Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	Exon_Number	t_depth	t_ref_count	t_alt_count	n_depth	n_ref_count	n_alt_count	all_effects	Allele	Gene	Feature	Feature_type	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	ALLELE_NUM	DISTANCE	STRAND	SYMBOL	SYMBOL_SOURCE	HGNC_ID	BIOTYPE	CANONICAL	CCDS	ENSP	SWISSPROT	TREMBL	UNIPARC	RefSeq	SIFT	PolyPhen	EXON	INTRON	DOMAINS	GMAF	AFR_MAF	AMR_MAF	ASN_MAF	EAS_MAF	EUR_MAF	SAS_MAF	AA_MAF	EA_MAF	CLIN_SIG	SOMATIC	PUBMED	MOTIF_NAME	MOTIF_POS	HIGH_INF_POS	MOTIF_SCORE_CHANGE	IMPACT	PICK	VARIANT_CLASS	TSL	HGVS_OFFSET	PHENO	MINIMISED	ExAC_AF	ExAC_AF_AFR	ExAC_AF_AMR	ExAC_AF_EAS	ExAC_AF_FIN	ExAC_AF_NFE	ExAC_AF_OTH	ExAC_AF_SAS	GENE_PHENO	FILTER	COSMIC	CENTERS	CONTEXT	DBVS	NCALLERS	Cancer_type
NEBL	0	.	GRCh37	10	21108359	21108359	+	Silent	SNP	C	C	T	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2049G>A	p.%3D	p.L683L	ENST00000377122	20/28	36	25	11	36	36	0	NEBL,synonymous_variant,p.%3D,ENST00000377122,;NEBL,intron_variant,,ENST00000377159,;NEBL,intron_variant,,ENST00000417816,;NEBL,non_coding_transcript_exon_variant,,ENST00000460652,;NEBL,upstream_gene_variant,,ENST00000473616,;NEBL,upstream_gene_variant,,ENST00000492325,;NEBL,non_coding_transcript_exon_variant,,ENST00000481592,;NEBL,non_coding_transcript_exon_variant,,ENST00000493005,;	T	ENSG00000078114	ENST00000377122	Transcript	synonymous_variant	2446	2049	683	L	ctG/ctA	COSM4013279	.	.	-1	NEBL	HGNC	16932	protein_coding	YES	CCDS7134.1	ENSP00000366326	NEBL_HUMAN	B0YJ47_HUMAN	UPI000012FEE8	.	.	.	20/28	.	PROSITE_profiles:PS51216,hmmpanther:PTHR11039,Pfam_domain:PF00880,SMART_domains:SM00227	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCACTCAGCTG	.	3	ESCA
KIAA1462	0	.	GRCh37	10	30317782	30317782	+	Missense_Mutation	SNP	C	C	T	rs190116152	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000375377	3/4	39	36	3	38	38	0	KIAA1462,missense_variant,p.Arg432Gln,ENST00000375377,;	T	ENSG00000165757	ENST00000375377	Transcript	missense_variant	1397	1295	432	R/Q	cGa/cAa	rs190116152	.	.	-1	KIAA1462	HGNC	29283	protein_coding	YES	CCDS41500.1	ENSP00000364526	JCAD_HUMAN	.	UPI00001D8117	.	deleterious(0)	probably_damaging(1)	3/4	.	Pfam_domain:PF15351	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATGTCGTAAC	byCluster|by1000G	4	ESCA
ANK3	0	.	GRCh37	10	61829891	61829891	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10748C>T	p.Thr3583Met	p.T3583M	ENST00000280772	37/44	58	31	26	39	39	0	ANK3,missense_variant,p.Thr3583Met,ENST00000280772,;ANK3,intron_variant,,ENST00000373827,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000355288,;ANK3,intron_variant,,ENST00000511043,;ANK3,intron_variant,,ENST00000503366,;	A	ENSG00000151150	ENST00000280772	Transcript	missense_variant	10940	10748	3583	T/M	aCg/aTg	COSM84012	.	.	-1	ANK3	HGNC	494	protein_coding	YES	CCDS7258.1	ENSP00000280772	ANK3_HUMAN	D6RFK6_HUMAN,D6RBY7_HUMAN,B1AQT1_HUMAN	UPI0000141BA9	.	.	probably_damaging(0.991)	37/44	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF15	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.T3583M|c.10748C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGCGTTGTA	.	5	ESCA
ZNF365	0	.	GRCh37	10	64415306	64415306	+	Intron	SNP	C	C	T	rs141356718	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1130-850C>T	.	.	ENST00000410046	.	33	22	10	31	31	0	ZNF365,synonymous_variant,p.%3D,ENST00000395251,;ZNF365,intron_variant,,ENST00000395249,;ZNF365,intron_variant,,ENST00000410046,;AC067751.1,upstream_gene_variant,,ENST00000579246,;ZNF365,non_coding_transcript_exon_variant,,ENST00000461412,;ZNF365,intron_variant,,ENST00000344640,;ZNF365,intron_variant,,ENST00000373784,;	T	ENSG00000138311	ENST00000410046	Transcript	intron_variant	.	.	.	.	.	rs141356718	.	.	1	ZNF365	HGNC	18194	protein_coding	YES	CCDS7264.1	ENSP00000387091	ZN365_HUMAN	C9J1G1_HUMAN	UPI00002323B9	.	.	.	.	5/7	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTGACGTTGT	byCluster|by1000G	5	ESCA
DNAJC12	0	.	GRCh37	10	69571381	69571381	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198G>A	p.%3D	p.L66L	ENST00000225171	3/5	38	20	18	35	35	0	DNAJC12,synonymous_variant,p.%3D,ENST00000339758,;DNAJC12,synonymous_variant,p.%3D,ENST00000483798,;DNAJC12,synonymous_variant,p.%3D,ENST00000225171,;RNU6-1250P,downstream_gene_variant,,ENST00000391218,;DNAJC12,3_prime_UTR_variant,,ENST00000480963,;DNAJC12,3_prime_UTR_variant,,ENST00000480180,;	T	ENSG00000108176	ENST00000225171	Transcript	synonymous_variant	351	198	66	L	ctG/ctA	.	.	.	-1	DNAJC12	HGNC	28908	protein_coding	YES	CCDS7271.1	ENSP00000225171	DJC12_HUMAN	Q6IAH1_HUMAN	UPI000012DAAA	.	.	.	3/5	.	PROSITE_profiles:PS50076,hmmpanther:PTHR24078:SF137,hmmpanther:PTHR24078,Pfam_domain:PF00226,Gene3D:1.10.287.110,SMART_domains:SM00271,Superfamily_domains:SSF46565,Prints_domain:PR00625	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGTCAGAAT	.	5	ESCA
MMP13	0	.	GRCh37	11	102826188	102826188	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.155T>A	p.Leu52His	p.L52H	ENST00000260302	2/10	48	45	3	37	37	0	MMP13,missense_variant,p.Leu52His,ENST00000260302,;MMP13,missense_variant,p.Leu52His,ENST00000340273,;	T	ENSG00000137745	ENST00000260302	Transcript	missense_variant	184	155	52	L/H	cTc/cAc	.	.	.	-1	MMP13	HGNC	7159	protein_coding	YES	CCDS8324.1	ENSP00000260302	MMP13_HUMAN	Q6LBE5_HUMAN	UPI00000422BC	.	tolerated(0.13)	benign(0.023)	2/10	.	hmmpanther:PTHR10201:SF130,hmmpanther:PTHR10201,Gene3D:3.40.390.10,Pfam_domain:PF01471,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF47090	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGCGAGATTT	.	2	ESCA
MRVI1	0	.	GRCh37	11	10650303	10650303	+	Missense_Mutation	SNP	G	G	A	rs373371120	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647C>T	p.Pro216Leu	p.P216L	ENST00000423302	6/21	42	33	8	32	32	0	MRVI1,missense_variant,p.Pro207Leu,ENST00000436272,;MRVI1,missense_variant,p.Pro125Leu,ENST00000547195,;MRVI1,missense_variant,p.Pro216Leu,ENST00000423302,;MRVI1,missense_variant,p.Pro207Leu,ENST00000531107,;MRVI1,missense_variant,p.Pro125Leu,ENST00000527509,;MRVI1,missense_variant,p.Pro125Leu,ENST00000552103,;MRVI1,missense_variant,p.Pro216Leu,ENST00000541483,;MRVI1,missense_variant,p.Pro207Leu,ENST00000421747,;MRVI1,5_prime_UTR_variant,,ENST00000424001,;MRVI1,5_prime_UTR_variant,,ENST00000545852,;MRVI1,5_prime_UTR_variant,,ENST00000558540,;MRVI1,5_prime_UTR_variant,,ENST00000534266,;MRVI1,downstream_gene_variant,,ENST00000529547,;MRVI1,downstream_gene_variant,,ENST00000531786,;MRVI1,downstream_gene_variant,,ENST00000532037,;MRVI1,missense_variant,p.Pro165Leu,ENST00000526414,;MRVI1,missense_variant,p.Pro112Leu,ENST00000533631,;MRVI1,3_prime_UTR_variant,,ENST00000529448,;	A	ENSG00000072952	ENST00000423302	Transcript	missense_variant	797	647	216	P/L	cCg/cTg	rs373371120,COSM1350631,COSM1350630	.	.	-1	MRVI1	HGNC	7237	protein_coding	YES	CCDS55746.1	ENSP00000412130	MRVI1_HUMAN	H0YI08_HUMAN,E9PRG4_HUMAN	UPI0001F78343	.	tolerated(0.07)	benign(0.013)	6/21	.	hmmpanther:PTHR15352:SF2,hmmpanther:PTHR15352	.	.	.	.	.	.	.	A:0	A:0.0002	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTGGCGGGGTG	byFrequency|byCluster	4	ESCA
OR4D5	0	.	GRCh37	11	123810418	123810418	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.95C>G	p.Ser32Cys	p.S32C	ENST00000307033	1/1	94	82	11	65	65	0	OR4D5,missense_variant,p.Ser32Cys,ENST00000307033,;OR6T1,downstream_gene_variant,,ENST00000321252,;	G	ENSG00000171014	ENST00000307033	Transcript	missense_variant	169	95	32	S/C	tCt/tGt	.	.	.	1	OR4D5	HGNC	14852	protein_coding	YES	CCDS31699.1	ENSP00000305970	OR4D5_HUMAN	.	UPI000003F227	.	tolerated(0.06)	benign(0.002)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF73,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCTCTGCTG	.	4	ESCA
IGSF22	0	.	GRCh37	11	18741278	18741278	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681G>C	p.Lys227Asn	p.K227N	ENST00000513874	7/23	84	46	38	53	53	0	IGSF22,missense_variant,p.Lys227Asn,ENST00000513874,;RP11-1081L13.4,intron_variant,,ENST00000527285,;IGSF22,downstream_gene_variant,,ENST00000412229,;IGSF22,missense_variant,p.Lys227Asn,ENST00000319338,;IGSF22,non_coding_transcript_exon_variant,,ENST00000504981,;	G	ENSG00000179057	ENST00000513874	Transcript	missense_variant	821	681	227	K/N	aaG/aaC	.	.	.	-1	IGSF22	HGNC	26750	protein_coding	YES	CCDS41625.2	ENSP00000421191	IGS22_HUMAN	.	UPI0001D3B05B	.	deleterious(0)	probably_damaging(0.917)	7/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR19900:SF53,hmmpanther:PTHR19900	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTCTTCTT	.	5	ESCA
SIRT3	0	.	GRCh37	11	233167	233167	+	Silent	SNP	C	C	T	rs148488998	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.522G>A	p.%3D	p.P174P	ENST00000382743	3/7	47	43	4	32	32	0	SIRT3,synonymous_variant,p.%3D,ENST00000529382,;SIRT3,synonymous_variant,p.%3D,ENST00000532956,;SIRT3,synonymous_variant,p.%3D,ENST00000528469,;SIRT3,synonymous_variant,p.%3D,ENST00000525319,;SIRT3,synonymous_variant,p.%3D,ENST00000524564,;SIRT3,synonymous_variant,p.%3D,ENST00000382743,;PSMD13,upstream_gene_variant,,ENST00000352303,;PSMD13,upstream_gene_variant,,ENST00000431206,;SIRT3,downstream_gene_variant,,ENST00000525237,;SIRT3,downstream_gene_variant,,ENST00000525776,;PSMD13,upstream_gene_variant,,ENST00000532097,;PSMD13,upstream_gene_variant,,ENST00000528906,;SIRT3,non_coding_transcript_exon_variant,,ENST00000531753,;SIRT3,non_coding_transcript_exon_variant,,ENST00000528702,;SIRT3,3_prime_UTR_variant,,ENST00000526854,;SIRT3,3_prime_UTR_variant,,ENST00000530067,;SIRT3,3_prime_UTR_variant,,ENST00000529055,;SIRT3,3_prime_UTR_variant,,ENST00000532837,;SIRT3,intron_variant,,ENST00000529937,;PSMD13,upstream_gene_variant,,ENST00000527047,;PSMD13,upstream_gene_variant,,ENST00000529372,;SIRT3,upstream_gene_variant,,ENST00000534381,;PSMD13,upstream_gene_variant,,ENST00000382671,;PSMD13,upstream_gene_variant,,ENST00000525665,;PSMD13,upstream_gene_variant,,ENST00000534590,;	T	ENSG00000142082	ENST00000382743	Transcript	synonymous_variant	625	522	174	P	ccG/ccA	rs148488998	.	.	-1	SIRT3	HGNC	14931	protein_coding	YES	CCDS7691.1	ENSP00000372191	SIR3_HUMAN	E9PNA0_HUMAN,E9PM52_HUMAN	UPI0000073D3C	.	.	.	3/7	.	PROSITE_profiles:PS50305,hmmpanther:PTHR11085:SF14,hmmpanther:PTHR11085,Pfam_domain:PF02146,Gene3D:3.30.1600.10,PIRSF_domain:PIRSF037938,Superfamily_domains:SSF52467	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTACGGGAG	byCluster	4	ESCA
PHF21A	0	.	GRCh37	11	45991391	45991391	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.674C>T	p.Thr225Ile	p.T225I	ENST00000418153	8/18	101	80	20	61	61	0	PHF21A,missense_variant,p.Thr226Ile,ENST00000257821,;PHF21A,missense_variant,p.Thr226Ile,ENST00000323180,;PHF21A,missense_variant,p.Thr225Ile,ENST00000418153,;PHF21A,downstream_gene_variant,,ENST00000524497,;PHF21A,downstream_gene_variant,,ENST00000531959,;PHF21A,downstream_gene_variant,,ENST00000525679,;PHF21A,upstream_gene_variant,,ENST00000527753,;PHF21A,non_coding_transcript_exon_variant,,ENST00000527401,;PHF21A,downstream_gene_variant,,ENST00000532883,;	A	ENSG00000135365	ENST00000418153	Transcript	missense_variant	874	674	225	T/I	aCt/aTt	COSM927117,COSM1585765	.	.	-1	PHF21A	HGNC	24156	protein_coding	YES	CCDS44578.1	ENSP00000398824	PF21A_HUMAN	E9PR02_HUMAN,E9PQM3_HUMAN,E9PNW9_HUMAN,E9PLV4_HUMAN	UPI000006E1CB	.	deleterious(0.01)	possibly_damaging(0.715)	8/18	.	hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF6	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGAGTGAGT	.	5	ESCA
OR5L2	0	.	GRCh37	11	55595411	55595411	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.717C>A	p.%3D	p.S239S	ENST00000378397	1/1	94	77	17	65	65	0	OR5L2,synonymous_variant,p.%3D,ENST00000378397,;	A	ENSG00000205030	ENST00000378397	Transcript	synonymous_variant	717	717	239	S	tcC/tcA	.	.	.	1	OR5L2	HGNC	8351	protein_coding	YES	CCDS31511.1	ENSP00000367650	OR5L2_HUMAN	.	UPI0000041C49	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF154,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCCACCTG	.	5	ESCA
C11orf35	0	.	GRCh37	11	556252	556252	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1197C>T	p.%3D	p.F399F	ENST00000329451	10/14	24	19	5	11	11	0	C11orf35,synonymous_variant,p.%3D,ENST00000329451,;C11orf35,downstream_gene_variant,,ENST00000486629,;RASSF7,upstream_gene_variant,,ENST00000431809,;C11orf35,downstream_gene_variant,,ENST00000441853,;RASSF7,upstream_gene_variant,,ENST00000397583,;RASSF7,upstream_gene_variant,,ENST00000344375,;RASSF7,upstream_gene_variant,,ENST00000397582,;LRRC56,downstream_gene_variant,,ENST00000270115,;RP11-496I9.1,upstream_gene_variant,,ENST00000527113,;RP11-496I9.1,upstream_gene_variant,,ENST00000533844,;RP11-496I9.1,upstream_gene_variant,,ENST00000527620,;RASSF7,upstream_gene_variant,,ENST00000524468,;C11orf35,non_coding_transcript_exon_variant,,ENST00000469990,;RASSF7,upstream_gene_variant,,ENST00000414138,;C11orf35,downstream_gene_variant,,ENST00000492515,;	A	ENSG00000185522	ENST00000329451	Transcript	synonymous_variant	1260	1197	399	F	ttC/ttT	.	.	.	-1	C11orf35	HGNC	28561	protein_coding	YES	CCDS7701.1	ENSP00000331167	CK035_HUMAN	.	UPI0000456441	.	.	.	10/14	.	hmmpanther:PTHR19956,hmmpanther:PTHR19956:SF5,Pfam_domain:PF00932,Gene3D:2.60.40.1260,Superfamily_domains:SSF74853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGGAAGCC	.	5	ESCA
OR8J3	0	.	GRCh37	11	55904509	55904509	+	Missense_Mutation	SNP	C	C	T	rs752411061	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686G>A	p.Arg229His	p.R229H	ENST00000301529	1/1	36	20	16	33	33	0	OR8J3,missense_variant,p.Arg229His,ENST00000301529,;OR5BN1P,upstream_gene_variant,,ENST00000532955,;	T	ENSG00000167822	ENST00000301529	Transcript	missense_variant	686	686	229	R/H	cGt/cAt	rs752411061	.	.	-1	OR8J3	HGNC	15312	protein_coding	YES	CCDS31520.1	ENSP00000301529	OR8J3_HUMAN	.	UPI0000061E99	.	tolerated(0.3)	benign(0.007)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF209,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAACGTATC	.	5	ESCA
OR5R1	0	.	GRCh37	11	56185376	56185376	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333G>A	p.%3D	p.E111E	ENST00000312253	1/1	34	18	16	27	27	0	OR5R1,synonymous_variant,p.%3D,ENST00000312253,;OR5AL1,downstream_gene_variant,,ENST00000327258,;OR5AL1,downstream_gene_variant,,ENST00000440231,;	T	ENSG00000174942	ENST00000312253	Transcript	synonymous_variant	333	333	111	E	gaG/gaA	.	.	.	-1	OR5R1	HGNC	14841	protein_coding	YES	CCDS31530.1	ENSP00000308595	OR5R1_HUMAN	.	UPI000004B225	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF89,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAACACTCAGT	.	3	ESCA
SPTBN2	0	.	GRCh37	11	66458832	66458832	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5488C>T	p.Arg1830Cys	p.R1830C	ENST00000533211	27/38	55	43	12	34	34	0	SPTBN2,missense_variant,p.Arg1830Cys,ENST00000533211,;SPTBN2,missense_variant,p.Arg1830Cys,ENST00000529997,;SPTBN2,missense_variant,p.Arg1830Cys,ENST00000309996,;SPTBN2,upstream_gene_variant,,ENST00000532650,;SPTBN2,upstream_gene_variant,,ENST00000532902,;SPTBN2,upstream_gene_variant,,ENST00000530775,;SPTBN2,upstream_gene_variant,,ENST00000528051,;SPTBN2,downstream_gene_variant,,ENST00000530665,;	A	ENSG00000173898	ENST00000533211	Transcript	missense_variant	5820	5488	1830	R/C	Cgc/Tgc	.	.	.	-1	SPTBN2	HGNC	11276	protein_coding	YES	CCDS8150.1	ENSP00000432568	SPTN2_HUMAN	E9PJZ2_HUMAN,C1KC08_HUMAN	UPI000013EF83	.	deleterious(0)	probably_damaging(0.989)	27/38	.	PIRSF_domain:PIRSF002297,SMART_domains:SM00150,Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCGCGGCCAG	.	5	ESCA
OMP	0	.	GRCh37	11	76814312	76814312	+	Missense_Mutation	SNP	G	G	A	rs376786233	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427G>A	p.Val143Ile	p.V143I	ENST00000529803	1/1	62	54	8	30	30	0	OMP,missense_variant,p.Val143Ile,ENST00000529803,;CAPN5,intron_variant,,ENST00000529629,;CAPN5,intron_variant,,ENST00000456580,;CAPN5,intron_variant,,ENST00000531028,;CAPN5,intron_variant,,ENST00000278559,;CAPN5,intron_variant,,ENST00000533889,;	A	ENSG00000254550	ENST00000529803	Transcript	missense_variant	427	427	143	V/I	Gtc/Atc	rs376786233	.	.	1	OMP	HGNC	8136	protein_coding	YES	CCDS53682.1	ENSP00000436376	OMP_HUMAN	.	UPI00001637C1	.	tolerated_low_confidence(0.87)	benign(0.001)	1/1	.	hmmpanther:PTHR15357,Gene3D:1f35A00,Pfam_domain:PF06554,Superfamily_domains:0037362	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTCGTCACC	byFrequency|byCluster	4	ESCA
MIR4300	0	.	GRCh37	11	81601792	81601792	+	RNA	SNP	A	A	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.87T>G	.	.	ENST00000581016	1/1	86	71	14	49	49	0	MIR4300,non_coding_transcript_exon_variant,,ENST00000581016,;RP11-179A16.1,intron_variant,,ENST00000500502,;RP11-179A16.1,intron_variant,,ENST00000530896,;	C	ENSG00000264110	ENST00000581016	Transcript	non_coding_transcript_exon_variant	87	.	.	.	.	.	.	.	-1	MIR4300	HGNC	38184	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCAGAAGT	.	5	ESCA
CREBZF	0	.	GRCh37	11	85372905	85372905	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1950A>G	.	.	ENST00000527447	1/1	62	47	15	35	35	0	CREBZF,3_prime_UTR_variant,,ENST00000398294,;CREBZF,3_prime_UTR_variant,,ENST00000527447,;CREBZF,intron_variant,,ENST00000534224,;CREBZF,intron_variant,,ENST00000531515,;CREBZF,3_prime_UTR_variant,,ENST00000490820,;CREBZF,intron_variant,,ENST00000260058,;CREBZF,intron_variant,,ENST00000525639,;CREBZF,intron_variant,,ENST00000527529,;CREBZF,intron_variant,,ENST00000528561,;CREBZF,downstream_gene_variant,,ENST00000528889,;	C	ENSG00000137504	ENST00000527447	Transcript	3_prime_UTR_variant	3242	.	.	.	.	.	.	.	-1	CREBZF	HGNC	24905	protein_coding	YES	CCDS41697.1	ENSP00000433459	ZHANG_HUMAN	.	UPI0000405F55	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATTTCAATT	.	5	ESCA
NAALAD2	0	.	GRCh37	11	89882244	89882244	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452A>T	p.Tyr151Phe	p.Y151F	ENST00000534061	4/19	154	100	53	101	101	0	NAALAD2,missense_variant,p.Tyr97Phe,ENST00000526637,;NAALAD2,missense_variant,p.Tyr151Phe,ENST00000375944,;NAALAD2,missense_variant,p.Tyr151Phe,ENST00000525171,;NAALAD2,missense_variant,p.Tyr151Phe,ENST00000534061,;NAALAD2,missense_variant,p.Tyr151Phe,ENST00000321955,;NAALAD2,downstream_gene_variant,,ENST00000525497,;NAALAD2,missense_variant,p.Tyr151Phe,ENST00000527493,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000524501,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000529090,;	T	ENSG00000077616	ENST00000534061	Transcript	missense_variant	682	452	151	Y/F	tAt/tTt	.	.	.	1	NAALAD2	HGNC	14526	protein_coding	YES	CCDS8288.1	ENSP00000432481	NALD2_HUMAN	E9PJ53_HUMAN,E9PII2_HUMAN	UPI0000031A85	.	tolerated(1)	benign(0.049)	4/19	.	Superfamily_domains:SSF52025,Gene3D:3.50.30.30,hmmpanther:PTHR10404:SF38,hmmpanther:PTHR10404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATATAATG	.	5	ESCA
GNPTAB	0	.	GRCh37	12	102158696	102158696	+	Missense_Mutation	SNP	C	C	G	rs281864985	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1999G>C	p.Glu667Gln	p.E667Q	ENST00000299314	13/21	38	26	12	30	30	0	GNPTAB,missense_variant,p.Glu667Gln,ENST00000299314,;GNPTAB,downstream_gene_variant,,ENST00000549940,;GNPTAB,upstream_gene_variant,,ENST00000550718,;RNU6-101P,downstream_gene_variant,,ENST00000410323,;GNPTAB,downstream_gene_variant,,ENST00000552009,;GNPTAB,upstream_gene_variant,,ENST00000549194,;	G	ENSG00000111670	ENST00000299314	Transcript	missense_variant	2262	1999	667	E/Q	Gag/Cag	rs281864985,CM094378	.	.	-1	GNPTAB	HGNC	29670	protein_coding	YES	CCDS9088.1	ENSP00000299314	GNPTA_HUMAN	Q9NV34_HUMAN,Q68CM9_HUMAN,F8VQW2_HUMAN	UPI000004CC0C	.	tolerated(0.07)	probably_damaging(0.947)	13/21	.	hmmpanther:PTHR24045:SF0,hmmpanther:PTHR24045	.	.	.	.	.	.	.	.	.	pathogenic	.	19659762	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCAAAAA	.	5	ESCA
DNAH10	0	.	GRCh37	12	124256179	124256179	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147A>G	p.%3D	p.L49L	ENST00000409039	3/78	33	18	14	24	24	0	DNAH10,synonymous_variant,p.%3D,ENST00000409039,;	G	ENSG00000197653	ENST00000409039	Transcript	synonymous_variant	172	147	49	L	ctA/ctG	.	.	.	1	DNAH10	HGNC	2941	protein_coding	YES	CCDS9255.2	ENSP00000386770	DYH10_HUMAN	.	UPI00014F7B89	.	.	.	3/78	.	hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTAGGCCA	.	5	ESCA
ERBB3	0	.	GRCh37	12	56494025	56494025	+	Missense_Mutation	SNP	G	G	T	rs756121964	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3197G>T	p.Cys1066Phe	p.C1066F	ENST00000267101	26/28	44	33	11	31	31	0	ERBB3,missense_variant,p.Cys1007Phe,ENST00000415288,;ERBB3,missense_variant,p.Cys423Phe,ENST00000450146,;ERBB3,missense_variant,p.Cys1066Phe,ENST00000267101,;ERBB3,missense_variant,p.Cys373Phe,ENST00000550070,;ERBB3,missense_variant,p.Cys307Phe,ENST00000553131,;ERBB3,missense_variant,p.Cys186Phe,ENST00000549832,;RP11-603J24.9,upstream_gene_variant,,ENST00000548861,;PA2G4,upstream_gene_variant,,ENST00000552766,;PA2G4,upstream_gene_variant,,ENST00000303305,;PA2G4,upstream_gene_variant,,ENST00000553057,;RP11-603J24.17,downstream_gene_variant,,ENST00000548595,;ERBB3,3_prime_UTR_variant,,ENST00000551085,;ERBB3,3_prime_UTR_variant,,ENST00000551242,;ERBB3,non_coding_transcript_exon_variant,,ENST00000552691,;ERBB3,downstream_gene_variant,,ENST00000550869,;ERBB3,downstream_gene_variant,,ENST00000548709,;ERBB3,downstream_gene_variant,,ENST00000549644,;ERBB3,downstream_gene_variant,,ENST00000549205,;	T	ENSG00000065361	ENST00000267101	Transcript	missense_variant	3637	3197	1066	C/F	tGc/tTc	rs756121964	.	.	1	ERBB3	HGNC	3431	protein_coding	YES	CCDS31833.1	ENSP00000267101	ERBB3_HUMAN	Q9NNX2_HUMAN,F8VX90_HUMAN,F8VW56_HUMAN,F8VW48_HUMAN,F8VRL0_HUMAN	UPI000012A113	.	tolerated(0.7)	benign(0.004)	26/28	.	hmmpanther:PTHR24416:SF88,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTGCCAGG	.	5	ESCA
CAPS2	0	.	GRCh37	12	75669885	75669885	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*138G>A	.	.	ENST00000409445	18/18	35	21	13	30	30	0	CAPS2,3_prime_UTR_variant,,ENST00000409445,;CAPS2,3_prime_UTR_variant,,ENST00000409799,;CAPS2,downstream_gene_variant,,ENST00000393284,;CAPS2,downstream_gene_variant,,ENST00000442339,;RP11-560G2.1,intron_variant,,ENST00000549953,;CAPS2,non_coding_transcript_exon_variant,,ENST00000409004,;CAPS2,downstream_gene_variant,,ENST00000336815,;CAPS2,downstream_gene_variant,,ENST00000328705,;	T	ENSG00000180881	ENST00000409445	Transcript	3_prime_UTR_variant	2009	.	.	.	.	.	.	.	-1	CAPS2	HGNC	16471	protein_coding	YES	CCDS9008.2	ENSP00000386959	CAYP2_HUMAN	F8VZC3_HUMAN	UPI000006D783	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAACGAATA	.	5	ESCA
ACSS3	0	.	GRCh37	12	81593158	81593158	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1289T>C	p.Val430Ala	p.V430A	ENST00000548058	9/16	29	23	6	23	23	0	ACSS3,missense_variant,p.Val429Ala,ENST00000261206,;ACSS3,missense_variant,p.Val430Ala,ENST00000548058,;ACSS3,missense_variant,p.Val112Ala,ENST00000548324,;ACSS3,missense_variant,p.Val50Ala,ENST00000546664,;ACSS3,non_coding_transcript_exon_variant,,ENST00000551745,;	C	ENSG00000111058	ENST00000548058	Transcript	missense_variant	2199	1289	430	V/A	gTa/gCa	.	.	.	1	ACSS3	HGNC	24723	protein_coding	YES	CCDS9022.1	ENSP00000449535	ACSS3_HUMAN	F8VZB4_HUMAN	UPI000007060A	.	tolerated(0.1)	benign(0.16)	9/16	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF0,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATGTAGAGA	.	5	ESCA
TUBA3C	0	.	GRCh37	13	19748204	19748204	+	Silent	SNP	G	G	A	rs1052403	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1152C>T	p.%3D	p.I384I	ENST00000400113	5/5	89	73	16	62	62	0	TUBA3C,synonymous_variant,p.%3D,ENST00000400113,;SMPD4P2,upstream_gene_variant,,ENST00000440167,;	A	ENSG00000198033	ENST00000400113	Transcript	synonymous_variant	1257	1152	384	I	atC/atT	rs1052403	.	.	-1	TUBA3C	HGNC	12408	protein_coding	YES	CCDS9284.1	ENSP00000382982	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	.	.	5/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Gene3D:1.10.287.600,Pfam_domain:PF03953,SMART_domains:SM00865,Superfamily_domains:SSF55307,Prints_domain:PR01161	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A383T|c.1147G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCGCGATGGC	.	5	ESCA
EIF5	0	.	GRCh37	14	103804756	103804757	+	In_Frame_Ins	INS	-	-	CAC	rs548001106	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553_555dupCCA	p.Pro185dup	p.P185dup	ENST00000216554	7/12	23	14	9	11	11	0	EIF5,inframe_insertion,p.Pro185dup,ENST00000216554,;EIF5,inframe_insertion,p.Pro185dup,ENST00000392715,;EIF5,inframe_insertion,p.Pro185dup,ENST00000558265,;EIF5,inframe_insertion,p.Pro185dup,ENST00000558506,;EIF5,downstream_gene_variant,,ENST00000560763,;EIF5,downstream_gene_variant,,ENST00000560338,;EIF5,downstream_gene_variant,,ENST00000561325,;EIF5,downstream_gene_variant,,ENST00000559532,;EIF5,downstream_gene_variant,,ENST00000558316,;EIF5,downstream_gene_variant,,ENST00000559130,;SNORA28,downstream_gene_variant,,ENST00000606769,;EIF5,upstream_gene_variant,,ENST00000561406,;EIF5,downstream_gene_variant,,ENST00000560877,;EIF5,downstream_gene_variant,,ENST00000560200,;EIF5,non_coding_transcript_exon_variant,,ENST00000561439,;EIF5,non_coding_transcript_exon_variant,,ENST00000559011,;EIF5,downstream_gene_variant,,ENST00000558551,;EIF5,downstream_gene_variant,,ENST00000561023,;EIF5,downstream_gene_variant,,ENST00000559923,;EIF5,upstream_gene_variant,,ENST00000558800,;EIF5,downstream_gene_variant,,ENST00000559249,;EIF5,upstream_gene_variant,,ENST00000561380,;	CAC	ENSG00000100664	ENST00000216554	Transcript	inframe_insertion	1208-1209	532-533	178	T/TP	aca/aCACca	rs548001106	.	.	1	EIF5	HGNC	3299	protein_coding	YES	CCDS9980.1	ENSP00000216554	IF5_HUMAN	H0YN40_HUMAN,H0YMJ8_HUMAN,H0YM54_HUMAN,H0YLZ1_HUMAN,H0YK29_HUMAN,H0YK11_HUMAN	UPI000012D3A5	.	.	.	7/12	.	hmmpanther:PTHR23001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	23	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTGAGACACCA	byCluster	2	ESCA
TRAV17	0	.	GRCh37	14	22466396	22466396	+	Missense_Mutation	SNP	G	G	A	rs368557894	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326G>A	p.Cys109Tyr	p.C109Y	ENST00000390445	2/2	19	14	4	11	11	0	TRAV17,missense_variant,p.Cys109Tyr,ENST00000390445,;TRAV18,upstream_gene_variant,,ENST00000390446,;	A	ENSG00000211797	ENST00000390445	Transcript	missense_variant	473	326	109	C/Y	tGt/tAt	rs368557894	.	.	1	TRAV17	HGNC	12113	TR_V_gene	YES	.	ENSP00000452087	.	.	UPI000011D121	.	deleterious(0)	probably_damaging(0.999)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19433:SF66,hmmpanther:PTHR19433,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTGTGCTA	byFrequency|byCluster	5	ESCA
KHNYN	0	.	GRCh37	14	24900129	24900130	+	Frame_Shift_Del	DEL	AG	AG	-	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.195_196delAG	p.Arg65SerfsTer16	p.R65Sfs*16	ENST00000251343	2/8	49	32	17	35	35	0	KHNYN,frameshift_variant,p.Arg65SerfsTer16,ENST00000251343,;KHNYN,frameshift_variant,p.Arg65SerfsTer16,ENST00000556842,;KHNYN,frameshift_variant,p.Arg65SerfsTer16,ENST00000553935,;KHNYN,frameshift_variant,p.Arg65SerfsTer16,ENST00000556510,;CBLN3,5_prime_UTR_variant,,ENST00000555436,;CBLN3,upstream_gene_variant,,ENST00000267406,;KHNYN,upstream_gene_variant,,ENST00000554268,;KHNYN,upstream_gene_variant,,ENST00000556255,;	-	ENSG00000100441	ENST00000251343	Transcript	frameshift_variant	332-333	193-194	65	R/X	AGa/a	.	.	.	1	KHNYN	HGNC	20166	protein_coding	YES	CCDS32058.1	ENSP00000251343	KHNYN_HUMAN	G3V3G3_HUMAN,G3V331_HUMAN	UPI000000CC1F	.	.	.	2/8	.	hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF28,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCAGCAGAGCCA	.	3	ESCA
MDGA2	0	.	GRCh37	14	47309545	47309545	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1589G>A	.	.	ENST00000426342	17/17	23	17	5	19	19	0	MDGA2,3_prime_UTR_variant,,ENST00000399222,;MDGA2,3_prime_UTR_variant,,ENST00000426342,;MDGA2,3_prime_UTR_variant,,ENST00000399232,;MDGA2,downstream_gene_variant,,ENST00000357362,;MDGA2,downstream_gene_variant,,ENST00000439988,;	T	ENSG00000139915	ENST00000426342	Transcript	3_prime_UTR_variant	4520	.	.	.	.	.	.	.	-1	MDGA2	HGNC	19835	protein_coding	YES	CCDS41948.1	ENSP00000405456	MDGA2_HUMAN	F8WE89_HUMAN	UPI0000213DB6	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTTAGA	.	5	ESCA
ESR2	0	.	GRCh37	14	64727213	64727213	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.906C>T	p.%3D	p.A302A	ENST00000341099	5/9	68	43	25	48	48	0	ESR2,synonymous_variant,p.%3D,ENST00000357782,;ESR2,synonymous_variant,p.%3D,ENST00000553796,;ESR2,synonymous_variant,p.%3D,ENST00000353772,;ESR2,synonymous_variant,p.%3D,ENST00000267525,;ESR2,synonymous_variant,p.%3D,ENST00000341099,;ESR2,synonymous_variant,p.%3D,ENST00000555278,;ESR2,synonymous_variant,p.%3D,ENST00000556275,;ESR2,synonymous_variant,p.%3D,ENST00000557772,;ESR2,synonymous_variant,p.%3D,ENST00000554572,;ESR2,synonymous_variant,p.%3D,ENST00000542956,;ESR2,synonymous_variant,p.%3D,ENST00000358599,;ESR2,non_coding_transcript_exon_variant,,ENST00000555483,;ESR2,non_coding_transcript_exon_variant,,ENST00000554520,;ESR2,non_coding_transcript_exon_variant,,ENST00000555783,;ESR2,synonymous_variant,p.%3D,ENST00000344288,;	A	ENSG00000140009	ENST00000341099	Transcript	synonymous_variant	1324	906	302	A	gcC/gcT	.	.	.	-1	ESR2	HGNC	3468	protein_coding	YES	CCDS9762.1	ENSP00000343925	ESR2_HUMAN	Q7LCB3_HUMAN,G3V5S2_HUMAN	UPI0000000964	.	.	.	5/9	.	hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF1,Pfam_domain:PF00104,Gene3D:1.10.565.10,PIRSF_domain:PIRSF500102,SMART_domains:SM00430,PIRSF_domain:PIRSF002527,Superfamily_domains:SSF48508,Prints_domain:PR00398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTCGGCCAA	.	5	ESCA
HSPA2	0	.	GRCh37	14	65009115	65009115	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1548C>T	p.%3D	p.D516D	ENST00000247207	1/1	42	39	3	20	20	0	HSPA2,synonymous_variant,p.%3D,ENST00000247207,;HSPA2,synonymous_variant,p.%3D,ENST00000394709,;RP11-973N13.4,upstream_gene_variant,,ENST00000554918,;HSPA2,downstream_gene_variant,,ENST00000554883,;	T	ENSG00000126803	ENST00000247207	Transcript	synonymous_variant	1930	1548	516	D	gaC/gaT	.	.	.	1	HSPA2	HGNC	5235	protein_coding	YES	CCDS9766.1	ENSP00000247207	HSP72_HUMAN	.	UPI000012CC6A	.	.	.	1/1	.	hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF142,Gene3D:2.60.34.10,Pfam_domain:PF00012,Superfamily_domains:SSF100920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGACGACAT	.	2	ESCA
HEATR4	0	.	GRCh37	14	73962027	73962027	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2690G>A	p.Gly897Glu	p.G897E	ENST00000553558	16/18	72	48	24	52	52	0	HEATR4,missense_variant,p.Gly897Glu,ENST00000553558,;HEATR4,missense_variant,p.Gly850Glu,ENST00000560393,;HEATR4,missense_variant,p.Gly897Glu,ENST00000334988,;HEATR4,upstream_gene_variant,,ENST00000565094,;C14orf169,downstream_gene_variant,,ENST00000531973,;AC005280.1,downstream_gene_variant,,ENST00000304061,;	T	ENSG00000187105	ENST00000553558	Transcript	missense_variant	3012	2690	897	G/E	gGa/gAa	.	.	.	-1	HEATR4	HGNC	16761	protein_coding	YES	CCDS9815.2	ENSP00000450444	HEAT4_HUMAN	H3BSP2_HUMAN,G3V5L2_HUMAN,G3V3Q5_HUMAN	UPI00001FD7FD	.	tolerated(1)	benign(0.004)	16/18	.	hmmpanther:PTHR12697,hmmpanther:PTHR12697:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTCCCATG	.	5	ESCA
COX8C	0	.	GRCh37	14	93813699	93813699	+	Missense_Mutation	SNP	G	G	A	rs746074705	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85G>A	p.Ala29Thr	p.A29T	ENST00000342144	1/2	32	14	17	12	12	0	COX8C,missense_variant,p.Ala29Thr,ENST00000342144,;UNC79,intron_variant,,ENST00000256339,;	A	ENSG00000187581	ENST00000342144	Transcript	missense_variant	163	85	29	A/T	Gcc/Acc	rs746074705	.	.	1	COX8C	HGNC	24382	protein_coding	YES	CCDS9910.1	ENSP00000340568	COX8C_HUMAN	.	UPI00001B6753	.	tolerated(0.59)	probably_damaging(0.948)	1/2	.	hmmpanther:PTHR16717,hmmpanther:PTHR16717:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTCGCCCAC	byFrequency	5	ESCA
PPP4R4	0	.	GRCh37	14	94710984	94710984	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1279C>T	p.%3D	p.L427L	ENST00000304338	12/25	23	17	5	20	20	0	PPP4R4,synonymous_variant,p.%3D,ENST00000304338,;	T	ENSG00000119698	ENST00000304338	Transcript	synonymous_variant	1433	1279	427	L	Ctg/Ttg	.	.	.	1	PPP4R4	HGNC	23788	protein_coding	YES	CCDS9921.1	ENSP00000305924	PP4R4_HUMAN	G3V431_HUMAN,G3V422_HUMAN	UPI000016223B	.	.	.	12/25	.	hmmpanther:PTHR21467,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCTGAAT	.	5	ESCA
CHSY1	0	.	GRCh37	15	101718437	101718437	+	Missense_Mutation	SNP	G	G	C	rs751688006	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1565C>G	p.Ser522Trp	p.S522W	ENST00000254190	3/3	46	36	9	29	29	0	CHSY1,missense_variant,p.Ser522Trp,ENST00000254190,;CHSY1,non_coding_transcript_exon_variant,,ENST00000543813,;CHSY1,downstream_gene_variant,,ENST00000561414,;CHSY1,downstream_gene_variant,,ENST00000560766,;	C	ENSG00000131873	ENST00000254190	Transcript	missense_variant	2041	1565	522	S/W	tCg/tGg	rs751688006	.	.	-1	CHSY1	HGNC	17198	protein_coding	YES	CCDS10390.1	ENSP00000254190	CHSS1_HUMAN	.	UPI000000DB6C	.	tolerated(0.05)	probably_damaging(0.941)	3/3	.	hmmpanther:PTHR12369,hmmpanther:PTHR12369:SF16,Pfam_domain:PF05679,Gene3D:3.90.550.10,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCGACCCA	.	5	ESCA
MAGEL2	0	.	GRCh37	15	23889169	23889169	+	Missense_Mutation	SNP	C	C	T	rs555657199	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1912G>A	p.Gly638Ser	p.G638S	ENST00000532292	1/1	28	20	7	12	12	0	MAGEL2,missense_variant,p.Gly638Ser,ENST00000532292,;AC124309.1,non_coding_transcript_exon_variant,,ENST00000314233,;	T	ENSG00000254585	ENST00000532292	Transcript	missense_variant	2007	1912	638	G/S	Ggc/Agc	rs555657199	.	.	-1	MAGEL2	HGNC	6814	protein_coding	YES	.	ENSP00000433433	.	Q6P3U4_HUMAN,Q2M1Q7_HUMAN,Q05BN9_HUMAN,H0YDD5_HUMAN	UPI00005A89F6	.	tolerated_low_confidence(0.12)	benign(0.053)	1/1	.	.	T:0.0008	T:0	T:0	.	T:0.004	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCCGTGGG	byFrequency|by1000G	5	ESCA
KLF13	0	.	GRCh37	15	31664583	31664583	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*81G>A	.	.	ENST00000307145	2/2	62	33	29	48	48	0	KLF13,3_prime_UTR_variant,,ENST00000307145,;KLF13,3_prime_UTR_variant,,ENST00000560473,;KLF13,downstream_gene_variant,,ENST00000558844,;KLF13,intron_variant,,ENST00000558921,;KLF13,upstream_gene_variant,,ENST00000558673,;	A	ENSG00000169926	ENST00000307145	Transcript	3_prime_UTR_variant	1306	.	.	.	.	.	.	.	1	KLF13	HGNC	13672	protein_coding	YES	CCDS10025.1	ENSP00000302456	KLF13_HUMAN	.	UPI000012DEDC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAGAACTT	.	5	ESCA
DUOXA2	0	.	GRCh37	15	45406923	45406923	+	Silent	SNP	C	C	T	rs757519712	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.120C>T	p.%3D	p.L40L	ENST00000323030	1/6	76	63	13	78	78	0	DUOXA2,synonymous_variant,p.%3D,ENST00000323030,;DUOXA1,downstream_gene_variant,,ENST00000267803,;DUOXA1,downstream_gene_variant,,ENST00000560572,;DUOXA1,downstream_gene_variant,,ENST00000558422,;DUOXA1,downstream_gene_variant,,ENST00000559014,;DUOX2,upstream_gene_variant,,ENST00000603300,;DUOX2,upstream_gene_variant,,ENST00000389039,;DUOXA1,downstream_gene_variant,,ENST00000430224,;DUOXA1,downstream_gene_variant,,ENST00000558996,;DUOXA2,synonymous_variant,p.%3D,ENST00000491993,;DUOXA2,non_coding_transcript_exon_variant,,ENST00000350243,;DUOX2,upstream_gene_variant,,ENST00000558383,;DUOXA1,downstream_gene_variant,,ENST00000559013,;	T	ENSG00000140274	ENST00000323030	Transcript	synonymous_variant	405	120	40	L	ctC/ctT	rs757519712	.	.	1	DUOXA2	HGNC	32698	protein_coding	YES	CCDS10118.2	ENSP00000319705	DOXA2_HUMAN	.	UPI000049DDDD	.	.	.	1/6	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Pfam_domain:PF10204,hmmpanther:PTHR31158:SF2,hmmpanther:PTHR31158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCATCTT	.	5	ESCA
TRPM7	0	.	GRCh37	15	50955214	50955214	+	Silent	SNP	C	C	T	rs771596024	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33G>A	p.%3D	p.L11L	ENST00000313478	2/39	30	25	5	23	23	0	TRPM7,synonymous_variant,p.%3D,ENST00000560955,;TRPM7,synonymous_variant,p.%3D,ENST00000313478,;	T	ENSG00000092439	ENST00000313478	Transcript	synonymous_variant	315	33	11	L	ttG/ttA	rs771596024	.	.	-1	TRPM7	HGNC	17994	protein_coding	YES	CCDS42035.1	ENSP00000320239	TRPM7_HUMAN	.	UPI0000071CBA	.	.	.	2/39	.	hmmpanther:PTHR13800:SF8,hmmpanther:PTHR13800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTGGTCAAAGT	.	2	ESCA
CHD2	0	.	GRCh37	15	93571110	93571110	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3175G>C	.	.	ENST00000394196	39/39	34	29	5	30	30	0	CHD2,3_prime_UTR_variant,,ENST00000394196,;	C	ENSG00000173575	ENST00000394196	Transcript	3_prime_UTR_variant	9730	.	.	.	.	.	.	.	1	CHD2	HGNC	1917	protein_coding	YES	CCDS10374.2	ENSP00000377747	CHD2_HUMAN	Q6AI05_HUMAN,Q3YLD6_HUMAN,Q3YLD5_HUMAN,G3V4S8_HUMAN,G3V418_HUMAN	UPI0000E8A85C	.	.	.	39/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTAGTGATT	.	5	ESCA
RRN3	0	.	GRCh37	16	15159153	15159153	+	Silent	SNP	G	G	A	rs773259277	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1629C>T	p.%3D	p.T543T	ENST00000198767	16/18	112	98	14	60	60	0	RRN3,synonymous_variant,p.%3D,ENST00000327307,;RRN3,synonymous_variant,p.%3D,ENST00000563559,;RRN3,synonymous_variant,p.%3D,ENST00000540462,;RRN3,synonymous_variant,p.%3D,ENST00000429751,;RRN3,synonymous_variant,p.%3D,ENST00000198767,;PDXDC1,intron_variant,,ENST00000535621,;	A	ENSG00000085721	ENST00000198767	Transcript	synonymous_variant	1713	1629	543	T	acC/acT	rs773259277	.	.	-1	RRN3	HGNC	30346	protein_coding	YES	CCDS10559.1	ENSP00000198767	RRN3_HUMAN	B4E3T2_HUMAN,B4DZL9_HUMAN	UPI000006E1BF	.	.	.	16/18	.	hmmpanther:PTHR12790,Pfam_domain:PF05327	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGCGGTACT	.	4	ESCA
SLC9A5	0	.	GRCh37	16	67288942	67288942	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.509G>T	p.Gly170Val	p.G170V	ENST00000299798	3/16	114	65	49	62	62	0	SLC9A5,missense_variant,p.Gly19Val,ENST00000566626,;SLC9A5,missense_variant,p.Gly170Val,ENST00000299798,;SLC9A5,intron_variant,,ENST00000566345,;SLC9A5,intron_variant,,ENST00000567247,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000561472,;SLC9A5,missense_variant,p.Trp152Cys,ENST00000564812,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000564704,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000563723,;SLC9A5,intron_variant,,ENST00000566638,;	T	ENSG00000135740	ENST00000299798	Transcript	missense_variant	574	509	170	G/V	gGc/gTc	.	.	.	1	SLC9A5	HGNC	11078	protein_coding	YES	CCDS42178.1	ENSP00000299798	SL9A5_HUMAN	.	UPI000012FD2D	.	deleterious(0)	possibly_damaging(0.908)	3/16	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF56,Pfam_domain:PF00999,TIGRFAM_domain:TIGR00840	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGGCTTAC	.	5	ESCA
PDPR	0	.	GRCh37	16	70154430	70154430	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35G>A	p.Arg12Lys	p.R12K	ENST00000288050	3/19	158	143	15	104	104	0	PDPR,missense_variant,p.Arg12Lys,ENST00000288050,;PDPR,missense_variant,p.Arg12Lys,ENST00000568530,;PDPR,intron_variant,,ENST00000398122,;PDPR,missense_variant,p.Arg12Lys,ENST00000565186,;PDPR,non_coding_transcript_exon_variant,,ENST00000561920,;	A	ENSG00000090857	ENST00000288050	Transcript	missense_variant	992	35	12	R/K	aGa/aAa	.	.	.	1	PDPR	HGNC	30264	protein_coding	YES	CCDS45520.1	ENSP00000288050	PDPR_HUMAN	H3BV59_HUMAN,H3BU60_HUMAN,B7ZAR9_HUMAN,B3KSE1_HUMAN,A8MT40_HUMAN	UPI00001FF513	.	tolerated_low_confidence(1)	benign(0.008)	3/19	.	hmmpanther:PTHR13847:SF146,hmmpanther:PTHR13847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGAAGACAAA	.	4	ESCA
SLC38A8	0	.	GRCh37	16	84050269	84050269	+	Silent	SNP	G	G	A	rs144115936	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1017C>T	p.%3D	p.A339A	ENST00000299709	8/10	29	21	8	10	10	0	SLC38A8,synonymous_variant,p.%3D,ENST00000299709,;SLC38A8,non_coding_transcript_exon_variant,,ENST00000568003,;	A	ENSG00000166558	ENST00000299709	Transcript	synonymous_variant	1017	1017	339	A	gcC/gcT	rs144115936	.	.	-1	SLC38A8	HGNC	32434	protein_coding	YES	CCDS32495.1	ENSP00000299709	S38A8_HUMAN	H3BUP5_HUMAN,H3BP02_HUMAN	UPI0000D61A1F	.	.	.	8/10	.	hmmpanther:PTHR22950:SF226,hmmpanther:PTHR22950,Pfam_domain:PF01490	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCGGCCAG	byCluster	4	ESCA
ATXN7L3	0	.	GRCh37	17	42270964	42270964	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*667G>T	.	.	ENST00000454077	12/12	10	8	2	10	10	0	ATXN7L3,3_prime_UTR_variant,,ENST00000591295,;ATXN7L3,3_prime_UTR_variant,,ENST00000389384,;ATXN7L3,3_prime_UTR_variant,,ENST00000454077,;TMUB2,downstream_gene_variant,,ENST00000589856,;ATXN7L3,downstream_gene_variant,,ENST00000589805,;TMUB2,downstream_gene_variant,,ENST00000319511,;TMUB2,downstream_gene_variant,,ENST00000587630,;TMUB2,downstream_gene_variant,,ENST00000357984,;TMUB2,downstream_gene_variant,,ENST00000587172,;TMUB2,downstream_gene_variant,,ENST00000446571,;TMUB2,downstream_gene_variant,,ENST00000589785,;TMUB2,downstream_gene_variant,,ENST00000590235,;ATXN7L3,downstream_gene_variant,,ENST00000590169,;TMUB2,downstream_gene_variant,,ENST00000592825,;ATXN7L3,downstream_gene_variant,,ENST00000587097,;ATXN7L3,downstream_gene_variant,,ENST00000590537,;TMUB2,downstream_gene_variant,,ENST00000587989,;TMUB2,downstream_gene_variant,,ENST00000538716,;TMUB2,downstream_gene_variant,,ENST00000589184,;ATXN7L3,downstream_gene_variant,,ENST00000593073,;ATXN7L3,downstream_gene_variant,,ENST00000587022,;ATXN7L3,downstream_gene_variant,,ENST00000591807,;TMUB2,downstream_gene_variant,,ENST00000588413,;ATXN7L3,downstream_gene_variant,,ENST00000586688,;ATXN7L3,downstream_gene_variant,,ENST00000589607,;TMUB2,downstream_gene_variant,,ENST00000587775,;TMUB2,downstream_gene_variant,,ENST00000587326,;	A	ENSG00000087152	ENST00000454077	Transcript	3_prime_UTR_variant	1732	.	.	.	.	.	.	.	-1	ATXN7L3	HGNC	25416	protein_coding	YES	CCDS45697.1	ENSP00000397259	AT7L3_HUMAN	K7ENZ2_HUMAN,K7EMZ3_HUMAN,K7EJK2_HUMAN,B4DKS1_HUMAN	UPI00001613AC	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCAACAAAAG	.	2	ESCA
TP53	0	.	GRCh37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524G>A	p.Arg175His	p.R175H	ENST00000269305	5/11	32	8	24	28	28	0	TP53,missense_variant,p.Arg175His,ENST00000413465,;TP53,missense_variant,p.Arg175His,ENST00000420246,;TP53,missense_variant,p.Arg175His,ENST00000269305,;TP53,missense_variant,p.Arg43His,ENST00000509690,;TP53,missense_variant,p.Arg175His,ENST00000359597,;TP53,missense_variant,p.Arg82His,ENST00000514944,;TP53,missense_variant,p.Arg175His,ENST00000445888,;TP53,missense_variant,p.Arg175His,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	714	524	175	R/H	cGc/cAc	CM951224,rs28934578,CM062017,TP53_g.12512G>T,TP53_g.12512G>C,TP53_g.12512G>A,COSM10718,COSM10648,COSM45416,COSM99914,COSM1679508,COSM99022,COSM1679510,COSM99023,COSM1679512,COSM3355994,COSM1640851,COSM1679509,COSM99024,COSM1679511	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.11)	benign(0.308)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660,21264207,24929325,25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R175H|c.524G>A|181,SITE|p.R43H|c.128G>A|183,SITE|p.R82H|c.245G>A|183,SITE|p.R175H|c.524G>A|124,SITE|p.R175H|c.524G>A|180,SITE|p.R175H|c.524G>A|926,SITE|p.R175H|c.524G>A|88,CODON|p.0?|c.1_1182del1182|6,CODON|p.R175L|c.524G>T|20,CODON|p.R175P|c.524G>C|6,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R43L|c.128G>T|3,CODON|p.R82L|c.245G>T|3,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.P177_C182delPHHERC|c.526_543del18|3,BUFFER|p.H179Y|c.534_535CC>TT|8,BUFFER|p.H179D|c.535C>G|12,BUFFER|p.H179Y|c.535C>T|4,BUFFER|p.H47Y|c.139C>T|15,BUFFER|p.H179Y|c.535C>T|5,BUFFER|p.H179Y|c.535C>T|88,BUFFER|p.H179N|c.535C>A|15,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H86Y|c.256C>T|14,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R82G|c.244C>G|5,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43G|c.127C>G|8,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175G|c.523C>G|16,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R174K|c.521G>A|5,BUFFER|p.R174W|c.520A>T|11,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V172D|c.515T>A|11,BUFFER|p.V172A|c.515T>C|4,BUFFER|p.V172G|c.515T>G|4,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGCGCCTC	byCluster	5	ESCA
MC5R	0	.	GRCh37	18	13826394	13826394	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630C>T	p.%3D	p.L210L	ENST00000324750	1/1	79	65	14	44	44	0	MC5R,synonymous_variant,p.%3D,ENST00000324750,;MC5R,downstream_gene_variant,,ENST00000589410,;AP001525.1,upstream_gene_variant,,ENST00000390194,;	T	ENSG00000176136	ENST00000324750	Transcript	synonymous_variant	852	630	210	L	ctC/ctT	.	.	.	1	MC5R	HGNC	6933	protein_coding	YES	CCDS11868.1	ENSP00000318077	MC5R_HUMAN	K7ER30_HUMAN	UPI0000050405	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR22750:SF5,hmmpanther:PTHR22750,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCCTGGC	.	5	ESCA
DTNA	0	.	GRCh37	18	32468493	32468493	+	Intron	DEL	T	T	-	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2035-1763delT	.	.	ENST00000598334	.	36	27	9	29	29	0	DTNA,3_prime_UTR_variant,,ENST00000444659,;DTNA,3_prime_UTR_variant,,ENST00000269190,;DTNA,3_prime_UTR_variant,,ENST00000399121,;DTNA,3_prime_UTR_variant,,ENST00000595022,;DTNA,3_prime_UTR_variant,,ENST00000283365,;DTNA,3_prime_UTR_variant,,ENST00000399097,;DTNA,intron_variant,,ENST00000590831,;DTNA,intron_variant,,ENST00000598334,;DTNA,downstream_gene_variant,,ENST00000399113,;DTNA,downstream_gene_variant,,ENST00000556414,;DTNA,downstream_gene_variant,,ENST00000591182,;DTNA,downstream_gene_variant,,ENST00000598142,;DTNA,downstream_gene_variant,,ENST00000269192,;DTNA,downstream_gene_variant,,ENST00000601125,;DTNA,intron_variant,,ENST00000592449,;	-	ENSG00000134769	ENST00000598334	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	DTNA	HGNC	3057	protein_coding	YES	CCDS59312.1	ENSP00000470152	.	M0QYX6_HUMAN,K7ERZ2_HUMAN,K7ERH7_HUMAN,K7ER73_HUMAN,K7ENJ7_HUMAN,K7EMN1_HUMAN,K7EJ84_HUMAN	UPI0001E92A2F	.	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAAATATTTTTT	.	2	ESCA
CDH7	0	.	GRCh37	18	63430217	63430217	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.139C>T	p.Arg47Cys	p.R47C	ENST00000397968	2/12	122	38	84	59	59	0	CDH7,missense_variant,p.Arg47Cys,ENST00000397968,;CDH7,missense_variant,p.Arg47Cys,ENST00000536984,;CDH7,missense_variant,p.Arg47Cys,ENST00000323011,;CDH7,upstream_gene_variant,,ENST00000581601,;	T	ENSG00000081138	ENST00000397968	Transcript	missense_variant	565	139	47	R/C	Cgc/Tgc	COSM193444	.	.	1	CDH7	HGNC	1766	protein_coding	YES	CCDS11993.1	ENSP00000381058	CADH7_HUMAN	.	UPI000013D269	.	deleterious(0)	probably_damaging(1)	2/12	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAGCGCAGC	.	5	ESCA
CDH19	0	.	GRCh37	18	64172263	64172263	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2105A>G	p.Lys702Arg	p.K702R	ENST00000262150	12/12	53	47	6	26	26	0	CDH19,missense_variant,p.Lys702Arg,ENST00000262150,;CDH19,downstream_gene_variant,,ENST00000540086,;CDH19,3_prime_UTR_variant,,ENST00000579658,;	C	ENSG00000071991	ENST00000262150	Transcript	missense_variant	2398	2105	702	K/R	aAg/aGg	.	.	.	-1	CDH19	HGNC	1758	protein_coding	YES	CCDS11994.1	ENSP00000262150	CAD19_HUMAN	Q96KY9_HUMAN,J3QS15_HUMAN,F8VVI9_HUMAN	UPI0000048ECF	.	tolerated(1)	probably_damaging(0.999)	12/12	.	hmmpanther:PTHR24027:SF255,hmmpanther:PTHR24027,Gene3D:4.10.900.10,Pfam_domain:PF01049	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAGCTTTTCC	.	4	ESCA
CDH19	0	.	GRCh37	18	64211432	64211432	+	Silent	SNP	G	G	A	rs371022067,rs770336548	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990C>T	p.%3D	p.Y330Y	ENST00000262150	7/12	124	53	71	41	41	0	CDH19,synonymous_variant,p.%3D,ENST00000540086,;CDH19,synonymous_variant,p.%3D,ENST00000262150,;CDH19,synonymous_variant,p.%3D,ENST00000454642,;CDH19,synonymous_variant,p.%3D,ENST00000579658,;	A	ENSG00000071991	ENST00000262150	Transcript	synonymous_variant	1283	990	330	Y	taC/taT	rs371022067,rs770336548	.	.	-1	CDH19	HGNC	1758	protein_coding	YES	CCDS11994.1	ENSP00000262150	CAD19_HUMAN	Q96KY9_HUMAN,J3QS15_HUMAN,F8VVI9_HUMAN	UPI0000048ECF	.	.	.	7/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF255,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	A:0,-:0.0007	A:0.0003,-:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACCGTAGTG	byFrequency|byCluster	5	ESCA
DSEL	0	.	GRCh37	18	65181541	65181541	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.335C>G	p.Thr112Arg	p.T112R	ENST00000310045	2/2	92	82	10	40	40	0	DSEL,missense_variant,p.Thr112Arg,ENST00000310045,;RP11-638L3.1,upstream_gene_variant,,ENST00000583687,;CTD-2541J13.2,downstream_gene_variant,,ENST00000583493,;CTD-2541J13.2,downstream_gene_variant,,ENST00000581951,;	C	ENSG00000171451	ENST00000310045	Transcript	missense_variant	1809	335	112	T/R	aCa/aGa	.	.	.	-1	DSEL	HGNC	18144	protein_coding	YES	CCDS11995.1	ENSP00000310565	DSEL_HUMAN	.	UPI00000740A1	.	tolerated(0.46)	benign(0.11)	2/2	.	hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTATGTTGGG	.	4	ESCA
HOOK2	0	.	GRCh37	19	12874386	12874386	+	Missense_Mutation	SNP	G	G	A	rs370952243	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1966C>T	p.Arg656Trp	p.R656W	ENST00000397668	22/23	56	38	17	45	45	0	HOOK2,missense_variant,p.Arg656Trp,ENST00000397668,;HOOK2,missense_variant,p.Arg654Trp,ENST00000264827,;HOOK2,downstream_gene_variant,,ENST00000589965,;HOOK2,non_coding_transcript_exon_variant,,ENST00000589915,;HOOK2,downstream_gene_variant,,ENST00000589398,;HOOK2,downstream_gene_variant,,ENST00000586710,;HOOK2,downstream_gene_variant,,ENST00000592259,;HOOK2,downstream_gene_variant,,ENST00000591839,;HOOK2,downstream_gene_variant,,ENST00000586188,;	A	ENSG00000095066	ENST00000397668	Transcript	missense_variant	2040	1966	656	R/W	Cgg/Tgg	rs370952243	.	.	-1	HOOK2	HGNC	19885	protein_coding	YES	CCDS42508.1	ENSP00000380785	HOOK2_HUMAN	K7ENU5_HUMAN,K7EMR5_HUMAN,K7EJ48_HUMAN	UPI00003D0BC0	.	deleterious(0.04)	possibly_damaging(0.568)	22/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947,Pfam_domain:PF05622	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCGCTGAC	byFrequency|byCluster	5	ESCA
KLHL26	0	.	GRCh37	19	18779978	18779978	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1771G>A	p.Asp591Asn	p.D591N	ENST00000300976	3/3	86	72	13	58	58	0	KLHL26,missense_variant,p.Asp591Asn,ENST00000300976,;KLHL26,intron_variant,,ENST00000599006,;KLHL26,downstream_gene_variant,,ENST00000595182,;KLHL26,downstream_gene_variant,,ENST00000595423,;KLHL26,downstream_gene_variant,,ENST00000596843,;KLHL26,downstream_gene_variant,,ENST00000600657,;	A	ENSG00000167487	ENST00000300976	Transcript	missense_variant	1861	1771	591	D/N	Gac/Aac	.	.	.	1	KLHL26	HGNC	25623	protein_coding	YES	CCDS12384.1	ENSP00000300976	KLH26_HUMAN	.	UPI0000071AC2	.	tolerated(0.15)	probably_damaging(0.94)	3/3	.	hmmpanther:PTHR24412:SF56,hmmpanther:PTHR24412,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGGGACCTG	.	5	ESCA
AC011467.1	0	.	GRCh37	19	22785662	22785662	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000408863	.	94	89	5	68	68	0	AC011467.1,downstream_gene_variant,,ENST00000408863,;RN7SL860P,downstream_gene_variant,,ENST00000473738,;CTC-457E21.3,non_coding_transcript_exon_variant,,ENST00000600260,;CTC-457E21.3,downstream_gene_variant,,ENST00000597408,;CTC-457E21.6,upstream_gene_variant,,ENST00000599738,;CTC-457E21.5,upstream_gene_variant,,ENST00000598658,;CTC-457E21.3,non_coding_transcript_exon_variant,,ENST00000596977,;CTC-457E21.5,upstream_gene_variant,,ENST00000594891,;	T	ENSG00000221790	ENST00000408863	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	72	1	AC011467.1	Clone_based_ensembl_gene	.	miRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATCCACAGG	.	2	ESCA
ZNF91	0	.	GRCh37	19	23542601	23542601	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3180A>G	p.Ile1060Met	p.I1060M	ENST00000300619	4/4	60	32	28	43	43	0	ZNF91,missense_variant,p.Ile1028Met,ENST00000397082,;ZNF91,missense_variant,p.Ile1060Met,ENST00000300619,;ZNF91,intron_variant,,ENST00000599743,;ZNF91,downstream_gene_variant,,ENST00000595533,;ZNF91,intron_variant,,ENST00000596989,;ZNF91,upstream_gene_variant,,ENST00000593341,;ZNF91,upstream_gene_variant,,ENST00000599281,;ZNF91,upstream_gene_variant,,ENST00000596528,;	C	ENSG00000167232	ENST00000300619	Transcript	missense_variant	3386	3180	1060	I/M	atA/atG	.	.	.	-1	ZNF91	HGNC	13166	protein_coding	YES	CCDS42541.1	ENSP00000300619	ZNF91_HUMAN	M0R186_HUMAN	UPI00002038F9	.	tolerated(0.22)	probably_damaging(0.974)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF100,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGATATAAA	.	5	ESCA
VSTM2B	0	.	GRCh37	19	30054821	30054821	+	Missense_Mutation	SNP	C	C	T	rs567862790	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838C>T	p.Arg280Cys	p.R280C	ENST00000335523	5/5	50	35	15	36	36	0	VSTM2B,missense_variant,p.Arg280Cys,ENST00000335523,;	T	ENSG00000187135	ENST00000335523	Transcript	missense_variant	923	838	280	R/C	Cgc/Tgc	rs567862790,COSM994376	.	.	1	VSTM2B	HGNC	33595	protein_coding	YES	CCDS46034.1	ENSP00000335038	VTM2B_HUMAN	.	UPI00001D8158	.	tolerated_low_confidence(0.17)	benign(0.037)	5/5	.	Low_complexity_(Seg):seg	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGCGCCTG	by1000G	5	ESCA
TBXA2R	0	.	GRCh37	19	3600557	3600557	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76G>A	p.Ala26Thr	p.A26T	ENST00000411851	2/4	60	48	11	43	43	0	TBXA2R,missense_variant,p.Ala26Thr,ENST00000589966,;TBXA2R,missense_variant,p.Ala26Thr,ENST00000411851,;TBXA2R,missense_variant,p.Ala26Thr,ENST00000375190,;TBXA2R,upstream_gene_variant,,ENST00000587717,;	T	ENSG00000006638	ENST00000411851	Transcript	missense_variant	290	76	26	A/T	Gcc/Acc	.	.	.	-1	TBXA2R	HGNC	11608	protein_coding	YES	CCDS54198.1	ENSP00000393333	TA2R_HUMAN	Q05C92_HUMAN	UPI00000711C4	.	tolerated(0.27)	probably_damaging(0.999)	2/4	.	Prints_domain:PR00429,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR11866:SF5,hmmpanther:PTHR11866	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGGCGATCA	.	5	ESCA
CHAF1A	0	.	GRCh37	19	4423372	4423372	+	Missense_Mutation	SNP	C	C	T	rs573779621	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1288C>T	p.Arg430Trp	p.R430W	ENST00000301280	6/15	29	21	7	32	32	0	CHAF1A,missense_variant,p.Arg430Trp,ENST00000301280,;CHAF1A,missense_variant,p.Arg196Trp,ENST00000587739,;CHAF1A,3_prime_UTR_variant,,ENST00000585371,;	T	ENSG00000167670	ENST00000301280	Transcript	missense_variant	1389	1288	430	R/W	Cgg/Tgg	rs573779621	.	.	1	CHAF1A	HGNC	1910	protein_coding	YES	CCDS32875.1	ENSP00000301280	CAF1A_HUMAN	.	UPI00002030F8	.	deleterious(0)	unknown(0)	6/15	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15272,hmmpanther:PTHR15272:SF0,Pfam_domain:PF11600	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAACGGTTA	by1000G	5	ESCA
DHDH	0	.	GRCh37	19	49448200	49448200	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10G>A	.	.	ENST00000221403	7/7	50	45	4	34	34	0	DHDH,3_prime_UTR_variant,,ENST00000221403,;DHDH,3_prime_UTR_variant,,ENST00000523250,;DHDH,3_prime_UTR_variant,,ENST00000522614,;DHDH,3_prime_UTR_variant,,ENST00000520557,;	A	ENSG00000104808	ENST00000221403	Transcript	3_prime_UTR_variant	1055	.	.	.	.	.	.	.	1	DHDH	HGNC	17887	protein_coding	YES	CCDS12741.1	ENSP00000221403	DHDH_HUMAN	.	UPI000006DD01	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCCGAATAA	.	4	ESCA
ZNF766	0	.	GRCh37	19	52793497	52793497	+	Silent	SNP	A	A	G	rs777241234	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453A>G	p.%3D	p.R151R	ENST00000439461	4/4	17	13	4	8	8	0	ZNF766,synonymous_variant,p.%3D,ENST00000359102,;ZNF766,synonymous_variant,p.%3D,ENST00000593703,;ZNF766,synonymous_variant,p.%3D,ENST00000593612,;ZNF766,synonymous_variant,p.%3D,ENST00000439461,;ZNF766,synonymous_variant,p.%3D,ENST00000595000,;ZNF766,3_prime_UTR_variant,,ENST00000599581,;ZNF766,downstream_gene_variant,,ENST00000600821,;ZNF766,downstream_gene_variant,,ENST00000595149,;CTD-2525I3.5,intron_variant,,ENST00000594865,;	G	ENSG00000196214	ENST00000439461	Transcript	synonymous_variant	496	453	151	R	agA/agG	rs777241234	.	.	1	ZNF766	HGNC	28063	protein_coding	YES	CCDS46163.1	ENSP00000409652	ZN766_HUMAN	M0R1P9_HUMAN,M0R139_HUMAN,M0QXI4_HUMAN	UPI0000202AF7	.	.	.	4/4	.	hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAAAGAATTTA	byCluster	3	ESCA
ZNF525	0	.	GRCh37	19	53887291	53887291	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2019C>G	.	.	ENST00000474037	4/4	28	17	11	18	18	0	ZNF525,3_prime_UTR_variant,,ENST00000474037,;ZNF525,3_prime_UTR_variant,,ENST00000467003,;ZNF525,intron_variant,,ENST00000593918,;ZNF525,intron_variant,,ENST00000475179,;ZNF525,downstream_gene_variant,,ENST00000355326,;ZNF525,non_coding_transcript_exon_variant,,ENST00000601790,;ZNF525,downstream_gene_variant,,ENST00000600148,;CTD-3141N22.1,upstream_gene_variant,,ENST00000459631,;	G	ENSG00000203326	ENST00000474037	Transcript	3_prime_UTR_variant	3593	.	.	.	.	.	.	.	1	ZNF525	HGNC	29423	protein_coding	YES	.	ENSP00000417696	.	J3KR62_HUMAN,J3KR51_HUMAN	UPI0000EE700C	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATCAGAAA	.	5	ESCA
LILRB3	0	.	GRCh37	19	54721222	54721222	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1718G>C	p.Arg573Thr	p.R573T	ENST00000245620	12/13	116	94	21	76	76	0	LILRB3,missense_variant,p.Arg572Thr,ENST00000424807,;LILRB3,missense_variant,p.Arg589Thr,ENST00000407860,;LILRA6,missense_variant,p.Arg573Thr,ENST00000270464,;LILRB3,missense_variant,p.Arg572Thr,ENST00000391750,;LILRA6,missense_variant,p.Arg572Thr,ENST00000440558,;LILRA6,missense_variant,p.Arg573Thr,ENST00000419410,;LILRB3,missense_variant,p.Arg573Thr,ENST00000245620,;LILRB3,missense_variant,p.Arg584Thr,ENST00000346401,;LILRA6,3_prime_UTR_variant,,ENST00000391735,;LILRB3,downstream_gene_variant,,ENST00000445347,;LILRB3,non_coding_transcript_exon_variant,,ENST00000469273,;LILRB3,3_prime_UTR_variant,,ENST00000414379,;LILRB3,non_coding_transcript_exon_variant,,ENST00000460208,;RPS9,intron_variant,,ENST00000448962,;LILRB3,downstream_gene_variant,,ENST00000436504,;LILRB3,downstream_gene_variant,,ENST00000468668,;	G	ENSG00000204577	ENST00000245620	Transcript	missense_variant	1720	1718	573	R/T	aGa/aCa	.	.	.	-1	LILRB3	HGNC	6607	protein_coding	YES	CCDS46175.1	ENSP00000245620	LIRB3_HUMAN	C9JWL8_HUMAN	UPI0000E04BFA	.	tolerated(0.34)	benign(0.001)	12/13	.	hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGTCTGTCC	.	5	ESCA
LILRB3	0	.	GRCh37	19	54725814	54725825	+	In_Frame_Del	DEL	GGAACAGGGCCT	GGAACAGGGCCT	-	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	GGAACAGGGCCT	GGAACAGGGCCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.533_544delAGGCCCTGTTCC	p.Gln178_Phe181del	p.Q178_F181del	ENST00000245620	4/13	38	26	12	32	32	0	LILRB3,inframe_deletion,p.Gln178_Phe181del,ENST00000424807,;LILRB3,inframe_deletion,p.Gln178_Phe181del,ENST00000407860,;LILRB3,inframe_deletion,p.Gln178_Phe181del,ENST00000391750,;LILRB3,inframe_deletion,p.Gln178_Phe181del,ENST00000245620,;LILRB3,inframe_deletion,p.Gln178_Phe181del,ENST00000346401,;LILRA6,intron_variant,,ENST00000270464,;LILRA6,intron_variant,,ENST00000391735,;LILRA6,intron_variant,,ENST00000440558,;LILRA6,intron_variant,,ENST00000419410,;LILRB3,downstream_gene_variant,,ENST00000445347,;CTB-83J4.1,upstream_gene_variant,,ENST00000601161,;LILRB3,upstream_gene_variant,,ENST00000469273,;LILRB3,inframe_deletion,p.Gln178_Phe181del,ENST00000414379,;RPS9,intron_variant,,ENST00000448962,;LILRB3,upstream_gene_variant,,ENST00000436504,;LILRB3,downstream_gene_variant,,ENST00000468668,;LILRB3,upstream_gene_variant,,ENST00000460208,;	-	ENSG00000204577	ENST00000245620	Transcript	inframe_deletion	535-546	533-544	178-182	QALFP/P	cAGGCCCTGTTCCct/cct	.	.	.	-1	LILRB3	HGNC	6607	protein_coding	YES	CCDS46175.1	ENSP00000245620	LIRB3_HUMAN	C9JWL8_HUMAN	UPI0000E04BFA	.	.	.	4/13	.	hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF32,Gene3D:2.60.40.10,Pfam_domain:PF13895,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCACAGGGAACAGGGCCTGGAAC	.	2	ESCA
ZNF582	0	.	GRCh37	19	56895667	56895667	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1119A>G	p.%3D	p.G373G	ENST00000301310	5/5	36	25	11	27	27	0	ZNF582,synonymous_variant,p.%3D,ENST00000586929,;ZNF582,synonymous_variant,p.%3D,ENST00000301310,;ZNF582,intron_variant,,ENST00000589143,;AC006116.12,upstream_gene_variant,,ENST00000589671,;ZNF542,downstream_gene_variant,,ENST00000467807,;ZNF542,downstream_gene_variant,,ENST00000495307,;ZNF542,downstream_gene_variant,,ENST00000490123,;ZNF582,downstream_gene_variant,,ENST00000593145,;ZNF582,downstream_gene_variant,,ENST00000587778,;SLC25A36P1,upstream_gene_variant,,ENST00000590111,;	C	ENSG00000018869	ENST00000301310	Transcript	synonymous_variant	1278	1119	373	G	ggA/ggG	.	.	.	-1	ZNF582	HGNC	26421	protein_coding	YES	CCDS33121.1	ENSP00000301310	ZN582_HUMAN	B4DQZ9_HUMAN	UPI000006D278	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF115,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTTCCACA	.	5	ESCA
SLC25A41	0	.	GRCh37	19	6433719	6433719	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-15G>A	.	.	ENST00000321510	1/7	26	17	9	24	24	0	SLC25A41,5_prime_UTR_variant,,ENST00000321510,;SLC25A23,downstream_gene_variant,,ENST00000601322,;SLC25A23,downstream_gene_variant,,ENST00000598908,;SLC25A23,downstream_gene_variant,,ENST00000595810,;SLC25A23,downstream_gene_variant,,ENST00000601760,;SLC25A41,5_prime_UTR_variant,,ENST00000458275,;SLC25A41,5_prime_UTR_variant,,ENST00000597558,;SLC25A23,downstream_gene_variant,,ENST00000264088,;SLC25A23,downstream_gene_variant,,ENST00000598704,;	T	ENSG00000181240	ENST00000321510	Transcript	5_prime_UTR_variant	55	.	.	.	.	.	.	.	-1	SLC25A41	HGNC	28533	protein_coding	YES	CCDS45937.1	ENSP00000322649	S2541_HUMAN	.	UPI00003751E5	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGACACCTG	.	5	ESCA
ZNF358	0	.	GRCh37	19	7584255	7584255	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.127C>T	p.Pro43Ser	p.P43S	ENST00000597229	2/2	53	50	3	32	32	0	ZNF358,missense_variant,p.Pro43Ser,ENST00000394341,;ZNF358,missense_variant,p.Pro43Ser,ENST00000597229,;ZNF358,missense_variant,p.Pro43Ser,ENST00000596712,;CTD-2207O23.12,3_prime_UTR_variant,,ENST00000599312,;MCOLN1,upstream_gene_variant,,ENST00000264079,;MCOLN1,upstream_gene_variant,,ENST00000601003,;CTD-2207O23.11,downstream_gene_variant,,ENST00000602083,;CTD-2207O23.12,non_coding_transcript_exon_variant,,ENST00000597384,;MCOLN1,upstream_gene_variant,,ENST00000394321,;MCOLN1,upstream_gene_variant,,ENST00000596390,;	T	ENSG00000198816	ENST00000597229	Transcript	missense_variant	297	127	43	P/S	Cca/Tca	.	.	.	1	ZNF358	HGNC	16838	protein_coding	YES	CCDS32890.2	ENSP00000472305	ZN358_HUMAN	M0R2S5_HUMAN	UPI0000201F0C	.	tolerated(0.36)	benign(0.024)	2/2	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGACCCAGAG	.	2	ESCA
MFN2	0	.	GRCh37	1	12066704	12066704	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1826C>G	p.Ser609Cys	p.S609C	ENST00000235329	16/19	68	47	21	48	48	0	MFN2,missense_variant,p.Ser609Cys,ENST00000235329,;MFN2,missense_variant,p.Ser609Cys,ENST00000444836,;	G	ENSG00000116688	ENST00000235329	Transcript	missense_variant	2148	1826	609	S/C	tCc/tGc	.	.	.	1	MFN2	HGNC	16877	protein_coding	YES	CCDS30587.1	ENSP00000235329	MFN2_HUMAN	Q5JXC5_HUMAN	UPI0000039854	.	deleterious(0.01)	benign(0.034)	16/19	.	hmmpanther:PTHR10465,hmmpanther:PTHR10465:SF1,Pfam_domain:PF04799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCCTCCTTGA	.	3	ESCA
FCRL4	0	.	GRCh37	1	157551430	157551430	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1140C>T	p.%3D	p.T380T	ENST00000271532	7/12	43	31	12	24	24	0	FCRL4,synonymous_variant,p.%3D,ENST00000271532,;FCRL4,non_coding_transcript_exon_variant,,ENST00000448509,;FCRL4,upstream_gene_variant,,ENST00000479869,;	A	ENSG00000163518	ENST00000271532	Transcript	synonymous_variant	1276	1140	380	T	acC/acT	.	.	.	-1	FCRL4	HGNC	18507	protein_coding	YES	CCDS1166.1	ENSP00000271532	FCRL4_HUMAN	.	UPI000006E26B	.	.	.	7/12	.	Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGGGTCTC	.	5	ESCA
ADCY10	0	.	GRCh37	1	167805612	167805612	+	Missense_Mutation	SNP	C	C	T	rs778523169	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3244G>A	p.Asp1082Asn	p.D1082N	ENST00000367851	23/33	18	7	10	13	13	0	ADCY10,missense_variant,p.Asp929Asn,ENST00000545172,;ADCY10,missense_variant,p.Asp1082Asn,ENST00000367851,;ADCY10,missense_variant,p.Asp990Asn,ENST00000367848,;ADCY10,intron_variant,,ENST00000485964,;	T	ENSG00000143199	ENST00000367851	Transcript	missense_variant	3429	3244	1082	D/N	Gac/Aac	rs778523169	.	.	-1	ADCY10	HGNC	21285	protein_coding	YES	CCDS1265.1	ENSP00000356825	ADCYA_HUMAN	.	UPI0000204D00	.	tolerated(0.81)	benign(0)	23/33	.	hmmpanther:PTHR16305:SF23,hmmpanther:PTHR16305,PIRSF_domain:PIRSF011131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCATTTT	.	5	ESCA
SLC9C2	0	.	GRCh37	1	173502849	173502849	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2062T>C	p.Cys688Arg	p.C688R	ENST00000367714	17/28	60	56	4	47	47	0	SLC9C2,missense_variant,p.Cys688Arg,ENST00000367714,;SLC9C2,3_prime_UTR_variant,,ENST00000536496,;SLC9C2,non_coding_transcript_exon_variant,,ENST00000466087,;	G	ENSG00000162753	ENST00000367714	Transcript	missense_variant	2485	2062	688	C/R	Tgt/Cgt	.	.	.	-1	SLC9C2	HGNC	28664	protein_coding	YES	CCDS1308.1	ENSP00000356687	SL9C2_HUMAN	F5H342_HUMAN	UPI0000197379	.	deleterious(0.01)	probably_damaging(0.933)	17/28	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10110:SF91,hmmpanther:PTHR10110,Gene3D:1.20.120.350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACACAAAAGA	.	2	ESCA
PAPPA2	0	.	GRCh37	1	176664899	176664899	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2650T>G	p.Cys884Gly	p.C884G	ENST00000367662	7/23	71	62	8	69	69	0	PAPPA2,missense_variant,p.Cys884Gly,ENST00000367662,;PAPPA2,downstream_gene_variant,,ENST00000367661,;	G	ENSG00000116183	ENST00000367662	Transcript	missense_variant	3814	2650	884	C/G	Tgc/Ggc	.	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	deleterious(0)	probably_damaging(0.999)	7/23	.	hmmpanther:PTHR19325:SF349,hmmpanther:PTHR19325,Gene3D:2.60.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGCTTGCACT	.	4	ESCA
UBR4	0	.	GRCh37	1	19440346	19440346	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11329-25G>C	.	.	ENST00000375254	.	37	31	6	30	30	0	UBR4,3_prime_UTR_variant,,ENST00000375218,;UBR4,intron_variant,,ENST00000375254,;UBR4,intron_variant,,ENST00000375217,;UBR4,intron_variant,,ENST00000375267,;UBR4,intron_variant,,ENST00000375226,;UBR4,upstream_gene_variant,,ENST00000494503,;UBR4,upstream_gene_variant,,ENST00000466969,;	G	ENSG00000127481	ENST00000375254	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	UBR4	HGNC	30313	protein_coding	YES	CCDS189.1	ENSP00000364403	UBR4_HUMAN	Q96HY5_HUMAN	UPI000021276F	.	.	.	.	76/105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTGTCAGGCT	.	3	ESCA
UBR4	0	.	GRCh37	1	19440388	19440388	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11328+51G>C	.	.	ENST00000375254	.	33	26	7	27	27	0	UBR4,missense_variant,p.Gln208His,ENST00000375218,;UBR4,intron_variant,,ENST00000375254,;UBR4,intron_variant,,ENST00000375217,;UBR4,intron_variant,,ENST00000375267,;UBR4,intron_variant,,ENST00000375226,;UBR4,upstream_gene_variant,,ENST00000494503,;UBR4,upstream_gene_variant,,ENST00000466969,;	G	ENSG00000127481	ENST00000375254	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	UBR4	HGNC	30313	protein_coding	YES	CCDS189.1	ENSP00000364403	UBR4_HUMAN	Q96HY5_HUMAN	UPI000021276F	.	.	.	.	76/105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCTTCTGATC	.	3	ESCA
KCNT2	0	.	GRCh37	1	196459055	196459055	+	Missense_Mutation	SNP	C	C	T	rs778987960	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188G>A	p.Arg63His	p.R63H	ENST00000294725	3/28	13	8	5	16	16	0	KCNT2,missense_variant,p.Arg63His,ENST00000609185,;KCNT2,missense_variant,p.Arg63His,ENST00000294725,;KCNT2,missense_variant,p.Arg63His,ENST00000367433,;KCNT2,missense_variant,p.Arg63His,ENST00000367431,;KCNT2,5_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,;	T	ENSG00000162687	ENST00000294725	Transcript	missense_variant	1104	188	63	R/H	cGc/cAc	rs778987960,COSM677351,COSM1127203	.	.	-1	KCNT2	HGNC	18866	protein_coding	YES	CCDS1384.1	ENSP00000294725	KCNT2_HUMAN	A9LNM6_HUMAN	UPI00001E0966	.	deleterious(0)	benign(0.34)	3/28	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9,Gene3D:1.10.287.70	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	ACAGGCGTATC	.	3	ESCA
PRKCZ	0	.	GRCh37	1	2113691	2113691	+	Intron	SNP	G	G	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1576-2331G>T	.	.	ENST00000378567	.	53	35	18	57	57	0	PRKCZ,intron_variant,,ENST00000400921,;PRKCZ,intron_variant,,ENST00000461106,;PRKCZ,intron_variant,,ENST00000378567,;PRKCZ,intron_variant,,ENST00000400920,;C1orf86,downstream_gene_variant,,ENST00000400919,;C1orf86,downstream_gene_variant,,ENST00000400918,;RP11-181G12.2,non_coding_transcript_exon_variant,,ENST00000333854,;RP11-181G12.2,non_coding_transcript_exon_variant,,ENST00000536678,;RP11-181G12.2,downstream_gene_variant,,ENST00000444529,;PRKCZ,intron_variant,,ENST00000479263,;C1orf86,downstream_gene_variant,,ENST00000469733,;PRKCZ,intron_variant,,ENST00000478770,;PRKCZ,intron_variant,,ENST00000505322,;C1orf86,downstream_gene_variant,,ENST00000414253,;C1orf86,downstream_gene_variant,,ENST00000428120,;	T	ENSG00000067606	ENST00000378567	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PRKCZ	HGNC	9412	protein_coding	YES	CCDS37.1	ENSP00000367830	KPCZ_HUMAN	J3KRP7_HUMAN,F2Z2H9_HUMAN,D6RGG1_HUMAN,D6RG01_HUMAN,D6REZ8_HUMAN,D6RDM0_HUMAN,D6RD31_HUMAN,D6RCN4_HUMAN,D6RC84_HUMAN,D6RBD4_HUMAN,D6RAU1_HUMAN,D6RAN5_HUMAN	UPI0000169EB7	.	.	.	.	16/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTGGGGGGC	.	5	ESCA
OBSCN	0	.	GRCh37	1	228511299	228511299	+	Missense_Mutation	SNP	G	G	A	rs375864261	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18515G>A	p.Arg6172His	p.R6172H	ENST00000570156	67/116	63	45	18	59	59	0	OBSCN,missense_variant,p.Arg2849His,ENST00000366707,;OBSCN,missense_variant,p.Arg2334His,ENST00000366709,;OBSCN,missense_variant,p.Arg5215His,ENST00000284548,;OBSCN,missense_variant,p.Arg5215His,ENST00000422127,;OBSCN,missense_variant,p.Arg6172His,ENST00000570156,;	A	ENSG00000154358	ENST00000570156	Transcript	missense_variant	18589	18515	6172	R/H	cGt/cAt	rs375864261	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	probably_damaging(0.999)	67/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCGTGTGG	byFrequency|byCluster	5	ESCA
GNG4	0	.	GRCh37	1	235715256	235715256	+	3'UTR	SNP	C	C	T	rs527657436	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*153G>A	.	.	ENST00000391854	4/4	14	10	4	8	8	0	GNG4,3_prime_UTR_variant,,ENST00000366598,;GNG4,3_prime_UTR_variant,,ENST00000366597,;GNG4,3_prime_UTR_variant,,ENST00000391854,;GNG4,3_prime_UTR_variant,,ENST00000450593,;GNG4,non_coding_transcript_exon_variant,,ENST00000484517,;	T	ENSG00000168243	ENST00000391854	Transcript	3_prime_UTR_variant	835	.	.	.	.	rs527657436	.	.	-1	GNG4	HGNC	4407	protein_coding	YES	CCDS1607.1	ENSP00000375727	GBG4_HUMAN	B1APZ0_HUMAN	UPI000012B22C	.	.	.	4/4	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCCACGAAGA	by1000G	3	ESCA
IL22RA1	0	.	GRCh37	1	24447957	24447957	+	Missense_Mutation	SNP	C	C	T	rs751761313	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1063G>A	p.Ala355Thr	p.A355T	ENST00000270800	7/7	74	66	8	78	78	0	IL22RA1,missense_variant,p.Ala355Thr,ENST00000270800,;	T	ENSG00000142677	ENST00000270800	Transcript	missense_variant	1102	1063	355	A/T	Gct/Act	rs751761313	.	.	-1	IL22RA1	HGNC	13700	protein_coding	YES	CCDS247.1	ENSP00000270800	I22R1_HUMAN	.	UPI0000071143	.	tolerated(0.2)	benign(0.004)	7/7	.	hmmpanther:PTHR20859:SF20,hmmpanther:PTHR20859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCAGCGTTTG	byFrequency	4	ESCA
PRDM16	0	.	GRCh37	1	3329081	3329081	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2320G>T	p.Asp774Tyr	p.D774Y	ENST00000270722	9/17	75	60	14	75	75	0	PRDM16,missense_variant,p.Asp774Tyr,ENST00000441472,;PRDM16,missense_variant,p.Asp775Tyr,ENST00000514189,;PRDM16,missense_variant,p.Asp583Tyr,ENST00000509860,;PRDM16,missense_variant,p.Asp774Tyr,ENST00000270722,;PRDM16,missense_variant,p.Asp774Tyr,ENST00000442529,;PRDM16,missense_variant,p.Asp775Tyr,ENST00000511072,;PRDM16,missense_variant,p.Asp775Tyr,ENST00000378398,;PRDM16,missense_variant,p.Asp774Tyr,ENST00000378391,;PRDM16,non_coding_transcript_exon_variant,,ENST00000512462,;	T	ENSG00000142611	ENST00000270722	Transcript	missense_variant	2369	2320	774	D/Y	Gat/Tat	.	.	.	1	PRDM16	HGNC	14000	protein_coding	YES	CCDS41236.2	ENSP00000270722	PRD16_HUMAN	.	UPI0000458A29	.	deleterious(0)	probably_damaging(0.986)	9/17	.	hmmpanther:PTHR24393:SF4,hmmpanther:PTHR24393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTGATCTC	.	5	ESCA
MRPS15	0	.	GRCh37	1	36923529	36923529	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.439C>T	p.Arg147Ter	p.R147*	ENST00000373116	6/8	74	56	18	46	46	0	MRPS15,stop_gained,p.Arg147Ter,ENST00000373116,;MRPS15,non_coding_transcript_exon_variant,,ENST00000462067,;MRPS15,non_coding_transcript_exon_variant,,ENST00000488606,;MRPS15,upstream_gene_variant,,ENST00000477040,;	A	ENSG00000116898	ENST00000373116	Transcript	stop_gained	601	439	147	R/*	Cga/Tga	.	.	.	-1	MRPS15	HGNC	14504	protein_coding	YES	CCDS411.1	ENSP00000362208	RT15_HUMAN	D3DPS9_HUMAN	UPI0000135287	.	.	.	6/8	.	Superfamily_domains:SSF47060,Pfam_domain:PF00312,Gene3D:1.10.287.10,hmmpanther:PTHR23321:SF26,hmmpanther:PTHR23321,HAMAP:MF_01343_B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTCGATGTT	.	5	ESCA
MOB3C	0	.	GRCh37	1	47075288	47075288	+	3'UTR	SNP	G	G	C	rs760790805	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39C>G	.	.	ENST00000271139	4/4	26	17	8	26	26	0	MOB3C,3_prime_UTR_variant,,ENST00000371940,;MOB3C,3_prime_UTR_variant,,ENST00000271139,;MOB3C,3_prime_UTR_variant,,ENST00000319928,;MKNK1,intron_variant,,ENST00000545730,;MKNK1,intron_variant,,ENST00000531769,;MOB3C,downstream_gene_variant,,ENST00000477318,;	C	ENSG00000142961	ENST00000271139	Transcript	3_prime_UTR_variant	903	.	.	.	.	rs760790805	.	.	-1	MOB3C	HGNC	29800	protein_coding	YES	CCDS539.1	ENSP00000271139	.	.	UPI000034ECBB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCAGATCGT	.	5	ESCA
TNNI3K	0	.	GRCh37	1	74957871	74957871	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2575A>G	p.Ser859Gly	p.S859G	ENST00000370891	25/27	63	57	6	48	48	0	TNNI3K,missense_variant,p.Ser859Gly,ENST00000370891,;FPGT-TNNI3K,missense_variant,p.Ser872Gly,ENST00000557284,;TNNI3K,missense_variant,p.Ser758Gly,ENST00000326637,;LRRC53,intron_variant,,ENST00000294635,;	G	ENSG00000116783	ENST00000370891	Transcript	missense_variant	2591	2575	859	S/G	Agt/Ggt	.	.	.	1	TNNI3K	HGNC	19661	protein_coding	YES	.	ENSP00000359928	TNI3K_HUMAN	A6NHC7_HUMAN	UPI00005E2707	.	tolerated_low_confidence(0.33)	benign(0.028)	25/27	.	hmmpanther:PTHR23257:SF63,hmmpanther:PTHR23257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCGGAGTCAT	.	4	ESCA
ACSS1	0	.	GRCh37	20	24993469	24993469	+	Silent	SNP	G	G	A	rs779037733	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1686C>T	p.%3D	p.T562T	ENST00000323482	11/14	121	109	12	44	44	0	ACSS1,synonymous_variant,p.%3D,ENST00000542618,;ACSS1,synonymous_variant,p.%3D,ENST00000323482,;ACSS1,synonymous_variant,p.%3D,ENST00000537502,;ACSS1,intron_variant,,ENST00000432802,;ACSS1,upstream_gene_variant,,ENST00000484396,;	A	ENSG00000154930	ENST00000323482	Transcript	synonymous_variant	1766	1686	562	T	acC/acT	rs779037733,COSM3544844,COSM3544845	.	.	-1	ACSS1	HGNC	16091	protein_coding	YES	CCDS13167.1	ENSP00000316924	ACS2L_HUMAN	Q658R1_HUMAN	UPI00001615FE	.	.	.	11/14	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF110,Gene3D:3.30.300.30,TIGRFAM_domain:TIGR02188,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGCGGTCCC	.	4	ESCA
NINL	0	.	GRCh37	20	25434171	25434171	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4065G>A	p.%3D	p.E1355E	ENST00000278886	24/24	89	70	18	34	33	0	NINL,synonymous_variant,p.%3D,ENST00000422516,;NINL,synonymous_variant,p.%3D,ENST00000278886,;GINS1,downstream_gene_variant,,ENST00000262460,;NINL,non_coding_transcript_exon_variant,,ENST00000464285,;NINL,downstream_gene_variant,,ENST00000496509,;GINS1,downstream_gene_variant,,ENST00000481735,;	T	ENSG00000101004	ENST00000278886	Transcript	synonymous_variant	4139	4065	1355	E	gaG/gaA	.	.	.	-1	NINL	HGNC	29163	protein_coding	YES	CCDS33452.1	ENSP00000278886	NINL_HUMAN	.	UPI0000206B64	.	.	.	24/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTCTCGGC	.	5	ESCA
NINL	0	.	GRCh37	20	25434213	25434213	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4023G>A	p.%3D	p.V1341V	ENST00000278886	24/24	83	66	16	35	35	0	NINL,synonymous_variant,p.%3D,ENST00000422516,;NINL,synonymous_variant,p.%3D,ENST00000278886,;NINL,non_coding_transcript_exon_variant,,ENST00000464285,;NINL,downstream_gene_variant,,ENST00000496509,;GINS1,downstream_gene_variant,,ENST00000481735,;	T	ENSG00000101004	ENST00000278886	Transcript	synonymous_variant	4097	4023	1341	V	gtG/gtA	.	.	.	-1	NINL	HGNC	29163	protein_coding	YES	CCDS33452.1	ENSP00000278886	NINL_HUMAN	.	UPI0000206B64	.	.	.	24/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTCACCAG	.	5	ESCA
SNTA1	0	.	GRCh37	20	31997973	31997973	+	Missense_Mutation	SNP	C	C	T	rs771369802	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1205G>A	p.Arg402Gln	p.R402Q	ENST00000217381	6/8	111	88	22	44	44	0	SNTA1,missense_variant,p.Arg402Gln,ENST00000217381,;	T	ENSG00000101400	ENST00000217381	Transcript	missense_variant	1477	1205	402	R/Q	cGg/cAg	rs771369802	.	.	-1	SNTA1	HGNC	11167	protein_coding	YES	CCDS13220.1	ENSP00000217381	SNTA1_HUMAN	B3KTR0_HUMAN	UPI0000135B08	.	tolerated(0.6)	benign(0.211)	6/8	.	hmmpanther:PTHR10554:SF6,hmmpanther:PTHR10554,SMART_domains:SM00233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCCGGTGA	byFrequency	5	ESCA
EPPIN	0	.	GRCh37	20	44174456	44174456	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92-47C>G	.	.	ENST00000555685	.	128	120	8	46	46	0	EPPIN,5_prime_UTR_variant,,ENST00000336443,;EPPIN-WFDC6,intron_variant,,ENST00000504988,;EPPIN,intron_variant,,ENST00000354280,;EPPIN,intron_variant,,ENST00000409554,;EPPIN,intron_variant,,ENST00000555685,;EPPIN,intron_variant,,ENST00000496898,;	C	ENSG00000101448	ENST00000555685	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	EPPIN	HGNC	15932	protein_coding	YES	CCDS56195.1	ENSP00000452085	EPPI_HUMAN	.	UPI0000E5A337	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATAGTGTCTCC	.	2	ESCA
FAM65C	0	.	GRCh37	20	49231294	49231294	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.336+1245C>T	.	.	ENST00000327979	.	93	83	10	44	44	0	FAM65C,intron_variant,,ENST00000327979,;FAM65C,intron_variant,,ENST00000535356,;FAM65C,intron_variant,,ENST00000045083,;MIR1302-5,non_coding_transcript_exon_variant,,ENST00000408164,;FAM65C,intron_variant,,ENST00000462493,;	A	ENSG00000042062	ENST00000327979	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	FAM65C	HGNC	16168	protein_coding	YES	CCDS13431.2	ENSP00000332663	FA65C_HUMAN	.	UPI0000DA5AF4	.	.	.	.	4/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTCTGAAAAA	.	3	ESCA
ARVCF	0	.	GRCh37	22	19958768	19958768	+	Missense_Mutation	SNP	C	C	T	rs72554700	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2872G>A	p.Val958Ile	p.V958I	ENST00000263207	19/20	46	37	8	30	30	0	ARVCF,missense_variant,p.Val958Ile,ENST00000263207,;ARVCF,missense_variant,p.Val889Ile,ENST00000406522,;ARVCF,missense_variant,p.Val895Ile,ENST00000344269,;ARVCF,missense_variant,p.Val952Ile,ENST00000406259,;ARVCF,missense_variant,p.Val895Ile,ENST00000401994,;COMT,downstream_gene_variant,,ENST00000428707,;COMT,downstream_gene_variant,,ENST00000407537,;COMT,downstream_gene_variant,,ENST00000361682,;COMT,downstream_gene_variant,,ENST00000449653,;COMT,downstream_gene_variant,,ENST00000412786,;COMT,downstream_gene_variant,,ENST00000406520,;COMT,downstream_gene_variant,,ENST00000403710,;ARVCF,downstream_gene_variant,,ENST00000480792,;ARVCF,intron_variant,,ENST00000495096,;COMT,downstream_gene_variant,,ENST00000207636,;	T	ENSG00000099889	ENST00000263207	Transcript	missense_variant	3164	2872	958	V/I	Gtt/Att	rs72554700	.	.	-1	ARVCF	HGNC	728	protein_coding	YES	CCDS13771.1	ENSP00000263207	ARVC_HUMAN	.	UPI00001260C8	.	deleterious_low_confidence(0.02)	probably_damaging(0.987)	19/20	.	hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF5	.	.	.	.	.	.	.	T:0.0002	T:0.0006	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAACGGGCT	byFrequency|byCluster	5	ESCA
ATXN10	0	.	GRCh37	22	46239555	46239555	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4A>T	.	.	ENST00000252934	12/12	82	51	31	43	43	0	ATXN10,3_prime_UTR_variant,,ENST00000402380,;ATXN10,3_prime_UTR_variant,,ENST00000381061,;ATXN10,3_prime_UTR_variant,,ENST00000252934,;ATXN10,downstream_gene_variant,,ENST00000493643,;	T	ENSG00000130638	ENST00000252934	Transcript	3_prime_UTR_variant	1697	.	.	.	.	.	.	.	1	ATXN10	HGNC	10549	protein_coding	YES	CCDS14070.1	ENSP00000252934	ATX10_HUMAN	Q9NTC6_HUMAN	UPI0000052A56	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATGAACTAC	.	5	ESCA
POLR2D	0	.	GRCh37	2	128604279	128604279	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1402A>G	.	.	ENST00000272645	4/4	20	9	10	9	9	0	POLR2D,3_prime_UTR_variant,,ENST00000272645,;POLR2D,3_prime_UTR_variant,,ENST00000409955,;POLR2D,downstream_gene_variant,,ENST00000409698,;RNU6-395P,downstream_gene_variant,,ENST00000365662,;RP5-935K16.1,upstream_gene_variant,,ENST00000602909,;POLR2D,downstream_gene_variant,,ENST00000487079,;AC006011.4,downstream_gene_variant,,ENST00000442758,;	C	ENSG00000144231	ENST00000272645	Transcript	3_prime_UTR_variant	1888	.	.	.	.	.	.	.	-1	POLR2D	HGNC	9191	protein_coding	YES	CCDS2151.1	ENSP00000272645	RPB4_HUMAN	Q587J0_HUMAN,Q53T47_HUMAN,E9PB93_HUMAN	UPI0000003EF2	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTTCTTCA	.	5	ESCA
LRP1B	0	.	GRCh37	2	140989056	140989056	+	3'UTR	SNP	C	C	G	rs541932143	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1699G>C	.	.	ENST00000389484	91/91	30	21	9	14	14	0	LRP1B,3_prime_UTR_variant,,ENST00000389484,;LRP1B,downstream_gene_variant,,ENST00000437977,;	G	ENSG00000168702	ENST00000389484	Transcript	3_prime_UTR_variant	16471	.	.	.	.	rs541932143	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	91/91	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCATTGT	by1000G	5	ESCA
PKP4	0	.	GRCh37	2	159526239	159526239	+	Silent	SNP	C	C	T	rs138568714	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2736C>T	p.%3D	p.Y912Y	ENST00000389759	17/22	32	23	8	23	23	0	PKP4,synonymous_variant,p.%3D,ENST00000389759,;PKP4,synonymous_variant,p.%3D,ENST00000389757,;AC005042.4,intron_variant,,ENST00000342892,;PKP4,downstream_gene_variant,,ENST00000495123,;PKP4,3_prime_UTR_variant,,ENST00000426248,;PKP4,non_coding_transcript_exon_variant,,ENST00000486254,;PKP4,non_coding_transcript_exon_variant,,ENST00000480171,;PKP4,downstream_gene_variant,,ENST00000483881,;	T	ENSG00000144283	ENST00000389759	Transcript	synonymous_variant	2848	2736	912	Y	taC/taT	rs138568714	.	.	1	PKP4	HGNC	9026	protein_coding	YES	CCDS33305.1	ENSP00000374409	PKP4_HUMAN	Q53TM5_HUMAN	UPI000044D379	.	.	.	17/22	.	hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF8,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATACGCCAT	byCluster	5	ESCA
PDE11A	0	.	GRCh37	2	178681580	178681580	+	Missense_Mutation	SNP	C	C	G	rs775823865	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1713G>C	p.Trp571Cys	p.W571C	ENST00000286063	9/20	23	17	6	11	11	0	PDE11A,missense_variant,p.Trp321Cys,ENST00000358450,;PDE11A,missense_variant,p.Trp571Cys,ENST00000286063,;PDE11A,missense_variant,p.Trp127Cys,ENST00000389683,;PDE11A,missense_variant,p.Trp213Cys,ENST00000449286,;PDE11A,missense_variant,p.Trp213Cys,ENST00000409504,;PDE11A,intron_variant,,ENST00000433879,;PDE11A,non_coding_transcript_exon_variant,,ENST00000492761,;PDE11A,non_coding_transcript_exon_variant,,ENST00000497003,;	G	ENSG00000128655	ENST00000286063	Transcript	missense_variant	2031	1713	571	W/C	tgG/tgC	rs775823865	.	.	-1	PDE11A	HGNC	8773	protein_coding	YES	CCDS33334.1	ENSP00000286063	PDE11_HUMAN	Q53S13_HUMAN,Q53S07_HUMAN,F8WAE1_HUMAN	UPI00001402C1	.	tolerated(0.17)	probably_damaging(0.99)	9/20	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF105,Superfamily_domains:SSF55781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCCCAGGA	.	5	ESCA
TTN	0	.	GRCh37	2	179647637	179647637	+	Missense_Mutation	SNP	C	C	T	rs371757623	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2996G>A	p.Arg999His	p.R999H	ENST00000589042	18/363	45	32	13	27	27	0	TTN,missense_variant,p.Arg999His,ENST00000360870,;TTN,missense_variant,p.Arg999His,ENST00000342992,;TTN,missense_variant,p.Arg953His,ENST00000342175,;TTN,missense_variant,p.Arg953His,ENST00000359218,;TTN,missense_variant,p.Arg999His,ENST00000589042,;TTN,missense_variant,p.Arg999His,ENST00000591111,;TTN,missense_variant,p.Arg953His,ENST00000460472,;TTN,downstream_gene_variant,,ENST00000436599,;RP11-88L24.4,downstream_gene_variant,,ENST00000582038,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	3221	2996	999	R/H	cGt/cAt	rs371757623,COSM3407365,COSM3407364,COSM3407361,COSM3407363,COSM3407362,COSM3407366	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	18/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGACGAGCA	byFrequency|byCluster	5	ESCA
SESTD1	0	.	GRCh37	2	179986657	179986657	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1283-1G>C	.	p.X428_splice	ENST00000428443	.	37	26	11	29	29	0	SESTD1,splice_acceptor_variant,,ENST00000428443,;snoU13,downstream_gene_variant,,ENST00000459087,;SESTD1,splice_acceptor_variant,,ENST00000335289,;SESTD1,splice_acceptor_variant,,ENST00000446758,;SESTD1,splice_acceptor_variant,,ENST00000426988,;	G	ENSG00000187231	ENST00000428443	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	SESTD1	HGNC	18379	protein_coding	YES	CCDS33338.1	ENSP00000415332	SESD1_HUMAN	Q7Z6D3_HUMAN,C9JHW6_HUMAN,C9J4X8_HUMAN	UPI0000043424	.	.	.	.	12/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATCTAAAA	.	5	ESCA
MYT1L	0	.	GRCh37	2	1926292	1926292	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1249T>C	p.Ser417Pro	p.S417P	ENST00000428368	10/25	56	45	11	46	46	0	MYT1L,missense_variant,p.Ser417Pro,ENST00000399161,;MYT1L,missense_variant,p.Ser417Pro,ENST00000428368,;MYT1L,missense_variant,p.Ser71Pro,ENST00000602387,;	G	ENSG00000186487	ENST00000428368	Transcript	missense_variant	1919	1249	417	S/P	Tcg/Ccg	.	.	.	-1	MYT1L	HGNC	7623	protein_coding	YES	CCDS46222.1	ENSP00000396103	MYT1L_HUMAN	.	UPI00004E55EA	.	deleterious(0)	probably_damaging(0.999)	10/25	.	hmmpanther:PTHR10816:SF11,hmmpanther:PTHR10816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCGAGTTCA	.	5	ESCA
PLCL1	0	.	GRCh37	2	198949317	198949317	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076G>T	p.Arg359Ile	p.R359I	ENST00000428675	2/6	57	47	10	44	44	0	PLCL1,missense_variant,p.Arg285Ile,ENST00000487695,;PLCL1,missense_variant,p.Arg359Ile,ENST00000428675,;PLCL1,missense_variant,p.Arg261Ile,ENST00000437704,;PLCL1,3_prime_UTR_variant,,ENST00000435320,;	T	ENSG00000115896	ENST00000428675	Transcript	missense_variant	1474	1076	359	R/I	aGa/aTa	.	.	.	1	PLCL1	HGNC	9063	protein_coding	YES	CCDS2326.2	ENSP00000402861	PLCL1_HUMAN	.	UPI000165BCF5	.	deleterious(0.01)	possibly_damaging(0.61)	2/6	.	hmmpanther:PTHR10336:SF76,hmmpanther:PTHR10336,Gene3D:1.10.238.10,Pfam_domain:PF09279,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E263K|c.787G>A|3,BUFFER|p.E361K|c.1081G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGAGATACG	.	5	ESCA
SATB2	0	.	GRCh37	2	200213817	200213817	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.780G>C	p.Gln260His	p.Q260H	ENST00000417098	7/11	167	160	6	140	140	0	SATB2,missense_variant,p.Gln260His,ENST00000260926,;SATB2,missense_variant,p.Gln142His,ENST00000428695,;SATB2,missense_variant,p.Gln201His,ENST00000443023,;SATB2,missense_variant,p.Gln260His,ENST00000417098,;SATB2,missense_variant,p.Gln260His,ENST00000457245,;SATB2,non_coding_transcript_exon_variant,,ENST00000483346,;	G	ENSG00000119042	ENST00000417098	Transcript	missense_variant	1597	780	260	Q/H	caG/caC	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	tolerated(0.15)	benign(0.002)	7/11	.	hmmpanther:PTHR15116,hmmpanther:PTHR15116:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAGCTGGTT	.	2	ESCA
AOX1	0	.	GRCh37	2	201470309	201470309	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.865G>T	p.Asp289Tyr	p.D289Y	ENST00000374700	10/35	61	48	13	42	42	0	AOX1,missense_variant,p.Asp289Tyr,ENST00000374700,;AOX1,downstream_gene_variant,,ENST00000454629,;AOX1,upstream_gene_variant,,ENST00000485106,;AOX1,upstream_gene_variant,,ENST00000465297,;AOX1,upstream_gene_variant,,ENST00000485965,;	T	ENSG00000138356	ENST00000374700	Transcript	missense_variant	1106	865	289	D/Y	Gat/Tat	.	.	.	1	AOX1	HGNC	553	protein_coding	YES	CCDS33360.1	ENSP00000363832	ADO_HUMAN	C9J244_HUMAN,B4DNI5_HUMAN	UPI0000071863	.	tolerated(0.11)	possibly_damaging(0.898)	10/35	.	PROSITE_profiles:PS51387,hmmpanther:PTHR11908,Gene3D:3.30.43.10,TIGRFAM_domain:TIGR02969,Pfam_domain:PF00941,PIRSF_domain:PIRSF000127,Superfamily_domains:SSF56176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTGATAGA	.	5	ESCA
FAM126B	0	.	GRCh37	2	201846546	201846546	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1040C>T	p.Ala347Val	p.A347V	ENST00000418596	12/12	41	29	11	24	24	0	FAM126B,missense_variant,p.Ala347Val,ENST00000418596,;AC005037.3,intron_variant,,ENST00000413848,;AC005037.3,downstream_gene_variant,,ENST00000332935,;FAM126B,3_prime_UTR_variant,,ENST00000286181,;	A	ENSG00000155744	ENST00000418596	Transcript	missense_variant	1228	1040	347	A/V	gCa/gTa	.	.	.	-1	FAM126B	HGNC	28593	protein_coding	YES	CCDS2335.1	ENSP00000393667	F126B_HUMAN	C9JTA1_HUMAN,C9JNS4_HUMAN,B3KW57_HUMAN	UPI0000074347	.	tolerated(0.68)	benign(0.027)	12/12	.	hmmpanther:PTHR31220:SF3,hmmpanther:PTHR31220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTGCATCA	.	5	ESCA
CCL20	0	.	GRCh37	2	228680209	228680209	+	Missense_Mutation	SNP	G	G	T	rs750593133	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116G>T	p.Arg39Leu	p.R39L	ENST00000358813	2/4	31	25	5	17	17	0	CCL20,missense_variant,p.Arg39Leu,ENST00000358813,;CCL20,missense_variant,p.Arg38Leu,ENST00000409189,;CCL20,non_coding_transcript_exon_variant,,ENST00000473642,;CCL20,non_coding_transcript_exon_variant,,ENST00000489160,;	T	ENSG00000115009	ENST00000358813	Transcript	missense_variant	174	116	39	R/L	cGt/cTt	rs750593133	.	.	1	CCL20	HGNC	10619	protein_coding	YES	CCDS2469.1	ENSP00000351671	CCL20_HUMAN	.	UPI00000339BD	.	tolerated(0.67)	benign(0.258)	2/4	.	hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF72,PROSITE_patterns:PS00472,Pfam_domain:PF00048,Gene3D:2.40.50.40,SMART_domains:SM00199,Superfamily_domains:SSF54117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACCGTATTC	byFrequency	5	ESCA
GIGYF2	0	.	GRCh37	2	233651989	233651989	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.728G>A	p.Arg243Gln	p.R243Q	ENST00000409451	11/31	53	47	6	40	40	0	GIGYF2,missense_variant,p.Arg170Gln,ENST00000423659,;GIGYF2,missense_variant,p.Arg221Gln,ENST00000373563,;GIGYF2,missense_variant,p.Arg243Gln,ENST00000409480,;GIGYF2,missense_variant,p.Arg221Gln,ENST00000409196,;GIGYF2,missense_variant,p.Arg52Gln,ENST00000445650,;GIGYF2,missense_variant,p.Arg243Gln,ENST00000409451,;GIGYF2,missense_variant,p.Arg221Gln,ENST00000440945,;GIGYF2,missense_variant,p.Arg221Gln,ENST00000409547,;GIGYF2,missense_variant,p.Arg52Gln,ENST00000452341,;GIGYF2,missense_variant,p.Arg48Gln,ENST00000421778,;GIGYF2,missense_variant,p.Arg243Gln,ENST00000373566,;GIGYF2,5_prime_UTR_variant,,ENST00000455139,;GIGYF2,5_prime_UTR_variant,,ENST00000436349,;GIGYF2,5_prime_UTR_variant,,ENST00000427649,;GIGYF2,5_prime_UTR_variant,,ENST00000424414,;GIGYF2,upstream_gene_variant,,ENST00000410033,;RNU6-107P,downstream_gene_variant,,ENST00000516643,;GIGYF2,downstream_gene_variant,,ENST00000424038,;GIGYF2,upstream_gene_variant,,ENST00000458528,;	A	ENSG00000204120	ENST00000409451	Transcript	missense_variant	954	728	243	R/Q	cGa/cAa	.	.	.	1	GIGYF2	HGNC	11960	protein_coding	YES	CCDS46542.1	ENSP00000387170	PERQ2_HUMAN	C9JZC0_HUMAN,C9JXQ0_HUMAN,C9JRZ2_HUMAN,C9JPV7_HUMAN,C9JHT0_HUMAN,C9JH18_HUMAN,C9J1A6_HUMAN,C9J0V6_HUMAN	UPI00003FEC8F	.	.	probably_damaging(0.992)	11/31	.	hmmpanther:PTHR14445:SF38,hmmpanther:PTHR14445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGCGACTAG	.	4	ESCA
COL6A3	0	.	GRCh37	2	238280601	238280601	+	Silent	SNP	G	G	A	rs765355858	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4059C>T	p.%3D	p.D1353D	ENST00000295550	9/44	28	16	11	33	33	0	COL6A3,synonymous_variant,p.%3D,ENST00000392003,;COL6A3,synonymous_variant,p.%3D,ENST00000472056,;COL6A3,synonymous_variant,p.%3D,ENST00000409809,;COL6A3,synonymous_variant,p.%3D,ENST00000295550,;COL6A3,synonymous_variant,p.%3D,ENST00000347401,;COL6A3,synonymous_variant,p.%3D,ENST00000346358,;COL6A3,synonymous_variant,p.%3D,ENST00000353578,;COL6A3,synonymous_variant,p.%3D,ENST00000392004,;	A	ENSG00000163359	ENST00000295550	Transcript	synonymous_variant	4512	4059	1353	D	gaC/gaT	rs765355858,COSM3391596,COSM3391597	.	.	-1	COL6A3	HGNC	2213	protein_coding	YES	CCDS33412.1	ENSP00000295550	CO6A3_HUMAN	Q8N4Z1_HUMAN,D9ZGF2_HUMAN	UPI0000456F39	.	.	.	9/44	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992,hmmpanther:PTHR22992:SF83,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTCGTCCAC	byFrequency	5	ESCA
PRKD3	0	.	GRCh37	2	37513341	37513341	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.889C>T	p.Arg297Cys	p.R297C	ENST00000379066	6/19	58	52	5	36	36	0	PRKD3,missense_variant,p.Arg297Cys,ENST00000234179,;PRKD3,missense_variant,p.Arg297Cys,ENST00000379066,;PRKD3,downstream_gene_variant,,ENST00000443187,;PRKD3,non_coding_transcript_exon_variant,,ENST00000494667,;PRKD3,non_coding_transcript_exon_variant,,ENST00000475912,;	A	ENSG00000115825	ENST00000379066	Transcript	missense_variant	1652	889	297	R/C	Cgc/Tgc	.	.	.	-1	PRKD3	HGNC	9408	protein_coding	YES	CCDS1789.1	ENSP00000368356	KPCD3_HUMAN	C9JKP8_HUMAN	UPI0000035B4D	.	deleterious(0)	probably_damaging(0.999)	6/19	.	PROSITE_profiles:PS50081,hmmpanther:PTHR22968,hmmpanther:PTHR22968:SF11,PROSITE_patterns:PS00479,Pfam_domain:PF00130,Gene3D:3.30.60.20,PIRSF_domain:PIRSF000552,SMART_domains:SM00109,Superfamily_domains:SSF57889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTGGCGAAAGA	.	3	ESCA
PSME4	0	.	GRCh37	2	54133795	54133795	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2883A>T	p.Lys961Asn	p.K961N	ENST00000404125	26/47	53	34	19	29	29	0	PSME4,missense_variant,p.Lys105Asn,ENST00000421748,;PSME4,missense_variant,p.Lys961Asn,ENST00000404125,;PSME4,3_prime_UTR_variant,,ENST00000389993,;PSME4,downstream_gene_variant,,ENST00000461810,;	A	ENSG00000068878	ENST00000404125	Transcript	missense_variant	2939	2883	961	K/N	aaA/aaT	.	.	.	-1	PSME4	HGNC	20635	protein_coding	YES	CCDS33197.2	ENSP00000384211	PSME4_HUMAN	.	UPI0000F3BE4A	.	tolerated(0.1)	benign(0.01)	26/47	.	hmmpanther:PTHR32170,hmmpanther:PTHR32170:SF0,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTTTTGTA	.	5	ESCA
ETAA1	0	.	GRCh37	2	67630697	67630697	+	Missense_Mutation	SNP	G	G	A	rs189478486	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.883G>A	p.Gly295Arg	p.G295R	ENST00000272342	5/6	35	29	6	18	18	0	ETAA1,missense_variant,p.Gly295Arg,ENST00000272342,;ETAA1,intron_variant,,ENST00000462772,;	A	ENSG00000143971	ENST00000272342	Transcript	missense_variant	1013	883	295	G/R	Gga/Aga	rs189478486	.	.	1	ETAA1	HGNC	24648	protein_coding	YES	CCDS1882.1	ENSP00000272342	ETAA1_HUMAN	.	UPI00001414BC	.	deleterious(0)	probably_damaging(1)	5/6	.	hmmpanther:PTHR16434:SF1,hmmpanther:PTHR16434,Pfam_domain:PF15350	A:0.0010	A:0	A:0.0058	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGCGGACAG	byFrequency|byCluster|by1000G	5	ESCA
KIAA1211L	0	.	GRCh37	2	99449396	99449396	+	Missense_Mutation	SNP	C	C	T	rs775652941	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304G>A	p.Gly102Arg	p.G102R	ENST00000397899	4/10	20	13	7	20	20	0	KIAA1211L,missense_variant,p.Gly116Arg,ENST00000415261,;KIAA1211L,missense_variant,p.Gly102Arg,ENST00000397899,;KIAA1211L,missense_variant,p.Gly116Arg,ENST00000428096,;KIAA1211L,missense_variant,p.Gly130Arg,ENST00000423771,;KIAA1211L,intron_variant,,ENST00000462314,;	T	ENSG00000196872	ENST00000397899	Transcript	missense_variant	636	304	102	G/R	Gga/Aga	rs775652941,COSM722723	.	.	-1	KIAA1211L	HGNC	33454	protein_coding	YES	CCDS42720.1	ENSP00000380996	K121L_HUMAN	.	UPI0000E59245	.	deleterious(0)	probably_damaging(0.98)	4/10	.	hmmpanther:PTHR22118:SF5,hmmpanther:PTHR22118	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTGTCCGGACT	byFrequency	4	ESCA
TIGIT	0	.	GRCh37	3	114018535	114018535	+	Silent	SNP	C	C	A	rs372970765	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483C>A	p.%3D	p.V161V	ENST00000486257	4/5	63	27	35	31	31	0	TIGIT,synonymous_variant,p.%3D,ENST00000461158,;TIGIT,synonymous_variant,p.%3D,ENST00000383671,;TIGIT,synonymous_variant,p.%3D,ENST00000484319,;TIGIT,synonymous_variant,p.%3D,ENST00000486257,;TIGIT,synonymous_variant,p.%3D,ENST00000481065,;TIGIT,downstream_gene_variant,,ENST00000485814,;	A	ENSG00000181847	ENST00000486257	Transcript	synonymous_variant	740	483	161	V	gtC/gtA	rs372970765	.	.	1	TIGIT	HGNC	26838	protein_coding	YES	CCDS2980.1	ENSP00000419085	TIGIT_HUMAN	C9JZW6_HUMAN,C9J0B0_HUMAN	UPI000013F7B8	.	.	.	4/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF62	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGTCGCGTT	byFrequency|byCluster	5	ESCA
SLC12A8	0	.	GRCh37	3	124854513	124854513	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736G>T	p.Gly246Ter	p.G246*	ENST00000393469	5/13	33	29	4	25	25	0	SLC12A8,stop_gained,p.Gly128Ter,ENST00000479826,;SLC12A8,stop_gained,p.Gly246Ter,ENST00000469902,;SLC12A8,stop_gained,p.Gly246Ter,ENST00000393469,;SLC12A8,stop_gained,p.Gly275Ter,ENST00000423114,;SLC12A8,splice_region_variant,,ENST00000314584,;SLC12A8,splice_region_variant,,ENST00000495105,;SLC12A8,splice_region_variant,,ENST00000485849,;SLC12A8,splice_region_variant,,ENST00000473262,;	A	ENSG00000221955	ENST00000393469	Transcript	stop_gained	786	736	246	G/*	Gga/Tga	.	.	.	-1	SLC12A8	HGNC	15595	protein_coding	YES	CCDS43143.1	ENSP00000377112	S12A8_HUMAN	C9IZN2_HUMAN	UPI000049DFB2	.	.	.	5/13	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11827:SF2,hmmpanther:PTHR11827,Pfam_domain:PF00324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATACCTGTAG	.	4	ESCA
WWTR1	0	.	GRCh37	3	149290715	149290715	+	Silent	SNP	G	G	C	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.504C>G	p.%3D	p.L168L	ENST00000465804	4/8	147	127	20	91	91	0	WWTR1,synonymous_variant,p.%3D,ENST00000472417,;WWTR1,synonymous_variant,p.%3D,ENST00000479238,;WWTR1,synonymous_variant,p.%3D,ENST00000360632,;WWTR1,synonymous_variant,p.%3D,ENST00000465804,;WWTR1,synonymous_variant,p.%3D,ENST00000467467,;	C	ENSG00000018408	ENST00000465804	Transcript	synonymous_variant	761	504	168	L	ctC/ctG	COSM3915112	.	.	-1	WWTR1	HGNC	24042	protein_coding	YES	CCDS3144.1	ENSP00000419465	WWTR1_HUMAN	C9JR84_HUMAN,C9JQS8_HUMAN,C9J588_HUMAN,C9J038_HUMAN	UPI000006D122	.	.	.	4/8	.	hmmpanther:PTHR17616,hmmpanther:PTHR17616:SF6	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGTGGAGGTT	.	3	ESCA
IGSF10	0	.	GRCh37	3	151165454	151165454	+	Missense_Mutation	SNP	C	C	T	rs746715734	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2315G>A	p.Arg772Gln	p.R772Q	ENST00000282466	4/6	113	106	6	50	50	0	IGSF10,missense_variant,p.Arg772Gln,ENST00000282466,;IGSF10,upstream_gene_variant,,ENST00000489791,;	T	ENSG00000152580	ENST00000282466	Transcript	missense_variant	2315	2315	772	R/Q	cGa/cAa	rs746715734,COSM3588829	.	.	-1	IGSF10	HGNC	26384	protein_coding	YES	CCDS3160.1	ENSP00000282466	IGS10_HUMAN	.	UPI00001D629A	.	tolerated(1)	benign(0.002)	4/6	.	hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCTCGCTTG	byFrequency	2	ESCA
TNIK	0	.	GRCh37	3	170846630	170846630	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1646delC	p.Pro549LeufsTer48	p.P549Lfs*48	ENST00000436636	16/33	17	5	11	11	11	0	TNIK,frameshift_variant,p.Pro520LeufsTer48,ENST00000470834,;TNIK,frameshift_variant,p.Pro549LeufsTer48,ENST00000436636,;TNIK,frameshift_variant,p.Pro520LeufsTer48,ENST00000369326,;TNIK,frameshift_variant,p.Pro549LeufsTer48,ENST00000284483,;TNIK,frameshift_variant,p.Pro520LeufsTer48,ENST00000357327,;TNIK,intron_variant,,ENST00000341852,;TNIK,intron_variant,,ENST00000475336,;TNIK,intron_variant,,ENST00000538048,;TNIK,intron_variant,,ENST00000488470,;TNIK,intron_variant,,ENST00000460047,;	-	ENSG00000154310	ENST00000436636	Transcript	frameshift_variant	1991	1646	549	P/X	cCt/ct	.	.	.	-1	TNIK	HGNC	30765	protein_coding	YES	CCDS46956.1	ENSP00000399511	TNIK_HUMAN	.	UPI000003ABDF	.	.	.	16/33	.	hmmpanther:PTHR24361:SF196,hmmpanther:PTHR24361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATGGCAGGGGAA	.	2	ESCA
CADPS	0	.	GRCh37	3	62384724	62384724	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*357C>T	.	.	ENST00000383710	30/30	24	15	9	33	33	0	CADPS,3_prime_UTR_variant,,ENST00000357948,;CADPS,3_prime_UTR_variant,,ENST00000283269,;CADPS,3_prime_UTR_variant,,ENST00000383710,;CADPS,3_prime_UTR_variant,,ENST00000473635,;CADPS,downstream_gene_variant,,ENST00000466621,;CADPS,non_coding_transcript_exon_variant,,ENST00000474560,;CADPS,non_coding_transcript_exon_variant,,ENST00000486172,;	A	ENSG00000163618	ENST00000383710	Transcript	3_prime_UTR_variant	4769	.	.	.	.	.	.	.	-1	CADPS	HGNC	1426	protein_coding	YES	CCDS46858.1	ENSP00000373215	CAPS1_HUMAN	.	UPI00001C036A	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGATGTACTT	.	5	ESCA
KBTBD8	0	.	GRCh37	3	67059087	67059087	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*278G>A	.	.	ENST00000417314	4/4	36	30	6	38	38	0	KBTBD8,3_prime_UTR_variant,,ENST00000417314,;KBTBD8,3_prime_UTR_variant,,ENST00000460576,;KBTBD8,3_prime_UTR_variant,,ENST00000295568,;KBTBD8,downstream_gene_variant,,ENST00000484414,;KBTBD8,downstream_gene_variant,,ENST00000469661,;	A	ENSG00000163376	ENST00000417314	Transcript	3_prime_UTR_variant	2133	.	.	.	.	.	.	.	1	KBTBD8	HGNC	30691	protein_coding	YES	CCDS2906.2	ENSP00000401878	KBTB8_HUMAN	C9JAA6_HUMAN,C9J331_HUMAN	UPI0000209974	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGGTACCA	.	5	ESCA
OTUD4	0	.	GRCh37	4	146059597	146059597	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2135A>T	p.Asn712Ile	p.N712I	ENST00000454497	21/21	67	51	16	62	62	0	OTUD4,missense_variant,p.Asn777Ile,ENST00000447906,;OTUD4,missense_variant,p.Asn712Ile,ENST00000454497,;OTUD4,intron_variant,,ENST00000455611,;	A	ENSG00000164164	ENST00000454497	Transcript	missense_variant	2273	2135	712	N/I	aAt/aTt	.	.	.	-1	OTUD4	HGNC	24949	protein_coding	YES	CCDS47139.1	ENSP00000409279	OTUD4_HUMAN	D6RA27_HUMAN	UPI0000DA6D4D	.	deleterious(0)	probably_damaging(0.988)	21/21	.	hmmpanther:PTHR12419,hmmpanther:PTHR12419:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCATTAACA	.	5	ESCA
TDO2	0	.	GRCh37	4	156831333	156831333	+	Silent	SNP	G	G	A	rs773821631	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588G>A	p.%3D	p.E196E	ENST00000536354	6/12	21	14	6	13	13	0	TDO2,synonymous_variant,p.%3D,ENST00000536354,;TDO2,downstream_gene_variant,,ENST00000506072,;TDO2,downstream_gene_variant,,ENST00000507590,;TDO2,upstream_gene_variant,,ENST00000510293,;TDO2,splice_region_variant,,ENST00000512584,;TDO2,downstream_gene_variant,,ENST00000509738,;	A	ENSG00000151790	ENST00000536354	Transcript	synonymous_variant	652	588	196	E	gaG/gaA	rs773821631	.	.	1	TDO2	HGNC	11708	protein_coding	YES	CCDS34086.1	ENSP00000444788	T23O_HUMAN	D6RB68_HUMAN,D6RA50_HUMAN	UPI00001367B7	.	.	.	6/12	.	HAMAP:MF_01972,hmmpanther:PTHR10138:SF1,hmmpanther:PTHR10138,Pfam_domain:PF03301,Superfamily_domains:SSF140959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGAGCAGGA	byFrequency	5	ESCA
FBN2	0	.	GRCh37	5	127615932	127615932	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7090G>T	p.Glu2364Ter	p.E2364*	ENST00000508053	62/71	19	17	2	16	16	0	FBN2,stop_gained,p.Glu2364Ter,ENST00000262464,;FBN2,stop_gained,p.Glu2364Ter,ENST00000508053,;	A	ENSG00000138829	ENST00000508053	Transcript	stop_gained	8065	7090	2364	E/*	Gag/Tag	.	.	.	-1	FBN2	HGNC	3604	protein_coding	YES	CCDS34222.1	ENSP00000424571	FBN2_HUMAN	.	UPI0000519468	.	.	.	62/71	.	Superfamily_domains:SSF57184,SMART_domains:SM00179,PIRSF_domain:PIRSF036312,SMART_domains:SM00181,Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS00010,PROSITE_patterns:PS01186,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF19,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACACTCACATC	.	2	ESCA
PCDHB10	0	.	GRCh37	5	140572114	140572114	+	5'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12T>C	.	.	ENST00000239446	1/1	29	11	17	49	49	0	PCDHB10,5_prime_UTR_variant,,ENST00000239446,;PCDHB9,downstream_gene_variant,,ENST00000316105,;	C	ENSG00000120324	ENST00000239446	Transcript	5_prime_UTR_variant	173	.	.	.	.	.	.	.	1	PCDHB10	HGNC	8681	protein_coding	YES	CCDS4252.1	ENSP00000239446	PCDBA_HUMAN	O95883_HUMAN	UPI0000048F2E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACGTATGCA	.	5	ESCA
MAP3K1	0	.	GRCh37	5	56189381	56189381	+	Silent	SNP	A	A	G	rs760319082	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4413A>G	p.%3D	p.P1471P	ENST00000399503	20/20	20	6	13	26	26	0	MAP3K1,synonymous_variant,p.%3D,ENST00000399503,;MAP3K1,non_coding_transcript_exon_variant,,ENST00000469188,;	G	ENSG00000095015	ENST00000399503	Transcript	synonymous_variant	4413	4413	1471	P	ccA/ccG	rs760319082	.	.	1	MAP3K1	HGNC	6848	protein_coding	YES	CCDS43318.1	ENSP00000382423	M3K1_HUMAN	.	UPI000015153B	.	.	.	20/20	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF255,hmmpanther:PTHR24361,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCATCGAT	.	5	ESCA
AK9	0	.	GRCh37	6	109854548	109854548	+	Missense_Mutation	SNP	C	C	T	rs774061625	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3476G>A	p.Arg1159His	p.R1159H	ENST00000424296	28/41	44	33	11	47	47	0	AK9,missense_variant,p.Arg238His,ENST00000341338,;AK9,missense_variant,p.Arg1159His,ENST00000424296,;AK9,missense_variant,p.Arg238His,ENST00000355283,;AK9,missense_variant,p.Arg94His,ENST00000491875,;AK9,upstream_gene_variant,,ENST00000470564,;	T	ENSG00000155085	ENST00000424296	Transcript	missense_variant	3553	3476	1159	R/H	cGc/cAc	rs774061625,COSM3975718,COSM1311457,COSM3975716,COSM1311455,COSM3975717,COSM1311456	.	.	-1	AK9	HGNC	33814	protein_coding	YES	CCDS55048.1	ENSP00000410186	KAD9_HUMAN	E9PPU7_HUMAN,E9PPM3_HUMAN	UPI0001A48FC8	.	deleterious(0)	probably_damaging(1)	28/41	.	hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF61,Pfam_domain:PF00406,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGAGGCGATCA	byFrequency	4	ESCA
NRSN1	0	.	GRCh37	6	24145969	24145969	+	Missense_Mutation	SNP	C	C	T	rs745509574	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383C>T	p.Thr128Met	p.T128M	ENST00000378491	4/4	54	50	3	48	48	0	NRSN1,missense_variant,p.Thr128Met,ENST00000378491,;NRSN1,missense_variant,p.Thr128Met,ENST00000378477,;NRSN1,downstream_gene_variant,,ENST00000378475,;NRSN1,downstream_gene_variant,,ENST00000378478,;NRSN1,intron_variant,,ENST00000468195,;	T	ENSG00000152954	ENST00000378491	Transcript	missense_variant	684	383	128	T/M	aCg/aTg	rs745509574	.	.	1	NRSN1	HGNC	17881	protein_coding	YES	CCDS4549.1	ENSP00000367752	NRSN1_HUMAN	Q5VTS0_HUMAN	UPI000003E7D6	.	tolerated(0.27)	benign(0.012)	4/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14796,hmmpanther:PTHR14796:SF2,Pfam_domain:PF14927	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCACGTCCA	byFrequency	2	ESCA
BRD2	0	.	GRCh37	6	32947844	32947844	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2186C>T	p.Ser729Phe	p.S729F	ENST00000395289	12/14	22	14	7	18	18	0	BRD2,missense_variant,p.Ser729Phe,ENST00000395289,;BRD2,missense_variant,p.Ser700Phe,ENST00000449025,;BRD2,missense_variant,p.Ser647Phe,ENST00000449085,;BRD2,missense_variant,p.Ser694Phe,ENST00000374825,;BRD2,missense_variant,p.Ser694Phe,ENST00000374831,;BRD2,missense_variant,p.Ser574Phe,ENST00000443797,;BRD2,missense_variant,p.Ser729Phe,ENST00000395287,;BRD2,downstream_gene_variant,,ENST00000607833,;BRD2,downstream_gene_variant,,ENST00000606059,;BRD2,downstream_gene_variant,,ENST00000456339,;BRD2,3_prime_UTR_variant,,ENST00000482914,;BRD2,non_coding_transcript_exon_variant,,ENST00000482838,;BRD2,non_coding_transcript_exon_variant,,ENST00000469132,;BRD2,downstream_gene_variant,,ENST00000481259,;BRD2,downstream_gene_variant,,ENST00000464592,;BRD2,downstream_gene_variant,,ENST00000495733,;BRD2,downstream_gene_variant,,ENST00000463639,;	T	ENSG00000204256	ENST00000395289	Transcript	missense_variant	3787	2186	729	S/F	tCc/tTc	COSM3873065	.	.	1	BRD2	HGNC	1103	protein_coding	YES	CCDS56420.1	ENSP00000378704	BRD2_HUMAN	U3KQA6_HUMAN	UPI0000227E6A	.	deleterious(0)	possibly_damaging(0.485)	12/14	.	PROSITE_profiles:PS51525,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF126	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATCCACAC	.	5	ESCA
ELOVL5	0	.	GRCh37	6	53133495	53133495	+	3'Flank	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000541407	.	21	14	7	12	12	0	ELOVL5,3_prime_UTR_variant,,ENST00000370918,;ELOVL5,3_prime_UTR_variant,,ENST00000542638,;ELOVL5,3_prime_UTR_variant,,ENST00000304434,;ELOVL5,downstream_gene_variant,,ENST00000541407,;	A	ENSG00000012660	ENST00000541407	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	62	-1	ELOVL5	HGNC	21308	protein_coding	YES	CCDS56433.1	ENSP00000438095	ELOV5_HUMAN	.	UPI0001AE72A0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTGCTTTTT	.	5	ESCA
DST	0	.	GRCh37	6	56494092	56494092	+	Silent	SNP	T	T	C	rs766624513	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2820A>G	p.%3D	p.Q940Q	ENST00000244364	18/84	69	36	33	60	60	0	DST,synonymous_variant,p.%3D,ENST00000439203,;DST,synonymous_variant,p.%3D,ENST00000446842,;DST,synonymous_variant,p.%3D,ENST00000370788,;DST,synonymous_variant,p.%3D,ENST00000244364,;DST,synonymous_variant,p.%3D,ENST00000520645,;DST,synonymous_variant,p.%3D,ENST00000370765,;DST,synonymous_variant,p.%3D,ENST00000370754,;DST,synonymous_variant,p.%3D,ENST00000361203,;DST,synonymous_variant,p.%3D,ENST00000370769,;DST,synonymous_variant,p.%3D,ENST00000312431,;DST,synonymous_variant,p.%3D,ENST00000421834,;DST,synonymous_variant,p.%3D,ENST00000518935,;DST,upstream_gene_variant,,ENST00000522360,;	C	ENSG00000151914	ENST00000244364	Transcript	synonymous_variant	3028	2820	940	Q	caA/caG	rs766624513	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	18/84	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF38,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTAATTGATC	byFrequency	5	ESCA
HTR1E	0	.	GRCh37	6	87725546	87725546	+	Missense_Mutation	SNP	G	G	A	rs373132619	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.494G>A	p.Arg165His	p.R165H	ENST00000305344	2/2	31	28	3	29	29	0	HTR1E,missense_variant,p.Arg165His,ENST00000305344,;	A	ENSG00000168830	ENST00000305344	Transcript	missense_variant	1197	494	165	R/H	cGc/cAc	rs373132619	.	.	1	HTR1E	HGNC	5291	protein_coding	YES	CCDS5006.1	ENSP00000307766	5HT1E_HUMAN	.	UPI000000126D	.	tolerated(0.08)	benign(0.005)	2/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF33,hmmpanther:PTHR24247,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R165C|c.493C>T|4	RADIA|MUTECT|MUSE|VARSCANS	CCGCCGCCTAA	byCluster	4	ESCA
VWDE	0	.	GRCh37	7	12409792	12409792	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2140C>A	p.His714Asn	p.H714N	ENST00000275358	12/29	51	29	22	58	58	0	VWDE,missense_variant,p.His714Asn,ENST00000275358,;VWDE,missense_variant,p.His714Asn,ENST00000452576,;VWDE,3_prime_UTR_variant,,ENST00000521169,;	T	ENSG00000146530	ENST00000275358	Transcript	missense_variant	2329	2140	714	H/N	Cat/Aat	.	.	.	-1	VWDE	HGNC	21897	protein_coding	YES	CCDS47544.1	ENSP00000275358	VWDE_HUMAN	.	UPI00006C0B98	.	tolerated(0.37)	benign(0.052)	12/29	.	hmmpanther:PTHR24048,hmmpanther:PTHR24048:SF67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGTTTTT	.	5	ESCA
EPHA1-AS1	0	.	GRCh37	7	143219877	143219877	+	RNA	SNP	G	G	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4353G>C	.	.	ENST00000429289	5/5	46	38	8	18	18	0	EPHA1-AS1,non_coding_transcript_exon_variant,,ENST00000429289,;	C	ENSG00000229153	ENST00000429289	Transcript	non_coding_transcript_exon_variant	4353	.	.	.	.	.	.	.	1	EPHA1-AS1	HGNC	27799	antisense	YES	.	.	.	.	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTGTAGATTGA	.	2	ESCA
NOBOX	0	.	GRCh37	7	144096926	144096926	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1078C>T	p.Arg360Ter	p.R360*	ENST00000467773	6/10	55	35	19	50	50	0	NOBOX,stop_gained,p.Arg243Ter,ENST00000223140,;NOBOX,stop_gained,p.Arg328Ter,ENST00000483238,;NOBOX,stop_gained,p.Arg360Ter,ENST00000467773,;	A	ENSG00000106410	ENST00000467773	Transcript	stop_gained	1078	1078	360	R/*	Cga/Tga	COSM1637522,COSM1637521	.	.	-1	NOBOX	HGNC	22448	protein_coding	YES	.	ENSP00000419457	NOBOX_HUMAN	.	UPI00019B220B	.	.	.	6/10	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF282,hmmpanther:PTHR24329,Gene3D:1.10.10.60,SMART_domains:SM00389	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCGCCACT	.	5	ESCA
LRRC61	0	.	GRCh37	7	150034279	150034279	+	Missense_Mutation	SNP	C	C	A	rs757569479	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329C>A	p.Ala110Asp	p.A110D	ENST00000359623	3/3	50	34	15	41	41	0	LRRC61,missense_variant,p.Ala110Asp,ENST00000359623,;LRRC61,missense_variant,p.Ala110Asp,ENST00000323078,;LRRC61,missense_variant,p.Ala110Asp,ENST00000493307,;RARRES2,downstream_gene_variant,,ENST00000482669,;RARRES2,downstream_gene_variant,,ENST00000223271,;ZBED6CL,downstream_gene_variant,,ENST00000343855,;RARRES2,downstream_gene_variant,,ENST00000467793,;RARRES2,downstream_gene_variant,,ENST00000466675,;RP4-584D14.7,upstream_gene_variant,,ENST00000563946,;RARRES2,downstream_gene_variant,,ENST00000478771,;	A	ENSG00000127399	ENST00000359623	Transcript	missense_variant	917	329	110	A/D	gCc/gAc	rs757569479	.	.	1	LRRC61	HGNC	21704	protein_coding	YES	CCDS5901.1	ENSP00000352642	LRC61_HUMAN	.	UPI000006F2E8	.	tolerated(0.16)	benign(0.218)	3/3	.	PROSITE_profiles:PS51450,hmmpanther:PTHR10588,hmmpanther:PTHR10588:SF201,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGGCCACCC	byFrequency	5	ESCA
DPP6	0	.	GRCh37	7	154681223	154681223	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2434G>A	p.Ala812Thr	p.A812T	ENST00000377770	25/26	32	26	6	32	32	0	DPP6,missense_variant,p.Ala705Thr,ENST00000427557,;DPP6,missense_variant,p.Ala812Thr,ENST00000377770,;DPP6,missense_variant,p.Ala750Thr,ENST00000332007,;DPP6,missense_variant,p.Ala748Thr,ENST00000404039,;DPP6,non_coding_transcript_exon_variant,,ENST00000480367,;	A	ENSG00000130226	ENST00000377770	Transcript	missense_variant	2575	2434	812	A/T	Gct/Act	.	.	.	1	DPP6	HGNC	3010	protein_coding	YES	.	ENSP00000367001	DPP6_HUMAN	Q75MI8_HUMAN,Q75MI7_HUMAN,Q75MF0_HUMAN	UPI00001AE746	.	deleterious(0.03)	benign(0.294)	25/26	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00326,hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGGCTAAT	.	5	ESCA
IQCE	0	.	GRCh37	7	2638117	2638117	+	Missense_Mutation	SNP	C	C	T	rs762486693	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1459C>T	p.Pro487Ser	p.P487S	ENST00000402050	17/22	90	54	35	59	59	0	IQCE,missense_variant,p.Pro436Ser,ENST00000404984,;IQCE,missense_variant,p.Pro487Ser,ENST00000402050,;IQCE,missense_variant,p.Pro471Ser,ENST00000438376,;IQCE,missense_variant,p.Pro422Ser,ENST00000325979,;IQCE,missense_variant,p.Pro67Ser,ENST00000423196,;IQCE,non_coding_transcript_exon_variant,,ENST00000486730,;IQCE,3_prime_UTR_variant,,ENST00000325997,;IQCE,non_coding_transcript_exon_variant,,ENST00000476665,;IQCE,non_coding_transcript_exon_variant,,ENST00000470731,;IQCE,non_coding_transcript_exon_variant,,ENST00000490913,;	T	ENSG00000106012	ENST00000402050	Transcript	missense_variant	1643	1459	487	P/S	Ccc/Tcc	rs762486693,COSM161760	.	.	1	IQCE	HGNC	29171	protein_coding	YES	CCDS43542.1	ENSP00000385597	IQCE_HUMAN	C9JX25_HUMAN,C9JP75_HUMAN	UPI000020E9EF	.	tolerated(0.36)	benign(0.024)	17/22	.	hmmpanther:PTHR22590	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCCCACT	byFrequency	5	ESCA
CDK13	0	.	GRCh37	7	40027387	40027387	+	Silent	SNP	C	C	T	rs137937704	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1401C>T	p.%3D	p.A467A	ENST00000181839	2/14	38	33	5	21	21	0	CDK13,synonymous_variant,p.%3D,ENST00000340829,;CDK13,synonymous_variant,p.%3D,ENST00000181839,;CDK13,upstream_gene_variant,,ENST00000484589,;	T	ENSG00000065883	ENST00000181839	Transcript	synonymous_variant	2006	1401	467	A	gcC/gcT	rs137937704	.	.	1	CDK13	HGNC	1733	protein_coding	YES	CCDS5461.1	ENSP00000181839	CDK13_HUMAN	.	UPI000013C5E3	.	.	.	2/14	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGCCGCAGA	byCluster	4	ESCA
GLI3	0	.	GRCh37	7	42005959	42005959	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2712C>T	p.%3D	p.R904R	ENST00000395925	15/15	46	28	17	34	34	0	GLI3,synonymous_variant,p.%3D,ENST00000395925,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,;	A	ENSG00000106571	ENST00000395925	Transcript	synonymous_variant	2797	2712	904	R	cgC/cgT	.	.	.	-1	GLI3	HGNC	4319	protein_coding	YES	CCDS5465.1	ENSP00000379258	GLI3_HUMAN	C9J9N4_HUMAN	UPI000020EE4C	.	.	.	15/15	.	hmmpanther:PTHR19818:SF5,hmmpanther:PTHR19818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCGGCGCGA	.	5	ESCA
PKHD1L1	0	.	GRCh37	8	110417360	110417360	+	Splice_Site	SNP	G	G	C	rs777507882	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1669+1G>C	.	p.X557_splice	ENST00000378402	.	56	41	15	35	35	0	PKHD1L1,splice_donor_variant,,ENST00000378402,;	C	ENSG00000205038	ENST00000378402	Transcript	splice_donor_variant	.	.	.	.	.	rs777507882	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	.	.	.	16/77	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTGGTAAGT	.	5	ESCA
SYBU	0	.	GRCh37	8	110587571	110587571	+	Missense_Mutation	SNP	G	G	A	rs372495769	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1556C>T	p.Ala519Val	p.A519V	ENST00000422135	8/8	50	47	3	26	26	0	SYBU,missense_variant,p.Ala519Val,ENST00000422135,;SYBU,missense_variant,p.Ala519Val,ENST00000433638,;SYBU,missense_variant,p.Ala451Val,ENST00000532779,;SYBU,missense_variant,p.Ala389Val,ENST00000529690,;SYBU,missense_variant,p.Ala519Val,ENST00000440310,;SYBU,missense_variant,p.Ala400Val,ENST00000533065,;SYBU,missense_variant,p.Ala518Val,ENST00000446070,;SYBU,missense_variant,p.Ala524Val,ENST00000424158,;SYBU,missense_variant,p.Ala313Val,ENST00000529175,;SYBU,missense_variant,p.Ala519Val,ENST00000408908,;SYBU,missense_variant,p.Ala400Val,ENST00000528331,;SYBU,missense_variant,p.Ala400Val,ENST00000408889,;SYBU,missense_variant,p.Ala518Val,ENST00000419099,;SYBU,missense_variant,p.Ala518Val,ENST00000528647,;SYBU,missense_variant,p.Ala519Val,ENST00000533171,;SYBU,missense_variant,p.Ala516Val,ENST00000399066,;SYBU,missense_variant,p.Ala519Val,ENST00000276646,;SYBU,missense_variant,p.Ala518Val,ENST00000533895,;SYBU,downstream_gene_variant,,ENST00000529190,;SYBU,downstream_gene_variant,,ENST00000528569,;SYBU,downstream_gene_variant,,ENST00000528045,;SYBU,downstream_gene_variant,,ENST00000533394,;SYBU,downstream_gene_variant,,ENST00000532189,;SYBU,downstream_gene_variant,,ENST00000527664,;SYBU,downstream_gene_variant,,ENST00000527707,;SYBU,downstream_gene_variant,,ENST00000528735,;SYBU,downstream_gene_variant,,ENST00000532594,;	A	ENSG00000147642	ENST00000422135	Transcript	missense_variant	2072	1556	519	A/V	gCg/gTg	rs372495769	.	.	-1	SYBU	HGNC	26011	protein_coding	YES	CCDS47912.1	ENSP00000407118	SYBU_HUMAN	E9PRT7_HUMAN,E9PQG2_HUMAN,E9PPS4_HUMAN,E9PPC2_HUMAN,E9PN31_HUMAN,E9PLB9_HUMAN,E9PL50_HUMAN,E9PK96_HUMAN,E9PJ11_HUMAN,E9PI48_HUMAN,B3KRD1_HUMAN	UPI00000407AB	.	tolerated(0.17)	benign(0.157)	8/8	.	hmmpanther:PTHR16208,hmmpanther:PTHR16208:SF4	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGACGCCAAG	byFrequency|byCluster	2	ESCA
C8orf48	0	.	GRCh37	8	13425527	13425527	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67A>C	.	.	ENST00000297324	1/1	85	75	10	45	45	0	C8orf48,3_prime_UTR_variant,,ENST00000297324,;RP11-145O15.3,intron_variant,,ENST00000529018,;	C	ENSG00000164743	ENST00000297324	Transcript	3_prime_UTR_variant	1176	.	.	.	.	.	.	.	1	C8orf48	HGNC	26345	protein_coding	YES	CCDS47809.1	ENSP00000297324	CH048_HUMAN	.	UPI000013E3F6	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACTAACTTA	.	4	ESCA
ARHGEF10	0	.	GRCh37	8	1853763	1853763	+	Silent	SNP	C	C	T	rs146717173	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1848C>T	p.%3D	p.L616L	ENST00000349830	17/29	120	104	16	57	57	0	ARHGEF10,synonymous_variant,p.%3D,ENST00000522435,;ARHGEF10,synonymous_variant,p.%3D,ENST00000262112,;ARHGEF10,synonymous_variant,p.%3D,ENST00000398564,;ARHGEF10,synonymous_variant,p.%3D,ENST00000349830,;ARHGEF10,synonymous_variant,p.%3D,ENST00000520359,;ARHGEF10,synonymous_variant,p.%3D,ENST00000518288,;ARHGEF10,downstream_gene_variant,,ENST00000398560,;ARHGEF10,non_coding_transcript_exon_variant,,ENST00000524212,;ARHGEF10,non_coding_transcript_exon_variant,,ENST00000523711,;ARHGEF10,downstream_gene_variant,,ENST00000520972,;	T	ENSG00000104728	ENST00000349830	Transcript	synonymous_variant	2033	1848	616	L	ctC/ctT	rs146717173	.	.	1	ARHGEF10	HGNC	14103	protein_coding	YES	CCDS34794.1	ENSP00000340297	ARHGA_HUMAN	.	UPI00005054FE	.	.	.	17/29	.	hmmpanther:PTHR12877:SF14,hmmpanther:PTHR12877,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCTCATTCG	byFrequency|byCluster	4	ESCA
SNAI2	0	.	GRCh37	8	49832626	49832626	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454G>A	p.Asp152Asn	p.D152N	ENST00000396822	3/4	97	82	15	47	47	0	SNAI2,missense_variant,p.Asp152Asn,ENST00000020945,;SNAI2,missense_variant,p.Asp152Asn,ENST00000396822,;	T	ENSG00000019549	ENST00000396822	Transcript	missense_variant	812	454	152	D/N	Gat/Aat	.	.	.	-1	SNAI2	HGNC	11094	protein_coding	YES	CCDS6146.1	ENSP00000380034	SNAI2_HUMAN	.	UPI0000135A3A	.	tolerated(0.24)	benign(0.121)	3/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR11389:SF400,hmmpanther:PTHR11389,Pfam_domain:PF13912,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATCGCAGT	.	5	ESCA
OTUD6B	0	.	GRCh37	8	92097035	92097035	+	Nonsense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.911T>G	p.Leu304Ter	p.L304*	ENST00000285420	7/7	23	20	3	12	12	0	OTUD6B,stop_gained,p.Leu173Ter,ENST00000404789,;OTUD6B,stop_gained,p.Leu304Ter,ENST00000285420,;OTUD6B,3_prime_UTR_variant,,ENST00000522894,;	G	ENSG00000155100	ENST00000285420	Transcript	stop_gained	1010	911	304	L/*	tTa/tGa	.	.	.	1	OTUD6B	HGNC	24281	protein_coding	YES	CCDS6253.2	ENSP00000285420	OTU6B_HUMAN	.	UPI0000E5AF0F	.	.	.	7/7	.	PROSITE_profiles:PS50802,hmmpanther:PTHR12419:SF1,hmmpanther:PTHR12419,Pfam_domain:PF02338,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCTTAGGAG	.	2	ESCA
GABBR2	0	.	GRCh37	9	101340276	101340276	+	Missense_Mutation	SNP	C	C	T	rs764365066	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400G>A	p.Val134Ile	p.V134I	ENST00000259455	2/19	59	53	6	42	42	0	GABBR2,missense_variant,p.Val134Ile,ENST00000259455,;	T	ENSG00000136928	ENST00000259455	Transcript	missense_variant	860	400	134	V/I	Gtc/Atc	rs764365066	.	.	-1	GABBR2	HGNC	4507	protein_coding	YES	CCDS6736.1	ENSP00000259455	GABR2_HUMAN	H9NIL8_HUMAN	UPI0000035832	.	tolerated(0.31)	probably_damaging(0.93)	2/19	.	Prints_domain:PR00248,Superfamily_domains:SSF53822,Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAGACGCCTC	byFrequency	4	ESCA
TNC	0	.	GRCh37	9	117825355	117825355	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000350763	13/28	101	62	38	50	50	0	TNC,missense_variant,p.Glu1292Lys,ENST00000350763,;TNC,missense_variant,p.Glu1292Lys,ENST00000423613,;TNC,intron_variant,,ENST00000345230,;TNC,intron_variant,,ENST00000542877,;TNC,intron_variant,,ENST00000544972,;TNC,intron_variant,,ENST00000346706,;TNC,intron_variant,,ENST00000537320,;TNC,intron_variant,,ENST00000341037,;TNC,intron_variant,,ENST00000535648,;TNC,intron_variant,,ENST00000340094,;TNC,non_coding_transcript_exon_variant,,ENST00000476680,;TNC,intron_variant,,ENST00000473855,;TNC,intron_variant,,ENST00000498724,;	T	ENSG00000041982	ENST00000350763	Transcript	missense_variant	4286	3874	1292	E/K	Gag/Aag	.	.	.	-1	TNC	HGNC	5318	protein_coding	YES	CCDS6811.1	ENSP00000265131	TENA_HUMAN	F5H5D6_HUMAN	UPI000013D5BD	.	tolerated(0.09)	benign(0.328)	13/28	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF38,hmmpanther:PTHR19143,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCCTGGA	.	5	ESCA
ODF2	0	.	GRCh37	9	131250255	131250255	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1487G>A	p.Arg496His	p.R496H	ENST00000434106	14/21	59	53	6	44	44	0	ODF2,missense_variant,p.Arg540His,ENST00000372814,;ODF2,missense_variant,p.Arg415His,ENST00000448249,;ODF2,missense_variant,p.Arg491His,ENST00000351030,;ODF2,missense_variant,p.Arg472His,ENST00000393527,;ODF2,missense_variant,p.Arg496His,ENST00000604420,;ODF2,missense_variant,p.Arg472His,ENST00000444119,;ODF2,missense_variant,p.Arg496His,ENST00000434106,;ODF2,missense_variant,p.Arg477His,ENST00000372791,;ODF2,missense_variant,p.Arg477His,ENST00000546203,;ODF2,missense_variant,p.Arg491His,ENST00000372807,;ODF2,missense_variant,p.Arg496His,ENST00000393533,;ODF2,downstream_gene_variant,,ENST00000421776,;ODF2,upstream_gene_variant,,ENST00000483070,;ODF2,downstream_gene_variant,,ENST00000535026,;	A	ENSG00000136811	ENST00000434106	Transcript	missense_variant	1850	1487	496	R/H	cGt/cAt	.	.	.	1	ODF2	HGNC	8114	protein_coding	YES	CCDS56588.1	ENSP00000403453	ODFP2_HUMAN	S4R462_HUMAN,Q9UNM2_HUMAN,Q6PJQ8_HUMAN,Q5T4C7_HUMAN	UPI0000211922	.	tolerated(0.09)	benign(0.005)	14/21	.	hmmpanther:PTHR23162:SF8,hmmpanther:PTHR23162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACACCGTCAGA	.	3	ESCA
PRRC2B	0	.	GRCh37	9	134363281	134363281	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6023G>T	p.Ser2008Ile	p.S2008I	ENST00000357304	27/31	73	49	23	52	52	0	PRRC2B,missense_variant,p.Ser15Ile,ENST00000320547,;PRRC2B,missense_variant,p.Ser2008Ile,ENST00000357304,;PRRC2B,missense_variant,p.Ser1314Ile,ENST00000405995,;PRRC2B,missense_variant,p.Ser1314Ile,ENST00000458550,;PRRC2B,missense_variant,p.Ser105Ile,ENST00000372249,;PRRC2B,downstream_gene_variant,,ENST00000451855,;SNORD62A,downstream_gene_variant,,ENST00000428514,;SNORD62B,upstream_gene_variant,,ENST00000426867,;PRRC2B,upstream_gene_variant,,ENST00000465931,;	T	ENSG00000130723	ENST00000357304	Transcript	missense_variant	6078	6023	2008	S/I	aGc/aTc	COSM204296	.	.	1	PRRC2B	HGNC	28121	protein_coding	YES	CCDS48044.1	ENSP00000349856	PRC2B_HUMAN	Q5JSZ9_HUMAN,B4E3S7_HUMAN	UPI00002374A3	.	deleterious(0)	possibly_damaging(0.501)	27/31	.	hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCAGCACCA	.	5	ESCA
ADAMTSL1	0	.	GRCh37	9	18775842	18775842	+	Silent	SNP	G	G	A	rs760762246	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2499G>A	p.%3D	p.P833P	ENST00000380548	18/29	50	36	14	48	48	0	ADAMTSL1,synonymous_variant,p.%3D,ENST00000380548,;ADAMTSL1,non_coding_transcript_exon_variant,,ENST00000380559,;	A	ENSG00000178031	ENST00000380548	Transcript	synonymous_variant	2838	2499	833	P	ccG/ccA	rs760762246,COSM455731	.	.	1	ADAMTSL1	HGNC	14632	protein_coding	YES	CCDS47954.1	ENSP00000369921	ATL1_HUMAN	H7BYE3_HUMAN	UPI000004FD83	.	.	.	18/29	.	PROSITE_profiles:PS50092,hmmpanther:PTHR13723:SF157,hmmpanther:PTHR13723,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGCCCCT	byFrequency	5	ESCA
TRPC5	0	.	GRCh37	X	111195502	111195502	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147G>T	p.Lys49Asn	p.K49N	ENST00000262839	2/11	25	9	16	14	14	0	TRPC5,missense_variant,p.Lys49Asn,ENST00000262839,;	A	ENSG00000072315	ENST00000262839	Transcript	missense_variant	1066	147	49	K/N	aaG/aaT	.	.	.	-1	TRPC5	HGNC	12337	protein_coding	YES	CCDS14561.1	ENSP00000262839	TRPC5_HUMAN	.	UPI00001374B6	.	deleterious(0)	probably_damaging(0.93)	2/11	.	hmmpanther:PTHR10117:SF24,hmmpanther:PTHR10117,Pfam_domain:PF12796,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGCTTCAC	.	5	ESCA
UPF3B	0	.	GRCh37	X	118975734	118975734	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588G>A	p.%3D	p.K196K	ENST00000276201	6/11	64	59	5	44	44	0	UPF3B,synonymous_variant,p.%3D,ENST00000345865,;UPF3B,synonymous_variant,p.%3D,ENST00000276201,;UPF3B,non_coding_transcript_exon_variant,,ENST00000478840,;	T	ENSG00000125351	ENST00000276201	Transcript	synonymous_variant	658	588	196	K	aaG/aaA	.	.	.	-1	UPF3B	HGNC	20439	protein_coding	YES	CCDS14588.1	ENSP00000276201	REN3B_HUMAN	I3XIE4_HUMAN	UPI000006D21C	.	.	.	6/11	.	hmmpanther:PTHR13112,hmmpanther:PTHR13112:SF1,Pfam_domain:PF03467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTGTCTTTTT	.	3	ESCA
GLUD2	0	.	GRCh37	X	120182347	120182347	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.809C>A	p.Ser270Tyr	p.S270Y	ENST00000328078	1/1	117	99	18	100	100	0	GLUD2,missense_variant,p.Ser270Tyr,ENST00000328078,;	A	ENSG00000182890	ENST00000328078	Transcript	missense_variant	886	809	270	S/Y	tCt/tAt	.	.	.	1	GLUD2	HGNC	4336	protein_coding	YES	CCDS14603.1	ENSP00000327589	DHE4_HUMAN	Q9BSD0_HUMAN	UPI0000129301	.	deleterious(0)	probably_damaging(0.991)	1/1	.	hmmpanther:PTHR11606:SF10,hmmpanther:PTHR11606,Gene3D:3.40.50.720,Pfam_domain:PF00208,SMART_domains:SM00839,Superfamily_domains:SSF51735,Prints_domain:PR00082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCTGCTA	.	4	ESCA
PCYT1B	0	.	GRCh37	X	24625955	24625955	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241G>A	p.Ala81Thr	p.A81T	ENST00000379144	3/8	24	19	4	25	25	0	PCYT1B,missense_variant,p.Ala81Thr,ENST00000379144,;PCYT1B,missense_variant,p.Ala63Thr,ENST00000379145,;PCYT1B,missense_variant,p.Ala81Thr,ENST00000356768,;PCYT1B,missense_variant,p.Ala55Thr,ENST00000496020,;	T	ENSG00000102230	ENST00000379144	Transcript	missense_variant	372	241	81	A/T	Gcc/Acc	.	.	.	-1	PCYT1B	HGNC	8755	protein_coding	YES	CCDS14213.1	ENSP00000368439	PCY1B_HUMAN	.	UPI000012864E	.	deleterious(0)	probably_damaging(0.958)	3/8	.	hmmpanther:PTHR10739:SF20,hmmpanther:PTHR10739,TIGRFAM_domain:TIGR00125,Pfam_domain:PF01467,Gene3D:3.40.50.620,Superfamily_domains:SSF52374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGGCGTATA	.	5	ESCA
MAGEB6	0	.	GRCh37	X	26213165	26213165	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1202G>C	p.Arg401Thr	p.R401T	ENST00000379034	2/2	76	39	37	67	67	0	MAGEB6,missense_variant,p.Arg401Thr,ENST00000379034,;GS1-466O4.3,upstream_gene_variant,,ENST00000450430,;	C	ENSG00000176746	ENST00000379034	Transcript	missense_variant	1351	1202	401	R/T	aGa/aCa	.	.	.	1	MAGEB6	HGNC	23796	protein_coding	YES	CCDS14217.1	ENSP00000368320	MAGB6_HUMAN	.	UPI00001413F4	.	deleterious(0)	benign(0.291)	2/2	.	hmmpanther:PTHR11736:SF67,hmmpanther:PTHR11736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGAGAGCAT	.	5	ESCA
DMD	0	.	GRCh37	X	33357448	33357448	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-66C>T	.	.	ENST00000288447	1/18	30	12	17	28	28	0	DMD,5_prime_UTR_variant,,ENST00000288447,;	A	ENSG00000198947	ENST00000288447	Transcript	5_prime_UTR_variant	111	.	.	.	.	.	.	.	-1	DMD	HGNC	2928	protein_coding	.	.	ENSP00000288447	.	Q9UPB5_HUMAN,Q9UMG1_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q7KZ40_HUMAN,Q548X2_HUMAN,Q4G0X0_HUMAN	UPI00004A0D95	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGTGCAAAA	.	5	ESCA
SSX1	0	.	GRCh37	X	48126361	48126361	+	3'UTR	SNP	C	C	T	rs782180899	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*77C>T	.	.	ENST00000376919	8/8	114	76	37	142	142	0	SSX1,3_prime_UTR_variant,,ENST00000376919,;	T	ENSG00000126752	ENST00000376919	Transcript	3_prime_UTR_variant	780	.	.	.	.	rs782180899	.	.	1	SSX1	HGNC	11335	protein_coding	YES	CCDS14290.1	ENSP00000366118	SSX1_HUMAN	.	UPI0000136052	.	.	.	8/8	.	.	T:0.0003	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGCGGCTC	by1000G	5	ESCA
CXorf67	0	.	GRCh37	X	51150911	51150911	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1043G>A	p.Arg348His	p.R348H	ENST00000342995	1/1	98	88	9	78	78	0	CXorf67,missense_variant,p.Arg348His,ENST00000342995,;RP11-348F1.2,intron_variant,,ENST00000455931,;	A	ENSG00000187690	ENST00000342995	Transcript	missense_variant	1145	1043	348	R/H	cGt/cAt	.	.	.	1	CXorf67	HGNC	33738	protein_coding	YES	.	ENSP00000342680	CX067_HUMAN	.	UPI000000DB6D	.	tolerated(0.25)	benign(0.062)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22467,hmmpanther:PTHR22467:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAGCCGTTCCA	.	3	ESCA
ZC3H12B	0	.	GRCh37	X	64709206	64709206	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.525C>A	p.Ser175Arg	p.S175R	ENST00000338957	1/5	30	26	4	25	25	0	ZC3H12B,missense_variant,p.Ser164Arg,ENST00000423889,;ZC3H12B,missense_variant,p.Ser175Arg,ENST00000338957,;	A	ENSG00000102053	ENST00000338957	Transcript	missense_variant	592	525	175	S/R	agC/agA	.	.	.	1	ZC3H12B	HGNC	17407	protein_coding	YES	CCDS48131.2	ENSP00000340839	.	E9PAJ6_HUMAN	UPI00001D7BEA	.	tolerated(0.41)	benign(0.024)	1/5	.	hmmpanther:PTHR12876:SF27,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAAGCCCTGA	.	4	ESCA
DIAPH2	0	.	GRCh37	X	96013192	96013192	+	Nonsense_Mutation	SNP	C	C	T	rs754269506	.	TCGA-IG-A3I8-01A-11D-A247-09	TCGA-IG-A3I8-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382C>T	p.Arg128Ter	p.R128*	ENST00000324765	4/27	46	42	3	30	30	0	DIAPH2,stop_gained,p.Arg117Ter,ENST00000373054,;DIAPH2,stop_gained,p.Arg128Ter,ENST00000355827,;DIAPH2,stop_gained,p.Arg128Ter,ENST00000324765,;DIAPH2,stop_gained,p.Arg128Ter,ENST00000373049,;DIAPH2,stop_gained,p.Arg128Ter,ENST00000373061,;	T	ENSG00000147202	ENST00000324765	Transcript	stop_gained	729	382	128	R/*	Cga/Tga	rs754269506	.	.	1	DIAPH2	HGNC	2877	protein_coding	YES	CCDS14467.1	ENSP00000321348	DIAP2_HUMAN	.	UPI00001293C8	.	.	.	4/27	.	PROSITE_profiles:PS51232,hmmpanther:PTHR23213:SF174,hmmpanther:PTHR23213,Pfam_domain:PF06371,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTACGAAAC	.	2	ESCA
CELF2	0	.	GRCh37	10	11299729	11299729	+	Silent	SNP	A	A	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432A>C	p.%3D	p.G144G	ENST00000450189	5/15	46	31	15	43	43	0	CELF2,synonymous_variant,p.%3D,ENST00000427450,;CELF2,synonymous_variant,p.%3D,ENST00000608830,;CELF2,synonymous_variant,p.%3D,ENST00000399850,;CELF2,synonymous_variant,p.%3D,ENST00000379261,;CELF2,synonymous_variant,p.%3D,ENST00000354897,;CELF2,synonymous_variant,p.%3D,ENST00000416382,;CELF2,synonymous_variant,p.%3D,ENST00000537122,;CELF2,synonymous_variant,p.%3D,ENST00000609692,;CELF2,synonymous_variant,p.%3D,ENST00000417956,;CELF2,synonymous_variant,p.%3D,ENST00000354440,;CELF2,synonymous_variant,p.%3D,ENST00000542579,;CELF2,synonymous_variant,p.%3D,ENST00000450189,;CELF2,synonymous_variant,p.%3D,ENST00000315874,;CELF2,3_prime_UTR_variant,,ENST00000609870,;	C	ENSG00000048740	ENST00000450189	Transcript	synonymous_variant	592	432	144	G	ggA/ggC	.	.	.	1	CELF2	HGNC	2550	protein_coding	YES	CCDS44355.1	ENSP00000389951	.	E9PC62_HUMAN,B4DIB6_HUMAN	UPI0000F58F21	.	.	.	5/15	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24622,hmmpanther:PTHR24622:SF164,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGGAATGGT	.	5	ESCA
NUDT5	0	.	GRCh37	10	12209761	12209761	+	Silent	SNP	G	G	A	rs148632115	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600C>T	p.%3D	p.Y200Y	ENST00000491614	10/10	29	17	11	27	27	0	NUDT5,synonymous_variant,p.%3D,ENST00000491614,;NUDT5,synonymous_variant,p.%3D,ENST00000378937,;NUDT5,synonymous_variant,p.%3D,ENST00000537776,;SEC61A2,intron_variant,,ENST00000304267,;SEC61A2,downstream_gene_variant,,ENST00000298428,;NUDT5,downstream_gene_variant,,ENST00000378927,;SEC61A2,downstream_gene_variant,,ENST00000379033,;SEC61A2,downstream_gene_variant,,ENST00000419021,;NUDT5,downstream_gene_variant,,ENST00000378940,;SEC61A2,downstream_gene_variant,,ENST00000379020,;NUDT5,non_coding_transcript_exon_variant,,ENST00000378952,;SEC61A2,non_coding_transcript_exon_variant,,ENST00000495368,;NUDT5,downstream_gene_variant,,ENST00000498825,;SEC61A2,synonymous_variant,p.%3D,ENST00000475268,;NUDT5,3_prime_UTR_variant,,ENST00000476462,;	A	ENSG00000165609	ENST00000491614	Transcript	synonymous_variant	996	600	200	Y	taC/taT	rs148632115	.	.	-1	NUDT5	HGNC	8052	protein_coding	YES	CCDS7089.1	ENSP00000419628	NUDT5_HUMAN	.	UPI00001308E1	.	.	.	10/10	.	hmmpanther:PTHR11839,hmmpanther:PTHR11839:SF1	.	.	.	.	.	.	.	A:0	A:0.0005	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGCGTAGGA	byCluster	5	ESCA
PSTK	0	.	GRCh37	10	124740046	124740046	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51A>T	p.Lys17Asn	p.K17N	ENST00000368887	1/7	22	0	21	11	11	0	PSTK,missense_variant,p.Lys17Asn,ENST00000368887,;PSTK,missense_variant,p.Lys18Asn,ENST00000406217,;PSTK,missense_variant,p.Lys17Asn,ENST00000405485,;PSTK,intron_variant,,ENST00000465232,;PSTK,upstream_gene_variant,,ENST00000497219,;PSTK,upstream_gene_variant,,ENST00000496079,;PSTK,upstream_gene_variant,,ENST00000483755,;PSTK,upstream_gene_variant,,ENST00000483455,;PSTK,upstream_gene_variant,,ENST00000493461,;	T	ENSG00000179988	ENST00000368887	Transcript	missense_variant	491	51	17	K/N	aaA/aaT	.	.	.	1	PSTK	HGNC	28578	protein_coding	YES	CCDS7633.1	ENSP00000357882	PSTK_HUMAN	.	UPI000013F992	.	deleterious(0.03)	benign(0.014)	1/7	.	Superfamily_domains:SSF52540,hmmpanther:PTHR20873	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGAAACGAGG	.	5	ESCA
MYO3A	0	.	GRCh37	10	26417469	26417469	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2262+2T>A	.	p.X754_splice	ENST00000265944	.	32	2	30	24	24	0	MYO3A,splice_donor_variant,,ENST00000265944,;MYO3A,intron_variant,,ENST00000543632,;	A	ENSG00000095777	ENST00000265944	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	MYO3A	HGNC	7601	protein_coding	YES	CCDS7148.1	ENSP00000265944	MYO3A_HUMAN	.	UPI000014140A	.	.	.	.	20/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGTAAGTC	.	5	ESCA
PITRM1	0	.	GRCh37	10	3208566	3208566	+	Silent	SNP	C	C	T	rs114690446	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.273G>A	p.%3D	p.Q91Q	ENST00000380989	4/27	26	18	8	19	18	1	PITRM1,synonymous_variant,p.%3D,ENST00000380989,;PITRM1,synonymous_variant,p.%3D,ENST00000451104,;PITRM1,synonymous_variant,p.%3D,ENST00000224949,;PITRM1-AS1,intron_variant,,ENST00000598280,;PITRM1-AS1,downstream_gene_variant,,ENST00000601046,;PITRM1,upstream_gene_variant,,ENST00000488065,;	T	ENSG00000107959	ENST00000380989	Transcript	synonymous_variant	312	273	91	Q	caG/caA	rs114690446,COSM1347606,COSM3746213,COSM3746212	.	.	-1	PITRM1	HGNC	17663	protein_coding	YES	CCDS55699.1	ENSP00000370377	PREP_HUMAN	.	UPI00015E00B2	.	.	.	4/27	.	hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF68,Gene3D:3.30.830.10,Superfamily_domains:SSF63411	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Q91Q|c.273G>A|5,CODON|p.Q91P|c.272A>C|5	SOMATICSNIPER|VARSCANS	CGGAACTGCAC	byCluster	2	ESCA
NRP1	0	.	GRCh37	10	33468385	33468385	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*619C>A	.	.	ENST00000265371	18/18	11	7	4	18	18	0	NRP1,3_prime_UTR_variant,,ENST00000374867,;NRP1,3_prime_UTR_variant,,ENST00000265371,;NRP1,3_prime_UTR_variant,,ENST00000374875,;NRP1,downstream_gene_variant,,ENST00000395995,;NRP1,downstream_gene_variant,,ENST00000413802,;	T	ENSG00000099250	ENST00000265371	Transcript	3_prime_UTR_variant	3917	.	.	.	.	.	.	.	-1	NRP1	HGNC	8004	protein_coding	YES	CCDS7177.1	ENSP00000265371	NRP1_HUMAN	Q9H2E0_HUMAN,Q9H2D9_HUMAN,Q9H2D8_HUMAN,Q9H2D7_HUMAN,Q7Z5M2_HUMAN	UPI000013D60A	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACGAGGTTTAG	.	3	ESCA
RP11-313J2.1	0	.	GRCh37	10	42832981	42832981	+	RNA	SNP	G	G	C	rs564760204	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.923C>G	.	.	ENST00000609841	3/3	39	19	20	41	41	0	RP11-313J2.1,non_coding_transcript_exon_variant,,ENST00000609841,;RP11-313J2.1,downstream_gene_variant,,ENST00000609034,;RP11-313J2.1,non_coding_transcript_exon_variant,,ENST00000423987,;	C	ENSG00000215146	ENST00000609841	Transcript	non_coding_transcript_exon_variant	923	.	.	.	.	rs564760204	.	.	-1	RP11-313J2.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	C:0.0002	C:0	C:0	.	C:0.001	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTAGGGTTT	by1000G	5	ESCA
CYP2C9	0	.	GRCh37	10	96702021	96702021	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404G>T	p.Gly135Val	p.G135V	ENST00000260682	3/9	87	67	19	80	80	0	CYP2C9,missense_variant,p.Gly135Val,ENST00000260682,;CYP2C9,non_coding_transcript_exon_variant,,ENST00000473496,;CYP2C9,non_coding_transcript_exon_variant,,ENST00000461906,;MTND4P20,upstream_gene_variant,,ENST00000424125,;	T	ENSG00000138109	ENST00000260682	Transcript	missense_variant	416	404	135	G/V	gGg/gTg	.	.	.	1	CYP2C9	HGNC	2623	protein_coding	YES	CCDS7437.1	ENSP00000260682	CP2C9_HUMAN	S5RV20_HUMAN,Q9UEH3_HUMAN	UPI0000128258	.	deleterious(0)	probably_damaging(0.999)	3/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF131,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGGGATGG	.	5	ESCA
DRD2	0	.	GRCh37	11	113283425	113283425	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.991G>C	p.Ala331Pro	p.A331P	ENST00000362072	7/8	156	115	41	103	102	0	DRD2,missense_variant,p.Ala331Pro,ENST00000542968,;DRD2,missense_variant,p.Ala330Pro,ENST00000544518,;DRD2,missense_variant,p.Ala331Pro,ENST00000362072,;DRD2,missense_variant,p.Ala333Pro,ENST00000355319,;DRD2,missense_variant,p.Ala302Pro,ENST00000346454,;DRD2,missense_variant,p.Ala333Pro,ENST00000538967,;DRD2,downstream_gene_variant,,ENST00000543292,;RP11-159N11.3,downstream_gene_variant,,ENST00000546284,;DRD2,downstream_gene_variant,,ENST00000535984,;DRD2,downstream_gene_variant,,ENST00000539420,;DRD2,downstream_gene_variant,,ENST00000540600,;	G	ENSG00000149295	ENST00000362072	Transcript	missense_variant	1336	991	331	A/P	Gcc/Ccc	.	.	.	-1	DRD2	HGNC	3023	protein_coding	YES	CCDS8361.1	ENSP00000354859	DRD2_HUMAN	Q6LDH7_HUMAN	UPI0000001315	.	tolerated(0.28)	benign(0.006)	7/8	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF68,Pfam_domain:PF00001,Prints_domain:PR00567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGGCATGCC	.	5	ESCA
OR8D4	0	.	GRCh37	11	123777707	123777707	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569C>T	p.Ser190Phe	p.S190F	ENST00000321355	1/1	25	22	3	35	35	0	OR8D4,missense_variant,p.Ser190Phe,ENST00000321355,;	T	ENSG00000181518	ENST00000321355	Transcript	missense_variant	599	569	190	S/F	tCc/tTc	COSM322420	.	.	1	OR8D4	HGNC	14840	protein_coding	YES	CCDS31698.1	ENSP00000325381	OR8D4_HUMAN	.	UPI0000040A83	.	deleterious(0.02)	probably_damaging(0.984)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF21,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCTCCAGCA	.	2	ESCA
SPA17	0	.	GRCh37	11	124543781	124543781	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1380G>C	.	.	ENST00000532692	1/4	10	3	7	9	9	0	SPA17,5_prime_UTR_variant,,ENST00000227135,;SPA17,5_prime_UTR_variant,,ENST00000532692,;SIAE,upstream_gene_variant,,ENST00000263593,;SIAE,upstream_gene_variant,,ENST00000545756,;SIAE,intron_variant,,ENST00000525730,;SPA17,upstream_gene_variant,,ENST00000529498,;SPA17,upstream_gene_variant,,ENST00000524614,;SIAE,upstream_gene_variant,,ENST00000533613,;SIAE,upstream_gene_variant,,ENST00000436137,;	C	ENSG00000064199	ENST00000532692	Transcript	5_prime_UTR_variant	42	.	.	.	.	.	.	.	1	SPA17	HGNC	11210	protein_coding	YES	CCDS8450.1	ENSP00000432305	SP17_HUMAN	.	UPI0000001617	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TTAAAGAAAAA	.	2	ESCA
FLI1	0	.	GRCh37	11	128651913	128651913	+	Missense_Mutation	SNP	A	A	C	rs766864970	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650A>C	p.Lys217Thr	p.K217T	ENST00000527786	5/9	48	40	7	49	49	0	FLI1,missense_variant,p.Lys151Thr,ENST00000281428,;FLI1,missense_variant,p.Lys24Thr,ENST00000525560,;FLI1,missense_variant,p.Lys184Thr,ENST00000344954,;FLI1,missense_variant,p.Lys184Thr,ENST00000534087,;FLI1,missense_variant,p.Lys217Thr,ENST00000527786,;FLI1,3_prime_UTR_variant,,ENST00000608303,;FLI1,3_prime_UTR_variant,,ENST00000429175,;	C	ENSG00000151702	ENST00000527786	Transcript	missense_variant	1139	650	217	K/T	aAa/aCa	rs766864970	.	.	1	FLI1	HGNC	3749	protein_coding	YES	CCDS44768.1	ENSP00000433488	.	.	UPI000012A972	.	tolerated(0.13)	benign(0.011)	5/9	.	hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCAAAGAAG	.	5	ESCA
CALCB	0	.	GRCh37	11	15096326	15096326	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.62G>C	p.Gly21Ala	p.G21A	ENST00000533448	2/5	41	27	14	36	36	0	CALCB,missense_variant,p.Gly21Ala,ENST00000533448,;CALCB,missense_variant,p.Gly21Ala,ENST00000324229,;CALCB,missense_variant,p.Gly32Ala,ENST00000523376,;	C	ENSG00000175868	ENST00000533448	Transcript	missense_variant	173	62	21	G/A	gGc/gCc	.	.	.	1	CALCB	HGNC	1438	protein_coding	YES	CCDS7820.1	ENSP00000433490	CALCB_HUMAN	.	UPI0000126E36	.	deleterious(0.04)	benign(0.422)	2/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10505,Pfam_domain:PF00214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGGGCAGCC	.	5	ESCA
ANO5	0	.	GRCh37	11	22294478	22294478	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2178C>T	p.%3D	p.S726S	ENST00000324559	19/22	53	40	13	47	47	0	ANO5,synonymous_variant,p.%3D,ENST00000324559,;ANO5,non_coding_transcript_exon_variant,,ENST00000532043,;	T	ENSG00000171714	ENST00000324559	Transcript	synonymous_variant	2495	2178	726	S	agC/agT	.	.	.	1	ANO5	HGNC	27337	protein_coding	YES	CCDS31444.1	ENSP00000315371	ANO5_HUMAN	.	UPI000035B19B	.	.	.	19/22	.	hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF23,Pfam_domain:PF04547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAGCATAGG	.	5	ESCA
LGR4	0	.	GRCh37	11	27389413	27389413	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1A>T	.	.	ENST00000379214	18/18	17	13	4	21	21	0	LGR4,3_prime_UTR_variant,,ENST00000389858,;LGR4,3_prime_UTR_variant,,ENST00000379214,;CCDC34,upstream_gene_variant,,ENST00000328697,;CCDC34,upstream_gene_variant,,ENST00000317945,;	A	ENSG00000205213	ENST00000379214	Transcript	3_prime_UTR_variant	3301	.	.	.	.	.	.	.	-1	LGR4	HGNC	13299	protein_coding	YES	CCDS31449.1	ENSP00000368516	LGR4_HUMAN	Q59ER8_HUMAN	UPI00000373E7	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTAGTTCAGT	.	5	ESCA
MPPED2	0	.	GRCh37	11	30439152	30439152	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565A>G	p.Asn189Asp	p.N189D	ENST00000358117	4/6	22	17	5	25	25	0	MPPED2,missense_variant,p.Asn189Asp,ENST00000448418,;MPPED2,missense_variant,p.Asn189Asp,ENST00000358117,;MPPED2,non_coding_transcript_exon_variant,,ENST00000529220,;MPPED2,non_coding_transcript_exon_variant,,ENST00000524667,;MPPED2,3_prime_UTR_variant,,ENST00000526437,;	C	ENSG00000066382	ENST00000358117	Transcript	missense_variant	688	565	189	N/D	Aac/Gac	.	.	.	-1	MPPED2	HGNC	1180	protein_coding	YES	CCDS7870.1	ENSP00000350833	MPPD2_HUMAN	F2Z346_HUMAN	UPI0000124E87	.	deleterious(0.01)	probably_damaging(0.952)	4/6	.	hmmpanther:PTHR12905:SF3,hmmpanther:PTHR12905,Pfam_domain:PF00149,PIRSF_domain:PIRSF035808,Superfamily_domains:SSF56300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGTTAAAGC	.	5	ESCA
OR52N5	0	.	GRCh37	11	5799447	5799447	+	Missense_Mutation	SNP	G	G	A	rs372227128	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418C>T	p.Arg140Cys	p.R140C	ENST00000317093	1/1	22	14	7	24	24	0	OR52N5,missense_variant,p.Arg140Cys,ENST00000317093,;TRIM5,intron_variant,,ENST00000412903,;TRIM5,intron_variant,,ENST00000380027,;	A	ENSG00000181009	ENST00000317093	Transcript	missense_variant	451	418	140	R/C	Cgt/Tgt	rs372227128,COSM283586	.	.	-1	OR52N5	HGNC	15231	protein_coding	YES	CCDS31397.1	ENSP00000322866	O52N5_HUMAN	.	UPI0000041BF9	.	deleterious(0.01)	benign(0.046)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF18,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAACGCAAAG	byCluster	5	ESCA
GIF	0	.	GRCh37	11	59612870	59612870	+	Missense_Mutation	SNP	A	A	T	rs762525615	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57T>A	p.Ser19Arg	p.S19R	ENST00000257248	1/9	26	20	6	23	23	0	GIF,missense_variant,p.Ser19Arg,ENST00000257248,;GIF,5_prime_UTR_variant,,ENST00000541311,;GIF,missense_variant,p.Ser19Arg,ENST00000525058,;GIF,non_coding_transcript_exon_variant,,ENST00000532070,;GIF,upstream_gene_variant,,ENST00000533847,;	T	ENSG00000134812	ENST00000257248	Transcript	missense_variant	105	57	19	S/R	agT/agA	rs762525615	.	.	-1	GIF	HGNC	4268	protein_coding	YES	CCDS7977.1	ENSP00000257248	IF_HUMAN	.	UPI0000001C67	.	deleterious(0.05)	possibly_damaging(0.845)	1/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10559,hmmpanther:PTHR10559:SF15,Pfam_domain:PF01122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGGGTACTAGT	.	4	ESCA
AHNAK	0	.	GRCh37	11	62292799	62292799	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9090C>T	p.%3D	p.F3030F	ENST00000378024	5/5	107	81	25	92	92	0	AHNAK,synonymous_variant,p.%3D,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;	A	ENSG00000124942	ENST00000378024	Transcript	synonymous_variant	9365	9090	3030	F	ttC/ttT	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	.	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCTGAATTT	.	5	ESCA
WDR74	0	.	GRCh37	11	62607112	62607112	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-70C>T	.	.	ENST00000525239	2/12	35	14	20	24	24	0	WDR74,5_prime_UTR_variant,,ENST00000525239,;WDR74,5_prime_UTR_variant,,ENST00000538098,;WDR74,5_prime_UTR_variant,,ENST00000278856,;WDR74,5_prime_UTR_variant,,ENST00000525752,;WDR74,5_prime_UTR_variant,,ENST00000529106,;WDR74,upstream_gene_variant,,ENST00000311713,;RNU2-2P,downstream_gene_variant,,ENST00000410396,;WDR74,upstream_gene_variant,,ENST00000540620,;WDR74,upstream_gene_variant,,ENST00000453708,;WDR74,upstream_gene_variant,,ENST00000544953,;WDR74,upstream_gene_variant,,ENST00000544831,;WDR74,upstream_gene_variant,,ENST00000545112,;WDR74,upstream_gene_variant,,ENST00000538277,;WDR74,upstream_gene_variant,,ENST00000538150,;WDR74,upstream_gene_variant,,ENST00000541930,;WDR74,upstream_gene_variant,,ENST00000542347,;	A	ENSG00000133316	ENST00000525239	Transcript	5_prime_UTR_variant	469	.	.	.	.	.	.	.	-1	WDR74	HGNC	25529	protein_coding	YES	CCDS44630.1	ENSP00000432119	WDR74_HUMAN	F5GYL6_HUMAN,E9PS41_HUMAN	UPI000013DB9A	.	.	.	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCCGATGCA	.	5	ESCA
RAB6A	0	.	GRCh37	11	73387840	73387840	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1103A>G	.	.	ENST00000310653	8/8	28	19	9	20	20	0	RAB6A,3_prime_UTR_variant,,ENST00000336083,;RAB6A,3_prime_UTR_variant,,ENST00000310653,;RAB6A,downstream_gene_variant,,ENST00000540771,;RAB6A,downstream_gene_variant,,ENST00000541973,;RAB6A,downstream_gene_variant,,ENST00000536566,;RAB6A,downstream_gene_variant,,ENST00000541588,;RAB6A,downstream_gene_variant,,ENST00000537446,;RAB6A,downstream_gene_variant,,ENST00000545625,;	C	ENSG00000175582	ENST00000310653	Transcript	3_prime_UTR_variant	2232	.	.	.	.	.	.	.	-1	RAB6A	HGNC	9786	protein_coding	YES	CCDS8223.1	ENSP00000311449	RAB6A_HUMAN	Q9UL30_HUMAN	UPI000002B21A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTATTCTGC	.	5	ESCA
MAML2	0	.	GRCh37	11	96074769	96074769	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291C>T	p.%3D	p.A97A	ENST00000524717	1/5	47	20	27	30	30	0	MAML2,synonymous_variant,p.%3D,ENST00000524717,;MIR1260B,downstream_gene_variant,,ENST00000582890,;	A	ENSG00000184384	ENST00000524717	Transcript	synonymous_variant	1576	291	97	A	gcC/gcT	.	.	.	-1	MAML2	HGNC	16259	protein_coding	YES	CCDS44714.1	ENSP00000434552	MAML2_HUMAN	.	UPI00001B4EFC	.	.	.	1/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTGGCGGT	.	5	ESCA
TAS2R8	0	.	GRCh37	12	10959271	10959271	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.309T>C	p.%3D	p.L103L	ENST00000240615	1/1	62	32	29	21	21	0	TAS2R8,synonymous_variant,p.%3D,ENST00000240615,;TAS2R9,downstream_gene_variant,,ENST00000240691,;TAS2R7,upstream_gene_variant,,ENST00000240687,;	G	ENSG00000121314	ENST00000240615	Transcript	synonymous_variant	622	309	103	L	ctT/ctC	.	.	.	-1	TAS2R8	HGNC	14915	protein_coding	YES	CCDS8632.1	ENSP00000240615	TA2R8_HUMAN	Q50KU2_HUMAN,Q50KU1_HUMAN	UPI0000038B10	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11394:SF31,hmmpanther:PTHR11394,Pfam_domain:PF05296,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTAAGGCA	.	5	ESCA
SCN8A	0	.	GRCh37	12	52159718	52159718	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2808G>C	p.Glu936Asp	p.E936D	ENST00000354534	16/27	97	54	43	98	98	0	SCN8A,missense_variant,p.Glu936Asp,ENST00000550891,;SCN8A,missense_variant,p.Glu936Asp,ENST00000354534,;SCN8A,missense_variant,p.Glu936Asp,ENST00000355133,;SCN8A,missense_variant,p.Glu936Asp,ENST00000545061,;	C	ENSG00000196876	ENST00000354534	Transcript	missense_variant	2986	2808	936	E/D	gaG/gaC	.	.	.	1	SCN8A	HGNC	10596	protein_coding	YES	CCDS44891.1	ENSP00000346534	SCN8A_HUMAN	Q9P2Q6_HUMAN,Q8WWN3_HUMAN	UPI000006FD85	.	deleterious(0)	probably_damaging(0.981)	16/27	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF132	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGAGTGGAT	.	5	ESCA
LRRC23	0	.	GRCh37	12	7016543	7016543	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555G>A	p.%3D	p.E185E	ENST00000007969	5/8	79	62	17	29	29	0	LRRC23,synonymous_variant,p.%3D,ENST00000436789,;LRRC23,synonymous_variant,p.%3D,ENST00000007969,;LRRC23,synonymous_variant,p.%3D,ENST00000443597,;LRRC23,synonymous_variant,p.%3D,ENST00000433346,;LRRC23,synonymous_variant,p.%3D,ENST00000323702,;LRRC23,intron_variant,,ENST00000429740,;LRRC23,downstream_gene_variant,,ENST00000415834,;LRRC23,downstream_gene_variant,,ENST00000449039,;LRRC23,downstream_gene_variant,,ENST00000457146,;LRRC23,3_prime_UTR_variant,,ENST00000451681,;LRRC23,3_prime_UTR_variant,,ENST00000431207,;LRRC23,3_prime_UTR_variant,,ENST00000428946,;LRRC23,downstream_gene_variant,,ENST00000486401,;	A	ENSG00000010626	ENST00000007969	Transcript	synonymous_variant	775	555	185	E	gaG/gaA	.	.	.	1	LRRC23	HGNC	19138	protein_coding	YES	CCDS8569.1	ENSP00000007969	LRC23_HUMAN	C9JQN5_HUMAN	UPI000013C506	.	.	.	5/8	.	Superfamily_domains:SSF52058,Gene3D:3.80.10.10,Pfam_domain:PF14580,hmmpanther:PTHR10588:SF204,hmmpanther:PTHR10588,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGAGCTTCG	.	5	ESCA
FNDC3A	0	.	GRCh37	13	49762729	49762729	+	Missense_Mutation	SNP	G	G	A	rs367719937	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1904G>A	p.Arg635His	p.R635H	ENST00000492622	17/26	79	36	43	58	58	0	FNDC3A,missense_variant,p.Arg635His,ENST00000541916,;FNDC3A,missense_variant,p.Arg635His,ENST00000492622,;FNDC3A,missense_variant,p.Arg579His,ENST00000398316,;FNDC3A,missense_variant,p.Arg635His,ENST00000484074,;COX7CP1,upstream_gene_variant,,ENST00000446556,;	A	ENSG00000102531	ENST00000492622	Transcript	missense_variant	2209	1904	635	R/H	cGt/cAt	rs367719937	.	.	1	FNDC3A	HGNC	20296	protein_coding	YES	CCDS41886.1	ENSP00000417257	FND3A_HUMAN	.	UPI0000229601	.	deleterious(0.03)	benign(0.108)	17/26	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR19900:SF38,hmmpanther:PTHR19900,PROSITE_profiles:PS50853	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATCGTTTAC	byCluster|by1000G	5	ESCA
SETDB2	0	.	GRCh37	13	50050669	50050669	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.399A>T	p.Glu133Asp	p.E133D	ENST00000317257	7/15	17	10	7	20	20	0	SETDB2,missense_variant,p.Glu121Asp,ENST00000258672,;SETDB2,missense_variant,p.Glu133Asp,ENST00000317257,;SETDB2,missense_variant,p.Glu121Asp,ENST00000354234,;	T	ENSG00000136169	ENST00000317257	Transcript	missense_variant	1224	399	133	E/D	gaA/gaT	.	.	.	1	SETDB2	HGNC	20263	protein_coding	YES	CCDS9417.1	ENSP00000326477	SETB2_HUMAN	Q8NDJ9_HUMAN	UPI000013CFF3	.	tolerated(0.56)	benign(0.013)	7/15	.	hmmpanther:PTHR22884:SF292,hmmpanther:PTHR22884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGAGAAAAAGA	.	4	ESCA
JAG2	0	.	GRCh37	14	105609908	105609908	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3152C>T	p.Ala1051Val	p.A1051V	ENST00000331782	25/26	43	28	14	40	40	0	JAG2,missense_variant,p.Ala1013Val,ENST00000347004,;JAG2,missense_variant,p.Ala1051Val,ENST00000331782,;JAG2,non_coding_transcript_exon_variant,,ENST00000546616,;JAG2,downstream_gene_variant,,ENST00000553244,;	A	ENSG00000184916	ENST00000331782	Transcript	missense_variant	3556	3152	1051	A/V	gCc/gTc	.	.	.	-1	JAG2	HGNC	6189	protein_coding	YES	CCDS9998.1	ENSP00000328169	JAG2_HUMAN	.	UPI0000167BD5	.	tolerated(0.16)	benign(0.26)	25/26	.	hmmpanther:PTHR24044:SF235,hmmpanther:PTHR24044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCGGCCACG	.	5	ESCA
AJUBA	0	.	GRCh37	14	23450545	23450545	+	Nonsense_Mutation	SNP	C	C	A	rs745365510	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.931G>T	p.Glu311Ter	p.E311*	ENST00000262713	1/8	15	2	13	10	10	0	AJUBA,stop_gained,p.Glu311Ter,ENST00000361265,;AJUBA,stop_gained,p.Glu85Ter,ENST00000553736,;AJUBA,stop_gained,p.Glu311Ter,ENST00000262713,;RP11-298I3.5,intron_variant,,ENST00000555074,;AJUBA,upstream_gene_variant,,ENST00000553911,;AJUBA,upstream_gene_variant,,ENST00000556731,;AJUBA,upstream_gene_variant,,ENST00000397388,;AJUBA,upstream_gene_variant,,ENST00000553592,;RP11-298I3.4,upstream_gene_variant,,ENST00000555294,;RP11-298I3.4,upstream_gene_variant,,ENST00000556503,;RP11-298I3.4,upstream_gene_variant,,ENST00000557615,;	A	ENSG00000129474	ENST00000262713	Transcript	stop_gained	1307	931	311	E/*	Gag/Tag	rs745365510	.	.	-1	AJUBA	HGNC	20250	protein_coding	YES	CCDS9581.1	ENSP00000262713	AJUBA_HUMAN	G3V5F5_HUMAN,G3V481_HUMAN	UPI0000040AEC	.	.	.	1/8	.	hmmpanther:PTHR24219,hmmpanther:PTHR24219:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCCTCCA	.	5	ESCA
ARID4A	0	.	GRCh37	14	58831580	58831580	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2773C>T	p.%3D	p.L925L	ENST00000355431	20/24	18	3	15	21	21	0	ARID4A,synonymous_variant,p.%3D,ENST00000355431,;ARID4A,synonymous_variant,p.%3D,ENST00000395168,;ARID4A,synonymous_variant,p.%3D,ENST00000417477,;ARID4A,synonymous_variant,p.%3D,ENST00000431317,;ARID4A,synonymous_variant,p.%3D,ENST00000348476,;ARID4A,downstream_gene_variant,,ENST00000469635,;ARID4A,upstream_gene_variant,,ENST00000466065,;	T	ENSG00000032219	ENST00000355431	Transcript	synonymous_variant	3146	2773	925	L	Ctg/Ttg	.	.	.	1	ARID4A	HGNC	9885	protein_coding	YES	CCDS9732.1	ENSP00000347602	ARI4A_HUMAN	H7C485_HUMAN,C9JIF4_HUMAN	UPI000013FD01	.	.	.	20/24	.	hmmpanther:PTHR13964:SF1,hmmpanther:PTHR13964	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAACTGACT	.	5	ESCA
AC114546.1	0	.	GRCh37	15	35271418	35271418	+	5'UTR	DEL	C	C	-	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-354delC	.	.	ENST00000391457	1/1	29	21	8	26	26	0	AC114546.1,5_prime_UTR_variant,,ENST00000391457,;ZNF770,3_prime_UTR_variant,,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;	-	ENSG00000212768	ENST00000391457	Transcript	5_prime_UTR_variant	867	.	.	.	.	.	.	.	1	AC114546.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000375288	.	Q9UHS9_HUMAN	UPI000006F036	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GACTCTCCCTGT	.	3	ESCA
CATSPER2	0	.	GRCh37	15	43931876	43931876	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682C>T	p.Gln228Ter	p.Q228*	ENST00000321596	6/13	35	26	8	39	39	0	CATSPER2,stop_gained,p.Gln228Ter,ENST00000355438,;CATSPER2,stop_gained,p.Gln228Ter,ENST00000354127,;CATSPER2,stop_gained,p.Gln234Ter,ENST00000381761,;CATSPER2,stop_gained,p.Gln228Ter,ENST00000396879,;CATSPER2,stop_gained,p.Gln228Ter,ENST00000321596,;STRC,intron_variant,,ENST00000541030,;RNU6-610P,upstream_gene_variant,,ENST00000384264,;CATSPER2,stop_gained,p.Gln228Ter,ENST00000433380,;CATSPER2,non_coding_transcript_exon_variant,,ENST00000469461,;CATSPER2,non_coding_transcript_exon_variant,,ENST00000415968,;CATSPER2,upstream_gene_variant,,ENST00000419262,;	A	ENSG00000166762	ENST00000321596	Transcript	stop_gained	882	682	228	Q/*	Caa/Taa	.	.	.	-1	CATSPER2	HGNC	18810	protein_coding	YES	CCDS10099.1	ENSP00000321463	CTSR2_HUMAN	E7EX46_HUMAN,B8ZZQ9_HUMAN	UPI000006DE3A	.	.	.	6/13	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTGAATTT	.	5	ESCA
UNC13C	0	.	GRCh37	15	54592555	54592555	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4252A>G	p.Ile1418Val	p.I1418V	ENST00000260323	12/32	32	18	13	31	31	0	UNC13C,missense_variant,p.Ile1416Val,ENST00000537900,;UNC13C,missense_variant,p.Ile1418Val,ENST00000545554,;UNC13C,missense_variant,p.Ile1418Val,ENST00000260323,;UNC13C,non_coding_transcript_exon_variant,,ENST00000561210,;	G	ENSG00000137766	ENST00000260323	Transcript	missense_variant	4252	4252	1418	I/V	Att/Gtt	.	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	deleterious_low_confidence(0)	probably_damaging(0.986)	12/32	.	hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCCATTTAT	.	5	ESCA
BNIP2	0	.	GRCh37	15	59956127	59956127	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*141A>G	.	.	ENST00000267859	10/10	25	12	12	22	22	0	BNIP2,3_prime_UTR_variant,,ENST00000439052,;BNIP2,3_prime_UTR_variant,,ENST00000267859,;BNIP2,3_prime_UTR_variant,,ENST00000607373,;BNIP2,3_prime_UTR_variant,,ENST00000415213,;AC092755.4,intron_variant,,ENST00000441746,;BNIP2,non_coding_transcript_exon_variant,,ENST00000478981,;BNIP2,downstream_gene_variant,,ENST00000560776,;	C	ENSG00000140299	ENST00000267859	Transcript	3_prime_UTR_variant	1543	.	.	.	.	.	.	.	-1	BNIP2	HGNC	1083	protein_coding	YES	CCDS10174.2	ENSP00000267859	.	J3KN59_HUMAN	UPI0000E59C57	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAATACAAA	.	5	ESCA
FBXL22	0	.	GRCh37	15	63889686	63889686	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.95T>C	p.Leu32Pro	p.L32P	ENST00000360587	1/2	30	16	14	27	27	0	FBXL22,missense_variant,p.Leu32Pro,ENST00000360587,;FBXL22,missense_variant,p.Leu32Pro,ENST00000534939,;FBXL22,missense_variant,p.Leu26Pro,ENST00000539570,;FBXL22,upstream_gene_variant,,ENST00000560325,;USP3-AS1,intron_variant,,ENST00000560962,;USP3-AS1,intron_variant,,ENST00000560622,;USP3-AS1,intron_variant,,ENST00000559737,;USP3-AS1,intron_variant,,ENST00000561191,;USP3-AS1,intron_variant,,ENST00000558831,;USP3-AS1,intron_variant,,ENST00000561256,;USP3-AS1,upstream_gene_variant,,ENST00000559861,;USP3,downstream_gene_variant,,ENST00000559257,;USP3,downstream_gene_variant,,ENST00000560202,;USP3,downstream_gene_variant,,ENST00000559192,;	C	ENSG00000197361	ENST00000360587	Transcript	missense_variant	135	95	32	L/P	cTt/cCt	.	.	.	1	FBXL22	HGNC	27537	protein_coding	YES	CCDS10187.2	ENSP00000353794	FXL22_HUMAN	.	UPI0000408A7A	.	deleterious_low_confidence(0)	probably_damaging(0.998)	1/2	.	Gene3D:1.20.1280.50,Pfam_domain:PF12937,Superfamily_domains:SSF81383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCTTGCCA	.	5	ESCA
AKAP13	0	.	GRCh37	15	86076844	86076844	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211C>A	p.Gln71Lys	p.Q71K	ENST00000361243	4/37	53	39	13	67	67	0	AKAP13,missense_variant,p.Gln71Lys,ENST00000560302,;AKAP13,missense_variant,p.Gln71Lys,ENST00000394518,;AKAP13,missense_variant,p.Gln71Lys,ENST00000559362,;AKAP13,missense_variant,p.Gln71Lys,ENST00000361243,;	A	ENSG00000170776	ENST00000361243	Transcript	missense_variant	292	211	71	Q/K	Cag/Aag	.	.	.	1	AKAP13	HGNC	371	protein_coding	YES	CCDS32320.1	ENSP00000354718	AKP13_HUMAN	H0YMI5_HUMAN,A8MYJ1_HUMAN	UPI00001A8BEB	.	tolerated(0.1)	benign(0.196)	4/37	.	hmmpanther:PTHR13944:SF4,hmmpanther:PTHR13944	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGCAGCTC	.	5	ESCA
RHBDF1	0	.	GRCh37	16	108636	108636	+	Silent	SNP	G	G	A	rs753678236	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2271C>T	p.%3D	p.F757F	ENST00000262316	18/18	12	8	4	19	19	0	RHBDF1,synonymous_variant,p.%3D,ENST00000448893,;RHBDF1,synonymous_variant,p.%3D,ENST00000262316,;RHBDF1,downstream_gene_variant,,ENST00000454039,;SNRNP25,downstream_gene_variant,,ENST00000383018,;SNRNP25,downstream_gene_variant,,ENST00000417493,;RHBDF1,downstream_gene_variant,,ENST00000450643,;SNRNP25,downstream_gene_variant,,ENST00000293861,;SNRNP25,downstream_gene_variant,,ENST00000493672,;RHBDF1,3_prime_UTR_variant,,ENST00000428730,;RHBDF1,downstream_gene_variant,,ENST00000487201,;RHBDF1,downstream_gene_variant,,ENST00000493647,;SNRNP25,downstream_gene_variant,,ENST00000397876,;SNRNP25,downstream_gene_variant,,ENST00000481947,;RHBDF1,downstream_gene_variant,,ENST00000417043,;RHBDF1,downstream_gene_variant,,ENST00000486045,;RHBDF1,downstream_gene_variant,,ENST00000482904,;SNRNP25,downstream_gene_variant,,ENST00000466183,;	A	ENSG00000007384	ENST00000262316	Transcript	synonymous_variant	2414	2271	757	F	ttC/ttT	rs753678236	.	.	-1	RHBDF1	HGNC	20561	protein_coding	YES	CCDS32344.1	ENSP00000262316	RHDF1_HUMAN	A2IDA2_HUMAN	UPI00001A5206	.	.	.	18/18	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22936:SF6,hmmpanther:PTHR22936,Gene3D:2xovA00,Pfam_domain:PF01694,Superfamily_domains:SSF144091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGAGGAAGAG	byCluster	3	ESCA
CIITA	0	.	GRCh37	16	11001871	11001871	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2522C>T	p.Thr841Met	p.T841M	ENST00000324288	11/20	63	49	14	39	39	0	CIITA,missense_variant,p.Thr841Met,ENST00000324288,;CIITA,intron_variant,,ENST00000381835,;CIITA,intron_variant,,ENST00000537380,;CIITA,non_coding_transcript_exon_variant,,ENST00000573309,;CIITA,non_coding_transcript_exon_variant,,ENST00000570546,;	T	ENSG00000179583	ENST00000324288	Transcript	missense_variant	2655	2522	841	T/M	aCg/aTg	.	.	.	1	CIITA	HGNC	7067	protein_coding	YES	CCDS10544.1	ENSP00000316328	C2TA_HUMAN	I3L2E5_HUMAN	UPI0000456914	.	deleterious(0)	benign(0.256)	11/20	.	hmmpanther:PTHR24106:SF104,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Superfamily_domains:SSF52047,Prints_domain:PR01719	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCACGCCTC	.	5	ESCA
MYH11	0	.	GRCh37	16	15835388	15835388	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2812C>T	p.%3D	p.L938L	ENST00000396324	23/42	35	13	21	25	25	0	MYH11,synonymous_variant,p.%3D,ENST00000452625,;MYH11,synonymous_variant,p.%3D,ENST00000576790,;MYH11,synonymous_variant,p.%3D,ENST00000300036,;MYH11,synonymous_variant,p.%3D,ENST00000396324,;AF001548.6,non_coding_transcript_exon_variant,,ENST00000577048,;MYH11,downstream_gene_variant,,ENST00000574119,;	A	ENSG00000133392	ENST00000396324	Transcript	synonymous_variant	2900	2812	938	L	Ctg/Ttg	.	.	.	-1	MYH11	HGNC	7569	protein_coding	YES	CCDS45423.1	ENSP00000379616	MYH11_HUMAN	Q68D89_HUMAN,Q66K75_HUMAN	UPI00005B7237	.	.	.	23/42	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF90257,Gene3D:1.20.5.340,hmmpanther:PTHR13140:SF335,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCAGGCGGG	.	5	ESCA
ITPRIPL2	0	.	GRCh37	16	19132331	19132331	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4940G>C	.	.	ENST00000381440	1/1	39	34	5	40	40	0	ITPRIPL2,3_prime_UTR_variant,,ENST00000381440,;ITPRIPL2,downstream_gene_variant,,ENST00000566735,;RP11-626G11.3,non_coding_transcript_exon_variant,,ENST00000567236,;CTD-2349B8.1,intron_variant,,ENST00000564808,;CTD-2349B8.1,intron_variant,,ENST00000568526,;	C	ENSG00000205730	ENST00000381440	Transcript	3_prime_UTR_variant	7078	.	.	.	.	.	.	.	1	ITPRIPL2	HGNC	27257	protein_coding	YES	CCDS32395.1	ENSP00000370849	IPIL2_HUMAN	.	UPI000023760C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAGAGGGAAA	.	2	ESCA
SYT17	0	.	GRCh37	16	19191850	19191850	+	Missense_Mutation	SNP	G	G	A	rs748717734	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320G>A	p.Arg107Gln	p.R107Q	ENST00000355377	4/8	27	21	5	29	29	0	SYT17,missense_variant,p.Arg46Gln,ENST00000562034,;SYT17,missense_variant,p.Arg46Gln,ENST00000568115,;SYT17,missense_variant,p.Arg107Gln,ENST00000355377,;SYT17,missense_variant,p.Arg46Gln,ENST00000566261,;SYT17,missense_variant,p.Arg103Gln,ENST00000562711,;SYT17,missense_variant,p.Arg46Gln,ENST00000570264,;SYT17,non_coding_transcript_exon_variant,,ENST00000562274,;SYT17,upstream_gene_variant,,ENST00000565183,;	A	ENSG00000103528	ENST00000355377	Transcript	missense_variant	718	320	107	R/Q	cGg/cAg	rs748717734	.	.	1	SYT17	HGNC	24119	protein_coding	YES	CCDS10575.1	ENSP00000347538	SYT17_HUMAN	H3BSP0_HUMAN,H3BRH9_HUMAN,H3BMD4_HUMAN	UPI000007297F	.	tolerated_low_confidence(0.11)	benign(0.002)	4/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GACGCGGAGGA	byFrequency	4	ESCA
SLX4	0	.	GRCh37	16	3652151	3652151	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.918G>A	p.Met306Ile	p.M306I	ENST00000294008	4/15	31	21	10	34	34	0	SLX4,missense_variant,p.Met306Ile,ENST00000294008,;SLX4,non_coding_transcript_exon_variant,,ENST00000486524,;SLX4,non_coding_transcript_exon_variant,,ENST00000466154,;	T	ENSG00000188827	ENST00000294008	Transcript	missense_variant	1559	918	306	M/I	atG/atA	.	.	.	-1	SLX4	HGNC	23845	protein_coding	YES	CCDS10506.2	ENSP00000294008	SLX4_HUMAN	.	UPI000050D2C5	.	deleterious(0)	probably_damaging(0.991)	4/15	.	hmmpanther:PTHR21541	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTTCATGGC	.	5	ESCA
FLCN	0	.	GRCh37	17	17122347	17122347	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1048C>T	p.Arg350Trp	p.R350W	ENST00000285071	9/14	87	64	22	33	33	0	FLCN,missense_variant,p.Arg350Trp,ENST00000285071,;MPRIP,downstream_gene_variant,,ENST00000578209,;FLCN,downstream_gene_variant,,ENST00000417064,;FLCN,downstream_gene_variant,,ENST00000389169,;RP11-45M22.4,missense_variant,p.Pro57Leu,ENST00000427497,;FLCN,non_coding_transcript_exon_variant,,ENST00000577591,;FLCN,downstream_gene_variant,,ENST00000466317,;FLCN,downstream_gene_variant,,ENST00000480316,;	A	ENSG00000154803	ENST00000285071	Transcript	missense_variant	1503	1048	350	R/W	Cgg/Tgg	.	.	.	-1	FLCN	HGNC	27310	protein_coding	YES	CCDS32579.1	ENSP00000285071	FLCN_HUMAN	J3QQZ7_HUMAN,C9J4C4_HUMAN	UPI0000071D7A	.	deleterious(0)	possibly_damaging(0.724)	9/14	.	hmmpanther:PTHR31441	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCCGGAGGG	.	5	ESCA
UBBP4	0	.	GRCh37	17	21731474	21731474	+	Silent	SNP	G	G	A	rs775578291	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549G>A	p.%3D	p.Q183Q	ENST00000578713	2/2	38	31	6	38	38	0	UBBP4,synonymous_variant,p.%3D,ENST00000578713,;UBBP4,3_prime_UTR_variant,,ENST00000583708,;UBBP4,3_prime_UTR_variant,,ENST00000584755,;UBBP4,intron_variant,,ENST00000581775,;UBBP4,downstream_gene_variant,,ENST00000584398,;UBBP4,downstream_gene_variant,,ENST00000581769,;	A	ENSG00000263563	ENST00000578713	Transcript	synonymous_variant	553	549	183	Q	caG/caA	rs775578291	.	.	1	UBBP4	HGNC	12467	protein_coding	YES	.	ENSP00000464265	.	J3QSA3_HUMAN,J3QRK5_HUMAN,J3KSM4_HUMAN,A8CGI2_HUMAN	UPI000268AF41	.	.	.	2/2	.	PROSITE_profiles:PS50053,hmmpanther:PTHR10666,PROSITE_patterns:PS00299,Gene3D:3.10.20.90,Pfam_domain:PF00240,SMART_domains:SM00213,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	ATCCAGGATGA	.	2	ESCA
UBBP4	0	.	GRCh37	17	21731478	21731478	+	Missense_Mutation	SNP	G	G	A	rs763004066	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553G>A	p.Glu185Lys	p.E185K	ENST00000578713	2/2	39	32	7	40	39	0	UBBP4,missense_variant,p.Glu185Lys,ENST00000578713,;UBBP4,3_prime_UTR_variant,,ENST00000583708,;UBBP4,3_prime_UTR_variant,,ENST00000584755,;UBBP4,intron_variant,,ENST00000581775,;UBBP4,downstream_gene_variant,,ENST00000584398,;UBBP4,downstream_gene_variant,,ENST00000581769,;	A	ENSG00000263563	ENST00000578713	Transcript	missense_variant	557	553	185	E/K	Gaa/Aaa	rs763004066	.	.	1	UBBP4	HGNC	12467	protein_coding	YES	.	ENSP00000464265	.	J3QSA3_HUMAN,J3QRK5_HUMAN,J3KSM4_HUMAN,A8CGI2_HUMAN	UPI000268AF41	.	tolerated(1)	benign(0.001)	2/2	.	PROSITE_profiles:PS50053,hmmpanther:PTHR10666,PROSITE_patterns:PS00299,Gene3D:3.10.20.90,Pfam_domain:PF00240,SMART_domains:SM00213,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	AGGATGAAGAA	.	2	ESCA
NLK	0	.	GRCh37	17	26523045	26523045	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1383C>T	.	.	ENST00000407008	11/11	39	23	16	34	34	0	NLK,3_prime_UTR_variant,,ENST00000407008,;NLK,downstream_gene_variant,,ENST00000584188,;NLK,intron_variant,,ENST00000496808,;NLK,downstream_gene_variant,,ENST00000584878,;AC061975.9,downstream_gene_variant,,ENST00000537819,;	T	ENSG00000087095	ENST00000407008	Transcript	3_prime_UTR_variant	3685	.	.	.	.	.	.	.	1	NLK	HGNC	29858	protein_coding	YES	CCDS11224.2	ENSP00000384625	NLK_HUMAN	H0YD75_HUMAN	UPI0000D48A70	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAGCAGAGT	.	5	ESCA
ACACA	0	.	GRCh37	17	35567390	35567390	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3698C>T	p.Thr1233Met	p.T1233M	ENST00000353139	30/56	48	25	22	36	36	0	ACACA,missense_variant,p.Thr1138Met,ENST00000360679,;ACACA,missense_variant,p.Thr1233Met,ENST00000353139,;ACACA,missense_variant,p.Thr1196Met,ENST00000394406,;ACACA,missense_variant,p.Thr1118Met,ENST00000335166,;ACACA,upstream_gene_variant,,ENST00000591119,;ACACA,non_coding_transcript_exon_variant,,ENST00000587598,;ACACA,intron_variant,,ENST00000587720,;	A	ENSG00000132142	ENST00000353139	Transcript	missense_variant	4180	3698	1233	T/M	aCg/aTg	.	.	.	-1	ACACA	HGNC	84	protein_coding	YES	CCDS42302.1	ENSP00000344789	ACACA_HUMAN	Q7Z5W8_HUMAN,K7EII5_HUMAN,K4DID9_HUMAN,B4DWK9_HUMAN,B4DK31_HUMAN,B4DIW1_HUMAN,B2ZZ90_HUMAN,A8MYL5_HUMAN	UPI00002263AC	.	tolerated(0.1)	probably_damaging(0.934)	30/56	.	hmmpanther:PTHR18866:SF89,hmmpanther:PTHR18866,Pfam_domain:PF08326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGCGTAGGG	.	5	ESCA
HOXB5	0	.	GRCh37	17	46670668	46670668	+	Missense_Mutation	SNP	G	G	A	rs755013825	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377C>T	p.Ser126Phe	p.S126F	ENST00000239151	1/2	110	69	41	60	60	0	HOXB5,missense_variant,p.Ser126Phe,ENST00000239151,;HOXB6,downstream_gene_variant,,ENST00000225648,;HOXB3,upstream_gene_variant,,ENST00000476342,;HOXB6,downstream_gene_variant,,ENST00000484302,;HOXB3,upstream_gene_variant,,ENST00000460160,;HOXB3,upstream_gene_variant,,ENST00000498678,;HOXB3,upstream_gene_variant,,ENST00000472863,;HOXB-AS3,intron_variant,,ENST00000487849,;HOXB-AS3,intron_variant,,ENST00000467155,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS3,intron_variant,,ENST00000474040,;HOXB-AS3,intron_variant,,ENST00000480872,;HOXB-AS3,intron_variant,,ENST00000476204,;HOXB-AS3,intron_variant,,ENST00000429755,;HOXB-AS3,intron_variant,,ENST00000492897,;HOXB-AS3,upstream_gene_variant,,ENST00000481995,;HOXB-AS3,upstream_gene_variant,,ENST00000466037,;HOXB-AS3,upstream_gene_variant,,ENST00000460041,;HOXB-AS3,upstream_gene_variant,,ENST00000477144,;HOXB-AS3,upstream_gene_variant,,ENST00000474324,;HOXB3,intron_variant,,ENST00000552000,;HOXB6,downstream_gene_variant,,ENST00000490419,;HOXB6,downstream_gene_variant,,ENST00000470193,;	A	ENSG00000120075	ENST00000239151	Transcript	missense_variant	656	377	126	S/F	tCc/tTc	rs755013825	.	.	-1	HOXB5	HGNC	5116	protein_coding	YES	CCDS11530.1	ENSP00000239151	HXB5_HUMAN	.	UPI000012CF58	.	deleterious(0.02)	benign(0.215)	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF165,hmmpanther:PTHR24326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTGGAGCTG	.	5	ESCA
ABCC3	0	.	GRCh37	17	48745338	48745338	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1750A>G	p.Met584Val	p.M584V	ENST00000285238	13/31	29	15	14	21	21	0	ABCC3,missense_variant,p.Met584Val,ENST00000285238,;ABCC3,downstream_gene_variant,,ENST00000427699,;ABCC3,downstream_gene_variant,,ENST00000513589,;ABCC3,upstream_gene_variant,,ENST00000503304,;ABCC3,missense_variant,p.Met584Val,ENST00000505699,;ABCC3,3_prime_UTR_variant,,ENST00000502426,;ABCC3,upstream_gene_variant,,ENST00000510633,;ABCC3,downstream_gene_variant,,ENST00000571855,;ABCC3,downstream_gene_variant,,ENST00000515585,;ABCC3,downstream_gene_variant,,ENST00000515070,;	G	ENSG00000108846	ENST00000285238	Transcript	missense_variant	1830	1750	584	M/V	Atg/Gtg	.	.	.	1	ABCC3	HGNC	54	protein_coding	YES	CCDS32681.1	ENSP00000285238	MRP3_HUMAN	Q96QA9_HUMAN,Q2M3C9_HUMAN	UPI000004B145	.	deleterious(0.04)	benign(0.005)	13/31	.	PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF199,TIGRFAM_domain:TIGR00957,Gene3D:2hydA01,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAACATGCTG	.	5	ESCA
SPAG9	0	.	GRCh37	17	49043483	49043483	+	3'UTR	SNP	C	C	A	rs141770749	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*150G>T	.	.	ENST00000262013	30/30	34	19	15	42	42	0	SPAG9,3_prime_UTR_variant,,ENST00000510283,;SPAG9,3_prime_UTR_variant,,ENST00000505279,;SPAG9,3_prime_UTR_variant,,ENST00000357122,;SPAG9,3_prime_UTR_variant,,ENST00000262013,;SPAG9,upstream_gene_variant,,ENST00000509724,;SPAG9,downstream_gene_variant,,ENST00000506500,;	A	ENSG00000008294	ENST00000262013	Transcript	3_prime_UTR_variant	4325	.	.	.	.	rs141770749	.	.	-1	SPAG9	HGNC	14524	protein_coding	YES	CCDS45740.1	ENSP00000262013	JIP4_HUMAN	H0Y981_HUMAN	UPI0000D60DF7	.	.	.	30/30	.	.	T:0.0006	T:0.0015	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGAACGGATT	byFrequency|byCluster|by1000G	5	ESCA
SPAG9	0	.	GRCh37	17	49091695	49091695	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1111G>T	p.Glu371Ter	p.E371*	ENST00000262013	9/30	34	16	17	23	23	0	SPAG9,stop_gained,p.Glu214Ter,ENST00000510283,;SPAG9,stop_gained,p.Glu357Ter,ENST00000357122,;SPAG9,stop_gained,p.Glu357Ter,ENST00000505279,;SPAG9,stop_gained,p.Glu371Ter,ENST00000262013,;SPAG9,stop_gained,p.Glu41Ter,ENST00000511795,;SPAG9,non_coding_transcript_exon_variant,,ENST00000576492,;SPAG9,non_coding_transcript_exon_variant,,ENST00000513547,;SPAG9,non_coding_transcript_exon_variant,,ENST00000514613,;SPAG9,non_coding_transcript_exon_variant,,ENST00000505173,;	A	ENSG00000008294	ENST00000262013	Transcript	stop_gained	1320	1111	371	E/*	Gag/Tag	.	.	.	-1	SPAG9	HGNC	14524	protein_coding	YES	CCDS45740.1	ENSP00000262013	JIP4_HUMAN	H0Y981_HUMAN	UPI0000D60DF7	.	.	.	9/30	.	hmmpanther:PTHR13886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTCTATGC	.	5	ESCA
USH1G	0	.	GRCh37	17	72915950	72915950	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.981C>T	p.%3D	p.H327H	ENST00000319642	2/3	116	87	29	45	45	0	USH1G,synonymous_variant,p.%3D,ENST00000319642,;OTOP2,upstream_gene_variant,,ENST00000580223,;OTOP2,upstream_gene_variant,,ENST00000331427,;USH1G,3_prime_UTR_variant,,ENST00000579243,;OTOP2,upstream_gene_variant,,ENST00000584711,;	A	ENSG00000182040	ENST00000319642	Transcript	synonymous_variant	1164	981	327	H	caC/caT	COSM1385867	.	.	-1	USH1G	HGNC	16356	protein_coding	YES	CCDS32725.1	ENSP00000320076	USH1G_HUMAN	.	UPI00001BC010	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCCGTGCAG	.	5	ESCA
SLC16A5	0	.	GRCh37	17	73096277	73096277	+	Silent	SNP	T	T	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.519T>A	p.%3D	p.L173L	ENST00000450736	4/6	72	51	20	45	45	0	SLC16A5,synonymous_variant,p.%3D,ENST00000584118,;SLC16A5,synonymous_variant,p.%3D,ENST00000329783,;SLC16A5,synonymous_variant,p.%3D,ENST00000450736,;SLC16A5,synonymous_variant,p.%3D,ENST00000580123,;SLC16A5,synonymous_variant,p.%3D,ENST00000578376,;SLC16A5,synonymous_variant,p.%3D,ENST00000538213,;SLC16A5,synonymous_variant,p.%3D,ENST00000584207,;SLC16A5,downstream_gene_variant,,ENST00000585293,;SLC16A5,downstream_gene_variant,,ENST00000582048,;	A	ENSG00000170190	ENST00000450736	Transcript	synonymous_variant	934	519	173	L	ctT/ctA	.	.	.	1	SLC16A5	HGNC	10926	protein_coding	YES	CCDS11713.1	ENSP00000390564	MOT6_HUMAN	J3QQW5_HUMAN,J3QL40_HUMAN,J3KT93_HUMAN	UPI0000000DC7	.	.	.	4/6	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11360:SF21,hmmpanther:PTHR11360,TIGRFAM_domain:TIGR00892,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTTGTCTT	.	5	ESCA
TP53	0	.	GRCh37	17	7577530	7577532	+	In_Frame_Del	DEL	TGG	TGG	-	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	TGG	TGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.749_751delCCA	p.Pro250_Ile251delinsLeu	p.P250_I251delinsL	ENST00000269305	7/11	70	6	64	48	48	0	TP53,inframe_deletion,p.Pro250_Ile251delinsLeu,ENST00000413465,;TP53,inframe_deletion,p.Pro250_Ile251delinsLeu,ENST00000420246,;TP53,inframe_deletion,p.Pro250_Ile251delinsLeu,ENST00000269305,;TP53,inframe_deletion,p.Pro118_Ile119delinsLeu,ENST00000509690,;TP53,inframe_deletion,p.Pro250_Ile251delinsLeu,ENST00000359597,;TP53,inframe_deletion,p.Pro250_Ile251delinsLeu,ENST00000445888,;TP53,inframe_deletion,p.Pro250_Ile251delinsLeu,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	-	ENSG00000141510	ENST00000269305	Transcript	inframe_deletion	939-941	749-751	250-251	PI/L	cCCAtc/ctc	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.L252_I254delLTI|c.754_762delCTCACCATC|4,CODON|p.L252_I254delLTI|c.751_759delATCCTCACC|4,CODON|p.L252delL|c.754_756delCTC|4,CODON|p.L252delL|c.754_756delCTC|9,CODON|p.L252delL|c.754_756delCTC|4,CODON|p.L252fs*93|c.754delC|5,CODON|p.L252F|c.754C>T|10,CODON|p.I251I|c.753C>A|3,CODON|p.I251N|c.752T>A|9,CODON|p.I251T|c.752T>C|6,CODON|p.I251T|c.752T>C|3,CODON|p.I251S|c.752T>G|12,CODON|p.I251T|c.752T>C|3,CODON|p.I251fs*94|c.751delA|6,CODON|p.I251L|c.751A>C|3,CODON|p.I251F|c.751A>T|8,CODON|p.P250P|c.750C>T|4,CODON|p.P250F|c.748_749CC>TT|3,BUFFER|p.I255delI|c.763_765delATC|8,BUFFER|p.I255delI|c.760_762delATC|3,BUFFER|p.I255fs*90|c.762delC|3,BUFFER|p.I255fs*9|c.762_763insN|3,BUFFER|p.I255V|c.763A>G|3,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|25,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254S|c.761T>G|9,BUFFER|p.I254N|c.761T>A|4,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254T|c.761T>C|3,BUFFER|p.I254F|c.760A>T|7,BUFFER|p.I254V|c.760A>G|6,BUFFER|p.I254fs*10|c.759_760insN|4,BUFFER|p.T253I|c.758C>T|4,BUFFER|p.T253N|c.758C>A|3,BUFFER|p.T253P|c.757A>C|3,BUFFER|p.T253S|c.757A>T|5,BUFFER|p.T253A|c.757A>G|3,BUFFER|p.L252P|c.755T>C|10,BUFFER|p.L252P|c.755T>C|3,BUFFER|p.L252P|c.755T>C|3,BUFFER|p.I251fs*94|c.748delC|4,BUFFER|p.P250L|c.749C>T|49,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250L|c.749C>T|8,BUFFER|p.P250L|c.749C>T|6,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250S|c.748C>T|12,BUFFER|p.R249fs*96|c.746delG|4,BUFFER|p.R249S|c.747G>T|31,BUFFER|p.R249S|c.747G>C|22,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|15,BUFFER|p.R249R|c.747G>A|6,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|314,BUFFER|p.R249S|c.747G>T|30,BUFFER|p.R249T|c.746G>C|3,BUFFER|p.R249M|c.746G>T|8,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249K|c.746G>A|17,BUFFER|p.R249M|c.746G>T|4,BUFFER|p.R249T|c.746G>C|20,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249M|c.746G>T|35,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R248Q|c.743_744GG>AA|5,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248R|c.744G>A|5,BUFFER|p.R248W|c.741_742CC>TT|15,BUFFER|p.R248Q|c.743G>A|113,BUFFER|p.R248Q|c.743G>A|633,BUFFER|p.R248L|c.743G>T|7,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|64,BUFFER|p.R155L|c.464G>T|12,BUFFER|p.R155P|c.464G>C|5,BUFFER|p.R248P|c.743G>C|17,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|42,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248L|c.743G>T|74,BUFFER|p.R155Q|c.464G>A|114,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248Q|c.743G>A|110,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87,BUFFER|p.N247N|c.741C>T|10,BUFFER|p.N247I|c.740A>T|7,BUFFER|p.N154I|c.461A>T|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247T|c.740A>C|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247S|c.740A>G|7,BUFFER|p.N247D|c.739A>G|5,BUFFER|p.N247Y|c.739A>T|3,BUFFER|p.M153I|c.459G>C|3,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>A|21,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>C|4	INDELOCATOR*|VARSCANI*|PINDEL	TGAGGATGGGCCTC	.	3	ESCA
TPGS2	0	.	GRCh37	18	34376768	34376768	+	Nonstop_Mutation	SNP	T	T	A	.	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903A>T	p.Ter301CysextTer32	p.*301Cext*32	ENST00000334295	7/7	43	30	13	19	19	0	TPGS2,stop_lost,p.Ter301CysextTer32,ENST00000334295,;TPGS2,stop_lost,p.Ter266CysextTer32,ENST00000593035,;TPGS2,stop_lost,p.Ter258CysextTer32,ENST00000383056,;TPGS2,intron_variant,,ENST00000590842,;TPGS2,intron_variant,,ENST00000587382,;TPGS2,intron_variant,,ENST00000587129,;TPGS2,intron_variant,,ENST00000591906,;TPGS2,downstream_gene_variant,,ENST00000589049,;TPGS2,intron_variant,,ENST00000590652,;TPGS2,intron_variant,,ENST00000590258,;TPGS2,downstream_gene_variant,,ENST00000590500,;TPGS2,downstream_gene_variant,,ENST00000591823,;TPGS2,downstream_gene_variant,,ENST00000590692,;TPGS2,downstream_gene_variant,,ENST00000585635,;	A	ENSG00000134779	ENST00000334295	Transcript	stop_lost	1331	903	301	*/C	tgA/tgT	COSM3362514	.	.	-1	TPGS2	HGNC	24561	protein_coding	YES	CCDS32817.1	ENSP00000335144	TPGS2_HUMAN	.	UPI0000201C11	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGCTCACTT	.	5	ESCA
NEDD4L	0	.	GRCh37	18	55996356	55996356	+	Silent	SNP	C	C	T	rs370529329	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.810C>T	p.%3D	p.P270P	ENST00000400345	10/31	9	5	4	9	9	0	NEDD4L,synonymous_variant,p.%3D,ENST00000456173,;NEDD4L,synonymous_variant,p.%3D,ENST00000256832,;NEDD4L,synonymous_variant,p.%3D,ENST00000586263,;NEDD4L,synonymous_variant,p.%3D,ENST00000357895,;NEDD4L,synonymous_variant,p.%3D,ENST00000400345,;NEDD4L,synonymous_variant,p.%3D,ENST00000431212,;NEDD4L,synonymous_variant,p.%3D,ENST00000435432,;NEDD4L,synonymous_variant,p.%3D,ENST00000456986,;NEDD4L,synonymous_variant,p.%3D,ENST00000356462,;NEDD4L,synonymous_variant,p.%3D,ENST00000587881,;NEDD4L,synonymous_variant,p.%3D,ENST00000256830,;NEDD4L,synonymous_variant,p.%3D,ENST00000586268,;NEDD4L,synonymous_variant,p.%3D,ENST00000382850,;NEDD4L,intron_variant,,ENST00000589054,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000592601,;NEDD4L,downstream_gene_variant,,ENST00000588066,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000590020,;NEDD4L,upstream_gene_variant,,ENST00000589167,;	T	ENSG00000049759	ENST00000400345	Transcript	synonymous_variant	1093	810	270	P	ccC/ccT	rs370529329	.	.	1	NEDD4L	HGNC	7728	protein_coding	YES	CCDS45872.1	ENSP00000383199	NED4L_HUMAN	K7ENS6_HUMAN,K7EN51_HUMAN	UPI000058E3AE	.	.	.	10/31	.	hmmpanther:PTHR11254:SF310,hmmpanther:PTHR11254,PIRSF_domain:PIRSF001569	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GTCCCCGAGGT	byFrequency|byCluster	2	ESCA
ALPK2	0	.	GRCh37	18	56247529	56247529	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479C>T	p.Ser160Leu	p.S160L	ENST00000361673	4/13	112	76	36	100	100	0	ALPK2,missense_variant,p.Ser160Leu,ENST00000361673,;ALPK2,non_coding_transcript_exon_variant,,ENST00000590642,;ALPK2,upstream_gene_variant,,ENST00000587399,;ALPK2,upstream_gene_variant,,ENST00000587842,;ALPK2,upstream_gene_variant,,ENST00000590662,;	A	ENSG00000198796	ENST00000361673	Transcript	missense_variant	693	479	160	S/L	tCa/tTa	.	.	.	-1	ALPK2	HGNC	20565	protein_coding	YES	CCDS11966.2	ENSP00000354991	ALPK2_HUMAN	.	UPI000022A768	.	deleterious(0.01)	benign(0.012)	4/13	.	hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGCTGACCTG	.	3	ESCA
PRKCSH	0	.	GRCh37	19	11548711	11548711	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211C>T	p.Pro71Ser	p.P71S	ENST00000252455	4/18	58	49	8	31	31	0	PRKCSH,missense_variant,p.Pro71Ser,ENST00000587509,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000589838,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000412601,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000593101,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000592741,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000591462,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000587327,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000589126,;PRKCSH,missense_variant,p.Pro71Ser,ENST00000252455,;PRKCSH,downstream_gene_variant,,ENST00000591946,;PRKCSH,downstream_gene_variant,,ENST00000588269,;CCDC151,upstream_gene_variant,,ENST00000356392,;CCDC151,upstream_gene_variant,,ENST00000545100,;CCDC151,upstream_gene_variant,,ENST00000591179,;CCDC151,upstream_gene_variant,,ENST00000586836,;snoU13,upstream_gene_variant,,ENST00000459022,;PRKCSH,non_coding_transcript_exon_variant,,ENST00000593104,;PRKCSH,non_coding_transcript_exon_variant,,ENST00000593053,;PRKCSH,upstream_gene_variant,,ENST00000589990,;CCDC151,upstream_gene_variant,,ENST00000593281,;CCDC151,upstream_gene_variant,,ENST00000591345,;	T	ENSG00000130175	ENST00000252455	Transcript	missense_variant	547	211	71	P/S	Cct/Tct	.	.	.	1	PRKCSH	HGNC	9411	protein_coding	YES	CCDS32911.1	ENSP00000252455	GLU2B_HUMAN	K7EPW7_HUMAN,K7EKX1_HUMAN,K7EJ70_HUMAN,K7EIP3_HUMAN	UPI000007007F	.	tolerated(0.08)	probably_damaging(0.974)	4/18	.	hmmpanther:PTHR12630,hmmpanther:PTHR12630:SF1,Gene3D:4.10.400.10,Pfam_domain:PF12999,Superfamily_domains:SSF57424	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGTCCTAAT	.	5	ESCA
ZNF440	0	.	GRCh37	19	11944594	11944594	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*815C>T	.	.	ENST00000304060	4/4	38	30	7	23	23	0	ZNF440,3_prime_UTR_variant,,ENST00000304060,;ZNF440,downstream_gene_variant,,ENST00000457526,;ZNF440,downstream_gene_variant,,ENST00000588954,;ZNF440,downstream_gene_variant,,ENST00000414255,;ZNF440,downstream_gene_variant,,ENST00000427505,;	T	ENSG00000171295	ENST00000304060	Transcript	3_prime_UTR_variant	2767	.	.	.	.	.	.	.	1	ZNF440	HGNC	20874	protein_coding	YES	CCDS42503.1	ENSP00000305373	ZN440_HUMAN	K7EJ55_HUMAN,C9JG89_HUMAN	UPI0000074249	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	AGCCTCGCACC	.	4	ESCA
WDR83	0	.	GRCh37	19	12780638	12780638	+	Missense_Mutation	SNP	G	G	A	rs746345300	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34G>A	p.Glu12Lys	p.E12K	ENST00000418543	3/11	60	46	14	28	28	0	WDR83,missense_variant,p.Glu12Lys,ENST00000242796,;WDR83,missense_variant,p.Glu12Lys,ENST00000418543,;WDR83OS,5_prime_UTR_variant,,ENST00000596731,;MAN2B1,upstream_gene_variant,,ENST00000486847,;WDR83OS,upstream_gene_variant,,ENST00000222190,;MAN2B1,upstream_gene_variant,,ENST00000598876,;MAN2B1,upstream_gene_variant,,ENST00000221363,;CTD-2192J16.24,upstream_gene_variant,,ENST00000597961,;WDR83OS,upstream_gene_variant,,ENST00000598732,;WDR83,upstream_gene_variant,,ENST00000547797,;MAN2B1,upstream_gene_variant,,ENST00000456935,;WDR83OS,downstream_gene_variant,,ENST00000600694,;MAN2B1,upstream_gene_variant,,ENST00000596512,;WDR83,missense_variant,p.Glu12Lys,ENST00000548381,;WDR83,missense_variant,p.Glu12Lys,ENST00000547481,;WDR83,missense_variant,p.Glu12Lys,ENST00000553179,;WDR83,non_coding_transcript_exon_variant,,ENST00000546754,;WDR83,non_coding_transcript_exon_variant,,ENST00000547255,;WDR83,non_coding_transcript_exon_variant,,ENST00000550939,;WDR83,non_coding_transcript_exon_variant,,ENST00000551329,;MAN2B1,upstream_gene_variant,,ENST00000466794,;WDR83,upstream_gene_variant,,ENST00000552700,;MAN2B1,upstream_gene_variant,,ENST00000600281,;WDR83,upstream_gene_variant,,ENST00000425834,;	A	ENSG00000123154	ENST00000418543	Transcript	missense_variant	383	34	12	E/K	Gag/Aag	rs746345300	.	.	1	WDR83	HGNC	32672	protein_coding	YES	CCDS12275.1	ENSP00000402653	WDR83_HUMAN	.	UPI000006DE5C	.	tolerated(0.18)	benign(0.265)	3/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22842,Gene3D:2.130.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCAGAGCTG	byFrequency	5	ESCA
USE1	0	.	GRCh37	19	17330466	17330466	+	Silent	SNP	G	G	A	rs146606083	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624G>A	p.%3D	p.A208A	ENST00000263897	8/8	31	28	3	34	34	0	USE1,synonymous_variant,p.%3D,ENST00000263897,;USE1,synonymous_variant,p.%3D,ENST00000445667,;USE1,3_prime_UTR_variant,,ENST00000379776,;USE1,3_prime_UTR_variant,,ENST00000596136,;USE1,downstream_gene_variant,,ENST00000593597,;USE1,downstream_gene_variant,,ENST00000595101,;USE1,3_prime_UTR_variant,,ENST00000594724,;USE1,3_prime_UTR_variant,,ENST00000600970,;USE1,downstream_gene_variant,,ENST00000594399,;USE1,downstream_gene_variant,,ENST00000601662,;USE1,downstream_gene_variant,,ENST00000601592,;	A	ENSG00000053501	ENST00000263897	Transcript	synonymous_variant	671	624	208	A	gcG/gcA	rs146606083	.	.	1	USE1	HGNC	30882	protein_coding	YES	CCDS46011.1	ENSP00000263897	USE1_HUMAN	M0QYT5_HUMAN	UPI000013F66C	.	.	.	8/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13050,Pfam_domain:PF09753	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGCGGACCA	byFrequency|byCluster|by1000G	2	ESCA
ZNF486	0	.	GRCh37	19	20308434	20308434	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915T>C	p.%3D	p.H305H	ENST00000335117	4/4	29	19	10	27	27	0	ZNF486,synonymous_variant,p.%3D,ENST00000335117,;CTC-260E6.6,intron_variant,,ENST00000586657,;CTC-260E6.6,intron_variant,,ENST00000593655,;CTC-260E6.6,intron_variant,,ENST00000585498,;	C	ENSG00000256229	ENST00000335117	Transcript	synonymous_variant	972	915	305	H	caT/caC	.	.	.	1	ZNF486	HGNC	20807	protein_coding	YES	CCDS46029.1	ENSP00000335042	ZN486_HUMAN	Q59FB0_HUMAN	UPI00002376E8	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF95,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCATCCTGC	.	5	ESCA
ZNF493	0	.	GRCh37	19	21608172	21608172	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*386C>T	.	.	ENST00000392288	4/4	15	9	5	10	10	0	ZNF493,3_prime_UTR_variant,,ENST00000355504,;ZNF493,3_prime_UTR_variant,,ENST00000392288,;ZNF493,downstream_gene_variant,,ENST00000596302,;CTD-2561J22.3,intron_variant,,ENST00000600810,;ZNF493,downstream_gene_variant,,ENST00000598152,;	T	ENSG00000196268	ENST00000392288	Transcript	3_prime_UTR_variant	2820	.	.	.	.	.	.	.	1	ZNF493	HGNC	23708	protein_coding	YES	CCDS42536.1	ENSP00000376110	ZN493_HUMAN	.	UPI000022ABBF	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AATGTCTCAAA	.	3	ESCA
ZNF43	0	.	GRCh37	19	21991047	21991047	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1792G>A	p.Glu598Lys	p.E598K	ENST00000354959	4/4	34	21	13	21	21	0	ZNF43,missense_variant,p.Glu592Lys,ENST00000595461,;ZNF43,missense_variant,p.Glu598Lys,ENST00000354959,;ZNF43,missense_variant,p.Glu592Lys,ENST00000594012,;ZNF43,missense_variant,p.Glu592Lys,ENST00000598381,;ZNF43,downstream_gene_variant,,ENST00000599906,;ZNF43,downstream_gene_variant,,ENST00000598288,;ZNF43,downstream_gene_variant,,ENST00000596899,;	T	ENSG00000198521	ENST00000354959	Transcript	missense_variant	1962	1792	598	E/K	Gaa/Aaa	.	.	.	-1	ZNF43	HGNC	13109	protein_coding	YES	CCDS12413.2	ENSP00000347045	ZNF43_HUMAN	M0R0T7_HUMAN,M0QYJ6_HUMAN,M0QXI2_HUMAN	UPI00001BD957	.	tolerated(0.05)	benign(0.393)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF220,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTCTTCAC	.	5	ESCA
TMPRSS9	0	.	GRCh37	19	2389893	2389893	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110G>A	p.Ser37Asn	p.S37N	ENST00000332578	1/17	65	40	24	27	27	0	TMPRSS9,missense_variant,p.Ser37Asn,ENST00000332578,;TMPRSS9,non_coding_transcript_exon_variant,,ENST00000395264,;	A	ENSG00000178297	ENST00000332578	Transcript	missense_variant	110	110	37	S/N	aGc/aAc	.	.	.	1	TMPRSS9	HGNC	30079	protein_coding	YES	CCDS12088.1	ENSP00000330264	TMPS9_HUMAN	.	UPI00001B4EC6	.	deleterious(0.02)	benign(0.209)	1/17	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PIRSF_domain:PIRSF037931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCAGCCTTG	.	5	ESCA
ZNF599	0	.	GRCh37	19	35250997	35250997	+	Missense_Mutation	SNP	G	G	A	rs143039488	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.709C>T	p.Arg237Cys	p.R237C	ENST00000329285	4/4	55	44	11	30	30	0	ZNF599,missense_variant,p.Arg237Cys,ENST00000329285,;ZNF599,downstream_gene_variant,,ENST00000587354,;	A	ENSG00000153896	ENST00000329285	Transcript	missense_variant	1083	709	237	R/C	Cgt/Tgt	rs143039488	.	.	-1	ZNF599	HGNC	26408	protein_coding	YES	CCDS32991.1	ENSP00000333802	ZN599_HUMAN	.	UPI0000071186	.	deleterious(0.04)	possibly_damaging(0.901)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF20,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	A:0.0007	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAACGACAGG	byFrequency|byCluster	5	ESCA
WDR87	0	.	GRCh37	19	38378468	38378468	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5726T>G	p.Leu1909Arg	p.L1909R	ENST00000303868	6/6	82	63	19	57	57	0	WDR87,missense_variant,p.Leu1948Arg,ENST00000447313,;WDR87,missense_variant,p.Leu1909Arg,ENST00000303868,;	C	ENSG00000171804	ENST00000303868	Transcript	missense_variant	5951	5726	1909	L/R	cTg/cGg	.	.	.	-1	WDR87	HGNC	29934	protein_coding	YES	CCDS46063.1	ENSP00000368025	WDR87_HUMAN	B4DXE9_HUMAN	UPI0001662BC1	.	.	probably_damaging(0.963)	6/6	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19852,hmmpanther:PTHR19852:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCCAGTTTC	.	5	ESCA
SLC6A16	0	.	GRCh37	19	49797779	49797779	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1261C>T	p.%3D	p.L421L	ENST00000335875	8/12	78	68	9	63	63	0	SLC6A16,synonymous_variant,p.%3D,ENST00000454748,;SLC6A16,synonymous_variant,p.%3D,ENST00000335875,;SLC6A16,5_prime_UTR_variant,,ENST00000598828,;SLC6A16,non_coding_transcript_exon_variant,,ENST00000598221,;	A	ENSG00000063127	ENST00000335875	Transcript	synonymous_variant	1503	1261	421	L	Cta/Tta	.	.	.	-1	SLC6A16	HGNC	13622	protein_coding	YES	CCDS42590.1	ENSP00000338627	S6A16_HUMAN	M0QYK3_HUMAN	UPI00001305CE	.	.	.	8/12	.	PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF48,hmmpanther:PTHR11616,Pfam_domain:PF00209	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCTAGGTTTA	.	4	ESCA
CCDC155	0	.	GRCh37	19	49910924	49910924	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.989C>T	p.Thr330Met	p.T330M	ENST00000447857	12/20	44	33	10	27	27	0	CCDC155,missense_variant,p.Thr330Met,ENST00000447857,;CCDC155,missense_variant,p.Thr294Met,ENST00000600570,;CCDC155,non_coding_transcript_exon_variant,,ENST00000596130,;CCDC155,non_coding_transcript_exon_variant,,ENST00000593362,;CCDC155,upstream_gene_variant,,ENST00000596419,;	T	ENSG00000161609	ENST00000447857	Transcript	missense_variant	1194	989	330	T/M	aCg/aTg	.	.	.	1	CCDC155	HGNC	26520	protein_coding	YES	CCDS46140.1	ENSP00000404220	KASH5_HUMAN	M0R1C7_HUMAN,M0QXW9_HUMAN,M0QXT3_HUMAN,M0QX09_HUMAN	UPI000006F690	.	deleterious(0.02)	benign(0.112)	12/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10159:SF289,hmmpanther:PTHR10159,Pfam_domain:PF14662	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGACGCAGG	.	5	ESCA
SIGLEC9	0	.	GRCh37	19	51633212	51633212	+	Intron	SNP	G	G	A	rs113526831	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1203+1445G>A	.	.	ENST00000440804	.	31	23	8	23	23	0	SIGLEC9,missense_variant,p.Arg423His,ENST00000250360,;SIGLEC9,intron_variant,,ENST00000440804,;SIGLEC9,downstream_gene_variant,,ENST00000599948,;	A	ENSG00000129450	ENST00000440804	Transcript	intron_variant	.	.	.	.	.	rs113526831	.	.	1	SIGLEC9	HGNC	10878	protein_coding	YES	CCDS56100.1	ENSP00000413861	.	.	UPI00017A75A8	.	.	.	.	6/6	.	.	.	.	.	.	.	.	A:0	A:0.0006	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGCTCCT	byFrequency|byCluster|by1000G	5	ESCA
CEACAM18	0	.	GRCh37	19	51981881	51981881	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168G>A	p.%3D	p.E56E	ENST00000451626	2/5	47	22	25	29	29	0	CEACAM18,synonymous_variant,p.%3D,ENST00000451626,;CEACAM18,5_prime_UTR_variant,,ENST00000396477,;	A	ENSG00000213822	ENST00000451626	Transcript	synonymous_variant	168	168	56	E	gaG/gaA	.	.	.	1	CEACAM18	HGNC	31949	protein_coding	YES	.	ENSP00000402203	.	.	UPI0000DD8506	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGGACCC	.	5	ESCA
ZNF264	0	.	GRCh37	19	57724047	57724047	+	Nonsense_Mutation	SNP	C	C	T	rs751802283	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1582C>T	p.Arg528Ter	p.R528*	ENST00000263095	4/4	65	54	11	44	44	0	ZNF264,stop_gained,p.Arg528Ter,ENST00000263095,;ZNF264,stop_gained,p.Arg528Ter,ENST00000536056,;ZNF264,downstream_gene_variant,,ENST00000597447,;	T	ENSG00000083844	ENST00000263095	Transcript	stop_gained	1996	1582	528	R/*	Cga/Tga	rs751802283,COSM1002116	.	.	1	ZNF264	HGNC	13057	protein_coding	YES	CCDS33127.1	ENSP00000263095	ZN264_HUMAN	M0QXF3_HUMAN	UPI000013C33B	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF96,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTCGACAT	byFrequency	5	ESCA
DVL1	0	.	GRCh37	1	1275451	1275451	+	Silent	SNP	G	G	A	rs560603838	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.876C>T	p.%3D	p.D292D	ENST00000378891	8/15	24	13	11	16	16	0	DVL1,synonymous_variant,p.%3D,ENST00000378891,;DVL1,synonymous_variant,p.%3D,ENST00000378888,;TAS1R3,downstream_gene_variant,,ENST00000339381,;DVL1,downstream_gene_variant,,ENST00000472445,;	A	ENSG00000107404	ENST00000378891	Transcript	synonymous_variant	923	876	292	D	gaC/gaT	rs560603838	.	.	-1	DVL1	HGNC	3084	protein_coding	YES	CCDS22.1	ENSP00000368169	DVL1_HUMAN	Q6PJD6_HUMAN,B7Z6B5_HUMAN,B7Z1E8_HUMAN	UPI000013D455	.	.	.	8/15	.	PROSITE_profiles:PS50106,hmmpanther:PTHR10878:SF5,hmmpanther:PTHR10878,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCGTCAGC	by1000G	5	ESCA
SEMA6C	0	.	GRCh37	1	151109548	151109548	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.759G>A	p.%3D	p.V253V	ENST00000368913	11/20	63	45	18	29	29	0	SEMA6C,synonymous_variant,p.%3D,ENST00000368914,;SEMA6C,synonymous_variant,p.%3D,ENST00000368913,;SEMA6C,synonymous_variant,p.%3D,ENST00000341697,;SEMA6C,synonymous_variant,p.%3D,ENST00000368912,;SEMA6C,downstream_gene_variant,,ENST00000485745,;SEMA6C,upstream_gene_variant,,ENST00000489944,;SEMA6C,upstream_gene_variant,,ENST00000464018,;SEMA6C,upstream_gene_variant,,ENST00000479820,;	T	ENSG00000143434	ENST00000368913	Transcript	synonymous_variant	888	759	253	V	gtG/gtA	.	.	.	-1	SEMA6C	HGNC	10740	protein_coding	YES	CCDS53364.1	ENSP00000357909	SEM6C_HUMAN	Q9UFI1_HUMAN	UPI00001414D0	.	.	.	11/20	.	Superfamily_domains:SSF101912,SMART_domains:SM00630,Pfam_domain:PF01403,Gene3D:2.130.10.10,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF11,PROSITE_profiles:PS51004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTGCACCTA	.	5	ESCA
FLG	0	.	GRCh37	1	152283351	152283351	+	Silent	SNP	G	G	T	.	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4011C>A	p.%3D	p.S1337S	ENST00000368799	3/3	283	229	54	115	115	0	FLG,synonymous_variant,p.%3D,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	T	ENSG00000143631	ENST00000368799	Transcript	synonymous_variant	4047	4011	1337	S	tcC/tcA	COSM3474041	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	.	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF21	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGAGGAAGA	.	4	ESCA
ETV3	0	.	GRCh37	1	157094737	157094737	+	Missense_Mutation	SNP	G	G	A	rs763695411	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1435C>T	p.Arg479Cys	p.R479C	ENST00000368192	5/5	45	36	8	26	26	0	ETV3,missense_variant,p.Arg479Cys,ENST00000368192,;CYCSP52,upstream_gene_variant,,ENST00000422857,;	A	ENSG00000117036	ENST00000368192	Transcript	missense_variant	1500	1435	479	R/C	Cgc/Tgc	rs763695411	.	.	-1	ETV3	HGNC	3492	protein_coding	YES	CCDS44250.1	ENSP00000357175	ETV3_HUMAN	.	UPI0000071047	.	deleterious_low_confidence(0)	probably_damaging(0.91)	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGCCGCT	.	5	ESCA
SPTA1	0	.	GRCh37	1	158612700	158612700	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4509A>G	p.%3D	p.K1503K	ENST00000368147	32/52	51	20	31	34	34	0	SPTA1,synonymous_variant,p.%3D,ENST00000368147,;SPTA1,upstream_gene_variant,,ENST00000465741,;	C	ENSG00000163554	ENST00000368147	Transcript	synonymous_variant	4690	4509	1503	K	aaA/aaG	.	.	.	-1	SPTA1	HGNC	11272	protein_coding	YES	CCDS41423.1	ENSP00000357129	SPTA1_HUMAN	O60686_HUMAN	UPI0000458906	.	.	.	32/52	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF240,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTGTTTTAG	.	5	ESCA
SLC19A2	0	.	GRCh37	1	169433861	169433861	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1226A>T	.	.	ENST00000236137	6/6	8	3	5	11	11	0	SLC19A2,3_prime_UTR_variant,,ENST00000367804,;SLC19A2,3_prime_UTR_variant,,ENST00000236137,;CCDC181,upstream_gene_variant,,ENST00000545005,;RP1-206D15.3,upstream_gene_variant,,ENST00000445428,;RP1-206D15.3,upstream_gene_variant,,ENST00000437857,;	A	ENSG00000117479	ENST00000236137	Transcript	3_prime_UTR_variant	2957	.	.	.	.	.	.	.	-1	SLC19A2	HGNC	10938	protein_coding	YES	CCDS1280.1	ENSP00000236137	S19A2_HUMAN	.	UPI0000036177	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGACATATACT	.	2	ESCA
METTL11B	0	.	GRCh37	1	170136782	170136782	+	Missense_Mutation	SNP	C	C	T	rs766426941	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736C>T	p.Arg246Trp	p.R246W	ENST00000439373	4/4	62	51	10	40	40	0	METTL11B,missense_variant,p.Arg246Trp,ENST00000439373,;METTL11B,downstream_gene_variant,,ENST00000367764,;	T	ENSG00000203740	ENST00000439373	Transcript	missense_variant	843	736	246	R/W	Cgg/Tgg	rs766426941	.	.	1	METTL11B	HGNC	31932	protein_coding	YES	CCDS44275.1	ENSP00000408058	NTM1B_HUMAN	.	UPI0000418EF1	.	tolerated(0.1)	benign(0.001)	4/4	.	hmmpanther:PTHR12753:SF2,hmmpanther:PTHR12753,Pfam_domain:PF05891,Gene3D:3.40.50.150,PIRSF_domain:PIRSF016958,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCCGGAGC	.	5	ESCA
SLC9C2	0	.	GRCh37	1	173556830	173556830	+	Missense_Mutation	SNP	C	C	T	rs539570027	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.497G>A	p.Arg166His	p.R166H	ENST00000367714	5/28	30	24	5	24	24	0	SLC9C2,missense_variant,p.Arg166His,ENST00000367714,;SLC9C2,missense_variant,p.Arg64His,ENST00000536496,;RP3-436N22.3,intron_variant,,ENST00000431459,;	T	ENSG00000162753	ENST00000367714	Transcript	missense_variant	920	497	166	R/H	cGt/cAt	rs539570027,COSM530938,COSM899751	.	.	-1	SLC9C2	HGNC	28664	protein_coding	YES	CCDS1308.1	ENSP00000356687	SL9C2_HUMAN	F5H342_HUMAN	UPI0000197379	.	tolerated(0.6)	benign(0.001)	5/28	.	hmmpanther:PTHR10110:SF91,hmmpanther:PTHR10110,Pfam_domain:PF00999	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAACGAAGA	by1000G	5	ESCA
LAMC1	0	.	GRCh37	1	183091210	183091210	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2225G>T	p.Cys742Phe	p.C742F	ENST00000258341	13/28	59	44	14	33	32	0	LAMC1,missense_variant,p.Cys742Phe,ENST00000258341,;LAMC1,upstream_gene_variant,,ENST00000466964,;	T	ENSG00000135862	ENST00000258341	Transcript	missense_variant	2482	2225	742	C/F	tGc/tTc	.	.	.	1	LAMC1	HGNC	6492	protein_coding	YES	CCDS1351.1	ENSP00000258341	LAMC1_HUMAN	R4GNC7_HUMAN	UPI000013CFC7	.	deleterious(0)	probably_damaging(1)	13/28	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF228,hmmpanther:PTHR10574,PROSITE_patterns:PS00022,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAACTGCAGAG	.	5	ESCA
DESI2	0	.	GRCh37	1	244870267	244870267	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1176T>G	.	.	ENST00000302550	5/5	26	22	3	22	22	0	DESI2,3_prime_UTR_variant,,ENST00000302550,;DESI2,downstream_gene_variant,,ENST00000263831,;	G	ENSG00000121644	ENST00000302550	Transcript	3_prime_UTR_variant	2140	.	.	.	.	.	.	.	1	DESI2	HGNC	24264	protein_coding	YES	CCDS1626.1	ENSP00000306528	DESI2_HUMAN	.	UPI0000038D6C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAACTGTCAC	.	4	ESCA
OR14K1	0	.	GRCh37	1	247902646	247902646	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.730A>G	p.Ile244Val	p.I244V	ENST00000283225	1/1	52	44	8	38	38	0	OR14K1,missense_variant,p.Ile244Val,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,;	G	ENSG00000153230	ENST00000283225	Transcript	missense_variant	730	730	244	I/V	Att/Gtt	.	.	.	1	OR14K1	HGNC	15025	protein_coding	YES	.	ENSP00000283225	O14K1_HUMAN	.	UPI0000041CBA	.	tolerated(0.68)	benign(0.016)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF242,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTCATTGTT	.	4	ESCA
EPHA10	0	.	GRCh37	1	38185713	38185713	+	Silent	SNP	C	C	A	rs780958682	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2430G>T	p.%3D	p.A810A	ENST00000373048	14/17	21	15	6	25	25	0	EPHA10,synonymous_variant,p.%3D,ENST00000373048,;EPHA10,synonymous_variant,p.%3D,ENST00000330210,;EPHA10,synonymous_variant,p.%3D,ENST00000427468,;EPHA10,3_prime_UTR_variant,,ENST00000540011,;EPHA10,non_coding_transcript_exon_variant,,ENST00000446149,;EPHA10,synonymous_variant,p.%3D,ENST00000534097,;EPHA10,3_prime_UTR_variant,,ENST00000437645,;EPHA10,3_prime_UTR_variant,,ENST00000432874,;EPHA10,downstream_gene_variant,,ENST00000453577,;	A	ENSG00000183317	ENST00000373048	Transcript	synonymous_variant	2430	2430	810	A	gcG/gcT	rs780958682,COSM1321101	.	.	-1	EPHA10	HGNC	19987	protein_coding	YES	CCDS41305.1	ENSP00000362139	EPHAA_HUMAN	.	UPI00001A41BD	.	.	.	14/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF267,hmmpanther:PTHR24416,Pfam_domain:PF07714,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF56112,Prints_domain:PR00109	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CATAGCGCTGG	byFrequency	4	ESCA
PTCH2	0	.	GRCh37	1	45294908	45294908	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1292delT	p.Leu431ArgfsTer103	p.L431Rfs*103	ENST00000372192	10/22	22	17	5	24	24	0	PTCH2,frameshift_variant,p.Leu431ArgfsTer103,ENST00000447098,;PTCH2,frameshift_variant,p.Leu431ArgfsTer103,ENST00000372192,;	-	ENSG00000117425	ENST00000372192	Transcript	frameshift_variant	1423	1292	431	L/X	cTg/cg	.	.	.	-1	PTCH2	HGNC	9586	protein_coding	YES	CCDS516.1	ENSP00000361266	PTC2_HUMAN	.	UPI00001328B8	.	.	.	10/22	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Superfamily_domains:SSF82866,Gene3D:2j8sB01,Pfam_domain:PF12349,TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF62,PROSITE_profiles:PS50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCAGCAGTACC	.	3	ESCA
PRDX1	0	.	GRCh37	1	45980307	45980307	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.386G>A	p.Gly129Asp	p.G129D	ENST00000262746	5/6	18	10	8	18	18	0	PRDX1,missense_variant,p.Gly129Asp,ENST00000319248,;PRDX1,missense_variant,p.Gly129Asp,ENST00000262746,;PRDX1,missense_variant,p.Gly27Asp,ENST00000372079,;PRDX1,missense_variant,p.Gly129Asp,ENST00000447184,;PRDX1,missense_variant,p.Gly129Asp,ENST00000424390,;MMACHC,downstream_gene_variant,,ENST00000401061,;PRDX1,downstream_gene_variant,,ENST00000483583,;MMACHC,downstream_gene_variant,,ENST00000477188,;	T	ENSG00000117450	ENST00000262746	Transcript	missense_variant	726	386	129	G/D	gGc/gAc	.	.	.	-1	PRDX1	HGNC	9352	protein_coding	YES	CCDS522.1	ENSP00000262746	PRDX1_HUMAN	.	UPI000002FC88	.	deleterious(0.02)	possibly_damaging(0.673)	5/6	.	Superfamily_domains:SSF52833,PIRSF_domain:PIRSF000239,Pfam_domain:PF00578,Gene3D:3.40.30.10,hmmpanther:PTHR10681:SF75,hmmpanther:PTHR10681,PROSITE_profiles:PS51352	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAGGCCCCTG	.	2	ESCA
SLC5A9	0	.	GRCh37	1	48695050	48695050	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.498G>T	p.%3D	p.L166L	ENST00000236495	5/15	23	18	4	20	20	0	SLC5A9,synonymous_variant,p.%3D,ENST00000420136,;SLC5A9,synonymous_variant,p.%3D,ENST00000533824,;SLC5A9,synonymous_variant,p.%3D,ENST00000438567,;SLC5A9,synonymous_variant,p.%3D,ENST00000236495,;RP5-1024N4.4,non_coding_transcript_exon_variant,,ENST00000606809,;SLC5A9,synonymous_variant,p.%3D,ENST00000441260,;SLC5A9,synonymous_variant,p.%3D,ENST00000425816,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000493837,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000527929,;	T	ENSG00000117834	ENST00000236495	Transcript	synonymous_variant	548	498	166	L	ctG/ctT	.	.	.	1	SLC5A9	HGNC	22146	protein_coding	YES	CCDS44136.1	ENSP00000236495	SC5A9_HUMAN	.	UPI0000251D94	.	.	.	5/15	.	Pfam_domain:PF00474,TIGRFAM_domain:TIGR00813,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF96,PROSITE_profiles:PS50283	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTGAAGAA	.	5	ESCA
NINL	0	.	GRCh37	20	25462723	25462723	+	Missense_Mutation	SNP	C	C	T	rs766249914	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1691G>A	p.Arg564His	p.R564H	ENST00000278886	14/24	100	76	24	46	46	0	NINL,missense_variant,p.Arg564His,ENST00000422516,;NINL,missense_variant,p.Arg564His,ENST00000278886,;NINL,upstream_gene_variant,,ENST00000336104,;NINL,non_coding_transcript_exon_variant,,ENST00000489780,;	T	ENSG00000101004	ENST00000278886	Transcript	missense_variant	1765	1691	564	R/H	cGc/cAc	rs766249914,COSM1730453	.	.	-1	NINL	HGNC	29163	protein_coding	YES	CCDS33452.1	ENSP00000278886	NINL_HUMAN	.	UPI0000206B64	.	tolerated(0.45)	benign(0.014)	14/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF12	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTTGCGGTCC	byFrequency	5	ESCA
NPBWR2	0	.	GRCh37	20	62737818	62737818	+	Missense_Mutation	SNP	C	C	T	rs753109352	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.367G>A	p.Val123Ile	p.V123I	ENST00000369768	1/1	53	35	17	36	36	0	NPBWR2,missense_variant,p.Val123Ile,ENST00000369768,;	T	ENSG00000125522	ENST00000369768	Transcript	missense_variant	707	367	123	V/I	Gtc/Atc	rs753109352	.	.	-1	NPBWR2	HGNC	4530	protein_coding	YES	CCDS13557.1	ENSP00000358783	NPBW2_HUMAN	.	UPI000013CBB3	.	tolerated(1)	benign(0)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24229:SF18,hmmpanther:PTHR24229,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCGACGGCCA	byFrequency	5	ESCA
TIAM1	0	.	GRCh37	21	32525396	32525396	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3228C>T	p.%3D	p.L1076L	ENST00000286827	19/29	50	38	11	46	46	0	TIAM1,synonymous_variant,p.%3D,ENST00000286827,;TIAM1,synonymous_variant,p.%3D,ENST00000541036,;	A	ENSG00000156299	ENST00000286827	Transcript	synonymous_variant	3700	3228	1076	L	ctC/ctT	.	.	.	-1	TIAM1	HGNC	11805	protein_coding	YES	CCDS13609.1	ENSP00000286827	TIAM1_HUMAN	C9JMB5_HUMAN	UPI000013DE6F	.	.	.	19/29	.	Superfamily_domains:SSF48065,SMART_domains:SM00325,Pfam_domain:PF00621,Gene3D:1.20.900.10,hmmpanther:PTHR22826:SF88,hmmpanther:PTHR22826,PROSITE_profiles:PS50010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTGAGAAA	.	5	ESCA
IGLV1-50	0	.	GRCh37	22	22681969	22681969	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.151G>C	p.Gly51Arg	p.G51R	ENST00000390291	2/2	54	44	9	36	36	0	IGLV1-50,missense_variant,p.Gly51Arg,ENST00000390291,;IGLV1-51,downstream_gene_variant,,ENST00000390290,;BMS1P20,downstream_gene_variant,,ENST00000426066,;	C	ENSG00000211645	ENST00000390291	Transcript	missense_variant	202	151	51	G/R	Ggt/Cgt	.	.	.	1	IGLV1-50	HGNC	5881	IG_V_gene	YES	.	ENSP00000374826	.	A2MYD3_HUMAN	UPI0000F30332	.	tolerated_low_confidence(0.07)	benign(0.005)	2/2	.	Superfamily_domains:SSF48726,SMART_domains:SM00406,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR23267:SF116,hmmpanther:PTHR23267,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCGGGTTAT	.	5	ESCA
PRAME	0	.	GRCh37	22	22891014	22891014	+	Silent	SNP	C	C	T	rs185120829	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1005G>A	p.%3D	p.S335S	ENST00000543184	5/5	24	17	6	14	14	0	PRAME,synonymous_variant,p.%3D,ENST00000398743,;PRAME,synonymous_variant,p.%3D,ENST00000398741,;PRAME,synonymous_variant,p.%3D,ENST00000402697,;PRAME,synonymous_variant,p.%3D,ENST00000543184,;PRAME,synonymous_variant,p.%3D,ENST00000539862,;PRAME,synonymous_variant,p.%3D,ENST00000424204,;PRAME,synonymous_variant,p.%3D,ENST00000405655,;PRAME,downstream_gene_variant,,ENST00000420709,;PRAME,downstream_gene_variant,,ENST00000406503,;PRAME,downstream_gene_variant,,ENST00000438888,;PRAME,downstream_gene_variant,,ENST00000439106,;PRAME,downstream_gene_variant,,ENST00000403441,;PRAME,downstream_gene_variant,,ENST00000476336,;PRAME,downstream_gene_variant,,ENST00000485532,;PRAME,non_coding_transcript_exon_variant,,ENST00000492657,;PRAME,downstream_gene_variant,,ENST00000442481,;	T	ENSG00000185686	ENST00000543184	Transcript	synonymous_variant	1868	1005	335	S	tcG/tcA	rs185120829,COSM389434	.	.	-1	PRAME	HGNC	9336	protein_coding	YES	CCDS13801.1	ENSP00000445675	PRAME_HUMAN	F5H4B1_HUMAN,E7EW99_HUMAN,E7EMH2_HUMAN,B7Z986_HUMAN,B5MD04_HUMAN,B5MCY4_HUMAN	UPI0000000DDA	.	.	.	5/5	.	hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF4,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047	T:0.0004	T:0.0008	T:0	.	T:0	T:0	T:0.001	T:0.0002	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCCGAAAG	byFrequency|byCluster|by1000G	5	ESCA
LRP1B	0	.	GRCh37	2	140990160	140990160	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*595A>G	.	.	ENST00000389484	91/91	43	36	7	24	24	0	LRP1B,3_prime_UTR_variant,,ENST00000389484,;LRP1B,3_prime_UTR_variant,,ENST00000437977,;	C	ENSG00000168702	ENST00000389484	Transcript	3_prime_UTR_variant	15367	.	.	.	.	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	91/91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAATTTTACA	.	5	ESCA
ARL5A	0	.	GRCh37	2	152684695	152684695	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-5C>G	.	.	ENST00000295087	1/6	62	34	27	21	21	0	ARL5A,5_prime_UTR_variant,,ENST00000295087,;ARL5A,intron_variant,,ENST00000428992,;CACNB4,downstream_gene_variant,,ENST00000360283,;CACNB4,downstream_gene_variant,,ENST00000539935,;ARL5A,non_coding_transcript_exon_variant,,ENST00000487723,;ARL5A,intron_variant,,ENST00000446896,;ARL5A,intron_variant,,ENST00000458140,;	C	ENSG00000162980	ENST00000295087	Transcript	5_prime_UTR_variant	308	.	.	.	.	.	.	.	-1	ARL5A	HGNC	696	protein_coding	YES	CCDS2195.1	ENSP00000295087	ARL5A_HUMAN	.	UPI0000125EE6	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCGGGCAG	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098909	178098909	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136T>C	p.Tyr46His	p.Y46H	ENST00000397062	2/5	55	43	12	63	63	0	NFE2L2,missense_variant,p.Tyr30His,ENST00000449627,;NFE2L2,missense_variant,p.Tyr30His,ENST00000423513,;NFE2L2,missense_variant,p.Tyr46His,ENST00000397062,;NFE2L2,missense_variant,p.Tyr30His,ENST00000446151,;NFE2L2,missense_variant,p.Tyr30His,ENST00000588123,;NFE2L2,missense_variant,p.Tyr45His,ENST00000586532,;NFE2L2,missense_variant,p.Tyr30His,ENST00000421929,;NFE2L2,missense_variant,p.Tyr30His,ENST00000464747,;NFE2L2,missense_variant,p.Tyr30His,ENST00000448782,;NFE2L2,missense_variant,p.Tyr30His,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	G	ENSG00000116044	ENST00000397062	Transcript	missense_variant	691	136	46	Y/H	Tat/Cat	.	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	tolerated(0.72)	benign(0.001)	2/5	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CTCATACTCTT	.	2	ESCA
ESPNL	0	.	GRCh37	2	239040155	239040155	+	Missense_Mutation	SNP	G	G	A	rs746042812	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2800G>A	p.Ala934Thr	p.A934T	ENST00000343063	9/9	12	7	5	11	11	0	ESPNL,missense_variant,p.Ala934Thr,ENST00000343063,;ESPNL,missense_variant,p.Ala566Thr,ENST00000409506,;ESPNL,missense_variant,p.Ala890Thr,ENST00000409169,;ESPNL,downstream_gene_variant,,ENST00000423032,;ESPNL,non_coding_transcript_exon_variant,,ENST00000477241,;	A	ENSG00000144488	ENST00000343063	Transcript	missense_variant	3063	2800	934	A/T	Gcc/Acc	rs746042812,COSM574203	.	.	1	ESPNL	HGNC	27937	protein_coding	YES	CCDS2525.1	ENSP00000339115	ESPNL_HUMAN	C9J6L8_HUMAN	UPI000022BC90	.	tolerated(0.19)	benign(0.009)	9/9	.	hmmpanther:PTHR24153,hmmpanther:PTHR24153:SF0	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCCCGCCTGG	.	3	ESCA
UBXN2A	0	.	GRCh37	2	24222791	24222791	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*54A>T	.	.	ENST00000309033	7/7	14	3	11	15	15	0	UBXN2A,3_prime_UTR_variant,,ENST00000535786,;UBXN2A,3_prime_UTR_variant,,ENST00000309033,;UBXN2A,3_prime_UTR_variant,,ENST00000404924,;RN7SL610P,upstream_gene_variant,,ENST00000463845,;UBXN2A,non_coding_transcript_exon_variant,,ENST00000446425,;	T	ENSG00000173960	ENST00000309033	Transcript	3_prime_UTR_variant	1078	.	.	.	.	.	.	.	1	UBXN2A	HGNC	27265	protein_coding	YES	CCDS1704.1	ENSP00000312107	UBX2A_HUMAN	.	UPI00001616AE	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TGGACATGCAA	.	4	ESCA
CAD	0	.	GRCh37	2	27456369	27456369	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3181A>T	p.Ser1061Cys	p.S1061C	ENST00000264705	20/44	39	30	9	23	23	0	CAD,missense_variant,p.Ser1061Cys,ENST00000264705,;CAD,missense_variant,p.Ser998Cys,ENST00000403525,;CAD,upstream_gene_variant,,ENST00000458503,;CAD,downstream_gene_variant,,ENST00000464159,;CAD,non_coding_transcript_exon_variant,,ENST00000475695,;CAD,upstream_gene_variant,,ENST00000479002,;CAD,downstream_gene_variant,,ENST00000491891,;	T	ENSG00000084774	ENST00000264705	Transcript	missense_variant	3343	3181	1061	S/C	Agc/Tgc	.	.	.	1	CAD	HGNC	1424	protein_coding	YES	CCDS1742.1	ENSP00000264705	PYR1_HUMAN	Q53SZ4_HUMAN,Q53SY7_HUMAN,G1UI39_HUMAN	UPI000013D558	.	deleterious(0.01)	probably_damaging(0.957)	20/44	.	PROSITE_profiles:PS50975,hmmpanther:PTHR11405:SF5,hmmpanther:PTHR11405,Gene3D:3.30.470.20,Pfam_domain:PF02786,TIGRFAM_domain:TIGR01369,Superfamily_domains:SSF56059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATCAGCCAG	.	5	ESCA
MSH6	0	.	GRCh37	2	48033609	48033609	+	Missense_Mutation	SNP	G	G	C	rs587779294	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3820G>C	p.Glu1274Gln	p.E1274Q	ENST00000234420	9/10	22	8	13	26	26	0	MSH6,missense_variant,p.Glu972Gln,ENST00000538136,;MSH6,missense_variant,p.Glu1274Gln,ENST00000234420,;MSH6,missense_variant,p.Glu1144Gln,ENST00000540021,;FBXO11,intron_variant,,ENST00000405808,;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000403359,;FBXO11,downstream_gene_variant,,ENST00000402508,;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,3_prime_UTR_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000470899,;FBXO11,downstream_gene_variant,,ENST00000465204,;	C	ENSG00000116062	ENST00000234420	Transcript	missense_variant	3972	3820	1274	E/Q	Gaa/Caa	rs587779294	.	.	1	MSH6	HGNC	7329	protein_coding	YES	CCDS1836.1	ENSP00000234420	MSH6_HUMAN	U3KQ72_HUMAN,F5H2F9_HUMAN,C9JH55_HUMAN,C9J8Y8_HUMAN,C9J7Y7_HUMAN	UPI00000405F8	.	deleterious(0)	probably_damaging(0.998)	9/10	.	hmmpanther:PTHR11361:SF31,hmmpanther:PTHR11361,Pfam_domain:PF00488,Gene3D:3.40.50.300,SMART_domains:SM00534,PIRSF_domain:PIRSF037677,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATGAATGT	.	5	ESCA
SPTBN1	0	.	GRCh37	2	54895849	54895850	+	3'UTR	INS	-	-	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*151dupG	.	.	ENST00000356805	36/36	23	14	8	14	14	0	SPTBN1,3_prime_UTR_variant,,ENST00000356805,;SPTBN1,non_coding_transcript_exon_variant,,ENST00000467371,;	G	ENSG00000115306	ENST00000356805	Transcript	3_prime_UTR_variant	7519-7520	.	.	.	.	.	.	.	1	SPTBN1	HGNC	11275	protein_coding	YES	CCDS33198.1	ENSP00000349259	SPTB2_HUMAN	Q53RC4_HUMAN,F8W6C1_HUMAN,D6W5C0_HUMAN,B2ZZ89_HUMAN	UPI0000DBEE4B	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CATTTCGGGGG	.	2	ESCA
STARD7	0	.	GRCh37	2	96852119	96852119	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*349A>T	.	.	ENST00000337288	8/8	48	39	8	30	30	0	STARD7,3_prime_UTR_variant,,ENST00000337288,;STARD7,downstream_gene_variant,,ENST00000462501,;STARD7,non_coding_transcript_exon_variant,,ENST00000479456,;	A	ENSG00000084090	ENST00000337288	Transcript	3_prime_UTR_variant	1846	.	.	.	.	.	.	.	-1	STARD7	HGNC	18063	protein_coding	YES	CCDS2017.2	ENSP00000338030	STAR7_HUMAN	C9JTD3_HUMAN	UPI0000001C0C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCGATGGTGG	.	5	ESCA
ZDHHC23	0	.	GRCh37	3	113672833	113672833	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448G>T	p.Gly150Cys	p.G150C	ENST00000330212	3/6	145	114	31	108	108	0	ZDHHC23,missense_variant,p.Gly144Cys,ENST00000498275,;ZDHHC23,missense_variant,p.Gly150Cys,ENST00000330212,;ZDHHC23,upstream_gene_variant,,ENST00000496083,;ZDHHC23,downstream_gene_variant,,ENST00000491556,;ZDHHC23,upstream_gene_variant,,ENST00000488129,;ZDHHC23,missense_variant,p.Gly150Cys,ENST00000478793,;	T	ENSG00000184307	ENST00000330212	Transcript	missense_variant	747	448	150	G/C	Ggc/Tgc	.	.	.	1	ZDHHC23	HGNC	28654	protein_coding	YES	CCDS33827.1	ENSP00000330485	ZDH23_HUMAN	C9JPJ8_HUMAN,B3KXV3_HUMAN	UPI0000209F9A	.	deleterious(0.04)	probably_damaging(0.993)	3/6	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGGGCTAC	.	5	ESCA
IFT122	0	.	GRCh37	3	129195555	129195555	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1211G>T	p.Ser404Ile	p.S404I	ENST00000296266	12/31	34	28	6	24	24	0	IFT122,missense_variant,p.Ser242Ile,ENST00000349441,;IFT122,missense_variant,p.Ser247Ile,ENST00000504021,;IFT122,missense_variant,p.Ser345Ile,ENST00000507564,;IFT122,missense_variant,p.Ser203Ile,ENST00000431818,;IFT122,missense_variant,p.Ser294Ile,ENST00000347300,;IFT122,missense_variant,p.Ser144Ile,ENST00000440957,;IFT122,missense_variant,p.Ser404Ile,ENST00000296266,;IFT122,missense_variant,p.Ser180Ile,ENST00000515783,;IFT122,missense_variant,p.Ser232Ile,ENST00000512157,;IFT122,missense_variant,p.Ser353Ile,ENST00000348417,;IFT122,downstream_gene_variant,,ENST00000511498,;IFT122,upstream_gene_variant,,ENST00000509522,;IFT122,downstream_gene_variant,,ENST00000509815,;IFT122,3_prime_UTR_variant,,ENST00000512220,;IFT122,non_coding_transcript_exon_variant,,ENST00000506507,;IFT122,non_coding_transcript_exon_variant,,ENST00000508654,;IFT122,upstream_gene_variant,,ENST00000512814,;IFT122,upstream_gene_variant,,ENST00000448668,;IFT122,upstream_gene_variant,,ENST00000513891,;	T	ENSG00000163913	ENST00000296266	Transcript	missense_variant	1403	1211	404	S/I	aGc/aTc	.	.	.	1	IFT122	HGNC	13556	protein_coding	YES	CCDS3060.1	ENSP00000296266	IF122_HUMAN	H7C3C0_HUMAN	UPI0000141042	.	deleterious(0)	possibly_damaging(0.817)	12/31	.	hmmpanther:PTHR12764:SF4,hmmpanther:PTHR12764	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCAGCACAG	.	5	ESCA
AGTR1	0	.	GRCh37	3	148460318	148460318	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*416G>T	.	.	ENST00000542281	4/4	18	12	5	19	19	0	AGTR1,3_prime_UTR_variant,,ENST00000404754,;AGTR1,3_prime_UTR_variant,,ENST00000542281,;AGTR1,3_prime_UTR_variant,,ENST00000418473,;AGTR1,3_prime_UTR_variant,,ENST00000402260,;AGTR1,3_prime_UTR_variant,,ENST00000497524,;AGTR1,3_prime_UTR_variant,,ENST00000349243,;AGTR1,downstream_gene_variant,,ENST00000461609,;AGTR1,downstream_gene_variant,,ENST00000474935,;AGTR1,downstream_gene_variant,,ENST00000475347,;	T	ENSG00000144891	ENST00000542281	Transcript	3_prime_UTR_variant	1942	.	.	.	.	.	.	.	1	AGTR1	HGNC	336	protein_coding	YES	CCDS3137.1	ENSP00000443186	AGTR1_HUMAN	Q53YY0_HUMAN,D3DNG8_HUMAN	UPI0000039D66	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAAGGGCAG	.	5	ESCA
PIK3CA	0	.	GRCh37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	T	rs121913279	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	21/21	21	9	11	17	17	0	PIK3CA,missense_variant,p.His1047Leu,ENST00000263967,;RP11-245C23.3,downstream_gene_variant,,ENST00000609807,;	T	ENSG00000121879	ENST00000263967	Transcript	missense_variant	3297	3140	1047	H/L	cAt/cTt	rs121913279,COSM776,COSM775,COSM249874,COSM94987,COSM94986	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	tolerated(0.44)	benign(0.085)	21/21	.	PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	pathogenic	0,1,1,1,1,1	25710561	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H1047L|c.3140A>T|236,SITE|p.H1047L|c.3140A>T|45,CODON|p.H1047Y|c.3139C>T|8,CODON|p.H1047Y|c.3139C>T|54,CODON|p.H1047R|c.3140A>G|1687,CODON|p.H1047R|c.3140A>G|242,BUFFER|p.M1043I|c.3129G>T|4,BUFFER|p.M1043I|c.3129G>A|8,BUFFER|p.M1043I|c.3129G>T|45,BUFFER|p.M1043I|c.3129G>A|22,BUFFER|p.M1043I|c.3129G>C|4,BUFFER|p.M1043I|c.3129G>C|6,BUFFER|p.N1044D|c.3130A>G|4,BUFFER|p.N1044Y|c.3130A>T|3,BUFFER|p.N1044S|c.3131A>G|5,BUFFER|p.N1044S|c.3131A>G|3,BUFFER|p.N1044K|c.3132T>G|5,BUFFER|p.N1044K|c.3132T>A|15,BUFFER|p.N1044K|c.3132T>A|7,BUFFER|p.D1045N|c.3133G>A|6,BUFFER|p.A1046T|c.3136G>A|6,BUFFER|p.A1046E|c.3137C>A|3,BUFFER|p.H1047Q|c.3141T>G|4,BUFFER|p.H1048R|c.3143A>G|6,BUFFER|p.H1048R|c.3143A>G|3,BUFFER|p.G1049S|c.3145G>A|16,BUFFER|p.G1049R|c.3145G>C|29,BUFFER|p.G1049R|c.3145G>C|5,BUFFER|p.G1049A|c.3146G>C|3,BUFFER|p.G1049D|c.3146G>A|4,BUFFER|p.G1049G|c.3147T>C|10,BUFFER|p.G1050S|c.3148G>A|3,BUFFER|p.G1050D|c.3149G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACATCATG	byFrequency|byCluster	5	ESCA
MCF2L2	0	.	GRCh37	3	182948802	182948802	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1866C>T	p.%3D	p.R622R	ENST00000328913	16/30	32	27	5	20	20	0	MCF2L2,synonymous_variant,p.%3D,ENST00000473233,;MCF2L2,synonymous_variant,p.%3D,ENST00000447025,;MCF2L2,synonymous_variant,p.%3D,ENST00000328913,;MCF2L2,non_coding_transcript_exon_variant,,ENST00000488149,;	A	ENSG00000053524	ENST00000328913	Transcript	synonymous_variant	2164	1866	622	R	cgC/cgT	.	.	.	-1	MCF2L2	HGNC	30319	protein_coding	YES	CCDS3243.1	ENSP00000328118	MF2L2_HUMAN	C9J326_HUMAN	UPI00001A962F	.	.	.	16/30	.	PROSITE_profiles:PS50010,hmmpanther:PTHR22826:SF89,hmmpanther:PTHR22826,Gene3D:1.20.900.10,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAATGCGCCT	.	5	ESCA
B3GNT5	0	.	GRCh37	3	182988947	182988947	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*224A>G	.	.	ENST00000326505	2/2	67	38	28	32	32	0	B3GNT5,3_prime_UTR_variant,,ENST00000460419,;B3GNT5,3_prime_UTR_variant,,ENST00000326505,;MCF2L2,intron_variant,,ENST00000328913,;MCF2L2,intron_variant,,ENST00000473233,;MCF2L2,intron_variant,,ENST00000447025,;B3GNT5,downstream_gene_variant,,ENST00000481531,;MCF2L2,downstream_gene_variant,,ENST00000414362,;B3GNT5,downstream_gene_variant,,ENST00000464191,;B3GNT5,downstream_gene_variant,,ENST00000464923,;B3GNT5,downstream_gene_variant,,ENST00000465010,;B3GNT5,intron_variant,,ENST00000480551,;B3GNT5,downstream_gene_variant,,ENST00000496270,;B3GNT5,downstream_gene_variant,,ENST00000493370,;B3GNT5,downstream_gene_variant,,ENST00000488301,;B3GNT5,downstream_gene_variant,,ENST00000477699,;MCF2L2,intron_variant,,ENST00000488149,;	G	ENSG00000176597	ENST00000326505	Transcript	3_prime_UTR_variant	1891	.	.	.	.	.	.	.	1	B3GNT5	HGNC	15684	protein_coding	YES	CCDS3244.1	ENSP00000316173	B3GN5_HUMAN	C9J5K2_HUMAN,C9J368_HUMAN,C9IYY0_HUMAN	UPI000003D75E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATATTATT	.	5	ESCA
RNU1-20P	0	.	GRCh37	3	192445098	192445098	+	3'Flank	SNP	T	T	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000363314	.	52	30	21	28	28	0	FGF12,5_prime_UTR_variant,,ENST00000418610,;FGF12,5_prime_UTR_variant,,ENST00000450716,;FGF12,5_prime_UTR_variant,,ENST00000445105,;FGF12,5_prime_UTR_variant,,ENST00000430714,;FGF12,intron_variant,,ENST00000448795,;FGF12,upstream_gene_variant,,ENST00000264730,;RNU1-20P,downstream_gene_variant,,ENST00000363314,;FGF12,non_coding_transcript_exon_variant,,ENST00000466144,;FGF12,non_coding_transcript_exon_variant,,ENST00000491636,;	G	ENSG00000200184	ENST00000363314	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2246	-1	RNU1-20P	HGNC	41946	snRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCCTTCCCC	.	5	ESCA
MUC4	0	.	GRCh37	3	195510962	195510962	+	Missense_Mutation	SNP	G	G	A	rs753697823	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7489C>T	p.Leu2497Phe	p.L2497F	ENST00000463781	2/25	577	511	66	354	354	0	MUC4,missense_variant,p.Leu2497Phe,ENST00000475231,;MUC4,missense_variant,p.Leu2497Phe,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.Leu2497Phe,ENST00000477086,;MUC4,missense_variant,p.Leu2497Phe,ENST00000466475,;MUC4,missense_variant,p.Leu2497Phe,ENST00000478156,;MUC4,missense_variant,p.Leu2497Phe,ENST00000470451,;MUC4,missense_variant,p.Leu2497Phe,ENST00000479406,;MUC4,missense_variant,p.Leu2497Phe,ENST00000477756,;MUC4,missense_variant,p.Leu2497Phe,ENST00000462323,;MUC4,missense_variant,p.Leu2497Phe,ENST00000480843,;	A	ENSG00000145113	ENST00000463781	Transcript	missense_variant	7949	7489	2497	L/F	Ctt/Ttt	rs753697823	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	probably_damaging(0.972)	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGAAGACGGG	byFrequency	4	ESCA
NRROS	0	.	GRCh37	3	196387351	196387351	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837G>A	p.%3D	p.L279L	ENST00000328557	3/3	48	22	26	36	36	0	NRROS,synonymous_variant,p.%3D,ENST00000328557,;PIGX,intron_variant,,ENST00000426755,;	A	ENSG00000174004	ENST00000328557	Transcript	synonymous_variant	1040	837	279	L	ctG/ctA	.	.	.	1	NRROS	HGNC	24613	protein_coding	YES	CCDS3319.1	ENSP00000328625	NRROS_HUMAN	.	UPI000000DA7E	.	.	.	3/3	.	Superfamily_domains:SSF52047,Gene3D:3.80.10.10,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF245,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTGCGCGA	.	5	ESCA
AZI2	0	.	GRCh37	3	28373342	28373342	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647+518G>T	.	.	ENST00000479665	.	39	23	16	26	26	0	AZI2,3_prime_UTR_variant,,ENST00000334100,;AZI2,3_prime_UTR_variant,,ENST00000457172,;AZI2,3_prime_UTR_variant,,ENST00000420543,;AZI2,intron_variant,,ENST00000429369,;AZI2,intron_variant,,ENST00000479665,;AZI2,downstream_gene_variant,,ENST00000414162,;AZI2,intron_variant,,ENST00000295748,;AZI2,non_coding_transcript_exon_variant,,ENST00000470234,;AZI2,non_coding_transcript_exon_variant,,ENST00000488978,;AZI2,intron_variant,,ENST00000492044,;AZI2,intron_variant,,ENST00000463512,;AZI2,downstream_gene_variant,,ENST00000462936,;AZI2,upstream_gene_variant,,ENST00000476174,;	A	ENSG00000163512	ENST00000479665	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AZI2	HGNC	24002	protein_coding	YES	CCDS2647.1	ENSP00000419371	AZI2_HUMAN	C9JVK8_HUMAN,C9JGA2_HUMAN	UPI000006CE34	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACTCTGATG	.	5	ESCA
LRIG1	0	.	GRCh37	3	66444546	66444546	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1386C>A	p.%3D	p.A462A	ENST00000273261	12/19	24	3	21	21	21	0	LRIG1,synonymous_variant,p.%3D,ENST00000383703,;LRIG1,synonymous_variant,p.%3D,ENST00000273261,;LRIG1,non_coding_transcript_exon_variant,,ENST00000496559,;LRIG1,non_coding_transcript_exon_variant,,ENST00000495037,;	T	ENSG00000144749	ENST00000273261	Transcript	synonymous_variant	1911	1386	462	A	gcC/gcA	.	.	.	-1	LRIG1	HGNC	17360	protein_coding	YES	CCDS33783.1	ENSP00000273261	LRIG1_HUMAN	.	UPI000004C5BE	.	.	.	12/19	.	Superfamily_domains:SSF52058,SMART_domains:SM00082,Gene3D:3.80.10.10,hmmpanther:PTHR24367:SF245,hmmpanther:PTHR24367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	ACAAAGGCCTG	.	4	ESCA
ROBO2	0	.	GRCh37	3	77681788	77681788	+	Intron	SNP	A	A	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3809-2233A>C	.	.	ENST00000487694	.	20	7	13	32	32	0	ROBO2,synonymous_variant,p.%3D,ENST00000332191,;ROBO2,intron_variant,,ENST00000461745,;ROBO2,intron_variant,,ENST00000475334,;ROBO2,intron_variant,,ENST00000487694,;ROBO2,upstream_gene_variant,,ENST00000490534,;ROBO2,non_coding_transcript_exon_variant,,ENST00000470802,;ROBO2,intron_variant,,ENST00000473767,;	C	ENSG00000185008	ENST00000487694	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ROBO2	HGNC	10250	protein_coding	YES	CCDS54609.1	ENSP00000417335	ROBO2_HUMAN	H9XFA4_HUMAN	UPI0000D891EC	.	.	.	.	24/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GATGGAACCAG	.	4	ESCA
HTR1F	0	.	GRCh37	3	88041494	88041494	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*494A>T	.	.	ENST00000319595	1/1	34	18	15	37	37	0	HTR1F,3_prime_UTR_variant,,ENST00000319595,;	T	ENSG00000179097	ENST00000319595	Transcript	3_prime_UTR_variant	1649	.	.	.	.	.	.	.	1	HTR1F	HGNC	5292	protein_coding	YES	CCDS2920.1	ENSP00000322924	5HT1F_HUMAN	Q9P2Q4_HUMAN	UPI00000503DF	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAAAGGGAG	.	5	ESCA
NAA15	0	.	GRCh37	4	140311559	140311559	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2321T>G	.	.	ENST00000296543	20/20	47	14	33	54	54	0	NAA15,3_prime_UTR_variant,,ENST00000296543,;NAA15,3_prime_UTR_variant,,ENST00000398947,;NAA15,intron_variant,,ENST00000515576,;NAA15,downstream_gene_variant,,ENST00000485905,;	G	ENSG00000164134	ENST00000296543	Transcript	3_prime_UTR_variant	5245	.	.	.	.	.	.	.	1	NAA15	HGNC	30782	protein_coding	YES	CCDS43270.1	ENSP00000296543	NAA15_HUMAN	.	UPI000004B631	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGTAGTAT	.	5	ESCA
KDR	0	.	GRCh37	4	55981097	55981097	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.602A>T	p.Glu201Val	p.E201V	ENST00000263923	5/30	13	8	5	21	21	0	KDR,missense_variant,p.Glu201Val,ENST00000263923,;KDR,non_coding_transcript_exon_variant,,ENST00000512566,;	A	ENSG00000128052	ENST00000263923	Transcript	missense_variant	898	602	201	E/V	gAa/gTa	.	.	.	-1	KDR	HGNC	6307	protein_coding	YES	CCDS3497.1	ENSP00000263923	VGFR2_HUMAN	B4DEK3_HUMAN	UPI000003AE04	.	deleterious(0)	possibly_damaging(0.864)	5/30	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TTGCTTCACAG	.	3	ESCA
AGPAT9	0	.	GRCh37	4	84457661	84457661	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-115G>A	.	.	ENST00000395226	2/13	16	4	12	16	16	0	AGPAT9,5_prime_UTR_variant,,ENST00000395226,;AGPAT9,5_prime_UTR_variant,,ENST00000264409,;AGPAT9,non_coding_transcript_exon_variant,,ENST00000506766,;AGPAT9,non_coding_transcript_exon_variant,,ENST00000509412,;AGPAT9,non_coding_transcript_exon_variant,,ENST00000514309,;	A	ENSG00000138678	ENST00000395226	Transcript	5_prime_UTR_variant	104	.	.	.	.	.	.	.	1	AGPAT9	HGNC	28157	protein_coding	YES	CCDS3606.1	ENSP00000378651	GPAT3_HUMAN	.	UPI000004B62F	.	.	.	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGTGAGTGC	.	5	ESCA
H2AFY	0	.	GRCh37	5	134705831	134705831	+	Silent	SNP	C	C	T	rs141756450	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174G>A	p.%3D	p.A58A	ENST00000511689	3/9	31	18	12	28	28	0	H2AFY,synonymous_variant,p.%3D,ENST00000510038,;H2AFY,synonymous_variant,p.%3D,ENST00000304332,;H2AFY,synonymous_variant,p.%3D,ENST00000312469,;H2AFY,synonymous_variant,p.%3D,ENST00000511689,;H2AFY,intron_variant,,ENST00000423969,;H2AFY,splice_region_variant,,ENST00000506532,;H2AFY,splice_region_variant,,ENST00000508785,;H2AFY,splice_region_variant,,ENST00000360597,;H2AFY,splice_region_variant,,ENST00000513210,;H2AFY,splice_region_variant,,ENST00000508120,;H2AFY,synonymous_variant,p.%3D,ENST00000506671,;H2AFY,splice_region_variant,,ENST00000506218,;H2AFY,splice_region_variant,,ENST00000507868,;H2AFY,non_coding_transcript_exon_variant,,ENST00000504197,;	T	ENSG00000113648	ENST00000511689	Transcript	synonymous_variant	768	174	58	A	gcG/gcA	rs141756450	.	.	-1	H2AFY	HGNC	4740	protein_coding	YES	CCDS4185.1	ENSP00000423563	H2AY_HUMAN	.	UPI00000723ED	.	.	.	3/9	.	hmmpanther:PTHR23430,hmmpanther:PTHR23430:SF20,Pfam_domain:PF00125,Gene3D:1.10.20.10,PIRSF_domain:PIRSF037942,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTCCGCTGT	byCluster	5	ESCA
SYNPO	0	.	GRCh37	5	150031518	150031518	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1623G>A	.	.	ENST00000394243	3/3	20	5	15	15	15	0	SYNPO,3_prime_UTR_variant,,ENST00000519664,;SYNPO,3_prime_UTR_variant,,ENST00000394243,;SYNPO,3_prime_UTR_variant,,ENST00000522122,;SYNPO,intron_variant,,ENST00000307662,;SYNPO,downstream_gene_variant,,ENST00000518872,;	A	ENSG00000171992	ENST00000394243	Transcript	3_prime_UTR_variant	4787	.	.	.	.	.	.	.	1	SYNPO	HGNC	30672	protein_coding	YES	CCDS54937.1	ENSP00000377789	SYNPO_HUMAN	Q71HJ6_HUMAN	UPI000013F943	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGAGGACCAC	.	5	ESCA
AACSP1	0	.	GRCh37	5	178201530	178201530	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.872G>A	.	.	ENST00000503486	7/11	17	12	4	16	16	0	AACSP1,non_coding_transcript_exon_variant,,ENST00000503486,;AACSP1,non_coding_transcript_exon_variant,,ENST00000521412,;AACSP1,non_coding_transcript_exon_variant,,ENST00000536654,;	T	ENSG00000250420	ENST00000503486	Transcript	non_coding_transcript_exon_variant	872	.	.	.	.	.	.	.	-1	AACSP1	HGNC	18226	processed_transcript	YES	.	.	.	.	.	.	.	.	7/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AACCGCGGGGT	.	4	ESCA
ADAMTS12	0	.	GRCh37	5	33892045	33892045	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-84C>G	.	.	ENST00000504830	1/24	13	3	9	13	13	0	ADAMTS12,5_prime_UTR_variant,,ENST00000515401,;ADAMTS12,5_prime_UTR_variant,,ENST00000504830,;ADAMTS12,5_prime_UTR_variant,,ENST00000352040,;RNU6-923P,upstream_gene_variant,,ENST00000364753,;ADAMTS12,upstream_gene_variant,,ENST00000509762,;	C	ENSG00000151388	ENST00000504830	Transcript	5_prime_UTR_variant	253	.	.	.	.	.	.	.	-1	ADAMTS12	HGNC	14605	protein_coding	YES	CCDS34140.1	ENSP00000422554	ATS12_HUMAN	.	UPI000013DC51	.	.	.	1/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AGCAGGAAGAT	.	4	ESCA
SLC45A2	0	.	GRCh37	5	33984553	33984553	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136G>T	p.Glu46Ter	p.E46*	ENST00000296589	1/7	26	20	6	38	38	0	SLC45A2,stop_gained,p.Glu46Ter,ENST00000342059,;SLC45A2,stop_gained,p.Glu46Ter,ENST00000382102,;SLC45A2,stop_gained,p.Glu46Ter,ENST00000345083,;SLC45A2,stop_gained,p.Glu46Ter,ENST00000509381,;SLC45A2,stop_gained,p.Glu46Ter,ENST00000296589,;SLC45A2,upstream_gene_variant,,ENST00000510600,;AMACR,downstream_gene_variant,,ENST00000502637,;AMACR,downstream_gene_variant,,ENST00000382085,;AMACR,downstream_gene_variant,,ENST00000382072,;AMACR,downstream_gene_variant,,ENST00000335606,;AMACR,downstream_gene_variant,,ENST00000514195,;SLC45A2,non_coding_transcript_exon_variant,,ENST00000505056,;AMACR,downstream_gene_variant,,ENST00000506639,;RP11-1084J3.4,downstream_gene_variant,,ENST00000382079,;	A	ENSG00000164175	ENST00000296589	Transcript	stop_gained	283	136	46	E/*	Gag/Tag	.	.	.	-1	SLC45A2	HGNC	16472	protein_coding	YES	CCDS3901.1	ENSP00000296589	S45A2_HUMAN	.	UPI00001AEC19	.	.	.	1/7	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,Pfam_domain:PF13347,Gene3D:1.20.1250.20,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTCTCTTC	.	5	ESCA
PIK3R1	0	.	GRCh37	5	67597163	67597163	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3734G>C	.	.	ENST00000521381	16/16	18	12	6	24	24	0	PIK3R1,3_prime_UTR_variant,,ENST00000274335,;PIK3R1,3_prime_UTR_variant,,ENST00000521381,;PIK3R1,3_prime_UTR_variant,,ENST00000396611,;PIK3R1,downstream_gene_variant,,ENST00000336483,;PIK3R1,downstream_gene_variant,,ENST00000521657,;PIK3R1,downstream_gene_variant,,ENST00000320694,;PIK3R1,downstream_gene_variant,,ENST00000523872,;PIK3R1,downstream_gene_variant,,ENST00000518813,;	C	ENSG00000145675	ENST00000521381	Transcript	3_prime_UTR_variant	6525	.	.	.	.	.	.	.	1	PIK3R1	HGNC	8979	protein_coding	YES	CCDS3993.1	ENSP00000428056	P85A_HUMAN	J7GXU7_HUMAN,J7GU64_HUMAN,E5RJY0_HUMAN,E5RHI0_HUMAN,E5RGI8_HUMAN,B3KWZ7_HUMAN	UPI000013D9FF	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCCAGGATGCT	.	3	ESCA
TAPBP	0	.	GRCh37	6	33271548	33271548	+	3'UTR	SNP	T	T	C	rs193144793	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4A>G	.	.	ENST00000426633	7/7	11	1	10	8	8	0	TAPBP,3_prime_UTR_variant,,ENST00000426633,;TAPBP,intron_variant,,ENST00000489157,;TAPBP,intron_variant,,ENST00000475304,;TAPBP,intron_variant,,ENST00000434618,;TAPBP,downstream_gene_variant,,ENST00000456592,;RGL2,upstream_gene_variant,,ENST00000444031,;TAPBP,downstream_gene_variant,,ENST00000467025,;RGL2,upstream_gene_variant,,ENST00000497454,;RGL2,upstream_gene_variant,,ENST00000425946,;RGL2,upstream_gene_variant,,ENST00000437840,;TAPBP,non_coding_transcript_exon_variant,,ENST00000480730,;TAPBP,downstream_gene_variant,,ENST00000437116,;	C	ENSG00000231925	ENST00000426633	Transcript	3_prime_UTR_variant	1690	.	.	.	.	rs193144793	.	.	-1	TAPBP	HGNC	11566	protein_coding	YES	CCDS34428.2	ENSP00000404833	.	.	UPI0000E5AD4C	.	.	.	7/7	.	.	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATATAGATT	by1000G	2	ESCA
MEP1A	0	.	GRCh37	6	46787380	46787380	+	Silent	SNP	C	C	T	rs776751972	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495C>T	p.%3D	p.H165H	ENST00000230588	7/14	69	13	56	47	47	0	MEP1A,synonymous_variant,p.%3D,ENST00000230588,;	T	ENSG00000112818	ENST00000230588	Transcript	synonymous_variant	504	495	165	H	caC/caT	rs776751972,COSM451583	.	.	1	MEP1A	HGNC	7015	protein_coding	YES	CCDS4918.1	ENSP00000230588	MEP1A_HUMAN	.	UPI000006E4E9	.	.	.	7/14	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF311,Gene3D:3.40.390.10,Pfam_domain:PF01400,PIRSF_domain:PIRSF001196,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00480	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCACGAGCA	byFrequency	5	ESCA
ZNF800	0	.	GRCh37	7	127011736	127011736	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*132A>G	.	.	ENST00000393313	6/6	26	19	7	20	20	0	ZNF800,3_prime_UTR_variant,,ENST00000393312,;ZNF800,3_prime_UTR_variant,,ENST00000393313,;ZNF800,3_prime_UTR_variant,,ENST00000265827,;ZNF800,downstream_gene_variant,,ENST00000436992,;ZNF800,downstream_gene_variant,,ENST00000434602,;ZNF800,intron_variant,,ENST00000485577,;	C	ENSG00000048405	ENST00000393313	Transcript	3_prime_UTR_variant	2719	.	.	.	.	.	.	.	-1	ZNF800	HGNC	27267	protein_coding	YES	CCDS5795.1	ENSP00000376989	ZN800_HUMAN	C9K0M9_HUMAN,C9JLY3_HUMAN,C9JHX9_HUMAN	UPI000020FA03	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAGTTGAAT	.	5	ESCA
FAM71F1	0	.	GRCh37	7	128370053	128370053	+	Silent	SNP	C	C	T	rs774672617	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951C>T	p.%3D	p.S317S	ENST00000315184	6/7	62	36	25	17	17	0	FAM71F1,synonymous_variant,p.%3D,ENST00000315184,;FAM71F1,synonymous_variant,p.%3D,ENST00000485070,;FAM71F1,downstream_gene_variant,,ENST00000466842,;FAM71F1,3_prime_UTR_variant,,ENST00000484425,;FAM71F1,downstream_gene_variant,,ENST00000471558,;	T	ENSG00000135248	ENST00000315184	Transcript	synonymous_variant	1004	951	317	S	tcC/tcT	rs774672617	.	.	1	FAM71F1	HGNC	30704	protein_coding	YES	CCDS5804.1	ENSP00000326652	F71F1_HUMAN	H7C4R1_HUMAN	UPI000006D961	.	.	.	6/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22574:SF10,hmmpanther:PTHR22574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCCGGCCT	byFrequency	5	ESCA
CHRM2	0	.	GRCh37	7	136700063	136700063	+	Missense_Mutation	SNP	T	T	A	.	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451T>A	p.Ser151Thr	p.S151T	ENST00000445907	3/3	28	22	6	19	19	0	CHRM2,missense_variant,p.Ser151Thr,ENST00000320658,;CHRM2,missense_variant,p.Ser151Thr,ENST00000401861,;CHRM2,missense_variant,p.Ser151Thr,ENST00000397608,;CHRM2,missense_variant,p.Ser151Thr,ENST00000402486,;CHRM2,missense_variant,p.Ser151Thr,ENST00000453373,;CHRM2,missense_variant,p.Ser151Thr,ENST00000445907,;hsa-mir-490,intron_variant,,ENST00000597642,;hsa-mir-490,intron_variant,,ENST00000586239,;hsa-mir-490,intron_variant,,ENST00000425981,;hsa-mir-490,intron_variant,,ENST00000592183,;hsa-mir-490,intron_variant,,ENST00000593789,;hsa-mir-490,intron_variant,,ENST00000598184,;hsa-mir-490,intron_variant,,ENST00000439694,;	A	ENSG00000181072	ENST00000445907	Transcript	missense_variant	979	451	151	S/T	Tct/Act	COSM1661137	.	.	1	CHRM2	HGNC	1951	protein_coding	YES	CCDS5843.1	ENSP00000399745	ACM2_HUMAN	Q96RH0_HUMAN,Q86SJ1_HUMAN,Q6SL56_HUMAN,A4D1Q0_HUMAN	UPI0000050410	.	deleterious(0)	probably_damaging(0.99)	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF57,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCTCTTTC	.	5	ESCA
DGKI	0	.	GRCh37	7	137374664	137374664	+	Silent	SNP	C	C	T	rs565718008	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486G>A	p.%3D	p.E162E	ENST00000288490	2/34	29	24	5	10	10	0	DGKI,synonymous_variant,p.%3D,ENST00000288490,;DGKI,synonymous_variant,p.%3D,ENST00000424189,;DGKI,synonymous_variant,p.%3D,ENST00000446122,;DGKI,intron_variant,,ENST00000453654,;DGKI,non_coding_transcript_exon_variant,,ENST00000483619,;DGKI,non_coding_transcript_exon_variant,,ENST00000470895,;	T	ENSG00000157680	ENST00000288490	Transcript	synonymous_variant	487	486	162	E	gaG/gaA	rs565718008	.	.	-1	DGKI	HGNC	2855	protein_coding	YES	CCDS5845.1	ENSP00000288490	DGKI_HUMAN	B3KR69_HUMAN	UPI000012DD23	.	.	.	2/34	.	hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCTCCTT	byCluster	5	ESCA
KIAA1549	0	.	GRCh37	7	138552846	138552846	+	Missense_Mutation	SNP	G	G	A	rs758674277	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4804C>T	p.Arg1602Cys	p.R1602C	ENST00000422774	15/20	58	42	15	27	27	0	KIAA1549,missense_variant,p.Arg1602Cys,ENST00000422774,;KIAA1549,missense_variant,p.Arg1552Cys,ENST00000242365,;KIAA1549,missense_variant,p.Arg1602Cys,ENST00000440172,;	A	ENSG00000122778	ENST00000422774	Transcript	missense_variant	4853	4804	1602	R/C	Cgc/Tgc	rs758674277	.	.	-1	KIAA1549	HGNC	22219	protein_coding	YES	CCDS56513.1	ENSP00000416040	K1549_HUMAN	.	UPI0001837EBD	.	deleterious(0)	probably_damaging(1)	15/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF4,Pfam_domain:PF12877	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGCGAGGCT	byCluster	5	ESCA
BRAF	0	.	GRCh37	7	140501216	140501216	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.856C>G	p.Leu286Val	p.L286V	ENST00000288602	6/18	37	22	15	24	24	0	BRAF,missense_variant,p.Leu286Val,ENST00000288602,;BRAF,3_prime_UTR_variant,,ENST00000497784,;	C	ENSG00000157764	ENST00000288602	Transcript	missense_variant	917	856	286	L/V	Ctt/Gtt	.	.	.	-1	BRAF	HGNC	1097	protein_coding	YES	CCDS5863.1	ENSP00000288602	BRAF_HUMAN	Q75MQ8_HUMAN,E5FF37_HUMAN,D7PBN4_HUMAN	UPI000013DF26	.	tolerated(0.26)	benign(0.101)	6/18	.	hmmpanther:PTHR23257:SF360,hmmpanther:PTHR23257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAAGTTGGT	.	5	ESCA
OR9A4	0	.	GRCh37	7	141619217	141619217	+	Missense_Mutation	SNP	G	G	C	rs782482254	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542G>C	p.Arg181Pro	p.R181P	ENST00000548136	1/1	37	32	4	26	26	0	OR9A4,missense_variant,p.Arg181Pro,ENST00000548136,;MGAM,intron_variant,,ENST00000465654,;MGAM,intron_variant,,ENST00000497554,;	C	ENSG00000258083	ENST00000548136	Transcript	missense_variant	601	542	181	R/P	cGa/cCa	rs782482254,COSM745320	.	.	1	OR9A4	HGNC	15095	protein_coding	YES	CCDS43661.1	ENSP00000448789	OR9A4_HUMAN	.	UPI0000041D24	.	tolerated(0.14)	probably_damaging(0.986)	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR24242:SF216,hmmpanther:PTHR24242,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACCGAGGGC	byFrequency	4	ESCA
ZNF767	0	.	GRCh37	7	149317094	149317094	+	RNA	SNP	C	C	A	.	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.521G>T	.	.	ENST00000463567	3/8	112	96	16	52	52	0	ZNF767,non_coding_transcript_exon_variant,,ENST00000472212,;ZNF767,non_coding_transcript_exon_variant,,ENST00000481762,;ZNF767,non_coding_transcript_exon_variant,,ENST00000463567,;ZNF767,non_coding_transcript_exon_variant,,ENST00000486492,;ZNF767,non_coding_transcript_exon_variant,,ENST00000493198,;ZNF767,non_coding_transcript_exon_variant,,ENST00000513792,;	A	ENSG00000133624	ENST00000463567	Transcript	non_coding_transcript_exon_variant	521	.	.	.	.	COSM3832249	.	.	-1	ZNF767	HGNC	21884	processed_transcript	YES	.	.	.	.	.	.	.	.	3/8	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODIFIER	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAATCTGGGA	.	4	ESCA
KMT2C	0	.	GRCh37	7	151878713	151878713	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6232A>G	p.Thr2078Ala	p.T2078A	ENST00000262189	36/59	56	46	10	27	27	0	KMT2C,missense_variant,p.Thr2078Ala,ENST00000355193,;KMT2C,missense_variant,p.Thr2078Ala,ENST00000262189,;KMT2C,intron_variant,,ENST00000558665,;KMT2C,upstream_gene_variant,,ENST00000360104,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;	C	ENSG00000055609	ENST00000262189	Transcript	missense_variant	6451	6232	2078	T/A	Aca/Gca	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	benign(0.033)	36/59	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGTCAAAG	.	5	ESCA
ADCY1	0	.	GRCh37	7	45614663	45614664	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.522dupT	p.Ala175CysfsTer62	p.A175Cfs*62	ENST00000297323	1/20	95	70	25	35	35	0	ADCY1,frameshift_variant,p.Ala175CysfsTer62,ENST00000297323,;ADCY1,5_prime_UTR_variant,,ENST00000432715,;	T	ENSG00000164742	ENST00000297323	Transcript	frameshift_variant	543-544	521-522	174	Y/YX	tat/taTt	.	.	.	1	ADCY1	HGNC	232	protein_coding	YES	CCDS34631.1	ENSP00000297323	ADCY1_HUMAN	Q8NFM5_HUMAN,D3DVL8_HUMAN	UPI0000199C4A	.	.	.	1/20	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11920:SF20,hmmpanther:PTHR11920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCCTATGCCT	.	3	ESCA
SNORA22	0	.	GRCh37	7	64530858	64530858	+	3'Flank	SNP	T	T	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000384614	.	98	55	42	55	55	0	SNORA22,downstream_gene_variant,,ENST00000384614,;SNORA15,upstream_gene_variant,,ENST00000384334,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000426828,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000419314,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000452026,;RP11-460N20.4,upstream_gene_variant,,ENST00000414799,;	C	ENSG00000207344	ENST00000384614	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4348	1	SNORA22	RFAM	.	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGATGATGG	.	5	ESCA
GS1-124K5.11	0	.	GRCh37	7	66006407	66006407	+	RNA	SNP	T	T	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1130A>T	.	.	ENST00000449307	1/2	67	36	31	30	30	0	GS1-124K5.11,non_coding_transcript_exon_variant,,ENST00000449307,;GS1-124K5.10,intron_variant,,ENST00000448776,;GS1-124K5.12,downstream_gene_variant,,ENST00000445080,;	A	ENSG00000229180	ENST00000449307	Transcript	non_coding_transcript_exon_variant	1130	.	.	.	.	.	.	.	-1	GS1-124K5.11	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCTGCAGG	.	5	ESCA
MLXIPL	0	.	GRCh37	7	73013902	73013902	+	Missense_Mutation	SNP	G	G	A	rs782609622	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1025C>T	p.Pro342Leu	p.P342L	ENST00000313375	8/17	48	30	18	18	18	0	MLXIPL,missense_variant,p.Pro342Leu,ENST00000313375,;MLXIPL,missense_variant,p.Pro249Leu,ENST00000434326,;MLXIPL,missense_variant,p.Pro249Leu,ENST00000395189,;MLXIPL,missense_variant,p.Pro342Leu,ENST00000429400,;MLXIPL,missense_variant,p.Pro342Leu,ENST00000354613,;MLXIPL,missense_variant,p.Pro175Leu,ENST00000453275,;MLXIPL,missense_variant,p.Pro342Leu,ENST00000414749,;MLXIPL,missense_variant,p.Pro342Leu,ENST00000345114,;MLXIPL,non_coding_transcript_exon_variant,,ENST00000476404,;MLXIPL,upstream_gene_variant,,ENST00000467221,;MLXIPL,downstream_gene_variant,,ENST00000488212,;	A	ENSG00000009950	ENST00000313375	Transcript	missense_variant	1073	1025	342	P/L	cCg/cTg	rs782609622,COSM3882255	.	.	-1	MLXIPL	HGNC	12744	protein_coding	YES	CCDS5553.1	ENSP00000320886	MLXPL_HUMAN	S5LSP3_HUMAN	UPI0000138F98	.	tolerated(0.19)	benign(0.075)	8/17	.	hmmpanther:PTHR15741:SF14,hmmpanther:PTHR15741	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCCGGGGGC	byFrequency	2	ESCA
MLXIPL	0	.	GRCh37	7	73013937	73013937	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990C>T	p.%3D	p.L330L	ENST00000313375	8/17	36	16	20	17	17	0	MLXIPL,synonymous_variant,p.%3D,ENST00000313375,;MLXIPL,synonymous_variant,p.%3D,ENST00000434326,;MLXIPL,synonymous_variant,p.%3D,ENST00000395189,;MLXIPL,synonymous_variant,p.%3D,ENST00000429400,;MLXIPL,synonymous_variant,p.%3D,ENST00000354613,;MLXIPL,synonymous_variant,p.%3D,ENST00000453275,;MLXIPL,synonymous_variant,p.%3D,ENST00000414749,;MLXIPL,synonymous_variant,p.%3D,ENST00000345114,;MLXIPL,non_coding_transcript_exon_variant,,ENST00000476404,;MLXIPL,non_coding_transcript_exon_variant,,ENST00000488212,;MLXIPL,upstream_gene_variant,,ENST00000467221,;	A	ENSG00000009950	ENST00000313375	Transcript	synonymous_variant	1038	990	330	L	ctC/ctT	.	.	.	-1	MLXIPL	HGNC	12744	protein_coding	YES	CCDS5553.1	ENSP00000320886	MLXPL_HUMAN	S5LSP3_HUMAN	UPI0000138F98	.	.	.	8/17	.	hmmpanther:PTHR15741:SF14,hmmpanther:PTHR15741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGAAGAGGGA	.	2	ESCA
KIAA1324L	0	.	GRCh37	7	86556124	86556124	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1198C>A	p.Pro400Thr	p.P400T	ENST00000450689	9/22	63	35	27	25	25	0	KIAA1324L,missense_variant,p.Pro233Thr,ENST00000416314,;KIAA1324L,missense_variant,p.Pro160Thr,ENST00000297222,;KIAA1324L,missense_variant,p.Pro400Thr,ENST00000444627,;KIAA1324L,missense_variant,p.Pro361Thr,ENST00000423294,;KIAA1324L,missense_variant,p.Pro400Thr,ENST00000450689,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;	T	ENSG00000164659	ENST00000450689	Transcript	missense_variant	1384	1198	400	P/T	Cct/Act	.	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	deleterious(0)	probably_damaging(0.984)	9/22	.	hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727,Gene3D:2.10.50.10,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGGGTTGC	.	5	ESCA
SAMD9L	0	.	GRCh37	7	92761326	92761326	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3959G>T	p.Ser1320Ile	p.S1320I	ENST00000318238	5/5	47	33	13	33	33	0	SAMD9L,missense_variant,p.Ser1320Ile,ENST00000318238,;SAMD9L,missense_variant,p.Ser1320Ile,ENST00000437805,;SAMD9L,missense_variant,p.Ser1320Ile,ENST00000411955,;SAMD9L,downstream_gene_variant,,ENST00000446033,;SAMD9L,downstream_gene_variant,,ENST00000446959,;SAMD9L,downstream_gene_variant,,ENST00000414791,;SAMD9L,downstream_gene_variant,,ENST00000439952,;	A	ENSG00000177409	ENST00000318238	Transcript	missense_variant	5176	3959	1320	S/I	aGt/aTt	.	.	.	-1	SAMD9L	HGNC	1349	protein_coding	YES	CCDS34681.1	ENSP00000326247	SAM9L_HUMAN	B4E3M1_HUMAN	UPI000020F567	.	deleterious(0.03)	possibly_damaging(0.481)	5/5	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGACTCTCT	.	5	ESCA
TFPI2	0	.	GRCh37	7	93516157	93516157	+	Missense_Mutation	SNP	C	C	T	rs149215949	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683G>A	p.Arg228Gln	p.R228Q	ENST00000222543	5/5	26	20	6	21	21	0	TFPI2,missense_variant,p.Arg117Gln,ENST00000545378,;TFPI2,missense_variant,p.Arg228Gln,ENST00000222543,;TFPI2,3_prime_UTR_variant,,ENST00000451238,;GNGT1,intron_variant,,ENST00000455502,;AC002076.10,upstream_gene_variant,,ENST00000435257,;TFPI2,downstream_gene_variant,,ENST00000461482,;	T	ENSG00000105825	ENST00000222543	Transcript	missense_variant	996	683	228	R/Q	cGg/cAg	rs149215949,COSM3942384	.	.	-1	TFPI2	HGNC	11761	protein_coding	YES	CCDS5632.1	ENSP00000222543	TFPI2_HUMAN	Q8NE89_HUMAN,Q8NAK6_HUMAN	UPI00000362E2	.	tolerated(0.36)	benign(0.015)	5/5	.	hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF89,PIRSF_domain:PIRSF001620	T:0.0014	T:0.0053	T:0	.	T:0	T:0	T:0	T:0.003	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCCGGATT	byFrequency|byCluster|by1000G	4	ESCA
PDAP1	0	.	GRCh37	7	98993772	98993772	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*533C>T	.	.	ENST00000350498	6/6	52	44	8	16	16	0	PDAP1,3_prime_UTR_variant,,ENST00000350498,;ARPC1B,downstream_gene_variant,,ENST00000451682,;ARPC1B,downstream_gene_variant,,ENST00000252725,;PDAP1,intron_variant,,ENST00000496335,;ARPC1B,downstream_gene_variant,,ENST00000463078,;ARPC1B,downstream_gene_variant,,ENST00000491294,;PDAP1,downstream_gene_variant,,ENST00000426447,;ARPC1B,downstream_gene_variant,,ENST00000481997,;	A	ENSG00000106244	ENST00000350498	Transcript	3_prime_UTR_variant	1360	.	.	.	.	.	.	.	-1	PDAP1	HGNC	14634	protein_coding	YES	CCDS5662.1	ENSP00000222968	HAP28_HUMAN	.	UPI000012CB07	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGGGCAGA	.	5	ESCA
LRP12	0	.	GRCh37	8	105509215	105509215	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1565G>C	p.Arg522Thr	p.R522T	ENST00000276654	5/7	56	30	26	22	22	0	LRP12,missense_variant,p.Arg111Thr,ENST00000523007,;LRP12,missense_variant,p.Arg522Thr,ENST00000276654,;LRP12,missense_variant,p.Arg503Thr,ENST00000424843,;LRP12,downstream_gene_variant,,ENST00000520770,;LRP12,upstream_gene_variant,,ENST00000518375,;LRP12,upstream_gene_variant,,ENST00000522046,;	G	ENSG00000147650	ENST00000276654	Transcript	missense_variant	1674	1565	522	R/T	aGa/aCa	.	.	.	-1	LRP12	HGNC	31708	protein_coding	YES	CCDS6303.1	ENSP00000276654	LRP12_HUMAN	E5RIW8_HUMAN,B3KWZ8_HUMAN	UPI0000047A9F	.	deleterious(0)	probably_damaging(0.996)	5/7	.	hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTCTCAGA	.	5	ESCA
TMEM71	0	.	GRCh37	8	133723099	133723099	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*114G>T	.	.	ENST00000356838	10/10	31	25	6	9	9	0	TMEM71,3_prime_UTR_variant,,ENST00000356838,;TMEM71,3_prime_UTR_variant,,ENST00000523829,;TMEM71,3_prime_UTR_variant,,ENST00000377901,;TMEM71,intron_variant,,ENST00000522780,;	A	ENSG00000165071	ENST00000356838	Transcript	3_prime_UTR_variant	1088	.	.	.	.	.	.	.	-1	TMEM71	HGNC	26572	protein_coding	YES	CCDS6366.1	ENSP00000349296	TMM71_HUMAN	E5RH69_HUMAN,E5RGD3_HUMAN	UPI000013E44E	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTCCATTAC	.	4	ESCA
FAM135B	0	.	GRCh37	8	139209800	139209800	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.782T>A	p.Val261Glu	p.V261E	ENST00000395297	8/20	30	21	9	23	23	0	FAM135B,missense_variant,p.Val261Glu,ENST00000395297,;FAM135B,missense_variant,p.Val261Glu,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;	T	ENSG00000147724	ENST00000395297	Transcript	missense_variant	953	782	261	V/E	gTg/gAg	.	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	tolerated(0.74)	benign(0.002)	8/20	.	hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATCACCAGG	.	5	ESCA
FAM135B	0	.	GRCh37	8	139268978	139268978	+	Missense_Mutation	SNP	C	C	T	rs376116724	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.322G>A	p.Asp108Asn	p.D108N	ENST00000395297	5/20	25	12	13	17	17	0	FAM135B,missense_variant,p.Asp108Asn,ENST00000160713,;FAM135B,missense_variant,p.Asp108Asn,ENST00000395297,;FAM135B,missense_variant,p.Asp108Asn,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;	T	ENSG00000147724	ENST00000395297	Transcript	missense_variant	493	322	108	D/N	Gat/Aat	rs376116724,COSM749102,COSM749103	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	tolerated(0.33)	benign(0.2)	5/20	.	hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCTACTT	byCluster	5	ESCA
PENK	0	.	GRCh37	8	57358329	57358329	+	Intron	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138+46T>C	.	.	ENST00000314922	.	88	64	23	32	32	0	PENK,missense_variant,p.Phe62Leu,ENST00000518770,;PENK,intron_variant,,ENST00000314922,;PENK,intron_variant,,ENST00000451791,;PENK,intron_variant,,ENST00000518974,;PENK,intron_variant,,ENST00000523051,;PENK,intron_variant,,ENST00000517415,;RP11-17A4.2,upstream_gene_variant,,ENST00000518662,;PENK,upstream_gene_variant,,ENST00000523274,;PENK,downstream_gene_variant,,ENST00000521153,;	G	ENSG00000181195	ENST00000314922	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PENK	HGNC	8831	protein_coding	YES	CCDS6168.1	ENSP00000324248	PENK_HUMAN	E5RFR1_HUMAN	UPI00001315A9	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGAAACTCTG	.	5	ESCA
CHD7	0	.	GRCh37	8	61765096	61765096	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5934A>T	p.%3D	p.V1978V	ENST00000423902	30/38	31	13	18	21	21	0	CHD7,synonymous_variant,p.%3D,ENST00000423902,;CHD7,intron_variant,,ENST00000524602,;CHD7,non_coding_transcript_exon_variant,,ENST00000527921,;CHD7,upstream_gene_variant,,ENST00000529472,;CHD7,upstream_gene_variant,,ENST00000531695,;	T	ENSG00000171316	ENST00000423902	Transcript	synonymous_variant	6413	5934	1978	V	gtA/gtT	.	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	.	30/38	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTATCCAC	.	5	ESCA
RRS1	0	.	GRCh37	8	67342179	67342179	+	Silent	SNP	G	G	T	rs765188633	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813G>T	p.%3D	p.L271L	ENST00000320270	1/1	35	19	15	13	13	0	RRS1,synonymous_variant,p.%3D,ENST00000320270,;ADHFE1,upstream_gene_variant,,ENST00000415254,;ADHFE1,upstream_gene_variant,,ENST00000396623,;ADHFE1,upstream_gene_variant,,ENST00000379385,;ADHFE1,upstream_gene_variant,,ENST00000523113,;RP11-346I3.4,upstream_gene_variant,,ENST00000499642,;ADHFE1,upstream_gene_variant,,ENST00000496501,;ADHFE1,upstream_gene_variant,,ENST00000422166,;ADHFE1,upstream_gene_variant,,ENST00000449512,;ADHFE1,upstream_gene_variant,,ENST00000424777,;ADHFE1,upstream_gene_variant,,ENST00000466920,;ADHFE1,upstream_gene_variant,,ENST00000443372,;ADHFE1,upstream_gene_variant,,ENST00000419955,;ADHFE1,upstream_gene_variant,,ENST00000426810,;ADHFE1,upstream_gene_variant,,ENST00000276576,;ADHFE1,upstream_gene_variant,,ENST00000431959,;ADHFE1,upstream_gene_variant,,ENST00000463261,;ADHFE1,upstream_gene_variant,,ENST00000396621,;	T	ENSG00000179041	ENST00000320270	Transcript	synonymous_variant	917	813	271	L	ctG/ctT	rs765188633	.	.	1	RRS1	HGNC	17083	protein_coding	YES	CCDS6189.1	ENSP00000322396	RRS1_HUMAN	.	UPI0000134B8A	.	.	.	1/1	.	hmmpanther:PTHR17602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTGCTTCG	byFrequency	5	ESCA
DCAF4L2	0	.	GRCh37	8	88885726	88885726	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474G>C	p.%3D	p.L158L	ENST00000319675	1/1	42	24	18	26	26	0	DCAF4L2,synonymous_variant,p.%3D,ENST00000319675,;	G	ENSG00000176566	ENST00000319675	Transcript	synonymous_variant	571	474	158	L	ctG/ctC	.	.	.	-1	DCAF4L2	HGNC	26657	protein_coding	YES	CCDS6245.1	ENSP00000316496	DC4L2_HUMAN	Q8N7W3_HUMAN	UPI0000072860	.	.	.	1/1	.	hmmpanther:PTHR22847:SF401,hmmpanther:PTHR22847,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A161A|c.483G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAGCAGCAC	.	5	ESCA
CALB1	0	.	GRCh37	8	91071580	91071580	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*821T>C	.	.	ENST00000265431	11/11	44	31	13	36	36	0	CALB1,3_prime_UTR_variant,,ENST00000265431,;CALB1,downstream_gene_variant,,ENST00000520613,;CALB1,downstream_gene_variant,,ENST00000523716,;CALB1,downstream_gene_variant,,ENST00000518457,;CALB1,non_coding_transcript_exon_variant,,ENST00000469032,;CALB1,downstream_gene_variant,,ENST00000522070,;CALB1,downstream_gene_variant,,ENST00000497376,;	G	ENSG00000104327	ENST00000265431	Transcript	3_prime_UTR_variant	1789	.	.	.	.	.	.	.	-1	CALB1	HGNC	1434	protein_coding	YES	CCDS6251.1	ENSP00000265431	CALB1_HUMAN	O75552_HUMAN,E5RIZ8_HUMAN,E5RG14_HUMAN,B7Z9J4_HUMAN	UPI000013D620	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGAAGTAT	.	5	ESCA
DMRT2	0	.	GRCh37	9	1056731	1056731	+	Missense_Mutation	SNP	C	C	G	rs760681935	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1144C>G	p.Arg382Gly	p.R382G	ENST00000382251	5/5	44	31	13	26	26	0	DMRT2,missense_variant,p.Arg382Gly,ENST00000302441,;DMRT2,missense_variant,p.Arg382Gly,ENST00000382251,;DMRT2,missense_variant,p.Arg382Gly,ENST00000358146,;DMRT2,3_prime_UTR_variant,,ENST00000259622,;DMRT2,3_prime_UTR_variant,,ENST00000382255,;DMRT2,downstream_gene_variant,,ENST00000412350,;	G	ENSG00000173253	ENST00000382251	Transcript	missense_variant	1473	1144	382	R/G	Cga/Gga	rs760681935	.	.	1	DMRT2	HGNC	2935	protein_coding	YES	CCDS6444.1	ENSP00000371686	DMRT2_HUMAN	.	UPI000013D066	.	deleterious_low_confidence(0.04)	benign(0.414)	5/5	.	hmmpanther:PTHR12322:SF59,hmmpanther:PTHR12322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCACGAGTC	byFrequency	5	ESCA
MAMDC4	0	.	GRCh37	9	139749014	139749017	+	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	GAGA	GAGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820_823delGAGA	p.Glu274GlnfsTer74	p.E274Qfs*74	ENST00000317446	8/27	17	11	6	18	18	0	MAMDC4,frameshift_variant,p.Glu274GlnfsTer74,ENST00000445819,;MAMDC4,frameshift_variant,p.Glu274GlnfsTer74,ENST00000317446,;PHPT1,downstream_gene_variant,,ENST00000545326,;PHPT1,downstream_gene_variant,,ENST00000371661,;PHPT1,downstream_gene_variant,,ENST00000247665,;MAMDC4,non_coding_transcript_exon_variant,,ENST00000485732,;PHPT1,downstream_gene_variant,,ENST00000497413,;MAMDC4,upstream_gene_variant,,ENST00000481327,;PHPT1,downstream_gene_variant,,ENST00000462205,;PHPT1,downstream_gene_variant,,ENST00000463215,;PHPT1,downstream_gene_variant,,ENST00000492540,;MAMDC4,upstream_gene_variant,,ENST00000479475,;	-	ENSG00000177943	ENST00000317446	Transcript	frameshift_variant	870-873	820-823	274-275	ET/X	GAGAca/ca	.	.	.	1	MAMDC4	HGNC	24083	protein_coding	YES	CCDS7010.1	ENSP00000319388	AEGP_HUMAN	.	UPI0000237828	.	.	.	8/27	.	PROSITE_profiles:PS50060,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF63,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GACTTTGAGACAGGC	.	2	ESCA
DCAF12	0	.	GRCh37	9	34093300	34093300	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1008C>A	p.%3D	p.S336S	ENST00000361264	7/9	63	45	17	54	54	0	DCAF12,synonymous_variant,p.%3D,ENST00000361264,;RP11-537H15.3,intron_variant,,ENST00000448245,;DCAF12,non_coding_transcript_exon_variant,,ENST00000466402,;	T	ENSG00000198876	ENST00000361264	Transcript	synonymous_variant	1350	1008	336	S	tcC/tcA	.	.	.	-1	DCAF12	HGNC	19911	protein_coding	YES	CCDS6549.1	ENSP00000355114	DCA12_HUMAN	.	UPI00000372E8	.	.	.	7/9	.	hmmpanther:PTHR19860:SF10,hmmpanther:PTHR19860,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTGGAACA	.	5	ESCA
DCAF12	0	.	GRCh37	9	34093301	34093301	+	Missense_Mutation	SNP	G	G	A	rs764970375	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1007C>T	p.Ser336Phe	p.S336F	ENST00000361264	7/9	63	45	17	54	54	0	DCAF12,missense_variant,p.Ser336Phe,ENST00000361264,;RP11-537H15.3,intron_variant,,ENST00000448245,;DCAF12,non_coding_transcript_exon_variant,,ENST00000466402,;	A	ENSG00000198876	ENST00000361264	Transcript	missense_variant	1349	1007	336	S/F	tCc/tTc	rs764970375	.	.	-1	DCAF12	HGNC	19911	protein_coding	YES	CCDS6549.1	ENSP00000355114	DCA12_HUMAN	.	UPI00000372E8	.	deleterious(0.01)	possibly_damaging(0.549)	7/9	.	hmmpanther:PTHR19860:SF10,hmmpanther:PTHR19860,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGGAACAG	.	5	ESCA
PTCH1	0	.	GRCh37	9	98231241	98231241	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2042delC	p.Pro681ArgfsTer12	p.P681Rfs*12	ENST00000331920	14/24	87	46	41	36	36	0	PTCH1,frameshift_variant,p.Pro680ArgfsTer12,ENST00000375274,;PTCH1,frameshift_variant,p.Pro681ArgfsTer12,ENST00000331920,;PTCH1,frameshift_variant,p.Pro615ArgfsTer12,ENST00000430669,;PTCH1,frameshift_variant,p.Pro530ArgfsTer12,ENST00000418258,;PTCH1,frameshift_variant,p.Pro530ArgfsTer12,ENST00000429896,;PTCH1,frameshift_variant,p.Pro530ArgfsTer12,ENST00000421141,;PTCH1,frameshift_variant,p.Pro346ArgfsTer?,ENST00000375271,;PTCH1,frameshift_variant,p.Pro615ArgfsTer12,ENST00000437951,;PTCH1,3_prime_UTR_variant,,ENST00000375290,;PTCH1,non_coding_transcript_exon_variant,,ENST00000549678,;	-	ENSG00000185920	ENST00000331920	Transcript	frameshift_variant	2342	2042	681	P/X	cCg/cg	COSM17459,COSM269965,COSM269966,COSM269964	.	.	-1	PTCH1	HGNC	9585	protein_coding	YES	CCDS6714.1	ENSP00000332353	PTC1_HUMAN	Q6TKQ0_HUMAN,F8VXL8_HUMAN,F8VQS6_HUMAN	UPI00001AFF9C	.	.	.	14/24	.	TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796:SF61,hmmpanther:PTHR10796	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P681L|c.2042C>T|3	INDELOCATOR*|VARSCANI*|PINDEL	GAGCGCGGCTCA	.	3	ESCA
BEX2	0	.	GRCh37	X	102564427	102564427	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*91T>G	.	.	ENST00000536889	3/3	21	10	11	13	13	0	BEX2,3_prime_UTR_variant,,ENST00000536889,;BEX2,3_prime_UTR_variant,,ENST00000372677,;BEX2,downstream_gene_variant,,ENST00000372674,;BEX2,downstream_gene_variant,,ENST00000449185,;	C	ENSG00000133134	ENST00000536889	Transcript	3_prime_UTR_variant	932	.	.	.	.	.	.	.	-1	BEX2	HGNC	30933	protein_coding	YES	CCDS55467.1	ENSP00000442521	BEX2_HUMAN	.	UPI0000D4D907	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTAACATCA	.	5	ESCA
FLNA	0	.	GRCh37	X	153590885	153590885	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2466C>A	p.%3D	p.I822I	ENST00000369850	17/48	96	56	39	40	40	0	FLNA,synonymous_variant,p.%3D,ENST00000422373,;FLNA,synonymous_variant,p.%3D,ENST00000360319,;FLNA,synonymous_variant,p.%3D,ENST00000344736,;FLNA,synonymous_variant,p.%3D,ENST00000369850,;FLNA,upstream_gene_variant,,ENST00000369856,;FLNA,upstream_gene_variant,,ENST00000466319,;FLNA,3_prime_UTR_variant,,ENST00000420627,;FLNA,upstream_gene_variant,,ENST00000490936,;FLNA,downstream_gene_variant,,ENST00000465144,;	T	ENSG00000196924	ENST00000369850	Transcript	synonymous_variant	2703	2466	822	I	atC/atA	.	.	.	-1	FLNA	HGNC	3754	protein_coding	YES	CCDS48194.1	ENSP00000358866	FLNA_HUMAN	Q96C61_HUMAN,Q86TQ3_HUMAN,Q6NXF2_HUMAN,Q60FE5_HUMAN	UPI000013C596	.	.	.	17/48	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50194,hmmpanther:PTHR11915:SF173,hmmpanther:PTHR11915,Gene3D:2.60.40.10,Pfam_domain:PF00630,SMART_domains:SM00557,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCGATGTC	.	5	ESCA
CHDC2	0	.	GRCh37	X	36117945	36117945	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801T>G	p.Phe267Leu	p.F267L	ENST00000313548	7/11	21	3	18	22	22	0	CHDC2,missense_variant,p.Phe267Leu,ENST00000313548,;CHDC2,missense_variant,p.Phe443Leu,ENST00000378660,;	G	ENSG00000176034	ENST00000313548	Transcript	missense_variant	987	801	267	F/L	ttT/ttG	.	.	.	1	CHDC2	HGNC	26708	protein_coding	YES	CCDS14238.1	ENSP00000324767	CHDC2_HUMAN	.	UPI000006F5CD	.	deleterious(0)	probably_damaging(0.997)	7/11	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTTGAAGC	.	5	ESCA
SSX5	0	.	GRCh37	X	48053592	48053592	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376G>A	p.Asp126Asn	p.D126N	ENST00000311798	5/9	80	26	53	77	77	0	SSX5,missense_variant,p.Asp85Asn,ENST00000347757,;SSX5,missense_variant,p.Asp126Asn,ENST00000311798,;SSX5,missense_variant,p.Asp85Asn,ENST00000376923,;SSX5,upstream_gene_variant,,ENST00000403001,;RP11-552E4.2,upstream_gene_variant,,ENST00000437312,;	T	ENSG00000165583	ENST00000311798	Transcript	missense_variant	429	376	126	D/N	Gat/Aat	.	.	.	-1	SSX5	HGNC	11339	protein_coding	YES	CCDS14288.1	ENSP00000312415	SSX5_HUMAN	.	UPI000013F201	.	deleterious(0)	probably_damaging(0.992)	5/9	.	hmmpanther:PTHR14112:SF4,hmmpanther:PTHR14112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTATCAAAAT	.	5	ESCA
HUWE1	0	.	GRCh37	X	53641613	53641613	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3QL-01A-11D-A247-09	TCGA-IG-A3QL-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2143C>A	p.Pro715Thr	p.P715T	ENST00000342160	22/83	25	20	4	23	23	0	HUWE1,missense_variant,p.Pro715Thr,ENST00000218328,;HUWE1,missense_variant,p.Pro715Thr,ENST00000342160,;HUWE1,missense_variant,p.Pro715Thr,ENST00000262854,;HUWE1,downstream_gene_variant,,ENST00000489876,;	T	ENSG00000086758	ENST00000342160	Transcript	missense_variant	2601	2143	715	P/T	Ccc/Acc	.	.	.	-1	HUWE1	HGNC	30892	protein_coding	YES	CCDS35301.1	ENSP00000340648	HUWE1_HUMAN	Q5H963_HUMAN	UPI00004A0DAC	.	.	possibly_damaging(0.647)	22/83	.	hmmpanther:PTHR11254:SF67,hmmpanther:PTHR11254,Pfam_domain:PF06025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TGGGGGAGGAG	.	2	ESCA
LZTS2	0	.	GRCh37	10	102762382	102762382	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.87G>C	p.%3D	p.V29V	ENST00000370220	1/4	74	58	16	61	61	0	LZTS2,synonymous_variant,p.%3D,ENST00000370223,;LZTS2,synonymous_variant,p.%3D,ENST00000370220,;LZTS2,synonymous_variant,p.%3D,ENST00000429732,;LZTS2,synonymous_variant,p.%3D,ENST00000481129,;LZTS2,synonymous_variant,p.%3D,ENST00000426584,;LZTS2,synonymous_variant,p.%3D,ENST00000454422,;LZTS2,non_coding_transcript_exon_variant,,ENST00000489526,;	C	ENSG00000107816	ENST00000370220	Transcript	synonymous_variant	3150	87	29	V	gtG/gtC	.	.	.	1	LZTS2	HGNC	29381	protein_coding	YES	CCDS7507.1	ENSP00000359240	LZTS2_HUMAN	S4R3W7_HUMAN,Q9BRY6_HUMAN,B1AL13_HUMAN,B1AL12_HUMAN,B1AL11_HUMAN	UPI00001BD944	.	.	.	1/4	.	HAMAP:MF_03026,hmmpanther:PTHR19354:SF4,hmmpanther:PTHR19354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGTGAGCAG	.	5	ESCA
DHTKD1	0	.	GRCh37	10	12126748	12126748	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520C>G	p.Gln174Glu	p.Q174E	ENST00000263035	3/17	46	43	3	36	36	0	DHTKD1,missense_variant,p.Gln174Glu,ENST00000437298,;DHTKD1,missense_variant,p.Gln174Glu,ENST00000263035,;DHTKD1,upstream_gene_variant,,ENST00000415935,;DHTKD1,intron_variant,,ENST00000465617,;	G	ENSG00000181192	ENST00000263035	Transcript	missense_variant	582	520	174	Q/E	Cag/Gag	.	.	.	1	DHTKD1	HGNC	23537	protein_coding	YES	CCDS7087.1	ENSP00000263035	DHTK1_HUMAN	.	UPI000013D38C	.	tolerated(0.28)	benign(0.071)	3/17	.	hmmpanther:PTHR23152,Gene3D:3.40.50.970,TIGRFAM_domain:TIGR00239,PIRSF_domain:PIRSF000157,Superfamily_domains:SSF52518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AATCTCAGGTA	.	2	ESCA
GPR26	0	.	GRCh37	10	125447475	125447475	+	Missense_Mutation	SNP	C	C	G	rs767515588	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813C>G	p.Ile271Met	p.I271M	ENST00000284674	3/3	32	26	6	32	32	0	GPR26,missense_variant,p.Ile271Met,ENST00000284674,;	G	ENSG00000154478	ENST00000284674	Transcript	missense_variant	866	813	271	I/M	atC/atG	rs767515588	.	.	1	GPR26	HGNC	4481	protein_coding	YES	CCDS7636.1	ENSP00000284674	GPR26_HUMAN	.	UPI000006E821	.	deleterious(0)	probably_damaging(0.985)	3/3	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24245:SF5,hmmpanther:PTHR24245,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATCGGCTC	.	5	ESCA
BCCIP	0	.	GRCh37	10	127541972	127541972	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*160T>G	.	.	ENST00000368759	8/8	18	13	5	8	8	0	BCCIP,3_prime_UTR_variant,,ENST00000368759,;DHX32,intron_variant,,ENST00000284688,;DHX32,intron_variant,,ENST00000368721,;DHX32,intron_variant,,ENST00000284690,;	G	ENSG00000107949	ENST00000368759	Transcript	3_prime_UTR_variant	1141	.	.	.	.	.	.	.	1	BCCIP	HGNC	978	protein_coding	YES	CCDS7649.1	ENSP00000357748	BCCIP_HUMAN	.	UPI0000073C44	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTTGTTTTCA	.	3	ESCA
ITGA8	0	.	GRCh37	10	15688954	15688954	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1098G>A	p.%3D	p.V366V	ENST00000378076	12/30	81	70	10	57	57	0	ITGA8,synonymous_variant,p.%3D,ENST00000378076,;ITGA8,upstream_gene_variant,,ENST00000468882,;	T	ENSG00000077943	ENST00000378076	Transcript	synonymous_variant	1452	1098	366	V	gtG/gtA	.	.	.	-1	ITGA8	HGNC	6144	protein_coding	YES	CCDS31155.1	ENSP00000367316	ITA8_HUMAN	.	UPI00001D80A0	.	.	.	12/30	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCTCACTTG	.	4	ESCA
OTUD1	0	.	GRCh37	10	23729743	23729743	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357C>G	p.Gln453Glu	p.Q453E	ENST00000376495	1/1	38	35	3	28	28	0	OTUD1,missense_variant,p.Gln453Glu,ENST00000376495,;	G	ENSG00000165312	ENST00000376495	Transcript	missense_variant	1546	1357	453	Q/E	Caa/Gaa	.	.	.	1	OTUD1	HGNC	27346	protein_coding	YES	CCDS44366.1	ENSP00000365678	OTUD1_HUMAN	.	UPI0000458A32	.	deleterious(0)	probably_damaging(0.93)	1/1	.	hmmpanther:PTHR12419:SF2,hmmpanther:PTHR12419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAACTCAAGTG	.	2	ESCA
ZNF438	0	.	GRCh37	10	31138696	31138696	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.638G>C	p.Ser213Thr	p.S213T	ENST00000436087	7/8	91	84	7	81	81	0	ZNF438,missense_variant,p.Ser203Thr,ENST00000452305,;ZNF438,missense_variant,p.Ser213Thr,ENST00000413025,;ZNF438,missense_variant,p.Ser213Thr,ENST00000361310,;ZNF438,missense_variant,p.Ser164Thr,ENST00000538351,;ZNF438,missense_variant,p.Ser213Thr,ENST00000442986,;ZNF438,missense_variant,p.Ser203Thr,ENST00000444692,;ZNF438,missense_variant,p.Ser213Thr,ENST00000436087,;ZNF438,missense_variant,p.Ser203Thr,ENST00000331737,;ZNF438,intron_variant,,ENST00000375311,;ZNF438,intron_variant,,ENST00000609683,;	G	ENSG00000183621	ENST00000436087	Transcript	missense_variant	1121	638	213	S/T	aGt/aCt	.	.	.	-1	ZNF438	HGNC	21029	protein_coding	YES	CCDS7168.1	ENSP00000406934	ZN438_HUMAN	Q5T427_HUMAN	UPI00001B3D8F	.	tolerated(0.58)	benign(0.031)	7/8	.	hmmpanther:PTHR24397:SF2,hmmpanther:PTHR24397	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAGACTGCCA	.	2	ESCA
RP11-313J2.1	0	.	GRCh37	10	42832735	42832735	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1169G>C	.	.	ENST00000609841	3/3	37	30	7	36	36	0	RP11-313J2.1,non_coding_transcript_exon_variant,,ENST00000609841,;RP11-313J2.1,downstream_gene_variant,,ENST00000609034,;RP11-313J2.1,non_coding_transcript_exon_variant,,ENST00000423987,;	G	ENSG00000215146	ENST00000609841	Transcript	non_coding_transcript_exon_variant	1169	.	.	.	.	.	.	.	-1	RP11-313J2.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTTCTCTCC	.	5	ESCA
WDFY4	0	.	GRCh37	10	50186394	50186394	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9332G>A	p.Arg3111Gln	p.R3111Q	ENST00000325239	59/61	25	21	4	32	32	0	WDFY4,missense_variant,p.Arg3111Gln,ENST00000325239,;WDFY4,missense_variant,p.Arg1198Gln,ENST00000265453,;WDFY4,3_prime_UTR_variant,,ENST00000413659,;RP11-523O18.5,intron_variant,,ENST00000428825,;WDFY4,non_coding_transcript_exon_variant,,ENST00000490507,;WDFY4,non_coding_transcript_exon_variant,,ENST00000465910,;WDFY4,downstream_gene_variant,,ENST00000497480,;	A	ENSG00000128815	ENST00000325239	Transcript	missense_variant	9359	9332	3111	R/Q	cGg/cAg	.	.	.	1	WDFY4	HGNC	29323	protein_coding	YES	CCDS44385.1	ENSP00000320563	WDFY4_HUMAN	Q6PIM1_HUMAN	UPI000176ADB8	.	tolerated(0.8)	benign(0)	59/61	.	hmmpanther:PTHR13743:SF52,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGACGGCCAG	.	2	ESCA
IL15RA	0	.	GRCh37	10	5994654	5994654	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*404C>G	.	.	ENST00000379977	7/7	28	24	4	13	13	0	IL15RA,3_prime_UTR_variant,,ENST00000397251,;IL15RA,3_prime_UTR_variant,,ENST00000525219,;IL15RA,3_prime_UTR_variant,,ENST00000397248,;IL15RA,3_prime_UTR_variant,,ENST00000379977,;IL15RA,intron_variant,,ENST00000435171,;IL15RA,downstream_gene_variant,,ENST00000532039,;IL15RA,downstream_gene_variant,,ENST00000379971,;IL15RA,downstream_gene_variant,,ENST00000528354,;IL15RA,downstream_gene_variant,,ENST00000397246,;IL15RA,downstream_gene_variant,,ENST00000530685,;IL15RA,downstream_gene_variant,,ENST00000447291,;IL15RA,downstream_gene_variant,,ENST00000397255,;IL15RA,downstream_gene_variant,,ENST00000397250,;IL15RA,non_coding_transcript_exon_variant,,ENST00000379972,;IL15RA,non_coding_transcript_exon_variant,,ENST00000534292,;IL15RA,non_coding_transcript_exon_variant,,ENST00000532948,;IL15RA,downstream_gene_variant,,ENST00000379974,;	C	ENSG00000134470	ENST00000379977	Transcript	3_prime_UTR_variant	1306	.	.	.	.	.	.	.	-1	IL15RA	HGNC	5978	protein_coding	YES	CCDS7074.1	ENSP00000369312	I15RA_HUMAN	.	UPI0000073D71	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAATTGACAGA	.	4	ESCA
CDH23	0	.	GRCh37	10	73499506	73499506	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4480G>C	p.Glu1494Gln	p.E1494Q	ENST00000224721	35/69	59	51	7	42	42	0	CDH23,missense_variant,p.Glu1494Gln,ENST00000224721,;C10orf105,upstream_gene_variant,,ENST00000398786,;CDH23,non_coding_transcript_exon_variant,,ENST00000398792,;	C	ENSG00000107736	ENST00000224721	Transcript	missense_variant	4485	4480	1494	E/Q	Gag/Cag	.	.	.	1	CDH23	HGNC	13733	protein_coding	.	.	ENSP00000224721	.	.	UPI0002B831D5	.	tolerated(0.53)	probably_damaging(0.943)	35/69	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF277,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGAGCTG	.	5	ESCA
POLR3A	0	.	GRCh37	10	79784318	79784318	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.634G>A	p.Gly212Arg	p.G212R	ENST00000372371	5/31	47	37	10	34	34	0	POLR3A,missense_variant,p.Gly212Arg,ENST00000372371,;POLR3A,upstream_gene_variant,,ENST00000484760,;	T	ENSG00000148606	ENST00000372371	Transcript	missense_variant	772	634	212	G/R	Gga/Aga	.	.	.	-1	POLR3A	HGNC	30074	protein_coding	YES	CCDS7354.1	ENSP00000361446	RPC1_HUMAN	Q8TCW4_HUMAN,Q8TCW3_HUMAN,Q8TCW2_HUMAN	UPI000007456A	.	tolerated(0.51)	benign(0.005)	5/31	.	hmmpanther:PTHR19376:SF31,hmmpanther:PTHR19376,Pfam_domain:PF04997,Superfamily_domains:SSF64484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCCCAGCA	.	5	ESCA
ZNF518A	0	.	GRCh37	10	97918367	97918367	+	RNA	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3145G>C	.	.	ENST00000534948	6/7	43	36	7	18	18	0	ZNF518A,non_coding_transcript_exon_variant,,ENST00000316045,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000567632,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000534948,;ZNF518A,intron_variant,,ENST00000563195,;ZNF518A,intron_variant,,ENST00000442635,;ZNF518A,downstream_gene_variant,,ENST00000478086,;ZNF518A,downstream_gene_variant,,ENST00000488700,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000371192,;	C	ENSG00000177853	ENST00000534948	Transcript	non_coding_transcript_exon_variant	3145	.	.	.	.	.	.	.	1	ZNF518A	HGNC	29009	processed_transcript	YES	.	.	.	.	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTAGAATCA	.	5	ESCA
YAP1	0	.	GRCh37	11	102094417	102094417	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1097C>G	p.Ser366Cys	p.S366C	ENST00000282441	7/9	85	71	14	53	53	0	YAP1,missense_variant,p.Ser188Cys,ENST00000524575,;YAP1,missense_variant,p.Ser312Cys,ENST00000526343,;YAP1,missense_variant,p.Ser316Cys,ENST00000345877,;YAP1,missense_variant,p.Ser120Cys,ENST00000529029,;YAP1,missense_variant,p.Ser354Cys,ENST00000537274,;YAP1,missense_variant,p.Ser350Cys,ENST00000531439,;YAP1,missense_variant,p.Ser366Cys,ENST00000282441,;YAP1,upstream_gene_variant,,ENST00000528834,;	G	ENSG00000137693	ENST00000282441	Transcript	missense_variant	1485	1097	366	S/C	tCt/tGt	.	.	.	1	YAP1	HGNC	16262	protein_coding	YES	CCDS44716.1	ENSP00000282441	YAP1_HUMAN	.	UPI00000746D8	.	deleterious(0.03)	benign(0.021)	7/9	.	hmmpanther:PTHR17616,hmmpanther:PTHR17616:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGTCTTCTC	.	5	ESCA
HTR3A	0	.	GRCh37	11	113856798	113856798	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624C>T	p.%3D	p.V208V	ENST00000355556	6/8	79	71	8	52	52	0	HTR3A,synonymous_variant,p.%3D,ENST00000355556,;HTR3A,synonymous_variant,p.%3D,ENST00000299961,;HTR3A,synonymous_variant,p.%3D,ENST00000504030,;HTR3A,synonymous_variant,p.%3D,ENST00000375498,;HTR3A,synonymous_variant,p.%3D,ENST00000506841,;HTR3A,intron_variant,,ENST00000535865,;HTR3A,non_coding_transcript_exon_variant,,ENST00000502622,;HTR3A,intron_variant,,ENST00000510849,;	T	ENSG00000166736	ENST00000355556	Transcript	synonymous_variant	857	624	208	V	gtC/gtT	.	.	.	1	HTR3A	HGNC	5297	protein_coding	YES	CCDS8366.2	ENSP00000347754	5HT3A_HUMAN	B3VRK0_HUMAN,B3VRJ5_HUMAN,B3VRI5_HUMAN,B3VRI0_HUMAN,B3VRH5_HUMAN,B3VRH0_HUMAN,B3VRG5_HUMAN,B3VRG0_HUMAN	UPI000013F7F1	.	.	.	6/8	.	hmmpanther:PTHR18945:SF52,hmmpanther:PTHR18945,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTGTCTTCAT	.	4	ESCA
DSCAML1	0	.	GRCh37	11	117302357	117302357	+	Missense_Mutation	SNP	G	G	C	rs781580901	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5447C>G	p.Ser1816Cys	p.S1816C	ENST00000321322	31/33	67	59	7	54	54	0	DSCAML1,missense_variant,p.Ser1546Cys,ENST00000527706,;DSCAML1,missense_variant,p.Ser1816Cys,ENST00000321322,;	C	ENSG00000177103	ENST00000321322	Transcript	missense_variant	5449	5447	1816	S/C	tCc/tGc	rs781580901	.	.	-1	DSCAML1	HGNC	14656	protein_coding	YES	CCDS8384.1	ENSP00000315465	DSCL1_HUMAN	.	UPI00000726E2	.	deleterious(0.02)	possibly_damaging(0.879)	31/33	.	hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTGGAGGCC	.	4	ESCA
KMT2A	0	.	GRCh37	11	118375063	118375063	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8456C>G	p.Ser2819Cys	p.S2819C	ENST00000534358	27/36	40	36	4	34	34	0	KMT2A,missense_variant,p.Ser2816Cys,ENST00000389506,;KMT2A,missense_variant,p.Ser2778Cys,ENST00000354520,;KMT2A,missense_variant,p.Ser2819Cys,ENST00000534358,;KMT2A,upstream_gene_variant,,ENST00000534085,;KMT2A,downstream_gene_variant,,ENST00000528278,;	G	ENSG00000118058	ENST00000534358	Transcript	missense_variant	8479	8456	2819	S/C	tCc/tGc	.	.	.	1	KMT2A	HGNC	7132	protein_coding	YES	CCDS55791.1	ENSP00000436786	KMT2A_HUMAN	Q9UPD0_HUMAN,Q9UM91_HUMAN,Q9HBJ4_HUMAN,B4DIJ7_HUMAN	UPI0001E5E732	.	.	probably_damaging(0.944)	27/36	.	hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCCTCCGACA	.	3	ESCA
BCL9L	0	.	GRCh37	11	118766721	118766721	+	3'UTR	DEL	G	G	-	rs561410565	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2403delC	.	.	ENST00000334801	8/8	40	33	7	25	25	0	BCL9L,3_prime_UTR_variant,,ENST00000334801,;CXCR5,3_prime_UTR_variant,,ENST00000292174,;BCL9L,downstream_gene_variant,,ENST00000526514,;BCL9L,downstream_gene_variant,,ENST00000530293,;BCL9L,downstream_gene_variant,,ENST00000526143,;	-	ENSG00000186174	ENST00000334801	Transcript	3_prime_UTR_variant	7868	.	.	.	.	rs561410565	.	.	-1	BCL9L	HGNC	23688	protein_coding	YES	CCDS8403.1	ENSP00000335320	BCL9L_HUMAN	E9PNR0_HUMAN	UPI0000192102	.	.	.	8/8	.	.	A:0.0020	A:0.0008	A:0	.	A:0	A:0	A:0.0092	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTCACGTGAGA	byFrequency|by1000G	3	ESCA
APLP2	0	.	GRCh37	11	130011951	130011951	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2172C>G	p.Ile724Met	p.I724M	ENST00000263574	17/18	47	43	4	20	20	0	APLP2,missense_variant,p.Ile712Met,ENST00000338167,;APLP2,missense_variant,p.Ile724Met,ENST00000263574,;APLP2,missense_variant,p.Ile512Met,ENST00000539648,;APLP2,missense_variant,p.Ile656Met,ENST00000528499,;APLP2,missense_variant,p.Ile619Met,ENST00000543137,;APLP2,missense_variant,p.Ile483Met,ENST00000345598,;APLP2,missense_variant,p.Ile722Met,ENST00000278756,;APLP2,3_prime_UTR_variant,,ENST00000533616,;APLP2,non_coding_transcript_exon_variant,,ENST00000525604,;APLP2,non_coding_transcript_exon_variant,,ENST00000530493,;APLP2,non_coding_transcript_exon_variant,,ENST00000533860,;	G	ENSG00000084234	ENST00000263574	Transcript	missense_variant	2244	2172	724	I/M	atC/atG	.	.	.	1	APLP2	HGNC	598	protein_coding	YES	CCDS8486.1	ENSP00000263574	APLP2_HUMAN	Q9UED0_HUMAN	UPI0000125CAE	.	deleterious(0)	probably_damaging(0.999)	17/18	.	Pfam_domain:PF10515,hmmpanther:PTHR23103:SF14,hmmpanther:PTHR23103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCATCAGCCA	.	3	ESCA
ADAMTS15	0	.	GRCh37	11	130318901	130318901	+	Silent	SNP	C	C	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33C>T	p.%3D	p.F11F	ENST00000299164	1/8	45	42	3	19	19	0	ADAMTS15,synonymous_variant,p.%3D,ENST00000299164,;	T	ENSG00000166106	ENST00000299164	Transcript	synonymous_variant	33	33	11	F	ttC/ttT	COSM415260	.	.	1	ADAMTS15	HGNC	16305	protein_coding	YES	CCDS8488.1	ENSP00000299164	ATS15_HUMAN	.	UPI000004F277	.	.	.	1/8	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR13723:SF39,hmmpanther:PTHR13723	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTTCGCCGG	.	2	ESCA
WT1	0	.	GRCh37	11	32452095	32452095	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647-1930G>A	.	.	ENST00000332351	.	50	46	4	42	42	0	WT1,5_prime_UTR_variant,,ENST00000379079,;WT1,5_prime_UTR_variant,,ENST00000530998,;WT1,intron_variant,,ENST00000332351,;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000452863,;WT1,upstream_gene_variant,,ENST00000527775,;WT1-AS,upstream_gene_variant,,ENST00000494911,;WT1,intron_variant,,ENST00000379077,;	T	ENSG00000184937	ENST00000332351	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	WT1	HGNC	12796	protein_coding	YES	CCDS7878.2	ENSP00000331327	.	Q6LBI3_HUMAN,J3KNN9_HUMAN,H0Y3F0_HUMAN,E9PPW3_HUMAN,E9PKS2_HUMAN,A8MN20_HUMAN,A0FJ58_HUMAN,A0FJ57_HUMAN	UPI0000D625D7	.	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGCCCAGGAG	.	3	ESCA
SLC1A2	0	.	GRCh37	11	35278066	35278066	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4375G>C	.	.	ENST00000278379	11/11	28	21	7	12	12	0	SLC1A2,3_prime_UTR_variant,,ENST00000395753,;SLC1A2,3_prime_UTR_variant,,ENST00000395750,;SLC1A2,3_prime_UTR_variant,,ENST00000278379,;SLC1A2,intron_variant,,ENST00000464522,;SLC1A2,downstream_gene_variant,,ENST00000479543,;	G	ENSG00000110436	ENST00000278379	Transcript	3_prime_UTR_variant	6383	.	.	.	.	.	.	.	-1	SLC1A2	HGNC	10940	protein_coding	YES	CCDS31459.1	ENSP00000278379	EAA2_HUMAN	A2A2U1_HUMAN	UPI0000129B12	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTCTAGGC	.	5	ESCA
OR4C15	0	.	GRCh37	11	55321806	55321806	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.24A>G	p.%3D	p.A8A	ENST00000314644	1/1	64	56	8	33	33	0	OR4C15,synonymous_variant,p.%3D,ENST00000314644,;	G	ENSG00000181939	ENST00000314644	Transcript	synonymous_variant	24	24	8	A	gcA/gcG	.	.	.	1	OR4C15	HGNC	15171	protein_coding	YES	CCDS31501.1	ENSP00000324958	OR4CF_HUMAN	.	UPI00003B288E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGCACTCAA	.	4	ESCA
OR4C15	0	.	GRCh37	11	55321807	55321807	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25C>A	p.Leu9Ile	p.L9I	ENST00000314644	1/1	64	56	8	34	34	0	OR4C15,missense_variant,p.Leu9Ile,ENST00000314644,;	A	ENSG00000181939	ENST00000314644	Transcript	missense_variant	25	25	9	L/I	Ctc/Atc	.	.	.	1	OR4C15	HGNC	15171	protein_coding	YES	CCDS31501.1	ENSP00000324958	OR4CF_HUMAN	.	UPI00003B288E	.	deleterious_low_confidence(0)	unknown(0)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCACTCAAT	.	4	ESCA
TRIM34	0	.	GRCh37	11	5665062	5665062	+	3'UTR	SNP	G	G	C	rs138040113	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*123G>C	.	.	ENST00000514226	8/8	33	28	5	34	34	0	TRIM34,3_prime_UTR_variant,,ENST00000514226,;TRIM34,3_prime_UTR_variant,,ENST00000429814,;TRIM6-TRIM34,3_prime_UTR_variant,,ENST00000457787,;TRIM6-TRIM34,3_prime_UTR_variant,,ENST00000354852,;HBG2,intron_variant,,ENST00000380259,;TRIM34,downstream_gene_variant,,ENST00000495668,;TRIM34,downstream_gene_variant,,ENST00000491385,;	C	ENSG00000258659	ENST00000514226	Transcript	3_prime_UTR_variant	1927	.	.	.	.	rs138040113	.	.	1	TRIM34	HGNC	10063	protein_coding	YES	CCDS31391.1	ENSP00000422947	TRI34_HUMAN	.	UPI000006F93F	.	.	.	8/8	.	.	C:0.0030	C:0.0098	C:0.0014	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTTGAGATG	byFrequency|byCluster|by1000G	2	ESCA
OR5AK2	0	.	GRCh37	11	56756448	56756448	+	Silent	SNP	G	G	A	rs775272882	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.60G>A	p.%3D	p.Q20Q	ENST00000326855	1/1	147	133	13	91	91	0	OR5AK2,synonymous_variant,p.%3D,ENST00000326855,;	A	ENSG00000181273	ENST00000326855	Transcript	synonymous_variant	102	60	20	Q	caG/caA	rs775272882,COSM429259	.	.	1	OR5AK2	HGNC	15251	protein_coding	YES	CCDS31538.1	ENSP00000322784	O5AK2_HUMAN	.	UPI0000041D03	.	.	.	1/1	.	hmmpanther:PTHR26452:SF47,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCCAGCATGA	byFrequency	3	ESCA
TRIM22	0	.	GRCh37	11	5717813	5717813	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351G>A	p.Trp117Ter	p.W117*	ENST00000379965	2/8	17	14	3	14	14	0	TRIM22,stop_gained,p.Trp117Ter,ENST00000414641,;TRIM22,stop_gained,p.Trp117Ter,ENST00000425490,;TRIM22,stop_gained,p.Trp117Ter,ENST00000454828,;TRIM22,stop_gained,p.Trp117Ter,ENST00000379965,;TRIM5,intron_variant,,ENST00000380027,;TRIM5,intron_variant,,ENST00000412903,;TRIM22,stop_gained,p.Trp28Ter,ENST00000414897,;TRIM22,non_coding_transcript_exon_variant,,ENST00000480395,;TRIM22,non_coding_transcript_exon_variant,,ENST00000460454,;	A	ENSG00000132274	ENST00000379965	Transcript	stop_gained	628	351	117	W/*	tgG/tgA	.	.	.	1	TRIM22	HGNC	16379	protein_coding	YES	CCDS41612.1	ENSP00000369299	TRI22_HUMAN	C9JIU5_HUMAN,C9J060_HUMAN	UPI0000074222	.	.	.	2/8	.	PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF265,Gene3D:1freA00,Pfam_domain:PF00643,SMART_domains:SM00336,Superfamily_domains:SSF57845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGGGTTTG	.	5	ESCA
MAP3K11	0	.	GRCh37	11	65373507	65373507	+	Missense_Mutation	SNP	C	C	T	rs764566604	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1649G>A	p.Arg550Gln	p.R550Q	ENST00000309100	7/10	60	51	8	35	35	0	MAP3K11,missense_variant,p.Arg550Gln,ENST00000309100,;MAP3K11,missense_variant,p.Arg293Gln,ENST00000530153,;MAP3K11,5_prime_UTR_variant,,ENST00000532507,;MAP3K11,downstream_gene_variant,,ENST00000526293,;MAP3K11,downstream_gene_variant,,ENST00000529839,;MAP3K11,non_coding_transcript_exon_variant,,ENST00000534432,;MAP3K11,3_prime_UTR_variant,,ENST00000524848,;MAP3K11,non_coding_transcript_exon_variant,,ENST00000526647,;MAP3K11,downstream_gene_variant,,ENST00000534110,;MAP3K11,downstream_gene_variant,,ENST00000524856,;MAP3K11,downstream_gene_variant,,ENST00000527304,;MAP3K11,downstream_gene_variant,,ENST00000533032,;MAP3K11,downstream_gene_variant,,ENST00000530949,;	T	ENSG00000173327	ENST00000309100	Transcript	missense_variant	2135	1649	550	R/Q	cGa/cAa	rs764566604	.	.	-1	MAP3K11	HGNC	6850	protein_coding	YES	CCDS8107.1	ENSP00000309597	M3K11_HUMAN	E9PLB1_HUMAN,E9PID4_HUMAN,B4DS76_HUMAN	UPI0000049BF7	.	tolerated(0.29)	possibly_damaging(0.885)	7/10	.	PIRSF_domain:PIRSF000556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGTCGGGGG	byFrequency	5	ESCA
NADSYN1	0	.	GRCh37	11	71188367	71188367	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.799-1074G>A	.	.	ENST00000319023	.	38	32	6	13	13	0	NADSYN1,5_prime_UTR_variant,,ENST00000539574,;NADSYN1,intron_variant,,ENST00000319023,;NADSYN1,upstream_gene_variant,,ENST00000530055,;NADSYN1,upstream_gene_variant,,ENST00000529840,;NADSYN1,upstream_gene_variant,,ENST00000526039,;NADSYN1,downstream_gene_variant,,ENST00000533769,;NADSYN1,3_prime_UTR_variant,,ENST00000525200,;NADSYN1,intron_variant,,ENST00000530534,;NADSYN1,downstream_gene_variant,,ENST00000529120,;NADSYN1,downstream_gene_variant,,ENST00000528509,;NADSYN1,upstream_gene_variant,,ENST00000527852,;NADSYN1,upstream_gene_variant,,ENST00000531236,;NADSYN1,upstream_gene_variant,,ENST00000527227,;	A	ENSG00000172890	ENST00000319023	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NADSYN1	HGNC	29832	protein_coding	YES	CCDS8201.1	ENSP00000326424	NADE_HUMAN	E9PNF5_HUMAN,E9PND0_HUMAN	UPI00001404C2	.	.	.	.	9/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACACGGACCG	.	4	ESCA
CHRDL2	0	.	GRCh37	11	74414394	74414394	+	Missense_Mutation	SNP	C	C	T	rs201003334	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.902G>A	p.Arg301His	p.R301H	ENST00000263671	8/12	201	185	15	75	75	0	CHRDL2,missense_variant,p.Arg301His,ENST00000263671,;CHRDL2,missense_variant,p.Arg101His,ENST00000525413,;CHRDL2,missense_variant,p.Arg301His,ENST00000376332,;CHRDL2,intron_variant,,ENST00000528789,;CHRDL2,non_coding_transcript_exon_variant,,ENST00000534159,;CHRDL2,3_prime_UTR_variant,,ENST00000528471,;CHRDL2,3_prime_UTR_variant,,ENST00000376324,;CHRDL2,3_prime_UTR_variant,,ENST00000534276,;AP001324.1,upstream_gene_variant,,ENST00000330802,;	T	ENSG00000054938	ENST00000263671	Transcript	missense_variant	1189	902	301	R/H	cGt/cAt	rs201003334	.	.	-1	CHRDL2	HGNC	24168	protein_coding	YES	CCDS8234.1	ENSP00000263671	CRDL2_HUMAN	.	UPI0000034E41	.	tolerated(0.54)	benign(0.001)	8/12	.	PROSITE_profiles:PS50184,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF226,PROSITE_patterns:PS01208,Pfam_domain:PF00093,SMART_domains:SM00214,Superfamily_domains:SSF57603	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGACGGCAG	byCluster|by1000G	2	ESCA
CYB5R2	0	.	GRCh37	11	7690913	7690913	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201G>A	p.%3D	p.R67R	ENST00000533558	4/9	74	70	4	46	46	0	CYB5R2,synonymous_variant,p.%3D,ENST00000527542,;CYB5R2,synonymous_variant,p.%3D,ENST00000299498,;CYB5R2,synonymous_variant,p.%3D,ENST00000524608,;CYB5R2,synonymous_variant,p.%3D,ENST00000299497,;CYB5R2,synonymous_variant,p.%3D,ENST00000524790,;CYB5R2,synonymous_variant,p.%3D,ENST00000436351,;CYB5R2,synonymous_variant,p.%3D,ENST00000531096,;CYB5R2,synonymous_variant,p.%3D,ENST00000533558,;CYB5R2,upstream_gene_variant,,ENST00000528585,;CYB5R2,upstream_gene_variant,,ENST00000534698,;CYB5R2,non_coding_transcript_exon_variant,,ENST00000534443,;CYB5R2,non_coding_transcript_exon_variant,,ENST00000526084,;CYB5R2,non_coding_transcript_exon_variant,,ENST00000532920,;CYB5R2,downstream_gene_variant,,ENST00000525307,;CYB5R2,upstream_gene_variant,,ENST00000532621,;	T	ENSG00000166394	ENST00000533558	Transcript	synonymous_variant	758	201	67	R	agG/agA	.	.	.	-1	CYB5R2	HGNC	24376	protein_coding	YES	CCDS7780.1	ENSP00000437041	NB5R2_HUMAN	E9PRM4_HUMAN,E9PMI2_HUMAN,E9PIV9_HUMAN	UPI000013E5AB	.	.	.	4/9	.	Prints_domain:PR00371,Prints_domain:PR00406,Superfamily_domains:SSF63380,Pfam_domain:PF00970,Gene3D:2.40.30.10,hmmpanther:PTHR19370,hmmpanther:PTHR19370:SF80,PROSITE_profiles:PS51384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAGCCCTGAC	.	2	ESCA
USP35	0	.	GRCh37	11	77907300	77907300	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>A	p.%3D	p.K3K	ENST00000529308	2/11	58	54	4	29	29	0	USP35,synonymous_variant,p.%3D,ENST00000529308,;USP35,intron_variant,,ENST00000528910,;USP35,intron_variant,,ENST00000530267,;USP35,upstream_gene_variant,,ENST00000526425,;USP35,upstream_gene_variant,,ENST00000441408,;USP35,intron_variant,,ENST00000530535,;USP35,upstream_gene_variant,,ENST00000530546,;	A	ENSG00000118369	ENST00000529308	Transcript	synonymous_variant	270	9	3	K	aaG/aaA	COSM932253	.	.	1	USP35	HGNC	20061	protein_coding	YES	CCDS41693.1	ENSP00000431876	UBP35_HUMAN	E9PRM2_HUMAN,E9PK78_HUMAN	UPI0000456553	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACAAGATCTT	.	2	ESCA
ZNF143	0	.	GRCh37	11	9522726	9522728	+	In_Frame_Del	DEL	AGG	AGG	-	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	AGG	AGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058_1060delGAG	p.Gly353del	p.G353del	ENST00000396602	11/16	73	63	10	28	28	0	ZNF143,inframe_deletion,p.Gly322del,ENST00000396597,;ZNF143,inframe_deletion,p.Gly353del,ENST00000396602,;ZNF143,inframe_deletion,p.Gly352del,ENST00000530463,;ZNF143,inframe_deletion,p.Gly352del,ENST00000396604,;ZNF143,inframe_deletion,p.Gly325del,ENST00000299606,;	-	ENSG00000166478	ENST00000396602	Transcript	inframe_deletion	1175-1177	1056-1058	352-353	TG/T	acAGGa/aca	.	.	.	1	ZNF143	HGNC	12928	protein_coding	YES	CCDS7799.2	ENSP00000379847	ZN143_HUMAN	E9PPB0_HUMAN,E9PJF2_HUMAN,C9JTC5_HUMAN,C9JCG1_HUMAN,C9J2G7_HUMAN	UPI00001F9D01	.	.	.	11/16	.	PROSITE_profiles:PS50157,hmmpanther:PTHR11389:SF362,hmmpanther:PTHR11389,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACACACAGGAGAAA	.	3	ESCA
FAM71C	0	.	GRCh37	12	100043170	100043170	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.720G>A	p.%3D	p.E240E	ENST00000324341	2/2	55	49	6	29	29	0	FAM71C,synonymous_variant,p.%3D,ENST00000324341,;ANKS1B,intron_variant,,ENST00000329257,;ANKS1B,intron_variant,,ENST00000549866,;ANKS1B,intron_variant,,ENST00000547010,;ANKS1B,intron_variant,,ENST00000547776,;ANKS1B,intron_variant,,ENST00000552232,;	A	ENSG00000180219	ENST00000324341	Transcript	synonymous_variant	1142	720	240	E	gaG/gaA	COSM3967908	.	.	1	FAM71C	HGNC	28594	protein_coding	YES	CCDS9072.1	ENSP00000315247	FA71C_HUMAN	.	UPI0000073857	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGAGATATG	.	4	ESCA
MAGOHB	0	.	GRCh37	12	10758710	10758710	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*164G>C	.	.	ENST00000320756	5/5	45	42	3	43	43	0	MAGOHB,3_prime_UTR_variant,,ENST00000539554,;MAGOHB,3_prime_UTR_variant,,ENST00000320756,;MAGOHB,3_prime_UTR_variant,,ENST00000381881,;MAGOHB,3_prime_UTR_variant,,ENST00000544850,;MAGOHB,non_coding_transcript_exon_variant,,ENST00000398874,;MAGOHB,non_coding_transcript_exon_variant,,ENST00000537852,;MAGOHB,downstream_gene_variant,,ENST00000545236,;MAGOHB,downstream_gene_variant,,ENST00000543929,;MAGOHB,downstream_gene_variant,,ENST00000540074,;MAGOHB,downstream_gene_variant,,ENST00000544176,;MAGOHB,downstream_gene_variant,,ENST00000546173,;	G	ENSG00000111196	ENST00000320756	Transcript	3_prime_UTR_variant	702	.	.	.	.	.	.	.	-1	MAGOHB	HGNC	25504	protein_coding	YES	CCDS8628.1	ENSP00000319240	MGN2_HUMAN	F5H6P7_HUMAN	UPI00000719E5	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGACTCAAGTA	.	2	ESCA
PXN	0	.	GRCh37	12	120649445	120649445	+	3'UTR	SNP	G	G	A	rs759367894	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*672C>T	.	.	ENST00000267257	11/11	44	41	3	17	17	0	PXN,3_prime_UTR_variant,,ENST00000228307,;PXN,3_prime_UTR_variant,,ENST00000458477,;PXN,3_prime_UTR_variant,,ENST00000267257,;PXN,3_prime_UTR_variant,,ENST00000424649,;PXN,3_prime_UTR_variant,,ENST00000397506,;PXN,3_prime_UTR_variant,,ENST00000536957,;PXN,downstream_gene_variant,,ENST00000550795,;PXN-AS1,intron_variant,,ENST00000535200,;PXN-AS1,intron_variant,,ENST00000542265,;PXN-AS1,downstream_gene_variant,,ENST00000539446,;PXN-AS1,downstream_gene_variant,,ENST00000538804,;PXN-AS1,downstream_gene_variant,,ENST00000542314,;PXN,downstream_gene_variant,,ENST00000538144,;PXN,non_coding_transcript_exon_variant,,ENST00000323871,;	A	ENSG00000089159	ENST00000267257	Transcript	3_prime_UTR_variant	2621	.	.	.	.	rs759367894	.	.	-1	PXN	HGNC	9718	protein_coding	YES	CCDS58281.1	ENSP00000267257	PAXI_HUMAN	F8W1E0_HUMAN,F8W0K8_HUMAN,F8W0G0_HUMAN	UPI000013C8CD	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCGGAGACG	.	2	ESCA
PLBD1	0	.	GRCh37	12	14664608	14664608	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.882C>T	p.%3D	p.S294S	ENST00000240617	7/11	67	59	8	33	33	0	PLBD1,synonymous_variant,p.%3D,ENST00000240617,;PLBD1,3_prime_UTR_variant,,ENST00000541618,;PLBD1,non_coding_transcript_exon_variant,,ENST00000541800,;	A	ENSG00000121316	ENST00000240617	Transcript	synonymous_variant	1535	882	294	S	agC/agT	.	.	.	-1	PLBD1	HGNC	26215	protein_coding	YES	CCDS31751.1	ENSP00000240617	PLBL1_HUMAN	F5H053_HUMAN	UPI00004565DA	.	.	.	7/11	.	hmmpanther:PTHR12370,Pfam_domain:PF04916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCACTGCTAAG	.	3	ESCA
LRTM2	0	.	GRCh37	12	1936680	1936680	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-190G>C	.	.	ENST00000543818	2/5	48	43	4	47	47	0	LRTM2,5_prime_UTR_variant,,ENST00000535041,;LRTM2,5_prime_UTR_variant,,ENST00000543818,;LRTM2,5_prime_UTR_variant,,ENST00000546167,;LRTM2,5_prime_UTR_variant,,ENST00000299194,;LRTM2,5_prime_UTR_variant,,ENST00000543694,;CACNA2D4,intron_variant,,ENST00000585732,;CACNA2D4,intron_variant,,ENST00000587995,;CACNA2D4,intron_variant,,ENST00000586184,;CACNA2D4,intron_variant,,ENST00000382722,;CACNA2D4,intron_variant,,ENST00000588077,;CACNA2D4,intron_variant,,ENST00000585708,;LRTM2,non_coding_transcript_exon_variant,,ENST00000539859,;LRTM2,non_coding_transcript_exon_variant,,ENST00000544489,;LRTM2,non_coding_transcript_exon_variant,,ENST00000545157,;LRTM2,non_coding_transcript_exon_variant,,ENST00000542529,;LRTM2,intron_variant,,ENST00000540378,;LRTM2,intron_variant,,ENST00000543730,;LRTM2,upstream_gene_variant,,ENST00000546157,;CACNA2D4,intron_variant,,ENST00000444595,;CACNA2D4,intron_variant,,ENST00000280663,;CACNA2D4,intron_variant,,ENST00000537784,;	C	ENSG00000166159	ENST00000543818	Transcript	5_prime_UTR_variant	653	.	.	.	.	.	.	.	1	LRTM2	HGNC	32443	protein_coding	YES	CCDS31726.1	ENSP00000446278	LRTM2_HUMAN	F5H2B4_HUMAN,F5GZY9_HUMAN	UPI00000714D3	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGGGAAGCA	.	4	ESCA
DBX2	0	.	GRCh37	12	45410229	45410229	+	Nonsense_Mutation	SNP	G	G	C	rs753569578	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.860C>G	p.Ser287Ter	p.S287*	ENST00000332700	4/4	75	64	10	56	56	0	DBX2,stop_gained,p.Ser287Ter,ENST00000332700,;	C	ENSG00000185610	ENST00000332700	Transcript	stop_gained	1032	860	287	S/*	tCa/tGa	rs753569578	.	.	-1	DBX2	HGNC	33186	protein_coding	YES	CCDS31781.1	ENSP00000331470	DBX2_HUMAN	.	UPI000041A784	.	.	.	4/4	.	hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTGAGTGC	.	5	ESCA
KANSL2	0	.	GRCh37	12	49065687	49065687	+	Missense_Mutation	SNP	G	G	C	rs769904804	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.604C>G	p.Arg202Gly	p.R202G	ENST00000420613	5/10	63	58	5	49	49	0	KANSL2,missense_variant,p.Arg7Gly,ENST00000357861,;KANSL2,missense_variant,p.Arg202Gly,ENST00000420613,;KANSL2,missense_variant,p.Arg202Gly,ENST00000553086,;KANSL2,missense_variant,p.Arg385Gly,ENST00000550347,;KANSL2,downstream_gene_variant,,ENST00000550931,;KANSL2,upstream_gene_variant,,ENST00000547087,;SNORA2B,upstream_gene_variant,,ENST00000384583,;KANSL2,missense_variant,p.Arg195Gly,ENST00000549574,;KANSL2,3_prime_UTR_variant,,ENST00000546701,;KANSL2,3_prime_UTR_variant,,ENST00000547582,;KANSL2,3_prime_UTR_variant,,ENST00000548147,;KANSL2,non_coding_transcript_exon_variant,,ENST00000547536,;	C	ENSG00000139620	ENST00000420613	Transcript	missense_variant	652	604	202	R/G	Cgt/Ggt	rs769904804,COSM3461404,COSM3461403,COSM3461405	.	.	-1	KANSL2	HGNC	26024	protein_coding	YES	CCDS44869.1	ENSP00000415436	KANL2_HUMAN	F8VRX7_HUMAN,F8VP38_HUMAN	UPI00001FC0EA	.	deleterious(0)	probably_damaging(0.984)	5/10	.	hmmpanther:PTHR13453,hmmpanther:PTHR13453:SF1	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAAACGAATTA	.	3	ESCA
TMEM194A	0	.	GRCh37	12	57472553	57472553	+	5'Flank	SNP	C	C	T	rs762686042	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000300128	.	77	73	4	55	55	0	TMEM194A,upstream_gene_variant,,ENST00000300128,;TMEM194A,upstream_gene_variant,,ENST00000379391,;TMEM194A,intron_variant,,ENST00000553654,;TMEM194A,upstream_gene_variant,,ENST00000554340,;	T	ENSG00000166881	ENST00000300128	Transcript	upstream_gene_variant	.	.	.	.	.	rs762686042	.	1	-1	TMEM194A	HGNC	29001	protein_coding	YES	CCDS44927.1	ENSP00000300128	T194A_HUMAN	.	UPI0000185F02	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCTCACGTG	.	2	ESCA
GLIPR1L1	0	.	GRCh37	12	75728517	75728517	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>A	p.%3D	p.L3L	ENST00000312442	1/5	97	84	12	54	54	0	GLIPR1L1,synonymous_variant,p.%3D,ENST00000378695,;GLIPR1L1,synonymous_variant,p.%3D,ENST00000312442,;CAPS2,intron_variant,,ENST00000436898,;CAPS2,intron_variant,,ENST00000442339,;CAPS2,intron_variant,,ENST00000552497,;CAPS2,intron_variant,,ENST00000551829,;CAPS2,upstream_gene_variant,,ENST00000409445,;CAPS2,upstream_gene_variant,,ENST00000409799,;CAPS2,intron_variant,,ENST00000486196,;CAPS2,intron_variant,,ENST00000336815,;CAPS2,intron_variant,,ENST00000328705,;CAPS2,upstream_gene_variant,,ENST00000493070,;	A	ENSG00000173401	ENST00000312442	Transcript	synonymous_variant	55	9	3	L	ctG/ctA	.	.	.	1	GLIPR1L1	HGNC	28392	protein_coding	YES	CCDS9009.1	ENSP00000310770	GPRL1_HUMAN	.	UPI00000721B3	.	.	.	1/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTCTGAAGAA	.	4	ESCA
NAV3	0	.	GRCh37	12	78569186	78569186	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5082G>C	p.Lys1694Asn	p.K1694N	ENST00000536525	25/39	110	100	9	89	89	0	NAV3,missense_variant,p.Lys1694Asn,ENST00000536525,;NAV3,missense_variant,p.Lys1694Asn,ENST00000397909,;NAV3,missense_variant,p.Lys323Asn,ENST00000550788,;NAV3,missense_variant,p.Lys1517Asn,ENST00000266692,;NAV3,missense_variant,p.Lys1694Asn,ENST00000228327,;NAV3,missense_variant,p.Lys589Asn,ENST00000552895,;NAV3,upstream_gene_variant,,ENST00000548948,;	C	ENSG00000067798	ENST00000536525	Transcript	missense_variant	5255	5082	1694	K/N	aaG/aaC	.	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	deleterious(0.01)	probably_damaging(0.925)	25/39	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	TCCAAGAAGAA	.	2	ESCA
CEP290	0	.	GRCh37	12	88481593	88481593	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4158C>G	p.Ile1386Met	p.I1386M	ENST00000552810	32/54	57	49	7	46	46	0	CEP290,missense_variant,p.Ile1386Met,ENST00000552810,;CEP290,missense_variant,p.Ile446Met,ENST00000397838,;CEP290,missense_variant,p.Ile1388Met,ENST00000309041,;CEP290,missense_variant,p.Ile446Met,ENST00000547691,;	C	ENSG00000198707	ENST00000552810	Transcript	missense_variant	4502	4158	1386	I/M	atC/atG	.	.	.	-1	CEP290	HGNC	29021	protein_coding	YES	CCDS55858.1	ENSP00000448012	CE290_HUMAN	.	UPI0000D60D15	.	.	probably_damaging(0.999)	32/54	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTGATTGT	.	5	ESCA
PCCA	0	.	GRCh37	13	100861714	100861714	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.597C>G	p.%3D	p.V199V	ENST00000376285	7/24	48	45	3	28	28	0	PCCA,synonymous_variant,p.%3D,ENST00000376286,;PCCA,synonymous_variant,p.%3D,ENST00000376279,;PCCA,synonymous_variant,p.%3D,ENST00000376285,;	G	ENSG00000175198	ENST00000376285	Transcript	synonymous_variant	635	597	199	V	gtC/gtG	.	.	.	1	PCCA	HGNC	8653	protein_coding	YES	CCDS9496.2	ENSP00000365462	PCCA_HUMAN	.	UPI0000070089	.	.	.	7/24	.	PROSITE_profiles:PS50975,PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF33,hmmpanther:PTHR18866,Gene3D:3.30.1490.20,Pfam_domain:PF02786,Superfamily_domains:SSF56059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTAGTCAAGGT	.	2	ESCA
CARKD	0	.	GRCh37	13	111286975	111286975	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.546+33C>T	.	.	ENST00000309957	.	50	46	4	46	46	0	CARKD,3_prime_UTR_variant,,ENST00000397191,;CARKD,intron_variant,,ENST00000309957,;CARKD,intron_variant,,ENST00000424185,;CARKD,intron_variant,,ENST00000458711,;CARKD,intron_variant,,ENST00000470164,;AL139385.1,upstream_gene_variant,,ENST00000545740,;	T	ENSG00000213995	ENST00000309957	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CARKD	HGNC	25576	protein_coding	YES	CCDS9513.1	ENSP00000311984	NNRD_HUMAN	.	UPI000013DD48	.	.	.	.	6/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGACTCCCGGA	.	3	ESCA
BRCA2	0	.	GRCh37	13	32954186	32954186	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9160C>T	p.Pro3054Ser	p.P3054S	ENST00000544455	24/28	79	74	5	63	63	0	BRCA2,missense_variant,p.Pro3054Ser,ENST00000544455,;BRCA2,missense_variant,p.Pro3054Ser,ENST00000380152,;BRCA2,missense_variant,p.Pro40Ser,ENST00000470094,;BRCA2,downstream_gene_variant,,ENST00000528762,;IFIT1P1,upstream_gene_variant,,ENST00000400497,;	T	ENSG00000139618	ENST00000544455	Transcript	missense_variant	9387	9160	3054	P/S	Ccc/Tcc	.	.	.	1	BRCA2	HGNC	1101	protein_coding	YES	CCDS9344.1	ENSP00000439902	BRCA2_HUMAN	Q9H4L3_HUMAN,Q8IU82_HUMAN,Q8IU77_HUMAN,Q8IU64_HUMAN,K4K7W0_HUMAN,K4JXT6_HUMAN,K4JTT2_HUMAN,E9PIQ1_HUMAN	UPI00001FCBCC	.	tolerated(0.36)	benign(0.06)	24/28	.	hmmpanther:PTHR11289:SF0,hmmpanther:PTHR11289,Pfam_domain:PF09104,Gene3D:2.40.50.140,PIRSF_domain:PIRSF002397,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAGCCCCTT	.	2	ESCA
PDS5B	0	.	GRCh37	13	33330027	33330027	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2989C>G	p.His997Asp	p.H997D	ENST00000315596	26/35	29	24	5	32	32	0	PDS5B,missense_variant,p.His997Asp,ENST00000315596,;PDS5B,upstream_gene_variant,,ENST00000447833,;PDS5B,missense_variant,p.His997Asp,ENST00000450460,;	G	ENSG00000083642	ENST00000315596	Transcript	missense_variant	3175	2989	997	H/D	Cac/Gac	.	.	.	1	PDS5B	HGNC	20418	protein_coding	YES	CCDS41878.1	ENSP00000313851	PDS5B_HUMAN	.	UPI000006D4A9	.	tolerated(0.1)	probably_damaging(0.977)	26/35	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF1,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATTCACCTT	.	5	ESCA
KBTBD6	0	.	GRCh37	13	41703267	41703267	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1356A>T	.	.	ENST00000379485	1/1	36	28	7	30	30	0	KBTBD6,3_prime_UTR_variant,,ENST00000379485,;KBTBD6,downstream_gene_variant,,ENST00000499385,;	A	ENSG00000165572	ENST00000379485	Transcript	3_prime_UTR_variant	3616	.	.	.	.	.	.	.	-1	KBTBD6	HGNC	25340	protein_coding	YES	CCDS9376.1	ENSP00000368799	KBTB6_HUMAN	.	UPI00001969BB	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGATATCAA	.	5	ESCA
KCTD4	0	.	GRCh37	13	45768277	45768277	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426C>T	p.%3D	p.F142F	ENST00000405872	2/2	46	42	4	30	30	0	KCTD4,synonymous_variant,p.%3D,ENST00000379108,;KCTD4,synonymous_variant,p.%3D,ENST00000405872,;GTF2F2,intron_variant,,ENST00000340473,;	A	ENSG00000180332	ENST00000405872	Transcript	synonymous_variant	830	426	142	F	ttC/ttT	.	.	.	-1	KCTD4	HGNC	23227	protein_coding	YES	CCDS9396.1	ENSP00000385144	KCTD4_HUMAN	.	UPI000013F484	.	.	.	2/2	.	hmmpanther:PTHR14499:SF9,hmmpanther:PTHR14499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCAAGAAAGT	.	3	ESCA
PPP1R2P4	0	.	GRCh37	13	47012009	47012009	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.317G>C	.	.	ENST00000535073	1/15	109	99	10	88	88	0	KIAA0226L,5_prime_UTR_variant,,ENST00000409879,;PPP1R2P4,non_coding_transcript_exon_variant,,ENST00000535073,;PPP1R2P4,non_coding_transcript_exon_variant,,ENST00000424051,;	G	ENSG00000241353	ENST00000535073	Transcript	non_coding_transcript_exon_variant	317	.	.	.	.	.	.	.	-1	PPP1R2P4	HGNC	16319	processed_pseudogene	YES	.	.	.	.	.	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGCTCCTCCT	.	3	ESCA
DOCK9	0	.	GRCh37	13	99538803	99538803	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2119C>G	p.Pro707Ala	p.P707A	ENST00000376460	19/57	27	23	4	25	25	0	DOCK9,missense_variant,p.Pro707Ala,ENST00000376460,;DOCK9,missense_variant,p.Pro707Ala,ENST00000442173,;DOCK9,missense_variant,p.Pro708Ala,ENST00000339416,;DOCK9,missense_variant,p.Pro719Ala,ENST00000448493,;DOCK9,downstream_gene_variant,,ENST00000473165,;	C	ENSG00000088387	ENST00000376460	Transcript	missense_variant	2200	2119	707	P/A	Cca/Gca	.	.	.	-1	DOCK9	HGNC	14132	protein_coding	YES	CCDS45062.1	ENSP00000365643	DOCK9_HUMAN	.	UPI000046FD7F	.	deleterious(0)	probably_damaging(0.999)	19/57	.	Pfam_domain:PF14429,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF77,PROSITE_profiles:PS51650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGGGTTTT	.	5	ESCA
DYNC1H1	0	.	GRCh37	14	102499768	102499768	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10360C>T	p.%3D	p.L3454L	ENST00000360184	54/78	30	25	5	26	26	0	DYNC1H1,synonymous_variant,p.%3D,ENST00000360184,;DYNC1H1,upstream_gene_variant,,ENST00000553423,;RP11-1017G21.4,downstream_gene_variant,,ENST00000553701,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557551,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557242,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000556791,;DYNC1H1,downstream_gene_variant,,ENST00000554854,;DYNC1H1,upstream_gene_variant,,ENST00000555800,;	T	ENSG00000197102	ENST00000360184	Transcript	synonymous_variant	10524	10360	3454	L	Ctg/Ttg	.	.	.	1	DYNC1H1	HGNC	2961	protein_coding	YES	CCDS9966.1	ENSP00000348965	DYHC1_HUMAN	Q92862_HUMAN,B4DSR6_HUMAN	UPI00001B515A	.	.	.	54/78	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10676:SF28,hmmpanther:PTHR10676,Pfam_domain:PF12777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTCCTGATC	.	5	ESCA
BTBD6	0	.	GRCh37	14	105716690	105716690	+	Missense_Mutation	SNP	C	C	A	rs774729758	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1139C>A	p.Ser380Tyr	p.S380Y	ENST00000392554	4/4	19	15	4	19	19	0	BTBD6,missense_variant,p.Ser380Tyr,ENST00000536364,;BTBD6,missense_variant,p.Ser380Tyr,ENST00000392554,;BTBD6,missense_variant,p.Ser380Tyr,ENST00000537513,;BTBD6,missense_variant,p.Ser305Tyr,ENST00000327471,;BTBD6,missense_variant,p.Ser305Tyr,ENST00000463376,;BRF1,intron_variant,,ENST00000379937,;BRF1,intron_variant,,ENST00000546417,;BRF1,intron_variant,,ENST00000546474,;BRF1,intron_variant,,ENST00000327359,;BRF1,intron_variant,,ENST00000440513,;BRF1,upstream_gene_variant,,ENST00000550208,;BRF1,upstream_gene_variant,,ENST00000550375,;BRF1,downstream_gene_variant,,ENST00000550692,;BRF1,upstream_gene_variant,,ENST00000552127,;BRF1,upstream_gene_variant,,ENST00000392557,;BRF1,upstream_gene_variant,,ENST00000446501,;BRF1,upstream_gene_variant,,ENST00000551787,;BRF1,upstream_gene_variant,,ENST00000379932,;BTBD6,downstream_gene_variant,,ENST00000392553,;	A	ENSG00000184887	ENST00000392554	Transcript	missense_variant	1436	1139	380	S/Y	tCt/tAt	rs774729758	.	.	1	BTBD6	HGNC	19897	protein_coding	YES	CCDS10002.2	ENSP00000376337	BTBD6_HUMAN	F8VPC8_HUMAN	UPI00001FDD27	.	tolerated(0.79)	benign(0.156)	4/4	.	hmmpanther:PTHR24413:SF4,hmmpanther:PTHR24413,Pfam_domain:PF08005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCTGGGA	.	5	ESCA
POTEM	0	.	GRCh37	14	20007579	20007579	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109C>G	p.Ser370Cys	p.S370C	ENST00000551509	6/11	21	16	5	13	13	0	POTEM,missense_variant,p.Ser370Cys,ENST00000551509,;RP11-244H18.1,intron_variant,,ENST00000547584,;RNU6-1268P,downstream_gene_variant,,ENST00000391214,;POTEM,missense_variant,p.Ser370Cys,ENST00000547848,;POTEM,3_prime_UTR_variant,,ENST00000547722,;CTD-2311B13.8,upstream_gene_variant,,ENST00000547150,;	C	ENSG00000187537	ENST00000551509	Transcript	missense_variant	1161	1109	370	S/C	tCt/tGt	.	.	.	-1	POTEM	HGNC	37096	protein_coding	YES	CCDS45076.1	ENSP00000452296	POTEM_HUMAN	.	UPI00006C1407	.	deleterious(0.02)	probably_damaging(0.987)	6/11	.	hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TTTCAGAAGAG	.	2	ESCA
OXA1L	0	.	GRCh37	14	23235862	23235862	+	Silent	SNP	T	T	C	rs764727247	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132T>C	p.%3D	p.G44G	ENST00000285848	1/10	56	49	7	29	29	0	OXA1L,synonymous_variant,p.%3D,ENST00000285848,;OXA1L,upstream_gene_variant,,ENST00000431881,;OXA1L,upstream_gene_variant,,ENST00000604262,;OXA1L,upstream_gene_variant,,ENST00000412791,;OXA1L,upstream_gene_variant,,ENST00000358043,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554857,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554730,;CTD-2555K7.2,upstream_gene_variant,,ENST00000553792,;OXA1L,upstream_gene_variant,,ENST00000442110,;OXA1L,upstream_gene_variant,,ENST00000556473,;OXA1L,upstream_gene_variant,,ENST00000473744,;OXA1L,upstream_gene_variant,,ENST00000495424,;OXA1L,upstream_gene_variant,,ENST00000481218,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554194,;OXA1L,upstream_gene_variant,,ENST00000557299,;OXA1L,upstream_gene_variant,,ENST00000483939,;	C	ENSG00000155463	ENST00000285848	Transcript	synonymous_variant	132	132	44	G	ggT/ggC	rs764727247	.	.	1	OXA1L	HGNC	8526	protein_coding	YES	CCDS9573.1	ENSP00000285848	.	S4R3Q9_HUMAN,J3KNA0_HUMAN,C9JC63_HUMAN	UPI000013DE11	.	.	.	1/10	.	hmmpanther:PTHR12428:SF16,hmmpanther:PTHR12428	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGGTTGTGG	byFrequency	4	ESCA
NPAS3	0	.	GRCh37	14	34029384	34029384	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526G>A	p.Glu176Lys	p.E176K	ENST00000356141	5/12	85	74	11	43	43	0	NPAS3,missense_variant,p.Glu146Lys,ENST00000548645,;NPAS3,missense_variant,p.Glu181Lys,ENST00000551492,;NPAS3,missense_variant,p.Glu163Lys,ENST00000357798,;NPAS3,missense_variant,p.Glu86Lys,ENST00000546849,;NPAS3,missense_variant,p.Glu176Lys,ENST00000356141,;NPAS3,missense_variant,p.Glu74Lys,ENST00000551008,;NPAS3,missense_variant,p.Glu72Lys,ENST00000547068,;NPAS3,missense_variant,p.Glu153Lys,ENST00000551634,;NPAS3,missense_variant,p.Glu144Lys,ENST00000346562,;NPAS3,missense_variant,p.Glu176Lys,ENST00000341321,;NPAS3,non_coding_transcript_exon_variant,,ENST00000549770,;NPAS3,upstream_gene_variant,,ENST00000552696,;	A	ENSG00000151322	ENST00000356141	Transcript	missense_variant	526	526	176	E/K	Gaa/Aaa	.	.	.	1	NPAS3	HGNC	19311	protein_coding	YES	CCDS53891.1	ENSP00000348460	NPAS3_HUMAN	.	UPI00000743C2	.	deleterious(0)	possibly_damaging(0.635)	5/12	.	PROSITE_profiles:PS50112,hmmpanther:PTHR23043:SF21,hmmpanther:PTHR23043,Pfam_domain:PF00989,Gene3D:3.30.450.20,SMART_domains:SM00091,Superfamily_domains:SSF55785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCGAAACA	.	5	ESCA
SAMD4A	0	.	GRCh37	14	55203862	55203862	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.836G>C	p.Arg279Thr	p.R279T	ENST00000392067	3/12	90	80	9	51	51	0	SAMD4A,missense_variant,p.Arg278Thr,ENST00000357634,;SAMD4A,missense_variant,p.Arg279Thr,ENST00000554335,;SAMD4A,missense_variant,p.Arg279Thr,ENST00000392067,;SAMD4A,intron_variant,,ENST00000251091,;SAMD4A,downstream_gene_variant,,ENST00000557013,;	C	ENSG00000020577	ENST00000392067	Transcript	missense_variant	836	836	279	R/T	aGa/aCa	.	.	.	1	SAMD4A	HGNC	23023	protein_coding	YES	CCDS32084.2	ENSP00000375919	SMAG1_HUMAN	J3QSW1_HUMAN	UPI0000229786	.	deleterious(0.01)	possibly_damaging(0.576)	3/12	.	hmmpanther:PTHR12515	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCTAGAGGAC	.	4	ESCA
MNAT1	0	.	GRCh37	14	61201556	61201556	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25G>A	.	.	ENST00000261245	1/8	81	77	4	39	39	0	MNAT1,5_prime_UTR_variant,,ENST00000261245,;MNAT1,5_prime_UTR_variant,,ENST00000539616,;MNAT1,non_coding_transcript_exon_variant,,ENST00000553354,;MNAT1,non_coding_transcript_exon_variant,,ENST00000555545,;MNAT1,non_coding_transcript_exon_variant,,ENST00000556764,;	A	ENSG00000020426	ENST00000261245	Transcript	5_prime_UTR_variant	77	.	.	.	.	.	.	.	1	MNAT1	HGNC	7181	protein_coding	YES	CCDS9750.1	ENSP00000261245	MAT1_HUMAN	H0YJ92_HUMAN	UPI000002FC14	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGCGAGAGT	.	2	ESCA
SGPP1	0	.	GRCh37	14	64151541	64151541	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1282C>G	.	.	ENST00000247225	3/3	47	41	5	30	30	0	SGPP1,3_prime_UTR_variant,,ENST00000247225,;	C	ENSG00000126821	ENST00000247225	Transcript	3_prime_UTR_variant	2703	.	.	.	.	.	.	.	-1	SGPP1	HGNC	17720	protein_coding	YES	CCDS9760.1	ENSP00000247225	SGPP1_HUMAN	.	UPI000006DEB2	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGTGAAAAT	.	4	ESCA
SYNE2	0	.	GRCh37	14	64457753	64457753	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2566G>A	p.Glu856Lys	p.E856K	ENST00000358025	21/116	45	36	8	29	29	0	SYNE2,missense_variant,p.Glu856Lys,ENST00000554584,;SYNE2,missense_variant,p.Glu856Lys,ENST00000358025,;SYNE2,missense_variant,p.Glu856Lys,ENST00000344113,;SYNE2,5_prime_UTR_variant,,ENST00000357395,;	A	ENSG00000054654	ENST00000358025	Transcript	missense_variant	2796	2566	856	E/K	Gaa/Aaa	COSM1515606	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	possibly_damaging(0.803)	21/116	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGGAACTT	.	5	ESCA
SYNE2	0	.	GRCh37	14	64469753	64469753	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4102C>T	p.His1368Tyr	p.H1368Y	ENST00000358025	30/116	26	23	3	15	15	0	SYNE2,missense_variant,p.His1368Tyr,ENST00000554584,;SYNE2,missense_variant,p.His1368Tyr,ENST00000358025,;SYNE2,missense_variant,p.His1368Tyr,ENST00000344113,;SYNE2,5_prime_UTR_variant,,ENST00000357395,;SYNE2,non_coding_transcript_exon_variant,,ENST00000557005,;	T	ENSG00000054654	ENST00000358025	Transcript	missense_variant	4332	4102	1368	H/Y	Cat/Tat	.	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	benign(0.004)	30/116	.	hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATTCATCTG	.	2	ESCA
HSPA2	0	.	GRCh37	14	65009364	65009364	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1797G>A	p.%3D	p.Q599Q	ENST00000247207	1/1	32	29	3	14	14	0	HSPA2,synonymous_variant,p.%3D,ENST00000247207,;HSPA2,synonymous_variant,p.%3D,ENST00000394709,;RP11-973N13.4,upstream_gene_variant,,ENST00000554918,;HSPA2,downstream_gene_variant,,ENST00000554883,;	A	ENSG00000126803	ENST00000247207	Transcript	synonymous_variant	2179	1797	599	Q	caG/caA	.	.	.	1	HSPA2	HGNC	5235	protein_coding	YES	CCDS9766.1	ENSP00000247207	HSP72_HUMAN	.	UPI000012CC6A	.	.	.	1/1	.	hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF142,Pfam_domain:PF00012,Gene3D:1.20.1270.10,Superfamily_domains:SSF100934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCAGAAAGA	.	4	ESCA
FAM71D	0	.	GRCh37	14	67669818	67669818	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.167G>C	p.Arg56Thr	p.R56T	ENST00000311864	4/9	60	52	8	52	52	0	FAM71D,missense_variant,p.Arg56Thr,ENST00000524532,;FAM71D,missense_variant,p.Arg56Thr,ENST00000530728,;FAM71D,upstream_gene_variant,,ENST00000556117,;FAM71D,intron_variant,,ENST00000531566,;FAM71D,missense_variant,p.Arg56Thr,ENST00000534174,;FAM71D,missense_variant,p.Arg56Thr,ENST00000311864,;FAM71D,3_prime_UTR_variant,,ENST00000556046,;FAM71D,downstream_gene_variant,,ENST00000524914,;RP11-125H8.1,downstream_gene_variant,,ENST00000553618,;	C	ENSG00000172717	ENST00000311864	Transcript	missense_variant	421	167	56	R/T	aGa/aCa	.	.	.	1	FAM71D	HGNC	20101	nonsense_mediated_decay	YES	CCDS9778.1	ENSP00000431905	FA71D_HUMAN	E9PPX0_HUMAN,E9PM27_HUMAN	UPI000013F210	.	deleterious(0)	probably_damaging(0.991)	4/9	.	hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACAGAAGAG	.	4	ESCA
ATP6V1D	0	.	GRCh37	14	67819642	67819642	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.157G>C	p.Glu53Gln	p.E53Q	ENST00000216442	2/9	130	116	13	70	70	0	ATP6V1D,missense_variant,p.Glu35Gln,ENST00000553687,;ATP6V1D,missense_variant,p.Glu5Gln,ENST00000555723,;ATP6V1D,missense_variant,p.Glu53Gln,ENST00000555012,;ATP6V1D,missense_variant,p.Glu53Gln,ENST00000554236,;ATP6V1D,missense_variant,p.Glu53Gln,ENST00000555474,;ATP6V1D,missense_variant,p.Glu53Gln,ENST00000216442,;ATP6V1D,intron_variant,,ENST00000555431,;ATP6V1D,upstream_gene_variant,,ENST00000553408,;ATP6V1D,missense_variant,p.Glu53Gln,ENST00000556058,;ATP6V1D,missense_variant,p.Glu53Gln,ENST00000554087,;ATP6V1D,splice_region_variant,,ENST00000555335,;ATP6V1D,non_coding_transcript_exon_variant,,ENST00000557244,;ATP6V1D,upstream_gene_variant,,ENST00000555625,;	G	ENSG00000100554	ENST00000216442	Transcript	missense_variant	708	157	53	E/Q	Gag/Cag	.	.	.	-1	ATP6V1D	HGNC	13527	protein_coding	YES	CCDS9780.1	ENSP00000216442	VATD_HUMAN	H0YJH8_HUMAN,G3V5S7_HUMAN,G3V341_HUMAN,G3V2S6_HUMAN	UPI000013818E	.	tolerated(0.16)	benign(0.053)	2/9	.	hmmpanther:PTHR11671,TIGRFAM_domain:TIGR00309,Pfam_domain:PF01813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCTCTATTA	.	4	ESCA
SIPA1L1	0	.	GRCh37	14	72055797	72055797	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1208G>C	p.Gly403Ala	p.G403A	ENST00000555818	2/22	100	90	10	47	47	0	SIPA1L1,missense_variant,p.Gly403Ala,ENST00000358550,;SIPA1L1,missense_variant,p.Gly403Ala,ENST00000381232,;SIPA1L1,missense_variant,p.Gly403Ala,ENST00000555818,;SIPA1L1,downstream_gene_variant,,ENST00000557151,;SIPA1L1,downstream_gene_variant,,ENST00000555652,;SIPA1L1,downstream_gene_variant,,ENST00000554362,;SIPA1L1,downstream_gene_variant,,ENST00000555989,;	C	ENSG00000197555	ENST00000555818	Transcript	missense_variant	1556	1208	403	G/A	gGa/gCa	.	.	.	1	SIPA1L1	HGNC	20284	protein_coding	YES	CCDS9807.1	ENSP00000450832	SI1L1_HUMAN	G3V4Z3_HUMAN	UPI00000443CB	.	deleterious(0)	probably_damaging(0.996)	2/22	.	hmmpanther:PTHR15711:SF10,hmmpanther:PTHR15711	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGGGAGATG	.	4	ESCA
ELMSAN1	0	.	GRCh37	14	74182388	74182388	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3616C>T	.	.	ENST00000286523	12/12	29	22	6	24	24	0	ELMSAN1,3_prime_UTR_variant,,ENST00000286523,;ELMSAN1,3_prime_UTR_variant,,ENST00000394071,;ELMSAN1,downstream_gene_variant,,ENST00000435371,;PNMA1,upstream_gene_variant,,ENST00000316836,;ELMSAN1,downstream_gene_variant,,ENST00000423556,;ELMSAN1,non_coding_transcript_exon_variant,,ENST00000476562,;ELMSAN1,downstream_gene_variant,,ENST00000451078,;ELMSAN1,downstream_gene_variant,,ENST00000478847,;	A	ENSG00000156030	ENST00000286523	Transcript	3_prime_UTR_variant	7537	.	.	.	.	.	.	.	-1	ELMSAN1	HGNC	19853	protein_coding	YES	CCDS9819.1	ENSP00000286523	EMSA1_HUMAN	F6RU81_HUMAN,C9JYU7_HUMAN	UPI00001FD815	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGCGAGCCC	.	5	ESCA
TGFB3	0	.	GRCh37	14	76447096	76447096	+	Missense_Mutation	SNP	G	G	C	rs766051522	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141C>G	p.Ile47Met	p.I47M	ENST00000238682	1/7	114	95	18	64	64	0	TGFB3,missense_variant,p.Ile47Met,ENST00000556285,;TGFB3,missense_variant,p.Ile47Met,ENST00000238682,;IFT43,upstream_gene_variant,,ENST00000314067,;TGFB3,non_coding_transcript_exon_variant,,ENST00000555193,;TGFB3,downstream_gene_variant,,ENST00000556674,;IFT43,intron_variant,,ENST00000555677,;	C	ENSG00000119699	ENST00000238682	Transcript	missense_variant	439	141	47	I/M	atC/atG	rs766051522	.	.	-1	TGFB3	HGNC	11769	protein_coding	YES	CCDS9846.1	ENSP00000238682	TGFB3_HUMAN	Q8WV88_HUMAN,Q6TV16_HUMAN,Q6TV15_HUMAN,Q6TV14_HUMAN,Q6LDJ6_HUMAN,A5YM40_HUMAN	UPI000000D8EC	.	deleterious(0)	probably_damaging(0.999)	1/7	.	hmmpanther:PTHR11848:SF34,hmmpanther:PTHR11848,Pfam_domain:PF00688,PIRSF_domain:PIRSF001787	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAAGATCTG	.	5	ESCA
TDP1	0	.	GRCh37	14	90446926	90446926	+	Silent	SNP	C	C	T	rs377532827	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.834C>T	p.%3D	p.V278V	ENST00000335725	8/17	93	84	9	58	58	0	TDP1,synonymous_variant,p.%3D,ENST00000553617,;TDP1,synonymous_variant,p.%3D,ENST00000393452,;TDP1,synonymous_variant,p.%3D,ENST00000555880,;TDP1,synonymous_variant,p.%3D,ENST00000554180,;TDP1,synonymous_variant,p.%3D,ENST00000393454,;TDP1,synonymous_variant,p.%3D,ENST00000335725,;TDP1,synonymous_variant,p.%3D,ENST00000357382,;TDP1,upstream_gene_variant,,ENST00000556063,;TDP1,non_coding_transcript_exon_variant,,ENST00000555565,;TDP1,synonymous_variant,p.%3D,ENST00000557782,;TDP1,synonymous_variant,p.%3D,ENST00000545686,;TDP1,3_prime_UTR_variant,,ENST00000555178,;TDP1,3_prime_UTR_variant,,ENST00000554976,;	T	ENSG00000042088	ENST00000335725	Transcript	synonymous_variant	1084	834	278	V	gtC/gtT	rs377532827	.	.	1	TDP1	HGNC	18884	protein_coding	YES	CCDS9888.1	ENSP00000337353	TYDP1_HUMAN	G3V5F9_HUMAN,G3V5B8_HUMAN,G3V554_HUMAN,G3V3Q0_HUMAN,G3V2U6_HUMAN,G3V2J6_HUMAN,B3KN41_HUMAN	UPI00000737ED	.	.	.	8/17	.	hmmpanther:PTHR12415:SF0,hmmpanther:PTHR12415,Pfam_domain:PF06087,Gene3D:3.30.870.10,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTGTCATACA	byFrequency|byCluster	4	ESCA
IFI27L2	0	.	GRCh37	14	94594153	94594153	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376G>C	p.Glu126Gln	p.E126Q	ENST00000238609	4/4	188	173	15	107	107	0	IFI27L2,missense_variant,p.Glu101Gln,ENST00000556727,;IFI27L2,missense_variant,p.Glu126Gln,ENST00000238609,;IFI27L2,non_coding_transcript_exon_variant,,ENST00000554909,;IFI27L2,non_coding_transcript_exon_variant,,ENST00000555558,;IFI27L2,downstream_gene_variant,,ENST00000556552,;IFI27L2,downstream_gene_variant,,ENST00000553601,;	G	ENSG00000119632	ENST00000238609	Transcript	missense_variant	476	376	126	E/Q	Gag/Cag	.	.	.	-1	IFI27L2	HGNC	19753	protein_coding	YES	CCDS9920.1	ENSP00000238609	I27L2_HUMAN	.	UPI0000049526	.	deleterious_low_confidence(0.01)	benign(0.403)	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTCTCTGACT	.	3	ESCA
SERPINA4	0	.	GRCh37	14	95033361	95033361	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.704T>A	p.Val235Asp	p.V235D	ENST00000557004	3/5	123	110	13	75	75	0	SERPINA4,missense_variant,p.Val235Asp,ENST00000555095,;SERPINA4,missense_variant,p.Val235Asp,ENST00000298841,;SERPINA4,missense_variant,p.Val235Asp,ENST00000557004,;SERPINA5,intron_variant,,ENST00000554220,;SERPINA5,intron_variant,,ENST00000553780,;	A	ENSG00000100665	ENST00000557004	Transcript	missense_variant	1125	704	235	V/D	gTt/gAt	.	.	.	1	SERPINA4	HGNC	8948	protein_coding	YES	CCDS9927.1	ENSP00000450838	KAIN_HUMAN	.	UPI000000CBEF	.	deleterious(0)	probably_damaging(0.998)	3/5	.	hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF157,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTATGTTGATG	.	4	ESCA
NPAP1	0	.	GRCh37	15	24927196	24927196	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2711G>C	.	.	ENST00000329468	1/1	43	38	5	20	20	0	NPAP1,3_prime_UTR_variant,,ENST00000329468,;	C	ENSG00000185823	ENST00000329468	Transcript	3_prime_UTR_variant	6656	.	.	.	.	.	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTAGCATAA	.	4	ESCA
CHRFAM7A	0	.	GRCh37	15	30653728	30653728	+	3'Flank	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000299847	.	55	46	9	48	48	0	CHRFAM7A,3_prime_UTR_variant,,ENST00000397827,;CHRFAM7A,downstream_gene_variant,,ENST00000299847,;CHRFAM7A,downstream_gene_variant,,ENST00000401522,;RP11-382B18.4,upstream_gene_variant,,ENST00000602453,;	G	ENSG00000166664	ENST00000299847	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	68	-1	CHRFAM7A	HGNC	15781	protein_coding	YES	CCDS32184.1	ENSP00000299847	CRFM7_HUMAN	Q693P7_HUMAN,H3BPP0_HUMAN	UPI000013E5F0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTCCTCAGTGT	.	3	ESCA
RYR3	0	.	GRCh37	15	34078107	34078107	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9513C>T	p.%3D	p.L3171L	ENST00000389232	66/104	45	38	6	31	31	0	RYR3,synonymous_variant,p.%3D,ENST00000389232,;RYR3,synonymous_variant,p.%3D,ENST00000415757,;	T	ENSG00000198838	ENST00000389232	Transcript	synonymous_variant	9583	9513	3171	L	ctC/ctT	.	.	.	1	RYR3	HGNC	10485	protein_coding	YES	CCDS45210.1	ENSP00000373884	RYR3_HUMAN	.	UPI0000E5B01A	.	.	.	66/104	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13715:SF16,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTCTCATCCT	.	4	ESCA
USP50	0	.	GRCh37	15	50792993	50792993	+	Silent	SNP	G	G	A	rs773444419	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.978C>T	p.%3D	p.F326F	ENST00000532404	7/7	61	56	4	31	31	0	USP50,synonymous_variant,p.%3D,ENST00000532404,;USP8,3_prime_UTR_variant,,ENST00000396444,;USP8,3_prime_UTR_variant,,ENST00000433963,;USP8,downstream_gene_variant,,ENST00000425032,;USP8,downstream_gene_variant,,ENST00000307179,;RP11-562A8.5,upstream_gene_variant,,ENST00000560159,;RP11-562A8.4,upstream_gene_variant,,ENST00000560380,;USP50,downstream_gene_variant,,ENST00000530218,;USP8,downstream_gene_variant,,ENST00000560379,;USP50,downstream_gene_variant,,ENST00000559105,;USP8,downstream_gene_variant,,ENST00000419830,;	A	ENSG00000170236	ENST00000532404	Transcript	synonymous_variant	1152	978	326	F	ttC/ttT	rs773444419	.	.	-1	USP50	HGNC	20079	protein_coding	YES	CCDS53944.1	ENSP00000434676	.	E9PP86_HUMAN	UPI0001CB7F8F	.	.	.	7/7	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF397,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGCAGAAAGC	.	2	ESCA
UNC13C	0	.	GRCh37	15	54860107	54860107	+	Missense_Mutation	SNP	C	C	G	rs371933638	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6068C>G	p.Ala2023Gly	p.A2023G	ENST00000260323	29/32	61	54	7	38	38	0	UNC13C,missense_variant,p.Ala2021Gly,ENST00000537900,;UNC13C,missense_variant,p.Ala2023Gly,ENST00000545554,;UNC13C,missense_variant,p.Ala2023Gly,ENST00000260323,;	G	ENSG00000137766	ENST00000260323	Transcript	missense_variant	6068	6068	2023	A/G	gCc/gGc	rs371933638	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	deleterious_low_confidence(0.04)	possibly_damaging(0.664)	29/32	.	PROSITE_profiles:PS51259,hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2,Pfam_domain:PF10540	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TGATGCCTTGA	byFrequency|byCluster	2	ESCA
MYO9A	0	.	GRCh37	15	72244100	72244100	+	Intron	SNP	C	C	G	rs761180470	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2302+18G>C	.	.	ENST00000356056	.	95	86	9	57	57	0	MYO9A,missense_variant,p.Asp369His,ENST00000566885,;MYO9A,intron_variant,,ENST00000424560,;MYO9A,intron_variant,,ENST00000564571,;MYO9A,intron_variant,,ENST00000356056,;MYO9A,intron_variant,,ENST00000444904,;MYO9A,intron_variant,,ENST00000563542,;MYO9A,intron_variant,,ENST00000566744,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563925,;MYO9A,intron_variant,,ENST00000563648,;MYO9A,intron_variant,,ENST00000567095,;	G	ENSG00000066933	ENST00000356056	Transcript	intron_variant	.	.	.	.	.	rs761180470	.	.	-1	MYO9A	HGNC	7608	protein_coding	YES	CCDS10239.1	ENSP00000348349	MYO9A_HUMAN	H3BSU8_HUMAN,H3BMS3_HUMAN	UPI000013D213	.	.	.	.	15/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTATCAGGAT	byFrequency	4	ESCA
ADPGK	0	.	GRCh37	15	73048618	73048618	+	Missense_Mutation	SNP	C	C	G	rs748487995	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814G>C	p.Glu272Gln	p.E272Q	ENST00000311669	5/7	91	75	16	49	49	0	ADPGK,missense_variant,p.Glu150Gln,ENST00000565814,;ADPGK,missense_variant,p.Glu272Gln,ENST00000311669,;ADPGK,intron_variant,,ENST00000563907,;ADPGK,upstream_gene_variant,,ENST00000456471,;ADPGK,intron_variant,,ENST00000567733,;ADPGK,3_prime_UTR_variant,,ENST00000567941,;ADPGK,3_prime_UTR_variant,,ENST00000569534,;ADPGK,non_coding_transcript_exon_variant,,ENST00000562621,;ADPGK,intron_variant,,ENST00000569517,;ADPGK,downstream_gene_variant,,ENST00000562286,;ADPGK,upstream_gene_variant,,ENST00000569693,;ADPGK,downstream_gene_variant,,ENST00000562823,;ADPGK,downstream_gene_variant,,ENST00000569058,;ADPGK,downstream_gene_variant,,ENST00000566509,;	G	ENSG00000159322	ENST00000311669	Transcript	missense_variant	908	814	272	E/Q	Gag/Cag	rs748487995	.	.	-1	ADPGK	HGNC	25250	protein_coding	YES	CCDS42057.1	ENSP00000312250	ADPGK_HUMAN	Q69YR1_HUMAN,H3BU35_HUMAN,H3BTH4_HUMAN	UPI0000039E98	.	tolerated(0.06)	benign(0.037)	5/7	.	PROSITE_profiles:PS51255,hmmpanther:PTHR21208,hmmpanther:PTHR21208:SF0,Gene3D:3.40.1190.20,Pfam_domain:PF04587,Superfamily_domains:SSF53613	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTCCTTGC	.	5	ESCA
PEAK1	0	.	GRCh37	15	77407012	77407012	+	Missense_Mutation	SNP	C	C	T	rs766575004	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4727G>A	p.Arg1576His	p.R1576H	ENST00000560626	7/7	64	53	11	38	38	0	PEAK1,missense_variant,p.Arg1576His,ENST00000560626,;PEAK1,missense_variant,p.Arg1576His,ENST00000312493,;	T	ENSG00000173517	ENST00000560626	Transcript	missense_variant	5203	4727	1576	R/H	cGc/cAc	rs766575004	.	.	-1	PEAK1	HGNC	29431	protein_coding	YES	CCDS42062.1	ENSP00000452796	PEAK1_HUMAN	H3BUZ5_HUMAN,H3BUE6_HUMAN	UPI00002378D0	.	deleterious(0)	probably_damaging(1)	7/7	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF5,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGCGAGAC	.	5	ESCA
HDGFRP3	0	.	GRCh37	15	83807341	83807341	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*681C>T	.	.	ENST00000299633	6/6	36	30	6	35	35	0	HDGFRP3,3_prime_UTR_variant,,ENST00000299633,;TM6SF1,intron_variant,,ENST00000561551,;HDGFRP3,intron_variant,,ENST00000568294,;TM6SF1,downstream_gene_variant,,ENST00000379386,;TM6SF1,downstream_gene_variant,,ENST00000322019,;TM6SF1,downstream_gene_variant,,ENST00000379390,;TM6SF1,downstream_gene_variant,,ENST00000565774,;TM6SF1,downstream_gene_variant,,ENST00000258909,;HDGFRP3,downstream_gene_variant,,ENST00000563790,;TM6SF1,downstream_gene_variant,,ENST00000379384,;	A	ENSG00000166503	ENST00000299633	Transcript	3_prime_UTR_variant	1897	.	.	.	.	.	.	.	-1	HDGFRP3	Uniprot_gn	.	protein_coding	YES	CCDS32314.1	ENSP00000299633	HDGR3_HUMAN	.	UPI000006D757	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGGGAAAAA	.	5	ESCA
ACAN	0	.	GRCh37	15	89398787	89398787	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2971G>A	p.Asp991Asn	p.D991N	ENST00000439576	12/18	35	28	6	30	30	0	ACAN,missense_variant,p.Asp991Asn,ENST00000559004,;ACAN,missense_variant,p.Asp991Asn,ENST00000439576,;ACAN,missense_variant,p.Asp991Asn,ENST00000561243,;ACAN,missense_variant,p.Asp991Asn,ENST00000352105,;ACAN,upstream_gene_variant,,ENST00000560601,;ACAN,downstream_gene_variant,,ENST00000558207,;	A	ENSG00000157766	ENST00000439576	Transcript	missense_variant	3345	2971	991	D/N	Gac/Aac	.	.	.	1	ACAN	HGNC	319	protein_coding	YES	CCDS53970.1	ENSP00000387356	.	Q6LE94_HUMAN,E7EX88_HUMAN	UPI0001B23381	.	deleterious(0.01)	possibly_damaging(0.893)	12/18	.	hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGAGGACATC	.	5	ESCA
SMG1	0	.	GRCh37	16	18823362	18823362	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10709C>T	p.Ser3570Leu	p.S3570L	ENST00000446231	61/63	97	85	12	44	44	0	SMG1,missense_variant,p.Ser3571Leu,ENST00000389467,;SMG1,missense_variant,p.Ser3460Leu,ENST00000565324,;SMG1,missense_variant,p.Ser3570Leu,ENST00000446231,;RP11-1035H13.2,non_coding_transcript_exon_variant,,ENST00000569096,;SMG1,non_coding_transcript_exon_variant,,ENST00000561940,;	A	ENSG00000157106	ENST00000446231	Transcript	missense_variant	11122	10709	3570	S/L	tCa/tTa	.	.	.	-1	SMG1	HGNC	30045	protein_coding	YES	CCDS45430.1	ENSP00000402515	SMG1_HUMAN	H3BPS6_HUMAN	UPI00004F8E22	.	tolerated(0.13)	benign(0.15)	61/63	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF59	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCTGATGTA	.	4	ESCA
MAZ	0	.	GRCh37	16	29821856	29821856	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*481C>T	.	.	ENST00000219782	6/6	84	71	12	55	55	0	MAZ,3_prime_UTR_variant,,ENST00000545521,;MAZ,3_prime_UTR_variant,,ENST00000566906,;MAZ,3_prime_UTR_variant,,ENST00000568544,;MAZ,3_prime_UTR_variant,,ENST00000568282,;MAZ,3_prime_UTR_variant,,ENST00000219782,;MAZ,3_prime_UTR_variant,,ENST00000562337,;MAZ,3_prime_UTR_variant,,ENST00000563402,;MAZ,3_prime_UTR_variant,,ENST00000322945,;MAZ,intron_variant,,ENST00000562594,;MAZ,intron_variant,,ENST00000568411,;PRRT2,upstream_gene_variant,,ENST00000562148,;PRRT2,upstream_gene_variant,,ENST00000567659,;MAZ,downstream_gene_variant,,ENST00000569978,;MAZ,downstream_gene_variant,,ENST00000563012,;MAZ,downstream_gene_variant,,ENST00000562557,;PRRT2,upstream_gene_variant,,ENST00000572820,;PRRT2,upstream_gene_variant,,ENST00000300797,;MAZ,downstream_gene_variant,,ENST00000567444,;PRRT2,upstream_gene_variant,,ENST00000358758,;AC009133.14,non_coding_transcript_exon_variant,,ENST00000569981,;AC009133.20,intron_variant,,ENST00000569039,;AC009133.15,upstream_gene_variant,,ENST00000566537,;AC009133.14,upstream_gene_variant,,ENST00000563806,;PRRT2,upstream_gene_variant,,ENST00000567551,;MAZ,upstream_gene_variant,,ENST00000568516,;MAZ,non_coding_transcript_exon_variant,,ENST00000565777,;MAZ,downstream_gene_variant,,ENST00000561855,;	T	ENSG00000103495	ENST00000219782	Transcript	3_prime_UTR_variant	2069	.	.	.	.	.	.	.	1	MAZ	HGNC	6914	protein_coding	YES	CCDS42144.1	ENSP00000219782	MAZ_HUMAN	Q9UJ31_HUMAN,Q8IUI2_HUMAN,I3L4Y2_HUMAN,I3L0M3_HUMAN	UPI00001AE621	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCTGTAA	.	5	ESCA
ZNF213	0	.	GRCh37	16	3190882	3190882	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.914G>A	p.Arg305Gln	p.R305Q	ENST00000396878	6/6	19	14	5	9	9	0	ZNF213,missense_variant,p.Arg147Gln,ENST00000416391,;ZNF213,missense_variant,p.Arg305Gln,ENST00000396878,;ZNF213,missense_variant,p.Arg305Gln,ENST00000576416,;ZNF213,missense_variant,p.Arg116Gln,ENST00000574575,;ZNF213,missense_variant,p.Arg305Gln,ENST00000574902,;ZNF213,3_prime_UTR_variant,,ENST00000572647,;CASP16,upstream_gene_variant,,ENST00000428155,;ZNF213,downstream_gene_variant,,ENST00000573771,;CASP16,upstream_gene_variant,,ENST00000571356,;ZNF213,3_prime_UTR_variant,,ENST00000576863,;ZNF213,non_coding_transcript_exon_variant,,ENST00000574928,;CASP16,upstream_gene_variant,,ENST00000575497,;	A	ENSG00000085644	ENST00000396878	Transcript	missense_variant	1389	914	305	R/Q	cGg/cAg	.	.	.	1	ZNF213	HGNC	13005	protein_coding	YES	CCDS10495.1	ENSP00000380087	ZN213_HUMAN	I3L2V8_HUMAN	UPI000007005C	.	tolerated(0.15)	benign(0.034)	6/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23226:SF58,hmmpanther:PTHR23226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCGCCGGCGCC	.	4	ESCA
GPT2	0	.	GRCh37	16	46952548	46952548	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916G>A	p.Val306Met	p.V306M	ENST00000340124	8/12	78	74	4	40	40	0	GPT2,missense_variant,p.Val306Met,ENST00000340124,;GPT2,missense_variant,p.Val206Met,ENST00000440783,;GPT2,non_coding_transcript_exon_variant,,ENST00000562801,;	A	ENSG00000166123	ENST00000340124	Transcript	missense_variant	1028	916	306	V/M	Gtg/Atg	.	.	.	1	GPT2	HGNC	18062	protein_coding	YES	CCDS10725.1	ENSP00000345282	ALAT2_HUMAN	B3KR40_HUMAN	UPI000004DBE2	.	deleterious(0.01)	probably_damaging(0.913)	8/12	.	hmmpanther:PTHR11751:SF311,hmmpanther:PTHR11751,Gene3D:3.40.640.10,Pfam_domain:PF00155,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAACGTGTAC	.	2	ESCA
SEPT12	0	.	GRCh37	16	4827743	4827743	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*55A>G	.	.	ENST00000268231	10/10	49	44	5	32	32	0	SEPT12,3_prime_UTR_variant,,ENST00000268231,;SEPT12,3_prime_UTR_variant,,ENST00000396693,;SEPT12,3_prime_UTR_variant,,ENST00000587603,;SEPT12,3_prime_UTR_variant,,ENST00000588241,;	C	ENSG00000140623	ENST00000268231	Transcript	3_prime_UTR_variant	1396	.	.	.	.	.	.	.	-1	SEPT12	HGNC	26348	protein_coding	YES	CCDS10522.1	ENSP00000268231	SEP12_HUMAN	K7EP92_HUMAN	UPI000007422A	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTGTGTTGA	.	4	ESCA
LONP2	0	.	GRCh37	16	48395764	48395764	+	3'Flank	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000285737	.	69	59	10	39	39	0	LONP2,missense_variant,p.Arg234Thr,ENST00000565867,;SIAH1,synonymous_variant,p.%3D,ENST00000380006,;SIAH1,synonymous_variant,p.%3D,ENST00000394725,;SIAH1,synonymous_variant,p.%3D,ENST00000356721,;LONP2,downstream_gene_variant,,ENST00000285737,;SIAH1,downstream_gene_variant,,ENST00000563745,;SIAH1,upstream_gene_variant,,ENST00000565620,;SIAH1,downstream_gene_variant,,ENST00000573005,;LONP2,downstream_gene_variant,,ENST00000564259,;LONP2,splice_acceptor_variant,,ENST00000565185,;SIAH1,synonymous_variant,p.%3D,ENST00000568007,;LONP2,non_coding_transcript_exon_variant,,ENST00000566719,;	C	ENSG00000102910	ENST00000285737	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4504	1	LONP2	HGNC	20598	protein_coding	YES	CCDS10734.1	ENSP00000285737	LONP2_HUMAN	Q9BU35_HUMAN	UPI000000DCD1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTAAGACTAA	.	4	ESCA
PAPD5	0	.	GRCh37	16	50261847	50261847	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1853C>T	p.Ser618Phe	p.S618F	ENST00000436909	12/13	107	82	25	50	50	0	PAPD5,missense_variant,p.Ser508Phe,ENST00000561678,;PAPD5,missense_variant,p.Ser618Phe,ENST00000436909,;PAPD5,missense_variant,p.Ser539Phe,ENST00000357464,;PAPD5,non_coding_transcript_exon_variant,,ENST00000573002,;PAPD5,non_coding_transcript_exon_variant,,ENST00000562717,;	T	ENSG00000121274	ENST00000436909	Transcript	missense_variant	1888	1853	618	S/F	tCt/tTt	.	.	.	1	PAPD5	HGNC	30758	protein_coding	YES	CCDS54006.1	ENSP00000396995	PAPD5_HUMAN	Q5EBM7_HUMAN,G4U4J3_HUMAN,B7ZLC1_HUMAN,B4DRJ7_HUMAN	UPI00017A7DC6	.	deleterious_low_confidence(0.02)	benign(0.343)	12/13	.	hmmpanther:PTHR23092,hmmpanther:PTHR23092:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTCTCAGG	.	5	ESCA
ADCY7	0	.	GRCh37	16	50345982	50345982	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2484G>A	p.%3D	p.K828K	ENST00000394697	21/26	68	64	4	35	35	0	ADCY7,synonymous_variant,p.%3D,ENST00000254235,;ADCY7,synonymous_variant,p.%3D,ENST00000394697,;ADCY7,downstream_gene_variant,,ENST00000537579,;BRD7,downstream_gene_variant,,ENST00000562383,;BRD7,downstream_gene_variant,,ENST00000394688,;BRD7,downstream_gene_variant,,ENST00000569774,;ADCY7,downstream_gene_variant,,ENST00000538642,;ADCY7,downstream_gene_variant,,ENST00000566433,;ADCY7,downstream_gene_variant,,ENST00000570187,;ADCY7,upstream_gene_variant,,ENST00000568930,;ADCY7,downstream_gene_variant,,ENST00000567277,;	A	ENSG00000121281	ENST00000394697	Transcript	synonymous_variant	2824	2484	828	K	aaG/aaA	.	.	.	1	ADCY7	HGNC	238	protein_coding	YES	CCDS10741.1	ENSP00000378187	ADCY7_HUMAN	I3L3Q5_HUMAN	UPI000004C5DB	.	.	.	21/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11920:SF273,hmmpanther:PTHR11920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAAGAAGAA	.	2	ESCA
PLLP	0	.	GRCh37	16	57290781	57290783	+	3'UTR	DEL	CCA	CCA	-	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	CCA	CCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*42_*44delTGG	.	.	ENST00000219207	4/4	31	26	5	24	24	0	PLLP,3_prime_UTR_variant,,ENST00000569059,;PLLP,3_prime_UTR_variant,,ENST00000219207,;ARL2BP,downstream_gene_variant,,ENST00000563234,;PLLP,downstream_gene_variant,,ENST00000564018,;ARL2BP,downstream_gene_variant,,ENST00000562023,;ARL2BP,downstream_gene_variant,,ENST00000219204,;RP11-407G23.3,upstream_gene_variant,,ENST00000564376,;	-	ENSG00000102934	ENST00000219207	Transcript	3_prime_UTR_variant	738-740	.	.	.	.	.	.	.	-1	PLLP	HGNC	18553	protein_coding	YES	CCDS10777.1	ENSP00000219207	PLLP_HUMAN	J3QLJ3_HUMAN	UPI0000131C07	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTGACCCAGCGGC	.	3	ESCA
SLC9A5	0	.	GRCh37	16	67292260	67292260	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1536G>A	p.%3D	p.L512L	ENST00000299798	10/16	69	60	9	35	35	0	SLC9A5,synonymous_variant,p.%3D,ENST00000299798,;SLC9A5,intron_variant,,ENST00000566626,;SLC9A5,intron_variant,,ENST00000566345,;SLC9A5,intron_variant,,ENST00000567247,;SLC9A5,downstream_gene_variant,,ENST00000561472,;SLC9A5,3_prime_UTR_variant,,ENST00000564812,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000564704,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000563723,;SLC9A5,intron_variant,,ENST00000566638,;CTC-277H1.7,upstream_gene_variant,,ENST00000573063,;	A	ENSG00000135740	ENST00000299798	Transcript	synonymous_variant	1601	1536	512	L	ctG/ctA	.	.	.	1	SLC9A5	HGNC	11078	protein_coding	YES	CCDS42178.1	ENSP00000299798	SL9A5_HUMAN	.	UPI000012FD2D	.	.	.	10/16	.	hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF56,TIGRFAM_domain:TIGR00840	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTGATGCG	.	4	ESCA
HSD11B2	0	.	GRCh37	16	67469707	67469707	+	Missense_Mutation	SNP	G	G	A	rs1139495	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442G>A	p.Val148Met	p.V148M	ENST00000326152	2/5	35	26	8	16	16	0	HSD11B2,missense_variant,p.Val148Met,ENST00000326152,;ATP6V0D1,downstream_gene_variant,,ENST00000290949,;ATP6V0D1,downstream_gene_variant,,ENST00000565835,;ATP6V0D1,downstream_gene_variant,,ENST00000602876,;ATP6V0D1,downstream_gene_variant,,ENST00000540149,;ATP6V0D1,downstream_gene_variant,,ENST00000564615,;RP11-297D21.2,upstream_gene_variant,,ENST00000567261,;HSD11B2,non_coding_transcript_exon_variant,,ENST00000567684,;ATP6V0D1,downstream_gene_variant,,ENST00000567694,;HSD11B2,3_prime_UTR_variant,,ENST00000566606,;ATP6V0D1,downstream_gene_variant,,ENST00000563064,;ATP6V0D1,downstream_gene_variant,,ENST00000561852,;HSD11B2,downstream_gene_variant,,ENST00000569303,;ATP6V0D1,downstream_gene_variant,,ENST00000564191,;ATP6V0D1,downstream_gene_variant,,ENST00000568620,;ATP6V0D1,downstream_gene_variant,,ENST00000564788,;ATP6V0D1,downstream_gene_variant,,ENST00000566322,;ATP6V0D1,downstream_gene_variant,,ENST00000567170,;ATP6V0D1,downstream_gene_variant,,ENST00000426604,;ATP6V0D1,downstream_gene_variant,,ENST00000563305,;AC009061.1,downstream_gene_variant,,ENST00000366223,;	A	ENSG00000176387	ENST00000326152	Transcript	missense_variant	574	442	148	V/M	Gtg/Atg	rs1139495	.	.	1	HSD11B2	HGNC	5209	protein_coding	YES	CCDS10837.1	ENSP00000316786	DHI2_HUMAN	.	UPI000014185A	.	deleterious(0)	possibly_damaging(0.807)	2/5	.	hmmpanther:PTHR24316:SF265,hmmpanther:PTHR24316,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCGTGCTA	byCluster|byHapMap|by1000G	4	ESCA
NFAT5	0	.	GRCh37	16	69737362	69737362	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7108G>T	.	.	ENST00000432919	15/15	102	70	32	68	68	0	NFAT5,3_prime_UTR_variant,,ENST00000349945,;NFAT5,3_prime_UTR_variant,,ENST00000393742,;NFAT5,3_prime_UTR_variant,,ENST00000432919,;NFAT5,3_prime_UTR_variant,,ENST00000354436,;NQO1,downstream_gene_variant,,ENST00000561500,;RP11-311C24.1,non_coding_transcript_exon_variant,,ENST00000561622,;NFAT5,3_prime_UTR_variant,,ENST00000426654,;	T	ENSG00000102908	ENST00000432919	Transcript	3_prime_UTR_variant	12966	.	.	.	.	.	.	.	1	NFAT5	HGNC	7774	protein_coding	YES	CCDS45518.1	ENSP00000396538	NFAT5_HUMAN	.	UPI000049DE1B	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAAGATAGG	.	5	ESCA
DDX19A	0	.	GRCh37	16	70390094	70390094	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237G>A	p.%3D	p.L79L	ENST00000302243	4/12	64	60	4	41	41	0	DDX19A,synonymous_variant,p.%3D,ENST00000302243,;DDX19A,synonymous_variant,p.%3D,ENST00000417604,;RP11-529K1.3,intron_variant,,ENST00000567706,;DDX19A,upstream_gene_variant,,ENST00000443119,;DDX19A,upstream_gene_variant,,ENST00000575878,;DDX19A,non_coding_transcript_exon_variant,,ENST00000569244,;DDX19A,non_coding_transcript_exon_variant,,ENST00000562509,;DDX19A,synonymous_variant,p.%3D,ENST00000569771,;DDX19A,3_prime_UTR_variant,,ENST00000566167,;DDX19A,3_prime_UTR_variant,,ENST00000561574,;DDX19A,3_prime_UTR_variant,,ENST00000562649,;DDX19A,non_coding_transcript_exon_variant,,ENST00000567012,;RP11-529K1.3,intron_variant,,ENST00000565116,;DDX19A,intron_variant,,ENST00000569319,;DDX19A,downstream_gene_variant,,ENST00000565195,;	A	ENSG00000168872	ENST00000302243	Transcript	synonymous_variant	400	237	79	L	ctG/ctA	.	.	.	1	DDX19A	HGNC	25628	protein_coding	YES	CCDS10889.1	ENSP00000306117	DD19A_HUMAN	Q69YM2_HUMAN,Q68DY7_HUMAN,H3BTB3_HUMAN	UPI000007100E	.	.	.	4/12	.	hmmpanther:PTHR24031:SF194,hmmpanther:PTHR24031,Gene3D:3.40.50.300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCTGCAACG	.	2	ESCA
FUK	0	.	GRCh37	16	70513177	70513177	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3024G>C	p.Met1008Ile	p.M1008I	ENST00000288078	23/24	70	65	5	45	45	0	FUK,missense_variant,p.Met499Ile,ENST00000571514,;FUK,missense_variant,p.Met1008Ile,ENST00000288078,;FUK,missense_variant,p.Met1014Ile,ENST00000378912,;COG4,downstream_gene_variant,,ENST00000565715,;COG4,downstream_gene_variant,,ENST00000323786,;FUK,3_prime_UTR_variant,,ENST00000498702,;FUK,non_coding_transcript_exon_variant,,ENST00000464499,;FUK,non_coding_transcript_exon_variant,,ENST00000485034,;COG4,downstream_gene_variant,,ENST00000564315,;COG4,downstream_gene_variant,,ENST00000482252,;COG4,downstream_gene_variant,,ENST00000564415,;FUK,downstream_gene_variant,,ENST00000573832,;COG4,downstream_gene_variant,,ENST00000530314,;COG4,downstream_gene_variant,,ENST00000526700,;	C	ENSG00000157353	ENST00000288078	Transcript	missense_variant	3256	3024	1008	M/I	atG/atC	.	.	.	1	FUK	HGNC	29500	protein_coding	YES	CCDS10891.2	ENSP00000288078	FUK_HUMAN	Q8N8I9_HUMAN,I3L3J1_HUMAN,I3L1X0_HUMAN,I3L171_HUMAN,I3L106_HUMAN,B2RDL5_HUMAN	UPI000013DEF1	.	tolerated(0.12)	benign(0.019)	23/24	.	hmmpanther:PTHR32463,hmmpanther:PTHR32463:SF0,Gene3D:3.30.70.890,Pfam_domain:PF08544,Superfamily_domains:SSF55060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTATGATGGA	.	2	ESCA
WDR90	0	.	GRCh37	16	715471	715471	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4312-208C>A	.	.	ENST00000293879	.	84	75	9	38	38	0	WDR90,5_prime_UTR_variant,,ENST00000547944,;WDR90,5_prime_UTR_variant,,ENST00000315764,;WDR90,intron_variant,,ENST00000549091,;WDR90,intron_variant,,ENST00000293879,;WDR90,upstream_gene_variant,,ENST00000551100,;RHOT2,upstream_gene_variant,,ENST00000315082,;RHOT2,upstream_gene_variant,,ENST00000563134,;WDR90,downstream_gene_variant,,ENST00000550739,;WDR90,upstream_gene_variant,,ENST00000546896,;RHOT2,upstream_gene_variant,,ENST00000561929,;WDR90,intron_variant,,ENST00000547543,;RHOT2,upstream_gene_variant,,ENST00000569943,;WDR90,downstream_gene_variant,,ENST00000548603,;WDR90,downstream_gene_variant,,ENST00000548844,;WDR90,non_coding_transcript_exon_variant,,ENST00000553080,;WDR90,intron_variant,,ENST00000552728,;WDR90,intron_variant,,ENST00000549024,;WDR90,intron_variant,,ENST00000547407,;RHOT2,upstream_gene_variant,,ENST00000569358,;RHOT2,upstream_gene_variant,,ENST00000568950,;WDR90,upstream_gene_variant,,ENST00000548448,;RHOT2,upstream_gene_variant,,ENST00000566214,;RHOT2,upstream_gene_variant,,ENST00000570092,;WDR90,downstream_gene_variant,,ENST00000546923,;RHOT2,upstream_gene_variant,,ENST00000569706,;RHOT2,upstream_gene_variant,,ENST00000569675,;WDR90,downstream_gene_variant,,ENST00000552683,;RHOT2,upstream_gene_variant,,ENST00000602564,;RHOT2,upstream_gene_variant,,ENST00000570280,;RHOT2,upstream_gene_variant,,ENST00000562333,;RHOT2,upstream_gene_variant,,ENST00000562708,;RHOT2,upstream_gene_variant,,ENST00000567017,;RHOT2,upstream_gene_variant,,ENST00000566965,;RHOT2,upstream_gene_variant,,ENST00000563776,;RHOT2,upstream_gene_variant,,ENST00000561983,;WDR90,downstream_gene_variant,,ENST00000550902,;RHOT2,upstream_gene_variant,,ENST00000568636,;WDR90,downstream_gene_variant,,ENST00000552943,;RHOT2,upstream_gene_variant,,ENST00000563637,;WDR90,downstream_gene_variant,,ENST00000546516,;RHOT2,upstream_gene_variant,,ENST00000562598,;	A	ENSG00000161996	ENST00000293879	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	WDR90	HGNC	26960	protein_coding	YES	CCDS42092.1	ENSP00000293879	WDR90_HUMAN	.	UPI0000D67C48	.	.	.	.	34/40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGGCTTGCT	.	2	ESCA
AP1G1	0	.	GRCh37	16	71765825	71765825	+	3'Flank	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000393512	.	61	51	10	31	31	0	AP1G1,3_prime_UTR_variant,,ENST00000569748,;AP1G1,3_prime_UTR_variant,,ENST00000423132,;AP1G1,3_prime_UTR_variant,,ENST00000564155,;AP1G1,3_prime_UTR_variant,,ENST00000433195,;AP1G1,3_prime_UTR_variant,,ENST00000299980,;AP1G1,downstream_gene_variant,,ENST00000393512,;RP11-432I5.4,downstream_gene_variant,,ENST00000563557,;AP1G1,downstream_gene_variant,,ENST00000570052,;	C	ENSG00000166747	ENST00000393512	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	463	-1	AP1G1	HGNC	555	protein_coding	YES	CCDS45522.1	ENSP00000377148	AP1G1_HUMAN	H3BV30_HUMAN,H3BS13_HUMAN,H3BRM7_HUMAN,H3BR36_HUMAN,H3BPN9_HUMAN,H3BN75_HUMAN,H3BN71_HUMAN,B3KNW1_HUMAN	UPI000016A4AD	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACAGATACA	.	5	ESCA
BCAR1	0	.	GRCh37	16	75298373	75298373	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26C>G	p.Ser9Cys	p.S9C	ENST00000418647	2/8	60	52	8	23	23	0	BCAR1,missense_variant,p.Ser9Cys,ENST00000418647,;BCAR1,5_prime_UTR_variant,,ENST00000546196,;BCAR1,intron_variant,,ENST00000393422,;BCAR1,intron_variant,,ENST00000538440,;BCAR1,intron_variant,,ENST00000535626,;BCAR1,intron_variant,,ENST00000563323,;BCAR1,intron_variant,,ENST00000420641,;BCAR1,upstream_gene_variant,,ENST00000568864,;BCAR1,missense_variant,p.Ser9Cys,ENST00000562556,;	C	ENSG00000050820	ENST00000418647	Transcript	missense_variant	310	26	9	S/C	tCt/tGt	.	.	.	-1	BCAR1	HGNC	971	protein_coding	YES	CCDS54040.1	ENSP00000391669	BCAR1_HUMAN	Q8NC57_HUMAN,H3BVF0_HUMAN,H3BU42_HUMAN,H3BTL5_HUMAN,H3BTB0_HUMAN,H3BSY4_HUMAN,H3BSB2_HUMAN,H3BQJ7_HUMAN,F5H855_HUMAN	UPI0001AE689B	.	deleterious_low_confidence(0)	benign(0.043)	2/8	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACAGAAGAG	.	5	ESCA
RBFOX1	0	.	GRCh37	16	7761756	7761756	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1009G>A	.	.	ENST00000311745	13/13	74	63	11	46	46	0	RBFOX1,3_prime_UTR_variant,,ENST00000355637,;RBFOX1,3_prime_UTR_variant,,ENST00000340209,;RBFOX1,3_prime_UTR_variant,,ENST00000311745,;RBFOX1,downstream_gene_variant,,ENST00000553186,;RBFOX1,downstream_gene_variant,,ENST00000535565,;RBFOX1,downstream_gene_variant,,ENST00000552089,;RBFOX1,downstream_gene_variant,,ENST00000567470,;RBFOX1,downstream_gene_variant,,ENST00000547338,;RBFOX1,downstream_gene_variant,,ENST00000436368,;RBFOX1,downstream_gene_variant,,ENST00000422070,;RBFOX1,downstream_gene_variant,,ENST00000550418,;RBFOX1,downstream_gene_variant,,ENST00000547372,;RBFOX1,downstream_gene_variant,,ENST00000570188,;	A	ENSG00000078328	ENST00000311745	Transcript	3_prime_UTR_variant	2518	.	.	.	.	.	.	.	1	RBFOX1	HGNC	18222	protein_coding	YES	CCDS10531.1	ENSP00000309117	RFOX1_HUMAN	.	UPI000006E29E	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTTAGAGACA	.	4	ESCA
DNAAF1	0	.	GRCh37	16	84199429	84199429	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.904G>A	p.Glu302Lys	p.E302K	ENST00000378553	7/12	51	42	9	46	46	0	DNAAF1,missense_variant,p.Glu302Lys,ENST00000378553,;DNAAF1,missense_variant,p.Glu302Lys,ENST00000334315,;DNAAF1,non_coding_transcript_exon_variant,,ENST00000567666,;DNAAF1,non_coding_transcript_exon_variant,,ENST00000563818,;DNAAF1,missense_variant,p.Glu302Lys,ENST00000563093,;DNAAF1,non_coding_transcript_exon_variant,,ENST00000570298,;	A	ENSG00000154099	ENST00000378553	Transcript	missense_variant	1028	904	302	E/K	Gaa/Aaa	COSM1479137	.	.	1	DNAAF1	HGNC	30539	protein_coding	YES	CCDS10943.2	ENSP00000367815	DAAF1_HUMAN	H3BP51_HUMAN	UPI000059D3C9	.	deleterious(0)	probably_damaging(0.985)	7/12	.	hmmpanther:PTHR10588,hmmpanther:PTHR10588:SF208	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTGAAAAG	.	5	ESCA
GINS2	0	.	GRCh37	16	85711917	85711917	+	Silent	SNP	G	G	A	rs199530196	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459C>T	p.%3D	p.I153I	ENST00000253462	5/5	63	56	7	41	41	0	GINS2,synonymous_variant,p.%3D,ENST00000253462,;GSE1,downstream_gene_variant,,ENST00000253458,;GSE1,downstream_gene_variant,,ENST00000405402,;GSE1,downstream_gene_variant,,ENST00000412692,;GINS2,downstream_gene_variant,,ENST00000595355,;GINS2,downstream_gene_variant,,ENST00000596233,;GSE1,downstream_gene_variant,,ENST00000393243,;GSE1,downstream_gene_variant,,ENST00000469381,;	A	ENSG00000131153	ENST00000253462	Transcript	synonymous_variant	560	459	153	I	atC/atT	rs199530196	.	.	-1	GINS2	HGNC	24575	protein_coding	YES	CCDS10953.1	ENSP00000253462	PSF2_HUMAN	M0R043_HUMAN,M0QXS3_HUMAN	UPI000006D930	.	.	.	5/5	.	Superfamily_domains:SSF158573,PIRSF_domain:PIRSF028998,Pfam_domain:PF05916,hmmpanther:PTHR12772	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTTGATCTC	byCluster|by1000G	4	ESCA
MYH13	0	.	GRCh37	17	10206759	10206759	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5523G>C	p.%3D	p.L1841L	ENST00000418404	37/41	93	85	8	61	61	0	MYH13,synonymous_variant,p.%3D,ENST00000418404,;MYH13,synonymous_variant,p.%3D,ENST00000252172,;RP11-401O9.4,intron_variant,,ENST00000609088,;	G	ENSG00000006788	ENST00000418404	Transcript	synonymous_variant	5687	5523	1841	L	ctG/ctC	.	.	.	-1	MYH13	HGNC	7571	protein_coding	YES	CCDS45613.1	ENSP00000404570	MYH13_HUMAN	.	UPI0000DB39EA	.	.	.	37/41	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF267,Pfam_domain:PF01576,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCTTCAGGGC	.	3	ESCA
MYH4	0	.	GRCh37	17	10354724	10354724	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3784G>A	p.Glu1262Lys	p.E1262K	ENST00000255381	28/40	79	70	9	55	55	0	MYH4,missense_variant,p.Glu1262Lys,ENST00000255381,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	T	ENSG00000264424	ENST00000255381	Transcript	missense_variant	3895	3784	1262	E/K	Gaa/Aaa	.	.	.	-1	MYH4	HGNC	7574	protein_coding	YES	CCDS11154.1	ENSP00000255381	MYH4_HUMAN	.	UPI000013CEAB	.	deleterious(0)	possibly_damaging(0.852)	28/40	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF278,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTTCACTAA	.	4	ESCA
INPP5K	0	.	GRCh37	17	1417222	1417222	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96C>T	p.%3D	p.L32L	ENST00000421807	2/12	44	40	4	18	18	0	INPP5K,synonymous_variant,p.%3D,ENST00000542125,;INPP5K,synonymous_variant,p.%3D,ENST00000575172,;INPP5K,synonymous_variant,p.%3D,ENST00000421807,;INPP5K,5_prime_UTR_variant,,ENST00000320345,;INPP5K,5_prime_UTR_variant,,ENST00000498390,;INPP5K,5_prime_UTR_variant,,ENST00000406424,;INPP5K,5_prime_UTR_variant,,ENST00000449479,;INPP5K,5_prime_UTR_variant,,ENST00000571274,;INPP5K,5_prime_UTR_variant,,ENST00000477910,;INPP5K,intron_variant,,ENST00000574561,;INPP5K,intron_variant,,ENST00000397335,;PITPNA,downstream_gene_variant,,ENST00000313486,;PITPNA,downstream_gene_variant,,ENST00000539476,;PITPNA-AS1,upstream_gene_variant,,ENST00000425081,;INPP5K,synonymous_variant,p.%3D,ENST00000573790,;INPP5K,synonymous_variant,p.%3D,ENST00000445774,;INPP5K,synonymous_variant,p.%3D,ENST00000576646,;INPP5K,3_prime_UTR_variant,,ENST00000574955,;INPP5K,intron_variant,,ENST00000350761,;INPP5K,upstream_gene_variant,,ENST00000460733,;	A	ENSG00000132376	ENST00000421807	Transcript	synonymous_variant	485	96	32	L	ctC/ctT	.	.	.	-1	INPP5K	HGNC	33882	protein_coding	YES	CCDS11004.1	ENSP00000413937	INP5K_HUMAN	K7EPG6_HUMAN,K7ENF7_HUMAN,I3L0Y0_HUMAN,C9JZB0_HUMAN,B7Z4V9_HUMAN	UPI000006EC12	.	.	.	2/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11200:SF117,hmmpanther:PTHR11200,Pfam_domain:PF03372,Gene3D:3.60.10.10,SMART_domains:SM00128,Superfamily_domains:SSF56219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCACTGAGATC	.	3	ESCA
RILP	0	.	GRCh37	17	1551189	1551189	+	Missense_Mutation	SNP	C	C	T	rs755684887	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.884G>A	p.Arg295Gln	p.R295Q	ENST00000301336	6/8	37	33	3	29	29	0	RILP,missense_variant,p.Arg148Gln,ENST00000574810,;RILP,missense_variant,p.Arg295Gln,ENST00000301336,;SCARF1,upstream_gene_variant,,ENST00000348987,;PRPF8,downstream_gene_variant,,ENST00000304992,;PRPF8,downstream_gene_variant,,ENST00000572621,;SCARF1,upstream_gene_variant,,ENST00000263071,;PRPF8,downstream_gene_variant,,ENST00000571958,;SCARF1,upstream_gene_variant,,ENST00000571272,;PRPF8,downstream_gene_variant,,ENST00000575116,;SCARF1,upstream_gene_variant,,ENST00000574545,;RILP,non_coding_transcript_exon_variant,,ENST00000570858,;RILP,non_coding_transcript_exon_variant,,ENST00000573398,;PRPF8,downstream_gene_variant,,ENST00000572723,;SCARF1,upstream_gene_variant,,ENST00000576012,;SCARF1,upstream_gene_variant,,ENST00000434376,;PRPF8,downstream_gene_variant,,ENST00000576585,;SCARF1,upstream_gene_variant,,ENST00000573852,;SCARF1,upstream_gene_variant,,ENST00000573867,;	T	ENSG00000167705	ENST00000301336	Transcript	missense_variant	1157	884	295	R/Q	cGg/cAg	rs755684887	.	.	-1	RILP	HGNC	30266	protein_coding	YES	CCDS11009.1	ENSP00000301336	RILP_HUMAN	.	UPI0000073C49	.	deleterious(0.04)	possibly_damaging(0.71)	6/8	.	hmmpanther:PTHR21502:SF7,hmmpanther:PTHR21502,Pfam_domain:PF11461,Superfamily_domains:0053655	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTCCGGACA	byFrequency	4	ESCA
TOM1L2	0	.	GRCh37	17	17788081	17788081	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.368C>T	p.Ala123Val	p.A123V	ENST00000379504	5/15	64	60	4	44	44	0	TOM1L2,missense_variant,p.Ala123Val,ENST00000379504,;TOM1L2,missense_variant,p.Ala73Val,ENST00000581396,;TOM1L2,missense_variant,p.Ala123Val,ENST00000535933,;TOM1L2,intron_variant,,ENST00000540946,;TOM1L2,intron_variant,,ENST00000542206,;TOM1L2,intron_variant,,ENST00000395739,;TOM1L2,intron_variant,,ENST00000318094,;TOM1L2,splice_region_variant,,ENST00000537091,;	A	ENSG00000175662	ENST00000379504	Transcript	missense_variant	452	368	123	A/V	gCa/gTa	.	.	.	-1	TOM1L2	HGNC	11984	protein_coding	YES	CCDS42270.1	ENSP00000368818	TM1L2_HUMAN	K7ENB0_HUMAN	UPI00001C09C6	.	deleterious(0.01)	possibly_damaging(0.481)	5/15	.	PROSITE_profiles:PS50179,hmmpanther:PTHR13856:SF31,hmmpanther:PTHR13856,Gene3D:1.25.40.90,Pfam_domain:PF00790,SMART_domains:SM00288,PIRSF_domain:PIRSF036948,Superfamily_domains:SSF48464	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCATGCCTGG	.	2	ESCA
TBC1D29	0	.	GRCh37	17	28887700	28887700	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144G>A	p.Met48Ile	p.M48I	ENST00000580161	4/6	86	78	8	82	82	0	TBC1D29,missense_variant,p.Met48Ile,ENST00000580161,;TBC1D29,missense_variant,p.Met48Ile,ENST00000579181,;TBC1D29,missense_variant,p.Met48Ile,ENST00000584297,;RP11-218M11.1,downstream_gene_variant,,ENST00000563063,;RP11-218M11.6,upstream_gene_variant,,ENST00000582125,;TBC1D29,non_coding_transcript_exon_variant,,ENST00000582511,;RP11-271K11.1,downstream_gene_variant,,ENST00000578471,;	A	ENSG00000266733	ENST00000580161	Transcript	missense_variant	2641	144	48	M/I	atG/atA	.	.	.	1	TBC1D29	HGNC	24509	protein_coding	YES	CCDS32606.1	ENSP00000462799	TBC29_HUMAN	.	UPI00000702F8	.	deleterious(0.02)	possibly_damaging(0.584)	4/6	.	hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF236,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGATGCTGAT	.	4	ESCA
SPATA22	0	.	GRCh37	17	3352231	3352231	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542C>G	p.Ser181Ter	p.S181*	ENST00000573128	6/9	148	141	6	88	88	0	SPATA22,stop_gained,p.Ser110Ter,ENST00000574797,;SPATA22,stop_gained,p.Ser181Ter,ENST00000573128,;SPATA22,stop_gained,p.Ser110Ter,ENST00000571553,;SPATA22,stop_gained,p.Ser165Ter,ENST00000541913,;SPATA22,stop_gained,p.Ser181Ter,ENST00000572969,;SPATA22,stop_gained,p.Ser181Ter,ENST00000575375,;SPATA22,stop_gained,p.Ser168Ter,ENST00000574051,;SPATA22,stop_gained,p.Ser181Ter,ENST00000268981,;SPATA22,stop_gained,p.Ser181Ter,ENST00000397168,;SPATA22,stop_gained,p.Ser138Ter,ENST00000355380,;SPATA22,downstream_gene_variant,,ENST00000572582,;SPATA22,downstream_gene_variant,,ENST00000571607,;	C	ENSG00000141255	ENST00000573128	Transcript	stop_gained	1026	542	181	S/*	tCa/tGa	.	.	.	-1	SPATA22	HGNC	30705	protein_coding	YES	CCDS11027.1	ENSP00000459580	SPT22_HUMAN	I3L517_HUMAN,I3L4D7_HUMAN,I3L2B9_HUMAN,I3L1L5_HUMAN	UPI0000140D16	.	.	.	6/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTGATGAA	.	2	ESCA
C17orf78	0	.	GRCh37	17	35746184	35746184	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.637C>T	p.Gln213Ter	p.Q213*	ENST00000300618	6/7	50	38	11	32	32	0	C17orf78,stop_gained,p.Gln213Ter,ENST00000300618,;C17orf78,missense_variant,p.Ser132Leu,ENST00000586700,;ACACA,intron_variant,,ENST00000416895,;ACACA,intron_variant,,ENST00000353139,;ACACA,intron_variant,,ENST00000451642,;ACACA,intron_variant,,ENST00000413318,;RP11-378E13.3,downstream_gene_variant,,ENST00000592238,;ACACA,intron_variant,,ENST00000587545,;ACACA,intron_variant,,ENST00000589665,;ACACA,intron_variant,,ENST00000456066,;	T	ENSG00000167230	ENST00000300618	Transcript	stop_gained	687	637	213	Q/*	Caa/Taa	.	.	.	1	C17orf78	HGNC	26831	protein_coding	YES	CCDS45655.1	ENSP00000300618	CQ078_HUMAN	.	UPI0000140B91	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTATCAATGC	.	5	ESCA
ATP2A3	0	.	GRCh37	17	3831294	3831294	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3120C>G	p.%3D	p.L1040L	ENST00000359983	22/23	55	51	4	43	43	0	ATP2A3,stop_gained,p.Ser145Ter,ENST00000570845,;ATP2A3,missense_variant,p.Gln116Glu,ENST00000572116,;ATP2A3,missense_variant,p.Gln191Glu,ENST00000397039,;ATP2A3,synonymous_variant,p.%3D,ENST00000359983,;ATP2A3,intron_variant,,ENST00000397043,;ATP2A3,intron_variant,,ENST00000309890,;ATP2A3,intron_variant,,ENST00000397035,;ATP2A3,intron_variant,,ENST00000397041,;ATP2A3,intron_variant,,ENST00000352011,;ATP2A3,intron_variant,,ENST00000574999,;ATP2A3,intron_variant,,ENST00000570773,;ATP2A3,downstream_gene_variant,,ENST00000576957,;ATP2A3,downstream_gene_variant,,ENST00000571245,;	C	ENSG00000074370	ENST00000359983	Transcript	synonymous_variant	3120	3120	1040	L	ctC/ctG	.	.	.	-1	ATP2A3	HGNC	813	protein_coding	YES	CCDS11042.1	ENSP00000353072	AT2A3_HUMAN	.	UPI0000161584	.	.	.	22/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCTGAGCAG	.	2	ESCA
KRT28	0	.	GRCh37	17	38948703	38948703	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1371G>C	p.Lys457Asn	p.K457N	ENST00000306658	8/8	63	58	5	41	41	0	KRT28,missense_variant,p.Lys457Asn,ENST00000306658,;	G	ENSG00000173908	ENST00000306658	Transcript	missense_variant	1437	1371	457	K/N	aaG/aaC	.	.	.	-1	KRT28	HGNC	30842	protein_coding	YES	CCDS11376.1	ENSP00000305263	K1C28_HUMAN	.	UPI0000246D70	.	deleterious_low_confidence(0.03)	possibly_damaging(0.691)	8/8	.	hmmpanther:PTHR23239:SF145,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTGTCTTGCC	.	3	ESCA
KRT9	0	.	GRCh37	17	39723652	39723652	+	Missense_Mutation	SNP	C	C	T	rs775942442	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1745G>A	p.Ser582Asn	p.S582N	ENST00000246662	7/8	189	165	24	93	93	0	KRT9,missense_variant,p.Ser349Asn,ENST00000588431,;KRT9,missense_variant,p.Ser582Asn,ENST00000246662,;	T	ENSG00000171403	ENST00000246662	Transcript	missense_variant	1811	1745	582	S/N	aGt/aAt	rs775942442	.	.	-1	KRT9	HGNC	6447	protein_coding	YES	CCDS32654.1	ENSP00000246662	K1C9_HUMAN	K7EQQ3_HUMAN	UPI00001AE6F7	.	deleterious_low_confidence(0)	unknown(0)	7/8	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCACTTCCT	.	4	ESCA
C17orf104	0	.	GRCh37	17	42743838	42743838	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559G>A	p.Asp187Asn	p.D187N	ENST00000409122	5/8	40	36	4	22	22	0	C17orf104,missense_variant,p.Asp21Asn,ENST00000432494,;C17orf104,missense_variant,p.Asp21Asn,ENST00000409464,;C17orf104,missense_variant,p.Asp187Asn,ENST00000409122,;C17orf104,missense_variant,p.Asp187Asn,ENST00000359945,;C17orf104,missense_variant,p.Asp21Asn,ENST00000456912,;C17orf104,downstream_gene_variant,,ENST00000425535,;C17orf104,upstream_gene_variant,,ENST00000472403,;	A	ENSG00000180336	ENST00000409122	Transcript	missense_variant	701	559	187	D/N	Gat/Aat	.	.	.	1	C17orf104	HGNC	26670	protein_coding	YES	CCDS45703.2	ENSP00000386452	CQ104_HUMAN	C9JYK8_HUMAN,C9J4A2_HUMAN	UPI0001881A86	.	tolerated(0.21)	benign(0.302)	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAATAGATACA	.	3	ESCA
LRRC37A4P	0	.	GRCh37	17	43585505	43585505	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4909G>C	.	.	ENST00000581296	12/12	132	114	17	97	96	1	RP11-798G7.5,intron_variant,,ENST00000253803,;LRRC37A4P,non_coding_transcript_exon_variant,,ENST00000579913,;LRRC37A4P,non_coding_transcript_exon_variant,,ENST00000581296,;LRRC37A4P,intron_variant,,ENST00000398305,;	G	ENSG00000214425	ENST00000581296	Transcript	non_coding_transcript_exon_variant	4909	.	.	.	.	.	.	.	-1	LRRC37A4P	HGNC	25479	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCTTCTCTGT	.	4	ESCA
INTS2	0	.	GRCh37	17	59949628	59949628	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2800C>G	p.Gln934Glu	p.Q934E	ENST00000444766	20/25	67	57	10	43	43	0	INTS2,missense_variant,p.Gln934Glu,ENST00000444766,;INTS2,missense_variant,p.Gln926Glu,ENST00000251334,;Y_RNA,downstream_gene_variant,,ENST00000365491,;INTS2,non_coding_transcript_exon_variant,,ENST00000583822,;	C	ENSG00000108506	ENST00000444766	Transcript	missense_variant	2876	2800	934	Q/E	Cag/Gag	.	.	.	-1	INTS2	HGNC	29241	protein_coding	YES	CCDS45750.1	ENSP00000414237	INT2_HUMAN	J3KRH0_HUMAN,J3KMZ7_HUMAN	UPI0000E5A03A	.	deleterious(0)	benign(0.186)	20/25	.	Pfam_domain:PF14750	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCTGAGCGG	.	2	ESCA
TEX2	0	.	GRCh37	17	62290620	62290620	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958G>T	p.Ala320Ser	p.A320S	ENST00000258991	2/12	36	33	3	21	21	0	TEX2,missense_variant,p.Ala320Ser,ENST00000584379,;TEX2,missense_variant,p.Ala320Ser,ENST00000258991,;TEX2,missense_variant,p.Ala320Ser,ENST00000583097,;TEX2,downstream_gene_variant,,ENST00000583922,;TEX2,upstream_gene_variant,,ENST00000583501,;TEX2,downstream_gene_variant,,ENST00000583738,;	A	ENSG00000136478	ENST00000258991	Transcript	missense_variant	1043	958	320	A/S	Gcc/Tcc	.	.	.	-1	TEX2	HGNC	30884	protein_coding	YES	CCDS11658.1	ENSP00000258991	TEX2_HUMAN	Q9NX99_HUMAN,J3QKY0_HUMAN,J3KRY2_HUMAN	UPI00001AE7BC	.	tolerated(0.34)	benign(0.155)	2/12	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAGGCTTTGG	.	2	ESCA
C17orf77	0	.	GRCh37	17	72588749	72588749	+	Silent	SNP	T	T	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564T>A	p.%3D	p.T188T	ENST00000392620	3/3	46	39	6	31	31	0	C17orf77,synonymous_variant,p.%3D,ENST00000328023,;C17orf77,synonymous_variant,p.%3D,ENST00000392620,;CD300LD,upstream_gene_variant,,ENST00000375352,;C17orf77,downstream_gene_variant,,ENST00000524389,;	A	ENSG00000182352	ENST00000392620	Transcript	synonymous_variant	926	564	188	T	acT/acA	.	.	.	1	C17orf77	HGNC	26480	protein_coding	YES	CCDS32721.1	ENSP00000376396	CQ077_HUMAN	E9PQI6_HUMAN	UPI00002001C6	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCACTTTGGG	.	4	ESCA
TP53	0	.	GRCh37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	rs28934574	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	8/11	50	36	13	35	35	0	TP53,missense_variant,p.Arg282Trp,ENST00000420246,;TP53,missense_variant,p.Arg282Trp,ENST00000269305,;TP53,missense_variant,p.Arg150Trp,ENST00000509690,;TP53,missense_variant,p.Arg282Trp,ENST00000359597,;TP53,missense_variant,p.Arg282Trp,ENST00000445888,;TP53,missense_variant,p.Arg282Trp,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1034	844	282	R/W	Cgg/Tgg	CM920678,CM056413,rs28934574,TP53_g.13824C>A,TP53_g.13824C>G,TP53_g.13824C>T,TP53_g.13824del,COSM43813,COSM10704,COSM10992,COSM44918,COSM99925,COSM99934,COSM3378339,COSM3675520,COSM1725698,COSM1636702	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.997)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	likely_benign,pathogenic	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1	25105660,25404506,22536362	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R282W|c.844C>T|49,SITE|p.R282W|c.844C>T|86,SITE|p.R282W|c.844C>T|450,SITE|p.R282W|c.844C>T|58,CODON|p.0?|c.1_1182del1182|6,CODON|p.R282R|c.846G>A|4,CODON|p.R282Q|c.845G>A|5,CODON|p.R282Q|c.845G>A|26,CODON|p.R282L|c.845G>T|3,CODON|p.R282Q|c.845G>A|3,CODON|p.R282P|c.845G>C|17,CODON|p.R282W|c.843_844CC>TT|10,BUFFER|p.E285E|c.855G>A|3,BUFFER|p.E285V|c.854A>T|3,BUFFER|p.E285G|c.854A>G|4,BUFFER|p.E285V|c.854A>T|17,BUFFER|p.E285V|c.854A>T|4,BUFFER|p.E285K|c.853G>A|19,BUFFER|p.E285*|c.853G>T|5,BUFFER|p.E285K|c.853G>A|114,BUFFER|p.E285*|c.853G>T|9,BUFFER|p.E285Q|c.853G>C|4,BUFFER|p.E285*|c.853G>T|25,BUFFER|p.E285K|c.853G>A|5,BUFFER|p.E285K|c.853G>A|9,BUFFER|p.T284T|c.852A>T|3,BUFFER|p.T284A|c.850A>G|3,BUFFER|p.T284P|c.850A>C|8,BUFFER|p.R283fs*62|c.847delC|3,BUFFER|p.R283P|c.848G>C|4,BUFFER|p.R283H|c.848G>A|12,BUFFER|p.R283L|c.848G>T|4,BUFFER|p.R283P|c.848G>C|24,BUFFER|p.R283C|c.847C>T|19,BUFFER|p.R282G|c.844C>G|5,BUFFER|p.R282G|c.844C>G|3,BUFFER|p.R282R|c.844C>A|3,BUFFER|p.R282G|c.844C>G|29,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12,BUFFER|p.D281V|c.842A>T|5,BUFFER|p.D281G|c.842A>G|10,BUFFER|p.D281H|c.841G>C|6,BUFFER|p.D281H|c.841G>C|28,BUFFER|p.D281H|c.841G>C|3,BUFFER|p.D281H|c.841G>C|4,BUFFER|p.D281Y|c.841G>T|7,BUFFER|p.D281N|c.841G>A|7,BUFFER|p.D281N|c.841G>A|3,BUFFER|p.D281Y|c.841G>T|13,BUFFER|p.D281Y|c.841G>T|4,BUFFER|p.D281N|c.841G>A|27,BUFFER|p.R280R|c.840A>G|3,BUFFER|p.R280S|c.840A>T|11,BUFFER|p.R280S|c.840A>C|6,BUFFER|p.R280T|c.839G>C|63,BUFFER|p.R280T|c.839G>C|4,BUFFER|p.R280I|c.839G>T|17,BUFFER|p.R280K|c.839G>A|17,BUFFER|p.R280K|c.839G>A|6,BUFFER|p.R280I|c.839G>T|4,BUFFER|p.R280K|c.839G>A|57,BUFFER|p.R280I|c.839G>T|3,BUFFER|p.R280T|c.839G>C|10,BUFFER|p.R280K|c.839G>A|11,BUFFER|p.R280*|c.838A>T|12,BUFFER|p.R280G|c.838A>G|6,BUFFER|p.R280G|c.838A>G|3,BUFFER|p.R280G|c.838A>G|23,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279E|c.836G>A|4,BUFFER|p.G279E|c.836G>A|34,BUFFER|p.G279V|c.836G>T|3,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278fs*67|c.833delC|3,BUFFER|p.P278F|c.832_833CC>TT|3,BUFFER|p.P278H|c.833C>A|15,BUFFER|p.P278R|c.833C>G|5,BUFFER|p.P278R|c.833C>G|30,BUFFER|p.P278R|c.833C>G|3,BUFFER|p.P278H|c.833C>A|3,BUFFER|p.P278L|c.833C>T|3,BUFFER|p.P278L|c.833C>T|11,BUFFER|p.P278L|c.833C>T|65,BUFFER|p.P278L|c.833C>T|8,BUFFER|p.P278fs*67|c.832delC|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCCGGTCTC	byFrequency|byCluster	5	ESCA
DNAH17	0	.	GRCh37	17	76423160	76423160	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12687G>C	p.Glu4229Asp	p.E4229D	ENST00000389840	78/81	50	41	8	27	27	0	DNAH17,missense_variant,p.Glu4201Asp,ENST00000585328,;DNAH17,missense_variant,p.Glu4229Asp,ENST00000389840,;PGS1,downstream_gene_variant,,ENST00000329897,;AC061992.1,downstream_gene_variant,,ENST00000600087,;PGS1,downstream_gene_variant,,ENST00000262764,;DNAH17,non_coding_transcript_exon_variant,,ENST00000586052,;DNAH17,non_coding_transcript_exon_variant,,ENST00000586850,;DNAH17,non_coding_transcript_exon_variant,,ENST00000592192,;PGS1,downstream_gene_variant,,ENST00000588281,;PGS1,downstream_gene_variant,,ENST00000586880,;DNAH17,missense_variant,p.Glu1407Asp,ENST00000591369,;DNAH17,non_coding_transcript_exon_variant,,ENST00000590227,;PGS1,downstream_gene_variant,,ENST00000589425,;DNAH17,upstream_gene_variant,,ENST00000591647,;PGS1,downstream_gene_variant,,ENST00000589426,;PGS1,downstream_gene_variant,,ENST00000588169,;	G	ENSG00000187775	ENST00000389840	Transcript	missense_variant	12812	12687	4229	E/D	gaG/gaC	.	.	.	-1	DNAH17	HGNC	2946	protein_coding	YES	.	ENSP00000374490	DYH17_HUMAN	.	UPI0001A5EE11	.	.	benign(0.018)	78/81	.	hmmpanther:PTHR10676:SF228,hmmpanther:PTHR10676,Pfam_domain:PF03028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCTCCAG	.	5	ESCA
DDC8	0	.	GRCh37	17	76888114	76888114	+	Nonsense_Mutation	SNP	G	G	A	rs769950393	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472C>T	p.Arg158Ter	p.R158*	ENST00000322630	3/3	37	31	6	24	24	0	DDC8,stop_gained,p.Arg158Ter,ENST00000322630,;TIMP2,intron_variant,,ENST00000536189,;DDC8,intron_variant,,ENST00000586713,;TIMP2,intron_variant,,ENST00000262768,;DDC8,downstream_gene_variant,,ENST00000590267,;DDC8,downstream_gene_variant,,ENST00000587052,;	A	ENSG00000178404	ENST00000322630	Transcript	stop_gained	638	472	158	R/*	Cga/Tga	rs769950393	.	.	-1	DDC8	Uniprot_gn	.	protein_coding	YES	CCDS58603.1	ENSP00000312767	DDC8_HUMAN	.	UPI0000071A46	.	.	.	3/3	.	hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTCGCTGGA	.	4	ESCA
CANT1	0	.	GRCh37	17	76989748	76989748	+	Missense_Mutation	SNP	C	C	G	rs200161867	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1090G>C	p.Glu364Gln	p.E364Q	ENST00000302345	4/4	61	49	12	44	44	0	CANT1,missense_variant,p.Glu364Gln,ENST00000302345,;CANT1,missense_variant,p.Glu364Gln,ENST00000591773,;CANT1,missense_variant,p.Glu364Gln,ENST00000392446,;CANT1,downstream_gene_variant,,ENST00000591625,;CANT1,downstream_gene_variant,,ENST00000586916,;CANT1,downstream_gene_variant,,ENST00000588075,;CANT1,downstream_gene_variant,,ENST00000592033,;CANT1,downstream_gene_variant,,ENST00000590370,;CANT1,downstream_gene_variant,,ENST00000588611,;CANT1,downstream_gene_variant,,ENST00000591811,;CANT1,downstream_gene_variant,,ENST00000591732,;CANT1,downstream_gene_variant,,ENST00000587242,;CANT1,downstream_gene_variant,,ENST00000592887,;CANT1,intron_variant,,ENST00000592228,;CANT1,downstream_gene_variant,,ENST00000588096,;	G	ENSG00000171302	ENST00000302345	Transcript	missense_variant	1585	1090	364	E/Q	Gag/Cag	rs200161867	.	.	-1	CANT1	HGNC	19721	protein_coding	YES	CCDS11760.1	ENSP00000307674	CANT1_HUMAN	K7EQT4_HUMAN,K7EMT2_HUMAN,K7EKT2_HUMAN,K7EIP9_HUMAN	UPI00000734F8	.	deleterious(0.03)	probably_damaging(0.961)	4/4	.	hmmpanther:PTHR13023:SF3,hmmpanther:PTHR13023,Pfam_domain:PF06079,Superfamily_domains:0049295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCGGATT	.	5	ESCA
TMEM105	0	.	GRCh37	17	79288254	79288254	+	Silent	SNP	G	G	C	rs777222122	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9C>G	p.%3D	p.L3L	ENST00000332900	2/3	78	65	12	49	49	0	TMEM105,synonymous_variant,p.%3D,ENST00000574093,;TMEM105,synonymous_variant,p.%3D,ENST00000332900,;	C	ENSG00000185332	ENST00000332900	Transcript	synonymous_variant	559	9	3	L	ctC/ctG	rs777222122	.	.	-1	TMEM105	HGNC	26794	protein_coding	YES	CCDS11781.1	ENSP00000329795	TM105_HUMAN	.	UPI0000071895	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTGAGAAG	.	5	ESCA
GREB1L	0	.	GRCh37	18	19029503	19029503	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1426G>C	p.Glu476Gln	p.E476Q	ENST00000580732	12/33	34	28	6	32	32	0	GREB1L,missense_variant,p.Glu476Gln,ENST00000424526,;GREB1L,missense_variant,p.Glu476Gln,ENST00000400483,;GREB1L,missense_variant,p.Glu476Gln,ENST00000580732,;GREB1L,missense_variant,p.Glu476Gln,ENST00000431264,;GREB1L,intron_variant,,ENST00000269218,;GREB1L,upstream_gene_variant,,ENST00000581327,;SNORD23,downstream_gene_variant,,ENST00000408212,;RP11-296E23.1,intron_variant,,ENST00000584611,;GREB1L,non_coding_transcript_exon_variant,,ENST00000578368,;GREB1L,non_coding_transcript_exon_variant,,ENST00000584446,;GREB1L,upstream_gene_variant,,ENST00000578955,;GREB1L,upstream_gene_variant,,ENST00000580683,;	C	ENSG00000141449	ENST00000580732	Transcript	missense_variant	1807	1426	476	E/Q	Gag/Cag	.	.	.	1	GREB1L	HGNC	31042	protein_coding	YES	CCDS45836.1	ENSP00000464162	GRB1L_HUMAN	.	UPI0001642876	.	deleterious(0)	probably_damaging(0.999)	12/33	.	hmmpanther:PTHR15720:SF12,hmmpanther:PTHR15720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATTTGAGCAA	.	2	ESCA
ESCO1	0	.	GRCh37	18	19109301	19109301	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1003G>C	.	.	ENST00000269214	12/12	16	12	3	20	20	0	ESCO1,3_prime_UTR_variant,,ENST00000269214,;GREB1L,downstream_gene_variant,,ENST00000580732,;ESCO1,3_prime_UTR_variant,,ENST00000383276,;	G	ENSG00000141446	ENST00000269214	Transcript	3_prime_UTR_variant	4464	.	.	.	.	.	.	.	-1	ESCO1	HGNC	24645	protein_coding	YES	CCDS32800.1	ENSP00000269214	ESCO1_HUMAN	.	UPI00001C1FF4	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTATTCTACAT	.	3	ESCA
SETBP1	0	.	GRCh37	18	42532279	42532279	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2974C>T	p.His992Tyr	p.H992Y	ENST00000282030	4/6	60	54	6	56	56	0	SETBP1,missense_variant,p.His992Tyr,ENST00000282030,;	T	ENSG00000152217	ENST00000282030	Transcript	missense_variant	3270	2974	992	H/Y	Cac/Tac	.	.	.	1	SETBP1	HGNC	15573	protein_coding	YES	CCDS11923.2	ENSP00000282030	SETBP_HUMAN	K7ES17_HUMAN	UPI0000201C54	.	deleterious(0.01)	benign(0.426)	4/6	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGATCACTAT	.	4	ESCA
DCC	0	.	GRCh37	18	50976874	50976874	+	Silent	SNP	G	G	A	rs746957136	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3234G>A	p.%3D	p.P1078P	ENST00000442544	23/29	106	89	17	63	63	0	DCC,synonymous_variant,p.%3D,ENST00000581580,;DCC,synonymous_variant,p.%3D,ENST00000442544,;	A	ENSG00000187323	ENST00000442544	Transcript	synonymous_variant	3850	3234	1078	P	ccG/ccA	rs746957136	.	.	1	DCC	HGNC	2701	protein_coding	YES	CCDS11952.1	ENSP00000389140	DCC_HUMAN	J3QQJ6_HUMAN	UPI00001AEDC6	.	.	.	23/29	.	hmmpanther:PTHR10489:SF68,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGCCAAT	byFrequency	5	ESCA
DSEL	0	.	GRCh37	18	65177721	65177721	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*486A>G	.	.	ENST00000310045	2/2	24	20	4	21	21	0	DSEL,3_prime_UTR_variant,,ENST00000310045,;CTD-2541J13.2,intron_variant,,ENST00000583493,;CTD-2541J13.2,intron_variant,,ENST00000581951,;	C	ENSG00000171451	ENST00000310045	Transcript	3_prime_UTR_variant	5629	.	.	.	.	.	.	.	-1	DSEL	HGNC	18144	protein_coding	YES	CCDS11995.1	ENSP00000310565	DSEL_HUMAN	.	UPI00000740A1	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAATTTTCT	.	2	ESCA
ICAM5	0	.	GRCh37	19	10401883	10401883	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218G>A	p.Arg73Gln	p.R73Q	ENST00000221980	2/11	32	29	3	23	23	0	ICAM5,missense_variant,p.Arg73Gln,ENST00000221980,;ICAM5,5_prime_UTR_variant,,ENST00000587398,;ICAM4,downstream_gene_variant,,ENST00000393717,;ICAM4,downstream_gene_variant,,ENST00000380770,;ICAM1,downstream_gene_variant,,ENST00000264832,;ICAM4,downstream_gene_variant,,ENST00000340992,;CTD-2369P2.8,upstream_gene_variant,,ENST00000589379,;ICAM5,non_coding_transcript_exon_variant,,ENST00000586004,;ICAM5,upstream_gene_variant,,ENST00000586480,;ICAM5,downstream_gene_variant,,ENST00000588912,;	A	ENSG00000105376	ENST00000221980	Transcript	missense_variant	281	218	73	R/Q	cGa/cAa	.	.	.	1	ICAM5	HGNC	5348	protein_coding	YES	CCDS12233.1	ENSP00000221980	ICAM5_HUMAN	K7EIL3_HUMAN	UPI000013C7E4	.	deleterious(0.01)	possibly_damaging(0.859)	2/11	.	hmmpanther:PTHR13771:SF6,hmmpanther:PTHR13771,Gene3D:2.60.40.10,Pfam_domain:PF03921,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCCGAAACG	.	2	ESCA
RGL3	0	.	GRCh37	19	11510589	11510589	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1706G>C	p.Arg569Thr	p.R569T	ENST00000393423	16/19	38	32	5	25	25	0	RGL3,missense_variant,p.Arg563Thr,ENST00000380456,;RGL3,missense_variant,p.Arg569Thr,ENST00000393423,;RGL3,upstream_gene_variant,,ENST00000568628,;RGL3,3_prime_UTR_variant,,ENST00000563726,;RGL3,3_prime_UTR_variant,,ENST00000562663,;RGL3,non_coding_transcript_exon_variant,,ENST00000566153,;RGL3,downstream_gene_variant,,ENST00000453604,;RGL3,upstream_gene_variant,,ENST00000566919,;RGL3,downstream_gene_variant,,ENST00000589032,;	G	ENSG00000205517	ENST00000393423	Transcript	missense_variant	1756	1706	569	R/T	aGa/aCa	.	.	.	-1	RGL3	HGNC	30282	protein_coding	YES	CCDS54221.1	ENSP00000377075	RGL3_HUMAN	.	UPI0001A5C4AD	.	tolerated(0.32)	unknown(0)	16/19	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCTGCTT	.	5	ESCA
ZNF700	0	.	GRCh37	19	12059541	12059541	+	Silent	SNP	C	C	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.702C>T	p.%3D	p.F234F	ENST00000254321	4/4	63	58	5	35	35	0	ZNF700,synonymous_variant,p.%3D,ENST00000254321,;ZNF700,synonymous_variant,p.%3D,ENST00000482090,;ZNF763,intron_variant,,ENST00000538752,;ZNF763,intron_variant,,ENST00000590798,;ZNF763,intron_variant,,ENST00000591944,;CTD-2006C1.12,intron_variant,,ENST00000586394,;ZNF763,intron_variant,,ENST00000591441,;ZNF763,upstream_gene_variant,,ENST00000586354,;	T	ENSG00000196757	ENST00000254321	Transcript	synonymous_variant	845	702	234	F	ttC/ttT	COSM1304008	.	.	1	ZNF700	HGNC	25292	protein_coding	YES	CCDS32915.1	ENSP00000254321	ZN700_HUMAN	.	UPI00000713C0	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF24,hmmpanther:PTHR24379,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTTTCAGTTT	.	3	ESCA
CACNA1A	0	.	GRCh37	19	13397432	13397432	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3438C>A	p.%3D	p.V1146V	ENST00000360228	20/47	30	25	5	26	26	0	CACNA1A,synonymous_variant,p.%3D,ENST00000573710,;CACNA1A,synonymous_variant,p.%3D,ENST00000360228,;	T	ENSG00000141837	ENST00000360228	Transcript	synonymous_variant	3438	3438	1146	V	gtC/gtA	.	.	.	-1	CACNA1A	HGNC	1388	protein_coding	YES	CCDS45998.1	ENSP00000353362	CAC1A_HUMAN	Q9UN69_HUMAN,Q9UHM9_HUMAN	UPI0000141565	.	.	.	20/47	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGTGACGAT	.	4	ESCA
DDX39A	0	.	GRCh37	19	14522410	14522410	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337G>T	p.Val113Leu	p.V113L	ENST00000242776	4/11	91	84	6	71	71	0	DDX39A,missense_variant,p.Val113Leu,ENST00000454233,;DDX39A,missense_variant,p.Val113Leu,ENST00000242776,;DDX39A,missense_variant,p.Val113Leu,ENST00000586993,;DDX39A,missense_variant,p.Val124Leu,ENST00000589675,;DDX39A,missense_variant,p.Val101Leu,ENST00000590315,;DDX39A,missense_variant,p.Val113Leu,ENST00000590239,;CD97,downstream_gene_variant,,ENST00000242786,;CD97,downstream_gene_variant,,ENST00000357355,;CD97,downstream_gene_variant,,ENST00000358600,;DDX39A,downstream_gene_variant,,ENST00000592632,;DDX39A,downstream_gene_variant,,ENST00000590696,;DDX39A,downstream_gene_variant,,ENST00000591275,;CTC-548K16.5,upstream_gene_variant,,ENST00000590626,;DDX39A,non_coding_transcript_exon_variant,,ENST00000592927,;DDX39A,downstream_gene_variant,,ENST00000593008,;DDX39A,missense_variant,p.Val113Leu,ENST00000588692,;DDX39A,missense_variant,p.Val113Leu,ENST00000324340,;DDX39A,splice_region_variant,,ENST00000589318,;DDX39A,splice_region_variant,,ENST00000588542,;DDX39A,splice_region_variant,,ENST00000590260,;DDX39A,splice_region_variant,,ENST00000586558,;DDX39A,upstream_gene_variant,,ENST00000592391,;DDX39A,upstream_gene_variant,,ENST00000587730,;DDX39A,upstream_gene_variant,,ENST00000590556,;DDX39A,upstream_gene_variant,,ENST00000593026,;	A	ENSG00000123136	ENST00000242776	Transcript	missense_variant	439	337	113	V/L	Gtg/Ttg	.	.	.	-1	DDX39A	HGNC	17821	protein_coding	YES	CCDS12308.1	ENSP00000242776	DX39A_HUMAN	K7ENP6_HUMAN,K7EN69_HUMAN,K7EL56_HUMAN,K7EIL8_HUMAN	UPI00000713A1	.	deleterious(0.04)	benign(0.048)	4/11	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF212,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTCACCTGGG	.	2	ESCA
NDUFB7	0	.	GRCh37	19	14677011	14677011	+	Silent	SNP	C	C	T	rs760199899	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348G>A	p.%3D	p.E116E	ENST00000215565	3/3	72	67	5	51	51	0	NDUFB7,synonymous_variant,p.%3D,ENST00000215565,;TECR,downstream_gene_variant,,ENST00000596073,;TECR,downstream_gene_variant,,ENST00000594545,;TECR,downstream_gene_variant,,ENST00000601187,;TECR,downstream_gene_variant,,ENST00000436007,;TECR,downstream_gene_variant,,ENST00000598715,;TECR,downstream_gene_variant,,ENST00000600083,;TECR,downstream_gene_variant,,ENST00000215567,;TECR,downstream_gene_variant,,ENST00000598298,;TECR,downstream_gene_variant,,ENST00000596164,;NDUFB7,3_prime_UTR_variant,,ENST00000593353,;TECR,downstream_gene_variant,,ENST00000601461,;TECR,downstream_gene_variant,,ENST00000598918,;TECR,downstream_gene_variant,,ENST00000594958,;TECR,downstream_gene_variant,,ENST00000598408,;TECR,downstream_gene_variant,,ENST00000600076,;TECR,downstream_gene_variant,,ENST00000600395,;TECR,downstream_gene_variant,,ENST00000599101,;TECR,downstream_gene_variant,,ENST00000593637,;TECR,downstream_gene_variant,,ENST00000601350,;TECR,downstream_gene_variant,,ENST00000598333,;TECR,downstream_gene_variant,,ENST00000593775,;TECR,downstream_gene_variant,,ENST00000597607,;TECR,downstream_gene_variant,,ENST00000596953,;TECR,downstream_gene_variant,,ENST00000601652,;TECR,downstream_gene_variant,,ENST00000598987,;TECR,downstream_gene_variant,,ENST00000594807,;	T	ENSG00000099795	ENST00000215565	Transcript	synonymous_variant	410	348	116	E	gaG/gaA	rs760199899	.	.	-1	NDUFB7	HGNC	7702	protein_coding	YES	CCDS12314.1	ENSP00000215565	NDUB7_HUMAN	.	UPI000013C68C	.	.	.	3/3	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR20900,hmmpanther:PTHR20900:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTTCTCCCG	byFrequency	2	ESCA
EMR2	0	.	GRCh37	19	14867093	14867093	+	Silent	SNP	C	C	G	rs148152299	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1149G>C	p.%3D	p.V383V	ENST00000315576	12/21	70	60	10	21	21	0	EMR2,synonymous_variant,p.%3D,ENST00000392964,;EMR2,synonymous_variant,p.%3D,ENST00000594076,;EMR2,synonymous_variant,p.%3D,ENST00000594294,;EMR2,synonymous_variant,p.%3D,ENST00000601345,;EMR2,synonymous_variant,p.%3D,ENST00000346057,;EMR2,synonymous_variant,p.%3D,ENST00000595839,;EMR2,synonymous_variant,p.%3D,ENST00000353005,;EMR2,synonymous_variant,p.%3D,ENST00000353876,;EMR2,synonymous_variant,p.%3D,ENST00000315576,;EMR2,synonymous_variant,p.%3D,ENST00000392965,;EMR2,synonymous_variant,p.%3D,ENST00000392967,;EMR2,synonymous_variant,p.%3D,ENST00000596991,;EMR2,synonymous_variant,p.%3D,ENST00000392962,;EMR2,synonymous_variant,p.%3D,ENST00000595208,;EMR2,non_coding_transcript_exon_variant,,ENST00000360222,;	G	ENSG00000127507	ENST00000315576	Transcript	synonymous_variant	1601	1149	383	V	gtG/gtC	rs148152299	.	.	-1	EMR2	HGNC	3337	protein_coding	YES	CCDS32935.1	ENSP00000319883	EMR2_HUMAN	.	UPI000016393A	.	.	.	12/21	.	hmmpanther:PTHR12011:SF179,hmmpanther:PTHR12011	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCATCACTGC	byCluster	5	ESCA
AKAP8	0	.	GRCh37	19	15483682	15483682	+	Missense_Mutation	SNP	G	G	A	rs779146472	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841C>T	p.Arg281Trp	p.R281W	ENST00000269701	5/14	37	34	3	27	27	0	AKAP8,missense_variant,p.Arg281Trp,ENST00000269701,;AKAP8,missense_variant,p.Arg95Trp,ENST00000598597,;AKAP8,3_prime_UTR_variant,,ENST00000599883,;AKAP8,non_coding_transcript_exon_variant,,ENST00000537303,;AKAP8,downstream_gene_variant,,ENST00000595416,;	A	ENSG00000105127	ENST00000269701	Transcript	missense_variant	902	841	281	R/W	Cgg/Tgg	rs779146472	.	.	-1	AKAP8	HGNC	378	protein_coding	YES	CCDS12329.1	ENSP00000269701	AKAP8_HUMAN	Q9UG73_HUMAN	UPI000012575C	.	deleterious(0.01)	benign(0.064)	5/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12190:SF5,hmmpanther:PTHR12190	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCCGAGGCT	.	2	ESCA
LINC00905	0	.	GRCh37	19	16146762	16146762	+	RNA	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1025G>C	.	.	ENST00000588117	4/5	39	33	5	25	25	0	LINC00905,non_coding_transcript_exon_variant,,ENST00000588117,;LINC00905,non_coding_transcript_exon_variant,,ENST00000588838,;LINC00905,downstream_gene_variant,,ENST00000602744,;LINC00905,downstream_gene_variant,,ENST00000602372,;LINC00905,downstream_gene_variant,,ENST00000397365,;LINC00905,downstream_gene_variant,,ENST00000602814,;LINC00905,non_coding_transcript_exon_variant,,ENST00000589071,;SNX33P1,non_coding_transcript_exon_variant,,ENST00000592116,;	C	ENSG00000167459	ENST00000588117	Transcript	non_coding_transcript_exon_variant	1025	.	.	.	.	.	.	.	1	LINC00905	HGNC	26334	lincRNA	YES	.	.	.	.	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTTGAGGTT	.	5	ESCA
UPF1	0	.	GRCh37	19	18972827	18972827	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2466G>A	p.%3D	p.E822E	ENST00000262803	18/24	44	36	8	22	22	0	UPF1,synonymous_variant,p.%3D,ENST00000599848,;UPF1,synonymous_variant,p.%3D,ENST00000262803,;UPF1,non_coding_transcript_exon_variant,,ENST00000596842,;UPF1,upstream_gene_variant,,ENST00000600689,;	A	ENSG00000005007	ENST00000262803	Transcript	synonymous_variant	2738	2466	822	E	gaG/gaA	.	.	.	1	UPF1	HGNC	9962	protein_coding	YES	CCDS12386.1	ENSP00000262803	RENT1_HUMAN	B3KY55_HUMAN	UPI0000001C89	.	.	.	18/24	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF340,Gene3D:3.40.50.300,Pfam_domain:PF13087,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAGATCGC	.	5	ESCA
UPF1	0	.	GRCh37	19	18972858	18972858	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2497G>A	p.Glu833Lys	p.E833K	ENST00000262803	18/24	47	40	7	21	21	0	UPF1,missense_variant,p.Glu844Lys,ENST00000599848,;UPF1,missense_variant,p.Glu833Lys,ENST00000262803,;UPF1,non_coding_transcript_exon_variant,,ENST00000596842,;UPF1,upstream_gene_variant,,ENST00000600689,;	A	ENSG00000005007	ENST00000262803	Transcript	missense_variant	2769	2497	833	E/K	Gag/Aag	.	.	.	1	UPF1	HGNC	9962	protein_coding	YES	CCDS12386.1	ENSP00000262803	RENT1_HUMAN	B3KY55_HUMAN	UPI0000001C89	.	deleterious(0)	probably_damaging(0.955)	18/24	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF340,Gene3D:3.40.50.300,Pfam_domain:PF13087,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACGCGAGAAG	.	4	ESCA
ZNF737	0	.	GRCh37	19	20735329	20735329	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.178A>G	p.Lys60Glu	p.K60E	ENST00000427401	3/4	79	71	7	43	43	0	ZNF737,missense_variant,p.Lys60Glu,ENST00000596797,;ZNF737,missense_variant,p.Lys60Glu,ENST00000427401,;ZNF737,5_prime_UTR_variant,,ENST00000594419,;CTC-513N18.7,downstream_gene_variant,,ENST00000595094,;ZNF737,3_prime_UTR_variant,,ENST00000597940,;	C	ENSG00000237440	ENST00000427401	Transcript	missense_variant	273	178	60	K/E	Aaa/Gaa	.	.	.	-1	ZNF737	HGNC	32468	protein_coding	YES	CCDS54238.1	ENSP00000395733	ZN737_HUMAN	M0R1D1_HUMAN	UPI0000198506	.	deleterious(0.03)	benign(0.008)	3/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24384:SF93,hmmpanther:PTHR24384,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TTTTTTTCCTT	.	3	ESCA
PLEKHF1	0	.	GRCh37	19	30156563	30156563	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-17+151C>G	.	.	ENST00000436066	.	34	30	3	36	36	0	PLEKHF1,5_prime_UTR_variant,,ENST00000588833,;PLEKHF1,5_prime_UTR_variant,,ENST00000592810,;PLEKHF1,intron_variant,,ENST00000436066,;PLEKHF1,upstream_gene_variant,,ENST00000586888,;	G	ENSG00000166289	ENST00000436066	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PLEKHF1	HGNC	20764	protein_coding	YES	CCDS12417.1	ENSP00000389787	PKHF1_HUMAN	K7ELB8_HUMAN,K7EIX0_HUMAN,B4DWN9_HUMAN	UPI000006E165	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TGACTCCAGCC	.	2	ESCA
COX6B1	0	.	GRCh37	19	36149574	36149574	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*25G>C	.	.	ENST00000246554	4/4	37	32	5	23	23	0	COX6B1,3_prime_UTR_variant,,ENST00000392201,;COX6B1,3_prime_UTR_variant,,ENST00000246554,;COX6B1,3_prime_UTR_variant,,ENST00000590618,;COX6B1,3_prime_UTR_variant,,ENST00000592141,;	C	ENSG00000126267	ENST00000246554	Transcript	3_prime_UTR_variant	478	.	.	.	.	.	.	.	1	COX6B1	HGNC	2280	protein_coding	YES	CCDS12469.1	ENSP00000246554	CX6B1_HUMAN	.	UPI00000527BE	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCTGTCCTC	.	4	ESCA
ZNF585A	0	.	GRCh37	19	37641671	37641671	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*820C>T	.	.	ENST00000292841	6/6	44	39	5	31	31	0	ZNF585A,3_prime_UTR_variant,,ENST00000292841,;ZNF585A,3_prime_UTR_variant,,ENST00000356958,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF585A,downstream_gene_variant,,ENST00000355533,;ZNF585A,downstream_gene_variant,,ENST00000392157,;ZNF585A,intron_variant,,ENST00000588723,;ZNF585A,intron_variant,,ENST00000587817,;	A	ENSG00000196967	ENST00000292841	Transcript	3_prime_UTR_variant	3463	.	.	.	.	.	.	.	-1	ZNF585A	HGNC	26305	protein_coding	YES	CCDS12499.1	ENSP00000292841	Z585A_HUMAN	.	UPI000007213F	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CAACTGAGTTG	.	3	ESCA
TGFB1	0	.	GRCh37	19	41848072	41848072	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712+3G>T	.	.	ENST00000221930	.	55	47	8	44	44	0	TGFB1,splice_region_variant,,ENST00000221930,;TGFB1,upstream_gene_variant,,ENST00000598758,;TGFB1,splice_region_variant,,ENST00000600196,;TGFB1,non_coding_transcript_exon_variant,,ENST00000597453,;	A	ENSG00000105329	ENST00000221930	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	TGFB1	HGNC	11766	protein_coding	YES	CCDS33031.1	ENSP00000221930	TGFB1_HUMAN	Q7Z488_HUMAN,Q7Z487_HUMAN,Q5PY19_HUMAN	UPI000013C7E1	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE|VARSCANS	GGCCTCACCGT	.	3	ESCA
PHLDB3	0	.	GRCh37	19	43983562	43983562	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1669G>C	p.Asp557His	p.D557H	ENST00000292140	14/16	79	71	8	54	54	0	PHLDB3,missense_variant,p.Asp557His,ENST00000292140,;PHLDB3,downstream_gene_variant,,ENST00000600660,;PHLDB3,downstream_gene_variant,,ENST00000596141,;PHLDB3,non_coding_transcript_exon_variant,,ENST00000595498,;PHLDB3,downstream_gene_variant,,ENST00000598849,;	G	ENSG00000176531	ENST00000292140	Transcript	missense_variant	2030	1669	557	D/H	Gac/Cac	.	.	.	-1	PHLDB3	HGNC	30499	protein_coding	YES	CCDS12621.2	ENSP00000292140	PHLB3_HUMAN	M0R3I7_HUMAN,M0R038_HUMAN	UPI00015C725F	.	deleterious(0)	probably_damaging(1)	14/16	.	Superfamily_domains:SSF50729,SMART_domains:SM00233,Gene3D:2.30.29.30,Pfam_domain:PF00169,hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF15,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGGTCAAAGC	.	4	ESCA
CLPTM1	0	.	GRCh37	19	45476365	45476365	+	Silent	SNP	C	C	A	rs748937869	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207C>A	p.%3D	p.I69I	ENST00000337392	3/14	49	39	9	34	34	0	CLPTM1,synonymous_variant,p.%3D,ENST00000591304,;CLPTM1,synonymous_variant,p.%3D,ENST00000541297,;CLPTM1,synonymous_variant,p.%3D,ENST00000337392,;CLPTM1,5_prime_UTR_variant,,ENST00000546079,;CLPTM1,5_prime_UTR_variant,,ENST00000585961,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000588855,;CLPTM1,upstream_gene_variant,,ENST00000587537,;	A	ENSG00000104853	ENST00000337392	Transcript	synonymous_variant	357	207	69	I	atC/atA	rs748937869	.	.	1	CLPTM1	HGNC	2087	protein_coding	YES	CCDS12651.1	ENSP00000336994	CLPT1_HUMAN	K7EKQ7_HUMAN,B4DDS3_HUMAN	UPI0000072CBA	.	.	.	3/14	.	hmmpanther:PTHR21347,hmmpanther:PTHR21347:SF0,Pfam_domain:PF05602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCAGCAG	.	5	ESCA
AKT1S1	0	.	GRCh37	19	50372347	50372347	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*827C>T	.	.	ENST00000391835	5/5	16	9	7	15	15	0	AKT1S1,3_prime_UTR_variant,,ENST00000391835,;AKT1S1,3_prime_UTR_variant,,ENST00000391832,;AKT1S1,3_prime_UTR_variant,,ENST00000344175,;AKT1S1,3_prime_UTR_variant,,ENST00000391833,;AKT1S1,3_prime_UTR_variant,,ENST00000391831,;AKT1S1,3_prime_UTR_variant,,ENST00000391834,;PNKP,upstream_gene_variant,,ENST00000322344,;PNKP,upstream_gene_variant,,ENST00000600910,;PNKP,upstream_gene_variant,,ENST00000596014,;AKT1S1,downstream_gene_variant,,ENST00000391830,;PNKP,upstream_gene_variant,,ENST00000596726,;AKT1S1,downstream_gene_variant,,ENST00000599525,;PNKP,upstream_gene_variant,,ENST00000599543,;PNKP,upstream_gene_variant,,ENST00000600573,;PNKP,upstream_gene_variant,,ENST00000595792,;PNKP,upstream_gene_variant,,ENST00000594661,;PNKP,upstream_gene_variant,,ENST00000593946,;PNKP,upstream_gene_variant,,ENST00000598020,;	A	ENSG00000204673	ENST00000391835	Transcript	3_prime_UTR_variant	3031	.	.	.	.	.	.	.	-1	AKT1S1	HGNC	28426	protein_coding	YES	CCDS59410.1	ENSP00000375711	AKTS1_HUMAN	M0R2V8_HUMAN,H9KV91_HUMAN	UPI00004A2415	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGATCCC	.	5	ESCA
MYH14	0	.	GRCh37	19	50720965	50720965	+	Missense_Mutation	SNP	C	C	T	rs759687206	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499C>T	p.Arg167Cys	p.R167C	ENST00000601313	3/43	39	35	3	26	26	0	MYH14,missense_variant,p.Arg167Cys,ENST00000440075,;MYH14,missense_variant,p.Arg167Cys,ENST00000601313,;MYH14,missense_variant,p.Arg167Cys,ENST00000376970,;MYH14,missense_variant,p.Arg167Cys,ENST00000596571,;MYH14,missense_variant,p.Arg167Cys,ENST00000425460,;MYH14,missense_variant,p.Arg167Cys,ENST00000599920,;MYH14,missense_variant,p.Arg167Cys,ENST00000598205,;MYH14,missense_variant,p.Arg167Cys,ENST00000262269,;	T	ENSG00000105357	ENST00000601313	Transcript	missense_variant	529	499	167	R/C	Cgc/Tgc	rs759687206	.	.	1	MYH14	HGNC	23212	protein_coding	YES	CCDS54295.1	ENSP00000470298	MYH14_HUMAN	A1L2Z2_HUMAN	UPI0001641C2F	.	deleterious(0)	probably_damaging(1)	3/43	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF318,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|VARSCANS	AGAAGCGCCAC	.	2	ESCA
CTD-2583A14.10	0	.	GRCh37	19	58361636	58361636	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34-5836G>C	.	.	ENST00000598031	.	39	34	5	20	20	0	CTD-2583A14.10,intron_variant,,ENST00000598031,;ZNF587,intron_variant,,ENST00000423137,;CTD-2583A14.10,intron_variant,,ENST00000597134,;ZNF587B,intron_variant,,ENST00000316462,;CTD-2583A14.10,intron_variant,,ENST00000593873,;CTD-2583A14.10,intron_variant,,ENST00000596498,;CTD-2583A14.10,intron_variant,,ENST00000603271,;ZNF587,intron_variant,,ENST00000339656,;ZNF814,downstream_gene_variant,,ENST00000597342,;ZNF814,downstream_gene_variant,,ENST00000596604,;ZNF587B,downstream_gene_variant,,ENST00000442832,;ZNF814,downstream_gene_variant,,ENST00000597832,;ZNF814,non_coding_transcript_exon_variant,,ENST00000597652,;ZNF587,intron_variant,,ENST00000484707,;CTD-2583A14.10,intron_variant,,ENST00000604231,;ZNF814,downstream_gene_variant,,ENST00000595894,;	C	ENSG00000268750	ENST00000598031	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CTD-2583A14.10	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000471077	.	M0R178_HUMAN,M0R0V5_HUMAN,M0R0M6_HUMAN,M0R082_HUMAN,M0QXF5_HUMAN	UPI0003335060	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	ATGAAGACTGG	.	2	ESCA
ZNF497	0	.	GRCh37	19	58869445	58869445	+	Intron	SNP	G	G	A	rs541377091	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-15+410C>T	.	.	ENST00000311044	.	31	27	4	16	16	0	ZNF497,5_prime_UTR_variant,,ENST00000595763,;ZNF497,intron_variant,,ENST00000311044,;ZNF497,intron_variant,,ENST00000425453,;A1BG,upstream_gene_variant,,ENST00000600966,;A1BG,upstream_gene_variant,,ENST00000263100,;CTD-2619J13.9,non_coding_transcript_exon_variant,,ENST00000599952,;A1BG-AS1,downstream_gene_variant,,ENST00000593374,;A1BG-AS1,downstream_gene_variant,,ENST00000594950,;A1BG-AS1,downstream_gene_variant,,ENST00000600379,;A1BG-AS1,downstream_gene_variant,,ENST00000600686,;A1BG-AS1,downstream_gene_variant,,ENST00000595302,;CTD-2619J13.3,upstream_gene_variant,,ENST00000599889,;A1BG-AS1,downstream_gene_variant,,ENST00000593960,;A1BG-AS1,downstream_gene_variant,,ENST00000599728,;CTD-2619J13.8,non_coding_transcript_exon_variant,,ENST00000599109,;CTD-2619J13.8,upstream_gene_variant,,ENST00000600123,;CTD-2619J13.8,upstream_gene_variant,,ENST00000596636,;A1BG,upstream_gene_variant,,ENST00000595014,;	A	ENSG00000174586	ENST00000311044	Transcript	intron_variant	.	.	.	.	.	rs541377091	.	.	-1	ZNF497	HGNC	23714	protein_coding	YES	CCDS12977.1	ENSP00000311183	ZN497_HUMAN	.	UPI00001D819C	.	.	.	.	2/2	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GGCTGGAGGAC	by1000G	3	ESCA
ALKBH7	0	.	GRCh37	19	6375015	6375015	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*31G>C	.	.	ENST00000245812	4/4	57	53	4	41	41	0	ALKBH7,3_prime_UTR_variant,,ENST00000245812,;ALKBH7,3_prime_UTR_variant,,ENST00000599849,;ALKBH7,3_prime_UTR_variant,,ENST00000596657,;GTF2F1,downstream_gene_variant,,ENST00000593678,;PSPN,downstream_gene_variant,,ENST00000245810,;PSPN,downstream_gene_variant,,ENST00000597721,;GTF2F1,downstream_gene_variant,,ENST00000429701,;GTF2F1,downstream_gene_variant,,ENST00000394456,;	C	ENSG00000125652	ENST00000245812	Transcript	3_prime_UTR_variant	1085	.	.	.	.	.	.	.	1	ALKBH7	HGNC	21306	protein_coding	YES	CCDS12163.1	ENSP00000245812	ALKB7_HUMAN	M0QZH2_HUMAN	UPI0000039ED9	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTGTGAATAA	.	2	ESCA
PTBP1	0	.	GRCh37	19	806462	806462	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1025C>T	p.Ala342Val	p.A342V	ENST00000356948	10/15	62	55	7	49	49	0	PTBP1,missense_variant,p.Ala316Val,ENST00000349038,;PTBP1,missense_variant,p.Ala167Val,ENST00000585956,;PTBP1,missense_variant,p.Ala335Val,ENST00000394601,;PTBP1,missense_variant,p.Ala342Val,ENST00000356948,;PTBP1,intron_variant,,ENST00000350092,;PTBP1,downstream_gene_variant,,ENST00000589575,;PTBP1,downstream_gene_variant,,ENST00000586481,;PTBP1,downstream_gene_variant,,ENST00000585535,;PTBP1,downstream_gene_variant,,ENST00000587094,;MIR4745,downstream_gene_variant,,ENST00000577608,;PTBP1,non_coding_transcript_exon_variant,,ENST00000589883,;PTBP1,non_coding_transcript_exon_variant,,ENST00000586944,;PTBP1,non_coding_transcript_exon_variant,,ENST00000587136,;PTBP1,intron_variant,,ENST00000587191,;PTBP1,upstream_gene_variant,,ENST00000585932,;PTBP1,downstream_gene_variant,,ENST00000589569,;PTBP1,downstream_gene_variant,,ENST00000592804,;PTBP1,upstream_gene_variant,,ENST00000589770,;PTBP1,downstream_gene_variant,,ENST00000592113,;PTBP1,upstream_gene_variant,,ENST00000585856,;PTBP1,downstream_gene_variant,,ENST00000590887,;	T	ENSG00000011304	ENST00000356948	Transcript	missense_variant	1448	1025	342	A/V	gCg/gTg	.	.	.	1	PTBP1	HGNC	9583	protein_coding	YES	CCDS42456.1	ENSP00000349428	PTBP1_HUMAN	.	UPI00000720B7	.	tolerated(0.27)	possibly_damaging(0.506)	10/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11546,hmmpanther:PTHR11546:SF17,TIGRFAM_domain:TIGR01649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCGGCGGCGG	.	4	ESCA
MUC16	0	.	GRCh37	19	9084625	9084625	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7190C>G	p.Ser2397Ter	p.S2397*	ENST00000397910	1/84	91	80	10	50	50	0	MUC16,stop_gained,p.Ser2397Ter,ENST00000397910,;	C	ENSG00000181143	ENST00000397910	Transcript	stop_gained	7394	7190	2397	S/*	tCa/tGa	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	1/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTGAGATG	.	4	ESCA
HIAT1	0	.	GRCh37	1	100548803	100548803	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1038C>T	.	.	ENST00000370152	12/12	57	52	5	56	56	0	HIAT1,3_prime_UTR_variant,,ENST00000370152,;SASS6,downstream_gene_variant,,ENST00000535161,;SASS6,downstream_gene_variant,,ENST00000287482,;RP4-714D9.2,intron_variant,,ENST00000432294,;SASS6,downstream_gene_variant,,ENST00000462159,;	T	ENSG00000156875	ENST00000370152	Transcript	3_prime_UTR_variant	2647	.	.	.	.	.	.	.	1	HIAT1	HGNC	23363	protein_coding	YES	CCDS763.1	ENSP00000359171	HIAT1_HUMAN	.	UPI0000049F99	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTTTCATCTT	.	3	ESCA
MAD2L2	0	.	GRCh37	1	11735184	11735184	+	Silent	SNP	G	G	A	rs747572072	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549C>T	p.%3D	p.D183D	ENST00000235310	10/11	34	31	3	35	35	0	MAD2L2,synonymous_variant,p.%3D,ENST00000376669,;MAD2L2,synonymous_variant,p.%3D,ENST00000376692,;MAD2L2,synonymous_variant,p.%3D,ENST00000235310,;MAD2L2,synonymous_variant,p.%3D,ENST00000376672,;MAD2L2,synonymous_variant,p.%3D,ENST00000376667,;MAD2L2,downstream_gene_variant,,ENST00000456915,;FBXO6,downstream_gene_variant,,ENST00000449067,;FBXO6,downstream_gene_variant,,ENST00000376753,;MAD2L2,downstream_gene_variant,,ENST00000445656,;MAD2L2,downstream_gene_variant,,ENST00000376655,;FBXO6,downstream_gene_variant,,ENST00000474239,;MAD2L2,downstream_gene_variant,,ENST00000376664,;	A	ENSG00000116670	ENST00000235310	Transcript	synonymous_variant	1478	549	183	D	gaC/gaT	rs747572072	.	.	-1	MAD2L2	HGNC	6764	protein_coding	YES	CCDS134.1	ENSP00000235310	MD2L2_HUMAN	B1AK45_HUMAN	UPI0000000DF1	.	.	.	10/11	.	PROSITE_profiles:PS50815,hmmpanther:PTHR11842:SF10,hmmpanther:PTHR11842,Gene3D:1go4B00,Superfamily_domains:0040144	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGGGGTCATG	byFrequency	2	ESCA
SPAG17	0	.	GRCh37	1	118596628	118596628	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2811C>G	p.%3D	p.L937L	ENST00000336338	20/49	89	84	5	52	52	0	SPAG17,synonymous_variant,p.%3D,ENST00000336338,;SPAG17,downstream_gene_variant,,ENST00000477444,;	C	ENSG00000155761	ENST00000336338	Transcript	synonymous_variant	2877	2811	937	L	ctC/ctG	.	.	.	-1	SPAG17	HGNC	26620	protein_coding	YES	CCDS899.1	ENSP00000337804	SPG17_HUMAN	A7LBF9_HUMAN	UPI00001601FD	.	.	.	20/49	.	hmmpanther:PTHR21963	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCTTGAGAGA	.	2	ESCA
NOTCH2	0	.	GRCh37	1	120484162	120484162	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2968G>A	p.Glu990Lys	p.E990K	ENST00000256646	18/34	105	95	9	61	61	0	NOTCH2,missense_variant,p.Glu990Lys,ENST00000256646,;NOTCH2,upstream_gene_variant,,ENST00000478864,;	T	ENSG00000134250	ENST00000256646	Transcript	missense_variant	3188	2968	990	E/K	Gag/Aag	.	.	.	-1	NOTCH2	HGNC	7882	protein_coding	YES	CCDS908.1	ENSP00000256646	NOTC2_HUMAN	Q9UFD5_HUMAN,Q13560_HUMAN	UPI000013CF1D	.	deleterious(0)	probably_damaging(0.993)	18/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF4,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,SMART_domains:SM00179,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCACTCATTGA	.	3	ESCA
TNFRSF1B	0	.	GRCh37	1	12251047	12251047	+	Missense_Mutation	SNP	C	C	T	rs776727613	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212C>T	p.Ser71Leu	p.S71L	ENST00000376259	3/10	58	52	6	30	30	0	TNFRSF1B,missense_variant,p.Ser71Leu,ENST00000536782,;TNFRSF1B,missense_variant,p.Ser71Leu,ENST00000376259,;MIR4632,upstream_gene_variant,,ENST00000584158,;TNFRSF1B,non_coding_transcript_exon_variant,,ENST00000492361,;TNFRSF1B,upstream_gene_variant,,ENST00000489921,;	T	ENSG00000028137	ENST00000376259	Transcript	missense_variant	301	212	71	S/L	tCg/tTg	rs776727613	.	.	1	TNFRSF1B	HGNC	11917	protein_coding	YES	CCDS145.1	ENSP00000365435	TNR1B_HUMAN	Q9UIH2_HUMAN,Q9UIG9_HUMAN,Q6LBF2_HUMAN	UPI000002FAE1	.	tolerated(0.08)	benign(0.361)	3/10	.	PROSITE_profiles:PS50050,hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF108,PROSITE_patterns:PS00652,Pfam_domain:PF00020,Gene3D:2.10.50.10,SMART_domains:SM00208,Superfamily_domains:SSF57586	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTCGGACA	byFrequency	2	ESCA
VPS13D	0	.	GRCh37	1	12304375	12304375	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.248C>T	p.Ser83Phe	p.S83F	ENST00000358136	4/70	59	47	11	25	25	0	VPS13D,missense_variant,p.Ser83Phe,ENST00000358136,;VPS13D,missense_variant,p.Ser83Phe,ENST00000356315,;VPS13D,upstream_gene_variant,,ENST00000476169,;	T	ENSG00000048707	ENST00000358136	Transcript	missense_variant	378	248	83	S/F	tCc/tTc	.	.	.	1	VPS13D	HGNC	23595	protein_coding	YES	CCDS30588.1	ENSP00000350854	.	M0QXS2_HUMAN,J3KP14_HUMAN	UPI0000451CA9	.	.	probably_damaging(0.983)	4/70	.	hmmpanther:PTHR16166:SF93,hmmpanther:PTHR16166,Pfam_domain:PF12624	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCCAGCC	.	5	ESCA
APH1A	0	.	GRCh37	1	150238645	150238645	+	Intron	SNP	G	G	A	rs199517322	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734-51C>T	.	.	ENST00000369109	.	39	34	5	38	38	0	APH1A,3_prime_UTR_variant,,ENST00000360244,;APH1A,intron_variant,,ENST00000414276,;APH1A,intron_variant,,ENST00000369109,;APH1A,downstream_gene_variant,,ENST00000236017,;CA14,downstream_gene_variant,,ENST00000607082,;C1orf54,upstream_gene_variant,,ENST00000369102,;CA14,downstream_gene_variant,,ENST00000369111,;snoU13,downstream_gene_variant,,ENST00000458929,;APH1A,downstream_gene_variant,,ENST00000493092,;APH1A,downstream_gene_variant,,ENST00000461320,;APH1A,downstream_gene_variant,,ENST00000486308,;APH1A,downstream_gene_variant,,ENST00000476538,;APH1A,downstream_gene_variant,,ENST00000486720,;CA14,downstream_gene_variant,,ENST00000607751,;CA14,downstream_gene_variant,,ENST00000607652,;CA14,downstream_gene_variant,,ENST00000483993,;	A	ENSG00000117362	ENST00000369109	Transcript	intron_variant	.	.	.	.	.	rs199517322	.	.	-1	APH1A	HGNC	29509	protein_coding	YES	CCDS41390.1	ENSP00000358105	APH1A_HUMAN	.	UPI0000073CA3	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACTGACACA	byFrequency|byCluster	4	ESCA
SETDB1	0	.	GRCh37	1	150923931	150923931	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2304G>A	p.%3D	p.K768K	ENST00000271640	14/22	103	89	14	59	59	0	SETDB1,synonymous_variant,p.%3D,ENST00000498193,;SETDB1,synonymous_variant,p.%3D,ENST00000271640,;SETDB1,synonymous_variant,p.%3D,ENST00000368969,;SETDB1,downstream_gene_variant,,ENST00000534805,;SETDB1,intron_variant,,ENST00000459773,;	A	ENSG00000143379	ENST00000271640	Transcript	synonymous_variant	2494	2304	768	K	aaG/aaA	.	.	.	1	SETDB1	HGNC	10761	protein_coding	YES	CCDS44217.1	ENSP00000271640	SETB1_HUMAN	E9PS59_HUMAN,B0QZE6_HUMAN	UPI0000135897	.	.	.	14/22	.	PROSITE_profiles:PS50867,PROSITE_profiles:PS51573,hmmpanther:PTHR22884:SF323,hmmpanther:PTHR22884,Pfam_domain:PF05033,Gene3D:2.170.270.10,SMART_domains:SM00468,Superfamily_domains:SSF82199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACAAGAGACT	.	4	ESCA
SNAPIN	0	.	GRCh37	1	153631615	153631615	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.145G>C	p.Glu49Gln	p.E49Q	ENST00000368685	2/4	81	71	9	47	47	0	SNAPIN,missense_variant,p.Glu49Gln,ENST00000368685,;ILF2,downstream_gene_variant,,ENST00000361891,;SNAPIN,non_coding_transcript_exon_variant,,ENST00000478558,;SNAPIN,non_coding_transcript_exon_variant,,ENST00000474959,;SNAPIN,intron_variant,,ENST00000462880,;ILF2,downstream_gene_variant,,ENST00000480213,;	C	ENSG00000143553	ENST00000368685	Transcript	missense_variant	235	145	49	E/Q	Gag/Cag	.	.	.	1	SNAPIN	HGNC	17145	protein_coding	YES	CCDS1049.1	ENSP00000357674	SNAPN_HUMAN	.	UPI000003E7DC	.	tolerated(0.57)	benign(0.013)	2/4	.	hmmpanther:PTHR31305,Pfam_domain:PF14712,PIRSF_domain:PIRSF037631	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGAGAGAGC	.	4	ESCA
LMNA	0	.	GRCh37	1	156107633	156107633	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1698+99C>A	.	.	ENST00000368300	.	19	15	3	16	16	0	LMNA,3_prime_UTR_variant,,ENST00000392353,;LMNA,3_prime_UTR_variant,,ENST00000368301,;LMNA,3_prime_UTR_variant,,ENST00000368297,;LMNA,3_prime_UTR_variant,,ENST00000361308,;LMNA,intron_variant,,ENST00000368299,;LMNA,intron_variant,,ENST00000347559,;LMNA,intron_variant,,ENST00000473598,;LMNA,intron_variant,,ENST00000508500,;LMNA,intron_variant,,ENST00000448611,;LMNA,intron_variant,,ENST00000368300,;LMNA,downstream_gene_variant,,ENST00000504687,;LMNA,non_coding_transcript_exon_variant,,ENST00000496738,;LMNA,downstream_gene_variant,,ENST00000502357,;LMNA,downstream_gene_variant,,ENST00000459904,;LMNA,downstream_gene_variant,,ENST00000502751,;LMNA,downstream_gene_variant,,ENST00000470199,;LMNA,downstream_gene_variant,,ENST00000469565,;LMNA,non_coding_transcript_exon_variant,,ENST00000498722,;LMNA,intron_variant,,ENST00000506981,;LMNA,downstream_gene_variant,,ENST00000515824,;LMNA,downstream_gene_variant,,ENST00000515459,;LMNA,downstream_gene_variant,,ENST00000368298,;	A	ENSG00000160789	ENST00000368300	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LMNA	HGNC	6636	protein_coding	YES	CCDS1129.1	ENSP00000357283	LMNA_HUMAN	Q5I6Y5_HUMAN	UPI000012E20D	.	.	.	.	10/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTTCATTAA	.	4	ESCA
SPTA1	0	.	GRCh37	1	158592856	158592856	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6037C>G	p.Leu2013Val	p.L2013V	ENST00000368147	43/52	35	32	3	35	35	0	SPTA1,missense_variant,p.Leu2013Val,ENST00000368147,;SPTA1,non_coding_transcript_exon_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000484520,;SPTA1,upstream_gene_variant,,ENST00000492934,;	C	ENSG00000163554	ENST00000368147	Transcript	missense_variant	6218	6037	2013	L/V	Ctg/Gtg	.	.	.	-1	SPTA1	HGNC	11272	protein_coding	YES	CCDS41423.1	ENSP00000357129	SPTA1_HUMAN	O60686_HUMAN	UPI0000458906	.	tolerated(0.79)	possibly_damaging(0.822)	43/52	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF240,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A2011V|c.6032C>T|7	MUTECT|MUSE	CAGCAGAGCGG	.	2	ESCA
COPA	0	.	GRCh37	1	160268910	160268910	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1839C>G	p.Ile613Met	p.I613M	ENST00000368069	18/33	81	77	4	43	43	0	COPA,missense_variant,p.Ile613Met,ENST00000368069,;COPA,missense_variant,p.Ile604Met,ENST00000241704,;COPA,non_coding_transcript_exon_variant,,ENST00000545284,;	C	ENSG00000122218	ENST00000368069	Transcript	missense_variant	1917	1839	613	I/M	atC/atG	.	.	.	-1	COPA	HGNC	2230	protein_coding	YES	CCDS41424.1	ENSP00000357048	COPA_HUMAN	.	UPI0000074301	.	deleterious(0.03)	benign(0.037)	18/33	.	hmmpanther:PTHR19876,Pfam_domain:PF04053,PIRSF_domain:PIRSF003354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTTGATCAG	.	2	ESCA
COPA	0	.	GRCh37	1	160276271	160276271	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315A>T	p.Asn439Tyr	p.N439Y	ENST00000368069	15/33	42	39	3	27	27	0	COPA,missense_variant,p.Asn439Tyr,ENST00000368069,;COPA,missense_variant,p.Asn439Tyr,ENST00000241704,;COPA,upstream_gene_variant,,ENST00000481522,;COPA,downstream_gene_variant,,ENST00000481040,;	A	ENSG00000122218	ENST00000368069	Transcript	missense_variant	1393	1315	439	N/Y	Aat/Tat	.	.	.	-1	COPA	HGNC	2230	protein_coding	YES	CCDS41424.1	ENSP00000357048	COPA_HUMAN	.	UPI0000074301	.	deleterious(0)	probably_damaging(0.914)	15/33	.	hmmpanther:PTHR19876,Pfam_domain:PF04053,PIRSF_domain:PIRSF003354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATTCTTGA	.	2	ESCA
PLEKHM2	0	.	GRCh37	1	16043265	16043265	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.231C>G	p.Ile77Met	p.I77M	ENST00000375799	3/20	43	39	4	28	28	0	PLEKHM2,missense_variant,p.Ile77Met,ENST00000375793,;PLEKHM2,missense_variant,p.Ile77Met,ENST00000375799,;PLEKHM2,intron_variant,,ENST00000462455,;	G	ENSG00000116786	ENST00000375799	Transcript	missense_variant	458	231	77	I/M	atC/atG	.	.	.	1	PLEKHM2	HGNC	29131	protein_coding	YES	CCDS44063.1	ENSP00000364956	PKHM2_HUMAN	.	UPI00001C1D9C	.	deleterious(0)	possibly_damaging(0.857)	3/20	.	PROSITE_profiles:PS50826,Pfam_domain:PF02759,Superfamily_domains:0052343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCATCAAGCA	.	3	ESCA
MROH9	0	.	GRCh37	1	170959080	170959080	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964T>C	p.%3D	p.L322L	ENST00000367759	11/22	97	91	6	51	51	0	MROH9,synonymous_variant,p.%3D,ENST00000367759,;MROH9,synonymous_variant,p.%3D,ENST00000367758,;MROH9,upstream_gene_variant,,ENST00000426136,;	C	ENSG00000117501	ENST00000367759	Transcript	synonymous_variant	1118	964	322	L	Ttg/Ctg	.	.	.	1	MROH9	HGNC	26287	protein_coding	YES	CCDS53429.1	ENSP00000356733	MROH9_HUMAN	.	UPI0001B09232	.	.	.	11/22	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTGTTGACA	.	2	ESCA
KLHL20	0	.	GRCh37	1	173744844	173744844	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501G>C	p.Gly501Arg	p.G501R	ENST00000209884	10/12	73	67	6	34	34	0	KLHL20,missense_variant,p.Gly312Arg,ENST00000546011,;KLHL20,missense_variant,p.Gly501Arg,ENST00000209884,;	C	ENSG00000076321	ENST00000209884	Transcript	missense_variant	1637	1501	501	G/R	Ggc/Cgc	.	.	.	1	KLHL20	HGNC	25056	protein_coding	YES	CCDS1310.1	ENSP00000209884	KLH20_HUMAN	.	UPI0000227E1A	.	deleterious(0.04)	possibly_damaging(0.489)	10/12	.	Superfamily_domains:0052715,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Gene3D:1k3iA02,Pfam_domain:PF01344,hmmpanther:PTHR24412:SF177,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCTAGGCTGT	.	3	ESCA
HMCN1	0	.	GRCh37	1	185902877	185902877	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1749C>G	p.Phe583Leu	p.F583L	ENST00000271588	11/107	146	129	16	73	73	0	HMCN1,missense_variant,p.Phe583Leu,ENST00000367492,;HMCN1,missense_variant,p.Phe583Leu,ENST00000271588,;	G	ENSG00000143341	ENST00000271588	Transcript	missense_variant	1978	1749	583	F/L	ttC/ttG	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	benign(0.122)	11/107	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAATTCAACGA	.	3	ESCA
HMCN1	0	.	GRCh37	1	185902924	185902924	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1796C>G	p.Ser599Ter	p.S599*	ENST00000271588	11/107	148	138	10	67	67	0	HMCN1,stop_gained,p.Ser599Ter,ENST00000367492,;HMCN1,stop_gained,p.Ser599Ter,ENST00000271588,;	G	ENSG00000143341	ENST00000271588	Transcript	stop_gained	2025	1796	599	S/*	tCa/tGa	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	.	11/107	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50835,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGATCATCAG	.	2	ESCA
GOLT1A	0	.	GRCh37	1	204167466	204167466	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120G>C	.	.	ENST00000308302	5/5	64	60	4	52	52	0	GOLT1A,3_prime_UTR_variant,,ENST00000308302,;KISS1,upstream_gene_variant,,ENST00000367194,;GOLT1A,downstream_gene_variant,,ENST00000475517,;	G	ENSG00000174567	ENST00000308302	Transcript	3_prime_UTR_variant	705	.	.	.	.	.	.	.	-1	GOLT1A	HGNC	24766	protein_coding	YES	CCDS1443.1	ENSP00000308535	GOT1A_HUMAN	.	UPI000005287E	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGACTTGGG	.	2	ESCA
PLEKHA6	0	.	GRCh37	1	204228389	204228389	+	Missense_Mutation	SNP	C	C	T	rs771389862	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000272203	8/23	34	30	4	24	24	0	PLEKHA6,missense_variant,p.Arg355Gln,ENST00000414478,;PLEKHA6,missense_variant,p.Arg335Gln,ENST00000272203,;PLEKHA6,downstream_gene_variant,,ENST00000485632,;	T	ENSG00000143850	ENST00000272203	Transcript	missense_variant	1321	1004	335	R/Q	cGg/cAg	rs771389862	.	.	-1	PLEKHA6	HGNC	17053	protein_coding	YES	CCDS1444.1	ENSP00000272203	PKHA6_HUMAN	.	UPI000013D935	.	deleterious(0.04)	benign(0.006)	8/23	.	hmmpanther:PTHR12752:SF5,hmmpanther:PTHR12752	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTCCGAAGG	byFrequency	4	ESCA
PLXNA2	0	.	GRCh37	1	208390941	208390941	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327C>T	p.%3D	p.L109L	ENST00000367033	2/32	98	88	9	53	53	0	PLXNA2,synonymous_variant,p.%3D,ENST00000367033,;PLXNA2,upstream_gene_variant,,ENST00000460870,;	A	ENSG00000076356	ENST00000367033	Transcript	synonymous_variant	1085	327	109	L	ctC/ctT	.	.	.	-1	PLXNA2	HGNC	9100	protein_coding	YES	CCDS31013.1	ENSP00000356000	PLXA2_HUMAN	.	UPI000022B239	.	.	.	2/32	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTGGTGAGGGT	.	3	ESCA
FAM71A	0	.	GRCh37	1	212798703	212798703	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484G>A	p.Asp162Asn	p.D162N	ENST00000294829	1/1	60	55	4	27	27	0	FAM71A,missense_variant,p.Asp162Asn,ENST00000294829,;ATF3,downstream_gene_variant,,ENST00000341491,;ATF3,downstream_gene_variant,,ENST00000366987,;RP11-338C15.5,non_coding_transcript_exon_variant,,ENST00000427949,;ATF3,downstream_gene_variant,,ENST00000492118,;	A	ENSG00000162771	ENST00000294829	Transcript	missense_variant	915	484	162	D/N	Gac/Aac	.	.	.	1	FAM71A	HGNC	26541	protein_coding	YES	CCDS1507.1	ENSP00000294829	FA71A_HUMAN	.	UPI000013E1C2	.	deleterious(0.02)	possibly_damaging(0.84)	1/1	.	hmmpanther:PTHR22574:SF9,hmmpanther:PTHR22574,Pfam_domain:PF12480	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGATGACCTC	.	2	ESCA
RRP15	0	.	GRCh37	1	218480911	218480911	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642G>A	p.%3D	p.L214L	ENST00000366932	4/5	92	83	9	43	43	0	RRP15,synonymous_variant,p.%3D,ENST00000366932,;RRP15,downstream_gene_variant,,ENST00000491428,;	A	ENSG00000067533	ENST00000366932	Transcript	synonymous_variant	672	642	214	L	ttG/ttA	COSM678502	.	.	1	RRP15	HGNC	24255	protein_coding	YES	CCDS1520.2	ENSP00000355899	RRP15_HUMAN	.	UPI0000205BC1	.	.	.	4/5	.	Pfam_domain:PF07890,hmmpanther:PTHR13245	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTGAGAGG	.	4	ESCA
MIA3	0	.	GRCh37	1	222826624	222826624	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4264G>C	p.Glu1422Gln	p.E1422Q	ENST00000344922	15/28	71	65	6	39	39	0	MIA3,missense_variant,p.Glu1422Gln,ENST00000344922,;MIA3,missense_variant,p.Glu946Gln,ENST00000354906,;MIA3,missense_variant,p.Glu300Gln,ENST00000340535,;MIA3,missense_variant,p.Glu1422Gln,ENST00000344441,;MIA3,intron_variant,,ENST00000344507,;MIA3,downstream_gene_variant,,ENST00000467190,;MIA3,downstream_gene_variant,,ENST00000495210,;	C	ENSG00000154305	ENST00000344922	Transcript	missense_variant	4289	4264	1422	E/Q	Gag/Cag	.	.	.	1	MIA3	HGNC	24008	protein_coding	YES	CCDS41470.1	ENSP00000340900	MIA3_HUMAN	.	UPI00001D75B3	.	deleterious(0)	benign(0.338)	15/28	.	hmmpanther:PTHR23158:SF37,hmmpanther:PTHR23158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCTGAGGGT	.	2	ESCA
DNAH14	0	.	GRCh37	1	225576110	225576110	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9777G>A	p.%3D	p.L3259L	ENST00000445597	57/61	73	64	8	35	35	0	DNAH14,synonymous_variant,p.%3D,ENST00000445597,;DNAH14,synonymous_variant,p.%3D,ENST00000430092,;DNAH14,synonymous_variant,p.%3D,ENST00000439375,;DNAH14,upstream_gene_variant,,ENST00000428003,;DNAH14,3_prime_UTR_variant,,ENST00000327794,;	A	ENSG00000185842	ENST00000445597	Transcript	synonymous_variant	9777	9777	3259	L	ctG/ctA	.	.	.	1	DNAH14	HGNC	2945	protein_coding	.	.	ENSP00000409472	DYH14_HUMAN	C9JU64_HUMAN	UPI0001642868	.	.	.	57/61	.	Pfam_domain:PF03028,hmmpanther:PTHR10676:SF132,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCACTGAGTTC	.	3	ESCA
RYR2	0	.	GRCh37	1	237895425	237895425	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11015G>C	p.Ser3672Thr	p.S3672T	ENST00000366574	78/105	60	51	8	33	33	0	RYR2,missense_variant,p.Ser3656Thr,ENST00000542537,;RYR2,missense_variant,p.Ser3672Thr,ENST00000366574,;RYR2,missense_variant,p.Ser3670Thr,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,;RYR2,downstream_gene_variant,,ENST00000609253,;	C	ENSG00000198626	ENST00000366574	Transcript	missense_variant	11332	11015	3672	S/T	aGt/aCt	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	possibly_damaging(0.735)	78/105	.	hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTAGTCGGA	.	5	ESCA
CHML	0	.	GRCh37	1	241798714	241798714	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355C>G	p.Leu119Val	p.L119V	ENST00000366553	1/1	26	22	3	17	17	0	CHML,missense_variant,p.Leu119Val,ENST00000366553,;OPN3,intron_variant,,ENST00000331838,;OPN3,intron_variant,,ENST00000366554,;OPN3,intron_variant,,ENST00000469376,;OPN3,intron_variant,,ENST00000490673,;OPN3,intron_variant,,ENST00000478849,;OPN3,intron_variant,,ENST00000463155,;	C	ENSG00000203668	ENST00000366553	Transcript	missense_variant	519	355	119	L/V	Ctg/Gtg	.	.	.	-1	CHML	HGNC	1941	protein_coding	YES	CCDS31073.1	ENSP00000355511	RAE2_HUMAN	.	UPI0000073C74	.	tolerated(0.1)	benign(0.049)	1/1	.	hmmpanther:PTHR11787,hmmpanther:PTHR11787:SF6,PIRSF_domain:PIRSF016550,Superfamily_domains:SSF51905,Prints_domain:PR00893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	CTGCAGAGCAC	.	3	ESCA
OR2T1	0	.	GRCh37	1	248570267	248570267	+	Silent	SNP	C	C	G	rs762761236	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972C>G	p.%3D	p.L324L	ENST00000366474	1/1	77	73	4	46	46	0	OR2T1,synonymous_variant,p.%3D,ENST00000366474,;	G	ENSG00000175143	ENST00000366474	Transcript	synonymous_variant	972	972	324	L	ctC/ctG	rs762761236	.	.	1	OR2T1	HGNC	8277	protein_coding	YES	CCDS31115.1	ENSP00000355430	OR2T1_HUMAN	.	UPI00003B2872	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF125,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCTCTCTGT	.	2	ESCA
AHDC1	0	.	GRCh37	1	27877849	27877849	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778G>C	p.Glu260Gln	p.E260Q	ENST00000374011	6/7	74	67	7	46	46	0	AHDC1,missense_variant,p.Glu260Gln,ENST00000247087,;AHDC1,missense_variant,p.Glu260Gln,ENST00000374011,;AHDC1,downstream_gene_variant,,ENST00000490295,;AHDC1,downstream_gene_variant,,ENST00000487743,;	G	ENSG00000126705	ENST00000374011	Transcript	missense_variant	1747	778	260	E/Q	Gag/Cag	.	.	.	-1	AHDC1	HGNC	25230	protein_coding	YES	CCDS30652.1	ENSP00000363123	AHDC1_HUMAN	.	UPI0000418EA1	.	tolerated_low_confidence(0.13)	possibly_damaging(0.607)	6/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15617,hmmpanther:PTHR15617:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCTAGCA	.	4	ESCA
THEMIS2	0	.	GRCh37	1	28209200	28209200	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1365C>G	p.%3D	p.V455V	ENST00000373921	4/6	54	45	8	29	29	0	THEMIS2,synonymous_variant,p.%3D,ENST00000456990,;THEMIS2,synonymous_variant,p.%3D,ENST00000373921,;THEMIS2,synonymous_variant,p.%3D,ENST00000328928,;THEMIS2,intron_variant,,ENST00000373927,;THEMIS2,intron_variant,,ENST00000373925,;THEMIS2,downstream_gene_variant,,ENST00000442118,;THEMIS2,downstream_gene_variant,,ENST00000427466,;THEMIS2,non_coding_transcript_exon_variant,,ENST00000482828,;THEMIS2,non_coding_transcript_exon_variant,,ENST00000467258,;THEMIS2,downstream_gene_variant,,ENST00000466068,;THEMIS2,upstream_gene_variant,,ENST00000492877,;	G	ENSG00000130775	ENST00000373921	Transcript	synonymous_variant	1369	1365	455	V	gtC/gtG	.	.	.	1	THEMIS2	HGNC	16839	protein_coding	YES	CCDS41290.1	ENSP00000363031	THMS2_HUMAN	.	UPI00001A796C	.	.	.	4/6	.	hmmpanther:PTHR15215,hmmpanther:PTHR15215:SF2,Pfam_domain:PF12736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTCAAGGT	.	5	ESCA
TRNAU1AP	0	.	GRCh37	1	28907438	28907438	+	3'Flank	SNP	A	A	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000373830	.	54	48	6	45	45	0	TRNAU1AP,downstream_gene_variant,,ENST00000373830,;SNHG12,non_coding_transcript_exon_variant,,ENST00000384342,;SNORD99,upstream_gene_variant,,ENST00000408612,;SNHG12,upstream_gene_variant,,ENST00000384584,;SNHG12,upstream_gene_variant,,ENST00000384581,;SNHG12,intron_variant,,ENST00000475441,;SNHG12,intron_variant,,ENST00000531126,;SNHG12,intron_variant,,ENST00000483436,;SNHG12,intron_variant,,ENST00000488745,;TRNAU1AP,downstream_gene_variant,,ENST00000491577,;TRNAU1AP,downstream_gene_variant,,ENST00000484775,;TRNAU1AP,downstream_gene_variant,,ENST00000480930,;SNHG12,non_coding_transcript_exon_variant,,ENST00000474814,;SNHG12,non_coding_transcript_exon_variant,,ENST00000481368,;SNHG12,non_coding_transcript_exon_variant,,ENST00000464612,;SNHG12,intron_variant,,ENST00000461448,;SNHG12,intron_variant,,ENST00000461832,;SNHG12,intron_variant,,ENST00000464115,;SNHG12,intron_variant,,ENST00000470977,;SNHG12,intron_variant,,ENST00000481220,;	G	ENSG00000180098	ENST00000373830	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2387	1	TRNAU1AP	HGNC	30813	protein_coding	YES	CCDS324.1	ENSP00000362936	TSAP1_HUMAN	.	UPI00000437E6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGTATTTTC	.	4	ESCA
GJA9	0	.	GRCh37	1	39340430	39340430	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1341C>T	p.%3D	p.F447F	ENST00000357771	2/2	60	53	7	35	35	0	GJA9,synonymous_variant,p.%3D,ENST00000357771,;GJA9,synonymous_variant,p.%3D,ENST00000360786,;GJA9,intron_variant,,ENST00000454994,;MYCBP,upstream_gene_variant,,ENST00000397572,;RP5-864K19.4,intron_variant,,ENST00000443161,;RP5-864K19.4,intron_variant,,ENST00000456813,;RP5-864K19.4,intron_variant,,ENST00000433671,;MYCBP,non_coding_transcript_exon_variant,,ENST00000489803,;MYCBP,intron_variant,,ENST00000489575,;MYCBP,upstream_gene_variant,,ENST00000465771,;MYCBP,upstream_gene_variant,,ENST00000462027,;MYCBP,upstream_gene_variant,,ENST00000495043,;MYCBP,upstream_gene_variant,,ENST00000494695,;	A	ENSG00000131233	ENST00000357771	Transcript	synonymous_variant	1622	1341	447	F	ttC/ttT	.	.	.	-1	GJA9	HGNC	19155	protein_coding	YES	CCDS432.1	ENSP00000350415	CXA9_HUMAN	.	UPI000006E09A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCTGAACTG	.	4	ESCA
IPP	0	.	GRCh37	1	46193360	46193360	+	Nonsense_Mutation	SNP	G	G	A	rs753607426	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.991C>T	p.Gln331Ter	p.Q331*	ENST00000396478	5/9	66	57	9	51	51	0	IPP,stop_gained,p.Gln331Ter,ENST00000396478,;IPP,stop_gained,p.Gln331Ter,ENST00000359942,;	A	ENSG00000197429	ENST00000396478	Transcript	stop_gained	1094	991	331	Q/*	Cag/Tag	rs753607426	.	.	-1	IPP	HGNC	6108	protein_coding	YES	CCDS30702.1	ENSP00000379739	IPP_HUMAN	.	UPI000012D80B	.	.	.	5/9	.	hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF35,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,SMART_domains:SM00612	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R333Q|c.998G>A|3	RADIA|MUTECT|MUSE|VARSCANS	AGCCTGATGAA	.	4	ESCA
PODN	0	.	GRCh37	1	53544495	53544495	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1457C>T	p.Ser486Leu	p.S486L	ENST00000312553	8/11	66	59	6	50	50	0	PODN,missense_variant,p.Ser486Leu,ENST00000312553,;PODN,missense_variant,p.Ser467Leu,ENST00000371500,;PODN,missense_variant,p.Ser344Leu,ENST00000395871,;RP11-334A14.5,intron_variant,,ENST00000447867,;PODN,non_coding_transcript_exon_variant,,ENST00000490650,;PODN,non_coding_transcript_exon_variant,,ENST00000471285,;	T	ENSG00000174348	ENST00000312553	Transcript	missense_variant	1464	1457	486	S/L	tCg/tTg	COSM1320992	.	.	1	PODN	HGNC	23174	protein_coding	YES	CCDS573.1	ENSP00000308315	PODN_HUMAN	.	UPI000034ECE9	.	deleterious(0.01)	probably_damaging(0.999)	8/11	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51450,hmmpanther:PTHR24369:SF12,hmmpanther:PTHR24369,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00364,SMART_domains:SM00369,Superfamily_domains:SSF52058,Superfamily_domains:SSF52058,Prints_domain:PR00019	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTGTCGGGCA	.	3	ESCA
RPE65	0	.	GRCh37	1	68910473	68910473	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339G>T	p.Lys113Asn	p.K113N	ENST00000262340	4/14	32	29	3	20	20	0	RPE65,missense_variant,p.Lys113Asn,ENST00000262340,;	A	ENSG00000116745	ENST00000262340	Transcript	missense_variant	393	339	113	K/N	aaG/aaT	.	.	.	-1	RPE65	HGNC	10294	protein_coding	YES	CCDS643.1	ENSP00000262340	RPE65_HUMAN	Q2EKB8_HUMAN,C7FEP0_HUMAN	UPI000004346C	.	deleterious(0)	possibly_damaging(0.872)	4/14	.	hmmpanther:PTHR10543,hmmpanther:PTHR10543:SF7,Pfam_domain:PF03055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATTCTTGCA	.	4	ESCA
PAX1	0	.	GRCh37	20	21695534	21695534	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*93C>G	.	.	ENST00000398485	5/5	27	23	4	15	15	0	PAX1,3_prime_UTR_variant,,ENST00000444366,;PAX1,3_prime_UTR_variant,,ENST00000398485,;	G	ENSG00000125813	ENST00000398485	Transcript	3_prime_UTR_variant	1752	.	.	.	.	.	.	.	1	PAX1	HGNC	8615	protein_coding	YES	CCDS13146.2	ENSP00000381499	PAX1_HUMAN	.	UPI000179A786	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CGTCTCCGTCT	.	2	ESCA
PCED1A	0	.	GRCh37	20	2818908	2818908	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811G>T	p.Val271Leu	p.V271L	ENST00000360652	6/8	79	71	8	43	43	0	PCED1A,missense_variant,p.Val271Leu,ENST00000439542,;PCED1A,missense_variant,p.Val36Leu,ENST00000474714,;PCED1A,missense_variant,p.Val271Leu,ENST00000360652,;PCED1A,missense_variant,p.Val220Leu,ENST00000448755,;PCED1A,missense_variant,p.Val220Leu,ENST00000356872,;VPS16,upstream_gene_variant,,ENST00000417508,;VPS16,upstream_gene_variant,,ENST00000380469,;VPS16,upstream_gene_variant,,ENST00000453689,;VPS16,upstream_gene_variant,,ENST00000380445,;PCED1A,intron_variant,,ENST00000487501,;	A	ENSG00000132635	ENST00000360652	Transcript	missense_variant	1314	811	271	V/L	Gtg/Ttg	.	.	.	-1	PCED1A	HGNC	16212	protein_coding	YES	CCDS13035.1	ENSP00000353868	PED1A_HUMAN	.	UPI00001285EE	.	tolerated(0.06)	possibly_damaging(0.737)	6/8	.	hmmpanther:PTHR14469:SF3,hmmpanther:PTHR14469	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCACGCCCC	.	4	ESCA
PLCG1	0	.	GRCh37	20	39788339	39788339	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311C>T	p.Ser104Leu	p.S104L	ENST00000373272	2/32	73	69	4	40	40	0	PLCG1,missense_variant,p.Ser104Leu,ENST00000373272,;PLCG1,missense_variant,p.Ser104Leu,ENST00000373271,;PLCG1,missense_variant,p.Ser104Leu,ENST00000244007,;PLCG1,non_coding_transcript_exon_variant,,ENST00000483646,;PLCG1,non_coding_transcript_exon_variant,,ENST00000490253,;PLCG1,upstream_gene_variant,,ENST00000492148,;PLCG1,upstream_gene_variant,,ENST00000470528,;	T	ENSG00000124181	ENST00000373272	Transcript	missense_variant	716	311	104	S/L	tCa/tTa	.	.	.	1	PLCG1	HGNC	9065	protein_coding	YES	CCDS13313.1	ENSP00000362369	PLCG1_HUMAN	.	UPI00001B94DD	.	tolerated(0.33)	benign(0.04)	2/32	.	PROSITE_profiles:PS50003,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF52,Gene3D:2.30.29.30,SMART_domains:SM00233,PIRSF_domain:PIRSF000952,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGTCACATT	.	2	ESCA
PTPRT	0	.	GRCh37	20	41306583	41306583	+	Missense_Mutation	SNP	C	C	G	rs571224137	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076G>C	p.Arg359Pro	p.R359P	ENST00000373187	7/31	84	78	6	43	43	0	PTPRT,missense_variant,p.Arg359Pro,ENST00000373201,;PTPRT,missense_variant,p.Arg359Pro,ENST00000356100,;PTPRT,missense_variant,p.Arg359Pro,ENST00000373198,;PTPRT,missense_variant,p.Arg359Pro,ENST00000373193,;PTPRT,missense_variant,p.Arg359Pro,ENST00000373184,;PTPRT,missense_variant,p.Arg359Pro,ENST00000373190,;PTPRT,missense_variant,p.Arg359Pro,ENST00000373187,;	G	ENSG00000196090	ENST00000373187	Transcript	missense_variant	1076	1076	359	R/P	cGa/cCa	rs571224137,COSM4098547,COSM4098548	.	.	-1	PTPRT	HGNC	9682	protein_coding	YES	CCDS42874.1	ENSP00000362283	PTPRT_HUMAN	.	UPI0000246C03	.	tolerated(0.07)	possibly_damaging(0.856)	7/31	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCACTCGGATC	by1000G	2	ESCA
GDAP1L1	0	.	GRCh37	20	42908227	42908227	+	3'UTR	SNP	C	C	G	rs761344936	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*287C>G	.	.	ENST00000342560	6/6	53	45	8	45	45	0	GDAP1L1,stop_gained,p.Ser97Ter,ENST00000447658,;GDAP1L1,3_prime_UTR_variant,,ENST00000342560,;GDAP1L1,downstream_gene_variant,,ENST00000537864,;GDAP1L1,downstream_gene_variant,,ENST00000438466,;	G	ENSG00000124194	ENST00000342560	Transcript	3_prime_UTR_variant	1479	.	.	.	.	rs761344936	.	.	1	GDAP1L1	HGNC	4213	protein_coding	YES	CCDS13328.1	ENSP00000341782	GD1L1_HUMAN	H0UIB3_HUMAN,B7Z4H3_HUMAN	UPI0000038D5C	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCTCAAGAT	.	5	ESCA
WISP2	0	.	GRCh37	20	43353384	43353384	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283G>C	p.Glu95Gln	p.E95Q	ENST00000372868	4/5	117	105	12	68	68	0	WISP2,missense_variant,p.Glu95Gln,ENST00000190983,;WISP2,missense_variant,p.Glu95Gln,ENST00000372868,;WISP2,intron_variant,,ENST00000372865,;RP11-445H22.4,intron_variant,,ENST00000445420,;RP11-445H22.4,intron_variant,,ENST00000427303,;RP11-445H22.4,intron_variant,,ENST00000427598,;WISP2,non_coding_transcript_exon_variant,,ENST00000465000,;WISP2,non_coding_transcript_exon_variant,,ENST00000471629,;WISP2,downstream_gene_variant,,ENST00000497421,;	C	ENSG00000064205	ENST00000372868	Transcript	missense_variant	626	283	95	E/Q	Gag/Cag	.	.	.	1	WISP2	HGNC	12770	protein_coding	YES	CCDS13336.1	ENSP00000361959	WISP2_HUMAN	.	UPI0000037219	.	tolerated(0.24)	benign(0.097)	4/5	.	hmmpanther:PTHR11348,hmmpanther:PTHR11348:SF16,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGCAGAGGAC	.	3	ESCA
YWHAB	0	.	GRCh37	20	43533668	43533668	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484A>G	p.Met162Val	p.M162V	ENST00000372839	5/7	50	30	19	24	24	0	YWHAB,missense_variant,p.Met162Val,ENST00000353703,;YWHAB,missense_variant,p.Met162Val,ENST00000372839,;YWHAB,downstream_gene_variant,,ENST00000428262,;YWHAB,downstream_gene_variant,,ENST00000445830,;YWHAB,non_coding_transcript_exon_variant,,ENST00000479421,;YWHAB,non_coding_transcript_exon_variant,,ENST00000477896,;YWHAB,upstream_gene_variant,,ENST00000479758,;	G	ENSG00000166913	ENST00000372839	Transcript	missense_variant	758	484	162	M/V	Atg/Gtg	.	.	.	1	YWHAB	HGNC	12849	protein_coding	YES	CCDS13339.1	ENSP00000361930	1433B_HUMAN	Q4VY20_HUMAN,Q4VY19_HUMAN	UPI000013C714	.	deleterious_low_confidence(0)	probably_damaging(0.998)	5/7	.	hmmpanther:PTHR18860,Pfam_domain:PF00244,Gene3D:3iquA00,PIRSF_domain:PIRSF000868,SMART_domains:SM00101,Superfamily_domains:SSF48445,Prints_domain:PR00305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAAATGCAG	.	5	ESCA
SEMG2	0	.	GRCh37	20	43850642	43850642	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369T>C	p.%3D	p.F123F	ENST00000372769	2/3	58	46	11	37	37	0	SEMG2,synonymous_variant,p.%3D,ENST00000372769,;	C	ENSG00000124157	ENST00000372769	Transcript	synonymous_variant	459	369	123	F	ttT/ttC	.	.	.	1	SEMG2	HGNC	10743	protein_coding	YES	CCDS13346.1	ENSP00000361855	SEMG2_HUMAN	.	UPI0000135845	.	.	.	2/3	.	hmmpanther:PTHR10547,hmmpanther:PTHR10547:SF6,Pfam_domain:PF05474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTTCACAT	.	5	ESCA
SDC4	0	.	GRCh37	20	43955594	43955594	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*310C>G	.	.	ENST00000372733	5/5	24	20	4	14	14	0	SDC4,3_prime_UTR_variant,,ENST00000372733,;SDC4,3_prime_UTR_variant,,ENST00000537976,;	C	ENSG00000124145	ENST00000372733	Transcript	3_prime_UTR_variant	947	.	.	.	.	.	.	.	-1	SDC4	HGNC	10661	protein_coding	YES	CCDS13350.1	ENSP00000361818	SDC4_HUMAN	B4E1S6_HUMAN	UPI000003B45C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCATGGTCAGT	.	2	ESCA
PCIF1	0	.	GRCh37	20	44567713	44567713	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75G>C	p.Gln25His	p.Q25H	ENST00000372409	3/17	71	63	8	43	43	0	PCIF1,missense_variant,p.Gln25His,ENST00000372409,;	C	ENSG00000100982	ENST00000372409	Transcript	missense_variant	439	75	25	Q/H	caG/caC	.	.	.	1	PCIF1	HGNC	16200	protein_coding	YES	CCDS13388.1	ENSP00000361486	PCIF1_HUMAN	.	UPI000000D717	.	tolerated(0.35)	benign(0.001)	3/17	.	hmmpanther:PTHR21727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATCAGAGCCA	.	4	ESCA
ELMO2	0	.	GRCh37	20	44994961	44994961	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1038T>C	.	.	ENST00000290246	22/22	94	76	18	56	56	0	ELMO2,3_prime_UTR_variant,,ENST00000372176,;ELMO2,3_prime_UTR_variant,,ENST00000396391,;ELMO2,3_prime_UTR_variant,,ENST00000452857,;ELMO2,3_prime_UTR_variant,,ENST00000290246,;SLC35C2,upstream_gene_variant,,ENST00000543605,;SLC35C2,upstream_gene_variant,,ENST00000372229,;SLC35C2,upstream_gene_variant,,ENST00000243896,;ELMO2,downstream_gene_variant,,ENST00000454865,;ELMO2,downstream_gene_variant,,ENST00000439931,;SLC35C2,upstream_gene_variant,,ENST00000372230,;SLC35C2,upstream_gene_variant,,ENST00000317734,;ELMO2,downstream_gene_variant,,ENST00000445496,;SLC35C2,upstream_gene_variant,,ENST00000372227,;ELMO2,downstream_gene_variant,,ENST00000352077,;SLC35C2,upstream_gene_variant,,ENST00000484188,;ELMO2,downstream_gene_variant,,ENST00000464448,;SLC35C2,upstream_gene_variant,,ENST00000484318,;SLC35C2,upstream_gene_variant,,ENST00000481809,;ELMO2,3_prime_UTR_variant,,ENST00000467800,;	G	ENSG00000062598	ENST00000290246	Transcript	3_prime_UTR_variant	3396	.	.	.	.	.	.	.	-1	ELMO2	HGNC	17233	protein_coding	YES	CCDS13398.1	ENSP00000290246	ELMO2_HUMAN	Q7Z5G9_HUMAN,Q5JVZ4_HUMAN,Q5BLP5_HUMAN,F5GZP8_HUMAN	UPI000013F6C4	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCCAATGTG	.	5	ESCA
CHGB	0	.	GRCh37	20	5904375	5904375	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1585C>G	p.Leu529Val	p.L529V	ENST00000378961	4/5	21	15	6	13	13	0	CHGB,missense_variant,p.Leu529Val,ENST00000378961,;CHGB,downstream_gene_variant,,ENST00000455042,;RP5-967N21.2,downstream_gene_variant,,ENST00000400619,;	G	ENSG00000089199	ENST00000378961	Transcript	missense_variant	1789	1585	529	L/V	Ctc/Gtc	.	.	.	1	CHGB	HGNC	1930	protein_coding	YES	CCDS13092.1	ENSP00000368244	SCG1_HUMAN	.	UPI000013C63D	.	tolerated(0.28)	benign(0.022)	4/5	.	Pfam_domain:PF01271,hmmpanther:PTHR10583:SF3,hmmpanther:PTHR10583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTCTCCAG	.	5	ESCA
LSM14B	0	.	GRCh37	20	60701373	60701373	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.305C>T	p.Ser102Phe	p.S102F	ENST00000279068	3/9	63	55	8	46	46	0	LSM14B,missense_variant,p.Ser102Phe,ENST00000279069,;LSM14B,missense_variant,p.Ser102Phe,ENST00000279068,;LSM14B,missense_variant,p.Ser128Phe,ENST00000400318,;LSM14B,missense_variant,p.Ser102Phe,ENST00000370915,;LSM14B,missense_variant,p.Ser102Phe,ENST00000253001,;LSM14B,5_prime_UTR_variant,,ENST00000361670,;	T	ENSG00000149657	ENST00000279068	Transcript	missense_variant	465	305	102	S/F	tCt/tTt	COSM3972649,COSM3972648,COSM3972647,COSM3972650	.	.	1	LSM14B	HGNC	15887	protein_coding	YES	CCDS46626.1	ENSP00000279068	LS14B_HUMAN	.	UPI0000073028	.	deleterious(0)	benign(0.377)	3/9	.	hmmpanther:PTHR13586:SF1,hmmpanther:PTHR13586	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTTCTGCCT	.	4	ESCA
SLCO4A1	0	.	GRCh37	20	61297920	61297920	+	Missense_Mutation	SNP	G	G	A	rs141088861	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1465G>A	p.Gly489Ser	p.G489S	ENST00000217159	7/12	62	56	6	48	48	0	SLCO4A1,missense_variant,p.Gly489Ser,ENST00000370507,;SLCO4A1,missense_variant,p.Gly489Ser,ENST00000217159,;SLCO4A1,upstream_gene_variant,,ENST00000451793,;RP11-93B14.5,non_coding_transcript_exon_variant,,ENST00000433126,;RP11-93B14.5,non_coding_transcript_exon_variant,,ENST00000411824,;RP11-93B14.5,non_coding_transcript_exon_variant,,ENST00000451648,;SLCO4A1,non_coding_transcript_exon_variant,,ENST00000470412,;SLCO4A1,upstream_gene_variant,,ENST00000466961,;SLCO4A1,upstream_gene_variant,,ENST00000497919,;SLCO4A1,upstream_gene_variant,,ENST00000495889,;SLCO4A1,upstream_gene_variant,,ENST00000466818,;SLCO4A1,missense_variant,p.Gly489Ser,ENST00000497209,;	A	ENSG00000101187	ENST00000217159	Transcript	missense_variant	1670	1465	489	G/S	Ggc/Agc	rs141088861	.	.	1	SLCO4A1	HGNC	10953	protein_coding	YES	CCDS13501.1	ENSP00000217159	SO4A1_HUMAN	.	UPI00000557C6	.	tolerated(0.87)	benign(0.001)	7/12	.	PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF66,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137	A:0.0006	A:0.0015	A:0.0014	.	A:0	A:0	A:0	A:0.0011	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTACGGCGGG	byFrequency|byCluster|by1000G	4	ESCA
DIDO1	0	.	GRCh37	20	61510579	61510579	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6C>T	.	.	ENST00000266070	16/16	58	45	13	54	54	0	DIDO1,3_prime_UTR_variant,,ENST00000266070,;DIDO1,3_prime_UTR_variant,,ENST00000395343,;	A	ENSG00000101191	ENST00000266070	Transcript	3_prime_UTR_variant	7055	.	.	.	.	.	.	.	-1	DIDO1	HGNC	2680	protein_coding	YES	CCDS33506.1	ENSP00000266070	DIDO1_HUMAN	.	UPI0000206380	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCGGGGCGT	.	5	ESCA
DIDO1	0	.	GRCh37	20	61510742	61510742	+	Missense_Mutation	SNP	C	C	T	rs768093655	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6566G>A	p.Arg2189Gln	p.R2189Q	ENST00000266070	16/16	92	83	9	67	67	0	DIDO1,missense_variant,p.Arg2189Gln,ENST00000266070,;DIDO1,missense_variant,p.Arg2189Gln,ENST00000395343,;	T	ENSG00000101191	ENST00000266070	Transcript	missense_variant	6892	6566	2189	R/Q	cGg/cAg	rs768093655	.	.	-1	DIDO1	HGNC	2680	protein_coding	YES	CCDS33506.1	ENSP00000266070	DIDO1_HUMAN	.	UPI0000206380	.	.	unknown(0)	16/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14914:SF7,hmmpanther:PTHR14914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTCCCGGTCG	.	3	ESCA
TIAM1	0	.	GRCh37	21	32638328	32638328	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.961C>T	p.Gln321Ter	p.Q321*	ENST00000286827	5/29	106	100	6	61	61	0	TIAM1,stop_gained,p.Gln321Ter,ENST00000286827,;TIAM1,stop_gained,p.Gln321Ter,ENST00000541036,;TIAM1,downstream_gene_variant,,ENST00000455508,;TIAM1,intron_variant,,ENST00000469412,;	A	ENSG00000156299	ENST00000286827	Transcript	stop_gained	1433	961	321	Q/*	Cag/Tag	.	.	.	-1	TIAM1	HGNC	11805	protein_coding	YES	CCDS13609.1	ENSP00000286827	TIAM1_HUMAN	C9JMB5_HUMAN	UPI000013DE6F	.	.	.	5/29	.	hmmpanther:PTHR22826:SF88,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCTGAGTTG	.	2	ESCA
CHAF1B	0	.	GRCh37	21	37775142	37775142	+	Silent	SNP	C	C	T	rs750325132	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.750C>T	p.%3D	p.L250L	ENST00000314103	8/14	77	69	7	47	47	0	CHAF1B,synonymous_variant,p.%3D,ENST00000314103,;CHAF1B,non_coding_transcript_exon_variant,,ENST00000481458,;CHAF1B,downstream_gene_variant,,ENST00000480486,;	T	ENSG00000159259	ENST00000314103	Transcript	synonymous_variant	901	750	250	L	ctC/ctT	rs750325132	.	.	1	CHAF1B	HGNC	1911	protein_coding	YES	CCDS13644.1	ENSP00000315700	CAF1B_HUMAN	.	UPI0000126DD1	.	.	.	8/14	.	hmmpanther:PTHR15271,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCTCACGCC	.	4	ESCA
PRDM15	0	.	GRCh37	21	43221625	43221625	+	Silent	SNP	C	C	T	rs766824100	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4299G>A	p.%3D	p.P1433P	ENST00000269844	31/31	67	62	5	62	62	0	PRDM15,synonymous_variant,p.%3D,ENST00000269844,;PRDM15,synonymous_variant,p.%3D,ENST00000422911,;PRDM15,synonymous_variant,p.%3D,ENST00000398548,;PRDM15,synonymous_variant,p.%3D,ENST00000447207,;PRDM15,synonymous_variant,p.%3D,ENST00000538201,;PRDM15,non_coding_transcript_exon_variant,,ENST00000470586,;PRDM15,downstream_gene_variant,,ENST00000465955,;PRDM15,downstream_gene_variant,,ENST00000495217,;PRDM15,downstream_gene_variant,,ENST00000477633,;PRDM15,synonymous_variant,p.%3D,ENST00000433067,;PRDM15,synonymous_variant,p.%3D,ENST00000447016,;PRDM15,3_prime_UTR_variant,,ENST00000449395,;PRDM15,3_prime_UTR_variant,,ENST00000441787,;PRDM15,non_coding_transcript_exon_variant,,ENST00000486812,;	T	ENSG00000141956	ENST00000269844	Transcript	synonymous_variant	4410	4299	1433	P	ccG/ccA	rs766824100	.	.	-1	PRDM15	HGNC	13999	protein_coding	YES	CCDS13676.1	ENSP00000269844	PRD15_HUMAN	.	UPI0000456FFA	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTCCGGCTG	byFrequency	2	ESCA
PDXK	0	.	GRCh37	21	45152385	45152385	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88-1565G>C	.	.	ENST00000291565	.	61	51	10	63	63	0	PDXK,missense_variant,p.Glu43Gln,ENST00000327574,;PDXK,intron_variant,,ENST00000398081,;PDXK,intron_variant,,ENST00000468090,;PDXK,intron_variant,,ENST00000291565,;PDXK,intron_variant,,ENST00000476313,;PDXK,intron_variant,,ENST00000498040,;PDXK,intron_variant,,ENST00000398085,;PDXK,intron_variant,,ENST00000470029,;PDXK,intron_variant,,ENST00000472777,;PDXK,upstream_gene_variant,,ENST00000481512,;PDXK,downstream_gene_variant,,ENST00000438837,;	C	ENSG00000160209	ENST00000291565	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PDXK	HGNC	8819	protein_coding	YES	CCDS13699.1	ENSP00000291565	PDXK_HUMAN	G1UI32_HUMAN	UPI0000131524	.	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGAAAAT	.	5	ESCA
CLTCL1	0	.	GRCh37	22	19241719	19241719	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.282G>C	p.Glu94Asp	p.E94D	ENST00000263200	3/33	68	58	10	37	37	0	CLTCL1,missense_variant,p.Glu115Asp,ENST00000449918,;CLTCL1,missense_variant,p.Glu94Asp,ENST00000427926,;CLTCL1,missense_variant,p.Glu94Asp,ENST00000263200,;CLTCL1,missense_variant,p.Glu94Asp,ENST00000353891,;SNORA15,downstream_gene_variant,,ENST00000516131,;CLTCL1,missense_variant,p.Glu94Asp,ENST00000505027,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000413132,;KRT18P62,upstream_gene_variant,,ENST00000446618,;	G	ENSG00000070371	ENST00000263200	Transcript	missense_variant	355	282	94	E/D	gaG/gaC	.	.	.	-1	CLTCL1	HGNC	2093	protein_coding	YES	CCDS46662.1	ENSP00000445677	CLH2_HUMAN	.	UPI0000127ABE	.	tolerated(0.31)	benign(0.438)	3/33	.	hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Gene3D:3gc3B00,PIRSF_domain:PIRSF002290,Superfamily_domains:0046096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATCTCAAT	.	5	ESCA
TRMT2A	0	.	GRCh37	22	20104018	20104018	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142G>A	p.Gly48Arg	p.G48R	ENST00000252136	2/12	70	66	4	53	53	0	TRMT2A,missense_variant,p.Gly48Arg,ENST00000403707,;TRMT2A,missense_variant,p.Gly36Arg,ENST00000445045,;TRMT2A,missense_variant,p.Gly48Arg,ENST00000439169,;TRMT2A,missense_variant,p.Gly48Arg,ENST00000404751,;TRMT2A,missense_variant,p.Gly48Arg,ENST00000252136,;RANBP1,intron_variant,,ENST00000430524,;RANBP1,intron_variant,,ENST00000432879,;RANBP1,upstream_gene_variant,,ENST00000411892,;RANBP1,upstream_gene_variant,,ENST00000331821,;DGCR8,downstream_gene_variant,,ENST00000351989,;RANBP1,upstream_gene_variant,,ENST00000421656,;TRMT2A,upstream_gene_variant,,ENST00000444256,;RANBP1,upstream_gene_variant,,ENST00000418705,;TRMT2A,upstream_gene_variant,,ENST00000444845,;RANBP1,upstream_gene_variant,,ENST00000402752,;DGCR8,downstream_gene_variant,,ENST00000383024,;RANBP1,upstream_gene_variant,,ENST00000423859,;DGCR8,downstream_gene_variant,,ENST00000407755,;RANBP1,upstream_gene_variant,,ENST00000416427,;AC006547.8,upstream_gene_variant,,ENST00000412713,;TRMT2A,upstream_gene_variant,,ENST00000480460,;RANBP1,upstream_gene_variant,,ENST00000467920,;TRMT2A,upstream_gene_variant,,ENST00000492988,;TRMT2A,upstream_gene_variant,,ENST00000488335,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000494641,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000464535,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000468917,;RANBP1,intron_variant,,ENST00000435265,;TRMT2A,upstream_gene_variant,,ENST00000494820,;TRMT2A,upstream_gene_variant,,ENST00000480339,;DGCR8,downstream_gene_variant,,ENST00000498171,;TRMT2A,upstream_gene_variant,,ENST00000463710,;TRMT2A,upstream_gene_variant,,ENST00000487378,;DGCR8,downstream_gene_variant,,ENST00000495826,;TRMT2A,upstream_gene_variant,,ENST00000487668,;RANBP1,upstream_gene_variant,,ENST00000488484,;TRMT2A,upstream_gene_variant,,ENST00000459644,;TRMT2A,upstream_gene_variant,,ENST00000471040,;	T	ENSG00000099899	ENST00000252136	Transcript	missense_variant	531	142	48	G/R	Ggg/Agg	.	.	.	-1	TRMT2A	HGNC	24974	protein_coding	YES	CCDS13774.1	ENSP00000252136	TRM2A_HUMAN	C9K041_HUMAN	UPI00001BBFC5	.	tolerated(0.12)	benign(0.006)	2/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11061:SF24,hmmpanther:PTHR11061	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCCCCAGCGC	.	2	ESCA
ADRBK2	0	.	GRCh37	22	26000407	26000407	+	Missense_Mutation	SNP	C	C	G	rs759800976	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177C>G	p.Phe59Leu	p.F59L	ENST00000324198	2/21	89	73	16	49	48	0	ADRBK2,missense_variant,p.Phe59Leu,ENST00000324198,;ADRBK2,missense_variant,p.Phe37Leu,ENST00000455558,;	G	ENSG00000100077	ENST00000324198	Transcript	missense_variant	369	177	59	F/L	ttC/ttG	rs759800976	.	.	1	ADRBK2	HGNC	290	protein_coding	YES	CCDS13832.1	ENSP00000317578	ARBK2_HUMAN	Q8N433_HUMAN	UPI0000050EDB	.	deleterious(0.03)	probably_damaging(0.989)	2/21	.	PROSITE_profiles:PS50132,hmmpanther:PTHR24355:SF17,hmmpanther:PTHR24355,Pfam_domain:PF00615,SMART_domains:SM00315,Superfamily_domains:SSF48097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCAATCA	byFrequency	4	ESCA
PES1	0	.	GRCh37	22	30983347	30983347	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.294G>C	p.Lys98Asn	p.K98N	ENST00000354694	4/15	157	151	6	68	68	0	PES1,missense_variant,p.Lys98Asn,ENST00000402284,;PES1,missense_variant,p.Lys98Asn,ENST00000354694,;PES1,missense_variant,p.Lys98Asn,ENST00000335214,;PES1,5_prime_UTR_variant,,ENST00000405677,;PES1,5_prime_UTR_variant,,ENST00000402281,;PES1,non_coding_transcript_exon_variant,,ENST00000433575,;PES1,3_prime_UTR_variant,,ENST00000406208,;PES1,non_coding_transcript_exon_variant,,ENST00000466614,;PES1,non_coding_transcript_exon_variant,,ENST00000477762,;	G	ENSG00000100029	ENST00000354694	Transcript	missense_variant	401	294	98	K/N	aaG/aaC	.	.	.	-1	PES1	HGNC	8848	protein_coding	YES	CCDS13880.1	ENSP00000346725	PESC_HUMAN	B3KXD6_HUMAN,B2RDF2_HUMAN	UPI0000001618	.	deleterious(0.02)	probably_damaging(0.991)	4/15	.	HAMAP:MF_03028,hmmpanther:PTHR12221,Pfam_domain:PF06732	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGCTCTTCCC	.	2	ESCA
RFPL2	0	.	GRCh37	22	32587193	32587193	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703C>G	p.Arg235Gly	p.R235G	ENST00000400237	5/5	175	164	11	102	102	0	RFPL2,missense_variant,p.Arg235Gly,ENST00000400237,;RFPL2,missense_variant,p.Arg145Gly,ENST00000248983,;RFPL2,missense_variant,p.Arg174Gly,ENST00000248980,;RFPL2,missense_variant,p.Arg145Gly,ENST00000400236,;RFPL2,non_coding_transcript_exon_variant,,ENST00000489846,;	C	ENSG00000128253	ENST00000400237	Transcript	missense_variant	1639	703	235	R/G	Cgc/Ggc	.	.	.	-1	RFPL2	HGNC	9979	protein_coding	YES	CCDS43009.2	ENSP00000383096	RFPL2_HUMAN	.	UPI000013CC66	.	tolerated(0.46)	benign(0.004)	5/5	.	PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF211,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAGCGAGGGG	.	2	ESCA
TOM1	0	.	GRCh37	22	35743592	35743592	+	3'UTR	SNP	G	G	A	rs537063040	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*390G>A	.	.	ENST00000411850	15/15	60	46	14	52	52	0	TOM1,3_prime_UTR_variant,,ENST00000449058,;TOM1,3_prime_UTR_variant,,ENST00000411850,;TOM1,3_prime_UTR_variant,,ENST00000425375,;TOM1,3_prime_UTR_variant,,ENST00000382034,;TOM1,3_prime_UTR_variant,,ENST00000436462,;TOM1,3_prime_UTR_variant,,ENST00000447733,;TOM1,3_prime_UTR_variant,,ENST00000404284,;TOM1,3_prime_UTR_variant,,ENST00000424387,;TOM1,non_coding_transcript_exon_variant,,ENST00000492723,;	A	ENSG00000100284	ENST00000411850	Transcript	3_prime_UTR_variant	1997	.	.	.	.	rs537063040	.	.	1	TOM1	HGNC	11982	protein_coding	YES	CCDS46696.1	ENSP00000413697	TOM1_HUMAN	B0QY02_HUMAN	UPI000000DB48	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCGAGGCC	.	5	ESCA
CSF2RB	0	.	GRCh37	22	37326490	37326490	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792G>A	p.%3D	p.V264V	ENST00000403662	7/14	75	58	16	49	49	0	CSF2RB,synonymous_variant,p.%3D,ENST00000536485,;CSF2RB,synonymous_variant,p.%3D,ENST00000421539,;CSF2RB,synonymous_variant,p.%3D,ENST00000406230,;CSF2RB,synonymous_variant,p.%3D,ENST00000403662,;CSF2RB,synonymous_variant,p.%3D,ENST00000262825,;	A	ENSG00000100368	ENST00000403662	Transcript	synonymous_variant	1014	792	264	V	gtG/gtA	.	.	.	1	CSF2RB	HGNC	2436	protein_coding	YES	CCDS13936.1	ENSP00000384053	IL3RB_HUMAN	B0QY07_HUMAN	UPI0000128C9F	.	.	.	7/14	.	Superfamily_domains:SSF49265,PIRSF_domain:PIRSF001956,Pfam_domain:PF09240,Gene3D:2.60.40.10,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTGAGGAA	.	5	ESCA
ELFN2	0	.	GRCh37	22	37770925	37770925	+	Missense_Mutation	SNP	G	G	A	rs762221074	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650C>T	p.Ser217Leu	p.S217L	ENST00000402918	3/3	188	162	26	115	115	0	ELFN2,missense_variant,p.Ser217Leu,ENST00000402918,;RP1-63G5.5,intron_variant,,ENST00000430883,;RP1-63G5.5,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000424973,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000451509,;	A	ENSG00000166897	ENST00000402918	Transcript	missense_variant	1436	650	217	S/L	tCg/tTg	rs762221074	.	.	-1	ELFN2	HGNC	29396	protein_coding	YES	CCDS33642.1	ENSP00000385277	PPR29_HUMAN	.	UPI000004E87D	.	deleterious(0)	benign(0.283)	3/3	.	hmmpanther:PTHR24367:SF248,hmmpanther:PTHR24367,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGGCGACTCA	byFrequency	4	ESCA
RRP7A	0	.	GRCh37	22	42908866	42908866	+	3'UTR	SNP	C	C	T	rs771890558	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50G>A	.	.	ENST00000323013	7/7	64	58	6	42	42	0	RRP7A,3_prime_UTR_variant,,ENST00000323013,;SERHL,downstream_gene_variant,,ENST00000359906,;SERHL,downstream_gene_variant,,ENST00000421475,;RRP7A,downstream_gene_variant,,ENST00000483303,;RRP7A,downstream_gene_variant,,ENST00000416699,;SERHL,downstream_gene_variant,,ENST00000455578,;	T	ENSG00000189306	ENST00000323013	Transcript	3_prime_UTR_variant	909	.	.	.	.	rs771890558	.	.	-1	RRP7A	HGNC	24286	protein_coding	YES	CCDS14036.1	ENSP00000321449	RRP7A_HUMAN	.	UPI000013C6B7	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCCTCGCCTC	.	3	ESCA
BRD1	0	.	GRCh37	22	50217944	50217944	+	Missense_Mutation	SNP	G	G	A	rs753681600	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22C>T	p.His8Tyr	p.H8Y	ENST00000216267	1/12	38	26	12	9	9	0	BRD1,missense_variant,p.His8Tyr,ENST00000457780,;BRD1,missense_variant,p.His8Tyr,ENST00000216267,;BRD1,missense_variant,p.His8Tyr,ENST00000404034,;BRD1,missense_variant,p.His8Tyr,ENST00000404760,;BRD1,upstream_gene_variant,,ENST00000542442,;BRD1,upstream_gene_variant,,ENST00000342989,;BRD1,upstream_gene_variant,,ENST00000459821,;BRD1,upstream_gene_variant,,ENST00000494833,;BRD1,upstream_gene_variant,,ENST00000438393,;	A	ENSG00000100425	ENST00000216267	Transcript	missense_variant	509	22	8	H/Y	Cat/Tat	rs753681600	.	.	-1	BRD1	HGNC	1102	protein_coding	YES	CCDS14080.1	ENSP00000216267	BRD1_HUMAN	Q659H0_HUMAN	UPI0000126ACA	.	tolerated(0.22)	possibly_damaging(0.716)	1/12	.	hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGATGACATC	.	5	ESCA
SLC9A4	0	.	GRCh37	2	103141509	103141509	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1845C>G	p.%3D	p.L615L	ENST00000295269	10/12	70	63	6	38	38	0	SLC9A4,synonymous_variant,p.%3D,ENST00000295269,;	G	ENSG00000180251	ENST00000295269	Transcript	synonymous_variant	2302	1845	615	L	ctC/ctG	.	.	.	1	SLC9A4	HGNC	11077	protein_coding	YES	CCDS33264.1	ENSP00000295269	SL9A4_HUMAN	.	UPI000047F996	.	.	.	10/12	.	hmmpanther:PTHR10110:SF103,hmmpanther:PTHR10110,TIGRFAM_domain:TIGR00840	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACCTCAAACC	.	4	ESCA
NOL10	0	.	GRCh37	2	10799328	10799328	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726G>C	p.Leu242Phe	p.L242F	ENST00000381685	10/21	61	53	7	39	39	0	NOL10,missense_variant,p.Leu133Phe,ENST00000431319,;NOL10,missense_variant,p.Leu242Phe,ENST00000381685,;NOL10,missense_variant,p.Leu242Phe,ENST00000345985,;NOL10,missense_variant,p.Leu216Phe,ENST00000538384,;NOL10,missense_variant,p.Leu192Phe,ENST00000542668,;	G	ENSG00000115761	ENST00000381685	Transcript	missense_variant	832	726	242	L/F	ttG/ttC	.	.	.	-1	NOL10	HGNC	25862	protein_coding	YES	CCDS1673.2	ENSP00000371101	NOL10_HUMAN	F5H6G7_HUMAN	UPI000006F6E2	.	deleterious(0)	probably_damaging(0.925)	10/21	.	hmmpanther:PTHR14927:SF0,hmmpanther:PTHR14927,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGGTCAAGGC	.	4	ESCA
DARS	0	.	GRCh37	2	136743200	136743200	+	5'UTR	SNP	G	G	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-162C>A	.	.	ENST00000264161	1/16	44	38	6	21	21	0	DARS,5_prime_UTR_variant,,ENST00000264161,;DARS,intron_variant,,ENST00000456565,;DARS,intron_variant,,ENST00000449218,;DARS,intron_variant,,ENST00000441323,;DARS,upstream_gene_variant,,ENST00000537273,;AC093391.2,intron_variant,,ENST00000444406,;AC093391.2,intron_variant,,ENST00000446492,;AC093391.2,intron_variant,,ENST00000419808,;AC093391.2,intron_variant,,ENST00000438432,;DARS,upstream_gene_variant,,ENST00000435076,;DARS,upstream_gene_variant,,ENST00000474184,;	T	ENSG00000115866	ENST00000264161	Transcript	5_prime_UTR_variant	55	.	.	.	.	.	.	.	-1	DARS	HGNC	2678	protein_coding	YES	CCDS2180.1	ENSP00000264161	SYDC_HUMAN	Q68CR9_HUMAN,Q53T60_HUMAN,Q53R85_HUMAN,D3DP78_HUMAN,C9JQM9_HUMAN,C9JLC1_HUMAN,C9J7S3_HUMAN	UPI000013639B	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCGCGAGAGC	.	2	ESCA
LRP1B	0	.	GRCh37	2	141143523	141143523	+	Silent	SNP	G	G	T	rs752743011	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10470C>A	p.%3D	p.P3490P	ENST00000389484	67/91	43	32	11	34	34	0	LRP1B,synonymous_variant,p.%3D,ENST00000389484,;	T	ENSG00000168702	ENST00000389484	Transcript	synonymous_variant	11442	10470	3490	P	ccC/ccA	rs752743011,COSM1007003	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	67/91	.	PROSITE_profiles:PS50068,PROSITE_patterns:PS01209,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D3491N|c.10471G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATCGGGAAT	byFrequency	5	ESCA
COBLL1	0	.	GRCh37	2	165561596	165561596	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1016G>C	p.Arg339Thr	p.R339T	ENST00000342193	7/14	51	43	7	24	24	0	COBLL1,missense_variant,p.Arg339Thr,ENST00000375458,;COBLL1,missense_variant,p.Arg377Thr,ENST00000409184,;COBLL1,missense_variant,p.Arg339Thr,ENST00000342193,;COBLL1,missense_variant,p.Arg377Thr,ENST00000392717,;COBLL1,missense_variant,p.Arg405Thr,ENST00000194871,;COBLL1,non_coding_transcript_exon_variant,,ENST00000491126,;COBLL1,non_coding_transcript_exon_variant,,ENST00000434366,;COBLL1,missense_variant,p.Arg352Thr,ENST00000456171,;COBLL1,non_coding_transcript_exon_variant,,ENST00000493868,;COBLL1,non_coding_transcript_exon_variant,,ENST00000460238,;	G	ENSG00000082438	ENST00000342193	Transcript	missense_variant	1232	1016	339	R/T	aGa/aCa	.	.	.	-1	COBLL1	HGNC	23571	protein_coding	YES	CCDS2223.2	ENSP00000341360	COBL1_HUMAN	C9JWZ0_HUMAN,C9JAU3_HUMAN,B3KMG7_HUMAN	UPI000007132B	.	deleterious(0.02)	benign(0.281)	7/14	.	hmmpanther:PTHR21557:SF2,hmmpanther:PTHR21557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTCTTCCT	.	5	ESCA
TTC21B	0	.	GRCh37	2	166788351	166788351	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811G>C	p.Glu271Gln	p.E271Q	ENST00000243344	8/29	98	86	12	64	64	0	TTC21B,missense_variant,p.Glu271Gln,ENST00000243344,;TTC21B-AS1,upstream_gene_variant,,ENST00000440322,;TTC21B-AS1,upstream_gene_variant,,ENST00000443032,;TTC21B,non_coding_transcript_exon_variant,,ENST00000464374,;TTC21B-AS1,upstream_gene_variant,,ENST00000446624,;	G	ENSG00000123607	ENST00000243344	Transcript	missense_variant	949	811	271	E/Q	Gaa/Caa	.	.	.	-1	TTC21B	HGNC	25660	protein_coding	YES	CCDS33315.1	ENSP00000243344	TT21B_HUMAN	B3KU32_HUMAN	UPI000020900A	.	tolerated(0.65)	benign(0.091)	8/29	.	hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF1,Gene3D:1.25.40.10,Superfamily_domains:SSF81901	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTCCAGCT	.	4	ESCA
XIRP2	0	.	GRCh37	2	168101829	168101829	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3927A>G	p.%3D	p.V1309V	ENST00000409195	9/11	65	57	8	57	57	0	XIRP2,synonymous_variant,p.%3D,ENST00000409273,;XIRP2,synonymous_variant,p.%3D,ENST00000409195,;XIRP2,synonymous_variant,p.%3D,ENST00000295237,;XIRP2,intron_variant,,ENST00000409605,;XIRP2,intron_variant,,ENST00000420519,;XIRP2,intron_variant,,ENST00000409756,;XIRP2,intron_variant,,ENST00000409043,;XIRP2,intron_variant,,ENST00000409728,;	G	ENSG00000163092	ENST00000409195	Transcript	synonymous_variant	4016	3927	1309	V	gtA/gtG	.	.	.	1	XIRP2	HGNC	14303	protein_coding	YES	CCDS42769.1	ENSP00000386840	.	J3KNB1_HUMAN	UPI0000E9BBED	.	.	.	9/11	.	Pfam_domain:PF08043,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1,PROSITE_profiles:PS51389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATGTAAAAAG	.	4	ESCA
ABCB11	0	.	GRCh37	2	169870832	169870832	+	Missense_Mutation	SNP	C	C	G	rs775156203	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.131G>C	p.Arg44Thr	p.R44T	ENST00000263817	4/28	52	46	5	40	40	0	ABCB11,missense_variant,p.Arg44Thr,ENST00000263817,;	G	ENSG00000073734	ENST00000263817	Transcript	missense_variant	256	131	44	R/T	aGa/aCa	rs775156203	.	.	-1	ABCB11	HGNC	42	protein_coding	YES	CCDS46444.1	ENSP00000263817	ABCBB_HUMAN	Q9UIL3_HUMAN,Q53S60_HUMAN,B4DYQ0_HUMAN	UPI0000163BFA	.	tolerated(0.42)	benign(0.044)	4/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAACTCTAACG	.	3	ESCA
HNRNPA3	0	.	GRCh37	2	178086396	178086396	+	3'Flank	SNP	G	G	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000392524	.	39	30	9	32	32	0	HNRNPA3,3_prime_UTR_variant,,ENST00000411529,;HNRNPA3,downstream_gene_variant,,ENST00000435711,;HNRNPA3,downstream_gene_variant,,ENST00000432457,;HNRNPA3,downstream_gene_variant,,ENST00000392524,;HNRNPA3,downstream_gene_variant,,ENST00000483137,;	T	ENSG00000170144	ENST00000392524	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1583	1	HNRNPA3	HGNC	24941	protein_coding	YES	CCDS2273.1	ENSP00000376309	ROA3_HUMAN	Q8NFG3_HUMAN	UPI00001BE8DE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAAGCACAG	.	5	ESCA
TTC30B	0	.	GRCh37	2	178417447	178417447	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45C>T	p.%3D	p.T15T	ENST00000408939	1/1	48	37	11	49	49	0	TTC30B,synonymous_variant,p.%3D,ENST00000408939,;	A	ENSG00000196659	ENST00000408939	Transcript	synonymous_variant	296	45	15	T	acC/acT	.	.	.	-1	TTC30B	HGNC	26425	protein_coding	YES	CCDS42784.1	ENSP00000386181	TT30B_HUMAN	.	UPI000013DE25	.	.	.	1/1	.	PROSITE_profiles:PS50293,hmmpanther:PTHR20931,hmmpanther:PTHR20931:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGCGGTGAA	.	5	ESCA
OSBPL6	0	.	GRCh37	2	179197727	179197727	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616G>C	p.Glu206Gln	p.E206Q	ENST00000392505	8/26	46	43	3	33	33	0	OSBPL6,missense_variant,p.Glu206Gln,ENST00000409631,;OSBPL6,missense_variant,p.Glu206Gln,ENST00000409045,;OSBPL6,missense_variant,p.Glu185Gln,ENST00000315022,;OSBPL6,missense_variant,p.Glu206Gln,ENST00000359685,;OSBPL6,missense_variant,p.Glu206Gln,ENST00000392505,;OSBPL6,missense_variant,p.Glu206Gln,ENST00000190611,;OSBPL6,missense_variant,p.Glu206Gln,ENST00000357080,;OSBPL6,downstream_gene_variant,,ENST00000477097,;	C	ENSG00000079156	ENST00000392505	Transcript	missense_variant	1160	616	206	E/Q	Gaa/Caa	.	.	.	1	OSBPL6	HGNC	16388	protein_coding	YES	CCDS56150.1	ENSP00000376293	OSBL6_HUMAN	.	UPI0000E5A29F	.	tolerated(0.26)	benign(0.395)	8/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10972:SF76,hmmpanther:PTHR10972	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTGAATCC	.	2	ESCA
TTN	0	.	GRCh37	2	179425563	179425563	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85296G>A	p.%3D	p.L28432L	ENST00000589042	326/363	85	77	8	52	51	0	TTN,synonymous_variant,p.%3D,ENST00000359218,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000342175,;TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;	T	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	85521	85296	28432	L	ctG/ctA	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	326/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCTTCAGTGT	.	3	ESCA
MYT1L	0	.	GRCh37	2	1795777	1795777	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3417T>A	p.Asp1139Glu	p.D1139E	ENST00000428368	25/25	18	14	4	22	22	0	MYT1L,missense_variant,p.Asp1141Glu,ENST00000399161,;MYT1L,missense_variant,p.Asp139Glu,ENST00000407844,;MYT1L,missense_variant,p.Asp1139Glu,ENST00000428368,;MYT1L,intron_variant,,ENST00000399157,;	T	ENSG00000186487	ENST00000428368	Transcript	missense_variant	4087	3417	1139	D/E	gaT/gaA	.	.	.	-1	MYT1L	HGNC	7623	protein_coding	YES	CCDS46222.1	ENSP00000396103	MYT1L_HUMAN	.	UPI00004E55EA	.	tolerated(1)	benign(0.004)	25/25	.	hmmpanther:PTHR10816:SF11,hmmpanther:PTHR10816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	ATTGGATCCTA	.	3	ESCA
DNAH7	0	.	GRCh37	2	196912149	196912149	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.325A>G	p.Thr109Ala	p.T109A	ENST00000312428	5/65	80	68	12	49	49	0	DNAH7,missense_variant,p.Thr109Ala,ENST00000410072,;DNAH7,missense_variant,p.Thr84Ala,ENST00000427816,;DNAH7,missense_variant,p.Thr109Ala,ENST00000312428,;	C	ENSG00000118997	ENST00000312428	Transcript	missense_variant	426	325	109	T/A	Act/Gct	.	.	.	-1	DNAH7	HGNC	18661	protein_coding	YES	CCDS42794.1	ENSP00000311273	DYH7_HUMAN	C9JUY3_HUMAN	UPI0000141B95	.	tolerated(0.27)	benign(0.004)	5/65	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGTAGATG	.	5	ESCA
CD28	0	.	GRCh37	2	204600220	204600220	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*585C>G	.	.	ENST00000324106	4/4	73	67	5	62	62	0	CD28,3_prime_UTR_variant,,ENST00000324106,;CD28,3_prime_UTR_variant,,ENST00000374481,;CD28,downstream_gene_variant,,ENST00000458610,;CD28,downstream_gene_variant,,ENST00000374478,;	G	ENSG00000178562	ENST00000324106	Transcript	3_prime_UTR_variant	1397	.	.	.	.	.	.	.	1	CD28	HGNC	1653	protein_coding	YES	CCDS2361.1	ENSP00000324890	CD28_HUMAN	.	UPI0000043F4D	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTGTCTTTTA	.	2	ESCA
NRP2	0	.	GRCh37	2	206660251	206660251	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*469C>T	.	.	ENST00000360409	17/17	20	17	3	21	21	0	NRP2,3_prime_UTR_variant,,ENST00000360409,;NRP2,3_prime_UTR_variant,,ENST00000540178,;NRP2,downstream_gene_variant,,ENST00000357785,;NRP2,downstream_gene_variant,,ENST00000540841,;NRP2,downstream_gene_variant,,ENST00000412873,;NRP2,downstream_gene_variant,,ENST00000467850,;	T	ENSG00000118257	ENST00000360409	Transcript	3_prime_UTR_variant	4056	.	.	.	.	.	.	.	1	NRP2	HGNC	8005	protein_coding	YES	CCDS2364.1	ENSP00000353582	NRP2_HUMAN	C9JH98_HUMAN	UPI000014020F	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTTCAGCCT	.	2	ESCA
SCG2	0	.	GRCh37	2	224463090	224463090	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.911C>T	p.Ser304Leu	p.S304L	ENST00000305409	2/2	57	49	8	38	38	0	SCG2,missense_variant,p.Ser304Leu,ENST00000305409,;SCG2,downstream_gene_variant,,ENST00000433889,;SCG2,downstream_gene_variant,,ENST00000421386,;	A	ENSG00000171951	ENST00000305409	Transcript	missense_variant	1144	911	304	S/L	tCa/tTa	.	.	.	-1	SCG2	HGNC	10575	protein_coding	YES	CCDS2457.1	ENSP00000304133	SCG2_HUMAN	C9JQI2_HUMAN,C9JDT0_HUMAN	UPI000013EA45	.	tolerated(0.06)	probably_damaging(1)	2/2	.	hmmpanther:PTHR15119,hmmpanther:PTHR15119:SF0,Pfam_domain:PF01271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTGAGAGT	.	5	ESCA
RHBDD1	0	.	GRCh37	2	227700798	227700798	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-397G>C	.	.	ENST00000392062	1/9	42	39	3	39	39	0	RHBDD1,5_prime_UTR_variant,,ENST00000423616,;RHBDD1,5_prime_UTR_variant,,ENST00000448992,;RHBDD1,5_prime_UTR_variant,,ENST00000341329,;RHBDD1,5_prime_UTR_variant,,ENST00000437454,;RHBDD1,5_prime_UTR_variant,,ENST00000392062,;RHBDD1,5_prime_UTR_variant,,ENST00000443477,;RHBDD1,intron_variant,,ENST00000424132,;RHBDD1,upstream_gene_variant,,ENST00000436481,;RHBDD1,non_coding_transcript_exon_variant,,ENST00000539613,;RHBDD1,upstream_gene_variant,,ENST00000450679,;	C	ENSG00000144468	ENST00000392062	Transcript	5_prime_UTR_variant	128	.	.	.	.	.	.	.	1	RHBDD1	HGNC	23081	protein_coding	YES	CCDS2464.1	ENSP00000375914	RHBL4_HUMAN	C9K011_HUMAN,C9JQK8_HUMAN,C9JAS2_HUMAN,C9J4C7_HUMAN,C9J1R4_HUMAN	UPI0000047AE4	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGTAGAGAGC	.	2	ESCA
COL4A4	0	.	GRCh37	2	227896937	227896937	+	Missense_Mutation	SNP	C	C	G	rs767770757	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3633G>C	p.Glu1211Asp	p.E1211D	ENST00000396625	39/48	30	26	4	20	20	0	COL4A4,missense_variant,p.Glu1211Asp,ENST00000329662,;COL4A4,missense_variant,p.Glu1211Asp,ENST00000396625,;	G	ENSG00000081052	ENST00000396625	Transcript	missense_variant	3841	3633	1211	E/D	gaG/gaC	rs767770757	.	.	-1	COL4A4	HGNC	2206	protein_coding	YES	CCDS42828.1	ENSP00000379866	CO4A4_HUMAN	.	UPI000013D987	.	.	unknown(0)	39/48	.	hmmpanther:PTHR24021:SF5,hmmpanther:PTHR24021,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCTCTCTCCCC	.	3	ESCA
ARMC9	0	.	GRCh37	2	232137712	232137712	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1255G>A	p.Glu419Lys	p.E419K	ENST00000349938	14/21	96	81	14	72	72	0	ARMC9,missense_variant,p.Glu61Lys,ENST00000446447,;ARMC9,missense_variant,p.Glu419Lys,ENST00000349938,;ARMC9,missense_variant,p.Glu122Lys,ENST00000424740,;ARMC9,missense_variant,p.Glu136Lys,ENST00000436339,;ARMC9,non_coding_transcript_exon_variant,,ENST00000483477,;ARMC9,missense_variant,p.Glu47Lys,ENST00000428662,;ARMC9,non_coding_transcript_exon_variant,,ENST00000481520,;ARMC9,non_coding_transcript_exon_variant,,ENST00000467698,;	A	ENSG00000135931	ENST00000349938	Transcript	missense_variant	1449	1255	419	E/K	Gag/Aag	COSM331309,COSM331310	.	.	1	ARMC9	HGNC	20730	protein_coding	YES	CCDS2484.1	ENSP00000258417	ARMC9_HUMAN	C9JW07_HUMAN	UPI00001AE7AC	.	tolerated(0.55)	benign(0.175)	14/21	.	hmmpanther:PTHR14881,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGGAGGGA	.	5	ESCA
SRSF7	0	.	GRCh37	2	38973295	38973295	+	Missense_Mutation	SNP	G	G	C	rs771774999	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.653C>G	p.Pro218Arg	p.P218R	ENST00000313117	7/8	53	46	6	43	43	0	SRSF7,missense_variant,p.Pro218Arg,ENST00000313117,;SRSF7,missense_variant,p.Pro215Arg,ENST00000409276,;SRSF7,intron_variant,,ENST00000452806,;SRSF7,intron_variant,,ENST00000446327,;GALM,downstream_gene_variant,,ENST00000434934,;SRSF7,3_prime_UTR_variant,,ENST00000431066,;SRSF7,3_prime_UTR_variant,,ENST00000425778,;SRSF7,3_prime_UTR_variant,,ENST00000443213,;SRSF7,3_prime_UTR_variant,,ENST00000432873,;SRSF7,3_prime_UTR_variant,,ENST00000425941,;SRSF7,non_coding_transcript_exon_variant,,ENST00000477635,;SRSF7,non_coding_transcript_exon_variant,,ENST00000487773,;SRSF7,downstream_gene_variant,,ENST00000415527,;	C	ENSG00000115875	ENST00000313117	Transcript	missense_variant	891	653	218	P/R	cCa/cGa	rs771774999	.	.	-1	SRSF7	HGNC	10789	protein_coding	YES	CCDS33183.1	ENSP00000325905	SRSF7_HUMAN	.	UPI000000D853	.	deleterious(0.01)	unknown(0)	7/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10548	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTTGGAGAT	.	4	ESCA
ABCG5	0	.	GRCh37	2	44065707	44065707	+	Silent	SNP	G	G	A	rs375829761	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.112C>T	p.%3D	p.L38L	ENST00000260645	1/13	59	52	6	56	56	0	ABCG5,synonymous_variant,p.%3D,ENST00000260645,;ABCG5,5_prime_UTR_variant,,ENST00000405322,;ABCG5,5_prime_UTR_variant,,ENST00000543989,;ABCG8,upstream_gene_variant,,ENST00000272286,;ABCG5,5_prime_UTR_variant,,ENST00000486512,;ABCG5,5_prime_UTR_variant,,ENST00000409962,;	A	ENSG00000138075	ENST00000260645	Transcript	synonymous_variant	252	112	38	L	Ctg/Ttg	rs375829761	.	.	-1	ABCG5	HGNC	13886	protein_coding	YES	CCDS1814.1	ENSP00000260645	ABCG5_HUMAN	Q96QZ3_HUMAN,Q96QZ2_HUMAN,Q53T83_HUMAN,Q53QN9_HUMAN,Q2T9G2_HUMAN	UPI0000046560	.	.	.	1/13	.	hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF193	.	.	.	.	.	.	.	C:0.0002	C:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCAGGCTGT	byFrequency|byCluster	4	ESCA
CCDC88A	0	.	GRCh37	2	55544775	55544775	+	Missense_Mutation	SNP	G	G	C	rs375580003	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3524C>G	p.Ser1175Cys	p.S1175C	ENST00000336838	20/33	27	24	3	30	30	0	CCDC88A,missense_variant,p.Ser1175Cys,ENST00000413716,;CCDC88A,missense_variant,p.Ser221Cys,ENST00000412148,;CCDC88A,missense_variant,p.Ser1176Cys,ENST00000436346,;CCDC88A,missense_variant,p.Ser157Cys,ENST00000456975,;CCDC88A,missense_variant,p.Ser1176Cys,ENST00000263630,;CCDC88A,missense_variant,p.Ser1175Cys,ENST00000336838,;CCDC88A,missense_variant,p.Ser351Cys,ENST00000426576,;AC012358.8,intron_variant,,ENST00000608103,;AC012358.8,intron_variant,,ENST00000600219,;AC012358.8,intron_variant,,ENST00000594078,;AC012358.8,intron_variant,,ENST00000599475,;AC012358.8,intron_variant,,ENST00000599352,;AC012358.8,downstream_gene_variant,,ENST00000366287,;CCDC88A,non_coding_transcript_exon_variant,,ENST00000474059,;CCDC88A,upstream_gene_variant,,ENST00000476903,;	C	ENSG00000115355	ENST00000336838	Transcript	missense_variant	4058	3524	1175	S/C	tCt/tGt	rs375580003,COSM1021851,COSM1592253	.	.	-1	CCDC88A	HGNC	25523	protein_coding	YES	CCDS46288.1	ENSP00000338728	GRDN_HUMAN	C9J225_HUMAN,B4DSN0_HUMAN	UPI00005B7220	.	deleterious(0.01)	benign(0.321)	20/33	.	hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF30	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAGAGATTCA	byFrequency|byCluster	2	ESCA
XPO1	0	.	GRCh37	2	61765363	61765363	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-673C>G	.	.	ENST00000401558	1/25	84	71	13	73	73	0	XPO1,5_prime_UTR_variant,,ENST00000401558,;XPO1,5_prime_UTR_variant,,ENST00000406957,;XPO1,intron_variant,,ENST00000436018,;XPO1,intron_variant,,ENST00000443240,;XPO1,upstream_gene_variant,,ENST00000404992,;XPO1,upstream_gene_variant,,ENST00000457483,;XPO1,upstream_gene_variant,,ENST00000422552,;XPO1,upstream_gene_variant,,ENST00000449444,;XPO1,upstream_gene_variant,,ENST00000451765,;XPO1,upstream_gene_variant,,ENST00000420673,;XPO1,upstream_gene_variant,,ENST00000481214,;XPO1,upstream_gene_variant,,ENST00000495003,;XPO1,5_prime_UTR_variant,,ENST00000428210,;	C	ENSG00000082898	ENST00000401558	Transcript	5_prime_UTR_variant	56	.	.	.	.	.	.	.	-1	XPO1	HGNC	12825	protein_coding	YES	CCDS33205.1	ENSP00000384863	XPO1_HUMAN	C9JV99_HUMAN,C9JQ02_HUMAN,C9JKM9_HUMAN,C9JF49_HUMAN,C9J673_HUMAN,C9IZS4_HUMAN,C9IYM2_HUMAN,B7ZB16_HUMAN,B3KWD0_HUMAN	UPI0000001C23	.	.	.	1/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCGGCCGC	.	5	ESCA
WDR92	0	.	GRCh37	2	68384711	68384711	+	5'Flank	SNP	G	G	C	rs756876994	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000295121	.	76	72	4	57	57	0	WDR92,upstream_gene_variant,,ENST00000409164,;WDR92,upstream_gene_variant,,ENST00000406245,;PNO1,upstream_gene_variant,,ENST00000263657,;WDR92,upstream_gene_variant,,ENST00000295121,;WDR92,upstream_gene_variant,,ENST00000492039,;RP11-474G23.1,missense_variant,p.Ala293Gly,ENST00000406334,;WDR92,upstream_gene_variant,,ENST00000468984,;PNO1,upstream_gene_variant,,ENST00000430742,;	C	ENSG00000243667	ENST00000295121	Transcript	upstream_gene_variant	.	.	.	.	.	rs756876994	.	19	-1	WDR92	HGNC	25176	protein_coding	YES	CCDS1884.1	ENSP00000295121	WDR92_HUMAN	Q8ND98_HUMAN,Q86YQ0_HUMAN	UPI000006F50D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTGGCTGTA	.	2	ESCA
PPP3R1	0	.	GRCh37	2	68406383	68406383	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1712C>T	.	.	ENST00000234310	6/6	28	25	3	27	27	0	PPP3R1,3_prime_UTR_variant,,ENST00000234310,;PPP3R1,downstream_gene_variant,,ENST00000409752,;PNO1,downstream_gene_variant,,ENST00000263657,;PPP3R1,downstream_gene_variant,,ENST00000409377,;RP11-474G23.2,upstream_gene_variant,,ENST00000609955,;RP11-474G23.1,intron_variant,,ENST00000406334,;PNO1,downstream_gene_variant,,ENST00000488728,;	A	ENSG00000221823	ENST00000234310	Transcript	3_prime_UTR_variant	2629	.	.	.	.	.	.	.	-1	PPP3R1	HGNC	9317	protein_coding	YES	CCDS46310.1	ENSP00000234310	CANB1_HUMAN	F6U1T9_HUMAN	UPI00000012AE	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACTGATCCA	.	2	ESCA
CLEC4F	0	.	GRCh37	2	71036285	71036285	+	3'UTR	SNP	G	G	T	rs782796759	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*118C>A	.	.	ENST00000272367	7/7	73	58	15	40	40	0	CLEC4F,3_prime_UTR_variant,,ENST00000272367,;CLEC4F,intron_variant,,ENST00000426626,;AC007395.4,downstream_gene_variant,,ENST00000451333,;	T	ENSG00000152672	ENST00000272367	Transcript	3_prime_UTR_variant	1965	.	.	.	.	rs782796759	.	.	-1	CLEC4F	HGNC	25357	protein_coding	YES	CCDS1910.1	ENSP00000272367	CLC4F_HUMAN	.	UPI0000376BCC	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTGACATG	byFrequency	5	ESCA
RTKN	0	.	GRCh37	2	74657797	74657797	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319G>C	p.Asp107His	p.D107H	ENST00000272430	3/12	73	67	6	55	55	0	RTKN,missense_variant,p.Asp107His,ENST00000272430,;RTKN,missense_variant,p.Asp94His,ENST00000305557,;RTKN,missense_variant,p.Asp57His,ENST00000233330,;WDR54,downstream_gene_variant,,ENST00000348227,;WDR54,downstream_gene_variant,,ENST00000409791,;RTKN,non_coding_transcript_exon_variant,,ENST00000479256,;WDR54,downstream_gene_variant,,ENST00000469321,;RTKN,downstream_gene_variant,,ENST00000484453,;RTKN,non_coding_transcript_exon_variant,,ENST00000469859,;RTKN,downstream_gene_variant,,ENST00000464094,;WDR54,downstream_gene_variant,,ENST00000465134,;RTKN,upstream_gene_variant,,ENST00000492013,;RTKN,downstream_gene_variant,,ENST00000472518,;WDR54,downstream_gene_variant,,ENST00000468778,;RTKN,downstream_gene_variant,,ENST00000460968,;WDR54,downstream_gene_variant,,ENST00000482605,;	G	ENSG00000114993	ENST00000272430	Transcript	missense_variant	402	319	107	D/H	Gac/Cac	.	.	.	-1	RTKN	HGNC	10466	protein_coding	YES	CCDS33226.1	ENSP00000272430	RTKN_HUMAN	.	UPI0000031F56	.	tolerated(0.07)	possibly_damaging(0.738)	3/12	.	hmmpanther:PTHR21538,hmmpanther:PTHR21538:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTGTCAGAAG	.	3	ESCA
LRRTM4	0	.	GRCh37	2	77746526	77746526	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.469C>T	p.Arg157Trp	p.R157W	ENST00000409093	3/4	40	36	4	40	40	0	LRRTM4,missense_variant,p.Arg157Trp,ENST00000409088,;LRRTM4,missense_variant,p.Arg157Trp,ENST00000409093,;LRRTM4,missense_variant,p.Arg158Trp,ENST00000409282,;LRRTM4,missense_variant,p.Arg157Trp,ENST00000409884,;LRRTM4,missense_variant,p.Arg158Trp,ENST00000409911,;LRRTM4,downstream_gene_variant,,ENST00000456154,;	A	ENSG00000176204	ENST00000409093	Transcript	missense_variant	806	469	157	R/W	Cgg/Tgg	COSM1409655,COSM1409654	.	.	-1	LRRTM4	HGNC	19411	protein_coding	YES	CCDS46346.1	ENSP00000386357	LRRT4_HUMAN	C9JM64_HUMAN	UPI0000047808	.	deleterious(0)	probably_damaging(1)	3/4	.	hmmpanther:PTHR24369:SF1,hmmpanther:PTHR24369,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTCCGAAGGC	.	3	ESCA
REG1A	0	.	GRCh37	2	79349978	79349978	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333G>A	p.Trp111Ter	p.W111*	ENST00000233735	5/6	44	39	5	30	30	0	REG1A,stop_gained,p.Trp111Ter,ENST00000233735,;REG1A,non_coding_transcript_exon_variant,,ENST00000485184,;REG1A,downstream_gene_variant,,ENST00000488524,;REG1A,downstream_gene_variant,,ENST00000461579,;	A	ENSG00000115386	ENST00000233735	Transcript	stop_gained	436	333	111	W/*	tgG/tgA	.	.	.	1	REG1A	HGNC	9951	protein_coding	YES	CCDS1964.1	ENSP00000233735	REG1A_HUMAN	Q2TBE1_HUMAN	UPI000012E72D	.	.	.	5/6	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF25,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R109H|c.326G>A|4,BUFFER|p.R110H|c.329G>A|4	RADIA|MUTECT|MUSE|VARSCANS	CGCTGGCACTG	.	4	ESCA
FOXI3	0	.	GRCh37	2	88748296	88748296	+	RNA	SNP	A	A	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.770T>C	.	.	ENST00000398142	2/2	37	33	4	25	25	0	FOXI3,non_coding_transcript_exon_variant,,ENST00000398142,;FOXI3,non_coding_transcript_exon_variant,,ENST00000428390,;	G	ENSG00000214336	ENST00000398142	Transcript	non_coding_transcript_exon_variant	770	.	.	.	.	.	.	.	-1	FOXI3	HGNC	35123	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCCATTGTC	.	4	ESCA
MBOAT2	0	.	GRCh37	2	8997283	8997283	+	3'UTR	SNP	A	A	G	rs575548110	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1526T>C	.	.	ENST00000305997	13/13	44	41	3	25	25	0	MBOAT2,3_prime_UTR_variant,,ENST00000305997,;MBOAT2,downstream_gene_variant,,ENST00000486484,;MBOAT2,downstream_gene_variant,,ENST00000471753,;MBOAT2,downstream_gene_variant,,ENST00000486315,;MBOAT2,downstream_gene_variant,,ENST00000473432,;	G	ENSG00000143797	ENST00000305997	Transcript	3_prime_UTR_variant	3288	.	.	.	.	rs575548110	.	.	-1	MBOAT2	HGNC	25193	protein_coding	YES	CCDS1660.1	ENSP00000302177	MBOA2_HUMAN	B0AZU0_HUMAN	UPI0000231CFB	.	.	.	13/13	.	.	G:0.0008	G:0	G:0	.	G:0.004	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAGAGAGAG	byFrequency|by1000G	2	ESCA
CNNM4	0	.	GRCh37	2	97475504	97475504	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*250G>T	.	.	ENST00000377075	7/7	52	44	8	43	43	0	CNNM4,3_prime_UTR_variant,,ENST00000540067,;CNNM4,3_prime_UTR_variant,,ENST00000377075,;RP11-353K11.1,downstream_gene_variant,,ENST00000608609,;CNNM4,downstream_gene_variant,,ENST00000496186,;	T	ENSG00000158158	ENST00000377075	Transcript	3_prime_UTR_variant	2676	.	.	.	.	.	.	.	1	CNNM4	HGNC	105	protein_coding	YES	CCDS2024.2	ENSP00000366275	CNNM4_HUMAN	.	UPI0000207C95	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTGAGAGA	.	5	ESCA
IGSF11	0	.	GRCh37	3	118753547	118753547	+	5'UTR	SNP	G	G	T	rs541504678	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-118C>A	.	.	ENST00000393775	1/7	16	7	8	9	9	0	IGSF11,5_prime_UTR_variant,,ENST00000489689,;IGSF11,5_prime_UTR_variant,,ENST00000393775,;IGSF11,5_prime_UTR_variant,,ENST00000480431,;IGSF11,5_prime_UTR_variant,,ENST00000491903,;IGSF11,intron_variant,,ENST00000425327,;IGSF11,intron_variant,,ENST00000354673,;IGSF11,intron_variant,,ENST00000441144,;IGSF11,intron_variant,,ENST00000494802,;	T	ENSG00000144847	ENST00000393775	Transcript	5_prime_UTR_variant	189	.	.	.	.	rs541504678	.	.	-1	IGSF11	HGNC	16669	protein_coding	YES	CCDS46891.1	ENSP00000377370	IGS11_HUMAN	C9JAD3_HUMAN,C9IZX3_HUMAN	UPI000013D9B3	.	.	.	1/7	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCGGGCCGCT	by1000G	3	ESCA
KALRN	0	.	GRCh37	3	124132352	124132352	+	Missense_Mutation	SNP	G	G	C	rs779442681	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2376G>C	p.Leu792Phe	p.L792F	ENST00000240874	14/34	44	39	5	29	29	0	KALRN,missense_variant,p.Leu792Phe,ENST00000240874,;KALRN,missense_variant,p.Leu792Phe,ENST00000460856,;KALRN,missense_variant,p.Leu770Phe,ENST00000354186,;KALRN,missense_variant,p.Leu792Phe,ENST00000360013,;KALRN,non_coding_transcript_exon_variant,,ENST00000484224,;KALRN,non_coding_transcript_exon_variant,,ENST00000393501,;	C	ENSG00000160145	ENST00000240874	Transcript	missense_variant	2533	2376	792	L/F	ttG/ttC	rs779442681	.	.	1	KALRN	HGNC	4814	protein_coding	YES	CCDS3027.1	ENSP00000240874	KALRN_HUMAN	.	UPI000012C095	.	deleterious(0)	probably_damaging(0.986)	14/34	.	hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACTTGCTTCG	.	4	ESCA
ZNF148	0	.	GRCh37	3	125032181	125032181	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304C>G	p.Gln102Glu	p.Q102E	ENST00000360647	4/9	99	94	5	66	66	0	ZNF148,missense_variant,p.Gln102Glu,ENST00000485866,;ZNF148,missense_variant,p.Gln102Glu,ENST00000492394,;ZNF148,missense_variant,p.Gln102Glu,ENST00000360647,;ZNF148,missense_variant,p.Gln102Glu,ENST00000484491,;ZNF148,intron_variant,,ENST00000544464,;ZNF148,intron_variant,,ENST00000468369,;ZNF148,downstream_gene_variant,,ENST00000471196,;ZNF148,downstream_gene_variant,,ENST00000495019,;ZNF148,downstream_gene_variant,,ENST00000465763,;DUTP1,downstream_gene_variant,,ENST00000493631,;DUTP1,downstream_gene_variant,,ENST00000596826,;	C	ENSG00000163848	ENST00000360647	Transcript	missense_variant	790	304	102	Q/E	Caa/Gaa	COSM3846082	.	.	-1	ZNF148	HGNC	12933	protein_coding	YES	CCDS3031.1	ENSP00000353863	ZN148_HUMAN	C9K0U4_HUMAN,C9JRX0_HUMAN,C9J6Y6_HUMAN	UPI000013C2FF	.	tolerated(0.38)	benign(0.237)	4/9	.	hmmpanther:PTHR11389:SF324,hmmpanther:PTHR11389	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTTGAGGAA	.	2	ESCA
DNAJB8	0	.	GRCh37	3	128182345	128182345	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-257C>G	.	.	ENST00000469083	2/2	38	30	8	20	20	0	DNAJB8,5_prime_UTR_variant,,ENST00000319153,;DNAJB8,5_prime_UTR_variant,,ENST00000469083,;DNAJB8-AS1,upstream_gene_variant,,ENST00000471626,;	C	ENSG00000179407	ENST00000469083	Transcript	5_prime_UTR_variant	2302	.	.	.	.	.	.	.	-1	DNAJB8	HGNC	23699	protein_coding	YES	CCDS3048.1	ENSP00000417418	DNJB8_HUMAN	.	UPI0000129437	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCAGAGTGG	.	5	ESCA
PLXND1	0	.	GRCh37	3	129324787	129324787	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696C>A	p.Phe232Leu	p.F232L	ENST00000324093	1/36	19	16	3	20	20	0	PLXND1,missense_variant,p.Phe232Leu,ENST00000393239,;PLXND1,missense_variant,p.Phe232Leu,ENST00000324093,;	T	ENSG00000004399	ENST00000324093	Transcript	missense_variant	875	696	232	F/L	ttC/ttA	COSM4113390,COSM4113391	.	.	-1	PLXND1	HGNC	9107	protein_coding	YES	CCDS33854.1	ENSP00000317128	PLXD1_HUMAN	Q6P657_HUMAN	UPI00003671AD	.	deleterious(0.01)	probably_damaging(0.993)	1/36	.	PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF7,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTCGAAGCG	.	2	ESCA
SLCO2A1	0	.	GRCh37	3	133664007	133664007	+	Missense_Mutation	SNP	C	C	G	rs779203269	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1393G>C	p.Glu465Gln	p.E465Q	ENST00000310926	10/14	54	46	7	39	39	0	SLCO2A1,missense_variant,p.Glu389Gln,ENST00000493729,;SLCO2A1,missense_variant,p.Glu465Gln,ENST00000310926,;SLCO2A1,synonymous_variant,p.%3D,ENST00000481359,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000462770,;SLCO2A1,downstream_gene_variant,,ENST00000477061,;	G	ENSG00000174640	ENST00000310926	Transcript	missense_variant	1667	1393	465	E/Q	Gag/Cag	rs779203269	.	.	-1	SLCO2A1	HGNC	10955	protein_coding	YES	CCDS3084.1	ENSP00000311291	SO2A1_HUMAN	Q4LEJ9_HUMAN	UPI000013F0AD	.	deleterious(0)	probably_damaging(0.998)	10/14	.	Superfamily_domains:SSF100895,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,Pfam_domain:PF07648,Gene3D:3.30.60.30,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF14,PROSITE_profiles:PS51465,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACTCGATTC	byFrequency	5	ESCA
MRAS	0	.	GRCh37	3	138121105	138121105	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.621C>T	p.%3D	p.I207I	ENST00000289104	6/6	62	50	12	37	37	0	MRAS,synonymous_variant,p.%3D,ENST00000464896,;MRAS,synonymous_variant,p.%3D,ENST00000474559,;MRAS,synonymous_variant,p.%3D,ENST00000423968,;MRAS,synonymous_variant,p.%3D,ENST00000289104,;MRAS,downstream_gene_variant,,ENST00000494949,;MRAS,downstream_gene_variant,,ENST00000478647,;	T	ENSG00000158186	ENST00000289104	Transcript	synonymous_variant	1268	621	207	I	atC/atT	.	.	.	1	MRAS	HGNC	7227	protein_coding	YES	CCDS3100.1	ENSP00000289104	RASM_HUMAN	Q6FGP0_HUMAN,C9J8Q6_HUMAN,C9J601_HUMAN	UPI0000001253	.	.	.	6/6	.	SMART_domains:SM00176,PROSITE_profiles:PS51421	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGATCTTGTG	.	5	ESCA
ATR	0	.	GRCh37	3	142224118	142224118	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5059G>C	p.Asp1687His	p.D1687H	ENST00000350721	29/47	39	36	3	29	29	0	ATR,missense_variant,p.Asp1623His,ENST00000383101,;ATR,missense_variant,p.Asp1687His,ENST00000350721,;	G	ENSG00000175054	ENST00000350721	Transcript	missense_variant	5181	5059	1687	D/H	Gat/Cat	COSM728976	.	.	-1	ATR	HGNC	882	protein_coding	YES	CCDS3124.1	ENSP00000343741	ATR_HUMAN	.	UPI0000031A31	.	deleterious(0)	probably_damaging(1)	29/47	.	PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64,Gene3D:1.25.40.10	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCATCAGGTT	.	3	ESCA
TSC22D2	0	.	GRCh37	3	150176626	150176626	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*203C>T	.	.	ENST00000361875	4/4	47	41	5	29	29	0	TSC22D2,3_prime_UTR_variant,,ENST00000361875,;TSC22D2,3_prime_UTR_variant,,ENST00000361136,;TSC22D2,3_prime_UTR_variant,,ENST00000466814,;TSC22D2,3_prime_UTR_variant,,ENST00000480589,;TSC22D2,non_coding_transcript_exon_variant,,ENST00000460316,;TSC22D2,downstream_gene_variant,,ENST00000485421,;	T	ENSG00000196428	ENST00000361875	Transcript	3_prime_UTR_variant	3562	.	.	.	.	.	.	.	1	TSC22D2	HGNC	29095	protein_coding	YES	CCDS3149.1	ENSP00000354543	T22D2_HUMAN	.	UPI00000722E0	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCATCAGTAC	.	4	ESCA
MBNL1	0	.	GRCh37	3	152132747	152132747	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.192G>C	p.Glu64Asp	p.E64D	ENST00000282486	3/10	113	108	5	74	74	0	MBNL1,missense_variant,p.Glu64Asp,ENST00000545754,;MBNL1,missense_variant,p.Glu64Asp,ENST00000282486,;MBNL1,missense_variant,p.Glu64Asp,ENST00000485509,;MBNL1,missense_variant,p.Glu64Asp,ENST00000324196,;MBNL1,missense_variant,p.Glu8Asp,ENST00000459747,;MBNL1,missense_variant,p.Glu64Asp,ENST00000498502,;MBNL1,missense_variant,p.Glu7Asp,ENST00000493459,;MBNL1,missense_variant,p.Glu64Asp,ENST00000357472,;MBNL1,missense_variant,p.Glu64Asp,ENST00000463374,;MBNL1,missense_variant,p.Glu64Asp,ENST00000465907,;MBNL1,missense_variant,p.Glu64Asp,ENST00000282488,;MBNL1,missense_variant,p.Glu64Asp,ENST00000492948,;MBNL1,missense_variant,p.Glu64Asp,ENST00000324210,;MBNL1,missense_variant,p.Glu64Asp,ENST00000355460,;MBNL1,missense_variant,p.Glu64Asp,ENST00000485910,;MBNL1,missense_variant,p.Glu63Asp,ENST00000464596,;MBNL1,5_prime_UTR_variant,,ENST00000460591,;MBNL1,5_prime_UTR_variant,,ENST00000495875,;MBNL1,upstream_gene_variant,,ENST00000478535,;MBNL1,upstream_gene_variant,,ENST00000460166,;	C	ENSG00000152601	ENST00000282486	Transcript	missense_variant	2034	192	64	E/D	gaG/gaC	.	.	.	1	MBNL1	HGNC	6923	protein_coding	YES	CCDS3165.1	ENSP00000282486	MBNL1_HUMAN	C9JCX1_HUMAN,C9J7P7_HUMAN	UPI000003B440	.	tolerated(0.17)	probably_damaging(0.995)	3/10	.	PROSITE_profiles:PS50103,hmmpanther:PTHR12675,hmmpanther:PTHR12675:SF7,SMART_domains:SM00356	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGAGAACTG	.	2	ESCA
C3orf55	0	.	GRCh37	3	157289013	157289013	+	Missense_Mutation	SNP	C	C	G	rs192031896	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.131C>G	p.Ser44Cys	p.S44C	ENST00000449199	3/5	128	110	18	95	95	0	C3orf55,missense_variant,p.Ser44Cys,ENST00000312275,;C3orf55,missense_variant,p.Ser44Cys,ENST00000449199,;C3orf55,missense_variant,p.Ser44Cys,ENST00000426338,;C3orf55,missense_variant,p.Ser44Cys,ENST00000459838,;C3orf55,intron_variant,,ENST00000461040,;C3orf55,downstream_gene_variant,,ENST00000468043,;C3orf55,downstream_gene_variant,,ENST00000498159,;	G	ENSG00000174899	ENST00000449199	Transcript	missense_variant	272	131	44	S/C	tCt/tGt	rs192031896	.	.	1	C3orf55	HGNC	25146	protein_coding	YES	CCDS46943.1	ENSP00000413228	CC055_HUMAN	.	UPI0000161AB6	.	deleterious(0)	probably_damaging(0.991)	3/5	.	hmmpanther:PTHR16201:SF38,hmmpanther:PTHR16201	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCTCTCTGG	byCluster|by1000G	5	ESCA
IL1RAP	0	.	GRCh37	3	190367130	190367130	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1345+3499C>G	.	.	ENST00000317757	.	54	44	9	22	22	0	IL1RAP,3_prime_UTR_variant,,ENST00000412504,;IL1RAP,3_prime_UTR_variant,,ENST00000072516,;IL1RAP,3_prime_UTR_variant,,ENST00000447382,;IL1RAP,intron_variant,,ENST00000317757,;IL1RAP,intron_variant,,ENST00000443369,;IL1RAP,downstream_gene_variant,,ENST00000439062,;IL1RAP,3_prime_UTR_variant,,ENST00000413869,;IL1RAP,3_prime_UTR_variant,,ENST00000342550,;	G	ENSG00000196083	ENST00000317757	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	IL1RAP	HGNC	5995	protein_coding	YES	CCDS54696.1	ENSP00000314807	IL1AP_HUMAN	Q8N9C1_HUMAN,C9JT28_HUMAN,C9J1D9_HUMAN	UPI000020A9C1	.	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATCTATGT	.	5	ESCA
CCDC50	0	.	GRCh37	3	191087747	191087747	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370G>C	p.Glu124Gln	p.E124Q	ENST00000392456	5/12	94	88	6	54	54	0	CCDC50,missense_variant,p.Glu124Gln,ENST00000392456,;CCDC50,missense_variant,p.Glu124Gln,ENST00000392455,;CCDC50,non_coding_transcript_exon_variant,,ENST00000460064,;	C	ENSG00000152492	ENST00000392456	Transcript	missense_variant	960	370	124	E/Q	Gag/Cag	.	.	.	1	CCDC50	HGNC	18111	protein_coding	YES	CCDS33912.1	ENSP00000376250	CCD50_HUMAN	.	UPI000018F5EF	.	deleterious(0)	probably_damaging(0.999)	5/12	.	Pfam_domain:PF15295,hmmpanther:PTHR22115:SF1,hmmpanther:PTHR22115,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAAGAGAAA	.	2	ESCA
MUC4	0	.	GRCh37	3	195512668	195512668	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5783C>G	p.Ser1928Ter	p.S1928*	ENST00000463781	2/25	512	491	20	217	217	0	MUC4,stop_gained,p.Ser1928Ter,ENST00000475231,;MUC4,stop_gained,p.Ser1928Ter,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,stop_gained,p.Ser1928Ter,ENST00000477086,;MUC4,stop_gained,p.Ser1928Ter,ENST00000466475,;MUC4,stop_gained,p.Ser1928Ter,ENST00000478156,;MUC4,stop_gained,p.Ser1928Ter,ENST00000470451,;MUC4,stop_gained,p.Ser1928Ter,ENST00000479406,;MUC4,stop_gained,p.Ser1928Ter,ENST00000477756,;MUC4,stop_gained,p.Ser1928Ter,ENST00000462323,;MUC4,stop_gained,p.Ser1928Ter,ENST00000480843,;	C	ENSG00000145113	ENST00000463781	Transcript	stop_gained	6243	5783	1928	S/*	tCa/tGa	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A1929V|c.5786C>T|3	MUTECT|MUSE	ATGCTGAGGAA	.	2	ESCA
EPM2AIP1	0	.	GRCh37	3	37033360	37033360	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209C>G	p.%3D	p.V403V	ENST00000322716	1/1	32	29	3	22	22	0	EPM2AIP1,synonymous_variant,p.%3D,ENST00000322716,;MLH1,upstream_gene_variant,,ENST00000455445,;MLH1,upstream_gene_variant,,ENST00000441265,;MLH1,upstream_gene_variant,,ENST00000231790,;MLH1,upstream_gene_variant,,ENST00000429117,;MLH1,upstream_gene_variant,,ENST00000456676,;MLH1,upstream_gene_variant,,ENST00000539477,;MLH1,upstream_gene_variant,,ENST00000458205,;MLH1,upstream_gene_variant,,ENST00000435176,;MLH1,upstream_gene_variant,,ENST00000536378,;MLH1,upstream_gene_variant,,ENST00000466900,;MLH1,upstream_gene_variant,,ENST00000492474,;MLH1,upstream_gene_variant,,ENST00000476172,;MLH1,upstream_gene_variant,,ENST00000485889,;MLH1,upstream_gene_variant,,ENST00000432299,;MLH1,upstream_gene_variant,,ENST00000457004,;MLH1,upstream_gene_variant,,ENST00000442249,;MLH1,upstream_gene_variant,,ENST00000454028,;	C	ENSG00000178567	ENST00000322716	Transcript	synonymous_variant	1436	1209	403	V	gtC/gtG	.	.	.	-1	EPM2AIP1	HGNC	19735	protein_coding	YES	CCDS46790.1	ENSP00000406027	EPMIP_HUMAN	.	UPI0000073486	.	.	.	1/1	.	hmmpanther:PTHR11697:SF82,hmmpanther:PTHR11697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAAAGACTTT	.	2	ESCA
TMEM110-MUSTN1	0	.	GRCh37	3	52876944	52876944	+	Silent	SNP	G	G	C	rs147058360	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.651C>G	p.%3D	p.L217L	ENST00000504329	7/10	84	78	6	67	67	0	TMEM110-MUSTN1,synonymous_variant,p.%3D,ENST00000514466,;TMEM110,synonymous_variant,p.%3D,ENST00000355083,;TMEM110-MUSTN1,synonymous_variant,p.%3D,ENST00000504329,;TMEM110,downstream_gene_variant,,ENST00000485356,;TMEM110,upstream_gene_variant,,ENST00000482155,;TMEM110,non_coding_transcript_exon_variant,,ENST00000464769,;TMEM110,upstream_gene_variant,,ENST00000477591,;TMEM110-MUSTN1,upstream_gene_variant,,ENST00000495552,;	C	ENSG00000248592	ENST00000504329	Transcript	synonymous_variant	763	651	217	L	ctC/ctG	rs147058360	.	.	-1	TMEM110-MUSTN1	HGNC	38834	protein_coding	YES	CCDS56264.1	ENSP00000422941	.	A8MSY1_HUMAN	UPI000020AD4B	.	.	.	7/10	.	Pfam_domain:PF12400,hmmpanther:PTHR31735,hmmpanther:PTHR31735:SF2	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCATGAGGAA	byCluster	2	ESCA
DNAH12	0	.	GRCh37	3	57399535	57399535	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5901G>A	p.%3D	p.L1967L	ENST00000351747	39/59	24	21	3	22	22	0	DNAH12,synonymous_variant,p.%3D,ENST00000351747,;DNAH12,synonymous_variant,p.%3D,ENST00000495027,;	T	ENSG00000174844	ENST00000351747	Transcript	synonymous_variant	6082	5901	1967	L	ttG/ttA	.	.	.	-1	DNAH12	HGNC	2943	protein_coding	.	.	ENSP00000295937	DYH12_HUMAN	O15436_HUMAN	UPI00017AA3A8	.	.	.	39/59	.	hmmpanther:PTHR10676:SF250,hmmpanther:PTHR10676,Pfam_domain:PF12775,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTCCAATGC	.	2	ESCA
AIMP1	0	.	GRCh37	4	107246215	107246215	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.121G>C	p.Glu41Gln	p.E41Q	ENST00000394701	2/7	29	23	6	28	28	0	AIMP1,missense_variant,p.Glu17Gln,ENST00000358008,;AIMP1,missense_variant,p.Glu17Gln,ENST00000442366,;AIMP1,missense_variant,p.Glu41Gln,ENST00000394701,;AIMP1,missense_variant,p.Glu17Gln,ENST00000510207,;TBCK,upstream_gene_variant,,ENST00000273980,;	C	ENSG00000164022	ENST00000394701	Transcript	missense_variant	162	121	41	E/Q	Gag/Cag	.	.	.	1	AIMP1	HGNC	10648	protein_coding	YES	CCDS47121.1	ENSP00000378191	AIMP1_HUMAN	D6R937_HUMAN	UPI00005A76B9	.	tolerated(0.32)	probably_damaging(0.999)	2/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11586,hmmpanther:PTHR11586:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GTGCAGAGGCA	.	4	ESCA
GAR1	0	.	GRCh37	4	110745646	110745646	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*59C>G	.	.	ENST00000226796	7/7	34	31	3	28	28	0	GAR1,3_prime_UTR_variant,,ENST00000226796,;GAR1,3_prime_UTR_variant,,ENST00000394631,;RRH,upstream_gene_variant,,ENST00000317735,;GAR1,downstream_gene_variant,,ENST00000506840,;GAR1,downstream_gene_variant,,ENST00000503671,;	G	ENSG00000109534	ENST00000226796	Transcript	3_prime_UTR_variant	977	.	.	.	.	.	.	.	1	GAR1	HGNC	14264	protein_coding	YES	CCDS34050.1	ENSP00000226796	GAR1_HUMAN	.	UPI0000070C13	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTTCTACTA	.	2	ESCA
AGA	0	.	GRCh37	4	178352704	178352704	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*158G>A	.	.	ENST00000264595	9/9	23	19	4	14	14	0	AGA,3_prime_UTR_variant,,ENST00000264595,;AGA,downstream_gene_variant,,ENST00000510635,;AGA,downstream_gene_variant,,ENST00000502310,;AGA,downstream_gene_variant,,ENST00000506853,;	T	ENSG00000038002	ENST00000264595	Transcript	3_prime_UTR_variant	1327	.	.	.	.	.	.	.	-1	AGA	HGNC	318	protein_coding	YES	CCDS3829.1	ENSP00000264595	ASPG_HUMAN	Q6LD43_HUMAN	UPI000013D53C	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|VARSCANS	AATTTCAGATA	.	3	ESCA
PDLIM3	0	.	GRCh37	4	186456520	186456520	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69C>T	p.%3D	p.F23F	ENST00000284770	1/8	48	42	6	42	42	0	PDLIM3,synonymous_variant,p.%3D,ENST00000284770,;PDLIM3,synonymous_variant,p.%3D,ENST00000284771,;PDLIM3,synonymous_variant,p.%3D,ENST00000284767,;PDLIM3,synonymous_variant,p.%3D,ENST00000505886,;PDLIM3,synonymous_variant,p.%3D,ENST00000512293,;PDLIM3,non_coding_transcript_exon_variant,,ENST00000515261,;PDLIM3,non_coding_transcript_exon_variant,,ENST00000504355,;PDLIM3,non_coding_transcript_exon_variant,,ENST00000504011,;	A	ENSG00000154553	ENST00000284770	Transcript	synonymous_variant	143	69	23	F	ttC/ttT	.	.	.	-1	PDLIM3	HGNC	20767	protein_coding	YES	CCDS3844.1	ENSP00000284770	PDLI3_HUMAN	.	UPI000013DDB6	.	.	.	1/8	.	PROSITE_profiles:PS50106,hmmpanther:PTHR24214:SF7,hmmpanther:PTHR24214,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTGAAGTC	.	4	ESCA
TBC1D19	0	.	GRCh37	4	26744169	26744169	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1267C>T	p.Gln423Ter	p.Q423*	ENST00000264866	18/21	55	44	10	49	49	0	TBC1D19,stop_gained,p.Gln358Ter,ENST00000511789,;TBC1D19,stop_gained,p.Gln423Ter,ENST00000264866,;TBC1D19,non_coding_transcript_exon_variant,,ENST00000502873,;	T	ENSG00000109680	ENST00000264866	Transcript	stop_gained	1545	1267	423	Q/*	Caa/Taa	.	.	.	1	TBC1D19	HGNC	25624	protein_coding	YES	CCDS3439.1	ENSP00000264866	TBC19_HUMAN	.	UPI000004A0E3	.	.	.	18/21	.	PROSITE_profiles:PS50086,hmmpanther:PTHR16110,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTCAAACT	.	5	ESCA
HTN3	0	.	GRCh37	4	70896442	70896442	+	Intron	SNP	T	T	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13-3T>G	.	.	ENST00000530128	.	104	87	16	77	77	0	HTN3,splice_region_variant,,ENST00000526767,;HTN3,splice_region_variant,,ENST00000381057,;HTN3,splice_region_variant,,ENST00000530128,;HTN3,splice_region_variant,,ENST00000528003,;HTN3,splice_region_variant,,ENST00000533547,;HTN3,splice_region_variant,,ENST00000529625,;	G	ENSG00000205649	ENST00000530128	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	HTN3	HGNC	5284	protein_coding	YES	CCDS33999.1	ENSP00000432561	HIS3_HUMAN	.	UPI000012C7A2	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTATAGGAC	.	4	ESCA
SH3TC1	0	.	GRCh37	4	8242607	8242607	+	Silent	SNP	C	C	T	rs778116596	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3936C>T	p.%3D	p.N1312N	ENST00000245105	18/18	53	45	8	45	45	0	SH3TC1,synonymous_variant,p.%3D,ENST00000245105,;SH3TC1,synonymous_variant,p.%3D,ENST00000539824,;SH3TC1,synonymous_variant,p.%3D,ENST00000512966,;SH3TC1,3_prime_UTR_variant,,ENST00000515682,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000502350,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000502559,;SH3TC1,downstream_gene_variant,,ENST00000502669,;SH3TC1,downstream_gene_variant,,ENST00000508183,;SH3TC1,downstream_gene_variant,,ENST00000511002,;SH3TC1,downstream_gene_variant,,ENST00000506360,;	T	ENSG00000125089	ENST00000245105	Transcript	synonymous_variant	4003	3936	1312	N	aaC/aaT	rs778116596	.	.	1	SH3TC1	HGNC	26009	protein_coding	YES	CCDS3399.1	ENSP00000245105	S3TC1_HUMAN	F5GXD3_HUMAN,E7EQR1_HUMAN,D6RC98_HUMAN	UPI000013CB93	.	.	.	18/18	.	Superfamily_domains:SSF48452,hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAACGTCCG	byFrequency	4	ESCA
UNC5C	0	.	GRCh37	4	96222865	96222865	+	Missense_Mutation	SNP	G	G	A	rs767605519	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382C>T	p.Arg128Cys	p.R128C	ENST00000453304	3/16	36	32	4	32	32	0	UNC5C,missense_variant,p.Arg128Cys,ENST00000506749,;UNC5C,missense_variant,p.Arg128Cys,ENST00000513796,;UNC5C,missense_variant,p.Arg128Cys,ENST00000453304,;UNC5C,missense_variant,p.Arg128Cys,ENST00000504962,;	A	ENSG00000182168	ENST00000453304	Transcript	missense_variant	731	382	128	R/C	Cgc/Tgc	rs767605519,COSM1541008	.	.	-1	UNC5C	HGNC	12569	protein_coding	YES	CCDS3643.1	ENSP00000406022	UNC5C_HUMAN	Q4W5H4_HUMAN	UPI000004E6A5	.	deleterious(0)	probably_damaging(0.995)	3/16	.	Superfamily_domains:SSF48726,Gene3D:2.60.40.10,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGCGCGAAA	byFrequency	4	ESCA
PPIP5K2	0	.	GRCh37	5	102488444	102488444	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1121C>A	p.Ser374Tyr	p.S374Y	ENST00000321521	10/30	57	48	9	45	45	0	PPIP5K2,missense_variant,p.Ser374Tyr,ENST00000414217,;PPIP5K2,missense_variant,p.Ser374Tyr,ENST00000358359,;PPIP5K2,missense_variant,p.Ser374Tyr,ENST00000321521,;PPIP5K2,missense_variant,p.Ser296Tyr,ENST00000507921,;PPIP5K2,downstream_gene_variant,,ENST00000507310,;PPIP5K2,non_coding_transcript_exon_variant,,ENST00000513500,;	A	ENSG00000145725	ENST00000321521	Transcript	missense_variant	1694	1121	374	S/Y	tCt/tAt	.	.	.	1	PPIP5K2	HGNC	29035	protein_coding	YES	CCDS34207.1	ENSP00000313070	VIP2_HUMAN	K7EPT7_HUMAN,D6RFG4_HUMAN	UPI000006E414	.	tolerated(0.2)	benign(0.43)	10/30	.	Superfamily_domains:SSF53254,hmmpanther:PTHR12750:SF10,hmmpanther:PTHR12750	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACATCTGGAA	.	5	ESCA
PAIP2	0	.	GRCh37	5	138677596	138677596	+	5'Flank	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000394795	.	110	105	5	75	75	0	PAIP2,5_prime_UTR_variant,,ENST00000265192,;PAIP2,5_prime_UTR_variant,,ENST00000511706,;PAIP2,5_prime_UTR_variant,,ENST00000507755,;PAIP2,upstream_gene_variant,,ENST00000394795,;PAIP2,upstream_gene_variant,,ENST00000510080,;PAIP2,non_coding_transcript_exon_variant,,ENST00000511381,;PAIP2,non_coding_transcript_exon_variant,,ENST00000510409,;PAIP2,upstream_gene_variant,,ENST00000507415,;	A	ENSG00000120727	ENST00000394795	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	535	1	PAIP2	HGNC	17970	protein_coding	YES	CCDS4211.1	ENSP00000378275	PAIP2_HUMAN	D6RA77_HUMAN	UPI0000049FBF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGGGGAGCGG	.	2	ESCA
PCDHA2	0	.	GRCh37	5	140174599	140174599	+	Missense_Mutation	SNP	C	C	G	rs781893367	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50C>G	p.Ser17Trp	p.S17W	ENST00000526136	1/4	58	50	8	36	36	0	PCDHA2,missense_variant,p.Ser17Trp,ENST00000378132,;PCDHA2,missense_variant,p.Ser17Trp,ENST00000526136,;PCDHA2,missense_variant,p.Ser17Trp,ENST00000520672,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA1,intron_variant,,ENST00000394633,;	G	ENSG00000204969	ENST00000526136	Transcript	missense_variant	50	50	17	S/W	tCg/tGg	rs781893367	.	.	1	PCDHA2	HGNC	8668	protein_coding	YES	CCDS54914.1	ENSP00000431748	PCDA2_HUMAN	.	UPI00001273C9	.	tolerated_low_confidence(0.21)	benign(0.024)	1/4	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTCTCGCTTC	.	4	ESCA
PCDHB1	0	.	GRCh37	5	140431453	140431453	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398T>C	p.Phe133Ser	p.F133S	ENST00000306549	1/1	28	22	5	30	30	0	PCDHB1,missense_variant,p.Phe133Ser,ENST00000306549,;	C	ENSG00000171815	ENST00000306549	Transcript	missense_variant	475	398	133	F/S	tTc/tCc	.	.	.	1	PCDHB1	HGNC	8680	protein_coding	YES	CCDS4243.1	ENSP00000307234	PCDB1_HUMAN	.	UPI000013EB56	.	deleterious(0)	probably_damaging(0.997)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF88,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTTTCCTAA	.	5	ESCA
PCDHB6	0	.	GRCh37	5	140530592	140530592	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.754G>A	p.Glu252Lys	p.E252K	ENST00000231136	1/1	43	35	8	32	32	0	PCDHB6,missense_variant,p.Glu116Lys,ENST00000543635,;PCDHB6,missense_variant,p.Glu252Lys,ENST00000231136,;PCDHB17,upstream_gene_variant,,ENST00000539533,;	A	ENSG00000113211	ENST00000231136	Transcript	missense_variant	754	754	252	E/K	Gag/Aag	.	.	.	1	PCDHB6	HGNC	8691	protein_coding	YES	CCDS4248.1	ENSP00000231136	PCDB6_HUMAN	F5H446_HUMAN	UPI00001273E2	.	deleterious(0)	probably_damaging(1)	1/1	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTGAGAAC	.	5	ESCA
KCTD16	0	.	GRCh37	5	143586365	143586365	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88A>C	p.Asn30His	p.N30H	ENST00000507359	2/3	35	32	3	13	13	0	KCTD16,missense_variant,p.Asn30His,ENST00000507359,;KCTD16,missense_variant,p.Asn30His,ENST00000512467,;	C	ENSG00000183775	ENST00000507359	Transcript	missense_variant	1179	88	30	N/H	Aat/Cat	.	.	.	1	KCTD16	HGNC	29244	protein_coding	YES	CCDS34260.1	ENSP00000426548	KCD16_HUMAN	.	UPI000004A046	.	deleterious(0)	probably_damaging(0.999)	2/3	.	Superfamily_domains:SSF54695,SMART_domains:SM00225,Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR14499:SF28,hmmpanther:PTHR14499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTGAATGTC	.	2	ESCA
ATP10B	0	.	GRCh37	5	160114974	160114974	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108G>C	p.%3D	p.G36G	ENST00000327245	5/26	72	67	5	35	35	0	ATP10B,synonymous_variant,p.%3D,ENST00000327245,;CTC-529G1.1,intron_variant,,ENST00000524198,;ATP10B,non_coding_transcript_exon_variant,,ENST00000518411,;ATP10B,non_coding_transcript_exon_variant,,ENST00000520098,;ATP10B,downstream_gene_variant,,ENST00000520975,;ATP10B,non_coding_transcript_exon_variant,,ENST00000521033,;ATP10B,non_coding_transcript_exon_variant,,ENST00000517802,;ATP10B,upstream_gene_variant,,ENST00000326831,;	G	ENSG00000118322	ENST00000327245	Transcript	synonymous_variant	955	108	36	G	ggG/ggC	.	.	.	-1	ATP10B	HGNC	13543	protein_coding	YES	CCDS43394.1	ENSP00000313600	AT10B_HUMAN	.	UPI0000191DAE	.	.	.	5/26	.	hmmpanther:PTHR24092:SF42,hmmpanther:PTHR24092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTCTCCCTTT	.	2	ESCA
CDH18	0	.	GRCh37	5	19473394	19473394	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2314C>A	p.Pro772Thr	p.P772T	ENST00000507958	15/15	72	53	18	45	45	0	CDH18,missense_variant,p.Pro772Thr,ENST00000382275,;CDH18,missense_variant,p.Pro772Thr,ENST00000274170,;CDH18,missense_variant,p.Pro772Thr,ENST00000507958,;CDH18,downstream_gene_variant,,ENST00000515257,;CDH18,downstream_gene_variant,,ENST00000506372,;CDH18,downstream_gene_variant,,ENST00000502796,;CDH18,non_coding_transcript_exon_variant,,ENST00000510297,;	T	ENSG00000145526	ENST00000507958	Transcript	missense_variant	3305	2314	772	P/T	Ccc/Acc	COSM1620196,COSM1620195	.	.	-1	CDH18	HGNC	1757	protein_coding	YES	CCDS3889.1	ENSP00000425093	CAD18_HUMAN	.	UPI0000126DBD	.	deleterious(0)	probably_damaging(0.999)	15/15	.	Pfam_domain:PF01049,Gene3D:4.10.900.10,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF106	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGGGTCCCC	.	5	ESCA
SLC1A3	0	.	GRCh37	5	36687911	36687911	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1540C>T	.	.	ENST00000265113	10/10	25	21	3	20	20	0	SLC1A3,3_prime_UTR_variant,,ENST00000265113,;SLC1A3,3_prime_UTR_variant,,ENST00000381918,;CTD-2353F22.1,intron_variant,,ENST00000510740,;SLC1A3,downstream_gene_variant,,ENST00000506178,;	T	ENSG00000079215	ENST00000265113	Transcript	3_prime_UTR_variant	3645	.	.	.	.	.	.	.	1	SLC1A3	HGNC	10941	protein_coding	YES	CCDS3919.1	ENSP00000265113	EAA1_HUMAN	E7EUV6_HUMAN,E7EUS7_HUMAN	UPI0000129B0F	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCTCCCAGGT	.	3	ESCA
NIPBL	0	.	GRCh37	5	36975895	36975895	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.886A>G	p.Ile296Val	p.I296V	ENST00000282516	9/47	44	37	6	25	25	0	NIPBL,missense_variant,p.Ile296Val,ENST00000448238,;NIPBL,missense_variant,p.Ile296Val,ENST00000282516,;NIPBL,non_coding_transcript_exon_variant,,ENST00000504430,;NIPBL,non_coding_transcript_exon_variant,,ENST00000505998,;	G	ENSG00000164190	ENST00000282516	Transcript	missense_variant	1385	886	296	I/V	Atc/Gtc	.	.	.	1	NIPBL	HGNC	28862	protein_coding	YES	CCDS3920.1	ENSP00000282516	NIPBL_HUMAN	A2RRA7_HUMAN	UPI00003761B5	.	deleterious_low_confidence(0)	benign(0.025)	9/47	.	hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CTTTAATCCTA	.	4	ESCA
HCN1	0	.	GRCh37	5	45260968	45260968	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1055G>C	.	.	ENST00000303230	8/8	61	54	7	59	59	0	HCN1,3_prime_UTR_variant,,ENST00000303230,;	G	ENSG00000164588	ENST00000303230	Transcript	3_prime_UTR_variant	3786	.	.	.	.	.	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTTTCTCTAC	.	4	ESCA
SMN2	0	.	GRCh37	5	69372363	69372363	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.850C>G	p.Gln284Glu	p.Q284E	ENST00000380743	8/9	42	35	7	42	42	0	SMN2,missense_variant,p.Gln252Glu,ENST00000380742,;SMN2,missense_variant,p.Gln217Glu,ENST00000511812,;SMN2,missense_variant,p.Gln284Glu,ENST00000380743,;SMN2,intron_variant,,ENST00000380741,;RN7SL9P,downstream_gene_variant,,ENST00000584813,;SMN2,missense_variant,p.Gln36Glu,ENST00000507458,;SMN2,non_coding_transcript_exon_variant,,ENST00000505346,;SMN2,non_coding_transcript_exon_variant,,ENST00000514914,;SMN2,intron_variant,,ENST00000506734,;	G	ENSG00000205571	ENST00000380743	Transcript	missense_variant	924	850	284	Q/E	Caa/Gaa	.	.	.	1	SMN2	HGNC	11118	protein_coding	YES	CCDS4007.1	ENSP00000370119	SMN_HUMAN	Q9UNT8_HUMAN	UPI00000000BB	.	deleterious(0.05)	benign(0.002)	8/9	.	Pfam_domain:PF06003,hmmpanther:PTHR12664	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AAAATCAAAAA	.	4	ESCA
OTP	0	.	GRCh37	5	76932724	76932724	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369C>T	p.%3D	p.F123F	ENST00000306422	2/3	101	94	7	91	91	0	OTP,synonymous_variant,p.%3D,ENST00000306422,;OTP,non_coding_transcript_exon_variant,,ENST00000515716,;	A	ENSG00000171540	ENST00000306422	Transcript	synonymous_variant	1508	369	123	F	ttC/ttT	COSM3617999	.	.	-1	OTP	HGNC	8518	protein_coding	YES	CCDS4039.1	ENSP00000302814	OTP_HUMAN	.	UPI0000021CAA	.	.	.	2/3	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF274,hmmpanther:PTHR24329,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGCGAAGCT	.	2	ESCA
MSH3	0	.	GRCh37	5	79950579	79950579	+	Silent	SNP	C	C	G	rs564921007	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33C>G	p.%3D	p.L11L	ENST00000265081	1/24	27	24	3	27	27	0	MSH3,synonymous_variant,p.%3D,ENST00000265081,;DHFR,5_prime_UTR_variant,,ENST00000439211,;DHFR,upstream_gene_variant,,ENST00000504396,;DHFR,upstream_gene_variant,,ENST00000511032,;MTRNR2L2,upstream_gene_variant,,ENST00000604882,;DHFR,upstream_gene_variant,,ENST00000505337,;MSH3,upstream_gene_variant,,ENST00000512531,;DHFR,upstream_gene_variant,,ENST00000513048,;DHFR,upstream_gene_variant,,ENST00000508282,;DHFR,upstream_gene_variant,,ENST00000513314,;	G	ENSG00000113318	ENST00000265081	Transcript	synonymous_variant	113	33	11	L	ctC/ctG	rs564921007,COSM1311352,COSM3828533	.	.	1	MSH3	HGNC	7326	protein_coding	YES	CCDS34195.1	ENSP00000265081	MSH3_HUMAN	.	UPI0000DBEE85	.	.	.	1/24	.	Low_complexity_(Seg):seg	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGCCTCGCTGC	byFrequency|byCluster|by1000G	2	ESCA
MEF2C	0	.	GRCh37	5	88017557	88017557	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*864G>A	.	.	ENST00000340208	12/12	55	45	10	53	53	0	MEF2C,3_prime_UTR_variant,,ENST00000504921,;MEF2C,3_prime_UTR_variant,,ENST00000510942,;MEF2C,3_prime_UTR_variant,,ENST00000514028,;MEF2C,3_prime_UTR_variant,,ENST00000506554,;MEF2C,3_prime_UTR_variant,,ENST00000340208,;MEF2C,3_prime_UTR_variant,,ENST00000424173,;MEF2C,3_prime_UTR_variant,,ENST00000437473,;MEF2C,downstream_gene_variant,,ENST00000514015,;MEF2C,downstream_gene_variant,,ENST00000508569,;MEF2C,downstream_gene_variant,,ENST00000539796,;CTC-467M3.1,intron_variant,,ENST00000510274,;MEF2C,downstream_gene_variant,,ENST00000510980,;	T	ENSG00000081189	ENST00000340208	Transcript	3_prime_UTR_variant	2722	.	.	.	.	.	.	.	-1	MEF2C	HGNC	6996	protein_coding	YES	CCDS54878.1	ENSP00000340874	MEF2C_HUMAN	H0YNI2_HUMAN,D6RJA7_HUMAN,D6RJ95_HUMAN,D6RG14_HUMAN	UPI0000D9B539	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTCATGGC	.	5	ESCA
BEND3	0	.	GRCh37	6	107391610	107391610	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785C>G	p.Ser262Ter	p.S262*	ENST00000429433	5/5	77	69	8	44	44	0	BEND3,stop_gained,p.Ser262Ter,ENST00000429433,;BEND3,stop_gained,p.Ser262Ter,ENST00000369042,;	C	ENSG00000178409	ENST00000429433	Transcript	stop_gained	1435	785	262	S/*	tCa/tGa	.	.	.	-1	BEND3	HGNC	23040	protein_coding	YES	CCDS34507.1	ENSP00000411268	BEND3_HUMAN	.	UPI00001D80D7	.	.	.	5/5	.	PROSITE_profiles:PS51457	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCCTGACAGG	.	4	ESCA
LAMA4	0	.	GRCh37	6	112443245	112443245	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4447G>C	p.Glu1483Gln	p.E1483Q	ENST00000230538	32/39	78	69	9	49	49	0	LAMA4,missense_variant,p.Glu1483Gln,ENST00000230538,;LAMA4,missense_variant,p.Glu1476Gln,ENST00000424408,;LAMA4,missense_variant,p.Glu1476Gln,ENST00000522006,;LAMA4,missense_variant,p.Glu1476Gln,ENST00000389463,;LAMA4,non_coding_transcript_exon_variant,,ENST00000604740,;LAMA4,downstream_gene_variant,,ENST00000521693,;	G	ENSG00000112769	ENST00000230538	Transcript	missense_variant	4845	4447	1483	E/Q	Gaa/Caa	.	.	.	-1	LAMA4	HGNC	6484	protein_coding	YES	CCDS43491.1	ENSP00000230538	LAMA4_HUMAN	E5RK79_HUMAN,E5RHF3_HUMAN,E5RFQ2_HUMAN,E5RFD7_HUMAN	UPI000013C937	.	tolerated(0.28)	benign(0.022)	32/39	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF174,Gene3D:2.60.120.200,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTTCAAACT	.	4	ESCA
LAMA4	0	.	GRCh37	6	112496650	112496650	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1222G>A	p.Glu408Lys	p.E408K	ENST00000230538	11/39	42	38	4	22	22	0	LAMA4,missense_variant,p.Glu408Lys,ENST00000230538,;LAMA4,missense_variant,p.Glu401Lys,ENST00000424408,;LAMA4,missense_variant,p.Glu401Lys,ENST00000522006,;LAMA4,missense_variant,p.Glu401Lys,ENST00000389463,;LAMA4,downstream_gene_variant,,ENST00000368640,;LAMA4,downstream_gene_variant,,ENST00000521732,;LAMA4,non_coding_transcript_exon_variant,,ENST00000521187,;	T	ENSG00000112769	ENST00000230538	Transcript	missense_variant	1620	1222	408	E/K	Gag/Aag	.	.	.	-1	LAMA4	HGNC	6484	protein_coding	YES	CCDS43491.1	ENSP00000230538	LAMA4_HUMAN	E5RK79_HUMAN,E5RHF3_HUMAN,E5RFQ2_HUMAN,E5RFD7_HUMAN	UPI000013C937	.	tolerated(0.67)	benign(0.007)	11/39	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF174,Pfam_domain:PF06008	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGCTCTTCCC	.	3	ESCA
SYNE1	0	.	GRCh37	6	152644662	152644662	+	Missense_Mutation	SNP	C	C	G	rs555495237	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15868G>C	p.Glu5290Gln	p.E5290Q	ENST00000367255	82/146	42	36	5	26	26	0	SYNE1,missense_variant,p.Glu5219Gln,ENST00000448038,;SYNE1,missense_variant,p.Glu5290Gln,ENST00000367255,;SYNE1,missense_variant,p.Glu5219Gln,ENST00000423061,;SYNE1,missense_variant,p.Glu4983Gln,ENST00000341594,;SYNE1,missense_variant,p.Glu5290Gln,ENST00000265368,;SYNE1,non_coding_transcript_exon_variant,,ENST00000490135,;	G	ENSG00000131018	ENST00000367255	Transcript	missense_variant	16470	15868	5290	E/Q	Gag/Cag	rs555495237	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	benign(0.004)	82/146	.	SMART_domains:SM00150,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGCTCTTCCC	by1000G	3	ESCA
SCAF8	0	.	GRCh37	6	155153402	155153402	+	Missense_Mutation	SNP	C	C	A	rs745485641	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2689C>A	p.Leu897Met	p.L897M	ENST00000367178	20/20	57	53	4	30	30	0	SCAF8,missense_variant,p.Leu963Met,ENST00000367186,;SCAF8,missense_variant,p.Leu897Met,ENST00000367178,;SCAF8,missense_variant,p.Leu897Met,ENST00000417268,;TIAM2,upstream_gene_variant,,ENST00000461783,;TIAM2,upstream_gene_variant,,ENST00000460692,;TIAM2,upstream_gene_variant,,ENST00000535064,;	A	ENSG00000213079	ENST00000367178	Transcript	missense_variant	3265	2689	897	L/M	Ctg/Atg	rs745485641	.	.	1	SCAF8	HGNC	20959	protein_coding	YES	CCDS5247.1	ENSP00000356146	SCAF8_HUMAN	Q9H8B2_HUMAN,Q8NDE9_HUMAN	UPI0000070A1C	.	deleterious_low_confidence(0.03)	benign(0.343)	20/20	.	hmmpanther:PTHR14124:SF4,hmmpanther:PTHR14124	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACTTCTGGGA	.	2	ESCA
ACAT2	0	.	GRCh37	6	160196340	160196340	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.629G>A	p.Arg210Lys	p.R210K	ENST00000367048	5/9	61	53	7	43	43	0	ACAT2,missense_variant,p.Arg239Lys,ENST00000541436,;ACAT2,missense_variant,p.Arg210Lys,ENST00000367048,;TCP1,downstream_gene_variant,,ENST00000392168,;TCP1,downstream_gene_variant,,ENST00000321394,;TCP1,downstream_gene_variant,,ENST00000539756,;TCP1,downstream_gene_variant,,ENST00000544255,;TCP1,downstream_gene_variant,,ENST00000420894,;SNORA20,downstream_gene_variant,,ENST00000384662,;ACAT2,non_coding_transcript_exon_variant,,ENST00000472052,;ACAT2,downstream_gene_variant,,ENST00000467951,;TCP1,downstream_gene_variant,,ENST00000546204,;	A	ENSG00000120437	ENST00000367048	Transcript	missense_variant	2389	629	210	R/K	aGa/aAa	.	.	.	1	ACAT2	HGNC	94	protein_coding	YES	CCDS5268.1	ENSP00000356015	THIC_HUMAN	.	UPI000013CA85	.	tolerated(0.28)	benign(0.005)	5/9	.	hmmpanther:PTHR18919:SF80,hmmpanther:PTHR18919,TIGRFAM_domain:TIGR01930,Pfam_domain:PF00108,Gene3D:3.40.47.10,PIRSF_domain:PIRSF000429,Superfamily_domains:SSF53901	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTAGAAAAG	.	4	ESCA
ZNF311	0	.	GRCh37	6	28963076	28963076	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1703C>G	p.Ser568Ter	p.S568*	ENST00000377179	7/7	66	56	10	30	30	0	ZNF311,stop_gained,p.Ser568Ter,ENST00000377179,;ZNF311,non_coding_transcript_exon_variant,,ENST00000483450,;	C	ENSG00000197935	ENST00000377179	Transcript	stop_gained	2216	1703	568	S/*	tCa/tGa	.	.	.	-1	ZNF311	HGNC	13847	protein_coding	YES	CCDS34357.1	ENSP00000366384	ZN311_HUMAN	.	UPI000020D71E	.	.	.	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF273,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTGAACTA	.	5	ESCA
SLC44A4	0	.	GRCh37	6	31833354	31833354	+	Missense_Mutation	SNP	C	C	G	rs537294061	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1607G>C	p.Cys536Ser	p.C536S	ENST00000229729	16/21	39	34	5	35	35	0	SLC44A4,missense_variant,p.Cys536Ser,ENST00000229729,;SLC44A4,missense_variant,p.Cys460Ser,ENST00000544672,;SLC44A4,missense_variant,p.Cys494Ser,ENST00000375562,;SLC44A4,downstream_gene_variant,,ENST00000414427,;NEU1,upstream_gene_variant,,ENST00000375631,;SLC44A4,upstream_gene_variant,,ENST00000487680,;NEU1,upstream_gene_variant,,ENST00000495807,;SLC44A4,downstream_gene_variant,,ENST00000475563,;NEU1,upstream_gene_variant,,ENST00000491768,;NEU1,upstream_gene_variant,,ENST00000480384,;SLC44A4,downstream_gene_variant,,ENST00000479777,;	G	ENSG00000204385	ENST00000229729	Transcript	missense_variant	1628	1607	536	C/S	tGc/tCc	rs537294061	.	.	-1	SLC44A4	HGNC	13941	protein_coding	YES	CCDS4724.2	ENSP00000229729	CTL4_HUMAN	.	UPI00004702CE	.	deleterious(0.03)	probably_damaging(0.955)	16/21	.	hmmpanther:PTHR12385,hmmpanther:PTHR12385:SF37,Pfam_domain:PF04515	A:0.0006	A:0	A:0	.	A:0	A:0	A:0.0031	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGATGCAGCGG	byFrequency|by1000G	4	ESCA
B3GALT4	0	.	GRCh37	6	33246327	33246327	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1131G>C	p.Gln377His	p.Q377H	ENST00000451237	1/1	39	36	3	39	39	0	B3GALT4,missense_variant,p.Gln377His,ENST00000451237,;RPS18,downstream_gene_variant,,ENST00000474973,;WDR46,downstream_gene_variant,,ENST00000444176,;WDR46,downstream_gene_variant,,ENST00000374617,;RPS18,downstream_gene_variant,,ENST00000439602,;RPS18,downstream_gene_variant,,ENST00000476222,;WDR46,downstream_gene_variant,,ENST00000461951,;B3GALT4,upstream_gene_variant,,ENST00000606990,;RPS18,downstream_gene_variant,,ENST00000472218,;RPS18,downstream_gene_variant,,ENST00000496813,;RPS18,downstream_gene_variant,,ENST00000490191,;WDR46,downstream_gene_variant,,ENST00000473611,;RPS18,downstream_gene_variant,,ENST00000479802,;RPS18,downstream_gene_variant,,ENST00000474626,;WDR46,downstream_gene_variant,,ENST00000489905,;	C	ENSG00000235863	ENST00000451237	Transcript	missense_variant	1411	1131	377	Q/H	caG/caC	.	.	.	1	B3GALT4	HGNC	919	protein_coding	YES	CCDS34425.1	ENSP00000390784	B3GT4_HUMAN	Q5STJ7_HUMAN	UPI0000126710	.	tolerated_low_confidence(1)	benign(0)	1/1	.	hmmpanther:PTHR11214:SF77,hmmpanther:PTHR11214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCAGAGCTG	.	2	ESCA
CDKN1A	0	.	GRCh37	6	36652282	36652282	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404G>C	p.Gly135Ala	p.G135A	ENST00000405375	2/3	42	39	3	23	23	0	CDKN1A,missense_variant,p.Gly135Ala,ENST00000244741,;CDKN1A,missense_variant,p.Gly135Ala,ENST00000373711,;CDKN1A,missense_variant,p.Gly169Ala,ENST00000448526,;CDKN1A,missense_variant,p.Gly135Ala,ENST00000405375,;CDKN1A,non_coding_transcript_exon_variant,,ENST00000459970,;CDKN1A,downstream_gene_variant,,ENST00000462537,;CDKN1A,downstream_gene_variant,,ENST00000478800,;	C	ENSG00000124762	ENST00000405375	Transcript	missense_variant	639	404	135	G/A	gGa/gCa	.	.	.	1	CDKN1A	HGNC	1784	protein_coding	YES	CCDS4824.1	ENSP00000384849	CDN1A_HUMAN	.	UPI0000048F7B	.	tolerated(0.08)	benign(0.197)	2/3	.	hmmpanther:PTHR10265,hmmpanther:PTHR10265:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCTGGAGACT	.	2	ESCA
FRS3	0	.	GRCh37	6	41739196	41739196	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640G>A	p.Glu214Lys	p.E214K	ENST00000373018	7/7	134	128	6	70	70	0	FRS3,missense_variant,p.Glu214Lys,ENST00000259748,;FRS3,missense_variant,p.Glu214Lys,ENST00000373018,;FRS3,downstream_gene_variant,,ENST00000422888,;FRS3,downstream_gene_variant,,ENST00000426290,;FRS3,downstream_gene_variant,,ENST00000466420,;	T	ENSG00000137218	ENST00000373018	Transcript	missense_variant	892	640	214	E/K	Gag/Aag	COSM161158	.	.	-1	FRS3	HGNC	16970	protein_coding	YES	CCDS4860.1	ENSP00000362109	FRS3_HUMAN	A6PVU0_HUMAN	UPI0000073ACA	.	tolerated(0.08)	probably_damaging(0.947)	7/7	.	hmmpanther:PTHR21258:SF39,hmmpanther:PTHR21258	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCCTCAGGCA	.	2	ESCA
MEA1	0	.	GRCh37	6	42980987	42980987	+	Missense_Mutation	SNP	C	C	G	rs201793021	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.169G>C	p.Glu57Gln	p.E57Q	ENST00000244711	2/4	85	74	11	61	61	0	MEA1,missense_variant,p.Glu57Gln,ENST00000244711,;PPP2R5D,downstream_gene_variant,,ENST00000461010,;PPP2R5D,downstream_gene_variant,,ENST00000486843,;KLHDC3,upstream_gene_variant,,ENST00000326974,;PPP2R5D,downstream_gene_variant,,ENST00000485511,;PPP2R5D,downstream_gene_variant,,ENST00000394110,;PPP2R5D,downstream_gene_variant,,ENST00000470467,;KLHDC3,upstream_gene_variant,,ENST00000332245,;PPP2R5D,downstream_gene_variant,,ENST00000472118,;KLHDC3,upstream_gene_variant,,ENST00000244670,;PPP2R5D,downstream_gene_variant,,ENST00000230402,;PPP2R5D,downstream_gene_variant,,ENST00000482315,;	G	ENSG00000124733	ENST00000244711	Transcript	missense_variant	324	169	57	E/Q	Gag/Cag	rs201793021	.	.	-1	MEA1	HGNC	6986	protein_coding	YES	CCDS4879.1	ENSP00000244711	MEA1_HUMAN	.	UPI000007291B	.	deleterious(0.04)	possibly_damaging(0.673)	2/4	.	Pfam_domain:PF06910,hmmpanther:PTHR17005:SF2,hmmpanther:PTHR17005,Low_complexity_(Seg):seg	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTCTTCCT	byCluster|by1000G	4	ESCA
GCLC	0	.	GRCh37	6	53362976	53362976	+	3'UTR	DEL	T	T	-	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*578delA	.	.	ENST00000229416	16/16	68	62	6	32	32	0	GCLC,3_prime_UTR_variant,,ENST00000229416,;GCLC,non_coding_transcript_exon_variant,,ENST00000515580,;GCLC,non_coding_transcript_exon_variant,,ENST00000509541,;GCLC,downstream_gene_variant,,ENST00000504353,;GCLC,downstream_gene_variant,,ENST00000510837,;	-	ENSG00000001084	ENST00000229416	Transcript	3_prime_UTR_variant	2976	.	.	.	.	.	.	.	-1	GCLC	HGNC	4311	protein_coding	YES	CCDS4952.1	ENSP00000229416	GSH1_HUMAN	Q14TF0_HUMAN,D6R959_HUMAN,B4E2I4_HUMAN	UPI000000D970	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAAGCTTGGGG	.	3	ESCA
DST	0	.	GRCh37	6	56324949	56324949	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15233G>C	p.Arg5078Thr	p.R5078T	ENST00000244364	83/84	42	37	4	38	38	0	DST,missense_variant,p.Arg7153Thr,ENST00000446842,;DST,missense_variant,p.Arg5282Thr,ENST00000370788,;DST,missense_variant,p.Arg5078Thr,ENST00000244364,;DST,missense_variant,p.Arg7368Thr,ENST00000361203,;DST,missense_variant,p.Arg7657Thr,ENST00000370754,;DST,missense_variant,p.Arg7479Thr,ENST00000370769,;DST,missense_variant,p.Arg166Thr,ENST00000523292,;DST,missense_variant,p.Arg5364Thr,ENST00000421834,;DST,3_prime_UTR_variant,,ENST00000312431,;DST,non_coding_transcript_exon_variant,,ENST00000523597,;DST,non_coding_transcript_exon_variant,,ENST00000466429,;DST,non_coding_transcript_exon_variant,,ENST00000482156,;DST,non_coding_transcript_exon_variant,,ENST00000518464,;DST,downstream_gene_variant,,ENST00000524216,;	G	ENSG00000151914	ENST00000244364	Transcript	missense_variant	15441	15233	5078	R/T	aGa/aCa	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	possibly_damaging(0.755)	83/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGACTCTGGCA	.	3	ESCA
ME1	0	.	GRCh37	6	83947511	83947511	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951G>C	p.Leu317Phe	p.L317F	ENST00000369705	9/14	61	55	6	32	32	0	ME1,missense_variant,p.Leu151Phe,ENST00000541327,;ME1,missense_variant,p.Leu317Phe,ENST00000369705,;ME1,missense_variant,p.Leu242Phe,ENST00000543031,;	G	ENSG00000065833	ENST00000369705	Transcript	missense_variant	1068	951	317	L/F	ttG/ttC	.	.	.	-1	ME1	HGNC	6983	protein_coding	YES	CCDS34492.1	ENSP00000358719	MAOX_HUMAN	F5H4W0_HUMAN,B4DZ70_HUMAN	UPI000000127E	.	deleterious(0)	possibly_damaging(0.647)	9/14	.	hmmpanther:PTHR23406,hmmpanther:PTHR23406:SF17,Pfam_domain:PF03949,Gene3D:3.40.50.720,PIRSF_domain:PIRSF000106,SMART_domains:SM00919,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTCCAAGGC	.	3	ESCA
MDN1	0	.	GRCh37	6	90402667	90402667	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10082C>G	p.Ser3361Cys	p.S3361C	ENST00000369393	63/102	28	23	4	39	39	0	MDN1,missense_variant,p.Ser3361Cys,ENST00000369393,;MDN1,missense_variant,p.Ser3361Cys,ENST00000428876,;	C	ENSG00000112159	ENST00000369393	Transcript	missense_variant	10198	10082	3361	S/C	tCt/tGt	.	.	.	-1	MDN1	HGNC	18302	protein_coding	YES	CCDS5024.1	ENSP00000358400	MDN1_HUMAN	M0QXR3_HUMAN	UPI000013C4B8	.	.	possibly_damaging(0.853)	63/102	.	hmmpanther:PTHR22908:SF58,hmmpanther:PTHR22908,PIRSF_domain:PIRSF010340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCAGACCGT	.	5	ESCA
NRCAM	0	.	GRCh37	7	107789071	107789071	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1284G>C	.	.	ENST00000379028	33/33	52	44	8	42	42	0	NRCAM,3_prime_UTR_variant,,ENST00000351718,;NRCAM,3_prime_UTR_variant,,ENST00000413765,;NRCAM,3_prime_UTR_variant,,ENST00000379024,;NRCAM,3_prime_UTR_variant,,ENST00000379028,;NRCAM,downstream_gene_variant,,ENST00000379022,;NRCAM,downstream_gene_variant,,ENST00000445634,;NRCAM,downstream_gene_variant,,ENST00000425651,;NRCAM,non_coding_transcript_exon_variant,,ENST00000522550,;NRCAM,downstream_gene_variant,,ENST00000415105,;	G	ENSG00000091129	ENST00000379028	Transcript	3_prime_UTR_variant	5670	.	.	.	.	.	.	.	-1	NRCAM	HGNC	7994	protein_coding	YES	CCDS47686.1	ENSP00000368314	NRCAM_HUMAN	C9JUR7_HUMAN,C9JF43_HUMAN,B3KRX0_HUMAN	UPI00005E2661	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCTGAAA	.	5	ESCA
TMEM209	0	.	GRCh37	7	129832592	129832592	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.645G>C	p.Leu215Phe	p.L215F	ENST00000397622	6/15	80	65	15	65	65	0	TMEM209,missense_variant,p.Leu214Phe,ENST00000336804,;TMEM209,missense_variant,p.Leu215Phe,ENST00000473456,;TMEM209,missense_variant,p.Leu215Phe,ENST00000397622,;TMEM209,missense_variant,p.Leu214Phe,ENST00000462753,;RP11-775D22.3,intron_variant,,ENST00000483283,;	G	ENSG00000146842	ENST00000397622	Transcript	missense_variant	768	645	215	L/F	ttG/ttC	.	.	.	-1	TMEM209	HGNC	21898	protein_coding	YES	CCDS47712.1	ENSP00000380747	TM209_HUMAN	C9J5K4_HUMAN	UPI000020FAA2	.	tolerated(0.16)	benign(0.093)	6/15	.	hmmpanther:PTHR21780:SF0,hmmpanther:PTHR21780,Pfam_domain:PF09786	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTCAATCC	.	5	ESCA
BPGM	0	.	GRCh37	7	134346821	134346821	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562C>G	p.His188Asp	p.H188D	ENST00000393132	3/4	64	59	4	36	36	0	BPGM,missense_variant,p.His188Asp,ENST00000344924,;BPGM,missense_variant,p.His188Asp,ENST00000393132,;BPGM,missense_variant,p.His188Asp,ENST00000418040,;BPGM,downstream_gene_variant,,ENST00000443095,;	G	ENSG00000172331	ENST00000393132	Transcript	missense_variant	1051	562	188	H/D	Cat/Gat	.	.	.	1	BPGM	HGNC	1093	protein_coding	YES	CCDS5833.1	ENSP00000376840	PMGE_HUMAN	C9JH23_HUMAN	UPI0000163BD9	.	deleterious(0)	possibly_damaging(0.869)	3/4	.	HAMAP:MF_01039,hmmpanther:PTHR11931:SF11,hmmpanther:PTHR11931,Pfam_domain:PF00300,TIGRFAM_domain:TIGR01258,Gene3D:3.40.50.1240,SMART_domains:SM00855,Superfamily_domains:SSF53254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCTCATGGA	.	2	ESCA
SLC13A4	0	.	GRCh37	7	135386446	135386446	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693G>C	p.Lys231Asn	p.K231N	ENST00000354042	7/16	194	167	27	163	163	0	SLC13A4,missense_variant,p.Lys231Asn,ENST00000354042,;RP11-644N4.1,upstream_gene_variant,,ENST00000609370,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000471405,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000480376,;	G	ENSG00000164707	ENST00000354042	Transcript	missense_variant	1383	693	231	K/N	aaG/aaC	.	.	.	-1	SLC13A4	HGNC	15827	protein_coding	YES	CCDS5840.1	ENSP00000297282	S13A4_HUMAN	.	UPI00000343D9	.	tolerated(0.34)	benign(0.004)	7/16	.	Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTTCTTGCC	.	4	ESCA
TMEM178B	0	.	GRCh37	7	141177055	141177055	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6469C>G	.	.	ENST00000565468	4/4	36	32	4	21	21	0	TMEM178B,3_prime_UTR_variant,,ENST00000565468,;	G	ENSG00000261115	ENST00000565468	Transcript	3_prime_UTR_variant	7433	.	.	.	.	.	.	.	1	TMEM178B	HGNC	44112	protein_coding	YES	CCDS59086.1	ENSP00000456594	T178B_HUMAN	.	UPI0000E217DE	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTATCTGTAA	.	4	ESCA
KMT2C	0	.	GRCh37	7	151859780	151859780	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10882G>A	p.Asp3628Asn	p.D3628N	ENST00000262189	43/59	64	51	12	35	35	0	KMT2C,missense_variant,p.Asp3628Asn,ENST00000355193,;KMT2C,missense_variant,p.Asp214Asn,ENST00000424877,;KMT2C,missense_variant,p.Asp1134Asn,ENST00000360104,;KMT2C,missense_variant,p.Asp3628Asn,ENST00000262189,;KMT2C,upstream_gene_variant,,ENST00000418061,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;	T	ENSG00000055609	ENST00000262189	Transcript	missense_variant	11101	10882	3628	D/N	Gat/Aat	COSM1743793,COSM1743792	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	possibly_damaging(0.816)	43/59	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATATCTGAAT	.	5	ESCA
PSMG3	0	.	GRCh37	7	1608892	1608892	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84C>T	p.%3D	p.F28F	ENST00000288607	1/2	58	51	7	17	17	0	PSMG3,synonymous_variant,p.%3D,ENST00000252329,;PSMG3,synonymous_variant,p.%3D,ENST00000404674,;PSMG3,synonymous_variant,p.%3D,ENST00000288607,;PSMG3-AS1,upstream_gene_variant,,ENST00000533935,;PSMG3-AS1,upstream_gene_variant,,ENST00000437621,;PSMG3-AS1,upstream_gene_variant,,ENST00000532358,;PSMG3-AS1,upstream_gene_variant,,ENST00000524978,;PSMG3-AS1,upstream_gene_variant,,ENST00000437964,;PSMG3-AS1,upstream_gene_variant,,ENST00000457484,;	A	ENSG00000157778	ENST00000288607	Transcript	synonymous_variant	738	84	28	F	ttC/ttT	.	.	.	-1	PSMG3	HGNC	22420	protein_coding	YES	CCDS5327.1	ENSP00000288607	PSMG3_HUMAN	.	UPI0000070DA3	.	.	.	1/2	.	hmmpanther:PTHR31051:SF1,hmmpanther:PTHR31051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTGAAGGC	.	4	ESCA
STK31	0	.	GRCh37	7	23826213	23826213	+	Missense_Mutation	SNP	C	C	G	rs754081338	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2361C>G	p.Asp787Glu	p.D787E	ENST00000355870	19/24	96	62	34	52	52	0	STK31,missense_variant,p.Asp764Glu,ENST00000428484,;STK31,missense_variant,p.Asp764Glu,ENST00000354639,;STK31,missense_variant,p.Asp787Glu,ENST00000355870,;STK31,missense_variant,p.Asp787Glu,ENST00000433467,;STK31,non_coding_transcript_exon_variant,,ENST00000405627,;	G	ENSG00000196335	ENST00000355870	Transcript	missense_variant	2480	2361	787	D/E	gaC/gaG	rs754081338	.	.	1	STK31	HGNC	11407	protein_coding	YES	CCDS5386.1	ENSP00000348132	STK31_HUMAN	Q75MZ9_HUMAN,F8W6E7_HUMAN,E9PRQ0_HUMAN,C9JQW5_HUMAN,B3KY91_HUMAN	UPI0000167B73	.	tolerated(1)	benign(0)	19/24	.	PROSITE_profiles:PS50011,hmmpanther:PTHR12302:SF0,hmmpanther:PTHR12302,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGACTCAGG	.	5	ESCA
CHST12	0	.	GRCh37	7	2472467	2472467	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193G>A	p.Asp65Asn	p.D65N	ENST00000258711	2/2	128	116	11	58	58	0	CHST12,missense_variant,p.Asp65Asn,ENST00000258711,;CHST12,missense_variant,p.Asp65Asn,ENST00000432336,;AC004840.9,upstream_gene_variant,,ENST00000313156,;	A	ENSG00000136213	ENST00000258711	Transcript	missense_variant	328	193	65	D/N	Gat/Aat	.	.	.	1	CHST12	HGNC	17423	protein_coding	YES	CCDS5333.1	ENSP00000258711	CHSTC_HUMAN	C9J991_HUMAN	UPI000004C65C	.	tolerated(0.24)	benign(0.011)	2/2	.	hmmpanther:PTHR12137,hmmpanther:PTHR12137:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTCCGATGTC	.	3	ESCA
HOXA13	0	.	GRCh37	7	27236841	27236841	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*976G>C	.	.	ENST00000222753	2/2	32	28	4	15	15	0	HOXA13,3_prime_UTR_variant,,ENST00000222753,;RP1-170O19.14,upstream_gene_variant,,ENST00000523331,;HOTTIP,upstream_gene_variant,,ENST00000472494,;HOTTIP,upstream_gene_variant,,ENST00000521028,;HOTTIP,upstream_gene_variant,,ENST00000421733,;HOTTIP,upstream_gene_variant,,ENST00000605136,;HOXA13,upstream_gene_variant,,ENST00000518136,;	G	ENSG00000106031	ENST00000222753	Transcript	3_prime_UTR_variant	2172	.	.	.	.	.	.	.	-1	HOXA13	HGNC	5102	protein_coding	YES	CCDS5412.1	ENSP00000222753	HXA13_HUMAN	.	UPI000013C812	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ATTTTCATTCT	.	3	ESCA
STARD3NL	0	.	GRCh37	7	38259194	38259194	+	Missense_Mutation	SNP	G	G	C	rs376265781	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.582G>C	p.Glu194Asp	p.E194D	ENST00000009041	7/9	129	112	17	67	67	0	STARD3NL,missense_variant,p.Glu176Asp,ENST00000434197,;STARD3NL,missense_variant,p.Glu194Asp,ENST00000396013,;STARD3NL,missense_variant,p.Glu187Asp,ENST00000544203,;STARD3NL,missense_variant,p.Glu194Asp,ENST00000009041,;STARD3NL,missense_variant,p.Glu194Asp,ENST00000429075,;STARD3NL,downstream_gene_variant,,ENST00000440144,;STARD3NL,downstream_gene_variant,,ENST00000453225,;STARD3NL,non_coding_transcript_exon_variant,,ENST00000471550,;	C	ENSG00000010270	ENST00000009041	Transcript	missense_variant	839	582	194	E/D	gaG/gaC	rs376265781	.	.	1	STARD3NL	HGNC	19169	protein_coding	YES	CCDS5455.1	ENSP00000009041	MENTO_HUMAN	C9JPX5_HUMAN,C9JJ39_HUMAN,C9J3F5_HUMAN,A4D1X0_HUMAN	UPI000000DCAC	.	tolerated(0.28)	benign(0.006)	7/9	.	Pfam_domain:PF10457,hmmpanther:PTHR12136,PROSITE_profiles:PS51439	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAGAGGGC	byCluster	5	ESCA
C7orf72	0	.	GRCh37	7	50198667	50198667	+	Missense_Mutation	SNP	G	G	T	rs768430057	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1219G>T	p.Asp407Tyr	p.D407Y	ENST00000297001	9/9	92	56	36	49	49	0	C7orf72,missense_variant,p.Asp407Tyr,ENST00000297001,;	T	ENSG00000164500	ENST00000297001	Transcript	missense_variant	1269	1219	407	D/Y	Gac/Tac	rs768430057	.	.	1	C7orf72	HGNC	22564	protein_coding	YES	CCDS47585.1	ENSP00000297001	CG072_HUMAN	.	UPI00001D7424	.	deleterious(0.04)	probably_damaging(0.957)	9/9	.	Pfam_domain:PF15073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTGACCTC	.	5	ESCA
TNRC18	0	.	GRCh37	7	5396810	5396810	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4931C>T	p.Ser1644Leu	p.S1644L	ENST00000430969	16/30	99	88	10	45	45	0	TNRC18,missense_variant,p.Ser134Leu,ENST00000440081,;TNRC18,missense_variant,p.Ser1644Leu,ENST00000430969,;TNRC18,missense_variant,p.Ser1644Leu,ENST00000399537,;	A	ENSG00000182095	ENST00000430969	Transcript	missense_variant	5280	4931	1644	S/L	tCg/tTg	.	.	.	-1	TNRC18	HGNC	11962	protein_coding	YES	CCDS47534.1	ENSP00000395538	TNC18_HUMAN	H7C3U5_HUMAN,C9J9K1_HUMAN	UPI00016632FD	.	.	possibly_damaging(0.479)	16/30	.	hmmpanther:PTHR12505:SF21,hmmpanther:PTHR12505	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGCGACTTC	.	4	ESCA
VSTM2A	0	.	GRCh37	7	54610260	54610260	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-164C>T	.	.	ENST00000407838	1/5	37	34	3	14	14	0	VSTM2A,5_prime_UTR_variant,,ENST00000402026,;VSTM2A,5_prime_UTR_variant,,ENST00000302287,;VSTM2A,5_prime_UTR_variant,,ENST00000404951,;VSTM2A,5_prime_UTR_variant,,ENST00000407838,;VSTM2A,upstream_gene_variant,,ENST00000402613,;VSTM2A,upstream_gene_variant,,ENST00000466888,;VSTM2A,upstream_gene_variant,,ENST00000498834,;VSTM2A,upstream_gene_variant,,ENST00000469952,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000495904,;	T	ENSG00000170419	ENST00000407838	Transcript	5_prime_UTR_variant	243	.	.	.	.	.	.	.	1	VSTM2A	HGNC	28499	protein_coding	YES	CCDS5512.2	ENSP00000384967	VTM2A_HUMAN	.	UPI0000EE7EC1	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAATCGCAAT	.	2	ESCA
CRCP	0	.	GRCh37	7	65617257	65617257	+	Silent	SNP	C	C	A	rs746821960	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.360C>A	p.%3D	p.V120V	ENST00000395326	6/6	34	30	4	23	23	0	CRCP,synonymous_variant,p.%3D,ENST00000338592,;CRCP,synonymous_variant,p.%3D,ENST00000431089,;CRCP,synonymous_variant,p.%3D,ENST00000398684,;CRCP,synonymous_variant,p.%3D,ENST00000415001,;CRCP,synonymous_variant,p.%3D,ENST00000395326,;AC068533.7,downstream_gene_variant,,ENST00000450043,;RP5-1132H15.1,intron_variant,,ENST00000435524,;CRCP,non_coding_transcript_exon_variant,,ENST00000492264,;CRCP,3_prime_UTR_variant,,ENST00000360415,;	A	ENSG00000241258	ENST00000395326	Transcript	synonymous_variant	718	360	120	V	gtC/gtA	rs746821960	.	.	1	CRCP	HGNC	17888	protein_coding	YES	CCDS5532.1	ENSP00000378736	RPC9_HUMAN	.	UPI0000128406	.	.	.	6/6	.	Superfamily_domains:SSF47819,SMART_domains:SM00657,Pfam_domain:PF03874,hmmpanther:PTHR15561:SF0,hmmpanther:PTHR15561	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCGTCACCAG	.	3	ESCA
CRCP	0	.	GRCh37	7	65617267	65617267	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370C>T	p.%3D	p.L124L	ENST00000395326	6/6	33	30	3	22	22	0	CRCP,synonymous_variant,p.%3D,ENST00000338592,;CRCP,synonymous_variant,p.%3D,ENST00000431089,;CRCP,synonymous_variant,p.%3D,ENST00000398684,;CRCP,synonymous_variant,p.%3D,ENST00000415001,;CRCP,synonymous_variant,p.%3D,ENST00000395326,;AC068533.7,downstream_gene_variant,,ENST00000450043,;RP5-1132H15.1,intron_variant,,ENST00000435524,;CRCP,non_coding_transcript_exon_variant,,ENST00000492264,;CRCP,3_prime_UTR_variant,,ENST00000360415,;	T	ENSG00000241258	ENST00000395326	Transcript	synonymous_variant	728	370	124	L	Ctg/Ttg	.	.	.	1	CRCP	HGNC	17888	protein_coding	YES	CCDS5532.1	ENSP00000378736	RPC9_HUMAN	.	UPI0000128406	.	.	.	6/6	.	Superfamily_domains:SSF47819,SMART_domains:SM00657,hmmpanther:PTHR15561:SF0,hmmpanther:PTHR15561	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCATTCTGCCT	.	2	ESCA
GLCCI1	0	.	GRCh37	7	8127833	8127833	+	3'UTR	DEL	T	T	-	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1675delT	.	.	ENST00000223145	8/8	29	15	14	13	13	0	GLCCI1,3_prime_UTR_variant,,ENST00000223145,;GLCCI1,non_coding_transcript_exon_variant,,ENST00000482540,;GLCCI1,intron_variant,,ENST00000438949,;GLCCI1,downstream_gene_variant,,ENST00000491947,;GLCCI1,downstream_gene_variant,,ENST00000489405,;	-	ENSG00000106415	ENST00000223145	Transcript	3_prime_UTR_variant	3866	.	.	.	.	.	.	.	1	GLCCI1	HGNC	18713	protein_coding	YES	CCDS34601.1	ENSP00000223145	GLCI1_HUMAN	.	UPI00001907F7	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CATTGATTTTTT	.	2	ESCA
ZNF804B	0	.	GRCh37	7	88963860	88963860	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1564G>C	p.Asp522His	p.D522H	ENST00000333190	4/4	29	25	4	35	35	0	ZNF804B,missense_variant,p.Asp522His,ENST00000333190,;	C	ENSG00000182348	ENST00000333190	Transcript	missense_variant	2173	1564	522	D/H	Gac/Cac	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	tolerated(0.57)	benign(0.025)	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGAAGACCAA	.	4	ESCA
RNF19A	0	.	GRCh37	8	101270645	101270645	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*139G>A	.	.	ENST00000519449	11/11	50	43	7	37	37	0	RNF19A,3_prime_UTR_variant,,ENST00000519449,;RNF19A,3_prime_UTR_variant,,ENST00000341084,;SPAG1,intron_variant,,ENST00000519409,;RNF19A,downstream_gene_variant,,ENST00000523255,;RNF19A,downstream_gene_variant,,ENST00000523644,;RNF19A,downstream_gene_variant,,ENST00000520071,;RNF19A,downstream_gene_variant,,ENST00000520903,;	T	ENSG00000034677	ENST00000519449	Transcript	3_prime_UTR_variant	2973	.	.	.	.	.	.	.	-1	RNF19A	HGNC	13432	protein_coding	YES	CCDS6286.1	ENSP00000428968	RN19A_HUMAN	E7ETB2_HUMAN,E7EQV8_HUMAN,E7EQ63_HUMAN,A3KCU8_HUMAN	UPI000013D5E6	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTGCTGAAC	.	2	ESCA
TMEM71	0	.	GRCh37	8	133759306	133759306	+	Intron	SNP	G	G	C	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315-3C>G	.	.	ENST00000356838	.	83	74	9	65	65	0	TMEM71,synonymous_variant,p.%3D,ENST00000519016,;TMEM71,synonymous_variant,p.%3D,ENST00000522334,;TMEM71,synonymous_variant,p.%3D,ENST00000523829,;TMEM71,synonymous_variant,p.%3D,ENST00000377901,;TMEM71,splice_region_variant,,ENST00000356838,;TMEM71,downstream_gene_variant,,ENST00000519187,;TMEM71,downstream_gene_variant,,ENST00000519304,;TMEM71,non_coding_transcript_exon_variant,,ENST00000517538,;	C	ENSG00000165071	ENST00000356838	Transcript	splice_region_variant	.	.	.	.	.	COSM3715885,COSM3715886	.	.	-1	TMEM71	HGNC	26572	protein_coding	YES	CCDS6366.1	ENSP00000349296	TMM71_HUMAN	E5RH69_HUMAN,E5RGD3_HUMAN	UPI000013E44E	.	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTACTGAGGTT	.	4	ESCA
PLEC	0	.	GRCh37	8	144996792	144996792	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7716G>A	p.%3D	p.E2572E	ENST00000322810	31/32	62	49	12	21	21	0	PLEC,synonymous_variant,p.%3D,ENST00000322810,;PLEC,synonymous_variant,p.%3D,ENST00000527096,;PLEC,synonymous_variant,p.%3D,ENST00000345136,;PLEC,synonymous_variant,p.%3D,ENST00000357649,;PLEC,synonymous_variant,p.%3D,ENST00000398774,;PLEC,synonymous_variant,p.%3D,ENST00000354589,;PLEC,synonymous_variant,p.%3D,ENST00000356346,;PLEC,synonymous_variant,p.%3D,ENST00000436759,;PLEC,synonymous_variant,p.%3D,ENST00000354958,;PLEC,intron_variant,,ENST00000527303,;	T	ENSG00000178209	ENST00000322810	Transcript	synonymous_variant	7886	7716	2572	E	gaG/gaA	.	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	.	31/32	.	hmmpanther:PTHR11915:SF247,hmmpanther:PTHR11915,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATCTCCAG	.	5	ESCA
CDCA2	0	.	GRCh37	8	25364100	25364100	+	Missense_Mutation	SNP	C	C	T	rs773590003	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1918C>T	p.Arg640Cys	p.R640C	ENST00000330560	15/15	36	28	8	35	34	1	CDCA2,missense_variant,p.Arg625Cys,ENST00000380665,;CDCA2,missense_variant,p.Arg640Cys,ENST00000330560,;CDCA2,non_coding_transcript_exon_variant,,ENST00000521098,;	T	ENSG00000184661	ENST00000330560	Transcript	missense_variant	2395	1918	640	R/C	Cgt/Tgt	rs773590003,COSM1098473	.	.	1	CDCA2	HGNC	14623	protein_coding	YES	CCDS6049.1	ENSP00000328228	CDCA2_HUMAN	.	UPI000013DF9A	.	deleterious(0.01)	benign(0.305)	15/15	.	hmmpanther:PTHR21603:SF2,hmmpanther:PTHR21603	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	TTTTGCGTCAT	byFrequency	3	ESCA
CSMD1	0	.	GRCh37	8	3889611	3889611	+	Missense_Mutation	SNP	G	G	T	rs773355949	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426C>A	p.Ser142Arg	p.S142R	ENST00000537824	4/70	24	19	5	19	19	0	CSMD1,missense_variant,p.Ser142Arg,ENST00000400186,;CSMD1,missense_variant,p.Ser142Arg,ENST00000542608,;CSMD1,missense_variant,p.Ser142Arg,ENST00000602723,;CSMD1,missense_variant,p.Ser142Arg,ENST00000539096,;CSMD1,missense_variant,p.Ser142Arg,ENST00000537824,;CSMD1,missense_variant,p.Ser142Arg,ENST00000602557,;CSMD1,missense_variant,p.Ser142Arg,ENST00000520002,;	T	ENSG00000183117	ENST00000537824	Transcript	missense_variant	426	426	142	S/R	agC/agA	rs773355949	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	probably_damaging(0.998)	4/70	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGTGGCTAGG	byFrequency	2	ESCA
C8orf34	0	.	GRCh37	8	69434053	69434053	+	Missense_Mutation	SNP	C	C	T	rs150489120	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785C>T	p.Ser262Phe	p.S262F	ENST00000518698	6/14	69	64	5	36	36	0	C8orf34,missense_variant,p.Ser176Phe,ENST00000539993,;C8orf34,missense_variant,p.Ser151Phe,ENST00000337103,;C8orf34,missense_variant,p.Ser176Phe,ENST00000348340,;C8orf34,missense_variant,p.Ser262Phe,ENST00000518698,;C8orf34,non_coding_transcript_exon_variant,,ENST00000349492,;C8orf34,missense_variant,p.Ser151Phe,ENST00000521406,;RPS15AP25,downstream_gene_variant,,ENST00000489168,;	T	ENSG00000165084	ENST00000518698	Transcript	missense_variant	1076	785	262	S/F	tCt/tTt	rs150489120,COSM3650561,COSM3650562	.	.	1	C8orf34	HGNC	30905	protein_coding	YES	CCDS6203.2	ENSP00000427820	CH034_HUMAN	.	UPI000021D12D	.	deleterious(0.02)	probably_damaging(0.968)	6/14	.	hmmpanther:PTHR32000,hmmpanther:PTHR32000:SF2	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAATTCTTCTC	byCluster	2	ESCA
SDC2	0	.	GRCh37	8	97622686	97622686	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*910C>T	.	.	ENST00000302190	5/5	89	84	5	46	46	0	SDC2,3_prime_UTR_variant,,ENST00000302190,;SDC2,downstream_gene_variant,,ENST00000522911,;SDC2,downstream_gene_variant,,ENST00000521590,;SDC2,downstream_gene_variant,,ENST00000523877,;SDC2,downstream_gene_variant,,ENST00000518385,;SDC2,downstream_gene_variant,,ENST00000519914,;	T	ENSG00000169439	ENST00000302190	Transcript	3_prime_UTR_variant	2437	.	.	.	.	.	.	.	1	SDC2	HGNC	10659	protein_coding	YES	CCDS6272.1	ENSP00000307046	SDC2_HUMAN	E5RJB8_HUMAN,E9PBI9_HUMAN,E5RHU3_HUMAN,B4DT61_HUMAN	UPI000013E7A4	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGCCTCTGA	.	2	ESCA
C8orf47	0	.	GRCh37	8	99076803	99076803	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-95G>C	.	.	ENST00000318528	1/3	121	115	6	75	75	0	C8orf47,5_prime_UTR_variant,,ENST00000545282,;C8orf47,5_prime_UTR_variant,,ENST00000318528,;	C	ENSG00000177459	ENST00000318528	Transcript	5_prime_UTR_variant	265	.	.	.	.	.	.	.	1	C8orf47	HGNC	26823	protein_coding	YES	CCDS34929.1	ENSP00000315614	CH047_HUMAN	.	UPI0000210389	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTGGAGAAA	.	2	ESCA
STX17	0	.	GRCh37	9	102713413	102713413	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.261G>A	p.%3D	p.L87L	ENST00000259400	4/8	68	54	13	36	36	0	STX17,synonymous_variant,p.%3D,ENST00000534052,;STX17,synonymous_variant,p.%3D,ENST00000525640,;STX17,synonymous_variant,p.%3D,ENST00000259400,;STX17,3_prime_UTR_variant,,ENST00000531035,;STX17,non_coding_transcript_exon_variant,,ENST00000525847,;STX17,non_coding_transcript_exon_variant,,ENST00000525579,;STX17,synonymous_variant,p.%3D,ENST00000524405,;STX17,3_prime_UTR_variant,,ENST00000529340,;STX17,3_prime_UTR_variant,,ENST00000525342,;	A	ENSG00000136874	ENST00000259400	Transcript	synonymous_variant	397	261	87	L	ctG/ctA	.	.	.	1	STX17	HGNC	11432	protein_coding	YES	CCDS6745.1	ENSP00000259400	STX17_HUMAN	E9PJW1_HUMAN	UPI000013D04E	.	.	.	4/8	.	Superfamily_domains:SSF47661,hmmpanther:PTHR19957:SF81,hmmpanther:PTHR19957,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTGAAGAG	.	5	ESCA
TRIM32	0	.	GRCh37	9	119463567	119463567	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1584G>A	.	.	ENST00000450136	2/2	66	58	8	35	35	0	TRIM32,3_prime_UTR_variant,,ENST00000373983,;TRIM32,3_prime_UTR_variant,,ENST00000450136,;ASTN2,intron_variant,,ENST00000373996,;ASTN2,intron_variant,,ENST00000373986,;ASTN2,intron_variant,,ENST00000361209,;ASTN2,intron_variant,,ENST00000313400,;ASTN2,intron_variant,,ENST00000361477,;TRIM32,downstream_gene_variant,,ENST00000411410,;	A	ENSG00000119401	ENST00000450136	Transcript	3_prime_UTR_variant	3707	.	.	.	.	.	.	.	1	TRIM32	HGNC	16380	protein_coding	YES	CCDS6817.1	ENSP00000408292	TRI32_HUMAN	Q5JVY0_HUMAN	UPI000012CDB9	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAATGATGTT	.	4	ESCA
NOTCH1	0	.	GRCh37	9	139404376	139404377	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2777dupT	p.Asn927GlnfsTer17	p.N927Qfs*17	ENST00000277541	18/34	81	62	19	49	49	0	NOTCH1,frameshift_variant,p.Asn927GlnfsTer17,ENST00000277541,;	A	ENSG00000148400	ENST00000277541	Transcript	frameshift_variant	2853-2854	2777-2778	926	I/IX	atc/atTc	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	18/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,Pfam_domain:PF00008,Gene3D:2gy5A03,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGTTGATGCC	.	3	ESCA
RUSC2	0	.	GRCh37	9	35547582	35547582	+	Missense_Mutation	SNP	C	C	T	rs765030082	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1064C>T	p.Ser355Phe	p.S355F	ENST00000455600	2/12	41	29	12	21	21	0	RUSC2,missense_variant,p.Ser355Phe,ENST00000361226,;RUSC2,missense_variant,p.Ser355Phe,ENST00000455600,;RUSC2,downstream_gene_variant,,ENST00000468041,;	T	ENSG00000198853	ENST00000455600	Transcript	missense_variant	1633	1064	355	S/F	tCt/tTt	rs765030082	.	.	1	RUSC2	HGNC	23625	protein_coding	YES	CCDS35008.1	ENSP00000393922	RUSC2_HUMAN	.	UPI00001C1EB0	.	deleterious(0)	possibly_damaging(0.828)	2/12	.	hmmpanther:PTHR15591,hmmpanther:PTHR15591:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCTCTTCTC	.	5	ESCA
RECK	0	.	GRCh37	9	36112352	36112352	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1939G>A	p.Gly647Arg	p.G647R	ENST00000377966	16/21	80	58	22	60	60	0	RECK,missense_variant,p.Gly647Arg,ENST00000377966,;	A	ENSG00000122707	ENST00000377966	Transcript	missense_variant	2505	1939	647	G/R	Ggg/Agg	.	.	.	1	RECK	HGNC	11345	protein_coding	YES	CCDS6597.1	ENSP00000367202	RECK_HUMAN	.	UPI0000133587	.	deleterious(0)	probably_damaging(1)	16/21	.	PROSITE_profiles:PS51465,hmmpanther:PTHR13487,PROSITE_patterns:PS00282,Pfam_domain:PF07648,Gene3D:3.30.60.30,SMART_domains:SM00280,Superfamily_domains:SSF100895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAATGGGCGC	.	5	ESCA
CCIN	0	.	GRCh37	9	36169685	36169685	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186G>T	p.Met62Ile	p.M62I	ENST00000335119	1/1	41	36	5	23	23	0	CCIN,missense_variant,p.Met62Ile,ENST00000335119,;	T	ENSG00000185972	ENST00000335119	Transcript	missense_variant	297	186	62	M/I	atG/atT	.	.	.	1	CCIN	HGNC	1568	protein_coding	YES	CCDS6599.1	ENSP00000334996	CALI_HUMAN	Q8WX35_HUMAN	UPI000006EB8E	.	tolerated(0.71)	benign(0.001)	1/1	.	Superfamily_domains:SSF54695,SMART_domains:SM00225,Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF163,PROSITE_profiles:PS50097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACATGAAGAC	.	4	ESCA
SLC25A51	0	.	GRCh37	9	37888332	37888332	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216G>A	p.%3D	p.L72L	ENST00000377716	3/3	105	76	29	65	65	0	SLC25A51,synonymous_variant,p.%3D,ENST00000377716,;SLC25A51,synonymous_variant,p.%3D,ENST00000380590,;SLC25A51,synonymous_variant,p.%3D,ENST00000242275,;SLC25A51,intron_variant,,ENST00000496760,;RP11-613M10.9,intron_variant,,ENST00000540557,;RP11-3J10.4,downstream_gene_variant,,ENST00000436507,;	T	ENSG00000122696	ENST00000377716	Transcript	synonymous_variant	960	216	72	L	ttG/ttA	.	.	.	-1	SLC25A51	HGNC	23323	protein_coding	YES	CCDS6614.1	ENSP00000366945	S2551_HUMAN	.	UPI000003615E	.	.	.	3/3	.	Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF253,PROSITE_profiles:PS50920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTCAACTG	.	5	ESCA
CDC37L1	0	.	GRCh37	9	4697838	4697838	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.706G>C	p.Asp236His	p.D236H	ENST00000381854	5/7	96	83	12	61	61	0	CDC37L1,missense_variant,p.Asp236His,ENST00000381854,;CDC37L1,missense_variant,p.Asp236His,ENST00000381858,;	C	ENSG00000106993	ENST00000381854	Transcript	missense_variant	908	706	236	D/H	Gat/Cat	.	.	.	1	CDC37L1	HGNC	17179	protein_coding	YES	CCDS6454.1	ENSP00000371278	CD37L_HUMAN	.	UPI000006E86C	.	deleterious(0)	probably_damaging(0.994)	5/7	.	hmmpanther:PTHR12800:SF2,hmmpanther:PTHR12800,Pfam_domain:PF08565,SMART_domains:SM01070,Superfamily_domains:0044500	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGGATCCA	.	5	ESCA
COL4A6	0	.	GRCh37	X	107400267	107400267	+	Missense_Mutation	SNP	C	C	T	rs773301536	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5039G>A	p.Arg1680Gln	p.R1680Q	ENST00000372216	45/45	39	28	11	18	18	0	COL4A6,missense_variant,p.Arg1680Gln,ENST00000372216,;COL4A6,missense_variant,p.Arg1622Gln,ENST00000538570,;COL4A6,missense_variant,p.Arg1680Gln,ENST00000394872,;COL4A6,missense_variant,p.Arg1679Gln,ENST00000334504,;COL4A6,missense_variant,p.Arg214Gln,ENST00000418180,;COL4A6,missense_variant,p.Arg1655Gln,ENST00000545689,;ATG4A,downstream_gene_variant,,ENST00000372254,;ATG4A,downstream_gene_variant,,ENST00000372232,;ATG4A,downstream_gene_variant,,ENST00000345734,;ATG4A,downstream_gene_variant,,ENST00000545696,;ATG4A,downstream_gene_variant,,ENST00000474825,;COL4A6,downstream_gene_variant,,ENST00000487645,;ATG4A,downstream_gene_variant,,ENST00000489247,;ATG4A,downstream_gene_variant,,ENST00000372246,;ATG4A,downstream_gene_variant,,ENST00000343524,;	T	ENSG00000197565	ENST00000372216	Transcript	missense_variant	5140	5039	1680	R/Q	cGa/cAa	rs773301536	.	.	-1	COL4A6	HGNC	2208	protein_coding	YES	CCDS14541.1	ENSP00000361290	CO4A6_HUMAN	B4DU54_HUMAN	UPI000049E122	.	.	benign(0.101)	45/45	.	PROSITE_profiles:PS51403,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF164,Gene3D:1t60D00,Pfam_domain:PF01413,SMART_domains:SM00111,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACTCGAGTG	byFrequency	5	ESCA
AMOT	0	.	GRCh37	X	112058657	112058657	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1321C>T	p.Leu441Phe	p.L441F	ENST00000371959	2/11	64	56	7	26	26	0	AMOT,missense_variant,p.Leu441Phe,ENST00000371959,;AMOT,missense_variant,p.Leu209Phe,ENST00000371962,;AMOT,missense_variant,p.Leu32Phe,ENST00000304758,;AMOT,missense_variant,p.Leu441Phe,ENST00000524145,;AMOT,missense_variant,p.Leu209Phe,ENST00000371958,;	A	ENSG00000126016	ENST00000371959	Transcript	missense_variant	1321	1321	441	L/F	Ctc/Ttc	.	.	.	-1	AMOT	HGNC	17810	protein_coding	YES	CCDS48154.1	ENSP00000361027	AMOT_HUMAN	E7ERM3_HUMAN	UPI000050ED33	.	.	unknown(0)	2/11	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14826,hmmpanther:PTHR14826:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGAGGATCT	.	4	ESCA
IL9R	0	.	GRCh37	X	155227398	155227398	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-27C>T	.	.	ENST00000244174	1/9	185	162	23	122	122	0	IL9R,5_prime_UTR_variant,,ENST00000369423,;IL9R,5_prime_UTR_variant,,ENST00000244174,;IL9R,5_prime_UTR_variant,,ENST00000540897,;IL9R,5_prime_UTR_variant,,ENST00000424344,;IL9R,upstream_gene_variant,,ENST00000489233,;	T	ENSG00000124334	ENST00000244174	Transcript	5_prime_UTR_variant	153	.	.	.	.	.	.	.	1	IL9R	HGNC	6030	protein_coding	YES	CCDS14771.4	ENSP00000244174	IL9R_HUMAN	.	UPI000016864A	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCTCCAGGT	.	4	ESCA
REPS2	0	.	GRCh37	X	17169130	17169130	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3526G>C	.	.	ENST00000357277	18/18	50	35	14	27	27	0	REPS2,3_prime_UTR_variant,,ENST00000357277,;REPS2,3_prime_UTR_variant,,ENST00000303843,;REPS2,downstream_gene_variant,,ENST00000380064,;REPS2,downstream_gene_variant,,ENST00000469714,;REPS2,downstream_gene_variant,,ENST00000470686,;	C	ENSG00000169891	ENST00000357277	Transcript	3_prime_UTR_variant	5680	.	.	.	.	.	.	.	1	REPS2	HGNC	9963	protein_coding	YES	CCDS14180.2	ENSP00000349824	REPS2_HUMAN	.	UPI00001BBB18	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATTGAGCTA	.	5	ESCA
BEND2	0	.	GRCh37	X	18221839	18221839	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.689T>G	p.Phe230Cys	p.F230C	ENST00000380033	5/14	76	63	13	27	27	0	BEND2,missense_variant,p.Phe230Cys,ENST00000380030,;BEND2,missense_variant,p.Phe230Cys,ENST00000380033,;	C	ENSG00000177324	ENST00000380033	Transcript	missense_variant	822	689	230	F/C	tTc/tGc	.	.	.	-1	BEND2	HGNC	28509	protein_coding	YES	CCDS14184.1	ENSP00000369372	BEND2_HUMAN	.	UPI000013FE0F	.	tolerated(0.27)	benign(0.002)	5/14	.	hmmpanther:PTHR16213,hmmpanther:PTHR16213:SF44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCGAAACAA	.	5	ESCA
DDX3X	0	.	GRCh37	X	41206955	41206955	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1972G>C	p.Asp658His	p.D658H	ENST00000399959	17/17	20	14	6	15	15	0	DDX3X,missense_variant,p.Asp658His,ENST00000399959,;DDX3X,missense_variant,p.Asp135His,ENST00000441189,;DDX3X,missense_variant,p.Asp642His,ENST00000457138,;DDX3X,downstream_gene_variant,,ENST00000542215,;RN7SL15P,upstream_gene_variant,,ENST00000582825,;DDX3X,non_coding_transcript_exon_variant,,ENST00000478993,;	C	ENSG00000215301	ENST00000399959	Transcript	missense_variant	2827	1972	658	D/H	Gac/Cac	.	.	.	1	DDX3X	HGNC	2745	protein_coding	YES	CCDS43931.1	ENSP00000382840	DDX3X_HUMAN	Q59GX6_HUMAN	UPI000013CB6D	.	deleterious(0)	unknown(0)	17/17	.	hmmpanther:PTHR24031:SF195,hmmpanther:PTHR24031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGGTTGACTGG	.	2	ESCA
ASB12	0	.	GRCh37	X	63445264	63445264	+	Missense_Mutation	SNP	C	C	A	rs34689841	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267G>T	p.Leu89Phe	p.L89F	ENST00000362002	2/3	30	19	10	15	15	0	ASB12,missense_variant,p.Leu80Phe,ENST00000396130,;MTMR8,missense_variant,p.Leu464Phe,ENST00000453546,;ASB12,missense_variant,p.Leu89Phe,ENST00000362002,;	A	ENSG00000198881	ENST00000362002	Transcript	missense_variant	460	267	89	L/F	ttG/ttT	rs34689841	.	.	-1	ASB12	HGNC	19763	protein_coding	YES	CCDS14378.2	ENSP00000355195	ASB12_HUMAN	.	UPI000013DA93	.	deleterious(0.01)	probably_damaging(0.985)	2/3	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24120,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	T:0.0016	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTGCAAACA	byFrequency|byCluster	4	ESCA
P2RY4	0	.	GRCh37	X	69478523	69478523	+	Missense_Mutation	SNP	G	G	A	rs775969220	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.952C>T	p.Arg318Cys	p.R318C	ENST00000374519	1/1	63	42	20	36	36	0	P2RY4,missense_variant,p.Arg318Cys,ENST00000374519,;	A	ENSG00000186912	ENST00000374519	Transcript	missense_variant	1132	952	318	R/C	Cgt/Tgt	rs775969220,COSM268272	.	.	-1	P2RY4	HGNC	8542	protein_coding	YES	CCDS14398.1	ENSP00000363643	P2RY4_HUMAN	C6G7W3_HUMAN	UPI000002E776	.	tolerated(0.15)	benign(0.024)	1/1	.	Prints_domain:PR01066,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR24231:SF21,hmmpanther:PTHR24231	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACGGAGCT	byFrequency	5	ESCA
ZMYM3	0	.	GRCh37	X	70471431	70471431	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.688G>A	p.Ala230Thr	p.A230T	ENST00000353904	3/25	36	17	18	16	16	0	ZMYM3,missense_variant,p.Ala230Thr,ENST00000373982,;ZMYM3,missense_variant,p.Ala230Thr,ENST00000373988,;ZMYM3,missense_variant,p.Ala230Thr,ENST00000373978,;ZMYM3,missense_variant,p.Ala230Thr,ENST00000373984,;ZMYM3,missense_variant,p.Ala230Thr,ENST00000314425,;ZMYM3,missense_variant,p.Ala230Thr,ENST00000373998,;ZMYM3,missense_variant,p.Ala230Thr,ENST00000373981,;ZMYM3,missense_variant,p.Ala230Thr,ENST00000353904,;ZMYM3,non_coding_transcript_exon_variant,,ENST00000489332,;	T	ENSG00000147130	ENST00000353904	Transcript	missense_variant	876	688	230	A/T	Gcg/Acg	.	.	.	-1	ZMYM3	HGNC	13054	protein_coding	YES	CCDS14409.1	ENSP00000343909	ZMYM3_HUMAN	.	UPI000013C339	.	deleterious_low_confidence(0.05)	benign(0.014)	3/25	.	hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCGCCTTCG	.	5	ESCA
XIST	0	.	GRCh37	X	73065478	73065478	+	RNA	SNP	G	G	C	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.7111C>G	.	.	ENST00000429829	1/6	43	39	4	25	25	0	XIST,non_coding_transcript_exon_variant,,ENST00000429829,;XIST,upstream_gene_variant,,ENST00000602863,;	C	ENSG00000229807	ENST00000429829	Transcript	non_coding_transcript_exon_variant	7111	.	.	.	.	.	.	.	-1	XIST	HGNC	12810	lincRNA	YES	.	.	.	.	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CATCTGAGAGT	.	3	ESCA
SLC16A2	0	.	GRCh37	X	73749129	73749129	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1252C>G	p.Leu418Val	p.L418V	ENST00000587091	5/6	55	50	5	32	32	0	SLC16A2,missense_variant,p.Leu418Val,ENST00000587091,;SLC16A2,missense_variant,p.Leu492Val,ENST00000276033,;SLC16A2,intron_variant,,ENST00000590447,;	G	ENSG00000147100	ENST00000587091	Transcript	missense_variant	1429	1252	418	L/V	Ctt/Gtt	COSM3914228	.	.	1	SLC16A2	HGNC	10923	protein_coding	YES	CCDS14426.2	ENSP00000465734	MOT8_HUMAN	.	UPI000019C3D5	.	tolerated(0.11)	benign(0.264)	5/6	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,Gene3D:1.20.1250.20,Pfam_domain:PF07690,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF123,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTGTCTTTTC	.	3	ESCA
BRWD3	0	.	GRCh37	X	80001094	80001094	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565G>C	p.Asp189His	p.D189H	ENST00000373275	7/41	47	38	9	33	33	0	BRWD3,missense_variant,p.Asp189His,ENST00000373275,;BRWD3,non_coding_transcript_exon_variant,,ENST00000478415,;	G	ENSG00000165288	ENST00000373275	Transcript	missense_variant	782	565	189	D/H	Gac/Cac	.	.	.	-1	BRWD3	HGNC	17342	protein_coding	YES	CCDS14447.1	ENSP00000362372	BRWD3_HUMAN	.	UPI000045785B	.	deleterious(0)	probably_damaging(0.995)	7/41	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGTCAAATG	.	5	ESCA
FAM9B	0	.	GRCh37	X	8997386	8997386	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355G>C	p.Glu119Gln	p.E119Q	ENST00000327220	6/9	69	60	9	39	39	0	FAM9B,missense_variant,p.Glu159Gln,ENST00000362066,;FAM9B,missense_variant,p.Glu119Gln,ENST00000428477,;FAM9B,missense_variant,p.Glu119Gln,ENST00000327220,;FAM9B,3_prime_UTR_variant,,ENST00000472522,;FAM9B,non_coding_transcript_exon_variant,,ENST00000461107,;	G	ENSG00000177138	ENST00000327220	Transcript	missense_variant	720	355	119	E/Q	Gag/Cag	.	.	.	-1	FAM9B	HGNC	18404	protein_coding	YES	CCDS14132.1	ENSP00000318716	FAM9B_HUMAN	.	UPI000012A419	.	tolerated(0.33)	possibly_damaging(0.537)	6/9	.	Pfam_domain:PF04803,hmmpanther:PTHR19368:SF2,hmmpanther:PTHR19368,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCTTTCT	.	5	ESCA
DIAPH2	0	.	GRCh37	X	96502803	96502803	+	Missense_Mutation	SNP	G	G	C	rs763576938	.	TCGA-IG-A3Y9-01A-12D-A247-09	TCGA-IG-A3Y9-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2809G>C	p.Glu937Gln	p.E937Q	ENST00000324765	23/27	79	65	14	51	51	0	DIAPH2,missense_variant,p.Glu933Gln,ENST00000373054,;DIAPH2,missense_variant,p.Glu937Gln,ENST00000355827,;DIAPH2,missense_variant,p.Glu937Gln,ENST00000324765,;DIAPH2,missense_variant,p.Glu937Gln,ENST00000373049,;DIAPH2,missense_variant,p.Glu937Gln,ENST00000373061,;	C	ENSG00000147202	ENST00000324765	Transcript	missense_variant	3156	2809	937	E/Q	Gaa/Caa	rs763576938,COSM1126484	.	.	1	DIAPH2	HGNC	2877	protein_coding	YES	CCDS14467.1	ENSP00000321348	DIAP2_HUMAN	.	UPI00001293C8	.	tolerated(0.36)	possibly_damaging(0.475)	23/27	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF174,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGAAAAT	byFrequency	5	ESCA
C10orf76	0	.	GRCh37	10	103771512	103771512	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.799C>A	p.Gln267Lys	p.Q267K	ENST00000370033	11/26	42	35	7	25	25	0	C10orf76,missense_variant,p.Gln267Lys,ENST00000370033,;	T	ENSG00000120029	ENST00000370033	Transcript	missense_variant	919	799	267	Q/K	Caa/Aaa	COSM914081	.	.	-1	C10orf76	HGNC	25788	protein_coding	YES	CCDS41563.1	ENSP00000359050	CJ076_HUMAN	.	UPI000047005B	.	tolerated(0.32)	benign(0.01)	11/26	.	hmmpanther:PTHR13608:SF3,hmmpanther:PTHR13608,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTGGTGTT	.	5	ESCA
ACADSB	0	.	GRCh37	10	124806738	124806738	+	Missense_Mutation	SNP	C	C	T	rs756796542	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.914C>T	p.Ala305Val	p.A305V	ENST00000358776	8/11	45	41	3	44	44	0	ACADSB,missense_variant,p.Ala305Val,ENST00000358776,;ACADSB,missense_variant,p.Ala203Val,ENST00000368869,;ACADSB,non_coding_transcript_exon_variant,,ENST00000496730,;	T	ENSG00000196177	ENST00000358776	Transcript	missense_variant	928	914	305	A/V	gCg/gTg	rs756796542	.	.	1	ACADSB	HGNC	91	protein_coding	YES	CCDS7634.1	ENSP00000357873	ACDSB_HUMAN	B4DQ51_HUMAN	UPI00001251DF	.	deleterious(0)	probably_damaging(0.988)	8/11	.	hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF212,Gene3D:1.20.140.10,Pfam_domain:PF00441,PIRSF_domain:PIRSF016578,Superfamily_domains:SSF47203	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACTGGCGCAAG	byFrequency	2	ESCA
MASTL	0	.	GRCh37	10	27459382	27459382	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1494T>C	p.%3D	p.S498S	ENST00000375940	8/12	32	28	4	46	46	0	MASTL,synonymous_variant,p.%3D,ENST00000375946,;MASTL,synonymous_variant,p.%3D,ENST00000375940,;MASTL,synonymous_variant,p.%3D,ENST00000342386,;MASTL,non_coding_transcript_exon_variant,,ENST00000477034,;	C	ENSG00000120539	ENST00000375940	Transcript	synonymous_variant	1551	1494	498	S	agT/agC	.	.	.	1	MASTL	HGNC	19042	protein_coding	YES	CCDS53502.1	ENSP00000365107	GWL_HUMAN	.	UPI000004060D	.	.	.	8/12	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24356,SMART_domains:SM00220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAAGTCAACA	.	4	ESCA
FRMPD2	0	.	GRCh37	10	49440312	49440312	+	Nonsense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1014T>G	p.Tyr338Ter	p.Y338*	ENST00000374201	10/29	36	28	8	26	26	0	FRMPD2,stop_gained,p.Tyr338Ter,ENST00000374201,;FRMPD2,stop_gained,p.Tyr307Ter,ENST00000407470,;FRMPD2,stop_gained,p.Tyr314Ter,ENST00000305531,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000486151,;	C	ENSG00000170324	ENST00000374201	Transcript	stop_gained	1317	1014	338	Y/*	taT/taG	.	.	.	-1	FRMPD2	HGNC	28572	protein_coding	YES	CCDS31195.1	ENSP00000363317	FRPD2_HUMAN	.	UPI0000D60F5F	.	.	.	10/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAAATAGGA	.	5	ESCA
PDGFD	0	.	GRCh37	11	103780276	103780276	+	3'UTR	SNP	A	A	G	rs527264660	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*146T>C	.	.	ENST00000393158	7/7	90	78	12	56	56	0	PDGFD,3_prime_UTR_variant,,ENST00000302251,;PDGFD,3_prime_UTR_variant,,ENST00000393158,;	G	ENSG00000170962	ENST00000393158	Transcript	3_prime_UTR_variant	1439	.	.	.	.	rs527264660	.	.	-1	PDGFD	HGNC	30620	protein_coding	YES	CCDS41703.1	ENSP00000376865	PDGFD_HUMAN	.	UPI0000034811	.	.	.	7/7	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAAAGCAAG	by1000G	5	ESCA
CASP12	0	.	GRCh37	11	104762081	104762081	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483C>A	p.%3D	p.S161S	ENST00000422698	4/8	83	72	11	63	63	0	CASP12,synonymous_variant,p.%3D,ENST00000375726,;CASP12,synonymous_variant,p.%3D,ENST00000446862,;CASP12,synonymous_variant,p.%3D,ENST00000508062,;CASP12,synonymous_variant,p.%3D,ENST00000441710,;CASP12,synonymous_variant,p.%3D,ENST00000422698,;CASP12,intron_variant,,ENST00000494737,;CASP12,intron_variant,,ENST00000448103,;CASP12,intron_variant,,ENST00000433738,;CASP12,intron_variant,,ENST00000447913,;CASP12,3_prime_UTR_variant,,ENST00000417998,;CASP12,intron_variant,,ENST00000458137,;	T	ENSG00000204403	ENST00000422698	Transcript	synonymous_variant	502	483	161	S	tcC/tcA	.	.	.	-1	CASP12	HGNC	19004	protein_coding	YES	CCDS55785.1	ENSP00000427128	CASPC_HUMAN	.	UPI000040532B	.	.	.	4/8	.	Superfamily_domains:SSF52129,SMART_domains:SM00115,PIRSF_domain:PIRSF038001,Gene3D:3.40.50.1460,Pfam_domain:PF00656,hmmpanther:PTHR10454:SF134,hmmpanther:PTHR10454,PROSITE_profiles:PS50208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGAGGACTG	.	5	ESCA
VWA5A	0	.	GRCh37	11	123989252	123989252	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482A>G	p.Asp161Gly	p.D161G	ENST00000456829	6/19	58	52	5	42	42	0	VWA5A,missense_variant,p.Asp177Gly,ENST00000392744,;VWA5A,missense_variant,p.Asp161Gly,ENST00000456829,;VWA5A,missense_variant,p.Asp161Gly,ENST00000449321,;VWA5A,missense_variant,p.Asp161Gly,ENST00000360334,;VWA5A,missense_variant,p.Asp161Gly,ENST00000361352,;VWA5A,missense_variant,p.Asp161Gly,ENST00000392748,;VWA5A,downstream_gene_variant,,ENST00000533623,;	G	ENSG00000110002	ENST00000456829	Transcript	missense_variant	733	482	161	D/G	gAc/gGc	.	.	.	1	VWA5A	HGNC	6658	protein_coding	YES	CCDS8444.1	ENSP00000407726	VMA5A_HUMAN	.	UPI0000158B80	.	tolerated(0.48)	benign(0.001)	6/19	.	hmmpanther:PTHR10338:SF100,hmmpanther:PTHR10338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAAGGACAGTT	.	3	ESCA
DCDC1	0	.	GRCh37	11	31112986	31112986	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2191G>T	p.Ala731Ser	p.A731S	ENST00000597505	15/36	64	61	3	45	45	0	DCDC1,missense_variant,p.Ala731Ser,ENST00000597505,;DCDC1,non_coding_transcript_exon_variant,,ENST00000437348,;DCDC1,3_prime_UTR_variant,,ENST00000342355,;	A	ENSG00000170959	ENST00000597505	Transcript	missense_variant	2191	2191	731	A/S	Gct/Tct	.	.	.	-1	DCDC1	HGNC	20625	protein_coding	.	.	ENSP00000472625	.	M0R2J8_HUMAN	UPI0002A47319	.	tolerated(0.41)	benign(0.193)	15/36	.	PROSITE_profiles:PS50231,Superfamily_domains:SSF50370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCAGCAGCCT	.	2	ESCA
OR10Q1	0	.	GRCh37	11	57995724	57995724	+	Silent	SNP	G	G	A	rs142217876	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624C>T	p.%3D	p.S208S	ENST00000316770	1/1	72	65	6	41	41	0	OR10Q1,synonymous_variant,p.%3D,ENST00000316770,;	A	ENSG00000180475	ENST00000316770	Transcript	synonymous_variant	667	624	208	S	agC/agT	rs142217876	.	.	-1	OR10Q1	HGNC	15134	protein_coding	YES	CCDS31547.1	ENSP00000314324	O10Q1_HUMAN	.	UPI0000041C4C	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF253,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	T:0	T:0.0006	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGATGCTCAC	byCluster	3	ESCA
LGALS12	0	.	GRCh37	11	63276016	63276016	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136-9C>A	.	.	ENST00000340246	.	134	123	10	119	119	0	LGALS12,5_prime_UTR_variant,,ENST00000425950,;LGALS12,5_prime_UTR_variant,,ENST00000415491,;LGALS12,intron_variant,,ENST00000255684,;LGALS12,intron_variant,,ENST00000340246,;LGALS12,intron_variant,,ENST00000394618,;	A	ENSG00000133317	ENST00000340246	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LGALS12	HGNC	15788	protein_coding	YES	CCDS44633.1	ENSP00000339374	.	G5E970_HUMAN	UPI000014130D	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTTTCTTGTT	.	3	ESCA
ANO1	0	.	GRCh37	11	70009403	70009403	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1907C>T	p.Pro636Leu	p.P636L	ENST00000355303	19/26	92	78	14	42	42	0	ANO1,missense_variant,p.Pro578Leu,ENST00000316296,;ANO1,missense_variant,p.Pro490Leu,ENST00000398543,;ANO1,missense_variant,p.Pro636Leu,ENST00000355303,;ANO1,missense_variant,p.Pro345Leu,ENST00000531349,;ANO1,missense_variant,p.Pro636Leu,ENST00000538023,;ANO1,missense_variant,p.Pro490Leu,ENST00000530676,;ANO1,downstream_gene_variant,,ENST00000531300,;ANO1,upstream_gene_variant,,ENST00000529636,;	T	ENSG00000131620	ENST00000355303	Transcript	missense_variant	2212	1907	636	P/L	cCg/cTg	.	.	.	1	ANO1	HGNC	21625	protein_coding	YES	CCDS44663.1	ENSP00000347454	ANO1_HUMAN	.	UPI000013CE03	.	deleterious(0)	probably_damaging(1)	19/26	.	hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13,Pfam_domain:PF04547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCCCGGGCG	.	5	ESCA
CTSC	0	.	GRCh37	11	88045627	88045627	+	Silent	SNP	G	G	A	rs375899934	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.414C>T	p.%3D	p.T138T	ENST00000227266	3/7	57	49	7	47	47	0	CTSC,synonymous_variant,p.%3D,ENST00000527018,;CTSC,synonymous_variant,p.%3D,ENST00000227266,;CTSC,non_coding_transcript_exon_variant,,ENST00000533865,;	A	ENSG00000109861	ENST00000227266	Transcript	synonymous_variant	529	414	138	T	acC/acT	rs375899934	.	.	-1	CTSC	HGNC	2528	protein_coding	YES	CCDS8282.1	ENSP00000227266	CATC_HUMAN	I3V9T0_HUMAN	UPI000006D22D	.	.	.	3/7	.	Superfamily_domains:SSF75001,Gene3D:2djfA00,Pfam_domain:PF08773,hmmpanther:PTHR12411:SF314,hmmpanther:PTHR12411	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCGGTGAA	byFrequency|byCluster	5	ESCA
TAS2R31	0	.	GRCh37	12	11183984	11183984	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-50C>T	.	.	ENST00000390675	1/1	15	11	4	11	11	0	TAS2R31,5_prime_UTR_variant,,ENST00000390675,;AC018630.1,upstream_gene_variant,,ENST00000601123,;PRR4,intron_variant,,ENST00000539853,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;TAS2R14,intron_variant,,ENST00000381852,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000536086,;PRR4,intron_variant,,ENST00000534923,;PRR4,intron_variant,,ENST00000541456,;	A	ENSG00000256436	ENST00000390675	Transcript	5_prime_UTR_variant	23	.	.	.	.	.	.	.	-1	TAS2R31	HGNC	19113	protein_coding	YES	CCDS53747.1	ENSP00000375093	T2R31_HUMAN	.	UPI000000D820	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGGAGTTGGT	.	2	ESCA
NOS1	0	.	GRCh37	12	117703277	117703277	+	Silent	SNP	G	G	A	rs765418769	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1980C>T	p.%3D	p.T660T	ENST00000338101	11/29	114	106	8	92	92	0	NOS1,synonymous_variant,p.%3D,ENST00000317775,;NOS1,synonymous_variant,p.%3D,ENST00000338101,;NOS1,3_prime_UTR_variant,,ENST00000344089,;	A	ENSG00000089250	ENST00000338101	Transcript	synonymous_variant	1985	1980	660	T	acC/acT	rs765418769	.	.	-1	NOS1	HGNC	7872	protein_coding	YES	CCDS55890.1	ENSP00000337459	NOS1_HUMAN	A0PJJ7_HUMAN	UPI00001FBC10	.	.	.	11/29	.	Superfamily_domains:SSF56512,PIRSF_domain:PIRSF000333,Pfam_domain:PF02898,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACTCGGTGGC	byFrequency	2	ESCA
GCN1L1	0	.	GRCh37	12	120580662	120580662	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5579A>T	p.Glu1860Val	p.E1860V	ENST00000300648	43/58	41	38	3	45	45	0	GCN1L1,missense_variant,p.Glu1860Val,ENST00000300648,;GCN1L1,upstream_gene_variant,,ENST00000547263,;	A	ENSG00000089154	ENST00000300648	Transcript	missense_variant	5592	5579	1860	E/V	gAg/gTg	.	.	.	-1	GCN1L1	HGNC	4199	protein_coding	YES	CCDS41847.1	ENSP00000300648	GCN1L_HUMAN	B4DM32_HUMAN	UPI00001FBC69	.	.	probably_damaging(0.926)	43/58	.	Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCCTCAGAG	.	2	ESCA
KRT121P	0	.	GRCh37	12	52649170	52649170	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.923G>A	.	.	ENST00000257935	4/11	44	39	4	41	41	0	KRT86,intron_variant,,ENST00000544024,;KRT86,intron_variant,,ENST00000553310,;KRT121P,non_coding_transcript_exon_variant,,ENST00000529785,;KRT7,downstream_gene_variant,,ENST00000548657,;KRT121P,non_coding_transcript_exon_variant,,ENST00000257935,;KRT121P,non_coding_transcript_exon_variant,,ENST00000534226,;	T	ENSG00000135477	ENST00000257935	Transcript	non_coding_transcript_exon_variant	923	.	.	.	.	.	.	.	-1	KRT121P	HGNC	30198	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	4/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGGCCCTTAG	.	3	ESCA
AVIL	0	.	GRCh37	12	58204170	58204170	+	Silent	SNP	G	G	T	rs547034263	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723C>A	p.%3D	p.I241I	ENST00000257861	6/19	58	47	11	61	61	0	AVIL,synonymous_variant,p.%3D,ENST00000257861,;AVIL,synonymous_variant,p.%3D,ENST00000537081,;AVIL,downstream_gene_variant,,ENST00000549994,;TSFM,downstream_gene_variant,,ENST00000548851,;RNU6-1083P,upstream_gene_variant,,ENST00000384022,;RP11-571M6.18,upstream_gene_variant,,ENST00000602327,;AVIL,upstream_gene_variant,,ENST00000550083,;AVIL,3_prime_UTR_variant,,ENST00000549851,;AVIL,non_coding_transcript_exon_variant,,ENST00000548843,;AVIL,upstream_gene_variant,,ENST00000549753,;AVIL,upstream_gene_variant,,ENST00000550537,;AVIL,upstream_gene_variant,,ENST00000549548,;	T	ENSG00000135407	ENST00000257861	Transcript	synonymous_variant	1154	723	241	I	atC/atA	rs547034263,COSM238920	.	.	-1	AVIL	HGNC	14188	protein_coding	YES	CCDS8959.1	ENSP00000257861	AVIL_HUMAN	F8VVU1_HUMAN	UPI000013CF93	.	.	.	6/19	.	Superfamily_domains:SSF82754,hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF33	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTATGATCTC	by1000G	5	ESCA
CHD4	0	.	GRCh37	12	6707388	6707388	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1686G>A	p.%3D	p.Q562Q	ENST00000357008	11/40	104	90	13	90	90	0	CHD4,synonymous_variant,p.%3D,ENST00000544040,;CHD4,synonymous_variant,p.%3D,ENST00000544484,;CHD4,synonymous_variant,p.%3D,ENST00000309577,;CHD4,synonymous_variant,p.%3D,ENST00000357008,;CHD4,downstream_gene_variant,,ENST00000545584,;CHD4,downstream_gene_variant,,ENST00000545942,;CHD4,upstream_gene_variant,,ENST00000536999,;CHD4,downstream_gene_variant,,ENST00000535810,;CHD4,downstream_gene_variant,,ENST00000430771,;	T	ENSG00000111642	ENST00000357008	Transcript	synonymous_variant	1850	1686	562	Q	caG/caA	.	.	.	-1	CHD4	HGNC	1919	protein_coding	YES	CCDS8552.1	ENSP00000349508	CHD4_HUMAN	F5H6N4_HUMAN	UPI000013C8EF	.	.	.	11/40	.	PROSITE_profiles:PS50013,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF554,Pfam_domain:PF00385,Gene3D:2.40.50.40,SMART_domains:SM00298,Superfamily_domains:SSF54160	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTACCTGCAG	.	4	ESCA
MGAT4C	0	.	GRCh37	12	86373140	86373140	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1364G>T	p.Cys455Phe	p.C455F	ENST00000604798	8/8	81	72	9	61	61	0	MGAT4C,missense_variant,p.Cys455Phe,ENST00000548651,;MGAT4C,missense_variant,p.Cys455Phe,ENST00000552808,;MGAT4C,missense_variant,p.Cys455Phe,ENST00000332156,;MGAT4C,missense_variant,p.Cys455Phe,ENST00000604798,;MGAT4C,missense_variant,p.Cys455Phe,ENST00000549405,;MGAT4C,missense_variant,p.Cys484Phe,ENST00000393205,;MGAT4C,downstream_gene_variant,,ENST00000547225,;MGAT4C,downstream_gene_variant,,ENST00000552435,;	A	ENSG00000182050	ENST00000604798	Transcript	missense_variant	2569	1364	455	C/F	tGt/tTt	COSM469001	.	.	-1	MGAT4C	HGNC	30871	protein_coding	YES	CCDS9030.1	ENSP00000474896	MGT4C_HUMAN	F8VWY2_HUMAN	UPI00001B002C	.	deleterious(0)	probably_damaging(0.999)	8/8	.	hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF8	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATACAATGT	.	4	ESCA
MIR1197	0	.	GRCh37	14	101491915	101491915	+	RNA	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.15G>A	.	.	ENST00000408818	1/1	177	162	15	144	144	0	MIR1197,non_coding_transcript_exon_variant,,ENST00000408818,;MIR379,downstream_gene_variant,,ENST00000362218,;MIR329-1,upstream_gene_variant,,ENST00000385028,;MIR758,upstream_gene_variant,,ENST00000390227,;MIR494,upstream_gene_variant,,ENST00000349529,;MIR411,downstream_gene_variant,,ENST00000362239,;MIR1193,upstream_gene_variant,,ENST00000408109,;MIR329-2,upstream_gene_variant,,ENST00000385029,;MIR323A,upstream_gene_variant,,ENST00000362199,;MIR299,downstream_gene_variant,,ENST00000385016,;MIR380,upstream_gene_variant,,ENST00000362112,;	A	ENSG00000221745	ENST00000408818	Transcript	non_coding_transcript_exon_variant	15	.	.	.	.	.	.	.	1	MIR1197	HGNC	35376	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TATTTGAAGAT	.	3	ESCA
MMP14	0	.	GRCh37	14	23310779	23310779	+	Missense_Mutation	SNP	C	C	T	rs554056813	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188C>T	p.Ala63Val	p.A63V	ENST00000311852	2/10	83	68	15	71	71	0	MMP14,missense_variant,p.Ala63Val,ENST00000311852,;MMP14,missense_variant,p.Ala69Val,ENST00000548761,;MMP14,downstream_gene_variant,,ENST00000547279,;MMP14,non_coding_transcript_exon_variant,,ENST00000548162,;MMP14,non_coding_transcript_exon_variant,,ENST00000547074,;MMP14,upstream_gene_variant,,ENST00000547596,;	T	ENSG00000157227	ENST00000311852	Transcript	missense_variant	449	188	63	A/V	gCg/gTg	rs554056813	.	.	1	MMP14	HGNC	7160	protein_coding	YES	CCDS9577.1	ENSP00000308208	MMP14_HUMAN	.	UPI0000048136	.	deleterious(0.01)	benign(0.342)	2/10	.	hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF24,Gene3D:3.40.390.10,Pfam_domain:PF01471,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF47090	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAGCGGCCA	byCluster	5	ESCA
MYH7	0	.	GRCh37	14	23886458	23886458	+	Missense_Mutation	SNP	G	G	A	rs139646545	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4423C>T	p.Arg1475Cys	p.R1475C	ENST00000355349	32/40	65	49	15	37	37	0	MYH7,missense_variant,p.Arg1475Cys,ENST00000355349,;MIR208B,downstream_gene_variant,,ENST00000401172,;CTD-2201G16.1,downstream_gene_variant,,ENST00000557368,;	A	ENSG00000092054	ENST00000355349	Transcript	missense_variant	4586	4423	1475	R/C	Cgc/Tgc	CM050711,rs139646545	.	.	-1	MYH7	HGNC	7577	protein_coding	YES	CCDS9601.1	ENSP00000347507	MYH7_HUMAN	Q59EV3_HUMAN,L0L5E6_HUMAN,A8CLN2_HUMAN,A8CLL2_HUMAN,A6N931_HUMAN,A6N930_HUMAN	UPI000014019B	.	deleterious(0.01)	possibly_damaging(0.654)	32/40	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF279,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	A:0	A:0.0001	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCGAGCCT	byCluster	5	ESCA
TXNDC16	0	.	GRCh37	14	52899183	52899183	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2317G>T	p.Val773Leu	p.V773L	ENST00000281741	21/21	76	65	10	69	69	0	TXNDC16,missense_variant,p.Val773Leu,ENST00000281741,;	A	ENSG00000087301	ENST00000281741	Transcript	missense_variant	2689	2317	773	V/L	Gtg/Ttg	.	.	.	-1	TXNDC16	HGNC	19965	protein_coding	YES	CCDS32083.1	ENSP00000281741	TXD16_HUMAN	G3V2S5_HUMAN,B7ZME4_HUMAN	UPI000059D245	.	tolerated(0.49)	benign(0.001)	21/21	.	hmmpanther:PTHR22699,hmmpanther:PTHR22699:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCACATCTG	.	5	ESCA
COX16	0	.	GRCh37	14	70826373	70826373	+	5'UTR	SNP	A	A	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-69T>C	.	.	ENST00000389912	1/4	29	23	6	14	14	0	COX16,5_prime_UTR_variant,,ENST00000389912,;RNU2-51P,upstream_gene_variant,,ENST00000410708,;COX16,non_coding_transcript_exon_variant,,ENST00000557612,;SYNJ2BP-COX16,intron_variant,,ENST00000555276,;COX16,upstream_gene_variant,,ENST00000555601,;	G	ENSG00000133983	ENST00000389912	Transcript	5_prime_UTR_variant	76	.	.	.	.	.	.	.	-1	COX16	HGNC	20213	protein_coding	YES	CCDS9802.1	ENSP00000374562	COX16_HUMAN	B8XYC5_HUMAN	UPI000004A06F	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGCTCACGCTC	.	4	ESCA
NRXN3	0	.	GRCh37	14	80327777	80327777	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2885-229G>A	.	.	ENST00000554719	.	86	63	23	78	78	0	NRXN3,missense_variant,p.Glu462Lys,ENST00000557594,;NRXN3,intron_variant,,ENST00000554719,;NRXN3,intron_variant,,ENST00000281127,;NRXN3,intron_variant,,ENST00000335750,;NRXN3,intron_variant,,ENST00000428277,;NRXN3,intron_variant,,ENST00000556003,;NRXN3,3_prime_UTR_variant,,ENST00000555387,;NRXN3,3_prime_UTR_variant,,ENST00000554738,;	A	ENSG00000021645	ENST00000554719	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCGAAACT	.	5	ESCA
GREM1	0	.	GRCh37	15	33025546	33025546	+	3'UTR	SNP	A	A	T	rs182520997	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2100A>T	.	.	ENST00000300177	2/2	34	26	8	25	25	0	GREM1,3_prime_UTR_variant,,ENST00000300177,;GREM1,3_prime_UTR_variant,,ENST00000322805,;GREM1,downstream_gene_variant,,ENST00000560830,;GREM1,downstream_gene_variant,,ENST00000560677,;	T	ENSG00000166923	ENST00000300177	Transcript	3_prime_UTR_variant	2844	.	.	.	.	rs182520997	.	.	1	GREM1	HGNC	2001	protein_coding	YES	CCDS10029.1	ENSP00000300177	GREM1_HUMAN	A6XAA7_HUMAN	UPI0000073D48	.	.	.	2/2	.	.	G:0.0004	G:0	G:0	.	G:0.002	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGAGGAAA	byFrequency|by1000G	5	ESCA
FBN1	0	.	GRCh37	15	48808454	48808454	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1253G>T	p.Gly418Val	p.G418V	ENST00000316623	11/66	26	23	3	33	33	0	FBN1,missense_variant,p.Gly418Val,ENST00000316623,;FBN1,intron_variant,,ENST00000537463,;	A	ENSG00000166147	ENST00000316623	Transcript	missense_variant	1709	1253	418	G/V	gGc/gTc	.	.	.	-1	FBN1	HGNC	3603	protein_coding	YES	CCDS32232.1	ENSP00000325527	FBN1_HUMAN	Q75N89_HUMAN,Q75N88_HUMAN,H0YN80_HUMAN	UPI0000163B0B	.	.	benign(0)	11/66	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,PIRSF_domain:PIRSF036312	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAAGCCAGGA	.	4	ESCA
SLTM	0	.	GRCh37	15	59189346	59189346	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1195G>C	p.Asp399His	p.D399H	ENST00000380516	9/21	64	58	6	44	44	0	SLTM,missense_variant,p.Asp381His,ENST00000249736,;SLTM,missense_variant,p.Asp399His,ENST00000380516,;SLTM,5_prime_UTR_variant,,ENST00000536328,;RNF111,intron_variant,,ENST00000559757,;SLTM,downstream_gene_variant,,ENST00000559880,;SLTM,upstream_gene_variant,,ENST00000432750,;SLTM,downstream_gene_variant,,ENST00000558486,;SLTM,downstream_gene_variant,,ENST00000560682,;AC025918.2,downstream_gene_variant,,ENST00000452467,;SLTM,downstream_gene_variant,,ENST00000557950,;SLTM,synonymous_variant,p.%3D,ENST00000558756,;SLTM,synonymous_variant,p.%3D,ENST00000492526,;SLTM,3_prime_UTR_variant,,ENST00000559305,;SLTM,3_prime_UTR_variant,,ENST00000557924,;SLTM,non_coding_transcript_exon_variant,,ENST00000473359,;SLTM,non_coding_transcript_exon_variant,,ENST00000497088,;SLTM,downstream_gene_variant,,ENST00000480144,;SLTM,upstream_gene_variant,,ENST00000558734,;SLTM,downstream_gene_variant,,ENST00000560532,;	G	ENSG00000137776	ENST00000380516	Transcript	missense_variant	1283	1195	399	D/H	Gat/Cat	.	.	.	-1	SLTM	HGNC	20709	protein_coding	YES	CCDS10168.2	ENSP00000369887	SLTM_HUMAN	H0YKH2_HUMAN,A8K5V8_HUMAN	UPI0000039EA4	.	deleterious(0)	unknown(0)	9/21	.	PROSITE_profiles:PS50102,hmmpanther:PTHR15683,hmmpanther:PTHR15683:SF5,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAAATCAGCAG	.	3	ESCA
FURIN	0	.	GRCh37	15	91420169	91420169	+	Missense_Mutation	SNP	C	C	T	rs138939644	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.416C>T	p.Ala139Val	p.A139V	ENST00000268171	5/16	68	61	6	61	61	0	FURIN,missense_variant,p.Ala139Val,ENST00000268171,;FURIN,missense_variant,p.Ala137Val,ENST00000560824,;FURIN,downstream_gene_variant,,ENST00000559353,;FURIN,upstream_gene_variant,,ENST00000558794,;FURIN,upstream_gene_variant,,ENST00000560018,;	T	ENSG00000140564	ENST00000268171	Transcript	missense_variant	695	416	139	A/V	gCg/gTg	rs138939644	.	.	1	FURIN	HGNC	8568	protein_coding	YES	CCDS10364.1	ENSP00000268171	FURIN_HUMAN	H0YNB5_HUMAN,H0YKB2_HUMAN	UPI0000000CC7	.	tolerated(0.1)	benign(0.006)	5/16	.	Superfamily_domains:SSF52743,Gene3D:3.40.50.200,hmmpanther:PTHR10795:SF325,hmmpanther:PTHR10795	.	.	.	.	.	.	.	T:0	T:0.0006	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGGGCGCAGG	byCluster|by1000G	3	ESCA
MCTP2	0	.	GRCh37	15	94942290	94942290	+	Missense_Mutation	SNP	C	C	T	rs528835766	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1889C>T	p.Pro630Leu	p.P630L	ENST00000357742	14/22	45	41	4	26	26	0	MCTP2,missense_variant,p.Pro218Leu,ENST00000557742,;MCTP2,missense_variant,p.Pro218Leu,ENST00000331706,;MCTP2,missense_variant,p.Pro630Leu,ENST00000357742,;MCTP2,missense_variant,p.Pro630Leu,ENST00000451018,;MCTP2,splice_region_variant,,ENST00000456504,;MCTP2,upstream_gene_variant,,ENST00000557505,;	T	ENSG00000140563	ENST00000357742	Transcript	missense_variant	1889	1889	630	P/L	cCg/cTg	rs528835766	.	.	1	MCTP2	HGNC	25636	protein_coding	YES	CCDS32338.1	ENSP00000350377	MCTP2_HUMAN	Q9NPN6_HUMAN	UPI0000D613A2	.	deleterious(0.03)	possibly_damaging(0.475)	14/22	.	hmmpanther:PTHR16122,hmmpanther:PTHR16122:SF5	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TAATCCGGTAA	by1000G	3	ESCA
KIAA0430	0	.	GRCh37	16	15733071	15733071	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20C>A	p.Thr7Asn	p.T7N	ENST00000396368	2/27	60	51	9	76	76	0	KIAA0430,missense_variant,p.Thr7Asn,ENST00000551742,;KIAA0430,missense_variant,p.Thr7Asn,ENST00000602337,;KIAA0430,missense_variant,p.Thr7Asn,ENST00000549219,;KIAA0430,missense_variant,p.Thr7Asn,ENST00000540441,;KIAA0430,missense_variant,p.Thr7Asn,ENST00000548025,;KIAA0430,missense_variant,p.Thr7Asn,ENST00000396368,;KIAA0430,5_prime_UTR_variant,,ENST00000344181,;NDE1,upstream_gene_variant,,ENST00000396353,;NDE1,upstream_gene_variant,,ENST00000396355,;MIR484,upstream_gene_variant,,ENST00000606601,;KIAA0430,missense_variant,p.Thr7Asn,ENST00000552553,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000548216,;	T	ENSG00000166783	ENST00000396368	Transcript	missense_variant	227	20	7	T/N	aCt/aAt	.	.	.	-1	KIAA0430	HGNC	29562	protein_coding	YES	CCDS10562.2	ENSP00000379654	MARF1_HUMAN	F8VRS5_HUMAN	UPI00006881BC	.	deleterious_low_confidence(0.04)	benign(0.169)	2/27	.	hmmpanther:PTHR14379:SF3,hmmpanther:PTHR14379	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCAGTTCCG	.	5	ESCA
PRSS22	0	.	GRCh37	16	2905760	2905760	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.374G>C	p.Trp125Ser	p.W125S	ENST00000161006	4/6	30	25	5	21	21	0	PRSS22,missense_variant,p.Trp125Ser,ENST00000161006,;PRSS22,intron_variant,,ENST00000571228,;LA16c-325D7.1,upstream_gene_variant,,ENST00000577140,;PRSS22,non_coding_transcript_exon_variant,,ENST00000577177,;PRSS22,non_coding_transcript_exon_variant,,ENST00000574768,;PRSS22,3_prime_UTR_variant,,ENST00000576381,;PRSS22,non_coding_transcript_exon_variant,,ENST00000572061,;PRSS22,non_coding_transcript_exon_variant,,ENST00000575164,;PRSS22,downstream_gene_variant,,ENST00000570950,;	G	ENSG00000005001	ENST00000161006	Transcript	missense_variant	440	374	125	W/S	tGg/tCg	.	.	.	-1	PRSS22	HGNC	14368	protein_coding	YES	CCDS10481.1	ENSP00000161006	BSSP4_HUMAN	.	UPI0000126AFA	.	tolerated(0.14)	benign(0.068)	4/6	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24253:SF6,hmmpanther:PTHR24253,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACCCAGGCA	.	4	ESCA
MT1A	0	.	GRCh37	16	56678679	56678679	+	3'Flank	SNP	A	A	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000290705	.	99	84	14	88	88	0	MT1A,downstream_gene_variant,,ENST00000290705,;MT1DP,non_coding_transcript_exon_variant,,ENST00000463480,;RP11-249C24.11,upstream_gene_variant,,ENST00000568608,;MT1CP,upstream_gene_variant,,ENST00000379816,;MT1DP,downstream_gene_variant,,ENST00000486551,;MT1CP,upstream_gene_variant,,ENST00000567054,;	T	ENSG00000205362	ENST00000290705	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4680	1	MT1A	HGNC	7393	protein_coding	YES	CCDS32454.1	ENSP00000290705	MT1A_HUMAN	.	UPI000000D79B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAAAAGGGG	.	5	ESCA
MYH13	0	.	GRCh37	17	10206736	10206736	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5546G>A	p.Arg1849His	p.R1849H	ENST00000418404	37/41	99	88	11	74	74	0	MYH13,missense_variant,p.Arg1849His,ENST00000418404,;MYH13,missense_variant,p.Arg1849His,ENST00000252172,;RP11-401O9.4,intron_variant,,ENST00000609088,;	T	ENSG00000006788	ENST00000418404	Transcript	missense_variant	5710	5546	1849	R/H	cGc/cAc	.	.	.	-1	MYH13	HGNC	7571	protein_coding	YES	CCDS45613.1	ENSP00000404570	MYH13_HUMAN	.	UPI0000DB39EA	.	deleterious(0)	probably_damaging(0.997)	37/41	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF267,Pfam_domain:PF01576,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTGCGTTCG	.	4	ESCA
SUPT6H	0	.	GRCh37	17	27002030	27002030	+	Missense_Mutation	SNP	G	G	T	rs376272646	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388G>T	p.Asp130Tyr	p.D130Y	ENST00000314616	5/37	62	53	9	34	34	0	SUPT6H,missense_variant,p.Asp130Tyr,ENST00000314616,;SUPT6H,missense_variant,p.Asp130Tyr,ENST00000347486,;SUPT6H,downstream_gene_variant,,ENST00000577713,;AC010761.13,upstream_gene_variant,,ENST00000578819,;SUPT6H,non_coding_transcript_exon_variant,,ENST00000584285,;SUPT6H,downstream_gene_variant,,ENST00000584312,;	T	ENSG00000109111	ENST00000314616	Transcript	missense_variant	671	388	130	D/Y	Gat/Tat	rs376272646,COSM705821	.	.	1	SUPT6H	HGNC	11470	protein_coding	YES	CCDS32596.1	ENSP00000319104	SPT6H_HUMAN	J3QS64_HUMAN	UPI000015FFA7	.	deleterious(0)	unknown(0)	5/37	.	PIRSF_domain:PIRSF036947,hmmpanther:PTHR10145:SF6,hmmpanther:PTHR10145,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	A:0.0005	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGACGATGAC	byFrequency|byCluster	3	ESCA
FLOT2	0	.	GRCh37	17	27209414	27209414	+	Missense_Mutation	SNP	C	C	T	rs376860005	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520G>A	p.Val174Met	p.V174M	ENST00000394908	6/11	76	68	8	87	87	0	FLOT2,missense_variant,p.Val229Met,ENST00000394906,;FLOT2,missense_variant,p.Val174Met,ENST00000585169,;FLOT2,missense_variant,p.Val174Met,ENST00000394908,;FLOT2,missense_variant,p.Val108Met,ENST00000465427,;FLOT2,non_coding_transcript_exon_variant,,ENST00000577789,;FLOT2,intron_variant,,ENST00000584569,;FLOT2,3_prime_UTR_variant,,ENST00000580805,;FLOT2,3_prime_UTR_variant,,ENST00000586827,;FLOT2,non_coding_transcript_exon_variant,,ENST00000593158,;FLOT2,downstream_gene_variant,,ENST00000582174,;FLOT2,downstream_gene_variant,,ENST00000581509,;FLOT2,downstream_gene_variant,,ENST00000580313,;	T	ENSG00000132589	ENST00000394908	Transcript	missense_variant	625	520	174	V/M	Gtg/Atg	rs376860005	.	.	-1	FLOT2	HGNC	3758	protein_coding	YES	CCDS11245.2	ENSP00000378368	FLOT2_HUMAN	Q6FG43_HUMAN	UPI00001AE777	.	tolerated(0.09)	benign(0.067)	6/11	.	hmmpanther:PTHR13806,hmmpanther:PTHR13806:SF17,Pfam_domain:PF01145,SMART_domains:SM00244,Superfamily_domains:0050593	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCACGGCAG	byFrequency|byCluster	4	ESCA
CDK5R1	0	.	GRCh37	17	30815527	30815527	+	Missense_Mutation	SNP	G	G	T	rs769214004	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000313401	2/2	51	43	8	48	48	0	CDK5R1,missense_variant,p.Asp297Tyr,ENST00000313401,;CDK5R1,3_prime_UTR_variant,,ENST00000584792,;MYO1D,downstream_gene_variant,,ENST00000394649,;MYO1D,downstream_gene_variant,,ENST00000318217,;CDK5R1,3_prime_UTR_variant,,ENST00000584716,;	T	ENSG00000176749	ENST00000313401	Transcript	missense_variant	1578	889	297	D/Y	Gac/Tac	rs769214004	.	.	1	CDK5R1	HGNC	1775	protein_coding	YES	CCDS11273.1	ENSP00000318486	CD5R1_HUMAN	.	UPI000012738E	.	deleterious(0)	possibly_damaging(0.642)	2/2	.	PIRSF_domain:PIRSF009324,hmmpanther:PTHR23401,hmmpanther:PTHR23401:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGGAGGACAAG	byFrequency	4	ESCA
KRT25	0	.	GRCh37	17	38910113	38910113	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668A>T	p.Glu223Val	p.E223V	ENST00000312150	3/8	85	74	11	68	68	0	KRT25,missense_variant,p.Glu223Val,ENST00000312150,;	A	ENSG00000204897	ENST00000312150	Transcript	missense_variant	729	668	223	E/V	gAg/gTg	.	.	.	-1	KRT25	HGNC	30839	protein_coding	YES	CCDS11373.1	ENSP00000310573	K1C25_HUMAN	.	UPI000019B3C3	.	deleterious(0)	possibly_damaging(0.904)	3/8	.	Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF160	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTACCTCTTTA	.	4	ESCA
KRT34	0	.	GRCh37	17	39538436	39538436	+	Silent	SNP	G	G	A	rs374587752	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189C>T	p.%3D	p.C63C	ENST00000394001	1/7	142	127	15	113	113	0	KRT34,synonymous_variant,p.%3D,ENST00000394001,;	A	ENSG00000131737	ENST00000394001	Transcript	synonymous_variant	220	189	63	C	tgC/tgT	rs374587752	.	.	-1	KRT34	HGNC	6452	protein_coding	YES	CCDS11390.1	ENSP00000377570	KRT34_HUMAN	.	UPI000013CD0C	.	.	.	1/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF165,hmmpanther:PTHR23239	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCACGCAGGG	byFrequency|byCluster	4	ESCA
ACADVL	0	.	GRCh37	17	7127680	7127680	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1642G>A	p.Val548Ile	p.V548I	ENST00000543245	17/21	71	63	8	54	54	0	ACADVL,missense_variant,p.Val145Ile,ENST00000542255,;ACADVL,missense_variant,p.Cys105Tyr,ENST00000579546,;ACADVL,missense_variant,p.Val525Ile,ENST00000356839,;ACADVL,missense_variant,p.Val548Ile,ENST00000543245,;ACADVL,missense_variant,p.Val503Ile,ENST00000350303,;DLG4,upstream_gene_variant,,ENST00000399510,;ACADVL,downstream_gene_variant,,ENST00000584103,;DVL2,downstream_gene_variant,,ENST00000575458,;DVL2,downstream_gene_variant,,ENST00000575756,;DVL2,downstream_gene_variant,,ENST00000575086,;DVL2,downstream_gene_variant,,ENST00000005340,;DVL2,downstream_gene_variant,,ENST00000574143,;ACADVL,downstream_gene_variant,,ENST00000583312,;ACADVL,downstream_gene_variant,,ENST00000579886,;MIR324,upstream_gene_variant,,ENST00000362183,;ACADVL,non_coding_transcript_exon_variant,,ENST00000583074,;DVL2,downstream_gene_variant,,ENST00000574642,;ACADVL,downstream_gene_variant,,ENST00000577857,;ACADVL,downstream_gene_variant,,ENST00000581562,;ACADVL,missense_variant,p.Cys169Tyr,ENST00000583858,;ACADVL,3_prime_UTR_variant,,ENST00000322910,;ACADVL,non_coding_transcript_exon_variant,,ENST00000579391,;ACADVL,non_coding_transcript_exon_variant,,ENST00000585203,;ACADVL,non_coding_transcript_exon_variant,,ENST00000578711,;ACADVL,non_coding_transcript_exon_variant,,ENST00000582450,;ACADVL,non_coding_transcript_exon_variant,,ENST00000578319,;ACADVL,non_coding_transcript_exon_variant,,ENST00000578809,;ACADVL,non_coding_transcript_exon_variant,,ENST00000579425,;ACADVL,non_coding_transcript_exon_variant,,ENST00000583850,;ACADVL,non_coding_transcript_exon_variant,,ENST00000579894,;ACADVL,upstream_gene_variant,,ENST00000583848,;ACADVL,downstream_gene_variant,,ENST00000578421,;DVL2,downstream_gene_variant,,ENST00000573354,;ACADVL,downstream_gene_variant,,ENST00000582379,;ACADVL,downstream_gene_variant,,ENST00000579286,;DVL2,downstream_gene_variant,,ENST00000576840,;ACADVL,downstream_gene_variant,,ENST00000580263,;ACADVL,downstream_gene_variant,,ENST00000577191,;DVL2,downstream_gene_variant,,ENST00000577154,;ACADVL,upstream_gene_variant,,ENST00000578033,;ACADVL,downstream_gene_variant,,ENST00000578269,;DVL2,downstream_gene_variant,,ENST00000571745,;DVL2,downstream_gene_variant,,ENST00000574591,;ACADVL,downstream_gene_variant,,ENST00000582356,;DVL2,downstream_gene_variant,,ENST00000576285,;ACADVL,downstream_gene_variant,,ENST00000583760,;ACADVL,downstream_gene_variant,,ENST00000577433,;ACADVL,downstream_gene_variant,,ENST00000582166,;ACADVL,downstream_gene_variant,,ENST00000578824,;ACADVL,downstream_gene_variant,,ENST00000580365,;DVL2,downstream_gene_variant,,ENST00000572285,;ACADVL,downstream_gene_variant,,ENST00000578579,;ACADVL,downstream_gene_variant,,ENST00000582056,;ACADVL,downstream_gene_variant,,ENST00000581378,;	A	ENSG00000072778	ENST00000543245	Transcript	missense_variant	1663	1642	548	V/I	Gtc/Atc	.	.	.	1	ACADVL	HGNC	92	protein_coding	YES	CCDS58509.1	ENSP00000438689	ACADV_HUMAN	B3KPA6_HUMAN	UPI0002064F84	.	tolerated(0.08)	benign(0.019)	17/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACTTGTCCAC	.	4	ESCA
GALR2	0	.	GRCh37	17	74071023	74071023	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59G>A	p.Gly20Asp	p.G20D	ENST00000329003	1/2	35	28	6	36	36	0	GALR2,missense_variant,p.Gly20Asp,ENST00000329003,;ZACN,upstream_gene_variant,,ENST00000392503,;SRP68,upstream_gene_variant,,ENST00000307877,;ZACN,upstream_gene_variant,,ENST00000334586,;SRP68,upstream_gene_variant,,ENST00000355113,;SRP68,upstream_gene_variant,,ENST00000539137,;ZACN,intron_variant,,ENST00000591500,;SRP68,upstream_gene_variant,,ENST00000591272,;SRP68,upstream_gene_variant,,ENST00000592704,;ZACN,upstream_gene_variant,,ENST00000524242,;ZACN,upstream_gene_variant,,ENST00000425015,;ZACN,upstream_gene_variant,,ENST00000421794,;	A	ENSG00000182687	ENST00000329003	Transcript	missense_variant	149	59	20	G/D	gGc/gAc	.	.	.	1	GALR2	HGNC	4133	protein_coding	YES	CCDS11739.1	ENSP00000329684	GALR2_HUMAN	.	UPI000004B247	.	tolerated(0.14)	benign(0.123)	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24230,hmmpanther:PTHR24230:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GGGAGGCTGGC	.	3	ESCA
TP53	0	.	GRCh37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524G>A	p.Arg175His	p.R175H	ENST00000269305	5/11	34	24	10	34	34	0	TP53,missense_variant,p.Arg175His,ENST00000413465,;TP53,missense_variant,p.Arg175His,ENST00000420246,;TP53,missense_variant,p.Arg175His,ENST00000269305,;TP53,missense_variant,p.Arg43His,ENST00000509690,;TP53,missense_variant,p.Arg175His,ENST00000359597,;TP53,missense_variant,p.Arg82His,ENST00000514944,;TP53,missense_variant,p.Arg175His,ENST00000445888,;TP53,missense_variant,p.Arg175His,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	714	524	175	R/H	cGc/cAc	CM951224,rs28934578,CM062017,TP53_g.12512G>T,TP53_g.12512G>C,TP53_g.12512G>A,COSM10718,COSM10648,COSM45416,COSM99914,COSM1679508,COSM99022,COSM1679510,COSM99023,COSM1679512,COSM3355994,COSM1640851,COSM1679509,COSM99024,COSM1679511	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.11)	benign(0.308)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660,21264207,24929325,25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R175H|c.524G>A|181,SITE|p.R43H|c.128G>A|183,SITE|p.R82H|c.245G>A|183,SITE|p.R175H|c.524G>A|124,SITE|p.R175H|c.524G>A|180,SITE|p.R175H|c.524G>A|926,SITE|p.R175H|c.524G>A|88,CODON|p.0?|c.1_1182del1182|6,CODON|p.R175L|c.524G>T|20,CODON|p.R175P|c.524G>C|6,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R43L|c.128G>T|3,CODON|p.R82L|c.245G>T|3,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.P177_C182delPHHERC|c.526_543del18|3,BUFFER|p.H179Y|c.534_535CC>TT|8,BUFFER|p.H179D|c.535C>G|12,BUFFER|p.H179Y|c.535C>T|4,BUFFER|p.H47Y|c.139C>T|15,BUFFER|p.H179Y|c.535C>T|5,BUFFER|p.H179Y|c.535C>T|88,BUFFER|p.H179N|c.535C>A|15,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H86Y|c.256C>T|14,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R82G|c.244C>G|5,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43G|c.127C>G|8,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175G|c.523C>G|16,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R174K|c.521G>A|5,BUFFER|p.R174W|c.520A>T|11,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V172D|c.515T>A|11,BUFFER|p.V172A|c.515T>C|4,BUFFER|p.V172G|c.515T>G|4,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAGCGCCTC	byCluster	5	ESCA
CCDC57	0	.	GRCh37	17	80115510	80115510	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99G>A	.	.	ENST00000392343	15/15	91	80	11	89	89	0	CCDC57,3_prime_UTR_variant,,ENST00000392343,;CCDC57,intron_variant,,ENST00000389641,;CCDC57,intron_variant,,ENST00000419322,;CCDC57,intron_variant,,ENST00000392347,;RP11-1376P16.1,upstream_gene_variant,,ENST00000582774,;RP11-1376P16.2,downstream_gene_variant,,ENST00000579979,;CCDC57,non_coding_transcript_exon_variant,,ENST00000327026,;CCDC57,upstream_gene_variant,,ENST00000475635,;	T	ENSG00000176155	ENST00000392343	Transcript	3_prime_UTR_variant	2710	.	.	.	.	.	.	.	-1	CCDC57	HGNC	27564	protein_coding	YES	.	ENSP00000376154	CCD57_HUMAN	.	UPI000022A20F	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGTCCC	.	4	ESCA
LDLRAD4	0	.	GRCh37	18	13646376	13646376	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*720T>A	.	.	ENST00000361205	7/7	16	8	8	20	20	0	LDLRAD4,3_prime_UTR_variant,,ENST00000361205,;LDLRAD4,3_prime_UTR_variant,,ENST00000359446,;LDLRAD4,3_prime_UTR_variant,,ENST00000399848,;LDLRAD4,3_prime_UTR_variant,,ENST00000585931,;LDLRAD4,downstream_gene_variant,,ENST00000587757,;LDLRAD4,downstream_gene_variant,,ENST00000592991,;LDLRAD4,downstream_gene_variant,,ENST00000586765,;RP11-701H16.4,upstream_gene_variant,,ENST00000588397,;LDLRAD4,downstream_gene_variant,,ENST00000586207,;LDLRAD4,non_coding_transcript_exon_variant,,ENST00000435606,;LDLRAD4,non_coding_transcript_exon_variant,,ENST00000361303,;	A	ENSG00000168675	ENST00000361205	Transcript	3_prime_UTR_variant	2309	.	.	.	.	.	.	.	1	LDLRAD4	HGNC	1224	protein_coding	YES	CCDS32793.1	ENSP00000354753	LRAD4_HUMAN	K7EMG1_HUMAN,K7EKD6_HUMAN,K7EJM9_HUMAN	UPI0000126BCF	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTTGGGGA	.	5	ESCA
RBBP8	0	.	GRCh37	18	20596862	20596862	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2429G>T	p.Gly810Val	p.G810V	ENST00000399722	17/19	29	24	5	36	36	0	RBBP8,missense_variant,p.Gly810Val,ENST00000399722,;RBBP8,missense_variant,p.Gly235Cys,ENST00000583057,;RBBP8,missense_variant,p.Gly815Val,ENST00000360790,;RBBP8,missense_variant,p.Gly810Val,ENST00000327155,;RBBP8,5_prime_UTR_variant,,ENST00000581687,;RBBP8,intron_variant,,ENST00000399725,;	T	ENSG00000101773	ENST00000399722	Transcript	missense_variant	2780	2429	810	G/V	gGg/gTg	COSM987026	.	.	1	RBBP8	HGNC	9891	protein_coding	YES	CCDS11875.1	ENSP00000382628	COM1_HUMAN	J3QRM0_HUMAN,J3QLW6_HUMAN,J3QLH2_HUMAN,J3QL93_HUMAN,J3KSA4_HUMAN,F6Q6H0_HUMAN	UPI000013D1A9	.	deleterious(0)	probably_damaging(0.965)	17/19	.	hmmpanther:PTHR15107,hmmpanther:PTHR15107:SF2,Pfam_domain:PF08573	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTTGGGCACA	.	3	ESCA
LSM7	0	.	GRCh37	19	2328428	2328428	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55A>T	p.Ile19Phe	p.I19F	ENST00000252622	2/4	45	37	7	57	57	0	LSM7,missense_variant,p.Ile19Phe,ENST00000252622,;AC004410.3,upstream_gene_variant,,ENST00000586111,;SPPL2B,upstream_gene_variant,,ENST00000592845,;SPPL2B,upstream_gene_variant,,ENST00000590982,;SPPL2B,upstream_gene_variant,,ENST00000586377,;SPPL2B,upstream_gene_variant,,ENST00000452401,;SPPL2B,upstream_gene_variant,,ENST00000585725,;SPPL2B,upstream_gene_variant,,ENST00000592738,;SPPL2B,upstream_gene_variant,,ENST00000590295,;SPPL2B,upstream_gene_variant,,ENST00000382189,;SPPL2B,upstream_gene_variant,,ENST00000586332,;LSM7,upstream_gene_variant,,ENST00000589532,;LSM7,missense_variant,p.Ile18Phe,ENST00000585395,;LSM7,missense_variant,p.Ile19Phe,ENST00000585409,;LSM7,non_coding_transcript_exon_variant,,ENST00000591745,;LSM7,non_coding_transcript_exon_variant,,ENST00000587502,;LSM7,upstream_gene_variant,,ENST00000591515,;SPPL2B,upstream_gene_variant,,ENST00000593198,;	A	ENSG00000130332	ENST00000252622	Transcript	missense_variant	109	55	19	I/F	Atc/Ttc	.	.	.	-1	LSM7	HGNC	20470	protein_coding	YES	CCDS45907.1	ENSP00000252622	LSM7_HUMAN	.	UPI000012E96B	.	deleterious(0.01)	possibly_damaging(0.493)	2/4	.	hmmpanther:PTHR10553,Gene3D:2.30.30.100,Pfam_domain:PF01423,SMART_domains:SM00651,PIRSF_domain:PIRSF037188,Superfamily_domains:SSF50182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCGATGTACT	.	5	ESCA
LSM7	0	.	GRCh37	19	2328429	2328429	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54C>A	p.Tyr18Ter	p.Y18*	ENST00000252622	2/4	45	38	7	58	58	0	LSM7,stop_gained,p.Tyr18Ter,ENST00000252622,;AC004410.3,upstream_gene_variant,,ENST00000586111,;SPPL2B,upstream_gene_variant,,ENST00000592845,;SPPL2B,upstream_gene_variant,,ENST00000590982,;SPPL2B,upstream_gene_variant,,ENST00000586377,;SPPL2B,upstream_gene_variant,,ENST00000452401,;SPPL2B,upstream_gene_variant,,ENST00000585725,;SPPL2B,upstream_gene_variant,,ENST00000592738,;SPPL2B,upstream_gene_variant,,ENST00000590295,;SPPL2B,upstream_gene_variant,,ENST00000382189,;SPPL2B,upstream_gene_variant,,ENST00000586332,;LSM7,upstream_gene_variant,,ENST00000589532,;LSM7,stop_gained,p.Tyr17Ter,ENST00000585395,;LSM7,stop_gained,p.Tyr18Ter,ENST00000585409,;LSM7,non_coding_transcript_exon_variant,,ENST00000591745,;LSM7,non_coding_transcript_exon_variant,,ENST00000587502,;LSM7,upstream_gene_variant,,ENST00000591515,;SPPL2B,upstream_gene_variant,,ENST00000593198,;	T	ENSG00000130332	ENST00000252622	Transcript	stop_gained	108	54	18	Y/*	taC/taA	.	.	.	-1	LSM7	HGNC	20470	protein_coding	YES	CCDS45907.1	ENSP00000252622	LSM7_HUMAN	.	UPI000012E96B	.	.	.	2/4	.	hmmpanther:PTHR10553,Gene3D:2.30.30.100,Pfam_domain:PF01423,SMART_domains:SM00651,PIRSF_domain:PIRSF037188,Superfamily_domains:SSF50182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGATGTACTT	.	5	ESCA
ZNF536	0	.	GRCh37	19	30936232	30936232	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1763T>C	p.Val588Ala	p.V588A	ENST00000355537	2/5	50	41	8	51	51	0	ZNF536,missense_variant,p.Val588Ala,ENST00000585628,;ZNF536,missense_variant,p.Val588Ala,ENST00000355537,;ZNF536,downstream_gene_variant,,ENST00000591488,;	C	ENSG00000198597	ENST00000355537	Transcript	missense_variant	1910	1763	588	V/A	gTg/gCg	.	.	.	1	ZNF536	HGNC	29025	protein_coding	YES	CCDS32984.1	ENSP00000347730	ZN536_HUMAN	K7EKT4_HUMAN,K7EJP8_HUMAN	UPI000006ED3E	.	tolerated(1)	benign(0.001)	2/5	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAAGTGGGCA	.	5	ESCA
ZFP14	0	.	GRCh37	19	36832184	36832184	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544A>G	p.Ile182Val	p.I182V	ENST00000270001	5/5	62	47	15	41	41	0	ZFP14,missense_variant,p.Ile182Val,ENST00000270001,;	C	ENSG00000142065	ENST00000270001	Transcript	missense_variant	660	544	182	I/V	Att/Gtt	.	.	.	-1	ZFP14	HGNC	29312	protein_coding	YES	CCDS33002.1	ENSP00000270001	ZFP14_HUMAN	.	UPI000013AD55	.	tolerated(0.47)	possibly_damaging(0.593)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF253,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R183C|c.547C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGAATAAAGG	.	5	ESCA
KLKP1	0	.	GRCh37	19	51391278	51391278	+	RNA	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.640G>T	.	.	ENST00000600104	1/2	234	195	39	211	211	0	KLKP1,non_coding_transcript_exon_variant,,ENST00000600104,;KLKP1,intron_variant,,ENST00000597246,;KLKP1,non_coding_transcript_exon_variant,,ENST00000595979,;KLKP1,upstream_gene_variant,,ENST00000358534,;	A	ENSG00000197588	ENST00000600104	Transcript	non_coding_transcript_exon_variant	640	.	.	.	.	.	.	.	-1	KLKP1	HGNC	21260	processed_transcript	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGACCATTC	.	4	ESCA
MIR518D	0	.	GRCh37	19	54238132	54238132	+	RNA	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2C>A	.	.	ENST00000385014	1/1	82	75	7	74	74	0	MIR518D,non_coding_transcript_exon_variant,,ENST00000385014,;MIR518A1,downstream_gene_variant,,ENST00000385068,;RNU6-980P,upstream_gene_variant,,ENST00000516925,;MIR518E,downstream_gene_variant,,ENST00000385252,;MIR516B1,upstream_gene_variant,,ENST00000385211,;MIR518A2,upstream_gene_variant,,ENST00000384966,;	A	ENSG00000207747	ENST00000385014	Transcript	non_coding_transcript_exon_variant	2	.	.	.	.	.	.	.	1	MIR518D	HGNC	32121	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGATCCCATG	.	4	ESCA
MUC16	0	.	GRCh37	19	9063245	9063245	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.24201A>G	p.%3D	p.G8067G	ENST00000397910	3/84	154	137	17	153	153	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;	C	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	24405	24201	8067	G	ggA/ggG	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	3/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATGTCCAGA	.	4	ESCA
OLFM3	0	.	GRCh37	1	102270448	102270448	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723T>A	p.%3D	p.T241T	ENST00000370103	6/6	46	37	9	41	41	0	OLFM3,synonymous_variant,p.%3D,ENST00000338858,;OLFM3,synonymous_variant,p.%3D,ENST00000370103,;OLFM3,3_prime_UTR_variant,,ENST00000536598,;OLFM3,non_coding_transcript_exon_variant,,ENST00000462354,;OLFM3,non_coding_transcript_exon_variant,,ENST00000465523,;	T	ENSG00000118733	ENST00000370103	Transcript	synonymous_variant	937	723	241	T	acT/acA	.	.	.	-1	OLFM3	HGNC	17990	protein_coding	YES	CCDS30781.1	ENSP00000359121	NOE3_HUMAN	.	UPI000002AF6A	.	.	.	6/6	.	PROSITE_profiles:PS51132,hmmpanther:PTHR23192:SF36,hmmpanther:PTHR23192,Pfam_domain:PF02191,SMART_domains:SM00284,Superfamily_domains:SSF50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTAGTATA	.	5	ESCA
IGSF3	0	.	GRCh37	1	117142808	117142808	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1844T>A	p.Leu615Ter	p.L615*	ENST00000369483	8/12	79	66	12	62	62	0	IGSF3,stop_gained,p.Leu615Ter,ENST00000318837,;IGSF3,stop_gained,p.Leu595Ter,ENST00000369486,;IGSF3,stop_gained,p.Leu615Ter,ENST00000369483,;	T	ENSG00000143061	ENST00000369483	Transcript	stop_gained	2549	1844	615	L/*	tTg/tAg	.	.	.	-1	IGSF3	HGNC	5950	protein_coding	YES	CCDS30814.1	ENSP00000358495	IGSF3_HUMAN	.	UPI0000140437	.	.	.	8/12	.	hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF21,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCAAGTCA	.	5	ESCA
OTUD7B	0	.	GRCh37	1	149916658	149916658	+	Missense_Mutation	SNP	C	C	T	rs782204756	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1630G>A	p.Gly544Ser	p.G544S	ENST00000369135	12/12	42	35	7	43	43	0	OTUD7B,missense_variant,p.Gly544Ser,ENST00000369135,;OTUD7B,downstream_gene_variant,,ENST00000417191,;	T	ENSG00000163113	ENST00000369135	Transcript	missense_variant	1925	1630	544	G/S	Ggc/Agc	rs782204756,COSM4021916	.	.	-1	OTUD7B	HGNC	16683	protein_coding	YES	CCDS41389.1	ENSP00000358131	OTU7B_HUMAN	Q5SZ59_HUMAN	UPI000020415D	.	tolerated(0.18)	benign(0.103)	12/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF11	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCCGCTGC	byFrequency	5	ESCA
FLG	0	.	GRCh37	1	152282420	152282420	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4942G>C	p.Glu1648Gln	p.E1648Q	ENST00000368799	3/3	182	160	21	193	193	0	FLG,missense_variant,p.Glu1648Gln,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	G	ENSG00000143631	ENST00000368799	Transcript	missense_variant	4978	4942	1648	E/Q	Gag/Cag	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	benign(0.403)	3/3	.	hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTCTCTGCAG	.	4	ESCA
KIF17	0	.	GRCh37	1	20998480	20998480	+	Silent	SNP	G	G	A	rs764516097	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2673C>T	p.%3D	p.G891G	ENST00000247986	12/15	134	117	16	85	85	0	KIF17,synonymous_variant,p.%3D,ENST00000247986,;KIF17,synonymous_variant,p.%3D,ENST00000375044,;KIF17,synonymous_variant,p.%3D,ENST00000400463,;KIF17,non_coding_transcript_exon_variant,,ENST00000498225,;KIF17,non_coding_transcript_exon_variant,,ENST00000490034,;KIF17,non_coding_transcript_exon_variant,,ENST00000477167,;KIF17,non_coding_transcript_exon_variant,,ENST00000462858,;KIF17,downstream_gene_variant,,ENST00000463389,;	A	ENSG00000117245	ENST00000247986	Transcript	synonymous_variant	2984	2673	891	G	ggC/ggT	rs764516097	.	.	-1	KIF17	HGNC	19167	protein_coding	YES	CCDS213.1	ENSP00000247986	KIF17_HUMAN	.	UPI0000185F1A	.	.	.	12/15	.	hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF415	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E888K|c.2662G>A|3	RADIA|MUTECT|MUSE|VARSCANS	CAGAAGCCGTT	.	4	ESCA
TAF5L	0	.	GRCh37	1	229730759	229730759	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1055C>T	p.Ala352Val	p.A352V	ENST00000258281	5/5	51	45	6	41	41	0	TAF5L,missense_variant,p.Ala352Val,ENST00000258281,;TAF5L,missense_variant,p.Ala352Val,ENST00000366676,;TAF5L,downstream_gene_variant,,ENST00000366675,;	A	ENSG00000135801	ENST00000258281	Transcript	missense_variant	1221	1055	352	A/V	gCg/gTg	.	.	.	-1	TAF5L	HGNC	17304	protein_coding	YES	CCDS1581.1	ENSP00000258281	TAF5L_HUMAN	.	UPI0000073E93	.	tolerated(0.12)	benign(0.008)	5/5	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19879,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCCGCGAGG	.	4	ESCA
OR2T2	0	.	GRCh37	1	248616580	248616580	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482C>T	p.Thr161Ile	p.T161I	ENST00000342927	1/1	70	55	15	57	57	0	OR2T2,missense_variant,p.Thr161Ile,ENST00000342927,;	T	ENSG00000196240	ENST00000342927	Transcript	missense_variant	504	482	161	T/I	aCt/aTt	.	.	.	1	OR2T2	HGNC	14725	protein_coding	YES	CCDS31116.1	ENSP00000343062	OR2T2_HUMAN	.	UPI0000048DB0	.	deleterious(0.03)	possibly_damaging(0.756)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF18,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GCTGACTCCTG	.	3	ESCA
BAI2	0	.	GRCh37	1	32196688	32196688	+	Missense_Mutation	SNP	C	C	T	rs751030662	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4093G>A	p.Gly1365Ser	p.G1365S	ENST00000373658	29/33	61	41	19	39	39	0	BAI2,missense_variant,p.Gly1353Ser,ENST00000398538,;BAI2,missense_variant,p.Gly1365Ser,ENST00000373658,;BAI2,missense_variant,p.Gly1298Ser,ENST00000398547,;BAI2,missense_variant,p.Gly1332Ser,ENST00000527361,;BAI2,missense_variant,p.Gly1280Ser,ENST00000398556,;BAI2,missense_variant,p.Gly1332Ser,ENST00000257070,;BAI2,missense_variant,p.Gly1265Ser,ENST00000398542,;BAI2,missense_variant,p.Gly1365Ser,ENST00000373655,;BAI2,missense_variant,p.Gly974Ser,ENST00000440175,;BAI2,non_coding_transcript_exon_variant,,ENST00000465239,;BAI2,non_coding_transcript_exon_variant,,ENST00000465256,;BAI2,downstream_gene_variant,,ENST00000484002,;BAI2,non_coding_transcript_exon_variant,,ENST00000530999,;BAI2,non_coding_transcript_exon_variant,,ENST00000525655,;	T	ENSG00000121753	ENST00000373658	Transcript	missense_variant	4435	4093	1365	G/S	Ggt/Agt	rs751030662	.	.	-1	BAI2	HGNC	944	protein_coding	YES	CCDS346.2	ENSP00000362762	BAI2_HUMAN	.	UPI0000E2A42F	.	tolerated(0.37)	benign(0.001)	29/33	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACCGCCAG	byFrequency	5	ESCA
CDCA8	0	.	GRCh37	1	38158196	38158196	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-167G>A	.	.	ENST00000373055	1/10	45	39	6	34	34	0	CDCA8,5_prime_UTR_variant,,ENST00000327331,;CDCA8,5_prime_UTR_variant,,ENST00000373055,;C1orf109,upstream_gene_variant,,ENST00000486637,;C1orf109,upstream_gene_variant,,ENST00000491981,;C1orf109,upstream_gene_variant,,ENST00000464085,;C1orf109,upstream_gene_variant,,ENST00000477060,;C1orf109,upstream_gene_variant,,ENST00000488137,;C1orf109,upstream_gene_variant,,ENST00000358011,;C1orf109,upstream_gene_variant,,ENST00000461359,;C1orf109,upstream_gene_variant,,ENST00000472584,;C1orf109,upstream_gene_variant,,ENST00000464178,;C1orf109,upstream_gene_variant,,ENST00000491797,;C1orf109,upstream_gene_variant,,ENST00000498448,;C1orf109,upstream_gene_variant,,ENST00000494120,;	A	ENSG00000134690	ENST00000373055	Transcript	5_prime_UTR_variant	107	.	.	.	.	.	.	.	1	CDCA8	HGNC	14629	protein_coding	YES	CCDS424.1	ENSP00000362146	BOREA_HUMAN	.	UPI000007033D	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCCGCTCTC	.	2	ESCA
ZCCHC11	0	.	GRCh37	1	52889301	52889301	+	3'UTR	DEL	T	T	-	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*306delA	.	.	ENST00000257177	30/30	50	45	5	26	26	0	ZCCHC11,3_prime_UTR_variant,,ENST00000494469,;ZCCHC11,3_prime_UTR_variant,,ENST00000257177,;ZCCHC11,3_prime_UTR_variant,,ENST00000371544,;ZCCHC11,intron_variant,,ENST00000528457,;ZCCHC11,downstream_gene_variant,,ENST00000471623,;PRPF38A,downstream_gene_variant,,ENST00000257181,;ZCCHC11,non_coding_transcript_exon_variant,,ENST00000466440,;ZCCHC11,intron_variant,,ENST00000527941,;	-	ENSG00000134744	ENST00000257177	Transcript	3_prime_UTR_variant	5389	.	.	.	.	.	.	.	-1	ZCCHC11	HGNC	28981	protein_coding	YES	CCDS30715.1	ENSP00000257177	TUT4_HUMAN	H0YEY0_HUMAN,E9PQS7_HUMAN,E9PJN7_HUMAN	UPI00001D7D0C	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAACATAAAAT	.	3	ESCA
DMRTB1	0	.	GRCh37	1	53930386	53930386	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827C>A	p.Pro276Gln	p.P276Q	ENST00000371445	3/4	148	136	12	116	116	0	DMRTB1,missense_variant,p.Pro276Gln,ENST00000371445,;DMRTB1,downstream_gene_variant,,ENST00000463126,;	A	ENSG00000143006	ENST00000371445	Transcript	missense_variant	882	827	276	P/Q	cCg/cAg	.	.	.	1	DMRTB1	HGNC	13913	protein_coding	YES	CCDS581.1	ENSP00000360500	DMRTB_HUMAN	I6L9A0_HUMAN	UPI000006FF4C	.	tolerated(0.27)	possibly_damaging(0.881)	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCACCGCTTC	.	3	ESCA
LZTS3	0	.	GRCh37	20	3146868	3146868	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598C>A	p.Leu200Met	p.L200M	ENST00000329152	2/3	97	77	20	88	88	0	LZTS3,missense_variant,p.Leu200Met,ENST00000329152,;LZTS3,missense_variant,p.Leu200Met,ENST00000360342,;LZTS3,missense_variant,p.Leu200Met,ENST00000337576,;	T	ENSG00000088899	ENST00000329152	Transcript	missense_variant	1996	598	200	L/M	Ctg/Atg	.	.	.	-1	LZTS3	Uniprot_gn	.	protein_coding	YES	.	ENSP00000332123	LZTS3_HUMAN	.	UPI0000139A8C	.	tolerated(0.11)	probably_damaging(0.969)	2/3	.	hmmpanther:PTHR19354:SF6,hmmpanther:PTHR19354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCAGTCCGC	.	5	ESCA
TOMM34	0	.	GRCh37	20	43571821	43571821	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.859C>T	p.Leu287Phe	p.L287F	ENST00000372813	7/7	60	55	5	54	54	0	TOMM34,missense_variant,p.Leu287Phe,ENST00000372813,;PABPC1L,intron_variant,,ENST00000372819,;PABPC1L,intron_variant,,ENST00000372826,;PABPC1L,downstream_gene_variant,,ENST00000255136,;PABPC1L,downstream_gene_variant,,ENST00000372822,;PABPC1L,downstream_gene_variant,,ENST00000372824,;PABPC1L,downstream_gene_variant,,ENST00000217073,;PABPC1L,downstream_gene_variant,,ENST00000217075,;PABPC1L,downstream_gene_variant,,ENST00000537323,;PABPC1L,intron_variant,,ENST00000490798,;PABPC1L,downstream_gene_variant,,ENST00000489068,;PABPC1L,downstream_gene_variant,,ENST00000482486,;PABPC1L,downstream_gene_variant,,ENST00000476056,;PABPC1L,downstream_gene_variant,,ENST00000474208,;PABPC1L,downstream_gene_variant,,ENST00000479873,;	A	ENSG00000025772	ENST00000372813	Transcript	missense_variant	1012	859	287	L/F	Ctc/Ttc	.	.	.	-1	TOMM34	HGNC	15746	protein_coding	YES	CCDS13340.1	ENSP00000361900	TOM34_HUMAN	.	UPI0000130CB3	.	deleterious(0.01)	probably_damaging(0.998)	7/7	.	Superfamily_domains:SSF48452,SMART_domains:SM00028,Gene3D:1.25.40.10,Pfam_domain:PF07719,hmmpanther:PTHR22904:SF31,hmmpanther:PTHR22904,PROSITE_profiles:PS50293,PROSITE_profiles:PS50005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAGGAGGTTGC	.	3	ESCA
ZNF831	0	.	GRCh37	20	57829715	57829715	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4951C>A	p.Leu1651Met	p.L1651M	ENST00000371030	5/5	10	7	3	19	19	0	ZNF831,missense_variant,p.Leu1651Met,ENST00000371030,;	A	ENSG00000124203	ENST00000371030	Transcript	missense_variant	4951	4951	1651	L/M	Ctg/Atg	.	.	.	1	ZNF831	HGNC	16167	protein_coding	YES	CCDS42894.1	ENSP00000360069	ZN831_HUMAN	.	UPI00001D82E4	.	deleterious(0)	probably_damaging(0.997)	5/5	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGTCTGGAA	.	2	ESCA
TNRC6B	0	.	GRCh37	22	40719728	40719728	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*483T>G	.	.	ENST00000454349	23/23	38	25	13	36	26	10	TNRC6B,3_prime_UTR_variant,,ENST00000454349,;TNRC6B,3_prime_UTR_variant,,ENST00000301923,;TNRC6B,3_prime_UTR_variant,,ENST00000335727,;TNRC6B,downstream_gene_variant,,ENST00000446273,;TNRC6B,downstream_gene_variant,,ENST00000402203,;	G	ENSG00000100354	ENST00000454349	Transcript	3_prime_UTR_variant	6196	.	.	.	.	.	.	.	1	TNRC6B	HGNC	29190	protein_coding	YES	CCDS54533.1	ENSP00000401946	TNR6B_HUMAN	.	UPI00017A6F19	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTGTTGGGGG	.	2	ESCA
ROCK2	0	.	GRCh37	2	11351835	11351835	+	Silent	SNP	G	G	A	rs770615625	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2175C>T	p.%3D	p.I725I	ENST00000315872	18/33	90	78	12	83	83	0	ROCK2,synonymous_variant,p.%3D,ENST00000315872,;ROCK2,synonymous_variant,p.%3D,ENST00000401753,;ROCK2,downstream_gene_variant,,ENST00000261535,;	A	ENSG00000134318	ENST00000315872	Transcript	synonymous_variant	2624	2175	725	I	atC/atT	rs770615625	.	.	-1	ROCK2	HGNC	10252	protein_coding	YES	CCDS42654.1	ENSP00000317985	ROCK2_HUMAN	Q14DU5_HUMAN,E9PF63_HUMAN	UPI000034ECB0	.	.	.	18/33	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22988:SF24,hmmpanther:PTHR22988,PIRSF_domain:PIRSF037568	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCGATGGA	byFrequency	5	ESCA
CNTNAP5	0	.	GRCh37	2	125232348	125232348	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951A>T	p.Lys317Asn	p.K317N	ENST00000431078	7/24	47	41	5	44	44	0	CNTNAP5,missense_variant,p.Lys317Asn,ENST00000431078,;	T	ENSG00000155052	ENST00000431078	Transcript	missense_variant	1315	951	317	K/N	aaA/aaT	.	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	deleterious(0.01)	probably_damaging(0.999)	7/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAAAACCTGG	.	4	ESCA
TRIB2	0	.	GRCh37	2	12881283	12881283	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*363C>A	.	.	ENST00000155926	3/3	53	48	5	48	48	0	TRIB2,3_prime_UTR_variant,,ENST00000381465,;TRIB2,3_prime_UTR_variant,,ENST00000155926,;MIR3125,downstream_gene_variant,,ENST00000579927,;	A	ENSG00000071575	ENST00000155926	Transcript	3_prime_UTR_variant	2814	.	.	.	.	.	.	.	1	TRIB2	HGNC	30809	protein_coding	YES	CCDS1683.1	ENSP00000155926	TRIB2_HUMAN	F8WA18_HUMAN	UPI0000051C55	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTGGCATCGC	.	3	ESCA
MBD5	0	.	GRCh37	2	149243434	149243434	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2969A>G	p.Gln990Arg	p.Q990R	ENST00000407073	11/15	74	64	10	49	49	0	MBD5,missense_variant,p.Gln990Arg,ENST00000407073,;MBD5,missense_variant,p.Gln1223Arg,ENST00000404807,;MBD5,missense_variant,p.Gln963Arg,ENST00000416015,;MBD5,non_coding_transcript_exon_variant,,ENST00000496893,;	G	ENSG00000204406	ENST00000407073	Transcript	missense_variant	3966	2969	990	Q/R	cAg/cGg	.	.	.	1	MBD5	HGNC	20444	protein_coding	YES	CCDS33302.1	ENSP00000386049	MBD5_HUMAN	.	UPI0000208C40	.	tolerated(0.07)	unknown(0)	11/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16112,hmmpanther:PTHR16112:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTACCAGAATC	.	4	ESCA
TTN	0	.	GRCh37	2	179400859	179400859	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100615G>C	p.Asp33539His	p.D33539H	ENST00000589042	357/363	62	57	5	63	63	0	TTN,missense_variant,p.Asp24599His,ENST00000359218,;TTN,missense_variant,p.Asp24474His,ENST00000460472,;TTN,missense_variant,p.Asp31898His,ENST00000591111,;TTN,missense_variant,p.Asp33539His,ENST00000589042,;TTN,missense_variant,p.Asp24666His,ENST00000342175,;TTN,missense_variant,p.Asp30971His,ENST00000342992,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589434,;TTN-AS1,intron_variant,,ENST00000588716,;TTN-AS1,intron_variant,,ENST00000589391,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000592182,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592836,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000591466,;TTN-AS1,intron_variant,,ENST00000591867,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000585358,;TTN-AS1,intron_variant,,ENST00000589842,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000590040,;TTN-AS1,intron_variant,,ENST00000450692,;TTN-AS1,intron_variant,,ENST00000431259,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000588257,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000588244,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000588804,;TTN-AS1,intron_variant,,ENST00000585487,;TTN-AS1,upstream_gene_variant,,ENST00000438095,;RP11-65L3.4,upstream_gene_variant,,ENST00000604692,;TTN-AS1,downstream_gene_variant,,ENST00000585625,;TTN-AS1,downstream_gene_variant,,ENST00000587568,;TTN-AS1,upstream_gene_variant,,ENST00000415561,;TTN-AS1,downstream_gene_variant,,ENST00000587944,;TTN-AS1,downstream_gene_variant,,ENST00000589355,;TTN-AS1,downstream_gene_variant,,ENST00000442329,;TTN-AS1,downstream_gene_variant,,ENST00000604571,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	100840	100615	33539	D/H	Gat/Cat	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	357/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCATCTGCAA	.	3	ESCA
NT5C1B	0	.	GRCh37	2	18765855	18765855	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.828C>T	p.%3D	p.D276D	ENST00000359846	5/10	61	58	3	53	53	0	NT5C1B,synonymous_variant,p.%3D,ENST00000359846,;NT5C1B,synonymous_variant,p.%3D,ENST00000304081,;NT5C1B,synonymous_variant,p.%3D,ENST00000600945,;NT5C1B-RDH14,synonymous_variant,p.%3D,ENST00000532967,;NT5C1B-RDH14,synonymous_variant,p.%3D,ENST00000444297,;NT5C1B,upstream_gene_variant,,ENST00000418427,;NT5C1B,downstream_gene_variant,,ENST00000416783,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,downstream_gene_variant,,ENST00000460052,;NT5C1B,missense_variant,p.Thr194Met,ENST00000406971,;NT5C1B,non_coding_transcript_exon_variant,,ENST00000490687,;	A	ENSG00000185013	ENST00000359846	Transcript	synonymous_variant	906	828	276	D	gaC/gaT	COSM1013866	.	.	-1	NT5C1B	HGNC	17818	protein_coding	YES	CCDS33150.1	ENSP00000352904	5NT1B_HUMAN	B4DZ86_HUMAN	UPI000035B1B0	.	.	.	5/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGTCGTCCTC	.	2	ESCA
ABCB6	0	.	GRCh37	2	220083133	220083133	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263T>A	p.Leu88Gln	p.L88Q	ENST00000265316	1/19	59	51	7	60	60	0	ABCB6,missense_variant,p.Leu88Gln,ENST00000265316,;ABCB6,missense_variant,p.Leu88Gln,ENST00000439002,;ATG9A,downstream_gene_variant,,ENST00000429920,;ATG9A,downstream_gene_variant,,ENST00000361242,;ATG9A,downstream_gene_variant,,ENST00000409422,;ATG9A,downstream_gene_variant,,ENST00000396761,;ATG9A,downstream_gene_variant,,ENST00000409618,;ABCB6,upstream_gene_variant,,ENST00000295750,;ABCB6,missense_variant,p.Leu23Gln,ENST00000448398,;ABCB6,missense_variant,p.Leu6Gln,ENST00000417678,;ATG9A,3_prime_UTR_variant,,ENST00000446716,;ATG9A,downstream_gene_variant,,ENST00000475339,;ABCB6,upstream_gene_variant,,ENST00000497882,;ABCB6,upstream_gene_variant,,ENST00000492953,;ABCB6,upstream_gene_variant,,ENST00000494639,;ABCB6,upstream_gene_variant,,ENST00000452545,;ABCB6,upstream_gene_variant,,ENST00000496984,;ABCB6,upstream_gene_variant,,ENST00000492543,;ATG9A,downstream_gene_variant,,ENST00000409033,;	T	ENSG00000115657	ENST00000265316	Transcript	missense_variant	580	263	88	L/Q	cTg/cAg	.	.	.	-1	ABCB6	HGNC	47	protein_coding	YES	CCDS2436.1	ENSP00000265316	ABCB6_HUMAN	U3THN0_HUMAN,H7C1R6_HUMAN	UPI000004C4BA	.	deleterious(0.04)	possibly_damaging(0.866)	1/19	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGGCCAGGGGC	.	3	ESCA
RAB10	0	.	GRCh37	2	26359719	26359719	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1829G>A	.	.	ENST00000264710	6/6	31	27	4	22	22	0	RAB10,3_prime_UTR_variant,,ENST00000264710,;RAB10,downstream_gene_variant,,ENST00000473035,;RAB10,downstream_gene_variant,,ENST00000462003,;RAB10,downstream_gene_variant,,ENST00000495146,;AC011742.3,downstream_gene_variant,,ENST00000443818,;	A	ENSG00000084733	ENST00000264710	Transcript	3_prime_UTR_variant	2931	.	.	.	.	.	.	.	1	RAB10	HGNC	9759	protein_coding	YES	CCDS1720.1	ENSP00000264710	RAB10_HUMAN	Q9UL28_HUMAN,Q53T70_HUMAN,Q53SX4_HUMAN	UPI0000001263	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACTTGACTTT	.	4	ESCA
XDH	0	.	GRCh37	2	31605935	31605935	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.970A>C	p.Thr324Pro	p.T324P	ENST00000379416	11/36	67	61	6	77	77	0	XDH,missense_variant,p.Thr324Pro,ENST00000379416,;XDH,non_coding_transcript_exon_variant,,ENST00000491727,;XDH,downstream_gene_variant,,ENST00000476043,;	G	ENSG00000158125	ENST00000379416	Transcript	missense_variant	1019	970	324	T/P	Aca/Cca	.	.	.	-1	XDH	HGNC	12805	protein_coding	YES	CCDS1775.1	ENSP00000368727	XDH_HUMAN	Q585T6_HUMAN	UPI0000036BC9	.	deleterious(0.01)	probably_damaging(0.982)	11/36	.	Superfamily_domains:SSF56176,PIRSF_domain:PIRSF000127,TIGRFAM_domain:TIGR02963,Gene3D:3.30.465.10,Pfam_domain:PF00941,hmmpanther:PTHR11908:SF32,hmmpanther:PTHR11908,PROSITE_profiles:PS51387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCTGTCTTTT	.	3	ESCA
COX7A2L	0	.	GRCh37	2	42588509	42588509	+	5'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-208G>T	.	.	ENST00000378669	2/4	12	8	3	10	10	0	COX7A2L,5_prime_UTR_variant,,ENST00000378669,;COX7A2L,upstream_gene_variant,,ENST00000234301,;COX7A2L,upstream_gene_variant,,ENST00000468711,;COX7A2L,upstream_gene_variant,,ENST00000463055,;COX7A2L,intron_variant,,ENST00000607768,;COX7A2L,upstream_gene_variant,,ENST00000482463,;COX7A2L,downstream_gene_variant,,ENST00000423797,;COX7A2L,upstream_gene_variant,,ENST00000464443,;	A	ENSG00000115944	ENST00000378669	Transcript	5_prime_UTR_variant	623	.	.	.	.	.	.	.	-1	COX7A2L	HGNC	2289	protein_coding	YES	CCDS1808.1	ENSP00000367938	COX7R_HUMAN	Q6FGA0_HUMAN	UPI0000127C56	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAAAACCAGCT	.	3	ESCA
CTNNA2	0	.	GRCh37	2	80875525	80875525	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*528C>A	.	.	ENST00000466387	22/22	90	80	10	88	88	0	CTNNA2,3_prime_UTR_variant,,ENST00000496558,;CTNNA2,3_prime_UTR_variant,,ENST00000466387,;CTNNA2,3_prime_UTR_variant,,ENST00000541047,;CTNNA2,3_prime_UTR_variant,,ENST00000343114,;CTNNA2,3_prime_UTR_variant,,ENST00000402739,;CTNNA2,downstream_gene_variant,,ENST00000540488,;CTNNA2,downstream_gene_variant,,ENST00000361291,;	A	ENSG00000066032	ENST00000466387	Transcript	3_prime_UTR_variant	3970	.	.	.	.	.	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTAACTGAGG	.	4	ESCA
MSL2	0	.	GRCh37	3	135869879	135869879	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*110A>G	.	.	ENST00000309993	2/2	43	38	5	52	52	0	MSL2,3_prime_UTR_variant,,ENST00000309993,;MSL2,3_prime_UTR_variant,,ENST00000434835,;MSL2,downstream_gene_variant,,ENST00000491050,;MSL2,downstream_gene_variant,,ENST00000473093,;PPP2R3A,downstream_gene_variant,,ENST00000264977,;MSL2,downstream_gene_variant,,ENST00000481989,;TDGF1P6,upstream_gene_variant,,ENST00000463873,;	C	ENSG00000174579	ENST00000309993	Transcript	3_prime_UTR_variant	2577	.	.	.	.	.	.	.	-1	MSL2	HGNC	25544	protein_coding	YES	CCDS33861.1	ENSP00000311827	MSL2_HUMAN	C9J5S2_HUMAN,C9IZG7_HUMAN,C9IZ03_HUMAN	UPI000020A2D7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTGATACAAG	.	4	ESCA
PIK3CA	0	.	GRCh37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	10/21	81	51	29	59	59	0	PIK3CA,missense_variant,p.Glu545Lys,ENST00000263967,;PIK3CA,upstream_gene_variant,,ENST00000462255,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	1790	1633	545	E/K	Gag/Aag	rs104886003,COSM763,COSM27133,COSM125370,COSM295672	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	deleterious(0.02)	probably_damaging(0.959)	10/21	.	PROSITE_profiles:PS51545,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Pfam_domain:PF00613,Gene3D:1.25.40.70,SMART_domains:SM00145,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	not_provided,pathogenic	0,1,1,1,1	21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E545K|c.1633G>A|227,SITE|p.E545K|c.1633G>A|1153,CODON|p.T544N|c.1631C>A|3,BUFFER|p.E542Q|c.1624G>C|8,BUFFER|p.E542K|c.1624G>A|115,BUFFER|p.E542K|c.1624G>A|758,BUFFER|p.E542G|c.1625A>G|3,BUFFER|p.E542V|c.1625A>T|14,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.E542V|c.1625A>T|5,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.I543V|c.1627A>G|3,BUFFER|p.E545Q|c.1633G>C|30,BUFFER|p.E545Q|c.1633G>C|9,BUFFER|p.E545A|c.1634A>C|130,BUFFER|p.E545V|c.1634A>T|4,BUFFER|p.E545A|c.1634A>C|11,BUFFER|p.E545G|c.1634A>G|14,BUFFER|p.E545G|c.1634A>G|90,BUFFER|p.E545D|c.1635G>T|13,BUFFER|p.E545D|c.1635G>C|11,BUFFER|p.E545D|c.1635G>T|4,BUFFER|p.Q546K|c.1636C>A|119,BUFFER|p.Q546E|c.1636C>G|15,BUFFER|p.Q546K|c.1636C>A|18,BUFFER|p.Q546R|c.1637A>G|20,BUFFER|p.Q546P|c.1637A>C|22,BUFFER|p.Q546P|c.1637A>C|7,BUFFER|p.Q546L|c.1637A>T|8,BUFFER|p.Q546R|c.1637A>G|41,BUFFER|p.Q546H|c.1638G>T|7,BUFFER|p.E547K|c.1639G>A|11,BUFFER|p.E547G|c.1640A>G|5,BUFFER|p.E547G|c.1640A>G|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTGAGCAG	byCluster	5	ESCA
TRANK1	0	.	GRCh37	3	36873577	36873577	+	Missense_Mutation	SNP	C	C	G	rs377104234	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7365G>C	p.Glu2455Asp	p.E2455D	ENST00000429976	21/23	69	61	8	76	76	0	TRANK1,missense_variant,p.Glu1905Asp,ENST00000428977,;TRANK1,missense_variant,p.Glu1905Asp,ENST00000301807,;TRANK1,missense_variant,p.Glu2455Asp,ENST00000429976,;	G	ENSG00000168016	ENST00000429976	Transcript	missense_variant	7613	7365	2455	E/D	gaG/gaC	rs377104234	.	.	-1	TRANK1	HGNC	29011	protein_coding	YES	CCDS46789.2	ENSP00000416168	TRNK1_HUMAN	B7WP88_HUMAN	UPI00017BE82B	.	tolerated(0.06)	benign(0.006)	21/23	.	hmmpanther:PTHR21529:SF5,hmmpanther:PTHR21529	.	.	.	.	.	.	.	T:0.0003	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAAGCTCCTT	byFrequency|byCluster	4	ESCA
TGM4	0	.	GRCh37	3	44959625	44959625	+	3'Flank	SNP	C	C	T	rs140195587	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000296125	.	107	96	11	96	96	0	ZDHHC3,missense_variant,p.Arg117His,ENST00000339420,;ZDHHC3,downstream_gene_variant,,ENST00000443879,;TGM4,downstream_gene_variant,,ENST00000296125,;ZDHHC3,non_coding_transcript_exon_variant,,ENST00000466084,;	T	ENSG00000163810	ENST00000296125	Transcript	downstream_gene_variant	.	.	.	.	.	rs140195587	.	3143	1	TGM4	HGNC	11780	protein_coding	YES	CCDS2723.1	ENSP00000296125	TGM4_HUMAN	Q9UBL5_HUMAN	UPI0000136CCD	.	.	.	.	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	A:0.0007	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGGCGCTCG	byCluster|by1000G	4	ESCA
FAT4	0	.	GRCh37	4	126371928	126371928	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9757C>T	p.Gln3253Ter	p.Q3253*	ENST00000394329	9/17	43	38	5	37	37	0	FAT4,stop_gained,p.Gln3253Ter,ENST00000394329,;FAT4,stop_gained,p.Gln1551Ter,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,;	T	ENSG00000196159	ENST00000394329	Transcript	stop_gained	9770	9757	3253	Q/*	Caa/Taa	COSM1050957,COSM1050956	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	.	9/17	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACTCAAGGC	.	4	ESCA
TRIM61	0	.	GRCh37	4	165891024	165891024	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.131G>A	p.Trp44Ter	p.W44*	ENST00000329314	3/5	190	178	12	145	145	0	TRIM61,stop_gained,p.Trp44Ter,ENST00000329314,;RP11-366M4.11,non_coding_transcript_exon_variant,,ENST00000508856,;RP11-366M4.8,intron_variant,,ENST00000596751,;	T	ENSG00000183439	ENST00000329314	Transcript	stop_gained	744	131	44	W/*	tGg/tAg	.	.	.	-1	TRIM61	HGNC	24339	protein_coding	YES	CCDS34093.1	ENSP00000332288	TRI61_HUMAN	.	UPI00004CEC1B	.	.	.	3/5	.	PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF304,Pfam_domain:PF15227,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTCCAGGAC	.	2	ESCA
FAM149A	0	.	GRCh37	4	187079298	187079298	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729+425C>T	.	.	ENST00000227065	.	32	19	12	23	23	0	FAM149A,intron_variant,,ENST00000514153,;FAM149A,intron_variant,,ENST00000389354,;FAM149A,intron_variant,,ENST00000502970,;FAM149A,intron_variant,,ENST00000503432,;FAM149A,intron_variant,,ENST00000227065,;FAM149A,intron_variant,,ENST00000356371,;FAM149A,downstream_gene_variant,,ENST00000504330,;FAM149A,downstream_gene_variant,,ENST00000509574,;FAM149A,downstream_gene_variant,,ENST00000510790,;FAM149A,non_coding_transcript_exon_variant,,ENST00000513030,;FAM149A,non_coding_transcript_exon_variant,,ENST00000514829,;FAM149A,intron_variant,,ENST00000515078,;RP11-173M11.2,non_coding_transcript_exon_variant,,ENST00000504462,;	T	ENSG00000109794	ENST00000227065	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	FAM149A	HGNC	24527	protein_coding	YES	CCDS34117.1	ENSP00000227065	F149A_HUMAN	D6RGX1_HUMAN,D6RC92_HUMAN,D6RAL4_HUMAN	UPI00001C1E1F	.	.	.	.	8/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCCGGCAG	.	5	ESCA
ZNF300	0	.	GRCh37	5	150275679	150275679	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1170A>G	p.Ile390Met	p.I390M	ENST00000446148	7/7	84	77	6	70	70	0	ZNF300,missense_variant,p.Ile338Met,ENST00000418587,;ZNF300,missense_variant,p.Ile374Met,ENST00000274599,;ZNF300,missense_variant,p.Ile374Met,ENST00000394226,;ZNF300,missense_variant,p.Ile390Met,ENST00000446148,;ZNF300,3_prime_UTR_variant,,ENST00000427179,;IRGM,intron_variant,,ENST00000520549,;	C	ENSG00000145908	ENST00000446148	Transcript	missense_variant	1598	1170	390	I/M	atA/atG	.	.	.	-1	ZNF300	HGNC	13091	protein_coding	YES	CCDS54940.1	ENSP00000397178	.	J3KQF6_HUMAN	UPI0001AE74AD	.	deleterious(0)	probably_damaging(0.999)	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF288,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTATGTATTCT	.	2	ESCA
TSPYL4	0	.	GRCh37	6	116574350	116574350	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822C>T	p.%3D	p.D274D	ENST00000420283	1/1	64	59	5	59	59	0	TSPYL4,synonymous_variant,p.%3D,ENST00000420283,;NT5DC1,downstream_gene_variant,,ENST00000319550,;DSE,upstream_gene_variant,,ENST00000540275,;DSE,upstream_gene_variant,,ENST00000430252,;RP3-486I3.7,upstream_gene_variant,,ENST00000448740,;	A	ENSG00000187189	ENST00000420283	Transcript	synonymous_variant	912	822	274	D	gaC/gaT	.	.	.	-1	TSPYL4	HGNC	21559	protein_coding	YES	CCDS5106.1	ENSP00000410943	TSYL4_HUMAN	Q69YV8_HUMAN	UPI00001BBB76	.	.	.	1/1	.	Superfamily_domains:SSF143113,Pfam_domain:PF00956,hmmpanther:PTHR11875:SF33,hmmpanther:PTHR11875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCATGTCTTC	.	3	ESCA
TNXB	0	.	GRCh37	6	32017091	32017091	+	5'Flank	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000451343	.	87	74	12	58	58	0	TNXB,missense_variant,p.His3236Arg,ENST00000375247,;TNXB,missense_variant,p.His3238Arg,ENST00000375244,;TNXB,upstream_gene_variant,,ENST00000451343,;TNXB,upstream_gene_variant,,ENST00000490077,;	C	ENSG00000168477	ENST00000451343	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3186	-1	TNXB	HGNC	11976	protein_coding	YES	CCDS4736.1	ENSP00000407685	TENX_HUMAN	B6RHJ5_HUMAN	UPI0000000E8E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCGTGGAGG	.	5	ESCA
KIFC1	0	.	GRCh37	6	33374195	33374195	+	Missense_Mutation	SNP	C	C	T	rs112635529	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1759C>T	p.Arg587Trp	p.R587W	ENST00000428849	8/11	69	55	13	50	50	0	KIFC1,missense_variant,p.Arg587Trp,ENST00000428849,;PHF1,upstream_gene_variant,,ENST00000374512,;PHF1,upstream_gene_variant,,ENST00000374516,;KIFC1,downstream_gene_variant,,ENST00000450504,;PHF1,upstream_gene_variant,,ENST00000428274,;PHF1,upstream_gene_variant,,ENST00000427004,;PHF1,upstream_gene_variant,,ENST00000459809,;KIFC1,downstream_gene_variant,,ENST00000486695,;KIFC1,non_coding_transcript_exon_variant,,ENST00000494554,;PHF1,upstream_gene_variant,,ENST00000487667,;PHF1,upstream_gene_variant,,ENST00000495509,;	T	ENSG00000237649	ENST00000428849	Transcript	missense_variant	2209	1759	587	R/W	Cgg/Tgg	rs112635529	.	.	1	KIFC1	HGNC	6389	protein_coding	YES	CCDS34430.1	ENSP00000393963	KIFC1_HUMAN	.	UPI000012DDB8	.	deleterious(0)	benign(0.393)	8/11	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCGGGAA	.	5	ESCA
KCND2	0	.	GRCh37	7	119914701	119914701	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15G>A	p.%3D	p.V5V	ENST00000331113	1/6	97	86	11	85	85	0	KCND2,synonymous_variant,p.%3D,ENST00000331113,;	A	ENSG00000184408	ENST00000331113	Transcript	synonymous_variant	980	15	5	V	gtG/gtA	.	.	.	1	KCND2	HGNC	6238	protein_coding	YES	CCDS5776.1	ENSP00000333496	KCND2_HUMAN	A4D0V9_HUMAN,Q75LS7_HUMAN	UPI0000073D37	.	.	.	1/6	.	Cleavage_site_(Signalp):SignalP-noTM,Pfam_domain:PF11601	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A3V|c.8C>T|3	RADIA|MUTECT|MUSE|VARSCANS	GGGGTGGCAGC	.	4	ESCA
GRM8	0	.	GRCh37	7	126173452	126173452	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1984A>C	p.Ser662Arg	p.S662R	ENST00000339582	9/11	51	46	5	58	58	0	GRM8,missense_variant,p.Ser662Arg,ENST00000358373,;GRM8,missense_variant,p.Ser662Arg,ENST00000444921,;GRM8,missense_variant,p.Ser662Arg,ENST00000339582,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,missense_variant,p.Ser662Arg,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,;	G	ENSG00000179603	ENST00000339582	Transcript	missense_variant	2793	1984	662	S/R	Agc/Cgc	.	.	.	-1	GRM8	HGNC	4600	protein_coding	YES	CCDS5794.1	ENSP00000344173	GRM8_HUMAN	E7ETK3_HUMAN,C9J7I1_HUMAN	UPI000012F085	.	tolerated(0.05)	probably_damaging(0.999)	9/11	.	PROSITE_profiles:PS50259,hmmpanther:PTHR24060:SF26,hmmpanther:PTHR24060,Pfam_domain:PF00003,Prints_domain:PR00593,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGCTGAAAC	.	4	ESCA
TNPO3	0	.	GRCh37	7	128641132	128641132	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.853G>A	p.Ala285Thr	p.A285T	ENST00000265388	6/23	55	48	7	37	37	0	TNPO3,missense_variant,p.Ala285Thr,ENST00000393245,;TNPO3,missense_variant,p.Ala285Thr,ENST00000471166,;TNPO3,missense_variant,p.Ala285Thr,ENST00000471234,;TNPO3,missense_variant,p.Ala219Thr,ENST00000482320,;TNPO3,missense_variant,p.Ala285Thr,ENST00000265388,;	T	ENSG00000064419	ENST00000265388	Transcript	missense_variant	997	853	285	A/T	Gca/Aca	.	.	.	-1	TNPO3	HGNC	17103	protein_coding	YES	CCDS5809.1	ENSP00000265388	TNPO3_HUMAN	E9PFH4_HUMAN,B3KMX1_HUMAN	UPI0000072FAB	.	tolerated(0.12)	benign(0.347)	6/23	.	hmmpanther:PTHR12363,hmmpanther:PTHR12363:SF5,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACGTGCCACGG	.	4	ESCA
ZNF212	0	.	GRCh37	7	148951091	148951091	+	Missense_Mutation	SNP	G	G	A	rs774957598	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000335870	5/5	50	45	5	33	33	0	ZNF212,missense_variant,p.Arg358Gln,ENST00000335870,;ZNF212,downstream_gene_variant,,ENST00000481584,;ZNF212,downstream_gene_variant,,ENST00000462724,;ZNF212,downstream_gene_variant,,ENST00000488917,;ZNF212,downstream_gene_variant,,ENST00000486371,;	A	ENSG00000170260	ENST00000335870	Transcript	missense_variant	1201	1073	358	R/Q	cGg/cAg	rs774957598	.	.	1	ZNF212	HGNC	13004	protein_coding	YES	CCDS5896.1	ENSP00000338572	ZN212_HUMAN	.	UPI000013CEE2	.	tolerated(0.74)	benign(0.007)	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF42,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCACGGCTGA	byFrequency	3	ESCA
HOXA9	0	.	GRCh37	7	27202906	27202906	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*316T>C	.	.	ENST00000343483	2/2	34	30	3	19	19	0	HOXA9,3_prime_UTR_variant,,ENST00000343483,;RP1-170O19.20,downstream_gene_variant,,ENST00000470747,;HOXA9,downstream_gene_variant,,ENST00000396345,;RP1-170O19.21,downstream_gene_variant,,ENST00000602610,;HOXA9,non_coding_transcript_exon_variant,,ENST00000497089,;HOXA9,downstream_gene_variant,,ENST00000489695,;HOXA9,downstream_gene_variant,,ENST00000487384,;RP1-170O19.20,downstream_gene_variant,,ENST00000465941,;	G	ENSG00000078399	ENST00000343483	Transcript	3_prime_UTR_variant	1208	.	.	.	.	.	.	.	-1	HOXA9	HGNC	5109	protein_coding	YES	CCDS5409.1	ENSP00000343619	HXA9_HUMAN	.	UPI0000000CA4	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAGGAACAGG	.	3	ESCA
NPSR1	0	.	GRCh37	7	34768375	34768375	+	Intron	SNP	G	G	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280+44079G>T	.	.	ENST00000359791	.	87	60	26	72	72	0	NPSR1,intron_variant,,ENST00000381539,;NPSR1,intron_variant,,ENST00000381553,;NPSR1,intron_variant,,ENST00000360581,;NPSR1,intron_variant,,ENST00000359791,;NPSR1,intron_variant,,ENST00000531252,;NPSR1,intron_variant,,ENST00000381542,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000436945,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000535640,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000442669,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000358772,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000419766,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000537560,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000544556,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000431669,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000439852,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000539747,;NPSR1-AS1,non_coding_transcript_exon_variant,,ENST00000428922,;NPSR1,intron_variant,,ENST00000381544,;NPSR1,intron_variant,,ENST00000396095,;	T	ENSG00000187258	ENST00000359791	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NPSR1	HGNC	23631	protein_coding	YES	CCDS5443.1	ENSP00000352839	NPSR1_HUMAN	.	UPI0000353D0F	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGATGGGCAT	.	3	ESCA
KIAA1324L	0	.	GRCh37	7	86567530	86567530	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1001A>G	p.Glu334Gly	p.E334G	ENST00000450689	8/22	67	49	18	94	93	0	KIAA1324L,missense_variant,p.Glu167Gly,ENST00000416314,;KIAA1324L,missense_variant,p.Glu94Gly,ENST00000297222,;KIAA1324L,missense_variant,p.Glu334Gly,ENST00000444627,;KIAA1324L,missense_variant,p.Glu295Gly,ENST00000423294,;KIAA1324L,missense_variant,p.Glu334Gly,ENST00000450689,;KIAA1324L,downstream_gene_variant,,ENST00000398276,;KIAA1324L,splice_region_variant,,ENST00000394714,;	C	ENSG00000164659	ENST00000450689	Transcript	missense_variant	1187	1001	334	E/G	gAg/gGg	.	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	tolerated(0.26)	benign(0.007)	8/22	.	hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727,Gene3D:3.90.10.10,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCTCTGCA	.	5	ESCA
RPL8	0	.	GRCh37	8	146015762	146015762	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.593G>T	p.Arg198Leu	p.R198L	ENST00000262584	5/6	76	72	4	67	67	0	RPL8,missense_variant,p.Arg89Leu,ENST00000527914,;RPL8,missense_variant,p.Arg198Leu,ENST00000394920,;RPL8,missense_variant,p.Arg198Leu,ENST00000262584,;RPL8,missense_variant,p.Arg177Leu,ENST00000533397,;RPL8,missense_variant,p.Arg198Leu,ENST00000528957,;RPL8,missense_variant,p.Arg198Leu,ENST00000532702,;ZNF34,upstream_gene_variant,,ENST00000534445,;ZNF34,upstream_gene_variant,,ENST00000429371,;ZNF34,upstream_gene_variant,,ENST00000343459,;RN7SL395P,downstream_gene_variant,,ENST00000462960,;RPL8,non_coding_transcript_exon_variant,,ENST00000528296,;RPL8,non_coding_transcript_exon_variant,,ENST00000529163,;RPL8,3_prime_UTR_variant,,ENST00000531975,;RPL8,3_prime_UTR_variant,,ENST00000529920,;RPL8,non_coding_transcript_exon_variant,,ENST00000526668,;RPL8,non_coding_transcript_exon_variant,,ENST00000534781,;RPL8,downstream_gene_variant,,ENST00000531767,;RPL8,downstream_gene_variant,,ENST00000525232,;ZNF34,upstream_gene_variant,,ENST00000527740,;	A	ENSG00000161016	ENST00000262584	Transcript	missense_variant	826	593	198	R/L	cGa/cTa	.	.	.	-1	RPL8	HGNC	10368	protein_coding	YES	CCDS6433.1	ENSP00000262584	RL8_HUMAN	G3V1A1_HUMAN,E9PKZ0_HUMAN	UPI000000419E	.	tolerated(0.09)	benign(0.139)	5/6	.	HAMAP:MF_01320_A,hmmpanther:PTHR13691,hmmpanther:PTHR13691:SF16,PROSITE_patterns:PS00467,Gene3D:4.10.950.10,Pfam_domain:PF03947,PIRSF_domain:PIRSF002158,Superfamily_domains:SSF50104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTACTCGTGGC	.	2	ESCA
PDLIM2	0	.	GRCh37	8	22442854	22442854	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1232C>A	p.Ser411Tyr	p.S411Y	ENST00000308354	6/10	91	85	6	79	79	0	PDLIM2,missense_variant,p.Ser161Tyr,ENST00000265810,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000426493,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000429812,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000456545,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000397760,;PDLIM2,missense_variant,p.Ser411Tyr,ENST00000308354,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000339162,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000409141,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000409417,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000397761,;PDLIM2,missense_variant,p.Ser161Tyr,ENST00000452226,;AC037459.4,upstream_gene_variant,,ENST00000430850,;PDLIM2,downstream_gene_variant,,ENST00000436754,;AC037459.4,upstream_gene_variant,,ENST00000450780,;AC037459.4,upstream_gene_variant,,ENST00000447849,;PDLIM2,non_coding_transcript_exon_variant,,ENST00000448520,;PDLIM2,upstream_gene_variant,,ENST00000443561,;PDLIM2,3_prime_UTR_variant,,ENST00000416159,;PDLIM2,non_coding_transcript_exon_variant,,ENST00000491330,;PDLIM2,upstream_gene_variant,,ENST00000464275,;	A	ENSG00000120913	ENST00000308354	Transcript	missense_variant	1271	1232	411	S/Y	tCc/tAc	.	.	.	1	PDLIM2	HGNC	13992	protein_coding	YES	CCDS6032.2	ENSP00000312634	PDLI2_HUMAN	C9K0F0_HUMAN,C9JSR2_HUMAN,C9JS55_HUMAN,C9J760_HUMAN,C9J0X3_HUMAN,B3KPU0_HUMAN	UPI0000E5AE4E	.	deleterious(0.02)	probably_damaging(0.916)	6/10	.	hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTTCCCCGG	.	2	ESCA
ADRA1A	0	.	GRCh37	8	26721737	26721737	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.750C>T	p.%3D	p.S250S	ENST00000380586	1/3	72	64	7	54	54	0	ADRA1A,synonymous_variant,p.%3D,ENST00000380573,;ADRA1A,synonymous_variant,p.%3D,ENST00000276393,;ADRA1A,synonymous_variant,p.%3D,ENST00000380586,;ADRA1A,synonymous_variant,p.%3D,ENST00000380572,;ADRA1A,synonymous_variant,p.%3D,ENST00000354550,;ADRA1A,synonymous_variant,p.%3D,ENST00000380587,;ADRA1A,synonymous_variant,p.%3D,ENST00000380581,;ADRA1A,synonymous_variant,p.%3D,ENST00000358857,;ADRA1A,synonymous_variant,p.%3D,ENST00000380582,;ADRA1A,synonymous_variant,p.%3D,ENST00000519229,;ADRA1A,synonymous_variant,p.%3D,ENST00000521711,;ADRA1A,synonymous_variant,p.%3D,ENST00000519096,;	A	ENSG00000120907	ENST00000380586	Transcript	synonymous_variant	1186	750	250	S	agC/agT	.	.	.	-1	ADRA1A	HGNC	277	protein_coding	YES	CCDS34869.1	ENSP00000369960	ADA1A_HUMAN	Q7KYZ9_HUMAN,B0ZBD3_HUMAN	UPI000066DA42	.	.	.	1/3	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF16,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Prints_domain:PR00557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGCGCTGGC	.	4	ESCA
TRIM35	0	.	GRCh37	8	27168552	27168552	+	Silent	SNP	G	G	C	rs758144604	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201C>G	p.%3D	p.A67A	ENST00000305364	1/6	94	86	7	58	58	0	TRIM35,synonymous_variant,p.%3D,ENST00000521253,;TRIM35,synonymous_variant,p.%3D,ENST00000305364,;PTK2B,upstream_gene_variant,,ENST00000338238,;PTK2B,upstream_gene_variant,,ENST00000544172,;PTK2B,upstream_gene_variant,,ENST00000397501,;PTK2B,upstream_gene_variant,,ENST00000522338,;PTK2B,upstream_gene_variant,,ENST00000519650,;TRIM35,upstream_gene_variant,,ENST00000519219,;	C	ENSG00000104228	ENST00000305364	Transcript	synonymous_variant	285	201	67	A	gcC/gcG	rs758144604	.	.	-1	TRIM35	HGNC	16285	protein_coding	YES	CCDS6056.2	ENSP00000301924	TRI35_HUMAN	.	UPI00001649FB	.	.	.	1/6	.	hmmpanther:PTHR24103:SF213,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGTCGGCGGG	.	3	ESCA
PLAG1	0	.	GRCh37	8	57073749	57073749	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5053G>A	.	.	ENST00000316981	5/5	44	37	6	35	35	0	PLAG1,3_prime_UTR_variant,,ENST00000316981,;PLAG1,downstream_gene_variant,,ENST00000423799,;PLAG1,downstream_gene_variant,,ENST00000522009,;	T	ENSG00000181690	ENST00000316981	Transcript	3_prime_UTR_variant	7036	.	.	.	.	.	.	.	-1	PLAG1	HGNC	9045	protein_coding	YES	CCDS6165.1	ENSP00000325546	PLAG1_HUMAN	A7IT80_HUMAN,A7IT79_HUMAN	UPI000013FF2F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TACAACAGTAG	.	4	ESCA
TSPYL5	0	.	GRCh37	8	98289607	98289607	+	Missense_Mutation	SNP	C	C	A	rs751121246	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.466G>T	p.Ala156Ser	p.A156S	ENST00000322128	1/1	54	47	7	37	37	0	TSPYL5,missense_variant,p.Ala156Ser,ENST00000322128,;	A	ENSG00000180543	ENST00000322128	Transcript	missense_variant	570	466	156	A/S	Gcg/Tcg	rs751121246	.	.	-1	TSPYL5	HGNC	29367	protein_coding	YES	CCDS34927.1	ENSP00000322802	TSYL5_HUMAN	.	UPI0000210364	.	tolerated(0.68)	benign(0.1)	1/1	.	hmmpanther:PTHR11875:SF30,hmmpanther:PTHR11875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCCGCGGTGC	.	4	ESCA
CDK5RAP2	0	.	GRCh37	9	123216129	123216129	+	Missense_Mutation	SNP	G	G	A	rs148134702	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2398C>T	p.Arg800Trp	p.R800W	ENST00000349780	21/38	65	49	15	61	61	0	CDK5RAP2,missense_variant,p.Arg194Trp,ENST00000416449,;CDK5RAP2,missense_variant,p.Arg800Trp,ENST00000349780,;CDK5RAP2,missense_variant,p.Arg800Trp,ENST00000360190,;CDK5RAP2,missense_variant,p.Arg768Trp,ENST00000360822,;CDK5RAP2,missense_variant,p.Arg800Trp,ENST00000359309,;CDK5RAP2,intron_variant,,ENST00000479584,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000483412,;	A	ENSG00000136861	ENST00000349780	Transcript	missense_variant	2578	2398	800	R/W	Cgg/Tgg	rs148134702	.	.	-1	CDK5RAP2	HGNC	18672	protein_coding	YES	CCDS6823.1	ENSP00000343818	CK5P2_HUMAN	F8WBJ0_HUMAN,C9K0C9_HUMAN	UPI0000367673	.	tolerated(0.22)	probably_damaging(0.973)	21/38	.	hmmpanther:PTHR13895,hmmpanther:PTHR13895:SF13	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCGTACCA	byCluster|by1000G	5	ESCA
CERCAM	0	.	GRCh37	9	131186871	131186871	+	Silent	SNP	C	C	T	rs142843167	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.744C>T	p.%3D	p.F248F	ENST00000372838	5/13	43	38	5	45	44	0	CERCAM,synonymous_variant,p.%3D,ENST00000372842,;CERCAM,synonymous_variant,p.%3D,ENST00000372838,;CERCAM,synonymous_variant,p.%3D,ENST00000420512,;CERCAM,downstream_gene_variant,,ENST00000447915,;CERCAM,downstream_gene_variant,,ENST00000411852,;CERCAM,downstream_gene_variant,,ENST00000420034,;CERCAM,non_coding_transcript_exon_variant,,ENST00000483893,;CERCAM,upstream_gene_variant,,ENST00000487001,;CERCAM,downstream_gene_variant,,ENST00000493788,;CERCAM,non_coding_transcript_exon_variant,,ENST00000463535,;CERCAM,downstream_gene_variant,,ENST00000483737,;	T	ENSG00000167123	ENST00000372838	Transcript	synonymous_variant	1142	744	248	F	ttC/ttT	rs142843167,COSM1105564,COSM1598058	.	.	1	CERCAM	HGNC	23723	protein_coding	YES	CCDS6901.2	ENSP00000361929	GT253_HUMAN	B7ZBT0_HUMAN,B7ZBS9_HUMAN,B7ZBS8_HUMAN	UPI000046FF85	.	.	.	5/13	.	Superfamily_domains:SSF53448,hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF9	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCTTCGCCTA	byCluster	3	ESCA
VPS13A	0	.	GRCh37	9	79985362	79985362	+	Silent	SNP	C	C	T	rs200321658	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8775C>T	p.%3D	p.T2925T	ENST00000360280	65/72	70	60	9	71	71	0	VPS13A,synonymous_variant,p.%3D,ENST00000357409,;VPS13A,synonymous_variant,p.%3D,ENST00000376634,;VPS13A,synonymous_variant,p.%3D,ENST00000376636,;VPS13A,synonymous_variant,p.%3D,ENST00000360280,;	T	ENSG00000197969	ENST00000360280	Transcript	synonymous_variant	9035	8775	2925	T	acC/acT	rs200321658	.	.	1	VPS13A	HGNC	1908	protein_coding	YES	CCDS6655.1	ENSP00000353422	VP13A_HUMAN	.	UPI0000210B7A	.	.	.	65/72	.	hmmpanther:PTHR16166,hmmpanther:PTHR16166:SF22	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCACCGGTGC	byCluster|by1000G	4	ESCA
GLA	0	.	GRCh37	X	100656624	100656624	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543A>G	p.%3D	p.A181A	ENST00000218516	3/7	65	60	5	51	51	0	GLA,synonymous_variant,p.%3D,ENST00000218516,;RPL36A-HNRNPH2,intron_variant,,ENST00000409338,;RPL36A-HNRNPH2,intron_variant,,ENST00000409170,;GLA,non_coding_transcript_exon_variant,,ENST00000479445,;GLA,non_coding_transcript_exon_variant,,ENST00000486121,;GLA,non_coding_transcript_exon_variant,,ENST00000480513,;GLA,upstream_gene_variant,,ENST00000468823,;GLA,upstream_gene_variant,,ENST00000466414,;GLA,synonymous_variant,p.%3D,ENST00000493905,;	C	ENSG00000102393	ENST00000218516	Transcript	synonymous_variant	565	543	181	A	gcA/gcG	.	.	.	-1	GLA	HGNC	4296	protein_coding	YES	CCDS14484.1	ENSP00000218516	AGAL_HUMAN	Q6LER7_HUMAN,Q53Y83_HUMAN	UPI0000033A30	.	.	.	3/7	.	hmmpanther:PTHR11452,hmmpanther:PTHR11452:SF15,Gene3D:3.20.20.70,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATCTGCCAA	.	2	ESCA
AMOT	0	.	GRCh37	X	112058876	112058876	+	Missense_Mutation	SNP	G	G	A	rs762357605	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1102C>T	p.Arg368Cys	p.R368C	ENST00000371959	2/11	57	39	17	42	42	0	AMOT,missense_variant,p.Arg368Cys,ENST00000371959,;AMOT,missense_variant,p.Arg136Cys,ENST00000371962,;AMOT,missense_variant,p.Arg368Cys,ENST00000524145,;AMOT,missense_variant,p.Arg136Cys,ENST00000371958,;AMOT,5_prime_UTR_variant,,ENST00000304758,;	A	ENSG00000126016	ENST00000371959	Transcript	missense_variant	1102	1102	368	R/C	Cgt/Tgt	rs762357605	.	.	-1	AMOT	HGNC	17810	protein_coding	YES	CCDS48154.1	ENSP00000361027	AMOT_HUMAN	E7ERM3_HUMAN	UPI000050ED33	.	.	unknown(0)	2/11	.	hmmpanther:PTHR14826,hmmpanther:PTHR14826:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACGGTAAT	byFrequency	5	ESCA
HS6ST2	0	.	GRCh37	X	131761460	131761460	+	3'Flank	SNP	C	C	A	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000521489	.	76	66	9	42	42	0	HS6ST2,3_prime_UTR_variant,,ENST00000370836,;HS6ST2,downstream_gene_variant,,ENST00000521489,;HS6ST2,downstream_gene_variant,,ENST00000406696,;HS6ST2,downstream_gene_variant,,ENST00000370833,;	A	ENSG00000171004	ENST00000521489	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	538	-1	HS6ST2	HGNC	19133	protein_coding	YES	CCDS48170.1	ENSP00000429473	H6ST2_HUMAN	B7Z2U5_HUMAN	UPI0000E59259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGATTCCAGTA	.	4	ESCA
EGFL6	0	.	GRCh37	X	13621508	13621508	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473G>T	p.Cys158Phe	p.C158F	ENST00000380602	5/12	39	35	4	41	41	0	EGFL6,missense_variant,p.Cys158Phe,ENST00000380602,;EGFL6,missense_variant,p.Cys158Phe,ENST00000361306,;	T	ENSG00000198759	ENST00000380602	Transcript	missense_variant	713	473	158	C/F	tGt/tTt	.	.	.	1	EGFL6	HGNC	3235	protein_coding	YES	CCDS55370.1	ENSP00000369976	EGFL6_HUMAN	.	UPI0000034CAE	.	deleterious(0)	probably_damaging(0.994)	5/12	.	hmmpanther:PTHR24050:SF18,hmmpanther:PTHR24050,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGTGTCCAT	.	2	ESCA
FAM47C	0	.	GRCh37	X	37027957	37027957	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1474G>A	p.Asp492Asn	p.D492N	ENST00000358047	1/1	73	55	17	76	76	0	FAM47C,missense_variant,p.Asp492Asn,ENST00000358047,;	A	ENSG00000198173	ENST00000358047	Transcript	missense_variant	1526	1474	492	D/N	Gac/Aac	COSM1467829,COSM1467828	.	.	1	FAM47C	HGNC	25301	protein_coding	YES	CCDS35227.1	ENSP00000367913	FA47C_HUMAN	.	UPI000041ABF8	.	tolerated_low_confidence(0.09)	benign(0.348)	1/1	.	hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCGACACT	.	5	ESCA
BRWD3	0	.	GRCh37	X	79940990	79940990	+	Missense_Mutation	SNP	C	C	G	rs775638823	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4051G>C	p.Glu1351Gln	p.E1351Q	ENST00000373275	36/41	52	44	7	47	47	0	BRWD3,missense_variant,p.Glu1351Gln,ENST00000373275,;BRWD3,non_coding_transcript_exon_variant,,ENST00000473691,;	G	ENSG00000165288	ENST00000373275	Transcript	missense_variant	4268	4051	1351	E/Q	Gaa/Caa	rs775638823	.	.	-1	BRWD3	HGNC	17342	protein_coding	YES	CCDS14447.1	ENSP00000362372	BRWD3_HUMAN	.	UPI000045785B	.	tolerated_low_confidence(0.32)	benign(0.054)	36/41	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50014,hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266,Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCTGGAA	.	5	ESCA
HMGN5	0	.	GRCh37	X	80371790	80371790	+	Silent	SNP	G	G	T	.	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180C>A	p.%3D	p.A60A	ENST00000358130	6/7	29	26	3	39	39	0	HMGN5,synonymous_variant,p.%3D,ENST00000358130,;HMGN5,synonymous_variant,p.%3D,ENST00000451455,;HMGN5,synonymous_variant,p.%3D,ENST00000436386,;HMGN5,synonymous_variant,p.%3D,ENST00000430960,;HMGN5,synonymous_variant,p.%3D,ENST00000447319,;HMGN5,synonymous_variant,p.%3D,ENST00000373250,;HMGN5,non_coding_transcript_exon_variant,,ENST00000491275,;	T	ENSG00000198157	ENST00000358130	Transcript	synonymous_variant	509	180	60	A	gcC/gcA	COSM1125906	.	.	-1	HMGN5	HGNC	8013	protein_coding	YES	CCDS14448.1	ENSP00000350848	HMGN5_HUMAN	Q5JSL0_HUMAN,Q5JSK8_HUMAN,Q5JSK7_HUMAN	UPI0000130542	.	.	.	6/7	.	hmmpanther:PTHR23145,Pfam_domain:PF01101,SMART_domains:SM00527	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A60A|c.180C>A|3	MUTECT|MUSE	GCTTGGGCACT	.	2	ESCA
SATL1	0	.	GRCh37	X	84362459	84362459	+	Missense_Mutation	SNP	G	G	C	rs762180135	.	TCGA-IG-A3YA-01A-11D-A247-09	TCGA-IG-A3YA-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516C>G	p.Leu506Val	p.L506V	ENST00000509231	1/5	93	63	29	75	75	0	SATL1,missense_variant,p.Leu506Val,ENST00000509231,;SATL1,missense_variant,p.Leu319Val,ENST00000332921,;SATL1,missense_variant,p.Leu319Val,ENST00000395409,;	C	ENSG00000184788	ENST00000509231	Transcript	missense_variant	1596	1516	506	L/V	Ctg/Gtg	rs762180135	.	.	-1	SATL1	HGNC	27992	protein_coding	YES	CCDS35343.2	ENSP00000425421	.	E9PB72_HUMAN	UPI000041ABBC	.	tolerated(0.33)	probably_damaging(0.91)	1/5	.	hmmpanther:PTHR10545,hmmpanther:PTHR10545:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCAGGCCTG	byFrequency	5	ESCA
UROS	0	.	GRCh37	10	127491497	127491497	+	Intron	SNP	G	G	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394+4485C>A	.	.	ENST00000368797	.	25	12	12	31	31	0	UROS,3_prime_UTR_variant,,ENST00000368778,;UROS,intron_variant,,ENST00000368797,;UROS,intron_variant,,ENST00000368786,;UROS,intron_variant,,ENST00000420761,;UROS,downstream_gene_variant,,ENST00000368774,;UROS,intron_variant,,ENST00000462490,;UROS,upstream_gene_variant,,ENST00000464267,;UROS,upstream_gene_variant,,ENST00000465577,;	T	ENSG00000188690	ENST00000368797	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	UROS	HGNC	12592	protein_coding	YES	CCDS7648.1	ENSP00000357787	HEM4_HUMAN	.	UPI000012C4A4	.	.	.	.	6/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	AGGATGCGGCT	.	3	ESCA
MRC1	0	.	GRCh37	10	18155626	18155626	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1919C>T	p.Thr640Met	p.T640M	ENST00000239761	12/30	16	11	5	19	19	0	MRC1,missense_variant,p.Thr640Met,ENST00000239761,;RP11-457D2.3,upstream_gene_variant,,ENST00000442231,;	T	ENSG00000120586	ENST00000239761	Transcript	missense_variant	2022	1919	640	T/M	aCg/aTg	.	.	.	1	MRC1	HGNC	7228	protein_coding	YES	CCDS7123.1	ENSP00000239761	MRC1_HUMAN	B4DLK9_HUMAN	UPI000012EB9A	.	deleterious(0.01)	probably_damaging(0.993)	12/30	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF55,Gene3D:3.10.100.10,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CACGACGACTC	.	2	ESCA
ANKRD30A	0	.	GRCh37	10	37507906	37507906	+	Splice_Site	SNP	A	A	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3100-2A>T	.	p.X1034_splice	ENST00000361713	.	25	14	10	10	10	0	ANKRD30A,splice_acceptor_variant,,ENST00000374660,;ANKRD30A,splice_acceptor_variant,,ENST00000361713,;ANKRD30A,splice_acceptor_variant,,ENST00000602533,;	T	ENSG00000148513	ENST00000361713	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ANKRD30A	HGNC	17234	protein_coding	YES	CCDS7193.1	ENSP00000354432	AN30A_HUMAN	R4GNA2_HUMAN	UPI0000458879	.	.	.	.	33/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTTAGGTTT	.	5	ESCA
BICC1	0	.	GRCh37	10	60573752	60573752	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2533+6C>T	.	.	ENST00000373886	.	75	28	47	78	78	0	BICC1,missense_variant,p.Arg473Cys,ENST00000263103,;BICC1,splice_region_variant,,ENST00000373886,;	T	ENSG00000122870	ENST00000373886	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	BICC1	HGNC	19351	protein_coding	YES	CCDS31206.1	ENSP00000362993	BICC1_HUMAN	.	UPI000059D156	.	.	.	.	18/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAGCGTTGT	.	5	ESCA
ARHGEF12	0	.	GRCh37	11	120317153	120317153	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1387C>T	p.His463Tyr	p.H463Y	ENST00000397843	17/41	21	16	4	10	10	0	ARHGEF12,missense_variant,p.His360Tyr,ENST00000532993,;ARHGEF12,missense_variant,p.His463Tyr,ENST00000397843,;ARHGEF12,missense_variant,p.His444Tyr,ENST00000356641,;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000525960,;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000528225,;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000529970,;ARHGEF12,upstream_gene_variant,,ENST00000525222,;ARHGEF12,upstream_gene_variant,,ENST00000532823,;	T	ENSG00000196914	ENST00000397843	Transcript	missense_variant	1553	1387	463	H/Y	Cac/Tac	.	.	.	1	ARHGEF12	HGNC	14193	protein_coding	YES	CCDS41727.1	ENSP00000380942	ARHGC_HUMAN	E9PMR6_HUMAN	UPI00000708ED	.	deleterious(0.01)	benign(0.317)	17/41	.	Superfamily_domains:SSF48097,Pfam_domain:PF09128,hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGCCACTAT	.	5	ESCA
TECTA	0	.	GRCh37	11	121000704	121000704	+	Missense_Mutation	SNP	C	C	T	rs139132568	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2725C>T	p.Arg909Cys	p.R909C	ENST00000392793	10/24	30	26	4	30	30	0	TECTA,missense_variant,p.Arg909Cys,ENST00000264037,;TECTA,missense_variant,p.Arg909Cys,ENST00000392793,;	T	ENSG00000109927	ENST00000392793	Transcript	missense_variant	2996	2725	909	R/C	Cgc/Tgc	rs139132568,COSM2157444	.	.	1	TECTA	HGNC	11720	protein_coding	YES	CCDS8434.1	ENSP00000376543	TECTA_HUMAN	.	UPI000045659D	.	tolerated(0.06)	possibly_damaging(0.892)	10/24	.	SMART_domains:SM00832,Pfam_domain:PF08742,hmmpanther:PTHR11339,PROSITE_profiles:PS51233	.	.	.	.	.	.	.	T:0	T:0.0005	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAGCCGCTCC	byCluster	2	ESCA
IGF2	0	.	GRCh37	11	2161524	2161524	+	Translation_Start_Site	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3G>C	p.Met1?	p.M1?	ENST00000434045	2/5	53	26	26	70	70	0	IGF2,start_lost,p.Met1?,ENST00000434045,;IGF2,intron_variant,,ENST00000381389,;IGF2,intron_variant,,ENST00000300632,;IGF2,upstream_gene_variant,,ENST00000381395,;IGF2,upstream_gene_variant,,ENST00000381406,;IGF2,upstream_gene_variant,,ENST00000416167,;IGF2,upstream_gene_variant,,ENST00000381392,;IGF2,upstream_gene_variant,,ENST00000418738,;IGF2-AS,upstream_gene_variant,,ENST00000381363,;IGF2-AS,upstream_gene_variant,,ENST00000381361,;IGF2-AS,upstream_gene_variant,,ENST00000445504,;INS-IGF2,intron_variant,,ENST00000356578,;	G	ENSG00000167244	ENST00000434045	Transcript	start_lost	388	3	1	M/I	atG/atC	.	.	.	-1	IGF2	HGNC	5466	protein_coding	YES	CCDS44517.1	ENSP00000391826	IGF2_HUMAN	E3UN46_HUMAN	UPI0001751501	.	deleterious_low_confidence(0)	possibly_damaging(0.775)	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAACCATCTC	.	5	ESCA
TSSC2	0	.	GRCh37	11	3424158	3424158	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.817C>T	.	.	ENST00000529482	7/9	82	77	5	111	111	0	TSSC2,non_coding_transcript_exon_variant,,ENST00000529482,;TSSC2,non_coding_transcript_exon_variant,,ENST00000533775,;TSSC2,downstream_gene_variant,,ENST00000526284,;TSSC2,intron_variant,,ENST00000450217,;	T	ENSG00000223756	ENST00000529482	Transcript	non_coding_transcript_exon_variant	817	.	.	.	.	.	.	.	1	TSSC2	HGNC	12384	processed_transcript	YES	.	.	.	.	.	.	.	.	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACTTCTCCAT	.	2	ESCA
OR52K1	0	.	GRCh37	11	4510932	4510932	+	Missense_Mutation	SNP	C	C	T	rs768055536	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.802C>T	p.Arg268Cys	p.R268C	ENST00000307632	1/1	74	48	26	55	55	0	OR52K1,missense_variant,p.Arg268Cys,ENST00000307632,;	T	ENSG00000196778	ENST00000307632	Transcript	missense_variant	824	802	268	R/C	Cgc/Tgc	rs768055536,COSM3986168	.	.	1	OR52K1	HGNC	15222	protein_coding	YES	CCDS31352.1	ENSP00000302422	O52K1_HUMAN	.	UPI00001AEE74	.	deleterious(0.04)	benign(0.008)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF21,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R268H|c.803G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCCCGCCAT	byFrequency	5	ESCA
DDB2	0	.	GRCh37	11	47260399	47260400	+	Frame_Shift_Del	DEL	GA	GA	-	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	GA	GA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3_*4delGA	.	.	ENST00000256996	10/10	28	25	3	25	25	0	DDB2,frameshift_variant,,ENST00000378603,;DDB2,frameshift_variant,,ENST00000256996,;DDB2,frameshift_variant,,ENST00000378600,;DDB2,3_prime_UTR_variant,,ENST00000378601,;ACP2,downstream_gene_variant,,ENST00000256997,;ACP2,downstream_gene_variant,,ENST00000529444,;ACP2,downstream_gene_variant,,ENST00000537863,;ACP2,downstream_gene_variant,,ENST00000529663,;ACP2,downstream_gene_variant,,ENST00000533929,;ACP2,downstream_gene_variant,,ENST00000527256,;ACP2,downstream_gene_variant,,ENST00000534752,;ACP2,downstream_gene_variant,,ENST00000524769,;ACP2,downstream_gene_variant,,ENST00000525230,;ACP2,downstream_gene_variant,,ENST00000531547,;ACP2,downstream_gene_variant,,ENST00000531004,;ACP2,downstream_gene_variant,,ENST00000534448,;	-	ENSG00000134574	ENST00000256996	Transcript	frameshift_variant	1478-1479	1283-1284	428	*/X	tGA/t	.	.	.	1	DDB2	HGNC	2718	protein_coding	YES	CCDS7927.1	ENSP00000256996	DDB2_HUMAN	.	UPI000000D90C	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GGAAGTGAGAGAC	.	2	ESCA
MS4A8	0	.	GRCh37	11	60470906	60470906	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.275C>T	p.Thr92Met	p.T92M	ENST00000300226	3/7	103	89	14	78	78	0	MS4A8,missense_variant,p.Thr74Met,ENST00000525458,;MS4A8,missense_variant,p.Thr92Met,ENST00000529752,;MS4A8,missense_variant,p.Thr92Met,ENST00000300226,;MS4A8,3_prime_UTR_variant,,ENST00000532816,;MS4A8,non_coding_transcript_exon_variant,,ENST00000533354,;MS4A8,non_coding_transcript_exon_variant,,ENST00000533691,;MS4A8,non_coding_transcript_exon_variant,,ENST00000532953,;MS4A8,non_coding_transcript_exon_variant,,ENST00000450141,;MS4A8,downstream_gene_variant,,ENST00000534316,;	T	ENSG00000166959	ENST00000300226	Transcript	missense_variant	478	275	92	T/M	aCg/aTg	COSM3397950	.	.	1	MS4A8	HGNC	13380	protein_coding	YES	CCDS7990.1	ENSP00000300226	M4A8_HUMAN	.	UPI0000047F97	.	tolerated(0.09)	possibly_damaging(0.672)	3/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23320:SF14,hmmpanther:PTHR23320,Pfam_domain:PF04103	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A91V|c.272C>T|4	RADIA|MUTECT|MUSE|VARSCANS	GGCGACGGTTC	.	4	ESCA
DNAJC4	0	.	GRCh37	11	63998025	63998027	+	5'UTR	DEL	CTT	CTT	-	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-300_-298delTCT	.	.	ENST00000321685	2/7	24	16	8	26	26	0	DNAJC4,5_prime_UTR_variant,,ENST00000321685,;DNAJC4,upstream_gene_variant,,ENST00000355040,;TRPT1,upstream_gene_variant,,ENST00000317459,;TRPT1,upstream_gene_variant,,ENST00000545812,;TRPT1,upstream_gene_variant,,ENST00000394547,;TRPT1,upstream_gene_variant,,ENST00000541278,;TRPT1,upstream_gene_variant,,ENST00000546089,;VEGFB,upstream_gene_variant,,ENST00000426086,;VEGFB,upstream_gene_variant,,ENST00000309422,;TRPT1,upstream_gene_variant,,ENST00000394546,;NUDT22,downstream_gene_variant,,ENST00000428347,;NUDT22,downstream_gene_variant,,ENST00000279206,;DNAJC4,upstream_gene_variant,,ENST00000535246,;NUDT22,downstream_gene_variant,,ENST00000539325,;NUDT22,downstream_gene_variant,,ENST00000441250,;DNAJC4,upstream_gene_variant,,ENST00000321460,;RP11-783K16.14,intron_variant,,ENST00000534988,;RP11-783K16.14,downstream_gene_variant,,ENST00000539963,;TRPT1,upstream_gene_variant,,ENST00000540472,;NUDT22,3_prime_UTR_variant,,ENST00000534929,;NUDT22,downstream_gene_variant,,ENST00000535000,;NUDT22,downstream_gene_variant,,ENST00000422364,;DNAJC4,upstream_gene_variant,,ENST00000537109,;TRPT1,upstream_gene_variant,,ENST00000536234,;NUDT22,downstream_gene_variant,,ENST00000545184,;TRPT1,upstream_gene_variant,,ENST00000539595,;NUDT22,downstream_gene_variant,,ENST00000543501,;DNAJC4,upstream_gene_variant,,ENST00000543685,;DNAJC4,upstream_gene_variant,,ENST00000542376,;DNAJC4,upstream_gene_variant,,ENST00000536006,;NUDT22,downstream_gene_variant,,ENST00000537707,;TRPT1,upstream_gene_variant,,ENST00000542040,;DNAJC4,upstream_gene_variant,,ENST00000538961,;TRPT1,upstream_gene_variant,,ENST00000537907,;NUDT22,downstream_gene_variant,,ENST00000537094,;DNAJC4,upstream_gene_variant,,ENST00000543791,;DNAJC4,upstream_gene_variant,,ENST00000540945,;TRPT1,upstream_gene_variant,,ENST00000539436,;NUDT22,downstream_gene_variant,,ENST00000543358,;	-	ENSG00000110011	ENST00000321685	Transcript	5_prime_UTR_variant	164-166	.	.	.	.	.	.	.	1	DNAJC4	HGNC	5271	protein_coding	YES	CCDS41666.1	ENSP00000396896	DNJC4_HUMAN	.	UPI000000DA95	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCCTCCTTCTCCC	.	3	ESCA
APBB1	0	.	GRCh37	11	6423342	6423342	+	Missense_Mutation	SNP	C	C	T	rs772042074	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1352G>A	p.Arg451His	p.R451H	ENST00000299402	8/14	60	41	19	50	50	0	APBB1,missense_variant,p.Arg192His,ENST00000608704,;APBB1,missense_variant,p.Arg192His,ENST00000608394,;APBB1,missense_variant,p.Arg231His,ENST00000530885,;APBB1,missense_variant,p.Arg451His,ENST00000299402,;APBB1,missense_variant,p.Arg451His,ENST00000609360,;APBB1,missense_variant,p.Arg192His,ENST00000529890,;APBB1,missense_variant,p.Arg451His,ENST00000389906,;APBB1,missense_variant,p.Arg192His,ENST00000608645,;APBB1,missense_variant,p.Arg216His,ENST00000609331,;APBB1,missense_variant,p.Arg451His,ENST00000311051,;APBB1,missense_variant,p.Arg231His,ENST00000608655,;APBB1,5_prime_UTR_variant,,ENST00000529519,;APBB1,downstream_gene_variant,,ENST00000532020,;APBB1,missense_variant,p.Arg451His,ENST00000608435,;APBB1,non_coding_transcript_exon_variant,,ENST00000533139,;APBB1,non_coding_transcript_exon_variant,,ENST00000533407,;APBB1,non_coding_transcript_exon_variant,,ENST00000529778,;APBB1,non_coding_transcript_exon_variant,,ENST00000534188,;APBB1,non_coding_transcript_exon_variant,,ENST00000524626,;APBB1,non_coding_transcript_exon_variant,,ENST00000526925,;	T	ENSG00000166313	ENST00000299402	Transcript	missense_variant	1452	1352	451	R/H	cGc/cAc	rs772042074	.	.	-1	APBB1	HGNC	581	protein_coding	YES	CCDS31410.1	ENSP00000299402	APBB1_HUMAN	.	UPI0000070BF7	.	deleterious(0)	probably_damaging(0.949)	8/14	.	Superfamily_domains:SSF50729,SMART_domains:SM00462,Gene3D:2.30.29.30,Pfam_domain:PF00640,hmmpanther:PTHR14058,hmmpanther:PTHR14058:SF5,PROSITE_profiles:PS01179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACGCGGATG	.	5	ESCA
LRP5	0	.	GRCh37	11	68174018	68174018	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1833delG	p.Cys612AlafsTer23	p.C612Afs*23	ENST00000294304	9/23	78	62	16	58	58	0	LRP5,frameshift_variant,p.Cys612AlafsTer23,ENST00000294304,;LRP5,upstream_gene_variant,,ENST00000528714,;LRP5,3_prime_UTR_variant,,ENST00000529993,;LRP5,downstream_gene_variant,,ENST00000528890,;	-	ENSG00000162337	ENST00000294304	Transcript	frameshift_variant	1934	1828	610	G/X	Ggg/gg	CM053295,CM053961	.	.	1	LRP5	HGNC	6697	protein_coding	YES	CCDS8181.1	ENSP00000294304	LRP5_HUMAN	E9PHY1_HUMAN	UPI0000073246	.	.	.	9/23	.	Superfamily_domains:SSF57196,PIRSF_domain:PIRSF036314,SMART_domains:SM00181,Gene3D:2.10.25.10,Pfam_domain:PF14670,hmmpanther:PTHR10529:SF202,hmmpanther:PTHR10529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGAACGGGGGG	.	3	ESCA
KIAA1731	0	.	GRCh37	11	93464336	93464336	+	3'Flank	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000325212	.	37	26	11	20	20	0	KIAA1731,downstream_gene_variant,,ENST00000531404,;KIAA1731,downstream_gene_variant,,ENST00000344196,;KIAA1731,downstream_gene_variant,,ENST00000325212,;KIAA1731,downstream_gene_variant,,ENST00000411936,;KIAA1731,downstream_gene_variant,,ENST00000531700,;KIAA1731,downstream_gene_variant,,ENST00000529185,;TAF1D,downstream_gene_variant,,ENST00000448108,;SNORA1,downstream_gene_variant,,ENST00000384107,;MIR1304,downstream_gene_variant,,ENST00000408243,;SNORD5,downstream_gene_variant,,ENST00000459342,;SNORA8,downstream_gene_variant,,ENST00000384574,;SNORA32,upstream_gene_variant,,ENST00000384072,;SNORA40,downstream_gene_variant,,ENST00000388090,;SNORD6,downstream_gene_variant,,ENST00000365444,;SNORA18,downstream_gene_variant,,ENST00000384416,;SNORA25,upstream_gene_variant,,ENST00000384384,;TAF1D,non_coding_transcript_exon_variant,,ENST00000546088,;TAF1D,non_coding_transcript_exon_variant,,ENST00000530089,;TAF1D,3_prime_UTR_variant,,ENST00000540232,;TAF1D,3_prime_UTR_variant,,ENST00000393259,;TAF1D,3_prime_UTR_variant,,ENST00000526015,;TAF1D,3_prime_UTR_variant,,ENST00000323981,;TAF1D,3_prime_UTR_variant,,ENST00000527169,;TAF1D,non_coding_transcript_exon_variant,,ENST00000530769,;TAF1D,non_coding_transcript_exon_variant,,ENST00000529435,;TAF1D,non_coding_transcript_exon_variant,,ENST00000529900,;TAF1D,non_coding_transcript_exon_variant,,ENST00000534079,;TAF1D,non_coding_transcript_exon_variant,,ENST00000525928,;TAF1D,downstream_gene_variant,,ENST00000533794,;TAF1D,downstream_gene_variant,,ENST00000528734,;TAF1D,downstream_gene_variant,,ENST00000527068,;TAF1D,downstream_gene_variant,,ENST00000529794,;	C	ENSG00000166004	ENST00000325212	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	814	1	KIAA1731	HGNC	29366	protein_coding	YES	CCDS44708.1	ENSP00000316681	K1731_HUMAN	E9PM20_HUMAN	UPI0000251F0E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGTCATCT	.	5	ESCA
FKBP4	0	.	GRCh37	12	2909017	2909017	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673T>C	p.Tyr225His	p.Y225H	ENST00000001008	6/10	37	31	6	24	24	0	FKBP4,missense_variant,p.Tyr225His,ENST00000001008,;FKBP4,upstream_gene_variant,,ENST00000539181,;FKBP4,downstream_gene_variant,,ENST00000538622,;FKBP4,upstream_gene_variant,,ENST00000544366,;RP4-816N1.6,intron_variant,,ENST00000547834,;RP4-816N1.7,intron_variant,,ENST00000547042,;FKBP4,downstream_gene_variant,,ENST00000540260,;FKBP4,splice_region_variant,,ENST00000543037,;FKBP4,downstream_gene_variant,,ENST00000543769,;	C	ENSG00000004478	ENST00000001008	Transcript	missense_variant	860	673	225	Y/H	Tat/Cat	.	.	.	1	FKBP4	HGNC	3720	protein_coding	YES	CCDS8512.1	ENSP00000001008	FKBP4_HUMAN	F5H1U3_HUMAN	UPI000013C4D0	.	deleterious(0.01)	possibly_damaging(0.614)	6/10	.	PROSITE_profiles:PS50059,hmmpanther:PTHR10516:SF25,hmmpanther:PTHR10516,Gene3D:3.10.50.40,Pfam_domain:PF00254,Superfamily_domains:SSF54534	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCTATGCT	.	5	ESCA
SLC38A2	0	.	GRCh37	12	46753241	46753241	+	3'UTR	SNP	C	C	T	rs188209713	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1653G>A	.	.	ENST00000256689	16/16	25	15	10	34	34	0	SLC38A2,3_prime_UTR_variant,,ENST00000256689,;SLC38A2,3_prime_UTR_variant,,ENST00000551374,;SLC38A2,downstream_gene_variant,,ENST00000548870,;SLC38A2,downstream_gene_variant,,ENST00000548111,;SLC38A2,3_prime_UTR_variant,,ENST00000549258,;SLC38A2,downstream_gene_variant,,ENST00000548785,;SLC38A2,downstream_gene_variant,,ENST00000552414,;SLC38A2,downstream_gene_variant,,ENST00000552703,;SLC38A2,downstream_gene_variant,,ENST00000546520,;SLC38A2,downstream_gene_variant,,ENST00000548236,;	T	ENSG00000134294	ENST00000256689	Transcript	3_prime_UTR_variant	3619	.	.	.	.	rs188209713	.	.	-1	SLC38A2	HGNC	13448	protein_coding	YES	CCDS8749.1	ENSP00000256689	S38A2_HUMAN	.	UPI000000121A	.	.	.	16/16	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATGCGTAAC	by1000G	5	ESCA
GPR84	0	.	GRCh37	12	54757553	54757553	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.83T>G	p.Val28Gly	p.V28G	ENST00000551809	1/1	42	13	29	46	46	0	GPR84,missense_variant,p.Val28Gly,ENST00000551809,;GPR84,missense_variant,p.Val28Gly,ENST00000267015,;RP11-753H16.3,intron_variant,,ENST00000550474,;RP11-753H16.5,intron_variant,,ENST00000552785,;	C	ENSG00000139572	ENST00000551809	Transcript	missense_variant	719	83	28	V/G	gTg/gGg	COSM191388	.	.	-1	GPR84	HGNC	4535	protein_coding	YES	CCDS8878.1	ENSP00000450310	GPR84_HUMAN	.	UPI00000421DF	.	deleterious(0.01)	benign(0.046)	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24230:SF59,hmmpanther:PTHR24230,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCACCCCC	.	5	ESCA
PPFIA2	0	.	GRCh37	12	81747054	81747054	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1838C>G	p.Pro613Arg	p.P613R	ENST00000549396	17/33	82	31	51	62	62	0	PPFIA2,missense_variant,p.Pro595Arg,ENST00000333447,;PPFIA2,missense_variant,p.Pro539Arg,ENST00000407050,;PPFIA2,missense_variant,p.Pro180Arg,ENST00000541570,;PPFIA2,missense_variant,p.Pro514Arg,ENST00000443686,;PPFIA2,missense_variant,p.Pro460Arg,ENST00000550359,;PPFIA2,missense_variant,p.Pro194Arg,ENST00000553058,;PPFIA2,missense_variant,p.Pro613Arg,ENST00000548586,;PPFIA2,missense_variant,p.Pro613Arg,ENST00000549396,;PPFIA2,missense_variant,p.Pro595Arg,ENST00000549325,;PPFIA2,missense_variant,p.Pro613Arg,ENST00000550584,;PPFIA2,missense_variant,p.Pro613Arg,ENST00000552948,;PPFIA2,5_prime_UTR_variant,,ENST00000541017,;PPFIA2,downstream_gene_variant,,ENST00000548670,;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,upstream_gene_variant,,ENST00000549917,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,;	C	ENSG00000139220	ENST00000549396	Transcript	missense_variant	1999	1838	613	P/R	cCt/cGt	COSM3465957,COSM3465958	.	.	-1	PPFIA2	HGNC	9246	protein_coding	YES	CCDS55857.1	ENSP00000450337	LIPA2_HUMAN	H0YHK3_HUMAN,F8W1Y8_HUMAN,F8VU88_HUMAN	UPI0000168655	.	tolerated(0.09)	benign(0.002)	17/33	.	hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAAAGGGTGG	.	5	ESCA
RASA3	0	.	GRCh37	13	114793367	114793367	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486G>T	p.%3D	p.G162G	ENST00000334062	6/24	46	26	20	40	40	0	RASA3,missense_variant,p.Ala131Ser,ENST00000542651,;RASA3,synonymous_variant,p.%3D,ENST00000389544,;RASA3,synonymous_variant,p.%3D,ENST00000334062,;	A	ENSG00000185989	ENST00000334062	Transcript	synonymous_variant	608	486	162	G	ggG/ggT	.	.	.	-1	RASA3	HGNC	20331	protein_coding	YES	CCDS32016.1	ENSP00000335029	RASA3_HUMAN	F8W6X8_HUMAN	UPI000000DBC1	.	.	.	6/24	.	PROSITE_profiles:PS50004,hmmpanther:PTHR10194:SF53,hmmpanther:PTHR10194,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTGCCCATT	.	5	ESCA
NDRG2	0	.	GRCh37	14	21487296	21487296	+	Missense_Mutation	SNP	C	C	T	rs747046310	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740G>A	p.Arg247His	p.R247H	ENST00000556147	11/16	50	41	9	38	38	0	NDRG2,missense_variant,p.Arg233His,ENST00000350792,;NDRG2,missense_variant,p.Arg233His,ENST00000555158,;NDRG2,missense_variant,p.Arg233His,ENST00000556008,;NDRG2,missense_variant,p.Arg160His,ENST00000556366,;NDRG2,missense_variant,p.Arg233His,ENST00000554143,;NDRG2,missense_variant,p.Arg233His,ENST00000397856,;NDRG2,missense_variant,p.Arg204His,ENST00000397855,;NDRG2,missense_variant,p.Arg204His,ENST00000298684,;NDRG2,missense_variant,p.Arg247His,ENST00000556147,;NDRG2,missense_variant,p.Arg247His,ENST00000298687,;NDRG2,missense_variant,p.Arg247His,ENST00000397858,;NDRG2,missense_variant,p.Arg247His,ENST00000397847,;NDRG2,missense_variant,p.Arg247His,ENST00000553867,;NDRG2,missense_variant,p.Arg247His,ENST00000397851,;NDRG2,missense_variant,p.Arg163His,ENST00000553593,;NDRG2,missense_variant,p.Arg233His,ENST00000555026,;NDRG2,missense_variant,p.Arg243His,ENST00000403829,;NDRG2,missense_variant,p.Arg233His,ENST00000553503,;NDRG2,missense_variant,p.Arg247His,ENST00000397853,;NDRG2,missense_variant,p.Arg233His,ENST00000397844,;NDRG2,missense_variant,p.Arg160His,ENST00000554104,;NDRG2,missense_variant,p.Arg233His,ENST00000556974,;NDRG2,missense_variant,p.Arg233His,ENST00000360463,;NDRG2,intron_variant,,ENST00000557633,;NDRG2,downstream_gene_variant,,ENST00000554489,;NDRG2,downstream_gene_variant,,ENST00000554561,;NDRG2,downstream_gene_variant,,ENST00000556329,;NDRG2,downstream_gene_variant,,ENST00000554483,;NDRG2,downstream_gene_variant,,ENST00000557274,;NDRG2,downstream_gene_variant,,ENST00000555733,;NDRG2,downstream_gene_variant,,ENST00000554472,;NDRG2,downstream_gene_variant,,ENST00000554415,;NDRG2,downstream_gene_variant,,ENST00000556561,;NDRG2,downstream_gene_variant,,ENST00000556688,;NDRG2,downstream_gene_variant,,ENST00000557182,;NDRG2,downstream_gene_variant,,ENST00000555142,;NDRG2,downstream_gene_variant,,ENST00000557264,;NDRG2,downstream_gene_variant,,ENST00000449431,;NDRG2,downstream_gene_variant,,ENST00000555869,;NDRG2,downstream_gene_variant,,ENST00000555384,;NDRG2,downstream_gene_variant,,ENST00000556457,;NDRG2,downstream_gene_variant,,ENST00000553442,;NDRG2,downstream_gene_variant,,ENST00000554833,;NDRG2,downstream_gene_variant,,ENST00000556924,;NDRG2,downstream_gene_variant,,ENST00000554398,;NDRG2,downstream_gene_variant,,ENST00000553563,;NDRG2,downstream_gene_variant,,ENST00000557149,;NDRG2,downstream_gene_variant,,ENST00000556420,;NDRG2,downstream_gene_variant,,ENST00000555657,;NDRG2,downstream_gene_variant,,ENST00000557169,;NDRG2,downstream_gene_variant,,ENST00000554893,;NDRG2,downstream_gene_variant,,ENST00000557676,;NDRG2,downstream_gene_variant,,ENST00000553784,;NDRG2,downstream_gene_variant,,ENST00000554531,;NDRG2,downstream_gene_variant,,ENST00000554419,;NDRG2,downstream_gene_variant,,ENST00000554094,;NDRG2,non_coding_transcript_exon_variant,,ENST00000554277,;NDRG2,3_prime_UTR_variant,,ENST00000557353,;NDRG2,non_coding_transcript_exon_variant,,ENST00000553793,;NDRG2,non_coding_transcript_exon_variant,,ENST00000557416,;NDRG2,non_coding_transcript_exon_variant,,ENST00000556716,;TPPP2,upstream_gene_variant,,ENST00000533755,;NDRG2,downstream_gene_variant,,ENST00000557167,;NDRG2,upstream_gene_variant,,ENST00000555650,;NDRG2,downstream_gene_variant,,ENST00000557616,;NDRG2,downstream_gene_variant,,ENST00000554379,;NDRG2,downstream_gene_variant,,ENST00000557669,;NDRG2,downstream_gene_variant,,ENST00000366204,;NDRG2,downstream_gene_variant,,ENST00000555695,;NDRG2,downstream_gene_variant,,ENST00000557113,;NDRG2,downstream_gene_variant,,ENST00000557198,;NDRG2,downstream_gene_variant,,ENST00000557728,;NDRG2,downstream_gene_variant,,ENST00000555767,;NDRG2,downstream_gene_variant,,ENST00000553567,;NDRG2,downstream_gene_variant,,ENST00000553741,;NDRG2,downstream_gene_variant,,ENST00000553862,;NDRG2,downstream_gene_variant,,ENST00000553900,;NDRG2,downstream_gene_variant,,ENST00000557318,;NDRG2,downstream_gene_variant,,ENST00000557305,;	T	ENSG00000165795	ENST00000556147	Transcript	missense_variant	1681	740	247	R/H	cGt/cAt	rs747046310	.	.	-1	NDRG2	HGNC	14460	protein_coding	YES	CCDS9565.1	ENSP00000451712	NDRG2_HUMAN	G3V5S0_HUMAN,G3V5P9_HUMAN,G3V5L7_HUMAN,G3V5B5_HUMAN,G3V578_HUMAN,G3V552_HUMAN,G3V4T9_HUMAN,G3V3P1_HUMAN,G3V3D5_HUMAN,G3V383_HUMAN,G3V358_HUMAN,G3V2T2_HUMAN,G3V2S0_HUMAN,G3V2I9_HUMAN	UPI000012FEDE	.	deleterious(0)	probably_damaging(0.995)	11/16	.	hmmpanther:PTHR11034:SF17,hmmpanther:PTHR11034,Gene3D:3.40.50.1820,Pfam_domain:PF03096,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCACGCTCA	byFrequency	5	ESCA
AP1G2	0	.	GRCh37	14	24031497	24031499	+	In_Frame_Del	DEL	TTG	TTG	-	rs772214302	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	TTG	TTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1626_1628delCAA	p.Asn543del	p.N543del	ENST00000308724	15/21	35	29	6	28	28	0	AP1G2,inframe_deletion,p.Asn543del,ENST00000308724,;AP1G2,inframe_deletion,p.Asn39del,ENST00000554477,;AP1G2,inframe_deletion,p.Asn543del,ENST00000397120,;THTPA,downstream_gene_variant,,ENST00000556545,;THTPA,downstream_gene_variant,,ENST00000404535,;AP1G2,downstream_gene_variant,,ENST00000556843,;THTPA,downstream_gene_variant,,ENST00000288014,;AP1G2,downstream_gene_variant,,ENST00000557189,;THTPA,downstream_gene_variant,,ENST00000554970,;THTPA,downstream_gene_variant,,ENST00000556015,;THTPA,downstream_gene_variant,,ENST00000554789,;RP11-66N24.3,intron_variant,,ENST00000555968,;RP11-66N24.4,downstream_gene_variant,,ENST00000553985,;RP11-66N24.4,downstream_gene_variant,,ENST00000555446,;RP11-66N24.4,downstream_gene_variant,,ENST00000556354,;AP1G2,splice_region_variant,,ENST00000555510,;AP1G2,downstream_gene_variant,,ENST00000555118,;AP1G2,downstream_gene_variant,,ENST00000556277,;AP1G2,splice_region_variant,,ENST00000535852,;AP1G2,splice_region_variant,,ENST00000460049,;AP1G2,splice_region_variant,,ENST00000465445,;AP1G2,non_coding_transcript_exon_variant,,ENST00000554554,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556966,;AP1G2,non_coding_transcript_exon_variant,,ENST00000554982,;AP1G2,downstream_gene_variant,,ENST00000556943,;AP1G2,downstream_gene_variant,,ENST00000556741,;AP1G2,downstream_gene_variant,,ENST00000554069,;AP1G2,downstream_gene_variant,,ENST00000555789,;AP1G2,downstream_gene_variant,,ENST00000554312,;AP1G2,downstream_gene_variant,,ENST00000553685,;AP1G2,downstream_gene_variant,,ENST00000556743,;AP1G2,downstream_gene_variant,,ENST00000554816,;AP1G2,downstream_gene_variant,,ENST00000557132,;AP1G2,downstream_gene_variant,,ENST00000553756,;AP1G2,upstream_gene_variant,,ENST00000557391,;AP1G2,downstream_gene_variant,,ENST00000557162,;AP1G2,upstream_gene_variant,,ENST00000554892,;AP1G2,downstream_gene_variant,,ENST00000557619,;AP1G2,downstream_gene_variant,,ENST00000555974,;AP1G2,downstream_gene_variant,,ENST00000554977,;AP1G2,downstream_gene_variant,,ENST00000557482,;AP1G2,downstream_gene_variant,,ENST00000555896,;AP1G2,downstream_gene_variant,,ENST00000556152,;AP1G2,downstream_gene_variant,,ENST00000553629,;	-	ENSG00000213983	ENST00000308724	Transcript	inframe_deletion	2382-2384	1626-1628	542-543	NN/N	aaCAAc/aac	rs772214302	.	.	-1	AP1G2	HGNC	556	protein_coding	YES	CCDS9602.1	ENSP00000312442	AP1G2_HUMAN	Q86U41_HUMAN,Q86U03_HUMAN,G3V532_HUMAN,G3V3Z2_HUMAN,G3V2V9_HUMAN	UPI0000124FE8	.	.	.	15/21	.	hmmpanther:PTHR22780:SF22,hmmpanther:PTHR22780,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037094,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTTACTTGTTGTC	byFrequency|byCluster	3	ESCA
AP1G2	0	.	GRCh37	14	24035498	24035498	+	Missense_Mutation	SNP	C	C	T	rs748909761	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460G>A	p.Val154Met	p.V154M	ENST00000308724	3/21	49	35	14	41	41	0	AP1G2,missense_variant,p.Val154Met,ENST00000308724,;AP1G2,missense_variant,p.Val154Met,ENST00000557189,;AP1G2,missense_variant,p.Val154Met,ENST00000397120,;AP1G2,downstream_gene_variant,,ENST00000556843,;JPH4,downstream_gene_variant,,ENST00000544177,;AP1G2,upstream_gene_variant,,ENST00000554477,;JPH4,downstream_gene_variant,,ENST00000397118,;JPH4,downstream_gene_variant,,ENST00000356300,;RP11-66N24.3,non_coding_transcript_exon_variant,,ENST00000555968,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000555118,;AP1G2,upstream_gene_variant,,ENST00000555510,;AP1G2,3_prime_UTR_variant,,ENST00000556943,;AP1G2,3_prime_UTR_variant,,ENST00000553756,;AP1G2,non_coding_transcript_exon_variant,,ENST00000554069,;AP1G2,non_coding_transcript_exon_variant,,ENST00000554312,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556743,;AP1G2,non_coding_transcript_exon_variant,,ENST00000535852,;AP1G2,non_coding_transcript_exon_variant,,ENST00000460049,;AP1G2,non_coding_transcript_exon_variant,,ENST00000557619,;AP1G2,non_coding_transcript_exon_variant,,ENST00000557482,;AP1G2,non_coding_transcript_exon_variant,,ENST00000555896,;AP1G2,non_coding_transcript_exon_variant,,ENST00000553629,;AP1G2,non_coding_transcript_exon_variant,,ENST00000465445,;AP1G2,upstream_gene_variant,,ENST00000556741,;AP1G2,upstream_gene_variant,,ENST00000555789,;AP1G2,downstream_gene_variant,,ENST00000553685,;AP1G2,downstream_gene_variant,,ENST00000554816,;AP1G2,upstream_gene_variant,,ENST00000557132,;AP1G2,upstream_gene_variant,,ENST00000557162,;AP1G2,upstream_gene_variant,,ENST00000555974,;AP1G2,upstream_gene_variant,,ENST00000554977,;AP1G2,upstream_gene_variant,,ENST00000554554,;AP1G2,upstream_gene_variant,,ENST00000556966,;AP1G2,upstream_gene_variant,,ENST00000554982,;AP1G2,upstream_gene_variant,,ENST00000556152,;	T	ENSG00000213983	ENST00000308724	Transcript	missense_variant	1216	460	154	V/M	Gtg/Atg	rs748909761,COSM3980104	.	.	-1	AP1G2	HGNC	556	protein_coding	YES	CCDS9602.1	ENSP00000312442	AP1G2_HUMAN	Q86U41_HUMAN,Q86U03_HUMAN,G3V532_HUMAN,G3V3Z2_HUMAN,G3V2V9_HUMAN	UPI0000124FE8	.	deleterious(0.02)	probably_damaging(0.953)	3/21	.	hmmpanther:PTHR22780:SF22,hmmpanther:PTHR22780,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037094,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCACGTAGG	byFrequency	5	ESCA
SEC23A	0	.	GRCh37	14	39532558	39532558	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1368C>T	p.%3D	p.T456T	ENST00000307712	12/20	51	39	12	53	53	0	SEC23A,synonymous_variant,p.%3D,ENST00000307712,;SEC23A,synonymous_variant,p.%3D,ENST00000536508,;SEC23A,synonymous_variant,p.%3D,ENST00000545328,;SEC23A,synonymous_variant,p.%3D,ENST00000537403,;SEC23A,downstream_gene_variant,,ENST00000553925,;	A	ENSG00000100934	ENST00000307712	Transcript	synonymous_variant	1886	1368	456	T	acC/acT	.	.	.	-1	SEC23A	HGNC	10701	protein_coding	YES	CCDS9668.1	ENSP00000306881	SC23A_HUMAN	G3V5K1_HUMAN,G3V3G5_HUMAN,G3V2R6_HUMAN,B3KXI2_HUMAN	UPI000013EC46	.	.	.	12/20	.	hmmpanther:PTHR11141,hmmpanther:PTHR11141:SF5,Pfam_domain:PF08033,Gene3D:2nutA01,Superfamily_domains:SSF81995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTAAGGTTGT	.	5	ESCA
C14orf39	0	.	GRCh37	14	60903487	60903487	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*76A>G	.	.	ENST00000321731	18/18	23	17	6	15	15	0	C14orf39,3_prime_UTR_variant,,ENST00000321731,;C14orf39,3_prime_UTR_variant,,ENST00000557138,;C14orf39,intron_variant,,ENST00000498565,;	C	ENSG00000179008	ENST00000321731	Transcript	3_prime_UTR_variant	2000	.	.	.	.	.	.	.	-1	C14orf39	HGNC	19849	protein_coding	YES	CCDS9746.1	ENSP00000324920	S6OS1_HUMAN	G3V493_HUMAN,G3V3U9_HUMAN	UPI0000140C15	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCATGTTTT	.	5	ESCA
RGS6	0	.	GRCh37	14	72939647	72939647	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.604G>A	p.Val202Ile	p.V202I	ENST00000553525	9/18	54	48	6	37	37	0	RGS6,missense_variant,p.Val202Ile,ENST00000406236,;RGS6,missense_variant,p.Val202Ile,ENST00000553530,;RGS6,missense_variant,p.Val202Ile,ENST00000553525,;RGS6,missense_variant,p.Val202Ile,ENST00000556437,;RGS6,missense_variant,p.Val63Ile,ENST00000554782,;RGS6,missense_variant,p.Val202Ile,ENST00000407322,;RGS6,missense_variant,p.Val202Ile,ENST00000555571,;RGS6,missense_variant,p.Val202Ile,ENST00000355512,;RGS6,missense_variant,p.Val202Ile,ENST00000404301,;RGS6,missense_variant,p.Val133Ile,ENST00000434263,;RGS6,missense_variant,p.Val202Ile,ENST00000343854,;RGS6,missense_variant,p.Val202Ile,ENST00000402788,;RGS6,non_coding_transcript_exon_variant,,ENST00000555368,;RGS6,non_coding_transcript_exon_variant,,ENST00000553690,;RGS6,missense_variant,p.Val202Ile,ENST00000554474,;RGS6,upstream_gene_variant,,ENST00000554734,;	A	ENSG00000182732	ENST00000553525	Transcript	missense_variant	1127	604	202	V/I	Gtc/Atc	.	.	.	1	RGS6	HGNC	10002	protein_coding	YES	CCDS55924.1	ENSP00000451030	RGS6_HUMAN	Q59FJ8_HUMAN	UPI00001698D0	.	deleterious(0)	benign(0.338)	9/18	.	hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGATGTCCAC	.	4	ESCA
SLC12A6	0	.	GRCh37	15	34525808	34525810	+	3'UTR	DEL	TTA	TTA	-	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	TTA	TTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*272_*274delTAA	.	.	ENST00000354181	26/26	31	15	16	20	20	0	SLC12A6,3_prime_UTR_variant,,ENST00000560611,;SLC12A6,3_prime_UTR_variant,,ENST00000397702,;SLC12A6,3_prime_UTR_variant,,ENST00000560164,;SLC12A6,3_prime_UTR_variant,,ENST00000354181,;SLC12A6,3_prime_UTR_variant,,ENST00000458406,;SLC12A6,3_prime_UTR_variant,,ENST00000397707,;SLC12A6,3_prime_UTR_variant,,ENST00000290209,;SLC12A6,3_prime_UTR_variant,,ENST00000451844,;SLC12A6,downstream_gene_variant,,ENST00000558589,;EMC4,downstream_gene_variant,,ENST00000267750,;EMC4,downstream_gene_variant,,ENST00000559421,;EMC4,downstream_gene_variant,,ENST00000249209,;EMC4,downstream_gene_variant,,ENST00000557879,;EMC4,downstream_gene_variant,,ENST00000560947,;SLC12A6,downstream_gene_variant,,ENST00000558667,;EMC4,downstream_gene_variant,,ENST00000559078,;SLC12A6,3_prime_UTR_variant,,ENST00000559664,;SLC12A6,3_prime_UTR_variant,,ENST00000561080,;SLC12A6,3_prime_UTR_variant,,ENST00000559523,;SLC12A6,downstream_gene_variant,,ENST00000559076,;SLC12A6,downstream_gene_variant,,ENST00000559441,;SLC12A6,downstream_gene_variant,,ENST00000558950,;EMC4,downstream_gene_variant,,ENST00000558102,;EMC4,downstream_gene_variant,,ENST00000558205,;EMC4,downstream_gene_variant,,ENST00000561246,;	-	ENSG00000140199	ENST00000354181	Transcript	3_prime_UTR_variant	4218-4220	.	.	.	.	.	.	.	-1	SLC12A6	HGNC	10914	protein_coding	YES	CCDS58352.1	ENSP00000346112	S12A6_HUMAN	H0YNJ5_HUMAN,H0YKL8_HUMAN,H0YKJ2_HUMAN,H0YKE6_HUMAN	UPI0000135427	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	AGCTTGTTAATTCT	.	2	ESCA
HYPK	0	.	GRCh37	15	44092665	44092665	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-104-28G>A	.	.	ENST00000406925	.	34	27	7	21	21	0	HYPK,5_prime_UTR_variant,,ENST00000442995,;SERF2,5_prime_UTR_variant,,ENST00000600633,;SERF2,intron_variant,,ENST00000594896,;HYPK,intron_variant,,ENST00000406925,;SERF2,downstream_gene_variant,,ENST00000430901,;HYPK,upstream_gene_variant,,ENST00000458412,;SERINC4,upstream_gene_variant,,ENST00000249714,;SERINC4,upstream_gene_variant,,ENST00000299969,;SERINC4,upstream_gene_variant,,ENST00000319327,;SERF2,downstream_gene_variant,,ENST00000409646,;SERF2,downstream_gene_variant,,ENST00000409291,;MFAP1,downstream_gene_variant,,ENST00000267812,;HYPK,non_coding_transcript_exon_variant,,ENST00000498605,;HYPK,upstream_gene_variant,,ENST00000497142,;SERF2,3_prime_UTR_variant,,ENST00000448830,;SERF2,intron_variant,,ENST00000409617,;MFAP1,downstream_gene_variant,,ENST00000484386,;SERINC4,upstream_gene_variant,,ENST00000412697,;RP11-296A16.1,upstream_gene_variant,,ENST00000417761,;SERF2,downstream_gene_variant,,ENST00000445816,;SERINC4,upstream_gene_variant,,ENST00000457418,;SERINC4,upstream_gene_variant,,ENST00000476490,;SERINC4,upstream_gene_variant,,ENST00000448553,;	A	ENSG00000242028	ENST00000406925	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	HYPK	HGNC	18418	protein_coding	YES	CCDS10104.1	ENSP00000384474	HYPK_HUMAN	.	UPI000000D937	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTGAGAGA	.	5	ESCA
LDHAL6B	0	.	GRCh37	15	59499600	59499600	+	Missense_Mutation	SNP	C	C	T	rs756211974	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.461C>T	p.Thr154Met	p.T154M	ENST00000307144	1/1	80	65	15	51	51	0	LDHAL6B,missense_variant,p.Thr154Met,ENST00000307144,;MYO1E,intron_variant,,ENST00000559269,;MYO1E,intron_variant,,ENST00000560749,;MYO1E,intron_variant,,ENST00000288235,;MYO1E,downstream_gene_variant,,ENST00000559489,;MYO1E,upstream_gene_variant,,ENST00000558182,;MYO1E,intron_variant,,ENST00000560642,;	T	ENSG00000171989	ENST00000307144	Transcript	missense_variant	559	461	154	T/M	aCg/aTg	rs756211974	.	.	1	LDHAL6B	HGNC	21481	protein_coding	YES	CCDS10171.1	ENSP00000302393	LDH6B_HUMAN	.	UPI000012E326	.	deleterious(0.02)	probably_damaging(0.976)	1/1	.	HAMAP:MF_00488,hmmpanther:PTHR11540,hmmpanther:PTHR11540:SF11,Gene3D:3.40.50.720,Pfam_domain:PF00056,TIGRFAM_domain:TIGR01771,PIRSF_domain:PIRSF000102,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAACGCGCC	byFrequency	5	ESCA
RP11-114H24.7	0	.	GRCh37	15	78217292	78217292	+	3'Flank	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000565869	.	113	64	49	91	91	0	RP11-114H24.7,downstream_gene_variant,,ENST00000565869,;RP11-114H24.2,non_coding_transcript_exon_variant,,ENST00000567226,;RP11-114H24.2,non_coding_transcript_exon_variant,,ENST00000562938,;	A	ENSG00000261244	ENST00000565869	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2931	1	RP11-114H24.7	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGTGGCAAC	.	5	ESCA
GNPTG	0	.	GRCh37	16	1402138	1402138	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88G>A	p.Val30Met	p.V30M	ENST00000204679	2/11	23	14	9	18	18	0	GNPTG,missense_variant,p.Val53Met,ENST00000529110,;GNPTG,missense_variant,p.Val30Met,ENST00000204679,;TSR3,upstream_gene_variant,,ENST00000007390,;BAIAP3,downstream_gene_variant,,ENST00000421665,;BAIAP3,downstream_gene_variant,,ENST00000568887,;BAIAP3,downstream_gene_variant,,ENST00000397488,;BAIAP3,downstream_gene_variant,,ENST00000561793,;BAIAP3,downstream_gene_variant,,ENST00000426824,;BAIAP3,downstream_gene_variant,,ENST00000562208,;BAIAP3,downstream_gene_variant,,ENST00000566162,;BAIAP3,downstream_gene_variant,,ENST00000324385,;BAIAP3,downstream_gene_variant,,ENST00000397489,;BAIAP3,downstream_gene_variant,,ENST00000564213,;GNPTG,missense_variant,p.Val30Met,ENST00000526820,;GNPTG,missense_variant,p.Val30Met,ENST00000527876,;GNPTG,non_coding_transcript_exon_variant,,ENST00000527168,;GNPTG,non_coding_transcript_exon_variant,,ENST00000529957,;GNPTG,non_coding_transcript_exon_variant,,ENST00000527137,;GNPTG,non_coding_transcript_exon_variant,,ENST00000534197,;BAIAP3,downstream_gene_variant,,ENST00000566389,;TSR3,upstream_gene_variant,,ENST00000566296,;	A	ENSG00000090581	ENST00000204679	Transcript	missense_variant	131	88	30	V/M	Gtg/Atg	.	.	.	1	GNPTG	HGNC	23026	protein_coding	YES	CCDS10436.1	ENSP00000204679	GNPTG_HUMAN	Q96RZ2_HUMAN	UPI0000073F3C	.	deleterious(0)	probably_damaging(0.992)	2/11	.	hmmpanther:PTHR12630,hmmpanther:PTHR12630:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGGTGGAG	.	5	ESCA
CNOT1	0	.	GRCh37	16	58577404	58577404	+	Intron	SNP	T	T	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4434+107A>C	.	.	ENST00000317147	.	34	27	6	27	27	0	CNOT1,missense_variant,p.Asn1514Thr,ENST00000441024,;CNOT1,intron_variant,,ENST00000317147,;CNOT1,intron_variant,,ENST00000569240,;CNOT1,intron_variant,,ENST00000245138,;CNOT1,downstream_gene_variant,,ENST00000567285,;CNOT1,upstream_gene_variant,,ENST00000568917,;CNOT1,downstream_gene_variant,,ENST00000567133,;SNORA46,downstream_gene_variant,,ENST00000384762,;CNOT1,intron_variant,,ENST00000566240,;CNOT1,intron_variant,,ENST00000567188,;CNOT1,upstream_gene_variant,,ENST00000563283,;	G	ENSG00000125107	ENST00000317147	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CNOT1	HGNC	7877	protein_coding	YES	CCDS10799.1	ENSP00000320949	CNOT1_HUMAN	H3BUY8_HUMAN,H3BT18_HUMAN,H3BPF1_HUMAN,B7Z6X2_HUMAN,B3KS60_HUMAN	UPI00001FF2F6	.	.	.	.	31/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GATTATTAAGA	.	3	ESCA
PDPR	0	.	GRCh37	16	70190707	70190707	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2565C>G	p.%3D	p.L855L	ENST00000288050	19/19	134	119	15	101	101	0	PDPR,synonymous_variant,p.%3D,ENST00000542659,;PDPR,synonymous_variant,p.%3D,ENST00000288050,;PDPR,synonymous_variant,p.%3D,ENST00000398122,;PDPR,synonymous_variant,p.%3D,ENST00000568530,;PDPR,synonymous_variant,p.%3D,ENST00000567046,;PDPR,downstream_gene_variant,,ENST00000563930,;PDPR,downstream_gene_variant,,ENST00000569042,;PDPR,downstream_gene_variant,,ENST00000567896,;RP11-296I10.3,intron_variant,,ENST00000566989,;RP11-296I10.3,downstream_gene_variant,,ENST00000502126,;PDPR,non_coding_transcript_exon_variant,,ENST00000562100,;PDPR,3_prime_UTR_variant,,ENST00000565186,;PDPR,3_prime_UTR_variant,,ENST00000564563,;	G	ENSG00000090857	ENST00000288050	Transcript	synonymous_variant	3522	2565	855	L	ctC/ctG	.	.	.	1	PDPR	HGNC	30264	protein_coding	YES	CCDS45520.1	ENSP00000288050	PDPR_HUMAN	H3BV59_HUMAN,H3BU60_HUMAN,B7ZAR9_HUMAN,B3KSE1_HUMAN,A8MT40_HUMAN	UPI00001FF513	.	.	.	19/19	.	Superfamily_domains:SSF101790	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCTCTACCC	.	4	ESCA
CLEC3A	0	.	GRCh37	16	78062008	78062008	+	Missense_Mutation	SNP	G	G	T	rs757280362	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147G>T	p.Lys49Asn	p.K49N	ENST00000299642	2/3	48	35	12	28	28	0	CLEC3A,missense_variant,p.Lys40Asn,ENST00000575655,;CLEC3A,missense_variant,p.Lys49Asn,ENST00000299642,;RP11-281J9.2,intron_variant,,ENST00000563114,;CLEC3A,upstream_gene_variant,,ENST00000565808,;CLEC3A,intron_variant,,ENST00000567430,;	T	ENSG00000166509	ENST00000299642	Transcript	missense_variant	232	147	49	K/N	aaG/aaT	rs757280362	.	.	1	CLEC3A	HGNC	2052	protein_coding	YES	CCDS10927.2	ENSP00000299642	.	J3KNC9_HUMAN	UPI00001FFC6A	.	tolerated(0.1)	benign(0.009)	2/3	.	hmmpanther:PTHR22799,hmmpanther:PTHR22799:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACAAGGATGG	byFrequency	5	ESCA
MSLNL	0	.	GRCh37	16	820093	820093	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2892C>T	p.%3D	p.H964H	ENST00000293892	15/16	25	13	12	20	20	0	MSLNL,synonymous_variant,p.%3D,ENST00000442466,;MSLNL,synonymous_variant,p.%3D,ENST00000543963,;MSLNL,synonymous_variant,p.%3D,ENST00000293892,;MSLN,downstream_gene_variant,,ENST00000382862,;MSLN,downstream_gene_variant,,ENST00000566269,;MSLN,downstream_gene_variant,,ENST00000569566,;MSLN,downstream_gene_variant,,ENST00000563651,;MSLN,downstream_gene_variant,,ENST00000561896,;MSLN,downstream_gene_variant,,ENST00000566549,;MSLN,downstream_gene_variant,,ENST00000563941,;MSLN,downstream_gene_variant,,ENST00000545450,;MIR662,upstream_gene_variant,,ENST00000384847,;MSLNL,downstream_gene_variant,,ENST00000537221,;	A	ENSG00000162006	ENST00000293892	Transcript	synonymous_variant	2892	2892	964	H	caC/caT	.	.	.	-1	MSLNL	HGNC	14170	protein_coding	YES	.	ENSP00000293892	MSLNL_HUMAN	.	UPI0000072242	.	.	.	15/16	.	hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTGGTGGGT	.	5	ESCA
CDH15	0	.	GRCh37	16	89261646	89261646	+	3'UTR	SNP	C	C	T	rs759711205	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*83C>T	.	.	ENST00000289746	14/14	10	7	3	9	9	0	CDH15,3_prime_UTR_variant,,ENST00000289746,;SLC22A31,downstream_gene_variant,,ENST00000562855,;SLC22A31,downstream_gene_variant,,ENST00000603735,;SLC22A31,downstream_gene_variant,,ENST00000562916,;SLC22A31,downstream_gene_variant,,ENST00000568161,;SLC22A31,downstream_gene_variant,,ENST00000563595,;	T	ENSG00000129910	ENST00000289746	Transcript	3_prime_UTR_variant	2593	.	.	.	.	rs759711205	.	.	1	CDH15	HGNC	1754	protein_coding	YES	CCDS10976.1	ENSP00000289746	CAD15_HUMAN	.	UPI0000126DAF	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCCCGACCC	.	2	ESCA
PIGS	0	.	GRCh37	17	26883215	26883215	+	Nonsense_Mutation	SNP	G	G	A	rs762251130	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150C>T	p.Arg384Ter	p.R384*	ENST00000308360	10/12	80	69	10	74	74	0	PIGS,stop_gained,p.Arg376Ter,ENST00000395346,;PIGS,stop_gained,p.Arg384Ter,ENST00000308360,;PIGS,stop_gained,p.Arg323Ter,ENST00000543734,;UNC119,upstream_gene_variant,,ENST00000335765,;UNC119,upstream_gene_variant,,ENST00000484980,;UNC119,upstream_gene_variant,,ENST00000301032,;UNC119,upstream_gene_variant,,ENST00000581945,;UNC119,upstream_gene_variant,,ENST00000444148,;PIGS,downstream_gene_variant,,ENST00000465444,;PIGS,downstream_gene_variant,,ENST00000580968,;PIGS,3_prime_UTR_variant,,ENST00000268758,;PIGS,non_coding_transcript_exon_variant,,ENST00000492429,;PIGS,non_coding_transcript_exon_variant,,ENST00000487231,;RP11-192H23.4,intron_variant,,ENST00000481916,;UNC119,upstream_gene_variant,,ENST00000578434,;PIGS,downstream_gene_variant,,ENST00000484580,;PIGS,downstream_gene_variant,,ENST00000584080,;PIGS,downstream_gene_variant,,ENST00000582615,;PIGS,downstream_gene_variant,,ENST00000577620,;	A	ENSG00000087111	ENST00000308360	Transcript	stop_gained	1526	1150	384	R/*	Cga/Tga	rs762251130	.	.	-1	PIGS	HGNC	14937	protein_coding	YES	CCDS11235.1	ENSP00000309430	PIGS_HUMAN	Q9BVC1_HUMAN,Q96IR5_HUMAN,F5H019_HUMAN	UPI000013D7D9	.	.	.	10/12	.	Pfam_domain:PF10510,hmmpanther:PTHR21072,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACTCGCACCA	byFrequency	4	ESCA
KCNH4	0	.	GRCh37	17	40321669	40321669	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1416G>C	p.%3D	p.G472G	ENST00000264661	9/17	75	26	49	61	61	0	KCNH4,synonymous_variant,p.%3D,ENST00000264661,;KCNH4,synonymous_variant,p.%3D,ENST00000607371,;	G	ENSG00000089558	ENST00000264661	Transcript	synonymous_variant	1749	1416	472	G	ggG/ggC	.	.	.	-1	KCNH4	HGNC	6253	protein_coding	YES	CCDS11420.1	ENSP00000264661	KCNH4_HUMAN	.	UPI000012DCA8	.	.	.	9/17	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF378,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR01463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTTCCCGAA	.	5	ESCA
DCAF7	0	.	GRCh37	17	61671337	61671337	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000415273	.	34	11	22	25	25	0	DCAF7,3_prime_UTR_variant,,ENST00000310827,;DCAF7,downstream_gene_variant,,ENST00000431926,;DCAF7,downstream_gene_variant,,ENST00000415273,;DCAF7,non_coding_transcript_exon_variant,,ENST00000577702,;DCAF7,intron_variant,,ENST00000580091,;DCAF7,intron_variant,,ENST00000582103,;	T	ENSG00000136485	ENST00000415273	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4190	1	DCAF7	HGNC	30915	protein_coding	YES	.	ENSP00000403920	.	B4E039_HUMAN	UPI00017A838F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCCTTGCA	.	5	ESCA
EIF5A	0	.	GRCh37	17	7211849	7211849	+	Intron	SNP	A	A	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70-1085A>T	.	.	ENST00000336452	.	101	76	24	80	80	0	EIF5A,5_prime_UTR_variant,,ENST00000571955,;EIF5A,5_prime_UTR_variant,,ENST00000576930,;EIF5A,5_prime_UTR_variant,,ENST00000416016,;EIF5A,intron_variant,,ENST00000336458,;EIF5A,intron_variant,,ENST00000336452,;EIF5A,intron_variant,,ENST00000572815,;EIF5A,intron_variant,,ENST00000573542,;EIF5A,intron_variant,,ENST00000419711,;EIF5A,intron_variant,,ENST00000573714,;GPS2,downstream_gene_variant,,ENST00000574458,;GPS2,downstream_gene_variant,,ENST00000573684,;GPS2,downstream_gene_variant,,ENST00000380728,;GPS2,downstream_gene_variant,,ENST00000570780,;GPS2,downstream_gene_variant,,ENST00000577040,;GPS2,downstream_gene_variant,,ENST00000391950,;GPS2,downstream_gene_variant,,ENST00000389167,;EIF5A,intron_variant,,ENST00000575001,;EIF5A,intron_variant,,ENST00000355068,;RP11-542C16.2,downstream_gene_variant,,ENST00000315601,;GPS2,downstream_gene_variant,,ENST00000571569,;GPS2,downstream_gene_variant,,ENST00000571697,;GPS2,downstream_gene_variant,,ENST00000572172,;GPS2,downstream_gene_variant,,ENST00000573807,;GPS2,downstream_gene_variant,,ENST00000572363,;RP11-542C16.2,downstream_gene_variant,,ENST00000575474,;	T	ENSG00000132507	ENST00000336452	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	EIF5A	HGNC	3300	protein_coding	YES	CCDS45601.1	ENSP00000336702	IF5A1_HUMAN	I3L397_HUMAN	UPI00001B5C0C	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGAGCTTT	.	5	ESCA
RECQL5	0	.	GRCh37	17	73621887	73621887	+	3'Flank	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000317905	.	46	39	7	35	35	0	RECQL5,downstream_gene_variant,,ENST00000423245,;RECQL5,downstream_gene_variant,,ENST00000317905,;RECQL5,downstream_gene_variant,,ENST00000580707,;RECQL5,downstream_gene_variant,,ENST00000582548,;RECQL5,downstream_gene_variant,,ENST00000581825,;MYO15B,non_coding_transcript_exon_variant,,ENST00000578382,;MYO15B,intron_variant,,ENST00000580262,;MYO15B,intron_variant,,ENST00000580414,;MYO15B,downstream_gene_variant,,ENST00000577948,;RECQL5,downstream_gene_variant,,ENST00000443199,;MYO15B,downstream_gene_variant,,ENST00000580096,;MYO15B,downstream_gene_variant,,ENST00000583140,;MYO15B,downstream_gene_variant,,ENST00000578220,;MYO15B,downstream_gene_variant,,ENST00000577296,;MYO15B,downstream_gene_variant,,ENST00000582597,;MYO15B,downstream_gene_variant,,ENST00000579052,;MYO15B,downstream_gene_variant,,ENST00000577986,;RECQL5,downstream_gene_variant,,ENST00000585205,;RECQL5,downstream_gene_variant,,ENST00000579265,;MYO15B,downstream_gene_variant,,ENST00000577613,;RECQL5,downstream_gene_variant,,ENST00000578865,;MYO15B,downstream_gene_variant,,ENST00000579048,;	A	ENSG00000108469	ENST00000317905	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1047	-1	RECQL5	HGNC	9950	protein_coding	YES	CCDS42380.1	ENSP00000317636	RECQ5_HUMAN	Q9BW80_HUMAN,Q9BSD6_HUMAN,J3QLU0_HUMAN,J3KTQ2_HUMAN	UPI0000133477	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCAGCAGTCA	.	4	ESCA
TP53	0	.	GRCh37	17	7578547	7578547	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383delC	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	5/11	59	35	24	25	25	0	TP53,frameshift_variant,p.Pro128LeufsTer?,ENST00000508793,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000413465,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000420246,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000269305,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000359597,;TP53,frameshift_variant,p.Pro35LeufsTer42,ENST00000514944,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000445888,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000455263,;TP53,incomplete_terminal_codon_variant,p.%3D,ENST00000503591,;TP53,5_prime_UTR_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	573	383	128	P/X	cCt/ct	TP53_g.12371C>T,TP53_g.12371C>G,COSM45131	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.Y126_K132delYSPALNK|c.376_396del21|6,CODON|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.N131delN|c.393_395delCAA|4,BUFFER|p.K132R|c.395A>G|5,BUFFER|p.K132T|c.395A>C|7,BUFFER|p.K39T|c.116A>C|3,BUFFER|p.K132R|c.395A>G|39,BUFFER|p.K132M|c.395A>T|10,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K39R|c.116A>G|7,BUFFER|p.K132Q|c.394A>C|13,BUFFER|p.K39E|c.115A>G|3,BUFFER|p.K132*|c.394A>T|5,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|19,BUFFER|p.N131delN|c.391_393delAAC|8,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131I|c.392A>T|7,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131S|c.392A>G|5,BUFFER|p.N38I|c.113A>T|3,BUFFER|p.N131Y|c.391A>T|8,BUFFER|p.L130L|c.390C>T|4,BUFFER|p.L130H|c.389T>A|5,BUFFER|p.L130P|c.389T>C|5,BUFFER|p.L130R|c.389T>G|8,BUFFER|p.L130F|c.388C>T|13,BUFFER|p.L130V|c.388C>G|5,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L130V|c.388C>G|3,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L37F|c.109C>T|7,BUFFER|p.L130F|c.388C>T|3,BUFFER|p.L130V|c.388C>G|5,BUFFER|p.L37V|c.109C>G|5,BUFFER|p.L130F|c.388C>T|4,BUFFER|p.L130V|c.388C>G|15,BUFFER|p.P128L|c.383C>T|3,BUFFER|p.P128fs*42|c.382delC|3,BUFFER|p.P128S|c.382C>T|7,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S127Y|c.380C>A|10,BUFFER|p.S34F|c.101C>T|11,BUFFER|p.S127F|c.380C>T|4,BUFFER|p.S127F|c.380C>T|33,BUFFER|p.S127F|c.380C>T|3,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S34P|c.100T>C|4,BUFFER|p.S34T|c.100T>A|4,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.S127P|c.379T>C|8,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127T|c.379T>A|10,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>G|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>A|4,BUFFER|p.Y33*|c.99C>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y33C|c.98A>G|6,BUFFER|p.Y126C|c.377A>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y126C|c.377A>G|9,BUFFER|p.Y126S|c.377A>C|3,BUFFER|p.Y126C|c.377A>G|5,BUFFER|p.Y126N|c.376T>A|7,BUFFER|p.Y33D|c.97T>G|7,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.Y126D|c.376T>G|10,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.?|c.97-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|10,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.97-1G>A|20,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>T|9,BUFFER|p.?|c.376-2A>G|4,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.97-2A>T|3,BUFFER|p.?|c.97-2A>G|10,BUFFER|p.?|c.376-2A>G|17,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-2A>G|6,BUFFER|p.?|c.376-2A>C|4,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-4A>G|3	INDELOCATOR*|VARSCANI*|PINDEL	AGGGCAGGGGAG	.	3	ESCA
DNAH2	0	.	GRCh37	17	7658190	7658190	+	Intron	SNP	G	G	A	rs150770956	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1905-2219G>A	.	.	ENST00000572933	.	37	27	10	24	24	0	DNAH2,intron_variant,,ENST00000389173,;DNAH2,intron_variant,,ENST00000572933,;RPL29P2,non_coding_transcript_exon_variant,,ENST00000498671,;RPL29P2,downstream_gene_variant,,ENST00000488409,;	A	ENSG00000183914	ENST00000572933	Transcript	intron_variant	.	.	.	.	.	rs150770956	.	.	1	DNAH2	HGNC	2948	protein_coding	YES	CCDS32551.1	ENSP00000458355	DYH2_HUMAN	.	UPI00005B2F0D	.	.	.	.	12/85	.	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAACGTGAGG	by1000G	5	ESCA
DNAH2	0	.	GRCh37	17	7669692	7669692	+	Missense_Mutation	SNP	C	C	T	rs138479117	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3568C>T	p.Arg1190Trp	p.R1190W	ENST00000572933	22/86	41	18	22	20	20	0	DNAH2,missense_variant,p.Arg1190Trp,ENST00000389173,;DNAH2,missense_variant,p.Arg1190Trp,ENST00000572933,;DNAH2,intron_variant,,ENST00000574518,;	T	ENSG00000183914	ENST00000572933	Transcript	missense_variant	5028	3568	1190	R/W	Cgg/Tgg	rs138479117,COSM985179	.	.	1	DNAH2	HGNC	2948	protein_coding	YES	CCDS32551.1	ENSP00000458355	DYH2_HUMAN	.	UPI00005B2F0D	.	.	probably_damaging(0.945)	22/86	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0002	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTGCGGGCC	byCluster|by1000G	4	ESCA
SPDYE4	0	.	GRCh37	17	8658868	8658868	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455A>G	p.Gln152Arg	p.Q152R	ENST00000328794	4/6	230	83	147	174	174	0	SPDYE4,missense_variant,p.Gln81Arg,ENST00000580999,;SPDYE4,missense_variant,p.Gln152Arg,ENST00000328794,;SPDYE4,3_prime_UTR_variant,,ENST00000582989,;	C	ENSG00000183318	ENST00000328794	Transcript	missense_variant	632	455	152	Q/R	cAa/cGa	.	.	.	-1	SPDYE4	HGNC	35463	protein_coding	YES	CCDS45609.1	ENSP00000329522	SPDE4_HUMAN	.	UPI0000DD83CC	.	tolerated(0.1)	benign(0.21)	4/6	.	hmmpanther:PTHR31156:SF9,hmmpanther:PTHR31156,Pfam_domain:PF11357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTATTGCCAC	.	5	ESCA
DTNA	0	.	GRCh37	18	32470965	32470965	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*561G>A	.	.	ENST00000598334	20/20	40	25	14	42	42	0	DTNA,3_prime_UTR_variant,,ENST00000444659,;DTNA,3_prime_UTR_variant,,ENST00000269190,;DTNA,3_prime_UTR_variant,,ENST00000399121,;DTNA,3_prime_UTR_variant,,ENST00000598334,;DTNA,3_prime_UTR_variant,,ENST00000595022,;DTNA,3_prime_UTR_variant,,ENST00000283365,;DTNA,3_prime_UTR_variant,,ENST00000399097,;DTNA,downstream_gene_variant,,ENST00000590831,;DTNA,downstream_gene_variant,,ENST00000556414,;DTNA,downstream_gene_variant,,ENST00000591182,;DTNA,downstream_gene_variant,,ENST00000598142,;DTNA,downstream_gene_variant,,ENST00000269192,;DTNA,downstream_gene_variant,,ENST00000601125,;DTNA,non_coding_transcript_exon_variant,,ENST00000592449,;	A	ENSG00000134769	ENST00000598334	Transcript	3_prime_UTR_variant	3062	.	.	.	.	.	.	.	1	DTNA	HGNC	3057	protein_coding	YES	CCDS59312.1	ENSP00000470152	.	M0QYX6_HUMAN,K7ERZ2_HUMAN,K7ERH7_HUMAN,K7ER73_HUMAN,K7ENJ7_HUMAN,K7EMN1_HUMAN,K7EJ84_HUMAN	UPI0001E92A2F	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCGATTCC	.	5	ESCA
C19orf66	0	.	GRCh37	19	10200373	10200373	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234+2T>C	.	p.X78_splice	ENST00000253110	.	37	17	19	34	34	0	C19orf66,splice_donor_variant,,ENST00000593131,;C19orf66,splice_donor_variant,,ENST00000591813,;C19orf66,splice_donor_variant,,ENST00000590378,;C19orf66,splice_donor_variant,,ENST00000397881,;C19orf66,splice_donor_variant,,ENST00000253110,;ANGPTL6,downstream_gene_variant,,ENST00000253109,;ANGPTL6,downstream_gene_variant,,ENST00000589181,;ANGPTL6,downstream_gene_variant,,ENST00000592641,;CTD-2240E14.4,non_coding_transcript_exon_variant,,ENST00000589622,;C19orf66,splice_donor_variant,,ENST00000585919,;C19orf66,splice_donor_variant,,ENST00000587609,;C19orf66,splice_donor_variant,,ENST00000586889,;C19orf66,splice_donor_variant,,ENST00000587710,;ANGPTL6,downstream_gene_variant,,ENST00000586910,;C19orf66,upstream_gene_variant,,ENST00000586730,;C19orf66,downstream_gene_variant,,ENST00000592551,;	C	ENSG00000130813	ENST00000253110	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	C19orf66	HGNC	25649	protein_coding	YES	CCDS45957.1	ENSP00000253110	CS066_HUMAN	.	UPI00002032C7	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGGTGAGTT	.	5	ESCA
CARM1	0	.	GRCh37	19	11032856	11032856	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*423G>A	.	.	ENST00000327064	16/16	104	83	21	71	71	0	CARM1,3_prime_UTR_variant,,ENST00000327064,;CARM1,3_prime_UTR_variant,,ENST00000344150,;YIPF2,downstream_gene_variant,,ENST00000585858,;YIPF2,downstream_gene_variant,,ENST00000586575,;YIPF2,downstream_gene_variant,,ENST00000586748,;YIPF2,downstream_gene_variant,,ENST00000591872,;YIPF2,downstream_gene_variant,,ENST00000589971,;YIPF2,downstream_gene_variant,,ENST00000587943,;YIPF2,downstream_gene_variant,,ENST00000588347,;YIPF2,downstream_gene_variant,,ENST00000253031,;YIPF2,downstream_gene_variant,,ENST00000590329,;CARM1,downstream_gene_variant,,ENST00000586298,;YIPF2,downstream_gene_variant,,ENST00000592646,;CARM1,3_prime_UTR_variant,,ENST00000586221,;YIPF2,downstream_gene_variant,,ENST00000588962,;CARM1,downstream_gene_variant,,ENST00000592516,;CARM1,downstream_gene_variant,,ENST00000590699,;CARM1,downstream_gene_variant,,ENST00000586508,;	A	ENSG00000142453	ENST00000327064	Transcript	3_prime_UTR_variant	2440	.	.	.	.	.	.	.	1	CARM1	HGNC	23393	protein_coding	YES	CCDS12250.1	ENSP00000325690	CARM1_HUMAN	.	UPI000004B825	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAACGGACGT	.	5	ESCA
DOCK6	0	.	GRCh37	19	11354034	11354034	+	Missense_Mutation	SNP	C	C	T	rs748891692	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1286G>A	p.Arg429His	p.R429H	ENST00000294618	12/48	76	60	16	54	54	0	DOCK6,missense_variant,p.Arg429His,ENST00000294618,;C19orf80,downstream_gene_variant,,ENST00000252453,;C19orf80,downstream_gene_variant,,ENST00000587543,;C19orf80,downstream_gene_variant,,ENST00000591200,;DOCK6,downstream_gene_variant,,ENST00000585609,;DOCK6,upstream_gene_variant,,ENST00000591750,;	T	ENSG00000130158	ENST00000294618	Transcript	missense_variant	1298	1286	429	R/H	cGc/cAc	rs748891692	.	.	-1	DOCK6	HGNC	19189	protein_coding	YES	CCDS45975.1	ENSP00000294618	DOCK6_HUMAN	.	UPI000059D66F	.	deleterious(0.04)	benign(0.38)	12/48	.	hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACGGCGGCGG	.	5	ESCA
WIZ	0	.	GRCh37	19	15538262	15538262	+	Silent	SNP	G	G	A	rs558510562	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612C>T	p.%3D	p.H204H	ENST00000263381	4/8	69	64	4	92	92	0	WIZ,synonymous_variant,p.%3D,ENST00000545156,;WIZ,synonymous_variant,p.%3D,ENST00000263381,;WIZ,synonymous_variant,p.%3D,ENST00000599686,;WIZ,synonymous_variant,p.%3D,ENST00000389282,;WIZ,synonymous_variant,p.%3D,ENST00000599910,;WIZ,upstream_gene_variant,,ENST00000600632,;	A	ENSG00000011451	ENST00000263381	Transcript	synonymous_variant	826	612	204	H	caC/caT	rs558510562	.	.	-1	WIZ	HGNC	30917	protein_coding	YES	CCDS42516.1	ENSP00000263381	WIZ_HUMAN	M0QXF8_HUMAN	UPI000041F888	.	.	.	4/8	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13894,PROSITE_patterns:PS00028,hmmpanther:PTHR24402:SF162,hmmpanther:PTHR24402,PROSITE_profiles:PS50157	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCGCGTGGCT	by1000G	2	ESCA
NWD1	0	.	GRCh37	19	16860996	16860996	+	Silent	SNP	C	C	T	rs757776142	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1543C>T	p.%3D	p.L515L	ENST00000524140	6/19	37	21	15	36	36	0	NWD1,synonymous_variant,p.%3D,ENST00000339803,;NWD1,synonymous_variant,p.%3D,ENST00000524140,;NWD1,synonymous_variant,p.%3D,ENST00000552788,;NWD1,synonymous_variant,p.%3D,ENST00000379808,;NWD1,synonymous_variant,p.%3D,ENST00000549814,;NWD1,synonymous_variant,p.%3D,ENST00000523826,;NWD1,3_prime_UTR_variant,,ENST00000438489,;NWD1,3_prime_UTR_variant,,ENST00000518676,;	T	ENSG00000188039	ENST00000524140	Transcript	synonymous_variant	1961	1543	515	L	Ctg/Ttg	rs757776142	.	.	1	NWD1	HGNC	27619	protein_coding	YES	CCDS32945.2	ENSP00000428579	NWD1_HUMAN	.	UPI0000D6173E	.	.	.	6/19	.	hmmpanther:PTHR22847:SF273,hmmpanther:PTHR22847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACGCTGAGC	.	5	ESCA
ZNF43	0	.	GRCh37	19	22018958	22018958	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-118G>A	.	.	ENST00000354959	1/4	40	30	9	34	34	0	ZNF43,5_prime_UTR_variant,,ENST00000599906,;ZNF43,5_prime_UTR_variant,,ENST00000354959,;ZNF43,intron_variant,,ENST00000595461,;ZNF43,intron_variant,,ENST00000593551,;ZNF43,intron_variant,,ENST00000598288,;ZNF43,intron_variant,,ENST00000596899,;ZNF43,intron_variant,,ENST00000594012,;ZNF43,intron_variant,,ENST00000598381,;ZNF43,downstream_gene_variant,,ENST00000593886,;	T	ENSG00000198521	ENST00000354959	Transcript	5_prime_UTR_variant	53	.	.	.	.	.	.	.	-1	ZNF43	HGNC	13109	protein_coding	YES	CCDS12413.2	ENSP00000347045	ZNF43_HUMAN	M0R0T7_HUMAN,M0QYJ6_HUMAN,M0QXI2_HUMAN	UPI00001BD957	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGACGCAGA	.	5	ESCA
B3GNT8	0	.	GRCh37	19	41931756	41931756	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.928T>C	p.Tyr310His	p.Y310H	ENST00000321702	3/3	47	26	21	39	39	0	B3GNT8,missense_variant,p.Tyr310His,ENST00000321702,;BCKDHA,downstream_gene_variant,,ENST00000457836,;BCKDHA,downstream_gene_variant,,ENST00000544905,;BCKDHA,downstream_gene_variant,,ENST00000595085,;CTC-435M10.3,downstream_gene_variant,,ENST00000540732,;BCKDHA,downstream_gene_variant,,ENST00000269980,;BCKDHA,downstream_gene_variant,,ENST00000542943,;BCKDHA,downstream_gene_variant,,ENST00000541315,;CTC-435M10.6,intron_variant,,ENST00000598887,;B3GNT8,intron_variant,,ENST00000601616,;B3GNT8,downstream_gene_variant,,ENST00000601379,;BCKDHA,downstream_gene_variant,,ENST00000535632,;BCKDHA,downstream_gene_variant,,ENST00000538423,;BCKDHA,downstream_gene_variant,,ENST00000545787,;	G	ENSG00000177191	ENST00000321702	Transcript	missense_variant	1382	928	310	Y/H	Tac/Cac	.	.	.	-1	B3GNT8	HGNC	24139	protein_coding	YES	CCDS12582.1	ENSP00000312700	B3GN8_HUMAN	.	UPI0000140C01	.	deleterious(0)	probably_damaging(0.999)	3/3	.	Low_complexity_(Seg):seg,Pfam_domain:PF01762,hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF87	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACGTAGCCAC	.	5	ESCA
ZNF526	0	.	GRCh37	19	42730789	42730789	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*221A>G	.	.	ENST00000301215	3/3	30	23	7	30	30	0	ZNF526,3_prime_UTR_variant,,ENST00000301215,;GSK3A,downstream_gene_variant,,ENST00000398249,;GSK3A,downstream_gene_variant,,ENST00000222330,;ZNF526,downstream_gene_variant,,ENST00000597945,;GSK3A,downstream_gene_variant,,ENST00000493059,;GSK3A,downstream_gene_variant,,ENST00000453535,;	G	ENSG00000167625	ENST00000301215	Transcript	3_prime_UTR_variant	2459	.	.	.	.	.	.	.	1	ZNF526	HGNC	29415	protein_coding	YES	CCDS12598.1	ENSP00000301215	ZN526_HUMAN	M0R395_HUMAN,H9ZYJ3_HUMAN	UPI00001C2011	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTGATCTGT	.	5	ESCA
PSG4	0	.	GRCh37	19	43699171	43699171	+	Missense_Mutation	SNP	C	C	T	rs576741968	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964G>A	p.Asp322Asn	p.D322N	ENST00000405312	4/6	237	135	102	170	170	0	PSG4,missense_variant,p.Asp200Asn,ENST00000596907,;PSG4,missense_variant,p.Asp114Asn,ENST00000597374,;PSG4,missense_variant,p.Asp208Asn,ENST00000599746,;PSG4,missense_variant,p.Asp322Asn,ENST00000405312,;PSG4,missense_variant,p.Asp229Asn,ENST00000433626,;PSG4,intron_variant,,ENST00000599391,;PSG4,intron_variant,,ENST00000244295,;PSG4,downstream_gene_variant,,ENST00000451895,;PSG4,downstream_gene_variant,,ENST00000600572,;PSG4,downstream_gene_variant,,ENST00000599371,;PSG4,3_prime_UTR_variant,,ENST00000595949,;PSG4,3_prime_UTR_variant,,ENST00000601041,;PSG4,non_coding_transcript_exon_variant,,ENST00000597349,;PSG4,downstream_gene_variant,,ENST00000495316,;PSG4,upstream_gene_variant,,ENST00000490769,;PSG4,downstream_gene_variant,,ENST00000596199,;	T	ENSG00000243137	ENST00000405312	Transcript	missense_variant	1202	964	322	D/N	Gac/Aac	rs576741968,COSM3535187	.	.	-1	PSG4	HGNC	9521	protein_coding	YES	CCDS46093.1	ENSP00000384770	PSG4_HUMAN	M0QYU2_HUMAN	UPI000034ECBA	.	tolerated(0.63)	benign(0)	4/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF105,hmmpanther:PTHR19955,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGTCACTGC	byCluster	5	ESCA
PRKD2	0	.	GRCh37	19	47201016	47201016	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213G>T	p.Val405Phe	p.V405F	ENST00000433867	9/19	41	32	9	22	22	0	PRKD2,missense_variant,p.Val405Phe,ENST00000433867,;PRKD2,missense_variant,p.Val405Phe,ENST00000291281,;PRKD2,missense_variant,p.Val405Phe,ENST00000595515,;PRKD2,missense_variant,p.Val248Phe,ENST00000600194,;PRKD2,missense_variant,p.Val248Phe,ENST00000601806,;PRKD2,downstream_gene_variant,,ENST00000601605,;PRKD2,upstream_gene_variant,,ENST00000597589,;PRKD2,upstream_gene_variant,,ENST00000599019,;	A	ENSG00000105287	ENST00000433867	Transcript	missense_variant	1691	1213	405	V/F	Gtt/Ttt	.	.	.	-1	PRKD2	HGNC	17293	protein_coding	YES	CCDS12689.1	ENSP00000393978	KPCD2_HUMAN	M0R346_HUMAN,M0R2R2_HUMAN,M0R012_HUMAN	UPI000013E03A	.	deleterious(0)	benign(0.184)	9/19	.	Superfamily_domains:SSF50729,PIRSF_domain:PIRSF000552,SMART_domains:SM00233,Pfam_domain:PF00169,Gene3D:2.30.29.30,hmmpanther:PTHR22968,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAACCACCC	.	5	ESCA
SIGLEC9	0	.	GRCh37	19	51633206	51633206	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1203+1439C>T	.	.	ENST00000440804	.	39	32	7	20	20	0	SIGLEC9,missense_variant,p.Ser421Phe,ENST00000250360,;SIGLEC9,intron_variant,,ENST00000440804,;SIGLEC9,downstream_gene_variant,,ENST00000599948,;	T	ENSG00000129450	ENST00000440804	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SIGLEC9	HGNC	10878	protein_coding	YES	CCDS56100.1	ENSP00000413861	.	.	UPI00017A75A8	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCTGCCC	.	5	ESCA
ZNF667	0	.	GRCh37	19	56972059	56972059	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159delT	p.Gly54ValfsTer9	p.G54Vfs*9	ENST00000504904	5/7	37	28	9	20	20	0	ZNF667,frameshift_variant,p.Gly54ValfsTer9,ENST00000591790,;ZNF667,frameshift_variant,p.Gly147ValfsTer9,ENST00000342634,;ZNF667,frameshift_variant,p.Gly54ValfsTer9,ENST00000587555,;ZNF667,frameshift_variant,p.Gly54ValfsTer9,ENST00000292069,;ZNF667,frameshift_variant,p.Gly54ValfsTer9,ENST00000589946,;ZNF667,frameshift_variant,p.Gly54ValfsTer9,ENST00000504904,;ZNF667,frameshift_variant,p.Gly54ValfsTer9,ENST00000592189,;	-	ENSG00000198046	ENST00000504904	Transcript	frameshift_variant	879	159	53	L/X	ctT/ct	.	.	.	-1	ZNF667	HGNC	28854	protein_coding	YES	CCDS12944.1	ENSP00000439402	ZN667_HUMAN	K7ERY5_HUMAN,K7EIE0_HUMAN	UPI0000202CEE	.	.	.	5/7	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTACCAAGCGA	.	3	ESCA
ZNF558	0	.	GRCh37	19	8933377	8933377	+	5'UTR	SNP	G	G	A	rs183660540	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-42C>T	.	.	ENST00000601372	5/10	26	19	7	19	19	0	ZNF558,5_prime_UTR_variant,,ENST00000301475,;ZNF558,5_prime_UTR_variant,,ENST00000601372,;ZNF558,upstream_gene_variant,,ENST00000444186,;CTD-2529P6.3,intron_variant,,ENST00000594006,;ZNF558,downstream_gene_variant,,ENST00000596172,;ZNF558,downstream_gene_variant,,ENST00000599938,;ZNF558,downstream_gene_variant,,ENST00000595786,;ZNF558,non_coding_transcript_exon_variant,,ENST00000597304,;	A	ENSG00000167785	ENST00000601372	Transcript	5_prime_UTR_variant	671	.	.	.	.	rs183660540	.	.	-1	ZNF558	HGNC	26422	protein_coding	YES	CCDS12208.1	ENSP00000471277	ZN558_HUMAN	B7Z798_HUMAN	UPI000006D81E	.	.	.	5/10	.	.	A:0.0008	.	.	.	.	.	.	C:0.0011	C:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGACGCTCCT	byFrequency|byCluster|by1000G	5	ESCA
ZNF697	0	.	GRCh37	1	120162907	120162907	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2421G>T	.	.	ENST00000421812	3/3	19	13	6	16	16	0	ZNF697,3_prime_UTR_variant,,ENST00000421812,;	A	ENSG00000143067	ENST00000421812	Transcript	3_prime_UTR_variant	4179	.	.	.	.	.	.	.	-1	ZNF697	HGNC	32034	protein_coding	YES	CCDS44202.1	ENSP00000396857	ZN697_HUMAN	Q8N508_HUMAN	UPI0000DD78D7	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCTCCACTC	.	5	ESCA
CCNL2	0	.	GRCh37	1	1328774	1328781	+	Splice_Site	DEL	ACCATGAG	ACCATGAG	-	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	ACCATGAG	ACCATGAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.654_659+2delCTCATGGT	.	p.X218_splice	ENST00000400809	5/11	49	28	21	23	23	0	CCNL2,splice_donor_variant,,ENST00000400809,;CCNL2,splice_donor_variant,,ENST00000408918,;CCNL2,splice_donor_variant,,ENST00000408952,;CCNL2,downstream_gene_variant,,ENST00000497013,;CCNL2,splice_donor_variant,,ENST00000471930,;CCNL2,upstream_gene_variant,,ENST00000505849,;CCNL2,upstream_gene_variant,,ENST00000469113,;CCNL2,splice_donor_variant,,ENST00000481223,;CCNL2,splice_donor_variant,,ENST00000482621,;CCNL2,splice_donor_variant,,ENST00000496007,;CCNL2,splice_donor_variant,,ENST00000488340,;CCNL2,non_coding_transcript_exon_variant,,ENST00000473872,;CCNL2,upstream_gene_variant,,ENST00000463260,;CCNL2,upstream_gene_variant,,ENST00000480479,;CCNL2,downstream_gene_variant,,ENST00000463895,;CCNL2,upstream_gene_variant,,ENST00000418865,;CCNL2,downstream_gene_variant,,ENST00000425598,;CCNL2,upstream_gene_variant,,ENST00000480646,;CCNL2,upstream_gene_variant,,ENST00000482365,;CCNL2,upstream_gene_variant,,ENST00000492998,;	-	ENSG00000221978	ENST00000400809	Transcript	splice_donor_variant	660-?	654-?	218-?	.	.	.	.	.	-1	CCNL2	HGNC	20570	protein_coding	YES	CCDS30557.1	ENSP00000383611	CCNL2_HUMAN	J3QSH2_HUMAN,B4DE38_HUMAN	UPI00000713F5	.	.	.	5/11	5/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAACTCACCATGAGGTCTG	.	3	ESCA
ADAMTSL4	0	.	GRCh37	1	150524746	150524746	+	5'UTR	SNP	G	G	A	rs374642601	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-19G>A	.	.	ENST00000271643	3/19	55	25	30	27	27	0	ADAMTSL4,5_prime_UTR_variant,,ENST00000271643,;ADAMTSL4,5_prime_UTR_variant,,ENST00000369038,;ADAMTSL4,5_prime_UTR_variant,,ENST00000369039,;ADAMTSL4,5_prime_UTR_variant,,ENST00000369041,;AL356356.1,downstream_gene_variant,,ENST00000538795,;MIR4257,downstream_gene_variant,,ENST00000581735,;RP11-54A4.2,intron_variant,,ENST00000442435,;ADAMTSL4,downstream_gene_variant,,ENST00000483335,;	A	ENSG00000143382	ENST00000271643	Transcript	5_prime_UTR_variant	218	.	.	.	.	rs374642601	.	.	1	ADAMTSL4	HGNC	19706	protein_coding	YES	CCDS955.1	ENSP00000271643	ATL4_HUMAN	Q9UFG7_HUMAN,A8KAH2_HUMAN	UPI00001E0572	.	.	.	3/19	.	.	.	.	.	.	.	.	.	A:0.0005	A:0.0004	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTGGGGCAG	byFrequency|byCluster	5	ESCA
ATP13A2	0	.	GRCh37	1	17319071	17319071	+	Silent	SNP	C	C	T	rs200184146	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1755G>A	p.%3D	p.L585L	ENST00000326735	17/29	43	32	10	42	42	0	ATP13A2,synonymous_variant,p.%3D,ENST00000503552,;ATP13A2,synonymous_variant,p.%3D,ENST00000452699,;ATP13A2,synonymous_variant,p.%3D,ENST00000341676,;ATP13A2,synonymous_variant,p.%3D,ENST00000326735,;ATP13A2,upstream_gene_variant,,ENST00000502418,;ATP13A2,downstream_gene_variant,,ENST00000506174,;RP1-37C10.3,intron_variant,,ENST00000446261,;ATP13A2,downstream_gene_variant,,ENST00000502860,;ATP13A2,downstream_gene_variant,,ENST00000463860,;ATP13A2,upstream_gene_variant,,ENST00000466561,;ATP13A2,downstream_gene_variant,,ENST00000509392,;	T	ENSG00000159363	ENST00000326735	Transcript	synonymous_variant	1789	1755	585	L	ctG/ctA	rs200184146	.	.	-1	ATP13A2	HGNC	30213	protein_coding	YES	CCDS175.1	ENSP00000327214	AT132_HUMAN	Q8N4D4_HUMAN	UPI0000049724	.	.	.	17/29	.	hmmpanther:PTHR24093:SF86,hmmpanther:PTHR24093,Gene3D:3.40.1110.10,Pfam_domain:PF12710,TIGRFAM_domain:TIGR01657,Superfamily_domains:SSF81660	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCCAGGAC	byCluster|by1000G	5	ESCA
TNR	0	.	GRCh37	1	175293656	175293656	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3794-1G>T	.	p.X1265_splice	ENST00000367674	.	54	43	11	36	36	0	TNR,splice_acceptor_variant,,ENST00000367674,;TNR,splice_acceptor_variant,,ENST00000263525,;RP3-518E13.2,intron_variant,,ENST00000569593,;	A	ENSG00000116147	ENST00000367674	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	TNR	HGNC	11953	protein_coding	YES	CCDS1318.1	ENSP00000356646	TENR_HUMAN	A1L306_HUMAN	UPI000013D41C	.	.	.	.	21/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCCTGCAA	.	5	ESCA
NMNAT2	0	.	GRCh37	1	183219973	183219973	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1803G>A	.	.	ENST00000287713	11/11	26	20	6	27	27	0	NMNAT2,3_prime_UTR_variant,,ENST00000294868,;NMNAT2,3_prime_UTR_variant,,ENST00000287713,;NMNAT2,downstream_gene_variant,,ENST00000464047,;	T	ENSG00000157064	ENST00000287713	Transcript	3_prime_UTR_variant	3062	.	.	.	.	.	.	.	-1	NMNAT2	HGNC	16789	protein_coding	YES	CCDS1353.1	ENSP00000287713	NMNA2_HUMAN	.	UPI00000706AB	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCCGCAAT	.	5	ESCA
EXOC8	0	.	GRCh37	1	231472386	231472386	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1106A>G	p.Asp369Gly	p.D369G	ENST00000360394	1/1	46	36	9	16	16	0	EXOC8,missense_variant,p.Asp369Gly,ENST00000360394,;EXOC8,missense_variant,p.Asp365Gly,ENST00000366645,;SPRTN,upstream_gene_variant,,ENST00000008440,;SPRTN,upstream_gene_variant,,ENST00000366644,;SPRTN,upstream_gene_variant,,ENST00000295050,;SPRTN,upstream_gene_variant,,ENST00000391858,;SPRTN,upstream_gene_variant,,ENST00000492437,;	C	ENSG00000116903	ENST00000360394	Transcript	missense_variant	1193	1106	369	D/G	gAt/gGt	.	.	.	-1	EXOC8	HGNC	24659	protein_coding	YES	CCDS1593.1	ENSP00000353564	EXOC8_HUMAN	.	UPI000006EA2C	.	tolerated(0.43)	benign(0)	1/1	.	hmmpanther:PTHR21426,Superfamily_domains:SSF74788	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTATCTTCC	.	5	ESCA
PCNXL2	0	.	GRCh37	1	233394198	233394198	+	Silent	SNP	G	G	A	rs771369510	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1410C>T	p.%3D	p.Y470Y	ENST00000258229	5/34	46	22	24	22	22	0	PCNXL2,synonymous_variant,p.%3D,ENST00000258229,;PCNXL2,5_prime_UTR_variant,,ENST00000430153,;PCNXL2,upstream_gene_variant,,ENST00000475463,;	A	ENSG00000135749	ENST00000258229	Transcript	synonymous_variant	1645	1410	470	Y	taC/taT	rs771369510	.	.	-1	PCNXL2	HGNC	8736	protein_coding	YES	CCDS44335.1	ENSP00000258229	PCX2_HUMAN	B3KNZ5_HUMAN	UPI0000F58F23	.	.	.	5/34	.	hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCCGTAGCC	byFrequency	5	ESCA
ZMYM6	0	.	GRCh37	1	35480667	35480667	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.525G>A	p.%3D	p.E175E	ENST00000357182	5/16	57	41	15	44	44	0	ZMYM6,synonymous_variant,p.%3D,ENST00000357182,;ZMYM6,synonymous_variant,p.%3D,ENST00000415531,;ZMYM6,synonymous_variant,p.%3D,ENST00000373340,;ZMYM6,downstream_gene_variant,,ENST00000373333,;ZMYM6,downstream_gene_variant,,ENST00000317538,;ZMYM6,non_coding_transcript_exon_variant,,ENST00000493328,;ZMYM6,downstream_gene_variant,,ENST00000460607,;ZMYM6,upstream_gene_variant,,ENST00000472971,;RP11-244H3.4,synonymous_variant,p.%3D,ENST00000487874,;	T	ENSG00000163867	ENST00000357182	Transcript	synonymous_variant	753	525	175	E	gaG/gaA	.	.	.	-1	ZMYM6	HGNC	13050	protein_coding	YES	CCDS387.2	ENSP00000349708	ZMYM6_HUMAN	Q7L9K1_HUMAN,A4Z946_HUMAN	UPI000040EBC6	.	.	.	5/16	.	hmmpanther:PTHR11697:SF92,hmmpanther:PTHR11697,SMART_domains:SM00746	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAGCTCATA	.	5	ESCA
SLFNL1	0	.	GRCh37	1	41483479	41483479	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785T>C	p.Val262Ala	p.V262A	ENST00000359345	2/4	44	26	18	31	31	0	SLFNL1,missense_variant,p.Val262Ala,ENST00000302946,;SLFNL1,missense_variant,p.Val262Ala,ENST00000397197,;SLFNL1,missense_variant,p.Val262Ala,ENST00000372613,;SLFNL1,missense_variant,p.Val262Ala,ENST00000439569,;SLFNL1,missense_variant,p.Val203Ala,ENST00000372611,;SLFNL1,missense_variant,p.Val262Ala,ENST00000359345,;	G	ENSG00000171790	ENST00000359345	Transcript	missense_variant	3362	785	262	V/A	gTa/gCa	.	.	.	-1	SLFNL1	HGNC	26313	protein_coding	YES	CCDS460.1	ENSP00000352299	SLNL1_HUMAN	.	UPI000013E83F	.	deleterious(0.03)	probably_damaging(0.947)	2/4	.	Pfam_domain:PF04326,hmmpanther:PTHR12155:SF19,hmmpanther:PTHR12155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTACTCCC	.	5	ESCA
C1orf173	0	.	GRCh37	1	75055150	75055150	+	Intron	SNP	T	T	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2176+165A>C	.	.	ENST00000326665	.	8	5	3	8	8	0	C1orf173,3_prime_UTR_variant,,ENST00000420661,;C1orf173,intron_variant,,ENST00000326665,;RP4-612J11.1,upstream_gene_variant,,ENST00000416017,;	G	ENSG00000178965	ENST00000326665	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	C1orf173	HGNC	25346	protein_coding	YES	CCDS30755.1	ENSP00000322609	CA173_HUMAN	.	UPI0000237200	.	.	.	.	12/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAACTGAAAA	.	2	ESCA
DSN1	0	.	GRCh37	20	35396375	35396375	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426C>A	p.Phe142Leu	p.F142L	ENST00000426836	4/11	31	10	20	20	20	0	DSN1,missense_variant,p.Phe142Leu,ENST00000447406,;DSN1,missense_variant,p.Phe142Leu,ENST00000373745,;DSN1,missense_variant,p.Phe42Leu,ENST00000438549,;DSN1,missense_variant,p.Phe35Leu,ENST00000373734,;DSN1,missense_variant,p.Phe126Leu,ENST00000448110,;DSN1,missense_variant,p.Phe70Leu,ENST00000373740,;DSN1,missense_variant,p.Phe142Leu,ENST00000426836,;DSN1,missense_variant,p.Phe142Leu,ENST00000373750,;DSN1,non_coding_transcript_exon_variant,,ENST00000492703,;DSN1,non_coding_transcript_exon_variant,,ENST00000473615,;DSN1,non_coding_transcript_exon_variant,,ENST00000480153,;	T	ENSG00000149636	ENST00000426836	Transcript	missense_variant	799	426	142	F/L	ttC/ttA	.	.	.	-1	DSN1	HGNC	16165	protein_coding	YES	CCDS13286.1	ENSP00000389810	DSN1_HUMAN	Q5JW58_HUMAN,Q5JW57_HUMAN,Q5JW53_HUMAN	UPI0000128621	.	tolerated(0.13)	probably_damaging(0.999)	4/11	.	hmmpanther:PTHR14778,Pfam_domain:PF08202	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTGGAAACT	.	5	ESCA
MYO18B	0	.	GRCh37	22	26164786	26164786	+	Silent	SNP	C	C	T	rs369200662	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903C>T	p.%3D	p.D301D	ENST00000335473	4/44	42	33	8	48	47	0	MYO18B,synonymous_variant,p.%3D,ENST00000335473,;MYO18B,synonymous_variant,p.%3D,ENST00000407587,;MYO18B,synonymous_variant,p.%3D,ENST00000536101,;MYO18B,synonymous_variant,p.%3D,ENST00000539302,;MYO18B,upstream_gene_variant,,ENST00000418374,;	T	ENSG00000133454	ENST00000335473	Transcript	synonymous_variant	1153	903	301	D	gaC/gaT	rs369200662	.	.	1	MYO18B	HGNC	18150	protein_coding	YES	CCDS54507.1	ENSP00000334563	.	Q8N903_HUMAN	UPI0000207402	.	.	.	4/44	.	hmmpanther:PTHR13140:SF254,hmmpanther:PTHR13140	.	.	.	.	.	.	.	T:0.0003	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGACGTAGG	byCluster	5	ESCA
UBXN4	0	.	GRCh37	2	136537813	136537813	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1246G>C	p.Gly416Arg	p.G416R	ENST00000272638	12/13	87	64	22	70	70	0	UBXN4,missense_variant,p.Gly416Arg,ENST00000272638,;UBXN4,non_coding_transcript_exon_variant,,ENST00000490163,;UBXN4,downstream_gene_variant,,ENST00000471246,;	C	ENSG00000144224	ENST00000272638	Transcript	missense_variant	1557	1246	416	G/R	Gga/Cga	.	.	.	1	UBXN4	HGNC	14860	protein_coding	YES	CCDS42761.1	ENSP00000272638	UBXN4_HUMAN	B3KTD5_HUMAN	UPI0000074226	.	deleterious(0.01)	benign(0.23)	12/13	.	hmmpanther:PTHR13020	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTGGGAACA	.	5	ESCA
KIF5C	0	.	GRCh37	2	149633197	149633197	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11C>T	p.Pro4Leu	p.P4L	ENST00000435030	1/26	90	25	65	18	18	0	KIF5C,missense_variant,p.Pro4Leu,ENST00000435030,;AC105402.4,intron_variant,,ENST00000601658,;AC105402.4,downstream_gene_variant,,ENST00000446781,;AC105402.3,upstream_gene_variant,,ENST00000413336,;	T	ENSG00000168280	ENST00000435030	Transcript	missense_variant	379	11	4	P/L	cCa/cTa	.	.	.	1	KIF5C	HGNC	6325	protein_coding	YES	.	ENSP00000393379	KIF5C_HUMAN	Q9UFW7_HUMAN,Q57Z91_HUMAN,Q57YV6_HUMAN,Q57YV5_HUMAN,Q53QT4_HUMAN,C9JWB9_HUMAN	UPI000012DDB7	.	tolerated(0.06)	benign(0.008)	1/26	.	hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF365	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGATCCAGCCG	.	4	ESCA
KIF5C	0	.	GRCh37	2	149840246	149840246	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1682T>A	p.Ile561Lys	p.I561K	ENST00000435030	15/26	213	42	171	68	68	0	KIF5C,missense_variant,p.Ile329Lys,ENST00000397413,;KIF5C,missense_variant,p.Ile561Lys,ENST00000435030,;KIF5C,missense_variant,p.Ile466Lys,ENST00000414838,;KIF5C,non_coding_transcript_exon_variant,,ENST00000464066,;KIF5C,non_coding_transcript_exon_variant,,ENST00000460377,;	A	ENSG00000168280	ENST00000435030	Transcript	missense_variant	2050	1682	561	I/K	aTa/aAa	.	.	.	1	KIF5C	HGNC	6325	protein_coding	YES	.	ENSP00000393379	KIF5C_HUMAN	Q9UFW7_HUMAN,Q57Z91_HUMAN,Q57YV6_HUMAN,Q57YV5_HUMAN,Q53QT4_HUMAN,C9JWB9_HUMAN	UPI000012DDB7	.	deleterious(0.03)	possibly_damaging(0.822)	15/26	.	hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF365	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGATAGGTG	.	5	ESCA
NEB	0	.	GRCh37	2	152525591	152525591	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4561G>A	p.Glu1521Lys	p.E1521K	ENST00000397345	39/182	62	46	15	42	42	0	NEB,missense_variant,p.Glu1521Lys,ENST00000603639,;NEB,missense_variant,p.Glu1521Lys,ENST00000172853,;NEB,missense_variant,p.Glu1521Lys,ENST00000427231,;NEB,missense_variant,p.Glu1521Lys,ENST00000397345,;NEB,missense_variant,p.Glu1521Lys,ENST00000604864,;NEB,missense_variant,p.Glu1521Lys,ENST00000409198,;NEB,non_coding_transcript_exon_variant,,ENST00000484968,;	T	ENSG00000183091	ENST00000397345	Transcript	missense_variant	4764	4561	1521	E/K	Gaa/Aaa	.	.	.	-1	NEB	HGNC	7720	protein_coding	YES	CCDS54407.1	ENSP00000380505	.	H7C2D0_HUMAN,F8WCL5_HUMAN	UPI0002065BA0	.	.	benign(0.048)	39/182	.	PROSITE_profiles:PS51216,hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATTCAGGGT	.	5	ESCA
TTC21B	0	.	GRCh37	2	166756357	166756357	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2791C>T	p.Gln931Ter	p.Q931*	ENST00000243344	21/29	49	38	11	42	42	0	TTC21B,stop_gained,p.Gln931Ter,ENST00000243344,;TTC21B,non_coding_transcript_exon_variant,,ENST00000484129,;	A	ENSG00000123607	ENST00000243344	Transcript	stop_gained	2929	2791	931	Q/*	Caa/Taa	.	.	.	-1	TTC21B	HGNC	25660	protein_coding	YES	CCDS33315.1	ENSP00000243344	TT21B_HUMAN	B3KU32_HUMAN	UPI000020900A	.	.	.	21/29	.	PROSITE_profiles:PS50293,hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF1,Gene3D:1.25.40.10,Pfam_domain:PF14559,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTGTGCCA	.	5	ESCA
FAM171B	0	.	GRCh37	2	187615950	187615950	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814C>G	p.Gln272Glu	p.Q272E	ENST00000304698	5/8	124	107	17	63	63	0	FAM171B,missense_variant,p.Gln272Glu,ENST00000304698,;	G	ENSG00000144369	ENST00000304698	Transcript	missense_variant	1017	814	272	Q/E	Caa/Gaa	.	.	.	1	FAM171B	HGNC	29412	protein_coding	YES	CCDS33347.1	ENSP00000304108	F171B_HUMAN	A8K122_HUMAN	UPI0000161631	.	tolerated(0.31)	benign(0.009)	5/8	.	Pfam_domain:PF10577,hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATTCAAGTT	.	5	ESCA
HECW2	0	.	GRCh37	2	197184302	197184302	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1312G>T	p.Glu438Ter	p.E438*	ENST00000260983	9/29	44	40	4	19	19	0	HECW2,stop_gained,p.Glu438Ter,ENST00000260983,;HECW2,stop_gained,p.Glu82Ter,ENST00000409111,;	A	ENSG00000138411	ENST00000260983	Transcript	stop_gained	1495	1312	438	E/*	Gag/Tag	.	.	.	-1	HECW2	HGNC	29853	protein_coding	YES	CCDS33354.1	ENSP00000260983	HECW2_HUMAN	C9JPI9_HUMAN,C9JHL2_HUMAN	UPI00001A75E8	.	.	.	9/29	.	hmmpanther:PTHR11254:SF127,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTCTCAGAGC	.	3	ESCA
MAP2	0	.	GRCh37	2	210559188	210559188	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2294A>T	p.Glu765Val	p.E765V	ENST00000360351	7/15	16	8	8	11	11	0	MAP2,missense_variant,p.Glu761Val,ENST00000447185,;MAP2,missense_variant,p.Glu765Val,ENST00000360351,;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000199940,;MAP2,intron_variant,,ENST00000392194,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000482864,;MAP2,intron_variant,,ENST00000471619,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,;MAP2,upstream_gene_variant,,ENST00000475600,;	T	ENSG00000078018	ENST00000360351	Transcript	missense_variant	2800	2294	765	E/V	gAg/gTg	.	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	deleterious(0.02)	probably_damaging(0.948)	7/15	.	hmmpanther:PTHR11501:SF15,hmmpanther:PTHR11501,Pfam_domain:PF08377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAAGAGGAAG	.	5	ESCA
PKDCC	0	.	GRCh37	2	42285555	42285555	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*727G>A	.	.	ENST00000294964	7/7	20	13	7	19	19	0	PKDCC,3_prime_UTR_variant,,ENST00000294964,;PKDCC,downstream_gene_variant,,ENST00000480099,;PKDCC,non_coding_transcript_exon_variant,,ENST00000490302,;PKDCC,downstream_gene_variant,,ENST00000470578,;PKDCC,downstream_gene_variant,,ENST00000401498,;PKDCC,downstream_gene_variant,,ENST00000475241,;PKDCC,downstream_gene_variant,,ENST00000485578,;PKDCC,downstream_gene_variant,,ENST00000492861,;PKDCC,downstream_gene_variant,,ENST00000475868,;	A	ENSG00000162878	ENST00000294964	Transcript	3_prime_UTR_variant	2389	.	.	.	.	.	.	.	1	PKDCC	HGNC	25123	protein_coding	YES	CCDS33186.2	ENSP00000294964	PKDCC_HUMAN	.	UPI0000EE25C6	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCGAGTTT	.	5	ESCA
SOX11	0	.	GRCh37	2	5839423	5839423	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5244G>C	.	.	ENST00000322002	1/1	29	17	12	40	40	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	C	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	6625	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAGGATATT	.	5	ESCA
ZDHHC23	0	.	GRCh37	3	113676531	113676531	+	Intron	SNP	T	T	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041-679T>A	.	.	ENST00000330212	.	116	74	42	63	63	0	ZDHHC23,intron_variant,,ENST00000498275,;ZDHHC23,intron_variant,,ENST00000330212,;ZDHHC23,upstream_gene_variant,,ENST00000496083,;ZDHHC23,downstream_gene_variant,,ENST00000491556,;ZDHHC23,non_coding_transcript_exon_variant,,ENST00000488129,;ZDHHC23,intron_variant,,ENST00000478793,;	A	ENSG00000184307	ENST00000330212	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZDHHC23	HGNC	28654	protein_coding	YES	CCDS33827.1	ENSP00000330485	ZDH23_HUMAN	C9JPJ8_HUMAN,B3KXV3_HUMAN	UPI0000209F9A	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAACTTATTT	.	5	ESCA
KIAA1257	0	.	GRCh37	3	128707650	128707650	+	Missense_Mutation	SNP	G	G	A	rs757373715	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.374C>T	p.Pro125Leu	p.P125L	ENST00000265068	3/8	78	64	14	56	56	0	KIAA1257,missense_variant,p.Pro13Leu,ENST00000515659,;KIAA1257,missense_variant,p.Pro125Leu,ENST00000511438,;KIAA1257,missense_variant,p.Pro125Leu,ENST00000265068,;KIAA1257,non_coding_transcript_exon_variant,,ENST00000510149,;	A	ENSG00000114656	ENST00000265068	Transcript	missense_variant	542	374	125	P/L	cCg/cTg	rs757373715	.	.	-1	KIAA1257	HGNC	29231	protein_coding	YES	CCDS46905.1	ENSP00000265068	K1257_HUMAN	.	UPI00001C1DE3	.	deleterious(0)	probably_damaging(0.983)	3/8	.	Pfam_domain:PF15084	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCCGGCAGA	byFrequency	5	ESCA
TRPC1	0	.	GRCh37	3	142462342	142462342	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343T>C	p.%3D	p.L115L	ENST00000476941	3/13	52	40	12	42	42	0	TRPC1,synonymous_variant,p.%3D,ENST00000476941,;TRPC1,intron_variant,,ENST00000273482,;TRPC1,intron_variant,,ENST00000460401,;	C	ENSG00000144935	ENST00000476941	Transcript	synonymous_variant	829	343	115	L	Ttg/Ctg	.	.	.	1	TRPC1	HGNC	12333	protein_coding	YES	CCDS58856.1	ENSP00000419313	TRPC1_HUMAN	.	UPI00001374A4	.	.	.	3/13	.	hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF3,Gene3D:1.25.40.20,Pfam_domain:PF12796,TIGRFAM_domain:TIGR00870,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTTTGGTG	.	5	ESCA
MBNL1	0	.	GRCh37	3	152175980	152175980	+	Intron	SNP	A	A	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1111-1080A>G	.	.	ENST00000282486	.	75	44	30	48	48	0	MBNL1,missense_variant,p.Met322Val,ENST00000485509,;MBNL1,missense_variant,p.Met322Val,ENST00000324196,;MBNL1,intron_variant,,ENST00000478535,;MBNL1,intron_variant,,ENST00000545754,;MBNL1,intron_variant,,ENST00000282486,;MBNL1,intron_variant,,ENST00000498502,;MBNL1,intron_variant,,ENST00000493459,;MBNL1,intron_variant,,ENST00000357472,;MBNL1,intron_variant,,ENST00000463374,;MBNL1,intron_variant,,ENST00000465907,;MBNL1,intron_variant,,ENST00000282488,;MBNL1,intron_variant,,ENST00000492948,;MBNL1,intron_variant,,ENST00000324210,;MBNL1,intron_variant,,ENST00000355460,;MBNL1,intron_variant,,ENST00000485910,;MBNL1,intron_variant,,ENST00000464596,;RP11-362A9.3,intron_variant,,ENST00000463255,;MBNL1,downstream_gene_variant,,ENST00000460166,;MBNL1,non_coding_transcript_exon_variant,,ENST00000497971,;	G	ENSG00000152601	ENST00000282486	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MBNL1	HGNC	6923	protein_coding	YES	CCDS3165.1	ENSP00000282486	MBNL1_HUMAN	C9JCX1_HUMAN,C9J7P7_HUMAN	UPI000003B440	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAAATGGTA	.	5	ESCA
MUC4	0	.	GRCh37	3	195509034	195509034	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9417C>G	p.%3D	p.V3139V	ENST00000463781	2/25	217	146	71	169	168	0	MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000470451,;MUC4,synonymous_variant,p.%3D,ENST00000477086,;MUC4,synonymous_variant,p.%3D,ENST00000466475,;MUC4,synonymous_variant,p.%3D,ENST00000478156,;MUC4,synonymous_variant,p.%3D,ENST00000479406,;MUC4,synonymous_variant,p.%3D,ENST00000477756,;MUC4,synonymous_variant,p.%3D,ENST00000462323,;MUC4,synonymous_variant,p.%3D,ENST00000480843,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,;	C	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	9877	9417	3139	V	gtC/gtG	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A3136P|c.9406G>C|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTGACAGG	.	5	ESCA
PLA2G12A	0	.	GRCh37	4	110650791	110650791	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175G>A	p.Glu59Lys	p.E59K	ENST00000243501	1/4	50	39	11	36	36	0	PLA2G12A,missense_variant,p.Glu59Lys,ENST00000243501,;PLA2G12A,missense_variant,p.Glu59Lys,ENST00000502283,;PLA2G12A,missense_variant,p.Glu59Lys,ENST00000507961,;	T	ENSG00000123739	ENST00000243501	Transcript	missense_variant	443	175	59	E/K	Gag/Aag	.	.	.	-1	PLA2G12A	HGNC	18554	protein_coding	YES	CCDS3686.1	ENSP00000243501	PG12A_HUMAN	Q542Y6_HUMAN	UPI0000001BF6	.	tolerated(1)	benign(0.012)	1/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12824,hmmpanther:PTHR12824:SF7,Pfam_domain:PF06951,Superfamily_domains:SSF48619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTCGCCTC	.	5	ESCA
BOD1L1	0	.	GRCh37	4	13590374	13590374	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8252G>T	p.Gly2751Val	p.G2751V	ENST00000040738	15/26	38	14	24	38	38	0	BOD1L1,missense_variant,p.Gly2751Val,ENST00000040738,;BOD1L1,non_coding_transcript_exon_variant,,ENST00000511119,;	A	ENSG00000038219	ENST00000040738	Transcript	missense_variant	8388	8252	2751	G/V	gGt/gTt	.	.	.	-1	BOD1L1	HGNC	31792	protein_coding	YES	CCDS3411.2	ENSP00000040738	BD1L1_HUMAN	.	UPI000066D9E3	.	.	benign(0.101)	15/26	.	hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGACCGCTT	.	5	ESCA
FBXW7	0	.	GRCh37	4	153247289	153247289	+	Missense_Mutation	SNP	G	G	C	rs149680468	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	10/12	47	34	13	43	43	0	FBXW7,missense_variant,p.Arg505Gly,ENST00000603548,;FBXW7,missense_variant,p.Arg425Gly,ENST00000263981,;FBXW7,missense_variant,p.Arg387Gly,ENST00000296555,;FBXW7,missense_variant,p.Arg329Gly,ENST00000393956,;FBXW7,missense_variant,p.Arg505Gly,ENST00000281708,;FBXW7,missense_variant,p.Arg505Gly,ENST00000603841,;FBXW7,non_coding_transcript_exon_variant,,ENST00000603821,;FBXW7,upstream_gene_variant,,ENST00000604316,;FBXW7,downstream_gene_variant,,ENST00000604069,;	C	ENSG00000109670	ENST00000281708	Transcript	missense_variant	2743	1513	505	R/G	Cgc/Ggc	rs149680468,COSM33763,COSM22975,COSM99604,COSM99606,COSM732380,COSM108572,COSM1154290,COSM1133711,COSM1149853,COSM108571,COSM732382,COSM99605,COSM74637,COSM99603,COSM732381	.	.	-1	FBXW7	HGNC	16712	protein_coding	YES	CCDS3777.1	ENSP00000281708	FBXW7_HUMAN	S4R3N3_HUMAN,H9CWI3_HUMAN,H9CWI2_HUMAN,G0Z2K0_HUMAN,A7BJS8_HUMAN	UPI000007007E	.	deleterious(0)	probably_damaging(1)	10/12	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Pfam_domain:PF00400,Gene3D:2.130.10.10,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF116,PROSITE_profiles:PS50294,PROSITE_profiles:PS50082	.	.	.	.	.	.	.	.	.	not_provided	1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	21499247	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R387G|c.1159C>G|7,SITE|p.R505G|c.1513C>G|11,SITE|p.R505G|c.1513C>G|11,SITE|p.R425G|c.1273C>G|11,CODON|p.R505L|c.1514G>T|8,CODON|p.R505?|c.1514G>H|14,CODON|p.R505H|c.1514G>A|3,BUFFER|p.R266G|c.796C>G|11,BUFFER|p.R266C|c.796C>T|32,BUFFER|p.R425C|c.1273C>T|33,BUFFER|p.R505C|c.1513C>T|32,BUFFER|p.R505S|c.1513C>A|3,BUFFER|p.R505C|c.1513C>T|66,BUFFER|p.R387C|c.1159C>T|19	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCGGACTG	.	5	ESCA
RP11-1398P2.1	0	.	GRCh37	4	1576058	1576058	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.310G>C	.	.	ENST00000466692	2/2	42	14	27	28	28	0	RP11-1398P2.1,non_coding_transcript_exon_variant,,ENST00000466692,;	G	ENSG00000244459	ENST00000466692	Transcript	non_coding_transcript_exon_variant	310	.	.	.	.	.	.	.	-1	RP11-1398P2.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCCTGCAG	.	5	ESCA
CCDC149	0	.	GRCh37	4	24809937	24809937	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*74C>T	.	.	ENST00000504487	12/12	49	30	18	19	19	0	CCDC149,3_prime_UTR_variant,,ENST00000502801,;CCDC149,3_prime_UTR_variant,,ENST00000389609,;CCDC149,3_prime_UTR_variant,,ENST00000504487,;CCDC149,3_prime_UTR_variant,,ENST00000428116,;CCDC149,downstream_gene_variant,,ENST00000507096,;	A	ENSG00000181982	ENST00000504487	Transcript	3_prime_UTR_variant	1671	.	.	.	.	.	.	.	-1	CCDC149	HGNC	25405	protein_coding	YES	CCDS47036.1	ENSP00000425715	CC149_HUMAN	.	UPI00005A7F29	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGCGCACCA	.	5	ESCA
PCDH7	0	.	GRCh37	4	30724999	30725000	+	In_Frame_Ins	INS	-	-	GCA	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1958_1960dupAGC	p.Gln653dup	p.Q653dup	ENST00000543491	1/3	51	29	22	36	36	0	PCDH7,inframe_insertion,p.Gln343dup,ENST00000511884,;PCDH7,inframe_insertion,p.Gln653dup,ENST00000543491,;PCDH7,inframe_insertion,p.Gln653dup,ENST00000361762,;PCDH7,intron_variant,,ENST00000507864,;	GCA	ENSG00000169851	ENST00000543491	Transcript	inframe_insertion	1955-1956	1955-1956	652	L/LQ	ttg/ttGCAg	.	.	.	1	PCDH7	HGNC	8659	protein_coding	YES	CCDS54753.1	ENSP00000441802	.	F5GWJ1_HUMAN	UPI0001CB27C3	.	.	.	1/3	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF14,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAACTTGCAGC	.	3	ESCA
TLR10	0	.	GRCh37	4	38775505	38775505	+	Silent	SNP	G	G	C	rs755099618	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1707C>G	p.%3D	p.L569L	ENST00000308973	4/4	138	133	5	84	83	1	TLR10,synonymous_variant,p.%3D,ENST00000508334,;TLR10,synonymous_variant,p.%3D,ENST00000361424,;TLR10,synonymous_variant,p.%3D,ENST00000308973,;TLR10,synonymous_variant,p.%3D,ENST00000506111,;TLR10,downstream_gene_variant,,ENST00000502321,;TLR10,downstream_gene_variant,,ENST00000507953,;	C	ENSG00000174123	ENST00000308973	Transcript	synonymous_variant	2313	1707	569	L	ctC/ctG	rs755099618	.	.	-1	TLR10	HGNC	15634	protein_coding	YES	CCDS3445.1	ENSP00000308925	TLR10_HUMAN	D6RHW6_HUMAN	UPI0000048F1C	.	.	.	4/4	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF131,PIRSF_domain:PIRSF037595,SMART_domains:SM00082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGTGGAGATG	.	2	ESCA
TLR10	0	.	GRCh37	4	38776722	38776722	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490C>G	p.His164Asp	p.H164D	ENST00000308973	4/4	85	78	7	36	36	0	TLR10,missense_variant,p.His164Asp,ENST00000508334,;TLR10,missense_variant,p.His164Asp,ENST00000361424,;TLR10,missense_variant,p.His164Asp,ENST00000308973,;TLR10,missense_variant,p.His164Asp,ENST00000506111,;TLR10,downstream_gene_variant,,ENST00000502321,;TLR10,downstream_gene_variant,,ENST00000507953,;	C	ENSG00000174123	ENST00000308973	Transcript	missense_variant	1096	490	164	H/D	Cat/Gat	.	.	.	-1	TLR10	HGNC	15634	protein_coding	YES	CCDS3445.1	ENSP00000308925	TLR10_HUMAN	D6RHW6_HUMAN	UPI0000048F1C	.	deleterious(0.03)	benign(0.009)	4/4	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF131,Gene3D:3.80.10.10,PIRSF_domain:PIRSF037595,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGATGAGCAA	.	3	ESCA
GRXCR1	0	.	GRCh37	4	43032468	43032468	+	Nonsense_Mutation	SNP	C	C	T	rs761349153	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.784C>T	p.Arg262Ter	p.R262*	ENST00000399770	4/4	157	140	17	47	47	0	GRXCR1,stop_gained,p.Arg262Ter,ENST00000399770,;	T	ENSG00000215203	ENST00000399770	Transcript	stop_gained	784	784	262	R/*	Cga/Tga	rs761349153,COSM174288	.	.	1	GRXCR1	HGNC	31673	protein_coding	YES	CCDS43225.1	ENSP00000382670	GRCR1_HUMAN	.	UPI00004191A5	.	.	.	4/4	.	hmmpanther:PTHR10168:SF65,hmmpanther:PTHR10168	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R262*|c.784C>T|5,BUFFER|p.R262Q|c.785G>A|5	RADIA|MUTECT|MUSE|VARSCANS	TGTTTCGAAAC	byFrequency	4	ESCA
TEC	0	.	GRCh37	4	48141032	48141032	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1543C>T	p.%3D	p.L515L	ENST00000381501	16/18	14	10	4	15	15	0	TEC,synonymous_variant,p.%3D,ENST00000381501,;TXK,upstream_gene_variant,,ENST00000264316,;TEC,downstream_gene_variant,,ENST00000511471,;TXK,upstream_gene_variant,,ENST00000510457,;TEC,3_prime_UTR_variant,,ENST00000515146,;TEC,3_prime_UTR_variant,,ENST00000505452,;TEC,non_coding_transcript_exon_variant,,ENST00000511150,;	A	ENSG00000135605	ENST00000381501	Transcript	synonymous_variant	1701	1543	515	L	Ctg/Ttg	.	.	.	-1	TEC	HGNC	11719	protein_coding	YES	CCDS3481.1	ENSP00000370912	TEC_HUMAN	Q14219_HUMAN	UPI000013CFAE	.	.	.	16/18	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF219,hmmpanther:PTHR24418,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCAGAACAT	.	2	ESCA
PCDHA10	0	.	GRCh37	5	140236873	140236873	+	Missense_Mutation	SNP	C	C	T	rs782208845	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1240C>T	p.Arg414Cys	p.R414C	ENST00000307360	1/4	144	54	90	99	99	0	PCDHA10,missense_variant,p.Arg414Cys,ENST00000506939,;PCDHA10,missense_variant,p.Arg414Cys,ENST00000307360,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA9,intron_variant,,ENST00000532602,;AC005609.1,downstream_gene_variant,,ENST00000502505,;PCDHA9,downstream_gene_variant,,ENST00000378122,;PCDHA14,upstream_gene_variant,,ENST00000506751,;	T	ENSG00000250120	ENST00000307360	Transcript	missense_variant	1240	1240	414	R/C	Cgc/Tgc	rs782208845,COSM736168,COSM736167	.	.	1	PCDHA10	HGNC	8664	protein_coding	YES	CCDS54921.1	ENSP00000304234	PCDAA_HUMAN	.	UPI00001273D3	.	deleterious_low_confidence(0.02)	benign(0.344)	1/4	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028:SF76,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACCGCGAG	.	5	ESCA
SLC6A3	0	.	GRCh37	5	1403165	1403165	+	Missense_Mutation	SNP	G	G	T	rs781299950	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1639C>A	p.His547Asn	p.H547N	ENST00000270349	13/15	45	34	11	26	26	0	SLC6A3,missense_variant,p.His547Asn,ENST00000270349,;SLC6A3,missense_variant,p.His547Asn,ENST00000453492,;SLC6A3,upstream_gene_variant,,ENST00000512002,;	T	ENSG00000142319	ENST00000270349	Transcript	missense_variant	1767	1639	547	H/N	Cac/Aac	rs781299950	.	.	-1	SLC6A3	HGNC	11049	protein_coding	YES	CCDS3863.1	ENSP00000270349	SC6A3_HUMAN	Q6LC27_HUMAN,H0YBA7_HUMAN	UPI000013548F	.	tolerated(0.51)	benign(0.002)	13/15	.	Prints_domain:PR01202,Superfamily_domains:0053687,Pfam_domain:PF00209,hmmpanther:PTHR11616:SF38,hmmpanther:PTHR11616,PROSITE_profiles:PS50267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGTGGGGGG	byFrequency	5	ESCA
ADAMTS2	0	.	GRCh37	5	178541072	178541072	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3432C>G	p.%3D	p.L1144L	ENST00000251582	22/22	86	66	20	52	52	0	ADAMTS2,synonymous_variant,p.%3D,ENST00000251582,;ADAMTS2,non_coding_transcript_exon_variant,,ENST00000522937,;ADAMTS2,downstream_gene_variant,,ENST00000523450,;	C	ENSG00000087116	ENST00000251582	Transcript	synonymous_variant	3534	3432	1144	L	ctC/ctG	.	.	.	-1	ADAMTS2	HGNC	218	protein_coding	YES	CCDS4444.1	ENSP00000251582	ATS2_HUMAN	.	UPI00001AE729	.	.	.	22/22	.	hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTGAGAGG	.	5	ESCA
MAP1B	0	.	GRCh37	5	71495635	71495635	+	Silent	SNP	C	C	T	rs543732551	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6453C>T	p.%3D	p.S2151S	ENST00000296755	5/7	21	11	10	37	37	0	MAP1B,synonymous_variant,p.%3D,ENST00000296755,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000513526,;	T	ENSG00000131711	ENST00000296755	Transcript	synonymous_variant	6751	6453	2151	S	agC/agT	rs543732551	.	.	1	MAP1B	HGNC	6836	protein_coding	YES	CCDS4012.1	ENSP00000296755	MAP1B_HUMAN	D6RGJ3_HUMAN,D6RA40_HUMAN	UPI000013E382	.	.	.	5/7	.	hmmpanther:PTHR13843,hmmpanther:PTHR13843:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAGCGAGTC	.	5	ESCA
FAM184A	0	.	GRCh37	6	119288068	119288068	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2965G>C	p.Asp989His	p.D989H	ENST00000338891	15/18	65	38	27	43	43	0	FAM184A,missense_variant,p.Asp152His,ENST00000521043,;FAM184A,missense_variant,p.Asp940His,ENST00000521531,;FAM184A,missense_variant,p.Asp820His,ENST00000368475,;FAM184A,missense_variant,p.Asp820His,ENST00000352896,;FAM184A,missense_variant,p.Asp989His,ENST00000338891,;FAM184A,missense_variant,p.Asp50His,ENST00000368472,;FAM184A,upstream_gene_variant,,ENST00000517987,;FAM184A,upstream_gene_variant,,ENST00000481884,;RP11-351A11.1,intron_variant,,ENST00000518570,;FAM184A,missense_variant,p.Asp244His,ENST00000475529,;FAM184A,upstream_gene_variant,,ENST00000482219,;	G	ENSG00000111879	ENST00000338891	Transcript	missense_variant	3409	2965	989	D/H	Gat/Cat	.	.	.	-1	FAM184A	HGNC	20991	protein_coding	YES	CCDS43499.1	ENSP00000342604	F184A_HUMAN	.	UPI0000470B36	.	deleterious(0)	probably_damaging(1)	15/18	.	hmmpanther:PTHR18870,hmmpanther:PTHR18870:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATCTTCTG	.	5	ESCA
SLC35D3	0	.	GRCh37	6	137245224	137245248	+	Frame_Shift_Del	DEL	CCTGGACCTTCCCGGGCTGGAAGGA	CCTGGACCTTCCCGGGCTGGAAGGA	-	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	CCTGGACCTTCCCGGGCTGGAAGGA	CCTGGACCTTCCCGGGCTGGAAGGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.643_667delTGGACCTTCCCGGGCTGGAAGGACC	p.Trp215ArgfsTer12	p.W215Rfs*12	ENST00000331858	2/2	29	22	7	17	17	0	SLC35D3,frameshift_variant,p.Trp215ArgfsTer12,ENST00000331858,;	-	ENSG00000182747	ENST00000331858	Transcript	frameshift_variant	806-830	641-665	214-222	AWTFPGWKD/X	gCCTGGACCTTCCCGGGCTGGAAGGAc/gc	.	.	.	1	SLC35D3	HGNC	15621	protein_coding	YES	CCDS34544.1	ENSP00000333591	S35D3_HUMAN	.	UPI00003673E9	.	.	.	2/2	.	Pfam_domain:PF03151,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCCACGCCTGGACCTTCCCGGGCTGGAAGGACCCGG	.	2	ESCA
HIST1H3F	0	.	GRCh37	6	26250521	26250522	+	Frame_Shift_Ins	INS	-	-	GAGCCCC	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306_312dupGGGGCTC	p.Phe105GlyfsTer4	p.F105Gfs*4	ENST00000446824	1/1	129	109	20	81	81	0	HIST1H3F,frameshift_variant,p.Phe105GlyfsTer4,ENST00000446824,;HIST1H4G,upstream_gene_variant,,ENST00000244537,;HIST1H2BH,upstream_gene_variant,,ENST00000356350,;	GAGCCCC	ENSG00000256316	ENST00000446824	Transcript	frameshift_variant	314-315	312-313	104-105	-/GAX	-/GGGGCTC	.	.	.	-1	HIST1H3F	HGNC	4773	protein_coding	YES	CCDS4600.1	ENSP00000444823	H31_HUMAN	.	UPI00000003C7	.	.	.	1/1	.	hmmpanther:PTHR11426,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTCAAAGAGCC	.	2	ESCA
C6orf25	0	.	GRCh37	6	31692792	31692792	+	Missense_Mutation	SNP	C	C	T	rs748914079	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.667C>T	p.Arg223Cys	p.R223C	ENST00000375806	6/6	14	6	7	10	10	0	C6orf25,missense_variant,p.Pro229Leu,ENST00000375809,;C6orf25,missense_variant,p.Pro185Leu,ENST00000375804,;C6orf25,missense_variant,p.Arg223Cys,ENST00000375806,;C6orf25,missense_variant,p.Arg179Cys,ENST00000375814,;C6orf25,missense_variant,p.Arg199Cys,ENST00000375805,;C6orf25,3_prime_UTR_variant,,ENST00000375810,;DDAH2,downstream_gene_variant,,ENST00000375787,;DDAH2,downstream_gene_variant,,ENST00000375792,;DDAH2,downstream_gene_variant,,ENST00000375789,;DDAH2,downstream_gene_variant,,ENST00000437288,;LY6G6C,upstream_gene_variant,,ENST00000375819,;C6orf25,downstream_gene_variant,,ENST00000480039,;LY6G6C,upstream_gene_variant,,ENST00000495859,;DDAH2,downstream_gene_variant,,ENST00000416410,;DDAH2,downstream_gene_variant,,ENST00000436437,;DDAH2,downstream_gene_variant,,ENST00000483792,;DDAH2,downstream_gene_variant,,ENST00000480913,;C6orf25,3_prime_UTR_variant,,ENST00000485548,;C6orf25,non_coding_transcript_exon_variant,,ENST00000471545,;C6orf25,non_coding_transcript_exon_variant,,ENST00000460663,;DDAH2,downstream_gene_variant,,ENST00000488119,;C6orf25,downstream_gene_variant,,ENST00000466312,;DDAH2,downstream_gene_variant,,ENST00000469963,;	T	ENSG00000204420	ENST00000375806	Transcript	missense_variant	667	667	223	R/C	Cgc/Tgc	rs748914079	.	.	1	C6orf25	HGNC	13937	protein_coding	YES	CCDS4715.1	ENSP00000364964	G6B_HUMAN	.	UPI000006DE84	.	tolerated_low_confidence(0.2)	benign(0.002)	6/6	.	Pfam_domain:PF15096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	GGCCCCGCCGG	byFrequency	4	ESCA
ZNF318	0	.	GRCh37	6	43305847	43305847	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5889G>C	p.Lys1963Asn	p.K1963N	ENST00000361428	10/10	40	26	13	18	18	0	ZNF318,missense_variant,p.Lys1963Asn,ENST00000361428,;ZNF318,intron_variant,,ENST00000606599,;ZNF318,intron_variant,,ENST00000318149,;ZNF318,intron_variant,,ENST00000605935,;	G	ENSG00000171467	ENST00000361428	Transcript	missense_variant	5967	5889	1963	K/N	aaG/aaC	.	.	.	-1	ZNF318	HGNC	13578	protein_coding	YES	CCDS4895.2	ENSP00000354964	ZN318_HUMAN	.	UPI000049E044	.	.	benign(0.002)	10/10	.	hmmpanther:PTHR15577:SF2,hmmpanther:PTHR15577	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCTTGTT	.	5	ESCA
POLH	0	.	GRCh37	6	43565542	43565542	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600G>A	p.Met200Ile	p.M200I	ENST00000372236	5/11	71	59	12	47	47	0	POLH,missense_variant,p.Met200Ile,ENST00000372226,;POLH,missense_variant,p.Met138Ile,ENST00000535400,;POLH,missense_variant,p.Met200Ile,ENST00000372236,;	A	ENSG00000170734	ENST00000372236	Transcript	missense_variant	895	600	200	M/I	atG/atA	.	.	.	1	POLH	HGNC	9181	protein_coding	YES	CCDS4902.1	ENSP00000361310	POLH_HUMAN	Q5JTF2_HUMAN,B4DG64_HUMAN,B3KN75_HUMAN	UPI000006F8FD	.	tolerated(0.09)	benign(0.039)	5/11	.	PROSITE_profiles:PS50173,hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF11,Gene3D:3.30.70.270,Pfam_domain:PF00817,PIRSF_domain:PIRSF036603,Superfamily_domains:SSF56672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAATGAGAGC	.	5	ESCA
MDN1	0	.	GRCh37	6	90385858	90385858	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12608A>C	p.His4203Pro	p.H4203P	ENST00000369393	77/102	39	28	10	26	26	0	MDN1,missense_variant,p.His4203Pro,ENST00000369393,;MDN1,missense_variant,p.His4203Pro,ENST00000428876,;RP1-122O8.7,downstream_gene_variant,,ENST00000438877,;MDN1,upstream_gene_variant,,ENST00000468568,;	G	ENSG00000112159	ENST00000369393	Transcript	missense_variant	12724	12608	4203	H/P	cAt/cCt	.	.	.	-1	MDN1	HGNC	18302	protein_coding	YES	CCDS5024.1	ENSP00000358400	MDN1_HUMAN	M0QXR3_HUMAN	UPI000013C4B8	.	.	possibly_damaging(0.642)	77/102	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22908:SF58,hmmpanther:PTHR22908,PIRSF_domain:PIRSF010340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCATGCCGT	.	5	ESCA
FUT9	0	.	GRCh37	6	96662829	96662829	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10718C>A	.	.	ENST00000302103	3/3	30	22	8	27	27	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	A	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	12124	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCCTGCTG	.	5	ESCA
SLC13A4	0	.	GRCh37	7	135406264	135406264	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.107C>T	p.Ser36Leu	p.S36L	ENST00000354042	2/16	30	19	11	22	22	0	SLC13A4,missense_variant,p.Ser36Leu,ENST00000378428,;SLC13A4,missense_variant,p.Ser36Leu,ENST00000422620,;SLC13A4,missense_variant,p.Ser36Leu,ENST00000354042,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000471405,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000478310,;	A	ENSG00000164707	ENST00000354042	Transcript	missense_variant	797	107	36	S/L	tCg/tTg	.	.	.	-1	SLC13A4	HGNC	15827	protein_coding	YES	CCDS5840.1	ENSP00000297282	S13A4_HUMAN	.	UPI00000343D9	.	tolerated(0.12)	benign(0.407)	2/16	.	Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACGAGGCC	.	5	ESCA
GRM3	0	.	GRCh37	7	86274000	86274000	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-329C>T	.	.	ENST00000361669	1/6	70	60	9	51	51	0	GRM3,5_prime_UTR_variant,,ENST00000536043,;GRM3,5_prime_UTR_variant,,ENST00000454217,;GRM3,5_prime_UTR_variant,,ENST00000361669,;GRM3,5_prime_UTR_variant,,ENST00000546348,;GRM3,upstream_gene_variant,,ENST00000439827,;GRM3,upstream_gene_variant,,ENST00000421579,;GRM3,upstream_gene_variant,,ENST00000394720,;	T	ENSG00000198822	ENST00000361669	Transcript	5_prime_UTR_variant	771	.	.	.	.	.	.	.	1	GRM3	HGNC	4595	protein_coding	YES	CCDS5600.1	ENSP00000355316	GRM3_HUMAN	C9JUH9_HUMAN,C9JIT1_HUMAN,A4D1D0_HUMAN	UPI0000153EFC	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCTGCGCGCA	.	4	ESCA
ASNS	0	.	GRCh37	7	97481732	97481732	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1525A>G	p.Thr509Ala	p.T509A	ENST00000175506	14/14	64	27	37	49	49	0	ASNS,missense_variant,p.Thr509Ala,ENST00000394309,;ASNS,missense_variant,p.Thr426Ala,ENST00000437628,;ASNS,missense_variant,p.Thr509Ala,ENST00000175506,;ASNS,missense_variant,p.Thr426Ala,ENST00000455086,;ASNS,missense_variant,p.Thr488Ala,ENST00000444334,;ASNS,missense_variant,p.Thr509Ala,ENST00000394308,;ASNS,missense_variant,p.Thr488Ala,ENST00000422745,;ASNS,3_prime_UTR_variant,,ENST00000454046,;ASNS,non_coding_transcript_exon_variant,,ENST00000487714,;ASNS,downstream_gene_variant,,ENST00000462436,;	C	ENSG00000070669	ENST00000175506	Transcript	missense_variant	2054	1525	509	T/A	Act/Gct	.	.	.	-1	ASNS	HGNC	753	protein_coding	YES	CCDS5652.1	ENSP00000175506	ASNS_HUMAN	C9JT45_HUMAN,C9JM09_HUMAN,C9JLA3_HUMAN,C9J605_HUMAN,C9J057_HUMAN	UPI0000169F55	.	tolerated(0.16)	benign(0.081)	14/14	.	hmmpanther:PTHR11772:SF5,hmmpanther:PTHR11772,Gene3D:3.40.50.620,PIRSF_domain:PIRSF001589,Superfamily_domains:SSF52402	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAGTATTGA	.	5	ESCA
CSMD3	0	.	GRCh37	8	113277777	113277777	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9551G>C	p.Arg3184Thr	p.R3184T	ENST00000297405	60/71	70	39	31	46	46	0	CSMD3,missense_variant,p.Arg3114Thr,ENST00000352409,;CSMD3,missense_variant,p.Arg3015Thr,ENST00000455883,;CSMD3,missense_variant,p.Arg3184Thr,ENST00000297405,;CSMD3,missense_variant,p.Arg2454Thr,ENST00000339701,;CSMD3,missense_variant,p.Arg3144Thr,ENST00000343508,;	G	ENSG00000164796	ENST00000297405	Transcript	missense_variant	9796	9551	3184	R/T	aGa/aCa	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	deleterious(0.03)	probably_damaging(0.93)	60/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATATCTCAGT	.	5	ESCA
ST18	0	.	GRCh37	8	53126769	53126769	+	Missense_Mutation	SNP	T	T	A	rs775154209	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.49A>T	p.Thr17Ser	p.T17S	ENST00000276480	7/26	89	62	26	63	63	0	ST18,missense_variant,p.Thr17Ser,ENST00000517580,;ST18,missense_variant,p.Thr17Ser,ENST00000276480,;ST18,downstream_gene_variant,,ENST00000519118,;ST18,non_coding_transcript_exon_variant,,ENST00000517456,;ST18,non_coding_transcript_exon_variant,,ENST00000518037,;ST18,non_coding_transcript_exon_variant,,ENST00000521549,;ST18,non_coding_transcript_exon_variant,,ENST00000520257,;ST18,downstream_gene_variant,,ENST00000518545,;ST18,missense_variant,p.Thr17Ser,ENST00000521824,;ST18,missense_variant,p.Thr17Ser,ENST00000521582,;ST18,missense_variant,p.Thr17Ser,ENST00000522251,;	A	ENSG00000147488	ENST00000276480	Transcript	missense_variant	733	49	17	T/S	Acc/Tcc	rs775154209	.	.	-1	ST18	HGNC	18695	protein_coding	YES	CCDS6149.1	ENSP00000276480	ST18_HUMAN	E5RHS3_HUMAN	UPI0000046C30	.	tolerated(0.35)	benign(0.01)	7/26	.	hmmpanther:PTHR10816:SF9,hmmpanther:PTHR10816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCGGTTCCTT	.	5	ESCA
PTDSS1	0	.	GRCh37	8	97345832	97345832	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*38G>C	.	.	ENST00000517309	13/13	24	15	9	14	13	0	PTDSS1,3_prime_UTR_variant,,ENST00000517309,;PTDSS1,3_prime_UTR_variant,,ENST00000455950,;PTDSS1,intron_variant,,ENST00000522072,;PTDSS1,3_prime_UTR_variant,,ENST00000337004,;PTDSS1,non_coding_transcript_exon_variant,,ENST00000517982,;	C	ENSG00000156471	ENST00000517309	Transcript	3_prime_UTR_variant	1786	.	.	.	.	.	.	.	1	PTDSS1	HGNC	9587	protein_coding	YES	CCDS6271.1	ENSP00000430548	PTSS1_HUMAN	Q9BUQ5_HUMAN	UPI0000132810	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCTAGAACTG	.	3	ESCA
FOXE1	0	.	GRCh37	9	100618166	100618166	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*848C>G	.	.	ENST00000375123	1/1	28	7	20	22	22	0	FOXE1,3_prime_UTR_variant,,ENST00000375123,;	G	ENSG00000178919	ENST00000375123	Transcript	3_prime_UTR_variant	2631	.	.	.	.	.	.	.	1	FOXE1	HGNC	3806	protein_coding	YES	CCDS35078.1	ENSP00000364265	FOXE1_HUMAN	.	UPI0000167B2F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCCAGGCA	.	5	ESCA
TXN	0	.	GRCh37	9	113018831	113018831	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-116C>G	.	.	ENST00000374517	1/5	20	10	10	13	12	1	TXN,5_prime_UTR_variant,,ENST00000374517,;TXN,upstream_gene_variant,,ENST00000374515,;	C	ENSG00000136810	ENST00000374517	Transcript	5_prime_UTR_variant	90	.	.	.	.	.	.	.	-1	TXN	HGNC	12435	protein_coding	YES	CCDS35103.1	ENSP00000363641	THIO_HUMAN	H9ZYJ2_HUMAN	UPI000011065C	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CGCCCGGCGTG	.	2	ESCA
ASTN2	0	.	GRCh37	9	119188344	119188344	+	Missense_Mutation	SNP	C	C	A	rs200117563	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3653G>T	p.Arg1218Leu	p.R1218L	ENST00000361209	22/22	31	26	4	30	30	0	ASTN2,missense_variant,p.Arg1265Leu,ENST00000373996,;ASTN2,missense_variant,p.Arg370Leu,ENST00000288520,;ASTN2,missense_variant,p.Arg1269Leu,ENST00000313400,;ASTN2,missense_variant,p.Arg1218Leu,ENST00000361209,;ASTN2,missense_variant,p.Arg321Leu,ENST00000361477,;ASTN2,missense_variant,p.Arg321Leu,ENST00000341734,;ASTN2,missense_variant,p.Arg992Leu,ENST00000373986,;	A	ENSG00000148219	ENST00000361209	Transcript	missense_variant	3785	3653	1218	R/L	cGa/cTa	rs200117563	.	.	-1	ASTN2	HGNC	17021	protein_coding	YES	CCDS6815.1	ENSP00000354504	ASTN2_HUMAN	B7ZKP3_HUMAN,B2RCB6_HUMAN	UPI00002116D7	.	deleterious(0.01)	unknown(0)	22/22	.	hmmpanther:PTHR16592	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGTCGCCGT	byCluster	4	ESCA
SPTAN1	0	.	GRCh37	9	131370264	131370264	+	Frame_Shift_Del	DEL	G	G	-	rs762216368	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4280delG	p.Arg1427LeufsTer13	p.R1427Lfs*13	ENST00000372739	33/57	79	69	10	60	60	0	SPTAN1,frameshift_variant,p.Arg1427LeufsTer13,ENST00000372739,;SPTAN1,frameshift_variant,p.Arg1427LeufsTer13,ENST00000358161,;SPTAN1,frameshift_variant,p.Arg1427LeufsTer13,ENST00000372731,;SPTAN1,non_coding_transcript_exon_variant,,ENST00000461855,;SPTAN1,upstream_gene_variant,,ENST00000476825,;	-	ENSG00000197694	ENST00000372739	Transcript	frameshift_variant	4390	4280	1427	R/X	cGt/ct	rs762216368	.	.	1	SPTAN1	HGNC	11273	protein_coding	YES	CCDS48036.1	ENSP00000361824	SPTN1_HUMAN	.	UPI000045894C	.	.	.	33/57	.	hmmpanther:PTHR11915:SF250,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGAGCGTGCAG	byFrequency	3	ESCA
LCN6	0	.	GRCh37	9	139642865	139642865	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71G>C	p.Gly24Ala	p.G24A	ENST00000341206	1/7	88	24	64	63	63	0	LCN6,missense_variant,p.Gly24Ala,ENST00000341206,;LCN6,upstream_gene_variant,,ENST00000476567,;LCN6,upstream_gene_variant,,ENST00000480584,;LCN6,upstream_gene_variant,,ENST00000497749,;LCN6,upstream_gene_variant,,ENST00000471509,;LCN6,upstream_gene_variant,,ENST00000494091,;LCN6,upstream_gene_variant,,ENST00000480347,;LCN6,missense_variant,p.Gly14Ala,ENST00000435202,;	G	ENSG00000267206	ENST00000341206	Transcript	missense_variant	116	71	24	G/A	gGa/gCa	.	.	.	-1	LCN6	HGNC	17337	protein_coding	YES	CCDS7005.1	ENSP00000339621	LCN6_HUMAN	K7ERN5_HUMAN,H7C1C5_HUMAN	UPI0000047820	.	tolerated(0.94)	probably_damaging(0.982)	1/7	.	hmmpanther:PTHR11430,hmmpanther:PTHR11430:SF10,Gene3D:2.40.128.20,Superfamily_domains:SSF50814	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCCCAAC	.	5	ESCA
TAF1L	0	.	GRCh37	9	32630449	32630449	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5129G>A	p.Arg1710Lys	p.R1710K	ENST00000242310	1/1	154	55	99	118	118	0	TAF1L,missense_variant,p.Arg1710Lys,ENST00000242310,;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,;AL589642.1,non_coding_transcript_exon_variant,,ENST00000541085,;	T	ENSG00000122728	ENST00000242310	Transcript	missense_variant	5219	5129	1710	R/K	aGg/aAg	.	.	.	-1	TAF1L	HGNC	18056	protein_coding	YES	CCDS35003.1	ENSP00000418379	TAF1L_HUMAN	.	UPI000007408A	.	tolerated_low_confidence(0.38)	benign(0.062)	1/1	.	hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0,PIRSF_domain:PIRSF003047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCCTACCT	.	5	ESCA
MIRLET7F1	0	.	GRCh37	9	96938644	96938644	+	RNA	SNP	A	A	T	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.16A>T	.	.	ENST00000362202	1/1	51	13	38	34	34	0	MIRLET7F1,non_coding_transcript_exon_variant,,ENST00000362202,;RP11-2B6.3,intron_variant,,ENST00000602703,;MIRLET7D,upstream_gene_variant,,ENST00000362263,;MIRLET7A1,downstream_gene_variant,,ENST00000362295,;MIRLET7DHG,downstream_gene_variant,,ENST00000602602,;MIRLET7DHG,downstream_gene_variant,,ENST00000416309,;RP11-2B6.2,upstream_gene_variant,,ENST00000602652,;	T	ENSG00000199072	ENST00000362202	Transcript	non_coding_transcript_exon_variant	16	.	.	.	.	.	.	.	1	MIRLET7F1	HGNC	31483	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGTAGATTG	.	5	ESCA
PNMA3	0	.	GRCh37	X	152228013	152228013	+	3'UTR	SNP	C	C	T	rs782597055	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1209C>T	.	.	ENST00000447306	2/2	47	10	36	29	29	0	PNMA3,3_prime_UTR_variant,,ENST00000447306,;PNMA3,3_prime_UTR_variant,,ENST00000370265,;PNMA3,downstream_gene_variant,,ENST00000370264,;PNMA3,3_prime_UTR_variant,,ENST00000424805,;	T	ENSG00000183837	ENST00000447306	Transcript	3_prime_UTR_variant	2937	.	.	.	.	rs782597055	.	.	1	PNMA3	HGNC	18742	protein_coding	YES	CCDS35435.2	ENSP00000407642	PNMA3_HUMAN	.	UPI00002123C6	.	.	.	2/2	.	.	T:0.0003	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGACGCCCA	by1000G	5	ESCA
WASH6P	0	.	GRCh37	X	155255244	155255248	+	RNA	DEL	GGGAC	GGGAC	AT	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	GGGAC	GGGAC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4160_4164delGGGACinsAT	.	.	ENST00000461007	2/2	144	115	29	100	100	0	WASH6P,non_coding_transcript_exon_variant,,ENST00000340131,;AJ271736.10,non_coding_transcript_exon_variant,,ENST00000285718,;WASH6P,non_coding_transcript_exon_variant,,ENST00000484415,;WASH6P,non_coding_transcript_exon_variant,,ENST00000492963,;WASH6P,non_coding_transcript_exon_variant,,ENST00000461007,;WASH6P,non_coding_transcript_exon_variant,,ENST00000460206,;WASH6P,non_coding_transcript_exon_variant,,ENST00000496301,;WASH6P,downstream_gene_variant,,ENST00000476066,;WASH6P,downstream_gene_variant,,ENST00000475594,;WASH6P,downstream_gene_variant,,ENST00000464205,;WASH6P,downstream_gene_variant,,ENST00000482170,;WASH6P,downstream_gene_variant,,ENST00000469624,;WASH6P,downstream_gene_variant,,ENST00000479401,;WASH6P,downstream_gene_variant,,ENST00000496011,;WASH6P,downstream_gene_variant,,ENST00000483079,;WASH6P,downstream_gene_variant,,ENST00000483286,;AJ271736.10,downstream_gene_variant,,ENST00000483543,;DDX11L16,downstream_gene_variant,,ENST00000445777,;DDX11L16,downstream_gene_variant,,ENST00000507418,;WASH6P,downstream_gene_variant,,ENST00000359512,;	AT	ENSG00000182484	ENST00000461007	Transcript	non_coding_transcript_exon_variant	4160-4164	.	.	.	.	.	.	.	1	WASH6P	HGNC	31685	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATGGGGGGACGGCTC	.	3	ESCA
PHF8	0	.	GRCh37	X	53970565	53970565	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-IG-A3YB-01A-11D-A247-09	TCGA-IG-A3YB-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2757+2T>G	.	p.X919_splice	ENST00000357988	.	53	17	36	36	36	0	PHF8,splice_donor_variant,,ENST00000443302,;PHF8,splice_donor_variant,,ENST00000396282,;PHF8,splice_donor_variant,,ENST00000322659,;PHF8,splice_donor_variant,,ENST00000357988,;PHF8,splice_donor_variant,,ENST00000338154,;PHF8,splice_donor_variant,,ENST00000338946,;PHF8,splice_donor_variant,,ENST00000470103,;	C	ENSG00000172943	ENST00000357988	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	PHF8	HGNC	20672	protein_coding	YES	CCDS55420.1	ENSP00000350676	PHF8_HUMAN	Q5JPR8_HUMAN,B3KMV4_HUMAN,B0QZZ4_HUMAN,B0QZZ3_HUMAN,B0QZZ2_HUMAN,B0QZE1_HUMAN	UPI00001C2071	.	.	.	.	20/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTACCTGC	.	5	ESCA
ARMC3	0	.	GRCh37	10	23292215	23292215	+	Missense_Mutation	SNP	C	C	T	rs148669748	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1603C>T	p.Arg535Trp	p.R535W	ENST00000298032	13/19	20	15	5	51	51	0	ARMC3,missense_variant,p.Arg535Trp,ENST00000409983,;ARMC3,missense_variant,p.Arg535Trp,ENST00000409049,;ARMC3,missense_variant,p.Arg535Trp,ENST00000298032,;ARMC3,missense_variant,p.Arg272Trp,ENST00000376528,;ARMC3,upstream_gene_variant,,ENST00000491803,;	T	ENSG00000165309	ENST00000298032	Transcript	missense_variant	1687	1603	535	R/W	Cgg/Tgg	rs148669748	.	.	1	ARMC3	HGNC	30964	protein_coding	YES	CCDS7142.1	ENSP00000298032	ARMC3_HUMAN	C9JC46_HUMAN,B4DXS3_HUMAN	UPI0000161785	.	deleterious(0)	possibly_damaging(0.841)	13/19	.	hmmpanther:PTHR23315:SF48,hmmpanther:PTHR23315	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GAACTCGGAAA	byCluster	4	ESCA
ZNF488	0	.	GRCh37	10	48370969	48370969	+	Missense_Mutation	SNP	A	A	G	rs140082282	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437A>G	p.Lys146Arg	p.K146R	ENST00000395702	2/2	16	8	8	68	68	0	ZNF488,missense_variant,p.Lys146Arg,ENST00000395702,;ZNF488,missense_variant,p.Lys39Arg,ENST00000586537,;ZNF488,3_prime_UTR_variant,,ENST00000494156,;ZNF488,downstream_gene_variant,,ENST00000444585,;ZNF488,downstream_gene_variant,,ENST00000442001,;ZNF488,downstream_gene_variant,,ENST00000433077,;ZNF488,downstream_gene_variant,,ENST00000436850,;ZNF488,downstream_gene_variant,,ENST00000412534,;ZNF488,downstream_gene_variant,,ENST00000425196,;	G	ENSG00000165388	ENST00000395702	Transcript	missense_variant	664	437	146	K/R	aAa/aGa	rs140082282	.	.	1	ZNF488	HGNC	23535	protein_coding	YES	CCDS7217.1	ENSP00000379054	ZN488_HUMAN	Q05CE0_HUMAN,A2AH66_HUMAN,A2AH65_HUMAN,A2AH64_HUMAN,A2AH63_HUMAN,A2AH62_HUMAN,A2AH61_HUMAN	UPI00000736CF	.	deleterious(0.02)	benign(0.007)	2/2	.	hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF1	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAAAGTCT	byCluster	5	ESCA
GRAMD1B	0	.	GRCh37	11	123480536	123480536	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1262A>T	p.Asn421Ile	p.N421I	ENST00000529750	12/20	28	22	6	92	92	0	GRAMD1B,missense_variant,p.Asn421Ile,ENST00000322282,;GRAMD1B,missense_variant,p.Asn417Ile,ENST00000534764,;GRAMD1B,missense_variant,p.Asn421Ile,ENST00000529750,;GRAMD1B,missense_variant,p.Asn428Ile,ENST00000456860,;GRAMD1B,missense_variant,p.Asn381Ile,ENST00000529432,;GRAMD1B,missense_variant,p.Asn112Ile,ENST00000450171,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;GRAMD1B,upstream_gene_variant,,ENST00000525945,;	T	ENSG00000023171	ENST00000529750	Transcript	missense_variant	1589	1262	421	N/I	aAt/aTt	.	.	.	1	GRAMD1B	HGNC	29214	protein_coding	YES	CCDS53720.1	ENSP00000436500	GRM1B_HUMAN	.	UPI00005C3025	.	tolerated(0.07)	benign(0.032)	12/20	.	hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGAATGGAA	.	5	ESCA
OR8G1	0	.	GRCh37	11	124121122	124121122	+	Missense_Mutation	SNP	A	A	G	rs753266210	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.700A>G	p.Arg234Gly	p.R234G	ENST00000341493	1/3	61	56	4	134	134	0	OR8G1,missense_variant,p.Arg234Gly,ENST00000341493,;OR8G1,missense_variant,p.Arg234Gly,ENST00000534473,;	G	ENSG00000197849	ENST00000341493	Transcript	missense_variant	700	700	234	R/G	Agg/Ggg	rs753266210	.	.	1	OR8G1	HGNC	8484	protein_coding	YES	.	ENSP00000476313	.	.	UPI00004565A2	.	deleterious_low_confidence(0)	probably_damaging(0.945)	1/3	.	Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF73,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGCAGGTCC	byFrequency	2	ESCA
OR8G5	0	.	GRCh37	11	124135103	124135105	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383_385delCCT	p.Ser128del	p.S128del	ENST00000524943	1/1	67	57	10	177	177	0	OR8G5,inframe_deletion,p.Ser128del,ENST00000524943,;OR8G1,intron_variant,,ENST00000341493,;	-	ENSG00000255298	ENST00000524943	Transcript	inframe_deletion	381-383	381-383	127-128	IS/I	atCTCc/atc	.	.	.	1	OR8G5	HGNC	19622	protein_coding	YES	CCDS66256.1	ENSP00000477014	OR8G5_HUMAN	B2RND3_HUMAN	UPI00003B286B	.	.	.	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452:SF73,hmmpanther:PTHR26452,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATCATCTCCTACC	.	3	ESCA
LRRC56	0	.	GRCh37	11	550123	550123	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.475C>A	p.Leu159Met	p.L159M	ENST00000270115	8/14	36	30	5	101	101	0	LRRC56,missense_variant,p.Leu159Met,ENST00000270115,;C11orf35,downstream_gene_variant,,ENST00000329451,;C11orf35,downstream_gene_variant,,ENST00000469990,;	A	ENSG00000161328	ENST00000270115	Transcript	missense_variant	975	475	159	L/M	Ctg/Atg	.	.	.	1	LRRC56	HGNC	25430	protein_coding	YES	CCDS7700.1	ENSP00000270115	LRC56_HUMAN	.	UPI000007425F	.	deleterious(0)	probably_damaging(0.999)	8/14	.	Superfamily_domains:SSF52058,Gene3D:3.80.10.10,hmmpanther:PTHR22708:SF0,hmmpanther:PTHR22708,PROSITE_profiles:PS51450,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCTGCTGGAA	.	3	ESCA
PC	0	.	GRCh37	11	66616073	66616073	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*297T>A	.	.	ENST00000393960	23/23	35	30	5	82	82	0	PC,3_prime_UTR_variant,,ENST00000393958,;PC,3_prime_UTR_variant,,ENST00000393955,;PC,3_prime_UTR_variant,,ENST00000393960,;PC,3_prime_UTR_variant,,ENST00000529047,;RCE1,downstream_gene_variant,,ENST00000524506,;RCE1,downstream_gene_variant,,ENST00000525356,;RCE1,downstream_gene_variant,,ENST00000309657,;PC,non_coding_transcript_exon_variant,,ENST00000528224,;PC,downstream_gene_variant,,ENST00000530259,;RCE1,downstream_gene_variant,,ENST00000534645,;PC,downstream_gene_variant,,ENST00000529352,;RCE1,downstream_gene_variant,,ENST00000533277,;RCE1,downstream_gene_variant,,ENST00000524849,;RCE1,downstream_gene_variant,,ENST00000532775,;RCE1,downstream_gene_variant,,ENST00000534822,;RCE1,downstream_gene_variant,,ENST00000530610,;	T	ENSG00000173599	ENST00000393960	Transcript	3_prime_UTR_variant	4116	.	.	.	.	.	.	.	-1	PC	HGNC	8636	protein_coding	YES	CCDS8152.1	ENSP00000377532	PYC_HUMAN	E9PS68_HUMAN	UPI0000132BC4	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGATAGGACC	.	4	ESCA
KIAA1033	0	.	GRCh37	12	105562252	105562252	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1543A>G	.	.	ENST00000332180	33/33	14	9	5	43	43	0	KIAA1033,3_prime_UTR_variant,,ENST00000332180,;APPL2,downstream_gene_variant,,ENST00000258530,;KIAA1033,downstream_gene_variant,,ENST00000547171,;KIAA1033,3_prime_UTR_variant,,ENST00000550053,;APPL2,downstream_gene_variant,,ENST00000547439,;KIAA1033,downstream_gene_variant,,ENST00000550036,;	G	ENSG00000136051	ENST00000332180	Transcript	3_prime_UTR_variant	5152	.	.	.	.	.	.	.	1	KIAA1033	HGNC	29174	protein_coding	YES	CCDS41826.1	ENSP00000328062	WASH7_HUMAN	F8W1W1_HUMAN,F8VQX3_HUMAN,F8VNZ5_HUMAN	UPI00001C1F3B	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTATATCAAA	.	5	ESCA
ACACB	0	.	GRCh37	12	109702980	109702980	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7008G>C	p.Glu2336Asp	p.E2336D	ENST00000338432	51/53	19	12	6	80	79	0	ACACB,missense_variant,p.Glu2266Asp,ENST00000377854,;ACACB,missense_variant,p.Glu2336Asp,ENST00000377848,;ACACB,missense_variant,p.Glu2336Asp,ENST00000338432,;ACACB,3_prime_UTR_variant,,ENST00000543201,;ACACB,3_prime_UTR_variant,,ENST00000538526,;ACACB,non_coding_transcript_exon_variant,,ENST00000537279,;	C	ENSG00000076555	ENST00000338432	Transcript	missense_variant	7127	7008	2336	E/D	gaG/gaC	.	.	.	1	ACACB	HGNC	85	protein_coding	YES	CCDS31898.1	ENSP00000341044	ACACB_HUMAN	F5H5C3_HUMAN,E9PEW7_HUMAN	UPI0000DBEEFB	.	deleterious(0.01)	possibly_damaging(0.908)	51/53	.	hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF84,Gene3D:3.90.226.10,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGGACCA	.	5	ESCA
ALDH2	0	.	GRCh37	12	112241777	112241778	+	Splice_Site	DEL	TG	TG	-	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	TG	TG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1521+2_1521+3delTG	.	p.X507_splice	ENST00000261733	12/13	57	47	10	77	77	0	ALDH2,splice_donor_variant,,ENST00000416293,;ALDH2,splice_donor_variant,,ENST00000261733,;ALDH2,splice_donor_variant,,ENST00000549106,;ALDH2,splice_donor_variant,,ENST00000548536,;	-	ENSG00000111275	ENST00000261733	Transcript	splice_donor_variant	1582-?	1521-?	507-?	.	.	.	.	.	1	ALDH2	HGNC	404	protein_coding	YES	CCDS9155.1	ENSP00000261733	ALDH2_HUMAN	Q9UN17_HUMAN,B4YAH7_HUMAN,B0LUF9_HUMAN	UPI0000129293	.	.	.	12/13	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAAACTGTGAGT	.	3	ESCA
SOX5	0	.	GRCh37	12	23999004	23999004	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394C>T	p.Pro132Ser	p.P132S	ENST00000451604	3/15	23	17	5	52	52	0	SOX5,missense_variant,p.Pro119Ser,ENST00000309359,;SOX5,missense_variant,p.Pro119Ser,ENST00000381381,;SOX5,missense_variant,p.Pro122Ser,ENST00000541847,;SOX5,missense_variant,p.Pro119Ser,ENST00000546136,;SOX5,missense_variant,p.Pro97Ser,ENST00000441133,;SOX5,missense_variant,p.Pro97Ser,ENST00000537393,;SOX5,missense_variant,p.Pro119Ser,ENST00000541536,;SOX5,missense_variant,p.Pro132Ser,ENST00000451604,;SOX5,missense_variant,p.Pro122Ser,ENST00000545921,;SOX5,missense_variant,p.Pro119Ser,ENST00000538083,;SOX5,missense_variant,p.Pro122Ser,ENST00000367206,;	A	ENSG00000134532	ENST00000451604	Transcript	missense_variant	496	394	132	P/S	Cct/Tct	.	.	.	-1	SOX5	HGNC	11201	protein_coding	YES	CCDS8699.1	ENSP00000398273	SOX5_HUMAN	T2CYZ2_HUMAN,F5GWL1_HUMAN	UPI000007405E	.	deleterious(0)	probably_damaging(0.998)	3/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGGAGTTC	.	5	ESCA
PCBP2	0	.	GRCh37	12	53848620	53848620	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36C>A	p.%3D	p.V12V	ENST00000359462	2/15	28	24	3	103	103	0	PCBP2,synonymous_variant,p.%3D,ENST00000550192,;PCBP2,synonymous_variant,p.%3D,ENST00000455667,;PCBP2,synonymous_variant,p.%3D,ENST00000552980,;PCBP2,synonymous_variant,p.%3D,ENST00000546463,;PCBP2,synonymous_variant,p.%3D,ENST00000550520,;PCBP2,synonymous_variant,p.%3D,ENST00000359282,;PCBP2,synonymous_variant,p.%3D,ENST00000552819,;PCBP2,synonymous_variant,p.%3D,ENST00000552296,;PCBP2,synonymous_variant,p.%3D,ENST00000551104,;PCBP2,synonymous_variant,p.%3D,ENST00000359462,;PCBP2,synonymous_variant,p.%3D,ENST00000541275,;PCBP2,synonymous_variant,p.%3D,ENST00000437231,;PCBP2,synonymous_variant,p.%3D,ENST00000439930,;PCBP2,synonymous_variant,p.%3D,ENST00000447282,;PCBP2,synonymous_variant,p.%3D,ENST00000548933,;PCBP2,synonymous_variant,p.%3D,ENST00000549863,;PCBP2,synonymous_variant,p.%3D,ENST00000603815,;PCBP2,upstream_gene_variant,,ENST00000562264,;PCBP2,synonymous_variant,p.%3D,ENST00000546652,;PCBP2,non_coding_transcript_exon_variant,,ENST00000550910,;RP11-793H13.8,non_coding_transcript_exon_variant,,ENST00000547717,;PCBP2,upstream_gene_variant,,ENST00000550585,;PCBP2,upstream_gene_variant,,ENST00000547987,;PCBP2,upstream_gene_variant,,ENST00000548190,;	A	ENSG00000197111	ENST00000359462	Transcript	synonymous_variant	359	36	12	V	gtC/gtA	.	.	.	1	PCBP2	HGNC	8648	protein_coding	YES	CCDS44900.1	ENSP00000352438	PCBP2_HUMAN	H3BSP4_HUMAN,F8W0G4_HUMAN,F8VTZ0_HUMAN	UPI0000161C69	.	.	.	2/15	.	Superfamily_domains:SSF54791,SMART_domains:SM00322,hmmpanther:PTHR10288:SF97,hmmpanther:PTHR10288	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AATGTCACTCT	.	3	ESCA
GDF3	0	.	GRCh37	12	7842645	7842645	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.924C>T	p.%3D	p.S308S	ENST00000329913	2/2	30	25	5	71	71	0	GDF3,synonymous_variant,p.%3D,ENST00000329913,;	A	ENSG00000184344	ENST00000329913	Transcript	synonymous_variant	972	924	308	S	tcC/tcT	.	.	.	-1	GDF3	HGNC	4218	protein_coding	YES	CCDS8581.1	ENSP00000331745	GDF3_HUMAN	.	UPI0000049E0E	.	.	.	2/2	.	PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF38,hmmpanther:PTHR11848,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAATTGGAGCT	.	4	ESCA
FGF14	0	.	GRCh37	13	102379101	102379101	+	Missense_Mutation	SNP	G	G	C	rs558694053	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483C>G	p.Ile161Met	p.I161M	ENST00000376131	4/5	36	25	11	76	76	0	FGF14,missense_variant,p.Ile156Met,ENST00000376143,;FGF14,missense_variant,p.Ile161Met,ENST00000376131,;ITGBL1,downstream_gene_variant,,ENST00000415285,;	C	ENSG00000102466	ENST00000376131	Transcript	missense_variant	579	483	161	I/M	atC/atG	rs558694053	.	.	-1	FGF14	HGNC	3671	protein_coding	YES	CCDS9500.1	ENSP00000365301	FGF14_HUMAN	.	UPI000000D898	.	tolerated(0.09)	possibly_damaging(0.452)	4/5	.	hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF18,Pfam_domain:PF00167,Gene3D:2.80.10.50,SMART_domains:SM00442,Superfamily_domains:SSF50353,Prints_domain:PR00262,Prints_domain:PR00263	A:0.0018	A:0	A:0	.	A:0	A:0	A:0.0092	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTAGATTAC	byFrequency|byCluster|by1000G	2	ESCA
RP11-596D21.1	0	.	GRCh37	14	31774121	31774121	+	3'Flank	SNP	G	G	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000551799	.	18	12	6	41	41	0	HEATR5A,missense_variant,p.Cys1743Trp,ENST00000543095,;HEATR5A,missense_variant,p.Cys1737Trp,ENST00000389961,;HEATR5A,missense_variant,p.Cys1371Trp,ENST00000538864,;HEATR5A,missense_variant,p.Cys1737Trp,ENST00000439348,;HEATR5A,missense_variant,p.Cys1450Trp,ENST00000439727,;RP11-596D21.1,downstream_gene_variant,,ENST00000551799,;	C	ENSG00000257831	ENST00000551799	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2176	1	RP11-596D21.1	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P1734S|c.5200C>T|3,BUFFER|p.P1734S|c.5200C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGAGCACAC	.	5	ESCA
MPP5	0	.	GRCh37	14	67799567	67799567	+	Missense_Mutation	SNP	C	C	T	rs774877439	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1922C>T	p.Thr641Met	p.T641M	ENST00000261681	15/15	26	22	4	67	67	0	MPP5,missense_variant,p.Thr607Met,ENST00000555925,;MPP5,missense_variant,p.Thr641Met,ENST00000261681,;ATP6V1D,downstream_gene_variant,,ENST00000553408,;ATP6V1D,intron_variant,,ENST00000553974,;ATP6V1D,intron_variant,,ENST00000554087,;ATP6V1D,downstream_gene_variant,,ENST00000555625,;	T	ENSG00000072415	ENST00000261681	Transcript	missense_variant	2583	1922	641	T/M	aCg/aTg	rs774877439,COSM470141	.	.	1	MPP5	HGNC	18669	protein_coding	YES	CCDS9779.1	ENSP00000261681	MPP5_HUMAN	G3V2H1_HUMAN	UPI0000046FB9	.	tolerated(0.54)	probably_damaging(0.939)	15/15	.	PROSITE_profiles:PS50052,hmmpanther:PTHR23122:SF32,hmmpanther:PTHR23122,Pfam_domain:PF00625,Gene3D:3.40.50.300,SMART_domains:SM00072,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.T641M|c.1922C>T|3	RADIA|MUSE	TGATACGGCAA	.	2	ESCA
NRXN3	0	.	GRCh37	14	80329492	80329492	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000554719	.	17	8	8	48	48	0	NRXN3,3_prime_UTR_variant,,ENST00000281127,;NRXN3,3_prime_UTR_variant,,ENST00000428277,;NRXN3,downstream_gene_variant,,ENST00000554719,;NRXN3,downstream_gene_variant,,ENST00000557594,;NRXN3,downstream_gene_variant,,ENST00000335750,;NRXN3,downstream_gene_variant,,ENST00000556003,;NRXN3,downstream_gene_variant,,ENST00000555387,;NRXN3,downstream_gene_variant,,ENST00000554738,;	T	ENSG00000021645	ENST00000554719	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	706	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCCCGAATG	.	5	ESCA
FMN1	0	.	GRCh37	15	33066543	33066543	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3559C>T	p.Arg1187Cys	p.R1187C	ENST00000334528	17/17	22	15	6	90	90	0	FMN1,missense_variant,p.Arg1410Cys,ENST00000559047,;FMN1,missense_variant,p.Arg1312Cys,ENST00000561249,;FMN1,missense_variant,p.Arg1187Cys,ENST00000334528,;FMN1,non_coding_transcript_exon_variant,,ENST00000558882,;	A	ENSG00000248905	ENST00000334528	Transcript	missense_variant	3559	3559	1187	R/C	Cgt/Tgt	.	.	.	-1	FMN1	HGNC	3768	protein_coding	YES	CCDS45209.1	ENSP00000333950	FMN1_HUMAN	.	UPI00004086C3	.	deleterious(0.01)	benign(0.349)	17/17	.	hmmpanther:PTHR13037,hmmpanther:PTHR13037:SF8,Prints_domain:PR00828	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACGCAGTC	.	5	ESCA
THSD4	0	.	GRCh37	15	72040919	72040919	+	Frame_Shift_Del	DEL	G	G	-	rs767893556	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2401delG	p.Glu801SerfsTer22	p.E801Sfs*22	ENST00000355327	14/18	59	50	9	112	112	0	THSD4,frameshift_variant,p.Glu801SerfsTer22,ENST00000355327,;THSD4,frameshift_variant,p.Glu441SerfsTer22,ENST00000357769,;THSD4,frameshift_variant,p.Glu801SerfsTer22,ENST00000261862,;THSD4,non_coding_transcript_exon_variant,,ENST00000567838,;	-	ENSG00000187720	ENST00000355327	Transcript	frameshift_variant	2535	2401	801	E/X	Gag/ag	rs767893556	.	.	1	THSD4	HGNC	25835	protein_coding	YES	CCDS10238.2	ENSP00000347484	THSD4_HUMAN	.	UPI00001A797D	.	.	.	14/18	.	PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF16,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCACCGAGTGG	byFrequency	3	ESCA
MYO9A	0	.	GRCh37	15	72190310	72190310	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4534A>G	p.Met1512Val	p.M1512V	ENST00000356056	25/42	69	65	4	160	160	0	MYO9A,missense_variant,p.Met291Val,ENST00000561618,;MYO9A,missense_variant,p.Met1512Val,ENST00000424560,;MYO9A,missense_variant,p.Met1512Val,ENST00000564571,;MYO9A,missense_variant,p.Met1132Val,ENST00000566885,;MYO9A,missense_variant,p.Met1512Val,ENST00000356056,;MYO9A,missense_variant,p.Met1493Val,ENST00000444904,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563542,;MYO9A,upstream_gene_variant,,ENST00000568781,;	C	ENSG00000066933	ENST00000356056	Transcript	missense_variant	5007	4534	1512	M/V	Atg/Gtg	.	.	.	-1	MYO9A	HGNC	7608	protein_coding	YES	CCDS10239.1	ENSP00000348349	MYO9A_HUMAN	H3BSU8_HUMAN,H3BMS3_HUMAN	UPI000013D213	.	deleterious_low_confidence(0)	benign(0.129)	25/42	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF9,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCATCTCTT	.	2	ESCA
RPUSD1	0	.	GRCh37	16	836115	836115	+	Silent	SNP	G	G	A	rs144842334	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774C>T	p.%3D	p.P258P	ENST00000561734	5/5	15	10	4	33	33	0	RPUSD1,synonymous_variant,p.%3D,ENST00000565377,;RPUSD1,synonymous_variant,p.%3D,ENST00000007264,;RPUSD1,synonymous_variant,p.%3D,ENST00000567114,;RPUSD1,synonymous_variant,p.%3D,ENST00000569601,;RPUSD1,synonymous_variant,p.%3D,ENST00000561734,;RPUSD1,3_prime_UTR_variant,,ENST00000565809,;RPUSD1,downstream_gene_variant,,ENST00000563560,;MSLNL,upstream_gene_variant,,ENST00000543963,;CHTF18,upstream_gene_variant,,ENST00000426047,;MSLNL,upstream_gene_variant,,ENST00000293892,;CHTF18,upstream_gene_variant,,ENST00000455171,;MSLNL,upstream_gene_variant,,ENST00000442466,;CHTF18,upstream_gene_variant,,ENST00000262315,;RPUSD1,downstream_gene_variant,,ENST00000562070,;CHTF18,upstream_gene_variant,,ENST00000317063,;CHTF18,upstream_gene_variant,,ENST00000570058,;CHTF18,upstream_gene_variant,,ENST00000491530,;CHTF18,upstream_gene_variant,,ENST00000440239,;RPUSD1,downstream_gene_variant,,ENST00000565503,;RPUSD1,downstream_gene_variant,,ENST00000567283,;CHTF18,upstream_gene_variant,,ENST00000479976,;CHTF18,upstream_gene_variant,,ENST00000464728,;CHTF18,upstream_gene_variant,,ENST00000484349,;CHTF18,upstream_gene_variant,,ENST00000563545,;CHTF18,upstream_gene_variant,,ENST00000569270,;CHTF18,upstream_gene_variant,,ENST00000471202,;CHTF18,upstream_gene_variant,,ENST00000567620,;	A	ENSG00000007376	ENST00000561734	Transcript	synonymous_variant	1018	774	258	P	ccC/ccT	rs144842334	.	.	-1	RPUSD1	HGNC	14173	protein_coding	YES	CCDS10426.1	ENSP00000455026	RUSD1_HUMAN	H3BSG4_HUMAN,H3BQN8_HUMAN	UPI0000073C11	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10436,hmmpanther:PTHR10436:SF92	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCGGGGGT	byCluster	5	ESCA
SREBF1	0	.	GRCh37	17	17718043	17718043	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2711A>T	p.Lys904Met	p.K904M	ENST00000355815	16/20	22	18	4	49	49	0	SREBF1,missense_variant,p.Lys874Met,ENST00000338854,;SREBF1,missense_variant,p.Lys620Met,ENST00000395757,;SREBF1,missense_variant,p.Lys904Met,ENST00000355815,;SREBF1,missense_variant,p.Lys874Met,ENST00000261646,;SREBF1,downstream_gene_variant,,ENST00000423161,;RAI1,downstream_gene_variant,,ENST00000261641,;SREBF1,upstream_gene_variant,,ENST00000486311,;SREBF1,upstream_gene_variant,,ENST00000478616,;RAI1,downstream_gene_variant,,ENST00000353383,;SREBF1,downstream_gene_variant,,ENST00000577897,;SREBF1,downstream_gene_variant,,ENST00000435530,;MIR33B,upstream_gene_variant,,ENST00000385104,;SREBF1,downstream_gene_variant,,ENST00000583732,;RAI1,downstream_gene_variant,,ENST00000582514,;SREBF1,3_prime_UTR_variant,,ENST00000395756,;SREBF1,3_prime_UTR_variant,,ENST00000395751,;SREBF1,non_coding_transcript_exon_variant,,ENST00000490796,;SREBF1,non_coding_transcript_exon_variant,,ENST00000581707,;SREBF1,intron_variant,,ENST00000447641,;SREBF1,downstream_gene_variant,,ENST00000583080,;SREBF1,downstream_gene_variant,,ENST00000487401,;SREBF1,downstream_gene_variant,,ENST00000584760,;SREBF1,downstream_gene_variant,,ENST00000469356,;SREBF1,upstream_gene_variant,,ENST00000578469,;SREBF1,downstream_gene_variant,,ENST00000471445,;SREBF1,upstream_gene_variant,,ENST00000485080,;SREBF1,downstream_gene_variant,,ENST00000580540,;SREBF1,downstream_gene_variant,,ENST00000470247,;	A	ENSG00000072310	ENST00000355815	Transcript	missense_variant	2881	2711	904	K/M	aAg/aTg	.	.	.	-1	SREBF1	HGNC	11289	protein_coding	YES	CCDS32583.1	ENSP00000348069	SRBP1_HUMAN	J3QLB6_HUMAN,B5MD58_HUMAN	UPI00004432F6	.	deleterious(0)	probably_damaging(0.996)	16/20	.	hmmpanther:PTHR12565,hmmpanther:PTHR12565:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCACTTGGCC	.	2	ESCA
PGAP3	0	.	GRCh37	17	37842243	37842243	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211G>A	p.Glu71Lys	p.E71K	ENST00000300658	2/8	25	22	3	54	54	0	PGAP3,missense_variant,p.Glu71Lys,ENST00000429199,;PGAP3,missense_variant,p.Glu71Lys,ENST00000579146,;PGAP3,missense_variant,p.Glu71Lys,ENST00000300658,;PGAP3,missense_variant,p.Glu71Lys,ENST00000378011,;PGAP3,5_prime_UTR_variant,,ENST00000584856,;ERBB2,upstream_gene_variant,,ENST00000578199,;ERBB2,upstream_gene_variant,,ENST00000406381,;ERBB2,upstream_gene_variant,,ENST00000584601,;PGAP3,missense_variant,p.Glu67Lys,ENST00000584620,;PGAP3,non_coding_transcript_exon_variant,,ENST00000309862,;PGAP3,intron_variant,,ENST00000582276,;PGAP3,upstream_gene_variant,,ENST00000580898,;ERBB2,upstream_gene_variant,,ENST00000584014,;PGAP3,upstream_gene_variant,,ENST00000577337,;	T	ENSG00000161395	ENST00000300658	Transcript	missense_variant	304	211	71	E/K	Gag/Aag	.	.	.	-1	PGAP3	HGNC	23719	protein_coding	YES	CCDS32641.1	ENSP00000300658	PGAP3_HUMAN	J3QQL0_HUMAN,B4DVJ3_HUMAN	UPI0000039EAA	.	tolerated(0.12)	benign(0.035)	2/8	.	Pfam_domain:PF04080,hmmpanther:PTHR13148:SF0,hmmpanther:PTHR13148	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACACTCATACT	.	2	ESCA
KRTAP4-3	0	.	GRCh37	17	39324398	39324398	+	Silent	SNP	G	G	A	rs369294684	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27C>T	p.%3D	p.V9V	ENST00000391356	1/1	70	60	10	185	185	0	KRTAP4-3,synonymous_variant,p.%3D,ENST00000391356,;	A	ENSG00000196156	ENST00000391356	Transcript	synonymous_variant	27	27	9	V	gtC/gtT	rs369294684	.	.	-1	KRTAP4-3	HGNC	18908	protein_coding	YES	CCDS42331.1	ENSP00000375151	KRA43_HUMAN	.	UPI00006C17BA	.	.	.	1/1	.	hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GAGCAGACAGA	byFrequency|byCluster	2	ESCA
CLTC	0	.	GRCh37	17	57697397	57697397	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96C>T	.	.	ENST00000269122	1/32	69	51	18	158	158	0	CLTC,5_prime_UTR_variant,,ENST00000269122,;CLTC,5_prime_UTR_variant,,ENST00000580081,;CLTC,5_prime_UTR_variant,,ENST00000393043,;CLTC,5_prime_UTR_variant,,ENST00000579456,;CLTC,5_prime_UTR_variant,,ENST00000584313,;	T	ENSG00000141367	ENST00000269122	Transcript	5_prime_UTR_variant	179	.	.	.	.	.	.	.	1	CLTC	HGNC	2092	protein_coding	YES	CCDS32696.1	ENSP00000269122	CLH1_HUMAN	Q49AL0_HUMAN	UPI0000127ABD	.	.	.	1/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTCCCCCC	.	5	ESCA
TP53	0	.	GRCh37	17	7578493	7578493	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	5/11	21	12	9	53	53	0	TP53,stop_gained,p.Trp146Ter,ENST00000508793,;TP53,stop_gained,p.Trp146Ter,ENST00000413465,;TP53,stop_gained,p.Trp139Ter,ENST00000604348,;TP53,stop_gained,p.Trp146Ter,ENST00000420246,;TP53,stop_gained,p.Trp146Ter,ENST00000269305,;TP53,stop_gained,p.Trp14Ter,ENST00000509690,;TP53,stop_gained,p.Trp146Ter,ENST00000359597,;TP53,stop_gained,p.Trp53Ter,ENST00000514944,;TP53,stop_gained,p.Trp146Ter,ENST00000445888,;TP53,stop_gained,p.Trp146Ter,ENST00000455263,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	stop_gained	627	437	146	W/*	tGg/tAg	CM107391,TP53_g.12425G>C,TP53_g.12425G>T,TP53_g.12425G>A,COSM43609,COSM46220,COSM1158445,COSM417960,COSM1158446,COSM417961,COSM417963,COSM1158448,COSM3378359,COSM1640860,COSM1158447,COSM417962	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.W14*|c.41G>A|9,SITE|p.W146*|c.437G>A|3,SITE|p.W146*|c.437G>A|9,SITE|p.W53*|c.158G>A|9,SITE|p.W146*|c.437G>A|7,SITE|p.W146*|c.437G>A|9,SITE|p.W146*|c.437G>A|43,CODON|p.0?|c.1_1182del1182|6,CODON|p.W146*|c.438G>A|5,CODON|p.W146*|c.438G>A|4,CODON|p.W53*|c.159G>A|5,CODON|p.W146*|c.438G>A|34,CODON|p.W146*|c.438G>A|3,CODON|p.W14*|c.42G>A|5,BUFFER|p.T150fs*16|c.448_460del13|4,BUFFER|p.S149S|c.447C>T|6,BUFFER|p.S149F|c.446C>T|5,BUFFER|p.S149fs*32|c.444_445insN|5,BUFFER|p.S149P|c.445T>C|4,BUFFER|p.D148N|c.442G>A|5,BUFFER|p.V147V|c.441T>G|3,BUFFER|p.V147G|c.440T>G|8,BUFFER|p.V147D|c.440T>A|3,BUFFER|p.V147fs*23|c.439delG|7,BUFFER|p.V147I|c.439G>A|6,BUFFER|p.W146R|c.436T>C|4,BUFFER|p.L145L|c.435G>A|3,BUFFER|p.L145R|c.434T>G|7,BUFFER|p.L145P|c.434T>C|17,BUFFER|p.L145Q|c.434T>A|19,BUFFER|p.L145L|c.433C>T|4,BUFFER|p.Q144H|c.432G>C|3,BUFFER|p.Q144fs*26|c.430delC|3,BUFFER|p.Q144R|c.431A>G|5,BUFFER|p.Q144L|c.431A>T|9,BUFFER|p.Q144P|c.431A>C|5,BUFFER|p.Q12*|c.34C>T|10,BUFFER|p.Q144*|c.430C>T|3,BUFFER|p.Q144*|c.430C>T|39,BUFFER|p.Q144*|c.430C>T|10,BUFFER|p.Q51*|c.151C>T|10,BUFFER|p.Q144*|c.430C>T|9,BUFFER|p.Q144*|c.430C>T|3,BUFFER|p.V11A|c.32T>C|4,BUFFER|p.V143E|c.428T>A|6,BUFFER|p.V143A|c.428T>C|3,BUFFER|p.V143A|c.428T>C|4,BUFFER|p.V143A|c.428T>C|16,BUFFER|p.V50A|c.149T>C|4,BUFFER|p.V143M|c.427G>A|4,BUFFER|p.V143L|c.427G>T|3,BUFFER|p.V143M|c.427G>A|3,BUFFER|p.V143M|c.427G>A|22,BUFFER|p.V11M|c.31G>A|4,BUFFER|p.V50M|c.148G>A|4,BUFFER|p.V143M|c.427G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACCCACAGC	.	5	ESCA
GUCY2D	0	.	GRCh37	17	7919550	7919550	+	Missense_Mutation	SNP	C	C	A	rs768597548	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3166C>A	p.Leu1056Ile	p.L1056I	ENST00000254854	18/20	39	30	9	90	90	0	GUCY2D,missense_variant,p.Leu1056Ile,ENST00000254854,;GUCY2D,non_coding_transcript_exon_variant,,ENST00000574510,;	A	ENSG00000132518	ENST00000254854	Transcript	missense_variant	3316	3166	1056	L/I	Cta/Ata	rs768597548	.	.	1	GUCY2D	HGNC	4689	protein_coding	YES	CCDS11127.1	ENSP00000254854	GUC2D_HUMAN	.	UPI0000128C1C	.	deleterious(0.01)	probably_damaging(0.999)	18/20	.	hmmpanther:PTHR11920:SF228,hmmpanther:PTHR11920,Gene3D:3.30.70.1230,Pfam_domain:PF00211,Superfamily_domains:SSF55073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGGCTAGTG	.	5	ESCA
CHST9	0	.	GRCh37	18	24495846	24495846	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*377G>C	.	.	ENST00000284224	6/6	13	9	3	39	39	0	CHST9,3_prime_UTR_variant,,ENST00000581714,;CHST9,3_prime_UTR_variant,,ENST00000580774,;CHST9,3_prime_UTR_variant,,ENST00000284224,;AQP4-AS1,intron_variant,,ENST00000578701,;AQP4-AS1,intron_variant,,ENST00000582605,;AQP4-AS1,intron_variant,,ENST00000568797,;AQP4-AS1,intron_variant,,ENST00000579964,;	G	ENSG00000154080	ENST00000284224	Transcript	3_prime_UTR_variant	1987	.	.	.	.	.	.	.	-1	CHST9	HGNC	19898	protein_coding	YES	CCDS42422.1	ENSP00000284224	CHST9_HUMAN	.	UPI000006EC67	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	ATATTCATGCA	.	4	ESCA
B4GALT6	0	.	GRCh37	18	29210978	29210978	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.720C>A	p.Tyr240Ter	p.Y240*	ENST00000306851	6/9	27	19	7	80	80	0	B4GALT6,stop_gained,p.Tyr201Ter,ENST00000383131,;B4GALT6,stop_gained,p.Tyr201Ter,ENST00000237019,;B4GALT6,stop_gained,p.Tyr240Ter,ENST00000306851,;B4GALT6,non_coding_transcript_exon_variant,,ENST00000578114,;	T	ENSG00000118276	ENST00000306851	Transcript	stop_gained	1017	720	240	Y/*	taC/taA	COSM987650	.	.	-1	B4GALT6	HGNC	929	protein_coding	YES	CCDS11900.1	ENSP00000306459	B4GT6_HUMAN	Q6NT00_HUMAN,J3QQY9_HUMAN	UPI0000126721	.	.	.	6/9	.	hmmpanther:PTHR19300,hmmpanther:PTHR19300:SF29,Pfam_domain:PF13733,Gene3D:3.90.550.10,Superfamily_domains:SSF53448,Prints_domain:PR02050	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCGTAATA	.	5	ESCA
COL5A3	0	.	GRCh37	19	10083616	10083616	+	Silent	SNP	C	C	T	rs758613882	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3753G>A	p.%3D	p.E1251E	ENST00000264828	51/67	38	29	9	77	77	0	COL5A3,synonymous_variant,p.%3D,ENST00000264828,;COL5A3,upstream_gene_variant,,ENST00000461214,;	T	ENSG00000080573	ENST00000264828	Transcript	synonymous_variant	3839	3753	1251	E	gaG/gaA	rs758613882	.	.	-1	COL5A3	HGNC	14864	protein_coding	YES	CCDS12222.1	ENSP00000264828	CO5A3_HUMAN	.	UPI00002032A3	.	.	.	51/67	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF400	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCTCTCC	byFrequency	5	ESCA
SCN1B	0	.	GRCh37	19	35524873	35524873	+	Silent	SNP	C	C	T	rs769132369	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.678C>T	p.%3D	p.S226S	ENST00000415950	3/3	29	18	11	99	99	0	SCN1B,synonymous_variant,p.%3D,ENST00000415950,;SCN1B,intron_variant,,ENST00000595652,;SCN1B,intron_variant,,ENST00000262631,;CTD-2527I21.9,upstream_gene_variant,,ENST00000601692,;SCN1B,intron_variant,,ENST00000596348,;SCN1B,upstream_gene_variant,,ENST00000602150,;	T	ENSG00000105711	ENST00000415950	Transcript	synonymous_variant	678	678	226	S	tcC/tcT	rs769132369	.	.	1	SCN1B	HGNC	10586	protein_coding	YES	CCDS46047.1	ENSP00000396915	SCN1B_HUMAN	.	UPI00000473F0	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	benign	.	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTCCGGGTA	.	5	ESCA
DYRK1B	0	.	GRCh37	19	40319120	40319120	+	Silent	SNP	G	G	A	rs746346346	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624C>T	p.%3D	p.G208G	ENST00000593685	6/11	27	24	3	57	57	0	DYRK1B,synonymous_variant,p.%3D,ENST00000597639,;DYRK1B,synonymous_variant,p.%3D,ENST00000593685,;DYRK1B,synonymous_variant,p.%3D,ENST00000348817,;DYRK1B,synonymous_variant,p.%3D,ENST00000430012,;DYRK1B,synonymous_variant,p.%3D,ENST00000323039,;DYRK1B,downstream_gene_variant,,ENST00000601972,;DYRK1B,downstream_gene_variant,,ENST00000600611,;DYRK1B,non_coding_transcript_exon_variant,,ENST00000601696,;	A	ENSG00000105204	ENST00000593685	Transcript	synonymous_variant	1093	624	208	G	ggC/ggT	rs746346346,COSM996429,COSM1590096	.	.	-1	DYRK1B	HGNC	3092	protein_coding	YES	CCDS12543.1	ENSP00000469863	DYR1B_HUMAN	M0R131_HUMAN	UPI0000001059	.	.	.	6/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF27,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGACGCCGCG	byFrequency	2	ESCA
FAM83E	0	.	GRCh37	19	49113245	49113245	+	Missense_Mutation	SNP	G	G	A	rs748353296	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.646C>T	p.Arg216Cys	p.R216C	ENST00000263266	3/5	32	24	8	74	74	0	FAM83E,missense_variant,p.Arg216Cys,ENST00000263266,;FAM83E,downstream_gene_variant,,ENST00000593772,;SPACA4,downstream_gene_variant,,ENST00000321762,;FAM83E,downstream_gene_variant,,ENST00000595110,;FAM83E,downstream_gene_variant,,ENST00000599126,;	A	ENSG00000105523	ENST00000263266	Transcript	missense_variant	836	646	216	R/C	Cgt/Tgt	rs748353296	.	.	-1	FAM83E	HGNC	25972	protein_coding	YES	CCDS42587.1	ENSP00000263266	FA83E_HUMAN	M0QZ37_HUMAN	UPI000013D3D9	.	deleterious(0)	probably_damaging(0.996)	3/5	.	hmmpanther:PTHR16181:SF6,hmmpanther:PTHR16181,Gene3D:3.30.870.10,Pfam_domain:PF07894,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACGGACAT	.	5	ESCA
ZNF432	0	.	GRCh37	19	52550148	52550148	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-27G>A	.	.	ENST00000594154	2/5	43	33	9	89	89	0	ZNF432,5_prime_UTR_variant,,ENST00000221315,;ZNF432,5_prime_UTR_variant,,ENST00000598745,;ZNF432,5_prime_UTR_variant,,ENST00000594154,;ZNF432,5_prime_UTR_variant,,ENST00000601310,;ZNF432,5_prime_UTR_variant,,ENST00000597273,;ZNF432,5_prime_UTR_variant,,ENST00000600368,;ZNF432,downstream_gene_variant,,ENST00000598446,;	T	ENSG00000256087	ENST00000594154	Transcript	5_prime_UTR_variant	187	.	.	.	.	.	.	.	-1	ZNF432	HGNC	20810	protein_coding	YES	CCDS12848.1	ENSP00000470488	ZN432_HUMAN	M0R258_HUMAN,M0R0H8_HUMAN,M0R0E2_HUMAN	UPI0000139CDC	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGCACCTG	.	5	ESCA
ZNF671	0	.	GRCh37	19	58232292	58232292	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1162C>A	p.Gln388Lys	p.Q388K	ENST00000317398	4/4	25	21	4	67	67	0	ZNF671,missense_variant,p.Gln388Lys,ENST00000317398,;ZNF671,missense_variant,p.Gln290Lys,ENST00000335820,;AC003006.7,intron_variant,,ENST00000594684,;ZNF551,downstream_gene_variant,,ENST00000596085,;ZNF671,downstream_gene_variant,,ENST00000596939,;AC003006.7,intron_variant,,ENST00000599221,;ZNF671,downstream_gene_variant,,ENST00000599961,;ZNF671,downstream_gene_variant,,ENST00000594803,;ZNF671,3_prime_UTR_variant,,ENST00000601584,;ZNF671,3_prime_UTR_variant,,ENST00000600125,;	T	ENSG00000083814	ENST00000317398	Transcript	missense_variant	1258	1162	388	Q/K	Cag/Aag	.	.	.	-1	ZNF671	HGNC	26279	protein_coding	YES	CCDS12961.1	ENSP00000321848	ZN671_HUMAN	C9J3V7_HUMAN	UPI000013C612	.	tolerated(0.35)	benign(0.358)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24390:SF44,hmmpanther:PTHR24390,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCCTGGTGTC	.	3	ESCA
OVGP1	0	.	GRCh37	1	111957574	111957574	+	Missense_Mutation	SNP	C	C	A	rs773134849	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1549G>T	p.Val517Leu	p.V517L	ENST00000369732	11/11	21	18	3	92	92	0	OVGP1,missense_variant,p.Val517Leu,ENST00000369732,;OVGP1,downstream_gene_variant,,ENST00000540696,;OVGP1,downstream_gene_variant,,ENST00000481495,;OVGP1,downstream_gene_variant,,ENST00000494622,;	A	ENSG00000085465	ENST00000369732	Transcript	missense_variant	1605	1549	517	V/L	Gtg/Ttg	rs773134849	.	.	-1	OVGP1	HGNC	8524	protein_coding	YES	CCDS834.1	ENSP00000358747	OVGP1_HUMAN	Q9UJZ3_HUMAN	UPI0000130C53	.	tolerated_low_confidence(0.14)	benign(0.072)	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G584G|c.1752G>A|4,BUFFER|p.G520G|c.1560G>A|4	MUTECT|MUSE	GGTCACAGACT	byFrequency	2	ESCA
APH1A	0	.	GRCh37	1	150238905	150238905	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.733+28C>T	.	.	ENST00000369109	.	30	27	3	89	89	0	APH1A,3_prime_UTR_variant,,ENST00000360244,;APH1A,intron_variant,,ENST00000414276,;APH1A,intron_variant,,ENST00000369109,;APH1A,downstream_gene_variant,,ENST00000236017,;CA14,downstream_gene_variant,,ENST00000607082,;C1orf54,upstream_gene_variant,,ENST00000369102,;CA14,downstream_gene_variant,,ENST00000369111,;snoU13,downstream_gene_variant,,ENST00000458929,;APH1A,non_coding_transcript_exon_variant,,ENST00000461320,;APH1A,downstream_gene_variant,,ENST00000493092,;APH1A,downstream_gene_variant,,ENST00000486308,;APH1A,downstream_gene_variant,,ENST00000476538,;APH1A,downstream_gene_variant,,ENST00000486720,;CA14,downstream_gene_variant,,ENST00000607652,;CA14,downstream_gene_variant,,ENST00000483993,;	A	ENSG00000117362	ENST00000369109	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	APH1A	HGNC	29509	protein_coding	YES	CCDS41390.1	ENSP00000358105	APH1A_HUMAN	.	UPI0000073CA3	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCAGGCGATC	.	2	ESCA
UHMK1	0	.	GRCh37	1	162492706	162492706	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*366G>C	.	.	ENST00000489294	8/8	56	48	7	161	161	0	UHMK1,3_prime_UTR_variant,,ENST00000545294,;UHMK1,3_prime_UTR_variant,,ENST00000489294,;UHMK1,3_prime_UTR_variant,,ENST00000538489,;UHMK1,non_coding_transcript_exon_variant,,ENST00000282169,;	C	ENSG00000152332	ENST00000489294	Transcript	3_prime_UTR_variant	1784	.	.	.	.	.	.	.	1	UHMK1	HGNC	19683	protein_coding	YES	CCDS1239.1	ENSP00000420270	UHMK1_HUMAN	.	UPI000000DCCA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTGGTGACA	.	4	ESCA
HSPB7	0	.	GRCh37	1	16342202	16342202	+	Missense_Mutation	SNP	G	G	A	rs757356294	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.386C>T	p.Pro129Leu	p.P129L	ENST00000311890	3/3	37	31	6	67	67	0	HSPB7,missense_variant,p.Pro134Leu,ENST00000487046,;HSPB7,missense_variant,p.Pro83Leu,ENST00000463576,;HSPB7,missense_variant,p.Pro129Leu,ENST00000311890,;HSPB7,missense_variant,p.Pro124Leu,ENST00000411503,;HSPB7,missense_variant,p.Pro204Leu,ENST00000375718,;HSPB7,missense_variant,p.Pro133Leu,ENST00000406363,;HSPB7,downstream_gene_variant,,ENST00000545268,;CLCNKA,upstream_gene_variant,,ENST00000464764,;HSPB7,non_coding_transcript_exon_variant,,ENST00000442459,;	A	ENSG00000173641	ENST00000311890	Transcript	missense_variant	1213	386	129	P/L	cCg/cTg	rs757356294	.	.	-1	HSPB7	HGNC	5249	protein_coding	YES	CCDS30611.1	ENSP00000310111	HSPB7_HUMAN	.	UPI0000000C78	.	deleterious(0)	probably_damaging(1)	3/3	.	PROSITE_profiles:PS01031,hmmpanther:PTHR11527:SF21,hmmpanther:PTHR11527,Pfam_domain:PF00011,Gene3D:2.60.40.790,Superfamily_domains:SSF49764	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCGGCAGC	byFrequency	5	ESCA
MGST3	0	.	GRCh37	1	165620279	165620279	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146A>T	p.Glu49Val	p.E49V	ENST00000367889	3/6	53	45	8	116	116	0	MGST3,missense_variant,p.Glu63Val,ENST00000367886,;MGST3,missense_variant,p.Glu49Val,ENST00000367889,;MGST3,missense_variant,p.Glu49Val,ENST00000367884,;MGST3,missense_variant,p.Glu63Val,ENST00000367885,;MGST3,missense_variant,p.Glu49Val,ENST00000367888,;MGST3,missense_variant,p.Glu63Val,ENST00000367883,;MGST3,non_coding_transcript_exon_variant,,ENST00000477450,;MGST3,downstream_gene_variant,,ENST00000461759,;MGST3,non_coding_transcript_exon_variant,,ENST00000488688,;MGST3,non_coding_transcript_exon_variant,,ENST00000495447,;MGST3,non_coding_transcript_exon_variant,,ENST00000609263,;MGST3,upstream_gene_variant,,ENST00000494074,;MGST3,downstream_gene_variant,,ENST00000461308,;	T	ENSG00000143198	ENST00000367889	Transcript	missense_variant	586	146	49	E/V	gAa/gTa	.	.	.	1	MGST3	HGNC	7064	protein_coding	YES	CCDS1249.1	ENSP00000356864	MGST3_HUMAN	Q2F833_HUMAN	UPI000012BC86	.	deleterious(0)	benign(0.209)	3/6	.	hmmpanther:PTHR10250,hmmpanther:PTHR10250:SF14,Pfam_domain:PF01124,Gene3D:1.20.120.550,Superfamily_domains:SSF161084	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGAAAATG	.	5	ESCA
CFHR3	0	.	GRCh37	1	196758866	196758866	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614-309G>C	.	.	ENST00000367425	.	19	13	6	59	59	0	CFHR3,3_prime_UTR_variant,,ENST00000471440,;CFHR3,intron_variant,,ENST00000367425,;CFHR3,intron_variant,,ENST00000391985,;CFHR3,intron_variant,,ENST00000367427,;CFHR3,upstream_gene_variant,,ENST00000461558,;	C	ENSG00000116785	ENST00000367425	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CFHR3	HGNC	16980	protein_coding	YES	CCDS30958.1	ENSP00000356395	FHR3_HUMAN	.	UPI000012A73C	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTAGTCCCA	.	5	ESCA
PROX1	0	.	GRCh37	1	214171007	214171007	+	Missense_Mutation	SNP	C	C	T	rs368029419	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129C>T	p.Arg377Cys	p.R377C	ENST00000366958	2/5	19	15	4	35	35	0	PROX1,missense_variant,p.Arg377Cys,ENST00000498508,;PROX1,missense_variant,p.Arg377Cys,ENST00000366958,;PROX1,missense_variant,p.Arg377Cys,ENST00000261454,;PROX1,missense_variant,p.Arg377Cys,ENST00000435016,;PROX1,downstream_gene_variant,,ENST00000607425,;PROX1,downstream_gene_variant,,ENST00000471129,;	T	ENSG00000117707	ENST00000366958	Transcript	missense_variant	1737	1129	377	R/C	Cgc/Tgc	rs368029419	.	.	1	PROX1	HGNC	9459	protein_coding	YES	CCDS31021.1	ENSP00000355925	PROX1_HUMAN	U3KPY6_HUMAN,C9JU29_HUMAN,B4DP41_HUMAN	UPI0000071D14	.	tolerated(0.08)	possibly_damaging(0.761)	2/5	.	hmmpanther:PTHR12198:SF2,hmmpanther:PTHR12198	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCCCGCCAG	byCluster	3	ESCA
CHRM3	0	.	GRCh37	1	240072404	240072404	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1653C>T	p.%3D	p.F551F	ENST00000255380	5/5	28	20	7	74	74	0	CHRM3,synonymous_variant,p.%3D,ENST00000255380,;CHRM3,downstream_gene_variant,,ENST00000448020,;	T	ENSG00000133019	ENST00000255380	Transcript	synonymous_variant	2432	1653	551	F	ttC/ttT	.	.	.	1	CHRM3	HGNC	1952	protein_coding	YES	CCDS1616.1	ENSP00000255380	ACM3_HUMAN	Q8NG01_HUMAN,B1AN12_HUMAN	UPI0000050453	.	.	.	5/5	.	hmmpanther:PTHR24249:SF61,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00243	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTCAGAAC	.	5	ESCA
CEP170	0	.	GRCh37	1	243363956	243363956	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.360G>A	p.%3D	p.Q120Q	ENST00000366542	6/20	31	21	9	74	74	0	CEP170,synonymous_variant,p.%3D,ENST00000336415,;CEP170,synonymous_variant,p.%3D,ENST00000366544,;CEP170,synonymous_variant,p.%3D,ENST00000522191,;CEP170,synonymous_variant,p.%3D,ENST00000366542,;CEP170,synonymous_variant,p.%3D,ENST00000366543,;CEP170,downstream_gene_variant,,ENST00000523424,;	T	ENSG00000143702	ENST00000366542	Transcript	synonymous_variant	412	360	120	Q	caG/caA	.	.	.	-1	CEP170	HGNC	28920	protein_coding	YES	CCDS44339.1	ENSP00000355500	CE170_HUMAN	Q9NSN9_HUMAN,E5RJT5_HUMAN,E5RIH6_HUMAN,E5RFU8_HUMAN	UPI0000470238	.	.	.	6/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GACAACTGAAG	.	4	ESCA
HNRNPU	0	.	GRCh37	1	245025801	245025803	+	In_Frame_Del	DEL	TCT	TCT	-	rs747301226	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	TCT	TCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837_839delAGA	p.Glu279del	p.E279del	ENST00000283179	3/14	51	39	11	119	119	0	HNRNPU,inframe_deletion,p.Glu56del,ENST00000440865,;HNRNPU,inframe_deletion,p.Glu279del,ENST00000283179,;HNRNPU,inframe_deletion,p.Glu260del,ENST00000444376,;RP11-11N7.4,upstream_gene_variant,,ENST00000610145,;HNRNPU,non_coding_transcript_exon_variant,,ENST00000483966,;HNRNPU,non_coding_transcript_exon_variant,,ENST00000476241,;HNRNPU,upstream_gene_variant,,ENST00000465881,;HNRNPU,upstream_gene_variant,,ENST00000366525,;	-	ENSG00000153187	ENST00000283179	Transcript	inframe_deletion	1001-1003	837-839	279-280	ED/D	gaAGAt/gat	rs747301226	.	.	-1	HNRNPU	HGNC	5048	protein_coding	YES	CCDS41479.1	ENSP00000283179	HNRPU_HUMAN	Q9UEL2_HUMAN,Q96BA7_HUMAN,Q7Z4Q5_HUMAN	UPI000040E1C8	.	.	.	3/14	.	PROSITE_profiles:PS50188,hmmpanther:PTHR12381:SF11,hmmpanther:PTHR12381	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTTCATCTTCTTC	.	2	ESCA
OR2M2	0	.	GRCh37	1	248344165	248344165	+	Missense_Mutation	SNP	G	G	A	rs758856171	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.878G>A	p.Arg293His	p.R293H	ENST00000359682	1/1	59	52	6	157	157	0	OR2M2,missense_variant,p.Arg293His,ENST00000359682,;	A	ENSG00000198601	ENST00000359682	Transcript	missense_variant	878	878	293	R/H	cGc/cAc	rs758856171,COSM2233207	.	.	1	OR2M2	HGNC	8268	protein_coding	YES	CCDS31106.1	ENSP00000352710	OR2M2_HUMAN	.	UPI00001612E4	.	deleterious(0.03)	benign(0.009)	1/1	.	hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF204,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCCGCAACA	byFrequency|byCluster	4	ESCA
NOL9	0	.	GRCh37	1	6610498	6610498	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.574A>G	p.Lys192Glu	p.K192E	ENST00000377705	2/12	41	35	6	94	94	0	NOL9,missense_variant,p.Lys192Glu,ENST00000377705,;TAS1R1,upstream_gene_variant,,ENST00000351136,;TAS1R1,upstream_gene_variant,,ENST00000333172,;TAS1R1,upstream_gene_variant,,ENST00000328191,;NOL9,non_coding_transcript_exon_variant,,ENST00000460777,;NOL9,intron_variant,,ENST00000464665,;RP11-58A11.2,downstream_gene_variant,,ENST00000456162,;	C	ENSG00000162408	ENST00000377705	Transcript	missense_variant	607	574	192	K/E	Aaa/Gaa	.	.	.	-1	NOL9	HGNC	26265	protein_coding	YES	CCDS80.1	ENSP00000366934	NOL9_HUMAN	.	UPI00003664C8	.	deleterious(0)	benign(0.242)	2/12	.	hmmpanther:PTHR12755:SF3,hmmpanther:PTHR12755,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTTCAGTT	.	5	ESCA
SEL1L2	0	.	GRCh37	20	13850839	13850840	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114dupA	p.Ile372AsnfsTer25	p.I372Nfs*25	ENST00000378072	13/18	43	35	8	66	66	0	SEL1L2,frameshift_variant,p.Ile372AsnfsTer25,ENST00000284951,;SEL1L2,frameshift_variant,p.Ile372AsnfsTer25,ENST00000378072,;SEL1L2,non_coding_transcript_exon_variant,,ENST00000486903,;SEL1L2,non_coding_transcript_exon_variant,,ENST00000492548,;SEL1L2,3_prime_UTR_variant,,ENST00000423870,;SEL1L2,upstream_gene_variant,,ENST00000475649,;	T	ENSG00000101251	ENST00000378072	Transcript	frameshift_variant	1196-1197	1114-1115	372	I/NX	atc/aAtc	.	.	.	-1	SEL1L2	HGNC	15897	protein_coding	YES	CCDS59443.1	ENSP00000367312	SE1L2_HUMAN	C9JNX3_HUMAN	UPI000003BCBF	.	.	.	13/18	.	hmmpanther:PTHR11102:SF53,hmmpanther:PTHR11102,Gene3D:1.25.40.10,SMART_domains:SM00671,Superfamily_domains:SSF81901	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|VARSCANS*|PINDEL|SOMATICSNIPER*	GGCCGATTGCA	.	5	ESCA
ZHX3	0	.	GRCh37	20	39831306	39831306	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2251C>A	p.Pro751Thr	p.P751T	ENST00000309060	4/5	20	16	4	57	57	0	ZHX3,missense_variant,p.Pro751Thr,ENST00000540170,;ZHX3,missense_variant,p.Pro751Thr,ENST00000432768,;ZHX3,missense_variant,p.Pro751Thr,ENST00000559234,;ZHX3,missense_variant,p.Pro751Thr,ENST00000544979,;ZHX3,missense_variant,p.Pro751Thr,ENST00000309060,;ZHX3,missense_variant,p.Pro751Thr,ENST00000560361,;ZHX3,missense_variant,p.Pro460Thr,ENST00000421422,;ZHX3,intron_variant,,ENST00000558993,;ZHX3,intron_variant,,ENST00000557816,;ZHX3,downstream_gene_variant,,ENST00000436099,;ZHX3,downstream_gene_variant,,ENST00000419740,;ZHX3,downstream_gene_variant,,ENST00000373261,;ZHX3,downstream_gene_variant,,ENST00000436440,;ZHX3,downstream_gene_variant,,ENST00000441102,;ZHX3,upstream_gene_variant,,ENST00000559436,;ZHX3,3_prime_UTR_variant,,ENST00000560364,;	T	ENSG00000174306	ENST00000309060	Transcript	missense_variant	2667	2251	751	P/T	Cct/Act	.	.	.	-1	ZHX3	HGNC	15935	protein_coding	YES	CCDS13315.1	ENSP00000312222	ZHX3_HUMAN	H0YMK8_HUMAN,F6YD28_HUMAN,F6XGA7_HUMAN,F6UQN6_HUMAN,F6UBH9_HUMAN,F6S7L4_HUMAN	UPI000000D72C	.	tolerated(0.08)	benign(0.002)	4/5	.	hmmpanther:PTHR15467:SF6,hmmpanther:PTHR15467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	CTCAGGGTCAC	.	2	ESCA
TIMP3	0	.	GRCh37	22	33255426	33255426	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62C>G	.	.	ENST00000266085	5/5	30	23	7	61	61	0	TIMP3,3_prime_UTR_variant,,ENST00000266085,;SYN3,intron_variant,,ENST00000358763,;SYN3,intron_variant,,ENST00000332840,;SYN3,intron_variant,,ENST00000462268,;Z98256.1,downstream_gene_variant,,ENST00000327661,;	G	ENSG00000100234	ENST00000266085	Transcript	3_prime_UTR_variant	999	.	.	.	.	.	.	.	1	TIMP3	HGNC	11822	protein_coding	YES	CCDS13911.1	ENSP00000266085	TIMP3_HUMAN	.	UPI000005F30A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTAACTCTTC	.	2	ESCA
OSBPL6	0	.	GRCh37	2	179247154	179247154	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1616A>T	p.Asp539Val	p.D539V	ENST00000392505	17/26	16	12	3	76	76	0	OSBPL6,missense_variant,p.Asp478Val,ENST00000409631,;OSBPL6,missense_variant,p.Asp483Val,ENST00000409045,;OSBPL6,missense_variant,p.Asp518Val,ENST00000315022,;OSBPL6,missense_variant,p.Asp478Val,ENST00000359685,;OSBPL6,missense_variant,p.Asp539Val,ENST00000392505,;OSBPL6,missense_variant,p.Asp514Val,ENST00000190611,;OSBPL6,missense_variant,p.Asp447Val,ENST00000357080,;	T	ENSG00000079156	ENST00000392505	Transcript	missense_variant	2160	1616	539	D/V	gAt/gTt	COSM4087072,COSM4087071,COSM4087070	.	.	1	OSBPL6	HGNC	16388	protein_coding	YES	CCDS56150.1	ENSP00000376293	OSBL6_HUMAN	.	UPI0000E5A29F	.	deleterious(0)	probably_damaging(0.984)	17/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10972:SF76,hmmpanther:PTHR10972	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGATGATG	.	5	ESCA
DYTN	0	.	GRCh37	2	207516442	207516442	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*100A>G	.	.	ENST00000452335	12/12	16	13	3	35	35	0	DYTN,3_prime_UTR_variant,,ENST00000452335,;AC010731.4,downstream_gene_variant,,ENST00000453816,;AC010731.4,downstream_gene_variant,,ENST00000441223,;AC010731.4,downstream_gene_variant,,ENST00000543490,;	C	ENSG00000232125	ENST00000452335	Transcript	3_prime_UTR_variant	1954	.	.	.	.	.	.	.	-1	DYTN	HGNC	23279	protein_coding	YES	CCDS46502.1	ENSP00000396593	DYTN_HUMAN	.	UPI0000EE0AB9	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACACTAAACT	.	5	ESCA
MSH6	0	.	GRCh37	2	48010277	48010277	+	5'UTR	SNP	T	T	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96T>A	.	.	ENST00000234420	1/10	28	21	7	54	54	0	MSH6,5_prime_UTR_variant,,ENST00000234420,;MSH6,intron_variant,,ENST00000606499,;MSH6,upstream_gene_variant,,ENST00000411819,;MSH6,upstream_gene_variant,,ENST00000538136,;MSH6,upstream_gene_variant,,ENST00000420813,;MSH6,upstream_gene_variant,,ENST00000455383,;MSH6,upstream_gene_variant,,ENST00000540021,;RNU6-688P,downstream_gene_variant,,ENST00000516063,;MSH6,upstream_gene_variant,,ENST00000493177,;MSH6,5_prime_UTR_variant,,ENST00000445503,;MSH6,5_prime_UTR_variant,,ENST00000456246,;	A	ENSG00000116062	ENST00000234420	Transcript	5_prime_UTR_variant	57	.	.	.	.	.	.	.	1	MSH6	HGNC	7329	protein_coding	YES	CCDS1836.1	ENSP00000234420	MSH6_HUMAN	U3KQ72_HUMAN,F5H2F9_HUMAN,C9JH55_HUMAN,C9J8Y8_HUMAN,C9J7Y7_HUMAN	UPI00000405F8	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCCTCCCCC	.	5	ESCA
MED12L	0	.	GRCh37	3	150883635	150883635	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360G>C	p.Val454Leu	p.V454L	ENST00000474524	10/43	20	17	3	88	88	0	MED12L,missense_variant,p.Val454Leu,ENST00000474524,;MED12L,missense_variant,p.Val454Leu,ENST00000422248,;MED12L,missense_variant,p.Val314Leu,ENST00000273432,;MED12L,missense_variant,p.Val454Leu,ENST00000309237,;	C	ENSG00000144893	ENST00000474524	Transcript	missense_variant	1398	1360	454	V/L	Gtg/Ctg	.	.	.	1	MED12L	HGNC	16050	protein_coding	YES	CCDS33876.1	ENSP00000417235	MD12L_HUMAN	.	UPI000020A46B	.	tolerated(0.58)	benign(0.168)	10/43	.	hmmpanther:PTHR12796,hmmpanther:PTHR12796:SF5,Pfam_domain:PF12145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGGGGTGACT	.	2	ESCA
PHC3	0	.	GRCh37	3	169889088	169889088	+	Intron	SNP	T	T	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.414+73A>G	.	.	ENST00000495893	.	33	28	4	55	55	0	PHC3,3_prime_UTR_variant,,ENST00000497658,;PHC3,3_prime_UTR_variant,,ENST00000481639,;PHC3,intron_variant,,ENST00000465896,;PHC3,intron_variant,,ENST00000474275,;PHC3,intron_variant,,ENST00000484931,;PHC3,intron_variant,,ENST00000495893,;PHC3,intron_variant,,ENST00000494943,;PHC3,intron_variant,,ENST00000467570,;PHC3,intron_variant,,ENST00000466189,;PHC3,intron_variant,,ENST00000475729,;PHC3,non_coding_transcript_exon_variant,,ENST00000491258,;PHC3,non_coding_transcript_exon_variant,,ENST00000490723,;PHC3,intron_variant,,ENST00000479467,;PHC3,intron_variant,,ENST00000472330,;	C	ENSG00000173889	ENST00000495893	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PHC3	HGNC	15682	protein_coding	YES	CCDS46952.1	ENSP00000420294	PHC3_HUMAN	C9JYH7_HUMAN	UPI00004DF1A6	.	.	.	.	4/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAAATAACAA	.	4	ESCA
NKD2	0	.	GRCh37	5	1034951	1034951	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.L169L	ENST00000296849	7/10	19	15	4	43	43	0	NKD2,synonymous_variant,p.%3D,ENST00000537972,;NKD2,synonymous_variant,p.%3D,ENST00000274150,;NKD2,synonymous_variant,p.%3D,ENST00000296849,;NKD2,upstream_gene_variant,,ENST00000382730,;NKD2,non_coding_transcript_exon_variant,,ENST00000523688,;NKD2,non_coding_transcript_exon_variant,,ENST00000519933,;NKD2,upstream_gene_variant,,ENST00000513296,;	T	ENSG00000145506	ENST00000296849	Transcript	synonymous_variant	736	507	169	L	ctC/ctT	.	.	.	1	NKD2	HGNC	17046	protein_coding	YES	CCDS3859.1	ENSP00000296849	NKD2_HUMAN	.	UPI0000073E19	.	.	.	7/10	.	hmmpanther:PTHR22611,hmmpanther:PTHR22611:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCCTCCGTGT	.	3	ESCA
JADE2	0	.	GRCh37	5	133915605	133915605	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*598G>A	.	.	ENST00000395003	11/11	30	23	6	80	80	0	JADE2,3_prime_UTR_variant,,ENST00000395003,;JADE2,downstream_gene_variant,,ENST00000282605,;JADE2,downstream_gene_variant,,ENST00000402835,;JADE2,downstream_gene_variant,,ENST00000361895,;JADE2,downstream_gene_variant,,ENST00000470876,;JADE2,downstream_gene_variant,,ENST00000430087,;	A	ENSG00000043143	ENST00000395003	Transcript	3_prime_UTR_variant	3150	.	.	.	.	.	.	.	1	JADE2	HGNC	22984	protein_coding	YES	CCDS4176.1	ENSP00000378451	JADE2_HUMAN	D6R9B8_HUMAN,C9J929_HUMAN	UPI00002331C9	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCGTATCA	.	5	ESCA
PCDHB17	0	.	GRCh37	5	140537168	140537168	+	Missense_Mutation	SNP	G	G	A	rs782224131	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1592G>A	p.Arg531His	p.R531H	ENST00000539533	1/1	85	79	6	236	236	0	PCDHB17,missense_variant,p.Arg531His,ENST00000539533,;PCDHB6,downstream_gene_variant,,ENST00000543635,;PCDHB6,downstream_gene_variant,,ENST00000231136,;	A	ENSG00000255622	ENST00000539533	Transcript	missense_variant	1592	1592	531	R/H	cGc/cAc	rs782224131	.	.	1	PCDHB17	Uniprot_gn	.	protein_coding	YES	.	ENSP00000438685	.	Q96T98_HUMAN	UPI000006CE19	.	tolerated_low_confidence(0.2)	benign(0.067)	1/1	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTCCGCGTGG	.	2	ESCA
SLC6A3	0	.	GRCh37	5	1443252	1443252	+	Missense_Mutation	SNP	G	G	A	rs533057143	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61C>T	p.Pro21Ser	p.P21S	ENST00000270349	2/15	27	23	4	64	64	0	SLC6A3,missense_variant,p.Pro21Ser,ENST00000270349,;SLC6A3,missense_variant,p.Pro21Ser,ENST00000453492,;SLC6A3,upstream_gene_variant,,ENST00000513308,;	A	ENSG00000142319	ENST00000270349	Transcript	missense_variant	189	61	21	P/S	Ccc/Tcc	rs533057143	.	.	-1	SLC6A3	HGNC	11049	protein_coding	YES	CCDS3863.1	ENSP00000270349	SC6A3_HUMAN	Q6LC27_HUMAN,H0YBA7_HUMAN	UPI000013548F	.	tolerated(0.59)	benign(0.002)	2/15	.	Prints_domain:PR01202,hmmpanther:PTHR11616:SF38,hmmpanther:PTHR11616	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTGGGCTCCT	by1000G	3	ESCA
IL7R	0	.	GRCh37	5	35876573	35876573	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1365C>G	p.Phe455Leu	p.F455L	ENST00000303115	8/8	39	35	4	69	69	0	IL7R,missense_variant,p.Phe455Leu,ENST00000303115,;IL7R,3_prime_UTR_variant,,ENST00000343305,;IL7R,3_prime_UTR_variant,,ENST00000505093,;IL7R,downstream_gene_variant,,ENST00000505875,;IL7R,downstream_gene_variant,,ENST00000506850,;IL7R,3_prime_UTR_variant,,ENST00000514217,;IL7R,downstream_gene_variant,,ENST00000509668,;	G	ENSG00000168685	ENST00000303115	Transcript	missense_variant	1494	1365	455	F/L	ttC/ttG	.	.	.	1	IL7R	HGNC	6024	protein_coding	YES	CCDS3911.1	ENSP00000306157	IL7RA_HUMAN	D6RG28_HUMAN,D6RCR9_HUMAN	UPI000013E861	.	deleterious(0)	probably_damaging(0.999)	8/8	.	hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|VARSCANS	AGCTTCTACCA	.	3	ESCA
PTGER4	0	.	GRCh37	5	40681944	40681944	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.849C>G	p.Ile283Met	p.I283M	ENST00000302472	2/3	17	11	6	40	40	0	PTGER4,missense_variant,p.Ile283Met,ENST00000302472,;PTGER4,non_coding_transcript_exon_variant,,ENST00000509543,;PTGER4,non_coding_transcript_exon_variant,,ENST00000513635,;PTGER4,non_coding_transcript_exon_variant,,ENST00000512578,;PTGER4,downstream_gene_variant,,ENST00000514343,;	G	ENSG00000171522	ENST00000302472	Transcript	missense_variant	1873	849	283	I/M	atC/atG	.	.	.	1	PTGER4	HGNC	9596	protein_coding	YES	CCDS3930.1	ENSP00000302846	PE2R4_HUMAN	A0PJF5_HUMAN	UPI000005042F	.	deleterious(0)	probably_damaging(0.948)	2/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11866:SF6,hmmpanther:PTHR11866,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01788	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCTGCTC	.	5	ESCA
AP3B1	0	.	GRCh37	5	77511947	77511947	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.718G>C	p.Gly240Arg	p.G240R	ENST00000255194	7/27	29	21	7	67	67	0	AP3B1,missense_variant,p.Gly240Arg,ENST00000255194,;AP3B1,missense_variant,p.Gly191Arg,ENST00000519295,;	G	ENSG00000132842	ENST00000255194	Transcript	missense_variant	894	718	240	G/R	Ggg/Cgg	.	.	.	-1	AP3B1	HGNC	566	protein_coding	YES	CCDS4041.1	ENSP00000255194	AP3B1_HUMAN	E5RJ68_HUMAN	UPI00001AE77D	.	deleterious(0)	probably_damaging(0.998)	7/27	.	hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF10,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037096,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCCCCACT	.	5	ESCA
ADCY2	0	.	GRCh37	5	7827274	7827274	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*290C>A	.	.	ENST00000338316	25/25	35	28	7	93	93	0	ADCY2,3_prime_UTR_variant,,ENST00000338316,;C5orf49,downstream_gene_variant,,ENST00000509627,;C5orf49,downstream_gene_variant,,ENST00000399810,;ADCY2,downstream_gene_variant,,ENST00000537121,;ADCY2,non_coding_transcript_exon_variant,,ENST00000489501,;	A	ENSG00000078295	ENST00000338316	Transcript	3_prime_UTR_variant	3655	.	.	.	.	.	.	.	1	ADCY2	HGNC	233	protein_coding	YES	CCDS3872.2	ENSP00000342952	ADCY2_HUMAN	Q7RTV6_HUMAN,Q71UM8_HUMAN,D6REB8_HUMAN	UPI000066D9F2	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTCTTAAG	.	5	ESCA
C6orf118	0	.	GRCh37	6	165715349	165715349	+	Missense_Mutation	SNP	C	C	G	rs770270029	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462G>C	p.Glu154Asp	p.E154D	ENST00000230301	2/9	21	16	4	57	57	0	C6orf118,missense_variant,p.Glu50Asp,ENST00000543069,;C6orf118,missense_variant,p.Glu154Asp,ENST00000230301,;	G	ENSG00000112539	ENST00000230301	Transcript	missense_variant	483	462	154	E/D	gaG/gaC	rs770270029	.	.	-1	C6orf118	HGNC	21233	protein_coding	YES	CCDS5288.1	ENSP00000230301	CF118_HUMAN	.	UPI0000367401	.	tolerated(0.23)	benign(0.055)	2/9	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E157K|c.469G>A|3,BUFFER|p.E53K|c.157G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCCTCTCT	.	5	ESCA
TRIM27	0	.	GRCh37	6	28875015	28875015	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.944C>T	p.Ser315Leu	p.S315L	ENST00000377199	7/8	23	19	4	85	85	0	TRIM27,missense_variant,p.Ser315Leu,ENST00000377199,;TRIM27,missense_variant,p.Ser315Leu,ENST00000377194,;TRIM27,missense_variant,p.Ser50Leu,ENST00000414543,;TRIM27,splice_region_variant,,ENST00000467742,;TRIM27,downstream_gene_variant,,ENST00000498117,;TRIM27,non_coding_transcript_exon_variant,,ENST00000481474,;	A	ENSG00000204713	ENST00000377199	Transcript	missense_variant	1301	944	315	S/L	tCa/tTa	.	.	.	-1	TRIM27	HGNC	9975	protein_coding	YES	CCDS4654.1	ENSP00000366404	TRI27_HUMAN	Q9NZT8_HUMAN	UPI0000000DCE	.	tolerated(0.36)	benign(0.011)	7/8	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF271,hmmpanther:PTHR24103,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCTGAGTAT	.	4	ESCA
ZNRD1-AS1	0	.	GRCh37	6	29974769	29974769	+	Intron	SNP	T	T	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1346+231A>T	.	.	ENST00000376797	.	54	33	20	146	146	0	ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;ZNRD1-AS1,intron_variant,,ENST00000376797,;HLA-J,non_coding_transcript_exon_variant,,ENST00000462773,;HLA-J,non_coding_transcript_exon_variant,,ENST00000469281,;HLA-J,intron_variant,,ENST00000495278,;HLA-J,non_coding_transcript_exon_variant,,ENST00000494367,;HCG4P3,non_coding_transcript_exon_variant,,ENST00000458060,;	A	ENSG00000204623	ENST00000376797	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ZNRD1-AS1	HGNC	13924	antisense	YES	.	.	.	.	.	.	.	.	.	10/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACTGGGCG	.	5	ESCA
EYS	0	.	GRCh37	6	65146103	65146103	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5891G>A	p.Arg1964Lys	p.R1964K	ENST00000503581	28/43	30	24	5	66	66	0	EYS,missense_variant,p.Arg1964Lys,ENST00000370616,;EYS,missense_variant,p.Arg1964Lys,ENST00000370621,;EYS,missense_variant,p.Arg1964Lys,ENST00000503581,;	T	ENSG00000188107	ENST00000503581	Transcript	missense_variant	6429	5891	1964	R/K	aGa/aAa	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	tolerated(0.98)	benign(0.001)	28/43	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTCTAACA	.	5	ESCA
EYS	0	.	GRCh37	6	66200582	66200582	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767T>A	p.Ile256Lys	p.I256K	ENST00000503581	5/43	29	24	5	72	72	0	EYS,missense_variant,p.Ile256Lys,ENST00000342421,;EYS,missense_variant,p.Ile256Lys,ENST00000393380,;EYS,missense_variant,p.Ile256Lys,ENST00000370616,;EYS,missense_variant,p.Ile256Lys,ENST00000503581,;EYS,missense_variant,p.Ile256Lys,ENST00000370621,;EYS,missense_variant,p.Ile256Lys,ENST00000370618,;EYS,3_prime_UTR_variant,,ENST00000471279,;EYS,non_coding_transcript_exon_variant,,ENST00000489873,;	T	ENSG00000188107	ENST00000503581	Transcript	missense_variant	1305	767	256	I/K	aTa/aAa	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	tolerated(0.73)	probably_damaging(0.965)	5/43	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048,Gene3D:2.10.25.10,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAATTATTTCT	.	4	ESCA
MUC3A	0	.	GRCh37	7	100609893	100609893	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2533A>G	p.Thr845Ala	p.T845A	ENST00000319509	9/11	107	101	6	158	158	0	MUC3A,missense_variant,p.Thr277Ala,ENST00000422757,;MUC3A,missense_variant,p.Thr845Ala,ENST00000319509,;MUC12,upstream_gene_variant,,ENST00000536621,;MUC12,upstream_gene_variant,,ENST00000379442,;RP11-395B7.2,intron_variant,,ENST00000420080,;RP11-395B7.2,upstream_gene_variant,,ENST00000434775,;MUC3A,3_prime_UTR_variant,,ENST00000414964,;MUC3A,non_coding_transcript_exon_variant,,ENST00000483133,;MUC3A,non_coding_transcript_exon_variant,,ENST00000480291,;RP11-395B7.2,upstream_gene_variant,,ENST00000438198,;	G	ENSG00000169894	ENST00000319509	Transcript	missense_variant	2533	2533	845	T/A	Aca/Gca	.	.	.	1	MUC3A	HGNC	7513	protein_coding	YES	.	ENSP00000324834	.	J3QST7_HUMAN,I0CMK2_HUMAN,H9XFA8_HUMAN	UPI000198CE7F	.	tolerated(0.58)	benign(0.034)	9/11	.	hmmpanther:PTHR24041,hmmpanther:PTHR24041:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGGAACAGGT	.	2	ESCA
NRCAM	0	.	GRCh37	7	107872803	107872803	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394G>T	p.Ala132Ser	p.A132S	ENST00000379028	7/33	66	59	6	76	76	0	NRCAM,missense_variant,p.Ala132Ser,ENST00000379022,;NRCAM,missense_variant,p.Ala126Ser,ENST00000351718,;NRCAM,missense_variant,p.Ala126Ser,ENST00000417701,;NRCAM,missense_variant,p.Ala132Ser,ENST00000413765,;NRCAM,missense_variant,p.Ala132Ser,ENST00000379024,;NRCAM,missense_variant,p.Ala132Ser,ENST00000379028,;NRCAM,missense_variant,p.Ala132Ser,ENST00000425651,;NRCAM,downstream_gene_variant,,ENST00000418239,;NRCAM,downstream_gene_variant,,ENST00000419936,;NRCAM,downstream_gene_variant,,ENST00000456431,;NRCAM,downstream_gene_variant,,ENST00000442580,;	A	ENSG00000091129	ENST00000379028	Transcript	missense_variant	865	394	132	A/S	Gca/Tca	.	.	.	-1	NRCAM	HGNC	7994	protein_coding	YES	CCDS47686.1	ENSP00000368314	NRCAM_HUMAN	C9JUR7_HUMAN,C9JF43_HUMAN,B3KRX0_HUMAN	UPI00005E2661	.	deleterious(0.02)	probably_damaging(0.999)	7/33	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF554,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AACTGCAGCTC	.	3	ESCA
FAM183B	0	.	GRCh37	7	38725145	38725145	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53C>T	.	.	ENST00000409072	2/2	21	17	4	34	34	0	FAM183B,3_prime_UTR_variant,,ENST00000409072,;	A	ENSG00000164556	ENST00000409072	Transcript	3_prime_UTR_variant	1396	.	.	.	.	.	.	.	-1	FAM183B	HGNC	34511	protein_coding	YES	.	ENSP00000386657	F183B_HUMAN	.	UPI000020EE1E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTAGGCAGT	.	5	ESCA
ERV3-1	0	.	GRCh37	7	64452476	64452476	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.929A>T	p.Glu310Val	p.E310V	ENST00000394323	2/2	35	30	5	96	96	0	ERV3-1,missense_variant,p.Glu310Val,ENST00000394323,;ZNF117,upstream_gene_variant,,ENST00000282869,;ZNF117,intron_variant,,ENST00000487644,;	A	ENSG00000213462	ENST00000394323	Transcript	missense_variant	1430	929	310	E/V	gAa/gTa	.	.	.	-1	ERV3-1	HGNC	3454	protein_coding	YES	CCDS47595.1	ENSP00000391594	ENR1_HUMAN	.	UPI000023FEAF	.	deleterious(0.01)	possibly_damaging(0.891)	2/2	.	hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTAGTTCCCTT	.	4	ESCA
SEMA3C	0	.	GRCh37	7	80432008	80432008	+	Missense_Mutation	SNP	C	C	T	rs766485092	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.889G>A	p.Gly297Ser	p.G297S	ENST00000265361	9/18	31	28	3	45	45	0	SEMA3C,missense_variant,p.Gly297Ser,ENST00000265361,;SEMA3C,missense_variant,p.Gly315Ser,ENST00000544525,;SEMA3C,missense_variant,p.Gly149Ser,ENST00000536800,;SEMA3C,missense_variant,p.Gly297Ser,ENST00000419255,;SEMA3C,upstream_gene_variant,,ENST00000475955,;SEMA3C,3_prime_UTR_variant,,ENST00000458729,;	T	ENSG00000075223	ENST00000265361	Transcript	missense_variant	1451	889	297	G/S	Ggc/Agc	rs766485092	.	.	-1	SEMA3C	HGNC	10725	protein_coding	YES	CCDS5596.1	ENSP00000265361	SEM3C_HUMAN	Q75MX0_HUMAN,Q75L25_HUMAN	UPI000011C137	.	deleterious(0)	probably_damaging(1)	9/18	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF25,hmmpanther:PTHR11036,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGGCCGTCTT	byFrequency	2	ESCA
CACNA2D1	0	.	GRCh37	7	81964469	81964469	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.276C>T	p.%3D	p.N92N	ENST00000356860	3/39	24	19	4	75	75	0	CACNA2D1,synonymous_variant,p.%3D,ENST00000356253,;CACNA2D1,synonymous_variant,p.%3D,ENST00000356860,;CACNA2D1,synonymous_variant,p.%3D,ENST00000423588,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000484706,;	A	ENSG00000153956	ENST00000356860	Transcript	synonymous_variant	615	276	92	N	aaC/aaT	.	.	.	-1	CACNA2D1	HGNC	1399	protein_coding	YES	CCDS5598.1	ENSP00000349320	CA2D1_HUMAN	Q9UDU5_HUMAN,Q9UDQ3_HUMAN,Q9UDL7_HUMAN,O95026_HUMAN	UPI00003674CD	.	.	.	3/39	.	hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTGTTGCT	.	5	ESCA
SAMD9L	0	.	GRCh37	7	92765282	92765282	+	Translation_Start_Site	SNP	C	C	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3G>C	p.Met1?	p.M1?	ENST00000318238	5/5	55	35	19	53	53	0	SAMD9L,start_lost,p.Met1?,ENST00000446033,;SAMD9L,start_lost,p.Met1?,ENST00000446959,;SAMD9L,start_lost,p.Met1?,ENST00000318238,;SAMD9L,start_lost,p.Met1?,ENST00000414791,;SAMD9L,start_lost,p.Met1?,ENST00000437805,;SAMD9L,start_lost,p.Met1?,ENST00000411955,;SAMD9L,start_lost,p.Met1?,ENST00000439952,;	G	ENSG00000177409	ENST00000318238	Transcript	start_lost	1220	3	1	M/I	atG/atC	.	.	.	-1	SAMD9L	HGNC	1349	protein_coding	YES	CCDS34681.1	ENSP00000326247	SAM9L_HUMAN	B4E3M1_HUMAN	UPI000020F567	.	deleterious(0)	probably_damaging(0.999)	5/5	.	hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACTCATATC	.	5	ESCA
TFPI2	0	.	GRCh37	7	93519957	93519957	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34C>A	p.Leu12Met	p.L12M	ENST00000222543	1/5	12	6	5	17	17	0	TFPI2,missense_variant,p.Leu12Met,ENST00000545378,;TFPI2,missense_variant,p.Leu12Met,ENST00000222543,;GNGT1,intron_variant,,ENST00000455502,;TFPI2,upstream_gene_variant,,ENST00000451238,;AC002076.10,upstream_gene_variant,,ENST00000435257,;TFPI2,non_coding_transcript_exon_variant,,ENST00000461482,;	T	ENSG00000105825	ENST00000222543	Transcript	missense_variant	347	34	12	L/M	Ctg/Atg	.	.	.	-1	TFPI2	HGNC	11761	protein_coding	YES	CCDS5632.1	ENSP00000222543	TFPI2_HUMAN	Q8NE89_HUMAN,Q8NAK6_HUMAN	UPI00000362E2	.	deleterious(0.02)	possibly_damaging(0.86)	1/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF89,PIRSF_domain:PIRSF001620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGCAGAATCG	.	3	ESCA
ZFPM2	0	.	GRCh37	8	106431482	106431482	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.151G>C	p.Gly51Arg	p.G51R	ENST00000407775	2/8	33	30	3	47	47	0	ZFPM2,missense_variant,p.Gly51Arg,ENST00000407775,;ZFPM2,5_prime_UTR_variant,,ENST00000520492,;ZFPM2,5_prime_UTR_variant,,ENST00000520027,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000524235,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522160,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000511341,;RP11-127H5.1,3_prime_UTR_variant,,ENST00000518180,;	C	ENSG00000169946	ENST00000407775	Transcript	missense_variant	401	151	51	G/R	Ggg/Cgg	.	.	.	1	ZFPM2	HGNC	16700	protein_coding	YES	CCDS47908.1	ENSP00000384179	FOG2_HUMAN	Q9NPQ0_HUMAN,F5H542_HUMAN,E7ET52_HUMAN,E5RJX0_HUMAN	UPI000057A0B4	.	tolerated(0.24)	benign(0.145)	2/8	.	hmmpanther:PTHR12958:SF5,hmmpanther:PTHR12958	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATTTGGGCCT	.	4	ESCA
NAP1L3	0	.	GRCh37	X	92927199	92927199	+	Silent	SNP	T	T	G	novel	.	TCGA-IG-A3YC-01A-11D-A247-09	TCGA-IG-A3YC-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1105A>C	p.%3D	p.R369R	ENST00000373079	1/1	11	8	3	35	35	0	NAP1L3,synonymous_variant,p.%3D,ENST00000475430,;NAP1L3,synonymous_variant,p.%3D,ENST00000373079,;FAM133A,upstream_gene_variant,,ENST00000355813,;FAM133A,upstream_gene_variant,,ENST00000538690,;FAM133A,upstream_gene_variant,,ENST00000332647,;FAM133A,upstream_gene_variant,,ENST00000322139,;	G	ENSG00000186310	ENST00000373079	Transcript	synonymous_variant	1369	1105	369	R	Aga/Cga	.	.	.	-1	NAP1L3	HGNC	7639	protein_coding	YES	CCDS14465.1	ENSP00000362171	NP1L3_HUMAN	.	UPI0000167B31	.	.	.	1/1	.	Superfamily_domains:SSF143113,Pfam_domain:PF00956,hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTCTGAAGT	.	2	ESCA
CHUK	0	.	GRCh37	10	101967073	101967073	+	Missense_Mutation	SNP	T	T	C	rs769905171	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1145A>G	p.Tyr382Cys	p.Y382C	ENST00000370397	11/21	23	16	7	12	12	0	CHUK,missense_variant,p.Tyr382Cys,ENST00000370397,;	C	ENSG00000213341	ENST00000370397	Transcript	missense_variant	1232	1145	382	Y/C	tAt/tGt	rs769905171	.	.	-1	CHUK	HGNC	1974	protein_coding	YES	CCDS7488.1	ENSP00000359424	IKKA_HUMAN	.	UPI000013D6C7	.	tolerated(0.18)	benign(0.081)	11/21	.	hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCATATAGCTA	.	2	ESCA
ZDHHC6	0	.	GRCh37	10	114190319	114190319	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*243C>T	.	.	ENST00000369405	11/11	20	16	4	21	21	0	ZDHHC6,3_prime_UTR_variant,,ENST00000369405,;ZDHHC6,downstream_gene_variant,,ENST00000369404,;ACSL5,downstream_gene_variant,,ENST00000356116,;ACSL5,downstream_gene_variant,,ENST00000354273,;ACSL5,downstream_gene_variant,,ENST00000433418,;ACSL5,downstream_gene_variant,,ENST00000354655,;ACSL5,downstream_gene_variant,,ENST00000393081,;ACSL5,downstream_gene_variant,,ENST00000369410,;ACSL5,downstream_gene_variant,,ENST00000496328,;ZDHHC6,downstream_gene_variant,,ENST00000471035,;ZDHHC6,downstream_gene_variant,,ENST00000482410,;	A	ENSG00000023041	ENST00000369405	Transcript	3_prime_UTR_variant	1909	.	.	.	.	.	.	.	-1	ZDHHC6	HGNC	19160	protein_coding	YES	CCDS7574.1	ENSP00000358413	ZDHC6_HUMAN	.	UPI00000373E8	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTGGATGAA	.	2	ESCA
FANK1	0	.	GRCh37	10	127693454	127693454	+	Missense_Mutation	SNP	C	C	G	rs779721250	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.541C>G	p.Leu181Val	p.L181V	ENST00000368693	7/11	118	87	30	108	108	0	FANK1,missense_variant,p.Leu76Val,ENST00000456942,;FANK1,missense_variant,p.Leu181Val,ENST00000368693,;FANK1,missense_variant,p.Leu159Val,ENST00000368691,;FANK1,missense_variant,p.Leu175Val,ENST00000368695,;FANK1,splice_region_variant,,ENST00000492670,;FANK1,splice_region_variant,,ENST00000464130,;FANK1,non_coding_transcript_exon_variant,,ENST00000477963,;	G	ENSG00000203780	ENST00000368693	Transcript	missense_variant	645	541	181	L/V	Cta/Gta	rs779721250	.	.	1	FANK1	HGNC	23527	protein_coding	YES	CCDS31309.1	ENSP00000357682	FANK1_HUMAN	C9JD80_HUMAN,A6NH44_HUMAN	UPI000046FFD6	.	deleterious(0.01)	possibly_damaging(0.578)	7/11	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24183,hmmpanther:PTHR24183:SF1,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTCTAATG	byFrequency	5	ESCA
FAM196A	0	.	GRCh37	10	128935704	128935704	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*397G>C	.	.	ENST00000522781	6/6	18	13	5	15	15	0	FAM196A,3_prime_UTR_variant,,ENST00000522781,;FAM196A,3_prime_UTR_variant,,ENST00000424811,;DOCK1,intron_variant,,ENST00000280333,;	G	ENSG00000188916	ENST00000522781	Transcript	3_prime_UTR_variant	2393	.	.	.	.	.	.	.	-1	FAM196A	HGNC	33859	protein_coding	YES	CCDS31312.1	ENSP00000429763	F196A_HUMAN	.	UPI00001C0E37	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTCATT	.	5	ESCA
MKI67	0	.	GRCh37	10	129913420	129913420	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1252C>G	p.Leu418Val	p.L418V	ENST00000368654	7/15	43	27	16	49	49	0	MKI67,missense_variant,p.Leu418Val,ENST00000368654,;MKI67,intron_variant,,ENST00000368653,;MKI67,downstream_gene_variant,,ENST00000478293,;MKI67,upstream_gene_variant,,ENST00000484853,;	C	ENSG00000148773	ENST00000368654	Transcript	missense_variant	1628	1252	418	L/V	Ctc/Gtc	.	.	.	-1	MKI67	HGNC	7107	protein_coding	YES	CCDS7659.1	ENSP00000357643	KI67_HUMAN	.	UPI000013DB54	.	tolerated(0.11)	possibly_damaging(0.681)	7/15	.	hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAGATTTT	.	5	ESCA
FRMD4A	0	.	GRCh37	10	13699399	13699399	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2190C>G	p.Phe730Leu	p.F730L	ENST00000357447	22/25	24	16	7	26	26	0	FRMD4A,missense_variant,p.Phe730Leu,ENST00000357447,;FRMD4A,missense_variant,p.Phe715Leu,ENST00000358621,;FRMD4A,missense_variant,p.Phe730Leu,ENST00000378503,;RP11-295P9.3,downstream_gene_variant,,ENST00000601460,;RP11-295P9.3,intron_variant,,ENST00000593351,;RP11-295P9.3,downstream_gene_variant,,ENST00000599639,;FRMD4A,upstream_gene_variant,,ENST00000475325,;RP11-295P9.3,downstream_gene_variant,,ENST00000600511,;RP11-295P9.3,downstream_gene_variant,,ENST00000600249,;RP11-295P9.3,downstream_gene_variant,,ENST00000593358,;FRMD4A,upstream_gene_variant,,ENST00000495956,;RP11-295P9.3,downstream_gene_variant,,ENST00000601758,;RP11-295P9.3,downstream_gene_variant,,ENST00000596499,;RP11-295P9.3,downstream_gene_variant,,ENST00000596235,;RP11-295P9.3,downstream_gene_variant,,ENST00000430721,;RP11-295P9.3,downstream_gene_variant,,ENST00000594575,;RP11-295P9.3,downstream_gene_variant,,ENST00000419851,;RP11-295P9.3,downstream_gene_variant,,ENST00000597920,;RP11-295P9.3,downstream_gene_variant,,ENST00000598625,;	C	ENSG00000151474	ENST00000357447	Transcript	missense_variant	2559	2190	730	F/L	ttC/ttG	.	.	.	-1	FRMD4A	HGNC	25491	protein_coding	YES	CCDS7101.1	ENSP00000350032	FRM4A_HUMAN	F8WAN4_HUMAN	UPI0000366665	.	tolerated(0.12)	benign(0.005)	22/25	.	hmmpanther:PTHR23281:SF12,hmmpanther:PTHR23281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTAGAAGTC	.	5	ESCA
SVIL	0	.	GRCh37	10	29821901	29821901	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1395G>C	p.%3D	p.V465V	ENST00000375398	10/40	40	31	9	37	37	0	SVIL,synonymous_variant,p.%3D,ENST00000355867,;SVIL,synonymous_variant,p.%3D,ENST00000375398,;SVIL,intron_variant,,ENST00000375400,;	G	ENSG00000197321	ENST00000375398	Transcript	synonymous_variant	1845	1395	465	V	gtG/gtC	.	.	.	-1	SVIL	HGNC	11480	protein_coding	YES	CCDS7164.1	ENSP00000364547	SVIL_HUMAN	Q569J5_HUMAN	UPI0000366678	.	.	.	10/40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCACTAG	.	5	ESCA
C10ORF68	0	.	GRCh37	10	33140807	33140807	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1697G>C	p.Gly566Ala	p.G566A	ENST00000302316	20/23	31	22	8	20	20	0	C10ORF68,missense_variant,p.Gly570Ala,ENST00000375028,;C10ORF68,missense_variant,p.Gly525Ala,ENST00000375030,;C10ORF68,missense_variant,p.Gly630Ala,ENST00000375025,;C10ORF68,missense_variant,p.Gly566Ala,ENST00000302316,;	C	ENSG00000150076	ENST00000302316	Transcript	missense_variant	2170	1697	566	G/A	gGt/gCt	.	.	.	1	C10ORF68	Uniprot_gn	.	nonsense_mediated_decay	YES	CCDS31177.1	ENSP00000303710	CJ068_HUMAN	.	UPI000049DCE8	.	tolerated(0.07)	benign(0.013)	20/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGGTCCAA	.	5	ESCA
ZNF487	0	.	GRCh37	10	43977046	43977046	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303C>T	p.%3D	p.G101G	ENST00000437590	4/4	31	25	6	39	39	0	ZNF487,synonymous_variant,p.%3D,ENST00000456416,;ZNF487,synonymous_variant,p.%3D,ENST00000431662,;ZNF487,synonymous_variant,p.%3D,ENST00000315429,;ZNF487,synonymous_variant,p.%3D,ENST00000437590,;	T	ENSG00000243660	ENST00000437590	Transcript	synonymous_variant	530	303	101	G	ggC/ggT	.	.	.	1	ZNF487	HGNC	23488	protein_coding	YES	.	ENSP00000392335	.	B7Z7S5_HUMAN	UPI00019151EB	.	.	.	4/4	.	hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF116	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGGCAACTG	.	5	ESCA
PRKG1	0	.	GRCh37	10	53667299	53667299	+	Missense_Mutation	SNP	T	T	C	rs769855764	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731T>C	p.Ile244Thr	p.I244T	ENST00000373980	5/18	52	30	21	61	61	0	PRKG1,missense_variant,p.Ile102Thr,ENST00000373976,;PRKG1,missense_variant,p.Ile229Thr,ENST00000401604,;PRKG1,missense_variant,p.Ile217Thr,ENST00000373985,;PRKG1,missense_variant,p.Ile244Thr,ENST00000373980,;	C	ENSG00000185532	ENST00000373980	Transcript	missense_variant	1148	731	244	I/T	aTc/aCc	rs769855764	.	.	1	PRKG1	HGNC	9414	protein_coding	YES	CCDS7244.1	ENSP00000363092	KGP1_HUMAN	.	UPI000012DDCD	.	tolerated(0.64)	benign(0.006)	5/18	.	PROSITE_profiles:PS50042,hmmpanther:PTHR24353:SF61,hmmpanther:PTHR24353,Gene3D:2.60.120.10,SMART_domains:SM00100,PIRSF_domain:PIRSF000559,Superfamily_domains:SSF51206,Prints_domain:PR00104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGATCCTCA	.	5	ESCA
MMP13	0	.	GRCh37	11	102822858	102822858	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682T>C	p.%3D	p.L228L	ENST00000260302	5/10	17	9	7	35	35	0	MMP13,synonymous_variant,p.%3D,ENST00000260302,;MMP13,synonymous_variant,p.%3D,ENST00000340273,;	G	ENSG00000137745	ENST00000260302	Transcript	synonymous_variant	711	682	228	L	Tta/Cta	.	.	.	-1	MMP13	HGNC	7159	protein_coding	YES	CCDS8324.1	ENSP00000260302	MMP13_HUMAN	Q6LBE5_HUMAN	UPI00000422BC	.	.	.	5/10	.	hmmpanther:PTHR10201:SF130,hmmpanther:PTHR10201,Gene3D:3.40.390.10,Pfam_domain:PF00413,SMART_domains:SM00235,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF55486,Prints_domain:PR00138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F224F|c.672C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTAAGGAGT	.	5	ESCA
CARD18	0	.	GRCh37	11	105009559	105009559	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.254C>T	p.Ser85Leu	p.S85L	ENST00000530950	2/3	52	47	5	66	66	0	CARD18,missense_variant,p.Ser46Leu,ENST00000532895,;CARD18,missense_variant,p.Ser46Leu,ENST00000526823,;CARD18,missense_variant,p.Ser85Leu,ENST00000530950,;	A	ENSG00000255501	ENST00000530950	Transcript	missense_variant	254	254	85	S/L	tCa/tTa	.	.	.	-1	CARD18	HGNC	28861	protein_coding	YES	CCDS53705.1	ENSP00000436691	CAR18_HUMAN	G5EA35_HUMAN	UPI000012D143	.	tolerated(0.13)	benign(0.007)	2/3	.	PROSITE_profiles:PS50209,hmmpanther:PTHR10454:SF136,hmmpanther:PTHR10454,Pfam_domain:PF00619,Gene3D:1.10.533.10,Superfamily_domains:SSF47986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Q82Q|c.246A>G|3	MUTECT|MUSE	TCTTTGAGGCA	.	2	ESCA
TRAPPC4	0	.	GRCh37	11	118890872	118890872	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363C>G	p.Ile121Met	p.I121M	ENST00000533632	3/5	30	27	3	23	23	0	TRAPPC4,missense_variant,p.Ile121Met,ENST00000533632,;TRAPPC4,missense_variant,p.Ile78Met,ENST00000528230,;TRAPPC4,missense_variant,p.Ile121Met,ENST00000359005,;TRAPPC4,missense_variant,p.Ile121Met,ENST00000533058,;TRAPPC4,intron_variant,,ENST00000434101,;TRAPPC4,intron_variant,,ENST00000525303,;SLC37A4,downstream_gene_variant,,ENST00000357590,;SLC37A4,downstream_gene_variant,,ENST00000330775,;CCDC84,downstream_gene_variant,,ENST00000334418,;RPS25,upstream_gene_variant,,ENST00000527673,;SLC37A4,downstream_gene_variant,,ENST00000545985,;SLC37A4,downstream_gene_variant,,ENST00000538950,;MIR3656,downstream_gene_variant,,ENST00000577421,;SLC37A4,downstream_gene_variant,,ENST00000527992,;RPS25,upstream_gene_variant,,ENST00000528547,;SLC37A4,downstream_gene_variant,,ENST00000525039,;SLC37A4,downstream_gene_variant,,ENST00000530407,;SLC37A4,downstream_gene_variant,,ENST00000525102,;SLC37A4,downstream_gene_variant,,ENST00000529510,;SLC37A4,downstream_gene_variant,,ENST00000525372,;TRAPPC4,upstream_gene_variant,,ENST00000526141,;TRAPPC4,3_prime_UTR_variant,,ENST00000525079,;TRAPPC4,non_coding_transcript_exon_variant,,ENST00000447216,;TRAPPC4,non_coding_transcript_exon_variant,,ENST00000531290,;TRAPPC4,non_coding_transcript_exon_variant,,ENST00000533149,;TRAPPC4,intron_variant,,ENST00000533012,;SLC37A4,downstream_gene_variant,,ENST00000532085,;TRAPPC4,upstream_gene_variant,,ENST00000524797,;CCDC84,downstream_gene_variant,,ENST00000532132,;TRAPPC4,downstream_gene_variant,,ENST00000527680,;RPS25,upstream_gene_variant,,ENST00000527791,;CCDC84,downstream_gene_variant,,ENST00000527356,;SLC37A4,downstream_gene_variant,,ENST00000524428,;RPS25,upstream_gene_variant,,ENST00000524864,;SLC37A4,downstream_gene_variant,,ENST00000526275,;CCDC84,downstream_gene_variant,,ENST00000526463,;RPS25,upstream_gene_variant,,ENST00000527853,;RPS25,upstream_gene_variant,,ENST00000532567,;CCDC84,downstream_gene_variant,,ENST00000533787,;	G	ENSG00000196655	ENST00000533632	Transcript	missense_variant	727	363	121	I/M	atC/atG	COSM428529	.	.	1	TRAPPC4	HGNC	19943	protein_coding	YES	CCDS8407.1	ENSP00000436005	TPPC4_HUMAN	G3V1A0_HUMAN	UPI0000052E23	.	tolerated(0.16)	probably_damaging(0.97)	3/5	.	Superfamily_domains:SSF64356,Gene3D:2j3wA00,Pfam_domain:PF04099,hmmpanther:PTHR23249,hmmpanther:PTHR23249:SF15	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCATCGGCTC	.	2	ESCA
OPCML	0	.	GRCh37	11	132286874	132286874	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3213T>A	.	.	ENST00000331898	7/7	43	35	8	41	41	0	OPCML,3_prime_UTR_variant,,ENST00000524381,;OPCML,3_prime_UTR_variant,,ENST00000331898,;OPCML,downstream_gene_variant,,ENST00000374778,;OPCML,downstream_gene_variant,,ENST00000541867,;OPCML,downstream_gene_variant,,ENST00000529038,;	T	ENSG00000183715	ENST00000331898	Transcript	3_prime_UTR_variant	4830	.	.	.	.	.	.	.	-1	OPCML	HGNC	8143	protein_coding	YES	CCDS8492.1	ENSP00000330862	OPCM_HUMAN	B7ZLQ0_HUMAN,B2CZX3_HUMAN,A8K0Y0_HUMAN	UPI0000055AE0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGAAGGGGA	.	4	ESCA
SLC5A12	0	.	GRCh37	11	26713971	26713971	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1153+65C>T	.	.	ENST00000396005	.	45	35	10	53	53	0	SLC5A12,3_prime_UTR_variant,,ENST00000280467,;SLC5A12,intron_variant,,ENST00000396005,;SLC5A12,downstream_gene_variant,,ENST00000533617,;SLC5A12,intron_variant,,ENST00000527405,;	A	ENSG00000148942	ENST00000396005	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SLC5A12	HGNC	28750	protein_coding	YES	CCDS7860.2	ENSP00000379326	SC5AC_HUMAN	E9PLZ7_HUMAN	UPI000003ED2C	.	.	.	.	9/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGGATTTT	.	5	ESCA
DNAJC24	0	.	GRCh37	11	31447855	31447855	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272G>T	p.Gly91Val	p.G91V	ENST00000465995	4/5	29	17	11	24	24	0	DNAJC24,missense_variant,p.Gly91Val,ENST00000465995,;DNAJC24,3_prime_UTR_variant,,ENST00000536040,;DNAJC24,non_coding_transcript_exon_variant,,ENST00000524747,;DNAJC24,non_coding_transcript_exon_variant,,ENST00000530125,;DNAJC24,missense_variant,p.Gly8Val,ENST00000395949,;DNAJC24,3_prime_UTR_variant,,ENST00000527731,;DNAJC24,3_prime_UTR_variant,,ENST00000526042,;	T	ENSG00000170946	ENST00000465995	Transcript	missense_variant	378	272	91	G/V	gGa/gTa	.	.	.	1	DNAJC24	HGNC	26979	protein_coding	YES	CCDS7873.2	ENSP00000417548	DJC24_HUMAN	.	UPI0000160EAB	.	tolerated(0.16)	possibly_damaging(0.53)	4/5	.	hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAGGACCAG	.	5	ESCA
LRRC4C	0	.	GRCh37	11	40137250	40137250	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.593A>T	p.Asn198Ile	p.N198I	ENST00000278198	2/2	23	19	4	20	20	0	LRRC4C,missense_variant,p.Asn198Ile,ENST00000528697,;LRRC4C,missense_variant,p.Asn198Ile,ENST00000278198,;LRRC4C,missense_variant,p.Asn198Ile,ENST00000530763,;LRRC4C,missense_variant,p.Asn198Ile,ENST00000527150,;LRRC4C,downstream_gene_variant,,ENST00000533474,;	A	ENSG00000148948	ENST00000278198	Transcript	missense_variant	2557	593	198	N/I	aAc/aTc	.	.	.	-1	LRRC4C	HGNC	29317	protein_coding	YES	CCDS31464.1	ENSP00000278198	LRC4C_HUMAN	E9PLP4_HUMAN	UPI000000D9A7	.	deleterious(0)	probably_damaging(0.994)	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24369:SF8,hmmpanther:PTHR24369,Gene3D:3.80.10.10,Pfam_domain:PF13306,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAAGTTGGAC	.	4	ESCA
OR4C12	0	.	GRCh37	11	50003299	50003299	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.739T>G	p.Leu247Val	p.L247V	ENST00000335238	1/1	43	37	5	38	38	0	OR4C12,missense_variant,p.Leu247Val,ENST00000335238,;	C	ENSG00000221954	ENST00000335238	Transcript	missense_variant	773	739	247	L/V	Tta/Gta	COSM4033453	.	.	-1	OR4C12	HGNC	15168	protein_coding	YES	CCDS31496.1	ENSP00000334418	OR4CC_HUMAN	.	UPI0000041E30	.	deleterious_low_confidence(0)	possibly_damaging(0.447)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF9,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F248L|c.744C>A|3	RADIA|MUTECT|MUSE|VARSCANS	GAATAAGACAA	.	4	ESCA
OR5D14	0	.	GRCh37	11	55563633	55563633	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.602T>G	p.Leu201Arg	p.L201R	ENST00000335605	1/1	108	78	30	109	109	0	OR5D14,missense_variant,p.Leu201Arg,ENST00000335605,;	G	ENSG00000186113	ENST00000335605	Transcript	missense_variant	602	602	201	L/R	cTt/cGt	.	.	.	1	OR5D14	HGNC	15281	protein_coding	YES	CCDS31508.1	ENSP00000334456	OR5DE_HUMAN	.	UPI000004B1F6	.	deleterious(0.02)	possibly_damaging(0.653)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF67,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCTTTTCA	.	5	ESCA
STX3	0	.	GRCh37	11	59568757	59568757	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*460G>A	.	.	ENST00000337979	11/11	47	35	11	26	26	0	STX3,3_prime_UTR_variant,,ENST00000535361,;STX3,3_prime_UTR_variant,,ENST00000529177,;STX3,3_prime_UTR_variant,,ENST00000300150,;STX3,3_prime_UTR_variant,,ENST00000337979,;STX3,downstream_gene_variant,,ENST00000528805,;STX3,downstream_gene_variant,,ENST00000530221,;MRPL16,downstream_gene_variant,,ENST00000300151,;STX3,downstream_gene_variant,,ENST00000437946,;STX3,downstream_gene_variant,,ENST00000533637,;	A	ENSG00000166900	ENST00000337979	Transcript	3_prime_UTR_variant	1877	.	.	.	.	.	.	.	1	STX3	HGNC	11438	protein_coding	YES	CCDS7975.1	ENSP00000338562	STX3_HUMAN	Q53YE2_HUMAN,F8W9Y0_HUMAN,E9PN33_HUMAN	UPI000016786E	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAAGAAGGC	.	5	ESCA
RBMXL2	0	.	GRCh37	11	7112042	7112042	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*512C>A	.	.	ENST00000306904	1/1	48	38	10	43	43	0	RBMXL2,3_prime_UTR_variant,,ENST00000306904,;	A	ENSG00000170748	ENST00000306904	Transcript	3_prime_UTR_variant	1878	.	.	.	.	.	.	.	1	RBMXL2	HGNC	17886	protein_coding	YES	CCDS7777.1	ENSP00000304139	RMXL2_HUMAN	.	UPI000013EBA5	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAACAACAA	.	5	ESCA
PDE2A	0	.	GRCh37	11	72297162	72297162	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1134delC	p.Ser379AlafsTer98	p.S379Afs*98	ENST00000334456	14/31	147	135	12	55	55	0	PDE2A,frameshift_variant,p.Ser370AlafsTer98,ENST00000540345,;PDE2A,frameshift_variant,p.Ser379AlafsTer98,ENST00000334456,;PDE2A,frameshift_variant,p.Ser264AlafsTer98,ENST00000418754,;PDE2A,frameshift_variant,p.Ser203AlafsTer98,ENST00000475807,;PDE2A,frameshift_variant,p.Ser372AlafsTer98,ENST00000544570,;PDE2A,frameshift_variant,p.Ser370AlafsTer98,ENST00000444035,;PDE2A,frameshift_variant,p.Ser141AlafsTer?,ENST00000538299,;PDE2A,frameshift_variant,p.Ser123AlafsTer98,ENST00000376450,;PDE2A,upstream_gene_variant,,ENST00000542223,;PDE2A,upstream_gene_variant,,ENST00000420501,;PDE2A,upstream_gene_variant,,ENST00000441209,;RP11-169D4.2,intron_variant,,ENST00000545254,;PDE2A,3_prime_UTR_variant,,ENST00000539367,;PDE2A,downstream_gene_variant,,ENST00000543750,;PDE2A,downstream_gene_variant,,ENST00000536308,;PDE2A,downstream_gene_variant,,ENST00000490749,;PDE2A,downstream_gene_variant,,ENST00000543575,;	-	ENSG00000186642	ENST00000334456	Transcript	frameshift_variant	1380	1134	378	T/X	acC/ac	.	.	.	-1	PDE2A	HGNC	8777	protein_coding	YES	CCDS8216.1	ENSP00000334910	PDE2A_HUMAN	F5GXX2_HUMAN,C9JPD5_HUMAN	UPI000003B340	.	.	.	14/31	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF102,SMART_domains:SM00065,Superfamily_domains:SSF55781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTGCTGGTGAG	.	3	ESCA
PDE2A	0	.	GRCh37	11	72297198	72297198	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1098C>T	p.%3D	p.I366I	ENST00000334456	14/31	108	94	14	45	45	0	PDE2A,synonymous_variant,p.%3D,ENST00000540345,;PDE2A,synonymous_variant,p.%3D,ENST00000334456,;PDE2A,synonymous_variant,p.%3D,ENST00000418754,;PDE2A,synonymous_variant,p.%3D,ENST00000475807,;PDE2A,synonymous_variant,p.%3D,ENST00000544570,;PDE2A,synonymous_variant,p.%3D,ENST00000444035,;PDE2A,synonymous_variant,p.%3D,ENST00000538299,;PDE2A,synonymous_variant,p.%3D,ENST00000376450,;PDE2A,upstream_gene_variant,,ENST00000542223,;PDE2A,upstream_gene_variant,,ENST00000420501,;PDE2A,upstream_gene_variant,,ENST00000441209,;RP11-169D4.2,intron_variant,,ENST00000545254,;PDE2A,3_prime_UTR_variant,,ENST00000539367,;PDE2A,downstream_gene_variant,,ENST00000543750,;PDE2A,downstream_gene_variant,,ENST00000536308,;PDE2A,downstream_gene_variant,,ENST00000490749,;PDE2A,downstream_gene_variant,,ENST00000543575,;	A	ENSG00000186642	ENST00000334456	Transcript	synonymous_variant	1344	1098	366	I	atC/atT	.	.	.	-1	PDE2A	HGNC	8777	protein_coding	YES	CCDS8216.1	ENSP00000334910	PDE2A_HUMAN	F5GXX2_HUMAN,C9JPD5_HUMAN	UPI000003B340	.	.	.	14/31	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF102,Gene3D:3.30.450.40,Pfam_domain:PF01590,SMART_domains:SM00065,Superfamily_domains:SSF55781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCTGGATCAC	.	3	ESCA
ACACB	0	.	GRCh37	12	109673410	109673410	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4405-1G>A	.	p.X1469_splice	ENST00000338432	.	80	72	8	81	81	0	ACACB,splice_acceptor_variant,,ENST00000377854,;ACACB,splice_acceptor_variant,,ENST00000543201,;ACACB,splice_acceptor_variant,,ENST00000377848,;ACACB,splice_acceptor_variant,,ENST00000338432,;ACACB,splice_acceptor_variant,,ENST00000542524,;ACACB,splice_acceptor_variant,,ENST00000538526,;	A	ENSG00000076555	ENST00000338432	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ACACB	HGNC	85	protein_coding	YES	CCDS31898.1	ENSP00000341044	ACACB_HUMAN	F5H5C3_HUMAN,E9PEW7_HUMAN	UPI0000DBEEFB	.	.	.	.	32/52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTGCAGAAAGA	.	3	ESCA
MLEC	0	.	GRCh37	12	121138090	121138090	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3742C>T	.	.	ENST00000228506	5/5	46	31	15	48	48	0	MLEC,3_prime_UTR_variant,,ENST00000228506,;MLEC,downstream_gene_variant,,ENST00000412616,;MLEC,downstream_gene_variant,,ENST00000535656,;MLEC,downstream_gene_variant,,ENST00000545525,;RP11-173P15.3,upstream_gene_variant,,ENST00000541383,;RP11-173P15.3,upstream_gene_variant,,ENST00000535720,;MLEC,intron_variant,,ENST00000535413,;	T	ENSG00000110917	ENST00000228506	Transcript	3_prime_UTR_variant	5049	.	.	.	.	.	.	.	1	MLEC	HGNC	28973	protein_coding	YES	CCDS9206.1	ENSP00000228506	MLEC_HUMAN	F5H1S8_HUMAN	UPI000013938A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCCCTCCC	.	5	ESCA
KDM2B	0	.	GRCh37	12	121878953	121878953	+	Missense_Mutation	SNP	C	C	T	rs781826750	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3368G>A	p.Arg1123Gln	p.R1123Q	ENST00000377071	20/23	20	14	5	19	19	0	KDM2B,missense_variant,p.Arg491Gln,ENST00000542973,;KDM2B,missense_variant,p.Arg1123Gln,ENST00000377071,;KDM2B,missense_variant,p.Arg1054Gln,ENST00000377069,;KDM2B,intron_variant,,ENST00000536437,;KDM2B,non_coding_transcript_exon_variant,,ENST00000536036,;KDM2B,non_coding_transcript_exon_variant,,ENST00000538503,;KDM2B,intron_variant,,ENST00000543025,;KDM2B,downstream_gene_variant,,ENST00000538243,;	T	ENSG00000089094	ENST00000377071	Transcript	missense_variant	3441	3368	1123	R/Q	cGg/cAg	rs781826750	.	.	-1	KDM2B	HGNC	13610	protein_coding	YES	CCDS41850.1	ENSP00000366271	KDM2B_HUMAN	F5H7T7_HUMAN,F5H6N6_HUMAN,F5H4A7_HUMAN,F5GXC2_HUMAN	UPI000006F36E	.	deleterious(0.02)	probably_damaging(0.996)	20/23	.	hmmpanther:PTHR23123:SF10,hmmpanther:PTHR23123,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCGCCGGATG	.	5	ESCA
DDX51	0	.	GRCh37	12	132625429	132625429	+	Missense_Mutation	SNP	C	C	T	rs772880022	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1387G>A	p.Asp463Asn	p.D463N	ENST00000397333	9/15	41	27	13	37	37	0	DDX51,missense_variant,p.Asp463Asn,ENST00000397333,;NOC4L,upstream_gene_variant,,ENST00000330579,;NOC4L,upstream_gene_variant,,ENST00000541954,;DDX51,non_coding_transcript_exon_variant,,ENST00000329073,;DDX51,non_coding_transcript_exon_variant,,ENST00000545991,;DDX51,upstream_gene_variant,,ENST00000462829,;DDX51,upstream_gene_variant,,ENST00000541489,;DDX51,downstream_gene_variant,,ENST00000546058,;	T	ENSG00000185163	ENST00000397333	Transcript	missense_variant	1426	1387	463	D/N	Gat/Aat	rs772880022	.	.	-1	DDX51	HGNC	20082	protein_coding	YES	CCDS41865.1	ENSP00000380495	DDX51_HUMAN	.	UPI000049DD95	.	tolerated(0.26)	benign(0.004)	9/15	.	hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF68,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATCTTCCA	byFrequency	5	ESCA
SLCO1B3	0	.	GRCh37	12	21028192	21028192	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.751G>C	p.Asp251His	p.D251H	ENST00000381545	9/16	179	124	55	147	147	0	SLCO1B3,missense_variant,p.Asp251His,ENST00000553473,;SLCO1B3,missense_variant,p.Asp251His,ENST00000261196,;SLCO1B3,missense_variant,p.Asp251His,ENST00000540853,;SLCO1B3,missense_variant,p.Asp75His,ENST00000544370,;LST3,missense_variant,p.Asp251His,ENST00000540229,;SLCO1B3,missense_variant,p.Asp251His,ENST00000381545,;SLCO1B7,intron_variant,,ENST00000554957,;LST3,intron_variant,,ENST00000381541,;	C	ENSG00000111700	ENST00000381545	Transcript	missense_variant	970	751	251	D/H	Gac/Cac	COSM138864	.	.	1	SLCO1B3	HGNC	10961	protein_coding	YES	CCDS8684.1	ENSP00000370956	SO1B3_HUMAN	F5H8K0_HUMAN	UPI000013544A	.	deleterious(0)	probably_damaging(0.999)	9/16	.	PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF89,hmmpanther:PTHR11388,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAGGACTCT	.	5	ESCA
DYRK4	0	.	GRCh37	12	4714126	4714126	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.828C>G	p.Ile276Met	p.I276M	ENST00000540757	9/13	47	33	13	39	39	0	DYRK4,missense_variant,p.Ile276Met,ENST00000540757,;DYRK4,missense_variant,p.Ile391Met,ENST00000542744,;DYRK4,missense_variant,p.Ile276Met,ENST00000010132,;DYRK4,missense_variant,p.Ile276Met,ENST00000543431,;DYRK4,upstream_gene_variant,,ENST00000545342,;RP11-500M8.7,missense_variant,p.Ile6Met,ENST00000536588,;DYRK4,non_coding_transcript_exon_variant,,ENST00000545571,;DYRK4,non_coding_transcript_exon_variant,,ENST00000540644,;DYRK4,non_coding_transcript_exon_variant,,ENST00000536137,;DYRK4,upstream_gene_variant,,ENST00000541024,;RP11-234B24.5,upstream_gene_variant,,ENST00000538921,;	G	ENSG00000010219	ENST00000540757	Transcript	missense_variant	988	828	276	I/M	atC/atG	.	.	.	1	DYRK4	HGNC	3095	protein_coding	YES	CCDS8530.1	ENSP00000441755	DYRK4_HUMAN	D3JEN3_HUMAN,D3JEN2_HUMAN,B4DQW1_HUMAN	UPI000006E05C	.	deleterious(0.01)	probably_damaging(0.999)	9/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR24058:SF22,hmmpanther:PTHR24058,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATCCTGGG	.	5	ESCA
DIP2B	0	.	GRCh37	12	51135289	51135289	+	Missense_Mutation	SNP	C	C	T	rs772210044	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4445C>T	p.Ser1482Leu	p.S1482L	ENST00000301180	37/38	64	54	10	50	50	0	DIP2B,missense_variant,p.Ser1482Leu,ENST00000301180,;Y_RNA,upstream_gene_variant,,ENST00000363558,;DIP2B,3_prime_UTR_variant,,ENST00000546732,;	T	ENSG00000066084	ENST00000301180	Transcript	missense_variant	4479	4445	1482	S/L	tCg/tTg	rs772210044	.	.	1	DIP2B	HGNC	29284	protein_coding	YES	CCDS31799.1	ENSP00000301180	DIP2B_HUMAN	Q96IB4_HUMAN	UPI0000406CA1	.	deleterious(0)	probably_damaging(0.994)	37/38	.	hmmpanther:PTHR22754:SF22,hmmpanther:PTHR22754,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTCGGTGT	.	5	ESCA
DGKA	0	.	GRCh37	12	56347519	56347520	+	Frame_Shift_Del	DEL	CC	CC	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	CC	CC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2175_2176delCCinsT	p.Arg726AlafsTer9	p.R726Afs*9	ENST00000331886	24/24	48	34	14	26	26	0	DGKA,frameshift_variant,p.Arg726AlafsTer9,ENST00000394147,;DGKA,frameshift_variant,p.Arg726AlafsTer9,ENST00000331886,;DGKA,frameshift_variant,p.Arg726AlafsTer9,ENST00000551156,;PMEL,downstream_gene_variant,,ENST00000549233,;PMEL,downstream_gene_variant,,ENST00000546543,;PMEL,downstream_gene_variant,,ENST00000536427,;PMEL,downstream_gene_variant,,ENST00000549404,;PMEL,downstream_gene_variant,,ENST00000552882,;PMEL,downstream_gene_variant,,ENST00000360714,;PMEL,downstream_gene_variant,,ENST00000548493,;PMEL,downstream_gene_variant,,ENST00000449260,;PMEL,downstream_gene_variant,,ENST00000548747,;PMEL,downstream_gene_variant,,ENST00000550447,;PMEL,downstream_gene_variant,,ENST00000550464,;PMEL,downstream_gene_variant,,ENST00000539511,;PMEL,downstream_gene_variant,,ENST00000549418,;DGKA,downstream_gene_variant,,ENST00000552903,;DGKA,downstream_gene_variant,,ENST00000555218,;PMEL,downstream_gene_variant,,ENST00000547137,;PMEL,downstream_gene_variant,,ENST00000548803,;DGKA,non_coding_transcript_exon_variant,,ENST00000549079,;PMEL,downstream_gene_variant,,ENST00000548689,;PMEL,downstream_gene_variant,,ENST00000549564,;DGKA,3_prime_UTR_variant,,ENST00000402956,;DGKA,non_coding_transcript_exon_variant,,ENST00000552478,;DGKA,non_coding_transcript_exon_variant,,ENST00000551296,;DGKA,non_coding_transcript_exon_variant,,ENST00000551739,;DGKA,non_coding_transcript_exon_variant,,ENST00000548491,;DGKA,downstream_gene_variant,,ENST00000553084,;DGKA,downstream_gene_variant,,ENST00000550957,;PMEL,downstream_gene_variant,,ENST00000550762,;PMEL,downstream_gene_variant,,ENST00000556802,;DGKA,downstream_gene_variant,,ENST00000551585,;PMEL,downstream_gene_variant,,ENST00000549430,;PMEL,downstream_gene_variant,,ENST00000550590,;	T	ENSG00000065357	ENST00000331886	Transcript	frameshift_variant	2629-2630	2175-2176	725-726	PR/PX	ccCCgc/ccTgc	.	.	.	1	DGKA	HGNC	2849	protein_coding	YES	CCDS8896.1	ENSP00000328405	DGKA_HUMAN	G3V4I3_HUMAN,G3V327_HUMAN,F8W1M3_HUMAN,F8W1H7_HUMAN,F8VWX8_HUMAN,F8VNZ9_HUMAN,C9JM35_HUMAN	UPI000007417B	.	.	.	24/24	.	hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	PINDEL|SOMATICSNIPER*|VARSCANI*|INDELOCATOR*|MUSE*|VARSCANS*	ACCCCCCCGCTCC	.	6	ESCA
GRIP1	0	.	GRCh37	12	66742575	66742575	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*224C>A	.	.	ENST00000398016	24/24	8	5	3	8	8	0	GRIP1,3_prime_UTR_variant,,ENST00000286445,;GRIP1,3_prime_UTR_variant,,ENST00000398016,;GRIP1,3_prime_UTR_variant,,ENST00000359742,;GRIP1,downstream_gene_variant,,ENST00000538211,;GRIP1,downstream_gene_variant,,ENST00000538164,;GRIP1,downstream_gene_variant,,ENST00000540854,;snoU13,downstream_gene_variant,,ENST00000458887,;GRIP1,downstream_gene_variant,,ENST00000535323,;	T	ENSG00000155974	ENST00000398016	Transcript	3_prime_UTR_variant	3524	.	.	.	.	.	.	.	-1	GRIP1	HGNC	18708	protein_coding	YES	CCDS41807.1	ENSP00000381098	GRIP1_HUMAN	F5H5I0_HUMAN,F5H4P8_HUMAN,F5H424_HUMAN	UPI0000DD8148	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGACTGGCAGG	.	2	ESCA
BEST3	0	.	GRCh37	12	70048704	70048704	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1990G>C	p.Glu664Gln	p.E664Q	ENST00000330891	10/10	52	47	5	50	50	0	BEST3,missense_variant,p.Glu664Gln,ENST00000330891,;BEST3,missense_variant,p.Glu558Gln,ENST00000553096,;BEST3,missense_variant,p.Glu451Gln,ENST00000488961,;BEST3,intron_variant,,ENST00000331471,;BEST3,intron_variant,,ENST00000547208,;	G	ENSG00000127325	ENST00000330891	Transcript	missense_variant	2217	1990	664	E/Q	Gag/Cag	.	.	.	-1	BEST3	HGNC	17105	protein_coding	YES	CCDS8992.2	ENSP00000332413	BEST3_HUMAN	F8VVZ2_HUMAN	UPI000006E397	.	tolerated_low_confidence(0.17)	possibly_damaging(0.556)	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCCTCAGTTT	.	3	ESCA
NAV3	0	.	GRCh37	12	78582430	78582430	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5862G>A	p.%3D	p.L1954L	ENST00000536525	32/39	50	41	9	42	42	0	NAV3,synonymous_variant,p.%3D,ENST00000536525,;NAV3,synonymous_variant,p.%3D,ENST00000397909,;NAV3,synonymous_variant,p.%3D,ENST00000550788,;NAV3,synonymous_variant,p.%3D,ENST00000266692,;NAV3,synonymous_variant,p.%3D,ENST00000228327,;NAV3,synonymous_variant,p.%3D,ENST00000552895,;NAV3,intron_variant,,ENST00000552300,;NAV3,downstream_gene_variant,,ENST00000548948,;	A	ENSG00000067798	ENST00000536525	Transcript	synonymous_variant	6035	5862	1954	L	ctG/ctA	.	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	.	.	32/39	.	hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTGAGCTC	.	5	ESCA
CEP290	0	.	GRCh37	12	88524980	88524980	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457G>A	p.Glu153Lys	p.E153K	ENST00000552810	7/54	71	53	18	42	42	0	CEP290,missense_variant,p.Glu153Lys,ENST00000552810,;CEP290,missense_variant,p.Glu153Lys,ENST00000309041,;CEP290,intron_variant,,ENST00000550962,;CEP290,upstream_gene_variant,,ENST00000604024,;CEP290,upstream_gene_variant,,ENST00000397838,;CEP290,downstream_gene_variant,,ENST00000552770,;CEP290,missense_variant,p.Glu119Lys,ENST00000547926,;	T	ENSG00000198707	ENST00000552810	Transcript	missense_variant	801	457	153	E/K	Gag/Aag	.	.	.	-1	CEP290	HGNC	29021	protein_coding	YES	CCDS55858.1	ENSP00000448012	CE290_HUMAN	.	UPI0000D60D15	.	.	probably_damaging(0.999)	7/54	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCATTTC	.	5	ESCA
RP11-726G1.1	0	.	GRCh37	12	9728249	9728249	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.7248C>G	.	.	ENST00000520314	12/12	98	71	27	67	67	0	RP11-726G1.1,non_coding_transcript_exon_variant,,ENST00000520314,;RP11-726G1.1,downstream_gene_variant,,ENST00000518709,;	G	ENSG00000214776	ENST00000520314	Transcript	non_coding_transcript_exon_variant	7248	.	.	.	.	.	.	.	1	RP11-726G1.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGCCCTAGC	.	5	ESCA
LINC00452	0	.	GRCh37	13	114622591	114622591	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.795C>T	.	.	ENST00000609661	5/8	49	46	3	57	57	0	LINC00452,non_coding_transcript_exon_variant,,ENST00000426859,;LINC00452,non_coding_transcript_exon_variant,,ENST00000609661,;	T	ENSG00000229373	ENST00000609661	Transcript	non_coding_transcript_exon_variant	795	.	.	.	.	.	.	.	1	LINC00452	HGNC	42800	lincRNA	YES	.	.	.	.	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCACCTGGAA	.	2	ESCA
ZDHHC20	0	.	GRCh37	13	21975811	21975811	+	Missense_Mutation	SNP	T	T	C	rs751466481	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454A>G	p.Met152Val	p.M152V	ENST00000382466	6/12	73	59	14	56	56	0	ZDHHC20,missense_variant,p.Met152Val,ENST00000400590,;ZDHHC20,missense_variant,p.Met152Val,ENST00000415724,;ZDHHC20,missense_variant,p.Met89Val,ENST00000542645,;ZDHHC20,missense_variant,p.Met152Val,ENST00000382466,;ZDHHC20,missense_variant,p.Met152Val,ENST00000320220,;ZDHHC20,downstream_gene_variant,,ENST00000422251,;ZDHHC20,non_coding_transcript_exon_variant,,ENST00000494731,;	C	ENSG00000180776	ENST00000382466	Transcript	missense_variant	567	454	152	M/V	Atg/Gtg	rs751466481	.	.	-1	ZDHHC20	HGNC	20749	protein_coding	YES	CCDS45017.1	ENSP00000371905	ZDH20_HUMAN	I6L9D4_HUMAN	UPI00003B90E3	.	deleterious(0)	benign(0.236)	6/12	.	PROSITE_profiles:PS50216,hmmpanther:PTHR22883:SF14,hmmpanther:PTHR22883,Pfam_domain:PF01529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCATCTTAA	.	5	ESCA
LNX2	0	.	GRCh37	13	28122482	28122482	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2063G>A	p.Ser688Asn	p.S688N	ENST00000316334	10/10	27	18	9	25	25	0	LNX2,missense_variant,p.Ser688Asn,ENST00000316334,;	T	ENSG00000139517	ENST00000316334	Transcript	missense_variant	2193	2063	688	S/N	aGc/aAc	.	.	.	-1	LNX2	HGNC	20421	protein_coding	YES	CCDS9323.1	ENSP00000325929	LNX2_HUMAN	.	UPI000012E7A7	.	deleterious(0)	probably_damaging(0.998)	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGGCTGCCA	.	5	ESCA
STARD13	0	.	GRCh37	13	33692207	33692207	+	Missense_Mutation	SNP	T	T	C	rs553359255	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2276A>G	p.Tyr759Cys	p.Y759C	ENST00000336934	8/14	64	51	13	52	52	0	STARD13,missense_variant,p.Tyr759Cys,ENST00000336934,;STARD13,missense_variant,p.Tyr751Cys,ENST00000255486,;STARD13,missense_variant,p.Tyr641Cys,ENST00000399365,;STARD13,upstream_gene_variant,,ENST00000491333,;	C	ENSG00000133121	ENST00000336934	Transcript	missense_variant	2393	2276	759	Y/C	tAt/tGt	rs553359255,COSM1513761	.	.	-1	STARD13	HGNC	19164	protein_coding	YES	CCDS9348.1	ENSP00000338785	STA13_HUMAN	B3KT04_HUMAN,B2R789_HUMAN	UPI000006226E	.	deleterious(0)	probably_damaging(0.992)	8/14	.	PROSITE_profiles:PS50238,hmmpanther:PTHR12659:SF6,hmmpanther:PTHR12659,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	C:0.0002	C:0	C:0.0014	.	C:0	C:0	C:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGATAGATA	by1000G	5	ESCA
NBEA	0	.	GRCh37	13	36245305	36245305	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*177G>A	.	.	ENST00000400445	58/58	40	33	7	41	41	0	NBEA,3_prime_UTR_variant,,ENST00000400445,;NBEA,3_prime_UTR_variant,,ENST00000540320,;NBEA,3_prime_UTR_variant,,ENST00000379922,;NBEA,3_prime_UTR_variant,,ENST00000310336,;NBEA,3_prime_UTR_variant,,ENST00000537702,;NBEA,3_prime_UTR_variant,,ENST00000379939,;NBEA,non_coding_transcript_exon_variant,,ENST00000461581,;	A	ENSG00000172915	ENST00000400445	Transcript	3_prime_UTR_variant	9552	.	.	.	.	.	.	.	1	NBEA	HGNC	7648	protein_coding	YES	CCDS45026.1	ENSP00000383295	NBEA_HUMAN	.	UPI00004FF92F	.	.	.	58/58	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTCACGACTGA	.	3	ESCA
IGHV1-46	0	.	GRCh37	14	106967495	106967495	+	5'UTR	SNP	T	T	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11A>C	.	.	ENST00000390622	1/2	28	22	6	45	45	0	IGHV1-46,5_prime_UTR_variant,,ENST00000390622,;IGHV1-45,upstream_gene_variant,,ENST00000390621,;LINC00221,intron_variant,,ENST00000433371,;IGHVII-46-1,downstream_gene_variant,,ENST00000519794,;	G	ENSG00000211962	ENST00000390622	Transcript	5_prime_UTR_variant	294	.	.	.	.	.	.	.	-1	IGHV1-46	HGNC	5554	IG_V_gene	YES	.	ENSP00000375031	.	.	UPI0000113ACE	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACTTTCCT	.	5	ESCA
TRAV29DV5	0	.	GRCh37	14	22631624	22631624	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216C>G	p.Phe72Leu	p.F72L	ENST00000390458	2/2	20	15	4	11	11	0	TRAV29DV5,missense_variant,p.Phe72Leu,ENST00000390458,;TRAV30,upstream_gene_variant,,ENST00000557168,;	G	ENSG00000211810	ENST00000390458	Transcript	missense_variant	327	216	72	F/L	ttC/ttG	.	.	.	1	TRAV29DV5	HGNC	12127	TR_V_gene	YES	.	ENSP00000452209	.	A0JD25_HUMAN	UPI000011D12B	.	tolerated(1)	benign(0.014)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19343,hmmpanther:PTHR19343:SF1,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTCCTGAT	.	5	ESCA
DCAF11	0	.	GRCh37	14	24584027	24584027	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-689C>T	.	.	ENST00000446197	1/15	37	26	10	38	38	0	DCAF11,5_prime_UTR_variant,,ENST00000560713,;DCAF11,5_prime_UTR_variant,,ENST00000558215,;NRL,5_prime_UTR_variant,,ENST00000561028,;DCAF11,5_prime_UTR_variant,,ENST00000560901,;DCAF11,5_prime_UTR_variant,,ENST00000559115,;DCAF11,5_prime_UTR_variant,,ENST00000559796,;NRL,5_prime_UTR_variant,,ENST00000558280,;DCAF11,5_prime_UTR_variant,,ENST00000561375,;DCAF11,5_prime_UTR_variant,,ENST00000559017,;DCAF11,5_prime_UTR_variant,,ENST00000446197,;DCAF11,5_prime_UTR_variant,,ENST00000559382,;DCAF11,5_prime_UTR_variant,,ENST00000557810,;DCAF11,upstream_gene_variant,,ENST00000396936,;DCAF11,upstream_gene_variant,,ENST00000559354,;DCAF11,upstream_gene_variant,,ENST00000559593,;DCAF11,upstream_gene_variant,,ENST00000559144,;DCAF11,upstream_gene_variant,,ENST00000561001,;DCAF11,upstream_gene_variant,,ENST00000560459,;DCAF11,upstream_gene_variant,,ENST00000396941,;DCAF11,upstream_gene_variant,,ENST00000561041,;DCAF11,upstream_gene_variant,,ENST00000558638,;PCK2,downstream_gene_variant,,ENST00000559171,;DCAF11,upstream_gene_variant,,ENST00000559288,;DCAF11,upstream_gene_variant,,ENST00000558408,;DCAF11,upstream_gene_variant,,ENST00000559396,;DCAF11,non_coding_transcript_exon_variant,,ENST00000557809,;DCAF11,non_coding_transcript_exon_variant,,ENST00000561056,;DCAF11,upstream_gene_variant,,ENST00000560171,;DCAF11,upstream_gene_variant,,ENST00000561016,;DCAF11,upstream_gene_variant,,ENST00000557952,;DCAF11,5_prime_UTR_variant,,ENST00000557802,;DCAF11,upstream_gene_variant,,ENST00000558624,;DCAF11,upstream_gene_variant,,ENST00000558706,;DCAF11,upstream_gene_variant,,ENST00000560046,;DCAF11,upstream_gene_variant,,ENST00000326009,;DCAF11,upstream_gene_variant,,ENST00000559451,;DCAF11,upstream_gene_variant,,ENST00000560457,;DCAF11,upstream_gene_variant,,ENST00000557888,;DCAF11,upstream_gene_variant,,ENST00000558914,;DCAF11,upstream_gene_variant,,ENST00000560614,;	T	ENSG00000100897	ENST00000446197	Transcript	5_prime_UTR_variant	39	.	.	.	.	.	.	.	1	DCAF11	HGNC	20258	protein_coding	YES	CCDS9610.1	ENSP00000415556	DCA11_HUMAN	H0YNS2_HUMAN,H0YNK2_HUMAN,H0YMZ4_HUMAN,H0YM56_HUMAN,H0YLQ1_HUMAN,H0YL64_HUMAN,H0YKR8_HUMAN	UPI0000073AB2	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGCGTGAC	.	5	ESCA
KIAA0586	0	.	GRCh37	14	58920065	58920065	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1289-3C>G	.	.	ENST00000354386	.	39	29	9	44	44	0	KIAA0586,splice_region_variant,,ENST00000261244,;KIAA0586,splice_region_variant,,ENST00000423743,;KIAA0586,splice_region_variant,,ENST00000354386,;KIAA0586,splice_region_variant,,ENST00000556134,;KIAA0586,downstream_gene_variant,,ENST00000555833,;KIAA0586,splice_region_variant,,ENST00000538571,;	G	ENSG00000100578	ENST00000354386	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	KIAA0586	HGNC	19960	protein_coding	YES	CCDS58320.1	ENSP00000346359	TALD3_HUMAN	.	UPI0001AE6998	.	.	.	.	10/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTCAGGAA	.	4	ESCA
PLEK2	0	.	GRCh37	14	67878826	67878826	+	5'UTR	SNP	C	C	G	rs759247558	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-50G>C	.	.	ENST00000216446	1/9	13	8	5	14	14	0	PLEK2,5_prime_UTR_variant,,ENST00000216446,;PLEK2,non_coding_transcript_exon_variant,,ENST00000557388,;PLEK2,upstream_gene_variant,,ENST00000553387,;	G	ENSG00000100558	ENST00000216446	Transcript	5_prime_UTR_variant	92	.	.	.	.	rs759247558	.	.	-1	PLEK2	HGNC	19238	protein_coding	YES	CCDS9782.1	ENSP00000216446	PLEK2_HUMAN	.	UPI0000035D89	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCCTCGCGCT	byFrequency	2	ESCA
ADAM21	0	.	GRCh37	14	70925471	70925471	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1255C>G	p.Gln419Glu	p.Q419E	ENST00000603540	2/2	92	79	12	96	96	0	ADAM21,missense_variant,p.Gln419Glu,ENST00000603540,;ADAM21,missense_variant,p.Gln419Glu,ENST00000267499,;RP11-486O13.4,intron_variant,,ENST00000556646,;	G	ENSG00000139985	ENST00000603540	Transcript	missense_variant	1513	1255	419	Q/E	Cag/Gag	.	.	.	1	ADAM21	HGNC	200	protein_coding	YES	CCDS9804.1	ENSP00000474385	ADA21_HUMAN	.	UPI000013D756	.	tolerated(1)	benign(0.014)	2/2	.	Superfamily_domains:SSF57552,SMART_domains:SM00050,Gene3D:3.40.390.10,Pfam_domain:PF00200,hmmpanther:PTHR11905:SF116,hmmpanther:PTHR11905,PROSITE_profiles:PS50214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAGCAGTGT	.	4	ESCA
SERPINA1	0	.	GRCh37	14	94847363	94847363	+	Missense_Mutation	SNP	C	C	G	rs763249215	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.762G>C	p.Gln254His	p.Q254H	ENST00000448921	5/7	44	38	5	72	72	0	SERPINA1,missense_variant,p.Gln254His,ENST00000448921,;SERPINA1,missense_variant,p.Gln254His,ENST00000449399,;SERPINA1,missense_variant,p.Gln254His,ENST00000355814,;SERPINA1,missense_variant,p.Gln254His,ENST00000404814,;SERPINA1,missense_variant,p.Gln254His,ENST00000393088,;SERPINA1,missense_variant,p.Gln254His,ENST00000393087,;SERPINA1,missense_variant,p.Gln254His,ENST00000437397,;SERPINA1,missense_variant,p.Gln254His,ENST00000402629,;SERPINA1,missense_variant,p.Gln254His,ENST00000440909,;SERPINA1,downstream_gene_variant,,ENST00000556955,;SERPINA1,downstream_gene_variant,,ENST00000554720,;SERPINA1,downstream_gene_variant,,ENST00000557492,;SERPINA1,downstream_gene_variant,,ENST00000557118,;SERPINA1,downstream_gene_variant,,ENST00000553327,;SERPINA1,downstream_gene_variant,,ENST00000556091,;SERPINA1,downstream_gene_variant,,ENST00000555289,;SERPINA1,missense_variant,p.Gln254His,ENST00000489769,;	G	ENSG00000197249	ENST00000448921	Transcript	missense_variant	1335	762	254	Q/H	caG/caC	rs763249215,COSM3943930	.	.	-1	SERPINA1	HGNC	8941	protein_coding	YES	CCDS9925.1	ENSP00000416066	A1AT_HUMAN	Q3I0J7_HUMAN,G3V5R8_HUMAN,G3V544_HUMAN,G3V4I7_HUMAN,G3V387_HUMAN,G3V2B9_HUMAN,E9KL23_HUMAN,A6YP93_HUMAN	UPI000000CBEC	.	tolerated(1)	benign(0.001)	5/7	.	Superfamily_domains:SSF56574,SMART_domains:SM00093,Pfam_domain:PF00079,Gene3D:2.30.39.10,hmmpanther:PTHR11461:SF150,hmmpanther:PTHR11461	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|VARSCANS	CAGTGCTGGAT	.	3	ESCA
SYNE3	0	.	GRCh37	14	95918609	95918609	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1249A>T	p.Ile417Phe	p.I417F	ENST00000334258	6/17	41	24	16	59	59	0	SYNE3,missense_variant,p.Ile174Phe,ENST00000554873,;SYNE3,missense_variant,p.Ile417Phe,ENST00000334258,;SYNE3,missense_variant,p.Ile417Phe,ENST00000557275,;SYNE3,missense_variant,p.Ile417Phe,ENST00000553340,;SYNE3,non_coding_transcript_exon_variant,,ENST00000555759,;	A	ENSG00000176438	ENST00000334258	Transcript	missense_variant	1264	1249	417	I/F	Atc/Ttc	.	.	.	-1	SYNE3	HGNC	19861	protein_coding	YES	CCDS9935.1	ENSP00000334308	SYNE3_HUMAN	.	UPI0000246F54	.	deleterious(0)	benign(0.128)	6/17	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGATGACAC	.	5	ESCA
MKRN3	0	.	GRCh37	15	23811569	23811569	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640G>A	p.Gly214Ser	p.G214S	ENST00000314520	1/1	65	37	27	49	49	0	MKRN3,missense_variant,p.Gly214Ser,ENST00000314520,;MKRN3,intron_variant,,ENST00000564592,;MKRN3,intron_variant,,ENST00000568252,;MIR4508,upstream_gene_variant,,ENST00000584178,;RP11-73C9.1,downstream_gene_variant,,ENST00000563044,;MKRN3,upstream_gene_variant,,ENST00000568945,;MKRN3,intron_variant,,ENST00000570112,;	A	ENSG00000179455	ENST00000314520	Transcript	missense_variant	1116	640	214	G/S	Ggc/Agc	.	.	.	1	MKRN3	HGNC	7114	protein_coding	YES	CCDS10013.1	ENSP00000313881	MKRN3_HUMAN	.	UPI000000DAA1	.	deleterious(0.03)	probably_damaging(0.963)	1/1	.	hmmpanther:PTHR11224,hmmpanther:PTHR11224:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGGGGCCGC	.	5	ESCA
MAGEL2	0	.	GRCh37	15	23890265	23890265	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.816C>G	p.%3D	p.S272S	ENST00000532292	1/1	69	53	16	90	90	0	MAGEL2,synonymous_variant,p.%3D,ENST00000532292,;AC124309.1,non_coding_transcript_exon_variant,,ENST00000314233,;	C	ENSG00000254585	ENST00000532292	Transcript	synonymous_variant	911	816	272	S	tcC/tcG	.	.	.	-1	MAGEL2	HGNC	6814	protein_coding	YES	.	ENSP00000433433	.	Q6P3U4_HUMAN,Q2M1Q7_HUMAN,Q05BN9_HUMAN,H0YDD5_HUMAN	UPI00005A89F6	.	.	.	1/1	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGACGGAGGT	.	5	ESCA
HERC2	0	.	GRCh37	15	28437270	28437270	+	Missense_Mutation	SNP	G	G	A	rs759989490	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8288C>T	p.Ser2763Phe	p.S2763F	ENST00000261609	53/93	17	14	3	29	29	0	HERC2,missense_variant,p.Ser2763Phe,ENST00000261609,;HERC2,non_coding_transcript_exon_variant,,ENST00000567869,;	A	ENSG00000128731	ENST00000261609	Transcript	missense_variant	8397	8288	2763	S/F	tCt/tTt	rs759989490,COSM1191818	.	.	-1	HERC2	HGNC	4868	protein_coding	YES	CCDS10021.1	ENSP00000261609	HERC2_HUMAN	.	UPI00004578F7	.	.	possibly_damaging(0.495)	53/93	.	PROSITE_profiles:PS51284,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF308,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.R2762G|c.8284C>G|4	MUTECT|MUSE	TTCCAGAACGG	.	2	ESCA
ZNF770	0	.	GRCh37	15	35274883	35274883	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753G>T	p.Lys251Asn	p.K251N	ENST00000356321	3/3	35	12	22	26	26	0	ZNF770,missense_variant,p.Lys251Asn,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	A	ENSG00000198146	ENST00000356321	Transcript	missense_variant	1098	753	251	K/N	aaG/aaT	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	tolerated(0.5)	benign(0.07)	3/3	.	hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGCCTCTTCTT	.	3	ESCA
ZNF770	0	.	GRCh37	15	35274940	35274940	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696G>A	p.%3D	p.L232L	ENST00000356321	3/3	53	28	25	34	34	0	ZNF770,synonymous_variant,p.%3D,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	T	ENSG00000198146	ENST00000356321	Transcript	synonymous_variant	1041	696	232	L	ctG/ctA	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	.	.	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCTTCAGAAG	.	3	ESCA
ZNF770	0	.	GRCh37	15	35274965	35274965	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.671G>C	p.Gly224Ala	p.G224A	ENST00000356321	3/3	53	28	25	35	35	0	ZNF770,missense_variant,p.Gly224Ala,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	G	ENSG00000198146	ENST00000356321	Transcript	missense_variant	1016	671	224	G/A	gGa/gCa	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	deleterious(0.01)	probably_damaging(1)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAAATCCTTTT	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275079	35275079	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.557G>T	p.Arg186Met	p.R186M	ENST00000356321	3/3	44	24	19	23	23	0	ZNF770,missense_variant,p.Arg186Met,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	A	ENSG00000198146	ENST00000356321	Transcript	missense_variant	902	557	186	R/M	aGg/aTg	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	deleterious(0)	probably_damaging(0.963)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGGCCTCTGA	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275110	35275110	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526G>C	p.Asp176His	p.D176H	ENST00000356321	3/3	45	28	16	29	29	0	ZNF770,missense_variant,p.Asp176His,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	G	ENSG00000198146	ENST00000356321	Transcript	missense_variant	871	526	176	D/H	Gat/Cat	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	deleterious(0.01)	probably_damaging(0.984)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTATCAAGTT	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275194	35275194	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442G>C	p.Asp148His	p.D148H	ENST00000356321	3/3	35	24	11	34	34	0	ZNF770,missense_variant,p.Asp148His,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	G	ENSG00000198146	ENST00000356321	Transcript	missense_variant	787	442	148	D/H	Gat/Cat	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	deleterious(0.03)	possibly_damaging(0.885)	3/3	.	hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGATCAGACT	.	2	ESCA
ZNF770	0	.	GRCh37	15	35275227	35275227	+	Nonsense_Mutation	SNP	C	C	A	rs777391880	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.409G>T	p.Glu137Ter	p.E137*	ENST00000356321	3/3	39	26	12	49	49	0	ZNF770,stop_gained,p.Glu137Ter,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	A	ENSG00000198146	ENST00000356321	Transcript	stop_gained	754	409	137	E/*	Gaa/Taa	rs777391880	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	.	.	3/3	.	hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTTCCTCTG	.	2	ESCA
ZNF770	0	.	GRCh37	15	35275230	35275230	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.406G>T	p.Glu136Ter	p.E136*	ENST00000356321	3/3	45	27	18	49	49	0	ZNF770,stop_gained,p.Glu136Ter,ENST00000356321,;ZNF770,downstream_gene_variant,,ENST00000559564,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	A	ENSG00000198146	ENST00000356321	Transcript	stop_gained	751	406	136	E/*	Gag/Tag	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	.	.	3/3	.	hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTCCTCTGTGG	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275289	35275289	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347G>C	p.Arg116Thr	p.R116T	ENST00000356321	3/3	64	38	25	44	44	0	ZNF770,missense_variant,p.Arg116Thr,ENST00000559564,;ZNF770,missense_variant,p.Arg116Thr,ENST00000356321,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	G	ENSG00000198146	ENST00000356321	Transcript	missense_variant	692	347	116	R/T	aGa/aCa	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	tolerated(0.12)	possibly_damaging(0.632)	3/3	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCAATCTTCTG	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275292	35275292	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.344G>A	p.Arg115Lys	p.R115K	ENST00000356321	3/3	63	38	24	44	44	0	ZNF770,missense_variant,p.Arg115Lys,ENST00000559564,;ZNF770,missense_variant,p.Arg115Lys,ENST00000356321,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	T	ENSG00000198146	ENST00000356321	Transcript	missense_variant	689	344	115	R/K	aGa/aAa	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	tolerated(0.37)	benign(0.015)	3/3	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATCTTCTGACC	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275345	35275345	+	Silent	SNP	C	C	A	rs760396768	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291G>T	p.%3D	p.V97V	ENST00000356321	3/3	59	39	20	44	44	0	ZNF770,synonymous_variant,p.%3D,ENST00000559564,;ZNF770,synonymous_variant,p.%3D,ENST00000356321,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	A	ENSG00000198146	ENST00000356321	Transcript	synonymous_variant	636	291	97	V	gtG/gtT	rs760396768	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	.	.	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCTTCACAAA	byFrequency	3	ESCA
ZNF770	0	.	GRCh37	15	35275357	35275357	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279G>A	p.%3D	p.L93L	ENST00000356321	3/3	61	42	18	44	44	0	ZNF770,synonymous_variant,p.%3D,ENST00000559564,;ZNF770,synonymous_variant,p.%3D,ENST00000356321,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	T	ENSG00000198146	ENST00000356321	Transcript	synonymous_variant	624	279	93	L	ctG/ctA	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	.	.	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCTTCAGATT	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275442	35275442	+	Missense_Mutation	SNP	C	C	G	rs779925410	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194G>C	p.Arg65Thr	p.R65T	ENST00000356321	3/3	71	50	21	74	74	0	ZNF770,missense_variant,p.Arg65Thr,ENST00000559564,;ZNF770,missense_variant,p.Arg65Thr,ENST00000356321,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	G	ENSG00000198146	ENST00000356321	Transcript	missense_variant	539	194	65	R/T	aGa/aCa	rs779925410	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	deleterious(0)	probably_damaging(0.999)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTTGTCTAAAG	.	3	ESCA
ZNF770	0	.	GRCh37	15	35275464	35275464	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>A	p.Asp58Asn	p.D58N	ENST00000356321	3/3	68	49	19	82	82	0	ZNF770,missense_variant,p.Asp58Asn,ENST00000559564,;ZNF770,missense_variant,p.Asp58Asn,ENST00000356321,;AC114546.1,downstream_gene_variant,,ENST00000391457,;	T	ENSG00000198146	ENST00000356321	Transcript	missense_variant	517	172	58	D/N	Gat/Aat	.	.	.	-1	ZNF770	HGNC	26061	protein_coding	YES	CCDS10042.1	ENSP00000348673	ZN770_HUMAN	H0YM59_HUMAN	UPI00001D776B	.	tolerated(0.48)	possibly_damaging(0.805)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF208,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CACATCACATT	.	3	ESCA
ZNF106	0	.	GRCh37	15	42749300	42749300	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.104A>G	p.Tyr35Cys	p.Y35C	ENST00000263805	1/19	31	18	13	40	40	0	ZNF106,missense_variant,p.Tyr58Cys,ENST00000567041,;ZNF106,missense_variant,p.Tyr58Cys,ENST00000564754,;ZNF106,missense_variant,p.Tyr35Cys,ENST00000263805,;ZNF106,intron_variant,,ENST00000565611,;ZNF106,intron_variant,,ENST00000565948,;ZNF106,intron_variant,,ENST00000565380,;	C	ENSG00000103994	ENST00000263805	Transcript	missense_variant	431	104	35	Y/C	tAt/tGt	.	.	.	-1	ZNF106	HGNC	12886	protein_coding	YES	CCDS32208.1	ENSP00000263805	ZN106_HUMAN	H3BNX5_HUMAN	UPI000006D6CC	.	deleterious(0)	probably_damaging(0.999)	1/19	.	hmmpanther:PTHR14435,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCATATGCA	.	5	ESCA
TTC23	0	.	GRCh37	15	99768848	99768848	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70C>G	p.His24Asp	p.H24D	ENST00000394132	5/14	50	43	7	50	50	0	TTC23,missense_variant,p.His24Asp,ENST00000560235,;TTC23,missense_variant,p.His24Asp,ENST00000560772,;TTC23,missense_variant,p.His24Asp,ENST00000394129,;TTC23,missense_variant,p.His24Asp,ENST00000561365,;TTC23,missense_variant,p.His24Asp,ENST00000262074,;TTC23,missense_variant,p.His24Asp,ENST00000558078,;TTC23,missense_variant,p.His24Asp,ENST00000558663,;TTC23,missense_variant,p.His24Asp,ENST00000394132,;TTC23,missense_variant,p.His24Asp,ENST00000558613,;TTC23,missense_variant,p.His24Asp,ENST00000394130,;TTC23,missense_variant,p.His24Asp,ENST00000394136,;TTC23,missense_variant,p.His24Asp,ENST00000560279,;TTC23,missense_variant,p.His24Asp,ENST00000560860,;TTC23,missense_variant,p.His24Asp,ENST00000394135,;TTC23,missense_variant,p.His24Asp,ENST00000459771,;TTC23,non_coding_transcript_exon_variant,,ENST00000468436,;	C	ENSG00000103852	ENST00000394132	Transcript	missense_variant	888	70	24	H/D	Cat/Gat	.	.	.	-1	TTC23	HGNC	25730	protein_coding	YES	CCDS10379.2	ENSP00000377690	TTC23_HUMAN	H0YNV8_HUMAN,H0YNH7_HUMAN,H0YN45_HUMAN,H0YMN1_HUMAN,H0YM10_HUMAN,H0YKN9_HUMAN,B3KMY5_HUMAN	UPI00004525C9	.	deleterious_low_confidence(0.03)	benign(0.005)	5/14	.	hmmpanther:PTHR14485:SF1,hmmpanther:PTHR14485	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTATGAGTGA	.	5	ESCA
LRRC28	0	.	GRCh37	15	99816796	99816796	+	Missense_Mutation	SNP	C	C	G	rs773574636	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.184C>G	p.Gln62Glu	p.Q62E	ENST00000301981	3/10	77	70	7	58	58	0	LRRC28,missense_variant,p.Gln62Glu,ENST00000301981,;LRRC28,missense_variant,p.Gln62Glu,ENST00000558861,;LRRC28,missense_variant,p.Gln17Glu,ENST00000561276,;LRRC28,missense_variant,p.Gln62Glu,ENST00000447360,;LRRC28,missense_variant,p.Gln62Glu,ENST00000422500,;LRRC28,missense_variant,p.Gln62Glu,ENST00000442993,;LRRC28,missense_variant,p.Gln62Glu,ENST00000331450,;LRRC28,intron_variant,,ENST00000558172,;LRRC28,intron_variant,,ENST00000558879,;LRRC28,non_coding_transcript_exon_variant,,ENST00000558500,;LRRC28,non_coding_transcript_exon_variant,,ENST00000559399,;LRRC28,missense_variant,p.Gln62Glu,ENST00000561253,;LRRC28,intron_variant,,ENST00000558471,;LRRC28,intron_variant,,ENST00000559433,;	G	ENSG00000168904	ENST00000301981	Transcript	missense_variant	424	184	62	Q/E	Cag/Gag	rs773574636	.	.	1	LRRC28	HGNC	28355	protein_coding	YES	CCDS10380.1	ENSP00000304923	LRC28_HUMAN	Q8NB41_HUMAN,H0YNW4_HUMAN,H0YKF6_HUMAN,B4DK22_HUMAN	UPI000000DBCB	.	tolerated(0.15)	possibly_damaging(0.487)	3/10	.	Superfamily_domains:SSF52058,SMART_domains:SM00369,Pfam_domain:PF13855,Gene3D:3.80.10.10,hmmpanther:PTHR23155:SF433,hmmpanther:PTHR23155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTGCTCAGAAG	byFrequency	3	ESCA
BAIAP3	0	.	GRCh37	16	1393012	1393012	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1365C>G	p.%3D	p.A455A	ENST00000324385	14/34	33	24	9	52	52	0	BAIAP3,synonymous_variant,p.%3D,ENST00000426824,;BAIAP3,synonymous_variant,p.%3D,ENST00000562208,;BAIAP3,synonymous_variant,p.%3D,ENST00000421665,;BAIAP3,synonymous_variant,p.%3D,ENST00000568887,;BAIAP3,synonymous_variant,p.%3D,ENST00000397488,;BAIAP3,synonymous_variant,p.%3D,ENST00000324385,;BAIAP3,synonymous_variant,p.%3D,ENST00000397489,;BAIAP3,upstream_gene_variant,,ENST00000561793,;BAIAP3,upstream_gene_variant,,ENST00000566162,;BAIAP3,upstream_gene_variant,,ENST00000564213,;BAIAP3,upstream_gene_variant,,ENST00000566389,;BAIAP3,upstream_gene_variant,,ENST00000561602,;BAIAP3,downstream_gene_variant,,ENST00000565665,;BAIAP3,upstream_gene_variant,,ENST00000567203,;BAIAP3,upstream_gene_variant,,ENST00000568198,;BAIAP3,downstream_gene_variant,,ENST00000567825,;	G	ENSG00000007516	ENST00000324385	Transcript	synonymous_variant	1523	1365	455	A	gcC/gcG	.	.	.	1	BAIAP3	HGNC	948	protein_coding	YES	CCDS10434.1	ENSP00000324510	BAIP3_HUMAN	.	UPI0000071E58	.	.	.	14/34	.	hmmpanther:PTHR15015,hmmpanther:PTHR15015:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGCCGTGCT	.	5	ESCA
DNAH3	0	.	GRCh37	16	20966359	20966359	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10847C>T	p.Pro3616Leu	p.P3616L	ENST00000261383	55/62	17	11	5	21	21	0	DNAH3,missense_variant,p.Pro3616Leu,ENST00000261383,;DNAH3,3_prime_UTR_variant,,ENST00000415178,;	A	ENSG00000158486	ENST00000261383	Transcript	missense_variant	10847	10847	3616	P/L	cCa/cTa	.	.	.	-1	DNAH3	HGNC	2949	protein_coding	YES	CCDS10594.1	ENSP00000261383	DYH3_HUMAN	.	UPI00001100F2	.	deleterious(0)	probably_damaging(0.996)	55/62	.	Pfam_domain:PF03028,hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATGGATAG	.	5	ESCA
PKD1	0	.	GRCh37	16	2139786	2139786	+	Missense_Mutation	SNP	G	G	C	rs767235360	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12854C>G	p.Thr4285Ser	p.T4285S	ENST00000262304	46/46	21	16	5	16	16	0	PKD1,missense_variant,p.Thr4285Ser,ENST00000262304,;PKD1,missense_variant,p.Thr4284Ser,ENST00000423118,;TSC2,downstream_gene_variant,,ENST00000439673,;TSC2,downstream_gene_variant,,ENST00000219476,;TSC2,downstream_gene_variant,,ENST00000568454,;TSC2,downstream_gene_variant,,ENST00000569110,;TSC2,downstream_gene_variant,,ENST00000401874,;TSC2,downstream_gene_variant,,ENST00000353929,;TSC2,downstream_gene_variant,,ENST00000350773,;TSC2,downstream_gene_variant,,ENST00000382538,;MIR1225,downstream_gene_variant,,ENST00000408729,;RP11-304L19.1,upstream_gene_variant,,ENST00000570072,;RP11-304L19.1,upstream_gene_variant,,ENST00000563284,;PKD1,non_coding_transcript_exon_variant,,ENST00000472577,;PKD1,downstream_gene_variant,,ENST00000568796,;PKD1,downstream_gene_variant,,ENST00000561668,;TSC2,downstream_gene_variant,,ENST00000569930,;PKD1,downstream_gene_variant,,ENST00000567355,;TSC2,downstream_gene_variant,,ENST00000497886,;PKD1,downstream_gene_variant,,ENST00000487932,;PKD1,downstream_gene_variant,,ENST00000485120,;PKD1,downstream_gene_variant,,ENST00000562425,;TSC2,downstream_gene_variant,,ENST00000439117,;PKD1,downstream_gene_variant,,ENST00000472659,;PKD1,downstream_gene_variant,,ENST00000564313,;	C	ENSG00000008710	ENST00000262304	Transcript	missense_variant	13063	12854	4285	T/S	aCt/aGt	rs767235360	.	.	-1	PKD1	HGNC	9008	protein_coding	YES	CCDS32369.1	ENSP00000262304	PKD1_HUMAN	O75276_HUMAN	UPI00001B0454	.	.	benign(0.001)	46/46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCAGTGGCC	.	2	ESCA
RP11-368J21.3	0	.	GRCh37	16	22558146	22558146	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1128C>G	.	.	ENST00000550753	1/9	41	37	4	48	48	0	RP11-368J21.3,non_coding_transcript_exon_variant,,ENST00000550753,;RP11-368J21.3,upstream_gene_variant,,ENST00000548889,;	G	ENSG00000257838	ENST00000550753	Transcript	non_coding_transcript_exon_variant	1128	.	.	.	.	.	.	.	1	RP11-368J21.3	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCTCGGTCA	.	4	ESCA
ABCC12	0	.	GRCh37	16	48117642	48117642	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4064C>A	p.Ala1355Glu	p.A1355E	ENST00000311303	29/29	55	41	14	53	53	0	ABCC12,missense_variant,p.Ala1355Glu,ENST00000311303,;ABCC12,3_prime_UTR_variant,,ENST00000416054,;ABCC12,3_prime_UTR_variant,,ENST00000448542,;ABCC12,downstream_gene_variant,,ENST00000532355,;ABCC12,3_prime_UTR_variant,,ENST00000532494,;ABCC12,3_prime_UTR_variant,,ENST00000529504,;ABCC12,3_prime_UTR_variant,,ENST00000497206,;ABCC12,3_prime_UTR_variant,,ENST00000534418,;ABCC12,3_prime_UTR_variant,,ENST00000529084,;ABCC12,downstream_gene_variant,,ENST00000526251,;	T	ENSG00000140798	ENST00000311303	Transcript	missense_variant	4410	4064	1355	A/E	gCa/gAa	.	.	.	-1	ABCC12	HGNC	14640	protein_coding	YES	CCDS10730.1	ENSP00000311030	MRP9_HUMAN	E9PHY2_HUMAN	UPI0000456987	.	deleterious(0)	possibly_damaging(0.764)	29/29	.	hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF10,Gene3D:3.40.50.300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTGCTGCT	.	5	ESCA
SALL1	0	.	GRCh37	16	51170299	51170299	+	3'UTR	DEL	A	A	-	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*724delT	.	.	ENST00000251020	3/3	70	57	13	47	47	0	SALL1,3_prime_UTR_variant,,ENST00000251020,;SALL1,3_prime_UTR_variant,,ENST00000440970,;SALL1,downstream_gene_variant,,ENST00000541611,;SALL1,downstream_gene_variant,,ENST00000570206,;SALL1,downstream_gene_variant,,ENST00000566102,;	-	ENSG00000103449	ENST00000251020	Transcript	3_prime_UTR_variant	4733	.	.	.	.	.	.	.	-1	SALL1	HGNC	10524	protein_coding	YES	CCDS10747.1	ENSP00000251020	SALL1_HUMAN	H3BSM9_HUMAN	UPI000013CCD8	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACTACCAAAACA	.	3	ESCA
AMFR	0	.	GRCh37	16	56396627	56396627	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*194C>G	.	.	ENST00000290649	14/14	43	31	12	42	42	0	AMFR,3_prime_UTR_variant,,ENST00000290649,;AMFR,3_prime_UTR_variant,,ENST00000492830,;AMFR,downstream_gene_variant,,ENST00000567738,;AMFR,non_coding_transcript_exon_variant,,ENST00000568325,;AMFR,non_coding_transcript_exon_variant,,ENST00000566757,;AMFR,downstream_gene_variant,,ENST00000566334,;AMFR,downstream_gene_variant,,ENST00000563285,;	C	ENSG00000159461	ENST00000290649	Transcript	3_prime_UTR_variant	2337	.	.	.	.	.	.	.	-1	AMFR	HGNC	463	protein_coding	YES	CCDS10758.1	ENSP00000290649	AMFR_HUMAN	Q6PGR1_HUMAN,Q1RN03_HUMAN,H3BSK3_HUMAN,H3BQM3_HUMAN	UPI000013EDCA	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAAGAGAAA	.	5	ESCA
CES3	0	.	GRCh37	16	66997813	66997813	+	Missense_Mutation	SNP	C	C	T	rs148620443	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535C>T	p.Arg179Cys	p.R179C	ENST00000303334	4/13	45	38	7	52	52	0	CES3,missense_variant,p.Arg179Cys,ENST00000394037,;CES3,missense_variant,p.Arg179Cys,ENST00000303334,;CES3,upstream_gene_variant,,ENST00000543856,;RP11-361L15.4,downstream_gene_variant,,ENST00000566869,;CES3,missense_variant,p.Arg179Cys,ENST00000570236,;CES3,3_prime_UTR_variant,,ENST00000566453,;CES3,downstream_gene_variant,,ENST00000566746,;CES3,downstream_gene_variant,,ENST00000568118,;CES3,upstream_gene_variant,,ENST00000564715,;	T	ENSG00000172828	ENST00000303334	Transcript	missense_variant	606	535	179	R/C	Cgc/Tgc	rs148620443,COSM3402408	.	.	1	CES3	HGNC	1865	protein_coding	YES	CCDS10826.1	ENSP00000304782	EST3_HUMAN	.	UPI0000047824	.	deleterious(0.01)	probably_damaging(0.994)	4/13	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF163	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0.0005	T:0.0008	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTACCGCCTT	byCluster|by1000G	5	ESCA
CA5A	0	.	GRCh37	16	87921625	87921625	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*110G>C	.	.	ENST00000309893	7/7	93	75	17	70	70	0	CA5A,3_prime_UTR_variant,,ENST00000309893,;GS1-21A4.1,downstream_gene_variant,,ENST00000562644,;CA5A,downstream_gene_variant,,ENST00000566402,;GS1-21A4.2,upstream_gene_variant,,ENST00000604757,;	G	ENSG00000174990	ENST00000309893	Transcript	3_prime_UTR_variant	1094	.	.	.	.	.	.	.	-1	CA5A	HGNC	1377	protein_coding	YES	CCDS10965.1	ENSP00000309649	CAH5A_HUMAN	.	UPI0000126DF3	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTCATGCT	.	5	ESCA
MYH2	0	.	GRCh37	17	10429074	10429074	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4307T>C	p.Leu1436Pro	p.L1436P	ENST00000245503	31/40	47	44	3	55	55	0	MYH2,missense_variant,p.Leu1436Pro,ENST00000245503,;MYH2,missense_variant,p.Leu1436Pro,ENST00000397183,;MYH2,intron_variant,,ENST00000532183,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	G	ENSG00000125414	ENST00000245503	Transcript	missense_variant	4692	4307	1436	L/P	cTt/cCt	.	.	.	-1	MYH2	HGNC	7572	protein_coding	YES	CCDS11156.1	ENSP00000245503	MYH2_HUMAN	J3QLR0_HUMAN,E7EX84_HUMAN,C9JIX4_HUMAN	UPI000012FB6C	.	deleterious(0.01)	benign(0.278)	31/40	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF90257,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF314	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCAAGCATG	.	2	ESCA
KSR1	0	.	GRCh37	17	25877646	25877646	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-128C>T	.	.	ENST00000398988	3/22	57	47	10	59	59	0	KSR1,missense_variant,p.Ala95Val,ENST00000319524,;KSR1,missense_variant,p.Ala95Val,ENST00000509603,;KSR1,5_prime_UTR_variant,,ENST00000398988,;KSR1,5_prime_UTR_variant,,ENST00000268763,;KSR1,5_prime_UTR_variant,,ENST00000580163,;KSR1,5_prime_UTR_variant,,ENST00000583370,;KSR1,non_coding_transcript_exon_variant,,ENST00000582311,;	T	ENSG00000141068	ENST00000398988	Transcript	5_prime_UTR_variant	318	.	.	.	.	.	.	.	1	KSR1	HGNC	6465	protein_coding	YES	CCDS58532.1	ENSP00000381958	.	J3QSG8_HUMAN,J3QR75_HUMAN,J3QKR8_HUMAN,H7BYU0_HUMAN	UPI00005B2F0C	.	.	.	3/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGGCTCCCG	.	5	ESCA
PROCA1	0	.	GRCh37	17	27037996	27037996	+	Intron	SNP	T	T	C	rs11655758	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.91+592A>G	.	.	ENST00000301039	.	22	16	6	25	24	1	PROCA1,5_prime_UTR_variant,,ENST00000439862,;PROCA1,intron_variant,,ENST00000581289,;PROCA1,intron_variant,,ENST00000301039,;RAB34,downstream_gene_variant,,ENST00000583538,;RAB34,downstream_gene_variant,,ENST00000430132,;RAB34,downstream_gene_variant,,ENST00000301043,;RAB34,downstream_gene_variant,,ENST00000419712,;RAB34,downstream_gene_variant,,ENST00000395242,;RAB34,downstream_gene_variant,,ENST00000395243,;RAB34,downstream_gene_variant,,ENST00000415040,;RAB34,downstream_gene_variant,,ENST00000395245,;RAB34,downstream_gene_variant,,ENST00000436730,;RAB34,downstream_gene_variant,,ENST00000353676,;RAB34,downstream_gene_variant,,ENST00000447716,;PROCA1,upstream_gene_variant,,ENST00000415329,;RAB34,downstream_gene_variant,,ENST00000412625,;RAB34,downstream_gene_variant,,ENST00000450529,;RAB34,downstream_gene_variant,,ENST00000453384,;PROCA1,non_coding_transcript_exon_variant,,ENST00000578097,;PROCA1,non_coding_transcript_exon_variant,,ENST00000422880,;PROCA1,non_coding_transcript_exon_variant,,ENST00000579650,;PROCA1,upstream_gene_variant,,ENST00000584073,;PROCA1,intron_variant,,ENST00000473751,;PROCA1,upstream_gene_variant,,ENST00000495203,;RAB34,downstream_gene_variant,,ENST00000481501,;RAB34,downstream_gene_variant,,ENST00000496866,;RAB34,downstream_gene_variant,,ENST00000474704,;RAB34,downstream_gene_variant,,ENST00000422279,;RAB34,downstream_gene_variant,,ENST00000484161,;	C	ENSG00000167525	ENST00000301039	Transcript	intron_variant	.	.	.	.	.	rs11655758	.	.	-1	PROCA1	HGNC	28600	protein_coding	YES	CCDS11239.1	ENSP00000301039	PRCA1_HUMAN	K7ESJ9_HUMAN	UPI000006D0EE	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TAGGGTGGGAA	suspect|byCluster|byHapMap	2	ESCA
LIG3	0	.	GRCh37	17	33318055	33318055	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.963G>C	p.Leu321Phe	p.L321F	ENST00000378526	5/20	41	30	11	37	37	0	LIG3,missense_variant,p.Leu50Phe,ENST00000585740,;LIG3,missense_variant,p.Leu321Phe,ENST00000378526,;LIG3,missense_variant,p.Leu321Phe,ENST00000262327,;LIG3,missense_variant,p.Leu330Phe,ENST00000585941,;LIG3,downstream_gene_variant,,ENST00000592690,;LIG3,downstream_gene_variant,,ENST00000586407,;LIG3,3_prime_UTR_variant,,ENST00000588109,;LIG3,non_coding_transcript_exon_variant,,ENST00000586435,;LIG3,upstream_gene_variant,,ENST00000588713,;LIG3,downstream_gene_variant,,ENST00000590181,;LIG3,upstream_gene_variant,,ENST00000590630,;LIG3,upstream_gene_variant,,ENST00000586058,;	C	ENSG00000005156	ENST00000378526	Transcript	missense_variant	1096	963	321	L/F	ttG/ttC	COSM1302651,COSM1302650	.	.	1	LIG3	HGNC	6600	protein_coding	YES	CCDS11284.2	ENSP00000367787	DNLI3_HUMAN	E5KLB5_HUMAN,K7EQB6_HUMAN,K7ENR9_HUMAN,C4B7Q3_HUMAN,B7Z6I3_HUMAN	UPI0000350B71	.	deleterious(0)	probably_damaging(0.988)	5/20	.	hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF11,Gene3D:1x9nA01,TIGRFAM_domain:TIGR00574,Pfam_domain:PF04675,Superfamily_domains:0050884	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AACTTGAACGA	.	4	ESCA
AP2B1	0	.	GRCh37	17	33953659	33953659	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736C>A	p.Pro246Thr	p.P246T	ENST00000312678	7/22	399	386	13	397	397	0	AP2B1,missense_variant,p.Pro246Thr,ENST00000589344,;AP2B1,missense_variant,p.Pro246Thr,ENST00000262325,;AP2B1,missense_variant,p.Pro246Thr,ENST00000312678,;AP2B1,missense_variant,p.Pro208Thr,ENST00000592545,;AP2B1,missense_variant,p.Pro189Thr,ENST00000538556,;AP2B1,missense_variant,p.Pro246Thr,ENST00000537622,;AP2B1,non_coding_transcript_exon_variant,,ENST00000545922,;AP2B1,non_coding_transcript_exon_variant,,ENST00000591561,;AP2B1,3_prime_UTR_variant,,ENST00000592191,;AP2B1,intron_variant,,ENST00000588116,;	A	ENSG00000006125	ENST00000312678	Transcript	missense_variant	866	736	246	P/T	Ccc/Acc	.	.	.	1	AP2B1	HGNC	563	protein_coding	YES	CCDS32621.1	ENSP00000314414	AP2B1_HUMAN	Q96EL6_HUMAN,K7ERB2_HUMAN,K7EN71_HUMAN,K7EJX1_HUMAN	UPI000006DD97	.	deleterious(0)	probably_damaging(0.944)	7/22	.	hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF9,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF002291,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACTCCCCGG	.	2	ESCA
SYNRG	0	.	GRCh37	17	35902238	35902238	+	Missense_Mutation	SNP	G	G	C	rs372539300	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3038C>G	p.Ser1013Cys	p.S1013C	ENST00000339208	15/22	62	43	19	38	38	0	SYNRG,missense_variant,p.Ser935Cys,ENST00000345615,;SYNRG,missense_variant,p.Ser84Cys,ENST00000591427,;SYNRG,missense_variant,p.Ser935Cys,ENST00000394378,;SYNRG,missense_variant,p.Ser890Cys,ENST00000502449,;SYNRG,missense_variant,p.Ser807Cys,ENST00000591288,;SYNRG,missense_variant,p.Ser934Cys,ENST00000585472,;SYNRG,missense_variant,p.Ser1013Cys,ENST00000339208,;SYNRG,missense_variant,p.Ser1013Cys,ENST00000346661,;SYNRG,non_coding_transcript_exon_variant,,ENST00000421408,;SYNRG,upstream_gene_variant,,ENST00000508220,;	C	ENSG00000006114	ENST00000339208	Transcript	missense_variant	3179	3038	1013	S/C	tCt/tGt	rs372539300	.	.	-1	SYNRG	HGNC	557	protein_coding	YES	CCDS11321.1	ENSP00000343610	SYNRG_HUMAN	.	UPI000013C4EA	.	deleterious_low_confidence(0)	probably_damaging(0.999)	15/22	.	hmmpanther:PTHR15463	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	C:0.0002	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGAGAGGCA	byCluster|by1000G	5	ESCA
PSMB3	0	.	GRCh37	17	36909465	36909465	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66C>T	p.%3D	p.I22I	ENST00000225426	2/6	34	28	5	53	53	0	PSMB3,synonymous_variant,p.%3D,ENST00000579088,;PSMB3,synonymous_variant,p.%3D,ENST00000225426,;PCGF2,upstream_gene_variant,,ENST00000578109,;PCGF2,upstream_gene_variant,,ENST00000579882,;PCGF2,upstream_gene_variant,,ENST00000360797,;PCGF2,upstream_gene_variant,,ENST00000580830,;CTB-58E17.5,downstream_gene_variant,,ENST00000539023,;RNU6-866P,downstream_gene_variant,,ENST00000516469,;PSMB3,synonymous_variant,p.%3D,ENST00000584662,;PSMB3,synonymous_variant,p.%3D,ENST00000579729,;	T	ENSG00000108294	ENST00000225426	Transcript	synonymous_variant	157	66	22	I	atC/atT	.	.	.	1	PSMB3	HGNC	9540	protein_coding	YES	CCDS11328.1	ENSP00000225426	PSB3_HUMAN	J3QKR3_HUMAN	UPI00001325B3	.	.	.	2/6	.	PROSITE_profiles:PS51476,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF49,PROSITE_patterns:PS00854,Gene3D:3.60.20.10,Pfam_domain:PF00227,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCATCGCTGC	.	4	ESCA
CA10	0	.	GRCh37	17	49710983	49710983	+	Missense_Mutation	SNP	T	T	G	rs765690627	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.818A>C	p.Asn273Thr	p.N273T	ENST00000451037	8/9	33	23	9	47	47	0	CA10,missense_variant,p.Asn273Thr,ENST00000285273,;CA10,missense_variant,p.Asn198Thr,ENST00000570565,;CA10,missense_variant,p.Asn273Thr,ENST00000575181,;CA10,missense_variant,p.Asn279Thr,ENST00000340813,;CA10,missense_variant,p.Asn273Thr,ENST00000451037,;CA10,missense_variant,p.Asn273Thr,ENST00000442502,;CA10,downstream_gene_variant,,ENST00000571918,;CA10,3_prime_UTR_variant,,ENST00000571371,;	G	ENSG00000154975	ENST00000451037	Transcript	missense_variant	1759	818	273	N/T	aAc/aCc	rs765690627,COSM1247045	.	.	-1	CA10	HGNC	1369	protein_coding	YES	CCDS32684.1	ENSP00000405388	CAH10_HUMAN	I3L375_HUMAN,B4DGL6_HUMAN	UPI000000167C	.	deleterious(0.02)	benign(0.249)	8/9	.	PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF91,Gene3D:3.10.200.10,Pfam_domain:PF00194,SMART_domains:SM01057,Superfamily_domains:SSF51069	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGGTTCTGG	.	5	ESCA
AKAP1	0	.	GRCh37	17	55193552	55193552	+	Missense_Mutation	SNP	G	G	A	rs189625721	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2362G>A	p.Glu788Lys	p.E788K	ENST00000337714	7/11	46	36	9	43	43	0	AKAP1,missense_variant,p.Glu21Lys,ENST00000572560,;AKAP1,missense_variant,p.Glu788Lys,ENST00000571629,;AKAP1,missense_variant,p.Glu788Lys,ENST00000337714,;AKAP1,missense_variant,p.Glu788Lys,ENST00000572557,;AKAP1,missense_variant,p.Glu77Lys,ENST00000575032,;AKAP1,missense_variant,p.Glu788Lys,ENST00000539273,;AKAP1,downstream_gene_variant,,ENST00000576295,;AKAP1,3_prime_UTR_variant,,ENST00000481416,;AKAP1,intron_variant,,ENST00000573326,;	A	ENSG00000121057	ENST00000337714	Transcript	missense_variant	2595	2362	788	E/K	Gaa/Aaa	rs189625721	.	.	1	AKAP1	HGNC	367	protein_coding	YES	CCDS11594.1	ENSP00000337736	AKAP1_HUMAN	I3L3L9_HUMAN,I3L3K1_HUMAN,I3L364_HUMAN,I3L2N7_HUMAN,I3L2A2_HUMAN,I3L0K6_HUMAN	UPI0000125778	.	deleterious(0)	probably_damaging(0.911)	7/11	.	PROSITE_profiles:PS50304,hmmpanther:PTHR12727,Pfam_domain:PF00567,Gene3D:2.30.30.140,SMART_domains:SM00333,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAACGAAGTG	byCluster|by1000G	5	ESCA
COG1	0	.	GRCh37	17	71197644	71197644	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1678T>C	p.Tyr560His	p.Y560H	ENST00000299886	7/14	35	19	16	32	32	0	COG1,missense_variant,p.Tyr560His,ENST00000438720,;COG1,missense_variant,p.Tyr560His,ENST00000299886,;COG1,upstream_gene_variant,,ENST00000582512,;COG1,upstream_gene_variant,,ENST00000582672,;RP11-143K11.5,downstream_gene_variant,,ENST00000580671,;COG1,upstream_gene_variant,,ENST00000577844,;COG1,upstream_gene_variant,,ENST00000577238,;COG1,downstream_gene_variant,,ENST00000582587,;COG1,upstream_gene_variant,,ENST00000580271,;	C	ENSG00000166685	ENST00000299886	Transcript	missense_variant	1758	1678	560	Y/H	Tac/Cac	.	.	.	1	COG1	HGNC	6545	protein_coding	YES	CCDS11692.1	ENSP00000299886	COG1_HUMAN	J3KSY3_HUMAN	UPI0000127E34	.	deleterious(0)	benign(0.019)	7/14	.	hmmpanther:PTHR31658,hmmpanther:PTHR31658:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGATACGCA	.	5	ESCA
TMEM104	0	.	GRCh37	17	72781707	72781707	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132C>T	p.%3D	p.V44V	ENST00000335464	3/10	61	34	27	37	37	0	TMEM104,synonymous_variant,p.%3D,ENST00000582330,;TMEM104,synonymous_variant,p.%3D,ENST00000582773,;TMEM104,synonymous_variant,p.%3D,ENST00000335464,;TMEM104,intron_variant,,ENST00000578764,;TMEM104,intron_variant,,ENST00000417024,;TMEM104,non_coding_transcript_exon_variant,,ENST00000584246,;	T	ENSG00000109066	ENST00000335464	Transcript	synonymous_variant	294	132	44	V	gtC/gtT	.	.	.	1	TMEM104	HGNC	25984	protein_coding	YES	CCDS32723.1	ENSP00000334849	TM104_HUMAN	.	UPI00002001C9	.	.	.	3/10	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR16189:SF0,hmmpanther:PTHR16189,Pfam_domain:PF01490	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGTCAGCCT	.	5	ESCA
SLC16A5	0	.	GRCh37	17	73096682	73096682	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.924C>T	p.%3D	p.F308F	ENST00000450736	4/6	46	40	6	28	28	0	SLC16A5,synonymous_variant,p.%3D,ENST00000329783,;SLC16A5,synonymous_variant,p.%3D,ENST00000450736,;SLC16A5,synonymous_variant,p.%3D,ENST00000580123,;SLC16A5,synonymous_variant,p.%3D,ENST00000578376,;SLC16A5,synonymous_variant,p.%3D,ENST00000538213,;SLC16A5,downstream_gene_variant,,ENST00000584118,;SLC16A5,downstream_gene_variant,,ENST00000584207,;SLC16A5,downstream_gene_variant,,ENST00000585293,;SLC16A5,downstream_gene_variant,,ENST00000582048,;	T	ENSG00000170190	ENST00000450736	Transcript	synonymous_variant	1339	924	308	F	ttC/ttT	.	.	.	1	SLC16A5	HGNC	10926	protein_coding	YES	CCDS11713.1	ENSP00000390564	MOT6_HUMAN	J3QQW5_HUMAN,J3QL40_HUMAN,J3KT93_HUMAN	UPI0000000DC7	.	.	.	4/6	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11360:SF21,hmmpanther:PTHR11360,TIGRFAM_domain:TIGR00892,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTTCAGCCT	.	4	ESCA
SLC16A5	0	.	GRCh37	17	73102226	73102226	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*98A>C	.	.	ENST00000450736	6/6	25	20	5	10	10	0	SLC16A5,3_prime_UTR_variant,,ENST00000329783,;SLC16A5,3_prime_UTR_variant,,ENST00000450736,;SLC16A5,3_prime_UTR_variant,,ENST00000580123,;ARMC7,upstream_gene_variant,,ENST00000581078,;ARMC7,upstream_gene_variant,,ENST00000245543,;ARMC7,upstream_gene_variant,,ENST00000584947,;SLC16A5,downstream_gene_variant,,ENST00000578376,;SLC16A5,downstream_gene_variant,,ENST00000538213,;ARMC7,upstream_gene_variant,,ENST00000582136,;	C	ENSG00000170190	ENST00000450736	Transcript	3_prime_UTR_variant	2031	.	.	.	.	.	.	.	1	SLC16A5	HGNC	10926	protein_coding	YES	CCDS11713.1	ENSP00000390564	MOT6_HUMAN	J3QQW5_HUMAN,J3QL40_HUMAN,J3KT93_HUMAN	UPI0000000DC7	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGCAAAATA	.	5	ESCA
SMIM6	0	.	GRCh37	17	73643892	73643892	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247G>C	.	.	ENST00000579469	2/2	56	46	10	20	20	0	SMIM6,3_prime_UTR_variant,,ENST00000556126,;SMIM6,3_prime_UTR_variant,,ENST00000579469,;RECQL5,intron_variant,,ENST00000578201,;RECQL5,intron_variant,,ENST00000423245,;RECQL5,intron_variant,,ENST00000317905,;RECQL5,downstream_gene_variant,,ENST00000584999,;RECQL5,downstream_gene_variant,,ENST00000420326,;RECQL5,downstream_gene_variant,,ENST00000340830,;RECQL5,downstream_gene_variant,,ENST00000580078,;RECQL5,downstream_gene_variant,,ENST00000579274,;RECQL5,intron_variant,,ENST00000582464,;	C	ENSG00000259120	ENST00000579469	Transcript	3_prime_UTR_variant	792	.	.	.	.	.	.	.	1	SMIM6	HGNC	40032	protein_coding	YES	CCDS54166.1	ENSP00000463361	SMIM6_HUMAN	.	UPI000005275F	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCAGAACCC	.	5	ESCA
TP53	0	.	GRCh37	17	7577106	7577106	+	Missense_Mutation	SNP	G	G	A	rs17849781	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	8/11	224	162	61	332	332	0	TP53,missense_variant,p.Pro278Ser,ENST00000420246,;TP53,missense_variant,p.Pro278Ser,ENST00000269305,;TP53,missense_variant,p.Pro146Ser,ENST00000509690,;TP53,missense_variant,p.Pro278Ser,ENST00000359597,;TP53,missense_variant,p.Pro278Ser,ENST00000445888,;TP53,missense_variant,p.Pro278Ser,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1022	832	278	P/S	Cct/Tct	CM052927,CX0910928,rs17849781,CM011015,TP53_g.13812C>G,TP53_g.13812C>A,TP53_g.13812del,TP53_g.13812C>T,COSM43697,COSM10939,COSM10814,COSM45178,COSM368635,COSM139044,COSM99725,COSM3421932,COSM3773297,COSM3717626,COSM1646810,COSM1646809,COSM3421931	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.03)	probably_damaging(1)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P278S|c.832C>T|4,SITE|p.P278S|c.832C>T|3,SITE|p.P278S|c.832C>T|8,SITE|p.P278S|c.832C>T|55,CODON|p.0?|c.1_1182del1182|6,CODON|p.P278fs*67|c.833delC|3,CODON|p.P278F|c.832_833CC>TT|3,CODON|p.P278H|c.833C>A|15,CODON|p.P278R|c.833C>G|5,CODON|p.P278R|c.833C>G|30,CODON|p.P278R|c.833C>G|3,CODON|p.P278H|c.833C>A|3,CODON|p.P278L|c.833C>T|3,CODON|p.P278L|c.833C>T|11,CODON|p.P278L|c.833C>T|65,CODON|p.P278L|c.833C>T|8,CODON|p.P278fs*67|c.832delC|3,BUFFER|p.R282W|c.843_844CC>TT|10,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12,BUFFER|p.D281V|c.842A>T|5,BUFFER|p.D281G|c.842A>G|10,BUFFER|p.D281H|c.841G>C|6,BUFFER|p.D281H|c.841G>C|28,BUFFER|p.D281H|c.841G>C|3,BUFFER|p.D281H|c.841G>C|4,BUFFER|p.D281Y|c.841G>T|7,BUFFER|p.D281N|c.841G>A|7,BUFFER|p.D281N|c.841G>A|3,BUFFER|p.D281Y|c.841G>T|13,BUFFER|p.D281Y|c.841G>T|4,BUFFER|p.D281N|c.841G>A|27,BUFFER|p.R280R|c.840A>G|3,BUFFER|p.R280S|c.840A>T|11,BUFFER|p.R280S|c.840A>C|6,BUFFER|p.R280T|c.839G>C|63,BUFFER|p.R280T|c.839G>C|4,BUFFER|p.R280I|c.839G>T|17,BUFFER|p.R280K|c.839G>A|17,BUFFER|p.R280K|c.839G>A|6,BUFFER|p.R280I|c.839G>T|4,BUFFER|p.R280K|c.839G>A|57,BUFFER|p.R280I|c.839G>T|3,BUFFER|p.R280T|c.839G>C|10,BUFFER|p.R280K|c.839G>A|11,BUFFER|p.R280*|c.838A>T|12,BUFFER|p.R280G|c.838A>G|6,BUFFER|p.R280G|c.838A>G|3,BUFFER|p.R280G|c.838A>G|23,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279E|c.836G>A|4,BUFFER|p.G279E|c.836G>A|34,BUFFER|p.G279V|c.836G>T|3,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278T|c.832C>A|29,BUFFER|p.P278A|c.832C>G|25,BUFFER|p.P278T|c.832C>A|8,BUFFER|p.P278A|c.832C>G|4,BUFFER|p.P278A|c.832C>G|10,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGGACAGG	.	5	ESCA
RNF138	0	.	GRCh37	18	29709260	29709260	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*110C>G	.	.	ENST00000261593	8/8	31	24	6	15	15	0	RNF138,3_prime_UTR_variant,,ENST00000257190,;RNF138,3_prime_UTR_variant,,ENST00000261593,;RNF138,3_prime_UTR_variant,,ENST00000577999,;GAREM,intron_variant,,ENST00000583696,;RNF138,downstream_gene_variant,,ENST00000580499,;RP11-53I6.4,upstream_gene_variant,,ENST00000583138,;	G	ENSG00000134758	ENST00000261593	Transcript	3_prime_UTR_variant	1306	.	.	.	.	.	.	.	1	RNF138	HGNC	17765	protein_coding	YES	CCDS11903.1	ENSP00000261593	RN138_HUMAN	J3KSI2_HUMAN,J3KRU4_HUMAN	UPI00000702BA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATTCAGTCA	.	5	ESCA
NOL4	0	.	GRCh37	18	31432285	31432285	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*521C>T	.	.	ENST00000261592	11/11	50	43	7	18	18	0	NOL4,3_prime_UTR_variant,,ENST00000261592,;NOL4,3_prime_UTR_variant,,ENST00000269185,;NOL4,3_prime_UTR_variant,,ENST00000535384,;NOL4,downstream_gene_variant,,ENST00000589544,;NOL4,downstream_gene_variant,,ENST00000538587,;NOL4,downstream_gene_variant,,ENST00000535475,;NOL4,downstream_gene_variant,,ENST00000590712,;NOL4,downstream_gene_variant,,ENST00000586314,;	A	ENSG00000101746	ENST00000261592	Transcript	3_prime_UTR_variant	2736	.	.	.	.	.	.	.	-1	NOL4	HGNC	7870	protein_coding	YES	CCDS11907.2	ENSP00000261592	NOL4_HUMAN	.	UPI000059D504	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACAAGTTTGA	.	4	ESCA
NOL4	0	.	GRCh37	18	31432316	31432316	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*490T>C	.	.	ENST00000261592	11/11	48	38	10	22	22	0	NOL4,3_prime_UTR_variant,,ENST00000261592,;NOL4,3_prime_UTR_variant,,ENST00000269185,;NOL4,3_prime_UTR_variant,,ENST00000535384,;NOL4,downstream_gene_variant,,ENST00000589544,;NOL4,downstream_gene_variant,,ENST00000538587,;NOL4,downstream_gene_variant,,ENST00000535475,;NOL4,downstream_gene_variant,,ENST00000590712,;NOL4,downstream_gene_variant,,ENST00000586314,;	G	ENSG00000101746	ENST00000261592	Transcript	3_prime_UTR_variant	2705	.	.	.	.	.	.	.	-1	NOL4	HGNC	7870	protein_coding	YES	CCDS11907.2	ENSP00000261592	NOL4_HUMAN	.	UPI000059D504	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATAAAAATT	.	5	ESCA
SLC39A6	0	.	GRCh37	18	33689687	33689687	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2137G>T	p.Asp713Tyr	p.D713Y	ENST00000269187	10/10	33	28	5	19	19	0	SLC39A6,missense_variant,p.Asp713Tyr,ENST00000269187,;SLC39A6,missense_variant,p.Asp713Tyr,ENST00000590986,;SLC39A6,downstream_gene_variant,,ENST00000586829,;SLC39A6,downstream_gene_variant,,ENST00000440549,;	A	ENSG00000141424	ENST00000269187	Transcript	missense_variant	2351	2137	713	D/Y	Gat/Tat	.	.	.	-1	SLC39A6	HGNC	18607	protein_coding	YES	CCDS42428.1	ENSP00000269187	S39A6_HUMAN	K7EQ91_HUMAN	UPI000004EC93	.	deleterious(0)	probably_damaging(1)	10/10	.	hmmpanther:PTHR12191,hmmpanther:PTHR12191:SF8,Pfam_domain:PF02535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGCATCATTGT	.	3	ESCA
SETBP1	0	.	GRCh37	18	42532361	42532361	+	Missense_Mutation	SNP	G	G	A	rs140544874	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3056G>A	p.Arg1019His	p.R1019H	ENST00000282030	4/6	62	47	15	31	31	0	SETBP1,missense_variant,p.Arg1019His,ENST00000282030,;	A	ENSG00000152217	ENST00000282030	Transcript	missense_variant	3352	3056	1019	R/H	cGt/cAt	rs140544874,COSM126101	.	.	1	SETBP1	HGNC	15573	protein_coding	YES	CCDS11923.2	ENSP00000282030	SETBP_HUMAN	K7ES17_HUMAN	UPI0000201C54	.	deleterious(0.01)	probably_damaging(0.997)	4/6	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF322,SMART_domains:SM00384	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCGTGGTA	byCluster	5	ESCA
ATP5A1	0	.	GRCh37	18	43675034	43675034	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124C>A	p.His42Asn	p.H42N	ENST00000282050	3/13	67	53	13	37	37	0	ATP5A1,missense_variant,p.His42Asn,ENST00000590665,;ATP5A1,missense_variant,p.His42Asn,ENST00000590406,;ATP5A1,missense_variant,p.His42Asn,ENST00000282050,;ATP5A1,missense_variant,p.His42Asn,ENST00000398752,;ATP5A1,missense_variant,p.His42Asn,ENST00000589252,;ATP5A1,5_prime_UTR_variant,,ENST00000589869,;ATP5A1,5_prime_UTR_variant,,ENST00000590324,;ATP5A1,5_prime_UTR_variant,,ENST00000592989,;ATP5A1,5_prime_UTR_variant,,ENST00000593152,;ATP5A1,non_coding_transcript_exon_variant,,ENST00000591267,;ATP5A1,missense_variant,p.His42Asn,ENST00000590156,;ATP5A1,missense_variant,p.His42Asn,ENST00000592364,;ATP5A1,synonymous_variant,p.%3D,ENST00000585650,;ATP5A1,3_prime_UTR_variant,,ENST00000591981,;ATP5A1,3_prime_UTR_variant,,ENST00000586592,;ATP5A1,non_coding_transcript_exon_variant,,ENST00000590448,;ATP5A1,non_coding_transcript_exon_variant,,ENST00000588390,;ATP5A1,upstream_gene_variant,,ENST00000589611,;	T	ENSG00000152234	ENST00000282050	Transcript	missense_variant	269	124	42	H/N	Cat/Aat	.	.	.	-1	ATP5A1	HGNC	823	protein_coding	YES	CCDS11927.1	ENSP00000282050	ATPA_HUMAN	K7EQH4_HUMAN,K7ERX7_HUMAN,K7EK77_HUMAN,K7EJP1_HUMAN,B4DGW3_HUMAN	UPI000006221A	.	tolerated_low_confidence(0.32)	benign(0)	3/13	.	hmmpanther:PTHR15184,hmmpanther:PTHR15184:SF39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATGAGTGT	.	5	ESCA
ZNF823	0	.	GRCh37	19	11835025	11835025	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175G>C	p.Ala59Pro	p.A59P	ENST00000341191	3/4	61	46	15	65	65	0	ZNF823,missense_variant,p.Ala15Pro,ENST00000431998,;ZNF823,missense_variant,p.Ala59Pro,ENST00000341191,;ZNF823,intron_variant,,ENST00000545749,;ZNF823,intron_variant,,ENST00000440527,;ZNF823,intron_variant,,ENST00000586121,;CTC-499B15.6,downstream_gene_variant,,ENST00000586983,;	G	ENSG00000197933	ENST00000341191	Transcript	missense_variant	329	175	59	A/P	Gcc/Ccc	.	.	.	-1	ZNF823	HGNC	30936	protein_coding	YES	CCDS45981.1	ENSP00000340683	ZN823_HUMAN	K7EN93_HUMAN,C9J2N8_HUMAN,B7Z8D4_HUMAN	UPI0000203407	.	tolerated(0.55)	benign(0.001)	3/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24379:SF27,hmmpanther:PTHR24379,SMART_domains:SM00349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGCATTTT	.	5	ESCA
CALR	0	.	GRCh37	19	13054423	13054423	+	Missense_Mutation	SNP	G	G	A	rs750961102	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1033G>A	p.Glu345Lys	p.E345K	ENST00000316448	8/9	34	26	8	40	40	0	CALR,missense_variant,p.Glu130Lys,ENST00000586760,;CALR,missense_variant,p.Glu345Lys,ENST00000316448,;RAD23A,upstream_gene_variant,,ENST00000541222,;CALR,downstream_gene_variant,,ENST00000588454,;RAD23A,upstream_gene_variant,,ENST00000316856,;RAD23A,upstream_gene_variant,,ENST00000592268,;RAD23A,upstream_gene_variant,,ENST00000586534,;CTC-425F1.4,downstream_gene_variant,,ENST00000589120,;RAD23A,upstream_gene_variant,,ENST00000588826,;CALR,non_coding_transcript_exon_variant,,ENST00000586803,;CALR,downstream_gene_variant,,ENST00000590325,;RAD23A,upstream_gene_variant,,ENST00000588329,;CALR,downstream_gene_variant,,ENST00000587486,;RAD23A,upstream_gene_variant,,ENST00000591499,;CALR,upstream_gene_variant,,ENST00000586967,;RAD23A,upstream_gene_variant,,ENST00000593114,;	A	ENSG00000179218	ENST00000316448	Transcript	missense_variant	1106	1033	345	E/K	Gag/Aag	rs750961102	.	.	1	CALR	HGNC	1455	protein_coding	YES	CCDS12288.1	ENSP00000320866	CALR_HUMAN	B4E2Y9_HUMAN	UPI000004CEC9	.	tolerated(0.2)	benign(0.07)	8/9	.	hmmpanther:PTHR11073,hmmpanther:PTHR11073:SF8,PIRSF_domain:PIRSF002356	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAACGAGACG	byFrequency	5	ESCA
CCDC130	0	.	GRCh37	19	13862599	13862599	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-24G>C	.	.	ENST00000586600	3/11	34	30	4	33	33	0	CCDC130,5_prime_UTR_variant,,ENST00000221554,;CCDC130,5_prime_UTR_variant,,ENST00000586600,;CCDC130,intron_variant,,ENST00000586666,;CCDC130,upstream_gene_variant,,ENST00000588809,;CCDC130,non_coding_transcript_exon_variant,,ENST00000588071,;CCDC130,non_coding_transcript_exon_variant,,ENST00000540216,;CCDC130,non_coding_transcript_exon_variant,,ENST00000593174,;	C	ENSG00000104957	ENST00000586600	Transcript	5_prime_UTR_variant	480	.	.	.	.	.	.	.	1	CCDC130	HGNC	28118	protein_coding	YES	CCDS12296.1	ENSP00000465776	CC130_HUMAN	K7EPA5_HUMAN,K7ELI4_HUMAN	UPI0000071AFB	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTGAGGAC	.	4	ESCA
ZSWIM4	0	.	GRCh37	19	13919937	13919937	+	Silent	SNP	C	C	G	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915C>G	p.%3D	p.L305L	ENST00000254323	5/13	19	13	6	30	30	0	ZSWIM4,synonymous_variant,p.%3D,ENST00000254323,;ZSWIM4,synonymous_variant,p.%3D,ENST00000440752,;ZSWIM4,synonymous_variant,p.%3D,ENST00000590508,;	G	ENSG00000132003	ENST00000254323	Transcript	synonymous_variant	1104	915	305	L	ctC/ctG	COSM1304074	.	.	1	ZSWIM4	HGNC	25704	protein_coding	YES	CCDS32924.1	ENSP00000254323	ZSWM4_HUMAN	Q9HA55_HUMAN	UPI00001C2005	.	.	.	5/13	.	hmmpanther:PTHR22619,hmmpanther:PTHR22619:SF4	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTCATGAC	.	5	ESCA
DDX39A	0	.	GRCh37	19	14522366	14522366	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381G>C	p.Gln127His	p.Q127H	ENST00000242776	4/11	55	44	11	72	72	0	DDX39A,missense_variant,p.Gln127His,ENST00000454233,;DDX39A,missense_variant,p.Gln127His,ENST00000242776,;DDX39A,missense_variant,p.Gln138His,ENST00000589675,;DDX39A,missense_variant,p.Gln115His,ENST00000590315,;DDX39A,missense_variant,p.Gln127His,ENST00000590239,;CD97,downstream_gene_variant,,ENST00000242786,;CD97,downstream_gene_variant,,ENST00000357355,;CD97,downstream_gene_variant,,ENST00000358600,;DDX39A,downstream_gene_variant,,ENST00000586993,;DDX39A,downstream_gene_variant,,ENST00000592632,;DDX39A,downstream_gene_variant,,ENST00000590696,;DDX39A,downstream_gene_variant,,ENST00000591275,;CTC-548K16.5,upstream_gene_variant,,ENST00000590626,;DDX39A,non_coding_transcript_exon_variant,,ENST00000592927,;DDX39A,downstream_gene_variant,,ENST00000593008,;DDX39A,missense_variant,p.Gln127His,ENST00000588692,;DDX39A,missense_variant,p.Gln127His,ENST00000324340,;DDX39A,non_coding_transcript_exon_variant,,ENST00000589318,;DDX39A,non_coding_transcript_exon_variant,,ENST00000588542,;DDX39A,non_coding_transcript_exon_variant,,ENST00000590260,;DDX39A,non_coding_transcript_exon_variant,,ENST00000586558,;DDX39A,non_coding_transcript_exon_variant,,ENST00000590556,;DDX39A,upstream_gene_variant,,ENST00000592391,;DDX39A,upstream_gene_variant,,ENST00000587730,;DDX39A,upstream_gene_variant,,ENST00000593026,;	G	ENSG00000123136	ENST00000242776	Transcript	missense_variant	483	381	127	Q/H	caG/caC	.	.	.	-1	DDX39A	HGNC	17821	protein_coding	YES	CCDS12308.1	ENSP00000242776	DX39A_HUMAN	K7ENP6_HUMAN,K7EN69_HUMAN,K7EL56_HUMAN,K7EIL8_HUMAN	UPI00000713A1	.	deleterious(0)	possibly_damaging(0.774)	4/11	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF212,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATCTGGAA	.	5	ESCA
SSBP4	0	.	GRCh37	19	18543996	18543996	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964G>C	p.Glu322Gln	p.E322Q	ENST00000270061	15/18	28	21	6	19	19	0	SSBP4,missense_variant,p.Glu300Gln,ENST00000348495,;SSBP4,missense_variant,p.Glu93Gln,ENST00000593641,;SSBP4,missense_variant,p.Glu322Gln,ENST00000270061,;ISYNA1,downstream_gene_variant,,ENST00000338128,;ISYNA1,downstream_gene_variant,,ENST00000581800,;SSBP4,downstream_gene_variant,,ENST00000597724,;SSBP4,upstream_gene_variant,,ENST00000599699,;ISYNA1,downstream_gene_variant,,ENST00000581672,;ISYNA1,downstream_gene_variant,,ENST00000457269,;ISYNA1,downstream_gene_variant,,ENST00000578963,;ISYNA1,downstream_gene_variant,,ENST00000317018,;ISYNA1,downstream_gene_variant,,ENST00000578352,;ISYNA1,downstream_gene_variant,,ENST00000545187,;ISYNA1,downstream_gene_variant,,ENST00000583534,;SSBP4,downstream_gene_variant,,ENST00000602088,;SSBP4,downstream_gene_variant,,ENST00000601357,;SSBP4,downstream_gene_variant,,ENST00000600628,;SSBP4,downstream_gene_variant,,ENST00000598159,;SSBP4,non_coding_transcript_exon_variant,,ENST00000601444,;SSBP4,downstream_gene_variant,,ENST00000607020,;SSBP4,downstream_gene_variant,,ENST00000601614,;ISYNA1,downstream_gene_variant,,ENST00000583309,;ISYNA1,downstream_gene_variant,,ENST00000577820,;SSBP4,downstream_gene_variant,,ENST00000600244,;ISYNA1,downstream_gene_variant,,ENST00000582770,;ISYNA1,downstream_gene_variant,,ENST00000582811,;SSBP4,downstream_gene_variant,,ENST00000601919,;ISYNA1,downstream_gene_variant,,ENST00000583816,;ISYNA1,downstream_gene_variant,,ENST00000577916,;ISYNA1,downstream_gene_variant,,ENST00000582287,;	C	ENSG00000130511	ENST00000270061	Transcript	missense_variant	1258	964	322	E/Q	Gag/Cag	.	.	.	1	SSBP4	HGNC	15676	protein_coding	YES	CCDS12378.1	ENSP00000270061	SSBP4_HUMAN	.	UPI0000135F98	.	deleterious_low_confidence(0.01)	probably_damaging(0.999)	15/18	.	Pfam_domain:PF04503,hmmpanther:PTHR12610:SF7,hmmpanther:PTHR12610	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGATGGAGCCT	.	5	ESCA
ZNF101	0	.	GRCh37	19	19779734	19779734	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39C>T	.	.	ENST00000592502	1/4	77	61	15	110	110	0	ZNF101,5_prime_UTR_variant,,ENST00000415784,;ZNF101,5_prime_UTR_variant,,ENST00000541458,;ZNF101,5_prime_UTR_variant,,ENST00000444249,;ZNF101,5_prime_UTR_variant,,ENST00000592502,;ZNF101,5_prime_UTR_variant,,ENST00000318110,;	T	ENSG00000181896	ENST00000592502	Transcript	5_prime_UTR_variant	72	.	.	.	.	.	.	.	1	ZNF101	HGNC	12881	protein_coding	YES	CCDS32971.1	ENSP00000468049	ZN101_HUMAN	Q96F93_HUMAN,Q0VDG9_HUMAN,K7ENV8_HUMAN	UPI0000074138	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCCAGCC	.	5	ESCA
ZNF724P	0	.	GRCh37	19	23414089	23414089	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205G>A	p.Glu69Lys	p.E69K	ENST00000418100	3/4	59	54	4	78	78	0	ZNF724P,missense_variant,p.Glu63Lys,ENST00000597537,;ZNF724P,missense_variant,p.Glu69Lys,ENST00000418100,;ZNF724P,missense_variant,p.Glu69Lys,ENST00000597037,;	T	ENSG00000196081	ENST00000418100	Transcript	missense_variant	323	205	69	E/K	Gag/Aag	COSM1293763,COSM1293762	.	.	-1	ZNF724P	HGNC	32460	protein_coding	YES	.	ENSP00000413411	ZN724_HUMAN	M0R3J2_HUMAN	UPI0000EE61E4	.	tolerated(0.12)	possibly_damaging(0.636)	3/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24384:SF101,hmmpanther:PTHR24384	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCTCATGTC	.	2	ESCA
TLE2	0	.	GRCh37	19	3005824	3005824	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1643delC	p.Pro548GlnfsTer130	p.P548Qfs*130	ENST00000262953	16/20	58	45	13	33	33	0	TLE2,frameshift_variant,p.Pro215GlnfsTer130,ENST00000447365,;TLE2,frameshift_variant,p.Pro426GlnfsTer130,ENST00000455444,;TLE2,frameshift_variant,p.Pro562GlnfsTer130,ENST00000426948,;TLE2,frameshift_variant,p.Pro197GlnfsTer?,ENST00000589364,;TLE2,frameshift_variant,p.Pro426GlnfsTer130,ENST00000443826,;TLE2,frameshift_variant,p.Pro548GlnfsTer130,ENST00000262953,;TLE2,frameshift_variant,p.Pro549GlnfsTer130,ENST00000590536,;TLE2,frameshift_variant,p.Pro562GlnfsTer130,ENST00000591529,;TLE2,intron_variant,,ENST00000586422,;TLE2,downstream_gene_variant,,ENST00000586492,;TLE2,downstream_gene_variant,,ENST00000589205,;TLE2,downstream_gene_variant,,ENST00000587672,;	-	ENSG00000065717	ENST00000262953	Transcript	frameshift_variant	1906	1643	548	P/X	cCa/ca	.	.	.	-1	TLE2	HGNC	11838	protein_coding	YES	CCDS45911.1	ENSP00000262953	TLE2_HUMAN	.	UPI0000137038	.	.	.	16/20	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR10814:SF4,hmmpanther:PTHR10814,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGCTGGGGCT	.	3	ESCA
PSG10P	0	.	GRCh37	19	43348520	43348520	+	RNA	SNP	C	C	T	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1489G>A	.	.	ENST00000501199	6/6	172	123	48	161	161	0	PSG8,intron_variant,,ENST00000401467,;PSG10P,non_coding_transcript_exon_variant,,ENST00000597171,;PSG10P,non_coding_transcript_exon_variant,,ENST00000501199,;	T	ENSG00000248257	ENST00000501199	Transcript	non_coding_transcript_exon_variant	1489	.	.	.	.	COSM997513	.	.	-1	PSG10P	HGNC	9515	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODIFIER	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTCGACTG	.	5	ESCA
CLEC11A	0	.	GRCh37	19	51226822	51226822	+	Missense_Mutation	SNP	C	C	A	rs370035526	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40C>A	p.Gln14Lys	p.Q14K	ENST00000250340	1/4	28	19	8	37	37	0	CLEC11A,missense_variant,p.Gln14Lys,ENST00000250340,;CLEC11A,missense_variant,p.Gln14Lys,ENST00000599973,;SHANK1,upstream_gene_variant,,ENST00000391814,;	A	ENSG00000105472	ENST00000250340	Transcript	missense_variant	237	40	14	Q/K	Cag/Aag	rs370035526	.	.	1	CLEC11A	HGNC	10576	protein_coding	YES	CCDS12800.1	ENSP00000250340	CLC11_HUMAN	.	UPI0000073E53	.	deleterious_low_confidence(0.01)	benign(0.156)	1/4	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22799:SF1,hmmpanther:PTHR22799	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCCAGCTC	byFrequency|byCluster	5	ESCA
ZNF525	0	.	GRCh37	19	53884541	53884541	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.709C>T	p.His237Tyr	p.H237Y	ENST00000474037	4/4	47	39	8	67	67	0	ZNF525,missense_variant,p.His201Tyr,ENST00000467003,;ZNF525,missense_variant,p.His237Tyr,ENST00000474037,;ZNF525,intron_variant,,ENST00000593918,;ZNF525,intron_variant,,ENST00000475179,;ZNF525,upstream_gene_variant,,ENST00000355326,;ZNF525,downstream_gene_variant,,ENST00000491101,;ZNF525,downstream_gene_variant,,ENST00000600148,;ZNF525,upstream_gene_variant,,ENST00000601790,;CTD-3141N22.1,upstream_gene_variant,,ENST00000459631,;	T	ENSG00000203326	ENST00000474037	Transcript	missense_variant	843	709	237	H/Y	Cat/Tat	.	.	.	1	ZNF525	HGNC	29423	protein_coding	YES	.	ENSP00000417696	.	J3KR62_HUMAN,J3KR51_HUMAN	UPI0000EE700C	.	deleterious(0.02)	benign(0.001)	4/4	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24407:SF12,hmmpanther:PTHR24407,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATTCATCTA	.	5	ESCA
SUV420H2	0	.	GRCh37	19	55859477	55859477	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*660G>C	.	.	ENST00000255613	9/9	44	34	10	49	49	0	SUV420H2,3_prime_UTR_variant,,ENST00000255613,;COX6B2,downstream_gene_variant,,ENST00000326529,;COX6B2,downstream_gene_variant,,ENST00000590900,;COX6B2,downstream_gene_variant,,ENST00000593184,;AC020922.1,downstream_gene_variant,,ENST00000539076,;COX6B2,downstream_gene_variant,,ENST00000588572,;SUV420H2,downstream_gene_variant,,ENST00000402499,;SUV420H2,downstream_gene_variant,,ENST00000460956,;COX6B2,downstream_gene_variant,,ENST00000586191,;SUV420H2,downstream_gene_variant,,ENST00000587442,;COX6B2,downstream_gene_variant,,ENST00000589879,;COX6B2,downstream_gene_variant,,ENST00000588586,;SUV420H2,3_prime_UTR_variant,,ENST00000445196,;SUV420H2,downstream_gene_variant,,ENST00000592631,;SUV420H2,downstream_gene_variant,,ENST00000474492,;SUV420H2,downstream_gene_variant,,ENST00000464185,;SUV420H2,downstream_gene_variant,,ENST00000589338,;CTD-2105E13.6,downstream_gene_variant,,ENST00000591954,;SUV420H2,downstream_gene_variant,,ENST00000468951,;	C	ENSG00000133247	ENST00000255613	Transcript	3_prime_UTR_variant	2297	.	.	.	.	.	.	.	1	SUV420H2	HGNC	28405	protein_coding	YES	CCDS12922.1	ENSP00000255613	SV422_HUMAN	.	UPI000000DABC	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGTTATA	.	5	ESCA
C19orf18	0	.	GRCh37	19	58472903	58472903	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388G>C	p.Glu130Gln	p.E130Q	ENST00000314391	5/6	22	19	3	30	30	0	C19orf18,missense_variant,p.Glu130Gln,ENST00000314391,;	G	ENSG00000177025	ENST00000314391	Transcript	missense_variant	490	388	130	E/Q	Gag/Cag	.	.	.	-1	C19orf18	HGNC	28642	protein_coding	YES	CCDS12967.1	ENSP00000321519	CS018_HUMAN	.	UPI000006D09E	.	deleterious(0)	possibly_damaging(0.859)	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCAGCCT	.	2	ESCA
MUC16	0	.	GRCh37	19	9075971	9075971	+	Silent	SNP	T	T	A	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11475A>T	p.%3D	p.P3825P	ENST00000397910	3/84	37	26	11	29	29	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;	A	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	11679	11475	3825	P	ccA/ccT	COSM568615,COSM568614	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	3/84	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G3826E|c.11477G>A|3,BUFFER|p.G3826E|c.11477G>A|3	RADIA|MUTECT|MUSE	TGCCCTGGATG	.	3	ESCA
AMY2B	0	.	GRCh37	1	104113141	104113141	+	Intron	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-46-1038A>G	.	.	ENST00000361355	.	83	77	5	117	117	0	AMY2B,intron_variant,,ENST00000435302,;AMY2B,intron_variant,,ENST00000361355,;AMY2B,intron_variant,,ENST00000453959,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,intron_variant,,ENST00000477657,;ACTG1P4,non_coding_transcript_exon_variant,,ENST00000425123,;	G	ENSG00000240038	ENST00000361355	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	AMY2B	HGNC	478	protein_coding	YES	CCDS782.1	ENSP00000354610	AMY2B_HUMAN	C9JWK7_HUMAN,C9J2Z5_HUMAN	UPI0000000CB1	.	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCACCATGAAG	.	2	ESCA
CSDE1	0	.	GRCh37	1	115259567	115259567	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1223G>A	.	.	ENST00000438362	20/20	15	11	4	11	11	0	CSDE1,3_prime_UTR_variant,,ENST00000358528,;CSDE1,3_prime_UTR_variant,,ENST00000339438,;CSDE1,3_prime_UTR_variant,,ENST00000438362,;CSDE1,downstream_gene_variant,,ENST00000369530,;CSDE1,downstream_gene_variant,,ENST00000261443,;NRAS,upstream_gene_variant,,ENST00000369535,;CSDE1,downstream_gene_variant,,ENST00000530886,;CSDE1,downstream_gene_variant,,ENST00000534699,;CSDE1,downstream_gene_variant,,ENST00000483407,;CSDE1,downstream_gene_variant,,ENST00000483030,;CSDE1,downstream_gene_variant,,ENST00000530784,;	T	ENSG00000009307	ENST00000438362	Transcript	3_prime_UTR_variant	4137	.	.	.	.	.	.	.	-1	CSDE1	HGNC	29905	protein_coding	YES	CCDS55626.1	ENSP00000407724	.	Q9UG93_HUMAN,G5E9Q2_HUMAN,E9PLD4_HUMAN,E9PKN4_HUMAN	UPI0000D99B0F	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATTCGCTTC	.	5	ESCA
SRGAP2B	0	.	GRCh37	1	144013980	144013980	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.995C>G	.	.	ENST00000467933	3/5	91	79	12	77	77	0	SRGAP2B,non_coding_transcript_exon_variant,,ENST00000467933,;SRGAP2B,non_coding_transcript_exon_variant,,ENST00000491897,;	G	ENSG00000196369	ENST00000467933	Transcript	non_coding_transcript_exon_variant	995	.	.	.	.	.	.	.	1	SRGAP2B	HGNC	35237	processed_transcript	YES	.	.	.	.	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCTCCAGGA	.	4	ESCA
BCL9	0	.	GRCh37	1	147086253	147086253	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398C>T	p.Ser133Phe	p.S133F	ENST00000234739	6/10	46	39	6	58	58	0	BCL9,missense_variant,p.Ser133Phe,ENST00000234739,;BCL9,non_coding_transcript_exon_variant,,ENST00000473292,;BCL9,downstream_gene_variant,,ENST00000497938,;	T	ENSG00000116128	ENST00000234739	Transcript	missense_variant	1138	398	133	S/F	tCc/tTc	.	.	.	1	BCL9	HGNC	1008	protein_coding	YES	CCDS30833.1	ENSP00000234739	BCL9_HUMAN	.	UPI000013C9B9	.	tolerated(0.09)	benign(0.002)	6/10	.	hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAGTCCCAGG	.	4	ESCA
BCL9	0	.	GRCh37	1	147096909	147096909	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*149G>C	.	.	ENST00000234739	10/10	39	32	7	35	35	0	BCL9,3_prime_UTR_variant,,ENST00000234739,;ACP6,downstream_gene_variant,,ENST00000609196,;	C	ENSG00000116128	ENST00000234739	Transcript	3_prime_UTR_variant	5170	.	.	.	.	.	.	.	1	BCL9	HGNC	1008	protein_coding	YES	CCDS30833.1	ENSP00000234739	BCL9_HUMAN	.	UPI000013C9B9	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCGAGAATGT	.	5	ESCA
OR10X1	0	.	GRCh37	1	158549211	158549211	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479T>A	p.Leu160His	p.L160H	ENST00000368150	1/1	32	27	4	35	35	0	OR10X1,missense_variant,p.Leu160His,ENST00000368150,;	T	ENSG00000186400	ENST00000368150	Transcript	missense_variant	479	479	160	L/H	cTt/cAt	.	.	.	-1	OR10X1	HGNC	14995	protein_coding	YES	CCDS30900.1	ENSP00000357132	O10X1_HUMAN	.	UPI000004CA20	.	deleterious(0.01)	benign(0.182)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF195,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACAAGTTGT	.	4	ESCA
FCGR2C	0	.	GRCh37	1	161561031	161561031	+	5'Flank	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000543859	.	44	35	8	50	50	0	FCGR2B,intron_variant,,ENST00000403078,;FCGR2B,intron_variant,,ENST00000367960,;FCGR2B,intron_variant,,ENST00000428605,;FCGR2B,intron_variant,,ENST00000367962,;FCGR3A,intron_variant,,ENST00000540048,;FCGR2C,upstream_gene_variant,,ENST00000543859,;FCGR2C,non_coding_transcript_exon_variant,,ENST00000473530,;FCGR2C,non_coding_transcript_exon_variant,,ENST00000482226,;FCGR2C,non_coding_transcript_exon_variant,,ENST00000473712,;FCGR2C,non_coding_transcript_exon_variant,,ENST00000465075,;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR2C,downstream_gene_variant,,ENST00000502411,;FCGR2C,upstream_gene_variant,,ENST00000507374,;FCGR2C,upstream_gene_variant,,ENST00000467903,;FCGR2C,downstream_gene_variant,,ENST00000496692,;FCGR2C,synonymous_variant,p.%3D,ENST00000466542,;	T	ENSG00000244682	ENST00000543859	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4312	1	FCGR2C	HGNC	15626	protein_coding	YES	.	ENSP00000444663	.	Q8TEX8_HUMAN	UPI000006E0EC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AAGGTCACATT	.	3	ESCA
FMO4	0	.	GRCh37	1	171303853	171303853	+	Missense_Mutation	SNP	C	C	G	rs776094653	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1131C>G	p.Ile377Met	p.I377M	ENST00000367749	8/10	33	19	13	19	19	0	FMO4,missense_variant,p.Ile377Met,ENST00000367749,;FMO4,non_coding_transcript_exon_variant,,ENST00000480136,;FMO4,intron_variant,,ENST00000475780,;FMO4,downstream_gene_variant,,ENST00000462992,;	G	ENSG00000076258	ENST00000367749	Transcript	missense_variant	1461	1131	377	I/M	atC/atG	rs776094653	.	.	1	FMO4	HGNC	3772	protein_coding	YES	CCDS1295.1	ENSP00000356723	FMO4_HUMAN	.	UPI000013C52B	.	tolerated(0.09)	probably_damaging(0.984)	8/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23023,hmmpanther:PTHR23023:SF74,Pfam_domain:PF00743,Gene3D:3.50.50.60,PIRSF_domain:PIRSF000332,Superfamily_domains:SSF51905,Prints_domain:PR00370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATCTTATC	.	5	ESCA
RASAL2	0	.	GRCh37	1	178062346	178062346	+	5'Flank	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000367649	.	38	32	6	35	35	0	RASAL2,upstream_gene_variant,,ENST00000367649,;RASAL2,upstream_gene_variant,,ENST00000448150,;RASAL2-AS1,non_coding_transcript_exon_variant,,ENST00000419458,;RASAL2-AS1,non_coding_transcript_exon_variant,,ENST00000452867,;RASAL2-AS1,non_coding_transcript_exon_variant,,ENST00000421505,;	A	ENSG00000075391	ENST00000367649	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	930	1	RASAL2	HGNC	9874	protein_coding	YES	CCDS1321.2	ENSP00000356621	NGAP_HUMAN	Q8IW42_HUMAN,Q6P4F9_HUMAN	UPI00019B254F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTGAGAGG	.	5	ESCA
TDRD5	0	.	GRCh37	1	179659934	179659934	+	Silent	SNP	G	G	A	rs371987660	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2964G>A	p.%3D	p.L988L	ENST00000444136	18/18	43	34	8	29	29	0	TDRD5,synonymous_variant,p.%3D,ENST00000367614,;TDRD5,synonymous_variant,p.%3D,ENST00000417329,;TDRD5,synonymous_variant,p.%3D,ENST00000444136,;TDRD5,synonymous_variant,p.%3D,ENST00000294848,;	A	ENSG00000162782	ENST00000444136	Transcript	synonymous_variant	3214	2964	988	L	ttG/ttA	rs371987660	.	.	1	TDRD5	HGNC	20614	protein_coding	YES	CCDS55663.1	ENSP00000406052	TDRD5_HUMAN	.	UPI000022AC96	.	.	.	18/18	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTGATTTT	byFrequency|byCluster	5	ESCA
EMC1	0	.	GRCh37	1	19559457	19559457	+	Missense_Mutation	SNP	C	C	G	rs753353617	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1605G>C	p.Met535Ile	p.M535I	ENST00000477853	14/23	88	71	16	100	100	0	EMC1,missense_variant,p.Met513Ile,ENST00000375208,;EMC1,missense_variant,p.Met534Ile,ENST00000375199,;EMC1,missense_variant,p.Met535Ile,ENST00000477853,;RP1-43E13.2,intron_variant,,ENST00000437898,;EMC1,upstream_gene_variant,,ENST00000494770,;	G	ENSG00000127463	ENST00000477853	Transcript	missense_variant	1648	1605	535	M/I	atG/atC	rs753353617	.	.	-1	EMC1	HGNC	28957	protein_coding	YES	CCDS190.1	ENSP00000420608	EMC1_HUMAN	.	UPI0000070A23	.	deleterious(0.01)	benign(0.059)	14/23	.	hmmpanther:PTHR21573,hmmpanther:PTHR21573:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATCATCTT	.	5	ESCA
ASPM	0	.	GRCh37	1	197071323	197071323	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7058G>A	p.Arg2353Lys	p.R2353K	ENST00000367409	18/28	61	39	21	48	48	0	ASPM,missense_variant,p.Arg2353Lys,ENST00000367409,;ASPM,intron_variant,,ENST00000367408,;ASPM,intron_variant,,ENST00000294732,;	T	ENSG00000066279	ENST00000367409	Transcript	missense_variant	7315	7058	2353	R/K	aGa/aAa	.	.	.	-1	ASPM	HGNC	19048	protein_coding	YES	CCDS1389.1	ENSP00000356379	ASPM_HUMAN	.	UPI0000458904	.	tolerated(0.22)	benign(0.042)	18/28	.	PROSITE_profiles:PS50096,hmmpanther:PTHR25069:SF115,hmmpanther:PTHR25069,Pfam_domain:PF00612,SMART_domains:SM00015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATATCTCATA	.	5	ESCA
CD46	0	.	GRCh37	1	207967081	207967081	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*145G>C	.	.	ENST00000322875	13/13	35	26	9	12	12	0	CD46,3_prime_UTR_variant,,ENST00000360212,;CD46,3_prime_UTR_variant,,ENST00000441839,;CD46,3_prime_UTR_variant,,ENST00000322918,;CD46,3_prime_UTR_variant,,ENST00000358170,;CD46,3_prime_UTR_variant,,ENST00000354848,;CD46,3_prime_UTR_variant,,ENST00000367042,;CD46,3_prime_UTR_variant,,ENST00000357714,;CD46,3_prime_UTR_variant,,ENST00000367047,;CD46,3_prime_UTR_variant,,ENST00000361067,;CD46,3_prime_UTR_variant,,ENST00000367041,;CD46,3_prime_UTR_variant,,ENST00000322875,;CD46,intron_variant,,ENST00000462968,;CD46,downstream_gene_variant,,ENST00000480003,;CD46,non_coding_transcript_exon_variant,,ENST00000488596,;CD46,non_coding_transcript_exon_variant,,ENST00000469535,;	C	ENSG00000117335	ENST00000322875	Transcript	3_prime_UTR_variant	1501	.	.	.	.	.	.	.	1	CD46	HGNC	6953	protein_coding	YES	CCDS1482.1	ENSP00000313875	MCP_HUMAN	Q06C42_HUMAN	UPI000015FF6E	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTTGATGCT	.	2	ESCA
USH2A	0	.	GRCh37	1	216144008	216144008	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6916G>A	p.Val2306Ile	p.V2306I	ENST00000307340	36/72	38	21	17	55	55	0	USH2A,missense_variant,p.Val2306Ile,ENST00000366943,;USH2A,missense_variant,p.Val2306Ile,ENST00000307340,;	T	ENSG00000042781	ENST00000307340	Transcript	missense_variant	7303	6916	2306	V/I	Gtc/Atc	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	benign(0.244)	36/72	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGACTCTGA	.	5	ESCA
SPATA17	0	.	GRCh37	1	217856693	217856693	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385G>A	p.Asp129Asn	p.D129N	ENST00000366933	5/11	39	35	4	30	30	0	SPATA17,missense_variant,p.Asp129Asn,ENST00000366933,;SPATA17,3_prime_UTR_variant,,ENST00000470448,;	A	ENSG00000162814	ENST00000366933	Transcript	missense_variant	440	385	129	D/N	Gat/Aat	.	.	.	1	SPATA17	HGNC	25184	protein_coding	YES	CCDS1519.1	ENSP00000355900	SPT17_HUMAN	R4GN71_HUMAN	UPI00000717C2	.	deleterious(0.05)	benign(0.009)	5/11	.	hmmpanther:PTHR22706,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S125*|c.374C>G|5	RADIA|MUTECT|VARSCANS	CCAATGATGCA	.	3	ESCA
SIPA1L2	0	.	GRCh37	1	232607242	232607242	+	Silent	SNP	G	G	A	rs200442380	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2118C>T	p.%3D	p.I706I	ENST00000366630	7/22	71	29	42	44	44	0	SIPA1L2,synonymous_variant,p.%3D,ENST00000366630,;SIPA1L2,synonymous_variant,p.%3D,ENST00000262861,;	A	ENSG00000116991	ENST00000366630	Transcript	synonymous_variant	2477	2118	706	I	atC/atT	rs200442380	.	.	-1	SIPA1L2	HGNC	23800	protein_coding	YES	CCDS41474.1	ENSP00000355589	SI1L2_HUMAN	.	UPI00001D7D6A	.	.	.	7/22	.	Superfamily_domains:0043732,Pfam_domain:PF02145,hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711,PROSITE_profiles:PS50085	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGACGATGTC	by1000G	5	ESCA
RPL11	0	.	GRCh37	1	24019156	24019156	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64C>G	p.Leu22Val	p.L22V	ENST00000374550	2/6	32	26	6	32	32	0	RPL11,missense_variant,p.Leu20Val,ENST00000443624,;RPL11,missense_variant,p.Leu20Val,ENST00000458455,;RPL11,missense_variant,p.Leu22Val,ENST00000374550,;RPL11,non_coding_transcript_exon_variant,,ENST00000467075,;RPL11,non_coding_transcript_exon_variant,,ENST00000482370,;	G	ENSG00000142676	ENST00000374550	Transcript	missense_variant	109	64	22	L/V	Ctc/Gtc	.	.	.	1	RPL11	HGNC	10301	protein_coding	YES	CCDS238.1	ENSP00000363676	RL11_HUMAN	Q5VVD0_HUMAN,Q5VVC9_HUMAN	UPI00000019F7	.	tolerated(0.3)	benign(0.37)	2/6	.	hmmpanther:PTHR11994,Gene3D:3.30.1440.10,Pfam_domain:PF00281,PIRSF_domain:PIRSF002161,Superfamily_domains:SSF55282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTCTCAAC	.	5	ESCA
PLD5	0	.	GRCh37	1	242271125	242271125	+	Silent	SNP	A	A	G	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1087T>C	p.%3D	p.L363L	ENST00000536534	8/10	46	43	3	35	35	0	PLD5,synonymous_variant,p.%3D,ENST00000536534,;PLD5,synonymous_variant,p.%3D,ENST00000427495,;PLD5,synonymous_variant,p.%3D,ENST00000442594,;PLD5,3_prime_UTR_variant,,ENST00000366545,;PLD5,3_prime_UTR_variant,,ENST00000314833,;	G	ENSG00000180287	ENST00000536534	Transcript	synonymous_variant	1329	1087	363	L	Ttg/Ctg	COSM3771670,COSM3771669	.	.	-1	PLD5	HGNC	26879	protein_coding	YES	CCDS1621.2	ENSP00000440896	PLD5_HUMAN	J3KP61_HUMAN	UPI000040E1A4	.	.	.	8/10	.	hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185,Pfam_domain:PF13918,Gene3D:3.30.870.10,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCAAGTCTG	.	2	ESCA
OR14K1	0	.	GRCh37	1	247902091	247902091	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175T>A	p.Phe59Ile	p.F59I	ENST00000283225	1/1	95	89	6	76	76	0	OR14K1,missense_variant,p.Phe59Ile,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,;	A	ENSG00000153230	ENST00000283225	Transcript	missense_variant	175	175	59	F/I	Ttt/Att	.	.	.	1	OR14K1	HGNC	15025	protein_coding	YES	.	ENSP00000283225	O14K1_HUMAN	.	UPI0000041CBA	.	deleterious(0.01)	probably_damaging(0.965)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF242,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTACTTTTTC	.	2	ESCA
SZT2	0	.	GRCh37	1	43916150	43916150	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10127G>A	p.%3D	p.%3D	ENST00000562955	71/71	26	23	3	23	23	0	SZT2,stop_retained_variant,p.%3D,ENST00000372442,;SZT2,stop_retained_variant,p.%3D,ENST00000562955,;HYI,downstream_gene_variant,,ENST00000487366,;HYI,downstream_gene_variant,,ENST00000372425,;HYI,downstream_gene_variant,,ENST00000486909,;HYI,downstream_gene_variant,,ENST00000583037,;HYI,downstream_gene_variant,,ENST00000372434,;HYI,downstream_gene_variant,,ENST00000372433,;HYI,downstream_gene_variant,,ENST00000470662,;HYI,downstream_gene_variant,,ENST00000372430,;HYI,downstream_gene_variant,,ENST00000372432,;HYI,downstream_gene_variant,,ENST00000372426,;SZT2-AS1,upstream_gene_variant,,ENST00000396885,;HYI-AS1,upstream_gene_variant,,ENST00000444386,;SZT2,non_coding_transcript_exon_variant,,ENST00000460536,;HYI,downstream_gene_variant,,ENST00000483618,;HYI,downstream_gene_variant,,ENST00000469587,;HYI,downstream_gene_variant,,ENST00000496142,;HYI,downstream_gene_variant,,ENST00000372427,;	A	ENSG00000198198	ENST00000562955	Transcript	stop_retained_variant	10127	10127	3376	*	tGa/tAa	.	.	.	1	SZT2	HGNC	29040	protein_coding	YES	CCDS30694.2	ENSP00000457168	SZT2_HUMAN	.	UPI0001E24F46	.	.	.	71/71	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCTGAGGGA	.	2	ESCA
CCDC163P	0	.	GRCh37	1	45963037	45963037	+	Missense_Mutation	SNP	G	G	T	rs746392850	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196C>A	p.Pro66Thr	p.P66T	ENST00000488405	3/4	14	11	3	30	30	0	CCDC163P,missense_variant,p.Pro66Thr,ENST00000490551,;CCDC163P,missense_variant,p.Pro66Thr,ENST00000432082,;CCDC163P,missense_variant,p.Pro66Thr,ENST00000488405,;MMACHC,upstream_gene_variant,,ENST00000401061,;CCDC163P,non_coding_transcript_exon_variant,,ENST00000486476,;CCDC163P,non_coding_transcript_exon_variant,,ENST00000502793,;CCDC163P,missense_variant,p.Pro66Thr,ENST00000415578,;CCDC163P,missense_variant,p.Pro66Thr,ENST00000514299,;CCDC163P,intron_variant,,ENST00000515561,;	T	ENSG00000236624	ENST00000488405	Transcript	missense_variant	440	196	66	P/T	Cct/Act	rs746392850	.	.	-1	CCDC163P	HGNC	27003	protein_coding	YES	.	ENSP00000432622	.	E9PPK7_HUMAN	UPI000019722E	.	deleterious_low_confidence(0.04)	possibly_damaging(0.803)	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCAGGAGTGA	.	2	ESCA
BEND5	0	.	GRCh37	1	49193621	49193621	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1203C>G	p.Ile401Met	p.I401M	ENST00000371833	6/6	55	46	8	68	68	0	BEND5,missense_variant,p.Ile401Met,ENST00000371833,;AGBL4,intron_variant,,ENST00000371839,;AGBL4,intron_variant,,ENST00000416121,;AGBL4,intron_variant,,ENST00000371838,;BEND5,non_coding_transcript_exon_variant,,ENST00000476096,;BEND5,non_coding_transcript_exon_variant,,ENST00000476079,;BEND5,non_coding_transcript_exon_variant,,ENST00000463562,;	C	ENSG00000162373	ENST00000371833	Transcript	missense_variant	1290	1203	401	I/M	atC/atG	.	.	.	-1	BEND5	HGNC	25668	protein_coding	YES	CCDS552.2	ENSP00000360899	BEND5_HUMAN	.	UPI00002042F4	.	deleterious(0)	probably_damaging(0.999)	6/6	.	PROSITE_profiles:PS51457,hmmpanther:PTHR14628	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATGATTTT	.	5	ESCA
USP1	0	.	GRCh37	1	62907260	62907260	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272A>G	p.Tyr91Cys	p.Y91C	ENST00000339950	3/9	36	25	10	26	26	0	USP1,missense_variant,p.Tyr91Cys,ENST00000371146,;USP1,missense_variant,p.Tyr91Cys,ENST00000452143,;USP1,missense_variant,p.Tyr91Cys,ENST00000339950,;USP1,downstream_gene_variant,,ENST00000442679,;	G	ENSG00000162607	ENST00000339950	Transcript	missense_variant	1087	272	91	Y/C	tAt/tGt	.	.	.	1	USP1	HGNC	12607	protein_coding	YES	CCDS621.1	ENSP00000343526	UBP1_HUMAN	C9JWX4_HUMAN,C9JC88_HUMAN	UPI00001379D4	.	deleterious(0)	probably_damaging(1)	3/9	.	Superfamily_domains:SSF54001,Pfam_domain:PF00443,PROSITE_patterns:PS00972,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF378,PROSITE_profiles:PS50235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCTATCTTA	.	5	ESCA
DLEU2L	0	.	GRCh37	1	64014721	64014721	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-258C>T	.	.	ENST00000371086	1/2	33	28	5	30	30	0	DLEU2L,5_prime_UTR_variant,,ENST00000371086,;DLEU2L,5_prime_UTR_variant,,ENST00000340052,;EFCAB7,intron_variant,,ENST00000371088,;EFCAB7,intron_variant,,ENST00000496956,;ITGB3BP,intron_variant,,ENST00000478138,;EFCAB7,intron_variant,,ENST00000460678,;	T	ENSG00000116652	ENST00000371086	Transcript	5_prime_UTR_variant	134	.	.	.	.	.	.	.	1	DLEU2L	HGNC	13225	protein_coding	YES	.	ENSP00000360127	.	Q5JX12_HUMAN	UPI0000470A6D	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCGCCGGAA	.	4	ESCA
DNAJC11	0	.	GRCh37	1	6704700	6704700	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015G>T	p.Ala339Ser	p.A339S	ENST00000377577	10/16	23	17	6	20	20	0	DNAJC11,missense_variant,p.Ala249Ser,ENST00000377573,;DNAJC11,missense_variant,p.Ala339Ser,ENST00000294401,;DNAJC11,missense_variant,p.Ala339Ser,ENST00000377577,;DNAJC11,missense_variant,p.Ala301Ser,ENST00000542246,;DNAJC11,intron_variant,,ENST00000349363,;DNAJC11,intron_variant,,ENST00000451196,;DNAJC11,downstream_gene_variant,,ENST00000426784,;DNAJC11,non_coding_transcript_exon_variant,,ENST00000472414,;DNAJC11,non_coding_transcript_exon_variant,,ENST00000465508,;DNAJC11,downstream_gene_variant,,ENST00000473993,;	A	ENSG00000007923	ENST00000377577	Transcript	missense_variant	1139	1015	339	A/S	Gct/Tct	.	.	.	-1	DNAJC11	HGNC	25570	protein_coding	YES	CCDS87.1	ENSP00000366800	DJC11_HUMAN	F5H1N1_HUMAN,B3KTC6_HUMAN	UPI000020544B	.	deleterious(0.03)	benign(0.04)	10/16	.	hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGCTCCGT	.	5	ESCA
PRKACB	0	.	GRCh37	1	84701429	84701429	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*441C>G	.	.	ENST00000370685	10/10	73	50	23	73	73	0	PRKACB,3_prime_UTR_variant,,ENST00000394839,;PRKACB,3_prime_UTR_variant,,ENST00000370689,;PRKACB,3_prime_UTR_variant,,ENST00000394838,;PRKACB,3_prime_UTR_variant,,ENST00000370685,;PRKACB,3_prime_UTR_variant,,ENST00000370682,;	G	ENSG00000142875	ENST00000370685	Transcript	3_prime_UTR_variant	1729	.	.	.	.	.	.	.	1	PRKACB	HGNC	9381	protein_coding	YES	CCDS693.1	ENSP00000359719	KAPCB_HUMAN	.	UPI00001A9CCB	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTCTAATA	.	5	ESCA
TGFBR3	0	.	GRCh37	1	92193264	92193264	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837C>G	p.%3D	p.V279V	ENST00000212355	7/17	31	26	5	35	35	0	TGFBR3,synonymous_variant,p.%3D,ENST00000525962,;TGFBR3,synonymous_variant,p.%3D,ENST00000370399,;TGFBR3,synonymous_variant,p.%3D,ENST00000212355,;TGFBR3,synonymous_variant,p.%3D,ENST00000465892,;TGFBR3,downstream_gene_variant,,ENST00000468996,;TGFBR3,3_prime_UTR_variant,,ENST00000532540,;TGFBR3,3_prime_UTR_variant,,ENST00000533089,;TGFBR3,non_coding_transcript_exon_variant,,ENST00000529608,;	C	ENSG00000069702	ENST00000212355	Transcript	synonymous_variant	1303	837	279	V	gtC/gtG	.	.	.	-1	TGFBR3	HGNC	11774	protein_coding	YES	CCDS30770.1	ENSP00000212355	TGBR3_HUMAN	E9PAW7_HUMAN	UPI000049D997	.	.	.	7/17	.	hmmpanther:PTHR14002,hmmpanther:PTHR14002:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTTGACAGA	.	5	ESCA
TGFBR3	0	.	GRCh37	1	92224237	92224237	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.317C>T	p.Ser106Phe	p.S106F	ENST00000212355	4/17	49	43	6	58	58	0	TGFBR3,missense_variant,p.Ser106Phe,ENST00000525962,;TGFBR3,missense_variant,p.Ser106Phe,ENST00000370399,;TGFBR3,missense_variant,p.Ser106Phe,ENST00000212355,;TGFBR3,missense_variant,p.Ser106Phe,ENST00000465892,;TGFBR3,non_coding_transcript_exon_variant,,ENST00000468996,;TGFBR3,3_prime_UTR_variant,,ENST00000532540,;TGFBR3,3_prime_UTR_variant,,ENST00000533089,;	A	ENSG00000069702	ENST00000212355	Transcript	missense_variant	783	317	106	S/F	tCc/tTc	COSM1667705	.	.	-1	TGFBR3	HGNC	11774	protein_coding	YES	CCDS30770.1	ENSP00000212355	TGBR3_HUMAN	E9PAW7_HUMAN	UPI000049D997	.	deleterious(0)	probably_damaging(1)	4/17	.	hmmpanther:PTHR14002,hmmpanther:PTHR14002:SF5	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GTGGGGAGTTG	.	3	ESCA
VSX1	0	.	GRCh37	20	25053267	25053267	+	3'Flank	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000376709	.	57	41	15	70	70	0	VSX1,missense_variant,p.Leu274Ser,ENST00000424574,;VSX1,missense_variant,p.Trp214Arg,ENST00000451258,;VSX1,intron_variant,,ENST00000429762,;VSX1,intron_variant,,ENST00000444511,;VSX1,downstream_gene_variant,,ENST00000376709,;VSX1,missense_variant,p.Trp214Arg,ENST00000409958,;VSX1,missense_variant,p.Leu274Ser,ENST00000409285,;VSX1,downstream_gene_variant,,ENST00000557285,;	G	ENSG00000100987	ENST00000376709	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2837	-1	VSX1	HGNC	12723	protein_coding	YES	CCDS13168.1	ENSP00000365899	VSX1_HUMAN	.	UPI0000138E43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCAATGTC	.	5	ESCA
TPX2	0	.	GRCh37	20	30380547	30380547	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1423G>C	p.Glu475Gln	p.E475Q	ENST00000300403	13/18	32	20	11	29	29	0	TPX2,missense_variant,p.Glu475Gln,ENST00000300403,;TPX2,missense_variant,p.Glu511Gln,ENST00000340513,;	C	ENSG00000088325	ENST00000300403	Transcript	missense_variant	1951	1423	475	E/Q	Gaa/Caa	.	.	.	1	TPX2	HGNC	1249	protein_coding	YES	CCDS13190.1	ENSP00000300403	TPX2_HUMAN	Q96FC3_HUMAN,Q643R0_HUMAN,B3KM90_HUMAN	UPI00000015BB	.	tolerated(0.06)	possibly_damaging(0.517)	13/18	.	hmmpanther:PTHR14326,hmmpanther:PTHR14326:SF9,Pfam_domain:PF12214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTGAAAAG	.	5	ESCA
HCK	0	.	GRCh37	20	30671780	30671780	+	Missense_Mutation	SNP	G	G	A	rs200896933	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616G>A	p.Gly206Arg	p.G206R	ENST00000375852	7/13	26	23	3	24	24	0	HCK,missense_variant,p.Gly185Arg,ENST00000520553,;HCK,missense_variant,p.Gly205Arg,ENST00000375862,;HCK,missense_variant,p.Gly206Arg,ENST00000375852,;HCK,missense_variant,p.Gly184Arg,ENST00000518730,;HCK,missense_variant,p.Gly186Arg,ENST00000534862,;HCK,missense_variant,p.Gly185Arg,ENST00000538448,;HCK,3_prime_UTR_variant,,ENST00000486475,;HCK,3_prime_UTR_variant,,ENST00000262651,;	A	ENSG00000101336	ENST00000375852	Transcript	missense_variant	780	616	206	G/R	Ggg/Agg	rs200896933	.	.	1	HCK	HGNC	4840	protein_coding	YES	CCDS33460.1	ENSP00000365012	.	J3KPD6_HUMAN	UPI000013D2F5	.	deleterious(0)	probably_damaging(0.987)	7/13	.	PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF181,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAACGGGGGC	byFrequency|byCluster	2	ESCA
CHD6	0	.	GRCh37	20	40045236	40045236	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6478A>G	p.Ile2160Val	p.I2160V	ENST00000373233	33/37	42	34	7	31	31	0	CHD6,missense_variant,p.Ile2160Val,ENST00000373233,;CHD6,upstream_gene_variant,,ENST00000480022,;	C	ENSG00000124177	ENST00000373233	Transcript	missense_variant	6656	6478	2160	I/V	Atc/Gtc	.	.	.	-1	CHD6	HGNC	19057	protein_coding	YES	CCDS13317.1	ENSP00000362330	CHD6_HUMAN	.	UPI0000168656	.	tolerated(1)	benign(0.001)	33/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGATCTGGG	.	5	ESCA
GMEB2	0	.	GRCh37	20	62223484	62223484	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843C>G	p.%3D	p.L281L	ENST00000266068	8/9	24	14	10	24	24	0	GMEB2,synonymous_variant,p.%3D,ENST00000266068,;GMEB2,synonymous_variant,p.%3D,ENST00000370069,;GMEB2,synonymous_variant,p.%3D,ENST00000370077,;	C	ENSG00000101216	ENST00000266068	Transcript	synonymous_variant	1322	843	281	L	ctC/ctG	.	.	.	-1	GMEB2	HGNC	4371	protein_coding	YES	CCDS13528.1	ENSP00000266068	GMEB2_HUMAN	Q659E7_HUMAN,Q5JTV1_HUMAN	UPI000012B8AD	.	.	.	8/9	.	hmmpanther:PTHR10417,hmmpanther:PTHR10417:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTGAGAAG	.	5	ESCA
TTC3	0	.	GRCh37	21	38462544	38462544	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438C>A	p.Phe146Leu	p.F146L	ENST00000399017	6/46	37	32	5	36	36	0	TTC3,missense_variant,p.Phe146Leu,ENST00000354749,;TTC3,missense_variant,p.Phe146Leu,ENST00000355666,;TTC3,missense_variant,p.Phe146Leu,ENST00000418766,;TTC3,missense_variant,p.Phe146Leu,ENST00000399010,;TTC3,missense_variant,p.Phe146Leu,ENST00000450533,;TTC3,missense_variant,p.Phe146Leu,ENST00000399017,;TTC3,intron_variant,,ENST00000438055,;TTC3,intron_variant,,ENST00000540756,;TTC3,non_coding_transcript_exon_variant,,ENST00000479930,;TTC3,non_coding_transcript_exon_variant,,ENST00000485402,;TTC3,non_coding_transcript_exon_variant,,ENST00000484047,;TTC3,intron_variant,,ENST00000492275,;TTC3,intron_variant,,ENST00000481605,;TTC3,intron_variant,,ENST00000494243,;TTC3,intron_variant,,ENST00000463216,;TTC3,upstream_gene_variant,,ENST00000491952,;TTC3,upstream_gene_variant,,ENST00000460328,;	A	ENSG00000182670	ENST00000399017	Transcript	missense_variant	3185	438	146	F/L	ttC/ttA	.	.	.	1	TTC3	HGNC	12393	protein_coding	YES	CCDS13651.1	ENSP00000381981	TTC3_HUMAN	E9PMS7_HUMAN,E9PMP8_HUMAN	UPI00001B043E	.	tolerated(0.29)	benign(0.004)	6/46	.	hmmpanther:PTHR17550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TCATTCCTTAT	.	3	ESCA
LINC00205	0	.	GRCh37	21	46716123	46716123	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.245C>G	.	.	ENST00000433465	2/2	38	28	10	44	44	0	LINC00205,non_coding_transcript_exon_variant,,ENST00000433465,;LINC00315,downstream_gene_variant,,ENST00000441947,;BX322557.10,downstream_gene_variant,,ENST00000400362,;	G	ENSG00000223768	ENST00000433465	Transcript	non_coding_transcript_exon_variant	245	.	.	.	.	.	.	.	1	LINC00205	HGNC	16420	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCTCCCTCC	.	5	ESCA
CCT8L2	0	.	GRCh37	22	17072414	17072414	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027A>T	p.Arg343Trp	p.R343W	ENST00000359963	1/1	48	38	10	61	61	0	CCT8L2,missense_variant,p.Arg343Trp,ENST00000359963,;FABP5P11,downstream_gene_variant,,ENST00000430910,;	A	ENSG00000198445	ENST00000359963	Transcript	missense_variant	1287	1027	343	R/W	Agg/Tgg	.	.	.	-1	CCT8L2	HGNC	15553	protein_coding	YES	CCDS13738.1	ENSP00000353048	TCPQM_HUMAN	.	UPI000006CF87	.	deleterious(0)	possibly_damaging(0.61)	1/1	.	Superfamily_domains:SSF52029,Pfam_domain:PF00118,Gene3D:3.50.7.10,hmmpanther:PTHR11353:SF70,hmmpanther:PTHR11353,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCTCTGGG	.	5	ESCA
DGCR2	0	.	GRCh37	22	19028769	19028769	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1198G>C	p.Asp400His	p.D400H	ENST00000263196	9/10	34	26	7	35	35	0	DGCR2,missense_variant,p.Asp400His,ENST00000263196,;DGCR2,missense_variant,p.Asp359His,ENST00000537045,;DGCR2,3_prime_UTR_variant,,ENST00000545799,;Y_RNA,upstream_gene_variant,,ENST00000384012,;DGCR11,downstream_gene_variant,,ENST00000609958,;DGCR2,missense_variant,p.Asp176His,ENST00000389262,;DGCR2,non_coding_transcript_exon_variant,,ENST00000467659,;	G	ENSG00000070413	ENST00000263196	Transcript	missense_variant	1446	1198	400	D/H	Gat/Cat	.	.	.	-1	DGCR2	HGNC	2845	protein_coding	YES	CCDS33598.1	ENSP00000263196	IDD_HUMAN	B7Z8B7_HUMAN,B7Z3C4_HUMAN	UPI0000001613	.	deleterious(0)	probably_damaging(0.998)	9/10	.	hmmpanther:PTHR15256	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAATCAAAGC	.	5	ESCA
CLTCL1	0	.	GRCh37	22	19263189	19263189	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207G>C	p.Glu69Asp	p.E69D	ENST00000263200	2/33	41	37	3	39	39	0	CLTCL1,missense_variant,p.Glu69Asp,ENST00000449918,;CLTCL1,missense_variant,p.Glu69Asp,ENST00000427926,;CLTCL1,missense_variant,p.Glu69Asp,ENST00000263200,;CLTCL1,missense_variant,p.Glu69Asp,ENST00000353891,;CLTCL1,missense_variant,p.Glu69Asp,ENST00000505027,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000413132,;	G	ENSG00000070371	ENST00000263200	Transcript	missense_variant	280	207	69	E/D	gaG/gaC	.	.	.	-1	CLTCL1	HGNC	2093	protein_coding	YES	CCDS46662.1	ENSP00000445677	CLH2_HUMAN	.	UPI0000127ABE	.	tolerated(1)	benign(0.006)	2/33	.	hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Gene3D:3gc3B00,PIRSF_domain:PIRSF002290,Superfamily_domains:0046096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCACTCTCTGC	.	3	ESCA
C22orf23	0	.	GRCh37	22	38343465	38343465	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>C	p.Asp58His	p.D58H	ENST00000249079	4/7	37	33	4	59	59	0	C22orf23,missense_variant,p.Asp58His,ENST00000403305,;C22orf23,missense_variant,p.Asp58His,ENST00000422191,;C22orf23,missense_variant,p.Asp58His,ENST00000403026,;C22orf23,missense_variant,p.Asp58His,ENST00000249079,;C22orf23,missense_variant,p.Asp58His,ENST00000418863,;MICALL1,downstream_gene_variant,,ENST00000215957,;RP5-1039K5.17,upstream_gene_variant,,ENST00000609976,;	G	ENSG00000128346	ENST00000249079	Transcript	missense_variant	429	172	58	D/H	Gat/Cat	.	.	.	-1	C22orf23	HGNC	18589	protein_coding	YES	CCDS13962.1	ENSP00000249079	EVG1_HUMAN	B0QYM2_HUMAN,B0QYM1_HUMAN	UPI0000001601	.	deleterious(0.04)	possibly_damaging(0.863)	4/7	.	Pfam_domain:PF05250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCATCTCCTC	.	2	ESCA
TOB2	0	.	GRCh37	22	41832168	41832168	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*147G>A	.	.	ENST00000327492	2/2	14	9	5	10	10	0	TOB2,3_prime_UTR_variant,,ENST00000327492,;TOB2,downstream_gene_variant,,ENST00000434408,;CTA-223H9.9,downstream_gene_variant,,ENST00000609612,;	T	ENSG00000183864	ENST00000327492	Transcript	3_prime_UTR_variant	1889	.	.	.	.	.	.	.	-1	TOB2	HGNC	11980	protein_coding	YES	CCDS14015.1	ENSP00000331305	TOB2_HUMAN	B0QXZ4_HUMAN	UPI00001370FC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATTCCGTGC	.	2	ESCA
TCF20	0	.	GRCh37	22	42557353	42557353	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*56G>T	.	.	ENST00000359486	5/5	49	42	7	82	82	0	TCF20,missense_variant,p.Trp1937Cys,ENST00000335626,;TCF20,3_prime_UTR_variant,,ENST00000404876,;TCF20,3_prime_UTR_variant,,ENST00000359486,;	A	ENSG00000100207	ENST00000359486	Transcript	3_prime_UTR_variant	6076	.	.	.	.	.	.	.	-1	TCF20	HGNC	11631	protein_coding	YES	CCDS14033.1	ENSP00000352463	TCF20_HUMAN	I3L1M7_HUMAN	UPI00001A95D9	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCCACAG	.	4	ESCA
TRMU	0	.	GRCh37	22	46752874	46752874	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1237G>T	p.Asp413Tyr	p.D413Y	ENST00000290846	11/11	34	24	10	60	60	0	TRMU,missense_variant,p.Asp413Tyr,ENST00000290846,;TRMU,3_prime_UTR_variant,,ENST00000381019,;TRMU,downstream_gene_variant,,ENST00000424260,;CELSR1,downstream_gene_variant,,ENST00000262738,;TRMU,downstream_gene_variant,,ENST00000486620,;TRMU,downstream_gene_variant,,ENST00000463785,;TRMU,downstream_gene_variant,,ENST00000485175,;TRMU,3_prime_UTR_variant,,ENST00000456595,;TRMU,3_prime_UTR_variant,,ENST00000441818,;TRMU,3_prime_UTR_variant,,ENST00000381021,;TRMU,3_prime_UTR_variant,,ENST00000457572,;TRMU,3_prime_UTR_variant,,ENST00000453630,;TRMU,non_coding_transcript_exon_variant,,ENST00000485559,;TRMU,non_coding_transcript_exon_variant,,ENST00000491612,;TRMU,non_coding_transcript_exon_variant,,ENST00000470831,;TRMU,downstream_gene_variant,,ENST00000479648,;CELSR1,downstream_gene_variant,,ENST00000473624,;	T	ENSG00000100416	ENST00000290846	Transcript	missense_variant	1577	1237	413	D/Y	Gat/Tat	COSM3555478	.	.	1	TRMU	HGNC	25481	protein_coding	YES	CCDS14075.1	ENSP00000290846	MTU1_HUMAN	.	UPI00000411E1	.	deleterious_low_confidence(0.03)	benign(0.079)	11/11	.	hmmpanther:PTHR11933,hmmpanther:PTHR11933:SF9	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGATGGT	.	5	ESCA
NMS	0	.	GRCh37	2	101093850	101093850	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235G>C	p.Glu79Gln	p.E79Q	ENST00000376865	5/10	58	51	7	46	46	0	NMS,missense_variant,p.Glu79Gln,ENST00000376865,;	C	ENSG00000204640	ENST00000376865	Transcript	missense_variant	242	235	79	E/Q	Gag/Cag	.	.	.	1	NMS	HGNC	32203	protein_coding	YES	CCDS33259.1	ENSP00000366061	NMS_HUMAN	.	UPI00004C7A83	.	deleterious(0.02)	benign(0.255)	5/10	.	hmmpanther:PTHR32414	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAGGAGGCA	.	4	ESCA
PROC	0	.	GRCh37	2	128183756	128183756	+	Missense_Mutation	SNP	C	C	T	rs121918143	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631C>T	p.Arg211Trp	p.R211W	ENST00000234071	7/9	31	24	7	15	15	0	PROC,missense_variant,p.Arg245Trp,ENST00000409048,;PROC,missense_variant,p.Arg266Trp,ENST00000453608,;PROC,missense_variant,p.Arg211Trp,ENST00000422777,;PROC,missense_variant,p.Arg211Trp,ENST00000234071,;PROC,intron_variant,,ENST00000402125,;PROC,downstream_gene_variant,,ENST00000429925,;PROC,downstream_gene_variant,,ENST00000427769,;PROC,downstream_gene_variant,,ENST00000442644,;MIR4783,upstream_gene_variant,,ENST00000580343,;PROC,non_coding_transcript_exon_variant,,ENST00000464089,;PROC,downstream_gene_variant,,ENST00000419985,;PROC,downstream_gene_variant,,ENST00000474030,;PROC,downstream_gene_variant,,ENST00000431364,;	T	ENSG00000115718	ENST00000234071	Transcript	missense_variant	718	631	211	R/W	Cgg/Tgg	rs121918143,CM880060	.	.	1	PROC	HGNC	9451	protein_coding	YES	CCDS2145.1	ENSP00000234071	PROC_HUMAN	Q8J004_HUMAN,Q8J003_HUMAN,Q6V7X9_HUMAN,E7EVH6_HUMAN,E7EU72_HUMAN,B4DPC8_HUMAN	UPI0000001646	.	tolerated(0.18)	benign(0.302)	7/9	.	hmmpanther:PTHR24278:SF0,hmmpanther:PTHR24278,PIRSF_domain:PIRSF001143,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	T:0	T:0.0001	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCGCGGCTC	byFrequency|byCluster	4	ESCA
PTPN18	0	.	GRCh37	2	131128322	131128322	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801G>A	p.Met267Ile	p.M267I	ENST00000175756	10/15	44	35	8	62	62	0	PTPN18,missense_variant,p.Met267Ile,ENST00000175756,;PTPN18,missense_variant,p.Met72Ile,ENST00000409022,;PTPN18,missense_variant,p.Met160Ile,ENST00000347849,;PTPN18,non_coding_transcript_exon_variant,,ENST00000464576,;PTPN18,non_coding_transcript_exon_variant,,ENST00000490812,;PTPN18,non_coding_transcript_exon_variant,,ENST00000490137,;PTPN18,non_coding_transcript_exon_variant,,ENST00000462996,;PTPN18,upstream_gene_variant,,ENST00000462321,;PTPN18,upstream_gene_variant,,ENST00000481492,;PTPN18,downstream_gene_variant,,ENST00000483617,;PTPN18,downstream_gene_variant,,ENST00000495400,;PTPN18,downstream_gene_variant,,ENST00000428843,;PTPN18,downstream_gene_variant,,ENST00000489215,;	A	ENSG00000072135	ENST00000175756	Transcript	missense_variant	902	801	267	M/I	atG/atA	.	.	.	1	PTPN18	HGNC	9649	protein_coding	YES	CCDS2161.1	ENSP00000175756	PTN18_HUMAN	B4DNE5_HUMAN	UPI000013C5D0	.	tolerated(0.3)	benign(0.063)	10/15	.	PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF223,Gene3D:3.90.190.10,Pfam_domain:PF00102,SMART_domains:SM00404,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATGAGGAA	.	5	ESCA
MBD5	0	.	GRCh37	2	149226195	149226195	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683G>C	p.Gly228Ala	p.G228A	ENST00000407073	9/15	31	21	9	23	23	0	MBD5,missense_variant,p.Gly228Ala,ENST00000407073,;MBD5,missense_variant,p.Gly228Ala,ENST00000404807,;MBD5,upstream_gene_variant,,ENST00000416015,;	C	ENSG00000204406	ENST00000407073	Transcript	missense_variant	1680	683	228	G/A	gGt/gCt	.	.	.	1	MBD5	HGNC	20444	protein_coding	YES	CCDS33302.1	ENSP00000386049	MBD5_HUMAN	.	UPI0000208C40	.	deleterious(0.01)	possibly_damaging(0.899)	9/15	.	hmmpanther:PTHR16112,hmmpanther:PTHR16112:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAGGTTCCC	.	5	ESCA
ARL6IP6	0	.	GRCh37	2	153575184	153575184	+	Missense_Mutation	SNP	G	G	A	rs776807699	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.46G>A	p.Gly16Ser	p.G16S	ENST00000326446	1/4	47	38	8	58	58	0	ARL6IP6,missense_variant,p.Gly16Ser,ENST00000326446,;PRPF40A,upstream_gene_variant,,ENST00000410080,;PRPF40A,upstream_gene_variant,,ENST00000493468,;PRPF40A,upstream_gene_variant,,ENST00000545856,;PRPF40A,upstream_gene_variant,,ENST00000448428,;ARL6IP6,intron_variant,,ENST00000495469,;ARL6IP6,upstream_gene_variant,,ENST00000463690,;PRPF40A,upstream_gene_variant,,ENST00000486100,;ARL6IP6,upstream_gene_variant,,ENST00000425034,;PRPF40A,upstream_gene_variant,,ENST00000450303,;ARL6IP6,upstream_gene_variant,,ENST00000455875,;PRPF40A,upstream_gene_variant,,ENST00000489741,;PRPF40A,upstream_gene_variant,,ENST00000354363,;	A	ENSG00000177917	ENST00000326446	Transcript	missense_variant	757	46	16	G/S	Ggt/Agt	rs776807699	.	.	1	ARL6IP6	HGNC	24048	protein_coding	YES	CCDS2197.1	ENSP00000315357	AR6P6_HUMAN	.	UPI000006EA01	.	tolerated_low_confidence(0.08)	benign(0.024)	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCGGTCCC	.	5	ESCA
GPD2	0	.	GRCh37	2	157426011	157426011	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1437C>G	p.%3D	p.L479L	ENST00000310454	11/17	14	10	4	31	31	0	GPD2,synonymous_variant,p.%3D,ENST00000310454,;GPD2,synonymous_variant,p.%3D,ENST00000409674,;GPD2,synonymous_variant,p.%3D,ENST00000438166,;GPD2,synonymous_variant,p.%3D,ENST00000409125,;GPD2,intron_variant,,ENST00000540309,;GPD2,synonymous_variant,p.%3D,ENST00000409861,;GPD2,upstream_gene_variant,,ENST00000464846,;	G	ENSG00000115159	ENST00000310454	Transcript	synonymous_variant	1809	1437	479	L	ctC/ctG	.	.	.	1	GPD2	HGNC	4456	protein_coding	YES	CCDS2202.1	ENSP00000308610	GPDM_HUMAN	Q53T76_HUMAN,Q53RD0_HUMAN,F8W6E4_HUMAN,F5GYK7_HUMAN,E7EM56_HUMAN	UPI000013F012	.	.	.	11/17	.	hmmpanther:PTHR11985:SF1,hmmpanther:PTHR11985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACACTCTACAT	.	4	ESCA
SLC4A10	0	.	GRCh37	2	162751319	162751319	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1325A>C	p.Lys442Thr	p.K442T	ENST00000446997	11/27	51	44	7	37	37	0	SLC4A10,missense_variant,p.Lys442Thr,ENST00000446997,;SLC4A10,missense_variant,p.Lys442Thr,ENST00000421911,;SLC4A10,missense_variant,p.Lys412Thr,ENST00000272716,;SLC4A10,missense_variant,p.Lys412Thr,ENST00000415876,;SLC4A10,missense_variant,p.Lys423Thr,ENST00000375514,;SLC4A10,3_prime_UTR_variant,,ENST00000535165,;SLC4A10,non_coding_transcript_exon_variant,,ENST00000493021,;SLC4A10,missense_variant,p.Lys412Thr,ENST00000446228,;	C	ENSG00000144290	ENST00000446997	Transcript	missense_variant	1418	1325	442	K/T	aAa/aCa	.	.	.	1	SLC4A10	HGNC	13811	protein_coding	YES	CCDS54411.1	ENSP00000393066	S4A10_HUMAN	.	UPI00001D4707	.	deleterious(0.02)	probably_damaging(0.996)	11/27	.	hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Gene3D:1hynR00,TIGRFAM_domain:TIGR00834,Superfamily_domains:SSF55804,Prints_domain:PR01232	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCAAAAATG	.	4	ESCA
SCN3A	0	.	GRCh37	2	165996004	165996004	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2134C>T	p.%3D	p.L712L	ENST00000283254	14/28	26	19	7	32	32	0	SCN3A,synonymous_variant,p.%3D,ENST00000440431,;SCN3A,synonymous_variant,p.%3D,ENST00000360093,;SCN3A,synonymous_variant,p.%3D,ENST00000283254,;SCN3A,synonymous_variant,p.%3D,ENST00000409101,;	A	ENSG00000153253	ENST00000283254	Transcript	synonymous_variant	2602	2134	712	L	Ctg/Ttg	.	.	.	-1	SCN3A	HGNC	10590	protein_coding	YES	CCDS33312.1	ENSP00000283254	SCN3A_HUMAN	F5H4V8_HUMAN,C9JBM7_HUMAN	UPI000002A665	.	.	.	14/28	.	hmmpanther:PTHR10037:SF200,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGTCAGAATGC	.	2	ESCA
SCN1A	0	.	GRCh37	2	166900304	166900304	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1918A>C	p.Lys640Gln	p.K640Q	ENST00000303395	11/26	53	41	11	50	50	0	SCN1A,missense_variant,p.Lys640Gln,ENST00000409050,;SCN1A,missense_variant,p.Lys640Gln,ENST00000423058,;SCN1A,missense_variant,p.Lys640Gln,ENST00000303395,;SCN1A,missense_variant,p.Lys640Gln,ENST00000375405,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000595268,;	G	ENSG00000144285	ENST00000303395	Transcript	missense_variant	1918	1918	640	K/Q	Aag/Cag	.	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	deleterious(0.03)	probably_damaging(0.986)	11/26	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF133,Pfam_domain:PF11933	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTTCCCAT	.	5	ESCA
TTN	0	.	GRCh37	2	179658217	179658217	+	Missense_Mutation	SNP	C	C	T	rs768211726	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1450G>A	p.Asp484Asn	p.D484N	ENST00000589042	9/363	64	56	8	56	56	0	TTN,missense_variant,p.Asp80Asn,ENST00000436599,;TTN,missense_variant,p.Asp484Asn,ENST00000360870,;TTN,missense_variant,p.Asp484Asn,ENST00000342992,;TTN,missense_variant,p.Asp484Asn,ENST00000342175,;TTN,missense_variant,p.Asp484Asn,ENST00000359218,;TTN,missense_variant,p.Asp484Asn,ENST00000589042,;TTN,missense_variant,p.Asp484Asn,ENST00000591111,;TTN,missense_variant,p.Asp484Asn,ENST00000460472,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	1675	1450	484	D/N	Gat/Aat	rs768211726,COSM3574451,COSM350512,COSM350511,COSM3574450,COSM3574447,COSM3574449,COSM350510,COSM350509,COSM3574448,COSM3574452,COSM350513	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	9/363	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF09042	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTATCGGCGG	byFrequency	4	ESCA
CCDC141	0	.	GRCh37	2	179730512	179730512	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2706G>C	p.Met902Ile	p.M902I	ENST00000420890	17/24	85	69	15	102	102	0	CCDC141,missense_variant,p.Met902Ile,ENST00000420890,;CCDC141,missense_variant,p.Met902Ile,ENST00000443758,;CCDC141,missense_variant,p.Met346Ile,ENST00000343876,;CCDC141,missense_variant,p.Met327Ile,ENST00000295723,;	G	ENSG00000163492	ENST00000420890	Transcript	missense_variant	2824	2706	902	M/I	atG/atC	.	.	.	-1	CCDC141	HGNC	26821	protein_coding	YES	.	ENSP00000395995	.	H7C0P1_HUMAN,E7ERF0_HUMAN	UPI0000EE2F1C	.	tolerated(0.14)	benign(0.002)	17/24	.	hmmpanther:PTHR19897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCATGGC	.	5	ESCA
BZW1	0	.	GRCh37	2	201682946	201682946	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.745G>C	p.Glu249Gln	p.E249Q	ENST00000452790	8/12	46	33	13	33	33	0	BZW1,missense_variant,p.Glu249Gln,ENST00000452790,;BZW1,missense_variant,p.Glu221Gln,ENST00000409226,;BZW1,missense_variant,p.Glu217Gln,ENST00000409600,;BZW1,missense_variant,p.Glu217Gln,ENST00000410110,;BZW1,downstream_gene_variant,,ENST00000447069,;BZW1,downstream_gene_variant,,ENST00000452206,;BZW1,upstream_gene_variant,,ENST00000359893,;BZW1,downstream_gene_variant,,ENST00000450637,;BZW1,downstream_gene_variant,,ENST00000419090,;BZW1,splice_region_variant,,ENST00000463310,;BZW1,downstream_gene_variant,,ENST00000464483,;BZW1,downstream_gene_variant,,ENST00000460660,;BZW1,upstream_gene_variant,,ENST00000491576,;	C	ENSG00000082153	ENST00000452790	Transcript	missense_variant	797	745	249	E/Q	Gaa/Caa	.	.	.	1	BZW1	HGNC	18380	protein_coding	YES	CCDS56155.1	ENSP00000394316	BZW1_HUMAN	Q3LIC9_HUMAN,D3DN77_HUMAN,C9JWF5_HUMAN,C9JFN4_HUMAN,C9J188_HUMAN,C9IZ80_HUMAN	UPI00006C0604	.	deleterious(0.02)	possibly_damaging(0.623)	8/12	.	hmmpanther:PTHR14208,hmmpanther:PTHR14208:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAGGAACTC	.	5	ESCA
RAPH1	0	.	GRCh37	2	204303018	204303018	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1142G>C	.	.	ENST00000319170	14/14	31	25	6	23	23	0	ABI2,3_prime_UTR_variant,,ENST00000295851,;RAPH1,3_prime_UTR_variant,,ENST00000319170,;RAPH1,intron_variant,,ENST00000457812,;RAPH1,downstream_gene_variant,,ENST00000423104,;RAPH1,downstream_gene_variant,,ENST00000419464,;RAPH1,downstream_gene_variant,,ENST00000374488,;RAPH1,downstream_gene_variant,,ENST00000439222,;RAPH1,downstream_gene_variant,,ENST00000374493,;RAPH1,downstream_gene_variant,,ENST00000374489,;RAPH1,downstream_gene_variant,,ENST00000308091,;ABI2,downstream_gene_variant,,ENST00000464761,;	G	ENSG00000173166	ENST00000319170	Transcript	3_prime_UTR_variant	5195	.	.	.	.	.	.	.	-1	RAPH1	HGNC	14436	protein_coding	YES	CCDS2359.1	ENSP00000316543	RAPH1_HUMAN	C9JLG4_HUMAN	UPI000020940F	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACACCTGTA	.	5	ESCA
MAP2	0	.	GRCh37	2	210597411	210597411	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2290T>G	.	.	ENST00000360351	15/15	40	34	6	22	22	0	MAP2,3_prime_UTR_variant,,ENST00000360351,;MAP2,3_prime_UTR_variant,,ENST00000392194,;MAP2,downstream_gene_variant,,ENST00000447185,;MAP2,downstream_gene_variant,,ENST00000199940,;MAP2,downstream_gene_variant,,ENST00000361559,;MAP2,downstream_gene_variant,,ENST00000475600,;	G	ENSG00000078018	ENST00000360351	Transcript	3_prime_UTR_variant	8280	.	.	.	.	.	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTCTTTAAA	.	4	ESCA
APOB	0	.	GRCh37	2	21238336	21238336	+	Silent	SNP	G	G	A	rs140456702	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3414C>T	p.%3D	p.L1138L	ENST00000233242	22/29	73	60	13	51	51	0	APOB,synonymous_variant,p.%3D,ENST00000233242,;	A	ENSG00000084674	ENST00000233242	Transcript	synonymous_variant	3542	3414	1138	L	ctC/ctT	rs140456702,COSM1565109	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	.	22/29	.	hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGAGGAT	byCluster	5	ESCA
NCL	0	.	GRCh37	2	232327928	232327928	+	Missense_Mutation	SNP	C	C	T	rs375715628	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118G>A	p.Asp40Asn	p.D40N	ENST00000322723	2/14	67	59	8	66	66	0	NCL,missense_variant,p.Asp24Asn,ENST00000454824,;NCL,missense_variant,p.Asp24Asn,ENST00000436894,;NCL,missense_variant,p.Asp24Asn,ENST00000417652,;NCL,missense_variant,p.Asp40Asn,ENST00000322723,;NCL,missense_variant,p.Asp24Asn,ENST00000453992,;NCL,upstream_gene_variant,,ENST00000356936,;SNORD82,upstream_gene_variant,,ENST00000365530,;NCL,non_coding_transcript_exon_variant,,ENST00000484328,;NCL,non_coding_transcript_exon_variant,,ENST00000461347,;NCL,upstream_gene_variant,,ENST00000494618,;	T	ENSG00000115053	ENST00000322723	Transcript	missense_variant	359	118	40	D/N	Gat/Aat	rs375715628	.	.	-1	NCL	HGNC	7667	protein_coding	YES	CCDS33397.1	ENSP00000318195	NUCL_HUMAN	C9JYW2_HUMAN,C9JWL1_HUMAN,C9JLB1_HUMAN,C9J1H7_HUMAN,B3KM80_HUMAN	UPI0000456F25	.	.	unknown(0)	2/14	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	T:0.0005	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTATCATCTT	byFrequency|byCluster	4	ESCA
AGBL5	0	.	GRCh37	2	27276293	27276293	+	Missense_Mutation	SNP	G	G	A	rs373073782	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239G>A	p.Arg80Gln	p.R80Q	ENST00000360131	3/15	18	13	5	10	10	0	AGBL5,missense_variant,p.Arg80Gln,ENST00000360131,;AGBL5,missense_variant,p.Arg80Gln,ENST00000453161,;AGBL5,missense_variant,p.Arg80Gln,ENST00000323064,;AGBL5,downstream_gene_variant,,ENST00000421915,;AGBL5,downstream_gene_variant,,ENST00000451003,;AGBL5,downstream_gene_variant,,ENST00000437006,;AGBL5-AS1,upstream_gene_variant,,ENST00000444217,;RP11-503P10.1,downstream_gene_variant,,ENST00000607407,;AGBL5,missense_variant,p.Arg80Gln,ENST00000487078,;AGBL5,non_coding_transcript_exon_variant,,ENST00000477136,;AGBL5,non_coding_transcript_exon_variant,,ENST00000489683,;	A	ENSG00000084693	ENST00000360131	Transcript	missense_variant	398	239	80	R/Q	cGg/cAg	rs373073782	.	.	1	AGBL5	HGNC	26147	protein_coding	YES	CCDS1732.3	ENSP00000353249	CBPC5_HUMAN	C9JTY1_HUMAN,C9JQG9_HUMAN,C9JHM6_HUMAN,C9JCE1_HUMAN	UPI000006FE54	.	tolerated(0.11)	benign(0.056)	3/15	.	hmmpanther:PTHR12756	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCCGGGGAG	byCluster|by1000G	5	ESCA
PREPL	0	.	GRCh37	2	44586763	44586763	+	Missense_Mutation	SNP	T	T	C	rs761628820	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92A>G	p.Tyr31Cys	p.Y31C	ENST00000409936	2/15	68	45	22	38	38	0	PREPL,missense_variant,p.Tyr31Cys,ENST00000260648,;PREPL,missense_variant,p.Tyr31Cys,ENST00000410081,;PREPL,missense_variant,p.Tyr31Cys,ENST00000378511,;PREPL,missense_variant,p.Tyr31Cys,ENST00000378520,;PREPL,missense_variant,p.Tyr31Cys,ENST00000409936,;PREPL,missense_variant,p.Tyr31Cys,ENST00000409272,;PREPL,missense_variant,p.Tyr31Cys,ENST00000438314,;PREPL,intron_variant,,ENST00000409957,;PREPL,intron_variant,,ENST00000541738,;PREPL,intron_variant,,ENST00000409411,;CAMKMT,upstream_gene_variant,,ENST00000407131,;CAMKMT,upstream_gene_variant,,ENST00000378494,;CAMKMT,upstream_gene_variant,,ENST00000403853,;CAMKMT,upstream_gene_variant,,ENST00000402247,;PREPL,intron_variant,,ENST00000477410,;PREPL,intron_variant,,ENST00000540817,;PREPL,missense_variant,p.Tyr31Cys,ENST00000426481,;PREPL,missense_variant,p.Tyr31Cys,ENST00000425263,;CAMKMT,upstream_gene_variant,,ENST00000454433,;	C	ENSG00000138078	ENST00000409936	Transcript	missense_variant	530	92	31	Y/C	tAt/tGt	rs761628820	.	.	-1	PREPL	HGNC	30228	protein_coding	YES	CCDS33190.1	ENSP00000386543	PPCEL_HUMAN	C9JMT4_HUMAN	UPI0000208358	.	tolerated_low_confidence(0.21)	benign(0)	2/15	.	hmmpanther:PTHR11757,hmmpanther:PTHR11757:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTATAGTGA	.	5	ESCA
EML6	0	.	GRCh37	2	55122100	55122100	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2791A>G	p.Met931Val	p.M931V	ENST00000356458	19/41	91	48	42	50	50	0	EML6,missense_variant,p.Met931Val,ENST00000356458,;	G	ENSG00000214595	ENST00000356458	Transcript	missense_variant	3311	2791	931	M/V	Atg/Gtg	.	.	.	1	EML6	HGNC	35412	protein_coding	YES	CCDS46286.1	ENSP00000348842	EMAL6_HUMAN	.	UPI00006C0432	.	tolerated(0.3)	benign(0.017)	19/41	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13720:SF8,hmmpanther:PTHR13720,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATATGTTT	.	5	ESCA
SOX11	0	.	GRCh37	2	5835839	5835839	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1660G>A	.	.	ENST00000322002	1/1	79	60	18	78	78	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,upstream_gene_variant,,ENST00000455579,;AC108025.2,upstream_gene_variant,,ENST00000453678,;AC107057.2,upstream_gene_variant,,ENST00000458264,;AC108025.2,upstream_gene_variant,,ENST00000420221,;	A	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	3041	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGTGAGGCT	.	5	ESCA
MEIS1	0	.	GRCh37	2	66665074	66665074	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218G>A	p.Arg73Lys	p.R73K	ENST00000272369	2/13	28	18	10	20	20	0	MEIS1,missense_variant,p.Arg73Lys,ENST00000488550,;MEIS1,missense_variant,p.Arg73Lys,ENST00000560281,;MEIS1,missense_variant,p.Arg41Lys,ENST00000444274,;MEIS1,missense_variant,p.Arg73Lys,ENST00000407092,;MEIS1,missense_variant,p.Arg71Lys,ENST00000398506,;MEIS1,missense_variant,p.Arg73Lys,ENST00000272369,;MEIS1,upstream_gene_variant,,ENST00000495021,;MEIS1,upstream_gene_variant,,ENST00000437869,;AC092669.1,downstream_gene_variant,,ENST00000454595,;MEIS1-AS2,downstream_gene_variant,,ENST00000439433,;MEIS1-AS3,upstream_gene_variant,,ENST00000454167,;MEIS1,non_coding_transcript_exon_variant,,ENST00000490726,;MEIS1,non_coding_transcript_exon_variant,,ENST00000496248,;MEIS1,missense_variant,p.Arg73Lys,ENST00000491706,;MEIS1,upstream_gene_variant,,ENST00000498705,;MEIS1,upstream_gene_variant,,ENST00000466811,;MEIS1,upstream_gene_variant,,ENST00000409622,;	A	ENSG00000143995	ENST00000272369	Transcript	missense_variant	675	218	73	R/K	aGa/aAa	.	.	.	1	MEIS1	HGNC	7000	protein_coding	YES	CCDS46309.1	ENSP00000272369	MEIS1_HUMAN	Q8IZZ2_HUMAN,Q53RD5_HUMAN,Q53R57_HUMAN	UPI000000DA5A	.	tolerated(0.07)	benign(0.354)	2/13	.	hmmpanther:PTHR11850:SF63,hmmpanther:PTHR11850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGAGATA	.	5	ESCA
ALMS1P	0	.	GRCh37	2	73899496	73899496	+	RNA	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.368G>C	.	.	ENST00000450720	3/7	33	29	4	24	24	0	ALMS1P,non_coding_transcript_exon_variant,,ENST00000450720,;ALMS1P,non_coding_transcript_exon_variant,,ENST00000428767,;	C	ENSG00000163016	ENST00000450720	Transcript	non_coding_transcript_exon_variant	368	.	.	.	.	.	.	.	1	ALMS1P	HGNC	29586	processed_transcript	YES	.	.	.	.	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCAGCGAGGCT	.	3	ESCA
SEMA4F	0	.	GRCh37	2	74902360	74902360	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1221C>G	p.Phe407Leu	p.F407L	ENST00000357877	10/14	30	18	12	43	43	0	SEMA4F,missense_variant,p.Phe407Leu,ENST00000357877,;SEMA4F,missense_variant,p.Phe252Leu,ENST00000339773,;SEMA4F,downstream_gene_variant,,ENST00000453930,;SEMA4F,downstream_gene_variant,,ENST00000434486,;SEMA4F,intron_variant,,ENST00000473350,;SEMA4F,3_prime_UTR_variant,,ENST00000420077,;SEMA4F,3_prime_UTR_variant,,ENST00000446927,;SEMA4F,downstream_gene_variant,,ENST00000458114,;	G	ENSG00000135622	ENST00000357877	Transcript	missense_variant	1370	1221	407	F/L	ttC/ttG	.	.	.	1	SEMA4F	HGNC	10734	protein_coding	YES	CCDS1955.1	ENSP00000350547	SEM4F_HUMAN	.	UPI0000001BF5	.	deleterious(0)	probably_damaging(0.999)	10/14	.	Superfamily_domains:SSF101912,SMART_domains:SM00630,Pfam_domain:PF01403,Gene3D:2.130.10.10,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF72,PROSITE_profiles:PS51004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCATCCG	.	5	ESCA
DNAH6	0	.	GRCh37	2	84864352	84864352	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4672G>C	p.Glu1558Gln	p.E1558Q	ENST00000389394	31/77	23	15	8	21	21	0	DNAH6,missense_variant,p.Glu1558Gln,ENST00000237449,;DNAH6,missense_variant,p.Glu1558Gln,ENST00000398278,;DNAH6,missense_variant,p.Glu1558Gln,ENST00000389394,;	C	ENSG00000115423	ENST00000389394	Transcript	missense_variant	4809	4672	1558	E/Q	Gag/Cag	.	.	.	1	DNAH6	HGNC	2951	protein_coding	YES	CCDS46348.1	ENSP00000374045	DYH6_HUMAN	B0I1R8_HUMAN	UPI000163AC9D	.	deleterious(0.01)	benign(0.261)	31/77	.	hmmpanther:PTHR10676:SF136,hmmpanther:PTHR10676,Pfam_domain:PF12774,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTGAGGGG	.	5	ESCA
SMYD1	0	.	GRCh37	2	88405881	88405881	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1019A>C	p.Glu340Ala	p.E340A	ENST00000419482	8/10	73	66	7	71	71	0	SMYD1,missense_variant,p.Glu327Ala,ENST00000444564,;SMYD1,missense_variant,p.Glu340Ala,ENST00000419482,;SMYD1,intron_variant,,ENST00000438570,;	C	ENSG00000115593	ENST00000419482	Transcript	missense_variant	1104	1019	340	E/A	gAg/gCg	.	.	.	1	SMYD1	HGNC	20986	protein_coding	YES	CCDS33240.1	ENSP00000393453	SMYD1_HUMAN	Q5GJ33_HUMAN	UPI000006EB68	.	tolerated(0.09)	benign(0.035)	8/10	.	hmmpanther:PTHR12197:SF16,hmmpanther:PTHR12197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAGGAGCCAG	.	3	ESCA
MYH15	0	.	GRCh37	3	108129652	108129652	+	Missense_Mutation	SNP	C	C	T	rs368421301	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4333G>A	p.Gly1445Arg	p.G1445R	ENST00000273353	32/42	17	14	3	10	10	0	MYH15,missense_variant,p.Gly1445Arg,ENST00000273353,;MYH15,non_coding_transcript_exon_variant,,ENST00000478998,;	T	ENSG00000144821	ENST00000273353	Transcript	missense_variant	4390	4333	1445	G/R	Ggg/Agg	rs368421301	.	.	-1	MYH15	HGNC	31073	protein_coding	YES	CCDS43127.1	ENSP00000273353	MYH15_HUMAN	H9XFA0_HUMAN	UPI0000253B6F	.	deleterious(0.02)	benign(0.111)	32/42	.	Pfam_domain:PF01576,hmmpanther:PTHR13140:SF263,hmmpanther:PTHR13140	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCCCGAGGT	byFrequency|byCluster	2	ESCA
PHLDB2	0	.	GRCh37	3	111694519	111694519	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1109G>C	.	.	ENST00000431670	18/18	47	43	4	21	21	0	PHLDB2,3_prime_UTR_variant,,ENST00000393923,;PHLDB2,3_prime_UTR_variant,,ENST00000412622,;PHLDB2,3_prime_UTR_variant,,ENST00000481953,;PHLDB2,3_prime_UTR_variant,,ENST00000495180,;PHLDB2,3_prime_UTR_variant,,ENST00000431670,;PHLDB2,3_prime_UTR_variant,,ENST00000393925,;ABHD10,upstream_gene_variant,,ENST00000494817,;ABHD10,upstream_gene_variant,,ENST00000273359,;ABHD10,upstream_gene_variant,,ENST00000534857,;PHLDB2,non_coding_transcript_exon_variant,,ENST00000486886,;ABHD10,upstream_gene_variant,,ENST00000491580,;ABHD10,upstream_gene_variant,,ENST00000497293,;ABHD10,upstream_gene_variant,,ENST00000493784,;	C	ENSG00000144824	ENST00000431670	Transcript	3_prime_UTR_variant	5282	.	.	.	.	.	.	.	1	PHLDB2	HGNC	29573	protein_coding	YES	CCDS46886.1	ENSP00000405405	PHLB2_HUMAN	Q8NEI7_HUMAN,Q659D2_HUMAN	UPI0000457152	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TTTTAGTTAAT	.	2	ESCA
GRAMD1C	0	.	GRCh37	3	113619947	113619947	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>C	p.Glu204Gln	p.E204Q	ENST00000358160	7/18	41	35	6	22	22	0	GRAMD1C,missense_variant,p.Glu204Gln,ENST00000358160,;GRAMD1C,missense_variant,p.Glu37Gln,ENST00000472026,;GRAMD1C,5_prime_UTR_variant,,ENST00000440446,;GRAMD1C,5_prime_UTR_variant,,ENST00000462838,;GRAMD1C,5_prime_UTR_variant,,ENST00000452134,;GRAMD1C,intron_variant,,ENST00000488680,;GRAMD1C,non_coding_transcript_exon_variant,,ENST00000479212,;GRAMD1C,non_coding_transcript_exon_variant,,ENST00000463760,;GRAMD1C,downstream_gene_variant,,ENST00000486457,;GRAMD1C,missense_variant,p.Glu172Gln,ENST00000472384,;GRAMD1C,3_prime_UTR_variant,,ENST00000484714,;	C	ENSG00000178075	ENST00000358160	Transcript	missense_variant	1102	610	204	E/Q	Gag/Cag	.	.	.	1	GRAMD1C	HGNC	25252	protein_coding	YES	CCDS33826.1	ENSP00000350881	GRM1C_HUMAN	C9J7B8_HUMAN,A8KA99_HUMAN	UPI00001AF15F	.	deleterious(0.01)	possibly_damaging(0.548)	7/18	.	hmmpanther:PTHR23319:SF1,hmmpanther:PTHR23319	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCTGAGGAG	.	2	ESCA
B4GALT4	0	.	GRCh37	3	118948751	118948751	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196G>A	p.Glu66Lys	p.E66K	ENST00000483209	3/8	81	72	9	67	67	0	B4GALT4,missense_variant,p.Glu66Lys,ENST00000483209,;B4GALT4,missense_variant,p.Glu19Lys,ENST00000471675,;B4GALT4,missense_variant,p.Glu66Lys,ENST00000475803,;B4GALT4,missense_variant,p.Glu66Lys,ENST00000467604,;B4GALT4,missense_variant,p.Glu66Lys,ENST00000393765,;B4GALT4,missense_variant,p.Glu66Lys,ENST00000359213,;B4GALT4,missense_variant,p.Glu66Lys,ENST00000479150,;B4GALT4,intron_variant,,ENST00000491906,;B4GALT4,downstream_gene_variant,,ENST00000473887,;B4GALT4,downstream_gene_variant,,ENST00000493932,;B4GALT4,downstream_gene_variant,,ENST00000459778,;B4GALT4,downstream_gene_variant,,ENST00000459820,;B4GALT4,downstream_gene_variant,,ENST00000470111,;B4GALT4-AS1,intron_variant,,ENST00000470790,;B4GALT4,intron_variant,,ENST00000460321,;B4GALT4,downstream_gene_variant,,ENST00000460395,;B4GALT4,downstream_gene_variant,,ENST00000472471,;B4GALT4,downstream_gene_variant,,ENST00000487579,;B4GALT4,downstream_gene_variant,,ENST00000484595,;B4GALT4,missense_variant,p.Glu66Lys,ENST00000480814,;	T	ENSG00000121578	ENST00000483209	Transcript	missense_variant	838	196	66	E/K	Gaa/Aaa	.	.	.	-1	B4GALT4	HGNC	927	protein_coding	YES	CCDS2986.1	ENSP00000420161	B4GT4_HUMAN	C9JY38_HUMAN,C9JY35_HUMAN,C9JE00_HUMAN,C9J644_HUMAN,C9J5S0_HUMAN,C9J4S5_HUMAN,C9J3R8_HUMAN,B2RAZ5_HUMAN	UPI00000389DB	.	tolerated(0.44)	benign(0.004)	3/8	.	hmmpanther:PTHR19300,hmmpanther:PTHR19300:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTTCATTAG	.	4	ESCA
FSTL1	0	.	GRCh37	3	120122126	120122126	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657C>G	p.%3D	p.L219L	ENST00000295633	8/11	46	38	8	27	27	0	FSTL1,synonymous_variant,p.%3D,ENST00000480823,;FSTL1,synonymous_variant,p.%3D,ENST00000295633,;FSTL1,synonymous_variant,p.%3D,ENST00000424703,;FSTL1,downstream_gene_variant,,ENST00000468098,;FSTL1,upstream_gene_variant,,ENST00000488318,;	C	ENSG00000163430	ENST00000295633	Transcript	synonymous_variant	1014	657	219	L	ctC/ctG	.	.	.	-1	FSTL1	HGNC	3972	protein_coding	YES	CCDS2998.1	ENSP00000295633	FSTL1_HUMAN	Q9BZQ0_HUMAN,C9J5G4_HUMAN	UPI00000422DB	.	.	.	8/11	.	PROSITE_profiles:PS50222,hmmpanther:PTHR10913:SF38,hmmpanther:PTHR10913,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTGAGAAA	.	5	ESCA
TMEM40	0	.	GRCh37	3	12776026	12776026	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247A>T	.	.	ENST00000314124	12/12	28	24	4	34	34	0	TMEM40,3_prime_UTR_variant,,ENST00000435575,;TMEM40,3_prime_UTR_variant,,ENST00000435218,;TMEM40,3_prime_UTR_variant,,ENST00000314124,;TMEM40,downstream_gene_variant,,ENST00000431022,;TMEM40,downstream_gene_variant,,ENST00000428020,;TMEM40,downstream_gene_variant,,ENST00000264728,;TMEM40,downstream_gene_variant,,ENST00000476331,;TMEM40,downstream_gene_variant,,ENST00000480698,;TMEM40,downstream_gene_variant,,ENST00000485124,;	A	ENSG00000088726	ENST00000314124	Transcript	3_prime_UTR_variant	1306	.	.	.	.	.	.	.	-1	TMEM40	HGNC	25620	protein_coding	YES	CCDS2613.1	ENSP00000322837	TMM40_HUMAN	.	UPI00000732A9	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCCTCAGGC	.	2	ESCA
EPHB1	0	.	GRCh37	3	134880869	134880869	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1432G>C	p.Glu478Gln	p.E478Q	ENST00000398015	7/16	79	68	10	46	46	0	EPHB1,missense_variant,p.Glu39Gln,ENST00000493838,;EPHB1,missense_variant,p.Glu478Gln,ENST00000398015,;	C	ENSG00000154928	ENST00000398015	Transcript	missense_variant	1802	1432	478	E/Q	Gag/Cag	.	.	.	1	EPHB1	HGNC	3392	protein_coding	YES	CCDS46921.1	ENSP00000381097	EPHB1_HUMAN	C9K090_HUMAN,C9JB88_HUMAN,C9J6S4_HUMAN,C9J466_HUMAN,B3KTB2_HUMAN	UPI000012A07E	.	tolerated(0.16)	benign(0.099)	7/16	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,Pfam_domain:PF00041,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATGAGTTC	.	5	ESCA
NCK1	0	.	GRCh37	3	136664643	136664643	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.445A>C	p.Asn149His	p.N149H	ENST00000481752	3/4	120	102	17	88	88	0	NCK1,missense_variant,p.Asn85His,ENST00000469404,;NCK1,missense_variant,p.Asn149His,ENST00000481752,;NCK1,missense_variant,p.Asn149His,ENST00000288986,;NCK1,intron_variant,,ENST00000467911,;NCK1,intron_variant,,ENST00000496489,;NCK1,intron_variant,,ENST00000488930,;NCK1,downstream_gene_variant,,ENST00000485096,;NCK1,downstream_gene_variant,,ENST00000491539,;IL20RB,upstream_gene_variant,,ENST00000484501,;NCK1,non_coding_transcript_exon_variant,,ENST00000482071,;	C	ENSG00000158092	ENST00000481752	Transcript	missense_variant	609	445	149	N/H	Aat/Cat	.	.	.	1	NCK1	HGNC	7664	protein_coding	YES	CCDS3092.1	ENSP00000417273	NCK1_HUMAN	C9K098_HUMAN,C9JVV5_HUMAN,C9J0K5_HUMAN	UPI000012FE3E	.	tolerated(0.08)	possibly_damaging(0.811)	3/4	.	Prints_domain:PR00452,Superfamily_domains:SSF50044,SMART_domains:SM00326,PIRSF_domain:PIRSF037874,Gene3D:2.30.30.40,Pfam_domain:PF14604,hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF11,PROSITE_profiles:PS50002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTACAATGGA	.	4	ESCA
TRIM42	0	.	GRCh37	3	140401907	140401907	+	Missense_Mutation	SNP	C	C	G	rs775891829	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.945C>G	p.Phe315Leu	p.F315L	ENST00000286349	2/5	65	52	12	41	41	0	TRIM42,missense_variant,p.Phe315Leu,ENST00000286349,;	G	ENSG00000155890	ENST00000286349	Transcript	missense_variant	1136	945	315	F/L	ttC/ttG	rs775891829	.	.	1	TRIM42	HGNC	19014	protein_coding	YES	CCDS3113.1	ENSP00000286349	TRI42_HUMAN	.	UPI00001AEAE0	.	tolerated(0.3)	benign(0)	2/5	.	PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF273,Pfam_domain:PF00643,SMART_domains:SM00336,Superfamily_domains:SSF57845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTCTCTTT	.	5	ESCA
SLC25A36	0	.	GRCh37	3	140675495	140675495	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168C>G	p.%3D	p.V56V	ENST00000324194	2/7	76	67	9	46	46	0	SLC25A36,synonymous_variant,p.%3D,ENST00000507429,;SLC25A36,synonymous_variant,p.%3D,ENST00000453248,;SLC25A36,synonymous_variant,p.%3D,ENST00000446041,;SLC25A36,synonymous_variant,p.%3D,ENST00000513887,;SLC25A36,synonymous_variant,p.%3D,ENST00000324194,;SLC25A36,non_coding_transcript_exon_variant,,ENST00000393015,;SLC25A36,synonymous_variant,p.%3D,ENST00000512506,;SLC25A36,synonymous_variant,p.%3D,ENST00000502594,;SLC25A36,synonymous_variant,p.%3D,ENST00000512023,;SLC25A36,non_coding_transcript_exon_variant,,ENST00000515813,;SLC25A36,non_coding_transcript_exon_variant,,ENST00000502756,;	G	ENSG00000114120	ENST00000324194	Transcript	synonymous_variant	336	168	56	V	gtC/gtG	.	.	.	1	SLC25A36	HGNC	25554	protein_coding	YES	CCDS46927.1	ENSP00000320688	S2536_HUMAN	.	UPI000006D558	.	.	.	2/7	.	PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF180,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTGTCAACCG	.	4	ESCA
PCOLCE2	0	.	GRCh37	3	142557648	142557648	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.674G>A	p.Arg225Lys	p.R225K	ENST00000295992	5/9	77	69	7	36	36	0	PCOLCE2,missense_variant,p.Arg225Lys,ENST00000485766,;PCOLCE2,missense_variant,p.Arg225Lys,ENST00000295992,;PCOLCE2,3_prime_UTR_variant,,ENST00000480473,;PCOLCE2,non_coding_transcript_exon_variant,,ENST00000483986,;	T	ENSG00000163710	ENST00000295992	Transcript	missense_variant	981	674	225	R/K	aGa/aAa	.	.	.	-1	PCOLCE2	HGNC	8739	protein_coding	YES	CCDS3127.1	ENSP00000295992	PCOC2_HUMAN	H7C5D5_HUMAN	UPI0000073F93	.	tolerated(1)	benign(0.006)	5/9	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF40,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTAGCA	.	4	ESCA
ZIC4	0	.	GRCh37	3	147124224	147124224	+	5'Flank	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000525172	.	34	28	6	20	20	0	ZIC4,5_prime_UTR_variant,,ENST00000383075,;ZIC4,5_prime_UTR_variant,,ENST00000463250,;ZIC4,5_prime_UTR_variant,,ENST00000491672,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,upstream_gene_variant,,ENST00000484399,;ZIC4,upstream_gene_variant,,ENST00000425731,;ZIC4,upstream_gene_variant,,ENST00000473123,;ZIC1,upstream_gene_variant,,ENST00000282928,;ZIC4,upstream_gene_variant,,ENST00000462748,;ZIC4,upstream_gene_variant,,ENST00000525172,;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC4,non_coding_transcript_exon_variant,,ENST00000464144,;ZIC1,intron_variant,,ENST00000472523,;	T	ENSG00000174963	ENST00000525172	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2153	-1	ZIC4	HGNC	20393	protein_coding	YES	CCDS54652.1	ENSP00000435509	ZIC4_HUMAN	C9JZU7_HUMAN,C9JD04_HUMAN,C9J6T3_HUMAN,B3KPI4_HUMAN	UPI0001914D88	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACCCCTCCA	.	4	ESCA
TSC22D2	0	.	GRCh37	3	150176665	150176665	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*242G>A	.	.	ENST00000361875	4/4	28	24	4	12	12	0	TSC22D2,3_prime_UTR_variant,,ENST00000361875,;TSC22D2,3_prime_UTR_variant,,ENST00000361136,;TSC22D2,3_prime_UTR_variant,,ENST00000466814,;TSC22D2,downstream_gene_variant,,ENST00000480589,;TSC22D2,non_coding_transcript_exon_variant,,ENST00000460316,;TSC22D2,downstream_gene_variant,,ENST00000485421,;	A	ENSG00000196428	ENST00000361875	Transcript	3_prime_UTR_variant	3601	.	.	.	.	.	.	.	1	TSC22D2	HGNC	29095	protein_coding	YES	CCDS3149.1	ENSP00000354543	T22D2_HUMAN	.	UPI00000722E0	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAGCGAGCAA	.	2	ESCA
SCHIP1	0	.	GRCh37	3	159557928	159557928	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-46C>T	.	.	ENST00000445224	1/7	50	41	9	35	35	0	SCHIP1,5_prime_UTR_variant,,ENST00000445224,;IQCJ-SCHIP1,intron_variant,,ENST00000527095,;IQCJ-SCHIP1,intron_variant,,ENST00000476809,;IQCJ-SCHIP1,intron_variant,,ENST00000473061,;IQCJ-SCHIP1,intron_variant,,ENST00000337808,;IQCJ-SCHIP1,intron_variant,,ENST00000485419,;IQCJ-SCHIP1,intron_variant,,ENST00000460298,;IQCJ-SCHIP1,intron_variant,,ENST00000412423,;SCHIP1,non_coding_transcript_exon_variant,,ENST00000483730,;SCHIP1,5_prime_UTR_variant,,ENST00000495954,;SCHIP1,non_coding_transcript_exon_variant,,ENST00000472483,;SCHIP1,non_coding_transcript_exon_variant,,ENST00000461058,;	T	ENSG00000151967	ENST00000445224	Transcript	5_prime_UTR_variant	279	.	.	.	.	.	.	.	1	SCHIP1	HGNC	15678	protein_coding	YES	CCDS56294.1	ENSP00000404860	SCHI1_HUMAN	.	UPI000020A51C	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCTCGCTCA	.	4	ESCA
SMC4	0	.	GRCh37	3	160135727	160135727	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1654G>C	p.Glu552Gln	p.E552Q	ENST00000357388	11/24	40	35	5	19	19	0	SMC4,missense_variant,p.Glu552Gln,ENST00000344722,;SMC4,missense_variant,p.Glu552Gln,ENST00000462787,;SMC4,missense_variant,p.Glu552Gln,ENST00000360111,;SMC4,missense_variant,p.Glu527Gln,ENST00000469762,;SMC4,missense_variant,p.Glu552Gln,ENST00000357388,;SMC4,downstream_gene_variant,,ENST00000489573,;SMC4,downstream_gene_variant,,ENST00000497984,;SMC4,downstream_gene_variant,,ENST00000487747,;SMC4,downstream_gene_variant,,ENST00000494612,;SMC4,3_prime_UTR_variant,,ENST00000469858,;SMC4,non_coding_transcript_exon_variant,,ENST00000462668,;SMC4,non_coding_transcript_exon_variant,,ENST00000484799,;RP11-432B6.3,intron_variant,,ENST00000483754,;SMC4,downstream_gene_variant,,ENST00000493695,;SMC4,downstream_gene_variant,,ENST00000465563,;SMC4,downstream_gene_variant,,ENST00000468653,;SMC4,downstream_gene_variant,,ENST00000467263,;SMC4,upstream_gene_variant,,ENST00000497203,;	C	ENSG00000113810	ENST00000357388	Transcript	missense_variant	2105	1654	552	E/Q	Gaa/Caa	.	.	.	1	SMC4	HGNC	14013	protein_coding	YES	CCDS3189.1	ENSP00000349961	SMC4_HUMAN	C9JWF0_HUMAN,C9JVD8_HUMAN,C9JR83_HUMAN,C9JJ64_HUMAN,C9J9E4_HUMAN,C9J578_HUMAN,C9IYK2_HUMAN	UPI000006DA0A	.	tolerated(0.09)	benign(0.052)	11/24	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF148,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACTGAACAA	.	4	ESCA
SLC7A14	0	.	GRCh37	3	170198910	170198910	+	Silent	SNP	G	G	A	rs375259922	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1161C>T	p.%3D	p.A387A	ENST00000231706	7/8	37	26	10	18	18	0	SLC7A14,synonymous_variant,p.%3D,ENST00000231706,;CLDN11,intron_variant,,ENST00000486975,;CLDN11,intron_variant,,ENST00000451576,;CLDN11,intron_variant,,ENST00000480067,;CLDN11,intron_variant,,ENST00000471373,;	A	ENSG00000013293	ENST00000231706	Transcript	synonymous_variant	1477	1161	387	A	gcC/gcT	rs375259922	.	.	-1	SLC7A14	HGNC	29326	protein_coding	YES	CCDS33892.1	ENSP00000231706	S7A14_HUMAN	.	UPI0000051F6B	.	.	.	7/8	.	Transmembrane_helices:TMhelix,Pfam_domain:PF13520,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF250	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCAGGCCAC	byCluster	5	ESCA
EIF5A2	0	.	GRCh37	3	170607019	170607019	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4130G>C	.	.	ENST00000295822	5/5	56	47	9	23	23	0	EIF5A2,3_prime_UTR_variant,,ENST00000295822,;EIF5A2,downstream_gene_variant,,ENST00000474096,;EIF5A2,downstream_gene_variant,,ENST00000487522,;EIF5A2,downstream_gene_variant,,ENST00000460117,;	G	ENSG00000163577	ENST00000295822	Transcript	3_prime_UTR_variant	4778	.	.	.	.	.	.	.	-1	EIF5A2	HGNC	3301	protein_coding	YES	CCDS3214.1	ENSP00000295822	IF5A2_HUMAN	C9J4W5_HUMAN	UPI0000035FC3	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTCAGGCA	.	5	ESCA
PIK3CA	0	.	GRCh37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	10/21	120	98	22	60	60	0	PIK3CA,missense_variant,p.Glu545Lys,ENST00000263967,;PIK3CA,upstream_gene_variant,,ENST00000462255,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	1790	1633	545	E/K	Gag/Aag	rs104886003,COSM763,COSM27133,COSM125370,COSM295672	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	deleterious(0.02)	probably_damaging(0.959)	10/21	.	PROSITE_profiles:PS51545,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Pfam_domain:PF00613,Gene3D:1.25.40.70,SMART_domains:SM00145,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	not_provided,pathogenic	0,1,1,1,1	21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E545K|c.1633G>A|227,SITE|p.E545K|c.1633G>A|1153,CODON|p.T544N|c.1631C>A|3,BUFFER|p.E542Q|c.1624G>C|8,BUFFER|p.E542K|c.1624G>A|115,BUFFER|p.E542K|c.1624G>A|758,BUFFER|p.E542G|c.1625A>G|3,BUFFER|p.E542V|c.1625A>T|14,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.E542V|c.1625A>T|5,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.I543V|c.1627A>G|3,BUFFER|p.E545Q|c.1633G>C|30,BUFFER|p.E545Q|c.1633G>C|9,BUFFER|p.E545A|c.1634A>C|130,BUFFER|p.E545V|c.1634A>T|4,BUFFER|p.E545A|c.1634A>C|11,BUFFER|p.E545G|c.1634A>G|14,BUFFER|p.E545G|c.1634A>G|90,BUFFER|p.E545D|c.1635G>T|13,BUFFER|p.E545D|c.1635G>C|11,BUFFER|p.E545D|c.1635G>T|4,BUFFER|p.Q546K|c.1636C>A|119,BUFFER|p.Q546E|c.1636C>G|15,BUFFER|p.Q546K|c.1636C>A|18,BUFFER|p.Q546R|c.1637A>G|20,BUFFER|p.Q546P|c.1637A>C|22,BUFFER|p.Q546P|c.1637A>C|7,BUFFER|p.Q546L|c.1637A>T|8,BUFFER|p.Q546R|c.1637A>G|41,BUFFER|p.Q546H|c.1638G>T|7,BUFFER|p.E547K|c.1639G>A|11,BUFFER|p.E547G|c.1640A>G|5,BUFFER|p.E547G|c.1640A>G|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTGAGCAG	byCluster	5	ESCA
LEPREL1	0	.	GRCh37	3	189838136	189838136	+	Missense_Mutation	SNP	C	C	A	rs200731219	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385G>T	p.Gly129Trp	p.G129W	ENST00000319332	1/15	34	22	12	14	14	0	LEPREL1,missense_variant,p.Gly129Trp,ENST00000319332,;LEPREL1,intron_variant,,ENST00000426003,;LEPREL1,intron_variant,,ENST00000427335,;LEPREL1,upstream_gene_variant,,ENST00000444866,;LEPREL1-AS1,upstream_gene_variant,,ENST00000412203,;	A	ENSG00000090530	ENST00000319332	Transcript	missense_variant	583	385	129	G/W	Ggg/Tgg	rs200731219	.	.	-1	LEPREL1	HGNC	19317	protein_coding	YES	CCDS3294.1	ENSP00000316881	P3H2_HUMAN	D3DNV8_HUMAN,C9JSL4_HUMAN,C9J313_HUMAN	UPI000007460B	.	deleterious(0)	probably_damaging(0.998)	1/15	.	hmmpanther:PTHR14049,hmmpanther:PTHR14049:SF1	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCCGAGGC	byFrequency|byCluster	5	ESCA
OPA1	0	.	GRCh37	3	193335055	193335055	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.537G>A	p.%3D	p.L179L	ENST00000361908	4/30	38	35	3	25	25	0	OPA1,synonymous_variant,p.%3D,ENST00000419435,;OPA1,synonymous_variant,p.%3D,ENST00000361828,;OPA1,synonymous_variant,p.%3D,ENST00000392438,;OPA1,synonymous_variant,p.%3D,ENST00000434811,;OPA1,synonymous_variant,p.%3D,ENST00000361510,;OPA1,synonymous_variant,p.%3D,ENST00000392436,;OPA1,synonymous_variant,p.%3D,ENST00000361908,;OPA1,intron_variant,,ENST00000392437,;OPA1,intron_variant,,ENST00000361715,;OPA1,intron_variant,,ENST00000361150,;OPA1-AS1,downstream_gene_variant,,ENST00000433105,;OPA1-AS1,downstream_gene_variant,,ENST00000444085,;OPA1,non_coding_transcript_exon_variant,,ENST00000487986,;OPA1,upstream_gene_variant,,ENST00000497189,;	A	ENSG00000198836	ENST00000361908	Transcript	synonymous_variant	771	537	179	L	ttG/ttA	.	.	.	1	OPA1	HGNC	8140	protein_coding	YES	CCDS33917.1	ENSP00000354681	OPA1_HUMAN	Q6PEK6_HUMAN,E5KLJ7_HUMAN,C9JY58_HUMAN	UPI0000422960	.	.	.	4/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTATTGAAGGA	.	2	ESCA
ZNF860	0	.	GRCh37	3	32031299	32031299	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.728C>G	p.Ser243Ter	p.S243*	ENST00000360311	2/2	93	49	43	76	76	0	ZNF860,stop_gained,p.Ser243Ter,ENST00000360311,;OSBPL10,intron_variant,,ENST00000479173,;ZNF860,downstream_gene_variant,,ENST00000489408,;	G	ENSG00000197385	ENST00000360311	Transcript	stop_gained	1277	728	243	S/*	tCa/tGa	.	.	.	1	ZNF860	HGNC	34513	protein_coding	YES	CCDS46784.1	ENSP00000373274	ZN860_HUMAN	.	UPI0000D61AE9	.	.	.	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF1,Gene3D:3.30.160.60,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCTCACTCT	.	5	ESCA
CLASP2	0	.	GRCh37	3	33592770	33592770	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000468888	30/39	42	36	6	23	23	0	CLASP2,missense_variant,p.Glu107Gln,ENST00000480385,;CLASP2,missense_variant,p.Glu532Gln,ENST00000307312,;CLASP2,missense_variant,p.Glu1042Gln,ENST00000359576,;CLASP2,missense_variant,p.Glu810Gln,ENST00000461133,;CLASP2,missense_variant,p.Glu1051Gln,ENST00000468888,;CLASP2,missense_variant,p.Glu1050Gln,ENST00000399362,;CLASP2,missense_variant,p.Glu820Gln,ENST00000539981,;CLASP2,missense_variant,p.Glu830Gln,ENST00000480013,;COX6CP10,upstream_gene_variant,,ENST00000416832,;	G	ENSG00000163539	ENST00000468888	Transcript	missense_variant	3198	3151	1051	E/Q	Gaa/Caa	.	.	.	-1	CLASP2	HGNC	17078	protein_coding	YES	.	ENSP00000419974	.	Q6N029_HUMAN,Q07A20_HUMAN,E7EW49_HUMAN,B2RTR1_HUMAN	UPI0001B7944B	.	deleterious(0.01)	benign(0.057)	30/39	.	hmmpanther:PTHR21567:SF30,hmmpanther:PTHR21567,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.K1045Q|c.3133A>C|3,BUFFER|p.K822Q|c.2464A>C|3,BUFFER|p.K832Q|c.2494A>C|3	RADIA|MUTECT|MUSE|VARSCANS	GGGTTCTGTTG	.	4	ESCA
PDCD6IP	0	.	GRCh37	3	33870405	33870405	+	Nonsense_Mutation	SNP	C	C	T	rs777618163	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.793C>T	p.Gln265Ter	p.Q265*	ENST00000457054	7/18	59	45	14	45	45	0	PDCD6IP,stop_gained,p.Gln260Ter,ENST00000307296,;PDCD6IP,stop_gained,p.Gln265Ter,ENST00000457054,;PDCD6IP,downstream_gene_variant,,ENST00000413073,;PDCD6IP,non_coding_transcript_exon_variant,,ENST00000482561,;PDCD6IP,downstream_gene_variant,,ENST00000477798,;PDCD6IP,downstream_gene_variant,,ENST00000484478,;PDCD6IP,stop_gained,p.Gln70Ter,ENST00000412887,;PDCD6IP,non_coding_transcript_exon_variant,,ENST00000487821,;PDCD6IP,downstream_gene_variant,,ENST00000435909,;PDCD6IP,downstream_gene_variant,,ENST00000459659,;PDCD6IP,downstream_gene_variant,,ENST00000494810,;	T	ENSG00000170248	ENST00000457054	Transcript	stop_gained	948	793	265	Q/*	Cag/Tag	rs777618163	.	.	1	PDCD6IP	HGNC	8766	protein_coding	YES	CCDS54561.1	ENSP00000411825	PDC6I_HUMAN	.	UPI00004121D3	.	.	.	7/18	.	PROSITE_profiles:PS51180,hmmpanther:PTHR23030:SF19,hmmpanther:PTHR23030,Pfam_domain:PF03097,Gene3D:2xs1A01,SMART_domains:SM01041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATCAGTCT	.	5	ESCA
ZNF501	0	.	GRCh37	3	44777740	44777740	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1011G>C	.	.	ENST00000396048	3/3	24	16	8	26	26	0	ZNF501,3_prime_UTR_variant,,ENST00000396048,;KIAA1143,downstream_gene_variant,,ENST00000484437,;ZNF501,downstream_gene_variant,,ENST00000491543,;ZNF501,downstream_gene_variant,,ENST00000484233,;ZNF501,downstream_gene_variant,,ENST00000486486,;	C	ENSG00000186446	ENST00000396048	Transcript	3_prime_UTR_variant	2264	.	.	.	.	.	.	.	1	ZNF501	HGNC	23717	protein_coding	YES	CCDS2720.2	ENSP00000379363	ZN501_HUMAN	Q15923_HUMAN	UPI00005A76A1	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATGAAAAA	.	5	ESCA
ROBO1	0	.	GRCh37	3	78689030	78689030	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2901C>A	p.%3D	p.I967I	ENST00000464233	22/31	44	36	8	33	33	0	ROBO1,synonymous_variant,p.%3D,ENST00000464233,;ROBO1,synonymous_variant,p.%3D,ENST00000495273,;ROBO1,synonymous_variant,p.%3D,ENST00000436010,;ROBO1,synonymous_variant,p.%3D,ENST00000467549,;ROBO1,non_coding_transcript_exon_variant,,ENST00000498428,;	T	ENSG00000169855	ENST00000464233	Transcript	synonymous_variant	3015	2901	967	I	atC/atA	.	.	.	-1	ROBO1	HGNC	10249	protein_coding	YES	CCDS54611.1	ENSP00000420321	ROBO1_HUMAN	.	UPI00000713D9	.	.	.	22/31	.	hmmpanther:PTHR10489:SF107,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACTGATGTT	.	4	ESCA
STX19	0	.	GRCh37	3	93733383	93733383	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731G>C	p.Gly244Ala	p.G244A	ENST00000315099	2/2	57	53	4	29	29	0	STX19,missense_variant,p.Gly244Ala,ENST00000315099,;ARL13B,intron_variant,,ENST00000394222,;ARL13B,intron_variant,,ENST00000303097,;ARL13B,intron_variant,,ENST00000535334,;ARL13B,intron_variant,,ENST00000471138,;ARL13B,intron_variant,,ENST00000539730,;ARL13B,intron_variant,,ENST00000486562,;ARL13B,intron_variant,,ENST00000335438,;ARL13B,intron_variant,,ENST00000460371,;	G	ENSG00000178750	ENST00000315099	Transcript	missense_variant	988	731	244	G/A	gGa/gCa	.	.	.	-1	STX19	HGNC	19300	protein_coding	YES	CCDS33793.1	ENSP00000320679	STX19_HUMAN	.	UPI00000471EA	.	tolerated(0.32)	probably_damaging(1)	2/2	.	PROSITE_profiles:PS50192,hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF29,PROSITE_patterns:PS00914,Gene3D:1.20.5.110,Pfam_domain:PF05739,SMART_domains:SM00397,Superfamily_domains:SSF47661	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCTCCTTGT	.	2	ESCA
H2AFZ	0	.	GRCh37	4	100870839	100870839	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.62C>T	p.Ser21Leu	p.S21L	ENST00000296417	2/5	12	6	6	17	17	0	H2AFZ,missense_variant,p.Ser21Leu,ENST00000296417,;DNAJB14,upstream_gene_variant,,ENST00000442697,;RP11-15B17.1,upstream_gene_variant,,ENST00000507494,;RP11-15B17.1,upstream_gene_variant,,ENST00000501976,;RP11-15B17.1,upstream_gene_variant,,ENST00000514624,;H2AFZ,non_coding_transcript_exon_variant,,ENST00000529158,;DNAJB14,upstream_gene_variant,,ENST00000471738,;H2AFZ,non_coding_transcript_exon_variant,,ENST00000511319,;H2AFZ,non_coding_transcript_exon_variant,,ENST00000511348,;H2AFZ,non_coding_transcript_exon_variant,,ENST00000527366,;H2AFZ,non_coding_transcript_exon_variant,,ENST00000511203,;DNAJB14,upstream_gene_variant,,ENST00000398991,;DNAJB14,upstream_gene_variant,,ENST00000474664,;DNAJB14,upstream_gene_variant,,ENST00000334223,;DNAJB14,upstream_gene_variant,,ENST00000469942,;DNAJB14,upstream_gene_variant,,ENST00000426476,;	A	ENSG00000164032	ENST00000296417	Transcript	missense_variant	280	62	21	S/L	tCg/tTg	COSM4120982	.	.	-1	H2AFZ	HGNC	4741	protein_coding	YES	CCDS3654.1	ENSP00000296417	H2AZ_HUMAN	.	UPI0000000FEF	.	tolerated(0.13)	benign(0.11)	2/5	.	hmmpanther:PTHR23430:SF34,hmmpanther:PTHR23430,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCTGCGAGCGG	.	3	ESCA
UBE2D3	0	.	GRCh37	4	103720628	103720628	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340G>C	p.Asp114His	p.D114H	ENST00000357194	6/7	28	19	8	28	28	0	UBE2D3,missense_variant,p.Asp112His,ENST00000453744,;UBE2D3,missense_variant,p.Asp83His,ENST00000502404,;UBE2D3,missense_variant,p.Asp112His,ENST00000321805,;UBE2D3,missense_variant,p.Asp112His,ENST00000349311,;UBE2D3,missense_variant,p.Asp83His,ENST00000505207,;UBE2D3,missense_variant,p.Asp114His,ENST00000357194,;UBE2D3,missense_variant,p.Asp112His,ENST00000343106,;UBE2D3,missense_variant,p.Asp112His,ENST00000338145,;UBE2D3,missense_variant,p.Asp106His,ENST00000350435,;UBE2D3,missense_variant,p.Asp112His,ENST00000394804,;UBE2D3,missense_variant,p.Asp112His,ENST00000394801,;UBE2D3,missense_variant,p.Asp83His,ENST00000504211,;UBE2D3,missense_variant,p.Asp112His,ENST00000394803,;UBE2D3,missense_variant,p.Asp83His,ENST00000507845,;UBE2D3,downstream_gene_variant,,ENST00000508238,;UBE2D3,downstream_gene_variant,,ENST00000502690,;UBE2D3,downstream_gene_variant,,ENST00000508476,;UBE2D3,downstream_gene_variant,,ENST00000508249,;UBE2D3,3_prime_UTR_variant,,ENST00000505307,;UBE2D3,3_prime_UTR_variant,,ENST00000508635,;UBE2D3,3_prime_UTR_variant,,ENST00000510129,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000508474,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000503742,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000505009,;UBE2D3,downstream_gene_variant,,ENST00000503418,;UBE2D3,downstream_gene_variant,,ENST00000510599,;UBE2D3,downstream_gene_variant,,ENST00000508974,;UBE2D3,downstream_gene_variant,,ENST00000508818,;UBE2D3,downstream_gene_variant,,ENST00000502563,;UBE2D3,downstream_gene_variant,,ENST00000514755,;	G	ENSG00000109332	ENST00000357194	Transcript	missense_variant	492	340	114	D/H	Gat/Cat	.	.	.	-1	UBE2D3	HGNC	12476	protein_coding	YES	CCDS3659.1	ENSP00000349722	UB2D3_HUMAN	D6RFM0_HUMAN,D6RAW0_HUMAN,D6RAH7_HUMAN	UPI00001B31EA	.	deleterious_low_confidence(0)	probably_damaging(0.949)	6/7	.	PROSITE_profiles:PS50127,hmmpanther:PTHR24068:SF48,hmmpanther:PTHR24068,Gene3D:3.10.110.10,Pfam_domain:PF00179,SMART_domains:SM00212,Superfamily_domains:SSF54495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGATCACATA	.	5	ESCA
ARHGEF38	0	.	GRCh37	4	106588313	106588313	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1717C>T	p.His573Tyr	p.H573Y	ENST00000420470	12/14	39	31	8	35	35	0	ARHGEF38,missense_variant,p.His573Tyr,ENST00000420470,;ARHGEF38,non_coding_transcript_exon_variant,,ENST00000508036,;	T	ENSG00000236699	ENST00000420470	Transcript	missense_variant	1861	1717	573	H/Y	Cat/Tat	.	.	.	1	ARHGEF38	HGNC	25968	protein_coding	YES	CCDS56338.1	ENSP00000416125	ARH38_HUMAN	.	UPI0001D3B6A5	.	tolerated(0.49)	benign(0.09)	12/14	.	hmmpanther:PTHR22834:SF18,hmmpanther:PTHR22834,Gene3D:2.30.30.40,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTCATCGC	.	5	ESCA
PLK4	0	.	GRCh37	4	128819601	128819601	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2818G>C	p.Glu940Gln	p.E940Q	ENST00000270861	16/16	35	29	6	38	38	0	PLK4,missense_variant,p.Glu186Gln,ENST00000508113,;PLK4,missense_variant,p.Glu908Gln,ENST00000513090,;PLK4,missense_variant,p.Glu862Gln,ENST00000515069,;PLK4,missense_variant,p.Glu879Gln,ENST00000507249,;PLK4,missense_variant,p.Glu940Gln,ENST00000270861,;PLK4,missense_variant,p.Glu899Gln,ENST00000514379,;PLK4,non_coding_transcript_exon_variant,,ENST00000510192,;	C	ENSG00000142731	ENST00000270861	Transcript	missense_variant	3092	2818	940	E/Q	Gaa/Caa	.	.	.	1	PLK4	HGNC	11397	protein_coding	YES	CCDS3735.1	ENSP00000270861	PLK4_HUMAN	.	UPI000007426E	.	tolerated(0.29)	benign(0.177)	16/16	.	PROSITE_profiles:PS50078,hmmpanther:PTHR24345,hmmpanther:PTHR24345:SF50,Pfam_domain:PF00659,Superfamily_domains:SSF82615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGAGAAAAT	.	5	ESCA
DCLK2	0	.	GRCh37	4	151153530	151153530	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1392G>A	p.%3D	p.V464V	ENST00000302176	10/17	33	27	6	48	48	0	DCLK2,synonymous_variant,p.%3D,ENST00000302176,;DCLK2,synonymous_variant,p.%3D,ENST00000296550,;DCLK2,synonymous_variant,p.%3D,ENST00000506325,;DCLK2,synonymous_variant,p.%3D,ENST00000411937,;	A	ENSG00000170390	ENST00000302176	Transcript	synonymous_variant	1392	1392	464	V	gtG/gtA	.	.	.	1	DCLK2	HGNC	19002	protein_coding	YES	CCDS47142.2	ENSP00000303887	DCLK2_HUMAN	.	UPI0000D615C9	.	.	.	10/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF122,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CGAGTGAAACA	.	4	ESCA
FAM198B	0	.	GRCh37	4	159092457	159092457	+	Missense_Mutation	SNP	C	C	A	rs781338886	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71G>T	p.Arg24Leu	p.R24L	ENST00000393807	2/6	20	10	9	19	19	0	FAM198B,missense_variant,p.Arg24Leu,ENST00000296530,;FAM198B,missense_variant,p.Arg24Leu,ENST00000393807,;FAM198B,missense_variant,p.Arg24Leu,ENST00000592057,;FAM198B,missense_variant,p.Arg24Leu,ENST00000585682,;FAM198B,upstream_gene_variant,,ENST00000593260,;FAM198B,downstream_gene_variant,,ENST00000587787,;FAM198B,upstream_gene_variant,,ENST00000592586,;RP11-597D13.9,non_coding_transcript_exon_variant,,ENST00000509463,;RP11-597D13.9,non_coding_transcript_exon_variant,,ENST00000503611,;RP11-597D13.9,upstream_gene_variant,,ENST00000514381,;RP11-597D13.9,upstream_gene_variant,,ENST00000505532,;FAM198B,intron_variant,,ENST00000589306,;	A	ENSG00000164125	ENST00000393807	Transcript	missense_variant	478	71	24	R/L	cGt/cTt	rs781338886,COSM4123151,COSM4123150,COSM4123152	.	.	-1	FAM198B	HGNC	25312	protein_coding	YES	CCDS34087.1	ENSP00000377396	F198B_HUMAN	K7EK71_HUMAN	UPI00003672A2	.	tolerated(0.19)	benign(0.002)	2/6	.	hmmpanther:PTHR15905,hmmpanther:PTHR15905:SF1	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTACGCACC	byFrequency	5	ESCA
TLL1	0	.	GRCh37	4	167023330	167023330	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1302C>T	.	.	ENST00000061240	21/21	27	23	4	9	9	0	TLL1,3_prime_UTR_variant,,ENST00000061240,;TLL1,downstream_gene_variant,,ENST00000507499,;TLL1,downstream_gene_variant,,ENST00000509505,;	T	ENSG00000038295	ENST00000061240	Transcript	3_prime_UTR_variant	4991	.	.	.	.	.	.	.	1	TLL1	HGNC	11843	protein_coding	YES	CCDS3811.1	ENSP00000061240	TLL1_HUMAN	D6RCE0_HUMAN	UPI0000072EED	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGATCCTCCT	.	4	ESCA
DDX60L	0	.	GRCh37	4	169377190	169377190	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837A>T	p.Leu279Phe	p.L279F	ENST00000260184	7/38	27	17	10	24	24	0	DDX60L,missense_variant,p.Leu279Phe,ENST00000511577,;DDX60L,missense_variant,p.Leu279Phe,ENST00000505890,;DDX60L,missense_variant,p.Leu7Phe,ENST00000505863,;DDX60L,missense_variant,p.Leu279Phe,ENST00000260184,;	A	ENSG00000181381	ENST00000260184	Transcript	missense_variant	1058	837	279	L/F	ttA/ttT	.	.	.	-1	DDX60L	HGNC	26429	protein_coding	YES	CCDS47161.1	ENSP00000260184	DDX6L_HUMAN	D6RIU1_HUMAN,D6RBA2_HUMAN,D6RB62_HUMAN	UPI0001553B03	.	deleterious(0.04)	possibly_damaging(0.862)	7/38	.	hmmpanther:PTHR11752,hmmpanther:PTHR11752:SF56	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTACTAAGAC	.	5	ESCA
LAP3	0	.	GRCh37	4	17600162	17600162	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1161C>G	p.%3D	p.L387L	ENST00000226299	10/13	34	26	8	49	49	0	LAP3,synonymous_variant,p.%3D,ENST00000226299,;LAP3,synonymous_variant,p.%3D,ENST00000606142,;LAP3,intron_variant,,ENST00000513105,;AC006160.5,intron_variant,,ENST00000511010,;RN7SL315P,upstream_gene_variant,,ENST00000580348,;LAP3,non_coding_transcript_exon_variant,,ENST00000503467,;LAP3,non_coding_transcript_exon_variant,,ENST00000504614,;	G	ENSG00000002549	ENST00000226299	Transcript	synonymous_variant	1435	1161	387	L	ctC/ctG	.	.	.	1	LAP3	HGNC	18449	protein_coding	YES	CCDS3422.1	ENSP00000226299	AMPL_HUMAN	.	UPI000014F97D	.	.	.	10/13	.	HAMAP:MF_00181,hmmpanther:PTHR11963,hmmpanther:PTHR11963:SF13,Gene3D:3.40.630.10,Pfam_domain:PF00883,Superfamily_domains:SSF53187,Prints_domain:PR00481	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCTCAATGC	.	2	ESCA
WDR17	0	.	GRCh37	4	177052858	177052858	+	Missense_Mutation	SNP	G	G	C	rs778731861	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1139G>C	p.Gly380Ala	p.G380A	ENST00000280190	8/31	68	61	7	81	81	0	WDR17,missense_variant,p.Gly363Ala,ENST00000507824,;WDR17,missense_variant,p.Gly129Ala,ENST00000505894,;WDR17,missense_variant,p.Gly380Ala,ENST00000280190,;WDR17,missense_variant,p.Gly356Ala,ENST00000508596,;WDR17,missense_variant,p.Gly356Ala,ENST00000393643,;	C	ENSG00000150627	ENST00000280190	Transcript	missense_variant	1295	1139	380	G/A	gGa/gCa	rs778731861	.	.	1	WDR17	HGNC	16661	protein_coding	YES	CCDS3825.1	ENSP00000280190	WDR17_HUMAN	Q0QD35_HUMAN,E7EP77_HUMAN	UPI000019C575	.	tolerated(0.16)	benign(0.358)	8/31	.	hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF344,Gene3D:2.130.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TATGGGAGCTA	.	3	ESCA
LIMCH1	0	.	GRCh37	4	41699228	41699228	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*26T>C	.	.	ENST00000313860	27/27	28	24	4	30	30	0	LIMCH1,3_prime_UTR_variant,,ENST00000512820,;LIMCH1,3_prime_UTR_variant,,ENST00000503057,;LIMCH1,3_prime_UTR_variant,,ENST00000508501,;LIMCH1,3_prime_UTR_variant,,ENST00000508466,;LIMCH1,3_prime_UTR_variant,,ENST00000511496,;LIMCH1,3_prime_UTR_variant,,ENST00000381753,;LIMCH1,3_prime_UTR_variant,,ENST00000512946,;LIMCH1,3_prime_UTR_variant,,ENST00000512632,;LIMCH1,3_prime_UTR_variant,,ENST00000313860,;LIMCH1,3_prime_UTR_variant,,ENST00000513024,;LIMCH1,3_prime_UTR_variant,,ENST00000514096,;LIMCH1,3_prime_UTR_variant,,ENST00000396595,;LIMCH1,3_prime_UTR_variant,,ENST00000509277,;RP11-227F19.5,upstream_gene_variant,,ENST00000506475,;LIMCH1,non_coding_transcript_exon_variant,,ENST00000505705,;LIMCH1,non_coding_transcript_exon_variant,,ENST00000515785,;	C	ENSG00000064042	ENST00000313860	Transcript	3_prime_UTR_variant	3332	.	.	.	.	.	.	.	1	LIMCH1	HGNC	29191	protein_coding	YES	CCDS33977.1	ENSP00000316891	LIMC1_HUMAN	D6RJ93_HUMAN,D6RGH8_HUMAN,D6R8Y0_HUMAN	UPI0000D61554	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	ATCACTCACCA	.	2	ESCA
ATP8A1	0	.	GRCh37	4	42505477	42505477	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2141G>T	p.Gly714Val	p.G714V	ENST00000381668	24/37	56	49	6	49	49	0	ATP8A1,missense_variant,p.Gly714Val,ENST00000381668,;ATP8A1,missense_variant,p.Gly699Val,ENST00000264449,;ATP8A1,missense_variant,p.Gly65Val,ENST00000514372,;	A	ENSG00000124406	ENST00000381668	Transcript	missense_variant	2373	2141	714	G/V	gGc/gTc	.	.	.	-1	ATP8A1	HGNC	13531	protein_coding	YES	CCDS3466.1	ENSP00000371084	AT8A1_HUMAN	H0YAJ4_HUMAN	UPI0000125063	.	deleterious(0.01)	benign(0.301)	24/37	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF56,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01652,Pfam_domain:PF12710,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GAGAGCCTTCA	.	3	ESCA
GNPDA2	0	.	GRCh37	4	44704577	44704577	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*521T>C	.	.	ENST00000295448	7/7	48	41	6	56	56	0	GNPDA2,3_prime_UTR_variant,,ENST00000295448,;GNPDA2,3_prime_UTR_variant,,ENST00000507917,;GNPDA2,intron_variant,,ENST00000608855,;GNPDA2,intron_variant,,ENST00000609092,;GNPDA2,downstream_gene_variant,,ENST00000509756,;GUF1,downstream_gene_variant,,ENST00000281543,;GNPDA2,downstream_gene_variant,,ENST00000507534,;RP11-700J17.2,upstream_gene_variant,,ENST00000610267,;GUF1,downstream_gene_variant,,ENST00000511493,;GNPDA2,downstream_gene_variant,,ENST00000511187,;GUF1,downstream_gene_variant,,ENST00000506793,;	G	ENSG00000163281	ENST00000295448	Transcript	3_prime_UTR_variant	1509	.	.	.	.	.	.	.	-1	GNPDA2	HGNC	21526	protein_coding	YES	CCDS3469.1	ENSP00000295448	GNPI2_HUMAN	.	UPI000004D013	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATATATAGCA	.	5	ESCA
GABRA2	0	.	GRCh37	4	46252361	46252361	+	Nonsense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1320T>G	p.Tyr440Ter	p.Y440*	ENST00000510861	10/10	41	25	15	28	28	0	GABRA2,stop_gained,p.Tyr440Ter,ENST00000510861,;GABRA2,stop_gained,p.Tyr440Ter,ENST00000356504,;GABRA2,stop_gained,p.Tyr500Ter,ENST00000507069,;GABRA2,stop_gained,p.Tyr440Ter,ENST00000381620,;GABRA2,stop_gained,p.Tyr445Ter,ENST00000540012,;GABRA2,stop_gained,p.Tyr440Ter,ENST00000514090,;GABRA2,3_prime_UTR_variant,,ENST00000513005,;GABRA2,3_prime_UTR_variant,,ENST00000510233,;	C	ENSG00000151834	ENST00000510861	Transcript	stop_gained	1494	1320	440	Y/*	taT/taG	.	.	.	-1	GABRA2	HGNC	4076	protein_coding	YES	CCDS3471.1	ENSP00000421828	GBRA2_HUMAN	Q4W5L8_HUMAN,D6RBL7_HUMAN,D6RBK9_HUMAN,D6RB77_HUMAN	UPI000013DC88	.	.	.	10/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF218,hmmpanther:PTHR18945,Gene3D:1.20.58.390,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR00253,Prints_domain:PR01079	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAAATATGT	.	5	ESCA
ERVMER34-1	0	.	GRCh37	4	53610238	53610238	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1450G>A	p.Gly484Arg	p.G484R	ENST00000443173	3/3	39	36	3	33	33	0	ERVMER34-1,missense_variant,p.Gly484Arg,ENST00000540758,;ERVMER34-1,missense_variant,p.Gly484Arg,ENST00000440542,;ERVMER34-1,missense_variant,p.Gly484Arg,ENST00000443173,;SNORA26,upstream_gene_variant,,ENST00000391188,;ERVMER34-1,intron_variant,,ENST00000454756,;	T	ENSG00000226887	ENST00000443173	Transcript	missense_variant	2311	1450	484	G/R	Gga/Aga	.	.	.	-1	ERVMER34-1	HGNC	42970	protein_coding	YES	.	ENSP00000460602	MER34_HUMAN	.	UPI000006F57C	.	tolerated_low_confidence(0.2)	probably_damaging(0.979)	3/3	.	hmmpanther:PTHR10424:SF42,hmmpanther:PTHR10424	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCTCCCACTT	.	2	ESCA
AASDH	0	.	GRCh37	4	57215467	57215467	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2450C>T	p.Ser817Leu	p.S817L	ENST00000205214	11/15	25	21	4	31	31	0	AASDH,missense_variant,p.Ser332Leu,ENST00000434343,;AASDH,missense_variant,p.Ser664Leu,ENST00000602986,;AASDH,missense_variant,p.Ser817Leu,ENST00000451613,;AASDH,missense_variant,p.Ser817Leu,ENST00000205214,;AASDH,missense_variant,p.Ser817Leu,ENST00000502617,;AASDH,missense_variant,p.Ser717Leu,ENST00000513376,;AASDH,3_prime_UTR_variant,,ENST00000503808,;AASDH,3_prime_UTR_variant,,ENST00000514745,;	A	ENSG00000157426	ENST00000205214	Transcript	missense_variant	2631	2450	817	S/L	tCa/tTa	.	.	.	-1	AASDH	HGNC	23993	protein_coding	YES	CCDS3504.1	ENSP00000205214	ACSF4_HUMAN	G3V0G4_HUMAN	UPI000020B8EF	.	deleterious(0)	probably_damaging(0.97)	11/15	.	Superfamily_domains:SSF50998,Pfam_domain:PF13360,Gene3D:2.140.10.10,hmmpanther:PTHR24095:SF43,hmmpanther:PTHR24095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGCTGAGGAT	.	3	ESCA
PKD2	0	.	GRCh37	4	88957371	88957371	+	Splice_Site	SNP	G	G	T	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.710-1G>T	.	p.X237_splice	ENST00000237596	.	9	6	3	19	19	0	PKD2,splice_acceptor_variant,,ENST00000237596,;PKD2,non_coding_transcript_exon_variant,,ENST00000506367,;PKD2,non_coding_transcript_exon_variant,,ENST00000506727,;	T	ENSG00000118762	ENST00000237596	Transcript	splice_acceptor_variant	.	.	.	.	.	COSM1058697	.	.	1	PKD2	HGNC	9009	protein_coding	YES	CCDS3627.1	ENSP00000237596	PKD2_HUMAN	Q9UEU6_HUMAN,B7Z2D4_HUMAN,B4DFN3_HUMAN,B4DE45_HUMAN	UPI000013CA1D	.	.	.	.	2/14	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTCCAGTGACC	.	2	ESCA
SLCO4C1	0	.	GRCh37	5	101572434	101572434	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128C>G	.	.	ENST00000310954	13/13	46	41	5	42	42	0	SLCO4C1,3_prime_UTR_variant,,ENST00000310954,;AC008948.1,downstream_gene_variant,,ENST00000597120,;	C	ENSG00000173930	ENST00000310954	Transcript	3_prime_UTR_variant	2590	.	.	.	.	.	.	.	-1	SLCO4C1	HGNC	23612	protein_coding	YES	CCDS34205.1	ENSP00000309741	SO4C1_HUMAN	Q63HP3_HUMAN	UPI00001C10B6	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTGATTAT	.	4	ESCA
PCDHB14	0	.	GRCh37	5	140604233	140604233	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1156C>G	p.Gln386Glu	p.Q386E	ENST00000239449	1/1	46	40	6	43	43	0	PCDHB14,missense_variant,p.Gln386Glu,ENST00000239449,;PCDHB14,missense_variant,p.Gln233Glu,ENST00000515856,;	G	ENSG00000120327	ENST00000239449	Transcript	missense_variant	1156	1156	386	Q/E	Caa/Gaa	.	.	.	1	PCDHB14	HGNC	8685	protein_coding	YES	CCDS4256.1	ENSP00000239449	PCDBE_HUMAN	B4DPE2_HUMAN	UPI00001273E7	.	tolerated_low_confidence(0.11)	benign(0.26)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTATTCAAGAT	.	4	ESCA
PCDHGB7	0	.	GRCh37	5	140799311	140799311	+	Missense_Mutation	SNP	G	G	C	rs760207269	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1885G>C	p.Val629Leu	p.V629L	ENST00000398594	1/4	33	26	7	41	41	0	PCDHGB7,missense_variant,p.Val629Leu,ENST00000398594,;PCDHGB6,intron_variant,,ENST00000520790,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGA10,intron_variant,,ENST00000398610,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGA11,upstream_gene_variant,,ENST00000398587,;PCDHGA11,upstream_gene_variant,,ENST00000518882,;	C	ENSG00000254122	ENST00000398594	Transcript	missense_variant	1885	1885	629	V/L	Gtg/Ctg	rs760207269	.	.	1	PCDHGB7	HGNC	8714	protein_coding	YES	CCDS47293.1	ENSP00000381594	PCDGJ_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000007141F	.	deleterious(0.02)	benign(0.05)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF113,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GCATGGTGCGT	byFrequency	4	ESCA
KCTD16	0	.	GRCh37	5	143853706	143853706	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29A>C	.	.	ENST00000507359	3/3	21	17	4	19	19	0	KCTD16,3_prime_UTR_variant,,ENST00000507359,;KCTD16,3_prime_UTR_variant,,ENST00000512467,;	C	ENSG00000183775	ENST00000507359	Transcript	3_prime_UTR_variant	2407	.	.	.	.	.	.	.	1	KCTD16	HGNC	29244	protein_coding	YES	CCDS34260.1	ENSP00000426548	KCD16_HUMAN	.	UPI000004A046	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAAAAAAG	.	5	ESCA
CD74	0	.	GRCh37	5	149792285	149792285	+	Missense_Mutation	SNP	G	G	C	rs776339297	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.28C>G	p.Arg10Gly	p.R10G	ENST00000009530	1/9	28	23	5	43	43	0	CD74,missense_variant,p.Arg10Gly,ENST00000524315,;CD74,missense_variant,p.Arg10Gly,ENST00000353334,;CD74,missense_variant,p.Arg10Gly,ENST00000377795,;CD74,missense_variant,p.Arg5Gly,ENST00000518797,;CD74,missense_variant,p.Arg10Gly,ENST00000009530,;CD74,missense_variant,p.Arg10Gly,ENST00000523813,;CD74,missense_variant,p.Arg7Gly,ENST00000523208,;CD74,missense_variant,p.Arg10Gly,ENST00000522246,;CD74,non_coding_transcript_exon_variant,,ENST00000522153,;CD74,non_coding_transcript_exon_variant,,ENST00000517752,;CD74,non_coding_transcript_exon_variant,,ENST00000523836,;CD74,non_coding_transcript_exon_variant,,ENST00000517791,;	C	ENSG00000019582	ENST00000009530	Transcript	missense_variant	30	28	10	R/G	Cgg/Ggg	rs776339297,COSM145212,COSM1317148	.	.	-1	CD74	HGNC	1697	protein_coding	YES	CCDS47309.1	ENSP00000009530	HG2A_HUMAN	O78208_HUMAN,O19685_HUMAN	UPI000012C6BB	.	tolerated_low_confidence(0.13)	benign(0)	1/9	.	hmmpanther:PTHR14093:SF14,hmmpanther:PTHR14093	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R10W|c.28C>T|3	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TTCCCGACAGC	.	4	ESCA
DCTN4	0	.	GRCh37	5	150088540	150088540	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000446090	.	63	53	10	36	36	0	DCTN4,3_prime_UTR_variant,,ENST00000424236,;DCTN4,3_prime_UTR_variant,,ENST00000447998,;DCTN4,downstream_gene_variant,,ENST00000446090,;	T	ENSG00000132912	ENST00000446090	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1880	-1	DCTN4	HGNC	15518	protein_coding	YES	CCDS47310.1	ENSP00000414906	DCTN4_HUMAN	Q9NSJ5_HUMAN,E5RGG1_HUMAN	UPI0000EE3766	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTCCAAAG	.	5	ESCA
DCTN4	0	.	GRCh37	5	150095155	150095155	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1162G>A	p.Glu388Lys	p.E388K	ENST00000446090	13/14	51	45	5	62	62	0	DCTN4,missense_variant,p.Glu388Lys,ENST00000446090,;DCTN4,missense_variant,p.Glu324Lys,ENST00000424236,;DCTN4,missense_variant,p.Glu381Lys,ENST00000447998,;DCTN4,downstream_gene_variant,,ENST00000518909,;	T	ENSG00000132912	ENST00000446090	Transcript	missense_variant	1204	1162	388	E/K	Gaa/Aaa	.	.	.	-1	DCTN4	HGNC	15518	protein_coding	YES	CCDS47310.1	ENSP00000414906	DCTN4_HUMAN	Q9NSJ5_HUMAN,E5RGG1_HUMAN	UPI0000EE3766	.	tolerated(0.18)	benign(0.046)	13/14	.	Pfam_domain:PF05502,hmmpanther:PTHR13034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGTTCTGCCA	.	4	ESCA
EBF1	0	.	GRCh37	5	158158109	158158109	+	Missense_Mutation	SNP	G	G	C	rs779178390	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1093C>G	p.Arg365Gly	p.R365G	ENST00000313708	11/16	31	19	11	23	23	0	EBF1,missense_variant,p.Arg334Gly,ENST00000380654,;EBF1,missense_variant,p.Arg365Gly,ENST00000313708,;EBF1,missense_variant,p.Arg357Gly,ENST00000517373,;EBF1,non_coding_transcript_exon_variant,,ENST00000518836,;EBF1,non_coding_transcript_exon_variant,,ENST00000523464,;EBF1,non_coding_transcript_exon_variant,,ENST00000519890,;EBF1,non_coding_transcript_exon_variant,,ENST00000522192,;EBF1,non_coding_transcript_exon_variant,,ENST00000519739,;	C	ENSG00000164330	ENST00000313708	Transcript	missense_variant	1376	1093	365	R/G	Cgg/Ggg	rs779178390	.	.	-1	EBF1	HGNC	3126	protein_coding	YES	CCDS4343.1	ENSP00000322898	COE1_HUMAN	.	UPI000000D95E	.	deleterious(0.01)	possibly_damaging(0.707)	11/16	.	hmmpanther:PTHR10747	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCCGAGGAA	.	5	ESCA
MAT2B	0	.	GRCh37	5	162945935	162945935	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*566A>T	.	.	ENST00000321757	7/7	47	42	5	37	37	0	MAT2B,3_prime_UTR_variant,,ENST00000321757,;MAT2B,3_prime_UTR_variant,,ENST00000280969,;MAT2B,3_prime_UTR_variant,,ENST00000518095,;MAT2B,downstream_gene_variant,,ENST00000421814,;MAT2B,non_coding_transcript_exon_variant,,ENST00000521838,;MAT2B,non_coding_transcript_exon_variant,,ENST00000523606,;MAT2B,downstream_gene_variant,,ENST00000520449,;	T	ENSG00000038274	ENST00000321757	Transcript	3_prime_UTR_variant	1710	.	.	.	.	.	.	.	1	MAT2B	HGNC	6905	protein_coding	YES	CCDS4365.1	ENSP00000325425	MAT2B_HUMAN	.	UPI0000037B81	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATAGCAGTTTA	.	2	ESCA
IRX2	0	.	GRCh37	5	2747574	2747574	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*23+81G>A	.	.	ENST00000382611	.	30	22	8	33	33	0	IRX2,3_prime_UTR_variant,,ENST00000302057,;IRX2,intron_variant,,ENST00000382611,;C5orf38,upstream_gene_variant,,ENST00000334000,;C5orf38,upstream_gene_variant,,ENST00000457752,;C5orf38,upstream_gene_variant,,ENST00000397835,;C5orf38,upstream_gene_variant,,ENST00000505778,;C5orf38,upstream_gene_variant,,ENST00000515640,;IRX2,downstream_gene_variant,,ENST00000502957,;C5orf38,upstream_gene_variant,,ENST00000503940,;C5orf38,upstream_gene_variant,,ENST00000505106,;	T	ENSG00000170561	ENST00000382611	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	IRX2	HGNC	14359	protein_coding	YES	CCDS3868.1	ENSP00000372056	IRX2_HUMAN	.	UPI00001B6456	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATGACCAGAA	.	2	ESCA
BDP1	0	.	GRCh37	5	70782376	70782376	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000358731	9/39	53	42	11	35	35	0	BDP1,missense_variant,p.Glu379Gln,ENST00000358731,;BDP1,5_prime_UTR_variant,,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;	C	ENSG00000145734	ENST00000358731	Transcript	missense_variant	1398	1135	379	E/Q	Gag/Cag	.	.	.	1	BDP1	HGNC	13652	protein_coding	YES	CCDS43328.1	ENSP00000351575	BDP1_HUMAN	.	UPI000020CA90	.	deleterious(0)	probably_damaging(0.999)	9/39	.	hmmpanther:PTHR22929:SF0,hmmpanther:PTHR22929	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAGAGAAA	.	5	ESCA
IQGAP2	0	.	GRCh37	5	75888710	75888710	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.867G>A	p.%3D	p.L289L	ENST00000274364	9/36	56	49	7	46	46	0	IQGAP2,synonymous_variant,p.%3D,ENST00000514350,;IQGAP2,synonymous_variant,p.%3D,ENST00000505766,;IQGAP2,synonymous_variant,p.%3D,ENST00000274364,;IQGAP2,5_prime_UTR_variant,,ENST00000379730,;IQGAP2,upstream_gene_variant,,ENST00000504815,;	A	ENSG00000145703	ENST00000274364	Transcript	synonymous_variant	1164	867	289	L	ctG/ctA	COSM3994446	.	.	1	IQGAP2	HGNC	6111	protein_coding	YES	CCDS34188.1	ENSP00000274364	IQGA2_HUMAN	E7EWC2_HUMAN,D6R939_HUMAN	UPI000020CB2C	.	.	.	9/36	.	hmmpanther:PTHR14149,hmmpanther:PTHR14149:SF12	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTGACACA	.	4	ESCA
CMYA5	0	.	GRCh37	5	79095325	79095325	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12096C>T	p.%3D	p.F4032F	ENST00000446378	13/13	61	43	17	39	39	0	CMYA5,synonymous_variant,p.%3D,ENST00000446378,;CTC-431G16.2,intron_variant,,ENST00000421252,;CMYA5,non_coding_transcript_exon_variant,,ENST00000506603,;	T	ENSG00000164309	ENST00000446378	Transcript	synonymous_variant	12127	12096	4032	F	ttC/ttT	.	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	.	13/13	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7,Pfam_domain:PF00622,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCATCAT	.	5	ESCA
MAK	0	.	GRCh37	6	10803989	10803989	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.627C>G	p.Ile209Met	p.I209M	ENST00000313243	7/14	28	20	7	40	40	0	MAK,missense_variant,p.Ile209Met,ENST00000354489,;MAK,missense_variant,p.Ile209Met,ENST00000538030,;MAK,missense_variant,p.Ile209Met,ENST00000474039,;MAK,missense_variant,p.Ile209Met,ENST00000313243,;MAK,missense_variant,p.Ile209Met,ENST00000536370,;SYCP2L,intron_variant,,ENST00000543878,;TMEM14B,intron_variant,,ENST00000489137,;RP11-637O19.3,intron_variant,,ENST00000480294,;TMEM14B,intron_variant,,ENST00000473166,;TMEM14B,intron_variant,,ENST00000467229,;TMEM14B,intron_variant,,ENST00000463448,;TMEM14B,intron_variant,,ENST00000460341,;TMEM14B,intron_variant,,ENST00000463100,;TMEM14B,downstream_gene_variant,,ENST00000478732,;TMEM14B,downstream_gene_variant,,ENST00000473807,;	C	ENSG00000111837	ENST00000313243	Transcript	missense_variant	1010	627	209	I/M	atC/atG	.	.	.	-1	MAK	HGNC	6816	protein_coding	YES	CCDS4516.1	ENSP00000313021	MAK_HUMAN	.	UPI0000001BCD	.	deleterious(0.01)	probably_damaging(0.961)	7/14	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF113,hmmpanther:PTHR24055,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAAGATTTC	.	5	ESCA
FOXO3	0	.	GRCh37	6	109003415	109003415	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2420C>T	.	.	ENST00000406360	3/3	27	21	6	30	30	0	FOXO3,3_prime_UTR_variant,,ENST00000406360,;FOXO3,3_prime_UTR_variant,,ENST00000343882,;FOXO3,downstream_gene_variant,,ENST00000540898,;	T	ENSG00000118689	ENST00000406360	Transcript	3_prime_UTR_variant	4785	.	.	.	.	.	.	.	1	FOXO3	HGNC	3821	protein_coding	YES	CCDS5068.1	ENSP00000385824	FOXO3_HUMAN	B4DVZ6_HUMAN	UPI000012ADEA	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCTCATTTA	.	5	ESCA
FIG4	0	.	GRCh37	6	110112718	110112718	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2320C>T	p.Gln774Ter	p.Q774*	ENST00000230124	20/23	22	17	5	18	18	0	FIG4,stop_gained,p.Gln497Ter,ENST00000441478,;FIG4,stop_gained,p.Gln774Ter,ENST00000230124,;FIG4,stop_gained,p.Gln81Ter,ENST00000419951,;	T	ENSG00000112367	ENST00000230124	Transcript	stop_gained	2444	2320	774	Q/*	Cag/Tag	.	.	.	1	FIG4	HGNC	16873	protein_coding	YES	CCDS5078.1	ENSP00000230124	FIG4_HUMAN	Q5TCS4_HUMAN,Q5JRV4_HUMAN	UPI000000D9A3	.	.	.	20/23	.	hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTCAGCGC	.	5	ESCA
HIVEP1	0	.	GRCh37	6	12122460	12122460	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2432A>T	p.Lys811Met	p.K811M	ENST00000379388	4/9	26	19	6	22	22	0	HIVEP1,missense_variant,p.Lys811Met,ENST00000379388,;HIVEP1,intron_variant,,ENST00000442081,;HIVEP1,downstream_gene_variant,,ENST00000487103,;HIVEP1,upstream_gene_variant,,ENST00000541134,;HIVEP1,downstream_gene_variant,,ENST00000491710,;HIVEP1,downstream_gene_variant,,ENST00000478545,;HIVEP1,upstream_gene_variant,,ENST00000399469,;	T	ENSG00000095951	ENST00000379388	Transcript	missense_variant	2764	2432	811	K/M	aAg/aTg	.	.	.	1	HIVEP1	HGNC	4920	protein_coding	YES	CCDS43426.1	ENSP00000368698	ZEP1_HUMAN	C9JZF8_HUMAN,C9JAW2_HUMAN,C9J2N3_HUMAN	UPI000020D52B	.	deleterious(0)	probably_damaging(1)	4/9	.	hmmpanther:PTHR23233:SF48,hmmpanther:PTHR23233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGAAGTCAC	.	5	ESCA
CTAGE9	0	.	GRCh37	6	132031038	132031038	+	Missense_Mutation	SNP	C	C	G	rs556536036	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1120G>C	p.Glu374Gln	p.E374Q	ENST00000314099	1/1	54	39	14	51	51	0	CTAGE9,missense_variant,p.Glu374Gln,ENST00000314099,;ENPP3,intron_variant,,ENST00000358229,;ENPP3,intron_variant,,ENST00000357639,;ENPP3,intron_variant,,ENST00000414305,;	G	ENSG00000236761	ENST00000314099	Transcript	missense_variant	1169	1120	374	E/Q	Gaa/Caa	rs556536036	.	.	-1	CTAGE9	HGNC	37275	protein_coding	YES	CCDS47475.1	ENSP00000395587	CTGE9_HUMAN	.	UPI0000073347	.	tolerated(0.06)	possibly_damaging(0.607)	1/1	.	hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF39	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	ACTTTCAAAAT	by1000G	3	ESCA
MAP7	0	.	GRCh37	6	136664548	136664548	+	3'Flank	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000454590	.	60	45	15	53	53	0	MAP7,3_prime_UTR_variant,,ENST00000354570,;MAP7,downstream_gene_variant,,ENST00000544465,;MAP7,downstream_gene_variant,,ENST00000454590,;MAP7,downstream_gene_variant,,ENST00000438100,;MAP7,downstream_gene_variant,,ENST00000432797,;	A	ENSG00000135525	ENST00000454590	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	133	-1	MAP7	HGNC	6869	protein_coding	YES	CCDS56455.1	ENSP00000414712	MAP7_HUMAN	.	UPI0001AE72EF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACAGACTTC	.	5	ESCA
MAP3K5	0	.	GRCh37	6	137015331	137015331	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1200G>A	p.Met400Ile	p.M400I	ENST00000359015	7/30	62	51	10	46	46	0	MAP3K5,missense_variant,p.Met400Ile,ENST00000359015,;	T	ENSG00000197442	ENST00000359015	Transcript	missense_variant	1561	1200	400	M/I	atG/atA	.	.	.	-1	MAP3K5	HGNC	6857	protein_coding	YES	CCDS5179.1	ENSP00000351908	M3K5_HUMAN	A6NIA0_HUMAN	UPI000012EAD5	.	tolerated(0.63)	benign(0.001)	7/30	.	hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF332,Pfam_domain:PF13281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAACATATC	.	5	ESCA
SAMD5	0	.	GRCh37	6	147885655	147885655	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63T>G	.	.	ENST00000367474	2/2	47	43	4	38	38	0	SAMD5,3_prime_UTR_variant,,ENST00000367474,;SAMD5,intron_variant,,ENST00000566741,;	G	ENSG00000203727	ENST00000367474	Transcript	3_prime_UTR_variant	587	.	.	.	.	.	.	.	1	SAMD5	HGNC	21180	protein_coding	YES	CCDS34548.1	ENSP00000356444	SAMD5_HUMAN	.	UPI000022CCF8	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CATATTTAGAA	.	2	ESCA
SYNE1	0	.	GRCh37	6	152675868	152675868	+	Missense_Mutation	SNP	C	C	T	rs577389543	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10852G>A	p.Glu3618Lys	p.E3618K	ENST00000367255	67/146	85	69	16	83	83	0	SYNE1,missense_variant,p.Glu3625Lys,ENST00000448038,;SYNE1,missense_variant,p.Glu3618Lys,ENST00000367255,;SYNE1,missense_variant,p.Glu3625Lys,ENST00000423061,;SYNE1,missense_variant,p.Glu3589Lys,ENST00000341594,;SYNE1,missense_variant,p.Glu3618Lys,ENST00000265368,;SYNE1,non_coding_transcript_exon_variant,,ENST00000471834,;	T	ENSG00000131018	ENST00000367255	Transcript	missense_variant	11454	10852	3618	E/K	Gag/Aag	rs577389543	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	probably_damaging(0.997)	67/146	.	Superfamily_domains:SSF46966,SMART_domains:SM00150,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCTGCTG	by1000G	5	ESCA
SYNE1	0	.	GRCh37	6	152792774	152792774	+	Silent	SNP	G	G	A	rs369178017	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1590C>T	p.%3D	p.Y530Y	ENST00000367255	16/146	49	40	9	38	38	0	SYNE1,synonymous_variant,p.%3D,ENST00000466159,;SYNE1,synonymous_variant,p.%3D,ENST00000423061,;SYNE1,synonymous_variant,p.%3D,ENST00000537750,;SYNE1,synonymous_variant,p.%3D,ENST00000367255,;SYNE1,synonymous_variant,p.%3D,ENST00000413186,;SYNE1,synonymous_variant,p.%3D,ENST00000341594,;SYNE1,synonymous_variant,p.%3D,ENST00000367248,;SYNE1,synonymous_variant,p.%3D,ENST00000495090,;SYNE1,synonymous_variant,p.%3D,ENST00000448038,;SYNE1,synonymous_variant,p.%3D,ENST00000367253,;SYNE1,synonymous_variant,p.%3D,ENST00000265368,;SYNE1,non_coding_transcript_exon_variant,,ENST00000535896,;SYNE1,non_coding_transcript_exon_variant,,ENST00000481502,;SYNE1,3_prime_UTR_variant,,ENST00000474655,;SYNE1,non_coding_transcript_exon_variant,,ENST00000468937,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,;	A	ENSG00000131018	ENST00000367255	Transcript	synonymous_variant	2192	1590	530	Y	taC/taT	rs369178017	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	.	16/146	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCGTACTT	byCluster	5	ESCA
PHF10	0	.	GRCh37	6	170117959	170117959	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369G>C	p.%3D	p.L123L	ENST00000339209	4/12	23	17	5	16	16	0	PHF10,synonymous_variant,p.%3D,ENST00000366780,;PHF10,synonymous_variant,p.%3D,ENST00000339209,;PHF10,non_coding_transcript_exon_variant,,ENST00000464779,;PHF10,non_coding_transcript_exon_variant,,ENST00000480008,;	G	ENSG00000130024	ENST00000339209	Transcript	synonymous_variant	493	369	123	L	ctG/ctC	.	.	.	-1	PHF10	HGNC	18250	protein_coding	YES	CCDS5308.2	ENSP00000341805	PHF10_HUMAN	S5FMB0_HUMAN	UPI0000EE1F6E	.	.	.	4/12	.	hmmpanther:PTHR10615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R36R|c.108A>G|6,BUFFER|p.R124R|c.372A>G|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCAGGTA	.	5	ESCA
MUC21	0	.	GRCh37	6	30954627	30954627	+	Silent	SNP	C	C	T	rs755308293	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.675C>T	p.%3D	p.A225A	ENST00000376296	2/3	82	53	29	115	115	0	MUC21,synonymous_variant,p.%3D,ENST00000376296,;MUC21,5_prime_UTR_variant,,ENST00000486149,;	T	ENSG00000204544	ENST00000376296	Transcript	synonymous_variant	916	675	225	A	gcC/gcT	rs755308293	.	.	1	MUC21	HGNC	21661	protein_coding	YES	CCDS34388.1	ENSP00000365473	MUC21_HUMAN	.	UPI000047030C	.	.	.	2/3	.	Low_complexity_(Seg):seg,Pfam_domain:PF05647	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCCACCAA	.	5	ESCA
DNAH8	0	.	GRCh37	6	38919237	38919237	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11741T>G	p.Leu3914Arg	p.L3914R	ENST00000359357	80/91	30	23	7	24	24	0	DNAH8,missense_variant,p.Leu3914Arg,ENST00000359357,;DNAH8,missense_variant,p.Leu4119Arg,ENST00000327475,;DNAH8,missense_variant,p.Leu3878Arg,ENST00000441566,;DNAH8,missense_variant,p.Leu4131Arg,ENST00000449981,;RP1-207H1.3,intron_variant,,ENST00000416948,;	G	ENSG00000124721	ENST00000359357	Transcript	missense_variant	11995	11741	3914	L/R	cTg/cGg	.	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	probably_damaging(1)	80/91	.	Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCCTGTCCA	.	5	ESCA
FOXP4	0	.	GRCh37	6	41567156	41567156	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*482G>C	.	.	ENST00000373060	17/17	24	20	4	23	23	0	FOXP4,3_prime_UTR_variant,,ENST00000373063,;FOXP4,3_prime_UTR_variant,,ENST00000307972,;FOXP4,3_prime_UTR_variant,,ENST00000409208,;FOXP4,3_prime_UTR_variant,,ENST00000373057,;FOXP4,3_prime_UTR_variant,,ENST00000373060,;MIR4641,downstream_gene_variant,,ENST00000578353,;	C	ENSG00000137166	ENST00000373060	Transcript	3_prime_UTR_variant	2983	.	.	.	.	.	.	.	1	FOXP4	HGNC	20842	protein_coding	YES	CCDS34447.1	ENSP00000362151	FOXP4_HUMAN	Q8N4A5_HUMAN,Q69YN9_HUMAN	UPI000007462D	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGAAGAAAGA	.	4	ESCA
HCRTR2	0	.	GRCh37	6	55039452	55039452	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.67G>A	p.Glu23Lys	p.E23K	ENST00000370862	1/7	43	27	16	45	45	0	HCRTR2,missense_variant,p.Glu23Lys,ENST00000370862,;	A	ENSG00000137252	ENST00000370862	Transcript	missense_variant	403	67	23	E/K	Gaa/Aaa	.	.	.	1	HCRTR2	HGNC	4849	protein_coding	YES	CCDS4956.1	ENSP00000359899	OX2R_HUMAN	S4X0W3_HUMAN,A6N9G8_HUMAN	UPI000013D07A	.	tolerated(0.8)	benign(0.006)	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAATGAAACT	.	5	ESCA
DST	0	.	GRCh37	6	56329512	56329512	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14819-950C>G	.	.	ENST00000244364	.	47	38	9	39	39	0	DST,missense_variant,p.Ser7042Cys,ENST00000446842,;DST,missense_variant,p.Ser5171Cys,ENST00000370788,;DST,missense_variant,p.Ser7257Cys,ENST00000361203,;DST,missense_variant,p.Ser7546Cys,ENST00000370754,;DST,missense_variant,p.Ser7368Cys,ENST00000370769,;DST,missense_variant,p.Ser5253Cys,ENST00000421834,;DST,intron_variant,,ENST00000244364,;DST,intron_variant,,ENST00000312431,;DST,intron_variant,,ENST00000523292,;DST,intron_variant,,ENST00000523597,;DST,non_coding_transcript_exon_variant,,ENST00000524216,;DST,intron_variant,,ENST00000482156,;DST,upstream_gene_variant,,ENST00000466429,;DST,upstream_gene_variant,,ENST00000518464,;	C	ENSG00000151914	ENST00000244364	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	.	80/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGAGTTT	.	5	ESCA
EYS	0	.	GRCh37	6	65300411	65300411	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5349T>G	p.Asp1783Glu	p.D1783E	ENST00000503581	26/43	23	19	4	18	18	0	EYS,missense_variant,p.Asp1783Glu,ENST00000370616,;EYS,missense_variant,p.Asp1783Glu,ENST00000370621,;EYS,missense_variant,p.Asp1783Glu,ENST00000503581,;EYS,downstream_gene_variant,,ENST00000330816,;	C	ENSG00000188107	ENST00000503581	Transcript	missense_variant	5887	5349	1783	D/E	gaT/gaG	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	tolerated_low_confidence(0.15)	benign(0.183)	26/43	.	hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAAAATCAGG	.	4	ESCA
TMEM30A	0	.	GRCh37	6	75974998	75974998	+	Silent	SNP	G	G	A	rs370998387	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402C>T	p.%3D	p.Y134Y	ENST00000230461	3/7	57	43	13	31	31	0	TMEM30A,synonymous_variant,p.%3D,ENST00000370050,;TMEM30A,synonymous_variant,p.%3D,ENST00000230461,;TMEM30A,synonymous_variant,p.%3D,ENST00000475111,;TMEM30A,synonymous_variant,p.%3D,ENST00000518161,;	A	ENSG00000112697	ENST00000230461	Transcript	synonymous_variant	732	402	134	Y	taC/taT	rs370998387	.	.	-1	TMEM30A	HGNC	16667	protein_coding	YES	CCDS4983.1	ENSP00000230461	CC50A_HUMAN	E5RG19_HUMAN	UPI0000071AE1	.	.	.	3/7	.	hmmpanther:PTHR10926,hmmpanther:PTHR10926:SF17,Pfam_domain:PF03381,PIRSF_domain:PIRSF015840	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCACGTAACG	byCluster	5	ESCA
ZNF292	0	.	GRCh37	6	87968551	87968551	+	Missense_Mutation	SNP	C	C	T	rs764982950	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5204C>T	p.Ser1735Leu	p.S1735L	ENST00000369577	8/8	35	32	3	21	21	0	ZNF292,missense_variant,p.Ser1735Leu,ENST00000369577,;ZNF292,missense_variant,p.Ser1730Leu,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,downstream_gene_variant,,ENST00000466062,;	T	ENSG00000188994	ENST00000369577	Transcript	missense_variant	5247	5204	1735	S/L	tCa/tTa	rs764982950	.	.	1	ZNF292	HGNC	18410	protein_coding	YES	CCDS47457.1	ENSP00000358590	ZN292_HUMAN	Q6ZS01_HUMAN,Q6P495_HUMAN,Q3MN16_HUMAN	UPI000020D2CC	.	deleterious_low_confidence(0.01)	benign(0.434)	8/8	.	hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAATTCATGCA	byFrequency	2	ESCA
CNR1	0	.	GRCh37	6	88853810	88853810	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1184T>A	p.Ile395Asn	p.I395N	ENST00000537554	2/2	26	21	4	23	23	0	CNR1,missense_variant,p.Ile395Asn,ENST00000369499,;CNR1,missense_variant,p.Ile395Asn,ENST00000428600,;CNR1,missense_variant,p.Ile395Asn,ENST00000535130,;CNR1,missense_variant,p.Ile334Asn,ENST00000549716,;CNR1,missense_variant,p.Ile395Asn,ENST00000369501,;CNR1,missense_variant,p.Ile362Asn,ENST00000468898,;CNR1,missense_variant,p.Ile395Asn,ENST00000537554,;CNR1,missense_variant,p.Ile395Asn,ENST00000549890,;CNR1,3_prime_UTR_variant,,ENST00000362094,;CNR1,downstream_gene_variant,,ENST00000551417,;	T	ENSG00000118432	ENST00000537554	Transcript	missense_variant	4747	1184	395	I/N	aTc/aAc	.	.	.	-1	CNR1	HGNC	2159	protein_coding	YES	CCDS5015.1	ENSP00000441046	CNR1_HUMAN	S5TLS4_HUMAN,Q9BYY6_HUMAN,F8W187_HUMAN	UPI00000008AA	.	deleterious(0)	probably_damaging(0.987)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF10,Pfam_domain:PF00001,Gene3D:1.20.1070.10,PIRSF_domain:PIRSF037995,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGATGGGG	.	5	ESCA
CASP8AP2	0	.	GRCh37	6	90575968	90575968	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4396C>G	.	.	ENST00000551025	8/9	19	11	7	18	18	0	CASP8AP2,non_coding_transcript_exon_variant,,ENST00000551025,;CASP8AP2,non_coding_transcript_exon_variant,,ENST00000237177,;CASP8AP2,intron_variant,,ENST00000548224,;CASP8AP2,downstream_gene_variant,,ENST00000419040,;CASP8AP2,downstream_gene_variant,,ENST00000552401,;	G	ENSG00000118412	ENST00000551025	Transcript	non_coding_transcript_exon_variant	4396	.	.	.	.	.	.	.	1	CASP8AP2	HGNC	1510	processed_transcript	YES	.	.	.	.	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACACATGTA	.	5	ESCA
CASP8AP2	0	.	GRCh37	6	90577632	90577632	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.6060C>G	.	.	ENST00000551025	8/9	44	32	12	41	41	0	CASP8AP2,non_coding_transcript_exon_variant,,ENST00000551025,;CASP8AP2,non_coding_transcript_exon_variant,,ENST00000237177,;CASP8AP2,intron_variant,,ENST00000548224,;	G	ENSG00000118412	ENST00000551025	Transcript	non_coding_transcript_exon_variant	6060	.	.	.	.	.	.	.	1	CASP8AP2	HGNC	1510	processed_transcript	YES	.	.	.	.	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTCATTGT	.	5	ESCA
CASP8AP2	0	.	GRCh37	6	90578545	90578545	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.6973C>G	.	.	ENST00000551025	8/9	19	13	5	15	15	0	CASP8AP2,non_coding_transcript_exon_variant,,ENST00000551025,;CASP8AP2,non_coding_transcript_exon_variant,,ENST00000237177,;CASP8AP2,intron_variant,,ENST00000548224,;	G	ENSG00000118412	ENST00000551025	Transcript	non_coding_transcript_exon_variant	6973	.	.	.	.	.	.	.	1	CASP8AP2	HGNC	1510	processed_transcript	YES	.	.	.	.	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCATAAA	.	5	ESCA
POLR2J	0	.	GRCh37	7	102119272	102119272	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36C>G	p.%3D	p.L12L	ENST00000292614	1/4	62	47	15	60	60	0	POLR2J,synonymous_variant,p.%3D,ENST00000393794,;POLR2J,synonymous_variant,p.%3D,ENST00000292614,;RASA4B,downstream_gene_variant,,ENST00000465829,;RASA4B,downstream_gene_variant,,ENST00000541662,;RASA4B,downstream_gene_variant,,ENST00000306682,;AC093668.3,upstream_gene_variant,,ENST00000607525,;RP11-514P8.8,downstream_gene_variant,,ENST00000481893,;RASA4B,downstream_gene_variant,,ENST00000467351,;RASA4B,downstream_gene_variant,,ENST00000495352,;RASA4B,downstream_gene_variant,,ENST00000488284,;RASA4B,downstream_gene_variant,,ENST00000477184,;AC093668.2,downstream_gene_variant,,ENST00000538869,;	C	ENSG00000005075	ENST00000292614	Transcript	synonymous_variant	83	36	12	L	ctC/ctG	.	.	.	-1	POLR2J	HGNC	9197	protein_coding	YES	CCDS5724.1	ENSP00000292614	RPB11_HUMAN	.	UPI000000B2C2	.	.	.	1/4	.	hmmpanther:PTHR13946:SF25,hmmpanther:PTHR13946,Gene3D:3.30.1360.10,Superfamily_domains:SSF55257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGAAGAGCAA	.	5	ESCA
ATP6V1F	0	.	GRCh37	7	128502673	128502673	+	5'Flank	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000492758	.	8	5	3	8	8	0	ATP6V1F,upstream_gene_variant,,ENST00000249289,;FLNC,downstream_gene_variant,,ENST00000346177,;FLNC,downstream_gene_variant,,ENST00000325888,;ATP6V1F,upstream_gene_variant,,ENST00000492758,;RP11-309L24.4,upstream_gene_variant,,ENST00000461420,;RP11-309L24.2,non_coding_transcript_exon_variant,,ENST00000469965,;KCP,downstream_gene_variant,,ENST00000297801,;KCP,non_coding_transcript_exon_variant,,ENST00000492679,;	C	ENSG00000128524	ENST00000492758	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	285	1	ATP6V1F	HGNC	16832	protein_coding	YES	CCDS56511.1	ENSP00000417378	VATF_HUMAN	.	UPI000020FA6C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGTTGAACGA	.	2	ESCA
TRPV5	0	.	GRCh37	7	142622526	142622526	+	Intron	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1122+98T>G	.	.	ENST00000265310	.	17	11	6	31	30	0	TRPV5,3_prime_UTR_variant,,ENST00000442623,;TRPV5,intron_variant,,ENST00000439304,;TRPV5,intron_variant,,ENST00000265310,;	C	ENSG00000127412	ENST00000265310	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TRPV5	HGNC	3145	protein_coding	YES	CCDS5875.1	ENSP00000265310	TRPV5_HUMAN	Q9H480_HUMAN	UPI0000052B76	.	.	.	.	8/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAACCCAG	.	5	ESCA
OR2F2	0	.	GRCh37	7	143632789	143632789	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464A>C	p.Asn155Thr	p.N155T	ENST00000408955	1/1	73	57	15	94	93	0	OR2F2,missense_variant,p.Asn155Thr,ENST00000408955,;	C	ENSG00000221910	ENST00000408955	Transcript	missense_variant	531	464	155	N/T	aAc/aCc	.	.	.	1	OR2F2	HGNC	8247	protein_coding	YES	CCDS43666.1	ENSP00000386222	OR2F2_HUMAN	.	UPI0000041C25	.	tolerated(0.19)	benign(0.124)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26453:SF63,hmmpanther:PTHR26453,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCAACTCTC	.	5	ESCA
ARHGEF5	0	.	GRCh37	7	144069488	144069488	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3942C>T	p.%3D	p.F1314F	ENST00000056217	8/15	23	19	4	18	18	0	ARHGEF5,synonymous_variant,p.%3D,ENST00000056217,;ARHGEF5,synonymous_variant,p.%3D,ENST00000471847,;ARHGEF5,synonymous_variant,p.%3D,ENST00000474817,;	T	ENSG00000050327	ENST00000056217	Transcript	synonymous_variant	4116	3942	1314	F	ttC/ttT	.	.	.	1	ARHGEF5	HGNC	13209	protein_coding	YES	CCDS34771.1	ENSP00000056217	ARHG5_HUMAN	H9XFB6_HUMAN	UPI00004028DC	.	.	.	8/15	.	PROSITE_profiles:PS50010,hmmpanther:PTHR12845:SF2,hmmpanther:PTHR12845,PROSITE_patterns:PS00741,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CCCTTCCAACG	.	2	ESCA
ZNF212	0	.	GRCh37	7	148950660	148950660	+	Silent	SNP	C	C	A	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642C>A	p.%3D	p.V214V	ENST00000335870	5/5	86	68	18	103	102	1	ZNF212,synonymous_variant,p.%3D,ENST00000481584,;ZNF212,synonymous_variant,p.%3D,ENST00000335870,;ZNF212,3_prime_UTR_variant,,ENST00000488917,;ZNF212,downstream_gene_variant,,ENST00000462724,;ZNF212,downstream_gene_variant,,ENST00000486371,;	A	ENSG00000170260	ENST00000335870	Transcript	synonymous_variant	770	642	214	V	gtC/gtA	COSM3832240	.	.	1	ZNF212	HGNC	13004	protein_coding	YES	CCDS5896.1	ENSP00000338572	ZN212_HUMAN	.	UPI000013CEE2	.	.	.	5/5	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF42	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTCATGAT	.	5	ESCA
HDAC9	0	.	GRCh37	7	18706043	18706043	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1675G>A	p.Glu559Lys	p.E559K	ENST00000441542	11/25	27	22	5	28	28	0	HDAC9,missense_variant,p.Glu515Lys,ENST00000401921,;HDAC9,missense_variant,p.Glu556Lys,ENST00000405010,;HDAC9,missense_variant,p.Glu512Lys,ENST00000428307,;HDAC9,missense_variant,p.Glu559Lys,ENST00000441542,;HDAC9,missense_variant,p.Glu554Lys,ENST00000417496,;HDAC9,missense_variant,p.Glu543Lys,ENST00000406072,;HDAC9,missense_variant,p.Glu556Lys,ENST00000406451,;HDAC9,missense_variant,p.Glu528Lys,ENST00000456174,;HDAC9,missense_variant,p.Glu556Lys,ENST00000432645,;HDAC9,missense_variant,p.Glu479Lys,ENST00000524023,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;	A	ENSG00000048052	ENST00000441542	Transcript	missense_variant	1675	1675	559	E/K	Gaa/Aaa	.	.	.	1	HDAC9	HGNC	14065	protein_coding	YES	CCDS47553.1	ENSP00000408617	HDAC9_HUMAN	Q8N926_HUMAN,Q75N15_HUMAN,Q75N14_HUMAN,Q75N10_HUMAN,C9JLX1_HUMAN,C9J835_HUMAN,C9J1W4_HUMAN,C9IZS0_HUMAN	UPI000019AB75	.	tolerated(0.13)	benign(0.138)	11/25	.	hmmpanther:PTHR10625:SF116,hmmpanther:PTHR10625,PIRSF_domain:PIRSF037911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATGAAGAT	.	5	ESCA
ITGB8	0	.	GRCh37	7	20454505	20454505	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4885A>G	.	.	ENST00000222573	14/14	70	45	25	34	34	0	ITGB8,3_prime_UTR_variant,,ENST00000222573,;ITGB8,downstream_gene_variant,,ENST00000537992,;	G	ENSG00000105855	ENST00000222573	Transcript	3_prime_UTR_variant	7879	.	.	.	.	.	.	.	1	ITGB8	HGNC	6163	protein_coding	YES	CCDS5370.1	ENSP00000222573	ITB8_HUMAN	B4DHD4_HUMAN	UPI000012DA14	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTAGCCTC	.	5	ESCA
IL6	0	.	GRCh37	7	22765763	22765763	+	5'UTR	SNP	G	G	A	rs529548126	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-199G>A	.	.	ENST00000404625	1/6	33	30	3	20	20	0	IL6,5_prime_UTR_variant,,ENST00000404625,;IL6,upstream_gene_variant,,ENST00000401630,;IL6,upstream_gene_variant,,ENST00000420258,;IL6,upstream_gene_variant,,ENST00000258743,;IL6,upstream_gene_variant,,ENST00000401651,;IL6,upstream_gene_variant,,ENST00000426291,;IL6,upstream_gene_variant,,ENST00000406575,;IL6,upstream_gene_variant,,ENST00000407492,;AC073072.5,non_coding_transcript_exon_variant,,ENST00000325042,;IL6,upstream_gene_variant,,ENST00000485300,;IL6,upstream_gene_variant,,ENST00000464710,;	A	ENSG00000136244	ENST00000404625	Transcript	5_prime_UTR_variant	261	.	.	.	.	rs529548126	.	.	1	IL6	HGNC	6018	protein_coding	YES	CCDS5375.1	ENSP00000385675	IL6_HUMAN	Q75MH2_HUMAN,H9C875_HUMAN,C9J5B0_HUMAN,B5MC21_HUMAN	UPI000002C4A6	.	.	.	1/6	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTCCGTAGTT	by1000G	2	ESCA
SKAP2	0	.	GRCh37	7	26709727	26709727	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1072G>C	p.Asp358His	p.D358H	ENST00000345317	12/13	96	66	29	68	68	0	SKAP2,missense_variant,p.Asp186His,ENST00000539623,;SKAP2,missense_variant,p.Asp358His,ENST00000345317,;	G	ENSG00000005020	ENST00000345317	Transcript	missense_variant	1386	1072	358	D/H	Gat/Cat	.	.	.	-1	SKAP2	HGNC	15687	protein_coding	YES	CCDS5400.1	ENSP00000005587	SKAP2_HUMAN	B7Z5R3_HUMAN	UPI0000073C8C	.	deleterious(0)	probably_damaging(0.971)	12/13	.	PROSITE_profiles:PS50002,hmmpanther:PTHR15129:SF2,hmmpanther:PTHR15129,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCATACA	.	5	ESCA
YAE1D1	0	.	GRCh37	7	39610125	39610125	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150A>G	p.Ile50Met	p.I50M	ENST00000223273	2/3	69	54	15	45	45	0	YAE1D1,missense_variant,p.Ile50Met,ENST00000448268,;YAE1D1,missense_variant,p.Ile50Met,ENST00000223273,;YAE1D1,missense_variant,p.Ile50Met,ENST00000432096,;AC011290.4,upstream_gene_variant,,ENST00000439751,;YAE1D1,non_coding_transcript_exon_variant,,ENST00000469737,;YAE1D1,non_coding_transcript_exon_variant,,ENST00000474392,;YAE1D1,non_coding_transcript_exon_variant,,ENST00000485025,;AC011290.5,upstream_gene_variant,,ENST00000438427,;	G	ENSG00000241127	ENST00000223273	Transcript	missense_variant	193	150	50	I/M	atA/atG	.	.	.	1	YAE1D1	HGNC	24857	protein_coding	YES	CCDS5459.1	ENSP00000223273	YAED1_HUMAN	.	UPI0000074023	.	deleterious(0)	possibly_damaging(0.629)	2/3	.	hmmpanther:PTHR18829,hmmpanther:PTHR18829:SF0,Pfam_domain:PF09811	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAATAGATGC	.	5	ESCA
DDX56	0	.	GRCh37	7	44613437	44613437	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58C>G	p.Gln20Glu	p.Q20E	ENST00000258772	1/14	25	20	4	28	28	0	DDX56,missense_variant,p.Gln20Glu,ENST00000258772,;DDX56,missense_variant,p.Gln20Glu,ENST00000431640,;TMED4,downstream_gene_variant,,ENST00000289577,;TMED4,downstream_gene_variant,,ENST00000457408,;DDX56,upstream_gene_variant,,ENST00000448192,;DDX56,upstream_gene_variant,,ENST00000485367,;DDX56,upstream_gene_variant,,ENST00000467318,;DDX56,missense_variant,p.Gln20Glu,ENST00000421223,;DDX56,missense_variant,p.Gln20Glu,ENST00000446987,;DDX56,missense_variant,p.Gln20Glu,ENST00000415758,;DDX56,non_coding_transcript_exon_variant,,ENST00000479440,;DDX56,upstream_gene_variant,,ENST00000473924,;DDX56,upstream_gene_variant,,ENST00000433257,;	C	ENSG00000136271	ENST00000258772	Transcript	missense_variant	165	58	20	Q/E	Cag/Gag	.	.	.	-1	DDX56	HGNC	18193	protein_coding	YES	CCDS5492.1	ENSP00000258772	DDX56_HUMAN	G3V0G3_HUMAN	UPI0000037BB1	.	tolerated(0.05)	benign(0.01)	1/14	.	PROSITE_profiles:PS51195,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF96,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCTGAAGGA	.	5	ESCA
ABCA13	0	.	GRCh37	7	48520703	48520703	+	Nonsense_Mutation	SNP	C	C	G	rs762477935	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13046C>G	p.Ser4349Ter	p.S4349*	ENST00000435803	46/62	88	64	23	61	61	0	ABCA13,stop_gained,p.Ser4349Ter,ENST00000435803,;ABCA13,stop_gained,p.Ser79Ter,ENST00000544596,;ABCA13,stop_gained,p.Ser122Ter,ENST00000411975,;ABCA13,stop_gained,p.Ser615Ter,ENST00000453246,;	G	ENSG00000179869	ENST00000435803	Transcript	stop_gained	13070	13046	4349	S/*	tCa/tGa	rs762477935	.	.	1	ABCA13	HGNC	14638	protein_coding	YES	CCDS47584.1	ENSP00000411096	ABCAD_HUMAN	.	UPI00001A95EA	.	.	.	46/62	.	hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCAGGCT	.	5	ESCA
ZNF107	0	.	GRCh37	7	64167974	64167974	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1292A>G	p.Lys431Arg	p.K431R	ENST00000395391	4/4	30	20	10	27	27	0	ZNF107,missense_variant,p.Lys431Arg,ENST00000344930,;ZNF107,missense_variant,p.Lys431Arg,ENST00000395391,;ZNF107,missense_variant,p.Lys431Arg,ENST00000423627,;ZNF107,downstream_gene_variant,,ENST00000360117,;	G	ENSG00000196247	ENST00000395391	Transcript	missense_variant	2667	1292	431	K/R	aAg/aGg	.	.	.	1	ZNF107	HGNC	12887	protein_coding	YES	CCDS5527.1	ENSP00000378789	ZN107_HUMAN	Q9H3U2_HUMAN,C9JSF9_HUMAN	UPI000000DBC2	.	tolerated(0.13)	probably_damaging(0.928)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF121,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATAAGAAAA	.	5	ESCA
SBDS	0	.	GRCh37	7	66453338	66453338	+	3'UTR	SNP	G	G	A	rs754935115	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*20C>T	.	.	ENST00000246868	5/5	71	59	12	41	41	0	SBDS,3_prime_UTR_variant,,ENST00000246868,;SBDS,3_prime_UTR_variant,,ENST00000414306,;SBDS,downstream_gene_variant,,ENST00000463579,;SBDS,downstream_gene_variant,,ENST00000490953,;	A	ENSG00000126524	ENST00000246868	Transcript	3_prime_UTR_variant	957	.	.	.	.	rs754935115	.	.	-1	SBDS	HGNC	19440	protein_coding	YES	CCDS5537.1	ENSP00000246868	SBDS_HUMAN	.	UPI000013559C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGAGGTGAA	.	5	ESCA
NPTX2	0	.	GRCh37	7	98258711	98258711	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*770T>C	.	.	ENST00000265634	5/5	60	52	8	57	57	0	NPTX2,3_prime_UTR_variant,,ENST00000265634,;NPTX2,downstream_gene_variant,,ENST00000466102,;	C	ENSG00000106236	ENST00000265634	Transcript	3_prime_UTR_variant	2231	.	.	.	.	.	.	.	1	NPTX2	HGNC	7953	protein_coding	YES	CCDS5657.1	ENSP00000265634	NPTX2_HUMAN	.	UPI000013040F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCGTTGCAG	.	4	ESCA
RIMS2	0	.	GRCh37	8	105001620	105001620	+	Missense_Mutation	SNP	G	G	A	rs199654709	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3015G>A	p.Met1005Ile	p.M1005I	ENST00000406091	17/24	40	34	6	45	45	0	RIMS2,missense_variant,p.Met1005Ile,ENST00000406091,;RIMS2,missense_variant,p.Met797Ile,ENST00000408894,;RIMS2,missense_variant,p.Met1005Ile,ENST00000504942,;RIMS2,missense_variant,p.Met797Ile,ENST00000507740,;RIMS2,missense_variant,p.Met844Ile,ENST00000262231,;RIMS2,missense_variant,p.Met783Ile,ENST00000436393,;	A	ENSG00000176406	ENST00000406091	Transcript	missense_variant	3015	3015	1005	M/I	atG/atA	rs199654709	.	.	1	RIMS2	HGNC	17283	protein_coding	YES	CCDS55269.1	ENSP00000384892	RIMS2_HUMAN	E9PFB6_HUMAN	UPI0001597063	.	tolerated_low_confidence(0.44)	benign(0.001)	17/24	.	hmmpanther:PTHR12157:SF15,hmmpanther:PTHR12157	.	.	.	.	.	.	.	A:0	A:0.0007	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCATGGATGA	byCluster	2	ESCA
DPYS	0	.	GRCh37	8	105456593	105456593	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.676G>A	p.Glu226Lys	p.E226K	ENST00000351513	4/10	30	21	9	48	47	0	DPYS,missense_variant,p.Glu226Lys,ENST00000351513,;DPYS,downstream_gene_variant,,ENST00000521573,;DPYS,non_coding_transcript_exon_variant,,ENST00000519217,;	T	ENSG00000147647	ENST00000351513	Transcript	missense_variant	809	676	226	E/K	Gag/Aag	.	.	.	-1	DPYS	HGNC	3013	protein_coding	YES	CCDS6302.1	ENSP00000276651	DPYS_HUMAN	.	UPI000012986F	.	deleterious(0)	probably_damaging(1)	4/10	.	hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,Pfam_domain:PF01979,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR02033,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGCCTCCACTG	.	4	ESCA
DPYS	0	.	GRCh37	8	105456626	105456626	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.643G>A	p.Glu215Lys	p.E215K	ENST00000351513	4/10	18	12	5	41	41	0	DPYS,missense_variant,p.Glu215Lys,ENST00000351513,;DPYS,downstream_gene_variant,,ENST00000521573,;DPYS,upstream_gene_variant,,ENST00000519217,;	T	ENSG00000147647	ENST00000351513	Transcript	missense_variant	776	643	215	E/K	Gag/Aag	.	.	.	-1	DPYS	HGNC	3013	protein_coding	YES	CCDS6302.1	ENSP00000276651	DPYS_HUMAN	.	UPI000012986F	.	deleterious(0)	possibly_damaging(0.815)	4/10	.	hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,Pfam_domain:PF01979,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR02033,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	GCCCTCAGGGC	.	3	ESCA
CSMD3	0	.	GRCh37	8	113256737	113256737	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10288C>T	p.His3430Tyr	p.H3430Y	ENST00000297405	65/71	46	35	11	42	42	0	CSMD3,missense_variant,p.His3360Tyr,ENST00000352409,;CSMD3,missense_variant,p.His3261Tyr,ENST00000455883,;CSMD3,missense_variant,p.His3430Tyr,ENST00000297405,;CSMD3,missense_variant,p.His2700Tyr,ENST00000339701,;CSMD3,missense_variant,p.His3390Tyr,ENST00000343508,;CSMD3,non_coding_transcript_exon_variant,,ENST00000534172,;	A	ENSG00000164796	ENST00000297405	Transcript	missense_variant	10533	10288	3430	H/Y	Cat/Tat	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.28)	benign(0.002)	65/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCATGAGATG	.	5	ESCA
KIAA1456	0	.	GRCh37	8	12879455	12879455	+	Silent	SNP	C	C	T	rs371288288	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1267C>T	p.%3D	p.L423L	ENST00000524591	5/5	14	8	6	16	16	0	KIAA1456,synonymous_variant,p.%3D,ENST00000524591,;KIAA1456,intron_variant,,ENST00000447063,;KIAA1456,non_coding_transcript_exon_variant,,ENST00000529978,;KIAA1456,downstream_gene_variant,,ENST00000529706,;	T	ENSG00000250305	ENST00000524591	Transcript	synonymous_variant	1756	1267	423	L	Ctg/Ttg	rs371288288	.	.	1	KIAA1456	HGNC	26725	protein_coding	YES	CCDS47808.1	ENSP00000432695	K1456_HUMAN	E9PK20_HUMAN	UPI0001596892	.	.	.	5/5	.	Gene3D:3.40.50.150,hmmpanther:PTHR13069,hmmpanther:PTHR13069:SF25	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTCTGCTC	byFrequency|byCluster	5	ESCA
TG	0	.	GRCh37	8	134125817	134125817	+	Missense_Mutation	SNP	C	C	G	rs771026858	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7724C>G	p.Ser2575Cys	p.S2575C	ENST00000220616	44/48	52	43	8	43	43	0	TG,missense_variant,p.Ser2575Cys,ENST00000220616,;TG,missense_variant,p.Ser945Cys,ENST00000542445,;TG,missense_variant,p.Ser24Cys,ENST00000521107,;TG,missense_variant,p.Ser2518Cys,ENST00000377869,;TG,missense_variant,p.Ser708Cys,ENST00000519543,;TG,missense_variant,p.Ser1031Cys,ENST00000519178,;TG,3_prime_UTR_variant,,ENST00000523756,;TG,non_coding_transcript_exon_variant,,ENST00000522809,;TG,downstream_gene_variant,,ENST00000522996,;	G	ENSG00000042832	ENST00000220616	Transcript	missense_variant	7764	7724	2575	S/C	tCc/tGc	rs771026858	.	.	1	TG	HGNC	11764	protein_coding	YES	CCDS34944.1	ENSP00000220616	THYG_HUMAN	Q9NYM1_HUMAN,Q9NYD9_HUMAN,E5RG33_HUMAN	UPI000013C79F	.	deleterious(0.05)	possibly_damaging(0.781)	44/48	.	Superfamily_domains:SSF53474,PIRSF_domain:PIRSF001831,Pfam_domain:PF00135,Gene3D:3.40.50.1820,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF142	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCCTTCT	.	5	ESCA
MSR1	0	.	GRCh37	8	16021760	16021760	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Glu211Lys	p.E211K	ENST00000262101	5/10	26	17	8	36	36	0	MSR1,start_lost,p.Glu1?,ENST00000522672,;MSR1,missense_variant,p.Glu211Lys,ENST00000350896,;MSR1,missense_variant,p.Glu211Lys,ENST00000355282,;MSR1,missense_variant,p.Glu229Lys,ENST00000445506,;MSR1,missense_variant,p.Glu211Lys,ENST00000262101,;MSR1,missense_variant,p.Glu211Lys,ENST00000381998,;MSR1,splice_region_variant,,ENST00000536385,;MSR1,missense_variant,p.Arg35Lys,ENST00000519060,;	T	ENSG00000038945	ENST00000262101	Transcript	missense_variant	753	631	211	E/K	Gaa/Aaa	COSM3646790,COSM3646791	.	.	-1	MSR1	HGNC	7376	protein_coding	YES	CCDS5995.1	ENSP00000262101	MSRE_HUMAN	E5RFW8_HUMAN	UPI000012F686	.	tolerated(0.27)	benign(0.341)	5/10	.	hmmpanther:PTHR24021:SF10,hmmpanther:PTHR24021,Prints_domain:PR01408	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCCTGTA	.	5	ESCA
LPL	0	.	GRCh37	8	19824479	19824479	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1658C>G	.	.	ENST00000311322	10/10	34	26	8	37	37	0	LPL,3_prime_UTR_variant,,ENST00000311322,;	G	ENSG00000175445	ENST00000311322	Transcript	3_prime_UTR_variant	3556	.	.	.	.	.	.	.	1	LPL	HGNC	6677	protein_coding	YES	CCDS6012.1	ENSP00000309757	LIPL_HUMAN	Q71UV2_HUMAN,Q4JIZ7_HUMAN,E7EW14_HUMAN,E5RJI0_HUMAN,E5RHN7_HUMAN	UPI0000036334	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TGGCTCCGAAA	.	2	ESCA
GPR124	0	.	GRCh37	8	37698775	37698775	+	Silent	SNP	G	G	A	rs774366183	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2919G>A	p.%3D	p.L973L	ENST00000412232	19/19	89	80	9	51	51	0	GPR124,synonymous_variant,p.%3D,ENST00000412232,;GPR124,synonymous_variant,p.%3D,ENST00000315215,;BRF2,downstream_gene_variant,,ENST00000220659,;BRF2,downstream_gene_variant,,ENST00000520601,;	A	ENSG00000020181	ENST00000412232	Transcript	synonymous_variant	2932	2919	973	L	ctG/ctA	rs774366183	.	.	1	GPR124	HGNC	17849	protein_coding	YES	CCDS6097.2	ENSP00000406367	GP124_HUMAN	.	UPI00004AE50D	.	.	.	19/19	.	hmmpanther:PTHR12011:SF33,hmmpanther:PTHR12011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCTGAGGGG	byFrequency	4	ESCA
LSM1	0	.	GRCh37	8	38021034	38021034	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*154C>T	.	.	ENST00000311351	4/4	63	58	5	15	15	0	LSM1,3_prime_UTR_variant,,ENST00000520755,;LSM1,3_prime_UTR_variant,,ENST00000311351,;RP11-90P5.7,downstream_gene_variant,,ENST00000521915,;RP11-90P5.2,non_coding_transcript_exon_variant,,ENST00000520598,;LSM1,non_coding_transcript_exon_variant,,ENST00000520286,;LSM1,non_coding_transcript_exon_variant,,ENST00000522515,;LSM1,downstream_gene_variant,,ENST00000523511,;	A	ENSG00000175324	ENST00000311351	Transcript	3_prime_UTR_variant	952	.	.	.	.	.	.	.	-1	LSM1	HGNC	20472	protein_coding	YES	CCDS6103.1	ENSP00000310596	LSM1_HUMAN	.	UPI000012E963	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TACACGATTTC	.	3	ESCA
RGS20	0	.	GRCh37	8	54764502	54764502	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43C>T	p.His15Tyr	p.H15Y	ENST00000297313	1/6	39	29	10	29	29	0	RGS20,missense_variant,p.His15Tyr,ENST00000297313,;RGS20,missense_variant,p.His15Tyr,ENST00000344277,;RGS20,missense_variant,p.His15Tyr,ENST00000523280,;RGS20,missense_variant,p.His15Tyr,ENST00000517659,;	T	ENSG00000147509	ENST00000297313	Transcript	missense_variant	135	43	15	H/Y	Cat/Tat	.	.	.	1	RGS20	HGNC	14600	protein_coding	YES	CCDS6155.1	ENSP00000297313	RGS20_HUMAN	B3KSW4_HUMAN	UPI000013383C	.	tolerated_low_confidence(0.14)	benign(0.002)	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAACATTTC	.	5	ESCA
PDE7A	0	.	GRCh37	8	66753636	66753636	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108C>T	p.%3D	p.F36F	ENST00000401827	1/13	39	32	7	59	59	0	PDE7A,synonymous_variant,p.%3D,ENST00000401827,;PDE7A,synonymous_variant,p.%3D,ENST00000396642,;PDE7A,upstream_gene_variant,,ENST00000523253,;CTD-2532N20.1,upstream_gene_variant,,ENST00000607622,;PDE7A,non_coding_transcript_exon_variant,,ENST00000519231,;PDE7A,non_coding_transcript_exon_variant,,ENST00000519626,;	A	ENSG00000205268	ENST00000401827	Transcript	synonymous_variant	552	108	36	F	ttC/ttT	.	.	.	-1	PDE7A	HGNC	8791	protein_coding	YES	CCDS56538.1	ENSP00000385632	PDE7A_HUMAN	Q86V65_HUMAN,Q7Z7I0_HUMAN	UPI0000127BFD	.	.	.	1/13	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCCGAAGAG	.	4	ESCA
FAM92A1	0	.	GRCh37	8	94738686	94738686	+	Nonsense_Mutation	SNP	C	C	G	rs759135660	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.722C>G	p.Ser241Ter	p.S241*	ENST00000518322	8/9	53	37	15	58	58	0	FAM92A1,stop_gained,p.Ser86Ter,ENST00000519679,;FAM92A1,stop_gained,p.Ser86Ter,ENST00000521641,;FAM92A1,stop_gained,p.Ser203Ter,ENST00000423990,;FAM92A1,stop_gained,p.Ser241Ter,ENST00000518322,;FAM92A1,stop_gained,p.Ser86Ter,ENST00000517718,;RBM12B,downstream_gene_variant,,ENST00000399300,;RBM12B,downstream_gene_variant,,ENST00000517700,;FAM92A1,non_coding_transcript_exon_variant,,ENST00000520363,;RBM12B,downstream_gene_variant,,ENST00000520961,;FAM92A1,stop_gained,p.Ser241Ter,ENST00000452913,;FAM92A1,3_prime_UTR_variant,,ENST00000518116,;FAM92A1,3_prime_UTR_variant,,ENST00000359421,;FAM92A1,non_coding_transcript_exon_variant,,ENST00000523577,;	G	ENSG00000188343	ENST00000518322	Transcript	stop_gained	863	722	241	S/*	tCa/tGa	rs759135660	.	.	1	FAM92A1	HGNC	30452	protein_coding	YES	CCDS47892.1	ENSP00000429367	F92A1_HUMAN	E5RID3_HUMAN,E5RHA4_HUMAN,E5RGE3_HUMAN,E5RFS7_HUMAN,E5RFH7_HUMAN	UPI000156FA8B	.	.	.	8/9	.	hmmpanther:PTHR21223:SF4,hmmpanther:PTHR21223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTCAAAGT	.	5	ESCA
ESRP1	0	.	GRCh37	8	95718708	95718708	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*591T>G	.	.	ENST00000433389	16/16	12	6	6	10	10	0	ESRP1,3_prime_UTR_variant,,ENST00000454170,;ESRP1,3_prime_UTR_variant,,ENST00000433389,;ESRP1,3_prime_UTR_variant,,ENST00000423620,;ESRP1,3_prime_UTR_variant,,ENST00000358397,;ESRP1,3_prime_UTR_variant,,ENST00000519505,;ESRP1,3_prime_UTR_variant,,ENST00000517610,;ESRP1,non_coding_transcript_exon_variant,,ENST00000523347,;KB-1090H4.2,downstream_gene_variant,,ENST00000522972,;	G	ENSG00000104413	ENST00000433389	Transcript	3_prime_UTR_variant	2827	.	.	.	.	.	.	.	1	ESRP1	HGNC	25966	protein_coding	YES	CCDS47897.1	ENSP00000405738	ESRP1_HUMAN	E5RI26_HUMAN,E5RGE9_HUMAN	UPI0000210327	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACAAATTAAAT	.	3	ESCA
STXBP1	0	.	GRCh37	9	130374641	130374641	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-42C>T	.	.	ENST00000373302	1/20	39	22	16	45	45	0	STXBP1,5_prime_UTR_variant,,ENST00000373302,;STXBP1,5_prime_UTR_variant,,ENST00000373299,;STXBP1,upstream_gene_variant,,ENST00000476182,;	T	ENSG00000136854	ENST00000373302	Transcript	5_prime_UTR_variant	98	.	.	.	.	.	.	.	1	STXBP1	HGNC	11444	protein_coding	YES	CCDS6874.1	ENSP00000362399	STXB1_HUMAN	.	UPI0000006C0B	.	.	.	1/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGTCGCGGG	.	5	ESCA
SET	0	.	GRCh37	9	131457259	131457259	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*316C>T	.	.	ENST00000372692	8/8	44	38	5	41	41	0	SET,3_prime_UTR_variant,,ENST00000322030,;SET,3_prime_UTR_variant,,ENST00000372688,;SET,3_prime_UTR_variant,,ENST00000372692,;SET,downstream_gene_variant,,ENST00000409104,;SET,downstream_gene_variant,,ENST00000372686,;SET,downstream_gene_variant,,ENST00000466009,;SET,downstream_gene_variant,,ENST00000477806,;SET,downstream_gene_variant,,ENST00000480217,;SET,downstream_gene_variant,,ENST00000485056,;SET,downstream_gene_variant,,ENST00000480536,;	T	ENSG00000119335	ENST00000372692	Transcript	3_prime_UTR_variant	1430	.	.	.	.	.	.	.	1	SET	HGNC	10760	protein_coding	YES	CCDS48037.1	ENSP00000361777	SET_HUMAN	Q5VXV3_HUMAN,B2REB7_HUMAN	UPI000006D7FF	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TCGCTCTGCTG	.	2	ESCA
COL5A1	0	.	GRCh37	9	137734324	137734324	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*175G>C	.	.	ENST00000371817	66/66	12	8	4	16	16	0	COL5A1,3_prime_UTR_variant,,ENST00000371817,;	C	ENSG00000130635	ENST00000371817	Transcript	3_prime_UTR_variant	6106	.	.	.	.	.	.	.	1	COL5A1	HGNC	2209	protein_coding	YES	CCDS6982.1	ENSP00000360882	CO5A1_HUMAN	Q9UML4_HUMAN,Q96HC0_HUMAN,Q59EE7_HUMAN	UPI0000210EE3	.	.	.	66/66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAACAGAGGGA	.	3	ESCA
LRRC19	0	.	GRCh37	9	26993489	26993489	+	3'UTR	SNP	A	A	T	rs190659202	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2030T>A	.	.	ENST00000380055	5/5	34	27	7	22	22	0	LRRC19,3_prime_UTR_variant,,ENST00000380055,;IFT74,intron_variant,,ENST00000429045,;IFT74,intron_variant,,ENST00000443698,;IFT74,intron_variant,,ENST00000433700,;IFT74,intron_variant,,ENST00000380062,;IFT74,downstream_gene_variant,,ENST00000517866,;IFT74,downstream_gene_variant,,ENST00000519968,;LRRC19,downstream_gene_variant,,ENST00000482770,;IFT74,downstream_gene_variant,,ENST00000494236,;	T	ENSG00000184434	ENST00000380055	Transcript	3_prime_UTR_variant	3254	.	.	.	.	rs190659202	.	.	-1	LRRC19	HGNC	23379	protein_coding	YES	CCDS6518.1	ENSP00000369395	LRC19_HUMAN	.	UPI000006E34A	.	.	.	5/5	.	.	G:0.0004	G:0.0008	G:0.0014	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTATTTTA	byFrequency|by1000G	5	ESCA
CTSL	0	.	GRCh37	9	90344621	90344621	+	Missense_Mutation	SNP	G	G	T	rs774766552	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.755G>T	p.Gly252Val	p.G252V	ENST00000343150	6/8	32	14	18	32	32	0	CTSL,missense_variant,p.Gly252Val,ENST00000340342,;CTSL,missense_variant,p.Gly252Val,ENST00000343150,;CTSL,downstream_gene_variant,,ENST00000342020,;CTSL,non_coding_transcript_exon_variant,,ENST00000375894,;CTSL,non_coding_transcript_exon_variant,,ENST00000495822,;CTSL,downstream_gene_variant,,ENST00000482054,;	T	ENSG00000135047	ENST00000343150	Transcript	missense_variant	1645	755	252	G/V	gGt/gTt	rs774766552	.	.	1	CTSL	HGNC	2537	protein_coding	YES	CCDS6675.1	ENSP00000345344	CATL1_HUMAN	Q9HBQ7_HUMAN,Q8NG13_HUMAN,Q5K630_HUMAN	UPI000004CAA2	.	deleterious(0.04)	probably_damaging(0.926)	6/8	.	Superfamily_domains:SSF54001,SMART_domains:SM00645,Gene3D:3.90.70.10,Pfam_domain:PF00112,hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF306	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGGTCATG	byFrequency	5	ESCA
ERCC6L2	0	.	GRCh37	9	98729010	98729010	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8C>T	.	.	ENST00000288985	14/14	45	31	14	71	71	0	ERCC6L2,3_prime_UTR_variant,,ENST00000437817,;ERCC6L2,3_prime_UTR_variant,,ENST00000288985,;ERCC6L2,intron_variant,,ENST00000402838,;ERCC6L2,non_coding_transcript_exon_variant,,ENST00000466840,;ERCC6L2,intron_variant,,ENST00000470362,;ERCC6L2,3_prime_UTR_variant,,ENST00000456993,;ERCC6L2,intron_variant,,ENST00000479391,;	T	ENSG00000182150	ENST00000288985	Transcript	3_prime_UTR_variant	2452	.	.	.	.	.	.	.	1	ERCC6L2	HGNC	26922	protein_coding	YES	CCDS35072.1	ENSP00000288985	RAD26_HUMAN	.	UPI000046FE3C	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTCTGA	.	5	ESCA
ZNF510	0	.	GRCh37	9	99521732	99521732	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1380T>A	p.Tyr460Ter	p.Y460*	ENST00000375231	6/6	64	42	21	49	49	0	ZNF510,stop_gained,p.Tyr460Ter,ENST00000375231,;ZNF510,stop_gained,p.Tyr460Ter,ENST00000223428,;ZNF510,downstream_gene_variant,,ENST00000374641,;ZNF510,downstream_gene_variant,,ENST00000472201,;	T	ENSG00000081386	ENST00000375231	Transcript	stop_gained	2031	1380	460	Y/*	taT/taA	.	.	.	-1	ZNF510	HGNC	29161	protein_coding	YES	CCDS35074.1	ENSP00000364379	ZN510_HUMAN	Q6NUI8_HUMAN	UPI0000139E9E	.	.	.	6/6	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,hmmpanther:PTHR24392:SF21,hmmpanther:PTHR24392,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTATAGGG	.	5	ESCA
ACTRT1	0	.	GRCh37	X	127185305	127185305	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.881T>G	p.Leu294Arg	p.L294R	ENST00000371124	1/1	30	16	13	25	25	0	ACTRT1,missense_variant,p.Leu294Arg,ENST00000371124,;	C	ENSG00000123165	ENST00000371124	Transcript	missense_variant	1078	881	294	L/R	cTt/cGt	COSM4106508	.	.	-1	ACTRT1	HGNC	24027	protein_coding	YES	CCDS14611.1	ENSP00000360165	ACTT1_HUMAN	.	UPI0000072276	.	deleterious(0)	benign(0.23)	1/1	.	hmmpanther:PTHR11937:SF153,hmmpanther:PTHR11937,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAAAGTTTA	.	5	ESCA
OR13H1	0	.	GRCh37	X	130678783	130678783	+	Missense_Mutation	SNP	G	G	A	rs761571973	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736G>A	p.Val246Met	p.V246M	ENST00000338616	1/1	22	15	7	26	26	0	OR13H1,missense_variant,p.Val246Met,ENST00000338616,;	A	ENSG00000171054	ENST00000338616	Transcript	missense_variant	834	736	246	V/M	Gtg/Atg	rs761571973,COSM3390424	.	.	1	OR13H1	HGNC	14755	protein_coding	YES	CCDS35396.1	ENSP00000340748	O13H1_HUMAN	.	UPI000003CAC9	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF76,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACCGTGGTG	byFrequency	5	ESCA
GPR112	0	.	GRCh37	X	135429032	135429032	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3167C>T	p.Ser1056Leu	p.S1056L	ENST00000394143	6/26	31	12	19	24	24	0	GPR112,missense_variant,p.Ser993Leu,ENST00000287534,;GPR112,missense_variant,p.Ser1056Leu,ENST00000370652,;GPR112,missense_variant,p.Ser1056Leu,ENST00000394143,;GPR112,missense_variant,p.Ser851Leu,ENST00000394141,;GPR112,missense_variant,p.Ser851Leu,ENST00000412101,;	T	ENSG00000156920	ENST00000394143	Transcript	missense_variant	3458	3167	1056	S/L	tCa/tTa	.	.	.	1	GPR112	HGNC	18992	protein_coding	YES	CCDS35409.1	ENSP00000377699	GP112_HUMAN	.	UPI00004CEC5B	.	deleterious(0.05)	benign(0.006)	6/26	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCTCAACTA	.	5	ESCA
SPANXN3	0	.	GRCh37	X	142596676	142596676	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394G>C	p.Glu132Gln	p.E132Q	ENST00000370503	2/2	44	31	13	44	44	0	SPANXN3,missense_variant,p.Glu132Gln,ENST00000370503,;GS1-256O22.5,intron_variant,,ENST00000431432,;	G	ENSG00000189252	ENST00000370503	Transcript	missense_variant	478	394	132	E/Q	Gaa/Caa	.	.	.	-1	SPANXN3	HGNC	33176	protein_coding	YES	CCDS35418.1	ENSP00000359534	SPXN3_HUMAN	.	UPI000016004A	.	tolerated_low_confidence(0.14)	probably_damaging(0.968)	2/2	.	hmmpanther:PTHR23425:SF6,hmmpanther:PTHR23425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S134S|c.402T>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCAGATA	.	5	ESCA
TKTL1	0	.	GRCh37	X	153524131	153524131	+	5'UTR	SNP	C	C	A	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-82C>A	.	.	ENST00000369915	1/13	46	39	7	45	45	0	TKTL1,5_prime_UTR_variant,,ENST00000369915,;TKTL1,upstream_gene_variant,,ENST00000217905,;TEX28,upstream_gene_variant,,ENST00000428625,;TEX28,upstream_gene_variant,,ENST00000361930,;TEX28,upstream_gene_variant,,ENST00000369926,;TKTL1,upstream_gene_variant,,ENST00000439635,;	A	ENSG00000007350	ENST00000369915	Transcript	5_prime_UTR_variant	108	.	.	.	.	.	.	.	1	TKTL1	HGNC	11835	protein_coding	YES	CCDS35448.1	ENSP00000358931	TKTL1_HUMAN	Q5TYJ8_HUMAN,B7Z7I0_HUMAN	UPI0000211D08	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACGCACTGGGC	.	4	ESCA
SHROOM4	0	.	GRCh37	X	50339534	50339534	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*161A>G	.	.	ENST00000376020	9/9	18	8	10	14	14	0	SHROOM4,3_prime_UTR_variant,,ENST00000376020,;SHROOM4,3_prime_UTR_variant,,ENST00000289292,;SHROOM4,3_prime_UTR_variant,,ENST00000460112,;SHROOM4,upstream_gene_variant,,ENST00000483955,;	C	ENSG00000158352	ENST00000376020	Transcript	3_prime_UTR_variant	4669	.	.	.	.	.	.	.	-1	SHROOM4	HGNC	29215	protein_coding	YES	CCDS35277.1	ENSP00000365188	SHRM4_HUMAN	.	UPI00001C2068	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGGTTAGGA	.	2	ESCA
SLC7A3	0	.	GRCh37	X	70148789	70148789	+	Missense_Mutation	SNP	G	G	C	rs755932893	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.434C>G	p.Ser145Cys	p.S145C	ENST00000374299	3/12	16	10	6	21	21	0	SLC7A3,missense_variant,p.Ser145Cys,ENST00000374299,;SLC7A3,missense_variant,p.Ser145Cys,ENST00000298085,;	C	ENSG00000165349	ENST00000374299	Transcript	missense_variant	579	434	145	S/C	tCt/tGt	rs755932893	.	.	-1	SLC7A3	HGNC	11061	protein_coding	YES	CCDS14404.1	ENSP00000363417	CTR3_HUMAN	.	UPI0000049F96	.	deleterious(0)	probably_damaging(0.992)	3/12	.	hmmpanther:PTHR11785:SF209,hmmpanther:PTHR11785,TIGRFAM_domain:TIGR00906,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTAGAGATG	byFrequency	5	ESCA
FAM133A	0	.	GRCh37	X	92964880	92964880	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A4P3-01A-11D-A27G-09	TCGA-IG-A4P3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462G>T	p.Lys154Asn	p.K154N	ENST00000538690	5/5	29	14	14	24	24	0	FAM133A,missense_variant,p.Lys154Asn,ENST00000355813,;FAM133A,missense_variant,p.Lys154Asn,ENST00000538690,;FAM133A,missense_variant,p.Lys154Asn,ENST00000332647,;FAM133A,missense_variant,p.Lys154Asn,ENST00000322139,;	T	ENSG00000179083	ENST00000538690	Transcript	missense_variant	1023	462	154	K/N	aaG/aaT	.	.	.	1	FAM133A	HGNC	26748	protein_coding	YES	CCDS14466.1	ENSP00000441389	F133A_HUMAN	.	UPI000006FB0A	.	deleterious_low_confidence(0.04)	unknown(0)	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31911:SF4,hmmpanther:PTHR31911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAAGGAGTC	.	5	ESCA
CILP2	0	.	GRCh37	19	19656499	19656499	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4QT-01A-21D-A27G-09	TCGA-IG-A4QT-10A-02D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3145C>T	p.%3D	p.L1049L	ENST00000291495	8/8	47	44	3	58	58	0	CILP2,synonymous_variant,p.%3D,ENST00000291495,;CILP2,synonymous_variant,p.%3D,ENST00000586018,;CILP2,downstream_gene_variant,,ENST00000588333,;	T	ENSG00000160161	ENST00000291495	Transcript	synonymous_variant	3230	3145	1049	L	Ctg/Ttg	.	.	.	1	CILP2	HGNC	24213	protein_coding	YES	CCDS12405.1	ENSP00000291495	CILP2_HUMAN	.	UPI000013E04D	.	.	.	8/8	.	hmmpanther:PTHR15031:SF0,hmmpanther:PTHR15031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATGCTGGCC	.	2	ESCA
C19orf55	0	.	GRCh37	19	36249058	36249058	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4QT-01A-21D-A27G-09	TCGA-IG-A4QT-10A-02D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-59C>T	.	.	ENST00000544099	1/11	29	25	4	34	34	0	C19orf55,5_prime_UTR_variant,,ENST00000301165,;C19orf55,5_prime_UTR_variant,,ENST00000544099,;C19orf55,5_prime_UTR_variant,,ENST00000396908,;C19orf55,5_prime_UTR_variant,,ENST00000444637,;C19orf55,upstream_gene_variant,,ENST00000421853,;C19orf55,upstream_gene_variant,,ENST00000542134,;C19orf55,upstream_gene_variant,,ENST00000537459,;HSPB6,upstream_gene_variant,,ENST00000004982,;LIN37,downstream_gene_variant,,ENST00000301159,;C19orf55,upstream_gene_variant,,ENST00000545674,;C19orf55,upstream_gene_variant,,ENST00000536950,;LIN37,downstream_gene_variant,,ENST00000591163,;HSPB6,upstream_gene_variant,,ENST00000592984,;HSPB6,upstream_gene_variant,,ENST00000587965,;AC002398.11,upstream_gene_variant,,ENST00000591091,;AC002398.12,downstream_gene_variant,,ENST00000587767,;C19orf55,upstream_gene_variant,,ENST00000544876,;AC002398.9,downstream_gene_variant,,ENST00000591613,;C19orf55,upstream_gene_variant,,ENST00000601095,;LIN37,downstream_gene_variant,,ENST00000590890,;C19orf55,upstream_gene_variant,,ENST00000600988,;C19orf55,upstream_gene_variant,,ENST00000535581,;LIN37,downstream_gene_variant,,ENST00000595455,;LIN37,downstream_gene_variant,,ENST00000590706,;C19orf55,upstream_gene_variant,,ENST00000539771,;LIN37,downstream_gene_variant,,ENST00000587108,;	T	ENSG00000167595	ENST00000544099	Transcript	5_prime_UTR_variant	5	.	.	.	.	.	.	.	1	C19orf55	HGNC	25204	protein_coding	YES	.	ENSP00000467267	.	K7EP81_HUMAN	UPI00006CA356	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AGATGCGCGCG	.	2	ESCA
UBXN6	0	.	GRCh37	19	4453480	4453480	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A4QT-01A-21D-A27G-09	TCGA-IG-A4QT-10A-02D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287G>A	p.Ser96Asn	p.S96N	ENST00000301281	3/11	22	18	4	18	18	0	UBXN6,missense_variant,p.Ser96Asn,ENST00000301281,;UBXN6,missense_variant,p.Ser69Asn,ENST00000591919,;UBXN6,missense_variant,p.Ser72Asn,ENST00000592515,;UBXN6,missense_variant,p.Ser43Asn,ENST00000394765,;CTB-50L17.16,downstream_gene_variant,,ENST00000591414,;CTB-50L17.16,downstream_gene_variant,,ENST00000590989,;CTB-50L17.9,upstream_gene_variant,,ENST00000592034,;UBXN6,upstream_gene_variant,,ENST00000588238,;UBXN6,upstream_gene_variant,,ENST00000593024,;UBXN6,upstream_gene_variant,,ENST00000592358,;	T	ENSG00000167671	ENST00000301281	Transcript	missense_variant	412	287	96	S/N	aGc/aAc	.	.	.	-1	UBXN6	HGNC	14928	protein_coding	YES	CCDS12129.1	ENSP00000301281	UBXN6_HUMAN	.	UPI000004EF28	.	tolerated(0.5)	benign(0.001)	3/11	.	hmmpanther:PTHR23153,hmmpanther:PTHR23153:SF35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CGGGGCTCCCG	.	2	ESCA
AK4	0	.	GRCh37	1	65693038	65693038	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A4QT-01A-21D-A27G-09	TCGA-IG-A4QT-10A-02D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1178C>T	.	.	ENST00000395334	6/6	47	44	3	51	51	0	AK4,3_prime_UTR_variant,,ENST00000327299,;AK4,3_prime_UTR_variant,,ENST00000395334,;AK4,3_prime_UTR_variant,,ENST00000545314,;AK4,downstream_gene_variant,,ENST00000546702,;AK4,downstream_gene_variant,,ENST00000470888,;AK4,downstream_gene_variant,,ENST00000479060,;AK4,downstream_gene_variant,,ENST00000474968,;AK4,downstream_gene_variant,,ENST00000497030,;	T	ENSG00000162433	ENST00000395334	Transcript	3_prime_UTR_variant	2208	.	.	.	.	.	.	.	1	AK4	HGNC	363	protein_coding	YES	CCDS629.1	ENSP00000378743	KAD4_HUMAN	D3DQ64_HUMAN	UPI000011E13C	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACAGCTTTAT	.	2	ESCA
ZDHHC8P1	0	.	GRCh37	22	23733627	23733627	+	RNA	SNP	G	G	A	novel	.	TCGA-IG-A4QT-01A-21D-A27G-09	TCGA-IG-A4QT-10A-02D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1673C>T	.	.	ENST00000420968	6/6	20	17	3	22	22	0	ZDHHC8P1,non_coding_transcript_exon_variant,,ENST00000255890,;ZDHHC8P1,non_coding_transcript_exon_variant,,ENST00000433168,;ZDHHC8P1,non_coding_transcript_exon_variant,,ENST00000420968,;ZDHHC8P1,downstream_gene_variant,,ENST00000456279,;CES5AP1,upstream_gene_variant,,ENST00000415114,;KB-1269D1.8,upstream_gene_variant,,ENST00000512987,;	A	ENSG00000133519	ENST00000420968	Transcript	non_coding_transcript_exon_variant	1673	.	.	.	.	.	.	.	-1	ZDHHC8P1	HGNC	26461	processed_transcript	YES	.	.	.	.	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCACGGCAAAC	.	2	ESCA
RELN	0	.	GRCh37	7	103202030	103202030	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A4QT-01A-21D-A27G-09	TCGA-IG-A4QT-10A-02D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5478G>A	p.%3D	p.G1826G	ENST00000428762	36/65	43	38	5	38	37	1	RELN,synonymous_variant,p.%3D,ENST00000424685,;RELN,synonymous_variant,p.%3D,ENST00000428762,;RELN,synonymous_variant,p.%3D,ENST00000343529,;	T	ENSG00000189056	ENST00000428762	Transcript	synonymous_variant	5638	5478	1826	G	ggG/ggA	.	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	.	.	36/65	.	hmmpanther:PTHR11841	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATTCCCCCT	.	2	ESCA
EGR3	0	.	GRCh37	8	22545648	22545648	+	3'UTR	SNP	T	T	A	rs397840873,rs539384628	.	TCGA-IG-A4QT-01A-21D-A27G-09	TCGA-IG-A4QT-10A-02D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2338A>T	.	.	ENST00000317216	2/2	45	42	3	50	50	0	EGR3,3_prime_UTR_variant,,ENST00000317216,;EGR3,downstream_gene_variant,,ENST00000522910,;EGR3,downstream_gene_variant,,ENST00000519492,;RP11-459E5.1,upstream_gene_variant,,ENST00000523627,;CTD-3247F14.2,upstream_gene_variant,,ENST00000566457,;EGR3,downstream_gene_variant,,ENST00000524088,;EGR3,downstream_gene_variant,,ENST00000518773,;	A	ENSG00000179388	ENST00000317216	Transcript	3_prime_UTR_variant	3860	.	.	.	.	rs397840873,rs539384628	.	.	-1	EGR3	HGNC	3240	protein_coding	YES	CCDS6033.1	ENSP00000318057	EGR3_HUMAN	B4DH80_HUMAN	UPI0000129E0F	.	.	.	2/2	.	.	A:0.0010	A:0.003	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTTAAACA	byFrequency|by1000G	2	ESCA
CDHR1	0	.	GRCh37	10	85962761	85962761	+	Missense_Mutation	SNP	C	C	A	rs537851141	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.665C>A	p.Ala222Asp	p.A222D	ENST00000372117	8/17	62	57	5	51	51	0	CDHR1,missense_variant,p.Ala222Asp,ENST00000372117,;CDHR1,missense_variant,p.Ala222Asp,ENST00000332904,;CDHR1,5_prime_UTR_variant,,ENST00000440770,;	A	ENSG00000148600	ENST00000372117	Transcript	missense_variant	768	665	222	A/D	gCt/gAt	rs537851141	.	.	1	CDHR1	HGNC	14550	protein_coding	YES	CCDS7372.1	ENSP00000361189	CDHR1_HUMAN	F1T0L2_HUMAN	UPI0000161C2F	.	tolerated(0.66)	benign(0.009)	8/17	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24027:SF2,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGGGCTGATG	byCluster|by1000G	3	ESCA
PI4K2A	0	.	GRCh37	10	99433595	99433595	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*96G>T	.	.	ENST00000370649	10/10	8	2	6	9	9	0	PI4K2A,3_prime_UTR_variant,,ENST00000370649,;PI4K2A,3_prime_UTR_variant,,ENST00000555577,;PI4K2A,3_prime_UTR_variant,,ENST00000370631,;AVPI1,downstream_gene_variant,,ENST00000370626,;	T	ENSG00000249967	ENST00000370649	Transcript	3_prime_UTR_variant	1776	.	.	.	.	.	.	.	1	PI4K2A	Uniprot_gn	30031	protein_coding	YES	.	ENSP00000359683	.	E9PAM4_HUMAN	UPI0001AE6D73	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GAGCAGCACCT	.	2	ESCA
CASP1	0	.	GRCh37	11	104901182	104901182	+	Missense_Mutation	SNP	T	T	C	rs376117763	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502A>G	p.Ile168Val	p.I168V	ENST00000533400	5/9	38	30	8	27	27	0	CASP1,missense_variant,p.Ile168Val,ENST00000436863,;CASP1,missense_variant,p.Ile147Val,ENST00000393136,;CASP1,missense_variant,p.Ile131Val,ENST00000527979,;CASP1,missense_variant,p.Ile75Val,ENST00000446369,;CASP1,missense_variant,p.Ile147Val,ENST00000593315,;CASP1,missense_variant,p.Ile168Val,ENST00000533400,;CASP1,missense_variant,p.Ile17Val,ENST00000532439,;CASP1,missense_variant,p.Ile168Val,ENST00000598974,;CASP1,missense_variant,p.Ile147Val,ENST00000525825,;CASP1,missense_variant,p.Ile75Val,ENST00000526568,;CASP1,missense_variant,p.Ile129Val,ENST00000528974,;CASP1,missense_variant,p.Ile75Val,ENST00000534497,;CASP1,missense_variant,p.Ile75Val,ENST00000594519,;CASP1,intron_variant,,ENST00000415981,;CASP1,intron_variant,,ENST00000353247,;CASP1,intron_variant,,ENST00000531166,;CASP1,missense_variant,p.Tyr108Cys,ENST00000529871,;CASP1,non_coding_transcript_exon_variant,,ENST00000526511,;CASP1,downstream_gene_variant,,ENST00000532520,;CASP1,downstream_gene_variant,,ENST00000528424,;CASP1,upstream_gene_variant,,ENST00000527625,;	C	ENSG00000137752	ENST00000533400	Transcript	missense_variant	538	502	168	I/V	Atc/Gtc	rs376117763	.	.	-1	CASP1	HGNC	1499	protein_coding	YES	CCDS8330.1	ENSP00000433138	CASP1_HUMAN	.	UPI000003AEF8	.	deleterious(0.02)	probably_damaging(0.998)	5/9	.	PROSITE_profiles:PS50208,hmmpanther:PTHR10454:SF34,hmmpanther:PTHR10454,Gene3D:3.40.50.1460,Pfam_domain:PF00656,SMART_domains:SM00115,PIRSF_domain:PIRSF038001,Superfamily_domains:SSF52129,Prints_domain:PR00376	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGATAATGA	.	5	ESCA
MUC2	0	.	GRCh37	11	1093845	1093845	+	Silent	SNP	G	G	A	rs753684218	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5664G>A	p.%3D	p.T1888T	ENST00000441003	30/49	22	12	9	21	21	0	MUC2,synonymous_variant,p.%3D,ENST00000333592,;MUC2,synonymous_variant,p.%3D,ENST00000441003,;MUC2,intron_variant,,ENST00000361558,;MUC2,downstream_gene_variant,,ENST00000359061,;	A	ENSG00000198788	ENST00000441003	Transcript	synonymous_variant	5691	5664	1888	T	acG/acA	rs753684218	.	.	1	MUC2	HGNC	7512	protein_coding	YES	.	ENSP00000415183	.	Q9UMI9_HUMAN,Q9HBC6_HUMAN,H0Y2U6_HUMAN,E7EUV1_HUMAN	UPI00006C10F2	.	.	.	30/49	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCACGGCCCC	byFrequency	5	ESCA
PCSK7	0	.	GRCh37	11	117079693	117079693	+	Silent	SNP	T	T	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1611A>T	p.%3D	p.P537P	ENST00000320934	13/17	122	106	16	94	94	0	PCSK7,synonymous_variant,p.%3D,ENST00000320934,;PCSK7,synonymous_variant,p.%3D,ENST00000540028,;TAGLN,downstream_gene_variant,,ENST00000525531,;TAGLN,downstream_gene_variant,,ENST00000529622,;TAGLN,downstream_gene_variant,,ENST00000530649,;TAGLN,downstream_gene_variant,,ENST00000532870,;TAGLN,downstream_gene_variant,,ENST00000278968,;TAGLN,downstream_gene_variant,,ENST00000392951,;PCSK7,non_coding_transcript_exon_variant,,ENST00000533135,;PCSK7,upstream_gene_variant,,ENST00000529458,;PCSK7,non_coding_transcript_exon_variant,,ENST00000532810,;PCSK7,non_coding_transcript_exon_variant,,ENST00000534529,;PCSK7,non_coding_transcript_exon_variant,,ENST00000527037,;PCSK7,intron_variant,,ENST00000528973,;TAGLN,downstream_gene_variant,,ENST00000533863,;PCSK7,upstream_gene_variant,,ENST00000527861,;PCSK7,upstream_gene_variant,,ENST00000531573,;	A	ENSG00000160613	ENST00000320934	Transcript	synonymous_variant	2242	1611	537	P	ccA/ccT	.	.	.	-1	PCSK7	HGNC	8748	protein_coding	YES	CCDS8382.1	ENSP00000325917	PCSK7_HUMAN	E9PMC0_HUMAN,E9PLM0_HUMAN,E9PIW7_HUMAN,B3KUH2_HUMAN	UPI0000070E4E	.	.	.	13/17	.	hmmpanther:PTHR10795:SF9,hmmpanther:PTHR10795,Pfam_domain:PF01483,Gene3D:2.60.120.260,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCCGTGGGTG	.	4	ESCA
FXYD2	0	.	GRCh37	11	117691332	117691332	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6+49G>T	.	.	ENST00000292079	.	31	27	4	33	33	0	FXYD2,intron_variant,,ENST00000532119,;FXYD6-FXYD2,intron_variant,,ENST00000532984,;FXYD2,intron_variant,,ENST00000260287,;FXYD2,intron_variant,,ENST00000292079,;FXYD2,intron_variant,,ENST00000528014,;DSCAML1,upstream_gene_variant,,ENST00000525836,;RP11-728F11.3,non_coding_transcript_exon_variant,,ENST00000531850,;RP11-728F11.3,intron_variant,,ENST00000596805,;FXYD2,upstream_gene_variant,,ENST00000514385,;FXYD2,non_coding_transcript_exon_variant,,ENST00000533281,;FXYD2,intron_variant,,ENST00000534383,;FXYD2,downstream_gene_variant,,ENST00000317594,;	A	ENSG00000137731	ENST00000292079	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	FXYD2	HGNC	4026	protein_coding	YES	CCDS8386.1	ENSP00000292079	ATNG_HUMAN	.	UPI00001262A8	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCTCCCAAGCC	.	3	ESCA
KIAA1549L	0	.	GRCh37	11	33620438	33620438	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3933C>G	p.%3D	p.P1311P	ENST00000321505	12/20	25	19	5	17	17	0	KIAA1549L,synonymous_variant,p.%3D,ENST00000321505,;KIAA1549L,synonymous_variant,p.%3D,ENST00000526400,;KIAA1549L,synonymous_variant,p.%3D,ENST00000389726,;KIAA1549L,3_prime_UTR_variant,,ENST00000265654,;	G	ENSG00000110427	ENST00000321505	Transcript	synonymous_variant	4113	3933	1311	P	ccC/ccG	.	.	.	1	KIAA1549L	HGNC	24836	protein_coding	YES	CCDS44565.2	ENSP00000315295	K154L_HUMAN	.	UPI0000E59322	.	.	.	12/20	.	Pfam_domain:PF12877,hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCCCAGAA	.	5	ESCA
NUP160	0	.	GRCh37	11	47837042	47837042	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1675C>T	p.%3D	p.L559L	ENST00000378460	13/36	31	24	7	25	25	0	NUP160,synonymous_variant,p.%3D,ENST00000528501,;NUP160,synonymous_variant,p.%3D,ENST00000528071,;NUP160,synonymous_variant,p.%3D,ENST00000530326,;NUP160,synonymous_variant,p.%3D,ENST00000378460,;Y_RNA,downstream_gene_variant,,ENST00000517065,;NUP160,non_coding_transcript_exon_variant,,ENST00000531016,;	A	ENSG00000030066	ENST00000378460	Transcript	synonymous_variant	1722	1675	559	L	Ctg/Ttg	.	.	.	-1	NUP160	HGNC	18017	protein_coding	YES	CCDS31484.1	ENSP00000367721	NU160_HUMAN	.	UPI0000185FEB	.	.	.	13/36	.	hmmpanther:PTHR21286,Pfam_domain:PF11715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAGGCACA	.	5	ESCA
OR5T1	0	.	GRCh37	11	56043679	56043679	+	Missense_Mutation	SNP	G	G	C	rs752406520	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565G>C	p.Val189Leu	p.V189L	ENST00000313033	1/1	95	77	18	89	89	0	OR5T1,missense_variant,p.Val189Leu,ENST00000313033,;	C	ENSG00000181698	ENST00000313033	Transcript	missense_variant	651	565	189	V/L	Gtc/Ctc	rs752406520,COSM1286894	.	.	1	OR5T1	HGNC	14821	protein_coding	YES	CCDS31525.1	ENSP00000323612	OR5T1_HUMAN	.	UPI000004B22E	.	deleterious(0.02)	benign(0.292)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24248:SF33,hmmpanther:PTHR24248,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCATGTCTTT	byFrequency	5	ESCA
OR5M8	0	.	GRCh37	11	56258778	56258778	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69A>T	p.Gln23His	p.Q23H	ENST00000327216	1/1	14	11	3	21	21	0	OR5M8,missense_variant,p.Gln23His,ENST00000327216,;CTD-3051L14.13,upstream_gene_variant,,ENST00000525853,;	A	ENSG00000181371	ENST00000327216	Transcript	missense_variant	94	69	23	Q/H	caA/caT	.	.	.	-1	OR5M8	HGNC	14846	protein_coding	YES	CCDS31533.1	ENSP00000323354	OR5M8_HUMAN	.	UPI00000405CC	.	deleterious(0.01)	benign(0.114)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452:SF146,hmmpanther:PTHR26452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAATTTGTAA	.	2	ESCA
MS4A10	0	.	GRCh37	11	60559760	60559760	+	Missense_Mutation	SNP	C	C	T	rs770181560	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326C>T	p.Ala109Val	p.A109V	ENST00000308287	4/8	28	24	4	46	46	0	MS4A10,missense_variant,p.Ala109Val,ENST00000308287,;	T	ENSG00000172689	ENST00000308287	Transcript	missense_variant	422	326	109	A/V	gCg/gTg	rs770181560	.	.	1	MS4A10	HGNC	13368	protein_coding	YES	CCDS7992.1	ENSP00000311862	M4A10_HUMAN	.	UPI000023754A	.	tolerated(0.44)	benign(0.029)	4/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23320:SF5,hmmpanther:PTHR23320,Pfam_domain:PF04103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A109A|c.327G>A|3	RADIA|MUTECT|MUSE|VARSCANS	CTTGGCGATAA	byFrequency	4	ESCA
FLRT1	0	.	GRCh37	11	63885526	63885526	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1787A>C	p.Lys596Thr	p.K596T	ENST00000246841	2/2	44	38	6	28	28	0	FLRT1,missense_variant,p.Lys596Thr,ENST00000246841,;MACROD1,intron_variant,,ENST00000255681,;RP11-21A7A.3,downstream_gene_variant,,ENST00000543817,;MACROD1,intron_variant,,ENST00000543422,;MACROD1,intron_variant,,ENST00000542359,;MACROD1,intron_variant,,ENST00000545464,;	C	ENSG00000126500	ENST00000246841	Transcript	missense_variant	2830	1787	596	K/T	aAa/aCa	.	.	.	1	FLRT1	HGNC	3760	protein_coding	YES	CCDS8057.1	ENSP00000246841	FLRT1_HUMAN	O43408_HUMAN	UPI0000039F94	.	tolerated(0.08)	benign(0.061)	2/2	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGAAAAAGG	.	4	ESCA
ESRRA	0	.	GRCh37	11	64081712	64081713	+	Frame_Shift_Ins	INS	-	-	GTGC	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.446_449dupTGCG	p.Leu151AlafsTer56	p.L151Afs*56	ENST00000405666	4/7	42	29	13	31	31	0	ESRRA,frameshift_variant,p.Leu151AlafsTer56,ENST00000405666,;ESRRA,frameshift_variant,p.Leu151AlafsTer56,ENST00000000442,;ESRRA,frameshift_variant,p.Leu151AlafsTer55,ENST00000406310,;ESRRA,frameshift_variant,p.Leu8AlafsTer56,ENST00000539594,;TRMT112,downstream_gene_variant,,ENST00000544844,;PRDX5,upstream_gene_variant,,ENST00000265462,;ESRRA,upstream_gene_variant,,ENST00000545035,;TRMT112,downstream_gene_variant,,ENST00000535750,;TRMT112,downstream_gene_variant,,ENST00000308774,;PRDX5,upstream_gene_variant,,ENST00000352435,;PRDX5,upstream_gene_variant,,ENST00000347941,;TRMT112,downstream_gene_variant,,ENST00000539854,;TRMT112,downstream_gene_variant,,ENST00000535126,;ESRRA,splice_region_variant,,ENST00000467987,;TRMT112,downstream_gene_variant,,ENST00000537918,;	GTGC	ENSG00000173153	ENST00000405666	Transcript	frameshift_variant	678-679	444-445	148-149	-/VX	-/GTGC	.	.	.	1	ESRRA	HGNC	3471	protein_coding	YES	CCDS41667.1	ENSP00000384851	ERR1_HUMAN	Q96I02_HUMAN,Q96F89_HUMAN,Q569H8_HUMAN,F5H0E9_HUMAN,F5GWT5_HUMAN	UPI0000167B87	.	.	.	4/7	.	PROSITE_profiles:PS51030,hmmpanther:PTHR24084,Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527,PIRSF_domain:PIRSF500939,Superfamily_domains:SSF57716,Superfamily_domains:SSF48508,Prints_domain:PR00398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAAGGAGTGCG	.	3	ESCA
FRMD8	0	.	GRCh37	11	65154535	65154535	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.28C>A	p.Gln10Lys	p.Q10K	ENST00000317568	2/11	78	67	11	68	68	0	FRMD8,missense_variant,p.Gln10Lys,ENST00000533782,;FRMD8,missense_variant,p.Gln10Lys,ENST00000526201,;FRMD8,missense_variant,p.Gln10Lys,ENST00000355991,;FRMD8,missense_variant,p.Gln10Lys,ENST00000416776,;FRMD8,missense_variant,p.Gln10Lys,ENST00000531296,;FRMD8,missense_variant,p.Gln10Lys,ENST00000317568,;FRMD8,missense_variant,p.Gln10Lys,ENST00000525156,;SLC25A45,upstream_gene_variant,,ENST00000377152,;SLC25A45,upstream_gene_variant,,ENST00000530936,;SLC25A45,upstream_gene_variant,,ENST00000398802,;SLC25A45,upstream_gene_variant,,ENST00000360662,;SLC25A45,upstream_gene_variant,,ENST00000417511,;SLC25A45,upstream_gene_variant,,ENST00000294187,;SLC25A45,upstream_gene_variant,,ENST00000534028,;FRMD8,non_coding_transcript_exon_variant,,ENST00000528854,;SLC25A45,upstream_gene_variant,,ENST00000529431,;SLC25A45,upstream_gene_variant,,ENST00000533629,;SLC25A45,upstream_gene_variant,,ENST00000524438,;SLC25A45,upstream_gene_variant,,ENST00000529962,;SLC25A45,upstream_gene_variant,,ENST00000526898,;SLC25A45,upstream_gene_variant,,ENST00000531791,;	A	ENSG00000126391	ENST00000317568	Transcript	missense_variant	191	28	10	Q/K	Cag/Aag	.	.	.	1	FRMD8	HGNC	25462	protein_coding	YES	CCDS8102.1	ENSP00000319726	FRMD8_HUMAN	Q96MK6_HUMAN,E9PRA3_HUMAN	UPI000000DAAC	.	tolerated(0.67)	benign(0.081)	2/11	.	hmmpanther:PTHR13283	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGGGCAGCCC	.	4	ESCA
NLRP14	0	.	GRCh37	11	7064621	7064621	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1364C>G	p.Ser455Cys	p.S455C	ENST00000299481	4/12	26	22	4	36	36	0	NLRP14,missense_variant,p.Ser455Cys,ENST00000299481,;	G	ENSG00000158077	ENST00000299481	Transcript	missense_variant	1710	1364	455	S/C	tCt/tGt	.	.	.	1	NLRP14	HGNC	22939	protein_coding	YES	CCDS7776.1	ENSP00000299481	NAL14_HUMAN	.	UPI0000167F6E	.	tolerated(0.14)	benign(0.004)	4/12	.	hmmpanther:PTHR24106:SF82,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TCAATCTGATG	.	2	ESCA
NOX4	0	.	GRCh37	11	89223663	89223663	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116A>G	p.Gln39Arg	p.Q39R	ENST00000263317	2/18	45	27	18	51	51	0	NOX4,missense_variant,p.Gln39Arg,ENST00000375979,;NOX4,missense_variant,p.Gln15Arg,ENST00000535633,;NOX4,missense_variant,p.Gln15Arg,ENST00000527956,;NOX4,missense_variant,p.Gln15Arg,ENST00000542487,;NOX4,missense_variant,p.Gln15Arg,ENST00000343727,;NOX4,missense_variant,p.Gln60Arg,ENST00000413594,;NOX4,missense_variant,p.Gln15Arg,ENST00000532825,;NOX4,missense_variant,p.Gln39Arg,ENST00000393282,;NOX4,missense_variant,p.Gln39Arg,ENST00000531342,;NOX4,missense_variant,p.Gln39Arg,ENST00000534731,;NOX4,missense_variant,p.Gln39Arg,ENST00000263317,;NOX4,missense_variant,p.Gln39Arg,ENST00000525196,;NOX4,missense_variant,p.Gln15Arg,ENST00000424319,;NOX4,5_prime_UTR_variant,,ENST00000527626,;NOX4,intron_variant,,ENST00000528341,;NOX4,missense_variant,p.Gln39Arg,ENST00000529343,;NOX4,non_coding_transcript_exon_variant,,ENST00000525278,;	C	ENSG00000086991	ENST00000263317	Transcript	missense_variant	355	116	39	Q/R	cAa/cGa	.	.	.	-1	NOX4	HGNC	7891	protein_coding	YES	CCDS8285.1	ENSP00000263317	NOX4_HUMAN	E7EMD7_HUMAN	UPI000045655B	.	tolerated(0.48)	benign(0)	2/18	.	hmmpanther:PTHR11972	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTTGGTTA	.	5	ESCA
FAT3	0	.	GRCh37	11	92590461	92590461	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11447G>A	p.Ser3816Asn	p.S3816N	ENST00000298047	19/27	28	21	6	33	33	0	FAT3,missense_variant,p.Ser151Asn,ENST00000533797,;FAT3,missense_variant,p.Ser3816Asn,ENST00000298047,;FAT3,missense_variant,p.Ser3816Asn,ENST00000409404,;FAT3,missense_variant,p.Ser3666Asn,ENST00000525166,;	A	ENSG00000165323	ENST00000298047	Transcript	missense_variant	11464	11447	3816	S/N	aGc/aAc	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	benign(0.005)	19/27	.	SMART_domains:SM00181,Gene3D:2.60.120.200,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCAGCAGGA	.	5	ESCA
CCDC82	0	.	GRCh37	11	96104185	96104185	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000278520	6/9	53	48	5	56	56	0	CCDC82,stop_gained,p.Gln401Ter,ENST00000542662,;CCDC82,stop_gained,p.Gln401Ter,ENST00000278520,;CCDC82,stop_gained,p.Gln401Ter,ENST00000423339,;	A	ENSG00000149231	ENST00000278520	Transcript	stop_gained	1630	1201	401	Q/*	Caa/Taa	.	.	.	-1	CCDC82	HGNC	26282	protein_coding	YES	CCDS8307.1	ENSP00000278520	CCD82_HUMAN	F5H777_HUMAN,E9PMD6_HUMAN	UPI000007367A	.	.	.	6/9	.	Pfam_domain:PF13926,hmmpanther:PTHR14689,hmmpanther:PTHR14689:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATATTGCTCTT	.	3	ESCA
NR1H4	0	.	GRCh37	12	100897237	100897238	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77dupT	p.Met27HisfsTer62	p.M27Hfs*62	ENST00000551379	1/9	62	52	10	71	71	0	NR1H4,frameshift_variant,p.Met6HisfsTer47,ENST00000551184,;NR1H4,frameshift_variant,p.Met27HisfsTer62,ENST00000551379,;NR1H4,frameshift_variant,p.Met27HisfsTer62,ENST00000188403,;NR1H4,intron_variant,,ENST00000392986,;NR1H4,intron_variant,,ENST00000549996,;NR1H4,intron_variant,,ENST00000548884,;NR1H4,intron_variant,,ENST00000546380,;NR1H4,intron_variant,,ENST00000321046,;NR1H4,intron_variant,,ENST00000548621,;	T	ENSG00000012504	ENST00000551379	Transcript	frameshift_variant	100-101	72-73	24-25	-/X	-/T	.	.	.	1	NR1H4	HGNC	7967	protein_coding	YES	CCDS55876.1	ENSP00000447149	NR1H4_HUMAN	B7Z423_HUMAN	UPI000006E701	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCAGGATTTTT	.	3	ESCA
TAOK3	0	.	GRCh37	12	118627816	118627816	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1195-70G>T	.	.	ENST00000392533	.	42	38	4	38	38	0	TAOK3,5_prime_UTR_variant,,ENST00000537952,;TAOK3,intron_variant,,ENST00000392533,;TAOK3,intron_variant,,ENST00000537822,;TAOK3,intron_variant,,ENST00000540561,;TAOK3,intron_variant,,ENST00000419821,;TAOK3,intron_variant,,ENST00000537305,;	A	ENSG00000135090	ENST00000392533	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TAOK3	HGNC	18133	protein_coding	YES	CCDS9188.1	ENSP00000376317	TAOK3_HUMAN	G3V1Q8_HUMAN,F5H7G4_HUMAN,F5H5E0_HUMAN,F5H5C7_HUMAN,F5H3L7_HUMAN,F5H005_HUMAN,F5GY38_HUMAN,F5GX96_HUMAN,F5GWV8_HUMAN	UPI000007231B	.	.	.	.	13/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TCTCACCCCTC	.	2	ESCA
CREBL2	0	.	GRCh37	12	12794940	12794940	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8A>G	.	.	ENST00000228865	4/4	59	44	15	54	54	0	CREBL2,3_prime_UTR_variant,,ENST00000228865,;CREBL2,downstream_gene_variant,,ENST00000540224,;	G	ENSG00000111269	ENST00000228865	Transcript	3_prime_UTR_variant	652	.	.	.	.	.	.	.	1	CREBL2	HGNC	2350	protein_coding	YES	CCDS8651.1	ENSP00000228865	CRBL2_HUMAN	.	UPI0000070749	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTATATAAAG	.	5	ESCA
TSPAN9	0	.	GRCh37	12	3390480	3390480	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549G>A	p.%3D	p.T183T	ENST00000011898	7/9	32	23	9	29	29	0	TSPAN9,synonymous_variant,p.%3D,ENST00000407263,;TSPAN9,synonymous_variant,p.%3D,ENST00000011898,;TSPAN9,synonymous_variant,p.%3D,ENST00000537971,;TSPAN9,downstream_gene_variant,,ENST00000431374,;TSPAN9,downstream_gene_variant,,ENST00000492305,;TSPAN9,downstream_gene_variant,,ENST00000444315,;	A	ENSG00000011105	ENST00000011898	Transcript	synonymous_variant	710	549	183	T	acG/acA	.	.	.	1	TSPAN9	HGNC	21640	protein_coding	YES	CCDS8520.1	ENSP00000011898	TSN9_HUMAN	.	UPI000004F1F1	.	.	.	7/9	.	Superfamily_domains:0037997,PIRSF_domain:PIRSF002419,Pfam_domain:PF00335,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACCACGCCTTT	.	4	ESCA
CAND1	0	.	GRCh37	12	67705481	67705481	+	Silent	SNP	A	A	G	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3369A>G	p.%3D	p.T1123T	ENST00000545606	14/15	49	40	8	45	45	0	CAND1,synonymous_variant,p.%3D,ENST00000545606,;CAND1,synonymous_variant,p.%3D,ENST00000544619,;CAND1,downstream_gene_variant,,ENST00000540319,;	G	ENSG00000111530	ENST00000545606	Transcript	synonymous_variant	3806	3369	1123	T	acA/acG	COSM3720453	.	.	1	CAND1	HGNC	30688	protein_coding	YES	CCDS8977.1	ENSP00000442318	CAND1_HUMAN	F5H6I6_HUMAN,B3KMG3_HUMAN	UPI0000037CC5	.	.	.	14/15	.	hmmpanther:PTHR12696:SF1,hmmpanther:PTHR12696,Gene3D:1.25.10.10,Pfam_domain:PF08623,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACATTTTT	.	5	ESCA
ZNF384	0	.	GRCh37	12	6775955	6775955	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*925G>A	.	.	ENST00000396801	11/11	30	27	3	28	28	0	ZNF384,3_prime_UTR_variant,,ENST00000361959,;ZNF384,3_prime_UTR_variant,,ENST00000396801,;ZNF384,3_prime_UTR_variant,,ENST00000319770,;ZNF384,3_prime_UTR_variant,,ENST00000355772,;ZNF384,3_prime_UTR_variant,,ENST00000396795,;ING4,upstream_gene_variant,,ENST00000444704,;ING4,upstream_gene_variant,,ENST00000467678,;ING4,upstream_gene_variant,,ENST00000423703,;ZNF384,downstream_gene_variant,,ENST00000396799,;ING4,upstream_gene_variant,,ENST00000493873,;ING4,upstream_gene_variant,,ENST00000412586,;ING4,upstream_gene_variant,,ENST00000446105,;ING4,upstream_gene_variant,,ENST00000396807,;ZNF384,downstream_gene_variant,,ENST00000545946,;ING4,upstream_gene_variant,,ENST00000341550,;RP4-761J14.8,intron_variant,,ENST00000589924,;RP4-761J14.8,upstream_gene_variant,,ENST00000586338,;ING4,upstream_gene_variant,,ENST00000437149,;ING4,upstream_gene_variant,,ENST00000493267,;ING4,upstream_gene_variant,,ENST00000479301,;ING4,upstream_gene_variant,,ENST00000472002,;ING4,upstream_gene_variant,,ENST00000469749,;ING4,upstream_gene_variant,,ENST00000488381,;	T	ENSG00000126746	ENST00000396801	Transcript	3_prime_UTR_variant	2867	.	.	.	.	.	.	.	-1	ZNF384	HGNC	11955	protein_coding	YES	CCDS44817.1	ENSP00000380019	ZN384_HUMAN	F5H3Z9_HUMAN,F5H105_HUMAN,F5H0D6_HUMAN,F5GYZ1_HUMAN,D3DUR9_HUMAN,B4DQU6_HUMAN,A9X425_HUMAN	UPI00001AE6F8	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGGCCGTGA	.	2	ESCA
SOX1	0	.	GRCh37	13	112725839	112725839	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2691C>T	.	.	ENST00000330949	1/1	11	5	5	13	13	0	SOX1,3_prime_UTR_variant,,ENST00000330949,;	T	ENSG00000182968	ENST00000330949	Transcript	3_prime_UTR_variant	3927	.	.	.	.	.	.	.	1	SOX1	HGNC	11189	protein_coding	YES	CCDS9523.1	ENSP00000330218	SOX1_HUMAN	.	UPI0000190FB0	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTTCCCCGCC	.	3	ESCA
IFT88	0	.	GRCh37	13	21189967	21189967	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1175C>A	p.Ala392Glu	p.A392E	ENST00000319980	16/28	17	11	5	34	34	0	IFT88,missense_variant,p.Ala392Glu,ENST00000319980,;IFT88,missense_variant,p.Ala383Glu,ENST00000351808,;IFT88,missense_variant,p.Ala392Glu,ENST00000382778,;IFT88,missense_variant,p.Ala364Glu,ENST00000537103,;RNU2-7P,downstream_gene_variant,,ENST00000410794,;IFT88,non_coding_transcript_exon_variant,,ENST00000482172,;IFT88,non_coding_transcript_exon_variant,,ENST00000461115,;	A	ENSG00000032742	ENST00000319980	Transcript	missense_variant	1502	1175	392	A/E	gCa/gAa	.	.	.	1	IFT88	HGNC	20606	protein_coding	YES	CCDS31944.1	ENSP00000323580	IFT88_HUMAN	F6SRW8_HUMAN	UPI0000160108	.	deleterious(0)	probably_damaging(0.989)	16/28	.	hmmpanther:PTHR23083:SF6,hmmpanther:PTHR23083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGCAAAAC	.	5	ESCA
OR4Q3	0	.	GRCh37	14	20216269	20216269	+	Missense_Mutation	SNP	C	C	T	rs187324686	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683C>T	p.Thr228Ile	p.T228I	ENST00000331723	1/1	39	31	8	50	50	0	OR4Q3,missense_variant,p.Thr228Ile,ENST00000331723,;OR4N2,intron_variant,,ENST00000557414,;OR11K2P,intron_variant,,ENST00000593630,;	T	ENSG00000182652	ENST00000331723	Transcript	missense_variant	683	683	228	T/I	aCa/aTa	rs187324686	.	.	1	OR4Q3	HGNC	15426	protein_coding	YES	CCDS32020.1	ENSP00000330049	OR4Q3_HUMAN	.	UPI0000061EF0	.	tolerated(0.15)	possibly_damaging(0.816)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF208,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAACACACT	by1000G	5	ESCA
OR4K1	0	.	GRCh37	14	20403917	20403917	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92T>C	p.Phe31Ser	p.F31S	ENST00000285600	1/1	66	55	11	84	84	0	OR4K1,missense_variant,p.Phe31Ser,ENST00000285600,;	C	ENSG00000155249	ENST00000285600	Transcript	missense_variant	151	92	31	F/S	tTc/tCc	COSM469741	.	.	1	OR4K1	HGNC	14726	protein_coding	YES	CCDS32025.1	ENSP00000285600	OR4K1_HUMAN	.	UPI0000041B4A	.	tolerated(0.08)	probably_damaging(0.998)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF182,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTTCTCTA	.	5	ESCA
NOVA1	0	.	GRCh37	14	26915623	26915623	+	3'UTR	DEL	G	G	-	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1542delC	.	.	ENST00000539517	5/5	88	75	13	71	71	0	NOVA1,3_prime_UTR_variant,,ENST00000539517,;NOVA1,3_prime_UTR_variant,,ENST00000465357,;NOVA1,downstream_gene_variant,,ENST00000549146,;NOVA1,downstream_gene_variant,,ENST00000347476,;NOVA1,downstream_gene_variant,,ENST00000549571,;NOVA1,downstream_gene_variant,,ENST00000267422,;NOVA1,downstream_gene_variant,,ENST00000449198,;NOVA1,3_prime_UTR_variant,,ENST00000483536,;NOVA1,downstream_gene_variant,,ENST00000546546,;	-	ENSG00000139910	ENST00000539517	Transcript	3_prime_UTR_variant	3384	.	.	.	.	.	.	.	-1	NOVA1	HGNC	7886	protein_coding	YES	CCDS32061.1	ENSP00000438875	NOVA1_HUMAN	F8VW64_HUMAN,B7Z770_HUMAN	UPI000013D74E	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCACAGAAAGG	.	3	ESCA
ARHGAP5	0	.	GRCh37	14	32623846	32623846	+	Missense_Mutation	SNP	A	A	G	rs779238726	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4201A>G	p.Ile1401Val	p.I1401V	ENST00000345122	7/7	44	36	7	31	31	0	ARHGAP5,missense_variant,p.Ile1400Val,ENST00000432921,;ARHGAP5,missense_variant,p.Ile1401Val,ENST00000539826,;ARHGAP5,missense_variant,p.Ile136Val,ENST00000396582,;ARHGAP5,missense_variant,p.Ile140Val,ENST00000433497,;ARHGAP5,missense_variant,p.Ile1401Val,ENST00000345122,;ARHGAP5,missense_variant,p.Ile1400Val,ENST00000556611,;ARHGAP5,downstream_gene_variant,,ENST00000554090,;ARHGAP5,3_prime_UTR_variant,,ENST00000557643,;ARHGAP5,non_coding_transcript_exon_variant,,ENST00000216743,;	G	ENSG00000100852	ENST00000345122	Transcript	missense_variant	4516	4201	1401	I/V	Atc/Gtc	rs779238726	.	.	1	ARHGAP5	HGNC	675	protein_coding	YES	CCDS32062.1	ENSP00000371897	RHG05_HUMAN	G3V5I7_HUMAN,G3V444_HUMAN,G3V360_HUMAN	UPI000057B85C	.	tolerated(0.85)	benign(0)	7/7	.	PROSITE_profiles:PS50238,hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF4,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAAATCAAC	byFrequency	5	ESCA
MAP4K5	0	.	GRCh37	14	50895961	50895961	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2182delT	p.Ser728ProfsTer4	p.S728Pfs*4	ENST00000013125	28/32	36	30	6	27	27	0	MAP4K5,frameshift_variant,p.Ser728ProfsTer4,ENST00000013125,;MAP4K5,non_coding_transcript_exon_variant,,ENST00000554990,;	-	ENSG00000012983	ENST00000013125	Transcript	frameshift_variant	2501	2182	728	S/X	Tcc/cc	.	.	.	-1	MAP4K5	HGNC	6867	protein_coding	YES	.	ENSP00000013125	M4K5_HUMAN	G3V5C6_HUMAN,G3V4T8_HUMAN,G3V3V7_HUMAN	UPI00015DFDAA	.	.	.	28/32	.	PROSITE_profiles:PS50219,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF203,Pfam_domain:PF00780,PIRSF_domain:PIRSF038172,SMART_domains:SM00036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAATGGAATCTA	.	3	ESCA
ZBTB1	0	.	GRCh37	14	64991355	64991355	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*991C>G	.	.	ENST00000394712	2/2	23	16	7	38	38	0	ZBTB1,3_prime_UTR_variant,,ENST00000394712,;ZBTB1,intron_variant,,ENST00000358738,;ZBTB1,downstream_gene_variant,,ENST00000555321,;ZBTB1,downstream_gene_variant,,ENST00000554015,;ZBTB1,downstream_gene_variant,,ENST00000553583,;ZBTB1,downstream_gene_variant,,ENST00000556965,;RP11-973N13.4,intron_variant,,ENST00000554918,;	G	ENSG00000126804	ENST00000394712	Transcript	3_prime_UTR_variant	3524	.	.	.	.	.	.	.	1	ZBTB1	HGNC	20259	protein_coding	YES	CCDS45126.1	ENSP00000378201	ZBTB1_HUMAN	G3V447_HUMAN,G3V3N0_HUMAN,G3V2I8_HUMAN	UPI00001FD6B2	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	GAGATCAATTA	.	3	ESCA
GALC	0	.	GRCh37	14	88431853	88431853	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1029A>G	p.%3D	p.V343V	ENST00000261304	9/17	31	28	3	20	20	0	GALC,synonymous_variant,p.%3D,ENST00000393568,;GALC,synonymous_variant,p.%3D,ENST00000544807,;GALC,synonymous_variant,p.%3D,ENST00000393569,;GALC,synonymous_variant,p.%3D,ENST00000261304,;GALC,non_coding_transcript_exon_variant,,ENST00000557520,;GALC,synonymous_variant,p.%3D,ENST00000555000,;GALC,3_prime_UTR_variant,,ENST00000557316,;GALC,non_coding_transcript_exon_variant,,ENST00000474294,;GALC,downstream_gene_variant,,ENST00000477716,;	C	ENSG00000054983	ENST00000261304	Transcript	synonymous_variant	1136	1029	343	V	gtA/gtG	.	.	.	-1	GALC	HGNC	4115	protein_coding	YES	CCDS9878.2	ENSP00000261304	GALC_HUMAN	.	UPI00001FD982	.	.	.	9/17	.	Superfamily_domains:SSF51445,Pfam_domain:PF02057,Gene3D:3.20.20.80,hmmpanther:PTHR15172,hmmpanther:PTHR15172:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGATACCCA	.	4	ESCA
IGHV4OR15-8	0	.	GRCh37	15	22473170	22473170	+	Missense_Mutation	SNP	G	G	A	rs748884810	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.101C>T	p.Ser34Leu	p.S34L	ENST00000557788	2/2	163	152	11	176	176	0	IGHV4OR15-8,missense_variant,p.Ser34Leu,ENST00000557788,;	A	ENSG00000259261	ENST00000557788	Transcript	missense_variant	101	101	34	S/L	tCg/tTg	rs748884810	.	.	-1	IGHV4OR15-8	HGNC	5658	IG_V_gene	YES	.	ENSP00000473987	IV4F8_HUMAN	.	UPI0003335098	.	deleterious(0.04)	benign(0.143)	2/2	.	Superfamily_domains:SSF48726,Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF86,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCCGAAGGC	byFrequency	2	ESCA
GOLGA6L1	0	.	GRCh37	15	22742849	22742849	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234C>A	p.Gln412Lys	p.Q412K	ENST00000316397	8/9	32	14	18	37	37	0	GOLGA6L1,missense_variant,p.Gln412Lys,ENST00000316397,;GOLGA6L1,missense_variant,p.Gln362Lys,ENST00000560659,;RP11-566K19.3,downstream_gene_variant,,ENST00000560026,;	A	ENSG00000197414	ENST00000316397	Transcript	missense_variant	1325	1234	412	Q/K	Cag/Aag	.	.	.	1	GOLGA6L1	HGNC	37444	protein_coding	YES	CCDS53919.1	ENSP00000320207	.	I3L087_HUMAN	UPI0001929533	.	.	unknown(0)	8/9	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23143,hmmpanther:PTHR23143:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	AGAGGCAGGAG	.	3	ESCA
ZNF609	0	.	GRCh37	15	64967549	64967549	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2496A>T	p.%3D	p.G832G	ENST00000326648	4/9	17	8	8	17	17	0	ZNF609,synonymous_variant,p.%3D,ENST00000326648,;RNU6-549P,downstream_gene_variant,,ENST00000384433,;ZNF609,downstream_gene_variant,,ENST00000559364,;ZNF609,downstream_gene_variant,,ENST00000558680,;	T	ENSG00000180357	ENST00000326648	Transcript	synonymous_variant	2624	2496	832	G	ggA/ggT	.	.	.	1	ZNF609	HGNC	29003	protein_coding	YES	CCDS32270.1	ENSP00000316527	ZN609_HUMAN	.	UPI00001D7783	.	.	.	4/9	.	hmmpanther:PTHR21564,hmmpanther:PTHR21564:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGGAGCTGA	.	5	ESCA
NPRL3	0	.	GRCh37	16	139733	139733	+	Silent	SNP	G	G	A	rs559760517	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1329C>T	p.%3D	p.N443N	ENST00000399953	11/14	45	38	6	30	30	0	NPRL3,synonymous_variant,p.%3D,ENST00000399953,;NPRL3,synonymous_variant,p.%3D,ENST00000399951,;MPG,downstream_gene_variant,,ENST00000436333,;MPG,downstream_gene_variant,,ENST00000356432,;MPG,downstream_gene_variant,,ENST00000397817,;MPG,downstream_gene_variant,,ENST00000219431,;Z69720.2,upstream_gene_variant,,ENST00000601483,;NPRL3,non_coding_transcript_exon_variant,,ENST00000405960,;NPRL3,non_coding_transcript_exon_variant,,ENST00000428323,;NPRL3,downstream_gene_variant,,ENST00000473674,;NPRL3,downstream_gene_variant,,ENST00000464069,;NPRL3,3_prime_UTR_variant,,ENST00000399957,;NPRL3,3_prime_UTR_variant,,ENST00000445810,;NPRL3,non_coding_transcript_exon_variant,,ENST00000463178,;	A	ENSG00000103148	ENST00000399953	Transcript	synonymous_variant	1732	1329	443	N	aaC/aaT	rs559760517	.	.	-1	NPRL3	HGNC	14124	protein_coding	YES	.	ENSP00000382834	NPRL3_HUMAN	.	UPI00004568D2	.	.	.	11/14	.	hmmpanther:PTHR13153	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGGCGTTGGG	by1000G	3	ESCA
RPS15A	0	.	GRCh37	16	18795982	18795983	+	Intron	INS	-	-	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.299+77dupT	.	.	ENST00000322989	.	19	9	10	19	19	0	RPS15A,3_prime_UTR_variant,,ENST00000576436,;RPS15A,3_prime_UTR_variant,,ENST00000569083,;RPS15A,intron_variant,,ENST00000563579,;RPS15A,intron_variant,,ENST00000563390,;RPS15A,intron_variant,,ENST00000565420,;RPS15A,intron_variant,,ENST00000322989,;RP11-1035H13.3,downstream_gene_variant,,ENST00000567078,;RPS15A,non_coding_transcript_exon_variant,,ENST00000575669,;RPS15A,downstream_gene_variant,,ENST00000573554,;RPS15A,intron_variant,,ENST00000576008,;RPS15A,intron_variant,,ENST00000574723,;RPS15A,intron_variant,,ENST00000569365,;RPS15A,intron_variant,,ENST00000562935,;RPS15A,intron_variant,,ENST00000572008,;	A	ENSG00000134419	ENST00000322989	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RPS15A	HGNC	10389	protein_coding	YES	CCDS10571.1	ENSP00000318646	RS15A_HUMAN	I3L3P7_HUMAN,B2R4W8_HUMAN	UPI0000002488	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAAAGAAAAA	.	2	ESCA
KNOP1	0	.	GRCh37	16	19718330	19718330	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1279A>T	p.Lys427Ter	p.K427*	ENST00000219837	5/5	35	25	10	50	50	0	KNOP1,stop_gained,p.Lys106Ter,ENST00000568230,;KNOP1,stop_gained,p.Lys427Ter,ENST00000219837,;C16orf62,downstream_gene_variant,,ENST00000542027,;KNOP1,downstream_gene_variant,,ENST00000567367,;AC002550.5,non_coding_transcript_exon_variant,,ENST00000565916,;KNOP1,downstream_gene_variant,,ENST00000565844,;	A	ENSG00000103550	ENST00000219837	Transcript	stop_gained	1358	1279	427	K/*	Aag/Tag	.	.	.	-1	KNOP1	HGNC	34404	protein_coding	YES	CCDS42127.1	ENSP00000219837	KNOP1_HUMAN	H3BNU8_HUMAN,H3BMC9_HUMAN	UPI00001982F5	.	.	.	5/5	.	Pfam_domain:PF15477,hmmpanther:PTHR22426	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACTTCCAGC	.	5	ESCA
SYNGR3	0	.	GRCh37	16	2044035	2044035	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*962C>T	.	.	ENST00000248121	4/4	20	17	3	38	38	0	SYNGR3,3_prime_UTR_variant,,ENST00000248121,;SYNGR3,downstream_gene_variant,,ENST00000568896,;SYNGR3,downstream_gene_variant,,ENST00000563869,;ZNF598,downstream_gene_variant,,ENST00000562103,;ZNF598,downstream_gene_variant,,ENST00000431526,;SYNGR3,downstream_gene_variant,,ENST00000562045,;ZNF598,downstream_gene_variant,,ENST00000563630,;AC005606.15,upstream_gene_variant,,ENST00000567515,;AC005606.14,upstream_gene_variant,,ENST00000565041,;ZNF598,downstream_gene_variant,,ENST00000567008,;ZNF598,downstream_gene_variant,,ENST00000565396,;ZNF598,downstream_gene_variant,,ENST00000564556,;SYNGR3,downstream_gene_variant,,ENST00000564642,;ZNF598,downstream_gene_variant,,ENST00000562988,;	T	ENSG00000127561	ENST00000248121	Transcript	3_prime_UTR_variant	1810	.	.	.	.	.	.	.	1	SYNGR3	HGNC	11501	protein_coding	YES	CCDS10456.1	ENSP00000248121	SNG3_HUMAN	.	UPI0000135B32	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCAACACCAA	.	2	ESCA
SALL1	0	.	GRCh37	16	51169890	51169890	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1133C>G	.	.	ENST00000251020	3/3	33	30	3	38	38	0	SALL1,3_prime_UTR_variant,,ENST00000251020,;SALL1,3_prime_UTR_variant,,ENST00000440970,;SALL1,downstream_gene_variant,,ENST00000541611,;SALL1,downstream_gene_variant,,ENST00000570206,;SALL1,downstream_gene_variant,,ENST00000566102,;	C	ENSG00000103449	ENST00000251020	Transcript	3_prime_UTR_variant	5142	.	.	.	.	.	.	.	-1	SALL1	HGNC	10524	protein_coding	YES	CCDS10747.1	ENSP00000251020	SALL1_HUMAN	H3BSM9_HUMAN	UPI000013CCD8	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ACACAGTATTT	.	3	ESCA
RLTPR	0	.	GRCh37	16	67688336	67688336	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3323G>A	p.Arg1108His	p.R1108H	ENST00000334583	31/38	77	66	11	54	54	0	RLTPR,missense_variant,p.Arg1108His,ENST00000334583,;RLTPR,missense_variant,p.Arg1072His,ENST00000545661,;ACD,downstream_gene_variant,,ENST00000219251,;ACD,downstream_gene_variant,,ENST00000602850,;ACD,downstream_gene_variant,,ENST00000393919,;ACD,downstream_gene_variant,,ENST00000602320,;ACD,downstream_gene_variant,,ENST00000602382,;RLTPR,non_coding_transcript_exon_variant,,ENST00000602924,;ACD,downstream_gene_variant,,ENST00000602860,;ACD,downstream_gene_variant,,ENST00000602656,;RLTPR,upstream_gene_variant,,ENST00000602368,;ACD,downstream_gene_variant,,ENST00000602945,;RLTPR,upstream_gene_variant,,ENST00000602705,;ACD,downstream_gene_variant,,ENST00000602519,;RLTPR,downstream_gene_variant,,ENST00000602321,;RLTPR,downstream_gene_variant,,ENST00000602931,;ACD,downstream_gene_variant,,ENST00000602622,;RLTPR,downstream_gene_variant,,ENST00000602633,;RLTPR,downstream_gene_variant,,ENST00000602562,;	A	ENSG00000159753	ENST00000334583	Transcript	missense_variant	3651	3323	1108	R/H	cGt/cAt	.	.	.	1	RLTPR	HGNC	27089	protein_coding	YES	CCDS45513.1	ENSP00000334958	LR16C_HUMAN	.	UPI00005194F2	.	deleterious(0)	probably_damaging(0.996)	31/38	.	hmmpanther:PTHR24112:SF41,hmmpanther:PTHR24112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTCGTTCAA	.	4	ESCA
CNTNAP4	0	.	GRCh37	16	76523630	76523630	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1711G>T	p.Val571Phe	p.V571F	ENST00000478060	12/23	9	6	3	18	18	0	CNTNAP4,missense_variant,p.Val571Phe,ENST00000478060,;CNTNAP4,missense_variant,p.Val595Phe,ENST00000377504,;CNTNAP4,missense_variant,p.Val643Phe,ENST00000307431,;CNTNAP4,missense_variant,p.Val647Phe,ENST00000476707,;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000469667,;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000469589,;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,;	T	ENSG00000152910	ENST00000478060	Transcript	missense_variant	1711	1711	571	V/F	Gtc/Ttc	.	.	.	1	CNTNAP4	HGNC	18747	protein_coding	YES	CCDS10924.2	ENSP00000418741	CNTP4_HUMAN	H3BPC8_HUMAN	UPI000059D3C6	.	deleterious(0.01)	benign(0.167)	12/23	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAAGAGTCAGA	.	3	ESCA
C16orf72	0	.	GRCh37	16	9211276	9211276	+	3'UTR	SNP	A	A	T	rs772495076	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*507A>T	.	.	ENST00000327827	4/4	63	51	12	56	56	0	C16orf72,3_prime_UTR_variant,,ENST00000327827,;RP11-473I1.10,downstream_gene_variant,,ENST00000574616,;	T	ENSG00000182831	ENST00000327827	Transcript	3_prime_UTR_variant	1732	.	.	.	.	rs772495076	.	.	1	C16orf72	HGNC	30103	protein_coding	YES	CCDS10538.1	ENSP00000331720	CP072_HUMAN	.	UPI00001E0574	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTAATTAT	byCluster	5	ESCA
MYH2	0	.	GRCh37	17	10431151	10431151	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3785T>C	p.Leu1262Pro	p.L1262P	ENST00000245503	28/40	57	41	16	40	40	0	MYH2,missense_variant,p.Leu1262Pro,ENST00000245503,;MYH2,missense_variant,p.Leu1262Pro,ENST00000397183,;MYH2,intron_variant,,ENST00000532183,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	G	ENSG00000125414	ENST00000245503	Transcript	missense_variant	4170	3785	1262	L/P	cTg/cCg	.	.	.	-1	MYH2	HGNC	7572	protein_coding	YES	CCDS11156.1	ENSP00000245503	MYH2_HUMAN	J3QLR0_HUMAN,E7EX84_HUMAN,C9JIX4_HUMAN	UPI000012FB6C	.	deleterious(0)	benign(0.278)	28/40	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF90257,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF314	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTCAGTTGG	.	5	ESCA
RAI1	0	.	GRCh37	17	17696252	17696252	+	5'UTR	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11C>G	.	.	ENST00000353383	3/6	30	10	20	23	23	0	RAI1,5_prime_UTR_variant,,ENST00000353383,;RAI1,5_prime_UTR_variant,,ENST00000471135,;RAI1,5_prime_UTR_variant,,ENST00000395774,;RAI1,upstream_gene_variant,,ENST00000261641,;	G	ENSG00000108557	ENST00000353383	Transcript	5_prime_UTR_variant	459	.	.	.	.	.	.	.	1	RAI1	HGNC	9834	protein_coding	YES	CCDS11188.1	ENSP00000323074	RAI1_HUMAN	J3QLL5_HUMAN,A8MXE8_HUMAN	UPI0000200AAF	.	.	.	3/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAACCAGCCC	.	5	ESCA
KRT15	0	.	GRCh37	17	39670288	39670288	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1358A>G	p.Lys453Arg	p.K453R	ENST00000254043	8/8	29	23	6	17	17	0	KRT15,missense_variant,p.Lys453Arg,ENST00000393976,;KRT15,missense_variant,p.Lys453Arg,ENST00000254043,;KRT15,missense_variant,p.Lys288Arg,ENST00000393974,;KRT15,3_prime_UTR_variant,,ENST00000393981,;KRT15,downstream_gene_variant,,ENST00000458290,;KRT15,non_coding_transcript_exon_variant,,ENST00000586794,;KRT15,non_coding_transcript_exon_variant,,ENST00000474031,;KRT15,downstream_gene_variant,,ENST00000470004,;KRT15,downstream_gene_variant,,ENST00000497016,;KRT15,downstream_gene_variant,,ENST00000463447,;	C	ENSG00000171346	ENST00000254043	Transcript	missense_variant	4944	1358	453	K/R	aAg/aGg	.	.	.	-1	KRT15	HGNC	6421	protein_coding	YES	CCDS11398.1	ENSP00000254043	K1C15_HUMAN	.	UPI000013CE0E	.	tolerated(0.28)	benign(0.437)	8/8	.	hmmpanther:PTHR23239:SF164,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTCTTGTGG	.	5	ESCA
ANKFY1	0	.	GRCh37	17	4080500	4080500	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2822C>A	p.Ser941Ter	p.S941*	ENST00000570535	19/25	35	27	7	26	26	0	ANKFY1,stop_gained,p.Ser900Ter,ENST00000574367,;ANKFY1,stop_gained,p.Ser899Ter,ENST00000341657,;ANKFY1,stop_gained,p.Ser941Ter,ENST00000570535,;CYB5D2,intron_variant,,ENST00000573984,;ANKFY1,3_prime_UTR_variant,,ENST00000572412,;ANKFY1,downstream_gene_variant,,ENST00000572564,;ANKFY1,downstream_gene_variant,,ENST00000571547,;	T	ENSG00000185722	ENST00000570535	Transcript	stop_gained	2939	2822	941	S/*	tCa/tAa	COSM3795631	.	.	-1	ANKFY1	HGNC	20763	protein_coding	YES	CCDS58502.1	ENSP00000459943	ANFY1_HUMAN	I3L1Z9_HUMAN	UPI00003FECB0	.	.	.	19/25	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24189,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTGAATTC	.	5	ESCA
SPAG9	0	.	GRCh37	17	49072830	49072830	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2033T>A	p.Leu678Gln	p.L678Q	ENST00000262013	17/30	26	18	8	23	23	0	SPAG9,missense_variant,p.Leu521Gln,ENST00000510283,;SPAG9,missense_variant,p.Leu664Gln,ENST00000357122,;SPAG9,missense_variant,p.Leu668Gln,ENST00000505279,;SPAG9,missense_variant,p.Leu678Gln,ENST00000262013,;SPAG9,upstream_gene_variant,,ENST00000513906,;SPAG9,non_coding_transcript_exon_variant,,ENST00000514613,;SPAG9,non_coding_transcript_exon_variant,,ENST00000506483,;SPAG9,non_coding_transcript_exon_variant,,ENST00000505173,;SPAG9,downstream_gene_variant,,ENST00000513827,;SPAG9,upstream_gene_variant,,ENST00000513746,;SPAG9,downstream_gene_variant,,ENST00000515685,;SPAG9,upstream_gene_variant,,ENST00000514205,;	T	ENSG00000008294	ENST00000262013	Transcript	missense_variant	2242	2033	678	L/Q	cTg/cAg	.	.	.	-1	SPAG9	HGNC	14524	protein_coding	YES	CCDS45740.1	ENSP00000262013	JIP4_HUMAN	H0Y981_HUMAN	UPI0000D60DF7	.	deleterious(0)	probably_damaging(0.996)	17/30	.	hmmpanther:PTHR13886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCCAGAGGT	.	5	ESCA
LPO	0	.	GRCh37	17	56329698	56329698	+	Silent	SNP	C	C	T	rs369628308	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936C>T	p.%3D	p.S312S	ENST00000262290	8/13	47	36	10	38	38	0	LPO,synonymous_variant,p.%3D,ENST00000421678,;LPO,synonymous_variant,p.%3D,ENST00000262290,;LPO,synonymous_variant,p.%3D,ENST00000543544,;LPO,synonymous_variant,p.%3D,ENST00000582328,;LPO,downstream_gene_variant,,ENST00000581008,;LPO,synonymous_variant,p.%3D,ENST00000389576,;LPO,3_prime_UTR_variant,,ENST00000580890,;LPO,downstream_gene_variant,,ENST00000578403,;LPO,downstream_gene_variant,,ENST00000580346,;LPO,downstream_gene_variant,,ENST00000578643,;	T	ENSG00000167419	ENST00000262290	Transcript	synonymous_variant	1252	936	312	S	tcC/tcT	rs369628308,COSM393316	.	.	1	LPO	HGNC	6678	protein_coding	YES	CCDS32689.1	ENSP00000262290	PERL_HUMAN	J3QSD8_HUMAN,F5H386_HUMAN	UPI0000131631	.	.	.	8/13	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF53,hmmpanther:PTHR11475,Pfam_domain:PF03098,Gene3D:1.10.640.10,Superfamily_domains:SSF48113	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCCGAGCC	byFrequency|byCluster	5	ESCA
TP53	0	.	GRCh37	17	7577114	7577114	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	8/11	262	129	133	286	286	0	TP53,missense_variant,p.Cys275Phe,ENST00000420246,;TP53,missense_variant,p.Cys275Phe,ENST00000269305,;TP53,missense_variant,p.Cys143Phe,ENST00000509690,;TP53,missense_variant,p.Cys275Phe,ENST00000359597,;TP53,missense_variant,p.Cys275Phe,ENST00000445888,;TP53,missense_variant,p.Cys275Phe,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1014	824	275	C/F	tGt/tTt	CM951234,CM076568,TP53_g.13804G>A,TP53_g.13804del,TP53_g.13804G>C,TP53_g.13804G>T,COSM10701,COSM10893,COSM45413,COSM44178,COSM165084,COSM99932,COSM1167915,COSM318164,COSM3403255,COSM3723938,COSM1637959,COSM2744531,COSM1728541	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.983)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.C275F|c.824G>T|10,SITE|p.C275F|c.824G>T|43,SITE|p.C275F|c.824G>T|5,CODON|p.0?|c.1_1182del1182|6,CODON|p.C275C|c.825T>C|4,CODON|p.C275W|c.825T>G|8,CODON|p.C275*|c.825T>A|3,CODON|p.C275S|c.824G>C|4,CODON|p.C275Y|c.824G>A|5,CODON|p.C275Y|c.824G>A|54,CODON|p.C275Y|c.824G>A|5,CODON|p.C275Y|c.824G>A|11,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278fs*67|c.833delC|3,BUFFER|p.P278F|c.832_833CC>TT|3,BUFFER|p.P278H|c.833C>A|15,BUFFER|p.P278R|c.833C>G|5,BUFFER|p.P278R|c.833C>G|30,BUFFER|p.P278R|c.833C>G|3,BUFFER|p.P278H|c.833C>A|3,BUFFER|p.P278L|c.833C>T|3,BUFFER|p.P278L|c.833C>T|11,BUFFER|p.P278L|c.833C>T|65,BUFFER|p.P278L|c.833C>T|8,BUFFER|p.P278fs*67|c.832delC|3,BUFFER|p.P278T|c.832C>A|29,BUFFER|p.P278A|c.832C>G|25,BUFFER|p.P278T|c.832C>A|8,BUFFER|p.P278A|c.832C>G|4,BUFFER|p.P278A|c.832C>G|10,BUFFER|p.P278S|c.832C>T|4,BUFFER|p.P278S|c.832C>T|3,BUFFER|p.P278S|c.832C>T|8,BUFFER|p.P278S|c.832C>T|55,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273L|c.818G>T|98,BUFFER|p.R273P|c.818G>C|4,BUFFER|p.R273H|c.818G>A|116,BUFFER|p.R273H|c.818G>A|64,BUFFER|p.R273H|c.818G>A|588,BUFFER|p.R273L|c.818G>T|5,BUFFER|p.R273H|c.818G>A|83,BUFFER|p.R273P|c.818G>C|29,BUFFER|p.R273L|c.818G>T|18,BUFFER|p.R273L|c.818G>T|12,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCACAAACA	.	5	ESCA
PTPN2	0	.	GRCh37	18	12859247	12859247	+	Silent	SNP	G	G	T	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76C>A	p.%3D	p.R26R	ENST00000309660	2/9	60	48	12	47	47	0	PTPN2,synonymous_variant,p.%3D,ENST00000309660,;PTPN2,synonymous_variant,p.%3D,ENST00000327283,;PTPN2,synonymous_variant,p.%3D,ENST00000591115,;PTPN2,synonymous_variant,p.%3D,ENST00000353319,;PTPN2,5_prime_UTR_variant,,ENST00000592059,;PTPN2,non_coding_transcript_exon_variant,,ENST00000589086,;PTPN2,synonymous_variant,p.%3D,ENST00000592776,;PTPN2,intron_variant,,ENST00000591305,;PTPN2,intron_variant,,ENST00000589216,;	T	ENSG00000175354	ENST00000309660	Transcript	synonymous_variant	170	76	26	R	Cga/Aga	COSM263172,COSM3524261	.	.	-1	PTPN2	HGNC	9650	protein_coding	YES	CCDS11865.1	ENSP00000311857	PTN2_HUMAN	K7ER87_HUMAN,D3DUJ3_HUMAN	UPI000017284E	.	.	.	2/9	.	Superfamily_domains:SSF52799,PIRSF_domain:PIRSF000926,SMART_domains:SM00194,Gene3D:3.90.190.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF200,PROSITE_profiles:PS50055	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCGAATTT	.	5	ESCA
TYK2	0	.	GRCh37	19	10461607	10461607	+	Missense_Mutation	SNP	G	G	A	rs143538128	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3467C>T	p.Ala1156Val	p.A1156V	ENST00000525621	25/25	29	22	7	34	34	0	TYK2,missense_variant,p.Ala1156Val,ENST00000525621,;TYK2,missense_variant,p.Ala1156Val,ENST00000264818,;TYK2,missense_variant,p.Ala33Val,ENST00000525976,;TYK2,missense_variant,p.Ala971Val,ENST00000524462,;TYK2,synonymous_variant,p.%3D,ENST00000530560,;TYK2,downstream_gene_variant,,ENST00000529739,;TYK2,non_coding_transcript_exon_variant,,ENST00000529422,;TYK2,downstream_gene_variant,,ENST00000592137,;TYK2,non_coding_transcript_exon_variant,,ENST00000530220,;TYK2,non_coding_transcript_exon_variant,,ENST00000524470,;TYK2,downstream_gene_variant,,ENST00000527481,;TYK2,downstream_gene_variant,,ENST00000529412,;TYK2,downstream_gene_variant,,ENST00000534228,;	A	ENSG00000105397	ENST00000525621	Transcript	missense_variant	3949	3467	1156	A/V	gCg/gTg	rs143538128	.	.	-1	TYK2	HGNC	12440	protein_coding	YES	CCDS12236.1	ENSP00000431885	TYK2_HUMAN	E9PQM4_HUMAN,E9PQL2_HUMAN,E9PM19_HUMAN	UPI000013D573	.	deleterious(0.01)	possibly_damaging(0.863)	25/25	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF68,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,PIRSF_domain:PIRSF000636,Superfamily_domains:SSF56112	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGACGCCTCT	byCluster|by1000G	5	ESCA
EPOR	0	.	GRCh37	19	11492471	11492471	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482A>T	p.His161Leu	p.H161L	ENST00000222139	4/8	72	24	48	28	28	0	EPOR,missense_variant,p.His161Leu,ENST00000592375,;EPOR,missense_variant,p.His161Leu,ENST00000222139,;SWSAP1,downstream_gene_variant,,ENST00000312423,;EPOR,missense_variant,p.His196Leu,ENST00000591958,;EPOR,3_prime_UTR_variant,,ENST00000586890,;EPOR,3_prime_UTR_variant,,ENST00000588859,;EPOR,non_coding_transcript_exon_variant,,ENST00000588681,;EPOR,non_coding_transcript_exon_variant,,ENST00000589402,;RGL3,downstream_gene_variant,,ENST00000563726,;EPOR,upstream_gene_variant,,ENST00000590927,;RGL3,downstream_gene_variant,,ENST00000562663,;	A	ENSG00000187266	ENST00000222139	Transcript	missense_variant	587	482	161	H/L	cAc/cTc	.	.	.	-1	EPOR	HGNC	3416	protein_coding	YES	CCDS12260.1	ENSP00000222139	EPOR_HUMAN	I6R7G3_HUMAN	UPI000012A0AD	.	tolerated(0.1)	benign(0.268)	4/8	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23037:SF7,hmmpanther:PTHR23037,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,PIRSF_domain:PIRSF001959,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACGTGGCCG	.	5	ESCA
FARSA	0	.	GRCh37	19	13041426	13041427	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284dupT	p.Met95IlefsTer27	p.M95Ifs*27	ENST00000314606	2/13	80	72	8	32	32	0	FARSA,frameshift_variant,p.Met95IlefsTer27,ENST00000587981,;FARSA,frameshift_variant,p.Met135IlefsTer27,ENST00000588025,;FARSA,frameshift_variant,p.Met95IlefsTer27,ENST00000314606,;FARSA,frameshift_variant,p.Met95IlefsTer27,ENST00000423140,;FARSA,intron_variant,,ENST00000593021,;FARSA,upstream_gene_variant,,ENST00000587488,;CTC-425F1.2,intron_variant,,ENST00000592636,;FARSA,frameshift_variant,p.Met95IlefsTer27,ENST00000586146,;FARSA,splice_region_variant,,ENST00000588965,;FARSA,splice_region_variant,,ENST00000592662,;FARSA,non_coding_transcript_exon_variant,,ENST00000586280,;	A	ENSG00000179115	ENST00000314606	Transcript	frameshift_variant	303-304	284-285	95	M/IX	atg/atTg	.	.	.	-1	FARSA	HGNC	3592	protein_coding	YES	CCDS12287.1	ENSP00000320309	SYFA_HUMAN	Q6IBR2_HUMAN	UPI0000136413	.	.	.	2/13	.	hmmpanther:PTHR11538:SF15,hmmpanther:PTHR11538	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTACCATAAG	.	3	ESCA
MVB12A	0	.	GRCh37	19	17534317	17534317	+	Missense_Mutation	SNP	G	G	A	rs773765047	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.424G>A	p.Gly142Ser	p.G142S	ENST00000317040	5/9	58	46	11	37	37	0	MVB12A,missense_variant,p.Gly142Ser,ENST00000529939,;MVB12A,missense_variant,p.Gly142Ser,ENST00000543795,;MVB12A,missense_variant,p.Gly50Ser,ENST00000528911,;MVB12A,missense_variant,p.Gly3Ser,ENST00000528604,;MVB12A,missense_variant,p.Gly50Ser,ENST00000600514,;MVB12A,missense_variant,p.Gly142Ser,ENST00000317040,;MVB12A,missense_variant,p.Gly10Ser,ENST00000594784,;MVB12A,synonymous_variant,p.%3D,ENST00000528515,;MVB12A,intron_variant,,ENST00000392702,;MVB12A,downstream_gene_variant,,ENST00000528659,;CTD-2521M24.9,downstream_gene_variant,,ENST00000599975,;CTD-2521M24.9,downstream_gene_variant,,ENST00000601007,;CTD-2521M24.6,upstream_gene_variant,,ENST00000593957,;CTD-2521M24.8,upstream_gene_variant,,ENST00000597028,;MVB12A,downstream_gene_variant,,ENST00000529490,;MVB12A,non_coding_transcript_exon_variant,,ENST00000524382,;MVB12A,downstream_gene_variant,,ENST00000528732,;MVB12A,downstream_gene_variant,,ENST00000526234,;MVB12A,downstream_gene_variant,,ENST00000528997,;	A	ENSG00000141971	ENST00000317040	Transcript	missense_variant	1479	424	142	G/S	Ggc/Agc	rs773765047	.	.	1	MVB12A	HGNC	25153	protein_coding	YES	CCDS12359.1	ENSP00000324810	MB12A_HUMAN	E9PLZ8_HUMAN,E9PLL0_HUMAN	UPI0000039EC7	.	tolerated(0.23)	probably_damaging(1)	5/9	.	PROSITE_profiles:PS51498,hmmpanther:PTHR31612:SF1,hmmpanther:PTHR31612,Pfam_domain:PF10240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGGCTTT	.	5	ESCA
ZNF90	0	.	GRCh37	19	20228869	20228870	+	Frame_Shift_Ins	INS	-	-	A	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.513dupA	p.Pro172ThrfsTer21	p.P172Tfs*21	ENST00000418063	4/4	52	43	9	44	44	0	ZNF90,frameshift_variant,p.Pro172ThrfsTer21,ENST00000418063,;ZNF90,intron_variant,,ENST00000474284,;ZNF90,intron_variant,,ENST00000469078,;ZNF90,upstream_gene_variant,,ENST00000484032,;ZNF90,downstream_gene_variant,,ENST00000473524,;	A	ENSG00000213988	ENST00000418063	Transcript	frameshift_variant	618-619	506-507	169	G/GX	gga/ggAa	TMP_ESP_19_20228870_20228869	.	.	1	ZNF90	HGNC	13165	protein_coding	YES	CCDS46028.1	ENSP00000410466	ZNF90_HUMAN	.	UPI00002376E6	.	.	.	4/4	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF92,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	HIGH	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TACTGGAAAAA	.	2	ESCA
ZNF676	0	.	GRCh37	19	22363052	22363052	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1467C>A	p.Phe489Leu	p.F489L	ENST00000397121	3/3	58	38	20	27	27	0	ZNF676,missense_variant,p.Phe489Leu,ENST00000397121,;	T	ENSG00000196109	ENST00000397121	Transcript	missense_variant	1785	1467	489	F/L	ttC/ttA	.	.	.	-1	ZNF676	HGNC	20429	protein_coding	YES	CCDS42539.1	ENSP00000380310	ZN676_HUMAN	.	UPI00002376EC	.	tolerated(0.41)	benign(0.01)	3/3	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF112,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGAGAACGT	.	5	ESCA
TSHZ3	0	.	GRCh37	19	31770292	31770292	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.407T>C	p.Leu136Pro	p.L136P	ENST00000240587	2/2	54	51	3	67	67	0	TSHZ3,missense_variant,p.Leu136Pro,ENST00000240587,;TSHZ3,3_prime_UTR_variant,,ENST00000560707,;	G	ENSG00000121297	ENST00000240587	Transcript	missense_variant	735	407	136	L/P	cTc/cCc	.	.	.	-1	TSHZ3	HGNC	30700	protein_coding	YES	CCDS12421.2	ENSP00000240587	TSH3_HUMAN	A1L0U7_HUMAN	UPI0000202000	.	deleterious(0)	benign(0.401)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTGAGGTTG	.	2	ESCA
KRTDAP	0	.	GRCh37	19	35978335	35978335	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295C>A	p.Gln99Lys	p.Q99K	ENST00000338897	6/6	75	47	28	70	70	0	KRTDAP,missense_variant,p.Gln99Lys,ENST00000338897,;KRTDAP,missense_variant,p.Gln85Lys,ENST00000484218,;KRTDAP,non_coding_transcript_exon_variant,,ENST00000479340,;	T	ENSG00000188508	ENST00000338897	Transcript	missense_variant	384	295	99	Q/K	Cag/Aag	.	.	.	-1	KRTDAP	HGNC	16313	protein_coding	YES	CCDS12462.1	ENSP00000339251	KTDAP_HUMAN	.	UPI0000035979	.	tolerated_low_confidence(0.06)	probably_damaging(0.968)	6/6	.	Pfam_domain:PF15200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTGGGCAT	.	5	ESCA
PTPRS	0	.	GRCh37	19	5214590	5214590	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4476G>A	p.%3D	p.R1492R	ENST00000357368	29/38	20	17	3	11	11	0	PTPRS,synonymous_variant,p.%3D,ENST00000353284,;PTPRS,synonymous_variant,p.%3D,ENST00000587303,;PTPRS,synonymous_variant,p.%3D,ENST00000372412,;PTPRS,synonymous_variant,p.%3D,ENST00000588012,;PTPRS,synonymous_variant,p.%3D,ENST00000262963,;PTPRS,synonymous_variant,p.%3D,ENST00000357368,;PTPRS,synonymous_variant,p.%3D,ENST00000592099,;PTPRS,synonymous_variant,p.%3D,ENST00000348075,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,;PTPRS,downstream_gene_variant,,ENST00000589851,;	T	ENSG00000105426	ENST00000357368	Transcript	synonymous_variant	4710	4476	1492	R	cgG/cgA	.	.	.	-1	PTPRS	HGNC	9681	protein_coding	YES	CCDS45930.1	ENSP00000349932	PTPRS_HUMAN	K7ESP0_HUMAN,K7ERX4_HUMAN	UPI000059D63E	.	.	.	29/38	.	Superfamily_domains:SSF52799,SMART_domains:SM00194,Pfam_domain:PF00102,Gene3D:3.90.190.10,hmmpanther:PTHR19134:SF204,hmmpanther:PTHR19134,PROSITE_profiles:PS50055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAGCCGCGT	.	2	ESCA
ZNF616	0	.	GRCh37	19	52619109	52619109	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1308T>C	p.%3D	p.T436T	ENST00000600228	4/4	37	31	6	41	41	0	ZNF616,synonymous_variant,p.%3D,ENST00000600228,;ZNF616,3_prime_UTR_variant,,ENST00000330123,;ZNF616,downstream_gene_variant,,ENST00000596290,;	G	ENSG00000204611	ENST00000600228	Transcript	synonymous_variant	1570	1308	436	T	acT/acC	.	.	.	-1	ZNF616	HGNC	28062	protein_coding	YES	CCDS33090.1	ENSP00000471000	ZN616_HUMAN	M0QXF0_HUMAN	UPI0000140D49	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF275,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTAAGTTTT	.	5	ESCA
ZNF880	0	.	GRCh37	19	52887840	52887840	+	Missense_Mutation	SNP	G	G	A	rs756887152	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1007G>A	p.Gly336Asp	p.G336D	ENST00000422689	4/4	27	19	8	44	44	0	ZNF880,missense_variant,p.Gly336Asp,ENST00000422689,;ZNF880,downstream_gene_variant,,ENST00000600321,;ZNF880,downstream_gene_variant,,ENST00000424032,;CTD-3018O17.3,downstream_gene_variant,,ENST00000601562,;CTD-3018O17.3,downstream_gene_variant,,ENST00000594119,;	A	ENSG00000221923	ENST00000422689	Transcript	missense_variant	1022	1007	336	G/D	gGt/gAt	rs756887152	.	.	1	ZNF880	HGNC	37249	protein_coding	YES	CCDS46164.1	ENSP00000406318	ZN880_HUMAN	.	UPI00001D818D	.	tolerated(0.5)	benign(0.001)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF108,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGGGTTCAG	.	5	ESCA
DPRX	0	.	GRCh37	19	54139880	54139880	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214A>G	p.Lys72Glu	p.K72E	ENST00000376650	3/3	28	24	4	35	35	0	DPRX,missense_variant,p.Lys72Glu,ENST00000376650,;	G	ENSG00000204595	ENST00000376650	Transcript	missense_variant	265	214	72	K/E	Aag/Gag	.	.	.	1	DPRX	HGNC	32166	protein_coding	YES	CCDS33103.1	ENSP00000365838	DPRX_HUMAN	.	UPI00004ED62B	.	deleterious(0.01)	probably_damaging(0.991)	3/3	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF299,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTCAAGAAA	.	4	ESCA
BRSK1	0	.	GRCh37	19	55817695	55817695	+	Missense_Mutation	SNP	G	G	A	rs769516314	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1966G>A	p.Val656Ile	p.V656I	ENST00000309383	17/19	47	40	6	41	41	0	BRSK1,missense_variant,p.Val351Ile,ENST00000326848,;BRSK1,missense_variant,p.Val656Ile,ENST00000309383,;BRSK1,missense_variant,p.Val672Ile,ENST00000590333,;BRSK1,downstream_gene_variant,,ENST00000585418,;BRSK1,downstream_gene_variant,,ENST00000591774,;BRSK1,downstream_gene_variant,,ENST00000588584,;BRSK1,downstream_gene_variant,,ENST00000586626,;	A	ENSG00000160469	ENST00000309383	Transcript	missense_variant	2243	1966	656	V/I	Gtc/Atc	rs769516314,COSM193236,COSM193237	.	.	1	BRSK1	HGNC	18994	protein_coding	YES	CCDS12921.1	ENSP00000310649	BRSK1_HUMAN	K7EM68_HUMAN,J3KNK0_HUMAN	UPI0000070495	.	deleterious(0.03)	possibly_damaging(0.874)	17/19	.	hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF130	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCCGTCTTC	.	4	ESCA
MUC16	0	.	GRCh37	19	9084850	9084850	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6965C>T	p.Ala2322Val	p.A2322V	ENST00000397910	1/84	116	99	16	111	111	0	MUC16,missense_variant,p.Ala2322Val,ENST00000397910,;	A	ENSG00000181143	ENST00000397910	Transcript	missense_variant	7169	6965	2322	A/V	gCt/gTt	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	1/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCAGCAGAG	.	4	ESCA
MUC16	0	.	GRCh37	19	9090486	9090486	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1329T>A	p.%3D	p.S443S	ENST00000397910	1/84	45	36	9	70	70	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;	T	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	1533	1329	443	S	tcT/tcA	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	1/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGCAGAGGT	.	5	ESCA
CCNL2	0	.	GRCh37	1	1326172	1326172	+	Missense_Mutation	SNP	T	T	A	rs777264153	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.733A>T	p.Ile245Phe	p.I245F	ENST00000400809	6/11	27	13	13	21	21	0	CCNL2,missense_variant,p.Ile245Phe,ENST00000400809,;CCNL2,missense_variant,p.Ile23Phe,ENST00000408952,;CCNL2,downstream_gene_variant,,ENST00000408918,;CCNL2,downstream_gene_variant,,ENST00000497013,;CCNL2,non_coding_transcript_exon_variant,,ENST00000505849,;CCNL2,non_coding_transcript_exon_variant,,ENST00000469113,;CCNL2,downstream_gene_variant,,ENST00000471930,;CCNL2,3_prime_UTR_variant,,ENST00000481223,;CCNL2,3_prime_UTR_variant,,ENST00000482621,;CCNL2,3_prime_UTR_variant,,ENST00000488340,;CCNL2,non_coding_transcript_exon_variant,,ENST00000480479,;CCNL2,non_coding_transcript_exon_variant,,ENST00000418865,;CCNL2,non_coding_transcript_exon_variant,,ENST00000496007,;CCNL2,non_coding_transcript_exon_variant,,ENST00000480646,;CCNL2,non_coding_transcript_exon_variant,,ENST00000482365,;CCNL2,non_coding_transcript_exon_variant,,ENST00000492998,;CCNL2,upstream_gene_variant,,ENST00000463260,;CCNL2,downstream_gene_variant,,ENST00000463895,;CCNL2,downstream_gene_variant,,ENST00000473872,;CCNL2,downstream_gene_variant,,ENST00000425598,;	A	ENSG00000221978	ENST00000400809	Transcript	missense_variant	739	733	245	I/F	Att/Ttt	rs777264153	.	.	-1	CCNL2	HGNC	20570	protein_coding	YES	CCDS30557.1	ENSP00000383611	CCNL2_HUMAN	J3QSH2_HUMAN,B4DE38_HUMAN	UPI00000713F5	.	deleterious(0)	probably_damaging(0.999)	6/11	.	Superfamily_domains:SSF47954,SMART_domains:SM00385,PIRSF_domain:PIRSF036580,Pfam_domain:PF02984,Gene3D:1.10.472.10,hmmpanther:PTHR10026:SF45,hmmpanther:PTHR10026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAATGCAGG	.	5	ESCA
OR6N1	0	.	GRCh37	1	158735878	158735878	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595G>T	p.Asp199Tyr	p.D199Y	ENST00000335094	1/1	15	12	3	17	17	0	OR6N1,missense_variant,p.Asp199Tyr,ENST00000335094,;	A	ENSG00000197403	ENST00000335094	Transcript	missense_variant	615	595	199	D/Y	Gat/Tat	COSM676043	.	.	-1	OR6N1	HGNC	15034	protein_coding	YES	CCDS30905.1	ENSP00000335535	OR6N1_HUMAN	.	UPI000003FE15	.	deleterious(0.03)	probably_damaging(0.997)	1/1	.	Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26453:SF123,hmmpanther:PTHR26453,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAATCTACTA	.	2	ESCA
COPA	0	.	GRCh37	1	160302324	160302324	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.410A>G	p.Tyr137Cys	p.Y137C	ENST00000368069	6/33	37	33	4	13	13	0	COPA,missense_variant,p.Tyr137Cys,ENST00000368069,;COPA,missense_variant,p.Tyr137Cys,ENST00000241704,;COPA,downstream_gene_variant,,ENST00000541366,;	C	ENSG00000122218	ENST00000368069	Transcript	missense_variant	488	410	137	Y/C	tAt/tGt	.	.	.	-1	COPA	HGNC	2230	protein_coding	YES	CCDS41424.1	ENSP00000357048	COPA_HUMAN	.	UPI0000074301	.	deleterious(0)	probably_damaging(0.999)	6/33	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19876,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,PIRSF_domain:PIRSF003354,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCACATAATGG	.	2	ESCA
NHLH1	0	.	GRCh37	1	160340918	160340918	+	Missense_Mutation	SNP	G	G	A	rs775174622	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397G>A	p.Val133Ile	p.V133I	ENST00000302101	2/2	37	34	3	20	20	0	NHLH1,missense_variant,p.Val133Ile,ENST00000302101,;	A	ENSG00000171786	ENST00000302101	Transcript	missense_variant	843	397	133	V/I	Gtc/Atc	rs775174622	.	.	1	NHLH1	HGNC	7817	protein_coding	YES	CCDS1204.1	ENSP00000302189	HEN1_HUMAN	Q5T203_HUMAN	UPI000012C5FE	.	deleterious_low_confidence(0.04)	benign(0.007)	2/2	.	hmmpanther:PTHR13864:SF17,hmmpanther:PTHR13864,SMART_domains:SM00353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGACGTCTGA	.	2	ESCA
DUSP27	0	.	GRCh37	1	167096073	167096073	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1705G>T	p.Glu569Ter	p.E569*	ENST00000361200	6/6	23	13	9	18	18	0	DUSP27,stop_gained,p.Glu569Ter,ENST00000361200,;DUSP27,stop_gained,p.Glu569Ter,ENST00000443333,;DUSP27,stop_gained,p.Glu569Ter,ENST00000271385,;DUSP27,intron_variant,,ENST00000485151,;	T	ENSG00000198842	ENST00000361200	Transcript	stop_gained	1871	1705	569	E/*	Gag/Tag	.	.	.	1	DUSP27	HGNC	25034	protein_coding	YES	CCDS30932.1	ENSP00000354483	DUS27_HUMAN	.	UPI000040DFF5	.	.	.	6/6	.	hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGTGAGCCC	.	5	ESCA
CRB1	0	.	GRCh37	1	197297560	197297560	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.79T>C	p.Cys27Arg	p.C27R	ENST00000367400	2/12	38	17	20	25	25	0	CRB1,missense_variant,p.Cys27Arg,ENST00000367399,;CRB1,missense_variant,p.Cys27Arg,ENST00000538660,;CRB1,missense_variant,p.Cys27Arg,ENST00000367400,;CRB1,5_prime_UTR_variant,,ENST00000535699,;CRB1,upstream_gene_variant,,ENST00000543483,;CRB1,missense_variant,p.Cys27Arg,ENST00000484075,;CRB1,non_coding_transcript_exon_variant,,ENST00000475659,;	C	ENSG00000134376	ENST00000367400	Transcript	missense_variant	214	79	27	C/R	Tgc/Cgc	.	.	.	1	CRB1	HGNC	2343	protein_coding	YES	CCDS1390.1	ENSP00000356370	CRUM1_HUMAN	B7Z824_HUMAN	UPI0000073345	.	deleterious(0.01)	possibly_damaging(0.714)	2/12	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24049	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTTGCAAT	.	5	ESCA
MAPKAPK2	0	.	GRCh37	1	206858691	206858691	+	Silent	SNP	C	C	G	rs781902222	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117C>G	p.%3D	p.P39P	ENST00000367103	1/10	25	16	9	10	10	0	MAPKAPK2,synonymous_variant,p.%3D,ENST00000294981,;MAPKAPK2,synonymous_variant,p.%3D,ENST00000367103,;SNORD112,downstream_gene_variant,,ENST00000517044,;DYRK3,downstream_gene_variant,,ENST00000489878,;	G	ENSG00000162889	ENST00000367103	Transcript	synonymous_variant	310	117	39	P	ccC/ccG	rs781902222	.	.	1	MAPKAPK2	HGNC	6887	protein_coding	YES	CCDS31001.1	ENSP00000356070	MAPK2_HUMAN	.	UPI0000112289	.	.	.	1/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24349,hmmpanther:PTHR24349:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGCCCCCGCA	.	2	ESCA
MIA3	0	.	GRCh37	1	222826634	222826634	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4274A>G	p.Asn1425Ser	p.N1425S	ENST00000344922	15/28	61	56	4	28	28	0	MIA3,missense_variant,p.Asn1425Ser,ENST00000344922,;MIA3,missense_variant,p.Asn949Ser,ENST00000354906,;MIA3,missense_variant,p.Asn303Ser,ENST00000340535,;MIA3,missense_variant,p.Asn1425Ser,ENST00000344441,;MIA3,intron_variant,,ENST00000344507,;MIA3,downstream_gene_variant,,ENST00000467190,;MIA3,downstream_gene_variant,,ENST00000495210,;	G	ENSG00000154305	ENST00000344922	Transcript	missense_variant	4299	4274	1425	N/S	aAt/aGt	.	.	.	1	MIA3	HGNC	24008	protein_coding	YES	CCDS41470.1	ENSP00000340900	MIA3_HUMAN	.	UPI00001D75B3	.	tolerated(0.3)	benign(0.007)	15/28	.	hmmpanther:PTHR23158:SF37,hmmpanther:PTHR23158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAAAATAAAG	.	2	ESCA
OBSCN	0	.	GRCh37	1	228487173	228487173	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13424A>G	p.Tyr4475Cys	p.Y4475C	ENST00000570156	50/116	132	109	23	98	98	0	OBSCN,missense_variant,p.Tyr1165Cys,ENST00000366707,;OBSCN,missense_variant,p.Tyr1322Cys,ENST00000483539,;OBSCN,missense_variant,p.Tyr4475Cys,ENST00000570156,;OBSCN,3_prime_UTR_variant,,ENST00000359599,;OBSCN,intron_variant,,ENST00000366709,;OBSCN,intron_variant,,ENST00000284548,;OBSCN,intron_variant,,ENST00000422127,;RP5-1139B12.4,intron_variant,,ENST00000602778,;OBSCN,upstream_gene_variant,,ENST00000602685,;OBSCN,upstream_gene_variant,,ENST00000602832,;OBSCN,downstream_gene_variant,,ENST00000494839,;	G	ENSG00000154358	ENST00000570156	Transcript	missense_variant	13498	13424	4475	Y/C	tAc/tGc	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	probably_damaging(1)	50/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGTACTCAT	.	5	ESCA
TSNAX	0	.	GRCh37	1	231700352	231700352	+	Missense_Mutation	SNP	G	G	A	rs767689300	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.574G>A	p.Ala192Thr	p.A192T	ENST00000366639	6/6	59	56	3	57	57	0	TSNAX,missense_variant,p.Ala192Thr,ENST00000366639,;TSNAX,downstream_gene_variant,,ENST00000413309,;TSNAX,non_coding_transcript_exon_variant,,ENST00000475168,;TSNAX-DISC1,intron_variant,,ENST00000602885,;TSNAX-DISC1,intron_variant,,ENST00000602956,;TSNAX-DISC1,intron_variant,,ENST00000602634,;TSNAX-DISC1,intron_variant,,ENST00000602567,;TSNAX-DISC1,intron_variant,,ENST00000602962,;	A	ENSG00000116918	ENST00000366639	Transcript	missense_variant	732	574	192	A/T	Gct/Act	rs767689300	.	.	1	TSNAX	HGNC	12380	protein_coding	YES	CCDS1596.1	ENSP00000355599	TSNAX_HUMAN	Q9NRI2_HUMAN	UPI0000137768	.	deleterious(0)	probably_damaging(0.953)	6/6	.	Superfamily_domains:0047790,Gene3D:1j1jA02,Pfam_domain:PF01997,hmmpanther:PTHR10741,hmmpanther:PTHR10741:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTGGCTGAC	.	2	ESCA
OR2M2	0	.	GRCh37	1	248343907	248343907	+	Missense_Mutation	SNP	T	T	C	rs535058818	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.620T>C	p.Leu207Pro	p.L207P	ENST00000359682	1/1	99	93	5	99	99	0	OR2M2,missense_variant,p.Leu207Pro,ENST00000359682,;	C	ENSG00000198601	ENST00000359682	Transcript	missense_variant	620	620	207	L/P	cTt/cCt	rs535058818	.	.	1	OR2M2	HGNC	8268	protein_coding	YES	CCDS31106.1	ENSP00000352710	OR2M2_HUMAN	.	UPI00001612E4	.	deleterious(0)	probably_damaging(0.988)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF204,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	A:0.0010	A:0.003	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATGCTTGTTT	byFrequency|by1000G	2	ESCA
BSDC1	0	.	GRCh37	1	32846840	32846840	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438A>G	p.%3D	p.P146P	ENST00000446293	5/11	25	21	4	19	19	0	BSDC1,synonymous_variant,p.%3D,ENST00000449308,;BSDC1,synonymous_variant,p.%3D,ENST00000341071,;BSDC1,synonymous_variant,p.%3D,ENST00000413080,;BSDC1,synonymous_variant,p.%3D,ENST00000455895,;BSDC1,synonymous_variant,p.%3D,ENST00000446293,;BSDC1,synonymous_variant,p.%3D,ENST00000530485,;BSDC1,synonymous_variant,p.%3D,ENST00000526031,;BSDC1,synonymous_variant,p.%3D,ENST00000419121,;BSDC1,synonymous_variant,p.%3D,ENST00000527163,;BSDC1,synonymous_variant,p.%3D,ENST00000444377,;BSDC1,3_prime_UTR_variant,,ENST00000373520,;BSDC1,non_coding_transcript_exon_variant,,ENST00000474414,;BSDC1,intron_variant,,ENST00000527513,;BSDC1,downstream_gene_variant,,ENST00000530753,;BSDC1,downstream_gene_variant,,ENST00000530876,;	C	ENSG00000160058	ENST00000446293	Transcript	synonymous_variant	454	438	146	P	ccA/ccG	.	.	.	-1	BSDC1	HGNC	25501	protein_coding	YES	CCDS44103.1	ENSP00000397759	BSDC1_HUMAN	.	UPI00017A7DA9	.	.	.	5/11	.	hmmpanther:PTHR16019:SF5,hmmpanther:PTHR16019,Superfamily_domains:SSF140383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTGCTGGGTC	.	4	ESCA
ZMYM4	0	.	GRCh37	1	35857881	35857881	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2656A>G	p.Ile886Val	p.I886V	ENST00000314607	16/30	35	29	6	41	41	0	ZMYM4,missense_variant,p.Ile546Val,ENST00000457946,;ZMYM4,missense_variant,p.Ile797Val,ENST00000373297,;ZMYM4,missense_variant,p.Ile886Val,ENST00000314607,;ZMYM4,upstream_gene_variant,,ENST00000470175,;	G	ENSG00000146463	ENST00000314607	Transcript	missense_variant	2736	2656	886	I/V	Ata/Gta	.	.	.	1	ZMYM4	HGNC	13055	protein_coding	YES	CCDS389.1	ENSP00000322915	ZMYM4_HUMAN	.	UPI0000203EE6	.	tolerated(0.05)	probably_damaging(0.995)	16/30	.	hmmpanther:PTHR11697:SF87,hmmpanther:PTHR11697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTATAGCC	.	5	ESCA
LPHN2	0	.	GRCh37	1	82456953	82456954	+	3'UTR	INS	-	-	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*130dupA	.	.	ENST00000319517	20/20	31	20	11	36	36	0	LPHN2,3_prime_UTR_variant,,ENST00000370730,;LPHN2,3_prime_UTR_variant,,ENST00000335786,;LPHN2,3_prime_UTR_variant,,ENST00000370713,;LPHN2,3_prime_UTR_variant,,ENST00000370717,;LPHN2,3_prime_UTR_variant,,ENST00000370727,;LPHN2,3_prime_UTR_variant,,ENST00000370725,;LPHN2,3_prime_UTR_variant,,ENST00000319517,;LPHN2,3_prime_UTR_variant,,ENST00000271029,;LPHN2,3_prime_UTR_variant,,ENST00000370728,;LPHN2,3_prime_UTR_variant,,ENST00000359929,;LPHN2,3_prime_UTR_variant,,ENST00000370715,;LPHN2,3_prime_UTR_variant,,ENST00000370723,;LPHN2,3_prime_UTR_variant,,ENST00000402328,;LPHN2,3_prime_UTR_variant,,ENST00000370721,;LPHN2,3_prime_UTR_variant,,ENST00000394879,;LPHN2,3_prime_UTR_variant,,ENST00000449420,;LPHN2,non_coding_transcript_exon_variant,,ENST00000469377,;LPHN2,downstream_gene_variant,,ENST00000472424,;LPHN2,downstream_gene_variant,,ENST00000464775,;LPHN2,downstream_gene_variant,,ENST00000464551,;	A	ENSG00000117114	ENST00000319517	Transcript	3_prime_UTR_variant	4552-4553	.	.	.	.	.	.	.	1	LPHN2	HGNC	18582	protein_coding	YES	CCDS689.1	ENSP00000322270	LPHN2_HUMAN	.	UPI000005046B	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGTGTAAAAA	.	3	ESCA
PRKACB	0	.	GRCh37	1	84639015	84639015	+	Intron	SNP	G	G	A	rs756910770	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188-5845G>A	.	.	ENST00000370685	.	40	28	12	91	89	1	PRKACB,missense_variant,p.Arg5His,ENST00000446538,;PRKACB,missense_variant,p.Arg5His,ENST00000394838,;PRKACB,missense_variant,p.Arg5His,ENST00000370682,;PRKACB,missense_variant,p.Arg4His,ENST00000394839,;PRKACB,missense_variant,p.Arg4His,ENST00000370680,;PRKACB,missense_variant,p.Arg5His,ENST00000436133,;PRKACB,missense_variant,p.Arg4His,ENST00000450730,;PRKACB,intron_variant,,ENST00000417530,;PRKACB,intron_variant,,ENST00000370685,;PRKACB,intron_variant,,ENST00000370688,;PRKACB,intron_variant,,ENST00000413538,;PRKACB,intron_variant,,ENST00000370684,;PRKACB,intron_variant,,ENST00000370689,;PRKACB,intron_variant,,ENST00000432111,;PRKACB,intron_variant,,ENST00000470673,;	A	ENSG00000142875	ENST00000370685	Transcript	intron_variant	.	.	.	.	.	rs756910770	.	.	1	PRKACB	HGNC	9381	protein_coding	YES	CCDS693.1	ENSP00000359719	KAPCB_HUMAN	.	UPI00001A9CCB	.	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCACGCAAAT	byFrequency	5	ESCA
KIF16B	0	.	GRCh37	20	16488617	16488617	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.685A>G	p.Ile229Val	p.I229V	ENST00000408042	7/23	48	37	10	41	41	0	KIF16B,missense_variant,p.Ile229Val,ENST00000408042,;KIF16B,missense_variant,p.Ile229Val,ENST00000354981,;KIF16B,missense_variant,p.Ile229Val,ENST00000355755,;KIF16B,5_prime_UTR_variant,,ENST00000378003,;	C	ENSG00000089177	ENST00000408042	Transcript	missense_variant	843	685	229	I/V	Atc/Gtc	.	.	.	-1	KIF16B	HGNC	15869	protein_coding	YES	CCDS56178.1	ENSP00000384164	KI16B_HUMAN	.	UPI00003BF77C	.	deleterious(0.01)	benign(0.108)	7/23	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF400,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGATGGTGA	.	5	ESCA
PCSK2	0	.	GRCh37	20	17208123	17208123	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.173G>A	p.Arg58Gln	p.R58Q	ENST00000262545	1/12	19	16	3	12	12	0	PCSK2,missense_variant,p.Arg58Gln,ENST00000262545,;PCSK2,missense_variant,p.Arg39Gln,ENST00000377899,;PCSK2,missense_variant,p.Arg58Gln,ENST00000536609,;PCSK2,upstream_gene_variant,,ENST00000470007,;	A	ENSG00000125851	ENST00000262545	Transcript	missense_variant	488	173	58	R/Q	cGa/cAa	.	.	.	1	PCSK2	HGNC	8744	protein_coding	YES	CCDS13125.1	ENSP00000262545	NEC2_HUMAN	Q9UM69_HUMAN	UPI0000000C6E	.	tolerated(0.3)	benign(0.408)	1/12	.	hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF11,Gene3D:1kn6A00,Superfamily_domains:SSF54897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTCCGAAAGG	.	2	ESCA
L3MBTL1	0	.	GRCh37	20	42157355	42157355	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855C>A	p.%3D	p.A285A	ENST00000427442	8/22	33	29	3	29	29	0	L3MBTL1,synonymous_variant,p.%3D,ENST00000444063,;L3MBTL1,synonymous_variant,p.%3D,ENST00000422861,;L3MBTL1,synonymous_variant,p.%3D,ENST00000373134,;L3MBTL1,synonymous_variant,p.%3D,ENST00000373135,;L3MBTL1,synonymous_variant,p.%3D,ENST00000427442,;L3MBTL1,synonymous_variant,p.%3D,ENST00000418998,;L3MBTL1,non_coding_transcript_exon_variant,,ENST00000457824,;L3MBTL1,non_coding_transcript_exon_variant,,ENST00000485334,;L3MBTL1,non_coding_transcript_exon_variant,,ENST00000430781,;L3MBTL1,upstream_gene_variant,,ENST00000373133,;L3MBTL1,upstream_gene_variant,,ENST00000497347,;L3MBTL1,upstream_gene_variant,,ENST00000445228,;	A	ENSG00000185513	ENST00000427442	Transcript	synonymous_variant	1014	855	285	A	gcC/gcA	.	.	.	1	L3MBTL1	HGNC	15905	protein_coding	YES	CCDS46602.2	ENSP00000402107	LMBL1_HUMAN	B0QYN5_HUMAN,B0QYN4_HUMAN	UPI0001E18E26	.	.	.	8/22	.	PROSITE_profiles:PS51079,hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF69,SMART_domains:SM00561	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGGCCATTAC	.	3	ESCA
ZNF335	0	.	GRCh37	20	44598230	44598230	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302G>C	p.Gly101Ala	p.G101A	ENST00000322927	3/28	43	37	6	32	32	0	ZNF335,missense_variant,p.Gly101Ala,ENST00000322927,;ZNF335,intron_variant,,ENST00000426788,;ZNF335,non_coding_transcript_exon_variant,,ENST00000476822,;ZNF335,upstream_gene_variant,,ENST00000494955,;	G	ENSG00000198026	ENST00000322927	Transcript	missense_variant	403	302	101	G/A	gGc/gCc	.	.	.	-1	ZNF335	HGNC	15807	protein_coding	YES	CCDS13389.1	ENSP00000325326	ZN335_HUMAN	.	UPI0000001BC3	.	tolerated(0.15)	benign(0.003)	3/28	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24403:SF31,hmmpanther:PTHR24403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCGCCTGTC	.	5	ESCA
ANKRD20A11P	0	.	GRCh37	21	15323581	15323581	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.987G>A	.	.	ENST00000451663	10/25	141	120	20	146	146	0	ANKRD20A11P,splice_region_variant,,ENST00000429521,;ANKRD20A11P,splice_region_variant,,ENST00000344693,;ANKRD20A11P,splice_region_variant,,ENST00000432875,;ANKRD20A11P,splice_region_variant,,ENST00000428576,;ANKRD20A11P,splice_region_variant,,ENST00000451663,;	T	ENSG00000215559	ENST00000451663	Transcript	splice_region_variant	987	.	.	.	.	.	.	.	-1	ANKRD20A11P	HGNC	42024	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	10/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGTCCTACA	.	4	ESCA
SON	0	.	GRCh37	21	34924731	34924731	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3194C>A	p.Ser1065Tyr	p.S1065Y	ENST00000356577	3/12	47	38	9	38	38	0	SON,missense_variant,p.Ser1065Tyr,ENST00000381679,;SON,missense_variant,p.Ser1065Tyr,ENST00000300278,;SON,missense_variant,p.Ser1065Tyr,ENST00000356577,;SON,missense_variant,p.Ser60Tyr,ENST00000436227,;SON,missense_variant,p.Ser1065Tyr,ENST00000290239,;SON,intron_variant,,ENST00000381692,;SON,upstream_gene_variant,,ENST00000421541,;SON,missense_variant,p.Ser1065Tyr,ENST00000455528,;	A	ENSG00000159140	ENST00000356577	Transcript	missense_variant	3669	3194	1065	S/Y	tCc/tAc	.	.	.	1	SON	HGNC	11183	protein_coding	YES	CCDS13629.1	ENSP00000348984	SON_HUMAN	.	UPI0000140BFD	.	.	possibly_damaging(0.608)	3/12	.	hmmpanther:PTHR12813:SF26,hmmpanther:PTHR12813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCTCCATGA	.	5	ESCA
ERG	0	.	GRCh37	21	39817494	39817494	+	Silent	SNP	G	G	A	rs545954647	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90C>T	p.%3D	p.Y30Y	ENST00000417133	4/12	49	39	9	50	49	1	ERG,synonymous_variant,p.%3D,ENST00000398910,;ERG,synonymous_variant,p.%3D,ENST00000288319,;ERG,synonymous_variant,p.%3D,ENST00000442448,;ERG,synonymous_variant,p.%3D,ENST00000429727,;ERG,synonymous_variant,p.%3D,ENST00000398919,;ERG,synonymous_variant,p.%3D,ENST00000398905,;ERG,synonymous_variant,p.%3D,ENST00000417133,;ERG,synonymous_variant,p.%3D,ENST00000398911,;ERG,synonymous_variant,p.%3D,ENST00000398907,;ERG,intron_variant,,ENST00000398897,;ERG,intron_variant,,ENST00000453032,;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,non_coding_transcript_exon_variant,,ENST00000481609,;ERG,non_coding_transcript_exon_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;	A	ENSG00000157554	ENST00000417133	Transcript	synonymous_variant	276	90	30	Y	taC/taT	rs545954647	.	.	-1	ERG	HGNC	3446	protein_coding	YES	CCDS46648.1	ENSP00000414150	ERG_HUMAN	Q16031_HUMAN,B4DVX5_HUMAN	UPI000018681C	.	.	.	4/12	.	hmmpanther:PTHR11849:SF161,hmmpanther:PTHR11849	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCCGTAGGC	byFrequency|byCluster	5	ESCA
ATF4	0	.	GRCh37	22	39918415	39918415	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864C>G	p.Asn288Lys	p.N288K	ENST00000337304	2/2	41	34	7	47	47	0	ATF4,missense_variant,p.Asn288Lys,ENST00000396680,;ATF4,missense_variant,p.Asn288Lys,ENST00000337304,;ATF4,missense_variant,p.Asn288Lys,ENST00000404241,;MIEF1,downstream_gene_variant,,ENST00000325301,;	G	ENSG00000128272	ENST00000337304	Transcript	missense_variant	1746	864	288	N/K	aaC/aaG	.	.	.	1	ATF4	HGNC	786	protein_coding	YES	CCDS13996.1	ENSP00000336790	ATF4_HUMAN	Q96AQ3_HUMAN,B4DJD4_HUMAN	UPI000000DABF	.	deleterious(0)	possibly_damaging(0.883)	2/2	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF57959,SMART_domains:SM00338,Gene3D:1.20.5.170,Pfam_domain:PF00170,PROSITE_patterns:PS00036,hmmpanther:PTHR13044:SF2,hmmpanther:PTHR13044,PROSITE_profiles:PS50217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAAAACAAGAC	.	4	ESCA
HDAC10	0	.	GRCh37	22	50688799	50688799	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291+57G>A	.	.	ENST00000216271	.	58	52	6	36	36	0	HDAC10,intron_variant,,ENST00000349505,;HDAC10,intron_variant,,ENST00000216271,;HDAC10,intron_variant,,ENST00000448072,;MAPK12,downstream_gene_variant,,ENST00000215659,;MAPK12,downstream_gene_variant,,ENST00000395780,;MAPK12,non_coding_transcript_exon_variant,,ENST00000497036,;HDAC10,intron_variant,,ENST00000470965,;HDAC10,intron_variant,,ENST00000498366,;HDAC10,intron_variant,,ENST00000497483,;HDAC10,intron_variant,,ENST00000483222,;HDAC10,intron_variant,,ENST00000496909,;HDAC10,intron_variant,,ENST00000489424,;HDAC10,non_coding_transcript_exon_variant,,ENST00000482213,;HDAC10,intron_variant,,ENST00000454936,;HDAC10,intron_variant,,ENST00000429374,;HDAC10,intron_variant,,ENST00000415993,;HDAC10,upstream_gene_variant,,ENST00000475965,;HDAC10,upstream_gene_variant,,ENST00000471375,;HDAC10,upstream_gene_variant,,ENST00000496235,;HDAC10,upstream_gene_variant,,ENST00000488270,;HDAC10,upstream_gene_variant,,ENST00000477814,;MAPK12,downstream_gene_variant,,ENST00000488504,;MAPK12,downstream_gene_variant,,ENST00000482969,;MAPK12,downstream_gene_variant,,ENST00000497738,;MAPK12,downstream_gene_variant,,ENST00000467891,;MAPK12,downstream_gene_variant,,ENST00000496942,;HDAC10,upstream_gene_variant,,ENST00000470378,;HDAC10,upstream_gene_variant,,ENST00000476310,;HDAC10,upstream_gene_variant,,ENST00000497952,;	T	ENSG00000100429	ENST00000216271	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	HDAC10	HGNC	18128	protein_coding	YES	CCDS14088.1	ENSP00000216271	HDA10_HUMAN	.	UPI000012C3A6	.	.	.	.	3/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGAACGCTCA	.	4	ESCA
SCN2A	0	.	GRCh37	2	166245183	166245183	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4867A>T	p.Thr1623Ser	p.T1623S	ENST00000357398	27/27	86	69	16	81	81	0	SCN2A,missense_variant,p.Thr1623Ser,ENST00000283256,;SCN2A,missense_variant,p.Thr1623Ser,ENST00000375437,;SCN2A,missense_variant,p.Thr1623Ser,ENST00000375427,;SCN2A,missense_variant,p.Thr1623Ser,ENST00000357398,;	T	ENSG00000136531	ENST00000357398	Transcript	missense_variant	5157	4867	1623	T/S	Acc/Tcc	.	.	.	1	SCN2A	HGNC	10588	protein_coding	YES	CCDS33313.1	ENSP00000349973	SCN2A_HUMAN	F8T7W7_HUMAN	UPI000002A663	.	tolerated(0.06)	benign(0.247)	27/27	.	hmmpanther:PTHR10037:SF133,hmmpanther:PTHR10037,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTACCCTG	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098809	178098809	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236A>G	p.Glu79Gly	p.E79G	ENST00000397062	2/5	91	55	35	99	99	0	NFE2L2,missense_variant,p.Glu63Gly,ENST00000449627,;NFE2L2,missense_variant,p.Glu63Gly,ENST00000423513,;NFE2L2,missense_variant,p.Glu79Gly,ENST00000397062,;NFE2L2,missense_variant,p.Glu63Gly,ENST00000446151,;NFE2L2,missense_variant,p.Glu63Gly,ENST00000588123,;NFE2L2,missense_variant,p.Glu78Gly,ENST00000586532,;NFE2L2,missense_variant,p.Glu63Gly,ENST00000421929,;NFE2L2,missense_variant,p.Glu63Gly,ENST00000464747,;NFE2L2,missense_variant,p.Glu63Gly,ENST00000448782,;NFE2L2,missense_variant,p.Glu63Gly,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	C	ENSG00000116044	ENST00000397062	Transcript	missense_variant	791	236	79	E/G	gAg/gGg	COSM1529470,COSM132960	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E82D|c.246A>C|3,BUFFER|p.E82D|c.246A>T|6,BUFFER|p.E82G|c.245A>G|7,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81D|c.242G>A|6,BUFFER|p.G81V|c.242G>T|7,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.G81S|c.241G>A|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79K|c.235G>A|10,BUFFER|p.E79Q|c.235G>C|11,BUFFER|p.D77V|c.230A>T|5,BUFFER|p.D77G|c.230A>G|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCTCTTCA	.	5	ESCA
TTN	0	.	GRCh37	2	179433512	179433512	+	Missense_Mutation	SNP	G	G	A	rs758010128	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77347C>T	p.Arg25783Trp	p.R25783W	ENST00000589042	326/363	23	11	11	23	23	0	TTN,missense_variant,p.Arg16843Trp,ENST00000359218,;TTN,missense_variant,p.Arg24142Trp,ENST00000591111,;TTN,missense_variant,p.Arg25783Trp,ENST00000589042,;TTN,missense_variant,p.Arg16910Trp,ENST00000342175,;TTN,missense_variant,p.Arg23215Trp,ENST00000342992,;TTN,missense_variant,p.Arg16718Trp,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;	A	ENSG00000155657	ENST00000589042	Transcript	missense_variant	77572	77347	25783	R/W	Cgg/Tgg	rs758010128	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	326/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACCGAGGAT	.	5	ESCA
PTH2R	0	.	GRCh37	2	209345854	209345854	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041C>T	p.%3D	p.T347T	ENST00000272847	10/13	39	31	8	48	48	0	PTH2R,synonymous_variant,p.%3D,ENST00000272847,;AC019185.4,intron_variant,,ENST00000424628,;PTH2R,non_coding_transcript_exon_variant,,ENST00000413482,;	T	ENSG00000144407	ENST00000272847	Transcript	synonymous_variant	1254	1041	347	T	acC/acT	.	.	.	1	PTH2R	HGNC	9609	protein_coding	YES	CCDS2383.1	ENSP00000272847	PTH2R_HUMAN	Q53T35_HUMAN,Q53SF6_HUMAN,B4DFN8_HUMAN	UPI000005041E	.	.	.	10/13	.	Superfamily_domains:SSF81321,Pfam_domain:PF00002,hmmpanther:PTHR12011:SF69,hmmpanther:PTHR12011,PROSITE_profiles:PS50261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACCAATGC	.	5	ESCA
NYAP2	0	.	GRCh37	2	226516200	226516200	+	Silent	SNP	T	T	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1881T>A	p.%3D	p.P627P	ENST00000272907	6/6	52	43	8	48	48	0	NYAP2,synonymous_variant,p.%3D,ENST00000272907,;	A	ENSG00000144460	ENST00000272907	Transcript	synonymous_variant	2294	1881	627	P	ccT/ccA	.	.	.	1	NYAP2	HGNC	29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	NYAP2_HUMAN	.	UPI00001C1DB6	.	.	.	6/6	.	hmmpanther:PTHR22633,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCTCCTCC	.	5	ESCA
KIF1A	0	.	GRCh37	2	241724476	241724476	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650C>T	p.Ser217Phe	p.S217F	ENST00000498729	7/50	58	30	27	39	39	0	KIF1A,missense_variant,p.Ser25Phe,ENST00000428768,;KIF1A,missense_variant,p.Ser217Phe,ENST00000498729,;KIF1A,missense_variant,p.Ser217Phe,ENST00000320389,;KIF1A,missense_variant,p.Ser217Phe,ENST00000404283,;KIF1A,downstream_gene_variant,,ENST00000448728,;	A	ENSG00000130294	ENST00000498729	Transcript	missense_variant	897	650	217	S/F	tCc/tTc	.	.	.	-1	KIF1A	HGNC	888	protein_coding	YES	CCDS58757.1	ENSP00000438388	KIF1A_HUMAN	G1UI30_HUMAN,C9JBH1_HUMAN	UPI0002065B81	.	deleterious(0)	probably_damaging(1)	7/50	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF361,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTGGGAGCGA	.	5	ESCA
KIAA1841	0	.	GRCh37	2	61361295	61361295	+	Missense_Mutation	SNP	C	C	A	rs777489264	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2052C>A	p.Asp684Glu	p.D684E	ENST00000295031	21/22	68	53	14	75	75	0	KIAA1841,missense_variant,p.Asp684Glu,ENST00000295031,;KIAA1841,non_coding_transcript_exon_variant,,ENST00000462959,;	A	ENSG00000162929	ENST00000295031	Transcript	missense_variant	2429	2052	684	D/E	gaC/gaA	rs777489264,COSM287788	.	.	1	KIAA1841	HGNC	29387	protein_coding	.	CCDS1867.1	ENSP00000295031	K1841_HUMAN	.	UPI0000456DC6	.	tolerated_low_confidence(0.36)	unknown(0)	21/22	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGACGGCAC	byFrequency	5	ESCA
EMC3	0	.	GRCh37	3	10016090	10016091	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389dupT	p.Met130IlefsTer20	p.M130Ifs*20	ENST00000245046	4/8	63	43	20	52	52	0	EMC3,frameshift_variant,p.Met130IlefsTer20,ENST00000245046,;EMC3,frameshift_variant,p.Met168IlefsTer20,ENST00000429759,;EMC3,downstream_gene_variant,,ENST00000470827,;EMC3,non_coding_transcript_exon_variant,,ENST00000497557,;EMC3,non_coding_transcript_exon_variant,,ENST00000487465,;	A	ENSG00000125037	ENST00000245046	Transcript	frameshift_variant	848-849	389-390	130	M/IX	atg/atTg	.	.	.	-1	EMC3	HGNC	23999	protein_coding	YES	CCDS2594.1	ENSP00000245046	EMC3_HUMAN	S4R3U9_HUMAN	UPI000006E80F	.	.	.	4/8	.	PIRSF_domain:PIRSF010045,Pfam_domain:PF01956,hmmpanther:PTHR13116:SF7,hmmpanther:PTHR13116,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATGTCATGTT	.	3	ESCA
DPPA4	0	.	GRCh37	3	109050582	109050582	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389A>G	p.Lys130Arg	p.K130R	ENST00000335658	4/7	62	53	9	52	52	0	DPPA4,missense_variant,p.Lys130Arg,ENST00000335658,;DPPA4,downstream_gene_variant,,ENST00000477303,;DPPA4,splice_region_variant,,ENST00000463966,;DPPA4,splice_region_variant,,ENST00000478791,;DPPA4,splice_region_variant,,ENST00000487299,;DPPA4,splice_region_variant,,ENST00000495679,;DPPA4,downstream_gene_variant,,ENST00000489281,;DPPA4,upstream_gene_variant,,ENST00000475135,;	C	ENSG00000121570	ENST00000335658	Transcript	missense_variant	444	389	130	K/R	aAg/aGg	.	.	.	-1	DPPA4	HGNC	19200	protein_coding	YES	CCDS33814.1	ENSP00000335306	DPPA4_HUMAN	C9J7A7_HUMAN	UPI000022C153	.	tolerated(0.09)	benign(0.374)	4/7	.	hmmpanther:PTHR16073,hmmpanther:PTHR16073:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACCTTTTGA	.	5	ESCA
ILDR1	0	.	GRCh37	3	121712109	121712109	+	Missense_Mutation	SNP	C	C	T	rs757986659	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1487G>A	p.Arg496His	p.R496H	ENST00000344209	7/8	65	49	16	49	49	0	ILDR1,missense_variant,p.Arg407His,ENST00000393631,;ILDR1,missense_variant,p.Arg452His,ENST00000273691,;ILDR1,missense_variant,p.Arg496His,ENST00000344209,;ILDR1,missense_variant,p.Arg464His,ENST00000462014,;ILDR1,non_coding_transcript_exon_variant,,ENST00000460554,;	T	ENSG00000145103	ENST00000344209	Transcript	missense_variant	1614	1487	496	R/H	cGc/cAc	rs757986659,COSM272802,COSM272803	.	.	-1	ILDR1	HGNC	28741	protein_coding	YES	CCDS56271.1	ENSP00000345667	ILDR1_HUMAN	.	UPI00003FF1E2	.	tolerated(0.06)	benign(0.001)	7/8	.	hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF3	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGGCGGTGG	byFrequency	5	ESCA
MB21D2	0	.	GRCh37	3	192515061	192515061	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1114G>T	.	.	ENST00000392452	2/2	20	16	3	18	18	0	MB21D2,3_prime_UTR_variant,,ENST00000392452,;	A	ENSG00000180611	ENST00000392452	Transcript	3_prime_UTR_variant	2911	.	.	.	.	.	.	.	-1	MB21D2	HGNC	30438	protein_coding	YES	CCDS3302.2	ENSP00000376246	M21D2_HUMAN	A8K332_HUMAN	UPI000013FAFE	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCCTGCCA	.	5	ESCA
ACAP2	0	.	GRCh37	3	194995529	194995529	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4528G>C	.	.	ENST00000326793	23/23	40	36	4	50	50	0	ACAP2,3_prime_UTR_variant,,ENST00000326793,;XXYLT1,upstream_gene_variant,,ENST00000310380,;ACAP2,downstream_gene_variant,,ENST00000472860,;XXYLT1,upstream_gene_variant,,ENST00000455281,;	G	ENSG00000114331	ENST00000326793	Transcript	3_prime_UTR_variant	7096	.	.	.	.	.	.	.	-1	ACAP2	HGNC	16469	protein_coding	YES	CCDS33924.1	ENSP00000324287	ACAP2_HUMAN	C9J8L1_HUMAN	UPI0000141A1A	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AATTACTTAAG	.	3	ESCA
CMC1	0	.	GRCh37	3	28364113	28364113	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2993A>G	.	.	ENST00000466830	4/4	45	27	18	64	64	0	CMC1,3_prime_UTR_variant,,ENST00000466830,;AZI2,3_prime_UTR_variant,,ENST00000479665,;AZI2,intron_variant,,ENST00000429369,;CMC1,downstream_gene_variant,,ENST00000423894,;CMC1,downstream_gene_variant,,ENST00000418849,;AZI2,non_coding_transcript_exon_variant,,ENST00000295748,;CMC1,downstream_gene_variant,,ENST00000495428,;CMC1,downstream_gene_variant,,ENST00000469102,;CMC1,downstream_gene_variant,,ENST00000467644,;CMC1,downstream_gene_variant,,ENST00000482499,;AZI2,downstream_gene_variant,,ENST00000476174,;CMC1,downstream_gene_variant,,ENST00000396610,;CMC1,downstream_gene_variant,,ENST00000477739,;AZI2,downstream_gene_variant,,ENST00000492044,;CMC1,downstream_gene_variant,,ENST00000334841,;AZI2,downstream_gene_variant,,ENST00000463512,;	G	ENSG00000187118	ENST00000466830	Transcript	3_prime_UTR_variant	3513	.	.	.	.	.	.	.	1	CMC1	HGNC	28783	protein_coding	YES	CCDS33722.1	ENSP00000418348	COXM1_HUMAN	.	UPI0000161ABD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTATGCAT	.	5	ESCA
CSRNP1	0	.	GRCh37	3	39184426	39184426	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120C>A	.	.	ENST00000273153	5/5	10	5	5	20	20	0	CSRNP1,3_prime_UTR_variant,,ENST00000514182,;CSRNP1,3_prime_UTR_variant,,ENST00000273153,;TTC21A,downstream_gene_variant,,ENST00000440121,;TTC21A,downstream_gene_variant,,ENST00000301819,;TTC21A,downstream_gene_variant,,ENST00000431162,;TTC21A,downstream_gene_variant,,ENST00000493856,;TTC21A,downstream_gene_variant,,ENST00000472866,;TTC21A,downstream_gene_variant,,ENST00000460460,;TTC21A,downstream_gene_variant,,ENST00000430597,;	T	ENSG00000144655	ENST00000273153	Transcript	3_prime_UTR_variant	2068	.	.	.	.	.	.	.	-1	CSRNP1	HGNC	14300	protein_coding	YES	CCDS2682.1	ENSP00000273153	CSRN1_HUMAN	.	UPI0000044242	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTGTGCACAT	.	3	ESCA
ALS2CL	0	.	GRCh37	3	46721933	46721933	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1535C>T	p.Ala512Val	p.A512V	ENST00000318962	14/26	37	32	4	45	45	0	ALS2CL,missense_variant,p.Ala512Val,ENST00000318962,;ALS2CL,missense_variant,p.Ala512Val,ENST00000415953,;ALS2CL,upstream_gene_variant,,ENST00000383742,;ALS2CL,missense_variant,p.Arg511Trp,ENST00000434140,;ALS2CL,3_prime_UTR_variant,,ENST00000450172,;ALS2CL,3_prime_UTR_variant,,ENST00000431015,;ALS2CL,3_prime_UTR_variant,,ENST00000423707,;ALS2CL,upstream_gene_variant,,ENST00000486301,;	A	ENSG00000178038	ENST00000318962	Transcript	missense_variant	1619	1535	512	A/V	gCg/gTg	.	.	.	-1	ALS2CL	HGNC	20605	protein_coding	YES	CCDS2743.1	ENSP00000313670	AL2CL_HUMAN	G3V0I7_HUMAN	UPI00001B5641	.	tolerated(0.38)	benign(0.292)	14/26	.	Superfamily_domains:0038399,SMART_domains:SM00698,Pfam_domain:PF02493,Gene3D:1h3iA01,hmmpanther:PTHR23084,hmmpanther:PTHR23084:SF114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCCGCCTGG	.	4	ESCA
CADM2	0	.	GRCh37	3	85008594	85008594	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-165G>A	.	.	ENST00000383699	1/10	11	8	3	16	16	0	CADM2,5_prime_UTR_variant,,ENST00000383699,;CADM2,upstream_gene_variant,,ENST00000407528,;CADM2,non_coding_transcript_exon_variant,,ENST00000485126,;CADM2,non_coding_transcript_exon_variant,,ENST00000473523,;	A	ENSG00000175161	ENST00000383699	Transcript	5_prime_UTR_variant	463	.	.	.	.	.	.	.	1	CADM2	HGNC	29849	protein_coding	.	CCDS54613.1	ENSP00000373200	CADM2_HUMAN	G3XHN7_HUMAN,G3XHN4_HUMAN	UPI0000035DF5	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCTGCTGCC	.	2	ESCA
CADM2	0	.	GRCh37	3	85008595	85008595	+	5'UTR	SNP	C	C	A	rs562625024	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-164C>A	.	.	ENST00000383699	1/10	11	8	3	16	16	0	CADM2,5_prime_UTR_variant,,ENST00000383699,;CADM2,upstream_gene_variant,,ENST00000407528,;CADM2,non_coding_transcript_exon_variant,,ENST00000485126,;CADM2,non_coding_transcript_exon_variant,,ENST00000473523,;	A	ENSG00000175161	ENST00000383699	Transcript	5_prime_UTR_variant	464	.	.	.	.	rs562625024	.	.	1	CADM2	HGNC	29849	protein_coding	.	CCDS54613.1	ENSP00000373200	CADM2_HUMAN	G3XHN7_HUMAN,G3XHN4_HUMAN	UPI0000035DF5	.	.	.	1/10	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTGCTGCCG	by1000G	2	ESCA
THUMPD3	0	.	GRCh37	3	9426231	9426231	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1383A>T	p.%3D	p.V461V	ENST00000345094	10/10	23	19	4	15	15	0	THUMPD3,synonymous_variant,p.%3D,ENST00000345094,;THUMPD3,synonymous_variant,p.%3D,ENST00000416603,;THUMPD3,synonymous_variant,p.%3D,ENST00000515662,;THUMPD3,synonymous_variant,p.%3D,ENST00000452837,;THUMPD3,downstream_gene_variant,,ENST00000441127,;SETD5-AS1,intron_variant,,ENST00000468186,;SETD5-AS1,downstream_gene_variant,,ENST00000520396,;SETD5-AS1,downstream_gene_variant,,ENST00000520447,;SETD5-AS1,downstream_gene_variant,,ENST00000521267,;SETD5-AS1,downstream_gene_variant,,ENST00000520629,;SETD5-AS1,downstream_gene_variant,,ENST00000523354,;SETD5-AS1,downstream_gene_variant,,ENST00000467069,;SETD5-AS1,downstream_gene_variant,,ENST00000521609,;SETD5-AS1,downstream_gene_variant,,ENST00000522525,;SETD5-AS1,downstream_gene_variant,,ENST00000519043,;THUMPD3,non_coding_transcript_exon_variant,,ENST00000464045,;THUMPD3,downstream_gene_variant,,ENST00000484006,;THUMPD3,downstream_gene_variant,,ENST00000461636,;	T	ENSG00000134077	ENST00000345094	Transcript	synonymous_variant	1717	1383	461	V	gtA/gtT	.	.	.	1	THUMPD3	HGNC	24493	protein_coding	YES	CCDS2573.1	ENSP00000339532	THUM3_HUMAN	C9JP31_HUMAN,C9J9V2_HUMAN	UPI000006E64E	.	.	.	10/10	.	hmmpanther:PTHR14911:SF12,hmmpanther:PTHR14911,Gene3D:3.40.50.150,Pfam_domain:PF01170	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACGTATGGCG	.	2	ESCA
COL25A1	0	.	GRCh37	4	109780831	109780831	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1301A>C	p.Asn434Thr	p.N434T	ENST00000399132	24/38	65	56	9	76	76	0	COL25A1,missense_variant,p.Asn415Thr,ENST00000399127,;COL25A1,missense_variant,p.Asn434Thr,ENST00000399132,;COL25A1,missense_variant,p.Asn434Thr,ENST00000399126,;COL25A1,missense_variant,p.Asn362Thr,ENST00000494183,;	G	ENSG00000188517	ENST00000399132	Transcript	missense_variant	1832	1301	434	N/T	aAc/aCc	.	.	.	-1	COL25A1	HGNC	18603	protein_coding	YES	CCDS43258.1	ENSP00000382083	COPA1_HUMAN	D6R8Y2_HUMAN	UPI0000225CD2	.	deleterious(0)	possibly_damaging(0.833)	24/38	.	hmmpanther:PTHR24023:SF412,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.N432N|c.1296C>T|3,BUFFER|p.N432N|c.1296C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGTTGCCG	.	5	ESCA
BOD1L1	0	.	GRCh37	4	13616992	13616992	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.503G>A	p.Gly168Glu	p.G168E	ENST00000040738	3/26	55	47	8	112	112	0	BOD1L1,missense_variant,p.Gly168Glu,ENST00000040738,;BOD1L1,3_prime_UTR_variant,,ENST00000482713,;	T	ENSG00000038219	ENST00000040738	Transcript	missense_variant	639	503	168	G/E	gGa/gAa	.	.	.	-1	BOD1L1	HGNC	31792	protein_coding	YES	CCDS3411.2	ENSP00000040738	BD1L1_HUMAN	.	UPI000066D9E3	.	.	benign(0.001)	3/26	.	hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTTCCTTCC	.	5	ESCA
WDR17	0	.	GRCh37	4	177041086	177041086	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448C>T	p.Pro150Ser	p.P150S	ENST00000280190	5/31	41	32	9	57	57	0	WDR17,missense_variant,p.Pro150Ser,ENST00000507824,;WDR17,missense_variant,p.Pro24Ser,ENST00000505894,;WDR17,missense_variant,p.Pro150Ser,ENST00000280190,;WDR17,missense_variant,p.Pro126Ser,ENST00000508596,;WDR17,missense_variant,p.Pro126Ser,ENST00000393643,;WDR17,synonymous_variant,p.%3D,ENST00000513261,;	T	ENSG00000150627	ENST00000280190	Transcript	missense_variant	604	448	150	P/S	Cca/Tca	.	.	.	1	WDR17	HGNC	16661	protein_coding	YES	CCDS3825.1	ENSP00000280190	WDR17_HUMAN	Q0QD35_HUMAN,E7EP77_HUMAN	UPI000019C575	.	tolerated(0.1)	probably_damaging(0.999)	5/31	.	hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF344,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCCCACTG	.	5	ESCA
ZNF721	0	.	GRCh37	4	436616	436616	+	Missense_Mutation	SNP	T	T	G	rs534408130	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1640A>C	p.His547Pro	p.H547P	ENST00000511833	3/3	52	39	13	55	55	0	ZNF721,missense_variant,p.His535Pro,ENST00000338977,;ZNF721,missense_variant,p.His547Pro,ENST00000511833,;ZNF721,intron_variant,,ENST00000506646,;ZNF721,downstream_gene_variant,,ENST00000505900,;ZNF721,intron_variant,,ENST00000507078,;ABCA11P,intron_variant,,ENST00000514396,;ABCA11P,intron_variant,,ENST00000451020,;ABCA11P,intron_variant,,ENST00000507854,;ZNF721,intron_variant,,ENST00000515578,;	G	ENSG00000182903	ENST00000511833	Transcript	missense_variant	1834	1640	547	H/P	cAt/cCt	rs534408130	.	.	-1	ZNF721	HGNC	29425	protein_coding	YES	CCDS46991.1	ENSP00000428878	ZN721_HUMAN	.	UPI0000E9B4A9	.	deleterious(0)	probably_damaging(1)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24376,hmmpanther:PTHR24376:SF16,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	C:0.0002	C:0	C:0	.	C:0.001	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTATGTACA	by1000G	5	ESCA
GK2	0	.	GRCh37	4	80328426	80328426	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.929G>C	p.Arg310Thr	p.R310T	ENST00000358842	1/1	44	35	8	47	47	0	GK2,missense_variant,p.Arg310Thr,ENST00000358842,;	G	ENSG00000196475	ENST00000358842	Transcript	missense_variant	947	929	310	R/T	aGa/aCa	.	.	.	-1	GK2	HGNC	4291	protein_coding	YES	CCDS3585.1	ENSP00000351706	GLPK2_HUMAN	.	UPI000011E629	.	tolerated(0.19)	benign(0.297)	1/1	.	Superfamily_domains:SSF53067,PIRSF_domain:PIRSF000538,Pfam_domain:PF02782,Gene3D:3.30.420.40,TIGRFAM_domain:TIGR01311,hmmpanther:PTHR10196:SF46,hmmpanther:PTHR10196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCTGCCT	.	5	ESCA
CCT5	0	.	GRCh37	5	10258535	10258535	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.761C>A	p.Pro254Gln	p.P254Q	ENST00000280326	6/11	18	14	4	17	17	0	CCT5,missense_variant,p.Pro254Gln,ENST00000280326,;CCT5,missense_variant,p.Pro161Gln,ENST00000506600,;CCT5,missense_variant,p.Pro233Gln,ENST00000503026,;CCT5,missense_variant,p.Pro216Gln,ENST00000515676,;CCT5,missense_variant,p.Pro199Gln,ENST00000515390,;CCT5,3_prime_UTR_variant,,ENST00000512975,;CCT5,3_prime_UTR_variant,,ENST00000503454,;CCT5,non_coding_transcript_exon_variant,,ENST00000423695,;CCT5,non_coding_transcript_exon_variant,,ENST00000509846,;CCT5,non_coding_transcript_exon_variant,,ENST00000514674,;CCT5,downstream_gene_variant,,ENST00000510326,;CCT5,downstream_gene_variant,,ENST00000508451,;CCT5,downstream_gene_variant,,ENST00000511700,;CCT5,upstream_gene_variant,,ENST00000511995,;	A	ENSG00000150753	ENST00000280326	Transcript	missense_variant	1181	761	254	P/Q	cCa/cAa	.	.	.	1	CCT5	HGNC	1618	protein_coding	YES	CCDS3877.1	ENSP00000280326	TCPE_HUMAN	Q9HB74_HUMAN,Q9BU08_HUMAN,Q96GI1_HUMAN,B7ZAR1_HUMAN	UPI0000001C34	.	deleterious(0)	probably_damaging(0.992)	6/11	.	hmmpanther:PTHR11353,Pfam_domain:PF00118,TIGRFAM_domain:TIGR02343,Gene3D:3.50.7.10,Superfamily_domains:SSF52029	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	ATGTCCATTTG	.	3	ESCA
SEC24A	0	.	GRCh37	5	134063408	134063408	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2624T>A	.	.	ENST00000398844	23/23	29	23	6	67	67	0	SEC24A,3_prime_UTR_variant,,ENST00000398844,;	A	ENSG00000113615	ENST00000398844	Transcript	3_prime_UTR_variant	6194	.	.	.	.	.	.	.	1	SEC24A	HGNC	10703	protein_coding	YES	CCDS43363.1	ENSP00000381823	SC24A_HUMAN	.	UPI0000185FF9	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAATGTGCT	.	5	ESCA
PCDHA7	0	.	GRCh37	5	140214386	140214386	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418C>G	p.Leu140Val	p.L140V	ENST00000525929	1/4	42	35	7	30	30	0	PCDHA7,missense_variant,p.Leu140Val,ENST00000378125,;PCDHA7,missense_variant,p.Leu140Val,ENST00000525929,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	G	ENSG00000204963	ENST00000525929	Transcript	missense_variant	418	418	140	L/V	Ctg/Gtg	.	.	.	1	PCDHA7	HGNC	8673	protein_coding	YES	CCDS54918.1	ENSP00000436426	PCDA7_HUMAN	.	UPI00001273CF	.	tolerated_low_confidence(0.15)	benign(0.111)	1/4	.	Superfamily_domains:SSF49313,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATCTGTTC	.	4	ESCA
TNIP1	0	.	GRCh37	5	150410284	150410284	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1901G>C	p.Gly634Ala	p.G634A	ENST00000389378	18/18	25	20	5	42	42	0	TNIP1,missense_variant,p.Gly581Ala,ENST00000520931,;TNIP1,missense_variant,p.Gly634Ala,ENST00000389378,;TNIP1,missense_variant,p.Gly634Ala,ENST00000521591,;TNIP1,missense_variant,p.Gly570Ala,ENST00000523200,;TNIP1,missense_variant,p.Gly538Arg,ENST00000524280,;TNIP1,missense_variant,p.Gly634Ala,ENST00000315050,;TNIP1,missense_variant,p.Gly634Ala,ENST00000522226,;TNIP1,intron_variant,,ENST00000517504,;TNIP1,intron_variant,,ENST00000518977,;TNIP1,intron_variant,,ENST00000523338,;GPX3,downstream_gene_variant,,ENST00000517973,;GPX3,downstream_gene_variant,,ENST00000520059,;GPX3,downstream_gene_variant,,ENST00000521632,;GPX3,downstream_gene_variant,,ENST00000388825,;GPX3,downstream_gene_variant,,ENST00000521650,;GPX3,downstream_gene_variant,,ENST00000521722,;TNIP1,downstream_gene_variant,,ENST00000521423,;TNIP1,3_prime_UTR_variant,,ENST00000519339,;TNIP1,non_coding_transcript_exon_variant,,ENST00000522574,;GPX3,downstream_gene_variant,,ENST00000520597,;GPX3,downstream_gene_variant,,ENST00000519214,;TNIP1,downstream_gene_variant,,ENST00000517329,;	G	ENSG00000145901	ENST00000389378	Transcript	missense_variant	2490	1901	634	G/A	gGg/gCg	.	.	.	-1	TNIP1	HGNC	16903	protein_coding	YES	CCDS34280.1	ENSP00000374029	TNIP1_HUMAN	E7EWG2_HUMAN,E7EW68_HUMAN,E7EW15_HUMAN,B7Z5B0_HUMAN,A4F1X2_HUMAN,A4F1W8_HUMAN	UPI000000DCDC	.	tolerated_low_confidence(0.61)	benign(0.196)	18/18	.	hmmpanther:PTHR31882:SF3,hmmpanther:PTHR31882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCCCCTCA	.	5	ESCA
SNCB	0	.	GRCh37	5	176047523	176047523	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*289G>A	.	.	ENST00000310112	7/7	29	25	4	32	32	0	SNCB,3_prime_UTR_variant,,ENST00000393693,;SNCB,3_prime_UTR_variant,,ENST00000310112,;SNCB,downstream_gene_variant,,ENST00000506696,;SNCB,downstream_gene_variant,,ENST00000510387,;SNCB,downstream_gene_variant,,ENST00000508006,;	T	ENSG00000074317	ENST00000310112	Transcript	3_prime_UTR_variant	945	.	.	.	.	.	.	.	-1	SNCB	HGNC	11140	protein_coding	YES	CCDS4406.1	ENSP00000308057	SYUB_HUMAN	G4Y816_HUMAN	UPI000003173C	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AAACACATAGA	.	3	ESCA
RMND5B	0	.	GRCh37	5	177569912	177569912	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.345G>C	p.Gln115His	p.Q115H	ENST00000515098	6/12	23	20	3	21	21	0	RMND5B,missense_variant,p.Gln115His,ENST00000313386,;RMND5B,missense_variant,p.Gln102His,ENST00000542098,;RMND5B,missense_variant,p.Gln115His,ENST00000515098,;RMND5B,missense_variant,p.Gln115His,ENST00000507457,;RMND5B,downstream_gene_variant,,ENST00000508647,;RMND5B,downstream_gene_variant,,ENST00000502814,;RMND5B,3_prime_UTR_variant,,ENST00000512811,;RMND5B,3_prime_UTR_variant,,ENST00000512663,;RMND5B,non_coding_transcript_exon_variant,,ENST00000513162,;RMND5B,non_coding_transcript_exon_variant,,ENST00000507575,;RMND5B,non_coding_transcript_exon_variant,,ENST00000515360,;RMND5B,upstream_gene_variant,,ENST00000507937,;	C	ENSG00000145916	ENST00000515098	Transcript	missense_variant	696	345	115	Q/H	caG/caC	COSM1066450	.	.	1	RMND5B	HGNC	26181	protein_coding	YES	CCDS4431.1	ENSP00000420875	RMD5B_HUMAN	Q659D3_HUMAN,D6RIF9_HUMAN,D6RFK1_HUMAN,D6RER3_HUMAN	UPI0000037C23	.	tolerated(0.06)	benign(0.001)	6/12	.	hmmpanther:PTHR12170,hmmpanther:PTHR12170:SF6	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GAACAGCAGCA	.	3	ESCA
AACSP1	0	.	GRCh37	5	178199531	178199531	+	RNA	SNP	C	C	T	rs540200724	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1005G>A	.	.	ENST00000503486	8/11	34	30	4	36	36	0	AACSP1,non_coding_transcript_exon_variant,,ENST00000503486,;AACSP1,non_coding_transcript_exon_variant,,ENST00000521412,;AACSP1,non_coding_transcript_exon_variant,,ENST00000536654,;	T	ENSG00000250420	ENST00000503486	Transcript	non_coding_transcript_exon_variant	1005	.	.	.	.	rs540200724	.	.	-1	AACSP1	HGNC	18226	processed_transcript	YES	.	.	.	.	.	.	.	.	8/11	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGGCGTGCC	by1000G	4	ESCA
PRDM9	0	.	GRCh37	5	23526968	23526968	+	Missense_Mutation	SNP	T	T	C	rs200381384	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1771T>C	p.Trp591Arg	p.W591R	ENST00000296682	11/11	51	39	12	63	63	0	PRDM9,missense_variant,p.Trp591Arg,ENST00000296682,;	C	ENSG00000164256	ENST00000296682	Transcript	missense_variant	1953	1771	591	W/R	Tgg/Cgg	rs200381384	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	tolerated(0.61)	benign(0.003)	11/11	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	C:0.0007	C:0.0004	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGCTGGCAG	byCluster	4	ESCA
CDH10	0	.	GRCh37	5	24487994	24487994	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2145T>C	p.%3D	p.N715N	ENST00000264463	12/12	26	17	9	47	47	0	CDH10,synonymous_variant,p.%3D,ENST00000264463,;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,;	G	ENSG00000040731	ENST00000264463	Transcript	synonymous_variant	2653	2145	715	N	aaT/aaC	.	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	.	.	12/12	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Gene3D:4.10.900.10,Pfam_domain:PF01049	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTCATTAAT	.	5	ESCA
ROS1	0	.	GRCh37	6	117709183	117709183	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1774A>G	p.Ser592Gly	p.S592G	ENST00000368508	13/43	19	12	7	23	23	0	ROS1,missense_variant,p.Ser592Gly,ENST00000368508,;ROS1,intron_variant,,ENST00000368507,;GOPC,intron_variant,,ENST00000467125,;	C	ENSG00000047936	ENST00000368508	Transcript	missense_variant	1973	1774	592	S/G	Agt/Ggt	.	.	.	-1	ROS1	HGNC	10261	protein_coding	YES	CCDS5116.1	ENSP00000357494	ROS1_HUMAN	.	UPI000013D467	.	tolerated_low_confidence(0.25)	benign(0)	13/43	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF304,hmmpanther:PTHR24416,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACTGATCA	.	5	ESCA
KIAA0408	0	.	GRCh37	6	127771344	127771344	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.289C>A	p.His97Asn	p.H97N	ENST00000483725	3/6	25	17	8	30	30	0	KIAA0408,missense_variant,p.His97Asn,ENST00000483725,;KIAA0408,missense_variant,p.His109Asn,ENST00000487331,;SOGA3,3_prime_UTR_variant,,ENST00000556132,;SOGA3,3_prime_UTR_variant,,ENST00000368268,;KIAA0408,upstream_gene_variant,,ENST00000465254,;SOGA3,downstream_gene_variant,,ENST00000474293,;SOGA3,3_prime_UTR_variant,,ENST00000464495,;SOGA3,3_prime_UTR_variant,,ENST00000473298,;SOGA3,3_prime_UTR_variant,,ENST00000481848,;KIAA0408,non_coding_transcript_exon_variant,,ENST00000368281,;KIAA0408,non_coding_transcript_exon_variant,,ENST00000472335,;	T	ENSG00000189367	ENST00000483725	Transcript	missense_variant	626	289	97	H/N	Cac/Aac	.	.	.	-1	KIAA0408	HGNC	21636	protein_coding	YES	CCDS34531.1	ENSP00000435150	K0408_HUMAN	.	UPI00001C0BD7	.	tolerated(0.07)	benign(0.009)	3/6	.	hmmpanther:PTHR15705,Pfam_domain:PF14818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGTGATTCG	.	5	ESCA
PTPRK	0	.	GRCh37	6	128642852	128642852	+	Intron	SNP	A	A	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495+332T>A	.	.	ENST00000368213	.	11	8	3	12	12	0	PTPRK,3_prime_UTR_variant,,ENST00000525459,;PTPRK,intron_variant,,ENST00000532331,;PTPRK,intron_variant,,ENST00000368215,;PTPRK,intron_variant,,ENST00000368227,;PTPRK,intron_variant,,ENST00000490332,;PTPRK,intron_variant,,ENST00000368207,;PTPRK,intron_variant,,ENST00000368226,;PTPRK,intron_variant,,ENST00000368210,;PTPRK,intron_variant,,ENST00000368213,;PTPRK,intron_variant,,ENST00000524534,;PTPRK,intron_variant,,ENST00000524481,;PTPRK,intron_variant,,ENST00000495748,;PTPRK,intron_variant,,ENST00000429595,;PTPRK,3_prime_UTR_variant,,ENST00000392449,;PTPRK,intron_variant,,ENST00000531050,;PTPRK,downstream_gene_variant,,ENST00000532751,;	T	ENSG00000152894	ENST00000368213	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PTPRK	HGNC	9674	protein_coding	YES	CCDS47473.1	ENSP00000357196	PTPRK_HUMAN	.	UPI0001747A04	.	.	.	.	3/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAGAATCTGT	.	2	ESCA
MOXD1	0	.	GRCh37	6	132649624	132649624	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.773A>G	p.Tyr258Cys	p.Y258C	ENST00000367963	5/12	47	40	7	48	48	0	MOXD1,missense_variant,p.Tyr190Cys,ENST00000336749,;MOXD1,missense_variant,p.Tyr258Cys,ENST00000367963,;MOXD1,upstream_gene_variant,,ENST00000489128,;	C	ENSG00000079931	ENST00000367963	Transcript	missense_variant	892	773	258	Y/C	tAt/tGt	.	.	.	-1	MOXD1	HGNC	21063	protein_coding	YES	CCDS5152.2	ENSP00000356940	MOXD1_HUMAN	.	UPI000003F04F	.	deleterious(0)	probably_damaging(1)	5/12	.	Superfamily_domains:SSF49742,Gene3D:1yi9A01,Pfam_domain:PF01082,hmmpanther:PTHR10157,hmmpanther:PTHR10157:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGATAGCAC	.	5	ESCA
IGF2R	0	.	GRCh37	6	160481680	160481680	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3193C>T	p.Arg1065Ter	p.R1065*	ENST00000356956	23/48	91	79	12	97	97	0	IGF2R,stop_gained,p.Arg1065Ter,ENST00000356956,;	T	ENSG00000197081	ENST00000356956	Transcript	stop_gained	3341	3193	1065	R/*	Cga/Tga	.	.	.	1	IGF2R	HGNC	5467	protein_coding	YES	CCDS5273.1	ENSP00000349437	MPRI_HUMAN	A0N9R7_HUMAN,A0N9R6_HUMAN	UPI0000072478	.	.	.	23/48	.	hmmpanther:PTHR10439:SF4,hmmpanther:PTHR10439,Gene3D:2.70.130.10,Pfam_domain:PF00878,Superfamily_domains:SSF50911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATCCGAAAC	.	4	ESCA
SERPINB9	0	.	GRCh37	6	2892151	2892151	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639C>G	p.%3D	p.R213R	ENST00000380698	6/7	15	11	3	17	17	0	SERPINB9,synonymous_variant,p.%3D,ENST00000380698,;	C	ENSG00000170542	ENST00000380698	Transcript	synonymous_variant	729	639	213	R	cgC/cgG	.	.	.	-1	SERPINB9	HGNC	8955	protein_coding	YES	CCDS4478.1	ENSP00000370074	SPB9_HUMAN	Q6N0A8_HUMAN	UPI000000121F	.	.	.	6/7	.	Superfamily_domains:SSF56574,SMART_domains:SM00093,Pfam_domain:PF00079,Gene3D:2.30.39.10,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TGCGCGCGCAC	.	4	ESCA
WDR46	0	.	GRCh37	6	33255939	33255939	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547G>A	p.Ala183Thr	p.A183T	ENST00000374617	5/15	28	20	8	29	29	0	WDR46,missense_variant,p.Ala118Thr,ENST00000444176,;WDR46,missense_variant,p.Ala183Thr,ENST00000374617,;PFDN6,upstream_gene_variant,,ENST00000395131,;PFDN6,upstream_gene_variant,,ENST00000374607,;PFDN6,upstream_gene_variant,,ENST00000374610,;RGL2,downstream_gene_variant,,ENST00000497454,;PFDN6,upstream_gene_variant,,ENST00000463584,;PFDN6,upstream_gene_variant,,ENST00000374606,;WDR46,non_coding_transcript_exon_variant,,ENST00000477718,;WDR46,non_coding_transcript_exon_variant,,ENST00000468157,;RGL2,downstream_gene_variant,,ENST00000471319,;RGL2,downstream_gene_variant,,ENST00000437840,;RGL2,downstream_gene_variant,,ENST00000491168,;B3GALT4,downstream_gene_variant,,ENST00000606990,;WDR46,non_coding_transcript_exon_variant,,ENST00000481025,;PFDN6,upstream_gene_variant,,ENST00000395134,;WDR46,upstream_gene_variant,,ENST00000488944,;PFDN6,upstream_gene_variant,,ENST00000491382,;RGL2,downstream_gene_variant,,ENST00000476616,;WDR46,upstream_gene_variant,,ENST00000489905,;RGL2,downstream_gene_variant,,ENST00000483151,;	T	ENSG00000227057	ENST00000374617	Transcript	missense_variant	904	547	183	A/T	Gca/Aca	.	.	.	-1	WDR46	HGNC	13923	protein_coding	YES	CCDS4772.1	ENSP00000363746	WDR46_HUMAN	.	UPI000045741F	.	tolerated(0.96)	benign(0.424)	5/15	.	hmmpanther:PTHR14085,hmmpanther:PTHR14085:SF3,Gene3D:2.130.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTGCAATGT	.	5	ESCA
ANKS1A	0	.	GRCh37	6	34985823	34985823	+	Missense_Mutation	SNP	C	C	T	rs779266197	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1997C>T	p.Ser666Leu	p.S666L	ENST00000360359	11/24	22	11	11	29	29	0	ANKS1A,missense_variant,p.Ser666Leu,ENST00000360359,;ANKS1A,intron_variant,,ENST00000535627,;	T	ENSG00000064999	ENST00000360359	Transcript	missense_variant	2135	1997	666	S/L	tCg/tTg	rs779266197	.	.	1	ANKS1A	HGNC	20961	protein_coding	YES	CCDS4798.1	ENSP00000353518	ANS1A_HUMAN	.	UPI00001C1E4D	.	deleterious(0.03)	possibly_damaging(0.716)	11/24	.	hmmpanther:PTHR24174	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCTCGGAGT	.	5	ESCA
COL21A1	0	.	GRCh37	6	55988863	55988863	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1755C>A	p.Phe585Leu	p.F585L	ENST00000244728	16/30	20	15	5	34	34	0	COL21A1,missense_variant,p.Phe582Leu,ENST00000370819,;COL21A1,missense_variant,p.Phe585Leu,ENST00000244728,;COL21A1,missense_variant,p.Phe585Leu,ENST00000535941,;COL21A1,downstream_gene_variant,,ENST00000456983,;COL21A1,downstream_gene_variant,,ENST00000469682,;COL21A1,missense_variant,p.Phe49Leu,ENST00000488912,;	T	ENSG00000124749	ENST00000244728	Transcript	missense_variant	2153	1755	585	F/L	ttC/ttA	.	.	.	-1	COL21A1	HGNC	17025	protein_coding	YES	CCDS55025.1	ENSP00000244728	COLA1_HUMAN	A6PVD9_HUMAN	UPI0000071DFE	.	tolerated(0.67)	benign(0.004)	16/30	.	Pfam_domain:PF01391,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	ACCTTGAAACC	.	4	ESCA
LGSN	0	.	GRCh37	6	63990251	63990251	+	Missense_Mutation	SNP	C	C	G	rs780163823	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1205G>C	p.Gly402Ala	p.G402A	ENST00000370657	4/4	37	31	6	33	33	0	LGSN,missense_variant,p.Gly402Ala,ENST00000370657,;LGSN,3_prime_UTR_variant,,ENST00000370658,;LGSN,intron_variant,,ENST00000485906,;	G	ENSG00000146166	ENST00000370657	Transcript	missense_variant	1239	1205	402	G/A	gGc/gCc	rs780163823	.	.	-1	LGSN	HGNC	21016	protein_coding	YES	CCDS4964.1	ENSP00000359691	LGSN_HUMAN	.	UPI000013DA35	.	deleterious(0.01)	possibly_damaging(0.656)	4/4	.	Superfamily_domains:SSF55931,Gene3D:3.30.590.10,Pfam_domain:PF00120,hmmpanther:PTHR20852,hmmpanther:PTHR20852:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTGCCTTTC	.	5	ESCA
IBTK	0	.	GRCh37	6	82921212	82921212	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2369G>A	p.Arg790Lys	p.R790K	ENST00000306270	14/29	21	14	7	44	44	0	IBTK,missense_variant,p.Arg790Lys,ENST00000510291,;IBTK,missense_variant,p.Arg589Lys,ENST00000503631,;IBTK,missense_variant,p.Arg790Lys,ENST00000306270,;RNU6-130P,upstream_gene_variant,,ENST00000411112,;IBTK,3_prime_UTR_variant,,ENST00000503400,;IBTK,non_coding_transcript_exon_variant,,ENST00000505222,;IBTK,non_coding_transcript_exon_variant,,ENST00000369751,;	T	ENSG00000005700	ENST00000306270	Transcript	missense_variant	2919	2369	790	R/K	aGa/aAa	.	.	.	-1	IBTK	HGNC	17853	protein_coding	YES	CCDS34490.1	ENSP00000305721	IBTK_HUMAN	.	UPI000041929F	.	deleterious(0.01)	probably_damaging(0.99)	14/29	.	PROSITE_profiles:PS50097,hmmpanther:PTHR22872,hmmpanther:PTHR22872:SF2,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGTCTAGCA	.	5	ESCA
MUC12	0	.	GRCh37	7	100657300	100657300	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15745C>T	p.Leu5249Phe	p.L5249F	ENST00000536621	9/12	48	33	14	24	24	0	MUC12,missense_variant,p.Leu5249Phe,ENST00000536621,;MUC12,missense_variant,p.Leu5392Phe,ENST00000379442,;RP11-395B7.4,downstream_gene_variant,,ENST00000448513,;RP11-395B7.4,downstream_gene_variant,,ENST00000441882,;MUC12,upstream_gene_variant,,ENST00000473098,;MUC12,upstream_gene_variant,,ENST00000467414,;MUC12,missense_variant,p.Leu66Phe,ENST00000305119,;MUC12,upstream_gene_variant,,ENST00000474482,;	T	ENSG00000205277	ENST00000536621	Transcript	missense_variant	15745	15745	5249	L/F	Ctc/Ttc	.	.	.	1	MUC12	HGNC	7510	protein_coding	YES	CCDS55139.1	ENSP00000441929	.	F5GWV9_HUMAN	UPI0001B25898	.	.	possibly_damaging(0.773)	9/12	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGCTCGCA	.	5	ESCA
DUS4L	0	.	GRCh37	7	107217834	107217834	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783C>G	p.Ile261Met	p.I261M	ENST00000265720	8/8	103	94	9	76	76	0	DUS4L,missense_variant,p.Ile140Met,ENST00000402620,;DUS4L,missense_variant,p.Ile261Met,ENST00000265720,;BCAP29,upstream_gene_variant,,ENST00000479917,;BCAP29,upstream_gene_variant,,ENST00000379119,;BCAP29,upstream_gene_variant,,ENST00000465919,;BCAP29,upstream_gene_variant,,ENST00000421217,;BCAP29,upstream_gene_variant,,ENST00000473124,;BCAP29,upstream_gene_variant,,ENST00000445771,;BCAP29,upstream_gene_variant,,ENST00000005259,;BCAP29,upstream_gene_variant,,ENST00000457837,;BCAP29,upstream_gene_variant,,ENST00000379117,;RP4-593H12.1,downstream_gene_variant,,ENST00000610269,;BCAP29,upstream_gene_variant,,ENST00000466094,;BCAP29,upstream_gene_variant,,ENST00000494086,;DUS4L,3_prime_UTR_variant,,ENST00000431839,;DUS4L,3_prime_UTR_variant,,ENST00000436411,;DUS4L,3_prime_UTR_variant,,ENST00000422290,;DUS4L,3_prime_UTR_variant,,ENST00000443233,;DUS4L,non_coding_transcript_exon_variant,,ENST00000485825,;DUS4L,downstream_gene_variant,,ENST00000497798,;DUS4L,downstream_gene_variant,,ENST00000471763,;BCAP29,upstream_gene_variant,,ENST00000482371,;DUS4L,downstream_gene_variant,,ENST00000458611,;BCAP29,upstream_gene_variant,,ENST00000442065,;BCAP29,upstream_gene_variant,,ENST00000486326,;	G	ENSG00000105865	ENST00000265720	Transcript	missense_variant	1145	783	261	I/M	atC/atG	.	.	.	1	DUS4L	HGNC	21517	protein_coding	YES	CCDS5745.1	ENSP00000265720	DUS4L_HUMAN	A4D0R5_HUMAN,F8WEL2_HUMAN,B4DFH2_HUMAN	UPI000006DD5D	.	deleterious(0)	possibly_damaging(0.781)	8/8	.	hmmpanther:PTHR11082,hmmpanther:PTHR11082:SF25,Pfam_domain:PF01207,PIRSF_domain:PIRSF006621,Superfamily_domains:SSF51395	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCATCTGGGA	.	3	ESCA
SCIN	0	.	GRCh37	7	12644288	12644288	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.666G>A	p.%3D	p.K222K	ENST00000297029	4/16	54	49	5	56	56	0	SCIN,synonymous_variant,p.%3D,ENST00000518849,;SCIN,synonymous_variant,p.%3D,ENST00000523729,;SCIN,synonymous_variant,p.%3D,ENST00000297029,;SCIN,splice_region_variant,,ENST00000445618,;SCIN,splice_region_variant,,ENST00000519209,;SCIN,splice_region_variant,,ENST00000486980,;SCIN,synonymous_variant,p.%3D,ENST00000341757,;	A	ENSG00000006747	ENST00000297029	Transcript	synonymous_variant	767	666	222	K	aaG/aaA	.	.	.	1	SCIN	HGNC	21695	protein_coding	YES	CCDS47545.1	ENSP00000297029	ADSV_HUMAN	Q8NBV9_HUMAN,Q75MG0_HUMAN	UPI000013C4DF	.	.	.	4/16	.	hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF14,Gene3D:3.40.20.10,SMART_domains:SM00262,Superfamily_domains:SSF55753	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATAAAGGTATT	.	3	ESCA
MKLN1	0	.	GRCh37	7	131175644	131175644	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3157C>G	.	.	ENST00000352689	18/18	25	20	5	25	25	0	MKLN1,3_prime_UTR_variant,,ENST00000352689,;MKLN1,downstream_gene_variant,,ENST00000421797,;RP11-180C16.1,downstream_gene_variant,,ENST00000610193,;MKLN1,downstream_gene_variant,,ENST00000498778,;MKLN1,downstream_gene_variant,,ENST00000458153,;MKLN1,downstream_gene_variant,,ENST00000468830,;	G	ENSG00000128585	ENST00000352689	Transcript	3_prime_UTR_variant	5405	.	.	.	.	.	.	.	1	MKLN1	HGNC	7109	protein_coding	YES	CCDS34754.1	ENSP00000323527	MKLN1_HUMAN	F8WEY7_HUMAN,C9JXB0_HUMAN,C9JWX9_HUMAN,C9JVL5_HUMAN,C9J7E8_HUMAN	UPI0000034CB0	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATCTAGCC	.	5	ESCA
TRPV5	0	.	GRCh37	7	142622702	142622702	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1044C>T	p.%3D	p.V348V	ENST00000265310	8/15	46	40	5	40	40	0	TRPV5,synonymous_variant,p.%3D,ENST00000442623,;TRPV5,synonymous_variant,p.%3D,ENST00000439304,;TRPV5,synonymous_variant,p.%3D,ENST00000265310,;	A	ENSG00000127412	ENST00000265310	Transcript	synonymous_variant	1393	1044	348	V	gtC/gtT	.	.	.	-1	TRPV5	HGNC	3145	protein_coding	YES	CCDS5875.1	ENSP00000265310	TRPV5_HUMAN	Q9H480_HUMAN	UPI0000052B76	.	.	.	8/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10582:SF11,hmmpanther:PTHR10582,TIGRFAM_domain:TIGR00870,Prints_domain:PR01765	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGTAGACGCA	.	4	ESCA
DGKB	0	.	GRCh37	7	14661089	14661089	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1201A>G	p.Ser401Gly	p.S401G	ENST00000403951	15/26	110	95	14	103	103	0	DGKB,missense_variant,p.Ser401Gly,ENST00000258767,;DGKB,missense_variant,p.Ser382Gly,ENST00000444700,;DGKB,missense_variant,p.Ser401Gly,ENST00000403951,;DGKB,missense_variant,p.Ser400Gly,ENST00000402815,;DGKB,missense_variant,p.Ser393Gly,ENST00000407950,;DGKB,missense_variant,p.Ser401Gly,ENST00000406247,;DGKB,missense_variant,p.Ser401Gly,ENST00000399322,;DGKB,non_coding_transcript_exon_variant,,ENST00000403963,;DGKB,non_coding_transcript_exon_variant,,ENST00000471732,;DGKB,non_coding_transcript_exon_variant,,ENST00000477401,;	C	ENSG00000136267	ENST00000403951	Transcript	missense_variant	1621	1201	401	S/G	Agt/Ggt	.	.	.	-1	DGKB	HGNC	2850	protein_coding	YES	CCDS47547.1	ENSP00000385780	DGKB_HUMAN	C9JA18_HUMAN,B7Z3B3_HUMAN	UPI0000033B9B	.	tolerated(0.2)	benign(0)	15/26	.	hmmpanther:PTHR11255:SF32,hmmpanther:PTHR11255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCACTCTTTT	.	4	ESCA
NOS3	0	.	GRCh37	7	150707823	150707823	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2824G>T	p.Val942Phe	p.V942F	ENST00000297494	22/27	34	22	12	28	28	0	NOS3,missense_variant,p.Val736Phe,ENST00000461406,;NOS3,missense_variant,p.Val942Phe,ENST00000297494,;NOS3,missense_variant,p.Val236Phe,ENST00000475017,;ATG9B,downstream_gene_variant,,ENST00000444312,;ATG9B,downstream_gene_variant,,ENST00000605938,;ATG9B,downstream_gene_variant,,ENST00000377974,;NOS3,non_coding_transcript_exon_variant,,ENST00000477227,;NOS3,non_coding_transcript_exon_variant,,ENST00000468293,;ATG9B,downstream_gene_variant,,ENST00000476282,;ATG9B,downstream_gene_variant,,ENST00000498521,;ATG9B,downstream_gene_variant,,ENST00000464855,;ATG9B,downstream_gene_variant,,ENST00000494791,;ATG9B,downstream_gene_variant,,ENST00000473698,;NOS3,downstream_gene_variant,,ENST00000473057,;ATG9B,downstream_gene_variant,,ENST00000486407,;ATG9B,downstream_gene_variant,,ENST00000471797,;ATG9B,downstream_gene_variant,,ENST00000404733,;NOS3,upstream_gene_variant,,ENST00000475454,;ATG9B,downstream_gene_variant,,ENST00000469530,;	T	ENSG00000164867	ENST00000297494	Transcript	missense_variant	3181	2824	942	V/F	Gtc/Ttc	.	.	.	1	NOS3	HGNC	7876	protein_coding	YES	CCDS5912.1	ENSP00000297494	NOS3_HUMAN	Q96P37_HUMAN,Q96J98_HUMAN,O14937_HUMAN,E7ESA7_HUMAN	UPI000013E417	.	deleterious(0)	possibly_damaging(0.847)	22/27	.	PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF66,Pfam_domain:PF00667,Gene3D:2.40.30.10,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF63380,Prints_domain:PR00371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCAGTCAGC	.	5	ESCA
CDCA7L	0	.	GRCh37	7	21941742	21941742	+	3'UTR	SNP	A	A	G	rs113159246	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*198T>C	.	.	ENST00000406877	10/10	23	18	5	27	27	0	CDCA7L,3_prime_UTR_variant,,ENST00000406877,;CDCA7L,3_prime_UTR_variant,,ENST00000373934,;CDCA7L,3_prime_UTR_variant,,ENST00000356195,;CDCA7L,downstream_gene_variant,,ENST00000435717,;DNAH11,downstream_gene_variant,,ENST00000328843,;DNAH11,downstream_gene_variant,,ENST00000409508,;CDCA7L,downstream_gene_variant,,ENST00000465490,;CDCA7L,non_coding_transcript_exon_variant,,ENST00000488845,;DNAH11,downstream_gene_variant,,ENST00000479878,;CDCA7L,downstream_gene_variant,,ENST00000489669,;	G	ENSG00000164649	ENST00000406877	Transcript	3_prime_UTR_variant	1843	.	.	.	.	rs113159246	.	.	-1	CDCA7L	HGNC	30777	protein_coding	YES	CCDS5374.1	ENSP00000383986	CDA7L_HUMAN	C9JFL7_HUMAN	UPI000000D840	.	.	.	10/10	.	.	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCTATATAG	by1000G	2	ESCA
AMZ1	0	.	GRCh37	7	2740059	2740059	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-27G>A	.	.	ENST00000312371	2/7	15	7	8	9	9	0	AMZ1,5_prime_UTR_variant,,ENST00000407112,;AMZ1,5_prime_UTR_variant,,ENST00000312371,;AMZ1,upstream_gene_variant,,ENST00000489665,;AMZ1,upstream_gene_variant,,ENST00000485540,;AMZ1,upstream_gene_variant,,ENST00000480560,;	A	ENSG00000174945	ENST00000312371	Transcript	5_prime_UTR_variant	342	.	.	.	.	.	.	.	1	AMZ1	HGNC	22231	protein_coding	YES	CCDS34589.1	ENSP00000308149	AMZ1_HUMAN	B4DIY9_HUMAN,A4D202_HUMAN	UPI00001C1E77	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCCAGGAGTG	.	3	ESCA
HEATR2	0	.	GRCh37	7	769417	769417	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.713G>C	p.Gly238Ala	p.G238A	ENST00000297440	2/13	65	57	7	48	48	0	HEATR2,missense_variant,p.Gly238Ala,ENST00000313147,;HEATR2,missense_variant,p.Gly238Ala,ENST00000297440,;HEATR2,missense_variant,p.Gly40Ala,ENST00000440747,;HEATR2,intron_variant,,ENST00000437419,;PRKAR1B,upstream_gene_variant,,ENST00000403562,;PRKAR1B,upstream_gene_variant,,ENST00000417852,;PRKAR1B,upstream_gene_variant,,ENST00000537384,;HEATR2,non_coding_transcript_exon_variant,,ENST00000438961,;PRKAR1B,upstream_gene_variant,,ENST00000478198,;PRKAR1B,upstream_gene_variant,,ENST00000488474,;	C	ENSG00000164818	ENST00000297440	Transcript	missense_variant	733	713	238	G/A	gGc/gCc	.	.	.	1	HEATR2	HGNC	26013	protein_coding	YES	CCDS34580.1	ENSP00000297440	HEAT2_HUMAN	.	UPI0000D61BE2	.	deleterious(0.01)	probably_damaging(0.986)	2/13	.	hmmpanther:PTHR16216:SF2,hmmpanther:PTHR16216,Pfam_domain:PF13646,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTGGCAACG	.	4	ESCA
ZNF804B	0	.	GRCh37	7	88965830	88965830	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3534T>C	p.%3D	p.L1178L	ENST00000333190	4/4	55	50	5	42	41	0	ZNF804B,synonymous_variant,p.%3D,ENST00000333190,;	C	ENSG00000182348	ENST00000333190	Transcript	synonymous_variant	4143	3534	1178	L	ctT/ctC	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	.	.	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CATCTTCGAGT	.	3	ESCA
FBXO43	0	.	GRCh37	8	101145905	101145905	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*125T>C	.	.	ENST00000428847	5/5	28	19	9	40	40	0	FBXO43,3_prime_UTR_variant,,ENST00000428847,;RGS22,upstream_gene_variant,,ENST00000520117,;FBXO43,3_prime_UTR_variant,,ENST00000517806,;FBXO43,downstream_gene_variant,,ENST00000520987,;	G	ENSG00000156509	ENST00000428847	Transcript	3_prime_UTR_variant	2569	.	.	.	.	.	.	.	-1	FBXO43	HGNC	28521	protein_coding	YES	CCDS47904.1	ENSP00000403293	FBX43_HUMAN	.	UPI000013DE8F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAATATATAC	.	5	ESCA
NKX2-6	0	.	GRCh37	8	23560288	23560288	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.582G>T	p.Lys194Asn	p.K194N	ENST00000325017	2/2	58	47	10	39	39	0	NKX2-6,missense_variant,p.Lys194Asn,ENST00000325017,;NKX2-6,missense_variant,p.Lys112Asn,ENST00000418222,;RP11-175E9.1,upstream_gene_variant,,ENST00000523874,;	A	ENSG00000180053	ENST00000325017	Transcript	missense_variant	582	582	194	K/N	aaG/aaT	.	.	.	-1	NKX2-6	HGNC	32940	protein_coding	YES	.	ENSP00000320089	NKX26_HUMAN	C9JML6_HUMAN	UPI000016092C	.	deleterious(0)	possibly_damaging(0.522)	2/2	.	hmmpanther:PTHR24340:SF15,hmmpanther:PTHR24340,SMART_domains:SM00389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCGACTTGTC	.	5	ESCA
EFCAB1	0	.	GRCh37	8	49644005	49644005	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116T>C	p.Val39Ala	p.V39A	ENST00000262103	2/6	31	23	7	43	43	0	EFCAB1,missense_variant,p.Val39Ala,ENST00000262103,;EFCAB1,intron_variant,,ENST00000523092,;EFCAB1,intron_variant,,ENST00000433756,;EFCAB1,upstream_gene_variant,,ENST00000523008,;EFCAB1,upstream_gene_variant,,ENST00000522254,;EFCAB1,intron_variant,,ENST00000521721,;EFCAB1,intron_variant,,ENST00000521002,;EFCAB1,intron_variant,,ENST00000521701,;EFCAB1,upstream_gene_variant,,ENST00000519425,;	G	ENSG00000034239	ENST00000262103	Transcript	missense_variant	197	116	39	V/A	gTa/gCa	.	.	.	-1	EFCAB1	HGNC	25678	protein_coding	YES	CCDS6145.1	ENSP00000262103	EFCB1_HUMAN	.	UPI000006E520	.	tolerated(1)	benign(0)	2/6	.	hmmpanther:PTHR23055,hmmpanther:PTHR23055:SF75,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTACTCCT	.	5	ESCA
VCPIP1	0	.	GRCh37	8	67547064	67547064	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3341C>T	p.Ser1114Phe	p.S1114F	ENST00000310421	3/3	21	17	4	32	32	0	VCPIP1,missense_variant,p.Ser1114Phe,ENST00000310421,;	A	ENSG00000175073	ENST00000310421	Transcript	missense_variant	3600	3341	1114	S/F	tCt/tTt	.	.	.	-1	VCPIP1	HGNC	30897	protein_coding	YES	CCDS6192.1	ENSP00000309031	VCIP1_HUMAN	.	UPI00001D3EF3	.	deleterious_low_confidence(0)	probably_damaging(0.996)	3/3	.	hmmpanther:PTHR14843,hmmpanther:PTHR14843:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TAGAAGAAACC	.	4	ESCA
CALB1	0	.	GRCh37	8	91095045	91095045	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-120C>G	.	.	ENST00000265431	1/11	19	16	3	19	19	0	CALB1,5_prime_UTR_variant,,ENST00000265431,;CALB1,intron_variant,,ENST00000514406,;CALB1,intron_variant,,ENST00000520613,;CALB1,intron_variant,,ENST00000523716,;CALB1,upstream_gene_variant,,ENST00000518457,;CALB1,non_coding_transcript_exon_variant,,ENST00000482702,;CALB1,upstream_gene_variant,,ENST00000473670,;CALB1,upstream_gene_variant,,ENST00000476853,;	C	ENSG00000104327	ENST00000265431	Transcript	5_prime_UTR_variant	63	.	.	.	.	.	.	.	-1	CALB1	HGNC	1434	protein_coding	YES	CCDS6251.1	ENSP00000265431	CALB1_HUMAN	O75552_HUMAN,E5RIZ8_HUMAN,E5RG14_HUMAN,B7Z9J4_HUMAN	UPI000013D620	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCGCGGGCGC	.	2	ESCA
TMEM246	0	.	GRCh37	9	104238534	104238534	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841A>G	p.Met281Val	p.M281V	ENST00000374851	4/4	24	17	7	28	28	0	TMEM246,missense_variant,p.Met281Val,ENST00000374851,;TMEM246,missense_variant,p.Met281Val,ENST00000374847,;TMEM246,missense_variant,p.Met281Val,ENST00000374848,;RP11-490D19.6,intron_variant,,ENST00000425734,;RP11-490D19.6,intron_variant,,ENST00000431507,;RP11-490D19.6,intron_variant,,ENST00000450109,;RP11-490D19.6,intron_variant,,ENST00000424154,;	C	ENSG00000165152	ENST00000374851	Transcript	missense_variant	1989	841	281	M/V	Atg/Gtg	.	.	.	-1	TMEM246	HGNC	28180	protein_coding	YES	CCDS6757.1	ENSP00000363984	TM246_HUMAN	.	UPI000006D08E	.	tolerated(0.51)	benign(0)	4/4	.	hmmpanther:PTHR31410,hmmpanther:PTHR31410:SF1,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCTCATGTATA	.	4	ESCA
NOTCH1	0	.	GRCh37	9	139411817	139411817	+	Missense_Mutation	SNP	C	C	T	rs753661188	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1462G>A	p.Glu488Lys	p.E488K	ENST00000277541	9/34	58	42	16	20	20	0	NOTCH1,missense_variant,p.Glu488Lys,ENST00000277541,;MIR4673,downstream_gene_variant,,ENST00000584777,;	T	ENSG00000148400	ENST00000277541	Transcript	missense_variant	1538	1462	488	E/K	Gag/Aag	rs753661188	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	deleterious(0.01)	possibly_damaging(0.812)	9/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184,Prints_domain:PR01983	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G484V|c.1451G>T|3,BUFFER|p.G484V|c.1451G>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCTCGCAGT	byFrequency	5	ESCA
ZNF658	0	.	GRCh37	9	40774731	40774731	+	Missense_Mutation	SNP	C	C	T	rs759327187	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544G>A	p.Ala182Thr	p.A182T	ENST00000602553	5/5	92	85	7	98	98	0	ZNF658,missense_variant,p.Ala180Thr,ENST00000441795,;ZNF658,missense_variant,p.Ala182Thr,ENST00000377626,;ZNF658,missense_variant,p.Ala182Thr,ENST00000602553,;ZNF658,missense_variant,p.Ala182Thr,ENST00000479710,;	T	ENSG00000196409	ENST00000602553	Transcript	missense_variant	839	544	182	A/T	Gct/Act	rs759327187	.	.	-1	ZNF658	HGNC	25226	protein_coding	YES	CCDS35023.1	ENSP00000473484	ZN658_HUMAN	B3KNB1_HUMAN	UPI000046D388	.	tolerated(1)	benign(0)	5/5	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF256	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGAGCTTTCT	.	2	ESCA
SMC5	0	.	GRCh37	9	72915086	72915086	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1434A>G	p.%3D	p.K478K	ENST00000361138	10/25	51	24	27	36	36	0	SMC5,synonymous_variant,p.%3D,ENST00000361138,;	G	ENSG00000198887	ENST00000361138	Transcript	synonymous_variant	1492	1434	478	K	aaA/aaG	.	.	.	1	SMC5	HGNC	20465	protein_coding	YES	CCDS6632.1	ENSP00000354957	SMC5_HUMAN	.	UPI000036763A	.	.	.	10/25	.	hmmpanther:PTHR19306:SF1,hmmpanther:PTHR19306,Pfam_domain:PF02463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAAACAAAG	.	5	ESCA
CTSL3P	0	.	GRCh37	9	90388070	90388070	+	RNA	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.297G>A	.	.	ENST00000412179	3/5	121	108	13	108	108	0	CTSL3P,non_coding_transcript_exon_variant,,ENST00000354530,;CTSL3P,non_coding_transcript_exon_variant,,ENST00000412179,;	A	ENSG00000188029	ENST00000412179	Transcript	non_coding_transcript_exon_variant	297	.	.	.	.	.	.	.	1	CTSL3P	HGNC	33132	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGAAGGGGAA	.	4	ESCA
MAP7D3	0	.	GRCh37	X	135313964	135313964	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1152A>G	p.%3D	p.A384A	ENST00000316077	8/19	14	10	4	9	9	0	MAP7D3,synonymous_variant,p.%3D,ENST00000370663,;MAP7D3,synonymous_variant,p.%3D,ENST00000370661,;MAP7D3,synonymous_variant,p.%3D,ENST00000370660,;MAP7D3,synonymous_variant,p.%3D,ENST00000316077,;MAP7D3,upstream_gene_variant,,ENST00000477124,;MAP7D3,upstream_gene_variant,,ENST00000495432,;MAP7D3,upstream_gene_variant,,ENST00000489788,;	C	ENSG00000129680	ENST00000316077	Transcript	synonymous_variant	1373	1152	384	A	gcA/gcG	.	.	.	-1	MAP7D3	HGNC	25742	protein_coding	YES	CCDS44004.1	ENSP00000318086	MA7D3_HUMAN	.	UPI00001C207C	.	.	.	8/19	.	hmmpanther:PTHR15073:SF5,hmmpanther:PTHR15073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGATGCTAC	.	2	ESCA
PLXNB3	0	.	GRCh37	X	153044743	153044743	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*249G>A	.	.	ENST00000538966	37/37	37	23	14	41	41	0	PLXNB3,3_prime_UTR_variant,,ENST00000538966,;SRPK3,5_prime_UTR_variant,,ENST00000489426,;PLXNB3,3_prime_UTR_variant,,ENST00000538776,;PLXNB3,3_prime_UTR_variant,,ENST00000361971,;PLXNB3,downstream_gene_variant,,ENST00000411613,;SRPK3,upstream_gene_variant,,ENST00000370108,;SRPK3,upstream_gene_variant,,ENST00000370100,;PLXNB3,downstream_gene_variant,,ENST00000455214,;PLXNB3,downstream_gene_variant,,ENST00000448847,;SRPK3,upstream_gene_variant,,ENST00000430541,;SRPK3,upstream_gene_variant,,ENST00000393786,;PLXNB3,downstream_gene_variant,,ENST00000538282,;SRPK3,upstream_gene_variant,,ENST00000370104,;SRPK3,upstream_gene_variant,,ENST00000370101,;PLXNB3,non_coding_transcript_exon_variant,,ENST00000472415,;PLXNB3,non_coding_transcript_exon_variant,,ENST00000469190,;PLXNB3,downstream_gene_variant,,ENST00000485980,;PLXNB3,downstream_gene_variant,,ENST00000482654,;	A	ENSG00000198753	ENST00000538966	Transcript	3_prime_UTR_variant	6319	.	.	.	.	.	.	.	1	PLXNB3	HGNC	9105	protein_coding	YES	CCDS55536.1	ENSP00000442736	PLXB3_HUMAN	.	UPI0001AFF680	.	.	.	37/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTGCCTGC	.	5	ESCA
L1CAM	0	.	GRCh37	X	153130787	153130787	+	Missense_Mutation	SNP	C	C	T	rs782505398	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2716G>A	p.Ala906Thr	p.A906T	ENST00000370060	21/29	19	9	9	11	11	0	L1CAM,missense_variant,p.Ala908Thr,ENST00000538883,;L1CAM,missense_variant,p.Ala906Thr,ENST00000370060,;L1CAM,missense_variant,p.Ala901Thr,ENST00000370055,;L1CAM,missense_variant,p.Ala901Thr,ENST00000361981,;L1CAM,missense_variant,p.Ala908Thr,ENST00000543994,;L1CAM,missense_variant,p.Ala906Thr,ENST00000361699,;L1CAM,missense_variant,p.Ala906Thr,ENST00000370057,;L1CAM,upstream_gene_variant,,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000455590,;L1CAM,non_coding_transcript_exon_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000484652,;L1CAM,upstream_gene_variant,,ENST00000491983,;	T	ENSG00000198910	ENST00000370060	Transcript	missense_variant	2906	2716	906	A/T	Gcc/Acc	rs782505398	.	.	-1	L1CAM	HGNC	6470	protein_coding	YES	CCDS14733.1	ENSP00000359077	L1CAM_HUMAN	Q86SE4_HUMAN,Q7Z3Z9_HUMAN,Q7Z2J9_HUMAN,Q7Z2J8_HUMAN,Q7Z2J6_HUMAN,Q7Z2J0_HUMAN,Q7Z2I3_HUMAN,Q7Z2H2_HUMAN,Q7Z2F9_HUMAN,E9PHJ4_HUMAN,E7EPI4_HUMAN	UPI0000126E89	.	tolerated(0.42)	benign(0.39)	21/29	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF42,Gene3D:2.60.40.10,Pfam_domain:PF00041,Superfamily_domains:SSF49265	T:0.0005	T:0	T:0	.	T:0.002	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGCGGGCC	byFrequency|byCluster|by1000G	5	ESCA
F8	0	.	GRCh37	X	154158117	154158117	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3948A>G	p.Ile1316Met	p.I1316M	ENST00000360256	14/26	30	27	3	30	30	0	F8,missense_variant,p.Ile1316Met,ENST00000360256,;	C	ENSG00000185010	ENST00000360256	Transcript	missense_variant	4149	3948	1316	I/M	atA/atG	.	.	.	-1	F8	HGNC	3546	protein_coding	YES	CCDS35457.1	ENSP00000353393	FA8_HUMAN	Q9UQQ5_HUMAN,Q71UI6_HUMAN,Q2VF45_HUMAN,Q003V9_HUMAN,Q003V5_HUMAN,A0FJ19_HUMAN,A0A2G6_HUMAN	UPI000012A416	.	tolerated(1)	benign(0.001)	14/26	.	hmmpanther:PTHR10127:SF50,hmmpanther:PTHR10127,PIRSF_domain:PIRSF000354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGATATCCT	.	2	ESCA
FOXR2	0	.	GRCh37	X	55651695	55651695	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*615C>A	.	.	ENST00000339140	1/1	32	21	10	39	39	0	FOXR2,3_prime_UTR_variant,,ENST00000339140,;	A	ENSG00000189299	ENST00000339140	Transcript	3_prime_UTR_variant	1863	.	.	.	.	.	.	.	1	FOXR2	HGNC	30469	protein_coding	YES	CCDS35308.1	ENSP00000427329	FOXR2_HUMAN	.	UPI00001603CE	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAACGTCCT	.	5	ESCA
ZXDB	0	.	GRCh37	X	57619961	57619961	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1480T>C	p.Ser494Pro	p.S494P	ENST00000374888	1/1	27	20	7	22	22	0	ZXDB,missense_variant,p.Ser494Pro,ENST00000374888,;	C	ENSG00000198455	ENST00000374888	Transcript	missense_variant	1693	1480	494	S/P	Tct/Cct	.	.	.	1	ZXDB	HGNC	13199	protein_coding	YES	CCDS35313.1	ENSP00000364023	ZXDB_HUMAN	.	UPI000013C495	.	deleterious(0)	probably_damaging(0.991)	1/1	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF00096,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR19818:SF72,hmmpanther:PTHR19818,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAATCTTTC	.	5	ESCA
ASB12	0	.	GRCh37	X	63444300	63444300	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.872C>A	p.Ala291Asp	p.A291D	ENST00000362002	3/3	28	13	15	21	21	0	ASB12,missense_variant,p.Ala282Asp,ENST00000396130,;MTMR8,missense_variant,p.Ala666Asp,ENST00000453546,;ASB12,missense_variant,p.Ala291Asp,ENST00000362002,;	T	ENSG00000198881	ENST00000362002	Transcript	missense_variant	1065	872	291	A/D	gCc/gAc	.	.	.	-1	ASB12	HGNC	19763	protein_coding	YES	CCDS14378.2	ENSP00000355195	ASB12_HUMAN	.	UPI000013DA93	.	tolerated(0.2)	probably_damaging(0.951)	3/3	.	hmmpanther:PTHR24120,Pfam_domain:PF07525,SMART_domains:SM00969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAAGGCTCTG	.	5	ESCA
KIAA2022	0	.	GRCh37	X	73963734	73963734	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-IG-A50L-01A-11D-A27G-09	TCGA-IG-A50L-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658A>G	p.Thr220Ala	p.T220A	ENST00000055682	3/4	26	15	10	23	23	0	KIAA2022,missense_variant,p.Thr220Ala,ENST00000055682,;KIAA2022,upstream_gene_variant,,ENST00000424929,;	C	ENSG00000050030	ENST00000055682	Transcript	missense_variant	1270	658	220	T/A	Act/Gct	COSM1125257	.	.	-1	KIAA2022	HGNC	29433	protein_coding	YES	CCDS35337.1	ENSP00000055682	K2022_HUMAN	.	UPI00001C207B	.	tolerated(1)	benign(0.001)	3/4	.	hmmpanther:PTHR10322:SF2,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAGTTTCTC	.	5	ESCA
C10orf90	0	.	GRCh37	10	128193492	128193492	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277G>A	p.Gly93Arg	p.G93R	ENST00000284694	3/9	46	40	6	33	33	0	C10orf90,missense_variant,p.Gly46Arg,ENST00000488181,;C10orf90,missense_variant,p.Gly46Arg,ENST00000356858,;C10orf90,missense_variant,p.Gly46Arg,ENST00000392694,;C10orf90,missense_variant,p.Gly93Arg,ENST00000432642,;C10orf90,missense_variant,p.Gly93Arg,ENST00000284694,;C10orf90,missense_variant,p.Gly93Arg,ENST00000454341,;C10orf90,missense_variant,p.Gly190Arg,ENST00000544758,;C10orf90,upstream_gene_variant,,ENST00000424927,;C10orf90,non_coding_transcript_exon_variant,,ENST00000368674,;C10orf90,3_prime_UTR_variant,,ENST00000463082,;	T	ENSG00000154493	ENST00000284694	Transcript	missense_variant	398	277	93	G/R	Gga/Aga	.	.	.	-1	C10orf90	HGNC	26563	protein_coding	YES	CCDS31310.1	ENSP00000284694	CJ090_HUMAN	S4R3N7_HUMAN,Q5T025_HUMAN	UPI00001D808F	.	tolerated(0.16)	benign(0.007)	3/9	.	hmmpanther:PTHR21553:SF10,hmmpanther:PTHR21553	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTCCGCTGC	.	5	ESCA
PITRM1	0	.	GRCh37	10	3212331	3212331	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124C>G	p.Leu42Val	p.L42V	ENST00000380989	2/27	71	64	7	55	55	0	PITRM1,missense_variant,p.Leu42Val,ENST00000380989,;PITRM1,missense_variant,p.Leu42Val,ENST00000224949,;PITRM1,intron_variant,,ENST00000451104,;PITRM1-AS1,downstream_gene_variant,,ENST00000598280,;PITRM1,upstream_gene_variant,,ENST00000488065,;	C	ENSG00000107959	ENST00000380989	Transcript	missense_variant	163	124	42	L/V	Cta/Gta	.	.	.	-1	PITRM1	HGNC	17663	protein_coding	YES	CCDS55699.1	ENSP00000370377	PREP_HUMAN	.	UPI00015E00B2	.	tolerated(0.6)	benign(0.001)	2/27	.	hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF68	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCTAGTTTAT	.	3	ESCA
ZNF503	0	.	GRCh37	10	77158178	77158179	+	3'UTR	DEL	AT	AT	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	AT	AT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*328_*329delAT	.	.	ENST00000372524	2/2	14	8	6	10	10	0	ZNF503,3_prime_UTR_variant,,ENST00000372524,;ZNF503,downstream_gene_variant,,ENST00000535216,;RP11-399K21.11,intron_variant,,ENST00000418818,;ZNF503-AS2,upstream_gene_variant,,ENST00000425916,;ZNF503-AS2,upstream_gene_variant,,ENST00000486015,;ZNF503-AS2,upstream_gene_variant,,ENST00000466942,;ZNF503-AS2,upstream_gene_variant,,ENST00000438638,;	-	ENSG00000165655	ENST00000372524	Transcript	3_prime_UTR_variant	2756-2757	.	.	.	.	.	.	.	-1	ZNF503	HGNC	23589	protein_coding	YES	CCDS7350.1	ENSP00000361602	ZN503_HUMAN	B3KXM8_HUMAN	UPI000004A951	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCTAACATAAATA	.	2	ESCA
GRID1	0	.	GRCh37	10	87379698	87379698	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2286C>T	p.%3D	p.G762G	ENST00000327946	14/16	61	51	10	44	44	0	GRID1,synonymous_variant,p.%3D,ENST00000536331,;GRID1,synonymous_variant,p.%3D,ENST00000327946,;GRID1,intron_variant,,ENST00000464741,;	A	ENSG00000182771	ENST00000327946	Transcript	synonymous_variant	2372	2286	762	G	ggC/ggT	.	.	.	-1	GRID1	HGNC	4575	protein_coding	YES	CCDS31236.1	ENSP00000330148	GRID1_HUMAN	B7Z7L0_HUMAN	UPI00001D8051	.	.	.	14/16	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF108,Pfam_domain:PF00060,Pfam_domain:PF00497,SMART_domains:SM00079,Superfamily_domains:SSF53850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTTGCCGAT	.	4	ESCA
RDX	0	.	GRCh37	11	110104066	110104066	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1483G>C	p.Glu495Gln	p.E495Q	ENST00000405097	13/16	93	77	16	92	92	0	RDX,missense_variant,p.Glu495Gln,ENST00000343115,;RDX,missense_variant,p.Glu359Gln,ENST00000544551,;RDX,missense_variant,p.Glu165Gln,ENST00000530085,;RDX,missense_variant,p.Glu148Gln,ENST00000528900,;RDX,missense_variant,p.Glu495Gln,ENST00000528498,;RDX,missense_variant,p.Glu495Gln,ENST00000405097,;RDX,intron_variant,,ENST00000530301,;RDX,missense_variant,p.Glu495Gln,ENST00000530749,;RDX,3_prime_UTR_variant,,ENST00000530131,;RDX,non_coding_transcript_exon_variant,,ENST00000527537,;RDX,non_coding_transcript_exon_variant,,ENST00000532461,;RDX,non_coding_transcript_exon_variant,,ENST00000533961,;	G	ENSG00000137710	ENST00000405097	Transcript	missense_variant	1793	1483	495	E/Q	Gaa/Caa	.	.	.	-1	RDX	HGNC	9944	protein_coding	YES	CCDS58174.1	ENSP00000384136	RADI_HUMAN	Q9NST9_HUMAN,E9PQ82_HUMAN,E9PNV3_HUMAN,E9PKN5_HUMAN,B0YJ88_HUMAN	UPI0000EE3914	.	tolerated(0.15)	benign(0.168)	13/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23281,Pfam_domain:PF00769,PIRSF_domain:PIRSF002305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTCAGCAT	.	5	ESCA
GLB1L3	0	.	GRCh37	11	134179627	134179627	+	Missense_Mutation	SNP	G	G	A	rs766442756	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1069G>A	p.Gly357Arg	p.G357R	ENST00000431683	11/20	26	20	6	21	21	0	GLB1L3,missense_variant,p.Gly357Arg,ENST00000431683,;GLB1L3,downstream_gene_variant,,ENST00000389887,;GLB1L3,missense_variant,p.Gly42Arg,ENST00000455971,;GLB1L3,non_coding_transcript_exon_variant,,ENST00000410100,;GLB1L3,non_coding_transcript_exon_variant,,ENST00000486034,;GLB1L3,non_coding_transcript_exon_variant,,ENST00000467068,;GLB1L3,intron_variant,,ENST00000498012,;	A	ENSG00000166105	ENST00000431683	Transcript	missense_variant	1069	1069	357	G/R	Ggg/Agg	rs766442756	.	.	1	GLB1L3	HGNC	25147	protein_coding	YES	CCDS44780.1	ENSP00000396615	GLBL3_HUMAN	.	UPI0001633637	.	tolerated(0.23)	possibly_damaging(0.625)	11/20	.	hmmpanther:PTHR23421,hmmpanther:PTHR23421:SF59,Gene3D:3.20.20.80,Pfam_domain:PF01301,PIRSF_domain:PIRSF006336,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCGGGAAG	.	5	ESCA
KIF18A	0	.	GRCh37	11	28080629	28080629	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1792G>A	p.Glu598Lys	p.E598K	ENST00000263181	13/17	73	58	15	63	63	0	KIF18A,missense_variant,p.Glu598Lys,ENST00000263181,;MIR610,downstream_gene_variant,,ENST00000385139,;	T	ENSG00000121621	ENST00000263181	Transcript	missense_variant	2083	1792	598	E/K	Gaa/Aaa	.	.	.	-1	KIF18A	HGNC	29441	protein_coding	YES	CCDS7867.1	ENSP00000263181	KI18A_HUMAN	.	UPI0000037CCC	.	deleterious(0.04)	benign(0.427)	13/17	.	hmmpanther:PTHR24115:SF399,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCAAAAG	.	5	ESCA
SIGIRR	0	.	GRCh37	11	406002	406002	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1127C>T	p.Ser376Leu	p.S376L	ENST00000431843	10/10	53	43	10	36	36	0	SIGIRR,missense_variant,p.Ser108Leu,ENST00000526395,;SIGIRR,missense_variant,p.Ser376Leu,ENST00000397632,;SIGIRR,missense_variant,p.Ser376Leu,ENST00000431843,;SIGIRR,missense_variant,p.Ser96Leu,ENST00000528845,;SIGIRR,missense_variant,p.Ser376Leu,ENST00000332725,;SIGIRR,synonymous_variant,p.%3D,ENST00000382520,;SIGIRR,synonymous_variant,p.%3D,ENST00000531205,;SIGIRR,downstream_gene_variant,,ENST00000528058,;PKP3,downstream_gene_variant,,ENST00000525642,;SIGIRR,downstream_gene_variant,,ENST00000528209,;PKP3,downstream_gene_variant,,ENST00000331563,;SIGIRR,downstream_gene_variant,,ENST00000530494,;SIGIRR,downstream_gene_variant,,ENST00000530683,;SIGIRR,downstream_gene_variant,,ENST00000527136,;SIGIRR,downstream_gene_variant,,ENST00000528116,;SIGIRR,downstream_gene_variant,,ENST00000529486,;SIGIRR,downstream_gene_variant,,ENST00000525299,;SIGIRR,downstream_gene_variant,,ENST00000534217,;SIGIRR,downstream_gene_variant,,ENST00000528698,;SIGIRR,downstream_gene_variant,,ENST00000526788,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000527987,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000527295,;SIGIRR,downstream_gene_variant,,ENST00000528536,;SIGIRR,downstream_gene_variant,,ENST00000525070,;SIGIRR,downstream_gene_variant,,ENST00000534145,;	A	ENSG00000185187	ENST00000431843	Transcript	missense_variant	1434	1127	376	S/L	tCg/tTg	.	.	.	-1	SIGIRR	HGNC	30575	protein_coding	YES	CCDS31325.1	ENSP00000403104	SIGIR_HUMAN	.	UPI000049DD22	.	deleterious(0.04)	benign(0.006)	10/10	.	hmmpanther:PTHR11890:SF2,hmmpanther:PTHR11890	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCGAGACC	.	5	ESCA
MYBPC3	0	.	GRCh37	11	47372796	47372796	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.286G>A	p.Glu96Lys	p.E96K	ENST00000545968	2/35	43	35	8	44	44	0	MYBPC3,missense_variant,p.Glu96Lys,ENST00000545968,;MYBPC3,missense_variant,p.Glu96Lys,ENST00000256993,;MYBPC3,missense_variant,p.Glu96Lys,ENST00000399249,;SPI1,downstream_gene_variant,,ENST00000378538,;SPI1,downstream_gene_variant,,ENST00000227163,;SPI1,downstream_gene_variant,,ENST00000533030,;MYBPC3,missense_variant,p.Glu96Lys,ENST00000544791,;	T	ENSG00000134571	ENST00000545968	Transcript	missense_variant	341	286	96	E/K	Gag/Aag	.	.	.	-1	MYBPC3	HGNC	7551	protein_coding	YES	CCDS53621.1	ENSP00000442795	MYPC3_HUMAN	B6D426_HUMAN	UPI000006EEAA	.	deleterious_low_confidence(0.02)	benign(0.22)	2/35	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCTCTATGA	.	5	ESCA
OR5W2	0	.	GRCh37	11	55681251	55681251	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.808C>A	p.Gln270Lys	p.Q270K	ENST00000344514	1/1	31	22	9	29	29	0	OR5W2,missense_variant,p.Gln270Lys,ENST00000344514,;	T	ENSG00000187612	ENST00000344514	Transcript	missense_variant	808	808	270	Q/K	Caa/Aaa	.	.	.	-1	OR5W2	HGNC	15299	protein_coding	YES	CCDS31513.1	ENSP00000342448	OR5W2_HUMAN	.	UPI0000061E8D	.	tolerated(0.07)	benign(0.144)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF58,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTGATCTA	.	5	ESCA
OR5T3	0	.	GRCh37	11	56020238	56020250	+	Frame_Shift_Del	DEL	TACATATAGTGGC	TACATATAGTGGC	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	TACATATAGTGGC	TACATATAGTGGC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.568_580delATAGTGGCTACAT	p.Ile190LeufsTer45	p.I190Lfs*45	ENST00000303059	1/1	125	108	17	110	110	0	OR5T3,frameshift_variant,p.Ile190LeufsTer45,ENST00000303059,;	-	ENSG00000172489	ENST00000303059	Transcript	frameshift_variant	563-575	563-575	188-192	IHIVA/X	aTACATATAGTGGCt/at	.	.	.	1	OR5T3	HGNC	15297	protein_coding	YES	CCDS31524.1	ENSP00000305403	OR5T3_HUMAN	.	UPI0000061E96	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTACTATACATATAGTGGCTACAT	.	3	ESCA
SLC22A6	0	.	GRCh37	11	62751107	62751107	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530C>A	p.Thr177Asn	p.T177N	ENST00000377871	3/10	43	35	8	50	50	0	SLC22A6,missense_variant,p.Thr177Asn,ENST00000377871,;SLC22A6,missense_variant,p.Thr177Asn,ENST00000421062,;SLC22A6,missense_variant,p.Thr177Asn,ENST00000458333,;SLC22A6,missense_variant,p.Thr177Asn,ENST00000360421,;SLC22A6,non_coding_transcript_exon_variant,,ENST00000537349,;SLC22A6,missense_variant,p.Asp169Glu,ENST00000540654,;	T	ENSG00000197901	ENST00000377871	Transcript	missense_variant	797	530	177	T/N	aCc/aAc	.	.	.	-1	SLC22A6	HGNC	10970	protein_coding	YES	CCDS31591.1	ENSP00000367102	S22A6_HUMAN	.	UPI00000747EC	.	deleterious(0)	probably_damaging(0.925)	3/10	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24064:SF205,hmmpanther:PTHR24064,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00898,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCAGGTCCCT	.	5	ESCA
MALAT1	0	.	GRCh37	11	65272188	65272189	+	RNA	DEL	TA	TA	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.6956_6957delTA	.	.	ENST00000534336	1/1	133	119	14	63	63	0	MALAT1,non_coding_transcript_exon_variant,,ENST00000534336,;MALAT1,downstream_gene_variant,,ENST00000508832,;MALAT1,downstream_gene_variant,,ENST00000544868,;	-	ENSG00000251562	ENST00000534336	Transcript	non_coding_transcript_exon_variant	6956-6957	.	.	.	.	.	.	.	1	MALAT1	HGNC	29665	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAAATTAAACTG	.	3	ESCA
B3GNT1	0	.	GRCh37	11	66114251	66114251	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766G>A	p.Val256Met	p.V256M	ENST00000311181	1/2	22	18	4	20	20	0	B3GNT1,missense_variant,p.Val256Met,ENST00000311181,;BRMS1,upstream_gene_variant,,ENST00000359957,;BRMS1,upstream_gene_variant,,ENST00000524699,;RP11-867G23.8,upstream_gene_variant,,ENST00000531602,;BRMS1,upstream_gene_variant,,ENST00000530756,;BRMS1,upstream_gene_variant,,ENST00000425825,;RP11-867G23.8,upstream_gene_variant,,ENST00000581155,;RP11-867G23.8,upstream_gene_variant,,ENST00000580881,;BRMS1,upstream_gene_variant,,ENST00000529544,;BRMS1,upstream_gene_variant,,ENST00000530238,;BRMS1,upstream_gene_variant,,ENST00000534617,;BRMS1,upstream_gene_variant,,ENST00000527375,;BRMS1,upstream_gene_variant,,ENST00000525127,;	T	ENSG00000174684	ENST00000311181	Transcript	missense_variant	913	766	256	V/M	Gtg/Atg	.	.	.	-1	B3GNT1	HGNC	15685	protein_coding	YES	CCDS8136.1	ENSP00000309096	B3GN1_HUMAN	B4DGI0_HUMAN	UPI00000358A1	.	deleterious(0)	probably_damaging(0.999)	1/2	.	hmmpanther:PTHR12270:SF20,hmmpanther:PTHR12270,Pfam_domain:PF13896	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCACCAGCG	.	5	ESCA
KDM2A	0	.	GRCh37	11	67023301	67023301	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*775C>T	.	.	ENST00000529006	21/21	42	36	6	44	44	0	KDM2A,3_prime_UTR_variant,,ENST00000398645,;KDM2A,3_prime_UTR_variant,,ENST00000308783,;KDM2A,3_prime_UTR_variant,,ENST00000530342,;KDM2A,3_prime_UTR_variant,,ENST00000529006,;KDM2A,non_coding_transcript_exon_variant,,ENST00000531696,;KDM2A,non_coding_transcript_exon_variant,,ENST00000524657,;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;	T	ENSG00000173120	ENST00000529006	Transcript	3_prime_UTR_variant	4710	.	.	.	.	.	.	.	1	KDM2A	HGNC	13606	protein_coding	YES	CCDS44657.1	ENSP00000432786	KDM2A_HUMAN	I3VM54_HUMAN,I3VM53_HUMAN	UPI00001678A9	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATTCTGAGA	.	4	ESCA
OR2D3	0	.	GRCh37	11	6943135	6943135	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903G>C	p.Leu301Phe	p.L301F	ENST00000317834	1/1	67	57	9	42	42	0	OR2D3,missense_variant,p.Leu301Phe,ENST00000317834,;ZNF215,upstream_gene_variant,,ENST00000414517,;ZNF215,upstream_gene_variant,,ENST00000278319,;ZNF215,upstream_gene_variant,,ENST00000529755,;ZNF215,upstream_gene_variant,,ENST00000527171,;	C	ENSG00000178358	ENST00000317834	Transcript	missense_variant	931	903	301	L/F	ttG/ttC	.	.	.	1	OR2D3	HGNC	15146	protein_coding	YES	CCDS31417.1	ENSP00000320560	OR2D3_HUMAN	.	UPI0000041C7D	.	deleterious(0.02)	benign(0.295)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF136,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTTGAACCC	.	5	ESCA
SHANK2	0	.	GRCh37	11	70333138	70333138	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3263G>A	p.Arg1088His	p.R1088H	ENST00000338508	32/33	183	175	8	33	33	0	SHANK2,missense_variant,p.Arg491His,ENST00000409161,;SHANK2,missense_variant,p.Arg366His,ENST00000424924,;SHANK2,missense_variant,p.Arg708His,ENST00000423696,;SHANK2,missense_variant,p.Arg711His,ENST00000294018,;SHANK2,missense_variant,p.Arg1088His,ENST00000338508,;SHANK2,missense_variant,p.Arg492His,ENST00000449833,;SHANK2,intron_variant,,ENST00000412252,;SHANK2,downstream_gene_variant,,ENST00000409530,;SHANK2,downstream_gene_variant,,ENST00000357171,;SHANK2,downstream_gene_variant,,ENST00000449116,;	T	ENSG00000162105	ENST00000338508	Transcript	missense_variant	3263	3263	1088	R/H	cGc/cAc	.	.	.	-1	SHANK2	HGNC	14295	protein_coding	YES	.	ENSP00000345193	.	C9JFP8_HUMAN,A6NHU9_HUMAN	UPI00020653A9	.	deleterious(0)	benign(0.254)	32/33	.	hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTCGCGGACG	.	2	ESCA
XRRA1	0	.	GRCh37	11	74638501	74638501	+	Missense_Mutation	SNP	G	G	C	rs748191489	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433C>G	p.Leu145Val	p.L145V	ENST00000340360	7/19	49	36	12	54	54	0	XRRA1,missense_variant,p.Leu153Val,ENST00000525407,;XRRA1,missense_variant,p.Leu145Val,ENST00000527087,;XRRA1,missense_variant,p.Leu145Val,ENST00000340360,;XRRA1,5_prime_UTR_variant,,ENST00000528219,;XRRA1,5_prime_UTR_variant,,ENST00000321448,;XRRA1,intron_variant,,ENST00000531852,;XRRA1,non_coding_transcript_exon_variant,,ENST00000533598,;XRRA1,non_coding_transcript_exon_variant,,ENST00000534798,;XRRA1,intron_variant,,ENST00000534041,;XRRA1,downstream_gene_variant,,ENST00000524430,;XRRA1,downstream_gene_variant,,ENST00000529400,;XRRA1,5_prime_UTR_variant,,ENST00000531849,;XRRA1,intron_variant,,ENST00000530562,;	C	ENSG00000166435	ENST00000340360	Transcript	missense_variant	765	433	145	L/V	Ctg/Gtg	rs748191489	.	.	-1	XRRA1	HGNC	18868	protein_coding	YES	CCDS44680.1	ENSP00000339918	XRRA1_HUMAN	E9PJ58_HUMAN	UPI0001572CC6	.	deleterious(0)	probably_damaging(0.997)	7/19	.	PROSITE_profiles:PS51450,hmmpanther:PTHR22710,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCAGTTCCT	.	5	ESCA
UTP20	0	.	GRCh37	12	101683933	101683933	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616C>A	p.Leu206Ile	p.L206I	ENST00000261637	7/62	36	29	7	32	32	0	UTP20,missense_variant,p.Leu206Ile,ENST00000261637,;UTP20,non_coding_transcript_exon_variant,,ENST00000551825,;UTP20,non_coding_transcript_exon_variant,,ENST00000551998,;	A	ENSG00000120800	ENST00000261637	Transcript	missense_variant	790	616	206	L/I	Ctt/Att	.	.	.	1	UTP20	HGNC	17897	protein_coding	YES	CCDS9081.1	ENSP00000261637	UTP20_HUMAN	.	UPI00001FB38B	.	deleterious(0.04)	benign(0.323)	7/62	.	hmmpanther:PTHR17695:SF11,hmmpanther:PTHR17695,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCACTTTTC	.	5	ESCA
ALDH1L2	0	.	GRCh37	12	105459083	105459083	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.748G>C	p.Asp250His	p.D250H	ENST00000258494	6/23	23	18	4	18	18	0	ALDH1L2,missense_variant,p.Asp250His,ENST00000424857,;ALDH1L2,missense_variant,p.Asp250His,ENST00000258494,;ALDH1L2,3_prime_UTR_variant,,ENST00000552270,;ALDH1L2,non_coding_transcript_exon_variant,,ENST00000549335,;	G	ENSG00000136010	ENST00000258494	Transcript	missense_variant	889	748	250	D/H	Gat/Cat	.	.	.	-1	ALDH1L2	HGNC	26777	protein_coding	YES	CCDS31891.1	ENSP00000258494	AL1L2_HUMAN	.	UPI00000477A9	.	deleterious_low_confidence(0)	probably_damaging(1)	6/23	.	Pfam_domain:PF02911,Gene3D:3.10.25.10,PIRSF_domain:PIRSF036489,Superfamily_domains:SSF50486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATCATGAC	.	5	ESCA
NAA25	0	.	GRCh37	12	112464841	112464841	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2494G>A	.	.	ENST00000261745	24/24	20	13	7	27	27	0	NAA25,3_prime_UTR_variant,,ENST00000261745,;ERP29,downstream_gene_variant,,ENST00000455836,;ERP29,downstream_gene_variant,,ENST00000261735,;ERP29,downstream_gene_variant,,ENST00000546477,;NAA25,downstream_gene_variant,,ENST00000552527,;NAA25,downstream_gene_variant,,ENST00000548181,;NAA25,downstream_gene_variant,,ENST00000549711,;	T	ENSG00000111300	ENST00000261745	Transcript	3_prime_UTR_variant	5662	.	.	.	.	.	.	.	-1	NAA25	HGNC	25783	protein_coding	YES	CCDS9159.1	ENSP00000261745	NAA25_HUMAN	.	UPI00001FBB50	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACATCAGATA	.	5	ESCA
HECTD4	0	.	GRCh37	12	112654172	112654172	+	Silent	SNP	G	G	A	rs372763829	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6951C>T	p.%3D	p.N2317N	ENST00000550722	48/76	20	16	4	16	16	0	HECTD4,synonymous_variant,p.%3D,ENST00000430131,;HECTD4,synonymous_variant,p.%3D,ENST00000550722,;HECTD4,synonymous_variant,p.%3D,ENST00000377560,;HECTD4,non_coding_transcript_exon_variant,,ENST00000550968,;HECTD4,downstream_gene_variant,,ENST00000552437,;	A	ENSG00000173064	ENST00000550722	Transcript	synonymous_variant	7347	6951	2317	N	aaC/aaT	rs372763829	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	.	48/76	.	hmmpanther:PTHR11254:SF286,hmmpanther:PTHR11254	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	CGGCCGTTGCT	.	3	ESCA
RBM19	0	.	GRCh37	12	114400104	114400104	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.152C>T	p.Ser51Phe	p.S51F	ENST00000545145	2/25	49	37	11	40	40	0	RBM19,missense_variant,p.Ser51Phe,ENST00000545145,;RBM19,missense_variant,p.Ser51Phe,ENST00000392561,;RBM19,missense_variant,p.Ser51Phe,ENST00000261741,;RBM19,non_coding_transcript_exon_variant,,ENST00000546876,;	A	ENSG00000122965	ENST00000545145	Transcript	missense_variant	231	152	51	S/F	tCc/tTc	.	.	.	-1	RBM19	HGNC	29098	protein_coding	YES	CCDS9172.1	ENSP00000442053	RBM19_HUMAN	.	UPI000013D1EC	.	deleterious(0)	probably_damaging(0.926)	2/25	.	PROSITE_profiles:PS50102,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCGGACTTG	.	5	ESCA
CAMKK2	0	.	GRCh37	12	121691134	121691134	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1049C>T	p.Thr350Met	p.T350M	ENST00000324774	10/17	37	30	6	45	45	0	CAMKK2,missense_variant,p.Thr350Met,ENST00000412367,;CAMKK2,missense_variant,p.Thr350Met,ENST00000324774,;CAMKK2,missense_variant,p.Thr350Met,ENST00000347034,;CAMKK2,missense_variant,p.Thr350Met,ENST00000404169,;CAMKK2,missense_variant,p.Thr137Met,ENST00000545538,;CAMKK2,missense_variant,p.Thr350Met,ENST00000538733,;CAMKK2,missense_variant,p.Thr350Met,ENST00000392473,;CAMKK2,missense_variant,p.Thr350Met,ENST00000402834,;CAMKK2,missense_variant,p.Thr350Met,ENST00000337174,;CAMKK2,missense_variant,p.Thr350Met,ENST00000392474,;CAMKK2,missense_variant,p.Thr350Met,ENST00000446440,;CAMKK2,non_coding_transcript_exon_variant,,ENST00000535524,;	A	ENSG00000110931	ENST00000324774	Transcript	missense_variant	1878	1049	350	T/M	aCg/aTg	COSM328679	.	.	-1	CAMKK2	HGNC	1470	protein_coding	YES	CCDS9216.1	ENSP00000312741	KKCC2_HUMAN	Q8IZW1_HUMAN,F5H4I7_HUMAN,F5H360_HUMAN	UPI000013D208	.	deleterious(0)	probably_damaging(0.999)	10/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF178,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGGCGTGCCC	.	4	ESCA
SETD1B	0	.	GRCh37	12	122252029	122252029	+	Silent	SNP	C	C	T	rs753493280	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1908C>T	p.%3D	p.G636G	ENST00000267197	6/17	37	30	7	34	34	0	SETD1B,synonymous_variant,p.%3D,ENST00000604567,;SETD1B,synonymous_variant,p.%3D,ENST00000542440,;SETD1B,synonymous_variant,p.%3D,ENST00000267197,;	T	ENSG00000139718	ENST00000267197	Transcript	synonymous_variant	1914	1908	636	G	ggC/ggT	rs753493280	.	.	1	SETD1B	HGNC	29187	protein_coding	YES	CCDS53838.1	ENSP00000267197	SET1B_HUMAN	.	UPI00006C12ED	.	.	.	6/17	.	hmmpanther:PTHR22884:SF296,hmmpanther:PTHR22884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGCGAGGA	.	5	ESCA
DNAH10	0	.	GRCh37	12	124315090	124315090	+	Intron	SNP	C	C	T	rs371307774	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4038-3C>T	.	.	ENST00000409039	.	45	40	5	29	29	0	DNAH10,splice_region_variant,,ENST00000409039,;DNAH10,upstream_gene_variant,,ENST00000497783,;	T	ENSG00000197653	ENST00000409039	Transcript	splice_region_variant	.	.	.	.	.	rs371307774	.	.	1	DNAH10	HGNC	2941	protein_coding	YES	CCDS9255.2	ENSP00000386770	DYH10_HUMAN	.	UPI00014F7B89	.	.	.	.	24/77	.	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GCTTTCAGGCA	byCluster	3	ESCA
GOLGA3	0	.	GRCh37	12	133351871	133351871	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3999G>C	p.Glu1333Asp	p.E1333D	ENST00000204726	22/24	53	45	7	57	57	0	GOLGA3,missense_variant,p.Glu1333Asp,ENST00000204726,;GOLGA3,missense_variant,p.Glu1333Asp,ENST00000450791,;GOLGA3,missense_variant,p.Glu1333Asp,ENST00000456883,;GOLGA3,non_coding_transcript_exon_variant,,ENST00000541013,;	G	ENSG00000090615	ENST00000204726	Transcript	missense_variant	4558	3999	1333	E/D	gaG/gaC	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	tolerated(0.13)	benign(0.071)	22/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902:SF20,hmmpanther:PTHR18902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCTCCAA	.	5	ESCA
TUBA1C	0	.	GRCh37	12	49666495	49666495	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835G>A	p.Glu279Lys	p.E279K	ENST00000301072	4/4	112	87	25	63	63	0	TUBA1C,missense_variant,p.Glu349Lys,ENST00000541364,;TUBA1C,missense_variant,p.Glu279Lys,ENST00000301072,;TUBA1C,downstream_gene_variant,,ENST00000549183,;RP11-161H23.5,non_coding_transcript_exon_variant,,ENST00000550468,;TUBA1C,3_prime_UTR_variant,,ENST00000552448,;TUBA1C,non_coding_transcript_exon_variant,,ENST00000548470,;TUBA1C,downstream_gene_variant,,ENST00000549818,;TUBA1C,downstream_gene_variant,,ENST00000552125,;	A	ENSG00000167553	ENST00000301072	Transcript	missense_variant	1110	835	279	E/K	Gag/Aag	.	.	.	1	TUBA1C	HGNC	20768	protein_coding	YES	CCDS8782.1	ENSP00000301072	TBA1C_HUMAN	F8VXZ7_HUMAN,F8VX09_HUMAN,F8VWV9_HUMAN,F8VRZ4_HUMAN,F8VRK0_HUMAN	UPI000013698C	.	deleterious_low_confidence(0)	possibly_damaging(0.579)	4/4	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Pfam_domain:PF03953,Gene3D:3.30.1330.20,SMART_domains:SM00865,Superfamily_domains:SSF55307,Prints_domain:PR01162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTGAGAAA	.	5	ESCA
PDE1B	0	.	GRCh37	12	54967206	54967206	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.904C>T	p.Arg302Ter	p.R302*	ENST00000243052	9/16	35	23	12	30	30	0	PDE1B,stop_gained,p.Arg261Ter,ENST00000538346,;PDE1B,stop_gained,p.Arg282Ter,ENST00000550620,;PDE1B,stop_gained,p.Arg302Ter,ENST00000243052,;PPP1R1A,downstream_gene_variant,,ENST00000547431,;PDE1B,non_coding_transcript_exon_variant,,ENST00000394277,;PDE1B,non_coding_transcript_exon_variant,,ENST00000542335,;PDE1B,3_prime_UTR_variant,,ENST00000550285,;PDE1B,non_coding_transcript_exon_variant,,ENST00000548855,;PDE1B,upstream_gene_variant,,ENST00000552774,;	T	ENSG00000123360	ENST00000243052	Transcript	stop_gained	1340	904	302	R/*	Cga/Tga	.	.	.	1	PDE1B	HGNC	8775	protein_coding	YES	CCDS8882.1	ENSP00000243052	PDE1B_HUMAN	Q7Z364_HUMAN,B4DK72_HUMAN,B3KX78_HUMAN	UPI0000001607	.	.	.	9/16	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF83,Pfam_domain:PF00233,Gene3D:1.10.1300.10,SMART_domains:SM00471,Superfamily_domains:SSF109604,Prints_domain:PR00387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCCGATTG	.	5	ESCA
STAT2	0	.	GRCh37	12	56739972	56739972	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2060G>A	p.Arg687Gln	p.R687Q	ENST00000314128	22/24	44	40	4	18	18	0	STAT2,missense_variant,p.Arg683Gln,ENST00000557235,;STAT2,missense_variant,p.Arg687Gln,ENST00000314128,;STAT2,downstream_gene_variant,,ENST00000418572,;STAT2,non_coding_transcript_exon_variant,,ENST00000556539,;STAT2,downstream_gene_variant,,ENST00000557252,;STAT2,non_coding_transcript_exon_variant,,ENST00000555488,;STAT2,downstream_gene_variant,,ENST00000555519,;STAT2,downstream_gene_variant,,ENST00000556140,;STAT2,downstream_gene_variant,,ENST00000557199,;	T	ENSG00000170581	ENST00000314128	Transcript	missense_variant	2084	2060	687	R/Q	cGg/cAg	.	.	.	-1	STAT2	HGNC	11363	protein_coding	YES	CCDS8917.1	ENSP00000315768	STAT2_HUMAN	R9QG81_HUMAN,R9QE65_HUMAN,Q6LD48_HUMAN	UPI00000473FC	.	tolerated(0.86)	benign(0.003)	22/24	.	hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF41,Gene3D:3.30.505.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCTCCGTTCC	.	3	ESCA
NAV3	0	.	GRCh37	12	78225248	78225248	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7G>C	p.Val3Leu	p.V3L	ENST00000536525	1/39	31	25	5	20	20	0	NAV3,missense_variant,p.Val3Leu,ENST00000536525,;NAV3,missense_variant,p.Val3Leu,ENST00000397909,;NAV3,missense_variant,p.Val3Leu,ENST00000266692,;NAV3,missense_variant,p.Val3Leu,ENST00000228327,;NAV3,missense_variant,p.Val3Leu,ENST00000549464,;	C	ENSG00000067798	ENST00000536525	Transcript	missense_variant	180	7	3	V/L	Gtt/Ctt	COSM1493025	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	deleterious_low_confidence(0.01)	probably_damaging(0.994)	1/39	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TGCCTGTTCTT	.	4	ESCA
M6PR	0	.	GRCh37	12	9094338	9094338	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*76C>G	.	.	ENST00000000412	7/7	26	22	4	18	18	0	M6PR,3_prime_UTR_variant,,ENST00000543704,;M6PR,3_prime_UTR_variant,,ENST00000000412,;M6PR,intron_variant,,ENST00000539143,;M6PR,intron_variant,,ENST00000544193,;PHC1,downstream_gene_variant,,ENST00000543824,;M6PR,downstream_gene_variant,,ENST00000544245,;PHC1,downstream_gene_variant,,ENST00000536844,;PHC1,downstream_gene_variant,,ENST00000433083,;M6PR,downstream_gene_variant,,ENST00000537621,;PHC1,downstream_gene_variant,,ENST00000544916,;PHC1,downstream_gene_variant,,ENST00000542346,;M6PR,downstream_gene_variant,,ENST00000543159,;M6PR,downstream_gene_variant,,ENST00000543845,;M6PR,3_prime_UTR_variant,,ENST00000541507,;M6PR,downstream_gene_variant,,ENST00000543258,;M6PR,downstream_gene_variant,,ENST00000543834,;PHC1,downstream_gene_variant,,ENST00000540574,;M6PR,downstream_gene_variant,,ENST00000540837,;PHC1,downstream_gene_variant,,ENST00000535510,;	C	ENSG00000003056	ENST00000000412	Transcript	3_prime_UTR_variant	1379	.	.	.	.	.	.	.	-1	M6PR	HGNC	6752	protein_coding	YES	CCDS8598.1	ENSP00000000412	MPRD_HUMAN	Q96AH2_HUMAN,F5H4U1_HUMAN,F5GXU0_HUMAN,F5GXE0_HUMAN	UPI000004E7FC	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTTGAGACT	.	2	ESCA
PZP	0	.	GRCh37	12	9354962	9354962	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433T>C	p.Phe145Leu	p.F145L	ENST00000261336	4/36	60	50	10	55	55	0	PZP,missense_variant,p.Phe145Leu,ENST00000261336,;PZP,missense_variant,p.Phe14Leu,ENST00000381997,;PZP,3_prime_UTR_variant,,ENST00000535230,;	G	ENSG00000126838	ENST00000261336	Transcript	missense_variant	462	433	145	F/L	Ttc/Ctc	.	.	.	-1	PZP	HGNC	9750	protein_coding	YES	CCDS8600.1	ENSP00000261336	PZP_HUMAN	.	UPI000013D168	.	deleterious(0.02)	possibly_damaging(0.867)	4/36	.	Pfam_domain:PF01835,hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF87	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGAATCTTA	.	5	ESCA
N4BP2L2	0	.	GRCh37	13	33017928	33017928	+	Missense_Mutation	SNP	G	G	A	rs777929333	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.746C>T	p.Pro249Leu	p.P249L	ENST00000399396	7/10	37	27	10	39	39	0	N4BP2L2,missense_variant,p.Pro234Leu,ENST00000504114,;N4BP2L2,missense_variant,p.Pro234Leu,ENST00000357505,;N4BP2L2,missense_variant,p.Pro249Leu,ENST00000399396,;N4BP2L2,missense_variant,p.Pro678Leu,ENST00000505213,;N4BP2L2,intron_variant,,ENST00000446957,;N4BP2L2,non_coding_transcript_exon_variant,,ENST00000380121,;N4BP2L2,non_coding_transcript_exon_variant,,ENST00000503296,;N4BP2L2,downstream_gene_variant,,ENST00000473025,;N4BP2L2,non_coding_transcript_exon_variant,,ENST00000509076,;	A	ENSG00000244754	ENST00000399396	Transcript	missense_variant	768	746	249	P/L	cCa/cTa	rs777929333	.	.	-1	N4BP2L2	HGNC	26916	protein_coding	YES	CCDS45024.1	ENSP00000382328	N42L2_HUMAN	Q6ZV26_HUMAN,B4DPY1_HUMAN	UPI00015C73C2	.	tolerated(0.12)	benign(0.039)	7/10	.	hmmpanther:PTHR13308,hmmpanther:PTHR13308:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.K250N|c.750G>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTGGTGTG	.	5	ESCA
MAB21L1	0	.	GRCh37	13	36049877	36049877	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.399G>A	p.%3D	p.Q133Q	ENST00000379919	1/1	20	17	3	26	26	0	MAB21L1,synonymous_variant,p.%3D,ENST00000379919,;NBEA,intron_variant,,ENST00000400445,;NBEA,intron_variant,,ENST00000540320,;NBEA,intron_variant,,ENST00000310336,;NBEA,intron_variant,,ENST00000379939,;NBEA,upstream_gene_variant,,ENST00000537702,;	T	ENSG00000180660	ENST00000379919	Transcript	synonymous_variant	956	399	133	Q	caG/caA	.	.	.	-1	MAB21L1	HGNC	6757	protein_coding	YES	CCDS9353.1	ENSP00000369251	MB211_HUMAN	F1T0A2_HUMAN	UPI0000022CD2	.	.	.	1/1	.	hmmpanther:PTHR10656:SF38,hmmpanther:PTHR10656,Pfam_domain:PF03281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCGTCTGAAA	.	2	ESCA
PCDH17	0	.	GRCh37	13	58208621	58208621	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1941G>A	p.%3D	p.T647T	ENST00000377918	1/4	10	7	3	16	16	0	PCDH17,synonymous_variant,p.%3D,ENST00000377918,;PCDH17,synonymous_variant,p.%3D,ENST00000484979,;	A	ENSG00000118946	ENST00000377918	Transcript	synonymous_variant	1967	1941	647	T	acG/acA	.	.	.	1	PCDH17	HGNC	14267	protein_coding	YES	CCDS31986.1	ENSP00000367151	PCD17_HUMAN	.	UPI00001FCE5B	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF41,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGCACGCTGCA	.	3	ESCA
KLHL1	0	.	GRCh37	13	70514337	70514337	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.849G>A	p.%3D	p.E283E	ENST00000377844	4/11	44	27	16	41	41	0	KLHL1,synonymous_variant,p.%3D,ENST00000545028,;KLHL1,synonymous_variant,p.%3D,ENST00000377844,;	T	ENSG00000150361	ENST00000377844	Transcript	synonymous_variant	1609	849	283	E	gaG/gaA	.	.	.	-1	KLHL1	HGNC	6352	protein_coding	YES	CCDS9445.1	ENSP00000367075	KLHL1_HUMAN	Q96RF4_HUMAN	UPI000004B136	.	.	.	4/11	.	hmmpanther:PTHR24412:SF75,hmmpanther:PTHR24412,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTCTCAAT	.	5	ESCA
CEP170B	0	.	GRCh37	14	105355974	105355974	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3757G>A	p.Ala1253Thr	p.A1253T	ENST00000414716	13/19	78	64	14	60	60	0	CEP170B,missense_variant,p.Ala1253Thr,ENST00000414716,;CEP170B,missense_variant,p.Ala1218Thr,ENST00000556508,;CEP170B,missense_variant,p.Ala1183Thr,ENST00000418279,;CEP170B,missense_variant,p.Ala1289Thr,ENST00000453495,;CEP170B,upstream_gene_variant,,ENST00000251181,;	A	ENSG00000099814	ENST00000414716	Transcript	missense_variant	3985	3757	1253	A/T	Gct/Act	.	.	.	1	CEP170B	HGNC	20362	protein_coding	YES	CCDS45175.1	ENSP00000404151	C170B_HUMAN	E9PFC1_HUMAN	UPI00001FDCF7	.	tolerated(0.18)	benign(0.06)	13/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF18,Pfam_domain:PF15308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAGGGCTGGC	.	4	ESCA
TRAV12-1	0	.	GRCh37	14	22309930	22309930	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311C>T	p.Ser104Leu	p.S104L	ENST00000390433	2/2	31	23	7	30	30	0	TRAV12-1,missense_variant,p.Ser104Leu,ENST00000390433,;TRAV8-2,upstream_gene_variant,,ENST00000390434,;	T	ENSG00000211785	ENST00000390433	Transcript	missense_variant	314	311	104	S/L	tCa/tTa	.	.	.	1	TRAV12-1	HGNC	12105	TR_V_gene	YES	.	ENSP00000445405	.	.	UPI000011C708	.	deleterious(0.01)	probably_damaging(0.998)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19343,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATTCAGCCA	.	5	ESCA
MAGEL2	0	.	GRCh37	15	23890125	23890125	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956G>T	p.Trp319Leu	p.W319L	ENST00000532292	1/1	60	45	14	45	45	0	MAGEL2,missense_variant,p.Trp319Leu,ENST00000532292,;AC124309.1,non_coding_transcript_exon_variant,,ENST00000314233,;	A	ENSG00000254585	ENST00000532292	Transcript	missense_variant	1051	956	319	W/L	tGg/tTg	.	.	.	-1	MAGEL2	HGNC	6814	protein_coding	YES	.	ENSP00000433433	.	Q6P3U4_HUMAN,Q2M1Q7_HUMAN,Q05BN9_HUMAN,H0YDD5_HUMAN	UPI00005A89F6	.	deleterious(0.03)	probably_damaging(0.996)	1/1	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCCAGTCA	.	5	ESCA
SNORD116-13	0	.	GRCh37	15	25324260	25324260	+	RNA	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.56G>A	.	.	ENST00000384408	1/1	63	56	7	65	65	0	SNORD116-13,non_coding_transcript_exon_variant,,ENST00000384408,;SNORD116-12,downstream_gene_variant,,ENST00000384468,;SNORD116-15,upstream_gene_variant,,ENST00000384445,;SNORD116-10,downstream_gene_variant,,ENST00000363791,;SNORD116-16,upstream_gene_variant,,ENST00000384533,;SNORD116-17,upstream_gene_variant,,ENST00000383929,;SNORD116-14,upstream_gene_variant,,ENST00000383894,;SNORD116-11,downstream_gene_variant,,ENST00000383882,;SNHG14,intron_variant,,ENST00000549804,;SNHG14,upstream_gene_variant,,ENST00000546682,;SNHG14,intron_variant,,ENST00000383025,;	A	ENSG00000207137	ENST00000384408	Transcript	non_coding_transcript_exon_variant	56	.	.	.	.	.	.	.	1	SNORD116-13	HGNC	33079	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGTGGGAACT	.	4	ESCA
SNORD115-40	0	.	GRCh37	15	25486890	25486890	+	5'Flank	SNP	G	G	C	rs374539447	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000606510	.	77	67	10	50	50	0	SNORD115-40,upstream_gene_variant,,ENST00000606510,;SNORD115-37,downstream_gene_variant,,ENST00000363768,;SNORD115-41,upstream_gene_variant,,ENST00000363608,;SNORD115-39,upstream_gene_variant,,ENST00000363694,;SNORD115-38,downstream_gene_variant,,ENST00000365037,;SNHG14,intron_variant,,ENST00000453082,;	C	ENSG00000272460	ENST00000606510	Transcript	upstream_gene_variant	.	.	.	.	.	rs374539447	.	1871	1	SNORD115-40	HGNC	33059	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A:0	A:0.0003	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE	TCTACGTTGGG	byFrequency|byCluster	2	ESCA
HERC2	0	.	GRCh37	15	28361836	28361836	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13584G>T	p.%3D	p.V4528V	ENST00000261609	88/93	40	33	7	31	31	0	HERC2,synonymous_variant,p.%3D,ENST00000261609,;HERC2,non_coding_transcript_exon_variant,,ENST00000568206,;HERC2,non_coding_transcript_exon_variant,,ENST00000566635,;HERC2,upstream_gene_variant,,ENST00000562136,;	A	ENSG00000128731	ENST00000261609	Transcript	synonymous_variant	13693	13584	4528	V	gtG/gtT	.	.	.	-1	HERC2	HGNC	4868	protein_coding	YES	CCDS10021.1	ENSP00000261609	HERC2_HUMAN	.	UPI00004578F7	.	.	.	88/93	.	PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF308,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGCACGGG	.	5	ESCA
MTMR10	0	.	GRCh37	15	31266646	31266646	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.345G>A	p.%3D	p.K115K	ENST00000435680	5/16	40	30	9	39	39	0	MTMR10,synonymous_variant,p.%3D,ENST00000425768,;MTMR10,synonymous_variant,p.%3D,ENST00000563714,;MTMR10,synonymous_variant,p.%3D,ENST00000435680,;MTMR10,upstream_gene_variant,,ENST00000314404,;MTMR10,synonymous_variant,p.%3D,ENST00000567567,;MTMR10,synonymous_variant,p.%3D,ENST00000568604,;MTMR10,3_prime_UTR_variant,,ENST00000564787,;MTMR10,non_coding_transcript_exon_variant,,ENST00000565728,;MTMR10,upstream_gene_variant,,ENST00000568547,;	T	ENSG00000166912	ENST00000435680	Transcript	synonymous_variant	443	345	115	K	aaG/aaA	.	.	.	-1	MTMR10	HGNC	25999	protein_coding	YES	CCDS45204.1	ENSP00000402537	MTMRA_HUMAN	B4E157_HUMAN	UPI00001FE130	.	.	.	5/16	.	hmmpanther:PTHR10807:SF39,hmmpanther:PTHR10807,Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCTTGTG	.	5	ESCA
CASC5	0	.	GRCh37	15	40913867	40913867	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1483A>C	p.Met495Leu	p.M495L	ENST00000346991	11/27	28	24	4	21	21	0	CASC5,missense_variant,p.Met495Leu,ENST00000346991,;CASC5,missense_variant,p.Met469Leu,ENST00000399668,;CASC5,3_prime_UTR_variant,,ENST00000527044,;CASC5,non_coding_transcript_exon_variant,,ENST00000533001,;CASC5,intron_variant,,ENST00000534204,;CASC5,upstream_gene_variant,,ENST00000526913,;	C	ENSG00000137812	ENST00000346991	Transcript	missense_variant	1873	1483	495	M/L	Atg/Ctg	.	.	.	1	CASC5	HGNC	24054	protein_coding	YES	CCDS42023.1	ENSP00000335463	CASC5_HUMAN	.	UPI0000E59BD3	.	tolerated(0.15)	benign(0.011)	11/27	.	hmmpanther:PTHR16520,hmmpanther:PTHR16520:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	ATGCTATGTCT	.	4	ESCA
MAPKBP1	0	.	GRCh37	15	42116141	42116141	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4113G>T	p.Gln1371His	p.Q1371H	ENST00000456763	30/32	47	26	21	65	65	0	MAPKBP1,missense_variant,p.Gln1248His,ENST00000221214,;MAPKBP1,missense_variant,p.Gln1204His,ENST00000260357,;MAPKBP1,missense_variant,p.Gln1365His,ENST00000457542,;MAPKBP1,missense_variant,p.Gln1371His,ENST00000456763,;MAPKBP1,intron_variant,,ENST00000514566,;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000342159,;PLA2G4B,upstream_gene_variant,,ENST00000542534,;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000382448,;JMJD7,upstream_gene_variant,,ENST00000408047,;JMJD7,upstream_gene_variant,,ENST00000397299,;JMJD7,upstream_gene_variant,,ENST00000431823,;RP11-23P13.4,downstream_gene_variant,,ENST00000512295,;RP11-23P13.4,downstream_gene_variant,,ENST00000510176,;JMJD7,upstream_gene_variant,,ENST00000405106,;MAPKBP1,3_prime_UTR_variant,,ENST00000512970,;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,;MAPKBP1,downstream_gene_variant,,ENST00000506301,;MAPKBP1,downstream_gene_variant,,ENST00000502695,;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000491746,;MAPKBP1,downstream_gene_variant,,ENST00000508050,;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000490848,;MAPKBP1,downstream_gene_variant,,ENST00000512433,;	T	ENSG00000137802	ENST00000456763	Transcript	missense_variant	4309	4113	1371	Q/H	caG/caT	.	.	.	1	MAPKBP1	HGNC	29536	protein_coding	YES	CCDS45239.1	ENSP00000393099	MABP1_HUMAN	D6R9F7_HUMAN	UPI00002375CB	.	tolerated(0.37)	benign(0.003)	30/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCAGCAACT	.	5	ESCA
SNX1	0	.	GRCh37	15	64424089	64424089	+	Missense_Mutation	SNP	C	C	A	rs761562391	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1219C>A	p.Arg407Ser	p.R407S	ENST00000261889	11/15	33	16	17	30	30	0	SNX1,missense_variant,p.Arg407Ser,ENST00000559844,;SNX1,missense_variant,p.Arg189Ser,ENST00000560829,;SNX1,missense_variant,p.Arg407Ser,ENST00000353874,;SNX1,missense_variant,p.Arg407Ser,ENST00000261889,;SNX1,missense_variant,p.Arg342Ser,ENST00000561026,;SNX1,intron_variant,,ENST00000558040,;SNX1,upstream_gene_variant,,ENST00000560861,;SNX1,splice_region_variant,,ENST00000559339,;SNX1,splice_region_variant,,ENST00000559401,;SNX1,splice_region_variant,,ENST00000380285,;SNX1,splice_region_variant,,ENST00000560260,;SNX1,upstream_gene_variant,,ENST00000559961,;	A	ENSG00000028528	ENST00000261889	Transcript	missense_variant	1240	1219	407	R/S	Cgc/Agc	rs761562391	.	.	1	SNX1	HGNC	11172	protein_coding	YES	CCDS58371.1	ENSP00000261889	SNX1_HUMAN	H0YKT3_HUMAN	UPI000217BDBB	.	deleterious(0)	possibly_damaging(0.822)	11/15	.	hmmpanther:PTHR10555:SF129,hmmpanther:PTHR10555,Pfam_domain:PF09325,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTCCGCGTA	.	5	ESCA
CTD-2524L6.3	0	.	GRCh37	15	72105936	72105936	+	5'Flank	SNP	G	G	A	rs779314442	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000563041	.	33	25	8	24	24	0	CTD-2524L6.3,upstream_gene_variant,,ENST00000562658,;CTD-2524L6.3,upstream_gene_variant,,ENST00000561834,;CTD-2524L6.3,upstream_gene_variant,,ENST00000563041,;NR2E3,splice_region_variant,,ENST00000326995,;NR2E3,splice_region_variant,,ENST00000398840,;NR2E3,non_coding_transcript_exon_variant,,ENST00000562839,;NR2E3,non_coding_transcript_exon_variant,,ENST00000562925,;NR2E3,non_coding_transcript_exon_variant,,ENST00000561604,;NR2E3,non_coding_transcript_exon_variant,,ENST00000567496,;NR2E3,upstream_gene_variant,,ENST00000563709,;	A	ENSG00000260037	ENST00000563041	Transcript	upstream_gene_variant	.	.	.	.	.	rs779314442,COSM964523,COSM964524,COSM964522	.	4819	1	CTD-2524L6.3	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODIFIER	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCCACGGAGTT	.	4	ESCA
ISLR	0	.	GRCh37	15	74468116	74468116	+	Missense_Mutation	SNP	C	C	A	rs267604313	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.917C>A	p.Ala306Asp	p.A306D	ENST00000249842	2/2	34	30	4	29	29	0	ISLR,missense_variant,p.Ala306Asp,ENST00000249842,;ISLR,missense_variant,p.Ala306Asp,ENST00000395118,;STRA6,downstream_gene_variant,,ENST00000574278,;STRA6,downstream_gene_variant,,ENST00000323940,;ISLR,downstream_gene_variant,,ENST00000560862,;STRA6,downstream_gene_variant,,ENST00000572785,;ISLR,downstream_gene_variant,,ENST00000559510,;STRA6,downstream_gene_variant,,ENST00000449139,;STRA6,downstream_gene_variant,,ENST00000535552,;STRA6,downstream_gene_variant,,ENST00000563965,;STRA6,downstream_gene_variant,,ENST00000423167,;STRA6,downstream_gene_variant,,ENST00000416286,;STRA6,downstream_gene_variant,,ENST00000395105,;RP11-665J16.1,intron_variant,,ENST00000561647,;STRA6,downstream_gene_variant,,ENST00000574439,;STRA6,downstream_gene_variant,,ENST00000545137,;	A	ENSG00000129009	ENST00000249842	Transcript	missense_variant	1274	917	306	A/D	gCc/gAc	rs267604313	.	.	1	ISLR	HGNC	6133	protein_coding	YES	CCDS10260.1	ENSP00000249842	ISLR_HUMAN	H0YN67_HUMAN,H0YL90_HUMAN	UPI0000049E09	.	deleterious(0)	probably_damaging(0.999)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	not_provided	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCAGGCCTTTG	.	3	ESCA
WDR61	0	.	GRCh37	15	78580699	78580699	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588G>C	p.Leu196Phe	p.L196F	ENST00000267973	8/11	53	48	5	36	36	0	WDR61,missense_variant,p.Leu196Phe,ENST00000560569,;WDR61,missense_variant,p.Leu103Phe,ENST00000558459,;WDR61,missense_variant,p.Leu15Phe,ENST00000558453,;WDR61,missense_variant,p.Leu196Phe,ENST00000267973,;WDR61,missense_variant,p.Leu196Phe,ENST00000558311,;WDR61,missense_variant,p.Leu67Phe,ENST00000560807,;RP11-762H8.1,upstream_gene_variant,,ENST00000560057,;WDR61,downstream_gene_variant,,ENST00000558840,;WDR61,upstream_gene_variant,,ENST00000559332,;WDR61,3_prime_UTR_variant,,ENST00000559848,;WDR61,3_prime_UTR_variant,,ENST00000560610,;WDR61,downstream_gene_variant,,ENST00000559700,;WDR61,upstream_gene_variant,,ENST00000559940,;WDR61,downstream_gene_variant,,ENST00000560063,;WDR61,upstream_gene_variant,,ENST00000558412,;RP11-762H8.2,downstream_gene_variant,,ENST00000560331,;	G	ENSG00000140395	ENST00000267973	Transcript	missense_variant	860	588	196	L/F	ttG/ttC	.	.	.	-1	WDR61	HGNC	30300	protein_coding	YES	CCDS10300.1	ENSP00000267973	WDR61_HUMAN	H0YN81_HUMAN,H0YM76_HUMAN	UPI00000714F4	.	deleterious(0)	probably_damaging(0.989)	8/11	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR22841,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGGTCAAGGA	.	4	ESCA
CTSH	0	.	GRCh37	15	79220095	79220095	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659A>G	p.Lys220Arg	p.K220R	ENST00000220166	9/12	40	34	5	30	30	0	CTSH,missense_variant,p.Lys220Arg,ENST00000220166,;CTSH,downstream_gene_variant,,ENST00000528741,;CTSH,non_coding_transcript_exon_variant,,ENST00000534237,;CTSH,non_coding_transcript_exon_variant,,ENST00000534533,;CTSH,downstream_gene_variant,,ENST00000534038,;CTSH,downstream_gene_variant,,ENST00000528191,;CTSH,missense_variant,p.Arg111Gly,ENST00000525807,;CTSH,3_prime_UTR_variant,,ENST00000533777,;CTSH,non_coding_transcript_exon_variant,,ENST00000529612,;CTSH,non_coding_transcript_exon_variant,,ENST00000527138,;CTSH,upstream_gene_variant,,ENST00000527715,;CTSH,downstream_gene_variant,,ENST00000529263,;CTSH,downstream_gene_variant,,ENST00000529861,;	C	ENSG00000103811	ENST00000220166	Transcript	missense_variant	769	659	220	K/R	aAg/aGg	.	.	.	-1	CTSH	HGNC	2535	protein_coding	YES	CCDS10308.1	ENSP00000220166	CATH_HUMAN	Q68D46_HUMAN,E9PKT6_HUMAN	UPI000013C799	.	tolerated(0.17)	benign(0.02)	9/12	.	Superfamily_domains:SSF54001,SMART_domains:SM00645,Gene3D:3.90.70.10,Pfam_domain:PF00112,hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF101	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCCTTTCCA	.	4	ESCA
OTOA	0	.	GRCh37	16	21726332	21726332	+	Silent	SNP	G	G	A	rs746634223	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1347G>A	p.%3D	p.Q449Q	ENST00000388958	13/28	57	52	5	36	36	0	OTOA,synonymous_variant,p.%3D,ENST00000388956,;OTOA,synonymous_variant,p.%3D,ENST00000286149,;OTOA,synonymous_variant,p.%3D,ENST00000388957,;OTOA,synonymous_variant,p.%3D,ENST00000388958,;OTOA,non_coding_transcript_exon_variant,,ENST00000563871,;	A	ENSG00000155719	ENST00000388958	Transcript	synonymous_variant	1348	1347	449	Q	caG/caA	rs746634223	.	.	1	OTOA	HGNC	16378	protein_coding	YES	CCDS10600.2	ENSP00000373610	OTOAN_HUMAN	B4DZ38_HUMAN	UPI00005C8607	.	.	.	13/28	.	hmmpanther:PTHR23412:SF14,hmmpanther:PTHR23412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCCAGATGGG	.	3	ESCA
PPL	0	.	GRCh37	16	4938211	4938211	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2406G>A	p.%3D	p.E802E	ENST00000345988	20/22	64	51	12	54	54	0	PPL,synonymous_variant,p.%3D,ENST00000592772,;PPL,synonymous_variant,p.%3D,ENST00000590782,;PPL,synonymous_variant,p.%3D,ENST00000345988,;PPL,downstream_gene_variant,,ENST00000589090,;PPL,downstream_gene_variant,,ENST00000590093,;PPL,downstream_gene_variant,,ENST00000588556,;	T	ENSG00000118898	ENST00000345988	Transcript	synonymous_variant	2496	2406	802	E	gaG/gaA	.	.	.	-1	PPL	HGNC	9273	protein_coding	YES	CCDS10526.1	ENSP00000340510	PEPL_HUMAN	.	UPI00001AE832	.	.	.	20/22	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23169,SMART_domains:SM00150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTAACTCATA	.	5	ESCA
MYH13	0	.	GRCh37	17	10227347	10227347	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2926G>A	p.Glu976Lys	p.E976K	ENST00000418404	22/41	156	128	27	153	153	0	MYH13,missense_variant,p.Glu976Lys,ENST00000418404,;MYH13,missense_variant,p.Glu976Lys,ENST00000252172,;RP11-401O9.3,intron_variant,,ENST00000577743,;	T	ENSG00000006788	ENST00000418404	Transcript	missense_variant	3090	2926	976	E/K	Gag/Aag	COSM705210,COSM705211	.	.	-1	MYH13	HGNC	7571	protein_coding	YES	CCDS45613.1	ENSP00000404570	MYH13_HUMAN	.	UPI0000DB39EA	.	deleterious(0)	probably_damaging(0.98)	22/41	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF267,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTCTGTGG	.	5	ESCA
LGALS9C	0	.	GRCh37	17	18390984	18390984	+	Silent	SNP	C	C	T	rs749828933	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.357C>T	p.%3D	p.F119F	ENST00000328114	4/11	21	16	5	12	12	0	LGALS9C,synonymous_variant,p.%3D,ENST00000584941,;LGALS9C,synonymous_variant,p.%3D,ENST00000582333,;LGALS9C,synonymous_variant,p.%3D,ENST00000583322,;LGALS9C,synonymous_variant,p.%3D,ENST00000412421,;LGALS9C,synonymous_variant,p.%3D,ENST00000328114,;LGALS9C,synonymous_variant,p.%3D,ENST00000581545,;LGALS9C,downstream_gene_variant,,ENST00000578983,;LGALS9C,3_prime_UTR_variant,,ENST00000579773,;LGALS9C,3_prime_UTR_variant,,ENST00000580674,;LGALS9C,3_prime_UTR_variant,,ENST00000578563,;LGALS9C,3_prime_UTR_variant,,ENST00000577691,;LGALS9C,non_coding_transcript_exon_variant,,ENST00000584170,;LGALS9C,upstream_gene_variant,,ENST00000584127,;LGALS9C,upstream_gene_variant,,ENST00000577265,;LGALS9C,upstream_gene_variant,,ENST00000578450,;LGALS9C,downstream_gene_variant,,ENST00000582928,;	T	ENSG00000171916	ENST00000328114	Transcript	synonymous_variant	438	357	119	F	ttC/ttT	rs749828933,COSM976318	.	.	1	LGALS9C	HGNC	33874	protein_coding	YES	CCDS32587.1	ENSP00000329932	LEG9C_HUMAN	C9JHN9_HUMAN	UPI00006C1768	.	.	.	4/11	.	PROSITE_profiles:PS51304,hmmpanther:PTHR11346,hmmpanther:PTHR11346:SF91,Gene3D:2.60.120.200,Pfam_domain:PF00337,SMART_domains:SM00908,SMART_domains:SM00276,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTCTTCGTGCA	byFrequency	2	ESCA
SLC47A1	0	.	GRCh37	17	19470501	19470501	+	Silent	SNP	C	C	T	rs774900748	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269C>T	p.%3D	p.I423I	ENST00000270570	14/17	80	61	19	63	63	0	SLC47A1,synonymous_variant,p.%3D,ENST00000436810,;SLC47A1,synonymous_variant,p.%3D,ENST00000571335,;SLC47A1,synonymous_variant,p.%3D,ENST00000270570,;SLC47A1,synonymous_variant,p.%3D,ENST00000457293,;SLC47A1,synonymous_variant,p.%3D,ENST00000395585,;SLC47A1,intron_variant,,ENST00000575023,;RP11-1113L8.1,intron_variant,,ENST00000574267,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000575362,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000575377,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000495425,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000573009,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000497548,;	T	ENSG00000142494	ENST00000270570	Transcript	synonymous_variant	1355	1269	423	I	atC/atT	rs774900748	.	.	1	SLC47A1	HGNC	25588	protein_coding	YES	CCDS11209.1	ENSP00000270570	S47A1_HUMAN	B4E3B2_HUMAN,B4DPA7_HUMAN	UPI0000071042	.	.	.	14/17	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11206,hmmpanther:PTHR11206:SF73,Pfam_domain:PF01554,TIGRFAM_domain:TIGR00797	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATCGGGAT	byFrequency	5	ESCA
CPD	0	.	GRCh37	17	28712032	28712032	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772G>A	p.Gly258Ser	p.G258S	ENST00000225719	2/21	91	79	11	80	80	0	CPD,missense_variant,p.Gly11Ser,ENST00000543464,;CPD,missense_variant,p.Gly258Ser,ENST00000225719,;CPD,non_coding_transcript_exon_variant,,ENST00000583275,;	A	ENSG00000108582	ENST00000225719	Transcript	missense_variant	848	772	258	G/S	Ggt/Agt	.	.	.	1	CPD	HGNC	2301	protein_coding	YES	CCDS11257.1	ENSP00000225719	CBPD_HUMAN	.	UPI000000DAF7	.	deleterious(0.03)	probably_damaging(1)	2/21	.	hmmpanther:PTHR11532:SF40,hmmpanther:PTHR11532,PROSITE_patterns:PS00133,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCATGGTGGC	.	4	ESCA
NF1	0	.	GRCh37	17	29701376	29701376	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*203C>T	.	.	ENST00000358273	58/58	52	47	5	25	25	0	NF1,3_prime_UTR_variant,,ENST00000456735,;NF1,3_prime_UTR_variant,,ENST00000358273,;NF1,3_prime_UTR_variant,,ENST00000356175,;NF1,intron_variant,,ENST00000444181,;NF1,upstream_gene_variant,,ENST00000498569,;NF1,intron_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000422121,;NF1,downstream_gene_variant,,ENST00000579081,;	T	ENSG00000196712	ENST00000358273	Transcript	3_prime_UTR_variant	9106	.	.	.	.	.	.	.	1	NF1	HGNC	7765	protein_coding	YES	CCDS42292.1	ENSP00000351015	NF1_HUMAN	Q9UMU3_HUMAN,Q4W6X4_HUMAN,K7EP94_HUMAN	UPI000012FFAE	.	.	.	58/58	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTTCTTCTA	.	3	ESCA
KRTAP9-3	0	.	GRCh37	17	39389161	39389161	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.408G>C	p.Glu136Asp	p.E136D	ENST00000411528	1/1	166	139	27	149	149	0	KRTAP9-3,missense_variant,p.Glu136Asp,ENST00000411528,;	C	ENSG00000204873	ENST00000411528	Transcript	missense_variant	447	408	136	E/D	gaG/gaC	.	.	.	1	KRTAP9-3	HGNC	16927	protein_coding	YES	CCDS11385.1	ENSP00000392189	KRA93_HUMAN	.	UPI0000071C07	.	tolerated(0.23)	benign(0.44)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23262:SF46,hmmpanther:PTHR23262,Pfam_domain:PF13885	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGAGACCAC	.	5	ESCA
LINC00671	0	.	GRCh37	17	41031648	41031648	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.561G>A	.	.	ENST00000301683	4/6	74	66	7	51	51	0	LINC00671,non_coding_transcript_exon_variant,,ENST00000301683,;LINC00671,non_coding_transcript_exon_variant,,ENST00000431109,;LINC00671,non_coding_transcript_exon_variant,,ENST00000436546,;LINC00671,non_coding_transcript_exon_variant,,ENST00000417193,;	T	ENSG00000213373	ENST00000301683	Transcript	non_coding_transcript_exon_variant	561	.	.	.	.	.	.	.	-1	LINC00671	HGNC	44339	lincRNA	YES	.	.	.	.	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGACTCATCTC	.	4	ESCA
ACOX1	0	.	GRCh37	17	73975071	73975071	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84G>A	p.%3D	p.E28E	ENST00000293217	1/14	36	28	8	43	43	0	ACOX1,synonymous_variant,p.%3D,ENST00000293217,;ACOX1,synonymous_variant,p.%3D,ENST00000588176,;ACOX1,synonymous_variant,p.%3D,ENST00000301608,;ACOX1,5_prime_UTR_variant,,ENST00000537812,;TEN1,upstream_gene_variant,,ENST00000586891,;TEN1,upstream_gene_variant,,ENST00000416485,;ACOX1,upstream_gene_variant,,ENST00000576743,;TEN1,upstream_gene_variant,,ENST00000590676,;TEN1,upstream_gene_variant,,ENST00000588202,;TEN1,upstream_gene_variant,,ENST00000397640,;ACOX1,non_coding_transcript_exon_variant,,ENST00000591857,;ACOX1,synonymous_variant,p.%3D,ENST00000573078,;ACOX1,synonymous_variant,p.%3D,ENST00000589301,;ACOX1,synonymous_variant,p.%3D,ENST00000572047,;ACOX1,non_coding_transcript_exon_variant,,ENST00000592329,;TEN1-CDK3,upstream_gene_variant,,ENST00000567351,;TEN1-CDK3,upstream_gene_variant,,ENST00000569284,;	T	ENSG00000161533	ENST00000293217	Transcript	synonymous_variant	374	84	28	E	gaG/gaA	.	.	.	-1	ACOX1	HGNC	119	protein_coding	YES	CCDS11734.1	ENSP00000293217	ACOX1_HUMAN	.	UPI000013E0F5	.	.	.	1/14	.	hmmpanther:PTHR10909:SF263,hmmpanther:PTHR10909,Pfam_domain:PF14749,Gene3D:1.10.540.10,PIRSF_domain:PIRSF000168,Superfamily_domains:SSF56645	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTCTCGGG	.	4	ESCA
TP53	0	.	GRCh37	17	7577567	7577568	+	Frame_Shift_Del	DEL	AC	AC	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	AC	AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.713_714delGT	p.Cys238Ter	p.C238*	ENST00000269305	7/11	451	239	212	234	234	0	TP53,frameshift_variant,p.Cys238Ter,ENST00000413465,;TP53,frameshift_variant,p.Cys238Ter,ENST00000420246,;TP53,frameshift_variant,p.Cys238Ter,ENST00000269305,;TP53,frameshift_variant,p.Cys106Ter,ENST00000509690,;TP53,frameshift_variant,p.Cys238Ter,ENST00000359597,;TP53,frameshift_variant,p.Cys145Ter,ENST00000514944,;TP53,frameshift_variant,p.Cys238Ter,ENST00000445888,;TP53,frameshift_variant,p.Cys238Ter,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	903-904	713-714	238	C/X	tGT/t	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.N239_C242delNSSC|c.715_726del12|3,CODON|p.N239D|c.715A>G|11,CODON|p.N239D|c.715A>G|13,CODON|p.N239D|c.715A>G|44,CODON|p.N146D|c.436A>G|14,CODON|p.N239Y|c.715A>T|6,CODON|p.N239D|c.715A>G|14,CODON|p.N239fs*1|c.714_715insT|3,CODON|p.N239fs*25|c.714_715insN|12,CODON|p.N239fs*1|c.714_715insT|4,CODON|p.N239fs*1|c.714_715insT|3,CODON|p.N146fs*1|c.435_436insT|3,CODON|p.C238*|c.714T>A|4,CODON|p.C238W|c.714T>G|3,BUFFER|p.C242W|c.726C>G|3,BUFFER|p.C242*|c.726C>A|3,BUFFER|p.C242W|c.726C>G|3,BUFFER|p.C242W|c.726C>G|9,BUFFER|p.C149W|c.447C>G|3,BUFFER|p.C242S|c.725G>C|3,BUFFER|p.C242Y|c.725G>A|4,BUFFER|p.C242S|c.725G>C|4,BUFFER|p.C242Y|c.725G>A|42,BUFFER|p.C242Y|c.725G>A|4,BUFFER|p.C242F|c.725G>T|11,BUFFER|p.C149Y|c.446G>A|4,BUFFER|p.C242F|c.725G>T|11,BUFFER|p.C242S|c.725G>C|3,BUFFER|p.C242F|c.725G>T|71,BUFFER|p.C149S|c.446G>C|4,BUFFER|p.C149F|c.446G>T|11,BUFFER|p.C242F|c.725G>T|4,BUFFER|p.C242S|c.725G>C|20,BUFFER|p.C242S|c.725G>C|4,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.C149fs*5|c.444delC|5,BUFFER|p.C242fs*5|c.723delC|12,BUFFER|p.S241delS|c.721_723delTCC|3,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.S241F|c.722_723CC>TT|5,BUFFER|p.C242G|c.724T>G|6,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C149G|c.445T>G|3,BUFFER|p.C242S|c.724T>A|11,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242R|c.724T>C|12,BUFFER|p.C242fs*5|c.722delC|6,BUFFER|p.S241fs*6|c.721delT|9,BUFFER|p.S148F|c.443C>T|15,BUFFER|p.S241Y|c.722C>A|4,BUFFER|p.S241Y|c.722C>A|15,BUFFER|p.S241C|c.722C>G|28,BUFFER|p.S241C|c.722C>G|3,BUFFER|p.S148Y|c.443C>A|5,BUFFER|p.S241F|c.722C>T|15,BUFFER|p.S241F|c.722C>T|6,BUFFER|p.S241F|c.722C>T|83,BUFFER|p.S241C|c.722C>G|4,BUFFER|p.S241Y|c.722C>A|4,BUFFER|p.S241Y|c.722C>A|5,BUFFER|p.S241Y|c.722C>A|5,BUFFER|p.S148C|c.443C>G|4,BUFFER|p.S241F|c.722C>T|9,BUFFER|p.S241F|c.722C>T|14,BUFFER|p.S241T|c.721T>A|6,BUFFER|p.S241A|c.721T>G|10,BUFFER|p.S241P|c.721T>C|5,BUFFER|p.S240R|c.720T>A|4,BUFFER|p.S240R|c.720T>G|4,BUFFER|p.S240S|c.720T>C|3,BUFFER|p.S240I|c.719G>T|6,BUFFER|p.S240C|c.718A>T|3,BUFFER|p.S240G|c.718A>G|16,BUFFER|p.N239K|c.717C>G|5,BUFFER|p.N146S|c.437A>G|6,BUFFER|p.N239T|c.716A>C|6,BUFFER|p.N239S|c.716A>G|3,BUFFER|p.N239S|c.716A>G|6,BUFFER|p.N239S|c.716A>G|4,BUFFER|p.N239S|c.716A>G|25,BUFFER|p.N239S|c.716A>G|5,BUFFER|p.C238Y|c.713G>A|7,BUFFER|p.C238F|c.713G>T|12,BUFFER|p.C145F|c.434G>T|12,BUFFER|p.C238Y|c.713G>A|16,BUFFER|p.C238F|c.713G>T|11,BUFFER|p.C238Y|c.713G>A|15,BUFFER|p.C238Y|c.713G>A|65,BUFFER|p.C238F|c.713G>T|42,BUFFER|p.C238Y|c.713G>A|9,BUFFER|p.C238F|c.713G>T|6,BUFFER|p.C145Y|c.434G>A|16,BUFFER|p.C238F|c.713G>T|6,BUFFER|p.C238S|c.713G>C|8,BUFFER|p.C238G|c.712T>G|3,BUFFER|p.C145G|c.433T>G|3,BUFFER|p.C238G|c.712T>G|4,BUFFER|p.C238R|c.712T>C|17,BUFFER|p.C238G|c.712T>G|3,BUFFER|p.C238S|c.712T>A|12,BUFFER|p.M237I|c.711G>A|15,BUFFER|p.M237I|c.711G>T|7,BUFFER|p.M237I|c.711G>C|9,BUFFER|p.M237I|c.711G>A|78,BUFFER|p.M237I|c.711G>T|3,BUFFER|p.M237I|c.711G>A|10,BUFFER|p.M237I|c.711G>T|31,BUFFER|p.M144I|c.432G>T|7,BUFFER|p.M237I|c.711G>A|15,BUFFER|p.M237I|c.711G>T|6,BUFFER|p.M237I|c.711G>T|7,BUFFER|p.M144I|c.432G>A|15,BUFFER|p.M237I|c.711G>A|9,BUFFER|p.M237K|c.710T>A|9,BUFFER|p.M237R|c.710T>G|3,BUFFER|p.M237T|c.710T>C|3,BUFFER|p.M144T|c.431T>C|3,BUFFER|p.M237T|c.710T>C|3,BUFFER|p.M237T|c.710T>C|5,BUFFER|p.M144V|c.430A>G|3,BUFFER|p.M237V|c.709A>G|3,BUFFER|p.M237V|c.709A>G|3,BUFFER|p.M237L|c.709A>T|4,BUFFER|p.M237V|c.709A>G|10,BUFFER|p.Y236delY|c.706_708delTAC|4,BUFFER|p.Y236*|c.708C>G|3,BUFFER|p.Y143*|c.429C>A|4,BUFFER|p.Y236*|c.708C>A|4,BUFFER|p.Y236*|c.708C>A|4,BUFFER|p.Y236*|c.708C>A|11,BUFFER|p.Y236C|c.707A>G|5,BUFFER|p.Y236C|c.707A>G|4,BUFFER|p.Y236C|c.707A>G|11,BUFFER|p.Y236C|c.707A>G|55,BUFFER|p.Y143C|c.428A>G|12,BUFFER|p.Y236C|c.707A>G|11,BUFFER|p.Y236S|c.707A>C|4,BUFFER|p.Y236N|c.706T>A|3,BUFFER|p.Y236N|c.706T>A|16,BUFFER|p.Y236D|c.706T>G|7,BUFFER|p.Y236H|c.706T>C|10,BUFFER|p.Y143N|c.427T>A|3,BUFFER|p.Y236N|c.706T>A|3,BUFFER|p.N235T|c.704A>C|3,BUFFER|p.N235I|c.704A>T|4,BUFFER|p.N235S|c.704A>G|15,BUFFER|p.N235D|c.703A>G|7,BUFFER|p.Y234delY|c.700_702delTAC|3,BUFFER|p.Y234*|c.702C>A|4	INDELOCATOR*|VARSCANI*|PINDEL	ACTGTTACACATG	.	3	ESCA
TMC6	0	.	GRCh37	17	76109657	76109657	+	Missense_Mutation	SNP	C	C	T	rs760748540	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2326G>A	p.Glu776Lys	p.E776K	ENST00000590602	19/20	51	38	13	36	36	0	TMC6,missense_variant,p.Glu425Lys,ENST00000306591,;TMC6,missense_variant,p.Glu776Lys,ENST00000392467,;TMC6,missense_variant,p.Glu776Lys,ENST00000590602,;TMC6,missense_variant,p.Glu355Lys,ENST00000322933,;TMC6,missense_variant,p.Glu776Lys,ENST00000322914,;TMC6,missense_variant,p.Glu355Lys,ENST00000591436,;TNRC6C,downstream_gene_variant,,ENST00000301624,;TNRC6C,downstream_gene_variant,,ENST00000335749,;TNRC6C-AS1,upstream_gene_variant,,ENST00000589217,;TMC6,non_coding_transcript_exon_variant,,ENST00000592076,;TNRC6C-AS1,upstream_gene_variant,,ENST00000374976,;TMC6,non_coding_transcript_exon_variant,,ENST00000590494,;TMC6,non_coding_transcript_exon_variant,,ENST00000593044,;TMC6,downstream_gene_variant,,ENST00000589933,;TNRC6C-AS1,upstream_gene_variant,,ENST00000592939,;	T	ENSG00000141524	ENST00000590602	Transcript	missense_variant	2486	2326	776	E/K	Gag/Aag	rs760748540	.	.	-1	TMC6	HGNC	18021	protein_coding	YES	CCDS32748.1	ENSP00000465261	TMC6_HUMAN	Q96I77_HUMAN,Q7L2M4_HUMAN,K7ERH0_HUMAN,K7ENM6_HUMAN,K7ENC4_HUMAN	UPI000013D819	.	tolerated(0.08)	possibly_damaging(0.728)	19/20	.	hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCGTAGA	byFrequency	5	ESCA
GPS1	0	.	GRCh37	17	80011221	80011221	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.225C>T	p.%3D	p.Y75Y	ENST00000392358	2/13	36	28	8	25	25	0	GPS1,synonymous_variant,p.%3D,ENST00000583641,;GPS1,synonymous_variant,p.%3D,ENST00000392358,;GPS1,synonymous_variant,p.%3D,ENST00000578552,;GPS1,synonymous_variant,p.%3D,ENST00000583009,;GPS1,synonymous_variant,p.%3D,ENST00000320548,;GPS1,synonymous_variant,p.%3D,ENST00000581418,;GPS1,synonymous_variant,p.%3D,ENST00000581578,;GPS1,synonymous_variant,p.%3D,ENST00000580716,;GPS1,synonymous_variant,p.%3D,ENST00000355130,;GPS1,synonymous_variant,p.%3D,ENST00000583961,;GPS1,synonymous_variant,p.%3D,ENST00000582327,;GPS1,synonymous_variant,p.%3D,ENST00000306823,;GPS1,synonymous_variant,p.%3D,ENST00000583885,;GPS1,synonymous_variant,p.%3D,ENST00000585084,;DUS1L,downstream_gene_variant,,ENST00000538833,;DUS1L,downstream_gene_variant,,ENST00000542088,;DUS1L,downstream_gene_variant,,ENST00000306796,;RFNG,upstream_gene_variant,,ENST00000310496,;DUS1L,downstream_gene_variant,,ENST00000577574,;RFNG,upstream_gene_variant,,ENST00000578356,;GPS1,upstream_gene_variant,,ENST00000578168,;DUS1L,downstream_gene_variant,,ENST00000354321,;RFNG,upstream_gene_variant,,ENST00000429557,;RFNG,upstream_gene_variant,,ENST00000580928,;GPS1,downstream_gene_variant,,ENST00000584229,;GPS1,downstream_gene_variant,,ENST00000583983,;RFNG,upstream_gene_variant,,ENST00000584838,;GPS1,missense_variant,p.Thr42Met,ENST00000580627,;GPS1,3_prime_UTR_variant,,ENST00000580141,;GPS1,3_prime_UTR_variant,,ENST00000584460,;GPS1,3_prime_UTR_variant,,ENST00000580723,;GPS1,3_prime_UTR_variant,,ENST00000578392,;GPS1,non_coding_transcript_exon_variant,,ENST00000392357,;GPS1,non_coding_transcript_exon_variant,,ENST00000578642,;RFNG,upstream_gene_variant,,ENST00000584515,;RFNG,upstream_gene_variant,,ENST00000582478,;GPS1,upstream_gene_variant,,ENST00000578279,;RFNG,upstream_gene_variant,,ENST00000580953,;DUS1L,downstream_gene_variant,,ENST00000578846,;GPS1,upstream_gene_variant,,ENST00000583486,;RFNG,upstream_gene_variant,,ENST00000584463,;RFNG,upstream_gene_variant,,ENST00000583784,;RFNG,upstream_gene_variant,,ENST00000578676,;DUS1L,downstream_gene_variant,,ENST00000584871,;DUS1L,downstream_gene_variant,,ENST00000579854,;DUS1L,downstream_gene_variant,,ENST00000580731,;RFNG,upstream_gene_variant,,ENST00000580793,;	T	ENSG00000169727	ENST00000392358	Transcript	synonymous_variant	574	225	75	Y	taC/taT	.	.	.	1	GPS1	HGNC	4549	protein_coding	YES	CCDS11800.1	ENSP00000376167	CSN1_HUMAN	J3QS88_HUMAN,J3QL53_HUMAN,J3KTB0_HUMAN,J3KSA5_HUMAN,C9JFE4_HUMAN,A8K070_HUMAN	UPI0000231C2E	.	.	.	2/13	.	hmmpanther:PTHR14145:SF2,hmmpanther:PTHR14145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTACGTGGT	.	5	ESCA
GPS1	0	.	GRCh37	17	80015160	80015160	+	3'UTR	SNP	C	C	T	rs771415364	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*157C>T	.	.	ENST00000392358	13/13	70	62	7	48	48	0	GPS1,3_prime_UTR_variant,,ENST00000392358,;GPS1,3_prime_UTR_variant,,ENST00000578552,;GPS1,3_prime_UTR_variant,,ENST00000320548,;GPS1,3_prime_UTR_variant,,ENST00000578168,;GPS1,3_prime_UTR_variant,,ENST00000306823,;DUS1L,downstream_gene_variant,,ENST00000538833,;DUS1L,downstream_gene_variant,,ENST00000542088,;GPS1,downstream_gene_variant,,ENST00000583641,;DUS1L,downstream_gene_variant,,ENST00000578907,;GPS1,downstream_gene_variant,,ENST00000583009,;DUS1L,downstream_gene_variant,,ENST00000306796,;DUS1L,downstream_gene_variant,,ENST00000577574,;GPS1,downstream_gene_variant,,ENST00000581418,;GPS1,downstream_gene_variant,,ENST00000581578,;GPS1,downstream_gene_variant,,ENST00000580716,;GPS1,downstream_gene_variant,,ENST00000355130,;DUS1L,downstream_gene_variant,,ENST00000578176,;GPS1,downstream_gene_variant,,ENST00000583961,;GPS1,downstream_gene_variant,,ENST00000582327,;DUS1L,downstream_gene_variant,,ENST00000354321,;GPS1,downstream_gene_variant,,ENST00000583885,;GPS1,downstream_gene_variant,,ENST00000585084,;DUS1L,downstream_gene_variant,,ENST00000582529,;GPS1,downstream_gene_variant,,ENST00000584229,;GPS1,3_prime_UTR_variant,,ENST00000584460,;GPS1,non_coding_transcript_exon_variant,,ENST00000392357,;GPS1,non_coding_transcript_exon_variant,,ENST00000583486,;GPS1,downstream_gene_variant,,ENST00000580141,;GPS1,downstream_gene_variant,,ENST00000578279,;DUS1L,downstream_gene_variant,,ENST00000582407,;DUS1L,downstream_gene_variant,,ENST00000578846,;DUS1L,downstream_gene_variant,,ENST00000578264,;GPS1,downstream_gene_variant,,ENST00000580627,;GPS1,downstream_gene_variant,,ENST00000578642,;DUS1L,downstream_gene_variant,,ENST00000584871,;DUS1L,downstream_gene_variant,,ENST00000579854,;DUS1L,downstream_gene_variant,,ENST00000580731,;DUS1L,downstream_gene_variant,,ENST00000578428,;GPS1,downstream_gene_variant,,ENST00000580723,;GPS1,downstream_gene_variant,,ENST00000578392,;	T	ENSG00000169727	ENST00000392358	Transcript	3_prime_UTR_variant	2090	.	.	.	.	rs771415364	.	.	1	GPS1	HGNC	4549	protein_coding	YES	CCDS11800.1	ENSP00000376167	CSN1_HUMAN	J3QS88_HUMAN,J3QL53_HUMAN,J3KTB0_HUMAN,J3KSA5_HUMAN,C9JFE4_HUMAN,A8K070_HUMAN	UPI0000231C2E	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGGCGGCTG	.	4	ESCA
FASN	0	.	GRCh37	17	80059488	80059488	+	5'Flank	SNP	G	G	A	rs532024831	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000306749	.	22	14	8	20	20	0	CCDC57,3_prime_UTR_variant,,ENST00000389641,;CCDC57,3_prime_UTR_variant,,ENST00000392347,;CCDC57,intron_variant,,ENST00000583053,;CCDC57,downstream_gene_variant,,ENST00000392345,;FASN,upstream_gene_variant,,ENST00000306749,;CCDC57,non_coding_transcript_exon_variant,,ENST00000584717,;CCDC57,downstream_gene_variant,,ENST00000582100,;CCDC57,downstream_gene_variant,,ENST00000583593,;	A	ENSG00000169710	ENST00000306749	Transcript	upstream_gene_variant	.	.	.	.	.	rs532024831	.	3280	-1	FASN	HGNC	3594	protein_coding	YES	CCDS11801.1	ENSP00000304592	FAS_HUMAN	.	UPI000013EB82	.	.	.	.	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AACACGTAGGT	by1000G	4	ESCA
GLP2R	0	.	GRCh37	17	9760754	9760754	+	Missense_Mutation	SNP	C	C	T	rs114514574	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626C>T	p.Thr209Met	p.T209M	ENST00000262441	6/13	98	88	9	55	55	0	GLP2R,missense_variant,p.Thr29Met,ENST00000574745,;GLP2R,missense_variant,p.Thr29Met,ENST00000304773,;GLP2R,missense_variant,p.Thr209Met,ENST00000262441,;GLP2R,3_prime_UTR_variant,,ENST00000458005,;NPM1P45,upstream_gene_variant,,ENST00000583151,;	T	ENSG00000065325	ENST00000262441	Transcript	missense_variant	1139	626	209	T/M	aCg/aTg	rs114514574	.	.	1	GLP2R	HGNC	4325	protein_coding	YES	CCDS11150.1	ENSP00000262441	GLP2R_HUMAN	I3L151_HUMAN,I3L0P5_HUMAN,E9PC86_HUMAN	UPI0000050469	.	deleterious(0.02)	probably_damaging(1)	6/13	.	PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF269,Pfam_domain:PF00002,Superfamily_domains:SSF81321	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R210C|c.628C>T|4	RADIA|MUTECT|MUSE|VARSCANS	CTGCACGCGCA	byCluster|by1000G	4	ESCA
ST8SIA3	0	.	GRCh37	18	55021733	55021733	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280C>T	p.Arg94Trp	p.R94W	ENST00000324000	2/4	30	22	8	29	29	0	ST8SIA3,missense_variant,p.Arg94Trp,ENST00000324000,;ST8SIA3,upstream_gene_variant,,ENST00000586360,;	T	ENSG00000177511	ENST00000324000	Transcript	missense_variant	2314	280	94	R/W	Cgg/Tgg	COSM1582376	.	.	1	ST8SIA3	HGNC	14269	protein_coding	YES	CCDS32834.1	ENSP00000320431	SIA8C_HUMAN	Q59GW3_HUMAN	UPI000014126D	.	.	benign(0.399)	2/4	.	hmmpanther:PTHR11987:SF33,hmmpanther:PTHR11987,PIRSF_domain:PIRSF005557	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATCGGACA	.	5	ESCA
SLC25A42	0	.	GRCh37	19	19206999	19206999	+	Silent	SNP	G	G	A	rs758484747	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66G>A	p.%3D	p.S22S	ENST00000318596	2/8	46	37	8	30	30	0	SLC25A42,synonymous_variant,p.%3D,ENST00000318596,;SLC25A42,non_coding_transcript_exon_variant,,ENST00000597661,;SLC25A42,non_coding_transcript_exon_variant,,ENST00000594070,;	A	ENSG00000181035	ENST00000318596	Transcript	synonymous_variant	217	66	22	S	tcG/tcA	rs758484747,COSM3403979	.	.	1	SLC25A42	HGNC	28380	protein_coding	YES	CCDS32966.1	ENSP00000326693	S2542_HUMAN	.	UPI0000198748	.	.	.	2/8	.	hmmpanther:PTHR24089:SF242,hmmpanther:PTHR24089	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCGTCCGT	.	5	ESCA
PRX	0	.	GRCh37	19	40902249	40902249	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2010G>T	p.Met670Ile	p.M670I	ENST00000324001	7/7	50	42	8	26	26	0	PRX,missense_variant,p.Met670Ile,ENST00000324001,;PRX,3_prime_UTR_variant,,ENST00000291825,;	A	ENSG00000105227	ENST00000324001	Transcript	missense_variant	2281	2010	670	M/I	atG/atT	COSM4131848	.	.	-1	PRX	HGNC	13797	protein_coding	YES	CCDS33028.1	ENSP00000326018	PRAX_HUMAN	.	UPI000044CC1A	.	tolerated(0.39)	benign(0.043)	7/7	.	hmmpanther:PTHR23348:SF39,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGCATTTT	.	5	ESCA
CYP2A13	0	.	GRCh37	19	41594483	41594483	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.107G>T	p.Gly36Val	p.G36V	ENST00000330436	1/9	104	84	20	74	74	0	CYP2A13,missense_variant,p.Gly36Val,ENST00000330436,;	T	ENSG00000197838	ENST00000330436	Transcript	missense_variant	107	107	36	G/V	gGa/gTa	.	.	.	1	CYP2A13	HGNC	2608	protein_coding	YES	CCDS12571.1	ENSP00000332679	CP2AD_HUMAN	.	UPI000013E07A	.	deleterious(0)	probably_damaging(1)	1/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF96,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGGACCCA	.	5	ESCA
CYP2A13	0	.	GRCh37	19	41597723	41597723	+	Silent	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.741C>T	p.%3D	p.F247F	ENST00000330436	5/9	96	82	13	75	75	0	CYP2A13,synonymous_variant,p.%3D,ENST00000330436,;	T	ENSG00000197838	ENST00000330436	Transcript	synonymous_variant	741	741	247	F	ttC/ttT	COSM4078410,COSM1525208	.	.	1	CYP2A13	HGNC	2608	protein_coding	YES	CCDS12571.1	ENSP00000332679	CP2AD_HUMAN	.	UPI000013E07A	.	.	.	5/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF96,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACTTCATCGC	.	4	ESCA
TMEM91	0	.	GRCh37	19	41889782	41889782	+	3'UTR	SNP	C	C	T	rs757674912	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4C>T	.	.	ENST00000392002	4/4	28	25	3	26	26	0	TMEM91,missense_variant,p.Pro122Ser,ENST00000447302,;TMEM91,missense_variant,p.Pro58Ser,ENST00000546050,;TMEM91,synonymous_variant,p.%3D,ENST00000413014,;TMEM91,synonymous_variant,p.%3D,ENST00000544232,;TMEM91,synonymous_variant,p.%3D,ENST00000604123,;TMEM91,3_prime_UTR_variant,,ENST00000546362,;TMEM91,3_prime_UTR_variant,,ENST00000535712,;TMEM91,3_prime_UTR_variant,,ENST00000356385,;TMEM91,3_prime_UTR_variant,,ENST00000542945,;TMEM91,3_prime_UTR_variant,,ENST00000392002,;TMEM91,3_prime_UTR_variant,,ENST00000539627,;BCKDHA,intron_variant,,ENST00000595085,;CTC-435M10.3,intron_variant,,ENST00000540732,;TMEM91,intron_variant,,ENST00000436170,;EXOSC5,downstream_gene_variant,,ENST00000602129,;TMEM91,downstream_gene_variant,,ENST00000342187,;TMEM91,downstream_gene_variant,,ENST00000537354,;EXOSC5,downstream_gene_variant,,ENST00000596905,;EXOSC5,downstream_gene_variant,,ENST00000221233,;CTC-435M10.3,intron_variant,,ENST00000604424,;	T	ENSG00000142046	ENST00000392002	Transcript	3_prime_UTR_variant	1183	.	.	.	.	rs757674912	.	.	1	TMEM91	HGNC	32393	protein_coding	YES	CCDS42571.1	ENSP00000375859	TMM91_HUMAN	F8W6Q6_HUMAN,F5H665_HUMAN	UPI00001C11CE	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTTGCCCCTA	byFrequency	2	ESCA
RPS19	0	.	GRCh37	19	42373777	42373777	+	Missense_Mutation	SNP	A	A	G	rs782437157	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365A>G	p.Lys122Arg	p.K122R	ENST00000598742	5/6	41	31	9	26	26	0	RPS19,missense_variant,p.Lys48Arg,ENST00000221975,;RPS19,missense_variant,p.Lys122Arg,ENST00000598742,;RPS19,missense_variant,p.Lys122Arg,ENST00000593863,;RPS19,downstream_gene_variant,,ENST00000600467,;RPS19,downstream_gene_variant,,ENST00000598261,;RPS19,downstream_gene_variant,,ENST00000601492,;RPS19,downstream_gene_variant,,ENST00000598399,;	G	ENSG00000105372	ENST00000598742	Transcript	missense_variant	737	365	122	K/R	aAa/aGa	rs782437157	.	.	1	RPS19	HGNC	10402	protein_coding	YES	CCDS12588.1	ENSP00000470972	RS19_HUMAN	M0QXK4_HUMAN,B0ZBD0_HUMAN	UPI0000161C03	.	tolerated(1)	benign(0.011)	5/6	.	hmmpanther:PTHR11710,hmmpanther:PTHR11710:SF1,Gene3D:1.10.10.10,Pfam_domain:PF01090,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCAAACTGA	.	5	ESCA
C19orf10	0	.	GRCh37	19	4664885	4664885	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287+3G>A	.	.	ENST00000262947	.	74	59	14	65	65	0	C19orf10,splice_region_variant,,ENST00000262947,;C19orf10,splice_region_variant,,ENST00000599761,;C19orf10,splice_region_variant,,ENST00000599630,;C19orf10,splice_region_variant,,ENST00000596031,;	T	ENSG00000074842	ENST00000262947	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	C19orf10	HGNC	16948	protein_coding	YES	CCDS12133.1	ENSP00000262947	CS010_HUMAN	.	UPI00000711E5	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCTCACCTC	.	4	ESCA
PNMAL2	0	.	GRCh37	19	46995440	46995440	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1375C>T	.	.	ENST00000599531	1/1	45	33	11	46	46	0	PNMAL2,missense_variant,p.Pro247Ser,ENST00000377655,;PNMAL2,3_prime_UTR_variant,,ENST00000599531,;PPP5D1,intron_variant,,ENST00000602017,;AC011484.1,upstream_gene_variant,,ENST00000377652,;PNMAL2,intron_variant,,ENST00000594749,;PPP5D1,upstream_gene_variant,,ENST00000595691,;	A	ENSG00000204851	ENST00000599531	Transcript	3_prime_UTR_variant	4316	.	.	.	.	.	.	.	-1	PNMAL2	HGNC	29206	protein_coding	YES	CCDS59400.1	ENSP00000473036	.	M0R374_HUMAN	UPI0000237925	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGGCCCCC	.	5	ESCA
ODF3L2	0	.	GRCh37	19	472424	472424	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205G>A	p.Ala69Thr	p.A69T	ENST00000315489	2/4	69	59	10	101	101	0	ODF3L2,missense_variant,p.Ala69Thr,ENST00000315489,;ODF3L2,intron_variant,,ENST00000382696,;ODF3L2,non_coding_transcript_exon_variant,,ENST00000591681,;	T	ENSG00000181781	ENST00000315489	Transcript	missense_variant	441	205	69	A/T	Gcc/Acc	.	.	.	-1	ODF3L2	HGNC	26841	protein_coding	YES	CCDS12027.1	ENSP00000318029	OD3L2_HUMAN	.	UPI0000072898	.	deleterious(0.02)	probably_damaging(0.972)	2/4	.	hmmpanther:PTHR21580,hmmpanther:PTHR21580:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAGGCGGGAC	.	4	ESCA
MIR519D	0	.	GRCh37	19	54216635	54216635	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.35C>T	.	.	ENST00000385246	1/1	110	95	14	83	83	0	MIR519D,non_coding_transcript_exon_variant,,ENST00000385246,;MIR521-2,upstream_gene_variant,,ENST00000384818,;MIR517A,downstream_gene_variant,,ENST00000385001,;MIR524,downstream_gene_variant,,ENST00000385242,;MIR518C,downstream_gene_variant,,ENST00000384822,;	T	ENSG00000207981	ENST00000385246	Transcript	non_coding_transcript_exon_variant	35	.	.	.	.	.	.	.	1	MIR519D	HGNC	32112	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTTCTGTTT	.	4	ESCA
PRKCG	0	.	GRCh37	19	54407957	54407957	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1725C>G	p.%3D	p.P575P	ENST00000263431	16/18	35	31	3	28	28	0	PRKCG,synonymous_variant,p.%3D,ENST00000540413,;PRKCG,synonymous_variant,p.%3D,ENST00000263431,;PRKCG,intron_variant,,ENST00000542049,;CACNG7,upstream_gene_variant,,ENST00000391767,;CACNG7,upstream_gene_variant,,ENST00000468076,;	G	ENSG00000126583	ENST00000263431	Transcript	synonymous_variant	2007	1725	575	P	ccC/ccG	.	.	.	1	PRKCG	HGNC	9402	protein_coding	YES	CCDS12867.1	ENSP00000263431	KPCG_HUMAN	M0R0Z4_HUMAN,M0R0I9_HUMAN,H7BZ60_HUMAN	UPI000000DC69	.	.	.	16/18	.	Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000550,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF64,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.S579F|c.1736C>T|3,BUFFER|p.S579F|c.1736C>T|3	RADIA|MUTECT|VARSCANS	TACCCCAAGTC	.	3	ESCA
LILRA2	0	.	GRCh37	19	55085970	55085970	+	Silent	SNP	C	C	T	rs757664099	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.273C>T	p.%3D	p.H91H	ENST00000251377	4/9	92	82	9	82	82	0	LILRA2,synonymous_variant,p.%3D,ENST00000251376,;LILRA2,synonymous_variant,p.%3D,ENST00000391738,;LILRA2,synonymous_variant,p.%3D,ENST00000391737,;LILRA2,synonymous_variant,p.%3D,ENST00000439534,;LILRA2,synonymous_variant,p.%3D,ENST00000251377,;LILRB1,intron_variant,,ENST00000418536,;LILRB1,intron_variant,,ENST00000448689,;LILRB1,intron_variant,,ENST00000396321,;LILRA2,non_coding_transcript_exon_variant,,ENST00000495786,;LILRA2,upstream_gene_variant,,ENST00000472992,;	T	ENSG00000239998	ENST00000251377	Transcript	synonymous_variant	406	273	91	H	caC/caT	rs757664099	.	.	1	LILRA2	HGNC	6603	protein_coding	YES	CCDS46179.1	ENSP00000251377	LIRA2_HUMAN	E9PDF4_HUMAN	UPI0000034C01	.	.	.	4/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11738:SF90,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13895,PIRSF_domain:PIRSF001979,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACACGCAGG	.	4	ESCA
KIR2DL3	0	.	GRCh37	19	55264097	55264097	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*126G>A	.	.	ENST00000342376	8/8	12	5	7	22	22	0	KIR2DL3,3_prime_UTR_variant,,ENST00000342376,;KIR2DL4,intron_variant,,ENST00000396284,;KIR3DL1,intron_variant,,ENST00000541392,;KIR3DL1,intron_variant,,ENST00000538269,;KIR3DL1,intron_variant,,ENST00000402254,;KIR2DL3,intron_variant,,ENST00000434419,;CTB-61M7.1,intron_variant,,ENST00000400864,;KIR2DP1,upstream_gene_variant,,ENST00000415311,;	A	ENSG00000243772	ENST00000342376	Transcript	3_prime_UTR_variant	1183	.	.	.	.	.	.	.	1	KIR2DL3	HGNC	6331	protein_coding	YES	CCDS33107.1	ENSP00000342215	KI2L3_HUMAN	M4NBK9_HUMAN,M4N692_HUMAN,E3NZD8_HUMAN,Q9UPI8_HUMAN,C6EVR7_HUMAN	UPI000012DB1C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGGCGTGAGT	.	3	ESCA
MUC16	0	.	GRCh37	19	9005210	9005210	+	Silent	SNP	A	A	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39867T>G	p.%3D	p.S13289S	ENST00000397910	47/84	58	48	9	43	43	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;MUC16,synonymous_variant,p.%3D,ENST00000599436,;MUC16,upstream_gene_variant,,ENST00000380951,;MUC16,synonymous_variant,p.%3D,ENST00000601404,;MUC16,upstream_gene_variant,,ENST00000596768,;	C	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	40071	39867	13289	S	tcT/tcG	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	47/84	.	hmmpanther:PTHR14672,hmmpanther:PTHR14672:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCACAGAGCT	.	5	ESCA
VPS45	0	.	GRCh37	1	150048327	150048327	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306C>T	p.%3D	p.I102I	ENST00000369130	4/15	83	71	11	27	27	0	VPS45,synonymous_variant,p.%3D,ENST00000369130,;VPS45,synonymous_variant,p.%3D,ENST00000419023,;VPS45,synonymous_variant,p.%3D,ENST00000369128,;VPS45,synonymous_variant,p.%3D,ENST00000535106,;VPS45,non_coding_transcript_exon_variant,,ENST00000497638,;VPS45,non_coding_transcript_exon_variant,,ENST00000460366,;VPS45,non_coding_transcript_exon_variant,,ENST00000462852,;VPS45,upstream_gene_variant,,ENST00000477558,;	T	ENSG00000136631	ENST00000369130	Transcript	synonymous_variant	852	306	102	I	atC/atT	.	.	.	1	VPS45	HGNC	14579	protein_coding	YES	CCDS944.1	ENSP00000358126	VPS45_HUMAN	.	UPI00000015E6	.	.	.	4/15	.	hmmpanther:PTHR11679:SF3,hmmpanther:PTHR11679,Pfam_domain:PF00995,Gene3D:3.40.50.2060,PIRSF_domain:PIRSF005715,Superfamily_domains:SSF56815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGATCAGCAA	.	5	ESCA
S100A7A	0	.	GRCh37	1	153390558	153390558	+	5'UTR	SNP	G	G	C	rs750574641	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1G>C	.	.	ENST00000368729	2/3	79	63	16	57	57	0	S100A7A,5_prime_UTR_variant,,ENST00000368728,;S100A7A,5_prime_UTR_variant,,ENST00000368729,;S100A7A,5_prime_UTR_variant,,ENST00000329256,;	C	ENSG00000184330	ENST00000368729	Transcript	5_prime_UTR_variant	57	.	.	.	.	rs750574641	.	.	1	S100A7A	HGNC	21657	protein_coding	YES	CCDS30872.1	ENSP00000357718	S1A7A_HUMAN	.	UPI000000D89D	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAAGATGAG	.	5	ESCA
ATP13A2	0	.	GRCh37	1	17322751	17322751	+	Missense_Mutation	SNP	G	G	A	rs139065780	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351C>T	p.Arg451Trp	p.R451W	ENST00000326735	14/29	61	45	15	57	57	0	ATP13A2,missense_variant,p.Arg10Trp,ENST00000503552,;ATP13A2,missense_variant,p.Arg446Trp,ENST00000452699,;ATP13A2,missense_variant,p.Arg165Trp,ENST00000506174,;ATP13A2,missense_variant,p.Arg446Trp,ENST00000341676,;ATP13A2,missense_variant,p.Arg451Trp,ENST00000326735,;ATP13A2,downstream_gene_variant,,ENST00000508222,;ATP13A2,downstream_gene_variant,,ENST00000511957,;ATP13A2,downstream_gene_variant,,ENST00000510069,;RP1-37C10.3,intron_variant,,ENST00000446261,;ATP13A2,splice_region_variant,,ENST00000502860,;ATP13A2,splice_region_variant,,ENST00000463860,;ATP13A2,splice_region_variant,,ENST00000509392,;ATP13A2,upstream_gene_variant,,ENST00000466561,;	A	ENSG00000159363	ENST00000326735	Transcript	missense_variant	1385	1351	451	R/W	Cgg/Tgg	rs139065780	.	.	-1	ATP13A2	HGNC	30213	protein_coding	YES	CCDS175.1	ENSP00000327214	AT132_HUMAN	Q8N4D4_HUMAN	UPI0000049724	.	deleterious(0)	possibly_damaging(0.846)	14/29	.	hmmpanther:PTHR24093:SF86,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01494,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01657,Superfamily_domains:0049473	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCCGGTTTC	byCluster	5	ESCA
PAPPA2	0	.	GRCh37	1	176526316	176526316	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.858G>A	p.%3D	p.A286A	ENST00000367662	2/23	77	69	8	50	50	0	PAPPA2,synonymous_variant,p.%3D,ENST00000367661,;PAPPA2,synonymous_variant,p.%3D,ENST00000367662,;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,;	A	ENSG00000116183	ENST00000367662	Transcript	synonymous_variant	2022	858	286	A	gcG/gcA	.	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	.	.	2/23	.	Pfam_domain:PF13385,Gene3D:2.60.120.200,SMART_domains:SM00560,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGCGTTCAC	.	4	ESCA
STX6	0	.	GRCh37	1	180953825	180953825	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679C>T	p.His227Tyr	p.H227Y	ENST00000258301	7/8	41	36	5	30	30	0	STX6,missense_variant,p.His227Tyr,ENST00000258301,;STX6,missense_variant,p.His126Tyr,ENST00000542060,;AL162431.1,downstream_gene_variant,,ENST00000457152,;STX6,non_coding_transcript_exon_variant,,ENST00000469135,;STX6,downstream_gene_variant,,ENST00000496476,;	A	ENSG00000135823	ENST00000258301	Transcript	missense_variant	917	679	227	H/Y	Cat/Tat	.	.	.	-1	STX6	HGNC	11441	protein_coding	YES	CCDS1341.1	ENSP00000258301	STX6_HUMAN	B4DR17_HUMAN	UPI00000490D6	.	deleterious(0.02)	probably_damaging(0.999)	7/8	.	hmmpanther:PTHR12380:SF35,hmmpanther:PTHR12380,Gene3D:1.20.5.110,Pfam_domain:PF05739	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATATGAGATA	.	2	ESCA
SUSD4	0	.	GRCh37	1	223395313	223395313	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*221A>G	.	.	ENST00000343846	8/8	17	11	5	14	14	0	SUSD4,3_prime_UTR_variant,,ENST00000608996,;SUSD4,3_prime_UTR_variant,,ENST00000343846,;SUSD4,3_prime_UTR_variant,,ENST00000484758,;SUSD4,3_prime_UTR_variant,,ENST00000366878,;SUSD4,intron_variant,,ENST00000494793,;SUSD4,downstream_gene_variant,,ENST00000454695,;SUSD4,non_coding_transcript_exon_variant,,ENST00000478605,;SUSD4,downstream_gene_variant,,ENST00000483818,;	C	ENSG00000143502	ENST00000343846	Transcript	3_prime_UTR_variant	2328	.	.	.	.	.	.	.	-1	SUSD4	HGNC	25470	protein_coding	YES	CCDS41471.1	ENSP00000344219	SUSD4_HUMAN	B7Z469_HUMAN	UPI0000205CB5	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGGTTCCCC	.	5	ESCA
TAF5L	0	.	GRCh37	1	229745865	229745865	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235A>G	p.Asn79Asp	p.N79D	ENST00000258281	3/5	40	33	7	17	17	0	TAF5L,missense_variant,p.Asn79Asp,ENST00000258281,;TAF5L,missense_variant,p.Asn79Asp,ENST00000366675,;TAF5L,missense_variant,p.Asn79Asp,ENST00000366676,;TAF5L,downstream_gene_variant,,ENST00000366674,;TAF5L,non_coding_transcript_exon_variant,,ENST00000477957,;	C	ENSG00000135801	ENST00000258281	Transcript	missense_variant	401	235	79	N/D	Aat/Gat	.	.	.	-1	TAF5L	HGNC	17304	protein_coding	YES	CCDS1581.1	ENSP00000258281	TAF5L_HUMAN	.	UPI0000073E93	.	tolerated(0.55)	benign(0.002)	3/5	.	hmmpanther:PTHR19879,Pfam_domain:PF04494,Superfamily_domains:SSF160897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATTCCGCA	.	5	ESCA
PGBD5	0	.	GRCh37	1	230468761	230468761	+	Missense_Mutation	SNP	C	C	T	rs371374137	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895G>A	p.Ala299Thr	p.A299T	ENST00000525115	5/7	101	83	18	68	68	0	PGBD5,missense_variant,p.Ala398Thr,ENST00000321327,;PGBD5,missense_variant,p.Ala253Thr,ENST00000391860,;PGBD5,missense_variant,p.Ala299Thr,ENST00000525115,;PGBD5,non_coding_transcript_exon_variant,,ENST00000530424,;	T	ENSG00000177614	ENST00000525115	Transcript	missense_variant	919	895	299	A/T	Gcg/Acg	rs371374137,COSM425556	.	.	-1	PGBD5	HGNC	19405	protein_coding	YES	.	ENSP00000431404	PGBD5_HUMAN	.	UPI0001D34147	.	tolerated(0.47)	benign(0.002)	5/7	.	Pfam_domain:PF13843	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCGCGCGGA	byCluster	5	ESCA
RYR2	0	.	GRCh37	1	237794736	237794736	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6450G>C	p.Met2150Ile	p.M2150I	ENST00000366574	42/105	96	89	7	48	48	0	RYR2,missense_variant,p.Met2134Ile,ENST00000542537,;RYR2,missense_variant,p.Met2150Ile,ENST00000366574,;RYR2,missense_variant,p.Met2148Ile,ENST00000360064,;	C	ENSG00000198626	ENST00000366574	Transcript	missense_variant	6767	6450	2150	M/I	atG/atC	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	probably_damaging(0.987)	42/105	.	Pfam_domain:PF01365,Gene3D:1n4kA02,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTATGAATAA	.	2	ESCA
RYR2	0	.	GRCh37	1	237982455	237982455	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14553C>A	p.Phe4851Leu	p.F4851L	ENST00000366574	101/105	144	122	21	90	90	0	RYR2,missense_variant,p.Phe4835Leu,ENST00000542537,;RYR2,missense_variant,p.Phe4851Leu,ENST00000366574,;RYR2,missense_variant,p.Phe4857Leu,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000608590,;	A	ENSG00000198626	ENST00000366574	Transcript	missense_variant	14870	14553	4851	F/L	ttC/ttA	CM0911018	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	possibly_damaging(0.787)	101/105	.	Pfam_domain:PF00520,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTTCTT	.	4	ESCA
MARCKSL1	0	.	GRCh37	1	32800284	32800284	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502G>C	p.Glu168Gln	p.E168Q	ENST00000329421	2/2	140	131	9	128	128	0	MARCKSL1,missense_variant,p.Glu168Gln,ENST00000329421,;HDAC1,downstream_gene_variant,,ENST00000373548,;HDAC1,downstream_gene_variant,,ENST00000373541,;HDAC1,downstream_gene_variant,,ENST00000490081,;HDAC1,downstream_gene_variant,,ENST00000482310,;HDAC1,downstream_gene_variant,,ENST00000476391,;HDAC1,downstream_gene_variant,,ENST00000471488,;HDAC1,downstream_gene_variant,,ENST00000484305,;	G	ENSG00000175130	ENST00000329421	Transcript	missense_variant	848	502	168	E/Q	Gag/Cag	.	.	.	-1	MARCKSL1	HGNC	7142	protein_coding	YES	CCDS361.1	ENSP00000362638	MRP_HUMAN	.	UPI0000001300	.	deleterious(0.01)	unknown(0)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14353,hmmpanther:PTHR14353:SF2,Pfam_domain:PF02063	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCTCTTCTT	.	2	ESCA
RNF19B	0	.	GRCh37	1	33412087	33412087	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1065T>G	p.Ile355Met	p.I355M	ENST00000373456	4/9	41	34	7	28	28	0	RNF19B,missense_variant,p.Ile355Met,ENST00000373456,;RNF19B,missense_variant,p.Ile354Met,ENST00000235150,;RNF19B,missense_variant,p.Ile354Met,ENST00000356990,;	C	ENSG00000116514	ENST00000373456	Transcript	missense_variant	1065	1065	355	I/M	atT/atG	.	.	.	-1	RNF19B	HGNC	26886	protein_coding	YES	CCDS372.2	ENSP00000362555	RN19B_HUMAN	.	UPI00015D777B	.	deleterious(0)	probably_damaging(0.991)	4/9	.	hmmpanther:PTHR11685,hmmpanther:PTHR11685:SF109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACCAATCAA	.	5	ESCA
ZMYM1	0	.	GRCh37	1	35570262	35570262	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.699G>A	p.%3D	p.E233E	ENST00000373330	7/11	49	39	9	34	34	0	ZMYM1,synonymous_variant,p.%3D,ENST00000417119,;ZMYM1,synonymous_variant,p.%3D,ENST00000373330,;ZMYM1,synonymous_variant,p.%3D,ENST00000359858,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000373329,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000488455,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000463393,;ZMYM1,intron_variant,,ENST00000475654,;	A	ENSG00000197056	ENST00000373330	Transcript	synonymous_variant	873	699	233	E	gaG/gaA	.	.	.	1	ZMYM1	HGNC	26253	protein_coding	YES	CCDS41302.1	ENSP00000362427	ZMYM1_HUMAN	Q9H5R2_HUMAN,Q5SW02_HUMAN,Q5SVZ7_HUMAN	UPI0000203ED6	.	.	.	7/11	.	hmmpanther:PTHR11697:SF88,hmmpanther:PTHR11697,Pfam_domain:PF06467,SMART_domains:SM00746	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGAGAACTG	.	5	ESCA
LRRC47	0	.	GRCh37	1	3699225	3699226	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1412dupA	p.Val472GlyfsTer2	p.V472Gfs*2	ENST00000378251	5/7	100	81	19	67	67	0	LRRC47,frameshift_variant,p.Val472GlyfsTer2,ENST00000378251,;RP1-286D6.5,upstream_gene_variant,,ENST00000607459,;RN7SL574P,upstream_gene_variant,,ENST00000581512,;LRRC47,splice_region_variant,,ENST00000479239,;LRRC47,splice_region_variant,,ENST00000462356,;	T	ENSG00000130764	ENST00000378251	Transcript	frameshift_variant	1440-1441	1412-1413	471	K/KX	aag/aaAg	.	.	.	-1	LRRC47	HGNC	29207	protein_coding	YES	CCDS51.1	ENSP00000367498	LRC47_HUMAN	.	UPI000006DEDC	.	.	.	5/7	.	hmmpanther:PTHR10947:SF2,hmmpanther:PTHR10947,Pfam_domain:PF03483,SMART_domains:SM00873	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTACCTTTGT	.	3	ESCA
CEP104	0	.	GRCh37	1	3755527	3755527	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.891+1G>T	.	p.X297_splice	ENST00000378230	.	73	57	16	63	63	0	CEP104,splice_donor_variant,,ENST00000443466,;CEP104,splice_donor_variant,,ENST00000378230,;CEP104,downstream_gene_variant,,ENST00000428079,;CEP104,downstream_gene_variant,,ENST00000378223,;CEP104,upstream_gene_variant,,ENST00000460038,;CEP104,splice_donor_variant,,ENST00000494653,;CEP104,downstream_gene_variant,,ENST00000494951,;	A	ENSG00000116198	ENST00000378230	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	CEP104	HGNC	24866	protein_coding	YES	CCDS30571.1	ENSP00000367476	CE104_HUMAN	.	UPI0000139AA8	.	.	.	.	8/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCACCAGCT	.	5	ESCA
GUCA2B	0	.	GRCh37	1	42620500	42620500	+	Silent	SNP	C	C	T	rs144117245	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240C>T	p.%3D	p.C80C	ENST00000372581	2/3	21	15	6	10	10	0	GUCA2B,synonymous_variant,p.%3D,ENST00000372581,;	T	ENSG00000044012	ENST00000372581	Transcript	synonymous_variant	270	240	80	C	tgC/tgT	rs144117245	.	.	1	GUCA2B	HGNC	4683	protein_coding	YES	CCDS464.1	ENSP00000361662	GUC2B_HUMAN	.	UPI000002E39E	.	.	.	2/3	.	hmmpanther:PTHR11318:SF1,hmmpanther:PTHR11318,Gene3D:1o8rA00,Pfam_domain:PF02058,PIRSF_domain:PIRSF001849,Superfamily_domains:0041741,Prints_domain:PR00774,Prints_domain:PR00774	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0002	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGCGCCTC	byCluster|by1000G	4	ESCA
RAD54L	0	.	GRCh37	1	46733163	46733163	+	Silent	SNP	T	T	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.924T>A	p.%3D	p.T308T	ENST00000371975	9/18	25	17	7	28	28	0	RAD54L,synonymous_variant,p.%3D,ENST00000371975,;RAD54L,synonymous_variant,p.%3D,ENST00000442598,;RAD54L,upstream_gene_variant,,ENST00000488942,;LRRC41,splice_region_variant,,ENST00000496156,;RAD54L,non_coding_transcript_exon_variant,,ENST00000476687,;RAD54L,non_coding_transcript_exon_variant,,ENST00000472889,;RAD54L,non_coding_transcript_exon_variant,,ENST00000473251,;RAD54L,intron_variant,,ENST00000487700,;	A	ENSG00000085999	ENST00000371975	Transcript	synonymous_variant	1598	924	308	T	acT/acA	.	.	.	1	RAD54L	HGNC	9826	protein_coding	YES	CCDS532.1	ENSP00000361043	RAD54_HUMAN	.	UPI0000378007	.	.	.	9/18	.	PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF208,hmmpanther:PTHR10799,Pfam_domain:PF00176,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGACTTACCA	.	5	ESCA
CHD5	0	.	GRCh37	1	6196803	6196803	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2559G>T	p.Lys853Asn	p.K853N	ENST00000262450	16/42	32	27	5	22	22	0	CHD5,missense_variant,p.Lys853Asn,ENST00000262450,;CHD5,5_prime_UTR_variant,,ENST00000378021,;CHD5,missense_variant,p.Lys853Asn,ENST00000496404,;CHD5,missense_variant,p.Lys236Asn,ENST00000462991,;	A	ENSG00000116254	ENST00000262450	Transcript	missense_variant	2659	2559	853	K/N	aaG/aaT	.	.	.	-1	CHD5	HGNC	16816	protein_coding	YES	CCDS57.1	ENSP00000262450	CHD5_HUMAN	.	UPI000006CD03	.	deleterious(0)	probably_damaging(1)	16/42	.	PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF583,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTCTTGAG	.	5	ESCA
IL23R	0	.	GRCh37	1	67724329	67724329	+	Missense_Mutation	SNP	G	G	A	rs375054504	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1408G>A	p.Asp470Asn	p.D470N	ENST00000347310	11/11	33	29	4	32	32	0	IL23R,missense_variant,p.Asp232Asn,ENST00000425614,;IL23R,missense_variant,p.Asp470Asn,ENST00000347310,;IL23R,missense_variant,p.Asp215Asn,ENST00000395227,;IL23R,3_prime_UTR_variant,,ENST00000371002,;IL23R,non_coding_transcript_exon_variant,,ENST00000473881,;	A	ENSG00000162594	ENST00000347310	Transcript	missense_variant	1579	1408	470	D/N	Gac/Aac	rs375054504	.	.	1	IL23R	HGNC	19100	protein_coding	YES	CCDS637.1	ENSP00000321345	IL23R_HUMAN	D9N2T9_HUMAN,B6HY80_HUMAN	UPI000004CACD	.	tolerated(0.15)	benign(0.047)	11/11	.	hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF88	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTCGACAAT	byCluster	4	ESCA
BCAR3	0	.	GRCh37	1	94027359	94027359	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*439C>T	.	.	ENST00000370244	14/14	34	29	5	27	27	0	BCAR3,3_prime_UTR_variant,,ENST00000370243,;BCAR3,3_prime_UTR_variant,,ENST00000539242,;BCAR3,3_prime_UTR_variant,,ENST00000260502,;BCAR3,3_prime_UTR_variant,,ENST00000370247,;BCAR3,3_prime_UTR_variant,,ENST00000370244,;BCAR3,downstream_gene_variant,,ENST00000538653,;	A	ENSG00000137936	ENST00000370244	Transcript	3_prime_UTR_variant	3206	.	.	.	.	.	.	.	-1	BCAR3	HGNC	973	protein_coding	YES	CCDS745.1	ENSP00000359264	BCAR3_HUMAN	B3KNL6_HUMAN	UPI000000D971	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAAAGATGTA	.	4	ESCA
EDEM2	0	.	GRCh37	20	33719587	33719587	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703-1G>A	.	p.X235_splice	ENST00000374492	.	50	44	5	33	33	0	EDEM2,splice_acceptor_variant,,ENST00000540582,;EDEM2,splice_acceptor_variant,,ENST00000374491,;EDEM2,splice_acceptor_variant,,ENST00000374492,;EDEM2,splice_acceptor_variant,,ENST00000541621,;EDEM2,splice_acceptor_variant,,ENST00000542871,;	T	ENSG00000088298	ENST00000374492	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	EDEM2	HGNC	15877	protein_coding	YES	CCDS13247.1	ENSP00000363616	EDEM2_HUMAN	B4E1F4_HUMAN	UPI00001285D9	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGACCTGAGA	.	4	ESCA
DLGAP4	0	.	GRCh37	20	35156429	35156429	+	3'UTR	SNP	G	G	A	rs544923981	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*995G>A	.	.	ENST00000373913	13/13	160	143	16	91	91	0	DLGAP4,3_prime_UTR_variant,,ENST00000401952,;DLGAP4,3_prime_UTR_variant,,ENST00000339266,;DLGAP4,3_prime_UTR_variant,,ENST00000373913,;DLGAP4,downstream_gene_variant,,ENST00000373907,;DLGAP4,downstream_gene_variant,,ENST00000340491,;RP5-977B1.7,intron_variant,,ENST00000439595,;RP5-977B1.7,intron_variant,,ENST00000425233,;RP5-977B1.7,upstream_gene_variant,,ENST00000433238,;DLGAP4,non_coding_transcript_exon_variant,,ENST00000475894,;DLGAP4,downstream_gene_variant,,ENST00000477195,;DLGAP4,downstream_gene_variant,,ENST00000497862,;DLGAP4,downstream_gene_variant,,ENST00000478910,;DLGAP4,downstream_gene_variant,,ENST00000489701,;	A	ENSG00000080845	ENST00000373913	Transcript	3_prime_UTR_variant	4445	.	.	.	.	rs544923981	.	.	1	DLGAP4	HGNC	24476	protein_coding	YES	CCDS13274.1	ENSP00000363023	DLGP4_HUMAN	.	UPI000013D34B	.	.	.	13/13	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTCGGGGCA	by1000G	4	ESCA
TTI1	0	.	GRCh37	20	36640851	36640851	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1368G>C	p.%3D	p.L456L	ENST00000373448	3/9	66	58	8	34	34	0	TTI1,synonymous_variant,p.%3D,ENST00000449821,;TTI1,synonymous_variant,p.%3D,ENST00000373447,;TTI1,synonymous_variant,p.%3D,ENST00000373448,;TTI1,non_coding_transcript_exon_variant,,ENST00000487362,;	G	ENSG00000101407	ENST00000373448	Transcript	synonymous_variant	1607	1368	456	L	ctG/ctC	.	.	.	-1	TTI1	HGNC	29029	protein_coding	YES	CCDS13300.1	ENSP00000362547	TTI1_HUMAN	D6W4K3_HUMAN	UPI000012DB27	.	.	.	3/9	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF005250,Gene3D:1.25.10.10,hmmpanther:PTHR18460	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATTCAGATC	.	4	ESCA
PREX1	0	.	GRCh37	20	47248873	47248873	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4468C>A	p.Gln1490Lys	p.Q1490K	ENST00000371941	35/40	83	69	13	59	59	0	PREX1,stop_gained,p.Cys1524Ter,ENST00000396220,;PREX1,missense_variant,p.Gln1490Lys,ENST00000371941,;PREX1,stop_gained,p.Cys846Ter,ENST00000482556,;	T	ENSG00000124126	ENST00000371941	Transcript	missense_variant	4491	4468	1490	Q/K	Cag/Aag	.	.	.	-1	PREX1	HGNC	32594	protein_coding	YES	CCDS13410.1	ENSP00000361009	PREX1_HUMAN	.	UPI000013D375	.	deleterious(0.01)	benign(0.097)	35/40	.	hmmpanther:PTHR22829,hmmpanther:PTHR22829:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTGCAAAT	.	4	ESCA
KCNQ2	0	.	GRCh37	20	62038650	62038650	+	Missense_Mutation	SNP	C	C	G	rs545544936	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1966G>C	p.Glu656Gln	p.E656Q	ENST00000359125	17/17	56	46	10	46	46	0	KCNQ2,missense_variant,p.Glu656Gln,ENST00000359689,;KCNQ2,missense_variant,p.Glu656Gln,ENST00000359125,;KCNQ2,missense_variant,p.Glu664Gln,ENST00000354587,;KCNQ2,missense_variant,p.Glu664Gln,ENST00000370224,;KCNQ2,missense_variant,p.Glu628Gln,ENST00000360480,;KCNQ2,missense_variant,p.Glu638Gln,ENST00000357249,;KCNQ2,missense_variant,p.Glu625Gln,ENST00000344462,;	G	ENSG00000075043	ENST00000359125	Transcript	missense_variant	2141	1966	656	E/Q	Gag/Cag	rs545544936	.	.	-1	KCNQ2	HGNC	6296	protein_coding	YES	CCDS13520.1	ENSP00000352035	KCNQ2_HUMAN	.	UPI00001279ED	.	tolerated(0.29)	probably_damaging(0.987)	17/17	.	Pfam_domain:PF03520	T:0.0004	T:0.0008	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCGGTCT	byFrequency|by1000G	5	ESCA
HUNK	0	.	GRCh37	21	33340686	33340686	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.999C>G	p.%3D	p.T333T	ENST00000270112	6/11	42	34	8	34	34	0	HUNK,synonymous_variant,p.%3D,ENST00000270112,;HUNK,downstream_gene_variant,,ENST00000430354,;	G	ENSG00000142149	ENST00000270112	Transcript	synonymous_variant	1359	999	333	T	acC/acG	.	.	.	1	HUNK	HGNC	13326	protein_coding	YES	CCDS13610.1	ENSP00000270112	HUNK_HUMAN	.	UPI0000035B66	.	.	.	6/11	.	hmmpanther:PTHR24343:SF152,hmmpanther:PTHR24343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCACCTATCC	.	5	ESCA
SON	0	.	GRCh37	21	34926664	34926664	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5127T>C	p.%3D	p.P1709P	ENST00000356577	3/12	46	42	3	36	36	0	SON,synonymous_variant,p.%3D,ENST00000381679,;SON,synonymous_variant,p.%3D,ENST00000300278,;SON,synonymous_variant,p.%3D,ENST00000356577,;SON,synonymous_variant,p.%3D,ENST00000436227,;SON,synonymous_variant,p.%3D,ENST00000290239,;SON,intron_variant,,ENST00000381692,;SON,upstream_gene_variant,,ENST00000421541,;SON,synonymous_variant,p.%3D,ENST00000455528,;	C	ENSG00000159140	ENST00000356577	Transcript	synonymous_variant	5602	5127	1709	P	ccT/ccC	.	.	.	1	SON	HGNC	11183	protein_coding	YES	CCDS13629.1	ENSP00000348984	SON_HUMAN	.	UPI0000140BFD	.	.	.	3/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12813:SF26,hmmpanther:PTHR12813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTACCTCCCCC	.	2	ESCA
SPECC1L	0	.	GRCh37	22	24743079	24743079	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2678C>G	p.Ser893Ter	p.S893*	ENST00000314328	11/17	55	44	10	38	38	0	SPECC1L,stop_gained,p.Ser893Ter,ENST00000541492,;SPECC1L,stop_gained,p.Ser893Ter,ENST00000314328,;SPECC1L,stop_gained,p.Ser893Ter,ENST00000437398,;SPECC1L-ADORA2A,3_prime_UTR_variant,,ENST00000358654,;	G	ENSG00000100014	ENST00000314328	Transcript	stop_gained	2963	2678	893	S/*	tCa/tGa	.	.	.	1	SPECC1L	HGNC	29022	protein_coding	YES	CCDS33619.1	ENSP00000325785	CYTSA_HUMAN	C9JLY8_HUMAN,C9J8U1_HUMAN	UPI00001B64E9	.	.	.	11/17	.	hmmpanther:PTHR23167:SF18,hmmpanther:PTHR23167	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTCAACAT	.	5	ESCA
LIMK2	0	.	GRCh37	22	31656020	31656020	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.445G>C	p.Glu149Gln	p.E149Q	ENST00000340552	4/15	28	23	5	23	23	0	LIMK2,missense_variant,p.Glu149Gln,ENST00000333611,;LIMK2,missense_variant,p.Glu170Gln,ENST00000331728,;LIMK2,missense_variant,p.Glu149Gln,ENST00000340552,;LIMK2,missense_variant,p.Glu92Gln,ENST00000406516,;LIMK2,intron_variant,,ENST00000444929,;LIMK2,downstream_gene_variant,,ENST00000425203,;LIMK2,non_coding_transcript_exon_variant,,ENST00000465937,;LIMK2,downstream_gene_variant,,ENST00000462625,;	C	ENSG00000182541	ENST00000340552	Transcript	missense_variant	675	445	149	E/Q	Gag/Cag	.	.	.	1	LIMK2	HGNC	6614	protein_coding	YES	CCDS33637.1	ENSP00000339916	LIMK2_HUMAN	B5MC51_HUMAN	UPI0000169F37	.	tolerated(0.06)	benign(0.414)	4/15	.	PROSITE_profiles:PS50106,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF398,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTGGAGAGT	.	5	ESCA
ADSL	0	.	GRCh37	22	40754947	40754947	+	Missense_Mutation	SNP	C	C	T	rs371892194	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562C>T	p.Arg188Cys	p.R188C	ENST00000216194	5/13	38	23	15	39	39	0	ADSL,missense_variant,p.Arg202Cys,ENST00000454266,;ADSL,missense_variant,p.Arg188Cys,ENST00000216194,;ADSL,missense_variant,p.Arg188Cys,ENST00000342312,;ADSL,upstream_gene_variant,,ENST00000480775,;ADSL,non_coding_transcript_exon_variant,,ENST00000477111,;	T	ENSG00000239900	ENST00000216194	Transcript	missense_variant	618	562	188	R/C	Cgt/Tgt	rs371892194	.	.	1	ADSL	HGNC	291	protein_coding	YES	CCDS14001.1	ENSP00000216194	PUR8_HUMAN	B4DUM2_HUMAN	UPI0000132AC7	.	deleterious(0.03)	probably_damaging(0.982)	5/13	.	hmmpanther:PTHR11444,hmmpanther:PTHR11444:SF2,TIGRFAM_domain:TIGR00928,Gene3D:1.20.200.10,Pfam_domain:PF00206,Superfamily_domains:SSF48557	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAGCGTGTC	.	5	ESCA
EP300	0	.	GRCh37	22	41565522	41565539	+	In_Frame_Del	DEL	TTACCTCGATAGTGTTCA	TTACCTCGATAGTGTTCA	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	TTACCTCGATAGTGTTCA	TTACCTCGATAGTGTTCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4190_4207delACCTCGATAGTGTTCATT	p.Tyr1397_His1402del	p.Y1397_H1402del	ENST00000263253	26/31	30	19	11	31	31	0	EP300,inframe_deletion,p.Tyr1397_His1402del,ENST00000263253,;RNU6-375P,downstream_gene_variant,,ENST00000517050,;RP1-85F18.6,splice_donor_variant,,ENST00000415054,;	-	ENSG00000100393	ENST00000263253	Transcript	inframe_deletion	5407-5424	4188-4205	1396-1402	SYLDSVH/S	tcTTACCTCGATAGTGTTCAt/tct	.	.	.	1	EP300	HGNC	3373	protein_coding	YES	CCDS14010.1	ENSP00000263253	EP300_HUMAN	B5A250_HUMAN	UPI00001AE876	.	.	.	26/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF4,Pfam_domain:PF08214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.D1399N|c.4195G>A|8,CODON|p.D1399Y|c.4195G>T|4	INDELOCATOR*|VARSCANI*|PINDEL	CATATCTTACCTCGATAGTGTTCATTTCT	.	3	ESCA
CNTNAP5	0	.	GRCh37	2	125175095	125175095	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457C>T	p.Arg153Cys	p.R153C	ENST00000431078	4/24	54	47	6	43	43	0	CNTNAP5,missense_variant,p.Arg153Cys,ENST00000431078,;	T	ENSG00000155052	ENST00000431078	Transcript	missense_variant	821	457	153	R/C	Cgc/Tgc	.	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	deleterious(0.01)	probably_damaging(1)	4/24	.	PROSITE_profiles:PS50022,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Pfam_domain:PF00754,Gene3D:2.60.120.260,SMART_domains:SM00231,Superfamily_domains:SSF49899,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTTCGCTTT	.	4	ESCA
ZEB2	0	.	GRCh37	2	145271205	145271205	+	Intron	SNP	C	C	T	rs765338223	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73+3640G>A	.	.	ENST00000558170	.	13	7	6	12	12	0	ZEB2,3_prime_UTR_variant,,ENST00000465070,;ZEB2,3_prime_UTR_variant,,ENST00000462355,;ZEB2,3_prime_UTR_variant,,ENST00000470879,;ZEB2,intron_variant,,ENST00000303660,;ZEB2,intron_variant,,ENST00000427902,;ZEB2,intron_variant,,ENST00000558170,;ZEB2,intron_variant,,ENST00000444559,;ZEB2,intron_variant,,ENST00000392861,;ZEB2,intron_variant,,ENST00000431672,;ZEB2,intron_variant,,ENST00000539609,;ZEB2,intron_variant,,ENST00000435831,;ZEB2,intron_variant,,ENST00000409487,;ZEB2,intron_variant,,ENST00000409211,;ZEB2-AS1,upstream_gene_variant,,ENST00000609376,;ZEB2-AS1,upstream_gene_variant,,ENST00000609842,;ZEB2-AS1,upstream_gene_variant,,ENST00000610265,;ZEB2-AS1,upstream_gene_variant,,ENST00000595109,;ZEB2-AS1,upstream_gene_variant,,ENST00000427278,;ZEB2-AS1,upstream_gene_variant,,ENST00000602006,;ZEB2-AS1,upstream_gene_variant,,ENST00000608361,;ZEB2,intron_variant,,ENST00000434448,;ZEB2,intron_variant,,ENST00000484313,;ZEB2,intron_variant,,ENST00000453352,;ZEB2,intron_variant,,ENST00000493689,;ZEB2,intron_variant,,ENST00000479735,;ZEB2,downstream_gene_variant,,ENST00000475115,;ZEB2,downstream_gene_variant,,ENST00000464380,;ZEB2,intron_variant,,ENST00000461784,;ZEB2,intron_variant,,ENST00000560384,;ZEB2,intron_variant,,ENST00000465308,;ZEB2,intron_variant,,ENST00000472146,;ZEB2,intron_variant,,ENST00000476394,;	T	ENSG00000169554	ENST00000558170	Transcript	intron_variant	.	.	.	.	.	rs765338223	.	.	-1	ZEB2	HGNC	14881	protein_coding	YES	CCDS2186.1	ENSP00000454157	ZEB2_HUMAN	U3KPV5_HUMAN,Q53TG0_HUMAN,Q53TD9_HUMAN,E7EUW9_HUMAN,E7ESP8_HUMAN,C9JUQ1_HUMAN,C9JU62_HUMAN,A0JP08_HUMAN	UPI00001359A2	.	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CTTCCCGGGCT	.	4	ESCA
TTN	0	.	GRCh37	2	179399772	179399772	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.101570A>G	p.Gln33857Arg	p.Q33857R	ENST00000589042	358/363	54	40	13	46	46	0	TTN,missense_variant,p.Gln24917Arg,ENST00000359218,;TTN,missense_variant,p.Gln24792Arg,ENST00000460472,;TTN,missense_variant,p.Gln32216Arg,ENST00000591111,;TTN,missense_variant,p.Gln33857Arg,ENST00000589042,;TTN,missense_variant,p.Gln24984Arg,ENST00000342175,;TTN,missense_variant,p.Gln31289Arg,ENST00000342992,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589434,;TTN-AS1,intron_variant,,ENST00000588716,;TTN-AS1,intron_variant,,ENST00000589391,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000592182,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592836,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000591466,;TTN-AS1,intron_variant,,ENST00000591867,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000585358,;TTN-AS1,intron_variant,,ENST00000589842,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000590040,;TTN-AS1,intron_variant,,ENST00000450692,;TTN-AS1,intron_variant,,ENST00000442329,;TTN-AS1,intron_variant,,ENST00000431259,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000588257,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000588244,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000588804,;TTN-AS1,intron_variant,,ENST00000585487,;TTN-AS1,downstream_gene_variant,,ENST00000585625,;TTN-AS1,downstream_gene_variant,,ENST00000587568,;TTN-AS1,upstream_gene_variant,,ENST00000415561,;TTN-AS1,downstream_gene_variant,,ENST00000587944,;TTN-AS1,downstream_gene_variant,,ENST00000589355,;TTN-AS1,downstream_gene_variant,,ENST00000604571,;	C	ENSG00000155657	ENST00000589042	Transcript	missense_variant	101795	101570	33857	Q/R	cAg/cGg	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	358/363	.	PROSITE_profiles:PS50011,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:3.30.200.20,Pfam_domain:PF00069,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACCTGATCA	.	5	ESCA
TTN	0	.	GRCh37	2	179516013	179516013	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39582G>A	p.%3D	p.K13194K	ENST00000589042	208/363	25	22	3	27	27	0	TTN,synonymous_variant,p.%3D,ENST00000446966,;TTN,synonymous_variant,p.%3D,ENST00000426232,;TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,intron_variant,,ENST00000414766,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000589830,;	T	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	39807	39582	13194	K	aaG/aaA	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	208/363	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ACTTTCTTTTC	.	2	ESCA
SATB2	0	.	GRCh37	2	200213692	200213692	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.905T>A	p.Leu302His	p.L302H	ENST00000417098	7/11	165	143	21	141	141	0	SATB2,missense_variant,p.Leu302His,ENST00000260926,;SATB2,missense_variant,p.Leu184His,ENST00000428695,;SATB2,missense_variant,p.Leu243His,ENST00000443023,;SATB2,missense_variant,p.Leu302His,ENST00000417098,;SATB2,missense_variant,p.Leu302His,ENST00000457245,;SATB2,non_coding_transcript_exon_variant,,ENST00000483346,;	T	ENSG00000119042	ENST00000417098	Transcript	missense_variant	1722	905	302	L/H	cTt/cAt	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	deleterious(0)	probably_damaging(0.984)	7/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15116,hmmpanther:PTHR15116:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACTAAGCTGG	.	4	ESCA
TRPM8	0	.	GRCh37	2	234854530	234854530	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.730G>A	p.Asp244Asn	p.D244N	ENST00000324695	7/26	43	36	7	39	39	0	TRPM8,missense_variant,p.Asp244Asn,ENST00000324695,;TRPM8,5_prime_UTR_variant,,ENST00000433712,;TRPM8,downstream_gene_variant,,ENST00000409625,;TRPM8,downstream_gene_variant,,ENST00000355722,;AC005538.5,downstream_gene_variant,,ENST00000455991,;TRPM8,missense_variant,p.Asp244Asn,ENST00000444298,;	A	ENSG00000144481	ENST00000324695	Transcript	missense_variant	770	730	244	D/N	Gac/Aac	.	.	.	1	TRPM8	HGNC	17961	protein_coding	YES	CCDS33407.1	ENSP00000323926	TRPM8_HUMAN	.	UPI0000456F32	.	tolerated(0.09)	benign(0.276)	7/26	.	hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATGACTTC	.	5	ESCA
D2HGDH	0	.	GRCh37	2	242681932	242681932	+	Missense_Mutation	SNP	G	G	A	rs768540316	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433G>A	p.Glu145Lys	p.E145K	ENST00000321264	4/10	24	18	5	13	13	0	D2HGDH,missense_variant,p.Glu145Lys,ENST00000321264,;D2HGDH,missense_variant,p.Glu15Lys,ENST00000454048,;D2HGDH,missense_variant,p.Glu11Lys,ENST00000403782,;D2HGDH,missense_variant,p.Glu145Lys,ENST00000537090,;D2HGDH,missense_variant,p.Glu29Lys,ENST00000437164,;D2HGDH,missense_variant,p.Glu145Lys,ENST00000342518,;D2HGDH,upstream_gene_variant,,ENST00000417686,;D2HGDH,missense_variant,p.Glu145Lys,ENST00000400769,;D2HGDH,missense_variant,p.Glu145Lys,ENST00000436747,;	A	ENSG00000180902	ENST00000321264	Transcript	missense_variant	642	433	145	E/K	Gag/Aag	rs768540316	.	.	1	D2HGDH	HGNC	28358	protein_coding	YES	CCDS33426.1	ENSP00000315351	D2HDH_HUMAN	B5MCV2_HUMAN,B3KP72_HUMAN	UPI0000456F51	.	deleterious(0)	probably_damaging(0.998)	4/10	.	PROSITE_profiles:PS51387,hmmpanther:PTHR11748,hmmpanther:PTHR11748:SF35,Pfam_domain:PF01565,Gene3D:3.30.43.10,Superfamily_domains:SSF56176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACGAGATC	byFrequency	5	ESCA
NRBP1	0	.	GRCh37	2	27662714	27662714	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.985G>C	p.Glu329Gln	p.E329Q	ENST00000233557	12/19	55	41	13	37	37	0	NRBP1,missense_variant,p.Glu329Gln,ENST00000233557,;NRBP1,missense_variant,p.Glu337Gln,ENST00000379863,;NRBP1,missense_variant,p.Glu329Gln,ENST00000379852,;IFT172,downstream_gene_variant,,ENST00000260570,;KRTCAP3,upstream_gene_variant,,ENST00000543753,;KRTCAP3,upstream_gene_variant,,ENST00000452499,;KRTCAP3,upstream_gene_variant,,ENST00000407293,;KRTCAP3,upstream_gene_variant,,ENST00000288873,;NRBP1,non_coding_transcript_exon_variant,,ENST00000460499,;NRBP1,downstream_gene_variant,,ENST00000493768,;NRBP1,upstream_gene_variant,,ENST00000486701,;KRTCAP3,upstream_gene_variant,,ENST00000453171,;KRTCAP3,upstream_gene_variant,,ENST00000464699,;IFT172,downstream_gene_variant,,ENST00000507184,;IFT172,downstream_gene_variant,,ENST00000509128,;NRBP1,downstream_gene_variant,,ENST00000493746,;KRTCAP3,upstream_gene_variant,,ENST00000494572,;	C	ENSG00000115216	ENST00000233557	Transcript	missense_variant	1817	985	329	E/Q	Gaa/Caa	.	.	.	1	NRBP1	HGNC	7993	protein_coding	YES	CCDS1753.1	ENSP00000233557	NRBP_HUMAN	C9JHZ6_HUMAN,C9JDW7_HUMAN	UPI0000035B7E	.	deleterious(0)	probably_damaging(0.997)	12/19	.	hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF48,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTGAAGTG	.	5	ESCA
SLC4A1AP	0	.	GRCh37	2	27905115	27905115	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1764G>A	p.%3D	p.K588K	ENST00000326019	9/14	33	28	5	22	22	0	SLC4A1AP,synonymous_variant,p.%3D,ENST00000326019,;	A	ENSG00000163798	ENST00000326019	Transcript	synonymous_variant	2046	1764	588	K	aaG/aaA	.	.	.	1	SLC4A1AP	HGNC	13813	protein_coding	YES	CCDS33166.1	ENSP00000323837	NADAP_HUMAN	B4DV74_HUMAN	UPI000006F66B	.	.	.	9/14	.	hmmpanther:PTHR23308:SF2,hmmpanther:PTHR23308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CCTAGGACTGA	.	2	ESCA
ABCG8	0	.	GRCh37	2	44079810	44079810	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767C>T	p.Ser256Phe	p.S256F	ENST00000272286	6/13	40	30	9	38	38	0	ABCG8,missense_variant,p.Ser256Phe,ENST00000272286,;	T	ENSG00000143921	ENST00000272286	Transcript	missense_variant	857	767	256	S/F	tCc/tTc	COSM1531902	.	.	1	ABCG8	HGNC	13887	protein_coding	YES	CCDS1815.1	ENSP00000272286	ABCG8_HUMAN	Q96A01_HUMAN	UPI000004C4CD	.	deleterious(0.01)	possibly_damaging(0.809)	6/13	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19241,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTCCAGGC	.	5	ESCA
STON1-GTF2A1L	0	.	GRCh37	2	48906683	48906683	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*102C>T	.	.	ENST00000394754	11/11	21	18	3	18	18	0	STON1-GTF2A1L,3_prime_UTR_variant,,ENST00000309827,;GTF2A1L,3_prime_UTR_variant,,ENST00000430487,;STON1-GTF2A1L,3_prime_UTR_variant,,ENST00000394754,;GTF2A1L,3_prime_UTR_variant,,ENST00000403751,;STON1-GTF2A1L,3_prime_UTR_variant,,ENST00000405008,;GTF2A1L,intron_variant,,ENST00000508440,;STON1-GTF2A1L,intron_variant,,ENST00000402114,;STON1-GTF2A1L,downstream_gene_variant,,ENST00000394751,;	T	ENSG00000068781	ENST00000394754	Transcript	3_prime_UTR_variant	3765	.	.	.	.	.	.	.	1	STON1-GTF2A1L	HGNC	30651	protein_coding	YES	CCDS1840.1	ENSP00000378236	.	Q53S48_HUMAN	UPI000013C976	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTTCAAATT	.	2	ESCA
TTC31	0	.	GRCh37	2	74717254	74717254	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.232G>A	p.Asp78Asn	p.D78N	ENST00000233623	3/13	141	123	18	89	89	0	TTC31,missense_variant,p.Asp78Asn,ENST00000410003,;TTC31,missense_variant,p.Asp78Asn,ENST00000233623,;TTC31,intron_variant,,ENST00000442235,;TTC31,upstream_gene_variant,,ENST00000414247,;TTC31,intron_variant,,ENST00000463189,;TTC31,splice_region_variant,,ENST00000489152,;TTC31,splice_region_variant,,ENST00000464241,;TTC31,non_coding_transcript_exon_variant,,ENST00000459957,;TTC31,intron_variant,,ENST00000491252,;TTC31,intron_variant,,ENST00000424122,;TTC31,intron_variant,,ENST00000449459,;TTC31,upstream_gene_variant,,ENST00000487623,;	A	ENSG00000115282	ENST00000233623	Transcript	missense_variant	239	232	78	D/N	Gat/Aat	.	.	.	1	TTC31	HGNC	25759	protein_coding	YES	CCDS42701.1	ENSP00000233623	TTC31_HUMAN	G5E9H3_HUMAN	UPI0000D611C0	.	tolerated_low_confidence(0.05)	possibly_damaging(0.691)	3/13	.	hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF314	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCATGGTGGG	.	4	ESCA
ANKRD36BP2	0	.	GRCh37	2	89084344	89084344	+	RNA	SNP	A	A	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.712A>C	.	.	ENST00000393525	7/15	100	83	17	74	74	0	ANKRD36BP2,non_coding_transcript_exon_variant,,ENST00000393525,;ANKRD36BP2,non_coding_transcript_exon_variant,,ENST00000393515,;ANKRD36BP2,intron_variant,,ENST00000575193,;	C	ENSG00000230006	ENST00000393525	Transcript	non_coding_transcript_exon_variant	712	.	.	.	.	.	.	.	1	ANKRD36BP2	HGNC	33607	processed_transcript	YES	.	.	.	.	.	.	.	.	7/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCAGCCAA	.	5	ESCA
IMPG2	0	.	GRCh37	3	100948333	100948333	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3524G>C	p.Gly1175Ala	p.G1175A	ENST00000193391	17/19	106	92	14	55	55	0	IMPG2,missense_variant,p.Gly1175Ala,ENST00000193391,;	G	ENSG00000081148	ENST00000193391	Transcript	missense_variant	3712	3524	1175	G/A	gGa/gCa	COSM3380288	.	.	-1	IMPG2	HGNC	18362	protein_coding	YES	CCDS2940.1	ENSP00000193391	IMPG2_HUMAN	F1T0J3_HUMAN	UPI000013C605	.	tolerated(0.12)	benign(0.001)	17/19	.	hmmpanther:PTHR12199:SF4,hmmpanther:PTHR12199	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGTCCCTCA	.	5	ESCA
CD47	0	.	GRCh37	3	107764115	107764115	+	3'Flank	SNP	T	T	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000361309	.	23	17	6	24	24	0	CD47,3_prime_UTR_variant,,ENST00000355354,;CD47,downstream_gene_variant,,ENST00000398258,;CD47,downstream_gene_variant,,ENST00000517766,;CD47,downstream_gene_variant,,ENST00000361309,;CD47,non_coding_transcript_exon_variant,,ENST00000471694,;	G	ENSG00000196776	ENST00000361309	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1813	-1	CD47	HGNC	1682	protein_coding	YES	CCDS43126.1	ENSP00000355361	CD47_HUMAN	.	UPI0000049C6C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAATTTTAC	.	5	ESCA
ILDR1	0	.	GRCh37	3	121713102	121713102	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.705A>G	p.%3D	p.G235G	ENST00000344209	6/8	60	42	18	39	39	0	ILDR1,synonymous_variant,p.%3D,ENST00000393631,;ILDR1,synonymous_variant,p.%3D,ENST00000344209,;ILDR1,intron_variant,,ENST00000273691,;ILDR1,intron_variant,,ENST00000462014,;ILDR1,non_coding_transcript_exon_variant,,ENST00000460554,;	C	ENSG00000145103	ENST00000344209	Transcript	synonymous_variant	832	705	235	G	ggA/ggG	.	.	.	-1	ILDR1	HGNC	28741	protein_coding	YES	CCDS56271.1	ENSP00000345667	ILDR1_HUMAN	.	UPI00003FF1E2	.	.	.	6/8	.	hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTTTCCCAT	.	5	ESCA
PLXND1	0	.	GRCh37	3	129290394	129290394	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3294G>C	p.Gln1098His	p.Q1098H	ENST00000324093	17/36	53	47	6	31	31	0	PLXND1,missense_variant,p.Gln1098His,ENST00000393239,;PLXND1,missense_variant,p.Gln1098His,ENST00000324093,;PLXND1,non_coding_transcript_exon_variant,,ENST00000515191,;PLXND1,non_coding_transcript_exon_variant,,ENST00000511018,;PLXND1,non_coding_transcript_exon_variant,,ENST00000504767,;PLXND1,upstream_gene_variant,,ENST00000514990,;PLXND1,downstream_gene_variant,,ENST00000505505,;	G	ENSG00000004399	ENST00000324093	Transcript	missense_variant	3473	3294	1098	Q/H	caG/caC	.	.	.	-1	PLXND1	HGNC	9107	protein_coding	YES	CCDS33854.1	ENSP00000317128	PLXD1_HUMAN	Q6P657_HUMAN	UPI00003671AD	.	deleterious(0)	probably_damaging(0.997)	17/36	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF7,Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATTCTGCAC	.	2	ESCA
DNAJC13	0	.	GRCh37	3	132242519	132242519	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6022G>A	p.Glu2008Lys	p.E2008K	ENST00000260818	51/56	51	46	5	23	23	0	DNAJC13,missense_variant,p.Glu2008Lys,ENST00000260818,;DNAJC13,non_coding_transcript_exon_variant,,ENST00000463038,;DNAJC13,upstream_gene_variant,,ENST00000509279,;	A	ENSG00000138246	ENST00000260818	Transcript	missense_variant	6270	6022	2008	E/K	Gaa/Aaa	.	.	.	1	DNAJC13	HGNC	30343	protein_coding	YES	CCDS33857.1	ENSP00000260818	DJC13_HUMAN	.	UPI000022C1FD	.	deleterious(0.02)	benign(0.23)	51/56	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF25,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTTAGAAAAA	.	3	ESCA
COPB2	0	.	GRCh37	3	139077583	139077583	+	Intron	SNP	G	G	C	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2553+3C>G	.	.	ENST00000333188	.	73	63	10	37	37	0	COPB2,splice_region_variant,,ENST00000333188,;COPB2,splice_region_variant,,ENST00000503326,;COPB2,splice_region_variant,,ENST00000507777,;COPB2,intron_variant,,ENST00000512309,;MRPS22,downstream_gene_variant,,ENST00000495075,;MRPS22,downstream_gene_variant,,ENST00000465056,;MRPS22,downstream_gene_variant,,ENST00000310776,;MRPS22,downstream_gene_variant,,ENST00000478464,;COPB2,non_coding_transcript_exon_variant,,ENST00000502734,;MRPS22,downstream_gene_variant,,ENST00000492644,;MRPS22,downstream_gene_variant,,ENST00000480938,;MRPS22,downstream_gene_variant,,ENST00000498505,;	C	ENSG00000184432	ENST00000333188	Transcript	splice_region_variant	.	.	.	.	.	COSM4005277	.	.	-1	COPB2	HGNC	2232	protein_coding	YES	CCDS3108.1	ENSP00000329419	COPB2_HUMAN	D6RCL6_HUMAN,D6RBZ7_HUMAN,D6RBT6_HUMAN,D6RBG7_HUMAN,B4DZI8_HUMAN	UPI0000161FB4	.	.	.	.	20/21	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACTGACCTG	.	4	ESCA
CNTN6	0	.	GRCh37	3	1427311	1427311	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2534A>G	p.Asp845Gly	p.D845G	ENST00000446702	20/23	39	35	4	43	43	0	CNTN6,missense_variant,p.Asp773Gly,ENST00000539053,;CNTN6,missense_variant,p.Asp845Gly,ENST00000446702,;CNTN6,missense_variant,p.Asp845Gly,ENST00000350110,;CNTN6,3_prime_UTR_variant,,ENST00000397479,;	G	ENSG00000134115	ENST00000446702	Transcript	missense_variant	3161	2534	845	D/G	gAt/gGt	.	.	.	1	CNTN6	HGNC	2176	protein_coding	YES	CCDS2557.1	ENSP00000407822	CNTN6_HUMAN	F5H752_HUMAN	UPI0000072430	.	tolerated(0.15)	probably_damaging(0.923)	20/23	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF52,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACAGATGACT	.	4	ESCA
PLOD2	0	.	GRCh37	3	145806375	145806375	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003A>G	p.Lys335Glu	p.K335E	ENST00000282903	9/20	63	51	12	21	21	0	PLOD2,missense_variant,p.Lys335Glu,ENST00000360060,;PLOD2,missense_variant,p.Lys280Glu,ENST00000494950,;PLOD2,missense_variant,p.Lys335Glu,ENST00000282903,;PLOD2,upstream_gene_variant,,ENST00000461497,;RP11-274H2.2,intron_variant,,ENST00000480247,;PLOD2,splice_region_variant,,ENST00000460520,;PLOD2,upstream_gene_variant,,ENST00000478436,;	C	ENSG00000152952	ENST00000282903	Transcript	missense_variant	1181	1003	335	K/E	Aaa/Gaa	.	.	.	-1	PLOD2	HGNC	9082	protein_coding	YES	CCDS3132.1	ENSP00000282903	PLOD2_HUMAN	Q9Y6D3_HUMAN,Q96QU5_HUMAN,Q96AR9_HUMAN,E7ETU9_HUMAN	UPI0000049C44	.	tolerated(0.07)	benign(0.023)	9/20	.	hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF6,Gene3D:3.90.550.10,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTTGTTAT	.	5	ESCA
HPS3	0	.	GRCh37	3	148890255	148890255	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*246A>T	.	.	ENST00000296051	17/17	24	9	14	17	17	0	HPS3,3_prime_UTR_variant,,ENST00000296051,;CP,intron_variant,,ENST00000479771,;CP,downstream_gene_variant,,ENST00000264613,;CP,downstream_gene_variant,,ENST00000494544,;HPS3,downstream_gene_variant,,ENST00000460120,;HPS3,3_prime_UTR_variant,,ENST00000460822,;CP,intron_variant,,ENST00000481169,;HPS3,downstream_gene_variant,,ENST00000478525,;CP,downstream_gene_variant,,ENST00000460674,;CP,downstream_gene_variant,,ENST00000463556,;CP,downstream_gene_variant,,ENST00000474204,;CP,downstream_gene_variant,,ENST00000473296,;	T	ENSG00000163755	ENST00000296051	Transcript	3_prime_UTR_variant	3401	.	.	.	.	.	.	.	1	HPS3	HGNC	15597	protein_coding	YES	CCDS3140.1	ENSP00000296051	HPS3_HUMAN	Q8N3N1_HUMAN	UPI000000D989	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTAAGACAT	.	5	ESCA
KCNAB1	0	.	GRCh37	3	156254522	156254522	+	Missense_Mutation	SNP	G	G	C	rs749806247	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1246G>C	p.Asp416His	p.D416H	ENST00000490337	14/14	114	104	10	61	61	0	KCNAB1,missense_variant,p.Asp405His,ENST00000471742,;KCNAB1,missense_variant,p.Asp416His,ENST00000490337,;KCNAB1,missense_variant,p.Asp387His,ENST00000389636,;KCNAB1,missense_variant,p.Asp369His,ENST00000389634,;KCNAB1,missense_variant,p.Asp398His,ENST00000302490,;SSR3,downstream_gene_variant,,ENST00000265044,;KCNAB1,non_coding_transcript_exon_variant,,ENST00000497291,;	C	ENSG00000169282	ENST00000490337	Transcript	missense_variant	1310	1246	416	D/H	Gac/Cac	rs749806247	.	.	1	KCNAB1	HGNC	6228	protein_coding	YES	CCDS3174.1	ENSP00000419952	KCAB1_HUMAN	B7Z435_HUMAN	UPI000012E169	.	deleterious(0.02)	benign(0.104)	14/14	.	hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF127	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAGGACTAT	.	4	ESCA
RARRES1	0	.	GRCh37	3	158428682	158428682	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380C>G	p.Ser127Cys	p.S127C	ENST00000237696	3/6	130	95	34	72	71	0	RARRES1,missense_variant,p.Ser127Cys,ENST00000479756,;RARRES1,missense_variant,p.Ser127Cys,ENST00000237696,;RARRES1,intron_variant,,ENST00000498640,;RARRES1,upstream_gene_variant,,ENST00000462663,;	C	ENSG00000118849	ENST00000237696	Transcript	missense_variant	661	380	127	S/C	tCt/tGt	.	.	.	-1	RARRES1	HGNC	9867	protein_coding	YES	CCDS3184.1	ENSP00000237696	TIG1_HUMAN	.	UPI000006E088	.	deleterious(0.04)	probably_damaging(0.971)	3/6	.	Pfam_domain:PF06907,Gene3D:3.10.450.10,PIRSF_domain:PIRSF500784,PIRSF_domain:PIRSF011132,Superfamily_domains:SSF54403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCAGAACAT	.	5	ESCA
SEC62	0	.	GRCh37	3	169710777	169710777	+	Missense_Mutation	SNP	G	G	C	rs746138382	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1126G>C	p.Asp376His	p.D376H	ENST00000337002	8/8	59	53	6	18	18	0	SEC62,missense_variant,p.Asp376His,ENST00000480708,;SEC62,missense_variant,p.Asp376His,ENST00000337002,;SEC62,downstream_gene_variant,,ENST00000470355,;SEC62,downstream_gene_variant,,ENST00000469515,;	C	ENSG00000008952	ENST00000337002	Transcript	missense_variant	1184	1126	376	D/H	Gat/Cat	rs746138382	.	.	1	SEC62	HGNC	11846	protein_coding	YES	CCDS3210.1	ENSP00000337688	SEC62_HUMAN	D3DNQ1_HUMAN	UPI000007186C	.	deleterious_low_confidence(0.01)	unknown(0)	8/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12443:SF9,hmmpanther:PTHR12443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACAGATGGG	.	4	ESCA
PEX5L	0	.	GRCh37	3	179519395	179519397	+	3'UTR	DEL	TTC	TTC	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	TTC	TTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*219_*221delGAA	.	.	ENST00000467460	15/15	136	113	23	75	75	0	PEX5L,3_prime_UTR_variant,,ENST00000392649,;PEX5L,3_prime_UTR_variant,,ENST00000263962,;PEX5L,3_prime_UTR_variant,,ENST00000476138,;PEX5L,3_prime_UTR_variant,,ENST00000485199,;PEX5L,3_prime_UTR_variant,,ENST00000468741,;PEX5L,3_prime_UTR_variant,,ENST00000467460,;PEX5L,downstream_gene_variant,,ENST00000472994,;PEX5L,downstream_gene_variant,,ENST00000464614,;PEX5L,downstream_gene_variant,,ENST00000465751,;RP11-494H4.3,upstream_gene_variant,,ENST00000602704,;PEX5L,downstream_gene_variant,,ENST00000467440,;	-	ENSG00000114757	ENST00000467460	Transcript	3_prime_UTR_variant	2431-2433	.	.	.	.	.	.	.	-1	PEX5L	HGNC	30024	protein_coding	YES	CCDS3236.1	ENSP00000419975	PEX5R_HUMAN	C9JZE2_HUMAN,C9IZ09_HUMAN	UPI0000049CE2	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTTAATTCTTCTT	.	3	ESCA
YEATS2	0	.	GRCh37	3	183495464	183495464	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2712A>G	p.%3D	p.G904G	ENST00000305135	19/31	47	41	5	31	31	0	YEATS2,synonymous_variant,p.%3D,ENST00000432781,;YEATS2,synonymous_variant,p.%3D,ENST00000305135,;	G	ENSG00000163872	ENST00000305135	Transcript	synonymous_variant	2907	2712	904	G	ggA/ggG	.	.	.	1	YEATS2	HGNC	25489	protein_coding	YES	CCDS43175.1	ENSP00000306983	YETS2_HUMAN	.	UPI00001BB2B9	.	.	.	19/31	.	hmmpanther:PTHR23195,hmmpanther:PTHR23195:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGGACAGAA	.	4	ESCA
WDR6	0	.	GRCh37	3	49051540	49051540	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2663C>G	p.Pro888Arg	p.P888R	ENST00000395474	2/6	46	37	9	51	51	0	WDR6,missense_variant,p.Pro888Arg,ENST00000395474,;WDR6,missense_variant,p.Pro807Arg,ENST00000448293,;WDR6,missense_variant,p.Pro306Arg,ENST00000415265,;WDR6,missense_variant,p.Pro858Arg,ENST00000608424,;DALRD3,downstream_gene_variant,,ENST00000313778,;WDR6,downstream_gene_variant,,ENST00000419837,;WDR6,downstream_gene_variant,,ENST00000489427,;DALRD3,downstream_gene_variant,,ENST00000420952,;WDR6,downstream_gene_variant,,ENST00000491365,;DALRD3,downstream_gene_variant,,ENST00000438585,;DALRD3,downstream_gene_variant,,ENST00000441576,;DALRD3,downstream_gene_variant,,ENST00000341949,;DALRD3,downstream_gene_variant,,ENST00000395462,;WDR6,downstream_gene_variant,,ENST00000429900,;DALRD3,downstream_gene_variant,,ENST00000440857,;WDR6,downstream_gene_variant,,ENST00000438660,;DALRD3,downstream_gene_variant,,ENST00000492585,;DALRD3,downstream_gene_variant,,ENST00000496568,;WDR6,downstream_gene_variant,,ENST00000489684,;WDR6,downstream_gene_variant,,ENST00000461687,;WDR6,downstream_gene_variant,,ENST00000472878,;WDR6,3_prime_UTR_variant,,ENST00000452875,;WDR6,3_prime_UTR_variant,,ENST00000420783,;WDR6,non_coding_transcript_exon_variant,,ENST00000498023,;WDR6,non_coding_transcript_exon_variant,,ENST00000471162,;WDR6,downstream_gene_variant,,ENST00000488572,;DALRD3,downstream_gene_variant,,ENST00000498794,;DALRD3,downstream_gene_variant,,ENST00000481001,;DALRD3,downstream_gene_variant,,ENST00000467457,;DALRD3,downstream_gene_variant,,ENST00000484831,;DALRD3,downstream_gene_variant,,ENST00000472331,;DALRD3,downstream_gene_variant,,ENST00000498498,;WDR6,downstream_gene_variant,,ENST00000462064,;DALRD3,downstream_gene_variant,,ENST00000460505,;WDR6,downstream_gene_variant,,ENST00000473238,;WDR6,upstream_gene_variant,,ENST00000492780,;	G	ENSG00000178252	ENST00000395474	Transcript	missense_variant	2943	2663	888	P/R	cCa/cGa	COSM1670189	.	.	1	WDR6	HGNC	12758	protein_coding	YES	CCDS2782.2	ENSP00000378857	WDR6_HUMAN	Q8NDH0_HUMAN,Q6PKC6_HUMAN,Q6AZD6_HUMAN,E9PDU5_HUMAN	UPI0000E5A634	.	deleterious(0)	probably_damaging(0.999)	2/6	.	hmmpanther:PTHR14344	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCCAGAGA	.	5	ESCA
BSN	0	.	GRCh37	3	49693542	49693542	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6553G>C	p.Ala2185Pro	p.A2185P	ENST00000296452	5/12	29	22	6	29	29	0	BSN,missense_variant,p.Ala2185Pro,ENST00000296452,;BSN,downstream_gene_variant,,ENST00000467456,;	C	ENSG00000164061	ENST00000296452	Transcript	missense_variant	6667	6553	2185	A/P	Gcc/Ccc	COSM317054	.	.	1	BSN	HGNC	1117	protein_coding	YES	CCDS2800.1	ENSP00000296452	BSN_HUMAN	.	UPI000013E33C	.	.	unknown(0)	5/12	.	hmmpanther:PTHR14113:SF1,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAGCCACT	.	5	ESCA
KBTBD8	0	.	GRCh37	3	67059335	67059335	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*526T>A	.	.	ENST00000417314	4/4	33	26	7	30	30	0	KBTBD8,3_prime_UTR_variant,,ENST00000417314,;KBTBD8,3_prime_UTR_variant,,ENST00000295568,;KBTBD8,downstream_gene_variant,,ENST00000460576,;	A	ENSG00000163376	ENST00000417314	Transcript	3_prime_UTR_variant	2381	.	.	.	.	.	.	.	1	KBTBD8	HGNC	30691	protein_coding	YES	CCDS2906.2	ENSP00000401878	KBTB8_HUMAN	C9JAA6_HUMAN,C9J331_HUMAN	UPI0000209974	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGTTCTATT	.	5	ESCA
EBLN2	0	.	GRCh37	3	73111574	73111574	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342A>G	p.%3D	p.A114A	ENST00000533473	1/1	30	22	8	31	31	0	EBLN2,synonymous_variant,p.%3D,ENST00000533473,;PPP4R2,intron_variant,,ENST00000488810,;PPP4R2,intron_variant,,ENST00000356692,;PPP4R2,intron_variant,,ENST00000394284,;PPP4R2,intron_variant,,ENST00000295862,;PPP4R2,upstream_gene_variant,,ENST00000460360,;PPP4R2,downstream_gene_variant,,ENST00000476505,;PPP4R2,intron_variant,,ENST00000482242,;PPP4R2,downstream_gene_variant,,ENST00000470976,;	G	ENSG00000255423	ENST00000533473	Transcript	synonymous_variant	765	342	114	A	gcA/gcG	.	.	.	1	EBLN2	HGNC	25493	protein_coding	YES	CCDS54608.1	ENSP00000432104	EBLN2_HUMAN	.	UPI0000231C2D	.	.	.	1/1	.	Pfam_domain:PF06407,Gene3D:1n93X01,Superfamily_domains:0041272	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCACATAA	.	5	ESCA
CTBP1	0	.	GRCh37	4	1231526	1231526	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.195+445C>T	.	.	ENST00000290921	.	269	260	9	356	356	0	CTBP1,3_prime_UTR_variant,,ENST00000510568,;CTBP1,intron_variant,,ENST00000513420,;CTBP1,intron_variant,,ENST00000382952,;CTBP1,intron_variant,,ENST00000515399,;CTBP1,intron_variant,,ENST00000514210,;CTBP1,intron_variant,,ENST00000290921,;CTBP1,intron_variant,,ENST00000506180,;CTBP1,intron_variant,,ENST00000515690,;CTBP1,intron_variant,,ENST00000514495,;CTBP1,upstream_gene_variant,,ENST00000514669,;	A	ENSG00000159692	ENST00000290921	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CTBP1	HGNC	2494	protein_coding	YES	CCDS3348.1	ENSP00000290921	CTBP1_HUMAN	.	UPI0000128637	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAGGGAAAAC	.	2	ESCA
FAT4	0	.	GRCh37	4	126373683	126373683	+	Missense_Mutation	SNP	G	G	A	rs779800461	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11512G>A	p.Val3838Met	p.V3838M	ENST00000394329	9/17	48	43	4	48	48	0	FAT4,missense_variant,p.Val3838Met,ENST00000394329,;FAT4,missense_variant,p.Val2136Met,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,;	A	ENSG00000196159	ENST00000394329	Transcript	missense_variant	11525	11512	3838	V/M	Gtg/Atg	rs779800461	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	benign(0.056)	9/17	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,Gene3D:2gy5A03,SMART_domains:SM00181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATCGTGGCA	.	4	ESCA
ETFDH	0	.	GRCh37	4	159605747	159605747	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.409C>T	p.Pro137Ser	p.P137S	ENST00000511912	4/13	38	31	7	24	24	0	ETFDH,missense_variant,p.Pro90Ser,ENST00000307738,;ETFDH,missense_variant,p.Pro137Ser,ENST00000511912,;ETFDH,5_prime_UTR_variant,,ENST00000507475,;ETFDH,downstream_gene_variant,,ENST00000512251,;ETFDH,intron_variant,,ENST00000506422,;ETFDH,downstream_gene_variant,,ENST00000436096,;ETFDH,downstream_gene_variant,,ENST00000510353,;ETFDH,non_coding_transcript_exon_variant,,ENST00000514148,;	T	ENSG00000171503	ENST00000511912	Transcript	missense_variant	741	409	137	P/S	Cca/Tca	CM093456	.	.	1	ETFDH	HGNC	3483	protein_coding	YES	CCDS3800.1	ENSP00000426638	ETFD_HUMAN	D6RAD5_HUMAN,B4DEQ0_HUMAN	UPI000013EC48	.	deleterious(0.01)	probably_damaging(1)	4/13	.	Superfamily_domains:SSF51905,Gene3D:3.50.50.60,hmmpanther:PTHR10617,hmmpanther:PTHR10617:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AGGCTCCACTT	.	2	ESCA
FNIP2	0	.	GRCh37	4	159789786	159789786	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1998C>A	p.%3D	p.P666P	ENST00000264433	13/17	22	17	5	22	22	0	FNIP2,synonymous_variant,p.%3D,ENST00000379346,;FNIP2,synonymous_variant,p.%3D,ENST00000264433,;FNIP2,downstream_gene_variant,,ENST00000512986,;FNIP2,upstream_gene_variant,,ENST00000505130,;	A	ENSG00000052795	ENST00000264433	Transcript	synonymous_variant	2073	1998	666	P	ccC/ccA	.	.	.	1	FNIP2	HGNC	29280	protein_coding	YES	CCDS47155.1	ENSP00000264433	FNIP2_HUMAN	.	UPI00001C1E0A	.	.	.	13/17	.	hmmpanther:PTHR21634,hmmpanther:PTHR21634:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCCAGCTG	.	5	ESCA
GUF1	0	.	GRCh37	4	44691414	44691414	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1190G>A	p.Gly397Asp	p.G397D	ENST00000281543	10/17	38	35	3	42	42	0	GUF1,missense_variant,p.Gly397Asp,ENST00000281543,;GNPDA2,intron_variant,,ENST00000609092,;GNPDA2,intron_variant,,ENST00000608855,;RP11-700J17.1,downstream_gene_variant,,ENST00000610260,;GUF1,non_coding_transcript_exon_variant,,ENST00000506793,;GUF1,3_prime_UTR_variant,,ENST00000513775,;	A	ENSG00000151806	ENST00000281543	Transcript	missense_variant	1384	1190	397	G/D	gGt/gAt	.	.	.	1	GUF1	HGNC	25799	protein_coding	YES	CCDS3468.1	ENSP00000281543	GUF1_HUMAN	.	UPI000006FFEC	.	deleterious(0)	probably_damaging(1)	10/17	.	Superfamily_domains:SSF54980,Gene3D:3.30.70.870,TIGRFAM_domain:TIGR01393,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF97,HAMAP:MF_00071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGGGTGCTG	.	2	ESCA
ERVMER34-1	0	.	GRCh37	4	53610318	53610324	+	Frame_Shift_Del	DEL	TTAGACT	TTAGACT	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	TTAGACT	TTAGACT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1364_1370delAGTCTAA	p.Lys455IlefsTer12	p.K455Ifs*12	ENST00000443173	3/3	45	39	6	27	27	0	ERVMER34-1,frameshift_variant,p.Lys455IlefsTer12,ENST00000540758,;ERVMER34-1,frameshift_variant,p.Lys455IlefsTer12,ENST00000440542,;ERVMER34-1,frameshift_variant,p.Lys455IlefsTer12,ENST00000443173,;SNORA26,upstream_gene_variant,,ENST00000391188,;ERVMER34-1,intron_variant,,ENST00000454756,;	-	ENSG00000226887	ENST00000443173	Transcript	frameshift_variant	2225-2231	1364-1370	455-457	KSN/X	aAGTCTAAt/at	.	.	.	-1	ERVMER34-1	HGNC	42970	protein_coding	YES	.	ENSP00000460602	MER34_HUMAN	.	UPI000006F57C	.	.	.	3/3	.	Superfamily_domains:SSF58069,Gene3D:1.10.287.210,hmmpanther:PTHR10424:SF42,hmmpanther:PTHR10424,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTATATTAGACTTTATT	.	3	ESCA
UTP3	0	.	GRCh37	4	71555258	71555258	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864G>C	p.Arg288Ser	p.R288S	ENST00000254803	1/1	37	25	11	29	29	0	UTP3,missense_variant,p.Arg288Ser,ENST00000254803,;ENAM,downstream_gene_variant,,ENST00000472903,;	C	ENSG00000132467	ENST00000254803	Transcript	missense_variant	1063	864	288	R/S	agG/agC	.	.	.	1	UTP3	HGNC	24477	protein_coding	YES	CCDS3546.1	ENSP00000254803	SAS10_HUMAN	.	UPI0000073D63	.	deleterious(0)	benign(0.043)	1/1	.	hmmpanther:PTHR13237,hmmpanther:PTHR13237:SF8,Pfam_domain:PF04000	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTAGGAGAGT	.	5	ESCA
SEPT11	0	.	GRCh37	4	77949786	77949786	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958C>T	p.Gln320Ter	p.Q320*	ENST00000264893	8/10	30	24	6	24	24	0	SEPT11,stop_gained,p.Gln320Ter,ENST00000502584,;SEPT11,stop_gained,p.Gln49Ter,ENST00000506731,;SEPT11,stop_gained,p.Gln320Ter,ENST00000505788,;SEPT11,stop_gained,p.Gln312Ter,ENST00000510641,;SEPT11,stop_gained,p.Gln320Ter,ENST00000264893,;SEPT11,stop_gained,p.Gln330Ter,ENST00000510515,;SEPT11,stop_gained,p.Gln330Ter,ENST00000541121,;SEPT11,upstream_gene_variant,,ENST00000502401,;SEPT11,non_coding_transcript_exon_variant,,ENST00000512575,;SEPT11,upstream_gene_variant,,ENST00000513697,;SEPT11,upstream_gene_variant,,ENST00000513373,;	T	ENSG00000138758	ENST00000264893	Transcript	stop_gained	1159	958	320	Q/*	Cag/Tag	.	.	.	1	SEPT11	HGNC	25589	protein_coding	YES	CCDS34018.1	ENSP00000264893	SEP11_HUMAN	.	UPI000007399D	.	.	.	8/10	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF48,PIRSF_domain:PIRSF006698	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTCAGGAG	.	5	ESCA
DCP2	0	.	GRCh37	5	112350933	112350933	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1752C>T	.	.	ENST00000389063	11/11	34	30	4	17	17	0	DCP2,3_prime_UTR_variant,,ENST00000515408,;DCP2,3_prime_UTR_variant,,ENST00000389063,;DCP2,downstream_gene_variant,,ENST00000513585,;DCP2,downstream_gene_variant,,ENST00000543319,;	T	ENSG00000172795	ENST00000389063	Transcript	3_prime_UTR_variant	3213	.	.	.	.	.	.	.	1	DCP2	HGNC	24452	protein_coding	YES	CCDS34210.1	ENSP00000373715	DCP2_HUMAN	B7Z3U5_HUMAN	UPI000020C41B	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATTCCAGAC	.	4	ESCA
TSSK1B	0	.	GRCh37	5	112770525	112770525	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12T>C	p.%3D	p.A4A	ENST00000390666	1/1	22	18	4	20	20	0	TSSK1B,synonymous_variant,p.%3D,ENST00000390666,;MCC,intron_variant,,ENST00000408903,;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000383058,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,;	G	ENSG00000212122	ENST00000390666	Transcript	synonymous_variant	204	12	4	A	gcT/gcC	.	.	.	-1	TSSK1B	HGNC	14968	protein_coding	YES	CCDS4112.1	ENSP00000375081	TSSK1_HUMAN	A0ZT98_HUMAN	UPI000003C96E	.	.	.	1/1	.	hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACAGCAGCGTC	.	4	ESCA
SHROOM1	0	.	GRCh37	5	132158683	132158683	+	Silent	SNP	G	G	A	rs765300774	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2364C>T	p.%3D	p.V788V	ENST00000378679	10/10	16	13	3	13	13	0	SHROOM1,synonymous_variant,p.%3D,ENST00000319854,;SHROOM1,synonymous_variant,p.%3D,ENST00000378679,;SHROOM1,synonymous_variant,p.%3D,ENST00000378676,;SHROOM1,downstream_gene_variant,,ENST00000440118,;AC004775.5,upstream_gene_variant,,ENST00000607389,;SHROOM1,downstream_gene_variant,,ENST00000488072,;SHROOM1,downstream_gene_variant,,ENST00000495680,;SHROOM1,downstream_gene_variant,,ENST00000606676,;	A	ENSG00000164403	ENST00000378679	Transcript	synonymous_variant	3169	2364	788	V	gtC/gtT	rs765300774	.	.	-1	SHROOM1	HGNC	24084	protein_coding	YES	CCDS54902.1	ENSP00000367950	SHRM1_HUMAN	C9JXU1_HUMAN	UPI000036FD4D	.	.	.	10/10	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51307,hmmpanther:PTHR15012,Pfam_domain:PF08687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAATAGACGCG	byFrequency	2	ESCA
FSTL4	0	.	GRCh37	5	132939673	132939673	+	Translation_Start_Site	SNP	A	A	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2T>G	p.Met1?	p.M1?	ENST00000265342	2/16	23	20	3	16	16	0	FSTL4,start_lost,p.Met1?,ENST00000265342,;	C	ENSG00000053108	ENST00000265342	Transcript	start_lost	252	2	1	M/R	aTg/aGg	.	.	.	-1	FSTL4	HGNC	21389	protein_coding	YES	CCDS34238.1	ENSP00000265342	FSTL4_HUMAN	.	UPI000003AFB0	.	deleterious_low_confidence(0)	probably_damaging(0.99)	2/16	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTCATTTTG	.	2	ESCA
DNAH5	0	.	GRCh37	5	13776634	13776634	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9287G>A	p.Arg3096Gln	p.R3096Q	ENST00000265104	55/79	46	38	8	40	40	0	DNAH5,missense_variant,p.Arg3096Gln,ENST00000265104,;	T	ENSG00000039139	ENST00000265104	Transcript	missense_variant	9392	9287	3096	R/Q	cGa/cAa	COSM393010	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	possibly_damaging(0.553)	55/79	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,Pfam_domain:PF12780,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R3096Q|c.9287G>A|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTCGAAAT	.	5	ESCA
PCDHA7	0	.	GRCh37	5	140215259	140215259	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1291G>T	p.Gly431Cys	p.G431C	ENST00000525929	1/4	162	138	24	119	119	0	PCDHA7,missense_variant,p.Gly431Cys,ENST00000378125,;PCDHA7,missense_variant,p.Gly431Cys,ENST00000525929,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	T	ENSG00000204963	ENST00000525929	Transcript	missense_variant	1291	1291	431	G/C	Ggc/Tgc	.	.	.	1	PCDHA7	HGNC	8673	protein_coding	YES	CCDS54918.1	ENSP00000436426	PCDA7_HUMAN	.	UPI00001273CF	.	deleterious_low_confidence(0.02)	probably_damaging(0.925)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R428W|c.1282C>T|3,BUFFER|p.R428W|c.1282C>T|3	RADIA|MUTECT|MUSE|VARSCANS	ACGGGGGCTCG	.	4	ESCA
PCDHA9	0	.	GRCh37	5	140228251	140228251	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.171G>A	p.%3D	p.A57A	ENST00000532602	1/4	97	80	17	72	72	0	PCDHA9,synonymous_variant,p.%3D,ENST00000378122,;PCDHA9,synonymous_variant,p.%3D,ENST00000532602,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA8,downstream_gene_variant,,ENST00000378123,;	A	ENSG00000204961	ENST00000532602	Transcript	synonymous_variant	1204	171	57	A	gcG/gcA	COSM3696973,COSM3696972	.	.	1	PCDHA9	HGNC	8675	protein_coding	YES	CCDS54920.1	ENSP00000436042	PCDA9_HUMAN	.	UPI00001273D1	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,Pfam_domain:PF08266,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGGAGCT	.	5	ESCA
IL12B	0	.	GRCh37	5	158749446	158749446	+	Silent	SNP	C	C	T	rs569226644	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438G>A	p.%3D	p.T146T	ENST00000231228	4/8	40	35	5	26	26	0	IL12B,synonymous_variant,p.%3D,ENST00000231228,;AC008697.1,intron_variant,,ENST00000521472,;RNU4ATAC2P,downstream_gene_variant,,ENST00000408674,;	T	ENSG00000113302	ENST00000231228	Transcript	synonymous_variant	894	438	146	T	acG/acA	rs569226644	.	.	-1	IL12B	HGNC	5970	protein_coding	YES	CCDS4346.1	ENSP00000231228	IL12B_HUMAN	Q8N0X8_HUMAN,A1Z2L5_HUMAN	UPI00000358B7	.	.	.	4/8	.	Superfamily_domains:SSF49265,PIRSF_domain:PIRSF038007,Gene3D:2.60.40.10,Pfam_domain:PF10420,hmmpanther:PTHR11321	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTGTCGTCAG	byCluster|by1000G	4	ESCA
KCNIP1	0	.	GRCh37	5	169931422	169931422	+	5'Flank	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000411494	.	37	30	7	29	29	0	KCNIP1,5_prime_UTR_variant,,ENST00000390656,;KCNIP1,5_prime_UTR_variant,,ENST00000328939,;KCNIP1,5_prime_UTR_variant,,ENST00000520740,;KCNIP1,intron_variant,,ENST00000377360,;KCNIP1,upstream_gene_variant,,ENST00000411494,;KCNIP1,upstream_gene_variant,,ENST00000434108,;	T	ENSG00000182132	ENST00000411494	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	155	1	KCNIP1	HGNC	15521	protein_coding	YES	CCDS34286.1	ENSP00000395323	KCIP1_HUMAN	.	UPI000004A27F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTAGCCTCGC	.	2	ESCA
ZNF354B	0	.	GRCh37	5	178311377	178311377	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*85C>T	.	.	ENST00000322434	5/5	20	15	5	18	18	0	ZNF354B,3_prime_UTR_variant,,ENST00000322434,;ZNF354B,downstream_gene_variant,,ENST00000520377,;RNU1-39P,upstream_gene_variant,,ENST00000383897,;ZNF354B,non_coding_transcript_exon_variant,,ENST00000522624,;ZNF354B,non_coding_transcript_exon_variant,,ENST00000522714,;	T	ENSG00000178338	ENST00000322434	Transcript	3_prime_UTR_variant	2150	.	.	.	.	.	.	.	1	ZNF354B	HGNC	17197	protein_coding	YES	CCDS4439.1	ENSP00000327143	Z354B_HUMAN	E5RH89_HUMAN	UPI0000071A24	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTCTCATCAG	.	2	ESCA
HCN1	0	.	GRCh37	5	45262430	45262430	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2266C>T	p.Gln756Ter	p.Q756*	ENST00000303230	8/8	42	35	7	43	43	0	HCN1,stop_gained,p.Gln756Ter,ENST00000303230,;	A	ENSG00000164588	ENST00000303230	Transcript	stop_gained	2324	2266	756	Q/*	Cag/Tag	COSM236753	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	.	.	8/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10217:SF373,hmmpanther:PTHR10217	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTGTGGCT	.	5	ESCA
BHMT	0	.	GRCh37	5	78417107	78417107	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544G>A	p.Ala182Thr	p.A182T	ENST00000274353	5/8	41	36	5	41	41	0	BHMT,missense_variant,p.Ala182Thr,ENST00000274353,;BHMT,intron_variant,,ENST00000524080,;DMGDH,non_coding_transcript_exon_variant,,ENST00000518707,;DMGDH,non_coding_transcript_exon_variant,,ENST00000520388,;BHMT,non_coding_transcript_exon_variant,,ENST00000523508,;BHMT,non_coding_transcript_exon_variant,,ENST00000521279,;BHMT,downstream_gene_variant,,ENST00000520703,;BHMT,downstream_gene_variant,,ENST00000520335,;	A	ENSG00000145692	ENST00000274353	Transcript	missense_variant	651	544	182	A/T	Gca/Aca	.	.	.	1	BHMT	HGNC	1047	protein_coding	YES	CCDS4046.1	ENSP00000274353	BHMT1_HUMAN	.	UPI000006D864	.	deleterious(0.03)	possibly_damaging(0.584)	5/8	.	PROSITE_profiles:PS50970,hmmpanther:PTHR21091,hmmpanther:PTHR21091:SF94,Pfam_domain:PF02574,Gene3D:3.20.20.330,PIRSF_domain:PIRSF037505,Superfamily_domains:SSF82282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTGGCAGCA	.	4	ESCA
RHOBTB3	0	.	GRCh37	5	95128791	95128791	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1749C>A	p.His583Gln	p.H583Q	ENST00000379982	12/12	45	30	15	41	41	0	RHOBTB3,missense_variant,p.His214Gln,ENST00000504179,;RHOBTB3,missense_variant,p.Thr30Lys,ENST00000514198,;RHOBTB3,missense_variant,p.His86Gln,ENST00000503737,;RHOBTB3,missense_variant,p.His583Gln,ENST00000379982,;RHOBTB3,intron_variant,,ENST00000513091,;GLRX,intron_variant,,ENST00000508780,;RHOBTB3,downstream_gene_variant,,ENST00000510313,;GLRX,intron_variant,,ENST00000507605,;RHOBTB3,downstream_gene_variant,,ENST00000511558,;	A	ENSG00000164292	ENST00000379982	Transcript	missense_variant	2257	1749	583	H/Q	caC/caA	.	.	.	1	RHOBTB3	HGNC	18757	protein_coding	YES	CCDS4077.1	ENSP00000369318	RHBT3_HUMAN	.	UPI0000367303	.	deleterious(0.01)	possibly_damaging(0.592)	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCACAGATG	.	5	ESCA
SLC35F1	0	.	GRCh37	6	118635678	118635678	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*263G>C	.	.	ENST00000360388	8/8	56	52	4	54	54	0	SLC35F1,3_prime_UTR_variant,,ENST00000360388,;	C	ENSG00000196376	ENST00000360388	Transcript	3_prime_UTR_variant	1691	.	.	.	.	.	.	.	1	SLC35F1	HGNC	21483	protein_coding	YES	CCDS34524.1	ENSP00000353557	S35F1_HUMAN	B4DJ02_HUMAN,B3KY53_HUMAN	UPI00001609C1	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTGAATCA	.	2	ESCA
FUCA2	0	.	GRCh37	6	143828412	143828412	+	Missense_Mutation	SNP	C	C	T	rs757296473	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.374G>A	p.Gly125Asp	p.G125D	ENST00000002165	2/7	64	52	12	44	44	0	FUCA2,missense_variant,p.Gly125Asp,ENST00000438118,;FUCA2,missense_variant,p.Gly125Asp,ENST00000002165,;RP1-20N2.6,non_coding_transcript_exon_variant,,ENST00000591892,;RP1-20N2.6,downstream_gene_variant,,ENST00000610068,;RP1-20N2.6,downstream_gene_variant,,ENST00000593175,;RP1-20N2.6,downstream_gene_variant,,ENST00000593045,;RP1-20N2.6,downstream_gene_variant,,ENST00000591189,;RP1-20N2.6,downstream_gene_variant,,ENST00000590703,;RP1-20N2.6,downstream_gene_variant,,ENST00000415586,;RP1-20N2.6,downstream_gene_variant,,ENST00000589489,;RP1-20N2.6,downstream_gene_variant,,ENST00000589563,;FUCA2,non_coding_transcript_exon_variant,,ENST00000367585,;	T	ENSG00000001036	ENST00000002165	Transcript	missense_variant	430	374	125	G/D	gGt/gAt	rs757296473	.	.	-1	FUCA2	HGNC	4008	protein_coding	YES	CCDS5200.1	ENSP00000002165	FUCO2_HUMAN	.	UPI0000073C10	.	deleterious(0)	probably_damaging(0.993)	2/7	.	hmmpanther:PTHR10030,hmmpanther:PTHR10030:SF24,Pfam_domain:PF01120,Gene3D:3.20.20.80,SMART_domains:SM00812,PIRSF_domain:PIRSF001092,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCACCAGAG	.	5	ESCA
ESR1	0	.	GRCh37	6	152265629	152265629	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1082C>T	p.Ala361Val	p.A361V	ENST00000440973	6/10	27	24	3	13	13	0	ESR1,missense_variant,p.Ala361Val,ENST00000440973,;ESR1,missense_variant,p.Ala188Val,ENST00000427531,;ESR1,missense_variant,p.Ala361Val,ENST00000338799,;ESR1,missense_variant,p.Ala361Val,ENST00000443427,;ESR1,missense_variant,p.Ala361Val,ENST00000206249,;ESR1,intron_variant,,ENST00000406599,;ESR1,intron_variant,,ENST00000456483,;ESR1,intron_variant,,ENST00000415488,;ESR1,non_coding_transcript_exon_variant,,ENST00000482101,;	T	ENSG00000091831	ENST00000440973	Transcript	missense_variant	1452	1082	361	A/V	gCg/gTg	.	.	.	1	ESR1	HGNC	3467	protein_coding	YES	CCDS5234.1	ENSP00000405330	ESR1_HUMAN	Q9UE35_HUMAN,Q9UBT1_HUMAN,Q5T5H8_HUMAN,K7R989_HUMAN,K4Q331_HUMAN,K4PXX0_HUMAN,K4PX46_HUMAN,G4XH65_HUMAN,E3WH18_HUMAN,C8CJL0_HUMAN,C7FFR5_HUMAN,B6DU67_HUMAN	UPI000004A328	.	deleterious(0)	probably_damaging(0.999)	6/10	.	hmmpanther:PTHR24084:SF3,hmmpanther:PTHR24084,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,PIRSF_domain:PIRSF500101,PIRSF_domain:PIRSF002527,Superfamily_domains:SSF48508,Prints_domain:PR00398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CTGGGCGAAGA	.	2	ESCA
BTN3A3	0	.	GRCh37	6	26452498	26452498	+	Silent	SNP	G	G	A	rs757126334	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1614G>A	p.%3D	p.P538P	ENST00000244519	11/11	75	56	18	47	47	0	BTN3A3,synonymous_variant,p.%3D,ENST00000361232,;BTN3A3,synonymous_variant,p.%3D,ENST00000244519,;BTN3A3,synonymous_variant,p.%3D,ENST00000339789,;BTN3A3,downstream_gene_variant,,ENST00000490254,;BTN3A3,downstream_gene_variant,,ENST00000487272,;BTN3A3,non_coding_transcript_exon_variant,,ENST00000480110,;BTN3A3,downstream_gene_variant,,ENST00000477388,;BTN3A3,downstream_gene_variant,,ENST00000497681,;BTN3A3,downstream_gene_variant,,ENST00000483179,;	A	ENSG00000111801	ENST00000244519	Transcript	synonymous_variant	1857	1614	538	P	ccG/ccA	rs757126334	.	.	1	BTN3A3	HGNC	1140	protein_coding	YES	CCDS4611.1	ENSP00000244519	BT3A3_HUMAN	D0FY33_HUMAN,C9JUV8_HUMAN,C9JQT8_HUMAN,C9JNZ3_HUMAN,C9J877_HUMAN,C9J3Q8_HUMAN	UPI00000480EF	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCCGGGCTT	byFrequency	5	ESCA
SCUBE3	0	.	GRCh37	6	35211789	35211789	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2121G>A	p.%3D	p.Q707Q	ENST00000274938	17/22	43	36	7	41	41	0	SCUBE3,synonymous_variant,p.%3D,ENST00000394681,;SCUBE3,synonymous_variant,p.%3D,ENST00000274938,;	A	ENSG00000146197	ENST00000274938	Transcript	synonymous_variant	2121	2121	707	Q	caG/caA	.	.	.	1	SCUBE3	HGNC	13655	protein_coding	YES	CCDS4800.1	ENSP00000274938	SCUB3_HUMAN	Q7Z3I8_HUMAN	UPI0000074423	.	.	.	17/22	.	hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF2,Pfam_domain:PF07699,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCAGCCATG	.	5	ESCA
GSTA5	0	.	GRCh37	6	52697688	52697688	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.515C>T	p.Ser172Leu	p.S172L	ENST00000370989	5/6	72	34	38	67	67	0	GSTA5,missense_variant,p.Ser172Leu,ENST00000370989,;GSTA5,missense_variant,p.Ser172Leu,ENST00000284562,;GSTA5,non_coding_transcript_exon_variant,,ENST00000475052,;	A	ENSG00000182793	ENST00000370989	Transcript	missense_variant	545	515	172	S/L	tCg/tTg	.	.	.	-1	GSTA5	HGNC	19662	protein_coding	YES	CCDS4946.1	ENSP00000360028	GSTA5_HUMAN	.	UPI0000049038	.	deleterious(0.04)	benign(0.323)	5/6	.	Superfamily_domains:SSF47616,Pfam_domain:PF00043,Gene3D:1.20.1050.10,hmmpanther:PTHR11571:SF131,hmmpanther:PTHR11571,PROSITE_profiles:PS50405	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTCGAGTCA	.	5	ESCA
TFR2	0	.	GRCh37	7	100238796	100238796	+	Missense_Mutation	SNP	C	C	T	rs750603454	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.89G>A	p.Arg30Gln	p.R30Q	ENST00000462107	3/19	57	52	5	24	24	0	TFR2,missense_variant,p.Arg30Gln,ENST00000462107,;TFR2,missense_variant,p.Arg30Gln,ENST00000223051,;TFR2,missense_variant,p.Arg30Gln,ENST00000431692,;ACTL6B,downstream_gene_variant,,ENST00000160382,;TFR2,non_coding_transcript_exon_variant,,ENST00000474947,;TFR2,non_coding_transcript_exon_variant,,ENST00000465294,;ACTL6B,downstream_gene_variant,,ENST00000487125,;	T	ENSG00000106327	ENST00000462107	Transcript	missense_variant	377	89	30	R/Q	cGg/cAg	rs750603454	.	.	-1	TFR2	HGNC	11762	protein_coding	YES	CCDS34707.1	ENSP00000420525	TFR2_HUMAN	.	UPI0000136C99	.	tolerated_low_confidence(1)	benign(0.001)	3/19	.	hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTTTCCGGGGG	byFrequency	3	ESCA
RELN	0	.	GRCh37	7	103136182	103136182	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9357G>C	p.Met3119Ile	p.M3119I	ENST00000428762	57/65	247	229	18	88	88	0	RELN,missense_variant,p.Met3119Ile,ENST00000424685,;RELN,missense_variant,p.Met3119Ile,ENST00000428762,;RELN,missense_variant,p.Met3119Ile,ENST00000343529,;CTB-107G13.1,intron_variant,,ENST00000422488,;	G	ENSG00000189056	ENST00000428762	Transcript	missense_variant	9517	9357	3119	M/I	atG/atC	COSM1173271	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	tolerated(0.29)	benign(0.101)	57/65	.	hmmpanther:PTHR11841	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCATCATGTA	.	2	ESCA
AGMO	0	.	GRCh37	7	15427133	15427133	+	Silent	SNP	G	G	A	rs772554565	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855C>T	p.%3D	p.F285F	ENST00000342526	9/13	75	63	11	45	45	0	AGMO,synonymous_variant,p.%3D,ENST00000342526,;	A	ENSG00000187546	ENST00000342526	Transcript	synonymous_variant	1025	855	285	F	ttC/ttT	rs772554565,COSM1087718	.	.	-1	AGMO	HGNC	33784	protein_coding	YES	CCDS34604.1	ENSP00000341662	ALKMO_HUMAN	.	UPI0000050343	.	.	.	9/13	.	hmmpanther:PTHR21624	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCAGAATGT	byFrequency	4	ESCA
TWISTNB	0	.	GRCh37	7	19748503	19748503	+	Missense_Mutation	SNP	G	G	A	rs527876640	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.137C>T	p.Ser46Leu	p.S46L	ENST00000222567	1/4	60	49	10	40	40	0	TWISTNB,missense_variant,p.Ser46Leu,ENST00000222567,;MIR3146,upstream_gene_variant,,ENST00000580367,;	A	ENSG00000105849	ENST00000222567	Transcript	missense_variant	208	137	46	S/L	tCa/tTa	rs527876640	.	.	-1	TWISTNB	HGNC	18027	protein_coding	YES	CCDS34606.1	ENSP00000222567	RPA43_HUMAN	.	UPI000006CEF4	.	deleterious(0)	probably_damaging(0.999)	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGCATGAGTAG	byCluster	4	ESCA
SDK1	0	.	GRCh37	7	4247736	4247736	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5220C>G	p.Tyr1740Ter	p.Y1740*	ENST00000404826	37/45	95	83	11	37	37	0	SDK1,stop_gained,p.Tyr1740Ter,ENST00000404826,;SDK1,stop_gained,p.Tyr1720Ter,ENST00000389531,;SDK1,non_coding_transcript_exon_variant,,ENST00000476701,;	G	ENSG00000146555	ENST00000404826	Transcript	stop_gained	5359	5220	1740	Y/*	taC/taG	.	.	.	1	SDK1	HGNC	19307	protein_coding	YES	CCDS34590.1	ENSP00000385899	SDK1_HUMAN	.	UPI0000DBEEC4	.	.	.	37/45	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF36,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTTACTACTG	.	4	ESCA
GBAS	0	.	GRCh37	7	56066786	56066786	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*21C>T	.	.	ENST00000322090	10/10	57	43	14	40	40	0	GBAS,3_prime_UTR_variant,,ENST00000322090,;GBAS,3_prime_UTR_variant,,ENST00000446778,;GBAS,downstream_gene_variant,,ENST00000437587,;GBAS,3_prime_UTR_variant,,ENST00000415967,;GBAS,non_coding_transcript_exon_variant,,ENST00000497279,;	T	ENSG00000146729	ENST00000322090	Transcript	3_prime_UTR_variant	911	.	.	.	.	.	.	.	1	GBAS	HGNC	4179	protein_coding	YES	CCDS5521.1	ENSP00000313050	NIPS2_HUMAN	C9K068_HUMAN,C9J7B1_HUMAN	UPI00000015EB	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGCCTACA	.	5	ESCA
PCLO	0	.	GRCh37	7	82579600	82579600	+	Missense_Mutation	SNP	C	C	T	rs775369053	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10304G>A	p.Arg3435Gln	p.R3435Q	ENST00000333891	6/25	90	80	9	68	68	0	PCLO,missense_variant,p.Arg155Gln,ENST00000437081,;PCLO,missense_variant,p.Arg3435Gln,ENST00000333891,;PCLO,missense_variant,p.Arg3435Gln,ENST00000423517,;	T	ENSG00000186472	ENST00000333891	Transcript	missense_variant	10642	10304	3435	R/Q	cGa/cAa	rs775369053,COSM1452328,COSM1452327,COSM1452329	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	6/25	.	hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTTCGGGGA	byFrequency	4	ESCA
NXPH1	0	.	GRCh37	7	8791241	8791241	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658C>A	p.Gln220Lys	p.Q220K	ENST00000405863	3/3	51	43	8	32	32	0	NXPH1,missense_variant,p.Gln103Lys,ENST00000602349,;NXPH1,missense_variant,p.Gln220Lys,ENST00000405863,;NXPH1,downstream_gene_variant,,ENST00000429542,;NXPH1,downstream_gene_variant,,ENST00000438764,;NXPH1,non_coding_transcript_exon_variant,,ENST00000497400,;	A	ENSG00000122584	ENST00000405863	Transcript	missense_variant	1569	658	220	Q/K	Cag/Aag	.	.	.	1	NXPH1	HGNC	20693	protein_coding	YES	CCDS47540.1	ENSP00000384551	NXPH1_HUMAN	Q3LID8_HUMAN,C9JPD0_HUMAN,C9JE46_HUMAN,B4DJV1_HUMAN	UPI000000DC02	.	tolerated(0.09)	possibly_damaging(0.792)	3/3	.	hmmpanther:PTHR17103,hmmpanther:PTHR17103:SF13,Pfam_domain:PF06312,PIRSF_domain:PIRSF038019	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTACCAGGAG	.	5	ESCA
STEAP2	0	.	GRCh37	7	89859299	89859299	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1134T>C	p.%3D	p.S378S	ENST00000287908	4/5	75	33	42	55	55	0	STEAP2,synonymous_variant,p.%3D,ENST00000394629,;STEAP2,synonymous_variant,p.%3D,ENST00000402625,;STEAP2,synonymous_variant,p.%3D,ENST00000394632,;STEAP2,synonymous_variant,p.%3D,ENST00000394621,;STEAP2,synonymous_variant,p.%3D,ENST00000394626,;STEAP2,synonymous_variant,p.%3D,ENST00000287908,;STEAP2,synonymous_variant,p.%3D,ENST00000394622,;STEAP2,downstream_gene_variant,,ENST00000428074,;STEAP2,downstream_gene_variant,,ENST00000426158,;STEAP2,downstream_gene_variant,,ENST00000482369,;	C	ENSG00000157214	ENST00000287908	Transcript	synonymous_variant	1527	1134	378	S	tcT/tcC	.	.	.	1	STEAP2	HGNC	17885	protein_coding	YES	CCDS5615.1	ENSP00000287908	STEA2_HUMAN	C9JLP2_HUMAN,C9JHX5_HUMAN	UPI000013DEE0	.	.	.	4/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14239,hmmpanther:PTHR14239:SF6,Pfam_domain:PF01794	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTCTATCCC	.	5	ESCA
FAM86B1	0	.	GRCh37	8	12040280	12040280	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*835A>T	.	.	ENST00000448228	7/7	251	243	8	239	239	0	FAM86B1,3_prime_UTR_variant,,ENST00000448228,;FAM86B1,3_prime_UTR_variant,,ENST00000533852,;FAM86B1,downstream_gene_variant,,ENST00000321602,;FAM86B1,downstream_gene_variant,,ENST00000524571,;FAM86B1,downstream_gene_variant,,ENST00000533513,;FAM86B1,downstream_gene_variant,,ENST00000534520,;AC145124.1,downstream_gene_variant,,ENST00000579282,;FAM86B1,3_prime_UTR_variant,,ENST00000431227,;FAM86B1,3_prime_UTR_variant,,ENST00000529146,;FAM86B1,3_prime_UTR_variant,,ENST00000340537,;FAM86B1,3_prime_UTR_variant,,ENST00000534187,;FAM86B1,downstream_gene_variant,,ENST00000531833,;FAM86B1,downstream_gene_variant,,ENST00000530385,;FAM86B1,downstream_gene_variant,,ENST00000529060,;FAM86B1,downstream_gene_variant,,ENST00000529617,;FAM86B1,downstream_gene_variant,,ENST00000526708,;FAM86B1,downstream_gene_variant,,ENST00000530508,;FAM86B1,downstream_gene_variant,,ENST00000534732,;FAM86B1,downstream_gene_variant,,ENST00000524893,;FAM86B1,downstream_gene_variant,,ENST00000527300,;FAM86B1,downstream_gene_variant,,ENST00000525822,;ALG1L11P,downstream_gene_variant,,ENST00000511660,;FAM90A2P,upstream_gene_variant,,ENST00000511144,;	A	ENSG00000186523	ENST00000448228	Transcript	3_prime_UTR_variant	1776	.	.	.	.	.	.	.	-1	FAM86B1	HGNC	28268	protein_coding	YES	CCDS59512.1	ENSP00000407067	F86B1_HUMAN	H9XFB3_HUMAN	UPI0000F58EC4	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCTTCTTG	.	2	ESCA
KCNQ3	0	.	GRCh37	8	133192457	133192457	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724C>T	p.Arg242Trp	p.R242W	ENST00000388996	4/15	48	41	6	42	42	0	KCNQ3,missense_variant,p.Arg122Trp,ENST00000521134,;KCNQ3,missense_variant,p.Arg242Trp,ENST00000388996,;KCNQ3,missense_variant,p.Arg242Trp,ENST00000519445,;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,;	A	ENSG00000184156	ENST00000388996	Transcript	missense_variant	1145	724	242	R/W	Cgg/Tgg	.	.	.	-1	KCNQ3	HGNC	6297	protein_coding	YES	CCDS34943.1	ENSP00000373648	KCNQ3_HUMAN	.	UPI00001279F0	.	deleterious(0)	probably_damaging(0.967)	4/15	.	hmmpanther:PTHR11537:SF5,hmmpanther:PTHR11537,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR00169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTCCGGTCCA	.	4	ESCA
CYP11B2	0	.	GRCh37	8	143999142	143999142	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115G>C	p.Glu39Gln	p.E39Q	ENST00000323110	1/9	49	43	6	25	25	0	CYP11B2,missense_variant,p.Glu39Gln,ENST00000323110,;GML,downstream_gene_variant,,ENST00000522728,;	G	ENSG00000179142	ENST00000323110	Transcript	missense_variant	118	115	39	E/Q	Gaa/Caa	.	.	.	-1	CYP11B2	HGNC	2592	protein_coding	YES	CCDS6393.1	ENSP00000325822	C11B2_HUMAN	Q14098_HUMAN	UPI00001282CF	.	tolerated(0.05)	possibly_damaging(0.792)	1/9	.	hmmpanther:PTHR24279:SF46,hmmpanther:PTHR24279	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGCTTCAAACG	.	2	ESCA
PLEC	0	.	GRCh37	8	144989388	144989388	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*957C>G	.	.	ENST00000322810	32/32	24	17	6	21	21	0	PLEC,3_prime_UTR_variant,,ENST00000322810,;PLEC,3_prime_UTR_variant,,ENST00000345136,;PLEC,3_prime_UTR_variant,,ENST00000357649,;PLEC,3_prime_UTR_variant,,ENST00000398774,;PLEC,3_prime_UTR_variant,,ENST00000354589,;PLEC,3_prime_UTR_variant,,ENST00000356346,;PLEC,3_prime_UTR_variant,,ENST00000436759,;PLEC,3_prime_UTR_variant,,ENST00000354958,;PLEC,downstream_gene_variant,,ENST00000527096,;	C	ENSG00000178209	ENST00000322810	Transcript	3_prime_UTR_variant	15182	.	.	.	.	.	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTGCCCTT	.	5	ESCA
TMEM249	0	.	GRCh37	8	145577021	145577021	+	Missense_Mutation	SNP	C	C	A	rs782749441	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.695G>T	p.Ser232Ile	p.S232I	ENST00000398633	5/5	32	23	9	35	34	1	TMEM249,missense_variant,p.Gln200His,ENST00000526263,;TMEM249,missense_variant,p.Ser232Ile,ENST00000398633,;FBXL6,downstream_gene_variant,,ENST00000331890,;FBXL6,downstream_gene_variant,,ENST00000455319,;SLC52A2,upstream_gene_variant,,ENST00000524541,;SLC52A2,upstream_gene_variant,,ENST00000532815,;FBXL6,downstream_gene_variant,,ENST00000530687,;FBXL6,downstream_gene_variant,,ENST00000527000,;FBXL6,downstream_gene_variant,,ENST00000524909,;FBXL6,downstream_gene_variant,,ENST00000526524,;GS1-393G12.13,3_prime_UTR_variant,,ENST00000531225,;TMEM249,non_coding_transcript_exon_variant,,ENST00000526503,;FBXL6,downstream_gene_variant,,ENST00000530142,;FBXL6,downstream_gene_variant,,ENST00000529279,;FBXL6,downstream_gene_variant,,ENST00000524492,;	A	ENSG00000214597	ENST00000398633	Transcript	missense_variant	842	695	232	S/I	aGc/aTc	rs782749441	.	.	-1	TMEM249	HGNC	44155	protein_coding	YES	CCDS59117.1	ENSP00000381630	TM249_HUMAN	.	UPI000019984E	.	deleterious_low_confidence(0.03)	benign(0.048)	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGGCTGGAC	byFrequency	2	ESCA
NUGGC	0	.	GRCh37	8	27898648	27898648	+	Missense_Mutation	SNP	C	C	T	rs373371560	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1531G>A	p.Ala511Thr	p.A511T	ENST00000413272	13/19	27	24	3	32	32	0	NUGGC,missense_variant,p.Ala511Thr,ENST00000413272,;NUGGC,missense_variant,p.Ala511Thr,ENST00000341513,;	T	ENSG00000189233	ENST00000413272	Transcript	missense_variant	1674	1531	511	A/T	Gcc/Acc	rs373371560,COSM605037,COSM605036	.	.	-1	NUGGC	HGNC	33550	protein_coding	YES	CCDS47833.1	ENSP00000408697	SLIP_HUMAN	.	UPI0000237454	.	tolerated(0.2)	benign(0.04)	13/19	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGGCGAAGC	byFrequency|byCluster	2	ESCA
RAB11FIP1	0	.	GRCh37	8	37730432	37730432	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1888T>A	p.Leu630Met	p.L630M	ENST00000330843	4/6	76	47	29	22	22	0	RAB11FIP1,missense_variant,p.Leu630Met,ENST00000330843,;RAB11FIP1,intron_variant,,ENST00000524118,;RAB11FIP1,intron_variant,,ENST00000522727,;RAB11FIP1,intron_variant,,ENST00000287263,;RAB11FIP1,non_coding_transcript_exon_variant,,ENST00000523182,;RAB11FIP1,non_coding_transcript_exon_variant,,ENST00000522774,;	T	ENSG00000156675	ENST00000330843	Transcript	missense_variant	1901	1888	630	L/M	Ttg/Atg	.	.	.	-1	RAB11FIP1	HGNC	30265	protein_coding	YES	CCDS34882.1	ENSP00000331342	RFIP1_HUMAN	.	UPI0000D624B1	.	tolerated(0.06)	possibly_damaging(0.885)	4/6	.	hmmpanther:PTHR15746,hmmpanther:PTHR15746:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCAAGGGTG	.	5	ESCA
SLC20A2	0	.	GRCh37	8	42274276	42274276	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1045G>C	.	.	ENST00000342228	11/11	36	28	7	11	11	0	SLC20A2,3_prime_UTR_variant,,ENST00000342228,;SLC20A2,downstream_gene_variant,,ENST00000520262,;SLC20A2,downstream_gene_variant,,ENST00000520179,;	G	ENSG00000168575	ENST00000342228	Transcript	3_prime_UTR_variant	3374	.	.	.	.	.	.	.	-1	SLC20A2	HGNC	10947	protein_coding	YES	CCDS6132.1	ENSP00000340465	S20A2_HUMAN	E5RJW9_HUMAN,E5RIX1_HUMAN,E5RGJ6_HUMAN,E5RGG8_HUMAN	UPI000006DC58	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AATGTCAAAGC	.	3	ESCA
NPBWR1	0	.	GRCh37	8	53852501	53852501	+	Missense_Mutation	SNP	G	G	A	rs758280395	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34G>A	p.Ala12Thr	p.A12T	ENST00000331251	1/1	44	41	3	27	27	0	NPBWR1,missense_variant,p.Ala12Thr,ENST00000331251,;	A	ENSG00000183729	ENST00000331251	Transcript	missense_variant	1511	34	12	A/T	Gcc/Acc	rs758280395	.	.	1	NPBWR1	HGNC	4522	protein_coding	YES	CCDS6151.1	ENSP00000330284	NPBW1_HUMAN	H9NIL7_HUMAN	UPI000013EEF3	.	tolerated(0.56)	benign(0)	1/1	.	hmmpanther:PTHR24229:SF29,hmmpanther:PTHR24229,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCCGCCAAC	byFrequency	2	ESCA
SULF1	0	.	GRCh37	8	70405348	70405348	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-390-2652G>A	.	.	ENST00000260128	.	75	69	6	50	50	0	SULF1,5_prime_UTR_variant,,ENST00000419716,;SULF1,5_prime_UTR_variant,,ENST00000402687,;SULF1,intron_variant,,ENST00000525061,;SULF1,intron_variant,,ENST00000260128,;SULF1,intron_variant,,ENST00000529134,;SULF1,intron_variant,,ENST00000458141,;SULF1,intron_variant,,ENST00000528286,;SULF1,non_coding_transcript_exon_variant,,ENST00000529041,;	A	ENSG00000137573	ENST00000260128	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SULF1	HGNC	20391	protein_coding	YES	CCDS6204.1	ENSP00000260128	SULF1_HUMAN	Q96E28_HUMAN,E9PS14_HUMAN,E9PPQ3_HUMAN,E9PLS5_HUMAN,E9PJL8_HUMAN,E9PI06_HUMAN	UPI000003FD82	.	.	.	.	1/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTTTGAAGGC	.	3	ESCA
EYA1	0	.	GRCh37	8	72110634	72110634	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*941T>A	.	.	ENST00000340726	18/18	37	34	3	32	32	0	EYA1,3_prime_UTR_variant,,ENST00000388741,;EYA1,3_prime_UTR_variant,,ENST00000388742,;EYA1,3_prime_UTR_variant,,ENST00000340726,;EYA1,3_prime_UTR_variant,,ENST00000388740,;EYA1,3_prime_UTR_variant,,ENST00000303824,;EYA1,downstream_gene_variant,,ENST00000419131,;EYA1,downstream_gene_variant,,ENST00000388743,;RP11-326E22.1,intron_variant,,ENST00000521685,;EYA1,3_prime_UTR_variant,,ENST00000465115,;EYA1,downstream_gene_variant,,ENST00000496494,;	T	ENSG00000104313	ENST00000340726	Transcript	3_prime_UTR_variant	3360	.	.	.	.	.	.	.	-1	EYA1	HGNC	3519	protein_coding	YES	CCDS34906.1	ENSP00000342626	EYA1_HUMAN	Q4A4D0_HUMAN	UPI000012A3B3	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TACTGACACTT	.	2	ESCA
FABP4	0	.	GRCh37	8	82391122	82391122	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377C>T	p.Thr126Met	p.T126M	ENST00000256104	4/4	44	35	9	34	34	0	FABP4,missense_variant,p.Thr126Met,ENST00000256104,;RP11-157I4.4,intron_variant,,ENST00000524085,;FABP4,non_coding_transcript_exon_variant,,ENST00000518669,;FABP4,3_prime_UTR_variant,,ENST00000522659,;FABP4,non_coding_transcript_exon_variant,,ENST00000521734,;	A	ENSG00000170323	ENST00000256104	Transcript	missense_variant	473	377	126	T/M	aCg/aTg	.	.	.	-1	FABP4	HGNC	3559	protein_coding	YES	CCDS6230.1	ENSP00000256104	FABP4_HUMAN	E7DVW4_HUMAN	UPI000013CEEC	.	deleterious(0.01)	possibly_damaging(0.669)	4/4	.	Prints_domain:PR00178,Superfamily_domains:SSF50814,Gene3D:2.40.128.20,Pfam_domain:PF00061,hmmpanther:PTHR11955:SF71,hmmpanther:PTHR11955	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTCTCGTGGAA	.	4	ESCA
CNBD1	0	.	GRCh37	8	88297028	88297028	+	Silent	SNP	T	T	C	rs774645211	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.894T>C	p.%3D	p.Y298Y	ENST00000518476	7/11	37	31	6	33	33	0	CNBD1,synonymous_variant,p.%3D,ENST00000518476,;CNBD1,upstream_gene_variant,,ENST00000523299,;CNBD1,downstream_gene_variant,,ENST00000522427,;	C	ENSG00000176571	ENST00000518476	Transcript	synonymous_variant	945	894	298	Y	taT/taC	rs774645211	.	.	1	CNBD1	HGNC	26663	protein_coding	YES	CCDS55259.1	ENSP00000430073	CNBD1_HUMAN	.	UPI000006EA68	.	.	.	7/11	.	hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF124,Gene3D:2.60.120.10,Superfamily_domains:SSF51206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATATGCAAA	byFrequency	4	ESCA
SDC2	0	.	GRCh37	8	97622459	97622459	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*683T>A	.	.	ENST00000302190	5/5	46	38	8	32	32	0	SDC2,3_prime_UTR_variant,,ENST00000302190,;SDC2,downstream_gene_variant,,ENST00000522911,;SDC2,downstream_gene_variant,,ENST00000521590,;SDC2,downstream_gene_variant,,ENST00000523877,;SDC2,downstream_gene_variant,,ENST00000518385,;SDC2,downstream_gene_variant,,ENST00000519914,;	A	ENSG00000169439	ENST00000302190	Transcript	3_prime_UTR_variant	2210	.	.	.	.	.	.	.	1	SDC2	HGNC	10659	protein_coding	YES	CCDS6272.1	ENSP00000307046	SDC2_HUMAN	E5RJB8_HUMAN,E9PBI9_HUMAN,E5RHU3_HUMAN,B4DT61_HUMAN	UPI000013E7A4	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATATCTATCTA	.	2	ESCA
TSPYL5	0	.	GRCh37	8	98285805	98285805	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3014A>G	.	.	ENST00000322128	1/1	29	24	4	22	22	0	TSPYL5,3_prime_UTR_variant,,ENST00000322128,;	C	ENSG00000180543	ENST00000322128	Transcript	3_prime_UTR_variant	4372	.	.	.	.	.	.	.	-1	TSPYL5	HGNC	29367	protein_coding	YES	CCDS34927.1	ENSP00000322802	TSYL5_HUMAN	.	UPI0000210364	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTATTAACAG	.	5	ESCA
MTDH	0	.	GRCh37	8	98737255	98737255	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*357G>A	.	.	ENST00000336273	12/12	67	60	7	39	39	0	MTDH,3_prime_UTR_variant,,ENST00000519934,;MTDH,3_prime_UTR_variant,,ENST00000336273,;MTDH,downstream_gene_variant,,ENST00000521933,;MTDH,downstream_gene_variant,,ENST00000519293,;	A	ENSG00000147649	ENST00000336273	Transcript	3_prime_UTR_variant	2434	.	.	.	.	.	.	.	1	MTDH	HGNC	29608	protein_coding	YES	CCDS6274.1	ENSP00000338235	LYRIC_HUMAN	.	UPI0000061E17	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTTGCCTAC	.	4	ESCA
MATN2	0	.	GRCh37	8	98973737	98973737	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937G>C	p.Glu313Gln	p.E313Q	ENST00000520016	4/18	84	73	11	50	50	0	MATN2,missense_variant,p.Glu10Gln,ENST00000522270,;MATN2,missense_variant,p.Glu29Gln,ENST00000519585,;MATN2,missense_variant,p.Glu313Gln,ENST00000521689,;MATN2,missense_variant,p.Glu313Gln,ENST00000254898,;MATN2,missense_variant,p.Glu313Gln,ENST00000520016,;MATN2,missense_variant,p.Glu313Gln,ENST00000524308,;MATN2,missense_variant,p.Glu29Gln,ENST00000522025,;MATN2,missense_variant,p.Glu68Gln,ENST00000521041,;MATN2,intron_variant,,ENST00000518154,;MATN2,non_coding_transcript_exon_variant,,ENST00000523490,;	C	ENSG00000132561	ENST00000520016	Transcript	missense_variant	1061	937	313	E/Q	Gag/Cag	.	.	.	1	MATN2	HGNC	6908	protein_coding	YES	CCDS55264.1	ENSP00000430487	MATN2_HUMAN	E5RJM4_HUMAN	UPI000021037B	.	tolerated(0.43)	benign(0.101)	4/18	.	hmmpanther:PTHR22992:SF17,hmmpanther:PTHR22992,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTGAGGAT	.	5	ESCA
PPP3R2	0	.	GRCh37	9	104356900	104356900	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313G>A	p.Asp105Asn	p.D105N	ENST00000374806	1/1	48	40	7	50	50	0	PPP3R2,missense_variant,p.Asp105Asn,ENST00000374806,;GRIN3A,intron_variant,,ENST00000361820,;	T	ENSG00000188386	ENST00000374806	Transcript	missense_variant	384	313	105	D/N	Gat/Aat	COSM3652397	.	.	-1	PPP3R2	HGNC	9318	protein_coding	YES	CCDS6759.1	ENSP00000363939	CANB2_HUMAN	.	UPI0000035DAE	.	tolerated(0.08)	benign(0.257)	1/1	.	PROSITE_profiles:PS50222,hmmpanther:PTHR23056:SF29,hmmpanther:PTHR23056,PROSITE_patterns:PS00018,Pfam_domain:PF13499,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D103N|c.307G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATCCATGT	.	5	ESCA
CTNNAL1	0	.	GRCh37	9	111741738	111741738	+	Silent	SNP	C	C	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.924G>A	p.%3D	p.E308E	ENST00000325551	7/19	55	47	7	34	34	0	CTNNAL1,synonymous_variant,p.%3D,ENST00000325580,;CTNNAL1,synonymous_variant,p.%3D,ENST00000325551,;CTNNAL1,synonymous_variant,p.%3D,ENST00000374595,;CTNNAL1,upstream_gene_variant,,ENST00000488130,;	T	ENSG00000119326	ENST00000325551	Transcript	synonymous_variant	1011	924	308	E	gaG/gaA	COSM422008,COSM1103699	.	.	-1	CTNNAL1	HGNC	2512	protein_coding	YES	CCDS6775.1	ENSP00000320434	CTNL1_HUMAN	Q5JTQ9_HUMAN	UPI0000070AF1	.	.	.	7/19	.	hmmpanther:PTHR18914:SF8,hmmpanther:PTHR18914	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R307W|c.919C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCTCCCG	.	5	ESCA
BSPRY	0	.	GRCh37	9	116135698	116135698	+	3'Flank	SNP	C	C	G	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000374183	.	15	10	5	19	19	0	BSPRY,downstream_gene_variant,,ENST00000374183,;HDHD3,downstream_gene_variant,,ENST00000374180,;HDHD3,downstream_gene_variant,,ENST00000238379,;BSPRY,downstream_gene_variant,,ENST00000462085,;HDHD3,downstream_gene_variant,,ENST00000485934,;	G	ENSG00000119411	ENST00000374183	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2185	1	BSPRY	HGNC	18232	protein_coding	YES	CCDS43868.1	ENSP00000363298	BSPRY_HUMAN	.	UPI000013CA39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAGCTGGTT	.	2	ESCA
FOXD4	0	.	GRCh37	9	116344	116344	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*456C>T	.	.	ENST00000382500	1/1	204	186	17	160	160	0	FOXD4,3_prime_UTR_variant,,ENST00000382500,;CBWD1,downstream_gene_variant,,ENST00000377400,;CBWD1,downstream_gene_variant,,ENST00000356521,;RP11-143M1.4,upstream_gene_variant,,ENST00000416242,;CBWD1,downstream_gene_variant,,ENST00000475990,;	A	ENSG00000170122	ENST00000382500	Transcript	3_prime_UTR_variant	2074	.	.	.	.	.	.	.	-1	FOXD4	HGNC	3805	protein_coding	YES	CCDS34975.1	ENSP00000371940	FOXD4_HUMAN	.	UPI00001AFF18	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTTCTGAAATT	.	3	ESCA
DAB2IP	0	.	GRCh37	9	124538484	124538484	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3044C>T	p.Ala1015Val	p.A1015V	ENST00000259371	14/17	60	52	8	47	47	0	DAB2IP,missense_variant,p.Ala1043Val,ENST00000408936,;DAB2IP,missense_variant,p.Ala1015Val,ENST00000259371,;DAB2IP,missense_variant,p.Ala952Val,ENST00000373782,;DAB2IP,missense_variant,p.Ala919Val,ENST00000309989,;	T	ENSG00000136848	ENST00000259371	Transcript	missense_variant	3113	3044	1015	A/V	gCg/gTg	.	.	.	1	DAB2IP	HGNC	17294	protein_coding	YES	CCDS6833.2	ENSP00000259371	DAB2P_HUMAN	H0Y3A3_HUMAN,F8WA47_HUMAN,F6R503_HUMAN,B3KW96_HUMAN	UPI0000D77E70	.	tolerated(0.59)	benign(0.004)	14/17	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10194:SF26,hmmpanther:PTHR10194,Pfam_domain:PF12004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGGCGGTGC	.	2	ESCA
OR1L1	0	.	GRCh37	9	125424367	125424367	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.373G>T	p.Ala125Ser	p.A125S	ENST00000309623	1/1	99	83	15	88	88	0	OR1L1,missense_variant,p.Ala175Ser,ENST00000373686,;OR1L1,missense_variant,p.Ala125Ser,ENST00000309623,;	T	ENSG00000173679	ENST00000309623	Transcript	missense_variant	373	373	125	A/S	Gcc/Tcc	.	.	.	1	OR1L1	HGNC	8213	protein_coding	YES	CCDS35127.2	ENSP00000310773	.	.	UPI0000041E03	.	deleterious(0)	probably_damaging(0.991)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,PROSITE_patterns:PS00237,hmmpanther:PTHR26451:SF39,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGGCCATA	.	5	ESCA
ZMYND19	0	.	GRCh37	9	140476993	140476993	+	3'UTR	SNP	C	C	T	rs751144309	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2G>A	.	.	ENST00000298585	6/6	35	32	3	31	31	0	ZMYND19,3_prime_UTR_variant,,ENST00000298585,;DPH7,upstream_gene_variant,,ENST00000277540,;DPH7,upstream_gene_variant,,ENST00000481839,;ZMYND19,downstream_gene_variant,,ENST00000471957,;DPH7,upstream_gene_variant,,ENST00000470855,;DPH7,upstream_gene_variant,,ENST00000472113,;DPH7,upstream_gene_variant,,ENST00000460572,;DPH7,upstream_gene_variant,,ENST00000467768,;DPH7,upstream_gene_variant,,ENST00000479650,;DPH7,upstream_gene_variant,,ENST00000491359,;DPH7,upstream_gene_variant,,ENST00000476303,;DPH7,upstream_gene_variant,,ENST00000475100,;	T	ENSG00000165724	ENST00000298585	Transcript	3_prime_UTR_variant	913	.	.	.	.	rs751144309	.	.	-1	ZMYND19	HGNC	21146	protein_coding	YES	CCDS7048.1	ENSP00000298585	ZMY19_HUMAN	.	UPI0000022A7D	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCCCGTCAT	byFrequency	2	ESCA
ADAMTSL1	0	.	GRCh37	9	18776926	18776926	+	Missense_Mutation	SNP	C	C	T	rs376039296	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2699C>T	p.Pro900Leu	p.P900L	ENST00000380548	19/29	56	22	34	31	31	0	ADAMTSL1,missense_variant,p.Pro900Leu,ENST00000380548,;ADAMTSL1,non_coding_transcript_exon_variant,,ENST00000380559,;	T	ENSG00000178031	ENST00000380548	Transcript	missense_variant	3038	2699	900	P/L	cCg/cTg	rs376039296	.	.	1	ADAMTSL1	HGNC	14632	protein_coding	YES	CCDS47954.1	ENSP00000369921	ATL1_HUMAN	H7BYE3_HUMAN	UPI000004FD83	.	deleterious(0)	probably_damaging(0.951)	19/29	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13723:SF157,hmmpanther:PTHR13723,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCCGGCGC	byCluster	5	ESCA
DOCK8	0	.	GRCh37	9	399175	399175	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3150C>T	p.%3D	p.I1050I	ENST00000453981	26/48	70	60	10	51	51	0	DOCK8,synonymous_variant,p.%3D,ENST00000432829,;DOCK8,synonymous_variant,p.%3D,ENST00000453981,;DOCK8,synonymous_variant,p.%3D,ENST00000382331,;DOCK8,synonymous_variant,p.%3D,ENST00000469391,;DOCK8,synonymous_variant,p.%3D,ENST00000382329,;DOCK8,non_coding_transcript_exon_variant,,ENST00000495184,;	T	ENSG00000107099	ENST00000453981	Transcript	synonymous_variant	3262	3150	1050	I	atC/atT	.	.	.	1	DOCK8	HGNC	19191	protein_coding	YES	CCDS6440.2	ENSP00000408464	DOCK8_HUMAN	E2J6M5_HUMAN,C9J7A3_HUMAN,C9J613_HUMAN	UPI0000E0B9E5	.	.	.	26/48	.	hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF74	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATCAGCCT	.	5	ESCA
C9orf47	0	.	GRCh37	9	91609064	91609064	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2161C>T	.	.	ENST00000334490	3/3	20	14	5	16	16	0	C9orf47,3_prime_UTR_variant,,ENST00000334490,;C9orf47,3_prime_UTR_variant,,ENST00000375851,;S1PR3,intron_variant,,ENST00000358157,;C9orf47,downstream_gene_variant,,ENST00000375850,;S1PR3,upstream_gene_variant,,ENST00000375846,;	T	ENSG00000186354	ENST00000334490	Transcript	3_prime_UTR_variant	2838	.	.	.	.	.	.	.	1	C9orf47	HGNC	23669	protein_coding	YES	CCDS35062.1	ENSP00000335616	CI047_HUMAN	.	UPI00001C0EE0	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTCATCCC	.	5	ESCA
TEX13A	0	.	GRCh37	X	104464794	104464794	+	Silent	SNP	G	G	A	rs782644244	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288C>T	p.%3D	p.F96F	ENST00000413579	2/5	11	8	3	14	14	0	TEX13A,synonymous_variant,p.%3D,ENST00000413579,;TEX13A,synonymous_variant,p.%3D,ENST00000372578,;TEX13A,synonymous_variant,p.%3D,ENST00000372575,;IL1RAPL2,intron_variant,,ENST00000344799,;IL1RAPL2,intron_variant,,ENST00000372582,;	A	ENSG00000133149	ENST00000413579	Transcript	synonymous_variant	400	288	96	F	ttC/ttT	rs782644244	.	.	-1	TEX13A	HGNC	11735	protein_coding	YES	.	ENSP00000399753	TX13A_HUMAN	.	UPI0000042200	.	.	.	2/5	.	hmmpanther:PTHR23111,hmmpanther:PTHR23111:SF13,Pfam_domain:PF15186	A:0.0003	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGCGAAGCC	byCluster|by1000G	2	ESCA
NRK	0	.	GRCh37	X	105066676	105066676	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-163C>T	.	.	ENST00000428173	1/29	25	18	6	25	25	0	NRK,5_prime_UTR_variant,,ENST00000536164,;NRK,5_prime_UTR_variant,,ENST00000428173,;NRK,5_prime_UTR_variant,,ENST00000243300,;	T	ENSG00000123572	ENST00000428173	Transcript	5_prime_UTR_variant	141	.	.	.	.	.	.	.	1	NRK	HGNC	25391	protein_coding	YES	.	ENSP00000438378	.	F5H049_HUMAN,B7Z6I7_HUMAN	UPI00015E03BB	.	.	.	1/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACACGTTTC	.	5	ESCA
RBMXL3	0	.	GRCh37	X	114425871	114425871	+	Missense_Mutation	SNP	C	C	T	rs781927425	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1867C>T	p.Arg623Cys	p.R623C	ENST00000424776	1/1	78	58	19	58	58	0	RBMXL3,missense_variant,p.Arg623Cys,ENST00000424776,;LRCH2,intron_variant,,ENST00000538422,;LRCH2,intron_variant,,ENST00000317135,;	T	ENSG00000175718	ENST00000424776	Transcript	missense_variant	1909	1867	623	R/C	Cgc/Tgc	rs781927425	.	.	1	RBMXL3	HGNC	26859	protein_coding	YES	CCDS55478.1	ENSP00000417451	RMXL3_HUMAN	.	UPI0001932819	.	deleterious_low_confidence(0.01)	benign(0.255)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF325	T:0.0005	T:0	T:0	.	T:0.002	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACCGCTAC	byFrequency|byCluster|by1000G	5	ESCA
CSF2RA	0	.	GRCh37	X	1409284	1409284	+	Silent	SNP	G	G	T	.	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528G>T	p.%3D	p.V176V	ENST00000417535	5/12	108	89	19	96	96	0	CSF2RA,synonymous_variant,p.%3D,ENST00000381524,;CSF2RA,synonymous_variant,p.%3D,ENST00000381529,;CSF2RA,synonymous_variant,p.%3D,ENST00000355432,;CSF2RA,synonymous_variant,p.%3D,ENST00000355805,;CSF2RA,synonymous_variant,p.%3D,ENST00000432318,;CSF2RA,synonymous_variant,p.%3D,ENST00000419094,;CSF2RA,synonymous_variant,p.%3D,ENST00000501036,;CSF2RA,synonymous_variant,p.%3D,ENST00000361536,;CSF2RA,synonymous_variant,p.%3D,ENST00000417535,;CSF2RA,synonymous_variant,p.%3D,ENST00000412290,;CSF2RA,synonymous_variant,p.%3D,ENST00000381500,;CSF2RA,synonymous_variant,p.%3D,ENST00000381509,;CSF2RA,intron_variant,,ENST00000494969,;BX649553.1,upstream_gene_variant,,ENST00000583047,;BX649553.2,upstream_gene_variant,,ENST00000578699,;MIR3690,upstream_gene_variant,,ENST00000580266,;BX649553.4,upstream_gene_variant,,ENST00000580687,;BX649553.3,upstream_gene_variant,,ENST00000581137,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000493312,;CSF2RA,downstream_gene_variant,,ENST00000477940,;CSF2RA,upstream_gene_variant,,ENST00000498153,;CSF2RA,upstream_gene_variant,,ENST00000475259,;CSF2RA,downstream_gene_variant,,ENST00000478256,;CSF2RA,upstream_gene_variant,,ENST00000491683,;CSF2RA,synonymous_variant,p.%3D,ENST00000486791,;	T	ENSG00000198223	ENST00000417535	Transcript	synonymous_variant	554	528	176	V	gtG/gtT	COSM755095,COSM755096,COSM1151515	.	.	1	CSF2RA	HGNC	2435	protein_coding	YES	CCDS55359.1	ENSP00000394227	CSF2R_HUMAN	J3JS74_HUMAN,J3JS73_HUMAN	UPI000159C3E4	.	.	.	5/12	.	hmmpanther:PTHR23036:SF84,hmmpanther:PTHR23036,Gene3D:2.60.40.10,Pfam_domain:PF09240,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGTGGGATG	.	5	ESCA
RBBP7	0	.	GRCh37	X	16864049	16864050	+	Frame_Shift_Del	DEL	CT	CT	-	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	CT	CT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1242_1243delAG	p.Gly415ThrfsTer4	p.G415Tfs*4	ENST00000380084	11/12	20	13	6	16	16	0	RBBP7,frameshift_variant,p.Gly415ThrfsTer4,ENST00000380084,;RBBP7,frameshift_variant,p.Gly371ThrfsTer4,ENST00000380087,;RBBP7,frameshift_variant,p.Gly31ThrfsTer4,ENST00000425696,;RBBP7,frameshift_variant,p.Gly362ThrfsTer4,ENST00000404022,;TXLNG,downstream_gene_variant,,ENST00000380122,;RBBP7,downstream_gene_variant,,ENST00000444437,;TXLNG,downstream_gene_variant,,ENST00000398155,;TXLNG,downstream_gene_variant,,ENST00000485153,;RBBP7,non_coding_transcript_exon_variant,,ENST00000330735,;RBBP7,non_coding_transcript_exon_variant,,ENST00000465244,;RBBP7,non_coding_transcript_exon_variant,,ENST00000481586,;	-	ENSG00000102054	ENST00000380084	Transcript	frameshift_variant	1487-1488	1242-1243	414-415	GG/GX	ggAGga/ggga	.	.	.	-1	RBBP7	HGNC	9890	protein_coding	YES	CCDS56598.1	ENSP00000369424	RBBP7_HUMAN	Q5JNZ6_HUMAN,C9J7L0_HUMAN	UPI00001AE848	.	.	.	11/12	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF82,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTGTCCTCCATG	.	2	ESCA
KDM6A	0	.	GRCh37	X	44950110	44950110	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3878+1G>A	.	p.X1293_splice	ENST00000377967	.	29	15	14	35	35	0	KDM6A,splice_donor_variant,,ENST00000433797,;KDM6A,splice_donor_variant,,ENST00000414389,;KDM6A,splice_donor_variant,,ENST00000543216,;KDM6A,splice_donor_variant,,ENST00000431196,;KDM6A,splice_donor_variant,,ENST00000377967,;KDM6A,splice_donor_variant,,ENST00000382899,;KDM6A,splice_donor_variant,,ENST00000536777,;KDM6A,downstream_gene_variant,,ENST00000484732,;	A	ENSG00000147050	ENST00000377967	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	KDM6A	HGNC	12637	protein_coding	YES	CCDS14265.1	ENSP00000367203	KDM6A_HUMAN	Q68D33_HUMAN,Q59HG3_HUMAN,Q590H7_HUMAN	UPI000013DA92	.	.	.	.	26/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.0?|c.1_4206del4206|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTAAGTAAGT	.	5	ESCA
FAM46D	0	.	GRCh37	X	79698219	79698219	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A51D-01A-11D-A27G-09	TCGA-IG-A51D-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181G>A	p.Ala61Thr	p.A61T	ENST00000538312	5/5	22	15	6	23	23	0	FAM46D,missense_variant,p.Ala61Thr,ENST00000308293,;FAM46D,missense_variant,p.Ala61Thr,ENST00000538312,;	A	ENSG00000174016	ENST00000538312	Transcript	missense_variant	515	181	61	A/T	Gcc/Acc	.	.	.	1	FAM46D	HGNC	28399	protein_coding	YES	CCDS14446.1	ENSP00000443410	FA46D_HUMAN	.	UPI0000073CF3	.	tolerated(0.16)	benign(0.004)	5/5	.	Pfam_domain:PF07984,hmmpanther:PTHR12974:SF30,hmmpanther:PTHR12974	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATGCCAGA	.	5	ESCA
SFR1	0	.	GRCh37	10	105885465	105885465	+	3'UTR	SNP	C	C	T	rs762987254	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3C>T	.	.	ENST00000369727	4/4	34	28	6	20	20	0	SFR1,3_prime_UTR_variant,,ENST00000369729,;SFR1,3_prime_UTR_variant,,ENST00000369727,;SFR1,3_prime_UTR_variant,,ENST00000336358,;WDR96,downstream_gene_variant,,ENST00000357060,;WDR96,downstream_gene_variant,,ENST00000457071,;WDR96,downstream_gene_variant,,ENST00000428666,;WDR96,downstream_gene_variant,,ENST00000434629,;SFR1,downstream_gene_variant,,ENST00000463224,;	T	ENSG00000156384	ENST00000369727	Transcript	3_prime_UTR_variant	760	.	.	.	.	rs762987254	.	.	1	SFR1	HGNC	29574	protein_coding	YES	CCDS31279.1	ENSP00000358742	SFR1_HUMAN	.	UPI00001F9699	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATTCCTGAT	.	5	ESCA
BUB3	0	.	GRCh37	10	124924555	124924555	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1204C>T	.	.	ENST00000368865	8/8	57	44	13	39	39	0	BUB3,splice_region_variant,,ENST00000368859,;BUB3,splice_region_variant,,ENST00000368858,;BUB3,3_prime_UTR_variant,,ENST00000368865,;BUB3,downstream_gene_variant,,ENST00000407911,;BUB3,downstream_gene_variant,,ENST00000538238,;BUB3,downstream_gene_variant,,ENST00000481952,;	T	ENSG00000154473	ENST00000368865	Transcript	3_prime_UTR_variant	2400	.	.	.	.	.	.	.	1	BUB3	HGNC	1151	protein_coding	YES	CCDS7635.1	ENSP00000357858	BUB3_HUMAN	J3QT28_HUMAN,B4DDM6_HUMAN	UPI0000126B30	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCATTGC	.	5	ESCA
OPTN	0	.	GRCh37	10	13174166	13174166	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501A>G	p.Lys501Glu	p.K501E	ENST00000378748	14/16	51	44	6	37	37	0	OPTN,missense_variant,p.Lys501Glu,ENST00000378748,;OPTN,missense_variant,p.Lys495Glu,ENST00000378764,;OPTN,missense_variant,p.Lys501Glu,ENST00000378757,;OPTN,missense_variant,p.Lys501Glu,ENST00000263036,;OPTN,missense_variant,p.Lys501Glu,ENST00000378747,;OPTN,missense_variant,p.Lys495Glu,ENST00000378752,;OPTN,non_coding_transcript_exon_variant,,ENST00000469025,;	G	ENSG00000123240	ENST00000378748	Transcript	missense_variant	1863	1501	501	K/E	Aaa/Gaa	.	.	.	1	OPTN	HGNC	17142	protein_coding	YES	CCDS7094.1	ENSP00000368022	OPTN_HUMAN	.	UPI000013D38D	.	deleterious(0)	possibly_damaging(0.488)	14/16	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31553:SF2,hmmpanther:PTHR31553,Gene3D:1.20.5.990	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTGAAAGAG	.	4	ESCA
JAKMIP3	0	.	GRCh37	10	133930673	133930673	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228G>C	p.Lys76Asn	p.K76N	ENST00000298622	2/24	43	38	5	23	23	0	JAKMIP3,missense_variant,p.Lys76Asn,ENST00000298622,;	C	ENSG00000188385	ENST00000298622	Transcript	missense_variant	366	228	76	K/N	aaG/aaC	.	.	.	1	JAKMIP3	HGNC	23523	protein_coding	YES	CCDS44494.1	ENSP00000298622	JKIP3_HUMAN	.	UPI000157482F	.	deleterious(0)	probably_damaging(0.913)	2/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR18935:SF5,hmmpanther:PTHR18935	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAAGACAAA	.	4	ESCA
VENTX	0	.	GRCh37	10	135053603	135053603	+	Silent	SNP	C	C	T	rs767616096	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570C>T	p.%3D	p.S190S	ENST00000325980	3/3	72	42	30	75	75	0	VENTX,synonymous_variant,p.%3D,ENST00000325980,;	T	ENSG00000151650	ENST00000325980	Transcript	synonymous_variant	1081	570	190	S	tcC/tcT	rs767616096	.	.	1	VENTX	HGNC	13639	protein_coding	YES	CCDS7675.1	ENSP00000357556	VENTX_HUMAN	.	UPI0000070A25	.	.	.	3/3	.	hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCCGGGCC	byFrequency	5	ESCA
SPAG6	0	.	GRCh37	10	22690153	22690153	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1261C>G	p.Leu421Val	p.L421V	ENST00000376624	9/11	32	28	4	33	33	0	SPAG6,missense_variant,p.Leu421Val,ENST00000313311,;SPAG6,missense_variant,p.Leu421Val,ENST00000376624,;SPAG6,missense_variant,p.Leu497Val,ENST00000376603,;SPAG6,missense_variant,p.Leu182Val,ENST00000456231,;SPAG6,missense_variant,p.Leu396Val,ENST00000538630,;SPAG6,missense_variant,p.Leu182Val,ENST00000376601,;RP11-301N24.3,intron_variant,,ENST00000422675,;SPAG6,non_coding_transcript_exon_variant,,ENST00000487973,;SPAG6,non_coding_transcript_exon_variant,,ENST00000490361,;SPAG6,non_coding_transcript_exon_variant,,ENST00000488555,;	G	ENSG00000077327	ENST00000376624	Transcript	missense_variant	1403	1261	421	L/V	Cta/Gta	COSM1347243,COSM917051,COSM1745741,COSM1745742,COSM3414910	.	.	1	SPAG6	HGNC	11215	protein_coding	YES	CCDS7139.1	ENSP00000365811	SPAG6_HUMAN	.	UPI0000073ED7	.	deleterious(0.02)	probably_damaging(0.931)	9/11	.	hmmpanther:PTHR23314,hmmpanther:PTHR23314:SF1,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTCTATAT	.	2	ESCA
YME1L1	0	.	GRCh37	10	27434388	27434388	+	Silent	SNP	G	G	C	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471C>G	p.%3D	p.V157V	ENST00000326799	4/20	24	20	4	25	25	0	YME1L1,synonymous_variant,p.%3D,ENST00000326799,;YME1L1,synonymous_variant,p.%3D,ENST00000375972,;YME1L1,synonymous_variant,p.%3D,ENST00000396296,;YME1L1,synonymous_variant,p.%3D,ENST00000376016,;YME1L1,synonymous_variant,p.%3D,ENST00000427324,;YME1L1,3_prime_UTR_variant,,ENST00000477432,;YME1L1,intron_variant,,ENST00000491542,;	C	ENSG00000136758	ENST00000326799	Transcript	synonymous_variant	620	471	157	V	gtC/gtG	COSM917403	.	.	-1	YME1L1	HGNC	12843	protein_coding	YES	CCDS7152.1	ENSP00000318480	YMEL1_HUMAN	.	UPI000013DBDD	.	.	.	4/20	.	HAMAP:MF_01458,hmmpanther:PTHR23076,hmmpanther:PTHR23076:SF37	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGAGACATG	.	5	ESCA
ZEB1	0	.	GRCh37	10	31809970	31809970	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1710T>C	p.%3D	p.P570P	ENST00000361642	7/9	33	28	5	31	31	0	ZEB1,synonymous_variant,p.%3D,ENST00000560721,;ZEB1,synonymous_variant,p.%3D,ENST00000446923,;ZEB1,synonymous_variant,p.%3D,ENST00000361642,;ZEB1,synonymous_variant,p.%3D,ENST00000320985,;ZEB1,synonymous_variant,p.%3D,ENST00000542815,;ZEB1,downstream_gene_variant,,ENST00000424869,;ZEB1,downstream_gene_variant,,ENST00000558440,;ZEB1,downstream_gene_variant,,ENST00000559476,;ZEB1,downstream_gene_variant,,ENST00000561212,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558655,;ZEB1,downstream_gene_variant,,ENST00000558863,;	C	ENSG00000148516	ENST00000361642	Transcript	synonymous_variant	1773	1710	570	P	ccT/ccC	.	.	.	1	ZEB1	HGNC	11642	protein_coding	YES	CCDS53505.1	ENSP00000354487	ZEB1_HUMAN	F6TDF5_HUMAN	UPI000068F51D	.	.	.	7/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCCTGAGTC	.	4	ESCA
PARD3	0	.	GRCh37	10	34626223	34626223	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2549C>G	p.Ser850Ter	p.S850*	ENST00000374789	17/25	38	24	14	23	23	0	PARD3,stop_gained,p.Ser834Ter,ENST00000545693,;PARD3,stop_gained,p.Ser847Ter,ENST00000374788,;PARD3,stop_gained,p.Ser564Ter,ENST00000544292,;PARD3,stop_gained,p.Ser847Ter,ENST00000340077,;PARD3,stop_gained,p.Ser790Ter,ENST00000374790,;PARD3,stop_gained,p.Ser790Ter,ENST00000374794,;PARD3,stop_gained,p.Ser850Ter,ENST00000374789,;PARD3,stop_gained,p.Ser850Ter,ENST00000346874,;PARD3,intron_variant,,ENST00000545260,;PARD3,intron_variant,,ENST00000374776,;PARD3,intron_variant,,ENST00000374773,;PARD3,intron_variant,,ENST00000350537,;PARD3,upstream_gene_variant,,ENST00000466092,;	C	ENSG00000148498	ENST00000374789	Transcript	stop_gained	2875	2549	850	S/*	tCa/tGa	.	.	.	-1	PARD3	HGNC	16051	protein_coding	YES	CCDS7178.1	ENSP00000363921	PARD3_HUMAN	.	UPI0000073A9F	.	.	.	17/25	.	hmmpanther:PTHR16484:SF10,hmmpanther:PTHR16484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTGATTTT	.	5	ESCA
CCNYL2	0	.	GRCh37	10	42907305	42907305	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1127G>A	.	.	ENST00000483242	8/9	81	69	12	101	101	0	CCNYL2,non_coding_transcript_exon_variant,,ENST00000483242,;CCNYL2,non_coding_transcript_exon_variant,,ENST00000426433,;CCNYL2,non_coding_transcript_exon_variant,,ENST00000472090,;	T	ENSG00000182632	ENST00000483242	Transcript	non_coding_transcript_exon_variant	1127	.	.	.	.	.	.	.	-1	CCNYL2	HGNC	23495	processed_transcript	YES	.	.	.	.	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCATTCC	.	5	ESCA
ZNF488	0	.	GRCh37	10	48372131	48372131	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*576G>C	.	.	ENST00000395702	2/2	72	65	6	43	43	0	ZNF488,3_prime_UTR_variant,,ENST00000395702,;ZNF488,3_prime_UTR_variant,,ENST00000586537,;ZNF488,3_prime_UTR_variant,,ENST00000494156,;ZNF488,downstream_gene_variant,,ENST00000444585,;ZNF488,downstream_gene_variant,,ENST00000442001,;ZNF488,downstream_gene_variant,,ENST00000433077,;ZNF488,downstream_gene_variant,,ENST00000436850,;ZNF488,downstream_gene_variant,,ENST00000412534,;ZNF488,downstream_gene_variant,,ENST00000425196,;	C	ENSG00000165388	ENST00000395702	Transcript	3_prime_UTR_variant	1826	.	.	.	.	.	.	.	1	ZNF488	HGNC	23535	protein_coding	YES	CCDS7217.1	ENSP00000379054	ZN488_HUMAN	Q05CE0_HUMAN,A2AH66_HUMAN,A2AH65_HUMAN,A2AH64_HUMAN,A2AH63_HUMAN,A2AH62_HUMAN,A2AH61_HUMAN	UPI00000736CF	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCGTGAGTCT	.	3	ESCA
PLAC9	0	.	GRCh37	10	81904016	81904016	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200T>C	p.Val67Ala	p.V67A	ENST00000372263	3/4	78	70	8	60	60	0	PLAC9,missense_variant,p.Val67Ala,ENST00000372263,;PLAC9,missense_variant,p.Val25Ala,ENST00000372270,;PLAC9,intron_variant,,ENST00000372267,;PLAC9,non_coding_transcript_exon_variant,,ENST00000465660,;	C	ENSG00000189129	ENST00000372263	Transcript	missense_variant	242	200	67	V/A	gTg/gCg	.	.	.	1	PLAC9	HGNC	19255	protein_coding	YES	CCDS31232.1	ENSP00000361337	PLAC9_HUMAN	Q5JTB4_HUMAN	UPI0000161743	.	deleterious(0)	possibly_damaging(0.728)	3/4	.	Low_complexity_(Seg):seg,Pfam_domain:PF15205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGAGGTGAAAG	.	3	ESCA
KIF20B	0	.	GRCh37	10	91492754	91492754	+	Nonsense_Mutation	SNP	C	C	G	rs144738424	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2366C>G	p.Ser789Ter	p.S789*	ENST00000260753	19/33	21	15	6	22	22	0	KIF20B,stop_gained,p.Ser829Ter,ENST00000371728,;KIF20B,stop_gained,p.Ser829Ter,ENST00000416354,;KIF20B,stop_gained,p.Ser789Ter,ENST00000260753,;KIF20B,stop_gained,p.Ser829Ter,ENST00000394289,;KIF20B,non_coding_transcript_exon_variant,,ENST00000478929,;	G	ENSG00000138182	ENST00000260753	Transcript	stop_gained	2438	2366	789	S/*	tCa/tGa	rs144738424	.	.	1	KIF20B	HGNC	7212	protein_coding	YES	CCDS7407.1	ENSP00000260753	KI20B_HUMAN	.	UPI00001F9377	.	.	.	19/33	.	hmmpanther:PTHR23165	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTCAGAAA	byCluster	5	ESCA
ALDH18A1	0	.	GRCh37	10	97373617	97373617	+	Missense_Mutation	SNP	C	C	A	rs543845150	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1805G>T	p.Arg602Ile	p.R602I	ENST00000371224	15/18	69	58	11	51	51	0	ALDH18A1,missense_variant,p.Arg602Ile,ENST00000371224,;ALDH18A1,missense_variant,p.Arg600Ile,ENST00000371221,;ALDH18A1,non_coding_transcript_exon_variant,,ENST00000485428,;	A	ENSG00000059573	ENST00000371224	Transcript	missense_variant	1943	1805	602	R/I	aGa/aTa	rs543845150	.	.	-1	ALDH18A1	HGNC	9722	protein_coding	YES	CCDS7443.1	ENSP00000360268	P5CS_HUMAN	.	UPI0000131056	.	tolerated(0.41)	possibly_damaging(0.844)	15/18	.	hmmpanther:PTHR11063,hmmpanther:PTHR11063:SF8,TIGRFAM_domain:TIGR01092,Gene3D:3.40.309.10,TIGRFAM_domain:TIGR00407,Pfam_domain:PF00171,PIRSF_domain:PIRSF036429,Superfamily_domains:SSF53720	G:0.0002	G:0	G:0.0014	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCTGACT	by1000G	5	ESCA
DYNC2H1	0	.	GRCh37	11	103152935	103152935	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10810G>A	p.Val3604Ile	p.V3604I	ENST00000398093	73/90	36	26	9	29	29	0	DYNC2H1,missense_variant,p.Val3604Ile,ENST00000398093,;DYNC2H1,missense_variant,p.Val3597Ile,ENST00000375735,;DYNC2H1,intron_variant,,ENST00000334267,;DYNC2H1,non_coding_transcript_exon_variant,,ENST00000525306,;DYNC2H1,upstream_gene_variant,,ENST00000528670,;	A	ENSG00000187240	ENST00000398093	Transcript	missense_variant	10810	10810	3604	V/I	Gtt/Att	.	.	.	1	DYNC2H1	HGNC	2962	protein_coding	YES	CCDS44717.1	ENSP00000381167	DYHC2_HUMAN	.	UPI0000481AC7	.	.	benign(0.02)	73/90	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTTGTTGGA	.	5	ESCA
GRIA4	0	.	GRCh37	11	105850508	105850508	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*42G>A	.	.	ENST00000282499	17/17	29	20	8	28	28	0	GRIA4,3_prime_UTR_variant,,ENST00000282499,;GRIA4,3_prime_UTR_variant,,ENST00000530497,;GRIA4,3_prime_UTR_variant,,ENST00000393127,;GRIA4,downstream_gene_variant,,ENST00000525187,;RNU6-277P,upstream_gene_variant,,ENST00000516272,;GRIA4,non_coding_transcript_exon_variant,,ENST00000533094,;	A	ENSG00000152578	ENST00000282499	Transcript	3_prime_UTR_variant	3197	.	.	.	.	.	.	.	1	GRIA4	HGNC	4574	protein_coding	YES	CCDS8333.1	ENSP00000282499	GRIA4_HUMAN	E9PJZ5_HUMAN	UPI000013DCE6	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGTGACTGG	.	5	ESCA
NLRX1	0	.	GRCh37	11	119050456	119050456	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1726C>T	p.Gln576Ter	p.Q576*	ENST00000409109	7/10	87	78	8	85	85	0	NLRX1,stop_gained,p.Gln576Ter,ENST00000409109,;NLRX1,stop_gained,p.Gln576Ter,ENST00000292199,;NLRX1,stop_gained,p.Gln576Ter,ENST00000409991,;NLRX1,stop_gained,p.Gln576Ter,ENST00000409265,;NLRX1,stop_gained,p.Gln576Ter,ENST00000525863,;NLRX1,non_coding_transcript_exon_variant,,ENST00000469103,;NLRX1,non_coding_transcript_exon_variant,,ENST00000481860,;NLRX1,downstream_gene_variant,,ENST00000524562,;	T	ENSG00000160703	ENST00000409109	Transcript	stop_gained	2313	1726	576	Q/*	Cag/Tag	.	.	.	1	NLRX1	HGNC	29890	protein_coding	YES	CCDS8416.1	ENSP00000387334	NLRX1_HUMAN	C9JQE9_HUMAN,C9JLK8_HUMAN,C9J0R6_HUMAN,B7Z889_HUMAN	UPI0000161217	.	.	.	7/10	.	hmmpanther:PTHR24106:SF17,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCTCAGGCC	.	4	ESCA
DKK3	0	.	GRCh37	11	11985989	11985989	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*22G>C	.	.	ENST00000396505	8/8	50	38	12	32	32	0	DKK3,3_prime_UTR_variant,,ENST00000396505,;DKK3,3_prime_UTR_variant,,ENST00000450094,;DKK3,3_prime_UTR_variant,,ENST00000525493,;DKK3,3_prime_UTR_variant,,ENST00000326932,;DKK3,downstream_gene_variant,,ENST00000534511,;DKK3,downstream_gene_variant,,ENST00000529338,;DKK3,downstream_gene_variant,,ENST00000533813,;DKK3,non_coding_transcript_exon_variant,,ENST00000527132,;DKK3,downstream_gene_variant,,ENST00000528188,;DKK3,downstream_gene_variant,,ENST00000532873,;DKK3,downstream_gene_variant,,ENST00000525927,;DKK3,downstream_gene_variant,,ENST00000532372,;	G	ENSG00000050165	ENST00000396505	Transcript	3_prime_UTR_variant	1314	.	.	.	.	.	.	.	-1	DKK3	HGNC	2893	protein_coding	YES	CCDS7808.1	ENSP00000379762	DKK3_HUMAN	E9PKW6_HUMAN	UPI00001694CA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATCTACCC	.	5	ESCA
ZNF202	0	.	GRCh37	11	123597553	123597553	+	Missense_Mutation	SNP	C	C	T	rs575384396	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1099G>A	p.Glu367Lys	p.E367K	ENST00000336139	8/8	44	31	12	41	40	1	ZNF202,missense_variant,p.Glu367Lys,ENST00000529691,;ZNF202,missense_variant,p.Glu367Lys,ENST00000336139,;ZNF202,missense_variant,p.Glu367Lys,ENST00000530393,;ZNF202,downstream_gene_variant,,ENST00000528306,;ZNF202,downstream_gene_variant,,ENST00000533463,;ZNF202,downstream_gene_variant,,ENST00000526252,;ZNF202,downstream_gene_variant,,ENST00000529250,;ZNF202,downstream_gene_variant,,ENST00000530944,;	T	ENSG00000166261	ENST00000336139	Transcript	missense_variant	1462	1099	367	E/K	Gaa/Aaa	rs575384396	.	.	-1	ZNF202	HGNC	12994	protein_coding	YES	CCDS8443.1	ENSP00000337724	ZN202_HUMAN	E9PM99_HUMAN,E9PJL4_HUMAN	UPI000013E581	.	tolerated(0.09)	benign(0.383)	8/8	.	hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF194	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCATTAA	byFrequency|by1000G	4	ESCA
NELL1	0	.	GRCh37	11	21594756	21594756	+	Missense_Mutation	SNP	T	T	G	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2183T>G	p.Leu728Arg	p.L728R	ENST00000357134	19/20	64	46	18	58	58	0	NELL1,missense_variant,p.Leu671Arg,ENST00000325319,;NELL1,missense_variant,p.Leu728Arg,ENST00000357134,;NELL1,missense_variant,p.Leu756Arg,ENST00000298925,;NELL1,missense_variant,p.Leu681Arg,ENST00000532434,;NELL1,non_coding_transcript_exon_variant,,ENST00000529218,;	G	ENSG00000165973	ENST00000357134	Transcript	missense_variant	2335	2183	728	L/R	cTc/cGc	COSM4032084	.	.	1	NELL1	HGNC	7750	protein_coding	YES	CCDS7855.1	ENSP00000349654	NELL1_HUMAN	K9UUD5_HUMAN	UPI000013E53D	.	deleterious(0)	possibly_damaging(0.848)	19/20	.	PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,PROSITE_patterns:PS01208,Pfam_domain:PF00093,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCCACTCACTT	.	4	ESCA
SLC5A12	0	.	GRCh37	11	26719966	26719966	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938C>T	p.Ser313Leu	p.S313L	ENST00000396005	7/15	39	28	11	30	30	0	SLC5A12,missense_variant,p.Ser313Leu,ENST00000280467,;SLC5A12,missense_variant,p.Ser125Leu,ENST00000533617,;SLC5A12,missense_variant,p.Ser313Leu,ENST00000396005,;SLC5A12,missense_variant,p.Ser125Leu,ENST00000527405,;	A	ENSG00000148942	ENST00000396005	Transcript	missense_variant	1248	938	313	S/L	tCa/tTa	.	.	.	-1	SLC5A12	HGNC	28750	protein_coding	YES	CCDS7860.2	ENSP00000379326	SC5AC_HUMAN	E9PLZ7_HUMAN	UPI000003ED2C	.	deleterious(0.03)	benign(0.133)	7/15	.	hmmpanther:PTHR11819,Pfam_domain:PF00474,hmmpanther:PTHR11819:SF113,PROSITE_profiles:PS50283,TIGRFAM_domain:TIGR00813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTGAGATG	.	5	ESCA
DNAJC24	0	.	GRCh37	11	31392295	31392295	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1G>C	.	.	ENST00000465995	2/5	19	15	4	17	17	0	DNAJC24,5_prime_UTR_variant,,ENST00000465995,;DNAJC24,5_prime_UTR_variant,,ENST00000536040,;DCDC1,upstream_gene_variant,,ENST00000452803,;DNAJC24,non_coding_transcript_exon_variant,,ENST00000532385,;DNAJC24,non_coding_transcript_exon_variant,,ENST00000527601,;DNAJC24,5_prime_UTR_variant,,ENST00000526042,;DNAJC24,5_prime_UTR_variant,,ENST00000526529,;DNAJC24,5_prime_UTR_variant,,ENST00000525511,;DNAJC24,non_coding_transcript_exon_variant,,ENST00000529086,;DNAJC24,upstream_gene_variant,,ENST00000527731,;DCDC1,upstream_gene_variant,,ENST00000342355,;	C	ENSG00000170946	ENST00000465995	Transcript	5_prime_UTR_variant	106	.	.	.	.	.	.	.	1	DNAJC24	HGNC	26979	protein_coding	YES	CCDS7873.2	ENSP00000417548	DJC24_HUMAN	.	UPI0000160EAB	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGGATGAT	.	5	ESCA
ELF5	0	.	GRCh37	11	34515144	34515144	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267C>T	p.%3D	p.F89F	ENST00000312319	3/7	29	15	13	43	43	0	ELF5,synonymous_variant,p.%3D,ENST00000257832,;ELF5,synonymous_variant,p.%3D,ENST00000532417,;ELF5,synonymous_variant,p.%3D,ENST00000312319,;ELF5,intron_variant,,ENST00000429939,;ELF5,intron_variant,,ENST00000528709,;	A	ENSG00000135374	ENST00000312319	Transcript	synonymous_variant	497	267	89	F	ttC/ttT	.	.	.	-1	ELF5	HGNC	3320	protein_coding	YES	CCDS7892.1	ENSP00000311010	ELF5_HUMAN	A8K443_HUMAN	UPI000006EFE4	.	.	.	3/7	.	PROSITE_profiles:PS51433,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF15,Gene3D:1.10.150.50,Pfam_domain:PF02198,SMART_domains:SM00251,Superfamily_domains:SSF47769	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAGAAGGA	.	5	ESCA
RAG1	0	.	GRCh37	11	36596806	36596806	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1952C>G	p.Ser651Cys	p.S651C	ENST00000299440	2/2	45	36	8	39	39	0	RAG1,missense_variant,p.Ser651Cys,ENST00000299440,;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.Ser651Cys,ENST00000534663,;	G	ENSG00000166349	ENST00000299440	Transcript	missense_variant	2064	1952	651	S/C	tCt/tGt	.	.	.	1	RAG1	HGNC	9831	protein_coding	YES	CCDS7902.1	ENSP00000299440	RAG1_HUMAN	.	UPI000013E5A0	.	deleterious_low_confidence(0)	probably_damaging(0.995)	2/2	.	Pfam_domain:PF12940,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTCTGAAC	.	5	ESCA
PHF21A	0	.	GRCh37	11	45954387	45954387	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000418153	.	30	21	9	17	17	0	PHF21A,3_prime_UTR_variant,,ENST00000257821,;PHF21A,3_prime_UTR_variant,,ENST00000323180,;GYLTL1B,downstream_gene_variant,,ENST00000325468,;GYLTL1B,downstream_gene_variant,,ENST00000531526,;GYLTL1B,downstream_gene_variant,,ENST00000529052,;GYLTL1B,downstream_gene_variant,,ENST00000534410,;PHF21A,downstream_gene_variant,,ENST00000532028,;GYLTL1B,downstream_gene_variant,,ENST00000536139,;GYLTL1B,downstream_gene_variant,,ENST00000531847,;GYLTL1B,downstream_gene_variant,,ENST00000401752,;PHF21A,downstream_gene_variant,,ENST00000525676,;PHF21A,downstream_gene_variant,,ENST00000418153,;PHF21A,non_coding_transcript_exon_variant,,ENST00000527401,;GYLTL1B,downstream_gene_variant,,ENST00000528236,;PHF21A,downstream_gene_variant,,ENST00000534724,;PHF21A,downstream_gene_variant,,ENST00000530587,;GYLTL1B,downstream_gene_variant,,ENST00000530437,;	T	ENSG00000135365	ENST00000418153	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	645	-1	PHF21A	HGNC	24156	protein_coding	YES	CCDS44578.1	ENSP00000398824	PF21A_HUMAN	E9PR02_HUMAN,E9PQM3_HUMAN,E9PNW9_HUMAN,E9PLV4_HUMAN	UPI000006E1CB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACTCTACCA	.	5	ESCA
CREB3L1	0	.	GRCh37	11	46331554	46331554	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531G>C	p.Met177Ile	p.M177I	ENST00000529193	4/12	39	27	11	24	24	0	CREB3L1,missense_variant,p.Met177Ile,ENST00000288400,;CREB3L1,missense_variant,p.Met177Ile,ENST00000529193,;CREB3L1,upstream_gene_variant,,ENST00000530518,;CREB3L1,downstream_gene_variant,,ENST00000534787,;CREB3L1,upstream_gene_variant,,ENST00000527342,;	C	ENSG00000157613	ENST00000529193	Transcript	missense_variant	982	531	177	M/I	atG/atC	.	.	.	1	CREB3L1	HGNC	18856	protein_coding	YES	CCDS53620.1	ENSP00000434939	CR3L1_HUMAN	E9PK33_HUMAN	UPI000004ABFF	.	tolerated(0.24)	benign(0.003)	4/12	.	hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATGACTCA	.	5	ESCA
CHRM4	0	.	GRCh37	11	46407355	46407355	+	Silent	SNP	C	C	T	rs201352810	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753G>A	p.%3D	p.K251K	ENST00000433765	1/1	82	63	19	54	54	0	CHRM4,synonymous_variant,p.%3D,ENST00000433765,;MDK,downstream_gene_variant,,ENST00000395565,;MDK,downstream_gene_variant,,ENST00000407067,;MDK,downstream_gene_variant,,ENST00000359803,;MDK,downstream_gene_variant,,ENST00000405308,;MDK,downstream_gene_variant,,ENST00000533952,;MDK,downstream_gene_variant,,ENST00000441869,;MDK,downstream_gene_variant,,ENST00000395566,;MDK,downstream_gene_variant,,ENST00000395569,;MDK,downstream_gene_variant,,ENST00000533283,;MDK,downstream_gene_variant,,ENST00000481047,;MDK,downstream_gene_variant,,ENST00000489525,;MDK,downstream_gene_variant,,ENST00000490240,;	T	ENSG00000180720	ENST00000433765	Transcript	synonymous_variant	753	753	251	K	aaG/aaA	rs201352810	.	.	-1	CHRM4	HGNC	1953	protein_coding	YES	CCDS44581.1	ENSP00000409378	ACM4_HUMAN	.	UPI00001252BB	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF60,hmmpanther:PTHR24249,Pfam_domain:PF00001	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGCTTCAT	byFrequency|byCluster	5	ESCA
AMBRA1	0	.	GRCh37	11	46563842	46563842	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1455G>A	p.%3D	p.L485L	ENST00000314845	8/19	72	49	23	52	52	0	AMBRA1,synonymous_variant,p.%3D,ENST00000534300,;AMBRA1,synonymous_variant,p.%3D,ENST00000533727,;AMBRA1,synonymous_variant,p.%3D,ENST00000426438,;AMBRA1,synonymous_variant,p.%3D,ENST00000298834,;AMBRA1,synonymous_variant,p.%3D,ENST00000314845,;AMBRA1,synonymous_variant,p.%3D,ENST00000528950,;AMBRA1,synonymous_variant,p.%3D,ENST00000458649,;AMBRA1,downstream_gene_variant,,ENST00000524783,;AMBRA1,downstream_gene_variant,,ENST00000531542,;	T	ENSG00000110497	ENST00000314845	Transcript	synonymous_variant	1815	1455	485	L	ctG/ctA	.	.	.	-1	AMBRA1	HGNC	25990	protein_coding	YES	CCDS31475.1	ENSP00000318313	AMRA1_HUMAN	E9PL55_HUMAN	UPI0000237851	.	.	.	8/19	.	hmmpanther:PTHR22874:SF1,hmmpanther:PTHR22874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGTCAGGAG	.	5	ESCA
PSMC3	0	.	GRCh37	11	47447783	47447783	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.48G>A	p.%3D	p.K16K	ENST00000298852	1/12	71	66	5	74	74	0	PSMC3,synonymous_variant,p.%3D,ENST00000526993,;PSMC3,synonymous_variant,p.%3D,ENST00000531051,;PSMC3,synonymous_variant,p.%3D,ENST00000298852,;PSMC3,synonymous_variant,p.%3D,ENST00000530912,;PSMC3,5_prime_UTR_variant,,ENST00000602866,;PSMC3,upstream_gene_variant,,ENST00000524447,;PSMC3,upstream_gene_variant,,ENST00000530651,;PSMC3,synonymous_variant,p.%3D,ENST00000527906,;PSMC3,non_coding_transcript_exon_variant,,ENST00000528362,;PSMC3,non_coding_transcript_exon_variant,,ENST00000529500,;PSMC3,non_coding_transcript_exon_variant,,ENST00000531653,;PSMC3,upstream_gene_variant,,ENST00000530887,;	T	ENSG00000165916	ENST00000298852	Transcript	synonymous_variant	206	48	16	K	aaG/aaA	.	.	.	-1	PSMC3	HGNC	9549	protein_coding	YES	CCDS7935.1	ENSP00000298852	PRS6A_HUMAN	R4GNH3_HUMAN	UPI0000132389	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCATCTTCTC	.	2	ESCA
OR8H2	0	.	GRCh37	11	55872714	55872714	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196C>T	p.His66Tyr	p.H66Y	ENST00000313503	1/1	88	74	13	80	80	0	OR8H2,missense_variant,p.His66Tyr,ENST00000313503,;	T	ENSG00000181767	ENST00000313503	Transcript	missense_variant	196	196	66	H/Y	Cac/Tac	COSM322422	.	.	1	OR8H2	HGNC	15308	protein_coding	YES	CCDS31518.1	ENSP00000323982	OR8H2_HUMAN	.	UPI0000041D0C	.	deleterious(0.03)	probably_damaging(0.939)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L64F|c.190C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TTACTCACCTG	.	4	ESCA
OR8K5	0	.	GRCh37	11	55927085	55927085	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.709G>T	p.Ala237Ser	p.A237S	ENST00000313447	1/1	32	29	3	27	27	0	OR8K5,missense_variant,p.Ala237Ser,ENST00000313447,;	A	ENSG00000181752	ENST00000313447	Transcript	missense_variant	709	709	237	A/S	Gct/Tct	COSM1321614,COSM543225	.	.	-1	OR8K5	HGNC	15315	protein_coding	YES	CCDS31521.1	ENSP00000323853	OR8K5_HUMAN	.	UPI000004B231	.	deleterious_low_confidence(0.01)	benign(0.303)	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF60,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAGCCTTTT	.	2	ESCA
CLP1	0	.	GRCh37	11	57428246	57428246	+	Missense_Mutation	SNP	C	C	T	rs777290319	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616C>T	p.Arg206Cys	p.R206C	ENST00000533682	3/3	107	94	13	64	64	0	CLP1,missense_variant,p.Arg142Cys,ENST00000302731,;CLP1,missense_variant,p.Arg206Cys,ENST00000533682,;CLP1,missense_variant,p.Arg206Cys,ENST00000525602,;CLP1,missense_variant,p.Arg217Cys,ENST00000529430,;CLP1,downstream_gene_variant,,ENST00000529773,;CLP1,downstream_gene_variant,,ENST00000533905,;	T	ENSG00000172409	ENST00000533682	Transcript	missense_variant	1341	616	206	R/C	Cgt/Tgt	rs777290319,COSM1718427	.	.	1	CLP1	HGNC	16999	protein_coding	YES	CCDS7964.1	ENSP00000434995	CLP1_HUMAN	E9PKV5_HUMAN,E9PJM4_HUMAN	UPI000012754A	.	tolerated(0.06)	benign(0.021)	3/3	.	HAMAP:MF_03035,hmmpanther:PTHR12755:SF6,hmmpanther:PTHR12755,Pfam_domain:PF03205,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCGTTTA	byFrequency	4	ESCA
OR1S1	0	.	GRCh37	11	57982698	57982698	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482C>T	p.Ser161Leu	p.S161L	ENST00000309433	1/1	74	55	19	64	64	0	OR1S1,missense_variant,p.Ser161Leu,ENST00000309433,;	T	ENSG00000172774	ENST00000309433	Transcript	missense_variant	482	482	161	S/L	tCa/tTa	COSM4034148	.	.	1	OR1S1	HGNC	8227	protein_coding	YES	CCDS31546.1	ENSP00000311688	OR1S1_HUMAN	.	UPI0000041C51	.	tolerated(0.05)	benign(0.207)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF180,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCATGGT	.	5	ESCA
OR56A1	0	.	GRCh37	11	6048626	6048626	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.309C>A	p.%3D	p.A103A	ENST00000316650	1/1	81	62	18	66	66	0	OR56A1,synonymous_variant,p.%3D,ENST00000316650,;	T	ENSG00000180934	ENST00000316650	Transcript	synonymous_variant	346	309	103	A	gcC/gcA	.	.	.	-1	OR56A1	HGNC	14781	protein_coding	YES	CCDS31405.1	ENSP00000321246	O56A1_HUMAN	.	UPI000013FE4B	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF62,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGGCAGG	.	5	ESCA
FTH1	0	.	GRCh37	11	61734848	61734848	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50C>T	p.Ser17Leu	p.S17L	ENST00000273550	1/4	22	15	7	28	28	0	FTH1,missense_variant,p.Ser17Leu,ENST00000529191,;FTH1,missense_variant,p.Ser17Leu,ENST00000273550,;FTH1,missense_variant,p.Ser17Leu,ENST00000529631,;FTH1,missense_variant,p.Ser17Leu,ENST00000530019,;FTH1,splice_region_variant,,ENST00000529548,;FTH1,intron_variant,,ENST00000526640,;BEST1,downstream_gene_variant,,ENST00000378042,;BEST1,downstream_gene_variant,,ENST00000378043,;FTH1,upstream_gene_variant,,ENST00000532601,;BEST1,downstream_gene_variant,,ENST00000435278,;BEST1,downstream_gene_variant,,ENST00000449131,;BEST1,downstream_gene_variant,,ENST00000534553,;AP003733.1,upstream_gene_variant,,ENST00000601917,;BEST1,downstream_gene_variant,,ENST00000301774,;FTH1,missense_variant,p.Ser17Leu,ENST00000532829,;FTH1,missense_variant,p.Ser17Leu,ENST00000534180,;FTH1,non_coding_transcript_exon_variant,,ENST00000534719,;FTH1,non_coding_transcript_exon_variant,,ENST00000533138,;BEST1,downstream_gene_variant,,ENST00000524926,;BEST1,downstream_gene_variant,,ENST00000524877,;	A	ENSG00000167996	ENST00000273550	Transcript	missense_variant	285	50	17	S/L	tCa/tTa	.	.	.	-1	FTH1	HGNC	3976	protein_coding	YES	CCDS41655.1	ENSP00000273550	FRIH_HUMAN	Q6NS36_HUMAN,G3V1D1_HUMAN,E9PPQ4_HUMAN,A9JQE1_HUMAN	UPI000000122C	.	deleterious(0.02)	benign(0.012)	1/4	.	PROSITE_profiles:PS50905,hmmpanther:PTHR11431,hmmpanther:PTHR11431:SF37,Gene3D:1.20.1260.10,Superfamily_domains:SSF47240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTGAGTCC	.	5	ESCA
SLC22A10	0	.	GRCh37	11	63065028	63065028	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662-3C>G	.	.	ENST00000332793	.	73	61	12	63	63	0	SLC22A10,splice_region_variant,,ENST00000544661,;SLC22A10,splice_region_variant,,ENST00000535888,;SLC22A10,splice_region_variant,,ENST00000332793,;SLC22A10,intron_variant,,ENST00000526800,;SLC22A10,splice_region_variant,,ENST00000525620,;SLC22A10,splice_region_variant,,ENST00000533483,;SLC22A10,intron_variant,,ENST00000532724,;	G	ENSG00000184999	ENST00000332793	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	SLC22A10	HGNC	18057	protein_coding	YES	CCDS41661.1	ENSP00000327569	S22AA_HUMAN	B4DJY8_HUMAN	UPI0000D62620	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TCTTTCAGTTA	.	2	ESCA
BBS1	0	.	GRCh37	11	66299165	66299165	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1647G>T	p.Glu549Asp	p.E549D	ENST00000318312	16/17	89	70	19	53	53	0	BBS1,missense_variant,p.Glu549Asp,ENST00000318312,;BBS1,missense_variant,p.Glu452Asp,ENST00000455748,;CTD-3074O7.11,missense_variant,p.Glu586Asp,ENST00000419755,;BBS1,missense_variant,p.Glu420Asp,ENST00000393994,;ZDHHC24,intron_variant,,ENST00000526986,;CTD-3074O7.12,downstream_gene_variant,,ENST00000602427,;BBS1,downstream_gene_variant,,ENST00000529766,;BBS1,3_prime_UTR_variant,,ENST00000526760,;BBS1,non_coding_transcript_exon_variant,,ENST00000529955,;ZDHHC24,intron_variant,,ENST00000534073,;BBS1,downstream_gene_variant,,ENST00000527959,;	T	ENSG00000174483	ENST00000318312	Transcript	missense_variant	1698	1647	549	E/D	gaG/gaT	.	.	.	1	BBS1	HGNC	966	protein_coding	YES	CCDS8142.1	ENSP00000317469	BBS1_HUMAN	E9PQD9_HUMAN,E9PPR3_HUMAN	UPI0000073430	.	tolerated(0.16)	benign(0.084)	16/17	.	hmmpanther:PTHR20870:SF0,hmmpanther:PTHR20870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAGACCTT	.	5	ESCA
RBM14-RBM4	0	.	GRCh37	11	66384399	66384399	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.208A>T	p.Met70Leu	p.M70L	ENST00000412278	1/3	46	34	12	54	54	0	RBM14-RBM4,missense_variant,p.Met70Leu,ENST00000412278,;RBM14,missense_variant,p.Met70Leu,ENST00000310137,;RBM4,missense_variant,p.Met70Leu,ENST00000514361,;RBM14-RBM4,missense_variant,p.Met70Leu,ENST00000500635,;RBM14,missense_variant,p.Met70Leu,ENST00000443702,;RBM14,missense_variant,p.Met70Leu,ENST00000393979,;RBM14,missense_variant,p.Met70Leu,ENST00000409738,;RBM14,missense_variant,p.Met70Leu,ENST00000409372,;RBM4,5_prime_UTR_variant,,ENST00000503028,;RNU4-39P,upstream_gene_variant,,ENST00000362455,;RBM14-RBM4,non_coding_transcript_exon_variant,,ENST00000511114,;RBM14,non_coding_transcript_exon_variant,,ENST00000512283,;RBM14,upstream_gene_variant,,ENST00000496694,;RBM14,upstream_gene_variant,,ENST00000461478,;RBM14,upstream_gene_variant,,ENST00000460762,;RBM14-RBM4,missense_variant,p.Met70Leu,ENST00000421355,;	T	ENSG00000248643	ENST00000412278	Transcript	missense_variant	303	208	70	M/L	Atg/Ttg	.	.	.	1	RBM14-RBM4	HGNC	38840	protein_coding	YES	CCDS55774.1	ENSP00000388552	.	.	UPI0001641710	.	tolerated(0.53)	benign(0.035)	1/3	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF242,Gene3D:3.30.70.330,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGATGTCG	.	5	ESCA
GVINP1	0	.	GRCh37	11	6741187	6741187	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2018G>C	.	.	ENST00000526769	2/2	29	25	4	29	29	0	GVINP1,non_coding_transcript_exon_variant,,ENST00000526769,;GVINP1,non_coding_transcript_exon_variant,,ENST00000531871,;GVINP1,upstream_gene_variant,,ENST00000535670,;	G	ENSG00000254838	ENST00000526769	Transcript	non_coding_transcript_exon_variant	2018	.	.	.	.	.	.	.	-1	GVINP1	HGNC	25813	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTTCTTTTA	.	2	ESCA
LRP5	0	.	GRCh37	11	68125233	68125233	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.604A>T	p.Ile202Phe	p.I202F	ENST00000294304	3/23	73	59	13	61	61	0	LRP5,missense_variant,p.Ile202Phe,ENST00000294304,;LRP5,missense_variant,p.Ile202Phe,ENST00000529993,;	T	ENSG00000162337	ENST00000294304	Transcript	missense_variant	710	604	202	I/F	Atc/Ttc	.	.	.	1	LRP5	HGNC	6697	protein_coding	YES	CCDS8181.1	ENSP00000294304	LRP5_HUMAN	E9PHY1_HUMAN	UPI0000073246	.	deleterious(0)	probably_damaging(0.934)	3/23	.	Superfamily_domains:SSF63825,PIRSF_domain:PIRSF036314,SMART_domains:SM00135,Pfam_domain:PF00058,Gene3D:2.120.10.30,hmmpanther:PTHR10529:SF202,hmmpanther:PTHR10529,PROSITE_profiles:PS51120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACCATCGAC	.	5	ESCA
SHANK2	0	.	GRCh37	11	70332425	70332425	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3976G>C	p.Asp1326His	p.D1326H	ENST00000338508	32/33	42	30	12	32	32	0	SHANK2,missense_variant,p.Asp729His,ENST00000409161,;SHANK2,missense_variant,p.Asp604His,ENST00000424924,;SHANK2,missense_variant,p.Asp946His,ENST00000423696,;SHANK2,missense_variant,p.Asp949His,ENST00000294018,;SHANK2,missense_variant,p.Asp1326His,ENST00000338508,;SHANK2,missense_variant,p.Asp730His,ENST00000449833,;SHANK2,intron_variant,,ENST00000412252,;SHANK2,downstream_gene_variant,,ENST00000409530,;SHANK2,downstream_gene_variant,,ENST00000357171,;SHANK2,downstream_gene_variant,,ENST00000449116,;	G	ENSG00000162105	ENST00000338508	Transcript	missense_variant	3976	3976	1326	D/H	Gac/Cac	.	.	.	-1	SHANK2	HGNC	14295	protein_coding	YES	.	ENSP00000345193	.	C9JFP8_HUMAN,A6NHU9_HUMAN	UPI00020653A9	.	tolerated(0.07)	possibly_damaging(0.861)	32/33	.	hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGTCCAGCT	.	5	ESCA
PAK1	0	.	GRCh37	11	77103569	77103569	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4G>A	.	.	ENST00000278568	2/16	64	50	13	56	56	0	PAK1,5_prime_UTR_variant,,ENST00000278568,;PAK1,5_prime_UTR_variant,,ENST00000528633,;PAK1,5_prime_UTR_variant,,ENST00000528592,;PAK1,5_prime_UTR_variant,,ENST00000524847,;PAK1,5_prime_UTR_variant,,ENST00000529248,;PAK1,5_prime_UTR_variant,,ENST00000526968,;PAK1,5_prime_UTR_variant,,ENST00000356341,;PAK1,5_prime_UTR_variant,,ENST00000530617,;PAK1,intron_variant,,ENST00000528203,;PAK1,non_coding_transcript_exon_variant,,ENST00000533568,;PAK1,upstream_gene_variant,,ENST00000526910,;	T	ENSG00000149269	ENST00000278568	Transcript	5_prime_UTR_variant	527	.	.	.	.	.	.	.	-1	PAK1	HGNC	8590	protein_coding	YES	CCDS44687.1	ENSP00000278568	PAK1_HUMAN	E9PRP6_HUMAN,E9PQW5_HUMAN,E9PMP2_HUMAN,E9PM17_HUMAN,E9PKH9_HUMAN,E9PJF8_HUMAN	UPI000013DB7F	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATTGTCACCAC	.	4	ESCA
CCDC90B	0	.	GRCh37	11	82996871	82996871	+	Intron	SNP	C	C	T	rs773808305	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100+45G>A	.	.	ENST00000529689	.	24	21	3	17	17	0	CCDC90B,5_prime_UTR_variant,,ENST00000525503,;CCDC90B,5_prime_UTR_variant,,ENST00000529611,;CCDC90B,intron_variant,,ENST00000529073,;CCDC90B,intron_variant,,ENST00000529689,;CCDC90B,intron_variant,,ENST00000455220,;RP11-727A23.10,upstream_gene_variant,,ENST00000534572,;RP11-727A23.10,upstream_gene_variant,,ENST00000530045,;CCDC90B,non_coding_transcript_exon_variant,,ENST00000525916,;CCDC90B,3_prime_UTR_variant,,ENST00000528149,;CCDC90B,intron_variant,,ENST00000534753,;CCDC90B,intron_variant,,ENST00000527025,;CCDC90B,intron_variant,,ENST00000526265,;CCDC90B,intron_variant,,ENST00000260054,;CCDC90B,intron_variant,,ENST00000529312,;CCDC90B,intron_variant,,ENST00000529856,;CCDC90B,intron_variant,,ENST00000529745,;CCDC90B,intron_variant,,ENST00000533761,;CCDC90B,intron_variant,,ENST00000530253,;CCDC90B,intron_variant,,ENST00000526631,;	T	ENSG00000137500	ENST00000529689	Transcript	intron_variant	.	.	.	.	.	rs773808305	.	.	-1	CCDC90B	HGNC	28108	protein_coding	YES	CCDS8266.1	ENSP00000434724	CC90B_HUMAN	B3KP87_HUMAN	UPI0000037C9A	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTCTCCCTAG	.	2	ESCA
CD151	0	.	GRCh37	11	836150	836150	+	Missense_Mutation	SNP	C	C	A	rs746358515	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81C>A	p.Phe27Leu	p.F27L	ENST00000397420	3/9	32	26	5	41	41	0	CD151,missense_variant,p.Phe27Leu,ENST00000528867,;CD151,missense_variant,p.Phe27Leu,ENST00000528011,;CD151,missense_variant,p.Phe27Leu,ENST00000525718,;CD151,missense_variant,p.Phe27Leu,ENST00000397420,;CD151,missense_variant,p.Phe27Leu,ENST00000526439,;CD151,missense_variant,p.Phe27Leu,ENST00000525333,;CD151,missense_variant,p.Phe27Leu,ENST00000322008,;CD151,missense_variant,p.Phe27Leu,ENST00000527341,;CD151,missense_variant,p.Phe27Leu,ENST00000529810,;CD151,missense_variant,p.Phe27Leu,ENST00000524748,;CD151,missense_variant,p.Phe27Leu,ENST00000397421,;CD151,missense_variant,p.Phe27Leu,ENST00000530320,;CD151,missense_variant,p.Phe27Leu,ENST00000526693,;EFCAB4A,downstream_gene_variant,,ENST00000528542,;EFCAB4A,downstream_gene_variant,,ENST00000525077,;EFCAB4A,downstream_gene_variant,,ENST00000450448,;POLR2L,downstream_gene_variant,,ENST00000322028,;AP006621.8,upstream_gene_variant,,ENST00000532946,;CD151,upstream_gene_variant,,ENST00000525181,;CD151,missense_variant,p.Phe27Leu,ENST00000530726,;CD151,non_coding_transcript_exon_variant,,ENST00000531999,;CD151,non_coding_transcript_exon_variant,,ENST00000530155,;CD151,non_coding_transcript_exon_variant,,ENST00000532045,;CD151,non_coding_transcript_exon_variant,,ENST00000526661,;CD151,non_coding_transcript_exon_variant,,ENST00000525868,;EFCAB4A,downstream_gene_variant,,ENST00000526531,;POLR2L,downstream_gene_variant,,ENST00000534030,;EFCAB4A,downstream_gene_variant,,ENST00000527763,;CD151,upstream_gene_variant,,ENST00000532075,;EFCAB4A,downstream_gene_variant,,ENST00000528694,;EFCAB4A,downstream_gene_variant,,ENST00000530688,;	A	ENSG00000177697	ENST00000397420	Transcript	missense_variant	330	81	27	F/L	ttC/ttA	rs746358515	.	.	1	CD151	HGNC	1630	protein_coding	YES	CCDS7719.1	ENSP00000380565	CD151_HUMAN	K4DIB7_HUMAN,E9PSA1_HUMAN,E9PP93_HUMAN,E9PLZ6_HUMAN,E9PK37_HUMAN,E9PJE8_HUMAN,E9PJC8_HUMAN	UPI00001507D8	.	deleterious(0)	possibly_damaging(0.812)	3/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF167,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Prints_domain:PR00259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCTGGGT	.	5	ESCA
FAT3	0	.	GRCh37	11	92538330	92538330	+	Nonsense_Mutation	SNP	C	C	T	rs563792009	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8908C>T	p.Arg2970Ter	p.R2970*	ENST00000298047	10/27	40	31	9	31	31	0	FAT3,stop_gained,p.Arg2970Ter,ENST00000298047,;FAT3,stop_gained,p.Arg2970Ter,ENST00000409404,;FAT3,stop_gained,p.Arg2820Ter,ENST00000525166,;	T	ENSG00000165323	ENST00000298047	Transcript	stop_gained	8925	8908	2970	R/*	Cga/Tga	rs563792009,COSM3953958,COSM3953957	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	.	10/27	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTCGAGGA	by1000G	4	ESCA
TDG	0	.	GRCh37	12	104381123	104381123	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*255G>A	.	.	ENST00000392872	10/10	38	31	6	34	34	0	TDG,3_prime_UTR_variant,,ENST00000392872,;TDG,downstream_gene_variant,,ENST00000542036,;GLT8D2,downstream_gene_variant,,ENST00000548660,;TDG,downstream_gene_variant,,ENST00000544861,;TDG,downstream_gene_variant,,ENST00000266775,;GLT8D2,downstream_gene_variant,,ENST00000360814,;TDG,downstream_gene_variant,,ENST00000537100,;TDG,downstream_gene_variant,,ENST00000436021,;GLT8D2,downstream_gene_variant,,ENST00000546436,;AC078819.1,downstream_gene_variant,,ENST00000401157,;TDG,downstream_gene_variant,,ENST00000536395,;TDG,downstream_gene_variant,,ENST00000542926,;TDG,downstream_gene_variant,,ENST00000540956,;	A	ENSG00000139372	ENST00000392872	Transcript	3_prime_UTR_variant	1722	.	.	.	.	.	.	.	1	TDG	HGNC	11700	protein_coding	YES	CCDS9095.1	ENSP00000376611	TDG_HUMAN	F5H539_HUMAN,B4E127_HUMAN	UPI00000740E5	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTATGAAGAA	.	4	ESCA
CKAP4	0	.	GRCh37	12	106632149	106632149	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*653G>C	.	.	ENST00000378026	2/2	27	23	4	24	24	0	CKAP4,3_prime_UTR_variant,,ENST00000378026,;CKAP4,downstream_gene_variant,,ENST00000553039,;CKAP4,downstream_gene_variant,,ENST00000552828,;	G	ENSG00000136026	ENST00000378026	Transcript	3_prime_UTR_variant	2599	.	.	.	.	.	.	.	-1	CKAP4	HGNC	16991	protein_coding	YES	CCDS9103.1	ENSP00000367265	CKAP4_HUMAN	.	UPI00000723B9	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATTCAGAAC	.	4	ESCA
RIC8B	0	.	GRCh37	12	107281648	107281648	+	3'Flank	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000392839	.	12	10	2	13	13	0	RIC8B,3_prime_UTR_variant,,ENST00000392837,;RIC8B,downstream_gene_variant,,ENST00000355478,;RIC8B,downstream_gene_variant,,ENST00000549643,;RIC8B,downstream_gene_variant,,ENST00000392839,;RIC8B,downstream_gene_variant,,ENST00000546449,;RIC8B,downstream_gene_variant,,ENST00000462949,;RIC8B,downstream_gene_variant,,ENST00000551756,;RIC8B,downstream_gene_variant,,ENST00000470960,;	C	ENSG00000111785	ENST00000392839	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1084	1	RIC8B	HGNC	25555	protein_coding	YES	CCDS9109.2	ENSP00000376583	RIC8B_HUMAN	F8VR30_HUMAN	UPI00001FB46B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGAAGAAATT	.	2	ESCA
BTBD11	0	.	GRCh37	12	108051486	108051486	+	Silent	SNP	C	C	T	rs763125812	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3306C>T	p.%3D	p.S1102S	ENST00000280758	17/17	33	28	5	41	41	0	BTBD11,synonymous_variant,p.%3D,ENST00000494235,;BTBD11,synonymous_variant,p.%3D,ENST00000280758,;BTBD11,synonymous_variant,p.%3D,ENST00000420571,;BTBD11,synonymous_variant,p.%3D,ENST00000357167,;	T	ENSG00000151136	ENST00000280758	Transcript	synonymous_variant	3834	3306	1102	S	tcC/tcT	rs763125812	.	.	1	BTBD11	HGNC	23844	protein_coding	YES	CCDS31893.1	ENSP00000280758	BTBDB_HUMAN	B3KY13_HUMAN,B3KXB0_HUMAN	UPI000051901E	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTTCCGTGGT	.	3	ESCA
ACACB	0	.	GRCh37	12	109647044	109647044	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3135C>T	p.%3D	p.I1045I	ENST00000338432	21/53	79	67	11	77	77	0	ACACB,synonymous_variant,p.%3D,ENST00000377854,;ACACB,synonymous_variant,p.%3D,ENST00000377848,;ACACB,synonymous_variant,p.%3D,ENST00000338432,;	T	ENSG00000076555	ENST00000338432	Transcript	synonymous_variant	3254	3135	1045	I	atC/atT	.	.	.	1	ACACB	HGNC	85	protein_coding	YES	CCDS31898.1	ENSP00000341044	ACACB_HUMAN	F5H5C3_HUMAN,E9PEW7_HUMAN	UPI0000DBEEFB	.	.	.	21/53	.	hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF84,Pfam_domain:PF08326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGATCATGAC	.	4	ESCA
RNFT2	0	.	GRCh37	12	117204678	117204678	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.687C>G	p.%3D	p.L229L	ENST00000257575	6/11	67	54	13	60	60	0	RNFT2,synonymous_variant,p.%3D,ENST00000407967,;RNFT2,synonymous_variant,p.%3D,ENST00000392549,;RNFT2,synonymous_variant,p.%3D,ENST00000257575,;RNFT2,synonymous_variant,p.%3D,ENST00000319176,;RNFT2,3_prime_UTR_variant,,ENST00000547718,;	G	ENSG00000135119	ENST00000257575	Transcript	synonymous_variant	920	687	229	L	ctC/ctG	.	.	.	1	RNFT2	HGNC	25905	protein_coding	YES	CCDS44987.1	ENSP00000257575	RNFT2_HUMAN	.	UPI00001FBBF4	.	.	.	6/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15860:SF2,hmmpanther:PTHR15860	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCTATGT	.	5	ESCA
SPPL3	0	.	GRCh37	12	121202843	121202843	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114T>C	p.Phe372Leu	p.F372L	ENST00000353487	11/11	17	13	4	13	13	0	SPPL3,missense_variant,p.Phe372Leu,ENST00000353487,;SPPL3,downstream_gene_variant,,ENST00000543608,;SPPL3,downstream_gene_variant,,ENST00000536996,;SPPL3,downstream_gene_variant,,ENST00000543854,;RP11-173P15.7,upstream_gene_variant,,ENST00000542620,;SPPL3,non_coding_transcript_exon_variant,,ENST00000545209,;SPPL3,non_coding_transcript_exon_variant,,ENST00000392495,;	G	ENSG00000157837	ENST00000353487	Transcript	missense_variant	1618	1114	372	F/L	Ttc/Ctc	.	.	.	-1	SPPL3	HGNC	30424	protein_coding	YES	CCDS9208.1	ENSP00000288680	SPPL3_HUMAN	F5H7J2_HUMAN,F5H6I1_HUMAN,F5H4Y6_HUMAN,F5H4L1_HUMAN,F5H2A2_HUMAN	UPI0000013590	.	tolerated(0.14)	benign(0.017)	11/11	.	hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGAAAGGCT	.	2	ESCA
CLIP1	0	.	GRCh37	12	122865061	122865061	+	5'Flank	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000540338	.	37	29	8	31	31	0	CLIP1,5_prime_UTR_variant,,ENST00000535290,;CLIP1,5_prime_UTR_variant,,ENST00000537178,;CLIP1,5_prime_UTR_variant,,ENST00000302528,;CLIP1,5_prime_UTR_variant,,ENST00000539080,;CLIP1,5_prime_UTR_variant,,ENST00000361654,;CLIP1,5_prime_UTR_variant,,ENST00000358808,;CLIP1,5_prime_UTR_variant,,ENST00000537004,;CLIP1,5_prime_UTR_variant,,ENST00000540304,;CLIP1,upstream_gene_variant,,ENST00000540338,;CLIP1,5_prime_UTR_variant,,ENST00000541108,;	A	ENSG00000130779	ENST00000540338	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	20	-1	CLIP1	HGNC	10461	protein_coding	YES	CCDS58285.1	ENSP00000439093	CLIP1_HUMAN	F5H367_HUMAN,F5H270_HUMAN	UPI0000E00D4E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATTGATACA	.	2	ESCA
RILPL2	0	.	GRCh37	12	123907666	123907666	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530G>T	p.Arg177Ile	p.R177I	ENST00000280571	3/4	40	35	5	48	48	0	RILPL2,missense_variant,p.Arg177Ile,ENST00000280571,;	A	ENSG00000150977	ENST00000280571	Transcript	missense_variant	827	530	177	R/I	aGa/aTa	.	.	.	-1	RILPL2	HGNC	28787	protein_coding	YES	CCDS9248.1	ENSP00000280571	RIPL2_HUMAN	.	UPI00000722E4	.	tolerated(0.29)	benign(0.315)	3/4	.	hmmpanther:PTHR21502,Pfam_domain:PF11461,Superfamily_domains:0053655	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTCTCTTCTT	.	3	ESCA
EIF2B1	0	.	GRCh37	12	124111668	124111668	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405G>A	p.%3D	p.L135L	ENST00000424014	5/9	51	46	4	44	44	0	EIF2B1,synonymous_variant,p.%3D,ENST00000537073,;EIF2B1,synonymous_variant,p.%3D,ENST00000539951,;EIF2B1,synonymous_variant,p.%3D,ENST00000424014,;EIF2B1,intron_variant,,ENST00000534960,;EIF2B1,downstream_gene_variant,,ENST00000543940,;EIF2B1,downstream_gene_variant,,ENST00000452159,;	T	ENSG00000111361	ENST00000424014	Transcript	synonymous_variant	614	405	135	L	ctG/ctA	.	.	.	-1	EIF2B1	HGNC	3257	protein_coding	YES	CCDS31924.1	ENSP00000416250	EI2BA_HUMAN	.	UPI0000129AAE	.	.	.	5/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10233,hmmpanther:PTHR10233:SF18,Pfam_domain:PF01008,Gene3D:3.40.50.10470,Superfamily_domains:SSF100950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTCTCAGGAC	.	2	ESCA
EIF2B1	0	.	GRCh37	12	124111678	124111678	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.395G>A	p.Arg132Lys	p.R132K	ENST00000424014	5/9	45	42	3	42	42	0	EIF2B1,missense_variant,p.Arg132Lys,ENST00000537073,;EIF2B1,missense_variant,p.Arg119Lys,ENST00000539951,;EIF2B1,missense_variant,p.Arg132Lys,ENST00000424014,;EIF2B1,intron_variant,,ENST00000534960,;EIF2B1,downstream_gene_variant,,ENST00000543940,;EIF2B1,downstream_gene_variant,,ENST00000452159,;	T	ENSG00000111361	ENST00000424014	Transcript	missense_variant	604	395	132	R/K	aGa/aAa	.	.	.	-1	EIF2B1	HGNC	3257	protein_coding	YES	CCDS31924.1	ENSP00000416250	EI2BA_HUMAN	.	UPI0000129AAE	.	tolerated(0.24)	benign(0.137)	5/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10233,hmmpanther:PTHR10233:SF18,Pfam_domain:PF01008,Gene3D:3.40.50.10470,Superfamily_domains:SSF100950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACTCTGGAG	.	2	ESCA
DNAH10	0	.	GRCh37	12	124343712	124343712	+	Nonsense_Mutation	SNP	C	C	T	rs751867595	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6292C>T	p.Gln2098Ter	p.Q2098*	ENST00000409039	37/78	49	42	7	51	51	0	DNAH10,stop_gained,p.Gln2098Ter,ENST00000409039,;DNAH10,stop_gained,p.Gln581Ter,ENST00000497783,;	T	ENSG00000197653	ENST00000409039	Transcript	stop_gained	6317	6292	2098	Q/*	Caa/Taa	rs751867595	.	.	1	DNAH10	HGNC	2941	protein_coding	YES	CCDS9255.2	ENSP00000386770	DYH10_HUMAN	.	UPI00014F7B89	.	.	.	37/78	.	hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTCAAATG	.	4	ESCA
EMP1	0	.	GRCh37	12	13364445	13364446	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2dupT	p.Met1?	p.M1?	ENST00000256951	2/5	53	36	17	62	62	0	EMP1,frameshift_variant,p.Met1?,ENST00000538364,;EMP1,frameshift_variant,p.Met1?,ENST00000537612,;EMP1,frameshift_variant,p.Met1?,ENST00000542474,;EMP1,frameshift_variant,p.Met1?,ENST00000396301,;EMP1,frameshift_variant,p.Met1?,ENST00000256951,;EMP1,intron_variant,,ENST00000544053,;EMP1,intron_variant,,ENST00000431267,;EMP1,non_coding_transcript_exon_variant,,ENST00000542289,;EMP1,downstream_gene_variant,,ENST00000535134,;EMP1,non_coding_transcript_exon_variant,,ENST00000541935,;EMP1,upstream_gene_variant,,ENST00000546357,;EMP1,upstream_gene_variant,,ENST00000536383,;	T	ENSG00000134531	ENST00000256951	Transcript	frameshift_variant	200-201	1-2	1	M/IX	atg/aTtg	.	.	.	1	EMP1	HGNC	3333	protein_coding	YES	CCDS8660.1	ENSP00000256951	EMP1_HUMAN	J3KQX4_HUMAN	UPI000000DBC8	.	.	.	2/5	.	hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF6,Pfam_domain:PF00822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAACATGTTG	.	3	ESCA
ATF7IP	0	.	GRCh37	12	14589064	14589064	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1670C>G	p.Ser557Cys	p.S557C	ENST00000261168	4/15	17	9	8	15	15	0	ATF7IP,missense_variant,p.Ser557Cys,ENST00000261168,;ATF7IP,missense_variant,p.Ser557Cys,ENST00000540793,;ATF7IP,missense_variant,p.Ser556Cys,ENST00000543189,;ATF7IP,missense_variant,p.Ser565Cys,ENST00000544627,;ATF7IP,missense_variant,p.Ser556Cys,ENST00000536444,;ATF7IP,5_prime_UTR_variant,,ENST00000538511,;ATF7IP,intron_variant,,ENST00000545723,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000539659,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000541654,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000537653,;	G	ENSG00000171681	ENST00000261168	Transcript	missense_variant	1823	1670	557	S/C	tCt/tGt	.	.	.	1	ATF7IP	HGNC	20092	protein_coding	YES	CCDS8663.1	ENSP00000261168	MCAF1_HUMAN	F8WE35_HUMAN,F5H8I0_HUMAN,F5H6X8_HUMAN,F5H502_HUMAN,F5H3C4_HUMAN,F5H2W9_HUMAN,F5H2H9_HUMAN,F5H221_HUMAN,F5H1K9_HUMAN,F5GZ98_HUMAN,F5GZ10_HUMAN,F5GYR7_HUMAN,A8MV73_HUMAN	UPI00001FB6B1	.	deleterious_low_confidence(0)	possibly_damaging(0.843)	4/15	.	hmmpanther:PTHR23210:SF20,hmmpanther:PTHR23210	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTTCTAAAT	.	5	ESCA
IQSEC3	0	.	GRCh37	12	176445	176445	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397C>T	p.His133Tyr	p.H133Y	ENST00000538872	1/14	147	117	29	127	127	0	IQSEC3,missense_variant,p.His133Tyr,ENST00000538872,;IQSEC3,missense_variant,p.His133Tyr,ENST00000326261,;	T	ENSG00000120645	ENST00000538872	Transcript	missense_variant	515	397	133	H/Y	Cac/Tac	.	.	.	1	IQSEC3	HGNC	29193	protein_coding	YES	CCDS53728.1	ENSP00000437554	IQEC3_HUMAN	.	UPI0000DBEEF0	.	tolerated_low_confidence(0.13)	benign(0.127)	1/14	.	hmmpanther:PTHR10663:SF62,hmmpanther:PTHR10663	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTCACACA	.	5	ESCA
ABCC9	0	.	GRCh37	12	21981923	21981923	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3638C>T	p.Ser1213Leu	p.S1213L	ENST00000261200	29/38	35	24	11	32	32	0	ABCC9,missense_variant,p.Ser1177Leu,ENST00000345162,;ABCC9,missense_variant,p.Ser1213Leu,ENST00000261201,;ABCC9,missense_variant,p.Ser840Leu,ENST00000544039,;ABCC9,missense_variant,p.Ser1213Leu,ENST00000261200,;RP11-729I10.2,intron_variant,,ENST00000539874,;	A	ENSG00000069431	ENST00000261200	Transcript	missense_variant	3638	3638	1213	S/L	tCa/tTa	COSM3710606,COSM3710607	.	.	-1	ABCC9	HGNC	60	protein_coding	YES	CCDS8693.1	ENSP00000261200	ABCC9_HUMAN	Q8N9N1_HUMAN	UPI000013D13F	.	tolerated(0.07)	benign(0.022)	29/38	.	Superfamily_domains:SSF90123,Pfam_domain:PF00664,Gene3D:2hydA01,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,PROSITE_profiles:PS50929	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGAGAGA	.	5	ESCA
FGD4	0	.	GRCh37	12	32754265	32754265	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.744G>C	p.Glu248Asp	p.E248D	ENST00000427716	6/17	21	16	4	37	37	0	FGD4,missense_variant,p.Glu155Asp,ENST00000546442,;FGD4,missense_variant,p.Glu333Asp,ENST00000531134,;FGD4,missense_variant,p.Glu248Asp,ENST00000427716,;FGD4,missense_variant,p.Glu360Asp,ENST00000525053,;FGD4,missense_variant,p.Glu385Asp,ENST00000534526,;FGD4,5_prime_UTR_variant,,ENST00000381025,;FGD4,5_prime_UTR_variant,,ENST00000266482,;FGD4,3_prime_UTR_variant,,ENST00000494977,;FGD4,3_prime_UTR_variant,,ENST00000395740,;FGD4,3_prime_UTR_variant,,ENST00000493087,;FGD4,3_prime_UTR_variant,,ENST00000551984,;	C	ENSG00000139132	ENST00000427716	Transcript	missense_variant	1168	744	248	E/D	gaG/gaC	.	.	.	1	FGD4	HGNC	19125	protein_coding	YES	CCDS8727.1	ENSP00000394487	FGD4_HUMAN	J3KSS3_HUMAN,F8W1R0_HUMAN	UPI000004CCA6	.	tolerated(0.6)	benign(0.123)	6/17	.	PROSITE_profiles:PS50010,hmmpanther:PTHR12673:SF98,hmmpanther:PTHR12673,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGAGATGGT	.	5	ESCA
PKP2	0	.	GRCh37	12	32975511	32975511	+	Missense_Mutation	SNP	C	C	G	rs749196250	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1861G>C	p.Glu621Gln	p.E621Q	ENST00000070846	9/14	48	44	3	41	41	0	PKP2,missense_variant,p.Glu577Gln,ENST00000340811,;PKP2,missense_variant,p.Glu621Gln,ENST00000070846,;PKP2,non_coding_transcript_exon_variant,,ENST00000546498,;PKP2,non_coding_transcript_exon_variant,,ENST00000552612,;PKP2,upstream_gene_variant,,ENST00000549461,;	G	ENSG00000057294	ENST00000070846	Transcript	missense_variant	1886	1861	621	E/Q	Gag/Cag	rs749196250,COSM468288	.	.	-1	PKP2	HGNC	9024	protein_coding	YES	CCDS8731.1	ENSP00000070846	PKP2_HUMAN	.	UPI000013C576	.	deleterious(0)	benign(0.165)	9/14	.	hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCTCTGCCT	.	2	ESCA
KDM5A	0	.	GRCh37	12	431719	431719	+	Nonsense_Mutation	SNP	G	G	A	rs768653465	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2290C>T	p.Arg764Ter	p.R764*	ENST00000399788	17/28	22	17	4	20	20	0	KDM5A,stop_gained,p.Arg764Ter,ENST00000382815,;KDM5A,stop_gained,p.Arg383Ter,ENST00000544760,;KDM5A,stop_gained,p.Arg764Ter,ENST00000399788,;KDM5A,non_coding_transcript_exon_variant,,ENST00000541335,;KDM5A,downstream_gene_variant,,ENST00000540168,;	A	ENSG00000073614	ENST00000399788	Transcript	stop_gained	2653	2290	764	R/*	Cga/Tga	rs768653465	.	.	-1	KDM5A	HGNC	9886	protein_coding	YES	CCDS41736.1	ENSP00000382688	KDM5A_HUMAN	.	UPI0000DB2E73	.	.	.	17/28	.	hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17,Pfam_domain:PF08429	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTCGCAATT	.	5	ESCA
KCNA6	0	.	GRCh37	12	4922632	4922632	+	3'UTR	SNP	C	C	T	rs41276722	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1835C>T	.	.	ENST00000433855	1/2	27	22	4	31	31	0	KCNA6,3_prime_UTR_variant,,ENST00000433855,;GALNT8,intron_variant,,ENST00000542998,;KCNA6,downstream_gene_variant,,ENST00000280684,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,;	T	ENSG00000151079	ENST00000433855	Transcript	3_prime_UTR_variant	4291	.	.	.	.	rs41276722	.	.	1	KCNA6	HGNC	6225	protein_coding	YES	CCDS8534.1	ENSP00000408321	KCNA6_HUMAN	.	UPI00001279AD	.	.	.	1/2	.	.	T:0.0008	T:0	T:0.0014	.	T:0	T:0.002	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGATCCAAAG	byFrequency|byCluster|by1000G	5	ESCA
CERS5	0	.	GRCh37	12	50524336	50524336	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1171G>A	p.Glu391Lys	p.E391K	ENST00000317551	10/10	62	49	13	55	55	0	CERS5,missense_variant,p.Glu333Lys,ENST00000422340,;CERS5,missense_variant,p.Glu391Lys,ENST00000317551,;CERS5,3_prime_UTR_variant,,ENST00000550919,;CERS5,3_prime_UTR_variant,,ENST00000553122,;CERS5,downstream_gene_variant,,ENST00000550547,;RP4-605O3.4,intron_variant,,ENST00000548468,;CERS5,downstream_gene_variant,,ENST00000548942,;CERS5,downstream_gene_variant,,ENST00000547138,;CERS5,3_prime_UTR_variant,,ENST00000551697,;CERS5,3_prime_UTR_variant,,ENST00000547787,;CERS5,3_prime_UTR_variant,,ENST00000380189,;CERS5,non_coding_transcript_exon_variant,,ENST00000550079,;CERS5,non_coding_transcript_exon_variant,,ENST00000546406,;CERS5,non_coding_transcript_exon_variant,,ENST00000551005,;CERS5,downstream_gene_variant,,ENST00000546676,;CERS5,downstream_gene_variant,,ENST00000542320,;CERS5,downstream_gene_variant,,ENST00000551757,;CERS5,downstream_gene_variant,,ENST00000438450,;	T	ENSG00000139624	ENST00000317551	Transcript	missense_variant	1296	1171	391	E/K	Gaa/Aaa	.	.	.	-1	CERS5	HGNC	23749	protein_coding	YES	CCDS8801.1	ENSP00000325485	CERS5_HUMAN	F8W1K4_HUMAN	UPI000007101F	.	deleterious_low_confidence(0.02)	benign(0.014)	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCAGCCC	.	5	ESCA
CSRNP2	0	.	GRCh37	12	51455218	51455218	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2311G>A	.	.	ENST00000228515	5/5	30	26	4	22	22	0	CSRNP2,3_prime_UTR_variant,,ENST00000228515,;LETMD1,downstream_gene_variant,,ENST00000551477,;LETMD1,downstream_gene_variant,,ENST00000547008,;LETMD1,downstream_gene_variant,,ENST00000553043,;LETMD1,downstream_gene_variant,,ENST00000552739,;LETMD1,downstream_gene_variant,,ENST00000418425,;LETMD1,downstream_gene_variant,,ENST00000550814,;LETMD1,downstream_gene_variant,,ENST00000551931,;LETMD1,downstream_gene_variant,,ENST00000548251,;LETMD1,downstream_gene_variant,,ENST00000550929,;LETMD1,downstream_gene_variant,,ENST00000547256,;LETMD1,downstream_gene_variant,,ENST00000262055,;LETMD1,downstream_gene_variant,,ENST00000380123,;LETMD1,downstream_gene_variant,,ENST00000549340,;LETMD1,downstream_gene_variant,,ENST00000547660,;LETMD1,downstream_gene_variant,,ENST00000548516,;LETMD1,downstream_gene_variant,,ENST00000550446,;LETMD1,downstream_gene_variant,,ENST00000549395,;LETMD1,downstream_gene_variant,,ENST00000547029,;LETMD1,downstream_gene_variant,,ENST00000546814,;LETMD1,downstream_gene_variant,,ENST00000552645,;LETMD1,downstream_gene_variant,,ENST00000550100,;LETMD1,downstream_gene_variant,,ENST00000550274,;LETMD1,downstream_gene_variant,,ENST00000547555,;LETMD1,downstream_gene_variant,,ENST00000380135,;LETMD1,downstream_gene_variant,,ENST00000547318,;LETMD1,downstream_gene_variant,,ENST00000550715,;LETMD1,downstream_gene_variant,,ENST00000547877,;LETMD1,downstream_gene_variant,,ENST00000552433,;LETMD1,downstream_gene_variant,,ENST00000549686,;	T	ENSG00000110925	ENST00000228515	Transcript	3_prime_UTR_variant	4241	.	.	.	.	.	.	.	-1	CSRNP2	HGNC	16006	protein_coding	YES	CCDS8807.1	ENSP00000228515	CSRN2_HUMAN	F8W1G8_HUMAN,F8VZY2_HUMAN,F8VVN1_HUMAN,F8VTU0_HUMAN	UPI0000073111	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTATCTGCTT	.	4	ESCA
POU6F1	0	.	GRCh37	12	51583707	51583707	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*323C>T	.	.	ENST00000389243	11/11	28	18	10	36	36	0	POU6F1,3_prime_UTR_variant,,ENST00000389243,;POU6F1,3_prime_UTR_variant,,ENST00000550824,;POU6F1,3_prime_UTR_variant,,ENST00000333640,;POU6F1,downstream_gene_variant,,ENST00000552305,;	A	ENSG00000184271	ENST00000389243	Transcript	3_prime_UTR_variant	2169	.	.	.	.	.	.	.	-1	POU6F1	HGNC	9224	protein_coding	YES	CCDS31803.1	ENSP00000373895	PO6F1_HUMAN	F8VSI9_HUMAN	UPI0000131D97	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACAGGGAGT	.	5	ESCA
NEUROD4	0	.	GRCh37	12	55423762	55423762	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2543C>T	.	.	ENST00000242994	2/2	26	21	5	41	41	0	NEUROD4,3_prime_UTR_variant,,ENST00000242994,;	T	ENSG00000123307	ENST00000242994	Transcript	3_prime_UTR_variant	3917	.	.	.	.	.	.	.	1	NEUROD4	HGNC	13802	protein_coding	YES	CCDS8886.1	ENSP00000242994	NDF4_HUMAN	Q8IW56_HUMAN	UPI000013CB1E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TCCTCCCTTTT	.	4	ESCA
NAB2	0	.	GRCh37	12	57486239	57486239	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.966C>T	p.%3D	p.I322I	ENST00000300131	3/7	40	34	6	38	38	0	NAB2,synonymous_variant,p.%3D,ENST00000300131,;NAB2,synonymous_variant,p.%3D,ENST00000342556,;NAB2,intron_variant,,ENST00000357680,;STAT6,downstream_gene_variant,,ENST00000454075,;STAT6,downstream_gene_variant,,ENST00000538913,;STAT6,downstream_gene_variant,,ENST00000537215,;STAT6,downstream_gene_variant,,ENST00000300134,;STAT6,downstream_gene_variant,,ENST00000543873,;STAT6,downstream_gene_variant,,ENST00000556155,;STAT6,downstream_gene_variant,,ENST00000555318,;TMEM194A,upstream_gene_variant,,ENST00000553654,;NAB2,downstream_gene_variant,,ENST00000555857,;NAB2,downstream_gene_variant,,ENST00000554718,;NAB2,non_coding_transcript_exon_variant,,ENST00000554839,;STAT6,downstream_gene_variant,,ENST00000557563,;STAT6,downstream_gene_variant,,ENST00000555222,;STAT6,downstream_gene_variant,,ENST00000554764,;	T	ENSG00000166886	ENST00000300131	Transcript	synonymous_variant	1344	966	322	I	atC/atT	.	.	.	1	NAB2	HGNC	7627	protein_coding	YES	CCDS8930.1	ENSP00000300131	NAB2_HUMAN	.	UPI000012FC41	.	.	.	3/7	.	hmmpanther:PTHR12623,hmmpanther:PTHR12623:SF6,Pfam_domain:PF04905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATCAACGA	.	5	ESCA
OS9	0	.	GRCh37	12	58112103	58112103	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1309G>C	p.Glu437Gln	p.E437Q	ENST00000315970	11/15	28	21	7	28	28	0	OS9,missense_variant,p.Glu231Gln,ENST00000413095,;OS9,missense_variant,p.Glu438Gln,ENST00000257966,;OS9,missense_variant,p.Glu385Gln,ENST00000435406,;OS9,missense_variant,p.Glu405Gln,ENST00000551035,;OS9,missense_variant,p.Glu437Gln,ENST00000315970,;OS9,missense_variant,p.Glu437Gln,ENST00000552285,;OS9,missense_variant,p.Glu437Gln,ENST00000389142,;OS9,missense_variant,p.Glu437Gln,ENST00000389146,;OS9,missense_variant,p.Glu378Gln,ENST00000439210,;OS9,intron_variant,,ENST00000547079,;OS9,downstream_gene_variant,,ENST00000550372,;RP11-571M6.7,intron_variant,,ENST00000549477,;OS9,non_coding_transcript_exon_variant,,ENST00000549307,;OS9,non_coding_transcript_exon_variant,,ENST00000550202,;OS9,downstream_gene_variant,,ENST00000552787,;OS9,downstream_gene_variant,,ENST00000550699,;OS9,downstream_gene_variant,,ENST00000550438,;OS9,downstream_gene_variant,,ENST00000553208,;OS9,upstream_gene_variant,,ENST00000546916,;	C	ENSG00000135506	ENST00000315970	Transcript	missense_variant	1350	1309	437	E/Q	Gag/Cag	.	.	.	1	OS9	HGNC	16994	protein_coding	YES	CCDS31843.1	ENSP00000318165	OS9_HUMAN	Q9BR60_HUMAN	UPI0000130EAC	.	deleterious(0)	probably_damaging(0.999)	11/15	.	hmmpanther:PTHR15414,hmmpanther:PTHR15414:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTGAGAAG	.	5	ESCA
TBC1D15	0	.	GRCh37	12	72317933	72317933	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*949C>T	.	.	ENST00000550746	18/18	60	45	15	56	56	0	TBC1D15,3_prime_UTR_variant,,ENST00000550746,;TBC1D15,downstream_gene_variant,,ENST00000485960,;TBC1D15,downstream_gene_variant,,ENST00000319106,;TBC1D15,downstream_gene_variant,,ENST00000393309,;TBC1D15,downstream_gene_variant,,ENST00000546450,;TBC1D15,downstream_gene_variant,,ENST00000462788,;	T	ENSG00000121749	ENST00000550746	Transcript	3_prime_UTR_variant	3089	.	.	.	.	.	.	.	1	TBC1D15	HGNC	25694	protein_coding	YES	CCDS31858.1	ENSP00000448182	TBC15_HUMAN	Q9NSR4_HUMAN,F8VV61_HUMAN,A8K8E1_HUMAN	UPI000049DD7C	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCATGAG	.	5	ESCA
HAL	0	.	GRCh37	12	96389545	96389545	+	Silent	SNP	C	C	T	rs758513871	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144G>A	p.%3D	p.V48V	ENST00000261208	2/21	32	28	4	29	29	0	HAL,synonymous_variant,p.%3D,ENST00000261208,;HAL,synonymous_variant,p.%3D,ENST00000552509,;HAL,synonymous_variant,p.%3D,ENST00000538703,;HAL,5_prime_UTR_variant,,ENST00000541929,;HAL,upstream_gene_variant,,ENST00000546579,;RP11-256L6.3,upstream_gene_variant,,ENST00000551849,;HAL,synonymous_variant,p.%3D,ENST00000544080,;HAL,synonymous_variant,p.%3D,ENST00000546999,;HAL,upstream_gene_variant,,ENST00000549376,;	T	ENSG00000084110	ENST00000261208	Transcript	synonymous_variant	513	144	48	V	gtG/gtA	rs758513871	.	.	-1	HAL	HGNC	4806	protein_coding	YES	CCDS9058.1	ENSP00000261208	HUTH_HUMAN	Q2PH61_HUMAN,Q2PH60_HUMAN,Q2PH56_HUMAN	UPI000012CE8E	.	.	.	2/21	.	hmmpanther:PTHR10362,hmmpanther:PTHR10362:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATCCACGGA	.	4	ESCA
C12orf55	0	.	GRCh37	12	96974874	96974874	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3066C>G	p.Phe1022Leu	p.F1022L	ENST00000524981	22/68	36	32	4	47	47	0	C12orf55,missense_variant,p.Phe1022Leu,ENST00000524981,;C12orf55,non_coding_transcript_exon_variant,,ENST00000554108,;C12orf55,downstream_gene_variant,,ENST00000556591,;	G	ENSG00000188596	ENST00000524981	Transcript	missense_variant	3089	3066	1022	F/L	ttC/ttG	.	.	.	1	C12orf55	HGNC	26456	protein_coding	YES	.	ENSP00000431759	.	R4GNI2_HUMAN,E9PJL5_HUMAN	UPI0001F77A4D	.	tolerated(0.1)	benign(0.102)	22/68	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTTCCTGAC	.	2	ESCA
SMAD9	0	.	GRCh37	13	37422854	37422854	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000379826	7/7	28	18	9	27	27	0	SMAD9,stop_gained,p.Gln418Ter,ENST00000350148,;SMAD9,stop_gained,p.Gln455Ter,ENST00000379826,;SMAD9,stop_gained,p.Gln455Ter,ENST00000399275,;SMAD9-AS1,downstream_gene_variant,,ENST00000437983,;	A	ENSG00000120693	ENST00000379826	Transcript	stop_gained	1706	1363	455	Q/*	Cag/Tag	.	.	.	-1	SMAD9	HGNC	6774	protein_coding	YES	CCDS45032.1	ENSP00000369154	SMAD9_HUMAN	.	UPI0000135A85	.	.	.	7/7	.	Superfamily_domains:SSF49879,Gene3D:2.60.200.10,hmmpanther:PTHR13703:SF37,hmmpanther:PTHR13703,PROSITE_profiles:PS51076	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTGAGTCA	.	5	ESCA
ATP7B	0	.	GRCh37	13	52542702	52542702	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1585G>C	p.Glu529Gln	p.E529Q	ENST00000242839	4/21	37	32	4	23	23	0	ATP7B,missense_variant,p.Glu529Gln,ENST00000418097,;ATP7B,missense_variant,p.Glu529Gln,ENST00000344297,;ATP7B,missense_variant,p.Glu529Gln,ENST00000242839,;ATP7B,missense_variant,p.Glu418Gln,ENST00000400366,;ATP7B,missense_variant,p.Glu529Gln,ENST00000448424,;ATP7B,intron_variant,,ENST00000400370,;ATP7B,intron_variant,,ENST00000542656,;ATP7B,non_coding_transcript_exon_variant,,ENST00000482841,;ATP7B,non_coding_transcript_exon_variant,,ENST00000483772,;FABP5P2,downstream_gene_variant,,ENST00000439042,;	G	ENSG00000123191	ENST00000242839	Transcript	missense_variant	1742	1585	529	E/Q	Gag/Cag	.	.	.	-1	ATP7B	HGNC	870	protein_coding	YES	CCDS41892.1	ENSP00000242839	ATP7B_HUMAN	G1FFF2_HUMAN,D3KCZ0_HUMAN,C8BMD5_HUMAN,A6YQZ1_HUMAN	UPI00001FCE15	.	deleterious(0)	probably_damaging(0.999)	4/21	.	PROSITE_profiles:PS50846,hmmpanther:PTHR24093:SF239,hmmpanther:PTHR24093,Pfam_domain:PF00403,Gene3D:3.30.70.100,TIGRFAM_domain:TIGR00003,Superfamily_domains:SSF55008,Prints_domain:PR00942	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATCTCTGCCT	.	4	ESCA
UTP14C	0	.	GRCh37	13	52604065	52604065	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125C>T	p.%3D	p.F375F	ENST00000521776	2/2	24	16	7	22	22	0	UTP14C,synonymous_variant,p.%3D,ENST00000521776,;ALG11,downstream_gene_variant,,ENST00000523764,;ALG11,downstream_gene_variant,,ENST00000521508,;ALG11,downstream_gene_variant,,ENST00000519151,;	T	ENSG00000253797	ENST00000521776	Transcript	synonymous_variant	1858	1125	375	F	ttC/ttT	.	.	.	1	UTP14C	HGNC	20321	protein_coding	YES	CCDS31978.1	ENSP00000428619	UT14C_HUMAN	.	UPI000006DB4B	.	.	.	2/2	.	Pfam_domain:PF04615,hmmpanther:PTHR14150:SF16,hmmpanther:PTHR14150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTTCAGGAG	.	5	ESCA
EDNRB	0	.	GRCh37	13	78493499	78493499	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.219+33C>T	.	.	ENST00000377211	.	17	11	6	16	16	0	EDNRB,intron_variant,,ENST00000377211,;EDNRB,upstream_gene_variant,,ENST00000446573,;EDNRB,upstream_gene_variant,,ENST00000334286,;RNF219-AS1,upstream_gene_variant,,ENST00000607862,;EDNRB,upstream_gene_variant,,ENST00000475537,;	A	ENSG00000136160	ENST00000377211	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	EDNRB	HGNC	3180	protein_coding	YES	CCDS55902.1	ENSP00000366416	EDNRB_HUMAN	.	UPI0000046D5C	.	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATGATTTT	.	5	ESCA
SLITRK5	0	.	GRCh37	13	88331700	88331700	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1180G>A	.	.	ENST00000325089	2/2	41	31	10	39	39	0	SLITRK5,3_prime_UTR_variant,,ENST00000325089,;SLITRK5,downstream_gene_variant,,ENST00000400028,;	A	ENSG00000165300	ENST00000325089	Transcript	3_prime_UTR_variant	4276	.	.	.	.	.	.	.	1	SLITRK5	HGNC	20295	protein_coding	YES	CCDS9465.1	ENSP00000366283	SLIK5_HUMAN	.	UPI000015F6F7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATGGACTGT	.	5	ESCA
FARP1	0	.	GRCh37	13	99087937	99087937	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2251G>T	p.Asp751Tyr	p.D751Y	ENST00000319562	19/27	25	10	15	22	22	0	FARP1,missense_variant,p.Asp751Tyr,ENST00000319562,;FARP1,missense_variant,p.Asp751Tyr,ENST00000376586,;FARP1,missense_variant,p.Asp116Tyr,ENST00000423063,;FARP1,missense_variant,p.Asp751Tyr,ENST00000595437,;FARP1,missense_variant,p.Asp104Tyr,ENST00000596256,;FARP1-AS1,intron_variant,,ENST00000432229,;FARP1,downstream_gene_variant,,ENST00000597777,;	T	ENSG00000152767	ENST00000319562	Transcript	missense_variant	2516	2251	751	D/Y	Gac/Tac	.	.	.	1	FARP1	HGNC	3591	protein_coding	YES	CCDS9487.1	ENSP00000322926	FARP1_HUMAN	M0QYB0_HUMAN	UPI000007052C	.	deleterious(0)	probably_damaging(0.987)	19/27	.	hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF105,Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTGACAAT	.	5	ESCA
C14orf180	0	.	GRCh37	14	105052817	105052817	+	Missense_Mutation	SNP	G	G	C	rs777081129	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50G>C	p.Arg17Pro	p.R17P	ENST00000557649	2/5	117	106	11	112	112	0	C14orf180,missense_variant,p.Arg17Pro,ENST00000410013,;C14orf180,missense_variant,p.Arg17Pro,ENST00000557649,;C14orf180,missense_variant,p.Arg17Pro,ENST00000331952,;TMEM179,intron_variant,,ENST00000415614,;TMEM179,downstream_gene_variant,,ENST00000556320,;RP11-614O9.1,downstream_gene_variant,,ENST00000556073,;	C	ENSG00000184601	ENST00000557649	Transcript	missense_variant	386	50	17	R/P	cGa/cCa	rs777081129	.	.	1	C14orf180	HGNC	33795	protein_coding	YES	CCDS32166.1	ENSP00000452502	NRAC_HUMAN	.	UPI000000CC7A	.	tolerated(0.21)	benign(0)	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACACGACGTC	byFrequency	3	ESCA
LRP10	0	.	GRCh37	14	23345309	23345309	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1152G>C	p.Gln384His	p.Q384H	ENST00000359591	5/7	35	29	5	34	34	0	LRP10,missense_variant,p.Gln286His,ENST00000551466,;LRP10,missense_variant,p.Gln384His,ENST00000359591,;LRP10,missense_variant,p.Gln384His,ENST00000546834,;LRP10,upstream_gene_variant,,ENST00000470660,;LRP10,downstream_gene_variant,,ENST00000553002,;	C	ENSG00000197324	ENST00000359591	Transcript	missense_variant	1843	1152	384	Q/H	caG/caC	.	.	.	1	LRP10	HGNC	14553	protein_coding	YES	CCDS9578.1	ENSP00000352601	LRP10_HUMAN	Q6IAK3_HUMAN,Q66K21_HUMAN,Q5I0F9_HUMAN	UPI000000CC06	.	deleterious(0)	probably_damaging(0.999)	5/7	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529:SF198,hmmpanther:PTHR10529,Gene3D:4.10.400.10,SMART_domains:SM00192,Prints_domain:PR00261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACCAGACTTT	.	3	ESCA
LRP10	0	.	GRCh37	14	23345331	23345331	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1174G>A	p.Asp392Asn	p.D392N	ENST00000359591	5/7	40	33	6	46	46	0	LRP10,missense_variant,p.Asp294Asn,ENST00000551466,;LRP10,missense_variant,p.Asp392Asn,ENST00000359591,;LRP10,missense_variant,p.Asp392Asn,ENST00000546834,;LRP10,upstream_gene_variant,,ENST00000470660,;LRP10,downstream_gene_variant,,ENST00000553002,;	A	ENSG00000197324	ENST00000359591	Transcript	missense_variant	1865	1174	392	D/N	Gat/Aat	.	.	.	1	LRP10	HGNC	14553	protein_coding	YES	CCDS9578.1	ENSP00000352601	LRP10_HUMAN	Q6IAK3_HUMAN,Q66K21_HUMAN,Q5I0F9_HUMAN	UPI000000CC06	.	deleterious(0)	probably_damaging(1)	5/7	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529:SF198,hmmpanther:PTHR10529,Gene3D:4.10.400.10,SMART_domains:SM00192,Prints_domain:PR00261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCAGATGAG	.	2	ESCA
TINF2	0	.	GRCh37	14	24709275	24709276	+	Frame_Shift_Ins	INS	-	-	TT	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1214_1215dupAA	p.Gly406LysfsTer17	p.G406Kfs*17	ENST00000267415	8/9	77	60	17	45	45	0	TINF2,frameshift_variant,p.Gly406LysfsTer17,ENST00000267415,;TINF2,frameshift_variant,p.Gly371LysfsTer17,ENST00000540705,;TINF2,frameshift_variant,p.Gly71LysfsTer4,ENST00000560019,;TINF2,3_prime_UTR_variant,,ENST00000538777,;TINF2,3_prime_UTR_variant,,ENST00000399423,;TINF2,3_prime_UTR_variant,,ENST00000558566,;TINF2,3_prime_UTR_variant,,ENST00000559969,;GMPR2,downstream_gene_variant,,ENST00000560139,;GMPR2,downstream_gene_variant,,ENST00000559479,;GMPR2,downstream_gene_variant,,ENST00000559943,;GMPR2,downstream_gene_variant,,ENST00000399440,;GMPR2,downstream_gene_variant,,ENST00000559409,;GMPR2,downstream_gene_variant,,ENST00000558279,;GMPR2,downstream_gene_variant,,ENST00000559836,;GMPR2,downstream_gene_variant,,ENST00000558788,;TINF2,downstream_gene_variant,,ENST00000557921,;GMPR2,downstream_gene_variant,,ENST00000559910,;GMPR2,downstream_gene_variant,,ENST00000558748,;GMPR2,downstream_gene_variant,,ENST00000558483,;GMPR2,downstream_gene_variant,,ENST00000355299,;GMPR2,downstream_gene_variant,,ENST00000561035,;GMPR2,downstream_gene_variant,,ENST00000420554,;GMPR2,downstream_gene_variant,,ENST00000558932,;GMPR2,downstream_gene_variant,,ENST00000559104,;GMPR2,downstream_gene_variant,,ENST00000456667,;GMPR2,downstream_gene_variant,,ENST00000558865,;TINF2,downstream_gene_variant,,ENST00000559019,;TINF2,downstream_gene_variant,,ENST00000558476,;GMPR2,downstream_gene_variant,,ENST00000348719,;GMPR2,downstream_gene_variant,,ENST00000557854,;TINF2,downstream_gene_variant,,ENST00000558510,;GMPR2,downstream_gene_variant,,ENST00000558701,;GMPR2,downstream_gene_variant,,ENST00000560517,;TINF2,non_coding_transcript_exon_variant,,ENST00000557915,;TINF2,non_coding_transcript_exon_variant,,ENST00000558703,;TINF2,downstream_gene_variant,,ENST00000559549,;TINF2,downstream_gene_variant,,ENST00000557830,;GMPR2,downstream_gene_variant,,ENST00000558007,;GMPR2,downstream_gene_variant,,ENST00000559102,;GMPR2,downstream_gene_variant,,ENST00000559606,;TINF2,downstream_gene_variant,,ENST00000559147,;GMPR2,downstream_gene_variant,,ENST00000561038,;GMPR2,downstream_gene_variant,,ENST00000559287,;GMPR2,downstream_gene_variant,,ENST00000558760,;GMPR2,downstream_gene_variant,,ENST00000561130,;	TT	ENSG00000092330	ENST00000267415	Transcript	frameshift_variant	1557-1558	1215-1216	405-406	-/X	-/AA	.	.	.	-1	TINF2	HGNC	11824	protein_coding	YES	CCDS41936.1	ENSP00000267415	TINF2_HUMAN	Q86TZ8_HUMAN,H0YKA6_HUMAN,B3W5Q7_HUMAN	UPI0000136FAB	.	.	.	8/9	.	hmmpanther:PTHR15512:SF0,hmmpanther:PTHR15512	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTTCCTTCCC	.	3	ESCA
PRKD1	0	.	GRCh37	14	30068914	30068914	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2015C>G	p.Ser672Ter	p.S672*	ENST00000331968	14/18	30	22	8	45	45	0	PRKD1,stop_gained,p.Ser680Ter,ENST00000415220,;PRKD1,stop_gained,p.Ser672Ter,ENST00000331968,;PRKD1,upstream_gene_variant,,ENST00000490795,;	C	ENSG00000184304	ENST00000331968	Transcript	stop_gained	2245	2015	672	S/*	tCa/tGa	.	.	.	-1	PRKD1	HGNC	9407	protein_coding	YES	CCDS9637.1	ENSP00000333568	KPCD1_HUMAN	Q1KKQ2_HUMAN	UPI0000456761	.	.	.	14/18	.	Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000552,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR22968,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTGACAAG	.	5	ESCA
PNN	0	.	GRCh37	14	39652095	39652095	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1028A>C	.	.	ENST00000216832	9/9	109	81	28	104	104	0	PNN,3_prime_UTR_variant,,ENST00000216832,;PNN,downstream_gene_variant,,ENST00000553331,;PNN,downstream_gene_variant,,ENST00000557680,;PNN,downstream_gene_variant,,ENST00000554902,;	C	ENSG00000100941	ENST00000216832	Transcript	3_prime_UTR_variant	3249	.	.	.	.	.	.	.	1	PNN	HGNC	9162	protein_coding	YES	CCDS9671.1	ENSP00000216832	PININ_HUMAN	.	UPI000013C70D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTATCTGT	.	5	ESCA
FAM179B	0	.	GRCh37	14	45542772	45542772	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8A>T	.	.	ENST00000361577	19/19	24	19	5	15	15	0	FAM179B,3_prime_UTR_variant,,ENST00000556823,;FAM179B,3_prime_UTR_variant,,ENST00000382233,;FAM179B,3_prime_UTR_variant,,ENST00000361577,;FAM179B,3_prime_UTR_variant,,ENST00000361462,;FAM179B,3_prime_UTR_variant,,ENST00000557423,;	T	ENSG00000198718	ENST00000361577	Transcript	3_prime_UTR_variant	5385	.	.	.	.	.	.	.	1	FAM179B	HGNC	19959	protein_coding	YES	CCDS9681.1	ENSP00000355045	F179B_HUMAN	.	UPI00001C1F79	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCGATAAAA	.	5	ESCA
SOS2	0	.	GRCh37	14	50649280	50649280	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.759G>A	p.%3D	p.L253L	ENST00000216373	6/23	25	21	4	12	12	0	SOS2,synonymous_variant,p.%3D,ENST00000543680,;SOS2,synonymous_variant,p.%3D,ENST00000216373,;SOS2,non_coding_transcript_exon_variant,,ENST00000556469,;SOS2,upstream_gene_variant,,ENST00000555794,;	T	ENSG00000100485	ENST00000216373	Transcript	synonymous_variant	1034	759	253	L	ttG/ttA	.	.	.	-1	SOS2	HGNC	11188	protein_coding	YES	CCDS9697.1	ENSP00000216373	SOS2_HUMAN	B4DJ05_HUMAN	UPI000013C6E8	.	.	.	6/23	.	PROSITE_profiles:PS50010,hmmpanther:PTHR23113:SF150,hmmpanther:PTHR23113,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAGTCAATTC	.	4	ESCA
NIN	0	.	GRCh37	14	51188286	51188286	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000382041	.	8	5	3	9	9	0	NIN,3_prime_UTR_variant,,ENST00000389868,;NIN,3_prime_UTR_variant,,ENST00000245441,;NIN,3_prime_UTR_variant,,ENST00000530997,;NIN,downstream_gene_variant,,ENST00000324330,;NIN,downstream_gene_variant,,ENST00000382041,;NIN,downstream_gene_variant,,ENST00000389869,;NIN,downstream_gene_variant,,ENST00000382043,;RP11-248J18.3,downstream_gene_variant,,ENST00000602615,;NIN,3_prime_UTR_variant,,ENST00000476352,;NIN,downstream_gene_variant,,ENST00000555984,;	T	ENSG00000100503	ENST00000382041	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4272	-1	NIN	HGNC	14906	protein_coding	YES	CCDS32079.1	ENSP00000371472	NIN_HUMAN	H7C162_HUMAN,E9PJH9_HUMAN	UPI0000DBEF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTTCTGTGA	.	2	ESCA
SYNE2	0	.	GRCh37	14	64612848	64612848	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15546G>C	p.Leu5182Phe	p.L5182F	ENST00000358025	84/116	35	25	9	33	33	0	SYNE2,missense_variant,p.Leu5099Phe,ENST00000554584,;SYNE2,missense_variant,p.Leu1567Phe,ENST00000394768,;SYNE2,missense_variant,p.Leu5182Phe,ENST00000344113,;SYNE2,missense_variant,p.Leu1567Phe,ENST00000357395,;SYNE2,missense_variant,p.Leu5182Phe,ENST00000358025,;SYNE2,missense_variant,p.Leu1816Phe,ENST00000555002,;ESR2,intron_variant,,ENST00000556275,;ESR2,intron_variant,,ENST00000542956,;SYNE2,missense_variant,p.Leu144Phe,ENST00000555612,;	C	ENSG00000054654	ENST00000358025	Transcript	missense_variant	15776	15546	5182	L/F	ttG/ttC	.	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	probably_damaging(0.996)	84/116	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTGAACAA	.	5	ESCA
MPP5	0	.	GRCh37	14	67746085	67746085	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198G>C	p.Met66Ile	p.M66I	ENST00000261681	3/15	22	19	3	18	18	0	MPP5,missense_variant,p.Met32Ile,ENST00000557783,;MPP5,missense_variant,p.Met32Ile,ENST00000555925,;MPP5,missense_variant,p.Met66Ile,ENST00000556345,;MPP5,missense_variant,p.Met66Ile,ENST00000261681,;MPP5,downstream_gene_variant,,ENST00000557237,;	C	ENSG00000072415	ENST00000261681	Transcript	missense_variant	859	198	66	M/I	atG/atC	.	.	.	1	MPP5	HGNC	18669	protein_coding	YES	CCDS9779.1	ENSP00000261681	MPP5_HUMAN	G3V2H1_HUMAN	UPI0000046FB9	.	tolerated(0.33)	benign(0)	3/15	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23122:SF32,hmmpanther:PTHR23122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACATGAGGCG	.	2	ESCA
ZFYVE1	0	.	GRCh37	14	73460063	73460063	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.991C>T	p.His331Tyr	p.H331Y	ENST00000556143	4/12	38	33	4	25	25	0	ZFYVE1,missense_variant,p.His331Tyr,ENST00000553891,;ZFYVE1,missense_variant,p.His331Tyr,ENST00000318876,;ZFYVE1,missense_variant,p.His331Tyr,ENST00000556143,;	A	ENSG00000165861	ENST00000556143	Transcript	missense_variant	1712	991	331	H/Y	Cat/Tat	COSM343217	.	.	-1	ZFYVE1	HGNC	13180	protein_coding	YES	CCDS9811.1	ENSP00000450742	ZFYV1_HUMAN	.	UPI0000049888	.	deleterious(0.03)	benign(0.004)	4/12	.	hmmpanther:PTHR22835:SF151,hmmpanther:PTHR22835	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGATGATCTA	.	2	ESCA
RBM25	0	.	GRCh37	14	73586949	73586949	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*436G>A	.	.	ENST00000261973	19/19	66	48	18	62	62	0	RBM25,3_prime_UTR_variant,,ENST00000527432,;RBM25,3_prime_UTR_variant,,ENST00000261973,;RBM25,non_coding_transcript_exon_variant,,ENST00000527449,;RBM25,downstream_gene_variant,,ENST00000532683,;RBM25,downstream_gene_variant,,ENST00000528081,;	A	ENSG00000119707	ENST00000261973	Transcript	3_prime_UTR_variant	3253	.	.	.	.	.	.	.	1	RBM25	HGNC	23244	protein_coding	YES	CCDS32113.1	ENSP00000261973	RBM25_HUMAN	Q16083_HUMAN,E9PSE8_HUMAN,E9PQU5_HUMAN	UPI0000373D58	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCAGAAATG	.	5	ESCA
NOXRED1	0	.	GRCh37	14	77872265	77872265	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.896C>T	p.Ser299Phe	p.S299F	ENST00000380835	5/6	35	22	12	27	27	0	NOXRED1,missense_variant,p.Ser299Phe,ENST00000380835,;NOXRED1,downstream_gene_variant,,ENST00000298358,;NOXRED1,downstream_gene_variant,,ENST00000555603,;NOXRED1,non_coding_transcript_exon_variant,,ENST00000555901,;	A	ENSG00000165555	ENST00000380835	Transcript	missense_variant	1063	896	299	S/F	tCt/tTt	.	.	.	-1	NOXRED1	HGNC	20487	protein_coding	YES	CCDS45142.1	ENSP00000370215	NXRD1_HUMAN	G3V2D4_HUMAN	UPI0000407F20	.	tolerated(0.68)	benign(0.004)	5/6	.	hmmpanther:PTHR11645,hmmpanther:PTHR11645:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGAGACAAA	.	5	ESCA
CEP128	0	.	GRCh37	14	81251350	81251350	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2100C>A	p.%3D	p.L700L	ENST00000555265	15/25	84	73	11	61	61	0	CEP128,synonymous_variant,p.%3D,ENST00000555265,;CEP128,synonymous_variant,p.%3D,ENST00000281129,;CEP128,synonymous_variant,p.%3D,ENST00000554502,;	T	ENSG00000100629	ENST00000555265	Transcript	synonymous_variant	2476	2100	700	L	ctC/ctA	.	.	.	-1	CEP128	HGNC	20359	protein_coding	YES	CCDS32130.1	ENSP00000451162	CE128_HUMAN	Q9NS50_HUMAN,Q9HCB0_HUMAN,Q86TS1_HUMAN,G3V3U2_HUMAN,G3V3F4_HUMAN	UPI000022982E	.	.	.	15/25	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937:SF149,hmmpanther:PTHR18937	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGTGAGATC	.	5	ESCA
SPATA7	0	.	GRCh37	14	88904786	88904786	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*20C>G	.	.	ENST00000393545	12/12	34	25	9	18	18	0	SPATA7,3_prime_UTR_variant,,ENST00000356583,;SPATA7,3_prime_UTR_variant,,ENST00000045347,;SPATA7,3_prime_UTR_variant,,ENST00000393545,;SPATA7,3_prime_UTR_variant,,ENST00000556553,;SPATA7,intron_variant,,ENST00000554802,;SPATA7,intron_variant,,ENST00000556406,;SPATA7,non_coding_transcript_exon_variant,,ENST00000556666,;SPATA7,non_coding_transcript_exon_variant,,ENST00000553626,;SPATA7,downstream_gene_variant,,ENST00000553303,;	G	ENSG00000042317	ENST00000393545	Transcript	3_prime_UTR_variant	2109	.	.	.	.	.	.	.	1	SPATA7	HGNC	20423	protein_coding	YES	CCDS9883.1	ENSP00000377176	SPAT7_HUMAN	.	UPI00000712C7	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCTCAAATG	.	2	ESCA
PPP4R4	0	.	GRCh37	14	94722887	94722887	+	Silent	SNP	G	G	C	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1956G>C	p.%3D	p.V652V	ENST00000304338	17/25	36	27	8	28	28	0	PPP4R4,synonymous_variant,p.%3D,ENST00000304338,;	C	ENSG00000119698	ENST00000304338	Transcript	synonymous_variant	2110	1956	652	V	gtG/gtC	COSM3499249	.	.	1	PPP4R4	HGNC	23788	protein_coding	YES	CCDS9921.1	ENSP00000305924	PP4R4_HUMAN	G3V431_HUMAN,G3V422_HUMAN	UPI000016223B	.	.	.	17/25	.	hmmpanther:PTHR21467,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTGAGGAA	.	5	ESCA
GLRX5	0	.	GRCh37	14	95999711	95999711	+	5'Flank	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000331334	.	17	15	2	16	16	0	GLRX5,upstream_gene_variant,,ENST00000557731,;GLRX5,upstream_gene_variant,,ENST00000331334,;SCARNA13,non_coding_transcript_exon_variant,,ENST00000516672,;SNHG10,intron_variant,,ENST00000553559,;SNHG10,intron_variant,,ENST00000554169,;SNHG10,intron_variant,,ENST00000555866,;SNHG10,intron_variant,,ENST00000500370,;GLRX5,upstream_gene_variant,,ENST00000553672,;	T	ENSG00000182512	ENST00000331334	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1219	1	GLRX5	HGNC	20134	protein_coding	YES	CCDS9936.1	ENSP00000328570	GLRX5_HUMAN	.	UPI000000DC2E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTAGTGTTCAA	.	2	ESCA
UBE3A	0	.	GRCh37	15	25654293	25654293	+	5'Flank	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000397954	.	31	21	9	30	30	0	UBE3A,5_prime_UTR_variant,,ENST00000566215,;UBE3A,5_prime_UTR_variant,,ENST00000232165,;UBE3A,upstream_gene_variant,,ENST00000397954,;UBE3A,upstream_gene_variant,,ENST00000438097,;UBE3A,upstream_gene_variant,,ENST00000428984,;SNHG14,intron_variant,,ENST00000554726,;	C	ENSG00000114062	ENST00000397954	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	498	-1	UBE3A	HGNC	12496	protein_coding	YES	CCDS45192.1	ENSP00000381045	UBE3A_HUMAN	Q9UBN9_HUMAN,Q9H2G0_HUMAN,Q96GR7_HUMAN	UPI0000161F3B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGATTAAAA	.	5	ESCA
RPAP1	0	.	GRCh37	15	41816047	41816047	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2358G>A	p.%3D	p.E786E	ENST00000304330	17/25	59	37	22	34	34	0	RPAP1,synonymous_variant,p.%3D,ENST00000561603,;RPAP1,synonymous_variant,p.%3D,ENST00000565035,;RPAP1,synonymous_variant,p.%3D,ENST00000304330,;RPAP1,downstream_gene_variant,,ENST00000568413,;RPAP1,synonymous_variant,p.%3D,ENST00000562303,;RPAP1,downstream_gene_variant,,ENST00000561631,;RPAP1,upstream_gene_variant,,ENST00000565167,;RPAP1,upstream_gene_variant,,ENST00000564934,;	T	ENSG00000103932	ENST00000304330	Transcript	synonymous_variant	2475	2358	786	E	gaG/gaA	.	.	.	-1	RPAP1	HGNC	24567	protein_coding	YES	CCDS10079.1	ENSP00000306123	RPAP1_HUMAN	H3BPY8_HUMAN,H3BPM3_HUMAN	UPI000013D465	.	.	.	17/25	.	hmmpanther:PTHR21483:SF18,hmmpanther:PTHR21483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATCTCAGG	.	5	ESCA
LRRC57	0	.	GRCh37	15	42836236	42836236	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45C>A	.	.	ENST00000323443	5/5	35	26	9	25	25	0	LRRC57,3_prime_UTR_variant,,ENST00000323443,;LRRC57,3_prime_UTR_variant,,ENST00000563454,;LRRC57,3_prime_UTR_variant,,ENST00000397130,;SNAP23,intron_variant,,ENST00000563830,;SNAP23,intron_variant,,ENST00000568841,;SNAP23,intron_variant,,ENST00000563873,;HAUS2,upstream_gene_variant,,ENST00000568846,;HAUS2,upstream_gene_variant,,ENST00000562398,;HAUS2,upstream_gene_variant,,ENST00000568876,;HAUS2,upstream_gene_variant,,ENST00000260372,;LRRC57,downstream_gene_variant,,ENST00000570160,;LRRC57,non_coding_transcript_exon_variant,,ENST00000562868,;HAUS2,upstream_gene_variant,,ENST00000391623,;HAUS2,upstream_gene_variant,,ENST00000563479,;HAUS2,upstream_gene_variant,,ENST00000567640,;LRRC57,downstream_gene_variant,,ENST00000569830,;HAUS2,upstream_gene_variant,,ENST00000570178,;HAUS2,upstream_gene_variant,,ENST00000564279,;	T	ENSG00000180979	ENST00000323443	Transcript	3_prime_UTR_variant	1133	.	.	.	.	.	.	.	-1	LRRC57	HGNC	26719	protein_coding	YES	CCDS10089.1	ENSP00000326817	LRC57_HUMAN	H3BSW0_HUMAN	UPI000004F8C8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGGTTCTA	.	5	ESCA
MAP1A	0	.	GRCh37	15	43817462	43817462	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3791C>T	p.Ser1264Leu	p.S1264L	ENST00000300231	4/6	11	7	4	13	13	0	MAP1A,missense_variant,p.Ser1264Leu,ENST00000399453,;MAP1A,missense_variant,p.Ser1264Leu,ENST00000300231,;MAP1A,missense_variant,p.Ser1502Leu,ENST00000382031,;	T	ENSG00000166963	ENST00000300231	Transcript	missense_variant	4241	3791	1264	S/L	tCa/tTa	.	.	.	1	MAP1A	HGNC	6835	protein_coding	YES	CCDS42031.1	ENSP00000300231	MAP1A_HUMAN	.	UPI000013E63C	.	.	benign(0.005)	4/6	.	hmmpanther:PTHR13843:SF6,hmmpanther:PTHR13843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	AGCGTCACCTC	.	2	ESCA
SECISBP2L	0	.	GRCh37	15	49285065	49285065	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2682G>A	p.%3D	p.E894E	ENST00000559471	18/18	72	53	19	32	32	0	SECISBP2L,synonymous_variant,p.%3D,ENST00000261847,;SECISBP2L,synonymous_variant,p.%3D,ENST00000561428,;SECISBP2L,synonymous_variant,p.%3D,ENST00000559471,;SECISBP2L,downstream_gene_variant,,ENST00000380927,;Y_RNA,downstream_gene_variant,,ENST00000384377,;	T	ENSG00000138593	ENST00000559471	Transcript	synonymous_variant	2946	2682	894	E	gaG/gaA	.	.	.	-1	SECISBP2L	HGNC	28997	protein_coding	YES	CCDS53942.1	ENSP00000453854	SBP2L_HUMAN	J3KPI1_HUMAN	UPI00001C1F8B	.	.	.	18/18	.	hmmpanther:PTHR13284,hmmpanther:PTHR13284:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCTCATT	.	5	ESCA
VPS13C	0	.	GRCh37	15	62209602	62209602	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7993C>T	p.His2665Tyr	p.H2665Y	ENST00000261517	60/85	45	29	15	29	29	0	VPS13C,missense_variant,p.His2665Tyr,ENST00000261517,;VPS13C,missense_variant,p.His2665Tyr,ENST00000395896,;VPS13C,missense_variant,p.His2622Tyr,ENST00000249837,;VPS13C,missense_variant,p.His2622Tyr,ENST00000395898,;RN7SL613P,downstream_gene_variant,,ENST00000584412,;VPS13C,non_coding_transcript_exon_variant,,ENST00000558338,;	A	ENSG00000129003	ENST00000261517	Transcript	missense_variant	8067	7993	2665	H/Y	Cat/Tat	.	.	.	-1	VPS13C	HGNC	23594	protein_coding	YES	CCDS32257.1	ENSP00000261517	VP13C_HUMAN	B4E2S9_HUMAN,B3KW10_HUMAN	UPI000023B7D3	.	deleterious(0.02)	probably_damaging(0.999)	60/85	.	hmmpanther:PTHR16166:SF69,hmmpanther:PTHR16166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATGAATAA	.	5	ESCA
CCDC33	0	.	GRCh37	15	74565109	74565109	+	Intron	SNP	C	C	T	rs760680267	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639-3C>T	.	.	ENST00000398814	.	40	32	8	34	34	0	CCDC33,splice_region_variant,,ENST00000321288,;CCDC33,splice_region_variant,,ENST00000558659,;CCDC33,splice_region_variant,,ENST00000398814,;	T	ENSG00000140481	ENST00000398814	Transcript	splice_region_variant	.	.	.	.	.	rs760680267	.	.	1	CCDC33	HGNC	26552	protein_coding	YES	CCDS42058.1	ENSP00000381795	CCD33_HUMAN	.	UPI0000E671FE	.	.	.	.	6/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCCAGGGT	.	4	ESCA
ISG20	0	.	GRCh37	15	89182739	89182739	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142G>C	p.Glu48Gln	p.E48Q	ENST00000306072	2/4	76	62	14	50	50	0	ISG20,missense_variant,p.Glu48Gln,ENST00000559876,;ISG20,missense_variant,p.Glu48Gln,ENST00000379224,;ISG20,missense_variant,p.Glu48Gln,ENST00000306072,;ISG20,missense_variant,p.Glu48Gln,ENST00000560741,;ISG20,downstream_gene_variant,,ENST00000558992,;ISG20,non_coding_transcript_exon_variant,,ENST00000558942,;ISG20,non_coding_transcript_exon_variant,,ENST00000560573,;	C	ENSG00000172183	ENST00000306072	Transcript	missense_variant	500	142	48	E/Q	Gag/Cag	.	.	.	1	ISG20	HGNC	6130	protein_coding	YES	CCDS10345.1	ENSP00000306565	ISG20_HUMAN	.	UPI000006FE4D	.	tolerated(0.07)	benign(0.037)	2/4	.	Superfamily_domains:SSF53098,SMART_domains:SM00479,Gene3D:3.30.420.10,Pfam_domain:PF00929,hmmpanther:PTHR12801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGAGAGATC	.	5	ESCA
LMF1	0	.	GRCh37	16	1020870	1020870	+	Silent	SNP	G	G	A	rs746820872	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111C>T	p.%3D	p.P37P	ENST00000262301	1/11	24	19	4	20	20	0	LMF1,synonymous_variant,p.%3D,ENST00000399843,;LMF1,synonymous_variant,p.%3D,ENST00000539379,;LMF1,synonymous_variant,p.%3D,ENST00000262301,;LMF1,5_prime_UTR_variant,,ENST00000543238,;LMF1,intron_variant,,ENST00000570014,;LMF1,upstream_gene_variant,,ENST00000568897,;RP11-161M6.2,downstream_gene_variant,,ENST00000562570,;RP11-161M6.2,downstream_gene_variant,,ENST00000565139,;RP11-161M6.2,downstream_gene_variant,,ENST00000567961,;RP11-161M6.2,downstream_gene_variant,,ENST00000565467,;RP11-161M6.2,downstream_gene_variant,,ENST00000563863,;RP11-161M6.2,downstream_gene_variant,,ENST00000568394,;LMF1,non_coding_transcript_exon_variant,,ENST00000566609,;LMF1,synonymous_variant,p.%3D,ENST00000562226,;LMF1,synonymous_variant,p.%3D,ENST00000568964,;LMF1,synonymous_variant,p.%3D,ENST00000567595,;LMF1,intron_variant,,ENST00000545827,;	A	ENSG00000103227	ENST00000262301	Transcript	synonymous_variant	130	111	37	P	ccC/ccT	rs746820872	.	.	-1	LMF1	HGNC	14154	protein_coding	YES	CCDS45373.1	ENSP00000262301	LMF1_HUMAN	H3BVI4_HUMAN,H3BN37_HUMAN,B3KS80_HUMAN	UPI000006E366	.	.	.	1/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCGGGGCC	.	5	ESCA
UNKL	0	.	GRCh37	16	1463960	1463960	+	Silent	SNP	G	G	C	rs768298679	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174C>G	p.%3D	p.L58L	ENST00000389221	2/15	52	31	21	39	39	0	UNKL,synonymous_variant,p.%3D,ENST00000397462,;UNKL,synonymous_variant,p.%3D,ENST00000508903,;UNKL,synonymous_variant,p.%3D,ENST00000301712,;UNKL,synonymous_variant,p.%3D,ENST00000389221,;LA16c-312E8.2,downstream_gene_variant,,ENST00000568554,;UNKL,non_coding_transcript_exon_variant,,ENST00000503648,;UNKL,stop_gained,p.Ser43Ter,ENST00000382757,;UNKL,non_coding_transcript_exon_variant,,ENST00000566707,;	C	ENSG00000059145	ENST00000389221	Transcript	synonymous_variant	174	174	58	L	ctC/ctG	rs768298679	.	.	-1	UNKL	HGNC	14184	protein_coding	YES	.	ENSP00000373873	UNKL_HUMAN	D6RA68_HUMAN	UPI0001AE676E	.	.	.	2/15	.	hmmpanther:PTHR14493:SF37,hmmpanther:PTHR14493	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTTGAGGAA	.	5	ESCA
KIAA0430	0	.	GRCh37	16	15715632	15715632	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2597C>G	p.Ser866Ter	p.S866*	ENST00000396368	12/27	106	86	19	73	73	0	KIAA0430,stop_gained,p.Ser866Ter,ENST00000551742,;KIAA0430,stop_gained,p.Ser863Ter,ENST00000602337,;KIAA0430,stop_gained,p.Ser701Ter,ENST00000540441,;KIAA0430,stop_gained,p.Ser535Ter,ENST00000344181,;KIAA0430,stop_gained,p.Ser863Ter,ENST00000548025,;KIAA0430,stop_gained,p.Ser866Ter,ENST00000396368,;C16orf45,intron_variant,,ENST00000565857,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000551678,;KIAA0430,stop_gained,p.Ser866Ter,ENST00000552553,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000546864,;KIAA0430,upstream_gene_variant,,ENST00000552535,;	C	ENSG00000166783	ENST00000396368	Transcript	stop_gained	2804	2597	866	S/*	tCa/tGa	.	.	.	-1	KIAA0430	HGNC	29562	protein_coding	YES	CCDS10562.2	ENSP00000379654	MARF1_HUMAN	F8VRS5_HUMAN	UPI00006881BC	.	.	.	12/27	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF54928,SMART_domains:SM00360,Pfam_domain:PF13893,Gene3D:3.30.70.330,hmmpanther:PTHR14379:SF3,hmmpanther:PTHR14379,PROSITE_profiles:PS50102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGTGAGACC	.	5	ESCA
UMOD	0	.	GRCh37	16	20362149	20362149	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39-51C>G	.	.	ENST00000570689	.	37	34	3	20	20	0	UMOD,missense_variant,p.Gln20Glu,ENST00000396138,;UMOD,5_prime_UTR_variant,,ENST00000396134,;UMOD,5_prime_UTR_variant,,ENST00000576546,;UMOD,5_prime_UTR_variant,,ENST00000396142,;UMOD,5_prime_UTR_variant,,ENST00000574195,;UMOD,5_prime_UTR_variant,,ENST00000570757,;UMOD,intron_variant,,ENST00000577168,;UMOD,intron_variant,,ENST00000571174,;UMOD,intron_variant,,ENST00000573567,;UMOD,intron_variant,,ENST00000570689,;UMOD,intron_variant,,ENST00000570972,;UMOD,intron_variant,,ENST00000576688,;UMOD,intron_variant,,ENST00000302509,;UMOD,intron_variant,,ENST00000424589,;	C	ENSG00000169344	ENST00000570689	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	UMOD	HGNC	12559	protein_coding	YES	CCDS10583.1	ENSP00000460548	UROM_HUMAN	Q8NHW8_HUMAN,I3L4Y6_HUMAN,I3L4B0_HUMAN,I3L2J2_HUMAN,I3L1M3_HUMAN,I3L1A9_HUMAN,B3KXM9_HUMAN	UPI0000137E1A	.	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCTGATGTC	.	2	ESCA
MLST8	0	.	GRCh37	16	2259163	2259163	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*285G>T	.	.	ENST00000569417	9/9	12	9	3	9	9	0	MLST8,3_prime_UTR_variant,,ENST00000301725,;MLST8,3_prime_UTR_variant,,ENST00000397124,;MLST8,3_prime_UTR_variant,,ENST00000564088,;MLST8,3_prime_UTR_variant,,ENST00000301724,;MLST8,3_prime_UTR_variant,,ENST00000569417,;MLST8,3_prime_UTR_variant,,ENST00000565250,;MLST8,3_prime_UTR_variant,,ENST00000382450,;MLST8,downstream_gene_variant,,ENST00000562479,;MLST8,downstream_gene_variant,,ENST00000569457,;BRICD5,downstream_gene_variant,,ENST00000328540,;MLST8,downstream_gene_variant,,ENST00000563179,;PGP,downstream_gene_variant,,ENST00000333503,;BRICD5,downstream_gene_variant,,ENST00000566018,;MLST8,downstream_gene_variant,,ENST00000562352,;BRICD5,downstream_gene_variant,,ENST00000562360,;AC009065.3,upstream_gene_variant,,ENST00000517149,;RP11-304L19.8,upstream_gene_variant,,ENST00000561544,;MLST8,downstream_gene_variant,,ENST00000565926,;MLST8,downstream_gene_variant,,ENST00000561651,;MLST8,downstream_gene_variant,,ENST00000562844,;MLST8,downstream_gene_variant,,ENST00000564319,;MLST8,downstream_gene_variant,,ENST00000562043,;MLST8,3_prime_UTR_variant,,ENST00000566835,;MLST8,non_coding_transcript_exon_variant,,ENST00000568194,;MLST8,non_coding_transcript_exon_variant,,ENST00000562392,;MLST8,non_coding_transcript_exon_variant,,ENST00000568542,;MLST8,non_coding_transcript_exon_variant,,ENST00000563067,;MLST8,downstream_gene_variant,,ENST00000563107,;BRICD5,downstream_gene_variant,,ENST00000566795,;MLST8,downstream_gene_variant,,ENST00000566653,;MLST8,downstream_gene_variant,,ENST00000569848,;MLST8,downstream_gene_variant,,ENST00000567282,;MLST8,downstream_gene_variant,,ENST00000565687,;MLST8,downstream_gene_variant,,ENST00000567623,;MLST8,downstream_gene_variant,,ENST00000562239,;MLST8,downstream_gene_variant,,ENST00000570224,;PGP,downstream_gene_variant,,ENST00000562001,;MLST8,downstream_gene_variant,,ENST00000564294,;MLST8,downstream_gene_variant,,ENST00000564679,;MLST8,downstream_gene_variant,,ENST00000562851,;MLST8,downstream_gene_variant,,ENST00000567928,;MLST8,downstream_gene_variant,,ENST00000565330,;MLST8,downstream_gene_variant,,ENST00000565717,;MLST8,downstream_gene_variant,,ENST00000565269,;	T	ENSG00000167965	ENST00000569417	Transcript	3_prime_UTR_variant	1620	.	.	.	.	.	.	.	1	MLST8	HGNC	24825	protein_coding	YES	CCDS10462.2	ENSP00000456405	LST8_HUMAN	H3BQ74_HUMAN,H3BN58_HUMAN	UPI000006D8E8	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTCTGAGGCT	.	2	ESCA
CHP2	0	.	GRCh37	16	23769008	23769008	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*104C>G	.	.	ENST00000300113	7/7	30	22	8	16	16	0	CHP2,3_prime_UTR_variant,,ENST00000300113,;	G	ENSG00000166869	ENST00000300113	Transcript	3_prime_UTR_variant	1118	.	.	.	.	.	.	.	1	CHP2	HGNC	24927	protein_coding	YES	CCDS10617.1	ENSP00000300113	CHP2_HUMAN	A8K2I8_HUMAN	UPI000013E626	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTCGTTTC	.	5	ESCA
NTN3	0	.	GRCh37	16	2522730	2522730	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.957C>T	p.%3D	p.R319R	ENST00000293973	2/6	17	14	3	13	13	0	NTN3,synonymous_variant,p.%3D,ENST00000293973,;TBC1D24,upstream_gene_variant,,ENST00000293970,;TBC1D24,upstream_gene_variant,,ENST00000567020,;RP11-715J22.2,upstream_gene_variant,,ENST00000563775,;RP11-715J22.6,upstream_gene_variant,,ENST00000561847,;	T	ENSG00000162068	ENST00000293973	Transcript	synonymous_variant	1160	957	319	R	cgC/cgT	.	.	.	1	NTN3	HGNC	8030	protein_coding	YES	CCDS10469.1	ENSP00000293973	NET3_HUMAN	.	UPI000006ED30	.	.	.	2/6	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574,Pfam_domain:PF00053,Gene3D:2.10.25.10,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCCGCTGCCG	.	2	ESCA
ERVK13-1	0	.	GRCh37	16	2711935	2711935	+	RNA	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4793C>G	.	.	ENST00000568395	3/3	30	27	3	15	15	0	ERVK13-1,non_coding_transcript_exon_variant,,ENST00000568395,;ERVK13-1,non_coding_transcript_exon_variant,,ENST00000569465,;ERVK13-1,intron_variant,,ENST00000564340,;ERVK13-1,downstream_gene_variant,,ENST00000566343,;ERVK13-1,downstream_gene_variant,,ENST00000562807,;	C	ENSG00000260565	ENST00000568395	Transcript	non_coding_transcript_exon_variant	4793	.	.	.	.	.	.	.	-1	ERVK13-1	HGNC	27548	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AATAAGAGTAA	.	3	ESCA
GTF3C1	0	.	GRCh37	16	27475803	27475803	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5710G>A	p.Gly1904Arg	p.G1904R	ENST00000356183	34/37	103	82	20	73	73	0	GTF3C1,missense_variant,p.Gly1904Arg,ENST00000561623,;GTF3C1,missense_variant,p.Gly1904Arg,ENST00000356183,;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,downstream_gene_variant,,ENST00000567843,;GTF3C1,upstream_gene_variant,,ENST00000567806,;GTF3C1,non_coding_transcript_exon_variant,,ENST00000562609,;GTF3C1,upstream_gene_variant,,ENST00000564747,;	T	ENSG00000077235	ENST00000356183	Transcript	missense_variant	5726	5710	1904	G/R	Ggg/Agg	.	.	.	-1	GTF3C1	HGNC	4664	protein_coding	YES	CCDS32414.1	ENSP00000348510	TF3C1_HUMAN	Q7Z7H4_HUMAN,I3L1Z3_HUMAN	UPI00001FF123	.	tolerated(0.21)	benign(0.054)	34/37	.	hmmpanther:PTHR15180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCCATCTT	.	5	ESCA
PKMYT1	0	.	GRCh37	16	3023093	3023093	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1389-28C>T	.	.	ENST00000262300	.	43	26	16	45	45	0	PKMYT1,3_prime_UTR_variant,,ENST00000575040,;PAQR4,3_prime_UTR_variant,,ENST00000572687,;PAQR4,3_prime_UTR_variant,,ENST00000293978,;PAQR4,3_prime_UTR_variant,,ENST00000318782,;PKMYT1,intron_variant,,ENST00000262300,;PKMYT1,intron_variant,,ENST00000573944,;PKMYT1,intron_variant,,ENST00000431515,;PKMYT1,intron_variant,,ENST00000440027,;PKMYT1,intron_variant,,ENST00000574730,;PKMYT1,intron_variant,,ENST00000574385,;PKMYT1,downstream_gene_variant,,ENST00000572619,;KREMEN2,downstream_gene_variant,,ENST00000303746,;PAQR4,downstream_gene_variant,,ENST00000576565,;PKMYT1,downstream_gene_variant,,ENST00000574415,;PAQR4,downstream_gene_variant,,ENST00000574988,;PKMYT1,downstream_gene_variant,,ENST00000576268,;KREMEN2,downstream_gene_variant,,ENST00000571007,;KREMEN2,downstream_gene_variant,,ENST00000319500,;KREMEN2,downstream_gene_variant,,ENST00000572045,;KREMEN2,downstream_gene_variant,,ENST00000575885,;PKMYT1,downstream_gene_variant,,ENST00000572059,;KREMEN2,downstream_gene_variant,,ENST00000575769,;PKMYT1,downstream_gene_variant,,ENST00000575632,;PKMYT1,intron_variant,,ENST00000574333,;PKMYT1,upstream_gene_variant,,ENST00000571102,;PKMYT1,upstream_gene_variant,,ENST00000572832,;PKMYT1,intron_variant,,ENST00000575981,;PKMYT1,intron_variant,,ENST00000574680,;PKMYT1,intron_variant,,ENST00000382240,;	A	ENSG00000127564	ENST00000262300	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PKMYT1	HGNC	29650	protein_coding	YES	CCDS10486.1	ENSP00000262300	PMYT1_HUMAN	Q0IJ49_HUMAN,I3L4Y0_HUMAN,I3L4K3_HUMAN,I3L1H7_HUMAN,I3L136_HUMAN	UPI000004CF52	.	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGGATCCA	.	5	ESCA
ARMC5	0	.	GRCh37	16	31470831	31470831	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-15G>A	.	.	ENST00000268314	1/6	75	63	12	55	55	0	ARMC5,missense_variant,p.Glu28Lys,ENST00000538189,;ARMC5,missense_variant,p.Glu91Lys,ENST00000408912,;ARMC5,5_prime_UTR_variant,,ENST00000268314,;ARMC5,5_prime_UTR_variant,,ENST00000563544,;ARMC5,5_prime_UTR_variant,,ENST00000457010,;ARMC5,upstream_gene_variant,,ENST00000564900,;ARMC5,upstream_gene_variant,,ENST00000412665,;RP11-452L6.5,non_coding_transcript_exon_variant,,ENST00000564629,;ARMC5,upstream_gene_variant,,ENST00000564514,;	A	ENSG00000140691	ENST00000268314	Transcript	5_prime_UTR_variant	515	.	.	.	.	.	.	.	1	ARMC5	HGNC	25781	protein_coding	YES	CCDS45472.1	ENSP00000268314	ARMC5_HUMAN	.	UPI0000F6E6C0	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTGAGGCC	.	5	ESCA
MYLK3	0	.	GRCh37	16	46761262	46761262	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1800G>T	p.%3D	p.R600R	ENST00000394809	8/13	66	52	13	39	39	0	MYLK3,synonymous_variant,p.%3D,ENST00000536476,;MYLK3,synonymous_variant,p.%3D,ENST00000394809,;MYLK3,non_coding_transcript_exon_variant,,ENST00000569844,;MYLK3,non_coding_transcript_exon_variant,,ENST00000564731,;	A	ENSG00000140795	ENST00000394809	Transcript	synonymous_variant	1916	1800	600	R	cgG/cgT	.	.	.	-1	MYLK3	HGNC	29826	protein_coding	YES	CCDS10723.2	ENSP00000378288	MYLK3_HUMAN	.	UPI000059D380	.	.	.	8/13	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF45,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATCCGGTC	.	5	ESCA
LONP2	0	.	GRCh37	16	48295447	48295447	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.836C>A	p.Thr279Lys	p.T279K	ENST00000285737	5/15	44	38	6	17	17	0	LONP2,missense_variant,p.Thr235Lys,ENST00000535754,;LONP2,missense_variant,p.Thr279Lys,ENST00000285737,;LONP2,missense_variant,p.Thr235Lys,ENST00000416006,;LONP2,missense_variant,p.Thr279Lys,ENST00000566755,;LONP2,upstream_gene_variant,,ENST00000570174,;	A	ENSG00000102910	ENST00000285737	Transcript	missense_variant	929	836	279	T/K	aCa/aAa	.	.	.	1	LONP2	HGNC	20598	protein_coding	YES	CCDS10734.1	ENSP00000285737	LONP2_HUMAN	Q9BU35_HUMAN	UPI000000DCD1	.	tolerated(0.72)	benign(0.035)	5/15	.	HAMAP:MF_03121,hmmpanther:PTHR10046,hmmpanther:PTHR10046:SF24,TIGRFAM_domain:TIGR00763,PIRSF_domain:PIRSF001174	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGAACATCTA	.	2	ESCA
N4BP1	0	.	GRCh37	16	48575913	48575913	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*902C>G	.	.	ENST00000262384	7/7	33	23	10	23	23	0	N4BP1,3_prime_UTR_variant,,ENST00000262384,;N4BP1,downstream_gene_variant,,ENST00000565638,;N4BP1,downstream_gene_variant,,ENST00000565423,;N4BP1,downstream_gene_variant,,ENST00000564124,;N4BP1,downstream_gene_variant,,ENST00000569027,;	C	ENSG00000102921	ENST00000262384	Transcript	3_prime_UTR_variant	3830	.	.	.	.	.	.	.	-1	N4BP1	HGNC	29850	protein_coding	YES	CCDS45479.1	ENSP00000262384	N4BP1_HUMAN	I3L3R7_HUMAN	UPI000013D2A2	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGTGACCGG	.	5	ESCA
MT1H	0	.	GRCh37	16	56704480	56704480	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.91A>G	p.Lys31Glu	p.K31E	ENST00000332374	2/3	108	98	10	83	83	0	MT1H,missense_variant,p.Lys31Glu,ENST00000332374,;MT1H,missense_variant,p.Lys31Glu,ENST00000569155,;MT1G,upstream_gene_variant,,ENST00000379811,;MT1G,upstream_gene_variant,,ENST00000444837,;MT1G,upstream_gene_variant,,ENST00000568675,;MT1G,upstream_gene_variant,,ENST00000569500,;	G	ENSG00000205358	ENST00000332374	Transcript	missense_variant	162	91	31	K/E	Aag/Gag	.	.	.	1	MT1H	HGNC	7400	protein_coding	YES	CCDS10767.1	ENSP00000330587	MT1H_HUMAN	.	UPI000012F6DC	.	deleterious(0.02)	unknown(0)	2/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23299:SF4,hmmpanther:PTHR23299,PROSITE_patterns:PS00203,Gene3D:4mt2A00,Pfam_domain:PF00131,Superfamily_domains:SSF57868,Prints_domain:PR00860	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAAGAAGAGT	.	3	ESCA
CNGB1	0	.	GRCh37	16	58001173	58001173	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18G>C	p.Gln6His	p.Q6H	ENST00000251102	2/33	69	60	8	64	64	0	CNGB1,missense_variant,p.Gln6His,ENST00000564448,;CNGB1,missense_variant,p.Gln6His,ENST00000311183,;CNGB1,missense_variant,p.Gln6His,ENST00000562761,;CNGB1,missense_variant,p.Gln6His,ENST00000251102,;CNGB1,non_coding_transcript_exon_variant,,ENST00000567568,;	G	ENSG00000070729	ENST00000251102	Transcript	missense_variant	79	18	6	Q/H	caG/caC	.	.	.	-1	CNGB1	HGNC	2151	protein_coding	YES	CCDS42169.1	ENSP00000251102	CNGB1_HUMAN	H3BQC3_HUMAN	UPI000013CCDF	.	tolerated_low_confidence(0.05)	probably_damaging(0.969)	2/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCCTCTGGAC	.	4	ESCA
WASH4P	0	.	GRCh37	16	63247	63247	+	3'Flank	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000326592	.	21	17	4	11	11	0	WASH4P,downstream_gene_variant,,ENST00000326592,;DDX11L10,non_coding_transcript_exon_variant,,ENST00000513886,;Z84812.4,downstream_gene_variant,,ENST00000568710,;WASH4P,downstream_gene_variant,,ENST00000462860,;WASH4P,downstream_gene_variant,,ENST00000538848,;WASH4P,downstream_gene_variant,,ENST00000487568,;WASH4P,downstream_gene_variant,,ENST00000470283,;WASH4P,downstream_gene_variant,,ENST00000477365,;WASH4P,downstream_gene_variant,,ENST00000468574,;WASH4P,downstream_gene_variant,,ENST00000495251,;WASH4P,downstream_gene_variant,,ENST00000483390,;WASH4P,downstream_gene_variant,,ENST00000474799,;WASH4P,downstream_gene_variant,,ENST00000564273,;WASH4P,downstream_gene_variant,,ENST00000494585,;WASH4P,downstream_gene_variant,,ENST00000470725,;DDX11L10,non_coding_transcript_exon_variant,,ENST00000545636,;DDX11L10,non_coding_transcript_exon_variant,,ENST00000430178,;	A	ENSG00000234769	ENST00000326592	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	796	-1	WASH4P	HGNC	14126	protein_coding	YES	.	ENSP00000317542	WASH4_HUMAN	H3BUR0_HUMAN	UPI000066D93A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCAGGGATCCT	.	3	ESCA
EXOC3L1	0	.	GRCh37	16	67223572	67223572	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8C>G	p.Ser3Ter	p.S3*	ENST00000314586	2/14	71	66	5	71	71	0	EXOC3L1,stop_gained,p.Ser3Ter,ENST00000545725,;EXOC3L1,stop_gained,p.Ser3Ter,ENST00000563889,;EXOC3L1,stop_gained,p.Ser3Ter,ENST00000564418,;EXOC3L1,stop_gained,p.Ser3Ter,ENST00000314586,;E2F4,upstream_gene_variant,,ENST00000379378,;EXOC3L1,non_coding_transcript_exon_variant,,ENST00000562887,;E2F4,upstream_gene_variant,,ENST00000564718,;EXOC3L1,stop_gained,p.Ser3Ter,ENST00000564324,;E2F4,upstream_gene_variant,,ENST00000561904,;E2F4,upstream_gene_variant,,ENST00000568839,;E2F4,upstream_gene_variant,,ENST00000566368,;E2F4,upstream_gene_variant,,ENST00000565849,;E2F4,upstream_gene_variant,,ENST00000563238,;E2F4,upstream_gene_variant,,ENST00000568693,;E2F4,upstream_gene_variant,,ENST00000568485,;E2F4,upstream_gene_variant,,ENST00000567007,;E2F4,upstream_gene_variant,,ENST00000569573,;EXOC3L1,upstream_gene_variant,,ENST00000563536,;	C	ENSG00000179044	ENST00000314586	Transcript	stop_gained	249	8	3	S/*	tCa/tGa	.	.	.	-1	EXOC3L1	HGNC	27540	protein_coding	YES	CCDS10832.1	ENSP00000325674	EX3L1_HUMAN	H3BTH9_HUMAN	UPI000013F886	.	.	.	2/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCTGAGTCC	.	2	ESCA
HSD11B2	0	.	GRCh37	16	67470642	67470642	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.954C>T	p.%3D	p.L318L	ENST00000326152	5/5	64	56	8	40	40	0	HSD11B2,synonymous_variant,p.%3D,ENST00000326152,;ATP6V0D1,downstream_gene_variant,,ENST00000290949,;ATP6V0D1,downstream_gene_variant,,ENST00000565835,;ATP6V0D1,downstream_gene_variant,,ENST00000602876,;ATP6V0D1,downstream_gene_variant,,ENST00000540149,;ATP6V0D1,downstream_gene_variant,,ENST00000564615,;ATP6V0D1,downstream_gene_variant,,ENST00000567694,;HSD11B2,downstream_gene_variant,,ENST00000567684,;ATP6V0D1,downstream_gene_variant,,ENST00000563064,;ATP6V0D1,downstream_gene_variant,,ENST00000561852,;HSD11B2,downstream_gene_variant,,ENST00000566606,;HSD11B2,downstream_gene_variant,,ENST00000569303,;ATP6V0D1,downstream_gene_variant,,ENST00000564191,;ATP6V0D1,downstream_gene_variant,,ENST00000568620,;ATP6V0D1,downstream_gene_variant,,ENST00000564788,;ATP6V0D1,downstream_gene_variant,,ENST00000566322,;ATP6V0D1,downstream_gene_variant,,ENST00000567170,;ATP6V0D1,downstream_gene_variant,,ENST00000426604,;ATP6V0D1,downstream_gene_variant,,ENST00000563305,;AC009061.1,downstream_gene_variant,,ENST00000366223,;	T	ENSG00000176387	ENST00000326152	Transcript	synonymous_variant	1086	954	318	L	ctC/ctT	.	.	.	1	HSD11B2	HGNC	5209	protein_coding	YES	CCDS10837.1	ENSP00000316786	DHI2_HUMAN	.	UPI000014185A	.	.	.	5/5	.	hmmpanther:PTHR24316:SF265,hmmpanther:PTHR24316,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCTCACCCC	.	4	ESCA
HSD11B2	0	.	GRCh37	16	67471214	67471214	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*308C>T	.	.	ENST00000326152	5/5	50	44	6	26	26	0	HSD11B2,3_prime_UTR_variant,,ENST00000326152,;ATP6V0D1,downstream_gene_variant,,ENST00000290949,;ATP6V0D1,downstream_gene_variant,,ENST00000565835,;ATP6V0D1,downstream_gene_variant,,ENST00000602876,;ATP6V0D1,downstream_gene_variant,,ENST00000540149,;ATP6V0D1,downstream_gene_variant,,ENST00000564615,;ATP6V0D1,downstream_gene_variant,,ENST00000567694,;HSD11B2,downstream_gene_variant,,ENST00000567684,;ATP6V0D1,downstream_gene_variant,,ENST00000563064,;ATP6V0D1,downstream_gene_variant,,ENST00000561852,;HSD11B2,downstream_gene_variant,,ENST00000566606,;HSD11B2,downstream_gene_variant,,ENST00000569303,;ATP6V0D1,downstream_gene_variant,,ENST00000564191,;ATP6V0D1,downstream_gene_variant,,ENST00000568620,;ATP6V0D1,downstream_gene_variant,,ENST00000564788,;ATP6V0D1,downstream_gene_variant,,ENST00000566322,;ATP6V0D1,downstream_gene_variant,,ENST00000567170,;ATP6V0D1,downstream_gene_variant,,ENST00000426604,;ATP6V0D1,downstream_gene_variant,,ENST00000563305,;AC009061.1,downstream_gene_variant,,ENST00000366223,;	T	ENSG00000176387	ENST00000326152	Transcript	3_prime_UTR_variant	1658	.	.	.	.	.	.	.	1	HSD11B2	HGNC	5209	protein_coding	YES	CCDS10837.1	ENSP00000316786	DHI2_HUMAN	.	UPI000014185A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTTTCACAGG	.	4	ESCA
ACD	0	.	GRCh37	16	67693165	67693165	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.718G>T	p.Glu240Ter	p.E240*	ENST00000393919	6/12	56	48	8	32	32	0	ACD,stop_gained,p.Glu237Ter,ENST00000219251,;ACD,stop_gained,p.Glu98Ter,ENST00000602850,;ACD,stop_gained,p.Glu240Ter,ENST00000393919,;ACD,stop_gained,p.Glu158Ter,ENST00000602320,;ACD,stop_gained,p.Glu2Ter,ENST00000602382,;PARD6A,upstream_gene_variant,,ENST00000458121,;PARD6A,upstream_gene_variant,,ENST00000602551,;RLTPR,downstream_gene_variant,,ENST00000334583,;ENKD1,downstream_gene_variant,,ENST00000602644,;PARD6A,upstream_gene_variant,,ENST00000219255,;ENKD1,downstream_gene_variant,,ENST00000243878,;RLTPR,downstream_gene_variant,,ENST00000545661,;ENKD1,downstream_gene_variant,,ENST00000602409,;ACD,splice_region_variant,,ENST00000602945,;ACD,non_coding_transcript_exon_variant,,ENST00000602860,;ACD,non_coding_transcript_exon_variant,,ENST00000602519,;ACD,non_coding_transcript_exon_variant,,ENST00000602622,;PARD6A,upstream_gene_variant,,ENST00000602727,;ACD,upstream_gene_variant,,ENST00000602656,;RLTPR,downstream_gene_variant,,ENST00000602368,;ENKD1,downstream_gene_variant,,ENST00000602415,;ACD,downstream_gene_variant,,ENST00000602821,;RLTPR,downstream_gene_variant,,ENST00000602924,;ACD,downstream_gene_variant,,ENST00000602423,;ACD,downstream_gene_variant,,ENST00000602780,;RLTPR,downstream_gene_variant,,ENST00000602705,;ENKD1,downstream_gene_variant,,ENST00000602942,;ENKD1,downstream_gene_variant,,ENST00000602642,;	A	ENSG00000102977	ENST00000393919	Transcript	stop_gained	983	718	240	E/*	Gag/Tag	.	.	.	-1	ACD	HGNC	25070	protein_coding	YES	CCDS42181.1	ENSP00000377496	ACD_HUMAN	.	UPI0000246BB2	.	.	.	6/12	.	hmmpanther:PTHR14487:SF2,hmmpanther:PTHR14487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTCCCTAC	.	5	ESCA
NIP7	0	.	GRCh37	16	69373946	69373946	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94G>C	p.Asp32His	p.D32H	ENST00000254940	2/5	91	59	32	60	60	0	NIP7,missense_variant,p.Asp32His,ENST00000569637,;NIP7,missense_variant,p.Asp32His,ENST00000254941,;NIP7,missense_variant,p.Asp32His,ENST00000254940,;RP11-343C2.9,intron_variant,,ENST00000563634,;COG8,upstream_gene_variant,,ENST00000567493,;COG8,upstream_gene_variant,,ENST00000562595,;TMED6,downstream_gene_variant,,ENST00000288025,;NIP7,upstream_gene_variant,,ENST00000562523,;COG8,upstream_gene_variant,,ENST00000562081,;COG8,upstream_gene_variant,,ENST00000306875,;NIP7,upstream_gene_variant,,ENST00000567202,;NIP7,non_coding_transcript_exon_variant,,ENST00000562131,;NIP7,non_coding_transcript_exon_variant,,ENST00000565034,;NIP7,non_coding_transcript_exon_variant,,ENST00000563364,;RP11-343C2.7,intron_variant,,ENST00000570293,;RP11-343C2.7,intron_variant,,ENST00000564737,;TMED6,downstream_gene_variant,,ENST00000568748,;	C	ENSG00000132603	ENST00000254940	Transcript	missense_variant	494	94	32	D/H	Gat/Cat	.	.	.	1	NIP7	HGNC	24328	protein_coding	YES	CCDS10877.1	ENSP00000254940	NIP7_HUMAN	.	UPI000006FFF0	.	deleterious(0)	probably_damaging(0.974)	2/5	.	hmmpanther:PTHR23415,hmmpanther:PTHR23415:SF4,Pfam_domain:PF03657,PIRSF_domain:PIRSF017190,Superfamily_domains:SSF88802	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCGATGGC	.	5	ESCA
NPIPB15	0	.	GRCh37	16	74425817	74425817	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1171G>C	p.Glu391Gln	p.E391Q	ENST00000429990	7/7	204	193	11	153	153	0	NPIPB15,missense_variant,p.Glu391Gln,ENST00000429990,;	C	ENSG00000196436	ENST00000429990	Transcript	missense_variant	1267	1171	391	E/Q	Gag/Cag	.	.	.	1	NPIPB15	HGNC	34409	protein_coding	YES	.	ENSP00000411140	NPB15_HUMAN	.	UPI000198C783	.	deleterious_low_confidence(0.03)	benign(0.446)	7/7	.	hmmpanther:PTHR15438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A394T|c.1180G>A|3,BUFFER|p.A333T|c.997G>A|3	MUTECT|MUSE	AGAGGGAGGCC	.	2	ESCA
CHST6	0	.	GRCh37	16	75512762	75512762	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.965C>T	p.Ser322Leu	p.S322L	ENST00000332272	3/3	88	76	12	55	55	0	CHST6,missense_variant,p.Ser322Leu,ENST00000390664,;CHST6,missense_variant,p.Ser322Leu,ENST00000332272,;RP11-77K12.4,intron_variant,,ENST00000530512,;	A	ENSG00000183196	ENST00000332272	Transcript	missense_variant	1145	965	322	S/L	tCg/tTg	COSM1709401	.	.	-1	CHST6	HGNC	6938	protein_coding	YES	CCDS10918.1	ENSP00000328983	CHST6_HUMAN	.	UPI00000467C8	.	deleterious(0.02)	benign(0.311)	3/3	.	hmmpanther:PTHR10704:SF13,hmmpanther:PTHR10704,Pfam_domain:PF00685,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S322L|c.965C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACGAAGTC	.	5	ESCA
ADAMTS18	0	.	GRCh37	16	77317946	77317946	+	Missense_Mutation	SNP	G	G	C	rs147053635	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3573C>G	p.Phe1191Leu	p.F1191L	ENST00000282849	23/23	35	30	5	35	35	0	ADAMTS18,missense_variant,p.Phe1191Leu,ENST00000282849,;ADAMTS18,intron_variant,,ENST00000562332,;RP11-538I12.3,intron_variant,,ENST00000561672,;	C	ENSG00000140873	ENST00000282849	Transcript	missense_variant	3992	3573	1191	F/L	ttC/ttG	rs147053635	.	.	-1	ADAMTS18	HGNC	17110	protein_coding	YES	CCDS10926.1	ENSP00000282849	ATS18_HUMAN	.	UPI0000233610	.	tolerated(0.51)	benign(0.001)	23/23	.	PROSITE_profiles:PS50900,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF167,Pfam_domain:PF08686	A:0.0052	A:0	A:0	.	A:0.0218	A:0	A:0.0041	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAAGAAATC	byFrequency|byCluster|by1000G	4	ESCA
MSLN	0	.	GRCh37	16	812752	812752	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72G>T	p.%3D	p.L24L	ENST00000382862	2/17	124	71	53	103	103	0	MSLN,synonymous_variant,p.%3D,ENST00000563651,;MSLN,synonymous_variant,p.%3D,ENST00000382862,;MSLN,synonymous_variant,p.%3D,ENST00000566549,;MSLN,synonymous_variant,p.%3D,ENST00000563941,;MSLN,synonymous_variant,p.%3D,ENST00000569566,;MSLN,synonymous_variant,p.%3D,ENST00000545450,;MSLN,upstream_gene_variant,,ENST00000561896,;MSLN,upstream_gene_variant,,ENST00000566269,;	T	ENSG00000102854	ENST00000382862	Transcript	synonymous_variant	167	72	24	L	ctG/ctT	.	.	.	1	MSLN	HGNC	7371	protein_coding	YES	CCDS32356.1	ENSP00000372313	MSLN_HUMAN	H3BV92_HUMAN	UPI000004EC9C	.	.	.	2/17	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23412:SF6,hmmpanther:PTHR23412,Pfam_domain:PF06060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTGCTCTT	.	5	ESCA
GALNS	0	.	GRCh37	16	88909193	88909193	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165G>C	p.Glu55Asp	p.E55D	ENST00000268695	2/14	136	126	10	96	96	0	GALNS,missense_variant,p.Glu55Asp,ENST00000268695,;GALNS,intron_variant,,ENST00000542788,;GALNS,intron_variant,,ENST00000562831,;GALNS,non_coding_transcript_exon_variant,,ENST00000565364,;GALNS,upstream_gene_variant,,ENST00000561812,;GALNS,upstream_gene_variant,,ENST00000562931,;GALNS,3_prime_UTR_variant,,ENST00000568613,;GALNS,non_coding_transcript_exon_variant,,ENST00000562593,;GALNS,intron_variant,,ENST00000567525,;GALNS,upstream_gene_variant,,ENST00000566563,;GALNS,upstream_gene_variant,,ENST00000567779,;	G	ENSG00000141012	ENST00000268695	Transcript	missense_variant	254	165	55	E/D	gaG/gaC	CD041913	.	.	-1	GALNS	HGNC	4122	protein_coding	YES	CCDS10970.1	ENSP00000268695	GALNS_HUMAN	Q96I49_HUMAN,Q6YL38_HUMAN	UPI000012AF92	.	tolerated(0.07)	possibly_damaging(0.46)	2/14	.	hmmpanther:PTHR10342:SF27,hmmpanther:PTHR10342,Gene3D:3.40.720.10,Pfam_domain:PF00884,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGTCTCTCT	.	2	ESCA
FANCA	0	.	GRCh37	16	89805460	89805460	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4168-78G>A	.	.	ENST00000389301	.	76	59	17	36	36	0	FANCA,synonymous_variant,p.%3D,ENST00000561722,;ZNF276,3_prime_UTR_variant,,ENST00000289816,;FANCA,intron_variant,,ENST00000389301,;FANCA,intron_variant,,ENST00000567879,;FANCA,intron_variant,,ENST00000564475,;FANCA,intron_variant,,ENST00000568369,;FANCA,intron_variant,,ENST00000564870,;ZNF276,downstream_gene_variant,,ENST00000568064,;ZNF276,downstream_gene_variant,,ENST00000443381,;ZNF276,downstream_gene_variant,,ENST00000446326,;ZNF276,non_coding_transcript_exon_variant,,ENST00000563983,;FANCA,intron_variant,,ENST00000562424,;FANCA,downstream_gene_variant,,ENST00000564969,;ZNF276,downstream_gene_variant,,ENST00000564004,;FANCA,downstream_gene_variant,,ENST00000568626,;ZNF276,downstream_gene_variant,,ENST00000568295,;ZNF276,downstream_gene_variant,,ENST00000561536,;ZNF276,downstream_gene_variant,,ENST00000569901,;FANCA,downstream_gene_variant,,ENST00000305699,;FANCA,downstream_gene_variant,,ENST00000567988,;ZNF276,downstream_gene_variant,,ENST00000569582,;ZNF276,downstream_gene_variant,,ENST00000562530,;	T	ENSG00000187741	ENST00000389301	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	FANCA	HGNC	3582	protein_coding	YES	CCDS32515.1	ENSP00000373952	FANCA_HUMAN	H3BT53_HUMAN	UPI0000520A1A	.	.	.	.	41/42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATGCTGTGC	.	5	ESCA
GAS8	0	.	GRCh37	16	90110451	90110451	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*698C>G	.	.	ENST00000268699	11/11	19	16	3	18	18	0	GAS8,3_prime_UTR_variant,,ENST00000268699,;GAS8,downstream_gene_variant,,ENST00000536122,;URAHP,intron_variant,,ENST00000409873,;URAHP,intron_variant,,ENST00000517889,;URAHP,intron_variant,,ENST00000409768,;URAHP,intron_variant,,ENST00000521551,;GAS8,downstream_gene_variant,,ENST00000540721,;GAS8,3_prime_UTR_variant,,ENST00000566266,;GAS8,non_coding_transcript_exon_variant,,ENST00000569558,;GAS8,downstream_gene_variant,,ENST00000569399,;GAS8,downstream_gene_variant,,ENST00000568284,;GAS8,downstream_gene_variant,,ENST00000564789,;URAHP,intron_variant,,ENST00000610227,;	G	ENSG00000141013	ENST00000268699	Transcript	3_prime_UTR_variant	2257	.	.	.	.	.	.	.	1	GAS8	HGNC	4166	protein_coding	YES	CCDS10992.1	ENSP00000268699	GAS8_HUMAN	H3BUA7_HUMAN,H3BP65_HUMAN,H3BNL3_HUMAN,G3V1L5_HUMAN	UPI0000070A4C	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTATCTGGCC	.	2	ESCA
FAM83G	0	.	GRCh37	17	18882138	18882138	+	Missense_Mutation	SNP	C	C	T	rs777843624	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841G>A	p.Asp281Asn	p.D281N	ENST00000388995	5/6	27	20	6	56	56	0	FAM83G,missense_variant,p.Asp281Asn,ENST00000585154,;FAM83G,missense_variant,p.Asp281Asn,ENST00000388995,;FAM83G,missense_variant,p.Asp281Asn,ENST00000345041,;SLC5A10,intron_variant,,ENST00000417251,;SLC5A10,intron_variant,,ENST00000395647,;SLC5A10,intron_variant,,ENST00000395643,;SLC5A10,intron_variant,,ENST00000395642,;SLC5A10,intron_variant,,ENST00000395645,;SLC5A10,intron_variant,,ENST00000317977,;FAM83G,upstream_gene_variant,,ENST00000580115,;FAM83G,non_coding_transcript_exon_variant,,ENST00000399096,;	T	ENSG00000188522	ENST00000388995	Transcript	missense_variant	1065	841	281	D/N	Gac/Aac	rs777843624	.	.	-1	FAM83G	HGNC	32554	protein_coding	YES	CCDS42276.1	ENSP00000373647	FA83G_HUMAN	.	UPI0000E03260	.	deleterious(0)	probably_damaging(0.982)	5/6	.	hmmpanther:PTHR16181:SF5,hmmpanther:PTHR16181,Gene3D:3.30.870.10,Pfam_domain:PF07894,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGTCCGTCC	.	5	ESCA
FAM83G	0	.	GRCh37	17	18907093	18907093	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.262C>T	p.Gln88Ter	p.Q88*	ENST00000388995	2/6	47	27	20	64	64	0	FAM83G,stop_gained,p.Gln88Ter,ENST00000585154,;FAM83G,stop_gained,p.Gln88Ter,ENST00000388995,;FAM83G,stop_gained,p.Gln88Ter,ENST00000345041,;SLC5A10,intron_variant,,ENST00000417251,;SLC5A10,intron_variant,,ENST00000395647,;SLC5A10,intron_variant,,ENST00000395643,;SLC5A10,intron_variant,,ENST00000395642,;SLC5A10,intron_variant,,ENST00000395645,;SLC5A10,intron_variant,,ENST00000317977,;FAM83G,non_coding_transcript_exon_variant,,ENST00000399096,;	A	ENSG00000188522	ENST00000388995	Transcript	stop_gained	486	262	88	Q/*	Cag/Tag	COSM1302480	.	.	-1	FAM83G	HGNC	32554	protein_coding	YES	CCDS42276.1	ENSP00000373647	FA83G_HUMAN	.	UPI0000E03260	.	.	.	2/6	.	hmmpanther:PTHR16181:SF5,hmmpanther:PTHR16181,Pfam_domain:PF07894	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCCTGAGAGG	.	3	ESCA
FAM83G	0	.	GRCh37	17	18907111	18907111	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244C>T	p.Arg82Trp	p.R82W	ENST00000388995	2/6	61	33	27	81	81	0	FAM83G,missense_variant,p.Arg82Trp,ENST00000585154,;FAM83G,missense_variant,p.Arg82Trp,ENST00000388995,;FAM83G,missense_variant,p.Arg82Trp,ENST00000345041,;SLC5A10,intron_variant,,ENST00000417251,;SLC5A10,intron_variant,,ENST00000395647,;SLC5A10,intron_variant,,ENST00000395643,;SLC5A10,intron_variant,,ENST00000395642,;SLC5A10,intron_variant,,ENST00000395645,;SLC5A10,intron_variant,,ENST00000317977,;FAM83G,upstream_gene_variant,,ENST00000399096,;	A	ENSG00000188522	ENST00000388995	Transcript	missense_variant	468	244	82	R/W	Cgg/Tgg	.	.	.	-1	FAM83G	HGNC	32554	protein_coding	YES	CCDS42276.1	ENSP00000373647	FA83G_HUMAN	.	UPI0000E03260	.	deleterious(0)	probably_damaging(0.993)	2/6	.	hmmpanther:PTHR16181:SF5,hmmpanther:PTHR16181,Pfam_domain:PF07894	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCCCCGAGGGT	.	3	ESCA
NLK	0	.	GRCh37	17	26512224	26512224	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1169A>G	p.Tyr390Cys	p.Y390C	ENST00000407008	8/11	15	11	4	27	27	0	NLK,missense_variant,p.Tyr390Cys,ENST00000407008,;NLK,non_coding_transcript_exon_variant,,ENST00000584188,;NLK,missense_variant,p.Tyr338Cys,ENST00000496808,;	G	ENSG00000087095	ENST00000407008	Transcript	missense_variant	1887	1169	390	Y/C	tAt/tGt	.	.	.	1	NLK	HGNC	29858	protein_coding	YES	CCDS11224.2	ENSP00000384625	NLK_HUMAN	H0YD75_HUMAN	UPI0000D48A70	.	tolerated(0.06)	probably_damaging(0.99)	8/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF179,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCTATACCC	.	5	ESCA
NF1	0	.	GRCh37	17	29527461	29527461	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.910C>T	p.Arg304Ter	p.R304*	ENST00000358273	9/58	72	47	25	62	62	0	NF1,stop_gained,p.Arg304Ter,ENST00000431387,;NF1,stop_gained,p.Arg304Ter,ENST00000358273,;NF1,stop_gained,p.Arg304Ter,ENST00000356175,;NF1,upstream_gene_variant,,ENST00000456735,;NF1,stop_gained,p.Arg338Ter,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000487476,;	T	ENSG00000196712	ENST00000358273	Transcript	stop_gained	1293	910	304	R/*	Cga/Tga	CM087437,CS983483,COSM24486,COSM1666613	.	.	1	NF1	HGNC	7765	protein_coding	YES	CCDS42292.1	ENSP00000351015	NF1_HUMAN	Q9UMU3_HUMAN,Q4W6X4_HUMAN,K7EP94_HUMAN	UPI000012FFAE	.	.	.	9/58	.	hmmpanther:PTHR10194:SF60,hmmpanther:PTHR10194	.	.	.	.	.	.	.	.	.	.	0,0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R304*|c.910C>T|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTACGAAAA	.	5	ESCA
RFFL	0	.	GRCh37	17	33336237	33336237	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2750T>G	.	.	ENST00000315249	7/7	15	12	3	26	26	0	RFFL,3_prime_UTR_variant,,ENST00000315249,;RFFL,3_prime_UTR_variant,,ENST00000394597,;RFFL,3_prime_UTR_variant,,ENST00000378516,;RFFL,3_prime_UTR_variant,,ENST00000268850,;RFFL,3_prime_UTR_variant,,ENST00000584655,;RFFL,downstream_gene_variant,,ENST00000581039,;RFFL,downstream_gene_variant,,ENST00000413582,;RFFL,downstream_gene_variant,,ENST00000415395,;LIG3,downstream_gene_variant,,ENST00000378526,;RFFL,downstream_gene_variant,,ENST00000447669,;RAD51L3-RFFL,downstream_gene_variant,,ENST00000593039,;RP5-837J1.2,non_coding_transcript_exon_variant,,ENST00000578488,;RP5-837J1.2,downstream_gene_variant,,ENST00000415412,;RFFL,upstream_gene_variant,,ENST00000580569,;RFFL,downstream_gene_variant,,ENST00000584541,;LIG3,downstream_gene_variant,,ENST00000592244,;LIG3,downstream_gene_variant,,ENST00000593099,;	C	ENSG00000092871	ENST00000315249	Transcript	3_prime_UTR_variant	4065	.	.	.	.	.	.	.	-1	RFFL	HGNC	24821	protein_coding	YES	CCDS11286.1	ENSP00000326170	RFFL_HUMAN	J3QR17_HUMAN,C9JE27_HUMAN	UPI000006D6B9	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTTAATAAA	.	2	ESCA
MAP3K14-AS1	0	.	GRCh37	17	43344565	43344565	+	RNA	SNP	T	T	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1701T>A	.	.	ENST00000585780	2/3	80	29	51	77	77	0	MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000590100,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000591263,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000585351,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000586450,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000588504,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000588160,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000585346,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000592422,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000588698,;MAP3K14-AS1,non_coding_transcript_exon_variant,,ENST00000585780,;MAP3K14,splice_region_variant,,ENST00000587332,;MAP3K14,splice_region_variant,,ENST00000344686,;MAP3K14,downstream_gene_variant,,ENST00000376926,;MAP3K14,splice_region_variant,,ENST00000592267,;MAP3K14,downstream_gene_variant,,ENST00000586644,;	A	ENSG00000267278	ENST00000585780	Transcript	non_coding_transcript_exon_variant	1701	.	.	.	.	.	.	.	1	MAP3K14-AS1	HGNC	44359	antisense	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAATTCTGCA	.	5	ESCA
NLRP1	0	.	GRCh37	17	5433952	5433952	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3369G>A	p.%3D	p.V1123V	ENST00000572272	12/17	32	28	4	26	26	0	NLRP1,synonymous_variant,p.%3D,ENST00000572272,;NLRP1,synonymous_variant,p.%3D,ENST00000345221,;NLRP1,synonymous_variant,p.%3D,ENST00000269280,;NLRP1,synonymous_variant,p.%3D,ENST00000354411,;NLRP1,synonymous_variant,p.%3D,ENST00000577119,;NLRP1,synonymous_variant,p.%3D,ENST00000262467,;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,synonymous_variant,p.%3D,ENST00000544378,;NLRP1,3_prime_UTR_variant,,ENST00000571451,;	T	ENSG00000091592	ENST00000572272	Transcript	synonymous_variant	3369	3369	1123	V	gtG/gtA	.	.	.	-1	NLRP1	HGNC	14374	protein_coding	YES	CCDS42246.1	ENSP00000460475	NALP1_HUMAN	I3L2G5_HUMAN,I3L0S2_HUMAN	UPI0000038309	.	.	.	12/17	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF13,Pfam_domain:PF13553	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGGTCACCGC	.	2	ESCA
EPX	0	.	GRCh37	17	56271143	56271143	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415G>A	p.Glu139Lys	p.E139K	ENST00000225371	4/13	55	37	17	37	37	0	EPX,missense_variant,p.Glu139Lys,ENST00000225371,;	A	ENSG00000121053	ENST00000225371	Transcript	missense_variant	525	415	139	E/K	Gag/Aag	COSM170334	.	.	1	EPX	HGNC	3423	protein_coding	YES	CCDS11602.1	ENSP00000225371	PERE_HUMAN	.	UPI0000131629	.	tolerated(0.62)	benign(0.069)	4/13	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF49	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCGAGCGC	.	5	ESCA
BRIP1	0	.	GRCh37	17	59938866	59938866	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35G>A	p.Gly12Glu	p.G12E	ENST00000259008	2/20	31	15	16	21	21	0	BRIP1,missense_variant,p.Gly12Glu,ENST00000577913,;BRIP1,missense_variant,p.Gly12Glu,ENST00000259008,;BRIP1,missense_variant,p.Gly12Glu,ENST00000577598,;INTS2,downstream_gene_variant,,ENST00000444766,;	T	ENSG00000136492	ENST00000259008	Transcript	missense_variant	303	35	12	G/E	gGg/gAg	.	.	.	-1	BRIP1	HGNC	20473	protein_coding	YES	CCDS11631.1	ENSP00000259008	FANCJ_HUMAN	J3KS24_HUMAN	UPI000013D01F	.	deleterious(0)	probably_damaging(1)	2/20	.	PROSITE_profiles:PS51193,hmmpanther:PTHR11472:SF6,hmmpanther:PTHR11472,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCCCACCA	.	5	ESCA
KCNJ16	0	.	GRCh37	17	68130729	68130729	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1244G>C	.	.	ENST00000392670	4/4	65	35	29	55	55	0	KCNJ16,3_prime_UTR_variant,,ENST00000283936,;KCNJ16,3_prime_UTR_variant,,ENST00000589377,;KCNJ16,3_prime_UTR_variant,,ENST00000392671,;KCNJ16,3_prime_UTR_variant,,ENST00000585558,;KCNJ16,3_prime_UTR_variant,,ENST00000392670,;KCNJ16,downstream_gene_variant,,ENST00000587698,;KCNJ16,downstream_gene_variant,,ENST00000586462,;KCNJ16,downstream_gene_variant,,ENST00000591891,;KCNJ16,downstream_gene_variant,,ENST00000587892,;	C	ENSG00000153822	ENST00000392670	Transcript	3_prime_UTR_variant	2994	.	.	.	.	.	.	.	1	KCNJ16	HGNC	6262	protein_coding	YES	CCDS11687.1	ENSP00000376438	IRK16_HUMAN	K7ELL5_HUMAN,K7EKJ4_HUMAN	UPI000012D8B3	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATGATTAC	.	5	ESCA
KCNJ2	0	.	GRCh37	17	68174799	68174799	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2335G>C	.	.	ENST00000243457	2/2	31	12	19	15	15	0	KCNJ2,3_prime_UTR_variant,,ENST00000243457,;KCNJ2,downstream_gene_variant,,ENST00000535240,;	C	ENSG00000123700	ENST00000243457	Transcript	3_prime_UTR_variant	4002	.	.	.	.	.	.	.	1	KCNJ2	HGNC	6263	protein_coding	YES	CCDS11688.1	ENSP00000243457	IRK2_HUMAN	.	UPI000004F21A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTATGGGGGG	.	5	ESCA
TP53	0	.	GRCh37	17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	rs121912666	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	6/11	47	24	22	57	57	0	TP53,missense_variant,p.Tyr220Cys,ENST00000413465,;TP53,missense_variant,p.Tyr220Cys,ENST00000420246,;TP53,missense_variant,p.Tyr220Cys,ENST00000269305,;TP53,missense_variant,p.Tyr88Cys,ENST00000509690,;TP53,missense_variant,p.Tyr220Cys,ENST00000359597,;TP53,missense_variant,p.Tyr127Cys,ENST00000514944,;TP53,missense_variant,p.Tyr220Cys,ENST00000445888,;TP53,missense_variant,p.Tyr220Cys,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	849	659	220	Y/C	tAt/tGt	CM015378,CM951227,rs121912666,TP53_g.12728A>T,TP53_g.12728A>C,TP53_g.12728A>G,COSM10758,COSM43850,COSM1564197,COSM99720,COSM251427,COSM1564198,COSM251426,COSM99718,COSM1564199,COSM3355993,COSM3675523,COSM1644277,COSM3675522,COSM99719,COSM251428,COSM1564200	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Y220C|c.659A>G|264,SITE|p.Y220C|c.659A>G|63,SITE|p.Y127C|c.380A>G|63,SITE|p.Y220C|c.659A>G|25,SITE|p.Y220C|c.659A>G|61,SITE|p.Y220C|c.659A>G|33,CODON|p.0?|c.1_1182del1182|6,CODON|p.Y220*|c.660T>G|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y127S|c.380A>C|4,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y220S|c.659A>C|13,BUFFER|p.E224K|c.670G>A|4,BUFFER|p.E224*|c.670G>T|5,BUFFER|p.P223L|c.668C>T|3,BUFFER|p.P222P|c.666G>C|3,BUFFER|p.P222L|c.665C>T|4,BUFFER|p.P222T|c.664C>A|3,BUFFER|p.E221G|c.662A>G|3,BUFFER|p.E221fs*4|c.660_661insN|3,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E128*|c.382G>T|6,BUFFER|p.E221*|c.661G>T|10,BUFFER|p.?|c.252+10T>A|3,BUFFER|p.Y220N|c.658T>A|16,BUFFER|p.?|c.252+10T>C|4,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220H|c.658T>C|13,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.Y127H|c.379T>C|4,BUFFER|p.Y127N|c.379T>A|3,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.P219P|c.657C>T|3,BUFFER|p.Y220fs*27|c.655delC|4,BUFFER|p.V218delV|c.652_654delGTG|3,BUFFER|p.P219S|c.655C>T|4,BUFFER|p.V218G|c.653T>G|6,BUFFER|p.V218A|c.653T>C|3,BUFFER|p.V218E|c.653T>A|8,BUFFER|p.V218M|c.652G>A|7,BUFFER|p.V217A|c.650T>C|5,BUFFER|p.V217G|c.650T>G|4,BUFFER|p.V217E|c.650T>A|3,BUFFER|p.V218delV|c.646_648delGTG|8	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCATAGGGC	byFrequency|byCluster	5	ESCA
DNAH17	0	.	GRCh37	17	76525741	76525741	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3320G>C	p.Arg1107Thr	p.R1107T	ENST00000389840	22/81	107	81	26	77	77	0	DNAH17,missense_variant,p.Arg1104Thr,ENST00000585328,;DNAH17,missense_variant,p.Arg1107Thr,ENST00000389840,;RN7SL454P,downstream_gene_variant,,ENST00000492744,;	G	ENSG00000187775	ENST00000389840	Transcript	missense_variant	3445	3320	1107	R/T	aGa/aCa	.	.	.	-1	DNAH17	HGNC	2946	protein_coding	YES	.	ENSP00000374490	DYH17_HUMAN	.	UPI0001A5EE11	.	.	benign(0.005)	22/81	.	hmmpanther:PTHR10676:SF228,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTCTGGCG	.	5	ESCA
BAIAP2	0	.	GRCh37	17	79005303	79005303	+	5'Flank	SNP	T	T	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000321300	.	34	14	19	35	35	0	BAIAP2,upstream_gene_variant,,ENST00000428708,;BAIAP2,upstream_gene_variant,,ENST00000435091,;BAIAP2,upstream_gene_variant,,ENST00000571530,;BAIAP2,upstream_gene_variant,,ENST00000321300,;BAIAP2,upstream_gene_variant,,ENST00000575245,;BAIAP2,upstream_gene_variant,,ENST00000575712,;BAIAP2,upstream_gene_variant,,ENST00000575989,;BAIAP2,upstream_gene_variant,,ENST00000392411,;BAIAP2,upstream_gene_variant,,ENST00000321280,;BAIAP2-AS1,non_coding_transcript_exon_variant,,ENST00000573167,;BAIAP2-AS1,non_coding_transcript_exon_variant,,ENST00000542745,;BAIAP2-AS1,non_coding_transcript_exon_variant,,ENST00000577066,;BAIAP2,upstream_gene_variant,,ENST00000573894,;BAIAP2,upstream_gene_variant,,ENST00000570913,;BAIAP2,upstream_gene_variant,,ENST00000575750,;BAIAP2,upstream_gene_variant,,ENST00000572329,;BAIAP2,upstream_gene_variant,,ENST00000576470,;	A	ENSG00000175866	ENST00000321300	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3659	1	BAIAP2	HGNC	947	protein_coding	YES	CCDS11775.1	ENSP00000316338	BAIP2_HUMAN	I3L526_HUMAN,I3L327_HUMAN,I3L2M4_HUMAN,I3L1C8_HUMAN,I3L125_HUMAN,I3L113_HUMAN,I3L0Y9_HUMAN,I3L0M4_HUMAN	UPI000000D762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCTACTCT	.	5	ESCA
GUCY2D	0	.	GRCh37	17	7910834	7910834	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1554C>T	p.%3D	p.G518G	ENST00000254854	6/20	20	9	10	27	27	0	GUCY2D,synonymous_variant,p.%3D,ENST00000254854,;	T	ENSG00000132518	ENST00000254854	Transcript	synonymous_variant	1704	1554	518	G	ggC/ggT	.	.	.	1	GUCY2D	HGNC	4689	protein_coding	YES	CCDS11127.1	ENSP00000254854	GUC2D_HUMAN	.	UPI0000128C1C	.	.	.	6/20	.	hmmpanther:PTHR11920:SF228,hmmpanther:PTHR11920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGCACCTC	.	5	ESCA
NARF	0	.	GRCh37	17	80442792	80442792	+	Missense_Mutation	SNP	G	G	A	rs753702239	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937G>A	p.Glu313Lys	p.E313K	ENST00000309794	9/11	193	175	17	142	142	0	NARF,missense_variant,p.Glu359Lys,ENST00000457415,;NARF,missense_variant,p.Glu254Lys,ENST00000390006,;NARF,missense_variant,p.Glu313Lys,ENST00000309794,;NARF,missense_variant,p.Glu265Lys,ENST00000345415,;NARF,intron_variant,,ENST00000584513,;NARF,downstream_gene_variant,,ENST00000577410,;NARF,downstream_gene_variant,,ENST00000577432,;NARF,downstream_gene_variant,,ENST00000412079,;NARF-IT1,downstream_gene_variant,,ENST00000584012,;NARF,downstream_gene_variant,,ENST00000581743,;NARF,3_prime_UTR_variant,,ENST00000374611,;NARF,3_prime_UTR_variant,,ENST00000582907,;NARF,non_coding_transcript_exon_variant,,ENST00000583908,;NARF,non_coding_transcript_exon_variant,,ENST00000577812,;NARF,non_coding_transcript_exon_variant,,ENST00000578820,;NARF,non_coding_transcript_exon_variant,,ENST00000584445,;NARF,intron_variant,,ENST00000584965,;NARF,downstream_gene_variant,,ENST00000581202,;NARF,downstream_gene_variant,,ENST00000581795,;	A	ENSG00000141562	ENST00000309794	Transcript	missense_variant	1135	937	313	E/K	Gag/Aag	rs753702239	.	.	1	NARF	HGNC	29916	protein_coding	YES	CCDS32777.1	ENSP00000309899	NARF_HUMAN	J3QSD9_HUMAN,J3QRB0_HUMAN,J3QL28_HUMAN,J3KS03_HUMAN,B5KGZ1_HUMAN	UPI0000073D0C	.	tolerated(0.89)	benign(0.086)	9/11	.	Superfamily_domains:SSF53920,Pfam_domain:PF02906,hmmpanther:PTHR11615:SF124,hmmpanther:PTHR11615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAACGAGGAT	.	2	ESCA
NARF	0	.	GRCh37	17	80442801	80442801	+	Missense_Mutation	SNP	G	G	A	rs754722531	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.946G>A	p.Glu316Lys	p.E316K	ENST00000309794	9/11	196	179	17	148	148	0	NARF,missense_variant,p.Glu362Lys,ENST00000457415,;NARF,missense_variant,p.Glu257Lys,ENST00000390006,;NARF,missense_variant,p.Glu316Lys,ENST00000309794,;NARF,missense_variant,p.Glu268Lys,ENST00000345415,;NARF,intron_variant,,ENST00000584513,;NARF,downstream_gene_variant,,ENST00000577410,;NARF,downstream_gene_variant,,ENST00000577432,;NARF,downstream_gene_variant,,ENST00000412079,;NARF-IT1,downstream_gene_variant,,ENST00000584012,;NARF,downstream_gene_variant,,ENST00000581743,;NARF,3_prime_UTR_variant,,ENST00000374611,;NARF,3_prime_UTR_variant,,ENST00000582907,;NARF,non_coding_transcript_exon_variant,,ENST00000583908,;NARF,non_coding_transcript_exon_variant,,ENST00000577812,;NARF,non_coding_transcript_exon_variant,,ENST00000578820,;NARF,non_coding_transcript_exon_variant,,ENST00000584445,;NARF,intron_variant,,ENST00000584965,;NARF,downstream_gene_variant,,ENST00000581202,;NARF,downstream_gene_variant,,ENST00000581795,;	A	ENSG00000141562	ENST00000309794	Transcript	missense_variant	1144	946	316	E/K	Gag/Aag	rs754722531	.	.	1	NARF	HGNC	29916	protein_coding	YES	CCDS32777.1	ENSP00000309899	NARF_HUMAN	J3QSD9_HUMAN,J3QRB0_HUMAN,J3QL28_HUMAN,J3KS03_HUMAN,B5KGZ1_HUMAN	UPI0000073D0C	.	tolerated(0.68)	benign(0.013)	9/11	.	Superfamily_domains:SSF53920,Pfam_domain:PF02906,hmmpanther:PTHR11615:SF124,hmmpanther:PTHR11615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTGGAGGAG	.	2	ESCA
PER1	0	.	GRCh37	17	8045267	8045267	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3456G>A	p.Met1152Ile	p.M1152I	ENST00000317276	22/23	97	66	31	120	120	0	PER1,missense_variant,p.Met1152Ile,ENST00000317276,;PER1,missense_variant,p.Met1129Ile,ENST00000581082,;PER1,downstream_gene_variant,,ENST00000354903,;PER1,downstream_gene_variant,,ENST00000583559,;PER1,downstream_gene_variant,,ENST00000578089,;PER1,3_prime_UTR_variant,,ENST00000582719,;PER1,non_coding_transcript_exon_variant,,ENST00000583677,;PER1,non_coding_transcript_exon_variant,,ENST00000585284,;PER1,downstream_gene_variant,,ENST00000581395,;PER1,downstream_gene_variant,,ENST00000577424,;PER1,downstream_gene_variant,,ENST00000585095,;PER1,downstream_gene_variant,,ENST00000578950,;PER1,downstream_gene_variant,,ENST00000579098,;	T	ENSG00000179094	ENST00000317276	Transcript	missense_variant	3694	3456	1152	M/I	atG/atA	.	.	.	-1	PER1	HGNC	8845	protein_coding	YES	CCDS11131.1	ENSP00000314420	PER1_HUMAN	J3QLQ5_HUMAN,A2I2P6_HUMAN	UPI000013FFF5	.	tolerated(0.71)	benign(0.006)	22/23	.	hmmpanther:PTHR11269,hmmpanther:PTHR11269:SF8,Pfam_domain:PF12114,Gene3D:3.30.450.20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGTCATGTC	.	5	ESCA
TBCD	0	.	GRCh37	17	80879433	80879433	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2158C>T	p.His720Tyr	p.H720Y	ENST00000355528	25/39	86	74	12	53	53	0	TBCD,missense_variant,p.His112Tyr,ENST00000571712,;TBCD,missense_variant,p.His720Tyr,ENST00000539345,;TBCD,missense_variant,p.His720Tyr,ENST00000355528,;TBCD,missense_variant,p.His158Tyr,ENST00000576760,;TBCD,missense_variant,p.His206Tyr,ENST00000572953,;TBCD,missense_variant,p.His158Tyr,ENST00000574422,;TBCD,missense_variant,p.His179Tyr,ENST00000574975,;TBCD,downstream_gene_variant,,ENST00000576996,;TBCD,downstream_gene_variant,,ENST00000576160,;RP11-497H17.1,downstream_gene_variant,,ENST00000571113,;TBCD,non_coding_transcript_exon_variant,,ENST00000571618,;TBCD,non_coding_transcript_exon_variant,,ENST00000574886,;TBCD,non_coding_transcript_exon_variant,,ENST00000574818,;TBCD,non_coding_transcript_exon_variant,,ENST00000571796,;	T	ENSG00000141556	ENST00000355528	Transcript	missense_variant	2288	2158	720	H/Y	Cac/Tac	.	.	.	1	TBCD	HGNC	11581	protein_coding	YES	CCDS45818.1	ENSP00000347719	TBCD_HUMAN	I3L4D2_HUMAN,I3L439_HUMAN,I3L3H4_HUMAN,I3L1S3_HUMAN,I3L163_HUMAN,I3L131_HUMAN	UPI000020053F	.	tolerated(0.57)	benign(0.308)	25/39	.	hmmpanther:PTHR12658,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAGTCACTCC	.	4	ESCA
INO80C	0	.	GRCh37	18	33048694	33048694	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.568G>A	p.Asp190Asn	p.D190N	ENST00000441607	7/7	51	46	5	54	54	0	INO80C,missense_variant,p.Asp131Asn,ENST00000591139,;INO80C,missense_variant,p.Asp154Asn,ENST00000334598,;INO80C,missense_variant,p.Asp190Asn,ENST00000441607,;INO80C,missense_variant,p.Asp99Asn,ENST00000586489,;INO80C,missense_variant,p.Asp57Asn,ENST00000590757,;INO80C,synonymous_variant,p.%3D,ENST00000587450,;RP11-322E11.6,intron_variant,,ENST00000589258,;INO80C,intron_variant,,ENST00000592173,;RP11-322E11.5,upstream_gene_variant,,ENST00000593122,;RP11-322E11.5,upstream_gene_variant,,ENST00000591141,;RP11-322E11.5,upstream_gene_variant,,ENST00000586741,;	T	ENSG00000153391	ENST00000441607	Transcript	missense_variant	637	568	190	D/N	Gac/Aac	.	.	.	-1	INO80C	HGNC	26994	protein_coding	YES	CCDS45853.1	ENSP00000391457	IN80C_HUMAN	K7EIY8_HUMAN,K7EKI6_HUMAN	UPI0000201BD0	.	deleterious(0.02)	probably_damaging(0.997)	7/7	.	hmmpanther:PTHR31200,hmmpanther:PTHR31200:SF1,Pfam_domain:PF08265,SMART_domains:SM00993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGGTCTGTGT	.	3	ESCA
RPRD1A	0	.	GRCh37	18	33606966	33606966	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686G>A	p.Arg229Lys	p.R229K	ENST00000399022	6/7	44	37	6	33	33	0	RPRD1A,missense_variant,p.Arg193Lys,ENST00000588737,;RPRD1A,missense_variant,p.Arg82Lys,ENST00000585953,;RPRD1A,missense_variant,p.Arg193Lys,ENST00000337059,;RPRD1A,missense_variant,p.Arg193Lys,ENST00000590898,;RPRD1A,missense_variant,p.Arg229Lys,ENST00000357384,;RPRD1A,missense_variant,p.Arg229Lys,ENST00000319040,;RPRD1A,missense_variant,p.Arg229Lys,ENST00000399022,;RPRD1A,missense_variant,p.Arg229Lys,ENST00000589050,;RPRD1A,non_coding_transcript_exon_variant,,ENST00000591994,;	T	ENSG00000141425	ENST00000399022	Transcript	missense_variant	858	686	229	R/K	aGa/aAa	.	.	.	-1	RPRD1A	HGNC	25560	protein_coding	YES	CCDS11917.1	ENSP00000381984	RPR1A_HUMAN	K7ER50_HUMAN	UPI0000036029	.	deleterious(0.03)	benign(0.391)	6/7	.	hmmpanther:PTHR12460,hmmpanther:PTHR12460:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAATCTGCCA	.	4	ESCA
ZBTB14	0	.	GRCh37	18	5291265	5291265	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.942C>T	p.%3D	p.F314F	ENST00000357006	4/4	101	88	13	94	94	0	ZBTB14,synonymous_variant,p.%3D,ENST00000357006,;ZBTB14,synonymous_variant,p.%3D,ENST00000400143,;ZBTB14,downstream_gene_variant,,ENST00000582135,;ZBTB14,downstream_gene_variant,,ENST00000582388,;ZBTB14,downstream_gene_variant,,ENST00000578327,;ZBTB14,downstream_gene_variant,,ENST00000585253,;	A	ENSG00000198081	ENST00000357006	Transcript	synonymous_variant	1281	942	314	F	ttC/ttT	COSM4072619	.	.	-1	ZBTB14	HGNC	12860	protein_coding	YES	CCDS11837.1	ENSP00000349503	ZBT14_HUMAN	J3QLI2_HUMAN,J3QL74_HUMAN,J3KRQ2_HUMAN	UPI0000163BCB	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF47,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGTGAAACC	.	4	ESCA
WDR7	0	.	GRCh37	18	54363617	54363617	+	Missense_Mutation	SNP	C	C	G	rs150975555	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1502C>G	p.Ser501Cys	p.S501C	ENST00000254442	12/28	78	38	39	61	61	0	WDR7,missense_variant,p.Ser501Cys,ENST00000254442,;WDR7,missense_variant,p.Ser501Cys,ENST00000357574,;WDR7,intron_variant,,ENST00000589935,;WDR7,non_coding_transcript_exon_variant,,ENST00000585754,;	G	ENSG00000091157	ENST00000254442	Transcript	missense_variant	1713	1502	501	S/C	tCt/tGt	rs150975555	.	.	1	WDR7	HGNC	13490	protein_coding	YES	CCDS11962.1	ENSP00000254442	WDR7_HUMAN	K7ERP9_HUMAN,K7EPQ4_HUMAN,K7EMB8_HUMAN,K7ELZ4_HUMAN	UPI000013CE33	.	deleterious(0)	possibly_damaging(0.711)	12/28	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF48,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTCTGGAG	byCluster	5	ESCA
PHLPP1	0	.	GRCh37	18	60646373	60646373	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4863G>T	p.%3D	p.R1621R	ENST00000262719	17/17	22	12	10	29	29	0	PHLPP1,synonymous_variant,p.%3D,ENST00000400316,;PHLPP1,synonymous_variant,p.%3D,ENST00000262719,;	T	ENSG00000081913	ENST00000262719	Transcript	synonymous_variant	5097	4863	1621	R	cgG/cgT	.	.	.	1	PHLPP1	HGNC	20610	protein_coding	YES	CCDS45881.2	ENSP00000262719	PHLP1_HUMAN	.	UPI000051AE2E	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCGGAGGGC	.	5	ESCA
DSEL	0	.	GRCh37	18	65180716	65180716	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1160C>T	p.Ser387Leu	p.S387L	ENST00000310045	2/2	62	53	9	75	75	0	DSEL,missense_variant,p.Ser387Leu,ENST00000310045,;RP11-638L3.1,upstream_gene_variant,,ENST00000583687,;CTD-2541J13.2,non_coding_transcript_exon_variant,,ENST00000583493,;CTD-2541J13.2,downstream_gene_variant,,ENST00000581951,;	A	ENSG00000171451	ENST00000310045	Transcript	missense_variant	2634	1160	387	S/L	tCa/tTa	.	.	.	-1	DSEL	HGNC	18144	protein_coding	YES	CCDS11995.1	ENSP00000310565	DSEL_HUMAN	.	UPI00000740A1	.	deleterious(0)	probably_damaging(0.999)	2/2	.	hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTGAAGGA	.	5	ESCA
TMX3	0	.	GRCh37	18	66381131	66381133	+	In_Frame_Del	DEL	ACA	ACA	-	rs769980242	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	ACA	ACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51_53delTGT	p.Val18del	p.V18del	ENST00000299608	2/16	32	13	19	41	41	0	TMX3,inframe_deletion,p.Val18del,ENST00000443099,;TMX3,inframe_deletion,p.Val18del,ENST00000544714,;TMX3,inframe_deletion,p.Val18del,ENST00000562706,;TMX3,inframe_deletion,p.Val18del,ENST00000299608,;CCDC102B,upstream_gene_variant,,ENST00000584775,;CCDC102B,upstream_gene_variant,,ENST00000578970,;CCDC102B,upstream_gene_variant,,ENST00000582371,;CCDC102B,upstream_gene_variant,,ENST00000582077,;TMX3,inframe_deletion,p.Val18del,ENST00000564008,;TMX3,inframe_deletion,p.Val18del,ENST00000569053,;TMX3,inframe_deletion,p.Val18del,ENST00000564631,;TMX3,inframe_deletion,p.Val18del,ENST00000565918,;TMX3,5_prime_UTR_variant,,ENST00000569982,;CCDC102B,upstream_gene_variant,,ENST00000580292,;	-	ENSG00000166479	ENST00000299608	Transcript	inframe_deletion	368-370	51-53	17-18	VV/V	gtTGTa/gta	rs769980242	.	.	-1	TMX3	HGNC	24718	protein_coding	YES	CCDS32840.1	ENSP00000299608	TMX3_HUMAN	.	UPI000004A093	.	.	.	2/16	.	Cleavage_site_(Signalp):SignalP-noTM,PROSITE_profiles:PS51352,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF62	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCAAGTACAACAAC	byFrequency	3	ESCA
ANGPTL6	0	.	GRCh37	19	10204497	10204497	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.823G>A	p.Glu275Lys	p.E275K	ENST00000253109	4/6	66	48	18	55	55	0	ANGPTL6,missense_variant,p.Glu275Lys,ENST00000253109,;ANGPTL6,missense_variant,p.Glu275Lys,ENST00000589181,;ANGPTL6,missense_variant,p.Glu275Lys,ENST00000592641,;C19orf66,downstream_gene_variant,,ENST00000593131,;C19orf66,downstream_gene_variant,,ENST00000591813,;C19orf66,downstream_gene_variant,,ENST00000590378,;C19orf66,downstream_gene_variant,,ENST00000397881,;C19orf66,downstream_gene_variant,,ENST00000253110,;CTD-2240E14.4,upstream_gene_variant,,ENST00000589622,;ANGPTL6,downstream_gene_variant,,ENST00000586910,;C19orf66,downstream_gene_variant,,ENST00000586730,;C19orf66,downstream_gene_variant,,ENST00000585919,;C19orf66,downstream_gene_variant,,ENST00000587609,;C19orf66,downstream_gene_variant,,ENST00000586889,;C19orf66,downstream_gene_variant,,ENST00000587710,;	T	ENSG00000130812	ENST00000253109	Transcript	missense_variant	1062	823	275	E/K	Gaa/Aaa	.	.	.	-1	ANGPTL6	HGNC	23140	protein_coding	YES	CCDS12224.1	ENSP00000253109	ANGL6_HUMAN	.	UPI000004BA54	.	tolerated(0.26)	possibly_damaging(0.543)	4/6	.	PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF169,hmmpanther:PTHR19143,Gene3D:3.90.215.10,Pfam_domain:PF00147,SMART_domains:SM00186,Superfamily_domains:SSF56496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCATACA	.	5	ESCA
ICAM1	0	.	GRCh37	19	10395227	10395227	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1074G>A	p.%3D	p.L358L	ENST00000264832	5/7	21	17	4	31	31	0	ICAM1,synonymous_variant,p.%3D,ENST00000423829,;ICAM1,synonymous_variant,p.%3D,ENST00000264832,;ICAM1,downstream_gene_variant,,ENST00000588645,;ICAM4,upstream_gene_variant,,ENST00000393717,;ICAM4,upstream_gene_variant,,ENST00000380770,;ICAM4,upstream_gene_variant,,ENST00000340992,;CTD-2369P2.5,intron_variant,,ENST00000592893,;CTD-2369P2.8,downstream_gene_variant,,ENST00000589379,;ICAM1,downstream_gene_variant,,ENST00000585443,;ICAM1,downstream_gene_variant,,ENST00000592686,;	A	ENSG00000090339	ENST00000264832	Transcript	synonymous_variant	1399	1074	358	L	ctG/ctA	.	.	.	1	ICAM1	HGNC	5344	protein_coding	YES	CCDS12231.1	ENSP00000264832	ICAM1_HUMAN	B4DNT6_HUMAN	UPI000000D91C	.	.	.	5/7	.	hmmpanther:PTHR13771,hmmpanther:PTHR13771:SF5,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTGAAGGC	.	4	ESCA
RAVER1	0	.	GRCh37	19	10428108	10428108	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*22T>C	.	.	ENST00000293677	13/13	73	54	19	60	60	0	RAVER1,3_prime_UTR_variant,,ENST00000293677,;FDX1L,upstream_gene_variant,,ENST00000393708,;FDX1L,upstream_gene_variant,,ENST00000541276,;FDX1L,upstream_gene_variant,,ENST00000494368,;RAVER1,downstream_gene_variant,,ENST00000585935,;FDX1L,upstream_gene_variant,,ENST00000492239,;CTD-2369P2.12,3_prime_UTR_variant,,ENST00000586529,;RAVER1,non_coding_transcript_exon_variant,,ENST00000592208,;CTD-2369P2.10,upstream_gene_variant,,ENST00000452032,;FDX1L,upstream_gene_variant,,ENST00000453681,;FDX1L,upstream_gene_variant,,ENST00000486454,;FDX1L,upstream_gene_variant,,ENST00000460631,;RAVER1,downstream_gene_variant,,ENST00000593136,;FDX1L,upstream_gene_variant,,ENST00000343376,;CTD-2369P2.10,upstream_gene_variant,,ENST00000493771,;	G	ENSG00000161847	ENST00000293677	Transcript	3_prime_UTR_variant	2375	.	.	.	.	.	.	.	-1	RAVER1	HGNC	30296	protein_coding	YES	CCDS45960.1	ENSP00000293677	.	K7EQG2_HUMAN,E9PAU2_HUMAN	UPI0000E042A4	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGAGTTAT	.	5	ESCA
PDE4A	0	.	GRCh37	19	10579350	10579350	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000352831	.	43	33	9	46	46	0	PDE4A,3_prime_UTR_variant,,ENST00000380702,;PDE4A,downstream_gene_variant,,ENST00000293683,;PDE4A,downstream_gene_variant,,ENST00000592685,;PDE4A,downstream_gene_variant,,ENST00000352831,;PDE4A,downstream_gene_variant,,ENST00000440014,;PDE4A,downstream_gene_variant,,ENST00000344979,;PDE4A,downstream_gene_variant,,ENST00000589073,;PDE4A,downstream_gene_variant,,ENST00000590407,;	T	ENSG00000065989	ENST00000352831	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	181	1	PDE4A	HGNC	8780	protein_coding	YES	CCDS45961.1	ENSP00000270474	PDE4A_HUMAN	Q86V67_HUMAN	UPI0000047003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATCACAGC	.	5	ESCA
IER2	0	.	GRCh37	19	13264138	13264138	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138C>G	p.%3D	p.L46L	ENST00000588173	1/1	64	51	13	57	57	0	IER2,synonymous_variant,p.%3D,ENST00000587885,;IER2,synonymous_variant,p.%3D,ENST00000588173,;IER2,synonymous_variant,p.%3D,ENST00000292433,;STX10,upstream_gene_variant,,ENST00000587318,;STX10,upstream_gene_variant,,ENST00000587230,;STX10,upstream_gene_variant,,ENST00000588848,;STX10,upstream_gene_variant,,ENST00000593126,;STX10,upstream_gene_variant,,ENST00000589083,;STX10,upstream_gene_variant,,ENST00000242770,;STX10,upstream_gene_variant,,ENST00000343587,;STX10,upstream_gene_variant,,ENST00000591197,;CTC-250I14.6,non_coding_transcript_exon_variant,,ENST00000586483,;CTC-250I14.6,intron_variant,,ENST00000592882,;STX10,upstream_gene_variant,,ENST00000591843,;STX10,upstream_gene_variant,,ENST00000440593,;CTC-250I14.1,downstream_gene_variant,,ENST00000481802,;	G	ENSG00000160888	ENST00000588173	Transcript	synonymous_variant	1350	138	46	L	ctC/ctG	.	.	.	1	IER2	HGNC	28871	protein_coding	YES	CCDS12295.1	ENSP00000465617	IER2_HUMAN	.	UPI000006D032	.	.	.	1/1	.	hmmpanther:PTHR15895,hmmpanther:PTHR15895:SF4,Pfam_domain:PF05760	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTCTACCT	.	5	ESCA
PODNL1	0	.	GRCh37	19	14044798	14044798	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681C>T	p.%3D	p.L227L	ENST00000339560	7/8	46	35	11	44	44	0	PODNL1,missense_variant,p.His115Tyr,ENST00000585607,;PODNL1,synonymous_variant,p.%3D,ENST00000538517,;PODNL1,synonymous_variant,p.%3D,ENST00000588764,;PODNL1,synonymous_variant,p.%3D,ENST00000339560,;PODNL1,synonymous_variant,p.%3D,ENST00000586075,;PODNL1,synonymous_variant,p.%3D,ENST00000254320,;PODNL1,synonymous_variant,p.%3D,ENST00000591353,;PODNL1,synonymous_variant,p.%3D,ENST00000538371,;CC2D1A,downstream_gene_variant,,ENST00000589606,;CC2D1A,downstream_gene_variant,,ENST00000587508,;PODNL1,upstream_gene_variant,,ENST00000587954,;PODNL1,downstream_gene_variant,,ENST00000587458,;CC2D1A,downstream_gene_variant,,ENST00000318003,;PODNL1,upstream_gene_variant,,ENST00000588872,;PODNL1,non_coding_transcript_exon_variant,,ENST00000587288,;CC2D1A,downstream_gene_variant,,ENST00000586955,;CC2D1A,downstream_gene_variant,,ENST00000589138,;	A	ENSG00000132000	ENST00000339560	Transcript	synonymous_variant	955	681	227	L	ctC/ctT	.	.	.	-1	PODNL1	HGNC	26275	protein_coding	YES	CCDS12300.1	ENSP00000345175	PONL1_HUMAN	.	UPI0000366D47	.	.	.	7/8	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24369:SF59,hmmpanther:PTHR24369,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGATGAGATT	.	5	ESCA
TECR	0	.	GRCh37	19	14675792	14675792	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>T	p.%3D	p.L198L	ENST00000215567	9/13	45	35	10	61	61	0	TECR,synonymous_variant,p.%3D,ENST00000596073,;TECR,synonymous_variant,p.%3D,ENST00000594545,;TECR,synonymous_variant,p.%3D,ENST00000436007,;TECR,synonymous_variant,p.%3D,ENST00000600083,;TECR,synonymous_variant,p.%3D,ENST00000215567,;TECR,synonymous_variant,p.%3D,ENST00000598298,;TECR,intron_variant,,ENST00000601187,;NDUFB7,downstream_gene_variant,,ENST00000215565,;TECR,downstream_gene_variant,,ENST00000598715,;TECR,downstream_gene_variant,,ENST00000596164,;TECR,3_prime_UTR_variant,,ENST00000598333,;TECR,3_prime_UTR_variant,,ENST00000598987,;TECR,non_coding_transcript_exon_variant,,ENST00000601461,;TECR,non_coding_transcript_exon_variant,,ENST00000594958,;TECR,non_coding_transcript_exon_variant,,ENST00000598408,;TECR,non_coding_transcript_exon_variant,,ENST00000600395,;TECR,non_coding_transcript_exon_variant,,ENST00000599101,;TECR,non_coding_transcript_exon_variant,,ENST00000593637,;TECR,non_coding_transcript_exon_variant,,ENST00000601350,;TECR,non_coding_transcript_exon_variant,,ENST00000593775,;TECR,non_coding_transcript_exon_variant,,ENST00000597607,;TECR,non_coding_transcript_exon_variant,,ENST00000596953,;TECR,downstream_gene_variant,,ENST00000598918,;TECR,downstream_gene_variant,,ENST00000600076,;TECR,downstream_gene_variant,,ENST00000601652,;NDUFB7,downstream_gene_variant,,ENST00000593353,;TECR,downstream_gene_variant,,ENST00000594807,;	T	ENSG00000099797	ENST00000215567	Transcript	synonymous_variant	731	594	198	L	ctC/ctT	.	.	.	1	TECR	HGNC	4551	protein_coding	YES	CCDS12313.1	ENSP00000215567	TECR_HUMAN	M0R0N5_HUMAN,M0QXS1_HUMAN,B4DR74_HUMAN	UPI00000534C6	.	.	.	9/13	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50244,hmmpanther:PTHR10556:SF31,hmmpanther:PTHR10556,Pfam_domain:PF02544	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCTCGCCAT	.	5	ESCA
TPM4	0	.	GRCh37	19	16178531	16178531	+	Missense_Mutation	SNP	G	G	A	rs368923322	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>A	p.Glu33Lys	p.E33K	ENST00000538887	1/10	56	50	6	39	39	0	TPM4,missense_variant,p.Glu33Lys,ENST00000538887,;TPM4,missense_variant,p.Glu33Lys,ENST00000344824,;TPM4,missense_variant,p.Glu33Lys,ENST00000589897,;TPM4,5_prime_UTR_variant,,ENST00000586499,;CTD-2231E14.4,downstream_gene_variant,,ENST00000585520,;	A	ENSG00000167460	ENST00000538887	Transcript	missense_variant	184	97	33	E/K	Gag/Aag	rs368923322	.	.	1	TPM4	HGNC	12013	protein_coding	YES	CCDS46007.1	ENSP00000439135	TPM4_HUMAN	K7EPV9_HUMAN,K7EMU5_HUMAN,K7ELP0_HUMAN	UPI000002B5B9	.	deleterious(0.04)	possibly_damaging(0.847)	1/10	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19269:SF40,hmmpanther:PTHR19269,Gene3D:1.20.5.340,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCTGAGGAC	byCluster	4	ESCA
PDE4C	0	.	GRCh37	19	18324249	18324249	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1537A>G	p.Thr513Ala	p.T513A	ENST00000355502	17/19	90	85	5	97	97	0	PDE4C,missense_variant,p.Thr283Ala,ENST00000597297,;PDE4C,missense_variant,p.Thr513Ala,ENST00000594465,;PDE4C,missense_variant,p.Thr513Ala,ENST00000594617,;PDE4C,missense_variant,p.Thr481Ala,ENST00000262805,;PDE4C,missense_variant,p.Thr407Ala,ENST00000447275,;PDE4C,missense_variant,p.Thr228Ala,ENST00000598111,;PDE4C,missense_variant,p.Thr513Ala,ENST00000355502,;PDE4C,missense_variant,p.Thr282Ala,ENST00000539010,;AC068499.10,intron_variant,,ENST00000594805,;AC068499.10,downstream_gene_variant,,ENST00000599416,;PDE4C,3_prime_UTR_variant,,ENST00000599188,;PDE4C,non_coding_transcript_exon_variant,,ENST00000597360,;	C	ENSG00000105650	ENST00000355502	Transcript	missense_variant	2409	1537	513	T/A	Acc/Gcc	.	.	.	-1	PDE4C	HGNC	8782	protein_coding	YES	CCDS12373.1	ENSP00000347689	PDE4C_HUMAN	Q9UPJ5_HUMAN,Q9P1U3_HUMAN,Q32MM7_HUMAN,O76105_HUMAN,M0R1P5_HUMAN,B7Z2S3_HUMAN	UPI0000127BF8	.	deleterious(0)	probably_damaging(0.989)	17/19	.	hmmpanther:PTHR11347:SF94,hmmpanther:PTHR11347,Pfam_domain:PF00233,Gene3D:1.10.1300.10,SMART_domains:SM00471,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATGGTCTTGA	.	2	ESCA
KLHL26	0	.	GRCh37	19	18775188	18775188	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201G>C	p.%3D	p.L67L	ENST00000300976	2/3	37	27	9	37	37	0	KLHL26,synonymous_variant,p.%3D,ENST00000595182,;KLHL26,synonymous_variant,p.%3D,ENST00000300976,;KLHL26,synonymous_variant,p.%3D,ENST00000599006,;KLHL26,synonymous_variant,p.%3D,ENST00000595423,;KLHL26,non_coding_transcript_exon_variant,,ENST00000596843,;KLHL26,3_prime_UTR_variant,,ENST00000600657,;	C	ENSG00000167487	ENST00000300976	Transcript	synonymous_variant	291	201	67	L	ctG/ctC	.	.	.	1	KLHL26	HGNC	25623	protein_coding	YES	CCDS12384.1	ENSP00000300976	KLH26_HUMAN	.	UPI0000071AC2	.	.	.	2/3	.	PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF56,hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,PIRSF_domain:PIRSF037037,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTGACTAT	.	5	ESCA
ZNF101	0	.	GRCh37	19	19790859	19790859	+	Missense_Mutation	SNP	G	G	A	rs758983961	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000592502	4/4	40	33	7	31	31	0	ZNF101,missense_variant,p.Arg234Gln,ENST00000415784,;ZNF101,missense_variant,p.Arg354Gln,ENST00000592502,;ZNF101,downstream_gene_variant,,ENST00000541458,;ZNF101,downstream_gene_variant,,ENST00000444249,;ZNF101,upstream_gene_variant,,ENST00000586745,;ZNF101,missense_variant,p.Arg354Gln,ENST00000318110,;ZNF101,missense_variant,p.Arg65Gln,ENST00000585565,;ZNF101,downstream_gene_variant,,ENST00000415440,;	A	ENSG00000181896	ENST00000592502	Transcript	missense_variant	1171	1061	354	R/Q	cGa/cAa	rs758983961	.	.	1	ZNF101	HGNC	12881	protein_coding	YES	CCDS32971.1	ENSP00000468049	ZN101_HUMAN	Q96F93_HUMAN,Q0VDG9_HUMAN,K7ENV8_HUMAN	UPI0000074138	.	tolerated(0.71)	benign(0.416)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24379,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCGAAGAC	.	5	ESCA
ZNF253	0	.	GRCh37	19	19976767	19976767	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39G>C	.	.	ENST00000589717	1/4	72	47	24	67	67	0	ZNF253,5_prime_UTR_variant,,ENST00000592725,;ZNF253,5_prime_UTR_variant,,ENST00000355650,;ZNF253,5_prime_UTR_variant,,ENST00000589717,;ZNF253,non_coding_transcript_exon_variant,,ENST00000589668,;CTC-559E9.10,downstream_gene_variant,,ENST00000605360,;	C	ENSG00000256771	ENST00000589717	Transcript	5_prime_UTR_variant	54	.	.	.	.	.	.	.	1	ZNF253	HGNC	13497	protein_coding	YES	CCDS42532.1	ENSP00000468720	ZN253_HUMAN	K7EP55_HUMAN	UPI0000070CE8	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGAGAGCCA	.	5	ESCA
ZNF676	0	.	GRCh37	19	22379731	22379731	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-296G>A	.	.	ENST00000397121	1/3	13	9	4	9	9	0	ZNF676,5_prime_UTR_variant,,ENST00000397121,;	T	ENSG00000196109	ENST00000397121	Transcript	5_prime_UTR_variant	23	.	.	.	.	.	.	.	-1	ZNF676	HGNC	20429	protein_coding	YES	CCDS42539.1	ENSP00000380310	ZN676_HUMAN	.	UPI00002376EC	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATCCATAAC	.	2	ESCA
C19orf71	0	.	GRCh37	19	3543359	3543359	+	Silent	SNP	G	G	A	rs377153853	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210G>A	p.%3D	p.S70S	ENST00000329493	2/4	18	13	5	15	15	0	C19orf71,synonymous_variant,p.%3D,ENST00000329493,;MFSD12,intron_variant,,ENST00000389395,;MFSD12,intron_variant,,ENST00000398558,;MFSD12,downstream_gene_variant,,ENST00000355415,;MFSD12,downstream_gene_variant,,ENST00000592652,;MFSD12,downstream_gene_variant,,ENST00000589063,;MFSD12,downstream_gene_variant,,ENST00000589995,;AC005786.7,upstream_gene_variant,,ENST00000589360,;MFSD12,downstream_gene_variant,,ENST00000591878,;MFSD12,non_coding_transcript_exon_variant,,ENST00000589157,;MFSD12,downstream_gene_variant,,ENST00000588918,;MFSD12,upstream_gene_variant,,ENST00000585788,;MFSD12,downstream_gene_variant,,ENST00000585814,;	A	ENSG00000183397	ENST00000329493	Transcript	synonymous_variant	234	210	70	S	tcG/tcA	rs377153853	.	.	1	C19orf71	HGNC	34496	protein_coding	YES	CCDS45918.1	ENSP00000327950	CS071_HUMAN	.	UPI000041AAB7	.	.	.	2/4	.	Pfam_domain:PF15041,hmmpanther:PTHR31254	A:0.0010	A:0	A:0	.	A:0.005	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTCGGACGC	byFrequency|byCluster|by1000G	5	ESCA
ZNF850	0	.	GRCh37	19	37241489	37241489	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453C>G	p.Phe151Leu	p.F151L	ENST00000591344	5/5	162	124	38	152	152	0	ZNF850,missense_variant,p.Phe151Leu,ENST00000591344,;ZNF850,intron_variant,,ENST00000589390,;	C	ENSG00000267041	ENST00000591344	Transcript	missense_variant	612	453	151	F/L	ttC/ttG	.	.	.	-1	ZNF850	HGNC	27994	protein_coding	YES	CCDS59379.1	ENSP00000464976	ZN850_HUMAN	.	UPI00001D815D	.	deleterious(0.03)	possibly_damaging(0.878)	5/5	.	Gene3D:3.30.160.60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGAAAGT	.	5	ESCA
ZNF540	0	.	GRCh37	19	38039934	38039934	+	5'Flank	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000592533	.	52	40	11	55	55	0	ZNF540,upstream_gene_variant,,ENST00000592533,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000586139,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000589802,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000585578,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000592392,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000592575,;CTD-3064H18.4,non_coding_transcript_exon_variant,,ENST00000316807,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000591430,;ZNF571-AS1,upstream_gene_variant,,ENST00000586013,;ZNF571-AS1,upstream_gene_variant,,ENST00000590838,;ZNF571-AS1,upstream_gene_variant,,ENST00000588382,;ZNF571-AS1,upstream_gene_variant,,ENST00000589750,;ZNF571-AS1,upstream_gene_variant,,ENST00000587121,;ZNF793,downstream_gene_variant,,ENST00000586187,;	A	ENSG00000171817	ENST00000592533	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2374	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAAGAAACC	.	5	ESCA
ZNF540	0	.	GRCh37	19	38104049	38104049	+	Missense_Mutation	SNP	C	C	G	rs746897709	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1868C>G	p.Thr623Ser	p.T623S	ENST00000592533	5/5	43	31	12	36	36	0	ZNF540,missense_variant,p.Thr623Ser,ENST00000316433,;ZNF540,missense_variant,p.Thr623Ser,ENST00000343599,;ZNF540,missense_variant,p.Thr591Ser,ENST00000589117,;ZNF540,missense_variant,p.Thr623Ser,ENST00000592533,;ZNF540,downstream_gene_variant,,ENST00000586134,;ZNF540,downstream_gene_variant,,ENST00000590588,;ZFP30,downstream_gene_variant,,ENST00000589018,;ZNF540,downstream_gene_variant,,ENST00000586792,;ZNF540,downstream_gene_variant,,ENST00000589857,;ZNF540,non_coding_transcript_exon_variant,,ENST00000589285,;	G	ENSG00000171817	ENST00000592533	Transcript	missense_variant	2200	1868	623	T/S	aCt/aGt	rs746897709	.	.	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	tolerated(0.15)	benign(0.089)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF138,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTACTGAAC	.	5	ESCA
WDR87	0	.	GRCh37	19	38380747	38380747	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3447C>T	p.%3D	p.L1149L	ENST00000303868	6/6	91	74	17	79	79	0	WDR87,synonymous_variant,p.%3D,ENST00000447313,;WDR87,synonymous_variant,p.%3D,ENST00000303868,;	A	ENSG00000171804	ENST00000303868	Transcript	synonymous_variant	3672	3447	1149	L	ctC/ctT	.	.	.	-1	WDR87	HGNC	29934	protein_coding	YES	CCDS46063.1	ENSP00000368025	WDR87_HUMAN	B4DXE9_HUMAN	UPI0001662BC1	.	.	.	6/6	.	hmmpanther:PTHR19852,hmmpanther:PTHR19852:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGAGAGCTT	.	5	ESCA
ACTN4	0	.	GRCh37	19	39208683	39208683	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1260G>A	p.%3D	p.Q420Q	ENST00000252699	11/21	78	57	21	62	62	0	ACTN4,synonymous_variant,p.%3D,ENST00000252699,;ACTN4,synonymous_variant,p.%3D,ENST00000390009,;ACTN4,intron_variant,,ENST00000424234,;ACTN4,intron_variant,,ENST00000589528,;ACTN4,downstream_gene_variant,,ENST00000586538,;ACTN4,downstream_gene_variant,,ENST00000489451,;ACTN4,non_coding_transcript_exon_variant,,ENST00000588618,;	A	ENSG00000130402	ENST00000252699	Transcript	synonymous_variant	1336	1260	420	Q	caG/caA	.	.	.	1	ACTN4	HGNC	166	protein_coding	YES	CCDS12518.1	ENSP00000252699	ACTN4_HUMAN	Q96BG6_HUMAN	UPI0000125093	.	.	.	11/21	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF271,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCAGAAGGC	.	5	ESCA
DYRK1B	0	.	GRCh37	19	40320544	40320544	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496G>T	p.Asp166Tyr	p.D166Y	ENST00000593685	5/11	67	56	11	59	59	0	DYRK1B,missense_variant,p.Asp166Tyr,ENST00000597639,;DYRK1B,missense_variant,p.Asp166Tyr,ENST00000593685,;DYRK1B,missense_variant,p.Asp166Tyr,ENST00000348817,;DYRK1B,missense_variant,p.Asp166Tyr,ENST00000430012,;DYRK1B,missense_variant,p.Asp166Tyr,ENST00000600611,;DYRK1B,missense_variant,p.Asp166Tyr,ENST00000323039,;DYRK1B,downstream_gene_variant,,ENST00000601972,;FBL,downstream_gene_variant,,ENST00000597224,;FBL,downstream_gene_variant,,ENST00000595545,;FBL,downstream_gene_variant,,ENST00000601274,;FBL,downstream_gene_variant,,ENST00000221801,;FBL,downstream_gene_variant,,ENST00000593503,;DYRK1B,non_coding_transcript_exon_variant,,ENST00000601696,;FBL,downstream_gene_variant,,ENST00000594443,;	A	ENSG00000105204	ENST00000593685	Transcript	missense_variant	965	496	166	D/Y	Gac/Tac	.	.	.	-1	DYRK1B	HGNC	3092	protein_coding	YES	CCDS12543.1	ENSP00000469863	DYR1B_HUMAN	M0R131_HUMAN	UPI0000001059	.	deleterious(0)	probably_damaging(0.948)	5/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF27,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGTCATGCT	.	5	ESCA
CEACAM6	0	.	GRCh37	19	42265341	42265341	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609C>G	p.%3D	p.L203L	ENST00000199764	3/6	234	170	63	151	151	0	CEACAM6,synonymous_variant,p.%3D,ENST00000199764,;CEA,downstream_gene_variant,,ENST00000598976,;CEACAM6,downstream_gene_variant,,ENST00000595740,;CEA,downstream_gene_variant,,ENST00000435837,;AC011513.4,intron_variant,,ENST00000601409,;	G	ENSG00000086548	ENST00000199764	Transcript	synonymous_variant	827	609	203	L	ctC/ctG	.	.	.	1	CEACAM6	HGNC	1818	protein_coding	YES	CCDS12585.1	ENSP00000199764	CEAM6_HUMAN	Q13985_HUMAN,M0QYD3_HUMAN	UPI000006DF42	.	.	.	3/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF121,hmmpanther:PTHR19955,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACTCAGCGT	.	5	ESCA
SNRPD2	0	.	GRCh37	19	46190949	46190949	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.219G>A	p.Met73Ile	p.M73I	ENST00000342669	3/3	96	74	21	89	89	0	SNRPD2,missense_variant,p.Met73Ile,ENST00000588301,;SNRPD2,missense_variant,p.Met63Ile,ENST00000587367,;SNRPD2,missense_variant,p.Met63Ile,ENST00000391932,;SNRPD2,missense_variant,p.Met9Ile,ENST00000585392,;SNRPD2,missense_variant,p.Met63Ile,ENST00000588599,;SNRPD2,missense_variant,p.Met73Ile,ENST00000342669,;SNRPD2,3_prime_UTR_variant,,ENST00000590212,;QPCTL,upstream_gene_variant,,ENST00000012049,;GIPR,downstream_gene_variant,,ENST00000590918,;SNRPD2,downstream_gene_variant,,ENST00000587579,;	T	ENSG00000125743	ENST00000342669	Transcript	missense_variant	664	219	73	M/I	atG/atA	.	.	.	-1	SNRPD2	HGNC	11159	protein_coding	YES	CCDS33053.1	ENSP00000342374	SMD2_HUMAN	K7EJB5_HUMAN	UPI0000028222	.	tolerated(0.15)	benign(0.079)	3/3	.	hmmpanther:PTHR12777,Gene3D:2.30.30.100,Pfam_domain:PF01423,SMART_domains:SM00651,Superfamily_domains:SSF50182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCACATCTC	.	5	ESCA
DMPK	0	.	GRCh37	19	46283468	46283468	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-151G>A	.	.	ENST00000343373	1/14	33	28	5	24	24	0	DMPK,5_prime_UTR_variant,,ENST00000600757,;DMPK,5_prime_UTR_variant,,ENST00000343373,;DMPK,intron_variant,,ENST00000291270,;DMPK,intron_variant,,ENST00000458663,;AC011530.4,intron_variant,,ENST00000596586,;DMPK,intron_variant,,ENST00000596067,;DMPK,intron_variant,,ENST00000447742,;AC011530.4,intron_variant,,ENST00000595946,;DMPK,intron_variant,,ENST00000354227,;DMPK,upstream_gene_variant,,ENST00000593574,;DMWD,downstream_gene_variant,,ENST00000377735,;DMWD,downstream_gene_variant,,ENST00000270223,;DMWD,downstream_gene_variant,,ENST00000537879,;DMPK,upstream_gene_variant,,ENST00000596920,;DMPK,upstream_gene_variant,,ENST00000595361,;AC011530.4,splice_region_variant,,ENST00000597712,;DMPK,non_coding_transcript_exon_variant,,ENST00000598180,;DMPK,intron_variant,,ENST00000588522,;AC011530.4,intron_variant,,ENST00000593999,;DMPK,upstream_gene_variant,,ENST00000599392,;DMPK,upstream_gene_variant,,ENST00000600370,;DMPK,upstream_gene_variant,,ENST00000598191,;DMPK,upstream_gene_variant,,ENST00000596686,;DMPK,upstream_gene_variant,,ENST00000599002,;	T	ENSG00000104936	ENST00000343373	Transcript	5_prime_UTR_variant	394	.	.	.	.	.	.	.	-1	DMPK	HGNC	2933	protein_coding	YES	CCDS46119.1	ENSP00000345997	DMPK_HUMAN	E5KR08_HUMAN	UPI00001AF19C	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTTCCACCT	.	4	ESCA
DMPK	0	.	GRCh37	19	46283590	46283590	+	5'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-273G>C	.	.	ENST00000343373	1/14	63	46	16	55	55	0	DMPK,missense_variant,p.Glu30Gln,ENST00000596067,;DMPK,5_prime_UTR_variant,,ENST00000600757,;DMPK,5_prime_UTR_variant,,ENST00000343373,;DMPK,intron_variant,,ENST00000291270,;DMPK,intron_variant,,ENST00000458663,;AC011530.4,intron_variant,,ENST00000596586,;DMPK,intron_variant,,ENST00000447742,;AC011530.4,intron_variant,,ENST00000595946,;DMPK,intron_variant,,ENST00000354227,;DMPK,upstream_gene_variant,,ENST00000593574,;DMWD,downstream_gene_variant,,ENST00000377735,;DMWD,downstream_gene_variant,,ENST00000602829,;DMWD,downstream_gene_variant,,ENST00000270223,;DMWD,downstream_gene_variant,,ENST00000537879,;DMPK,upstream_gene_variant,,ENST00000596920,;DMPK,upstream_gene_variant,,ENST00000595361,;AC011530.4,stop_lost,p.Ter57SerextTer2,ENST00000597712,;DMPK,synonymous_variant,p.%3D,ENST00000588522,;DMPK,non_coding_transcript_exon_variant,,ENST00000598180,;AC011530.4,intron_variant,,ENST00000593999,;DMPK,upstream_gene_variant,,ENST00000599392,;DMPK,upstream_gene_variant,,ENST00000598191,;DMPK,upstream_gene_variant,,ENST00000596686,;DMPK,upstream_gene_variant,,ENST00000599002,;	G	ENSG00000104936	ENST00000343373	Transcript	5_prime_UTR_variant	272	.	.	.	.	.	.	.	-1	DMPK	HGNC	2933	protein_coding	YES	CCDS46119.1	ENSP00000345997	DMPK_HUMAN	E5KR08_HUMAN	UPI00001AF19C	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTCAGATG	.	5	ESCA
CALM3	0	.	GRCh37	19	47111561	47111561	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142G>T	p.Glu48Ter	p.E48*	ENST00000291295	3/6	38	32	6	30	30	0	CALM3,stop_gained,p.Glu12Ter,ENST00000599839,;CALM3,stop_gained,p.Glu48Ter,ENST00000291295,;CALM3,stop_gained,p.Glu48Ter,ENST00000597743,;CALM3,stop_gained,p.Glu12Ter,ENST00000391918,;CALM3,stop_gained,p.Glu12Ter,ENST00000598871,;CALM3,stop_gained,p.Glu12Ter,ENST00000594523,;CALM3,stop_gained,p.Glu48Ter,ENST00000596362,;CTB-12A17.3,downstream_gene_variant,,ENST00000597609,;CALM3,non_coding_transcript_exon_variant,,ENST00000482455,;CALM3,non_coding_transcript_exon_variant,,ENST00000477244,;CALM3,non_coding_transcript_exon_variant,,ENST00000595072,;CALM3,non_coding_transcript_exon_variant,,ENST00000597868,;CALM3,non_coding_transcript_exon_variant,,ENST00000486500,;CALM3,downstream_gene_variant,,ENST00000602169,;	T	ENSG00000160014	ENST00000291295	Transcript	stop_gained	341	142	48	E/*	Gag/Tag	.	.	.	1	CALM3	HGNC	1449	protein_coding	YES	CCDS33061.1	ENSP00000291295	CALM_HUMAN	Q96HY3_HUMAN,G3V361_HUMAN,B4DJ51_HUMAN	UPI00000000C1	.	.	.	3/6	.	PROSITE_profiles:PS50222,hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF155,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGAGCTG	.	5	ESCA
C5AR2	0	.	GRCh37	19	47844098	47844098	+	Silent	SNP	C	C	T	rs138403580	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42C>T	p.%3D	p.S14S	ENST00000595464	2/2	33	25	8	30	30	0	C5AR2,synonymous_variant,p.%3D,ENST00000257267,;C5AR2,synonymous_variant,p.%3D,ENST00000600626,;C5AR2,synonymous_variant,p.%3D,ENST00000595464,;	T	ENSG00000134830	ENST00000595464	Transcript	synonymous_variant	260	42	14	S	agC/agT	rs138403580	.	.	1	C5AR2	HGNC	4527	protein_coding	YES	CCDS12699.1	ENSP00000472620	C5AR2_HUMAN	.	UPI000003BCC8	.	.	.	2/2	.	hmmpanther:PTHR24225:SF1,hmmpanther:PTHR24225,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAGCGACCT	byFrequency|byCluster	5	ESCA
PRMT1	0	.	GRCh37	19	50185264	50185264	+	Missense_Mutation	SNP	C	C	T	rs750309006	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.290C>T	p.Ser97Leu	p.S97L	ENST00000454376	4/11	72	60	12	66	66	0	PRMT1,missense_variant,p.Ser51Leu,ENST00000526224,;PRMT1,missense_variant,p.Ser107Leu,ENST00000524771,;PRMT1,missense_variant,p.Ser51Leu,ENST00000534465,;PRMT1,missense_variant,p.Ser79Leu,ENST00000391851,;PRMT1,missense_variant,p.Ser73Leu,ENST00000529836,;PRMT1,missense_variant,p.Ser51Leu,ENST00000532489,;PRMT1,missense_variant,p.Ser97Leu,ENST00000454376,;PRMT1,missense_variant,p.Ser51Leu,ENST00000527382,;PRMT1,missense_variant,p.Ser51Leu,ENST00000529284,;PRMT1,missense_variant,p.Ser76Leu,ENST00000527412,;PRMT1,downstream_gene_variant,,ENST00000528623,;AC011495.1,upstream_gene_variant,,ENST00000581740,;PRMT1,upstream_gene_variant,,ENST00000530361,;PRMT1,upstream_gene_variant,,ENST00000530070,;PRMT1,3_prime_UTR_variant,,ENST00000534280,;PRMT1,non_coding_transcript_exon_variant,,ENST00000525616,;PRMT1,non_coding_transcript_exon_variant,,ENST00000534676,;PRMT1,downstream_gene_variant,,ENST00000525915,;PRMT1,upstream_gene_variant,,ENST00000528126,;PRMT1,upstream_gene_variant,,ENST00000529650,;	T	ENSG00000126457	ENST00000454376	Transcript	missense_variant	299	290	97	S/L	tCg/tTg	rs750309006	.	.	1	PRMT1	HGNC	5187	protein_coding	YES	CCDS46145.1	ENSP00000406162	.	H7C2I1_HUMAN,E9PQ98_HUMAN,E9PNR9_HUMAN,E9PKG1_HUMAN,E9PI83_HUMAN	UPI0000456CFB	.	deleterious(0)	possibly_damaging(0.832)	4/11	.	PROSITE_profiles:PS51678,hmmpanther:PTHR11006,hmmpanther:PTHR11006:SF54,Gene3D:3.40.50.150,Pfam_domain:PF13847,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCTCGGGCA	.	5	ESCA
NKG7	0	.	GRCh37	19	51875019	51875019	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*12G>C	.	.	ENST00000221978	4/4	33	27	5	37	37	0	NKG7,3_prime_UTR_variant,,ENST00000595217,;NKG7,3_prime_UTR_variant,,ENST00000221978,;NKG7,3_prime_UTR_variant,,ENST00000600427,;NKG7,3_prime_UTR_variant,,ENST00000593572,;NKG7,3_prime_UTR_variant,,ENST00000595157,;CLDND2,upstream_gene_variant,,ENST00000601435,;CLDND2,upstream_gene_variant,,ENST00000291715,;CLDND2,upstream_gene_variant,,ENST00000593841,;CTD-2616J11.11,upstream_gene_variant,,ENST00000600067,;	G	ENSG00000105374	ENST00000221978	Transcript	3_prime_UTR_variant	690	.	.	.	.	.	.	.	-1	NKG7	HGNC	7830	protein_coding	YES	CCDS12830.1	ENSP00000221978	NKG7_HUMAN	.	UPI00001301FE	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCGCTCTTGCC	.	3	ESCA
ZNF841	0	.	GRCh37	19	52568449	52568449	+	Missense_Mutation	SNP	G	G	C	rs754785449	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2686C>G	p.Gln896Glu	p.Q896E	ENST00000389534	7/7	79	60	19	72	72	0	ZNF841,missense_variant,p.Gln484Glu,ENST00000601738,;ZNF841,missense_variant,p.Gln896Glu,ENST00000389534,;ZNF841,missense_variant,p.Gln780Glu,ENST00000426391,;ZNF841,missense_variant,p.Gln472Glu,ENST00000359973,;ZNF841,missense_variant,p.Gln896Glu,ENST00000594295,;ZNF432,upstream_gene_variant,,ENST00000600368,;CTC-471J1.2,upstream_gene_variant,,ENST00000569091,;ZNF432,intron_variant,,ENST00000598446,;ZNF841,downstream_gene_variant,,ENST00000595599,;	C	ENSG00000197608	ENST00000389534	Transcript	missense_variant	3146	2686	896	Q/E	Cag/Gag	rs754785449	.	.	-1	ZNF841	HGNC	27611	protein_coding	YES	CCDS46161.1	ENSP00000374185	ZN841_HUMAN	M0QYV6_HUMAN	UPI00001D818B	.	tolerated(0.09)	benign(0.019)	7/7	.	PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTGATGTT	byFrequency	5	ESCA
ZNF880	0	.	GRCh37	19	52877592	52877592	+	Silent	SNP	G	G	A	rs770190506	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180G>A	p.%3D	p.E60E	ENST00000422689	3/4	43	34	9	44	44	0	ZNF880,synonymous_variant,p.%3D,ENST00000422689,;ZNF880,synonymous_variant,p.%3D,ENST00000344085,;ZNF880,synonymous_variant,p.%3D,ENST00000600321,;ZNF880,synonymous_variant,p.%3D,ENST00000424032,;ZNF880,synonymous_variant,p.%3D,ENST00000597976,;ZNF880,downstream_gene_variant,,ENST00000595099,;	A	ENSG00000221923	ENST00000422689	Transcript	synonymous_variant	195	180	60	E	gaG/gaA	rs770190506	.	.	1	ZNF880	HGNC	37249	protein_coding	YES	CCDS46164.1	ENSP00000406318	ZN880_HUMAN	.	UPI00001D818D	.	.	.	3/4	.	Superfamily_domains:0044637,SMART_domains:SM00349,hmmpanther:PTHR24377:SF108,hmmpanther:PTHR24377,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGAGCAAAG	.	5	ESCA
ZNF415	0	.	GRCh37	19	53625823	53625823	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-152G>A	.	.	ENST00000500065	2/4	39	33	6	32	32	0	ZNF415,5_prime_UTR_variant,,ENST00000595813,;ZNF415,5_prime_UTR_variant,,ENST00000500065,;ZNF415,5_prime_UTR_variant,,ENST00000599261,;ZNF415,intron_variant,,ENST00000440291,;ZNF415,intron_variant,,ENST00000596051,;ZNF415,intron_variant,,ENST00000455735,;ZNF415,intron_variant,,ENST00000600574,;ZNF415,intron_variant,,ENST00000601215,;ZNF415,intron_variant,,ENST00000448501,;ZNF415,intron_variant,,ENST00000601110,;ZNF415,intron_variant,,ENST00000601493,;ZNF415,intron_variant,,ENST00000243643,;ZNF415,intron_variant,,ENST00000594011,;ZNF415,intron_variant,,ENST00000597503,;ZNF415,intron_variant,,ENST00000595193,;ZNF415,intron_variant,,ENST00000421033,;ZNF415,intron_variant,,ENST00000595174,;ZNF415,intron_variant,,ENST00000597748,;ZNF347,downstream_gene_variant,,ENST00000601804,;ZNF415,non_coding_transcript_exon_variant,,ENST00000596106,;ZNF415,non_coding_transcript_exon_variant,,ENST00000602024,;ZNF415,non_coding_transcript_exon_variant,,ENST00000594286,;ZNF415,intron_variant,,ENST00000602110,;ZNF415,intron_variant,,ENST00000596683,;ZNF415,intron_variant,,ENST00000595359,;ZNF415,non_coding_transcript_exon_variant,,ENST00000600098,;ZNF415,intron_variant,,ENST00000600120,;ZNF415,intron_variant,,ENST00000598578,;ZNF415,intron_variant,,ENST00000598024,;ZNF415,intron_variant,,ENST00000597877,;	T	ENSG00000170954	ENST00000500065	Transcript	5_prime_UTR_variant	183	.	.	.	.	.	.	.	-1	ZNF415	HGNC	20636	protein_coding	YES	CCDS54313.1	ENSP00000439435	ZN415_HUMAN	.	UPI0000E04BC1	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTTCAGACT	.	4	ESCA
NLRP5	0	.	GRCh37	19	56515193	56515193	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174C>T	p.%3D	p.L58L	ENST00000390649	2/15	38	31	6	43	43	0	NLRP5,synonymous_variant,p.%3D,ENST00000390649,;NLRP5,synonymous_variant,p.%3D,ENST00000597673,;	T	ENSG00000171487	ENST00000390649	Transcript	synonymous_variant	174	174	58	L	ctC/ctT	.	.	.	1	NLRP5	HGNC	21269	protein_coding	YES	CCDS12938.1	ENSP00000375063	NALP5_HUMAN	.	UPI00001AEEBD	.	.	.	2/15	.	hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S61F|c.182C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCTCACCTT	.	5	ESCA
ZSCAN5B	0	.	GRCh37	19	56703331	56703331	+	Missense_Mutation	SNP	C	C	G	rs762833792	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.476G>C	p.Arg159Thr	p.R159T	ENST00000586855	3/5	77	63	14	62	62	0	ZSCAN5B,missense_variant,p.Arg159Thr,ENST00000589938,;ZSCAN5B,missense_variant,p.Arg159Thr,ENST00000586855,;ZSCAN5B,missense_variant,p.Arg159Thr,ENST00000358992,;ZSCAN5B,downstream_gene_variant,,ENST00000587032,;	G	ENSG00000197213	ENST00000586855	Transcript	missense_variant	790	476	159	R/T	aGa/aCa	rs762833792	.	.	-1	ZSCAN5B	HGNC	34246	protein_coding	YES	CCDS46203.1	ENSP00000466072	ZSA5B_HUMAN	K7ESD3_HUMAN,K7EJD1_HUMAN	UPI000059D7BA	.	tolerated(0.57)	benign(0.159)	3/5	.	hmmpanther:PTHR10032:SF163,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CGTCTCTCGGA	.	4	ESCA
VN1R1	0	.	GRCh37	19	57967238	57967238	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617G>T	p.Gly206Val	p.G206V	ENST00000321039	1/1	52	35	17	42	42	0	VN1R1,missense_variant,p.Gly206Val,ENST00000321039,;AC004076.9,intron_variant,,ENST00000596831,;AC004076.9,intron_variant,,ENST00000601945,;AC004076.9,intron_variant,,ENST00000415705,;VN1R107P,upstream_gene_variant,,ENST00000601784,;	A	ENSG00000178201	ENST00000321039	Transcript	missense_variant	617	617	206	G/V	gGa/gTa	.	.	.	-1	VN1R1	HGNC	13548	protein_coding	YES	CCDS12951.1	ENSP00000322339	VN1R1_HUMAN	.	UPI0000039957	.	tolerated(0.14)	possibly_damaging(0.474)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24062,hmmpanther:PTHR24062:SF43,Gene3D:1.20.1070.10,Pfam_domain:PF03402,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTATCCATAA	.	5	ESCA
ZNF256	0	.	GRCh37	19	58458845	58458845	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3C>T	.	.	ENST00000282308	1/3	71	64	7	73	73	0	ZNF256,5_prime_UTR_variant,,ENST00000282308,;ZNF256,5_prime_UTR_variant,,ENST00000598928,;	A	ENSG00000152454	ENST00000282308	Transcript	5_prime_UTR_variant	195	.	.	.	.	.	.	.	-1	ZNF256	HGNC	13049	protein_coding	YES	CCDS12966.1	ENSP00000282308	ZN256_HUMAN	.	UPI00001D69EC	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTGACTCT	.	4	ESCA
ALKBH7	0	.	GRCh37	19	6374962	6374962	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.644G>C	p.Gly215Ala	p.G215A	ENST00000245812	4/4	51	42	8	70	70	0	ALKBH7,missense_variant,p.Gly215Ala,ENST00000245812,;ALKBH7,missense_variant,p.Gly154Ala,ENST00000599849,;ALKBH7,missense_variant,p.Gly73Ala,ENST00000596657,;GTF2F1,downstream_gene_variant,,ENST00000593678,;PSPN,downstream_gene_variant,,ENST00000245810,;PSPN,downstream_gene_variant,,ENST00000597721,;GTF2F1,downstream_gene_variant,,ENST00000429701,;GTF2F1,downstream_gene_variant,,ENST00000394456,;	C	ENSG00000125652	ENST00000245812	Transcript	missense_variant	1032	644	215	G/A	gGa/gCa	.	.	.	1	ALKBH7	HGNC	21306	protein_coding	YES	CCDS12163.1	ENSP00000245812	ALKB7_HUMAN	M0QZH2_HUMAN	UPI0000039ED9	.	tolerated_low_confidence(0.35)	benign(0.014)	4/4	.	hmmpanther:PTHR21052:SF0,hmmpanther:PTHR21052	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGGACAGC	.	5	ESCA
MUC16	0	.	GRCh37	19	9010665	9010665	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38996C>T	p.Ser12999Phe	p.S12999F	ENST00000397910	38/84	52	45	7	79	79	0	MUC16,missense_variant,p.Ser12999Phe,ENST00000397910,;MUC16,upstream_gene_variant,,ENST00000599436,;MUC16,upstream_gene_variant,,ENST00000601404,;	A	ENSG00000181143	ENST00000397910	Transcript	missense_variant	39200	38996	12999	S/F	tCc/tTc	COSM229823	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	possibly_damaging(0.636)	38/84	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14672,hmmpanther:PTHR14672:SF0	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGGGAGGAT	.	5	ESCA
MUC16	0	.	GRCh37	19	9089301	9089301	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2514C>T	p.%3D	p.L838L	ENST00000397910	1/84	76	55	21	79	79	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;	A	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	2718	2514	838	L	ctC/ctT	COSM715142,COSM715141	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	1/84	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCTGAGAGT	.	5	ESCA
OLFM2	0	.	GRCh37	19	9971454	9971454	+	Missense_Mutation	SNP	G	G	A	rs375695569	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.80C>T	p.Pro27Leu	p.P27L	ENST00000264833	2/6	32	27	5	34	34	0	OLFM2,missense_variant,p.Pro27Leu,ENST00000264833,;OLFM2,missense_variant,p.Pro51Leu,ENST00000593091,;OLFM2,upstream_gene_variant,,ENST00000590841,;OLFM2,non_coding_transcript_exon_variant,,ENST00000590410,;OLFM2,upstream_gene_variant,,ENST00000592448,;	A	ENSG00000105088	ENST00000264833	Transcript	missense_variant	266	80	27	P/L	cCa/cTa	rs375695569	.	.	-1	OLFM2	HGNC	17189	protein_coding	YES	CCDS12221.1	ENSP00000264833	NOE2_HUMAN	K7EIS8_HUMAN	UPI000013D57B	.	deleterious(0)	probably_damaging(0.938)	2/6	.	hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF27,Pfam_domain:PF12308	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCTGGGTTC	byFrequency|byCluster	2	ESCA
GLTPD1	0	.	GRCh37	1	1263592	1263592	+	3'UTR	SNP	G	G	A	rs139436517	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*449G>A	.	.	ENST00000343938	3/3	44	38	6	33	33	0	GLTPD1,3_prime_UTR_variant,,ENST00000343938,;CPSF3L,upstream_gene_variant,,ENST00000419704,;CPSF3L,upstream_gene_variant,,ENST00000450926,;TAS1R3,upstream_gene_variant,,ENST00000339381,;CPSF3L,upstream_gene_variant,,ENST00000434694,;CPSF3L,upstream_gene_variant,,ENST00000527719,;CPSF3L,upstream_gene_variant,,ENST00000545578,;CPSF3L,upstream_gene_variant,,ENST00000530031,;CPSF3L,upstream_gene_variant,,ENST00000435064,;CPSF3L,upstream_gene_variant,,ENST00000526332,;CPSF3L,upstream_gene_variant,,ENST00000534345,;CPSF3L,upstream_gene_variant,,ENST00000421495,;CPSF3L,upstream_gene_variant,,ENST00000498476,;CPSF3L,upstream_gene_variant,,ENST00000540437,;CPSF3L,upstream_gene_variant,,ENST00000411962,;GLTPD1,downstream_gene_variant,,ENST00000488011,;GLTPD1,downstream_gene_variant,,ENST00000464957,;CPSF3L,upstream_gene_variant,,ENST00000490853,;CPSF3L,upstream_gene_variant,,ENST00000532952,;CPSF3L,upstream_gene_variant,,ENST00000493534,;CPSF3L,upstream_gene_variant,,ENST00000531019,;CPSF3L,upstream_gene_variant,,ENST00000530233,;CPSF3L,upstream_gene_variant,,ENST00000470679,;CPSF3L,upstream_gene_variant,,ENST00000430786,;CPSF3L,upstream_gene_variant,,ENST00000532772,;CPSF3L,upstream_gene_variant,,ENST00000323275,;CPSF3L,upstream_gene_variant,,ENST00000488042,;CPSF3L,upstream_gene_variant,,ENST00000528879,;CPSF3L,upstream_gene_variant,,ENST00000525285,;CPSF3L,upstream_gene_variant,,ENST00000526904,;CPSF3L,upstream_gene_variant,,ENST00000429572,;CPSF3L,upstream_gene_variant,,ENST00000458452,;CPSF3L,upstream_gene_variant,,ENST00000498173,;CPSF3L,upstream_gene_variant,,ENST00000496353,;CPSF3L,upstream_gene_variant,,ENST00000526797,;CPSF3L,upstream_gene_variant,,ENST00000526113,;CPSF3L,upstream_gene_variant,,ENST00000527098,;	A	ENSG00000224051	ENST00000343938	Transcript	3_prime_UTR_variant	1505	.	.	.	.	rs139436517	.	.	1	GLTPD1	HGNC	28116	protein_coding	YES	CCDS30555.1	ENSP00000343890	CPTP_HUMAN	S4S694_HUMAN,Q9UFH6_HUMAN,J3KST3_HUMAN	UPI00001AF6EA	.	.	.	3/3	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCCGTGCCT	by1000G	2	ESCA
PRAMEF2	0	.	GRCh37	1	12918848	12918848	+	5'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-17C>G	.	.	ENST00000240189	2/4	132	122	10	67	67	0	PRAMEF2,5_prime_UTR_variant,,ENST00000240189,;	G	ENSG00000120952	ENST00000240189	Transcript	5_prime_UTR_variant	71	.	.	.	.	.	.	.	1	PRAMEF2	HGNC	28841	protein_coding	YES	CCDS149.1	ENSP00000240189	PRAM2_HUMAN	.	UPI0000139EF9	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTCTTGCA	.	2	ESCA
ATAD3B	0	.	GRCh37	1	1431023	1431023	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1773G>C	p.Glu591Asp	p.E591D	ENST00000308647	16/16	100	94	6	78	78	0	ATAD3B,missense_variant,p.Glu591Asp,ENST00000308647,;ATAD3B,non_coding_transcript_exon_variant,,ENST00000472194,;ATAD3B,non_coding_transcript_exon_variant,,ENST00000474481,;ATAD3B,non_coding_transcript_exon_variant,,ENST00000485748,;	C	ENSG00000160072	ENST00000308647	Transcript	missense_variant	1889	1773	591	E/D	gaG/gaC	.	.	.	1	ATAD3B	HGNC	24007	protein_coding	YES	CCDS30.1	ENSP00000311766	ATD3B_HUMAN	Q9H834_HUMAN	UPI000013E044	.	tolerated_low_confidence(0.55)	benign(0)	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCGAGACCCT	.	2	ESCA
HIST2H2BF	0	.	GRCh37	1	149783597	149783597	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.282G>C	p.Glu94Asp	p.E94D	ENST00000545683	1/2	207	189	18	132	132	0	HIST2H2BF,missense_variant,p.Glu94Asp,ENST00000545683,;HIST2H2BF,missense_variant,p.Glu94Asp,ENST00000369167,;HIST2H2BF,missense_variant,p.Glu94Asp,ENST00000427880,;HIST2H3D,downstream_gene_variant,,ENST00000331491,;RP11-196G18.21,upstream_gene_variant,,ENST00000420462,;HIST2H2BF,non_coding_transcript_exon_variant,,ENST00000469483,;	G	ENSG00000203814	ENST00000545683	Transcript	missense_variant	332	282	94	E/D	gaG/gaC	.	.	.	-1	HIST2H2BF	HGNC	24700	protein_coding	YES	CCDS53359.1	ENSP00000445831	H2B2F_HUMAN	.	UPI00017A7443	.	deleterious_low_confidence(0.02)	benign(0.387)	1/2	.	hmmpanther:PTHR23428,PROSITE_patterns:PS00357,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGATCTCGCG	.	3	ESCA
CA14	0	.	GRCh37	1	150236222	150236222	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.892T>C	p.%3D	p.L298L	ENST00000369111	10/11	47	41	6	37	37	0	CA14,synonymous_variant,p.%3D,ENST00000369111,;CA14,intron_variant,,ENST00000607082,;APH1A,downstream_gene_variant,,ENST00000236017,;APH1A,downstream_gene_variant,,ENST00000360244,;APH1A,downstream_gene_variant,,ENST00000414276,;APH1A,downstream_gene_variant,,ENST00000369109,;C1orf54,upstream_gene_variant,,ENST00000369102,;snoU13,downstream_gene_variant,,ENST00000458929,;APH1A,downstream_gene_variant,,ENST00000461320,;APH1A,downstream_gene_variant,,ENST00000486308,;APH1A,downstream_gene_variant,,ENST00000476538,;APH1A,downstream_gene_variant,,ENST00000486720,;CA14,non_coding_transcript_exon_variant,,ENST00000607652,;CA14,downstream_gene_variant,,ENST00000607751,;CA14,downstream_gene_variant,,ENST00000483993,;	C	ENSG00000118298	ENST00000369111	Transcript	synonymous_variant	1862	892	298	L	Ttg/Ctg	.	.	.	1	CA14	HGNC	1372	protein_coding	YES	CCDS947.1	ENSP00000358107	CAH14_HUMAN	A8K3J4_HUMAN	UPI00000389EA	.	.	.	10/11	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAATCTTGGTT	.	4	ESCA
HAX1	0	.	GRCh37	1	154245820	154245820	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.62A>T	p.Asp21Val	p.D21V	ENST00000328703	2/7	56	31	24	31	31	0	HAX1,missense_variant,p.Asp21Val,ENST00000435087,;HAX1,missense_variant,p.Asp21Val,ENST00000328703,;HAX1,missense_variant,p.Asp21Val,ENST00000483970,;HAX1,intron_variant,,ENST00000532105,;HAX1,intron_variant,,ENST00000457918,;UBAP2L,downstream_gene_variant,,ENST00000428595,;UBAP2L,downstream_gene_variant,,ENST00000433615,;UBAP2L,downstream_gene_variant,,ENST00000271877,;UBAP2L,downstream_gene_variant,,ENST00000361546,;UBAP2L,downstream_gene_variant,,ENST00000428931,;UBAP2L,downstream_gene_variant,,ENST00000484819,;UBAP2L,downstream_gene_variant,,ENST00000493867,;HAX1,missense_variant,p.Asp21Val,ENST00000447768,;HAX1,non_coding_transcript_exon_variant,,ENST00000531435,;HAX1,non_coding_transcript_exon_variant,,ENST00000471326,;HAX1,non_coding_transcript_exon_variant,,ENST00000477780,;HAX1,upstream_gene_variant,,ENST00000492550,;HAX1,upstream_gene_variant,,ENST00000459914,;	T	ENSG00000143575	ENST00000328703	Transcript	missense_variant	275	62	21	D/V	gAt/gTt	.	.	.	1	HAX1	HGNC	16915	protein_coding	YES	CCDS1064.1	ENSP00000329002	HAX1_HUMAN	E9PIQ7_HUMAN	UPI000012C0B6	.	deleterious(0)	probably_damaging(0.983)	2/7	.	hmmpanther:PTHR14938,PIRSF_domain:PIRSF037634	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P22S|c.64C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGATCCCT	.	5	ESCA
SLC50A1	0	.	GRCh37	1	155110171	155110171	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.417C>A	p.Ser139Arg	p.S139R	ENST00000368404	4/6	98	73	25	55	55	0	SLC50A1,missense_variant,p.Ser84Arg,ENST00000368401,;SLC50A1,missense_variant,p.Ser74Arg,ENST00000484157,;SLC50A1,missense_variant,p.Ser139Arg,ENST00000368404,;SLC50A1,intron_variant,,ENST00000303343,;EFNA1,downstream_gene_variant,,ENST00000368406,;EFNA1,downstream_gene_variant,,ENST00000368407,;DPM3,downstream_gene_variant,,ENST00000341298,;DPM3,downstream_gene_variant,,ENST00000368400,;DPM3,downstream_gene_variant,,ENST00000368399,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000488609,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000475824,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000490770,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000490276,;SLC50A1,intron_variant,,ENST00000484027,;SLC50A1,intron_variant,,ENST00000368405,;SLC50A1,downstream_gene_variant,,ENST00000465546,;EFNA1,downstream_gene_variant,,ENST00000469878,;SLC50A1,upstream_gene_variant,,ENST00000479579,;EFNA1,downstream_gene_variant,,ENST00000474413,;EFNA1,downstream_gene_variant,,ENST00000497282,;SLC50A1,downstream_gene_variant,,ENST00000506037,;	A	ENSG00000169241	ENST00000368404	Transcript	missense_variant	479	417	139	S/R	agC/agA	.	.	.	1	SLC50A1	HGNC	30657	protein_coding	YES	CCDS1093.1	ENSP00000357389	SWET1_HUMAN	.	UPI00000361FB	.	deleterious(0.03)	possibly_damaging(0.888)	4/6	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10791,hmmpanther:PTHR10791:SF24,Pfam_domain:PF03083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCAGCATGTA	.	5	ESCA
RHBG	0	.	GRCh37	1	156347784	156347784	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378G>T	p.Met126Ile	p.M126I	ENST00000368249	3/10	61	51	10	48	48	0	RHBG,missense_variant,p.Met126Ile,ENST00000368249,;RHBG,missense_variant,p.Met57Ile,ENST00000255013,;RHBG,missense_variant,p.Met57Ile,ENST00000451864,;RHBG,missense_variant,p.Met57Ile,ENST00000400992,;RHBG,missense_variant,p.Met126Ile,ENST00000368246,;RHBG,intron_variant,,ENST00000537040,;RHBG,upstream_gene_variant,,ENST00000494874,;RHBG,missense_variant,p.Asp151Tyr,ENST00000446171,;RHBG,3_prime_UTR_variant,,ENST00000544720,;RHBG,3_prime_UTR_variant,,ENST00000368245,;RHBG,3_prime_UTR_variant,,ENST00000368247,;RHBG,non_coding_transcript_exon_variant,,ENST00000466013,;RHBG,upstream_gene_variant,,ENST00000477000,;	T	ENSG00000132677	ENST00000368249	Transcript	missense_variant	416	378	126	M/I	atG/atT	.	.	.	1	RHBG	HGNC	14572	protein_coding	YES	.	ENSP00000357232	RHBG_HUMAN	.	UPI00001411E0	.	tolerated(0.12)	benign(0.238)	3/10	.	Transmembrane_helices:TMhelix,Superfamily_domains:0044218,Gene3D:1.10.3430.10,Pfam_domain:PF00909,hmmpanther:PTHR11883,hmmpanther:PTHR11883:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCATGATCAA	.	5	ESCA
IQGAP3	0	.	GRCh37	1	156524141	156524141	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1334C>T	p.Ser445Leu	p.S445L	ENST00000361170	13/38	70	56	14	67	67	0	IQGAP3,missense_variant,p.Ser445Leu,ENST00000361170,;IQGAP3,missense_variant,p.Ser402Leu,ENST00000491900,;	A	ENSG00000183856	ENST00000361170	Transcript	missense_variant	1345	1334	445	S/L	tCa/tTa	.	.	.	-1	IQGAP3	HGNC	20669	protein_coding	YES	CCDS1144.1	ENSP00000354451	IQGA3_HUMAN	F2Z2E2_HUMAN	UPI000046FFDD	.	deleterious(0.02)	possibly_damaging(0.78)	13/38	.	hmmpanther:PTHR14149,hmmpanther:PTHR14149:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGAGAGC	.	5	ESCA
OR6P1	0	.	GRCh37	1	158533238	158533238	+	Missense_Mutation	SNP	G	G	A	rs749013393	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.157C>T	p.Pro53Ser	p.P53S	ENST00000334632	1/1	41	29	12	20	20	0	OR6P1,missense_variant,p.Pro53Ser,ENST00000334632,;	A	ENSG00000186440	ENST00000334632	Transcript	missense_variant	157	157	53	P/S	Cca/Tca	rs749013393	.	.	-1	OR6P1	HGNC	15036	protein_coding	YES	CCDS53391.1	ENSP00000334721	OR6P1_HUMAN	.	UPI000004B1FF	.	tolerated(0.99)	benign(0.002)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF73,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTGGAGCAA	byFrequency	5	ESCA
IFI16	0	.	GRCh37	1	159002344	159002344	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1192G>A	p.Asp398Asn	p.D398N	ENST00000368131	7/11	59	48	11	31	31	0	IFI16,missense_variant,p.Asp398Asn,ENST00000295809,;IFI16,missense_variant,p.Asp398Asn,ENST00000340979,;IFI16,missense_variant,p.Asp346Asn,ENST00000430894,;IFI16,missense_variant,p.Asp398Asn,ENST00000368132,;IFI16,missense_variant,p.Asp398Asn,ENST00000368131,;IFI16,missense_variant,p.Asp398Asn,ENST00000448393,;IFI16,missense_variant,p.Asp342Asn,ENST00000359709,;IFI16,non_coding_transcript_exon_variant,,ENST00000493884,;IFI16,non_coding_transcript_exon_variant,,ENST00000562225,;IFI16,non_coding_transcript_exon_variant,,ENST00000483916,;	A	ENSG00000163565	ENST00000368131	Transcript	missense_variant	1482	1192	398	D/N	Gac/Aac	.	.	.	1	IFI16	HGNC	5395	protein_coding	YES	CCDS1180.3	ENSP00000357113	IF16_HUMAN	H3BVE6_HUMAN,H3BR88_HUMAN,H3BR65_HUMAN,H3BM18_HUMAN	UPI00001412C9	.	tolerated(0.48)	probably_damaging(0.932)	7/11	.	hmmpanther:PTHR12200:SF5,hmmpanther:PTHR12200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATGACCCC	.	4	ESCA
DNAJC16	0	.	GRCh37	1	15901458	15901458	+	3'Flank	SNP	T	T	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000375847	.	33	28	5	17	17	0	DNAJC16,3_prime_UTR_variant,,ENST00000375849,;AGMAT,intron_variant,,ENST00000375826,;DNAJC16,downstream_gene_variant,,ENST00000375847,;DNAJC16,non_coding_transcript_exon_variant,,ENST00000483270,;DNAJC16,downstream_gene_variant,,ENST00000495523,;DNAJC16,downstream_gene_variant,,ENST00000475133,;	A	ENSG00000116138	ENST00000375847	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3230	1	DNAJC16	HGNC	29157	protein_coding	YES	CCDS30606.1	ENSP00000365007	DJC16_HUMAN	B3KMS3_HUMAN	UPI000000DBDB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAACATTTGTT	.	2	ESCA
CLCNKB	0	.	GRCh37	1	16382251	16382251	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1927G>A	p.Glu643Lys	p.E643K	ENST00000375679	18/20	76	72	4	65	65	0	CLCNKB,missense_variant,p.Glu643Lys,ENST00000375679,;CLCNKB,missense_variant,p.Glu473Lys,ENST00000375667,;CLCNKB,missense_variant,p.Glu131Lys,ENST00000431772,;FAM131C,downstream_gene_variant,,ENST00000375662,;FAM131C,downstream_gene_variant,,ENST00000494078,;	A	ENSG00000184908	ENST00000375679	Transcript	missense_variant	2038	1927	643	E/K	Gag/Aag	.	.	.	1	CLCNKB	HGNC	2027	protein_coding	YES	CCDS168.1	ENSP00000364831	CLCKB_HUMAN	.	UPI000040E261	.	tolerated(0.15)	benign(0.142)	18/20	.	Superfamily_domains:SSF54631,SMART_domains:SM00116,Pfam_domain:PF00571,Gene3D:3.10.580.10,hmmpanther:PTHR11689:SF78,hmmpanther:PTHR11689,PROSITE_profiles:PS51371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCATGAGGTA	.	2	ESCA
RXRG	0	.	GRCh37	1	165377516	165377516	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1086G>A	p.%3D	p.Q362Q	ENST00000359842	8/10	107	79	27	57	57	0	RXRG,synonymous_variant,p.%3D,ENST00000359842,;RXRG,downstream_gene_variant,,ENST00000470566,;	T	ENSG00000143171	ENST00000359842	Transcript	synonymous_variant	1389	1086	362	Q	caG/caA	.	.	.	-1	RXRG	HGNC	10479	protein_coding	YES	CCDS1248.1	ENSP00000352900	RXRG_HUMAN	F1D8Q7_HUMAN	UPI000004989F	.	.	.	8/10	.	hmmpanther:PTHR24083:SF83,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00545,Prints_domain:PR00398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCTGCAT	.	5	ESCA
TMCO1	0	.	GRCh37	1	165737460	165737460	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.270G>A	p.%3D	p.L90L	ENST00000367881	2/7	109	86	23	76	76	0	TMCO1,synonymous_variant,p.%3D,ENST00000392129,;TMCO1,synonymous_variant,p.%3D,ENST00000481278,;TMCO1,synonymous_variant,p.%3D,ENST00000367881,;TMCO1,5_prime_UTR_variant,,ENST00000464650,;TMCO1,5_prime_UTR_variant,,ENST00000580248,;RP11-466F5.8,upstream_gene_variant,,ENST00000423121,;TMCO1,synonymous_variant,p.%3D,ENST00000476143,;TMCO1,synonymous_variant,p.%3D,ENST00000465705,;	T	ENSG00000143183	ENST00000367881	Transcript	synonymous_variant	546	270	90	L	ctG/ctA	.	.	.	-1	TMCO1	HGNC	18188	protein_coding	YES	CCDS1251.2	ENSP00000356856	.	J9JIE6_HUMAN,J3QQY2_HUMAN	UPI0000EE3C5A	.	.	.	2/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR20917,Pfam_domain:PF01956,PIRSF_domain:PIRSF023322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A41A|c.123A>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCAGTCT	.	5	ESCA
F5	0	.	GRCh37	1	169524417	169524417	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118+3G>A	.	.	ENST00000367797	.	80	65	14	49	49	0	F5,splice_region_variant,,ENST00000367796,;F5,splice_region_variant,,ENST00000546081,;F5,splice_region_variant,,ENST00000367797,;	T	ENSG00000198734	ENST00000367797	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	F5	HGNC	3542	protein_coding	YES	CCDS1281.1	ENSP00000356771	FA5_HUMAN	Q8TD21_HUMAN,Q2HZZ1_HUMAN,Q1L610_HUMAN	UPI0000070F01	.	.	.	.	7/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACTCACTTG	.	4	ESCA
FMO2	0	.	GRCh37	1	171165874	171165874	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.408G>A	p.%3D	p.Q136Q	ENST00000441535	4/10	108	96	12	68	68	0	FMO2,synonymous_variant,p.%3D,ENST00000441535,;FMO2,synonymous_variant,p.%3D,ENST00000209929,;RP1-127D3.4,downstream_gene_variant,,ENST00000445909,;RP1-127D3.4,downstream_gene_variant,,ENST00000445290,;RP1-127D3.4,downstream_gene_variant,,ENST00000422841,;FMO2,non_coding_transcript_exon_variant,,ENST00000529935,;FMO2,intron_variant,,ENST00000489354,;FMO2,downstream_gene_variant,,ENST00000483192,;FMO2,downstream_gene_variant,,ENST00000462643,;	A	ENSG00000094963	ENST00000441535	Transcript	synonymous_variant	525	408	136	Q	caG/caA	COSM3802827	.	.	1	FMO2	HGNC	3770	protein_coding	YES	CCDS1293.1	ENSP00000405905	FMO2_HUMAN	B4E2Q9_HUMAN	UPI000013C672	.	.	.	4/10	.	hmmpanther:PTHR23023:SF84,hmmpanther:PTHR23023,Gene3D:3.50.50.60,Pfam_domain:PF00743,Superfamily_domains:SSF51905,Prints_domain:PR00370	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCAGAGTGC	.	4	ESCA
C1orf105	0	.	GRCh37	1	172437700	172437700	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.518G>C	p.Arg173Thr	p.R173T	ENST00000367727	7/7	38	32	5	20	20	0	C1orf105,missense_variant,p.Arg163Thr,ENST00000367725,;C1orf105,missense_variant,p.Arg173Thr,ENST00000367727,;C1orf105,downstream_gene_variant,,ENST00000488100,;C1orf105,non_coding_transcript_exon_variant,,ENST00000367726,;	C	ENSG00000180999	ENST00000367727	Transcript	missense_variant	716	518	173	R/T	aGa/aCa	.	.	.	1	C1orf105	HGNC	29591	protein_coding	YES	CCDS1301.1	ENSP00000356700	CA105_HUMAN	.	UPI000006D456	.	deleterious(0.01)	benign(0.402)	7/7	.	Pfam_domain:PF15081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCAGAAAGG	.	5	ESCA
CACNA1E	0	.	GRCh37	1	181752870	181752870	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5420C>G	p.Ser1807Cys	p.S1807C	ENST00000367573	40/48	89	61	28	79	79	0	CACNA1E,missense_variant,p.Ser1739Cys,ENST00000358338,;CACNA1E,missense_variant,p.Ser1414Cys,ENST00000367567,;CACNA1E,missense_variant,p.Ser1758Cys,ENST00000357570,;CACNA1E,missense_variant,p.Ser1788Cys,ENST00000360108,;CACNA1E,missense_variant,p.Ser1788Cys,ENST00000526775,;CACNA1E,missense_variant,p.Ser1807Cys,ENST00000367573,;CACNA1E,missense_variant,p.Ser1807Cys,ENST00000367570,;	G	ENSG00000198216	ENST00000367573	Transcript	missense_variant	5420	5420	1807	S/C	tCc/tGc	.	.	.	1	CACNA1E	HGNC	1392	protein_coding	YES	CCDS55664.1	ENSP00000356545	CAC1E_HUMAN	Q9UN68_HUMAN,Q9NYZ6_HUMAN,Q9NY05_HUMAN,E9PIE8_HUMAN	UPI00004588C2	.	deleterious(0)	possibly_damaging(0.7)	40/48	.	hmmpanther:PTHR10037:SF57,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTCCACAC	.	5	ESCA
HMCN1	0	.	GRCh37	1	186050412	186050412	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8673G>A	p.%3D	p.L2891L	ENST00000271588	56/107	52	46	5	42	42	0	HMCN1,synonymous_variant,p.%3D,ENST00000367492,;HMCN1,synonymous_variant,p.%3D,ENST00000271588,;	A	ENSG00000143341	ENST00000271588	Transcript	synonymous_variant	8902	8673	2891	L	ctG/ctA	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	.	56/107	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACTGATAGA	.	4	ESCA
UBR4	0	.	GRCh37	1	19510631	19510631	+	Silent	SNP	G	G	T	rs747148639	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1977C>A	p.%3D	p.T659T	ENST00000375254	16/106	31	25	6	20	20	0	UBR4,synonymous_variant,p.%3D,ENST00000375254,;UBR4,synonymous_variant,p.%3D,ENST00000375217,;UBR4,synonymous_variant,p.%3D,ENST00000375267,;UBR4,synonymous_variant,p.%3D,ENST00000375226,;	T	ENSG00000127481	ENST00000375254	Transcript	synonymous_variant	2005	1977	659	T	acC/acA	rs747148639	.	.	-1	UBR4	HGNC	30313	protein_coding	YES	CCDS189.1	ENSP00000364403	UBR4_HUMAN	Q96HY5_HUMAN	UPI000021276F	.	.	.	16/106	.	Superfamily_domains:SSF48371,hmmpanther:PTHR21725	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGAGGTGAT	.	5	ESCA
CAPZB	0	.	GRCh37	1	19683172	19683172	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.545C>G	p.Ser182Cys	p.S182C	ENST00000375142	6/10	88	82	6	51	51	0	CAPZB,missense_variant,p.Ser182Cys,ENST00000375142,;CAPZB,missense_variant,p.Ser170Cys,ENST00000375144,;CAPZB,missense_variant,p.Ser170Cys,ENST00000413711,;CAPZB,missense_variant,p.Ser211Cys,ENST00000433834,;CAPZB,missense_variant,p.Ser182Cys,ENST00000401084,;CAPZB,missense_variant,p.Ser182Cys,ENST00000264202,;CAPZB,missense_variant,p.Ser208Cys,ENST00000264203,;CAPZB,downstream_gene_variant,,ENST00000457768,;CAPZB,non_coding_transcript_exon_variant,,ENST00000459967,;CAPZB,downstream_gene_variant,,ENST00000489607,;	C	ENSG00000077549	ENST00000375142	Transcript	missense_variant	592	545	182	S/C	tCt/tGt	.	.	.	-1	CAPZB	HGNC	1491	protein_coding	YES	CCDS55579.1	ENSP00000364284	CAPZB_HUMAN	F6USW4_HUMAN	UPI0000126EDB	.	deleterious(0.02)	benign(0.008)	6/10	.	hmmpanther:PTHR10619,Pfam_domain:PF01115,Superfamily_domains:SSF90096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCAGATTTG	.	2	ESCA
ASPM	0	.	GRCh37	1	197059154	197059154	+	Missense_Mutation	SNP	G	G	A	rs201033114	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9890C>T	p.Ser3297Phe	p.S3297F	ENST00000367409	25/28	25	20	5	13	13	0	ASPM,missense_variant,p.Ser3297Phe,ENST00000367409,;ASPM,missense_variant,p.Ser962Phe,ENST00000367408,;ASPM,missense_variant,p.Ser1712Phe,ENST00000294732,;	A	ENSG00000066279	ENST00000367409	Transcript	missense_variant	10147	9890	3297	S/F	tCt/tTt	rs201033114	.	.	-1	ASPM	HGNC	19048	protein_coding	YES	CCDS1389.1	ENSP00000356379	ASPM_HUMAN	.	UPI0000458904	.	tolerated(0.19)	benign(0.009)	25/28	.	hmmpanther:PTHR25069:SF115,hmmpanther:PTHR25069,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	TTTTAGAAATT	byCluster|by1000G	3	ESCA
PPFIA4	0	.	GRCh37	1	203013536	203013536	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531G>A	p.%3D	p.E177E	ENST00000367240	5/29	44	30	13	41	41	0	PPFIA4,synonymous_variant,p.%3D,ENST00000367240,;PPFIA4,synonymous_variant,p.%3D,ENST00000447715,;PPFIA4,5_prime_UTR_variant,,ENST00000295706,;PPFIA4,upstream_gene_variant,,ENST00000414050,;PPFIA4,upstream_gene_variant,,ENST00000600426,;PPFIA4,upstream_gene_variant,,ENST00000601609,;	A	ENSG00000143847	ENST00000367240	Transcript	synonymous_variant	1058	531	177	E	gaG/gaA	.	.	.	1	PPFIA4	HGNC	9248	protein_coding	.	.	ENSP00000356209	.	B1APN9_HUMAN	UPI0001881B39	.	.	.	5/29	.	hmmpanther:PTHR12587:SF5,hmmpanther:PTHR12587,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAGCGAGT	.	5	ESCA
LAX1	0	.	GRCh37	1	203743776	203743776	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1164G>A	p.%3D	p.Q388Q	ENST00000442561	5/5	34	26	8	34	34	0	LAX1,synonymous_variant,p.%3D,ENST00000367217,;LAX1,synonymous_variant,p.%3D,ENST00000442561,;LAX1,non_coding_transcript_exon_variant,,ENST00000367215,;	A	ENSG00000122188	ENST00000442561	Transcript	synonymous_variant	1554	1164	388	Q	caG/caA	.	.	.	1	LAX1	HGNC	26005	protein_coding	YES	CCDS1441.2	ENSP00000406970	LAX1_HUMAN	.	UPI000007446D	.	.	.	5/5	.	hmmpanther:PTHR24091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCAGGGGCC	.	5	ESCA
SOX13	0	.	GRCh37	1	204086794	204086794	+	Missense_Mutation	SNP	C	C	T	rs764676220	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734C>T	p.Ser245Phe	p.S245F	ENST00000367204	7/14	56	44	12	30	30	0	SOX13,missense_variant,p.Ser245Phe,ENST00000367204,;SOX13,downstream_gene_variant,,ENST00000528591,;SOX13,downstream_gene_variant,,ENST00000525442,;SOX13,non_coding_transcript_exon_variant,,ENST00000272193,;SOX13,non_coding_transcript_exon_variant,,ENST00000367203,;SOX13,downstream_gene_variant,,ENST00000534185,;SOX13,downstream_gene_variant,,ENST00000530882,;SOX13,missense_variant,p.Ser106Phe,ENST00000480326,;SOX13,upstream_gene_variant,,ENST00000525258,;	T	ENSG00000143842	ENST00000367204	Transcript	missense_variant	843	734	245	S/F	tCc/tTc	rs764676220	.	.	1	SOX13	HGNC	11192	protein_coding	YES	CCDS44299.1	ENSP00000356172	SOX13_HUMAN	E9PPW0_HUMAN,E9PKD6_HUMAN,B4E3N9_HUMAN	UPI000034ECAB	.	tolerated(0.15)	benign(0.374)	7/14	.	hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTCCCAGC	.	5	ESCA
DYRK3	0	.	GRCh37	1	206822509	206822509	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*199A>G	.	.	ENST00000367109	3/3	53	40	13	57	57	0	DYRK3,3_prime_UTR_variant,,ENST00000367108,;DYRK3,3_prime_UTR_variant,,ENST00000367109,;DYRK3,downstream_gene_variant,,ENST00000441486,;DYRK3,downstream_gene_variant,,ENST00000367106,;DYRK3,intron_variant,,ENST00000489878,;	G	ENSG00000143479	ENST00000367109	Transcript	3_prime_UTR_variant	2134	.	.	.	.	.	.	.	1	DYRK3	HGNC	3094	protein_coding	YES	CCDS30999.1	ENSP00000356076	DYRK3_HUMAN	.	UPI0000071267	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAATATGC	.	5	ESCA
MUL1	0	.	GRCh37	1	20827622	20827622	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.620C>G	p.Ser207Cys	p.S207C	ENST00000264198	4/4	56	51	5	27	27	0	MUL1,missense_variant,p.Ser207Cys,ENST00000264198,;	C	ENSG00000090432	ENST00000264198	Transcript	missense_variant	757	620	207	S/C	tCt/tGt	.	.	.	-1	MUL1	HGNC	25762	protein_coding	YES	CCDS208.1	ENSP00000264198	MUL1_HUMAN	B7Z8S4_HUMAN	UPI00000361FC	.	tolerated(0.12)	benign(0.006)	4/4	.	hmmpanther:PTHR12183:SF4,hmmpanther:PTHR12183,Pfam_domain:PF12483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGACAGAGTTG	.	3	ESCA
LAMB3	0	.	GRCh37	1	209800282	209800282	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1527G>A	p.%3D	p.L509L	ENST00000391911	12/22	79	48	30	59	59	0	LAMB3,synonymous_variant,p.%3D,ENST00000356082,;LAMB3,synonymous_variant,p.%3D,ENST00000391911,;LAMB3,synonymous_variant,p.%3D,ENST00000367030,;MIR4260,upstream_gene_variant,,ENST00000583107,;	T	ENSG00000196878	ENST00000391911	Transcript	synonymous_variant	1917	1527	509	L	ctG/ctA	.	.	.	-1	LAMB3	HGNC	6490	protein_coding	YES	CCDS1487.1	ENSP00000375778	LAMB3_HUMAN	Q5THA1_HUMAN	UPI000012E76F	.	.	.	12/22	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF245,hmmpanther:PTHR10574,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,Superfamily_domains:SSF57196,Prints_domain:PR00011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATCAGGCC	.	5	ESCA
USH2A	0	.	GRCh37	1	215848443	215848443	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12810G>A	p.%3D	p.V4270V	ENST00000307340	63/72	53	39	14	35	35	0	USH2A,synonymous_variant,p.%3D,ENST00000366943,;USH2A,synonymous_variant,p.%3D,ENST00000307340,;	T	ENSG00000042781	ENST00000307340	Transcript	synonymous_variant	13197	12810	4270	V	gtG/gtA	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	.	63/72	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATATCACAGG	.	5	ESCA
USH2A	0	.	GRCh37	1	216420404	216420404	+	Missense_Mutation	SNP	C	C	T	rs142898216	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2332G>A	p.Asp778Asn	p.D778N	ENST00000307340	13/72	44	39	5	16	16	0	USH2A,missense_variant,p.Asp778Asn,ENST00000366942,;USH2A,missense_variant,p.Asp778Asn,ENST00000366943,;USH2A,missense_variant,p.Asp778Asn,ENST00000307340,;	T	ENSG00000042781	ENST00000307340	Transcript	missense_variant	2719	2332	778	D/N	Gac/Aac	rs142898216	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	possibly_damaging(0.533)	13/72	.	Prints_domain:PR00011,Superfamily_domains:SSF57196,SMART_domains:SM00180,Pfam_domain:PF00053,Gene3D:2.10.25.10,PROSITE_patterns:PS01248,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50027	.	.	.	.	.	.	.	A:0.0005	A:0	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GGTGTCACACT	byCluster	3	ESCA
NBPF3	0	.	GRCh37	1	21808259	21808259	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1603G>T	p.Asp535Tyr	p.D535Y	ENST00000318249	13/15	21	17	4	16	16	0	NBPF3,missense_variant,p.Asp479Tyr,ENST00000434838,;NBPF3,missense_variant,p.Asp535Tyr,ENST00000318249,;NBPF3,missense_variant,p.Asp479Tyr,ENST00000318220,;NBPF3,missense_variant,p.Asp523Tyr,ENST00000342104,;NBPF3,missense_variant,p.Asp465Tyr,ENST00000454000,;NBPF3,non_coding_transcript_exon_variant,,ENST00000469876,;NBPF3,downstream_gene_variant,,ENST00000477050,;	T	ENSG00000142794	ENST00000318249	Transcript	missense_variant	1953	1603	535	D/Y	Gat/Tat	.	.	.	1	NBPF3	HGNC	25076	protein_coding	YES	CCDS216.1	ENSP00000316782	NBPF3_HUMAN	.	UPI0000037D6C	.	deleterious(0)	possibly_damaging(0.773)	13/15	.	PROSITE_profiles:PS51316,hmmpanther:PTHR14199:SF15,hmmpanther:PTHR14199,Pfam_domain:PF06758	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACGTGGATGGT	.	2	ESCA
SLC30A10	0	.	GRCh37	1	220088979	220088979	+	Missense_Mutation	SNP	G	G	A	rs375331656	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1270C>T	p.His424Tyr	p.H424Y	ENST00000366926	4/4	70	52	18	30	30	0	SLC30A10,missense_variant,p.His179Tyr,ENST00000536446,;SLC30A10,missense_variant,p.His424Tyr,ENST00000366926,;SLC30A10,non_coding_transcript_exon_variant,,ENST00000484079,;SLC30A10,intron_variant,,ENST00000484239,;SLC30A10,3_prime_UTR_variant,,ENST00000356609,;	A	ENSG00000196660	ENST00000366926	Transcript	missense_variant	1432	1270	424	H/Y	Cac/Tac	rs375331656	.	.	-1	SLC30A10	HGNC	25355	protein_coding	YES	CCDS31026.1	ENSP00000355893	ZNT10_HUMAN	B3KR19_HUMAN	UPI000040E993	.	deleterious(0.05)	benign(0.016)	4/4	.	hmmpanther:PTHR11562:SF14,hmmpanther:PTHR11562	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACGTGAGCCA	byFrequency|byCluster	5	ESCA
EPHX1	0	.	GRCh37	1	226026976	226026976	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.651C>A	p.Phe217Leu	p.F217L	ENST00000366837	5/9	63	42	20	62	62	0	EPHX1,missense_variant,p.Phe217Leu,ENST00000366837,;EPHX1,missense_variant,p.Phe217Leu,ENST00000272167,;EPHX1,downstream_gene_variant,,ENST00000448202,;EPHX1,downstream_gene_variant,,ENST00000445856,;RP11-285F7.2,downstream_gene_variant,,ENST00000424332,;	A	ENSG00000143819	ENST00000366837	Transcript	missense_variant	847	651	217	F/L	ttC/ttA	.	.	.	1	EPHX1	HGNC	3401	protein_coding	YES	CCDS1547.1	ENSP00000355802	HYEP_HUMAN	R4SBI6_HUMAN,B1AQP9_HUMAN,B1AQP8_HUMAN	UPI000012CFF2	.	deleterious(0.03)	probably_damaging(0.983)	5/9	.	hmmpanther:PTHR21661,hmmpanther:PTHR21661:SF10,Gene3D:3.40.50.1820,Pfam_domain:PF00561,PIRSF_domain:PIRSF001112,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCCAGGA	.	5	ESCA
EPHX1	0	.	GRCh37	1	226032974	226032974	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1294T>A	p.Phe432Ile	p.F432I	ENST00000366837	9/9	63	56	7	46	46	0	EPHX1,missense_variant,p.Phe432Ile,ENST00000366837,;EPHX1,missense_variant,p.Phe432Ile,ENST00000272167,;TMEM63A,downstream_gene_variant,,ENST00000366835,;RP11-285F7.2,intron_variant,,ENST00000424332,;TMEM63A,downstream_gene_variant,,ENST00000496025,;TMEM63A,downstream_gene_variant,,ENST00000482753,;	A	ENSG00000143819	ENST00000366837	Transcript	missense_variant	1490	1294	432	F/I	Ttt/Att	.	.	.	1	EPHX1	HGNC	3401	protein_coding	YES	CCDS1547.1	ENSP00000355802	HYEP_HUMAN	R4SBI6_HUMAN,B1AQP9_HUMAN,B1AQP8_HUMAN	UPI000012CFF2	.	deleterious(0)	probably_damaging(1)	9/9	.	hmmpanther:PTHR21661,hmmpanther:PTHR21661:SF10,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF001112,Superfamily_domains:SSF53474,Prints_domain:PR00412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCACTTTGCG	.	4	ESCA
HTR1D	0	.	GRCh37	1	23520393	23520393	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320G>A	p.Gly107Asp	p.G107D	ENST00000374619	1/1	86	68	17	51	51	0	HTR1D,missense_variant,p.Gly107Asp,ENST00000314113,;HTR1D,missense_variant,p.Gly107Asp,ENST00000374619,;	T	ENSG00000179546	ENST00000374619	Transcript	missense_variant	830	320	107	G/D	gGc/gAc	COSM905787	.	.	-1	HTR1D	HGNC	5289	protein_coding	YES	CCDS231.1	ENSP00000363748	5HT1D_HUMAN	.	UPI00000503DE	.	deleterious(0)	probably_damaging(1)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF17,hmmpanther:PTHR24247,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGGCCAAAG	.	5	ESCA
RYR2	0	.	GRCh37	1	237954760	237954760	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13508G>A	p.Arg4503Lys	p.R4503K	ENST00000366574	93/105	88	70	18	76	76	0	RYR2,missense_variant,p.Arg4487Lys,ENST00000542537,;RYR2,missense_variant,p.Arg4503Lys,ENST00000366574,;RYR2,missense_variant,p.Arg4509Lys,ENST00000360064,;RYR2,upstream_gene_variant,,ENST00000608590,;	A	ENSG00000198626	ENST00000366574	Transcript	missense_variant	13825	13508	4503	R/K	aGa/aAa	COSM3418961,COSM3418960	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	possibly_damaging(0.694)	93/105	.	Pfam_domain:PF06459,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGAGAATGT	.	5	ESCA
RYR2	0	.	GRCh37	1	237955559	237955559	+	Missense_Mutation	SNP	G	G	A	rs371157286	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13718G>A	p.Arg4573His	p.R4573H	ENST00000366574	94/105	31	26	4	32	32	0	RYR2,missense_variant,p.Arg4557His,ENST00000542537,;RYR2,missense_variant,p.Arg4573His,ENST00000366574,;RYR2,missense_variant,p.Arg4579His,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000608590,;	A	ENSG00000198626	ENST00000366574	Transcript	missense_variant	14035	13718	4573	R/H	cGt/cAt	rs371157286	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	probably_damaging(0.98)	94/105	.	Pfam_domain:PF06459,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTGCGTATCT	byCluster	3	ESCA
GREM2	0	.	GRCh37	1	240654646	240654646	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1623C>G	.	.	ENST00000318160	2/2	35	28	7	24	24	0	GREM2,3_prime_UTR_variant,,ENST00000318160,;	C	ENSG00000180875	ENST00000318160	Transcript	3_prime_UTR_variant	2397	.	.	.	.	.	.	.	-1	GREM2	HGNC	17655	protein_coding	YES	CCDS31070.1	ENSP00000318650	GREM2_HUMAN	.	UPI000006F961	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGGTTTTC	.	5	ESCA
RP11-439E19.10	0	.	GRCh37	1	246943704	246943704	+	3'Flank	SNP	C	C	T	rs775171090	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000567832	.	59	44	14	36	36	0	RP11-439E19.3,non_coding_transcript_exon_variant,,ENST00000509202,;RP11-439E19.3,non_coding_transcript_exon_variant,,ENST00000421003,;RP11-439E19.3,non_coding_transcript_exon_variant,,ENST00000505748,;RP11-439E19.10,downstream_gene_variant,,ENST00000567832,;KIF28P,non_coding_transcript_exon_variant,,ENST00000451123,;KIF28P,downstream_gene_variant,,ENST00000508436,;KIF28P,non_coding_transcript_exon_variant,,ENST00000504864,;	T	ENSG00000260855	ENST00000567832	Transcript	downstream_gene_variant	.	.	.	.	.	rs775171090	.	4630	1	RP11-439E19.10	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGCGACTG	.	5	ESCA
NIPAL3	0	.	GRCh37	1	24766717	24766717	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.149C>T	p.Ala50Val	p.A50V	ENST00000374399	3/12	47	40	6	28	28	0	NIPAL3,missense_variant,p.Ala50Val,ENST00000358028,;NIPAL3,missense_variant,p.Ala50Val,ENST00000339255,;NIPAL3,missense_variant,p.Ala50Val,ENST00000428131,;NIPAL3,missense_variant,p.Ala50Val,ENST00000374399,;NIPAL3,5_prime_UTR_variant,,ENST00000003912,;	T	ENSG00000001461	ENST00000374399	Transcript	missense_variant	517	149	50	A/V	gCa/gTa	.	.	.	1	NIPAL3	HGNC	25233	protein_coding	YES	CCDS30631.1	ENSP00000363520	NPAL3_HUMAN	.	UPI000006FFD0	.	deleterious(0)	probably_damaging(0.936)	3/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12570,hmmpanther:PTHR12570:SF14,Pfam_domain:PF05653	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTGCACTTA	.	4	ESCA
OR2T11	0	.	GRCh37	1	248790179	248790179	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.251C>G	p.Ser84Cys	p.S84C	ENST00000330803	1/1	88	67	20	54	54	0	OR2T11,missense_variant,p.Ser84Cys,ENST00000330803,;	C	ENSG00000183130	ENST00000330803	Transcript	missense_variant	313	251	84	S/C	tCt/tGt	.	.	.	-1	OR2T11	HGNC	19574	protein_coding	YES	CCDS31122.1	ENSP00000328934	O2T11_HUMAN	.	UPI000004F23F	.	tolerated(0.17)	possibly_damaging(0.595)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF173,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTAGAAACC	.	5	ESCA
ZNF672	0	.	GRCh37	1	249141564	249141564	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.91C>T	p.Arg31Ter	p.R31*	ENST00000306562	4/4	66	59	7	44	44	0	ZNF672,stop_gained,p.Arg31Ter,ENST00000423362,;ZNF672,stop_gained,p.Arg31Ter,ENST00000428515,;ZNF672,stop_gained,p.Arg31Ter,ENST00000306562,;ZNF692,downstream_gene_variant,,ENST00000427146,;ZNF692,downstream_gene_variant,,ENST00000451251,;ZNF672,downstream_gene_variant,,ENST00000505503,;ZNF692,downstream_gene_variant,,ENST00000306601,;ZNF692,downstream_gene_variant,,ENST00000366471,;ZNF692,downstream_gene_variant,,ENST00000366469,;ZNF692,downstream_gene_variant,,ENST00000476503,;ZNF672,downstream_gene_variant,,ENST00000510904,;ZNF672,downstream_gene_variant,,ENST00000502697,;ZNF672,downstream_gene_variant,,ENST00000515369,;ZNF692,downstream_gene_variant,,ENST00000477070,;ZNF692,downstream_gene_variant,,ENST00000482023,;ZNF692,downstream_gene_variant,,ENST00000463519,;ZNF692,downstream_gene_variant,,ENST00000474351,;ZNF692,downstream_gene_variant,,ENST00000462037,;ZNF692,downstream_gene_variant,,ENST00000412341,;ZNF692,downstream_gene_variant,,ENST00000470787,;ZNF692,downstream_gene_variant,,ENST00000533927,;	T	ENSG00000171161	ENST00000306562	Transcript	stop_gained	837	91	31	R/*	Cga/Tga	.	.	.	1	ZNF672	HGNC	26179	protein_coding	YES	CCDS1638.1	ENSP00000421915	ZN672_HUMAN	D6RH11_HUMAN,D6RD56_HUMAN	UPI0000070D6C	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTGCGACAT	.	4	ESCA
PGBD2	0	.	GRCh37	1	249211564	249211564	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.781C>T	p.Pro261Ser	p.P261S	ENST00000329291	3/3	53	44	9	26	26	0	PGBD2,missense_variant,p.Pro258Ser,ENST00000539153,;PGBD2,missense_variant,p.Pro261Ser,ENST00000329291,;PGBD2,missense_variant,p.Pro10Ser,ENST00000355360,;RNU6-1205P,upstream_gene_variant,,ENST00000363625,;PGBD2,non_coding_transcript_exon_variant,,ENST00000462488,;	T	ENSG00000185220	ENST00000329291	Transcript	missense_variant	928	781	261	P/S	Ccc/Tcc	.	.	.	1	PGBD2	HGNC	19399	protein_coding	YES	CCDS31128.1	ENSP00000331643	PGBD2_HUMAN	.	UPI000016196D	.	tolerated(0.06)	possibly_damaging(0.461)	3/3	.	Pfam_domain:PF13843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCACCCTTG	.	5	ESCA
RHCE	0	.	GRCh37	1	25729208	25729208	+	Missense_Mutation	SNP	G	G	A	rs201407774	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365C>T	p.Ser122Leu	p.S122L	ENST00000294413	3/10	186	151	34	135	135	0	RHCE,missense_variant,p.Ser122Leu,ENST00000340849,;RHCE,missense_variant,p.Ser106Leu,ENST00000374352,;RHCE,missense_variant,p.Ser122Leu,ENST00000425135,;RHCE,missense_variant,p.Ser122Leu,ENST00000349438,;RHCE,missense_variant,p.Ser122Leu,ENST00000413854,;RHCE,missense_variant,p.Ser122Leu,ENST00000455194,;RHCE,missense_variant,p.Ser106Leu,ENST00000349320,;RHCE,missense_variant,p.Ser122Leu,ENST00000346452,;RHCE,missense_variant,p.Ser122Leu,ENST00000243186,;RHCE,missense_variant,p.Ser122Leu,ENST00000294413,;RHCE,upstream_gene_variant,,ENST00000527747,;AL031284.1,upstream_gene_variant,,ENST00000577655,;RHCE,non_coding_transcript_exon_variant,,ENST00000495048,;RHCE,3_prime_UTR_variant,,ENST00000533771,;RHCE,non_coding_transcript_exon_variant,,ENST00000527187,;RP3-469D22.1,downstream_gene_variant,,ENST00000541879,;RP3-469D22.1,downstream_gene_variant,,ENST00000419297,;	A	ENSG00000188672	ENST00000294413	Transcript	missense_variant	424	365	122	S/L	tCg/tTg	rs201407774,CM058209,BGMUT_777	.	.	-1	RHCE	HGNC	10008	protein_coding	YES	CCDS30635.1	ENSP00000294413	RHCE_HUMAN	Q9UP89_HUMAN,Q9UEC6_HUMAN,Q8NDV4_HUMAN,Q5UD29_HUMAN,D0AB04_HUMAN,D0AB03_HUMAN,B6ZCF8_HUMAN,B6ZCF7_HUMAN,A8YPS4_HUMAN	UPI00001D9627	.	deleterious(0.01)	benign(0.069)	3/10	.	Prints_domain:PR00342,Superfamily_domains:0044218,Gene3D:1.10.3430.10,Pfam_domain:PF00909,hmmpanther:PTHR11883:SF24,hmmpanther:PTHR11883,Transmembrane_helices:TMhelix	A:0.0002	A:0,A:0	A:0,A:0	.	A:0,A:0	A:0.001,A:0.001	A:0,A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCGACATA	byCluster|by1000G	5	ESCA
AL353354.1	0	.	GRCh37	1	28527133	28527133	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20A>G	p.His7Arg	p.H7R	ENST00000321830	1/2	40	27	12	34	34	0	AL353354.1,missense_variant,p.His7Arg,ENST00000321830,;AL353354.2,5_prime_UTR_variant,,ENST00000596102,;DNAJC8,3_prime_UTR_variant,,ENST00000263697,;DNAJC8,intron_variant,,ENST00000603289,;DNAJC8,non_coding_transcript_exon_variant,,ENST00000489277,;DNAJC8,downstream_gene_variant,,ENST00000470967,;	C	ENSG00000215902	ENST00000321830	Transcript	missense_variant	20	20	7	H/R	cAt/cGt	.	.	.	-1	AL353354.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000362959	.	H3BLX2_HUMAN	UPI00015E0B4A	.	.	unknown(0)	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACATGGTAC	.	5	ESCA
GMEB1	0	.	GRCh37	1	29028959	29028959	+	Missense_Mutation	SNP	C	C	T	rs201750134	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.638C>T	p.Thr213Met	p.T213M	ENST00000294409	7/10	77	61	16	41	41	0	GMEB1,missense_variant,p.Thr213Met,ENST00000294409,;GMEB1,missense_variant,p.Thr203Met,ENST00000373816,;GMEB1,missense_variant,p.Thr203Met,ENST00000361872,;GMEB1,non_coding_transcript_exon_variant,,ENST00000480454,;	T	ENSG00000162419	ENST00000294409	Transcript	missense_variant	728	638	213	T/M	aCg/aTg	rs201750134	.	.	1	GMEB1	HGNC	4370	protein_coding	YES	CCDS327.1	ENSP00000294409	GMEB1_HUMAN	.	UPI000012B8AB	.	tolerated(0.05)	benign(0.186)	7/10	.	hmmpanther:PTHR10417,hmmpanther:PTHR10417:SF3	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCACGCAGA	byCluster	5	ESCA
CCDC27	0	.	GRCh37	1	3673349	3673349	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606G>A	p.%3D	p.K202K	ENST00000294600	4/12	49	37	11	24	24	0	CCDC27,synonymous_variant,p.%3D,ENST00000294600,;CCDC27,missense_variant,p.Arg196Lys,ENST00000462521,;	A	ENSG00000162592	ENST00000294600	Transcript	synonymous_variant	690	606	202	K	aaG/aaA	.	.	.	1	CCDC27	HGNC	26546	protein_coding	YES	CCDS50.1	ENSP00000294600	CCD27_HUMAN	.	UPI000013E186	.	.	.	4/12	.	hmmpanther:PTHR18853,hmmpanther:PTHR18853:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGAAGAGGAG	.	5	ESCA
LEPRE1	0	.	GRCh37	1	43213395	43213395	+	Missense_Mutation	SNP	G	G	A	rs772830417	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1913C>T	p.Thr638Met	p.T638M	ENST00000236040	13/14	69	50	19	57	57	0	LEPRE1,missense_variant,p.Thr638Met,ENST00000397054,;LEPRE1,missense_variant,p.Thr638Met,ENST00000236040,;LEPRE1,missense_variant,p.Thr638Met,ENST00000296388,;LEPRE1,downstream_gene_variant,,ENST00000447502,;LEPRE1,splice_region_variant,,ENST00000462474,;LEPRE1,splice_region_variant,,ENST00000495874,;LEPRE1,splice_region_variant,,ENST00000460031,;LEPRE1,3_prime_UTR_variant,,ENST00000431412,;LEPRE1,downstream_gene_variant,,ENST00000481465,;LEPRE1,downstream_gene_variant,,ENST00000460831,;LEPRE1,upstream_gene_variant,,ENST00000472802,;	A	ENSG00000117385	ENST00000236040	Transcript	missense_variant	1954	1913	638	T/M	aCg/aTg	rs772830417	.	.	-1	LEPRE1	HGNC	19316	protein_coding	YES	CCDS57986.1	ENSP00000236040	P3H1_HUMAN	B4DTG8_HUMAN	UPI000013E32E	.	deleterious(0)	probably_damaging(0.983)	13/14	.	SMART_domains:SM00702,Pfam_domain:PF13640,hmmpanther:PTHR14049,hmmpanther:PTHR14049:SF5,PROSITE_profiles:PS51471	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCGTCACG	byFrequency	5	ESCA
ECHDC2	0	.	GRCh37	1	53387333	53387333	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13C>G	p.Leu5Val	p.L5V	ENST00000371522	1/10	15	11	3	16	16	0	ECHDC2,missense_variant,p.Leu5Val,ENST00000467988,;ECHDC2,missense_variant,p.Leu5Val,ENST00000358358,;ECHDC2,missense_variant,p.Leu5Val,ENST00000371522,;ECHDC2,5_prime_UTR_variant,,ENST00000536120,;ECHDC2,5_prime_UTR_variant,,ENST00000541281,;ECHDC2,non_coding_transcript_exon_variant,,ENST00000495920,;ECHDC2,upstream_gene_variant,,ENST00000544531,;ECHDC2,upstream_gene_variant,,ENST00000480312,;ECHDC2,missense_variant,p.Leu5Val,ENST00000476477,;ECHDC2,missense_variant,p.Leu5Val,ENST00000544365,;ECHDC2,missense_variant,p.Leu5Val,ENST00000542552,;ECHDC2,missense_variant,p.Leu5Val,ENST00000371520,;ECHDC2,non_coding_transcript_exon_variant,,ENST00000474789,;ECHDC2,non_coding_transcript_exon_variant,,ENST00000460612,;ECHDC2,upstream_gene_variant,,ENST00000488268,;RP4-631H13.6,downstream_gene_variant,,ENST00000420575,;RP4-631H13.4,downstream_gene_variant,,ENST00000436385,;	C	ENSG00000121310	ENST00000371522	Transcript	missense_variant	107	13	5	L/V	Ctg/Gtg	.	.	.	-1	ECHDC2	HGNC	23408	protein_coding	YES	CCDS55600.1	ENSP00000360577	ECHD2_HUMAN	Q8WY60_HUMAN,B7Z7N0_HUMAN	UPI0000204369	.	tolerated_low_confidence(0.05)	benign(0.352)	1/10	.	hmmpanther:PTHR11941,hmmpanther:PTHR11941:SF44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|VARSCANS	GCACAGAACGC	.	3	ESCA
NPHP4	0	.	GRCh37	1	5947473	5947473	+	Silent	SNP	G	G	A	rs371647995	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2358C>T	p.%3D	p.V786V	ENST00000378156	18/30	146	112	34	97	97	0	NPHP4,synonymous_variant,p.%3D,ENST00000378156,;NPHP4,non_coding_transcript_exon_variant,,ENST00000478423,;NPHP4,synonymous_variant,p.%3D,ENST00000489180,;NPHP4,3_prime_UTR_variant,,ENST00000378169,;NPHP4,3_prime_UTR_variant,,ENST00000466897,;NPHP4,upstream_gene_variant,,ENST00000470763,;	A	ENSG00000131697	ENST00000378156	Transcript	synonymous_variant	2624	2358	786	V	gtC/gtT	rs371647995,COSM3865907	.	.	-1	NPHP4	HGNC	19104	protein_coding	YES	CCDS44052.1	ENSP00000367398	NPHP4_HUMAN	.	UPI00001303E5	.	.	.	18/30	.	hmmpanther:PTHR31043:SF3,hmmpanther:PTHR31043	.	.	.	.	.	.	.	A:0	A:0.0002	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACGACCTC	byFrequency|byCluster	5	ESCA
ZBTB48	0	.	GRCh37	1	6642271	6642271	+	Missense_Mutation	SNP	G	G	A	rs549375724	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844G>A	p.Glu282Lys	p.E282K	ENST00000377674	3/11	68	53	15	44	44	0	ZBTB48,missense_variant,p.Glu282Lys,ENST00000435905,;ZBTB48,missense_variant,p.Glu37Lys,ENST00000488936,;ZBTB48,missense_variant,p.Glu282Lys,ENST00000377674,;ZBTB48,missense_variant,p.Glu282Lys,ENST00000319084,;TAS1R1,downstream_gene_variant,,ENST00000415267,;TAS1R1,downstream_gene_variant,,ENST00000351136,;TAS1R1,downstream_gene_variant,,ENST00000333172,;TAS1R1,downstream_gene_variant,,ENST00000328191,;TAS1R1,downstream_gene_variant,,ENST00000411823,;ZBTB48,upstream_gene_variant,,ENST00000498342,;ZBTB48,upstream_gene_variant,,ENST00000482360,;	A	ENSG00000204859	ENST00000377674	Transcript	missense_variant	1002	844	282	E/K	Gag/Aag	rs549375724	.	.	1	ZBTB48	HGNC	4930	protein_coding	YES	CCDS84.1	ENSP00000366902	ZBT48_HUMAN	Q6LCP1_HUMAN,Q5SY21_HUMAN,Q5SY20_HUMAN,K7EM76_HUMAN	UPI000012C932	.	tolerated(0.38)	benign(0.021)	3/11	.	hmmpanther:PTHR24375:SF5,hmmpanther:PTHR24375	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTGAGAAC	by1000G	5	ESCA
WDR63	0	.	GRCh37	1	85555813	85555813	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.755A>G	p.Asn252Ser	p.N252S	ENST00000294664	8/23	19	16	3	26	26	0	WDR63,missense_variant,p.Asn252Ser,ENST00000294664,;WDR63,intron_variant,,ENST00000326813,;WDR63,intron_variant,,ENST00000370596,;WDR63,missense_variant,p.Asn252Ser,ENST00000464801,;	G	ENSG00000162643	ENST00000294664	Transcript	missense_variant	935	755	252	N/S	aAt/aGt	.	.	.	1	WDR63	HGNC	30711	protein_coding	YES	CCDS702.1	ENSP00000294664	WDR63_HUMAN	.	UPI00000744F1	.	deleterious(0.02)	probably_damaging(0.94)	8/23	.	hmmpanther:PTHR12442:SF5,hmmpanther:PTHR12442	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAAAATGCTA	.	2	ESCA
GFI1	0	.	GRCh37	1	92941516	92941516	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*70C>G	.	.	ENST00000370332	7/7	45	34	11	48	48	0	GFI1,3_prime_UTR_variant,,ENST00000370332,;GFI1,3_prime_UTR_variant,,ENST00000294702,;GFI1,3_prime_UTR_variant,,ENST00000427103,;	C	ENSG00000162676	ENST00000370332	Transcript	3_prime_UTR_variant	1658	.	.	.	.	.	.	.	-1	GFI1	HGNC	4237	protein_coding	YES	CCDS30773.1	ENSP00000359357	GFI1_HUMAN	D3DT36_HUMAN	UPI000006D7FD	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCAGAGTGG	.	5	ESCA
SIRPB1	0	.	GRCh37	20	1592044	1592052	+	Intron	DEL	ACGTGGTCG	ACGTGGTCG	GTGTCA	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	ACGTGGTCG	ACGTGGTCG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76+8463_76+8471delCGACCACGTinsTGACAC	.	.	ENST00000381605	.	60	51	9	54	54	0	RP4-576H24.4,protein_altering_variant,p.His55_Val56delinsThr,ENST00000566961,;SIRPB1,protein_altering_variant,p.His130_Val131delinsThr,ENST00000279477,;SIRPB1,protein_altering_variant,p.His130_Val131delinsThr,ENST00000568365,;SIRPB1,protein_altering_variant,p.His7_Val8delinsThr,ENST00000569629,;RP4-576H24.4,intron_variant,,ENST00000564763,;SIRPB1,intron_variant,,ENST00000381605,;SIRPB1,intron_variant,,ENST00000381603,;SIRPB1,non_coding_transcript_exon_variant,,ENST00000381596,;SIRPB1,intron_variant,,ENST00000565775,;	GTGTCA	ENSG00000101307	ENST00000381605	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SIRPB1	HGNC	15928	protein_coding	YES	CCDS13019.1	ENSP00000371018	SIRB1_HUMAN	.	UPI000036700F	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.P128P|c.384C>T|3	INDELOCATOR*|PINDEL	AACTCCACGTGGTCGGGGCT	.	2	ESCA
RIN2	0	.	GRCh37	20	19981592	19981592	+	3'UTR	SNP	G	G	A	rs756129656	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*12G>A	.	.	ENST00000255006	12/12	17	13	4	25	25	0	RIN2,3_prime_UTR_variant,,ENST00000255006,;RIN2,3_prime_UTR_variant,,ENST00000440354,;RIN2,non_coding_transcript_exon_variant,,ENST00000484638,;	A	ENSG00000132669	ENST00000255006	Transcript	3_prime_UTR_variant	2996	.	.	.	.	rs756129656	.	.	1	RIN2	HGNC	18750	protein_coding	YES	CCDS56182.1	ENSP00000255006	RIN2_HUMAN	.	UPI00004709D0	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GGCGGGACTTC	.	4	ESCA
C20orf26	0	.	GRCh37	20	20269495	20269495	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3039C>G	p.%3D	p.L1013L	ENST00000245957	23/27	51	44	7	44	44	0	C20orf26,synonymous_variant,p.%3D,ENST00000245957,;C20orf26,intron_variant,,ENST00000377309,;C20orf26,non_coding_transcript_exon_variant,,ENST00000488640,;C20orf26,upstream_gene_variant,,ENST00000469994,;C20orf26,intron_variant,,ENST00000377308,;	G	ENSG00000089101	ENST00000245957	Transcript	synonymous_variant	3115	3039	1013	L	ctC/ctG	.	.	.	1	C20orf26	HGNC	15872	protein_coding	YES	CCDS33447.1	ENSP00000245957	CT026_HUMAN	C9JMV0_HUMAN,C9JHE8_HUMAN,C9J610_HUMAN	UPI0000206AE4	.	.	.	23/27	.	hmmpanther:PTHR21178:SF8,hmmpanther:PTHR21178,Gene3D:3.50.50.60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCTTTGA	.	4	ESCA
PAX1	0	.	GRCh37	20	21687102	21687102	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313C>A	p.Leu105Met	p.L105M	ENST00000398485	2/5	54	28	25	45	45	0	PAX1,missense_variant,p.Leu81Met,ENST00000444366,;PAX1,missense_variant,p.Leu105Met,ENST00000398485,;PAX1,intron_variant,,ENST00000460221,;PAX1,upstream_gene_variant,,ENST00000485038,;	A	ENSG00000125813	ENST00000398485	Transcript	missense_variant	367	313	105	L/M	Ctg/Atg	.	.	.	1	PAX1	HGNC	8615	protein_coding	YES	CCDS13146.2	ENSP00000381499	PAX1_HUMAN	.	UPI000179A786	.	deleterious(0)	probably_damaging(0.999)	2/5	.	PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF262,Pfam_domain:PF00292,Gene3D:1.10.10.10,SMART_domains:SM00351,Superfamily_domains:SSF46689,Prints_domain:PR00027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAGCTGGGC	.	5	ESCA
SIGLEC1	0	.	GRCh37	20	3674093	3674093	+	Splice_Site	SNP	C	C	T	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3508+1G>A	.	p.X1170_splice	ENST00000344754	.	55	48	7	67	67	0	SIGLEC1,splice_donor_variant,,ENST00000344754,;SIGLEC1,splice_donor_variant,,ENST00000202578,;SIGLEC1,upstream_gene_variant,,ENST00000419548,;	T	ENSG00000088827	ENST00000344754	Transcript	splice_donor_variant	.	.	.	.	.	COSM69290	.	.	-1	SIGLEC1	HGNC	11127	protein_coding	YES	CCDS13060.1	ENSP00000341141	SN_HUMAN	.	UPI0000049BA6	.	.	.	.	13/20	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTCACAGAGG	.	3	ESCA
CHD6	0	.	GRCh37	20	40084517	40084517	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2932G>A	p.Asp978Asn	p.D978N	ENST00000373233	19/37	59	48	11	40	40	0	CHD6,missense_variant,p.Asp978Asn,ENST00000373233,;CHD6,intron_variant,,ENST00000309279,;CHD6,intron_variant,,ENST00000440697,;RP4-620E11.4,downstream_gene_variant,,ENST00000423903,;	T	ENSG00000124177	ENST00000373233	Transcript	missense_variant	3110	2932	978	D/N	Gac/Aac	.	.	.	-1	CHD6	HGNC	19057	protein_coding	YES	CCDS13317.1	ENSP00000362330	CHD6_HUMAN	.	UPI0000168656	.	deleterious(0.01)	probably_damaging(0.983)	19/37	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF589,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGTCTTCTT	.	5	ESCA
R3HDML	0	.	GRCh37	20	42965973	42965973	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.176C>T	p.Ser59Phe	p.S59F	ENST00000217043	1/5	75	68	7	65	65	0	R3HDML,missense_variant,p.Ser59Phe,ENST00000217043,;	T	ENSG00000101074	ENST00000217043	Transcript	missense_variant	348	176	59	S/F	tCt/tTt	.	.	.	1	R3HDML	HGNC	16249	protein_coding	YES	CCDS13329.1	ENSP00000217043	CRSPL_HUMAN	.	UPI00000422F8	.	deleterious(0.02)	possibly_damaging(0.861)	1/5	.	hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF62,Gene3D:3.40.33.10,Superfamily_domains:SSF55797	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CATCTCTGTGA	.	3	ESCA
OLIG1	0	.	GRCh37	21	34444476	34444476	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1108G>A	.	.	ENST00000382348	1/1	58	39	19	75	75	0	OLIG1,3_prime_UTR_variant,,ENST00000333063,;OLIG1,3_prime_UTR_variant,,ENST00000426947,;OLIG1,3_prime_UTR_variant,,ENST00000382348,;AP000282.2,upstream_gene_variant,,ENST00000454622,;AP000282.2,upstream_gene_variant,,ENST00000420356,;OLIG1,non_coding_transcript_exon_variant,,ENST00000498799,;	A	ENSG00000184221	ENST00000382348	Transcript	3_prime_UTR_variant	2027	.	.	.	.	.	.	.	1	OLIG1	HGNC	16983	protein_coding	YES	CCDS42920.2	ENSP00000371785	OLIG1_HUMAN	Q59EM0_HUMAN	UPI0000130C80	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCAGGTCTT	.	5	ESCA
XKR3	0	.	GRCh37	22	17288835	17288835	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129C>A	p.%3D	p.L43L	ENST00000331428	2/4	18	12	5	32	32	0	XKR3,synonymous_variant,p.%3D,ENST00000331428,;	T	ENSG00000172967	ENST00000331428	Transcript	synonymous_variant	232	129	43	L	ctC/ctA	.	.	.	-1	XKR3	HGNC	28778	protein_coding	YES	CCDS42975.1	ENSP00000331704	XKR3_HUMAN	.	UPI000013EFAE	.	.	.	2/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14297,hmmpanther:PTHR14297:SF7,Pfam_domain:PF09815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTAGAGAAC	.	5	ESCA
MYO18B	0	.	GRCh37	22	26242238	26242238	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3540C>G	p.Ile1180Met	p.I1180M	ENST00000335473	19/44	35	19	15	37	37	0	MYO18B,missense_variant,p.Ile1180Met,ENST00000335473,;MYO18B,missense_variant,p.Ile1181Met,ENST00000407587,;MYO18B,missense_variant,p.Ile1180Met,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,;	G	ENSG00000133454	ENST00000335473	Transcript	missense_variant	3790	3540	1180	I/M	atC/atG	COSM579874	.	.	1	MYO18B	HGNC	18150	protein_coding	YES	CCDS54507.1	ENSP00000334563	.	Q8N903_HUMAN	UPI0000207402	.	deleterious(0.02)	probably_damaging(0.967)	19/44	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF254,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATCAAGCT	.	5	ESCA
CBX6	0	.	GRCh37	22	39261344	39261344	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*870C>G	.	.	ENST00000407418	5/5	18	8	10	14	14	0	CBX6,3_prime_UTR_variant,,ENST00000216083,;CBX6,3_prime_UTR_variant,,ENST00000407418,;CBX6,downstream_gene_variant,,ENST00000469420,;	C	ENSG00000183741	ENST00000407418	Transcript	3_prime_UTR_variant	2233	.	.	.	.	.	.	.	-1	CBX6	HGNC	1556	protein_coding	YES	CCDS13980.1	ENSP00000384490	CBX6_HUMAN	.	UPI00001271FD	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACTGAGGCG	.	5	ESCA
EP300	0	.	GRCh37	22	41565574	41565574	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4240T>G	p.Tyr1414Asp	p.Y1414D	ENST00000263253	26/31	21	12	9	20	20	0	EP300,missense_variant,p.Tyr1414Asp,ENST00000263253,;RNU6-375P,downstream_gene_variant,,ENST00000517050,;RP1-85F18.6,non_coding_transcript_exon_variant,,ENST00000415054,;	G	ENSG00000100393	ENST00000263253	Transcript	missense_variant	5459	4240	1414	Y/D	Tat/Gat	.	.	.	1	EP300	HGNC	3373	protein_coding	YES	CCDS14010.1	ENSP00000263253	EP300_HUMAN	B5A250_HUMAN	UPI00001AE876	.	.	probably_damaging(0.998)	26/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF4,Pfam_domain:PF08214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Y1414C|c.4241A>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTCTATCAT	.	5	ESCA
XRCC6	0	.	GRCh37	22	42033762	42033762	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740G>A	p.Arg247His	p.R247H	ENST00000359308	5/12	17	10	7	17	17	0	XRCC6,missense_variant,p.Arg247His,ENST00000405878,;XRCC6,missense_variant,p.Arg197His,ENST00000405506,;XRCC6,missense_variant,p.Arg247His,ENST00000359308,;XRCC6,missense_variant,p.Arg114His,ENST00000428575,;XRCC6,missense_variant,p.Arg206His,ENST00000402580,;XRCC6,missense_variant,p.Arg247His,ENST00000360079,;	A	ENSG00000196419	ENST00000359308	Transcript	missense_variant	1395	740	247	R/H	cGc/cAc	.	.	.	1	XRCC6	HGNC	4055	protein_coding	YES	CCDS14021.1	ENSP00000352257	XRCC6_HUMAN	F5H1I8_HUMAN	UPI0000000C8F	.	deleterious(0.01)	benign(0.134)	5/12	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12604,hmmpanther:PTHR12604:SF2,TIGRFAM_domain:TIGR00578,Gene3D:3.40.50.410,Pfam_domain:PF03731,PIRSF_domain:PIRSF003033,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCGCGCCA	.	5	ESCA
REV1	0	.	GRCh37	2	100017707	100017707	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3753A>G	p.%3D	p.T1251T	ENST00000258428	23/23	43	32	10	50	50	0	REV1,synonymous_variant,p.%3D,ENST00000258428,;REV1,synonymous_variant,p.%3D,ENST00000393445,;EIF5B,3_prime_UTR_variant,,ENST00000289371,;RP11-527J8.1,upstream_gene_variant,,ENST00000608144,;REV1,downstream_gene_variant,,ENST00000482595,;REV1,downstream_gene_variant,,ENST00000465835,;REV1,3_prime_UTR_variant,,ENST00000413697,;REV1,downstream_gene_variant,,ENST00000472000,;REV1,downstream_gene_variant,,ENST00000485487,;EIF5B,downstream_gene_variant,,ENST00000470023,;REV1,downstream_gene_variant,,ENST00000477121,;REV1,downstream_gene_variant,,ENST00000438366,;EIF5B,downstream_gene_variant,,ENST00000494190,;REV1,downstream_gene_variant,,ENST00000465086,;	C	ENSG00000135945	ENST00000258428	Transcript	synonymous_variant	3982	3753	1251	T	acA/acG	.	.	.	-1	REV1	HGNC	14060	protein_coding	YES	CCDS2045.1	ENSP00000258428	REV1_HUMAN	.	UPI0000073A14	.	.	.	23/23	.	PIRSF_domain:PIRSF036573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTATGTAAC	.	5	ESCA
REV1	0	.	GRCh37	2	100019123	100019123	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3525G>T	p.Trp1175Cys	p.W1175C	ENST00000258428	21/23	38	34	4	26	26	0	REV1,missense_variant,p.Trp1175Cys,ENST00000258428,;REV1,missense_variant,p.Trp1174Cys,ENST00000393445,;EIF5B,downstream_gene_variant,,ENST00000289371,;RP11-527J8.1,upstream_gene_variant,,ENST00000608144,;REV1,intron_variant,,ENST00000482595,;REV1,downstream_gene_variant,,ENST00000465835,;REV1,3_prime_UTR_variant,,ENST00000413697,;REV1,non_coding_transcript_exon_variant,,ENST00000465086,;REV1,downstream_gene_variant,,ENST00000472000,;REV1,downstream_gene_variant,,ENST00000485487,;EIF5B,downstream_gene_variant,,ENST00000470023,;REV1,downstream_gene_variant,,ENST00000477121,;REV1,downstream_gene_variant,,ENST00000438366,;EIF5B,downstream_gene_variant,,ENST00000494190,;	A	ENSG00000135945	ENST00000258428	Transcript	missense_variant	3754	3525	1175	W/C	tgG/tgT	.	.	.	-1	REV1	HGNC	14060	protein_coding	YES	CCDS2045.1	ENSP00000258428	REV1_HUMAN	.	UPI0000073A14	.	deleterious(0)	probably_damaging(0.999)	21/23	.	PIRSF_domain:PIRSF036573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTATCCATTC	.	4	ESCA
TAF1B	0	.	GRCh37	2	10008430	10008430	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.425C>G	p.Ser142Ter	p.S142*	ENST00000263663	6/15	27	23	4	25	25	0	TAF1B,stop_gained,p.Ser142Ter,ENST00000263663,;TAF1B,5_prime_UTR_variant,,ENST00000396242,;TAF1B,non_coding_transcript_exon_variant,,ENST00000402170,;TAF1B,non_coding_transcript_exon_variant,,ENST00000469895,;TAF1B,non_coding_transcript_exon_variant,,ENST00000480197,;TAF1B,stop_gained,p.Ser142Ter,ENST00000434858,;	G	ENSG00000115750	ENST00000263663	Transcript	stop_gained	613	425	142	S/*	tCa/tGa	.	.	.	1	TAF1B	HGNC	11533	protein_coding	YES	CCDS33143.1	ENSP00000263663	TAF1B_HUMAN	.	UPI0000208E44	.	.	.	6/15	.	hmmpanther:PTHR31576,hmmpanther:PTHR31576:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATTCAGACT	.	4	ESCA
SLC9A4	0	.	GRCh37	2	103120146	103120146	+	Silent	SNP	C	C	T	rs752491917	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.960C>T	p.%3D	p.L320L	ENST00000295269	3/12	66	62	4	30	30	0	SLC9A4,synonymous_variant,p.%3D,ENST00000295269,;SLC9A4,non_coding_transcript_exon_variant,,ENST00000492154,;	T	ENSG00000180251	ENST00000295269	Transcript	synonymous_variant	1417	960	320	L	ctC/ctT	rs752491917	.	.	1	SLC9A4	HGNC	11077	protein_coding	YES	CCDS33264.1	ENSP00000295269	SL9A4_HUMAN	.	UPI000047F996	.	.	.	3/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10110:SF103,hmmpanther:PTHR10110,Pfam_domain:PF00999,TIGRFAM_domain:TIGR00840	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCCTCTATCT	.	2	ESCA
GCC2	0	.	GRCh37	2	109089316	109089316	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2821G>A	p.Asp941Asn	p.D941N	ENST00000309863	7/23	43	35	7	33	33	0	GCC2,missense_variant,p.Asp103Asn,ENST00000492785,;GCC2,missense_variant,p.Asp941Asn,ENST00000309863,;GCC2,missense_variant,p.Asp904Asn,ENST00000409896,;GCC2,missense_variant,p.Asp113Asn,ENST00000462897,;GCC2,downstream_gene_variant,,ENST00000409821,;GCC2,downstream_gene_variant,,ENST00000485546,;GCC2,downstream_gene_variant,,ENST00000478207,;GCC2,3_prime_UTR_variant,,ENST00000482325,;GCC2,upstream_gene_variant,,ENST00000447558,;	A	ENSG00000135968	ENST00000309863	Transcript	missense_variant	3535	2821	941	D/N	Gat/Aat	.	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	tolerated(0.17)	benign(0.019)	7/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATGATCCT	.	5	ESCA
DPP10	0	.	GRCh37	2	116599859	116599859	+	Missense_Mutation	SNP	T	T	G	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2341T>G	p.Phe781Val	p.F781V	ENST00000393147	26/26	33	20	13	31	31	0	DPP10,missense_variant,p.Phe781Val,ENST00000393147,;DPP10,missense_variant,p.Phe727Val,ENST00000409163,;DPP10,missense_variant,p.Phe770Val,ENST00000310323,;DPP10,missense_variant,p.Phe777Val,ENST00000410059,;	G	ENSG00000175497	ENST00000393147	Transcript	missense_variant	2696	2341	781	F/V	Ttc/Gtc	COSM1250642,COSM1250640,COSM1250641,COSM1250639	.	.	1	DPP10	HGNC	20823	protein_coding	YES	CCDS54388.1	ENSP00000376855	DPP10_HUMAN	J3KQK8_HUMAN,C9J4M8_HUMAN	UPI00015E0A22	.	deleterious(0)	possibly_damaging(0.839)	26/26	.	hmmpanther:PTHR11731:SF21,hmmpanther:PTHR11731,Pfam_domain:PF00326,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTCTTCAGT	.	5	ESCA
GREB1	0	.	GRCh37	2	11765302	11765302	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4170G>C	p.Trp1390Cys	p.W1390C	ENST00000381486	24/33	52	38	14	54	54	0	GREB1,missense_variant,p.Trp1390Cys,ENST00000234142,;GREB1,missense_variant,p.Trp388Cys,ENST00000396123,;GREB1,missense_variant,p.Trp1390Cys,ENST00000381486,;	C	ENSG00000196208	ENST00000381486	Transcript	missense_variant	4470	4170	1390	W/C	tgG/tgC	COSM4084393	.	.	1	GREB1	HGNC	24885	protein_coding	YES	CCDS42655.1	ENSP00000370896	GREB1_HUMAN	.	UPI0000163937	.	tolerated(0.17)	probably_damaging(0.972)	24/33	.	hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGGCATTA	.	5	ESCA
TUBA3E	0	.	GRCh37	2	130949566	130949566	+	Silent	SNP	G	G	C	rs759535569	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1191C>G	p.%3D	p.L397L	ENST00000312988	5/5	63	47	15	49	49	0	TUBA3E,synonymous_variant,p.%3D,ENST00000312988,;MZT2B,downstream_gene_variant,,ENST00000457492,;MZT2B,downstream_gene_variant,,ENST00000425361,;MZT2B,downstream_gene_variant,,ENST00000455239,;MZT2B,downstream_gene_variant,,ENST00000281871,;MZT2B,downstream_gene_variant,,ENST00000409255,;MZT2B,downstream_gene_variant,,ENST00000491178,;MZT2B,downstream_gene_variant,,ENST00000480182,;	C	ENSG00000152086	ENST00000312988	Transcript	synonymous_variant	1292	1191	397	L	ctC/ctG	rs759535569	.	.	-1	TUBA3E	HGNC	20765	protein_coding	YES	CCDS2158.1	ENSP00000318197	TBA3E_HUMAN	F8VXZ7_HUMAN	UPI00001BE8EB	.	.	.	5/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Gene3D:1.10.287.600,Superfamily_domains:SSF55307,Prints_domain:PR01161,Prints_domain:PR01162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACATGAGATC	byFrequency	5	ESCA
GPR39	0	.	GRCh37	2	133174609	133174610	+	5'UTR	INS	-	-	GAA	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-7_-6insGAA	.	.	ENST00000329321	1/2	78	59	19	48	48	0	GPR39,5_prime_UTR_variant,,ENST00000329321,;	GAA	ENSG00000183840	ENST00000329321	Transcript	5_prime_UTR_variant	463-464	.	.	.	.	.	.	.	1	GPR39	HGNC	4496	protein_coding	YES	CCDS2170.1	ENSP00000327417	GPR39_HUMAN	Q53RU7_HUMAN,B3KVZ1_HUMAN,A4FVA5_HUMAN	UPI0000046406	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGCTCTTTCT	.	3	ESCA
NCKAP5	0	.	GRCh37	2	133541104	133541104	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3280G>C	p.Asp1094His	p.D1094H	ENST00000409261	14/20	84	61	23	58	58	0	NCKAP5,missense_variant,p.Asp1094His,ENST00000409261,;NCKAP5,missense_variant,p.Asp1094His,ENST00000317721,;NCKAP5,intron_variant,,ENST00000409213,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,upstream_gene_variant,,ENST00000473859,;	G	ENSG00000176771	ENST00000409261	Transcript	missense_variant	3654	3280	1094	D/H	Gat/Cat	.	.	.	-1	NCKAP5	HGNC	29847	protein_coding	YES	CCDS46418.1	ENSP00000387128	NCKP5_HUMAN	C9JYL7_HUMAN	UPI0000E07A3F	.	deleterious(0)	probably_damaging(0.922)	14/20	.	hmmpanther:PTHR21740:SF0,hmmpanther:PTHR21740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTATCATTCA	.	3	ESCA
STAM2	0	.	GRCh37	2	153032245	153032245	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-89C>G	.	.	ENST00000263904	1/14	30	22	7	28	28	0	STAM2,5_prime_UTR_variant,,ENST00000263904,;STAM2,non_coding_transcript_exon_variant,,ENST00000494589,;STAM2,non_coding_transcript_exon_variant,,ENST00000463854,;STAM2,upstream_gene_variant,,ENST00000482997,;	C	ENSG00000115145	ENST00000263904	Transcript	5_prime_UTR_variant	262	.	.	.	.	.	.	.	-1	STAM2	HGNC	11358	protein_coding	YES	CCDS2196.1	ENSP00000263904	STAM2_HUMAN	.	UPI0000071984	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTAGACCGC	.	5	ESCA
ZNF804A	0	.	GRCh37	2	185800688	185800688	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565A>C	p.Ser189Arg	p.S189R	ENST00000302277	4/4	23	18	5	24	24	0	ZNF804A,missense_variant,p.Ser189Arg,ENST00000302277,;	C	ENSG00000170396	ENST00000302277	Transcript	missense_variant	1159	565	189	S/R	Agt/Cgt	.	.	.	1	ZNF804A	HGNC	21711	protein_coding	YES	CCDS2291.1	ENSP00000303252	Z804A_HUMAN	.	UPI00001B4B18	.	tolerated(0.1)	benign(0.348)	4/4	.	hmmpanther:PTHR17614:SF13,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAAGTGCA	.	5	ESCA
SATB2	0	.	GRCh37	2	200298187	200298187	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.220G>C	p.Glu74Gln	p.E74Q	ENST00000417098	3/11	30	23	6	20	20	0	SATB2,missense_variant,p.Glu74Gln,ENST00000260926,;SATB2,missense_variant,p.Glu74Gln,ENST00000428695,;SATB2,missense_variant,p.Glu74Gln,ENST00000417098,;SATB2,missense_variant,p.Glu74Gln,ENST00000457245,;SATB2,intron_variant,,ENST00000443023,;SATB2,missense_variant,p.Glu74Gln,ENST00000440919,;	G	ENSG00000119042	ENST00000417098	Transcript	missense_variant	1037	220	74	E/Q	Gaa/Caa	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	tolerated(0.15)	benign(0.024)	3/11	.	hmmpanther:PTHR15116,hmmpanther:PTHR15116:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCAAGAG	.	5	ESCA
APOB	0	.	GRCh37	2	21229677	21229677	+	Missense_Mutation	SNP	C	C	T	rs776374541	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10063G>A	p.Glu3355Lys	p.E3355K	ENST00000233242	26/29	44	41	3	31	31	0	APOB,missense_variant,p.Glu3355Lys,ENST00000233242,;	T	ENSG00000084674	ENST00000233242	Transcript	missense_variant	10191	10063	3355	E/K	Gaa/Aaa	rs776374541	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	benign(0.084)	26/29	.	hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTTCAGCAT	.	2	ESCA
CHRND	0	.	GRCh37	2	233394716	233394716	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.687C>A	p.Asp229Glu	p.D229E	ENST00000258385	7/12	52	42	9	59	59	0	CHRND,missense_variant,p.Asp229Glu,ENST00000258385,;CHRND,missense_variant,p.Gln193Lys,ENST00000536614,;CHRND,missense_variant,p.Asp214Glu,ENST00000543200,;CHRND,intron_variant,,ENST00000457943,;PRSS56,downstream_gene_variant,,ENST00000449534,;CHRND,downstream_gene_variant,,ENST00000449596,;CHRND,missense_variant,p.Gln193Lys,ENST00000441621,;CHRND,3_prime_UTR_variant,,ENST00000446616,;CHRND,intron_variant,,ENST00000412233,;	A	ENSG00000135902	ENST00000258385	Transcript	missense_variant	719	687	229	D/E	gaC/gaA	.	.	.	1	CHRND	HGNC	1965	protein_coding	YES	CCDS2494.1	ENSP00000258385	ACHD_HUMAN	.	UPI000012525E	.	tolerated(0.55)	benign(0.001)	7/12	.	hmmpanther:PTHR18945:SF61,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02931,Gene3D:2.70.170.10,Superfamily_domains:0038932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGACAGCCC	.	5	ESCA
UBE2F	0	.	GRCh37	2	238949975	238949975	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554G>C	p.Arg185Thr	p.R185T	ENST00000272930	10/10	73	63	10	77	77	0	UBE2F,missense_variant,p.Arg161Thr,ENST00000409953,;UBE2F,missense_variant,p.Arg163Thr,ENST00000409332,;UBE2F,missense_variant,p.Arg153Thr,ENST00000414443,;UBE2F,missense_variant,p.Arg164Thr,ENST00000409633,;UBE2F,missense_variant,p.Arg185Thr,ENST00000272930,;UBE2F,downstream_gene_variant,,ENST00000434655,;UBE2F,downstream_gene_variant,,ENST00000416292,;UBE2F-SCLY,missense_variant,p.Arg131Thr,ENST00000449191,;UBE2F,3_prime_UTR_variant,,ENST00000455999,;UBE2F,3_prime_UTR_variant,,ENST00000454786,;UBE2F,3_prime_UTR_variant,,ENST00000445676,;UBE2F,3_prime_UTR_variant,,ENST00000417231,;UBE2F,3_prime_UTR_variant,,ENST00000433241,;UBE2F,3_prime_UTR_variant,,ENST00000441728,;UBE2F,3_prime_UTR_variant,,ENST00000439338,;UBE2F,non_coding_transcript_exon_variant,,ENST00000480828,;UBE2F,non_coding_transcript_exon_variant,,ENST00000472479,;UBE2F-SCLY,intron_variant,,ENST00000449891,;UBE2F,downstream_gene_variant,,ENST00000439780,;	C	ENSG00000184182	ENST00000272930	Transcript	missense_variant	748	554	185	R/T	aGa/aCa	.	.	.	1	UBE2F	HGNC	12480	protein_coding	YES	CCDS2523.1	ENSP00000272930	UBE2F_HUMAN	C9J9P8_HUMAN	UPI000007332C	.	deleterious(0)	possibly_damaging(0.877)	10/10	.	SMART_domains:SM00212,hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF56	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCAGATGAT	.	4	ESCA
TMEM214	0	.	GRCh37	2	27261971	27261971	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1464G>A	p.%3D	p.L488L	ENST00000238788	13/17	37	28	8	33	33	0	TMEM214,synonymous_variant,p.%3D,ENST00000444135,;TMEM214,synonymous_variant,p.%3D,ENST00000404032,;TMEM214,synonymous_variant,p.%3D,ENST00000238788,;TMEM214,downstream_gene_variant,,ENST00000425720,;AGBL5,upstream_gene_variant,,ENST00000421915,;TMEM214,synonymous_variant,p.%3D,ENST00000321326,;TMEM214,synonymous_variant,p.%3D,ENST00000434544,;TMEM214,3_prime_UTR_variant,,ENST00000435172,;TMEM214,downstream_gene_variant,,ENST00000460904,;TMEM214,upstream_gene_variant,,ENST00000469445,;TMEM214,upstream_gene_variant,,ENST00000460665,;TMEM214,downstream_gene_variant,,ENST00000495312,;TMEM214,downstream_gene_variant,,ENST00000478980,;TMEM214,downstream_gene_variant,,ENST00000475258,;	A	ENSG00000119777	ENST00000238788	Transcript	synonymous_variant	1526	1464	488	L	ttG/ttA	.	.	.	1	TMEM214	HGNC	25983	protein_coding	YES	CCDS42664.1	ENSP00000238788	TM214_HUMAN	B2RD07_HUMAN	UPI00003FF926	.	.	.	13/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13448,Pfam_domain:PF10151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTGTTGCTGCT	.	4	ESCA
IFT172	0	.	GRCh37	2	27670443	27670443	+	Missense_Mutation	SNP	G	G	A	rs202181028	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4598C>T	p.Thr1533Met	p.T1533M	ENST00000260570	42/48	37	32	4	31	31	0	IFT172,missense_variant,p.Thr1533Met,ENST00000260570,;KRTCAP3,downstream_gene_variant,,ENST00000452499,;KRTCAP3,downstream_gene_variant,,ENST00000407293,;KRTCAP3,downstream_gene_variant,,ENST00000543753,;KRTCAP3,downstream_gene_variant,,ENST00000288873,;IFT172,missense_variant,p.Thr57Met,ENST00000420854,;IFT172,3_prime_UTR_variant,,ENST00000509128,;IFT172,non_coding_transcript_exon_variant,,ENST00000480892,;IFT172,non_coding_transcript_exon_variant,,ENST00000507184,;IFT172,downstream_gene_variant,,ENST00000450564,;KRTCAP3,downstream_gene_variant,,ENST00000494572,;IFT172,upstream_gene_variant,,ENST00000494163,;IFT172,upstream_gene_variant,,ENST00000479419,;KRTCAP3,downstream_gene_variant,,ENST00000453171,;KRTCAP3,downstream_gene_variant,,ENST00000464699,;	A	ENSG00000138002	ENST00000260570	Transcript	missense_variant	4702	4598	1533	T/M	aCg/aTg	rs202181028	.	.	-1	IFT172	HGNC	30391	protein_coding	YES	CCDS1755.1	ENSP00000260570	IF172_HUMAN	H7C161_HUMAN	UPI0000353ABB	.	tolerated(0.07)	benign(0.013)	42/48	.	hmmpanther:PTHR15722,hmmpanther:PTHR15722:SF2	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATCGTCTTG	byCluster|by1000G	4	ESCA
GPR75	0	.	GRCh37	2	54081859	54081859	+	Missense_Mutation	SNP	T	T	C	rs775964311	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35A>G	p.Asn12Ser	p.N12S	ENST00000394705	2/2	43	30	12	39	39	0	GPR75,missense_variant,p.Asn12Ser,ENST00000394705,;ASB3,intron_variant,,ENST00000406625,;GPR75-ASB3,intron_variant,,ENST00000352846,;ASB3,intron_variant,,ENST00000498475,;ASB3,intron_variant,,ENST00000459916,;	C	ENSG00000119737	ENST00000394705	Transcript	missense_variant	306	35	12	N/S	aAt/aGt	rs775964311	.	.	-1	GPR75	HGNC	4526	protein_coding	YES	CCDS1849.1	ENSP00000378195	GPR75_HUMAN	.	UPI0000050454	.	tolerated_low_confidence(0.08)	possibly_damaging(0.477)	2/2	.	hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGGCATTGGGG	byFrequency	4	ESCA
MEIS1	0	.	GRCh37	2	66795917	66795917	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114+29C>T	.	.	ENST00000272369	.	39	24	14	9	9	0	MEIS1,3_prime_UTR_variant,,ENST00000488550,;MEIS1,intron_variant,,ENST00000495021,;MEIS1,intron_variant,,ENST00000444274,;MEIS1,intron_variant,,ENST00000407092,;MEIS1,intron_variant,,ENST00000272369,;MEIS1,intron_variant,,ENST00000398506,;MEIS1,downstream_gene_variant,,ENST00000450027,;MEIS1,downstream_gene_variant,,ENST00000606455,;MEIS1,downstream_gene_variant,,ENST00000560281,;MEIS1,intron_variant,,ENST00000409517,;MEIS1,intron_variant,,ENST00000542964,;MEIS1,downstream_gene_variant,,ENST00000475239,;	T	ENSG00000143995	ENST00000272369	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MEIS1	HGNC	7000	protein_coding	YES	CCDS46309.1	ENSP00000272369	MEIS1_HUMAN	Q8IZZ2_HUMAN,Q53RD5_HUMAN,Q53R57_HUMAN	UPI000000DA5A	.	.	.	.	11/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCCTCATTTT	.	3	ESCA
TACR1	0	.	GRCh37	2	75425863	75425863	+	Silent	SNP	C	C	T	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198G>A	p.%3D	p.V66V	ENST00000305249	1/5	77	55	22	48	48	0	TACR1,synonymous_variant,p.%3D,ENST00000305249,;TACR1,synonymous_variant,p.%3D,ENST00000409848,;	T	ENSG00000115353	ENST00000305249	Transcript	synonymous_variant	964	198	66	V	gtG/gtA	COSM3785324	.	.	-1	TACR1	HGNC	11526	protein_coding	YES	CCDS1958.1	ENSP00000303522	NK1R_HUMAN	Q53TR1_HUMAN,Q53TQ2_HUMAN	UPI0000039D68	.	.	.	1/5	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF14,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T67T|c.201G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCGTCACTGT	.	5	ESCA
TGOLN2	0	.	GRCh37	2	85548357	85548357	+	3'Flank	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000409232	.	18	12	6	10	10	0	TGOLN2,3_prime_UTR_variant,,ENST00000398263,;TGOLN2,3_prime_UTR_variant,,ENST00000282120,;TGOLN2,3_prime_UTR_variant,,ENST00000377386,;TGOLN2,downstream_gene_variant,,ENST00000409232,;TGOLN2,downstream_gene_variant,,ENST00000444342,;TGOLN2,downstream_gene_variant,,ENST00000409015,;AC093162.5,downstream_gene_variant,,ENST00000501107,;	A	ENSG00000152291	ENST00000409232	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	660	-1	TGOLN2	HGNC	15450	protein_coding	YES	CCDS56126.1	ENSP00000386443	.	F8WBK2_HUMAN	UPI000020880A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTAACGCATC	.	5	ESCA
SEMA4C	0	.	GRCh37	2	97530058	97530058	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>C	p.Glu342Gln	p.E342Q	ENST00000305476	10/15	75	71	4	53	53	0	SEMA4C,missense_variant,p.Glu342Gln,ENST00000305476,;SEMA4C,downstream_gene_variant,,ENST00000442264,;SEMA4C,downstream_gene_variant,,ENST00000449330,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000482925,;SEMA4C,upstream_gene_variant,,ENST00000467747,;SEMA4C,upstream_gene_variant,,ENST00000474420,;	G	ENSG00000168758	ENST00000305476	Transcript	missense_variant	1157	1024	342	E/Q	Gag/Cag	.	.	.	-1	SEMA4C	HGNC	10731	protein_coding	YES	CCDS2029.1	ENSP00000306844	SEM4C_HUMAN	Q8NBN9_HUMAN,Q6P5A5_HUMAN,Q53RE7_HUMAN,C9JV89_HUMAN,C9J4M7_HUMAN	UPI00001A7981	.	tolerated(0.07)	possibly_damaging(0.903)	10/15	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF16,hmmpanther:PTHR11036,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCTCAAACA	.	2	ESCA
ANKRD36	0	.	GRCh37	2	97877280	97877280	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3368-3C>G	.	.	ENST00000420699	.	220	191	29	165	165	0	ANKRD36,splice_region_variant,,ENST00000461153,;ANKRD36,splice_region_variant,,ENST00000420699,;ANKRD36,upstream_gene_variant,,ENST00000421946,;	G	ENSG00000135976	ENST00000420699	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	ANKRD36	HGNC	24079	protein_coding	YES	CCDS54379.1	ENSP00000391950	AN36A_HUMAN	.	UPI0001B23BB4	.	.	.	.	56/75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CTTTTCAGTGT	.	3	ESCA
SLC9C1	0	.	GRCh37	3	111997672	111997672	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.222G>A	p.Met74Ile	p.M74I	ENST00000305815	4/29	49	45	4	25	25	0	SLC9C1,start_lost,p.Met1?,ENST00000486574,;SLC9C1,missense_variant,p.Met74Ile,ENST00000487372,;SLC9C1,missense_variant,p.Met74Ile,ENST00000305815,;SLC9C1,non_coding_transcript_exon_variant,,ENST00000467397,;SLC9C1,missense_variant,p.Met74Ile,ENST00000471295,;	T	ENSG00000172139	ENST00000305815	Transcript	missense_variant	475	222	74	M/I	atG/atA	.	.	.	-1	SLC9C1	HGNC	31401	protein_coding	YES	CCDS33817.1	ENSP00000306627	SL9C1_HUMAN	C9J3M6_HUMAN	UPI00002372C5	.	tolerated(0.59)	benign(0.078)	4/29	.	hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF87,Pfam_domain:PF00999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGACTCATCCA	.	2	ESCA
CD200R1L	0	.	GRCh37	3	112534797	112534797	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13G>A	.	.	ENST00000398214	6/6	38	34	4	28	28	0	CD200R1L,3_prime_UTR_variant,,ENST00000488794,;CD200R1L,3_prime_UTR_variant,,ENST00000448932,;CD200R1L,3_prime_UTR_variant,,ENST00000398214,;RP11-180K7.1,downstream_gene_variant,,ENST00000496067,;CD200R1L,3_prime_UTR_variant,,ENST00000486723,;	T	ENSG00000206531	ENST00000398214	Transcript	3_prime_UTR_variant	1055	.	.	.	.	.	.	.	-1	CD200R1L	HGNC	24665	protein_coding	YES	CCDS43131.1	ENSP00000381272	MO2R2_HUMAN	.	UPI000042263C	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGACCCTTCC	.	4	ESCA
VGLL4	0	.	GRCh37	3	11600101	11600101	+	Missense_Mutation	SNP	G	G	A	rs377034464	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820C>T	p.Arg274Cys	p.R274C	ENST00000430365	5/5	100	85	14	94	94	0	VGLL4,missense_variant,p.Arg209Cys,ENST00000413604,;VGLL4,missense_variant,p.Arg188Cys,ENST00000451674,;VGLL4,missense_variant,p.Arg274Cys,ENST00000430365,;VGLL4,missense_variant,p.Arg268Cys,ENST00000273038,;VGLL4,missense_variant,p.Arg273Cys,ENST00000404339,;VGLL4,missense_variant,p.Arg184Cys,ENST00000424529,;ATG7,downstream_gene_variant,,ENST00000446450,;VGLL4,downstream_gene_variant,,ENST00000458499,;ATG7,downstream_gene_variant,,ENST00000354449,;VGLL4,downstream_gene_variant,,ENST00000445411,;ATG7,downstream_gene_variant,,ENST00000354956,;VGLL4,downstream_gene_variant,,ENST00000418000,;VGLL4,3_prime_UTR_variant,,ENST00000426568,;	A	ENSG00000144560	ENST00000430365	Transcript	missense_variant	1226	820	274	R/C	Cgc/Tgc	rs377034464	.	.	-1	VGLL4	HGNC	28966	protein_coding	YES	CCDS46754.1	ENSP00000404251	.	Q0H0I7_HUMAN,G5E9M9_HUMAN,G5E9M7_HUMAN,C9JX59_HUMAN,C9JBN2_HUMAN	UPI000013D995	.	deleterious_low_confidence(0.02)	probably_damaging(0.999)	5/5	.	hmmpanther:PTHR17604:SF1,hmmpanther:PTHR17604	T:0.0032	T:0	T:0	.	T:0	T:0	T:0.0164	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGCGAGAGG	byFrequency|byCluster|by1000G	4	ESCA
IGSF11	0	.	GRCh37	3	118621345	118621345	+	3'UTR	SNP	G	G	A	rs766982555	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*22C>T	.	.	ENST00000393775	7/7	69	51	17	49	49	0	IGSF11,3_prime_UTR_variant,,ENST00000425327,;IGSF11,3_prime_UTR_variant,,ENST00000441144,;IGSF11,3_prime_UTR_variant,,ENST00000489689,;IGSF11,3_prime_UTR_variant,,ENST00000393775,;IGSF11,3_prime_UTR_variant,,ENST00000354673,;IGSF11,3_prime_UTR_variant,,ENST00000491903,;	A	ENSG00000144847	ENST00000393775	Transcript	3_prime_UTR_variant	1624	.	.	.	.	rs766982555	.	.	-1	IGSF11	HGNC	16669	protein_coding	YES	CCDS46891.1	ENSP00000377370	IGS11_HUMAN	C9JAD3_HUMAN,C9IZX3_HUMAN	UPI000013D9B3	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTGAACAC	.	5	ESCA
MYLK	0	.	GRCh37	3	123419182	123419182	+	Missense_Mutation	SNP	C	C	G	rs773540567	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3133G>C	p.Glu1045Gln	p.E1045Q	ENST00000360304	18/34	78	63	15	53	53	0	MYLK,missense_variant,p.Glu1045Gln,ENST00000360304,;MYLK,missense_variant,p.Glu976Gln,ENST00000346322,;MYLK,missense_variant,p.Glu1045Gln,ENST00000360772,;MYLK,missense_variant,p.Glu1045Gln,ENST00000475616,;MYLK,missense_variant,p.Glu1045Gln,ENST00000359169,;MYLK,upstream_gene_variant,,ENST00000510775,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,non_coding_transcript_exon_variant,,ENST00000504946,;	G	ENSG00000065534	ENST00000360304	Transcript	missense_variant	3415	3133	1045	E/Q	Gag/Cag	rs773540567	.	.	-1	MYLK	HGNC	7590	protein_coding	YES	CCDS46896.1	ENSP00000353452	MYLK_HUMAN	Q06S79_HUMAN,Q05B98_HUMAN,Q05B97_HUMAN,D6R9C2_HUMAN,B4DUE3_HUMAN	UPI000020A0AE	.	deleterious(0.04)	benign(0.299)	18/34	.	hmmpanther:PTHR22964,hmmpanther:PTHR22964:SF44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCGGCAG	byFrequency	5	ESCA
CAND2	0	.	GRCh37	3	12873053	12873053	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3465G>T	p.Arg1155Ser	p.R1155S	ENST00000456430	14/15	41	29	12	34	34	0	CAND2,missense_variant,p.Arg1155Ser,ENST00000456430,;CAND2,missense_variant,p.Arg1038Ser,ENST00000295989,;CAND2,missense_variant,p.Arg83Ser,ENST00000454887,;RPL32,downstream_gene_variant,,ENST00000396957,;RPL32,downstream_gene_variant,,ENST00000273223,;RPL32,downstream_gene_variant,,ENST00000457131,;RPL32,downstream_gene_variant,,ENST00000429711,;RPL32,downstream_gene_variant,,ENST00000435983,;RPL32,downstream_gene_variant,,ENST00000396953,;RP11-767C1.2,downstream_gene_variant,,ENST00000606447,;	T	ENSG00000144712	ENST00000456430	Transcript	missense_variant	3506	3465	1155	R/S	agG/agT	.	.	.	1	CAND2	HGNC	30689	protein_coding	YES	CCDS54554.1	ENSP00000387641	CAND2_HUMAN	.	UPI00005795FA	.	deleterious(0)	possibly_damaging(0.72)	14/15	.	hmmpanther:PTHR12696,hmmpanther:PTHR12696:SF2,Gene3D:1.25.10.10,Pfam_domain:PF08623,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAGGGCCAC	.	5	ESCA
SOX14	0	.	GRCh37	3	137484324	137484324	+	Missense_Mutation	SNP	C	C	T	rs777197594	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.698C>T	p.Ser233Leu	p.S233L	ENST00000306087	1/1	51	46	5	46	46	0	SOX14,missense_variant,p.Ser233Leu,ENST00000306087,;	T	ENSG00000168875	ENST00000306087	Transcript	missense_variant	746	698	233	S/L	tCg/tTg	rs777197594,COSM204889	.	.	1	SOX14	HGNC	11193	protein_coding	YES	CCDS3094.1	ENSP00000305343	SOX14_HUMAN	.	UPI0000000B2D	.	tolerated_low_confidence(0.19)	benign(0.32)	1/1	.	hmmpanther:PTHR10270:SF107,hmmpanther:PTHR10270	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTATTCGTCAG	.	2	ESCA
PRR23B	0	.	GRCh37	3	138739627	138739627	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-124G>A	.	.	ENST00000329447	1/1	31	25	5	20	20	0	PRR23B,5_prime_UTR_variant,,ENST00000329447,;MRPS22,intron_variant,,ENST00000495075,;	T	ENSG00000184814	ENST00000329447	Transcript	5_prime_UTR_variant	142	.	.	.	.	.	.	.	-1	PRR23B	HGNC	33764	protein_coding	YES	CCDS33868.1	ENSP00000328768	PR23B_HUMAN	.	UPI00001C0F1A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGGGCGCAGG	.	4	ESCA
ZBTB38	0	.	GRCh37	3	141162094	141162094	+	Silent	SNP	C	C	G	rs147594598	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864C>G	p.%3D	p.S288S	ENST00000514251	4/4	41	27	13	24	24	0	ZBTB38,synonymous_variant,p.%3D,ENST00000441582,;ZBTB38,synonymous_variant,p.%3D,ENST00000321464,;ZBTB38,synonymous_variant,p.%3D,ENST00000509883,;ZBTB38,synonymous_variant,p.%3D,ENST00000514251,;ZBTB38,downstream_gene_variant,,ENST00000504673,;ZBTB38,downstream_gene_variant,,ENST00000507722,;ZBTB38,downstream_gene_variant,,ENST00000509813,;ZBTB38,downstream_gene_variant,,ENST00000503809,;ZBTB38,downstream_gene_variant,,ENST00000513570,;ZBTB38,downstream_gene_variant,,ENST00000510338,;ZBTB38,downstream_gene_variant,,ENST00000510726,;ZBTB38,downstream_gene_variant,,ENST00000513258,;ZBTB38,downstream_gene_variant,,ENST00000509842,;ZBTB38,upstream_gene_variant,,ENST00000512769,;	G	ENSG00000177311	ENST00000514251	Transcript	synonymous_variant	1143	864	288	S	tcC/tcG	rs147594598	.	.	1	ZBTB38	HGNC	26636	protein_coding	YES	CCDS43157.1	ENSP00000426387	ZBT38_HUMAN	Q9H6F0_HUMAN,D6RJE1_HUMAN,D6RHD1_HUMAN,D6RGK1_HUMAN,D6RE69_HUMAN,D6RC86_HUMAN,D6RBC4_HUMAN,D6RAC4_HUMAN,D6R9U6_HUMAN,D6R9J6_HUMAN,D6R9I1_HUMAN,B3KST1_HUMAN	UPI000020A364	.	.	.	4/4	.	hmmpanther:PTHR24397:SF23,hmmpanther:PTHR24397	T:0.0010	T:0.0038	T:0	.	T:0	T:0	T:0	T:0.0016	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATCCAACTT	byFrequency|byCluster|by1000G	5	ESCA
CP	0	.	GRCh37	3	148896253	148896253	+	Missense_Mutation	SNP	C	C	T	rs571448440	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2827G>A	p.Glu943Lys	p.E943K	ENST00000264613	16/19	81	66	15	33	33	0	CP,missense_variant,p.Glu943Lys,ENST00000264613,;CP,missense_variant,p.Glu78Lys,ENST00000479771,;CP,missense_variant,p.Glu726Lys,ENST00000494544,;HPS3,downstream_gene_variant,,ENST00000296051,;CP,missense_variant,p.Glu872Lys,ENST00000481169,;CP,non_coding_transcript_exon_variant,,ENST00000490639,;CP,non_coding_transcript_exon_variant,,ENST00000460674,;CP,non_coding_transcript_exon_variant,,ENST00000463556,;CP,upstream_gene_variant,,ENST00000474204,;CP,upstream_gene_variant,,ENST00000473296,;	T	ENSG00000047457	ENST00000264613	Transcript	missense_variant	3090	2827	943	E/K	Gag/Aag	rs571448440	.	.	-1	CP	HGNC	2295	protein_coding	YES	CCDS3141.1	ENSP00000264613	CERU_HUMAN	.	UPI000045718B	.	tolerated(0.55)	benign(0.008)	16/19	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF294,Gene3D:2.60.40.420,Superfamily_domains:SSF49503	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCGGGGT	byCluster|by1000G	5	ESCA
SERPINI2	0	.	GRCh37	3	167191546	167191546	+	Intron	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11+245A>G	.	.	ENST00000476257	.	46	27	18	33	33	0	SERPINI2,5_prime_UTR_variant,,ENST00000466903,;SERPINI2,5_prime_UTR_variant,,ENST00000461846,;SERPINI2,intron_variant,,ENST00000476257,;SERPINI2,intron_variant,,ENST00000264677,;WDR49,downstream_gene_variant,,ENST00000472600,;SERPINI2,upstream_gene_variant,,ENST00000471111,;SERPINI2,upstream_gene_variant,,ENST00000467583,;WDR49,downstream_gene_variant,,ENST00000453925,;WDR49,downstream_gene_variant,,ENST00000308378,;WDR49,downstream_gene_variant,,ENST00000476376,;WDR49,downstream_gene_variant,,ENST00000479765,;SERPINI2,upstream_gene_variant,,ENST00000465031,;	C	ENSG00000114204	ENST00000476257	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SERPINI2	HGNC	8945	protein_coding	YES	CCDS3200.1	ENSP00000420621	SPI2_HUMAN	C9J7N5_HUMAN	UPI0000135E26	.	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATATCTTAT	.	5	ESCA
SLC2A2	0	.	GRCh37	3	170732382	170732382	+	Missense_Mutation	SNP	C	C	T	rs150851401	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>A	p.Glu83Lys	p.E83K	ENST00000314251	3/11	160	130	30	115	115	0	SLC2A2,missense_variant,p.Glu83Lys,ENST00000314251,;SLC2A2,intron_variant,,ENST00000461867,;SLC2A2,intron_variant,,ENST00000382808,;SLC2A2,missense_variant,p.Glu83Lys,ENST00000497642,;SLC2A2,intron_variant,,ENST00000469787,;	T	ENSG00000163581	ENST00000314251	Transcript	missense_variant	327	247	83	E/K	Gag/Aag	rs150851401	.	.	-1	SLC2A2	HGNC	11006	protein_coding	YES	CCDS3215.1	ENSP00000323568	GTR2_HUMAN	Q6PAU8_HUMAN,C9J0E8_HUMAN	UPI000004EC97	.	tolerated(0.13)	benign(0.016)	3/11	.	PROSITE_profiles:PS50850,hmmpanther:PTHR24063,hmmpanther:PTHR24063:SF13,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00879	T:0.0004	T:0	T:0.0014	.	T:0	T:0.001	T:0	T:0	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCAGCCC	byFrequency|byCluster|by1000G	5	ESCA
MASP1	0	.	GRCh37	3	186937549	186937549	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*310C>T	.	.	ENST00000337774	16/16	79	70	9	54	54	0	MASP1,3_prime_UTR_variant,,ENST00000337774,;	A	ENSG00000127241	ENST00000337774	Transcript	3_prime_UTR_variant	2800	.	.	.	.	.	.	.	-1	MASP1	HGNC	6901	protein_coding	.	CCDS33907.1	ENSP00000336792	MASP1_HUMAN	C9JLU5_HUMAN	UPI0000161FB8	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTACGAGGTA	.	4	ESCA
ATP13A4	0	.	GRCh37	3	193210921	193210921	+	Missense_Mutation	SNP	C	C	T	rs767732804	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.410G>A	p.Arg137Lys	p.R137K	ENST00000342695	4/30	36	30	6	14	14	0	ATP13A4,missense_variant,p.Arg137Lys,ENST00000392443,;ATP13A4,missense_variant,p.Arg137Lys,ENST00000342695,;ATP13A4,missense_variant,p.Arg137Lys,ENST00000295548,;ATP13A4,3_prime_UTR_variant,,ENST00000450950,;ATP13A4,non_coding_transcript_exon_variant,,ENST00000490925,;	T	ENSG00000127249	ENST00000342695	Transcript	missense_variant	733	410	137	R/K	aGa/aAa	rs767732804	.	.	-1	ATP13A4	HGNC	25422	protein_coding	YES	CCDS3304.2	ENSP00000339182	AT134_HUMAN	.	UPI0000520D50	.	tolerated(0.43)	possibly_damaging(0.884)	4/30	.	hmmpanther:PTHR24093:SF279,hmmpanther:PTHR24093,Pfam_domain:PF12409,TIGRFAM_domain:TIGR01657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATATCTTATT	.	4	ESCA
TTC21A	0	.	GRCh37	3	39159627	39159627	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.784G>A	p.Glu262Lys	p.E262K	ENST00000431162	7/29	24	21	3	32	32	0	TTC21A,missense_variant,p.Glu221Lys,ENST00000440121,;TTC21A,missense_variant,p.Glu262Lys,ENST00000301819,;TTC21A,missense_variant,p.Glu262Lys,ENST00000431162,;TTC21A,missense_variant,p.Glu262Lys,ENST00000430597,;TTC21A,3_prime_UTR_variant,,ENST00000431559,;TTC21A,non_coding_transcript_exon_variant,,ENST00000493337,;TTC21A,non_coding_transcript_exon_variant,,ENST00000479954,;TTC21A,non_coding_transcript_exon_variant,,ENST00000459702,;	A	ENSG00000168026	ENST00000431162	Transcript	missense_variant	918	784	262	E/K	Gaa/Aaa	.	.	.	1	TTC21A	HGNC	30761	protein_coding	YES	CCDS46800.1	ENSP00000398211	TT21A_HUMAN	.	UPI00015D46B9	.	deleterious(0.01)	possibly_damaging(0.83)	7/29	.	hmmpanther:PTHR14699:SF2,hmmpanther:PTHR14699	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAGAGAAGGA	.	2	ESCA
DNAH1	0	.	GRCh37	3	52414133	52414133	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7590C>T	p.%3D	p.L2530L	ENST00000420323	48/78	28	17	11	30	30	0	DNAH1,synonymous_variant,p.%3D,ENST00000420323,;DNAH1,non_coding_transcript_exon_variant,,ENST00000486752,;DNAH1,upstream_gene_variant,,ENST00000488988,;	T	ENSG00000114841	ENST00000420323	Transcript	synonymous_variant	7851	7590	2530	L	ctC/ctT	.	.	.	1	DNAH1	HGNC	2940	protein_coding	YES	CCDS46842.1	ENSP00000401514	DYH1_HUMAN	.	UPI0001AE79D6	.	.	.	48/78	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTCATCAC	.	5	ESCA
MITF	0	.	GRCh37	3	69788713	69788713	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-36C>T	.	.	ENST00000352241	1/10	38	28	9	51	51	0	MITF,5_prime_UTR_variant,,ENST00000352241,;MITF,5_prime_UTR_variant,,ENST00000448226,;MITF,non_coding_transcript_exon_variant,,ENST00000461511,;MITF,non_coding_transcript_exon_variant,,ENST00000495741,;	T	ENSG00000187098	ENST00000352241	Transcript	5_prime_UTR_variant	128	.	.	.	.	.	.	.	1	MITF	HGNC	7105	protein_coding	YES	CCDS43106.1	ENSP00000295600	MITF_HUMAN	C9K0S7_HUMAN	UPI000002ADF8	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTCACTTT	.	5	ESCA
CRYBG3	0	.	GRCh37	3	97591374	97591374	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1336G>A	p.Asp446Asn	p.D446N	ENST00000419587	4/4	24	14	9	19	19	0	CRYBG3,missense_variant,p.Asp446Asn,ENST00000419587,;CRYBG3,upstream_gene_variant,,ENST00000182096,;	A	ENSG00000233280	ENST00000419587	Transcript	missense_variant	1503	1336	446	D/N	Gac/Aac	.	.	.	1	CRYBG3	Uniprot_gn	34427	protein_coding	YES	.	ENSP00000391551	.	B4DLE8_HUMAN	UPI00017A74DC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTGACACT	.	5	ESCA
CRYBG3	0	.	GRCh37	3	97591695	97591695	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1657G>A	p.Glu553Lys	p.E553K	ENST00000419587	4/4	23	20	3	24	24	0	CRYBG3,missense_variant,p.Glu553Lys,ENST00000419587,;CRYBG3,upstream_gene_variant,,ENST00000182096,;	A	ENSG00000233280	ENST00000419587	Transcript	missense_variant	1824	1657	553	E/K	Gag/Aag	.	.	.	1	CRYBG3	Uniprot_gn	34427	protein_coding	YES	.	ENSP00000391551	.	B4DLE8_HUMAN	UPI00017A74DC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATTGAGTCA	.	2	ESCA
SEC24D	0	.	GRCh37	4	119649764	119649764	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2910C>G	p.%3D	p.L970L	ENST00000280551	22/23	41	33	8	30	30	0	SEC24D,synonymous_variant,p.%3D,ENST00000379735,;SEC24D,synonymous_variant,p.%3D,ENST00000280551,;SEC24D,synonymous_variant,p.%3D,ENST00000511481,;SEC24D,3_prime_UTR_variant,,ENST00000429811,;SEC24D,non_coding_transcript_exon_variant,,ENST00000505134,;SEC24D,non_coding_transcript_exon_variant,,ENST00000502830,;SEC24D,downstream_gene_variant,,ENST00000511715,;	C	ENSG00000150961	ENST00000280551	Transcript	synonymous_variant	3149	2910	970	L	ctC/ctG	.	.	.	-1	SEC24D	HGNC	10706	protein_coding	YES	CCDS3710.1	ENSP00000280551	SC24D_HUMAN	E9PDM8_HUMAN,D6RGJ5_HUMAN	UPI00001AEA4F	.	.	.	22/23	.	hmmpanther:PTHR13803:SF6,hmmpanther:PTHR13803,Pfam_domain:PF00626,Gene3D:3.40.20.10,Superfamily_domains:SSF82754	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTGAGTTG	.	5	ESCA
FGF2	0	.	GRCh37	4	123817437	123817437	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3886C>A	.	.	ENST00000264498	3/3	45	39	6	37	37	0	FGF2,3_prime_UTR_variant,,ENST00000264498,;NUDT6,intron_variant,,ENST00000304430,;NUDT6,intron_variant,,ENST00000510735,;NUDT6,intron_variant,,ENST00000502270,;NUDT6,intron_variant,,ENST00000339154,;FGF2,downstream_gene_variant,,ENST00000608478,;NUDT6,upstream_gene_variant,,ENST00000608639,;NUDT6,intron_variant,,ENST00000503370,;NUDT6,intron_variant,,ENST00000512116,;NUDT6,downstream_gene_variant,,ENST00000513517,;	A	ENSG00000138685	ENST00000264498	Transcript	3_prime_UTR_variant	4821	.	.	.	.	.	.	.	1	FGF2	HGNC	3676	protein_coding	YES	CCDS34059.1	ENSP00000264498	FGF2_HUMAN	D9ZGF5_HUMAN	UPI0000367289	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGGCTTGGA	.	4	ESCA
POU4F2	0	.	GRCh37	4	147561864	147561864	+	Silent	SNP	C	C	T	rs572053159	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1134C>T	p.%3D	p.I378I	ENST00000281321	2/2	38	32	6	25	25	0	POU4F2,synonymous_variant,p.%3D,ENST00000281321,;AC093887.1,downstream_gene_variant,,ENST00000584185,;	T	ENSG00000151615	ENST00000281321	Transcript	synonymous_variant	1382	1134	378	I	atC/atT	rs572053159	.	.	1	POU4F2	HGNC	9219	protein_coding	YES	CCDS34074.1	ENSP00000281321	PO4F2_HUMAN	.	UPI000013DC6C	.	.	.	2/2	.	PROSITE_profiles:PS50071,hmmpanther:PTHR11636:SF41,hmmpanther:PTHR11636,PROSITE_patterns:PS00027,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A376A|c.1128C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATCGCGGA	byFrequency|byCluster	5	ESCA
SPOCK3	0	.	GRCh37	4	167656000	167656000	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*72C>G	.	.	ENST00000357154	12/12	44	38	6	44	44	0	SPOCK3,3_prime_UTR_variant,,ENST00000357154,;SPOCK3,3_prime_UTR_variant,,ENST00000511531,;SPOCK3,3_prime_UTR_variant,,ENST00000357545,;SPOCK3,3_prime_UTR_variant,,ENST00000506886,;SPOCK3,3_prime_UTR_variant,,ENST00000511269,;SPOCK3,3_prime_UTR_variant,,ENST00000421836,;SPOCK3,3_prime_UTR_variant,,ENST00000510741,;SPOCK3,3_prime_UTR_variant,,ENST00000535728,;SPOCK3,3_prime_UTR_variant,,ENST00000541354,;SPOCK3,3_prime_UTR_variant,,ENST00000512681,;SPOCK3,3_prime_UTR_variant,,ENST00000502330,;SPOCK3,3_prime_UTR_variant,,ENST00000504953,;SPOCK3,downstream_gene_variant,,ENST00000541637,;SPOCK3,downstream_gene_variant,,ENST00000534949,;SPOCK3,non_coding_transcript_exon_variant,,ENST00000507137,;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,;	C	ENSG00000196104	ENST00000357154	Transcript	3_prime_UTR_variant	1521	.	.	.	.	.	.	.	-1	SPOCK3	HGNC	13565	protein_coding	YES	CCDS54817.1	ENSP00000349677	TICN3_HUMAN	Q4W5S3_HUMAN,Q4W5E2_HUMAN,E7EMP8_HUMAN	UPI000004BA60	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAAGATAAT	.	4	ESCA
FAM184B	0	.	GRCh37	4	17638223	17638223	+	Silent	SNP	G	G	A	rs749548028	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2712C>T	p.%3D	p.P904P	ENST00000265018	15/18	47	35	11	54	53	1	FAM184B,synonymous_variant,p.%3D,ENST00000265018,;MED28,downstream_gene_variant,,ENST00000237380,;MED28,downstream_gene_variant,,ENST00000499786,;	A	ENSG00000047662	ENST00000265018	Transcript	synonymous_variant	2925	2712	904	P	ccC/ccT	rs749548028	.	.	-1	FAM184B	HGNC	29235	protein_coding	YES	CCDS47033.1	ENSP00000265018	F184B_HUMAN	.	UPI000020BD7C	.	.	.	15/18	.	hmmpanther:PTHR18870:SF8,hmmpanther:PTHR18870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCGGGCCT	.	5	ESCA
ZFP42	0	.	GRCh37	4	188926074	188926074	+	3'UTR	DEL	T	T	-	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1184delT	.	.	ENST00000326866	4/4	56	47	9	47	47	0	ZFP42,3_prime_UTR_variant,,ENST00000326866,;ZFP42,3_prime_UTR_variant,,ENST00000509524,;	-	ENSG00000179059	ENST00000326866	Transcript	3_prime_UTR_variant	2521	.	.	.	.	.	.	.	1	ZFP42	HGNC	30949	protein_coding	YES	CCDS3849.1	ENSP00000317686	ZFP42_HUMAN	.	UPI0000049CA7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTGTGATTTTTG	.	3	ESCA
GBA3	0	.	GRCh37	4	22694548	22694548	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-91C>T	.	.	ENST00000508166	1/5	59	52	6	47	47	0	GBA3,5_prime_UTR_variant,,ENST00000503442,;GBA3,5_prime_UTR_variant,,ENST00000508166,;	T	ENSG00000249948	ENST00000508166	Transcript	5_prime_UTR_variant	12	.	.	.	.	.	.	.	1	GBA3	HGNC	19069	polymorphic_pseudogene	YES	.	ENSP00000427458	.	.	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCTCATTTT	.	4	ESCA
RHOH	0	.	GRCh37	4	40244925	40244925	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-82G>C	.	.	ENST00000381799	3/3	70	60	10	60	60	0	RHOH,5_prime_UTR_variant,,ENST00000503941,;RHOH,5_prime_UTR_variant,,ENST00000508513,;RHOH,5_prime_UTR_variant,,ENST00000505618,;RHOH,5_prime_UTR_variant,,ENST00000381799,;RHOH,5_prime_UTR_variant,,ENST00000507851,;RHOH,5_prime_UTR_variant,,ENST00000511121,;RHOH,non_coding_transcript_exon_variant,,ENST00000515718,;RHOH,downstream_gene_variant,,ENST00000504638,;RHOH,downstream_gene_variant,,ENST00000515503,;RHOH,downstream_gene_variant,,ENST00000515702,;RHOH,downstream_gene_variant,,ENST00000511967,;RHOH,downstream_gene_variant,,ENST00000503754,;RHOH,downstream_gene_variant,,ENST00000513894,;RHOH,downstream_gene_variant,,ENST00000503978,;	C	ENSG00000168421	ENST00000381799	Transcript	5_prime_UTR_variant	643	.	.	.	.	.	.	.	1	RHOH	HGNC	686	protein_coding	YES	CCDS3458.1	ENSP00000371219	RHOH_HUMAN	Q6ICP4_HUMAN,D6RG23_HUMAN,D6RA52_HUMAN	UPI0000133892	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTGCTGAATGG	.	2	ESCA
USP46	0	.	GRCh37	4	53461615	53461615	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2191C>A	.	.	ENST00000441222	9/9	12	10	2	16	16	0	USP46,3_prime_UTR_variant,,ENST00000451218,;USP46,3_prime_UTR_variant,,ENST00000441222,;USP46,downstream_gene_variant,,ENST00000508499,;USP46,downstream_gene_variant,,ENST00000503060,;USP46,downstream_gene_variant,,ENST00000514536,;	T	ENSG00000109189	ENST00000441222	Transcript	3_prime_UTR_variant	3477	.	.	.	.	.	.	.	-1	USP46	HGNC	20075	protein_coding	YES	CCDS47053.1	ENSP00000407818	UBP46_HUMAN	.	UPI0000006C18	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAACTGTTTTA	.	2	ESCA
KIAA1211	0	.	GRCh37	4	57176886	57176886	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340G>C	p.Glu114Gln	p.E114Q	ENST00000504228	4/9	81	71	10	80	80	0	KIAA1211,missense_variant,p.Glu114Gln,ENST00000504228,;KIAA1211,missense_variant,p.Glu114Gln,ENST00000264229,;KIAA1211,missense_variant,p.Glu107Gln,ENST00000541073,;KIAA1211,non_coding_transcript_exon_variant,,ENST00000505410,;KIAA1211,downstream_gene_variant,,ENST00000503618,;	C	ENSG00000109265	ENST00000504228	Transcript	missense_variant	445	340	114	E/Q	Gag/Cag	.	.	.	1	KIAA1211	HGNC	29219	protein_coding	YES	CCDS43230.1	ENSP00000423366	K1211_HUMAN	.	UPI0000237309	.	deleterious(0.04)	probably_damaging(0.988)	4/9	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF350,Pfam_domain:PF15262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGTGAGATG	.	5	ESCA
CENPC	0	.	GRCh37	4	68378268	68378268	+	Silent	SNP	A	A	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1464T>G	p.%3D	p.T488T	ENST00000273853	9/19	30	25	5	23	23	0	CENPC,synonymous_variant,p.%3D,ENST00000273853,;CENPC,synonymous_variant,p.%3D,ENST00000506882,;CENPC,synonymous_variant,p.%3D,ENST00000513216,;CENPC,non_coding_transcript_exon_variant,,ENST00000506410,;CENPC,non_coding_transcript_exon_variant,,ENST00000510189,;CENPC,upstream_gene_variant,,ENST00000507196,;	C	ENSG00000145241	ENST00000273853	Transcript	synonymous_variant	1715	1464	488	T	acT/acG	.	.	.	-1	CENPC	HGNC	1854	protein_coding	YES	CCDS47063.1	ENSP00000273853	CENPC_HUMAN	.	UPI00004135A3	.	.	.	9/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16684,Pfam_domain:PF15620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTAGTGCT	.	5	ESCA
TMPRSS11F	0	.	GRCh37	4	68928855	68928855	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015+1548C>G	.	.	ENST00000356291	.	46	30	15	33	33	0	TMPRSS11F,intron_variant,,ENST00000356291,;UBA6-AS1,non_coding_transcript_exon_variant,,ENST00000511571,;UBA6-AS1,non_coding_transcript_exon_variant,,ENST00000500538,;UBA6-AS1,non_coding_transcript_exon_variant,,ENST00000499180,;SYT14L,non_coding_transcript_exon_variant,,ENST00000600441,;SYT14L,non_coding_transcript_exon_variant,,ENST00000481459,;SYT14L,non_coding_transcript_exon_variant,,ENST00000419424,;	C	ENSG00000198092	ENST00000356291	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TMPRSS11F	HGNC	29994	protein_coding	YES	CCDS3520.1	ENSP00000348639	TM11F_HUMAN	.	UPI0000251DE7	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATAGAGAAA	.	5	ESCA
CABS1	0	.	GRCh37	4	71201540	71201540	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.784G>A	p.Glu262Lys	p.E262K	ENST00000273936	1/2	45	42	3	28	28	0	CABS1,missense_variant,p.Glu262Lys,ENST00000273936,;	A	ENSG00000145309	ENST00000273936	Transcript	missense_variant	858	784	262	E/K	Gag/Aag	.	.	.	1	CABS1	HGNC	30710	protein_coding	YES	CCDS3539.1	ENSP00000273936	CABS1_HUMAN	.	UPI0000071735	.	deleterious(0)	possibly_damaging(0.908)	1/2	.	hmmpanther:PTHR22810,Pfam_domain:PF15367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGATGAGAAG	.	2	ESCA
AC093677.1	0	.	GRCh37	4	75023442	75023442	+	Nonsense_Mutation	SNP	A	A	T	rs746956328	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.644T>A	p.Leu215Ter	p.L215*	ENST00000600169	1/1	74	63	11	65	65	0	AC093677.1,stop_gained,p.Leu215Ter,ENST00000600169,;MTHFD2L,intron_variant,,ENST00000433372,;MTHFD2L,upstream_gene_variant,,ENST00000395759,;MTHFD2L,upstream_gene_variant,,ENST00000359107,;MTHFD2L,upstream_gene_variant,,ENST00000331145,;MTHFD2L,upstream_gene_variant,,ENST00000325278,;MTHFD2L,upstream_gene_variant,,ENST00000461101,;MTHFD2L,upstream_gene_variant,,ENST00000484725,;MTHFD2L,intron_variant,,ENST00000490698,;MTHFD2L,intron_variant,,ENST00000429335,;MTHFD2L,intron_variant,,ENST00000475291,;MTHFD2L,intron_variant,,ENST00000429519,;MTHFD2L,upstream_gene_variant,,ENST00000423607,;	T	ENSG00000269559	ENST00000600169	Transcript	stop_gained	644	644	215	L/*	tTg/tAg	rs746956328	.	.	-1	AC093677.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000469155	.	M0QXG7_HUMAN	UPI0000246E5D	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATCCAATTCC	.	4	ESCA
NAA11	0	.	GRCh37	4	80246828	80246828	+	Silent	SNP	C	C	T	rs762585511	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204G>A	p.%3D	p.P68P	ENST00000286794	1/2	34	21	13	21	21	0	NAA11,synonymous_variant,p.%3D,ENST00000286794,;NAA11,upstream_gene_variant,,ENST00000513733,;NAA11,upstream_gene_variant,,ENST00000511542,;	T	ENSG00000156269	ENST00000286794	Transcript	synonymous_variant	377	204	68	P	ccG/ccA	rs762585511,COSM448188,COSM734548	.	.	-1	NAA11	HGNC	28125	protein_coding	YES	CCDS47084.1	ENSP00000286794	NAA11_HUMAN	H0Y8T0_HUMAN	UPI00000467CA	.	.	.	1/2	.	Superfamily_domains:SSF55729,Gene3D:3.40.630.30,Pfam_domain:PF00583,hmmpanther:PTHR23091,hmmpanther:PTHR23091:SF205,PROSITE_profiles:PS51186	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P68P|c.204G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGCGGGAC	.	5	ESCA
DSPP	0	.	GRCh37	4	88534007	88534007	+	Silent	SNP	G	G	A	rs750546551	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.669G>A	p.%3D	p.G223G	ENST00000399271	4/5	54	47	7	45	45	0	DSPP,synonymous_variant,p.%3D,ENST00000282478,;DSPP,synonymous_variant,p.%3D,ENST00000399271,;RP11-742B18.1,intron_variant,,ENST00000506480,;	A	ENSG00000152591	ENST00000399271	Transcript	synonymous_variant	789	669	223	G	ggG/ggA	rs750546551	.	.	1	DSPP	HGNC	3054	protein_coding	YES	CCDS43248.1	ENSP00000382213	DSPP_HUMAN	B7SEZ4_HUMAN,B7SEY4_HUMAN	UPI00006BFF57	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGGACTAA	byFrequency	5	ESCA
PJA2	0	.	GRCh37	5	108714941	108714941	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>A	p.Asp83Asn	p.D83N	ENST00000361189	4/10	29	18	11	29	29	0	PJA2,missense_variant,p.Asp83Asn,ENST00000361189,;PJA2,missense_variant,p.Asp83Asn,ENST00000361557,;PJA2,non_coding_transcript_exon_variant,,ENST00000511624,;PJA2,downstream_gene_variant,,ENST00000512822,;	T	ENSG00000198961	ENST00000361189	Transcript	missense_variant	487	247	83	D/N	Gat/Aat	.	.	.	-1	PJA2	HGNC	17481	protein_coding	YES	CCDS4099.1	ENSP00000354775	PJA2_HUMAN	.	UPI000013D192	.	tolerated(0.41)	benign(0.132)	4/10	.	hmmpanther:PTHR15710,hmmpanther:PTHR15710:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGATCCAAAG	.	5	ESCA
KCNN2	0	.	GRCh37	5	113831919	113831919	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*40C>G	.	.	ENST00000512097	9/9	24	19	5	15	15	0	KCNN2,3_prime_UTR_variant,,ENST00000512097,;KCNN2,3_prime_UTR_variant,,ENST00000503706,;KCNN2,3_prime_UTR_variant,,ENST00000264773,;RP11-492A10.1,intron_variant,,ENST00000514115,;KCNN2,downstream_gene_variant,,ENST00000507750,;KCNN2,downstream_gene_variant,,ENST00000506812,;KCNN2,downstream_gene_variant,,ENST00000505491,;	G	ENSG00000080709	ENST00000512097	Transcript	3_prime_UTR_variant	2798	.	.	.	.	.	.	.	1	KCNN2	HGNC	6291	protein_coding	YES	CCDS4114.1	ENSP00000427120	KCNN2_HUMAN	.	UPI000013D56A	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GCCATCATATG	.	4	ESCA
AQPEP	0	.	GRCh37	5	115298659	115298659	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.345G>C	p.%3D	p.L115L	ENST00000357872	1/20	21	18	3	15	15	0	AQPEP,synonymous_variant,p.%3D,ENST00000357872,;AQPEP,5_prime_UTR_variant,,ENST00000395528,;AQPEP,synonymous_variant,p.%3D,ENST00000504467,;	C	ENSG00000172901	ENST00000357872	Transcript	synonymous_variant	469	345	115	L	ctG/ctC	.	.	.	1	AQPEP	Uniprot_gn	.	protein_coding	YES	CCDS4124.1	ENSP00000350541	AMPQ_HUMAN	.	UPI0000457329	.	.	.	1/20	.	Superfamily_domains:0038696,Pfam_domain:PF01433,hmmpanther:PTHR11533:SF31,hmmpanther:PTHR11533	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTGAGGCC	.	2	ESCA
PRRC1	0	.	GRCh37	5	126866085	126866085	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.754A>G	p.Ile252Val	p.I252V	ENST00000296666	5/9	45	35	9	32	32	0	PRRC1,missense_variant,p.Ile252Val,ENST00000442138,;PRRC1,missense_variant,p.Ile252Val,ENST00000296666,;PRRC1,missense_variant,p.Ile252Val,ENST00000512635,;	G	ENSG00000164244	ENST00000296666	Transcript	missense_variant	942	754	252	I/V	Atc/Gtc	.	.	.	1	PRRC1	HGNC	28164	protein_coding	YES	CCDS4143.1	ENSP00000296666	PRRC1_HUMAN	.	UPI0000073C8E	.	deleterious(0)	probably_damaging(0.994)	5/9	.	hmmpanther:PTHR23276,hmmpanther:PTHR23276:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATATCAGT	.	5	ESCA
CHSY3	0	.	GRCh37	5	129520357	129520357	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1522G>C	p.Glu508Gln	p.E508Q	ENST00000305031	3/3	47	41	6	24	24	0	CHSY3,missense_variant,p.Glu508Gln,ENST00000305031,;CHSY3,downstream_gene_variant,,ENST00000507545,;	C	ENSG00000198108	ENST00000305031	Transcript	missense_variant	1880	1522	508	E/Q	Gag/Cag	.	.	.	1	CHSY3	HGNC	24293	protein_coding	YES	CCDS34223.1	ENSP00000302629	CHSS3_HUMAN	Q1JTV1_HUMAN	UPI0000251E08	.	tolerated(0.32)	benign(0.098)	3/3	.	hmmpanther:PTHR12369,hmmpanther:PTHR12369:SF18,Pfam_domain:PF05679	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAATGAGAAT	.	4	ESCA
SLC22A4	0	.	GRCh37	5	131657980	131657980	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756C>T	p.%3D	p.F252F	ENST00000200652	4/10	157	122	35	124	124	0	SLC22A4,synonymous_variant,p.%3D,ENST00000200652,;AC034220.3,intron_variant,,ENST00000417795,;SLC22A4,non_coding_transcript_exon_variant,,ENST00000425923,;SLC22A4,downstream_gene_variant,,ENST00000491257,;	T	ENSG00000197208	ENST00000200652	Transcript	synonymous_variant	930	756	252	F	ttC/ttT	.	.	.	1	SLC22A4	HGNC	10968	protein_coding	YES	CCDS4153.1	ENSP00000200652	S22A4_HUMAN	D9N2T6_HUMAN	UPI000006DAB7	.	.	.	4/10	.	PROSITE_profiles:PS50850,hmmpanther:PTHR24064:SF5,hmmpanther:PTHR24064,Gene3D:1.20.1250.20,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00898,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTCATCAG	.	5	ESCA
JADE2	0	.	GRCh37	5	133915701	133915701	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*694C>A	.	.	ENST00000395003	11/11	32	28	4	36	36	0	JADE2,3_prime_UTR_variant,,ENST00000395003,;JADE2,downstream_gene_variant,,ENST00000282605,;JADE2,downstream_gene_variant,,ENST00000402835,;JADE2,downstream_gene_variant,,ENST00000361895,;JADE2,downstream_gene_variant,,ENST00000470876,;JADE2,downstream_gene_variant,,ENST00000430087,;	A	ENSG00000043143	ENST00000395003	Transcript	3_prime_UTR_variant	3246	.	.	.	.	.	.	.	1	JADE2	HGNC	22984	protein_coding	YES	CCDS4176.1	ENSP00000378451	JADE2_HUMAN	D6R9B8_HUMAN,C9J929_HUMAN	UPI00002331C9	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTTCCCAGA	.	4	ESCA
CATSPER3	0	.	GRCh37	5	134343646	134343646	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493-1G>A	.	p.X165_splice	ENST00000282611	.	59	44	15	47	47	0	CATSPER3,splice_acceptor_variant,,ENST00000282611,;PCBD2,splice_acceptor_variant,,ENST00000504352,;	A	ENSG00000152705	ENST00000282611	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	CATSPER3	HGNC	20819	protein_coding	YES	CCDS4181.1	ENSP00000282611	CTSR3_HUMAN	.	UPI0000034D60	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCAGACGCT	.	5	ESCA
KDM3B	0	.	GRCh37	5	137761139	137761139	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4279G>C	p.Glu1427Gln	p.E1427Q	ENST00000314358	17/24	94	69	25	81	81	0	KDM3B,missense_variant,p.Glu459Gln,ENST00000542866,;KDM3B,missense_variant,p.Glu1427Gln,ENST00000314358,;KDM3B,missense_variant,p.Glu1083Gln,ENST00000394866,;KDM3B,downstream_gene_variant,,ENST00000508386,;KDM3B,3_prime_UTR_variant,,ENST00000507996,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,non_coding_transcript_exon_variant,,ENST00000505756,;KDM3B,upstream_gene_variant,,ENST00000509468,;	C	ENSG00000120733	ENST00000314358	Transcript	missense_variant	4479	4279	1427	E/Q	Gag/Cag	.	.	.	1	KDM3B	HGNC	1337	protein_coding	YES	CCDS34242.1	ENSP00000326563	KDM3B_HUMAN	F5H275_HUMAN	UPI000020C6A8	.	tolerated(0.08)	possibly_damaging(0.677)	17/24	.	hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTCTGAGCTC	.	3	ESCA
KDM3B	0	.	GRCh37	5	137761147	137761147	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4287G>A	p.Trp1429Ter	p.W1429*	ENST00000314358	17/24	97	70	27	85	85	0	KDM3B,stop_gained,p.Trp461Ter,ENST00000542866,;KDM3B,stop_gained,p.Trp1429Ter,ENST00000314358,;KDM3B,stop_gained,p.Trp1085Ter,ENST00000394866,;KDM3B,downstream_gene_variant,,ENST00000508386,;KDM3B,3_prime_UTR_variant,,ENST00000507996,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,non_coding_transcript_exon_variant,,ENST00000505756,;KDM3B,upstream_gene_variant,,ENST00000509468,;	A	ENSG00000120733	ENST00000314358	Transcript	stop_gained	4487	4287	1429	W/*	tgG/tgA	.	.	.	1	KDM3B	HGNC	1337	protein_coding	YES	CCDS34242.1	ENSP00000326563	KDM3B_HUMAN	F5H275_HUMAN	UPI000020C6A8	.	.	.	17/24	.	hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCTGGAAGCC	.	3	ESCA
UBE2D2	0	.	GRCh37	5	138979986	138979986	+	Silent	SNP	A	A	T	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54A>T	p.%3D	p.P18P	ENST00000398733	2/7	30	23	6	35	35	0	UBE2D2,synonymous_variant,p.%3D,ENST00000398733,;UBE2D2,5_prime_UTR_variant,,ENST00000505548,;UBE2D2,5_prime_UTR_variant,,ENST00000511725,;UBE2D2,5_prime_UTR_variant,,ENST00000505007,;UBE2D2,5_prime_UTR_variant,,ENST00000253815,;UBE2D2,synonymous_variant,p.%3D,ENST00000398734,;UBE2D2,non_coding_transcript_exon_variant,,ENST00000510470,;UBE2D2,upstream_gene_variant,,ENST00000511691,;	T	ENSG00000131508	ENST00000398733	Transcript	synonymous_variant	680	54	18	P	ccA/ccT	COSM3946886	.	.	1	UBE2D2	HGNC	12475	protein_coding	YES	CCDS43369.1	ENSP00000381717	UB2D2_HUMAN	D6RFM0_HUMAN,D6RAW0_HUMAN	UPI0000006BD0	.	.	.	2/7	.	PROSITE_profiles:PS50127,hmmpanther:PTHR24068:SF48,hmmpanther:PTHR24068,Pfam_domain:PF00179,Gene3D:3.10.110.10,SMART_domains:SM00212,Superfamily_domains:SSF54495	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCAGCACA	.	5	ESCA
PCDHAC1	0	.	GRCh37	5	140307392	140307392	+	Silent	SNP	C	C	G	rs782194525	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915C>G	p.%3D	p.L305L	ENST00000253807	1/4	30	19	11	30	30	0	PCDHAC1,synonymous_variant,p.%3D,ENST00000253807,;PCDHAC1,synonymous_variant,p.%3D,ENST00000409700,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA13,intron_variant,,ENST00000289272,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA13,intron_variant,,ENST00000409494,;	G	ENSG00000248383	ENST00000253807	Transcript	synonymous_variant	915	915	305	L	ctC/ctG	rs782194525	.	.	1	PCDHAC1	HGNC	8676	protein_coding	YES	CCDS4241.1	ENSP00000253807	PCDC1_HUMAN	.	UPI000013CDF7	.	.	.	1/4	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF112,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGCTCTTGGA	byFrequency	5	ESCA
PCDHB1	0	.	GRCh37	5	140431922	140431922	+	Silent	SNP	C	C	G	rs782300922	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.867C>G	p.%3D	p.L289L	ENST00000306549	1/1	42	30	12	33	33	0	PCDHB1,synonymous_variant,p.%3D,ENST00000306549,;	G	ENSG00000171815	ENST00000306549	Transcript	synonymous_variant	944	867	289	L	ctC/ctG	rs782300922	.	.	1	PCDHB1	HGNC	8680	protein_coding	YES	CCDS4243.1	ENSP00000307234	PCDB1_HUMAN	.	UPI000013EB56	.	.	.	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF88,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTCAAGAC	byFrequency	5	ESCA
KCTD16	0	.	GRCh37	5	143853449	143853449	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059G>C	p.%3D	p.L353L	ENST00000507359	3/3	25	20	4	18	18	0	KCTD16,synonymous_variant,p.%3D,ENST00000507359,;KCTD16,synonymous_variant,p.%3D,ENST00000512467,;	C	ENSG00000183775	ENST00000507359	Transcript	synonymous_variant	2150	1059	353	L	ctG/ctC	.	.	.	1	KCTD16	HGNC	29244	protein_coding	YES	CCDS34260.1	ENSP00000426548	KCD16_HUMAN	.	UPI000004A046	.	.	.	3/3	.	hmmpanther:PTHR14499:SF28,hmmpanther:PTHR14499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGATCCA	.	5	ESCA
MED7	0	.	GRCh37	5	156565835	156565835	+	Missense_Mutation	SNP	T	T	A	rs148324701	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608A>T	p.His203Leu	p.H203L	ENST00000286317	2/2	80	55	25	71	71	0	MED7,missense_variant,p.His203Leu,ENST00000420343,;MED7,missense_variant,p.His203Leu,ENST00000286317,;HAVCR2,intron_variant,,ENST00000524219,;MED7,downstream_gene_variant,,ENST00000524289,;ITK,upstream_gene_variant,,ENST00000521769,;	A	ENSG00000155868	ENST00000286317	Transcript	missense_variant	990	608	203	H/L	cAt/cTt	rs148324701	.	.	-1	MED7	HGNC	2378	protein_coding	YES	CCDS4334.1	ENSP00000286317	MED7_HUMAN	Q6IAZ5_HUMAN,E5RIE8_HUMAN	UPI0000128565	.	tolerated(0.34)	benign(0)	2/2	.	hmmpanther:PTHR15498:SF45,hmmpanther:PTHR15498	C:0.0004	C:0.0008	C:0.0014	.	C:0	C:0	C:0	C:0.0007	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGATGTTCA	byFrequency|byCluster|by1000G	5	ESCA
GABRG2	0	.	GRCh37	5	161524723	161524723	+	Missense_Mutation	SNP	G	G	A	rs778814579	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.407G>A	p.Arg136Gln	p.R136Q	ENST00000414552	4/11	41	38	3	37	37	0	GABRG2,missense_variant,p.Arg41Gln,ENST00000393933,;GABRG2,missense_variant,p.Arg136Gln,ENST00000361925,;GABRG2,missense_variant,p.Arg136Gln,ENST00000356592,;GABRG2,missense_variant,p.Arg41Gln,ENST00000522053,;GABRG2,missense_variant,p.Arg136Gln,ENST00000414552,;GABRG2,3_prime_UTR_variant,,ENST00000522990,;GABRG2,3_prime_UTR_variant,,ENST00000523372,;	A	ENSG00000113327	ENST00000414552	Transcript	missense_variant	632	407	136	R/Q	cGa/cAa	rs778814579	.	.	1	GABRG2	HGNC	4087	protein_coding	YES	CCDS47333.1	ENSP00000410732	GBRG2_HUMAN	.	UPI00017503BD	.	tolerated(0.09)	probably_damaging(0.997)	4/11	.	Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945:SF498,hmmpanther:PTHR18945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCTCCGATTGA	byFrequency	2	ESCA
DOCK2	0	.	GRCh37	5	169097556	169097556	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179C>G	p.Pro60Arg	p.P60R	ENST00000256935	4/52	41	31	9	49	49	0	DOCK2,missense_variant,p.Pro60Arg,ENST00000256935,;DOCK2,non_coding_transcript_exon_variant,,ENST00000522138,;DOCK2,missense_variant,p.Pro60Arg,ENST00000524185,;	G	ENSG00000134516	ENST00000256935	Transcript	missense_variant	259	179	60	P/R	cCt/cGt	.	.	.	1	DOCK2	HGNC	2988	protein_coding	YES	CCDS4371.1	ENSP00000256935	DOCK2_HUMAN	Q5XG91_HUMAN,B3KXW9_HUMAN	UPI00001A38CC	.	deleterious(0)	probably_damaging(0.996)	4/52	.	PROSITE_profiles:PS50002,hmmpanther:PTHR23317:SF73,hmmpanther:PTHR23317,Pfam_domain:PF07653,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCCTAAGT	.	5	ESCA
CREBRF	0	.	GRCh37	5	172550174	172550174	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1773G>C	p.Gln591His	p.Q591H	ENST00000296953	8/9	28	23	5	22	22	0	CREBRF,missense_variant,p.Gln593His,ENST00000540014,;CREBRF,missense_variant,p.Gln591His,ENST00000296953,;CREBRF,non_coding_transcript_exon_variant,,ENST00000520464,;	C	ENSG00000164463	ENST00000296953	Transcript	missense_variant	2092	1773	591	Q/H	caG/caC	.	.	.	1	CREBRF	HGNC	24050	protein_coding	YES	CCDS34293.1	ENSP00000296953	CRERF_HUMAN	E5RI19_HUMAN,B3KV47_HUMAN	UPI000049E01D	.	deleterious(0.02)	benign(0.382)	8/9	.	hmmpanther:PTHR21552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCAGAAGCT	.	5	ESCA
CPEB4	0	.	GRCh37	5	173386077	173386077	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2937C>G	.	.	ENST00000265085	10/10	66	53	12	51	51	0	CPEB4,3_prime_UTR_variant,,ENST00000334035,;CPEB4,3_prime_UTR_variant,,ENST00000265085,;CPEB4,downstream_gene_variant,,ENST00000522336,;CPEB4,downstream_gene_variant,,ENST00000517880,;CPEB4,downstream_gene_variant,,ENST00000520867,;CPEB4,downstream_gene_variant,,ENST00000519467,;	G	ENSG00000113742	ENST00000265085	Transcript	3_prime_UTR_variant	6581	.	.	.	.	.	.	.	1	CPEB4	HGNC	21747	protein_coding	YES	CCDS4390.1	ENSP00000265085	CPEB4_HUMAN	.	UPI000020C179	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCAGATT	.	5	ESCA
FAM193B	0	.	GRCh37	5	176951721	176951721	+	Silent	SNP	G	G	C	rs374231278	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1761C>G	p.%3D	p.L587L	ENST00000514747	6/9	48	37	11	49	49	0	FAM193B,synonymous_variant,p.%3D,ENST00000329540,;FAM193B,synonymous_variant,p.%3D,ENST00000524677,;FAM193B,synonymous_variant,p.%3D,ENST00000443375,;FAM193B,synonymous_variant,p.%3D,ENST00000514747,;FAM193B,upstream_gene_variant,,ENST00000504130,;FAM193B,downstream_gene_variant,,ENST00000508298,;FAM193B,upstream_gene_variant,,ENST00000505241,;FAM193B,3_prime_UTR_variant,,ENST00000510479,;FAM193B,3_prime_UTR_variant,,ENST00000506955,;FAM193B,3_prime_UTR_variant,,ENST00000510163,;FAM193B,non_coding_transcript_exon_variant,,ENST00000505569,;FAM193B,upstream_gene_variant,,ENST00000513282,;FAM193B,upstream_gene_variant,,ENST00000506879,;FAM193B,downstream_gene_variant,,ENST00000513502,;FAM193B,upstream_gene_variant,,ENST00000507212,;	C	ENSG00000146067	ENST00000514747	Transcript	synonymous_variant	1810	1761	587	L	ctC/ctG	rs374231278	.	.	-1	FAM193B	HGNC	25524	protein_coding	YES	CCDS54954.1	ENSP00000422131	F193B_HUMAN	D6RDZ2_HUMAN,D6RC29_HUMAN,D6RAX9_HUMAN	UPI0001D3BB6A	.	.	.	6/9	.	hmmpanther:PTHR15109,hmmpanther:PTHR15109:SF3	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTTGAGTCT	byFrequency|byCluster	5	ESCA
PRLR	0	.	GRCh37	5	35068920	35068920	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.746G>C	p.Cys249Ser	p.C249S	ENST00000382002	8/10	42	38	4	23	23	0	PRLR,missense_variant,p.Cys249Ser,ENST00000310101,;PRLR,missense_variant,p.Cys249Ser,ENST00000382002,;PRLR,missense_variant,p.Cys148Ser,ENST00000342362,;PRLR,missense_variant,p.Cys148Ser,ENST00000511486,;PRLR,missense_variant,p.Cys249Ser,ENST00000542609,;PRLR,missense_variant,p.Cys249Ser,ENST00000231423,;PRLR,missense_variant,p.Cys249Ser,ENST00000513753,;PRLR,intron_variant,,ENST00000348262,;PRLR,intron_variant,,ENST00000397391,;PRLR,intron_variant,,ENST00000509934,;PRLR,3_prime_UTR_variant,,ENST00000509140,;PRLR,3_prime_UTR_variant,,ENST00000508107,;PRLR,intron_variant,,ENST00000514088,;	G	ENSG00000113494	ENST00000382002	Transcript	missense_variant	1173	746	249	C/S	tGt/tCt	.	.	.	-1	PRLR	HGNC	9446	protein_coding	YES	CCDS3909.1	ENSP00000371432	PRLR_HUMAN	D6RD41_HUMAN,D6RC67_HUMAN,D6RAN9_HUMAN,D6R9V7_HUMAN,D6R9P5_HUMAN	UPI0000132234	.	deleterious(0.02)	benign(0.209)	8/10	.	hmmpanther:PTHR23036:SF86,hmmpanther:PTHR23036,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAAACAGATG	.	3	ESCA
SPEF2	0	.	GRCh37	5	35779216	35779216	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4218-3C>T	.	.	ENST00000356031	.	62	55	7	31	31	0	SPEF2,splice_region_variant,,ENST00000440995,;SPEF2,splice_region_variant,,ENST00000356031,;SPEF2,upstream_gene_variant,,ENST00000303129,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,splice_region_variant,,ENST00000506526,;SPEF2,upstream_gene_variant,,ENST00000513078,;	T	ENSG00000152582	ENST00000356031	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	SPEF2	HGNC	26293	protein_coding	YES	CCDS43309.1	ENSP00000348314	SPEF2_HUMAN	.	UPI0001505B9F	.	.	.	.	29/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	ACTTTCAGTAC	.	2	ESCA
EGFLAM	0	.	GRCh37	5	38438418	38438418	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2325C>T	p.%3D	p.F775F	ENST00000354891	17/23	109	89	20	49	49	0	EGFLAM,synonymous_variant,p.%3D,ENST00000336740,;EGFLAM,synonymous_variant,p.%3D,ENST00000354891,;EGFLAM,synonymous_variant,p.%3D,ENST00000397202,;EGFLAM,synonymous_variant,p.%3D,ENST00000322350,;	T	ENSG00000164318	ENST00000354891	Transcript	synonymous_variant	2671	2325	775	F	ttC/ttT	.	.	.	1	EGFLAM	HGNC	26810	protein_coding	YES	CCDS56363.1	ENSP00000346964	EGFLA_HUMAN	D6RJD2_HUMAN	UPI000022C806	.	.	.	17/23	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10574:SF202,hmmpanther:PTHR10574,Gene3D:2.60.120.200,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCACCTC	.	5	ESCA
C7	0	.	GRCh37	5	40947882	40947882	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.917C>G	p.Ser306Cys	p.S306C	ENST00000313164	8/18	94	83	11	48	48	0	C7,missense_variant,p.Ser306Cys,ENST00000313164,;C7,downstream_gene_variant,,ENST00000508185,;	G	ENSG00000112936	ENST00000313164	Transcript	missense_variant	1276	917	306	S/C	tCt/tGt	.	.	.	1	C7	HGNC	1346	protein_coding	YES	CCDS47201.1	ENSP00000322061	CO7_HUMAN	.	UPI000020CA08	.	deleterious(0.01)	probably_damaging(0.992)	8/18	.	PROSITE_profiles:PS51412,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF312,Pfam_domain:PF01823,SMART_domains:SM00457	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAATCTGGGT	.	4	ESCA
MROH2B	0	.	GRCh37	5	41045946	41045946	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1738G>C	p.Glu580Gln	p.E580Q	ENST00000399564	18/42	115	91	24	62	62	0	MROH2B,missense_variant,p.Glu135Gln,ENST00000506092,;MROH2B,missense_variant,p.Glu580Gln,ENST00000399564,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,;MROH2B,downstream_gene_variant,,ENST00000508575,;	G	ENSG00000171495	ENST00000399564	Transcript	missense_variant	2189	1738	580	E/Q	Gaa/Caa	.	.	.	-1	MROH2B	HGNC	26857	protein_coding	YES	CCDS47202.1	ENSP00000382476	MRO2B_HUMAN	F5GZ06_HUMAN	UPI000020CA04	.	deleterious(0.02)	benign(0.138)	18/42	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF15,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATTCTTTGA	.	5	ESCA
GHR	0	.	GRCh37	5	42718722	42718722	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1113G>A	p.%3D	p.E371E	ENST00000230882	10/10	56	51	5	25	25	0	GHR,synonymous_variant,p.%3D,ENST00000230882,;GHR,synonymous_variant,p.%3D,ENST00000537449,;GHR,synonymous_variant,p.%3D,ENST00000357703,;GHR,non_coding_transcript_exon_variant,,ENST00000513625,;GHR,3_prime_UTR_variant,,ENST00000511135,;	A	ENSG00000112964	ENST00000230882	Transcript	synonymous_variant	1303	1113	371	E	gaG/gaA	COSM3616680	.	.	1	GHR	HGNC	4263	protein_coding	YES	CCDS3940.1	ENSP00000230882	GHR_HUMAN	Q9NRZ8_HUMAN,Q9HCW9_HUMAN,F5H7X2_HUMAN	UPI000012B416	.	.	.	10/10	.	Pfam_domain:PF12772,hmmpanther:PTHR23036:SF74,hmmpanther:PTHR23036	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CATGAGAAATC	.	3	ESCA
EMB	0	.	GRCh37	5	49694982	49694982	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*125G>T	.	.	ENST00000303221	9/9	104	69	35	59	58	0	EMB,3_prime_UTR_variant,,ENST00000514111,;EMB,3_prime_UTR_variant,,ENST00000303221,;EMB,3_prime_UTR_variant,,ENST00000508934,;EMB,downstream_gene_variant,,ENST00000506190,;EMB,non_coding_transcript_exon_variant,,ENST00000505896,;	A	ENSG00000170571	ENST00000303221	Transcript	3_prime_UTR_variant	1325	.	.	.	.	.	.	.	-1	EMB	HGNC	30465	protein_coding	YES	CCDS3953.1	ENSP00000302289	EMB_HUMAN	B7Z902_HUMAN	UPI0000160A6D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGCATGTT	.	5	ESCA
PARP8	0	.	GRCh37	5	49963923	49963923	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110C>G	p.Ser37Cys	p.S37C	ENST00000281631	2/26	354	241	112	215	215	0	PARP8,missense_variant,p.Ser37Cys,ENST00000503750,;PARP8,missense_variant,p.Ser37Cys,ENST00000514067,;PARP8,missense_variant,p.Ser37Cys,ENST00000513738,;PARP8,missense_variant,p.Ser37Cys,ENST00000503046,;PARP8,missense_variant,p.Ser37Cys,ENST00000502524,;PARP8,missense_variant,p.Ser37Cys,ENST00000515175,;PARP8,missense_variant,p.Ser37Cys,ENST00000505697,;PARP8,missense_variant,p.Ser37Cys,ENST00000281631,;PARP8,missense_variant,p.Ser37Cys,ENST00000503665,;PARP8,missense_variant,p.Ser16Cys,ENST00000505554,;PARP8,5_prime_UTR_variant,,ENST00000514342,;RP11-269M20.3,upstream_gene_variant,,ENST00000607844,;PARP8,non_coding_transcript_exon_variant,,ENST00000505180,;PARP8,non_coding_transcript_exon_variant,,ENST00000513414,;PARP8,non_coding_transcript_exon_variant,,ENST00000511363,;PARP8,non_coding_transcript_exon_variant,,ENST00000503561,;PARP8,non_coding_transcript_exon_variant,,ENST00000503790,;PARP8,missense_variant,p.Ser37Cys,ENST00000503707,;PARP8,missense_variant,p.Ser37Cys,ENST00000515166,;PARP8,missense_variant,p.Ser37Cys,ENST00000510303,;PARP8,missense_variant,p.Ser37Cys,ENST00000507812,;PARP8,non_coding_transcript_exon_variant,,ENST00000510040,;PARP8,intron_variant,,ENST00000503193,;PARP8,intron_variant,,ENST00000503888,;	G	ENSG00000151883	ENST00000281631	Transcript	missense_variant	268	110	37	S/C	tCc/tGc	.	.	.	1	PARP8	HGNC	26124	protein_coding	YES	CCDS3954.1	ENSP00000281631	PARP8_HUMAN	D6RGZ9_HUMAN	UPI0000073D19	.	deleterious_low_confidence(0.01)	benign(0.28)	2/26	.	hmmpanther:PTHR21328,hmmpanther:PTHR21328:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTCCACCT	.	5	ESCA
KIAA0947	0	.	GRCh37	5	5464326	5464326	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4879G>C	p.Glu1627Gln	p.E1627Q	ENST00000296564	13/19	30	20	10	22	22	0	KIAA0947,missense_variant,p.Glu1627Gln,ENST00000296564,;	C	ENSG00000164151	ENST00000296564	Transcript	missense_variant	5101	4879	1627	E/Q	Gag/Cag	.	.	.	1	KIAA0947	HGNC	29154	protein_coding	YES	CCDS47187.1	ENSP00000296564	K0947_HUMAN	.	UPI00015542F9	.	deleterious(0)	probably_damaging(1)	13/19	.	hmmpanther:PTHR11852,hmmpanther:PTHR11852:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAAGAGGTG	.	5	ESCA
KIAA0947	0	.	GRCh37	5	5465301	5465301	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5854G>C	p.Glu1952Gln	p.E1952Q	ENST00000296564	13/19	27	20	7	17	17	0	KIAA0947,missense_variant,p.Glu1952Gln,ENST00000296564,;	C	ENSG00000164151	ENST00000296564	Transcript	missense_variant	6076	5854	1952	E/Q	Gag/Cag	.	.	.	1	KIAA0947	HGNC	29154	protein_coding	YES	CCDS47187.1	ENSP00000296564	K0947_HUMAN	.	UPI00015542F9	.	deleterious(0)	probably_damaging(0.999)	13/19	.	hmmpanther:PTHR11852,hmmpanther:PTHR11852:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCAAGAGAAG	.	5	ESCA
IL6ST	0	.	GRCh37	5	55250687	55250687	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1401C>G	p.Ile467Met	p.I467M	ENST00000381298	11/17	50	40	10	49	49	0	IL6ST,missense_variant,p.Ile467Met,ENST00000336909,;IL6ST,missense_variant,p.Ile467Met,ENST00000381298,;IL6ST,missense_variant,p.Ile467Met,ENST00000502326,;IL6ST,3_prime_UTR_variant,,ENST00000522633,;IL6ST,3_prime_UTR_variant,,ENST00000381287,;IL6ST,intron_variant,,ENST00000381293,;IL6ST,intron_variant,,ENST00000536319,;IL6ST,intron_variant,,ENST00000381294,;IL6ST,intron_variant,,ENST00000381286,;IL6ST,upstream_gene_variant,,ENST00000423954,;IL6ST,3_prime_UTR_variant,,ENST00000503773,;IL6ST,upstream_gene_variant,,ENST00000583149,;IL6ST,downstream_gene_variant,,ENST00000506241,;	C	ENSG00000134352	ENST00000381298	Transcript	missense_variant	1714	1401	467	I/M	atC/atG	.	.	.	-1	IL6ST	HGNC	6021	protein_coding	YES	CCDS3971.1	ENSP00000370698	IL6RB_HUMAN	.	UPI000013CF29	.	tolerated(0.08)	benign(0.07)	11/17	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF25,hmmpanther:PTHR23036,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTGATACA	.	5	ESCA
PDE4D	0	.	GRCh37	5	58334993	58334993	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.809-195G>A	.	.	ENST00000340635	.	15	10	5	14	14	0	PDE4D,5_prime_UTR_variant,,ENST00000358923,;PDE4D,intron_variant,,ENST00000505453,;PDE4D,intron_variant,,ENST00000503258,;PDE4D,intron_variant,,ENST00000546160,;PDE4D,intron_variant,,ENST00000360047,;PDE4D,intron_variant,,ENST00000340635,;PDE4D,intron_variant,,ENST00000405755,;PDE4D,intron_variant,,ENST00000507116,;PDE4D,intron_variant,,ENST00000502484,;RP11-266N13.2,upstream_gene_variant,,ENST00000500224,;PDE4D,intron_variant,,ENST00000405053,;PDE4D,non_coding_transcript_exon_variant,,ENST00000515011,;PDE4D,intron_variant,,ENST00000309641,;	T	ENSG00000113448	ENST00000340635	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PDE4D	HGNC	8783	protein_coding	YES	CCDS47213.1	ENSP00000345502	PDE4D_HUMAN	D6RHE0_HUMAN	UPI0000050EB1	.	.	.	.	5/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGCCTCGGGGA	.	4	ESCA
TNPO1	0	.	GRCh37	5	72161504	72161504	+	Missense_Mutation	SNP	A	A	G	rs113424229	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544A>G	p.Ile182Val	p.I182V	ENST00000337273	6/25	42	32	9	30	30	0	TNPO1,missense_variant,p.Ile174Val,ENST00000506351,;TNPO1,missense_variant,p.Ile132Val,ENST00000454282,;TNPO1,missense_variant,p.Ile132Val,ENST00000523768,;TNPO1,missense_variant,p.Ile182Val,ENST00000337273,;TNPO1,intron_variant,,ENST00000447967,;TNPO1,non_coding_transcript_exon_variant,,ENST00000511754,;TNPO1,non_coding_transcript_exon_variant,,ENST00000518279,;TNPO1,intron_variant,,ENST00000506528,;TNPO1,downstream_gene_variant,,ENST00000513944,;TNPO1,downstream_gene_variant,,ENST00000509030,;TNPO1,intron_variant,,ENST00000520850,;	G	ENSG00000083312	ENST00000337273	Transcript	missense_variant	970	544	182	I/V	Atc/Gtc	rs113424229	.	.	1	TNPO1	HGNC	6401	protein_coding	YES	CCDS43329.1	ENSP00000336712	TNPO1_HUMAN	S4R398_HUMAN	UPI000020CAB6	.	tolerated(0.64)	benign(0)	6/25	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR10527:SF21,hmmpanther:PTHR10527	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAACATCATG	.	5	ESCA
EDIL3	0	.	GRCh37	5	83680212	83680212	+	5'UTR	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-20C>A	.	.	ENST00000296591	1/11	63	44	19	87	87	0	EDIL3,5_prime_UTR_variant,,ENST00000296591,;EDIL3,upstream_gene_variant,,ENST00000380138,;CTD-2269F5.1,upstream_gene_variant,,ENST00000509406,;CTD-2269F5.1,upstream_gene_variant,,ENST00000507060,;CTD-2269F5.1,upstream_gene_variant,,ENST00000502253,;CTD-2269F5.1,upstream_gene_variant,,ENST00000514696,;CTD-2269F5.1,upstream_gene_variant,,ENST00000515688,;	T	ENSG00000164176	ENST00000296591	Transcript	5_prime_UTR_variant	400	.	.	.	.	.	.	.	-1	EDIL3	HGNC	3173	protein_coding	YES	CCDS4062.1	ENSP00000296591	EDIL3_HUMAN	.	UPI000004D126	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACGTGACCCC	.	5	ESCA
MBLAC2	0	.	GRCh37	5	89755780	89755780	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1204C>T	.	.	ENST00000316610	2/2	48	37	11	39	39	0	MBLAC2,3_prime_UTR_variant,,ENST00000316610,;	A	ENSG00000176055	ENST00000316610	Transcript	3_prime_UTR_variant	2520	.	.	.	.	.	.	.	-1	MBLAC2	HGNC	33711	protein_coding	YES	CCDS4067.1	ENSP00000314776	MBLC2_HUMAN	.	UPI00001975AC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGTGGGA	.	5	ESCA
GCM2	0	.	GRCh37	6	10876178	10876178	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528G>A	p.%3D	p.K176K	ENST00000379491	4/5	66	42	24	61	61	0	GCM2,synonymous_variant,p.%3D,ENST00000379491,;SYCP2L,intron_variant,,ENST00000543878,;RP11-637O19.3,intron_variant,,ENST00000480294,;	T	ENSG00000124827	ENST00000379491	Transcript	synonymous_variant	676	528	176	K	aaG/aaA	.	.	.	-1	GCM2	HGNC	4198	protein_coding	YES	CCDS4517.1	ENSP00000368805	GCM2_HUMAN	D3GDV6_HUMAN	UPI0000073DE7	.	.	.	4/5	.	hmmpanther:PTHR12414,hmmpanther:PTHR12414:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTCTTGAT	.	5	ESCA
HDDC2	0	.	GRCh37	6	125623117	125623117	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39C>G	.	.	ENST00000398153	1/6	24	20	4	16	16	0	HDDC2,5_prime_UTR_variant,,ENST00000398153,;HDDC2,5_prime_UTR_variant,,ENST00000368377,;HDDC2,5_prime_UTR_variant,,ENST00000608284,;HDDC2,upstream_gene_variant,,ENST00000608295,;HDDC2,non_coding_transcript_exon_variant,,ENST00000609574,;HDDC2,5_prime_UTR_variant,,ENST00000318787,;HDDC2,upstream_gene_variant,,ENST00000609477,;HDDC2,upstream_gene_variant,,ENST00000608461,;	C	ENSG00000111906	ENST00000398153	Transcript	5_prime_UTR_variant	5	.	.	.	.	.	.	.	-1	HDDC2	HGNC	21078	protein_coding	YES	CCDS43503.1	ENSP00000381220	HDDC2_HUMAN	H0UI53_HUMAN,H0UI52_HUMAN	UPI0000070B81	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGGCGAAGCT	.	2	ESCA
LAMA2	0	.	GRCh37	6	129724965	129724965	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5727-1G>C	.	p.X1909_splice	ENST00000421865	.	31	26	4	32	32	0	LAMA2,splice_acceptor_variant,,ENST00000421865,;	C	ENSG00000196569	ENST00000421865	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	LAMA2	HGNC	6482	protein_coding	YES	CCDS5138.1	ENSP00000400365	LAMA2_HUMAN	Q59H37_HUMAN	UPI00003673E0	.	.	.	.	39/64	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCAGAATCC	.	5	ESCA
KIAA1244	0	.	GRCh37	6	138649248	138649248	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5092G>C	p.Asp1698His	p.D1698H	ENST00000251691	32/34	10	5	5	8	8	0	KIAA1244,missense_variant,p.Asp1698His,ENST00000251691,;	C	ENSG00000112379	ENST00000251691	Transcript	missense_variant	5258	5092	1698	D/H	Gat/Cat	.	.	.	1	KIAA1244	HGNC	21213	protein_coding	YES	CCDS5189.2	ENSP00000251691	BIG3_HUMAN	C5NM88_HUMAN,B5MDV5_HUMAN	UPI000150AF4A	.	deleterious(0.02)	possibly_damaging(0.823)	32/34	.	hmmpanther:PTHR10663:SF13,hmmpanther:PTHR10663	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCTGATGAA	.	2	ESCA
SHPRH	0	.	GRCh37	6	146268631	146268631	+	Missense_Mutation	SNP	C	C	T	rs577017273	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210G>A	p.Glu404Lys	p.E404K	ENST00000367505	6/30	35	25	9	31	31	0	SHPRH,missense_variant,p.Glu404Lys,ENST00000275233,;SHPRH,missense_variant,p.Glu404Lys,ENST00000438092,;SHPRH,missense_variant,p.Glu404Lys,ENST00000367505,;SHPRH,missense_variant,p.Glu404Lys,ENST00000367503,;SHPRH,missense_variant,p.Glu293Lys,ENST00000519632,;SHPRH,missense_variant,p.Glu382Lys,ENST00000433355,;SHPRH,splice_region_variant,,ENST00000521977,;	T	ENSG00000146414	ENST00000367505	Transcript	missense_variant	1475	1210	404	E/K	Gag/Aag	rs577017273	.	.	-1	SHPRH	HGNC	19336	protein_coding	YES	CCDS43513.2	ENSP00000356475	SHPRH_HUMAN	.	UPI0000458A24	.	tolerated_low_confidence(0.07)	probably_damaging(0.979)	6/30	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF552,Pfam_domain:PF00176,SMART_domains:SM00487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCTCGGGAA	byCluster	5	ESCA
CMAHP	0	.	GRCh37	6	25093789	25093789	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1798G>C	.	.	ENST00000377989	10/14	47	32	14	46	46	0	CMAHP,non_coding_transcript_exon_variant,,ENST00000377989,;CMAHP,non_coding_transcript_exon_variant,,ENST00000493257,;CMAHP,non_coding_transcript_exon_variant,,ENST00000490939,;CMAHP,non_coding_transcript_exon_variant,,ENST00000436589,;CMAHP,non_coding_transcript_exon_variant,,ENST00000377993,;CMAHP,downstream_gene_variant,,ENST00000424282,;	G	ENSG00000168405	ENST00000377989	Transcript	non_coding_transcript_exon_variant	1798	.	.	.	.	.	.	.	-1	CMAHP	HGNC	2098	processed_transcript	YES	.	.	.	.	.	.	.	.	10/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTATTCTTTTA	.	5	ESCA
LRRC16A	0	.	GRCh37	6	25495435	25495435	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1317G>T	p.Glu439Asp	p.E439D	ENST00000329474	16/37	36	27	9	30	30	0	LRRC16A,missense_variant,p.Glu439Asp,ENST00000329474,;	T	ENSG00000079691	ENST00000329474	Transcript	missense_variant	1685	1317	439	E/D	gaG/gaT	.	.	.	1	LRRC16A	HGNC	21581	protein_coding	YES	CCDS54973.1	ENSP00000331983	LR16A_HUMAN	.	UPI00004588AB	.	tolerated(0.46)	benign(0.109)	16/37	.	hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF39,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGAGCCCTT	.	5	ESCA
HIST1H4E	0	.	GRCh37	6	26205238	26205238	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*54C>T	.	.	ENST00000360441	1/1	39	33	6	24	24	0	HIST1H4E,3_prime_UTR_variant,,ENST00000360441,;HIST1H2BF,downstream_gene_variant,,ENST00000359985,;RP1-34B20.4,downstream_gene_variant,,ENST00000405418,;	T	ENSG00000198518	ENST00000360441	Transcript	3_prime_UTR_variant	381	.	.	.	.	.	.	.	1	HIST1H4E	HGNC	4790	protein_coding	YES	CCDS4593.1	ENSP00000353624	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTTCAGGGC	.	2	ESCA
HIST1H3E	0	.	GRCh37	6	26225602	26225602	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.220G>C	p.Glu74Gln	p.E74Q	ENST00000360408	1/1	136	115	21	104	104	0	HIST1H3E,missense_variant,p.Glu74Gln,ENST00000360408,;	C	ENSG00000196966	ENST00000360408	Transcript	missense_variant	220	220	74	E/Q	Gaa/Caa	.	.	.	1	HIST1H3E	HGNC	4769	protein_coding	YES	CCDS4596.1	ENSP00000353581	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0.02)	probably_damaging(0.996)	1/1	.	hmmpanther:PTHR11426,PROSITE_patterns:PS00959,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGAGAAATA	.	5	ESCA
OR11A1	0	.	GRCh37	6	29394838	29394838	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.581G>A	p.Arg194Lys	p.R194K	ENST00000377149	5/5	37	29	8	25	25	0	OR11A1,missense_variant,p.Arg194Lys,ENST00000377149,;OR11A1,missense_variant,p.Arg194Lys,ENST00000377148,;OR11A1,missense_variant,p.Arg194Lys,ENST00000377147,;OR5V1,intron_variant,,ENST00000377154,;	T	ENSG00000204694	ENST00000377149	Transcript	missense_variant	1054	581	194	R/K	aGa/aAa	.	.	.	-1	OR11A1	HGNC	8176	protein_coding	YES	CCDS34363.1	ENSP00000366354	O11A1_HUMAN	.	UPI000000DCA8	.	tolerated(0.15)	benign(0.026)	5/5	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF178,hmmpanther:PTHR24242,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTCTGGGA	.	5	ESCA
TRIM10	0	.	GRCh37	6	30128405	30128405	+	Silent	SNP	G	G	A	rs762205559	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.231C>T	p.%3D	p.N77N	ENST00000449742	1/7	86	77	9	66	66	0	TRIM10,synonymous_variant,p.%3D,ENST00000376704,;TRIM10,synonymous_variant,p.%3D,ENST00000449742,;TRIM15,upstream_gene_variant,,ENST00000376688,;TRIM15,upstream_gene_variant,,ENST00000376694,;	A	ENSG00000204613	ENST00000449742	Transcript	synonymous_variant	307	231	77	N	aaC/aaT	rs762205559,COSM316129	.	.	-1	TRIM10	HGNC	10072	protein_coding	YES	CCDS34375.1	ENSP00000397073	TRI10_HUMAN	.	UPI000000D736	.	.	.	1/7	.	hmmpanther:PTHR24103:SF44,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCACGTTAGC	byFrequency	3	ESCA
EHMT2	0	.	GRCh37	6	31847870	31847870	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3624C>G	p.%3D	p.V1208V	ENST00000375537	28/28	88	62	25	106	106	0	EHMT2,synonymous_variant,p.%3D,ENST00000375528,;EHMT2,synonymous_variant,p.%3D,ENST00000395728,;EHMT2,synonymous_variant,p.%3D,ENST00000375530,;EHMT2,synonymous_variant,p.%3D,ENST00000375537,;EHMT2,downstream_gene_variant,,ENST00000436026,;SLC44A4,upstream_gene_variant,,ENST00000229729,;SLC44A4,upstream_gene_variant,,ENST00000414427,;SLC44A4,upstream_gene_variant,,ENST00000544672,;SLC44A4,upstream_gene_variant,,ENST00000375562,;EHMT2-AS1,upstream_gene_variant,,ENST00000434689,;EHMT2,non_coding_transcript_exon_variant,,ENST00000480912,;EHMT2,non_coding_transcript_exon_variant,,ENST00000478491,;SLC44A4,upstream_gene_variant,,ENST00000465707,;SLC44A4,upstream_gene_variant,,ENST00000462671,;EHMT2,non_coding_transcript_exon_variant,,ENST00000461880,;EHMT2,non_coding_transcript_exon_variant,,ENST00000494816,;EHMT2,downstream_gene_variant,,ENST00000477678,;	C	ENSG00000204371	ENST00000375537	Transcript	synonymous_variant	3631	3624	1208	V	gtC/gtG	.	.	.	-1	EHMT2	HGNC	14129	protein_coding	YES	CCDS4725.1	ENSP00000364687	EHMT2_HUMAN	.	UPI000013D085	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTTGACAGG	.	5	ESCA
TNXB	0	.	GRCh37	6	32023938	32023938	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8157G>C	p.Glu2719Asp	p.E2719D	ENST00000375247	24/44	36	26	10	40	40	0	TNXB,missense_variant,p.Glu2719Asp,ENST00000375247,;TNXB,missense_variant,p.Glu2719Asp,ENST00000375244,;	G	ENSG00000168477	ENST00000375247	Transcript	missense_variant	8359	8157	2719	E/D	gaG/gaC	.	.	.	-1	TNXB	HGNC	11976	protein_coding	.	.	ENSP00000364396	TENX_HUMAN	Q9NPK8_HUMAN,Q9NPK7_HUMAN,B6RHJ5_HUMAN	UPI000174F11D	.	.	probably_damaging(0.979)	24/44	.	Gene3D:2.60.40.10,hmmpanther:PTHR19143:SF190,hmmpanther:PTHR19143,PROSITE_profiles:PS50853,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTCTCTTC	.	5	ESCA
HLA-DQA2	0	.	GRCh37	6	32713702	32713702	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.466G>A	p.Glu156Lys	p.E156K	ENST00000374940	3/5	256	211	45	176	176	0	HLA-DQA2,missense_variant,p.Glu156Lys,ENST00000374940,;MIR3135B,downstream_gene_variant,,ENST00000581098,;	A	ENSG00000237541	ENST00000374940	Transcript	missense_variant	568	466	156	E/K	Gaa/Aaa	.	.	.	1	HLA-DQA2	HGNC	4943	protein_coding	YES	CCDS4753.1	ENSP00000364076	DQA2_HUMAN	O19697_HUMAN	UPI0000001086	.	tolerated(0.13)	benign(0.245)	3/5	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19944:SF54,hmmpanther:PTHR19944,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACAGAAGGT	.	4	ESCA
SYNGAP1	0	.	GRCh37	6	33408515	33408515	+	Silent	SNP	G	G	A	rs765453681	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1686G>A	p.%3D	p.P562P	ENST00000418600	11/19	55	44	10	41	41	0	SYNGAP1,synonymous_variant,p.%3D,ENST00000428982,;SYNGAP1,synonymous_variant,p.%3D,ENST00000418600,;SYNGAP1,synonymous_variant,p.%3D,ENST00000293748,;SYNGAP1,synonymous_variant,p.%3D,ENST00000449372,;MIR5004,downstream_gene_variant,,ENST00000579078,;SYNGAP1,non_coding_transcript_exon_variant,,ENST00000496374,;SYNGAP1,downstream_gene_variant,,ENST00000495633,;SYNGAP1,downstream_gene_variant,,ENST00000479510,;	A	ENSG00000197283	ENST00000418600	Transcript	synonymous_variant	1787	1686	562	P	ccG/ccA	rs765453681	.	.	1	SYNGAP1	HGNC	11497	protein_coding	YES	CCDS34434.2	ENSP00000403636	SYGP1_HUMAN	.	UPI0000470C44	.	.	.	11/19	.	PROSITE_profiles:PS50018,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF25,Gene3D:1.10.506.10,Pfam_domain:PF00616,SMART_domains:SM00323,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTCCCGAGGGA	.	3	ESCA
ITPR3	0	.	GRCh37	6	33653581	33653581	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5644G>C	p.Glu1882Gln	p.E1882Q	ENST00000374316	42/59	12	9	3	11	11	0	ITPR3,missense_variant,p.Glu1882Gln,ENST00000374316,;ITPR3,missense_variant,p.Glu1882Gln,ENST00000605930,;	C	ENSG00000096433	ENST00000374316	Transcript	missense_variant	6704	5644	1882	E/Q	Gag/Cag	.	.	.	1	ITPR3	HGNC	6182	protein_coding	YES	CCDS4783.1	ENSP00000363435	ITPR3_HUMAN	A6H8K3_HUMAN	UPI000013CB74	.	deleterious(0.01)	probably_damaging(0.984)	42/59	.	hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715,Pfam_domain:PF08454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTGTGAGAAC	.	2	ESCA
C6orf89	0	.	GRCh37	6	36867365	36867365	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166C>G	p.Gln56Glu	p.Q56E	ENST00000355190	2/8	34	24	9	27	27	0	C6orf89,missense_variant,p.Gln49Glu,ENST00000373685,;C6orf89,missense_variant,p.Gln56Glu,ENST00000355190,;C6orf89,missense_variant,p.Gln49Glu,ENST00000480824,;C6orf89,5_prime_UTR_variant,,ENST00000510325,;C6orf89,5_prime_UTR_variant,,ENST00000359359,;	G	ENSG00000198663	ENST00000355190	Transcript	missense_variant	329	166	56	Q/E	Cag/Gag	COSM3830372,COSM3830373	.	.	1	C6orf89	HGNC	21114	protein_coding	YES	CCDS4827.1	ENSP00000347322	CF089_HUMAN	Q5TDC5_HUMAN	UPI000035E870	.	deleterious(0.01)	probably_damaging(0.997)	2/8	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P60fs*7|c.172delC|7,BUFFER|p.Q61fs*10|c.171_172insC|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTCAGAGA	.	5	ESCA
PGC	0	.	GRCh37	6	41710116	41710116	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559C>G	p.Leu187Val	p.L187V	ENST00000373025	5/9	43	26	17	33	33	0	PGC,missense_variant,p.Leu187Val,ENST00000373025,;PGC,missense_variant,p.Leu108Val,ENST00000356667,;PGC,missense_variant,p.Leu187Val,ENST00000425343,;PGC,downstream_gene_variant,,ENST00000415707,;	C	ENSG00000096088	ENST00000373025	Transcript	missense_variant	622	559	187	L/V	Ctg/Gtg	.	.	.	-1	PGC	HGNC	8890	protein_coding	YES	CCDS4859.1	ENSP00000362116	PEPC_HUMAN	.	UPI00001315CC	.	tolerated(0.19)	benign(0.043)	5/9	.	hmmpanther:PTHR13683:SF242,hmmpanther:PTHR13683,Pfam_domain:PF00026,Gene3D:2.40.70.10,Superfamily_domains:SSF50630	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGACAGAGCAG	.	4	ESCA
FRS3	0	.	GRCh37	6	41744689	41744689	+	Missense_Mutation	SNP	C	C	T	rs367802861	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37G>A	p.Val13Ile	p.V13I	ENST00000373018	3/7	71	60	10	63	63	0	FRS3,missense_variant,p.Val13Ile,ENST00000422888,;FRS3,missense_variant,p.Val13Ile,ENST00000373018,;FRS3,missense_variant,p.Val37Ile,ENST00000426290,;FRS3,missense_variant,p.Val13Ile,ENST00000259748,;PRICKLE4,upstream_gene_variant,,ENST00000359201,;PRICKLE4,upstream_gene_variant,,ENST00000458694,;FRS3,non_coding_transcript_exon_variant,,ENST00000466420,;PRICKLE4,upstream_gene_variant,,ENST00000335515,;PRICKLE4,upstream_gene_variant,,ENST00000487182,;PRICKLE4,upstream_gene_variant,,ENST00000456057,;	T	ENSG00000137218	ENST00000373018	Transcript	missense_variant	289	37	13	V/I	Gtt/Att	rs367802861	.	.	-1	FRS3	HGNC	16970	protein_coding	YES	CCDS4860.1	ENSP00000362109	FRS3_HUMAN	A6PVU0_HUMAN	UPI0000073ACA	.	tolerated(1)	benign(0)	3/7	.	PROSITE_profiles:PS51064,hmmpanther:PTHR21258:SF39,hmmpanther:PTHR21258,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAACGCTGT	byFrequency|byCluster	5	ESCA
KLHDC3	0	.	GRCh37	6	42988714	42988714	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*243C>T	.	.	ENST00000326974	11/11	59	55	4	40	40	0	KLHDC3,3_prime_UTR_variant,,ENST00000332245,;KLHDC3,3_prime_UTR_variant,,ENST00000326974,;KLHDC3,3_prime_UTR_variant,,ENST00000244670,;RRP36,upstream_gene_variant,,ENST00000244496,;	T	ENSG00000124702	ENST00000326974	Transcript	3_prime_UTR_variant	1587	.	.	.	.	.	.	.	1	KLHDC3	HGNC	20704	protein_coding	YES	CCDS4880.1	ENSP00000313995	KLDC3_HUMAN	.	UPI0000036176	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTTCAGCTG	.	2	ESCA
CYP39A1	0	.	GRCh37	6	46607323	46607323	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396C>G	p.%3D	p.L132L	ENST00000275016	3/12	38	29	9	40	40	0	CYP39A1,synonymous_variant,p.%3D,ENST00000275016,;CYP39A1,upstream_gene_variant,,ENST00000480804,;	C	ENSG00000146233	ENST00000275016	Transcript	synonymous_variant	600	396	132	L	ctC/ctG	.	.	.	-1	CYP39A1	HGNC	17449	protein_coding	YES	CCDS4916.1	ENSP00000275016	CP39A_HUMAN	.	UPI000013DA3D	.	.	.	3/12	.	hmmpanther:PTHR24304,hmmpanther:PTHR24304:SF4,Pfam_domain:PF00067,Gene3D:1.10.630.10,PIRSF_domain:PIRSF000047,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATGGAGATT	.	5	ESCA
MCM3	0	.	GRCh37	6	52132674	52132674	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2196G>C	p.Gln732His	p.Q732H	ENST00000596288	14/17	178	132	46	146	146	0	MCM3,missense_variant,p.Gln182His,ENST00000421471,;MCM3,missense_variant,p.Gln641His,ENST00000419835,;MCM3,missense_variant,p.Gln687His,ENST00000229854,;MCM3,missense_variant,p.Gln732His,ENST00000596288,;	G	ENSG00000112118	ENST00000596288	Transcript	missense_variant	2224	2196	732	Q/H	caG/caC	.	.	.	-1	MCM3	HGNC	6945	protein_coding	YES	CCDS4940.2	ENSP00000472940	.	Q8NHX6_HUMAN,B4DWW4_HUMAN	UPI0000EE4F08	.	tolerated(0.15)	benign(0.332)	14/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11630,hmmpanther:PTHR11630:SF72	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCTGCTC	.	5	ESCA
FAM135A	0	.	GRCh37	6	71236164	71236164	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3377G>A	p.Arg1126Lys	p.R1126K	ENST00000418814	15/22	37	31	5	29	29	0	FAM135A,missense_variant,p.Arg913Lys,ENST00000457062,;FAM135A,missense_variant,p.Arg1126Lys,ENST00000505868,;FAM135A,missense_variant,p.Arg930Lys,ENST00000361499,;FAM135A,missense_variant,p.Arg706Lys,ENST00000505769,;FAM135A,missense_variant,p.Arg1126Lys,ENST00000418814,;FAM135A,missense_variant,p.Arg913Lys,ENST00000370479,;FAM135A,downstream_gene_variant,,ENST00000515323,;FAM135A,3_prime_UTR_variant,,ENST00000194672,;FAM135A,downstream_gene_variant,,ENST00000393299,;	A	ENSG00000082269	ENST00000418814	Transcript	missense_variant	3991	3377	1126	R/K	aGa/aAa	.	.	.	1	FAM135A	HGNC	21084	protein_coding	YES	CCDS55028.1	ENSP00000410768	F135A_HUMAN	D6RFG9_HUMAN,D6REA8_HUMAN,D6RC17_HUMAN	UPI000004A0FF	.	tolerated(0.38)	benign(0.001)	15/22	.	hmmpanther:PTHR12482,hmmpanther:PTHR12482:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAAGACTTA	.	5	ESCA
SNAP91	0	.	GRCh37	6	84371233	84371233	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.440G>C	p.Arg147Thr	p.R147T	ENST00000439399	5/30	28	21	7	34	34	0	SNAP91,missense_variant,p.Arg147Thr,ENST00000519779,;SNAP91,missense_variant,p.Arg147Thr,ENST00000439399,;SNAP91,missense_variant,p.Arg147Thr,ENST00000195649,;SNAP91,missense_variant,p.Arg147Thr,ENST00000369690,;SNAP91,missense_variant,p.Arg147Thr,ENST00000521931,;SNAP91,missense_variant,p.Arg147Thr,ENST00000437520,;SNAP91,missense_variant,p.Arg147Thr,ENST00000518309,;SNAP91,missense_variant,p.Arg147Thr,ENST00000521485,;SNAP91,missense_variant,p.Arg147Thr,ENST00000520302,;SNAP91,missense_variant,p.Arg147Thr,ENST00000428679,;SNAP91,missense_variant,p.Arg147Thr,ENST00000520213,;SNAP91,missense_variant,p.Arg147Thr,ENST00000369694,;SNAP91,missense_variant,p.Arg147Thr,ENST00000521743,;SNAP91,downstream_gene_variant,,ENST00000523484,;SNAP91,downstream_gene_variant,,ENST00000519825,;SNAP91,3_prime_UTR_variant,,ENST00000521616,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,intron_variant,,ENST00000522248,;	G	ENSG00000065609	ENST00000439399	Transcript	missense_variant	757	440	147	R/T	aGg/aCg	.	.	.	-1	SNAP91	HGNC	14986	protein_coding	YES	CCDS47455.1	ENSP00000400459	AP180_HUMAN	E5RK53_HUMAN,E5RK51_HUMAN,E5RJY3_HUMAN,E5RIJ5_HUMAN,E5RFU0_HUMAN,E5RFC6_HUMAN,B7Z2C2_HUMAN	UPI0000124FB3	.	deleterious(0)	unknown(0)	5/30	.	hmmpanther:PTHR22951,hmmpanther:PTHR22951:SF4,Pfam_domain:PF07651,Superfamily_domains:SSF48464	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCCTGGCA	.	5	ESCA
ZNF292	0	.	GRCh37	6	87966128	87966128	+	Silent	SNP	T	T	A	rs775192723	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2781T>A	p.%3D	p.T927T	ENST00000369577	8/8	23	17	6	15	15	0	ZNF292,synonymous_variant,p.%3D,ENST00000369577,;ZNF292,synonymous_variant,p.%3D,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,downstream_gene_variant,,ENST00000466062,;	A	ENSG00000188994	ENST00000369577	Transcript	synonymous_variant	2824	2781	927	T	acT/acA	rs775192723	.	.	1	ZNF292	HGNC	18410	protein_coding	YES	CCDS47457.1	ENSP00000358590	ZN292_HUMAN	Q6ZS01_HUMAN,Q6P495_HUMAN,Q3MN16_HUMAN	UPI000020D2CC	.	.	.	8/8	.	hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTACTCCTCT	byFrequency	5	ESCA
ZNF292	0	.	GRCh37	6	87971218	87971218	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7871A>G	p.His2624Arg	p.H2624R	ENST00000369577	8/8	26	18	8	15	15	0	ZNF292,missense_variant,p.His2624Arg,ENST00000369577,;ZNF292,missense_variant,p.His2619Arg,ENST00000339907,;ZNF292,downstream_gene_variant,,ENST00000496806,;	G	ENSG00000188994	ENST00000369577	Transcript	missense_variant	7914	7871	2624	H/R	cAt/cGt	.	.	.	1	ZNF292	HGNC	18410	protein_coding	YES	CCDS47457.1	ENSP00000358590	ZN292_HUMAN	Q6ZS01_HUMAN,Q6P495_HUMAN,Q3MN16_HUMAN	UPI000020D2CC	.	tolerated(0.26)	benign(0.045)	8/8	.	hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCCATTCAA	.	5	ESCA
MANEA	0	.	GRCh37	6	96054102	96054102	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210G>C	p.Glu404Gln	p.E404Q	ENST00000358812	5/5	23	15	7	24	24	0	MANEA,missense_variant,p.Glu404Gln,ENST00000358812,;MANEA,downstream_gene_variant,,ENST00000474553,;	C	ENSG00000172469	ENST00000358812	Transcript	missense_variant	1344	1210	404	E/Q	Gag/Cag	.	.	.	1	MANEA	HGNC	21072	protein_coding	YES	CCDS5032.1	ENSP00000351669	MANEA_HUMAN	.	UPI000020DF99	.	tolerated(0.08)	probably_damaging(0.999)	5/5	.	hmmpanther:PTHR13572:SF1,hmmpanther:PTHR13572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAATGAGTGG	.	5	ESCA
RELN	0	.	GRCh37	7	103175830	103175830	+	Missense_Mutation	SNP	G	G	C	rs751431158	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7282C>G	p.Arg2428Gly	p.R2428G	ENST00000428762	46/65	57	47	10	61	61	0	RELN,missense_variant,p.Arg2428Gly,ENST00000424685,;RELN,missense_variant,p.Arg2428Gly,ENST00000428762,;RELN,missense_variant,p.Arg2428Gly,ENST00000343529,;RELN,non_coding_transcript_exon_variant,,ENST00000478148,;	C	ENSG00000189056	ENST00000428762	Transcript	missense_variant	7442	7282	2428	R/G	Cgg/Ggg	rs751431158,COSM484573	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	tolerated(0.06)	benign(0.126)	46/65	.	hmmpanther:PTHR11841,Superfamily_domains:SSF50939	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCCGTTGCA	.	5	ESCA
SLC26A4	0	.	GRCh37	7	107334901	107334901	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1317G>A	p.%3D	p.G439G	ENST00000265715	11/21	52	42	10	43	43	0	SLC26A4,synonymous_variant,p.%3D,ENST00000544569,;SLC26A4,synonymous_variant,p.%3D,ENST00000265715,;SLC26A4,synonymous_variant,p.%3D,ENST00000543100,;SLC26A4,intron_variant,,ENST00000541474,;SLC26A4,non_coding_transcript_exon_variant,,ENST00000480841,;SLC26A4,non_coding_transcript_exon_variant,,ENST00000460748,;SLC26A4,non_coding_transcript_exon_variant,,ENST00000497446,;SLC26A4,intron_variant,,ENST00000477350,;	A	ENSG00000091137	ENST00000265715	Transcript	synonymous_variant	1541	1317	439	G	ggG/ggA	.	.	.	1	SLC26A4	HGNC	8818	protein_coding	YES	CCDS5746.1	ENSP00000265715	S26A4_HUMAN	Q75MC7_HUMAN,C9JQG1_HUMAN,B7Z266_HUMAN	UPI00001315A4	.	.	.	11/21	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11814:SF33,hmmpanther:PTHR11814,Pfam_domain:PF00916,TIGRFAM_domain:TIGR00815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGGAAGCT	.	5	ESCA
CFTR	0	.	GRCh37	7	117227862	117227862	+	Missense_Mutation	SNP	C	C	G	rs76554633	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1654C>G	p.Gln552Glu	p.Q552E	ENST00000003084	12/27	21	17	4	28	28	0	CFTR,missense_variant,p.Gln522Glu,ENST00000426809,;CFTR,missense_variant,p.Gln491Glu,ENST00000454343,;CFTR,missense_variant,p.Gln552Glu,ENST00000003084,;CFTR,downstream_gene_variant,,ENST00000472848,;AC000111.5,upstream_gene_variant,,ENST00000448200,;	G	ENSG00000001626	ENST00000003084	Transcript	missense_variant	1786	1654	552	Q/E	Caa/Gaa	CM962464,CM910072,rs76554633	.	.	1	CFTR	HGNC	1884	protein_coding	YES	CCDS5773.1	ENSP00000003084	CFTR_HUMAN	Q9UML7_HUMAN,Q9UJ19_HUMAN,Q99989_HUMAN,Q6KEJ7_HUMAN,Q6KEJ4_HUMAN,Q6KEJ1_HUMAN,Q6KEI8_HUMAN,Q6KEI7_HUMAN,Q6KEI2_HUMAN,Q6KEH8_HUMAN,Q6KEH6_HUMAN,Q6KEH3_HUMAN,Q6KEG9_HUMAN,Q6KEG6_HUMAN,Q6KEG3_HUMAN,Q6KEF9_HUMAN,Q6KEF5_HUMAN,Q6KEE7_HUMAN,Q6KEE3_HUMAN,Q6KED8_HUMAN,Q6KED3_HUMAN,Q6KEC8_HUMAN,Q6KEC3_HUMAN,Q6KEB8_HUMAN,Q6KEB2_HUMAN,Q6KEA5_HUMAN,Q6KEA0_HUMAN,Q6KE95_HUMAN,Q5I6N7_HUMAN,Q5I6N6_HUMAN,Q5I6N5_HUMAN,Q5I6N4_HUMAN,Q5I6F9_HUMAN,C9J6L5_HUMAN,A4L9V0_HUMAN	UPI000013C4D4	.	deleterious(0)	probably_damaging(0.971)	12/27	.	PROSITE_profiles:PS50893,hmmpanther:PTHR24223:SF19,hmmpanther:PTHR24223,PROSITE_patterns:PS00211,Gene3D:3.40.50.300,Pfam_domain:PF00005,TIGRFAM_domain:TIGR01271,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGGTCAACGA	byCluster	2	ESCA
IMPDH1	0	.	GRCh37	7	128040880	128040880	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570G>A	p.%3D	p.R190R	ENST00000338791	7/17	85	54	31	82	82	0	IMPDH1,synonymous_variant,p.%3D,ENST00000419067,;IMPDH1,synonymous_variant,p.%3D,ENST00000470772,;IMPDH1,synonymous_variant,p.%3D,ENST00000338791,;IMPDH1,synonymous_variant,p.%3D,ENST00000497868,;IMPDH1,synonymous_variant,p.%3D,ENST00000378717,;IMPDH1,synonymous_variant,p.%3D,ENST00000348127,;IMPDH1,synonymous_variant,p.%3D,ENST00000354269,;IMPDH1,splice_region_variant,,ENST00000480861,;IMPDH1,intron_variant,,ENST00000496200,;IMPDH1,intron_variant,,ENST00000343214,;IMPDH1,intron_variant,,ENST00000489263,;IMPDH1,synonymous_variant,p.%3D,ENST00000484496,;IMPDH1,synonymous_variant,p.%3D,ENST00000469328,;IMPDH1,non_coding_transcript_exon_variant,,ENST00000491376,;IMPDH1,non_coding_transcript_exon_variant,,ENST00000496487,;IMPDH1,upstream_gene_variant,,ENST00000468842,;IMPDH1,downstream_gene_variant,,ENST00000473463,;	T	ENSG00000106348	ENST00000338791	Transcript	synonymous_variant	921	570	190	R	cgG/cgA	.	.	.	-1	IMPDH1	HGNC	6052	protein_coding	YES	CCDS34749.1	ENSP00000345096	IMDH1_HUMAN	.	UPI00001BDC74	.	.	.	7/17	.	HAMAP:MF_01964,hmmpanther:PTHR11911:SF74,hmmpanther:PTHR11911,Pfam_domain:PF00478,TIGRFAM_domain:TIGR01302,Gene3D:3.20.20.70,Superfamily_domains:SSF51412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCCGCAC	.	5	ESCA
PDIA4	0	.	GRCh37	7	148701243	148701243	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1581C>T	p.%3D	p.V527V	ENST00000286091	10/10	105	89	16	84	84	0	PDIA4,synonymous_variant,p.%3D,ENST00000286091,;PDIA4,downstream_gene_variant,,ENST00000466592,;	A	ENSG00000155660	ENST00000286091	Transcript	synonymous_variant	1814	1581	527	V	gtC/gtT	.	.	.	-1	PDIA4	HGNC	30167	protein_coding	YES	CCDS5893.1	ENSP00000286091	PDIA4_HUMAN	.	UPI000004062C	.	.	.	10/10	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51352,hmmpanther:PTHR18929:SF56,hmmpanther:PTHR18929,Pfam_domain:PF00085,TIGRFAM_domain:TIGR01130,Gene3D:3.40.30.10,PIRSF_domain:PIRSF036862,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTTGACGGG	.	4	ESCA
SLC4A2	0	.	GRCh37	7	150768592	150768592	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2091G>A	p.%3D	p.L697L	ENST00000485713	14/23	42	36	6	40	40	0	SLC4A2,synonymous_variant,p.%3D,ENST00000485713,;SLC4A2,synonymous_variant,p.%3D,ENST00000392826,;SLC4A2,synonymous_variant,p.%3D,ENST00000310317,;SLC4A2,synonymous_variant,p.%3D,ENST00000413384,;SLC4A2,synonymous_variant,p.%3D,ENST00000461735,;RP11-148K1.12,downstream_gene_variant,,ENST00000485974,;SLC4A2,upstream_gene_variant,,ENST00000482697,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000480107,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000493040,;SLC4A2,upstream_gene_variant,,ENST00000472204,;SLC4A2,downstream_gene_variant,,ENST00000469355,;SLC4A2,upstream_gene_variant,,ENST00000460010,;SLC4A2,downstream_gene_variant,,ENST00000494298,;SLC4A2,upstream_gene_variant,,ENST00000469467,;	A	ENSG00000164889	ENST00000485713	Transcript	synonymous_variant	3131	2091	697	L	ctG/ctA	.	.	.	1	SLC4A2	HGNC	11028	protein_coding	YES	CCDS5917.1	ENSP00000419412	B3A2_HUMAN	Q59GF1_HUMAN,C9JVC2_HUMAN,C9J9M9_HUMAN,C9J722_HUMAN,C9J459_HUMAN,C9J035_HUMAN	UPI000013EFE9	.	.	.	14/23	.	hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF14,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834,Gene3D:1bzkA00	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCTGAGTGA	.	4	ESCA
ABCF2	0	.	GRCh37	7	150912737	150912737	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1483G>C	p.Glu495Gln	p.E495Q	ENST00000222388	13/16	143	121	21	118	118	0	ABCF2,missense_variant,p.Glu495Gln,ENST00000287844,;ABCF2,missense_variant,p.Glu495Gln,ENST00000222388,;ABCF2,downstream_gene_variant,,ENST00000473874,;	G	ENSG00000033050	ENST00000222388	Transcript	missense_variant	1529	1483	495	E/Q	Gaa/Caa	.	.	.	-1	ABCF2	HGNC	71	protein_coding	YES	CCDS5922.1	ENSP00000222388	.	Q75MJ1_HUMAN,C9JZV3_HUMAN,C9JHK9_HUMAN	UPI000004C4C9	.	tolerated(0.37)	benign(0.259)	13/16	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50893,hmmpanther:PTHR19211:SF15,hmmpanther:PTHR19211,Pfam_domain:PF00005,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTCTTCCT	.	5	ESCA
GALNT11	0	.	GRCh37	7	151807728	151807728	+	Missense_Mutation	SNP	C	C	T	rs147464952	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1078C>T	p.Arg360Trp	p.R360W	ENST00000434507	9/14	19	14	5	20	20	0	GALNT11,missense_variant,p.Arg360Trp,ENST00000430044,;GALNT11,missense_variant,p.Arg360Trp,ENST00000320311,;GALNT11,missense_variant,p.Arg360Trp,ENST00000434507,;GALNT11,missense_variant,p.Arg279Trp,ENST00000452146,;GALNT11,downstream_gene_variant,,ENST00000422997,;GALNT11,splice_region_variant,,ENST00000491061,;GALNT11,splice_region_variant,,ENST00000447778,;GALNT11,upstream_gene_variant,,ENST00000431940,;	T	ENSG00000178234	ENST00000434507	Transcript	missense_variant	1515	1078	360	R/W	Cgg/Tgg	rs147464952,COSM1087493	.	.	1	GALNT11	HGNC	19875	protein_coding	YES	CCDS5930.1	ENSP00000416787	GLT11_HUMAN	C9JMT8_HUMAN,C9J8A7_HUMAN,C9J111_HUMAN	UPI000004C2AA	.	deleterious(0)	probably_damaging(1)	9/14	.	hmmpanther:PTHR11675:SF10,hmmpanther:PTHR11675,Gene3D:3.90.550.10,Pfam_domain:PF02709,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTCGGGTA	byCluster	5	ESCA
PTPRN2	0	.	GRCh37	7	157333462	157333462	+	Silent	SNP	C	C	T	rs765163209	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2994G>A	p.%3D	p.A998A	ENST00000389418	23/23	68	48	20	68	68	0	PTPRN2,synonymous_variant,p.%3D,ENST00000409483,;PTPRN2,synonymous_variant,p.%3D,ENST00000389416,;PTPRN2,synonymous_variant,p.%3D,ENST00000404321,;PTPRN2,synonymous_variant,p.%3D,ENST00000389418,;PTPRN2,synonymous_variant,p.%3D,ENST00000389413,;	T	ENSG00000155093	ENST00000389418	Transcript	synonymous_variant	3004	2994	998	A	gcG/gcA	rs765163209	.	.	-1	PTPRN2	HGNC	9677	protein_coding	YES	CCDS5947.1	ENSP00000374069	PTPR2_HUMAN	Q9NSR5_HUMAN	UPI000002E7C7	.	.	.	23/23	.	PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799,Prints_domain:PR00700	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAGCGCGAA	byFrequency	5	ESCA
HNRNPA2B1	0	.	GRCh37	7	26231674	26231674	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*306G>C	.	.	ENST00000354667	12/12	30	24	6	28	28	0	HNRNPA2B1,3_prime_UTR_variant,,ENST00000354667,;HNRNPA2B1,3_prime_UTR_variant,,ENST00000356674,;NFE2L3,downstream_gene_variant,,ENST00000056233,;HNRNPA2B1,upstream_gene_variant,,ENST00000476233,;HNRNPA2B1,non_coding_transcript_exon_variant,,ENST00000490912,;HNRNPA2B1,non_coding_transcript_exon_variant,,ENST00000463181,;HNRNPA2B1,intron_variant,,ENST00000360787,;HNRNPA2B1,downstream_gene_variant,,ENST00000495810,;	G	ENSG00000122566	ENST00000354667	Transcript	3_prime_UTR_variant	1537	.	.	.	.	.	.	.	-1	HNRNPA2B1	HGNC	5033	protein_coding	YES	CCDS43557.1	ENSP00000346694	ROA2_HUMAN	.	UPI000002F091	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCTACAC	.	5	ESCA
BMPER	0	.	GRCh37	7	34192911	34192911	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*26G>A	.	.	ENST00000297161	16/16	36	33	3	22	22	0	BMPER,3_prime_UTR_variant,,ENST00000297161,;BMPER,3_prime_UTR_variant,,ENST00000426693,;	A	ENSG00000164619	ENST00000297161	Transcript	3_prime_UTR_variant	2458	.	.	.	.	.	.	.	1	BMPER	HGNC	24154	protein_coding	YES	CCDS5442.1	ENSP00000297161	BMPER_HUMAN	.	UPI000006D462	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTCTGAAATC	.	2	ESCA
AEBP1	0	.	GRCh37	7	44147454	44147454	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787delA	p.Arg263GlyfsTer29	p.R263Gfs*29	ENST00000223357	5/21	87	61	26	35	35	0	AEBP1,frameshift_variant,p.Arg263GlyfsTer29,ENST00000223357,;AEBP1,intron_variant,,ENST00000455443,;AEBP1,downstream_gene_variant,,ENST00000449162,;AEBP1,upstream_gene_variant,,ENST00000450684,;MIR4649,upstream_gene_variant,,ENST00000582839,;AEBP1,upstream_gene_variant,,ENST00000454218,;AEBP1,upstream_gene_variant,,ENST00000434445,;AEBP1,upstream_gene_variant,,ENST00000413907,;AEBP1,upstream_gene_variant,,ENST00000431035,;AEBP1,upstream_gene_variant,,ENST00000453052,;	-	ENSG00000106624	ENST00000223357	Transcript	frameshift_variant	1091	786	262	R/X	agA/ag	.	.	.	1	AEBP1	HGNC	303	protein_coding	YES	CCDS5476.1	ENSP00000223357	AEBP1_HUMAN	B4DJB3_HUMAN	UPI00000746E2	.	.	.	5/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11532:SF48,hmmpanther:PTHR11532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGCAGAAGGAG	.	3	ESCA
FOXK1	0	.	GRCh37	7	4810620	4810620	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8525G>A	.	.	ENST00000328914	9/9	17	14	3	18	18	0	FOXK1,3_prime_UTR_variant,,ENST00000328914,;AP5Z1,upstream_gene_variant,,ENST00000401897,;AP5Z1,upstream_gene_variant,,ENST00000348624,;AP5Z1,upstream_gene_variant,,ENST00000477680,;AP5Z1,upstream_gene_variant,,ENST00000496303,;	A	ENSG00000164916	ENST00000328914	Transcript	3_prime_UTR_variant	10727	.	.	.	.	.	.	.	1	FOXK1	HGNC	23480	protein_coding	YES	CCDS34591.1	ENSP00000328720	FOXK1_HUMAN	B3KV39_HUMAN	UPI00004158EB	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTATGAAGTG	.	2	ESCA
WBSCR17	0	.	GRCh37	7	71177154	71177154	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*23A>G	.	.	ENST00000333538	11/11	28	19	9	19	19	0	WBSCR17,3_prime_UTR_variant,,ENST00000333538,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;	G	ENSG00000185274	ENST00000333538	Transcript	3_prime_UTR_variant	2454	.	.	.	.	.	.	.	1	WBSCR17	HGNC	16347	protein_coding	YES	CCDS5540.1	ENSP00000329654	GLTL3_HUMAN	Q68CW8_HUMAN,Q2L4S5_HUMAN,B3KRD2_HUMAN	UPI00000502D5	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGGAGCCTG	.	5	ESCA
CCDC146	0	.	GRCh37	7	76891437	76891437	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.987-1G>A	.	p.X329_splice	ENST00000285871	.	44	34	10	34	34	0	CCDC146,splice_acceptor_variant,,ENST00000285871,;CCDC146,splice_acceptor_variant,,ENST00000431197,;AC073635.5,upstream_gene_variant,,ENST00000476561,;CCDC146,splice_acceptor_variant,,ENST00000415740,;CCDC146,downstream_gene_variant,,ENST00000461882,;	A	ENSG00000135205	ENST00000285871	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	CCDC146	HGNC	29296	protein_coding	YES	CCDS34671.1	ENSP00000285871	CC146_HUMAN	Q7Z4Q3_HUMAN	UPI000020F44F	.	.	.	.	8/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACAGAGGGA	.	5	ESCA
SEMA3E	0	.	GRCh37	7	82997166	82997166	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2064G>T	p.Glu688Asp	p.E688D	ENST00000307792	17/17	70	51	19	84	84	0	SEMA3E,missense_variant,p.Glu628Asp,ENST00000427262,;SEMA3E,missense_variant,p.Glu688Asp,ENST00000307792,;	A	ENSG00000170381	ENST00000307792	Transcript	missense_variant	2532	2064	688	E/D	gaG/gaT	.	.	.	-1	SEMA3E	HGNC	10727	protein_coding	YES	CCDS34674.1	ENSP00000303212	SEM3E_HUMAN	F8WCZ5_HUMAN,C9JVH5_HUMAN	UPI0000135A68	.	tolerated(0.38)	benign(0.001)	17/17	.	hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCCTCCTC	.	5	ESCA
NXPH1	0	.	GRCh37	7	8473973	8473973	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-523G>A	.	.	ENST00000405863	1/3	71	47	23	46	46	0	NXPH1,5_prime_UTR_variant,,ENST00000405863,;NXPH1,upstream_gene_variant,,ENST00000602349,;NXPH1,upstream_gene_variant,,ENST00000429542,;NXPH1,upstream_gene_variant,,ENST00000438764,;	A	ENSG00000122584	ENST00000405863	Transcript	5_prime_UTR_variant	389	.	.	.	.	.	.	.	1	NXPH1	HGNC	20693	protein_coding	YES	CCDS47540.1	ENSP00000384551	NXPH1_HUMAN	Q3LID8_HUMAN,C9JPD0_HUMAN,C9JE46_HUMAN,B4DJV1_HUMAN	UPI000000DC02	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCCGAGAGT	.	5	ESCA
RUNDC3B	0	.	GRCh37	7	87258250	87258250	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111C>T	p.%3D	p.I37I	ENST00000338056	1/12	14	9	5	22	22	0	RUNDC3B,synonymous_variant,p.%3D,ENST00000338056,;RUNDC3B,synonymous_variant,p.%3D,ENST00000394654,;RUNDC3B,synonymous_variant,p.%3D,ENST00000493037,;ABCB1,intron_variant,,ENST00000265724,;ABCB1,intron_variant,,ENST00000416177,;snoU13,downstream_gene_variant,,ENST00000459484,;RUNDC3B,intron_variant,,ENST00000497788,;ABCB1,intron_variant,,ENST00000476862,;RUNDC3B,intron_variant,,ENST00000466676,;RUNDC3B,upstream_gene_variant,,ENST00000489461,;RUNDC3B,non_coding_transcript_exon_variant,,ENST00000476114,;	T	ENSG00000105784	ENST00000338056	Transcript	synonymous_variant	522	111	37	I	atC/atT	.	.	.	1	RUNDC3B	HGNC	30286	protein_coding	YES	CCDS5609.1	ENSP00000337732	RUN3B_HUMAN	.	UPI0000071425	.	.	.	1/12	.	hmmpanther:PTHR22835:SF124,hmmpanther:PTHR22835,Superfamily_domains:0052343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CTGATCACCGT	.	4	ESCA
CYP51A1	0	.	GRCh37	7	91752604	91752604	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916G>A	p.Glu306Lys	p.E306K	ENST00000003100	7/10	44	37	6	45	45	0	CYP51A1,missense_variant,p.Glu47Lys,ENST00000422867,;CYP51A1,missense_variant,p.Glu306Lys,ENST00000003100,;CYP51A1,missense_variant,p.Glu201Lys,ENST00000450723,;LRRD1,non_coding_transcript_exon_variant,,ENST00000422722,;	T	ENSG00000001630	ENST00000003100	Transcript	missense_variant	1082	916	306	E/K	Gaa/Aaa	.	.	.	-1	CYP51A1	HGNC	2649	protein_coding	YES	CCDS5623.1	ENSP00000003100	CP51A_HUMAN	.	UPI000013C4D5	.	deleterious(0.01)	probably_damaging(0.93)	7/10	.	hmmpanther:PTHR24286,hmmpanther:PTHR24286:SF25,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTCATCAT	.	5	ESCA
HEPACAM2	0	.	GRCh37	7	92844738	92844738	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.691G>A	p.Asp231Asn	p.D231N	ENST00000394468	3/10	62	55	7	58	58	0	HEPACAM2,missense_variant,p.Asp231Asn,ENST00000394468,;HEPACAM2,missense_variant,p.Asp219Asn,ENST00000440868,;HEPACAM2,missense_variant,p.Asp254Asn,ENST00000453812,;HEPACAM2,missense_variant,p.Asp219Asn,ENST00000341723,;	T	ENSG00000188175	ENST00000394468	Transcript	missense_variant	769	691	231	D/N	Gat/Aat	.	.	.	-1	HEPACAM2	HGNC	27364	protein_coding	YES	CCDS43616.1	ENSP00000377980	HECA2_HUMAN	.	UPI000013DA71	.	tolerated(0.11)	benign(0.031)	3/10	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF125,hmmpanther:PTHR19955,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATATCACTTT	.	4	ESCA
PEG10	0	.	GRCh37	7	94296325	94296325	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2479G>A	.	.	ENST00000482108	2/2	61	44	16	53	53	0	PEG10,3_prime_UTR_variant,,ENST00000482108,;PEG10,downstream_gene_variant,,ENST00000488574,;PEG10,intron_variant,,ENST00000465184,;PEG10,intron_variant,,ENST00000493935,;	A	ENSG00000242265	ENST00000482108	Transcript	3_prime_UTR_variant	3936	.	.	.	.	.	.	.	1	PEG10	HGNC	14005	protein_coding	YES	CCDS55126.1	ENSP00000417587	PEG10_HUMAN	B4DSP0_HUMAN	UPI0000047FA3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTGATGTG	.	5	ESCA
TRRAP	0	.	GRCh37	7	98601877	98601877	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10332G>C	p.Trp3444Cys	p.W3444C	ENST00000359863	67/72	45	34	11	31	31	0	TRRAP,missense_variant,p.Trp3415Cys,ENST00000355540,;TRRAP,missense_variant,p.Trp3433Cys,ENST00000446306,;TRRAP,missense_variant,p.Trp3173Cys,ENST00000456197,;TRRAP,missense_variant,p.Trp3444Cys,ENST00000359863,;AC004893.10,upstream_gene_variant,,ENST00000442161,;	C	ENSG00000196367	ENST00000359863	Transcript	missense_variant	10541	10332	3444	W/C	tgG/tgC	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	probably_damaging(0.999)	67/72	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTGGATCAA	.	5	ESCA
TRRAP	0	.	GRCh37	7	98601974	98601974	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10429G>A	p.Glu3477Lys	p.E3477K	ENST00000359863	67/72	37	26	11	36	36	0	TRRAP,missense_variant,p.Glu3448Lys,ENST00000355540,;TRRAP,missense_variant,p.Glu3466Lys,ENST00000446306,;TRRAP,missense_variant,p.Glu3206Lys,ENST00000456197,;TRRAP,missense_variant,p.Glu3477Lys,ENST00000359863,;AC004893.10,upstream_gene_variant,,ENST00000442161,;	A	ENSG00000196367	ENST00000359863	Transcript	missense_variant	10638	10429	3477	E/K	Gaa/Aaa	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	probably_damaging(0.926)	67/72	.	hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTGAAGTG	.	5	ESCA
VPS13B	0	.	GRCh37	8	100791077	100791077	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7672G>C	p.Glu2558Gln	p.E2558Q	ENST00000358544	42/62	64	53	11	53	53	0	VPS13B,missense_variant,p.Glu2558Gln,ENST00000358544,;VPS13B,missense_variant,p.Glu2533Gln,ENST00000357162,;VPS13B,3_prime_UTR_variant,,ENST00000395996,;VPS13B,downstream_gene_variant,,ENST00000518569,;	C	ENSG00000132549	ENST00000358544	Transcript	missense_variant	7783	7672	2558	E/Q	Gag/Cag	.	.	.	1	VPS13B	HGNC	2183	protein_coding	YES	CCDS6280.1	ENSP00000351346	VP13B_HUMAN	.	UPI00001D2D35	.	deleterious(0)	benign(0.403)	42/62	.	hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTAGAGTGC	.	5	ESCA
PKHD1L1	0	.	GRCh37	8	110374853	110374853	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44T>A	p.Leu15Gln	p.L15Q	ENST00000378402	1/78	95	69	25	74	74	0	PKHD1L1,missense_variant,p.Leu15Gln,ENST00000378402,;	A	ENSG00000205038	ENST00000378402	Transcript	missense_variant	148	44	15	L/Q	cTg/cAg	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	deleterious(0.01)	possibly_damaging(0.902)	1/78	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGCTGCTCC	.	5	ESCA
PKHD1L1	0	.	GRCh37	8	110408258	110408258	+	Missense_Mutation	SNP	G	G	C	rs751291729	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814G>C	p.Val272Leu	p.V272L	ENST00000378402	11/78	42	30	12	50	50	0	PKHD1L1,missense_variant,p.Val272Leu,ENST00000378402,;	C	ENSG00000205038	ENST00000378402	Transcript	missense_variant	918	814	272	V/L	Gtc/Ctc	rs751291729	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	deleterious(0.04)	benign(0.247)	11/78	.	Pfam_domain:PF01833,Gene3D:2.60.40.10,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGGTCACC	byFrequency	5	ESCA
KCNV1	0	.	GRCh37	8	110986468	110986468	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150C>T	p.%3D	p.F50F	ENST00000524391	2/4	85	66	19	37	37	0	KCNV1,synonymous_variant,p.%3D,ENST00000297404,;KCNV1,synonymous_variant,p.%3D,ENST00000524391,;RP11-696P8.2,intron_variant,,ENST00000530667,;	A	ENSG00000164794	ENST00000524391	Transcript	synonymous_variant	1183	150	50	F	ttC/ttT	COSM399235	.	.	-1	KCNV1	HGNC	18861	protein_coding	YES	CCDS6314.1	ENSP00000435954	KCNV1_HUMAN	Q76FP2_HUMAN,B4DMC1_HUMAN	UPI0000073DA5	.	.	.	2/4	.	hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF38,Pfam_domain:PF02214,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695,Prints_domain:PR01493	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCACGAAGCG	.	2	ESCA
GATA4	0	.	GRCh37	8	11615867	11615867	+	Silent	SNP	G	G	A	rs780419565	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1212G>A	p.%3D	p.K404K	ENST00000335135	7/7	44	31	13	39	39	0	GATA4,synonymous_variant,p.%3D,ENST00000532059,;GATA4,synonymous_variant,p.%3D,ENST00000335135,;GATA4,synonymous_variant,p.%3D,ENST00000528712,;C8orf49,upstream_gene_variant,,ENST00000525043,;GATA4,downstream_gene_variant,,ENST00000526716,;GATA4,non_coding_transcript_exon_variant,,ENST00000526021,;	A	ENSG00000136574	ENST00000335135	Transcript	synonymous_variant	1770	1212	404	K	aaG/aaA	rs780419565	.	.	1	GATA4	HGNC	4173	protein_coding	YES	CCDS5983.1	ENSP00000334458	GATA4_HUMAN	R4GND5_HUMAN,E9PRI5_HUMAN,E9PKS4_HUMAN,B3KUF4_HUMAN,B2ZBW1_HUMAN	UPI00001B3DC4	.	.	.	7/7	.	PIRSF_domain:PIRSF003028,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF154	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAGCTCTC	.	5	ESCA
ATAD2	0	.	GRCh37	8	124357292	124357292	+	Missense_Mutation	SNP	C	C	G	rs760609188	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2550G>C	p.Lys850Asn	p.K850N	ENST00000287394	19/28	40	37	3	23	23	0	ATAD2,missense_variant,p.Lys850Asn,ENST00000287394,;ATAD2,missense_variant,p.Lys168Asn,ENST00000521903,;RNU6-875P,downstream_gene_variant,,ENST00000516488,;MIR548D1,upstream_gene_variant,,ENST00000384971,;ATAD2,3_prime_UTR_variant,,ENST00000517666,;ATAD2,3_prime_UTR_variant,,ENST00000519124,;ATAD2,non_coding_transcript_exon_variant,,ENST00000521496,;	G	ENSG00000156802	ENST00000287394	Transcript	missense_variant	2658	2550	850	K/N	aaG/aaC	rs760609188	.	.	-1	ATAD2	HGNC	30123	protein_coding	YES	CCDS6343.1	ENSP00000287394	ATAD2_HUMAN	.	UPI0000052A8C	.	deleterious(0.01)	possibly_damaging(0.573)	19/28	.	hmmpanther:PTHR23069,hmmpanther:PTHR23069:SF1,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTCTCTTAGC	.	2	ESCA
GLI4	0	.	GRCh37	8	144358109	144358109	+	Missense_Mutation	SNP	C	C	G	rs13264624	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.266C>G	p.Ser89Cys	p.S89C	ENST00000340042	4/4	33	27	6	16	16	0	GLI4,missense_variant,p.Ser89Cys,ENST00000340042,;GLI4,missense_variant,p.Ser89Cys,ENST00000523522,;ZFP41,3_prime_UTR_variant,,ENST00000522452,;GLI4,intron_variant,,ENST00000517530,;GLI4,downstream_gene_variant,,ENST00000521682,;GLI4,downstream_gene_variant,,ENST00000344692,;GLI4,downstream_gene_variant,,ENST00000520021,;GLI4,downstream_gene_variant,,ENST00000517468,;RP13-582O9.5,downstream_gene_variant,,ENST00000523031,;RP13-582O9.5,downstream_gene_variant,,ENST00000519852,;RP13-582O9.5,downstream_gene_variant,,ENST00000518073,;RP13-582O9.5,downstream_gene_variant,,ENST00000517411,;GLI4,non_coding_transcript_exon_variant,,ENST00000522479,;GLI4,non_coding_transcript_exon_variant,,ENST00000523812,;GLI4,downstream_gene_variant,,ENST00000519876,;GLI4,non_coding_transcript_exon_variant,,ENST00000522033,;	G	ENSG00000250571	ENST00000340042	Transcript	missense_variant	351	266	89	S/C	tCt/tGt	rs13264624	.	.	1	GLI4	HGNC	4320	protein_coding	YES	CCDS6398.1	ENSP00000345024	GLI4_HUMAN	.	UPI0000070432	.	tolerated(0.06)	benign(0.125)	4/4	.	hmmpanther:PTHR24377:SF122,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TGGCTCTCAGG	.	3	ESCA
GLI4	0	.	GRCh37	8	144358344	144358344	+	Silent	SNP	C	C	G	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501C>G	p.%3D	p.V167V	ENST00000340042	4/4	37	31	6	24	24	0	GLI4,synonymous_variant,p.%3D,ENST00000340042,;GLI4,synonymous_variant,p.%3D,ENST00000523522,;GLI4,3_prime_UTR_variant,,ENST00000517530,;ZFP41,3_prime_UTR_variant,,ENST00000522452,;GLI4,downstream_gene_variant,,ENST00000521682,;GLI4,downstream_gene_variant,,ENST00000344692,;GLI4,downstream_gene_variant,,ENST00000517468,;GLI4,downstream_gene_variant,,ENST00000520021,;RP13-582O9.5,downstream_gene_variant,,ENST00000519852,;RP13-582O9.5,downstream_gene_variant,,ENST00000523031,;RP13-582O9.5,downstream_gene_variant,,ENST00000524335,;RP13-582O9.5,downstream_gene_variant,,ENST00000518073,;RP13-582O9.5,downstream_gene_variant,,ENST00000517411,;RP13-582O9.5,downstream_gene_variant,,ENST00000521207,;GLI4,non_coding_transcript_exon_variant,,ENST00000522479,;GLI4,non_coding_transcript_exon_variant,,ENST00000523812,;GLI4,downstream_gene_variant,,ENST00000519876,;GLI4,downstream_gene_variant,,ENST00000522033,;	G	ENSG00000250571	ENST00000340042	Transcript	synonymous_variant	586	501	167	V	gtC/gtG	COSM3768729	.	.	1	GLI4	HGNC	4320	protein_coding	YES	CCDS6398.1	ENSP00000345024	GLI4_HUMAN	.	UPI0000070432	.	.	.	4/4	.	hmmpanther:PTHR24377:SF122,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGTCAACTT	.	4	ESCA
PLEC	0	.	GRCh37	8	144997022	144997022	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7486G>A	p.Glu2496Lys	p.E2496K	ENST00000322810	31/32	64	55	9	38	38	0	PLEC,missense_variant,p.Glu2496Lys,ENST00000322810,;PLEC,missense_variant,p.Glu2382Lys,ENST00000527096,;PLEC,missense_variant,p.Glu2359Lys,ENST00000345136,;PLEC,missense_variant,p.Glu2363Lys,ENST00000357649,;PLEC,missense_variant,p.Glu2327Lys,ENST00000398774,;PLEC,missense_variant,p.Glu2359Lys,ENST00000354589,;PLEC,missense_variant,p.Glu2345Lys,ENST00000356346,;PLEC,missense_variant,p.Glu2386Lys,ENST00000436759,;PLEC,missense_variant,p.Glu2337Lys,ENST00000354958,;PLEC,intron_variant,,ENST00000527303,;	T	ENSG00000178209	ENST00000322810	Transcript	missense_variant	7656	7486	2496	E/K	Gag/Aag	.	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	possibly_damaging(0.688)	31/32	.	hmmpanther:PTHR11915:SF247,hmmpanther:PTHR11915,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCGCCA	.	4	ESCA
SLC39A4	0	.	GRCh37	8	145637923	145637923	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1943G>A	p.%3D	p.%3D	ENST00000301305	12/12	188	175	13	102	102	0	SLC39A4,stop_retained_variant,p.%3D,ENST00000276833,;SLC39A4,stop_retained_variant,p.%3D,ENST00000301305,;CPSF1,upstream_gene_variant,,ENST00000349769,;SLC39A4,downstream_gene_variant,,ENST00000526658,;CPSF1,upstream_gene_variant,,ENST00000531042,;GS1-393G12.14,downstream_gene_variant,,ENST00000607491,;SLC39A4,non_coding_transcript_exon_variant,,ENST00000532718,;SLC39A4,non_coding_transcript_exon_variant,,ENST00000531013,;SLC39A4,non_coding_transcript_exon_variant,,ENST00000530807,;SLC39A4,intron_variant,,ENST00000527148,;SLC39A4,downstream_gene_variant,,ENST00000531789,;SLC39A4,non_coding_transcript_exon_variant,,ENST00000529462,;	T	ENSG00000147804	ENST00000301305	Transcript	stop_retained_variant	2049	1943	648	*	tGa/tAa	.	.	.	-1	SLC39A4	HGNC	17129	protein_coding	YES	CCDS6424.1	ENSP00000301305	S39A4_HUMAN	Q9NX22_HUMAN	UPI00001AED01	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGTATCAGAAG	.	2	ESCA
GPT	0	.	GRCh37	8	145731375	145731375	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820-3C>T	.	.	ENST00000394955	.	45	31	13	39	39	0	GPT,splice_region_variant,,ENST00000528431,;GPT,splice_region_variant,,ENST00000394955,;MFSD3,upstream_gene_variant,,ENST00000301327,;PPP1R16A,downstream_gene_variant,,ENST00000435887,;PPP1R16A,downstream_gene_variant,,ENST00000528430,;PPP1R16A,downstream_gene_variant,,ENST00000292539,;CTD-2517M22.14,upstream_gene_variant,,ENST00000527086,;GPT,non_coding_transcript_exon_variant,,ENST00000534702,;GPT,non_coding_transcript_exon_variant,,ENST00000527165,;GPT,downstream_gene_variant,,ENST00000531330,;CTD-2517M22.14,upstream_gene_variant,,ENST00000528690,;MFSD3,upstream_gene_variant,,ENST00000534427,;MFSD3,upstream_gene_variant,,ENST00000528047,;PPP1R16A,downstream_gene_variant,,ENST00000526183,;MFSD3,upstream_gene_variant,,ENST00000526749,;GPT,downstream_gene_variant,,ENST00000527961,;GPT,downstream_gene_variant,,ENST00000354769,;	T	ENSG00000167701	ENST00000394955	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	GPT	HGNC	4552	protein_coding	YES	CCDS6430.1	ENSP00000378408	ALAT1_HUMAN	.	UPI0000001054	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCCAGGTG	.	5	ESCA
COMMD5	0	.	GRCh37	8	146076001	146076001	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*48G>C	.	.	ENST00000450361	2/2	65	60	4	34	34	0	COMMD5,3_prime_UTR_variant,,ENST00000305103,;COMMD5,3_prime_UTR_variant,,ENST00000450361,;COMMD5,3_prime_UTR_variant,,ENST00000402718,;ZNF7,downstream_gene_variant,,ENST00000325217,;COMMD5,downstream_gene_variant,,ENST00000533270,;ZNF7,downstream_gene_variant,,ENST00000525266,;ZNF250,downstream_gene_variant,,ENST00000543949,;COMMD5,downstream_gene_variant,,ENST00000529143,;AF235103.1,upstream_gene_variant,,ENST00000578937,;COMMD5,3_prime_UTR_variant,,ENST00000530332,;	G	ENSG00000170619	ENST00000450361	Transcript	3_prime_UTR_variant	1145	.	.	.	.	.	.	.	-1	COMMD5	HGNC	17902	protein_coding	YES	CCDS6436.1	ENSP00000394331	COMD5_HUMAN	E9PJE4_HUMAN	UPI000004A08E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCTCAGGTG	.	2	ESCA
BMP1	0	.	GRCh37	8	22056861	22056861	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2107+1928C>G	.	.	ENST00000306385	.	8	5	3	18	18	0	BMP1,missense_variant,p.Leu812Val,ENST00000397816,;BMP1,intron_variant,,ENST00000354870,;BMP1,intron_variant,,ENST00000306385,;BMP1,intron_variant,,ENST00000306349,;BMP1,downstream_gene_variant,,ENST00000397814,;BMP1,downstream_gene_variant,,ENST00000523749,;BMP1,3_prime_UTR_variant,,ENST00000521385,;BMP1,non_coding_transcript_exon_variant,,ENST00000522332,;BMP1,intron_variant,,ENST00000471755,;BMP1,intron_variant,,ENST00000483364,;BMP1,intron_variant,,ENST00000518913,;BMP1,intron_variant,,ENST00000520970,;BMP1,intron_variant,,ENST00000520626,;BMP1,intron_variant,,ENST00000520982,;BMP1,downstream_gene_variant,,ENST00000517324,;	G	ENSG00000168487	ENST00000306385	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	BMP1	HGNC	1067	protein_coding	YES	CCDS6026.1	ENSP00000305714	BMP1_HUMAN	.	UPI0000049818	.	.	.	.	15/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TCAGTCTGACC	.	2	ESCA
CCAR2	0	.	GRCh37	8	22477413	22477413	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*218A>G	.	.	ENST00000308511	21/21	95	79	16	85	85	0	CCAR2,3_prime_UTR_variant,,ENST00000389279,;CCAR2,3_prime_UTR_variant,,ENST00000520738,;CCAR2,3_prime_UTR_variant,,ENST00000308511,;CCAR2,3_prime_UTR_variant,,ENST00000520861,;BIN3,downstream_gene_variant,,ENST00000276416,;BIN3,downstream_gene_variant,,ENST00000399977,;BIN3,downstream_gene_variant,,ENST00000519513,;CCAR2,downstream_gene_variant,,ENST00000522599,;RP11-582J16.5,upstream_gene_variant,,ENST00000521025,;BIN3,downstream_gene_variant,,ENST00000519335,;BIN3,downstream_gene_variant,,ENST00000519863,;CCAR2,non_coding_transcript_exon_variant,,ENST00000520536,;CCAR2,non_coding_transcript_exon_variant,,ENST00000521436,;BIN3,downstream_gene_variant,,ENST00000520489,;BIN3,downstream_gene_variant,,ENST00000522687,;	G	ENSG00000158941	ENST00000308511	Transcript	3_prime_UTR_variant	3239	.	.	.	.	.	.	.	1	CCAR2	HGNC	23360	protein_coding	YES	CCDS34863.1	ENSP00000310670	CCAR2_HUMAN	E5RGU7_HUMAN,E5RFJ3_HUMAN,E2PSM9_HUMAN	UPI0000070A46	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTAAATACAA	.	5	ESCA
STC1	0	.	GRCh37	8	23702448	23702448	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.579C>G	p.%3D	p.L193L	ENST00000290271	4/4	53	34	19	44	44	0	STC1,synonymous_variant,p.%3D,ENST00000524323,;STC1,synonymous_variant,p.%3D,ENST00000290271,;	C	ENSG00000159167	ENST00000290271	Transcript	synonymous_variant	863	579	193	L	ctC/ctG	.	.	.	-1	STC1	HGNC	11373	protein_coding	YES	CCDS6043.1	ENSP00000290271	STC1_HUMAN	Q71UE5_HUMAN,B4DN22_HUMAN	UPI00001360B4	.	.	.	4/4	.	hmmpanther:PTHR11245:SF1,hmmpanther:PTHR11245,Pfam_domain:PF03298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAAGAGGCT	.	5	ESCA
LSM1	0	.	GRCh37	8	38033964	38033964	+	5'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-126G>C	.	.	ENST00000311351	1/4	16	10	6	11	11	0	LSM1,5_prime_UTR_variant,,ENST00000520755,;LSM1,5_prime_UTR_variant,,ENST00000311351,;BAG4,upstream_gene_variant,,ENST00000287322,;BAG4,upstream_gene_variant,,ENST00000432471,;LSM1,non_coding_transcript_exon_variant,,ENST00000522515,;LSM1,intron_variant,,ENST00000520286,;BAG4,upstream_gene_variant,,ENST00000521282,;LSM1,5_prime_UTR_variant,,ENST00000523511,;	G	ENSG00000175324	ENST00000311351	Transcript	5_prime_UTR_variant	271	.	.	.	.	.	.	.	-1	LSM1	HGNC	20472	protein_coding	YES	CCDS6103.1	ENSP00000310596	LSM1_HUMAN	.	UPI000012E963	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCTGCCC	.	5	ESCA
PLAT	0	.	GRCh37	8	42033373	42033373	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*138A>G	.	.	ENST00000220809	14/14	33	23	9	32	32	0	PLAT,3_prime_UTR_variant,,ENST00000220809,;PLAT,3_prime_UTR_variant,,ENST00000429089,;PLAT,3_prime_UTR_variant,,ENST00000429710,;PLAT,3_prime_UTR_variant,,ENST00000270189,;PLAT,3_prime_UTR_variant,,ENST00000352041,;PLAT,3_prime_UTR_variant,,ENST00000519510,;AP3M2,downstream_gene_variant,,ENST00000518421,;AP3M2,downstream_gene_variant,,ENST00000396926,;AP3M2,downstream_gene_variant,,ENST00000174653,;PLAT,downstream_gene_variant,,ENST00000524009,;PLAT,downstream_gene_variant,,ENST00000521042,;PLAT,downstream_gene_variant,,ENST00000522812,;AP3M2,downstream_gene_variant,,ENST00000520689,;	C	ENSG00000104368	ENST00000220809	Transcript	3_prime_UTR_variant	2084	.	.	.	.	.	.	.	-1	PLAT	HGNC	9051	protein_coding	YES	CCDS6126.1	ENSP00000220809	TPA_HUMAN	Q6LBF5_HUMAN,E5RHG4_HUMAN,E5RGA1_HUMAN	UPI0000000DD4	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCCTCTCCT	.	5	ESCA
RP1	0	.	GRCh37	8	55538983	55538983	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2541G>C	p.Leu847Phe	p.L847F	ENST00000220676	4/4	31	20	11	17	17	0	RP1,missense_variant,p.Leu847Phe,ENST00000220676,;	C	ENSG00000104237	ENST00000220676	Transcript	missense_variant	2689	2541	847	L/F	ttG/ttC	COSM461422	.	.	1	RP1	HGNC	10263	protein_coding	YES	CCDS6160.1	ENSP00000220676	RP1_HUMAN	A0FDN2_HUMAN	UPI000013455B	.	deleterious(0.03)	possibly_damaging(0.753)	4/4	.	hmmpanther:PTHR23005:SF4,hmmpanther:PTHR23005	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTTGAGAGG	.	5	ESCA
CA13	0	.	GRCh37	8	86195843	86195843	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2265G>A	.	.	ENST00000321764	7/7	53	37	15	69	69	0	CA13,3_prime_UTR_variant,,ENST00000321764,;	A	ENSG00000185015	ENST00000321764	Transcript	3_prime_UTR_variant	3356	.	.	.	.	.	.	.	1	CA13	HGNC	14914	protein_coding	YES	CCDS6236.1	ENSP00000318912	CAH13_HUMAN	.	UPI000004BEFC	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTTGAGTGG	.	5	ESCA
MMP16	0	.	GRCh37	8	89198796	89198796	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313G>A	p.Asp105Asn	p.D105N	ENST00000286614	3/10	48	39	8	43	43	0	MMP16,missense_variant,p.Asp105Asn,ENST00000286614,;MMP16,missense_variant,p.Asp122Asn,ENST00000522726,;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,;MMP16,non_coding_transcript_exon_variant,,ENST00000520568,;	T	ENSG00000156103	ENST00000286614	Transcript	missense_variant	595	313	105	D/N	Gac/Aac	.	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	deleterious(0)	possibly_damaging(0.849)	3/10	.	hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,PROSITE_patterns:PS00546,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF47090,Prints_domain:PR00138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTCAGGTA	.	5	ESCA
TNKS	0	.	GRCh37	8	9413446	9413446	+	5'UTR	SNP	G	G	A	rs375949097	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4G>A	.	.	ENST00000310430	1/27	59	49	10	67	67	0	TNKS,5_prime_UTR_variant,,ENST00000520408,;TNKS,5_prime_UTR_variant,,ENST00000310430,;TNKS,5_prime_UTR_variant,,ENST00000522110,;RP11-375N15.2,non_coding_transcript_exon_variant,,ENST00000607598,;	A	ENSG00000173273	ENST00000310430	Transcript	5_prime_UTR_variant	23	.	.	.	.	rs375949097	.	.	1	TNKS	HGNC	11941	protein_coding	YES	CCDS5974.1	ENSP00000311579	TNKS1_HUMAN	Q59FX0_HUMAN,E7EQ52_HUMAN	UPI000013F00D	.	.	.	1/27	.	.	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCCGAAGAT	byFrequency|byCluster	5	ESCA
OSR2	0	.	GRCh37	8	99963845	99963845	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855C>T	p.%3D	p.S285S	ENST00000297565	4/4	51	32	18	54	54	0	OSR2,missense_variant,p.Ala258Val,ENST00000435298,;OSR2,synonymous_variant,p.%3D,ENST00000297565,;OSR2,synonymous_variant,p.%3D,ENST00000457907,;OSR2,synonymous_variant,p.%3D,ENST00000522510,;OSR2,downstream_gene_variant,,ENST00000520951,;OSR2,downstream_gene_variant,,ENST00000518199,;OSR2,downstream_gene_variant,,ENST00000523368,;OSR2,downstream_gene_variant,,ENST00000520722,;OSR2,downstream_gene_variant,,ENST00000521044,;	T	ENSG00000164920	ENST00000297565	Transcript	synonymous_variant	1351	855	285	S	agC/agT	.	.	.	1	OSR2	HGNC	15830	protein_coding	YES	CCDS47901.1	ENSP00000297565	OSR2_HUMAN	E5RH47_HUMAN	UPI00001AEC4D	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR14196:SF4,hmmpanther:PTHR14196,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAGCTGCGA	.	5	ESCA
NANS	0	.	GRCh37	9	100840628	100840628	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.602C>T	p.Ser201Leu	p.S201L	ENST00000210444	4/6	39	16	22	46	46	0	NANS,missense_variant,p.Ser9Leu,ENST00000427646,;NANS,missense_variant,p.Ser201Leu,ENST00000210444,;NANS,missense_variant,p.Ser60Leu,ENST00000415280,;TRIM14,intron_variant,,ENST00000375098,;NANS,splice_region_variant,,ENST00000461452,;TRIM14,downstream_gene_variant,,ENST00000478530,;NANS,downstream_gene_variant,,ENST00000495319,;	T	ENSG00000095380	ENST00000210444	Transcript	missense_variant	672	602	201	S/L	tCg/tTg	.	.	.	1	NANS	HGNC	19237	protein_coding	YES	CCDS6733.1	ENSP00000210444	SIAS_HUMAN	.	UPI000013597F	.	tolerated(0.33)	benign(0.005)	4/6	.	hmmpanther:PTHR23416,hmmpanther:PTHR23416:SF1,Pfam_domain:PF03102,Gene3D:3.20.20.70,Superfamily_domains:SSF51569	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCGGTGA	.	5	ESCA
OR13C9	0	.	GRCh37	9	107379583	107379583	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903G>A	p.%3D	p.K301K	ENST00000259362	1/1	118	75	43	103	103	0	OR13C9,synonymous_variant,p.%3D,ENST00000259362,;	T	ENSG00000136839	ENST00000259362	Transcript	synonymous_variant	903	903	301	K	aaG/aaA	.	.	.	-1	OR13C9	HGNC	15104	protein_coding	YES	CCDS35093.1	ENSP00000259362	O13C9_HUMAN	Q8NGV4_HUMAN	UPI0000041D56	.	.	.	1/1	.	hmmpanther:PTHR26453:SF143,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATCCTTGTT	.	5	ESCA
NTNG2	0	.	GRCh37	9	135073473	135073473	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334T>C	p.Trp112Arg	p.W112R	ENST00000393229	3/8	66	36	29	52	52	0	NTNG2,missense_variant,p.Trp112Arg,ENST00000393228,;NTNG2,missense_variant,p.Trp112Arg,ENST00000372179,;NTNG2,missense_variant,p.Trp112Arg,ENST00000360670,;NTNG2,missense_variant,p.Trp112Arg,ENST00000393229,;	C	ENSG00000196358	ENST00000393229	Transcript	missense_variant	1110	334	112	W/R	Tgg/Cgg	.	.	.	1	NTNG2	HGNC	14288	protein_coding	YES	CCDS6946.1	ENSP00000376921	NTNG2_HUMAN	.	UPI0000367698	.	deleterious(0)	probably_damaging(1)	3/8	.	SMART_domains:SM00136,Pfam_domain:PF00055,hmmpanther:PTHR10574,PROSITE_profiles:PS51117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCTGGAGC	.	5	ESCA
TSC1	0	.	GRCh37	9	135787825	135787825	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757C>A	p.His253Asn	p.H253N	ENST00000298552	9/23	39	17	21	60	60	0	TSC1,missense_variant,p.His253Asn,ENST00000298552,;TSC1,missense_variant,p.His202Asn,ENST00000545250,;TSC1,missense_variant,p.His253Asn,ENST00000440111,;TSC1,missense_variant,p.His253Asn,ENST00000403810,;TSC1,non_coding_transcript_exon_variant,,ENST00000493467,;	T	ENSG00000165699	ENST00000298552	Transcript	missense_variant	979	757	253	H/N	Cat/Aat	.	.	.	-1	TSC1	HGNC	12362	protein_coding	YES	CCDS6956.1	ENSP00000298552	TSC1_HUMAN	.	UPI000013773E	.	deleterious(0.01)	possibly_damaging(0.589)	9/23	.	hmmpanther:PTHR15154,Pfam_domain:PF04388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATGAGTTT	.	5	ESCA
INPP5E	0	.	GRCh37	9	139327500	139327500	+	Missense_Mutation	SNP	C	C	T	rs779363781	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1187G>A	p.Arg396His	p.R396H	ENST00000371712	5/10	43	35	8	40	40	0	INPP5E,missense_variant,p.Arg396His,ENST00000371712,;	T	ENSG00000148384	ENST00000371712	Transcript	missense_variant	1590	1187	396	R/H	cGc/cAc	rs779363781,COSM1461077	.	.	-1	INPP5E	HGNC	21474	protein_coding	YES	CCDS7000.1	ENSP00000360777	INP5E_HUMAN	Q2YD81_HUMAN	UPI000014053C	.	deleterious(0)	probably_damaging(0.997)	5/10	.	hmmpanther:PTHR11200:SF114,hmmpanther:PTHR11200,Pfam_domain:PF03372,Gene3D:3.60.10.10,SMART_domains:SM00128,Superfamily_domains:SSF56219	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGATGCGTGTG	byFrequency	5	ESCA
WDR44	0	.	GRCh37	X	117583140	117583140	+	3'UTR	SNP	G	G	C	rs751579860	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*190G>C	.	.	ENST00000254029	20/20	26	13	13	16	16	0	WDR44,3_prime_UTR_variant,,ENST00000371822,;WDR44,3_prime_UTR_variant,,ENST00000371825,;WDR44,3_prime_UTR_variant,,ENST00000371848,;WDR44,3_prime_UTR_variant,,ENST00000254029,;	C	ENSG00000131725	ENST00000254029	Transcript	3_prime_UTR_variant	3327	.	.	.	.	rs751579860	.	.	1	WDR44	HGNC	30512	protein_coding	YES	CCDS14572.1	ENSP00000254029	WDR44_HUMAN	B7Z947_HUMAN	UPI000013CE0C	.	.	.	20/20	.	.	A:0.0005	A:0	A:0.0014	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTAGAATAA	byFrequency|by1000G	5	ESCA
DOCK11	0	.	GRCh37	X	117758549	117758549	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3519A>G	p.%3D	p.L1173L	ENST00000276202	32/53	31	15	16	28	28	0	DOCK11,synonymous_variant,p.%3D,ENST00000276204,;DOCK11,synonymous_variant,p.%3D,ENST00000276202,;	G	ENSG00000147251	ENST00000276202	Transcript	synonymous_variant	3582	3519	1173	L	ctA/ctG	.	.	.	1	DOCK11	HGNC	23483	protein_coding	YES	CCDS35373.1	ENSP00000276202	DOC11_HUMAN	B3KNP4_HUMAN	UPI000022DB8F	.	.	.	32/53	.	hmmpanther:PTHR23317:SF81,hmmpanther:PTHR23317,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTACTTTT	.	5	ESCA
HS6ST2	0	.	GRCh37	X	131761250	131761250	+	3'Flank	SNP	C	C	G	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000521489	.	43	22	20	36	36	0	HS6ST2,3_prime_UTR_variant,,ENST00000370836,;HS6ST2,downstream_gene_variant,,ENST00000521489,;HS6ST2,downstream_gene_variant,,ENST00000406696,;HS6ST2,downstream_gene_variant,,ENST00000370833,;	G	ENSG00000171004	ENST00000521489	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	748	-1	HS6ST2	HGNC	19133	protein_coding	YES	CCDS48170.1	ENSP00000429473	H6ST2_HUMAN	B7Z2U5_HUMAN	UPI0000E59259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTCAAGTT	.	5	ESCA
PHF6	0	.	GRCh37	X	133561862	133561862	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2502A>T	.	.	ENST00000332070	10/10	40	23	16	37	37	0	PHF6,3_prime_UTR_variant,,ENST00000394292,;PHF6,3_prime_UTR_variant,,ENST00000332070,;PHF6,3_prime_UTR_variant,,ENST00000370803,;PHF6,downstream_gene_variant,,ENST00000416404,;	T	ENSG00000156531	ENST00000332070	Transcript	3_prime_UTR_variant	3802	.	.	.	.	.	.	.	1	PHF6	HGNC	18145	protein_coding	YES	CCDS14639.1	ENSP00000329097	PHF6_HUMAN	B4E138_HUMAN	UPI0000074487	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTCACATGC	.	5	ESCA
PBDC1	0	.	GRCh37	X	75397537	75397537	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5B8-01A-11D-A28B-09	TCGA-IG-A5B8-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496G>A	p.Glu166Lys	p.E166K	ENST00000373358	6/6	25	13	12	9	9	0	PBDC1,missense_variant,p.Glu166Lys,ENST00000373358,;PBDC1,synonymous_variant,p.%3D,ENST00000373357,;	A	ENSG00000102390	ENST00000373358	Transcript	missense_variant	699	496	166	E/K	Gaa/Aaa	.	.	.	1	PBDC1	HGNC	28790	protein_coding	YES	CCDS14432.1	ENSP00000362456	PBDC1_HUMAN	Q9P0N4_HUMAN	UPI0000072009	.	tolerated(0.1)	benign(0.332)	6/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13410	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACAAAGAAGGA	.	3	ESCA
HSPA14	0	.	GRCh37	10	14884177	14884177	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221+2021G>A	.	.	ENST00000378372	.	10	4	6	15	15	0	HSPA14,intron_variant,,ENST00000378372,;HSPA14,intron_variant,,ENST00000441647,;HSPA14,intron_variant,,ENST00000437161,;CDNF,upstream_gene_variant,,ENST00000465530,;CDNF,upstream_gene_variant,,ENST00000378442,;HSPA14,non_coding_transcript_exon_variant,,ENST00000493178,;HSPA14,non_coding_transcript_exon_variant,,ENST00000493863,;CDNF,upstream_gene_variant,,ENST00000378441,;	A	ENSG00000187522	ENST00000378372	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	HSPA14	HGNC	29526	protein_coding	YES	CCDS7103.1	ENSP00000367623	HSP7E_HUMAN	B4DYI5_HUMAN	UPI000013D6A8	.	.	.	.	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCCTGAGAGG	.	3	ESCA
DDX50	0	.	GRCh37	10	70694630	70694630	+	Missense_Mutation	SNP	C	C	G	rs746818108	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1477C>G	p.Gln493Glu	p.Q493E	ENST00000373585	10/15	26	14	11	30	30	0	DDX50,missense_variant,p.Gln493Glu,ENST00000373585,;DDX50,non_coding_transcript_exon_variant,,ENST00000460470,;DDX50,intron_variant,,ENST00000466265,;	G	ENSG00000107625	ENST00000373585	Transcript	missense_variant	1584	1477	493	Q/E	Caa/Gaa	rs746818108	.	.	1	DDX50	HGNC	17906	protein_coding	YES	CCDS7283.1	ENSP00000362687	DDX50_HUMAN	Q9NTA9_HUMAN,B4DED6_HUMAN	UPI000006FBBF	.	tolerated(0.12)	benign(0.011)	10/15	.	PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF227,hmmpanther:PTHR24031,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATCAACCA	.	5	ESCA
ADAMTS14	0	.	GRCh37	10	72498630	72498630	+	Silent	SNP	G	G	A	rs749282565	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1641G>A	p.%3D	p.S547S	ENST00000373208	11/22	70	56	14	134	134	0	ADAMTS14,synonymous_variant,p.%3D,ENST00000373208,;ADAMTS14,synonymous_variant,p.%3D,ENST00000373207,;	A	ENSG00000138316	ENST00000373208	Transcript	synonymous_variant	1641	1641	547	S	tcG/tcA	rs749282565	.	.	1	ADAMTS14	HGNC	14899	protein_coding	YES	CCDS7307.1	ENSP00000362304	ATS14_HUMAN	.	UPI000013E57B	.	.	.	11/22	.	hmmpanther:PTHR13723:SF24,hmmpanther:PTHR13723	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTCGCCGGA	byFrequency	5	ESCA
PPP3CB	0	.	GRCh37	10	75197677	75197680	+	3'UTR	DEL	GAAG	GAAG	AAA	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	GAAG	GAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*320_*323delCTTCinsTTT	.	.	ENST00000394829	14/14	52	35	17	27	27	0	PPP3CB,3_prime_UTR_variant,,ENST00000544628,;PPP3CB,3_prime_UTR_variant,,ENST00000394828,;PPP3CB,3_prime_UTR_variant,,ENST00000394829,;PPP3CB,3_prime_UTR_variant,,ENST00000360663,;PPP3CB,downstream_gene_variant,,ENST00000430762,;MSS51,upstream_gene_variant,,ENST00000299432,;MSS51,upstream_gene_variant,,ENST00000487126,;	AAA	ENSG00000107758	ENST00000394829	Transcript	3_prime_UTR_variant	2033-2036	.	.	.	.	.	.	.	-1	PPP3CB	HGNC	9315	protein_coding	YES	CCDS44437.1	ENSP00000378306	PP2BB_HUMAN	Q9UMB2_HUMAN	UPI000006E24B	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	TCTACTGAAGGGGAA	.	5	ESCA
GUCY1A2	0	.	GRCh37	11	106647265	106647265	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1736A>G	p.His579Arg	p.H579R	ENST00000282249	6/9	42	32	10	57	56	1	GUCY1A2,missense_variant,p.His579Arg,ENST00000282249,;GUCY1A2,missense_variant,p.His579Arg,ENST00000526355,;GUCY1A2,missense_variant,p.His600Arg,ENST00000347596,;	C	ENSG00000152402	ENST00000282249	Transcript	missense_variant	2126	1736	579	H/R	cAc/cGc	COSM3749129,COSM3749130	.	.	-1	GUCY1A2	HGNC	4684	protein_coding	YES	CCDS58170.1	ENSP00000282249	GCYA2_HUMAN	.	UPI000002A79C	.	deleterious(0)	possibly_damaging(0.792)	6/9	.	PROSITE_profiles:PS50125,hmmpanther:PTHR11920:SF276,hmmpanther:PTHR11920,Pfam_domain:PF00211,Gene3D:3.30.70.1230,SMART_domains:SM00044,Superfamily_domains:SSF55073	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGTGGAGC	.	5	ESCA
OR10G8	0	.	GRCh37	11	123900990	123900990	+	Missense_Mutation	SNP	G	G	A	rs778953302	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.661G>A	p.Val221Ile	p.V221I	ENST00000431524	1/1	131	90	41	180	180	0	OR10G8,missense_variant,p.Val221Ile,ENST00000431524,;	A	ENSG00000234560	ENST00000431524	Transcript	missense_variant	694	661	221	V/I	Gtc/Atc	rs778953302,COSM1506991,COSM1127871	.	.	1	OR10G8	HGNC	14845	protein_coding	YES	CCDS31704.1	ENSP00000389072	O10G8_HUMAN	.	UPI0000040A8F	.	tolerated(0.3)	benign(0.05)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF146,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCGTCTGT	.	5	ESCA
ABCC8	0	.	GRCh37	11	17416732	17416732	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4398G>T	p.%3D	p.L1466L	ENST00000389817	36/39	26	20	6	16	16	0	ABCC8,synonymous_variant,p.%3D,ENST00000389817,;ABCC8,synonymous_variant,p.%3D,ENST00000302539,;ABCC8,downstream_gene_variant,,ENST00000528374,;ABCC8,3_prime_UTR_variant,,ENST00000531642,;ABCC8,3_prime_UTR_variant,,ENST00000526168,;ABCC8,intron_variant,,ENST00000526037,;ABCC8,intron_variant,,ENST00000525022,;ABCC8,downstream_gene_variant,,ENST00000531137,;ABCC8,downstream_gene_variant,,ENST00000527905,;ABCC8,downstream_gene_variant,,ENST00000532220,;ABCC8,downstream_gene_variant,,ENST00000531891,;	A	ENSG00000006071	ENST00000389817	Transcript	synonymous_variant	4467	4398	1466	L	ctG/ctT	.	.	.	-1	ABCC8	HGNC	59	protein_coding	YES	CCDS31437.1	ENSP00000374467	ABCC8_HUMAN	.	UPI0000DBEF32	.	.	.	36/39	.	PROSITE_profiles:PS50893,hmmpanther:PTHR24223:SF187,hmmpanther:PTHR24223,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CCTGGCAGTGC	.	4	ESCA
HTATIP2	0	.	GRCh37	11	20385843	20385843	+	Silent	SNP	C	C	T	rs775602858	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.162C>T	p.%3D	p.S54S	ENST00000419348	2/6	30	23	6	27	27	0	HTATIP2,synonymous_variant,p.%3D,ENST00000531058,;HTATIP2,synonymous_variant,p.%3D,ENST00000532505,;HTATIP2,synonymous_variant,p.%3D,ENST00000443524,;HTATIP2,synonymous_variant,p.%3D,ENST00000421577,;HTATIP2,synonymous_variant,p.%3D,ENST00000530266,;HTATIP2,synonymous_variant,p.%3D,ENST00000451739,;HTATIP2,synonymous_variant,p.%3D,ENST00000532081,;HTATIP2,synonymous_variant,p.%3D,ENST00000419348,;	T	ENSG00000109854	ENST00000419348	Transcript	synonymous_variant	231	162	54	S	tcC/tcT	rs775602858	.	.	1	HTATIP2	HGNC	16637	protein_coding	YES	CCDS44553.1	ENSP00000392985	HTAI2_HUMAN	.	UPI0001536775	.	.	.	2/6	.	Superfamily_domains:SSF51735,Gene3D:3.40.50.720,hmmpanther:PTHR14097:SF7,hmmpanther:PTHR14097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATCCGTCTT	.	5	ESCA
OR51G2	0	.	GRCh37	11	4936269	4936269	+	Missense_Mutation	SNP	C	C	T	rs767452142	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.625G>A	p.Val209Ile	p.V209I	ENST00000322013	1/1	43	34	8	45	45	0	OR51G2,missense_variant,p.Val209Ile,ENST00000322013,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	T	ENSG00000176893	ENST00000322013	Transcript	missense_variant	654	625	209	V/I	Gtc/Atc	rs767452142,COSM1508812	.	.	-1	OR51G2	HGNC	15198	protein_coding	YES	CCDS31365.1	ENSP00000322593	O51G2_HUMAN	.	UPI0000041C2F	.	tolerated(0.51)	benign(0.021)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF133,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGACGATGA	byFrequency	5	ESCA
UBQLN3	0	.	GRCh37	11	5529807	5529807	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.982G>T	p.Asp328Tyr	p.D328Y	ENST00000311659	2/2	37	25	12	25	25	0	UBQLN3,missense_variant,p.Asp328Tyr,ENST00000311659,;HBG2,intron_variant,,ENST00000380259,;HBE1,upstream_gene_variant,,ENST00000396895,;HBG2,upstream_gene_variant,,ENST00000380252,;HBE1,upstream_gene_variant,,ENST00000380237,;UBQLN3,downstream_gene_variant,,ENST00000445998,;AC104389.28,upstream_gene_variant,,ENST00000418729,;AC104389.28,upstream_gene_variant,,ENST00000415970,;AC104389.28,upstream_gene_variant,,ENST00000420465,;AC104389.28,upstream_gene_variant,,ENST00000420726,;	A	ENSG00000175520	ENST00000311659	Transcript	missense_variant	1130	982	328	D/Y	Gac/Tac	.	.	.	-1	UBQLN3	HGNC	12510	protein_coding	YES	CCDS7758.1	ENSP00000347997	UBQL3_HUMAN	C9IYQ4_HUMAN	UPI000006E3A0	.	deleterious(0.01)	benign(0.149)	2/2	.	hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGTCAGGTG	.	5	ESCA
KCNK4	0	.	GRCh37	11	64067761	64067761	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000539216	.	24	19	5	16	16	0	KCNK4,downstream_gene_variant,,ENST00000538767,;TEX40,upstream_gene_variant,,ENST00000328404,;TEX40,upstream_gene_variant,,ENST00000539943,;KCNK4,downstream_gene_variant,,ENST00000539216,;KCNK4,downstream_gene_variant,,ENST00000422670,;KCNK4,downstream_gene_variant,,ENST00000394525,;Y_RNA,downstream_gene_variant,,ENST00000384297,;RP11-783K16.10,non_coding_transcript_exon_variant,,ENST00000539086,;KCNK4,downstream_gene_variant,,ENST00000539651,;KCNK4,downstream_gene_variant,,ENST00000541349,;TEX40,upstream_gene_variant,,ENST00000535981,;KCNK4,downstream_gene_variant,,ENST00000536690,;KCNK4,downstream_gene_variant,,ENST00000453423,;KCNK4,downstream_gene_variant,,ENST00000545838,;KCNK4,downstream_gene_variant,,ENST00000538846,;	T	ENSG00000182450	ENST00000539216	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	382	1	KCNK4	HGNC	6279	protein_coding	YES	CCDS8067.1	ENSP00000444948	KCNK4_HUMAN	F5GZ20_HUMAN	UPI0000042377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCGCGTG	.	5	ESCA
RIN1	0	.	GRCh37	11	66103267	66103267	+	Silent	SNP	G	G	A	rs760724156	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348C>T	p.%3D	p.F116F	ENST00000311320	3/10	48	38	10	57	57	0	RIN1,synonymous_variant,p.%3D,ENST00000311320,;RIN1,synonymous_variant,p.%3D,ENST00000530056,;RIN1,synonymous_variant,p.%3D,ENST00000424433,;BRMS1,downstream_gene_variant,,ENST00000425825,;BRMS1,downstream_gene_variant,,ENST00000359957,;BRMS1,downstream_gene_variant,,ENST00000524699,;BRMS1,downstream_gene_variant,,ENST00000530756,;RP11-867G23.12,intron_variant,,ENST00000526655,;RIN1,upstream_gene_variant,,ENST00000524804,;RIN1,missense_variant,p.Ser56Leu,ENST00000530745,;RIN1,non_coding_transcript_exon_variant,,ENST00000526246,;RIN1,upstream_gene_variant,,ENST00000534824,;BRMS1,downstream_gene_variant,,ENST00000534617,;RIN1,upstream_gene_variant,,ENST00000528006,;BRMS1,downstream_gene_variant,,ENST00000527375,;BRMS1,downstream_gene_variant,,ENST00000525127,;BRMS1,downstream_gene_variant,,ENST00000530238,;	A	ENSG00000174791	ENST00000311320	Transcript	synonymous_variant	475	348	116	F	ttC/ttT	rs760724156,COSM3452035,COSM3452036	.	.	-1	RIN1	HGNC	18749	protein_coding	YES	CCDS31614.1	ENSP00000310406	RIN1_HUMAN	.	UPI000013F14D	.	.	.	3/10	.	PROSITE_profiles:PS50001,hmmpanther:PTHR23101:SF54,hmmpanther:PTHR23101,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACGAAGGA	byFrequency	5	ESCA
NPAS4	0	.	GRCh37	11	66191454	66191454	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1093G>A	p.Ala365Thr	p.A365T	ENST00000311034	7/8	28	18	10	23	23	0	NPAS4,missense_variant,p.Ala365Thr,ENST00000311034,;NPAS4,3_prime_UTR_variant,,ENST00000525148,;NPAS4,downstream_gene_variant,,ENST00000524617,;	A	ENSG00000174576	ENST00000311034	Transcript	missense_variant	1269	1093	365	A/T	Gca/Aca	.	.	.	1	NPAS4	HGNC	18983	protein_coding	YES	CCDS8138.1	ENSP00000311196	NPAS4_HUMAN	.	UPI0000074744	.	deleterious(0.01)	benign(0)	7/8	.	hmmpanther:PTHR23043:SF13,hmmpanther:PTHR23043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCGCAGCA	.	5	ESCA
BTBD11	0	.	GRCh37	12	108013823	108013823	+	Missense_Mutation	SNP	G	G	A	rs777803244	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2513G>A	p.Arg838His	p.R838H	ENST00000280758	11/17	37	33	4	72	72	0	BTBD11,missense_variant,p.Arg838His,ENST00000490090,;BTBD11,missense_variant,p.Arg838His,ENST00000280758,;BTBD11,missense_variant,p.Arg719His,ENST00000420571,;BTBD11,missense_variant,p.Arg375His,ENST00000357167,;RP11-128P10.1,upstream_gene_variant,,ENST00000548473,;	A	ENSG00000151136	ENST00000280758	Transcript	missense_variant	3041	2513	838	R/H	cGc/cAc	rs777803244,COSM296977	.	.	1	BTBD11	HGNC	23844	protein_coding	YES	CCDS31893.1	ENSP00000280758	BTBDB_HUMAN	B3KY13_HUMAN,B3KXB0_HUMAN	UPI000051901E	.	deleterious(0.03)	probably_damaging(0.964)	11/17	.	hmmpanther:PTHR24413:SF76,hmmpanther:PTHR24413	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCACCGCAGGC	byFrequency	2	ESCA
PLBD1	0	.	GRCh37	12	14706313	14706313	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.149C>G	p.Ala50Gly	p.A50G	ENST00000240617	2/11	74	44	29	39	39	0	PLBD1,missense_variant,p.Ala50Gly,ENST00000240617,;PLBD1,missense_variant,p.Ala3Gly,ENST00000540572,;RN7SKP134,downstream_gene_variant,,ENST00000363960,;PLBD1,intron_variant,,ENST00000541618,;	C	ENSG00000121316	ENST00000240617	Transcript	missense_variant	802	149	50	A/G	gCt/gGt	.	.	.	-1	PLBD1	HGNC	26215	protein_coding	YES	CCDS31751.1	ENSP00000240617	PLBL1_HUMAN	F5H053_HUMAN	UPI00004565DA	.	tolerated(0.26)	benign(0.257)	2/11	.	hmmpanther:PTHR12370,Pfam_domain:PF04916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCAGCAGGC	.	5	ESCA
SLCO1A2	0	.	GRCh37	12	21457384	21457384	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.566T>C	p.Phe189Ser	p.F189S	ENST00000307378	7/16	57	44	13	37	37	0	SLCO1A2,missense_variant,p.Phe187Ser,ENST00000390670,;SLCO1A2,missense_variant,p.Phe189Ser,ENST00000307378,;SLCO1A2,missense_variant,p.Phe57Ser,ENST00000537524,;SLCO1A2,missense_variant,p.Phe189Ser,ENST00000452078,;SLCO1A2,missense_variant,p.Phe57Ser,ENST00000458504,;SLCO1A2,downstream_gene_variant,,ENST00000453443,;SLCO1A2,downstream_gene_variant,,ENST00000413682,;SLCO1A2,downstream_gene_variant,,ENST00000422327,;SLCO1A2,3_prime_UTR_variant,,ENST00000544020,;SLCO1A2,3_prime_UTR_variant,,ENST00000544290,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000480394,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000463718,;	G	ENSG00000084453	ENST00000307378	Transcript	missense_variant	1287	566	189	F/S	tTt/tCt	.	.	.	-1	SLCO1A2	HGNC	10956	protein_coding	YES	CCDS8686.1	ENSP00000305974	SO1A2_HUMAN	C9K059_HUMAN,C9JUW6_HUMAN,C9JTF6_HUMAN,C9JHU9_HUMAN,C9JGK7_HUMAN,C9JG34_HUMAN,C9JCA7_HUMAN,B4DJE6_HUMAN	UPI0000037575	.	tolerated(0.72)	benign(0)	7/16	.	Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Gene3D:1.20.1250.20,hmmpanther:PTHR11388:SF16,hmmpanther:PTHR11388,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCAAATTTG	.	5	ESCA
KCNJ8	0	.	GRCh37	12	21918874	21918874	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058G>A	p.Cys353Tyr	p.C353Y	ENST00000240662	3/3	72	32	39	59	59	0	KCNJ8,missense_variant,p.Cys353Tyr,ENST00000240662,;RP11-59N23.1,intron_variant,,ENST00000542489,;	T	ENSG00000121361	ENST00000240662	Transcript	missense_variant	1404	1058	353	C/Y	tGc/tAc	.	.	.	-1	KCNJ8	HGNC	6269	protein_coding	YES	CCDS8692.1	ENSP00000240662	IRK8_HUMAN	F5GY12_HUMAN	UPI000012D8A3	.	tolerated(0.09)	probably_damaging(0.996)	3/3	.	hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF11,Pfam_domain:PF01007,Gene3D:2.60.40.1400,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81296,Prints_domain:PR01331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGCACCGT	.	5	ESCA
CACNA1C	0	.	GRCh37	12	2800324	2800324	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6520G>A	p.Glu2174Lys	p.E2174K	ENST00000347598	49/49	76	56	19	44	44	0	CACNA1C,missense_variant,p.Glu2126Lys,ENST00000399644,;CACNA1C,missense_variant,p.Glu2134Lys,ENST00000399595,;CACNA1C,missense_variant,p.Glu2197Lys,ENST00000406454,;CACNA1C,missense_variant,p.Glu2161Lys,ENST00000399617,;CACNA1C,missense_variant,p.Glu2174Lys,ENST00000347598,;CACNA1C,missense_variant,p.Glu2145Lys,ENST00000402845,;CACNA1C,missense_variant,p.Glu2161Lys,ENST00000327702,;CACNA1C,missense_variant,p.Glu2197Lys,ENST00000399634,;CACNA1C,missense_variant,p.Glu2126Lys,ENST00000399641,;CACNA1C,missense_variant,p.Glu2126Lys,ENST00000399603,;CACNA1C,missense_variant,p.Glu2143Lys,ENST00000399629,;CACNA1C,missense_variant,p.Glu2126Lys,ENST00000399601,;CACNA1C,missense_variant,p.Glu2126Lys,ENST00000399597,;CACNA1C,missense_variant,p.Glu2126Lys,ENST00000399655,;CACNA1C,missense_variant,p.Glu2146Lys,ENST00000399606,;CACNA1C,missense_variant,p.Glu2145Lys,ENST00000399637,;CACNA1C,missense_variant,p.Glu2151Lys,ENST00000335762,;CACNA1C,missense_variant,p.Glu2134Lys,ENST00000399591,;CACNA1C,missense_variant,p.Glu2145Lys,ENST00000399621,;CACNA1C,missense_variant,p.Glu2154Lys,ENST00000399638,;CACNA1C,missense_variant,p.Glu2167Lys,ENST00000344100,;CACNA1C,missense_variant,p.Glu2132Lys,ENST00000399649,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000544517,;CACNA1C-AS1,upstream_gene_variant,,ENST00000501371,;CACNA1C-AS1,upstream_gene_variant,,ENST00000541673,;	A	ENSG00000151067	ENST00000347598	Transcript	missense_variant	6520	6520	2174	E/K	Gag/Aag	.	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	deleterious_low_confidence(0)	benign(0.137)	49/49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAGGAGGAG	.	5	ESCA
DYRK4	0	.	GRCh37	12	4708255	4708255	+	Missense_Mutation	SNP	C	C	G	rs750043434	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.622C>G	p.Arg208Gly	p.R208G	ENST00000540757	7/13	148	138	10	97	97	0	DYRK4,missense_variant,p.Arg208Gly,ENST00000540757,;DYRK4,missense_variant,p.Arg208Gly,ENST00000010132,;DYRK4,missense_variant,p.Arg323Gly,ENST00000542744,;DYRK4,missense_variant,p.Arg208Gly,ENST00000543431,;DYRK4,downstream_gene_variant,,ENST00000536157,;DYRK4,upstream_gene_variant,,ENST00000540644,;RP11-234B24.5,downstream_gene_variant,,ENST00000538921,;	G	ENSG00000010219	ENST00000540757	Transcript	missense_variant	782	622	208	R/G	Cgg/Ggg	rs750043434,COSM3772621	.	.	1	DYRK4	HGNC	3095	protein_coding	YES	CCDS8530.1	ENSP00000441755	DYRK4_HUMAN	D3JEN3_HUMAN,D3JEN2_HUMAN,B4DQW1_HUMAN	UPI000006E05C	.	deleterious(0.01)	possibly_damaging(0.537)	7/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR24058:SF22,hmmpanther:PTHR24058,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGTTCGGCGC	byFrequency	2	ESCA
SLC38A4	0	.	GRCh37	12	47159383	47159383	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1101C>T	.	.	ENST00000447411	16/16	9	6	3	15	15	0	SLC38A4,3_prime_UTR_variant,,ENST00000447411,;SLC38A4,downstream_gene_variant,,ENST00000550670,;SLC38A4,downstream_gene_variant,,ENST00000266579,;	A	ENSG00000139209	ENST00000447411	Transcript	3_prime_UTR_variant	2952	.	.	.	.	.	.	.	-1	SLC38A4	HGNC	14679	protein_coding	YES	CCDS8750.1	ENSP00000389843	S38A4_HUMAN	F8VRD9_HUMAN,F8VQY9_HUMAN	UPI00000468F8	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAATGGATTT	.	2	ESCA
ESPL1	0	.	GRCh37	12	53668781	53668781	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1687G>T	p.Glu563Ter	p.E563*	ENST00000257934	7/31	35	27	8	46	46	0	ESPL1,stop_gained,p.Glu563Ter,ENST00000257934,;ESPL1,stop_gained,p.Glu563Ter,ENST00000552462,;ESPL1,downstream_gene_variant,,ENST00000550026,;ESPL1,3_prime_UTR_variant,,ENST00000552671,;ESPL1,upstream_gene_variant,,ENST00000535123,;	T	ENSG00000135476	ENST00000257934	Transcript	stop_gained	1778	1687	563	E/*	Gag/Tag	.	.	.	1	ESPL1	HGNC	16856	protein_coding	YES	CCDS8852.1	ENSP00000257934	ESPL1_HUMAN	H3BRX7_HUMAN	UPI00003668C3	.	.	.	7/31	.	hmmpanther:PTHR12792	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAAGGAGCTA	.	5	ESCA
TRHDE	0	.	GRCh37	12	72680484	72680484	+	Missense_Mutation	SNP	C	C	T	rs767303355	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.803C>T	p.Ser268Leu	p.S268L	ENST00000261180	2/19	57	37	19	47	47	0	TRHDE,missense_variant,p.Ser268Leu,ENST00000261180,;TRHDE,missense_variant,p.Ser34Leu,ENST00000547300,;TRHDE,non_coding_transcript_exon_variant,,ENST00000552503,;TRHDE,intron_variant,,ENST00000548156,;	T	ENSG00000072657	ENST00000261180	Transcript	missense_variant	899	803	268	S/L	tCg/tTg	rs767303355,COSM1705937	.	.	1	TRHDE	HGNC	30748	protein_coding	YES	CCDS9004.1	ENSP00000261180	TRHDE_HUMAN	.	UPI0000136D52	.	deleterious(0.01)	probably_damaging(0.983)	2/19	.	Superfamily_domains:0038696,Pfam_domain:PF01433,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S268L|c.803C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTCGCCTA	.	5	ESCA
NANOGP1	0	.	GRCh37	12	8051567	8051567	+	RNA	SNP	C	C	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.787C>A	.	.	ENST00000607111	3/4	215	194	21	135	135	0	NANOGP1,non_coding_transcript_exon_variant,,ENST00000607111,;RP11-277E18.2,upstream_gene_variant,,ENST00000533382,;NANOGP1,downstream_gene_variant,,ENST00000525030,;	A	ENSG00000176654	ENST00000607111	Transcript	non_coding_transcript_exon_variant	787	.	.	.	.	.	.	.	1	NANOGP1	HGNC	23099	processed_transcript	YES	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCCATC	.	4	ESCA
HAL	0	.	GRCh37	12	96384204	96384204	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822G>C	p.Trp274Cys	p.W274C	ENST00000261208	10/21	59	49	9	57	56	1	HAL,missense_variant,p.Trp66Cys,ENST00000541929,;HAL,missense_variant,p.Trp274Cys,ENST00000261208,;HAL,missense_variant,p.Trp262Cys,ENST00000552509,;HAL,missense_variant,p.Trp274Cys,ENST00000538703,;HAL,downstream_gene_variant,,ENST00000546579,;HAL,non_coding_transcript_exon_variant,,ENST00000551562,;HAL,3_prime_UTR_variant,,ENST00000544080,;HAL,3_prime_UTR_variant,,ENST00000546999,;HAL,non_coding_transcript_exon_variant,,ENST00000549376,;HAL,upstream_gene_variant,,ENST00000548636,;	G	ENSG00000084110	ENST00000261208	Transcript	missense_variant	1191	822	274	W/C	tgG/tgC	.	.	.	-1	HAL	HGNC	4806	protein_coding	YES	CCDS9058.1	ENSP00000261208	HUTH_HUMAN	Q2PH61_HUMAN,Q2PH60_HUMAN,Q2PH56_HUMAN	UPI000012CE8E	.	deleterious(0.01)	probably_damaging(0.997)	10/21	.	Superfamily_domains:SSF48557,Pfam_domain:PF00221,Gene3D:1.10.275.10,TIGRFAM_domain:TIGR01225,hmmpanther:PTHR10362,hmmpanther:PTHR10362:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGACCACAT	.	5	ESCA
ELK3	0	.	GRCh37	12	96588369	96588369	+	5'UTR	SNP	G	G	T	rs765556712	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-117G>T	.	.	ENST00000228741	1/5	15	11	4	16	16	0	ELK3,5_prime_UTR_variant,,ENST00000228741,;ELK3,5_prime_UTR_variant,,ENST00000547249,;ELK3,5_prime_UTR_variant,,ENST00000552142,;ELK3,upstream_gene_variant,,ENST00000547860,;	T	ENSG00000111145	ENST00000228741	Transcript	5_prime_UTR_variant	210	.	.	.	.	rs765556712	.	.	1	ELK3	HGNC	3325	protein_coding	YES	CCDS9060.1	ENSP00000228741	ELK3_HUMAN	F8VZQ0_HUMAN,F8VUJ0_HUMAN	UPI0000000E09	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCAGGATCTC	.	5	ESCA
GAS6	0	.	GRCh37	13	114541097	114541097	+	Silent	SNP	G	G	A	rs776379476	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534C>T	p.%3D	p.F178F	ENST00000327773	6/15	112	80	32	157	157	0	GAS6,synonymous_variant,p.%3D,ENST00000355761,;GAS6,synonymous_variant,p.%3D,ENST00000327773,;GAS6,synonymous_variant,p.%3D,ENST00000357389,;GAS6,upstream_gene_variant,,ENST00000450766,;GAS6,upstream_gene_variant,,ENST00000418959,;GAS6-AS1,non_coding_transcript_exon_variant,,ENST00000458001,;GAS6,upstream_gene_variant,,ENST00000610073,;GAS6,upstream_gene_variant,,ENST00000480426,;	A	ENSG00000183087	ENST00000327773	Transcript	synonymous_variant	681	534	178	F	ttC/ttT	rs776379476	.	.	-1	GAS6	HGNC	4168	protein_coding	YES	CCDS45072.1	ENSP00000331831	GAS6_HUMAN	B4DZY7_HUMAN	UPI0000073CCA	.	.	.	6/15	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24035:SF21,hmmpanther:PTHR24035,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,Pfam_domain:PF14670,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTGGAAGCT	.	5	ESCA
DCT	0	.	GRCh37	13	95114434	95114434	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.873C>T	p.%3D	p.D291D	ENST00000446125	5/10	51	30	20	68	68	0	DCT,synonymous_variant,p.%3D,ENST00000377028,;DCT,synonymous_variant,p.%3D,ENST00000446125,;AL139318.1,downstream_gene_variant,,ENST00000390768,;DCT,non_coding_transcript_exon_variant,,ENST00000490854,;DCT,synonymous_variant,p.%3D,ENST00000483392,;DCT,downstream_gene_variant,,ENST00000472871,;	A	ENSG00000080166	ENST00000446125	Transcript	synonymous_variant	1300	873	291	D	gaC/gaT	.	.	.	-1	DCT	HGNC	2709	protein_coding	YES	CCDS45060.1	ENSP00000392762	TYRP2_HUMAN	Q9NQD8_HUMAN,Q0PK43_HUMAN	UPI0000E13F02	.	.	.	5/10	.	Superfamily_domains:SSF48056,Pfam_domain:PF00264,Gene3D:1.10.1280.10,hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTAGTCATC	.	5	ESCA
ZBTB42	0	.	GRCh37	14	105269410	105269410	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*607G>T	.	.	ENST00000342537	1/1	20	13	7	19	19	0	ZBTB42,3_prime_UTR_variant,,ENST00000342537,;ZBTB42,downstream_gene_variant,,ENST00000555360,;	T	ENSG00000179627	ENST00000342537	Transcript	3_prime_UTR_variant	2161	.	.	.	.	.	.	.	1	ZBTB42	HGNC	32550	protein_coding	YES	CCDS45174.1	ENSP00000409107	ZBT42_HUMAN	.	UPI0001849D48	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGGTGGGGGGG	.	2	ESCA
MGA	0	.	GRCh37	15	42058227	42058227	+	Silent	SNP	A	A	C	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7947A>C	p.%3D	p.P2649P	ENST00000219905	24/24	35	23	12	31	31	0	MGA,synonymous_variant,p.%3D,ENST00000219905,;MGA,synonymous_variant,p.%3D,ENST00000570161,;MGA,synonymous_variant,p.%3D,ENST00000389936,;MGA,synonymous_variant,p.%3D,ENST00000545763,;MGA,synonymous_variant,p.%3D,ENST00000566586,;MGA,downstream_gene_variant,,ENST00000564190,;RP11-107F6.3,downstream_gene_variant,,ENST00000562063,;RP11-107F6.3,downstream_gene_variant,,ENST00000607504,;MGA,downstream_gene_variant,,ENST00000568255,;	C	ENSG00000174197	ENST00000219905	Transcript	synonymous_variant	8128	7947	2649	P	ccA/ccC	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	.	.	24/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCCACGAAT	.	5	ESCA
BNC1	0	.	GRCh37	15	83932769	83932769	+	Missense_Mutation	SNP	G	G	A	rs778484158	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234C>T	p.Arg412Trp	p.R412W	ENST00000345382	4/5	31	20	11	36	36	0	BNC1,missense_variant,p.Arg412Trp,ENST00000345382,;BNC1,missense_variant,p.Arg405Trp,ENST00000569704,;RP11-382A20.4,intron_variant,,ENST00000565495,;	A	ENSG00000169594	ENST00000345382	Transcript	missense_variant	1320	1234	412	R/W	Cgg/Tgg	rs778484158	.	.	-1	BNC1	HGNC	1081	protein_coding	YES	CCDS10324.1	ENSP00000307041	BNC1_HUMAN	.	UPI0000126796	.	deleterious(0)	probably_damaging(0.999)	4/5	.	hmmpanther:PTHR15021:SF1,hmmpanther:PTHR15021,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCGAGGGT	.	5	ESCA
CRYM	0	.	GRCh37	16	21270033	21270033	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69T>C	.	.	ENST00000219599	10/10	16	11	5	25	25	0	CRYM,3_prime_UTR_variant,,ENST00000396023,;CRYM,3_prime_UTR_variant,,ENST00000219599,;CRYM,3_prime_UTR_variant,,ENST00000543948,;CRYM,3_prime_UTR_variant,,ENST00000415987,;CRYM,intron_variant,,ENST00000570401,;CRYM,downstream_gene_variant,,ENST00000576703,;CRYM,intron_variant,,ENST00000574448,;CRYM,downstream_gene_variant,,ENST00000572113,;CRYM,downstream_gene_variant,,ENST00000571666,;	G	ENSG00000103316	ENST00000219599	Transcript	3_prime_UTR_variant	1280	.	.	.	.	.	.	.	-1	CRYM	HGNC	2418	protein_coding	YES	CCDS10597.1	ENSP00000219599	CRYM_HUMAN	I3NI53_HUMAN,I3L3J9_HUMAN,I3L325_HUMAN,H9KVC2_HUMAN	UPI00001284E5	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTACTCTA	.	2	ESCA
BEAN1	0	.	GRCh37	16	66511471	66511471	+	Missense_Mutation	SNP	G	G	A	rs758205983	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298G>A	p.Glu100Lys	p.E100K	ENST00000536005	4/5	27	19	7	19	19	0	BEAN1,missense_variant,p.Glu100Lys,ENST00000536005,;BEAN1,5_prime_UTR_variant,,ENST00000564819,;BEAN1,5_prime_UTR_variant,,ENST00000299694,;BEAN1,5_prime_UTR_variant,,ENST00000561796,;BEAN1,upstream_gene_variant,,ENST00000562146,;CTD-2258A20.5,intron_variant,,ENST00000569125,;CTD-2258A20.5,upstream_gene_variant,,ENST00000564618,;CTD-2258A20.5,upstream_gene_variant,,ENST00000567528,;BEAN1,intron_variant,,ENST00000563075,;BEAN1,5_prime_UTR_variant,,ENST00000562849,;RP11-403P17.5,intron_variant,,ENST00000561527,;RP11-403P17.5,intron_variant,,ENST00000561728,;	A	ENSG00000166546	ENST00000536005	Transcript	missense_variant	515	298	100	E/K	Gag/Aag	rs758205983	.	.	1	BEAN1	HGNC	24160	protein_coding	YES	CCDS54015.1	ENSP00000442793	BEAN1_HUMAN	.	UPI000164284B	.	deleterious(0.01)	benign(0.021)	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGACGAGCAC	.	5	ESCA
ZDHHC1	0	.	GRCh37	16	67440127	67440127	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228C>T	p.%3D	p.H76H	ENST00000348579	3/11	57	39	17	50	50	0	ZDHHC1,synonymous_variant,p.%3D,ENST00000348579,;ZDHHC1,upstream_gene_variant,,ENST00000562122,;ZDHHC1,non_coding_transcript_exon_variant,,ENST00000568650,;	A	ENSG00000159714	ENST00000348579	Transcript	synonymous_variant	570	228	76	H	caC/caT	.	.	.	-1	ZDHHC1	HGNC	17916	protein_coding	YES	CCDS10836.1	ENSP00000340299	ZDHC1_HUMAN	.	UPI000013C37E	.	.	.	3/11	.	hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTGGTGAGG	.	5	ESCA
CENPT	0	.	GRCh37	16	67866357	67866357	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201+1G>T	.	p.X67_splice	ENST00000562787	.	60	43	16	72	72	0	CENPT,splice_donor_variant,,ENST00000445712,;CENPT,splice_donor_variant,,ENST00000562787,;CENPT,splice_donor_variant,,ENST00000440851,;CENPT,splice_donor_variant,,ENST00000219172,;CENPT,splice_donor_variant,,ENST00000564817,;CENPT,splice_donor_variant,,ENST00000566758,;TSNAXIP1,downstream_gene_variant,,ENST00000415766,;CENPT,downstream_gene_variant,,ENST00000567985,;CENPT,downstream_gene_variant,,ENST00000565114,;CENPT,downstream_gene_variant,,ENST00000561593,;TSNAXIP1,downstream_gene_variant,,ENST00000431934,;TSNAXIP1,downstream_gene_variant,,ENST00000388833,;TSNAXIP1,downstream_gene_variant,,ENST00000561639,;CENPT,splice_donor_variant,,ENST00000564538,;CENPT,downstream_gene_variant,,ENST00000564346,;CENPT,downstream_gene_variant,,ENST00000564144,;CENPT,downstream_gene_variant,,ENST00000567482,;CENPT,downstream_gene_variant,,ENST00000568652,;CENPT,downstream_gene_variant,,ENST00000565132,;CENPT,downstream_gene_variant,,ENST00000565436,;CENPT,downstream_gene_variant,,ENST00000568765,;CENPT,downstream_gene_variant,,ENST00000565385,;CENPT,downstream_gene_variant,,ENST00000569094,;CENPT,downstream_gene_variant,,ENST00000569019,;CENPT,upstream_gene_variant,,ENST00000562947,;CENPT,splice_donor_variant,,ENST00000562338,;CENPT,splice_donor_variant,,ENST00000566067,;CENPT,splice_donor_variant,,ENST00000565157,;CENPT,splice_donor_variant,,ENST00000562513,;CENPT,splice_donor_variant,,ENST00000436104,;CENPT,splice_donor_variant,,ENST00000562462,;CENPT,splice_donor_variant,,ENST00000565713,;CENPT,splice_donor_variant,,ENST00000568069,;CENPT,splice_donor_variant,,ENST00000563885,;CENPT,non_coding_transcript_exon_variant,,ENST00000569862,;CENPT,non_coding_transcript_exon_variant,,ENST00000562483,;CENPT,non_coding_transcript_exon_variant,,ENST00000568564,;CENPT,non_coding_transcript_exon_variant,,ENST00000564128,;TSNAXIP1,downstream_gene_variant,,ENST00000565339,;TSNAXIP1,downstream_gene_variant,,ENST00000487120,;TSNAXIP1,downstream_gene_variant,,ENST00000466164,;TSNAXIP1,downstream_gene_variant,,ENST00000569504,;CENPT,upstream_gene_variant,,ENST00000574569,;TSNAXIP1,downstream_gene_variant,,ENST00000565558,;CENPT,upstream_gene_variant,,ENST00000568495,;TSNAXIP1,downstream_gene_variant,,ENST00000568990,;	A	ENSG00000102901	ENST00000562787	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	CENPT	HGNC	25787	protein_coding	YES	CCDS42182.1	ENSP00000457810	CENPT_HUMAN	H3BQ71_HUMAN,H3BMP6_HUMAN	UPI00001C1CDE	.	.	.	.	5/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTACCCTGG	.	5	ESCA
VPS9D1	0	.	GRCh37	16	89783106	89783106	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268+32G>A	.	.	ENST00000389386	.	55	45	10	62	62	0	VPS9D1,intron_variant,,ENST00000389386,;VPS9D1,intron_variant,,ENST00000561976,;ZNF276,upstream_gene_variant,,ENST00000446326,;ZNF276,upstream_gene_variant,,ENST00000568064,;ZNF276,upstream_gene_variant,,ENST00000443381,;ZNF276,upstream_gene_variant,,ENST00000289816,;VPS9D1-AS1,non_coding_transcript_exon_variant,,ENST00000562866,;VPS9D1-AS1,intron_variant,,ENST00000562298,;VPS9D1,intron_variant,,ENST00000563798,;ZNF276,upstream_gene_variant,,ENST00000568295,;ZNF276,upstream_gene_variant,,ENST00000563983,;VPS9D1,upstream_gene_variant,,ENST00000567379,;VPS9D1,upstream_gene_variant,,ENST00000568691,;ZNF276,upstream_gene_variant,,ENST00000562530,;	T	ENSG00000075399	ENST00000389386	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	VPS9D1	HGNC	13526	protein_coding	YES	CCDS42220.1	ENSP00000374037	VP9D1_HUMAN	H3BM58_HUMAN	UPI00001FF749	.	.	.	.	3/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGCCCCAGG	.	5	ESCA
KRT13	0	.	GRCh37	17	39657566	39657566	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1319C>T	p.Ser440Phe	p.S440F	ENST00000246635	8/8	43	40	3	55	55	0	KRT13,missense_variant,p.Ser440Phe,ENST00000246635,;KRT13,3_prime_UTR_variant,,ENST00000336861,;KRT13,downstream_gene_variant,,ENST00000590425,;KRT13,downstream_gene_variant,,ENST00000587435,;KRT13,downstream_gene_variant,,ENST00000587544,;AC019349.5,splice_region_variant,,ENST00000411759,;KRT13,non_coding_transcript_exon_variant,,ENST00000475217,;KRT13,downstream_gene_variant,,ENST00000587118,;KRT13,non_coding_transcript_exon_variant,,ENST00000468313,;KRT13,downstream_gene_variant,,ENST00000464634,;	A	ENSG00000171401	ENST00000246635	Transcript	missense_variant	1366	1319	440	S/F	tCt/tTt	.	.	.	-1	KRT13	HGNC	6415	protein_coding	YES	CCDS11396.1	ENSP00000246635	K1C13_HUMAN	K7ERE3_HUMAN,K7EMD9_HUMAN	UPI000013CBF6	.	tolerated(0.05)	benign(0.009)	8/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF121,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACAGAGGCA	.	2	ESCA
FTSJ3	0	.	GRCh37	17	61903427	61903427	+	Frame_Shift_Del	DEL	G	G	-	rs764050450	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.289delC	p.Arg97ValfsTer6	p.R97Vfs*6	ENST00000427159	5/21	43	34	9	47	47	0	FTSJ3,frameshift_variant,p.Arg97ValfsTer6,ENST00000580272,;FTSJ3,frameshift_variant,p.Arg97ValfsTer6,ENST00000581209,;FTSJ3,frameshift_variant,p.Arg97ValfsTer6,ENST00000427159,;PSMC5,upstream_gene_variant,,ENST00000581882,;PSMC5,upstream_gene_variant,,ENST00000579708,;PSMC5,upstream_gene_variant,,ENST00000375812,;PSMC5,upstream_gene_variant,,ENST00000585123,;FTSJ3,downstream_gene_variant,,ENST00000585145,;PSMC5,upstream_gene_variant,,ENST00000310144,;PSMC5,upstream_gene_variant,,ENST00000580864,;FTSJ3,downstream_gene_variant,,ENST00000584574,;PSMC5,upstream_gene_variant,,ENST00000581842,;PSMC5,upstream_gene_variant,,ENST00000584320,;PSMC5,upstream_gene_variant,,ENST00000582130,;FTSJ3,downstream_gene_variant,,ENST00000580295,;PSMC5,upstream_gene_variant,,ENST00000582420,;FTSJ3,3_prime_UTR_variant,,ENST00000579569,;FTSJ3,3_prime_UTR_variant,,ENST00000584193,;FTSJ3,non_coding_transcript_exon_variant,,ENST00000577263,;FTSJ3,non_coding_transcript_exon_variant,,ENST00000580290,;PSMC5,upstream_gene_variant,,ENST00000580265,;PSMC5,upstream_gene_variant,,ENST00000578570,;FTSJ3,downstream_gene_variant,,ENST00000582476,;PSMC5,upstream_gene_variant,,ENST00000579031,;FTSJ3,upstream_gene_variant,,ENST00000583901,;FTSJ3,upstream_gene_variant,,ENST00000580129,;PSMC5,upstream_gene_variant,,ENST00000581764,;PSMC5,upstream_gene_variant,,ENST00000584880,;FTSJ3,upstream_gene_variant,,ENST00000580376,;PSMC5,upstream_gene_variant,,ENST00000583283,;FTSJ3,upstream_gene_variant,,ENST00000583202,;PSMC5,upstream_gene_variant,,ENST00000584536,;PSMC5,upstream_gene_variant,,ENST00000580063,;FTSJ3,upstream_gene_variant,,ENST00000579831,;PSMC5,upstream_gene_variant,,ENST00000579147,;PSMC5,upstream_gene_variant,,ENST00000585242,;	-	ENSG00000108592	ENST00000427159	Transcript	frameshift_variant	935	289	97	R/X	Cgt/gt	rs764050450	.	.	-1	FTSJ3	HGNC	17136	protein_coding	YES	CCDS11644.1	ENSP00000396673	SPB1_HUMAN	J3QSE2_HUMAN,J3QRS5_HUMAN,J3QKT6_HUMAN,J3KS36_HUMAN	UPI000013C87B	.	.	.	5/21	.	HAMAP:MF_01547,HAMAP:MF_03163,hmmpanther:PTHR10920,hmmpanther:PTHR10920:SF13,Gene3D:3.40.50.150,Pfam_domain:PF01728,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TACAACGTTCTG	.	3	ESCA
MAP2K6	0	.	GRCh37	17	67538379	67538379	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*485G>A	.	.	ENST00000590474	12/12	34	28	5	37	37	0	MAP2K6,3_prime_UTR_variant,,ENST00000590474,;MAP2K6,downstream_gene_variant,,ENST00000589647,;MAP2K6,3_prime_UTR_variant,,ENST00000359094,;MAP2K6,downstream_gene_variant,,ENST00000592348,;	A	ENSG00000108984	ENST00000590474	Transcript	3_prime_UTR_variant	1777	.	.	.	.	.	.	.	1	MAP2K6	HGNC	6846	protein_coding	YES	CCDS11686.1	ENSP00000468348	MP2K6_HUMAN	K7ELM6_HUMAN,A8K3Y2_HUMAN	UPI000012F492	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TATAGGGCTTT	.	4	ESCA
TP53	0	.	GRCh37	17	7577105	7577105	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.833C>A	p.Pro278His	p.P278H	ENST00000269305	8/11	32	6	26	40	40	0	TP53,missense_variant,p.Pro278His,ENST00000420246,;TP53,missense_variant,p.Pro278His,ENST00000269305,;TP53,missense_variant,p.Pro146His,ENST00000509690,;TP53,missense_variant,p.Pro278His,ENST00000359597,;TP53,missense_variant,p.Pro278His,ENST00000445888,;TP53,missense_variant,p.Pro278His,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1023	833	278	P/H	cCt/cAt	CM961376,TP53_g.13813C>A,TP53_g.13813C>G,TP53_g.13813del,TP53_g.13813C>T,COSM10863,COSM10887,COSM44871,COSM43755,COSM129831,COSM300205,COSM333585,COSM1727548,COSM3773296,COSM3378341,COSM3388170,COSM1646811,COSM1646812,COSM1649338,COSM1727549	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P278H|c.833C>A|15,SITE|p.P278H|c.833C>A|3,CODON|p.0?|c.1_1182del1182|6,CODON|p.P278fs*67|c.833delC|3,CODON|p.P278F|c.832_833CC>TT|3,CODON|p.P278R|c.833C>G|5,CODON|p.P278R|c.833C>G|30,CODON|p.P278R|c.833C>G|3,CODON|p.P278L|c.833C>T|3,CODON|p.P278L|c.833C>T|11,CODON|p.P278L|c.833C>T|65,CODON|p.P278L|c.833C>T|8,CODON|p.P278fs*67|c.832delC|3,BUFFER|p.R282W|c.843_844CC>TT|10,BUFFER|p.R282G|c.844C>G|5,BUFFER|p.R282W|c.844C>T|49,BUFFER|p.R282G|c.844C>G|3,BUFFER|p.R282R|c.844C>A|3,BUFFER|p.R282W|c.844C>T|86,BUFFER|p.R282G|c.844C>G|29,BUFFER|p.R282W|c.844C>T|450,BUFFER|p.R282W|c.844C>T|58,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12,BUFFER|p.D281V|c.842A>T|5,BUFFER|p.D281G|c.842A>G|10,BUFFER|p.D281H|c.841G>C|6,BUFFER|p.D281H|c.841G>C|28,BUFFER|p.D281H|c.841G>C|3,BUFFER|p.D281H|c.841G>C|4,BUFFER|p.D281Y|c.841G>T|7,BUFFER|p.D281N|c.841G>A|7,BUFFER|p.D281N|c.841G>A|3,BUFFER|p.D281Y|c.841G>T|13,BUFFER|p.D281Y|c.841G>T|4,BUFFER|p.D281N|c.841G>A|27,BUFFER|p.R280R|c.840A>G|3,BUFFER|p.R280S|c.840A>T|11,BUFFER|p.R280S|c.840A>C|6,BUFFER|p.R280T|c.839G>C|63,BUFFER|p.R280T|c.839G>C|4,BUFFER|p.R280I|c.839G>T|17,BUFFER|p.R280K|c.839G>A|17,BUFFER|p.R280K|c.839G>A|6,BUFFER|p.R280I|c.839G>T|4,BUFFER|p.R280K|c.839G>A|57,BUFFER|p.R280I|c.839G>T|3,BUFFER|p.R280T|c.839G>C|10,BUFFER|p.R280K|c.839G>A|11,BUFFER|p.R280*|c.838A>T|12,BUFFER|p.R280G|c.838A>G|6,BUFFER|p.R280G|c.838A>G|3,BUFFER|p.R280G|c.838A>G|23,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279E|c.836G>A|4,BUFFER|p.G279E|c.836G>A|34,BUFFER|p.G279V|c.836G>T|3,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278T|c.832C>A|29,BUFFER|p.P278A|c.832C>G|25,BUFFER|p.P278T|c.832C>A|8,BUFFER|p.P278A|c.832C>G|4,BUFFER|p.P278A|c.832C>G|10,BUFFER|p.P278S|c.832C>T|4,BUFFER|p.P278S|c.832C>T|3,BUFFER|p.P278S|c.832C>T|8,BUFFER|p.P278S|c.832C>T|55,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCAGGACAG	.	5	ESCA
DSEL	0	.	GRCh37	18	65181701	65181701	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175G>C	p.Asp59His	p.D59H	ENST00000310045	2/2	21	16	4	26	26	0	DSEL,missense_variant,p.Asp59His,ENST00000310045,;RP11-638L3.1,upstream_gene_variant,,ENST00000583687,;CTD-2541J13.2,downstream_gene_variant,,ENST00000583493,;CTD-2541J13.2,downstream_gene_variant,,ENST00000581951,;	G	ENSG00000171451	ENST00000310045	Transcript	missense_variant	1649	175	59	D/H	Gat/Cat	.	.	.	-1	DSEL	HGNC	18144	protein_coding	YES	CCDS11995.1	ENSP00000310565	DSEL_HUMAN	.	UPI00000740A1	.	deleterious_low_confidence(0.04)	possibly_damaging(0.621)	2/2	.	hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATCTTGCA	.	5	ESCA
ZNF833P	0	.	GRCh37	19	11759238	11759238	+	RNA	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.357G>A	.	.	ENST00000344893	4/10	62	27	34	145	145	0	ZNF833P,non_coding_transcript_exon_variant,,ENST00000344893,;CTD-2006C1.6,non_coding_transcript_exon_variant,,ENST00000431363,;	A	ENSG00000197332	ENST00000344893	Transcript	non_coding_transcript_exon_variant	357	.	.	.	.	.	.	.	1	ZNF833P	HGNC	33819	lincRNA	YES	.	.	.	.	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCCGTCCCA	.	5	ESCA
PIK3R2	0	.	GRCh37	19	18280366	18280366	+	3'UTR	SNP	C	C	T	rs771945095	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*262C>T	.	.	ENST00000222254	16/16	57	47	10	63	63	0	PIK3R2,3_prime_UTR_variant,,ENST00000222254,;IFI30,upstream_gene_variant,,ENST00000407280,;IFI30,upstream_gene_variant,,ENST00000597802,;PIK3R2,3_prime_UTR_variant,,ENST00000593731,;PIK3R2,3_prime_UTR_variant,,ENST00000426902,;IFI30,upstream_gene_variant,,ENST00000600463,;PIK3R2,downstream_gene_variant,,ENST00000459743,;PIK3R2,downstream_gene_variant,,ENST00000464016,;	T	ENSG00000105647	ENST00000222254	Transcript	3_prime_UTR_variant	3049	.	.	.	.	rs771945095	.	.	1	PIK3R2	HGNC	8980	protein_coding	YES	CCDS12371.1	ENSP00000222254	P85B_HUMAN	Q96CK7_HUMAN,M0QYU3_HUMAN	UPI000006EF95	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTACGTGTC	.	4	ESCA
HAUS5	0	.	GRCh37	19	36111189	36111189	+	Silent	SNP	C	C	A	rs746696536	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1611C>A	p.%3D	p.L537L	ENST00000203166	17/19	54	33	21	74	74	0	HAUS5,synonymous_variant,p.%3D,ENST00000203166,;HAUS5,synonymous_variant,p.%3D,ENST00000590994,;HAUS5,3_prime_UTR_variant,,ENST00000379045,;HAUS5,3_prime_UTR_variant,,ENST00000587439,;HAUS5,3_prime_UTR_variant,,ENST00000424522,;HAUS5,non_coding_transcript_exon_variant,,ENST00000428854,;HAUS5,non_coding_transcript_exon_variant,,ENST00000430749,;HAUS5,non_coding_transcript_exon_variant,,ENST00000585968,;HAUS5,downstream_gene_variant,,ENST00000592291,;	A	ENSG00000249115	ENST00000203166	Transcript	synonymous_variant	1636	1611	537	L	ctC/ctA	rs746696536	.	.	1	HAUS5	HGNC	29130	protein_coding	YES	CCDS42550.1	ENSP00000439056	HAUS5_HUMAN	.	UPI0000169F45	.	.	.	17/19	.	Pfam_domain:PF14817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACTCCACAT	.	5	ESCA
ZNF540	0	.	GRCh37	19	38039849	38039849	+	5'Flank	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000592533	.	95	90	5	76	76	0	ZNF540,upstream_gene_variant,,ENST00000592533,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000585578,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000592575,;CTD-3064H18.4,non_coding_transcript_exon_variant,,ENST00000316807,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000591430,;ZNF571-AS1,upstream_gene_variant,,ENST00000586013,;ZNF571-AS1,upstream_gene_variant,,ENST00000590838,;ZNF571-AS1,upstream_gene_variant,,ENST00000586139,;ZNF571-AS1,upstream_gene_variant,,ENST00000589802,;ZNF571-AS1,upstream_gene_variant,,ENST00000588382,;ZNF571-AS1,upstream_gene_variant,,ENST00000592392,;ZNF571-AS1,upstream_gene_variant,,ENST00000589750,;ZNF571-AS1,upstream_gene_variant,,ENST00000587121,;ZNF793,downstream_gene_variant,,ENST00000586187,;	A	ENSG00000171817	ENST00000592533	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2459	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGCGTCTGT	.	2	ESCA
KCNA7	0	.	GRCh37	19	49574060	49574060	+	Missense_Mutation	SNP	C	C	T	rs531366512	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Val211Met	p.V211M	ENST00000221444	2/2	67	43	24	60	60	0	KCNA7,missense_variant,p.Val211Met,ENST00000221444,;	T	ENSG00000104848	ENST00000221444	Transcript	missense_variant	987	631	211	V/M	Gtg/Atg	rs531366512,COSM999203	.	.	-1	KCNA7	HGNC	6226	protein_coding	YES	CCDS12755.1	ENSP00000221444	KCNA7_HUMAN	.	UPI000004F638	.	tolerated(0.26)	benign(0.037)	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11537:SF19,hmmpanther:PTHR11537,Gene3D:1.20.120.350,Superfamily_domains:SSF81324,Prints_domain:PR00169	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCACGAAGA	by1000G	5	ESCA
PNKP	0	.	GRCh37	19	50367621	50367621	+	Missense_Mutation	SNP	G	G	A	rs3739185	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538C>T	p.Arg180Cys	p.R180C	ENST00000322344	5/17	39	33	6	34	34	0	PNKP,missense_variant,p.Arg180Cys,ENST00000600910,;PNKP,missense_variant,p.Arg180Cys,ENST00000596014,;PNKP,missense_variant,p.Arg180Cys,ENST00000600573,;PNKP,missense_variant,p.Arg180Cys,ENST00000322344,;PTOV1,downstream_gene_variant,,ENST00000601675,;PNKP,upstream_gene_variant,,ENST00000597965,;AKT1S1,downstream_gene_variant,,ENST00000391835,;AKT1S1,downstream_gene_variant,,ENST00000391832,;PTOV1,downstream_gene_variant,,ENST00000599732,;AKT1S1,downstream_gene_variant,,ENST00000344175,;AKT1S1,downstream_gene_variant,,ENST00000391831,;PTOV1,downstream_gene_variant,,ENST00000600603,;PNKP,downstream_gene_variant,,ENST00000599543,;PTOV1,downstream_gene_variant,,ENST00000391842,;PTOV1,downstream_gene_variant,,ENST00000597730,;PTOV1,downstream_gene_variant,,ENST00000601638,;PNKP,downstream_gene_variant,,ENST00000596726,;PTOV1,downstream_gene_variant,,ENST00000601093,;PTOV1,downstream_gene_variant,,ENST00000221557,;AKT1S1,downstream_gene_variant,,ENST00000391833,;AKT1S1,downstream_gene_variant,,ENST00000391834,;AC018766.4,upstream_gene_variant,,ENST00000596624,;PTOV1,downstream_gene_variant,,ENST00000598325,;PNKP,downstream_gene_variant,,ENST00000595792,;PNKP,3_prime_UTR_variant,,ENST00000593946,;PNKP,non_coding_transcript_exon_variant,,ENST00000594661,;PTOV1,downstream_gene_variant,,ENST00000597793,;PNKP,upstream_gene_variant,,ENST00000599454,;PNKP,upstream_gene_variant,,ENST00000595081,;PNKP,upstream_gene_variant,,ENST00000593706,;PTOV1,downstream_gene_variant,,ENST00000601612,;PNKP,upstream_gene_variant,,ENST00000601816,;PNKP,downstream_gene_variant,,ENST00000598020,;	A	ENSG00000039650	ENST00000322344	Transcript	missense_variant	648	538	180	R/C	Cgc/Tgc	rs3739185	.	.	-1	PNKP	HGNC	9154	protein_coding	YES	CCDS12783.1	ENSP00000323511	PNKP_HUMAN	M0R000_HUMAN,M0QYI1_HUMAN	UPI00000705EA	.	deleterious(0)	possibly_damaging(0.887)	5/17	.	hmmpanther:PTHR12083:SF9,hmmpanther:PTHR12083,TIGRFAM_domain:TIGR01663,TIGRFAM_domain:TIGR01662,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01664,Pfam_domain:PF08645,Superfamily_domains:SSF56784	T:0.0030	T:0.0113	T:0	.	T:0	T:0	T:0	T:0.0127	T:0	benign	.	17055652	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE|VARSCANS	AGAGCGTGTGG	byFrequency|byCluster|byHapMap|by1000G	3	ESCA
ATAD3C	0	.	GRCh37	1	1391664	1391664	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624C>A	p.%3D	p.P208P	ENST00000378785	7/12	27	19	8	42	42	0	ATAD3C,synonymous_variant,p.%3D,ENST00000378785,;ATAD3C,downstream_gene_variant,,ENST00000475091,;	A	ENSG00000215915	ENST00000378785	Transcript	synonymous_variant	1619	624	208	P	ccC/ccA	.	.	.	1	ATAD3C	HGNC	32151	protein_coding	YES	CCDS44039.1	ENSP00000368062	ATD3C_HUMAN	.	UPI00001619C0	.	.	.	7/12	.	hmmpanther:PTHR23075,hmmpanther:PTHR23075:SF5,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GCCCCCATGGG	.	2	ESCA
FCRL3	0	.	GRCh37	1	157648385	157648385	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*115G>A	.	.	ENST00000368184	15/15	20	14	6	20	20	0	FCRL3,3_prime_UTR_variant,,ENST00000368184,;FCRL3,intron_variant,,ENST00000368186,;FCRL3,splice_region_variant,,ENST00000494724,;FCRL3,splice_region_variant,,ENST00000480682,;FCRL3,non_coding_transcript_exon_variant,,ENST00000473231,;FCRL3,upstream_gene_variant,,ENST00000457799,;FCRL3,downstream_gene_variant,,ENST00000468507,;FCRL3,splice_region_variant,,ENST00000485028,;FCRL3,splice_region_variant,,ENST00000477837,;FCRL3,splice_region_variant,,ENST00000492769,;	T	ENSG00000160856	ENST00000368184	Transcript	3_prime_UTR_variant	2612	.	.	.	.	.	.	.	-1	FCRL3	HGNC	18506	protein_coding	YES	CCDS1167.1	ENSP00000357167	FCRL3_HUMAN	R4GNJ6_HUMAN	UPI000006D60E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATACCCTGCA	.	2	ESCA
DCAF6	0	.	GRCh37	1	167944174	167944174	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359T>A	p.Ile120Lys	p.I120K	ENST00000367840	4/22	118	113	5	107	107	0	DCAF6,missense_variant,p.Ile120Lys,ENST00000367840,;DCAF6,missense_variant,p.Ile120Lys,ENST00000312263,;DCAF6,missense_variant,p.Ile89Lys,ENST00000432587,;DCAF6,missense_variant,p.Ile120Lys,ENST00000367843,;DCAF6,non_coding_transcript_exon_variant,,ENST00000470919,;DCAF6,non_coding_transcript_exon_variant,,ENST00000491067,;DCAF6,non_coding_transcript_exon_variant,,ENST00000455334,;DCAF6,non_coding_transcript_exon_variant,,ENST00000450548,;DCAF6,missense_variant,p.Ile120Lys,ENST00000470721,;	A	ENSG00000143164	ENST00000367840	Transcript	missense_variant	453	359	120	I/K	aTa/aAa	.	.	.	1	DCAF6	HGNC	30002	protein_coding	YES	CCDS55657.1	ENSP00000356814	DCAF6_HUMAN	.	UPI00000743AB	.	deleterious(0)	probably_damaging(0.996)	4/22	.	PROSITE_profiles:PS50294,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF11,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTAATATTTT	.	2	ESCA
CACNA1E	0	.	GRCh37	1	181693605	181693605	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2075-1G>T	.	p.X692_splice	ENST00000367573	.	139	72	67	94	94	0	CACNA1E,splice_acceptor_variant,,ENST00000358338,;CACNA1E,splice_acceptor_variant,,ENST00000367567,;CACNA1E,splice_acceptor_variant,,ENST00000357570,;CACNA1E,splice_acceptor_variant,,ENST00000360108,;CACNA1E,splice_acceptor_variant,,ENST00000526775,;CACNA1E,splice_acceptor_variant,,ENST00000367573,;CACNA1E,splice_acceptor_variant,,ENST00000367570,;	T	ENSG00000198216	ENST00000367573	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	CACNA1E	HGNC	1392	protein_coding	YES	CCDS55664.1	ENSP00000356545	CAC1E_HUMAN	Q9UN68_HUMAN,Q9NYZ6_HUMAN,Q9NY05_HUMAN,E9PIE8_HUMAN	UPI00004588C2	.	.	.	.	16/47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCAGACACG	.	5	ESCA
CACNA1E	0	.	GRCh37	1	181727944	181727944	+	Silent	SNP	C	C	T	rs182225778	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4545C>T	p.%3D	p.I1515I	ENST00000367573	32/48	247	137	110	188	188	0	CACNA1E,synonymous_variant,p.%3D,ENST00000358338,;CACNA1E,synonymous_variant,p.%3D,ENST00000367567,;CACNA1E,synonymous_variant,p.%3D,ENST00000357570,;CACNA1E,synonymous_variant,p.%3D,ENST00000360108,;CACNA1E,synonymous_variant,p.%3D,ENST00000526775,;CACNA1E,synonymous_variant,p.%3D,ENST00000367573,;CACNA1E,synonymous_variant,p.%3D,ENST00000367570,;	T	ENSG00000198216	ENST00000367573	Transcript	synonymous_variant	4545	4545	1515	I	atC/atT	rs182225778,COSM3479720,COSM3479721,COSM3479719	.	.	1	CACNA1E	HGNC	1392	protein_coding	YES	CCDS55664.1	ENSP00000356545	CAC1E_HUMAN	Q9UN68_HUMAN,Q9NYZ6_HUMAN,Q9NY05_HUMAN,E9PIE8_HUMAN	UPI00004588C2	.	.	.	32/48	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,Gene3D:1.20.120.350,hmmpanther:PTHR10037:SF57,hmmpanther:PTHR10037,Transmembrane_helices:TMhelix	T:0.0006	T:0.0023	T:0	.	T:0	T:0	T:0	T:0.0023	T:0	.	0,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATCGCCTT	byFrequency|byCluster|by1000G	5	ESCA
PHLDA3	0	.	GRCh37	1	201434889	201434902	+	3'UTR	DEL	CCTGGGTACCAGGC	CCTGGGTACCAGGC	-	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	CCTGGGTACCAGGC	CCTGGGTACCAGGC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*467_*480delGCCTGGTACCCAGG	.	.	ENST00000367311	2/2	65	57	8	47	47	0	PHLDA3,3_prime_UTR_variant,,ENST00000367311,;PHLDA3,downstream_gene_variant,,ENST00000367309,;RP11-134G8.8,upstream_gene_variant,,ENST00000430471,;PHLDA3,downstream_gene_variant,,ENST00000497057,;PHLDA3,downstream_gene_variant,,ENST00000485436,;	-	ENSG00000174307	ENST00000367311	Transcript	3_prime_UTR_variant	1249-1262	.	.	.	.	.	.	.	-1	PHLDA3	HGNC	8934	protein_coding	YES	CCDS1412.1	ENSP00000356280	PHLA3_HUMAN	.	UPI00000716DA	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGTGGGCCTGGGTACCAGGCCCTGG	.	2	ESCA
HSPG2	0	.	GRCh37	1	22169271	22169271	+	Missense_Mutation	SNP	G	G	C	rs759625593	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8902C>G	p.Arg2968Gly	p.R2968G	ENST00000374695	67/97	95	77	17	92	92	0	HSPG2,missense_variant,p.Arg2968Gly,ENST00000374695,;HSPG2,downstream_gene_variant,,ENST00000453796,;HSPG2,downstream_gene_variant,,ENST00000430507,;HSPG2,upstream_gene_variant,,ENST00000374676,;	C	ENSG00000142798	ENST00000374695	Transcript	missense_variant	8982	8902	2968	R/G	Cgg/Ggg	rs759625593	.	.	-1	HSPG2	HGNC	5273	protein_coding	YES	CCDS30625.1	ENSP00000363827	PGBM_HUMAN	B6EU51_HUMAN	UPI0000212778	.	.	benign(0.326)	67/97	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF252,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCGGGCGG	.	5	ESCA
SUSD4	0	.	GRCh37	1	223408377	223408377	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725-5647C>T	.	.	ENST00000343846	.	31	9	21	50	50	0	SUSD4,missense_variant,p.Leu264Phe,ENST00000344029,;SUSD4,intron_variant,,ENST00000608996,;SUSD4,intron_variant,,ENST00000343846,;SUSD4,intron_variant,,ENST00000454695,;SUSD4,intron_variant,,ENST00000484758,;SUSD4,intron_variant,,ENST00000494793,;SUSD4,intron_variant,,ENST00000366878,;SUSD4,intron_variant,,ENST00000483818,;SUSD4,intron_variant,,ENST00000478605,;SUSD4,upstream_gene_variant,,ENST00000470249,;	A	ENSG00000143502	ENST00000343846	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SUSD4	HGNC	25470	protein_coding	YES	CCDS41471.1	ENSP00000344219	SUSD4_HUMAN	B7Z469_HUMAN	UPI0000205CB5	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAAGCACAG	.	5	ESCA
RP11-231P20.2	0	.	GRCh37	1	26551855	26551855	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1930+93G>A	.	.	ENST00000428812	.	12	5	7	12	12	0	RP11-231P20.2,non_coding_transcript_exon_variant,,ENST00000451482,;RP11-231P20.2,downstream_gene_variant,,ENST00000448341,;RP11-231P20.2,downstream_gene_variant,,ENST00000447201,;RP11-231P20.2,intron_variant,,ENST00000428812,;	A	ENSG00000236155	ENST00000428812	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RP11-231P20.2	Clone_based_vega_gene	.	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	5/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCGCCGTCTTC	.	3	ESCA
PCSK2	0	.	GRCh37	20	17465182	17465182	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2467G>T	.	.	ENST00000262545	12/12	36	25	11	14	14	0	PCSK2,3_prime_UTR_variant,,ENST00000262545,;PCSK2,3_prime_UTR_variant,,ENST00000377899,;PCSK2,downstream_gene_variant,,ENST00000536609,;PCSK2,downstream_gene_variant,,ENST00000459871,;	T	ENSG00000125851	ENST00000262545	Transcript	3_prime_UTR_variant	4699	.	.	.	.	.	.	.	1	PCSK2	HGNC	8744	protein_coding	YES	CCDS13125.1	ENSP00000262545	NEC2_HUMAN	Q9UM69_HUMAN	UPI0000000C6E	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTTGTAAAT	.	5	ESCA
SIGLEC1	0	.	GRCh37	20	3672113	3672113	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4465C>T	p.His1489Tyr	p.H1489Y	ENST00000344754	17/21	78	54	24	49	49	0	SIGLEC1,missense_variant,p.His1489Tyr,ENST00000344754,;SIGLEC1,missense_variant,p.His303Tyr,ENST00000419548,;SIGLEC1,missense_variant,p.His1489Tyr,ENST00000202578,;	A	ENSG00000088827	ENST00000344754	Transcript	missense_variant	4465	4465	1489	H/Y	Cac/Tac	.	.	.	-1	SIGLEC1	HGNC	11127	protein_coding	YES	CCDS13060.1	ENSP00000341141	SN_HUMAN	.	UPI0000049BA6	.	tolerated(0.61)	benign(0.008)	17/21	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF46,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGTGCAGCC	.	5	ESCA
KCNB1	0	.	GRCh37	20	48098775	48098775	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.243C>T	p.%3D	p.N81N	ENST00000371741	1/2	47	23	24	28	28	0	KCNB1,synonymous_variant,p.%3D,ENST00000371741,;	A	ENSG00000158445	ENST00000371741	Transcript	synonymous_variant	410	243	81	N	aaC/aaT	.	.	.	-1	KCNB1	HGNC	6231	protein_coding	YES	CCDS13418.1	ENSP00000360806	KCNB1_HUMAN	.	UPI000012DC80	.	.	.	1/2	.	Superfamily_domains:SSF54695,SMART_domains:SM00225,Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR11537:SF63,hmmpanther:PTHR11537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTCGTTGTC	.	5	ESCA
ZNF831	0	.	GRCh37	20	57766999	57766999	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.925G>A	p.Ala309Thr	p.A309T	ENST00000371030	1/5	65	57	8	31	31	0	ZNF831,missense_variant,p.Ala309Thr,ENST00000371030,;	A	ENSG00000124203	ENST00000371030	Transcript	missense_variant	925	925	309	A/T	Gcc/Acc	.	.	.	1	ZNF831	HGNC	16167	protein_coding	YES	CCDS42894.1	ENSP00000360069	ZN831_HUMAN	.	UPI00001D82E4	.	tolerated(0.1)	benign(0.006)	1/5	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGACCGCCGGG	.	2	ESCA
COL9A3	0	.	GRCh37	20	61472147	61472147	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63C>T	.	.	ENST00000343916	32/32	60	48	12	49	49	0	COL9A3,3_prime_UTR_variant,,ENST00000343916,;TCFL5,downstream_gene_variant,,ENST00000217162,;TCFL5,downstream_gene_variant,,ENST00000335351,;COL9A3,non_coding_transcript_exon_variant,,ENST00000467819,;COL9A3,non_coding_transcript_exon_variant,,ENST00000462700,;COL9A3,downstream_gene_variant,,ENST00000466532,;COL9A3,non_coding_transcript_exon_variant,,ENST00000466192,;COL9A3,downstream_gene_variant,,ENST00000472880,;COL9A3,downstream_gene_variant,,ENST00000481800,;COL9A3,downstream_gene_variant,,ENST00000469802,;COL9A3,downstream_gene_variant,,ENST00000469852,;COL9A3,downstream_gene_variant,,ENST00000490398,;DPH3P1,upstream_gene_variant,,ENST00000486648,;DPH3P1,upstream_gene_variant,,ENST00000502378,;	T	ENSG00000092758	ENST00000343916	Transcript	3_prime_UTR_variant	2121	.	.	.	.	.	.	.	1	COL9A3	HGNC	2219	protein_coding	YES	CCDS13505.1	ENSP00000341640	CO9A3_HUMAN	Q96IF4_HUMAN	UPI0000126D51	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGCGGGGG	.	5	ESCA
KRTAP13-2	0	.	GRCh37	21	31744251	31744251	+	Missense_Mutation	SNP	G	G	A	rs771266402	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281C>T	p.Thr94Met	p.T94M	ENST00000399889	1/1	79	54	25	97	97	0	KRTAP13-2,missense_variant,p.Thr94Met,ENST00000399889,;MIR4327,downstream_gene_variant,,ENST00000581194,;	A	ENSG00000182816	ENST00000399889	Transcript	missense_variant	307	281	94	T/M	aCg/aTg	rs771266402,COSM478482	.	.	-1	KRTAP13-2	HGNC	18923	protein_coding	YES	CCDS13589.1	ENSP00000382777	KR132_HUMAN	.	UPI000003B46A	.	tolerated(0.06)	benign(0.223)	1/1	.	Pfam_domain:PF05287,hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF17	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTCGTCTTG	.	5	ESCA
SON	0	.	GRCh37	21	34932448	34932448	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6657+367G>A	.	.	ENST00000356577	.	151	135	16	125	125	0	SON,3_prime_UTR_variant,,ENST00000300278,;SON,intron_variant,,ENST00000421541,;SON,intron_variant,,ENST00000381692,;SON,intron_variant,,ENST00000436227,;SON,intron_variant,,ENST00000290239,;SON,intron_variant,,ENST00000356577,;SON,downstream_gene_variant,,ENST00000381679,;DONSON,intron_variant,,ENST00000439593,;SON,intron_variant,,ENST00000455528,;	A	ENSG00000159140	ENST00000356577	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SON	HGNC	11183	protein_coding	YES	CCDS13629.1	ENSP00000348984	SON_HUMAN	.	UPI0000140BFD	.	.	.	.	6/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTATCGGGTGG	.	4	ESCA
SCUBE1	0	.	GRCh37	22	43617211	43617211	+	Missense_Mutation	SNP	C	C	T	rs140525929	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000360835	13/22	80	45	35	198	198	0	SCUBE1,missense_variant,p.Arg506Gln,ENST00000360835,;	T	ENSG00000159307	ENST00000360835	Transcript	missense_variant	1644	1517	506	R/Q	cGa/cAa	rs140525929	.	.	-1	SCUBE1	HGNC	13441	protein_coding	YES	CCDS14048.1	ENSP00000354080	SCUB1_HUMAN	.	UPI000020790F	.	tolerated(0.48)	benign(0.001)	13/22	.	hmmpanther:PTHR24046:SF4,hmmpanther:PTHR24046	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E509G|c.1526A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCTCGTGCC	byCluster	5	ESCA
MIOX	0	.	GRCh37	22	50927860	50927860	+	Missense_Mutation	SNP	C	C	A	rs555088706	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.621C>A	p.Phe207Leu	p.F207L	ENST00000216075	8/10	48	31	16	78	78	0	MIOX,missense_variant,p.Phe207Leu,ENST00000395732,;MIOX,missense_variant,p.Phe187Leu,ENST00000451761,;MIOX,missense_variant,p.Phe207Leu,ENST00000216075,;MIOX,intron_variant,,ENST00000395733,;ADM2,downstream_gene_variant,,ENST00000395738,;ADM2,downstream_gene_variant,,ENST00000362068,;	A	ENSG00000100253	ENST00000216075	Transcript	missense_variant	695	621	207	F/L	ttC/ttA	rs555088706	.	.	1	MIOX	HGNC	14522	protein_coding	YES	CCDS14092.1	ENSP00000216075	MIOX_HUMAN	.	UPI000012F148	.	tolerated(0.63)	benign(0.181)	8/10	.	hmmpanther:PTHR12588,Pfam_domain:PF05153,Superfamily_domains:SSF109604	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTTCTCACT	by1000G	5	ESCA
MARCO	0	.	GRCh37	2	119727700	119727700	+	Silent	SNP	G	G	T	rs765781526	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210G>T	p.%3D	p.L70L	ENST00000327097	3/17	15	11	4	16	16	0	MARCO,synonymous_variant,p.%3D,ENST00000327097,;MARCO,5_prime_UTR_variant,,ENST00000412481,;MARCO,5_prime_UTR_variant,,ENST00000541757,;	T	ENSG00000019169	ENST00000327097	Transcript	synonymous_variant	345	210	70	L	ctG/ctT	rs765781526,COSM1631259	.	.	1	MARCO	HGNC	6895	protein_coding	YES	CCDS2124.1	ENSP00000318916	MARCO_HUMAN	Q4ZG40_HUMAN,C9JKT8_HUMAN,B4DW79_HUMAN,B4DLJ6_HUMAN	UPI0000000DF8	.	.	.	3/17	.	hmmpanther:PTHR24021:SF16,hmmpanther:PTHR24021	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCTGCAGGC	.	5	ESCA
SCN1A	0	.	GRCh37	2	166847062	166847062	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*693G>T	.	.	ENST00000303395	26/26	32	15	17	22	22	0	SCN1A,3_prime_UTR_variant,,ENST00000423058,;SCN1A,3_prime_UTR_variant,,ENST00000303395,;SCN1A,3_prime_UTR_variant,,ENST00000375405,;SCN1A,downstream_gene_variant,,ENST00000409050,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000597623,;	A	ENSG00000144285	ENST00000303395	Transcript	3_prime_UTR_variant	6723	.	.	.	.	.	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTTCGCAAA	.	5	ESCA
ADAM23	0	.	GRCh37	2	207452839	207452839	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1813A>G	p.Lys605Glu	p.K605E	ENST00000264377	20/26	60	41	18	62	62	0	ADAM23,missense_variant,p.Lys605Glu,ENST00000374415,;ADAM23,missense_variant,p.Lys605Glu,ENST00000374416,;ADAM23,missense_variant,p.Lys605Glu,ENST00000264377,;	G	ENSG00000114948	ENST00000264377	Transcript	missense_variant	2141	1813	605	K/E	Aag/Gag	.	.	.	1	ADAM23	HGNC	202	protein_coding	YES	CCDS2369.1	ENSP00000264377	ADA23_HUMAN	Q53TK5_HUMAN,Q53TC0_HUMAN,Q53RX4_HUMAN	UPI0000044543	.	deleterious(0)	possibly_damaging(0.719)	20/26	.	SMART_domains:SM00608,Pfam_domain:PF08516,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCAAGACC	.	5	ESCA
COL4A4	0	.	GRCh37	2	227920748	227920748	+	Missense_Mutation	SNP	G	G	A	rs55948916	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2629C>T	p.Arg877Trp	p.R877W	ENST00000396625	30/48	60	41	19	52	52	0	COL4A4,missense_variant,p.Arg877Trp,ENST00000329662,;COL4A4,missense_variant,p.Arg877Trp,ENST00000396625,;	A	ENSG00000081052	ENST00000396625	Transcript	missense_variant	2837	2629	877	R/W	Cgg/Tgg	rs55948916	.	.	-1	COL4A4	HGNC	2206	protein_coding	YES	CCDS42828.1	ENSP00000379866	CO4A4_HUMAN	.	UPI000013D987	.	.	unknown(0)	30/48	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24021:SF5,hmmpanther:PTHR24021,Pfam_domain:PF01391	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0005	A:0.0004	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCCGTCCTG	byCluster|by1000G	5	ESCA
COPS8	0	.	GRCh37	2	238006331	238006331	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.576C>T	p.%3D	p.P192P	ENST00000354371	8/8	140	97	43	132	132	0	COPS8,synonymous_variant,p.%3D,ENST00000409334,;COPS8,synonymous_variant,p.%3D,ENST00000392008,;COPS8,synonymous_variant,p.%3D,ENST00000354371,;COPS8,synonymous_variant,p.%3D,ENST00000409629,;COPS8,synonymous_variant,p.%3D,ENST00000447464,;COPS8,non_coding_transcript_exon_variant,,ENST00000465362,;COPS8,downstream_gene_variant,,ENST00000470452,;COPS8,downstream_gene_variant,,ENST00000419015,;	T	ENSG00000198612	ENST00000354371	Transcript	synonymous_variant	1229	576	192	P	ccC/ccT	.	.	.	1	COPS8	HGNC	24335	protein_coding	YES	CCDS2517.1	ENSP00000346340	CSN8_HUMAN	.	UPI000006CD9B	.	.	.	8/8	.	hmmpanther:PTHR13339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACCCAATGA	.	5	ESCA
TRIM54	0	.	GRCh37	2	27529352	27529352	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1146C>T	p.%3D	p.A382A	ENST00000296098	9/10	93	70	22	89	89	0	TRIM54,synonymous_variant,p.%3D,ENST00000296098,;TRIM54,synonymous_variant,p.%3D,ENST00000380075,;MPV17,downstream_gene_variant,,ENST00000405076,;MPV17,downstream_gene_variant,,ENST00000380044,;UCN,downstream_gene_variant,,ENST00000296099,;MPV17,downstream_gene_variant,,ENST00000435114,;MPV17,downstream_gene_variant,,ENST00000402722,;MPV17,downstream_gene_variant,,ENST00000357186,;MPV17,downstream_gene_variant,,ENST00000233545,;MPV17,downstream_gene_variant,,ENST00000402310,;MPV17,downstream_gene_variant,,ENST00000430991,;MPV17,downstream_gene_variant,,ENST00000405983,;TRIM54,downstream_gene_variant,,ENST00000485306,;TRIM54,downstream_gene_variant,,ENST00000488321,;MPV17,downstream_gene_variant,,ENST00000426513,;MPV17,downstream_gene_variant,,ENST00000415514,;MPV17,downstream_gene_variant,,ENST00000489478,;	T	ENSG00000138100	ENST00000296098	Transcript	synonymous_variant	1416	1146	382	A	gcC/gcT	.	.	.	1	TRIM54	HGNC	16008	protein_coding	YES	CCDS1745.2	ENSP00000296098	TRI54_HUMAN	.	UPI000020814F	.	.	.	9/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCCCCAGA	.	5	ESCA
FAM98A	0	.	GRCh37	2	33809105	33809106	+	3'UTR	DEL	TT	TT	-	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*737_*738delAA	.	.	ENST00000238823	8/8	43	38	5	33	33	0	FAM98A,3_prime_UTR_variant,,ENST00000403368,;FAM98A,3_prime_UTR_variant,,ENST00000238823,;FAM98A,downstream_gene_variant,,ENST00000441530,;FAM98A,downstream_gene_variant,,ENST00000498340,;FAM98A,non_coding_transcript_exon_variant,,ENST00000474985,;FAM98A,downstream_gene_variant,,ENST00000492649,;FAM98A,downstream_gene_variant,,ENST00000475122,;	-	ENSG00000119812	ENST00000238823	Transcript	3_prime_UTR_variant	2435-2436	.	.	.	.	.	.	.	-1	FAM98A	HGNC	24520	protein_coding	YES	CCDS33179.1	ENSP00000238823	FA98A_HUMAN	C9J3G8_HUMAN,B4DT23_HUMAN	UPI000013F15A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GAGGAATTTGTTT	.	2	ESCA
PRKCE	0	.	GRCh37	2	46413592	46413592	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1572G>A	.	.	ENST00000306156	15/15	45	40	5	33	33	0	PRKCE,3_prime_UTR_variant,,ENST00000306156,;	A	ENSG00000171132	ENST00000306156	Transcript	3_prime_UTR_variant	4113	.	.	.	.	.	.	.	1	PRKCE	HGNC	9401	protein_coding	YES	CCDS1824.1	ENSP00000306124	KPCE_HUMAN	Q53RT0_HUMAN,L7RTI5_HUMAN,C9JR22_HUMAN	UPI000012DF6B	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGCATGTTCAG	.	3	ESCA
THNSL2	0	.	GRCh37	2	88474919	88474919	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570A>G	p.%3D	p.G190G	ENST00000324166	3/8	93	74	18	89	89	0	THNSL2,synonymous_variant,p.%3D,ENST00000377254,;THNSL2,synonymous_variant,p.%3D,ENST00000343544,;THNSL2,synonymous_variant,p.%3D,ENST00000402102,;THNSL2,synonymous_variant,p.%3D,ENST00000324166,;THNSL2,synonymous_variant,p.%3D,ENST00000358591,;THNSL2,synonymous_variant,p.%3D,ENST00000449349,;THNSL2,downstream_gene_variant,,ENST00000419759,;THNSL2,splice_region_variant,,ENST00000496844,;THNSL2,non_coding_transcript_exon_variant,,ENST00000475910,;THNSL2,upstream_gene_variant,,ENST00000476349,;	G	ENSG00000144115	ENST00000324166	Transcript	synonymous_variant	2261	570	190	G	ggA/ggG	.	.	.	1	THNSL2	HGNC	25602	protein_coding	YES	CCDS2002.2	ENSP00000327323	THNS2_HUMAN	C9J3J1_HUMAN	UPI00002088D9	.	.	.	3/8	.	hmmpanther:PTHR10314:SF89,hmmpanther:PTHR10314,Pfam_domain:PF00291,Gene3D:3.40.50.1100,TIGRFAM_domain:TIGR00260,Superfamily_domains:SSF53686	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGGAGGTGT	.	5	ESCA
LRRC15	0	.	GRCh37	3	194080470	194080470	+	Missense_Mutation	SNP	G	G	A	rs552954426	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1321C>T	p.Arg441Cys	p.R441C	ENST00000439944	2/2	57	44	13	41	41	0	LRRC15,missense_variant,p.Arg435Cys,ENST00000347624,;LRRC15,missense_variant,p.Arg441Cys,ENST00000439944,;LRRC15,missense_variant,p.Arg441Cys,ENST00000428839,;	A	ENSG00000172061	ENST00000439944	Transcript	missense_variant	1321	1321	441	R/C	Cgc/Tgc	rs552954426,COSM3591536,COSM3591535	.	.	-1	LRRC15	HGNC	20818	protein_coding	YES	CCDS46984.1	ENSP00000389128	LRC15_HUMAN	.	UPI000153D75D	.	deleterious(0)	possibly_damaging(0.847)	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24369:SF15,hmmpanther:PTHR24369,SMART_domains:SM00082,Superfamily_domains:SSF52058	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGCGGAGCG	by1000G	5	ESCA
ZNF654	0	.	GRCh37	3	88192469	88192469	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1667C>T	.	.	ENST00000309495	2/2	25	18	7	35	35	0	ZNF654,3_prime_UTR_variant,,ENST00000309495,;CGGBP1,intron_variant,,ENST00000462901,;CGGBP1,intron_variant,,ENST00000467332,;RP11-159G9.5,downstream_gene_variant,,ENST00000498458,;	T	ENSG00000175105	ENST00000309495	Transcript	3_prime_UTR_variant	3620	.	.	.	.	.	.	.	1	ZNF654	HGNC	25612	protein_coding	YES	CCDS46874.1	ENSP00000312141	ZN654_HUMAN	.	UPI0000DD0307	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTCTGTTA	.	5	ESCA
TLR10	0	.	GRCh37	4	38775539	38775539	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1673A>T	p.Asn558Ile	p.N558I	ENST00000308973	4/4	110	91	19	39	39	0	TLR10,missense_variant,p.Asn558Ile,ENST00000508334,;TLR10,missense_variant,p.Asn558Ile,ENST00000361424,;TLR10,missense_variant,p.Asn558Ile,ENST00000308973,;TLR10,missense_variant,p.Asn558Ile,ENST00000506111,;TLR10,downstream_gene_variant,,ENST00000502321,;TLR10,downstream_gene_variant,,ENST00000507953,;	A	ENSG00000174123	ENST00000308973	Transcript	missense_variant	2279	1673	558	N/I	aAc/aTc	.	.	.	-1	TLR10	HGNC	15634	protein_coding	YES	CCDS3445.1	ENSP00000308925	TLR10_HUMAN	D6RHW6_HUMAN	UPI0000048F1C	.	deleterious(0.04)	benign(0.235)	4/4	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF131,PIRSF_domain:PIRSF037595,SMART_domains:SM00082,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGGTTTAAA	.	5	ESCA
LIMCH1	0	.	GRCh37	4	41621228	41621228	+	Missense_Mutation	SNP	G	G	A	rs143218091	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.706G>A	p.Asp236Asn	p.D236N	ENST00000313860	8/27	58	53	5	43	43	0	LIMCH1,missense_variant,p.Asp236Asn,ENST00000512820,;LIMCH1,missense_variant,p.Asp77Asn,ENST00000503057,;LIMCH1,missense_variant,p.Asp77Asn,ENST00000509638,;LIMCH1,missense_variant,p.Asp236Asn,ENST00000508501,;LIMCH1,missense_variant,p.Asp71Asn,ENST00000508466,;LIMCH1,missense_variant,p.Asp77Asn,ENST00000511496,;LIMCH1,missense_variant,p.Asp82Asn,ENST00000381753,;LIMCH1,missense_variant,p.Asp236Asn,ENST00000512946,;LIMCH1,missense_variant,p.Asp236Asn,ENST00000512632,;LIMCH1,missense_variant,p.Asp84Asn,ENST00000509454,;LIMCH1,missense_variant,p.Asp77Asn,ENST00000446625,;LIMCH1,missense_variant,p.Asp236Asn,ENST00000313860,;LIMCH1,missense_variant,p.Asp77Asn,ENST00000513024,;LIMCH1,missense_variant,p.Asp89Asn,ENST00000514096,;LIMCH1,missense_variant,p.Asp82Asn,ENST00000396595,;LIMCH1,missense_variant,p.Asp82Asn,ENST00000509277,;	A	ENSG00000064042	ENST00000313860	Transcript	missense_variant	760	706	236	D/N	Gac/Aac	rs143218091	.	.	1	LIMCH1	HGNC	29191	protein_coding	YES	CCDS33977.1	ENSP00000316891	LIMC1_HUMAN	D6RJ93_HUMAN,D6RGH8_HUMAN,D6R8Y0_HUMAN	UPI0000D61554	.	deleterious(0)	probably_damaging(0.999)	8/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15551,hmmpanther:PTHR15551:SF3	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCCGACTTG	byCluster	2	ESCA
PDE6B	0	.	GRCh37	4	647448	647448	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712-193C>T	.	.	ENST00000496514	.	48	12	36	38	38	0	PDE6B,5_prime_UTR_variant,,ENST00000488061,;PDE6B,intron_variant,,ENST00000429163,;PDE6B,intron_variant,,ENST00000487902,;PDE6B,intron_variant,,ENST00000496514,;PDE6B,intron_variant,,ENST00000255622,;PDE6B,intron_variant,,ENST00000465426,;RP11-1191J2.2,non_coding_transcript_exon_variant,,ENST00000468356,;RP11-1191J2.2,intron_variant,,ENST00000599030,;RP11-1191J2.2,downstream_gene_variant,,ENST00000489312,;RP11-1191J2.2,upstream_gene_variant,,ENST00000598370,;PDE6B,intron_variant,,ENST00000474251,;PDE6B,intron_variant,,ENST00000476034,;PDE6B,intron_variant,,ENST00000467152,;	T	ENSG00000133256	ENST00000496514	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PDE6B	HGNC	8786	protein_coding	YES	CCDS33932.1	ENSP00000420295	PDE6B_HUMAN	H7C4P9_HUMAN,C9J628_HUMAN	UPI0000DBEE72	.	.	.	.	3/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCCGGGCC	.	5	ESCA
EPB41L4A	0	.	GRCh37	5	111481669	111481669	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1021G>A	.	.	ENST00000507810	13/14	81	55	26	85	85	0	EPB41L4A,non_coding_transcript_exon_variant,,ENST00000507810,;	T	ENSG00000129595	ENST00000507810	Transcript	non_coding_transcript_exon_variant	1021	.	.	.	.	.	.	.	-1	EPB41L4A	HGNC	13278	processed_transcript	.	.	.	.	.	.	.	.	.	13/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCCTTTCT	.	5	ESCA
IL3	0	.	GRCh37	5	131398418	131398418	+	Silent	SNP	G	G	A	rs750120195	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393G>A	p.%3D	p.T131T	ENST00000296870	5/5	44	36	8	40	40	0	IL3,synonymous_variant,p.%3D,ENST00000296870,;	A	ENSG00000164399	ENST00000296870	Transcript	synonymous_variant	571	393	131	T	acG/acA	rs750120195,COSM1433018	.	.	1	IL3	HGNC	6011	protein_coding	YES	CCDS4149.1	ENSP00000296870	IL3_HUMAN	.	UPI000002BEA8	.	.	.	5/5	.	hmmpanther:PTHR10079,Pfam_domain:PF02059,Gene3D:1.20.1250.10,PIRSF_domain:PIRSF001939,Superfamily_domains:SSF47266,Prints_domain:PR00430	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACGTTCTA	byFrequency	5	ESCA
DNAH5	0	.	GRCh37	5	13928260	13928260	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.220G>C	p.Val74Leu	p.V74L	ENST00000265104	3/79	36	29	6	30	30	0	DNAH5,missense_variant,p.Val74Leu,ENST00000265104,;DNAH5,non_coding_transcript_exon_variant,,ENST00000508040,;	G	ENSG00000039139	ENST00000265104	Transcript	missense_variant	325	220	74	V/L	Gtt/Ctt	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.001)	3/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAACAGCAA	.	5	ESCA
PCDHB4	0	.	GRCh37	5	140504087	140504087	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*119C>G	.	.	ENST00000194152	1/1	10	8	2	18	18	0	PCDHB4,3_prime_UTR_variant,,ENST00000194152,;AC005754.8,downstream_gene_variant,,ENST00000606030,;	G	ENSG00000081818	ENST00000194152	Transcript	3_prime_UTR_variant	2507	.	.	.	.	.	.	.	1	PCDHB4	HGNC	8689	protein_coding	YES	CCDS4246.1	ENSP00000194152	PCDB4_HUMAN	.	UPI00001273DF	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTACTCATGTC	.	2	ESCA
SLC36A3	0	.	GRCh37	5	150660711	150660711	+	Silent	SNP	G	G	A	rs748413637	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1131C>T	p.%3D	p.I377I	ENST00000377713	10/11	60	50	10	45	45	0	SLC36A3,synonymous_variant,p.%3D,ENST00000335230,;SLC36A3,synonymous_variant,p.%3D,ENST00000377713,;SLC36A3,non_coding_transcript_exon_variant,,ENST00000423071,;	A	ENSG00000186334	ENST00000377713	Transcript	synonymous_variant	1273	1131	377	I	atC/atT	rs748413637	.	.	-1	SLC36A3	HGNC	19659	protein_coding	YES	CCDS47316.1	ENSP00000366942	S36A3_HUMAN	.	UPI00005764D3	.	.	.	10/11	.	Pfam_domain:PF01490,hmmpanther:PTHR22950:SF203,hmmpanther:PTHR22950,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCCGATAGA	byFrequency	5	ESCA
FAM196B	0	.	GRCh37	5	169310673	169310673	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.230C>A	p.Pro77His	p.P77H	ENST00000377365	2/4	67	51	15	70	70	0	FAM196B,missense_variant,p.Pro77His,ENST00000377365,;DOCK2,intron_variant,,ENST00000540750,;DOCK2,intron_variant,,ENST00000256935,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,;	T	ENSG00000204767	ENST00000377365	Transcript	missense_variant	1612	230	77	P/H	cCc/cAc	.	.	.	-1	FAM196B	HGNC	37271	protein_coding	YES	CCDS47336.1	ENSP00000366582	F196B_HUMAN	.	UPI0000480500	.	deleterious(0.03)	possibly_damaging(0.875)	2/4	.	Pfam_domain:PF15265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTGGGGGGA	.	5	ESCA
C5orf60	0	.	GRCh37	5	179071806	179071806	+	Silent	SNP	G	G	A	rs772507674	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216C>T	p.%3D	p.S72S	ENST00000448248	1/6	109	87	21	127	127	0	C5orf60,synonymous_variant,p.%3D,ENST00000448248,;C5orf60,intron_variant,,ENST00000506142,;C5orf60,synonymous_variant,p.%3D,ENST00000513845,;C5orf60,synonymous_variant,p.%3D,ENST00000512899,;C5orf60,non_coding_transcript_exon_variant,,ENST00000503358,;C5orf60,non_coding_transcript_exon_variant,,ENST00000511063,;C5orf60,non_coding_transcript_exon_variant,,ENST00000513142,;C5orf60,non_coding_transcript_exon_variant,,ENST00000514664,;	A	ENSG00000204661	ENST00000448248	Transcript	synonymous_variant	242	216	72	S	agC/agT	rs772507674	.	.	-1	C5orf60	HGNC	27753	protein_coding	YES	CCDS47353.1	ENSP00000404583	CE060_HUMAN	.	UPI00004191D3	.	.	.	1/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCGCTGTC	byFrequency	5	ESCA
CDH10	0	.	GRCh37	5	24593471	24593471	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129G>T	p.Arg43Ser	p.R43S	ENST00000264463	2/12	60	46	14	44	44	0	CDH10,missense_variant,p.Arg43Ser,ENST00000264463,;RP11-116O11.1,intron_variant,,ENST00000510391,;CDH10,missense_variant,p.Arg43Ser,ENST00000510477,;	A	ENSG00000040731	ENST00000264463	Transcript	missense_variant	637	129	43	R/S	agG/agT	COSM3615265	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	tolerated(0.74)	benign(0.001)	2/12	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTCCTTGG	.	5	ESCA
CDH9	0	.	GRCh37	5	26881567	26881567	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2048G>C	p.Arg683Thr	p.R683T	ENST00000231021	12/12	70	54	16	57	57	0	CDH9,missense_variant,p.Arg683Thr,ENST00000231021,;CDH9,non_coding_transcript_exon_variant,,ENST00000505020,;	G	ENSG00000113100	ENST00000231021	Transcript	missense_variant	2221	2048	683	R/T	aGa/aCa	.	.	.	-1	CDH9	HGNC	1768	protein_coding	YES	CCDS3893.1	ENSP00000231021	CADH9_HUMAN	E7EPN0_HUMAN,D6RBT9_HUMAN	UPI000013C945	.	tolerated(0.5)	possibly_damaging(0.721)	12/12	.	Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF99	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCTTGCC	.	5	ESCA
PDZD2	0	.	GRCh37	5	32090983	32090983	+	Missense_Mutation	SNP	G	G	A	rs370676238	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7429G>A	p.Val2477Met	p.V2477M	ENST00000438447	20/25	46	36	9	28	28	0	PDZD2,missense_variant,p.Val2477Met,ENST00000438447,;PDZD2,missense_variant,p.Val2477Met,ENST00000282493,;	A	ENSG00000133401	ENST00000438447	Transcript	missense_variant	7817	7429	2477	V/M	Gtg/Atg	rs370676238	.	.	1	PDZD2	HGNC	18486	protein_coding	YES	CCDS34137.1	ENSP00000402033	PDZD2_HUMAN	B4DGS3_HUMAN	UPI000069648B	.	tolerated(0.06)	possibly_damaging(0.66)	20/25	.	hmmpanther:PTHR11324:SF16,hmmpanther:PTHR11324	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCCGTGTCC	byFrequency|byCluster	5	ESCA
RAB3C	0	.	GRCh37	5	57913496	57913496	+	Silent	SNP	C	C	T	rs554866418	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51C>T	p.%3D	p.Y17Y	ENST00000282878	2/5	27	15	12	27	27	0	RAB3C,synonymous_variant,p.%3D,ENST00000282878,;RAB3C,non_coding_transcript_exon_variant,,ENST00000513316,;	T	ENSG00000152932	ENST00000282878	Transcript	synonymous_variant	220	51	17	Y	taC/taT	rs554866418,COSM192796	.	.	1	RAB3C	HGNC	30269	protein_coding	YES	CCDS3976.1	ENSP00000282878	RAB3C_HUMAN	.	UPI0000133178	.	.	.	2/5	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTACGGCCA	by1000G	5	ESCA
RFX6	0	.	GRCh37	6	117252838	117252838	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*169G>T	.	.	ENST00000332958	19/19	20	12	8	18	18	0	RFX6,3_prime_UTR_variant,,ENST00000332958,;	T	ENSG00000185002	ENST00000332958	Transcript	3_prime_UTR_variant	2972	.	.	.	.	.	.	.	1	RFX6	HGNC	21478	protein_coding	YES	CCDS5113.1	ENSP00000332208	RFX6_HUMAN	.	UPI00001609BE	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTGCAGAG	.	5	ESCA
PLG	0	.	GRCh37	6	161139850	161139850	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076C>T	p.Thr359Met	p.T359M	ENST00000308192	9/19	48	33	14	52	52	0	PLG,missense_variant,p.Thr359Met,ENST00000308192,;PLG,intron_variant,,ENST00000297289,;	T	ENSG00000122194	ENST00000308192	Transcript	missense_variant	1139	1076	359	T/M	aCg/aTg	.	.	.	1	PLG	HGNC	9071	protein_coding	YES	CCDS5279.1	ENSP00000308938	PLMN_HUMAN	Q9UMI2_HUMAN,Q68DS2_HUMAN,Q5TEH5_HUMAN,B4DPH4_HUMAN	UPI000000D8B8	.	tolerated(0.17)	possibly_damaging(0.466)	9/19	.	hmmpanther:PTHR24259,hmmpanther:PTHR24259:SF70,PIRSF_domain:PIRSF001150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCACGGAAC	.	5	ESCA
HIST1H1A	0	.	GRCh37	6	26017957	26017968	+	Missense_Mutation	DEL	ACATGGTGACTA	ACATGGTGACTA	-	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	ACATGGTGACTA	ACATGGTGACTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-8_4delTAGTCACCATGT	.	.	ENST00000244573	1/1	45	33	12	61	61	0	HIST1H1A,coding_sequence_variant,,ENST00000244573,;HIST1H4A,upstream_gene_variant,,ENST00000359907,;HIST1H3A,upstream_gene_variant,,ENST00000357647,;U91328.22,downstream_gene_variant,,ENST00000608919,;HIST1H1PS2,downstream_gene_variant,,ENST00000437528,;	-	ENSG00000124610	ENST00000244573	Transcript	coding_sequence_variant	73-84	?-4	?-2	.	.	.	.	.	-1	HIST1H1A	HGNC	4715	protein_coding	YES	CCDS4569.1	ENSP00000244573	H11_HUMAN	.	UPI0000001BD8	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TTTCAGACATGGTGACTAACACA	.	2	ESCA
SRPK1	0	.	GRCh37	6	35837431	35837434	+	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	AGAG	AGAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1236_1239delCTCT	p.Ser413ValfsTer4	p.S413Vfs*4	ENST00000373825	11/16	81	55	26	94	94	0	SRPK1,frameshift_variant,p.Ser397ValfsTer4,ENST00000423325,;SRPK1,frameshift_variant,p.Ser429ValfsTer4,ENST00000361690,;SRPK1,frameshift_variant,p.Ser306ValfsTer4,ENST00000373822,;SRPK1,frameshift_variant,p.Ser413ValfsTer4,ENST00000373825,;SRPK1,downstream_gene_variant,,ENST00000510290,;SRPK1,downstream_gene_variant,,ENST00000373821,;SRPK1,non_coding_transcript_exon_variant,,ENST00000502969,;SRPK1,non_coding_transcript_exon_variant,,ENST00000346162,;SRPK1,upstream_gene_variant,,ENST00000507292,;	-	ENSG00000096063	ENST00000373825	Transcript	frameshift_variant	1522-1525	1236-1239	412-413	DS/X	gaCTCT/ga	.	.	.	-1	SRPK1	HGNC	11305	protein_coding	YES	CCDS47415.1	ENSP00000362931	SRPK1_HUMAN	D6RBF8_HUMAN	UPI000020DBDD	.	.	.	11/16	.	SMART_domains:SM00220,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF101,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTACAAGAGTCTGT	.	3	ESCA
EYS	0	.	GRCh37	6	66005908	66005908	+	Missense_Mutation	SNP	G	G	A	rs548565748	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1871C>T	p.Ser624Leu	p.S624L	ENST00000503581	12/43	41	31	10	53	53	0	EYS,missense_variant,p.Ser624Leu,ENST00000370616,;EYS,missense_variant,p.Ser624Leu,ENST00000370621,;EYS,missense_variant,p.Ser624Leu,ENST00000503581,;EYS,non_coding_transcript_exon_variant,,ENST00000447127,;EYS,non_coding_transcript_exon_variant,,ENST00000370615,;	A	ENSG00000188107	ENST00000503581	Transcript	missense_variant	2409	1871	624	S/L	tCg/tTg	rs548565748,COSM1081038	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	tolerated(1)	benign(0)	12/43	.	hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCGAAAGG	by1000G	5	ESCA
CPA1	0	.	GRCh37	7	130021558	130021558	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235C>G	p.Leu79Val	p.L79V	ENST00000011292	3/10	67	47	20	72	72	0	CPA1,missense_variant,p.Leu79Val,ENST00000011292,;CPA1,5_prime_UTR_variant,,ENST00000484324,;CPA1,5_prime_UTR_variant,,ENST00000476062,;CPA1,5_prime_UTR_variant,,ENST00000481342,;CPA1,intron_variant,,ENST00000604896,;CPA1,non_coding_transcript_exon_variant,,ENST00000491460,;CPA1,upstream_gene_variant,,ENST00000478096,;CPA1,upstream_gene_variant,,ENST00000479106,;CPA1,upstream_gene_variant,,ENST00000470838,;	G	ENSG00000091704	ENST00000011292	Transcript	missense_variant	385	235	79	L/V	Ctg/Gtg	.	.	.	1	CPA1	HGNC	2296	protein_coding	YES	CCDS5820.1	ENSP00000011292	CBPA1_HUMAN	C9JUZ4_HUMAN,C9JUF9_HUMAN,C9JQ63_HUMAN	UPI000004D332	.	deleterious(0)	probably_damaging(1)	3/10	.	Superfamily_domains:SSF54897,Gene3D:3.30.70.340,Pfam_domain:PF02244,hmmpanther:PTHR11705:SF15,hmmpanther:PTHR11705	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCTGGAG	.	5	ESCA
ZNF775	0	.	GRCh37	7	150095050	150095050	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1481G>T	p.Arg494Leu	p.R494L	ENST00000329630	3/3	28	11	16	27	27	0	ZNF775,missense_variant,p.Arg494Leu,ENST00000329630,;ZNF775,downstream_gene_variant,,ENST00000478789,;ZNF775,downstream_gene_variant,,ENST00000490973,;ZNF775,intron_variant,,ENST00000483664,;ZNF775,intron_variant,,ENST00000486297,;ZNF775,upstream_gene_variant,,ENST00000476489,;	T	ENSG00000196456	ENST00000329630	Transcript	missense_variant	1588	1481	494	R/L	cGc/cTc	.	.	.	1	ZNF775	HGNC	28501	protein_coding	YES	CCDS43678.1	ENSP00000330838	ZN775_HUMAN	C9JVG2_HUMAN,C9JAM7_HUMAN	UPI00001BDA25	.	deleterious(0)	probably_damaging(0.999)	3/3	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24409,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGCGCAACC	.	5	ESCA
EGFR	0	.	GRCh37	7	55273280	55273280	+	Silent	SNP	G	G	A	rs202156403	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3603G>A	p.%3D	p.A1201A	ENST00000275493	28/28	50	38	12	38	38	0	EGFR,synonymous_variant,p.%3D,ENST00000454757,;EGFR,synonymous_variant,p.%3D,ENST00000275493,;EGFR,intron_variant,,ENST00000442591,;EGFR,downstream_gene_variant,,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000485503,;	A	ENSG00000146648	ENST00000275493	Transcript	synonymous_variant	3780	3603	1201	A	gcG/gcA	rs202156403,COSM82120	.	.	1	EGFR	HGNC	3236	protein_coding	YES	CCDS5514.1	ENSP00000275493	EGFR_HUMAN	Q75MF2_HUMAN,I3WA73_HUMAN,I3WA72_HUMAN,G9MC81_HUMAN,F1JTL6_HUMAN,E9PFD7_HUMAN,C9JYS6_HUMAN,A7VN06_HUMAN	UPI000003E750	.	.	.	28/28	.	PIRSF_domain:PIRSF000619	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCGCGCCACA	byCluster	5	ESCA
TYW1	0	.	GRCh37	7	66461866	66461866	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-100C>T	.	.	ENST00000359626	1/16	61	48	13	67	67	0	TYW1,5_prime_UTR_variant,,ENST00000442959,;TYW1,5_prime_UTR_variant,,ENST00000359626,;SBDS,upstream_gene_variant,,ENST00000246868,;TYW1,intron_variant,,ENST00000491969,;TYW1,5_prime_UTR_variant,,ENST00000361660,;TYW1,non_coding_transcript_exon_variant,,ENST00000475392,;SBDS,upstream_gene_variant,,ENST00000490953,;SBDS,upstream_gene_variant,,ENST00000414306,;SBDS,upstream_gene_variant,,ENST00000463579,;	T	ENSG00000198874	ENST00000359626	Transcript	5_prime_UTR_variant	65	.	.	.	.	.	.	.	1	TYW1	HGNC	25598	protein_coding	YES	CCDS5538.1	ENSP00000352645	TYW1_HUMAN	B4DW16_HUMAN	UPI00003674A9	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACGCCGCTAA	.	5	ESCA
ZNF804B	0	.	GRCh37	7	88962883	88962883	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.587G>A	p.Arg196His	p.R196H	ENST00000333190	4/4	21	11	10	19	19	0	ZNF804B,missense_variant,p.Arg196His,ENST00000333190,;	A	ENSG00000182348	ENST00000333190	Transcript	missense_variant	1196	587	196	R/H	cGt/cAt	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	tolerated(0.68)	benign(0.022)	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGCGTTGTT	.	5	ESCA
DLX5	0	.	GRCh37	7	96649859	96649859	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*189G>A	.	.	ENST00000222598	3/3	40	32	7	44	44	0	DLX5,3_prime_UTR_variant,,ENST00000222598,;DLX5,downstream_gene_variant,,ENST00000486603,;DLX5,downstream_gene_variant,,ENST00000493764,;	T	ENSG00000105880	ENST00000222598	Transcript	3_prime_UTR_variant	1533	.	.	.	.	.	.	.	-1	DLX5	HGNC	2918	protein_coding	YES	CCDS5647.1	ENSP00000222598	DLX5_HUMAN	Q53Y73_HUMAN	UPI00001294B7	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTGCGCAAA	.	5	ESCA
DERL1	0	.	GRCh37	8	124027675	124027675	+	3'UTR	SNP	G	G	A	rs200496042	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*12C>T	.	.	ENST00000259512	8/8	46	33	12	45	45	0	DERL1,3_prime_UTR_variant,,ENST00000259512,;DERL1,3_prime_UTR_variant,,ENST00000419562,;DERL1,3_prime_UTR_variant,,ENST00000405944,;DERL1,downstream_gene_variant,,ENST00000519018,;DERL1,downstream_gene_variant,,ENST00000523036,;RP11-557C18.3,intron_variant,,ENST00000521258,;DERL1,non_coding_transcript_exon_variant,,ENST00000524119,;	A	ENSG00000136986	ENST00000259512	Transcript	3_prime_UTR_variant	1069	.	.	.	.	rs200496042	.	.	-1	DERL1	HGNC	28454	protein_coding	YES	CCDS6337.1	ENSP00000259512	DERL1_HUMAN	E5RGY0_HUMAN	UPI0000048EAA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	A:0	A:0.0003	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCCGAGGCC	byCluster	5	ESCA
ADAM28	0	.	GRCh37	8	24193159	24193159	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1567+5G>A	.	.	ENST00000265769	.	87	30	56	79	79	0	ADAM28,synonymous_variant,p.%3D,ENST00000437154,;ADAM28,synonymous_variant,p.%3D,ENST00000540823,;ADAM28,splice_region_variant,,ENST00000521629,;ADAM28,splice_region_variant,,ENST00000397649,;ADAM28,splice_region_variant,,ENST00000265769,;RP11-624C23.1,intron_variant,,ENST00000518988,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,;RP11-624C23.1,intron_variant,,ENST00000523700,;ADAM28,downstream_gene_variant,,ENST00000521110,;ADAM28,downstream_gene_variant,,ENST00000518516,;ADAM28,splice_region_variant,,ENST00000520448,;	A	ENSG00000042980	ENST00000265769	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	ADAM28	HGNC	206	protein_coding	YES	CCDS34865.1	ENSP00000265769	ADA28_HUMAN	E5RGY1_HUMAN	UPI000049E0B9	.	.	.	.	14/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAGGAGGAC	.	5	ESCA
CSMD1	0	.	GRCh37	8	2820079	2820079	+	Silent	SNP	G	G	A	rs752713861	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9537C>T	p.%3D	p.F3179F	ENST00000537824	61/70	31	23	8	44	44	0	CSMD1,synonymous_variant,p.%3D,ENST00000400186,;CSMD1,synonymous_variant,p.%3D,ENST00000542608,;CSMD1,synonymous_variant,p.%3D,ENST00000602723,;CSMD1,synonymous_variant,p.%3D,ENST00000335551,;CSMD1,synonymous_variant,p.%3D,ENST00000537824,;CSMD1,synonymous_variant,p.%3D,ENST00000602557,;CSMD1,synonymous_variant,p.%3D,ENST00000520002,;	A	ENSG00000183117	ENST00000537824	Transcript	synonymous_variant	9537	9537	3179	F	ttC/ttT	rs752713861	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	.	61/70	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF323,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGGAAGAA	.	5	ESCA
HNF4G	0	.	GRCh37	8	76471212	76471212	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1033T>C	p.Phe345Leu	p.F345L	ENST00000396423	8/10	28	23	5	44	44	0	HNF4G,missense_variant,p.Phe345Leu,ENST00000396423,;HNF4G,missense_variant,p.Phe308Leu,ENST00000354370,;	C	ENSG00000164749	ENST00000396423	Transcript	missense_variant	1157	1033	345	F/L	Ttt/Ctt	.	.	.	1	HNF4G	HGNC	5026	protein_coding	YES	CCDS6220.2	ENSP00000379701	HNF4G_HUMAN	F1D8Q4_HUMAN	UPI0000D47E07	.	tolerated(0.38)	benign(0.007)	8/10	.	hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Pfam_domain:PF00104,Superfamily_domains:SSF48508	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAGTTTGTT	.	5	ESCA
ZNF704	0	.	GRCh37	8	81552479	81552480	+	3'UTR	DEL	TA	TA	C	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1121_*1122delTAinsG	.	.	ENST00000327835	9/9	59	44	15	76	76	0	ZNF704,3_prime_UTR_variant,,ENST00000327835,;ZNF704,intron_variant,,ENST00000517379,;CKS1BP7,downstream_gene_variant,,ENST00000522230,;	C	ENSG00000164684	ENST00000327835	Transcript	3_prime_UTR_variant	2592-2593	.	.	.	.	.	.	.	-1	ZNF704	HGNC	32291	protein_coding	YES	CCDS34913.1	ENSP00000331462	ZN704_HUMAN	E5RGL7_HUMAN	UPI000035E754	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|SOMATICSNIPER*	ACATGCTAAAGCA	.	4	ESCA
NOTCH1	0	.	GRCh37	9	139413231	139413231	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.911delA	p.Asn304MetfsTer327	p.N304Mfs*327	ENST00000277541	6/34	140	57	83	87	87	0	NOTCH1,frameshift_variant,p.Asn304MetfsTer327,ENST00000277541,;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,;	-	ENSG00000148400	ENST00000277541	Transcript	frameshift_variant	987	911	304	N/X	aAt/at	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	6/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGCATTTGGC	.	3	ESCA
FAM154A	0	.	GRCh37	9	18928750	18928750	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725A>T	p.Gln242Leu	p.Q242L	ENST00000380534	4/4	93	86	6	90	90	0	FAM154A,missense_variant,p.Gln50Leu,ENST00000542071,;FAM154A,missense_variant,p.Gln242Leu,ENST00000380534,;FAM154A,3_prime_UTR_variant,,ENST00000380530,;	A	ENSG00000155875	ENST00000380534	Transcript	missense_variant	1005	725	242	Q/L	cAa/cTa	.	.	.	-1	FAM154A	HGNC	28566	protein_coding	YES	CCDS6487.1	ENSP00000369907	F154A_HUMAN	F6S232_HUMAN	UPI0000367609	.	tolerated(0.31)	benign(0.158)	4/4	.	hmmpanther:PTHR31516,hmmpanther:PTHR31516:SF5,Pfam_domain:PF05217,Pfam_domain:PF05217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGATTGTTTT	.	2	ESCA
KIAA2026	0	.	GRCh37	9	5922719	5922719	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3277C>T	p.Pro1093Ser	p.P1093S	ENST00000399933	8/8	41	26	15	49	49	0	KIAA2026,missense_variant,p.Pro1063Ser,ENST00000381461,;KIAA2026,missense_variant,p.Pro1093Ser,ENST00000399933,;KIAA2026,3_prime_UTR_variant,,ENST00000540714,;KIAA2026,upstream_gene_variant,,ENST00000436015,;	A	ENSG00000183354	ENST00000399933	Transcript	missense_variant	3277	3277	1093	P/S	Cct/Tct	.	.	.	-1	KIAA2026	HGNC	23378	protein_coding	YES	.	ENSP00000382815	K2026_HUMAN	.	UPI0001533DB0	.	tolerated(0.28)	benign(0.003)	8/8	.	hmmpanther:PTHR31095:SF2,hmmpanther:PTHR31095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAGGATCCA	.	5	ESCA
PTPRD	0	.	GRCh37	9	8486299	8486299	+	Missense_Mutation	SNP	G	G	T	rs142009246	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2518C>A	p.Leu840Ile	p.L840I	ENST00000381196	25/43	37	26	11	56	56	0	PTPRD,missense_variant,p.Leu818Ile,ENST00000358503,;PTPRD,missense_variant,p.Leu827Ile,ENST00000360074,;PTPRD,missense_variant,p.Leu840Ile,ENST00000381196,;PTPRD,missense_variant,p.Leu840Ile,ENST00000356435,;PTPRD,missense_variant,p.Leu840Ile,ENST00000540109,;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000486161,;PTPRD,intron_variant,,ENST00000397606,;PTPRD,intron_variant,,ENST00000355233,;PTPRD,intron_variant,,ENST00000397611,;PTPRD,intron_variant,,ENST00000537002,;PTPRD,non_coding_transcript_exon_variant,,ENST00000471274,;PTPRD,upstream_gene_variant,,ENST00000477552,;	T	ENSG00000153707	ENST00000381196	Transcript	missense_variant	3062	2518	840	L/I	Ctt/Att	rs142009246	.	.	-1	PTPRD	HGNC	9668	protein_coding	YES	CCDS43786.1	ENSP00000370593	PTPRD_HUMAN	C9J6E4_HUMAN,B4DK48_HUMAN	UPI0000132990	.	tolerated(0.11)	probably_damaging(0.987)	25/43	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	A:0	A:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAAGAGCAG	byFrequency|byCluster	5	ESCA
ARMCX3	0	.	GRCh37	X	100882700	100882700	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1591C>T	.	.	ENST00000341189	5/5	118	88	29	170	170	0	ARMCX3,3_prime_UTR_variant,,ENST00000341189,;ARMCX3,3_prime_UTR_variant,,ENST00000537169,;ARMCX3,downstream_gene_variant,,ENST00000479298,;ARMCX3,downstream_gene_variant,,ENST00000471229,;ARMCX3,downstream_gene_variant,,ENST00000491568,;ARMCX3-AS1,upstream_gene_variant,,ENST00000454228,;RP4-545K15.5,upstream_gene_variant,,ENST00000564612,;ARMCX3,downstream_gene_variant,,ENST00000467808,;ARMCX3,downstream_gene_variant,,ENST00000477980,;	T	ENSG00000102401	ENST00000341189	Transcript	3_prime_UTR_variant	3597	.	.	.	.	.	.	.	1	ARMCX3	HGNC	24065	protein_coding	YES	CCDS14489.1	ENSP00000340672	ARMX3_HUMAN	H3BV87_HUMAN,H3BM63_HUMAN	UPI000004C63E	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATCGAGCA	.	5	ESCA
COL4A5	0	.	GRCh37	X	107929290	107929290	+	Missense_Mutation	SNP	C	C	T	rs104886270	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4246C>T	p.Arg1416Cys	p.R1416C	ENST00000328300	48/53	34	26	7	68	68	0	COL4A5,missense_variant,p.Arg1416Cys,ENST00000328300,;COL4A5,missense_variant,p.Arg1410Cys,ENST00000361603,;COL4A5,missense_variant,p.Arg15Cys,ENST00000515658,;COL4A5,non_coding_transcript_exon_variant,,ENST00000489230,;	T	ENSG00000188153	ENST00000328300	Transcript	missense_variant	4490	4246	1416	R/C	Cgc/Tgc	CM960393,rs104886270	.	.	1	COL4A5	HGNC	2207	protein_coding	YES	CCDS35366.1	ENSP00000331902	CO4A5_HUMAN	H0Y9R8_HUMAN,B4DFF0_HUMAN	UPI000002A538	.	.	probably_damaging(0.993)	48/53	.	hmmpanther:PTHR24023:SF381,hmmpanther:PTHR24023,Pfam_domain:PF01391	T:0.0003	T:0.0008	T:0	.	T:0	T:0	T:0	T:0	T:0.0001	pathogenic	.	8651296	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGACGCAAT	byCluster|by1000G	5	ESCA
EIF2S3	0	.	GRCh37	X	24075597	24075597	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193C>T	p.His65Tyr	p.H65Y	ENST00000253039	3/12	38	24	13	61	61	0	EIF2S3,missense_variant,p.His65Tyr,ENST00000253039,;EIF2S3,missense_variant,p.His65Tyr,ENST00000423068,;EIF2S3,intron_variant,,ENST00000487075,;	T	ENSG00000130741	ENST00000253039	Transcript	missense_variant	446	193	65	H/Y	Cat/Tat	COSM1557255	.	.	1	EIF2S3	HGNC	3267	protein_coding	YES	CCDS14210.1	ENSP00000253039	IF2G_HUMAN	.	UPI0000163BD6	.	tolerated(0.27)	benign(0.013)	3/12	.	hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF94,Gene3D:3.40.50.300,Pfam_domain:PF00009,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTTCATACT	.	5	ESCA
NYX	0	.	GRCh37	X	41332755	41332755	+	Missense_Mutation	SNP	G	G	A	rs769075010	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.49G>A	p.Gly17Ser	p.G17S	ENST00000342595	2/2	18	12	6	34	34	0	NYX,missense_variant,p.Gly17Ser,ENST00000378220,;NYX,missense_variant,p.Gly17Ser,ENST00000342595,;NYX,non_coding_transcript_exon_variant,,ENST00000486842,;RP1-169I5.4,upstream_gene_variant,,ENST00000451718,;	A	ENSG00000188937	ENST00000342595	Transcript	missense_variant	505	49	17	G/S	Ggc/Agc	rs769075010	.	.	1	NYX	HGNC	8082	protein_coding	YES	CCDS14256.1	ENSP00000340328	NYX_HUMAN	.	UPI0000130B37	.	tolerated(0.63)	benign(0.001)	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,PROSITE_profiles:PS51257,hmmpanther:PTHR24369:SF29,hmmpanther:PTHR24369	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTCGGCCTG	byFrequency	2	ESCA
OTUD5	0	.	GRCh37	X	48779773	48779773	+	3'UTR	SNP	G	G	A	rs782405160	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*678C>T	.	.	ENST00000156084	9/9	15	12	3	37	37	0	OTUD5,3_prime_UTR_variant,,ENST00000376488,;OTUD5,3_prime_UTR_variant,,ENST00000396743,;OTUD5,3_prime_UTR_variant,,ENST00000156084,;OTUD5,3_prime_UTR_variant,,ENST00000455452,;PIM2,upstream_gene_variant,,ENST00000376509,;OTUD5,downstream_gene_variant,,ENST00000428668,;OTUD5,downstream_gene_variant,,ENST00000484499,;	A	ENSG00000068308	ENST00000156084	Transcript	3_prime_UTR_variant	2455	.	.	.	.	rs782405160	.	.	-1	OTUD5	HGNC	25402	protein_coding	YES	CCDS14313.1	ENSP00000156084	OTUD5_HUMAN	H7BZQ3_HUMAN	UPI000006ED2A	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCCGGCCTC	.	2	ESCA
AWAT1	0	.	GRCh37	X	69454560	69454560	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A5S3-01A-11D-A28B-09	TCGA-IG-A5S3-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15G>A	p.%3D	p.K5K	ENST00000374521	1/7	53	48	5	61	61	0	AWAT1,synonymous_variant,p.%3D,ENST00000374521,;AWAT1,non_coding_transcript_exon_variant,,ENST00000480702,;	A	ENSG00000204195	ENST00000374521	Transcript	synonymous_variant	56	15	5	K	aaG/aaA	.	.	.	1	AWAT1	HGNC	23252	protein_coding	YES	CCDS35321.1	ENSP00000363645	AWAT1_HUMAN	.	UPI00002122D8	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCAAGCAGCC	.	3	ESCA
SH3PXD2A	0	.	GRCh37	10	105358613	105358613	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2960A>G	.	.	ENST00000355946	14/14	9	6	3	13	13	0	SH3PXD2A,3_prime_UTR_variant,,ENST00000369774,;SH3PXD2A,3_prime_UTR_variant,,ENST00000355946,;SH3PXD2A,intron_variant,,ENST00000427662,;SH3PXD2A,downstream_gene_variant,,ENST00000540321,;SH3PXD2A,downstream_gene_variant,,ENST00000538130,;SH3PXD2A,downstream_gene_variant,,ENST00000420222,;SH3PXD2A,downstream_gene_variant,,ENST00000315994,;	C	ENSG00000107957	ENST00000355946	Transcript	3_prime_UTR_variant	6418	.	.	.	.	.	.	.	-1	SH3PXD2A	HGNC	23664	protein_coding	YES	CCDS31278.1	ENSP00000348215	SPD2A_HUMAN	.	UPI000041B175	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTAATATTCT	.	2	ESCA
PTER	0	.	GRCh37	10	16553247	16553247	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1042T>G	p.Phe348Val	p.F348V	ENST00000378000	6/6	36	16	20	39	39	0	PTER,missense_variant,p.Phe348Val,ENST00000298942,;PTER,missense_variant,p.Phe348Val,ENST00000378000,;PTER,missense_variant,p.Phe348Val,ENST00000535784,;PTER,missense_variant,p.Phe301Val,ENST00000423462,;C1QL3,downstream_gene_variant,,ENST00000298943,;	G	ENSG00000165983	ENST00000378000	Transcript	missense_variant	1288	1042	348	F/V	Ttc/Gtc	.	.	.	1	PTER	HGNC	9590	protein_coding	YES	CCDS7111.1	ENSP00000367239	PTER_HUMAN	.	UPI00000492E9	.	deleterious(0)	probably_damaging(0.926)	6/6	.	PROSITE_profiles:PS51347,hmmpanther:PTHR10819,Gene3D:3.20.20.140,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTTTCAAA	.	5	ESCA
GPRIN2	0	.	GRCh37	10	46999668	46999668	+	Missense_Mutation	SNP	C	C	T	rs781801723	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.788C>T	p.Ala263Val	p.A263V	ENST00000374314	1/1	19	13	6	33	33	0	GPRIN2,missense_variant,p.Ala263Val,ENST00000374314,;GPRIN2,missense_variant,p.Ala263Val,ENST00000374317,;	T	ENSG00000204175	ENST00000374314	Transcript	missense_variant	1743	788	263	A/V	gCg/gTg	rs781801723,COSM1253606	.	.	1	GPRIN2	HGNC	23730	protein_coding	YES	CCDS31192.1	ENSP00000363433	GRIN2_HUMAN	.	UPI000013ECB4	.	deleterious(0)	possibly_damaging(0.835)	1/1	.	hmmpanther:PTHR15718	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGTGGCGTCAG	byFrequency	4	ESCA
NET1	0	.	GRCh37	10	5494811	5494811	+	Intron	DEL	A	A	-	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.532-10delA	.	.	ENST00000355029	.	40	34	6	37	37	0	NET1,5_prime_UTR_variant,,ENST00000542715,;NET1,intron_variant,,ENST00000355029,;NET1,intron_variant,,ENST00000449083,;NET1,intron_variant,,ENST00000380359,;NET1,non_coding_transcript_exon_variant,,ENST00000486354,;NET1,intron_variant,,ENST00000465087,;NET1,upstream_gene_variant,,ENST00000484741,;	-	ENSG00000173848	ENST00000355029	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NET1	HGNC	14592	protein_coding	YES	CCDS41483.1	ENSP00000347134	ARHG8_HUMAN	Q5SQI5_HUMAN,B4E1Y1_HUMAN	UPI00001A9465	.	.	.	.	5/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TGCTGGATGTTT	.	2	ESCA
GLB1L3	0	.	GRCh37	11	134188557	134188557	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1812A>G	p.%3D	p.G604G	ENST00000431683	19/20	47	31	16	46	46	0	GLB1L3,synonymous_variant,p.%3D,ENST00000431683,;GLB1L3,3_prime_UTR_variant,,ENST00000455971,;GLB1L3,non_coding_transcript_exon_variant,,ENST00000486034,;GLB1L3,non_coding_transcript_exon_variant,,ENST00000467068,;GLB1L3,non_coding_transcript_exon_variant,,ENST00000498012,;GLB1L3,downstream_gene_variant,,ENST00000410100,;AP000859.4,upstream_gene_variant,,ENST00000525536,;	G	ENSG00000166105	ENST00000431683	Transcript	synonymous_variant	1812	1812	604	G	ggA/ggG	.	.	.	1	GLB1L3	HGNC	25147	protein_coding	YES	CCDS44780.1	ENSP00000396615	GLBL3_HUMAN	.	UPI0001633637	.	.	.	19/20	.	hmmpanther:PTHR23421,hmmpanther:PTHR23421:SF59,Gene3D:2.60.120.260,PIRSF_domain:PIRSF006336,Superfamily_domains:SSF49785,Prints_domain:PR00742	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGACGTAA	.	5	ESCA
CRY2	0	.	GRCh37	11	45891258	45891258	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147A>G	p.Ile383Val	p.I383V	ENST00000443527	7/12	32	21	11	35	35	0	CRY2,missense_variant,p.Ile383Val,ENST00000443527,;CRY2,missense_variant,p.Ile301Val,ENST00000417225,;CRY2,non_coding_transcript_exon_variant,,ENST00000496667,;CRY2,upstream_gene_variant,,ENST00000488962,;CRY2,downstream_gene_variant,,ENST00000525110,;CRY2,downstream_gene_variant,,ENST00000495237,;	G	ENSG00000121671	ENST00000443527	Transcript	missense_variant	1169	1147	383	I/V	Atc/Gtc	.	.	.	1	CRY2	HGNC	2385	protein_coding	YES	CCDS7915.2	ENSP00000406751	.	B4DZD6_HUMAN,B4DIJ2_HUMAN,A2I2P1_HUMAN	UPI000174F724	.	deleterious(0.03)	benign(0.424)	7/12	.	hmmpanther:PTHR11455,hmmpanther:PTHR11455:SF15,Gene3D:1owlA03,Pfam_domain:PF03441,Superfamily_domains:SSF48173	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCCATCATG	.	5	ESCA
FADS1	0	.	GRCh37	11	61583950	61583950	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375+77C>G	.	.	ENST00000350997	.	34	24	9	60	59	0	FADS2,5_prime_UTR_variant,,ENST00000522056,;FADS1,intron_variant,,ENST00000421879,;FADS2,intron_variant,,ENST00000257261,;FADS1,intron_variant,,ENST00000544309,;FADS1,intron_variant,,ENST00000350997,;FADS2,intron_variant,,ENST00000574708,;FADS1,intron_variant,,ENST00000448607,;FADS1,intron_variant,,ENST00000491310,;FADS2,intron_variant,,ENST00000522639,;FADS1,upstream_gene_variant,,ENST00000540767,;FADS1,upstream_gene_variant,,ENST00000545245,;FADS1,upstream_gene_variant,,ENST00000466716,;FADS1,upstream_gene_variant,,ENST00000539419,;FADS1,upstream_gene_variant,,ENST00000473263,;FADS1,upstream_gene_variant,,ENST00000545405,;FADS1,upstream_gene_variant,,ENST00000433932,;FADS1,upstream_gene_variant,,ENST00000542506,;FADS2,upstream_gene_variant,,ENST00000517839,;FADS1,upstream_gene_variant,,ENST00000544696,;MIR1908,upstream_gene_variant,,ENST00000410394,;FADS1,intron_variant,,ENST00000541683,;FADS1,upstream_gene_variant,,ENST00000545986,;FADS1,upstream_gene_variant,,ENST00000496123,;FADS1,intron_variant,,ENST00000424501,;	C	ENSG00000149485	ENST00000350997	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	FADS1	HGNC	3574	protein_coding	YES	CCDS8011.2	ENSP00000322229	FADS1_HUMAN	I3ZNT3_HUMAN,I3ZNS6_HUMAN,I3ZNS3_HUMAN,I3ZNS1_HUMAN,I3ZNN6_HUMAN,I3ZNL9_HUMAN,I3ZNL2_HUMAN,I3ZNH3_HUMAN,I3ZNE3_HUMAN,F5H8G5_HUMAN,F5H852_HUMAN,F5H5X5_HUMAN,F5H3P6_HUMAN,F5H2H3_HUMAN,F5H1Q7_HUMAN,F5H0Y2_HUMAN,F5GYH4_HUMAN,C9JJB3_HUMAN,C9J425_HUMAN	UPI00001AF33B	.	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCGGAGTG	.	5	ESCA
ARHGEF17	0	.	GRCh37	11	73068098	73068098	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3920C>T	p.Ser1307Phe	p.S1307F	ENST00000263674	8/21	33	25	8	41	41	0	ARHGEF17,missense_variant,p.Ser1307Phe,ENST00000263674,;AP002761.1,upstream_gene_variant,,ENST00000582555,;ARHGEF17,downstream_gene_variant,,ENST00000536170,;ARHGEF17,non_coding_transcript_exon_variant,,ENST00000537198,;	T	ENSG00000110237	ENST00000263674	Transcript	missense_variant	4270	3920	1307	S/F	tCt/tTt	.	.	.	1	ARHGEF17	HGNC	21726	protein_coding	YES	CCDS8221.1	ENSP00000263674	ARHGH_HUMAN	.	UPI000004980B	.	deleterious(0.01)	probably_damaging(0.983)	8/21	.	hmmpanther:PTHR12877:SF15,hmmpanther:PTHR12877,Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGTCTCTCT	.	5	ESCA
KIAA1731	0	.	GRCh37	11	93466281	93466281	+	3'Flank	SNP	T	T	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000325212	.	65	37	28	79	79	0	KIAA1731,downstream_gene_variant,,ENST00000344196,;TAF1D,downstream_gene_variant,,ENST00000532455,;TAF1D,downstream_gene_variant,,ENST00000448108,;KIAA1731,downstream_gene_variant,,ENST00000531404,;KIAA1731,downstream_gene_variant,,ENST00000325212,;KIAA1731,downstream_gene_variant,,ENST00000411936,;KIAA1731,downstream_gene_variant,,ENST00000531700,;SNORA1,upstream_gene_variant,,ENST00000384107,;SNORD5,downstream_gene_variant,,ENST00000459342,;SNORA8,upstream_gene_variant,,ENST00000384574,;SNORA40,downstream_gene_variant,,ENST00000388090,;SNORA18,downstream_gene_variant,,ENST00000384416,;MIR1304,downstream_gene_variant,,ENST00000408243,;SNORA32,upstream_gene_variant,,ENST00000384072,;SNORD6,upstream_gene_variant,,ENST00000365444,;SNORA25,upstream_gene_variant,,ENST00000384384,;TAF1D,non_coding_transcript_exon_variant,,ENST00000530089,;TAF1D,non_coding_transcript_exon_variant,,ENST00000546088,;TAF1D,downstream_gene_variant,,ENST00000532235,;TAF1D,3_prime_UTR_variant,,ENST00000533794,;TAF1D,3_prime_UTR_variant,,ENST00000540232,;TAF1D,3_prime_UTR_variant,,ENST00000323981,;TAF1D,3_prime_UTR_variant,,ENST00000527169,;TAF1D,3_prime_UTR_variant,,ENST00000393259,;TAF1D,3_prime_UTR_variant,,ENST00000526015,;TAF1D,non_coding_transcript_exon_variant,,ENST00000529794,;TAF1D,non_coding_transcript_exon_variant,,ENST00000529435,;TAF1D,non_coding_transcript_exon_variant,,ENST00000530769,;TAF1D,non_coding_transcript_exon_variant,,ENST00000525928,;TAF1D,downstream_gene_variant,,ENST00000528734,;TAF1D,downstream_gene_variant,,ENST00000527068,;TAF1D,downstream_gene_variant,,ENST00000534770,;TAF1D,upstream_gene_variant,,ENST00000529900,;TAF1D,upstream_gene_variant,,ENST00000534079,;	A	ENSG00000166004	ENST00000325212	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2759	1	KIAA1731	HGNC	29366	protein_coding	YES	CCDS44708.1	ENSP00000316681	K1731_HUMAN	E9PM20_HUMAN	UPI0000251F0E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACATTCATT	.	5	ESCA
VWF	0	.	GRCh37	12	6153592	6153592	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2307C>A	p.%3D	p.P769P	ENST00000261405	18/52	26	8	18	23	23	0	VWF,synonymous_variant,p.%3D,ENST00000261405,;VWF,intron_variant,,ENST00000538635,;	T	ENSG00000110799	ENST00000261405	Transcript	synonymous_variant	2562	2307	769	P	ccC/ccA	.	.	.	-1	VWF	HGNC	12726	protein_coding	YES	CCDS8539.1	ENSP00000261405	VWF_HUMAN	H2DLA2_HUMAN	UPI00001AE7EE	.	.	.	18/52	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF259,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGGGGGCCG	.	5	ESCA
KITLG	0	.	GRCh37	12	88910245	88910245	+	Missense_Mutation	SNP	C	C	T	rs771121084	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.386G>A	p.Ser129Asn	p.S129N	ENST00000228280	5/10	63	41	21	75	75	0	KITLG,missense_variant,p.Ser129Asn,ENST00000228280,;KITLG,missense_variant,p.Ser129Asn,ENST00000347404,;KITLG,intron_variant,,ENST00000357116,;KITLG,downstream_gene_variant,,ENST00000552044,;KITLG,non_coding_transcript_exon_variant,,ENST00000378535,;	T	ENSG00000049130	ENST00000228280	Transcript	missense_variant	569	386	129	S/N	aGc/aAc	rs771121084	.	.	-1	KITLG	HGNC	6343	protein_coding	YES	CCDS31868.1	ENSP00000228280	SCF_HUMAN	S4R442_HUMAN,S4R384_HUMAN	UPI000002D482	.	tolerated(0.64)	benign(0)	5/10	.	Superfamily_domains:SSF47266,PIRSF_domain:PIRSF015599,Gene3D:1.20.1250.10,Pfam_domain:PF02404,hmmpanther:PTHR11574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGCTCTTG	byFrequency	5	ESCA
KBTBD7	0	.	GRCh37	13	41767331	41767331	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1063C>T	p.Pro355Ser	p.P355S	ENST00000379483	1/1	44	38	6	51	51	0	KBTBD7,missense_variant,p.Pro355Ser,ENST00000379483,;	A	ENSG00000120696	ENST00000379483	Transcript	missense_variant	1372	1063	355	P/S	Ccc/Tcc	COSM3468902	.	.	-1	KBTBD7	HGNC	25266	protein_coding	YES	CCDS9377.1	ENSP00000368797	KBTB7_HUMAN	B4DS80_HUMAN	UPI0000071F8F	.	tolerated(0.27)	benign(0.407)	1/1	.	hmmpanther:PTHR24412:SF132,hmmpanther:PTHR24412,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAGGGATCTC	.	4	ESCA
NOMO2	0	.	GRCh37	16	18532148	18532148	+	Missense_Mutation	SNP	C	C	T	rs759016851	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2212G>A	p.Val738Met	p.V738M	ENST00000381474	19/32	223	185	38	324	323	1	NOMO2,missense_variant,p.Val738Met,ENST00000330537,;NOMO2,missense_variant,p.Val571Met,ENST00000543392,;NOMO2,missense_variant,p.Val738Met,ENST00000381474,;NOMO2,3_prime_UTR_variant,,ENST00000567831,;NOMO2,3_prime_UTR_variant,,ENST00000564991,;NOMO2,downstream_gene_variant,,ENST00000569051,;	T	ENSG00000185164	ENST00000381474	Transcript	missense_variant	2278	2212	738	V/M	Gtg/Atg	rs759016851,COSM967681	.	.	-1	NOMO2	HGNC	22652	protein_coding	YES	CCDS32394.1	ENSP00000370883	NOMO2_HUMAN	.	UPI00001AFC79	.	tolerated(0.12)	benign(0.054)	19/32	.	hmmpanther:PTHR23303	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTGCACGGGAG	byFrequency	3	ESCA
EFTUD2	0	.	GRCh37	17	42927927	42927927	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*715T>A	.	.	ENST00000426333	28/28	12	5	7	11	11	0	EFTUD2,3_prime_UTR_variant,,ENST00000426333,;EFTUD2,downstream_gene_variant,,ENST00000402521,;HIGD1B,downstream_gene_variant,,ENST00000587021,;EFTUD2,downstream_gene_variant,,ENST00000591382,;HIGD1B,downstream_gene_variant,,ENST00000591513,;EFTUD2,downstream_gene_variant,,ENST00000592576,;EFTUD2,downstream_gene_variant,,ENST00000590124,;HIGD1B,downstream_gene_variant,,ENST00000253410,;HIGD1B,downstream_gene_variant,,ENST00000590423,;EFTUD2,downstream_gene_variant,,ENST00000590367,;EFTUD2,downstream_gene_variant,,ENST00000586276,;EFTUD2,downstream_gene_variant,,ENST00000590977,;EFTUD2,downstream_gene_variant,,ENST00000588340,;EFTUD2,downstream_gene_variant,,ENST00000589769,;HIGD1B,downstream_gene_variant,,ENST00000586911,;	T	ENSG00000108883	ENST00000426333	Transcript	3_prime_UTR_variant	3932	.	.	.	.	.	.	.	-1	EFTUD2	HGNC	30858	protein_coding	YES	CCDS11489.1	ENSP00000392094	U5S1_HUMAN	K7EIV5_HUMAN,K7EIT3_HUMAN,B3KX19_HUMAN	UPI0000137931	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGGAAATCAA	.	3	ESCA
SCN4A	0	.	GRCh37	17	62022996	62022996	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3444G>A	p.%3D	p.V1148V	ENST00000435607	19/24	18	5	13	35	35	0	SCN4A,synonymous_variant,p.%3D,ENST00000435607,;SCN4A,synonymous_variant,p.%3D,ENST00000578147,;SCN4A,downstream_gene_variant,,ENST00000584310,;	T	ENSG00000007314	ENST00000435607	Transcript	synonymous_variant	3521	3444	1148	V	gtG/gtA	.	.	.	-1	SCN4A	HGNC	10591	protein_coding	YES	CCDS45761.1	ENSP00000396320	SCN4A_HUMAN	Q9H3L9_HUMAN	UPI0000201254	.	.	.	19/24	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF193,Pfam_domain:PF00520,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACCACCTG	.	5	ESCA
SEC14L1	0	.	GRCh37	17	75210142	75210142	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2144+41G>A	.	.	ENST00000392476	.	42	22	20	41	41	0	SEC14L1,3_prime_UTR_variant,,ENST00000588488,;SEC14L1,3_prime_UTR_variant,,ENST00000436233,;SEC14L1,3_prime_UTR_variant,,ENST00000591437,;SEC14L1,3_prime_UTR_variant,,ENST00000585618,;SEC14L1,3_prime_UTR_variant,,ENST00000413679,;SEC14L1,3_prime_UTR_variant,,ENST00000430767,;SEC14L1,3_prime_UTR_variant,,ENST00000431431,;SEC14L1,intron_variant,,ENST00000392476,;SEC14L1,intron_variant,,ENST00000443798,;SEC14L1,non_coding_transcript_exon_variant,,ENST00000588721,;SEC14L1,non_coding_transcript_exon_variant,,ENST00000587491,;SEC14L1,downstream_gene_variant,,ENST00000591413,;	A	ENSG00000129657	ENST00000392476	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SEC14L1	HGNC	10698	protein_coding	YES	CCDS42385.1	ENSP00000376268	S14L1_HUMAN	K7EQK4_HUMAN,K7ELU0_HUMAN,K7ELM0_HUMAN,K7EJ08_HUMAN,B4E0D1_HUMAN,B4DEZ7_HUMAN	UPI00006AB82A	.	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGACGGCCGCC	.	4	ESCA
TP53	0	.	GRCh37	17	7578176	7578176	+	Splice_Site	SNP	C	C	A	.	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672+1G>T	.	p.X224_splice	ENST00000269305	.	32	6	25	42	42	0	TP53,splice_donor_variant,,ENST00000413465,;TP53,splice_donor_variant,,ENST00000420246,;TP53,splice_donor_variant,,ENST00000269305,;TP53,splice_donor_variant,,ENST00000509690,;TP53,splice_donor_variant,,ENST00000359597,;TP53,splice_donor_variant,,ENST00000514944,;TP53,splice_donor_variant,,ENST00000445888,;TP53,splice_donor_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,splice_donor_variant,,ENST00000504937,;TP53,splice_donor_variant,,ENST00000504290,;TP53,splice_donor_variant,,ENST00000510385,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	splice_donor_variant	.	.	.	.	.	CS071266,TP53_g.12742G>T,TP53_g.12742G>A,TP53_g.12742del,TP53_g.12742G>C,COSM6906,COSM13586,COSM45367,COSM118941,COSM121038,COSM119013,COSM121039,COSM118939,COSM119011,COSM3388194,COSM3723947,COSM1638407,COSM2744696,COSM118940,COSM119012,COSM121040	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.672+1G>T|5,SITE|p.?|c.672+1G>T|3,SITE|p.?|c.393+1G>T|6,SITE|p.?|c.672+1G>T|16,SITE|p.?|c.672+1G>T|6,SITE|p.?|c.672+1G>T|6,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.?|c.672+2T>A|3,BUFFER|p.?|c.672+2T>A|3,BUFFER|p.?|c.672+2T>C|8,BUFFER|p.?|c.393+2T>A|3,BUFFER|p.?|c.672+2T>A|3,BUFFER|p.?|c.672+1G>A|4,BUFFER|p.?|c.393+1G>A|8,BUFFER|p.?|c.672+1G>A|8,BUFFER|p.?|c.672+1G>A|8,BUFFER|p.?|c.672+1G>C|3,BUFFER|p.?|c.672+1G>A|4,BUFFER|p.?|c.672+1G>A|19,BUFFER|p.E224D|c.672G>C|3,BUFFER|p.E224D|c.672G>C|8,BUFFER|p.E224E|c.672G>A|3,BUFFER|p.E224E|c.672G>A|9,BUFFER|p.E224E|c.672G>A|3,BUFFER|p.E131D|c.393G>C|3,BUFFER|p.E224D|c.672G>C|3,BUFFER|p.E224D|c.672G>T|7,BUFFER|p.E224E|c.672G>A|3,BUFFER|p.E131E|c.393G>A|3,BUFFER|p.E224K|c.670G>A|4,BUFFER|p.E224*|c.670G>T|5,BUFFER|p.P223L|c.668C>T|3,BUFFER|p.P222P|c.666G>C|3,BUFFER|p.P222L|c.665C>T|4,BUFFER|p.P222T|c.664C>A|3,BUFFER|p.E221G|c.662A>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGACCTCAG	.	5	ESCA
ROCK1	0	.	GRCh37	18	18530807	18530807	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*538A>G	.	.	ENST00000399799	33/33	79	33	45	56	56	0	ROCK1,3_prime_UTR_variant,,ENST00000399799,;ROCK1,downstream_gene_variant,,ENST00000578051,;ROCK1,downstream_gene_variant,,ENST00000584687,;	C	ENSG00000067900	ENST00000399799	Transcript	3_prime_UTR_variant	5544	.	.	.	.	.	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAGTGAGGG	.	5	ESCA
TGIF1	0	.	GRCh37	18	3456685	3456685	+	Intron	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630+107A>G	.	.	ENST00000330513	.	24	16	8	19	19	0	TGIF1,missense_variant,p.Lys117Arg,ENST00000551402,;TGIF1,intron_variant,,ENST00000345133,;TGIF1,intron_variant,,ENST00000577543,;TGIF1,intron_variant,,ENST00000401449,;TGIF1,intron_variant,,ENST00000551541,;TGIF1,intron_variant,,ENST00000472042,;TGIF1,intron_variant,,ENST00000552383,;TGIF1,intron_variant,,ENST00000549780,;TGIF1,intron_variant,,ENST00000551333,;TGIF1,intron_variant,,ENST00000343820,;TGIF1,intron_variant,,ENST00000546979,;TGIF1,intron_variant,,ENST00000548489,;TGIF1,intron_variant,,ENST00000405385,;TGIF1,intron_variant,,ENST00000549468,;TGIF1,intron_variant,,ENST00000407501,;TGIF1,intron_variant,,ENST00000549546,;TGIF1,intron_variant,,ENST00000549253,;TGIF1,intron_variant,,ENST00000330513,;TGIF1,intron_variant,,ENST00000550958,;TGIF1,intron_variant,,ENST00000400167,;	G	ENSG00000177426	ENST00000330513	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TGIF1	HGNC	11776	protein_coding	YES	CCDS11834.1	ENSP00000327959	TGIF1_HUMAN	F8VZH2_HUMAN,F8VXG3_HUMAN,F8VX54_HUMAN,F8VWK5_HUMAN,F8VW34_HUMAN,F8VVS9_HUMAN,F8VUY0_HUMAN	UPI0000140386	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAGAAGGAAT	.	2	ESCA
ZBTB14	0	.	GRCh37	18	5291775	5291775	+	Nonsense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432T>G	p.Tyr144Ter	p.Y144*	ENST00000357006	4/4	28	22	6	19	19	0	ZBTB14,stop_gained,p.Tyr144Ter,ENST00000357006,;ZBTB14,stop_gained,p.Tyr144Ter,ENST00000582135,;ZBTB14,stop_gained,p.Tyr144Ter,ENST00000582388,;ZBTB14,stop_gained,p.Tyr144Ter,ENST00000400143,;ZBTB14,downstream_gene_variant,,ENST00000578327,;ZBTB14,downstream_gene_variant,,ENST00000585253,;	C	ENSG00000198081	ENST00000357006	Transcript	stop_gained	771	432	144	Y/*	taT/taG	.	.	.	-1	ZBTB14	HGNC	12860	protein_coding	YES	CCDS11837.1	ENSP00000349503	ZBT14_HUMAN	J3QLI2_HUMAN,J3QL74_HUMAN,J3KRQ2_HUMAN	UPI0000163BCB	.	.	.	4/4	.	hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCAATACTT	.	5	ESCA
SOGA2	0	.	GRCh37	18	8793003	8793004	+	Frame_Shift_Ins	INS	-	-	C	rs754891814	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1902dupC	p.Val635ArgfsTer4	p.V635Rfs*4	ENST00000359865	8/17	32	21	11	24	24	0	SOGA2,frameshift_variant,p.Val635ArgfsTer4,ENST00000359865,;SOGA2,5_prime_UTR_variant,,ENST00000306285,;SOGA2,intron_variant,,ENST00000518815,;SOGA2,intron_variant,,ENST00000517570,;SOGA2,intron_variant,,ENST00000400050,;SOGA2,intron_variant,,ENST00000306329,;SOGA2,intron_variant,,ENST00000520495,;	C	ENSG00000168502	ENST00000359865	Transcript	frameshift_variant	2037-2038	1895-1896	632	G/GX	ggc/ggCc	rs754891814,COSM1389920	.	.	1	SOGA2	HGNC	29121	protein_coding	YES	CCDS11841.1	ENSP00000352927	SOGA2_HUMAN	J3QLE1_HUMAN	UPI0000456B5B	.	.	.	8/17	.	hmmpanther:PTHR15742:SF3,hmmpanther:PTHR15742	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	insertion	.	7	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAGGGGCCCCC	.	2	ESCA
WDR83OS	0	.	GRCh37	19	12780418	12780418	+	5'UTR	SNP	G	G	T	rs777148778	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-201C>A	.	.	ENST00000596731	1/4	8	5	3	9	9	0	WDR83OS,5_prime_UTR_variant,,ENST00000596731,;WDR83,intron_variant,,ENST00000418543,;WDR83,upstream_gene_variant,,ENST00000242796,;MAN2B1,upstream_gene_variant,,ENST00000486847,;WDR83OS,upstream_gene_variant,,ENST00000222190,;MAN2B1,upstream_gene_variant,,ENST00000598876,;MAN2B1,upstream_gene_variant,,ENST00000221363,;CTD-2192J16.24,upstream_gene_variant,,ENST00000597961,;WDR83OS,upstream_gene_variant,,ENST00000598732,;WDR83,upstream_gene_variant,,ENST00000547797,;MAN2B1,upstream_gene_variant,,ENST00000456935,;WDR83OS,downstream_gene_variant,,ENST00000600694,;MAN2B1,upstream_gene_variant,,ENST00000596512,;WDR83,non_coding_transcript_exon_variant,,ENST00000547255,;WDR83,intron_variant,,ENST00000546754,;WDR83,intron_variant,,ENST00000548381,;WDR83,intron_variant,,ENST00000553179,;MAN2B1,upstream_gene_variant,,ENST00000466794,;WDR83,upstream_gene_variant,,ENST00000550939,;WDR83,upstream_gene_variant,,ENST00000547481,;WDR83,upstream_gene_variant,,ENST00000552700,;WDR83,upstream_gene_variant,,ENST00000551329,;MAN2B1,upstream_gene_variant,,ENST00000600281,;WDR83,upstream_gene_variant,,ENST00000425834,;	T	ENSG00000105583	ENST00000596731	Transcript	5_prime_UTR_variant	1753	.	.	.	.	rs777148778	.	.	-1	WDR83OS	HGNC	30203	protein_coding	YES	CCDS12274.1	ENSP00000468969	ASTER_HUMAN	.	UPI0000003EE7	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAAGAACCT	.	2	ESCA
UQCRFS1	0	.	GRCh37	19	29698442	29698442	+	3'UTR	SNP	G	G	C	rs751732012	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13C>G	.	.	ENST00000304863	2/2	75	69	6	98	98	0	UQCRFS1,3_prime_UTR_variant,,ENST00000304863,;	C	ENSG00000169021	ENST00000304863	Transcript	3_prime_UTR_variant	1261	.	.	.	.	rs751732012	.	.	-1	UQCRFS1	HGNC	12587	protein_coding	YES	CCDS12415.1	ENSP00000306397	UCRI_HUMAN	.	UPI000013E9D6	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACTTGAGTCC	byFrequency	3	ESCA
ZBTB7A	0	.	GRCh37	19	4054661	4054661	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570G>A	p.%3D	p.A190A	ENST00000322357	2/3	97	58	39	158	158	0	ZBTB7A,synonymous_variant,p.%3D,ENST00000322357,;ZBTB7A,synonymous_variant,p.%3D,ENST00000601588,;	T	ENSG00000178951	ENST00000322357	Transcript	synonymous_variant	849	570	190	A	gcG/gcA	.	.	.	-1	ZBTB7A	HGNC	18078	protein_coding	YES	CCDS12119.1	ENSP00000323670	ZBT7A_HUMAN	.	UPI000006E9D9	.	.	.	2/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23229,hmmpanther:PTHR23229:SF69	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGACGCCCC	.	5	ESCA
KLK2	0	.	GRCh37	19	51379818	51379818	+	Silent	SNP	G	G	A	rs759727230	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297G>A	p.%3D	p.P99P	ENST00000325321	3/5	35	24	10	19	19	0	KLK2,synonymous_variant,p.%3D,ENST00000325321,;KLK2,synonymous_variant,p.%3D,ENST00000358049,;KLK2,5_prime_UTR_variant,,ENST00000599568,;KLK2,5_prime_UTR_variant,,ENST00000391810,;KLK2,5_prime_UTR_variant,,ENST00000593493,;KLK2,intron_variant,,ENST00000600690,;AC037199.1,upstream_gene_variant,,ENST00000594218,;KLK2,non_coding_transcript_exon_variant,,ENST00000596950,;KLK2,downstream_gene_variant,,ENST00000597509,;KLK2,missense_variant,p.Arg46His,ENST00000595316,;KLK2,missense_variant,p.Arg46His,ENST00000599121,;KLK2,missense_variant,p.Arg46His,ENST00000597727,;KLK2,synonymous_variant,p.%3D,ENST00000597439,;KLK2,3_prime_UTR_variant,,ENST00000594174,;KLK2,non_coding_transcript_exon_variant,,ENST00000600755,;KLK2,non_coding_transcript_exon_variant,,ENST00000600866,;KLK2,non_coding_transcript_exon_variant,,ENST00000599280,;KLK2,non_coding_transcript_exon_variant,,ENST00000601114,;KLK2,non_coding_transcript_exon_variant,,ENST00000595173,;KLK2,upstream_gene_variant,,ENST00000597911,;KLK2,downstream_gene_variant,,ENST00000601743,;KLK2,downstream_gene_variant,,ENST00000595375,;KLK2,upstream_gene_variant,,ENST00000595050,;KLK2,upstream_gene_variant,,ENST00000597461,;	A	ENSG00000167751	ENST00000325321	Transcript	synonymous_variant	522	297	99	P	ccG/ccA	rs759727230	.	.	1	KLK2	HGNC	6363	protein_coding	YES	CCDS12808.1	ENSP00000313581	KLK2_HUMAN	M0R2W5_HUMAN,M0R1T3_HUMAN,M0R0M4_HUMAN,B0AZU9_HUMAN	UPI000004CA0C	.	.	.	3/5	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24275,hmmpanther:PTHR24275:SF15,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCGCTCTA	byFrequency	5	ESCA
NLRP4	0	.	GRCh37	19	56369885	56369885	+	Missense_Mutation	SNP	G	G	A	rs149428225	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1126G>A	p.Val376Ile	p.V376I	ENST00000301295	3/10	28	24	4	27	27	0	NLRP4,missense_variant,p.Val376Ile,ENST00000301295,;NLRP4,missense_variant,p.Val376Ile,ENST00000346986,;NLRP4,missense_variant,p.Val301Ile,ENST00000587891,;NLRP4,upstream_gene_variant,,ENST00000589437,;NLRP4,downstream_gene_variant,,ENST00000587464,;	A	ENSG00000160505	ENST00000301295	Transcript	missense_variant	1548	1126	376	V/I	Gtc/Atc	rs149428225,COSM1001692	.	.	1	NLRP4	HGNC	22943	protein_coding	YES	CCDS12936.1	ENSP00000301295	NALP4_HUMAN	K7ES09_HUMAN	UPI000013E6FD	.	tolerated(1)	benign(0)	3/10	.	hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTCGTCTTT	byCluster|by1000G	4	ESCA
VN1R1	0	.	GRCh37	19	57967427	57967427	+	Missense_Mutation	SNP	T	T	A	rs769909938	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.428A>T	p.Asn143Ile	p.N143I	ENST00000321039	1/1	49	40	9	30	30	0	VN1R1,missense_variant,p.Asn143Ile,ENST00000321039,;AC004076.9,intron_variant,,ENST00000596831,;AC004076.9,intron_variant,,ENST00000601945,;AC004076.9,intron_variant,,ENST00000415705,;VN1R107P,upstream_gene_variant,,ENST00000601784,;	A	ENSG00000178201	ENST00000321039	Transcript	missense_variant	428	428	143	N/I	aAt/aTt	rs769909938	.	.	-1	VN1R1	HGNC	13548	protein_coding	YES	CCDS12951.1	ENSP00000322339	VN1R1_HUMAN	.	UPI0000039957	.	deleterious(0)	probably_damaging(0.932)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24062,hmmpanther:PTHR24062:SF43,Gene3D:1.20.1070.10,Pfam_domain:PF03402,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCATTGAGA	byFrequency	5	ESCA
MYO1F	0	.	GRCh37	19	8587367	8587367	+	Missense_Mutation	SNP	C	C	G	rs187667984	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3114G>C	p.Gln1038His	p.Q1038H	ENST00000338257	27/28	38	24	14	44	44	0	MYO1F,missense_variant,p.Gln1038His,ENST00000338257,;MYO1F,downstream_gene_variant,,ENST00000596245,;MYO1F,downstream_gene_variant,,ENST00000600885,;MYO1F,downstream_gene_variant,,ENST00000598005,;	G	ENSG00000142347	ENST00000338257	Transcript	missense_variant	3382	3114	1038	Q/H	caG/caC	rs187667984	.	.	-1	MYO1F	HGNC	7600	protein_coding	YES	CCDS42494.1	ENSP00000344871	MYO1F_HUMAN	Q14779_HUMAN,M0QXU2_HUMAN	UPI00001678F0	.	tolerated(0.14)	benign(0.195)	27/28	.	Superfamily_domains:SSF50044	T:0.0004	T:0	T:0	.	T:0.002	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGGCTGGGG	byFrequency|byCluster|by1000G	5	ESCA
GNAI3	0	.	GRCh37	1	110135566	110135566	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*622T>C	.	.	ENST00000369851	9/9	37	20	17	50	50	0	GNAI3,3_prime_UTR_variant,,ENST00000369851,;RNU6V,upstream_gene_variant,,ENST00000384105,;RP5-1160K1.3,upstream_gene_variant,,ENST00000436416,;	C	ENSG00000065135	ENST00000369851	Transcript	3_prime_UTR_variant	1797	.	.	.	.	.	.	.	1	GNAI3	HGNC	4387	protein_coding	YES	CCDS802.1	ENSP00000358867	GNAI3_HUMAN	Q5TZX1_HUMAN,C9J2Z2_HUMAN	UPI000004D205	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCTCAAAG	.	5	ESCA
ATP1A1	0	.	GRCh37	1	116932186	116932186	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880A>T	p.Ile294Phe	p.I294F	ENST00000537345	8/23	83	64	18	79	79	0	ATP1A1,missense_variant,p.Ile294Phe,ENST00000537345,;ATP1A1,missense_variant,p.Ile294Phe,ENST00000295598,;ATP1A1,missense_variant,p.Ile263Phe,ENST00000369496,;ATP1A1,downstream_gene_variant,,ENST00000418797,;ATP1A1,downstream_gene_variant,,ENST00000369494,;ATP1A1,non_coding_transcript_exon_variant,,ENST00000491156,;ATP1A1OS,downstream_gene_variant,,ENST00000608511,;ATP1A1,downstream_gene_variant,,ENST00000463382,;ATP1A1,downstream_gene_variant,,ENST00000488733,;	T	ENSG00000163399	ENST00000537345	Transcript	missense_variant	1243	880	294	I/F	Atc/Ttc	.	.	.	1	ATP1A1	HGNC	799	protein_coding	YES	CCDS53351.1	ENSP00000445306	AT1A1_HUMAN	Q5TC02_HUMAN,Q5TC01_HUMAN	UPI0001A471A4	.	deleterious(0.04)	possibly_damaging(0.512)	8/23	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24093:SF222,hmmpanther:PTHR24093,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01106,Superfamily_domains:0049473,Prints_domain:PR00121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACATCATC	.	5	ESCA
NBPF10	0	.	GRCh37	1	145304458	145304458	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1391A>G	p.Lys464Arg	p.K464R	ENST00000342960	10/84	487	397	89	381	381	0	NBPF10,missense_variant,p.Lys130Arg,ENST00000605176,;NBPF10,missense_variant,p.Lys193Arg,ENST00000369339,;NBPF10,missense_variant,p.Lys464Arg,ENST00000342960,;NBPF10,missense_variant,p.Lys193Arg,ENST00000369338,;NBPF10,3_prime_UTR_variant,,ENST00000448873,;NBPF10,missense_variant,p.Lys464Arg,ENST00000490598,;RP11-458D21.5,3_prime_UTR_variant,,ENST00000468030,;NBPF10,3_prime_UTR_variant,,ENST00000464433,;	G	ENSG00000163386	ENST00000342960	Transcript	missense_variant	1426	1391	464	K/R	aAg/aGg	.	.	.	1	NBPF10	HGNC	31992	protein_coding	YES	.	ENSP00000345684	.	S4R3H5_HUMAN,A6NDV3_HUMAN	UPI0001CE93AE	.	.	possibly_damaging(0.745)	10/84	.	PROSITE_profiles:PS51316,hmmpanther:PTHR14199,hmmpanther:PTHR14199:SF16,Pfam_domain:PF06758	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGAAGGCTG	.	4	ESCA
OTUD7B	0	.	GRCh37	1	149914361	149914361	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1395G>A	.	.	ENST00000369135	12/12	14	5	9	9	9	0	OTUD7B,3_prime_UTR_variant,,ENST00000369135,;OTUD7B,downstream_gene_variant,,ENST00000417191,;	T	ENSG00000163113	ENST00000369135	Transcript	3_prime_UTR_variant	4222	.	.	.	.	.	.	.	-1	OTUD7B	HGNC	16683	protein_coding	YES	CCDS41389.1	ENSP00000358131	OTU7B_HUMAN	Q5SZ59_HUMAN	UPI000020415D	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGCATCCCCAC	.	3	ESCA
CD5L	0	.	GRCh37	1	157805945	157805945	+	Missense_Mutation	SNP	G	G	A	rs377627339	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.56C>T	p.Ala19Val	p.A19V	ENST00000368174	3/6	27	19	7	8	8	0	CD5L,missense_variant,p.Ala19Val,ENST00000368174,;CD5L,splice_region_variant,,ENST00000484609,;	A	ENSG00000073754	ENST00000368174	Transcript	missense_variant	153	56	19	A/V	gCg/gTg	rs377627339,COSM159866,COSM676234	.	.	-1	CD5L	HGNC	1690	protein_coding	YES	CCDS1171.1	ENSP00000357156	CD5L_HUMAN	.	UPI000012738C	.	tolerated(0.15)	benign(0.035)	3/6	.	hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF246	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGACGCTGCA	byCluster	3	ESCA
SUCO	0	.	GRCh37	1	172579996	172579996	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*597A>T	.	.	ENST00000263688	24/24	34	28	6	12	12	0	SUCO,3_prime_UTR_variant,,ENST00000608151,;SUCO,3_prime_UTR_variant,,ENST00000367723,;SUCO,3_prime_UTR_variant,,ENST00000263688,;SUCO,downstream_gene_variant,,ENST00000610051,;RNU6-693P,downstream_gene_variant,,ENST00000516134,;SUCO,downstream_gene_variant,,ENST00000609685,;	T	ENSG00000094975	ENST00000263688	Transcript	3_prime_UTR_variant	4581	.	.	.	.	.	.	.	1	SUCO	HGNC	1240	protein_coding	YES	CCDS1303.1	ENSP00000263688	SUCO_HUMAN	.	UPI0000070BAC	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTAAGTCTG	.	2	ESCA
IER5	0	.	GRCh37	1	181059092	181059092	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*70G>C	.	.	ENST00000367577	1/1	43	29	14	32	32	0	IER5,3_prime_UTR_variant,,ENST00000367577,;RP11-309G3.3,upstream_gene_variant,,ENST00000606938,;	C	ENSG00000162783	ENST00000367577	Transcript	3_prime_UTR_variant	1455	.	.	.	.	.	.	.	1	IER5	HGNC	5393	protein_coding	YES	CCDS1343.1	ENSP00000356549	IER5_HUMAN	.	UPI000013E1C9	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCCGGCTGC	.	5	ESCA
PRELP	0	.	GRCh37	1	203445038	203445038	+	5'UTR	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-45G>T	.	.	ENST00000343110	1/3	82	47	34	68	68	0	PRELP,5_prime_UTR_variant,,ENST00000343110,;	T	ENSG00000188783	ENST00000343110	Transcript	5_prime_UTR_variant	83	.	.	.	.	.	.	.	1	PRELP	HGNC	9357	protein_coding	YES	CCDS1438.1	ENSP00000343924	PRELP_HUMAN	Q7Z4B2_HUMAN	UPI000013222E	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCAGAGCTG	.	5	ESCA
LRP8	0	.	GRCh37	1	53715213	53715214	+	Frame_Shift_Ins	INS	-	-	AA	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2690_2691dupTT	p.Asp898LeufsTer59	p.D898Lfs*59	ENST00000306052	18/19	47	33	14	28	28	0	LRP8,frameshift_variant,p.Asp728LeufsTer59,ENST00000347547,;LRP8,frameshift_variant,p.Asp898LeufsTer59,ENST00000306052,;LRP8,intron_variant,,ENST00000465675,;LRP8,intron_variant,,ENST00000371454,;LRP8,intron_variant,,ENST00000354412,;LRP8,3_prime_UTR_variant,,ENST00000480045,;LRP8,intron_variant,,ENST00000529670,;LRP8,downstream_gene_variant,,ENST00000459674,;	AA	ENSG00000157193	ENST00000306052	Transcript	frameshift_variant	2793-2794	2691-2692	897-898	-/X	-/TT	.	.	.	-1	LRP8	HGNC	6700	protein_coding	YES	CCDS578.1	ENSP00000303634	LRP8_HUMAN	.	UPI00001AF338	.	.	.	18/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCGATCAAAGC	.	3	ESCA
DMRTB1	0	.	GRCh37	1	53927253	53927253	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.685C>T	p.Pro229Ser	p.P229S	ENST00000371445	2/4	25	22	3	27	27	0	DMRTB1,missense_variant,p.Pro229Ser,ENST00000371445,;DMRTB1,non_coding_transcript_exon_variant,,ENST00000463126,;	T	ENSG00000143006	ENST00000371445	Transcript	missense_variant	740	685	229	P/S	Cct/Tct	.	.	.	1	DMRTB1	HGNC	13913	protein_coding	YES	CCDS581.1	ENSP00000360500	DMRTB_HUMAN	I6L9A0_HUMAN	UPI000006FF4C	.	tolerated(0.14)	benign(0.147)	2/4	.	hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCCTCCTGGC	.	4	ESCA
LRRIQ3	0	.	GRCh37	1	74492493	74492493	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4A>G	.	.	ENST00000354431	8/8	59	34	24	56	56	0	LRRIQ3,3_prime_UTR_variant,,ENST00000417067,;LRRIQ3,3_prime_UTR_variant,,ENST00000395089,;LRRIQ3,3_prime_UTR_variant,,ENST00000354431,;LRRIQ3,3_prime_UTR_variant,,ENST00000415760,;	C	ENSG00000162620	ENST00000354431	Transcript	3_prime_UTR_variant	2071	.	.	.	.	.	.	.	-1	LRRIQ3	HGNC	28318	protein_coding	YES	CCDS41350.1	ENSP00000346414	LRIQ3_HUMAN	.	UPI000155D493	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATTGATTC	.	5	ESCA
ITPA	0	.	GRCh37	20	3194687	3194687	+	Silent	SNP	G	G	A	rs763647607	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246G>A	p.%3D	p.G82G	ENST00000380113	4/8	59	26	33	79	79	0	ITPA,synonymous_variant,p.%3D,ENST00000399838,;ITPA,synonymous_variant,p.%3D,ENST00000380113,;ITPA,synonymous_variant,p.%3D,ENST00000455664,;ITPA,non_coding_transcript_exon_variant,,ENST00000490838,;ITPA,non_coding_transcript_exon_variant,,ENST00000460676,;ITPA,non_coding_transcript_exon_variant,,ENST00000483354,;ITPA,non_coding_transcript_exon_variant,,ENST00000460550,;ITPA,upstream_gene_variant,,ENST00000461029,;ITPA,non_coding_transcript_exon_variant,,ENST00000609835,;	A	ENSG00000125877	ENST00000380113	Transcript	synonymous_variant	438	246	82	G	ggG/ggA	rs763647607	.	.	1	ITPA	HGNC	6176	protein_coding	YES	CCDS13051.1	ENSP00000369456	ITPA_HUMAN	Q5NT82_HUMAN	UPI0000072BC2	.	.	.	4/8	.	HAMAP:MF_03148,hmmpanther:PTHR11067,Pfam_domain:PF01725,Gene3D:3.90.950.10,TIGRFAM_domain:TIGR00042,Superfamily_domains:SSF52972	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGGGCTCCC	.	5	ESCA
YPEL1	0	.	GRCh37	22	22053852	22053852	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1566G>A	.	.	ENST00000339468	5/5	12	8	4	12	12	0	YPEL1,3_prime_UTR_variant,,ENST00000339468,;PPIL2,3_prime_UTR_variant,,ENST00000335025,;YPEL1,downstream_gene_variant,,ENST00000403503,;PPIL2,downstream_gene_variant,,ENST00000398831,;PPIL2,downstream_gene_variant,,ENST00000412327,;PPIL2,downstream_gene_variant,,ENST00000406385,;PPIL2,downstream_gene_variant,,ENST00000456792,;PPIL2,downstream_gene_variant,,ENST00000492445,;PPIL2,downstream_gene_variant,,ENST00000446951,;YPEL1,downstream_gene_variant,,ENST00000477675,;PPIL2,downstream_gene_variant,,ENST00000462188,;PPIL2,downstream_gene_variant,,ENST00000417788,;	T	ENSG00000100027	ENST00000339468	Transcript	3_prime_UTR_variant	2310	.	.	.	.	.	.	.	-1	YPEL1	HGNC	12845	protein_coding	YES	CCDS13794.1	ENSP00000342832	YPEL1_HUMAN	.	UPI000013BE05	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTGACATGGG	.	3	ESCA
IGLV3-12	0	.	GRCh37	22	23115074	23115074	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.346C>T	p.Pro116Ser	p.P116S	ENST00000390313	2/2	43	19	24	38	38	0	IGLV3-12,missense_variant,p.Pro116Ser,ENST00000390313,;LL22NC03-24A12.8,upstream_gene_variant,,ENST00000415642,;	T	ENSG00000211667	ENST00000390313	Transcript	missense_variant	355	346	116	P/S	Ccc/Tcc	.	.	.	1	IGLV3-12	HGNC	5898	IG_V_gene	YES	.	ENSP00000374848	.	Q5NV85_HUMAN	UPI0000EE5A3E	.	tolerated_low_confidence(0.14)	benign(0.227)	2/2	.	PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATCCCACG	.	5	ESCA
RAB36	0	.	GRCh37	22	23503091	23503091	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843C>T	p.%3D	p.S281S	ENST00000263116	10/11	31	28	3	35	35	0	RAB36,synonymous_variant,p.%3D,ENST00000341989,;RAB36,synonymous_variant,p.%3D,ENST00000263116,;RAB36,downstream_gene_variant,,ENST00000420895,;	T	ENSG00000100228	ENST00000263116	Transcript	synonymous_variant	883	843	281	S	agC/agT	.	.	.	1	RAB36	HGNC	9775	protein_coding	YES	CCDS13805.1	ENSP00000263116	RAB36_HUMAN	.	UPI000013D3AA	.	.	.	10/11	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF451,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,SMART_domains:SM00175,SMART_domains:SM00176,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00177,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCAGCCGCGT	.	2	ESCA
MCHR1	0	.	GRCh37	22	41077184	41077184	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.521G>A	p.Gly174Asp	p.G174D	ENST00000249016	2/2	36	23	12	45	45	0	MCHR1,missense_variant,p.Gly174Asp,ENST00000249016,;MCHR1,intron_variant,,ENST00000381433,;MCHR1,non_coding_transcript_exon_variant,,ENST00000498400,;MCHR1,non_coding_transcript_exon_variant,,ENST00000465662,;	A	ENSG00000128285	ENST00000249016	Transcript	missense_variant	1217	521	174	G/D	gGc/gAc	.	.	.	1	MCHR1	HGNC	4479	protein_coding	YES	CCDS14004.1	ENSP00000249016	MCHR1_HUMAN	Q5IFI4_HUMAN	UPI0000073C67	.	deleterious(0.02)	probably_damaging(1)	2/2	.	Prints_domain:PR01507,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF00001,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF17,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGGCAATG	.	5	ESCA
BUB1	0	.	GRCh37	2	111398882	111398882	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2783+2C>A	.	p.X928_splice	ENST00000302759	.	33	22	11	22	22	0	BUB1,splice_donor_variant,,ENST00000302759,;BUB1,splice_donor_variant,,ENST00000535254,;BUB1,intron_variant,,ENST00000409311,;BUB1,downstream_gene_variant,,ENST00000478175,;BUB1,downstream_gene_variant,,ENST00000466333,;	T	ENSG00000169679	ENST00000302759	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	BUB1	HGNC	1148	protein_coding	YES	CCDS33273.1	ENSP00000302530	BUB1_HUMAN	Q9BXX5_HUMAN,C9JRC7_HUMAN,C9JQA4_HUMAN,C9IYH4_HUMAN	UPI00000012C4	.	.	.	.	22/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTGCCCGT	.	5	ESCA
MAP3K2	0	.	GRCh37	2	128075818	128075818	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1121A>T	p.Tyr374Phe	p.Y374F	ENST00000409947	13/17	36	21	15	53	53	0	MAP3K2,missense_variant,p.Tyr374Phe,ENST00000409947,;MAP3K2,missense_variant,p.Tyr374Phe,ENST00000344908,;RNU6-1147P,downstream_gene_variant,,ENST00000363380,;	A	ENSG00000169967	ENST00000409947	Transcript	missense_variant	1404	1121	374	Y/F	tAt/tTt	.	.	.	-1	MAP3K2	HGNC	6854	protein_coding	YES	CCDS46404.1	ENSP00000387246	M3K2_HUMAN	Q96K88_HUMAN,F8W6K3_HUMAN	UPI0000208C78	.	deleterious(0.01)	benign(0.349)	13/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF37,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCATAACAG	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098957	178098957	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	2/5	53	40	13	55	55	0	NFE2L2,missense_variant,p.Leu14Phe,ENST00000449627,;NFE2L2,missense_variant,p.Leu14Phe,ENST00000423513,;NFE2L2,missense_variant,p.Leu30Phe,ENST00000397062,;NFE2L2,missense_variant,p.Leu14Phe,ENST00000446151,;NFE2L2,missense_variant,p.Leu14Phe,ENST00000588123,;NFE2L2,missense_variant,p.Leu29Phe,ENST00000586532,;NFE2L2,missense_variant,p.Leu14Phe,ENST00000421929,;NFE2L2,missense_variant,p.Leu14Phe,ENST00000464747,;NFE2L2,missense_variant,p.Leu14Phe,ENST00000448782,;NFE2L2,missense_variant,p.Leu14Phe,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	A	ENSG00000116044	ENST00000397062	Transcript	missense_variant	643	88	30	L/F	Ctt/Ttt	COSM132854	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.L30F|c.88C>T|6,CODON|p.L30R|c.89T>G|7,BUFFER|p.G31E|c.92G>A|5,BUFFER|p.G31A|c.92G>C|7,BUFFER|p.D29G|c.86A>G|11,BUFFER|p.D29H|c.85G>C|12,BUFFER|p.D29N|c.85G>A|3,BUFFER|p.D29Y|c.85G>T|4,BUFFER|p.D27G|c.80A>G|3	MUTECT|MUSE	TCCAAGATCTA	.	2	ESCA
MYT1L	0	.	GRCh37	2	1795481	1795481	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*158A>T	.	.	ENST00000428368	25/25	38	30	7	47	47	0	MYT1L,3_prime_UTR_variant,,ENST00000399161,;MYT1L,3_prime_UTR_variant,,ENST00000407844,;MYT1L,3_prime_UTR_variant,,ENST00000428368,;MYT1L,intron_variant,,ENST00000399157,;	A	ENSG00000186487	ENST00000428368	Transcript	3_prime_UTR_variant	4383	.	.	.	.	.	.	.	-1	MYT1L	HGNC	7623	protein_coding	YES	CCDS46222.1	ENSP00000396103	MYT1L_HUMAN	.	UPI00004E55EA	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTATCTTTA	.	5	ESCA
TTN	0	.	GRCh37	2	179647001	179647001	+	Silent	SNP	G	G	A	rs141768043	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3318C>T	p.%3D	p.G1106G	ENST00000589042	20/363	36	22	14	28	28	0	TTN,synonymous_variant,p.%3D,ENST00000360870,;TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000342175,;TTN,synonymous_variant,p.%3D,ENST00000359218,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000460472,;TTN,downstream_gene_variant,,ENST00000436599,;RP11-88L24.4,downstream_gene_variant,,ENST00000582038,;	A	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	3543	3318	1106	G	ggC/ggT	rs141768043,COSM1178786,COSM1178785,COSM1178782,COSM1178784,COSM1178783,COSM1178787	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	20/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0.0007	A:0	likely_benign	0,1,1,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G1060G|c.3180C>T|5,SITE|p.G1106G|c.3318C>T|5,SITE|p.G1060G|c.3180C>T|5,SITE|p.G1106G|c.3318C>T|5,SITE|p.G1106G|c.3318C>T|5,SITE|p.G1060G|c.3180C>T|5	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCCGCCAAC	byCluster	4	ESCA
MYO1B	0	.	GRCh37	2	192280957	192280957	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3276G>T	p.Glu1092Asp	p.E1092D	ENST00000392318	30/31	38	22	15	49	49	0	MYO1B,missense_variant,p.Glu1063Asp,ENST00000392316,;MYO1B,missense_variant,p.Glu1092Asp,ENST00000392318,;MYO1B,missense_variant,p.Glu1034Asp,ENST00000339514,;MYO1B,missense_variant,p.Glu337Asp,ENST00000439065,;MYO1B,missense_variant,p.Glu171Asp,ENST00000427152,;MYO1B,missense_variant,p.Glu1092Asp,ENST00000304164,;MYO1B,non_coding_transcript_exon_variant,,ENST00000490069,;	T	ENSG00000128641	ENST00000392318	Transcript	missense_variant	3523	3276	1092	E/D	gaG/gaT	.	.	.	1	MYO1B	HGNC	7596	protein_coding	YES	CCDS46477.1	ENSP00000376132	MYO1B_HUMAN	Q14777_HUMAN,E7EQD9_HUMAN,C9K0I9_HUMAN,C9JYW1_HUMAN,C9JUP5_HUMAN,B0I1S9_HUMAN	UPI00001A9466	.	tolerated(0.47)	benign(0.014)	30/31	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF277,Pfam_domain:PF06017	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGAGATTTC	.	5	ESCA
AC096772.6	0	.	GRCh37	2	208687115	208687115	+	RNA	SNP	A	A	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.379T>G	.	.	ENST00000343987	1/2	72	45	27	104	104	0	AC096772.6,non_coding_transcript_exon_variant,,ENST00000343987,;	C	ENSG00000244567	ENST00000343987	Transcript	non_coding_transcript_exon_variant	379	.	.	.	.	.	.	.	-1	AC096772.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCAATTATG	.	5	ESCA
CTDSP1	0	.	GRCh37	2	219270431	219270431	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1283C>T	.	.	ENST00000273062	7/7	29	17	11	53	53	0	CTDSP1,3_prime_UTR_variant,,ENST00000273062,;CTDSP1,downstream_gene_variant,,ENST00000452977,;CTDSP1,downstream_gene_variant,,ENST00000431127,;CTDSP1,downstream_gene_variant,,ENST00000428361,;CTDSP1,downstream_gene_variant,,ENST00000443891,;MIR26B,downstream_gene_variant,,ENST00000362251,;CTDSP1,downstream_gene_variant,,ENST00000464255,;CTDSP1,downstream_gene_variant,,ENST00000473420,;CTDSP1,downstream_gene_variant,,ENST00000496785,;CTDSP1,downstream_gene_variant,,ENST00000498160,;CTDSP1,downstream_gene_variant,,ENST00000488627,;CTDSP1,downstream_gene_variant,,ENST00000491064,;CTDSP1,downstream_gene_variant,,ENST00000497677,;CTDSP1,downstream_gene_variant,,ENST00000482272,;CTDSP1,downstream_gene_variant,,ENST00000494067,;	T	ENSG00000144579	ENST00000273062	Transcript	3_prime_UTR_variant	2405	.	.	.	.	.	.	.	1	CTDSP1	HGNC	21614	protein_coding	YES	CCDS2416.1	ENSP00000273062	CTDS1_HUMAN	.	UPI000013007C	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGCGATTC	.	5	ESCA
STAMBP	0	.	GRCh37	2	74072312	74072312	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298T>C	p.Phe100Leu	p.F100L	ENST00000394070	4/10	46	27	19	52	52	0	STAMBP,missense_variant,p.Phe100Leu,ENST00000424659,;STAMBP,missense_variant,p.Phe100Leu,ENST00000409707,;STAMBP,missense_variant,p.Phe100Leu,ENST00000394070,;STAMBP,missense_variant,p.Phe100Leu,ENST00000536064,;STAMBP,missense_variant,p.Phe100Leu,ENST00000452725,;STAMBP,missense_variant,p.Phe100Leu,ENST00000394073,;STAMBP,missense_variant,p.Phe100Leu,ENST00000339566,;STAMBP,missense_variant,p.Phe100Leu,ENST00000432295,;STAMBP,non_coding_transcript_exon_variant,,ENST00000478946,;	C	ENSG00000124356	ENST00000394070	Transcript	missense_variant	801	298	100	F/L	Ttt/Ctt	.	.	.	1	STAMBP	HGNC	16950	protein_coding	YES	CCDS1929.1	ENSP00000377633	STABP_HUMAN	C9JZ93_HUMAN,C9JK83_HUMAN,C9JEK5_HUMAN	UPI0000038DA0	.	tolerated(0.06)	possibly_damaging(0.818)	4/10	.	hmmpanther:PTHR12947,hmmpanther:PTHR12947:SF8,Pfam_domain:PF08969,Gene3D:1.20.58.280,Superfamily_domains:0051729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCATTTCCC	.	5	ESCA
C2orf68	0	.	GRCh37	2	85838860	85838860	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.157A>T	p.Arg53Trp	p.R53W	ENST00000306336	2/4	29	18	11	35	35	0	C2orf68,missense_variant,p.Arg53Trp,ENST00000306336,;C2orf68,missense_variant,p.Arg53Trp,ENST00000409734,;USP39,upstream_gene_variant,,ENST00000323701,;USP39,upstream_gene_variant,,ENST00000409766,;USP39,upstream_gene_variant,,ENST00000448971,;USP39,upstream_gene_variant,,ENST00000442708,;USP39,upstream_gene_variant,,ENST00000409470,;USP39,upstream_gene_variant,,ENST00000409025,;USP39,upstream_gene_variant,,ENST00000450066,;C2orf68,non_coding_transcript_exon_variant,,ENST00000478626,;USP39,intron_variant,,ENST00000459775,;USP39,intron_variant,,ENST00000474572,;USP39,intron_variant,,ENST00000491659,;USP39,upstream_gene_variant,,ENST00000465282,;USP39,upstream_gene_variant,,ENST00000455732,;C2orf68,splice_region_variant,,ENST00000423181,;C2orf68,3_prime_UTR_variant,,ENST00000420686,;USP39,upstream_gene_variant,,ENST00000458268,;USP39,upstream_gene_variant,,ENST00000493829,;	A	ENSG00000168887	ENST00000306336	Transcript	missense_variant	202	157	53	R/W	Agg/Tgg	.	.	.	-1	C2orf68	HGNC	34353	protein_coding	YES	CCDS42704.1	ENSP00000304410	CB068_HUMAN	L7T9J5_HUMAN	UPI00002377B0	.	deleterious(0)	possibly_damaging(0.905)	2/4	.	Low_complexity_(Seg):seg,Pfam_domain:PF10573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGCCTCCTCA	.	2	ESCA
NIT2	0	.	GRCh37	3	100058768	100058768	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236A>T	p.Tyr79Phe	p.Y79F	ENST00000394140	3/10	113	60	53	65	65	0	NIT2,missense_variant,p.Tyr173Phe,ENST00000497785,;NIT2,missense_variant,p.Tyr79Phe,ENST00000394140,;NIT2,missense_variant,p.Tyr79Phe,ENST00000480073,;NIT2,3_prime_UTR_variant,,ENST00000460317,;NIT2,non_coding_transcript_exon_variant,,ENST00000478856,;NIT2,non_coding_transcript_exon_variant,,ENST00000472392,;NIT2,non_coding_transcript_exon_variant,,ENST00000465368,;	T	ENSG00000114021	ENST00000394140	Transcript	missense_variant	327	236	79	Y/F	tAt/tTt	.	.	.	1	NIT2	HGNC	29878	protein_coding	YES	CCDS33806.1	ENSP00000377696	NIT2_HUMAN	.	UPI000004A5A7	.	tolerated(0.16)	benign(0.057)	3/10	.	PROSITE_profiles:PS50263,hmmpanther:PTHR23088:SF20,hmmpanther:PTHR23088,Gene3D:3.60.110.10,Pfam_domain:PF00795,Superfamily_domains:SSF56317	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATATATCTCA	.	5	ESCA
CD200R1	0	.	GRCh37	3	112643345	112643345	+	Missense_Mutation	SNP	C	C	T	rs763301923	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916G>A	p.Val306Ile	p.V306I	ENST00000308611	7/8	93	73	20	47	47	0	CD200R1,missense_variant,p.Val306Ile,ENST00000308611,;CD200R1,missense_variant,p.Val283Ile,ENST00000471858,;CD200R1,intron_variant,,ENST00000295863,;CD200R1,downstream_gene_variant,,ENST00000440122,;CD200R1,downstream_gene_variant,,ENST00000490004,;	T	ENSG00000163606	ENST00000308611	Transcript	missense_variant	1181	916	306	V/I	Gtt/Att	rs763301923,COSM1327972	.	.	-1	CD200R1	HGNC	24235	protein_coding	YES	CCDS2969.1	ENSP00000311035	MO2R1_HUMAN	.	UPI000013E2BD	.	tolerated(0.17)	benign(0.025)	7/8	.	hmmpanther:PTHR21462:SF2,hmmpanther:PTHR21462	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAACAACTG	.	5	ESCA
GOLGB1	0	.	GRCh37	3	121400679	121400679	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8728T>C	p.%3D	p.L2910L	ENST00000393667	15/22	51	31	20	47	47	0	GOLGB1,synonymous_variant,p.%3D,ENST00000393667,;GOLGB1,synonymous_variant,p.%3D,ENST00000340645,;GOLGB1,3_prime_UTR_variant,,ENST00000482512,;GOLGB1,upstream_gene_variant,,ENST00000491690,;	G	ENSG00000173230	ENST00000393667	Transcript	synonymous_variant	8839	8728	2910	L	Tta/Cta	.	.	.	-1	GOLGB1	HGNC	4429	protein_coding	YES	CCDS58847.1	ENSP00000377275	GOGB1_HUMAN	C9J8Q0_HUMAN	UPI0001AE7645	.	.	.	15/22	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18887,hmmpanther:PTHR18887:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTAAGTATT	.	5	ESCA
ABTB1	0	.	GRCh37	3	127396675	127396675	+	Missense_Mutation	SNP	G	G	A	rs764861864	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1018G>A	p.Asp340Asn	p.D340N	ENST00000232744	10/12	17	13	4	10	10	0	ABTB1,missense_variant,p.Asp198Asn,ENST00000453791,;ABTB1,missense_variant,p.Asp198Asn,ENST00000468137,;ABTB1,missense_variant,p.Asp340Asn,ENST00000232744,;ABTB1,missense_variant,p.Asp198Asn,ENST00000393363,;ABTB1,non_coding_transcript_exon_variant,,ENST00000491633,;ABTB1,downstream_gene_variant,,ENST00000466612,;ABTB1,downstream_gene_variant,,ENST00000467179,;ABTB1,missense_variant,p.Asp123Asn,ENST00000497162,;ABTB1,3_prime_UTR_variant,,ENST00000475042,;ABTB1,non_coding_transcript_exon_variant,,ENST00000478298,;ABTB1,non_coding_transcript_exon_variant,,ENST00000464431,;ABTB1,non_coding_transcript_exon_variant,,ENST00000474129,;ABTB1,downstream_gene_variant,,ENST00000479280,;ABTB1,downstream_gene_variant,,ENST00000483857,;ABTB1,downstream_gene_variant,,ENST00000475265,;ABTB1,downstream_gene_variant,,ENST00000493365,;	A	ENSG00000114626	ENST00000232744	Transcript	missense_variant	1104	1018	340	D/N	Gac/Aac	rs764861864,COSM203661	.	.	1	ABTB1	HGNC	18275	protein_coding	YES	CCDS3045.1	ENSP00000232744	ABTB1_HUMAN	.	UPI0000035DA3	.	tolerated(0.18)	possibly_damaging(0.573)	10/12	.	PROSITE_profiles:PS50097,hmmpanther:PTHR24413:SF83,hmmpanther:PTHR24413,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAGCGACCAC	.	2	ESCA
STAG1	0	.	GRCh37	3	136056729	136056729	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*367A>C	.	.	ENST00000383202	34/34	39	34	5	19	19	0	STAG1,3_prime_UTR_variant,,ENST00000434713,;STAG1,3_prime_UTR_variant,,ENST00000383202,;PCCB,3_prime_UTR_variant,,ENST00000478469,;STAG1,3_prime_UTR_variant,,ENST00000236698,;PCCB,3_prime_UTR_variant,,ENST00000471595,;STAG1,downstream_gene_variant,,ENST00000536929,;STAG1,3_prime_UTR_variant,,ENST00000483235,;	G	ENSG00000118007	ENST00000383202	Transcript	3_prime_UTR_variant	4401	.	.	.	.	.	.	.	-1	STAG1	HGNC	11354	protein_coding	YES	CCDS3090.1	ENSP00000372689	STAG1_HUMAN	Q4LE48_HUMAN	UPI000020A2DE	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATATGTTTTTT	.	3	ESCA
CNTN6	0	.	GRCh37	3	1363504	1363504	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933delA	p.Gln311HisfsTer42	p.Q311Hfs*42	ENST00000446702	8/23	29	17	12	21	21	0	CNTN6,frameshift_variant,p.Gln239HisfsTer42,ENST00000539053,;CNTN6,frameshift_variant,p.Gln311HisfsTer42,ENST00000446702,;CNTN6,frameshift_variant,p.Gln311HisfsTer42,ENST00000350110,;CNTN6,3_prime_UTR_variant,,ENST00000397479,;	-	ENSG00000134115	ENST00000446702	Transcript	frameshift_variant	1559	932	311	Q/X	cAa/ca	.	.	.	1	CNTN6	HGNC	2176	protein_coding	YES	CCDS2557.1	ENSP00000407822	CNTN6_HUMAN	F5H752_HUMAN	UPI0000072430	.	.	.	8/23	.	hmmpanther:PTHR10489:SF52,hmmpanther:PTHR10489,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGGTCAACTCA	.	3	ESCA
MRPS25	0	.	GRCh37	3	15090343	15090343	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3605C>A	.	.	ENST00000253686	4/4	46	28	18	74	74	0	MRPS25,3_prime_UTR_variant,,ENST00000253686,;NR2C2,intron_variant,,ENST00000439011,;NR2C2,intron_variant,,ENST00000413194,;MRPS25,downstream_gene_variant,,ENST00000449354,;MRPS25,downstream_gene_variant,,ENST00000444840,;MRPS25,intron_variant,,ENST00000474866,;MRPS25,intron_variant,,ENST00000496484,;MRPS25,downstream_gene_variant,,ENST00000420267,;MRPS25,downstream_gene_variant,,ENST00000447299,;	T	ENSG00000131368	ENST00000253686	Transcript	3_prime_UTR_variant	4268	.	.	.	.	.	.	.	-1	MRPS25	HGNC	14511	protein_coding	YES	CCDS2622.1	ENSP00000253686	RT25_HUMAN	Q96Q22_HUMAN,E7EPW2_HUMAN	UPI00001352A0	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAATGTAACT	.	5	ESCA
SPATA16	0	.	GRCh37	3	172835311	172835311	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211G>T	p.Glu71Ter	p.E71*	ENST00000351008	2/11	89	68	20	64	64	0	SPATA16,stop_gained,p.Glu71Ter,ENST00000351008,;	A	ENSG00000144962	ENST00000351008	Transcript	stop_gained	395	211	71	E/*	Gaa/Taa	.	.	.	-1	SPATA16	HGNC	29935	protein_coding	YES	CCDS3221.1	ENSP00000341765	SPT16_HUMAN	.	UPI000013D9BF	.	.	.	2/11	.	Pfam_domain:PF15015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCTTTGA	.	5	ESCA
TBL1XR1	0	.	GRCh37	3	176742123	176742123	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1163C>G	.	.	ENST00000430069	16/16	71	47	24	29	29	0	TBL1XR1,3_prime_UTR_variant,,ENST00000457928,;TBL1XR1,3_prime_UTR_variant,,ENST00000430069,;TBL1XR1,non_coding_transcript_exon_variant,,ENST00000474363,;	C	ENSG00000177565	ENST00000430069	Transcript	3_prime_UTR_variant	2968	.	.	.	.	.	.	.	-1	TBL1XR1	HGNC	29529	protein_coding	YES	CCDS46961.1	ENSP00000405574	TBL1R_HUMAN	C9JY82_HUMAN,C9JTW8_HUMAN,C9JLJ1_HUMAN,C9JEC9_HUMAN,C9JCW4_HUMAN,C9JCK0_HUMAN,C9JBN1_HUMAN,C9J903_HUMAN,C9J7E1_HUMAN,C9J3H2_HUMAN,C9IYU9_HUMAN	UPI0000136A71	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCCGTTATC	.	5	ESCA
BDH1	0	.	GRCh37	3	197260430	197260430	+	Missense_Mutation	SNP	C	C	T	rs201898088	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86G>A	p.Arg29His	p.R29H	ENST00000392379	4/8	83	65	18	43	42	1	BDH1,missense_variant,p.Arg29His,ENST00000445160,;BDH1,missense_variant,p.Arg29His,ENST00000392379,;BDH1,missense_variant,p.Arg10His,ENST00000434143,;BDH1,missense_variant,p.Arg29His,ENST00000392378,;BDH1,missense_variant,p.Arg29His,ENST00000431056,;BDH1,missense_variant,p.Arg29His,ENST00000432819,;BDH1,missense_variant,p.Arg29His,ENST00000358186,;BDH1,splice_region_variant,,ENST00000446746,;BDH1,splice_region_variant,,ENST00000441275,;BDH1,non_coding_transcript_exon_variant,,ENST00000477015,;BDH1,non_coding_transcript_exon_variant,,ENST00000495285,;	T	ENSG00000161267	ENST00000392379	Transcript	missense_variant	488	86	29	R/H	cGc/cAc	rs201898088,COSM4116498	.	.	-1	BDH1	HGNC	1027	protein_coding	YES	CCDS3328.1	ENSP00000376184	BDH_HUMAN	E9PCG9_HUMAN,C9K0G7_HUMAN,C9JQ90_HUMAN,C9JEB9_HUMAN,C9JB83_HUMAN,A1E284_HUMAN	UPI0000126875	.	tolerated_low_confidence(0.17)	benign(0)	4/8	.	hmmpanther:PTHR24316,hmmpanther:PTHR24316:SF279	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|VARSCANS	GTGGGCGTCTG	byCluster	3	ESCA
CADM2	0	.	GRCh37	3	86116280	86116281	+	3'Flank	INS	-	-	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000405615	.	66	50	16	46	46	0	CADM2,3_prime_UTR_variant,,ENST00000383699,;CADM2,downstream_gene_variant,,ENST00000407528,;CADM2,downstream_gene_variant,,ENST00000405615,;	T	ENSG00000175161	ENST00000405615	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	347	1	CADM2	HGNC	29849	protein_coding	YES	CCDS33792.1	ENSP00000384193	CADM2_HUMAN	G3XHN8_HUMAN	UPI000013F077	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCCCATTTTT	.	3	ESCA
HS3ST1	0	.	GRCh37	4	11400816	11400816	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814C>T	p.Arg272Trp	p.R272W	ENST00000002596	2/2	32	27	4	44	44	0	HS3ST1,missense_variant,p.Arg272Trp,ENST00000002596,;HS3ST1,downstream_gene_variant,,ENST00000510712,;HS3ST1,downstream_gene_variant,,ENST00000514690,;	A	ENSG00000002587	ENST00000002596	Transcript	missense_variant	1989	814	272	R/W	Cgg/Tgg	COSM3599213	.	.	-1	HS3ST1	HGNC	5194	protein_coding	YES	CCDS3408.1	ENSP00000002596	HS3S1_HUMAN	Q05CH3_HUMAN,E9PDE3_HUMAN	UPI0000072A23	.	deleterious(0)	probably_damaging(0.999)	2/2	.	hmmpanther:PTHR10605:SF16,hmmpanther:PTHR10605,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCCCGGCCTT	.	4	ESCA
FGG	0	.	GRCh37	4	155528020	155528020	+	Silent	SNP	G	G	A	rs146218442	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.966C>T	p.%3D	p.G322G	ENST00000336098	8/9	22	9	12	42	42	0	FGG,synonymous_variant,p.%3D,ENST00000407946,;FGG,synonymous_variant,p.%3D,ENST00000336098,;FGG,synonymous_variant,p.%3D,ENST00000404648,;FGG,synonymous_variant,p.%3D,ENST00000405164,;FGG,downstream_gene_variant,,ENST00000443553,;FGG,downstream_gene_variant,,ENST00000393846,;FGG,non_coding_transcript_exon_variant,,ENST00000492082,;FGG,non_coding_transcript_exon_variant,,ENST00000465913,;FGG,downstream_gene_variant,,ENST00000473393,;FGG,downstream_gene_variant,,ENST00000464532,;FGG,downstream_gene_variant,,ENST00000465336,;	A	ENSG00000171557	ENST00000336098	Transcript	synonymous_variant	1005	966	322	G	ggC/ggT	rs146218442,COSM3409117	.	.	-1	FGG	HGNC	3694	protein_coding	YES	CCDS3788.1	ENSP00000336829	FIBG_HUMAN	C9JU00_HUMAN,C9JPQ9_HUMAN	UPI000012A78D	.	.	.	8/9	.	Superfamily_domains:SSF56496,SMART_domains:SM00186,Pfam_domain:PF00147,Gene3D:3.90.215.10,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF22,PROSITE_profiles:PS51406,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	A:0	A:0.0001	not_provided	0,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATCGCCAAA	byCluster	5	ESCA
ZNF732	0	.	GRCh37	4	265855	265855	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.791C>A	p.Thr264Asn	p.T264N	ENST00000419098	4/4	24	15	9	28	28	0	ZNF732,missense_variant,p.Thr264Asn,ENST00000419098,;RP11-478C6.5,upstream_gene_variant,,ENST00000507882,;RP11-478C6.6,upstream_gene_variant,,ENST00000511111,;	T	ENSG00000186777	ENST00000419098	Transcript	missense_variant	802	791	264	T/N	aCc/aAc	.	.	.	-1	ZNF732	HGNC	37138	protein_coding	YES	CCDS46990.1	ENSP00000415774	ZN732_HUMAN	.	UPI00017A8291	.	tolerated(0.78)	probably_damaging(0.987)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF81,hmmpanther:PTHR24384,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGGGTTGAG	.	5	ESCA
HTT	0	.	GRCh37	4	3109067	3109078	+	In_Frame_Del	DEL	GAATCAGTCCAG	GAATCAGTCCAG	-	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	GAATCAGTCCAG	GAATCAGTCCAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.666_677delATCAGTCCAGGA	p.Ser223_Glu226del	p.S223_E226del	ENST00000355072	6/67	26	20	6	29	29	0	HTT,inframe_deletion,p.Ser223_Glu226del,ENST00000355072,;	-	ENSG00000197386	ENST00000355072	Transcript	inframe_deletion	809-820	664-675	222-225	ESVQ/-	GAATCAGTCCAG/-	.	.	.	1	HTT	HGNC	4851	protein_coding	YES	CCDS43206.1	ENSP00000347184	HD_HUMAN	D3DVR8_HUMAN,D2CTD8_HUMAN,D2CTD7_HUMAN,D2CTD4_HUMAN,D2CTD2_HUMAN	UPI000013D567	.	.	.	6/67	.	hmmpanther:PTHR10170:SF10,hmmpanther:PTHR10170,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	VARSCANI*|PINDEL	CCCGAAGAATCAGTCCAGGAGAC	.	2	ESCA
DCUN1D4	0	.	GRCh37	4	52781950	52781950	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2200A>G	.	.	ENST00000334635	11/11	25	9	16	69	69	0	DCUN1D4,3_prime_UTR_variant,,ENST00000381441,;DCUN1D4,3_prime_UTR_variant,,ENST00000334635,;DCUN1D4,downstream_gene_variant,,ENST00000510808,;DCUN1D4,downstream_gene_variant,,ENST00000381437,;DCUN1D4,downstream_gene_variant,,ENST00000451288,;RP11-365H22.2,upstream_gene_variant,,ENST00000610270,;DCUN1D4,downstream_gene_variant,,ENST00000507659,;DCUN1D4,downstream_gene_variant,,ENST00000510587,;DCUN1D4,downstream_gene_variant,,ENST00000508257,;DCUN1D4,3_prime_UTR_variant,,ENST00000477560,;DCUN1D4,downstream_gene_variant,,ENST00000509376,;DCUN1D4,downstream_gene_variant,,ENST00000505634,;DCUN1D4,downstream_gene_variant,,ENST00000507741,;DCUN1D4,downstream_gene_variant,,ENST00000512199,;DCUN1D4,downstream_gene_variant,,ENST00000510518,;	G	ENSG00000109184	ENST00000334635	Transcript	3_prime_UTR_variant	3259	.	.	.	.	.	.	.	1	DCUN1D4	HGNC	28998	protein_coding	YES	CCDS33982.1	ENSP00000334625	DCNL4_HUMAN	B4DH26_HUMAN	UPI00001C1E10	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAATCAAC	.	5	ESCA
UBTD2	0	.	GRCh37	5	171638319	171638319	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*515G>T	.	.	ENST00000393792	3/3	29	17	12	38	38	0	UBTD2,3_prime_UTR_variant,,ENST00000393792,;	A	ENSG00000168246	ENST00000393792	Transcript	3_prime_UTR_variant	1626	.	.	.	.	.	.	.	-1	UBTD2	HGNC	24463	protein_coding	YES	CCDS4379.2	ENSP00000377381	UBTD2_HUMAN	B3KMW8_HUMAN,B2R886_HUMAN	UPI000020C12C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAACCTCAA	.	2	ESCA
CDH10	0	.	GRCh37	5	24491785	24491785	+	Silent	SNP	T	T	C	rs752469511	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1776A>G	p.%3D	p.Q592Q	ENST00000264463	11/12	37	23	14	22	22	0	CDH10,synonymous_variant,p.%3D,ENST00000264463,;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,;	C	ENSG00000040731	ENST00000264463	Transcript	synonymous_variant	2284	1776	592	Q	caA/caG	rs752469511	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	.	.	11/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,SMART_domains:SM00112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCTTGGCT	.	5	ESCA
MROH2B	0	.	GRCh37	5	41051168	41051168	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1255C>A	p.His419Asn	p.H419N	ENST00000399564	13/42	45	27	18	54	54	0	MROH2B,missense_variant,p.His419Asn,ENST00000399564,;MROH2B,5_prime_UTR_variant,,ENST00000506092,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000508575,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,;	T	ENSG00000171495	ENST00000399564	Transcript	missense_variant	1706	1255	419	H/N	Cat/Aat	.	.	.	-1	MROH2B	HGNC	26857	protein_coding	YES	CCDS47202.1	ENSP00000382476	MRO2B_HUMAN	F5GZ06_HUMAN	UPI000020CA04	.	tolerated(0.47)	benign(0.026)	13/42	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF15,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATGAAAGT	.	5	ESCA
RAB3C	0	.	GRCh37	5	58021834	58021834	+	Silent	SNP	A	A	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258A>C	p.%3D	p.T86T	ENST00000282878	3/5	37	17	20	29	29	0	RAB3C,synonymous_variant,p.%3D,ENST00000282878,;RAB3C,non_coding_transcript_exon_variant,,ENST00000507977,;	C	ENSG00000152932	ENST00000282878	Transcript	synonymous_variant	427	258	86	T	acA/acC	.	.	.	1	RAB3C	HGNC	30269	protein_coding	YES	CCDS3976.1	ENSP00000282878	RAB3C_HUMAN	.	UPI0000133178	.	.	.	3/5	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF445,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,Gene3D:3.40.50.300,SMART_domains:SM00174,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00175,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACACAGCAGG	.	5	ESCA
FCHO2	0	.	GRCh37	5	72385446	72385446	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1529T>C	.	.	ENST00000430046	26/26	86	50	35	83	83	0	FCHO2,3_prime_UTR_variant,,ENST00000341845,;FCHO2,3_prime_UTR_variant,,ENST00000430046,;FCHO2,downstream_gene_variant,,ENST00000512348,;	C	ENSG00000157107	ENST00000430046	Transcript	3_prime_UTR_variant	4078	.	.	.	.	.	.	.	1	FCHO2	HGNC	25180	protein_coding	YES	CCDS47230.1	ENSP00000393776	FCHO2_HUMAN	B4DEU7_HUMAN	UPI000019971A	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTATAATAA	.	5	ESCA
REV3L	0	.	GRCh37	6	111654555	111654555	+	Missense_Mutation	SNP	T	T	C	rs368840674	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7696A>G	p.Met2566Val	p.M2566V	ENST00000358835	24/33	51	37	14	51	51	0	REV3L,missense_variant,p.Met2488Val,ENST00000435970,;REV3L,missense_variant,p.Met2566Val,ENST00000358835,;REV3L,missense_variant,p.Met2566Val,ENST00000368802,;REV3L,missense_variant,p.Met2566Val,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000434009,;REV3L,3_prime_UTR_variant,,ENST00000422377,;	C	ENSG00000009413	ENST00000358835	Transcript	missense_variant	8151	7696	2566	M/V	Atg/Gtg	rs368840674	.	.	-1	REV3L	HGNC	9968	protein_coding	YES	CCDS5091.2	ENSP00000351697	DPOLZ_HUMAN	Q9UID5_HUMAN,C4TNX2_HUMAN,C4TNX1_HUMAN,C4TNX0_HUMAN,C4B7Q4_HUMAN	UPI0000140023	.	deleterious(0.01)	benign(0.1)	24/33	.	SMART_domains:SM00486,Pfam_domain:PF00136,hmmpanther:PTHR10322:SF16,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCATTGATT	.	5	ESCA
RAB32	0	.	GRCh37	6	146870631	146870632	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283dupT	p.Tyr95LeufsTer13	p.Y95Lfs*13	ENST00000367495	2/3	94	68	26	83	83	0	RAB32,frameshift_variant,p.Tyr95LeufsTer13,ENST00000367495,;	T	ENSG00000118508	ENST00000367495	Transcript	frameshift_variant	461-462	282-283	94-95	-/X	-/T	.	.	.	1	RAB32	HGNC	9772	protein_coding	YES	CCDS5210.1	ENSP00000356465	RAB32_HUMAN	.	UPI000000126A	.	.	.	2/3	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF440,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00176,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGAGTATACTA	.	3	ESCA
BAG6	0	.	GRCh37	6	31610093	31610093	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2041C>G	p.Pro681Ala	p.P681A	ENST00000375964	15/25	23	16	7	25	25	0	BAG6,missense_variant,p.Pro675Ala,ENST00000375976,;BAG6,missense_variant,p.Pro675Ala,ENST00000362049,;BAG6,missense_variant,p.Pro711Ala,ENST00000437771,;BAG6,missense_variant,p.Pro681Ala,ENST00000375964,;BAG6,missense_variant,p.Pro675Ala,ENST00000211379,;BAG6,missense_variant,p.Pro711Ala,ENST00000404765,;BAG6,intron_variant,,ENST00000439687,;BAG6,downstream_gene_variant,,ENST00000435080,;PRRC2A,downstream_gene_variant,,ENST00000376033,;BAG6,upstream_gene_variant,,ENST00000441793,;BAG6,downstream_gene_variant,,ENST00000453833,;BAG6,upstream_gene_variant,,ENST00000422948,;PRRC2A,downstream_gene_variant,,ENST00000376007,;BAG6,downstream_gene_variant,,ENST00000438149,;BAG6,non_coding_transcript_exon_variant,,ENST00000470875,;BAG6,upstream_gene_variant,,ENST00000464869,;BAG6,downstream_gene_variant,,ENST00000469182,;BAG6,upstream_gene_variant,,ENST00000464126,;BAG6,downstream_gene_variant,,ENST00000465348,;BAG6,downstream_gene_variant,,ENST00000462682,;PRRC2A,downstream_gene_variant,,ENST00000462617,;PRRC2A,downstream_gene_variant,,ENST00000482441,;PRRC2A,downstream_gene_variant,,ENST00000492691,;BAG6,upstream_gene_variant,,ENST00000462875,;	C	ENSG00000204463	ENST00000375964	Transcript	missense_variant	2355	2041	681	P/A	Cct/Gct	.	.	.	-1	BAG6	HGNC	13919	protein_coding	YES	CCDS47403.1	ENSP00000365131	BAG6_HUMAN	F6TC96_HUMAN,F6RG75_HUMAN	UPI000047029D	.	tolerated(0.36)	benign(0.025)	15/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGGGGAGC	.	2	ESCA
TJAP1	0	.	GRCh37	6	43469320	43469320	+	Missense_Mutation	SNP	G	G	A	rs370044590	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.185G>A	p.Arg62His	p.R62H	ENST00000372445	6/11	21	11	9	22	22	0	TJAP1,missense_variant,p.Arg62His,ENST00000372449,;TJAP1,missense_variant,p.Arg62His,ENST00000436109,;TJAP1,missense_variant,p.Arg62His,ENST00000372454,;TJAP1,missense_variant,p.Arg62His,ENST00000438588,;TJAP1,missense_variant,p.Arg62His,ENST00000372445,;TJAP1,missense_variant,p.Arg62His,ENST00000372444,;TJAP1,missense_variant,p.Arg20His,ENST00000454762,;TJAP1,missense_variant,p.Arg62His,ENST00000372452,;TJAP1,missense_variant,p.Arg62His,ENST00000259751,;TJAP1,missense_variant,p.Arg62His,ENST00000442878,;TJAP1,non_coding_transcript_exon_variant,,ENST00000478173,;TJAP1,non_coding_transcript_exon_variant,,ENST00000490050,;TJAP1,non_coding_transcript_exon_variant,,ENST00000459851,;TJAP1,non_coding_transcript_exon_variant,,ENST00000483640,;	A	ENSG00000137221	ENST00000372445	Transcript	missense_variant	561	185	62	R/H	cGc/cAc	rs370044590	.	.	1	TJAP1	HGNC	17949	protein_coding	YES	CCDS55004.1	ENSP00000361522	TJAP1_HUMAN	E2QRK7_HUMAN,B3KT40_HUMAN	UPI00004A3A96	.	tolerated(0.12)	probably_damaging(0.921)	6/11	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGACGCACTG	byFrequency|byCluster|by1000G	5	ESCA
SENP6	0	.	GRCh37	6	76388386	76388386	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1936A>G	p.Ile646Val	p.I646V	ENST00000447266	15/24	48	30	18	59	59	0	SENP6,missense_variant,p.Ile242Val,ENST00000541192,;SENP6,missense_variant,p.Ile536Val,ENST00000424947,;SENP6,missense_variant,p.Ile639Val,ENST00000327284,;SENP6,missense_variant,p.Ile639Val,ENST00000370010,;SENP6,missense_variant,p.Ile646Val,ENST00000370014,;SENP6,missense_variant,p.Ile646Val,ENST00000447266,;SENP6,missense_variant,p.Ile262Val,ENST00000503501,;SENP6,non_coding_transcript_exon_variant,,ENST00000476060,;SENP6,upstream_gene_variant,,ENST00000474906,;	G	ENSG00000112701	ENST00000447266	Transcript	missense_variant	2414	1936	646	I/V	Atc/Gtc	.	.	.	1	SENP6	HGNC	20944	protein_coding	YES	CCDS47454.1	ENSP00000402527	SENP6_HUMAN	H0Y4F4_HUMAN	UPI0000141B65	.	tolerated(1)	benign(0.015)	15/24	.	hmmpanther:PTHR12438:SF14,hmmpanther:PTHR12438,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCATCTTC	.	5	ESCA
HTR1E	0	.	GRCh37	6	87725923	87725923	+	Missense_Mutation	SNP	C	C	T	rs771278269	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.871C>T	p.Arg291Cys	p.R291C	ENST00000305344	2/2	48	36	12	67	67	0	HTR1E,missense_variant,p.Arg291Cys,ENST00000305344,;	T	ENSG00000168830	ENST00000305344	Transcript	missense_variant	1574	871	291	R/C	Cgc/Tgc	rs771278269,COSM484414	.	.	1	HTR1E	HGNC	5291	protein_coding	YES	CCDS5006.1	ENSP00000307766	5HT1E_HUMAN	.	UPI000000126D	.	deleterious(0)	probably_damaging(0.978)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF33,hmmpanther:PTHR24247,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCACGCATC	byFrequency	5	ESCA
ANKRD6	0	.	GRCh37	6	90276680	90276680	+	5'UTR	SNP	C	C	G	rs560424198	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16C>G	.	.	ENST00000522441	2/16	16	7	9	20	20	0	ANKRD6,5_prime_UTR_variant,,ENST00000520458,;ANKRD6,5_prime_UTR_variant,,ENST00000522441,;ANKRD6,5_prime_UTR_variant,,ENST00000523798,;ANKRD6,5_prime_UTR_variant,,ENST00000447838,;ANKRD6,5_prime_UTR_variant,,ENST00000518150,;ANKRD6,5_prime_UTR_variant,,ENST00000369408,;ANKRD6,5_prime_UTR_variant,,ENST00000522705,;ANKRD6,5_prime_UTR_variant,,ENST00000485637,;ANKRD6,5_prime_UTR_variant,,ENST00000465722,;ANKRD6,5_prime_UTR_variant,,ENST00000339746,;ANKRD6,5_prime_UTR_variant,,ENST00000522779,;ANKRD6,upstream_gene_variant,,ENST00000520793,;RP11-16C18.3,non_coding_transcript_exon_variant,,ENST00000438267,;RP11-16C18.3,non_coding_transcript_exon_variant,,ENST00000425588,;ANKRD6,intron_variant,,ENST00000520886,;LYRM2,downstream_gene_variant,,ENST00000520897,;	G	ENSG00000135299	ENST00000522441	Transcript	5_prime_UTR_variant	626	.	.	.	.	rs560424198	.	.	1	ANKRD6	HGNC	17280	protein_coding	YES	CCDS56441.1	ENSP00000430985	ANKR6_HUMAN	E5RJR9_HUMAN,E5RJ45_HUMAN,E5RIS1_HUMAN,E5RIJ4_HUMAN	UPI000020D325	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAAACCTTTCT	.	4	ESCA
FUT9	0	.	GRCh37	6	96663432	96663432	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11321A>C	.	.	ENST00000302103	3/3	17	8	9	20	20	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	C	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	12727	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTCTGACCTAA	.	4	ESCA
ZNHIT1	0	.	GRCh37	7	100867224	100867224	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450G>A	p.%3D	p.L150L	ENST00000305105	5/5	30	21	8	31	31	0	ZNHIT1,synonymous_variant,p.%3D,ENST00000305105,;ZNHIT1,non_coding_transcript_exon_variant,,ENST00000492315,;ZNHIT1,downstream_gene_variant,,ENST00000461205,;ZNHIT1,non_coding_transcript_exon_variant,,ENST00000485387,;	A	ENSG00000106400	ENST00000305105	Transcript	synonymous_variant	978	450	150	L	ctG/ctA	.	.	.	1	ZNHIT1	HGNC	21688	protein_coding	YES	CCDS5716.1	ENSP00000304593	ZNHI1_HUMAN	.	UPI0000073C91	.	.	.	5/5	.	hmmpanther:PTHR13093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTGAAGTG	.	5	ESCA
IMMP2L	0	.	GRCh37	7	111161482	111161482	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22G>T	p.Val8Leu	p.V8L	ENST00000405709	2/6	26	16	10	33	33	0	IMMP2L,missense_variant,p.Val8Leu,ENST00000437687,;IMMP2L,missense_variant,p.Val8Leu,ENST00000415362,;IMMP2L,missense_variant,p.Val8Leu,ENST00000452895,;IMMP2L,missense_variant,p.Val8Leu,ENST00000405709,;IMMP2L,missense_variant,p.Val8Leu,ENST00000452753,;IMMP2L,missense_variant,p.Val8Leu,ENST00000447215,;IMMP2L,missense_variant,p.Val8Leu,ENST00000331762,;IMMP2L,non_coding_transcript_exon_variant,,ENST00000492938,;	A	ENSG00000184903	ENST00000405709	Transcript	missense_variant	465	22	8	V/L	Gtg/Ttg	.	.	.	-1	IMMP2L	HGNC	14598	protein_coding	YES	CCDS5753.1	ENSP00000384966	IMP2L_HUMAN	C9JVB0_HUMAN,A4D0S9_HUMAN	UPI000006D162	.	tolerated(0.64)	benign(0)	2/6	.	hmmpanther:PTHR12383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCACCCACC	.	5	ESCA
SUMF2	0	.	GRCh37	7	56147218	56147218	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734-3C>T	.	.	ENST00000342190	.	31	15	15	54	54	0	SUMF2,splice_region_variant,,ENST00000275607,;SUMF2,splice_region_variant,,ENST00000395435,;SUMF2,splice_region_variant,,ENST00000437307,;SUMF2,splice_region_variant,,ENST00000451338,;SUMF2,splice_region_variant,,ENST00000342190,;SUMF2,splice_region_variant,,ENST00000395436,;SUMF2,splice_region_variant,,ENST00000413756,;SUMF2,splice_region_variant,,ENST00000434526,;PHKG1,downstream_gene_variant,,ENST00000432123,;SUMF2,downstream_gene_variant,,ENST00000413952,;PHKG1,downstream_gene_variant,,ENST00000452681,;PHKG1,downstream_gene_variant,,ENST00000446428,;PHKG1,downstream_gene_variant,,ENST00000297373,;PHKG1,downstream_gene_variant,,ENST00000537360,;PHKG1,downstream_gene_variant,,ENST00000489604,;SUMF2,splice_region_variant,,ENST00000452216,;SUMF2,splice_region_variant,,ENST00000531229,;SUMF2,splice_region_variant,,ENST00000423763,;SUMF2,splice_region_variant,,ENST00000438133,;SUMF2,splice_region_variant,,ENST00000436782,;SUMF2,3_prime_UTR_variant,,ENST00000447501,;PHKG1,downstream_gene_variant,,ENST00000395428,;PHKG1,downstream_gene_variant,,ENST00000471665,;SUMF2,downstream_gene_variant,,ENST00000529457,;SUMF2,downstream_gene_variant,,ENST00000461912,;	T	ENSG00000129103	ENST00000342190	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	SUMF2	HGNC	20415	protein_coding	YES	CCDS47589.1	ENSP00000341938	.	Q75LP3_HUMAN,F8WA42_HUMAN	UPI0001AE7021	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGGCAGGAT	.	5	ESCA
ZNF679	0	.	GRCh37	7	63726569	63726570	+	Frame_Shift_Ins	INS	-	-	A	.	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564dupA	p.Tyr189IlefsTer20	p.Y189Ifs*20	ENST00000421025	5/5	84	68	16	77	77	0	ZNF679,frameshift_variant,p.Tyr189IlefsTer20,ENST00000255746,;ZNF679,frameshift_variant,p.Tyr189IlefsTer20,ENST00000421025,;	A	ENSG00000197123	ENST00000421025	Transcript	frameshift_variant	827-828	558-559	186-187	-/X	-/A	COSM1451763	.	.	1	ZNF679	HGNC	28650	protein_coding	YES	CCDS47592.1	ENSP00000416809	ZN679_HUMAN	.	UPI000045756A	.	.	.	5/5	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF91,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	insertion	.	6	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAATGTAAAAA	.	3	ESCA
C7orf62	0	.	GRCh37	7	88424264	88424264	+	5'UTR	SNP	C	C	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-8G>T	.	.	ENST00000297203	2/2	42	24	17	34	34	0	C7orf62,5_prime_UTR_variant,,ENST00000297203,;ZNF804B,intron_variant,,ENST00000333190,;	A	ENSG00000164645	ENST00000297203	Transcript	5_prime_UTR_variant	179	.	.	.	.	.	.	.	-1	C7orf62	HGNC	22402	protein_coding	YES	CCDS34678.1	ENSP00000297203	CG062_HUMAN	.	UPI000005034C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTCTTATT	.	5	ESCA
GTPBP10	0	.	GRCh37	7	89984453	89984453	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.373G>A	p.Gly125Ser	p.G125S	ENST00000222511	4/10	54	51	3	72	72	0	GTPBP10,missense_variant,p.Gly125Ser,ENST00000222511,;GTPBP10,missense_variant,p.Gly142Ser,ENST00000450619,;GTPBP10,missense_variant,p.Gly116Ser,ENST00000426366,;GTPBP10,intron_variant,,ENST00000417207,;GTPBP10,intron_variant,,ENST00000257659,;GTPBP10,non_coding_transcript_exon_variant,,ENST00000474503,;GTPBP10,3_prime_UTR_variant,,ENST00000439832,;GTPBP10,3_prime_UTR_variant,,ENST00000421719,;GTPBP10,intron_variant,,ENST00000453512,;GTPBP10,intron_variant,,ENST00000380058,;GTPBP10,downstream_gene_variant,,ENST00000477972,;	A	ENSG00000105793	ENST00000222511	Transcript	missense_variant	439	373	125	G/S	Ggt/Agt	.	.	.	1	GTPBP10	HGNC	25106	protein_coding	YES	CCDS5617.1	ENSP00000222511	GTPBA_HUMAN	.	UPI00003674D7	.	deleterious(0)	probably_damaging(0.998)	4/10	.	hmmpanther:PTHR11702:SF25,hmmpanther:PTHR11702,Pfam_domain:PF01018,Gene3D:1udxA01,PIRSF_domain:PIRSF002401,Superfamily_domains:SSF82051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGTGGTAAA	.	2	ESCA
GRHL2	0	.	GRCh37	8	102555638	102555638	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.190C>T	p.Leu64Phe	p.L64F	ENST00000251808	2/16	48	20	28	41	41	0	GRHL2,missense_variant,p.Leu64Phe,ENST00000251808,;GRHL2,missense_variant,p.Leu48Phe,ENST00000395927,;GRHL2,non_coding_transcript_exon_variant,,ENST00000472106,;	T	ENSG00000083307	ENST00000251808	Transcript	missense_variant	528	190	64	L/F	Ctc/Ttc	.	.	.	1	GRHL2	HGNC	2799	protein_coding	YES	CCDS34931.1	ENSP00000251808	GRHL2_HUMAN	.	UPI000013CD16	.	deleterious(0)	probably_damaging(0.928)	2/16	.	hmmpanther:PTHR11037:SF17,hmmpanther:PTHR11037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCCTCGGC	.	5	ESCA
OXR1	0	.	GRCh37	8	107763910	107763910	+	3'Flank	SNP	A	A	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000442977	.	33	25	8	29	29	0	OXR1,3_prime_UTR_variant,,ENST00000312046,;OXR1,3_prime_UTR_variant,,ENST00000519415,;OXR1,3_prime_UTR_variant,,ENST00000445937,;OXR1,3_prime_UTR_variant,,ENST00000531443,;OXR1,3_prime_UTR_variant,,ENST00000452423,;OXR1,3_prime_UTR_variant,,ENST00000517566,;OXR1,3_prime_UTR_variant,,ENST00000449762,;OXR1,3_prime_UTR_variant,,ENST00000297447,;OXR1,downstream_gene_variant,,ENST00000442977,;OXR1,downstream_gene_variant,,ENST00000521592,;OXR1,3_prime_UTR_variant,,ENST00000435082,;	G	ENSG00000164830	ENST00000442977	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	509	1	OXR1	HGNC	15822	protein_coding	YES	CCDS56548.1	ENSP00000405424	OXR1_HUMAN	E9PLW2_HUMAN	UPI0001914BEA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATATATTA	.	5	ESCA
KIAA0196	0	.	GRCh37	8	126061249	126061249	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2378A>G	p.Lys793Arg	p.K793R	ENST00000318410	19/29	47	38	9	45	45	0	KIAA0196,missense_variant,p.Lys645Arg,ENST00000517845,;KIAA0196,missense_variant,p.Lys793Arg,ENST00000318410,;KIAA0196-AS1,downstream_gene_variant,,ENST00000519140,;KIAA0196,splice_region_variant,,ENST00000530856,;	C	ENSG00000164961	ENST00000318410	Transcript	missense_variant	2728	2378	793	K/R	aAg/aGg	.	.	.	-1	KIAA0196	HGNC	28984	protein_coding	YES	CCDS6355.1	ENSP00000318016	STRUM_HUMAN	Q53EL1_HUMAN,E7EQI7_HUMAN,E5RFU6_HUMAN	UPI000013943B	.	deleterious(0.01)	probably_damaging(0.978)	19/29	.	hmmpanther:PTHR15691,Pfam_domain:PF10266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACCTTCGTT	.	5	ESCA
ADAM28	0	.	GRCh37	8	24212065	24212065	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*148G>C	.	.	ENST00000265769	23/23	41	23	18	36	36	0	ADAM28,3_prime_UTR_variant,,ENST00000521629,;ADAM28,3_prime_UTR_variant,,ENST00000265769,;ADAM28,downstream_gene_variant,,ENST00000397649,;ADAM28,downstream_gene_variant,,ENST00000518326,;RP11-624C23.1,intron_variant,,ENST00000518988,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,;RP11-624C23.1,intron_variant,,ENST00000523700,;ADAM28,downstream_gene_variant,,ENST00000518737,;ADAM28,downstream_gene_variant,,ENST00000523236,;ADAM28,downstream_gene_variant,,ENST00000520448,;ADAM28,downstream_gene_variant,,ENST00000520665,;	C	ENSG00000042980	ENST00000265769	Transcript	3_prime_UTR_variant	2586	.	.	.	.	.	.	.	1	ADAM28	HGNC	206	protein_coding	YES	CCDS34865.1	ENSP00000265769	ADA28_HUMAN	E5RGY1_HUMAN	UPI000049E0B9	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTGAAGAGACT	.	4	ESCA
PRKDC	0	.	GRCh37	8	48733437	48733437	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9176C>T	p.Ser3059Phe	p.S3059F	ENST00000314191	67/87	82	58	23	56	56	0	PRKDC,missense_variant,p.Ser3059Phe,ENST00000338368,;PRKDC,missense_variant,p.Ser3059Phe,ENST00000314191,;PRKDC,non_coding_transcript_exon_variant,,ENST00000518216,;PRKDC,non_coding_transcript_exon_variant,,ENST00000523565,;	A	ENSG00000253729	ENST00000314191	Transcript	missense_variant	9233	9176	3059	S/F	tCc/tTc	.	.	.	-1	PRKDC	HGNC	9413	protein_coding	YES	.	ENSP00000313420	PRKDC_HUMAN	F5GX40_HUMAN	UPI000045790C	.	.	possibly_damaging(0.789)	67/87	.	PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF54,Pfam_domain:PF02259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGGGACTGG	.	5	ESCA
YTHDF3	0	.	GRCh37	8	64124416	64124417	+	3'UTR	INS	-	-	A	rs748343204	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2161dupA	.	.	ENST00000539294	5/5	43	35	8	27	27	0	YTHDF3,3_prime_UTR_variant,,ENST00000539294,;YTHDF3,3_prime_UTR_variant,,ENST00000517371,;YTHDF3,3_prime_UTR_variant,,ENST00000542911,;RP11-16E18.3,upstream_gene_variant,,ENST00000569835,;YTHDF3,non_coding_transcript_exon_variant,,ENST00000521674,;YTHDF3,downstream_gene_variant,,ENST00000520640,;YTHDF3,downstream_gene_variant,,ENST00000517303,;YTHDF3,3_prime_UTR_variant,,ENST00000524135,;	A	ENSG00000185728	ENST00000539294	Transcript	3_prime_UTR_variant	4223-4224	.	.	.	.	rs748343204	.	.	1	YTHDF3	HGNC	26465	protein_coding	YES	.	ENSP00000473496	.	R4GN55_HUMAN,R4GMX0_HUMAN	UPI0002C8850B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTTGGAAAAA	.	2	ESCA
CARD9	0	.	GRCh37	9	139262253	139262253	+	Missense_Mutation	SNP	C	C	A	rs141270365	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1105G>T	p.Ala369Ser	p.A369S	ENST00000371732	8/13	13	9	4	10	10	0	CARD9,missense_variant,p.Ala369Ser,ENST00000371732,;CARD9,missense_variant,p.Ala369Ser,ENST00000371734,;CARD9,downstream_gene_variant,,ENST00000315908,;DNLZ,upstream_gene_variant,,ENST00000371739,;DNLZ,upstream_gene_variant,,ENST00000371738,;CARD9,upstream_gene_variant,,ENST00000460290,;CARD9,3_prime_UTR_variant,,ENST00000489932,;CARD9,non_coding_transcript_exon_variant,,ENST00000481053,;CARD9,non_coding_transcript_exon_variant,,ENST00000485975,;CARD9,downstream_gene_variant,,ENST00000556340,;	A	ENSG00000187796	ENST00000371732	Transcript	missense_variant	1271	1105	369	A/S	Gca/Tca	rs141270365	.	.	-1	CARD9	HGNC	16391	protein_coding	YES	CCDS6997.1	ENSP00000360797	CARD9_HUMAN	.	UPI000013E4EB	.	tolerated(0.75)	benign(0.031)	8/13	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF3	T:0.0008	T:0.003	T:0	.	T:0	T:0	T:0	T:0.0014	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CTGTGCGTGCA	byFrequency|byCluster|by1000G	2	ESCA
NDOR1	0	.	GRCh37	9	140110968	140110968	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*100A>T	.	.	ENST00000371521	14/14	9	5	4	10	10	0	NDOR1,3_prime_UTR_variant,,ENST00000427047,;NDOR1,3_prime_UTR_variant,,ENST00000371521,;NDOR1,3_prime_UTR_variant,,ENST00000344894,;RNF208,downstream_gene_variant,,ENST00000392827,;RNF208,downstream_gene_variant,,ENST00000391553,;NDOR1,downstream_gene_variant,,ENST00000458322,;	T	ENSG00000188566	ENST00000371521	Transcript	3_prime_UTR_variant	2004	.	.	.	.	.	.	.	1	NDOR1	HGNC	29838	protein_coding	YES	CCDS48061.1	ENSP00000360576	NDOR1_HUMAN	.	UPI0000190A69	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGGACCAGC	.	2	ESCA
DCAF12	0	.	GRCh37	9	34089557	34089557	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1056C>A	p.%3D	p.I352I	ENST00000361264	8/9	64	44	19	47	47	0	DCAF12,synonymous_variant,p.%3D,ENST00000361264,;RP11-537H15.3,intron_variant,,ENST00000448245,;DCAF12,non_coding_transcript_exon_variant,,ENST00000466402,;	T	ENSG00000198876	ENST00000361264	Transcript	synonymous_variant	1398	1056	352	I	atC/atA	.	.	.	-1	DCAF12	HGNC	19911	protein_coding	YES	CCDS6549.1	ENSP00000355114	DCA12_HUMAN	.	UPI00000372E8	.	.	.	8/9	.	hmmpanther:PTHR19860:SF10,hmmpanther:PTHR19860,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATGATGTG	.	5	ESCA
FAM199X	0	.	GRCh37	X	103432909	103432909	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.918C>G	p.Asn306Lys	p.N306K	ENST00000493442	5/6	17	5	12	8	8	0	FAM199X,missense_variant,p.Asn306Lys,ENST00000493442,;FAM199X,intron_variant,,ENST00000299906,;	G	ENSG00000123575	ENST00000493442	Transcript	missense_variant	1084	918	306	N/K	aaC/aaG	.	.	.	1	FAM199X	HGNC	25195	protein_coding	YES	CCDS35364.1	ENSP00000417581	F199X_HUMAN	B0QYU2_HUMAN	UPI00001C2069	.	tolerated_low_confidence(0.81)	benign(0.282)	5/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32003:SF1,hmmpanther:PTHR32003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAAACTCCAG	.	3	ESCA
SOWAHD	0	.	GRCh37	X	118893519	118893519	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.889C>T	p.Arg297Trp	p.R297W	ENST00000343905	1/1	33	23	9	15	15	0	SOWAHD,missense_variant,p.Arg297Trp,ENST00000343905,;	T	ENSG00000187808	ENST00000343905	Transcript	missense_variant	944	889	297	R/W	Cgg/Tgg	.	.	.	1	SOWAHD	HGNC	32960	protein_coding	YES	CCDS43984.1	ENSP00000340975	SWAHD_HUMAN	.	UPI0000197588	.	deleterious(0)	probably_damaging(0.979)	1/1	.	hmmpanther:PTHR14491,hmmpanther:PTHR14491:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCCGGGTG	.	5	ESCA
KDM6A	0	.	GRCh37	X	44941834	44941834	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A625-01A-11D-A31U-09	TCGA-IG-A625-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3158A>T	p.Lys1053Ile	p.K1053I	ENST00000377967	21/29	36	7	28	56	56	0	KDM6A,missense_variant,p.Lys696Ile,ENST00000433797,;KDM6A,missense_variant,p.Lys651Ile,ENST00000414389,;KDM6A,missense_variant,p.Lys974Ile,ENST00000543216,;KDM6A,missense_variant,p.Lys1053Ile,ENST00000377967,;KDM6A,missense_variant,p.Lys1060Ile,ENST00000382899,;KDM6A,missense_variant,p.Lys1008Ile,ENST00000536777,;KDM6A,non_coding_transcript_exon_variant,,ENST00000485072,;KDM6A,non_coding_transcript_exon_variant,,ENST00000484732,;	T	ENSG00000147050	ENST00000377967	Transcript	missense_variant	3199	3158	1053	K/I	aAa/aTa	.	.	.	1	KDM6A	HGNC	12637	protein_coding	YES	CCDS14265.1	ENSP00000367203	KDM6A_HUMAN	Q68D33_HUMAN,Q59HG3_HUMAN,Q590H7_HUMAN	UPI000013DA92	.	deleterious(0)	probably_damaging(0.99)	21/29	.	hmmpanther:PTHR14017:SF9,hmmpanther:PTHR14017	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_4206del4206|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAAAAAGAA	.	5	ESCA
NOLC1	0	.	GRCh37	10	103920492	103920492	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1383G>T	p.Gln461His	p.Q461H	ENST00000605788	10/13	39	28	11	43	43	0	NOLC1,missense_variant,p.Gln470His,ENST00000370007,;NOLC1,missense_variant,p.Gln461His,ENST00000605788,;NOLC1,missense_variant,p.Gln462His,ENST00000488254,;NOLC1,missense_variant,p.Gln180His,ENST00000603742,;NOLC1,missense_variant,p.Gln471His,ENST00000405356,;NOLC1,downstream_gene_variant,,ENST00000476468,;NOLC1,downstream_gene_variant,,ENST00000461421,;NOLC1,non_coding_transcript_exon_variant,,ENST00000477977,;NOLC1,3_prime_UTR_variant,,ENST00000603946,;NOLC1,3_prime_UTR_variant,,ENST00000464969,;	T	ENSG00000166197	ENST00000605788	Transcript	missense_variant	1618	1383	461	Q/H	caG/caT	.	.	.	1	NOLC1	HGNC	15608	protein_coding	YES	CCDS7530.1	ENSP00000474710	NOLC1_HUMAN	Q96J17_HUMAN	UPI000013E575	.	deleterious_low_confidence(0)	unknown(0)	10/13	.	hmmpanther:PTHR23216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGGCTCC	.	5	ESCA
CCDC147	0	.	GRCh37	10	106139943	106139943	+	Silent	SNP	C	C	A	rs766901777	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1330C>A	p.%3D	p.R444R	ENST00000369704	9/18	94	61	33	91	91	0	CCDC147,synonymous_variant,p.%3D,ENST00000312902,;CCDC147,synonymous_variant,p.%3D,ENST00000369703,;CCDC147,synonymous_variant,p.%3D,ENST00000369704,;	A	ENSG00000120051	ENST00000369704	Transcript	synonymous_variant	1464	1330	444	R	Cgg/Agg	rs766901777,COSM537062	.	.	1	CCDC147	HGNC	26676	protein_coding	YES	CCDS31282.1	ENSP00000358718	CC147_HUMAN	B4DK97_HUMAN	UPI0000160405	.	.	.	9/18	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF26	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGACCGGTAC	.	5	ESCA
MICU1	0	.	GRCh37	10	74293533	74293533	+	Missense_Mutation	SNP	G	G	C	rs779752327	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.508C>G	p.Gln170Glu	p.Q170E	ENST00000361114	5/12	30	22	8	30	30	0	MICU1,missense_variant,p.Gln170Glu,ENST00000604238,;MICU1,missense_variant,p.Gln136Glu,ENST00000603011,;MICU1,missense_variant,p.Gln170Glu,ENST00000401998,;MICU1,missense_variant,p.Gln170Glu,ENST00000398761,;MICU1,missense_variant,p.Gln170Glu,ENST00000361114,;MICU1,upstream_gene_variant,,ENST00000603173,;MICU1,missense_variant,p.Gln13Glu,ENST00000476605,;	C	ENSG00000107745	ENST00000361114	Transcript	missense_variant	605	508	170	Q/E	Caa/Gaa	rs779752327	.	.	-1	MICU1	HGNC	1530	protein_coding	YES	CCDS55715.1	ENSP00000354415	MICU1_HUMAN	.	UPI0000035D9A	.	deleterious(0.02)	benign(0.206)	5/12	.	hmmpanther:PTHR12294:SF1,hmmpanther:PTHR12294,Gene3D:1.10.238.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTGATCCA	.	5	ESCA
PPP3CB	0	.	GRCh37	10	75196893	75196893	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1107C>G	.	.	ENST00000394829	14/14	55	35	20	48	48	0	PPP3CB,3_prime_UTR_variant,,ENST00000394828,;PPP3CB,3_prime_UTR_variant,,ENST00000394829,;PPP3CB,3_prime_UTR_variant,,ENST00000360663,;PPP3CB,downstream_gene_variant,,ENST00000430762,;PPP3CB,downstream_gene_variant,,ENST00000544628,;MSS51,upstream_gene_variant,,ENST00000299432,;MSS51,upstream_gene_variant,,ENST00000487126,;	C	ENSG00000107758	ENST00000394829	Transcript	3_prime_UTR_variant	2820	.	.	.	.	.	.	.	-1	PPP3CB	HGNC	9315	protein_coding	YES	CCDS44437.1	ENSP00000378306	PP2BB_HUMAN	Q9UMB2_HUMAN	UPI000006E24B	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTGACTTT	.	5	ESCA
VCL	0	.	GRCh37	10	75863596	75863596	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2041A>G	p.Ile681Val	p.I681V	ENST00000211998	15/22	94	57	37	87	87	0	VCL,missense_variant,p.Ile353Val,ENST00000436396,;VCL,missense_variant,p.Ile681Val,ENST00000211998,;VCL,missense_variant,p.Ile681Val,ENST00000372755,;VCL,intron_variant,,ENST00000417648,;VCL,non_coding_transcript_exon_variant,,ENST00000478896,;VCL,upstream_gene_variant,,ENST00000472585,;	G	ENSG00000035403	ENST00000211998	Transcript	missense_variant	2135	2041	681	I/V	Atc/Gtc	.	.	.	1	VCL	HGNC	12665	protein_coding	YES	CCDS7341.1	ENSP00000211998	VINC_HUMAN	Q5JQ13_HUMAN	UPI0000167B54	.	tolerated(0.05)	probably_damaging(0.986)	15/22	.	hmmpanther:PTHR18914:SF22,hmmpanther:PTHR18914,Gene3D:1.20.120.230,Pfam_domain:PF01044,Superfamily_domains:SSF47220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGTATCTTA	.	5	ESCA
RDX	0	.	GRCh37	11	110070376	110070376	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1776C>T	p.%3D	p.F592F	ENST00000405097	15/16	25	12	13	49	49	0	RDX,synonymous_variant,p.%3D,ENST00000528900,;RDX,synonymous_variant,p.%3D,ENST00000528498,;RDX,synonymous_variant,p.%3D,ENST00000530301,;RDX,synonymous_variant,p.%3D,ENST00000405097,;RDX,synonymous_variant,p.%3D,ENST00000530749,;	A	ENSG00000137710	ENST00000405097	Transcript	synonymous_variant	2086	1776	592	F	ttC/ttT	.	.	.	-1	RDX	HGNC	9944	protein_coding	YES	CCDS58174.1	ENSP00000384136	RADI_HUMAN	Q9NST9_HUMAN,E9PQ82_HUMAN,E9PNV3_HUMAN,E9PKN5_HUMAN,B0YJ88_HUMAN	UPI0000EE3914	.	.	.	15/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGGAACAA	.	5	ESCA
OR52B4	0	.	GRCh37	11	4389279	4389279	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>T	p.Ala83Ser	p.A83S	ENST00000408920	1/1	51	37	13	46	46	0	OR52B4,missense_variant,p.Ala83Ser,ENST00000408920,;	A	ENSG00000221996	ENST00000408920	Transcript	missense_variant	338	247	83	A/S	Gcc/Tcc	.	.	.	-1	OR52B4	HGNC	15209	protein_coding	YES	CCDS41609.1	ENSP00000386160	O52B4_HUMAN	.	UPI000013F0A2	.	deleterious(0.03)	benign(0.072)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF89,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGGCCTGAG	.	5	ESCA
EXT2	0	.	GRCh37	11	44165803	44165803	+	Intron	SNP	A	A	G	rs747999174	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1272+14115A>G	.	.	ENST00000395673	.	73	46	26	64	63	0	EXT2,missense_variant,p.Met394Val,ENST00000358681,;EXT2,intron_variant,,ENST00000533608,;EXT2,intron_variant,,ENST00000395673,;EXT2,intron_variant,,ENST00000343631,;EXT2,intron_variant,,ENST00000531161,;EXT2,intron_variant,,ENST00000534048,;EXT2,intron_variant,,ENST00000525559,;	G	ENSG00000151348	ENST00000395673	Transcript	intron_variant	.	.	.	.	.	rs747999174	.	.	1	EXT2	HGNC	3513	protein_coding	YES	CCDS53618.1	ENSP00000379032	EXT2_HUMAN	E9PNL9_HUMAN,E9PJA5_HUMAN	UPI0000EE3A5C	.	.	.	.	7/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCATGGAA	.	5	ESCA
OR52N4	0	.	GRCh37	11	5775951	5775951	+	5'UTR	SNP	C	C	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-20C>G	.	.	ENST00000317254	1/1	34	19	15	34	34	0	OR52N4,5_prime_UTR_variant,,ENST00000317254,;TRIM5,intron_variant,,ENST00000412903,;TRIM5,intron_variant,,ENST00000380027,;	G	ENSG00000181074	ENST00000317254	Transcript	5_prime_UTR_variant	29	.	.	.	.	.	.	.	1	OR52N4	HGNC	15230	protein_coding	YES	CCDS44528.1	ENSP00000323224	O52N4_HUMAN	.	UPI00001AF18B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTCATAAC	.	5	ESCA
FAM160A2	0	.	GRCh37	11	6238828	6238828	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2030G>A	p.Gly677Asp	p.G677D	ENST00000265978	9/12	32	20	11	53	53	0	FAM160A2,missense_variant,p.Gly677Asp,ENST00000265978,;FAM160A2,missense_variant,p.Gly663Asp,ENST00000449352,;FAM160A2,missense_variant,p.Gly663Asp,ENST00000524416,;FAM160A2,downstream_gene_variant,,ENST00000532797,;FAM160A2,upstream_gene_variant,,ENST00000529360,;	T	ENSG00000051009	ENST00000265978	Transcript	missense_variant	2389	2030	677	G/D	gGc/gAc	.	.	.	-1	FAM160A2	HGNC	25378	protein_coding	YES	CCDS7760.1	ENSP00000265978	F16A2_HUMAN	.	UPI000013D6B5	.	tolerated(0.11)	benign(0.002)	9/12	.	hmmpanther:PTHR21705,hmmpanther:PTHR21705:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGCCCTCT	.	5	ESCA
LRP5	0	.	GRCh37	11	68181296	68181296	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2643C>G	p.%3D	p.L881L	ENST00000294304	12/23	56	42	14	30	30	0	LRP5,synonymous_variant,p.%3D,ENST00000294304,;LRP5,downstream_gene_variant,,ENST00000528714,;LRP5,3_prime_UTR_variant,,ENST00000529993,;	G	ENSG00000162337	ENST00000294304	Transcript	synonymous_variant	2749	2643	881	L	ctC/ctG	.	.	.	1	LRP5	HGNC	6697	protein_coding	YES	CCDS8181.1	ENSP00000294304	LRP5_HUMAN	E9PHY1_HUMAN	UPI0000073246	.	.	.	12/23	.	Superfamily_domains:SSF63825,PIRSF_domain:PIRSF036314,Pfam_domain:PF00058,Gene3D:2.120.10.30,hmmpanther:PTHR10529:SF202,hmmpanther:PTHR10529,PROSITE_profiles:PS51120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTCATCCA	.	5	ESCA
ITGA7	0	.	GRCh37	12	56080031	56080031	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3196-959C>T	.	.	ENST00000553804	.	76	51	25	53	53	0	ITGA7,missense_variant,p.Ala1088Val,ENST00000394230,;ITGA7,missense_variant,p.Ala1128Val,ENST00000257880,;ITGA7,missense_variant,p.Ala1084Val,ENST00000394229,;ITGA7,synonymous_variant,p.%3D,ENST00000557555,;ITGA7,intron_variant,,ENST00000452168,;ITGA7,intron_variant,,ENST00000257879,;ITGA7,intron_variant,,ENST00000555728,;ITGA7,intron_variant,,ENST00000553804,;ITGA7,intron_variant,,ENST00000347027,;METTL7B,downstream_gene_variant,,ENST00000394252,;ITGA7,intron_variant,,ENST00000554327,;	A	ENSG00000135424	ENST00000553804	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ITGA7	HGNC	6143	protein_coding	YES	CCDS55832.1	ENSP00000452120	ITA7_HUMAN	.	UPI00003668CF	.	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACAGCCAGA	.	5	ESCA
DACH1	0	.	GRCh37	13	72441024	72441024	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-117G>A	.	.	ENST00000305425	1/11	14	4	10	23	23	0	DACH1,5_prime_UTR_variant,,ENST00000305425,;DACH1,5_prime_UTR_variant,,ENST00000313174,;DACH1,5_prime_UTR_variant,,ENST00000354591,;DACH1,upstream_gene_variant,,ENST00000359684,;	T	ENSG00000165659	ENST00000305425	Transcript	5_prime_UTR_variant	307	.	.	.	.	.	.	.	-1	DACH1	HGNC	2663	protein_coding	YES	CCDS41899.1	ENSP00000304994	DACH1_HUMAN	.	UPI00001FCE9E	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTCCGGGAG	.	5	ESCA
CLDN10	0	.	GRCh37	13	96230262	96230262	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681T>C	p.%3D	p.Y227Y	ENST00000299339	5/5	49	19	30	74	74	0	CLDN10,synonymous_variant,p.%3D,ENST00000376873,;CLDN10,synonymous_variant,p.%3D,ENST00000299339,;DZIP1,downstream_gene_variant,,ENST00000376829,;DZIP1,downstream_gene_variant,,ENST00000361396,;DZIP1,downstream_gene_variant,,ENST00000361156,;DZIP1,downstream_gene_variant,,ENST00000347108,;DZIP1,downstream_gene_variant,,ENST00000485031,;	C	ENSG00000134873	ENST00000299339	Transcript	synonymous_variant	710	681	227	Y	taT/taC	.	.	.	1	CLDN10	HGNC	2033	protein_coding	YES	CCDS9476.1	ENSP00000299339	CLD10_HUMAN	Q6IBF9_HUMAN,Q5W075_HUMAN	UPI0000127AB3	.	.	.	5/5	.	hmmpanther:PTHR12002:SF13,hmmpanther:PTHR12002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTATGTCTA	.	5	ESCA
OR11H12	0	.	GRCh37	14	19377922	19377922	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329C>A	p.Ala110Asp	p.A110D	ENST00000550708	1/1	138	112	26	114	114	0	OR11H12,missense_variant,p.Ala110Asp,ENST00000550708,;	A	ENSG00000257115	ENST00000550708	Transcript	missense_variant	401	329	110	A/D	gCt/gAt	.	.	.	1	OR11H12	HGNC	30738	protein_coding	YES	CCDS32017.1	ENSP00000449002	O11HC_HUMAN	.	UPI00004EAFF2	.	deleterious(0.01)	benign(0.084)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF201,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTTTGCTGGAT	.	2	ESCA
SUPT16H	0	.	GRCh37	14	21840137	21840137	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226A>G	p.Met76Val	p.M76V	ENST00000216297	3/26	106	83	22	68	68	0	SUPT16H,missense_variant,p.Met76Val,ENST00000216297,;SUPT16H,splice_region_variant,,ENST00000556309,;SUPT16H,3_prime_UTR_variant,,ENST00000557652,;SUPT16H,non_coding_transcript_exon_variant,,ENST00000556217,;SUPT16H,downstream_gene_variant,,ENST00000555752,;	C	ENSG00000092201	ENST00000216297	Transcript	missense_variant	565	226	76	M/V	Atg/Gtg	.	.	.	-1	SUPT16H	HGNC	11465	protein_coding	YES	CCDS9569.1	ENSP00000216297	SP16H_HUMAN	.	UPI0000035D5C	.	deleterious(0.01)	benign(0.007)	3/26	.	hmmpanther:PTHR13980:SF15,hmmpanther:PTHR13980,Pfam_domain:PF14826,Gene3D:3.40.350.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCATAAAGA	.	5	ESCA
TRAV34	0	.	GRCh37	14	22675763	22675763	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75G>A	p.%3D	p.E25E	ENST00000390461	2/2	78	55	22	65	65	0	TRAV34,synonymous_variant,p.%3D,ENST00000390461,;TRAV26-2,downstream_gene_variant,,ENST00000390460,;	A	ENSG00000211813	ENST00000390461	Transcript	synonymous_variant	87	75	25	E	gaG/gaA	.	.	.	1	TRAV34	HGNC	12133	TR_V_gene	YES	.	ENSP00000452002	.	.	UPI000011D12E	.	.	.	2/2	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50835,hmmpanther:PTHR19433:SF58,hmmpanther:PTHR19433,Pfam_domain:PF07686,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGCAGAG	.	5	ESCA
L2HGDH	0	.	GRCh37	14	50750625	50750625	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.667G>C	p.Glu223Gln	p.E223Q	ENST00000267436	5/10	111	62	49	88	88	0	L2HGDH,missense_variant,p.Glu223Gln,ENST00000421284,;L2HGDH,missense_variant,p.Glu223Gln,ENST00000261699,;L2HGDH,missense_variant,p.Glu223Gln,ENST00000267436,;L2HGDH,missense_variant,p.Glu223Gln,ENST00000555423,;L2HGDH,3_prime_UTR_variant,,ENST00000555610,;	G	ENSG00000087299	ENST00000267436	Transcript	missense_variant	1065	667	223	E/Q	Gaa/Caa	.	.	.	-1	L2HGDH	HGNC	20499	protein_coding	YES	CCDS9698.1	ENSP00000267436	L2HDH_HUMAN	.	UPI0000048F63	.	tolerated(0.25)	benign(0.043)	5/10	.	hmmpanther:PTHR13847:SF171,hmmpanther:PTHR13847,Pfam_domain:PF01266,Gene3D:3.50.50.60,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CATTTCAATAC	.	3	ESCA
PCNX	0	.	GRCh37	14	71502860	71502860	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3853T>A	p.Phe1285Ile	p.F1285I	ENST00000304743	19/36	48	27	20	56	56	0	PCNX,missense_variant,p.Phe344Ile,ENST00000554691,;PCNX,missense_variant,p.Phe1285Ile,ENST00000238570,;PCNX,missense_variant,p.Phe1174Ile,ENST00000439984,;PCNX,missense_variant,p.Phe1285Ile,ENST00000304743,;RP5-1163L11.2,upstream_gene_variant,,ENST00000555418,;	A	ENSG00000100731	ENST00000304743	Transcript	missense_variant	4299	3853	1285	F/I	Ttc/Atc	.	.	.	1	PCNX	HGNC	19740	protein_coding	YES	CCDS9806.1	ENSP00000304192	PCX1_HUMAN	Q05BT4_HUMAN	UPI000013E9BB	.	deleterious(0.01)	probably_damaging(0.997)	19/36	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12372:SF2,hmmpanther:PTHR12372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCTTCACA	.	5	ESCA
TRIP11	0	.	GRCh37	14	92472172	92472172	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2148G>A	p.Met716Ile	p.M716I	ENST00000267622	11/21	56	37	19	28	28	0	TRIP11,missense_variant,p.Met432Ile,ENST00000554357,;TRIP11,missense_variant,p.Met716Ile,ENST00000267622,;	T	ENSG00000100815	ENST00000267622	Transcript	missense_variant	2522	2148	716	M/I	atG/atA	.	.	.	-1	TRIP11	HGNC	12305	protein_coding	YES	CCDS9899.1	ENSP00000267622	TRIPB_HUMAN	G3V4R7_HUMAN	UPI000013D767	.	tolerated(0.27)	benign(0.001)	11/21	.	hmmpanther:PTHR18921:SF2,hmmpanther:PTHR18921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCCATTTT	.	5	ESCA
GOLGA8EP	0	.	GRCh37	15	23436943	23436943	+	Intron	SNP	A	A	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.149A>C	.	.	ENST00000526079	2/18	211	159	52	211	211	0	GOLGA8EP,splice_region_variant,,ENST00000526079,;GOLGA8EP,splice_region_variant,,ENST00000530246,;	C	ENSG00000175676	ENST00000526079	Transcript	splice_region_variant	149	.	.	.	.	.	.	.	1	GOLGA8EP	HGNC	32377	processed_transcript	YES	.	.	.	.	.	.	.	.	2/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTAAAAGA	.	4	ESCA
TLN2	0	.	GRCh37	15	63054541	63054541	+	Missense_Mutation	SNP	G	G	A	rs776245129	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4850G>A	p.Arg1617His	p.R1617H	ENST00000561311	38/58	73	50	23	71	70	1	TLN2,missense_variant,p.Arg531His,ENST00000494733,;TLN2,missense_variant,p.Arg1617His,ENST00000561311,;TLN2,missense_variant,p.Arg10His,ENST00000472902,;TLN2,missense_variant,p.Arg1617His,ENST00000306829,;TLN2,non_coding_transcript_exon_variant,,ENST00000489129,;TLN2,upstream_gene_variant,,ENST00000467297,;	A	ENSG00000171914	ENST00000561311	Transcript	missense_variant	5080	4850	1617	R/H	cGc/cAc	rs776245129	.	.	1	TLN2	HGNC	15447	protein_coding	YES	CCDS32261.1	ENSP00000453508	TLN2_HUMAN	.	UPI00001FE5FC	.	tolerated(0.06)	benign(0.002)	38/58	.	Gene3D:1.20.1440.10,hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTCGCACTG	byFrequency	5	ESCA
MEGF11	0	.	GRCh37	15	66274821	66274821	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400G>A	p.Asp134Asn	p.D134N	ENST00000409699	6/23	16	13	3	9	9	0	MEGF11,missense_variant,p.Asp134Asn,ENST00000409699,;MEGF11,missense_variant,p.Asp134Asn,ENST00000360698,;MEGF11,missense_variant,p.Asp59Asn,ENST00000395625,;MEGF11,missense_variant,p.Asp134Asn,ENST00000422354,;MEGF11,missense_variant,p.Asp59Asn,ENST00000288745,;MEGF11,5_prime_UTR_variant,,ENST00000395614,;	T	ENSG00000157890	ENST00000409699	Transcript	missense_variant	573	400	134	D/N	Gac/Aac	.	.	.	-1	MEGF11	HGNC	29635	protein_coding	YES	CCDS10213.2	ENSP00000386908	MEG11_HUMAN	C9JYE7_HUMAN	UPI00001FE6DA	.	deleterious(0.03)	possibly_damaging(0.851)	6/23	.	hmmpanther:PTHR24035:SF10,hmmpanther:PTHR24035,Gene3D:2gy5A03	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGTCGCAGC	.	2	ESCA
AKAP13	0	.	GRCh37	15	86287894	86287894	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8440G>C	p.Glu2814Gln	p.E2814Q	ENST00000361243	37/37	42	23	18	32	32	0	AKAP13,missense_variant,p.Glu2810Gln,ENST00000394518,;AKAP13,missense_variant,p.Glu2814Gln,ENST00000361243,;AKAP13,missense_variant,p.Glu1055Gln,ENST00000394510,;RP11-158M2.3,non_coding_transcript_exon_variant,,ENST00000558375,;AKAP13,non_coding_transcript_exon_variant,,ENST00000560579,;AKAP13,upstream_gene_variant,,ENST00000560185,;AKAP13,downstream_gene_variant,,ENST00000559391,;	C	ENSG00000170776	ENST00000361243	Transcript	missense_variant	8521	8440	2814	E/Q	Gag/Cag	.	.	.	1	AKAP13	HGNC	371	protein_coding	YES	CCDS32320.1	ENSP00000354718	AKP13_HUMAN	H0YMI5_HUMAN,A8MYJ1_HUMAN	UPI00001A8BEB	.	deleterious(0)	probably_damaging(0.998)	37/37	.	hmmpanther:PTHR13944:SF4,hmmpanther:PTHR13944	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAGAGATC	.	5	ESCA
FBXL19	0	.	GRCh37	16	30933892	30933892	+	5'Flank	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000380310	.	55	41	13	49	49	0	FBXL19,upstream_gene_variant,,ENST00000565690,;FBXL19,upstream_gene_variant,,ENST00000427128,;FBXL19,upstream_gene_variant,,ENST00000471231,;FBXL19,upstream_gene_variant,,ENST00000380310,;FBXL19,upstream_gene_variant,,ENST00000562798,;FBXL19,upstream_gene_variant,,ENST00000562319,;FBXL19,upstream_gene_variant,,ENST00000338343,;FBXL19-AS1,non_coding_transcript_exon_variant,,ENST00000563777,;	C	ENSG00000099364	ENST00000380310	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2004	1	FBXL19	HGNC	25300	protein_coding	YES	CCDS45465.1	ENSP00000369666	FXL19_HUMAN	H3BVB1_HUMAN,H3BQP6_HUMAN,H3BPZ0_HUMAN	UPI00015C725E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCCTTTCTC	.	5	ESCA
TIGD7	0	.	GRCh37	16	3350311	3350311	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304G>A	p.Glu102Lys	p.E102K	ENST00000396862	2/2	47	22	25	59	59	0	TIGD7,missense_variant,p.Glu102Lys,ENST00000268674,;TIGD7,missense_variant,p.Glu102Lys,ENST00000396862,;TIGD7,missense_variant,p.Glu102Lys,ENST00000573608,;ZNF263,3_prime_UTR_variant,,ENST00000575332,;ZNF263,intron_variant,,ENST00000574674,;TIGD7,downstream_gene_variant,,ENST00000570634,;TIGD7,downstream_gene_variant,,ENST00000573695,;TIGD7,downstream_gene_variant,,ENST00000576104,;TIGD7,downstream_gene_variant,,ENST00000571748,;TIGD7,downstream_gene_variant,,ENST00000572297,;TIGD7,downstream_gene_variant,,ENST00000574598,;	T	ENSG00000140993	ENST00000396862	Transcript	missense_variant	2133	304	102	E/K	Gag/Aag	.	.	.	-1	TIGD7	HGNC	18331	protein_coding	YES	CCDS10500.1	ENSP00000380071	TIGD7_HUMAN	I3L2A8_HUMAN	UPI0000072536	.	deleterious(0.03)	probably_damaging(0.998)	2/2	.	PROSITE_profiles:PS51253,hmmpanther:PTHR19303:SF224,hmmpanther:PTHR19303,Pfam_domain:PF03221,Gene3D:1.10.10.60,SMART_domains:SM00674,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTCCACGC	.	5	ESCA
KATNB1	0	.	GRCh37	16	57790343	57790343	+	Silent	SNP	G	G	A	rs781829852	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1794G>A	p.%3D	p.A598A	ENST00000379661	19/20	39	20	19	35	35	0	KATNB1,synonymous_variant,p.%3D,ENST00000563462,;KATNB1,synonymous_variant,p.%3D,ENST00000379661,;KIFC3,downstream_gene_variant,,ENST00000565270,;KIFC3,downstream_gene_variant,,ENST00000539578,;KIFC3,downstream_gene_variant,,ENST00000543930,;KIFC3,downstream_gene_variant,,ENST00000379655,;KIFC3,downstream_gene_variant,,ENST00000540079,;KATNB1,downstream_gene_variant,,ENST00000569627,;KIFC3,downstream_gene_variant,,ENST00000421376,;KIFC3,downstream_gene_variant,,ENST00000465878,;KIFC3,downstream_gene_variant,,ENST00000565397,;KATNB1,downstream_gene_variant,,ENST00000562592,;KIFC3,downstream_gene_variant,,ENST00000445690,;KIFC3,downstream_gene_variant,,ENST00000541240,;KIFC3,downstream_gene_variant,,ENST00000562903,;KATNB1,downstream_gene_variant,,ENST00000566726,;KATNB1,non_coding_transcript_exon_variant,,ENST00000569018,;KATNB1,non_coding_transcript_exon_variant,,ENST00000562542,;KATNB1,non_coding_transcript_exon_variant,,ENST00000566611,;KIFC3,downstream_gene_variant,,ENST00000564136,;KATNB1,downstream_gene_variant,,ENST00000563127,;KIFC3,downstream_gene_variant,,ENST00000565753,;	A	ENSG00000140854	ENST00000379661	Transcript	synonymous_variant	2186	1794	598	A	gcG/gcA	rs781829852	.	.	1	KATNB1	HGNC	6217	protein_coding	YES	CCDS10788.1	ENSP00000368982	KTNB1_HUMAN	H3BTV8_HUMAN,H3BPK1_HUMAN	UPI000007388F	.	.	.	19/20	.	HAMAP:MF_03022,hmmpanther:PTHR19845,Pfam_domain:PF13925	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGGCCCC	byFrequency	5	ESCA
ZNF23	0	.	GRCh37	16	71490014	71490014	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-183G>A	.	.	ENST00000393539	3/6	61	37	24	55	55	0	ZNF23,5_prime_UTR_variant,,ENST00000428724,;ZNF23,5_prime_UTR_variant,,ENST00000393539,;ZNF23,5_prime_UTR_variant,,ENST00000497160,;ZNF23,intron_variant,,ENST00000358700,;ZNF23,intron_variant,,ENST00000565718,;ZNF23,intron_variant,,ENST00000567340,;ZNF23,intron_variant,,ENST00000357254,;ZNF23,intron_variant,,ENST00000417828,;ZNF23,upstream_gene_variant,,ENST00000564528,;ZNF23,intron_variant,,ENST00000539742,;ZNF23,downstream_gene_variant,,ENST00000564588,;AC010547.9,3_prime_UTR_variant,,ENST00000561908,;ZNF23,upstream_gene_variant,,ENST00000576258,;	T	ENSG00000167377	ENST00000393539	Transcript	5_prime_UTR_variant	632	.	.	.	.	.	.	.	-1	ZNF23	HGNC	13023	protein_coding	YES	CCDS10900.1	ENSP00000377171	ZNF23_HUMAN	Q8NDP5_HUMAN,H3BPE6_HUMAN	UPI000013C406	.	.	.	3/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGATCCGTGA	.	5	ESCA
CCL14	0	.	GRCh37	17	34313811	34313811	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-55-71C>T	.	.	ENST00000536149	.	17	10	7	13	13	0	CCL14,5_prime_UTR_variant,,ENST00000480944,;CTB-186H2.3,3_prime_UTR_variant,,ENST00000591669,;CCL14,intron_variant,,ENST00000536149,;CCL14,upstream_gene_variant,,ENST00000394509,;CCL14,upstream_gene_variant,,ENST00000586216,;CCL14,upstream_gene_variant,,ENST00000435911,;CTB-186H2.3,downstream_gene_variant,,ENST00000593057,;CCL15-CCL14,intron_variant,,ENST00000481427,;CCL15-CCL14,intron_variant,,ENST00000495214,;	A	ENSG00000213494	ENST00000536149	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CCL14	HGNC	10612	protein_coding	YES	CCDS45652.1	ENSP00000441771	CCL14_HUMAN	.	UPI000002B47E	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTGGAAGG	.	5	ESCA
ACACA	0	.	GRCh37	17	35445997	35445997	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6904G>A	p.Asp2302Asn	p.D2302N	ENST00000353139	55/56	30	20	10	31	31	0	ACACA,missense_variant,p.Asp2207Asn,ENST00000360679,;ACACA,missense_variant,p.Asp2187Asn,ENST00000335166,;ACACA,missense_variant,p.Asp917Asn,ENST00000591119,;ACACA,missense_variant,p.Asp2302Asn,ENST00000353139,;ACACA,missense_variant,p.Asp2265Asn,ENST00000394406,;ACACA,missense_variant,p.Asp391Asn,ENST00000361253,;ACACA,upstream_gene_variant,,ENST00000586821,;ACACA,3_prime_UTR_variant,,ENST00000587233,;ACACA,non_coding_transcript_exon_variant,,ENST00000593055,;	T	ENSG00000132142	ENST00000353139	Transcript	missense_variant	7386	6904	2302	D/N	Gac/Aac	.	.	.	-1	ACACA	HGNC	84	protein_coding	YES	CCDS42302.1	ENSP00000344789	ACACA_HUMAN	Q7Z5W8_HUMAN,K7EII5_HUMAN,K4DID9_HUMAN,B4DWK9_HUMAN,B4DK31_HUMAN,B4DIW1_HUMAN,B2ZZ90_HUMAN,A8MYL5_HUMAN	UPI00002263AC	.	tolerated(0.09)	benign(0.005)	55/56	.	hmmpanther:PTHR18866:SF89,hmmpanther:PTHR18866,Gene3D:3.90.226.10,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTCCCAAA	.	5	ESCA
NLGN2	0	.	GRCh37	17	7322076	7322076	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*958G>C	.	.	ENST00000302926	7/7	35	22	12	22	22	0	NLGN2,3_prime_UTR_variant,,ENST00000302926,;NLGN2,downstream_gene_variant,,ENST00000570940,;NLGN2,downstream_gene_variant,,ENST00000575301,;SPEM1,upstream_gene_variant,,ENST00000323675,;RP11-104H15.7,upstream_gene_variant,,ENST00000575310,;	C	ENSG00000169992	ENST00000302926	Transcript	3_prime_UTR_variant	3539	.	.	.	.	.	.	.	1	NLGN2	HGNC	14290	protein_coding	YES	CCDS11103.1	ENSP00000305288	NLGN2_HUMAN	.	UPI0000049FD2	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGGAGGGG	.	5	ESCA
TP53	0	.	GRCh37	17	7577556	7577556	+	Missense_Mutation	SNP	C	C	T	rs121912655	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	7/11	45	8	36	41	41	0	TP53,missense_variant,p.Cys242Tyr,ENST00000413465,;TP53,missense_variant,p.Cys242Tyr,ENST00000420246,;TP53,missense_variant,p.Cys242Tyr,ENST00000269305,;TP53,missense_variant,p.Cys110Tyr,ENST00000509690,;TP53,missense_variant,p.Cys242Tyr,ENST00000359597,;TP53,missense_variant,p.Cys149Tyr,ENST00000514944,;TP53,missense_variant,p.Cys242Tyr,ENST00000445888,;TP53,missense_variant,p.Cys242Tyr,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	915	725	242	C/Y	tGc/tAc	CM910618,rs121912655,TP53_g.13362G>A,TP53_g.13362G>T,TP53_g.13362G>C,COSM11133,COSM10810,COSM10646,COSM251397,COSM129834,COSM1610838,COSM1610839,COSM251396,COSM129835,COSM3403262,COSM3717642,COSM3378347,COSM2744611,COSM1646852,COSM2744612,COSM1610840,COSM129836,COSM251398	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.C242Y|c.725G>A|4,SITE|p.C242Y|c.725G>A|42,SITE|p.C242Y|c.725G>A|4,SITE|p.C149Y|c.446G>A|4,CODON|p.0?|c.1_1182del1182|6,CODON|p.N239_C242delNSSC|c.715_726del12|3,CODON|p.C242W|c.726C>G|3,CODON|p.C242*|c.726C>A|3,CODON|p.C242W|c.726C>G|3,CODON|p.C242W|c.726C>G|9,CODON|p.C149W|c.447C>G|3,CODON|p.C242S|c.725G>C|3,CODON|p.C242S|c.725G>C|4,CODON|p.C242F|c.725G>T|11,CODON|p.C242F|c.725G>T|11,CODON|p.C242S|c.725G>C|3,CODON|p.C242F|c.725G>T|71,CODON|p.C149S|c.446G>C|4,CODON|p.C149F|c.446G>T|11,CODON|p.C242F|c.725G>T|4,CODON|p.C242S|c.725G>C|20,CODON|p.C242S|c.725G>C|4,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246L|c.736A>T|3,BUFFER|p.M153V|c.457A>G|7,BUFFER|p.M246V|c.736A>G|3,BUFFER|p.M246V|c.736A>G|35,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246V|c.736A>G|4,BUFFER|p.G245G|c.735C>T|5,BUFFER|p.G245D|c.734G>A|10,BUFFER|p.G245V|c.734G>T|3,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245A|c.734G>C|8,BUFFER|p.G152D|c.455G>A|23,BUFFER|p.G152V|c.455G>T|15,BUFFER|p.G245V|c.734G>T|10,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245D|c.734G>A|119,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245D|c.734G>A|7,BUFFER|p.G245V|c.734G>T|69,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245R|c.733G>C|14,BUFFER|p.G245S|c.733G>A|22,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152S|c.454G>A|56,BUFFER|p.G245C|c.733G>T|4,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245S|c.733G>A|340,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245C|c.733G>T|50,BUFFER|p.G245S|c.733G>A|39,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152C|c.454G>T|6,BUFFER|p.G152R|c.454G>C|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G151G|c.453C>T|3,BUFFER|p.G244G|c.732C>T|8,BUFFER|p.G244G|c.732C>A|6,BUFFER|p.G244fs*3|c.730delG|4,BUFFER|p.G151D|c.452G>A|8,BUFFER|p.G244D|c.731G>A|42,BUFFER|p.G244D|c.731G>A|3,BUFFER|p.G244D|c.731G>A|8,BUFFER|p.G244A|c.731G>C|8,BUFFER|p.G244D|c.731G>A|8,BUFFER|p.G244V|c.731G>T|15,BUFFER|p.G244C|c.730G>T|43,BUFFER|p.G244S|c.730G>A|6,BUFFER|p.G244C|c.730G>T|3,BUFFER|p.G244S|c.730G>A|5,BUFFER|p.G244C|c.730G>T|9,BUFFER|p.G244R|c.730G>C|5,BUFFER|p.G244C|c.730G>T|9,BUFFER|p.G244S|c.730G>A|9,BUFFER|p.G244S|c.730G>A|42,BUFFER|p.G151C|c.451G>T|9,BUFFER|p.G151S|c.451G>A|9,BUFFER|p.G244S|c.730G>A|8,BUFFER|p.G244C|c.730G>T|6,BUFFER|p.M243I|c.729G>A|5,BUFFER|p.M243T|c.728T>C|5,BUFFER|p.M243L|c.727A>C|4,BUFFER|p.M243V|c.727A>G|3,BUFFER|p.M243L|c.727A>T|6,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.C149fs*5|c.444delC|5,BUFFER|p.C242fs*5|c.723delC|12,BUFFER|p.S241delS|c.721_723delTCC|3,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.S241F|c.722_723CC>TT|5,BUFFER|p.C242G|c.724T>G|6,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C149G|c.445T>G|3,BUFFER|p.C242S|c.724T>A|11,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242R|c.724T>C|12,BUFFER|p.C242fs*5|c.722delC|6,BUFFER|p.S241fs*6|c.721delT|9,BUFFER|p.S148F|c.443C>T|15,BUFFER|p.S241Y|c.722C>A|4,BUFFER|p.S241Y|c.722C>A|15,BUFFER|p.S241C|c.722C>G|28,BUFFER|p.S241C|c.722C>G|3,BUFFER|p.S148Y|c.443C>A|5,BUFFER|p.S241F|c.722C>T|15,BUFFER|p.S241F|c.722C>T|6,BUFFER|p.S241F|c.722C>T|83,BUFFER|p.S241C|c.722C>G|4,BUFFER|p.S241Y|c.722C>A|4,BUFFER|p.S241Y|c.722C>A|5,BUFFER|p.S241Y|c.722C>A|5,BUFFER|p.S148C|c.443C>G|4,BUFFER|p.S241F|c.722C>T|9,BUFFER|p.S241F|c.722C>T|14,BUFFER|p.S241T|c.721T>A|6,BUFFER|p.S241A|c.721T>G|10,BUFFER|p.S241P|c.721T>C|5,BUFFER|p.S240R|c.720T>A|4,BUFFER|p.S240R|c.720T>G|4,BUFFER|p.S240S|c.720T>C|3,BUFFER|p.S240I|c.719G>T|6,BUFFER|p.S240C|c.718A>T|3,BUFFER|p.S240G|c.718A>G|16,BUFFER|p.N239K|c.717C>G|5,BUFFER|p.N146S|c.437A>G|6,BUFFER|p.N239T|c.716A>C|6,BUFFER|p.N239S|c.716A>G|3,BUFFER|p.N239S|c.716A>G|6,BUFFER|p.N239S|c.716A>G|4,BUFFER|p.N239S|c.716A>G|25,BUFFER|p.N239S|c.716A>G|5,BUFFER|p.N239D|c.715A>G|11,BUFFER|p.N239D|c.715A>G|13,BUFFER|p.N239D|c.715A>G|44,BUFFER|p.N146D|c.436A>G|14,BUFFER|p.N239Y|c.715A>T|6,BUFFER|p.N239D|c.715A>G|14,BUFFER|p.N239fs*1|c.714_715insT|3,BUFFER|p.N239fs*25|c.714_715insN|12,BUFFER|p.N239fs*1|c.714_715insT|4,BUFFER|p.N239fs*1|c.714_715insT|3,BUFFER|p.N146fs*1|c.435_436insT|3,BUFFER|p.C238*|c.714T>A|4,BUFFER|p.C238W|c.714T>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGCAGGAA	byCluster	5	ESCA
FOXK2	0	.	GRCh37	17	80559543	80559543	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*168C>G	.	.	ENST00000335255	9/9	40	23	17	33	33	0	FOXK2,3_prime_UTR_variant,,ENST00000335255,;RP13-638C3.4,downstream_gene_variant,,ENST00000576912,;FOXK2,non_coding_transcript_exon_variant,,ENST00000529652,;FOXK2,downstream_gene_variant,,ENST00000571989,;FOXK2,upstream_gene_variant,,ENST00000574694,;FOXK2,3_prime_UTR_variant,,ENST00000473637,;	G	ENSG00000141568	ENST00000335255	Transcript	3_prime_UTR_variant	2325	.	.	.	.	.	.	.	1	FOXK2	HGNC	6036	protein_coding	YES	CCDS11813.1	ENSP00000335677	FOXK2_HUMAN	E9PM37_HUMAN	UPI00001A8BEE	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACACTTGAA	.	5	ESCA
SMARCA4	0	.	GRCh37	19	11097213	11097213	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.704G>A	p.Gly235Asp	p.G235D	ENST00000429416	5/36	17	12	5	12	12	0	SMARCA4,missense_variant,p.Gly235Asp,ENST00000450717,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000358026,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000413806,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000590574,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000444061,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000344626,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000541122,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000429416,;SMARCA4,missense_variant,p.Gly235Asp,ENST00000589677,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;	A	ENSG00000127616	ENST00000429416	Transcript	missense_variant	985	704	235	G/D	gGc/gAc	.	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	benign(0.441)	5/36	.	hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCTGGCCCTG	.	4	ESCA
ZNF878	0	.	GRCh37	19	12154831	12154831	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1385C>T	p.Ser462Phe	p.S462F	ENST00000547628	4/4	49	34	15	54	54	0	ZNF878,missense_variant,p.Ser462Phe,ENST00000547628,;ZNF878,missense_variant,p.Ser509Phe,ENST00000602107,;CTD-2006C1.2,intron_variant,,ENST00000591898,;CTD-2006C1.2,intron_variant,,ENST00000476474,;CTD-2006C1.2,intron_variant,,ENST00000591838,;CTD-2006C1.10,intron_variant,,ENST00000547473,;	A	ENSG00000257446	ENST00000547628	Transcript	missense_variant	1523	1385	462	S/F	tCt/tTt	.	.	.	-1	ZNF878	HGNC	37246	protein_coding	YES	CCDS45984.2	ENSP00000447931	ZN878_HUMAN	.	UPI00001D8268	.	tolerated(0.7)	possibly_damaging(0.516)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24379,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGAAGAAATG	.	5	ESCA
CC2D1A	0	.	GRCh37	19	14038817	14038817	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2428G>C	p.Asp810His	p.D810H	ENST00000318003	23/29	154	106	47	160	160	0	CC2D1A,missense_variant,p.Asp810His,ENST00000589606,;CC2D1A,missense_variant,p.Asp265His,ENST00000587508,;CC2D1A,missense_variant,p.Asp810His,ENST00000318003,;PODNL1,downstream_gene_variant,,ENST00000538517,;PODNL1,downstream_gene_variant,,ENST00000339560,;PODNL1,downstream_gene_variant,,ENST00000254320,;PODNL1,downstream_gene_variant,,ENST00000587954,;PODNL1,downstream_gene_variant,,ENST00000588872,;PODNL1,downstream_gene_variant,,ENST00000538371,;CC2D1A,3_prime_UTR_variant,,ENST00000586955,;CC2D1A,non_coding_transcript_exon_variant,,ENST00000589138,;CC2D1A,downstream_gene_variant,,ENST00000589679,;CC2D1A,downstream_gene_variant,,ENST00000588932,;CC2D1A,downstream_gene_variant,,ENST00000589224,;	C	ENSG00000132024	ENST00000318003	Transcript	missense_variant	2669	2428	810	D/H	Gac/Cac	.	.	.	1	CC2D1A	HGNC	30237	protein_coding	YES	CCDS42512.1	ENSP00000313601	C2D1A_HUMAN	.	UPI0000203524	.	deleterious(0)	probably_damaging(1)	23/29	.	hmmpanther:PTHR13076,hmmpanther:PTHR13076:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATTGACCCT	.	5	ESCA
CYP4F22	0	.	GRCh37	19	15658995	15658995	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213G>T	p.Val405Phe	p.V405F	ENST00000269703	11/14	45	33	12	31	31	0	CYP4F22,missense_variant,p.Val405Phe,ENST00000269703,;CYP4F22,missense_variant,p.Val405Phe,ENST00000601005,;	T	ENSG00000171954	ENST00000269703	Transcript	missense_variant	1412	1213	405	V/F	Gtc/Ttc	.	.	.	1	CYP4F22	HGNC	26820	protein_coding	YES	CCDS12331.1	ENSP00000269703	CP4FN_HUMAN	.	UPI000013D84B	.	tolerated(0.06)	possibly_damaging(0.724)	11/14	.	hmmpanther:PTHR24290,hmmpanther:PTHR24290:SF68,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTGTCTCT	.	5	ESCA
PNMAL1	0	.	GRCh37	19	46973274	46973274	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1019G>T	p.Gly340Val	p.G340V	ENST00000313683	2/3	20	10	9	20	20	0	PNMAL1,missense_variant,p.Gly340Val,ENST00000438932,;PNMAL1,missense_variant,p.Gly340Val,ENST00000313683,;PNMAL1,intron_variant,,ENST00000602246,;	A	ENSG00000182013	ENST00000313683	Transcript	missense_variant	1325	1019	340	G/V	gGc/gTc	.	.	.	-1	PNMAL1	HGNC	25578	protein_coding	YES	CCDS33059.1	ENSP00000318131	PNML1_HUMAN	.	UPI0000231C97	.	deleterious(0.05)	probably_damaging(0.979)	2/3	.	hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF21,Pfam_domain:PF14893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGGCCACCA	.	5	ESCA
MIR517B	0	.	GRCh37	19	54224390	54224390	+	RNA	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.61G>A	.	.	ENST00000385102	1/1	122	59	63	189	189	0	MIR517B,mature_miRNA_variant,,ENST00000385102,;MIR521-2,downstream_gene_variant,,ENST00000384818,;MIR516B2,upstream_gene_variant,,ENST00000385190,;MIR520D,downstream_gene_variant,,ENST00000385002,;RNU6-803P,upstream_gene_variant,,ENST00000516034,;MIR520G,upstream_gene_variant,,ENST00000385064,;	A	ENSG00000207837	ENST00000385102	Transcript	mature_miRNA_variant	61	.	.	.	.	.	.	.	1	MIR517B	HGNC	32115	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGAGTGTTA	.	5	ESCA
ARHGEF18	0	.	GRCh37	19	7533811	7533811	+	Missense_Mutation	SNP	G	G	A	rs201204829	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3017G>A	p.Arg1006His	p.R1006H	ENST00000359920	17/20	23	16	6	16	16	0	ARHGEF18,missense_variant,p.Arg1006His,ENST00000359920,;ARHGEF18,missense_variant,p.Arg645His,ENST00000594665,;ARHGEF18,missense_variant,p.Arg848His,ENST00000319670,;CTD-2207O23.3,missense_variant,p.Arg964His,ENST00000593531,;	A	ENSG00000104880	ENST00000359920	Transcript	missense_variant	3270	3017	1006	R/H	cGc/cAc	rs201204829	.	.	1	ARHGEF18	HGNC	17090	protein_coding	YES	CCDS45946.1	ENSP00000352995	ARHGI_HUMAN	M0R125_HUMAN	UPI0000D6170D	.	deleterious(0.05)	benign(0.117)	17/20	.	hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF9	A:0.0004	A:0	A:0.0014	.	A:0	A:0	A:0.001	A:0	A:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGAGCGCCCCG	byFrequency|byCluster|by1000G	4	ESCA
RP11-403I13.8	0	.	GRCh37	1	149287545	149287545	+	RNA	SNP	G	G	A	rs371598228,rs760762172	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.95G>A	.	.	ENST00000433084	1/2	14	11	3	9	9	0	RP11-403I13.8,non_coding_transcript_exon_variant,,ENST00000433084,;LINC00869,downstream_gene_variant,,ENST00000424684,;RNU1-143P,upstream_gene_variant,,ENST00000516296,;	A	ENSG00000235999	ENST00000433084	Transcript	non_coding_transcript_exon_variant	95	.	.	.	.	rs371598228,rs760762172	.	.	1	RP11-403I13.8	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ACAAGGCCGTT	byCluster	2	ESCA
EPHA2	0	.	GRCh37	1	16475134	16475134	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562T>C	p.Cys188Arg	p.C188R	ENST00000358432	3/17	35	32	3	40	40	0	EPHA2,missense_variant,p.Cys188Arg,ENST00000358432,;EPHA2,non_coding_transcript_exon_variant,,ENST00000461614,;EPHA2,upstream_gene_variant,,ENST00000480202,;	G	ENSG00000142627	ENST00000358432	Transcript	missense_variant	717	562	188	C/R	Tgt/Cgt	.	.	.	-1	EPHA2	HGNC	3386	protein_coding	YES	CCDS169.1	ENSP00000351209	EPHA2_HUMAN	Q96HF4_HUMAN,Q8IZL0_HUMAN	UPI00000731AB	.	deleterious(0)	probably_damaging(0.989)	3/17	.	PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF306,hmmpanther:PTHR24416,PROSITE_patterns:PS00790,Pfam_domain:PF01404,Gene3D:2.60.120.260,PIRSF_domain:PIRSF000666,SMART_domains:SM00615,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACACAGGCAC	.	2	ESCA
PFKFB2	0	.	GRCh37	1	207236027	207236027	+	Missense_Mutation	SNP	C	C	T	rs757942412	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274C>T	p.Arg92Trp	p.R92W	ENST00000367080	4/15	61	37	24	81	81	0	PFKFB2,missense_variant,p.Arg92Trp,ENST00000367079,;PFKFB2,missense_variant,p.Arg92Trp,ENST00000367080,;PFKFB2,missense_variant,p.Arg59Trp,ENST00000545806,;PFKFB2,5_prime_UTR_variant,,ENST00000411990,;PFKFB2,upstream_gene_variant,,ENST00000541914,;PFKFB2,non_coding_transcript_exon_variant,,ENST00000464777,;	T	ENSG00000123836	ENST00000367080	Transcript	missense_variant	398	274	92	R/W	Cgg/Tgg	rs757942412	.	.	1	PFKFB2	HGNC	8873	protein_coding	YES	CCDS31004.1	ENSP00000356047	F262_HUMAN	B0FLL2_HUMAN	UPI000012A3F0	.	.	probably_damaging(0.991)	4/15	.	hmmpanther:PTHR10606:SF13,hmmpanther:PTHR10606,Gene3D:3.40.50.300,Pfam_domain:PF01591,PIRSF_domain:PIRSF000709,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCGGCAT	.	5	ESCA
EIF4G3	0	.	GRCh37	1	21268765	21268765	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732C>T	p.%3D	p.V244V	ENST00000602326	12/35	113	107	6	105	105	0	EIF4G3,synonymous_variant,p.%3D,ENST00000374927,;EIF4G3,synonymous_variant,p.%3D,ENST00000356916,;EIF4G3,synonymous_variant,p.%3D,ENST00000400422,;EIF4G3,synonymous_variant,p.%3D,ENST00000374937,;EIF4G3,synonymous_variant,p.%3D,ENST00000602326,;EIF4G3,synonymous_variant,p.%3D,ENST00000264211,;EIF4G3,5_prime_UTR_variant,,ENST00000536266,;EIF4G3,intron_variant,,ENST00000374935,;EIF4G3,upstream_gene_variant,,ENST00000544689,;EIF4G3,upstream_gene_variant,,ENST00000374933,;EIF4G3,upstream_gene_variant,,ENST00000485722,;	A	ENSG00000075151	ENST00000602326	Transcript	synonymous_variant	1316	732	244	V	gtC/gtT	.	.	.	-1	EIF4G3	HGNC	3298	protein_coding	YES	CCDS55580.1	ENSP00000473510	IF4G3_HUMAN	Q59GJ0_HUMAN,F5H564_HUMAN	UPI0001639589	.	.	.	12/35	.	hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGAGGACTAG	.	2	ESCA
ZNF496	0	.	GRCh37	1	247471852	247471852	+	Missense_Mutation	SNP	T	T	C	rs775076588	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.931A>G	p.Arg311Gly	p.R311G	ENST00000294753	8/9	68	48	19	68	68	0	ZNF496,missense_variant,p.Arg347Gly,ENST00000366498,;ZNF496,missense_variant,p.Arg236Gly,ENST00000461277,;ZNF496,missense_variant,p.Arg311Gly,ENST00000294753,;ZNF496,non_coding_transcript_exon_variant,,ENST00000462139,;	C	ENSG00000162714	ENST00000294753	Transcript	missense_variant	1396	931	311	R/G	Agg/Ggg	rs775076588	.	.	-1	ZNF496	HGNC	23713	protein_coding	YES	CCDS1631.1	ENSP00000294753	ZN496_HUMAN	.	UPI000007025B	.	tolerated(0.34)	benign(0.006)	8/9	.	hmmpanther:PTHR10032:SF212,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCTTCTTT	byFrequency	5	ESCA
OR11L1	0	.	GRCh37	1	248004325	248004325	+	Silent	SNP	A	A	G	rs184029383	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874T>C	p.%3D	p.L292L	ENST00000355784	1/1	50	38	11	26	26	0	OR11L1,synonymous_variant,p.%3D,ENST00000355784,;	G	ENSG00000197591	ENST00000355784	Transcript	synonymous_variant	930	874	292	L	Ttg/Ctg	rs184029383	.	.	-1	OR11L1	HGNC	14998	protein_coding	YES	CCDS31098.1	ENSP00000348033	O11L1_HUMAN	.	UPI0000061EBC	.	.	.	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26452:SF12,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237	C:0.0002	C:0	C:0	.	C:0.001	C:0	C:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCAAGCTGT	byCluster|by1000G	5	ESCA
AUNIP	0	.	GRCh37	1	26161543	26161543	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015C>A	p.Pro339Thr	p.P339T	ENST00000374298	3/3	39	21	18	42	42	0	AUNIP,missense_variant,p.Pro339Thr,ENST00000374298,;AUNIP,missense_variant,p.Pro339Thr,ENST00000538789,;MTFR1L,downstream_gene_variant,,ENST00000466284,;MTFR1L,downstream_gene_variant,,ENST00000374307,;MTFR1L,downstream_gene_variant,,ENST00000374303,;MTFR1L,downstream_gene_variant,,ENST00000474295,;MTFR1L,downstream_gene_variant,,ENST00000374301,;MTFR1L,downstream_gene_variant,,ENST00000524618,;MTFR1L,downstream_gene_variant,,ENST00000374300,;RP1-317E23.7,upstream_gene_variant,,ENST00000606617,;AUNIP,intron_variant,,ENST00000481602,;MTFR1L,downstream_gene_variant,,ENST00000469815,;MTFR1L,downstream_gene_variant,,ENST00000497956,;	T	ENSG00000127423	ENST00000374298	Transcript	missense_variant	1070	1015	339	P/T	Cct/Act	.	.	.	-1	AUNIP	HGNC	28363	protein_coding	YES	CCDS266.1	ENSP00000363416	AUNIP_HUMAN	.	UPI000006D2D0	.	tolerated(0.11)	benign(0.02)	3/3	.	hmmpanther:PTHR14526,hmmpanther:PTHR14526:SF2,Pfam_domain:PF15334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ATCAGGCTTCA	.	4	ESCA
AUNIP	0	.	GRCh37	1	26161544	26161544	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1014G>A	p.%3D	p.K338K	ENST00000374298	3/3	40	22	18	43	43	0	AUNIP,synonymous_variant,p.%3D,ENST00000374298,;AUNIP,synonymous_variant,p.%3D,ENST00000538789,;MTFR1L,downstream_gene_variant,,ENST00000466284,;MTFR1L,downstream_gene_variant,,ENST00000374307,;MTFR1L,downstream_gene_variant,,ENST00000374303,;MTFR1L,downstream_gene_variant,,ENST00000474295,;MTFR1L,downstream_gene_variant,,ENST00000374301,;MTFR1L,downstream_gene_variant,,ENST00000524618,;MTFR1L,downstream_gene_variant,,ENST00000374300,;RP1-317E23.7,upstream_gene_variant,,ENST00000606617,;AUNIP,intron_variant,,ENST00000481602,;MTFR1L,downstream_gene_variant,,ENST00000469815,;MTFR1L,downstream_gene_variant,,ENST00000497956,;	T	ENSG00000127423	ENST00000374298	Transcript	synonymous_variant	1069	1014	338	K	aaG/aaA	.	.	.	-1	AUNIP	HGNC	28363	protein_coding	YES	CCDS266.1	ENSP00000363416	AUNIP_HUMAN	.	UPI000006D2D0	.	.	.	3/3	.	hmmpanther:PTHR14526,hmmpanther:PTHR14526:SF2,Pfam_domain:PF15334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGGCTTCAG	.	5	ESCA
TOE1	0	.	GRCh37	1	45809288	45809288	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1447G>C	p.Val483Leu	p.V483L	ENST00000372090	8/8	38	23	14	37	37	0	TOE1,missense_variant,p.Val483Leu,ENST00000372090,;TOE1,missense_variant,p.Val403Leu,ENST00000539779,;MUTYH,upstream_gene_variant,,ENST00000372098,;MUTYH,upstream_gene_variant,,ENST00000412971,;MUTYH,upstream_gene_variant,,ENST00000531105,;MUTYH,upstream_gene_variant,,ENST00000372110,;MUTYH,upstream_gene_variant,,ENST00000355498,;MUTYH,upstream_gene_variant,,ENST00000450313,;MUTYH,upstream_gene_variant,,ENST00000372104,;MUTYH,upstream_gene_variant,,ENST00000372115,;TESK2,downstream_gene_variant,,ENST00000341771,;TESK2,downstream_gene_variant,,ENST00000538496,;MUTYH,upstream_gene_variant,,ENST00000528013,;MUTYH,upstream_gene_variant,,ENST00000448481,;MUTYH,upstream_gene_variant,,ENST00000456914,;MUTYH,upstream_gene_variant,,ENST00000372100,;MUTYH,upstream_gene_variant,,ENST00000488731,;MUTYH,upstream_gene_variant,,ENST00000529984,;TESK2,downstream_gene_variant,,ENST00000372086,;MUTYH,upstream_gene_variant,,ENST00000483127,;MUTYH,upstream_gene_variant,,ENST00000435155,;TESK2,downstream_gene_variant,,ENST00000372084,;MUTYH,upstream_gene_variant,,ENST00000354383,;MUTYH,upstream_gene_variant,,ENST00000528332,;TOE1,non_coding_transcript_exon_variant,,ENST00000495703,;TOE1,downstream_gene_variant,,ENST00000477731,;TESK2,downstream_gene_variant,,ENST00000486676,;TOE1,downstream_gene_variant,,ENST00000471337,;TOE1,downstream_gene_variant,,ENST00000460057,;MUTYH,upstream_gene_variant,,ENST00000525160,;MUTYH,upstream_gene_variant,,ENST00000481571,;MUTYH,upstream_gene_variant,,ENST00000534453,;MUTYH,upstream_gene_variant,,ENST00000475516,;MUTYH,upstream_gene_variant,,ENST00000470256,;MUTYH,upstream_gene_variant,,ENST00000474703,;MUTYH,upstream_gene_variant,,ENST00000485484,;MUTYH,upstream_gene_variant,,ENST00000461495,;MUTYH,upstream_gene_variant,,ENST00000481139,;MUTYH,upstream_gene_variant,,ENST00000492494,;MUTYH,upstream_gene_variant,,ENST00000467940,;MUTYH,upstream_gene_variant,,ENST00000479746,;MUTYH,upstream_gene_variant,,ENST00000476789,;MUTYH,upstream_gene_variant,,ENST00000462387,;MUTYH,upstream_gene_variant,,ENST00000483642,;	C	ENSG00000132773	ENST00000372090	Transcript	missense_variant	2030	1447	483	V/L	Gta/Cta	.	.	.	1	TOE1	HGNC	15954	protein_coding	YES	CCDS521.1	ENSP00000361162	TOE1_HUMAN	B3KSC7_HUMAN	UPI00000382DE	.	deleterious(0.02)	benign(0.334)	8/8	.	hmmpanther:PTHR15092,hmmpanther:PTHR15092:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTGTACCC	.	5	ESCA
USP1	0	.	GRCh37	1	62916244	62916244	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1950A>T	p.%3D	p.G650G	ENST00000339950	9/9	62	43	18	50	50	0	USP1,synonymous_variant,p.%3D,ENST00000371146,;USP1,synonymous_variant,p.%3D,ENST00000339950,;DOCK7,downstream_gene_variant,,ENST00000251157,;DOCK7,downstream_gene_variant,,ENST00000340370,;DOCK7,downstream_gene_variant,,ENST00000454575,;	T	ENSG00000162607	ENST00000339950	Transcript	synonymous_variant	2765	1950	650	G	ggA/ggT	.	.	.	1	USP1	HGNC	12607	protein_coding	YES	CCDS621.1	ENSP00000343526	UBP1_HUMAN	C9JWX4_HUMAN,C9JC88_HUMAN	UPI00001379D4	.	.	.	9/9	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF378,PROSITE_profiles:PS50235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGAAATAC	.	5	ESCA
LPAR3	0	.	GRCh37	1	85279550	85279550	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041C>T	p.%3D	p.V347V	ENST00000440886	2/2	49	31	17	42	42	0	LPAR3,synonymous_variant,p.%3D,ENST00000440886,;LPAR3,synonymous_variant,p.%3D,ENST00000370611,;LPAR3,downstream_gene_variant,,ENST00000491034,;	A	ENSG00000171517	ENST00000440886	Transcript	synonymous_variant	1080	1041	347	V	gtC/gtT	.	.	.	-1	LPAR3	HGNC	14298	protein_coding	YES	CCDS700.1	ENSP00000395389	LPAR3_HUMAN	.	UPI000003CAC0	.	.	.	2/2	.	hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF21,Prints_domain:PR01560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCAGACTGC	.	5	ESCA
GPCPD1	0	.	GRCh37	20	5548199	5548199	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1157A>T	p.Asp386Val	p.D386V	ENST00000379019	13/20	130	88	41	158	157	1	GPCPD1,missense_variant,p.Asp386Val,ENST00000379019,;GPCPD1,intron_variant,,ENST00000418646,;GPCPD1,non_coding_transcript_exon_variant,,ENST00000481038,;GPCPD1,non_coding_transcript_exon_variant,,ENST00000473797,;	A	ENSG00000125772	ENST00000379019	Transcript	missense_variant	1370	1157	386	D/V	gAt/gTt	.	.	.	-1	GPCPD1	HGNC	26957	protein_coding	YES	CCDS13090.1	ENSP00000368305	GPCP1_HUMAN	D3DW07_HUMAN	UPI0000062241	.	tolerated(0.16)	benign(0.033)	13/20	.	Superfamily_domains:SSF51695,Pfam_domain:PF03009,Gene3D:3.20.20.190,hmmpanther:PTHR22958,PROSITE_profiles:PS51704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCATCAAAT	.	5	ESCA
CCT8	0	.	GRCh37	21	30435686	30435686	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.928A>G	p.Ile310Val	p.I310V	ENST00000286788	8/15	26	16	9	36	36	0	CCT8,missense_variant,p.Ile256Val,ENST00000431234,;CCT8,missense_variant,p.Ile310Val,ENST00000286788,;CCT8,missense_variant,p.Ile291Val,ENST00000542732,;CCT8,missense_variant,p.Ile237Val,ENST00000540844,;CCT8,upstream_gene_variant,,ENST00000432178,;AF129075.5,upstream_gene_variant,,ENST00000457162,;CCT8,non_coding_transcript_exon_variant,,ENST00000470450,;CCT8,upstream_gene_variant,,ENST00000480359,;CCT8,downstream_gene_variant,,ENST00000494296,;CCT8,downstream_gene_variant,,ENST00000481059,;CCT8,non_coding_transcript_exon_variant,,ENST00000475205,;CCT8,upstream_gene_variant,,ENST00000496121,;CCT8,downstream_gene_variant,,ENST00000484403,;	C	ENSG00000156261	ENST00000286788	Transcript	missense_variant	1135	928	310	I/V	Atc/Gtc	COSM219967	.	.	-1	CCT8	HGNC	1623	protein_coding	YES	CCDS33528.1	ENSP00000286788	TCPQ_HUMAN	Q7Z759_HUMAN	UPI0000136B0D	.	tolerated(0.05)	benign(0.014)	8/15	.	Superfamily_domains:SSF52029,Gene3D:3.50.7.10,TIGRFAM_domain:TIGR02346,Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF60	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CATGATATTAT	.	4	ESCA
SYNJ1	0	.	GRCh37	21	34038771	34038771	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2041delA	p.Ile681SerfsTer17	p.I681Sfs*17	ENST00000433931	16/32	79	56	23	73	73	0	SYNJ1,frameshift_variant,p.Ile681SerfsTer17,ENST00000382499,;SYNJ1,frameshift_variant,p.Ile637SerfsTer17,ENST00000429236,;SYNJ1,frameshift_variant,p.Ile637SerfsTer17,ENST00000382491,;SYNJ1,frameshift_variant,p.Ile642SerfsTer17,ENST00000322229,;SYNJ1,frameshift_variant,p.Ile681SerfsTer17,ENST00000433931,;SYNJ1,frameshift_variant,p.Ile642SerfsTer17,ENST00000357345,;	-	ENSG00000159082	ENST00000433931	Transcript	frameshift_variant	2049	2041	681	I/X	Atc/tc	.	.	.	-1	SYNJ1	HGNC	11503	protein_coding	YES	CCDS33539.2	ENSP00000409667	.	J3KQV8_HUMAN,C9J1Z6_HUMAN	UPI0001A47572	.	.	.	16/32	.	Superfamily_domains:SSF56219,SMART_domains:SM00128,Gene3D:3.60.10.10,Pfam_domain:PF03372,hmmpanther:PTHR11200:SF126,hmmpanther:PTHR11200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCTGATAAAAA	.	3	ESCA
CECR7	0	.	GRCh37	22	17525823	17525823	+	RNA	SNP	G	G	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.836G>T	.	.	ENST00000441006	2/4	91	58	32	91	91	0	CECR7,non_coding_transcript_exon_variant,,ENST00000609932,;CECR7,non_coding_transcript_exon_variant,,ENST00000609596,;CECR7,non_coding_transcript_exon_variant,,ENST00000441006,;CECR7,non_coding_transcript_exon_variant,,ENST00000414401,;	T	ENSG00000237438	ENST00000441006	Transcript	non_coding_transcript_exon_variant	836	.	.	.	.	.	.	.	1	CECR7	HGNC	1845	lincRNA	YES	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGAGCAACT	.	5	ESCA
CECR7	0	.	GRCh37	22	17525824	17525824	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.837C>T	.	.	ENST00000441006	2/4	92	59	32	92	92	0	CECR7,non_coding_transcript_exon_variant,,ENST00000609932,;CECR7,non_coding_transcript_exon_variant,,ENST00000609596,;CECR7,non_coding_transcript_exon_variant,,ENST00000441006,;CECR7,non_coding_transcript_exon_variant,,ENST00000414401,;	T	ENSG00000237438	ENST00000441006	Transcript	non_coding_transcript_exon_variant	837	.	.	.	.	.	.	.	1	CECR7	HGNC	1845	lincRNA	YES	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGCAACTG	.	5	ESCA
FAM230B	0	.	GRCh37	22	21538128	21538128	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1114C>T	.	.	ENST00000451257	8/12	222	211	11	241	241	0	FAM230B,non_coding_transcript_exon_variant,,ENST00000451257,;FAM230B,intron_variant,,ENST00000415376,;FAM230B,downstream_gene_variant,,ENST00000421576,;KB-1592A4.14,upstream_gene_variant,,ENST00000417463,;FAM230B,downstream_gene_variant,,ENST00000424410,;FAM230B,downstream_gene_variant,,ENST00000446717,;	T	ENSG00000215498	ENST00000451257	Transcript	non_coding_transcript_exon_variant	1114	.	.	.	.	.	.	.	1	FAM230B	HGNC	32943	lincRNA	YES	.	.	.	.	.	.	.	.	8/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCATCGCCAG	.	2	ESCA
KB-1572G7.2	0	.	GRCh37	22	24025972	24025972	+	RNA	SNP	G	G	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2661C>A	.	.	ENST00000421064	10/12	19	16	3	14	14	0	RGL4,upstream_gene_variant,,ENST00000401461,;AP000347.2,non_coding_transcript_exon_variant,,ENST00000451919,;KB-1572G7.2,non_coding_transcript_exon_variant,,ENST00000421064,;GUSBP11,non_coding_transcript_exon_variant,,ENST00000422506,;AP000347.2,non_coding_transcript_exon_variant,,ENST00000458554,;KB-1572G7.2,non_coding_transcript_exon_variant,,ENST00000423913,;AP000347.2,non_coding_transcript_exon_variant,,ENST00000417194,;GUSBP11,non_coding_transcript_exon_variant,,ENST00000452737,;GUSBP11,non_coding_transcript_exon_variant,,ENST00000445682,;GUSBP11,non_coding_transcript_exon_variant,,ENST00000451837,;GUSBP11,non_coding_transcript_exon_variant,,ENST00000455485,;GUSBP11,non_coding_transcript_exon_variant,,ENST00000608454,;AP000347.2,non_coding_transcript_exon_variant,,ENST00000437862,;KB-1572G7.2,intron_variant,,ENST00000434893,;AP000347.2,intron_variant,,ENST00000438858,;RGL4,upstream_gene_variant,,ENST00000441897,;AP000347.2,intron_variant,,ENST00000435868,;	T	ENSG00000273000	ENST00000421064	Transcript	non_coding_transcript_exon_variant	2661	.	.	.	.	.	.	.	-1	KB-1572G7.2	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	10/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGCCGGAAAG	.	4	ESCA
TOB2	0	.	GRCh37	22	41832910	41832910	+	Missense_Mutation	SNP	T	T	C	rs776245257	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.440A>G	p.Asp147Gly	p.D147G	ENST00000327492	2/2	40	23	17	37	37	0	TOB2,missense_variant,p.Asp147Gly,ENST00000327492,;TOB2,downstream_gene_variant,,ENST00000434408,;	C	ENSG00000183864	ENST00000327492	Transcript	missense_variant	1147	440	147	D/G	gAc/gGc	rs776245257	.	.	-1	TOB2	HGNC	11980	protein_coding	YES	CCDS14015.1	ENSP00000331305	TOB2_HUMAN	B0QXZ4_HUMAN	UPI00001370FC	.	tolerated(0.39)	benign(0)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR17537:SF3,hmmpanther:PTHR17537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGTCCTGG	.	5	ESCA
SLC9A4	0	.	GRCh37	2	103124546	103124546	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1207G>T	p.Ala403Ser	p.A403S	ENST00000295269	5/12	78	55	22	60	60	0	SLC9A4,missense_variant,p.Ala403Ser,ENST00000295269,;SLC9A4,downstream_gene_variant,,ENST00000492154,;	T	ENSG00000180251	ENST00000295269	Transcript	missense_variant	1664	1207	403	A/S	Gct/Tct	.	.	.	1	SLC9A4	HGNC	11077	protein_coding	YES	CCDS33264.1	ENSP00000295269	SL9A4_HUMAN	.	UPI000047F996	.	tolerated(0.22)	benign(0.08)	5/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10110:SF103,hmmpanther:PTHR10110,Pfam_domain:PF00999,TIGRFAM_domain:TIGR00840	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTGCTCTC	.	5	ESCA
NBAS	0	.	GRCh37	2	15415836	15415836	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5496A>T	p.Lys1832Asn	p.K1832N	ENST00000281513	44/52	36	26	10	31	30	1	NBAS,missense_variant,p.Lys1712Asn,ENST00000441750,;NBAS,missense_variant,p.Lys1832Asn,ENST00000281513,;NBAS,missense_variant,p.Lys880Asn,ENST00000442506,;	A	ENSG00000151779	ENST00000281513	Transcript	missense_variant	5522	5496	1832	K/N	aaA/aaT	.	.	.	-1	NBAS	HGNC	15625	protein_coding	YES	CCDS1685.1	ENSP00000281513	NBAS_HUMAN	Q4ZG05_HUMAN,H7C007_HUMAN	UPI00001AEA68	.	deleterious(0.01)	benign(0.424)	44/52	.	hmmpanther:PTHR15922:SF2,hmmpanther:PTHR15922	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGGATTTTGGG	.	2	ESCA
BAZ2B	0	.	GRCh37	2	160206655	160206655	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4427C>T	p.Ala1476Val	p.A1476V	ENST00000392783	28/37	84	58	25	76	76	0	BAZ2B,missense_variant,p.Ala1442Val,ENST00000355831,;BAZ2B,missense_variant,p.Ala1440Val,ENST00000392782,;BAZ2B,missense_variant,p.Ala1376Val,ENST00000343439,;BAZ2B,missense_variant,p.Ala1476Val,ENST00000392783,;BAZ2B,upstream_gene_variant,,ENST00000426648,;BAZ2B,upstream_gene_variant,,ENST00000474437,;	A	ENSG00000123636	ENST00000392783	Transcript	missense_variant	4923	4427	1476	A/V	gCt/gTt	.	.	.	-1	BAZ2B	HGNC	963	protein_coding	YES	CCDS2209.2	ENSP00000376534	BAZ2B_HUMAN	Q8NC87_HUMAN,Q53TG3_HUMAN,C9JCA6_HUMAN	UPI0000D74C4A	.	.	possibly_damaging(0.715)	28/37	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF144	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTAGCTACT	.	5	ESCA
KCNH7	0	.	GRCh37	2	163279955	163279955	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000332142	9/16	122	83	39	108	108	0	KCNH7,missense_variant,p.Arg682Gln,ENST00000332142,;KCNH7,missense_variant,p.Arg675Gln,ENST00000328032,;	T	ENSG00000184611	ENST00000332142	Transcript	missense_variant	2145	2045	682	R/Q	cGa/cAa	COSM232583,COSM1255318,COSM3391043,COSM1255319	.	.	-1	KCNH7	HGNC	18863	protein_coding	YES	CCDS2219.1	ENSP00000331727	KCNH7_HUMAN	.	UPI0000167D11	.	deleterious(0)	probably_damaging(0.991)	9/16	.	hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Gene3D:3bpzA01,Superfamily_domains:SSF51206	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E685G|c.2054A>G|4,BUFFER|p.E678G|c.2033A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTCGCAGC	.	5	ESCA
SCN7A	0	.	GRCh37	2	167322493	167322493	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.669G>A	p.%3D	p.L223L	ENST00000409855	7/25	37	26	11	39	39	0	SCN7A,synonymous_variant,p.%3D,ENST00000409855,;SCN7A,synonymous_variant,p.%3D,ENST00000441411,;SCN7A,synonymous_variant,p.%3D,ENST00000419992,;SCN7A,synonymous_variant,p.%3D,ENST00000424326,;SCN7A,upstream_gene_variant,,ENST00000497562,;	T	ENSG00000136546	ENST00000409855	Transcript	synonymous_variant	796	669	223	L	ctG/ctA	.	.	.	-1	SCN7A	HGNC	10594	protein_coding	YES	CCDS46442.1	ENSP00000386796	SCN7A_HUMAN	Q16278_HUMAN,C9JW43_HUMAN,C9JII9_HUMAN	UPI0000209019	.	.	.	7/25	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,hmmpanther:PTHR10037:SF14,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCAGACC	.	5	ESCA
RAPGEF4	0	.	GRCh37	2	173894912	173894912	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2579T>G	p.Leu860Arg	p.L860R	ENST00000397081	26/31	46	29	17	53	53	0	RAPGEF4,missense_variant,p.Leu716Arg,ENST00000397087,;RAPGEF4,missense_variant,p.Leu860Arg,ENST00000409036,;RAPGEF4,missense_variant,p.Leu859Arg,ENST00000264111,;RAPGEF4,missense_variant,p.Leu640Arg,ENST00000535187,;RAPGEF4,missense_variant,p.Leu707Arg,ENST00000539331,;RAPGEF4,missense_variant,p.Leu689Arg,ENST00000538974,;RAPGEF4,missense_variant,p.Leu860Arg,ENST00000397081,;RAPGEF4,missense_variant,p.Leu707Arg,ENST00000540783,;RAPGEF4,missense_variant,p.Leu91Arg,ENST00000397085,;	G	ENSG00000091428	ENST00000397081	Transcript	missense_variant	2722	2579	860	L/R	cTg/cGg	.	.	.	1	RAPGEF4	HGNC	16626	protein_coding	YES	CCDS42775.1	ENSP00000380271	RPGF4_HUMAN	Q53TH3_HUMAN,Q53QY2_HUMAN,B7Z283_HUMAN,B7Z278_HUMAN	UPI000006D4C7	.	deleterious(0)	probably_damaging(0.998)	26/31	.	PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF175,Gene3D:2ii0A02,Pfam_domain:PF00617,SMART_domains:SM00147,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATCTGAATT	.	5	ESCA
GEN1	0	.	GRCh37	2	17963086	17963086	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2608delT	p.Ser870GlnfsTer6	p.S870Qfs*6	ENST00000381254	14/14	124	96	28	96	96	0	GEN1,frameshift_variant,p.Ser870GlnfsTer6,ENST00000381254,;GEN1,frameshift_variant,p.Ser870GlnfsTer6,ENST00000317402,;SMC6,intron_variant,,ENST00000428868,;SMC6,intron_variant,,ENST00000402989,;GEN1,downstream_gene_variant,,ENST00000528873,;	-	ENSG00000178295	ENST00000381254	Transcript	frameshift_variant	2821	2607	869	D/X	gaT/ga	.	.	.	1	GEN1	HGNC	26881	protein_coding	YES	CCDS1691.1	ENSP00000370653	GEN_HUMAN	E9PM30_HUMAN,E9PLG0_HUMAN	UPI00004113DA	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCAGATTCAAC	.	3	ESCA
CWC22	0	.	GRCh37	2	180810229	180810229	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2354C>T	p.Thr785Ile	p.T785I	ENST00000410053	20/20	65	42	23	36	36	0	CWC22,missense_variant,p.Thr785Ile,ENST00000410053,;CWC22,missense_variant,p.Thr785Ile,ENST00000295749,;CWC22,downstream_gene_variant,,ENST00000404136,;	A	ENSG00000163510	ENST00000410053	Transcript	missense_variant	2654	2354	785	T/I	aCa/aTa	.	.	.	-1	CWC22	HGNC	29322	protein_coding	YES	CCDS46465.1	ENSP00000387006	CWC22_HUMAN	B7WP74_HUMAN	UPI00001C1DAE	.	tolerated_low_confidence(0.45)	benign(0.001)	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATGTGTAC	.	5	ESCA
ANKAR	0	.	GRCh37	2	190561097	190561097	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1708+2T>C	.	p.X570_splice	ENST00000520309	.	100	66	34	94	94	0	ANKAR,splice_donor_variant,,ENST00000281412,;ANKAR,splice_donor_variant,,ENST00000313581,;ANKAR,splice_donor_variant,,ENST00000438402,;ANKAR,splice_donor_variant,,ENST00000431575,;ANKAR,splice_donor_variant,,ENST00000520309,;ANKAR,splice_donor_variant,,ENST00000464687,;ANKAR,downstream_gene_variant,,ENST00000461516,;ANKAR,splice_donor_variant,,ENST00000441800,;ANKAR,splice_donor_variant,,ENST00000433782,;ANKAR,downstream_gene_variant,,ENST00000467927,;	C	ENSG00000151687	ENST00000520309	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	ANKAR	HGNC	26350	protein_coding	YES	CCDS33351.2	ENSP00000427882	ANKAR_HUMAN	J3KQB7_HUMAN	UPI00001D7E11	.	.	.	.	7/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGTACCAT	.	5	ESCA
C2orf57	0	.	GRCh37	2	232458893	232458893	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*43C>G	.	.	ENST00000313965	1/1	45	31	13	31	31	0	C2orf57,3_prime_UTR_variant,,ENST00000313965,;	G	ENSG00000177673	ENST00000313965	Transcript	3_prime_UTR_variant	1319	.	.	.	.	.	.	.	1	C2orf57	HGNC	28563	protein_coding	YES	CCDS2487.1	ENSP00000315557	CB057_HUMAN	.	UPI000013F6CA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCCTCCAGAGA	.	4	ESCA
DHX57	0	.	GRCh37	2	39090566	39090566	+	Missense_Mutation	SNP	T	T	A	rs762040974	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320A>T	p.Asn107Ile	p.N107I	ENST00000295373	3/24	125	75	49	109	109	0	DHX57,missense_variant,p.Asn5Ile,ENST00000417233,;DHX57,missense_variant,p.Asn107Ile,ENST00000295373,;AC018693.6,downstream_gene_variant,,ENST00000442829,;DHX57,non_coding_transcript_exon_variant,,ENST00000479345,;DHX57,missense_variant,p.Asn5Ile,ENST00000457308,;DHX57,non_coding_transcript_exon_variant,,ENST00000474104,;DHX57,non_coding_transcript_exon_variant,,ENST00000460193,;	A	ENSG00000163214	ENST00000295373	Transcript	missense_variant	447	320	107	N/I	aAt/aTt	rs762040974	.	.	-1	DHX57	HGNC	20086	protein_coding	YES	CCDS1800.1	ENSP00000295373	DHX57_HUMAN	C9J207_HUMAN,B4DKW2_HUMAN	UPI0000231C8C	.	deleterious(0.04)	probably_damaging(0.973)	3/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGATTCTCA	.	5	ESCA
BCL11A	0	.	GRCh37	2	60689333	60689333	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.714T>G	p.Phe238Leu	p.F238L	ENST00000335712	4/4	88	54	34	80	80	0	BCL11A,missense_variant,p.Phe204Leu,ENST00000538214,;BCL11A,missense_variant,p.Phe204Leu,ENST00000358510,;BCL11A,missense_variant,p.Phe238Leu,ENST00000356842,;BCL11A,missense_variant,p.Phe238Leu,ENST00000335712,;BCL11A,intron_variant,,ENST00000359629,;BCL11A,intron_variant,,ENST00000537768,;BCL11A,non_coding_transcript_exon_variant,,ENST00000477659,;BCL11A,intron_variant,,ENST00000489516,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,upstream_gene_variant,,ENST00000479026,;	C	ENSG00000119866	ENST00000335712	Transcript	missense_variant	942	714	238	F/L	ttT/ttG	.	.	.	-1	BCL11A	HGNC	13221	protein_coding	YES	CCDS1862.1	ENSP00000338774	BC11A_HUMAN	D6W5D9_HUMAN,Q53TS1_HUMAN,Q53TE8_HUMAN	UPI000013DC00	.	deleterious(0.01)	probably_damaging(0.958)	4/4	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTAAAGGG	.	5	ESCA
C2orf42	0	.	GRCh37	2	70406666	70406666	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932C>G	p.Ser311Cys	p.S311C	ENST00000264434	4/10	81	54	26	84	84	0	C2orf42,missense_variant,p.Ser311Cys,ENST00000420306,;C2orf42,missense_variant,p.Ser311Cys,ENST00000264434,;C2orf42,downstream_gene_variant,,ENST00000425268,;C2orf42,downstream_gene_variant,,ENST00000428010,;C2orf42,downstream_gene_variant,,ENST00000457952,;C2orf42,downstream_gene_variant,,ENST00000417203,;C2orf42,downstream_gene_variant,,ENST00000428751,;C2orf42,downstream_gene_variant,,ENST00000447804,;C2orf42,downstream_gene_variant,,ENST00000419381,;C2orf42,downstream_gene_variant,,ENST00000417865,;C2orf42,downstream_gene_variant,,ENST00000487560,;C2orf42,downstream_gene_variant,,ENST00000470096,;C2orf42,downstream_gene_variant,,ENST00000464505,;C2orf42,downstream_gene_variant,,ENST00000495353,;	C	ENSG00000115998	ENST00000264434	Transcript	missense_variant	1312	932	311	S/C	tCt/tGt	.	.	.	-1	C2orf42	HGNC	26056	protein_coding	YES	CCDS1899.1	ENSP00000264434	CB042_HUMAN	C9JZF3_HUMAN,C9JV10_HUMAN,C9JS43_HUMAN,C9JKD5_HUMAN,C9JK51_HUMAN,C9JJF4_HUMAN,C9J5U1_HUMAN,C9J4L7_HUMAN	UPI0000037CF2	.	tolerated(0.1)	benign(0.298)	4/10	.	hmmpanther:PTHR13518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCAGATACT	.	5	ESCA
UBE2D3	0	.	GRCh37	4	103718113	103718113	+	3'Flank	SNP	C	C	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000357194	.	41	24	17	44	44	0	UBE2D3,3_prime_UTR_variant,,ENST00000453744,;UBE2D3,3_prime_UTR_variant,,ENST00000343106,;UBE2D3,3_prime_UTR_variant,,ENST00000394804,;UBE2D3,3_prime_UTR_variant,,ENST00000394801,;UBE2D3,3_prime_UTR_variant,,ENST00000394803,;UBE2D3,downstream_gene_variant,,ENST00000508238,;UBE2D3,downstream_gene_variant,,ENST00000502690,;UBE2D3,downstream_gene_variant,,ENST00000502404,;UBE2D3,downstream_gene_variant,,ENST00000321805,;UBE2D3,downstream_gene_variant,,ENST00000349311,;UBE2D3,downstream_gene_variant,,ENST00000505207,;UBE2D3,downstream_gene_variant,,ENST00000357194,;UBE2D3,downstream_gene_variant,,ENST00000508476,;UBE2D3,downstream_gene_variant,,ENST00000338145,;UBE2D3,downstream_gene_variant,,ENST00000350435,;UBE2D3,downstream_gene_variant,,ENST00000504211,;UBE2D3,downstream_gene_variant,,ENST00000507845,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000508474,;UBE2D3,downstream_gene_variant,,ENST00000505307,;UBE2D3,downstream_gene_variant,,ENST00000503742,;UBE2D3,downstream_gene_variant,,ENST00000508635,;UBE2D3,downstream_gene_variant,,ENST00000508974,;UBE2D3,downstream_gene_variant,,ENST00000502563,;UBE2D3,downstream_gene_variant,,ENST00000514755,;UBE2D3,downstream_gene_variant,,ENST00000510129,;UBE2D3,downstream_gene_variant,,ENST00000505009,;	G	ENSG00000109332	ENST00000357194	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	401	-1	UBE2D3	HGNC	12476	protein_coding	YES	CCDS3659.1	ENSP00000349722	UB2D3_HUMAN	D6RFM0_HUMAN,D6RAW0_HUMAN,D6RAH7_HUMAN	UPI00001B31EA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTCAAATC	.	5	ESCA
SPRY1	0	.	GRCh37	4	124323397	124323397	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.651A>G	p.%3D	p.E217E	ENST00000394339	2/2	47	31	16	53	53	0	SPRY1,synonymous_variant,p.%3D,ENST00000339241,;SPRY1,synonymous_variant,p.%3D,ENST00000394339,;SPRY1,downstream_gene_variant,,ENST00000508849,;SPRY1,downstream_gene_variant,,ENST00000505319,;SPRY1,downstream_gene_variant,,ENST00000507703,;SPRY1,downstream_gene_variant,,ENST00000515726,;	G	ENSG00000164056	ENST00000394339	Transcript	synonymous_variant	991	651	217	E	gaA/gaG	.	.	.	1	SPRY1	HGNC	11269	protein_coding	YES	CCDS3731.1	ENSP00000377871	SPY1_HUMAN	D6RIE6_HUMAN,D6RHD2_HUMAN,D6REX7_HUMAN	UPI0000035D8F	.	.	.	2/2	.	PROSITE_profiles:PS51227,hmmpanther:PTHR12365,hmmpanther:PTHR12365:SF10,Pfam_domain:PF05210	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAATATGG	.	5	ESCA
ANKRD50	0	.	GRCh37	4	125587726	125587726	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*947A>G	.	.	ENST00000504087	5/5	23	13	10	23	23	0	ANKRD50,3_prime_UTR_variant,,ENST00000504087,;ANKRD50,downstream_gene_variant,,ENST00000515641,;	C	ENSG00000151458	ENST00000504087	Transcript	3_prime_UTR_variant	6275	.	.	.	.	.	.	.	-1	ANKRD50	HGNC	29223	protein_coding	YES	CCDS34060.1	ENSP00000425658	ANR50_HUMAN	Q8TB46_HUMAN	UPI00002377E8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTATTTAGC	.	5	ESCA
CWH43	0	.	GRCh37	4	48994050	48994050	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454T>C	p.Ser152Pro	p.S152P	ENST00000226432	4/16	52	48	3	60	60	0	CWH43,missense_variant,p.Ser125Pro,ENST00000513409,;CWH43,missense_variant,p.Ser152Pro,ENST00000226432,;CWH43,missense_variant,p.Ser152Pro,ENST00000514053,;	C	ENSG00000109182	ENST00000226432	Transcript	missense_variant	637	454	152	S/P	Tcc/Ccc	.	.	.	1	CWH43	HGNC	26133	protein_coding	YES	CCDS3486.1	ENSP00000226432	PG2IP_HUMAN	E7EQL2_HUMAN,D6RDZ8_HUMAN	UPI000020BC89	.	tolerated(0.09)	benign(0.025)	4/16	.	hmmpanther:PTHR14859:SF0,hmmpanther:PTHR14859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATGTCCAAC	.	2	ESCA
USP46	0	.	GRCh37	4	53463254	53463254	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*552A>G	.	.	ENST00000441222	9/9	78	48	30	79	79	0	USP46,3_prime_UTR_variant,,ENST00000451218,;USP46,3_prime_UTR_variant,,ENST00000441222,;USP46,downstream_gene_variant,,ENST00000508499,;USP46,3_prime_UTR_variant,,ENST00000503060,;USP46,downstream_gene_variant,,ENST00000514536,;	C	ENSG00000109189	ENST00000441222	Transcript	3_prime_UTR_variant	1838	.	.	.	.	.	.	.	-1	USP46	HGNC	20075	protein_coding	YES	CCDS47053.1	ENSP00000407818	UBP46_HUMAN	.	UPI0000006C18	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGATGATTT	.	5	ESCA
RAI14	0	.	GRCh37	5	34687772	34687772	+	Intron	SNP	T	T	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-136-401T>A	.	.	ENST00000515799	.	31	25	6	39	39	0	RAI14,5_prime_UTR_variant,,ENST00000506376,;RAI14,intron_variant,,ENST00000512305,;RAI14,intron_variant,,ENST00000508315,;RAI14,intron_variant,,ENST00000514873,;RAI14,intron_variant,,ENST00000428746,;RAI14,intron_variant,,ENST00000504052,;RAI14,intron_variant,,ENST00000514036,;RAI14,intron_variant,,ENST00000512625,;RAI14,intron_variant,,ENST00000514527,;RAI14,intron_variant,,ENST00000265109,;RAI14,intron_variant,,ENST00000515799,;RAI14,intron_variant,,ENST00000513974,;RAI14,intron_variant,,ENST00000512629,;RAI14,intron_variant,,ENST00000503673,;RAI14,intron_variant,,ENST00000511652,;RAI14,upstream_gene_variant,,ENST00000507502,;RAI14,intron_variant,,ENST00000508777,;RAI14,intron_variant,,ENST00000505185,;RAI14,intron_variant,,ENST00000510386,;RAI14,intron_variant,,ENST00000515448,;RAI14,intron_variant,,ENST00000514931,;RAI14,intron_variant,,ENST00000503222,;RAI14,intron_variant,,ENST00000510319,;	A	ENSG00000039560	ENST00000515799	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RAI14	HGNC	14873	protein_coding	YES	CCDS54839.1	ENSP00000427123	RAI14_HUMAN	B3KMZ9_HUMAN	UPI00001B296B	.	.	.	.	3/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTTGAGCA	.	5	ESCA
JMY	0	.	GRCh37	5	78573804	78573804	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1104C>A	p.%3D	p.A368A	ENST00000396137	2/11	49	14	35	56	56	0	JMY,synonymous_variant,p.%3D,ENST00000396137,;	A	ENSG00000152409	ENST00000396137	Transcript	synonymous_variant	1566	1104	368	A	gcC/gcA	.	.	.	1	JMY	HGNC	28916	protein_coding	YES	CCDS4047.3	ENSP00000379441	JMY_HUMAN	.	UPI0000E5AC67	.	.	.	2/11	.	hmmpanther:PTHR23330,hmmpanther:PTHR23330:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCCTACAG	.	5	ESCA
MEF2C	0	.	GRCh37	5	88119631	88119631	+	5'UTR	SNP	G	G	A	rs758320958	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-26C>T	.	.	ENST00000340208	3/12	30	12	18	37	37	0	MEF2C,5_prime_UTR_variant,,ENST00000504921,;MEF2C,5_prime_UTR_variant,,ENST00000510942,;MEF2C,5_prime_UTR_variant,,ENST00000514015,;MEF2C,5_prime_UTR_variant,,ENST00000507984,;MEF2C,5_prime_UTR_variant,,ENST00000506554,;MEF2C,5_prime_UTR_variant,,ENST00000437473,;MEF2C,5_prime_UTR_variant,,ENST00000502983,;MEF2C,5_prime_UTR_variant,,ENST00000513252,;MEF2C,5_prime_UTR_variant,,ENST00000503075,;MEF2C,5_prime_UTR_variant,,ENST00000509373,;MEF2C,5_prime_UTR_variant,,ENST00000514028,;MEF2C,5_prime_UTR_variant,,ENST00000508610,;MEF2C,5_prime_UTR_variant,,ENST00000502831,;MEF2C,5_prime_UTR_variant,,ENST00000340208,;MEF2C,5_prime_UTR_variant,,ENST00000424173,;MEF2C,5_prime_UTR_variant,,ENST00000508569,;MEF2C,5_prime_UTR_variant,,ENST00000506716,;MEF2C,upstream_gene_variant,,ENST00000539796,;MEF2C,non_coding_transcript_exon_variant,,ENST00000515093,;MEF2C,downstream_gene_variant,,ENST00000509349,;MEF2C,non_coding_transcript_exon_variant,,ENST00000511086,;	A	ENSG00000081189	ENST00000340208	Transcript	5_prime_UTR_variant	381	.	.	.	.	rs758320958	.	.	-1	MEF2C	HGNC	6996	protein_coding	YES	CCDS54878.1	ENSP00000340874	MEF2C_HUMAN	H0YNI2_HUMAN,D6RJA7_HUMAN,D6RJ95_HUMAN,D6RG14_HUMAN	UPI0000D9B539	.	.	.	3/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTCGTCCCT	.	5	ESCA
SCAND3	0	.	GRCh37	6	28542921	28542921	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1561A>G	p.Ser521Gly	p.S521G	ENST00000452236	3/4	22	17	5	13	13	0	SCAND3,missense_variant,p.Ser521Gly,ENST00000452236,;SCAND3,downstream_gene_variant,,ENST00000530247,;	C	ENSG00000232040	ENST00000452236	Transcript	missense_variant	2179	1561	521	S/G	Agt/Ggt	.	.	.	-1	SCAND3	HGNC	13851	protein_coding	YES	CCDS34355.1	ENSP00000395259	SCND3_HUMAN	.	UPI00001618B7	.	tolerated_low_confidence(0.81)	benign(0)	3/4	.	PROSITE_profiles:PS50994,hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF90,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCACTTTCAC	.	2	ESCA
PACSIN1	0	.	GRCh37	6	34494065	34494065	+	5'UTR	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-18T>C	.	.	ENST00000538621	2/10	50	46	4	47	47	0	PACSIN1,5_prime_UTR_variant,,ENST00000538621,;PACSIN1,5_prime_UTR_variant,,ENST00000244458,;PACSIN1,5_prime_UTR_variant,,ENST00000374043,;PACSIN1,non_coding_transcript_exon_variant,,ENST00000486120,;PACSIN1,non_coding_transcript_exon_variant,,ENST00000487760,;PACSIN1,non_coding_transcript_exon_variant,,ENST00000493633,;	C	ENSG00000124507	ENST00000538621	Transcript	5_prime_UTR_variant	228	.	.	.	.	.	.	.	1	PACSIN1	HGNC	8570	protein_coding	YES	CCDS4793.1	ENSP00000439639	PACN1_HUMAN	Q5TZC3_HUMAN,F6U236_HUMAN	UPI000000D983	.	.	.	2/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCCATCCCCC	.	3	ESCA
EYS	0	.	GRCh37	6	64791750	64791750	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6570C>A	p.Tyr2190Ter	p.Y2190*	ENST00000503581	32/43	81	50	31	66	66	0	EYS,stop_gained,p.Tyr2190Ter,ENST00000370616,;EYS,stop_gained,p.Tyr2190Ter,ENST00000370621,;EYS,stop_gained,p.Tyr2190Ter,ENST00000503581,;	T	ENSG00000188107	ENST00000503581	Transcript	stop_gained	7108	6570	2190	Y/*	taC/taA	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	.	.	32/43	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTGTAAAG	.	5	ESCA
CTTNBP2	0	.	GRCh37	7	117365257	117365257	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4110A>G	p.Ile1370Met	p.I1370M	ENST00000160373	18/23	35	18	17	65	65	0	CTTNBP2,missense_variant,p.Ile858Met,ENST00000446636,;CTTNBP2,missense_variant,p.Ile1370Met,ENST00000160373,;CTTNBP2,3_prime_UTR_variant,,ENST00000441556,;CTTNBP2,intron_variant,,ENST00000445366,;	C	ENSG00000077063	ENST00000160373	Transcript	missense_variant	4202	4110	1370	I/M	atA/atG	.	.	.	-1	CTTNBP2	HGNC	15679	protein_coding	YES	CCDS5774.1	ENSP00000160373	CTTB2_HUMAN	Q20BG9_HUMAN,Q20BG7_HUMAN,C9JVQ6_HUMAN,C9JFC9_HUMAN,C9J720_HUMAN	UPI000006E94A	.	deleterious(0)	possibly_damaging(0.86)	18/23	.	hmmpanther:PTHR24166:SF11,hmmpanther:PTHR24166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACAATATTGC	.	5	ESCA
SDK1	0	.	GRCh37	7	4056935	4056935	+	Silent	SNP	C	C	T	rs562967510	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2553C>T	p.%3D	p.A851A	ENST00000404826	17/45	44	26	17	31	31	0	SDK1,synonymous_variant,p.%3D,ENST00000404826,;SDK1,synonymous_variant,p.%3D,ENST00000389531,;	T	ENSG00000146555	ENST00000404826	Transcript	synonymous_variant	2692	2553	851	A	gcC/gcT	rs562967510,COSM3832771	.	.	1	SDK1	HGNC	19307	protein_coding	YES	CCDS34590.1	ENSP00000385899	SDK1_HUMAN	.	UPI0000DBEEC4	.	.	.	17/45	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF36,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGGGCCGGTCT	by1000G	4	ESCA
POR	0	.	GRCh37	7	75609828	75609828	+	Intron	SNP	A	A	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.516+22A>G	.	.	ENST00000461988	.	71	45	25	71	71	0	POR,start_lost,p.Met1?,ENST00000450476,;POR,missense_variant,p.Met153Val,ENST00000447222,;POR,intron_variant,,ENST00000394893,;POR,intron_variant,,ENST00000461988,;POR,intron_variant,,ENST00000439963,;POR,intron_variant,,ENST00000545601,;POR,intron_variant,,ENST00000419840,;POR,downstream_gene_variant,,ENST00000439297,;POR,downstream_gene_variant,,ENST00000432753,;POR,downstream_gene_variant,,ENST00000414186,;POR,downstream_gene_variant,,ENST00000453773,;POR,downstream_gene_variant,,ENST00000426184,;POR,downstream_gene_variant,,ENST00000412521,;POR,upstream_gene_variant,,ENST00000439269,;POR,downstream_gene_variant,,ENST00000475509,;POR,3_prime_UTR_variant,,ENST00000448410,;POR,intron_variant,,ENST00000454934,;POR,intron_variant,,ENST00000412064,;POR,upstream_gene_variant,,ENST00000487247,;POR,upstream_gene_variant,,ENST00000495770,;POR,downstream_gene_variant,,ENST00000471238,;POR,upstream_gene_variant,,ENST00000460892,;POR,upstream_gene_variant,,ENST00000496888,;	G	ENSG00000127948	ENST00000461988	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	POR	HGNC	9208	protein_coding	YES	CCDS5579.1	ENSP00000419970	NCPR_HUMAN	Q59ED7_HUMAN,E7EMD0_HUMAN,C9JQ78_HUMAN	UPI000013D5F4	.	.	.	.	5/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTATGGGC	.	5	ESCA
PCLO	0	.	GRCh37	7	82586167	82586167	+	Missense_Mutation	SNP	C	C	T	rs533061339	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4102G>A	p.Asp1368Asn	p.D1368N	ENST00000333891	5/25	65	43	21	64	64	0	PCLO,missense_variant,p.Asp1368Asn,ENST00000333891,;PCLO,missense_variant,p.Asp1368Asn,ENST00000423517,;	T	ENSG00000186472	ENST00000333891	Transcript	missense_variant	4440	4102	1368	D/N	Gat/Aat	rs533061339	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	5/25	.	hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCGGAAG	by1000G	5	ESCA
PLEC	0	.	GRCh37	8	144989495	144989495	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*850G>T	.	.	ENST00000322810	32/32	14	3	11	11	11	0	PLEC,3_prime_UTR_variant,,ENST00000322810,;PLEC,3_prime_UTR_variant,,ENST00000345136,;PLEC,3_prime_UTR_variant,,ENST00000357649,;PLEC,3_prime_UTR_variant,,ENST00000398774,;PLEC,3_prime_UTR_variant,,ENST00000354589,;PLEC,3_prime_UTR_variant,,ENST00000356346,;PLEC,3_prime_UTR_variant,,ENST00000436759,;PLEC,3_prime_UTR_variant,,ENST00000354958,;PLEC,downstream_gene_variant,,ENST00000527096,;	A	ENSG00000178209	ENST00000322810	Transcript	3_prime_UTR_variant	15075	.	.	.	.	.	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGACCAGGG	.	5	ESCA
PCM1	0	.	GRCh37	8	17885213	17885213	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*42A>T	.	.	ENST00000325083	39/39	44	21	23	72	72	0	PCM1,3_prime_UTR_variant,,ENST00000325083,;PCM1,3_prime_UTR_variant,,ENST00000327578,;PCM1,3_prime_UTR_variant,,ENST00000519253,;PCM1,3_prime_UTR_variant,,ENST00000524226,;PCM1,3_prime_UTR_variant,,ENST00000522275,;PCM1,non_coding_transcript_exon_variant,,ENST00000519802,;PCM1,non_coding_transcript_exon_variant,,ENST00000523896,;PCM1,downstream_gene_variant,,ENST00000518877,;	T	ENSG00000078674	ENST00000325083	Transcript	3_prime_UTR_variant	6556	.	.	.	.	.	.	.	1	PCM1	HGNC	8727	protein_coding	YES	CCDS47812.1	ENSP00000327077	PCM1_HUMAN	E5RGQ4_HUMAN	UPI0000210A25	.	.	.	39/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTCAATGCA	.	5	ESCA
EBF2	0	.	GRCh37	8	25702068	25702068	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*57G>A	.	.	ENST00000520164	16/16	32	19	12	49	49	0	EBF2,3_prime_UTR_variant,,ENST00000408929,;EBF2,3_prime_UTR_variant,,ENST00000520164,;EBF2,downstream_gene_variant,,ENST00000535548,;RP11-299D14.2,upstream_gene_variant,,ENST00000520386,;	T	ENSG00000221818	ENST00000520164	Transcript	3_prime_UTR_variant	2323	.	.	.	.	.	.	.	-1	EBF2	HGNC	19090	protein_coding	YES	CCDS43726.1	ENSP00000430241	COE2_HUMAN	B7Z934_HUMAN,B2RNT0_HUMAN	UPI0000DD7EC9	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTCTTCAT	.	5	ESCA
ADRA1A	0	.	GRCh37	8	26627783	26627783	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269+15C>G	.	.	ENST00000380586	.	30	11	19	64	64	0	ADRA1A,missense_variant,p.Ser428Arg,ENST00000380573,;ADRA1A,missense_variant,p.Ser428Arg,ENST00000276393,;ADRA1A,intron_variant,,ENST00000380586,;ADRA1A,intron_variant,,ENST00000354550,;ADRA1A,intron_variant,,ENST00000380587,;ADRA1A,intron_variant,,ENST00000380581,;ADRA1A,intron_variant,,ENST00000380582,;ADRA1A,intron_variant,,ENST00000519229,;ADRA1A,non_coding_transcript_exon_variant,,ENST00000518621,;ADRA1A,intron_variant,,ENST00000521711,;ADRA1A,intron_variant,,ENST00000519096,;RP11-384C12.1,upstream_gene_variant,,ENST00000486251,;	C	ENSG00000120907	ENST00000380586	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ADRA1A	HGNC	277	protein_coding	YES	CCDS34869.1	ENSP00000369960	ADA1A_HUMAN	Q7KYZ9_HUMAN,B0ZBD3_HUMAN	UPI000066DA42	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAGCTTTT	.	5	ESCA
GALNT12	0	.	GRCh37	9	101594127	101594127	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805G>A	p.Gly269Arg	p.G269R	ENST00000375011	4/10	146	21	125	100	100	0	GALNT12,missense_variant,p.Gly269Arg,ENST00000375011,;	A	ENSG00000119514	ENST00000375011	Transcript	missense_variant	805	805	269	G/R	Ggg/Agg	.	.	.	1	GALNT12	HGNC	19877	protein_coding	YES	CCDS6737.1	ENSP00000364150	GLT12_HUMAN	.	UPI000004D295	.	tolerated(0.74)	probably_damaging(0.997)	4/10	.	hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF18,Gene3D:3.90.550.10,Pfam_domain:PF00535,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGGGGAAC	.	5	ESCA
SLC31A1	0	.	GRCh37	9	116024271	116024271	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1518C>T	.	.	ENST00000374212	5/5	60	4	56	42	42	0	SLC31A1,3_prime_UTR_variant,,ENST00000374212,;SLC31A1,intron_variant,,ENST00000374210,;CDC26,intron_variant,,ENST00000490408,;	T	ENSG00000136868	ENST00000374212	Transcript	3_prime_UTR_variant	2243	.	.	.	.	.	.	.	1	SLC31A1	HGNC	11016	protein_coding	YES	CCDS6789.1	ENSP00000363329	COPT1_HUMAN	Q9BT69_HUMAN	UPI0000127EC2	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAGCCAAAG	.	5	ESCA
BRINP1	0	.	GRCh37	9	121976407	121976407	+	Missense_Mutation	SNP	G	G	C	rs541790465	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712C>G	p.Leu238Val	p.L238V	ENST00000265922	6/8	92	73	19	54	54	0	BRINP1,missense_variant,p.Leu238Val,ENST00000265922,;BRINP1,missense_variant,p.Leu238Val,ENST00000373964,;	C	ENSG00000078725	ENST00000265922	Transcript	missense_variant	1174	712	238	L/V	Ctg/Gtg	rs541790465	.	.	-1	BRINP1	HGNC	2687	protein_coding	YES	CCDS6822.1	ENSP00000265922	BRNP1_HUMAN	B4DE75_HUMAN	UPI000013D6A7	.	deleterious(0)	possibly_damaging(0.899)	6/8	.	SMART_domains:SM00457,hmmpanther:PTHR15564:SF7,hmmpanther:PTHR15564	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAGATACT	by1000G	5	ESCA
FOXD4L6	0	.	GRCh37	9	69199991	69199991	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*368G>A	.	.	ENST00000377473	1/1	29	8	21	37	37	0	FOXD4L6,3_prime_UTR_variant,,ENST00000377473,;CBWD6,downstream_gene_variant,,ENST00000382399,;CBWD6,downstream_gene_variant,,ENST00000377449,;CBWD6,downstream_gene_variant,,ENST00000377457,;CBWD6,downstream_gene_variant,,ENST00000416428,;CBWD6,downstream_gene_variant,,ENST00000461037,;CBWD6,downstream_gene_variant,,ENST00000495626,;CBWD6,downstream_gene_variant,,ENST00000498101,;CBWD6,downstream_gene_variant,,ENST00000477430,;CBWD6,downstream_gene_variant,,ENST00000468061,;CBWD6,downstream_gene_variant,,ENST00000466320,;CBWD6,downstream_gene_variant,,ENST00000468763,;	T	ENSG00000204793	ENST00000377473	Transcript	3_prime_UTR_variant	2214	.	.	.	.	.	.	.	-1	FOXD4L6	HGNC	31986	protein_coding	YES	CCDS43826.1	ENSP00000366693	FX4L6_HUMAN	Q8WTR0_HUMAN	UPI0000519166	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	ATGCGCAAATC	.	2	ESCA
TRPM3	0	.	GRCh37	9	73240146	73240146	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1734C>T	p.%3D	p.R578R	ENST00000377110	13/25	58	38	20	32	32	0	TRPM3,synonymous_variant,p.%3D,ENST00000377111,;TRPM3,synonymous_variant,p.%3D,ENST00000377106,;TRPM3,synonymous_variant,p.%3D,ENST00000360823,;TRPM3,synonymous_variant,p.%3D,ENST00000358082,;TRPM3,synonymous_variant,p.%3D,ENST00000396292,;TRPM3,synonymous_variant,p.%3D,ENST00000396280,;TRPM3,synonymous_variant,p.%3D,ENST00000423814,;TRPM3,synonymous_variant,p.%3D,ENST00000408909,;TRPM3,synonymous_variant,p.%3D,ENST00000357533,;TRPM3,synonymous_variant,p.%3D,ENST00000377110,;TRPM3,synonymous_variant,p.%3D,ENST00000377105,;TRPM3,synonymous_variant,p.%3D,ENST00000396285,;	A	ENSG00000083067	ENST00000377110	Transcript	synonymous_variant	1978	1734	578	R	cgC/cgT	.	.	.	-1	TRPM3	HGNC	17992	protein_coding	YES	CCDS43835.1	ENSP00000366314	TRPM3_HUMAN	.	UPI0001596895	.	.	.	13/25	.	hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGAAGCGCTT	.	5	ESCA
TRPC5	0	.	GRCh37	X	111078315	111078315	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1730G>C	p.Trp577Ser	p.W577S	ENST00000262839	7/11	48	32	16	33	33	0	TRPC5,missense_variant,p.Trp577Ser,ENST00000262839,;	G	ENSG00000072315	ENST00000262839	Transcript	missense_variant	2649	1730	577	W/S	tGg/tCg	.	.	.	-1	TRPC5	HGNC	12337	protein_coding	YES	CCDS14561.1	ENSP00000262839	TRPC5_HUMAN	.	UPI00001374B6	.	deleterious(0)	probably_damaging(0.995)	7/11	.	hmmpanther:PTHR10117:SF24,hmmpanther:PTHR10117,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAGACCAGAAG	.	4	ESCA
DGKK	0	.	GRCh37	X	50122993	50122993	+	RNA	SNP	G	G	A	rs370221683	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2800C>T	.	.	ENST00000376025	19/28	37	14	22	35	35	0	DGKK,non_coding_transcript_exon_variant,,ENST00000376025,;DGKK,non_coding_transcript_exon_variant,,ENST00000546288,;	A	ENSG00000204466	ENST00000376025	Transcript	non_coding_transcript_exon_variant	2800	.	.	.	.	rs370221683	.	.	-1	DGKK	HGNC	32395	processed_transcript	YES	.	.	.	.	.	.	.	.	19/28	.	.	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTCGTTCTT	byCluster	5	ESCA
ITGB1BP2	0	.	GRCh37	X	70523687	70523687	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565A>T	p.Ile189Phe	p.I189F	ENST00000373829	8/11	26	4	22	15	15	0	ITGB1BP2,missense_variant,p.Ile189Phe,ENST00000373829,;ITGB1BP2,missense_variant,p.Ile171Phe,ENST00000538820,;NONO,downstream_gene_variant,,ENST00000276079,;NONO,downstream_gene_variant,,ENST00000373856,;NONO,downstream_gene_variant,,ENST00000535149,;NONO,downstream_gene_variant,,ENST00000373841,;ITGB1BP2,non_coding_transcript_exon_variant,,ENST00000465388,;ITGB1BP2,non_coding_transcript_exon_variant,,ENST00000483897,;ITGB1BP2,non_coding_transcript_exon_variant,,ENST00000475413,;NONO,downstream_gene_variant,,ENST00000472185,;NONO,downstream_gene_variant,,ENST00000473525,;NONO,downstream_gene_variant,,ENST00000490044,;NONO,downstream_gene_variant,,ENST00000474431,;AL590762.1,downstream_gene_variant,,ENST00000536900,;	T	ENSG00000147166	ENST00000373829	Transcript	missense_variant	638	565	189	I/F	Atc/Ttc	.	.	.	1	ITGB1BP2	HGNC	6154	protein_coding	YES	CCDS14411.1	ENSP00000362935	ITBP2_HUMAN	.	UPI000000103C	.	tolerated(0.08)	probably_damaging(0.951)	8/11	.	PROSITE_profiles:PS51401,hmmpanther:PTHR12621:SF8,hmmpanther:PTHR12621,Pfam_domain:PF04968	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCATCCAG	.	5	ESCA
DIAPH2	0	.	GRCh37	X	96396712	96396712	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2638A>G	p.Ile880Val	p.I880V	ENST00000324765	22/27	167	26	140	84	84	0	DIAPH2,missense_variant,p.Ile876Val,ENST00000373054,;DIAPH2,missense_variant,p.Ile880Val,ENST00000355827,;DIAPH2,missense_variant,p.Ile880Val,ENST00000324765,;DIAPH2,missense_variant,p.Ile880Val,ENST00000373049,;DIAPH2,missense_variant,p.Ile880Val,ENST00000373061,;	G	ENSG00000147202	ENST00000324765	Transcript	missense_variant	2985	2638	880	I/V	Att/Gtt	.	.	.	1	DIAPH2	HGNC	2877	protein_coding	YES	CCDS14467.1	ENSP00000321348	DIAP2_HUMAN	.	UPI00001293C8	.	deleterious(0.02)	possibly_damaging(0.475)	22/27	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF174,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTATTGCC	.	5	ESCA
SRPX2	0	.	GRCh37	X	99920277	99920277	+	Silent	SNP	T	T	G	novel	.	TCGA-IG-A6QS-01A-12D-A33E-09	TCGA-IG-A6QS-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570T>G	p.%3D	p.R190R	ENST00000373004	6/11	60	7	53	27	27	0	SRPX2,synonymous_variant,p.%3D,ENST00000373004,;	G	ENSG00000102359	ENST00000373004	Transcript	synonymous_variant	998	570	190	R	cgT/cgG	.	.	.	1	SRPX2	HGNC	30668	protein_coding	YES	CCDS14471.1	ENSP00000362095	SRPX2_HUMAN	.	UPI000006CCC6	.	.	.	6/11	.	PROSITE_profiles:PS50825,hmmpanther:PTHR19325:SF93,hmmpanther:PTHR19325,Pfam_domain:PF02494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACGTGAGAA	.	5	ESCA
ATRNL1	0	.	GRCh37	10	117309029	117309029	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3778G>A	p.Ala1260Thr	p.A1260T	ENST00000355044	26/29	50	41	8	67	67	0	ATRNL1,missense_variant,p.Ala311Thr,ENST00000423111,;ATRNL1,missense_variant,p.Ala1260Thr,ENST00000355044,;ATRNL1,missense_variant,p.Ala53Thr,ENST00000303745,;ATRNL1,non_coding_transcript_exon_variant,,ENST00000424738,;ATRNL1,non_coding_transcript_exon_variant,,ENST00000534530,;	A	ENSG00000107518	ENST00000355044	Transcript	missense_variant	3904	3778	1260	A/T	Gct/Act	.	.	.	1	ATRNL1	HGNC	29063	protein_coding	YES	CCDS7592.1	ENSP00000347152	ATRN1_HUMAN	.	UPI000021CCF8	.	tolerated(0.09)	probably_damaging(0.998)	26/29	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGGGCTTCT	.	5	ESCA
BNIP3	0	.	GRCh37	10	133784260	133784260	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.421G>A	p.Ala141Thr	p.A141T	ENST00000368636	5/6	90	65	25	101	101	0	BNIP3,missense_variant,p.Ala141Thr,ENST00000368636,;BNIP3,missense_variant,p.Ala141Thr,ENST00000540159,;	T	ENSG00000176171	ENST00000368636	Transcript	missense_variant	546	421	141	A/T	Gcc/Acc	COSM4012751	.	.	-1	BNIP3	HGNC	1084	protein_coding	YES	CCDS7663.1	ENSP00000357625	BNIP3_HUMAN	Q6NVY4_HUMAN,Q66K24_HUMAN,B4DHJ7_HUMAN	UPI00001301A0	.	tolerated(0.65)	benign(0.006)	5/6	.	hmmpanther:PTHR15186:SF4,hmmpanther:PTHR15186,Pfam_domain:PF06553	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGCCGTGC	.	5	ESCA
ITGB1	0	.	GRCh37	10	33214829	33214829	+	Silent	SNP	G	G	A	rs12261912	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756C>T	p.%3D	p.F252F	ENST00000396033	6/16	116	92	24	74	74	0	ITGB1,synonymous_variant,p.%3D,ENST00000374956,;ITGB1,synonymous_variant,p.%3D,ENST00000302278,;ITGB1,synonymous_variant,p.%3D,ENST00000423113,;ITGB1,synonymous_variant,p.%3D,ENST00000396033,;ITGB1,downstream_gene_variant,,ENST00000437302,;ITGB1,downstream_gene_variant,,ENST00000475184,;ITGB1,downstream_gene_variant,,ENST00000472147,;ITGB1,downstream_gene_variant,,ENST00000493758,;ITGB1,downstream_gene_variant,,ENST00000534049,;ITGB1,downstream_gene_variant,,ENST00000417122,;ITGB1,downstream_gene_variant,,ENST00000528877,;ITGB1,downstream_gene_variant,,ENST00000488494,;ITGB1,downstream_gene_variant,,ENST00000474568,;ITGB1,downstream_gene_variant,,ENST00000480226,;ITGB1,downstream_gene_variant,,ENST00000484088,;ITGB1,downstream_gene_variant,,ENST00000464001,;	A	ENSG00000150093	ENST00000396033	Transcript	synonymous_variant	892	756	252	F	ttC/ttT	rs12261912	.	.	-1	ITGB1	HGNC	6153	protein_coding	YES	CCDS7174.1	ENSP00000379350	ITB1_HUMAN	Q5T3E6_HUMAN,Q5T3E5_HUMAN,Q5T3E4_HUMAN,E9PQJ2_HUMAN,E9PLR6_HUMAN,E7ERX5_HUMAN,E7EQW5_HUMAN,C9JPK5_HUMAN,C9JJP8_HUMAN	UPI0000070EEB	.	.	.	6/16	.	Prints_domain:PR01186,Superfamily_domains:SSF53300,PIRSF_domain:PIRSF002512,SMART_domains:SM00187,Pfam_domain:PF00362,Gene3D:3.40.50.410,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF28	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATCGAAACC	byFrequency|byCluster|byHapMap|by1000G	5	ESCA
ZNF33A	0	.	GRCh37	10	38345270	38345270	+	Nonsense_Mutation	SNP	C	C	T	rs267602486	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2218C>T	p.Gln740Ter	p.Q740*	ENST00000374618	5/5	115	97	18	97	97	0	ZNF33A,stop_gained,p.Gln746Ter,ENST00000432900,;ZNF33A,stop_gained,p.Gln739Ter,ENST00000307441,;ZNF33A,stop_gained,p.Gln739Ter,ENST00000458705,;ZNF33A,stop_gained,p.Gln740Ter,ENST00000374618,;ZNF33A,intron_variant,,ENST00000469037,;ZNF33A,downstream_gene_variant,,ENST00000478556,;	T	ENSG00000189180	ENST00000374618	Transcript	stop_gained	2396	2218	740	Q/*	Cag/Tag	rs267602486,COSM1347753,COSM36621,COSM4165476	.	.	1	ZNF33A	HGNC	13096	protein_coding	YES	CCDS44372.1	ENSP00000363747	ZN33A_HUMAN	.	UPI0000161788	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF204,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	not_provided	0,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACATCAGAGA	.	4	ESCA
LARP4B	0	.	GRCh37	10	871242	871242	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1247C>T	p.Ser416Phe	p.S416F	ENST00000316157	12/17	56	42	14	78	78	0	LARP4B,missense_variant,p.Ser416Phe,ENST00000316157,;LARP4B,upstream_gene_variant,,ENST00000448368,;LARP4B,upstream_gene_variant,,ENST00000609318,;	A	ENSG00000107929	ENST00000316157	Transcript	missense_variant	1288	1247	416	S/F	tCt/tTt	.	.	.	-1	LARP4B	HGNC	28987	protein_coding	YES	CCDS31131.1	ENSP00000326128	LAR4B_HUMAN	B5MCU2_HUMAN	UPI00001F8C87	.	deleterious(0)	possibly_damaging(0.862)	12/17	.	hmmpanther:PTHR22792,hmmpanther:PTHR22792:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGAGATTTA	.	5	ESCA
PIK3AP1	0	.	GRCh37	10	98469469	98469469	+	Silent	SNP	C	C	T	rs777298829	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285G>A	p.%3D	p.P95P	ENST00000339364	2/17	50	40	10	47	47	0	PIK3AP1,synonymous_variant,p.%3D,ENST00000339364,;	T	ENSG00000155629	ENST00000339364	Transcript	synonymous_variant	405	285	95	P	ccG/ccA	rs777298829	.	.	-1	PIK3AP1	HGNC	30034	protein_coding	YES	CCDS31259.1	ENSP00000339826	BCAP_HUMAN	.	UPI00001F947F	.	.	.	2/17	.	hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTGCGGAGG	byFrequency	5	ESCA
ROBO4	0	.	GRCh37	11	124761271	124761271	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1872C>T	p.%3D	p.L624L	ENST00000306534	12/18	79	41	38	93	93	0	ROBO4,synonymous_variant,p.%3D,ENST00000306534,;ROBO4,synonymous_variant,p.%3D,ENST00000533054,;RP11-664I21.6,5_prime_UTR_variant,,ENST00000524433,;RP11-664I21.5,downstream_gene_variant,,ENST00000524453,;ROBO4,downstream_gene_variant,,ENST00000527279,;ROBO4,downstream_gene_variant,,ENST00000526899,;ROBO4,non_coding_transcript_exon_variant,,ENST00000534407,;ROBO4,non_coding_transcript_exon_variant,,ENST00000532216,;ROBO4,downstream_gene_variant,,ENST00000525182,;ROBO4,downstream_gene_variant,,ENST00000532300,;	A	ENSG00000154133	ENST00000306534	Transcript	synonymous_variant	2358	1872	624	L	ctC/ctT	.	.	.	-1	ROBO4	HGNC	17985	protein_coding	YES	CCDS8455.1	ENSP00000304945	ROBO4_HUMAN	B4DYV8_HUMAN	UPI000004A023	.	.	.	12/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10489:SF1,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGAGGCT	.	5	ESCA
CCDC15	0	.	GRCh37	11	124875054	124875054	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2357G>C	p.Arg786Thr	p.R786T	ENST00000344762	13/16	107	85	22	113	113	0	CCDC15,missense_variant,p.Arg786Thr,ENST00000344762,;CCDC15,missense_variant,p.Arg786Thr,ENST00000529051,;	C	ENSG00000149548	ENST00000344762	Transcript	missense_variant	2616	2357	786	R/T	aGa/aCa	.	.	.	1	CCDC15	HGNC	25798	protein_coding	YES	CCDS44756.1	ENSP00000341684	CCD15_HUMAN	.	UPI0000EE3BEA	.	deleterious(0)	probably_damaging(0.999)	13/16	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGAGAGAAC	.	5	ESCA
SRPR	0	.	GRCh37	11	126137496	126137499	+	Frame_Shift_Del	DEL	TTAA	TTAA	-	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	TTAA	TTAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310_313delTTAA	p.Leu104ValfsTer3	p.L104Vfs*3	ENST00000332118	3/14	39	28	11	56	56	0	SRPR,frameshift_variant,p.Leu76ValfsTer3,ENST00000532259,;SRPR,frameshift_variant,p.Leu104ValfsTer3,ENST00000332118,;FAM118B,downstream_gene_variant,,ENST00000533050,;FOXRED1,upstream_gene_variant,,ENST00000532125,;FOXRED1,upstream_gene_variant,,ENST00000442061,;FAM118B,downstream_gene_variant,,ENST00000360194,;FOXRED1,upstream_gene_variant,,ENST00000263578,;SRPR,non_coding_transcript_exon_variant,,ENST00000530680,;FOXRED1,upstream_gene_variant,,ENST00000533839,;FOXRED1,upstream_gene_variant,,ENST00000534011,;FOXRED1,upstream_gene_variant,,ENST00000526366,;SRPR,non_coding_transcript_exon_variant,,ENST00000528744,;FOXRED1,upstream_gene_variant,,ENST00000526525,;FAM118B,downstream_gene_variant,,ENST00000531935,;SRPR,upstream_gene_variant,,ENST00000531104,;FOXRED1,upstream_gene_variant,,ENST00000527004,;SRPR,upstream_gene_variant,,ENST00000527817,;FOXRED1,upstream_gene_variant,,ENST00000525770,;SRPR,upstream_gene_variant,,ENST00000532268,;FOXRED1,upstream_gene_variant,,ENST00000532101,;FOXRED1,upstream_gene_variant,,ENST00000525083,;FOXRED1,upstream_gene_variant,,ENST00000529802,;FOXRED1,upstream_gene_variant,,ENST00000534315,;FOXRED1,upstream_gene_variant,,ENST00000524751,;	-	ENSG00000182934	ENST00000332118	Transcript	frameshift_variant	465-468	310-313	104-105	LS/X	TTAAgt/gt	.	.	.	-1	SRPR	HGNC	11307	protein_coding	YES	CCDS31717.1	ENSP00000328023	SRPR_HUMAN	.	UPI0000135F5A	.	.	.	3/14	.	Superfamily_domains:SSF64356,Pfam_domain:PF04086,hmmpanther:PTHR11564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATAAACTTAAAGCAC	.	3	ESCA
ST14	0	.	GRCh37	11	130068269	130068269	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1526A>T	p.Asp509Val	p.D509V	ENST00000278742	13/19	56	30	26	84	84	0	ST14,missense_variant,p.Asp509Val,ENST00000278742,;ST14,downstream_gene_variant,,ENST00000530376,;ST14,downstream_gene_variant,,ENST00000524718,;ST14,downstream_gene_variant,,ENST00000530532,;	T	ENSG00000149418	ENST00000278742	Transcript	missense_variant	1944	1526	509	D/V	gAc/gTc	.	.	.	1	ST14	HGNC	11344	protein_coding	YES	CCDS8487.1	ENSP00000278742	ST14_HUMAN	Q8WVC1_HUMAN	UPI00000012E9	.	deleterious(0)	probably_damaging(0.999)	13/19	.	Prints_domain:PR00261,Superfamily_domains:SSF57424,SMART_domains:SM00192,PIRSF_domain:PIRSF036370,Pfam_domain:PF00057,Gene3D:4.10.400.10,hmmpanther:PTHR24256:SF20,hmmpanther:PTHR24256,PROSITE_profiles:PS50068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCGACAGTG	.	5	ESCA
PDE3B	0	.	GRCh37	11	14793560	14793560	+	Intron	SNP	A	A	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1029+27A>C	.	.	ENST00000282096	.	135	102	32	146	145	0	PDE3B,intron_variant,,ENST00000455098,;PDE3B,intron_variant,,ENST00000282096,;PDE3B,non_coding_transcript_exon_variant,,ENST00000534317,;	C	ENSG00000152270	ENST00000282096	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PDE3B	HGNC	8779	protein_coding	YES	CCDS7817.1	ENSP00000282096	PDE3B_HUMAN	.	UPI000013DCB7	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGAATATCT	.	5	ESCA
HSD17B12	0	.	GRCh37	11	43859885	43859885	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555G>A	p.%3D	p.L185L	ENST00000278353	8/11	59	44	14	73	73	0	HSD17B12,synonymous_variant,p.%3D,ENST00000278353,;HSD17B12,synonymous_variant,p.%3D,ENST00000531185,;RP11-613D13.5,intron_variant,,ENST00000530450,;RP11-613D13.5,upstream_gene_variant,,ENST00000499066,;RP11-613D13.5,upstream_gene_variant,,ENST00000524643,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000533802,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000532864,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000527213,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000534053,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000533090,;	A	ENSG00000149084	ENST00000278353	Transcript	synonymous_variant	674	555	185	L	ctG/ctA	.	.	.	1	HSD17B12	HGNC	18646	protein_coding	YES	CCDS7905.1	ENSP00000278353	DHB12_HUMAN	B4DWS6_HUMAN	UPI000004C79B	.	.	.	8/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24316:SF261,hmmpanther:PTHR24316,Gene3D:3.40.50.720,Pfam_domain:PF00106,PIRSF_domain:PIRSF000126,Superfamily_domains:SSF51735,Prints_domain:PR00080,Prints_domain:PR00081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTGAACAT	.	5	ESCA
OR4C11	0	.	GRCh37	11	55371598	55371598	+	Silent	SNP	G	G	A	rs767460262	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.252C>T	p.%3D	p.L84L	ENST00000302231	1/1	63	14	49	53	53	0	OR4C11,synonymous_variant,p.%3D,ENST00000302231,;	A	ENSG00000172188	ENST00000302231	Transcript	synonymous_variant	277	252	84	L	ctC/ctT	rs767460262	.	.	-1	OR4C11	HGNC	15167	protein_coding	YES	CCDS31503.1	ENSP00000306651	OR4CB_HUMAN	.	UPI000013E7AD	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF33,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAGAGAGC	.	5	ESCA
P2RX3	0	.	GRCh37	11	57117341	57117341	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.674C>T	p.Ala225Val	p.A225V	ENST00000263314	7/12	169	71	97	165	164	1	P2RX3,missense_variant,p.Ala225Val,ENST00000263314,;P2RX3,3_prime_UTR_variant,,ENST00000534820,;	T	ENSG00000109991	ENST00000263314	Transcript	missense_variant	708	674	225	A/V	gCg/gTg	.	.	.	1	P2RX3	HGNC	8534	protein_coding	YES	CCDS7953.1	ENSP00000263314	P2RX3_HUMAN	H0YDR6_HUMAN	UPI00000342EB	.	deleterious(0.01)	possibly_damaging(0.884)	7/12	.	hmmpanther:PTHR10125,hmmpanther:PTHR10125:SF8,Gene3D:3h9vA02,TIGRFAM_domain:TIGR00863,Pfam_domain:PF00864,Prints_domain:PR01310	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTGCGGGGC	.	5	ESCA
OR4D10	0	.	GRCh37	11	59245409	59245409	+	Silent	SNP	C	C	T	rs375485138	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.C169C	ENST00000530162	1/1	78	38	40	74	74	0	OR4D10,synonymous_variant,p.%3D,ENST00000530162,;	T	ENSG00000254466	ENST00000530162	Transcript	synonymous_variant	564	507	169	C	tgC/tgT	rs375485138	.	.	1	OR4D10	HGNC	15173	protein_coding	YES	CCDS53636.1	ENSP00000436424	OR4DA_HUMAN	.	UPI0000046485	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF111,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	T:0.0005	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGCGGACC	byFrequency|byCluster	5	ESCA
OOSP2	0	.	GRCh37	11	59807875	59807875	+	5'UTR	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-58G>A	.	.	ENST00000278855	1/4	67	46	21	81	81	0	OOSP2,5_prime_UTR_variant,,ENST00000278855,;OOSP2,upstream_gene_variant,,ENST00000532905,;OOSP2,upstream_gene_variant,,ENST00000527395,;	A	ENSG00000149507	ENST00000278855	Transcript	5_prime_UTR_variant	128	.	.	.	.	.	.	.	1	OOSP2	HGNC	26699	protein_coding	YES	CCDS7979.1	ENSP00000278855	OOSP2_HUMAN	.	UPI000000DC90	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCGCCACT	.	5	ESCA
INCENP	0	.	GRCh37	11	61897831	61897831	+	Silent	SNP	C	C	A	rs571110517	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>A	p.%3D	p.R278R	ENST00000394818	4/19	76	54	22	82	82	0	INCENP,synonymous_variant,p.%3D,ENST00000278849,;INCENP,synonymous_variant,p.%3D,ENST00000394818,;INCENP,downstream_gene_variant,,ENST00000533896,;INCENP,non_coding_transcript_exon_variant,,ENST00000528037,;INCENP,upstream_gene_variant,,ENST00000528375,;	A	ENSG00000149503	ENST00000394818	Transcript	synonymous_variant	1034	832	278	R	Cgg/Agg	rs571110517	.	.	1	INCENP	HGNC	6058	protein_coding	YES	CCDS44624.1	ENSP00000378295	INCE_HUMAN	E9PM67_HUMAN	UPI0000D7D6F3	.	.	.	4/19	.	hmmpanther:PTHR13142,hmmpanther:PTHR13142:SF1	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGGCGGGAG	by1000G	5	ESCA
GPR152	0	.	GRCh37	11	67219230	67219230	+	Silent	SNP	C	C	T	rs367572061	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.966G>A	p.%3D	p.P322P	ENST00000312457	1/1	61	46	14	78	78	0	GPR152,synonymous_variant,p.%3D,ENST00000312457,;CABP4,upstream_gene_variant,,ENST00000325656,;CABP4,upstream_gene_variant,,ENST00000438189,;CABP4,upstream_gene_variant,,ENST00000542233,;CABP4,upstream_gene_variant,,ENST00000542025,;CABP4,upstream_gene_variant,,ENST00000538060,;CABP4,upstream_gene_variant,,ENST00000545777,;CABP4,upstream_gene_variant,,ENST00000545040,;	T	ENSG00000175514	ENST00000312457	Transcript	synonymous_variant	971	966	322	P	ccG/ccA	rs367572061	.	.	-1	GPR152	HGNC	23622	protein_coding	YES	CCDS8165.1	ENSP00000310255	GP152_HUMAN	.	UPI000003B364	.	.	.	1/1	.	hmmpanther:PTHR11334:SF1,hmmpanther:PTHR11334,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCCGGCCG	byFrequency|byCluster	5	ESCA
KRTAP5-11	0	.	GRCh37	11	71293138	71293138	+	3'UTR	SNP	G	G	T	rs114237482	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*275C>A	.	.	ENST00000398530	1/1	111	88	23	59	59	0	KRTAP5-11,3_prime_UTR_variant,,ENST00000398530,;AP000867.1,3_prime_UTR_variant,,ENST00000343767,;KRTAP5-11,non_coding_transcript_exon_variant,,ENST00000526239,;KRTAP5-14P,upstream_gene_variant,,ENST00000502328,;	T	ENSG00000204571	ENST00000398530	Transcript	3_prime_UTR_variant	784	.	.	.	.	rs114237482	.	.	-1	KRTAP5-11	HGNC	23606	protein_coding	YES	CCDS41685.1	ENSP00000381541	KR511_HUMAN	.	UPI0000376063	.	.	.	1/1	.	.	A:0.0140	A:0.0507	A:0.0043	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAGGGAGAA	byFrequency|byCluster|by1000G	5	ESCA
FCHSD2	0	.	GRCh37	11	72853031	72853031	+	5'UTR	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-109T>A	.	.	ENST00000409418	1/20	43	25	17	47	47	0	FCHSD2,5_prime_UTR_variant,,ENST00000409314,;FCHSD2,5_prime_UTR_variant,,ENST00000409418,;FCHSD2,5_prime_UTR_variant,,ENST00000311172,;FCHSD2,upstream_gene_variant,,ENST00000458644,;FCHSD2,upstream_gene_variant,,ENST00000422375,;FCHSD2,upstream_gene_variant,,ENST00000409853,;	T	ENSG00000137478	ENST00000409418	Transcript	5_prime_UTR_variant	276	.	.	.	.	.	.	.	-1	FCHSD2	HGNC	29114	protein_coding	YES	CCDS8218.2	ENSP00000386722	FCSD2_HUMAN	C9JM66_HUMAN	UPI0000251F08	.	.	.	1/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAAGGAGC	.	5	ESCA
CCDC81	0	.	GRCh37	11	86120398	86120398	+	Silent	SNP	G	G	A	rs553491893	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209G>A	p.%3D	p.P403P	ENST00000445632	10/15	181	142	39	233	232	0	CCDC81,synonymous_variant,p.%3D,ENST00000528728,;CCDC81,synonymous_variant,p.%3D,ENST00000445632,;CCDC81,synonymous_variant,p.%3D,ENST00000278487,;CCDC81,synonymous_variant,p.%3D,ENST00000354755,;CCDC81,non_coding_transcript_exon_variant,,ENST00000530845,;CCDC81,non_coding_transcript_exon_variant,,ENST00000532215,;CCDC81,downstream_gene_variant,,ENST00000529603,;CCDC81,upstream_gene_variant,,ENST00000531587,;CCDC81,downstream_gene_variant,,ENST00000532466,;	A	ENSG00000149201	ENST00000445632	Transcript	synonymous_variant	1481	1209	403	P	ccG/ccA	rs553491893	.	.	1	CCDC81	HGNC	26281	protein_coding	YES	CCDS53691.1	ENSP00000415528	CCD81_HUMAN	B4DQN0_HUMAN	UPI0000E5BE97	.	.	.	10/15	.	hmmpanther:PTHR14362,hmmpanther:PTHR14362:SF2	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACCGGAATT	by1000G	5	ESCA
JRKL	0	.	GRCh37	11	96125434	96125437	+	3'UTR	DEL	TCTT	TCTT	-	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	TCTT	TCTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*47_*50delCTTT	.	.	ENST00000458427	1/1	41	26	15	40	40	0	JRKL,3_prime_UTR_variant,,ENST00000458427,;JRKL,3_prime_UTR_variant,,ENST00000332349,;CCDC82,upstream_gene_variant,,ENST00000542662,;CCDC82,upstream_gene_variant,,ENST00000538597,;CCDC82,upstream_gene_variant,,ENST00000278520,;JRKL,intron_variant,,ENST00000546177,;CCDC82,upstream_gene_variant,,ENST00000524836,;CCDC82,upstream_gene_variant,,ENST00000525786,;	-	ENSG00000183340	ENST00000458427	Transcript	3_prime_UTR_variant	2277-2280	.	.	.	.	.	.	.	1	JRKL	HGNC	6200	protein_coding	YES	CCDS8308.1	ENSP00000389989	JERKL_HUMAN	.	UPI0000167818	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	ACAAACTCTTTGCAA	.	2	ESCA
MYO1H	0	.	GRCh37	12	109831212	109831212	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205delT	p.Tyr69IlefsTer16	p.Y69Ifs*16	ENST00000310903	3/32	92	83	9	76	76	0	MYO1H,frameshift_variant,p.Tyr69IlefsTer16,ENST00000431443,;MYO1H,frameshift_variant,p.Tyr69IlefsTer16,ENST00000310903,;	-	ENSG00000174527	ENST00000310903	Transcript	frameshift_variant	309	203	68	L/X	cTt/ct	.	.	.	1	MYO1H	HGNC	13879	protein_coding	YES	CCDS53826.1	ENSP00000439182	.	S4R387_HUMAN,F5H3C6_HUMAN	UPI0001AFF951	.	.	.	3/32	.	Superfamily_domains:SSF52540,SMART_domains:SM00242,Pfam_domain:PF00063,hmmpanther:PTHR13140:SF353,hmmpanther:PTHR13140,PROSITE_profiles:PS51456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGGAACTTTATC	.	2	ESCA
ANKRD13A	0	.	GRCh37	12	110475748	110475748	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*389A>G	.	.	ENST00000261739	15/15	15	10	5	10	10	0	ANKRD13A,3_prime_UTR_variant,,ENST00000261739,;C12orf76,intron_variant,,ENST00000546651,;C12orf76,downstream_gene_variant,,ENST00000546627,;ANKRD13A,downstream_gene_variant,,ENST00000551491,;C12orf76,downstream_gene_variant,,ENST00000309050,;C12orf76,downstream_gene_variant,,ENST00000551185,;ANKRD13A,downstream_gene_variant,,ENST00000547419,;C12orf76,downstream_gene_variant,,ENST00000549724,;C12orf76,downstream_gene_variant,,ENST00000548936,;ANKRD13A,non_coding_transcript_exon_variant,,ENST00000553246,;ANKRD13A,non_coding_transcript_exon_variant,,ENST00000553251,;ANKRD13A,downstream_gene_variant,,ENST00000549826,;	G	ENSG00000076513	ENST00000261739	Transcript	3_prime_UTR_variant	2328	.	.	.	.	.	.	.	1	ANKRD13A	HGNC	21268	protein_coding	YES	CCDS9140.1	ENSP00000261739	AN13A_HUMAN	Q3ZTS7_HUMAN,B4DDL0_HUMAN,B3KMT9_HUMAN	UPI000004472C	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATATATAAGA	.	2	ESCA
PRB3	0	.	GRCh37	12	11420400	11420400	+	Silent	SNP	T	T	C	rs528598166	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657A>G	p.%3D	p.P219P	ENST00000381842	4/6	141	103	37	116	116	0	PRB3,synonymous_variant,p.%3D,ENST00000381842,;PRB3,synonymous_variant,p.%3D,ENST00000538488,;PRB3,synonymous_variant,p.%3D,ENST00000279573,;PRB3,intron_variant,,ENST00000440870,;PRB3,downstream_gene_variant,,ENST00000539835,;	C	ENSG00000197870	ENST00000381842	Transcript	synonymous_variant	695	657	219	P	ccA/ccG	rs528598166	.	.	-1	PRB3	HGNC	9339	protein_coding	YES	.	ENSP00000371264	PRB3_HUMAN	.	UPI0000E67202	.	.	.	4/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23203,hmmpanther:PTHR23203:SF4,Pfam_domain:PF15240,Pfam_domain:PF15240	C:0.0028	C:0.003	C:0	.	C:0.0089	C:0	C:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGGTGGGGG	byFrequency|by1000G	4	ESCA
CACNA2D4	0	.	GRCh37	12	1963175	1963175	+	Missense_Mutation	SNP	C	C	T	rs368331985	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2188G>A	p.Ala730Thr	p.A730T	ENST00000382722	23/38	65	35	29	56	56	0	CACNA2D4,missense_variant,p.Ala591Thr,ENST00000585732,;CACNA2D4,missense_variant,p.Ala705Thr,ENST00000587995,;CACNA2D4,missense_variant,p.Ala730Thr,ENST00000586184,;CACNA2D4,missense_variant,p.Ala730Thr,ENST00000382722,;CACNA2D4,missense_variant,p.Ala666Thr,ENST00000588077,;CACNA2D4,missense_variant,p.Ala666Thr,ENST00000585708,;CACNA2D4,intron_variant,,ENST00000539048,;CACNA2D4,missense_variant,p.Ala11Thr,ENST00000537784,;CACNA2D4,3_prime_UTR_variant,,ENST00000444595,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000280663,;	T	ENSG00000151062	ENST00000382722	Transcript	missense_variant	2551	2188	730	A/T	Gcg/Acg	rs368331985	.	.	-1	CACNA2D4	HGNC	20202	protein_coding	YES	CCDS44785.1	ENSP00000372169	CA2D4_HUMAN	.	UPI0000E593D9	.	deleterious(0.01)	possibly_damaging(0.797)	23/38	.	hmmpanther:PTHR10166:SF26,hmmpanther:PTHR10166	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D729D|c.2187C>T|3,BUFFER|p.D729D|c.2187C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCGCGTCAA	byFrequency|byCluster	5	ESCA
PDE3A	0	.	GRCh37	12	20774228	20774228	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1425-2A>C	.	p.X475_splice	ENST00000359062	.	73	57	15	54	54	0	PDE3A,splice_acceptor_variant,,ENST00000359062,;PDE3A,splice_acceptor_variant,,ENST00000544307,;	C	ENSG00000172572	ENST00000359062	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	PDE3A	HGNC	8778	protein_coding	YES	CCDS31754.1	ENSP00000351957	PDE3A_HUMAN	.	UPI000014175F	.	.	.	.	4/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTAGTCCT	.	5	ESCA
SLCO1C1	0	.	GRCh37	12	20874792	20874792	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.830G>C	p.Gly277Ala	p.G277A	ENST00000381552	8/15	61	50	11	70	70	0	SLCO1C1,missense_variant,p.Gly277Ala,ENST00000381552,;SLCO1C1,missense_variant,p.Gly277Ala,ENST00000545604,;SLCO1C1,missense_variant,p.Gly159Ala,ENST00000545102,;SLCO1C1,missense_variant,p.Gly277Ala,ENST00000266509,;SLCO1C1,missense_variant,p.Gly228Ala,ENST00000540354,;SLCO1C1,3_prime_UTR_variant,,ENST00000539415,;	C	ENSG00000139155	ENST00000381552	Transcript	missense_variant	1198	830	277	G/A	gGc/gCc	.	.	.	1	SLCO1C1	HGNC	13819	protein_coding	YES	CCDS53757.1	ENSP00000370964	SO1C1_HUMAN	.	UPI00004C3E1B	.	deleterious(0)	probably_damaging(0.999)	8/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF18,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTGGCTATC	.	5	ESCA
SCAF11	0	.	GRCh37	12	46318804	46318804	+	Missense_Mutation	SNP	T	T	C	rs150376258	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3613A>G	p.Ile1205Val	p.I1205V	ENST00000369367	12/15	138	112	25	122	122	0	SCAF11,missense_variant,p.Ile890Val,ENST00000465950,;SCAF11,missense_variant,p.Ile1205Val,ENST00000369367,;SCAF11,missense_variant,p.Ile1205Val,ENST00000419565,;SCAF11,missense_variant,p.Ile1013Val,ENST00000549162,;SCAF11,downstream_gene_variant,,ENST00000484275,;SCAF11,upstream_gene_variant,,ENST00000547654,;SCAF11,upstream_gene_variant,,ENST00000550629,;SCAF11,non_coding_transcript_exon_variant,,ENST00000547950,;SCAF11,downstream_gene_variant,,ENST00000547018,;SCAF11,upstream_gene_variant,,ENST00000550893,;	C	ENSG00000139218	ENST00000369367	Transcript	missense_variant	3847	3613	1205	I/V	Ata/Gta	rs150376258	.	.	-1	SCAF11	HGNC	10784	protein_coding	YES	CCDS8748.2	ENSP00000358374	SCAFB_HUMAN	F8VXG7_HUMAN	UPI0000D481F2	.	tolerated(0.94)	benign(0.002)	12/15	.	hmmpanther:PTHR15242:SF3,hmmpanther:PTHR15242	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTATAGGTA	byCluster	5	ESCA
KRR1	0	.	GRCh37	12	75897754	75897754	+	Missense_Mutation	SNP	C	C	A	rs761193901	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.761G>T	p.Arg254Leu	p.R254L	ENST00000229214	7/10	103	69	34	113	112	0	KRR1,missense_variant,p.Arg254Leu,ENST00000229214,;KRR1,intron_variant,,ENST00000438169,;GLIPR1,downstream_gene_variant,,ENST00000266659,;KRR1,non_coding_transcript_exon_variant,,ENST00000551070,;KRR1,downstream_gene_variant,,ENST00000550898,;KRR1,downstream_gene_variant,,ENST00000550023,;GLIPR1,downstream_gene_variant,,ENST00000536703,;	A	ENSG00000111615	ENST00000229214	Transcript	missense_variant	785	761	254	R/L	cGc/cTc	rs761193901,COSM1364229	.	.	-1	KRR1	HGNC	5176	protein_coding	YES	CCDS9012.1	ENSP00000229214	KRR1_HUMAN	.	UPI00001403EE	.	deleterious(0)	benign(0.366)	7/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12581,PIRSF_domain:PIRSF006515	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGCGTTTA	.	5	ESCA
KLRF1	0	.	GRCh37	12	9994939	9994939	+	Missense_Mutation	SNP	T	T	G	rs779826490	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.497T>G	p.Leu166Arg	p.L166R	ENST00000279544	5/6	72	55	17	73	73	0	KLRF1,missense_variant,p.Leu116Arg,ENST00000324214,;KLRF1,missense_variant,p.Leu166Arg,ENST00000279544,;KLRF1,intron_variant,,ENST00000354855,;KLRF1,intron_variant,,ENST00000537723,;KLRF1,stop_lost,p.Ter125GluextTer3,ENST00000545196,;KLRF1,synonymous_variant,p.%3D,ENST00000535631,;KLRF1,synonymous_variant,p.%3D,ENST00000279545,;	G	ENSG00000150045	ENST00000279544	Transcript	missense_variant	561	497	166	L/R	cTa/cGa	rs779826490	.	.	1	KLRF1	HGNC	13342	protein_coding	YES	CCDS41750.1	ENSP00000279544	KLRF1_HUMAN	.	UPI0000141308	.	tolerated(0.07)	benign(0.309)	5/6	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22800:SF134,hmmpanther:PTHR22800,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACCTAAGAC	byFrequency	5	ESCA
FGF14	0	.	GRCh37	13	103054074	103054074	+	5'UTR	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-46G>C	.	.	ENST00000376131	1/5	73	60	13	84	84	0	FGF14,5_prime_UTR_variant,,ENST00000376131,;RP11-811P12.3,intron_variant,,ENST00000418923,;	G	ENSG00000102466	ENST00000376131	Transcript	5_prime_UTR_variant	51	.	.	.	.	.	.	.	-1	FGF14	HGNC	3671	protein_coding	YES	CCDS9500.1	ENSP00000365301	FGF14_HUMAN	.	UPI000000D898	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTCACGTG	.	5	ESCA
TUBGCP3	0	.	GRCh37	13	113140238	113140238	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69C>T	.	.	ENST00000261965	22/22	27	22	5	36	36	0	TUBGCP3,3_prime_UTR_variant,,ENST00000261965,;TUBGCP3,non_coding_transcript_exon_variant,,ENST00000469302,;	A	ENSG00000126216	ENST00000261965	Transcript	3_prime_UTR_variant	2980	.	.	.	.	.	.	.	-1	TUBGCP3	HGNC	18598	protein_coding	YES	CCDS9525.1	ENSP00000261965	GCP3_HUMAN	.	UPI000000DB88	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGGACGTCAAT	.	3	ESCA
POMP	0	.	GRCh37	13	29242660	29242660	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.213G>A	p.%3D	p.Q71Q	ENST00000380842	4/6	52	42	9	63	63	0	POMP,synonymous_variant,p.%3D,ENST00000380842,;POMP,non_coding_transcript_exon_variant,,ENST00000460403,;	A	ENSG00000132963	ENST00000380842	Transcript	synonymous_variant	294	213	71	Q	caG/caA	.	.	.	1	POMP	HGNC	20330	protein_coding	YES	CCDS9331.1	ENSP00000370222	POMP_HUMAN	.	UPI000006E3C4	.	.	.	4/6	.	hmmpanther:PTHR12828:SF3,hmmpanther:PTHR12828,Pfam_domain:PF05348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCAGGGTCT	.	5	ESCA
MAB21L1	0	.	GRCh37	13	36049167	36049167	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29T>C	.	.	ENST00000379919	1/1	88	69	18	64	64	0	MAB21L1,3_prime_UTR_variant,,ENST00000379919,;NBEA,intron_variant,,ENST00000400445,;NBEA,intron_variant,,ENST00000540320,;NBEA,intron_variant,,ENST00000310336,;NBEA,intron_variant,,ENST00000379939,;NBEA,upstream_gene_variant,,ENST00000537702,;	G	ENSG00000180660	ENST00000379919	Transcript	3_prime_UTR_variant	1666	.	.	.	.	.	.	.	-1	MAB21L1	HGNC	6757	protein_coding	YES	CCDS9353.1	ENSP00000369251	MB211_HUMAN	F1T0A2_HUMAN	UPI0000022CD2	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTAATAATT	.	5	ESCA
KCNRG	0	.	GRCh37	13	50592451	50592451	+	Intron	SNP	A	A	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.579-1899A>C	.	.	ENST00000312942	.	71	54	16	63	63	0	TRIM13,3_prime_UTR_variant,,ENST00000378182,;KCNRG,intron_variant,,ENST00000360473,;KCNRG,intron_variant,,ENST00000312942,;TRIM13,downstream_gene_variant,,ENST00000420995,;TRIM13,intron_variant,,ENST00000478111,;TRIM13,intron_variant,,ENST00000474805,;	C	ENSG00000198553	ENST00000312942	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KCNRG	HGNC	18893	protein_coding	YES	CCDS9424.1	ENSP00000324191	KCNRG_HUMAN	.	UPI000000D8AF	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTAATTCT	.	5	ESCA
PPP2R5C	0	.	GRCh37	14	102392107	102392107	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*498T>G	.	.	ENST00000422945	16/16	32	22	10	49	49	0	PPP2R5C,3_prime_UTR_variant,,ENST00000350249,;PPP2R5C,3_prime_UTR_variant,,ENST00000422945,;PPP2R5C,3_prime_UTR_variant,,ENST00000328724,;PPP2R5C,3_prime_UTR_variant,,ENST00000334743,;PPP2R5C,downstream_gene_variant,,ENST00000555237,;PPP2R5C,downstream_gene_variant,,ENST00000557268,;PPP2R5C,downstream_gene_variant,,ENST00000554147,;PPP2R5C,downstream_gene_variant,,ENST00000557071,;	G	ENSG00000078304	ENST00000422945	Transcript	3_prime_UTR_variant	2262	.	.	.	.	.	.	.	1	PPP2R5C	HGNC	9311	protein_coding	YES	CCDS53912.1	ENSP00000412324	2A5G_HUMAN	H0YJ75_HUMAN	UPI0001A7AE62	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAATGGCTC	.	5	ESCA
RTN1	0	.	GRCh37	14	60193766	60193766	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1636G>T	p.Glu546Ter	p.E546*	ENST00000267484	3/9	64	41	22	102	102	0	RTN1,stop_gained,p.Glu546Ter,ENST00000267484,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,;	A	ENSG00000139970	ENST00000267484	Transcript	stop_gained	1972	1636	546	E/*	Gag/Tag	.	.	.	-1	RTN1	HGNC	10467	protein_coding	YES	CCDS9740.1	ENSP00000267484	RTN1_HUMAN	Q2NKQ5_HUMAN,Q2L7A7_HUMAN	UPI00001352DA	.	.	.	3/9	.	hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCTCAGGCT	.	5	ESCA
SYNE2	0	.	GRCh37	14	64491122	64491122	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5785T>C	p.Ser1929Pro	p.S1929P	ENST00000358025	39/116	36	23	12	50	50	0	SYNE2,missense_variant,p.Ser1929Pro,ENST00000554584,;SYNE2,missense_variant,p.Ser1929Pro,ENST00000358025,;SYNE2,missense_variant,p.Ser1929Pro,ENST00000344113,;SYNE2,5_prime_UTR_variant,,ENST00000357395,;SYNE2,non_coding_transcript_exon_variant,,ENST00000557005,;	C	ENSG00000054654	ENST00000358025	Transcript	missense_variant	6015	5785	1929	S/P	Tcc/Ccc	.	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	probably_damaging(0.999)	39/116	.	hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGTCCATA	.	5	ESCA
MOAP1	0	.	GRCh37	14	93648618	93648618	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*914A>G	.	.	ENST00000556883	2/2	30	18	12	30	30	0	MOAP1,3_prime_UTR_variant,,ENST00000556883,;MOAP1,3_prime_UTR_variant,,ENST00000298894,;RP11-371E8.4,upstream_gene_variant,,ENST00000557574,;TMEM251,upstream_gene_variant,,ENST00000283534,;TMEM251,upstream_gene_variant,,ENST00000415050,;RP11-371E8.4,upstream_gene_variant,,ENST00000557048,;RP11-371E8.4,upstream_gene_variant,,ENST00000554824,;	C	ENSG00000165943	ENST00000556883	Transcript	3_prime_UTR_variant	2455	.	.	.	.	.	.	.	-1	MOAP1	HGNC	16658	protein_coding	YES	CCDS9908.1	ENSP00000451594	MOAP1_HUMAN	.	UPI0000037797	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAACTAGATG	.	5	ESCA
NIPA2	0	.	GRCh37	15	23006588	23006588	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.716C>T	p.Ala239Val	p.A239V	ENST00000337451	8/8	51	44	7	31	31	0	NIPA2,missense_variant,p.Ala239Val,ENST00000398013,;NIPA2,missense_variant,p.Ala220Val,ENST00000539711,;NIPA2,missense_variant,p.Ala239Val,ENST00000398014,;NIPA2,missense_variant,p.Ala239Val,ENST00000337451,;NIPA2,missense_variant,p.Ala220Val,ENST00000359727,;CYFIP1,downstream_gene_variant,,ENST00000435939,;CYFIP1,downstream_gene_variant,,ENST00000560848,;CYFIP1,downstream_gene_variant,,ENST00000313077,;CYFIP1,downstream_gene_variant,,ENST00000561020,;	A	ENSG00000140157	ENST00000337451	Transcript	missense_variant	1329	716	239	A/V	gCc/gTc	.	.	.	-1	NIPA2	HGNC	17044	protein_coding	YES	CCDS10010.1	ENSP00000337618	NIPA2_HUMAN	H0YMQ7_HUMAN	UPI0000070013	.	deleterious(0)	probably_damaging(0.981)	8/8	.	hmmpanther:PTHR12570:SF1,hmmpanther:PTHR12570,Pfam_domain:PF05653	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGGGCCCTA	.	4	ESCA
NDN	0	.	GRCh37	15	23931297	23931297	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*102G>A	.	.	ENST00000331837	1/1	56	38	18	34	34	0	NDN,3_prime_UTR_variant,,ENST00000331837,;	T	ENSG00000182636	ENST00000331837	Transcript	3_prime_UTR_variant	1154	.	.	.	.	.	.	.	-1	NDN	HGNC	7675	protein_coding	YES	CCDS10014.1	ENSP00000332643	NECD_HUMAN	.	UPI000012FEF1	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACACGTGAA	.	5	ESCA
GABRG3	0	.	GRCh37	15	27778007	27778007	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1384G>A	p.Val462Ile	p.V462I	ENST00000333743	10/10	141	122	19	110	110	0	GABRG3,missense_variant,p.Val462Ile,ENST00000333743,;GABRG3,downstream_gene_variant,,ENST00000451330,;RP11-100M12.3,intron_variant,,ENST00000556642,;RP11-100M12.3,downstream_gene_variant,,ENST00000557170,;	A	ENSG00000182256	ENST00000333743	Transcript	missense_variant	1638	1384	462	V/I	Gtt/Att	.	.	.	1	GABRG3	HGNC	4088	protein_coding	YES	CCDS45195.1	ENSP00000331912	GBRG3_HUMAN	.	UPI000012AFCB	.	tolerated(0.43)	probably_damaging(0.978)	10/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF195,hmmpanther:PTHR18945,Gene3D:1.20.58.390,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR00253	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGGGTTGGA	.	4	ESCA
SEMA6D	0	.	GRCh37	15	48062933	48062933	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2173G>T	p.Val725Phe	p.V725F	ENST00000316364	19/19	24	13	10	20	20	0	SEMA6D,missense_variant,p.Val682Phe,ENST00000389432,;SEMA6D,missense_variant,p.Val189Phe,ENST00000560006,;SEMA6D,missense_variant,p.Val663Phe,ENST00000537942,;SEMA6D,missense_variant,p.Val663Phe,ENST00000358066,;SEMA6D,missense_variant,p.Val669Phe,ENST00000354744,;SEMA6D,missense_variant,p.Val650Phe,ENST00000389428,;SEMA6D,missense_variant,p.Val725Phe,ENST00000536845,;SEMA6D,missense_variant,p.Val706Phe,ENST00000389433,;SEMA6D,missense_variant,p.Val663Phe,ENST00000558014,;SEMA6D,missense_variant,p.Val725Phe,ENST00000316364,;SEMA6D,3_prime_UTR_variant,,ENST00000355997,;SEMA6D,3_prime_UTR_variant,,ENST00000558816,;SEMA6D,downstream_gene_variant,,ENST00000559064,;SEMA6D,downstream_gene_variant,,ENST00000558431,;	T	ENSG00000137872	ENST00000316364	Transcript	missense_variant	2612	2173	725	V/F	Gtc/Ttc	.	.	.	1	SEMA6D	HGNC	16770	protein_coding	YES	CCDS32225.1	ENSP00000324857	SEM6D_HUMAN	Q9HAH9_HUMAN,H0YMV0_HUMAN,H0YMA6_HUMAN,H0YL82_HUMAN	UPI000006E201	.	deleterious(0.05)	benign(0.439)	19/19	.	hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTGTCAAG	.	5	ESCA
FBN1	0	.	GRCh37	15	48702628	48702628	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*559G>C	.	.	ENST00000316623	66/66	48	33	15	64	64	0	FBN1,3_prime_UTR_variant,,ENST00000316623,;FBN1,downstream_gene_variant,,ENST00000561429,;FBN1,3_prime_UTR_variant,,ENST00000559133,;	G	ENSG00000166147	ENST00000316623	Transcript	3_prime_UTR_variant	9631	.	.	.	.	.	.	.	-1	FBN1	HGNC	3603	protein_coding	YES	CCDS32232.1	ENSP00000325527	FBN1_HUMAN	Q75N89_HUMAN,Q75N88_HUMAN,H0YN80_HUMAN	UPI0000163B0B	.	.	.	66/66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATACTCATA	.	5	ESCA
COX5A	0	.	GRCh37	15	75219207	75219207	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239A>G	p.Tyr80Cys	p.Y80C	ENST00000322347	3/5	48	36	12	76	76	0	COX5A,missense_variant,p.Tyr41Cys,ENST00000567270,;COX5A,missense_variant,p.Tyr80Cys,ENST00000322347,;COX5A,missense_variant,p.Tyr80Cys,ENST00000568783,;COX5A,missense_variant,p.Tyr80Cys,ENST00000564811,;COX5A,5_prime_UTR_variant,,ENST00000568517,;COX5A,intron_variant,,ENST00000562233,;	C	ENSG00000178741	ENST00000322347	Transcript	missense_variant	393	239	80	Y/C	tAt/tGt	.	.	.	-1	COX5A	HGNC	2267	protein_coding	YES	CCDS10273.1	ENSP00000317780	COX5A_HUMAN	Q71UP1_HUMAN,H3BRM5_HUMAN	UPI000007112F	.	deleterious(0.01)	probably_damaging(0.994)	3/5	.	hmmpanther:PTHR14200,hmmpanther:PTHR14200:SF11,Gene3D:1v54E00,Pfam_domain:PF02284,Superfamily_domains:0053246	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCATAGGTA	.	5	ESCA
LINGO1	0	.	GRCh37	15	77907091	77907091	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1158G>C	p.%3D	p.R386R	ENST00000355300	2/2	56	40	16	94	94	0	LINGO1,synonymous_variant,p.%3D,ENST00000355300,;LINGO1,synonymous_variant,p.%3D,ENST00000561030,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000567726,;LINGO1,downstream_gene_variant,,ENST00000561686,;LINGO1,downstream_gene_variant,,ENST00000566711,;LINGO1,downstream_gene_variant,,ENST00000557798,;LINGO1,downstream_gene_variant,,ENST00000564472,;	G	ENSG00000169783	ENST00000355300	Transcript	synonymous_variant	1333	1158	386	R	cgG/cgC	.	.	.	-1	LINGO1	HGNC	21205	protein_coding	YES	CCDS45313.1	ENSP00000347451	LIGO1_HUMAN	H3BQ49_HUMAN,H3BN48_HUMAN,H3BMW2_HUMAN,H3BMN3_HUMAN,H3BM59_HUMAN,H0YNK7_HUMAN	UPI00000377A0	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,Gene3D:3.80.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAGCCGCCA	.	5	ESCA
STARD5	0	.	GRCh37	15	81614790	81614790	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241G>A	p.Glu81Lys	p.E81K	ENST00000302824	3/6	40	14	26	61	61	0	STARD5,missense_variant,p.Glu81Lys,ENST00000302824,;RP11-761I4.3,upstream_gene_variant,,ENST00000559781,;RP11-761I4.3,upstream_gene_variant,,ENST00000560973,;STARD5,non_coding_transcript_exon_variant,,ENST00000559913,;STARD5,stop_retained_variant,p.%3D,ENST00000325346,;STARD5,3_prime_UTR_variant,,ENST00000560156,;STARD5,non_coding_transcript_exon_variant,,ENST00000560723,;	T	ENSG00000172345	ENST00000302824	Transcript	missense_variant	267	241	81	E/K	Gag/Aag	.	.	.	-1	STARD5	HGNC	18065	protein_coding	YES	CCDS10318.1	ENSP00000304032	STAR5_HUMAN	.	UPI0000136136	.	tolerated(1)	benign(0.01)	3/6	.	PROSITE_profiles:PS50848,hmmpanther:PTHR12136,hmmpanther:PTHR12136:SF44,Gene3D:3.30.530.20,Pfam_domain:PF01852,SMART_domains:SM00234,Superfamily_domains:SSF55961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTCATCCC	.	5	ESCA
MAN2A2	0	.	GRCh37	15	91459419	91459419	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2927T>C	p.Leu976Pro	p.L976P	ENST00000360468	19/22	104	40	63	151	151	0	MAN2A2,missense_variant,p.Leu619Pro,ENST00000557865,;MAN2A2,missense_variant,p.Leu108Pro,ENST00000560147,;MAN2A2,missense_variant,p.Leu976Pro,ENST00000360468,;MAN2A2,missense_variant,p.Leu150Pro,ENST00000557990,;MAN2A2,missense_variant,p.Leu166Pro,ENST00000430376,;MAN2A2,missense_variant,p.Leu976Pro,ENST00000559717,;MAN2A2,missense_variant,p.Leu484Pro,ENST00000431652,;MAN2A2,downstream_gene_variant,,ENST00000558171,;MAN2A2,downstream_gene_variant,,ENST00000560616,;AC068831.15,downstream_gene_variant,,ENST00000560522,;MAN2A2,non_coding_transcript_exon_variant,,ENST00000558538,;MAN2A2,intron_variant,,ENST00000560926,;MAN2A2,downstream_gene_variant,,ENST00000561240,;MAN2A2,upstream_gene_variant,,ENST00000559558,;MAN2A2,missense_variant,p.Leu186Pro,ENST00000561448,;MAN2A2,3_prime_UTR_variant,,ENST00000558161,;MAN2A2,3_prime_UTR_variant,,ENST00000560451,;MAN2A2,non_coding_transcript_exon_variant,,ENST00000560880,;MAN2A2,non_coding_transcript_exon_variant,,ENST00000559341,;MAN2A2,downstream_gene_variant,,ENST00000560505,;MAN2A2,downstream_gene_variant,,ENST00000560192,;MAN2A2,upstream_gene_variant,,ENST00000558374,;MAN2A2,upstream_gene_variant,,ENST00000559704,;MAN2A2,downstream_gene_variant,,ENST00000561047,;MAN2A2,downstream_gene_variant,,ENST00000559374,;	C	ENSG00000196547	ENST00000360468	Transcript	missense_variant	2945	2927	976	L/P	cTc/cCc	.	.	.	1	MAN2A2	HGNC	6825	protein_coding	YES	CCDS32332.1	ENSP00000353655	MA2A2_HUMAN	H0YNC8_HUMAN,H0YMU0_HUMAN,H0YL67_HUMAN,H0YK77_HUMAN,B7ZA35_HUMAN	UPI0000408EF0	.	deleterious(0)	probably_damaging(1)	19/22	.	Superfamily_domains:SSF74650,Pfam_domain:PF07748,Gene3D:2.70.98.30,hmmpanther:PTHR11607:SF24,hmmpanther:PTHR11607	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCTCAAGG	.	5	ESCA
ERI2	0	.	GRCh37	16	20809366	20809366	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1756C>G	p.Pro586Ala	p.P586A	ENST00000357967	9/9	61	39	22	73	73	0	ERI2,missense_variant,p.Pro493Ala,ENST00000563117,;ERI2,missense_variant,p.Pro321Ala,ENST00000389345,;ERI2,missense_variant,p.Pro493Ala,ENST00000564349,;ERI2,missense_variant,p.Pro586Ala,ENST00000357967,;ERI2,3_prime_UTR_variant,,ENST00000569729,;ERI2,intron_variant,,ENST00000300005,;ACSM3,downstream_gene_variant,,ENST00000562251,;ACSM3,downstream_gene_variant,,ENST00000569141,;ACSM3,downstream_gene_variant,,ENST00000289416,;ACSM3,downstream_gene_variant,,ENST00000450120,;ERI2,downstream_gene_variant,,ENST00000563537,;ACSM3,downstream_gene_variant,,ENST00000567387,;ERI2,downstream_gene_variant,,ENST00000565884,;ACSM3,downstream_gene_variant,,ENST00000567711,;ERI2,downstream_gene_variant,,ENST00000567562,;ERI2,3_prime_UTR_variant,,ENST00000568805,;ERI2,non_coding_transcript_exon_variant,,ENST00000562215,;ERI2,intron_variant,,ENST00000562987,;ERI2,downstream_gene_variant,,ENST00000567859,;ACSM3,downstream_gene_variant,,ENST00000567006,;	C	ENSG00000196678	ENST00000357967	Transcript	missense_variant	1799	1756	586	P/A	Cca/Gca	.	.	.	-1	ERI2	HGNC	30541	protein_coding	YES	CCDS45436.1	ENSP00000350651	ERI2_HUMAN	.	UPI0000EE8210	.	tolerated(0.55)	benign(0.156)	9/9	.	hmmpanther:PTHR23044:SF30,hmmpanther:PTHR23044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGGCTCTT	.	5	ESCA
TMEM159	0	.	GRCh37	16	21181911	21181911	+	Missense_Mutation	SNP	G	G	A	rs747501346	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250G>A	p.Val84Ile	p.V84I	ENST00000233047	3/5	87	66	20	70	70	0	TMEM159,missense_variant,p.Val108Ile,ENST00000451578,;TMEM159,missense_variant,p.Val84Ile,ENST00000572599,;TMEM159,missense_variant,p.Val84Ile,ENST00000261388,;TMEM159,missense_variant,p.Val84Ile,ENST00000233047,;TMEM159,missense_variant,p.Val84Ile,ENST00000572258,;TMEM159,downstream_gene_variant,,ENST00000577162,;TMEM159,non_coding_transcript_exon_variant,,ENST00000574092,;TMEM159,missense_variant,p.Val41Ile,ENST00000573688,;TMEM159,missense_variant,p.Val108Ile,ENST00000573487,;	A	ENSG00000011638	ENST00000233047	Transcript	missense_variant	718	250	84	V/I	Gtc/Atc	rs747501346	.	.	1	TMEM159	HGNC	30136	protein_coding	YES	CCDS10595.1	ENSP00000233047	TM159_HUMAN	.	UPI000013D178	.	deleterious(0.04)	benign(0.27)	3/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR14275:SF0,hmmpanther:PTHR14275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGGTCATA	byFrequency	5	ESCA
GSG1L	0	.	GRCh37	16	27840120	27840120	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820T>G	p.Phe274Val	p.F274V	ENST00000447459	5/7	63	27	35	47	47	0	GSG1L,missense_variant,p.Phe119Val,ENST00000380897,;GSG1L,missense_variant,p.Phe119Val,ENST00000569166,;GSG1L,missense_variant,p.Phe223Val,ENST00000395724,;GSG1L,missense_variant,p.Phe274Val,ENST00000447459,;GSG1L,missense_variant,p.Phe119Val,ENST00000380898,;GSG1L,3_prime_UTR_variant,,ENST00000562611,;	C	ENSG00000169181	ENST00000447459	Transcript	missense_variant	905	820	274	F/V	Ttc/Gtc	.	.	.	-1	GSG1L	HGNC	28283	protein_coding	YES	CCDS45450.1	ENSP00000394954	GSG1L_HUMAN	.	UPI0000EE765B	.	tolerated(0.12)	possibly_damaging(0.577)	5/7	.	hmmpanther:PTHR10671:SF35,hmmpanther:PTHR10671	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGAAGTACT	.	5	ESCA
ITGAM	0	.	GRCh37	16	31341216	31341216	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2969C>T	p.Thr990Ile	p.T990I	ENST00000544665	25/30	16	9	6	15	15	0	ITGAM,missense_variant,p.Thr989Ile,ENST00000287497,;ITGAM,missense_variant,p.Thr990Ile,ENST00000544665,;ITGAM,upstream_gene_variant,,ENST00000565142,;ITGAM,non_coding_transcript_exon_variant,,ENST00000569746,;ITGAM,non_coding_transcript_exon_variant,,ENST00000567178,;ITGAM,downstream_gene_variant,,ENST00000561838,;	T	ENSG00000169896	ENST00000544665	Transcript	missense_variant	3040	2969	990	T/I	aCc/aTc	.	.	.	1	ITGAM	HGNC	6149	protein_coding	YES	CCDS54004.1	ENSP00000441691	ITAM_HUMAN	B3KXM6_HUMAN	UPI000004B26A	.	tolerated(0.75)	benign(0.007)	25/30	.	hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Pfam_domain:PF08441,Superfamily_domains:SSF69179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GGTCACCTTCT	.	4	ESCA
SLX4	0	.	GRCh37	16	3656556	3656556	+	Missense_Mutation	SNP	C	C	T	rs147872182	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679G>A	p.Ala227Thr	p.A227T	ENST00000294008	3/15	51	26	24	59	59	0	SLX4,missense_variant,p.Ala227Thr,ENST00000294008,;SLX4,non_coding_transcript_exon_variant,,ENST00000486524,;SLX4,non_coding_transcript_exon_variant,,ENST00000466154,;	T	ENSG00000188827	ENST00000294008	Transcript	missense_variant	1320	679	227	A/T	Gct/Act	rs147872182,COSM970504	.	.	-1	SLX4	HGNC	23845	protein_coding	YES	CCDS10506.2	ENSP00000294008	SLX4_HUMAN	.	UPI000050D2C5	.	tolerated(0.48)	benign(0.027)	3/15	.	hmmpanther:PTHR21541	.	.	.	.	.	.	.	T:0.0007	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAGCGTGTC	byFrequency|byCluster	5	ESCA
ANKRD26P1	0	.	GRCh37	16	46534259	46534259	+	RNA	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.656G>A	.	.	ENST00000571006	3/10	32	17	15	33	33	0	ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000571006,;ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000566201,;ANKRD26P1,downstream_gene_variant,,ENST00000574898,;ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000569528,;	T	ENSG00000261239	ENST00000571006	Transcript	non_coding_transcript_exon_variant	656	.	.	.	.	.	.	.	-1	ANKRD26P1	HGNC	32955	processed_transcript	YES	.	.	.	.	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTGCCACTT	.	5	ESCA
CNEP1R1	0	.	GRCh37	16	50063691	50063691	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204A>T	p.%3D	p.I68I	ENST00000458059	4/7	114	94	20	92	92	0	CNEP1R1,synonymous_variant,p.%3D,ENST00000565556,;CNEP1R1,synonymous_variant,p.%3D,ENST00000562576,;CNEP1R1,synonymous_variant,p.%3D,ENST00000458059,;CNEP1R1,synonymous_variant,p.%3D,ENST00000427478,;CNEP1R1,synonymous_variant,p.%3D,ENST00000566093,;CNEP1R1,downstream_gene_variant,,ENST00000567712,;CNEP1R1,downstream_gene_variant,,ENST00000569647,;CNEP1R1,synonymous_variant,p.%3D,ENST00000565457,;CNEP1R1,intron_variant,,ENST00000389134,;CNEP1R1,intron_variant,,ENST00000566482,;CNEP1R1,intron_variant,,ENST00000568890,;	T	ENSG00000205423	ENST00000458059	Transcript	synonymous_variant	1110	204	68	I	atA/atT	.	.	.	1	CNEP1R1	HGNC	26759	protein_coding	YES	CCDS45480.1	ENSP00000405635	NEPR1_HUMAN	H3BUT5_HUMAN,H3BMF1_HUMAN	UPI000006FFD2	.	.	.	4/7	.	Pfam_domain:PF09771,hmmpanther:PTHR20996:SF1,hmmpanther:PTHR20996,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATAGACCC	.	5	ESCA
PAPD5	0	.	GRCh37	16	50264337	50264337	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1098C>G	.	.	ENST00000436909	13/13	54	34	19	37	37	0	PAPD5,3_prime_UTR_variant,,ENST00000436909,;PAPD5,3_prime_UTR_variant,,ENST00000357464,;PAPD5,downstream_gene_variant,,ENST00000561678,;PAPD5,non_coding_transcript_exon_variant,,ENST00000573002,;PAPD5,intron_variant,,ENST00000562717,;	G	ENSG00000121274	ENST00000436909	Transcript	3_prime_UTR_variant	3230	.	.	.	.	.	.	.	1	PAPD5	HGNC	30758	protein_coding	YES	CCDS54006.1	ENSP00000396995	PAPD5_HUMAN	Q5EBM7_HUMAN,G4U4J3_HUMAN,B7ZLC1_HUMAN,B4DRJ7_HUMAN	UPI00017A7DC6	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCTTATT	.	5	ESCA
CMTM2	0	.	GRCh37	16	66613777	66613777	+	Missense_Mutation	SNP	G	G	C	rs761550400	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267G>C	p.Glu89Asp	p.E89D	ENST00000268595	1/4	68	43	25	60	60	0	CMTM2,missense_variant,p.Glu89Asp,ENST00000268595,;CMTM2,missense_variant,p.Glu89Asp,ENST00000379486,;CMTM1,downstream_gene_variant,,ENST00000379500,;CMTM1,downstream_gene_variant,,ENST00000528324,;CMTM1,downstream_gene_variant,,ENST00000529506,;CMTM1,downstream_gene_variant,,ENST00000531885,;CMTM1,downstream_gene_variant,,ENST00000533953,;CMTM1,downstream_gene_variant,,ENST00000332695,;CKLF-CMTM1,downstream_gene_variant,,ENST00000527729,;CMTM1,downstream_gene_variant,,ENST00000328020,;CMTM1,downstream_gene_variant,,ENST00000533666,;CMTM1,downstream_gene_variant,,ENST00000336328,;CKLF-CMTM1,downstream_gene_variant,,ENST00000529718,;CMTM1,downstream_gene_variant,,ENST00000457188,;RP11-403P17.2,downstream_gene_variant,,ENST00000568430,;CMTM2,intron_variant,,ENST00000569316,;CMTM1,downstream_gene_variant,,ENST00000533078,;CMTM1,downstream_gene_variant,,ENST00000528484,;CMTM1,downstream_gene_variant,,ENST00000465057,;CMTM1,downstream_gene_variant,,ENST00000529386,;CMTM1,downstream_gene_variant,,ENST00000528441,;CMTM1,downstream_gene_variant,,ENST00000533915,;CMTM1,downstream_gene_variant,,ENST00000333001,;CMTM1,downstream_gene_variant,,ENST00000530141,;CMTM1,downstream_gene_variant,,ENST00000534143,;CMTM1,downstream_gene_variant,,ENST00000479381,;	C	ENSG00000140932	ENST00000268595	Transcript	missense_variant	418	267	89	E/D	gaG/gaC	rs761550400	.	.	1	CMTM2	HGNC	19173	protein_coding	YES	CCDS10814.1	ENSP00000268595	CKLF2_HUMAN	.	UPI0000073CB1	.	tolerated(0.18)	probably_damaging(0.953)	1/4	.	PROSITE_profiles:PS51225,hmmpanther:PTHR22776:SF15,hmmpanther:PTHR22776	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGAGATCAA	byFrequency	5	ESCA
FHOD1	0	.	GRCh37	16	67268058	67268058	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1548G>A	p.%3D	p.K516K	ENST00000258201	13/22	107	89	18	120	120	0	FHOD1,synonymous_variant,p.%3D,ENST00000258201,;TMEM208,downstream_gene_variant,,ENST00000304800,;TMEM208,downstream_gene_variant,,ENST00000563953,;TMEM208,downstream_gene_variant,,ENST00000565201,;TMEM208,downstream_gene_variant,,ENST00000563426,;FHOD1,3_prime_UTR_variant,,ENST00000561922,;FHOD1,3_prime_UTR_variant,,ENST00000568595,;FHOD1,non_coding_transcript_exon_variant,,ENST00000567752,;FHOD1,upstream_gene_variant,,ENST00000567561,;SLC9A5,upstream_gene_variant,,ENST00000564704,;TMEM208,downstream_gene_variant,,ENST00000564649,;TMEM208,downstream_gene_variant,,ENST00000563168,;FHOD1,upstream_gene_variant,,ENST00000567509,;FHOD1,upstream_gene_variant,,ENST00000566006,;TMEM208,downstream_gene_variant,,ENST00000567193,;FHOD1,downstream_gene_variant,,ENST00000562266,;TMEM208,downstream_gene_variant,,ENST00000562235,;FHOD1,upstream_gene_variant,,ENST00000569888,;TMEM208,downstream_gene_variant,,ENST00000563271,;FHOD1,upstream_gene_variant,,ENST00000569085,;	T	ENSG00000135723	ENST00000258201	Transcript	synonymous_variant	1796	1548	516	K	aaG/aaA	.	.	.	-1	FHOD1	HGNC	17905	protein_coding	YES	CCDS10834.1	ENSP00000258201	FHOD1_HUMAN	.	UPI000013CFB9	.	.	.	13/22	.	hmmpanther:PTHR23213:SF189,hmmpanther:PTHR23213	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCCTTGGG	.	5	ESCA
ZFP90	0	.	GRCh37	16	68598471	68598471	+	Missense_Mutation	SNP	C	C	A	rs375588905	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1781C>A	p.Thr594Asn	p.T594N	ENST00000570495	5/5	90	66	24	56	56	0	ZFP90,missense_variant,p.Thr594Asn,ENST00000563169,;ZFP90,missense_variant,p.Thr594Asn,ENST00000398253,;ZFP90,missense_variant,p.Thr594Asn,ENST00000570495,;ZFP90,intron_variant,,ENST00000573113,;ZFP90,downstream_gene_variant,,ENST00000573685,;ZFP90,downstream_gene_variant,,ENST00000562156,;ZFP90,downstream_gene_variant,,ENST00000564323,;ZFP90,3_prime_UTR_variant,,ENST00000564558,;ZFP90,non_coding_transcript_exon_variant,,ENST00000571720,;ZFP90,downstream_gene_variant,,ENST00000571809,;ZFP90,downstream_gene_variant,,ENST00000576805,;ZFP90,downstream_gene_variant,,ENST00000569323,;	A	ENSG00000184939	ENST00000570495	Transcript	missense_variant	2073	1781	594	T/N	aCc/aAc	rs375588905,COSM3421113	.	.	1	ZFP90	HGNC	23329	protein_coding	YES	CCDS42183.1	ENSP00000460547	ZFP90_HUMAN	I3L3M0_HUMAN,I3L1L4_HUMAN,H3BVC6_HUMAN	UPI000004C096	.	deleterious(0.03)	possibly_damaging(0.858)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF143,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAACCAACC	byFrequency|byCluster	5	ESCA
HYDIN	0	.	GRCh37	16	70942309	70942309	+	Missense_Mutation	SNP	C	C	T	rs774403280	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8242G>A	p.Ala2748Thr	p.A2748T	ENST00000393567	49/86	61	41	20	68	68	0	HYDIN,missense_variant,p.Ala2748Thr,ENST00000393567,;HYDIN,non_coding_transcript_exon_variant,,ENST00000309900,;	T	ENSG00000157423	ENST00000393567	Transcript	missense_variant	8393	8242	2748	A/T	Gcc/Acc	rs774403280	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	possibly_damaging(0.908)	49/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	ATTGGCTGGCA	.	3	ESCA
LDHD	0	.	GRCh37	16	75147474	75147474	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114A>G	p.Asn372Asp	p.N372D	ENST00000300051	8/11	49	25	24	42	42	0	LDHD,missense_variant,p.Asn372Asp,ENST00000300051,;LDHD,missense_variant,p.Asn349Asp,ENST00000450168,;ZNRF1,downstream_gene_variant,,ENST00000320619,;ZNRF1,downstream_gene_variant,,ENST00000568351,;ZNRF1,downstream_gene_variant,,ENST00000335325,;RP11-252E2.1,upstream_gene_variant,,ENST00000499110,;LDHD,downstream_gene_variant,,ENST00000569876,;ZNRF1,downstream_gene_variant,,ENST00000568844,;LDHD,downstream_gene_variant,,ENST00000568164,;	C	ENSG00000166816	ENST00000300051	Transcript	missense_variant	1161	1114	372	N/D	Aat/Gat	.	.	.	-1	LDHD	HGNC	19708	protein_coding	YES	CCDS10913.1	ENSP00000300051	LDHD_HUMAN	.	UPI0000062302	.	tolerated(0.76)	benign(0.019)	8/11	.	hmmpanther:PTHR11748:SF72,hmmpanther:PTHR11748,Pfam_domain:PF02913,Superfamily_domains:SSF55103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCATTGTGCC	.	5	ESCA
ZCCHC14	0	.	GRCh37	16	87440245	87440245	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3641C>T	.	.	ENST00000268616	13/13	23	16	7	25	25	0	ZCCHC14,3_prime_UTR_variant,,ENST00000268616,;ZCCHC14,downstream_gene_variant,,ENST00000561928,;MAP1LC3B,downstream_gene_variant,,ENST00000268607,;MAP1LC3B,downstream_gene_variant,,ENST00000565788,;MAP1LC3B,downstream_gene_variant,,ENST00000534986,;ZCCHC14,3_prime_UTR_variant,,ENST00000568020,;MAP1LC3B,downstream_gene_variant,,ENST00000570189,;MAP1LC3B,downstream_gene_variant,,ENST00000564844,;	A	ENSG00000140948	ENST00000268616	Transcript	3_prime_UTR_variant	6709	.	.	.	.	.	.	.	-1	ZCCHC14	HGNC	24134	protein_coding	YES	CCDS10961.1	ENSP00000268616	ZCH14_HUMAN	.	UPI00000705C4	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAACGCACGT	.	2	ESCA
SARM1	0	.	GRCh37	17	26708470	26708470	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617C>A	p.Ala206Glu	p.A206E	ENST00000457710	2/9	15	11	4	20	20	0	SARM1,missense_variant,p.Ala206Glu,ENST00000457710,;TMEM199,synonymous_variant,p.%3D,ENST00000509083,;SARM1,upstream_gene_variant,,ENST00000578128,;SARM1,non_coding_transcript_exon_variant,,ENST00000379061,;CTB-96E2.3,non_coding_transcript_exon_variant,,ENST00000591482,;SARM1,upstream_gene_variant,,ENST00000582323,;SARM1,upstream_gene_variant,,ENST00000003834,;SARM1,upstream_gene_variant,,ENST00000577870,;	A	ENSG00000004139	ENST00000457710	Transcript	missense_variant	1088	617	206	A/E	gCg/gAg	.	.	.	1	SARM1	HGNC	17074	protein_coding	YES	.	ENSP00000406738	.	.	UPI0000042801	.	tolerated(1)	benign(0.081)	2/9	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR22998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGGCGGTGC	.	2	ESCA
CPD	0	.	GRCh37	17	28706683	28706683	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.685C>A	p.Pro229Thr	p.P229T	ENST00000225719	1/21	22	15	6	15	15	0	CPD,missense_variant,p.Pro229Thr,ENST00000225719,;CPD,upstream_gene_variant,,ENST00000543464,;CPD,non_coding_transcript_exon_variant,,ENST00000583275,;	A	ENSG00000108582	ENST00000225719	Transcript	missense_variant	761	685	229	P/T	Ccc/Acc	.	.	.	1	CPD	HGNC	2301	protein_coding	YES	CCDS11257.1	ENSP00000225719	CBPD_HUMAN	.	UPI000000DAF7	.	tolerated(0.22)	benign(0.06)	1/21	.	hmmpanther:PTHR11532:SF40,hmmpanther:PTHR11532,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGAACCCCCC	.	5	ESCA
UNC45B	0	.	GRCh37	17	33495370	33495370	+	Missense_Mutation	SNP	G	G	A	rs201142835	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1442G>A	p.Arg481His	p.R481H	ENST00000268876	10/20	22	18	4	19	19	0	UNC45B,missense_variant,p.Arg481His,ENST00000378449,;UNC45B,missense_variant,p.Arg481His,ENST00000433649,;UNC45B,missense_variant,p.Arg481His,ENST00000268876,;UNC45B,missense_variant,p.Arg481His,ENST00000591048,;UNC45B,missense_variant,p.Arg481His,ENST00000394570,;RP11-799D4.3,upstream_gene_variant,,ENST00000585646,;	A	ENSG00000141161	ENST00000268876	Transcript	missense_variant	1539	1442	481	R/H	cGc/cAc	rs201142835,COSM560251	.	.	1	UNC45B	HGNC	14304	protein_coding	YES	CCDS11292.1	ENSP00000268876	UN45B_HUMAN	.	UPI0000074455	.	deleterious(0)	probably_damaging(0.999)	10/20	.	hmmpanther:PTHR22904:SF299,hmmpanther:PTHR22904,Pfam_domain:PF11701,Superfamily_domains:SSF48371	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GATCCGCACAC	byCluster|by1000G	2	ESCA
PSME3	0	.	GRCh37	17	40990730	40990730	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427A>G	p.Ile143Val	p.I143V	ENST00000293362	7/11	30	26	4	38	38	0	PSME3,missense_variant,p.Ile143Val,ENST00000293362,;PSME3,intron_variant,,ENST00000590720,;PSME3,intron_variant,,ENST00000589469,;PSME3,intron_variant,,ENST00000441946,;PSME3,intron_variant,,ENST00000585805,;PSME3,intron_variant,,ENST00000586114,;PSME3,intron_variant,,ENST00000541124,;PSME3,intron_variant,,ENST00000545225,;PSME3,intron_variant,,ENST00000592169,;PSME3,intron_variant,,ENST00000591152,;PSME3,downstream_gene_variant,,ENST00000592578,;PSME3,intron_variant,,ENST00000593111,;PSME3,intron_variant,,ENST00000586312,;PSME3,intron_variant,,ENST00000543428,;PSME3,downstream_gene_variant,,ENST00000591722,;	G	ENSG00000131467	ENST00000293362	Transcript	missense_variant	588	427	143	I/V	Ata/Gta	.	.	.	1	PSME3	HGNC	9570	protein_coding	YES	CCDS11442.1	ENSP00000293362	PSME3_HUMAN	.	UPI000002B1BA	.	tolerated_low_confidence(1)	benign(0)	7/11	.	hmmpanther:PTHR10660,hmmpanther:PTHR10660:SF4,Pfam_domain:PF02252,Gene3D:1.20.120.180,Superfamily_domains:SSF47216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCATATATGT	.	4	ESCA
ABCA6	0	.	GRCh37	17	67109433	67109433	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1971G>A	p.%3D	p.L657L	ENST00000284425	15/39	69	17	52	79	79	0	ABCA6,synonymous_variant,p.%3D,ENST00000284425,;ABCA6,downstream_gene_variant,,ENST00000592493,;ABCA6,non_coding_transcript_exon_variant,,ENST00000589803,;ABCA6,non_coding_transcript_exon_variant,,ENST00000590311,;	T	ENSG00000154262	ENST00000284425	Transcript	synonymous_variant	2146	1971	657	L	ctG/ctA	.	.	.	-1	ABCA6	HGNC	36	protein_coding	YES	CCDS11683.1	ENSP00000284425	ABCA6_HUMAN	.	UPI000013DD9D	.	.	.	15/39	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229:SF13,hmmpanther:PTHR19229,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCAGGAG	.	5	ESCA
EXOC7	0	.	GRCh37	17	74097765	74097765	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306A>C	p.Arg102Ser	p.R102S	ENST00000335146	3/20	58	43	14	49	49	0	EXOC7,missense_variant,p.Arg102Ser,ENST00000332065,;EXOC7,missense_variant,p.Arg102Ser,ENST00000335146,;EXOC7,missense_variant,p.Arg121Ser,ENST00000589507,;EXOC7,missense_variant,p.Arg61Ser,ENST00000467929,;EXOC7,missense_variant,p.Arg49Ser,ENST00000442951,;EXOC7,missense_variant,p.Arg102Ser,ENST00000411744,;EXOC7,missense_variant,p.Arg102Ser,ENST00000406660,;EXOC7,missense_variant,p.Arg102Ser,ENST00000589210,;EXOC7,missense_variant,p.Arg102Ser,ENST00000405575,;EXOC7,missense_variant,p.Arg102Ser,ENST00000607838,;EXOC7,missense_variant,p.Arg57Ser,ENST00000357231,;EXOC7,intron_variant,,ENST00000420116,;EXOC7,non_coding_transcript_exon_variant,,ENST00000405068,;	G	ENSG00000182473	ENST00000335146	Transcript	missense_variant	360	306	102	R/S	agA/agC	.	.	.	-1	EXOC7	HGNC	23214	protein_coding	YES	CCDS45782.1	ENSP00000334100	EXOC7_HUMAN	C9JME6_HUMAN,C9JKC2_HUMAN	UPI00001AFC78	.	deleterious(0)	benign(0.119)	3/20	.	Superfamily_domains:SSF74788,hmmpanther:PTHR12542:SF7,hmmpanther:PTHR12542	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCTCTGAT	.	5	ESCA
SENP3	0	.	GRCh37	17	7475192	7475192	+	Intron	SNP	T	T	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*387+4T>A	.	.	ENST00000429205	.	30	22	8	33	32	1	SENP3,splice_region_variant,,ENST00000429205,;SENP3,downstream_gene_variant,,ENST00000321337,;EIF4A1,upstream_gene_variant,,ENST00000584784,;EIF4A1,upstream_gene_variant,,ENST00000583802,;EIF4A1,upstream_gene_variant,,ENST00000581384,;EIF4A1,upstream_gene_variant,,ENST00000585024,;SENP3,downstream_gene_variant,,ENST00000582789,;EIF4A1,upstream_gene_variant,,ENST00000577929,;SENP3,downstream_gene_variant,,ENST00000581093,;EIF4A1,upstream_gene_variant,,ENST00000380512,;EIF4A1,upstream_gene_variant,,ENST00000584860,;SENP3,downstream_gene_variant,,ENST00000580231,;EIF4A1,upstream_gene_variant,,ENST00000582169,;EIF4A1,upstream_gene_variant,,ENST00000578495,;EIF4A1,upstream_gene_variant,,ENST00000578754,;EIF4A1,upstream_gene_variant,,ENST00000582746,;EIF4A1,upstream_gene_variant,,ENST00000293831,;EIF4A1,upstream_gene_variant,,ENST00000581770,;EIF4A1,upstream_gene_variant,,ENST00000583389,;EIF4A1,upstream_gene_variant,,ENST00000577269,;SNORD10,upstream_gene_variant,,ENST00000459579,;SNORA48,upstream_gene_variant,,ENST00000386847,;SENP3,non_coding_transcript_exon_variant,,ENST00000578813,;SENP3,non_coding_transcript_exon_variant,,ENST00000578868,;SENP3-EIF4A1,intron_variant,,ENST00000579777,;SENP3,downstream_gene_variant,,ENST00000580042,;SNORA67,upstream_gene_variant,,ENST00000581621,;SENP3,non_coding_transcript_exon_variant,,ENST00000581010,;EIF4A1,upstream_gene_variant,,ENST00000584798,;EIF4A1,upstream_gene_variant,,ENST00000577738,;EIF4A1,upstream_gene_variant,,ENST00000582213,;EIF4A1,upstream_gene_variant,,ENST00000580888,;EIF4A1,upstream_gene_variant,,ENST00000578476,;EIF4A1,upstream_gene_variant,,ENST00000582848,;EIF4A1,upstream_gene_variant,,ENST00000580886,;EIF4A1,upstream_gene_variant,,ENST00000577731,;EIF4A1,upstream_gene_variant,,ENST00000584054,;EIF4A1,upstream_gene_variant,,ENST00000580461,;EIF4A1,upstream_gene_variant,,ENST00000578324,;EIF4A1,upstream_gene_variant,,ENST00000584712,;EIF4A1,upstream_gene_variant,,ENST00000396527,;EIF4A1,upstream_gene_variant,,ENST00000584901,;EIF4A1,upstream_gene_variant,,ENST00000581544,;EIF4A1,upstream_gene_variant,,ENST00000579085,;EIF4A1,upstream_gene_variant,,ENST00000579139,;EIF4A1,upstream_gene_variant,,ENST00000583899,;	A	ENSG00000161956	ENST00000429205	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	SENP3	HGNC	17862	protein_coding	YES	.	ENSP00000403712	SENP3_HUMAN	.	UPI0000163BE7	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	ATATATATATA	.	2	ESCA
TP53	0	.	GRCh37	17	7578427	7578427	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.503A>G	p.His168Arg	p.H168R	ENST00000269305	5/11	26	10	16	44	44	0	TP53,missense_variant,p.His168Arg,ENST00000413465,;TP53,missense_variant,p.His168Arg,ENST00000420246,;TP53,missense_variant,p.His168Arg,ENST00000269305,;TP53,missense_variant,p.His36Arg,ENST00000509690,;TP53,missense_variant,p.His168Arg,ENST00000359597,;TP53,missense_variant,p.His75Arg,ENST00000514944,;TP53,missense_variant,p.His168Arg,ENST00000445888,;TP53,missense_variant,p.His168Arg,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	693	503	168	H/R	cAc/cGc	TP53_g.12491A>C,TP53_g.12491A>G,TP53_g.12491A>T,COSM43545,COSM44801,COSM96590,COSM44808,COSM3388206,COSM1480069,COSM562629,COSM3388209,COSM1480070,COSM562630,COSM1480072,COSM3388211,COSM562632,COSM3388208,COSM4139873,COSM3388207,COSM1649383,COSM4139872,COSM1480071,COSM3388210,COSM562631	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	possibly_damaging(0.733)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H75R|c.224A>G|3,SITE|p.H168R|c.503A>G|15,SITE|p.H168R|c.503A>G|3,SITE|p.H168R|c.503A>G|3,SITE|p.H168R|c.503A>G|3,SITE|p.H168R|c.503A>G|3,SITE|p.H36R|c.107A>G|3,CODON|p.0?|c.1_1182del1182|6,CODON|p.H168H|c.504C>T|4,CODON|p.H168L|c.503A>T|6,CODON|p.H168P|c.503A>C|12,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.E171G|c.512A>G|3,BUFFER|p.E78*|c.232G>T|4,BUFFER|p.E171*|c.511G>T|4,BUFFER|p.E171Q|c.511G>C|4,BUFFER|p.E39*|c.115G>T|4,BUFFER|p.E171*|c.511G>T|13,BUFFER|p.E171*|c.511G>T|4,BUFFER|p.E171K|c.511G>A|9,BUFFER|p.T170T|c.510G>A|6,BUFFER|p.T170M|c.509C>T|7,BUFFER|p.M169I|c.507G>A|7,BUFFER|p.M169T|c.506T>C|4,BUFFER|p.M169V|c.505A>G|3,BUFFER|p.H168Y|c.502C>T|9,BUFFER|p.Q167fs*13|c.499_500delCA|3,BUFFER|p.Q167Q|c.501G>A|3,BUFFER|p.Q167R|c.500A>G|4,BUFFER|p.Q167L|c.500A>T|3,BUFFER|p.Q167*|c.499C>T|5,BUFFER|p.Q167*|c.499C>T|5,BUFFER|p.Q167*|c.499C>T|26,BUFFER|p.Q35*|c.103C>T|5,BUFFER|p.Q74*|c.220C>T|5,BUFFER|p.Q167fs*14|c.497_498insC|3,BUFFER|p.S166*|c.497C>A|8,BUFFER|p.S166L|c.497C>T|5,BUFFER|p.S166*|c.497C>G|11,BUFFER|p.S166P|c.496T>C|6,BUFFER|p.Q165L|c.494A>T|3,BUFFER|p.Q72*|c.214C>T|6,BUFFER|p.Q33*|c.97C>T|6,BUFFER|p.Q165*|c.493C>T|30,BUFFER|p.Q165*|c.493C>T|6,BUFFER|p.Q165*|c.493C>T|4,BUFFER|p.Q165*|c.493C>T|6,BUFFER|p.Q165*|c.493C>T|4,BUFFER|p.K164N|c.492G>T|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATGTGCTGT	.	5	ESCA
ENPP7	0	.	GRCh37	17	77708928	77708928	+	Silent	SNP	C	C	T	rs77624421	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486C>T	p.%3D	p.I162I	ENST00000328313	3/6	51	15	36	48	48	0	ENPP7,synonymous_variant,p.%3D,ENST00000328313,;ENPP7,upstream_gene_variant,,ENST00000576512,;	T	ENSG00000182156	ENST00000328313	Transcript	synonymous_variant	707	486	162	I	atC/atT	rs77624421	.	.	1	ENPP7	HGNC	23764	protein_coding	YES	CCDS11763.1	ENSP00000332656	ENPP7_HUMAN	I3L3G5_HUMAN	UPI00001983C8	.	.	.	3/6	.	hmmpanther:PTHR10151:SF63,hmmpanther:PTHR10151,Gene3D:3.40.720.10,Pfam_domain:PF01663,Superfamily_domains:SSF53649	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	T:0.0009	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCATCGCACA	byFrequency|byCluster|by1000G	5	ESCA
ZNF750	0	.	GRCh37	17	80790167	80790167	+	Nonsense_Mutation	SNP	A	A	C	rs749514638	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.164T>G	p.Leu55Ter	p.L55*	ENST00000269394	2/3	69	19	50	59	59	0	ZNF750,stop_gained,p.Leu55Ter,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	C	ENSG00000141579	ENST00000269394	Transcript	stop_gained	998	164	55	L/*	tTa/tGa	rs749514638	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678,Pfam_domain:PF15269	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACTAAAGTA	.	5	ESCA
MEP1B	0	.	GRCh37	18	29784155	29784155	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.379T>C	p.Ser127Pro	p.S127P	ENST00000269202	7/15	116	95	20	117	117	0	MEP1B,missense_variant,p.Ser127Pro,ENST00000269202,;MEP1B,missense_variant,p.Ser95Pro,ENST00000581184,;MEP1B,missense_variant,p.Ser127Pro,ENST00000581447,;GAREM,intron_variant,,ENST00000583696,;MEP1B,downstream_gene_variant,,ENST00000579919,;	C	ENSG00000141434	ENST00000269202	Transcript	missense_variant	426	379	127	S/P	Tca/Cca	.	.	.	1	MEP1B	HGNC	7020	protein_coding	YES	CCDS45846.1	ENSP00000269202	MEP1B_HUMAN	J3KRK1_HUMAN	UPI0000201B8B	.	tolerated(0.17)	possibly_damaging(0.892)	7/15	.	hmmpanther:PTHR10127:SF312,hmmpanther:PTHR10127,Pfam_domain:PF01400,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001196,SMART_domains:SM00235,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCTTCAGTA	.	5	ESCA
C18orf54	0	.	GRCh37	18	51888438	51888438	+	Intron	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.589+120T>C	.	.	ENST00000300091	.	44	41	3	42	42	0	C18orf54,missense_variant,p.Tyr237His,ENST00000382911,;C18orf54,intron_variant,,ENST00000578138,;C18orf54,intron_variant,,ENST00000300091,;STARD6,upstream_gene_variant,,ENST00000581310,;STARD6,upstream_gene_variant,,ENST00000584040,;STARD6,upstream_gene_variant,,ENST00000577499,;C18orf54,upstream_gene_variant,,ENST00000582188,;	C	ENSG00000166845	ENST00000300091	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C18orf54	HGNC	13796	protein_coding	YES	CCDS11956.1	ENSP00000300091	LAS2_HUMAN	J3KS56_HUMAN,J3KRX3_HUMAN,I7HAS0_HUMAN,I7GY12_HUMAN	UPI0000074279	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAATTACCCA	.	2	ESCA
SOCS6	0	.	GRCh37	18	67992415	67992415	+	Missense_Mutation	SNP	G	G	A	rs755164587	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.511G>A	p.Val171Ile	p.V171I	ENST00000397942	2/2	53	27	25	35	35	0	SOCS6,missense_variant,p.Val171Ile,ENST00000578377,;SOCS6,missense_variant,p.Val171Ile,ENST00000397942,;SOCS6,missense_variant,p.Val171Ile,ENST00000582322,;	A	ENSG00000170677	ENST00000397942	Transcript	missense_variant	827	511	171	V/I	Gtc/Atc	rs755164587,COSM194425	.	.	1	SOCS6	HGNC	16833	protein_coding	YES	CCDS11998.1	ENSP00000381034	SOCS6_HUMAN	J3KTM7_HUMAN	UPI0000072C28	.	tolerated_low_confidence(0.22)	benign(0.022)	2/2	.	hmmpanther:PTHR10385:SF25,hmmpanther:PTHR10385	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGCGTCCGG	.	5	ESCA
FBXO15	0	.	GRCh37	18	71797743	71797743	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483delA	p.Lys161AsnfsTer3	p.K161Nfs*3	ENST00000419743	4/10	64	57	7	64	64	0	FBXO15,frameshift_variant,p.Lys124AsnfsTer3,ENST00000582526,;FBXO15,frameshift_variant,p.Lys161AsnfsTer3,ENST00000419743,;FBXO15,frameshift_variant,p.Lys85AsnfsTer3,ENST00000269500,;FBXO15,upstream_gene_variant,,ENST00000579517,;FBXO15,3_prime_UTR_variant,,ENST00000583443,;FBXO15,3_prime_UTR_variant,,ENST00000585174,;FBXO15,3_prime_UTR_variant,,ENST00000581214,;FBXO15,intron_variant,,ENST00000578399,;FBXO15,downstream_gene_variant,,ENST00000580552,;	-	ENSG00000141665	ENST00000419743	Transcript	frameshift_variant	563	483	161	K/X	aaA/aa	.	.	.	-1	FBXO15	HGNC	13617	protein_coding	YES	CCDS45884.1	ENSP00000393154	FBX15_HUMAN	J3QRE7_HUMAN	UPI00003CF23D	.	.	.	4/10	.	hmmpanther:PTHR20995:SF16,hmmpanther:PTHR20995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TATTTGTTTTGT	.	3	ESCA
NOTCH3	0	.	GRCh37	19	15289708	15289721	+	Frame_Shift_Del	DEL	ATGGCTGGGACTCG	ATGGCTGGGACTCG	-	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	ATGGCTGGGACTCG	ATGGCTGGGACTCG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3750_3763delCGAGTCCCAGCCAT	p.Cys1250TrpfsTer10	p.C1250Wfs*10	ENST00000263388	23/33	97	81	16	84	84	0	NOTCH3,frameshift_variant,p.Cys1250TrpfsTer10,ENST00000263388,;NOTCH3,frameshift_variant,p.Cys1197TrpfsTer10,ENST00000601011,;NOTCH3,non_coding_transcript_exon_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,;	-	ENSG00000074181	ENST00000263388	Transcript	frameshift_variant	3826-3839	3750-3763	1250-1255	CESQPC/WX	tgCGAGTCCCAGCCATgc/tggc	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	.	.	23/33	.	Superfamily_domains:SSF57184,Superfamily_domains:SSF57196,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Gene3D:2gy5A03,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTGGCATGGCTGGGACTCGCAGGG	.	3	ESCA
SIN3B	0	.	GRCh37	19	16980490	16980490	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2122G>A	p.Ala708Thr	p.A708T	ENST00000379803	14/20	99	76	23	77	76	1	SIN3B,missense_variant,p.Ala266Thr,ENST00000595541,;SIN3B,missense_variant,p.Ala676Thr,ENST00000248054,;SIN3B,missense_variant,p.Ala708Thr,ENST00000379803,;SIN3B,downstream_gene_variant,,ENST00000599880,;SIN3B,upstream_gene_variant,,ENST00000595900,;SIN3B,downstream_gene_variant,,ENST00000594372,;SIN3B,upstream_gene_variant,,ENST00000602204,;	A	ENSG00000127511	ENST00000379803	Transcript	missense_variant	2136	2122	708	A/T	Gcc/Acc	.	.	.	1	SIN3B	HGNC	19354	protein_coding	YES	CCDS32946.1	ENSP00000369131	SIN3B_HUMAN	.	UPI0000425EFA	.	tolerated(0.19)	benign(0.002)	14/20	.	hmmpanther:PTHR12346,hmmpanther:PTHR12346:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGCCTCC	.	4	ESCA
ZNF257	0	.	GRCh37	19	22272088	22272088	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1536G>A	p.%3D	p.E512E	ENST00000594947	4/4	120	102	17	82	82	0	ZNF257,synonymous_variant,p.%3D,ENST00000594947,;ZNF257,downstream_gene_variant,,ENST00000597927,;ZNF257,downstream_gene_variant,,ENST00000600162,;ZNF257,3_prime_UTR_variant,,ENST00000435820,;	A	ENSG00000197134	ENST00000594947	Transcript	synonymous_variant	1680	1536	512	E	gaG/gaA	.	.	.	1	ZNF257	HGNC	13498	protein_coding	YES	CCDS46030.1	ENSP00000470209	ZN257_HUMAN	M0R0N1_HUMAN	UPI0000E045CA	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF109,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGAGAAACC	.	4	ESCA
SGTA	0	.	GRCh37	19	2762546	2762546	+	Silent	SNP	G	G	A	rs747018743	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>T	p.%3D	p.N198N	ENST00000221566	7/12	22	15	7	22	22	0	SGTA,synonymous_variant,p.%3D,ENST00000221566,;SGTA,downstream_gene_variant,,ENST00000589251,;SGTA,upstream_gene_variant,,ENST00000591984,;	A	ENSG00000104969	ENST00000221566	Transcript	synonymous_variant	756	594	198	N	aaC/aaT	rs747018743,COSM3531902	.	.	-1	SGTA	HGNC	10819	protein_coding	YES	CCDS12094.1	ENSP00000221566	SGTA_HUMAN	K7ERW5_HUMAN,K7EMD6_HUMAN	UPI000013592E	.	.	.	7/12	.	hmmpanther:PTHR22904:SF316,hmmpanther:PTHR22904,Gene3D:1.25.40.10,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAGGTTGGA	byFrequency	5	ESCA
C19orf12	0	.	GRCh37	19	30193514	30193514	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*105C>G	.	.	ENST00000392278	3/3	24	14	10	43	43	0	C19orf12,3_prime_UTR_variant,,ENST00000392276,;C19orf12,3_prime_UTR_variant,,ENST00000392278,;C19orf12,3_prime_UTR_variant,,ENST00000323670,;C19orf12,3_prime_UTR_variant,,ENST00000592153,;C19orf12,downstream_gene_variant,,ENST00000591243,;C19orf12,non_coding_transcript_exon_variant,,ENST00000392275,;C19orf12,downstream_gene_variant,,ENST00000342680,;	C	ENSG00000131943	ENST00000392278	Transcript	3_prime_UTR_variant	691	.	.	.	.	.	.	.	-1	C19orf12	HGNC	25443	protein_coding	YES	CCDS42542.1	ENSP00000376103	CS012_HUMAN	K7EPS8_HUMAN	UPI0000DB2738	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGGAGATT	.	5	ESCA
GPI	0	.	GRCh37	19	34855878	34855878	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64C>T	p.Pro22Ser	p.P22S	ENST00000415930	1/18	37	30	7	34	34	0	GPI,missense_variant,p.Pro22Ser,ENST00000415930,;GPI,missense_variant,p.Pro22Ser,ENST00000587521,;GPI,missense_variant,p.Pro22Ser,ENST00000592277,;GPI,missense_variant,p.Pro22Ser,ENST00000587384,;GPI,upstream_gene_variant,,ENST00000591204,;GPI,upstream_gene_variant,,ENST00000590375,;GPI,upstream_gene_variant,,ENST00000589399,;GPI,upstream_gene_variant,,ENST00000588991,;GPI,upstream_gene_variant,,ENST00000589640,;GPI,upstream_gene_variant,,ENST00000586425,;GPI,upstream_gene_variant,,ENST00000356487,;GPI,upstream_gene_variant,,ENST00000592144,;GPI,upstream_gene_variant,,ENST00000589504,;	T	ENSG00000105220	ENST00000415930	Transcript	missense_variant	234	64	22	P/S	Ccc/Tcc	.	.	.	1	GPI	HGNC	4458	protein_coding	YES	CCDS54246.1	ENSP00000405573	G6PI_HUMAN	K7EPY4_HUMAN,K7ERK8_HUMAN,K7ELR7_HUMAN,K7EIL4_HUMAN,B4DE36_HUMAN	UPI00017A6DE4	.	tolerated_low_confidence(0.39)	benign(0.014)	1/18	.	hmmpanther:PTHR11469,hmmpanther:PTHR11469:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCCCCACT	.	5	ESCA
OPA3	0	.	GRCh37	19	46032328	46032328	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.529G>A	p.Ala177Thr	p.A177T	ENST00000323060	2/2	16	8	8	17	17	0	OPA3,missense_variant,p.Ala177Thr,ENST00000323060,;VASP,downstream_gene_variant,,ENST00000245932,;VASP,downstream_gene_variant,,ENST00000587444,;VASP,downstream_gene_variant,,ENST00000588273,;VASP,downstream_gene_variant,,ENST00000588463,;VASP,downstream_gene_variant,,ENST00000586014,;VASP,downstream_gene_variant,,ENST00000588482,;	T	ENSG00000125741	ENST00000323060	Transcript	missense_variant	607	529	177	A/T	Gcg/Acg	.	.	.	-1	OPA3	HGNC	8142	protein_coding	YES	CCDS33052.1	ENSP00000319817	OPA3_HUMAN	.	UPI0000140FD5	.	tolerated_low_confidence(0.63)	benign(0.008)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12499,hmmpanther:PTHR12499:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACGCCGGCG	.	5	ESCA
DPP9	0	.	GRCh37	19	4689690	4689690	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1641C>G	p.%3D	p.T547T	ENST00000262960	15/22	25	12	13	45	45	0	DPP9,synonymous_variant,p.%3D,ENST00000262960,;DPP9,synonymous_variant,p.%3D,ENST00000598800,;DPP9,synonymous_variant,p.%3D,ENST00000594671,;DPP9,synonymous_variant,p.%3D,ENST00000595327,;DPP9,downstream_gene_variant,,ENST00000597849,;DPP9,upstream_gene_variant,,ENST00000601720,;AC005594.3,downstream_gene_variant,,ENST00000381796,;DPP9,upstream_gene_variant,,ENST00000601173,;DPP9,non_coding_transcript_exon_variant,,ENST00000597145,;DPP9,non_coding_transcript_exon_variant,,ENST00000599998,;DPP9,non_coding_transcript_exon_variant,,ENST00000597253,;DPP9,downstream_gene_variant,,ENST00000599163,;DPP9,downstream_gene_variant,,ENST00000601764,;DPP9,upstream_gene_variant,,ENST00000597900,;	C	ENSG00000142002	ENST00000262960	Transcript	synonymous_variant	1919	1641	547	T	acC/acG	.	.	.	-1	DPP9	HGNC	18648	protein_coding	YES	CCDS45928.1	ENSP00000262960	DPP9_HUMAN	M0R3E8_HUMAN,M0R3C4_HUMAN,M0R2G6_HUMAN,M0R145_HUMAN,M0R0I1_HUMAN,M0QXN4_HUMAN,M0QXG6_HUMAN	UPI000004DB00	.	.	.	15/22	.	hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF109,Gene3D:2.140.10.30,Pfam_domain:PF00930,Superfamily_domains:SSF82171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTGGTGCC	.	5	ESCA
KLK9	0	.	GRCh37	19	51506391	51506391	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729G>C	p.Trp243Cys	p.W243C	ENST00000376832	5/7	75	58	17	97	97	0	KLK9,missense_variant,p.Trp243Cys,ENST00000376832,;KLK9,missense_variant,p.Trp243Cys,ENST00000594211,;KLK8,upstream_gene_variant,,ENST00000291726,;KLK8,upstream_gene_variant,,ENST00000347619,;KLK8,upstream_gene_variant,,ENST00000391806,;KLK8,upstream_gene_variant,,ENST00000320838,;KLK8,upstream_gene_variant,,ENST00000600767,;KLK8,upstream_gene_variant,,ENST00000595238,;KLK8,upstream_gene_variant,,ENST00000593490,;CTB-147C22.9,intron_variant,,ENST00000594512,;KLK8,upstream_gene_variant,,ENST00000598195,;KLK9,missense_variant,p.Trp243Cys,ENST00000250366,;KLK9,missense_variant,p.Trp84Cys,ENST00000599166,;KLK9,3_prime_UTR_variant,,ENST00000544410,;KLK8,upstream_gene_variant,,ENST00000594669,;KLK8,upstream_gene_variant,,ENST00000599710,;	G	ENSG00000213022	ENST00000376832	Transcript	missense_variant	763	729	243	W/C	tgG/tgC	.	.	.	-1	KLK9	HGNC	6370	protein_coding	YES	CCDS12816.1	ENSP00000366028	KLK9_HUMAN	Q2XQG6_HUMAN,Q2XQG4_HUMAN	UPI000004CA0A	.	deleterious(0)	probably_damaging(1)	5/7	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24259:SF72,hmmpanther:PTHR24259,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATCCAGTC	.	5	ESCA
ZNF557	0	.	GRCh37	19	7083472	7083472	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1010A>T	p.Gln337Leu	p.Q337L	ENST00000414706	8/8	83	67	16	85	85	0	ZNF557,missense_variant,p.Gln337Leu,ENST00000414706,;ZNF557,missense_variant,p.Gln330Leu,ENST00000439035,;ZNF557,missense_variant,p.Gln337Leu,ENST00000252840,;CTB-25J19.9,upstream_gene_variant,,ENST00000598826,;	T	ENSG00000130544	ENST00000414706	Transcript	missense_variant	1483	1010	337	Q/L	cAg/cTg	.	.	.	1	ZNF557	HGNC	28632	protein_coding	YES	CCDS42485.1	ENSP00000404065	ZN557_HUMAN	B2RD50_HUMAN	UPI000020324B	.	tolerated(0.58)	benign(0.016)	8/8	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF145,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACAGCACA	.	5	ESCA
PRAM1	0	.	GRCh37	19	8555253	8555253	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1944G>A	p.%3D	p.E648E	ENST00000423345	9/10	45	31	13	61	61	0	PRAM1,synonymous_variant,p.%3D,ENST00000255612,;PRAM1,synonymous_variant,p.%3D,ENST00000423345,;HNRNPM,downstream_gene_variant,,ENST00000596295,;HNRNPM,downstream_gene_variant,,ENST00000594907,;HNRNPM,downstream_gene_variant,,ENST00000325495,;HNRNPM,downstream_gene_variant,,ENST00000598999,;HNRNPM,downstream_gene_variant,,ENST00000597270,;HNRNPM,downstream_gene_variant,,ENST00000348943,;HNRNPM,downstream_gene_variant,,ENST00000600092,;HNRNPM,downstream_gene_variant,,ENST00000602219,;HNRNPM,downstream_gene_variant,,ENST00000597081,;PRAM1,non_coding_transcript_exon_variant,,ENST00000599698,;PRAM1,non_coding_transcript_exon_variant,,ENST00000594696,;HNRNPM,downstream_gene_variant,,ENST00000598603,;HNRNPM,downstream_gene_variant,,ENST00000600806,;	T	ENSG00000133246	ENST00000423345	Transcript	synonymous_variant	2465	1944	648	E	gaG/gaA	.	.	.	-1	PRAM1	HGNC	30091	protein_coding	YES	CCDS45954.2	ENSP00000408342	PRAM_HUMAN	.	UPI00001AE786	.	.	.	9/10	.	hmmpanther:PTHR16830:SF6,hmmpanther:PTHR16830,Gene3D:2.30.30.40,Pfam_domain:PF14603	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGTCTCCCT	.	5	ESCA
UFC1	0	.	GRCh37	1	161123890	161123890	+	Nonsense_Mutation	SNP	G	G	T	rs182746901	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103G>T	p.Glu35Ter	p.E35*	ENST00000368003	1/6	96	39	57	86	86	0	UFC1,stop_gained,p.Glu35Ter,ENST00000368003,;RP11-297K8.2,intron_variant,,ENST00000420498,;UFC1,non_coding_transcript_exon_variant,,ENST00000473766,;UFC1,non_coding_transcript_exon_variant,,ENST00000467540,;UFC1,non_coding_transcript_exon_variant,,ENST00000463735,;UFC1,non_coding_transcript_exon_variant,,ENST00000483191,;UFC1,intron_variant,,ENST00000482672,;	T	ENSG00000143222	ENST00000368003	Transcript	stop_gained	349	103	35	E/*	Gaa/Taa	rs182746901	.	.	1	UFC1	HGNC	26941	protein_coding	YES	CCDS1220.1	ENSP00000356982	UFC1_HUMAN	.	UPI00001275BD	.	.	.	1/6	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12921,Pfam_domain:PF08694,PIRSF_domain:PIRSF008716,Superfamily_domains:SSF54495	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGGAATAT	byCluster|by1000G	5	ESCA
ADAMTS4	0	.	GRCh37	1	161166195	161166195	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958-102G>A	.	.	ENST00000367996	.	16	7	9	20	20	0	ADAMTS4,3_prime_UTR_variant,,ENST00000367995,;ADAMTS4,intron_variant,,ENST00000367996,;NDUFS2,upstream_gene_variant,,ENST00000367993,;NDUFS2,upstream_gene_variant,,ENST00000496133,;ADAMTS4,upstream_gene_variant,,ENST00000478394,;NDUFS2,upstream_gene_variant,,ENST00000479948,;	T	ENSG00000158859	ENST00000367996	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ADAMTS4	HGNC	220	protein_coding	YES	CCDS1223.1	ENSP00000356975	ATS4_HUMAN	.	UPI000014194C	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCACTGTCA	.	5	ESCA
TADA1	0	.	GRCh37	1	166831610	166831610	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370C>T	p.Gln124Ter	p.Q124*	ENST00000367874	5/8	71	60	11	71	71	0	TADA1,stop_gained,p.Gln124Ter,ENST00000367874,;TADA1,non_coding_transcript_exon_variant,,ENST00000467021,;	A	ENSG00000152382	ENST00000367874	Transcript	stop_gained	464	370	124	Q/*	Caa/Taa	.	.	.	-1	TADA1	HGNC	30631	protein_coding	YES	CCDS1255.1	ENSP00000356848	TADA1_HUMAN	.	UPI00000709B6	.	.	.	5/8	.	hmmpanther:PTHR21277,Pfam_domain:PF12767	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATTGCTGGG	.	4	ESCA
DUSP27	0	.	GRCh37	1	167096645	167096645	+	Silent	SNP	G	G	A	rs139214807	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2277G>A	p.%3D	p.A759A	ENST00000361200	6/6	46	42	3	36	36	0	DUSP27,synonymous_variant,p.%3D,ENST00000361200,;DUSP27,synonymous_variant,p.%3D,ENST00000443333,;DUSP27,synonymous_variant,p.%3D,ENST00000271385,;DUSP27,intron_variant,,ENST00000485151,;	A	ENSG00000198842	ENST00000361200	Transcript	synonymous_variant	2443	2277	759	A	gcG/gcA	rs139214807	.	.	1	DUSP27	HGNC	25034	protein_coding	YES	CCDS30932.1	ENSP00000354483	DUS27_HUMAN	.	UPI000040DFF5	.	.	.	6/6	.	hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGCGGCTAG	byCluster	2	ESCA
MROH9	0	.	GRCh37	1	170985417	170985417	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1848C>G	p.Asp616Glu	p.D616E	ENST00000367759	17/22	122	87	35	96	96	0	MROH9,missense_variant,p.Asp616Glu,ENST00000367759,;MROH9,downstream_gene_variant,,ENST00000426136,;	G	ENSG00000117501	ENST00000367759	Transcript	missense_variant	2002	1848	616	D/E	gaC/gaG	.	.	.	1	MROH9	HGNC	26287	protein_coding	YES	CCDS53429.1	ENSP00000356733	MROH9_HUMAN	.	UPI0001B09232	.	deleterious(0)	probably_damaging(0.97)	17/22	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGACAAAGT	.	5	ESCA
C1orf105	0	.	GRCh37	1	172414300	172414300	+	Splice_Site	SNP	T	T	C	rs371586803	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.107+2T>C	.	p.X36_splice	ENST00000367727	.	54	41	13	57	57	0	C1orf105,splice_donor_variant,,ENST00000367727,;C1orf105,splice_donor_variant,,ENST00000488100,;PIGC,upstream_gene_variant,,ENST00000367728,;PIGC,upstream_gene_variant,,ENST00000258324,;PIGC,upstream_gene_variant,,ENST00000344529,;PIGC,upstream_gene_variant,,ENST00000478184,;PIGC,upstream_gene_variant,,ENST00000484368,;	C	ENSG00000180999	ENST00000367727	Transcript	splice_donor_variant	.	.	.	.	.	rs371586803	.	.	1	C1orf105	HGNC	29591	protein_coding	YES	CCDS1301.1	ENSP00000356700	CA105_HUMAN	.	UPI000006D456	.	.	.	.	2/6	.	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGGTAACCT	byCluster	5	ESCA
KIAA1614	0	.	GRCh37	1	180904863	180904863	+	Silent	SNP	G	G	A	rs377007881	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1818G>A	p.%3D	p.A606A	ENST00000367588	5/9	52	44	8	45	45	0	KIAA1614,synonymous_variant,p.%3D,ENST00000367588,;KIAA1614,synonymous_variant,p.%3D,ENST00000367587,;KIAA1614,intron_variant,,ENST00000483705,;	A	ENSG00000135835	ENST00000367588	Transcript	synonymous_variant	1873	1818	606	A	gcG/gcA	rs377007881	.	.	1	KIAA1614	HGNC	29327	protein_coding	YES	CCDS41442.1	ENSP00000356560	K1614_HUMAN	.	UPI00001C1D75	.	.	.	5/9	.	hmmpanther:PTHR17130,hmmpanther:PTHR17130:SF7	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGCGGAGGT	byFrequency|byCluster	4	ESCA
RGS1	0	.	GRCh37	1	192544903	192544903	+	5'UTR	SNP	G	G	A	rs772513476	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-20G>A	.	.	ENST00000367459	1/5	38	34	3	46	46	0	RGS1,5_prime_UTR_variant,,ENST00000469578,;RGS1,5_prime_UTR_variant,,ENST00000367459,;RGS1,non_coding_transcript_exon_variant,,ENST00000583155,;RGS1,non_coding_transcript_exon_variant,,ENST00000462589,;RGS1,non_coding_transcript_exon_variant,,ENST00000474373,;RGS1,upstream_gene_variant,,ENST00000498352,;	A	ENSG00000090104	ENST00000367459	Transcript	5_prime_UTR_variant	47	.	.	.	.	rs772513476	.	.	1	RGS1	HGNC	9991	protein_coding	YES	CCDS1375.2	ENSP00000356429	RGS1_HUMAN	.	UPI0000169CF2	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTAGCGCATAT	byFrequency	2	ESCA
CFH	0	.	GRCh37	1	196694303	196694303	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1749G>C	p.Lys583Asn	p.K583N	ENST00000367429	12/22	62	55	7	47	47	0	CFH,missense_variant,p.Lys583Asn,ENST00000367429,;CFH,non_coding_transcript_exon_variant,,ENST00000466229,;	C	ENSG00000000971	ENST00000367429	Transcript	missense_variant	1989	1749	583	K/N	aaG/aaC	.	.	.	1	CFH	HGNC	4883	protein_coding	YES	CCDS1385.1	ENSP00000356399	CFAH_HUMAN	.	UPI000013C4D1	.	deleterious(0.03)	possibly_damaging(0.485)	12/22	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF310,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCAAGAAAGA	.	4	ESCA
FAM43B	0	.	GRCh37	1	20879425	20879425	+	5'UTR	SNP	G	G	A	rs777944124	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-42G>A	.	.	ENST00000332947	1/1	25	16	9	36	36	0	FAM43B,5_prime_UTR_variant,,ENST00000332947,;	A	ENSG00000183114	ENST00000332947	Transcript	5_prime_UTR_variant	494	.	.	.	.	rs777944124	.	.	1	FAM43B	HGNC	31791	protein_coding	YES	CCDS209.1	ENSP00000331397	FA43B_HUMAN	.	UPI00001C0D42	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCCGGTGAG	.	5	ESCA
LAMB3	0	.	GRCh37	1	209788522	209788522	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*94C>A	.	.	ENST00000391911	22/22	21	17	3	24	24	0	LAMB3,3_prime_UTR_variant,,ENST00000356082,;LAMB3,3_prime_UTR_variant,,ENST00000391911,;LAMB3,3_prime_UTR_variant,,ENST00000367030,;LAMB3,downstream_gene_variant,,ENST00000455193,;CAMK1G,downstream_gene_variant,,ENST00000361322,;CAMK1G,downstream_gene_variant,,ENST00000009105,;CAMK1G,downstream_gene_variant,,ENST00000494990,;	T	ENSG00000196878	ENST00000391911	Transcript	3_prime_UTR_variant	4003	.	.	.	.	.	.	.	-1	LAMB3	HGNC	6490	protein_coding	YES	CCDS1487.1	ENSP00000375778	LAMB3_HUMAN	Q5THA1_HUMAN	UPI000012E76F	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAAAGTCTCC	.	4	ESCA
EPRS	0	.	GRCh37	1	220160602	220160602	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2920A>T	p.Lys974Ter	p.K974*	ENST00000366923	20/32	72	37	35	29	29	0	EPRS,stop_gained,p.Lys974Ter,ENST00000366923,;EPRS,downstream_gene_variant,,ENST00000609181,;snoU13,downstream_gene_variant,,ENST00000459217,;EPRS,upstream_gene_variant,,ENST00000485821,;	A	ENSG00000136628	ENST00000366923	Transcript	stop_gained	3190	2920	974	K/*	Aag/Tag	.	.	.	-1	EPRS	HGNC	3418	protein_coding	YES	CCDS31027.1	ENSP00000355890	SYEP_HUMAN	.	UPI0000205E8C	.	.	.	20/32	.	hmmpanther:PTHR10119:SF15,hmmpanther:PTHR10119,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTTTTCAG	.	5	ESCA
RGS7	0	.	GRCh37	1	240938980	240938980	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*483G>A	.	.	ENST00000366565	18/18	45	34	11	32	32	0	RGS7,3_prime_UTR_variant,,ENST00000440928,;RGS7,3_prime_UTR_variant,,ENST00000446183,;RGS7,3_prime_UTR_variant,,ENST00000366564,;RGS7,3_prime_UTR_variant,,ENST00000366565,;RGS7,3_prime_UTR_variant,,ENST00000366563,;RGS7,3_prime_UTR_variant,,ENST00000348120,;RGS7,intron_variant,,ENST00000331110,;RGS7,downstream_gene_variant,,ENST00000366562,;PRKRIRP8,upstream_gene_variant,,ENST00000447914,;	T	ENSG00000182901	ENST00000366565	Transcript	3_prime_UTR_variant	2329	.	.	.	.	.	.	.	-1	RGS7	HGNC	10003	protein_coding	YES	CCDS31071.1	ENSP00000355523	RGS7_HUMAN	.	UPI000040E182	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGACGAAGA	.	5	ESCA
OR2T8	0	.	GRCh37	1	248084839	248084839	+	Missense_Mutation	SNP	C	C	T	rs200305171	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520C>T	p.His174Tyr	p.H174Y	ENST00000319968	1/1	57	52	5	31	31	0	OR2T8,missense_variant,p.His174Tyr,ENST00000319968,;	T	ENSG00000177462	ENST00000319968	Transcript	missense_variant	520	520	174	H/Y	Cac/Tac	rs200305171	.	.	1	OR2T8	HGNC	15020	protein_coding	YES	CCDS31100.1	ENSP00000326225	OR2T8_HUMAN	.	UPI00001999E3	.	deleterious(0)	benign(0.163)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF147,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.I172I|c.516C>T|4	RADIA|VARSCANS	TCGATCACTTC	byFrequency|byCluster	2	ESCA
OR2T33	0	.	GRCh37	1	248436938	248436938	+	Missense_Mutation	SNP	A	A	C	rs544654849	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179T>G	p.Leu60Arg	p.L60R	ENST00000318021	1/1	70	56	14	89	89	0	OR2T33,missense_variant,p.Leu60Arg,ENST00000318021,;	C	ENSG00000177212	ENST00000318021	Transcript	missense_variant	201	179	60	L/R	cTc/cGc	rs544654849,COSM680429	.	.	-1	OR2T33	HGNC	31255	protein_coding	YES	CCDS31109.1	ENSP00000324687	O2T33_HUMAN	.	UPI000004B237	.	deleterious(0)	probably_damaging(0.992)	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF83,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGAGGAAG	by1000G	5	ESCA
OR2T11	0	.	GRCh37	1	248790191	248790191	+	Missense_Mutation	SNP	G	G	T	rs200166974	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239C>A	p.Ala80Glu	p.A80E	ENST00000330803	1/1	49	41	8	39	39	0	OR2T11,missense_variant,p.Ala80Glu,ENST00000330803,;	T	ENSG00000183130	ENST00000330803	Transcript	missense_variant	301	239	80	A/E	gCa/gAa	rs200166974	.	.	-1	OR2T11	HGNC	19574	protein_coding	YES	CCDS31122.1	ENSP00000328934	O2T11_HUMAN	.	UPI000004F23F	.	deleterious(0.01)	benign(0.016)	1/1	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF173,PROSITE_profiles:PS50262	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TGTCTGCCAGG	byCluster|by1000G	3	ESCA
RHD	0	.	GRCh37	1	25655647	25655647	+	3'UTR	SNP	T	T	C	rs778010642	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*232T>C	.	.	ENST00000328664	10/10	22	14	7	30	30	0	RHD,3_prime_UTR_variant,,ENST00000423810,;RHD,3_prime_UTR_variant,,ENST00000568195,;RHD,3_prime_UTR_variant,,ENST00000417538,;RHD,3_prime_UTR_variant,,ENST00000357542,;RHD,3_prime_UTR_variant,,ENST00000454452,;RHD,3_prime_UTR_variant,,ENST00000342055,;RHD,3_prime_UTR_variant,,ENST00000328664,;C1orf63,intron_variant,,ENST00000561867,;C1orf63,intron_variant,,ENST00000568996,;C1orf63,intron_variant,,ENST00000568399,;C1orf63,intron_variant,,ENST00000567741,;C1orf63,intron_variant,,ENST00000562018,;C1orf63,intron_variant,,ENST00000473314,;	C	ENSG00000187010	ENST00000328664	Transcript	3_prime_UTR_variant	1641	.	.	.	.	rs778010642	.	.	1	RHD	HGNC	10009	protein_coding	YES	CCDS262.1	ENSP00000331871	RHD_HUMAN	T2DL33_HUMAN,Q9UEC7_HUMAN,Q9UDZ3_HUMAN,Q8NFY2_HUMAN,Q6A1H1_HUMAN,Q5NDM5_HUMAN,Q49IM6_HUMAN,P78522_HUMAN,I2HA01_HUMAN,I2HA00_HUMAN,I0CKG6_HUMAN,G0TQY3_HUMAN,E7BAS5_HUMAN,D8MJ86_HUMAN,D8MJ84_HUMAN,D2CRH1_HUMAN,B4F4S7_HUMAN,B4F4S0_HUMAN,B2ZGQ0_HUMAN,A9P3T3_HUMAN,A7Y8S3_HUMAN,A0PFK1_HUMAN	UPI0000246EA2	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACATAACAA	byFrequency	5	ESCA
ARID1A	0	.	GRCh37	1	27101359	27101359	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4641C>T	p.%3D	p.S1547S	ENST00000324856	18/20	99	52	47	104	104	0	ARID1A,synonymous_variant,p.%3D,ENST00000374152,;ARID1A,synonymous_variant,p.%3D,ENST00000430799,;ARID1A,synonymous_variant,p.%3D,ENST00000324856,;ARID1A,intron_variant,,ENST00000457599,;ARID1A,intron_variant,,ENST00000540690,;ARID1A,intron_variant,,ENST00000466382,;ARID1A,upstream_gene_variant,,ENST00000532781,;	T	ENSG00000117713	ENST00000324856	Transcript	synonymous_variant	5012	4641	1547	S	tcC/tcT	.	.	.	1	ARID1A	HGNC	11110	protein_coding	YES	CCDS285.1	ENSP00000320485	ARI1A_HUMAN	Q96T01_HUMAN,Q96SY8_HUMAN,Q96SM7_HUMAN,E9PQW6_HUMAN,C1KEN7_HUMAN,A4FU79_HUMAN	UPI0000167B91	.	.	.	18/20	.	hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.W1545*|c.4635G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCCCATGG	.	5	ESCA
FABP3	0	.	GRCh37	1	31838684	31838684	+	3'UTR	SNP	C	C	T	rs371423628	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*49G>A	.	.	ENST00000373713	4/4	49	39	9	46	46	0	FABP3,3_prime_UTR_variant,,ENST00000373713,;ZCCHC17,downstream_gene_variant,,ENST00000546109,;ZCCHC17,downstream_gene_variant,,ENST00000344147,;ZCCHC17,downstream_gene_variant,,ENST00000422613,;FABP3,downstream_gene_variant,,ENST00000482018,;ZCCHC17,downstream_gene_variant,,ENST00000373714,;FABP3,non_coding_transcript_exon_variant,,ENST00000497275,;FABP3,3_prime_UTR_variant,,ENST00000498148,;	T	ENSG00000121769	ENST00000373713	Transcript	3_prime_UTR_variant	513	.	.	.	.	rs371423628	.	.	-1	FABP3	HGNC	3557	protein_coding	YES	CCDS342.1	ENSP00000362817	FABPH_HUMAN	S4R371_HUMAN	UPI000013CAC3	.	.	.	4/4	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGTCGAGGG	.	4	ESCA
PHC2	0	.	GRCh37	1	33796985	33796985	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1967G>A	p.Arg656His	p.R656H	ENST00000257118	11/14	88	64	23	86	86	0	PHC2,missense_variant,p.Arg657His,ENST00000419414,;PHC2,missense_variant,p.Arg121His,ENST00000373418,;PHC2,missense_variant,p.Arg627His,ENST00000431992,;PHC2,missense_variant,p.Arg262His,ENST00000373422,;PHC2,missense_variant,p.Arg121His,ENST00000373416,;PHC2,missense_variant,p.Arg656His,ENST00000257118,;MIR3605,downstream_gene_variant,,ENST00000583214,;PHC2,non_coding_transcript_exon_variant,,ENST00000486897,;PHC2,non_coding_transcript_exon_variant,,ENST00000493483,;PHC2,non_coding_transcript_exon_variant,,ENST00000485928,;PHC2,non_coding_transcript_exon_variant,,ENST00000473158,;PHC2,non_coding_transcript_exon_variant,,ENST00000467894,;	T	ENSG00000134686	ENST00000257118	Transcript	missense_variant	2021	1967	656	R/H	cGt/cAt	.	.	.	-1	PHC2	HGNC	3183	protein_coding	YES	CCDS378.1	ENSP00000257118	PHC2_HUMAN	.	UPI0000074391	.	tolerated(0.09)	probably_damaging(0.943)	11/14	.	PROSITE_profiles:PS51024,hmmpanther:PTHR12247:SF71,hmmpanther:PTHR12247	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAACGCTTG	.	5	ESCA
C1orf228	0	.	GRCh37	1	45189867	45189867	+	Silent	SNP	G	G	A	rs774296293	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.798G>A	p.%3D	p.L266L	ENST00000458657	8/13	52	39	12	37	37	0	C1orf228,synonymous_variant,p.%3D,ENST00000535358,;C1orf228,synonymous_variant,p.%3D,ENST00000458657,;C1orf228,synonymous_variant,p.%3D,ENST00000434068,;RNU5F-1,upstream_gene_variant,,ENST00000362507,;C1orf228,non_coding_transcript_exon_variant,,ENST00000446792,;C1orf228,non_coding_transcript_exon_variant,,ENST00000434520,;C1orf228,non_coding_transcript_exon_variant,,ENST00000444751,;C1orf228,non_coding_transcript_exon_variant,,ENST00000421398,;C1orf228,non_coding_transcript_exon_variant,,ENST00000427321,;C1orf228,non_coding_transcript_exon_variant,,ENST00000357508,;C1orf228,non_coding_transcript_exon_variant,,ENST00000424484,;C1orf228,non_coding_transcript_exon_variant,,ENST00000444525,;C1orf228,non_coding_transcript_exon_variant,,ENST00000440383,;C1orf228,non_coding_transcript_exon_variant,,ENST00000427336,;C1orf228,upstream_gene_variant,,ENST00000418779,;C1orf228,upstream_gene_variant,,ENST00000568406,;	A	ENSG00000198520	ENST00000458657	Transcript	synonymous_variant	1105	798	266	L	ctG/ctA	rs774296293	.	.	1	C1orf228	HGNC	34345	protein_coding	YES	CCDS53311.1	ENSP00000420716	CA228_HUMAN	F8WDG2_HUMAN,C9JCY2_HUMAN,C9JA22_HUMAN,C9J579_HUMAN,C9J477_HUMAN	UPI0000EE3082	.	.	.	8/13	.	Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTGATACC	.	5	ESCA
CCDC17	0	.	GRCh37	1	46088492	46088492	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.671C>T	p.Ser224Phe	p.S224F	ENST00000528266	5/13	160	84	76	138	138	0	CCDC17,missense_variant,p.Ser224Phe,ENST00000528266,;CCDC17,missense_variant,p.Ser192Phe,ENST00000343901,;CCDC17,missense_variant,p.Ser215Phe,ENST00000421127,;CCDC17,intron_variant,,ENST00000445048,;NASP,downstream_gene_variant,,ENST00000402363,;NASP,downstream_gene_variant,,ENST00000350030,;GPBP1L1,downstream_gene_variant,,ENST00000355105,;GPBP1L1,downstream_gene_variant,,ENST00000290795,;NASP,downstream_gene_variant,,ENST00000534450,;NASP,downstream_gene_variant,,ENST00000537798,;NASP,downstream_gene_variant,,ENST00000351223,;NASP,downstream_gene_variant,,ENST00000531612,;NASP,downstream_gene_variant,,ENST00000372052,;GPBP1L1,downstream_gene_variant,,ENST00000479235,;CCDC17,upstream_gene_variant,,ENST00000464739,;NASP,downstream_gene_variant,,ENST00000530073,;CCDC17,missense_variant,p.Ser192Phe,ENST00000479529,;CCDC17,3_prime_UTR_variant,,ENST00000372044,;CCDC17,non_coding_transcript_exon_variant,,ENST00000525599,;CCDC17,non_coding_transcript_exon_variant,,ENST00000482416,;CCDC17,non_coding_transcript_exon_variant,,ENST00000491755,;NASP,downstream_gene_variant,,ENST00000481782,;NASP,downstream_gene_variant,,ENST00000472408,;	A	ENSG00000159588	ENST00000528266	Transcript	missense_variant	819	671	224	S/F	tCc/tTc	.	.	.	-1	CCDC17	HGNC	26574	protein_coding	YES	CCDS44131.2	ENSP00000432172	CCD17_HUMAN	.	UPI0001AE78A9	.	deleterious(0.01)	possibly_damaging(0.807)	5/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGGGAGCTC	.	5	ESCA
LRRC41	0	.	GRCh37	1	46763994	46763994	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.248A>G	p.Tyr83Cys	p.Y83C	ENST00000343304	2/10	131	77	54	130	130	0	LRRC41,missense_variant,p.Tyr83Cys,ENST00000343304,;LRRC41,non_coding_transcript_exon_variant,,ENST00000469150,;LRRC41,non_coding_transcript_exon_variant,,ENST00000498402,;LRRC41,non_coding_transcript_exon_variant,,ENST00000472710,;	C	ENSG00000132128	ENST00000343304	Transcript	missense_variant	534	248	83	Y/C	tAt/tGt	.	.	.	-1	LRRC41	HGNC	16917	protein_coding	YES	CCDS533.1	ENSP00000343298	LRC41_HUMAN	.	UPI0000225CC7	.	deleterious(0)	probably_damaging(0.975)	2/10	.	hmmpanther:PTHR15354:SF1,hmmpanther:PTHR15354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAATATATA	.	5	ESCA
STIL	0	.	GRCh37	1	47746765	47746765	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1365G>T	p.Leu455Phe	p.L455F	ENST00000371877	12/17	85	58	27	72	72	0	STIL,missense_variant,p.Leu455Phe,ENST00000337817,;STIL,missense_variant,p.Leu455Phe,ENST00000396221,;STIL,missense_variant,p.Leu455Phe,ENST00000243182,;STIL,missense_variant,p.Leu408Phe,ENST00000447475,;STIL,missense_variant,p.Leu455Phe,ENST00000371877,;STIL,missense_variant,p.Leu455Phe,ENST00000360380,;STIL,upstream_gene_variant,,ENST00000436811,;STIL,non_coding_transcript_exon_variant,,ENST00000418131,;	A	ENSG00000123473	ENST00000371877	Transcript	missense_variant	1513	1365	455	L/F	ttG/ttT	.	.	.	-1	STIL	HGNC	10879	protein_coding	YES	CCDS41329.1	ENSP00000360944	STIL_HUMAN	.	UPI00002042D5	.	tolerated(0.13)	possibly_damaging(0.694)	12/17	.	hmmpanther:PTHR15128,hmmpanther:PTHR15128:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATCAAAGG	.	5	ESCA
LPHN2	0	.	GRCh37	1	82409141	82409141	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.886C>G	p.Leu296Val	p.L296V	ENST00000319517	5/20	49	38	11	33	33	0	LPHN2,missense_variant,p.Leu296Val,ENST00000370730,;LPHN2,missense_variant,p.Leu296Val,ENST00000335786,;LPHN2,missense_variant,p.Leu296Val,ENST00000370713,;LPHN2,missense_variant,p.Leu296Val,ENST00000370717,;LPHN2,missense_variant,p.Leu296Val,ENST00000370727,;LPHN2,missense_variant,p.Leu296Val,ENST00000370725,;LPHN2,missense_variant,p.Leu296Val,ENST00000319517,;LPHN2,missense_variant,p.Leu296Val,ENST00000271029,;LPHN2,missense_variant,p.Leu296Val,ENST00000370728,;LPHN2,missense_variant,p.Leu296Val,ENST00000359929,;LPHN2,missense_variant,p.Leu296Val,ENST00000370715,;LPHN2,missense_variant,p.Leu296Val,ENST00000370723,;LPHN2,missense_variant,p.Leu300Val,ENST00000370721,;LPHN2,missense_variant,p.Leu296Val,ENST00000394879,;LPHN2,missense_variant,p.Leu164Val,ENST00000449420,;LPHN2,intron_variant,,ENST00000469377,;	G	ENSG00000117114	ENST00000319517	Transcript	missense_variant	1102	886	296	L/V	Ctt/Gtt	.	.	.	1	LPHN2	HGNC	18582	protein_coding	YES	CCDS689.1	ENSP00000322270	LPHN2_HUMAN	.	UPI000005046B	.	deleterious(0)	probably_damaging(0.999)	5/20	.	PROSITE_profiles:PS51132,hmmpanther:PTHR12011:SF61,hmmpanther:PTHR12011,Pfam_domain:PF02191,SMART_domains:SM00284	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTCTTCGA	.	5	ESCA
ODF2L	0	.	GRCh37	1	86848664	86848664	+	Missense_Mutation	SNP	C	C	T	rs748708880	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457G>A	p.Glu153Lys	p.E153K	ENST00000359242	6/18	102	89	13	101	101	0	ODF2L,missense_variant,p.Glu22Lys,ENST00000394731,;ODF2L,missense_variant,p.Glu22Lys,ENST00000479890,;ODF2L,missense_variant,p.Glu153Lys,ENST00000370566,;ODF2L,missense_variant,p.Glu153Lys,ENST00000294678,;ODF2L,missense_variant,p.Glu153Lys,ENST00000359242,;ODF2L,missense_variant,p.Glu29Lys,ENST00000460698,;ODF2L,missense_variant,p.Glu153Lys,ENST00000317336,;ODF2L,missense_variant,p.Glu22Lys,ENST00000394733,;ODF2L,missense_variant,p.Glu153Lys,ENST00000370567,;ODF2L,downstream_gene_variant,,ENST00000478286,;ODF2L,downstream_gene_variant,,ENST00000486215,;ODF2L,3_prime_UTR_variant,,ENST00000488879,;ODF2L,non_coding_transcript_exon_variant,,ENST00000472368,;ODF2L,non_coding_transcript_exon_variant,,ENST00000480440,;ODF2L,non_coding_transcript_exon_variant,,ENST00000496592,;	T	ENSG00000122417	ENST00000359242	Transcript	missense_variant	739	457	153	E/K	Gaa/Aaa	rs748708880	.	.	-1	ODF2L	HGNC	29225	protein_coding	YES	CCDS41354.2	ENSP00000359600	ODF2L_HUMAN	B5ME44_HUMAN	UPI00001C1D6A	.	deleterious(0)	probably_damaging(0.944)	6/18	.	hmmpanther:PTHR23162:SF7,hmmpanther:PTHR23162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTTCAAATA	.	4	ESCA
DR1	0	.	GRCh37	1	93827094	93827094	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*898G>T	.	.	ENST00000370272	3/3	22	15	7	26	26	0	DR1,3_prime_UTR_variant,,ENST00000370272,;DR1,downstream_gene_variant,,ENST00000370267,;DR1,downstream_gene_variant,,ENST00000481583,;	T	ENSG00000117505	ENST00000370272	Transcript	3_prime_UTR_variant	2187	.	.	.	.	.	.	.	1	DR1	HGNC	3017	protein_coding	YES	CCDS744.1	ENSP00000359295	NC2B_HUMAN	Q658N3_HUMAN	UPI0000136997	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAAGAAATG	.	5	ESCA
FLRT3	0	.	GRCh37	20	14305782	14305782	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*421A>C	.	.	ENST00000378053	2/2	104	81	22	96	95	0	FLRT3,3_prime_UTR_variant,,ENST00000378053,;FLRT3,3_prime_UTR_variant,,ENST00000341420,;MACROD2,intron_variant,,ENST00000217246,;MACROD2,intron_variant,,ENST00000310348,;MACROD2,intron_variant,,ENST00000490428,;MACROD2,intron_variant,,ENST00000494602,;MACROD2,intron_variant,,ENST00000477147,;FLRT3,downstream_gene_variant,,ENST00000462077,;	G	ENSG00000125848	ENST00000378053	Transcript	3_prime_UTR_variant	2628	.	.	.	.	.	.	.	-1	FLRT3	HGNC	3762	protein_coding	YES	CCDS13121.1	ENSP00000367292	FLRT3_HUMAN	.	UPI0000001BE7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATTAATAC	.	5	ESCA
NKX2-2	0	.	GRCh37	20	21492752	21492752	+	Missense_Mutation	SNP	C	C	A	rs767138374	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>T	p.Asp211Tyr	p.D211Y	ENST00000377142	2/2	96	87	8	88	88	0	NKX2-2,missense_variant,p.Asp211Tyr,ENST00000377142,;NKX2-2-AS1,non_coding_transcript_exon_variant,,ENST00000549659,;	A	ENSG00000125820	ENST00000377142	Transcript	missense_variant	988	631	211	D/Y	Gac/Tac	rs767138374	.	.	-1	NKX2-2	HGNC	7835	protein_coding	YES	CCDS13145.1	ENSP00000366347	NKX22_HUMAN	.	UPI00001301E6	.	deleterious(0)	probably_damaging(0.994)	2/2	.	hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCCGTCCCTGA	.	3	ESCA
C20orf96	0	.	GRCh37	20	257338	257338	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912+96C>T	.	.	ENST00000360321	.	15	9	6	9	9	0	C20orf96,3_prime_UTR_variant,,ENST00000400269,;C20orf96,intron_variant,,ENST00000360321,;C20orf96,intron_variant,,ENST00000382369,;	A	ENSG00000196476	ENST00000360321	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	C20orf96	HGNC	16227	protein_coding	YES	CCDS12994.1	ENSP00000353470	CT096_HUMAN	.	UPI00001285F1	.	.	.	.	9/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	TGAGCGCCAGA	.	3	ESCA
ITCH	0	.	GRCh37	20	33097696	33097696	+	3'Flank	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000262650	.	73	48	25	65	65	0	ITCH,3_prime_UTR_variant,,ENST00000374864,;ITCH,downstream_gene_variant,,ENST00000535650,;ITCH,downstream_gene_variant,,ENST00000262650,;	G	ENSG00000078747	ENST00000262650	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1856	1	ITCH	HGNC	13890	protein_coding	YES	CCDS58768.1	ENSP00000262650	ITCH_HUMAN	.	UPI00000731C2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATTAAGAGA	.	5	ESCA
RBM12	0	.	GRCh37	20	34240263	34240263	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*183C>T	.	.	ENST00000374114	3/3	77	63	14	82	82	0	RBM12,3_prime_UTR_variant,,ENST00000374114,;RBM12,3_prime_UTR_variant,,ENST00000359646,;RBM12,3_prime_UTR_variant,,ENST00000374104,;CPNE1,intron_variant,,ENST00000352393,;CPNE1,intron_variant,,ENST00000414711,;CPNE1,intron_variant,,ENST00000458038,;CPNE1,intron_variant,,ENST00000397443,;CPNE1,intron_variant,,ENST00000434795,;CPNE1,intron_variant,,ENST00000317677,;CPNE1,intron_variant,,ENST00000397442,;CPNE1,intron_variant,,ENST00000440240,;CPNE1,intron_variant,,ENST00000412056,;CPNE1,intron_variant,,ENST00000317619,;CPNE1,intron_variant,,ENST00000430570,;CPNE1,intron_variant,,ENST00000416778,;CPNE1,intron_variant,,ENST00000435747,;CPNE1,intron_variant,,ENST00000420363,;CPNE1,intron_variant,,ENST00000439806,;CPNE1,intron_variant,,ENST00000437340,;CPNE1,intron_variant,,ENST00000397445,;CPNE1,intron_variant,,ENST00000414664,;CPNE1,intron_variant,,ENST00000397446,;CPNE1,intron_variant,,ENST00000437100,;RBM12,downstream_gene_variant,,ENST00000435161,;RBM12,downstream_gene_variant,,ENST00000424458,;RBM12,downstream_gene_variant,,ENST00000431148,;RNU6-759P,upstream_gene_variant,,ENST00000516740,;CPNE1,intron_variant,,ENST00000401607,;RP1-309K20.6,intron_variant,,ENST00000541176,;RP1-309K20.6,intron_variant,,ENST00000454607,;CPNE1,intron_variant,,ENST00000439669,;CPNE1,intron_variant,,ENST00000483359,;RP1-309K20.6,intron_variant,,ENST00000441563,;	A	ENSG00000244462	ENST00000374114	Transcript	3_prime_UTR_variant	3246	.	.	.	.	.	.	.	-1	RBM12	HGNC	9898	protein_coding	YES	CCDS13261.1	ENSP00000363228	RBM12_HUMAN	Q69YJ7_HUMAN,Q5JX62_HUMAN,A6PVI1_HUMAN,A6PVI0_HUMAN	UPI0000073D24	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACAGCAATG	.	5	ESCA
CHD6	0	.	GRCh37	20	40074302	40074302	+	Intron	SNP	C	C	G	rs371678888	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3877+3G>C	.	.	ENST00000373233	.	97	78	18	78	78	0	CHD6,splice_region_variant,,ENST00000373233,;CHD6,splice_region_variant,,ENST00000309279,;CHD6,splice_region_variant,,ENST00000440697,;	G	ENSG00000124177	ENST00000373233	Transcript	splice_region_variant	.	.	.	.	.	rs371678888	.	.	-1	CHD6	HGNC	19057	protein_coding	YES	CCDS13317.1	ENSP00000362330	CHD6_HUMAN	.	UPI0000168656	.	.	.	.	25/36	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACACACCAT	byCluster	4	ESCA
PIGT	0	.	GRCh37	20	44045206	44045206	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237G>T	p.Lys79Asn	p.K79N	ENST00000279036	2/12	65	52	12	56	56	0	PIGT,missense_variant,p.Lys79Asn,ENST00000543458,;PIGT,missense_variant,p.Lys79Asn,ENST00000372689,;PIGT,missense_variant,p.Lys79Asn,ENST00000279036,;PIGT,5_prime_UTR_variant,,ENST00000535404,;PIGT,intron_variant,,ENST00000432270,;PIGT,intron_variant,,ENST00000341555,;PIGT,intron_variant,,ENST00000545755,;PIGT,intron_variant,,ENST00000279035,;PIGT,missense_variant,p.Lys79Asn,ENST00000455050,;	T	ENSG00000124155	ENST00000279036	Transcript	missense_variant	317	237	79	K/N	aaG/aaT	COSM443901,COSM1134163	.	.	1	PIGT	HGNC	14938	protein_coding	YES	CCDS13353.1	ENSP00000279036	PIGT_HUMAN	B7Z1N3_HUMAN	UPI000003B0D0	.	tolerated(0.09)	probably_damaging(0.962)	2/12	.	hmmpanther:PTHR12959:SF11,hmmpanther:PTHR12959,Pfam_domain:PF04113	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGTATTC	.	5	ESCA
ARFGEF2	0	.	GRCh37	20	47649631	47649631	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5253C>T	p.%3D	p.L1751L	ENST00000371917	39/39	112	93	19	86	86	0	ARFGEF2,synonymous_variant,p.%3D,ENST00000371917,;	T	ENSG00000124198	ENST00000371917	Transcript	synonymous_variant	5253	5253	1751	L	ctC/ctT	.	.	.	1	ARFGEF2	HGNC	15853	protein_coding	YES	CCDS13411.1	ENSP00000360985	BIG2_HUMAN	Q59FR3_HUMAN	UPI000013D378	.	.	.	39/39	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF124,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTCCGAGC	.	5	ESCA
TMEM230	0	.	GRCh37	20	5093572	5093572	+	Intron	SNP	G	G	C	rs565592529	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.68+35C>G	.	.	ENST00000342308	.	19	9	9	16	16	0	TMEM230,5_prime_UTR_variant,,ENST00000379286,;TMEM230,5_prime_UTR_variant,,ENST00000379283,;TMEM230,5_prime_UTR_variant,,ENST00000379299,;TMEM230,5_prime_UTR_variant,,ENST00000379279,;TMEM230,intron_variant,,ENST00000342308,;TMEM230,intron_variant,,ENST00000202834,;TMEM230,upstream_gene_variant,,ENST00000379277,;TMEM230,upstream_gene_variant,,ENST00000379276,;PCNA,downstream_gene_variant,,ENST00000379143,;PCNA,downstream_gene_variant,,ENST00000379160,;Y_RNA,downstream_gene_variant,,ENST00000516558,;TMEM230,non_coding_transcript_exon_variant,,ENST00000492419,;	C	ENSG00000089063	ENST00000342308	Transcript	intron_variant	.	.	.	.	.	rs565592529	.	.	-1	TMEM230	HGNC	15876	protein_coding	YES	CCDS33438.1	ENSP00000341364	TM230_HUMAN	Q5JWB9_HUMAN	UPI0000470ABB	.	.	.	.	1/4	.	C:0.0026	C:0.0098	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGACGGTTCT	byFrequency|by1000G	5	ESCA
ZNF217	0	.	GRCh37	20	52185334	52185334	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*493C>T	.	.	ENST00000371471	6/6	65	53	12	40	40	0	ZNF217,3_prime_UTR_variant,,ENST00000302342,;ZNF217,3_prime_UTR_variant,,ENST00000371471,;ZNF217,downstream_gene_variant,,ENST00000437222,;RP4-724E16.2,intron_variant,,ENST00000424252,;	A	ENSG00000171940	ENST00000371471	Transcript	3_prime_UTR_variant	4066	.	.	.	.	.	.	.	-1	ZNF217	HGNC	13009	protein_coding	YES	CCDS13443.1	ENSP00000360526	ZN217_HUMAN	A2A326_HUMAN	UPI000013C323	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGCAGAAACT	.	4	ESCA
OPRL1	0	.	GRCh37	20	62730100	62730100	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1061A>G	p.Lys354Arg	p.K354R	ENST00000349451	6/6	31	25	6	42	42	0	OPRL1,missense_variant,p.Lys354Arg,ENST00000336866,;OPRL1,missense_variant,p.Lys354Arg,ENST00000355631,;OPRL1,missense_variant,p.Lys354Arg,ENST00000349451,;	G	ENSG00000125510	ENST00000349451	Transcript	missense_variant	1473	1061	354	K/R	aAg/aGg	.	.	.	1	OPRL1	HGNC	8155	protein_coding	YES	CCDS13556.1	ENSP00000336764	OPRX_HUMAN	.	UPI0000001C6D	.	tolerated(1)	benign(0.006)	6/6	.	hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF11,Prints_domain:PR00547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCAAGGACG	.	5	ESCA
PLCB1	0	.	GRCh37	20	8865304	8865304	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2808A>G	.	.	ENST00000338037	32/32	80	75	5	76	76	0	PLCB1,3_prime_UTR_variant,,ENST00000378641,;PLCB1,3_prime_UTR_variant,,ENST00000338037,;PLCB1,intron_variant,,ENST00000487210,;	G	ENSG00000182621	ENST00000338037	Transcript	3_prime_UTR_variant	6486	.	.	.	.	.	.	.	1	PLCB1	HGNC	15917	protein_coding	YES	CCDS13102.1	ENSP00000338185	PLCB1_HUMAN	.	UPI0000131A8F	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTAATATTGTT	.	2	ESCA
LZTR1	0	.	GRCh37	22	21341811	21341811	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339C>T	p.%3D	p.T113T	ENST00000215739	4/21	36	33	3	45	45	0	LZTR1,synonymous_variant,p.%3D,ENST00000215739,;LZTR1,synonymous_variant,p.%3D,ENST00000389355,;LZTR1,non_coding_transcript_exon_variant,,ENST00000479606,;LZTR1,intron_variant,,ENST00000480895,;LZTR1,upstream_gene_variant,,ENST00000497716,;LZTR1,3_prime_UTR_variant,,ENST00000443265,;LZTR1,intron_variant,,ENST00000414985,;LZTR1,upstream_gene_variant,,ENST00000492480,;LZTR1,downstream_gene_variant,,ENST00000493460,;LZTR1,upstream_gene_variant,,ENST00000461510,;	T	ENSG00000099949	ENST00000215739	Transcript	synonymous_variant	698	339	113	T	acC/acT	.	.	.	1	LZTR1	HGNC	6742	protein_coding	YES	CCDS33606.1	ENSP00000215739	LZTR1_HUMAN	B2R8T5_HUMAN	UPI000013C695	.	.	.	4/21	.	hmmpanther:PTHR23244:SF15,hmmpanther:PTHR23244,Gene3D:1zgkA00,Pfam_domain:PF13415,SMART_domains:SM00612,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GGGACCCCACC	.	2	ESCA
PPM1F	0	.	GRCh37	22	22274597	22274597	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2868G>A	.	.	ENST00000263212	8/8	27	23	4	31	31	0	PPM1F,3_prime_UTR_variant,,ENST00000407142,;PPM1F,3_prime_UTR_variant,,ENST00000263212,;PPM1F,downstream_gene_variant,,ENST00000397495,;PPM1F,downstream_gene_variant,,ENST00000538191,;PPM1F,downstream_gene_variant,,ENST00000496143,;PPM1F,downstream_gene_variant,,ENST00000484588,;	T	ENSG00000100034	ENST00000263212	Transcript	3_prime_UTR_variant	4339	.	.	.	.	.	.	.	-1	PPM1F	HGNC	19388	protein_coding	YES	CCDS13796.1	ENSP00000263212	PPM1F_HUMAN	Q6IPC0_HUMAN,Q0VGL7_HUMAN,C9J2F3_HUMAN,B5MCT7_HUMAN,A0M8Q2_HUMAN	UPI000012A61C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGACACGCCGG	.	3	ESCA
IGLC3	0	.	GRCh37	22	23248849	23248852	+	3'UTR	DEL	CCCA	CCCA	ACC	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	CCCA	CCCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*18_*21delCCCAinsACC	.	.	ENST00000390325	1/1	140	111	29	126	126	0	IGLC3,3_prime_UTR_variant,,ENST00000390325,;IGLJ3,downstream_gene_variant,,ENST00000390324,;IGLJ4,upstream_gene_variant,,ENST00000390326,;IGLC4,upstream_gene_variant,,ENST00000517690,;	ACC	ENSG00000211679	ENST00000390325	Transcript	3_prime_UTR_variant	338-341	.	.	.	.	.	.	.	1	IGLC3	HGNC	5857	IG_C_gene	YES	.	ENSP00000374857	.	.	UPI000059D869	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	PINDEL|VARSCANS*	TCACCCCCCACCACG	.	2	ESCA
DNAJB7	0	.	GRCh37	22	41256535	41256535	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*534G>A	.	.	ENST00000307221	1/1	36	15	21	50	50	0	DNAJB7,3_prime_UTR_variant,,ENST00000307221,;XPNPEP3,intron_variant,,ENST00000357137,;XPNPEP3,intron_variant,,ENST00000414396,;XPNPEP3,intron_variant,,ENST00000541156,;ST13,upstream_gene_variant,,ENST00000216218,;XPNPEP3,upstream_gene_variant,,ENST00000544094,;XPNPEP3,intron_variant,,ENST00000482652,;XPNPEP3,upstream_gene_variant,,ENST00000465258,;XPNPEP3,intron_variant,,ENST00000417688,;XPNPEP3,intron_variant,,ENST00000428799,;ST13,upstream_gene_variant,,ENST00000455824,;	T	ENSG00000172404	ENST00000307221	Transcript	3_prime_UTR_variant	1596	.	.	.	.	.	.	.	-1	DNAJB7	HGNC	24986	protein_coding	YES	CCDS14008.1	ENSP00000307197	DNJB7_HUMAN	.	UPI000006FBAD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTCTTCTA	.	5	ESCA
LCT	0	.	GRCh37	2	136562471	136562471	+	Missense_Mutation	SNP	C	C	T	rs757039689	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4330G>A	p.Val1444Met	p.V1444M	ENST00000264162	10/17	109	87	22	106	106	0	LCT,missense_variant,p.Val1444Met,ENST00000264162,;LCT,missense_variant,p.Val876Met,ENST00000452974,;	T	ENSG00000115850	ENST00000264162	Transcript	missense_variant	4341	4330	1444	V/M	Gtg/Atg	rs757039689	.	.	-1	LCT	HGNC	6530	protein_coding	YES	CCDS2178.1	ENSP00000264162	LPH_HUMAN	.	UPI000013D4D2	.	deleterious(0)	probably_damaging(0.998)	10/17	.	hmmpanther:PTHR10353,hmmpanther:PTHR10353:SF38,Gene3D:3.20.20.80,Pfam_domain:PF00232,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACACGCCCA	.	5	ESCA
LRP1B	0	.	GRCh37	2	141806552	141806552	+	Intron	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1789+3A>G	.	.	ENST00000389484	.	32	11	21	56	56	0	LRP1B,splice_region_variant,,ENST00000389484,;LRP1B,intron_variant,,ENST00000434794,;	C	ENSG00000168702	ENST00000389484	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	.	11/90	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTTACCAT	.	4	ESCA
BAZ2B	0	.	GRCh37	2	160175916	160175916	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*860T>C	.	.	ENST00000392783	37/37	83	61	21	46	46	0	BAZ2B,3_prime_UTR_variant,,ENST00000355831,;BAZ2B,3_prime_UTR_variant,,ENST00000392782,;BAZ2B,3_prime_UTR_variant,,ENST00000343439,;BAZ2B,3_prime_UTR_variant,,ENST00000392783,;BAZ2B,downstream_gene_variant,,ENST00000548440,;	G	ENSG00000123636	ENST00000392783	Transcript	3_prime_UTR_variant	7863	.	.	.	.	.	.	.	-1	BAZ2B	HGNC	963	protein_coding	YES	CCDS2209.2	ENSP00000376534	BAZ2B_HUMAN	Q8NC87_HUMAN,Q53TG3_HUMAN,C9JCA6_HUMAN	UPI0000D74C4A	.	.	.	37/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGACGCCA	.	5	ESCA
CHRNA1	0	.	GRCh37	2	175614679	175614679	+	Missense_Mutation	SNP	G	G	A	rs374391312	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1072C>T	p.Arg358Trp	p.R358W	ENST00000261007	8/10	24	19	5	33	33	0	CHRNA1,missense_variant,p.Arg251Trp,ENST00000409542,;CHRNA1,missense_variant,p.Arg333Trp,ENST00000409219,;CHRNA1,missense_variant,p.Arg333Trp,ENST00000348749,;CHRNA1,missense_variant,p.Arg358Trp,ENST00000261007,;CHRNA1,downstream_gene_variant,,ENST00000409323,;AC018890.6,intron_variant,,ENST00000442996,;CHRNA1,3_prime_UTR_variant,,ENST00000435083,;	A	ENSG00000138435	ENST00000261007	Transcript	missense_variant	1139	1072	358	R/W	Cgg/Tgg	CM086805,rs374391312	.	.	-1	CHRNA1	HGNC	1955	protein_coding	YES	CCDS33331.1	ENSP00000261007	ACHA_HUMAN	A9X444_HUMAN	UPI000012524E	.	deleterious(0)	probably_damaging(0.998)	8/10	.	hmmpanther:PTHR18945:SF74,hmmpanther:PTHR18945,Pfam_domain:PF02932,Gene3D:1.20.120.370,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCCGCACCC	byFrequency|byCluster	4	ESCA
HOXD10	0	.	GRCh37	2	176982185	176982185	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624G>A	p.%3D	p.Q208Q	ENST00000249501	1/2	108	66	41	108	108	0	HOXD10,synonymous_variant,p.%3D,ENST00000249501,;HOXD9,upstream_gene_variant,,ENST00000249499,;HOXD-AS2,downstream_gene_variant,,ENST00000440016,;HOXD10,intron_variant,,ENST00000549469,;HOXD10,intron_variant,,ENST00000490088,;	A	ENSG00000128710	ENST00000249501	Transcript	synonymous_variant	879	624	208	Q	caG/caA	.	.	.	1	HOXD10	HGNC	5133	protein_coding	YES	CCDS2266.1	ENSP00000249501	HXD10_HUMAN	.	UPI000013CC87	.	.	.	1/2	.	hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCAGGAGCC	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098810	178098810	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	2/5	131	82	49	92	92	0	NFE2L2,missense_variant,p.Glu63Lys,ENST00000449627,;NFE2L2,missense_variant,p.Glu63Lys,ENST00000423513,;NFE2L2,missense_variant,p.Glu79Lys,ENST00000397062,;NFE2L2,missense_variant,p.Glu63Lys,ENST00000446151,;NFE2L2,missense_variant,p.Glu63Lys,ENST00000588123,;NFE2L2,missense_variant,p.Glu78Lys,ENST00000586532,;NFE2L2,missense_variant,p.Glu63Lys,ENST00000421929,;NFE2L2,missense_variant,p.Glu63Lys,ENST00000464747,;NFE2L2,missense_variant,p.Glu63Lys,ENST00000448782,;NFE2L2,missense_variant,p.Glu63Lys,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	T	ENSG00000116044	ENST00000397062	Transcript	missense_variant	790	235	79	E/K	Gag/Aag	COSM132851,COSM120958,COSM1631472	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(0.999)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E79K|c.235G>A|10,BUFFER|p.E82D|c.246A>C|3,BUFFER|p.E82D|c.246A>T|6,BUFFER|p.E82G|c.245A>G|7,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81D|c.242G>A|6,BUFFER|p.G81V|c.242G>T|7,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.G81S|c.241G>A|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79Q|c.235G>C|11,BUFFER|p.D77V|c.230A>T|5,BUFFER|p.D77G|c.230A>G|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTCTTCAT	.	5	ESCA
AGPS	0	.	GRCh37	2	178333231	178333231	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1084C>T	p.His362Tyr	p.H362Y	ENST00000264167	10/20	178	113	64	113	113	0	AGPS,missense_variant,p.His362Tyr,ENST00000264167,;AGPS,intron_variant,,ENST00000409888,;	T	ENSG00000018510	ENST00000264167	Transcript	missense_variant	1230	1084	362	H/Y	Cac/Tac	.	.	.	1	AGPS	HGNC	327	protein_coding	YES	CCDS2275.1	ENSP00000264167	ADAS_HUMAN	Q53SN7_HUMAN,Q53SG6_HUMAN,Q53S12_HUMAN,B7Z3Q4_HUMAN	UPI00001254E8	.	deleterious(0)	possibly_damaging(0.862)	10/20	.	PROSITE_profiles:PS51387,hmmpanther:PTHR11748,hmmpanther:PTHR11748:SF3,Gene3D:3.30.465.10,Superfamily_domains:SSF56176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCACTTC	.	5	ESCA
DFNB59	0	.	GRCh37	2	179320838	179320838	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.509C>T	p.Ser170Leu	p.S170L	ENST00000409117	4/7	97	57	40	95	95	0	DFNB59,missense_variant,p.Ser118Leu,ENST00000442710,;DFNB59,missense_variant,p.Ser170Leu,ENST00000375129,;DFNB59,missense_variant,p.Ser170Leu,ENST00000409117,;PRKRA,upstream_gene_variant,,ENST00000438687,;PRKRA,upstream_gene_variant,,ENST00000325748,;DFNB59,non_coding_transcript_exon_variant,,ENST00000605419,;PRKRA,upstream_gene_variant,,ENST00000470200,;DFNB59,missense_variant,p.Ser51Leu,ENST00000444615,;DFNB59,non_coding_transcript_exon_variant,,ENST00000437056,;PRKRA,upstream_gene_variant,,ENST00000424699,;PRKRA,upstream_gene_variant,,ENST00000466165,;PRKRA,upstream_gene_variant,,ENST00000463882,;AC009948.7,downstream_gene_variant,,ENST00000437039,;	T	ENSG00000204311	ENST00000409117	Transcript	missense_variant	865	509	170	S/L	tCa/tTa	CD073602	.	.	1	DFNB59	HGNC	29502	protein_coding	YES	CCDS42787.1	ENSP00000386647	PJVK_HUMAN	A0PK15_HUMAN	UPI0000DAD718	.	tolerated(0.48)	possibly_damaging(0.737)	4/7	.	hmmpanther:PTHR16399:SF10,hmmpanther:PTHR16399,Pfam_domain:PF04598	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCTCACTGT	.	5	ESCA
TTN	0	.	GRCh37	2	179411010	179411010	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.95048G>T	p.Ser31683Ile	p.S31683I	ENST00000589042	342/363	74	46	27	50	50	0	TTN,missense_variant,p.Ser22743Ile,ENST00000359218,;TTN,missense_variant,p.Ser30042Ile,ENST00000591111,;TTN,missense_variant,p.Ser31683Ile,ENST00000589042,;TTN,missense_variant,p.Ser22810Ile,ENST00000342175,;TTN,missense_variant,p.Ser29115Ile,ENST00000342992,;TTN,missense_variant,p.Ser22618Ile,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;RP11-65L3.2,upstream_gene_variant,,ENST00000603415,;RP11-65L3.4,downstream_gene_variant,,ENST00000604692,;TTN-AS1,downstream_gene_variant,,ENST00000590040,;	A	ENSG00000155657	ENST00000589042	Transcript	missense_variant	95273	95048	31683	S/I	aGt/aTt	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	342/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCACTGTCA	.	5	ESCA
ANKRD44	0	.	GRCh37	2	197858322	197858322	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2353G>A	p.Ala785Thr	p.A785T	ENST00000424317	21/22	57	33	24	43	43	0	ANKRD44,missense_variant,p.Ala785Thr,ENST00000424317,;ANKRD44,missense_variant,p.Ala962Thr,ENST00000282272,;ANKRD44,missense_variant,p.Ala159Thr,ENST00000448801,;ANKRD44,downstream_gene_variant,,ENST00000337207,;ANKRD44,downstream_gene_variant,,ENST00000450567,;ANKRD44,downstream_gene_variant,,ENST00000328737,;ANKRD44,non_coding_transcript_exon_variant,,ENST00000486006,;ANKRD44,non_coding_transcript_exon_variant,,ENST00000493808,;	T	ENSG00000065413	ENST00000424317	Transcript	missense_variant	2353	2353	785	A/T	Gct/Act	.	.	.	-1	ANKRD44	HGNC	25259	protein_coding	.	.	ENSP00000403415	.	H7C209_HUMAN	UPI00018818D9	.	tolerated(0.1)	possibly_damaging(0.685)	21/22	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24158,hmmpanther:PTHR24158:SF19,Gene3D:1.25.40.20,Pfam_domain:PF00023,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAGCAAGTA	.	5	ESCA
PLEKHM3	0	.	GRCh37	2	208842214	208842214	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.707C>T	p.Ser236Leu	p.S236L	ENST00000427836	3/8	100	82	18	60	60	0	PLEKHM3,missense_variant,p.Ser236Leu,ENST00000457206,;PLEKHM3,missense_variant,p.Ser236Leu,ENST00000427836,;PLEKHM3,missense_variant,p.Ser236Leu,ENST00000389247,;PLEKHM3,upstream_gene_variant,,ENST00000447645,;	A	ENSG00000178385	ENST00000427836	Transcript	missense_variant	1197	707	236	S/L	tCa/tTa	.	.	.	-1	PLEKHM3	HGNC	34006	protein_coding	YES	CCDS42808.1	ENSP00000417003	PKHM3_HUMAN	.	UPI0000DBEE58	.	deleterious(0)	benign(0.342)	3/8	.	hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF10,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGTGAAAGT	.	5	ESCA
GLB1L	0	.	GRCh37	2	220103229	220103229	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1215G>C	p.Glu405Asp	p.E405D	ENST00000295759	13/17	101	62	39	74	74	0	GLB1L,missense_variant,p.Glu315Asp,ENST00000409640,;GLB1L,missense_variant,p.Glu405Asp,ENST00000295759,;GLB1L,missense_variant,p.Glu315Asp,ENST00000356283,;GLB1L,missense_variant,p.Glu405Asp,ENST00000392089,;ANKZF1,downstream_gene_variant,,ENST00000410034,;ANKZF1,downstream_gene_variant,,ENST00000409849,;GLB1L,downstream_gene_variant,,ENST00000440853,;GLB1L,downstream_gene_variant,,ENST00000424620,;GLB1L,downstream_gene_variant,,ENST00000428427,;ANKZF1,downstream_gene_variant,,ENST00000323348,;GLB1L,non_coding_transcript_exon_variant,,ENST00000497855,;GLB1L,downstream_gene_variant,,ENST00000471516,;ANKZF1,downstream_gene_variant,,ENST00000465550,;GLB1L,downstream_gene_variant,,ENST00000447002,;ANKZF1,downstream_gene_variant,,ENST00000460966,;ANKZF1,downstream_gene_variant,,ENST00000468387,;GLB1L,downstream_gene_variant,,ENST00000459951,;ANKZF1,downstream_gene_variant,,ENST00000467884,;ANKZF1,downstream_gene_variant,,ENST00000483188,;ANKZF1,downstream_gene_variant,,ENST00000477479,;ANKZF1,downstream_gene_variant,,ENST00000463792,;ANKZF1,downstream_gene_variant,,ENST00000496346,;GLB1L,downstream_gene_variant,,ENST00000467548,;ANKZF1,downstream_gene_variant,,ENST00000461731,;ANKZF1,downstream_gene_variant,,ENST00000494886,;	G	ENSG00000163521	ENST00000295759	Transcript	missense_variant	1529	1215	405	E/D	gaG/gaC	.	.	.	-1	GLB1L	HGNC	28129	protein_coding	YES	CCDS2437.1	ENSP00000295759	GLB1L_HUMAN	C9JE41_HUMAN,C9J1Y9_HUMAN	UPI000003ED32	.	deleterious(0.05)	probably_damaging(0.997)	13/17	.	PIRSF_domain:PIRSF006336,hmmpanther:PTHR23421,hmmpanther:PTHR23421:SF50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCCTCAAA	.	5	ESCA
FAM124B	0	.	GRCh37	2	225244631	225244631	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027G>A	p.Ala343Thr	p.A343T	ENST00000409685	2/2	70	64	6	60	60	0	FAM124B,missense_variant,p.Ala343Thr,ENST00000409685,;FAM124B,3_prime_UTR_variant,,ENST00000389874,;	T	ENSG00000124019	ENST00000409685	Transcript	missense_variant	1293	1027	343	A/T	Gcc/Acc	.	.	.	-1	FAM124B	HGNC	26224	protein_coding	YES	CCDS46527.1	ENSP00000386895	F124B_HUMAN	.	UPI00002096DA	.	tolerated(0.45)	benign(0.08)	2/2	.	hmmpanther:PTHR14715:SF2,hmmpanther:PTHR14715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTGGCCCCGG	.	3	ESCA
NGEF	0	.	GRCh37	2	233759339	233759339	+	Intron	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.989+127A>G	.	.	ENST00000264051	.	20	13	7	16	16	0	NGEF,3_prime_UTR_variant,,ENST00000409079,;NGEF,intron_variant,,ENST00000420650,;NGEF,intron_variant,,ENST00000373552,;NGEF,intron_variant,,ENST00000458735,;NGEF,intron_variant,,ENST00000264051,;NGEF,intron_variant,,ENST00000416114,;NGEF,intron_variant,,ENST00000539537,;NGEF,upstream_gene_variant,,ENST00000424488,;NGEF,upstream_gene_variant,,ENST00000461944,;	C	ENSG00000066248	ENST00000264051	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NGEF	HGNC	7807	protein_coding	YES	CCDS2500.1	ENSP00000264051	NGEF_HUMAN	C9JTV7_HUMAN,B4DDI2_HUMAN	UPI000013D4AE	.	.	.	.	6/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTATTATGG	.	2	ESCA
GBX2	0	.	GRCh37	2	237074317	237074317	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*240C>G	.	.	ENST00000306318	2/2	64	57	7	60	60	0	GBX2,3_prime_UTR_variant,,ENST00000306318,;GBX2,downstream_gene_variant,,ENST00000551105,;AC079135.1,upstream_gene_variant,,ENST00000483218,;AC079135.1,upstream_gene_variant,,ENST00000415226,;GBX2,downstream_gene_variant,,ENST00000465889,;	C	ENSG00000168505	ENST00000306318	Transcript	3_prime_UTR_variant	1685	.	.	.	.	.	.	.	-1	GBX2	HGNC	4186	protein_coding	YES	CCDS2515.1	ENSP00000302251	GBX2_HUMAN	.	UPI000012B273	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTATAGAGATA	.	4	ESCA
AQP12A	0	.	GRCh37	2	241631651	241631651	+	Missense_Mutation	SNP	C	C	T	rs779109324	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284C>T	p.Ser95Phe	p.S95F	ENST00000337801	2/4	104	81	23	97	97	0	AQP12A,missense_variant,p.Ser95Phe,ENST00000337801,;AQP12A,missense_variant,p.Ser107Phe,ENST00000429564,;AC011298.2,downstream_gene_variant,,ENST00000407635,;AC011298.2,downstream_gene_variant,,ENST00000600041,;AQP12A,upstream_gene_variant,,ENST00000474778,;AQP12A,upstream_gene_variant,,ENST00000471878,;AQP12A,upstream_gene_variant,,ENST00000460527,;	T	ENSG00000184945	ENST00000337801	Transcript	missense_variant	353	284	95	S/F	tCt/tTt	rs779109324	.	.	1	AQP12A	HGNC	19941	protein_coding	YES	.	ENSP00000337144	AQ12A_HUMAN	.	UPI00000743B9	.	deleterious(0)	probably_damaging(0.964)	2/4	.	hmmpanther:PTHR21191:SF8,hmmpanther:PTHR21191,Pfam_domain:PF00230,Gene3D:1.20.1080.10,PIRSF_domain:PIRSF017529,Superfamily_domains:SSF81338,Prints_domain:PR02025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTCTCTGC	.	5	ESCA
KIF3C	0	.	GRCh37	2	26203716	26203716	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1071C>G	p.%3D	p.R357R	ENST00000264712	1/8	117	109	7	88	88	0	KIF3C,synonymous_variant,p.%3D,ENST00000264712,;KIF3C,synonymous_variant,p.%3D,ENST00000405914,;KIF3C,synonymous_variant,p.%3D,ENST00000455394,;KIF3C,synonymous_variant,p.%3D,ENST00000417737,;KIF3C,upstream_gene_variant,,ENST00000475453,;	C	ENSG00000084731	ENST00000264712	Transcript	synonymous_variant	1651	1071	357	R	cgC/cgG	.	.	.	-1	KIF3C	HGNC	6321	protein_coding	YES	CCDS1719.1	ENSP00000264712	KIF3C_HUMAN	.	UPI000013D55A	.	.	.	1/8	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF349,hmmpanther:PTHR24115,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAAAGCGCAA	.	2	ESCA
SLC8A1	0	.	GRCh37	2	40656660	40656660	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.761G>T	p.Arg254Met	p.R254M	ENST00000403092	2/11	75	66	8	45	45	0	SLC8A1,missense_variant,p.Arg254Met,ENST00000408028,;SLC8A1,missense_variant,p.Arg254Met,ENST00000406785,;SLC8A1,missense_variant,p.Arg254Met,ENST00000542024,;SLC8A1,missense_variant,p.Arg254Met,ENST00000403092,;SLC8A1,missense_variant,p.Arg254Met,ENST00000405269,;SLC8A1,missense_variant,p.Arg254Met,ENST00000332839,;SLC8A1,missense_variant,p.Arg254Met,ENST00000542756,;SLC8A1,missense_variant,p.Arg254Met,ENST00000406391,;SLC8A1,missense_variant,p.Arg254Met,ENST00000405901,;SLC8A1,missense_variant,p.Arg254Met,ENST00000402441,;SLC8A1,downstream_gene_variant,,ENST00000448531,;SLC8A1,downstream_gene_variant,,ENST00000455476,;SLC8A1,downstream_gene_variant,,ENST00000417271,;SLC8A1,missense_variant,p.Arg251Met,ENST00000407929,;	A	ENSG00000183023	ENST00000403092	Transcript	missense_variant	795	761	254	R/M	aGg/aTg	.	.	.	-1	SLC8A1	HGNC	11068	protein_coding	YES	CCDS1806.1	ENSP00000384763	NAC1_HUMAN	Q6LAJ9_HUMAN,Q6LAJ8_HUMAN,Q4QQH3_HUMAN,E9PCL8_HUMAN,E9PB98_HUMAN	UPI000012FC46	.	deleterious(0)	probably_damaging(0.923)	2/11	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,TIGRFAM_domain:TIGR00845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTCCTATCC	.	4	ESCA
EML4	0	.	GRCh37	2	42558018	42558018	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*671A>C	.	.	ENST00000318522	23/23	72	48	24	62	62	0	EML4,3_prime_UTR_variant,,ENST00000318522,;EML4,downstream_gene_variant,,ENST00000401738,;COX7A2L,downstream_gene_variant,,ENST00000468711,;EML4,downstream_gene_variant,,ENST00000453191,;EML4,downstream_gene_variant,,ENST00000402711,;EML4,non_coding_transcript_exon_variant,,ENST00000406175,;	C	ENSG00000143924	ENST00000318522	Transcript	3_prime_UTR_variant	3879	.	.	.	.	.	.	.	1	EML4	HGNC	1316	protein_coding	YES	CCDS1807.1	ENSP00000320663	EMAL4_HUMAN	F2Z2B5_HUMAN	UPI0000140350	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCAACTCTG	.	5	ESCA
SLC3A1	0	.	GRCh37	2	44513196	44513204	+	In_Frame_Del	DEL	GGCACTTTG	GGCACTTTG	CGC	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	GGCACTTTG	GGCACTTTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.791_799delGGCACTTTGinsCGC	p.Trp264_Asp267delinsSerHis	p.W264_D267delinsSH	ENST00000260649	4/10	76	66	10	44	44	0	SLC3A1,protein_altering_variant,p.Trp264_Asp267delinsSerHis,ENST00000260649,;SLC3A1,protein_altering_variant,p.Trp264_Asp267delinsSerHis,ENST00000409387,;SLC3A1,protein_altering_variant,p.Trp264_Asp267delinsSerHis,ENST00000409229,;SLC3A1,protein_altering_variant,p.Trp264_Asp267delinsSerHis,ENST00000409741,;SLC3A1,protein_altering_variant,p.Trp264_Asp267delinsSerHis,ENST00000410056,;SLC3A1,protein_altering_variant,p.Trp42_Asp45delinsSerHis,ENST00000427285,;SLC3A1,5_prime_UTR_variant,,ENST00000409380,;	CGC	ENSG00000138079	ENST00000260649	Transcript	protein_altering_variant	867-875	791-799	264-267	WHFD/SH	tGGCACTTTGac/tCGCac	.	.	.	1	SLC3A1	HGNC	11025	protein_coding	YES	CCDS1819.1	ENSP00000260649	SLC31_HUMAN	E7ENC4_HUMAN	UPI000013D0F2	.	.	.	4/10	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF73,Gene3D:3.90.400.10,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	PINDEL|VARSCANS*	CCAGTTGGCACTTTGACGAA	.	2	ESCA
EPAS1	0	.	GRCh37	2	46607509	46607510	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1699dupA	p.Met567AsnfsTer44	p.M567Nfs*44	ENST00000263734	12/16	74	51	23	47	47	0	EPAS1,frameshift_variant,p.Met567AsnfsTer44,ENST00000263734,;EPAS1,upstream_gene_variant,,ENST00000468530,;EPAS1,non_coding_transcript_exon_variant,,ENST00000466465,;EPAS1,upstream_gene_variant,,ENST00000465318,;EPAS1,downstream_gene_variant,,ENST00000483692,;	A	ENSG00000116016	ENST00000263734	Transcript	frameshift_variant	2208-2209	1698-1699	566-567	-/X	-/A	.	.	.	1	EPAS1	HGNC	3374	protein_coding	YES	CCDS1825.1	ENSP00000263734	EPAS1_HUMAN	Q53SM6_HUMAN,C9J9N2_HUMAN,B3KW07_HUMAN	UPI000013D44F	.	.	.	12/16	.	hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTGCCATGAC	.	3	ESCA
MSH2	0	.	GRCh37	2	47702214	47702214	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1810G>A	p.Ala604Thr	p.A604T	ENST00000233146	12/16	106	70	35	87	87	0	MSH2,missense_variant,p.Ala604Thr,ENST00000406134,;MSH2,missense_variant,p.Ala604Thr,ENST00000233146,;MSH2,missense_variant,p.Ala538Thr,ENST00000543555,;	A	ENSG00000095002	ENST00000233146	Transcript	missense_variant	2033	1810	604	A/T	Gct/Act	.	.	.	1	MSH2	HGNC	7325	protein_coding	YES	CCDS1834.1	ENSP00000233146	MSH2_HUMAN	Q53RU4_HUMAN,C9J809_HUMAN,B4DL39_HUMAN	UPI00000405F6	.	deleterious(0.03)	probably_damaging(0.934)	12/16	.	hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF35,Pfam_domain:PF05192,SMART_domains:SM00533,PIRSF_domain:PIRSF005813,Superfamily_domains:SSF48334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATGCTGTT	.	5	ESCA
C2orf73	0	.	GRCh37	2	54562094	54562094	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.167A>G	p.Asn56Ser	p.N56S	ENST00000398634	2/5	78	62	15	73	73	0	C2orf73,missense_variant,p.Asn56Ser,ENST00000398634,;C2orf73,missense_variant,p.Asn62Ser,ENST00000486488,;C2orf73,intron_variant,,ENST00000447328,;C2orf73,intron_variant,,ENST00000405749,;C2orf73,intron_variant,,ENST00000491538,;C2orf73,intron_variant,,ENST00000317627,;C2orf73,intron_variant,,ENST00000414747,;	G	ENSG00000177994	ENST00000398634	Transcript	missense_variant	209	167	56	N/S	aAc/aGc	.	.	.	1	C2orf73	HGNC	26861	protein_coding	YES	CCDS46285.1	ENSP00000381631	CB073_HUMAN	B7ZM11_HUMAN	UPI00001C1DC4	.	tolerated(0.17)	benign(0.39)	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTAACACAA	.	5	ESCA
CCDC85A	0	.	GRCh37	2	56599497	56599497	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1336C>T	p.Gln446Ter	p.Q446*	ENST00000407595	4/6	120	76	44	61	60	1	CCDC85A,stop_gained,p.Gln446Ter,ENST00000407595,;RP11-482H16.1,intron_variant,,ENST00000607540,;	T	ENSG00000055813	ENST00000407595	Transcript	stop_gained	1838	1336	446	Q/*	Caa/Taa	.	.	.	1	CCDC85A	HGNC	29400	protein_coding	YES	CCDS46290.1	ENSP00000384040	CC85A_HUMAN	.	UPI00001C1DC1	.	.	.	4/6	.	hmmpanther:PTHR13546,hmmpanther:PTHR13546:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGGCAACCT	.	5	ESCA
SOX11	0	.	GRCh37	2	5840840	5840840	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6661T>C	.	.	ENST00000322002	1/1	65	55	10	54	54	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	C	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	8042	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTTTTCCG	.	5	ESCA
RP11-67L2.2	0	.	GRCh37	3	122606017	122606017	+	RNA	SNP	G	G	A	rs559372578	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.230G>A	.	.	ENST00000610128	1/1	44	33	11	46	46	0	RP11-67L2.2,non_coding_transcript_exon_variant,,ENST00000610128,;	A	ENSG00000273033	ENST00000610128	Transcript	non_coding_transcript_exon_variant	230	.	.	.	.	rs559372578	.	.	1	RP11-67L2.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGTCTGT	by1000G	5	ESCA
COL6A5	0	.	GRCh37	3	130098602	130098602	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009G>A	p.Gly337Arg	p.G337R	ENST00000265379	4/42	71	63	8	44	44	0	COL6A5,missense_variant,p.Gly337Arg,ENST00000432398,;COL6A5,missense_variant,p.Gly337Arg,ENST00000265379,;COL6A5,missense_variant,p.Gly337Arg,ENST00000312481,;	A	ENSG00000172752	ENST00000265379	Transcript	missense_variant	1503	1009	337	G/R	Gga/Aga	.	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	deleterious(0.01)	probably_damaging(0.99)	4/42	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF93,hmmpanther:PTHR22992,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACAAGGAGTG	.	4	ESCA
MSL2	0	.	GRCh37	3	135868065	135868065	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1924A>G	.	.	ENST00000309993	2/2	94	75	19	41	41	0	MSL2,3_prime_UTR_variant,,ENST00000309993,;PPP2R3A,downstream_gene_variant,,ENST00000264977,;MSL2,downstream_gene_variant,,ENST00000434835,;MSL2,downstream_gene_variant,,ENST00000481989,;PPP2R3A,downstream_gene_variant,,ENST00000490467,;MSL2,downstream_gene_variant,,ENST00000491050,;MSL2,downstream_gene_variant,,ENST00000473093,;PPP2R3A,downstream_gene_variant,,ENST00000334546,;	C	ENSG00000174579	ENST00000309993	Transcript	3_prime_UTR_variant	4391	.	.	.	.	.	.	.	-1	MSL2	HGNC	25544	protein_coding	YES	CCDS33861.1	ENSP00000311827	MSL2_HUMAN	C9J5S2_HUMAN,C9IZG7_HUMAN,C9IZ03_HUMAN	UPI000020A2D7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAATATATC	.	5	ESCA
STAG1	0	.	GRCh37	3	136056027	136056027	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1069A>T	.	.	ENST00000383202	34/34	160	143	17	106	106	0	STAG1,3_prime_UTR_variant,,ENST00000383202,;PCCB,3_prime_UTR_variant,,ENST00000478469,;STAG1,3_prime_UTR_variant,,ENST00000236698,;PCCB,3_prime_UTR_variant,,ENST00000471595,;STAG1,downstream_gene_variant,,ENST00000536929,;STAG1,downstream_gene_variant,,ENST00000434713,;STAG1,downstream_gene_variant,,ENST00000483235,;	A	ENSG00000118007	ENST00000383202	Transcript	3_prime_UTR_variant	5103	.	.	.	.	.	.	.	-1	STAG1	HGNC	11354	protein_coding	YES	CCDS3090.1	ENSP00000372689	STAG1_HUMAN	Q4LE48_HUMAN	UPI000020A2DE	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTATAATCA	.	4	ESCA
MRPS22	0	.	GRCh37	3	139074623	139074623	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.978T>A	p.Asn326Lys	p.N326K	ENST00000495075	9/10	162	131	30	89	89	0	MRPS22,missense_variant,p.Asn326Lys,ENST00000495075,;MRPS22,missense_variant,p.Asn326Lys,ENST00000310776,;MRPS22,missense_variant,p.Asn325Lys,ENST00000465056,;MRPS22,missense_variant,p.Asn285Lys,ENST00000478464,;COPB2,intron_variant,,ENST00000503326,;COPB2,downstream_gene_variant,,ENST00000333188,;COPB2,downstream_gene_variant,,ENST00000512309,;COPB2,downstream_gene_variant,,ENST00000507777,;MRPS22,downstream_gene_variant,,ENST00000480644,;MRPS22,3_prime_UTR_variant,,ENST00000498505,;MRPS22,non_coding_transcript_exon_variant,,ENST00000492644,;MRPS22,non_coding_transcript_exon_variant,,ENST00000480938,;COPB2,downstream_gene_variant,,ENST00000502734,;MRPS22,downstream_gene_variant,,ENST00000483545,;MRPS22,downstream_gene_variant,,ENST00000466690,;	A	ENSG00000175110	ENST00000495075	Transcript	missense_variant	1410	978	326	N/K	aaT/aaA	.	.	.	1	MRPS22	HGNC	14508	protein_coding	YES	CCDS3107.1	ENSP00000418008	RT22_HUMAN	Q96Q16_HUMAN	UPI0000042222	.	deleterious(0.02)	benign(0.003)	9/10	.	hmmpanther:PTHR13071:SF4,hmmpanther:PTHR13071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAATTTAAT	.	5	ESCA
TRPC1	0	.	GRCh37	3	142521063	142521063	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1634T>G	p.Leu545Arg	p.L545R	ENST00000476941	10/13	175	147	27	112	112	0	TRPC1,missense_variant,p.Leu511Arg,ENST00000273482,;TRPC1,missense_variant,p.Leu545Arg,ENST00000476941,;RNU7-47P,downstream_gene_variant,,ENST00000515978,;	G	ENSG00000144935	ENST00000476941	Transcript	missense_variant	2120	1634	545	L/R	cTt/cGt	.	.	.	1	TRPC1	HGNC	12333	protein_coding	YES	CCDS58856.1	ENSP00000419313	TRPC1_HUMAN	.	UPI00001374A4	.	deleterious(0.04)	probably_damaging(0.987)	10/13	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF3,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTCTTCTTG	.	4	ESCA
ZIC1	0	.	GRCh37	3	147130385	147130385	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1063G>C	p.Val355Leu	p.V355L	ENST00000282928	2/3	114	96	17	82	82	0	ZIC1,missense_variant,p.Val44Leu,ENST00000488404,;ZIC1,missense_variant,p.Val355Leu,ENST00000282928,;ZIC1,intron_variant,,ENST00000472523,;	C	ENSG00000152977	ENST00000282928	Transcript	missense_variant	1792	1063	355	V/L	Gtg/Ctg	.	.	.	1	ZIC1	HGNC	12872	protein_coding	YES	CCDS3136.1	ENSP00000282928	ZIC1_HUMAN	.	UPI000013DD09	.	deleterious(0)	probably_damaging(0.914)	2/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF26,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCACGTGCAC	.	4	ESCA
CAPN7	0	.	GRCh37	3	15248038	15248038	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36G>T	p.Gln12His	p.Q12H	ENST00000253693	1/21	51	36	15	64	64	0	CAPN7,missense_variant,p.Gln12His,ENST00000253693,;COL6A4P1,upstream_gene_variant,,ENST00000446690,;CAPN7,missense_variant,p.Gln12His,ENST00000418994,;CAPN7,missense_variant,p.Gln12His,ENST00000457023,;	T	ENSG00000131375	ENST00000253693	Transcript	missense_variant	289	36	12	Q/H	caG/caT	.	.	.	1	CAPN7	HGNC	1484	protein_coding	YES	CCDS2624.1	ENSP00000253693	CAN7_HUMAN	.	UPI0000038A6D	.	tolerated(0.17)	benign(0.004)	1/21	.	Superfamily_domains:SSF116846,SMART_domains:SM00745,Pfam_domain:PF04212,Gene3D:1.20.58.280,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCAGTTCGC	.	5	ESCA
IFT80	0	.	GRCh37	3	160117253	160117253	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-366G>A	.	.	ENST00000326448	1/20	98	89	9	54	54	0	IFT80,5_prime_UTR_variant,,ENST00000498409,;SMC4,5_prime_UTR_variant,,ENST00000357388,;IFT80,5_prime_UTR_variant,,ENST00000475677,;IFT80,5_prime_UTR_variant,,ENST00000326448,;IFT80,5_prime_UTR_variant,,ENST00000478536,;SMC4,intron_variant,,ENST00000497311,;IFT80,upstream_gene_variant,,ENST00000465537,;SMC4,upstream_gene_variant,,ENST00000465903,;IFT80,upstream_gene_variant,,ENST00000489004,;SMC4,upstream_gene_variant,,ENST00000360111,;IFT80,upstream_gene_variant,,ENST00000478370,;SMC4,upstream_gene_variant,,ENST00000485867,;IFT80,upstream_gene_variant,,ENST00000486856,;SMC4,upstream_gene_variant,,ENST00000344722,;SMC4,upstream_gene_variant,,ENST00000472991,;IFT80,upstream_gene_variant,,ENST00000496589,;SMC4,upstream_gene_variant,,ENST00000489573,;IFT80,upstream_gene_variant,,ENST00000468218,;SMC4,upstream_gene_variant,,ENST00000490207,;SMC4,upstream_gene_variant,,ENST00000462787,;SMC4,upstream_gene_variant,,ENST00000485645,;SMC4,upstream_gene_variant,,ENST00000469762,;SMC4,upstream_gene_variant,,ENST00000467468,;IFT80,non_coding_transcript_exon_variant,,ENST00000498145,;IFT80,non_coding_transcript_exon_variant,,ENST00000466326,;IFT80,upstream_gene_variant,,ENST00000468327,;SMC4,upstream_gene_variant,,ENST00000470240,;IFT80,upstream_gene_variant,,ENST00000465972,;SMC4,upstream_gene_variant,,ENST00000472282,;IFT80,upstream_gene_variant,,ENST00000477495,;IFT80,upstream_gene_variant,,ENST00000478460,;SMC4,upstream_gene_variant,,ENST00000497984,;IFT80,upstream_gene_variant,,ENST00000472773,;RP11-432B6.3,intron_variant,,ENST00000483754,;IFT80,upstream_gene_variant,,ENST00000467254,;SMC4,upstream_gene_variant,,ENST00000469858,;IFT80,upstream_gene_variant,,ENST00000487943,;SMC4,upstream_gene_variant,,ENST00000468653,;IFT80,upstream_gene_variant,,ENST00000482317,;	T	ENSG00000068885	ENST00000326448	Transcript	5_prime_UTR_variant	68	.	.	.	.	.	.	.	-1	IFT80	HGNC	29262	protein_coding	YES	CCDS3188.1	ENSP00000312778	IFT80_HUMAN	C9JUJ1_HUMAN,C9JUI1_HUMAN,C9JSB1_HUMAN,C9J6I5_HUMAN,C9J6G8_HUMAN,C9J627_HUMAN,C9IZR2_HUMAN	UPI0000160F16	.	.	.	1/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AATCCCTCGCT	.	3	ESCA
MECOM	0	.	GRCh37	3	168864376	168864376	+	5'Flank	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000264674	.	120	99	21	96	96	0	MECOM,5_prime_UTR_variant,,ENST00000468789,;MECOM,intron_variant,,ENST00000481315,;MECOM,intron_variant,,ENST00000464456,;MECOM,intron_variant,,ENST00000494292,;MECOM,upstream_gene_variant,,ENST00000472280,;MECOM,upstream_gene_variant,,ENST00000460890,;MECOM,upstream_gene_variant,,ENST00000487503,;MECOM,upstream_gene_variant,,ENST00000484519,;MECOM,upstream_gene_variant,,ENST00000392736,;MECOM,upstream_gene_variant,,ENST00000433243,;MECOM,upstream_gene_variant,,ENST00000475754,;MECOM,upstream_gene_variant,,ENST00000264674,;MECOM,upstream_gene_variant,,ENST00000494597,;MECOM,downstream_gene_variant,,ENST00000485957,;	A	ENSG00000085276	ENST00000264674	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	283	-1	MECOM	HGNC	3498	protein_coding	YES	CCDS54670.1	ENSP00000264674	EVI1_HUMAN	Q9UBK3_HUMAN,Q8IU84_HUMAN,E9PGE9_HUMAN,E7EU48_HUMAN,E7ERX0_HUMAN,E7EPY2_HUMAN,D3DNP4_HUMAN	UPI00015D43FA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAGACTGCGG	.	4	ESCA
FXR1	0	.	GRCh37	3	180688017	180688017	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1474G>A	p.Asp492Asn	p.D492N	ENST00000357559	15/17	82	74	8	52	52	0	FXR1,missense_variant,p.Asp93Asn,ENST00000482125,;FXR1,missense_variant,p.Asp492Asn,ENST00000357559,;FXR1,missense_variant,p.Asp443Asn,ENST00000491062,;FXR1,missense_variant,p.Asp492Asn,ENST00000445140,;FXR1,missense_variant,p.Asp479Asn,ENST00000480918,;FXR1,missense_variant,p.Asp407Asn,ENST00000305586,;FXR1,missense_variant,p.Asp407Asn,ENST00000468861,;FXR1,non_coding_transcript_exon_variant,,ENST00000476672,;FXR1,non_coding_transcript_exon_variant,,ENST00000475315,;FXR1,non_coding_transcript_exon_variant,,ENST00000472339,;FXR1,non_coding_transcript_exon_variant,,ENST00000481383,;FXR1,downstream_gene_variant,,ENST00000498658,;	A	ENSG00000114416	ENST00000357559	Transcript	missense_variant	1858	1474	492	D/N	Gat/Aat	.	.	.	1	FXR1	HGNC	4023	protein_coding	YES	CCDS3238.1	ENSP00000350170	FXR1_HUMAN	C9JZE0_HUMAN,C9JY20_HUMAN,C9J5B4_HUMAN,C9IZ22_HUMAN	UPI000013EA6E	.	deleterious_low_confidence(0)	probably_damaging(0.998)	15/17	.	hmmpanther:PTHR10603,hmmpanther:PTHR10603:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACTGATGCC	.	4	ESCA
PARL	0	.	GRCh37	3	183551536	183551547	+	Frame_Shift_Del	DEL	CGGAAGGAAAAT	CGGAAGGAAAAT	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	CGGAAGGAAAAT	CGGAAGGAAAAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895_906delATTTTCCTTCCGinsT	p.Ile299TyrfsTer29	p.I299Yfs*29	ENST00000317096	8/10	92	76	16	68	68	0	PARL,frameshift_variant,p.Ile249TyrfsTer29,ENST00000311101,;PARL,frameshift_variant,p.Ile91TyrfsTer29,ENST00000417784,;PARL,frameshift_variant,p.Ile299TyrfsTer29,ENST00000317096,;PARL,intron_variant,,ENST00000435888,;PARL,intron_variant,,ENST00000418450,;PARL,intron_variant,,ENST00000450375,;PARL,downstream_gene_variant,,ENST00000449306,;PARL,3_prime_UTR_variant,,ENST00000421484,;	A	ENSG00000175193	ENST00000317096	Transcript	frameshift_variant	956-967	895-906	299-302	IFLP/X	ATTTTCCTTCCG/T	.	.	.	-1	PARL	HGNC	18253	protein_coding	YES	CCDS3248.1	ENSP00000325421	PARL_HUMAN	.	UPI00000711C6	.	.	.	8/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22936,Gene3D:2xovA00,Pfam_domain:PF01694,Superfamily_domains:SSF144091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	GAACATCGGAAGGAAAATAATGG	.	2	ESCA
DYNC1LI1	0	.	GRCh37	3	32567838	32567838	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*453A>G	.	.	ENST00000273130	13/13	91	79	12	77	77	0	DYNC1LI1,3_prime_UTR_variant,,ENST00000273130,;DYNC1LI1,3_prime_UTR_variant,,ENST00000432458,;DYNC1LI1,non_coding_transcript_exon_variant,,ENST00000481915,;DYNC1LI1,downstream_gene_variant,,ENST00000472985,;	C	ENSG00000144635	ENST00000273130	Transcript	3_prime_UTR_variant	2129	.	.	.	.	.	.	.	-1	DYNC1LI1	HGNC	18745	protein_coding	YES	CCDS2654.1	ENSP00000273130	DC1L1_HUMAN	B3KM42_HUMAN	UPI000013D99D	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACGATTTTTC	.	4	ESCA
FAM19A4	0	.	GRCh37	3	68781385	68781385	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*908T>A	.	.	ENST00000295569	6/6	64	47	17	64	64	0	FAM19A4,3_prime_UTR_variant,,ENST00000295569,;	T	ENSG00000163377	ENST00000295569	Transcript	3_prime_UTR_variant	1824	.	.	.	.	.	.	.	-1	FAM19A4	HGNC	21591	protein_coding	YES	CCDS2907.1	ENSP00000295569	F19A4_HUMAN	C9JUW7_HUMAN	UPI0000071129	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTACAGTCTA	.	5	ESCA
ROBO2	0	.	GRCh37	3	77695632	77695632	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*426A>T	.	.	ENST00000487694	27/27	54	43	11	51	51	0	ROBO2,3_prime_UTR_variant,,ENST00000332191,;ROBO2,3_prime_UTR_variant,,ENST00000461745,;ROBO2,3_prime_UTR_variant,,ENST00000487694,;ROBO2,downstream_gene_variant,,ENST00000490534,;ROBO2,downstream_gene_variant,,ENST00000475334,;ROBO2,3_prime_UTR_variant,,ENST00000473767,;ROBO2,non_coding_transcript_exon_variant,,ENST00000470802,;	T	ENSG00000185008	ENST00000487694	Transcript	3_prime_UTR_variant	4890	.	.	.	.	.	.	.	1	ROBO2	HGNC	10250	protein_coding	YES	CCDS54609.1	ENSP00000417335	ROBO2_HUMAN	H9XFA4_HUMAN	UPI0000D891EC	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTAAATTT	.	5	ESCA
ROBO2	0	.	GRCh37	3	77695780	77695780	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*574G>T	.	.	ENST00000487694	27/27	33	26	7	30	30	0	ROBO2,3_prime_UTR_variant,,ENST00000332191,;ROBO2,3_prime_UTR_variant,,ENST00000461745,;ROBO2,3_prime_UTR_variant,,ENST00000487694,;ROBO2,downstream_gene_variant,,ENST00000490534,;ROBO2,downstream_gene_variant,,ENST00000475334,;ROBO2,3_prime_UTR_variant,,ENST00000473767,;ROBO2,non_coding_transcript_exon_variant,,ENST00000470802,;	T	ENSG00000185008	ENST00000487694	Transcript	3_prime_UTR_variant	5038	.	.	.	.	.	.	.	1	ROBO2	HGNC	10250	protein_coding	YES	CCDS54609.1	ENSP00000417335	ROBO2_HUMAN	H9XFA4_HUMAN	UPI0000D891EC	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCAGTTGGG	.	2	ESCA
CADM2	0	.	GRCh37	3	85961663	85961663	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.649C>G	p.Gln217Glu	p.Q217E	ENST00000405615	5/10	126	117	9	69	69	0	CADM2,missense_variant,p.Gln215Glu,ENST00000407528,;CADM2,missense_variant,p.Gln224Glu,ENST00000383699,;CADM2,missense_variant,p.Gln217Glu,ENST00000405615,;	G	ENSG00000175161	ENST00000405615	Transcript	missense_variant	649	649	217	Q/E	Cag/Gag	.	.	.	1	CADM2	HGNC	29849	protein_coding	YES	CCDS33792.1	ENSP00000384193	CADM2_HUMAN	G3XHN8_HUMAN	UPI000013F077	.	tolerated(0.08)	benign(0.021)	5/10	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF56,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCCTCAGGTA	.	2	ESCA
HTR1F	0	.	GRCh37	3	88039960	88039960	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61C>G	p.Pro21Ala	p.P21A	ENST00000319595	1/1	138	118	20	83	82	0	HTR1F,missense_variant,p.Pro21Ala,ENST00000319595,;	G	ENSG00000179097	ENST00000319595	Transcript	missense_variant	115	61	21	P/A	Cca/Gca	COSM269338	.	.	1	HTR1F	HGNC	5292	protein_coding	YES	CCDS2920.1	ENSP00000322924	5HT1F_HUMAN	Q9P2Q4_HUMAN	UPI00000503DF	.	tolerated(0.86)	benign(0.075)	1/1	.	hmmpanther:PTHR24247:SF34,hmmpanther:PTHR24247,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00515	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAATGCCATCC	.	4	ESCA
CGGBP1	0	.	GRCh37	3	88102996	88102996	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1627T>C	.	.	ENST00000398392	1/1	89	75	13	46	46	0	CGGBP1,3_prime_UTR_variant,,ENST00000309534,;CGGBP1,3_prime_UTR_variant,,ENST00000398392,;CGGBP1,downstream_gene_variant,,ENST00000482016,;CGGBP1,downstream_gene_variant,,ENST00000462901,;CGGBP1,downstream_gene_variant,,ENST00000467332,;CGGBP1,downstream_gene_variant,,ENST00000474441,;	G	ENSG00000163320	ENST00000398392	Transcript	3_prime_UTR_variant	3464	.	.	.	.	.	.	.	-1	CGGBP1	HGNC	1888	protein_coding	YES	CCDS43111.1	ENSP00000381429	CGBP1_HUMAN	C9JUJ0_HUMAN	UPI000006DF25	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCTAGGCAT	.	4	ESCA
ETNPPL	0	.	GRCh37	4	109674128	109674128	+	Missense_Mutation	SNP	C	C	G	rs772650876	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.541G>C	p.Asp181His	p.D181H	ENST00000296486	6/13	57	39	17	71	71	0	ETNPPL,missense_variant,p.Asp141His,ENST00000510706,;ETNPPL,missense_variant,p.Asp175His,ENST00000411864,;ETNPPL,missense_variant,p.Asp181His,ENST00000296486,;ETNPPL,missense_variant,p.Asp123His,ENST00000512646,;ETNPPL,downstream_gene_variant,,ENST00000512320,;ETNPPL,downstream_gene_variant,,ENST00000510723,;ETNPPL,3_prime_UTR_variant,,ENST00000505233,;ETNPPL,non_coding_transcript_exon_variant,,ENST00000511923,;ETNPPL,downstream_gene_variant,,ENST00000509402,;ETNPPL,upstream_gene_variant,,ENST00000503912,;	G	ENSG00000164089	ENST00000296486	Transcript	missense_variant	696	541	181	D/H	Gac/Cac	rs772650876,COSM4121251	.	.	-1	ETNPPL	HGNC	14404	protein_coding	YES	CCDS3682.1	ENSP00000296486	AT2L1_HUMAN	E7ENR6_HUMAN,D6RGG2_HUMAN	UPI000004B638	.	deleterious(0)	probably_damaging(0.961)	6/13	.	hmmpanther:PTHR11986,hmmpanther:PTHR11986:SF63,Pfam_domain:PF00202,Gene3D:3.40.640.10,PIRSF_domain:PIRSF000521,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGTCTTCTC	.	5	ESCA
ARHGAP10	0	.	GRCh37	4	148786095	148786095	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.585G>A	p.%3D	p.E195E	ENST00000336498	6/23	81	52	29	91	91	0	ARHGAP10,synonymous_variant,p.%3D,ENST00000336498,;ARHGAP10,non_coding_transcript_exon_variant,,ENST00000506054,;	A	ENSG00000071205	ENST00000336498	Transcript	synonymous_variant	824	585	195	E	gaG/gaA	.	.	.	1	ARHGAP10	HGNC	26099	protein_coding	YES	CCDS34075.1	ENSP00000336923	RHG10_HUMAN	Q8ND72_HUMAN,Q3KQX3_HUMAN	UPI000013EA63	.	.	.	6/23	.	hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF5,Gene3D:1y2oA00,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGAGTTTGT	.	5	ESCA
FGB	0	.	GRCh37	4	155488798	155488798	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544T>C	p.Tyr182His	p.Y182H	ENST00000302068	4/8	42	27	14	51	51	0	FGB,missense_variant,p.Tyr182His,ENST00000302068,;FGB,5_prime_UTR_variant,,ENST00000509493,;FGB,non_coding_transcript_exon_variant,,ENST00000502545,;FGB,non_coding_transcript_exon_variant,,ENST00000473984,;FGB,downstream_gene_variant,,ENST00000425838,;FGB,downstream_gene_variant,,ENST00000497097,;FGB,downstream_gene_variant,,ENST00000498375,;	C	ENSG00000171564	ENST00000302068	Transcript	missense_variant	607	544	182	Y/H	Tat/Cat	.	.	.	1	FGB	HGNC	3662	protein_coding	YES	CCDS3786.1	ENSP00000306099	FIBB_HUMAN	D6REL8_HUMAN,D3DP13_HUMAN,B4E1D3_HUMAN	UPI000012A778	.	tolerated(0.1)	possibly_damaging(0.873)	4/8	.	Superfamily_domains:SSF58010,Gene3D:1.20.5.50,Pfam_domain:PF08702,hmmpanther:PTHR19143:SF23,hmmpanther:PTHR19143	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AATTATATATA	.	3	ESCA
CDKN2AIP	0	.	GRCh37	4	184368914	184368914	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*334T>G	.	.	ENST00000504169	3/3	72	52	19	71	71	0	CDKN2AIP,3_prime_UTR_variant,,ENST00000302350,;CDKN2AIP,3_prime_UTR_variant,,ENST00000504169,;CDKN2AIP,downstream_gene_variant,,ENST00000510928,;CDKN2AIP,intron_variant,,ENST00000502924,;CDKN2AIP,downstream_gene_variant,,ENST00000506835,;	G	ENSG00000168564	ENST00000504169	Transcript	3_prime_UTR_variant	2284	.	.	.	.	.	.	.	1	CDKN2AIP	HGNC	24325	protein_coding	YES	CCDS34110.1	ENSP00000427108	CARF_HUMAN	B3KTW3_HUMAN	UPI000004A077	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATTAAGTT	.	5	ESCA
FAT1	0	.	GRCh37	4	187541055	187541055	+	Missense_Mutation	SNP	T	T	C	rs759239082	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6685A>G	p.Ile2229Val	p.I2229V	ENST00000441802	10/27	53	29	23	58	58	0	FAT1,missense_variant,p.Ile2229Val,ENST00000441802,;	C	ENSG00000083857	ENST00000441802	Transcript	missense_variant	6895	6685	2229	I/V	Att/Gtt	rs759239082	.	.	-1	FAT1	HGNC	3595	protein_coding	YES	CCDS47177.1	ENSP00000406229	FAT1_HUMAN	D6RCE4_HUMAN	UPI000051946B	.	.	benign(0.019)	10/27	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTAATAGTGA	.	5	ESCA
GABRG1	0	.	GRCh37	4	46042590	46042591	+	3'UTR	INS	-	-	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*414dupA	.	.	ENST00000295452	9/9	168	131	37	180	180	0	GABRG1,3_prime_UTR_variant,,ENST00000295452,;	T	ENSG00000163285	ENST00000295452	Transcript	3_prime_UTR_variant	1980-1981	.	.	.	.	.	.	.	-1	GABRG1	HGNC	4086	protein_coding	YES	CCDS3470.1	ENSP00000295452	GBRG1_HUMAN	.	UPI0000047AE2	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAGTCTTTTT	.	3	ESCA
HNRNPDL	0	.	GRCh37	4	83347630	83347630	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1178A>T	p.Tyr393Phe	p.Y393F	ENST00000295470	6/8	58	42	16	60	60	0	HNRNPDL,missense_variant,p.Tyr393Phe,ENST00000502762,;HNRNPDL,missense_variant,p.Tyr274Phe,ENST00000602300,;HNRNPDL,missense_variant,p.Tyr393Phe,ENST00000295470,;HNRNPDL,intron_variant,,ENST00000349655,;ENOPH1,upstream_gene_variant,,ENST00000273920,;ENOPH1,upstream_gene_variant,,ENST00000509635,;HNRNPDL,non_coding_transcript_exon_variant,,ENST00000514511,;HNRNPDL,non_coding_transcript_exon_variant,,ENST00000507721,;ENOPH1,upstream_gene_variant,,ENST00000505846,;	A	ENSG00000152795	ENST00000295470	Transcript	missense_variant	1354	1178	393	Y/F	tAt/tTt	.	.	.	-1	HNRNPDL	HGNC	5037	protein_coding	YES	CCDS3593.1	ENSP00000295470	HNRDL_HUMAN	B4DGN3_HUMAN	UPI0000073377	.	tolerated_low_confidence(0.19)	benign(0.431)	6/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCATATCCC	.	5	ESCA
CCSER1	0	.	GRCh37	4	92520186	92520186	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2681C>G	p.Thr894Ser	p.T894S	ENST00000509176	11/11	34	25	9	73	73	0	CCSER1,missense_variant,p.Thr894Ser,ENST00000509176,;CCSER1,missense_variant,p.Thr894Ser,ENST00000333691,;	G	ENSG00000184305	ENST00000509176	Transcript	missense_variant	2969	2681	894	T/S	aCt/aGt	.	.	.	1	CCSER1	HGNC	29349	protein_coding	YES	CCDS47099.1	ENSP00000425040	CCSE1_HUMAN	.	UPI00005A6104	.	tolerated_low_confidence(0.1)	benign(0.003)	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAACTCTAG	.	5	ESCA
MEGF10	0	.	GRCh37	5	126746293	126746293	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1130G>A	p.Ser377Asn	p.S377N	ENST00000274473	10/26	30	24	6	42	42	0	MEGF10,missense_variant,p.Ser377Asn,ENST00000508365,;MEGF10,missense_variant,p.Ser377Asn,ENST00000274473,;MEGF10,missense_variant,p.Ser377Asn,ENST00000418761,;MEGF10,missense_variant,p.Ser377Asn,ENST00000503335,;MEGF10,splice_region_variant,,ENST00000515002,;	A	ENSG00000145794	ENST00000274473	Transcript	missense_variant	1397	1130	377	S/N	aGc/aAc	.	.	.	1	MEGF10	HGNC	29634	protein_coding	YES	CCDS4142.1	ENSP00000274473	MEG10_HUMAN	.	UPI000006F868	.	deleterious(0.01)	possibly_damaging(0.88)	10/26	.	hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF75,Pfam_domain:PF00053,Gene3D:2gy5A03,SMART_domains:SM00180,SMART_domains:SM00181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATAGGTGAG	.	5	ESCA
PKD2L2	0	.	GRCh37	5	137225149	137225149	+	5'Flank	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000290431	.	31	18	13	43	43	0	PKD2L2,5_prime_UTR_variant,,ENST00000350250,;PKD2L2,5_prime_UTR_variant,,ENST00000508638,;PKD2L2,intron_variant,,ENST00000503015,;PKD2L2,upstream_gene_variant,,ENST00000508883,;PKD2L2,upstream_gene_variant,,ENST00000290431,;PKD2L2,upstream_gene_variant,,ENST00000502810,;MYOT,downstream_gene_variant,,ENST00000239926,;MYOT,downstream_gene_variant,,ENST00000421631,;PKD2L2,upstream_gene_variant,,ENST00000511176,;MYOT,downstream_gene_variant,,ENST00000515645,;RP11-381K20.2,upstream_gene_variant,,ENST00000508281,;RP11-381K20.2,upstream_gene_variant,,ENST00000514616,;MYOT,downstream_gene_variant,,ENST00000509812,;PKD2L2,5_prime_UTR_variant,,ENST00000414094,;MYOT,downstream_gene_variant,,ENST00000511254,;MYOT,downstream_gene_variant,,ENST00000508938,;	T	ENSG00000078795	ENST00000290431	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	9	1	PKD2L2	HGNC	9012	protein_coding	YES	CCDS43367.1	ENSP00000290431	PK2L2_HUMAN	D6RF71_HUMAN,D6RBX8_HUMAN	UPI000049E016	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGCGAACG	.	5	ESCA
TAF7	0	.	GRCh37	5	140698912	140698912	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.700G>T	p.Asp234Tyr	p.D234Y	ENST00000313368	1/1	23	8	15	31	31	0	TAF7,missense_variant,p.Asp234Tyr,ENST00000313368,;AC005618.1,downstream_gene_variant,,ENST00000535969,;	A	ENSG00000178913	ENST00000313368	Transcript	missense_variant	1419	700	234	D/Y	Gat/Tat	.	.	.	-1	TAF7	HGNC	11541	protein_coding	YES	CCDS4259.1	ENSP00000312709	TAF7_HUMAN	.	UPI00001367E8	.	deleterious(0)	possibly_damaging(0.73)	1/1	.	hmmpanther:PTHR12228,hmmpanther:PTHR12228:SF3,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCTTCAT	.	5	ESCA
STK10	0	.	GRCh37	5	171469136	171469136	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2750C>G	.	.	ENST00000176763	19/19	72	20	52	125	125	0	STK10,3_prime_UTR_variant,,ENST00000176763,;STK10,downstream_gene_variant,,ENST00000520476,;STK10,downstream_gene_variant,,ENST00000517360,;	C	ENSG00000072786	ENST00000176763	Transcript	3_prime_UTR_variant	6001	.	.	.	.	.	.	.	-1	STK10	HGNC	11388	protein_coding	YES	CCDS34290.1	ENSP00000176763	STK10_HUMAN	.	UPI0000136104	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCAGAGAAC	.	5	ESCA
GOLPH3	0	.	GRCh37	5	32126582	32126582	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633G>A	p.%3D	p.Q211Q	ENST00000265070	4/4	111	89	22	98	98	0	GOLPH3,synonymous_variant,p.%3D,ENST00000265070,;CTD-2152M20.2,upstream_gene_variant,,ENST00000503441,;GOLPH3,downstream_gene_variant,,ENST00000512668,;GOLPH3,3_prime_UTR_variant,,ENST00000503610,;	T	ENSG00000113384	ENST00000265070	Transcript	synonymous_variant	949	633	211	Q	caG/caA	.	.	.	-1	GOLPH3	HGNC	15452	protein_coding	YES	CCDS3896.1	ENSP00000265070	GOLP3_HUMAN	B3KQJ9_HUMAN,B3KS18_HUMAN,B3KQ71_HUMAN	UPI000006EEF4	.	.	.	4/4	.	Pfam_domain:PF05719,Gene3D:2zihB00,hmmpanther:PTHR12704:SF3,hmmpanther:PTHR12704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCGCTGCTT	.	5	ESCA
WDR41	0	.	GRCh37	5	76736675	76736675	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.845A>G	p.Asn282Ser	p.N282S	ENST00000296679	9/13	47	20	27	63	63	0	WDR41,missense_variant,p.Asn53Ser,ENST00000507654,;WDR41,missense_variant,p.Asn227Ser,ENST00000507029,;WDR41,missense_variant,p.Asn28Ser,ENST00000414719,;WDR41,missense_variant,p.Asn282Ser,ENST00000296679,;WDR41,missense_variant,p.Asn74Ser,ENST00000511791,;WDR41,missense_variant,p.Asn108Ser,ENST00000511630,;WDR41,missense_variant,p.Asn217Ser,ENST00000515253,;WDR41,upstream_gene_variant,,ENST00000512033,;WDR41,3_prime_UTR_variant,,ENST00000509701,;WDR41,3_prime_UTR_variant,,ENST00000505129,;WDR41,non_coding_transcript_exon_variant,,ENST00000502528,;WDR41,downstream_gene_variant,,ENST00000506307,;	C	ENSG00000164253	ENST00000296679	Transcript	missense_variant	1221	845	282	N/S	aAt/aGt	.	.	.	-1	WDR41	HGNC	25601	protein_coding	YES	CCDS4038.1	ENSP00000296679	WDR41_HUMAN	B4E2L4_HUMAN	UPI00000744EF	.	tolerated(0.54)	benign(0.009)	9/13	.	Superfamily_domains:SSF50978,Gene3D:2.130.10.10,hmmpanther:PTHR22805,hmmpanther:PTHR22805:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCATTTGAT	.	5	ESCA
PAPD4	0	.	GRCh37	5	78944904	78944904	+	Silent	SNP	G	G	A	rs768766761	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.918G>A	p.%3D	p.P306P	ENST00000453514	10/15	98	31	66	127	127	0	PAPD4,synonymous_variant,p.%3D,ENST00000423041,;PAPD4,synonymous_variant,p.%3D,ENST00000453514,;PAPD4,synonymous_variant,p.%3D,ENST00000296783,;PAPD4,synonymous_variant,p.%3D,ENST00000428308,;PAPD4,intron_variant,,ENST00000504233,;PAPD4,non_coding_transcript_exon_variant,,ENST00000504982,;PAPD4,non_coding_transcript_exon_variant,,ENST00000513735,;PAPD4,downstream_gene_variant,,ENST00000509227,;	A	ENSG00000164329	ENST00000453514	Transcript	synonymous_variant	1611	918	306	P	ccG/ccA	rs768766761	.	.	1	PAPD4	HGNC	26776	protein_coding	YES	CCDS4048.1	ENSP00000397563	GLD2_HUMAN	.	UPI000013E386	.	.	.	10/15	.	hmmpanther:PTHR12271,Gene3D:3.30.460.10,Superfamily_domains:SSF81631	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCCGTTAGT	byFrequency	5	ESCA
GCM2	0	.	GRCh37	6	10877517	10877517	+	Missense_Mutation	SNP	G	G	A	rs532834782	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199C>T	p.Arg67Cys	p.R67C	ENST00000379491	2/5	32	27	5	33	33	0	GCM2,missense_variant,p.Arg67Cys,ENST00000379491,;SYCP2L,intron_variant,,ENST00000543878,;RP11-637O19.2,upstream_gene_variant,,ENST00000436249,;RP11-637O19.3,intron_variant,,ENST00000480294,;	A	ENSG00000124827	ENST00000379491	Transcript	missense_variant	347	199	67	R/C	Cgc/Tgc	rs532834782	.	.	-1	GCM2	HGNC	4198	protein_coding	YES	CCDS4517.1	ENSP00000368805	GCM2_HUMAN	D3GDV6_HUMAN	UPI0000073DE7	.	deleterious(0)	probably_damaging(1)	2/5	.	PROSITE_profiles:PS50807,hmmpanther:PTHR12414,hmmpanther:PTHR12414:SF4,Pfam_domain:PF03615,Superfamily_domains:0041800	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	GTTGCGCATGG	by1000G	2	ESCA
SASH1	0	.	GRCh37	6	148872166	148872166	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2472A>T	.	.	ENST00000367467	20/20	37	11	26	56	56	0	SASH1,3_prime_UTR_variant,,ENST00000367467,;	T	ENSG00000111961	ENST00000367467	Transcript	3_prime_UTR_variant	6691	.	.	.	.	.	.	.	1	SASH1	HGNC	19182	protein_coding	YES	CCDS5212.1	ENSP00000356437	SASH1_HUMAN	.	UPI00003519AE	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCATAGAAAA	.	5	ESCA
RAET1G	0	.	GRCh37	6	150240472	150240472	+	Intron	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.350-12T>C	.	.	ENST00000367360	.	50	44	5	82	82	0	RAET1G,intron_variant,,ENST00000367360,;RAET1G,intron_variant,,ENST00000479265,;RP11-244K5.8,non_coding_transcript_exon_variant,,ENST00000606915,;RAET1E-AS1,non_coding_transcript_exon_variant,,ENST00000605899,;RAET1E-AS1,non_coding_transcript_exon_variant,,ENST00000446954,;RAET1G,intron_variant,,ENST00000367361,;	G	ENSG00000203722	ENST00000367360	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RAET1G	HGNC	16795	protein_coding	YES	CCDS43514.1	ENSP00000356329	RET1G_HUMAN	J7HEM2_HUMAN	UPI00003B0CBD	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATCAAAGAG	.	4	ESCA
OPRM1	0	.	GRCh37	6	154412611	154412611	+	Intron	SNP	C	C	T	rs79668187	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1443+4C>T	.	.	ENST00000434900	.	34	12	22	62	62	0	OPRM1,missense_variant,p.Arg390Cys,ENST00000428397,;OPRM1,splice_region_variant,,ENST00000337049,;OPRM1,splice_region_variant,,ENST00000360422,;OPRM1,splice_region_variant,,ENST00000452687,;OPRM1,splice_region_variant,,ENST00000330432,;OPRM1,splice_region_variant,,ENST00000435918,;OPRM1,splice_region_variant,,ENST00000518759,;OPRM1,splice_region_variant,,ENST00000414028,;OPRM1,splice_region_variant,,ENST00000419506,;OPRM1,splice_region_variant,,ENST00000434900,;OPRM1,splice_region_variant,,ENST00000524163,;OPRM1,splice_region_variant,,ENST00000522236,;OPRM1,splice_region_variant,,ENST00000520708,;OPRM1,splice_region_variant,,ENST00000522555,;OPRM1,splice_region_variant,,ENST00000229768,;OPRM1,downstream_gene_variant,,ENST00000520282,;OPRM1,splice_region_variant,,ENST00000519613,;OPRM1,splice_region_variant,,ENST00000521106,;OPRM1,non_coding_transcript_exon_variant,,ENST00000522382,;OPRM1,splice_region_variant,,ENST00000522739,;OPRM1,splice_region_variant,,ENST00000519083,;OPRM1,splice_region_variant,,ENST00000524150,;	T	ENSG00000112038	ENST00000434900	Transcript	splice_region_variant	.	.	.	.	.	rs79668187,COSM258746,COSM258747,COSM258748	.	.	1	OPRM1	HGNC	8156	protein_coding	YES	CCDS47503.1	ENSP00000394624	OPRM_HUMAN	Q7Z6A5_HUMAN,Q71V90_HUMAN,C9EA00_HUMAN,C9E9Z9_HUMAN,C7E9I8_HUMAN,B8K2Q5_HUMAN	UPI0001899627	.	.	.	.	5/5	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0	T:0.0006	.	0,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTACGCAGT	byCluster|by1000G	5	ESCA
TAGAP	0	.	GRCh37	6	159463326	159463326	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.149-50C>T	.	.	ENST00000367066	.	26	7	19	26	26	0	TAGAP,intron_variant,,ENST00000326965,;TAGAP,intron_variant,,ENST00000338313,;TAGAP,intron_variant,,ENST00000367066,;RP1-111C20.4,non_coding_transcript_exon_variant,,ENST00000606470,;RP1-111C20.4,non_coding_transcript_exon_variant,,ENST00000606466,;RP1-111C20.4,non_coding_transcript_exon_variant,,ENST00000607391,;RP1-111C20.4,downstream_gene_variant,,ENST00000607796,;	A	ENSG00000164691	ENST00000367066	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TAGAP	HGNC	15669	protein_coding	YES	CCDS5261.1	ENSP00000356033	TAGAP_HUMAN	.	UPI0000071CD5	.	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTAAGAAGCA	.	5	ESCA
MAP3K4	0	.	GRCh37	6	161494611	161494611	+	Silent	SNP	C	C	T	rs374997561	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2064C>T	p.%3D	p.D688D	ENST00000392142	5/27	42	37	5	54	54	0	MAP3K4,synonymous_variant,p.%3D,ENST00000366919,;MAP3K4,synonymous_variant,p.%3D,ENST00000348824,;MAP3K4,synonymous_variant,p.%3D,ENST00000366920,;MAP3K4,synonymous_variant,p.%3D,ENST00000392142,;MAP3K4,synonymous_variant,p.%3D,ENST00000544041,;MAP3K4,3_prime_UTR_variant,,ENST00000490904,;MAP3K4,non_coding_transcript_exon_variant,,ENST00000542851,;MAP3K4,downstream_gene_variant,,ENST00000542952,;	T	ENSG00000085511	ENST00000392142	Transcript	synonymous_variant	2212	2064	688	D	gaC/gaT	rs374997561	.	.	1	MAP3K4	HGNC	6856	protein_coding	YES	CCDS34565.1	ENSP00000375986	M3K4_HUMAN	F5H534_HUMAN	UPI00004574E1	.	.	.	5/27	.	hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF53	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTGACGCTTT	byFrequency|byCluster	4	ESCA
KIAA0319	0	.	GRCh37	6	24564464	24564464	+	Silent	SNP	C	C	T	rs571054596	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2397G>A	p.%3D	p.S799S	ENST00000378214	15/21	87	51	35	65	65	0	KIAA0319,synonymous_variant,p.%3D,ENST00000543707,;KIAA0319,synonymous_variant,p.%3D,ENST00000430948,;KIAA0319,synonymous_variant,p.%3D,ENST00000378214,;KIAA0319,synonymous_variant,p.%3D,ENST00000535378,;KIAA0319,synonymous_variant,p.%3D,ENST00000537886,;	T	ENSG00000137261	ENST00000378214	Transcript	synonymous_variant	2922	2397	799	S	tcG/tcA	rs571054596	.	.	-1	KIAA0319	HGNC	21580	protein_coding	YES	CCDS34348.1	ENSP00000367459	K0319_HUMAN	.	UPI000020D61A	.	.	.	15/21	.	Superfamily_domains:SSF49299,SMART_domains:SM00060,SMART_domains:SM00089,Gene3D:2.60.40.670,hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF194	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTCCGAGGC	by1000G	5	ESCA
OR2B2	0	.	GRCh37	6	27879293	27879293	+	Missense_Mutation	SNP	C	C	A	rs770021461	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805G>T	p.Asp269Tyr	p.D269Y	ENST00000303324	1/1	92	80	12	86	86	0	OR2B2,missense_variant,p.Asp269Tyr,ENST00000303324,;	A	ENSG00000168131	ENST00000303324	Transcript	missense_variant	882	805	269	D/Y	Gac/Tac	rs770021461	.	.	-1	OR2B2	HGNC	13966	protein_coding	YES	CCDS4641.1	ENSP00000304419	OR2B2_HUMAN	Q6IFA1_HUMAN	UPI000004187A	.	deleterious(0)	probably_damaging(0.977)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26453:SF115,hmmpanther:PTHR26453,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGGTCTTTGG	byFrequency	4	ESCA
HLA-F	0	.	GRCh37	6	29691240	29691240	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1C>T	.	.	ENST00000259951	1/7	107	72	35	97	97	0	HLA-F,5_prime_UTR_variant,,ENST00000376861,;HLA-F,5_prime_UTR_variant,,ENST00000259951,;HLA-F,5_prime_UTR_variant,,ENST00000440587,;HLA-F,5_prime_UTR_variant,,ENST00000334668,;HLA-F,5_prime_UTR_variant,,ENST00000414333,;HLA-F,upstream_gene_variant,,ENST00000444621,;HLA-F,upstream_gene_variant,,ENST00000434407,;HLA-F,upstream_gene_variant,,ENST00000429294,;HLA-F,non_coding_transcript_exon_variant,,ENST00000482257,;HLA-F,non_coding_transcript_exon_variant,,ENST00000462777,;HLA-F,intron_variant,,ENST00000489502,;HLA-F,upstream_gene_variant,,ENST00000485513,;HLA-F,upstream_gene_variant,,ENST00000486194,;HLA-F,upstream_gene_variant,,ENST00000484704,;HLA-F,upstream_gene_variant,,ENST00000465459,;HLA-F,upstream_gene_variant,,ENST00000475996,;HLA-F-AS1,downstream_gene_variant,,ENST00000399247,;HLA-F,upstream_gene_variant,,ENST00000606273,;HCG4P11,non_coding_transcript_exon_variant,,ENST00000427340,;RPL23AP1,downstream_gene_variant,,ENST00000428990,;	T	ENSG00000204642	ENST00000259951	Transcript	5_prime_UTR_variant	56	.	.	.	.	.	.	.	1	HLA-F	HGNC	4963	protein_coding	YES	CCDS43437.1	ENSP00000259951	HLAF_HUMAN	Q5JZ48_HUMAN,O78094_HUMAN,F6T2Q8_HUMAN	UPI000013D098	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGTCATGGC	.	5	ESCA
LRFN2	0	.	GRCh37	6	40399644	40399644	+	Silent	SNP	G	G	A	rs756121681	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209C>T	p.%3D	p.S403S	ENST00000338305	2/3	81	66	15	85	85	0	LRFN2,synonymous_variant,p.%3D,ENST00000338305,;	A	ENSG00000156564	ENST00000338305	Transcript	synonymous_variant	1752	1209	403	S	agC/agT	rs756121681	.	.	-1	LRFN2	HGNC	21226	protein_coding	YES	CCDS34443.1	ENSP00000345985	LRFN2_HUMAN	.	UPI00001C1E47	.	.	.	2/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTGCTGGA	byFrequency	5	ESCA
TDRD6	0	.	GRCh37	6	46657521	46657521	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1656T>C	p.%3D	p.Y552Y	ENST00000316081	1/4	173	99	73	135	135	0	TDRD6,synonymous_variant,p.%3D,ENST00000316081,;TDRD6,synonymous_variant,p.%3D,ENST00000544460,;TDRD6,upstream_gene_variant,,ENST00000450697,;RP11-446F17.3,upstream_gene_variant,,ENST00000422284,;RP11-446F17.3,upstream_gene_variant,,ENST00000571590,;RP11-446F17.3,upstream_gene_variant,,ENST00000434329,;	C	ENSG00000180113	ENST00000316081	Transcript	synonymous_variant	1656	1656	552	Y	taT/taC	.	.	.	1	TDRD6	HGNC	21339	protein_coding	YES	CCDS34470.1	ENSP00000346065	TDRD6_HUMAN	.	UPI0000251E8A	.	.	.	1/4	.	Superfamily_domains:SSF63748,SMART_domains:SM00333,Gene3D:2.30.30.140,Pfam_domain:PF00567,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7,PROSITE_profiles:PS50304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTATTATAG	.	5	ESCA
B3GAT2	0	.	GRCh37	6	71571660	71571660	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758T>A	p.Val253Asp	p.V253D	ENST00000230053	3/4	13	7	6	24	24	0	B3GAT2,missense_variant,p.Val253Asp,ENST00000230053,;SMAP1,3_prime_UTR_variant,,ENST00000370455,;SMAP1,downstream_gene_variant,,ENST00000316999,;SMAP1,downstream_gene_variant,,ENST00000370452,;	T	ENSG00000112309	ENST00000230053	Transcript	missense_variant	1367	758	253	V/D	gTc/gAc	.	.	.	-1	B3GAT2	HGNC	922	protein_coding	YES	CCDS4974.1	ENSP00000230053	B3GA2_HUMAN	A8K1V3_HUMAN	UPI000012670C	.	deleterious(0)	probably_damaging(0.999)	3/4	.	hmmpanther:PTHR10896:SF8,hmmpanther:PTHR10896,Gene3D:3.90.550.10,Pfam_domain:PF03360,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATGACTTGA	.	2	ESCA
PNRC1	0	.	GRCh37	6	89794188	89794188	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*273T>G	.	.	ENST00000336032	2/2	55	44	11	60	60	0	PNRC1,3_prime_UTR_variant,,ENST00000336032,;PNRC1,downstream_gene_variant,,ENST00000369472,;PNRC1,downstream_gene_variant,,ENST00000354922,;RP11-63L7.5,upstream_gene_variant,,ENST00000606729,;	G	ENSG00000146278	ENST00000336032	Transcript	3_prime_UTR_variant	1374	.	.	.	.	.	.	.	1	PNRC1	HGNC	17278	protein_coding	YES	CCDS5018.1	ENSP00000336931	PNRC1_HUMAN	Q49A59_HUMAN	UPI0000052C62	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGTATATA	.	5	ESCA
LRRC4	0	.	GRCh37	7	127669037	127669037	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1657C>T	p.Arg553Trp	p.R553W	ENST00000249363	2/2	50	37	12	64	64	0	LRRC4,missense_variant,p.Arg553Trp,ENST00000249363,;SND1,intron_variant,,ENST00000354725,;SND1,intron_variant,,ENST00000486037,;LRRC4,downstream_gene_variant,,ENST00000494115,;LRRC4,downstream_gene_variant,,ENST00000478726,;LRRC4,downstream_gene_variant,,ENST00000476782,;SND1,intron_variant,,ENST00000484767,;SND1,intron_variant,,ENST00000470723,;	A	ENSG00000128594	ENST00000249363	Transcript	missense_variant	1915	1657	553	R/W	Cgg/Tgg	COSM1447870	.	.	-1	LRRC4	HGNC	15586	protein_coding	YES	CCDS5799.1	ENSP00000249363	LRRC4_HUMAN	C9JA92_HUMAN,C9J7V8_HUMAN,C9J7K7_HUMAN	UPI0000049DF3	.	deleterious(0)	probably_damaging(0.952)	2/2	.	hmmpanther:PTHR24369:SF9,hmmpanther:PTHR24369	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCGCTTAC	.	5	ESCA
IGFBP3	0	.	GRCh37	7	45956987	45956987	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473C>T	p.Pro158Leu	p.P158L	ENST00000381083	2/5	41	32	9	44	44	0	IGFBP3,missense_variant,p.Pro152Leu,ENST00000275521,;IGFBP3,missense_variant,p.Pro42Leu,ENST00000448817,;IGFBP3,missense_variant,p.Pro158Leu,ENST00000381083,;IGFBP3,missense_variant,p.Pro4Leu,ENST00000428530,;IGFBP3,missense_variant,p.Pro14Leu,ENST00000417621,;IGFBP3,missense_variant,p.Pro55Leu,ENST00000381086,;IGFBP3,non_coding_transcript_exon_variant,,ENST00000465642,;IGFBP3,non_coding_transcript_exon_variant,,ENST00000460477,;IGFBP3,upstream_gene_variant,,ENST00000460209,;	A	ENSG00000146674	ENST00000381083	Transcript	missense_variant	584	473	158	P/L	cCg/cTg	.	.	.	-1	IGFBP3	HGNC	5472	protein_coding	YES	CCDS34632.1	ENSP00000370473	IBP3_HUMAN	B3KPF0_HUMAN	UPI00004F8E1F	.	tolerated(0.36)	benign(0.008)	2/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11551:SF3,hmmpanther:PTHR11551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGACGGGCTC	.	5	ESCA
SNORA15	0	.	GRCh37	7	64533839	64533839	+	3'Flank	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000384334	.	20	16	4	12	12	0	SNORA15,downstream_gene_variant,,ENST00000384334,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000426828,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000419314,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000452026,;RP11-460N20.4,upstream_gene_variant,,ENST00000414799,;	A	ENSG00000207062	ENST00000384334	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2789	1	SNORA15	RFAM	.	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CAGCAGAAGCA	.	2	ESCA
CALCR	0	.	GRCh37	7	93108802	93108802	+	Silent	SNP	A	A	T	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123T>A	p.%3D	p.L41L	ENST00000359558	5/16	21	12	9	33	33	0	CALCR,synonymous_variant,p.%3D,ENST00000421592,;CALCR,synonymous_variant,p.%3D,ENST00000426151,;CALCR,synonymous_variant,p.%3D,ENST00000394441,;CALCR,synonymous_variant,p.%3D,ENST00000359558,;CALCR,synonymous_variant,p.%3D,ENST00000360249,;MIR489,downstream_gene_variant,,ENST00000384923,;MIR653,downstream_gene_variant,,ENST00000385279,;CALCR,synonymous_variant,p.%3D,ENST00000415529,;CALCR,synonymous_variant,p.%3D,ENST00000423724,;	T	ENSG00000004948	ENST00000359558	Transcript	synonymous_variant	423	123	41	L	ctT/ctA	COSM1452960,COSM1452959	.	.	-1	CALCR	HGNC	1440	protein_coding	YES	CCDS55125.1	ENSP00000352561	.	.	UPI0001B8380B	.	.	.	5/16	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF84	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGAAGAAT	.	5	ESCA
VPS13B	0	.	GRCh37	8	100286546	100286546	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2636G>T	p.Cys879Phe	p.C879F	ENST00000358544	18/62	155	118	36	132	132	0	VPS13B,missense_variant,p.Cys879Phe,ENST00000395996,;VPS13B,missense_variant,p.Cys879Phe,ENST00000358544,;VPS13B,missense_variant,p.Cys879Phe,ENST00000357162,;VPS13B,upstream_gene_variant,,ENST00000522802,;VPS13B,missense_variant,p.Cys879Phe,ENST00000496144,;	T	ENSG00000132549	ENST00000358544	Transcript	missense_variant	2747	2636	879	C/F	tGt/tTt	.	.	.	1	VPS13B	HGNC	2183	protein_coding	YES	CCDS6280.1	ENSP00000351346	VP13B_HUMAN	.	UPI00001D2D35	.	deleterious(0)	possibly_damaging(0.831)	18/62	.	hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTGTGCCA	.	5	ESCA
SLC30A8	0	.	GRCh37	8	118188790	118188790	+	3'Flank	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000456015	.	54	46	8	66	66	0	SLC30A8,3_prime_UTR_variant,,ENST00000427715,;SLC30A8,downstream_gene_variant,,ENST00000456015,;SLC30A8,downstream_gene_variant,,ENST00000519688,;SLC30A8,downstream_gene_variant,,ENST00000521243,;	T	ENSG00000164756	ENST00000456015	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2460	1	SLC30A8	HGNC	20303	protein_coding	YES	CCDS6322.1	ENSP00000415011	ZNT8_HUMAN	E5RG87_HUMAN	UPI00001B00D6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAGCGCAGG	.	4	ESCA
DLC1	0	.	GRCh37	8	12946007	12946007	+	Silent	SNP	G	G	A	rs73552359	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4281C>T	p.%3D	p.Y1427Y	ENST00000276297	16/18	84	71	12	78	78	0	DLC1,synonymous_variant,p.%3D,ENST00000358919,;DLC1,synonymous_variant,p.%3D,ENST00000520226,;DLC1,synonymous_variant,p.%3D,ENST00000512044,;DLC1,synonymous_variant,p.%3D,ENST00000276297,;DLC1,non_coding_transcript_exon_variant,,ENST00000510318,;DLC1,non_coding_transcript_exon_variant,,ENST00000521730,;	A	ENSG00000164741	ENST00000276297	Transcript	synonymous_variant	4691	4281	1427	Y	taC/taT	rs73552359	.	.	-1	DLC1	HGNC	2897	protein_coding	YES	CCDS5989.1	ENSP00000276297	RHG07_HUMAN	.	UPI0000210275	.	.	.	16/18	.	PROSITE_profiles:PS50848,hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF2,Pfam_domain:PF01852,Gene3D:3.30.530.20,SMART_domains:SM00234,Superfamily_domains:SSF55961	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAACGTAGTC	byCluster|by1000G	4	ESCA
PLEC	0	.	GRCh37	8	144989774	144989774	+	3'UTR	SNP	G	G	A	rs530662366	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*571C>T	.	.	ENST00000322810	32/32	37	30	6	16	16	0	PLEC,3_prime_UTR_variant,,ENST00000322810,;PLEC,3_prime_UTR_variant,,ENST00000345136,;PLEC,3_prime_UTR_variant,,ENST00000357649,;PLEC,3_prime_UTR_variant,,ENST00000398774,;PLEC,3_prime_UTR_variant,,ENST00000354589,;PLEC,3_prime_UTR_variant,,ENST00000356346,;PLEC,3_prime_UTR_variant,,ENST00000436759,;PLEC,3_prime_UTR_variant,,ENST00000354958,;PLEC,downstream_gene_variant,,ENST00000527096,;	A	ENSG00000178209	ENST00000322810	Transcript	3_prime_UTR_variant	14796	.	.	.	.	rs530662366	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACGCCGGA	.	5	ESCA
SCRT1	0	.	GRCh37	8	145556067	145556067	+	3'UTR	SNP	G	G	T	rs564136317	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*780C>A	.	.	ENST00000332135	2/2	69	29	39	64	64	0	SCRT1,3_prime_UTR_variant,,ENST00000332135,;	T	ENSG00000170616	ENST00000332135	Transcript	3_prime_UTR_variant	1939	.	.	.	.	rs564136317	.	.	-1	SCRT1	HGNC	15950	protein_coding	YES	CCDS6421.1	ENSP00000331692	SCRT1_HUMAN	.	UPI0000071337	.	.	.	2/2	.	.	T:0.0008	T:0.003	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGGGGTGG	byFrequency|by1000G	5	ESCA
ZNF395	0	.	GRCh37	8	28218519	28218519	+	Silent	SNP	G	G	A	rs368064690	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>T	p.%3D	p.A41A	ENST00000344423	2/10	89	60	28	107	107	0	ZNF395,synonymous_variant,p.%3D,ENST00000520290,;ZNF395,synonymous_variant,p.%3D,ENST00000344423,;ZNF395,synonymous_variant,p.%3D,ENST00000517459,;ZNF395,synonymous_variant,p.%3D,ENST00000521185,;ZNF395,synonymous_variant,p.%3D,ENST00000522795,;ZNF395,synonymous_variant,p.%3D,ENST00000521912,;ZNF395,synonymous_variant,p.%3D,ENST00000523202,;ZNF395,synonymous_variant,p.%3D,ENST00000523095,;ZNF395,downstream_gene_variant,,ENST00000519730,;FBXO16,missense_variant,p.Arg342Cys,ENST00000521548,;	A	ENSG00000186918	ENST00000344423	Transcript	synonymous_variant	255	123	41	A	gcC/gcT	rs368064690,COSM1456483	.	.	-1	ZNF395	HGNC	18737	protein_coding	YES	CCDS6067.1	ENSP00000340494	ZN395_HUMAN	E5RH90_HUMAN,E5RGF1_HUMAN,E5RG59_HUMAN,E5RFV4_HUMAN	UPI0000073F08	.	.	.	2/10	.	hmmpanther:PTHR13006:SF6,hmmpanther:PTHR13006	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGCGGCCCC	byFrequency|byCluster	5	ESCA
PURG	0	.	GRCh37	8	30889849	30889849	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450G>A	p.%3D	p.Q150Q	ENST00000475541	1/1	30	21	9	24	24	0	PURG,synonymous_variant,p.%3D,ENST00000475541,;PURG,synonymous_variant,p.%3D,ENST00000339382,;PURG,synonymous_variant,p.%3D,ENST00000523392,;WRN,upstream_gene_variant,,ENST00000298139,;	T	ENSG00000172733	ENST00000475541	Transcript	synonymous_variant	1383	450	150	Q	caG/caA	.	.	.	-1	PURG	HGNC	17930	protein_coding	YES	CCDS6081.1	ENSP00000418721	PURG_HUMAN	K7ENC1_HUMAN	UPI000006F2C7	.	.	.	1/1	.	hmmpanther:PTHR12611:SF3,hmmpanther:PTHR12611,Pfam_domain:PF04845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTCTGCCT	.	5	ESCA
ADAM2	0	.	GRCh37	8	39679180	39679180	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.269A>T	p.Asn90Ile	p.N90I	ENST00000265708	5/21	123	73	50	98	98	0	ADAM2,missense_variant,p.Asn90Ile,ENST00000521880,;ADAM2,missense_variant,p.Asn90Ile,ENST00000265708,;ADAM2,missense_variant,p.Asn90Ile,ENST00000347580,;ADAM2,missense_variant,p.Asn90Ile,ENST00000379853,;ADAM2,splice_region_variant,,ENST00000523181,;	A	ENSG00000104755	ENST00000265708	Transcript	missense_variant	373	269	90	N/I	aAt/aTt	.	.	.	-1	ADAM2	HGNC	198	protein_coding	YES	CCDS34884.1	ENSP00000265708	ADAM2_HUMAN	.	UPI00001254C2	.	deleterious(0.04)	benign(0.063)	5/21	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF108,Pfam_domain:PF01562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAATTCTGA	.	5	ESCA
XKR4	0	.	GRCh37	8	56015428	56015428	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380G>A	p.Gly127Asp	p.G127D	ENST00000327381	1/3	23	20	3	22	22	0	XKR4,missense_variant,p.Gly127Asp,ENST00000327381,;	A	ENSG00000206579	ENST00000327381	Transcript	missense_variant	480	380	127	G/D	gGc/gAc	.	.	.	1	XKR4	HGNC	29394	protein_coding	YES	CCDS34893.1	ENSP00000328326	XKR4_HUMAN	.	UPI000016098C	.	deleterious(0.01)	probably_damaging(1)	1/3	.	Transmembrane_helices:TMhelix,Pfam_domain:PF09815,hmmpanther:PTHR32129:SF14,hmmpanther:PTHR32129	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTGGGCACAG	.	4	ESCA
CHD7	0	.	GRCh37	8	61754274	61754274	+	Silent	SNP	T	T	G	rs530345787	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4605T>G	p.%3D	p.A1535A	ENST00000423902	20/38	132	114	17	126	126	0	CHD7,synonymous_variant,p.%3D,ENST00000423902,;CHD7,intron_variant,,ENST00000524602,;	G	ENSG00000171316	ENST00000423902	Transcript	synonymous_variant	5084	4605	1535	A	gcT/gcG	rs530345787	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	.	20/38	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGCTAAGAA	.	4	ESCA
CHD7	0	.	GRCh37	8	61754275	61754275	+	Missense_Mutation	SNP	A	A	C	rs759574788	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4606A>C	p.Lys1536Gln	p.K1536Q	ENST00000423902	20/38	133	115	17	127	127	0	CHD7,missense_variant,p.Lys1536Gln,ENST00000423902,;CHD7,intron_variant,,ENST00000524602,;	C	ENSG00000171316	ENST00000423902	Transcript	missense_variant	5085	4606	1536	K/Q	Aag/Cag	rs759574788	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	probably_damaging(0.994)	20/38	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGCTAAGAAG	.	4	ESCA
CHD7	0	.	GRCh37	8	61754276	61754276	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4607A>G	p.Lys1536Arg	p.K1536R	ENST00000423902	20/38	133	115	17	128	128	0	CHD7,missense_variant,p.Lys1536Arg,ENST00000423902,;CHD7,intron_variant,,ENST00000524602,;	G	ENSG00000171316	ENST00000423902	Transcript	missense_variant	5086	4607	1536	K/R	aAg/aGg	COSM1457724,COSM1457723	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	probably_damaging(0.986)	20/38	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF551	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTAAGAAGG	.	4	ESCA
ARFGEF1	0	.	GRCh37	8	68110132	68110132	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1037A>T	.	.	ENST00000262215	39/39	64	33	31	68	68	0	ARFGEF1,3_prime_UTR_variant,,ENST00000262215,;ARFGEF1,intron_variant,,ENST00000520381,;ARFGEF1,downstream_gene_variant,,ENST00000518230,;ARFGEF1,downstream_gene_variant,,ENST00000518789,;CSPP1,downstream_gene_variant,,ENST00000262210,;CSPP1,downstream_gene_variant,,ENST00000412460,;CSPP1,downstream_gene_variant,,ENST00000519668,;ARFGEF1,intron_variant,,ENST00000522878,;ARFGEF1,downstream_gene_variant,,ENST00000517955,;CSPP1,downstream_gene_variant,,ENST00000521168,;CSPP1,downstream_gene_variant,,ENST00000521324,;ARFGEF1,non_coding_transcript_exon_variant,,ENST00000518290,;	A	ENSG00000066777	ENST00000262215	Transcript	3_prime_UTR_variant	6977	.	.	.	.	.	.	.	-1	ARFGEF1	HGNC	15772	protein_coding	YES	CCDS6199.1	ENSP00000262215	BIG1_HUMAN	E5RJN9_HUMAN,E5RJB2_HUMAN,E5RHZ1_HUMAN,B3KMS9_HUMAN	UPI000013D275	.	.	.	39/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACATTTCCA	.	5	ESCA
CRISPLD1	0	.	GRCh37	8	75932277	75932277	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1207C>G	p.Leu403Val	p.L403V	ENST00000262207	12/15	78	46	32	68	68	0	CRISPLD1,missense_variant,p.Leu403Val,ENST00000262207,;CRISPLD1,missense_variant,p.Leu217Val,ENST00000517786,;CRISPLD1,missense_variant,p.Leu215Val,ENST00000523524,;	G	ENSG00000121005	ENST00000262207	Transcript	missense_variant	1675	1207	403	L/V	Ctc/Gtc	.	.	.	1	CRISPLD1	HGNC	18206	protein_coding	YES	CCDS6219.1	ENSP00000262207	CRLD1_HUMAN	E5RJS4_HUMAN,B7Z8V9_HUMAN	UPI00000422F5	.	tolerated(0.06)	benign(0.151)	12/15	.	PROSITE_profiles:PS50820,hmmpanther:PTHR10334:SF73,hmmpanther:PTHR10334,Gene3D:1jbiA00,Pfam_domain:PF03815,SMART_domains:SM00603,Superfamily_domains:0039469	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAGCTCTGT	.	5	ESCA
PEX2	0	.	GRCh37	8	77896250	77896250	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165G>A	p.%3D	p.E55E	ENST00000419564	4/4	105	88	17	88	88	0	PEX2,synonymous_variant,p.%3D,ENST00000419564,;PEX2,synonymous_variant,p.%3D,ENST00000522527,;PEX2,synonymous_variant,p.%3D,ENST00000520103,;PEX2,synonymous_variant,p.%3D,ENST00000357039,;PEX2,synonymous_variant,p.%3D,ENST00000518986,;PEX2,downstream_gene_variant,,ENST00000519956,;PEX2,downstream_gene_variant,,ENST00000520203,;	T	ENSG00000164751	ENST00000419564	Transcript	synonymous_variant	630	165	55	E	gaG/gaA	.	.	.	-1	PEX2	HGNC	9717	protein_coding	YES	CCDS6221.1	ENSP00000400984	PEX2_HUMAN	E5RIW9_HUMAN	UPI000013E3FB	.	.	.	4/4	.	hmmpanther:PTHR12590,hmmpanther:PTHR12590:SF3,Pfam_domain:PF04757	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCACCTCTGG	.	5	ESCA
CIZ1	0	.	GRCh37	9	130928602	130928602	+	Silent	SNP	T	T	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2571A>C	p.%3D	p.T857T	ENST00000393608	17/17	87	59	28	140	140	0	CIZ1,synonymous_variant,p.%3D,ENST00000325721,;CIZ1,synonymous_variant,p.%3D,ENST00000372948,;CIZ1,synonymous_variant,p.%3D,ENST00000357558,;CIZ1,synonymous_variant,p.%3D,ENST00000415526,;CIZ1,synonymous_variant,p.%3D,ENST00000538431,;CIZ1,synonymous_variant,p.%3D,ENST00000372938,;CIZ1,synonymous_variant,p.%3D,ENST00000541172,;CIZ1,synonymous_variant,p.%3D,ENST00000277465,;CIZ1,synonymous_variant,p.%3D,ENST00000393608,;CIZ1,synonymous_variant,p.%3D,ENST00000372954,;C9orf16,downstream_gene_variant,,ENST00000372994,;CIZ1,non_coding_transcript_exon_variant,,ENST00000491487,;CIZ1,non_coding_transcript_exon_variant,,ENST00000485862,;CIZ1,non_coding_transcript_exon_variant,,ENST00000471773,;CIZ1,non_coding_transcript_exon_variant,,ENST00000461765,;CIZ1,non_coding_transcript_exon_variant,,ENST00000471839,;C9orf16,downstream_gene_variant,,ENST00000489240,;C9orf16,downstream_gene_variant,,ENST00000492588,;CIZ1,downstream_gene_variant,,ENST00000476727,;C9orf16,downstream_gene_variant,,ENST00000486420,;CIZ1,downstream_gene_variant,,ENST00000485001,;CIZ1,downstream_gene_variant,,ENST00000476541,;	G	ENSG00000148337	ENST00000393608	Transcript	synonymous_variant	2774	2571	857	T	acA/acC	.	.	.	-1	CIZ1	HGNC	16744	protein_coding	YES	CCDS6894.1	ENSP00000377232	CIZ1_HUMAN	Q9Y3F8_HUMAN,F6WSM2_HUMAN,F6VD24_HUMAN,B0EXJ7_HUMAN	UPI0000141722	.	.	.	17/17	.	hmmpanther:PTHR15491:SF9,hmmpanther:PTHR15491	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCTGTCAA	.	5	ESCA
COL5A1	0	.	GRCh37	9	137642670	137642670	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1604A>G	p.Lys535Arg	p.K535R	ENST00000371817	13/66	50	47	3	94	94	0	COL5A1,missense_variant,p.Lys535Arg,ENST00000371817,;	G	ENSG00000130635	ENST00000371817	Transcript	missense_variant	2018	1604	535	K/R	aAa/aGa	.	.	.	1	COL5A1	HGNC	2209	protein_coding	YES	CCDS6982.1	ENSP00000360882	CO5A1_HUMAN	Q9UML4_HUMAN,Q96HC0_HUMAN,Q59EE7_HUMAN	UPI0000210EE3	.	.	probably_damaging(0.986)	13/66	.	hmmpanther:PTHR24023:SF387,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCAAAGGCC	.	2	ESCA
BNC2	0	.	GRCh37	9	16436780	16436780	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1412G>T	p.Cys471Phe	p.C471F	ENST00000380672	6/7	84	75	9	100	100	0	BNC2,missense_variant,p.Cys376Phe,ENST00000545497,;BNC2,missense_variant,p.Cys404Phe,ENST00000380667,;BNC2,missense_variant,p.Cys471Phe,ENST00000380672,;BNC2,missense_variant,p.Cys471Phe,ENST00000380666,;BNC2,missense_variant,p.Cys428Phe,ENST00000418777,;BNC2,downstream_gene_variant,,ENST00000603713,;BNC2,upstream_gene_variant,,ENST00000411752,;BNC2,missense_variant,p.Cys471Phe,ENST00000484726,;	A	ENSG00000173068	ENST00000380672	Transcript	missense_variant	1470	1412	471	C/F	tGc/tTc	.	.	.	-1	BNC2	HGNC	30988	protein_coding	YES	CCDS6482.2	ENSP00000370047	BNC2_HUMAN	S4R351_HUMAN,Q06HC7_HUMAN,Q06HC2_HUMAN,Q06HB9_HUMAN,D3DRJ1_HUMAN	UPI000035E7B0	.	deleterious(0)	probably_damaging(0.999)	6/7	.	SMART_domains:SM00355,hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTGCATCGA	.	4	ESCA
C9orf53	0	.	GRCh37	9	21967209	21967209	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11G>A	p.Arg4His	p.R4H	ENST00000441769	1/1	15	11	4	38	38	0	C9orf53,missense_variant,p.Arg4His,ENST00000441769,;CDKN2A,downstream_gene_variant,,ENST00000578845,;CDKN2A,downstream_gene_variant,,ENST00000579755,;CDKN2A,downstream_gene_variant,,ENST00000494262,;CDKN2A,downstream_gene_variant,,ENST00000498628,;CDKN2A,downstream_gene_variant,,ENST00000530628,;CDKN2A,downstream_gene_variant,,ENST00000446177,;CDKN2A,downstream_gene_variant,,ENST00000304494,;CDKN2A,downstream_gene_variant,,ENST00000361570,;CDKN2A,downstream_gene_variant,,ENST00000498124,;CDKN2A,downstream_gene_variant,,ENST00000479692,;CDKN2A,downstream_gene_variant,,ENST00000579122,;CDKN2A,downstream_gene_variant,,ENST00000497750,;CDKN2A,downstream_gene_variant,,ENST00000380150,;CDKN2A,downstream_gene_variant,,ENST00000577854,;RP11-145E5.5,intron_variant,,ENST00000404796,;CDKN2A,downstream_gene_variant,,ENST00000380151,;	A	ENSG00000224854	ENST00000441769	Transcript	missense_variant	73	11	4	R/H	cGt/cAt	.	.	.	1	C9orf53	HGNC	23831	protein_coding	YES	.	ENSP00000414893	NSGX_HUMAN	.	UPI000013054C	.	.	unknown(0)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE	GCAGCGTGGAC	.	2	ESCA
C9orf47	0	.	GRCh37	9	91609691	91609691	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2788G>T	.	.	ENST00000334490	3/3	47	21	26	50	50	0	C9orf47,3_prime_UTR_variant,,ENST00000334490,;C9orf47,3_prime_UTR_variant,,ENST00000375851,;S1PR3,intron_variant,,ENST00000358157,;C9orf47,downstream_gene_variant,,ENST00000375850,;S1PR3,upstream_gene_variant,,ENST00000375846,;	T	ENSG00000186354	ENST00000334490	Transcript	3_prime_UTR_variant	3465	.	.	.	.	.	.	.	1	C9orf47	HGNC	23669	protein_coding	YES	CCDS35062.1	ENSP00000335616	CI047_HUMAN	.	UPI00001C0EE0	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGGGAAGCA	.	5	ESCA
TENM1	0	.	GRCh37	X	123680763	123680763	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2612G>A	p.Ser871Asn	p.S871N	ENST00000422452	15/32	22	2	20	34	34	0	TENM1,missense_variant,p.Ser871Asn,ENST00000422452,;TENM1,missense_variant,p.Ser871Asn,ENST00000371130,;	T	ENSG00000009694	ENST00000422452	Transcript	missense_variant	2676	2612	871	S/N	aGt/aAt	.	.	.	-1	TENM1	HGNC	8117	protein_coding	YES	CCDS55488.1	ENSP00000403954	TEN1_HUMAN	G3CAS6_HUMAN,B7ZMH4_HUMAN	UPI0000211B6A	.	deleterious(0.03)	probably_damaging(0.949)	15/32	.	hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTACTGTCC	.	5	ESCA
MAGEA3	0	.	GRCh37	X	151935214	151935214	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8C>T	.	.	ENST00000393902	3/3	151	142	9	97	97	0	MAGEA3,3_prime_UTR_variant,,ENST00000393902,;MAGEA3,3_prime_UTR_variant,,ENST00000370278,;MAGEA3,downstream_gene_variant,,ENST00000417212,;	A	ENSG00000221867	ENST00000393902	Transcript	3_prime_UTR_variant	1521	.	.	.	.	.	.	.	-1	MAGEA3	HGNC	6801	protein_coding	YES	CCDS14715.1	ENSP00000377480	MAGA3_HUMAN	E7EMU0_HUMAN,B9A060_HUMAN	UPI0000062194	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGTGCTCAG	.	2	ESCA
SPRY3	0	.	GRCh37	X	155007780	155007780	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3380C>T	.	.	ENST00000302805	2/2	79	47	31	51	51	0	SPRY3,3_prime_UTR_variant,,ENST00000302805,;	T	ENSG00000168939	ENST00000302805	Transcript	3_prime_UTR_variant	4678	.	.	.	.	.	.	.	1	SPRY3	HGNC	11271	protein_coding	YES	CCDS14769.4	ENSP00000302978	SPY3_HUMAN	.	UPI0000135E98	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAACAATTG	.	5	ESCA
WASIR1	0	.	GRCh37	X	155251425	155251425	+	5'Flank	SNP	G	G	C	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000399966	.	286	229	57	278	278	0	WASIR1,upstream_gene_variant,,ENST00000399966,;WASH6P,non_coding_transcript_exon_variant,,ENST00000340131,;WASH6P,non_coding_transcript_exon_variant,,ENST00000476066,;AJ271736.10,non_coding_transcript_exon_variant,,ENST00000285718,;WASH6P,non_coding_transcript_exon_variant,,ENST00000469624,;WASH6P,non_coding_transcript_exon_variant,,ENST00000479401,;WASH6P,non_coding_transcript_exon_variant,,ENST00000492963,;WASH6P,non_coding_transcript_exon_variant,,ENST00000496011,;WASH6P,non_coding_transcript_exon_variant,,ENST00000461007,;WASH6P,non_coding_transcript_exon_variant,,ENST00000460206,;WASH6P,upstream_gene_variant,,ENST00000475594,;WASH6P,upstream_gene_variant,,ENST00000464205,;WASH6P,upstream_gene_variant,,ENST00000482170,;WASH6P,upstream_gene_variant,,ENST00000484415,;WASH6P,upstream_gene_variant,,ENST00000483079,;WASH6P,upstream_gene_variant,,ENST00000483286,;WASH6P,upstream_gene_variant,,ENST00000496301,;AJ271736.10,non_coding_transcript_exon_variant,,ENST00000483543,;WASH6P,non_coding_transcript_exon_variant,,ENST00000359512,;DDX11L16,downstream_gene_variant,,ENST00000445777,;DDX11L16,downstream_gene_variant,,ENST00000507418,;	C	ENSG00000185203	ENST00000399966	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4923	-1	WASIR1	HGNC	38513	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AGATTGAGAAG	.	2	ESCA
WASIR1	0	.	GRCh37	X	155251430	155251430	+	5'Flank	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000399966	.	292	233	59	275	275	0	WASIR1,upstream_gene_variant,,ENST00000399966,;WASH6P,non_coding_transcript_exon_variant,,ENST00000340131,;WASH6P,non_coding_transcript_exon_variant,,ENST00000476066,;AJ271736.10,non_coding_transcript_exon_variant,,ENST00000285718,;WASH6P,non_coding_transcript_exon_variant,,ENST00000469624,;WASH6P,non_coding_transcript_exon_variant,,ENST00000479401,;WASH6P,non_coding_transcript_exon_variant,,ENST00000492963,;WASH6P,non_coding_transcript_exon_variant,,ENST00000496011,;WASH6P,non_coding_transcript_exon_variant,,ENST00000461007,;WASH6P,non_coding_transcript_exon_variant,,ENST00000460206,;WASH6P,upstream_gene_variant,,ENST00000475594,;WASH6P,upstream_gene_variant,,ENST00000464205,;WASH6P,upstream_gene_variant,,ENST00000482170,;WASH6P,upstream_gene_variant,,ENST00000484415,;WASH6P,upstream_gene_variant,,ENST00000483079,;WASH6P,upstream_gene_variant,,ENST00000483286,;WASH6P,upstream_gene_variant,,ENST00000496301,;AJ271736.10,non_coding_transcript_exon_variant,,ENST00000483543,;WASH6P,non_coding_transcript_exon_variant,,ENST00000359512,;DDX11L16,downstream_gene_variant,,ENST00000445777,;DDX11L16,downstream_gene_variant,,ENST00000507418,;	A	ENSG00000185203	ENST00000399966	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4928	-1	WASIR1	HGNC	38513	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GAGAAGATCAA	.	2	ESCA
TBC1D25	0	.	GRCh37	X	48417663	48417663	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.634G>A	p.Gly212Ser	p.G212S	ENST00000376771	5/6	17	3	14	24	24	0	TBC1D25,missense_variant,p.Gly212Ser,ENST00000376771,;TBC1D25,missense_variant,p.Gly228Ser,ENST00000418627,;TBC1D25,5_prime_UTR_variant,,ENST00000537536,;snoU13,downstream_gene_variant,,ENST00000459609,;TBC1D25,non_coding_transcript_exon_variant,,ENST00000476141,;TBC1D25,non_coding_transcript_exon_variant,,ENST00000494495,;TBC1D25,3_prime_UTR_variant,,ENST00000481090,;	A	ENSG00000068354	ENST00000376771	Transcript	missense_variant	975	634	212	G/S	Ggc/Agc	.	.	.	1	TBC1D25	HGNC	8092	protein_coding	YES	CCDS35242.1	ENSP00000365962	TBC25_HUMAN	B4DF03_HUMAN,B4DE92_HUMAN	UPI0000160685	.	deleterious(0)	probably_damaging(0.998)	5/6	.	hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF189,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGAGGGCCAG	.	5	ESCA
ARR3	0	.	GRCh37	X	69497288	69497288	+	Missense_Mutation	SNP	C	C	T	rs766517164	.	TCGA-IG-A8O2-01A-11D-A36J-09	TCGA-IG-A8O2-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.518C>T	p.Pro173Leu	p.P173L	ENST00000307959	9/17	36	27	9	45	45	0	ARR3,missense_variant,p.Pro173Leu,ENST00000374495,;ARR3,missense_variant,p.Pro173Leu,ENST00000307959,;RAB41,upstream_gene_variant,,ENST00000374473,;RAB41,upstream_gene_variant,,ENST00000276066,;RAB41,upstream_gene_variant,,ENST00000509895,;ARR3,downstream_gene_variant,,ENST00000480877,;	T	ENSG00000120500	ENST00000307959	Transcript	missense_variant	569	518	173	P/L	cCg/cTg	rs766517164,COSM1626067	.	.	1	ARR3	HGNC	710	protein_coding	YES	CCDS14399.1	ENSP00000311538	ARRC_HUMAN	D6RCT3_HUMAN	UPI0000457850	.	tolerated(0.29)	benign(0)	9/17	.	hmmpanther:PTHR11792,hmmpanther:PTHR11792:SF19	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCACCGGAGG	.	5	ESCA
KIF5B	0	.	GRCh37	10	32324841	32324841	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.793delA	p.Ile265PhefsTer18	p.I265Ffs*18	ENST00000302418	9/26	67	46	21	49	49	0	KIF5B,frameshift_variant,p.Ile265PhefsTer18,ENST00000302418,;	-	ENSG00000170759	ENST00000302418	Transcript	frameshift_variant	1251	793	265	I/X	Att/tt	.	.	.	-1	KIF5B	HGNC	6324	protein_coding	YES	CCDS7171.1	ENSP00000307078	KINH_HUMAN	A8K048_HUMAN	UPI000012DE68	.	.	.	9/26	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGAAATAACAT	.	3	ESCA
OR13A1	0	.	GRCh37	10	45798763	45798763	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*121G>A	.	.	ENST00000553795	4/4	15	11	4	20	20	0	OR13A1,3_prime_UTR_variant,,ENST00000553795,;OR13A1,3_prime_UTR_variant,,ENST00000536058,;OR13A1,downstream_gene_variant,,ENST00000374401,;	T	ENSG00000256574	ENST00000553795	Transcript	3_prime_UTR_variant	1417	.	.	.	.	.	.	.	-1	OR13A1	HGNC	14772	protein_coding	YES	CCDS31188.1	ENSP00000451950	O13A1_HUMAN	.	UPI000003FE0F	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CTCATCCATGC	.	3	ESCA
EIF4EBP2	0	.	GRCh37	10	72183444	72183444	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1941A>G	.	.	ENST00000373218	3/3	11	4	7	23	23	0	EIF4EBP2,3_prime_UTR_variant,,ENST00000373218,;	G	ENSG00000148730	ENST00000373218	Transcript	3_prime_UTR_variant	2327	.	.	.	.	.	.	.	1	EIF4EBP2	HGNC	3289	protein_coding	YES	CCDS7303.1	ENSP00000362314	4EBP2_HUMAN	.	UPI0000073D8C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAAAGAGAGGA	.	3	ESCA
SNCG	0	.	GRCh37	10	88719881	88719881	+	Missense_Mutation	SNP	G	G	A	rs371074090	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287G>A	p.Arg96His	p.R96H	ENST00000372017	3/5	35	23	11	27	27	0	SNCG,missense_variant,p.Arg96His,ENST00000372017,;SNCG,synonymous_variant,p.%3D,ENST00000348795,;MMRN2,intron_variant,,ENST00000474994,;MMRN2,intron_variant,,ENST00000609457,;MMRN2,upstream_gene_variant,,ENST00000372027,;SNCG,non_coding_transcript_exon_variant,,ENST00000465679,;SNCG,non_coding_transcript_exon_variant,,ENST00000483064,;MMRN2,upstream_gene_variant,,ENST00000608090,;MMRN2,upstream_gene_variant,,ENST00000608753,;	A	ENSG00000173267	ENST00000372017	Transcript	missense_variant	329	287	96	R/H	cGc/cAc	rs371074090	.	.	1	SNCG	HGNC	11141	protein_coding	YES	CCDS7380.1	ENSP00000361087	SYUG_HUMAN	Q6FHG5_HUMAN	UPI0000169F48	.	tolerated(0.06)	benign(0.027)	3/5	.	hmmpanther:PTHR13820,Gene3D:1xq8A00,Pfam_domain:PF01387,Superfamily_domains:0053543,Prints_domain:PR01214,Prints_domain:PR01211	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGCGCAAGG	byFrequency|byCluster	5	ESCA
CPEB3	0	.	GRCh37	10	93810663	93810663	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1306T>C	.	.	ENST00000265997	10/10	29	16	13	30	30	0	CPEB3,3_prime_UTR_variant,,ENST00000265997,;CPEB3,3_prime_UTR_variant,,ENST00000412050,;	G	ENSG00000107864	ENST00000265997	Transcript	3_prime_UTR_variant	3576	.	.	.	.	.	.	.	-1	CPEB3	HGNC	21746	protein_coding	YES	CCDS31246.1	ENSP00000265997	CPEB3_HUMAN	.	UPI000013F7DE	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAAGAGCTCA	.	5	ESCA
MMP27	0	.	GRCh37	11	102562551	102562551	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1488C>T	p.%3D	p.S496S	ENST00000260229	10/10	64	43	21	56	56	0	MMP27,synonymous_variant,p.%3D,ENST00000260229,;	A	ENSG00000137675	ENST00000260229	Transcript	synonymous_variant	1580	1488	496	S	agC/agT	COSM540607	.	.	-1	MMP27	HGNC	14250	protein_coding	YES	CCDS8319.1	ENSP00000260229	MMP27_HUMAN	.	UPI00001AE7D3	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAAGCTTAA	.	5	ESCA
DDX6	0	.	GRCh37	11	118661592	118661592	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-268+215G>A	.	.	ENST00000264018	.	113	59	53	112	112	0	DDX6,5_prime_UTR_variant,,ENST00000526070,;DDX6,intron_variant,,ENST00000264018,;DDX6,upstream_gene_variant,,ENST00000534980,;DDX6,intron_variant,,ENST00000525082,;DDX6,intron_variant,,ENST00000533239,;DDX6,upstream_gene_variant,,ENST00000531971,;	T	ENSG00000110367	ENST00000264018	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DDX6	HGNC	2747	protein_coding	YES	CCDS44751.1	ENSP00000264018	DDX6_HUMAN	B2R858_HUMAN	UPI000013D4A2	.	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTCCTACCA	.	5	ESCA
MUC5AC	0	.	GRCh37	11	1220217	1220217	+	RNA	SNP	C	C	T	rs773564635	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2902C>T	.	.	ENST00000358378	14/19	86	62	23	47	47	0	MUC5AC,non_coding_transcript_exon_variant,,ENST00000358378,;	T	ENSG00000215182	ENST00000358378	Transcript	non_coding_transcript_exon_variant	2902	.	.	.	.	rs773564635	.	.	1	MUC5AC	HGNC	7515	processed_transcript	.	.	.	.	.	.	.	.	.	14/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGCCCTGTG	byFrequency	5	ESCA
HPS5	0	.	GRCh37	11	18327774	18327774	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732G>A	p.%3D	p.R244R	ENST00000349215	7/23	97	89	7	67	67	0	HPS5,synonymous_variant,p.%3D,ENST00000531848,;HPS5,synonymous_variant,p.%3D,ENST00000438420,;HPS5,synonymous_variant,p.%3D,ENST00000349215,;HPS5,synonymous_variant,p.%3D,ENST00000396253,;	T	ENSG00000110756	ENST00000349215	Transcript	synonymous_variant	1010	732	244	R	agG/agA	.	.	.	-1	HPS5	HGNC	17022	protein_coding	YES	CCDS7836.1	ENSP00000265967	HPS5_HUMAN	F5GWM5_HUMAN	UPI000000D7E9	.	.	.	7/23	.	hmmpanther:PTHR23287:SF15,hmmpanther:PTHR23287,PIRSF_domain:PIRSF037475	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACATCCTAGA	.	2	ESCA
MUC15	0	.	GRCh37	11	26587287	26587287	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200A>C	p.Lys67Thr	p.K67T	ENST00000436318	2/4	64	42	21	50	50	0	MUC15,missense_variant,p.Lys40Thr,ENST00000455601,;MUC15,missense_variant,p.Lys67Thr,ENST00000281268,;MUC15,missense_variant,p.Lys67Thr,ENST00000527569,;MUC15,missense_variant,p.Lys67Thr,ENST00000436318,;MUC15,missense_variant,p.Lys67Thr,ENST00000529533,;ANO3,intron_variant,,ENST00000537978,;ANO3,intron_variant,,ENST00000531568,;ANO3,intron_variant,,ENST00000525139,;ANO3,intron_variant,,ENST00000256737,;ANO3,downstream_gene_variant,,ENST00000529242,;	G	ENSG00000169550	ENST00000436318	Transcript	missense_variant	334	200	67	K/T	aAa/aCa	.	.	.	-1	MUC15	HGNC	14956	protein_coding	YES	CCDS44557.1	ENSP00000416753	.	E9PII6_HUMAN	UPI0000D4B9CF	.	deleterious_low_confidence(0)	possibly_damaging(0.859)	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E64D|c.192A>T|5,BUFFER|p.E37D|c.111A>T|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTTTAAAA	.	5	ESCA
LIN7C	0	.	GRCh37	11	27518698	27518698	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1498A>G	.	.	ENST00000278193	5/5	55	37	18	22	22	0	LIN7C,3_prime_UTR_variant,,ENST00000524596,;LIN7C,3_prime_UTR_variant,,ENST00000278193,;	C	ENSG00000148943	ENST00000278193	Transcript	3_prime_UTR_variant	2113	.	.	.	.	.	.	.	-1	LIN7C	HGNC	17789	protein_coding	YES	CCDS7864.1	ENSP00000278193	LIN7C_HUMAN	.	UPI000000BB45	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTATTTTGA	.	5	ESCA
MPPED2	0	.	GRCh37	11	30431873	30431873	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1142A>T	.	.	ENST00000358117	6/6	45	32	13	36	36	0	MPPED2,3_prime_UTR_variant,,ENST00000358117,;MPPED2,intron_variant,,ENST00000448418,;MPPED2,downstream_gene_variant,,ENST00000529220,;MPPED2,downstream_gene_variant,,ENST00000524667,;MPPED2,downstream_gene_variant,,ENST00000526437,;	A	ENSG00000066382	ENST00000358117	Transcript	3_prime_UTR_variant	2150	.	.	.	.	.	.	.	-1	MPPED2	HGNC	1180	protein_coding	YES	CCDS7870.1	ENSP00000350833	MPPD2_HUMAN	F2Z346_HUMAN	UPI0000124E87	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGTAACAT	.	5	ESCA
API5	0	.	GRCh37	11	43364068	43364068	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8A>G	.	.	ENST00000531273	14/14	35	24	10	25	25	0	API5,synonymous_variant,p.%3D,ENST00000534695,;API5,3_prime_UTR_variant,,ENST00000455725,;API5,3_prime_UTR_variant,,ENST00000378852,;API5,3_prime_UTR_variant,,ENST00000420461,;API5,3_prime_UTR_variant,,ENST00000531273,;RP11-484D2.2,intron_variant,,ENST00000526220,;API5,downstream_gene_variant,,ENST00000529334,;	G	ENSG00000166181	ENST00000531273	Transcript	3_prime_UTR_variant	1722	.	.	.	.	.	.	.	1	API5	HGNC	594	protein_coding	YES	CCDS44572.1	ENSP00000431391	API5_HUMAN	.	UPI0000E229DE	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGACATCAGC	.	5	ESCA
ACCSL	0	.	GRCh37	11	44080171	44080171	+	Missense_Mutation	SNP	C	C	T	rs749322101	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1546C>T	p.Arg516Cys	p.R516C	ENST00000378832	13/14	35	29	6	32	32	0	ACCSL,missense_variant,p.Arg516Cys,ENST00000378832,;ACCSL,3_prime_UTR_variant,,ENST00000527145,;	T	ENSG00000205126	ENST00000378832	Transcript	missense_variant	1602	1546	516	R/C	Cgt/Tgt	rs749322101	.	.	1	ACCSL	HGNC	34391	protein_coding	YES	CCDS41636.1	ENSP00000368109	1A1L2_HUMAN	.	UPI000023785D	.	tolerated(0.21)	benign(0.007)	13/14	.	hmmpanther:PTHR11751:SF344,hmmpanther:PTHR11751,Pfam_domain:PF00155,Gene3D:3.90.1150.10,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCCCGTGGC	byFrequency	5	ESCA
CKAP5	0	.	GRCh37	11	46765717	46765718	+	Frame_Shift_Ins	INS	-	-	AGCA	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5954_5955insTGCT	p.Arg1986AlafsTer16	p.R1986Afs*16	ENST00000529230	44/44	48	36	12	32	32	0	CKAP5,frameshift_variant,p.Arg1993AlafsTer16,ENST00000415402,;CKAP5,frameshift_variant,p.Arg1926AlafsTer16,ENST00000354558,;CKAP5,frameshift_variant,p.Arg1926AlafsTer16,ENST00000312055,;CKAP5,frameshift_variant,p.Arg1986AlafsTer16,ENST00000529230,;CKAP5,3_prime_UTR_variant,,ENST00000525896,;F2,downstream_gene_variant,,ENST00000530231,;F2,downstream_gene_variant,,ENST00000311907,;CKAP5,non_coding_transcript_exon_variant,,ENST00000533413,;	AGCA	ENSG00000175216	ENST00000529230	Transcript	frameshift_variant	6001-6002	5954-5955	1985	L/LAX	ctc/ctTGCTc	.	.	.	-1	CKAP5	HGNC	28959	protein_coding	YES	CCDS31477.1	ENSP00000432768	CKAP5_HUMAN	E9PQH5_HUMAN	UPI000013F21E	.	.	.	44/44	.	hmmpanther:PTHR12609:SF0,hmmpanther:PTHR12609	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCCGGAGCTG	.	3	ESCA
RASSF7	0	.	GRCh37	11	562263	562263	+	Silent	SNP	G	G	A	rs770196669	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.309G>A	p.%3D	p.P103P	ENST00000397583	3/6	35	18	17	29	29	0	RASSF7,synonymous_variant,p.%3D,ENST00000431809,;RASSF7,synonymous_variant,p.%3D,ENST00000397583,;RASSF7,synonymous_variant,p.%3D,ENST00000397582,;RASSF7,synonymous_variant,p.%3D,ENST00000454668,;RASSF7,synonymous_variant,p.%3D,ENST00000344375,;C11orf35,upstream_gene_variant,,ENST00000329451,;C11orf35,upstream_gene_variant,,ENST00000486629,;C11orf35,upstream_gene_variant,,ENST00000441853,;RASSF7,downstream_gene_variant,,ENST00000528736,;MIR210HG,downstream_gene_variant,,ENST00000528245,;MIR210HG,downstream_gene_variant,,ENST00000533920,;MIR210HG,downstream_gene_variant,,ENST00000500447,;RP11-496I9.1,downstream_gene_variant,,ENST00000527113,;RP11-496I9.1,downstream_gene_variant,,ENST00000533844,;RP11-496I9.1,downstream_gene_variant,,ENST00000527620,;RASSF7,non_coding_transcript_exon_variant,,ENST00000524468,;RASSF7,missense_variant,p.Gly102Arg,ENST00000414138,;C11orf35,upstream_gene_variant,,ENST00000492515,;RASSF7,upstream_gene_variant,,ENST00000531112,;	A	ENSG00000099849	ENST00000397583	Transcript	synonymous_variant	742	309	103	P	ccG/ccA	rs770196669	.	.	1	RASSF7	HGNC	1166	protein_coding	YES	CCDS7702.1	ENSP00000380713	RASF7_HUMAN	E9PM39_HUMAN	UPI0000127A61	.	.	.	3/6	.	hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCCGGAACG	byFrequency	5	ESCA
APLNR	0	.	GRCh37	11	57004102	57004102	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377A>C	p.Asp126Ala	p.D126A	ENST00000606794	1/1	25	21	4	28	28	0	APLNR,missense_variant,p.Asp126Ala,ENST00000606794,;APLNR,missense_variant,p.Asp126Ala,ENST00000257254,;	G	ENSG00000134817	ENST00000606794	Transcript	missense_variant	574	377	126	D/A	gAc/gCc	.	.	.	-1	APLNR	HGNC	339	protein_coding	YES	CCDS7950.1	ENSP00000475344	APJ_HUMAN	.	UPI0000001622	.	deleterious(0)	probably_damaging(0.992)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF2,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCGGTCGAAG	.	4	ESCA
ASRGL1	0	.	GRCh37	11	62105564	62105564	+	Missense_Mutation	SNP	C	C	T	rs533515407	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115C>T	p.Arg39Trp	p.R39W	ENST00000415229	2/7	48	31	17	30	30	0	ASRGL1,missense_variant,p.Arg39Trp,ENST00000415229,;ASRGL1,missense_variant,p.Arg39Trp,ENST00000301776,;ASRGL1,5_prime_UTR_variant,,ENST00000535727,;RP11-703H8.7,upstream_gene_variant,,ENST00000400902,;ASRGL1,non_coding_transcript_exon_variant,,ENST00000526096,;ASRGL1,missense_variant,p.Arg39Trp,ENST00000534183,;ASRGL1,missense_variant,p.Arg39Trp,ENST00000529226,;ASRGL1,non_coding_transcript_exon_variant,,ENST00000534571,;ASRGL1,non_coding_transcript_exon_variant,,ENST00000525496,;	T	ENSG00000162174	ENST00000415229	Transcript	missense_variant	330	115	39	R/W	Cgg/Tgg	rs533515407	.	.	1	ASRGL1	HGNC	16448	protein_coding	YES	CCDS8019.1	ENSP00000400057	ASGL1_HUMAN	Q9BRH2_HUMAN	UPI000004BF00	.	deleterious(0)	possibly_damaging(0.773)	2/7	.	hmmpanther:PTHR10188,hmmpanther:PTHR10188:SF18,Pfam_domain:PF01112,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCCGGGAG	byCluster	5	ESCA
DNHD1	0	.	GRCh37	11	6588195	6588195	+	Missense_Mutation	SNP	T	T	C	rs747679287	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11456T>C	p.Ile3819Thr	p.I3819T	ENST00000254579	36/43	53	39	13	29	29	0	DNHD1,missense_variant,p.Ile3819Thr,ENST00000254579,;DNHD1,missense_variant,p.Ile67Thr,ENST00000525080,;DNHD1,missense_variant,p.Ile3819Thr,ENST00000527990,;DNHD1,upstream_gene_variant,,ENST00000527143,;DNHD1,non_coding_transcript_exon_variant,,ENST00000529821,;DNHD1,non_coding_transcript_exon_variant,,ENST00000525883,;DNHD1,non_coding_transcript_exon_variant,,ENST00000530197,;DNHD1,non_coding_transcript_exon_variant,,ENST00000533635,;DNHD1,intron_variant,,ENST00000534210,;DNHD1,downstream_gene_variant,,ENST00000526027,;DNHD1,downstream_gene_variant,,ENST00000524401,;DNHD1,downstream_gene_variant,,ENST00000531903,;DNHD1,upstream_gene_variant,,ENST00000532467,;	C	ENSG00000179532	ENST00000254579	Transcript	missense_variant	12020	11456	3819	I/T	aTa/aCa	rs747679287	.	.	1	DNHD1	HGNC	26532	protein_coding	YES	CCDS44532.1	ENSP00000254579	DNHD1_HUMAN	.	UPI0001929529	.	.	benign(0.047)	36/43	.	hmmpanther:PTHR10676:SF244,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACATAGTGA	byFrequency	5	ESCA
PRB3	0	.	GRCh37	12	11421033	11421033	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150C>T	p.%3D	p.T50T	ENST00000381842	3/6	106	71	35	76	76	0	PRB3,synonymous_variant,p.%3D,ENST00000381842,;PRB3,synonymous_variant,p.%3D,ENST00000538488,;PRB3,synonymous_variant,p.%3D,ENST00000279573,;PRB3,non_coding_transcript_exon_variant,,ENST00000440870,;PRB3,non_coding_transcript_exon_variant,,ENST00000539835,;	A	ENSG00000197870	ENST00000381842	Transcript	synonymous_variant	188	150	50	T	acC/acT	.	.	.	-1	PRB3	HGNC	9339	protein_coding	YES	.	ENSP00000371264	PRB3_HUMAN	.	UPI0000E67202	.	.	.	3/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23203,hmmpanther:PTHR23203:SF4,Pfam_domain:PF15240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGGGTACG	.	5	ESCA
PRB4	0	.	GRCh37	12	11461767	11461767	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150C>T	p.%3D	p.P50P	ENST00000279575	3/4	137	130	6	152	152	0	PRB4,synonymous_variant,p.%3D,ENST00000279575,;PRB4,synonymous_variant,p.%3D,ENST00000445719,;PRB4,synonymous_variant,p.%3D,ENST00000535904,;	A	ENSG00000230657	ENST00000279575	Transcript	synonymous_variant	184	150	50	P	ccC/ccT	.	.	.	-1	PRB4	HGNC	9340	protein_coding	YES	CCDS8641.1	ENSP00000279575	.	E9PAL0_HUMAN	UPI000013DBDC	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23203:SF4,hmmpanther:PTHR23203,Pfam_domain:PF15240,Prints_domain:PR01217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P50T|c.148C>A|4	MUTECT|MUSE	GGTGGGGGACG	.	2	ESCA
PDE3A	0	.	GRCh37	12	20801778	20801778	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2722A>G	p.Thr908Ala	p.T908A	ENST00000359062	13/16	79	56	23	59	59	0	PDE3A,missense_variant,p.Thr908Ala,ENST00000359062,;PDE3A,non_coding_transcript_exon_variant,,ENST00000544307,;	G	ENSG00000172572	ENST00000359062	Transcript	missense_variant	2762	2722	908	T/A	Act/Gct	.	.	.	1	PDE3A	HGNC	8778	protein_coding	YES	CCDS31754.1	ENSP00000351957	PDE3A_HUMAN	.	UPI000014175F	.	deleterious(0)	probably_damaging(0.999)	13/16	.	hmmpanther:PTHR11347:SF104,hmmpanther:PTHR11347,Pfam_domain:PF00233,Gene3D:1.10.1300.10,SMART_domains:SM00471,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCACTGAC	.	5	ESCA
KIF21A	0	.	GRCh37	12	39703470	39703471	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4194dupT	p.Thr1399TyrfsTer13	p.T1399Yfs*13	ENST00000361418	33/38	51	33	18	39	39	0	KIF21A,frameshift_variant,p.Thr700TyrfsTer13,ENST00000552961,;KIF21A,frameshift_variant,p.Thr1399TyrfsTer13,ENST00000361418,;KIF21A,frameshift_variant,p.Thr380TyrfsTer13,ENST00000551264,;KIF21A,frameshift_variant,p.Thr1362TyrfsTer13,ENST00000544797,;KIF21A,frameshift_variant,p.Thr1400TyrfsTer13,ENST00000395670,;KIF21A,frameshift_variant,p.Thr1346TyrfsTer13,ENST00000541463,;KIF21A,frameshift_variant,p.Thr1386TyrfsTer13,ENST00000361961,;KIF21A,downstream_gene_variant,,ENST00000547745,;KIF21A,non_coding_transcript_exon_variant,,ENST00000547733,;	A	ENSG00000139116	ENST00000361418	Transcript	frameshift_variant	4210-4211	4194-4195	1398-1399	-/X	-/T	.	.	.	-1	KIF21A	HGNC	19349	protein_coding	YES	CCDS53776.1	ENSP00000354878	KI21A_HUMAN	.	UPI0000212ED9	.	.	.	33/38	.	PROSITE_profiles:PS50294,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF398,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACTGGTATAAT	.	3	ESCA
GDF11	0	.	GRCh37	12	56143674	56143674	+	3'UTR	SNP	G	G	A	rs753525991	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8G>A	.	.	ENST00000257868	3/3	48	21	27	51	51	0	GDF11,splice_region_variant,,ENST00000546799,;GDF11,3_prime_UTR_variant,,ENST00000257868,;SARNP,downstream_gene_variant,,ENST00000444631,;SARNP,downstream_gene_variant,,ENST00000552884,;SARNP,downstream_gene_variant,,ENST00000546604,;	A	ENSG00000135414	ENST00000257868	Transcript	3_prime_UTR_variant	1269	.	.	.	.	rs753525991	.	.	1	GDF11	HGNC	4216	protein_coding	YES	CCDS8891.1	ENSP00000257868	GDF11_HUMAN	.	UPI000004C158	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGGATAGA	.	5	ESCA
ZC3H10	0	.	GRCh37	12	56515545	56515545	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1199C>T	p.Ser400Leu	p.S400L	ENST00000257940	3/3	18	5	12	16	16	0	ZC3H10,missense_variant,p.Ser400Leu,ENST00000257940,;ESYT1,intron_variant,,ENST00000551790,;ZC3H10,downstream_gene_variant,,ENST00000551880,;RPL41,downstream_gene_variant,,ENST00000546591,;ZC3H10,downstream_gene_variant,,ENST00000546903,;RPL41,downstream_gene_variant,,ENST00000501597,;ZC3H10,downstream_gene_variant,,ENST00000552345,;RP11-603J24.5,intron_variant,,ENST00000549438,;RP11-603J24.5,intron_variant,,ENST00000550947,;RP11-603J24.6,upstream_gene_variant,,ENST00000550840,;RPL41,downstream_gene_variant,,ENST00000546654,;ZC3H10,downstream_gene_variant,,ENST00000549973,;RPL41,downstream_gene_variant,,ENST00000546485,;RPL41,downstream_gene_variant,,ENST00000552314,;RPL41,downstream_gene_variant,,ENST00000358888,;	T	ENSG00000135482	ENST00000257940	Transcript	missense_variant	1475	1199	400	S/L	tCg/tTg	.	.	.	1	ZC3H10	HGNC	25893	protein_coding	YES	CCDS8903.1	ENSP00000257940	ZC3HA_HUMAN	F8VYY3_HUMAN,F8VSG0_HUMAN,F8VQT2_HUMAN	UPI0000070771	.	tolerated(0.11)	possibly_damaging(0.875)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12675	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATCGATGG	.	5	ESCA
BAZ2A	0	.	GRCh37	12	57030103	57030103	+	5'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-134T>C	.	.	ENST00000551812	1/29	26	12	13	29	29	0	BAZ2A,5_prime_UTR_variant,,ENST00000379441,;BAZ2A,5_prime_UTR_variant,,ENST00000551812,;BAZ2A,5_prime_UTR_variant,,ENST00000179765,;ATP5B,downstream_gene_variant,,ENST00000551570,;ATP5B,downstream_gene_variant,,ENST00000552104,;ATP5B,downstream_gene_variant,,ENST00000552959,;ATP5B,downstream_gene_variant,,ENST00000553007,;BAZ2A,upstream_gene_variant,,ENST00000549506,;ATP5B,downstream_gene_variant,,ENST00000552919,;ATP5B,downstream_gene_variant,,ENST00000262030,;ATP5B,downstream_gene_variant,,ENST00000551020,;BAZ2A,intron_variant,,ENST00000550730,;ATP5B,downstream_gene_variant,,ENST00000547808,;ATP5B,downstream_gene_variant,,ENST00000550162,;ATP5B,downstream_gene_variant,,ENST00000551182,;ATP5B,downstream_gene_variant,,ENST00000547250,;ATP5B,downstream_gene_variant,,ENST00000548474,;	G	ENSG00000076108	ENST00000551812	Transcript	5_prime_UTR_variant	61	.	.	.	.	.	.	.	-1	BAZ2A	HGNC	962	protein_coding	YES	CCDS44924.1	ENSP00000446880	BAZ2A_HUMAN	F8W053_HUMAN,F8VWQ3_HUMAN,F8VU39_HUMAN	UPI0000D4FED1	.	.	.	1/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGTATGCTT	.	5	ESCA
DCTN2	0	.	GRCh37	12	57927734	57927734	+	Splice_Site	SNP	A	A	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.684+2T>A	.	p.X228_splice	ENST00000434715	.	69	50	19	71	71	0	DCTN2,splice_donor_variant,,ENST00000543672,;DCTN2,splice_donor_variant,,ENST00000548249,;DCTN2,splice_donor_variant,,ENST00000550954,;DCTN2,splice_donor_variant,,ENST00000537439,;DCTN2,splice_donor_variant,,ENST00000546758,;DCTN2,splice_donor_variant,,ENST00000434715,;DCTN2,intron_variant,,ENST00000550086,;DCTN2,intron_variant,,ENST00000546670,;MBD6,downstream_gene_variant,,ENST00000355673,;MBD6,downstream_gene_variant,,ENST00000431731,;DCTN2,downstream_gene_variant,,ENST00000550750,;DCTN2,downstream_gene_variant,,ENST00000548949,;DCTN2,downstream_gene_variant,,ENST00000551611,;DCTN2,downstream_gene_variant,,ENST00000551400,;DCTN2,downstream_gene_variant,,ENST00000546965,;DCTN2,splice_donor_variant,,ENST00000549394,;DCTN2,splice_donor_variant,,ENST00000551872,;DCTN2,splice_donor_variant,,ENST00000552390,;DCTN2,splice_donor_variant,,ENST00000550201,;DCTN2,splice_donor_variant,,ENST00000550988,;DCTN2,intron_variant,,ENST00000548736,;DCTN2,downstream_gene_variant,,ENST00000547345,;MBD6,downstream_gene_variant,,ENST00000547844,;DCTN2,downstream_gene_variant,,ENST00000551142,;DCTN2,downstream_gene_variant,,ENST00000550576,;MBD6,downstream_gene_variant,,ENST00000547545,;DCTN2,downstream_gene_variant,,ENST00000547480,;	T	ENSG00000175203	ENST00000434715	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	DCTN2	HGNC	2712	protein_coding	YES	CCDS44930.1	ENSP00000408910	DCTN2_HUMAN	A8K8J9_HUMAN	UPI000004EFD1	.	.	.	.	9/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTTACTTTG	.	5	ESCA
LEMD3	0	.	GRCh37	12	65634765	65634765	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2203C>T	p.Arg735Ter	p.R735*	ENST00000308330	9/13	66	37	28	77	77	0	LEMD3,stop_gained,p.Arg735Ter,ENST00000308330,;LEMD3,non_coding_transcript_exon_variant,,ENST00000542032,;LEMD3,upstream_gene_variant,,ENST00000544506,;LEMD3,upstream_gene_variant,,ENST00000545026,;LEMD3,upstream_gene_variant,,ENST00000539442,;	T	ENSG00000174106	ENST00000308330	Transcript	stop_gained	2229	2203	735	R/*	Cga/Tga	CM104377	.	.	1	LEMD3	HGNC	28887	protein_coding	YES	CCDS8972.1	ENSP00000308369	MAN1_HUMAN	B4DI45_HUMAN	UPI000012EB75	.	.	.	9/13	.	hmmpanther:PTHR13428:SF9,hmmpanther:PTHR13428,Pfam_domain:PF09402	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACACGAAGA	.	5	ESCA
LIG4	0	.	GRCh37	13	108860848	108860848	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*33C>G	.	.	ENST00000356922	2/2	38	29	9	18	18	0	LIG4,3_prime_UTR_variant,,ENST00000405925,;LIG4,3_prime_UTR_variant,,ENST00000356922,;LIG4,3_prime_UTR_variant,,ENST00000442234,;	C	ENSG00000174405	ENST00000356922	Transcript	3_prime_UTR_variant	3042	.	.	.	.	.	.	.	-1	LIG4	HGNC	6601	protein_coding	YES	CCDS9508.1	ENSP00000349393	DNLI4_HUMAN	.	UPI00000742BF	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCAGATCAG	.	5	ESCA
FLT3	0	.	GRCh37	13	28623675	28623675	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.883-1G>A	.	p.X295_splice	ENST00000241453	.	35	10	24	40	40	0	FLT3,splice_acceptor_variant,,ENST00000241453,;FLT3,splice_acceptor_variant,,ENST00000537084,;FLT3,splice_acceptor_variant,,ENST00000380982,;FLT3,splice_acceptor_variant,,ENST00000380987,;	T	ENSG00000122025	ENST00000241453	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	FLT3	HGNC	3765	protein_coding	YES	CCDS31953.1	ENSP00000241453	FLT3_HUMAN	.	UPI00001FC90B	.	.	.	.	7/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCCCTAGGT	.	5	ESCA
DLEU7	0	.	GRCh37	13	51397464	51397464	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459+19860C>G	.	.	ENST00000400393	.	59	28	31	46	46	0	DLEU7,missense_variant,p.Leu218Val,ENST00000504404,;DLEU7,intron_variant,,ENST00000400393,;DLEU7-AS1,intron_variant,,ENST00000413510,;	C	ENSG00000186047	ENST00000400393	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DLEU7	HGNC	17567	protein_coding	YES	CCDS53869.1	ENSP00000420976	LEU7_HUMAN	.	UPI0000684279	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGAGATTCT	.	5	ESCA
DOCK9	0	.	GRCh37	13	99534153	99534153	+	Missense_Mutation	SNP	C	C	A	rs745870034	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2668G>T	p.Val890Leu	p.V890L	ENST00000376460	24/57	58	49	9	22	22	0	DOCK9,missense_variant,p.Val890Leu,ENST00000376460,;DOCK9,missense_variant,p.Val890Leu,ENST00000442173,;DOCK9,missense_variant,p.Val891Leu,ENST00000339416,;DOCK9,missense_variant,p.Val902Leu,ENST00000448493,;	A	ENSG00000088387	ENST00000376460	Transcript	missense_variant	2749	2668	890	V/L	Gtg/Ttg	rs745870034	.	.	-1	DOCK9	HGNC	14132	protein_coding	YES	CCDS45062.1	ENSP00000365643	DOCK9_HUMAN	.	UPI000046FD7F	.	tolerated(0.09)	possibly_damaging(0.658)	24/57	.	Superfamily_domains:SSF48371,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF77	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCACGTTAA	byFrequency	5	ESCA
ASPG	0	.	GRCh37	14	104570719	104570719	+	Missense_Mutation	SNP	G	G	T	rs749790590	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832G>T	p.Asp278Tyr	p.D278Y	ENST00000551177	8/16	110	61	48	79	79	0	ASPG,missense_variant,p.Asp278Tyr,ENST00000546892,;ASPG,missense_variant,p.Asp278Tyr,ENST00000551177,;ASPG,missense_variant,p.Asp278Tyr,ENST00000455920,;ASPG,intron_variant,,ENST00000551170,;ASPG,upstream_gene_variant,,ENST00000550583,;ASPG,upstream_gene_variant,,ENST00000549809,;ASPG,upstream_gene_variant,,ENST00000552126,;ASPG,upstream_gene_variant,,ENST00000556267,;ASPG,non_coding_transcript_exon_variant,,ENST00000548372,;	T	ENSG00000166183	ENST00000551177	Transcript	missense_variant	924	832	278	D/Y	Gac/Tac	rs749790590,COSM3494063,COSM3494064	.	.	1	ASPG	HGNC	20123	protein_coding	YES	CCDS45170.2	ENSP00000450040	LPP60_HUMAN	.	UPI00001D7B76	.	deleterious(0)	possibly_damaging(0.813)	8/16	.	hmmpanther:PTHR11707:SF3,hmmpanther:PTHR11707,Pfam_domain:PF00710,Gene3D:3.40.50.40,TIGRFAM_domain:TIGR00519,SMART_domains:SM00870,Superfamily_domains:SSF53774	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCGACCTG	byFrequency	5	ESCA
ZFHX2	0	.	GRCh37	14	23992792	23992792	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6359A>G	p.Glu2120Gly	p.E2120G	ENST00000419474	9/10	23	9	13	14	14	0	ZFHX2,missense_variant,p.Glu2120Gly,ENST00000419474,;RP11-66N24.4,intron_variant,,ENST00000553985,;RP11-66N24.4,intron_variant,,ENST00000556354,;RP11-66N24.4,intron_variant,,ENST00000554403,;ZFHX2,upstream_gene_variant,,ENST00000606808,;	C	ENSG00000136367	ENST00000419474	Transcript	missense_variant	6715	6359	2120	E/G	gAa/gGa	.	.	.	-1	ZFHX2	HGNC	20152	protein_coding	YES	CCDS55907.1	ENSP00000413418	ZFHX2_HUMAN	G3V3N5_HUMAN,C9JSX6_HUMAN	UPI000198D01B	.	.	unknown(0)	9/10	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF86,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTTCCTTG	.	5	ESCA
SLC39A9	0	.	GRCh37	14	69928356	69928357	+	3'Flank	INS	-	-	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000336643	.	18	12	5	18	18	0	SLC39A9,3_prime_UTR_variant,,ENST00000031146,;SLC39A9,intron_variant,,ENST00000556605,;SLC39A9,downstream_gene_variant,,ENST00000336643,;SLC39A9,downstream_gene_variant,,ENST00000557046,;SLC39A9,downstream_gene_variant,,ENST00000555245,;SLC39A9,intron_variant,,ENST00000555840,;SLC39A9,downstream_gene_variant,,ENST00000554023,;SLC39A9,downstream_gene_variant,,ENST00000538956,;	T	ENSG00000029364	ENST00000336643	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1088	1	SLC39A9	HGNC	20182	protein_coding	YES	CCDS9795.1	ENSP00000336887	S39A9_HUMAN	C4N9M8_HUMAN,B4DDK0_HUMAN	UPI0000040C12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTGTGTTTTT	.	2	ESCA
TRIP11	0	.	GRCh37	14	92470324	92470324	+	Silent	SNP	T	T	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3996A>T	p.%3D	p.A1332A	ENST00000267622	11/21	31	16	15	29	29	0	TRIP11,synonymous_variant,p.%3D,ENST00000554357,;TRIP11,synonymous_variant,p.%3D,ENST00000267622,;TRIP11,upstream_gene_variant,,ENST00000557017,;	A	ENSG00000100815	ENST00000267622	Transcript	synonymous_variant	4370	3996	1332	A	gcA/gcT	.	.	.	-1	TRIP11	HGNC	12305	protein_coding	YES	CCDS9899.1	ENSP00000267622	TRIPB_HUMAN	G3V4R7_HUMAN	UPI000013D767	.	.	.	11/21	.	hmmpanther:PTHR18921:SF2,hmmpanther:PTHR18921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTTGCTCT	.	5	ESCA
SNORD116-24	0	.	GRCh37	15	25339239	25339239	+	RNA	SNP	A	A	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.56A>T	.	.	ENST00000384549	1/1	92	50	41	95	95	0	SNORD116-24,non_coding_transcript_exon_variant,,ENST00000384549,;SNORD116-25,upstream_gene_variant,,ENST00000516517,;SNORD116-23,downstream_gene_variant,,ENST00000384645,;SNHG14,downstream_gene_variant,,ENST00000384430,;SNHG14,intron_variant,,ENST00000553108,;SNHG14,intron_variant,,ENST00000549804,;SNHG14,intron_variant,,ENST00000546682,;	T	ENSG00000207279	ENST00000384549	Transcript	non_coding_transcript_exon_variant	56	.	.	.	.	.	.	.	1	SNORD116-24	HGNC	33090	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTGAAAACT	.	5	ESCA
NUTM1	0	.	GRCh37	15	34649094	34649094	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2801G>A	p.Gly934Asp	p.G934D	ENST00000333756	7/7	26	20	6	19	19	0	NUTM1,missense_variant,p.Gly962Asp,ENST00000537011,;NUTM1,missense_variant,p.Gly934Asp,ENST00000333756,;NUTM1,missense_variant,p.Gly952Asp,ENST00000438749,;LPCAT4,downstream_gene_variant,,ENST00000314891,;LPCAT4,downstream_gene_variant,,ENST00000567507,;LPCAT4,downstream_gene_variant,,ENST00000563240,;LPCAT4,downstream_gene_variant,,ENST00000563748,;	A	ENSG00000184507	ENST00000333756	Transcript	missense_variant	2956	2801	934	G/D	gGc/gAc	.	.	.	1	NUTM1	HGNC	29919	protein_coding	YES	CCDS32190.1	ENSP00000329448	NUTM1_HUMAN	.	UPI000016159A	.	deleterious(0.03)	benign(0.086)	7/7	.	hmmpanther:PTHR22879:SF13,hmmpanther:PTHR22879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGGCAGGG	.	4	ESCA
CASC5	0	.	GRCh37	15	40914458	40914458	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2074A>G	p.Ile692Val	p.I692V	ENST00000346991	11/27	21	15	6	27	27	0	CASC5,missense_variant,p.Ile692Val,ENST00000346991,;CASC5,missense_variant,p.Ile666Val,ENST00000399668,;CASC5,3_prime_UTR_variant,,ENST00000527044,;CASC5,non_coding_transcript_exon_variant,,ENST00000533001,;CASC5,intron_variant,,ENST00000534204,;CASC5,upstream_gene_variant,,ENST00000526913,;	G	ENSG00000137812	ENST00000346991	Transcript	missense_variant	2464	2074	692	I/V	Ata/Gta	.	.	.	1	CASC5	HGNC	24054	protein_coding	YES	CCDS42023.1	ENSP00000335463	CASC5_HUMAN	.	UPI0000E59BD3	.	tolerated(0.36)	benign(0.009)	11/27	.	hmmpanther:PTHR16520,hmmpanther:PTHR16520:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGATAGCA	.	5	ESCA
MGA	0	.	GRCh37	15	42041627	42041627	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5822C>G	p.Ser1941Cys	p.S1941C	ENST00000219905	17/24	31	25	6	29	29	0	MGA,missense_variant,p.Ser589Cys,ENST00000564190,;MGA,missense_variant,p.Ser1941Cys,ENST00000219905,;MGA,missense_variant,p.Ser1941Cys,ENST00000570161,;MGA,missense_variant,p.Ser1732Cys,ENST00000545763,;MGA,missense_variant,p.Ser1902Cys,ENST00000389936,;MGA,missense_variant,p.Ser1732Cys,ENST00000566586,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,;	G	ENSG00000174197	ENST00000219905	Transcript	missense_variant	6003	5822	1941	S/C	tCt/tGt	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	deleterious(0)	probably_damaging(0.998)	17/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGTCTGGTA	.	4	ESCA
CTDSPL2	0	.	GRCh37	15	44817510	44817510	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1138A>G	.	.	ENST00000260327	13/13	44	38	6	51	51	0	CTDSPL2,3_prime_UTR_variant,,ENST00000558373,;CTDSPL2,3_prime_UTR_variant,,ENST00000260327,;CTDSPL2,3_prime_UTR_variant,,ENST00000396780,;CTDSPL2,downstream_gene_variant,,ENST00000558966,;EIF3J-AS1,downstream_gene_variant,,ENST00000560750,;CTDSPL2,downstream_gene_variant,,ENST00000559738,;CTDSPL2,non_coding_transcript_exon_variant,,ENST00000559175,;CTDSPL2,downstream_gene_variant,,ENST00000560620,;	G	ENSG00000137770	ENST00000260327	Transcript	3_prime_UTR_variant	3102	.	.	.	.	.	.	.	1	CTDSPL2	HGNC	26936	protein_coding	YES	CCDS10110.1	ENSP00000260327	CTSL2_HUMAN	H0YNW9_HUMAN,H0YNU2_HUMAN,H0YMH7_HUMAN	UPI000004A0B3	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TTAATATGCTC	.	3	ESCA
RP11-152L20.3	0	.	GRCh37	15	92715088	92715088	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.186-14617C>T	.	.	ENST00000561674	.	42	26	15	45	45	0	SLCO3A1,missense_variant,p.Ser692Asn,ENST00000424469,;RP11-152L20.3,intron_variant,,ENST00000561674,;RP11-24J19.1,intron_variant,,ENST00000557683,;SLCO3A1,non_coding_transcript_exon_variant,,ENST00000566477,;SLCO3A1,downstream_gene_variant,,ENST00000555892,;	A	ENSG00000260661	ENST00000561674	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RP11-152L20.3	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGCTGAG	.	5	ESCA
PRKCB	0	.	GRCh37	16	23847536	23847536	+	Missense_Mutation	SNP	G	G	A	rs771388864	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40G>A	p.Glu14Lys	p.E14K	ENST00000303531	1/17	18	12	6	17	17	0	PRKCB,missense_variant,p.Glu14Lys,ENST00000498058,;PRKCB,missense_variant,p.Glu14Lys,ENST00000303531,;PRKCB,missense_variant,p.Glu14Lys,ENST00000321728,;PRKCB,upstream_gene_variant,,ENST00000498739,;	A	ENSG00000166501	ENST00000303531	Transcript	missense_variant	192	40	14	E/K	Gag/Aag	rs771388864	.	.	1	PRKCB	HGNC	9395	protein_coding	YES	CCDS10619.1	ENSP00000305355	KPCB_HUMAN	I3L1Z0_HUMAN	UPI000002ACF9	.	tolerated(0.21)	benign(0.01)	1/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF63,PIRSF_domain:PIRSF000550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCGAGGAG	.	5	ESCA
RBBP6	0	.	GRCh37	16	24582688	24582688	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4301T>A	p.Leu1434Gln	p.L1434Q	ENST00000319715	18/18	32	23	8	34	34	0	RBBP6,missense_variant,p.Leu594Gln,ENST00000381039,;RBBP6,missense_variant,p.Leu1434Gln,ENST00000319715,;RBBP6,missense_variant,p.Leu1400Gln,ENST00000348022,;RBBP6,downstream_gene_variant,,ENST00000564314,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,;	A	ENSG00000122257	ENST00000319715	Transcript	missense_variant	4733	4301	1434	L/Q	cTg/cAg	.	.	.	1	RBBP6	HGNC	9889	protein_coding	YES	CCDS10621.1	ENSP00000317872	RBBP6_HUMAN	I3L3Y2_HUMAN,H3BUN0_HUMAN,H3BSK8_HUMAN	UPI00001A96B8	.	tolerated_low_confidence(0.09)	unknown(0)	18/18	.	hmmpanther:PTHR15439:SF1,hmmpanther:PTHR15439	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTCTGAATG	.	5	ESCA
XPO6	0	.	GRCh37	16	28128767	28128767	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1876G>T	p.Ala626Ser	p.A626S	ENST00000304658	15/24	24	17	7	24	24	0	XPO6,missense_variant,p.Ala626Ser,ENST00000304658,;XPO6,missense_variant,p.Ala612Ser,ENST00000565698,;XPO6,upstream_gene_variant,,ENST00000569216,;XPO6,non_coding_transcript_exon_variant,,ENST00000562408,;XPO6,intron_variant,,ENST00000564905,;	A	ENSG00000169180	ENST00000304658	Transcript	missense_variant	2377	1876	626	A/S	Gct/Tct	.	.	.	-1	XPO6	HGNC	19733	protein_coding	YES	CCDS42135.1	ENSP00000302790	XPO6_HUMAN	H3BUP8_HUMAN,H3BR41_HUMAN,D3DWF9_HUMAN	UPI000006F228	.	tolerated(0.06)	possibly_damaging(0.685)	15/24	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR21452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCAGCCAGGG	.	5	ESCA
NUPR1	0	.	GRCh37	16	28550253	28550253	+	5'UTR	SNP	T	T	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25A>T	.	.	ENST00000395641	1/3	45	30	14	50	50	0	NUPR1,5_prime_UTR_variant,,ENST00000324873,;NUPR1,5_prime_UTR_variant,,ENST00000395641,;NUPR1,5_prime_UTR_variant,,ENST00000567646,;	A	ENSG00000176046	ENST00000395641	Transcript	5_prime_UTR_variant	77	.	.	.	.	.	.	.	-1	NUPR1	HGNC	29990	protein_coding	YES	CCDS42137.1	ENSP00000379003	NUPR1_HUMAN	.	UPI000016955C	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCTCTCTT	.	5	ESCA
DDX19B	0	.	GRCh37	16	70351454	70351454	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.352A>G	p.Ile118Val	p.I118V	ENST00000288071	5/12	61	28	32	59	59	0	DDX19B,missense_variant,p.Ile9Val,ENST00000393657,;DDX19B,missense_variant,p.Ile118Val,ENST00000288071,;DDX19B,missense_variant,p.Ile105Val,ENST00000566216,;RP11-529K1.3,missense_variant,p.Ile118Val,ENST00000567706,;DDX19B,missense_variant,p.Ile9Val,ENST00000568625,;DDX19B,missense_variant,p.Ile123Val,ENST00000563206,;DDX19B,missense_variant,p.Ile9Val,ENST00000563392,;DDX19B,intron_variant,,ENST00000451014,;DDX19B,intron_variant,,ENST00000355992,;RP11-529K1.2,intron_variant,,ENST00000562077,;DDX19B,non_coding_transcript_exon_variant,,ENST00000570055,;DDX19B,downstream_gene_variant,,ENST00000569099,;DDX19B,3_prime_UTR_variant,,ENST00000562912,;DDX19B,3_prime_UTR_variant,,ENST00000568460,;DDX19B,non_coding_transcript_exon_variant,,ENST00000569224,;DDX19B,intron_variant,,ENST00000562519,;DDX19B,intron_variant,,ENST00000568408,;DDX19B,intron_variant,,ENST00000568008,;RP11-529K1.3,intron_variant,,ENST00000565116,;	G	ENSG00000157349	ENST00000288071	Transcript	missense_variant	597	352	118	I/V	Ata/Gta	.	.	.	1	DDX19B	HGNC	2742	protein_coding	YES	CCDS10888.1	ENSP00000288071	DD19B_HUMAN	Q2NL95_HUMAN,H3BN59_HUMAN,B4DL69_HUMAN	UPI000012907F	.	deleterious(0.01)	possibly_damaging(0.749)	5/12	.	PROSITE_profiles:PS51195,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF194,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGATACAA	.	5	ESCA
SPATA33	0	.	GRCh37	16	89724674	89724674	+	Missense_Mutation	SNP	G	G	A	rs767065039	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53G>A	p.Gly18Glu	p.G18E	ENST00000301031	2/3	104	84	19	71	70	1	SPATA33,missense_variant,p.Gly18Glu,ENST00000301031,;SPATA33,missense_variant,p.Gly25Glu,ENST00000566204,;SPATA33,missense_variant,p.Gly19Glu,ENST00000579310,;SPATA33,3_prime_UTR_variant,,ENST00000564238,;SPATA33,5_prime_UTR_variant,,ENST00000568929,;CHMP1A,upstream_gene_variant,,ENST00000397901,;CHMP1A,upstream_gene_variant,,ENST00000550102,;CHMP1A,upstream_gene_variant,,ENST00000535997,;CHMP1A,upstream_gene_variant,,ENST00000253475,;SPATA33,upstream_gene_variant,,ENST00000566857,;CHMP1A,upstream_gene_variant,,ENST00000547614,;SPATA33,missense_variant,p.Asp37Asn,ENST00000567827,;SPATA33,3_prime_UTR_variant,,ENST00000457689,;SPATA33,intron_variant,,ENST00000565890,;CHMP1A,upstream_gene_variant,,ENST00000549328,;CHMP1A,upstream_gene_variant,,ENST00000550872,;CHMP1A,upstream_gene_variant,,ENST00000551981,;	A	ENSG00000167523	ENST00000301031	Transcript	missense_variant	53	53	18	G/E	gGa/gAa	rs767065039	.	.	1	SPATA33	HGNC	26463	protein_coding	YES	CCDS10983.1	ENSP00000301031	SPT33_HUMAN	.	UPI000007159D	.	tolerated(0.37)	benign(0.002)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAAGGGATCCA	byFrequency	3	ESCA
SPATA33	0	.	GRCh37	16	89724680	89724680	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>T	p.Thr20Ile	p.T20I	ENST00000301031	2/3	104	83	20	72	72	0	SPATA33,missense_variant,p.Thr20Ile,ENST00000301031,;SPATA33,missense_variant,p.Thr27Ile,ENST00000566204,;SPATA33,missense_variant,p.Thr21Ile,ENST00000579310,;SPATA33,3_prime_UTR_variant,,ENST00000564238,;SPATA33,5_prime_UTR_variant,,ENST00000568929,;CHMP1A,upstream_gene_variant,,ENST00000397901,;CHMP1A,upstream_gene_variant,,ENST00000550102,;CHMP1A,upstream_gene_variant,,ENST00000535997,;CHMP1A,upstream_gene_variant,,ENST00000253475,;SPATA33,upstream_gene_variant,,ENST00000566857,;CHMP1A,upstream_gene_variant,,ENST00000547614,;SPATA33,missense_variant,p.Pro39Ser,ENST00000567827,;SPATA33,3_prime_UTR_variant,,ENST00000457689,;SPATA33,intron_variant,,ENST00000565890,;CHMP1A,upstream_gene_variant,,ENST00000549328,;CHMP1A,upstream_gene_variant,,ENST00000550872,;CHMP1A,upstream_gene_variant,,ENST00000551981,;	T	ENSG00000167523	ENST00000301031	Transcript	missense_variant	59	59	20	T/I	aCc/aTc	.	.	.	1	SPATA33	HGNC	26463	protein_coding	YES	CCDS10983.1	ENSP00000301031	SPT33_HUMAN	.	UPI000007159D	.	tolerated(0.23)	benign(0.001)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATCCACCTATT	.	3	ESCA
SPATA33	0	.	GRCh37	16	89724682	89724682	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61T>C	p.Tyr21His	p.Y21H	ENST00000301031	2/3	104	83	20	75	75	0	SPATA33,missense_variant,p.Tyr21His,ENST00000301031,;SPATA33,missense_variant,p.Tyr28His,ENST00000566204,;SPATA33,missense_variant,p.Tyr22His,ENST00000579310,;SPATA33,3_prime_UTR_variant,,ENST00000564238,;SPATA33,5_prime_UTR_variant,,ENST00000568929,;CHMP1A,upstream_gene_variant,,ENST00000397901,;CHMP1A,upstream_gene_variant,,ENST00000550102,;CHMP1A,upstream_gene_variant,,ENST00000535997,;CHMP1A,upstream_gene_variant,,ENST00000253475,;SPATA33,upstream_gene_variant,,ENST00000566857,;CHMP1A,upstream_gene_variant,,ENST00000547614,;SPATA33,synonymous_variant,p.%3D,ENST00000567827,;SPATA33,3_prime_UTR_variant,,ENST00000457689,;SPATA33,intron_variant,,ENST00000565890,;CHMP1A,upstream_gene_variant,,ENST00000549328,;CHMP1A,upstream_gene_variant,,ENST00000550872,;CHMP1A,upstream_gene_variant,,ENST00000551981,;	C	ENSG00000167523	ENST00000301031	Transcript	missense_variant	61	61	21	Y/H	Tat/Cat	.	.	.	1	SPATA33	HGNC	26463	protein_coding	YES	CCDS10983.1	ENSP00000301031	SPT33_HUMAN	.	UPI000007159D	.	tolerated(0.5)	benign(0.002)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCACCTATTCA	.	3	ESCA
TOP3A	0	.	GRCh37	17	18202892	18202892	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.971C>T	p.Pro324Leu	p.P324L	ENST00000321105	9/19	40	20	20	60	60	0	TOP3A,missense_variant,p.Pro299Leu,ENST00000580095,;TOP3A,missense_variant,p.Pro324Leu,ENST00000321105,;TOP3A,missense_variant,p.Pro229Leu,ENST00000542570,;TOP3A,5_prime_UTR_variant,,ENST00000540524,;TOP3A,downstream_gene_variant,,ENST00000584669,;TOP3A,missense_variant,p.Pro86Leu,ENST00000581536,;TOP3A,3_prime_UTR_variant,,ENST00000582981,;TOP3A,3_prime_UTR_variant,,ENST00000584582,;TOP3A,non_coding_transcript_exon_variant,,ENST00000583804,;TOP3A,non_coding_transcript_exon_variant,,ENST00000469739,;TOP3A,downstream_gene_variant,,ENST00000461127,;	A	ENSG00000177302	ENST00000321105	Transcript	missense_variant	1186	971	324	P/L	cCt/cTt	.	.	.	-1	TOP3A	HGNC	11992	protein_coding	YES	CCDS11194.1	ENSP00000321636	TOP3A_HUMAN	B4DSJ0_HUMAN,A8K398_HUMAN	UPI00001371A0	.	deleterious(0)	probably_damaging(1)	9/19	.	hmmpanther:PTHR11390,hmmpanther:PTHR11390:SF23,Pfam_domain:PF01131,Gene3D:2.70.20.10,SMART_domains:SM00437,Superfamily_domains:SSF56712	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGAGGCCGC	.	5	ESCA
MLLT6	0	.	GRCh37	17	36882710	36882710	+	3'UTR	SNP	C	C	T	rs12936439	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*859C>T	.	.	ENST00000325718	20/20	16	12	4	11	11	0	MLLT6,3_prime_UTR_variant,,ENST00000325718,;AC006449.1,downstream_gene_variant,,ENST00000595377,;CISD3,upstream_gene_variant,,ENST00000439660,;MLLT6,intron_variant,,ENST00000582830,;CISD3,upstream_gene_variant,,ENST00000578573,;MLLT6,non_coding_transcript_exon_variant,,ENST00000484263,;MLLT6,non_coding_transcript_exon_variant,,ENST00000494578,;CISD3,upstream_gene_variant,,ENST00000581668,;	T	ENSG00000108292	ENST00000325718	Transcript	3_prime_UTR_variant	4232	.	.	.	.	rs12936439	.	.	1	MLLT6	HGNC	7138	protein_coding	YES	CCDS11327.1	ENSP00000316426	AF17_HUMAN	.	UPI000013C86A	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	ATAGGCGCAGT	.	2	ESCA
TUBG2	0	.	GRCh37	17	40818726	40818726	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1264G>C	p.Asp422His	p.D422H	ENST00000251412	11/11	67	43	23	71	71	0	TUBG2,missense_variant,p.Asp422His,ENST00000251412,;PLEKHH3,downstream_gene_variant,,ENST00000412503,;PLEKHH3,downstream_gene_variant,,ENST00000591022,;PLEKHH3,downstream_gene_variant,,ENST00000293349,;PLEKHH3,downstream_gene_variant,,ENST00000456950,;TUBG2,non_coding_transcript_exon_variant,,ENST00000588870,;PLEKHH3,downstream_gene_variant,,ENST00000591476,;PLEKHH3,downstream_gene_variant,,ENST00000591196,;PLEKHH3,downstream_gene_variant,,ENST00000591490,;	C	ENSG00000037042	ENST00000251412	Transcript	missense_variant	1463	1264	422	D/H	Gac/Cac	.	.	.	1	TUBG2	HGNC	12419	protein_coding	YES	CCDS32658.1	ENSP00000251412	TBG2_HUMAN	.	UPI0000136A5C	.	deleterious(0.01)	possibly_damaging(0.836)	11/11	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF79,Gene3D:1.10.287.600,Superfamily_domains:SSF55307,Prints_domain:PR01164	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGGACAGG	.	5	ESCA
DDX5	0	.	GRCh37	17	62496054	62496054	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1832G>T	p.Gly611Val	p.G611V	ENST00000225792	13/13	36	17	19	28	28	0	DDX5,missense_variant,p.Gly611Val,ENST00000578804,;DDX5,missense_variant,p.Gly532Val,ENST00000450599,;DDX5,missense_variant,p.Gly611Val,ENST00000225792,;DDX5,downstream_gene_variant,,ENST00000584279,;DDX5,downstream_gene_variant,,ENST00000583212,;DDX5,downstream_gene_variant,,ENST00000581806,;DDX5,downstream_gene_variant,,ENST00000583239,;DDX5,downstream_gene_variant,,ENST00000579091,;DDX5,downstream_gene_variant,,ENST00000578190,;POLG2,upstream_gene_variant,,ENST00000539111,;DDX5,downstream_gene_variant,,ENST00000581697,;DDX5,downstream_gene_variant,,ENST00000585060,;DDX5,downstream_gene_variant,,ENST00000579996,;DDX5,downstream_gene_variant,,ENST00000585111,;DDX5,downstream_gene_variant,,ENST00000577787,;DDX5,downstream_gene_variant,,ENST00000577922,;MIR3064,downstream_gene_variant,,ENST00000581130,;MIR5047,downstream_gene_variant,,ENST00000579212,;DDX5,downstream_gene_variant,,ENST00000580026,;DDX5,downstream_gene_variant,,ENST00000581237,;DDX5,downstream_gene_variant,,ENST00000578491,;DDX5,3_prime_UTR_variant,,ENST00000540698,;DDX5,3_prime_UTR_variant,,ENST00000581693,;DDX5,non_coding_transcript_exon_variant,,ENST00000581230,;DDX5,downstream_gene_variant,,ENST00000584549,;DDX5,downstream_gene_variant,,ENST00000585223,;DDX5,downstream_gene_variant,,ENST00000579461,;DDX5,downstream_gene_variant,,ENST00000578758,;DDX5,downstream_gene_variant,,ENST00000578400,;DDX5,downstream_gene_variant,,ENST00000582326,;DDX5,downstream_gene_variant,,ENST00000583894,;DDX5,downstream_gene_variant,,ENST00000581551,;DDX5,downstream_gene_variant,,ENST00000583562,;POLG2,upstream_gene_variant,,ENST00000585141,;DDX5,downstream_gene_variant,,ENST00000583201,;POLG2,upstream_gene_variant,,ENST00000578997,;DDX5,downstream_gene_variant,,ENST00000585317,;	A	ENSG00000108654	ENST00000225792	Transcript	missense_variant	2234	1832	611	G/V	gGa/gTa	.	.	.	-1	DDX5	HGNC	2746	protein_coding	YES	CCDS11659.1	ENSP00000225792	DDX5_HUMAN	J3QS97_HUMAN,J3QRQ7_HUMAN,J3QRN5_HUMAN,J3QR62_HUMAN,J3QLG9_HUMAN,J3QKN9_HUMAN,J3KTQ4_HUMAN,J3KRZ1_HUMAN,J3KRX8_HUMAN	UPI000003B456	.	deleterious_low_confidence(0.03)	benign(0.034)	13/13	.	hmmpanther:PTHR24031:SF182,hmmpanther:PTHR24031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATCCTGTT	.	5	ESCA
TP53	0	.	GRCh37	17	7578291	7578291	+	Splice_Site	SNP	T	T	A	.	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560-2A>T	.	p.X187_splice	ENST00000269305	.	45	25	19	48	48	0	TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000269305,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000504937,;TP53,splice_acceptor_variant,,ENST00000505014,;TP53,splice_acceptor_variant,,ENST00000504290,;TP53,splice_acceptor_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	splice_acceptor_variant	.	.	.	.	.	CS941545,TP53_g.12627A>T,TP53_g.12627A>C,TP53_g.12627A>G,COSM18657,COSM45026,COSM45031,COSM1679503,COSM323926,COSM1679505,COSM323925,COSM1679507,COSM323927,COSM3773307,COSM1679504,COSM1679506,COSM323928	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	5/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.560-2A>T|5,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.A189_V197delAPPQHLIRV|c.565_591del27|4,BUFFER|p.P191delP|c.568_570delCCT|6,BUFFER|p.P190fs*57|c.569delC|4,BUFFER|p.P190L|c.569C>T|4,BUFFER|p.P97L|c.290C>T|6,BUFFER|p.P190L|c.569C>T|6,BUFFER|p.P190L|c.569C>T|30,BUFFER|p.P190R|c.569C>G|3,BUFFER|p.P190L|c.569C>T|6,BUFFER|p.P190L|c.569C>T|3,BUFFER|p.P58L|c.173C>T|6,BUFFER|p.P190T|c.568C>A|4,BUFFER|p.P190S|c.568C>T|8,BUFFER|p.A189V|c.566C>T|4,BUFFER|p.A189T|c.565G>A|3,BUFFER|p.G187G|c.561T>C|3,BUFFER|p.G187D|c.560G>A|7,BUFFER|p.G187V|c.560G>T|3,BUFFER|p.?|c.164-1G>A|7,BUFFER|p.?|c.560-1G>T|4,BUFFER|p.?|c.560-1G>A|20,BUFFER|p.?|c.164-1G>T|4,BUFFER|p.?|c.560-1G>A|7,BUFFER|p.?|c.560-1G>A|3,BUFFER|p.?|c.560-1G>T|4,BUFFER|p.?|c.281-1G>T|4,BUFFER|p.?|c.281-1G>A|7,BUFFER|p.?|c.560-1G>T|3,BUFFER|p.?|c.560-1G>A|7,BUFFER|p.?|c.560-1G>T|10,BUFFER|p.?|c.560-1G>C|6,BUFFER|p.?|c.560-2A>G|4,BUFFER|p.?|c.281-2A>G|4,BUFFER|p.?|c.164-2A>G|4,BUFFER|p.?|c.560-2A>G|4,BUFFER|p.?|c.560-2A>G|4,BUFFER|p.?|c.560-2A>G|8,BUFFER|p.?|c.560-2A>G|3,BUFFER|p.?|c.560-3T>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCTAAGAG	.	5	ESCA
UNC13A	0	.	GRCh37	19	17766135	17766135	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1340C>A	p.Ala447Asp	p.A447D	ENST00000519716	11/44	46	32	13	37	37	0	UNC13A,missense_variant,p.Ala447Asp,ENST00000252773,;UNC13A,missense_variant,p.Ala447Asp,ENST00000519716,;UNC13A,missense_variant,p.Ala447Asp,ENST00000550896,;UNC13A,missense_variant,p.Ala447Asp,ENST00000552293,;UNC13A,missense_variant,p.Ala447Asp,ENST00000551649,;UNC13A,missense_variant,p.Ala535Asp,ENST00000428389,;	T	ENSG00000130477	ENST00000519716	Transcript	missense_variant	1340	1340	447	A/D	gCc/gAc	.	.	.	-1	UNC13A	HGNC	23150	protein_coding	YES	CCDS46013.2	ENSP00000429562	UN13A_HUMAN	.	UPI00006C19A7	.	deleterious_low_confidence(0)	probably_damaging(0.914)	11/44	.	hmmpanther:PTHR10480	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGGCCCTG	.	5	ESCA
UNC13A	0	.	GRCh37	19	17766136	17766136	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1339G>T	p.Ala447Ser	p.A447S	ENST00000519716	11/44	44	30	13	36	36	0	UNC13A,missense_variant,p.Ala447Ser,ENST00000252773,;UNC13A,missense_variant,p.Ala447Ser,ENST00000519716,;UNC13A,missense_variant,p.Ala447Ser,ENST00000550896,;UNC13A,missense_variant,p.Ala447Ser,ENST00000552293,;UNC13A,missense_variant,p.Ala447Ser,ENST00000551649,;UNC13A,missense_variant,p.Ala535Ser,ENST00000428389,;	A	ENSG00000130477	ENST00000519716	Transcript	missense_variant	1339	1339	447	A/S	Gcc/Tcc	.	.	.	-1	UNC13A	HGNC	23150	protein_coding	YES	CCDS46013.2	ENSP00000429562	UN13A_HUMAN	.	UPI00006C19A7	.	tolerated_low_confidence(0.17)	possibly_damaging(0.676)	11/44	.	hmmpanther:PTHR10480	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGCCCTGG	.	5	ESCA
XRCC1	0	.	GRCh37	19	44055806	44055806	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1116G>A	p.%3D	p.Q372Q	ENST00000262887	10/17	66	46	20	46	46	0	XRCC1,synonymous_variant,p.%3D,ENST00000262887,;XRCC1,synonymous_variant,p.%3D,ENST00000543982,;XRCC1,downstream_gene_variant,,ENST00000594107,;XRCC1,downstream_gene_variant,,ENST00000599693,;L34079.2,downstream_gene_variant,,ENST00000594374,;XRCC1,downstream_gene_variant,,ENST00000598165,;L34079.3,upstream_gene_variant,,ENST00000597119,;XRCC1,3_prime_UTR_variant,,ENST00000597811,;XRCC1,downstream_gene_variant,,ENST00000595789,;XRCC1,downstream_gene_variant,,ENST00000598422,;	T	ENSG00000073050	ENST00000262887	Transcript	synonymous_variant	1664	1116	372	Q	caG/caA	.	.	.	-1	XRCC1	HGNC	12828	protein_coding	YES	CCDS12624.1	ENSP00000262887	XRCC1_HUMAN	M4WFF9_HUMAN	UPI000013D351	.	.	.	10/17	.	PROSITE_profiles:PS50172,hmmpanther:PTHR11370,hmmpanther:PTHR11370:SF1,Pfam_domain:PF00533,Gene3D:3.40.50.10190,SMART_domains:SM00292,Superfamily_domains:SSF52113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGACCTGGCT	.	5	ESCA
PVRL2	0	.	GRCh37	19	45381584	45381585	+	Intron	INS	-	-	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1042+3850dupT	.	.	ENST00000252483	.	59	44	15	29	29	0	PVRL2,frameshift_variant,p.Leu384ProfsTer55,ENST00000252485,;PVRL2,intron_variant,,ENST00000252483,;PVRL2,intron_variant,,ENST00000585601,;PVRL2,intron_variant,,ENST00000591581,;PVRL2,upstream_gene_variant,,ENST00000592018,;CTB-129P6.4,downstream_gene_variant,,ENST00000585408,;PVRL2,downstream_gene_variant,,ENST00000587386,;	T	ENSG00000130202	ENST00000252483	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PVRL2	HGNC	9707	protein_coding	YES	CCDS42576.1	ENSP00000252483	PVRL2_HUMAN	Q7Z458_HUMAN,Q7Z457_HUMAN,Q7Z456_HUMAN	UPI000004A2BF	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTTCATCCTG	.	3	ESCA
C19orf68	0	.	GRCh37	19	48675270	48675270	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211C>T	p.Leu71Phe	p.L71F	ENST00000328759	2/5	54	45	9	26	26	0	C19orf68,missense_variant,p.Leu71Phe,ENST00000328759,;LIG1,upstream_gene_variant,,ENST00000536218,;LIG1,upstream_gene_variant,,ENST00000593425,;LIG1,upstream_gene_variant,,ENST00000598938,;LIG1,upstream_gene_variant,,ENST00000427526,;LIG1,upstream_gene_variant,,ENST00000263274,;LIG1,upstream_gene_variant,,ENST00000596549,;ZNF114,upstream_gene_variant,,ENST00000597695,;C19orf68,non_coding_transcript_exon_variant,,ENST00000593921,;LIG1,upstream_gene_variant,,ENST00000599165,;LIG1,upstream_gene_variant,,ENST00000542460,;LIG1,upstream_gene_variant,,ENST00000594759,;LIG1,upstream_gene_variant,,ENST00000600055,;LIG1,upstream_gene_variant,,ENST00000601091,;	T	ENSG00000185453	ENST00000328759	Transcript	missense_variant	243	211	71	L/F	Ctc/Ttc	.	.	.	1	C19orf68	HGNC	34495	protein_coding	YES	.	ENSP00000331363	CS068_HUMAN	.	UPI0000366E3A	.	deleterious(0.02)	probably_damaging(0.999)	2/5	.	hmmpanther:PTHR10315:SF26,hmmpanther:PTHR10315	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGTGCTCAAG	.	5	ESCA
GRWD1	0	.	GRCh37	19	48956267	48956267	+	Silent	SNP	C	C	T	rs745453359	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1326C>T	p.%3D	p.R442R	ENST00000253237	7/7	30	23	7	18	18	0	GRWD1,synonymous_variant,p.%3D,ENST00000253237,;KCNJ14,upstream_gene_variant,,ENST00000342291,;GRWD1,downstream_gene_variant,,ENST00000598711,;	T	ENSG00000105447	ENST00000253237	Transcript	synonymous_variant	1559	1326	442	R	cgC/cgT	rs745453359	.	.	1	GRWD1	HGNC	21270	protein_coding	YES	CCDS12720.1	ENSP00000253237	GRWD1_HUMAN	M0QX71_HUMAN,A0MNN5_HUMAN	UPI000012BB5B	.	.	.	7/7	.	hmmpanther:PTHR22850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCGCACCAT	byFrequency	4	ESCA
KIR3DX1	0	.	GRCh37	19	55048095	55048095	+	Missense_Mutation	SNP	A	A	C	rs554102215	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662A>C	p.Tyr221Ser	p.Y221S	ENST00000221567	5/9	51	39	12	46	46	0	KIR3DX1,missense_variant,p.Tyr221Ser,ENST00000335056,;KIR3DX1,non_coding_transcript_exon_variant,,ENST00000482404,;KIR3DX1,missense_variant,p.Tyr221Ser,ENST00000221567,;KIR3DX1,splice_region_variant,,ENST00000447145,;KIR3DX1,intron_variant,,ENST00000465702,;KIR3DX1,intron_variant,,ENST00000446586,;KIR3DX1,intron_variant,,ENST00000471931,;KIR3DX1,intron_variant,,ENST00000434659,;	C	ENSG00000104970	ENST00000221567	Transcript	missense_variant	669	662	221	Y/S	tAc/tCc	rs554102215	.	.	1	KIR3DX1	HGNC	25043	nonsense_mediated_decay	YES	.	ENSP00000221567	KI3X1_HUMAN	.	UPI0000DE238B	.	tolerated(0.22)	benign(0.013)	5/9	.	hmmpanther:PTHR11738:SF91,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATACAAAA	by1000G	5	ESCA
MUC16	0	.	GRCh37	19	9066912	9066912	+	Missense_Mutation	SNP	G	G	A	rs780491549	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20534C>T	p.Thr6845Ile	p.T6845I	ENST00000397910	3/84	52	26	25	50	50	0	MUC16,missense_variant,p.Thr6845Ile,ENST00000397910,;	A	ENSG00000181143	ENST00000397910	Transcript	missense_variant	20738	20534	6845	T/I	aCa/aTa	rs780491549	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	3/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAATGTGTCT	.	5	ESCA
WDR18	0	.	GRCh37	19	991108	991108	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.769C>A	p.Pro257Thr	p.P257T	ENST00000251289	6/10	61	33	27	54	54	0	WDR18,missense_variant,p.Pro219Thr,ENST00000607440,;WDR18,missense_variant,p.Pro257Thr,ENST00000251289,;WDR18,missense_variant,p.Pro257Thr,ENST00000587001,;WDR18,upstream_gene_variant,,ENST00000590354,;WDR18,downstream_gene_variant,,ENST00000591997,;WDR18,missense_variant,p.Pro256Thr,ENST00000591985,;WDR18,3_prime_UTR_variant,,ENST00000585809,;WDR18,3_prime_UTR_variant,,ENST00000590397,;WDR18,non_coding_transcript_exon_variant,,ENST00000591276,;WDR18,downstream_gene_variant,,ENST00000586317,;WDR18,upstream_gene_variant,,ENST00000591155,;	A	ENSG00000065268	ENST00000251289	Transcript	missense_variant	792	769	257	P/T	Cca/Aca	.	.	.	1	WDR18	HGNC	17956	protein_coding	YES	CCDS12051.1	ENSP00000251289	WDR18_HUMAN	.	UPI000013CCF7	.	tolerated(0.63)	benign(0.005)	6/10	.	PROSITE_profiles:PS50294,hmmpanther:PTHR18763,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCACCCAGAG	.	5	ESCA
GPR88	0	.	GRCh37	1	101004692	101004692	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.170C>T	p.Ser57Leu	p.S57L	ENST00000315033	2/2	35	23	12	30	30	0	GPR88,missense_variant,p.Ser57Leu,ENST00000315033,;	T	ENSG00000181656	ENST00000315033	Transcript	missense_variant	609	170	57	S/L	tCg/tTg	.	.	.	1	GPR88	HGNC	4539	protein_coding	YES	CCDS772.1	ENSP00000314223	GPR88_HUMAN	.	UPI00001403B3	.	tolerated(0.51)	benign(0.016)	2/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF196,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTGTCGTCCT	.	5	ESCA
RNPC3	0	.	GRCh37	1	104068788	104068788	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96G>T	p.Arg32Ser	p.R32S	ENST00000533099	2/16	71	52	19	56	56	0	RNPC3,missense_variant,p.Arg32Ser,ENST00000524631,;RNPC3,missense_variant,p.Arg32Ser,ENST00000533099,;RNPC3,missense_variant,p.Arg32Ser,ENST00000531883,;RNPC3,missense_variant,p.Arg32Ser,ENST00000423855,;RNPC3,intron_variant,,ENST00000527062,;RN7SKP285,downstream_gene_variant,,ENST00000410137,;RP11-153F1.1,upstream_gene_variant,,ENST00000447322,;RP11-153F1.1,upstream_gene_variant,,ENST00000444810,;	T	ENSG00000185946	ENST00000533099	Transcript	missense_variant	332	96	32	R/S	agG/agT	.	.	.	1	RNPC3	HGNC	18666	protein_coding	YES	CCDS781.1	ENSP00000432886	RBM40_HUMAN	E9PPV2_HUMAN	UPI000006E703	.	deleterious(0)	probably_damaging(0.988)	2/16	.	PROSITE_profiles:PS50102,hmmpanther:PTHR16105:SF0,hmmpanther:PTHR16105,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAGGCACCT	.	5	ESCA
HENMT1	0	.	GRCh37	1	109202518	109202518	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12C>G	.	.	ENST00000370032	2/8	43	28	14	37	37	0	HENMT1,5_prime_UTR_variant,,ENST00000370031,;HENMT1,5_prime_UTR_variant,,ENST00000370032,;HENMT1,5_prime_UTR_variant,,ENST00000402983,;HENMT1,5_prime_UTR_variant,,ENST00000420055,;HENMT1,intron_variant,,ENST00000493676,;	C	ENSG00000162639	ENST00000370032	Transcript	5_prime_UTR_variant	410	.	.	.	.	.	.	.	-1	HENMT1	HGNC	26400	protein_coding	YES	CCDS787.1	ENSP00000359049	HENMT_HUMAN	.	UPI000013E19C	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGAAGTTTTG	.	5	ESCA
AMPD2	0	.	GRCh37	1	110163817	110163817	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.182G>A	p.Gly61Asp	p.G61D	ENST00000256578	1/18	46	26	20	41	41	0	AMPD2,missense_variant,p.Ala30Thr,ENST00000358729,;AMPD2,missense_variant,p.Gly61Asp,ENST00000256578,;AMPD2,missense_variant,p.Gly61Asp,ENST00000528667,;AMPD2,missense_variant,p.Gly32Asp,ENST00000369840,;AMPD2,intron_variant,,ENST00000474459,;AMPD2,intron_variant,,ENST00000342115,;AMPD2,intron_variant,,ENST00000531203,;AMPD2,intron_variant,,ENST00000531734,;AMPD2,upstream_gene_variant,,ENST00000528454,;AMPD2,upstream_gene_variant,,ENST00000527846,;AMPD2,downstream_gene_variant,,ENST00000469039,;AMPD2,upstream_gene_variant,,ENST00000393688,;AMPD2,intron_variant,,ENST00000526301,;AMPD2,upstream_gene_variant,,ENST00000459643,;AMPD2,missense_variant,p.Gly15Asp,ENST00000528270,;AMPD2,non_coding_transcript_exon_variant,,ENST00000486282,;AMPD2,upstream_gene_variant,,ENST00000534144,;	A	ENSG00000116337	ENST00000256578	Transcript	missense_variant	542	182	61	G/D	gGc/gAc	.	.	.	1	AMPD2	HGNC	469	protein_coding	YES	CCDS805.1	ENSP00000256578	AMPD2_HUMAN	E9PIJ1_HUMAN	UPI0000125956	.	deleterious_low_confidence(0.02)	benign(0.004)	1/18	.	hmmpanther:PTHR11359:SF3,hmmpanther:PTHR11359,PIRSF_domain:PIRSF001251	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGGCTCTG	.	5	ESCA
RBM15	0	.	GRCh37	1	110883931	110883931	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1904G>A	p.Ser635Asn	p.S635N	ENST00000369784	1/3	19	12	7	23	23	0	RBM15,missense_variant,p.Ser635Asn,ENST00000602849,;RBM15,missense_variant,p.Ser635Asn,ENST00000369784,;RBM15,missense_variant,p.Ser635Asn,ENST00000487146,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,;	A	ENSG00000162775	ENST00000369784	Transcript	missense_variant	2804	1904	635	S/N	aGc/aAc	.	.	.	1	RBM15	HGNC	14959	protein_coding	YES	CCDS822.1	ENSP00000358799	RBM15_HUMAN	.	UPI000013E1C5	.	tolerated(0.33)	benign(0.023)	1/3	.	hmmpanther:PTHR23189:SF43,hmmpanther:PTHR23189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAGCAGAG	.	5	ESCA
PTPN22	0	.	GRCh37	1	114414233	114414233	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13G>C	p.Glu5Gln	p.E5Q	ENST00000359785	1/21	41	32	8	38	38	0	PTPN22,missense_variant,p.Glu5Gln,ENST00000528414,;PTPN22,missense_variant,p.Glu5Gln,ENST00000420377,;PTPN22,missense_variant,p.Glu5Gln,ENST00000359785,;PTPN22,missense_variant,p.Glu5Gln,ENST00000460620,;PTPN22,missense_variant,p.Glu5Gln,ENST00000525799,;PTPN22,5_prime_UTR_variant,,ENST00000538253,;AP4B1-AS1,intron_variant,,ENST00000419536,;PTPN22,non_coding_transcript_exon_variant,,ENST00000534519,;PTPN22,missense_variant,p.Glu5Gln,ENST00000529045,;PTPN22,missense_variant,p.Glu5Gln,ENST00000532224,;PTPN22,non_coding_transcript_exon_variant,,ENST00000484147,;	G	ENSG00000134242	ENST00000359785	Transcript	missense_variant	149	13	5	E/Q	Gaa/Caa	.	.	.	-1	PTPN22	HGNC	9652	protein_coding	YES	CCDS863.1	ENSP00000352833	.	F5H2S8_HUMAN	UPI000013CF18	.	deleterious(0.01)	possibly_damaging(0.893)	1/21	.	hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF260,PIRSF_domain:PIRSF000930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTCTCTTT	.	5	ESCA
FAM72B	0	.	GRCh37	1	120854652	120854652	+	3'UTR	SNP	T	T	G	rs587770516	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66T>G	.	.	ENST00000369390	4/4	41	27	14	46	46	0	FAM72B,3_prime_UTR_variant,,ENST00000369390,;FAM72B,3_prime_UTR_variant,,ENST00000355228,;FAM72B,downstream_gene_variant,,ENST00000452190,;FAM72B,non_coding_transcript_exon_variant,,ENST00000471903,;	G	ENSG00000188610	ENST00000369390	Transcript	3_prime_UTR_variant	1345	.	.	.	.	rs587770516	.	.	1	FAM72B	HGNC	24805	protein_coding	YES	CCDS41374.1	ENSP00000358397	FA72B_HUMAN	Q5QP12_HUMAN	UPI000046FF4E	.	.	.	4/4	.	.	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CAACTTTAAAA	by1000G	4	ESCA
VPS13D	0	.	GRCh37	1	12416003	12416003	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9728delC	p.Pro3243LeufsTer8	p.P3243Lfs*8	ENST00000358136	48/70	78	63	15	40	40	0	VPS13D,frameshift_variant,p.Pro3243LeufsTer8,ENST00000358136,;VPS13D,frameshift_variant,p.Pro2065LeufsTer8,ENST00000011700,;VPS13D,frameshift_variant,p.Pro3218LeufsTer8,ENST00000356315,;VPS13D,non_coding_transcript_exon_variant,,ENST00000460333,;	-	ENSG00000048707	ENST00000358136	Transcript	frameshift_variant	9857	9727	3243	P/X	Cct/ct	.	.	.	1	VPS13D	HGNC	23595	protein_coding	YES	CCDS30588.1	ENSP00000350854	.	M0QXS2_HUMAN,J3KP14_HUMAN	UPI0000451CA9	.	.	.	48/70	.	hmmpanther:PTHR16166:SF93,hmmpanther:PTHR16166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATTCCACCTGGA	.	3	ESCA
RP11-277L2.3	0	.	GRCh37	1	149581283	149581283	+	5'Flank	SNP	C	C	T	rs369844172	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000447883	.	21	13	8	14	14	0	RP11-277L2.3,upstream_gene_variant,,ENST00000447883,;RP11-353N4.6,non_coding_transcript_exon_variant,,ENST00000598569,;RP11-353N4.6,intron_variant,,ENST00000419105,;RP11-353N4.6,intron_variant,,ENST00000455295,;RP11-353N4.6,intron_variant,,ENST00000594630,;RP11-353N4.6,intron_variant,,ENST00000443884,;RP11-353N4.6,intron_variant,,ENST00000434047,;RP11-353N4.6,intron_variant,,ENST00000417986,;RP11-353N4.6,downstream_gene_variant,,ENST00000593370,;RP11-353N4.6,downstream_gene_variant,,ENST00000453293,;RP11-353N4.6,intron_variant,,ENST00000444581,;RP11-353N4.6,downstream_gene_variant,,ENST00000452356,;	T	ENSG00000233368	ENST00000447883	Transcript	upstream_gene_variant	.	.	.	.	.	rs369844172	.	3987	-1	RP11-277L2.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	AAAGACATGAG	.	2	ESCA
FLG	0	.	GRCh37	1	152280506	152280506	+	Missense_Mutation	SNP	G	G	A	rs770039879	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6856C>T	p.His2286Tyr	p.H2286Y	ENST00000368799	3/3	239	225	14	183	183	0	FLG,missense_variant,p.His2286Tyr,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	A	ENSG00000143631	ENST00000368799	Transcript	missense_variant	6892	6856	2286	H/Y	Cac/Tac	rs770039879	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	benign(0.152)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCGTGATGGG	.	2	ESCA
UBQLN4	0	.	GRCh37	1	156020165	156020165	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658A>T	p.Met220Leu	p.M220L	ENST00000368309	4/11	35	22	13	47	47	0	UBQLN4,missense_variant,p.Met220Leu,ENST00000368309,;LAMTOR2,upstream_gene_variant,,ENST00000368302,;LAMTOR2,upstream_gene_variant,,ENST00000368305,;LAMTOR2,upstream_gene_variant,,ENST00000368304,;UBQLN4,intron_variant,,ENST00000472638,;LAMTOR2,upstream_gene_variant,,ENST00000489664,;LAMTOR2,upstream_gene_variant,,ENST00000487106,;	A	ENSG00000160803	ENST00000368309	Transcript	missense_variant	751	658	220	M/L	Atg/Ttg	.	.	.	-1	UBQLN4	HGNC	1237	protein_coding	YES	CCDS1127.1	ENSP00000357292	UBQL4_HUMAN	.	UPI000013E0AB	.	tolerated(0.41)	benign(0.008)	4/11	.	hmmpanther:PTHR10677:SF20,hmmpanther:PTHR10677,SMART_domains:SM00727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCATAATCA	.	5	ESCA
FHAD1	0	.	GRCh37	1	15717703	15717703	+	Intron	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1882-3A>G	.	.	ENST00000314740	.	58	37	20	51	51	0	FHAD1,splice_region_variant,,ENST00000314740,;FHAD1,splice_region_variant,,ENST00000529606,;FHAD1,intron_variant,,ENST00000314668,;FHAD1,intron_variant,,ENST00000417793,;FHAD1,intron_variant,,ENST00000358897,;FHAD1,intron_variant,,ENST00000375998,;FHAD1,downstream_gene_variant,,ENST00000375999,;FHAD1,splice_region_variant,,ENST00000471347,;FHAD1,splice_region_variant,,ENST00000472086,;FHAD1,non_coding_transcript_exon_variant,,ENST00000472449,;FHAD1,intron_variant,,ENST00000495195,;FHAD1,intron_variant,,ENST00000477846,;FHAD1,splice_region_variant,,ENST00000481324,;	G	ENSG00000142621	ENST00000314740	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	FHAD1	HGNC	29408	protein_coding	.	.	ENSP00000322979	.	B7WPP2_HUMAN	UPI0001AE77D0	.	.	.	.	14/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTGAAGAGA	.	4	ESCA
NUF2	0	.	GRCh37	1	163325168	163325168	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1304A>G	p.Asp435Gly	p.D435G	ENST00000271452	14/14	80	55	24	52	51	0	NUF2,missense_variant,p.Asp435Gly,ENST00000367900,;NUF2,missense_variant,p.Asp388Gly,ENST00000524800,;NUF2,missense_variant,p.Asp435Gly,ENST00000271452,;	G	ENSG00000143228	ENST00000271452	Transcript	missense_variant	1583	1304	435	D/G	gAc/gGc	.	.	.	1	NUF2	HGNC	14621	protein_coding	YES	CCDS1245.1	ENSP00000271452	NUF2_HUMAN	E9PKH1_HUMAN,B1AQT4_HUMAN,B1AQT3_HUMAN	UPI000006D211	.	deleterious(0.01)	benign(0.064)	14/14	.	hmmpanther:PTHR21650,hmmpanther:PTHR21650:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACGACGGTA	.	5	ESCA
PADI6	0	.	GRCh37	1	17707573	17707573	+	RNA	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.517G>A	.	.	ENST00000434762	5/16	52	35	17	51	51	0	PADI6,non_coding_transcript_exon_variant,,ENST00000434762,;PADI6,non_coding_transcript_exon_variant,,ENST00000358481,;	A	ENSG00000256049	ENST00000434762	Transcript	non_coding_transcript_exon_variant	517	.	.	.	.	.	.	.	1	PADI6	HGNC	20449	processed_transcript	YES	.	.	.	.	.	.	.	.	5/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGGGTGCCA	.	5	ESCA
NAV1	0	.	GRCh37	1	201791219	201791219	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2159G>A	.	.	ENST00000367296	30/30	44	34	10	48	48	0	NAV1,3_prime_UTR_variant,,ENST00000367297,;NAV1,3_prime_UTR_variant,,ENST00000367300,;NAV1,3_prime_UTR_variant,,ENST00000295624,;NAV1,3_prime_UTR_variant,,ENST00000367302,;NAV1,3_prime_UTR_variant,,ENST00000367296,;NAV1,3_prime_UTR_variant,,ENST00000367295,;IPO9-AS1,non_coding_transcript_exon_variant,,ENST00000421159,;IPO9-AS1,intron_variant,,ENST00000413035,;IPO9-AS1,intron_variant,,ENST00000421449,;	A	ENSG00000134369	ENST00000367296	Transcript	3_prime_UTR_variant	8213	.	.	.	.	.	.	.	1	NAV1	HGNC	15989	protein_coding	YES	CCDS1414.2	ENSP00000356265	NAV1_HUMAN	.	UPI00004562D4	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATGACAGG	.	5	ESCA
NFASC	0	.	GRCh37	1	204987868	204987868	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2201G>A	.	.	ENST00000339876	30/30	22	17	5	15	15	0	NFASC,3_prime_UTR_variant,,ENST00000367170,;NFASC,3_prime_UTR_variant,,ENST00000338515,;NFASC,3_prime_UTR_variant,,ENST00000360049,;NFASC,3_prime_UTR_variant,,ENST00000401399,;NFASC,3_prime_UTR_variant,,ENST00000367171,;NFASC,3_prime_UTR_variant,,ENST00000539706,;NFASC,3_prime_UTR_variant,,ENST00000339876,;NFASC,3_prime_UTR_variant,,ENST00000367169,;NFASC,3_prime_UTR_variant,,ENST00000367172,;NFASC,3_prime_UTR_variant,,ENST00000338586,;NFASC,downstream_gene_variant,,ENST00000404076,;NFASC,downstream_gene_variant,,ENST00000447819,;NFASC,downstream_gene_variant,,ENST00000425360,;NFASC,downstream_gene_variant,,ENST00000404907,;NFASC,downstream_gene_variant,,ENST00000413225,;NFASC,downstream_gene_variant,,ENST00000367173,;NFASC,downstream_gene_variant,,ENST00000430393,;NFASC,downstream_gene_variant,,ENST00000513543,;NFASC,non_coding_transcript_exon_variant,,ENST00000495396,;NFASC,non_coding_transcript_exon_variant,,ENST00000503221,;NFASC,downstream_gene_variant,,ENST00000504476,;	A	ENSG00000163531	ENST00000339876	Transcript	3_prime_UTR_variant	6252	.	.	.	.	.	.	.	1	NFASC	HGNC	29866	protein_coding	YES	CCDS53460.1	ENSP00000344786	NFASC_HUMAN	D6RHX4_HUMAN	UPI0000237208	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTGGATCTG	.	2	ESCA
RGS7	0	.	GRCh37	1	241031952	241031952	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544G>T	p.Asp182Tyr	p.D182Y	ENST00000366565	9/18	56	34	21	34	34	0	RGS7,missense_variant,p.Asp13Tyr,ENST00000440928,;RGS7,missense_variant,p.Asp156Tyr,ENST00000331110,;RGS7,missense_variant,p.Asp98Tyr,ENST00000446183,;RGS7,missense_variant,p.Asp129Tyr,ENST00000401882,;RGS7,missense_variant,p.Asp182Tyr,ENST00000366564,;RGS7,missense_variant,p.Asp182Tyr,ENST00000366565,;RGS7,missense_variant,p.Asp182Tyr,ENST00000366562,;RGS7,missense_variant,p.Asp182Tyr,ENST00000407727,;RGS7,missense_variant,p.Asp182Tyr,ENST00000366563,;RGS7,missense_variant,p.Asp129Tyr,ENST00000348120,;	A	ENSG00000182901	ENST00000366565	Transcript	missense_variant	926	544	182	D/Y	Gac/Tac	.	.	.	-1	RGS7	HGNC	10003	protein_coding	YES	CCDS31071.1	ENSP00000355523	RGS7_HUMAN	.	UPI000040E182	.	deleterious(0)	probably_damaging(0.999)	9/18	.	hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTCTCTCT	.	5	ESCA
RUNX3	0	.	GRCh37	1	25255542	25255542	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.324+536G>A	.	.	ENST00000399916	.	96	73	23	71	71	0	RUNX3,5_prime_UTR_variant,,ENST00000540420,;RUNX3,intron_variant,,ENST00000308873,;RUNX3,intron_variant,,ENST00000338888,;RUNX3,intron_variant,,ENST00000399916,;RUNX3,downstream_gene_variant,,ENST00000479341,;RUNX3,upstream_gene_variant,,ENST00000496967,;	T	ENSG00000020633	ENST00000399916	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RUNX3	HGNC	10473	protein_coding	YES	CCDS30633.1	ENSP00000382800	RUNX3_HUMAN	.	UPI000002B2FF	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACGCATAAT	.	5	ESCA
BSDC1	0	.	GRCh37	1	32841985	32841985	+	Missense_Mutation	SNP	C	C	T	rs759945487	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1085G>A	p.Gly362Asp	p.G362D	ENST00000446293	9/11	39	31	7	16	16	0	BSDC1,missense_variant,p.Gly345Asp,ENST00000449308,;BSDC1,missense_variant,p.Gly362Asp,ENST00000341071,;BSDC1,missense_variant,p.Gly284Asp,ENST00000413080,;BSDC1,missense_variant,p.Gly345Asp,ENST00000455895,;BSDC1,missense_variant,p.Gly362Asp,ENST00000446293,;BSDC1,missense_variant,p.Gly250Asp,ENST00000526031,;BSDC1,missense_variant,p.Gly289Asp,ENST00000419121,;BSDC1,downstream_gene_variant,,ENST00000530485,;BSDC1,downstream_gene_variant,,ENST00000527163,;BSDC1,upstream_gene_variant,,ENST00000463967,;BSDC1,missense_variant,p.Gly345Asp,ENST00000444377,;BSDC1,3_prime_UTR_variant,,ENST00000373520,;BSDC1,downstream_gene_variant,,ENST00000474414,;BSDC1,downstream_gene_variant,,ENST00000527513,;	T	ENSG00000160058	ENST00000446293	Transcript	missense_variant	1101	1085	362	G/D	gGc/gAc	rs759945487	.	.	-1	BSDC1	HGNC	25501	protein_coding	YES	CCDS44103.1	ENSP00000397759	BSDC1_HUMAN	.	UPI00017A7DA9	.	tolerated(0.23)	benign(0.415)	9/11	.	hmmpanther:PTHR16019:SF5,hmmpanther:PTHR16019	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGGCCGCCG	byFrequency	4	ESCA
PHC2	0	.	GRCh37	1	33841156	33841156	+	5'UTR	SNP	G	G	A	rs376278733	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16C>T	.	.	ENST00000257118	1/14	23	18	5	13	13	0	PHC2,5_prime_UTR_variant,,ENST00000431992,;PHC2,5_prime_UTR_variant,,ENST00000373416,;PHC2,5_prime_UTR_variant,,ENST00000419414,;PHC2,5_prime_UTR_variant,,ENST00000257118,;PHC2,non_coding_transcript_exon_variant,,ENST00000484692,;PHC2,non_coding_transcript_exon_variant,,ENST00000468406,;	A	ENSG00000134686	ENST00000257118	Transcript	5_prime_UTR_variant	39	.	.	.	.	rs376278733	.	.	-1	PHC2	HGNC	3183	protein_coding	YES	CCDS378.1	ENSP00000257118	PHC2_HUMAN	.	UPI0000074391	.	.	.	1/14	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGCGCAGTC	byCluster|by1000G	4	ESCA
SLC5A9	0	.	GRCh37	1	48694879	48694879	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.414+30C>A	.	.	ENST00000236495	.	28	19	9	34	34	0	SLC5A9,intron_variant,,ENST00000420136,;SLC5A9,intron_variant,,ENST00000533824,;SLC5A9,intron_variant,,ENST00000438567,;SLC5A9,intron_variant,,ENST00000236495,;RP5-1024N4.4,non_coding_transcript_exon_variant,,ENST00000606809,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000493837,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000527929,;SLC5A9,intron_variant,,ENST00000441260,;SLC5A9,intron_variant,,ENST00000425816,;	A	ENSG00000117834	ENST00000236495	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SLC5A9	HGNC	22146	protein_coding	YES	CCDS44136.1	ENSP00000236495	SC5A9_HUMAN	.	UPI0000251D94	.	.	.	.	4/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCCACAGC	.	5	ESCA
CDKN2C	0	.	GRCh37	1	51440096	51440096	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*154A>G	.	.	ENST00000262662	4/4	42	38	4	40	40	0	CDKN2C,3_prime_UTR_variant,,ENST00000371761,;CDKN2C,3_prime_UTR_variant,,ENST00000396148,;CDKN2C,3_prime_UTR_variant,,ENST00000262662,;	G	ENSG00000123080	ENST00000262662	Transcript	3_prime_UTR_variant	2695	.	.	.	.	.	.	.	1	CDKN2C	HGNC	1789	protein_coding	YES	CCDS555.1	ENSP00000262662	CDN2C_HUMAN	Q9P1T2_HUMAN,Q6ICV4_HUMAN	UPI0000047FD9	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGCTTATGAAT	.	3	ESCA
DEPDC1	0	.	GRCh37	1	68947259	68947259	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1799A>G	p.Asp600Gly	p.D600G	ENST00000456315	9/12	95	78	16	77	77	0	DEPDC1,missense_variant,p.Asp600Gly,ENST00000456315,;DEPDC1,missense_variant,p.Asp316Gly,ENST00000370966,;RP4-694A7.2,intron_variant,,ENST00000425820,;DEPDC1,3_prime_UTR_variant,,ENST00000489862,;DEPDC1,non_coding_transcript_exon_variant,,ENST00000488146,;	C	ENSG00000024526	ENST00000456315	Transcript	missense_variant	1914	1799	600	D/G	gAt/gGt	.	.	.	-1	DEPDC1	HGNC	22949	protein_coding	YES	CCDS44159.1	ENSP00000412292	DEP1A_HUMAN	E9PL61_HUMAN	UPI0000204557	.	deleterious(0.04)	benign(0.003)	9/12	.	hmmpanther:PTHR16206,hmmpanther:PTHR16206:SF12,Gene3D:1.10.555.10,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCATCGATG	.	5	ESCA
RBMXL1	0	.	GRCh37	1	89448294	89448294	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*43A>G	.	.	ENST00000399794	3/3	83	64	19	82	82	0	RBMXL1,3_prime_UTR_variant,,ENST00000321792,;RBMXL1,3_prime_UTR_variant,,ENST00000399794,;CCBL2,intron_variant,,ENST00000370485,;CCBL2,intron_variant,,ENST00000370486,;CCBL2,intron_variant,,ENST00000370491,;CCBL2,intron_variant,,ENST00000260508,;CCBL2,intron_variant,,ENST00000446900,;RBMXL1,downstream_gene_variant,,ENST00000413769,;	C	ENSG00000213516	ENST00000399794	Transcript	3_prime_UTR_variant	1932	.	.	.	.	.	.	.	-1	RBMXL1	HGNC	25073	protein_coding	YES	CCDS716.1	ENSP00000446099	RMXL1_HUMAN	Q2VIN3_HUMAN	UPI000006DA18	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTTGTTTC	.	5	ESCA
AGRN	0	.	GRCh37	1	989341	989341	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5860C>G	p.Arg1954Gly	p.R1954G	ENST00000379370	34/36	28	22	5	28	28	0	AGRN,missense_variant,p.Arg1954Gly,ENST00000379370,;AGRN,downstream_gene_variant,,ENST00000419249,;RP11-54O7.14,upstream_gene_variant,,ENST00000418300,;AGRN,non_coding_transcript_exon_variant,,ENST00000461111,;AGRN,downstream_gene_variant,,ENST00000492947,;	G	ENSG00000188157	ENST00000379370	Transcript	missense_variant	5910	5860	1954	R/G	Cgg/Ggg	.	.	.	1	AGRN	HGNC	329	protein_coding	YES	CCDS30551.1	ENSP00000368678	AGRIN_HUMAN	Q5XG79_HUMAN	UPI00001D7C8B	.	deleterious(0.01)	probably_damaging(0.96)	34/36	.	Superfamily_domains:SSF49899,SMART_domains:SM00282,Pfam_domain:PF00054,Gene3D:2.60.120.200,hmmpanther:PTHR10574:SF227,hmmpanther:PTHR10574,PROSITE_profiles:PS50025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTGCGGGTC	.	5	ESCA
SIRPG	0	.	GRCh37	20	1615955	1615955	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1039G>T	p.Val347Phe	p.V347F	ENST00000303415	4/6	96	61	35	58	58	0	SIRPG,missense_variant,p.Val314Phe,ENST00000381580,;SIRPG,missense_variant,p.Val347Phe,ENST00000303415,;SIRPG,intron_variant,,ENST00000381583,;SIRPG,intron_variant,,ENST00000216927,;SIRPG,intron_variant,,ENST00000344103,;RP11-77C3.3,intron_variant,,ENST00000456177,;RP11-77C3.3,intron_variant,,ENST00000437384,;SIRPG,upstream_gene_variant,,ENST00000497407,;SIRPG,upstream_gene_variant,,ENST00000478145,;	A	ENSG00000089012	ENST00000303415	Transcript	missense_variant	1104	1039	347	V/F	Gtc/Ttc	.	.	.	-1	SIRPG	HGNC	15757	protein_coding	YES	CCDS13020.2	ENSP00000305529	SIRPG_HUMAN	.	UPI00001AE5FD	.	tolerated(0.14)	benign(0.009)	4/6	.	hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF6,SMART_domains:SM00409	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGACCTCTA	.	5	ESCA
ZFP64	0	.	GRCh37	20	50701424	50701424	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1610G>C	p.Ser537Thr	p.S537T	ENST00000361387	9/9	32	20	11	21	21	0	ZFP64,missense_variant,p.Ser537Thr,ENST00000361387,;ZFP64,missense_variant,p.Ser318Thr,ENST00000371523,;ZFP64,intron_variant,,ENST00000371518,;ZFP64,downstream_gene_variant,,ENST00000395989,;ZFP64,downstream_gene_variant,,ENST00000456175,;ZFP64,downstream_gene_variant,,ENST00000477786,;ZFP64,downstream_gene_variant,,ENST00000467811,;	G	ENSG00000020256	ENST00000361387	Transcript	missense_variant	1671	1610	537	S/T	aGc/aCc	.	.	.	-1	ZFP64	HGNC	15940	protein_coding	.	CCDS13439.1	ENSP00000355179	ZF64B_HUMAN	.	UPI000013C56C	.	tolerated(0.19)	probably_damaging(0.977)	9/9	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24403:SF27,hmmpanther:PTHR24403,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGCTGCTG	.	5	ESCA
SAMSN1	0	.	GRCh37	21	15882700	15882700	+	Silent	SNP	G	G	A	.	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696C>T	p.%3D	p.F232F	ENST00000285670	6/9	54	31	23	32	32	0	SAMSN1,synonymous_variant,p.%3D,ENST00000400566,;SAMSN1,synonymous_variant,p.%3D,ENST00000285670,;SAMSN1,intron_variant,,ENST00000400564,;	A	ENSG00000155307	ENST00000285670	Transcript	synonymous_variant	871	696	232	F	ttC/ttT	COSM238138	.	.	-1	SAMSN1	HGNC	10528	protein_coding	YES	CCDS58786.1	ENSP00000285670	.	S6FRS6_HUMAN,F8WAA1_HUMAN	UPI000013DDFD	.	.	.	6/9	.	hmmpanther:PTHR12301,hmmpanther:PTHR12301:SF4,Pfam_domain:PF12485,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAGAATGG	.	5	ESCA
KRTAP13-2	0	.	GRCh37	21	31743873	31743873	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*131G>T	.	.	ENST00000399889	1/1	15	9	6	19	19	0	KRTAP13-2,3_prime_UTR_variant,,ENST00000399889,;MIR4327,downstream_gene_variant,,ENST00000581194,;	A	ENSG00000182816	ENST00000399889	Transcript	3_prime_UTR_variant	685	.	.	.	.	.	.	.	-1	KRTAP13-2	HGNC	18923	protein_coding	YES	CCDS13589.1	ENSP00000382777	KR132_HUMAN	.	UPI000003B46A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGTCCAGCC	.	5	ESCA
KRTAP13-4	0	.	GRCh37	21	31802694	31802694	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.101C>A	p.Ala34Asp	p.A34D	ENST00000334068	1/1	67	45	22	43	43	0	KRTAP13-4,missense_variant,p.Ala34Asp,ENST00000334068,;KRTAP13-3,upstream_gene_variant,,ENST00000390690,;	A	ENSG00000186971	ENST00000334068	Transcript	missense_variant	123	101	34	A/D	gCc/gAc	COSM1294022	.	.	1	KRTAP13-4	HGNC	18926	protein_coding	YES	CCDS13592.1	ENSP00000334834	KR134_HUMAN	.	UPI000003B46D	.	tolerated(1)	benign(0.002)	1/1	.	hmmpanther:PTHR19051:SF10,hmmpanther:PTHR19051,Pfam_domain:PF05287	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGCCCTCT	.	5	ESCA
POTEH	0	.	GRCh37	22	16256650	16256650	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29G>T	.	.	ENST00000343518	11/11	1151	1099	52	990	990	0	POTEH,3_prime_UTR_variant,,ENST00000343518,;POTEH,3_prime_UTR_variant,,ENST00000452800,;LA16c-3G11.7,upstream_gene_variant,,ENST00000417657,;LA16c-3G11.7,upstream_gene_variant,,ENST00000339523,;	A	ENSG00000198062	ENST00000343518	Transcript	3_prime_UTR_variant	1719	.	.	.	.	.	.	.	-1	POTEH	HGNC	133	protein_coding	YES	CCDS46658.1	ENSP00000340610	POTEH_HUMAN	.	UPI0000E5A425	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGGTCTTTTT	.	2	ESCA
GNB1L	0	.	GRCh37	22	19808147	19808147	+	Silent	SNP	C	C	T	rs368294430	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228G>A	p.%3D	p.T76T	ENST00000329517	4/8	94	68	26	84	84	0	GNB1L,synonymous_variant,p.%3D,ENST00000403325,;GNB1L,synonymous_variant,p.%3D,ENST00000405009,;GNB1L,synonymous_variant,p.%3D,ENST00000329517,;GNB1L,intron_variant,,ENST00000453108,;GNB1L,intron_variant,,ENST00000481086,;GNB1L,intron_variant,,ENST00000460402,;	T	ENSG00000185838	ENST00000329517	Transcript	synonymous_variant	465	228	76	T	acG/acA	rs368294430	.	.	-1	GNB1L	HGNC	4397	protein_coding	YES	CCDS13768.1	ENSP00000331313	GNB1L_HUMAN	.	UPI00000474FA	.	.	.	4/8	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR19854,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAGCGTCTG	byFrequency|byCluster	5	ESCA
SEC14L2	0	.	GRCh37	22	30811775	30811775	+	Missense_Mutation	SNP	A	A	G	rs748368938	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.692A>G	p.His231Arg	p.H231R	ENST00000312932	9/12	29	23	6	19	19	0	SEC14L2,missense_variant,p.His231Arg,ENST00000405717,;SEC14L2,missense_variant,p.His231Arg,ENST00000312932,;SEC14L2,missense_variant,p.His148Arg,ENST00000402592,;RP4-539M6.19,missense_variant,p.His65Arg,ENST00000439838,;SEC14L2,missense_variant,p.His157Arg,ENST00000403484,;SEC14L2,missense_variant,p.His177Arg,ENST00000428195,;RP4-539M6.19,intron_variant,,ENST00000439023,;RNF215,intron_variant,,ENST00000431544,;KIAA1658,downstream_gene_variant,,ENST00000598426,;RP4-539M6.20,upstream_gene_variant,,ENST00000608677,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000467218,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000483116,;RP4-539M6.19,intron_variant,,ENST00000454552,;SEC14L2,intron_variant,,ENST00000478762,;SEC14L2,intron_variant,,ENST00000464335,;	G	ENSG00000100003	ENST00000312932	Transcript	missense_variant	952	692	231	H/R	cAt/cGt	rs748368938	.	.	1	SEC14L2	HGNC	10699	protein_coding	YES	CCDS13876.1	ENSP00000316203	S14L2_HUMAN	C9JZI9_HUMAN,B7Z3Z8_HUMAN	UPI0000135433	.	tolerated(0.05)	benign(0.059)	9/12	.	PROSITE_profiles:PS50191,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF64,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAACATATCA	byCluster	5	ESCA
TRIOBP	0	.	GRCh37	22	38130534	38130534	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4191G>A	p.%3D	p.R1397R	ENST00000406386	9/24	95	73	21	63	63	0	TRIOBP,synonymous_variant,p.%3D,ENST00000406386,;NOL12,3_prime_UTR_variant,,ENST00000455236,;TRIOBP,3_prime_UTR_variant,,ENST00000344404,;	A	ENSG00000100106	ENST00000406386	Transcript	synonymous_variant	4446	4191	1397	R	agG/agA	.	.	.	1	TRIOBP	HGNC	17009	protein_coding	YES	CCDS43015.1	ENSP00000384312	TARA_HUMAN	F6WYE2_HUMAN,F6WMF4_HUMAN	UPI000067CB88	.	.	.	9/24	.	hmmpanther:PTHR17271:SF10,hmmpanther:PTHR17271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGGACATC	.	5	ESCA
EN1	0	.	GRCh37	2	119599892	119599892	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*622G>A	.	.	ENST00000295206	2/2	127	80	47	96	96	0	EN1,3_prime_UTR_variant,,ENST00000295206,;EN1,downstream_gene_variant,,ENST00000546667,;	T	ENSG00000163064	ENST00000295206	Transcript	3_prime_UTR_variant	2312	.	.	.	.	.	.	.	-1	EN1	HGNC	3342	protein_coding	YES	CCDS2123.1	ENSP00000295206	HME1_HUMAN	.	UPI000013E21D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGACAGACC	.	5	ESCA
FIGN	0	.	GRCh37	2	164468092	164468092	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250G>A	p.Asp84Asn	p.D84N	ENST00000333129	3/3	33	29	4	41	41	0	FIGN,missense_variant,p.Asp84Asn,ENST00000333129,;FIGN,intron_variant,,ENST00000409634,;FIGN,non_coding_transcript_exon_variant,,ENST00000482917,;	T	ENSG00000182263	ENST00000333129	Transcript	missense_variant	565	250	84	D/N	Gac/Aac	.	.	.	-1	FIGN	HGNC	13285	protein_coding	YES	CCDS2221.2	ENSP00000333836	FIGN_HUMAN	.	UPI000022BD13	.	tolerated(0.06)	benign(0.007)	3/3	.	hmmpanther:PTHR23074:SF14,hmmpanther:PTHR23074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGGTCCACAG	.	4	ESCA
ZNF804A	0	.	GRCh37	2	185802383	185802383	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2260G>T	p.Val754Phe	p.V754F	ENST00000302277	4/4	35	27	8	25	24	1	ZNF804A,missense_variant,p.Val754Phe,ENST00000302277,;	T	ENSG00000170396	ENST00000302277	Transcript	missense_variant	2854	2260	754	V/F	Gtt/Ttt	.	.	.	1	ZNF804A	HGNC	21711	protein_coding	YES	CCDS2291.1	ENSP00000303252	Z804A_HUMAN	.	UPI00001B4B18	.	deleterious(0)	possibly_damaging(0.656)	4/4	.	hmmpanther:PTHR17614:SF13,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	AGGCTGTTAAA	.	2	ESCA
FSIP2	0	.	GRCh37	2	186656763	186656763	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5167T>C	p.Ser1723Pro	p.S1723P	ENST00000343098	16/23	28	19	9	9	9	0	FSIP2,missense_variant,p.Ser1723Pro,ENST00000343098,;FSIP2,missense_variant,p.Ser1634Pro,ENST00000424728,;AC008174.3,intron_variant,,ENST00000436557,;AC008174.3,intron_variant,,ENST00000429929,;FSIP2,upstream_gene_variant,,ENST00000415915,;	C	ENSG00000188738	ENST00000343098	Transcript	missense_variant	5167	5167	1723	S/P	Tca/Cca	.	.	.	1	FSIP2	HGNC	21675	protein_coding	YES	CCDS54426.1	ENSP00000344403	.	J3QTJ6_HUMAN	UPI0001D420A1	.	.	benign(0.006)	16/23	.	hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGCATCATTT	.	3	ESCA
PLCL1	0	.	GRCh37	2	198953678	198953678	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2812G>T	p.Asp938Tyr	p.D938Y	ENST00000428675	3/6	54	34	19	35	35	0	PLCL1,missense_variant,p.Asp864Tyr,ENST00000487695,;PLCL1,missense_variant,p.Asp938Tyr,ENST00000428675,;PLCL1,missense_variant,p.Asp840Tyr,ENST00000437704,;PLCL1,3_prime_UTR_variant,,ENST00000435320,;	T	ENSG00000115896	ENST00000428675	Transcript	missense_variant	3210	2812	938	D/Y	Gac/Tac	.	.	.	1	PLCL1	HGNC	9063	protein_coding	YES	CCDS2326.2	ENSP00000402861	PLCL1_HUMAN	.	UPI000165BCF5	.	deleterious(0)	possibly_damaging(0.786)	3/6	.	hmmpanther:PTHR10336:SF76,hmmpanther:PTHR10336	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGTGACAAT	.	5	ESCA
ATG4B	0	.	GRCh37	2	242606219	242606219	+	Missense_Mutation	SNP	C	C	G	rs369000453	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.698C>G	p.Thr233Arg	p.T233R	ENST00000404914	8/13	13	10	3	11	11	0	ATG4B,missense_variant,p.Thr219Arg,ENST00000474739,;ATG4B,missense_variant,p.Thr233Arg,ENST00000404914,;ATG4B,missense_variant,p.Thr182Arg,ENST00000400771,;ATG4B,missense_variant,p.Thr70Arg,ENST00000428861,;ATG4B,missense_variant,p.Thr159Arg,ENST00000396411,;ATG4B,missense_variant,p.Thr233Arg,ENST00000405546,;ATG4B,missense_variant,p.Thr159Arg,ENST00000402096,;ATG4B,downstream_gene_variant,,ENST00000429899,;ATG4B,3_prime_UTR_variant,,ENST00000344376,;ATG4B,non_coding_transcript_exon_variant,,ENST00000494465,;ATG4B,non_coding_transcript_exon_variant,,ENST00000482507,;ATG4B,upstream_gene_variant,,ENST00000494132,;ATG4B,upstream_gene_variant,,ENST00000460211,;ATG4B,upstream_gene_variant,,ENST00000475693,;ATG4B,upstream_gene_variant,,ENST00000479941,;	G	ENSG00000168397	ENST00000404914	Transcript	missense_variant	801	698	233	T/R	aCg/aGg	rs369000453	.	.	1	ATG4B	HGNC	20790	protein_coding	YES	CCDS46564.1	ENSP00000384259	ATG4B_HUMAN	F8WD71_HUMAN,C9JVD5_HUMAN,C9J3C0_HUMAN,C9J1C1_HUMAN	UPI00001AF16F	.	deleterious(0)	benign(0.258)	8/13	.	hmmpanther:PTHR22624,hmmpanther:PTHR22624:SF39,Pfam_domain:PF03416,Superfamily_domains:SSF54001	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCACGGACA	byCluster|by1000G	2	ESCA
ING5	0	.	GRCh37	2	242662678	242662678	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672A>G	p.%3D	p.K224K	ENST00000313552	7/8	75	41	33	68	68	0	ING5,synonymous_variant,p.%3D,ENST00000406941,;ING5,synonymous_variant,p.%3D,ENST00000313552,;AC114730.11,downstream_gene_variant,,ENST00000435195,;ING5,non_coding_transcript_exon_variant,,ENST00000493578,;ING5,upstream_gene_variant,,ENST00000486061,;ING5,downstream_gene_variant,,ENST00000482774,;ING5,upstream_gene_variant,,ENST00000474238,;ING5,downstream_gene_variant,,ENST00000445620,;ING5,downstream_gene_variant,,ENST00000489509,;	G	ENSG00000168395	ENST00000313552	Transcript	synonymous_variant	698	672	224	K	aaA/aaG	.	.	.	1	ING5	HGNC	19421	protein_coding	YES	CCDS33425.1	ENSP00000322142	ING5_HUMAN	.	UPI00000702CD	.	.	.	7/8	.	Superfamily_domains:SSF57903,SMART_domains:SM00249,Pfam_domain:PF00628,Gene3D:3.30.40.10,PROSITE_patterns:PS01359,hmmpanther:PTHR10333:SF41,hmmpanther:PTHR10333,PROSITE_profiles:PS50016	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAAAGGAAA	.	5	ESCA
CAPN13	0	.	GRCh37	2	30957354	30957354	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1759C>G	p.Leu587Val	p.L587V	ENST00000295055	19/23	58	41	16	38	38	0	CAPN13,missense_variant,p.Leu587Val,ENST00000534090,;CAPN13,missense_variant,p.Leu587Val,ENST00000295055,;CAPN13,upstream_gene_variant,,ENST00000490786,;CAPN13,3_prime_UTR_variant,,ENST00000450650,;	C	ENSG00000162949	ENST00000295055	Transcript	missense_variant	1936	1759	587	L/V	Ctc/Gtc	.	.	.	-1	CAPN13	HGNC	16663	protein_coding	YES	CCDS46252.1	ENSP00000295055	CAN13_HUMAN	.	UPI00000463E5	.	tolerated(0.05)	benign(0.372)	19/23	.	hmmpanther:PTHR10183:SF37,hmmpanther:PTHR10183,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAGGAGGACTC	.	4	ESCA
CCDC85A	0	.	GRCh37	2	56612129	56612129	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*639C>T	.	.	ENST00000407595	6/6	87	68	19	55	55	0	CCDC85A,3_prime_UTR_variant,,ENST00000407595,;RP11-482H16.1,non_coding_transcript_exon_variant,,ENST00000607540,;	T	ENSG00000055813	ENST00000407595	Transcript	3_prime_UTR_variant	2803	.	.	.	.	.	.	.	1	CCDC85A	HGNC	29400	protein_coding	YES	CCDS46290.1	ENSP00000384040	CC85A_HUMAN	.	UPI00001C1DC1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGACGTTGT	.	5	ESCA
SOX11	0	.	GRCh37	2	5834576	5834576	+	3'UTR	SNP	G	G	T	rs34946300	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*397G>T	.	.	ENST00000322002	1/1	61	48	12	43	43	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,upstream_gene_variant,,ENST00000455579,;AC108025.2,upstream_gene_variant,,ENST00000453678,;AC107057.2,upstream_gene_variant,,ENST00000458264,;AC108025.2,upstream_gene_variant,,ENST00000420221,;	T	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	1778	.	.	.	.	rs34946300	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGAGGGG	.	5	ESCA
AFTPH	0	.	GRCh37	2	64796257	64796265	+	In_Frame_Del	DEL	GATATCCAT	GATATCCAT	-	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	GATATCCAT	GATATCCAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2122_2130delATCCATGAT	p.Ile708_Asp710del	p.I708_D710del	ENST00000238855	4/10	72	58	14	53	53	0	AFTPH,inframe_deletion,p.Ile708_Asp710del,ENST00000422803,;AFTPH,inframe_deletion,p.Ile339_Asp341del,ENST00000409183,;AFTPH,inframe_deletion,p.Ile708_Asp710del,ENST00000409933,;AFTPH,inframe_deletion,p.Ile708_Asp710del,ENST00000238855,;AFTPH,inframe_deletion,p.Ile708_Asp710del,ENST00000238856,;AFTPH,intron_variant,,ENST00000487769,;AFTPH,non_coding_transcript_exon_variant,,ENST00000498706,;	-	ENSG00000119844	ENST00000238855	Transcript	inframe_deletion	2433-2441	2119-2127	707-709	DIH/-	GATATCCAT/-	.	.	.	1	AFTPH	HGNC	25951	protein_coding	YES	CCDS46303.1	ENSP00000238855	AFTIN_HUMAN	.	UPI00003E1F8E	.	.	.	4/10	.	hmmpanther:PTHR16156:SF9,hmmpanther:PTHR16156,Pfam_domain:PF15045	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTACAGGATATCCATGATGC	.	3	ESCA
EIF5B	0	.	GRCh37	2	99977012	99977012	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246G>A	p.%3D	p.K82K	ENST00000289371	3/24	68	61	6	55	55	0	EIF5B,synonymous_variant,p.%3D,ENST00000289371,;	A	ENSG00000158417	ENST00000289371	Transcript	synonymous_variant	448	246	82	K	aaG/aaA	.	.	.	1	EIF5B	HGNC	30793	protein_coding	YES	CCDS42721.1	ENSP00000289371	IF2P_HUMAN	D3DVI5_HUMAN	UPI0000207EC7	.	.	.	3/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGAAGGTGAA	.	3	ESCA
TBC1D23	0	.	GRCh37	3	100029351	100029351	+	Silent	SNP	C	C	T	rs748159443	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1518C>T	p.%3D	p.I506I	ENST00000394144	14/19	74	59	15	42	42	0	TBC1D23,synonymous_variant,p.%3D,ENST00000344949,;TBC1D23,synonymous_variant,p.%3D,ENST00000394144,;TBC1D23,synonymous_variant,p.%3D,ENST00000475134,;TBC1D23,non_coding_transcript_exon_variant,,ENST00000486274,;TBC1D23,downstream_gene_variant,,ENST00000496167,;	T	ENSG00000036054	ENST00000394144	Transcript	synonymous_variant	1525	1518	506	I	atC/atT	rs748159443	.	.	1	TBC1D23	HGNC	25622	protein_coding	YES	CCDS56265.1	ENSP00000377700	TBC23_HUMAN	B3KS68_HUMAN	UPI000013D5E5	.	.	.	14/19	.	hmmpanther:PTHR13297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTATCAGTTT	.	5	ESCA
IMPG2	0	.	GRCh37	3	100963611	100963611	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1564T>C	p.Ser522Pro	p.S522P	ENST00000193391	13/19	40	18	21	26	26	0	IMPG2,missense_variant,p.Ser522Pro,ENST00000193391,;	G	ENSG00000081148	ENST00000193391	Transcript	missense_variant	1752	1564	522	S/P	Tca/Cca	.	.	.	-1	IMPG2	HGNC	18362	protein_coding	YES	CCDS2940.1	ENSP00000193391	IMPG2_HUMAN	F1T0J3_HUMAN	UPI000013C605	.	tolerated(0.24)	benign(0.004)	13/19	.	hmmpanther:PTHR12199:SF4,hmmpanther:PTHR12199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGACTCTT	.	5	ESCA
XRN1	0	.	GRCh37	3	142137304	142137304	+	Intron	SNP	A	A	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1346+42T>A	.	.	ENST00000264951	.	39	35	4	24	24	0	XRN1,3_prime_UTR_variant,,ENST00000544157,;XRN1,3_prime_UTR_variant,,ENST00000463916,;XRN1,intron_variant,,ENST00000392981,;XRN1,intron_variant,,ENST00000264951,;XRN1,downstream_gene_variant,,ENST00000477237,;RNU1-100P,downstream_gene_variant,,ENST00000365255,;XRN1,3_prime_UTR_variant,,ENST00000486211,;XRN1,intron_variant,,ENST00000472697,;XRN1,upstream_gene_variant,,ENST00000465507,;	T	ENSG00000114127	ENST00000264951	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	XRN1	HGNC	30654	protein_coding	YES	CCDS3123.1	ENSP00000264951	XRN1_HUMAN	C9JCZ8_HUMAN	UPI0000074113	.	.	.	.	12/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AATCTAATTTT	.	3	ESCA
P2RY14	0	.	GRCh37	3	150931563	150931563	+	Missense_Mutation	SNP	C	C	T	rs368040389	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542G>A	p.Arg181Gln	p.R181Q	ENST00000309170	3/3	48	42	6	24	24	0	P2RY14,missense_variant,p.Arg181Gln,ENST00000309170,;P2RY14,missense_variant,p.Arg181Gln,ENST00000424796,;MED12L,intron_variant,,ENST00000474524,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000273432,;P2RY14,downstream_gene_variant,,ENST00000494668,;	T	ENSG00000174944	ENST00000309170	Transcript	missense_variant	855	542	181	R/Q	cGg/cAg	rs368040389,COSM3588720	.	.	-1	P2RY14	HGNC	16442	protein_coding	YES	CCDS3156.1	ENSP00000308361	P2Y14_HUMAN	C9JAB5_HUMAN,A5JUU3_HUMAN	UPI0000050418	.	tolerated(0.07)	benign(0.007)	3/3	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24233:SF3,hmmpanther:PTHR24233,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTTCCGTCCC	byFrequency|byCluster	4	ESCA
MECOM	0	.	GRCh37	3	168810878	168810878	+	Frame_Shift_Del	DEL	G	G	-	rs540158912	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2663delC	p.Ser888CysfsTer46	p.S888Cfs*46	ENST00000264674	14/17	143	107	36	60	60	0	MECOM,frameshift_variant,p.Ser824CysfsTer46,ENST00000472280,;MECOM,frameshift_variant,p.Ser814CysfsTer46,ENST00000460814,;MECOM,frameshift_variant,p.Ser814CysfsTer46,ENST00000464456,;MECOM,frameshift_variant,p.Ser1002CysfsTer46,ENST00000494292,;MECOM,frameshift_variant,p.Ser823CysfsTer46,ENST00000468789,;MECOM,frameshift_variant,p.Ser824CysfsTer46,ENST00000433243,;MECOM,frameshift_variant,p.Ser823CysfsTer46,ENST00000392736,;MECOM,frameshift_variant,p.Ser888CysfsTer46,ENST00000264674,;	-	ENSG00000085276	ENST00000264674	Transcript	frameshift_variant	2802	2663	888	S/X	tCg/tg	rs540158912,COSM3203546,COSM3203545	.	.	-1	MECOM	HGNC	3498	protein_coding	YES	CCDS54670.1	ENSP00000264674	EVI1_HUMAN	Q9UBK3_HUMAN,Q8IU84_HUMAN,E9PGE9_HUMAN,E7EU48_HUMAN,E7ERX0_HUMAN,E7EPY2_HUMAN,D3DNP4_HUMAN	UPI00015D43FA	.	.	.	14/17	.	hmmpanther:PTHR24393	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCGACGATGTT	by1000G	3	ESCA
SKIL	0	.	GRCh37	3	170110118	170110118	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1968G>T	p.Gln656His	p.Q656H	ENST00000458537	6/6	44	34	10	27	27	0	SKIL,missense_variant,p.Gln656His,ENST00000458537,;SKIL,missense_variant,p.Gln656His,ENST00000259119,;SKIL,missense_variant,p.Gln610His,ENST00000413427,;SKIL,missense_variant,p.Gln636His,ENST00000426052,;SKIL,downstream_gene_variant,,ENST00000470571,;	T	ENSG00000136603	ENST00000458537	Transcript	missense_variant	2677	1968	656	Q/H	caG/caT	.	.	.	1	SKIL	HGNC	10897	protein_coding	YES	CCDS33890.1	ENSP00000415243	SKIL_HUMAN	C9J8R9_HUMAN	UPI000020A79D	.	tolerated(0.17)	benign(0.192)	6/6	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10005,hmmpanther:PTHR10005:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACAGGAACG	.	5	ESCA
CCDC39	0	.	GRCh37	3	180372723	180372723	+	Missense_Mutation	SNP	G	G	T	rs747179863	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757C>A	p.Gln253Lys	p.Q253K	ENST00000442201	7/20	104	77	27	65	65	0	CCDC39,missense_variant,p.Gln337Lys,ENST00000273654,;CCDC39,missense_variant,p.Gln253Lys,ENST00000442201,;CCDC39,missense_variant,p.Gln253Lys,ENST00000476379,;	T	ENSG00000145075	ENST00000442201	Transcript	missense_variant	877	757	253	Q/K	Cag/Aag	rs747179863	.	.	-1	CCDC39	HGNC	25244	protein_coding	YES	CCDS46964.1	ENSP00000405708	CCD39_HUMAN	.	UPI00015D7298	.	deleterious(0.03)	possibly_damaging(0.661)	7/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18962:SF0,hmmpanther:PTHR18962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTGCTTTA	.	5	ESCA
ABHD5	0	.	GRCh37	3	43753309	43753309	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615G>T	p.Leu205Phe	p.L205F	ENST00000458276	4/7	59	34	24	80	80	0	ABHD5,missense_variant,p.Leu37Phe,ENST00000413300,;ABHD5,missense_variant,p.Leu205Phe,ENST00000458276,;ABHD5,3_prime_UTR_variant,,ENST00000013894,;	T	ENSG00000011198	ENST00000458276	Transcript	missense_variant	738	615	205	L/F	ttG/ttT	.	.	.	1	ABHD5	HGNC	21396	protein_coding	YES	CCDS2711.1	ENSP00000390849	ABHD5_HUMAN	F8W7B5_HUMAN,F6K7K5_HUMAN,F6K7K4_HUMAN,C9JBM3_HUMAN,C9J1D1_HUMAN	UPI00000411E4	.	tolerated(0.17)	benign(0.049)	4/7	.	hmmpanther:PTHR10992,hmmpanther:PTHR10992:SF737,Pfam_domain:PF12697,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTGACTCC	.	5	ESCA
CRYBG3	0	.	GRCh37	3	97593312	97593312	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3274C>G	p.Leu1092Val	p.L1092V	ENST00000419587	4/4	45	22	22	25	25	0	CRYBG3,missense_variant,p.Leu1092Val,ENST00000419587,;CRYBG3,upstream_gene_variant,,ENST00000182096,;	G	ENSG00000233280	ENST00000419587	Transcript	missense_variant	3441	3274	1092	L/V	Ctc/Gtc	.	.	.	1	CRYBG3	Uniprot_gn	34427	protein_coding	YES	.	ENSP00000391551	.	B4DLE8_HUMAN	UPI00017A74DC	.	.	.	4/4	.	hmmpanther:PTHR11818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATCTCACA	.	5	ESCA
TET2	0	.	GRCh37	4	106159920	106159921	+	Intron	INS	-	-	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3409+1413dupT	.	.	ENST00000540549	.	20	8	12	12	12	0	TET2,3_prime_UTR_variant,,ENST00000305737,;TET2,3_prime_UTR_variant,,ENST00000394764,;TET2,intron_variant,,ENST00000413648,;TET2,intron_variant,,ENST00000540549,;TET2,intron_variant,,ENST00000380013,;TET2,intron_variant,,ENST00000545826,;TET2,intron_variant,,ENST00000513237,;TET2,downstream_gene_variant,,ENST00000514870,;TET2,intron_variant,,ENST00000265149,;	T	ENSG00000168769	ENST00000540549	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TET2	HGNC	25941	protein_coding	YES	CCDS47120.1	ENSP00000442788	TET2_HUMAN	E7EPB1_HUMAN,D6RE87_HUMAN	UPI00001D75E4	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TTGATATATTG	.	2	ESCA
ETNPPL	0	.	GRCh37	4	109674127	109674127	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542A>G	p.Asp181Gly	p.D181G	ENST00000296486	6/13	68	42	26	56	56	0	ETNPPL,missense_variant,p.Asp141Gly,ENST00000510706,;ETNPPL,missense_variant,p.Asp175Gly,ENST00000411864,;ETNPPL,missense_variant,p.Asp181Gly,ENST00000296486,;ETNPPL,missense_variant,p.Asp123Gly,ENST00000512646,;ETNPPL,downstream_gene_variant,,ENST00000512320,;ETNPPL,downstream_gene_variant,,ENST00000510723,;ETNPPL,3_prime_UTR_variant,,ENST00000505233,;ETNPPL,non_coding_transcript_exon_variant,,ENST00000511923,;ETNPPL,downstream_gene_variant,,ENST00000509402,;ETNPPL,upstream_gene_variant,,ENST00000503912,;	C	ENSG00000164089	ENST00000296486	Transcript	missense_variant	697	542	181	D/G	gAc/gGc	.	.	.	-1	ETNPPL	HGNC	14404	protein_coding	YES	CCDS3682.1	ENSP00000296486	AT2L1_HUMAN	E7ENR6_HUMAN,D6RGG2_HUMAN	UPI000004B638	.	tolerated(0.11)	benign(0.247)	6/13	.	hmmpanther:PTHR11986,hmmpanther:PTHR11986:SF63,Pfam_domain:PF00202,Gene3D:3.40.640.10,PIRSF_domain:PIRSF000521,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGGTCTTCT	.	5	ESCA
RP11-384K6.6	0	.	GRCh37	4	119552902	119552902	+	RNA	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2413C>G	.	.	ENST00000567913	10/10	30	24	5	21	21	0	RP11-384K6.6,non_coding_transcript_exon_variant,,ENST00000567913,;RP11-384K6.2,upstream_gene_variant,,ENST00000426314,;CICP16,downstream_gene_variant,,ENST00000502609,;CICP16,downstream_gene_variant,,ENST00000401754,;	G	ENSG00000260404	ENST00000567913	Transcript	non_coding_transcript_exon_variant	2413	.	.	.	.	.	.	.	1	RP11-384K6.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCCTCCAGAC	.	2	ESCA
FAM160A1	0	.	GRCh37	4	152571182	152571182	+	Silent	SNP	T	T	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1989T>G	p.%3D	p.A663A	ENST00000435205	11/14	52	35	17	48	48	0	FAM160A1,synonymous_variant,p.%3D,ENST00000435205,;FAM160A1,synonymous_variant,p.%3D,ENST00000505231,;	G	ENSG00000164142	ENST00000435205	Transcript	synonymous_variant	2564	1989	663	A	gcT/gcG	.	.	.	1	FAM160A1	HGNC	34237	protein_coding	YES	CCDS47146.1	ENSP00000413196	F16A1_HUMAN	D6RF38_HUMAN,D6RBF5_HUMAN,D6RAG2_HUMAN	UPI00015DE720	.	.	.	11/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21705:SF6,hmmpanther:PTHR21705	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGCTGCTAG	.	5	ESCA
TAPT1	0	.	GRCh37	4	16163076	16163076	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1855G>C	.	.	ENST00000405303	14/14	55	47	8	31	31	0	TAPT1,3_prime_UTR_variant,,ENST00000405303,;TAPT1,downstream_gene_variant,,ENST00000304584,;TAPT1,downstream_gene_variant,,ENST00000399920,;TAPT1,downstream_gene_variant,,ENST00000505603,;TAPT1,downstream_gene_variant,,ENST00000503858,;TAPT1,downstream_gene_variant,,ENST00000508886,;TAPT1,downstream_gene_variant,,ENST00000513782,;	G	ENSG00000169762	ENST00000405303	Transcript	3_prime_UTR_variant	3643	.	.	.	.	.	.	.	-1	TAPT1	HGNC	26887	protein_coding	YES	CCDS47030.1	ENSP00000385347	TAPT1_HUMAN	B4DJJ3_HUMAN	UPI0000253B29	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAACAGAAT	.	5	ESCA
QDPR	0	.	GRCh37	4	17506070	17506070	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227G>T	p.Gly76Val	p.G76V	ENST00000281243	3/7	48	40	8	55	55	0	QDPR,missense_variant,p.Gly76Val,ENST00000508623,;QDPR,missense_variant,p.Gly76Val,ENST00000513615,;QDPR,missense_variant,p.Gly76Val,ENST00000281243,;QDPR,missense_variant,p.Gly45Val,ENST00000428702,;QDPR,missense_variant,p.Gly52Val,ENST00000505710,;QDPR,missense_variant,p.Gly76Val,ENST00000507439,;QDPR,3_prime_UTR_variant,,ENST00000514300,;	A	ENSG00000151552	ENST00000281243	Transcript	missense_variant	407	227	76	G/V	gGt/gTt	.	.	.	-1	QDPR	HGNC	9752	protein_coding	YES	CCDS3421.1	ENSP00000281243	DHPR_HUMAN	.	UPI0000111B0A	.	deleterious(0)	probably_damaging(0.998)	3/7	.	hmmpanther:PTHR15104,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCACCCAAG	.	5	ESCA
LGI2	0	.	GRCh37	4	25013980	25013980	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.797T>A	p.Phe266Tyr	p.F266Y	ENST00000382114	7/8	40	26	14	55	55	0	LGI2,missense_variant,p.Phe266Tyr,ENST00000382114,;LGI2,intron_variant,,ENST00000512108,;	T	ENSG00000153012	ENST00000382114	Transcript	missense_variant	983	797	266	F/Y	tTc/tAc	.	.	.	-1	LGI2	HGNC	18710	protein_coding	YES	CCDS3431.1	ENSP00000371548	LGI2_HUMAN	.	UPI0000047256	.	deleterious(0)	possibly_damaging(0.747)	7/8	.	Pfam_domain:PF03736,hmmpanther:PTHR24367:SF21,hmmpanther:PTHR24367,PROSITE_profiles:PS50912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R267W|c.799C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGAAATTC	.	5	ESCA
ZNF595	0	.	GRCh37	4	53273	53273	+	5'UTR	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-110C>T	.	.	ENST00000526473	1/4	244	225	19	204	204	0	ZNF595,5_prime_UTR_variant,,ENST00000526473,;ZNF595,5_prime_UTR_variant,,ENST00000509152,;ZNF595,non_coding_transcript_exon_variant,,ENST00000339368,;ZNF595,non_coding_transcript_exon_variant,,ENST00000512065,;ZNF595,non_coding_transcript_exon_variant,,ENST00000507368,;Z95704.4,upstream_gene_variant,,ENST00000596885,;ZNF595,non_coding_transcript_exon_variant,,ENST00000502981,;Z95704.4,upstream_gene_variant,,ENST00000503774,;	T	ENSG00000197701	ENST00000526473	Transcript	5_prime_UTR_variant	64	.	.	.	.	.	.	.	1	ZNF595	HGNC	27196	protein_coding	YES	.	ENSP00000437878	.	F5H663_HUMAN	UPI00020651F4	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGGCTCCGG	.	2	ESCA
PCDHA4	0	.	GRCh37	5	140188667	140188667	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1895G>A	p.Ser632Asn	p.S632N	ENST00000530339	1/4	103	65	37	82	82	0	PCDHA4,missense_variant,p.Ser632Asn,ENST00000356878,;PCDHA4,missense_variant,p.Ser632Asn,ENST00000530339,;PCDHA4,missense_variant,p.Ser632Asn,ENST00000512229,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA2,downstream_gene_variant,,ENST00000520672,;	A	ENSG00000204967	ENST00000530339	Transcript	missense_variant	1895	1895	632	S/N	aGc/aAc	.	.	.	1	PCDHA4	HGNC	8670	protein_coding	YES	CCDS54916.1	ENSP00000435300	PCDA4_HUMAN	.	UPI00001273CC	.	deleterious_low_confidence(0)	possibly_damaging(0.827)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF82,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R635H|c.1904G>A|3,BUFFER|p.R635H|c.1904G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCAGCACAA	.	5	ESCA
CYFIP2	0	.	GRCh37	5	156787307	156787307	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2757C>G	p.%3D	p.L919L	ENST00000521420	24/30	56	25	31	66	66	0	CYFIP2,synonymous_variant,p.%3D,ENST00000377576,;CYFIP2,synonymous_variant,p.%3D,ENST00000541131,;CYFIP2,synonymous_variant,p.%3D,ENST00000318218,;CYFIP2,synonymous_variant,p.%3D,ENST00000435847,;CYFIP2,synonymous_variant,p.%3D,ENST00000347377,;CYFIP2,synonymous_variant,p.%3D,ENST00000522463,;CYFIP2,synonymous_variant,p.%3D,ENST00000521420,;CYFIP2,3_prime_UTR_variant,,ENST00000442283,;CTB-109A12.1,downstream_gene_variant,,ENST00000519499,;CTB-109A12.1,downstream_gene_variant,,ENST00000509655,;CYFIP2,3_prime_UTR_variant,,ENST00000517753,;CYFIP2,3_prime_UTR_variant,,ENST00000523119,;CYFIP2,3_prime_UTR_variant,,ENST00000523969,;CYFIP2,3_prime_UTR_variant,,ENST00000520759,;CYFIP2,3_prime_UTR_variant,,ENST00000519153,;CYFIP2,upstream_gene_variant,,ENST00000522892,;	G	ENSG00000055163	ENST00000521420	Transcript	synonymous_variant	2848	2757	919	L	ctC/ctG	.	.	.	1	CYFIP2	HGNC	13760	protein_coding	YES	.	ENSP00000430904	.	E7EVJ5_HUMAN	UPI0001D55E6B	.	.	.	24/30	.	hmmpanther:PTHR12195,hmmpanther:PTHR12195:SF1,Pfam_domain:PF05994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTCCAGTA	.	5	ESCA
C5orf45	0	.	GRCh37	5	179264464	179264464	+	Missense_Mutation	SNP	T	T	C	rs761368110	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.959A>G	p.Glu320Gly	p.E320G	ENST00000292586	7/7	33	29	4	28	28	0	C5orf45,missense_variant,p.Glu320Gly,ENST00000292586,;C5orf45,missense_variant,p.Glu265Gly,ENST00000376931,;C5orf45,missense_variant,p.Glu186Gly,ENST00000523084,;SQSTM1,3_prime_UTR_variant,,ENST00000389805,;C5orf45,3_prime_UTR_variant,,ENST00000518219,;SQSTM1,3_prime_UTR_variant,,ENST00000376929,;C5orf45,intron_variant,,ENST00000520698,;C5orf45,intron_variant,,ENST00000403396,;C5orf45,intron_variant,,ENST00000518235,;C5orf45,downstream_gene_variant,,ENST00000521333,;SQSTM1,downstream_gene_variant,,ENST00000510187,;SQSTM1,downstream_gene_variant,,ENST00000402874,;SQSTM1,downstream_gene_variant,,ENST00000360718,;C5orf45,non_coding_transcript_exon_variant,,ENST00000523267,;C5orf45,intron_variant,,ENST00000522663,;C5orf45,intron_variant,,ENST00000518950,;C5orf45,downstream_gene_variant,,ENST00000521675,;C5orf45,downstream_gene_variant,,ENST00000520900,;C5orf45,downstream_gene_variant,,ENST00000520150,;C5orf45,downstream_gene_variant,,ENST00000523835,;SQSTM1,downstream_gene_variant,,ENST00000466342,;C5orf45,downstream_gene_variant,,ENST00000521299,;C5orf45,downstream_gene_variant,,ENST00000520995,;C5orf45,downstream_gene_variant,,ENST00000524068,;C5orf45,downstream_gene_variant,,ENST00000523737,;C5orf45,downstream_gene_variant,,ENST00000522157,;C5orf45,downstream_gene_variant,,ENST00000519208,;	C	ENSG00000161010	ENST00000292586	Transcript	missense_variant	1050	959	320	E/G	gAg/gGg	rs761368110	.	.	-1	C5orf45	HGNC	30817	protein_coding	YES	CCDS34319.1	ENSP00000292586	CE045_HUMAN	E5RJC6_HUMAN	UPI000020CD05	.	tolerated(1)	benign(0.002)	7/7	.	hmmpanther:PTHR15863:SF2,hmmpanther:PTHR15863	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCCTCCAGG	.	2	ESCA
KIAA0947	0	.	GRCh37	5	5462676	5462676	+	Silent	SNP	A	A	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3229A>C	p.%3D	p.R1077R	ENST00000296564	13/19	70	42	27	24	24	0	KIAA0947,synonymous_variant,p.%3D,ENST00000296564,;	C	ENSG00000164151	ENST00000296564	Transcript	synonymous_variant	3451	3229	1077	R	Aga/Cga	.	.	.	1	KIAA0947	HGNC	29154	protein_coding	YES	CCDS47187.1	ENSP00000296564	K0947_HUMAN	.	UPI00015542F9	.	.	.	13/19	.	hmmpanther:PTHR11852,hmmpanther:PTHR11852:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGCAGAAAA	.	5	ESCA
ADCY2	0	.	GRCh37	5	7820737	7820737	+	Missense_Mutation	SNP	A	A	T	rs758742476	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3058A>T	p.Ile1020Phe	p.I1020F	ENST00000338316	24/25	78	56	22	35	35	0	ADCY2,missense_variant,p.Ile1020Phe,ENST00000338316,;ADCY2,missense_variant,p.Ile840Phe,ENST00000537121,;ADCY2,downstream_gene_variant,,ENST00000382531,;ADCY2,3_prime_UTR_variant,,ENST00000493243,;ADCY2,non_coding_transcript_exon_variant,,ENST00000489501,;	T	ENSG00000078295	ENST00000338316	Transcript	missense_variant	3147	3058	1020	I/F	Atc/Ttc	rs758742476	.	.	1	ADCY2	HGNC	233	protein_coding	YES	CCDS3872.2	ENSP00000342952	ADCY2_HUMAN	Q7RTV6_HUMAN,Q71UM8_HUMAN,D6REB8_HUMAN	UPI000066D9F2	.	deleterious(0)	probably_damaging(1)	24/25	.	Superfamily_domains:SSF55073,SMART_domains:SM00044,Pfam_domain:PF00211,Gene3D:3.30.70.1230,PROSITE_patterns:PS00452,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,PROSITE_profiles:PS50125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATATCTGG	.	5	ESCA
MBLAC2	0	.	GRCh37	5	89770101	89770101	+	Silent	SNP	C	C	T	rs751743463	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>A	p.%3D	p.A3A	ENST00000316610	1/2	33	21	12	28	28	0	MBLAC2,synonymous_variant,p.%3D,ENST00000316610,;MBLAC2,synonymous_variant,p.%3D,ENST00000514906,;POLR3G,5_prime_UTR_variant,,ENST00000505345,;POLR3G,5_prime_UTR_variant,,ENST00000503373,;POLR3G,intron_variant,,ENST00000512239,;POLR3G,upstream_gene_variant,,ENST00000504930,;POLR3G,upstream_gene_variant,,ENST00000514483,;POLR3G,upstream_gene_variant,,ENST00000503973,;POLR3G,upstream_gene_variant,,ENST00000399107,;	T	ENSG00000176055	ENST00000316610	Transcript	synonymous_variant	485	9	3	A	gcG/gcA	rs751743463	.	.	-1	MBLAC2	HGNC	33711	protein_coding	YES	CCDS4067.1	ENSP00000314776	MBLC2_HUMAN	.	UPI00001975AC	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGAGCGCCGA	.	5	ESCA
CRISP3	0	.	GRCh37	6	49700981	49700981	+	Missense_Mutation	SNP	C	C	T	rs377483373	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.517G>A	p.Val173Ile	p.V173I	ENST00000433368	6/8	66	49	16	50	50	0	CRISP3,missense_variant,p.Val163Ile,ENST00000263045,;CRISP3,missense_variant,p.Val181Ile,ENST00000371159,;CRISP3,missense_variant,p.Val173Ile,ENST00000354620,;CRISP3,missense_variant,p.Val150Ile,ENST00000393666,;CRISP3,missense_variant,p.Val173Ile,ENST00000433368,;CRISP3,missense_variant,p.Val60Ile,ENST00000423399,;	T	ENSG00000096006	ENST00000433368	Transcript	missense_variant	587	517	173	V/I	Gtt/Att	rs377483373	.	.	-1	CRISP3	HGNC	16904	protein_coding	YES	CCDS55019.1	ENSP00000389026	CRIS3_HUMAN	J3KQX0_HUMAN,I3L0A1_HUMAN	UPI0001DBC27E	.	tolerated(0.52)	benign(0.332)	6/8	.	Prints_domain:PR00837,Superfamily_domains:SSF55797,SMART_domains:SM00198,Pfam_domain:PF00188,Gene3D:3.40.33.10,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF162	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAACGAGGT	byFrequency|byCluster	5	ESCA
KHDRBS2	0	.	GRCh37	6	62757860	62757860	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259T>C	p.Ser87Pro	p.S87P	ENST00000281156	3/9	50	33	16	46	46	0	KHDRBS2,missense_variant,p.Ser87Pro,ENST00000281156,;	G	ENSG00000112232	ENST00000281156	Transcript	missense_variant	538	259	87	S/P	Tcc/Ccc	.	.	.	-1	KHDRBS2	HGNC	18114	protein_coding	YES	CCDS4963.1	ENSP00000281156	KHDR2_HUMAN	.	UPI000004D256	.	deleterious(0)	probably_damaging(0.977)	3/9	.	PROSITE_profiles:PS50084,hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF34,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGAGTTTC	.	5	ESCA
HIPK2	0	.	GRCh37	7	139416737	139416737	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97A>G	p.Ile33Val	p.I33V	ENST00000406875	2/15	50	35	15	34	34	0	HIPK2,missense_variant,p.Ile33Val,ENST00000342645,;HIPK2,missense_variant,p.Ile33Val,ENST00000428878,;HIPK2,missense_variant,p.Ile33Val,ENST00000406875,;	C	ENSG00000064393	ENST00000406875	Transcript	missense_variant	192	97	33	I/V	Ata/Gta	.	.	.	-1	HIPK2	HGNC	14402	protein_coding	YES	.	ENSP00000385571	HIPK2_HUMAN	A4D1R9_HUMAN	UPI000012C71E	.	tolerated(1)	benign(0)	2/15	.	hmmpanther:PTHR24058:SF45,hmmpanther:PTHR24058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTATTTTCA	.	5	ESCA
NPVF	0	.	GRCh37	7	25266259	25266259	+	Missense_Mutation	SNP	A	A	T	rs113088992	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.525T>A	p.Asp175Glu	p.D175E	ENST00000222674	2/3	107	60	47	48	48	0	NPVF,missense_variant,p.Asp175Glu,ENST00000222674,;	T	ENSG00000105954	ENST00000222674	Transcript	missense_variant	572	525	175	D/E	gaT/gaA	rs113088992	.	.	-1	NPVF	HGNC	13782	protein_coding	YES	CCDS5395.1	ENSP00000222674	NPVF_HUMAN	.	UPI000004CB0B	.	tolerated(0.17)	benign(0.006)	2/3	.	hmmpanther:PTHR14403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGATCGGG	byCluster	5	ESCA
AMPH	0	.	GRCh37	7	38468144	38468144	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182+1298G>T	.	.	ENST00000356264	.	57	38	18	50	50	0	AMPH,intron_variant,,ENST00000356264,;AMPH,intron_variant,,ENST00000428293,;AMPH,intron_variant,,ENST00000441628,;AMPH,intron_variant,,ENST00000325590,;AMPH,non_coding_transcript_exon_variant,,ENST00000471913,;AMPH,intron_variant,,ENST00000467580,;AMPH,intron_variant,,ENST00000462072,;AMPH,intron_variant,,ENST00000450124,;	A	ENSG00000078053	ENST00000356264	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AMPH	HGNC	471	protein_coding	YES	CCDS5456.1	ENSP00000348602	AMPH_HUMAN	Q9UQI5_HUMAN,Q9UQI4_HUMAN,Q9UQI3_HUMAN,Q9UQI2_HUMAN	UPI00001259EA	.	.	.	.	14/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTACTGTCT	.	5	ESCA
PCLO	0	.	GRCh37	7	82583743	82583743	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6526G>A	p.Val2176Ile	p.V2176I	ENST00000333891	5/25	42	28	13	30	30	0	PCLO,missense_variant,p.Val2176Ile,ENST00000333891,;PCLO,missense_variant,p.Val2176Ile,ENST00000423517,;PCLO,upstream_gene_variant,,ENST00000437081,;	T	ENSG00000186472	ENST00000333891	Transcript	missense_variant	6864	6526	2176	V/I	Gtc/Atc	.	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	5/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGGGACAGATG	.	4	ESCA
CROT	0	.	GRCh37	7	87020907	87020907	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1388C>G	p.Pro463Arg	p.P463R	ENST00000419147	15/19	49	34	14	31	31	0	CROT,missense_variant,p.Pro435Arg,ENST00000331536,;CROT,missense_variant,p.Pro463Arg,ENST00000419147,;CROT,missense_variant,p.Pro435Arg,ENST00000442291,;	G	ENSG00000005469	ENST00000419147	Transcript	missense_variant	1587	1388	463	P/R	cCt/cGt	.	.	.	1	CROT	HGNC	2366	protein_coding	YES	CCDS47634.1	ENSP00000413575	OCTC_HUMAN	B4DT97_HUMAN	UPI000020F4C5	.	deleterious(0)	probably_damaging(0.997)	15/19	.	hmmpanther:PTHR22589:SF8,hmmpanther:PTHR22589,Pfam_domain:PF00755,Superfamily_domains:SSF52777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCCCTGGTT	.	5	ESCA
CSMD3	0	.	GRCh37	8	114389317	114389317	+	Intron	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.178+59589C>T	.	.	ENST00000297405	.	17	12	4	10	10	0	CSMD3,5_prime_UTR_variant,,ENST00000343508,;CSMD3,intron_variant,,ENST00000352409,;CSMD3,intron_variant,,ENST00000455883,;CSMD3,intron_variant,,ENST00000297405,;CSMD3,intron_variant,,ENST00000497026,;CSMD3,intron_variant,,ENST00000493303,;RP11-709P2.1,non_coding_transcript_exon_variant,,ENST00000422478,;	A	ENSG00000164796	ENST00000297405	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	.	.	.	1/70	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTGGCGCTGGA	.	4	ESCA
ZNF623	0	.	GRCh37	8	144733440	144733440	+	Silent	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1398A>G	p.%3D	p.K466K	ENST00000501748	1/1	26	17	8	38	38	0	ZNF623,synonymous_variant,p.%3D,ENST00000501748,;ZNF623,synonymous_variant,p.%3D,ENST00000458270,;ZNF623,synonymous_variant,p.%3D,ENST00000526926,;	G	ENSG00000183309	ENST00000501748	Transcript	synonymous_variant	1487	1398	466	K	aaA/aaG	.	.	.	1	ZNF623	HGNC	29084	protein_coding	YES	CCDS34957.1	ENSP00000445979	ZN623_HUMAN	.	UPI00001AF7CB	.	.	.	1/1	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF244,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAAGGCTT	.	5	ESCA
TNFRSF10D	0	.	GRCh37	8	23006036	23006036	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285C>T	p.%3D	p.A95A	ENST00000312584	3/9	57	35	22	63	63	0	TNFRSF10D,synonymous_variant,p.%3D,ENST00000312584,;	A	ENSG00000173530	ENST00000312584	Transcript	synonymous_variant	380	285	95	A	gcC/gcT	.	.	.	-1	TNFRSF10D	HGNC	11907	protein_coding	YES	CCDS6038.1	ENSP00000310263	TR10D_HUMAN	.	UPI0000167BBC	.	.	.	3/9	.	hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF89,Gene3D:2.10.50.10,Superfamily_domains:SSF57586,Prints_domain:PR01956	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACAGGCTCC	.	5	ESCA
RALYL	0	.	GRCh37	8	85618195	85618195	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296-68619C>T	.	.	ENST00000517638	.	22	17	5	26	26	0	RALYL,5_prime_UTR_variant,,ENST00000523850,;RALYL,5_prime_UTR_variant,,ENST00000521376,;RALYL,intron_variant,,ENST00000521268,;RALYL,intron_variant,,ENST00000522455,;RALYL,intron_variant,,ENST00000517638,;RALYL,intron_variant,,ENST00000517988,;RALYL,intron_variant,,ENST00000521695,;RALYL,intron_variant,,ENST00000518566,;	T	ENSG00000184672	ENST00000517638	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RALYL	HGNC	27036	protein_coding	YES	CCDS55252.1	ENSP00000430128	.	G3V129_HUMAN,E5RIX9_HUMAN,E5RG71_HUMAN	UPI00002108E6	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCACAACCC	.	5	ESCA
RUNX1T1	0	.	GRCh37	8	92983023	92983023	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1435G>A	p.Val479Met	p.V479M	ENST00000436581	10/11	26	20	6	26	26	0	RUNX1T1,missense_variant,p.Val479Met,ENST00000436581,;RUNX1T1,missense_variant,p.Val468Met,ENST00000265814,;RUNX1T1,missense_variant,p.Val441Met,ENST00000518844,;RUNX1T1,missense_variant,p.Val468Met,ENST00000523629,;RUNX1T1,missense_variant,p.Val431Met,ENST00000360348,;RUNX1T1,missense_variant,p.Val431Met,ENST00000520724,;RUNX1T1,missense_variant,p.Val441Met,ENST00000396218,;RUNX1T1,missense_variant,p.Val431Met,ENST00000422361,;RUNX1T1,3_prime_UTR_variant,,ENST00000521751,;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000521078,;	T	ENSG00000079102	ENST00000436581	Transcript	missense_variant	1446	1435	479	V/M	Gtg/Atg	COSM1102411,COSM1102410	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	deleterious(0.02)	possibly_damaging(0.82)	10/11	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF5,Prints_domain:PR01875	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.A434V|c.1301C>T|4,BUFFER|p.A471V|c.1412C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACACGGCCT	.	5	ESCA
DNAJC25	0	.	GRCh37	9	114415683	114415683	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*181A>G	.	.	ENST00000313525	4/4	50	32	18	22	22	0	DNAJC25,3_prime_UTR_variant,,ENST00000313525,;DNAJC25-GNG10,intron_variant,,ENST00000374294,;DNAJC25,intron_variant,,ENST00000556107,;DNAJC25,3_prime_UTR_variant,,ENST00000463589,;DNAJC25,3_prime_UTR_variant,,ENST00000447096,;	G	ENSG00000059769	ENST00000313525	Transcript	3_prime_UTR_variant	1320	.	.	.	.	.	.	.	1	DNAJC25	HGNC	34187	protein_coding	YES	CCDS43862.1	ENSP00000320650	DJC25_HUMAN	.	UPI000006F186	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTATGATT	.	5	ESCA
TTLL11	0	.	GRCh37	9	124801548	124801548	+	Intron	SNP	T	T	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.829+3A>T	.	.	ENST00000321582	.	64	43	21	61	61	0	TTLL11,splice_region_variant,,ENST00000373776,;TTLL11,splice_region_variant,,ENST00000321582,;TTLL11,splice_region_variant,,ENST00000474723,;TTLL11,splice_region_variant,,ENST00000487468,;TTLL11,splice_region_variant,,ENST00000373778,;	A	ENSG00000175764	ENST00000321582	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	TTLL11	HGNC	18113	protein_coding	YES	CCDS48012.1	ENSP00000321346	.	F8W6M1_HUMAN	UPI0000E0BF7B	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGATACCTG	.	4	ESCA
IFNA4	0	.	GRCh37	9	21187114	21187114	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.417C>T	p.%3D	p.S139S	ENST00000421715	1/1	88	48	39	133	133	0	IFNA4,synonymous_variant,p.%3D,ENST00000421715,;IFNWP9,downstream_gene_variant,,ENST00000448683,;	A	ENSG00000236637	ENST00000421715	Transcript	synonymous_variant	485	417	139	S	tcC/tcT	.	.	.	-1	IFNA4	HGNC	5425	protein_coding	YES	CCDS6498.1	ENSP00000412897	IFNA4_HUMAN	Q9UMJ2_HUMAN	UPI000002BA77	.	.	.	1/1	.	Superfamily_domains:SSF47266,SMART_domains:SM00076,Pfam_domain:PF00143,Gene3D:1.20.1250.10,hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGGAGTC	.	5	ESCA
SPATA31E1	0	.	GRCh37	9	90503680	90503680	+	Silent	SNP	G	G	T	rs753454888	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4278G>T	p.%3D	p.S1426S	ENST00000325643	4/4	28	23	5	33	33	0	SPATA31E1,synonymous_variant,p.%3D,ENST00000325643,;	T	ENSG00000177992	ENST00000325643	Transcript	synonymous_variant	4344	4278	1426	S	tcG/tcT	rs753454888	.	.	1	SPATA31E1	HGNC	26672	protein_coding	YES	CCDS6676.1	ENSP00000322640	S31E1_HUMAN	.	UPI000036764A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	ACCTCGGGCGG	byFrequency	3	ESCA
SPRY3	0	.	GRCh37	X	155006011	155006011	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1611T>C	.	.	ENST00000302805	2/2	24	20	4	33	33	0	SPRY3,3_prime_UTR_variant,,ENST00000302805,;	C	ENSG00000168939	ENST00000302805	Transcript	3_prime_UTR_variant	2909	.	.	.	.	.	.	.	1	SPRY3	HGNC	11271	protein_coding	YES	CCDS14769.4	ENSP00000302978	SPY3_HUMAN	.	UPI0000135E98	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GTGCTTGCTCC	.	3	ESCA
MED14	0	.	GRCh37	X	40541948	40541948	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2272G>T	p.Gly758Cys	p.G758C	ENST00000324817	18/31	46	37	8	27	27	0	MED14,missense_variant,p.Gly758Cys,ENST00000324817,;MED14,non_coding_transcript_exon_variant,,ENST00000496531,;	A	ENSG00000180182	ENST00000324817	Transcript	missense_variant	2391	2272	758	G/C	Ggt/Tgt	.	.	.	-1	MED14	HGNC	2370	protein_coding	YES	CCDS14254.1	ENSP00000323720	MED14_HUMAN	.	UPI00001414B1	.	deleterious(0.01)	probably_damaging(0.922)	18/31	.	hmmpanther:PTHR12809,hmmpanther:PTHR12809:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCACCAACAG	.	5	ESCA
DGKK	0	.	GRCh37	X	50146073	50146073	+	RNA	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1354T>C	.	.	ENST00000376025	7/28	26	9	16	18	18	0	DGKK,non_coding_transcript_exon_variant,,ENST00000376025,;DGKK,non_coding_transcript_exon_variant,,ENST00000546288,;	G	ENSG00000204466	ENST00000376025	Transcript	non_coding_transcript_exon_variant	1354	.	.	.	.	.	.	.	-1	DGKK	HGNC	32395	processed_transcript	YES	.	.	.	.	.	.	.	.	7/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACCACAGGC	.	5	ESCA
PHKA1	0	.	GRCh37	X	71800902	71800902	+	Missense_Mutation	SNP	C	C	T	rs782814716	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3622G>A	p.Ala1208Thr	p.A1208T	ENST00000373542	32/32	59	26	33	43	43	0	PHKA1,missense_variant,p.Ala1166Thr,ENST00000373545,;PHKA1,missense_variant,p.Ala1195Thr,ENST00000339490,;PHKA1,missense_variant,p.Ala1208Thr,ENST00000373542,;PHKA1,missense_variant,p.Ala1136Thr,ENST00000541944,;PHKA1,missense_variant,p.Ala1225Thr,ENST00000373539,;	T	ENSG00000067177	ENST00000373542	Transcript	missense_variant	3782	3622	1208	A/T	Gcc/Acc	rs782814716	.	.	-1	PHKA1	HGNC	8925	protein_coding	YES	CCDS14421.1	ENSP00000362643	KPB1_HUMAN	.	UPI000013D340	.	deleterious(0)	benign(0.337)	32/32	.	hmmpanther:PTHR10749:SF4,hmmpanther:PTHR10749	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGCGGCTG	byFrequency	5	ESCA
PGK1	0	.	GRCh37	X	77381578	77381578	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*251A>T	.	.	ENST00000373316	11/11	14	4	9	12	12	0	PGK1,3_prime_UTR_variant,,ENST00000537456,;PGK1,3_prime_UTR_variant,,ENST00000373316,;PGK1,3_prime_UTR_variant,,ENST00000442431,;TAF9B,downstream_gene_variant,,ENST00000341864,;PGK1,non_coding_transcript_exon_variant,,ENST00000476531,;PGK1,downstream_gene_variant,,ENST00000491291,;PGK1,downstream_gene_variant,,ENST00000474281,;	T	ENSG00000102144	ENST00000373316	Transcript	3_prime_UTR_variant	1672	.	.	.	.	.	.	.	1	PGK1	HGNC	8896	protein_coding	YES	CCDS14438.1	ENSP00000362413	PGK1_HUMAN	B7Z7A9_HUMAN,B4DHM5_HUMAN	UPI00000727EE	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TGCATATATTT	.	4	ESCA
EIF1AY	0	.	GRCh37	Y	22751375	22751375	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97H-01A-11D-A387-09	TCGA-IG-A97H-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343A>G	p.Ile115Val	p.I115V	ENST00000361365	6/7	39	10	29	21	21	0	EIF1AY,missense_variant,p.Ile98Val,ENST00000382772,;EIF1AY,missense_variant,p.Ile115Val,ENST00000361365,;EIF1AY,non_coding_transcript_exon_variant,,ENST00000485584,;EIF1AY,non_coding_transcript_exon_variant,,ENST00000464196,;EIF1AY,downstream_gene_variant,,ENST00000465253,;	G	ENSG00000198692	ENST00000361365	Transcript	missense_variant	490	343	115	I/V	Atc/Gtc	.	.	.	1	EIF1AY	HGNC	3252	protein_coding	YES	CCDS14795.1	ENSP00000354722	IF1AY_HUMAN	.	UPI0000169E55	.	tolerated(0.19)	benign(0.017)	6/7	.	hmmpanther:PTHR21668,hmmpanther:PTHR21668:SF2,Gene3D:2.40.50.140,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAAAATCAAT	.	5	ESCA
FAM178A	0	.	GRCh37	10	102684710	102684710	+	Missense_Mutation	SNP	C	C	A	rs779981337	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1952C>A	p.Ser651Tyr	p.S651Y	ENST00000370269	5/19	33	22	11	36	36	0	FAM178A,missense_variant,p.Ser651Tyr,ENST00000370269,;FAM178A,missense_variant,p.Ser651Tyr,ENST00000370271,;FAM178A,missense_variant,p.Ser651Tyr,ENST00000238961,;	A	ENSG00000119906	ENST00000370269	Transcript	missense_variant	2084	1952	651	S/Y	tCt/tAt	rs779981337	.	.	1	FAM178A	HGNC	17814	protein_coding	YES	CCDS44470.1	ENSP00000359292	F178A_HUMAN	.	UPI0000458847	.	deleterious(0.01)	possibly_damaging(0.735)	5/19	.	hmmpanther:PTHR16046,hmmpanther:PTHR16046:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGATCTCAGT	.	5	ESCA
SH3PXD2A	0	.	GRCh37	10	105386894	105386894	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670A>T	p.Asn224Tyr	p.N224Y	ENST00000355946	9/14	49	34	15	51	51	0	SH3PXD2A,missense_variant,p.Asn91Tyr,ENST00000540321,;SH3PXD2A,missense_variant,p.Asn59Tyr,ENST00000538130,;SH3PXD2A,missense_variant,p.Asn179Tyr,ENST00000420222,;SH3PXD2A,missense_variant,p.Asn224Tyr,ENST00000369774,;SH3PXD2A,missense_variant,p.Asn224Tyr,ENST00000355946,;SH3PXD2A,missense_variant,p.Asn86Tyr,ENST00000427662,;SH3PXD2A,non_coding_transcript_exon_variant,,ENST00000315994,;	A	ENSG00000107957	ENST00000355946	Transcript	missense_variant	810	670	224	N/Y	Aat/Tat	.	.	.	-1	SH3PXD2A	HGNC	23664	protein_coding	YES	CCDS31278.1	ENSP00000348215	SPD2A_HUMAN	.	UPI000041B175	.	deleterious(0)	possibly_damaging(0.847)	9/14	.	PROSITE_profiles:PS50002,hmmpanther:PTHR15706,hmmpanther:PTHR15706:SF7,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATTCTGGG	.	5	ESCA
GPR158	0	.	GRCh37	10	25701176	25701176	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1112-3C>T	.	.	ENST00000376351	.	65	44	21	99	99	0	GPR158,splice_region_variant,,ENST00000376351,;	T	ENSG00000151025	ENST00000376351	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	GPR158	HGNC	23689	protein_coding	YES	CCDS31166.1	ENSP00000365529	GP158_HUMAN	.	UPI0000199875	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTCAGGAA	.	4	ESCA
DRGX	0	.	GRCh37	10	50598228	50598228	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200C>G	p.Thr67Ser	p.T67S	ENST00000434016	3/6	33	21	11	64	64	0	DRGX,missense_variant,p.Thr67Ser,ENST00000434016,;DRGX,missense_variant,p.Thr62Ser,ENST00000374139,;	C	ENSG00000165606	ENST00000434016	Transcript	missense_variant	200	200	67	T/S	aCc/aGc	.	.	.	-1	DRGX	HGNC	21536	protein_coding	YES	.	ENSP00000401653	.	C9JW76_HUMAN	UPI00006C1033	.	deleterious(0.04)	probably_damaging(0.992)	3/6	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF313,hmmpanther:PTHR24329,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGGTGAAG	.	5	ESCA
C10orf40	0	.	GRCh37	10	61719561	61719561	+	5'UTR	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-890G>C	.	.	ENST00000521074	2/3	68	51	16	76	76	0	C10orf40,5_prime_UTR_variant,,ENST00000521074,;C10orf40,5_prime_UTR_variant,,ENST00000444900,;C10orf40,upstream_gene_variant,,ENST00000430888,;	G	ENSG00000235931	ENST00000521074	Transcript	5_prime_UTR_variant	198	.	.	.	.	.	.	.	-1	C10orf40	HGNC	23524	protein_coding	YES	.	ENSP00000430990	CJ040_HUMAN	.	UPI00001600DA	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTCCTCGCAAA	.	4	ESCA
GHITM	0	.	GRCh37	10	85901340	85901340	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84G>A	p.%3D	p.V28V	ENST00000372134	2/9	62	42	19	96	96	0	GHITM,synonymous_variant,p.%3D,ENST00000372134,;RP11-338I21.1,upstream_gene_variant,,ENST00000606511,;	A	ENSG00000165678	ENST00000372134	Transcript	synonymous_variant	277	84	28	V	gtG/gtA	.	.	.	1	GHITM	HGNC	17281	protein_coding	YES	CCDS41542.1	ENSP00000361207	GHITM_HUMAN	Q9P099_HUMAN,Q658I8_HUMAN,Q5VT94_HUMAN,B4DPG9_HUMAN	UPI0000049DE6	.	.	.	2/9	.	Pfam_domain:PF12811	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGTGAAGAA	.	5	ESCA
TNKS2	0	.	GRCh37	10	93579775	93579783	+	In_Frame_Del	DEL	ATGCTAAAG	ATGCTAAAG	-	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	ATGCTAAAG	ATGCTAAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715_723delGCTAAAGAT	p.Ala239_Asp241del	p.A239_D241del	ENST00000371627	6/27	74	55	19	96	96	0	TNKS2,inframe_deletion,p.Ala239_Asp241del,ENST00000371627,;	-	ENSG00000107854	ENST00000371627	Transcript	inframe_deletion	1092-1100	713-721	238-241	HAKD/H	cATGCTAAAGat/cat	.	.	.	1	TNKS2	HGNC	15677	protein_coding	YES	CCDS7417.1	ENSP00000360689	TNKS2_HUMAN	.	UPI00000362BE	.	.	.	6/27	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24180,hmmpanther:PTHR24180:SF11,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01415	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGTCCATGCTAAAGATAAA	.	3	ESCA
CYP2C18	0	.	GRCh37	10	96495128	96495128	+	Missense_Mutation	SNP	T	T	A	rs775301825	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1400T>A	p.Ile467Asn	p.I467N	ENST00000285979	9/9	97	76	21	76	76	0	CYP2C18,missense_variant,p.Ile408Asn,ENST00000339022,;CYP2C18,missense_variant,p.Ile467Asn,ENST00000285979,;CYP2C19,intron_variant,,ENST00000464755,;	A	ENSG00000108242	ENST00000285979	Transcript	missense_variant	1599	1400	467	I/N	aTt/aAt	rs775301825	.	.	1	CYP2C18	HGNC	2620	protein_coding	YES	CCDS7435.1	ENSP00000285979	CP2CI_HUMAN	Q16750_HUMAN	UPI000013DE1D	.	deleterious(0)	probably_damaging(0.996)	9/9	.	hmmpanther:PTHR24300:SF123,hmmpanther:PTHR24300,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATATTGACA	.	5	ESCA
ANKRD2	0	.	GRCh37	10	99338347	99338347	+	Silent	SNP	C	C	T	rs140424419	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.522C>T	p.%3D	p.A174A	ENST00000307518	4/9	43	25	18	37	37	0	ANKRD2,synonymous_variant,p.%3D,ENST00000307518,;ANKRD2,synonymous_variant,p.%3D,ENST00000370655,;ANKRD2,synonymous_variant,p.%3D,ENST00000298808,;ANKRD2,synonymous_variant,p.%3D,ENST00000455090,;	T	ENSG00000165887	ENST00000307518	Transcript	synonymous_variant	789	522	174	A	gcC/gcT	rs140424419	.	.	1	ANKRD2	HGNC	495	protein_coding	YES	CCDS7466.1	ENSP00000306163	ANKR2_HUMAN	.	UPI0000231C90	.	.	.	4/9	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24126,hmmpanther:PTHR24126:SF3,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	T:0.0002	T:0.0004	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCCGACAC	byFrequency|byCluster	5	ESCA
GRAMD1B	0	.	GRCh37	11	123465506	123465506	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404G>A	p.Trp135Ter	p.W135*	ENST00000529750	5/20	29	13	15	40	40	0	GRAMD1B,stop_gained,p.Trp135Ter,ENST00000322282,;GRAMD1B,stop_gained,p.Trp142Ter,ENST00000456860,;GRAMD1B,stop_gained,p.Trp131Ter,ENST00000534764,;GRAMD1B,stop_gained,p.Trp95Ter,ENST00000529432,;GRAMD1B,stop_gained,p.Trp135Ter,ENST00000529750,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;SF3A3P2,downstream_gene_variant,,ENST00000528675,;	A	ENSG00000023171	ENST00000529750	Transcript	stop_gained	731	404	135	W/*	tGg/tAg	.	.	.	1	GRAMD1B	HGNC	29214	protein_coding	YES	CCDS53720.1	ENSP00000436500	GRM1B_HUMAN	.	UPI00005C3025	.	.	.	5/20	.	hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF3,Pfam_domain:PF02893,SMART_domains:SM00568	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AAATTGGATCT	.	4	ESCA
OR6X1	0	.	GRCh37	11	123624707	123624707	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520C>G	p.His174Asp	p.H174D	ENST00000327930	1/1	21	13	7	34	34	0	OR6X1,missense_variant,p.His174Asp,ENST00000327930,;	C	ENSG00000221931	ENST00000327930	Transcript	missense_variant	547	520	174	H/D	Cat/Gat	.	.	.	-1	OR6X1	HGNC	14737	protein_coding	YES	CCDS31695.1	ENSP00000333724	OR6X1_HUMAN	.	UPI000004B1D5	.	deleterious(0)	probably_damaging(0.998)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF30,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GAAATGACTGA	.	4	ESCA
PLEKHA7	0	.	GRCh37	11	16872792	16872792	+	Silent	SNP	G	G	A	rs367816429	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642C>T	p.%3D	p.Y214Y	ENST00000355661	8/23	37	26	10	51	51	0	PLEKHA7,synonymous_variant,p.%3D,ENST00000448080,;PLEKHA7,synonymous_variant,p.%3D,ENST00000531066,;PLEKHA7,synonymous_variant,p.%3D,ENST00000528376,;PLEKHA7,synonymous_variant,p.%3D,ENST00000355661,;PLEKHA7,intron_variant,,ENST00000532079,;PLEKHA7,downstream_gene_variant,,ENST00000529213,;PLEKHA7,downstream_gene_variant,,ENST00000528637,;	A	ENSG00000166689	ENST00000355661	Transcript	synonymous_variant	653	642	214	Y	taC/taT	rs367816429	.	.	-1	PLEKHA7	HGNC	27049	protein_coding	YES	CCDS31434.1	ENSP00000347883	PKHA7_HUMAN	E9PL74_HUMAN,E9PIK1_HUMAN	UPI0000456498	.	.	.	8/23	.	Superfamily_domains:SSF50729,SMART_domains:SM00233,Gene3D:2.30.29.30,Pfam_domain:PF00169,hmmpanther:PTHR12752:SF4,hmmpanther:PTHR12752,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCACGTAGCT	byCluster	5	ESCA
LUZP2	0	.	GRCh37	11	24518708	24518708	+	5'Flank	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000336930	.	11	4	6	15	15	0	LUZP2,upstream_gene_variant,,ENST00000529015,;LUZP2,upstream_gene_variant,,ENST00000336930,;LUZP2,upstream_gene_variant,,ENST00000533227,;LUZP2,non_coding_transcript_exon_variant,,ENST00000531187,;LUZP2,non_coding_transcript_exon_variant,,ENST00000449567,;LUZP2,non_coding_transcript_exon_variant,,ENST00000405855,;	C	ENSG00000187398	ENST00000336930	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	16	1	LUZP2	HGNC	23206	protein_coding	YES	CCDS31446.1	ENSP00000336817	LUZP2_HUMAN	.	UPI000019816C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGACAGAGCCG	.	3	ESCA
OR4A47	0	.	GRCh37	11	48510440	48510440	+	Missense_Mutation	SNP	C	C	G	rs758038674	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96C>G	p.Phe32Leu	p.F32L	ENST00000446524	1/1	69	62	6	91	91	0	OR4A47,missense_variant,p.Phe32Leu,ENST00000446524,;OR4R1P,upstream_gene_variant,,ENST00000529879,;OR4A48P,upstream_gene_variant,,ENST00000531359,;	G	ENSG00000237388	ENST00000446524	Transcript	missense_variant	172	96	32	F/L	ttC/ttG	rs758038674	.	.	1	OR4A47	HGNC	31266	protein_coding	YES	CCDS31490.1	ENSP00000412752	O4A47_HUMAN	.	UPI00001971E5	.	tolerated_low_confidence(0.14)	benign(0.005)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451:SF87,hmmpanther:PTHR26451,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTTCTACAT	.	4	ESCA
TRIM51HP	0	.	GRCh37	11	55062977	55062977	+	RNA	SNP	G	G	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.982C>A	.	.	ENST00000530412	2/5	305	234	71	282	282	0	TRIM51HP,non_coding_transcript_exon_variant,,ENST00000526016,;TRIM51HP,non_coding_transcript_exon_variant,,ENST00000530412,;	T	ENSG00000166007	ENST00000530412	Transcript	non_coding_transcript_exon_variant	982	.	.	.	.	.	.	.	-1	TRIM51HP	HGNC	43977	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCAGATCCT	.	5	ESCA
OR4A15	0	.	GRCh37	11	55135831	55135831	+	Missense_Mutation	SNP	C	C	G	rs151248769	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472C>G	p.Leu158Val	p.L158V	ENST00000314706	1/1	123	105	18	106	106	0	OR4A15,missense_variant,p.Leu158Val,ENST00000314706,;	G	ENSG00000181958	ENST00000314706	Transcript	missense_variant	472	472	158	L/V	Ctt/Gtt	rs151248769	.	.	1	OR4A15	HGNC	15152	protein_coding	YES	CCDS31500.1	ENSP00000325065	O4A15_HUMAN	.	UPI000004618F	.	deleterious_low_confidence(0)	probably_damaging(1)	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF63,PROSITE_profiles:PS50262	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCTTCAT	byCluster|by1000G	5	ESCA
OR8I2	0	.	GRCh37	11	55860877	55860877	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94C>G	p.Leu32Val	p.L32V	ENST00000302124	1/1	85	57	28	102	102	0	OR8I2,missense_variant,p.Leu32Val,ENST00000302124,;OR8I4P,downstream_gene_variant,,ENST00000526965,;	G	ENSG00000172154	ENST00000302124	Transcript	missense_variant	125	94	32	L/V	Ctc/Gtc	COSM543285	.	.	1	OR8I2	HGNC	15310	protein_coding	YES	CCDS31517.1	ENSP00000303864	OR8I2_HUMAN	H0YLY8_HUMAN	UPI0000041D16	.	deleterious(0.01)	probably_damaging(0.994)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTCTCTTC	.	5	ESCA
SDHAF2	0	.	GRCh37	11	61213450	61213450	+	Silent	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.408C>G	p.%3D	p.V136V	ENST00000301761	4/4	62	43	19	59	59	0	SDHAF2,stop_gained,p.Ser25Ter,ENST00000542074,;SDHAF2,synonymous_variant,p.%3D,ENST00000301761,;SDHAF2,3_prime_UTR_variant,,ENST00000537782,;SDHAF2,3_prime_UTR_variant,,ENST00000543265,;RP11-286N22.8,intron_variant,,ENST00000541135,;RN7SL23P,downstream_gene_variant,,ENST00000484055,;RP11-286N22.8,intron_variant,,ENST00000544025,;RP11-286N22.8,intron_variant,,ENST00000544880,;RP11-286N22.8,synonymous_variant,p.%3D,ENST00000543044,;SDHAF2,3_prime_UTR_variant,,ENST00000359614,;SDHAF2,3_prime_UTR_variant,,ENST00000542794,;RP11-286N22.8,intron_variant,,ENST00000544801,;RP11-286N22.8,intron_variant,,ENST00000538594,;RP11-286N22.8,intron_variant,,ENST00000536670,;	G	ENSG00000167985	ENST00000301761	Transcript	synonymous_variant	482	408	136	V	gtC/gtG	.	.	.	1	SDHAF2	HGNC	26034	protein_coding	YES	CCDS8007.1	ENSP00000301761	SDHF2_HUMAN	F5GYJ5_HUMAN	UPI0000039E6D	.	.	.	4/4	.	HAMAP:MF_03057,hmmpanther:PTHR12469,hmmpanther:PTHR12469:SF2,Pfam_domain:PF03937,Gene3D:1.10.150.250,Superfamily_domains:0042477	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGTCATGGC	.	5	ESCA
SPTBN2	0	.	GRCh37	11	66455366	66455367	+	Frame_Shift_Del	DEL	AA	AA	-	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	AA	AA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6473_6474delTT	p.Leu2158ArgfsTer130	p.L2158Rfs*130	ENST00000533211	34/38	35	24	11	45	45	0	SPTBN2,frameshift_variant,p.Leu2158ArgfsTer130,ENST00000533211,;SPTBN2,frameshift_variant,p.Leu2158ArgfsTer130,ENST00000309996,;SPTBN2,frameshift_variant,p.Leu2158ArgfsTer130,ENST00000529997,;SPTBN2,non_coding_transcript_exon_variant,,ENST00000532650,;SPTBN2,upstream_gene_variant,,ENST00000530775,;SPTBN2,downstream_gene_variant,,ENST00000532902,;SPTBN2,upstream_gene_variant,,ENST00000528051,;	-	ENSG00000173898	ENST00000533211	Transcript	frameshift_variant	6805-6806	6473-6474	2158	L/X	cTT/c	.	.	.	-1	SPTBN2	HGNC	11276	protein_coding	YES	CCDS8150.1	ENSP00000432568	SPTN2_HUMAN	E9PJZ2_HUMAN,C1KC08_HUMAN	UPI000013EF83	.	.	.	34/38	.	PIRSF_domain:PIRSF002297,SMART_domains:SM00150,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGCTCAAGTCTC	.	3	ESCA
PPFIBP2	0	.	GRCh37	11	7618827	7618827	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.409G>A	p.Glu137Lys	p.E137K	ENST00000299492	5/24	37	24	12	50	50	0	PPFIBP2,missense_variant,p.Glu25Lys,ENST00000528883,;PPFIBP2,missense_variant,p.Glu92Lys,ENST00000524548,;PPFIBP2,missense_variant,p.Glu137Lys,ENST00000527790,;PPFIBP2,missense_variant,p.Glu137Lys,ENST00000299492,;PPFIBP2,5_prime_UTR_variant,,ENST00000525597,;PPFIBP2,5_prime_UTR_variant,,ENST00000529575,;PPFIBP2,5_prime_UTR_variant,,ENST00000533792,;PPFIBP2,intron_variant,,ENST00000532926,;PPFIBP2,intron_variant,,ENST00000529021,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000530189,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000529321,;	A	ENSG00000166387	ENST00000299492	Transcript	missense_variant	797	409	137	E/K	Gaa/Aaa	.	.	.	1	PPFIBP2	HGNC	9250	protein_coding	YES	CCDS31419.1	ENSP00000299492	LIPB2_HUMAN	E9PP16_HUMAN,E9PMN3_HUMAN,E9PMH3_HUMAN,E9PK17_HUMAN,E9PJA0_HUMAN,E9PIK8_HUMAN,B3KM46_HUMAN	UPI00001C1EF8	.	tolerated(0.06)	probably_damaging(0.991)	5/24	.	hmmpanther:PTHR12587:SF18,hmmpanther:PTHR12587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGAGAAAAG	.	5	ESCA
FAT3	0	.	GRCh37	11	92085866	92085866	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588C>A	p.Tyr196Ter	p.Y196*	ENST00000298047	1/27	21	13	7	42	42	0	FAT3,stop_gained,p.Tyr196Ter,ENST00000541502,;FAT3,stop_gained,p.Tyr196Ter,ENST00000298047,;FAT3,stop_gained,p.Tyr196Ter,ENST00000409404,;FAT3,stop_gained,p.Tyr46Ter,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,;	A	ENSG00000165323	ENST00000298047	Transcript	stop_gained	605	588	196	Y/*	taC/taA	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	.	1/27	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTACTTTAA	.	5	ESCA
HSP90B1	0	.	GRCh37	12	104337535	104337535	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1910C>G	p.Ser637Cys	p.S637C	ENST00000299767	14/18	80	72	8	78	78	0	HSP90B1,missense_variant,p.Ser637Cys,ENST00000299767,;HSP90B1,upstream_gene_variant,,ENST00000550595,;HSP90B1,non_coding_transcript_exon_variant,,ENST00000548462,;HSP90B1,non_coding_transcript_exon_variant,,ENST00000552051,;HSP90B1,downstream_gene_variant,,ENST00000550479,;HSP90B1,downstream_gene_variant,,ENST00000551983,;	G	ENSG00000166598	ENST00000299767	Transcript	missense_variant	2092	1910	637	S/C	tCt/tGt	.	.	.	1	HSP90B1	HGNC	12028	protein_coding	YES	CCDS9094.1	ENSP00000299767	ENPL_HUMAN	Q5CAQ5_HUMAN,F8W026_HUMAN,B4DHT9_HUMAN	UPI0000129FBA	.	deleterious(0)	probably_damaging(0.994)	14/18	.	HAMAP:MF_00505,hmmpanther:PTHR11528,hmmpanther:PTHR11528:SF44,Pfam_domain:PF00183,PIRSF_domain:PIRSF002583,Superfamily_domains:0043579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTGTCTCAGC	.	3	ESCA
KIAA1033	0	.	GRCh37	12	105520920	105520920	+	Missense_Mutation	SNP	C	C	A	rs575817689	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1052C>A	p.Thr351Asn	p.T351N	ENST00000332180	13/33	128	98	30	119	119	0	KIAA1033,missense_variant,p.Thr351Asn,ENST00000332180,;KIAA1033,3_prime_UTR_variant,,ENST00000550053,;KIAA1033,non_coding_transcript_exon_variant,,ENST00000311317,;KIAA1033,downstream_gene_variant,,ENST00000547404,;	A	ENSG00000136051	ENST00000332180	Transcript	missense_variant	1139	1052	351	T/N	aCt/aAt	rs575817689	.	.	1	KIAA1033	HGNC	29174	protein_coding	YES	CCDS41826.1	ENSP00000328062	WASH7_HUMAN	F8W1W1_HUMAN,F8VQX3_HUMAN,F8VNZ5_HUMAN	UPI00001C1F3B	.	tolerated(0.25)	benign(0.23)	13/33	.	hmmpanther:PTHR31409,hmmpanther:PTHR31409:SF0,Pfam_domain:PF14745	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCACTCTAA	by1000G	5	ESCA
TBX5	0	.	GRCh37	12	114793304	114793304	+	3'UTR	SNP	C	C	G	rs756537403	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*33G>C	.	.	ENST00000310346	9/9	27	18	8	28	28	0	TBX5,3_prime_UTR_variant,,ENST00000405440,;TBX5,3_prime_UTR_variant,,ENST00000349716,;TBX5,3_prime_UTR_variant,,ENST00000310346,;	G	ENSG00000089225	ENST00000310346	Transcript	3_prime_UTR_variant	2257	.	.	.	.	rs756537403	.	.	-1	TBX5	HGNC	11604	protein_coding	YES	CCDS9173.1	ENSP00000309913	TBX5_HUMAN	.	UPI0000136AA2	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCTAGGA	.	5	ESCA
TESC	0	.	GRCh37	12	117486955	117486955	+	Missense_Mutation	SNP	C	C	T	rs761040708	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218G>A	p.Arg73His	p.R73H	ENST00000335209	4/8	55	42	13	68	68	0	TESC,missense_variant,p.Arg126His,ENST00000392545,;TESC,missense_variant,p.Arg73His,ENST00000335209,;TESC,missense_variant,p.Arg46His,ENST00000541210,;TESC,upstream_gene_variant,,ENST00000549210,;TESC,non_coding_transcript_exon_variant,,ENST00000535198,;TESC,missense_variant,p.Arg73His,ENST00000470612,;TESC,missense_variant,p.Arg73His,ENST00000462502,;TESC,non_coding_transcript_exon_variant,,ENST00000482176,;	T	ENSG00000088992	ENST00000335209	Transcript	missense_variant	405	218	73	R/H	cGc/cAc	rs761040708	.	.	-1	TESC	HGNC	26065	protein_coding	YES	CCDS9183.3	ENSP00000334785	CHP3_HUMAN	.	UPI0000136BF7	.	tolerated(0.35)	benign(0.004)	4/8	.	Superfamily_domains:SSF47473,Gene3D:1.10.238.10,hmmpanther:PTHR23056,hmmpanther:PTHR23056:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTGCGCAGG	.	5	ESCA
COQ5	0	.	GRCh37	12	120941457	120941457	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*130A>T	.	.	ENST00000288532	7/7	41	29	11	45	45	0	COQ5,3_prime_UTR_variant,,ENST00000288532,;COQ5,3_prime_UTR_variant,,ENST00000445328,;COQ5,downstream_gene_variant,,ENST00000552443,;Y_RNA,downstream_gene_variant,,ENST00000410669,;	A	ENSG00000110871	ENST00000288532	Transcript	3_prime_UTR_variant	1155	.	.	.	.	.	.	.	-1	COQ5	HGNC	28722	protein_coding	YES	CCDS31912.1	ENSP00000288532	COQ5_HUMAN	F8VVX6_HUMAN,F8VP53_HUMAN	UPI00001592AF	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCGATTCAAA	.	5	ESCA
KDM2B	0	.	GRCh37	12	121877875	121877875	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3614A>T	p.Gln1205Leu	p.Q1205L	ENST00000377071	22/23	41	33	7	45	45	0	KDM2B,missense_variant,p.Gln573Leu,ENST00000542973,;KDM2B,missense_variant,p.Gln1205Leu,ENST00000377071,;KDM2B,missense_variant,p.Gln1136Leu,ENST00000377069,;KDM2B,intron_variant,,ENST00000536437,;KDM2B,non_coding_transcript_exon_variant,,ENST00000536036,;KDM2B,non_coding_transcript_exon_variant,,ENST00000538503,;KDM2B,intron_variant,,ENST00000543025,;KDM2B,downstream_gene_variant,,ENST00000538243,;	A	ENSG00000089094	ENST00000377071	Transcript	missense_variant	3687	3614	1205	Q/L	cAg/cTg	.	.	.	-1	KDM2B	HGNC	13610	protein_coding	YES	CCDS41850.1	ENSP00000366271	KDM2B_HUMAN	F5H7T7_HUMAN,F5H6N6_HUMAN,F5H4A7_HUMAN,F5GXC2_HUMAN	UPI000006F36E	.	tolerated(0.13)	probably_damaging(0.989)	22/23	.	hmmpanther:PTHR23123:SF10,hmmpanther:PTHR23123,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCTGACCT	.	5	ESCA
DDX51	0	.	GRCh37	12	132625874	132625874	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1196C>T	p.Ala399Val	p.A399V	ENST00000397333	8/15	63	42	21	68	66	1	DDX51,missense_variant,p.Ala399Val,ENST00000397333,;NOC4L,upstream_gene_variant,,ENST00000330579,;NOC4L,upstream_gene_variant,,ENST00000541954,;DDX51,non_coding_transcript_exon_variant,,ENST00000329073,;DDX51,non_coding_transcript_exon_variant,,ENST00000545991,;DDX51,non_coding_transcript_exon_variant,,ENST00000546058,;DDX51,upstream_gene_variant,,ENST00000462829,;DDX51,upstream_gene_variant,,ENST00000541489,;	A	ENSG00000185163	ENST00000397333	Transcript	missense_variant	1235	1196	399	A/V	gCg/gTg	.	.	.	-1	DDX51	HGNC	20082	protein_coding	YES	CCDS41865.1	ENSP00000380495	DDX51_HUMAN	.	UPI000049DD95	.	tolerated(0.2)	benign(0.227)	8/15	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF68,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGTCCGCGGGG	.	4	ESCA
SYT10	0	.	GRCh37	12	33579301	33579301	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281C>G	p.Thr94Ser	p.T94S	ENST00000228567	2/7	76	55	20	76	76	0	SYT10,missense_variant,p.Thr94Ser,ENST00000228567,;SYT10,5_prime_UTR_variant,,ENST00000535526,;SYT10,upstream_gene_variant,,ENST00000567656,;SYT10,missense_variant,p.Thr94Ser,ENST00000539102,;	C	ENSG00000110975	ENST00000228567	Transcript	missense_variant	578	281	94	T/S	aCt/aGt	.	.	.	-1	SYT10	HGNC	19266	protein_coding	YES	CCDS8732.1	ENSP00000228567	SYT10_HUMAN	F5H2A8_HUMAN	UPI0000052B30	.	tolerated(1)	benign(0)	2/7	.	hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCGTAGTGATG	.	3	ESCA
KCNA5	0	.	GRCh37	12	5154277	5154277	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964G>A	p.Asp322Asn	p.D322N	ENST00000252321	1/1	16	13	3	29	29	0	KCNA5,missense_variant,p.Asp322Asn,ENST00000252321,;	A	ENSG00000130037	ENST00000252321	Transcript	missense_variant	1193	964	322	D/N	Gac/Aac	.	.	.	1	KCNA5	HGNC	6224	protein_coding	YES	CCDS8536.1	ENSP00000252321	KCNA5_HUMAN	.	UPI000013CD56	.	tolerated(0.07)	probably_damaging(0.998)	1/1	.	hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF25,Gene3D:1.20.120.350,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCCGACCCC	.	2	ESCA
KRT6A	0	.	GRCh37	12	52884517	52884517	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.913G>C	p.Glu305Gln	p.E305Q	ENST00000330722	5/9	148	137	11	177	177	0	KRT6A,missense_variant,p.Glu305Gln,ENST00000330722,;KRT6A,splice_region_variant,,ENST00000549600,;KRT6A,splice_region_variant,,ENST00000549754,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549898,;KRT6A,upstream_gene_variant,,ENST00000548735,;	G	ENSG00000205420	ENST00000330722	Transcript	missense_variant	982	913	305	E/Q	Gag/Cag	.	.	.	-1	KRT6A	HGNC	6443	protein_coding	YES	CCDS41786.1	ENSP00000369317	K2C6A_HUMAN	.	UPI000013CD4C	.	deleterious(0)	probably_damaging(0.99)	5/9	.	Pfam_domain:PF00038,hmmpanther:PTHR23239:SF141,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGCTCCTGCA	.	3	ESCA
HOXC9	0	.	GRCh37	12	54394503	54394503	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531G>A	p.%3D	p.L177L	ENST00000303450	1/2	18	14	4	20	20	0	HOXC9,synonymous_variant,p.%3D,ENST00000303450,;HOXC9,synonymous_variant,p.%3D,ENST00000508190,;HOXC6,intron_variant,,ENST00000509328,;HOXC6,intron_variant,,ENST00000504315,;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC-AS2,upstream_gene_variant,,ENST00000513533,;HOXC-AS2,upstream_gene_variant,,ENST00000604081,;HOXC-AS1,upstream_gene_variant,,ENST00000505700,;HOXC-AS1,upstream_gene_variant,,ENST00000512427,;HOXC9,intron_variant,,ENST00000504557,;	A	ENSG00000180806	ENST00000303450	Transcript	synonymous_variant	601	531	177	L	ctG/ctA	.	.	.	1	HOXC9	HGNC	5130	protein_coding	YES	CCDS8869.1	ENSP00000302836	HXC9_HUMAN	.	UPI000012CF79	.	.	.	1/2	.	hmmpanther:PTHR24326:SF145,hmmpanther:PTHR24326,Pfam_domain:PF04617,PIRSF_domain:PIRSF037109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A175A|c.525C>T|6	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GACCTGGACCC	.	4	ESCA
SARNP	0	.	GRCh37	12	56184369	56184369	+	Silent	SNP	T	T	A	rs200101615	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.414A>T	p.%3D	p.S138S	ENST00000336133	8/11	78	52	26	75	75	0	SARNP,synonymous_variant,p.%3D,ENST00000552080,;SARNP,synonymous_variant,p.%3D,ENST00000444631,;SARNP,synonymous_variant,p.%3D,ENST00000336133,;RP11-762I7.5,synonymous_variant,p.%3D,ENST00000546837,;SARNP,synonymous_variant,p.%3D,ENST00000546604,;SARNP,3_prime_UTR_variant,,ENST00000552884,;SARNP,downstream_gene_variant,,ENST00000552207,;	A	ENSG00000205323	ENST00000336133	Transcript	synonymous_variant	469	414	138	S	tcA/tcT	rs200101615	.	.	-1	SARNP	HGNC	24432	protein_coding	YES	CCDS8892.1	ENSP00000337632	SARNP_HUMAN	.	UPI0000034E15	.	.	.	8/11	.	hmmpanther:PTHR21594	.	.	.	.	.	.	.	C:0	C:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGATGACAG	byCluster	5	ESCA
DGKA	0	.	GRCh37	12	56334726	56334726	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1063A>G	p.Met355Val	p.M355V	ENST00000331886	13/24	39	28	10	44	44	0	DGKA,missense_variant,p.Met274Val,ENST00000555218,;DGKA,missense_variant,p.Met355Val,ENST00000394147,;DGKA,missense_variant,p.Met355Val,ENST00000331886,;DGKA,missense_variant,p.Met355Val,ENST00000551156,;DGKA,downstream_gene_variant,,ENST00000557080,;DGKA,downstream_gene_variant,,ENST00000547015,;DGKA,downstream_gene_variant,,ENST00000549629,;DGKA,downstream_gene_variant,,ENST00000556001,;DGKA,downstream_gene_variant,,ENST00000553783,;DGKA,downstream_gene_variant,,ENST00000546878,;DGKA,downstream_gene_variant,,ENST00000551707,;DGKA,upstream_gene_variant,,ENST00000552903,;DGKA,downstream_gene_variant,,ENST00000432422,;DGKA,downstream_gene_variant,,ENST00000549368,;DGKA,downstream_gene_variant,,ENST00000555090,;DGKA,downstream_gene_variant,,ENST00000555025,;DGKA,non_coding_transcript_exon_variant,,ENST00000549079,;DGKA,downstream_gene_variant,,ENST00000549323,;DGKA,3_prime_UTR_variant,,ENST00000553084,;DGKA,3_prime_UTR_variant,,ENST00000402956,;DGKA,3_prime_UTR_variant,,ENST00000557180,;DGKA,non_coding_transcript_exon_variant,,ENST00000552478,;DGKA,non_coding_transcript_exon_variant,,ENST00000548047,;DGKA,non_coding_transcript_exon_variant,,ENST00000554434,;DGKA,non_coding_transcript_exon_variant,,ENST00000551296,;DGKA,non_coding_transcript_exon_variant,,ENST00000552652,;DGKA,non_coding_transcript_exon_variant,,ENST00000551739,;DGKA,downstream_gene_variant,,ENST00000546995,;DGKA,downstream_gene_variant,,ENST00000549085,;DGKA,downstream_gene_variant,,ENST00000549097,;DGKA,downstream_gene_variant,,ENST00000547324,;DGKA,upstream_gene_variant,,ENST00000551585,;DGKA,downstream_gene_variant,,ENST00000550484,;DGKA,downstream_gene_variant,,ENST00000547358,;DGKA,downstream_gene_variant,,ENST00000550888,;DGKA,downstream_gene_variant,,ENST00000549986,;DGKA,downstream_gene_variant,,ENST00000552335,;DGKA,downstream_gene_variant,,ENST00000556344,;DGKA,downstream_gene_variant,,ENST00000546895,;DGKA,downstream_gene_variant,,ENST00000551615,;DGKA,downstream_gene_variant,,ENST00000548407,;DGKA,downstream_gene_variant,,ENST00000548479,;DGKA,downstream_gene_variant,,ENST00000548549,;DGKA,downstream_gene_variant,,ENST00000547535,;DGKA,downstream_gene_variant,,ENST00000552687,;	G	ENSG00000065357	ENST00000331886	Transcript	missense_variant	1517	1063	355	M/V	Atg/Gtg	.	.	.	1	DGKA	HGNC	2849	protein_coding	YES	CCDS8896.1	ENSP00000328405	DGKA_HUMAN	G3V4I3_HUMAN,G3V327_HUMAN,F8W1M3_HUMAN,F8W1H7_HUMAN,F8VWX8_HUMAN,F8VNZ9_HUMAN,C9JM35_HUMAN	UPI000007417B	.	tolerated(0.32)	benign(0)	13/24	.	hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACCATGGAT	.	5	ESCA
CHD4	0	.	GRCh37	12	6682395	6682395	+	Missense_Mutation	SNP	C	C	T	rs763955970	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5402G>A	p.Arg1801Gln	p.R1801Q	ENST00000357008	38/40	51	31	20	50	50	0	CHD4,missense_variant,p.Arg1826Gln,ENST00000544484,;CHD4,missense_variant,p.Arg1794Gln,ENST00000544040,;CHD4,missense_variant,p.Arg1829Gln,ENST00000309577,;CHD4,missense_variant,p.Arg1801Gln,ENST00000357008,;NOP2,upstream_gene_variant,,ENST00000545915,;NOP2,upstream_gene_variant,,ENST00000399466,;NOP2,upstream_gene_variant,,ENST00000322166,;NOP2,upstream_gene_variant,,ENST00000536124,;NOP2,upstream_gene_variant,,ENST00000540228,;NOP2,upstream_gene_variant,,ENST00000382421,;NOP2,upstream_gene_variant,,ENST00000542867,;NOP2,upstream_gene_variant,,ENST00000545200,;NOP2,upstream_gene_variant,,ENST00000541778,;NOP2,upstream_gene_variant,,ENST00000545492,;NOP2,upstream_gene_variant,,ENST00000542015,;CHD4,upstream_gene_variant,,ENST00000535717,;NOP2,upstream_gene_variant,,ENST00000538697,;NOP2,upstream_gene_variant,,ENST00000538420,;NOP2,upstream_gene_variant,,ENST00000546053,;	T	ENSG00000111642	ENST00000357008	Transcript	missense_variant	5566	5402	1801	R/Q	cGg/cAg	rs763955970,COSM1248206,COSM1248207,COSM1248205	.	.	-1	CHD4	HGNC	1919	protein_coding	YES	CCDS8552.1	ENSP00000349508	CHD4_HUMAN	F5H6N4_HUMAN	UPI000013C8EF	.	deleterious(0)	probably_damaging(0.986)	38/40	.	Pfam_domain:PF08074	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCCGGCGC	byCluster	5	ESCA
KERA	0	.	GRCh37	12	91445036	91445036	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*87C>T	.	.	ENST00000266719	3/3	15	11	4	29	29	0	KERA,3_prime_UTR_variant,,ENST00000266719,;	A	ENSG00000139330	ENST00000266719	Transcript	3_prime_UTR_variant	1394	.	.	.	.	.	.	.	-1	KERA	HGNC	6309	protein_coding	YES	CCDS9037.1	ENSP00000266719	KERA_HUMAN	.	UPI000000161F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATGACTTG	.	5	ESCA
MRPS31	0	.	GRCh37	13	41345279	41345279	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-7C>G	.	.	ENST00000323563	1/7	22	14	8	36	36	0	MRPS31,5_prime_UTR_variant,,ENST00000323563,;MRPS31,upstream_gene_variant,,ENST00000435009,;	C	ENSG00000102738	ENST00000323563	Transcript	5_prime_UTR_variant	31	.	.	.	.	.	.	.	-1	MRPS31	HGNC	16632	protein_coding	YES	CCDS9372.1	ENSP00000315397	RT31_HUMAN	.	UPI000013D1D3	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGAGACACG	.	5	ESCA
LRCH1	0	.	GRCh37	13	47224409	47224409	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381G>T	p.%3D	p.L127L	ENST00000389797	2/20	51	25	26	49	49	0	LRCH1,synonymous_variant,p.%3D,ENST00000389797,;LRCH1,synonymous_variant,p.%3D,ENST00000311191,;LRCH1,synonymous_variant,p.%3D,ENST00000389798,;LRCH1,non_coding_transcript_exon_variant,,ENST00000443945,;	T	ENSG00000136141	ENST00000389797	Transcript	synonymous_variant	518	381	127	L	ctG/ctT	.	.	.	1	LRCH1	HGNC	20309	protein_coding	YES	CCDS53865.1	ENSP00000374447	LRCH1_HUMAN	C9JWE0_HUMAN,C9J5B8_HUMAN	UPI00015DFE06	.	.	.	2/20	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23155:SF434,hmmpanther:PTHR23155,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCTGTATCA	.	5	ESCA
RPS4XP16	0	.	GRCh37	13	52035402	52035402	+	RNA	SNP	C	C	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.761C>A	.	.	ENST00000595905	2/2	64	45	19	59	59	0	INTS6-AS1,intron_variant,,ENST00000597745,;INTS6-AS1,intron_variant,,ENST00000595997,;INTS6-AS1,intron_variant,,ENST00000601572,;INTS6-AS1,intron_variant,,ENST00000596050,;INTS6-AS1,intron_variant,,ENST00000602089,;INTS6-AS1,intron_variant,,ENST00000594604,;INTS6-AS1,intron_variant,,ENST00000593709,;INTS6-AS1,intron_variant,,ENST00000593429,;INTS6-AS1,intron_variant,,ENST00000601318,;INTS6-AS1,intron_variant,,ENST00000598864,;INTS6-AS1,intron_variant,,ENST00000593672,;INTS6-AS1,intron_variant,,ENST00000594358,;INTS6-AS1,intron_variant,,ENST00000595424,;INTS6-AS1,intron_variant,,ENST00000595435,;INTS6-AS1,intron_variant,,ENST00000434512,;INTS6-AS1,intron_variant,,ENST00000594488,;INTS6-AS1,intron_variant,,ENST00000600477,;INTS6-AS1,intron_variant,,ENST00000594959,;INTS6-AS1,intron_variant,,ENST00000593928,;INTS6-AS1,intron_variant,,ENST00000601034,;INTS6-AS1,intron_variant,,ENST00000596180,;INTS6-AS1,intron_variant,,ENST00000599315,;INTS6-AS1,intron_variant,,ENST00000596303,;RPS4XP16,non_coding_transcript_exon_variant,,ENST00000595905,;RPS4XP16,downstream_gene_variant,,ENST00000596904,;RPS4XP16,non_coding_transcript_exon_variant,,ENST00000427198,;	A	ENSG00000224892	ENST00000595905	Transcript	non_coding_transcript_exon_variant	761	.	.	.	.	.	.	.	1	RPS4XP16	HGNC	36365	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACCATTGC	.	5	ESCA
SLITRK5	0	.	GRCh37	13	88328551	88328551	+	Missense_Mutation	SNP	C	C	T	rs113077003	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.908C>T	p.Thr303Met	p.T303M	ENST00000325089	2/2	41	29	12	69	69	0	SLITRK5,missense_variant,p.Thr303Met,ENST00000325089,;SLITRK5,missense_variant,p.Thr62Met,ENST00000400028,;	T	ENSG00000165300	ENST00000325089	Transcript	missense_variant	1127	908	303	T/M	aCg/aTg	rs113077003	.	.	1	SLITRK5	HGNC	20295	protein_coding	YES	CCDS9465.1	ENSP00000366283	SLIK5_HUMAN	.	UPI000015F6F7	.	tolerated(0.1)	benign(0.018)	2/2	.	hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCACGGGGT	byCluster	5	ESCA
DYNC1H1	0	.	GRCh37	14	102486374	102486374	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8488C>T	p.%3D	p.L2830L	ENST00000360184	42/78	76	56	19	71	71	0	DYNC1H1,synonymous_variant,p.%3D,ENST00000360184,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000555204,;	T	ENSG00000197102	ENST00000360184	Transcript	synonymous_variant	8652	8488	2830	L	Ctg/Ttg	.	.	.	1	DYNC1H1	HGNC	2961	protein_coding	YES	CCDS9966.1	ENSP00000348965	DYHC1_HUMAN	Q92862_HUMAN,B4DSR6_HUMAN	UPI00001B515A	.	.	.	42/78	.	hmmpanther:PTHR10676:SF28,hmmpanther:PTHR10676,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTCTGCGT	.	5	ESCA
IGHG4	0	.	GRCh37	14	106091101	106091101	+	Silent	SNP	G	G	C	rs749197844	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696C>G	p.%3D	p.P232P	ENST00000390543	4/4	259	226	33	230	230	0	IGHG4,synonymous_variant,p.%3D,ENST00000390543,;	C	ENSG00000211892	ENST00000390543	Transcript	synonymous_variant	696	696	232	P	ccC/ccG	rs749197844	.	.	-1	IGHG4	HGNC	5528	IG_C_gene	YES	.	ENSP00000374985	IGHG4_HUMAN	.	UPI0000047190	.	.	.	4/4	.	Superfamily_domains:SSF48726,Gene3D:2.60.40.10,Pfam_domain:PF07654,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF72,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATGGGGGCAG	byFrequency	4	ESCA
OR4N2	0	.	GRCh37	14	20295854	20295854	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>A	p.Val83Met	p.V83M	ENST00000315947	1/1	332	244	87	282	282	0	OR4N2,missense_variant,p.Val83Met,ENST00000557677,;OR4N2,missense_variant,p.Val83Met,ENST00000315947,;OR4N2,missense_variant,p.Val83Met,ENST00000568211,;OR4N2,downstream_gene_variant,,ENST00000557414,;	A	ENSG00000176294	ENST00000315947	Transcript	missense_variant	247	247	83	V/M	Gtg/Atg	.	.	.	1	OR4N2	HGNC	14742	protein_coding	YES	CCDS32022.1	ENSP00000319601	OR4N2_HUMAN	H3BTD8_HUMAN,G3V4W1_HUMAN,G3V3W5_HUMAN	UPI000004A5DF	.	tolerated(0.14)	benign(0.08)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF155,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTGGTGGAC	.	5	ESCA
OR4K14	0	.	GRCh37	14	20482578	20482578	+	Missense_Mutation	SNP	A	A	C	rs200567872	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775T>G	p.Tyr259Asp	p.Y259D	ENST00000305045	1/1	48	25	23	40	40	0	OR4K14,missense_variant,p.Tyr259Asp,ENST00000305045,;	C	ENSG00000169484	ENST00000305045	Transcript	missense_variant	775	775	259	Y/D	Tat/Gat	rs200567872	.	.	-1	OR4K14	HGNC	15352	protein_coding	YES	CCDS32027.1	ENSP00000305011	OR4KE_HUMAN	.	UPI0000041CED	.	deleterious(0)	probably_damaging(0.992)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF31,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R261W|c.781C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATAAACAA	.	5	ESCA
SYNE2	0	.	GRCh37	14	64427584	64427584	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.788-659G>C	.	.	ENST00000358025	.	24	18	5	12	12	0	SYNE2,3_prime_UTR_variant,,ENST00000341472,;SYNE2,intron_variant,,ENST00000554584,;SYNE2,intron_variant,,ENST00000357395,;SYNE2,intron_variant,,ENST00000358025,;SYNE2,intron_variant,,ENST00000344113,;SYNE2,downstream_gene_variant,,ENST00000356081,;	C	ENSG00000054654	ENST00000358025	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	.	.	8/115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATAGAGAGACC	.	4	ESCA
SPTB	0	.	GRCh37	14	65289846	65289846	+	5'UTR	SNP	G	G	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-34C>A	.	.	ENST00000389722	1/35	45	20	24	34	34	0	SPTB,5_prime_UTR_variant,,ENST00000556626,;SPTB,5_prime_UTR_variant,,ENST00000389722,;SPTB,5_prime_UTR_variant,,ENST00000542895,;SPTB,upstream_gene_variant,,ENST00000389721,;SPTB,upstream_gene_variant,,ENST00000389720,;	T	ENSG00000070182	ENST00000389722	Transcript	5_prime_UTR_variant	21	.	.	.	.	.	.	.	-1	SPTB	HGNC	11274	protein_coding	YES	CCDS32099.1	ENSP00000374372	SPTB1_HUMAN	Q71VG2_HUMAN,Q71VG1_HUMAN,Q71VG0_HUMAN,Q71VF9_HUMAN,Q71VF8_HUMAN,Q59FP5_HUMAN,O14726_HUMAN,O14725_HUMAN	UPI000053030D	.	.	.	1/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCAGTCTTC	.	5	ESCA
OCA2	0	.	GRCh37	15	28116298	28116298	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2244+2T>G	.	p.X748_splice	ENST00000354638	.	28	17	10	36	36	0	OCA2,splice_donor_variant,,ENST00000354638,;OCA2,splice_donor_variant,,ENST00000353809,;	C	ENSG00000104044	ENST00000354638	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	OCA2	HGNC	8101	protein_coding	YES	CCDS10020.1	ENSP00000346659	P_HUMAN	C9JDV3_HUMAN	UPI000013D158	.	.	.	.	21/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTCACCATG	.	5	ESCA
TJP1	0	.	GRCh37	15	30000830	30000830	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4783A>G	p.Ile1595Val	p.I1595V	ENST00000346128	25/28	56	39	16	79	79	0	TJP1,missense_variant,p.Ile1595Val,ENST00000356107,;TJP1,missense_variant,p.Ile67Val,ENST00000400007,;TJP1,missense_variant,p.Ile1519Val,ENST00000400011,;TJP1,missense_variant,p.Ile1595Val,ENST00000346128,;TJP1,missense_variant,p.Ile1515Val,ENST00000545208,;TJP1,upstream_gene_variant,,ENST00000579042,;	C	ENSG00000104067	ENST00000346128	Transcript	missense_variant	5258	4783	1595	I/V	Atc/Gtc	.	.	.	-1	TJP1	HGNC	11827	protein_coding	YES	CCDS42007.1	ENSP00000281537	ZO1_HUMAN	.	UPI000013DC83	.	tolerated_low_confidence(0.37)	benign(0)	25/28	.	hmmpanther:PTHR13865,hmmpanther:PTHR13865:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.H1596Q|c.4788T>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGATAGAGA	.	5	ESCA
MEIS2	0	.	GRCh37	15	37386766	37386766	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451A>G	p.Ile151Val	p.I151V	ENST00000561208	5/12	41	24	16	44	44	0	MEIS2,start_lost,p.Ile1?,ENST00000606653,;MEIS2,missense_variant,p.Ile151Val,ENST00000424352,;MEIS2,missense_variant,p.Ile5Val,ENST00000219869,;MEIS2,missense_variant,p.Ile5Val,ENST00000560697,;MEIS2,missense_variant,p.Ile151Val,ENST00000559561,;MEIS2,missense_variant,p.Ile63Val,ENST00000397620,;MEIS2,missense_variant,p.Ile5Val,ENST00000560617,;MEIS2,missense_variant,p.Ile10Val,ENST00000607277,;MEIS2,missense_variant,p.Ile63Val,ENST00000558313,;MEIS2,missense_variant,p.Ile63Val,ENST00000397624,;MEIS2,missense_variant,p.Ile151Val,ENST00000338564,;MEIS2,missense_variant,p.Ile138Val,ENST00000340545,;MEIS2,missense_variant,p.Ile151Val,ENST00000444725,;MEIS2,missense_variant,p.Ile138Val,ENST00000559085,;MEIS2,missense_variant,p.Ile151Val,ENST00000382766,;MEIS2,missense_variant,p.Ile138Val,ENST00000557796,;MEIS2,missense_variant,p.Ile151Val,ENST00000561208,;RP11-128A17.1,upstream_gene_variant,,ENST00000559509,;MEIS2,missense_variant,p.Ile151Val,ENST00000314177,;MEIS2,3_prime_UTR_variant,,ENST00000560570,;MEIS2,non_coding_transcript_exon_variant,,ENST00000561163,;MEIS2,non_coding_transcript_exon_variant,,ENST00000559129,;MEIS2,upstream_gene_variant,,ENST00000561422,;	C	ENSG00000134138	ENST00000561208	Transcript	missense_variant	870	451	151	I/V	Ata/Gta	COSM3744572,COSM3744573	.	.	-1	MEIS2	HGNC	7001	protein_coding	YES	CCDS10044.1	ENSP00000453793	MEIS2_HUMAN	H0YKN2_HUMAN,H0YKE5_HUMAN	UPI000012EEBC	.	deleterious(0.01)	possibly_damaging(0.861)	5/12	.	hmmpanther:PTHR11850:SF47,hmmpanther:PTHR11850	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTATTGCTT	.	5	ESCA
MGA	0	.	GRCh37	15	42003263	42003263	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2800C>T	p.%3D	p.L934L	ENST00000219905	8/24	43	30	12	42	42	0	MGA,synonymous_variant,p.%3D,ENST00000219905,;MGA,synonymous_variant,p.%3D,ENST00000563576,;MGA,synonymous_variant,p.%3D,ENST00000570161,;MGA,synonymous_variant,p.%3D,ENST00000545763,;MGA,synonymous_variant,p.%3D,ENST00000389936,;MGA,synonymous_variant,p.%3D,ENST00000566718,;MGA,synonymous_variant,p.%3D,ENST00000566586,;	T	ENSG00000174197	ENST00000219905	Transcript	synonymous_variant	2981	2800	934	L	Cta/Tta	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	.	.	8/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTCTAGGA	.	5	ESCA
SPTBN5	0	.	GRCh37	15	42155939	42155939	+	Missense_Mutation	SNP	C	C	T	rs753634857	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7112G>A	p.Arg2371Gln	p.R2371Q	ENST00000320955	41/68	42	31	11	32	32	0	SPTBN5,missense_variant,p.Arg2371Gln,ENST00000320955,;MIR4310,downstream_gene_variant,,ENST00000582950,;	T	ENSG00000137877	ENST00000320955	Transcript	missense_variant	7340	7112	2371	R/Q	cGa/cAa	rs753634857,COSM1227507	.	.	-1	SPTBN5	HGNC	15680	protein_coding	YES	CCDS61599.1	ENSP00000317790	SPTN5_HUMAN	.	UPI0000E59BE4	.	.	benign(0.004)	41/68	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF249,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTCGGGAC	byFrequency	5	ESCA
DIS3L	0	.	GRCh37	15	66610849	66610849	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057G>T	p.Glu353Ter	p.E353*	ENST00000319212	8/17	80	50	30	82	82	0	DIS3L,stop_gained,p.Glu353Ter,ENST00000319212,;DIS3L,stop_gained,p.Glu270Ter,ENST00000319194,;DIS3L,intron_variant,,ENST00000441424,;DIS3L,downstream_gene_variant,,ENST00000525109,;RP11-352G18.2,intron_variant,,ENST00000565993,;DIS3L,3_prime_UTR_variant,,ENST00000530537,;DIS3L,non_coding_transcript_exon_variant,,ENST00000565281,;DIS3L,non_coding_transcript_exon_variant,,ENST00000564909,;DIS3L,intron_variant,,ENST00000524795,;	T	ENSG00000166938	ENST00000319212	Transcript	stop_gained	1107	1057	353	E/*	Gaa/Taa	COSM555612,COSM555611	.	.	1	DIS3L	HGNC	28698	protein_coding	YES	CCDS45286.1	ENSP00000321711	DI3L1_HUMAN	E9PS35_HUMAN,E9PIL0_HUMAN,E9PI27_HUMAN,E9PI20_HUMAN	UPI000162779D	.	.	.	8/17	.	hmmpanther:PTHR23355,hmmpanther:PTHR23355:SF30	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAAGAAGAG	.	5	ESCA
IREB2	0	.	GRCh37	15	78790410	78790410	+	Silent	SNP	G	G	A	rs144816277	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2817G>A	p.%3D	p.S939S	ENST00000258886	22/22	43	37	5	41	41	0	IREB2,synonymous_variant,p.%3D,ENST00000258886,;IREB2,downstream_gene_variant,,ENST00000559091,;IREB2,3_prime_UTR_variant,,ENST00000558570,;	A	ENSG00000136381	ENST00000258886	Transcript	synonymous_variant	2966	2817	939	S	tcG/tcA	rs144816277	.	.	1	IREB2	HGNC	6115	protein_coding	YES	CCDS10302.1	ENSP00000258886	IREB2_HUMAN	H0YLE0_HUMAN	UPI00001C1F8E	.	.	.	22/22	.	hmmpanther:PTHR11670:SF31,hmmpanther:PTHR11670,Gene3D:3.20.19.10,TIGRFAM_domain:TIGR01341,Superfamily_domains:SSF52016	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S939L|c.2816C>T|3	RADIA|MUTECT|MUSE|VARSCANS	GCTTCGTTTGA	byCluster|by1000G	4	ESCA
WHAMM	0	.	GRCh37	15	83503179	83503179	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*891T>G	.	.	ENST00000286760	10/10	11	7	4	10	10	0	WHAMM,3_prime_UTR_variant,,ENST00000286760,;	G	ENSG00000156232	ENST00000286760	Transcript	3_prime_UTR_variant	3420	.	.	.	.	.	.	.	1	WHAMM	HGNC	30493	protein_coding	YES	CCDS45333.1	ENSP00000286760	WHAMM_HUMAN	.	UPI00001C1F94	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGATGTCAAGA	.	2	ESCA
FOPNL	0	.	GRCh37	16	15977900	15977900	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.191A>C	p.Asn64Thr	p.N64T	ENST00000255759	2/5	65	44	20	64	64	0	FOPNL,missense_variant,p.Asn64Thr,ENST00000573968,;FOPNL,missense_variant,p.Asn37Thr,ENST00000575938,;FOPNL,missense_variant,p.Asn64Thr,ENST00000573396,;FOPNL,missense_variant,p.Asn64Thr,ENST00000255759,;FOPNL,missense_variant,p.Asn64Thr,ENST00000575073,;FOPNL,missense_variant,p.Asn64Thr,ENST00000573429,;FOPNL,intron_variant,,ENST00000575744,;CTA-972D3.2,upstream_gene_variant,,ENST00000573856,;FOPNL,missense_variant,p.Asn64Thr,ENST00000572415,;FOPNL,missense_variant,p.Asn64Thr,ENST00000573087,;	G	ENSG00000133393	ENST00000255759	Transcript	missense_variant	221	191	64	N/T	aAc/aCc	.	.	.	-1	FOPNL	HGNC	26435	protein_coding	YES	CCDS10567.1	ENSP00000255759	FOPNL_HUMAN	I3L2N4_HUMAN	UPI000006F1B6	.	deleterious(0)	probably_damaging(0.998)	2/5	.	SMART_domains:SM00667,Pfam_domain:PF09398,hmmpanther:PTHR15431,PROSITE_profiles:PS50896	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTGTTGAAT	.	5	ESCA
NOXO1	0	.	GRCh37	16	2030148	2030148	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451C>G	p.Leu151Val	p.L151V	ENST00000397280	5/8	18	12	6	18	18	0	NOXO1,missense_variant,p.Leu145Val,ENST00000354249,;NOXO1,missense_variant,p.Leu150Val,ENST00000566005,;NOXO1,missense_variant,p.Leu151Val,ENST00000397280,;NOXO1,missense_variant,p.Leu146Val,ENST00000356120,;TBL3,3_prime_UTR_variant,,ENST00000568546,;AC005606.1,upstream_gene_variant,,ENST00000598236,;TBL3,downstream_gene_variant,,ENST00000332704,;GFER,upstream_gene_variant,,ENST00000248114,;GFER,upstream_gene_variant,,ENST00000567719,;NOXO1,downstream_gene_variant,,ENST00000567471,;GFER,upstream_gene_variant,,ENST00000561710,;GFER,upstream_gene_variant,,ENST00000569451,;AC005606.14,downstream_gene_variant,,ENST00000564438,;NOXO1,non_coding_transcript_exon_variant,,ENST00000563181,;TBL3,downstream_gene_variant,,ENST00000569792,;TBL3,downstream_gene_variant,,ENST00000564171,;TBL3,downstream_gene_variant,,ENST00000567615,;TBL3,downstream_gene_variant,,ENST00000569628,;GFER,upstream_gene_variant,,ENST00000565658,;NOXO1,upstream_gene_variant,,ENST00000569739,;	C	ENSG00000196408	ENST00000397280	Transcript	missense_variant	455	451	151	L/V	Ctt/Gtt	.	.	.	-1	NOXO1	HGNC	19404	protein_coding	YES	CCDS42101.1	ENSP00000380450	NOXO1_HUMAN	.	UPI000006E194	.	tolerated(0.28)	benign(0.002)	5/8	.	hmmpanther:PTHR15706:SF1,hmmpanther:PTHR15706	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAAGAGGCT	.	5	ESCA
DNAH3	0	.	GRCh37	16	21033361	21033361	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5708A>T	p.Lys1903Ile	p.K1903I	ENST00000261383	40/62	32	26	6	24	24	0	DNAH3,missense_variant,p.Lys1903Ile,ENST00000261383,;DNAH3,intron_variant,,ENST00000415178,;DNAH3,non_coding_transcript_exon_variant,,ENST00000572640,;DNAH3,intron_variant,,ENST00000572931,;	A	ENSG00000158486	ENST00000261383	Transcript	missense_variant	5708	5708	1903	K/I	aAa/aTa	.	.	.	-1	DNAH3	HGNC	2949	protein_coding	YES	CCDS10594.1	ENSP00000261383	DYH3_HUMAN	.	UPI00001100F2	.	deleterious(0)	benign(0.439)	40/62	.	hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAATTTACAA	.	5	ESCA
FBXL19	0	.	GRCh37	16	30958499	30958499	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2033C>T	p.Pro678Leu	p.P678L	ENST00000380310	11/11	39	35	4	51	51	0	FBXL19,missense_variant,p.Pro542Leu,ENST00000565690,;FBXL19,missense_variant,p.Pro570Leu,ENST00000427128,;FBXL19,missense_variant,p.Pro366Leu,ENST00000471231,;FBXL19,missense_variant,p.Pro678Leu,ENST00000380310,;FBXL19,missense_variant,p.Pro658Leu,ENST00000562319,;FBXL19,missense_variant,p.Pro658Leu,ENST00000338343,;FBXL19,synonymous_variant,p.%3D,ENST00000565939,;FBXL19,intron_variant,,ENST00000566320,;ORAI3,upstream_gene_variant,,ENST00000318663,;ORAI3,upstream_gene_variant,,ENST00000566237,;ORAI3,upstream_gene_variant,,ENST00000562699,;AC135048.13,upstream_gene_variant,,ENST00000562642,;AC135048.13,upstream_gene_variant,,ENST00000566056,;ORAI3,upstream_gene_variant,,ENST00000563161,;	T	ENSG00000099364	ENST00000380310	Transcript	missense_variant	2191	2033	678	P/L	cCc/cTc	.	.	.	1	FBXL19	HGNC	25300	protein_coding	YES	CCDS45465.1	ENSP00000369666	FXL19_HUMAN	H3BVB1_HUMAN,H3BQP6_HUMAN,H3BPZ0_HUMAN	UPI00015C725E	.	tolerated(0.13)	probably_damaging(0.927)	11/11	.	hmmpanther:PTHR23125:SF254,hmmpanther:PTHR23125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CGGGCCCCCTG	.	2	ESCA
POLR2C	0	.	GRCh37	16	57505846	57505846	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*815A>G	.	.	ENST00000219252	9/9	28	19	9	36	36	0	POLR2C,3_prime_UTR_variant,,ENST00000219252,;DOK4,downstream_gene_variant,,ENST00000566588,;DOK4,downstream_gene_variant,,ENST00000340099,;DOK4,downstream_gene_variant,,ENST00000564378,;DOK4,downstream_gene_variant,,ENST00000562737,;DOK4,downstream_gene_variant,,ENST00000567276,;DOK4,downstream_gene_variant,,ENST00000566936,;DOK4,downstream_gene_variant,,ENST00000569010,;DOK4,downstream_gene_variant,,ENST00000569538,;DOK4,downstream_gene_variant,,ENST00000569548,;DOK4,downstream_gene_variant,,ENST00000567175,;DOK4,downstream_gene_variant,,ENST00000562008,;DOK4,downstream_gene_variant,,ENST00000569250,;DOK4,downstream_gene_variant,,ENST00000568617,;DOK4,downstream_gene_variant,,ENST00000566705,;DOK4,downstream_gene_variant,,ENST00000567214,;DOK4,downstream_gene_variant,,ENST00000561918,;POLR2C,downstream_gene_variant,,ENST00000564651,;DOK4,downstream_gene_variant,,ENST00000563483,;POLR2C,downstream_gene_variant,,ENST00000563589,;POLR2C,downstream_gene_variant,,ENST00000563115,;DOK4,downstream_gene_variant,,ENST00000561659,;POLR2C,downstream_gene_variant,,ENST00000567982,;POLR2C,downstream_gene_variant,,ENST00000562953,;POLR2C,downstream_gene_variant,,ENST00000562599,;	G	ENSG00000102978	ENST00000219252	Transcript	3_prime_UTR_variant	1981	.	.	.	.	.	.	.	1	POLR2C	HGNC	9189	protein_coding	YES	CCDS10782.1	ENSP00000219252	RPB3_HUMAN	Q6FGR6_HUMAN	UPI00000012C1	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAAGGATA	.	5	ESCA
MMP15	0	.	GRCh37	16	58072241	58072241	+	Missense_Mutation	SNP	G	G	A	rs199590044	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383G>A	p.Arg128His	p.R128H	ENST00000219271	3/10	115	80	35	112	111	1	MMP15,missense_variant,p.Arg128His,ENST00000219271,;MMP15,upstream_gene_variant,,ENST00000570065,;	A	ENSG00000102996	ENST00000219271	Transcript	missense_variant	1168	383	128	R/H	cGt/cAt	rs199590044	.	.	1	MMP15	HGNC	7161	protein_coding	YES	CCDS10792.1	ENSP00000219271	MMP15_HUMAN	.	UPI000003DC75	.	deleterious(0)	probably_damaging(0.994)	3/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10201:SF25,hmmpanther:PTHR10201,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGCGTCGGA	byCluster|by1000G	5	ESCA
ZNF23	0	.	GRCh37	16	71482777	71482777	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1151G>C	p.Arg384Thr	p.R384T	ENST00000393539	6/6	82	59	23	96	96	0	ZNF23,missense_variant,p.Arg326Thr,ENST00000428724,;ZNF23,missense_variant,p.Arg384Thr,ENST00000393539,;ZNF23,missense_variant,p.Arg384Thr,ENST00000357254,;ZNF23,missense_variant,p.Arg384Thr,ENST00000417828,;ZNF23,missense_variant,p.Arg326Thr,ENST00000564528,;ZNF23,3_prime_UTR_variant,,ENST00000358700,;ZNF23,3_prime_UTR_variant,,ENST00000497160,;ZNF23,downstream_gene_variant,,ENST00000565718,;ZNF23,downstream_gene_variant,,ENST00000567340,;ZNF23,non_coding_transcript_exon_variant,,ENST00000539742,;AC010547.9,3_prime_UTR_variant,,ENST00000561908,;ZNF23,non_coding_transcript_exon_variant,,ENST00000576258,;	G	ENSG00000167377	ENST00000393539	Transcript	missense_variant	1965	1151	384	R/T	aGa/aCa	COSM1233719	.	.	-1	ZNF23	HGNC	13023	protein_coding	YES	CCDS10900.1	ENSP00000377171	ZNF23_HUMAN	Q8NDP5_HUMAN,H3BPE6_HUMAN	UPI000013C406	.	deleterious(0.03)	possibly_damaging(0.727)	6/6	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF180,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATTCTCTGA	.	5	ESCA
DPEP1	0	.	GRCh37	16	89704484	89704484	+	Missense_Mutation	SNP	G	G	A	rs147872447	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1090G>A	p.Glu364Lys	p.E364K	ENST00000393092	11/11	83	75	7	85	85	0	DPEP1,missense_variant,p.Glu364Lys,ENST00000261615,;DPEP1,missense_variant,p.Glu364Lys,ENST00000393092,;DPEP1,missense_variant,p.Glu364Lys,ENST00000421184,;DPEP1,downstream_gene_variant,,ENST00000570029,;DPEP1,downstream_gene_variant,,ENST00000568281,;DPEP1,non_coding_transcript_exon_variant,,ENST00000564281,;DPEP1,non_coding_transcript_exon_variant,,ENST00000564645,;DPEP1,downstream_gene_variant,,ENST00000561484,;DPEP1,downstream_gene_variant,,ENST00000565249,;	A	ENSG00000015413	ENST00000393092	Transcript	missense_variant	1381	1090	364	E/K	Gag/Aag	rs147872447	.	.	1	DPEP1	HGNC	3002	protein_coding	YES	CCDS10982.1	ENSP00000376807	DPEP1_HUMAN	H3BQS5_HUMAN,H3BP43_HUMAN	UPI000006DF95	.	tolerated(0.7)	benign(0.245)	11/11	.	PROSITE_profiles:PS51365,hmmpanther:PTHR10443:SF17,hmmpanther:PTHR10443,Gene3D:3.20.20.140,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	A:0.0002	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCCGAGGAG	byCluster	4	ESCA
SPATA33	0	.	GRCh37	16	89735825	89735825	+	Missense_Mutation	SNP	G	G	A	rs773277966	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340G>A	p.Glu114Lys	p.E114K	ENST00000301031	3/3	51	43	8	77	77	0	SPATA33,missense_variant,p.Glu115Lys,ENST00000579310,;SPATA33,missense_variant,p.Glu114Lys,ENST00000301031,;SPATA33,missense_variant,p.Glu121Lys,ENST00000566204,;SPATA33,3_prime_UTR_variant,,ENST00000457689,;SPATA33,3_prime_UTR_variant,,ENST00000565890,;SPATA33,downstream_gene_variant,,ENST00000567827,;	A	ENSG00000167523	ENST00000301031	Transcript	missense_variant	340	340	114	E/K	Gag/Aag	rs773277966	.	.	1	SPATA33	HGNC	26463	protein_coding	YES	CCDS10983.1	ENSP00000301031	SPT33_HUMAN	.	UPI000007159D	.	deleterious(0)	probably_damaging(0.981)	3/3	.	Pfam_domain:PF15382	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCGGGAGCCG	byFrequency	5	ESCA
VPS9D1	0	.	GRCh37	16	89785741	89785741	+	Intron	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100-231C>G	.	.	ENST00000389386	.	40	22	17	45	45	0	VPS9D1,5_prime_UTR_variant,,ENST00000561976,;VPS9D1,intron_variant,,ENST00000389386,;ZNF276,upstream_gene_variant,,ENST00000446326,;ZNF276,upstream_gene_variant,,ENST00000568064,;ZNF276,upstream_gene_variant,,ENST00000443381,;ZNF276,upstream_gene_variant,,ENST00000289816,;VPS9D1-AS1,downstream_gene_variant,,ENST00000562866,;VPS9D1-AS1,downstream_gene_variant,,ENST00000562298,;VPS9D1,intron_variant,,ENST00000563798,;ZNF276,upstream_gene_variant,,ENST00000569426,;ZNF276,upstream_gene_variant,,ENST00000568295,;ZNF276,upstream_gene_variant,,ENST00000563983,;ZNF276,upstream_gene_variant,,ENST00000561536,;ZNF276,upstream_gene_variant,,ENST00000562530,;ZNF276,upstream_gene_variant,,ENST00000563541,;	C	ENSG00000075399	ENST00000389386	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	VPS9D1	HGNC	13526	protein_coding	YES	CCDS42220.1	ENSP00000374037	VP9D1_HUMAN	H3BM58_HUMAN	UPI00001FF749	.	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTGAGAGA	.	5	ESCA
RP11-744K17.9	0	.	GRCh37	17	21909575	21909575	+	RNA	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.300G>C	.	.	ENST00000581223	2/2	26	18	8	27	27	0	RP11-744K17.9,non_coding_transcript_exon_variant,,ENST00000581223,;RP11-1109M24.8,upstream_gene_variant,,ENST00000578438,;RP11-1109M24.9,upstream_gene_variant,,ENST00000582046,;RP11-1109M24.7,downstream_gene_variant,,ENST00000582156,;RP11-1109M24.11,upstream_gene_variant,,ENST00000583831,;	C	ENSG00000266795	ENST00000581223	Transcript	non_coding_transcript_exon_variant	300	.	.	.	.	.	.	.	1	RP11-744K17.9	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGAGGAA	.	5	ESCA
CCL7	0	.	GRCh37	17	32598826	32598826	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5T>C	.	.	ENST00000378569	3/3	64	53	11	71	71	0	CCL7,3_prime_UTR_variant,,ENST00000394627,;CCL7,3_prime_UTR_variant,,ENST00000394630,;CCL7,3_prime_UTR_variant,,ENST00000200307,;CCL7,3_prime_UTR_variant,,ENST00000378569,;	C	ENSG00000108688	ENST00000378569	Transcript	3_prime_UTR_variant	375	.	.	.	.	.	.	.	1	CCL7	HGNC	10634	protein_coding	YES	CCDS11278.1	ENSP00000367832	CCL7_HUMAN	.	UPI0000047516	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACATTCATGA	.	5	ESCA
FAM187A	0	.	GRCh37	17	42981907	42981907	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.710G>A	p.Arg237Gln	p.R237Q	ENST00000331733	4/4	29	16	13	40	40	0	FAM187A,missense_variant,p.Arg237Gln,ENST00000331733,;FAM187A,missense_variant,p.Arg237Gln,ENST00000412523,;CCDC103,3_prime_UTR_variant,,ENST00000417826,;CCDC103,downstream_gene_variant,,ENST00000410027,;CCDC103,downstream_gene_variant,,ENST00000357776,;GFAP,downstream_gene_variant,,ENST00000253408,;GFAP,downstream_gene_variant,,ENST00000591880,;EFTUD2,upstream_gene_variant,,ENST00000426333,;CCDC103,downstream_gene_variant,,ENST00000577339,;GFAP,downstream_gene_variant,,ENST00000586125,;CCDC103,downstream_gene_variant,,ENST00000410006,;GFAP,downstream_gene_variant,,ENST00000588735,;AC015936.3,non_coding_transcript_exon_variant,,ENST00000441312,;GFAP,downstream_gene_variant,,ENST00000592706,;GFAP,downstream_gene_variant,,ENST00000592065,;GFAP,downstream_gene_variant,,ENST00000588640,;GFAP,downstream_gene_variant,,ENST00000589701,;GFAP,downstream_gene_variant,,ENST00000585543,;	A	ENSG00000214447	ENST00000331733	Transcript	missense_variant	2546	710	237	R/Q	cGg/cAg	.	.	.	1	FAM187A	HGNC	35153	protein_coding	YES	.	ENSP00000329499	F187A_HUMAN	.	UPI000013E667	.	tolerated(0.12)	benign(0.017)	4/4	.	hmmpanther:PTHR32178:SF3,hmmpanther:PTHR32178	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCGGAGCT	.	5	ESCA
SPOP	0	.	GRCh37	17	47688654	47688654	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.646G>A	p.Ala216Thr	p.A216T	ENST00000393331	8/12	74	49	25	72	72	0	SPOP,missense_variant,p.Ala216Thr,ENST00000393331,;SPOP,missense_variant,p.Ala216Thr,ENST00000504102,;SPOP,missense_variant,p.Ala216Thr,ENST00000347630,;SPOP,missense_variant,p.Ala216Thr,ENST00000509079,;SPOP,missense_variant,p.Ala216Thr,ENST00000505581,;SPOP,missense_variant,p.Ala216Thr,ENST00000503676,;SPOP,missense_variant,p.Ala216Thr,ENST00000393328,;SPOP,downstream_gene_variant,,ENST00000507970,;SPOP,3_prime_UTR_variant,,ENST00000509869,;SPOP,non_coding_transcript_exon_variant,,ENST00000504889,;SPOP,downstream_gene_variant,,ENST00000506399,;	T	ENSG00000121067	ENST00000393331	Transcript	missense_variant	1117	646	216	A/T	Gct/Act	.	.	.	-1	SPOP	HGNC	11254	protein_coding	YES	CCDS11551.1	ENSP00000377004	SPOP_HUMAN	D6RIS7_HUMAN,D6RGZ4_HUMAN,D6RFL7_HUMAN,D6RDV6_HUMAN,D6RDG8_HUMAN,D6RD94_HUMAN,D6RBH6_HUMAN,D6RA79_HUMAN,B4DUE7_HUMAN,B4DEE4_HUMAN	UPI0000003F5C	.	deleterious(0)	probably_damaging(0.928)	8/12	.	PROSITE_profiles:PS50097,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF97,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATAGCCTTGT	.	5	ESCA
MPO	0	.	GRCh37	17	56357257	56357257	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.367C>T	p.%3D	p.L123L	ENST00000225275	3/12	51	33	18	57	57	0	MPO,synonymous_variant,p.%3D,ENST00000340482,;MPO,synonymous_variant,p.%3D,ENST00000225275,;MPO,non_coding_transcript_exon_variant,,ENST00000580005,;MPO,upstream_gene_variant,,ENST00000578493,;MPO,upstream_gene_variant,,ENST00000581022,;	A	ENSG00000005381	ENST00000225275	Transcript	synonymous_variant	544	367	123	L	Cta/Tta	.	.	.	-1	MPO	HGNC	7218	protein_coding	YES	CCDS11604.1	ENSP00000225275	PERM_HUMAN	.	UPI0000131634	.	.	.	3/12	.	hmmpanther:PTHR11475:SF46,hmmpanther:PTHR11475	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTAGAGCCA	.	5	ESCA
INTS2	0	.	GRCh37	17	59955383	59955383	+	Missense_Mutation	SNP	G	G	A	rs754468707	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2345C>T	p.Ser782Phe	p.S782F	ENST00000444766	18/25	51	31	19	44	44	0	INTS2,missense_variant,p.Ser782Phe,ENST00000444766,;INTS2,missense_variant,p.Ser774Phe,ENST00000251334,;Y_RNA,upstream_gene_variant,,ENST00000365491,;INTS2,non_coding_transcript_exon_variant,,ENST00000583822,;INTS2,non_coding_transcript_exon_variant,,ENST00000584967,;	A	ENSG00000108506	ENST00000444766	Transcript	missense_variant	2421	2345	782	S/F	tCt/tTt	rs754468707	.	.	-1	INTS2	HGNC	29241	protein_coding	YES	CCDS45750.1	ENSP00000414237	INT2_HUMAN	J3KRH0_HUMAN,J3KMZ7_HUMAN	UPI0000E5A03A	.	deleterious(0.02)	probably_damaging(0.974)	18/25	.	Pfam_domain:PF14750	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCAGAGAGT	.	5	ESCA
hsa-mir-6080	0	.	GRCh37	17	62754401	62754401	+	RNA	SNP	C	C	T	rs766341020	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1800G>A	.	.	ENST00000400873	8/13	71	45	26	113	113	0	hsa-mir-6080,non_coding_transcript_exon_variant,,ENST00000578492,;hsa-mir-6080,non_coding_transcript_exon_variant,,ENST00000400873,;hsa-mir-6080,downstream_gene_variant,,ENST00000579125,;RP13-104F24.1,non_coding_transcript_exon_variant,,ENST00000584190,;RP11-927P21.5,downstream_gene_variant,,ENST00000579209,;	T	ENSG00000215769	ENST00000400873	Transcript	non_coding_transcript_exon_variant	1800	.	.	.	.	rs766341020	.	.	-1	hsa-mir-6080	miRBase	.	processed_transcript	YES	.	.	.	.	.	.	.	.	8/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATCAGGAA	byFrequency	5	ESCA
PLEKHM1P	0	.	GRCh37	17	62796231	62796231	+	RNA	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1923A>G	.	.	ENST00000578036	7/18	50	44	5	59	59	0	PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000578036,;PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000582986,;PLEKHM1P,downstream_gene_variant,,ENST00000580919,;PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000582201,;PLEKHM1P,downstream_gene_variant,,ENST00000440036,;	C	ENSG00000214176	ENST00000578036	Transcript	non_coding_transcript_exon_variant	1923	.	.	.	.	.	.	.	-1	PLEKHM1P	HGNC	35411	processed_transcript	.	.	.	.	.	.	.	.	.	7/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGTTTTCATCC	.	3	ESCA
ALOX12	0	.	GRCh37	17	6904970	6904970	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1001C>G	p.Ser334Ter	p.S334*	ENST00000251535	8/14	65	44	20	63	63	0	ALOX12,stop_gained,p.Ser334Ter,ENST00000251535,;AC027763.2,3_prime_UTR_variant,,ENST00000399540,;AC027763.2,intron_variant,,ENST00000399541,;AC027763.2,intron_variant,,ENST00000575889,;AC027763.2,intron_variant,,ENST00000574377,;AC027763.2,intron_variant,,ENST00000575727,;ALOX12,downstream_gene_variant,,ENST00000480801,;AC027763.2,downstream_gene_variant,,ENST00000573939,;RP11-589P10.7,intron_variant,,ENST00000572547,;AC027763.2,intron_variant,,ENST00000572385,;AC027763.2,intron_variant,,ENST00000571010,;AC027763.2,intron_variant,,ENST00000570562,;	G	ENSG00000108839	ENST00000251535	Transcript	stop_gained	1054	1001	334	S/*	tCa/tGa	.	.	.	1	ALOX12	HGNC	429	protein_coding	YES	CCDS11084.1	ENSP00000251535	LOX12_HUMAN	.	UPI000013CD03	.	.	.	8/14	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF48484,Pfam_domain:PF00305,Gene3D:3.10.450.60,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF4,PROSITE_profiles:PS51393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCAGACC	.	5	ESCA
TP53	0	.	GRCh37	17	7572939	7572940	+	Frame_Shift_Del	DEL	AG	AG	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1169_1170delCTinsA	p.Pro390GlnfsTer32	p.P390Qfs*32	ENST00000269305	11/11	66	49	17	45	45	0	TP53,frameshift_variant,p.Pro390GlnfsTer32,ENST00000445888,;TP53,frameshift_variant,p.Pro390GlnfsTer32,ENST00000269305,;TP53,3_prime_UTR_variant,,ENST00000420246,;TP53,3_prime_UTR_variant,,ENST00000576024,;TP53,3_prime_UTR_variant,,ENST00000455263,;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	1359-1360	1169-1170	390	P/X	cCT/cA	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	11/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	TGAGTCAGGCCCT	.	5	ESCA
TP53	0	.	GRCh37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	7/11	60	46	14	59	59	0	TP53,missense_variant,p.Arg248Gln,ENST00000413465,;TP53,missense_variant,p.Arg248Gln,ENST00000420246,;TP53,missense_variant,p.Arg248Gln,ENST00000269305,;TP53,missense_variant,p.Arg116Gln,ENST00000509690,;TP53,missense_variant,p.Arg248Gln,ENST00000359597,;TP53,missense_variant,p.Arg155Gln,ENST00000514944,;TP53,missense_variant,p.Arg248Gln,ENST00000445888,;TP53,missense_variant,p.Arg248Gln,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	933	743	248	R/Q	cGg/cAg	rs11540652,CM920675,TP53_g.13380G>A,TP53_g.13380G>C,TP53_g.13380G>T,TP53_g.13380del,COSM10662,COSM11491,COSM6549,COSM46135,COSM340105,COSM99602,COSM241995,COSM99020,COSM241994,COSM340106,COSM3356964,COSM3378346,COSM1640830,COSM1646857,COSM1646858,COSM99021,COSM241996,COSM340107	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25032700,20377871,18798306,15450681,25105660,21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R248Q|c.743G>A|113,SITE|p.R248Q|c.743G>A|633,SITE|p.R248Q|c.743G>A|64,SITE|p.R248Q|c.743G>A|42,SITE|p.R155Q|c.464G>A|114,SITE|p.R248Q|c.743G>A|110,CODON|p.0?|c.1_1182del1182|6,CODON|p.R248Q|c.743_744GG>AA|5,CODON|p.R248R|c.744G>A|5,CODON|p.R248W|c.741_742CC>TT|15,CODON|p.R248L|c.743G>T|7,CODON|p.R248L|c.743G>T|12,CODON|p.R155L|c.464G>T|12,CODON|p.R155P|c.464G>C|5,CODON|p.R248P|c.743G>C|17,CODON|p.R248L|c.743G>T|12,CODON|p.R248P|c.743G>C|5,CODON|p.R248L|c.743G>T|74,CODON|p.R248P|c.743G>C|5,BUFFER|p.L252_I254delLTI|c.754_762delCTCACCATC|4,BUFFER|p.L252_I254delLTI|c.751_759delATCCTCACC|4,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252delL|c.754_756delCTC|9,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252fs*93|c.754delC|5,BUFFER|p.L252F|c.754C>T|10,BUFFER|p.I251I|c.753C>A|3,BUFFER|p.I251N|c.752T>A|9,BUFFER|p.I251T|c.752T>C|6,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251S|c.752T>G|12,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251fs*94|c.751delA|6,BUFFER|p.I251L|c.751A>C|3,BUFFER|p.I251F|c.751A>T|8,BUFFER|p.P250P|c.750C>T|4,BUFFER|p.P250F|c.748_749CC>TT|3,BUFFER|p.I251fs*94|c.748delC|4,BUFFER|p.P250L|c.749C>T|49,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250L|c.749C>T|8,BUFFER|p.P250L|c.749C>T|6,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250S|c.748C>T|12,BUFFER|p.R249fs*96|c.746delG|4,BUFFER|p.R249S|c.747G>T|31,BUFFER|p.R249S|c.747G>C|22,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|15,BUFFER|p.R249R|c.747G>A|6,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|314,BUFFER|p.R249S|c.747G>T|30,BUFFER|p.R249T|c.746G>C|3,BUFFER|p.R249M|c.746G>T|8,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249K|c.746G>A|17,BUFFER|p.R249M|c.746G>T|4,BUFFER|p.R249T|c.746G>C|20,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249M|c.746G>T|35,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87,BUFFER|p.N247N|c.741C>T|10,BUFFER|p.N247I|c.740A>T|7,BUFFER|p.N154I|c.461A>T|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247T|c.740A>C|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247S|c.740A>G|7,BUFFER|p.N247D|c.739A>G|5,BUFFER|p.N247Y|c.739A>T|3,BUFFER|p.M153I|c.459G>C|3,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>A|21,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>C|4,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246R|c.737T>G|12,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246T|c.737T>C|8,BUFFER|p.M153R|c.458T>G|3,BUFFER|p.M246K|c.737T>A|7,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246L|c.736A>T|3,BUFFER|p.M153V|c.457A>G|7,BUFFER|p.M246V|c.736A>G|3,BUFFER|p.M246V|c.736A>G|35,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246V|c.736A>G|4,BUFFER|p.G245G|c.735C>T|5,BUFFER|p.G245D|c.734G>A|10,BUFFER|p.G245V|c.734G>T|3,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245A|c.734G>C|8,BUFFER|p.G152D|c.455G>A|23,BUFFER|p.G152V|c.455G>T|15,BUFFER|p.G245V|c.734G>T|10,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245D|c.734G>A|119,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245D|c.734G>A|7,BUFFER|p.G245V|c.734G>T|69,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245R|c.733G>C|14,BUFFER|p.G245S|c.733G>A|22,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152S|c.454G>A|56,BUFFER|p.G245C|c.733G>T|4,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245S|c.733G>A|340,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245C|c.733G>T|50,BUFFER|p.G245S|c.733G>A|39,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152C|c.454G>T|6,BUFFER|p.G152R|c.454G>C|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G151G|c.453C>T|3,BUFFER|p.G244G|c.732C>T|8,BUFFER|p.G244G|c.732C>A|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCCGGTTC	byFrequency|byCluster	5	ESCA
CBX4	0	.	GRCh37	17	77807252	77807252	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*506A>G	.	.	ENST00000269397	5/5	78	58	20	85	85	0	CBX4,3_prime_UTR_variant,,ENST00000269397,;CBX4,downstream_gene_variant,,ENST00000495122,;CBX4,downstream_gene_variant,,ENST00000448310,;CBX4,downstream_gene_variant,,ENST00000494546,;	C	ENSG00000141582	ENST00000269397	Transcript	3_prime_UTR_variant	2367	.	.	.	.	.	.	.	-1	CBX4	HGNC	1554	protein_coding	YES	CCDS32758.1	ENSP00000269397	CBX4_HUMAN	.	UPI000013D82E	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGATATAGA	.	5	ESCA
PIK3C3	0	.	GRCh37	18	39637872	39637872	+	Silent	SNP	A	A	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2289A>T	p.%3D	p.G763G	ENST00000262039	22/25	61	24	37	53	53	0	PIK3C3,synonymous_variant,p.%3D,ENST00000593098,;PIK3C3,synonymous_variant,p.%3D,ENST00000262039,;PIK3C3,synonymous_variant,p.%3D,ENST00000398870,;PIK3C3,5_prime_UTR_variant,,ENST00000588156,;PIK3C3,5_prime_UTR_variant,,ENST00000587261,;PIK3C3,intron_variant,,ENST00000588631,;	T	ENSG00000078142	ENST00000262039	Transcript	synonymous_variant	2375	2289	763	G	ggA/ggT	.	.	.	1	PIK3C3	HGNC	8974	protein_coding	YES	CCDS11920.1	ENSP00000262039	PK3C3_HUMAN	M0R2C5_HUMAN,M0R0W7_HUMAN,M0R0U1_HUMAN,M0R0G8_HUMAN,M0QZG0_HUMAN	UPI00000708CE	.	.	.	22/25	.	Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000587,SMART_domains:SM00146,Gene3D:1.10.1070.11,Pfam_domain:PF00454,hmmpanther:PTHR10048,PROSITE_profiles:PS50290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGGATATAT	.	5	ESCA
YES1	0	.	GRCh37	18	748017	748017	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.373G>C	p.Glu125Gln	p.E125Q	ENST00000584307	4/12	41	31	10	34	34	0	YES1,missense_variant,p.Glu125Gln,ENST00000314574,;YES1,missense_variant,p.Glu125Gln,ENST00000584307,;YES1,missense_variant,p.Glu130Gln,ENST00000577961,;YES1,downstream_gene_variant,,ENST00000577611,;	G	ENSG00000176105	ENST00000584307	Transcript	missense_variant	544	373	125	E/Q	Gaa/Caa	.	.	.	-1	YES1	HGNC	12841	protein_coding	YES	CCDS11824.1	ENSP00000462468	YES_HUMAN	.	UPI0000062316	.	tolerated(0.21)	benign(0.362)	4/12	.	PROSITE_profiles:PS50002,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF90,Gene3D:2.30.30.40,Pfam_domain:PF00018,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCCCTGC	.	5	ESCA
ZNF730	0	.	GRCh37	19	23328592	23328592	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.746T>A	p.Ile249Asn	p.I249N	ENST00000597761	4/4	51	39	12	46	46	0	ZNF730,missense_variant,p.Ile249Asn,ENST00000597761,;ZNF730,downstream_gene_variant,,ENST00000599195,;	A	ENSG00000183850	ENST00000597761	Transcript	missense_variant	945	746	249	I/N	aTt/aAt	.	.	.	1	ZNF730	HGNC	32470	protein_coding	YES	CCDS59371.1	ENSP00000472959	ZN730_HUMAN	.	UPI000035E7F4	.	deleterious(0.03)	probably_damaging(0.987)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF110,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAATTCATA	.	5	ESCA
CHST8	0	.	GRCh37	19	34263467	34263467	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774C>T	p.%3D	p.R258R	ENST00000262622	4/4	67	45	22	79	79	0	CHST8,synonymous_variant,p.%3D,ENST00000438847,;CHST8,synonymous_variant,p.%3D,ENST00000262622,;CHST8,synonymous_variant,p.%3D,ENST00000434302,;CHST8,downstream_gene_variant,,ENST00000591231,;	T	ENSG00000124302	ENST00000262622	Transcript	synonymous_variant	1532	774	258	R	cgC/cgT	.	.	.	1	CHST8	HGNC	15993	protein_coding	YES	CCDS12433.1	ENSP00000262622	CHST8_HUMAN	K7ENM3_HUMAN	UPI000006F966	.	.	.	4/4	.	Pfam_domain:PF03567,hmmpanther:PTHR12137:SF7,hmmpanther:PTHR12137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCGCGAGCC	.	5	ESCA
ZNF607	0	.	GRCh37	19	38189230	38189230	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1802C>T	p.Ala601Val	p.A601V	ENST00000355202	5/5	77	53	23	52	52	0	ZNF607,missense_variant,p.Ala600Val,ENST00000395835,;ZNF607,missense_variant,p.Ala601Val,ENST00000355202,;ZNF607,downstream_gene_variant,,ENST00000591664,;ZNF607,downstream_gene_variant,,ENST00000590670,;CTD-2528L19.4,intron_variant,,ENST00000586606,;CTD-2528L19.4,intron_variant,,ENST00000585547,;CTD-2528L19.4,intron_variant,,ENST00000591114,;ZNF607,downstream_gene_variant,,ENST00000586559,;CTD-2528L19.3,upstream_gene_variant,,ENST00000589357,;	A	ENSG00000198182	ENST00000355202	Transcript	missense_variant	2398	1802	601	A/V	gCt/gTt	.	.	.	-1	ZNF607	HGNC	28192	protein_coding	YES	CCDS33006.1	ENSP00000347338	ZN607_HUMAN	Q59G67_HUMAN,K7EN48_HUMAN	UPI000040BC07	.	tolerated(0.45)	benign(0.017)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF249,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAGCATGA	.	5	ESCA
EML2	0	.	GRCh37	19	46129982	46129982	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1325A>T	p.Lys442Met	p.K442M	ENST00000587152	11/22	72	48	23	82	82	0	EML2,missense_variant,p.Lys442Met,ENST00000587152,;EML2,missense_variant,p.Lys388Met,ENST00000536630,;EML2,missense_variant,p.Lys241Met,ENST00000245925,;EML2,missense_variant,p.Lys219Met,ENST00000586770,;EML2,missense_variant,p.Lys241Met,ENST00000589876,;EML2,missense_variant,p.Lys90Met,ENST00000588496,;EML2,intron_variant,,ENST00000588272,;EML2,upstream_gene_variant,,ENST00000590575,;EML2,non_coding_transcript_exon_variant,,ENST00000586902,;EML2,non_coding_transcript_exon_variant,,ENST00000590580,;EML2,missense_variant,p.Lys399Met,ENST00000399594,;EML2,missense_variant,p.Lys10Met,ENST00000590819,;EML2,missense_variant,p.Lys241Met,ENST00000588308,;EML2,3_prime_UTR_variant,,ENST00000592853,;EML2,3_prime_UTR_variant,,ENST00000586195,;EML2,non_coding_transcript_exon_variant,,ENST00000588000,;EML2,non_coding_transcript_exon_variant,,ENST00000588610,;EML2,downstream_gene_variant,,ENST00000587804,;	A	ENSG00000125746	ENST00000587152	Transcript	missense_variant	1510	1325	442	K/M	aAg/aTg	.	.	.	-1	EML2	HGNC	18035	protein_coding	YES	CCDS59399.1	ENSP00000468312	EMAL2_HUMAN	K7ESL7_HUMAN,K7ERY9_HUMAN,K7ERR2_HUMAN,K7EQR0_HUMAN,K7EKU5_HUMAN,K7EIM1_HUMAN	UPI0001DD21BF	.	deleterious(0)	probably_damaging(0.967)	11/22	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13720:SF22,hmmpanther:PTHR13720,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCTTGCTC	.	5	ESCA
ZNF578	0	.	GRCh37	19	53014575	53014575	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941C>T	p.Pro314Leu	p.P314L	ENST00000421239	6/6	104	72	32	108	108	0	ZNF578,missense_variant,p.Pro314Leu,ENST00000421239,;ZNF578,downstream_gene_variant,,ENST00000601120,;CTD-3099C6.5,non_coding_transcript_exon_variant,,ENST00000599143,;	T	ENSG00000258405	ENST00000421239	Transcript	missense_variant	1185	941	314	P/L	cCt/cTt	.	.	.	1	ZNF578	HGNC	26449	protein_coding	YES	CCDS54310.1	ENSP00000459216	ZN578_HUMAN	M0QZV4_HUMAN	UPI000048A457	.	tolerated(0.08)	benign(0.373)	6/6	.	Superfamily_domains:SSF57667,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF12,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G311S|c.931G>A|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAACCTTACA	.	5	ESCA
ZNF525	0	.	GRCh37	19	53884598	53884598	+	Nonsense_Mutation	SNP	C	C	T	rs753369536	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766C>T	p.Arg256Ter	p.R256*	ENST00000474037	4/4	79	74	5	101	101	0	ZNF525,stop_gained,p.Arg220Ter,ENST00000467003,;ZNF525,stop_gained,p.Arg256Ter,ENST00000474037,;ZNF525,intron_variant,,ENST00000593918,;ZNF525,intron_variant,,ENST00000475179,;ZNF525,upstream_gene_variant,,ENST00000355326,;ZNF525,downstream_gene_variant,,ENST00000491101,;ZNF525,downstream_gene_variant,,ENST00000600148,;ZNF525,upstream_gene_variant,,ENST00000601790,;CTD-3141N22.1,upstream_gene_variant,,ENST00000459631,;	T	ENSG00000203326	ENST00000474037	Transcript	stop_gained	900	766	256	R/*	Cga/Tga	rs753369536	.	.	1	ZNF525	HGNC	29423	protein_coding	YES	.	ENSP00000417696	.	J3KR62_HUMAN,J3KR51_HUMAN	UPI0000EE700C	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24407:SF12,hmmpanther:PTHR24407,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAAGCGATAC	byFrequency	2	ESCA
ZNRF4	0	.	GRCh37	19	5456256	5456256	+	Silent	SNP	C	C	T	rs769289392	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.754C>T	p.%3D	p.L252L	ENST00000222033	1/1	46	28	17	53	53	0	ZNRF4,synonymous_variant,p.%3D,ENST00000222033,;	T	ENSG00000105428	ENST00000222033	Transcript	synonymous_variant	831	754	252	L	Ctg/Ttg	rs769289392	.	.	1	ZNRF4	HGNC	17726	protein_coding	YES	CCDS42475.1	ENSP00000222033	ZNRF4_HUMAN	.	UPI0000366CF5	.	.	.	1/1	.	hmmpanther:PTHR22765:SF34,hmmpanther:PTHR22765	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTGCTGACC	.	5	ESCA
PEG3	0	.	GRCh37	19	57324921	57324921	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*122G>A	.	.	ENST00000326441	10/10	45	29	16	53	53	0	PEG3,3_prime_UTR_variant,,ENST00000423103,;PEG3,3_prime_UTR_variant,,ENST00000598410,;PEG3,3_prime_UTR_variant,,ENST00000326441,;ZIM2,intron_variant,,ENST00000221722,;ZIM2,intron_variant,,ENST00000601070,;ZIM2,intron_variant,,ENST00000593711,;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000391708,;PEG3,downstream_gene_variant,,ENST00000600833,;PEG3,downstream_gene_variant,,ENST00000599577,;PEG3,downstream_gene_variant,,ENST00000599534,;PEG3,downstream_gene_variant,,ENST00000593695,;PEG3,upstream_gene_variant,,ENST00000599565,;ZIM2,intron_variant,,ENST00000597281,;ZIM2,intron_variant,,ENST00000595671,;	T	ENSG00000198300	ENST00000326441	Transcript	3_prime_UTR_variant	5253	.	.	.	.	.	.	.	-1	PEG3	HGNC	8826	protein_coding	YES	CCDS12948.1	ENSP00000326581	PEG3_HUMAN	M0QXG1_HUMAN	UPI000006D36D	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGTCAGGTG	.	5	ESCA
FBN3	0	.	GRCh37	19	8203386	8203386	+	Missense_Mutation	SNP	C	C	T	rs778441811	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.928G>A	p.Gly310Ser	p.G310S	ENST00000600128	9/64	34	23	11	37	37	0	FBN3,missense_variant,p.Gly310Ser,ENST00000600128,;FBN3,missense_variant,p.Gly310Ser,ENST00000601739,;FBN3,missense_variant,p.Gly310Ser,ENST00000270509,;	T	ENSG00000142449	ENST00000600128	Transcript	missense_variant	1343	928	310	G/S	Ggc/Agc	rs778441811,COSM1564924	.	.	-1	FBN3	HGNC	18794	protein_coding	YES	CCDS12196.1	ENSP00000470498	FBN3_HUMAN	.	UPI000013D88F	.	tolerated(0.17)	possibly_damaging(0.871)	9/64	.	PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF0,Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,Superfamily_domains:SSF57581	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTGGCCGGCGA	byFrequency	4	ESCA
ACTL9	0	.	GRCh37	19	8808930	8808930	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.122T>G	p.Val41Gly	p.V41G	ENST00000324436	1/1	108	101	6	105	105	0	ACTL9,missense_variant,p.Val41Gly,ENST00000324436,;	C	ENSG00000181786	ENST00000324436	Transcript	missense_variant	243	122	41	V/G	gTg/gGg	.	.	.	-1	ACTL9	HGNC	28494	protein_coding	YES	CCDS12207.1	ENSP00000316674	ACTL9_HUMAN	.	UPI000014129E	.	tolerated(0.1)	benign(0.335)	1/1	.	hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGCCACCATG	.	2	ESCA
COL11A1	0	.	GRCh37	1	103471858	103471858	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1697T>C	p.Val566Ala	p.V566A	ENST00000370096	16/67	49	34	14	59	59	0	COL11A1,missense_variant,p.Val450Ala,ENST00000512756,;COL11A1,missense_variant,p.Val527Ala,ENST00000353414,;COL11A1,missense_variant,p.Val566Ala,ENST00000370096,;COL11A1,missense_variant,p.Val578Ala,ENST00000358392,;COL11A1,downstream_gene_variant,,ENST00000427239,;COL11A1,non_coding_transcript_exon_variant,,ENST00000461720,;COL11A1,upstream_gene_variant,,ENST00000475980,;	G	ENSG00000060718	ENST00000370096	Transcript	missense_variant	2010	1697	566	V/A	gTc/gCc	.	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	unknown(0)	16/67	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF42,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGACGCCT	.	5	ESCA
SLC16A4	0	.	GRCh37	1	110925488	110925488	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188G>A	p.Gly63Glu	p.G63E	ENST00000369779	3/9	73	68	5	79	79	0	SLC16A4,missense_variant,p.Gly63Glu,ENST00000369781,;SLC16A4,missense_variant,p.Gly63Glu,ENST00000369779,;SLC16A4,missense_variant,p.Gly63Glu,ENST00000472422,;SLC16A4,intron_variant,,ENST00000541986,;SLC16A4,intron_variant,,ENST00000437429,;SLC16A4,upstream_gene_variant,,ENST00000467986,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000590413,;SLC16A4,intron_variant,,ENST00000497687,;SLC16A4,intron_variant,,ENST00000492412,;SLC16A4,intron_variant,,ENST00000528649,;SLC16A4,intron_variant,,ENST00000461647,;	T	ENSG00000168679	ENST00000369779	Transcript	missense_variant	438	188	63	G/E	gGa/gAa	.	.	.	-1	SLC16A4	HGNC	10925	protein_coding	YES	CCDS823.1	ENSP00000358794	MOT5_HUMAN	.	UPI000004EE9B	.	deleterious(0)	probably_damaging(0.996)	3/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF14,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGATCCAATC	.	2	ESCA
KCND3	0	.	GRCh37	1	112533645	112533654	+	5'Flank	DEL	TCCCCGCCGC	TCCCCGCCGC	-	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	TCCCCGCCGC	TCCCCGCCGC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000315987	.	59	33	26	32	32	0	KCND3,upstream_gene_variant,,ENST00000302127,;KCND3,upstream_gene_variant,,ENST00000315987,;RP11-88H9.2,non_coding_transcript_exon_variant,,ENST00000428461,;RP11-88H9.2,non_coding_transcript_exon_variant,,ENST00000442751,;RP11-88H9.2,non_coding_transcript_exon_variant,,ENST00000438293,;	-	ENSG00000171385	ENST00000315987	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1868	-1	KCND3	HGNC	6239	protein_coding	YES	CCDS843.1	ENSP00000319591	KCND3_HUMAN	.	UPI000003050A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCGCAGTCCCCGCCGCTGGGC	.	3	ESCA
HORMAD1	0	.	GRCh37	1	150671191	150671191	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1124C>T	p.Ser375Phe	p.S375F	ENST00000361824	15/15	84	60	23	85	85	0	HORMAD1,missense_variant,p.Ser375Phe,ENST00000361824,;HORMAD1,missense_variant,p.Ser368Phe,ENST00000322343,;HORMAD1,missense_variant,p.Ser295Phe,ENST00000368995,;HORMAD1,missense_variant,p.Ser375Phe,ENST00000368993,;GOLPH3L,upstream_gene_variant,,ENST00000540514,;GOLPH3L,upstream_gene_variant,,ENST00000271732,;GOLPH3L,upstream_gene_variant,,ENST00000427665,;RNU6-1042P,upstream_gene_variant,,ENST00000384204,;HORMAD1,non_coding_transcript_exon_variant,,ENST00000470397,;HORMAD1,non_coding_transcript_exon_variant,,ENST00000486497,;GOLPH3L,upstream_gene_variant,,ENST00000479757,;	A	ENSG00000143452	ENST00000361824	Transcript	missense_variant	1230	1124	375	S/F	tCt/tTt	.	.	.	-1	HORMAD1	HGNC	25245	protein_coding	YES	CCDS967.1	ENSP00000355167	HORM1_HUMAN	.	UPI000000DBE5	.	tolerated(0.06)	benign(0.033)	15/15	.	hmmpanther:PTHR21518:SF4,hmmpanther:PTHR21518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGAAGAATCA	.	5	ESCA
S100A11	0	.	GRCh37	1	152009416	152009416	+	5'UTR	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25C>G	.	.	ENST00000271638	1/3	126	80	46	115	115	0	S100A11,5_prime_UTR_variant,,ENST00000271638,;NBPF18P,intron_variant,,ENST00000432386,;S100A11,intron_variant,,ENST00000478109,;	C	ENSG00000163191	ENST00000271638	Transcript	5_prime_UTR_variant	96	.	.	.	.	.	.	.	-1	S100A11	HGNC	10488	protein_coding	YES	CCDS1009.1	ENSP00000271638	S10AB_HUMAN	.	UPI0000034180	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGAGGCTGT	.	5	ESCA
FLG	0	.	GRCh37	1	152283278	152283278	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4084C>G	p.Gln1362Glu	p.Q1362E	ENST00000368799	3/3	198	151	47	223	223	0	FLG,missense_variant,p.Gln1362Glu,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	C	ENSG00000143631	ENST00000368799	Transcript	missense_variant	4120	4084	1362	Q/E	Cag/Gag	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	benign(0.149)	3/3	.	hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF21,Pfam_domain:PF03516	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTGGTGGC	.	5	ESCA
NPR1	0	.	GRCh37	1	153660146	153660146	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2129C>T	p.Ala710Val	p.A710V	ENST00000368680	14/22	55	38	17	51	51	0	NPR1,missense_variant,p.Ala710Val,ENST00000368680,;NPR1,upstream_gene_variant,,ENST00000368677,;	T	ENSG00000169418	ENST00000368680	Transcript	missense_variant	2601	2129	710	A/V	gCt/gTt	.	.	.	1	NPR1	HGNC	7943	protein_coding	YES	CCDS1051.1	ENSP00000357669	ANPRA_HUMAN	.	UPI0000125B3D	.	tolerated(0.19)	benign(0.297)	14/22	.	PROSITE_profiles:PS50011,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF232,Pfam_domain:PF07714,Gene3D:1.10.510.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGCTTCAC	.	5	ESCA
SLC25A44	0	.	GRCh37	1	156182430	156182440	+	3'UTR	ONP	TGGAAACCTGA	TGGAAACCTGA	GGAAACCTGAT	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	TGGAAACCTGA	TGGAAACCTGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2207_*2218delCTGGAAACCTGAinsCGGAAACCTGAT	.	.	ENST00000359511	4/4	56	43	13	73	73	0	SLC25A44,3_prime_UTR_variant,,ENST00000359511,;PMF1,upstream_gene_variant,,ENST00000567140,;PMF1-BGLAP,upstream_gene_variant,,ENST00000368276,;PMF1,upstream_gene_variant,,ENST00000368273,;PMF1-BGLAP,upstream_gene_variant,,ENST00000490491,;PMF1,upstream_gene_variant,,ENST00000565805,;PMF1,upstream_gene_variant,,ENST00000368277,;SLC25A44,downstream_gene_variant,,ENST00000423538,;PMF1,upstream_gene_variant,,ENST00000368279,;PMF1-BGLAP,upstream_gene_variant,,ENST00000320139,;SLC25A44,non_coding_transcript_exon_variant,,ENST00000469537,;SLC25A44,downstream_gene_variant,,ENST00000468973,;PMF1,upstream_gene_variant,,ENST00000606952,;PMF1,upstream_gene_variant,,ENST00000497069,;PMF1,upstream_gene_variant,,ENST00000466489,;	CGGAAACCTGAT	ENSG00000160785	ENST00000359511	Transcript	3_prime_UTR_variant	3324-3335	.	.	.	.	.	.	.	1	SLC25A44	HGNC	29036	protein_coding	YES	CCDS1133.1	ENSP00000352497	S2544_HUMAN	.	UPI0000073CAD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	GGAGACTGGAAACCTGATTGGA	.	2	ESCA
SLC25A44	0	.	GRCh37	1	156182440	156182441	+	3'UTR	INS	-	-	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2220dupT	.	.	ENST00000359511	4/4	53	37	15	74	74	0	SLC25A44,3_prime_UTR_variant,,ENST00000359511,;PMF1,upstream_gene_variant,,ENST00000567140,;PMF1-BGLAP,upstream_gene_variant,,ENST00000368276,;PMF1,upstream_gene_variant,,ENST00000368273,;PMF1-BGLAP,upstream_gene_variant,,ENST00000490491,;PMF1,upstream_gene_variant,,ENST00000565805,;PMF1,upstream_gene_variant,,ENST00000368277,;SLC25A44,downstream_gene_variant,,ENST00000423538,;PMF1,upstream_gene_variant,,ENST00000368279,;PMF1-BGLAP,upstream_gene_variant,,ENST00000320139,;SLC25A44,non_coding_transcript_exon_variant,,ENST00000469537,;SLC25A44,downstream_gene_variant,,ENST00000468973,;PMF1,upstream_gene_variant,,ENST00000606952,;PMF1,upstream_gene_variant,,ENST00000497069,;PMF1,upstream_gene_variant,,ENST00000466489,;	T	ENSG00000160785	ENST00000359511	Transcript	3_prime_UTR_variant	3335-3336	.	.	.	.	.	.	.	1	SLC25A44	HGNC	29036	protein_coding	YES	CCDS1133.1	ENSP00000352497	S2544_HUMAN	.	UPI0000073CAD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACCTGATTGGA	.	2	ESCA
MROH9	0	.	GRCh37	1	170959002	170959002	+	Nonsense_Mutation	SNP	A	A	T	rs760051072	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.886A>T	p.Lys296Ter	p.K296*	ENST00000367759	11/22	84	66	18	110	110	0	MROH9,stop_gained,p.Lys296Ter,ENST00000367759,;MROH9,stop_gained,p.Lys296Ter,ENST00000367758,;MROH9,upstream_gene_variant,,ENST00000426136,;	T	ENSG00000117501	ENST00000367759	Transcript	stop_gained	1040	886	296	K/*	Aag/Tag	rs760051072	.	.	1	MROH9	HGNC	26287	protein_coding	YES	CCDS53429.1	ENSP00000356733	MROH9_HUMAN	.	UPI0001B09232	.	.	.	11/22	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTAAGATC	.	5	ESCA
PADI1	0	.	GRCh37	1	17563814	17563814	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1319G>C	p.Gly440Ala	p.G440A	ENST00000375471	12/16	33	22	11	43	43	0	PADI1,missense_variant,p.Gly440Ala,ENST00000375471,;PADI1,5_prime_UTR_variant,,ENST00000537499,;PADI1,5_prime_UTR_variant,,ENST00000413717,;PADI1,intron_variant,,ENST00000536552,;PADI1,upstream_gene_variant,,ENST00000460293,;	C	ENSG00000142623	ENST00000375471	Transcript	missense_variant	1411	1319	440	G/A	gGt/gCt	.	.	.	1	PADI1	HGNC	18367	protein_coding	YES	CCDS178.1	ENSP00000364620	PADI1_HUMAN	B4DQP2_HUMAN,B4DDP3_HUMAN	UPI000013D8A2	.	tolerated(0.54)	benign(0.422)	12/16	.	hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF9,Pfam_domain:PF03068,PIRSF_domain:PIRSF001247,Superfamily_domains:SSF55909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCGGTGGGC	.	5	ESCA
KIF21B	0	.	GRCh37	1	200967542	200967542	+	Silent	SNP	G	G	A	rs756280671	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2047C>T	p.%3D	p.L683L	ENST00000422435	14/35	55	51	4	59	59	0	KIF21B,synonymous_variant,p.%3D,ENST00000422435,;KIF21B,synonymous_variant,p.%3D,ENST00000360529,;KIF21B,synonymous_variant,p.%3D,ENST00000461742,;KIF21B,synonymous_variant,p.%3D,ENST00000332129,;KIF21B,downstream_gene_variant,,ENST00000534043,;	A	ENSG00000116852	ENST00000422435	Transcript	synonymous_variant	2364	2047	683	L	Ctg/Ttg	rs756280671	.	.	-1	KIF21B	HGNC	29442	protein_coding	YES	CCDS58056.1	ENSP00000411831	KI21B_HUMAN	.	UPI0000153E7C	.	.	.	14/35	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCAGCTGTG	.	2	ESCA
HIST3H2A	0	.	GRCh37	1	228645538	228645538	+	5'UTR	SNP	G	G	A	rs780054377	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-20C>T	.	.	ENST00000366695	1/1	41	27	14	36	36	0	HIST3H2A,5_prime_UTR_variant,,ENST00000366695,;HIST3H2BB,upstream_gene_variant,,ENST00000369160,;MIR4666A,upstream_gene_variant,,ENST00000580160,;	A	ENSG00000181218	ENST00000366695	Transcript	5_prime_UTR_variant	23	.	.	.	.	rs780054377	.	.	-1	HIST3H2A	HGNC	20507	protein_coding	YES	CCDS1573.1	ENSP00000355656	H2A3_HUMAN	.	UPI0000073CEF	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAGACAAC	byFrequency	5	ESCA
KDM1A	0	.	GRCh37	1	23395626	23395626	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1395G>A	p.%3D	p.L465L	ENST00000400181	12/21	67	47	20	81	81	0	KDM1A,synonymous_variant,p.%3D,ENST00000356634,;KDM1A,synonymous_variant,p.%3D,ENST00000542151,;KDM1A,synonymous_variant,p.%3D,ENST00000400181,;KDM1A,upstream_gene_variant,,ENST00000465864,;RP1-184J9.2,intron_variant,,ENST00000427154,;	A	ENSG00000004487	ENST00000400181	Transcript	synonymous_variant	1499	1395	465	L	ttG/ttA	.	.	.	1	KDM1A	HGNC	29079	protein_coding	YES	CCDS53278.1	ENSP00000383042	KDM1A_HUMAN	.	UPI0000403137	.	.	.	12/21	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10742:SF245,hmmpanther:PTHR10742,Pfam_domain:PF01593,Gene3D:1.10.287.80,PIRSF_domain:PIRSF038051,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTGAAAGA	.	5	ESCA
LYST	0	.	GRCh37	1	235826107	235826107	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*133C>T	.	.	ENST00000389794	53/53	28	19	9	26	26	0	LYST,3_prime_UTR_variant,,ENST00000389793,;LYST,3_prime_UTR_variant,,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000473037,;	A	ENSG00000143669	ENST00000389794	Transcript	3_prime_UTR_variant	11714	.	.	.	.	.	.	.	-1	LYST	HGNC	1968	protein_coding	YES	CCDS31062.1	ENSP00000374444	LYST_HUMAN	.	UPI000020509E	.	.	.	53/53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATGAATAG	.	2	ESCA
ERO1LB	0	.	GRCh37	1	236399539	236399539	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626+39G>A	.	.	ENST00000354619	.	47	27	20	38	38	0	ERO1LB,3_prime_UTR_variant,,ENST00000327333,;ERO1LB,intron_variant,,ENST00000354619,;ERO1LB,downstream_gene_variant,,ENST00000366589,;	T	ENSG00000086619	ENST00000354619	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ERO1LB	HGNC	14355	protein_coding	YES	CCDS31064.1	ENSP00000346635	ERO1B_HUMAN	Q5TAE8_HUMAN,Q5T1H5_HUMAN	UPI00004700B5	.	.	.	.	7/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCTATCA	.	5	ESCA
TRIM62	0	.	GRCh37	1	33612835	33612835	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1371G>A	p.%3D	p.Q457Q	ENST00000291416	5/5	24	13	11	27	27	0	TRIM62,synonymous_variant,p.%3D,ENST00000291416,;TRIM62,synonymous_variant,p.%3D,ENST00000543586,;	T	ENSG00000116525	ENST00000291416	Transcript	synonymous_variant	1605	1371	457	Q	caG/caA	.	.	.	-1	TRIM62	HGNC	25574	protein_coding	YES	CCDS376.1	ENSP00000291416	TRI62_HUMAN	.	UPI000004E050	.	.	.	5/5	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF30,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCTGGCC	.	5	ESCA
CLSPN	0	.	GRCh37	1	36214021	36214021	+	Silent	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2457C>G	p.%3D	p.V819V	ENST00000318121	13/25	43	34	8	45	45	0	CLSPN,synonymous_variant,p.%3D,ENST00000318121,;CLSPN,synonymous_variant,p.%3D,ENST00000520551,;CLSPN,synonymous_variant,p.%3D,ENST00000373220,;CLSPN,synonymous_variant,p.%3D,ENST00000251195,;RP11-435D7.3,downstream_gene_variant,,ENST00000373226,;CLSPN,non_coding_transcript_exon_variant,,ENST00000517467,;	C	ENSG00000092853	ENST00000318121	Transcript	synonymous_variant	2515	2457	819	V	gtC/gtG	.	.	.	-1	CLSPN	HGNC	19715	protein_coding	YES	CCDS396.1	ENSP00000312995	CLSPN_HUMAN	.	UPI0000161087	.	.	.	13/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14396	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTGACCAA	.	5	ESCA
TEKT2	0	.	GRCh37	1	36552424	36552424	+	Missense_Mutation	SNP	T	T	C	rs201956071	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608T>C	p.Val203Ala	p.V203A	ENST00000207457	5/10	64	36	28	35	35	0	TEKT2,missense_variant,p.Val203Ala,ENST00000207457,;ADPRHL2,upstream_gene_variant,,ENST00000373178,;TEKT2,upstream_gene_variant,,ENST00000473120,;RP4-665N4.4,upstream_gene_variant,,ENST00000446354,;TEKT2,3_prime_UTR_variant,,ENST00000469024,;	C	ENSG00000092850	ENST00000207457	Transcript	missense_variant	735	608	203	V/A	gTt/gCt	rs201956071	.	.	1	TEKT2	HGNC	11725	protein_coding	YES	CCDS401.1	ENSP00000207457	TEKT2_HUMAN	.	UPI0000001C3D	.	tolerated(0.38)	benign(0.005)	5/10	.	Pfam_domain:PF03148,hmmpanther:PTHR19960,hmmpanther:PTHR19960:SF7	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGGTTGACC	byCluster|by1000G	5	ESCA
HEYL	0	.	GRCh37	1	40092733	40092733	+	Missense_Mutation	SNP	C	C	T	rs762466594	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433G>A	p.Val145Ile	p.V145I	ENST00000372852	5/5	49	34	15	62	62	0	HEYL,missense_variant,p.Val145Ile,ENST00000372852,;HEYL,missense_variant,p.Val117Ile,ENST00000535435,;	T	ENSG00000163909	ENST00000372852	Transcript	missense_variant	753	433	145	V/I	Gtc/Atc	rs762466594,COSM909328	.	.	-1	HEYL	HGNC	4882	protein_coding	YES	CCDS439.1	ENSP00000361943	HEYL_HUMAN	F5H3V9_HUMAN	UPI000013E317	.	tolerated(0.64)	benign(0.042)	5/5	.	PROSITE_profiles:PS51054,hmmpanther:PTHR10985:SF10,hmmpanther:PTHR10985,Pfam_domain:PF07527,SMART_domains:SM00511,Superfamily_domains:0053813	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGACGGGGT	byFrequency	5	ESCA
PRPF38A	0	.	GRCh37	1	52882816	52882816	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*454C>T	.	.	ENST00000257181	10/10	26	16	9	50	50	0	PRPF38A,3_prime_UTR_variant,,ENST00000257181,;ZCCHC11,intron_variant,,ENST00000528457,;PRPF38A,downstream_gene_variant,,ENST00000474048,;ZCCHC11,intron_variant,,ENST00000527941,;	T	ENSG00000134748	ENST00000257181	Transcript	3_prime_UTR_variant	1579	.	.	.	.	.	.	.	1	PRPF38A	HGNC	25930	protein_coding	YES	CCDS567.1	ENSP00000257181	PR38A_HUMAN	.	UPI000006D9C2	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCCAGCAG	.	4	ESCA
GTF2B	0	.	GRCh37	1	89318844	89318844	+	3'UTR	SNP	T	T	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*52A>C	.	.	ENST00000370500	7/7	72	47	24	84	84	0	GTF2B,3_prime_UTR_variant,,ENST00000370500,;GTF2B,downstream_gene_variant,,ENST00000418217,;GTF2B,downstream_gene_variant,,ENST00000448623,;GTF2B,downstream_gene_variant,,ENST00000494819,;	G	ENSG00000137947	ENST00000370500	Transcript	3_prime_UTR_variant	1122	.	.	.	.	.	.	.	-1	GTF2B	HGNC	4648	protein_coding	YES	CCDS715.1	ENSP00000359531	TF2B_HUMAN	.	UPI0000136C21	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTATGTACA	.	5	ESCA
GBP5	0	.	GRCh37	1	89730518	89730518	+	Missense_Mutation	SNP	C	C	T	rs143883598	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1000G>A	p.Asp334Asn	p.D334N	ENST00000343435	8/12	117	87	30	103	103	0	GBP5,missense_variant,p.Asp334Asn,ENST00000443807,;GBP5,missense_variant,p.Asp334Asn,ENST00000343435,;GBP5,missense_variant,p.Asp334Asn,ENST00000370459,;RP4-620F22.2,intron_variant,,ENST00000437128,;GBP5,intron_variant,,ENST00000490568,;GBP5,upstream_gene_variant,,ENST00000471171,;GBP5,non_coding_transcript_exon_variant,,ENST00000481145,;	T	ENSG00000154451	ENST00000343435	Transcript	missense_variant	1537	1000	334	D/N	Gac/Aac	rs143883598	.	.	-1	GBP5	HGNC	19895	protein_coding	YES	CCDS722.1	ENSP00000340396	GBP5_HUMAN	E7ETN8_HUMAN	UPI000004B6D7	.	deleterious(0.03)	benign(0.16)	8/12	.	hmmpanther:PTHR10751:SF40,hmmpanther:PTHR10751,Pfam_domain:PF02841,Gene3D:1f5nA01,Superfamily_domains:0037397	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTCATAGT	byCluster	5	ESCA
CLSTN1	0	.	GRCh37	1	9789388	9789388	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1178C>G	.	.	ENST00000377298	19/19	33	28	4	37	37	0	CLSTN1,3_prime_UTR_variant,,ENST00000435891,;CLSTN1,3_prime_UTR_variant,,ENST00000377298,;CLSTN1,3_prime_UTR_variant,,ENST00000361311,;CLSTN1,3_prime_UTR_variant,,ENST00000377288,;PIK3CD,downstream_gene_variant,,ENST00000361110,;PIK3CD,downstream_gene_variant,,ENST00000536656,;PIK3CD,downstream_gene_variant,,ENST00000377346,;CLSTN1,non_coding_transcript_exon_variant,,ENST00000477264,;	C	ENSG00000171603	ENST00000377298	Transcript	3_prime_UTR_variant	4917	.	.	.	.	.	.	.	-1	CLSTN1	HGNC	17447	protein_coding	YES	CCDS30580.1	ENSP00000366513	CSTN1_HUMAN	.	UPI0000127B95	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTAGACCAT	.	2	ESCA
BTBD3	0	.	GRCh37	20	11904537	11904537	+	3'UTR	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*223T>A	.	.	ENST00000405977	5/5	48	42	6	47	47	0	BTBD3,3_prime_UTR_variant,,ENST00000254977,;BTBD3,3_prime_UTR_variant,,ENST00000399006,;BTBD3,3_prime_UTR_variant,,ENST00000405977,;BTBD3,3_prime_UTR_variant,,ENST00000378226,;BTBD3,downstream_gene_variant,,ENST00000430557,;BTBD3,downstream_gene_variant,,ENST00000422390,;BTBD3,downstream_gene_variant,,ENST00000455911,;BTBD3,downstream_gene_variant,,ENST00000473180,;BTBD3,downstream_gene_variant,,ENST00000471120,;BTBD3,downstream_gene_variant,,ENST00000488503,;BTBD3,downstream_gene_variant,,ENST00000473416,;BTBD3,downstream_gene_variant,,ENST00000449299,;	A	ENSG00000132640	ENST00000405977	Transcript	3_prime_UTR_variant	2417	.	.	.	.	.	.	.	1	BTBD3	HGNC	15854	protein_coding	YES	CCDS13113.1	ENSP00000384545	BTBD3_HUMAN	Q9NST6_HUMAN,Q52M42_HUMAN,B4DK27_HUMAN,B0QYR1_HUMAN,B0QYR0_HUMAN,B0QYQ9_HUMAN	UPI0000126B03	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGCTTTGTG	.	2	ESCA
ZNF343	0	.	GRCh37	20	2464529	2464529	+	Nonsense_Mutation	SNP	G	G	A	rs766928129	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1078C>T	p.Arg360Ter	p.R360*	ENST00000278772	6/6	87	72	15	84	84	0	ZNF343,stop_gained,p.Arg360Ter,ENST00000278772,;ZNF343,downstream_gene_variant,,ENST00000445484,;ZNF343,non_coding_transcript_exon_variant,,ENST00000465019,;RP4-734P14.4,intron_variant,,ENST00000461548,;	A	ENSG00000088876	ENST00000278772	Transcript	stop_gained	1566	1078	360	R/*	Cga/Tga	rs766928129	.	.	-1	ZNF343	HGNC	16017	protein_coding	YES	CCDS13028.1	ENSP00000278772	ZN343_HUMAN	.	UPI000013DB8F	.	.	.	6/6	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24381:SF97,hmmpanther:PTHR24381,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCGCCCAC	.	5	ESCA
NCOA3	0	.	GRCh37	20	46282984	46282985	+	3'Flank	INS	-	-	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000371998	.	51	40	10	31	31	0	NCOA3,3_prime_UTR_variant,,ENST00000341724,;NCOA3,3_prime_UTR_variant,,ENST00000371997,;NCOA3,3_prime_UTR_variant,,ENST00000372004,;SULF2,downstream_gene_variant,,ENST00000359930,;SULF2,downstream_gene_variant,,ENST00000484875,;NCOA3,downstream_gene_variant,,ENST00000371998,;SULF2,downstream_gene_variant,,ENST00000361612,;SULF2,downstream_gene_variant,,ENST00000467815,;SULF2,downstream_gene_variant,,ENST00000495544,;SULF2,downstream_gene_variant,,ENST00000479472,;SULF2,downstream_gene_variant,,ENST00000479970,;	T	ENSG00000124151	ENST00000371998	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	621	1	NCOA3	HGNC	7670	protein_coding	YES	CCDS13407.1	ENSP00000361066	NCOA3_HUMAN	Q569F6_HUMAN,B4DYT5_HUMAN	UPI000012FE45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTATGATTTTT	.	2	ESCA
BCAS4	0	.	GRCh37	20	49434786	49434786	+	Silent	SNP	C	C	T	rs200095102	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.219C>T	p.%3D	p.L73L	ENST00000358791	2/6	60	49	11	49	49	0	BCAS4,synonymous_variant,p.%3D,ENST00000358791,;BCAS4,synonymous_variant,p.%3D,ENST00000371608,;BCAS4,synonymous_variant,p.%3D,ENST00000445038,;BCAS4,synonymous_variant,p.%3D,ENST00000609336,;BCAS4,synonymous_variant,p.%3D,ENST00000262591,;BCAS4,non_coding_transcript_exon_variant,,ENST00000485049,;BCAS4,synonymous_variant,p.%3D,ENST00000463943,;	T	ENSG00000124243	ENST00000358791	Transcript	synonymous_variant	319	219	73	L	ctC/ctT	rs200095102	.	.	1	BCAS4	HGNC	14367	protein_coding	YES	CCDS33487.1	ENSP00000351642	BCAS4_HUMAN	.	UPI0000070BBB	.	.	.	2/6	.	hmmpanther:PTHR16230,hmmpanther:PTHR16230:SF5	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAGGCT	byCluster	5	ESCA
LAMA5	0	.	GRCh37	20	60886990	60886990	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9621C>T	p.%3D	p.Y3207Y	ENST00000252999	70/80	154	118	36	126	126	0	LAMA5,synonymous_variant,p.%3D,ENST00000252999,;ADRM1,downstream_gene_variant,,ENST00000253003,;LAMA5,upstream_gene_variant,,ENST00000492698,;LAMA5,synonymous_variant,p.%3D,ENST00000370691,;LAMA5,non_coding_transcript_exon_variant,,ENST00000462415,;LAMA5,non_coding_transcript_exon_variant,,ENST00000491036,;LAMA5,upstream_gene_variant,,ENST00000495695,;LAMA5,downstream_gene_variant,,ENST00000468786,;LAMA5,downstream_gene_variant,,ENST00000471042,;	A	ENSG00000130702	ENST00000252999	Transcript	synonymous_variant	9688	9621	3207	Y	taC/taT	.	.	.	-1	LAMA5	HGNC	6485	protein_coding	YES	CCDS33502.1	ENSP00000252999	LAMA5_HUMAN	O75079_HUMAN	UPI0000161FDC	.	.	.	70/80	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10574:SF261,hmmpanther:PTHR10574,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCTGTAGAA	.	5	ESCA
URB1	0	.	GRCh37	21	33765205	33765205	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15G>C	p.Lys5Asn	p.K5N	ENST00000382751	1/39	16	10	6	18	18	0	URB1,missense_variant,p.Lys5Asn,ENST00000382751,;C21orf119,upstream_gene_variant,,ENST00000534991,;	G	ENSG00000142207	ENST00000382751	Transcript	missense_variant	131	15	5	K/N	aaG/aaC	.	.	.	-1	URB1	HGNC	17344	protein_coding	YES	CCDS46645.1	ENSP00000372199	NPA1P_HUMAN	.	UPI0000185F65	.	deleterious(0)	probably_damaging(0.994)	1/39	.	hmmpanther:PTHR13500	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTTGGG	.	5	ESCA
POLDIP3	0	.	GRCh37	22	42981144	42981144	+	3'UTR	SNP	C	C	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*653G>T	.	.	ENST00000252115	9/9	33	26	7	31	31	0	POLDIP3,3_prime_UTR_variant,,ENST00000339677,;POLDIP3,3_prime_UTR_variant,,ENST00000348657,;POLDIP3,3_prime_UTR_variant,,ENST00000252115,;POLDIP3,downstream_gene_variant,,ENST00000451060,;RRP7B,upstream_gene_variant,,ENST00000357802,;RRP7B,upstream_gene_variant,,ENST00000437211,;POLDIP3,downstream_gene_variant,,ENST00000491021,;RRP7B,upstream_gene_variant,,ENST00000421116,;RRP7B,upstream_gene_variant,,ENST00000458605,;POLDIP3,3_prime_UTR_variant,,ENST00000445215,;RRP7B,upstream_gene_variant,,ENST00000566851,;	A	ENSG00000100227	ENST00000252115	Transcript	3_prime_UTR_variant	2024	.	.	.	.	.	.	.	-1	POLDIP3	HGNC	23782	protein_coding	YES	CCDS14038.1	ENSP00000252115	PDIP3_HUMAN	Q96DI9_HUMAN	UPI000006EEA7	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGACGACAC	.	5	ESCA
FLJ27365	0	.	GRCh37	22	46508717	46508717	+	3'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2827A>G	.	.	ENST00000360737	5/5	63	47	16	47	47	0	FLJ27365,3_prime_UTR_variant,,ENST00000360737,;MIR4763,upstream_gene_variant,,ENST00000581461,;MIRLET7B,upstream_gene_variant,,ENST00000385140,;MIRLET7A3,downstream_gene_variant,,ENST00000362116,;FLJ27365,downstream_gene_variant,,ENST00000435439,;	G	ENSG00000197182	ENST00000360737	Transcript	3_prime_UTR_variant	3469	.	.	.	.	.	.	.	1	FLJ27365	Uniprot_gn	.	protein_coding	YES	.	ENSP00000353966	.	Q6ZNQ0_HUMAN,B1AKH8_HUMAN	UPI00001C11DA	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAATATCTGC	.	5	ESCA
BAZ2B	0	.	GRCh37	2	160176749	160176750	+	3'UTR	INS	-	-	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*26dupT	.	.	ENST00000392783	37/37	56	45	11	51	51	0	BAZ2B,3_prime_UTR_variant,,ENST00000355831,;BAZ2B,3_prime_UTR_variant,,ENST00000392782,;BAZ2B,3_prime_UTR_variant,,ENST00000343439,;BAZ2B,3_prime_UTR_variant,,ENST00000392783,;BAZ2B,downstream_gene_variant,,ENST00000548440,;	A	ENSG00000123636	ENST00000392783	Transcript	3_prime_UTR_variant	7029-7030	.	.	.	.	.	.	.	-1	BAZ2B	HGNC	963	protein_coding	YES	CCDS2209.2	ENSP00000376534	BAZ2B_HUMAN	Q8NC87_HUMAN,Q53TG3_HUMAN,C9JCA6_HUMAN	UPI0000D74C4A	.	.	.	37/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAAGGAAAAA	.	2	ESCA
XIRP2	0	.	GRCh37	2	168104729	168104729	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6827T>A	p.Phe2276Tyr	p.F2276Y	ENST00000409195	9/11	28	19	8	39	39	0	XIRP2,missense_variant,p.Phe2054Tyr,ENST00000409273,;XIRP2,missense_variant,p.Phe2276Tyr,ENST00000409195,;XIRP2,missense_variant,p.Phe2276Tyr,ENST00000295237,;XIRP2,intron_variant,,ENST00000409605,;XIRP2,intron_variant,,ENST00000420519,;XIRP2,intron_variant,,ENST00000409756,;XIRP2,intron_variant,,ENST00000409043,;XIRP2,intron_variant,,ENST00000409728,;	A	ENSG00000163092	ENST00000409195	Transcript	missense_variant	6916	6827	2276	F/Y	tTt/tAt	.	.	.	1	XIRP2	HGNC	14303	protein_coding	YES	CCDS42769.1	ENSP00000386840	.	J3KNB1_HUMAN	UPI0000E9BBED	.	.	benign(0.251)	9/11	.	hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTTTAACC	.	5	ESCA
FKBP7	0	.	GRCh37	2	179330499	179330499	+	Nonstop_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.667T>C	p.Ter223GlnextTer10	p.*223Qext*10	ENST00000424785	4/4	52	38	14	63	63	0	FKBP7,stop_lost,p.Ter222GlnextTer?,ENST00000434643,;FKBP7,stop_lost,p.Ter223GlnextTer10,ENST00000424785,;DFNB59,downstream_gene_variant,,ENST00000442710,;DFNB59,downstream_gene_variant,,ENST00000375129,;DFNB59,downstream_gene_variant,,ENST00000409117,;FKBP7,non_coding_transcript_exon_variant,,ENST00000470945,;FKBP7,non_coding_transcript_exon_variant,,ENST00000464248,;FKBP7,3_prime_UTR_variant,,ENST00000233092,;FKBP7,3_prime_UTR_variant,,ENST00000419184,;FKBP7,3_prime_UTR_variant,,ENST00000435079,;FKBP7,downstream_gene_variant,,ENST00000412612,;DFNB59,downstream_gene_variant,,ENST00000437056,;	G	ENSG00000079150	ENST00000424785	Transcript	stop_lost	726	667	223	*/Q	Tag/Cag	.	.	.	-1	FKBP7	HGNC	3723	protein_coding	YES	CCDS2280.1	ENSP00000413152	FKBP7_HUMAN	.	UPI000002A9BC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCTATAGTT	.	5	ESCA
TTN	0	.	GRCh37	2	179580465	179580465	+	Missense_Mutation	SNP	C	C	G	rs745818225	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25676G>C	p.Arg8559Thr	p.R8559T	ENST00000589042	89/363	26	15	11	29	29	0	TTN,missense_variant,p.Arg7315Thr,ENST00000342992,;TTN,missense_variant,p.Arg8559Thr,ENST00000589042,;TTN,missense_variant,p.Arg8242Thr,ENST00000591111,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,downstream_gene_variant,,ENST00000592630,;TTN-AS1,downstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000589830,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	25901	25676	8559	R/T	aGa/aCa	rs745818225,COSM2706447,COSM2706448	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	89/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATTCTTGAA	.	5	ESCA
LANCL1	0	.	GRCh37	2	211336800	211336800	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.82C>G	p.Leu28Val	p.L28V	ENST00000443314	2/9	37	26	11	74	74	0	LANCL1,missense_variant,p.Leu28Val,ENST00000450366,;LANCL1,missense_variant,p.Leu28Val,ENST00000448951,;LANCL1,missense_variant,p.Leu28Val,ENST00000431941,;LANCL1,missense_variant,p.Leu28Val,ENST00000443314,;LANCL1,missense_variant,p.Leu28Val,ENST00000441020,;LANCL1,missense_variant,p.Leu28Val,ENST00000233714,;AC007970.1,downstream_gene_variant,,ENST00000420418,;AC007970.1,downstream_gene_variant,,ENST00000416344,;LANCL1,missense_variant,p.Leu28Val,ENST00000453956,;	C	ENSG00000115365	ENST00000443314	Transcript	missense_variant	425	82	28	L/V	Ctg/Gtg	.	.	.	-1	LANCL1	HGNC	6508	protein_coding	YES	CCDS2392.1	ENSP00000388713	LANC1_HUMAN	Q53TN2_HUMAN,E9PHS0_HUMAN	UPI0000073D7C	.	tolerated(0.24)	benign(0.028)	2/9	.	hmmpanther:PTHR12736,hmmpanther:PTHR12736:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCAGCTAGA	.	5	ESCA
USP37	0	.	GRCh37	2	219319578	219319579	+	3'UTR	INS	-	-	TTCA	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*71_*74dupTGAA	.	.	ENST00000258399	26/26	32	26	6	45	45	0	USP37,3_prime_UTR_variant,,ENST00000258399,;USP37,3_prime_UTR_variant,,ENST00000418019,;USP37,3_prime_UTR_variant,,ENST00000415516,;USP37,3_prime_UTR_variant,,ENST00000454775,;VIL1,downstream_gene_variant,,ENST00000248444,;	TTCA	ENSG00000135913	ENST00000258399	Transcript	3_prime_UTR_variant	3427-3428	.	.	.	.	.	.	.	-1	USP37	HGNC	20063	protein_coding	YES	CCDS2418.1	ENSP00000258399	UBP37_HUMAN	.	UPI0000160023	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTCCTTCAG	.	3	ESCA
PID1	0	.	GRCh37	2	229890405	229890405	+	Silent	SNP	G	G	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.690C>A	p.%3D	p.I230I	ENST00000392054	4/4	30	22	8	35	35	0	PID1,synonymous_variant,p.%3D,ENST00000409462,;PID1,synonymous_variant,p.%3D,ENST00000354069,;PID1,synonymous_variant,p.%3D,ENST00000392055,;PID1,synonymous_variant,p.%3D,ENST00000392054,;PID1,intron_variant,,ENST00000482518,;PID1,downstream_gene_variant,,ENST00000534952,;	T	ENSG00000153823	ENST00000392054	Transcript	synonymous_variant	1030	690	230	I	atC/atA	.	.	.	-1	PID1	HGNC	26084	protein_coding	YES	CCDS2471.1	ENSP00000375907	PCLI1_HUMAN	Q4ZG81_HUMAN	UPI00001C0AF7	.	.	.	4/4	.	hmmpanther:PTHR16265,hmmpanther:PTHR16265:SF0,Pfam_domain:PF14719,SMART_domains:SM00462	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGGATCCG	.	5	ESCA
TRPM8	0	.	GRCh37	2	234856184	234856184	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.942+385C>T	.	.	ENST00000324695	.	74	54	20	74	74	0	TRPM8,5_prime_UTR_variant,,ENST00000433712,;TRPM8,intron_variant,,ENST00000324695,;TRPM8,downstream_gene_variant,,ENST00000409625,;TRPM8,downstream_gene_variant,,ENST00000355722,;AC005538.5,intron_variant,,ENST00000455991,;TRPM8,3_prime_UTR_variant,,ENST00000444298,;	T	ENSG00000144481	ENST00000324695	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TRPM8	HGNC	17961	protein_coding	YES	CCDS33407.1	ENSP00000323926	TRPM8_HUMAN	.	UPI0000456F32	.	.	.	.	8/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTCCAGAC	.	5	ESCA
NCOA1	0	.	GRCh37	2	24888748	24888748	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.220G>A	p.Val74Ile	p.V74I	ENST00000406961	6/23	35	27	8	30	30	0	NCOA1,missense_variant,p.Val74Ile,ENST00000348332,;NCOA1,missense_variant,p.Val74Ile,ENST00000288599,;NCOA1,missense_variant,p.Val74Ile,ENST00000406961,;NCOA1,missense_variant,p.Val74Ile,ENST00000395856,;NCOA1,missense_variant,p.Val74Ile,ENST00000538539,;NCOA1,missense_variant,p.Val74Ile,ENST00000405141,;NCOA1,intron_variant,,ENST00000407230,;	A	ENSG00000084676	ENST00000406961	Transcript	missense_variant	872	220	74	V/I	Gtc/Atc	.	.	.	1	NCOA1	HGNC	7668	protein_coding	YES	CCDS1712.1	ENSP00000385216	NCOA1_HUMAN	.	UPI000006E1F7	.	deleterious(0)	possibly_damaging(0.472)	6/23	.	PROSITE_profiles:PS50888,hmmpanther:PTHR10684:SF1,hmmpanther:PTHR10684,Gene3D:4.10.280.10,PIRSF_domain:PIRSF038181,SMART_domains:SM00353,Superfamily_domains:SSF47459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACAGTCGAT	.	5	ESCA
PREPL	0	.	GRCh37	2	44559648	44559648	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1303G>A	p.Asp435Asn	p.D435N	ENST00000409936	9/15	69	45	23	80	80	0	PREPL,missense_variant,p.Asp435Asn,ENST00000409936,;PREPL,missense_variant,p.Asp346Asn,ENST00000409957,;PREPL,missense_variant,p.Asp435Asn,ENST00000260648,;PREPL,missense_variant,p.Asp346Asn,ENST00000541738,;PREPL,missense_variant,p.Asp346Asn,ENST00000409411,;PREPL,missense_variant,p.Asp435Asn,ENST00000409272,;PREPL,missense_variant,p.Asp435Asn,ENST00000410081,;PREPL,missense_variant,p.Asp373Asn,ENST00000378511,;PREPL,intron_variant,,ENST00000378520,;PREPL,missense_variant,p.Asp435Asn,ENST00000425263,;PREPL,missense_variant,p.Asp435Asn,ENST00000426481,;	T	ENSG00000138078	ENST00000409936	Transcript	missense_variant	1741	1303	435	D/N	Gac/Aac	.	.	.	-1	PREPL	HGNC	30228	protein_coding	YES	CCDS33190.1	ENSP00000386543	PPCEL_HUMAN	C9JMT4_HUMAN	UPI0000208358	.	tolerated(0.49)	benign(0.379)	9/15	.	hmmpanther:PTHR11757,hmmpanther:PTHR11757:SF3,Gene3D:3.40.50.1820	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTCTTCAT	.	5	ESCA
ZNF514	0	.	GRCh37	2	95824709	95824709	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96+276G>A	.	.	ENST00000295208	.	40	25	15	24	24	0	ZNF514,5_prime_UTR_variant,,ENST00000411425,;ZNF514,intron_variant,,ENST00000447814,;ZNF514,intron_variant,,ENST00000295208,;ZNF514,upstream_gene_variant,,ENST00000496060,;	T	ENSG00000144026	ENST00000295208	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ZNF514	HGNC	25894	protein_coding	YES	CCDS2011.1	ENSP00000295208	ZN514_HUMAN	Q658L7_HUMAN	UPI0000070647	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAACCTGAT	.	5	ESCA
ZNF514	0	.	GRCh37	2	95824710	95824710	+	Intron	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96+275G>C	.	.	ENST00000295208	.	40	25	15	24	24	0	ZNF514,5_prime_UTR_variant,,ENST00000411425,;ZNF514,intron_variant,,ENST00000447814,;ZNF514,intron_variant,,ENST00000295208,;ZNF514,upstream_gene_variant,,ENST00000496060,;	G	ENSG00000144026	ENST00000295208	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ZNF514	HGNC	25894	protein_coding	YES	CCDS2011.1	ENSP00000295208	ZN514_HUMAN	Q658L7_HUMAN	UPI0000070647	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAACCTGATG	.	5	ESCA
NAA50	0	.	GRCh37	3	113440550	113440550	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*57A>G	.	.	ENST00000240922	5/5	66	44	22	92	92	0	NAA50,3_prime_UTR_variant,,ENST00000240922,;NAA50,3_prime_UTR_variant,,ENST00000493454,;NAA50,3_prime_UTR_variant,,ENST00000493900,;NAA50,3_prime_UTR_variant,,ENST00000477813,;NAA50,3_prime_UTR_variant,,ENST00000497525,;NAA50,3_prime_UTR_variant,,ENST00000497255,;NAA50,downstream_gene_variant,,ENST00000478020,;NAA50,downstream_gene_variant,,ENST00000467022,;NAA50,3_prime_UTR_variant,,ENST00000481432,;	C	ENSG00000121579	ENST00000240922	Transcript	3_prime_UTR_variant	892	.	.	.	.	.	.	.	-1	NAA50	HGNC	29533	protein_coding	YES	CCDS2975.1	ENSP00000240922	NAA50_HUMAN	B0AZT5_HUMAN	UPI000003B017	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAATGGGCC	.	5	ESCA
GSK3B	0	.	GRCh37	3	119582439	119582439	+	Missense_Mutation	SNP	C	C	T	rs775606264	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.962G>A	p.Arg321Gln	p.R321Q	ENST00000316626	10/12	53	31	22	63	63	0	GSK3B,missense_variant,p.Arg321Gln,ENST00000316626,;GSK3B,missense_variant,p.Arg308Gln,ENST00000264235,;GSK3B,non_coding_transcript_exon_variant,,ENST00000473886,;	T	ENSG00000082701	ENST00000316626	Transcript	missense_variant	1194	962	321	R/Q	cGa/cAa	rs775606264,COSM1036811,COSM1036812	.	.	-1	GSK3B	HGNC	4617	protein_coding	YES	CCDS2996.1	ENSP00000324806	GSK3B_HUMAN	.	UPI000002ACBB	.	deleterious(0.01)	possibly_damaging(0.477)	10/12	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24057,hmmpanther:PTHR24057:SF8,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTCGGGGT	.	5	ESCA
ACKR4	0	.	GRCh37	3	132319381	132319405	+	Frame_Shift_Del	DEL	TCCTCACAATAGTTTTCGTCATTGG	TCCTCACAATAGTTTTCGTCATTGG	-	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	TCCTCACAATAGTTTTCGTCATTGG	TCCTCACAATAGTTTTCGTCATTGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.140_164delTCCTCACAATAGTTTTCGTCATTGG	p.Phe47TyrfsTer8	p.F47Yfs*8	ENST00000249887	2/2	88	76	12	99	99	0	ACKR4,frameshift_variant,p.Phe47TyrfsTer8,ENST00000249887,;ACAD11,intron_variant,,ENST00000264990,;ACAD11,intron_variant,,ENST00000545291,;ACAD11,intron_variant,,ENST00000355458,;ACAD11,intron_variant,,ENST00000507705,;NPHP3,intron_variant,,ENST00000471702,;ACAD11,intron_variant,,ENST00000496418,;ACAD11,intron_variant,,ENST00000477604,;ACAD11,intron_variant,,ENST00000487024,;ACAD11,intron_variant,,ENST00000485198,;ACAD11,intron_variant,,ENST00000469042,;ACAD11,intron_variant,,ENST00000510100,;ACKR4,upstream_gene_variant,,ENST00000509820,;	-	ENSG00000129048	ENST00000249887	Transcript	frameshift_variant	236-260	140-164	47-55	FLTIVFVIG/X	tTCCTCACAATAGTTTTCGTCATTGGa/ta	.	.	.	1	ACKR4	HGNC	1611	protein_coding	YES	CCDS3075.1	ENSP00000249887	ACKR4_HUMAN	H0Y9Z2_HUMAN	UPI0000039DBA	.	.	.	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24227:SF35,hmmpanther:PTHR24227,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01558,Prints_domain:PR00237,Prints_domain:PR00657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTGTATTCCTCACAATAGTTTTCGTCATTGGACTTG	.	3	ESCA
SLITRK3	0	.	GRCh37	3	164905307	164905307	+	3'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*378A>G	.	.	ENST00000475390	2/2	84	38	45	52	52	0	SLITRK3,3_prime_UTR_variant,,ENST00000475390,;SLITRK3,3_prime_UTR_variant,,ENST00000241274,;SLITRK3,downstream_gene_variant,,ENST00000497724,;	C	ENSG00000121871	ENST00000475390	Transcript	3_prime_UTR_variant	3756	.	.	.	.	.	.	.	-1	SLITRK3	HGNC	23501	protein_coding	YES	CCDS3197.1	ENSP00000420091	SLIK3_HUMAN	C9K0R4_HUMAN	UPI000004F259	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATAGTTACTG	.	5	ESCA
NLGN1	0	.	GRCh37	3	173999902	173999902	+	3'UTR	SNP	G	G	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*809G>T	.	.	ENST00000457714	7/7	82	66	16	51	50	0	NLGN1,3_prime_UTR_variant,,ENST00000457714,;NLGN1,3_prime_UTR_variant,,ENST00000361589,;NLGN1,intron_variant,,ENST00000545397,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000469564,;NLGN1,downstream_gene_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;	T	ENSG00000169760	ENST00000457714	Transcript	3_prime_UTR_variant	3710	.	.	.	.	.	.	.	1	NLGN1	HGNC	14291	protein_coding	YES	CCDS3222.1	ENSP00000392500	NLGN1_HUMAN	.	UPI0000072F54	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAAGGTATT	.	5	ESCA
ATP13A3	0	.	GRCh37	3	194146182	194146182	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3202A>G	p.Ile1068Val	p.I1068V	ENST00000439040	30/33	60	44	16	44	44	0	ATP13A3,missense_variant,p.Ile1068Val,ENST00000256031,;ATP13A3,missense_variant,p.Ile1068Val,ENST00000439040,;ATP13A3,upstream_gene_variant,,ENST00000429136,;	C	ENSG00000133657	ENST00000439040	Transcript	missense_variant	3994	3202	1068	I/V	Ata/Gta	.	.	.	-1	ATP13A3	HGNC	24113	protein_coding	YES	CCDS43187.1	ENSP00000416508	AT133_HUMAN	C9JAP7_HUMAN,C9J7Z7_HUMAN	UPI000049DFC3	.	tolerated(0.44)	benign(0.023)	30/33	.	hmmpanther:PTHR24093:SF249,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01657,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTATATTAT	.	5	ESCA
FAM86DP	0	.	GRCh37	3	75478287	75478287	+	Intron	SNP	C	C	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.379G>T	.	.	ENST00000459803	4/8	123	70	52	224	224	0	FAM86DP,splice_region_variant,,ENST00000459803,;FAM86DP,intron_variant,,ENST00000489609,;FAM86DP,intron_variant,,ENST00000484945,;FAM86DP,intron_variant,,ENST00000491583,;FAM86DP,intron_variant,,ENST00000478666,;FAM86DP,intron_variant,,ENST00000497543,;FAM86DP,splice_region_variant,,ENST00000477247,;	A	ENSG00000244026	ENST00000459803	Transcript	splice_region_variant	379	.	.	.	.	.	.	.	-1	FAM86DP	HGNC	32659	processed_transcript	YES	.	.	.	.	.	.	.	.	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATACCAGCAA	.	5	ESCA
ROBO2	0	.	GRCh37	3	77671452	77671452	+	Missense_Mutation	SNP	C	C	G	rs755603547	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3677C>G	p.Ser1226Cys	p.S1226C	ENST00000487694	24/27	42	31	11	72	72	0	ROBO2,missense_variant,p.Ser1210Cys,ENST00000332191,;ROBO2,missense_variant,p.Ser1210Cys,ENST00000461745,;ROBO2,missense_variant,p.Ser42Cys,ENST00000475334,;ROBO2,missense_variant,p.Ser1226Cys,ENST00000487694,;ROBO2,downstream_gene_variant,,ENST00000490991,;ROBO2,downstream_gene_variant,,ENST00000469233,;ROBO2,3_prime_UTR_variant,,ENST00000473767,;	G	ENSG00000185008	ENST00000487694	Transcript	missense_variant	3956	3677	1226	S/C	tCt/tGt	rs755603547	.	.	1	ROBO2	HGNC	10250	protein_coding	YES	CCDS54609.1	ENSP00000417335	ROBO2_HUMAN	H9XFA4_HUMAN	UPI0000D891EC	.	tolerated(0.06)	possibly_damaging(0.7)	24/27	.	hmmpanther:PTHR10489:SF27,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCTGATT	byFrequency	5	ESCA
ROBO1	0	.	GRCh37	3	78646931	78646931	+	3'UTR	SNP	A	A	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1132T>G	.	.	ENST00000464233	31/31	45	26	18	51	51	0	ROBO1,3_prime_UTR_variant,,ENST00000464233,;ROBO1,3_prime_UTR_variant,,ENST00000436010,;ROBO1,downstream_gene_variant,,ENST00000495273,;ROBO1,downstream_gene_variant,,ENST00000467549,;ROBO1,downstream_gene_variant,,ENST00000466906,;	C	ENSG00000169855	ENST00000464233	Transcript	3_prime_UTR_variant	6202	.	.	.	.	.	.	.	-1	ROBO1	HGNC	10249	protein_coding	YES	CCDS54611.1	ENSP00000420321	ROBO1_HUMAN	.	UPI00000713D9	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGTATGCAT	.	5	ESCA
CYP2U1	0	.	GRCh37	4	108866175	108866175	+	Silent	SNP	C	C	T	rs778117975	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.540C>T	p.%3D	p.F180F	ENST00000332884	2/5	55	42	13	78	78	0	CYP2U1,synonymous_variant,p.%3D,ENST00000332884,;CYP2U1,5_prime_UTR_variant,,ENST00000508453,;RP11-286E11.1,intron_variant,,ENST00000513071,;RP11-286E11.2,upstream_gene_variant,,ENST00000512428,;	T	ENSG00000155016	ENST00000332884	Transcript	synonymous_variant	815	540	180	F	ttC/ttT	rs778117975	.	.	1	CYP2U1	HGNC	20582	protein_coding	YES	CCDS34047.1	ENSP00000333212	CP2U1_HUMAN	E9PGH5_HUMAN,B4DQW9_HUMAN	UPI0000044231	.	.	.	2/5	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF51,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTCTCTCA	.	5	ESCA
NDNF	0	.	GRCh37	4	121957628	121957628	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498C>A	p.Gln500Lys	p.Q500K	ENST00000379692	4/4	70	46	24	73	73	0	NDNF,missense_variant,p.Gln500Lys,ENST00000379692,;NDNF,downstream_gene_variant,,ENST00000515757,;NDNF,downstream_gene_variant,,ENST00000511408,;NDNF,downstream_gene_variant,,ENST00000506900,;	T	ENSG00000173376	ENST00000379692	Transcript	missense_variant	2025	1498	500	Q/K	Caa/Aaa	.	.	.	-1	NDNF	HGNC	26256	protein_coding	YES	CCDS3717.2	ENSP00000369014	NDNF_HUMAN	D6RF18_HUMAN,D6R972_HUMAN	UPI00001D6985	.	tolerated(0.29)	benign(0.119)	4/4	.	hmmpanther:PTHR14619,hmmpanther:PTHR14619:SF1,Pfam_domain:PF10179,SMART_domains:SM00060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTGGTTTT	.	5	ESCA
TENM3	0	.	GRCh37	4	183713835	183713835	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6010A>G	p.Ile2004Val	p.I2004V	ENST00000511685	26/28	40	19	20	78	77	0	TENM3,missense_variant,p.Ile2004Val,ENST00000511685,;TENM3,missense_variant,p.Ile2004Val,ENST00000406950,;	G	ENSG00000218336	ENST00000511685	Transcript	missense_variant	6133	6010	2004	I/V	Att/Gtt	.	.	.	1	TENM3	HGNC	29944	protein_coding	YES	CCDS47165.1	ENSP00000424226	TEN3_HUMAN	G3CAS9_HUMAN,D6RGC5_HUMAN	UPI00006C0820	.	tolerated(0.06)	benign(0.141)	26/28	.	hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGATTTTC	.	5	ESCA
GRXCR1	0	.	GRCh37	4	42965095	42965095	+	Nonsense_Mutation	SNP	C	C	T	rs754115014	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.571C>T	p.Arg191Ter	p.R191*	ENST00000399770	2/4	61	40	20	103	103	0	GRXCR1,stop_gained,p.Arg191Ter,ENST00000399770,;	T	ENSG00000215203	ENST00000399770	Transcript	stop_gained	571	571	191	R/*	Cga/Tga	rs754115014,COSM1618849,COSM1253848	.	.	1	GRXCR1	HGNC	31673	protein_coding	YES	CCDS43225.1	ENSP00000382670	GRCR1_HUMAN	.	UPI00004191A5	.	.	.	2/4	.	PROSITE_profiles:PS51354,hmmpanther:PTHR10168:SF65,hmmpanther:PTHR10168,Pfam_domain:PF00462,Gene3D:3.40.30.10,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.R190Q|c.569G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGACGAGTT	byFrequency	5	ESCA
TMPRSS11B	0	.	GRCh37	4	69096947	69096947	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660A>G	p.%3D	p.L220L	ENST00000332644	7/10	53	38	15	42	42	0	TMPRSS11B,synonymous_variant,p.%3D,ENST00000332644,;TMPRSS11B,upstream_gene_variant,,ENST00000510856,;TMPRSS11B,downstream_gene_variant,,ENST00000502365,;RP11-646E20.6,upstream_gene_variant,,ENST00000514295,;	C	ENSG00000185873	ENST00000332644	Transcript	synonymous_variant	822	660	220	L	ctA/ctG	.	.	.	-1	TMPRSS11B	HGNC	25398	protein_coding	YES	CCDS3521.1	ENSP00000330475	TM11B_HUMAN	.	UPI000013E249	.	.	.	7/10	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF90,Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF037941,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATAATAGCCA	.	5	ESCA
PARM1	0	.	GRCh37	4	75959102	75959102	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.779C>T	p.Ala260Val	p.A260V	ENST00000307428	3/4	53	36	17	72	72	0	PARM1,missense_variant,p.Ala260Val,ENST00000307428,;PARM1,missense_variant,p.Ala18Val,ENST00000513238,;RP11-44F21.2,intron_variant,,ENST00000513770,;	T	ENSG00000169116	ENST00000307428	Transcript	missense_variant	991	779	260	A/V	gCc/gTc	.	.	.	1	PARM1	HGNC	24536	protein_coding	YES	CCDS47077.1	ENSP00000370224	PARM1_HUMAN	.	UPI000004457B	.	tolerated(0.17)	possibly_damaging(0.768)	3/4	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCGCCGCCA	.	5	ESCA
PRDM8	0	.	GRCh37	4	81123458	81123458	+	Missense_Mutation	SNP	A	A	T	rs764924018	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.842A>T	p.Gln281Leu	p.Q281L	ENST00000339711	10/10	18	14	4	10	10	0	PRDM8,missense_variant,p.Gln281Leu,ENST00000504452,;PRDM8,missense_variant,p.Gln281Leu,ENST00000515013,;PRDM8,missense_variant,p.Gln281Leu,ENST00000339711,;PRDM8,missense_variant,p.Gln281Leu,ENST00000415738,;	T	ENSG00000152784	ENST00000339711	Transcript	missense_variant	2073	842	281	Q/L	cAg/cTg	rs764924018	.	.	1	PRDM8	HGNC	13993	protein_coding	YES	CCDS43243.1	ENSP00000339764	PRDM8_HUMAN	Q05CA1_HUMAN,E9PEH0_HUMAN	UPI0000422A1D	.	tolerated_low_confidence(0.35)	benign(0)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCAGAGCC	byFrequency	5	ESCA
MARCH6	0	.	GRCh37	5	10410318	10410318	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621G>T	p.Glu541Ter	p.E541*	ENST00000274140	18/26	66	40	26	90	90	0	MARCH6,stop_gained,p.Glu493Ter,ENST00000449913,;MARCH6,stop_gained,p.Glu239Ter,ENST00000510792,;MARCH6,stop_gained,p.Glu541Ter,ENST00000274140,;MARCH6,stop_gained,p.Glu436Ter,ENST00000503788,;MARCH6,upstream_gene_variant,,ENST00000505253,;MARCH6,non_coding_transcript_exon_variant,,ENST00000511802,;MARCH6,non_coding_transcript_exon_variant,,ENST00000512449,;	T	ENSG00000145495	ENST00000274140	Transcript	stop_gained	1753	1621	541	E/*	Gaa/Taa	COSM3428805	.	.	1	MARCH6	HGNC	30550	protein_coding	YES	CCDS34135.1	ENSP00000274140	MARH6_HUMAN	.	UPI00001B94D6	.	.	.	18/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13145:SF0,hmmpanther:PTHR13145	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTCGAACAG	.	5	ESCA
APC	0	.	GRCh37	5	112176831	112176831	+	Missense_Mutation	SNP	C	C	T	rs371686531	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5540C>T	p.Thr1847Met	p.T1847M	ENST00000457016	16/16	38	25	12	60	60	0	APC,missense_variant,p.Thr1847Met,ENST00000257430,;APC,missense_variant,p.Thr1847Met,ENST00000457016,;APC,missense_variant,p.Thr1847Met,ENST00000508376,;APC,downstream_gene_variant,,ENST00000507379,;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000502371,;APC,downstream_gene_variant,,ENST00000514164,;	T	ENSG00000134982	ENST00000457016	Transcript	missense_variant	5920	5540	1847	T/M	aCg/aTg	rs371686531	.	.	1	APC	HGNC	583	protein_coding	YES	CCDS4107.1	ENSP00000413133	APC_HUMAN	Q9UM98_HUMAN,Q9P119_HUMAN,Q9HAW6_HUMAN,Q4LE70_HUMAN,E9PFT7_HUMAN,D6RFL6_HUMAN,B2ZRE1_HUMAN,A5HB97_HUMAN,A5HB96_HUMAN,A5HB95_HUMAN,A5HB94_HUMAN,A1YIQ7_HUMAN	UPI000013CF60	.	.	probably_damaging(0.973)	16/16	.	hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11,Pfam_domain:PF05923	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACACGCCTA	byFrequency|byCluster	5	ESCA
SEMA6A	0	.	GRCh37	5	115781045	115781045	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1264G>C	.	.	ENST00000343348	19/19	39	29	10	36	36	0	SEMA6A,3_prime_UTR_variant,,ENST00000343348,;SEMA6A,downstream_gene_variant,,ENST00000510263,;SEMA6A,downstream_gene_variant,,ENST00000515129,;SEMA6A,downstream_gene_variant,,ENST00000257414,;SEMA6A,downstream_gene_variant,,ENST00000513137,;SEMA6A,downstream_gene_variant,,ENST00000282394,;SEMA6A,downstream_gene_variant,,ENST00000503865,;CTB-118N6.3,upstream_gene_variant,,ENST00000512128,;CTB-118N6.3,upstream_gene_variant,,ENST00000510682,;CTB-118N6.3,upstream_gene_variant,,ENST00000514214,;CTB-118N6.3,upstream_gene_variant,,ENST00000508424,;CTB-118N6.3,upstream_gene_variant,,ENST00000508640,;SEMA6A,downstream_gene_variant,,ENST00000506114,;AC010296.1,upstream_gene_variant,,ENST00000542571,;	G	ENSG00000092421	ENST00000343348	Transcript	3_prime_UTR_variant	5145	.	.	.	.	.	.	.	-1	SEMA6A	HGNC	10738	protein_coding	YES	CCDS47256.1	ENSP00000345512	SEM6A_HUMAN	D6RCR0_HUMAN,D6RAG9_HUMAN	UPI000020C463	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TAACCCCACGA	.	4	ESCA
NPY6R	0	.	GRCh37	5	137144064	137144064	+	RNA	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.612T>C	.	.	ENST00000510937	2/2	64	41	23	67	67	0	NPY6R,non_coding_transcript_exon_variant,,ENST00000510937,;NPY6R,non_coding_transcript_exon_variant,,ENST00000503807,;	C	ENSG00000226306	ENST00000510937	Transcript	non_coding_transcript_exon_variant	612	.	.	.	.	.	.	.	1	NPY6R	HGNC	7959	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCTCTCAT	.	5	ESCA
DNAH5	0	.	GRCh37	5	13737400	13737400	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11416G>C	p.Glu3806Gln	p.E3806Q	ENST00000265104	66/79	46	43	3	54	54	0	DNAH5,missense_variant,p.Glu3806Gln,ENST00000265104,;	G	ENSG00000039139	ENST00000265104	Transcript	missense_variant	11521	11416	3806	E/Q	Gaa/Caa	COSM1741407	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.403)	66/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AACTTCTGTCT	.	2	ESCA
EBF1	0	.	GRCh37	5	158140134	158140134	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213G>A	p.Ala405Thr	p.A405T	ENST00000313708	13/16	76	71	5	59	59	0	EBF1,missense_variant,p.Ala374Thr,ENST00000380654,;EBF1,missense_variant,p.Ala405Thr,ENST00000313708,;EBF1,missense_variant,p.Ala397Thr,ENST00000517373,;EBF1,non_coding_transcript_exon_variant,,ENST00000518836,;EBF1,non_coding_transcript_exon_variant,,ENST00000519890,;EBF1,non_coding_transcript_exon_variant,,ENST00000522192,;EBF1,non_coding_transcript_exon_variant,,ENST00000519739,;	T	ENSG00000164330	ENST00000313708	Transcript	missense_variant	1496	1213	405	A/T	Gcc/Acc	COSM1204857	.	.	-1	EBF1	HGNC	3126	protein_coding	YES	CCDS4343.1	ENSP00000322898	COE1_HUMAN	.	UPI000000D95E	.	deleterious_low_confidence(0.04)	benign(0.21)	13/16	.	hmmpanther:PTHR10747	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D406N|c.1216G>A|3	MUTECT|MUSE	GTCGGCCGCTC	.	2	ESCA
GABRG2	0	.	GRCh37	5	161522567	161522567	+	Missense_Mutation	SNP	T	T	A	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326T>A	p.Met109Lys	p.M109K	ENST00000414552	3/11	49	42	7	57	57	0	GABRG2,missense_variant,p.Met14Lys,ENST00000393933,;GABRG2,missense_variant,p.Met109Lys,ENST00000361925,;GABRG2,missense_variant,p.Met109Lys,ENST00000356592,;GABRG2,missense_variant,p.Met14Lys,ENST00000522053,;GABRG2,missense_variant,p.Met109Lys,ENST00000414552,;GABRG2,missense_variant,p.Met109Lys,ENST00000522990,;GABRG2,splice_region_variant,,ENST00000523372,;	A	ENSG00000113327	ENST00000414552	Transcript	missense_variant	551	326	109	M/K	aTg/aAg	COSM1619986	.	.	1	GABRG2	HGNC	4087	protein_coding	YES	CCDS47333.1	ENSP00000410732	GBRG2_HUMAN	.	UPI00017503BD	.	deleterious(0)	benign(0.406)	3/11	.	Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945:SF498,hmmpanther:PTHR18945	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATATGGTGA	.	5	ESCA
NIPBL	0	.	GRCh37	5	36972125	36972125	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.850A>T	p.Ser284Cys	p.S284C	ENST00000282516	8/47	38	24	14	62	62	0	NIPBL,missense_variant,p.Ser284Cys,ENST00000448238,;NIPBL,missense_variant,p.Ser284Cys,ENST00000282516,;NIPBL,non_coding_transcript_exon_variant,,ENST00000504430,;NIPBL,non_coding_transcript_exon_variant,,ENST00000505998,;	T	ENSG00000164190	ENST00000282516	Transcript	missense_variant	1349	850	284	S/C	Agt/Tgt	.	.	.	1	NIPBL	HGNC	28862	protein_coding	YES	CCDS3920.1	ENSP00000282516	NIPBL_HUMAN	A2RRA7_HUMAN	UPI00003761B5	.	deleterious_low_confidence(0)	probably_damaging(0.997)	8/47	.	hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAAGTGAA	.	5	ESCA
DAB2	0	.	GRCh37	5	39425034	39425034	+	5'UTR	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-230T>C	.	.	ENST00000320816	1/15	9	6	3	14	14	0	DAB2,5_prime_UTR_variant,,ENST00000339788,;DAB2,5_prime_UTR_variant,,ENST00000320816,;DAB2,5_prime_UTR_variant,,ENST00000545653,;DAB2,5_prime_UTR_variant,,ENST00000515700,;DAB2,intron_variant,,ENST00000511792,;DAB2,upstream_gene_variant,,ENST00000503513,;DAB2,intron_variant,,ENST00000509457,;DAB2,upstream_gene_variant,,ENST00000511536,;DAB2,upstream_gene_variant,,ENST00000515269,;C9,upstream_gene_variant,,ENST00000483232,;DAB2,non_coding_transcript_exon_variant,,ENST00000502388,;DAB2,upstream_gene_variant,,ENST00000507539,;	G	ENSG00000153071	ENST00000320816	Transcript	5_prime_UTR_variant	239	.	.	.	.	.	.	.	-1	DAB2	HGNC	2662	protein_coding	YES	CCDS34149.1	ENSP00000313391	DAB2_HUMAN	D6RIA5_HUMAN,D6RGZ1_HUMAN,D6REB1_HUMAN	UPI0000169E27	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGCCACTCCC	.	2	ESCA
HCN1	0	.	GRCh37	5	45261098	45261098	+	3'UTR	SNP	C	C	G	rs559025160	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*925G>C	.	.	ENST00000303230	8/8	42	29	12	43	43	0	HCN1,3_prime_UTR_variant,,ENST00000303230,;	G	ENSG00000164588	ENST00000303230	Transcript	3_prime_UTR_variant	3656	.	.	.	.	rs559025160	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	.	.	8/8	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCGAGCA	by1000G	5	ESCA
HCN1	0	.	GRCh37	5	45262772	45262772	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1924C>T	p.Pro642Ser	p.P642S	ENST00000303230	8/8	62	49	12	58	58	0	HCN1,missense_variant,p.Pro642Ser,ENST00000303230,;	A	ENSG00000164588	ENST00000303230	Transcript	missense_variant	1982	1924	642	P/S	Cct/Tct	.	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	tolerated(0.49)	benign(0)	8/8	.	hmmpanther:PTHR10217:SF373,hmmpanther:PTHR10217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGGATAAT	.	5	ESCA
CTD-2324F15.2	0	.	GRCh37	5	6312341	6312341	+	RNA	DEL	T	T	-	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.632delA	.	.	ENST00000507444	2/2	37	29	7	42	42	0	CTD-2324F15.2,non_coding_transcript_exon_variant,,ENST00000507444,;	-	ENSG00000250490	ENST00000507444	Transcript	non_coding_transcript_exon_variant	632	.	.	.	.	.	.	.	-1	CTD-2324F15.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGGTGATTTTTT	.	2	ESCA
MAP1B	0	.	GRCh37	5	71495574	71495574	+	Missense_Mutation	SNP	C	C	T	rs747707013	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6392C>T	p.Pro2131Leu	p.P2131L	ENST00000296755	5/7	43	30	13	34	34	0	MAP1B,missense_variant,p.Pro2131Leu,ENST00000296755,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000513526,;	T	ENSG00000131711	ENST00000296755	Transcript	missense_variant	6690	6392	2131	P/L	cCg/cTg	rs747707013	.	.	1	MAP1B	HGNC	6836	protein_coding	YES	CCDS4012.1	ENSP00000296755	MAP1B_HUMAN	D6RGJ3_HUMAN,D6RA40_HUMAN	UPI000013E382	.	.	benign(0.253)	5/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13843,hmmpanther:PTHR13843:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCACCGCCTC	byFrequency	5	ESCA
ZDHHC11	0	.	GRCh37	5	840629	840629	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.765C>T	p.%3D	p.L255L	ENST00000283441	5/13	69	55	13	87	87	0	ZDHHC11,synonymous_variant,p.%3D,ENST00000283441,;ZDHHC11,synonymous_variant,p.%3D,ENST00000511193,;ZDHHC11,synonymous_variant,p.%3D,ENST00000511539,;ZDHHC11,synonymous_variant,p.%3D,ENST00000424784,;ZDHHC11,non_coding_transcript_exon_variant,,ENST00000503758,;ZDHHC11,intron_variant,,ENST00000508951,;ZDHHC11,synonymous_variant,p.%3D,ENST00000507800,;ZDHHC11,downstream_gene_variant,,ENST00000503880,;ZDHHC11,downstream_gene_variant,,ENST00000512190,;ZDHHC11,downstream_gene_variant,,ENST00000505815,;	A	ENSG00000188818	ENST00000283441	Transcript	synonymous_variant	1149	765	255	L	ctC/ctT	.	.	.	-1	ZDHHC11	HGNC	19158	protein_coding	YES	CCDS3857.1	ENSP00000283441	ZDH11_HUMAN	.	UPI000013C384	.	.	.	5/13	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22883:SF22,hmmpanther:PTHR22883,Pfam_domain:PF01529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATGAGCAG	.	5	ESCA
SYNE1	0	.	GRCh37	6	152652910	152652910	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12910G>A	p.Glu4304Lys	p.E4304K	ENST00000367255	78/146	69	55	13	75	75	0	SYNE1,missense_variant,p.Glu4233Lys,ENST00000448038,;SYNE1,missense_variant,p.Glu4304Lys,ENST00000367255,;SYNE1,missense_variant,p.Glu4233Lys,ENST00000423061,;SYNE1,missense_variant,p.Glu4169Lys,ENST00000341594,;SYNE1,missense_variant,p.Glu4304Lys,ENST00000265368,;SYNE1,non_coding_transcript_exon_variant,,ENST00000490135,;SYNE1,downstream_gene_variant,,ENST00000471834,;	T	ENSG00000131018	ENST00000367255	Transcript	missense_variant	13512	12910	4304	E/K	Gag/Aag	.	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	benign(0.242)	78/146	.	Superfamily_domains:SSF46966,Superfamily_domains:SSF46966,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCTCTATCA	.	5	ESCA
OR2B6	0	.	GRCh37	6	27925834	27925834	+	Missense_Mutation	SNP	G	G	C	rs369732488	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.816G>C	p.Lys272Asn	p.K272N	ENST00000244623	1/1	56	41	15	55	55	0	OR2B6,missense_variant,p.Lys272Asn,ENST00000244623,;	C	ENSG00000124657	ENST00000244623	Transcript	missense_variant	816	816	272	K/N	aaG/aaC	rs369732488	.	.	1	OR2B6	HGNC	8241	protein_coding	YES	CCDS4642.1	ENSP00000244623	OR2B6_HUMAN	.	UPI000003F061	.	deleterious(0)	probably_damaging(0.994)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF202,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAAGATGGT	byFrequency|byCluster	5	ESCA
MSH5	0	.	GRCh37	6	31725827	31725827	+	Intron	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015-115C>T	.	.	ENST00000375703	.	23	18	5	11	11	0	MSH5,5_prime_UTR_variant,,ENST00000395853,;MSH5,intron_variant,,ENST00000375740,;MSH5,intron_variant,,ENST00000375755,;MSH5,intron_variant,,ENST00000375750,;MSH5,intron_variant,,ENST00000534153,;MSH5,intron_variant,,ENST00000450148,;MSH5,intron_variant,,ENST00000375742,;MSH5,intron_variant,,ENST00000375703,;MSH5,intron_variant,,ENST00000431848,;SAPCD1,upstream_gene_variant,,ENST00000415669,;SAPCD1,upstream_gene_variant,,ENST00000425424,;MSH5,upstream_gene_variant,,ENST00000429846,;SAPCD1,upstream_gene_variant,,ENST00000433778,;RNU6-850P,upstream_gene_variant,,ENST00000516934,;MSH5,intron_variant,,ENST00000468602,;MSH5-SAPCD1,upstream_gene_variant,,ENST00000491552,;MSH5-SAPCD1,intron_variant,,ENST00000493662,;MSH5,intron_variant,,ENST00000423982,;MSH5,intron_variant,,ENST00000463144,;MSH5,intron_variant,,ENST00000468136,;MSH5,upstream_gene_variant,,ENST00000494646,;MSH5-SAPCD1,upstream_gene_variant,,ENST00000498473,;MSH5-SAPCD1,upstream_gene_variant,,ENST00000476085,;MSH5,upstream_gene_variant,,ENST00000467319,;MSH5,upstream_gene_variant,,ENST00000484309,;MSH5,upstream_gene_variant,,ENST00000494458,;MSH5,downstream_gene_variant,,ENST00000497269,;	T	ENSG00000204410	ENST00000375703	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MSH5	HGNC	7328	protein_coding	YES	CCDS34410.1	ENSP00000364855	MSH5_HUMAN	Q5SSR2_HUMAN	UPI0000070722	.	.	.	.	12/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTCCCTCT	.	5	ESCA
DNAH8	0	.	GRCh37	6	38828241	38828241	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5316G>T	p.Met1772Ile	p.M1772I	ENST00000359357	41/91	55	31	24	53	53	0	DNAH8,missense_variant,p.Met1772Ile,ENST00000359357,;DNAH8,missense_variant,p.Met1977Ile,ENST00000327475,;DNAH8,missense_variant,p.Met1772Ile,ENST00000441566,;DNAH8,missense_variant,p.Met1989Ile,ENST00000449981,;DNAH8,upstream_gene_variant,,ENST00000394393,;	T	ENSG00000124721	ENST00000359357	Transcript	missense_variant	5570	5316	1772	M/I	atG/atT	.	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	benign(0.206)	41/91	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATGCATAT	.	5	ESCA
CENPQ	0	.	GRCh37	6	49460500	49460500	+	3'UTR	SNP	A	A	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*512A>T	.	.	ENST00000335783	9/9	44	33	11	28	28	0	CENPQ,3_prime_UTR_variant,,ENST00000335783,;	T	ENSG00000031691	ENST00000335783	Transcript	3_prime_UTR_variant	1413	.	.	.	.	.	.	.	1	CENPQ	HGNC	21347	protein_coding	YES	CCDS4925.1	ENSP00000337289	CENPQ_HUMAN	.	UPI000020DE7B	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAGATATGC	.	5	ESCA
LMBRD1	0	.	GRCh37	6	70506734	70506734	+	Missense_Mutation	SNP	C	C	G	rs779667411	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40G>C	p.Gly14Arg	p.G14R	ENST00000370577	1/16	50	35	15	66	66	0	LMBRD1,missense_variant,p.Gly14Arg,ENST00000370577,;LMBRD1,missense_variant,p.Gly14Arg,ENST00000472827,;	G	ENSG00000168216	ENST00000370577	Transcript	missense_variant	270	40	14	G/R	Ggc/Cgc	rs779667411	.	.	-1	LMBRD1	HGNC	23038	protein_coding	YES	CCDS4969.1	ENSP00000359609	LMBD1_HUMAN	.	UPI000003ED25	.	deleterious(0)	probably_damaging(1)	1/16	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR16130:SF2,hmmpanther:PTHR16130	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCCGATCA	.	5	ESCA
FAM135A	0	.	GRCh37	6	71236398	71236398	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3611A>C	p.Gln1204Pro	p.Q1204P	ENST00000418814	15/22	26	17	8	16	16	0	FAM135A,missense_variant,p.Gln991Pro,ENST00000457062,;FAM135A,missense_variant,p.Gln1204Pro,ENST00000505868,;FAM135A,missense_variant,p.Gln1008Pro,ENST00000361499,;FAM135A,missense_variant,p.Gln784Pro,ENST00000505769,;FAM135A,missense_variant,p.Gln1204Pro,ENST00000418814,;FAM135A,missense_variant,p.Gln991Pro,ENST00000370479,;FAM135A,downstream_gene_variant,,ENST00000515323,;FAM135A,3_prime_UTR_variant,,ENST00000194672,;FAM135A,downstream_gene_variant,,ENST00000393299,;	C	ENSG00000082269	ENST00000418814	Transcript	missense_variant	4225	3611	1204	Q/P	cAa/cCa	.	.	.	1	FAM135A	HGNC	21084	protein_coding	YES	CCDS55028.1	ENSP00000410768	F135A_HUMAN	D6RFG9_HUMAN,D6REA8_HUMAN,D6RC17_HUMAN	UPI000004A0FF	.	tolerated(0.21)	benign(0.397)	15/22	.	hmmpanther:PTHR12482,hmmpanther:PTHR12482:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AATACAAGCGT	.	4	ESCA
RIMS1	0	.	GRCh37	6	73100340	73100340	+	Silent	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4407C>T	p.%3D	p.S1469S	ENST00000521978	30/34	50	35	15	49	49	0	RIMS1,synonymous_variant,p.%3D,ENST00000491071,;RIMS1,synonymous_variant,p.%3D,ENST00000517827,;RIMS1,synonymous_variant,p.%3D,ENST00000453976,;RIMS1,synonymous_variant,p.%3D,ENST00000522291,;RIMS1,synonymous_variant,p.%3D,ENST00000538414,;RIMS1,synonymous_variant,p.%3D,ENST00000522211,;RIMS1,synonymous_variant,p.%3D,ENST00000520567,;RIMS1,synonymous_variant,p.%3D,ENST00000518273,;RIMS1,synonymous_variant,p.%3D,ENST00000517960,;RIMS1,synonymous_variant,p.%3D,ENST00000517433,;RIMS1,synonymous_variant,p.%3D,ENST00000523963,;RIMS1,synonymous_variant,p.%3D,ENST00000425662,;RIMS1,synonymous_variant,p.%3D,ENST00000264839,;RIMS1,synonymous_variant,p.%3D,ENST00000401910,;RIMS1,synonymous_variant,p.%3D,ENST00000348717,;RIMS1,synonymous_variant,p.%3D,ENST00000521978,;RIMS1,synonymous_variant,p.%3D,ENST00000370420,;RIMS1,5_prime_UTR_variant,,ENST00000414192,;RIMS1,non_coding_transcript_exon_variant,,ENST00000431478,;RIMS1,non_coding_transcript_exon_variant,,ENST00000463023,;	T	ENSG00000079841	ENST00000521978	Transcript	synonymous_variant	4407	4407	1469	S	agC/agT	.	.	.	1	RIMS1	HGNC	17282	protein_coding	YES	CCDS47449.1	ENSP00000428417	RIMS1_HUMAN	.	UPI00001908FB	.	.	.	30/34	.	hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGCACAGA	.	5	ESCA
GPR63	0	.	GRCh37	6	97246324	97246324	+	3'UTR	SNP	C	C	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*24G>C	.	.	ENST00000229955	2/2	41	26	15	47	47	0	GPR63,3_prime_UTR_variant,,ENST00000417980,;GPR63,3_prime_UTR_variant,,ENST00000229955,;RP3-417O22.3,downstream_gene_variant,,ENST00000442184,;	G	ENSG00000112218	ENST00000229955	Transcript	3_prime_UTR_variant	1630	.	.	.	.	.	.	.	-1	GPR63	HGNC	13302	protein_coding	YES	CCDS5036.1	ENSP00000229955	GPR63_HUMAN	A8K1C4_HUMAN	UPI0000037594	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCACCCAAAAT	.	4	ESCA
TAS2R16	0	.	GRCh37	7	122634852	122634852	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837C>T	p.%3D	p.S279S	ENST00000249284	1/1	49	33	15	53	53	0	TAS2R16,synonymous_variant,p.%3D,ENST00000249284,;	A	ENSG00000128519	ENST00000249284	Transcript	synonymous_variant	903	837	279	S	agC/agT	.	.	.	-1	TAS2R16	HGNC	14921	protein_coding	YES	CCDS5785.1	ENSP00000249284	T2R16_HUMAN	Q50KN6_HUMAN	UPI0000038B18	.	.	.	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11394,Pfam_domain:PF05296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTGCTCAG	.	5	ESCA
POT1	0	.	GRCh37	7	124569039	124569039	+	5'UTR	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-397A>G	.	.	ENST00000357628	2/19	23	18	5	27	27	0	POT1,5_prime_UTR_variant,,ENST00000446993,;POT1,5_prime_UTR_variant,,ENST00000357628,;POT1,5_prime_UTR_variant,,ENST00000609702,;POT1,5_prime_UTR_variant,,ENST00000393329,;POT1-AS1,upstream_gene_variant,,ENST00000449642,;POT1-AS1,upstream_gene_variant,,ENST00000429134,;POT1-AS1,upstream_gene_variant,,ENST00000453342,;POT1-AS1,upstream_gene_variant,,ENST00000435452,;POT1,non_coding_transcript_exon_variant,,ENST00000461288,;POT1,non_coding_transcript_exon_variant,,ENST00000464453,;POT1,non_coding_transcript_exon_variant,,ENST00000608261,;POT1,non_coding_transcript_exon_variant,,ENST00000608437,;POT1,5_prime_UTR_variant,,ENST00000609106,;	C	ENSG00000128513	ENST00000357628	Transcript	5_prime_UTR_variant	203	.	.	.	.	.	.	.	-1	POT1	HGNC	17284	protein_coding	YES	CCDS5793.1	ENSP00000350249	POTE1_HUMAN	C9JPG9_HUMAN,A8MTK3_HUMAN	UPI0000073E3F	.	.	.	2/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAATCTGAC	.	2	ESCA
TRPV6	0	.	GRCh37	7	142569373	142569374	+	3'UTR	DEL	GA	GA	-	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	GA	GA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*86_*87delTC	.	.	ENST00000359396	15/15	50	36	14	37	37	0	TRPV6,3_prime_UTR_variant,,ENST00000359396,;EPHB6,downstream_gene_variant,,ENST00000442129,;EPHB6,downstream_gene_variant,,ENST00000411471,;TRPV6,downstream_gene_variant,,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000392957,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;TRPV6,non_coding_transcript_exon_variant,,ENST00000487077,;TRPV6,non_coding_transcript_exon_variant,,ENST00000463646,;EPHB6,downstream_gene_variant,,ENST00000471581,;EPHB6,downstream_gene_variant,,ENST00000422643,;EPHB6,downstream_gene_variant,,ENST00000486511,;EPHB6,downstream_gene_variant,,ENST00000466783,;EPHB6,downstream_gene_variant,,ENST00000425995,;TRPV6,downstream_gene_variant,,ENST00000474388,;	-	ENSG00000165125	ENST00000359396	Transcript	3_prime_UTR_variant	2510-2511	.	.	.	.	.	.	.	-1	TRPV6	HGNC	14006	protein_coding	YES	CCDS5874.1	ENSP00000352358	TRPV6_HUMAN	Q9NXZ3_HUMAN,Q8NBV5_HUMAN,C9J9W0_HUMAN	UPI000000D91B	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GGAGATGAGACCT	.	2	ESCA
MACC1	0	.	GRCh37	7	20199486	20199486	+	Silent	SNP	G	G	A	rs146810957	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.498C>T	p.%3D	p.H166H	ENST00000400331	5/7	19	12	6	31	31	0	MACC1,synonymous_variant,p.%3D,ENST00000589011,;MACC1,synonymous_variant,p.%3D,ENST00000400331,;MACC1,synonymous_variant,p.%3D,ENST00000332878,;MACC1,downstream_gene_variant,,ENST00000471019,;	A	ENSG00000183742	ENST00000400331	Transcript	synonymous_variant	807	498	166	H	caC/caT	rs146810957	.	.	-1	MACC1	HGNC	30215	protein_coding	YES	CCDS5369.1	ENSP00000383185	MACC1_HUMAN	.	UPI00001B2F47	.	.	.	5/7	.	hmmpanther:PTHR15603,hmmpanther:PTHR15603:SF1	A:0.0004	A:0	A:0.0014	.	A:0	A:0	A:0.001	A:0.0002	A:0.0006	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCGTGTAG	byFrequency|byCluster|by1000G	5	ESCA
NACAD	0	.	GRCh37	7	45122609	45122609	+	Missense_Mutation	SNP	C	C	T	rs775145169	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3170G>A	p.Arg1057Gln	p.R1057Q	ENST00000490531	2/8	52	37	15	44	44	0	NACAD,missense_variant,p.Arg1057Gln,ENST00000490531,;NACAD,upstream_gene_variant,,ENST00000460409,;	T	ENSG00000136274	ENST00000490531	Transcript	missense_variant	3190	3170	1057	R/Q	cGa/cAa	rs775145169	.	.	-1	NACAD	HGNC	22196	protein_coding	YES	CCDS47582.1	ENSP00000420477	NACAD_HUMAN	.	UPI00001D747D	.	tolerated(0.29)	benign(0.001)	2/8	.	hmmpanther:PTHR21713:SF1,hmmpanther:PTHR21713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCTCGCGCT	.	5	ESCA
PKHD1L1	0	.	GRCh37	8	110457161	110457161	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5063C>A	p.Ser1688Tyr	p.S1688Y	ENST00000378402	38/78	58	49	8	36	36	0	PKHD1L1,missense_variant,p.Ser1688Tyr,ENST00000378402,;	A	ENSG00000205038	ENST00000378402	Transcript	missense_variant	5167	5063	1688	S/Y	tCt/tAt	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	deleterious(0.05)	benign(0.014)	38/78	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF213,Pfam_domain:PF01833,Gene3D:2.60.40.10,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTGCAG	.	4	ESCA
MTBP	0	.	GRCh37	8	121463519	121463521	+	In_Frame_Del	DEL	GAA	GAA	-	rs372780440	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	GAA	GAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390_392delAGA	p.Glu130del	p.E130del	ENST00000305949	4/22	50	42	8	39	39	0	MTBP,inframe_deletion,p.Glu130del,ENST00000305949,;MTBP,inframe_deletion,p.Glu130del,ENST00000523373,;MTBP,non_coding_transcript_exon_variant,,ENST00000522308,;MTBP,non_coding_transcript_exon_variant,,ENST00000456899,;	-	ENSG00000172167	ENST00000305949	Transcript	inframe_deletion	427-429	382-384	128	E/-	GAA/-	rs372780440,COSM1454578	.	.	1	MTBP	HGNC	7417	protein_coding	YES	CCDS6333.1	ENSP00000303398	MTBP_HUMAN	.	UPI00000703F0	.	.	.	4/22	.	hmmpanther:PTHR14382,hmmpanther:PTHR14382:SF1,Pfam_domain:PF14918	-:0.0010	-:0.0038	-:0	.	-:0	-:0	-:0	-:0.0023	-:0	.	0,1	.	.	.	.	.	MODERATE	.	deletion	.	8	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTTTTGAAGAAGA	byFrequency|byCluster|by1000G	2	ESCA
PTK2	0	.	GRCh37	8	141799622	141799622	+	Silent	SNP	C	C	T	rs748726361	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1128G>A	p.%3D	p.L376L	ENST00000340930	14/33	55	48	6	45	45	0	PTK2,synonymous_variant,p.%3D,ENST00000538769,;PTK2,synonymous_variant,p.%3D,ENST00000519654,;PTK2,synonymous_variant,p.%3D,ENST00000521059,;PTK2,synonymous_variant,p.%3D,ENST00000340930,;PTK2,synonymous_variant,p.%3D,ENST00000519419,;PTK2,synonymous_variant,p.%3D,ENST00000395218,;PTK2,synonymous_variant,p.%3D,ENST00000535192,;PTK2,synonymous_variant,p.%3D,ENST00000521986,;PTK2,synonymous_variant,p.%3D,ENST00000523539,;PTK2,synonymous_variant,p.%3D,ENST00000517887,;PTK2,synonymous_variant,p.%3D,ENST00000522684,;PTK2,non_coding_transcript_exon_variant,,ENST00000523746,;PTK2,synonymous_variant,p.%3D,ENST00000521981,;PTK2,synonymous_variant,p.%3D,ENST00000524202,;PTK2,synonymous_variant,p.%3D,ENST00000521250,;PTK2,3_prime_UTR_variant,,ENST00000519993,;	T	ENSG00000169398	ENST00000340930	Transcript	synonymous_variant	1283	1128	376	L	ttG/ttA	rs748726361	.	.	-1	PTK2	HGNC	9611	protein_coding	YES	CCDS56557.1	ENSP00000341189	FAK1_HUMAN	E5RJQ2_HUMAN,E5RIK4_HUMAN,E5RI72_HUMAN,E5RHK7_HUMAN,E5RHD8_HUMAN,E5RH48_HUMAN,E5RH08_HUMAN,E5RH01_HUMAN,E5RGA6_HUMAN,E5RG86_HUMAN,E5RG80_HUMAN,E5RG66_HUMAN,E5RFW9_HUMAN	UPI0001E8F57E	.	.	.	14/33	.	hmmpanther:PTHR24418:SF78,hmmpanther:PTHR24418	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGCCAACCT	.	4	ESCA
TMEM66	0	.	GRCh37	8	29921356	29921356	+	3'UTR	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*48C>G	.	.	ENST00000256255	6/6	69	54	14	65	65	0	TMEM66,stop_gained,p.Ser343Ter,ENST00000521265,;TMEM66,3_prime_UTR_variant,,ENST00000545648,;TMEM66,3_prime_UTR_variant,,ENST00000536273,;TMEM66,3_prime_UTR_variant,,ENST00000523127,;TMEM66,3_prime_UTR_variant,,ENST00000256255,;TMEM66,downstream_gene_variant,,ENST00000522794,;TMEM66,downstream_gene_variant,,ENST00000518296,;TMEM66,3_prime_UTR_variant,,ENST00000518174,;TMEM66,3_prime_UTR_variant,,ENST00000520303,;TMEM66,downstream_gene_variant,,ENST00000521934,;TMEM66,downstream_gene_variant,,ENST00000518340,;	C	ENSG00000133872	ENST00000256255	Transcript	3_prime_UTR_variant	1326	.	.	.	.	.	.	.	-1	TMEM66	HGNC	28789	protein_coding	YES	CCDS6074.1	ENSP00000256255	SARAF_HUMAN	E5RHW0_HUMAN,B7Z307_HUMAN	UPI0000035F61	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATGAAAAA	.	5	ESCA
KAT6A	0	.	GRCh37	8	41792124	41792124	+	Missense_Mutation	SNP	T	T	C	rs754427391	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3614A>G	p.Gln1205Arg	p.Q1205R	ENST00000396930	18/18	101	71	30	103	103	0	KAT6A,missense_variant,p.Gln1205Arg,ENST00000396930,;KAT6A,missense_variant,p.Gln1205Arg,ENST00000406337,;KAT6A,missense_variant,p.Gln1205Arg,ENST00000265713,;KAT6A,downstream_gene_variant,,ENST00000418721,;	C	ENSG00000083168	ENST00000396930	Transcript	missense_variant	4158	3614	1205	Q/R	cAg/cGg	rs754427391	.	.	-1	KAT6A	HGNC	13013	protein_coding	YES	CCDS6124.1	ENSP00000380136	KAT6A_HUMAN	A5PKX7_HUMAN	UPI000013D666	.	.	benign(0.366)	18/18	.	hmmpanther:PTHR10615:SF26,hmmpanther:PTHR10615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCTGGATC	byFrequency	5	ESCA
GEM	0	.	GRCh37	8	95262302	95262302	+	3'UTR	SNP	T	T	C	rs528039915	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*236A>G	.	.	ENST00000297596	5/5	23	17	5	25	25	0	GEM,3_prime_UTR_variant,,ENST00000297596,;GEM,3_prime_UTR_variant,,ENST00000396194,;	C	ENSG00000164949	ENST00000297596	Transcript	3_prime_UTR_variant	1392	.	.	.	.	rs528039915	.	.	-1	GEM	HGNC	4234	protein_coding	YES	CCDS6261.1	ENSP00000297596	GEM_HUMAN	E5RJF9_HUMAN	UPI000012B3BC	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCTAAAGA	.	5	ESCA
PALM2-AKAP2	0	.	GRCh37	9	112932713	112932714	+	3'UTR	INS	-	-	G	rs202059217	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1944dupG	.	.	ENST00000374530	11/11	23	16	7	20	20	0	PALM2-AKAP2,3_prime_UTR_variant,,ENST00000374530,;AKAP2,3_prime_UTR_variant,,ENST00000374525,;AKAP2,downstream_gene_variant,,ENST00000259318,;AKAP2,downstream_gene_variant,,ENST00000434623,;PALM2-AKAP2,downstream_gene_variant,,ENST00000302798,;AKAP2,downstream_gene_variant,,ENST00000510514,;AKAP2,downstream_gene_variant,,ENST00000555236,;AKAP2,downstream_gene_variant,,ENST00000482335,;AKAP2,downstream_gene_variant,,ENST00000485762,;AKAP2,downstream_gene_variant,,ENST00000495980,;	G	ENSG00000157654	ENST00000374530	Transcript	3_prime_UTR_variant	5428-5429	.	.	.	.	rs202059217	.	.	1	PALM2-AKAP2	HGNC	33529	protein_coding	YES	CCDS35100.1	ENSP00000363654	.	.	UPI0000125755	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GACTTTGGGGG	by1000G	2	ESCA
ANGPTL2	0	.	GRCh37	9	129850289	129850289	+	3'UTR	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*929C>T	.	.	ENST00000373425	5/5	28	17	11	35	35	0	ANGPTL2,3_prime_UTR_variant,,ENST00000373425,;ANGPTL2,3_prime_UTR_variant,,ENST00000373417,;RALGPS1,intron_variant,,ENST00000394022,;RALGPS1,intron_variant,,ENST00000424082,;RALGPS1,intron_variant,,ENST00000373436,;RALGPS1,intron_variant,,ENST00000259351,;RALGPS1,intron_variant,,ENST00000373434,;	A	ENSG00000136859	ENST00000373425	Transcript	3_prime_UTR_variant	3029	.	.	.	.	.	.	.	-1	ANGPTL2	HGNC	490	protein_coding	YES	CCDS6868.1	ENSP00000362524	ANGL2_HUMAN	Q8NCH7_HUMAN,Q8N2J9_HUMAN	UPI0000049E07	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTGGAGCCC	.	5	ESCA
SPTAN1	0	.	GRCh37	9	131388230	131388230	+	Silent	SNP	T	T	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6252T>G	p.%3D	p.L2084L	ENST00000372739	48/57	54	24	29	52	52	0	SPTAN1,synonymous_variant,p.%3D,ENST00000372739,;SPTAN1,synonymous_variant,p.%3D,ENST00000358161,;SPTAN1,synonymous_variant,p.%3D,ENST00000372731,;SPTAN1,downstream_gene_variant,,ENST00000491712,;	G	ENSG00000197694	ENST00000372739	Transcript	synonymous_variant	6362	6252	2084	L	ctT/ctG	.	.	.	1	SPTAN1	HGNC	11273	protein_coding	YES	CCDS48036.1	ENSP00000361824	SPTN1_HUMAN	.	UPI000045894C	.	.	.	48/57	.	hmmpanther:PTHR11915:SF250,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTTCTGGA	.	5	ESCA
CEL	0	.	GRCh37	9	135940034	135940034	+	Silent	SNP	G	G	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234G>A	p.%3D	p.L78L	ENST00000372080	3/11	39	32	6	54	54	0	CEL,synonymous_variant,p.%3D,ENST00000351304,;CEL,synonymous_variant,p.%3D,ENST00000372080,;	A	ENSG00000170835	ENST00000372080	Transcript	synonymous_variant	250	234	78	L	ctG/ctA	.	.	.	1	CEL	HGNC	1848	protein_coding	YES	CCDS43896.1	ENSP00000361151	.	Q9UMB1_HUMAN	UPI000013E8C6	.	.	.	3/11	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTGAAGGC	.	5	ESCA
C9orf135	0	.	GRCh37	9	72521031	72521031	+	Missense_Mutation	SNP	T	T	A	.	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.669T>A	p.Ser223Arg	p.S223R	ENST00000377197	6/6	75	50	24	80	80	0	C9orf135,missense_variant,p.Ser223Arg,ENST00000377197,;C9orf135,3_prime_UTR_variant,,ENST00000527647,;C9orf135,non_coding_transcript_exon_variant,,ENST00000466872,;C9orf135,3_prime_UTR_variant,,ENST00000529131,;C9orf135,3_prime_UTR_variant,,ENST00000529446,;	A	ENSG00000204711	ENST00000377197	Transcript	missense_variant	756	669	223	S/R	agT/agA	COSM3907748	.	.	1	C9orf135	HGNC	31422	protein_coding	YES	CCDS35041.1	ENSP00000366402	CI135_HUMAN	E9PIA3_HUMAN	UPI00001AEC57	.	tolerated(0.52)	benign(0.015)	6/6	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTAGTGGGCC	.	5	ESCA
SPATA31D1	0	.	GRCh37	9	84605932	84605932	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547G>C	p.Asp183His	p.D183H	ENST00000344803	4/4	94	60	34	107	107	0	SPATA31D1,missense_variant,p.Asp183His,ENST00000344803,;SPATA31D1,downstream_gene_variant,,ENST00000603921,;	C	ENSG00000214929	ENST00000344803	Transcript	missense_variant	594	547	183	D/H	Gac/Cac	.	.	.	1	SPATA31D1	HGNC	37283	protein_coding	YES	CCDS47986.1	ENSP00000341988	S31D1_HUMAN	.	UPI00001C10A6	.	deleterious(0.04)	benign(0.045)	4/4	.	hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGACCTA	.	5	ESCA
TAF7L	0	.	GRCh37	X	100531514	100531514	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.952T>C	p.Tyr318His	p.Y318H	ENST00000372907	10/13	19	9	10	12	12	0	TAF7L,missense_variant,p.Tyr232His,ENST00000356784,;TAF7L,missense_variant,p.Tyr318His,ENST00000372907,;TAF7L,intron_variant,,ENST00000372905,;TAF7L,intron_variant,,ENST00000324762,;	G	ENSG00000102387	ENST00000372907	Transcript	missense_variant	964	952	318	Y/H	Tat/Cat	.	.	.	-1	TAF7L	HGNC	11548	protein_coding	YES	CCDS35347.1	ENSP00000361998	TAF7L_HUMAN	.	UPI0000212176	.	tolerated(0.34)	benign(0.059)	10/13	.	hmmpanther:PTHR12228,hmmpanther:PTHR12228:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATATTCTA	.	5	ESCA
MAGEA4	0	.	GRCh37	X	151092505	151092505	+	Silent	SNP	C	C	A	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369C>A	p.%3D	p.R123R	ENST00000360243	3/3	51	12	38	45	45	0	MAGEA4,synonymous_variant,p.%3D,ENST00000416020,;MAGEA4,synonymous_variant,p.%3D,ENST00000370335,;MAGEA4,synonymous_variant,p.%3D,ENST00000276344,;MAGEA4,synonymous_variant,p.%3D,ENST00000448295,;MAGEA4,synonymous_variant,p.%3D,ENST00000393921,;MAGEA4,synonymous_variant,p.%3D,ENST00000431971,;MAGEA4,synonymous_variant,p.%3D,ENST00000425182,;MAGEA4,synonymous_variant,p.%3D,ENST00000431963,;MAGEA4,synonymous_variant,p.%3D,ENST00000370337,;MAGEA4,synonymous_variant,p.%3D,ENST00000393920,;MAGEA4,synonymous_variant,p.%3D,ENST00000441865,;MAGEA4,synonymous_variant,p.%3D,ENST00000370340,;MAGEA4,synonymous_variant,p.%3D,ENST00000430273,;MAGEA4,synonymous_variant,p.%3D,ENST00000360243,;MAGEA4,synonymous_variant,p.%3D,ENST00000457310,;	A	ENSG00000147381	ENST00000360243	Transcript	synonymous_variant	636	369	123	R	cgC/cgA	.	.	.	1	MAGEA4	HGNC	6802	protein_coding	YES	CCDS14702.1	ENSP00000353379	MAGA4_HUMAN	C9JZJ5_HUMAN,C9JK50_HUMAN,C9JIR1_HUMAN,C9J9C2_HUMAN,B4DTE6_HUMAN	UPI000013EA1F	.	.	.	3/3	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF48,hmmpanther:PTHR11736,Pfam_domain:PF01454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCGCAAGTA	.	5	ESCA
MAP3K15	0	.	GRCh37	X	19390939	19390939	+	Silent	SNP	T	T	C	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2940A>G	p.%3D	p.P980P	ENST00000338883	22/29	23	4	18	21	21	0	MAP3K15,synonymous_variant,p.%3D,ENST00000469203,;MAP3K15,synonymous_variant,p.%3D,ENST00000359173,;MAP3K15,synonymous_variant,p.%3D,ENST00000338883,;Y_RNA,upstream_gene_variant,,ENST00000365274,;MAP3K15,non_coding_transcript_exon_variant,,ENST00000518578,;MAP3K15,non_coding_transcript_exon_variant,,ENST00000470101,;	C	ENSG00000180815	ENST00000338883	Transcript	synonymous_variant	2940	2940	980	P	ccA/ccG	.	.	.	-1	MAP3K15	HGNC	31689	protein_coding	YES	.	ENSP00000345629	M3K15_HUMAN	E7EWI5_HUMAN	UPI0000E444D0	.	.	.	22/29	.	hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCGTCTGGAAC	.	4	ESCA
PRDX4	0	.	GRCh37	X	23685653	23685653	+	5'UTR	SNP	C	C	G	rs760429953	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-35C>G	.	.	ENST00000379341	1/7	10	3	7	8	8	0	PRDX4,5_prime_UTR_variant,,ENST00000379341,;PRDX4,intron_variant,,ENST00000379349,;PRDX4,upstream_gene_variant,,ENST00000379331,;PRDX4,non_coding_transcript_exon_variant,,ENST00000495599,;	G	ENSG00000123131	ENST00000379341	Transcript	5_prime_UTR_variant	91	.	.	.	.	rs760429953	.	.	1	PRDX4	HGNC	17169	protein_coding	YES	CCDS14206.1	ENSP00000368646	PRDX4_HUMAN	.	UPI00001314E8	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCTCGCGCC	.	2	ESCA
PABPC1L2A	0	.	GRCh37	X	72297621	72297621	+	3'UTR	SNP	C	C	T	novel	.	TCGA-IG-A97I-01A-11D-A387-09	TCGA-IG-A97I-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1002G>A	.	.	ENST00000373519	1/1	23	19	4	17	17	0	PABPC1L2A,3_prime_UTR_variant,,ENST00000373519,;PABPC1L2A,downstream_gene_variant,,ENST00000453389,;RP11-493K23.4,upstream_gene_variant,,ENST00000454388,;	T	ENSG00000186288	ENST00000373519	Transcript	3_prime_UTR_variant	1731	.	.	.	.	.	.	.	-1	PABPC1L2A	HGNC	27989	protein_coding	YES	CCDS35334.1	ENSP00000362618	PAP1M_HUMAN	.	UPI00001C207A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AGTGACCAGGA	.	2	ESCA
GLRX3	0	.	GRCh37	10	131964815	131964815	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523C>T	p.Gln175Ter	p.Q175*	ENST00000368644	5/12	16	6	10	33	33	0	GLRX3,stop_gained,p.Gln175Ter,ENST00000368644,;GLRX3,stop_gained,p.Gln175Ter,ENST00000331244,;GLRX3,stop_gained,p.Gln175Ter,ENST00000481034,;	T	ENSG00000108010	ENST00000368644	Transcript	stop_gained	545	523	175	Q/*	Cag/Tag	.	.	.	1	GLRX3	HGNC	15987	protein_coding	YES	CCDS7661.1	ENSP00000357633	GLRX3_HUMAN	.	UPI000006E4EA	.	.	.	5/12	.	PROSITE_profiles:PS51354,hmmpanther:PTHR10293,hmmpanther:PTHR10293:SF40,Gene3D:3.40.30.10,Pfam_domain:PF00462,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCAGTTT	.	5	ESCA
NEBL	0	.	GRCh37	10	21097518	21097518	+	Silent	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2682A>T	p.%3D	p.G894G	ENST00000377122	26/28	55	27	27	61	61	0	NEBL,synonymous_variant,p.%3D,ENST00000377122,;NEBL,intron_variant,,ENST00000377159,;NEBL,intron_variant,,ENST00000417816,;NEBL,downstream_gene_variant,,ENST00000493005,;MTND1P21,downstream_gene_variant,,ENST00000412991,;	A	ENSG00000078114	ENST00000377122	Transcript	synonymous_variant	3079	2682	894	G	ggA/ggT	.	.	.	-1	NEBL	HGNC	16932	protein_coding	YES	CCDS7134.1	ENSP00000366326	NEBL_HUMAN	B0YJ47_HUMAN	UPI000012FEE8	.	.	.	26/28	.	hmmpanther:PTHR11039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTCTCCGAG	.	5	ESCA
CASC10	0	.	GRCh37	10	21783676	21783676	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*853G>T	.	.	ENST00000377113	2/2	47	27	19	38	38	0	CASC10,3_prime_UTR_variant,,ENST00000377113,;MIR1915,downstream_gene_variant,,ENST00000410139,;	A	ENSG00000204682	ENST00000377113	Transcript	3_prime_UTR_variant	1712	.	.	.	.	.	.	.	-1	CASC10	HGNC	31448	protein_coding	YES	CCDS31163.1	ENSP00000366317	CSC10_HUMAN	.	UPI0000198ED5	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTCCCTCG	.	5	ESCA
ANKRD30A	0	.	GRCh37	10	37506700	37506700	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2993G>A	p.Arg998Lys	p.R998K	ENST00000361713	33/36	33	12	21	50	50	0	ANKRD30A,missense_variant,p.Arg1117Lys,ENST00000374660,;ANKRD30A,missense_variant,p.Arg998Lys,ENST00000361713,;ANKRD30A,missense_variant,p.Arg998Lys,ENST00000602533,;	A	ENSG00000148513	ENST00000361713	Transcript	missense_variant	3092	2993	998	R/K	aGa/aAa	.	.	.	1	ANKRD30A	HGNC	17234	protein_coding	YES	CCDS7193.1	ENSP00000354432	AN30A_HUMAN	R4GNA2_HUMAN	UPI0000458879	.	tolerated(1)	benign(0.364)	33/36	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAGAATCG	.	5	ESCA
OR13A1	0	.	GRCh37	10	45799654	45799654	+	Missense_Mutation	SNP	G	G	A	rs756684773	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217C>T	p.Leu73Phe	p.L73F	ENST00000553795	4/4	125	52	73	54	54	0	OR13A1,missense_variant,p.Leu73Phe,ENST00000374401,;OR13A1,missense_variant,p.Leu73Phe,ENST00000553795,;OR13A1,missense_variant,p.Leu73Phe,ENST00000536058,;	A	ENSG00000256574	ENST00000553795	Transcript	missense_variant	526	217	73	L/F	Ctc/Ttc	rs756684773	.	.	-1	OR13A1	HGNC	14772	protein_coding	YES	CCDS31188.1	ENSP00000451950	O13A1_HUMAN	.	UPI000003FE0F	.	deleterious(0.01)	probably_damaging(1)	4/4	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF81,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAGCCCAG	.	5	ESCA
RP11-50E11.3	0	.	GRCh37	10	52390924	52390924	+	RNA	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2113A>T	.	.	ENST00000443374	4/4	189	83	106	85	85	0	RP11-50E11.3,non_coding_transcript_exon_variant,,ENST00000443374,;RP11-50E11.3,downstream_gene_variant,,ENST00000609579,;RP11-50E11.2,upstream_gene_variant,,ENST00000437111,;	T	ENSG00000226200	ENST00000443374	Transcript	non_coding_transcript_exon_variant	2113	.	.	.	.	.	.	.	1	RP11-50E11.3	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGAACTCGG	.	5	ESCA
ADAMTS14	0	.	GRCh37	10	72520180	72520188	+	In_Frame_Del	DEL	CATTCCCGG	CATTCCCGG	-	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	CATTCCCGG	CATTCCCGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3253_3261delATTCCCGGC	p.Ile1085_Gly1087del	p.I1085_G1087del	ENST00000373208	22/22	48	36	12	30	30	0	ADAMTS14,inframe_deletion,p.Ile1085_Gly1087del,ENST00000373208,;ADAMTS14,inframe_deletion,p.Ile1082_Gly1084del,ENST00000373207,;	-	ENSG00000138316	ENST00000373208	Transcript	inframe_deletion	3252-3260	3252-3260	1084-1087	SIPG/S	tcCATTCCCGGc/tcc	.	.	.	1	ADAMTS14	HGNC	14899	protein_coding	YES	CCDS7307.1	ENSP00000362304	ATS14_HUMAN	.	UPI000013E57B	.	.	.	22/22	.	PROSITE_profiles:PS50900,hmmpanther:PTHR13723:SF24,hmmpanther:PTHR13723	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	CTGCTCCATTCCCGGCTACC	.	2	ESCA
CDH23	0	.	GRCh37	10	73434919	73434919	+	Silent	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.275T>C	p.%3D	p.S92S	ENST00000442677	3/17	44	30	13	29	29	0	CDH23,synonymous_variant,p.%3D,ENST00000442677,;CDH23,synonymous_variant,p.%3D,ENST00000466757,;CDH23,synonymous_variant,p.%3D,ENST00000224721,;CDH23,synonymous_variant,p.%3D,ENST00000299366,;	C	ENSG00000107736	ENST00000442677	Transcript	synonymous_variant	275	276	92	S	agT/agC	.	.	.	1	CDH23	HGNC	13733	protein_coding	.	.	ENSP00000388894	.	.	UPI0002B83372	.	.	.	3/17	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24027:SF277,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGTGATGA	.	5	ESCA
ITIH5	0	.	GRCh37	10	7611724	7611724	+	Missense_Mutation	SNP	C	C	A	rs772412778	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2056G>T	p.Val686Leu	p.V686L	ENST00000256861	12/14	47	32	14	44	44	0	ITIH5,missense_variant,p.Val468Leu,ENST00000446830,;ITIH5,missense_variant,p.Val472Leu,ENST00000298441,;ITIH5,missense_variant,p.Val686Leu,ENST00000256861,;ITIH5,intron_variant,,ENST00000397146,;ITIH5,downstream_gene_variant,,ENST00000397145,;ITIH5,non_coding_transcript_exon_variant,,ENST00000473591,;ITIH5,non_coding_transcript_exon_variant,,ENST00000492668,;ITIH5,downstream_gene_variant,,ENST00000434980,;ITIH5,downstream_gene_variant,,ENST00000468389,;ITIH5,downstream_gene_variant,,ENST00000476417,;	A	ENSG00000123243	ENST00000256861	Transcript	missense_variant	2135	2056	686	V/L	Gtg/Ttg	rs772412778	.	.	-1	ITIH5	HGNC	21449	protein_coding	YES	.	ENSP00000256861	ITIH5_HUMAN	.	UPI00001F8AF3	.	deleterious(0)	possibly_damaging(0.902)	12/14	.	hmmpanther:PTHR10338:SF62,hmmpanther:PTHR10338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCACAACAA	byFrequency	5	ESCA
CC2D2B	0	.	GRCh37	10	97786972	97786972	+	Silent	SNP	C	C	T	.	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843C>T	p.%3D	p.I281I	ENST00000410012	11/12	75	19	55	92	92	0	CC2D2B,stop_gained,p.Arg133Ter,ENST00000371198,;CC2D2B,synonymous_variant,p.%3D,ENST00000410012,;CC2D2B,intron_variant,,ENST00000344386,;ENTPD1-AS1,non_coding_transcript_exon_variant,,ENST00000458228,;ENTPD1-AS1,intron_variant,,ENST00000416301,;ENTPD1-AS1,intron_variant,,ENST00000454638,;ENTPD1-AS1,intron_variant,,ENST00000451364,;ENTPD1-AS1,intron_variant,,ENST00000452728,;ENTPD1-AS1,intron_variant,,ENST00000449197,;RP11-690P14.4,3_prime_UTR_variant,,ENST00000475252,;	T	ENSG00000188649	ENST00000410012	Transcript	synonymous_variant	1054	843	281	I	atC/atT	COSM3808098,COSM1971397	.	.	1	CC2D2B	HGNC	31666	protein_coding	YES	CCDS53560.1	ENSP00000386988	C2D2B_HUMAN	.	UPI0001A4205F	.	.	.	11/12	.	hmmpanther:PTHR20837,hmmpanther:PTHR20837:SF2	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATCGAAAG	.	5	ESCA
ZBED5	0	.	GRCh37	11	10874919	10874919	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1574A>T	p.Asp525Val	p.D525V	ENST00000432999	3/3	36	21	15	32	32	0	ZBED5,missense_variant,p.Asp525Val,ENST00000432999,;ZBED5,missense_variant,p.Asp525Val,ENST00000413761,;ZBED5,downstream_gene_variant,,ENST00000528289,;ZBED5,downstream_gene_variant,,ENST00000534690,;ZBED5,downstream_gene_variant,,ENST00000526852,;ZBED5,downstream_gene_variant,,ENST00000526020,;ZBED5-AS1,upstream_gene_variant,,ENST00000529014,;ZBED5-AS1,upstream_gene_variant,,ENST00000501079,;ZBED5,intron_variant,,ENST00000533925,;ZBED5,intron_variant,,ENST00000525350,;ZBED5,downstream_gene_variant,,ENST00000530570,;	A	ENSG00000236287	ENST00000432999	Transcript	missense_variant	2073	1574	525	D/V	gAt/gTt	.	.	.	-1	ZBED5	HGNC	30803	protein_coding	YES	.	ENSP00000398106	ZBED5_HUMAN	E9PNT1_HUMAN,E9PM71_HUMAN,E9PJT5_HUMAN,E9PJ57_HUMAN	UPI000013CCBF	.	deleterious(0)	possibly_damaging(0.596)	3/3	.	Superfamily_domains:SSF53098,hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF86	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAATCAAAG	.	5	ESCA
GRAMD1B	0	.	GRCh37	11	123480972	123480972	+	Silent	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1416G>T	p.%3D	p.V472V	ENST00000529750	13/20	61	34	27	57	57	0	GRAMD1B,synonymous_variant,p.%3D,ENST00000322282,;GRAMD1B,synonymous_variant,p.%3D,ENST00000529750,;GRAMD1B,synonymous_variant,p.%3D,ENST00000456860,;GRAMD1B,synonymous_variant,p.%3D,ENST00000529432,;GRAMD1B,synonymous_variant,p.%3D,ENST00000450171,;GRAMD1B,downstream_gene_variant,,ENST00000534764,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;GRAMD1B,upstream_gene_variant,,ENST00000525945,;	T	ENSG00000023171	ENST00000529750	Transcript	synonymous_variant	1743	1416	472	V	gtG/gtT	.	.	.	1	GRAMD1B	HGNC	29214	protein_coding	YES	CCDS53720.1	ENSP00000436500	GRM1B_HUMAN	.	UPI00005C3025	.	.	.	13/20	.	hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGTGCCCTA	.	5	ESCA
NELL1	0	.	GRCh37	11	21592425	21592425	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2096G>A	p.Gly699Asp	p.G699D	ENST00000357134	18/20	36	23	12	78	78	0	NELL1,missense_variant,p.Gly642Asp,ENST00000325319,;NELL1,missense_variant,p.Gly699Asp,ENST00000357134,;NELL1,missense_variant,p.Gly727Asp,ENST00000298925,;NELL1,missense_variant,p.Gly652Asp,ENST00000532434,;NELL1,non_coding_transcript_exon_variant,,ENST00000529218,;	A	ENSG00000165973	ENST00000357134	Transcript	missense_variant	2248	2096	699	G/D	gGt/gAt	.	.	.	1	NELL1	HGNC	7750	protein_coding	YES	CCDS7855.1	ENSP00000349654	NELL1_HUMAN	K9UUD5_HUMAN	UPI000013E53D	.	tolerated(0.1)	probably_damaging(0.956)	18/20	.	PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,Pfam_domain:PF00093,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATGGTCACA	.	5	ESCA
ELP4	0	.	GRCh37	11	31616430	31616430	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495G>T	p.Gln165His	p.Q165H	ENST00000350638	4/10	54	30	23	39	39	0	ELP4,missense_variant,p.Gln165His,ENST00000379163,;ELP4,missense_variant,p.Gln165His,ENST00000395934,;ELP4,missense_variant,p.Gln165His,ENST00000350638,;ELP4,missense_variant,p.Gln165His,ENST00000474374,;	T	ENSG00000109911	ENST00000350638	Transcript	missense_variant	530	495	165	Q/H	caG/caT	.	.	.	1	ELP4	HGNC	1171	protein_coding	YES	CCDS7875.2	ENSP00000298937	ELP4_HUMAN	Q9H4R8_HUMAN	UPI0000074047	.	deleterious(0)	probably_damaging(0.994)	4/10	.	hmmpanther:PTHR12896:SF1,hmmpanther:PTHR12896,Pfam_domain:PF05625	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCAGTTATT	.	5	ESCA
WT1	0	.	GRCh37	11	32439125	32439125	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.948G>T	p.Lys316Asn	p.K316N	ENST00000332351	4/10	97	58	38	63	63	0	WT1,missense_variant,p.Lys67Asn,ENST00000527775,;WT1,missense_variant,p.Lys316Asn,ENST00000332351,;WT1,missense_variant,p.Lys316Asn,ENST00000448076,;WT1,missense_variant,p.Lys316Asn,ENST00000452863,;WT1,missense_variant,p.Lys104Asn,ENST00000379079,;WT1,missense_variant,p.Lys7Asn,ENST00000527882,;WT1,missense_variant,p.Lys104Asn,ENST00000530998,;WT1,missense_variant,p.Lys316Asn,ENST00000379077,;	A	ENSG00000184937	ENST00000332351	Transcript	missense_variant	1233	948	316	K/N	aaG/aaT	.	.	.	-1	WT1	HGNC	12796	protein_coding	YES	CCDS7878.2	ENSP00000331327	.	Q6LBI3_HUMAN,J3KNN9_HUMAN,H0Y3F0_HUMAN,E9PPW3_HUMAN,E9PKS2_HUMAN,A8MN20_HUMAN,A0FJ58_HUMAN,A0FJ57_HUMAN	UPI0000D625D7	.	deleterious_low_confidence(0)	probably_damaging(0.998)	4/10	.	hmmpanther:PTHR10042:SF3,hmmpanther:PTHR10042,Pfam_domain:PF02165	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCCCTTTAA	.	5	ESCA
OR8H1	0	.	GRCh37	11	56058051	56058051	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.488G>C	p.Ser163Thr	p.S163T	ENST00000313022	1/1	52	29	23	33	33	0	OR8H1,missense_variant,p.Ser163Thr,ENST00000313022,;	G	ENSG00000181693	ENST00000313022	Transcript	missense_variant	516	488	163	S/T	aGc/aCc	COSM1703982	.	.	-1	OR8H1	HGNC	14824	protein_coding	YES	CCDS31526.1	ENSP00000323595	OR8H1_HUMAN	.	UPI0000041BC0	.	tolerated(0.15)	benign(0.082)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGCTCATC	.	5	ESCA
EIF1AD	0	.	GRCh37	11	65766009	65766009	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*61A>G	.	.	ENST00000312234	6/6	36	20	16	33	33	0	EIF1AD,3_prime_UTR_variant,,ENST00000525767,;EIF1AD,3_prime_UTR_variant,,ENST00000533544,;EIF1AD,3_prime_UTR_variant,,ENST00000529964,;EIF1AD,3_prime_UTR_variant,,ENST00000526451,;EIF1AD,3_prime_UTR_variant,,ENST00000312234,;BANF1,upstream_gene_variant,,ENST00000533166,;BANF1,upstream_gene_variant,,ENST00000527348,;EIF1AD,downstream_gene_variant,,ENST00000527249,;EIF1AD,downstream_gene_variant,,ENST00000530462,;EIF1AD,downstream_gene_variant,,ENST00000532707,;BANF1,upstream_gene_variant,,ENST00000312175,;BANF1,upstream_gene_variant,,ENST00000445560,;BANF1,upstream_gene_variant,,ENST00000530204,;EIF1AD,downstream_gene_variant,,ENST00000527051,;BANF1,upstream_gene_variant,,ENST00000528648,;BANF1,upstream_gene_variant,,ENST00000524628,;BANF1,upstream_gene_variant,,ENST00000524663,;EIF1AD,downstream_gene_variant,,ENST00000529973,;EIF1AD,downstream_gene_variant,,ENST00000526449,;	C	ENSG00000175376	ENST00000312234	Transcript	3_prime_UTR_variant	894	.	.	.	.	.	.	.	-1	EIF1AD	HGNC	28147	protein_coding	YES	CCDS8124.1	ENSP00000309175	EIF1A_HUMAN	E9PS76_HUMAN,E9PS30_HUMAN,E9PRR8_HUMAN,E9PNH5_HUMAN,E9PLI6_HUMAN	UPI0000070E9C	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATGTCCAAG	.	5	ESCA
PDE2A	0	.	GRCh37	11	72301270	72301270	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.722A>G	p.Asp241Gly	p.D241G	ENST00000334456	9/31	57	28	29	35	35	0	PDE2A,missense_variant,p.Asp232Gly,ENST00000540345,;PDE2A,missense_variant,p.Asp241Gly,ENST00000334456,;PDE2A,missense_variant,p.Asp126Gly,ENST00000418754,;PDE2A,missense_variant,p.Asp65Gly,ENST00000475807,;PDE2A,missense_variant,p.Asp234Gly,ENST00000544570,;PDE2A,missense_variant,p.Asp232Gly,ENST00000444035,;PDE2A,intron_variant,,ENST00000376450,;PDE2A,upstream_gene_variant,,ENST00000538299,;PDE2A,downstream_gene_variant,,ENST00000538749,;RP11-169D4.2,downstream_gene_variant,,ENST00000545254,;PDE2A,3_prime_UTR_variant,,ENST00000539367,;PDE2A,3_prime_UTR_variant,,ENST00000536308,;PDE2A,downstream_gene_variant,,ENST00000543750,;PDE2A,downstream_gene_variant,,ENST00000490749,;PDE2A,downstream_gene_variant,,ENST00000541998,;PDE2A,downstream_gene_variant,,ENST00000543575,;	C	ENSG00000186642	ENST00000334456	Transcript	missense_variant	968	722	241	D/G	gAt/gGt	.	.	.	-1	PDE2A	HGNC	8777	protein_coding	YES	CCDS8216.1	ENSP00000334910	PDE2A_HUMAN	F5GXX2_HUMAN,C9JPD5_HUMAN	UPI000003B340	.	deleterious(0.01)	possibly_damaging(0.691)	9/31	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF102,Gene3D:3.30.450.40,SMART_domains:SM00065,Superfamily_domains:SSF55781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCATCCAGG	.	5	ESCA
CEND1	0	.	GRCh37	11	788361	788361	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216C>T	p.%3D	p.L72L	ENST00000330106	2/2	85	40	45	65	65	0	CEND1,synonymous_variant,p.%3D,ENST00000330106,;SLC25A22,downstream_gene_variant,,ENST00000528606,;SLC25A22,downstream_gene_variant,,ENST00000526152,;SLC25A22,downstream_gene_variant,,ENST00000532484,;SLC25A22,downstream_gene_variant,,ENST00000533385,;SLC25A22,downstream_gene_variant,,ENST00000531214,;SLC25A22,downstream_gene_variant,,ENST00000527723,;SLC25A22,downstream_gene_variant,,ENST00000528936,;SLC25A22,downstream_gene_variant,,ENST00000320230,;SLC25A22,downstream_gene_variant,,ENST00000531437,;SLC25A22,downstream_gene_variant,,ENST00000481290,;SLC25A22,downstream_gene_variant,,ENST00000531514,;SLC25A22,downstream_gene_variant,,ENST00000456706,;AP006621.5,downstream_gene_variant,,ENST00000530083,;CEND1,non_coding_transcript_exon_variant,,ENST00000524587,;AP006621.5,downstream_gene_variant,,ENST00000525941,;SLC25A22,downstream_gene_variant,,ENST00000527734,;SLC25A22,downstream_gene_variant,,ENST00000529351,;	A	ENSG00000184524	ENST00000330106	Transcript	synonymous_variant	392	216	72	L	ctC/ctT	.	.	.	-1	CEND1	HGNC	24153	protein_coding	YES	CCDS7714.1	ENSP00000328336	CEND_HUMAN	.	UPI0000126A16	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTGAGAAG	.	5	ESCA
CREBZF	0	.	GRCh37	11	85373850	85373850	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1005T>A	.	.	ENST00000527447	1/1	75	38	37	73	73	0	CREBZF,3_prime_UTR_variant,,ENST00000527447,;CREBZF,intron_variant,,ENST00000398294,;CREBZF,intron_variant,,ENST00000534224,;CREBZF,intron_variant,,ENST00000531515,;CREBZF,intron_variant,,ENST00000260058,;CREBZF,intron_variant,,ENST00000528889,;CREBZF,intron_variant,,ENST00000525639,;CREBZF,intron_variant,,ENST00000527529,;CREBZF,intron_variant,,ENST00000528561,;CREBZF,intron_variant,,ENST00000490820,;	T	ENSG00000137504	ENST00000527447	Transcript	3_prime_UTR_variant	2297	.	.	.	.	.	.	.	-1	CREBZF	HGNC	24905	protein_coding	YES	CCDS41697.1	ENSP00000433459	ZHANG_HUMAN	.	UPI0000405F55	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTAATACAA	.	5	ESCA
ALKBH2	0	.	GRCh37	12	109526157	109526157	+	Missense_Mutation	SNP	C	C	T	rs772106516	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640G>A	p.Val214Ile	p.V214I	ENST00000429722	4/4	74	13	60	52	52	0	ALKBH2,stop_gained,p.Trp147Ter,ENST00000440112,;ALKBH2,missense_variant,p.Val214Ile,ENST00000429722,;ALKBH2,missense_variant,p.Val214Ile,ENST00000343075,;USP30,downstream_gene_variant,,ENST00000392784,;USP30,downstream_gene_variant,,ENST00000257548,;ALKBH2,downstream_gene_variant,,ENST00000543444,;ALKBH2,downstream_gene_variant,,ENST00000536358,;ALKBH2,downstream_gene_variant,,ENST00000536242,;ALKBH2,downstream_gene_variant,,ENST00000536720,;USP30,downstream_gene_variant,,ENST00000470117,;USP30,downstream_gene_variant,,ENST00000479219,;USP30,downstream_gene_variant,,ENST00000491362,;	T	ENSG00000189046	ENST00000429722	Transcript	missense_variant	1004	640	214	V/I	Gtc/Atc	rs772106516	.	.	-1	ALKBH2	HGNC	32487	protein_coding	YES	CCDS31897.1	ENSP00000398181	ALKB2_HUMAN	F5H5X2_HUMAN,F5GZZ0_HUMAN	UPI0000160F58	.	tolerated(0.17)	benign(0.009)	4/4	.	PROSITE_profiles:PS51471,hmmpanther:PTHR31573,hmmpanther:PTHR31573:SF1,Gene3D:3i3qA00,Pfam_domain:PF13532,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGACCACCG	.	5	ESCA
HECTD4	0	.	GRCh37	12	112696393	112696393	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2597T>C	p.Leu866Ser	p.L866S	ENST00000550722	20/76	71	12	59	80	80	0	HECTD4,missense_variant,p.Leu580Ser,ENST00000430131,;HECTD4,missense_variant,p.Leu866Ser,ENST00000550722,;HECTD4,missense_variant,p.Leu830Ser,ENST00000377560,;RP3-521E19.2,non_coding_transcript_exon_variant,,ENST00000547401,;HECTD4,non_coding_transcript_exon_variant,,ENST00000547352,;HECTD4,non_coding_transcript_exon_variant,,ENST00000311694,;	G	ENSG00000173064	ENST00000550722	Transcript	missense_variant	2993	2597	866	L/S	tTg/tCg	.	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	possibly_damaging(0.879)	20/76	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCAACGCC	.	5	ESCA
NOS1	0	.	GRCh37	12	117718602	117718602	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1452C>T	p.%3D	p.L484L	ENST00000338101	7/29	116	75	40	105	105	0	NOS1,synonymous_variant,p.%3D,ENST00000317775,;NOS1,synonymous_variant,p.%3D,ENST00000338101,;NOS1,3_prime_UTR_variant,,ENST00000344089,;	A	ENSG00000089250	ENST00000338101	Transcript	synonymous_variant	1457	1452	484	L	ctC/ctT	.	.	.	-1	NOS1	HGNC	7872	protein_coding	YES	CCDS55890.1	ENSP00000337459	NOS1_HUMAN	A0PJJ7_HUMAN	UPI00001FBC10	.	.	.	7/29	.	Superfamily_domains:SSF56512,PIRSF_domain:PIRSF000333,Gene3D:3.90.340.10,Pfam_domain:PF02898,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGATGAGCTG	.	5	ESCA
HNF1A	0	.	GRCh37	12	121431999	121431999	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.746C>G	p.Ser249Ter	p.S249*	ENST00000257555	4/10	59	29	30	41	41	0	HNF1A,stop_gained,p.Ser249Ter,ENST00000541395,;HNF1A,stop_gained,p.Ser249Ter,ENST00000400024,;HNF1A,stop_gained,p.Ser249Ter,ENST00000402929,;HNF1A,stop_gained,p.Ser132Ter,ENST00000543427,;HNF1A,stop_gained,p.Ser249Ter,ENST00000544413,;HNF1A,stop_gained,p.Ser249Ter,ENST00000257555,;HNF1A,intron_variant,,ENST00000538626,;HNF1A,intron_variant,,ENST00000535955,;HNF1A,stop_gained,p.Ser297Ter,ENST00000560968,;HNF1A,missense_variant,p.His187Asp,ENST00000538646,;HNF1A,3_prime_UTR_variant,,ENST00000540108,;HNF1A,intron_variant,,ENST00000544574,;HNF1A,intron_variant,,ENST00000541924,;HNF1A,upstream_gene_variant,,ENST00000543255,;	G	ENSG00000135100	ENST00000257555	Transcript	stop_gained	972	746	249	S/*	tCa/tGa	.	.	.	1	HNF1A	HGNC	11621	protein_coding	YES	CCDS9209.1	ENSP00000257555	.	E0YMJ2_HUMAN,E0YMJ1_HUMAN,B8YNW1_HUMAN,B8YNU9_HUMAN	UPI000013CF6C	.	.	.	4/10	.	PROSITE_profiles:PS50071,hmmpanther:PTHR11568:SF4,hmmpanther:PTHR11568,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.Q250_G255delQAQGLG|c.747_764del18|4,BUFFER|p.Q250P|c.749A>C|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATCACAGG	.	5	ESCA
HNF1A	0	.	GRCh37	12	121432189	121432189	+	Silent	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936C>G	p.%3D	p.L312L	ENST00000257555	4/10	36	21	15	40	40	0	HNF1A,synonymous_variant,p.%3D,ENST00000541395,;HNF1A,synonymous_variant,p.%3D,ENST00000400024,;HNF1A,synonymous_variant,p.%3D,ENST00000402929,;HNF1A,synonymous_variant,p.%3D,ENST00000543427,;HNF1A,synonymous_variant,p.%3D,ENST00000544413,;HNF1A,synonymous_variant,p.%3D,ENST00000257555,;HNF1A,intron_variant,,ENST00000538626,;HNF1A,intron_variant,,ENST00000535955,;HNF1A,missense_variant,p.Ser250Cys,ENST00000538646,;HNF1A,3_prime_UTR_variant,,ENST00000540108,;HNF1A,intron_variant,,ENST00000560968,;HNF1A,intron_variant,,ENST00000544574,;HNF1A,intron_variant,,ENST00000541924,;HNF1A,upstream_gene_variant,,ENST00000543255,;	G	ENSG00000135100	ENST00000257555	Transcript	synonymous_variant	1162	936	312	L	ctC/ctG	.	.	.	1	HNF1A	HGNC	11621	protein_coding	YES	CCDS9209.1	ENSP00000257555	.	E0YMJ2_HUMAN,E0YMJ1_HUMAN,B8YNW1_HUMAN,B8YNU9_HUMAN	UPI000013CF6C	.	.	.	4/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11568:SF4,hmmpanther:PTHR11568,Pfam_domain:PF04812	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCTCCCC	.	5	ESCA
CLIP1	0	.	GRCh37	12	122763382	122763382	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3873G>T	p.Glu1291Asp	p.E1291D	ENST00000540338	22/25	30	4	25	41	41	0	CLIP1,missense_variant,p.Glu1245Asp,ENST00000537178,;CLIP1,missense_variant,p.Glu1280Asp,ENST00000302528,;CLIP1,missense_variant,p.Glu1169Asp,ENST00000361654,;CLIP1,missense_variant,p.Glu866Asp,ENST00000545889,;CLIP1,missense_variant,p.Glu1280Asp,ENST00000358808,;CLIP1,missense_variant,p.Glu1291Asp,ENST00000540338,;CLIP1,upstream_gene_variant,,ENST00000540539,;CLIP1,non_coding_transcript_exon_variant,,ENST00000536634,;CLIP1,non_coding_transcript_exon_variant,,ENST00000543205,;CLIP1,non_coding_transcript_exon_variant,,ENST00000538120,;CLIP1,upstream_gene_variant,,ENST00000501271,;	A	ENSG00000130779	ENST00000540338	Transcript	missense_variant	3915	3873	1291	E/D	gaG/gaT	.	.	.	-1	CLIP1	HGNC	10461	protein_coding	YES	CCDS58285.1	ENSP00000439093	CLIP1_HUMAN	F5H367_HUMAN,F5H270_HUMAN	UPI0000E00D4E	.	deleterious(0)	probably_damaging(0.977)	22/25	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAGCTCCAA	.	5	ESCA
TUBA1B	0	.	GRCh37	12	49521825	49521825	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1272T>C	p.%3D	p.D424D	ENST00000336023	4/4	156	124	32	134	134	0	TUBA1B,synonymous_variant,p.%3D,ENST00000336023,;TUBA1B,downstream_gene_variant,,ENST00000549870,;TUBA1B,downstream_gene_variant,,ENST00000550367,;TUBA1B,downstream_gene_variant,,ENST00000552984,;TUBA1B,downstream_gene_variant,,ENST00000547476,;RP11-386G11.10,non_coding_transcript_exon_variant,,ENST00000548149,;RP11-386G11.10,non_coding_transcript_exon_variant,,ENST00000552893,;RP11-386G11.10,non_coding_transcript_exon_variant,,ENST00000547387,;RP11-386G11.10,upstream_gene_variant,,ENST00000547712,;Y_RNA,downstream_gene_variant,,ENST00000363439,;RP11-386G11.10,upstream_gene_variant,,ENST00000551496,;TUBA1B,3_prime_UTR_variant,,ENST00000547765,;TUBA1B,non_coding_transcript_exon_variant,,ENST00000332858,;TUBA1B,downstream_gene_variant,,ENST00000551324,;	G	ENSG00000123416	ENST00000336023	Transcript	synonymous_variant	1367	1272	424	D	gaT/gaC	.	.	.	-1	TUBA1B	HGNC	18809	protein_coding	YES	CCDS31792.1	ENSP00000336799	TBA1B_HUMAN	F8VXZ7_HUMAN,F8VX09_HUMAN,F8VWV9_HUMAN,F8VRZ4_HUMAN,F8VRK0_HUMAN,C9JDS9_HUMAN	UPI00000015EA	.	.	.	4/4	.	hmmpanther:PTHR11588:SF65,hmmpanther:PTHR11588,Gene3D:1.10.287.600,Superfamily_domains:SSF55307,Prints_domain:PR01162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCCATATCTTC	.	3	ESCA
TUBA1B	0	.	GRCh37	12	49521828	49521828	+	Silent	SNP	T	T	C	rs747107430	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269A>G	p.%3D	p.E423E	ENST00000336023	4/4	156	122	34	142	142	0	TUBA1B,synonymous_variant,p.%3D,ENST00000336023,;TUBA1B,downstream_gene_variant,,ENST00000549870,;TUBA1B,downstream_gene_variant,,ENST00000550367,;TUBA1B,downstream_gene_variant,,ENST00000552984,;TUBA1B,downstream_gene_variant,,ENST00000547476,;RP11-386G11.10,non_coding_transcript_exon_variant,,ENST00000548149,;RP11-386G11.10,non_coding_transcript_exon_variant,,ENST00000552893,;RP11-386G11.10,non_coding_transcript_exon_variant,,ENST00000547387,;RP11-386G11.10,upstream_gene_variant,,ENST00000547712,;Y_RNA,downstream_gene_variant,,ENST00000363439,;RP11-386G11.10,upstream_gene_variant,,ENST00000551496,;TUBA1B,3_prime_UTR_variant,,ENST00000547765,;TUBA1B,non_coding_transcript_exon_variant,,ENST00000332858,;TUBA1B,downstream_gene_variant,,ENST00000551324,;	C	ENSG00000123416	ENST00000336023	Transcript	synonymous_variant	1364	1269	423	E	gaA/gaG	rs747107430	.	.	-1	TUBA1B	HGNC	18809	protein_coding	YES	CCDS31792.1	ENSP00000336799	TBA1B_HUMAN	F8VXZ7_HUMAN,F8VX09_HUMAN,F8VWV9_HUMAN,F8VRZ4_HUMAN,F8VRK0_HUMAN,C9JDS9_HUMAN	UPI00000015EA	.	.	.	4/4	.	hmmpanther:PTHR11588:SF65,hmmpanther:PTHR11588,Gene3D:1.10.287.600,Superfamily_domains:SSF55307,Prints_domain:PR01162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATATCTTCACG	byFrequency	3	ESCA
IRAK3	0	.	GRCh37	12	66638728	66638728	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1087G>A	p.Val363Ile	p.V363I	ENST00000261233	10/12	44	30	14	36	36	0	IRAK3,missense_variant,p.Val363Ile,ENST00000261233,;IRAK3,missense_variant,p.Val302Ile,ENST00000457197,;	A	ENSG00000090376	ENST00000261233	Transcript	missense_variant	1508	1087	363	V/I	Gta/Ata	.	.	.	1	IRAK3	HGNC	17020	protein_coding	YES	CCDS8975.1	ENSP00000261233	IRAK3_HUMAN	.	UPI000013D14A	.	deleterious(0.02)	possibly_damaging(0.889)	10/12	.	Superfamily_domains:SSF56112,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24419,hmmpanther:PTHR24419:SF7,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAGGTAATA	.	5	ESCA
FRY	0	.	GRCh37	13	32839672	32839672	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7866delA	p.Glu2622AspfsTer10	p.E2622Dfs*10	ENST00000380250	54/61	158	112	46	63	63	0	FRY,frameshift_variant,p.Glu2622AspfsTer10,ENST00000380250,;FRY,5_prime_UTR_variant,,ENST00000542859,;FRY,frameshift_variant,p.Glu58AspfsTer10,ENST00000477712,;FRY,non_coding_transcript_exon_variant,,ENST00000602645,;	-	ENSG00000073910	ENST00000380250	Transcript	frameshift_variant	8361	7865	2622	E/X	gAa/ga	.	.	.	1	FRY	HGNC	20367	protein_coding	YES	CCDS41875.1	ENSP00000369600	FRY_HUMAN	Q96KW3_HUMAN,F5H4D2_HUMAN	UPI000046FD40	.	.	.	54/61	.	hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTTTGAATGCA	.	3	ESCA
ZAR1L	0	.	GRCh37	13	32885527	32885527	+	Missense_Mutation	SNP	T	T	C	rs754190339	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.536A>G	p.Glu179Gly	p.E179G	ENST00000533490	3/6	42	22	19	41	41	0	ZAR1L,missense_variant,p.Glu179Gly,ENST00000345108,;ZAR1L,missense_variant,p.Glu179Gly,ENST00000533490,;BRCA2,upstream_gene_variant,,ENST00000544455,;BRCA2,upstream_gene_variant,,ENST00000530893,;BRCA2,upstream_gene_variant,,ENST00000380152,;	C	ENSG00000189167	ENST00000533490	Transcript	missense_variant	955	536	179	E/G	gAg/gGg	rs754190339	.	.	-1	ZAR1L	HGNC	37116	protein_coding	YES	CCDS45023.1	ENSP00000437289	ZAR1L_HUMAN	.	UPI00006C1387	.	deleterious(0.05)	possibly_damaging(0.462)	3/6	.	hmmpanther:PTHR31054:SF4,hmmpanther:PTHR31054	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCTCCTGC	.	5	ESCA
BRCA2	0	.	GRCh37	13	32906495	32906495	+	Nonsense_Mutation	SNP	G	G	T	rs397508009	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880G>T	p.Glu294Ter	p.E294*	ENST00000544455	10/28	180	106	73	108	108	0	BRCA2,stop_gained,p.Glu294Ter,ENST00000544455,;BRCA2,stop_gained,p.Glu171Ter,ENST00000530893,;BRCA2,stop_gained,p.Glu294Ter,ENST00000380152,;	T	ENSG00000139618	ENST00000544455	Transcript	stop_gained	1107	880	294	E/*	Gaa/Taa	rs397508009	.	.	1	BRCA2	HGNC	1101	protein_coding	YES	CCDS9344.1	ENSP00000439902	BRCA2_HUMAN	Q9H4L3_HUMAN,Q8IU82_HUMAN,Q8IU77_HUMAN,Q8IU64_HUMAN,K4K7W0_HUMAN,K4JXT6_HUMAN,K4JTT2_HUMAN,E9PIQ1_HUMAN	UPI00001FCBCC	.	.	.	10/28	.	hmmpanther:PTHR11289:SF0,hmmpanther:PTHR11289,PIRSF_domain:PIRSF002397	.	.	.	.	.	.	.	.	.	not_provided	.	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATGAAGTA	.	5	ESCA
KL	0	.	GRCh37	13	33635154	33635154	+	Silent	SNP	A	A	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1938A>C	p.%3D	p.G646G	ENST00000380099	4/5	24	15	8	26	26	0	KL,synonymous_variant,p.%3D,ENST00000380099,;KL,3_prime_UTR_variant,,ENST00000426690,;KL,non_coding_transcript_exon_variant,,ENST00000487852,;	C	ENSG00000133116	ENST00000380099	Transcript	synonymous_variant	1946	1938	646	G	ggA/ggC	.	.	.	1	KL	HGNC	6344	protein_coding	YES	CCDS9347.1	ENSP00000369442	KLOT_HUMAN	G3XKV3_HUMAN	UPI000013CEBA	.	.	.	4/5	.	hmmpanther:PTHR10353:SF10,hmmpanther:PTHR10353,Gene3D:3.20.20.80,Pfam_domain:PF00232,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGACTGCC	.	5	ESCA
SOHLH2	0	.	GRCh37	13	36748661	36748661	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1064A>T	p.Gln355Leu	p.Q355L	ENST00000554962	13/16	45	19	26	66	66	0	SOHLH2,missense_variant,p.Gln278Leu,ENST00000379881,;CCDC169-SOHLH2,missense_variant,p.Gln355Leu,ENST00000511166,;SOHLH2,missense_variant,p.Gln355Leu,ENST00000554962,;	A	ENSG00000120669	ENST00000554962	Transcript	missense_variant	1366	1064	355	Q/L	cAa/cTa	.	.	.	-1	SOHLH2	HGNC	26026	protein_coding	YES	CCDS55896.1	ENSP00000451542	SOLH2_HUMAN	.	UPI00017A803A	.	deleterious(0)	possibly_damaging(0.534)	13/16	.	hmmpanther:PTHR16223:SF16,hmmpanther:PTHR16223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGTTGTTTC	.	5	ESCA
UCHL3	0	.	GRCh37	13	76179918	76179918	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.663A>G	p.%3D	p.R221R	ENST00000377595	9/9	36	12	23	29	29	0	UCHL3,synonymous_variant,p.%3D,ENST00000377595,;UCHL3,synonymous_variant,p.%3D,ENST00000419068,;RP11-173B14.5,intron_variant,,ENST00000568735,;RP11-173B14.5,intron_variant,,ENST00000568302,;UCHL3,non_coding_transcript_exon_variant,,ENST00000606347,;UCHL3,non_coding_transcript_exon_variant,,ENST00000607339,;RP11-29G8.3,intron_variant,,ENST00000570285,;RP11-29G8.3,intron_variant,,ENST00000563635,;	G	ENSG00000118939	ENST00000377595	Transcript	synonymous_variant	693	663	221	R	agA/agG	.	.	.	1	UCHL3	HGNC	12515	protein_coding	YES	CCDS9453.1	ENSP00000366819	UCHL3_HUMAN	.	UPI000004D00E	.	.	.	9/9	.	hmmpanther:PTHR10589:SF24,hmmpanther:PTHR10589,Gene3D:3.40.532.10,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAAGATTTAA	.	5	ESCA
FOXG1	0	.	GRCh37	14	29237215	29237215	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.730C>A	p.Arg244Ser	p.R244S	ENST00000382535	2/2	58	12	46	62	62	0	FOXG1,missense_variant,p.Arg244Ser,ENST00000313071,;FOXG1,missense_variant,p.Arg244Ser,ENST00000382535,;C14orf23,upstream_gene_variant,,ENST00000552957,;C14orf23,upstream_gene_variant,,ENST00000399387,;C14orf23,upstream_gene_variant,,ENST00000548213,;RP11-966I7.1,upstream_gene_variant,,ENST00000549487,;RP11-966I7.1,upstream_gene_variant,,ENST00000551395,;RP11-966I7.1,upstream_gene_variant,,ENST00000546560,;	A	ENSG00000176165	ENST00000382535	Transcript	missense_variant	1099	730	244	R/S	Cgc/Agc	CM111914,RettBASE_FOXG1:c.730C>T	.	.	1	FOXG1	HGNC	3811	protein_coding	YES	CCDS9636.1	ENSP00000371975	FOXG1_HUMAN	.	UPI00001AE46C	.	deleterious(0)	probably_damaging(1)	2/2	.	PROSITE_profiles:PS50039,hmmpanther:PTHR25042:SF8,hmmpanther:PTHR25042,Pfam_domain:PF00250,Gene3D:1.10.10.10,SMART_domains:SM00339,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCGCGCCAC	.	5	ESCA
KLHL28	0	.	GRCh37	14	45397793	45397793	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*438C>G	.	.	ENST00000396128	5/5	27	20	7	27	27	0	KLHL28,3_prime_UTR_variant,,ENST00000396128,;KLHL28,downstream_gene_variant,,ENST00000355081,;	C	ENSG00000179454	ENST00000396128	Transcript	3_prime_UTR_variant	2274	.	.	.	.	.	.	.	-1	KLHL28	HGNC	19741	protein_coding	YES	CCDS9680.1	ENSP00000379434	KLH28_HUMAN	J3KRJ0_HUMAN,G3V5Y9_HUMAN,G3V4Y0_HUMAN,G3V2P9_HUMAN	UPI00001FD46D	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGTATCA	.	5	ESCA
ARID4A	0	.	GRCh37	14	58831520	58831520	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2713G>C	p.Glu905Gln	p.E905Q	ENST00000355431	20/24	63	38	24	49	49	0	ARID4A,missense_variant,p.Glu905Gln,ENST00000355431,;ARID4A,missense_variant,p.Glu905Gln,ENST00000395168,;ARID4A,missense_variant,p.Glu583Gln,ENST00000417477,;ARID4A,missense_variant,p.Glu905Gln,ENST00000431317,;ARID4A,missense_variant,p.Glu905Gln,ENST00000348476,;ARID4A,downstream_gene_variant,,ENST00000469635,;ARID4A,upstream_gene_variant,,ENST00000466065,;	C	ENSG00000032219	ENST00000355431	Transcript	missense_variant	3086	2713	905	E/Q	Gaa/Caa	.	.	.	1	ARID4A	HGNC	9885	protein_coding	YES	CCDS9732.1	ENSP00000347602	ARI4A_HUMAN	H7C485_HUMAN,C9JIF4_HUMAN	UPI000013FD01	.	tolerated_low_confidence(0.1)	benign(0.089)	20/24	.	hmmpanther:PTHR13964:SF1,hmmpanther:PTHR13964	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTGAAAGA	.	5	ESCA
HERC2P3	0	.	GRCh37	15	20663127	20663127	+	RNA	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1175A>G	.	.	ENST00000428453	9/27	242	168	74	209	209	0	HERC2P3,non_coding_transcript_exon_variant,,ENST00000437318,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000428453,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000430598,;HERC2P3,downstream_gene_variant,,ENST00000412154,;HERC2P3,upstream_gene_variant,,ENST00000440774,;HERC2P3,downstream_gene_variant,,ENST00000414804,;HERC2P3,upstream_gene_variant,,ENST00000426501,;HERC2P3,upstream_gene_variant,,ENST00000440441,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000429926,;HERC2P3,upstream_gene_variant,,ENST00000424611,;HERC2P3,downstream_gene_variant,,ENST00000456027,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000429257,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000544900,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000545640,;	C	ENSG00000180229	ENST00000428453	Transcript	non_coding_transcript_exon_variant	1175	.	.	.	.	.	.	.	-1	HERC2P3	HGNC	4871	processed_transcript	YES	.	.	.	.	.	.	.	.	9/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGACCTCTTCC	.	5	ESCA
TUBGCP5	0	.	GRCh37	15	22846926	22846926	+	Missense_Mutation	SNP	G	G	C	rs549962518	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801G>C	p.Glu267Asp	p.E267D	ENST00000283645	8/23	99	66	33	85	85	0	TUBGCP5,missense_variant,p.Glu267Asp,ENST00000283645,;TUBGCP5,missense_variant,p.Glu267Asp,ENST00000453949,;TUBGCP5,downstream_gene_variant,,ENST00000558664,;TUBGCP5,upstream_gene_variant,,ENST00000559846,;	C	ENSG00000153575	ENST00000283645	Transcript	missense_variant	931	801	267	E/D	gaG/gaC	rs549962518	.	.	1	TUBGCP5	HGNC	18600	protein_coding	YES	CCDS10008.1	ENSP00000283645	GCP5_HUMAN	.	UPI000012B2EE	.	deleterious(0.01)	possibly_damaging(0.908)	8/23	.	hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF33	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGAGACTCA	by1000G	5	ESCA
TRPM1	0	.	GRCh37	15	31334235	31334235	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2057A>C	p.Lys686Thr	p.K686T	ENST00000542188	16/27	75	40	34	46	46	0	TRPM1,missense_variant,p.Lys647Thr,ENST00000558445,;TRPM1,missense_variant,p.Lys686Thr,ENST00000542188,;TRPM1,missense_variant,p.Lys571Thr,ENST00000558768,;TRPM1,missense_variant,p.Lys669Thr,ENST00000256552,;TRPM1,missense_variant,p.Lys647Thr,ENST00000397795,;TRPM1,intron_variant,,ENST00000559177,;RP11-348B17.1,intron_variant,,ENST00000561299,;TRPM1,3_prime_UTR_variant,,ENST00000560801,;	G	ENSG00000134160	ENST00000542188	Transcript	missense_variant	2371	2057	686	K/T	aAg/aCg	.	.	.	-1	TRPM1	HGNC	7146	protein_coding	YES	CCDS58347.1	ENSP00000437849	TRPM1_HUMAN	H0YKU7_HUMAN	UPI0001DBB3A9	.	deleterious(0.01)	probably_damaging(0.999)	16/27	.	hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGCTTGCAG	.	5	ESCA
C15orf41	0	.	GRCh37	15	37101143	37101143	+	3'UTR	SNP	G	G	A	rs778687093	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*489G>A	.	.	ENST00000566621	11/11	17	10	7	28	28	0	C15orf41,3_prime_UTR_variant,,ENST00000563167,;C15orf41,3_prime_UTR_variant,,ENST00000437989,;C15orf41,3_prime_UTR_variant,,ENST00000338183,;C15orf41,3_prime_UTR_variant,,ENST00000567389,;C15orf41,3_prime_UTR_variant,,ENST00000566621,;C15orf41,downstream_gene_variant,,ENST00000569302,;C15orf41,downstream_gene_variant,,ENST00000562489,;C15orf41,downstream_gene_variant,,ENST00000562877,;C15orf41,non_coding_transcript_exon_variant,,ENST00000565792,;CSNK1A1P1,intron_variant,,ENST00000430593,;C15orf41,downstream_gene_variant,,ENST00000566932,;C15orf41,non_coding_transcript_exon_variant,,ENST00000566677,;	A	ENSG00000186073	ENST00000566621	Transcript	3_prime_UTR_variant	1585	.	.	.	.	rs778687093	.	.	1	C15orf41	HGNC	26929	protein_coding	YES	CCDS45215.1	ENSP00000455397	CO041_HUMAN	H3BNF9_HUMAN	UPI00001FE1DF	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAGCGCAAAC	.	5	ESCA
CHP1	0	.	GRCh37	15	41573994	41573994	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2407A>T	.	.	ENST00000334660	7/7	91	59	32	61	61	0	CHP1,3_prime_UTR_variant,,ENST00000334660,;CHP1,downstream_gene_variant,,ENST00000560397,;OIP5-AS1,upstream_gene_variant,,ENST00000500949,;OIP5-AS1,upstream_gene_variant,,ENST00000561275,;OIP5-AS1,upstream_gene_variant,,ENST00000557993,;OIP5-AS1,upstream_gene_variant,,ENST00000559368,;OIP5-AS1,upstream_gene_variant,,ENST00000560706,;OIP5-AS1,upstream_gene_variant,,ENST00000561226,;OIP5-AS1,upstream_gene_variant,,ENST00000558945,;OIP5-AS1,upstream_gene_variant,,ENST00000501665,;CHP1,downstream_gene_variant,,ENST00000558351,;CHP1,downstream_gene_variant,,ENST00000392151,;OIP5-AS1,upstream_gene_variant,,ENST00000560545,;CHP1,downstream_gene_variant,,ENST00000560784,;CHP1,downstream_gene_variant,,ENST00000560411,;OIP5-AS1,upstream_gene_variant,,ENST00000558457,;	T	ENSG00000187446	ENST00000334660	Transcript	3_prime_UTR_variant	3235	.	.	.	.	.	.	.	1	CHP1	HGNC	17433	protein_coding	YES	CCDS10073.1	ENSP00000335632	CHP1_HUMAN	.	UPI000013D461	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGTATAGCA	.	5	ESCA
DUOX2	0	.	GRCh37	15	45399110	45399110	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1751C>T	p.Pro584Leu	p.P584L	ENST00000603300	15/34	53	30	23	33	33	0	DUOX2,missense_variant,p.Pro584Leu,ENST00000389039,;DUOX2,missense_variant,p.Pro584Leu,ENST00000603300,;DUOX2,non_coding_transcript_exon_variant,,ENST00000558383,;	A	ENSG00000140279	ENST00000603300	Transcript	missense_variant	1954	1751	584	P/L	cCc/cTc	.	.	.	-1	DUOX2	HGNC	13273	protein_coding	YES	CCDS10117.1	ENSP00000475084	DUOX2_HUMAN	S6B490_HUMAN	UPI000013D775	.	deleterious(0)	possibly_damaging(0.535)	15/34	.	hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGGGTGCA	.	5	ESCA
SECISBP2L	0	.	GRCh37	15	49319599	49319599	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.998G>C	p.Arg333Thr	p.R333T	ENST00000559471	7/18	79	44	34	70	70	0	SECISBP2L,missense_variant,p.Arg333Thr,ENST00000261847,;SECISBP2L,missense_variant,p.Arg250Thr,ENST00000559424,;SECISBP2L,missense_variant,p.Arg333Thr,ENST00000559471,;SECISBP2L,missense_variant,p.Arg95Thr,ENST00000380927,;	G	ENSG00000138593	ENST00000559471	Transcript	missense_variant	1262	998	333	R/T	aGa/aCa	.	.	.	-1	SECISBP2L	HGNC	28997	protein_coding	YES	CCDS53942.1	ENSP00000453854	SBP2L_HUMAN	J3KPI1_HUMAN	UPI00001C1F8B	.	deleterious(0)	possibly_damaging(0.57)	7/18	.	hmmpanther:PTHR13284,hmmpanther:PTHR13284:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCTAGAA	.	5	ESCA
ATP8B4	0	.	GRCh37	15	50226248	50226248	+	Silent	SNP	G	G	C	rs761916821	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1419C>G	p.%3D	p.L473L	ENST00000284509	15/28	35	28	6	34	34	0	ATP8B4,synonymous_variant,p.%3D,ENST00000559829,;ATP8B4,synonymous_variant,p.%3D,ENST00000284509,;ATP8B4,synonymous_variant,p.%3D,ENST00000557955,;ATP8B4,3_prime_UTR_variant,,ENST00000558906,;ATP8B4,3_prime_UTR_variant,,ENST00000559726,;ATP8B4,upstream_gene_variant,,ENST00000558458,;	C	ENSG00000104043	ENST00000284509	Transcript	synonymous_variant	1561	1419	473	L	ctC/ctG	rs761916821	.	.	-1	ATP8B4	HGNC	13536	protein_coding	YES	CCDS32238.1	ENSP00000284509	AT8B4_HUMAN	H0YMB5_HUMAN	UPI0000055904	.	.	.	15/28	.	hmmpanther:PTHR24092:SF46,hmmpanther:PTHR24092,Gene3D:3.40.1110.10,Pfam_domain:PF12710,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGGCAGAGAGC	byFrequency	4	ESCA
PTPN9	0	.	GRCh37	15	75759850	75759850	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1260C>A	.	.	ENST00000306726	13/13	27	16	11	23	23	0	PTPN9,3_prime_UTR_variant,,ENST00000306726,;PTPN9,downstream_gene_variant,,ENST00000563835,;PTPN9,downstream_gene_variant,,ENST00000568108,;	T	ENSG00000169410	ENST00000306726	Transcript	3_prime_UTR_variant	3555	.	.	.	.	.	.	.	-1	PTPN9	HGNC	9661	protein_coding	YES	CCDS10280.1	ENSP00000303554	PTN9_HUMAN	.	UPI0000000CAC	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGTGAAGCT	.	5	ESCA
LINC00052	0	.	GRCh37	15	88121415	88121416	+	RNA	DEL	CA	CA	-	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.284_285delCA	.	.	ENST00000560153	3/3	37	27	10	27	27	0	LINC00052,non_coding_transcript_exon_variant,,ENST00000560153,;RP11-648K4.2,intron_variant,,ENST00000560439,;	-	ENSG00000259527	ENST00000560153	Transcript	non_coding_transcript_exon_variant	284-285	.	.	.	.	.	.	.	1	LINC00052	HGNC	26455	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAATCTCAGTCTC	.	3	ESCA
TUFM	0	.	GRCh37	16	28855330	28855330	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015delC	p.Arg339GlyfsTer46	p.R339Gfs*46	ENST00000313511	8/10	211	156	55	87	87	0	TUFM,frameshift_variant,p.Arg339GlyfsTer46,ENST00000313511,;SH2B1,upstream_gene_variant,,ENST00000322610,;SH2B1,upstream_gene_variant,,ENST00000563591,;SH2B1,upstream_gene_variant,,ENST00000567536,;MIR4721,upstream_gene_variant,,ENST00000577590,;TUFM,3_prime_UTR_variant,,ENST00000565012,;TUFM,non_coding_transcript_exon_variant,,ENST00000569217,;TUFM,downstream_gene_variant,,ENST00000561644,;	-	ENSG00000178952	ENST00000313511	Transcript	frameshift_variant	1154	1015	339	R/X	Cgg/gg	.	.	.	-1	TUFM	HGNC	12420	protein_coding	YES	CCDS10642.1	ENSP00000322439	EFTU_HUMAN	.	UPI0000049FD5	.	.	.	8/10	.	Superfamily_domains:SSF50447,Gene3D:2.40.30.10,Pfam_domain:PF03144,TIGRFAM_domain:TIGR00485,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCCCCGCCGCA	.	3	ESCA
ITGAL	0	.	GRCh37	16	30495433	30495433	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.856-1G>A	.	p.X286_splice	ENST00000356798	.	47	32	15	47	47	0	ITGAL,splice_acceptor_variant,,ENST00000356798,;ITGAL,splice_acceptor_variant,,ENST00000454514,;ITGAL,splice_acceptor_variant,,ENST00000358164,;ITGAL,intron_variant,,ENST00000433423,;ITGAL,downstream_gene_variant,,ENST00000569725,;ITGAL,downstream_gene_variant,,ENST00000564118,;RNU7-61P,upstream_gene_variant,,ENST00000515897,;RP11-297C4.2,intron_variant,,ENST00000569459,;RP11-297C4.3,upstream_gene_variant,,ENST00000562525,;ITGAL,downstream_gene_variant,,ENST00000565348,;ITGAL,upstream_gene_variant,,ENST00000568012,;ITGAL,splice_acceptor_variant,,ENST00000566149,;ITGAL,intron_variant,,ENST00000568926,;ITGAL,upstream_gene_variant,,ENST00000564935,;ITGAL,downstream_gene_variant,,ENST00000562857,;ITGAL,downstream_gene_variant,,ENST00000565864,;	A	ENSG00000005844	ENST00000356798	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ITGAL	HGNC	6148	protein_coding	YES	CCDS32433.1	ENSP00000349252	ITAL_HUMAN	I3L468_HUMAN,H3BNL5_HUMAN	UPI000013C4FF	.	.	.	.	8/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACAGATTGG	.	5	ESCA
FAM65A	0	.	GRCh37	16	67577003	67577004	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2375dupT	p.Met792IlefsTer32	p.M792Ifs*32	ENST00000422602	13/22	109	75	34	72	72	0	FAM65A,frameshift_variant,p.Met786IlefsTer32,ENST00000428437,;FAM65A,frameshift_variant,p.Met792IlefsTer32,ENST00000422602,;FAM65A,frameshift_variant,p.Met792IlefsTer32,ENST00000540839,;FAM65A,frameshift_variant,p.Met772IlefsTer32,ENST00000042381,;FAM65A,frameshift_variant,p.Met776IlefsTer32,ENST00000379312,;FAM65A,downstream_gene_variant,,ENST00000566559,;FAM65A,downstream_gene_variant,,ENST00000569253,;FAM65A,downstream_gene_variant,,ENST00000569179,;FAM65A,upstream_gene_variant,,ENST00000568959,;FAM65A,downstream_gene_variant,,ENST00000562755,;FAM65A,downstream_gene_variant,,ENST00000566920,;FAM65A,downstream_gene_variant,,ENST00000565176,;FAM65A,downstream_gene_variant,,ENST00000566907,;FAM65A,downstream_gene_variant,,ENST00000562116,;CTD-2012K14.4,upstream_gene_variant,,ENST00000564717,;CTD-2012K14.3,upstream_gene_variant,,ENST00000563083,;CTD-2012K14.2,upstream_gene_variant,,ENST00000567122,;FAM65A,downstream_gene_variant,,ENST00000566522,;FAM65A,non_coding_transcript_exon_variant,,ENST00000569733,;FAM65A,non_coding_transcript_exon_variant,,ENST00000564616,;FAM65A,upstream_gene_variant,,ENST00000565190,;FAM65A,downstream_gene_variant,,ENST00000561534,;FAM65A,upstream_gene_variant,,ENST00000565679,;FAM65A,downstream_gene_variant,,ENST00000569474,;FAM65A,downstream_gene_variant,,ENST00000566730,;FAM65A,downstream_gene_variant,,ENST00000566815,;	T	ENSG00000039523	ENST00000422602	Transcript	frameshift_variant	2470-2471	2374-2375	792	M/IX	atg/aTtg	.	.	.	1	FAM65A	HGNC	25836	protein_coding	YES	CCDS54026.1	ENSP00000400099	FA65A_HUMAN	H3BQI5_HUMAN,H3BV02_HUMAN,H3BUP6_HUMAN,H3BSV5_HUMAN,H3BS40_HUMAN	UPI0001AE68C6	.	.	.	13/22	.	hmmpanther:PTHR15829,hmmpanther:PTHR15829:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGCCATGGCT	.	3	ESCA
TMEM231	0	.	GRCh37	16	75573669	75573669	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*223G>C	.	.	ENST00000568377	6/6	14	7	7	15	15	0	TMEM231,3_prime_UTR_variant,,ENST00000258173,;TMEM231,3_prime_UTR_variant,,ENST00000568377,;TMEM231,3_prime_UTR_variant,,ENST00000565067,;CHST5,upstream_gene_variant,,ENST00000565039,;CHST5,upstream_gene_variant,,ENST00000336257,;RP11-77K12.8,downstream_gene_variant,,ENST00000564489,;TMEM231,downstream_gene_variant,,ENST00000569294,;TMEM231,downstream_gene_variant,,ENST00000564576,;TMEM231,3_prime_UTR_variant,,ENST00000562410,;TMEM231,non_coding_transcript_exon_variant,,ENST00000564318,;RP11-77K12.7,intron_variant,,ENST00000460606,;TMEM231,downstream_gene_variant,,ENST00000570006,;	G	ENSG00000205084	ENST00000568377	Transcript	3_prime_UTR_variant	1300	.	.	.	.	.	.	.	-1	TMEM231	HGNC	37234	protein_coding	YES	.	ENSP00000476267	.	B7Z5I3_HUMAN	UPI0000E5DA67	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTCCAGGA	.	5	ESCA
UBBP4	0	.	GRCh37	17	21731342	21731342	+	Intron	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505-88G>A	.	.	ENST00000578713	.	100	81	19	122	122	0	UBBP4,missense_variant,p.Arg215Lys,ENST00000584755,;UBBP4,3_prime_UTR_variant,,ENST00000583708,;UBBP4,intron_variant,,ENST00000581775,;UBBP4,intron_variant,,ENST00000578713,;UBBP4,downstream_gene_variant,,ENST00000584398,;UBBP4,downstream_gene_variant,,ENST00000581769,;	A	ENSG00000263563	ENST00000578713	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	UBBP4	HGNC	12467	protein_coding	YES	.	ENSP00000464265	.	J3QSA3_HUMAN,J3QRK5_HUMAN,J3KSM4_HUMAN,A8CGI2_HUMAN	UPI000268AF41	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGAAGGAGTC	.	3	ESCA
UBBP4	0	.	GRCh37	17	21731357	21731357	+	Intron	SNP	C	C	T	rs778477472	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505-73C>T	.	.	ENST00000578713	.	109	81	28	102	102	0	UBBP4,missense_variant,p.Thr220Ile,ENST00000584755,;UBBP4,3_prime_UTR_variant,,ENST00000583708,;UBBP4,intron_variant,,ENST00000581775,;UBBP4,intron_variant,,ENST00000578713,;UBBP4,downstream_gene_variant,,ENST00000584398,;UBBP4,downstream_gene_variant,,ENST00000581769,;	T	ENSG00000263563	ENST00000578713	Transcript	intron_variant	.	.	.	.	.	rs778477472	.	.	1	UBBP4	HGNC	12467	protein_coding	YES	.	ENSP00000464265	.	J3QSA3_HUMAN,J3QRK5_HUMAN,J3KSM4_HUMAN,A8CGI2_HUMAN	UPI000268AF41	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGCACCTGGT	byFrequency	3	ESCA
SSH2	0	.	GRCh37	17	27958092	27958092	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4039G>C	p.Ala1347Pro	p.A1347P	ENST00000269033	15/15	37	26	10	24	24	0	SSH2,missense_variant,p.Ala1347Pro,ENST00000269033,;SSH2,missense_variant,p.Ala1374Pro,ENST00000540801,;SSH2,intron_variant,,ENST00000577991,;RP11-68I3.2,intron_variant,,ENST00000581474,;	G	ENSG00000141298	ENST00000269033	Transcript	missense_variant	4191	4039	1347	A/P	Gcc/Ccc	.	.	.	-1	SSH2	HGNC	30580	protein_coding	YES	CCDS11253.1	ENSP00000269033	SSH2_HUMAN	J3KSQ9_HUMAN	UPI00001D6272	.	deleterious_low_confidence(0)	probably_damaging(0.984)	15/15	.	hmmpanther:PTHR10159:SF106,hmmpanther:PTHR10159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGGCATACT	.	5	ESCA
NF1	0	.	GRCh37	17	29670040	29670040	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7076T>C	p.Val2359Ala	p.V2359A	ENST00000358273	48/58	59	12	47	37	37	0	NF1,missense_variant,p.Val72Ala,ENST00000417592,;NF1,missense_variant,p.Val152Ala,ENST00000444181,;NF1,missense_variant,p.Val2359Ala,ENST00000358273,;NF1,missense_variant,p.Val2004Ala,ENST00000456735,;NF1,missense_variant,p.Val2338Ala,ENST00000356175,;NF1,missense_variant,p.Val74Ala,ENST00000581790,;NF1,missense_variant,p.Val154Ala,ENST00000471572,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,non_coding_transcript_exon_variant,,ENST00000584328,;NF1,non_coding_transcript_exon_variant,,ENST00000582892,;AK4P1,upstream_gene_variant,,ENST00000581275,;	C	ENSG00000196712	ENST00000358273	Transcript	missense_variant	7459	7076	2359	V/A	gTa/gCa	.	.	.	1	NF1	HGNC	7765	protein_coding	YES	CCDS42292.1	ENSP00000351015	NF1_HUMAN	Q9UMU3_HUMAN,Q4W6X4_HUMAN,K7EP94_HUMAN	UPI000012FFAE	.	deleterious(0)	benign(0.444)	48/58	.	Superfamily_domains:SSF48371,hmmpanther:PTHR10194:SF60,hmmpanther:PTHR10194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGTATTTA	.	5	ESCA
P2RX5	0	.	GRCh37	17	3591966	3591966	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841C>T	p.%3D	p.L281L	ENST00000225328	8/12	85	59	25	83	83	0	P2RX5,synonymous_variant,p.%3D,ENST00000435558,;P2RX5,synonymous_variant,p.%3D,ENST00000552050,;P2RX5,synonymous_variant,p.%3D,ENST00000552276,;P2RX5,synonymous_variant,p.%3D,ENST00000551178,;P2RX5,synonymous_variant,p.%3D,ENST00000547178,;P2RX5,synonymous_variant,p.%3D,ENST00000345901,;P2RX5,synonymous_variant,p.%3D,ENST00000225328,;P2RX5,synonymous_variant,p.%3D,ENST00000552723,;P2RX5,non_coding_transcript_exon_variant,,ENST00000550772,;P2RX5-TAX1BP3,synonymous_variant,p.%3D,ENST00000550383,;P2RX5,upstream_gene_variant,,ENST00000552456,;P2RX5,downstream_gene_variant,,ENST00000547933,;	A	ENSG00000083454	ENST00000225328	Transcript	synonymous_variant	1240	841	281	L	Ctg/Ttg	.	.	.	-1	P2RX5	HGNC	8536	protein_coding	YES	CCDS11034.1	ENSP00000225328	P2RX5_HUMAN	.	UPI0000074324	.	.	.	8/12	.	hmmpanther:PTHR10125:SF12,hmmpanther:PTHR10125,Pfam_domain:PF00864,TIGRFAM_domain:TIGR00863,Gene3D:3h9vA02	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCAGACGGC	.	5	ESCA
DNAJC7	0	.	GRCh37	17	40128676	40128676	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*75C>T	.	.	ENST00000457167	14/14	87	60	27	92	92	0	DNAJC7,3_prime_UTR_variant,,ENST00000457167,;DNAJC7,3_prime_UTR_variant,,ENST00000587727,;DNAJC7,3_prime_UTR_variant,,ENST00000426588,;CNP,3_prime_UTR_variant,,ENST00000393892,;CNP,downstream_gene_variant,,ENST00000393888,;CNP,downstream_gene_variant,,ENST00000472031,;CNP,downstream_gene_variant,,ENST00000591072,;DNAJC7,downstream_gene_variant,,ENST00000316603,;CNP,downstream_gene_variant,,ENST00000592105,;DNAJC7,3_prime_UTR_variant,,ENST00000588814,;CNP,downstream_gene_variant,,ENST00000486438,;DNAJC7,downstream_gene_variant,,ENST00000585693,;CNP,downstream_gene_variant,,ENST00000592861,;	A	ENSG00000168259	ENST00000457167	Transcript	3_prime_UTR_variant	1797	.	.	.	.	.	.	.	-1	DNAJC7	HGNC	12392	protein_coding	YES	CCDS45677.1	ENSP00000406463	DNJC7_HUMAN	K7ER44_HUMAN,K7EN19_HUMAN,K7EK03_HUMAN,K7EJV7_HUMAN,K7EJL5_HUMAN,K7EJE9_HUMAN	UPI000013EC47	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAGGAGGTG	.	5	ESCA
STAT3	0	.	GRCh37	17	40466587	40466587	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1176C>A	.	.	ENST00000264657	24/24	155	101	54	122	122	0	STAT3,3_prime_UTR_variant,,ENST00000264657,;STAT3,downstream_gene_variant,,ENST00000588969,;STAT5A,downstream_gene_variant,,ENST00000546010,;STAT5A,downstream_gene_variant,,ENST00000590949,;STAT5A,downstream_gene_variant,,ENST00000452307,;STAT5A,downstream_gene_variant,,ENST00000345506,;STAT5A,downstream_gene_variant,,ENST00000588868,;STAT5A,downstream_gene_variant,,ENST00000587646,;STAT3,downstream_gene_variant,,ENST00000585517,;STAT3,downstream_gene_variant,,ENST00000404395,;STAT3,downstream_gene_variant,,ENST00000389272,;STAT3,downstream_gene_variant,,ENST00000491272,;STAT3,downstream_gene_variant,,ENST00000462286,;STAT3,downstream_gene_variant,,ENST00000462269,;STAT5A,downstream_gene_variant,,ENST00000468096,;	T	ENSG00000168610	ENST00000264657	Transcript	3_prime_UTR_variant	3802	.	.	.	.	.	.	.	-1	STAT3	HGNC	11364	protein_coding	YES	CCDS32656.1	ENSP00000264657	STAT3_HUMAN	G8JLH9_HUMAN	UPI0000031047	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAGATCAA	.	5	ESCA
ITGB3	0	.	GRCh37	17	45364556	45364556	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.898C>T	p.His300Tyr	p.H300Y	ENST00000559488	6/15	61	42	19	51	51	0	ITGB3,missense_variant,p.His253Tyr,ENST00000435993,;ITGB3,missense_variant,p.His300Tyr,ENST00000571680,;ITGB3,missense_variant,p.His300Tyr,ENST00000559488,;ITGB3,missense_variant,p.His289Tyr,ENST00000560629,;ITGB3,upstream_gene_variant,,ENST00000573377,;	T	ENSG00000259207	ENST00000559488	Transcript	missense_variant	914	898	300	H/Y	Cat/Tat	.	.	.	1	ITGB3	HGNC	6156	protein_coding	YES	CCDS11511.1	ENSP00000452786	ITB3_HUMAN	F2X0V0_HUMAN,F1C634_HUMAN,F1C632_HUMAN,F1C630_HUMAN	UPI000013D240	.	deleterious(0.03)	benign(0.141)	6/15	.	hmmpanther:PTHR10082:SF25,hmmpanther:PTHR10082,Pfam_domain:PF00362,Gene3D:3.40.50.410,PIRSF_domain:PIRSF002512,SMART_domains:SM00187,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGTCATGTT	.	5	ESCA
CLTC	0	.	GRCh37	17	57758783	57758783	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3193T>C	p.Phe1065Leu	p.F1065L	ENST00000269122	20/32	47	24	22	38	38	0	CLTC,missense_variant,p.Phe1065Leu,ENST00000269122,;CLTC,missense_variant,p.Phe1065Leu,ENST00000393043,;CLTC,intron_variant,,ENST00000579456,;CLTC,upstream_gene_variant,,ENST00000475458,;CLTC,upstream_gene_variant,,ENST00000472651,;PTRH2,intron_variant,,ENST00000587935,;CLTC,downstream_gene_variant,,ENST00000579815,;CLTC,upstream_gene_variant,,ENST00000496076,;	C	ENSG00000141367	ENST00000269122	Transcript	missense_variant	3467	3193	1065	F/L	Ttt/Ctt	.	.	.	1	CLTC	HGNC	2092	protein_coding	YES	CCDS32696.1	ENSP00000269122	CLH1_HUMAN	Q49AL0_HUMAN	UPI0000127ABD	.	deleterious(0.01)	benign(0.265)	20/32	.	PROSITE_profiles:PS50236,hmmpanther:PTHR10292:SF7,hmmpanther:PTHR10292,Gene3D:1.25.40.10,Pfam_domain:PF00637,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGTTTGAA	.	5	ESCA
DDX5	0	.	GRCh37	17	62499111	62499111	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916G>T	p.Glu306Ter	p.E306*	ENST00000225792	8/13	74	35	39	38	38	0	DDX5,stop_gained,p.Glu306Ter,ENST00000578804,;DDX5,stop_gained,p.Glu92Ter,ENST00000579996,;DDX5,stop_gained,p.Glu227Ter,ENST00000450599,;DDX5,stop_gained,p.Glu144Ter,ENST00000577787,;DDX5,stop_gained,p.Glu306Ter,ENST00000225792,;DDX5,downstream_gene_variant,,ENST00000584279,;DDX5,downstream_gene_variant,,ENST00000583212,;CEP95,upstream_gene_variant,,ENST00000553412,;DDX5,downstream_gene_variant,,ENST00000581806,;DDX5,downstream_gene_variant,,ENST00000583239,;DDX5,downstream_gene_variant,,ENST00000579091,;CEP95,upstream_gene_variant,,ENST00000556440,;DDX5,downstream_gene_variant,,ENST00000578190,;CEP95,upstream_gene_variant,,ENST00000581056,;DDX5,downstream_gene_variant,,ENST00000581697,;DDX5,downstream_gene_variant,,ENST00000585060,;CEP95,upstream_gene_variant,,ENST00000580188,;DDX5,downstream_gene_variant,,ENST00000585111,;DDX5,downstream_gene_variant,,ENST00000577922,;MIR3064,upstream_gene_variant,,ENST00000581130,;MIR5047,upstream_gene_variant,,ENST00000579212,;DDX5,non_coding_transcript_exon_variant,,ENST00000578491,;DDX5,upstream_gene_variant,,ENST00000580026,;DDX5,downstream_gene_variant,,ENST00000584500,;DDX5,downstream_gene_variant,,ENST00000583699,;DDX5,upstream_gene_variant,,ENST00000581237,;DDX5,3_prime_UTR_variant,,ENST00000540698,;DDX5,3_prime_UTR_variant,,ENST00000581693,;DDX5,non_coding_transcript_exon_variant,,ENST00000584549,;DDX5,non_coding_transcript_exon_variant,,ENST00000579461,;DDX5,non_coding_transcript_exon_variant,,ENST00000582326,;DDX5,non_coding_transcript_exon_variant,,ENST00000583894,;DDX5,non_coding_transcript_exon_variant,,ENST00000581551,;DDX5,non_coding_transcript_exon_variant,,ENST00000581230,;DDX5,non_coding_transcript_exon_variant,,ENST00000583201,;DDX5,downstream_gene_variant,,ENST00000585223,;CEP95,upstream_gene_variant,,ENST00000579860,;DDX5,upstream_gene_variant,,ENST00000578758,;CEP95,upstream_gene_variant,,ENST00000553956,;DDX5,downstream_gene_variant,,ENST00000578400,;DDX5,downstream_gene_variant,,ENST00000583562,;DDX5,upstream_gene_variant,,ENST00000585317,;	A	ENSG00000108654	ENST00000225792	Transcript	stop_gained	1318	916	306	E/*	Gaa/Taa	.	.	.	-1	DDX5	HGNC	2746	protein_coding	YES	CCDS11659.1	ENSP00000225792	DDX5_HUMAN	J3QS97_HUMAN,J3QRQ7_HUMAN,J3QRN5_HUMAN,J3QR62_HUMAN,J3QLG9_HUMAN,J3QKN9_HUMAN,J3KTQ4_HUMAN,J3KRZ1_HUMAN,J3KRX8_HUMAN	UPI000003B456	.	.	.	8/13	.	hmmpanther:PTHR24031:SF182,hmmpanther:PTHR24031,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCAAGTG	.	5	ESCA
TP53	0	.	GRCh37	17	7578257	7578257	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	6/11	120	21	99	82	82	0	TP53,stop_gained,p.Glu198Ter,ENST00000413465,;TP53,stop_gained,p.Glu198Ter,ENST00000420246,;TP53,stop_gained,p.Glu198Ter,ENST00000269305,;TP53,stop_gained,p.Glu66Ter,ENST00000509690,;TP53,stop_gained,p.Glu198Ter,ENST00000359597,;TP53,stop_gained,p.Glu105Ter,ENST00000514944,;TP53,stop_gained,p.Glu198Ter,ENST00000445888,;TP53,stop_gained,p.Glu198Ter,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	782	592	198	E/*	Gaa/Taa	TP53_g.12661G>T,TP53_g.12661G>C,TP53_g.12661del,TP53_g.12661G>A,COSM45449,COSM43690,COSM44241,COSM44702,COSM118013,COSM391541,COSM118010,COSM391542,COSM118011,COSM391544,COSM3522696,COSM1750370,COSM118012,COSM391543	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E198*|c.592G>T|5,SITE|p.E198*|c.592G>T|4,SITE|p.E105*|c.313G>T|9,SITE|p.E198*|c.592G>T|27,SITE|p.E198*|c.592G>T|9,SITE|p.E66*|c.196G>T|9,SITE|p.E198*|c.592G>T|9,CODON|p.0?|c.1_1182del1182|6,BUFFER|p.L201F|c.603G>T|3,BUFFER|p.L201F|c.603G>C|4,BUFFER|p.N200fs*47|c.598delA|5,BUFFER|p.G199V|c.596G>T|10,BUFFER|p.G106V|c.317G>T|6,BUFFER|p.G67V|c.200G>T|6,BUFFER|p.G199V|c.596G>T|6,BUFFER|p.G199V|c.596G>T|6,BUFFER|p.G199E|c.596G>A|11,BUFFER|p.G199*|c.595G>T|5,BUFFER|p.G199R|c.595G>A|9,BUFFER|p.A189_V197delAPPQHLIRV|c.565_591del27|4,BUFFER|p.E198K|c.592G>A|5,BUFFER|p.V197G|c.590T>G|15,BUFFER|p.V197E|c.590T>A|8,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.V65L|c.193G>T|3,BUFFER|p.V197M|c.589G>A|12,BUFFER|p.V197L|c.589G>T|5,BUFFER|p.V104L|c.310G>T|3,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.R196R|c.588A>G|4,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R196P|c.587G>C|18,BUFFER|p.R64P|c.191G>C|7,BUFFER|p.R196Q|c.587G>A|4,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R103P|c.308G>C|7,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196*|c.585_586CC>TT|7,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R64fs*>27|c.190delC|3,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R103fs*51|c.307delC|3,BUFFER|p.R196fs*51|c.586delC|7,BUFFER|p.R64*|c.190C>T|65,BUFFER|p.R196*|c.586C>T|45,BUFFER|p.R196*|c.586C>T|33,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R103*|c.307C>T|64,BUFFER|p.R196*|c.586C>T|180,BUFFER|p.I102N|c.305T>A|10,BUFFER|p.I102T|c.305T>C|21,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I63S|c.188T>G|3,BUFFER|p.I195T|c.584T>C|88,BUFFER|p.I195N|c.584T>A|4,BUFFER|p.I195T|c.584T>C|21,BUFFER|p.I63N|c.188T>A|10,BUFFER|p.I195T|c.584T>C|12,BUFFER|p.I63T|c.188T>C|21,BUFFER|p.I195T|c.584T>C|21,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I195N|c.584T>A|23,BUFFER|p.I195T|c.584T>C|10,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I195S|c.584T>G|7,BUFFER|p.I195F|c.583A>T|6,BUFFER|p.I195F|c.583A>T|28,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.I63F|c.187A>T|9,BUFFER|p.I102F|c.304A>T|9,BUFFER|p.I195F|c.583A>T|5,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.L194L|c.582T>C|3,BUFFER|p.L62R|c.185T>G|17,BUFFER|p.L194R|c.581T>G|50,BUFFER|p.L194R|c.581T>G|11,BUFFER|p.L194H|c.581T>A|6,BUFFER|p.L194P|c.581T>C|9,BUFFER|p.L101R|c.302T>G|17,BUFFER|p.L194R|c.581T>G|9,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194R|c.581T>G|17	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTCCACTC	.	5	ESCA
TBCD	0	.	GRCh37	17	80847552	80847552	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1542C>A	p.Phe514Leu	p.F514L	ENST00000355528	16/39	95	69	26	55	55	0	TBCD,missense_variant,p.Phe514Leu,ENST00000539345,;TBCD,missense_variant,p.Phe128Leu,ENST00000397466,;TBCD,missense_variant,p.Phe20Leu,ENST00000571316,;TBCD,missense_variant,p.Phe514Leu,ENST00000355528,;TBCD,5_prime_UTR_variant,,ENST00000571712,;TBCD,5_prime_UTR_variant,,ENST00000576760,;TBCD,5_prime_UTR_variant,,ENST00000576996,;TBCD,5_prime_UTR_variant,,ENST00000572984,;TBCD,5_prime_UTR_variant,,ENST00000576160,;TBCD,upstream_gene_variant,,ENST00000572953,;TBCD,upstream_gene_variant,,ENST00000574975,;TBCD,intron_variant,,ENST00000574801,;	A	ENSG00000141556	ENST00000355528	Transcript	missense_variant	1672	1542	514	F/L	ttC/ttA	.	.	.	1	TBCD	HGNC	11581	protein_coding	YES	CCDS45818.1	ENSP00000347719	TBCD_HUMAN	I3L4D2_HUMAN,I3L439_HUMAN,I3L3H4_HUMAN,I3L1S3_HUMAN,I3L163_HUMAN,I3L131_HUMAN	UPI000020053F	.	deleterious(0)	probably_damaging(0.983)	16/39	.	hmmpanther:PTHR12658,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCCAGGA	.	5	ESCA
ROCK1	0	.	GRCh37	18	18529846	18529846	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1499T>A	.	.	ENST00000399799	33/33	91	77	13	48	48	0	ROCK1,3_prime_UTR_variant,,ENST00000399799,;ROCK1,downstream_gene_variant,,ENST00000578051,;ROCK1,downstream_gene_variant,,ENST00000584687,;	T	ENSG00000067900	ENST00000399799	Transcript	3_prime_UTR_variant	6505	.	.	.	.	.	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCATAAATTA	.	4	ESCA
ZNF516	0	.	GRCh37	18	74154846	74154846	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165G>A	p.%3D	p.K55K	ENST00000443185	3/8	30	23	7	32	32	0	ZNF516,synonymous_variant,p.%3D,ENST00000443185,;ZNF516,synonymous_variant,p.%3D,ENST00000532857,;ZNF516,non_coding_transcript_exon_variant,,ENST00000524431,;	T	ENSG00000101493	ENST00000443185	Transcript	synonymous_variant	483	165	55	K	aaG/aaA	.	.	.	-1	ZNF516	HGNC	28990	protein_coding	YES	.	ENSP00000394757	ZN516_HUMAN	F5H2K2_HUMAN	UPI00001394A1	.	.	.	3/8	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF3,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGCTTGCG	.	4	ESCA
SALL3	0	.	GRCh37	18	76752159	76752159	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168C>G	p.Cys56Trp	p.C56W	ENST00000537592	2/3	62	41	21	55	55	0	SALL3,missense_variant,p.Cys56Trp,ENST00000537592,;SALL3,missense_variant,p.Cys56Trp,ENST00000575389,;SALL3,5_prime_UTR_variant,,ENST00000536229,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,non_coding_transcript_exon_variant,,ENST00000572928,;	G	ENSG00000256463	ENST00000537592	Transcript	missense_variant	168	168	56	C/W	tgC/tgG	.	.	.	1	SALL3	HGNC	10527	protein_coding	YES	CCDS12013.1	ENSP00000441823	SALL3_HUMAN	.	UPI000013E5A7	.	deleterious(0)	unknown(0)	2/3	.	hmmpanther:PTHR23233:SF46,hmmpanther:PTHR23233,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.C57C|c.171C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATGCTGCGC	.	5	ESCA
CTDP1	0	.	GRCh37	18	77473021	77473021	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.913G>A	p.Glu305Lys	p.E305K	ENST00000299543	7/13	50	29	21	38	38	0	CTDP1,missense_variant,p.Glu237Lys,ENST00000591598,;CTDP1,missense_variant,p.Glu305Lys,ENST00000075430,;CTDP1,missense_variant,p.Glu305Lys,ENST00000299543,;	A	ENSG00000060069	ENST00000299543	Transcript	missense_variant	1060	913	305	E/K	Gaa/Aaa	.	.	.	1	CTDP1	HGNC	2498	protein_coding	YES	CCDS12017.1	ENSP00000299543	CTDP1_HUMAN	K7EPW4_HUMAN	UPI000013C57B	.	deleterious(0)	probably_damaging(1)	7/13	.	PROSITE_profiles:PS50969,hmmpanther:PTHR23081:SF0,hmmpanther:PTHR23081,TIGRFAM_domain:TIGR02250,Gene3D:3.40.50.1000,Pfam_domain:PF03031,SMART_domains:SM00577,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCGAGAAGAT	.	5	ESCA
DNMT1	0	.	GRCh37	19	10254519	10254519	+	Silent	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3039A>G	p.%3D	p.K1013K	ENST00000359526	29/41	65	36	29	28	28	0	DNMT1,synonymous_variant,p.%3D,ENST00000340748,;DNMT1,synonymous_variant,p.%3D,ENST00000540357,;DNMT1,synonymous_variant,p.%3D,ENST00000359526,;DNMT1,non_coding_transcript_exon_variant,,ENST00000589538,;DNMT1,upstream_gene_variant,,ENST00000593049,;DNMT1,3_prime_UTR_variant,,ENST00000592705,;DNMT1,non_coding_transcript_exon_variant,,ENST00000586588,;DNMT1,upstream_gene_variant,,ENST00000588913,;DNMT1,upstream_gene_variant,,ENST00000587197,;DNMT1,upstream_gene_variant,,ENST00000587604,;DNMT1,upstream_gene_variant,,ENST00000589091,;DNMT1,upstream_gene_variant,,ENST00000589351,;DNMT1,upstream_gene_variant,,ENST00000591239,;	C	ENSG00000130816	ENST00000359526	Transcript	synonymous_variant	3219	3039	1013	K	aaA/aaG	.	.	.	-1	DNMT1	HGNC	2976	protein_coding	YES	CCDS45958.1	ENSP00000352516	DNMT1_HUMAN	K7ELB1_HUMAN,K7EKC3_HUMAN,I6L9H2_HUMAN,B3KVA0_HUMAN	UPI000002A823	.	.	.	29/41	.	PROSITE_profiles:PS51038,hmmpanther:PTHR10629:SF11,hmmpanther:PTHR10629,Pfam_domain:PF01426,PIRSF_domain:PIRSF037404,SMART_domains:SM00439	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTCTTTGAT	.	5	ESCA
DAZAP1	0	.	GRCh37	19	1434963	1434963	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*52G>A	.	.	ENST00000233078	12/12	53	36	17	59	59	0	DAZAP1,3_prime_UTR_variant,,ENST00000233078,;DAZAP1,3_prime_UTR_variant,,ENST00000336761,;DAZAP1,3_prime_UTR_variant,,ENST00000591999,;DAZAP1,3_prime_UTR_variant,,ENST00000587079,;RPS15,upstream_gene_variant,,ENST00000591804,;RPS15,upstream_gene_variant,,ENST00000593052,;RPS15,upstream_gene_variant,,ENST00000233609,;RPS15,upstream_gene_variant,,ENST00000586686,;DAZAP1,downstream_gene_variant,,ENST00000592453,;RPS15,upstream_gene_variant,,ENST00000589656,;RPS15,upstream_gene_variant,,ENST00000591032,;RPS15,upstream_gene_variant,,ENST00000586656,;RPS15,upstream_gene_variant,,ENST00000586096,;RPS15,upstream_gene_variant,,ENST00000585665,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000585485,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000589874,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000589484,;RPS15,upstream_gene_variant,,ENST00000592623,;RPS15,upstream_gene_variant,,ENST00000592588,;RPS15,upstream_gene_variant,,ENST00000592700,;	A	ENSG00000071626	ENST00000233078	Transcript	3_prime_UTR_variant	1437	.	.	.	.	.	.	.	1	DAZAP1	HGNC	2683	protein_coding	YES	CCDS12065.1	ENSP00000233078	DAZP1_HUMAN	Q5IRM7_HUMAN,B3KS63_HUMAN	UPI00000728D6	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTGAACTC	.	5	ESCA
NOTCH3	0	.	GRCh37	19	15300201	15300201	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1075C>A	p.Pro359Thr	p.P359T	ENST00000263388	7/33	53	29	23	32	32	0	NOTCH3,missense_variant,p.Pro359Thr,ENST00000263388,;NOTCH3,missense_variant,p.Pro358Thr,ENST00000601011,;	T	ENSG00000074181	ENST00000263388	Transcript	missense_variant	1151	1075	359	P/T	Ccc/Acc	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	deleterious(0.02)	probably_damaging(1)	7/33	.	Superfamily_domains:SSF57196,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,Gene3D:2.10.25.10,Pfam_domain:PF00008,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGGGTTGC	.	5	ESCA
PIK3R2	0	.	GRCh37	19	18273933	18273933	+	Silent	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1266C>G	p.%3D	p.L422L	ENST00000222254	10/16	44	27	17	48	48	0	PIK3R2,synonymous_variant,p.%3D,ENST00000222254,;PIK3R2,synonymous_variant,p.%3D,ENST00000593731,;PIK3R2,synonymous_variant,p.%3D,ENST00000426902,;PIK3R2,upstream_gene_variant,,ENST00000464016,;PIK3R2,downstream_gene_variant,,ENST00000474310,;PIK3R2,downstream_gene_variant,,ENST00000600533,;	G	ENSG00000105647	ENST00000222254	Transcript	synonymous_variant	1866	1266	422	L	ctC/ctG	.	.	.	1	PIK3R2	HGNC	8980	protein_coding	YES	CCDS12371.1	ENSP00000222254	P85B_HUMAN	Q96CK7_HUMAN,M0QYU3_HUMAN	UPI000006EF95	.	.	.	10/16	.	PROSITE_profiles:PS50001,hmmpanther:PTHR10155:SF1,hmmpanther:PTHR10155,Gene3D:3.30.505.10,Superfamily_domains:SSF55550,Prints_domain:PR00678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCTACCC	.	5	ESCA
ZNF90	0	.	GRCh37	19	20228938	20228938	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.575A>T	p.Lys192Met	p.K192M	ENST00000418063	4/4	70	43	27	66	66	0	ZNF90,missense_variant,p.Lys192Met,ENST00000418063,;ZNF90,intron_variant,,ENST00000474284,;ZNF90,intron_variant,,ENST00000469078,;ZNF90,upstream_gene_variant,,ENST00000484032,;ZNF90,downstream_gene_variant,,ENST00000473524,;	T	ENSG00000213988	ENST00000418063	Transcript	missense_variant	687	575	192	K/M	aAg/aTg	.	.	.	1	ZNF90	HGNC	13165	protein_coding	YES	CCDS46028.1	ENSP00000410466	ZNF90_HUMAN	.	UPI00002376E6	.	deleterious(0.01)	probably_damaging(0.995)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF92,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATAAGAAAA	.	5	ESCA
JSRP1	0	.	GRCh37	19	2254447	2254447	+	Silent	SNP	G	G	A	rs775914552	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144C>T	p.%3D	p.P48P	ENST00000300961	3/7	91	64	26	73	72	0	JSRP1,synonymous_variant,p.%3D,ENST00000586471,;JSRP1,synonymous_variant,p.%3D,ENST00000300961,;JSRP1,synonymous_variant,p.%3D,ENST00000593238,;AMH,downstream_gene_variant,,ENST00000592877,;AMH,downstream_gene_variant,,ENST00000221496,;MIR4321,downstream_gene_variant,,ENST00000592276,;AMH,downstream_gene_variant,,ENST00000609455,;AMH,downstream_gene_variant,,ENST00000589313,;	A	ENSG00000167476	ENST00000300961	Transcript	synonymous_variant	209	144	48	P	ccC/ccT	rs775914552	.	.	-1	JSRP1	HGNC	24963	protein_coding	YES	CCDS12086.1	ENSP00000300961	JSPR1_HUMAN	K7EKG1_HUMAN	UPI000006EA5D	.	.	.	3/7	.	hmmpanther:PTHR22397,hmmpanther:PTHR22397:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACGTGGGGCAC	.	4	ESCA
TLE2	0	.	GRCh37	19	3025060	3025060	+	Silent	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.252G>C	p.%3D	p.L84L	ENST00000262953	5/20	99	53	46	67	67	0	TLE2,synonymous_variant,p.%3D,ENST00000455444,;TLE2,synonymous_variant,p.%3D,ENST00000592584,;TLE2,synonymous_variant,p.%3D,ENST00000262953,;TLE2,synonymous_variant,p.%3D,ENST00000590536,;TLE2,synonymous_variant,p.%3D,ENST00000587137,;TLE2,synonymous_variant,p.%3D,ENST00000591529,;TLE2,synonymous_variant,p.%3D,ENST00000426948,;TLE2,synonymous_variant,p.%3D,ENST00000443826,;TLE2,synonymous_variant,p.%3D,ENST00000586422,;TLE2,5_prime_UTR_variant,,ENST00000447365,;TLE2,intron_variant,,ENST00000591457,;TLE2,upstream_gene_variant,,ENST00000589364,;TLE2,non_coding_transcript_exon_variant,,ENST00000590183,;TLE2,upstream_gene_variant,,ENST00000589291,;TLE2,upstream_gene_variant,,ENST00000587217,;TLE2,non_coding_transcript_exon_variant,,ENST00000590101,;TLE2,non_coding_transcript_exon_variant,,ENST00000587893,;TLE2,non_coding_transcript_exon_variant,,ENST00000592305,;TLE2,non_coding_transcript_exon_variant,,ENST00000591720,;TLE2,non_coding_transcript_exon_variant,,ENST00000587770,;	G	ENSG00000065717	ENST00000262953	Transcript	synonymous_variant	515	252	84	L	ctG/ctC	.	.	.	-1	TLE2	HGNC	11838	protein_coding	YES	CCDS45911.1	ENSP00000262953	TLE2_HUMAN	.	UPI0000137038	.	.	.	5/20	.	hmmpanther:PTHR10814:SF4,hmmpanther:PTHR10814,Pfam_domain:PF03920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCTCAGACG	.	5	ESCA
CEBPA	0	.	GRCh37	19	33791575	33791575	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*669C>G	.	.	ENST00000498907	1/1	14	9	5	17	17	0	CEBPA,3_prime_UTR_variant,,ENST00000498907,;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.11,intron_variant,,ENST00000589932,;CTD-2540B15.7,upstream_gene_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;AC008738.1,non_coding_transcript_exon_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,;	C	ENSG00000245848	ENST00000498907	Transcript	3_prime_UTR_variant	1896	.	.	.	.	.	.	.	-1	CEBPA	HGNC	1833	protein_coding	YES	CCDS54243.1	ENSP00000427514	CEBPA_HUMAN	Q6P3S4_HUMAN	UPI0000167F92	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCGCAGTG	.	5	ESCA
FFAR3	0	.	GRCh37	19	35849910	35849910	+	Missense_Mutation	SNP	G	G	A	rs763567775	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118G>A	p.Val40Met	p.V40M	ENST00000327809	2/2	121	101	19	84	84	0	FFAR3,missense_variant,p.Val40Met,ENST00000327809,;FFAR3,missense_variant,p.Val40Met,ENST00000594310,;	A	ENSG00000185897	ENST00000327809	Transcript	missense_variant	319	118	40	V/M	Gtg/Atg	rs763567775	.	.	1	FFAR3	HGNC	4499	protein_coding	YES	CCDS12459.1	ENSP00000328230	FFAR3_HUMAN	.	UPI0000001C3F	.	deleterious(0.05)	benign(0.149)	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF31,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTCGTGGGC	byFrequency	4	ESCA
KMT2B	0	.	GRCh37	19	36211861	36211861	+	Missense_Mutation	SNP	C	C	T	rs747570960	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1612C>T	p.Arg538Cys	p.R538C	ENST00000222270	3/37	39	23	16	40	40	0	KMT2B,missense_variant,p.Arg538Cys,ENST00000222270,;KMT2B,missense_variant,p.Arg538Cys,ENST00000420124,;KMT2B,intron_variant,,ENST00000341701,;ZBTB32,downstream_gene_variant,,ENST00000392197,;ZBTB32,downstream_gene_variant,,ENST00000262630,;ZBTB32,downstream_gene_variant,,ENST00000426659,;KMT2B,non_coding_transcript_exon_variant,,ENST00000607650,;KMT2B,intron_variant,,ENST00000606995,;ZBTB32,downstream_gene_variant,,ENST00000481182,;	T	ENSG00000272333	ENST00000222270	Transcript	missense_variant	1612	1612	538	R/C	Cgt/Tgt	rs747570960	.	.	1	KMT2B	Uniprot_gn	15840	protein_coding	YES	CCDS46055.1	ENSP00000222270	KMT2B_HUMAN	.	UPI00001376B5	.	.	probably_damaging(0.973)	3/37	.	hmmpanther:PTHR22884:SF280,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCCGTGTC	.	5	ESCA
FCGBP	0	.	GRCh37	19	40368702	40368702	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12646C>T	p.Leu4216Phe	p.L4216F	ENST00000221347	28/36	229	203	26	169	169	0	FCGBP,missense_variant,p.Leu4216Phe,ENST00000221347,;	A	ENSG00000090920	ENST00000221347	Transcript	missense_variant	12654	12646	4216	L/F	Ctc/Ttc	.	.	.	-1	FCGBP	HGNC	13572	protein_coding	YES	CCDS12546.1	ENSP00000221347	FCGBP_HUMAN	.	UPI00001B0455	.	.	possibly_damaging(0.849)	28/36	.	PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF244,hmmpanther:PTHR11339,Pfam_domain:PF00094,SMART_domains:SM00216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGAGCCCGC	.	4	ESCA
CYP2B6	0	.	GRCh37	19	41510046	41510046	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312C>T	p.%3D	p.V104V	ENST00000324071	2/9	92	49	43	68	68	0	CYP2B6,synonymous_variant,p.%3D,ENST00000593831,;CYP2B6,synonymous_variant,p.%3D,ENST00000330446,;CYP2B6,synonymous_variant,p.%3D,ENST00000324071,;CYP2B6,non_coding_transcript_exon_variant,,ENST00000598834,;CYP2B6,upstream_gene_variant,,ENST00000594187,;	T	ENSG00000197408	ENST00000324071	Transcript	synonymous_variant	319	312	104	V	gtC/gtT	.	.	.	1	CYP2B6	HGNC	2615	protein_coding	YES	CCDS12570.1	ENSP00000324648	CP2B6_HUMAN	Q9UNX8_HUMAN,F2X1B0_HUMAN	UPI000012823F	.	.	.	2/9	.	hmmpanther:PTHR24300:SF146,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGTCGACCC	.	5	ESCA
RSPH6A	0	.	GRCh37	19	46299318	46299318	+	Missense_Mutation	SNP	C	C	T	rs145529811	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1963G>A	p.Glu655Lys	p.E655K	ENST00000221538	6/6	118	65	53	66	66	0	RSPH6A,missense_variant,p.Glu391Lys,ENST00000600188,;RSPH6A,missense_variant,p.Glu655Lys,ENST00000221538,;RSPH6A,synonymous_variant,p.%3D,ENST00000597055,;DMWD,upstream_gene_variant,,ENST00000377735,;DMWD,upstream_gene_variant,,ENST00000270223,;DMWD,upstream_gene_variant,,ENST00000598237,;DMWD,upstream_gene_variant,,ENST00000601370,;	T	ENSG00000104941	ENST00000221538	Transcript	missense_variant	2106	1963	655	E/K	Gag/Aag	rs145529811	.	.	-1	RSPH6A	HGNC	14241	protein_coding	YES	CCDS12675.1	ENSP00000221538	RSH6A_HUMAN	M0R103_HUMAN	UPI0000037C58	.	tolerated(0.06)	benign(0.051)	6/6	.	hmmpanther:PTHR13159,hmmpanther:PTHR13159:SF1,Pfam_domain:PF04712	.	.	.	.	.	.	.	T:0.0005	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCGGGGC	.	5	ESCA
RASIP1	0	.	GRCh37	19	49228078	49228078	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2267A>G	p.Glu756Gly	p.E756G	ENST00000222145	9/12	70	46	24	43	43	0	RASIP1,missense_variant,p.Glu756Gly,ENST00000222145,;RASIP1,downstream_gene_variant,,ENST00000599291,;RASIP1,downstream_gene_variant,,ENST00000594232,;RASIP1,non_coding_transcript_exon_variant,,ENST00000601530,;	C	ENSG00000105538	ENST00000222145	Transcript	missense_variant	2472	2267	756	E/G	gAg/gGg	.	.	.	-1	RASIP1	HGNC	24716	protein_coding	YES	CCDS12731.1	ENSP00000222145	RAIN_HUMAN	Q9NX72_HUMAN,Q7L251_HUMAN,B3KVR5_HUMAN	UPI000020283D	.	tolerated(0.11)	possibly_damaging(0.766)	9/12	.	PROSITE_profiles:PS51126,hmmpanther:PTHR16027:SF4,hmmpanther:PTHR16027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGCTCCAAG	.	5	ESCA
SNRNP70	0	.	GRCh37	19	49604727	49604727	+	Silent	SNP	C	C	T	rs373191644	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474C>T	p.%3D	p.H158H	ENST00000598441	7/10	154	90	63	125	125	0	SNRNP70,synonymous_variant,p.%3D,ENST00000221448,;SNRNP70,synonymous_variant,p.%3D,ENST00000598441,;SNRNP70,synonymous_variant,p.%3D,ENST00000598984,;SNRNP70,downstream_gene_variant,,ENST00000601411,;SNRNP70,synonymous_variant,p.%3D,ENST00000595231,;SNRNP70,synonymous_variant,p.%3D,ENST00000401730,;SNRNP70,synonymous_variant,p.%3D,ENST00000601065,;SNRNP70,non_coding_transcript_exon_variant,,ENST00000599687,;SNRNP70,upstream_gene_variant,,ENST00000544278,;	T	ENSG00000104852	ENST00000598441	Transcript	synonymous_variant	698	474	158	H	caC/caT	rs373191644	.	.	1	SNRNP70	HGNC	11150	protein_coding	YES	CCDS12756.1	ENSP00000472998	RU17_HUMAN	Q9UFS1_HUMAN,M0QX04_HUMAN	UPI00001352E4	.	.	.	7/10	.	PROSITE_profiles:PS50102,hmmpanther:PTHR13952:SF5,hmmpanther:PTHR13952,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	T:0.0005	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCACTGTGA	byFrequency|byCluster	5	ESCA
CCDC106	0	.	GRCh37	19	56162797	56162797	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462G>T	p.Gln154His	p.Q154H	ENST00000586790	4/5	40	24	16	43	43	0	CCDC106,missense_variant,p.Gln154His,ENST00000591578,;CCDC106,missense_variant,p.Gln154His,ENST00000588740,;CCDC106,missense_variant,p.Gln119His,ENST00000591241,;CCDC106,missense_variant,p.Gln154His,ENST00000592996,;CCDC106,missense_variant,p.Gln154His,ENST00000586790,;CCDC106,missense_variant,p.Gln154His,ENST00000308964,;U2AF2,upstream_gene_variant,,ENST00000308924,;U2AF2,upstream_gene_variant,,ENST00000450554,;CCDC106,downstream_gene_variant,,ENST00000593069,;CCDC106,downstream_gene_variant,,ENST00000587213,;CCDC106,downstream_gene_variant,,ENST00000586864,;U2AF2,upstream_gene_variant,,ENST00000587196,;U2AF2,upstream_gene_variant,,ENST00000588850,;	T	ENSG00000173581	ENST00000586790	Transcript	missense_variant	1366	462	154	Q/H	caG/caT	.	.	.	1	CCDC106	HGNC	30181	protein_coding	YES	CCDS33118.1	ENSP00000465757	CC106_HUMAN	K7ES29_HUMAN,K7ER22_HUMAN,K7EMP7_HUMAN	UPI0000072074	.	tolerated(0.07)	benign(0.444)	4/5	.	hmmpanther:PTHR16477,hmmpanther:PTHR16477:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCAGAAGCA	.	5	ESCA
NLRP4	0	.	GRCh37	19	56370074	56370074	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315C>G	p.Leu439Val	p.L439V	ENST00000301295	3/10	65	42	22	50	50	0	NLRP4,missense_variant,p.Leu5Val,ENST00000589437,;NLRP4,missense_variant,p.Leu439Val,ENST00000301295,;NLRP4,missense_variant,p.Leu439Val,ENST00000346986,;NLRP4,missense_variant,p.Leu364Val,ENST00000587891,;NLRP4,downstream_gene_variant,,ENST00000587464,;	G	ENSG00000160505	ENST00000301295	Transcript	missense_variant	1737	1315	439	L/V	Ctg/Gtg	.	.	.	1	NLRP4	HGNC	22943	protein_coding	YES	CCDS12936.1	ENSP00000301295	NALP4_HUMAN	K7ES09_HUMAN	UPI000013E6FD	.	tolerated(0.3)	benign(0.097)	3/10	.	hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G442R|c.1324G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTCTGAAG	.	5	ESCA
AURKC	0	.	GRCh37	19	57744878	57744878	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486G>A	p.%3D	p.V162V	ENST00000302804	5/7	53	34	19	51	51	0	AURKC,synonymous_variant,p.%3D,ENST00000598785,;AURKC,synonymous_variant,p.%3D,ENST00000302804,;AURKC,synonymous_variant,p.%3D,ENST00000599062,;AURKC,synonymous_variant,p.%3D,ENST00000448930,;AURKC,synonymous_variant,p.%3D,ENST00000415300,;AURKC,intron_variant,,ENST00000594599,;AURKC,3_prime_UTR_variant,,ENST00000596375,;AURKC,3_prime_UTR_variant,,ENST00000601799,;	A	ENSG00000105146	ENST00000302804	Transcript	synonymous_variant	672	486	162	V	gtG/gtA	.	.	.	1	AURKC	HGNC	11391	protein_coding	YES	CCDS33128.1	ENSP00000302898	AURKC_HUMAN	.	UPI000013610A	.	.	.	5/7	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24350,hmmpanther:PTHR24350:SF3,PROSITE_patterns:PS00108,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTGATTCA	.	5	ESCA
ZNF561	0	.	GRCh37	19	9720818	9720818	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*58C>G	.	.	ENST00000302851	6/6	41	26	14	35	35	0	ZNF561,3_prime_UTR_variant,,ENST00000326044,;ZNF561,3_prime_UTR_variant,,ENST00000424629,;ZNF561,3_prime_UTR_variant,,ENST00000302851,;ZNF561,3_prime_UTR_variant,,ENST00000354661,;ZNF561,downstream_gene_variant,,ENST00000444611,;ZNF561,downstream_gene_variant,,ENST00000465974,;ZNF561,downstream_gene_variant,,ENST00000495503,;ZNF561,intron_variant,,ENST00000444802,;ZNF561,downstream_gene_variant,,ENST00000483768,;ZNF561,downstream_gene_variant,,ENST00000494276,;ZNF561,downstream_gene_variant,,ENST00000457965,;ZNF561,downstream_gene_variant,,ENST00000443819,;	C	ENSG00000171469	ENST00000302851	Transcript	3_prime_UTR_variant	1883	.	.	.	.	.	.	.	-1	ZNF561	HGNC	28684	protein_coding	YES	CCDS12216.2	ENSP00000303915	ZN561_HUMAN	F8WAU2_HUMAN,C9JQP3_HUMAN,C9J7U2_HUMAN,B4E2Q8_HUMAN,A8KAD9_HUMAN	UPI000037525C	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTAGGACAA	.	5	ESCA
COL11A1	0	.	GRCh37	1	103352542	103352542	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4679G>T	p.Gly1560Val	p.G1560V	ENST00000370096	63/67	79	46	32	76	76	0	COL11A1,missense_variant,p.Gly1444Val,ENST00000512756,;COL11A1,missense_variant,p.Gly1521Val,ENST00000353414,;COL11A1,missense_variant,p.Gly1560Val,ENST00000370096,;COL11A1,missense_variant,p.Gly1572Val,ENST00000358392,;	A	ENSG00000060718	ENST00000370096	Transcript	missense_variant	4992	4679	1560	G/V	gGc/gTc	.	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	unknown(0)	63/67	.	hmmpanther:PTHR24023:SF42,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATGCCTTCA	.	5	ESCA
STXBP3	0	.	GRCh37	1	109351459	109351459	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1739A>G	p.Asn580Ser	p.N580S	ENST00000370008	19/19	96	62	34	82	82	0	STXBP3,missense_variant,p.Asn580Ser,ENST00000370008,;STXBP3,downstream_gene_variant,,ENST00000472099,;	G	ENSG00000116266	ENST00000370008	Transcript	missense_variant	1789	1739	580	N/S	aAt/aGt	.	.	.	1	STXBP3	HGNC	11446	protein_coding	YES	CCDS790.1	ENSP00000359025	STXB3_HUMAN	.	UPI000000DC53	.	tolerated(0.89)	benign(0)	19/19	.	Superfamily_domains:SSF56815,PIRSF_domain:PIRSF005715,Gene3D:3.40.50.1910,hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTGAATAAAC	.	3	ESCA
STRIP1	0	.	GRCh37	1	110589335	110589335	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1450C>T	p.Gln484Ter	p.Q484*	ENST00000369795	13/21	125	76	49	89	89	0	STRIP1,stop_gained,p.Gln484Ter,ENST00000369795,;STRIP1,stop_gained,p.Gln389Ter,ENST00000369796,;STRIP1,upstream_gene_variant,,ENST00000461054,;STRIP1,3_prime_UTR_variant,,ENST00000485775,;STRIP1,non_coding_transcript_exon_variant,,ENST00000535003,;STRIP1,non_coding_transcript_exon_variant,,ENST00000473429,;STRIP1,downstream_gene_variant,,ENST00000539541,;	T	ENSG00000143093	ENST00000369795	Transcript	stop_gained	1472	1450	484	Q/*	Cag/Tag	.	.	.	1	STRIP1	HGNC	25916	protein_coding	YES	CCDS30798.1	ENSP00000358810	STRP1_HUMAN	.	UPI0000160E65	.	.	.	13/21	.	hmmpanther:PTHR13239,hmmpanther:PTHR13239:SF5,Pfam_domain:PF11882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCACAGATG	.	5	ESCA
PRAMEF6	0	.	GRCh37	1	13001128	13001128	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555G>A	p.%3D	p.L185L	ENST00000376189	3/4	54	39	15	90	90	0	PRAMEF6,synonymous_variant,p.%3D,ENST00000415464,;PRAMEF6,synonymous_variant,p.%3D,ENST00000355096,;PRAMEF6,synonymous_variant,p.%3D,ENST00000376189,;PRAMEF6,intron_variant,,ENST00000376192,;	T	ENSG00000232423	ENST00000376189	Transcript	synonymous_variant	655	555	185	L	ctG/ctA	.	.	.	-1	PRAMEF6	HGNC	30583	protein_coding	YES	CCDS30594.1	ENSP00000365360	PRAM6_HUMAN	.	UPI0000418E57	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ATTTTCAGCTT	.	2	ESCA
OR10Z1	0	.	GRCh37	1	158576363	158576363	+	Silent	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.135T>A	p.%3D	p.I45I	ENST00000361284	1/1	45	31	14	42	42	0	OR10Z1,synonymous_variant,p.%3D,ENST00000361284,;SPTA1,downstream_gene_variant,,ENST00000368147,;SPTA1,downstream_gene_variant,,ENST00000485680,;	A	ENSG00000198967	ENST00000361284	Transcript	synonymous_variant	135	135	45	I	atT/atA	.	.	.	1	OR10Z1	HGNC	14996	protein_coding	YES	CCDS30901.1	ENSP00000354707	O10Z1_HUMAN	.	UPI000004CA23	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATTATCAT	.	5	ESCA
DARC	0	.	GRCh37	1	159176230	159176230	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1007G>A	p.Ser336Asn	p.S336N	ENST00000368121	1/1	75	57	18	45	45	0	DARC,missense_variant,p.Ser334Asn,ENST00000368122,;DARC,missense_variant,p.Ser334Asn,ENST00000537147,;DARC,missense_variant,p.Ser336Asn,ENST00000368121,;CADM3,downstream_gene_variant,,ENST00000368124,;CADM3,downstream_gene_variant,,ENST00000368125,;DARC,downstream_gene_variant,,ENST00000435307,;CTA-134P22.2,intron_variant,,ENST00000609696,;CTA-134P22.2,upstream_gene_variant,,ENST00000415675,;	A	ENSG00000213088	ENST00000368121	Transcript	missense_variant	1030	1007	336	S/N	aGc/aAc	.	.	.	1	DARC	HGNC	4035	protein_coding	YES	CCDS44252.1	ENSP00000357103	ACKR1_HUMAN	Q5Y7A1_HUMAN,Q5JY94_HUMAN,Q4VBN9_HUMAN	UPI000013E1B0	.	tolerated(0.06)	benign(0.15)	1/1	.	hmmpanther:PTHR14181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAAGCAAAT	.	5	ESCA
DARC	0	.	GRCh37	1	159176231	159176231	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1008C>A	p.Ser336Arg	p.S336R	ENST00000368121	1/1	73	55	18	45	45	0	DARC,missense_variant,p.Ser334Arg,ENST00000368122,;DARC,missense_variant,p.Ser334Arg,ENST00000537147,;DARC,missense_variant,p.Ser336Arg,ENST00000368121,;CADM3,downstream_gene_variant,,ENST00000368124,;CADM3,downstream_gene_variant,,ENST00000368125,;DARC,downstream_gene_variant,,ENST00000435307,;CTA-134P22.2,intron_variant,,ENST00000609696,;CTA-134P22.2,upstream_gene_variant,,ENST00000415675,;	A	ENSG00000213088	ENST00000368121	Transcript	missense_variant	1031	1008	336	S/R	agC/agA	.	.	.	1	DARC	HGNC	4035	protein_coding	YES	CCDS44252.1	ENSP00000357103	ACKR1_HUMAN	Q5Y7A1_HUMAN,Q5JY94_HUMAN,Q4VBN9_HUMAN	UPI000013E1B0	.	tolerated(0.08)	benign(0.007)	1/1	.	hmmpanther:PTHR14181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGCAAATC	.	5	ESCA
TNN	0	.	GRCh37	1	175096207	175096207	+	Missense_Mutation	SNP	G	G	C	rs762282016	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3031G>C	p.Asp1011His	p.D1011H	ENST00000239462	13/19	78	52	26	84	84	0	TNN,missense_variant,p.Asp1011His,ENST00000239462,;	C	ENSG00000120332	ENST00000239462	Transcript	missense_variant	3144	3031	1011	D/H	Gat/Cat	rs762282016	.	.	1	TNN	HGNC	22942	protein_coding	YES	CCDS30943.1	ENSP00000239462	TENN_HUMAN	.	UPI00001D7DA9	.	deleterious(0)	probably_damaging(0.976)	13/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF167,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCCCAGATGGC	.	4	ESCA
RASSF5	0	.	GRCh37	1	206760161	206760162	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109dupA	p.Asp370GlufsTer7	p.D370Efs*7	ENST00000355294	6/6	55	43	12	33	33	0	RASSF5,frameshift_variant,p.Cys332MetfsTer12,ENST00000367117,;RASSF5,frameshift_variant,p.Asp370GlufsTer7,ENST00000355294,;RASSF5,frameshift_variant,p.Asp217GlufsTer7,ENST00000304534,;EIF2D,downstream_gene_variant,,ENST00000367114,;EIF2D,downstream_gene_variant,,ENST00000271764,;RASSF5,non_coding_transcript_exon_variant,,ENST00000491368,;RASSF5,non_coding_transcript_exon_variant,,ENST00000481486,;EIF2D,intron_variant,,ENST00000472709,;	A	ENSG00000136653	ENST00000355294	Transcript	frameshift_variant	1165-1166	1108-1109	370	D/EX	gat/gAat	.	.	.	1	RASSF5	HGNC	17609	protein_coding	YES	CCDS30998.1	ENSP00000347443	RASF5_HUMAN	.	UPI0000072CF5	.	.	.	6/6	.	PROSITE_profiles:PS50951,hmmpanther:PTHR22738,hmmpanther:PTHR22738:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTGGGATGCC	.	3	ESCA
RASSF5	0	.	GRCh37	1	206761653	206761653	+	3'Flank	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000355294	.	9	5	4	11	11	0	RASSF5,3_prime_UTR_variant,,ENST00000304534,;EIF2D,downstream_gene_variant,,ENST00000367114,;RASSF5,downstream_gene_variant,,ENST00000367117,;RASSF5,downstream_gene_variant,,ENST00000355294,;EIF2D,downstream_gene_variant,,ENST00000271764,;RASSF5,non_coding_transcript_exon_variant,,ENST00000491368,;RASSF5,non_coding_transcript_exon_variant,,ENST00000481486,;EIF2D,intron_variant,,ENST00000472709,;	A	ENSG00000136653	ENST00000355294	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	609	1	RASSF5	HGNC	17609	protein_coding	YES	CCDS30998.1	ENSP00000347443	RASF5_HUMAN	.	UPI0000072CF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGATACCAG	.	2	ESCA
IL10	0	.	GRCh37	1	206943229	206943229	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389T>C	p.Leu130Pro	p.L130P	ENST00000423557	4/5	57	23	33	41	41	0	IL10,missense_variant,p.Leu130Pro,ENST00000423557,;IL10,non_coding_transcript_exon_variant,,ENST00000471071,;IL10,non_coding_transcript_exon_variant,,ENST00000367099,;	G	ENSG00000136634	ENST00000423557	Transcript	missense_variant	448	389	130	L/P	cTt/cCt	.	.	.	-1	IL10	HGNC	5962	protein_coding	YES	CCDS1467.1	ENSP00000412237	IL10_HUMAN	Q71UZ1_HUMAN,Q6LBF4_HUMAN,Q6FGW4_HUMAN	UPI0000034E50	.	deleterious(0)	probably_damaging(1)	4/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11585,hmmpanther:PTHR11585:SF1,Pfam_domain:PF00726,Gene3D:1.20.1250.10,SMART_domains:SM00188,Superfamily_domains:SSF47266,Prints_domain:PR01294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGAAGAAAT	.	5	ESCA
USH2A	0	.	GRCh37	1	216073502	216073502	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7509C>T	p.%3D	p.Y2503Y	ENST00000307340	40/72	45	26	19	57	57	0	USH2A,synonymous_variant,p.%3D,ENST00000366943,;USH2A,synonymous_variant,p.%3D,ENST00000307340,;RP5-1111A8.3,intron_variant,,ENST00000414995,;	A	ENSG00000042781	ENST00000307340	Transcript	synonymous_variant	7896	7509	2503	Y	taC/taT	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	.	40/72	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGTGTACGG	.	5	ESCA
KDM1A	0	.	GRCh37	1	23408804	23408804	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2390A>G	p.Tyr797Cys	p.Y797C	ENST00000400181	20/21	55	34	20	50	50	0	KDM1A,missense_variant,p.Tyr797Cys,ENST00000542151,;KDM1A,missense_variant,p.Tyr773Cys,ENST00000356634,;KDM1A,missense_variant,p.Tyr225Cys,ENST00000494920,;KDM1A,missense_variant,p.Tyr797Cys,ENST00000400181,;LUZP1,downstream_gene_variant,,ENST00000374623,;KDM1A,downstream_gene_variant,,ENST00000465864,;LUZP1,downstream_gene_variant,,ENST00000418342,;LUZP1,downstream_gene_variant,,ENST00000302291,;RP1-184J9.2,intron_variant,,ENST00000427154,;KDM1A,non_coding_transcript_exon_variant,,ENST00000602503,;	G	ENSG00000004487	ENST00000400181	Transcript	missense_variant	2494	2390	797	Y/C	tAt/tGt	.	.	.	1	KDM1A	HGNC	29079	protein_coding	YES	CCDS53278.1	ENSP00000383042	KDM1A_HUMAN	.	UPI0000403137	.	deleterious(0)	probably_damaging(1)	20/21	.	hmmpanther:PTHR10742:SF245,hmmpanther:PTHR10742,Pfam_domain:PF01593,PIRSF_domain:PIRSF038051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACTATGATT	.	5	ESCA
ZNF436	0	.	GRCh37	1	23686276	23686276	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2186A>G	.	.	ENST00000314011	4/4	108	65	42	81	81	0	ZNF436,3_prime_UTR_variant,,ENST00000314011,;ZNF436,downstream_gene_variant,,ENST00000374608,;	C	ENSG00000125945	ENST00000314011	Transcript	3_prime_UTR_variant	3736	.	.	.	.	.	.	.	-1	ZNF436	HGNC	20814	protein_coding	YES	CCDS233.1	ENSP00000313582	ZN436_HUMAN	Q15921_HUMAN	UPI0000001669	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTATGGAGA	.	5	ESCA
ACTN2	0	.	GRCh37	1	236889280	236889280	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496G>T	p.Ala166Ser	p.A166S	ENST00000366578	5/21	51	33	17	42	42	0	ACTN2,missense_variant,p.Ala166Ser,ENST00000542672,;ACTN2,missense_variant,p.Ala166Ser,ENST00000366578,;ACTN2,non_coding_transcript_exon_variant,,ENST00000492634,;	T	ENSG00000077522	ENST00000366578	Transcript	missense_variant	662	496	166	A/S	Gct/Tct	.	.	.	1	ACTN2	HGNC	164	protein_coding	YES	CCDS1613.1	ENSP00000355537	ACTN2_HUMAN	B7Z4P8_HUMAN	UPI0000125088	.	deleterious(0.02)	probably_damaging(0.999)	5/21	.	Superfamily_domains:SSF47576,SMART_domains:SM00033,Gene3D:1.10.418.10,Pfam_domain:PF00307,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,PROSITE_profiles:PS50021	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTGCTCCT	.	5	ESCA
ZBTB18	0	.	GRCh37	1	244219732	244219732	+	3'UTR	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1060T>A	.	.	ENST00000358704	2/2	92	63	29	71	71	0	ZBTB18,3_prime_UTR_variant,,ENST00000358704,;	A	ENSG00000179456	ENST00000358704	Transcript	3_prime_UTR_variant	2805	.	.	.	.	.	.	.	1	ZBTB18	HGNC	13030	protein_coding	YES	CCDS1622.1	ENSP00000351539	ZBT18_HUMAN	.	UPI000034ECE2	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATATAAATG	.	5	ESCA
ARID1A	0	.	GRCh37	1	27088764	27088764	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2373C>A	p.Asn791Lys	p.N791K	ENST00000324856	7/20	112	65	47	69	69	0	ARID1A,missense_variant,p.Asn791Lys,ENST00000457599,;ARID1A,missense_variant,p.Asn408Lys,ENST00000374152,;ARID1A,missense_variant,p.Asn791Lys,ENST00000324856,;RN7SL501P,upstream_gene_variant,,ENST00000578818,;ARID1A,upstream_gene_variant,,ENST00000430291,;	A	ENSG00000117713	ENST00000324856	Transcript	missense_variant	2744	2373	791	N/K	aaC/aaA	.	.	.	1	ARID1A	HGNC	11110	protein_coding	YES	CCDS285.1	ENSP00000320485	ARI1A_HUMAN	Q96T01_HUMAN,Q96SY8_HUMAN,Q96SM7_HUMAN,E9PQW6_HUMAN,C1KEN7_HUMAN,A4FU79_HUMAN	UPI0000167B91	.	.	unknown(0)	7/20	.	hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Q790*|c.2368C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAACTCCAT	.	5	ESCA
GPATCH3	0	.	GRCh37	1	27216997	27216997	+	3'UTR	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*504A>T	.	.	ENST00000361720	7/7	11	6	5	13	13	0	GPATCH3,3_prime_UTR_variant,,ENST00000361720,;GPATCH3,3_prime_UTR_variant,,ENST00000445019,;GPN2,upstream_gene_variant,,ENST00000431781,;GPATCH3,downstream_gene_variant,,ENST00000450844,;GPN2,upstream_gene_variant,,ENST00000374135,;GPN2,upstream_gene_variant,,ENST00000374133,;GPN2,upstream_gene_variant,,ENST00000461282,;GPN2,upstream_gene_variant,,ENST00000477418,;	A	ENSG00000198746	ENST00000361720	Transcript	3_prime_UTR_variant	2106	.	.	.	.	.	.	.	-1	GPATCH3	HGNC	25720	protein_coding	YES	CCDS290.1	ENSP00000354645	GPTC3_HUMAN	Q5JYG5_HUMAN,B4E015_HUMAN	UPI000003E830	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCTTTATTCT	.	3	ESCA
MACF1	0	.	GRCh37	1	39823313	39823313	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5505G>A	p.%3D	p.E1835E	ENST00000545844	40/94	71	45	25	62	62	0	MACF1,synonymous_variant,p.%3D,ENST00000372925,;MACF1,synonymous_variant,p.%3D,ENST00000361689,;MACF1,synonymous_variant,p.%3D,ENST00000289893,;MACF1,synonymous_variant,p.%3D,ENST00000564288,;MACF1,synonymous_variant,p.%3D,ENST00000530262,;MACF1,synonymous_variant,p.%3D,ENST00000539005,;MACF1,synonymous_variant,p.%3D,ENST00000372915,;MACF1,synonymous_variant,p.%3D,ENST00000317713,;MACF1,synonymous_variant,p.%3D,ENST00000567887,;MACF1,synonymous_variant,p.%3D,ENST00000545844,;MACF1,non_coding_transcript_exon_variant,,ENST00000476350,;	A	ENSG00000127603	ENST00000545844	Transcript	synonymous_variant	5613	5505	1835	E	gaG/gaA	.	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	.	40/94	.	Superfamily_domains:SSF46966,SMART_domains:SM00150,Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915:SF37,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGAGAAAGA	.	5	ESCA
LPHN2	0	.	GRCh37	1	82421722	82421722	+	Silent	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1944C>G	p.%3D	p.V648V	ENST00000319517	9/20	73	44	29	85	85	0	LPHN2,synonymous_variant,p.%3D,ENST00000370730,;LPHN2,synonymous_variant,p.%3D,ENST00000335786,;LPHN2,synonymous_variant,p.%3D,ENST00000370713,;LPHN2,synonymous_variant,p.%3D,ENST00000370717,;LPHN2,synonymous_variant,p.%3D,ENST00000370727,;LPHN2,synonymous_variant,p.%3D,ENST00000370725,;LPHN2,synonymous_variant,p.%3D,ENST00000319517,;LPHN2,synonymous_variant,p.%3D,ENST00000271029,;LPHN2,synonymous_variant,p.%3D,ENST00000370728,;LPHN2,synonymous_variant,p.%3D,ENST00000359929,;LPHN2,synonymous_variant,p.%3D,ENST00000370715,;LPHN2,synonymous_variant,p.%3D,ENST00000370723,;LPHN2,synonymous_variant,p.%3D,ENST00000370721,;LPHN2,synonymous_variant,p.%3D,ENST00000394879,;LPHN2,synonymous_variant,p.%3D,ENST00000449420,;LPHN2,non_coding_transcript_exon_variant,,ENST00000468283,;LPHN2,intron_variant,,ENST00000469377,;	G	ENSG00000117114	ENST00000319517	Transcript	synonymous_variant	2160	1944	648	V	gtC/gtG	.	.	.	1	LPHN2	HGNC	18582	protein_coding	YES	CCDS689.1	ENSP00000322270	LPHN2_HUMAN	.	UPI000005046B	.	.	.	9/20	.	hmmpanther:PTHR12011:SF61,hmmpanther:PTHR12011,Pfam_domain:PF12003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGTCTCAAT	.	5	ESCA
ZNF217	0	.	GRCh37	20	52184614	52184614	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1213A>G	.	.	ENST00000371471	6/6	30	11	19	27	27	0	ZNF217,3_prime_UTR_variant,,ENST00000302342,;ZNF217,3_prime_UTR_variant,,ENST00000371471,;ZNF217,downstream_gene_variant,,ENST00000437222,;RP4-724E16.2,intron_variant,,ENST00000424252,;	C	ENSG00000171940	ENST00000371471	Transcript	3_prime_UTR_variant	4786	.	.	.	.	.	.	.	-1	ZNF217	HGNC	13009	protein_coding	YES	CCDS13443.1	ENSP00000360526	ZN217_HUMAN	A2A326_HUMAN	UPI000013C323	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAATGTTAC	.	5	ESCA
ZBP1	0	.	GRCh37	20	56179817	56179817	+	Missense_Mutation	SNP	G	G	A	rs762891234	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1102C>T	p.Pro368Ser	p.P368S	ENST00000371173	8/8	113	57	55	54	54	0	ZBP1,missense_variant,p.Pro345Ser,ENST00000340462,;ZBP1,missense_variant,p.Pro293Ser,ENST00000395822,;ZBP1,missense_variant,p.Pro368Ser,ENST00000371173,;ZBP1,downstream_gene_variant,,ENST00000343535,;ZBP1,downstream_gene_variant,,ENST00000453793,;RP4-718J7.4,upstream_gene_variant,,ENST00000424850,;ZBP1,non_coding_transcript_exon_variant,,ENST00000461547,;	A	ENSG00000124256	ENST00000371173	Transcript	missense_variant	1280	1102	368	P/S	Ccc/Tcc	rs762891234	.	.	-1	ZBP1	HGNC	16176	protein_coding	YES	CCDS13461.1	ENSP00000360215	ZBP1_HUMAN	.	UPI000013CB5B	.	tolerated(0.47)	benign(0.007)	8/8	.	hmmpanther:PTHR14966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGGGACGAC	byFrequency	5	ESCA
GRIK1	0	.	GRCh37	21	30909427	30909427	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*124G>A	.	.	ENST00000327783	18/18	13	7	6	18	18	0	GRIK1,3_prime_UTR_variant,,ENST00000327783,;GRIK1,3_prime_UTR_variant,,ENST00000399914,;GRIK1,3_prime_UTR_variant,,ENST00000399913,;GRIK1,3_prime_UTR_variant,,ENST00000389125,;BACH1,intron_variant,,ENST00000468059,;BACH1,intron_variant,,ENST00000422809,;GRIK1,downstream_gene_variant,,ENST00000389124,;GRIK1,downstream_gene_variant,,ENST00000535441,;	T	ENSG00000171189	ENST00000327783	Transcript	3_prime_UTR_variant	3006	.	.	.	.	.	.	.	-1	GRIK1	HGNC	4579	protein_coding	.	.	ENSP00000327687	.	Q9UNN1_HUMAN,Q71UA3_HUMAN,E7ENK3_HUMAN	UPI0000E5A39C	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TATATCTGTAT	.	3	ESCA
C2CD2	0	.	GRCh37	21	43305835	43305835	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3398G>A	.	.	ENST00000380486	14/14	8	4	4	16	16	0	C2CD2,3_prime_UTR_variant,,ENST00000449165,;C2CD2,3_prime_UTR_variant,,ENST00000329623,;C2CD2,3_prime_UTR_variant,,ENST00000380486,;SNORA3,downstream_gene_variant,,ENST00000515969,;C2CD2,downstream_gene_variant,,ENST00000482186,;C2CD2,downstream_gene_variant,,ENST00000482084,;	T	ENSG00000157617	ENST00000380486	Transcript	3_prime_UTR_variant	5731	.	.	.	.	.	.	.	-1	C2CD2	HGNC	1266	protein_coding	YES	CCDS42933.1	ENSP00000369853	CU025_HUMAN	.	UPI0000206BBE	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCGGTGG	.	2	ESCA
COL18A1	0	.	GRCh37	21	46897715	46897715	+	Missense_Mutation	SNP	C	C	T	rs369114408	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597C>T	p.Arg533Trp	p.R533W	ENST00000355480	7/41	90	49	40	99	99	0	COL18A1,missense_variant,p.Arg768Trp,ENST00000359759,;COL18A1,missense_variant,p.Arg533Trp,ENST00000355480,;COL18A1,missense_variant,p.Arg353Trp,ENST00000400337,;	T	ENSG00000182871	ENST00000355480	Transcript	missense_variant	1639	1597	533	R/W	Cgg/Tgg	rs369114408	.	.	1	COL18A1	HGNC	2195	protein_coding	YES	CCDS42972.1	ENSP00000347665	COIA1_HUMAN	D3DSM5_HUMAN	UPI000016A19D	.	.	unknown(0)	7/41	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF390	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0011	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCCGGGCA	byCluster|by1000G	5	ESCA
AC002472.1	0	.	GRCh37	22	21363916	21363916	+	5'Flank	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000547793	.	28	15	13	20	20	0	AC002472.1,upstream_gene_variant,,ENST00000547793,;THAP7-AS1,non_coding_transcript_exon_variant,,ENST00000452284,;THAP7-AS1,non_coding_transcript_exon_variant,,ENST00000436079,;TUBA3FP,intron_variant,,ENST00000292748,;TUBA3FP,intron_variant,,ENST00000422086,;P2RX6,upstream_gene_variant,,ENST00000591411,;TUBA3FP,upstream_gene_variant,,ENST00000442739,;	G	ENSG00000269103	ENST00000547793	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3180	-1	AC002472.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000446823	.	H0YHC8_HUMAN	UPI00015DF7A3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCACAAATCA	.	5	ESCA
CBX7	0	.	GRCh37	22	39527231	39527231	+	3'UTR	SNP	T	T	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2665A>T	.	.	ENST00000216133	6/6	103	69	34	76	76	0	CBX7,3_prime_UTR_variant,,ENST00000216133,;CBX7,downstream_gene_variant,,ENST00000401405,;CBX7,downstream_gene_variant,,ENST00000434260,;CBX7,intron_variant,,ENST00000475962,;CBX7,downstream_gene_variant,,ENST00000490741,;	A	ENSG00000100307	ENST00000216133	Transcript	3_prime_UTR_variant	3627	.	.	.	.	.	.	.	-1	CBX7	HGNC	1557	protein_coding	YES	CCDS13986.1	ENSP00000216133	CBX7_HUMAN	.	UPI00001271FE	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCTCCGCA	.	5	ESCA
CCNT2	0	.	GRCh37	2	135714570	135714570	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2352A>T	.	.	ENST00000264157	9/9	36	14	21	31	31	0	CCNT2,3_prime_UTR_variant,,ENST00000264157,;CCNT2,3_prime_UTR_variant,,ENST00000295238,;CCNT2,downstream_gene_variant,,ENST00000438691,;CCNT2,downstream_gene_variant,,ENST00000446247,;CCNT2,downstream_gene_variant,,ENST00000452521,;CCNT2,downstream_gene_variant,,ENST00000537343,;CCNT2,downstream_gene_variant,,ENST00000452839,;CCNT2,downstream_gene_variant,,ENST00000419781,;	T	ENSG00000082258	ENST00000264157	Transcript	3_prime_UTR_variant	4575	.	.	.	.	.	.	.	1	CCNT2	HGNC	1600	protein_coding	YES	CCDS2174.1	ENSP00000264157	CCNT2_HUMAN	.	UPI000013E228	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGCAGCCAG	.	5	ESCA
ZNF804A	0	.	GRCh37	2	185803054	185803054	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2931G>C	p.Glu977Asp	p.E977D	ENST00000302277	4/4	45	16	28	49	49	0	ZNF804A,missense_variant,p.Glu977Asp,ENST00000302277,;	C	ENSG00000170396	ENST00000302277	Transcript	missense_variant	3525	2931	977	E/D	gaG/gaC	.	.	.	1	ZNF804A	HGNC	21711	protein_coding	YES	CCDS2291.1	ENSP00000303252	Z804A_HUMAN	.	UPI00001B4B18	.	tolerated(0.05)	probably_damaging(0.935)	4/4	.	hmmpanther:PTHR17614:SF13,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGAGGCCCT	.	5	ESCA
BMPR2	0	.	GRCh37	2	203430435	203430440	+	3'UTR	DEL	CTACAT	CTACAT	-	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	CTACAT	CTACAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5766_*5771delCTACAT	.	.	ENST00000374580	13/13	29	4	25	31	31	0	BMPR2,3_prime_UTR_variant,,ENST00000374574,;BMPR2,3_prime_UTR_variant,,ENST00000374580,;	-	ENSG00000204217	ENST00000374580	Transcript	3_prime_UTR_variant	9422-9427	.	.	.	.	.	.	.	1	BMPR2	HGNC	1078	protein_coding	YES	CCDS33361.1	ENSP00000363708	BMPR2_HUMAN	.	UPI0000126A3B	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAAACCCTACATTAATC	.	3	ESCA
NYAP2	0	.	GRCh37	2	226447490	226447490	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357A>G	p.Arg453Gly	p.R453G	ENST00000272907	4/6	70	65	4	67	67	0	NYAP2,missense_variant,p.Arg453Gly,ENST00000272907,;NYAP2,intron_variant,,ENST00000409269,;	G	ENSG00000144460	ENST00000272907	Transcript	missense_variant	1770	1357	453	R/G	Agg/Ggg	COSM1255724	.	.	1	NYAP2	HGNC	29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	NYAP2_HUMAN	.	UPI00001C1DB6	.	deleterious(0)	probably_damaging(0.996)	4/6	.	hmmpanther:PTHR22633	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAAAAGGCCT	.	2	ESCA
KIF1A	0	.	GRCh37	2	241679744	241679744	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3787C>A	p.Pro1263Thr	p.P1263T	ENST00000498729	36/50	89	23	66	76	76	0	KIF1A,missense_variant,p.Pro1263Thr,ENST00000498729,;KIF1A,missense_variant,p.Pro1162Thr,ENST00000320389,;KIF1A,missense_variant,p.Pro1263Thr,ENST00000404283,;KIF1A,missense_variant,p.Pro86Thr,ENST00000431776,;KIF1A,downstream_gene_variant,,ENST00000415042,;KIF1A,upstream_gene_variant,,ENST00000494452,;	T	ENSG00000130294	ENST00000498729	Transcript	missense_variant	4034	3787	1263	P/T	Cca/Aca	.	.	.	-1	KIF1A	HGNC	888	protein_coding	YES	CCDS58757.1	ENSP00000438388	KIF1A_HUMAN	G1UI30_HUMAN,C9JBH1_HUMAN	UPI0002065B81	.	deleterious(0.03)	probably_damaging(1)	36/50	.	hmmpanther:PTHR24115:SF361,hmmpanther:PTHR24115,Pfam_domain:PF12473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATGGCATGC	.	5	ESCA
CAD	0	.	GRCh37	2	27459359	27459359	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4282A>G	p.Ile1428Val	p.I1428V	ENST00000264705	26/44	30	18	11	24	24	0	CAD,missense_variant,p.Ile73Val,ENST00000458503,;CAD,missense_variant,p.Ile1428Val,ENST00000264705,;CAD,missense_variant,p.Ile1365Val,ENST00000403525,;CAD,upstream_gene_variant,,ENST00000456311,;CAD,upstream_gene_variant,,ENST00000491461,;CAD,downstream_gene_variant,,ENST00000464159,;CAD,downstream_gene_variant,,ENST00000479002,;CAD,downstream_gene_variant,,ENST00000475695,;CAD,downstream_gene_variant,,ENST00000491891,;CAD,upstream_gene_variant,,ENST00000487239,;	G	ENSG00000084774	ENST00000264705	Transcript	missense_variant	4444	4282	1428	I/V	Atc/Gtc	.	.	.	1	CAD	HGNC	1424	protein_coding	YES	CCDS1742.1	ENSP00000264705	PYR1_HUMAN	Q53SZ4_HUMAN,Q53SY7_HUMAN,G1UI39_HUMAN	UPI000013D558	.	deleterious(0.01)	benign(0.102)	26/44	.	hmmpanther:PTHR11405:SF5,hmmpanther:PTHR11405,Gene3D:3.40.50.1380,TIGRFAM_domain:TIGR01369,SMART_domains:SM00851,Superfamily_domains:SSF52335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATCATCGAT	.	5	ESCA
RNASEH1	0	.	GRCh37	2	3593197	3593197	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*178A>G	.	.	ENST00000315212	8/8	23	4	19	12	12	0	RNASEH1,3_prime_UTR_variant,,ENST00000315212,;RP13-512J5.1,intron_variant,,ENST00000438485,;RNASEH1,3_prime_UTR_variant,,ENST00000436842,;RNASEH1,downstream_gene_variant,,ENST00000464986,;RNASEH1,downstream_gene_variant,,ENST00000454734,;	C	ENSG00000171865	ENST00000315212	Transcript	3_prime_UTR_variant	1395	.	.	.	.	.	.	.	-1	RNASEH1	HGNC	18466	protein_coding	YES	CCDS1647.1	ENSP00000313350	RNH1_HUMAN	E5KN15_HUMAN,F8WD93_HUMAN,B3KUD4_HUMAN	UPI00001343BC	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATATACTTA	.	5	ESCA
EFEMP1	0	.	GRCh37	2	56097965	56097965	+	Missense_Mutation	SNP	T	T	A	rs567386311	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210A>T	p.Arg404Trp	p.R404W	ENST00000394555	10/11	42	29	13	39	39	0	EFEMP1,missense_variant,p.Arg404Trp,ENST00000355426,;EFEMP1,missense_variant,p.Arg404Trp,ENST00000394554,;EFEMP1,missense_variant,p.Arg266Trp,ENST00000424836,;EFEMP1,missense_variant,p.Arg404Trp,ENST00000394555,;	A	ENSG00000115380	ENST00000394555	Transcript	missense_variant	1646	1210	404	R/W	Agg/Tgg	rs567386311	.	.	-1	EFEMP1	HGNC	3218	protein_coding	YES	CCDS1857.1	ENSP00000378058	FBLN3_HUMAN	Q580Q6_HUMAN,Q53TA7_HUMAN,C9JUM4_HUMAN,C9JQX7_HUMAN,C9JPZ9_HUMAN,C9J8S9_HUMAN,C9J4J8_HUMAN,C9J4H7_HUMAN	UPI0000000C12	.	deleterious(0)	probably_damaging(0.999)	10/11	.	hmmpanther:PTHR24048:SF68,hmmpanther:PTHR24048	C:0.0002	C:0	C:0.0014	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCTATCAG	by1000G	5	ESCA
RHO	0	.	GRCh37	3	129247687	129247687	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111C>A	p.Phe37Leu	p.F37L	ENST00000296271	1/5	78	54	24	64	63	1	RHO,missense_variant,p.Phe37Leu,ENST00000296271,;	A	ENSG00000163914	ENST00000296271	Transcript	missense_variant	205	111	37	F/L	ttC/ttA	.	.	.	1	RHO	HGNC	10012	protein_coding	YES	CCDS3063.1	ENSP00000296271	OPSD_HUMAN	.	UPI0000046CE6	.	deleterious(0.02)	possibly_damaging(0.474)	1/5	.	hmmpanther:PTHR24240:SF15,hmmpanther:PTHR24240,Pfam_domain:PF10413,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCTCCAT	.	5	ESCA
SLITRK3	0	.	GRCh37	3	164907755	164907755	+	Missense_Mutation	SNP	C	C	A	rs763531605	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864G>T	p.Glu288Asp	p.E288D	ENST00000475390	2/2	125	63	62	74	74	0	SLITRK3,missense_variant,p.Glu288Asp,ENST00000475390,;SLITRK3,missense_variant,p.Glu288Asp,ENST00000241274,;SLITRK3,downstream_gene_variant,,ENST00000497724,;	A	ENSG00000121871	ENST00000475390	Transcript	missense_variant	1308	864	288	E/D	gaG/gaT	rs763531605	.	.	-1	SLITRK3	HGNC	23501	protein_coding	YES	CCDS3197.1	ENSP00000420091	SLIK3_HUMAN	C9K0R4_HUMAN	UPI000004F259	.	tolerated(0.24)	probably_damaging(0.984)	2/2	.	hmmpanther:PTHR24373:SF14,hmmpanther:PTHR24373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTACCTCAGA	byFrequency	5	ESCA
PDCD10	0	.	GRCh37	3	167401716	167401716	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*380A>G	.	.	ENST00000392750	9/9	109	95	13	45	45	0	PDCD10,3_prime_UTR_variant,,ENST00000497056,;PDCD10,3_prime_UTR_variant,,ENST00000392750,;PDCD10,3_prime_UTR_variant,,ENST00000473645,;PDCD10,downstream_gene_variant,,ENST00000479121,;PDCD10,downstream_gene_variant,,ENST00000492396,;PDCD10,downstream_gene_variant,,ENST00000492139,;PDCD10,downstream_gene_variant,,ENST00000461494,;PDCD10,downstream_gene_variant,,ENST00000470131,;PDCD10,downstream_gene_variant,,ENST00000462725,;PDCD10,downstream_gene_variant,,ENST00000487947,;PDCD10,downstream_gene_variant,,ENST00000471885,;PDCD10,downstream_gene_variant,,ENST00000475915,;	C	ENSG00000114209	ENST00000392750	Transcript	3_prime_UTR_variant	1437	.	.	.	.	.	.	.	-1	PDCD10	HGNC	8761	protein_coding	YES	CCDS3202.1	ENSP00000376506	PDC10_HUMAN	C9JSA3_HUMAN,C9JND6_HUMAN,C9J932_HUMAN,C9J6F3_HUMAN,C9J5C3_HUMAN,C9J363_HUMAN	UPI0000071E33	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTTATTGAAT	.	4	ESCA
FNDC3B	0	.	GRCh37	3	172116120	172116120	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*855C>A	.	.	ENST00000336824	26/26	76	69	7	28	28	0	FNDC3B,3_prime_UTR_variant,,ENST00000415807,;FNDC3B,3_prime_UTR_variant,,ENST00000336824,;FNDC3B,downstream_gene_variant,,ENST00000416957,;	A	ENSG00000075420	ENST00000336824	Transcript	3_prime_UTR_variant	4569	.	.	.	.	.	.	.	1	FNDC3B	HGNC	24670	protein_coding	YES	CCDS3217.1	ENSP00000338523	FND3B_HUMAN	.	UPI00001AE8B2	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGACCAGAAT	.	4	ESCA
NAALADL2	0	.	GRCh37	3	174814895	174814895	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359G>A	p.Cys120Tyr	p.C120Y	ENST00000454872	2/14	116	103	12	56	56	0	NAALADL2,missense_variant,p.Cys103Tyr,ENST00000434257,;NAALADL2,missense_variant,p.Cys120Tyr,ENST00000454872,;NAALADL2-AS3,intron_variant,,ENST00000453180,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000473253,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000485853,;NAALADL2-AS3,intron_variant,,ENST00000436929,;	A	ENSG00000177694	ENST00000454872	Transcript	missense_variant	487	359	120	C/Y	tGc/tAc	.	.	.	1	NAALADL2	HGNC	23219	protein_coding	YES	CCDS46960.1	ENSP00000404705	NADL2_HUMAN	C9JQ86_HUMAN	UPI0000161608	.	tolerated(0.97)	benign(0.023)	2/14	.	hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGCTGCAACT	.	4	ESCA
CCDC39	0	.	GRCh37	3	180334633	180334633	+	Nonsense_Mutation	SNP	A	A	C	rs377454931	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2387T>G	p.Leu796Ter	p.L796*	ENST00000442201	17/20	174	138	36	65	65	0	CCDC39,stop_gained,p.Leu796Ter,ENST00000442201,;CCDC39,3_prime_UTR_variant,,ENST00000273654,;TTC14,intron_variant,,ENST00000382584,;CCDC39,upstream_gene_variant,,ENST00000489868,;CCDC39,upstream_gene_variant,,ENST00000473854,;CCDC39,3_prime_UTR_variant,,ENST00000476379,;	C	ENSG00000145075	ENST00000442201	Transcript	stop_gained	2507	2387	796	L/*	tTa/tGa	rs377454931	.	.	-1	CCDC39	HGNC	25244	protein_coding	YES	CCDS46964.1	ENSP00000405708	CCD39_HUMAN	.	UPI00015D7298	.	.	.	17/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18962:SF0,hmmpanther:PTHR18962	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTAATTTT	byFrequency|byCluster	5	ESCA
LAMP3	0	.	GRCh37	3	182871996	182871996	+	Missense_Mutation	SNP	G	G	A	rs114675283	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.233C>T	p.Ala78Val	p.A78V	ENST00000265598	2/6	80	72	8	26	26	0	LAMP3,missense_variant,p.Ala78Val,ENST00000265598,;LAMP3,missense_variant,p.Ala54Val,ENST00000470251,;LAMP3,missense_variant,p.Ala78Val,ENST00000476015,;LAMP3,missense_variant,p.Ala54Val,ENST00000466939,;LAMP3,downstream_gene_variant,,ENST00000486686,;	A	ENSG00000078081	ENST00000265598	Transcript	missense_variant	489	233	78	A/V	gCg/gTg	rs114675283	.	.	-1	LAMP3	HGNC	14582	protein_coding	YES	CCDS3242.1	ENSP00000265598	LAMP3_HUMAN	E7ETP9_HUMAN,C9JYP5_HUMAN,C9JDI8_HUMAN	UPI000006DB7A	.	tolerated(0.16)	benign(0.148)	2/6	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51407	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCCGCTGTT	byFrequency|byCluster|by1000G	4	ESCA
KLHL6	0	.	GRCh37	3	183209898	183209898	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1683C>G	p.Tyr561Ter	p.Y561*	ENST00000341319	7/7	195	134	60	87	87	0	KLHL6,stop_gained,p.Tyr561Ter,ENST00000341319,;KLHL6,stop_gained,p.Tyr550Ter,ENST00000468734,;KLHL6,non_coding_transcript_exon_variant,,ENST00000489245,;	C	ENSG00000172578	ENST00000341319	Transcript	stop_gained	1719	1683	561	Y/*	taC/taG	.	.	.	-1	KLHL6	HGNC	18653	protein_coding	YES	CCDS3245.2	ENSP00000341342	KLHL6_HUMAN	.	UPI0000169CB9	.	.	.	7/7	.	hmmpanther:PTHR24411:SF4,hmmpanther:PTHR24411,Pfam_domain:PF01344,Gene3D:1zgkA00,SMART_domains:SM00612,PIRSF_domain:PIRSF037037,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGATGTAGAG	.	5	ESCA
YEATS2	0	.	GRCh37	3	183472028	183472029	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1266dupT	p.Gly423TrpfsTer22	p.G423Wfs*22	ENST00000305135	11/31	154	134	20	54	54	0	YEATS2,frameshift_variant,p.Gly423TrpfsTer22,ENST00000305135,;	T	ENSG00000163872	ENST00000305135	Transcript	frameshift_variant	1460-1461	1265-1266	422	H/HX	cat/caTt	.	.	.	1	YEATS2	HGNC	25489	protein_coding	YES	CCDS43175.1	ENSP00000306983	YETS2_HUMAN	.	UPI00001BB2B9	.	.	.	11/31	.	hmmpanther:PTHR23195,hmmpanther:PTHR23195:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCCCATGGCA	.	3	ESCA
ABCC5	0	.	GRCh37	3	183702524	183702524	+	Intron	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592-1729C>T	.	.	ENST00000334444	.	73	58	15	30	30	0	ABCC5,3_prime_UTR_variant,,ENST00000427120,;ABCC5,3_prime_UTR_variant,,ENST00000382494,;ABCC5,3_prime_UTR_variant,,ENST00000392579,;ABCC5,intron_variant,,ENST00000334444,;ABCC5,intron_variant,,ENST00000265586,;ABCC5,downstream_gene_variant,,ENST00000437341,;ABCC5,upstream_gene_variant,,ENST00000492216,;ABCC5,3_prime_UTR_variant,,ENST00000443376,;ABCC5,intron_variant,,ENST00000437205,;ABCC5,downstream_gene_variant,,ENST00000438979,;	A	ENSG00000114770	ENST00000334444	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ABCC5	HGNC	56	protein_coding	YES	CCDS43176.1	ENSP00000333926	MRP5_HUMAN	C9JZL5_HUMAN	UPI000004A33C	.	.	.	.	5/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAAGAAGAT	.	5	ESCA
KLHL40	0	.	GRCh37	3	42727547	42727547	+	Missense_Mutation	SNP	C	C	T	rs763489381	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437C>T	p.Ala146Val	p.A146V	ENST00000287777	1/6	31	16	15	29	29	0	KLHL40,missense_variant,p.Ala146Val,ENST00000287777,;	T	ENSG00000157119	ENST00000287777	Transcript	missense_variant	537	437	146	A/V	gCg/gTg	rs763489381	.	.	1	KLHL40	HGNC	30372	protein_coding	YES	CCDS2703.1	ENSP00000287777	KLH40_HUMAN	.	UPI000000D866	.	deleterious(0.01)	possibly_damaging(0.523)	1/6	.	hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF22,Pfam_domain:PF07707,SMART_domains:SM00875,PIRSF_domain:PIRSF037037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCGCGCGTC	byFrequency	5	ESCA
BSN	0	.	GRCh37	3	49699718	49699718	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10440C>A	p.%3D	p.G3480G	ENST00000296452	6/12	168	38	130	127	125	2	BSN,synonymous_variant,p.%3D,ENST00000296452,;	A	ENSG00000164061	ENST00000296452	Transcript	synonymous_variant	10554	10440	3480	G	ggC/ggA	.	.	.	1	BSN	HGNC	1117	protein_coding	YES	CCDS2800.1	ENSP00000296452	BSN_HUMAN	.	UPI000013E33C	.	.	.	6/12	.	hmmpanther:PTHR14113:SF1,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GCGGGCCCCAA	.	3	ESCA
SSUH2	0	.	GRCh37	3	8677462	8677492	+	Frame_Shift_Del	DEL	CAGTCATAGCTGGGCAGTCTCTCCAGGAGCT	CAGTCATAGCTGGGCAGTCTCTCCAGGAGCT	-	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	CAGTCATAGCTGGGCAGTCTCTCCAGGAGCT	CAGTCATAGCTGGGCAGTCTCTCCAGGAGCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.80_110delAGCTCCTGGAGAGACTGCCCAGCTATGACTG	p.Glu27GlyfsTer38	p.E27Gfs*38	ENST00000544814	2/12	82	23	59	56	56	0	SSUH2,frameshift_variant,p.Glu27GlyfsTer38,ENST00000427408,;SSUH2,frameshift_variant,p.Glu27GlyfsTer38,ENST00000544814,;SSUH2,5_prime_UTR_variant,,ENST00000317371,;SSUH2,5_prime_UTR_variant,,ENST00000341795,;SSUH2,5_prime_UTR_variant,,ENST00000415132,;SSUH2,non_coding_transcript_exon_variant,,ENST00000466215,;SSUH2,non_coding_transcript_exon_variant,,ENST00000484585,;SSUH2,non_coding_transcript_exon_variant,,ENST00000483845,;SSUH2,upstream_gene_variant,,ENST00000492435,;SSUH2,frameshift_variant,p.Glu27GlyfsTer136,ENST00000413305,;SSUH2,coding_sequence_variant,,ENST00000420394,;SSUH2,3_prime_UTR_variant,,ENST00000455157,;SSUH2,3_prime_UTR_variant,,ENST00000435138,;SSUH2,non_coding_transcript_exon_variant,,ENST00000495366,;	-	ENSG00000125046	ENST00000544814	Transcript	frameshift_variant	120-150	80-110	27-37	ELLERLPSYDW/X	gAGCTCCTGGAGAGACTGCCCAGCTATGACTGg/gg	.	.	.	-1	SSUH2	HGNC	24809	protein_coding	YES	CCDS58815.1	ENSP00000439378	SSUH2_HUMAN	C9JZA7_HUMAN	UPI000206527B	.	.	.	2/12	.	hmmpanther:PTHR15852:SF7,hmmpanther:PTHR15852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAAGCCAGTCATAGCTGGGCAGTCTCTCCAGGAGCTCTGTG	.	3	ESCA
SLC39A8	0	.	GRCh37	4	103184318	103184318	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1266G>A	p.%3D	p.K422K	ENST00000394833	8/8	40	13	27	65	64	0	SLC39A8,synonymous_variant,p.%3D,ENST00000356736,;SLC39A8,synonymous_variant,p.%3D,ENST00000394833,;SLC39A8,synonymous_variant,p.%3D,ENST00000424970,;	T	ENSG00000138821	ENST00000394833	Transcript	synonymous_variant	1743	1266	422	K	aaG/aaA	.	.	.	-1	SLC39A8	HGNC	20862	protein_coding	YES	CCDS3656.1	ENSP00000378310	S39A8_HUMAN	.	UPI0000046C4E	.	.	.	8/8	.	hmmpanther:PTHR12191:SF2,hmmpanther:PTHR12191,Pfam_domain:PF02535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTACCTTTTC	.	5	ESCA
FGA	0	.	GRCh37	4	155505175	155505176	+	3'UTR	INS	-	-	TT	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99_*100dupAA	.	.	ENST00000302053	6/6	58	32	26	72	72	0	FGA,3_prime_UTR_variant,,ENST00000302053,;FGA,downstream_gene_variant,,ENST00000403106,;	TT	ENSG00000171560	ENST00000302053	Transcript	3_prime_UTR_variant	2780-2781	.	.	.	.	.	.	.	-1	FGA	HGNC	3661	protein_coding	YES	CCDS3787.1	ENSP00000306361	FIBA_HUMAN	Q86Z09_HUMAN	UPI000012A75A	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAGGAATTTTT	.	3	ESCA
GABRA2	0	.	GRCh37	4	46263847	46263864	+	Intron	DEL	GATGTCTTTAATGTCAGT	GATGTCTTTAATGTCAGT	TCTTTAATGTCAGGA	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	GATGTCTTTAATGTCAGT	GATGTCTTTAATGTCAGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059+79_1059+96delACTGACATTAAAGACATCinsTCCTGACATTAAAGA	.	.	ENST00000510861	.	27	8	19	33	33	0	GABRA2,3_prime_UTR_variant,,ENST00000515082,;GABRA2,intron_variant,,ENST00000510861,;GABRA2,intron_variant,,ENST00000356504,;GABRA2,intron_variant,,ENST00000507069,;GABRA2,intron_variant,,ENST00000381620,;GABRA2,intron_variant,,ENST00000540012,;GABRA2,intron_variant,,ENST00000514090,;GABRA2,intron_variant,,ENST00000513005,;GABRA2,intron_variant,,ENST00000510233,;	TCTTTAATGTCAGGA	ENSG00000151834	ENST00000510861	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	GABRA2	HGNC	4076	protein_coding	YES	CCDS3471.1	ENSP00000421828	GBRA2_HUMAN	Q4W5L8_HUMAN,D6RBL7_HUMAN,D6RBK9_HUMAN,D6RB77_HUMAN	UPI000013DC88	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|PINDEL	TATATGGATGTCTTTAATGTCAGTTTTTA	.	2	ESCA
USP46	0	.	GRCh37	4	53463586	53463586	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*220G>C	.	.	ENST00000441222	9/9	25	21	4	17	17	0	USP46,3_prime_UTR_variant,,ENST00000451218,;USP46,3_prime_UTR_variant,,ENST00000441222,;USP46,downstream_gene_variant,,ENST00000508499,;USP46,3_prime_UTR_variant,,ENST00000503060,;USP46,downstream_gene_variant,,ENST00000514536,;	G	ENSG00000109189	ENST00000441222	Transcript	3_prime_UTR_variant	1506	.	.	.	.	.	.	.	-1	USP46	HGNC	20075	protein_coding	YES	CCDS47053.1	ENSP00000407818	UBP46_HUMAN	.	UPI0000006C18	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCAGACTACAA	.	3	ESCA
CABS1	0	.	GRCh37	4	71201456	71201456	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.700C>G	p.Leu234Val	p.L234V	ENST00000273936	1/2	22	15	7	24	24	0	CABS1,missense_variant,p.Leu234Val,ENST00000273936,;	G	ENSG00000145309	ENST00000273936	Transcript	missense_variant	774	700	234	L/V	Ctt/Gtt	.	.	.	1	CABS1	HGNC	30710	protein_coding	YES	CCDS3539.1	ENSP00000273936	CABS1_HUMAN	.	UPI0000071735	.	tolerated(0.15)	possibly_damaging(0.899)	1/2	.	hmmpanther:PTHR22810,Pfam_domain:PF15367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCCTTGAA	.	5	ESCA
SHROOM3	0	.	GRCh37	4	77661188	77661188	+	Missense_Mutation	SNP	G	G	A	rs761894567	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1862G>A	p.Arg621Lys	p.R621K	ENST00000296043	5/11	43	33	10	33	33	0	SHROOM3,missense_variant,p.Arg621Lys,ENST00000296043,;SHROOM3,intron_variant,,ENST00000469923,;SHROOM3,downstream_gene_variant,,ENST00000473602,;SHROOM3,downstream_gene_variant,,ENST00000481002,;SHROOM3,non_coding_transcript_exon_variant,,ENST00000486758,;	A	ENSG00000138771	ENST00000296043	Transcript	missense_variant	2815	1862	621	R/K	aGg/aAg	rs761894567	.	.	1	SHROOM3	HGNC	30422	protein_coding	YES	CCDS3579.2	ENSP00000296043	SHRM3_HUMAN	.	UPI0000E5AC1C	.	tolerated(0.21)	benign(0.007)	5/11	.	hmmpanther:PTHR15012:SF33,hmmpanther:PTHR15012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCAGGCTCT	.	5	ESCA
WDFY3	0	.	GRCh37	4	85731437	85731437	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1948G>A	p.Gly650Arg	p.G650R	ENST00000295888	14/68	32	20	11	23	23	0	WDFY3,missense_variant,p.Gly650Arg,ENST00000295888,;WDFY3,missense_variant,p.Gly650Arg,ENST00000322366,;WDFY3-AS1,non_coding_transcript_exon_variant,,ENST00000510449,;WDFY3,upstream_gene_variant,,ENST00000505923,;WDFY3,non_coding_transcript_exon_variant,,ENST00000426414,;	T	ENSG00000163625	ENST00000295888	Transcript	missense_variant	2356	1948	650	G/R	Gga/Aga	.	.	.	-1	WDFY3	HGNC	20751	protein_coding	YES	CCDS3609.1	ENSP00000295888	WDFY3_HUMAN	D6RJE4_HUMAN,A7E1Z6_HUMAN	UPI000013E2C7	.	deleterious(0)	probably_damaging(1)	14/68	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR13743:SF55,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATCCTCCAA	.	5	ESCA
GRID2	0	.	GRCh37	4	94376819	94376819	+	Missense_Mutation	SNP	G	G	C	rs757620916	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1552G>C	p.Asp518His	p.D518H	ENST00000282020	11/16	17	3	13	21	21	0	GRID2,missense_variant,p.Asp518His,ENST00000282020,;GRID2,missense_variant,p.Asp423His,ENST00000510992,;	C	ENSG00000152208	ENST00000282020	Transcript	missense_variant	1810	1552	518	D/H	Gac/Cac	rs757620916,COSM1328340	.	.	1	GRID2	HGNC	4576	protein_coding	YES	CCDS3637.1	ENSP00000282020	GRID2_HUMAN	Q4W5S4_HUMAN,Q4W5L9_HUMAN,Q4W5F4_HUMAN,Q4W5B7_HUMAN,D6R976_HUMAN	UPI00001AEA78	.	deleterious(0)	probably_damaging(0.996)	11/16	.	hmmpanther:PTHR18966:SF109,hmmpanther:PTHR18966,Gene3D:3.40.190.10,Pfam_domain:PF00497,SMART_domains:SM00079,Superfamily_domains:SSF53850	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGACATA	.	5	ESCA
FAM170A	0	.	GRCh37	5	118970255	118970255	+	Missense_Mutation	SNP	T	T	C	rs528739250	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.812T>C	p.Met271Thr	p.M271T	ENST00000335286	3/5	33	24	9	33	33	0	FAM170A,missense_variant,p.Met271Thr,ENST00000515256,;FAM170A,intron_variant,,ENST00000509264,;FAM170A,missense_variant,p.Met271Thr,ENST00000335286,;FAM170A,missense_variant,p.Met224Thr,ENST00000379555,;FAM170A,missense_variant,p.Met224Thr,ENST00000504819,;HSD17B4,intron_variant,,ENST00000515235,;	C	ENSG00000164334	ENST00000335286	Transcript	missense_variant	983	812	271	M/T	aTg/aCg	rs528739250	.	.	1	FAM170A	HGNC	27963	nonsense_mediated_decay	YES	CCDS43353.1	ENSP00000334285	F170A_HUMAN	.	UPI00001C1E37	.	tolerated(0.1)	benign(0.033)	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACATGGAAT	byFrequency|byCluster	5	ESCA
CXCL14	0	.	GRCh37	5	134907182	134907182	+	3'UTR	SNP	G	G	T	rs773211331	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*361C>A	.	.	ENST00000337225	4/4	42	28	13	35	35	0	CXCL14,3_prime_UTR_variant,,ENST00000337225,;CXCL14,3_prime_UTR_variant,,ENST00000512158,;CTC-321K16.1,intron_variant,,ENST00000509372,;	T	ENSG00000145824	ENST00000337225	Transcript	3_prime_UTR_variant	1162	.	.	.	.	rs773211331	.	.	-1	CXCL14	HGNC	10640	protein_coding	YES	CCDS4188.1	ENSP00000337065	CXL14_HUMAN	.	UPI000003B10C	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCGGGCGC	byCluster	5	ESCA
KCTD16	0	.	GRCh37	5	143854159	143854159	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*482C>A	.	.	ENST00000507359	3/3	50	35	15	42	42	0	KCTD16,3_prime_UTR_variant,,ENST00000507359,;KCTD16,downstream_gene_variant,,ENST00000512467,;	A	ENSG00000183775	ENST00000507359	Transcript	3_prime_UTR_variant	2860	.	.	.	.	.	.	.	1	KCTD16	HGNC	29244	protein_coding	YES	CCDS34260.1	ENSP00000426548	KCD16_HUMAN	.	UPI000004A046	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCACTCAAA	.	5	ESCA
ANKH	0	.	GRCh37	5	14769140	14769140	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257C>T	p.Ala86Val	p.A86V	ENST00000284268	2/12	53	22	31	45	45	0	ANKH,missense_variant,p.Ala86Val,ENST00000284268,;ANKH,non_coding_transcript_exon_variant,,ENST00000503389,;ANKH,non_coding_transcript_exon_variant,,ENST00000513115,;	A	ENSG00000154122	ENST00000284268	Transcript	missense_variant	588	257	86	A/V	gCc/gTc	.	.	.	-1	ANKH	HGNC	15492	protein_coding	YES	CCDS3885.1	ENSP00000284268	ANKH_HUMAN	B3KMG4_HUMAN	UPI000003F535	.	tolerated(0.45)	probably_damaging(0.998)	2/12	.	Transmembrane_helices:TMhelix,Pfam_domain:PF07260	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACGGCTTTG	.	5	ESCA
GABRA1	0	.	GRCh37	5	161300308	161300308	+	Silent	SNP	G	G	A	rs190024862	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441G>A	p.%3D	p.R147R	ENST00000428797	6/11	61	55	5	53	53	0	GABRA1,synonymous_variant,p.%3D,ENST00000444819,;GABRA1,synonymous_variant,p.%3D,ENST00000420560,;GABRA1,synonymous_variant,p.%3D,ENST00000437025,;GABRA1,synonymous_variant,p.%3D,ENST00000428797,;GABRA1,synonymous_variant,p.%3D,ENST00000393943,;GABRA1,synonymous_variant,p.%3D,ENST00000023897,;GABRA1,downstream_gene_variant,,ENST00000519621,;GABRA1,non_coding_transcript_exon_variant,,ENST00000519542,;	A	ENSG00000022355	ENST00000428797	Transcript	synonymous_variant	796	441	147	R	cgG/cgA	rs190024862	.	.	1	GABRA1	HGNC	4075	protein_coding	YES	CCDS4357.1	ENSP00000393097	GBRA1_HUMAN	E5RK60_HUMAN,E5RJS3_HUMAN	UPI000012AF95	.	.	.	6/11	.	hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0	T:0.0005	benign	.	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGCGGATCAC	byCluster|by1000G	3	ESCA
GABRA1	0	.	GRCh37	5	161300309	161300309	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442A>T	p.Ile148Phe	p.I148F	ENST00000428797	6/11	60	54	5	53	53	0	GABRA1,missense_variant,p.Ile148Phe,ENST00000444819,;GABRA1,missense_variant,p.Ile148Phe,ENST00000420560,;GABRA1,missense_variant,p.Ile148Phe,ENST00000437025,;GABRA1,missense_variant,p.Ile148Phe,ENST00000428797,;GABRA1,missense_variant,p.Ile148Phe,ENST00000393943,;GABRA1,missense_variant,p.Ile148Phe,ENST00000023897,;GABRA1,downstream_gene_variant,,ENST00000519621,;GABRA1,non_coding_transcript_exon_variant,,ENST00000519542,;	T	ENSG00000022355	ENST00000428797	Transcript	missense_variant	797	442	148	I/F	Atc/Ttc	.	.	.	1	GABRA1	HGNC	4075	protein_coding	YES	CCDS4357.1	ENSP00000393097	GBRA1_HUMAN	E5RK60_HUMAN,E5RJS3_HUMAN	UPI000012AF95	.	deleterious(0.03)	possibly_damaging(0.528)	6/11	.	hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCGGATCACA	.	3	ESCA
BASP1	0	.	GRCh37	5	17276654	17276654	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*645T>C	.	.	ENST00000322611	2/2	78	28	49	57	57	0	BASP1,3_prime_UTR_variant,,ENST00000322611,;BASP1,downstream_gene_variant,,ENST00000606445,;	C	ENSG00000176788	ENST00000322611	Transcript	3_prime_UTR_variant	1589	.	.	.	.	.	.	.	1	BASP1	HGNC	957	protein_coding	YES	CCDS3888.1	ENSP00000319281	BASP1_HUMAN	U3KQP0_HUMAN	UPI0000140E98	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCCTACTTA	.	5	ESCA
CDH6	0	.	GRCh37	5	31323519	31323519	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*104C>A	.	.	ENST00000265071	12/12	31	24	7	13	13	0	CDH6,3_prime_UTR_variant,,ENST00000265071,;CDH6,downstream_gene_variant,,ENST00000504835,;	A	ENSG00000113361	ENST00000265071	Transcript	3_prime_UTR_variant	2742	.	.	.	.	.	.	.	1	CDH6	HGNC	1765	protein_coding	YES	CCDS3894.1	ENSP00000265071	CADH6_HUMAN	.	UPI0000126D9B	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTTCCAAAA	.	5	ESCA
PLCXD3	0	.	GRCh37	5	41307118	41307118	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6601T>A	.	.	ENST00000377801	3/3	58	43	14	57	57	0	PLCXD3,3_prime_UTR_variant,,ENST00000328457,;PLCXD3,3_prime_UTR_variant,,ENST00000377801,;	T	ENSG00000182836	ENST00000377801	Transcript	3_prime_UTR_variant	7642	.	.	.	.	.	.	.	-1	PLCXD3	HGNC	31822	protein_coding	YES	CCDS34150.1	ENSP00000367032	PLCX3_HUMAN	B3KXD1_HUMAN	UPI0000049DBB	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTAAGAAC	.	5	ESCA
MED10	0	.	GRCh37	5	6372690	6372690	+	Missense_Mutation	SNP	C	C	T	rs775786804	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334G>A	p.Glu112Lys	p.E112K	ENST00000255764	4/4	121	88	33	72	72	0	MED10,missense_variant,p.Glu112Lys,ENST00000255764,;MED10,non_coding_transcript_exon_variant,,ENST00000503112,;MED10,downstream_gene_variant,,ENST00000504058,;	T	ENSG00000133398	ENST00000255764	Transcript	missense_variant	445	334	112	E/K	Gaa/Aaa	rs775786804	.	.	-1	MED10	HGNC	28760	protein_coding	YES	CCDS34134.1	ENSP00000255764	MED10_HUMAN	.	UPI000007379B	.	tolerated(0.06)	benign(0.315)	4/4	.	Pfam_domain:PF09748,hmmpanther:PTHR13345	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTTCTTGAA	.	5	ESCA
BRD9	0	.	GRCh37	5	878475	878475	+	Silent	SNP	C	C	T	rs145445077	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1266G>A	p.%3D	p.A422A	ENST00000467963	11/16	54	35	18	45	45	0	BRD9,synonymous_variant,p.%3D,ENST00000467963,;BRD9,synonymous_variant,p.%3D,ENST00000323510,;BRD9,synonymous_variant,p.%3D,ENST00000388890,;BRD9,synonymous_variant,p.%3D,ENST00000483173,;BRD9,3_prime_UTR_variant,,ENST00000435709,;BRD9,non_coding_transcript_exon_variant,,ENST00000494422,;BRD9,non_coding_transcript_exon_variant,,ENST00000519838,;BRD9,synonymous_variant,p.%3D,ENST00000519112,;BRD9,synonymous_variant,p.%3D,ENST00000518251,;BRD9,3_prime_UTR_variant,,ENST00000489816,;BRD9,3_prime_UTR_variant,,ENST00000495265,;BRD9,3_prime_UTR_variant,,ENST00000466684,;BRD9,3_prime_UTR_variant,,ENST00000490814,;BRD9,non_coding_transcript_exon_variant,,ENST00000493082,;BRD9,non_coding_transcript_exon_variant,,ENST00000483234,;BRD9,non_coding_transcript_exon_variant,,ENST00000495794,;BRD9,non_coding_transcript_exon_variant,,ENST00000475706,;BRD9,upstream_gene_variant,,ENST00000523139,;	T	ENSG00000028310	ENST00000467963	Transcript	synonymous_variant	1433	1266	422	A	gcG/gcA	rs145445077	.	.	-1	BRD9	HGNC	25818	protein_coding	YES	CCDS34127.2	ENSP00000419765	BRD9_HUMAN	.	UPI000020BEBE	.	.	.	11/16	.	Pfam_domain:PF12024,hmmpanther:PTHR22881,hmmpanther:PTHR22881:SF4	T:0.0010	T:0.0038	T:0	.	T:0	T:0	T:0	T:0.0009	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAGCGCACA	byFrequency|byCluster|by1000G	5	ESCA
PRDM1	0	.	GRCh37	6	106553478	106553478	+	Silent	SNP	G	G	A	rs777578275	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1443G>A	p.%3D	p.P481P	ENST00000369096	5/7	30	8	21	50	50	0	PRDM1,synonymous_variant,p.%3D,ENST00000369096,;PRDM1,synonymous_variant,p.%3D,ENST00000369091,;PRDM1,synonymous_variant,p.%3D,ENST00000369089,;PRDM1,downstream_gene_variant,,ENST00000450060,;	A	ENSG00000057657	ENST00000369096	Transcript	synonymous_variant	1677	1443	481	P	ccG/ccA	rs777578275	.	.	1	PRDM1	HGNC	9346	protein_coding	YES	CCDS5054.2	ENSP00000358092	PRDM1_HUMAN	Q5T4E8_HUMAN,B2REA5_HUMAN	UPI0000D49069	.	.	.	5/7	.	hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF339,PIRSF_domain:PIRSF013212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCGGAGCA	byFrequency	5	ESCA
ENPP3	0	.	GRCh37	6	132059220	132059220	+	Silent	SNP	A	A	G	rs769019983	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2217A>G	p.%3D	p.E739E	ENST00000414305	24/26	118	74	44	87	87	0	ENPP3,synonymous_variant,p.%3D,ENST00000357639,;ENPP3,synonymous_variant,p.%3D,ENST00000414305,;ENPP3,3_prime_UTR_variant,,ENST00000358229,;	G	ENSG00000154269	ENST00000414305	Transcript	synonymous_variant	2545	2217	739	E	gaA/gaG	rs769019983	.	.	1	ENPP3	HGNC	3358	protein_coding	YES	CCDS5148.1	ENSP00000406261	ENPP3_HUMAN	Q9UNI4_HUMAN,Q9NQM9_HUMAN,Q9H515_HUMAN,F5GY67_HUMAN	UPI000013DD9F	.	.	.	24/26	.	hmmpanther:PTHR10151:SF55,hmmpanther:PTHR10151,Pfam_domain:PF01223,Gene3D:1g8tA00,SMART_domains:SM00892,SMART_domains:SM00477,Superfamily_domains:SSF54060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGAAAGAAA	.	5	ESCA
ADAT2	0	.	GRCh37	6	143749461	143749461	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*139C>T	.	.	ENST00000237283	6/6	17	9	8	16	16	0	ADAT2,3_prime_UTR_variant,,ENST00000606514,;ADAT2,3_prime_UTR_variant,,ENST00000237283,;	A	ENSG00000189007	ENST00000237283	Transcript	3_prime_UTR_variant	730	.	.	.	.	.	.	.	-1	ADAT2	HGNC	21172	protein_coding	YES	CCDS43511.1	ENSP00000237283	ADAT2_HUMAN	.	UPI00001A3A7E	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAACAGAGCAA	.	5	ESCA
GRM1	0	.	GRCh37	6	146708117	146708117	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1694G>T	p.Cys565Phe	p.C565F	ENST00000361719	7/9	108	91	16	84	84	0	GRM1,missense_variant,p.Cys565Phe,ENST00000282753,;GRM1,missense_variant,p.Cys565Phe,ENST00000392299,;GRM1,missense_variant,p.Cys565Phe,ENST00000361719,;GRM1,missense_variant,p.Cys565Phe,ENST00000507907,;GRM1,missense_variant,p.Cys565Phe,ENST00000355289,;GRM1,missense_variant,p.Cys565Phe,ENST00000492807,;	T	ENSG00000152822	ENST00000361719	Transcript	missense_variant	2164	1694	565	C/F	tGt/tTt	.	.	.	1	GRM1	HGNC	4593	protein_coding	YES	CCDS5209.1	ENSP00000354896	GRM1_HUMAN	.	UPI000013DCFD	.	deleterious(0.03)	probably_damaging(0.999)	7/9	.	hmmpanther:PTHR24060:SF29,hmmpanther:PTHR24060,PROSITE_patterns:PS00980,Pfam_domain:PF07562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTGTGACT	.	5	ESCA
TULP4	0	.	GRCh37	6	158735106	158735106	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58C>T	p.%3D	p.L20L	ENST00000367097	1/14	35	21	13	38	38	0	TULP4,synonymous_variant,p.%3D,ENST00000367097,;TULP4,synonymous_variant,p.%3D,ENST00000367094,;RP11-732M18.3,downstream_gene_variant,,ENST00000432358,;	T	ENSG00000130338	ENST00000367097	Transcript	synonymous_variant	1415	58	20	L	Ctg/Ttg	.	.	.	1	TULP4	HGNC	15530	protein_coding	YES	CCDS34561.1	ENSP00000356064	TULP4_HUMAN	.	UPI000013CD76	.	.	.	1/14	.	hmmpanther:PTHR16517,hmmpanther:PTHR16517:SF2,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.C19Y|c.56G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGCCTGTCC	.	5	ESCA
NUP153	0	.	GRCh37	6	17615773	17615773	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*555C>T	.	.	ENST00000262077	22/22	105	81	23	46	46	0	NUP153,3_prime_UTR_variant,,ENST00000262077,;NUP153,downstream_gene_variant,,ENST00000537253,;FAM8A1,downstream_gene_variant,,ENST00000259963,;RNU6-190P,upstream_gene_variant,,ENST00000384154,;	A	ENSG00000124789	ENST00000262077	Transcript	3_prime_UTR_variant	4983	.	.	.	.	.	.	.	-1	NUP153	HGNC	8062	protein_coding	YES	CCDS4541.1	ENSP00000262077	NU153_HUMAN	.	UPI000013D251	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAAGTCCTT	.	5	ESCA
SLC17A2	0	.	GRCh37	6	25913642	25913642	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1192C>T	p.%3D	p.L398L	ENST00000360488	11/11	93	66	27	55	55	0	SLC17A2,missense_variant,p.Ser447Phe,ENST00000377850,;SLC17A2,synonymous_variant,p.%3D,ENST00000360488,;SLC17A2,3_prime_UTR_variant,,ENST00000265425,;	A	ENSG00000112337	ENST00000360488	Transcript	synonymous_variant	1610	1192	398	L	Ctg/Ttg	.	.	.	-1	SLC17A2	HGNC	10930	protein_coding	YES	CCDS4567.1	ENSP00000353677	NPT3_HUMAN	.	UPI0000000DB7	.	.	.	11/11	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAGACAGG	.	5	ESCA
HIST1H2AI	0	.	GRCh37	6	27775992	27775992	+	Missense_Mutation	SNP	C	C	A	rs768930206	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5C>A	p.Ser2Tyr	p.S2Y	ENST00000358739	1/1	98	77	20	65	65	0	HIST1H2AI,missense_variant,p.Ser2Tyr,ENST00000358739,;HIST1H2BL,upstream_gene_variant,,ENST00000377401,;HIST1H3H,upstream_gene_variant,,ENST00000369163,;HIST1H4PS1,downstream_gene_variant,,ENST00000406085,;	A	ENSG00000196747	ENST00000358739	Transcript	missense_variant	94	5	2	S/Y	tCt/tAt	rs768930206	.	.	1	HIST1H2AI	HGNC	4725	protein_coding	YES	CCDS4626.1	ENSP00000351589	H2A1_HUMAN	A4FTV9_HUMAN,A3KPC7_HUMAN	UPI0000000E01	.	deleterious_low_confidence(0)	benign(0.184)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23430,hmmpanther:PTHR23430:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGTCTGGGC	.	5	ESCA
FAM217A	0	.	GRCh37	6	4073518	4073518	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.293T>C	p.Ile98Thr	p.I98T	ENST00000274673	6/7	95	68	27	59	59	0	FAM217A,missense_variant,p.Ile35Thr,ENST00000498677,;FAM217A,missense_variant,p.Ile98Thr,ENST00000274673,;FAM217A,downstream_gene_variant,,ENST00000492651,;snoU13,upstream_gene_variant,,ENST00000516859,;FAM217A,non_coding_transcript_exon_variant,,ENST00000469157,;FAM217A,non_coding_transcript_exon_variant,,ENST00000380188,;FAM217A,downstream_gene_variant,,ENST00000478714,;	G	ENSG00000145975	ENST00000274673	Transcript	missense_variant	697	293	98	I/T	aTa/aCa	.	.	.	-1	FAM217A	HGNC	21362	protein_coding	YES	CCDS4489.1	ENSP00000274673	F217A_HUMAN	C9J6U0_HUMAN,C9J5H0_HUMAN	UPI0000160AA7	.	tolerated(0.94)	benign(0.002)	6/7	.	hmmpanther:PTHR22145,hmmpanther:PTHR22145:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTATGGTA	.	5	ESCA
BCKDHB	0	.	GRCh37	6	80878608	80878608	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.494C>T	p.Ala165Val	p.A165V	ENST00000320393	5/10	131	65	65	95	95	0	BCKDHB,missense_variant,p.Ala165Val,ENST00000369760,;BCKDHB,missense_variant,p.Ala165Val,ENST00000356489,;BCKDHB,missense_variant,p.Ala165Val,ENST00000320393,;BCKDHB,missense_variant,p.Ala165Val,ENST00000545529,;	T	ENSG00000083123	ENST00000320393	Transcript	missense_variant	541	494	165	A/V	gCc/gTc	.	.	.	1	BCKDHB	HGNC	987	protein_coding	YES	CCDS4994.1	ENSP00000318351	ODBB_HUMAN	Q6LCK9_HUMAN,B7ZB80_HUMAN	UPI0000001C97	.	deleterious(0)	probably_damaging(0.978)	5/10	.	hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF21,Pfam_domain:PF02779,Gene3D:3.40.50.970,SMART_domains:SM00861,Superfamily_domains:SSF52518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGCCAAGT	.	5	ESCA
MDN1	0	.	GRCh37	6	90384069	90384069	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13001delT	p.Leu4334ArgfsTer14	p.L4334Rfs*14	ENST00000369393	79/102	58	52	6	26	26	0	MDN1,frameshift_variant,p.Leu4334ArgfsTer14,ENST00000369393,;MDN1,frameshift_variant,p.Leu4334ArgfsTer14,ENST00000428876,;RP1-122O8.7,intron_variant,,ENST00000438877,;MDN1,upstream_gene_variant,,ENST00000468568,;	-	ENSG00000112159	ENST00000369393	Transcript	frameshift_variant	13117	13001	4334	L/X	cTg/cg	.	.	.	-1	MDN1	HGNC	18302	protein_coding	YES	CCDS5024.1	ENSP00000358400	MDN1_HUMAN	M0QXR3_HUMAN	UPI000013C4B8	.	.	.	79/102	.	hmmpanther:PTHR22908:SF58,hmmpanther:PTHR22908,PIRSF_domain:PIRSF010340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTTCCAGGCAG	.	3	ESCA
ST7-OT4	0	.	GRCh37	7	116596724	116596724	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.317T>C	p.Leu106Pro	p.L106P	ENST00000397750	4/5	38	16	22	42	42	0	ST7-OT4,missense_variant,p.Leu8Pro,ENST00000597499,;ST7-OT4,missense_variant,p.Leu106Pro,ENST00000397751,;ST7-OT4,missense_variant,p.Leu106Pro,ENST00000397750,;ST7,intron_variant,,ENST00000393449,;ST7,intron_variant,,ENST00000417919,;ST7,intron_variant,,ENST00000446490,;ST7,intron_variant,,ENST00000393451,;ST7,intron_variant,,ENST00000393446,;ST7,intron_variant,,ENST00000323984,;ST7,intron_variant,,ENST00000265437,;ST7,intron_variant,,ENST00000421345,;ST7-AS1,upstream_gene_variant,,ENST00000456775,;ST7-OT4,intron_variant,,ENST00000471110,;ST7-OT4,intron_variant,,ENST00000470996,;ST7-OT4,intron_variant,,ENST00000466018,;ST7,intron_variant,,ENST00000438863,;ST7,intron_variant,,ENST00000443979,;	C	ENSG00000214188	ENST00000397750	Transcript	missense_variant	858	317	106	L/P	cTc/cCc	.	.	.	1	ST7-OT4	HGNC	18835	protein_coding	YES	.	ENSP00000380858	.	A8MTU0_HUMAN	UPI000020F980	.	deleterious_low_confidence(0)	possibly_damaging(0.883)	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCTCAATA	.	5	ESCA
MOXD2P	0	.	GRCh37	7	141942747	141942747	+	RNA	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1234C>A	.	.	ENST00000460233	8/11	30	19	11	28	28	0	MOXD2P,non_coding_transcript_exon_variant,,ENST00000477615,;MOXD2P,non_coding_transcript_exon_variant,,ENST00000460233,;	T	ENSG00000240268	ENST00000460233	Transcript	non_coding_transcript_exon_variant	1234	.	.	.	.	.	.	.	-1	MOXD2P	HGNC	33605	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	8/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTAGCAGGT	.	5	ESCA
RNY5	0	.	GRCh37	7	148638591	148638591	+	RNA	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.12G>T	.	.	ENST00000516501	1/1	65	46	19	33	33	0	RNY5,non_coding_transcript_exon_variant,,ENST00000516501,;	T	ENSG00000252310	ENST00000516501	Transcript	non_coding_transcript_exon_variant	12	.	.	.	.	.	.	.	1	RNY5	HGNC	10248	misc_RNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGAGTGTTG	.	5	ESCA
ABCB5	0	.	GRCh37	7	20744391	20744391	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2382G>C	p.Leu794Phe	p.L794F	ENST00000404938	20/28	64	48	15	24	24	0	ABCB5,missense_variant,p.Leu349Phe,ENST00000258738,;ABCB5,missense_variant,p.Leu794Phe,ENST00000404938,;	C	ENSG00000004846	ENST00000404938	Transcript	missense_variant	3034	2382	794	L/F	ttG/ttC	.	.	.	1	ABCB5	HGNC	46	protein_coding	YES	CCDS55090.1	ENSP00000384881	ABCB5_HUMAN	.	UPI000173A253	.	deleterious(0)	probably_damaging(0.998)	20/28	.	PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF2,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTGACAAC	.	5	ESCA
DPY19L1	0	.	GRCh37	7	34971135	34971135	+	3'UTR	SNP	T	T	G	rs781051508	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50A>C	.	.	ENST00000310974	22/22	141	101	39	77	77	0	DPY19L1,3_prime_UTR_variant,,ENST00000310974,;DPY19L1,downstream_gene_variant,,ENST00000428054,;	G	ENSG00000173852	ENST00000310974	Transcript	3_prime_UTR_variant	2223	.	.	.	.	rs781051508	.	.	-1	DPY19L1	HGNC	22205	protein_coding	YES	CCDS43567.1	ENSP00000308695	D19L1_HUMAN	.	UPI000067CB92	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACATTAAAA	.	5	ESCA
TNRC18	0	.	GRCh37	7	5414008	5414008	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2907G>T	p.%3D	p.G969G	ENST00000430969	10/30	34	29	4	17	17	0	TNRC18,synonymous_variant,p.%3D,ENST00000430969,;TNRC18,synonymous_variant,p.%3D,ENST00000399537,;TNRC18,downstream_gene_variant,,ENST00000413081,;	A	ENSG00000182095	ENST00000430969	Transcript	synonymous_variant	3256	2907	969	G	ggG/ggT	.	.	.	-1	TNRC18	HGNC	11962	protein_coding	YES	CCDS47534.1	ENSP00000395538	TNC18_HUMAN	H7C3U5_HUMAN,C9J9K1_HUMAN	UPI00016632FD	.	.	.	10/30	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12505:SF21,hmmpanther:PTHR12505	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCAGCCCGGG	.	4	ESCA
TYW1B	0	.	GRCh37	7	72281191	72281191	+	Missense_Mutation	SNP	C	C	T	rs782217657	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298G>A	p.Glu100Lys	p.E100K	ENST00000438904	4/9	159	98	61	124	123	0	TYW1B,missense_variant,p.Glu100Lys,ENST00000438904,;TYW1B,intron_variant,,ENST00000438125,;TYW1B,intron_variant,,ENST00000437915,;TYW1B,missense_variant,p.Glu100Lys,ENST00000435769,;	T	ENSG00000254184	ENST00000438904	Transcript	missense_variant	397	298	100	E/K	Gaa/Aaa	rs782217657	.	.	-1	TYW1B	HGNC	33908	protein_coding	YES	.	ENSP00000477404	.	.	UPI0002065470	.	deleterious(0.04)	probably_damaging(0.986)	4/9	.	PROSITE_profiles:PS50902,hmmpanther:PTHR13930,hmmpanther:PTHR13930:SF0,Pfam_domain:PF00258,Gene3D:3.40.50.360,Superfamily_domains:SSF52218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTCGGTTG	byFrequency	5	ESCA
PHTF2	0	.	GRCh37	7	77585121	77585121	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*926A>G	.	.	ENST00000416283	18/18	18	11	7	12	12	0	PHTF2,3_prime_UTR_variant,,ENST00000307305,;PHTF2,3_prime_UTR_variant,,ENST00000416283,;PHTF2,3_prime_UTR_variant,,ENST00000422959,;PHTF2,3_prime_UTR_variant,,ENST00000248550,;PHTF2,3_prime_UTR_variant,,ENST00000275575,;PHTF2,downstream_gene_variant,,ENST00000470215,;	G	ENSG00000006576	ENST00000416283	Transcript	3_prime_UTR_variant	3308	.	.	.	.	.	.	.	1	PHTF2	HGNC	13411	protein_coding	YES	CCDS47621.1	ENSP00000400958	PHTF2_HUMAN	.	UPI0000E674D3	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAAATGAAC	.	5	ESCA
KRIT1	0	.	GRCh37	7	91851268	91851268	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1511C>T	p.Pro504Leu	p.P504L	ENST00000394507	15/20	182	141	41	89	89	0	KRIT1,missense_variant,p.Pro456Leu,ENST00000394503,;KRIT1,missense_variant,p.Pro504Leu,ENST00000394505,;KRIT1,missense_variant,p.Pro504Leu,ENST00000412043,;KRIT1,missense_variant,p.Pro504Leu,ENST00000340022,;KRIT1,missense_variant,p.Pro504Leu,ENST00000394507,;KRIT1,downstream_gene_variant,,ENST00000445516,;KRIT1,non_coding_transcript_exon_variant,,ENST00000475770,;KRIT1,non_coding_transcript_exon_variant,,ENST00000486261,;	A	ENSG00000001631	ENST00000394507	Transcript	missense_variant	2295	1511	504	P/L	cCt/cTt	.	.	.	-1	KRIT1	HGNC	1573	protein_coding	YES	CCDS5624.1	ENSP00000378015	KRIT1_HUMAN	C9JXI9_HUMAN,C9JSG7_HUMAN,C9JJM9_HUMAN,C9JI47_HUMAN,C9JF32_HUMAN,C9JEW7_HUMAN,C9JD81_HUMAN,C9JBN7_HUMAN,C9J718_HUMAN,C9J3W7_HUMAN,A4D1F7_HUMAN	UPI000006F5AA	.	deleterious(0)	benign(0.305)	15/20	.	PROSITE_profiles:PS50057,hmmpanther:PTHR13283,SMART_domains:SM00295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGAGGTGTT	.	5	ESCA
FER1L6	0	.	GRCh37	8	124988147	124988147	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693G>C	p.Leu231Phe	p.L231F	ENST00000522917	9/41	79	45	33	66	66	0	FER1L6,missense_variant,p.Leu231Phe,ENST00000522917,;FER1L6,missense_variant,p.Leu231Phe,ENST00000399018,;	C	ENSG00000214814	ENST00000522917	Transcript	missense_variant	899	693	231	L/F	ttG/ttC	.	.	.	1	FER1L6	HGNC	28065	protein_coding	YES	CCDS43767.1	ENSP00000428280	FR1L6_HUMAN	.	UPI0000E9B4AA	.	deleterious(0)	probably_damaging(1)	9/41	.	hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546,Pfam_domain:PF08151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTGATCCC	.	5	ESCA
DLGAP2	0	.	GRCh37	8	1497582	1497582	+	Silent	SNP	C	C	T	rs758466387	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723C>T	p.%3D	p.G241G	ENST00000421627	2/12	23	5	18	24	24	0	DLGAP2,synonymous_variant,p.%3D,ENST00000520901,;DLGAP2,synonymous_variant,p.%3D,ENST00000421627,;	T	ENSG00000198010	ENST00000421627	Transcript	synonymous_variant	857	723	241	G	ggC/ggT	rs758466387	.	.	1	DLGAP2	HGNC	2906	protein_coding	YES	CCDS47760.1	ENSP00000400258	DLGP2_HUMAN	.	UPI000021BFBC	.	.	.	2/12	.	hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCCCCGT	.	5	ESCA
CHRNA2	0	.	GRCh37	8	27320896	27320896	+	Missense_Mutation	SNP	C	C	T	rs368791756	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1064G>A	p.Arg355His	p.R355H	ENST00000407991	6/7	14	2	11	27	27	0	CHRNA2,missense_variant,p.Arg355His,ENST00000407991,;CHRNA2,missense_variant,p.Arg340His,ENST00000240132,;CHRNA2,missense_variant,p.Arg355His,ENST00000520933,;PTK2B,downstream_gene_variant,,ENST00000338238,;PTK2B,downstream_gene_variant,,ENST00000517339,;PTK2B,downstream_gene_variant,,ENST00000420218,;PTK2B,downstream_gene_variant,,ENST00000544172,;PTK2B,downstream_gene_variant,,ENST00000397501,;PTK2B,downstream_gene_variant,,ENST00000346049,;CHRNA2,3_prime_UTR_variant,,ENST00000523695,;CHRNA2,non_coding_transcript_exon_variant,,ENST00000523529,;CHRNA2,intron_variant,,ENST00000520600,;CHRNA2,downstream_gene_variant,,ENST00000522008,;PTK2B,downstream_gene_variant,,ENST00000522245,;	T	ENSG00000120903	ENST00000407991	Transcript	missense_variant	1673	1064	355	R/H	cGc/cAc	rs368791756	.	.	-1	CHRNA2	HGNC	1956	protein_coding	YES	CCDS6059.1	ENSP00000385026	ACHA2_HUMAN	E5RK67_HUMAN,E5RHQ4_HUMAN,E5RGT4_HUMAN,E5RGP6_HUMAN	UPI000013CA9F	.	deleterious(0)	probably_damaging(1)	6/7	.	hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF83,Gene3D:1.20.120.370,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAGCGGTGG	byFrequency|byCluster	5	ESCA
NRG1	0	.	GRCh37	8	32618077	32618077	+	Intron	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1283+153C>T	.	.	ENST00000356819	.	8	0	8	10	10	0	NRG1,3_prime_UTR_variant,,ENST00000523079,;NRG1,intron_variant,,ENST00000338921,;NRG1,intron_variant,,ENST00000287842,;NRG1,intron_variant,,ENST00000539990,;NRG1,intron_variant,,ENST00000521670,;NRG1,intron_variant,,ENST00000519301,;NRG1,intron_variant,,ENST00000356819,;NRG1,intron_variant,,ENST00000341377,;NRG1,intron_variant,,ENST00000518104,;NRG1,intron_variant,,ENST00000523534,;NRG1,intron_variant,,ENST00000405005,;NRG1,intron_variant,,ENST00000287845,;NRG1,downstream_gene_variant,,ENST00000519240,;NRG1,downstream_gene_variant,,ENST00000522402,;NRG1,downstream_gene_variant,,ENST00000522569,;	T	ENSG00000157168	ENST00000356819	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NRG1	HGNC	7997	protein_coding	YES	CCDS6083.1	ENSP00000349275	NRG1_HUMAN	Q7RTW5_HUMAN,B7Z168_HUMAN	UPI000013DED7	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCTCTTTGT	.	2	ESCA
PENK	0	.	GRCh37	8	57354245	57354245	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390G>C	p.Glu130Asp	p.E130D	ENST00000314922	2/2	84	58	25	83	83	0	PENK,missense_variant,p.Glu130Asp,ENST00000314922,;PENK,missense_variant,p.Glu130Asp,ENST00000451791,;PENK,intron_variant,,ENST00000517415,;PENK,downstream_gene_variant,,ENST00000518974,;PENK,downstream_gene_variant,,ENST00000523051,;PENK,downstream_gene_variant,,ENST00000518770,;RP11-17A4.2,upstream_gene_variant,,ENST00000518662,;PENK,non_coding_transcript_exon_variant,,ENST00000523274,;PENK,upstream_gene_variant,,ENST00000520589,;PENK,downstream_gene_variant,,ENST00000521153,;	G	ENSG00000181195	ENST00000314922	Transcript	missense_variant	467	390	130	E/D	gaG/gaC	.	.	.	-1	PENK	HGNC	8831	protein_coding	YES	CCDS6168.1	ENSP00000324248	PENK_HUMAN	E5RFR1_HUMAN	UPI00001315A9	.	tolerated(0.1)	benign(0.071)	2/2	.	Prints_domain:PR01029,hmmpanther:PTHR11438:SF3,hmmpanther:PTHR11438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATCTCACT	.	5	ESCA
ZFHX4	0	.	GRCh37	8	77779442	77779442	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2641G>A	.	.	ENST00000521891	11/11	58	36	22	42	42	0	ZFHX4,3_prime_UTR_variant,,ENST00000455469,;ZFHX4,3_prime_UTR_variant,,ENST00000521891,;ZFHX4,downstream_gene_variant,,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000050961,;	A	ENSG00000091656	ENST00000521891	Transcript	3_prime_UTR_variant	13940	.	.	.	.	.	.	.	1	ZFHX4	HGNC	30939	protein_coding	YES	CCDS47878.2	ENSP00000430497	.	Q9H7F3_HUMAN,Q86WW5_HUMAN,Q6DK57_HUMAN,G3V138_HUMAN,E5RI93_HUMAN,E5RHS1_HUMAN,E5RGK3_HUMAN,E5RG79_HUMAN	UPI0000424CC7	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTGAACTT	.	5	ESCA
FSD1L	0	.	GRCh37	9	108210341	108210341	+	5'Flank	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000481272	.	52	34	18	46	46	0	FSD1L,5_prime_UTR_variant,,ENST00000374710,;FSD1L,5_prime_UTR_variant,,ENST00000374716,;FSD1L,5_prime_UTR_variant,,ENST00000495708,;FSD1L,upstream_gene_variant,,ENST00000484973,;FSD1L,upstream_gene_variant,,ENST00000539376,;FSD1L,upstream_gene_variant,,ENST00000481272,;FSD1L,upstream_gene_variant,,ENST00000394926,;FSD1L,upstream_gene_variant,,ENST00000480279,;FSD1L,non_coding_transcript_exon_variant,,ENST00000469022,;	T	ENSG00000106701	ENST00000481272	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	42	1	FSD1L	HGNC	13753	protein_coding	YES	CCDS47999.1	ENSP00000417492	FSD1L_HUMAN	Q8N450_HUMAN	UPI0001931361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTGACTACGG	.	5	ESCA
TSC1	0	.	GRCh37	9	135782727	135782727	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1294C>G	p.Leu432Val	p.L432V	ENST00000298552	13/23	62	36	26	26	26	0	TSC1,missense_variant,p.Leu432Val,ENST00000298552,;TSC1,missense_variant,p.Leu381Val,ENST00000545250,;TSC1,missense_variant,p.Leu432Val,ENST00000440111,;TSC1,downstream_gene_variant,,ENST00000403810,;TSC1,downstream_gene_variant,,ENST00000493467,;	C	ENSG00000165699	ENST00000298552	Transcript	missense_variant	1516	1294	432	L/V	Cta/Gta	.	.	.	-1	TSC1	HGNC	12362	protein_coding	YES	CCDS6956.1	ENSP00000298552	TSC1_HUMAN	.	UPI000013773E	.	tolerated(0.17)	benign(0.078)	13/23	.	hmmpanther:PTHR15154,Pfam_domain:PF04388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTAGACATG	.	5	ESCA
C9orf96	0	.	GRCh37	9	136260761	136260761	+	Missense_Mutation	SNP	G	G	A	rs782474036	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.737G>A	p.Arg246His	p.R246H	ENST00000371957	9/18	53	28	24	39	39	0	C9orf96,missense_variant,p.Arg246His,ENST00000371957,;C9orf96,5_prime_UTR_variant,,ENST00000371955,;C9orf96,non_coding_transcript_exon_variant,,ENST00000462310,;C9orf96,non_coding_transcript_exon_variant,,ENST00000477284,;	A	ENSG00000198870	ENST00000371957	Transcript	missense_variant	844	737	246	R/H	cGc/cAc	rs782474036,COSM1674933,COSM1674932	.	.	1	C9orf96	HGNC	28669	protein_coding	YES	CCDS35169.1	ENSP00000361025	SGK71_HUMAN	.	UPI00001D763E	.	deleterious(0.03)	possibly_damaging(0.485)	9/18	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24363:SF3,hmmpanther:PTHR24363,Gene3D:1.10.510.10,Pfam_domain:PF00069,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCGCCAGA	byFrequency	5	ESCA
QSOX2	0	.	GRCh37	9	139103122	139103122	+	Missense_Mutation	SNP	C	C	T	rs757462508	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1537G>A	p.Gly513Ser	p.G513S	ENST00000358701	11/12	37	33	4	42	42	0	QSOX2,missense_variant,p.Gly281Ser,ENST00000455222,;QSOX2,missense_variant,p.Gly513Ser,ENST00000358701,;	T	ENSG00000165661	ENST00000358701	Transcript	missense_variant	1575	1537	513	G/S	Ggc/Agc	rs757462508	.	.	-1	QSOX2	HGNC	30249	protein_coding	YES	CCDS35178.1	ENSP00000351536	QSOX2_HUMAN	.	UPI00004A7AC1	.	tolerated(1)	benign(0.01)	11/12	.	PROSITE_profiles:PS51324,hmmpanther:PTHR22897:SF7,hmmpanther:PTHR22897,Gene3D:1.20.120.310,Pfam_domain:PF04777,Superfamily_domains:SSF69000	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGGCCGTTCA	byFrequency	4	ESCA
SDCCAG3	0	.	GRCh37	9	139298600	139298600	+	Missense_Mutation	SNP	C	C	T	rs762736506	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1115G>A	p.Gly372Asp	p.G372D	ENST00000357365	9/10	32	15	17	42	42	0	SDCCAG3,missense_variant,p.Gly104Asp,ENST00000417512,;SDCCAG3,missense_variant,p.Gly349Asp,ENST00000298537,;SDCCAG3,missense_variant,p.Gly372Asp,ENST00000357365,;SDCCAG3,missense_variant,p.Gly299Asp,ENST00000371725,;SDCCAG3,downstream_gene_variant,,ENST00000446833,;SDCCAG3,downstream_gene_variant,,ENST00000371723,;SDCCAG3,non_coding_transcript_exon_variant,,ENST00000466579,;SDCCAG3,non_coding_transcript_exon_variant,,ENST00000486441,;SDCCAG3,non_coding_transcript_exon_variant,,ENST00000461693,;SDCCAG3,downstream_gene_variant,,ENST00000468963,;SDCCAG3,upstream_gene_variant,,ENST00000481114,;	T	ENSG00000165689	ENST00000357365	Transcript	missense_variant	1245	1115	372	G/D	gGc/gAc	rs762736506	.	.	-1	SDCCAG3	HGNC	10667	protein_coding	YES	CCDS43904.1	ENSP00000349929	SDCG3_HUMAN	.	UPI00006C511A	.	deleterious(0.03)	benign(0.366)	9/10	.	hmmpanther:PTHR31259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGCCGCAC	.	5	ESCA
TTC39B	0	.	GRCh37	9	15307166	15307166	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.156G>C	p.Glu52Asp	p.E52D	ENST00000512701	1/20	43	15	28	64	64	0	TTC39B,missense_variant,p.Glu52Asp,ENST00000512701,;TTC39B,missense_variant,p.Glu52Asp,ENST00000297615,;TTC39B,missense_variant,p.Glu52Asp,ENST00000380850,;TTC39B,missense_variant,p.Glu14Asp,ENST00000506891,;TTC39B,5_prime_UTR_variant,,ENST00000541445,;TTC39B,5_prime_UTR_variant,,ENST00000355694,;TTC39B,non_coding_transcript_exon_variant,,ENST00000505732,;	G	ENSG00000155158	ENST00000512701	Transcript	missense_variant	193	156	52	E/D	gaG/gaC	.	.	.	-1	TTC39B	HGNC	23704	protein_coding	YES	CCDS6477.2	ENSP00000422496	TT39B_HUMAN	.	UPI0001BE810F	.	tolerated_low_confidence(0.42)	benign(0.007)	1/20	.	hmmpanther:PTHR31859,hmmpanther:PTHR31859:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAACTCAGA	.	5	ESCA
RP11-435O5.4	0	.	GRCh37	9	98278926	98278926	+	3'Flank	SNP	G	G	C	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000604650	.	44	9	34	40	40	0	PTCH1,missense_variant,p.Asp59Glu,ENST00000375274,;PTCH1,5_prime_UTR_variant,,ENST00000430669,;PTCH1,5_prime_UTR_variant,,ENST00000468211,;PTCH1,5_prime_UTR_variant,,ENST00000437951,;RP11-435O5.4,downstream_gene_variant,,ENST00000604650,;PTCH1,non_coding_transcript_exon_variant,,ENST00000551425,;PTCH1,missense_variant,p.Asp5Glu,ENST00000551623,;	C	ENSG00000271659	ENST00000604650	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2124	1	RP11-435O5.4	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTGTCTCC	.	5	ESCA
BEX1	0	.	GRCh37	X	102317850	102317850	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.353A>C	p.His118Pro	p.H118P	ENST00000372728	3/3	86	45	40	40	40	0	BEX1,missense_variant,p.His118Pro,ENST00000372728,;	G	ENSG00000133169	ENST00000372728	Transcript	missense_variant	593	353	118	H/P	cAt/cCt	.	.	.	-1	BEX1	HGNC	1036	protein_coding	YES	CCDS35354.1	ENSP00000361813	BEX1_HUMAN	.	UPI0000073F72	.	deleterious(0)	probably_damaging(0.945)	3/3	.	hmmpanther:PTHR19430,Pfam_domain:PF04538,PIRSF_domain:PIRSF008633	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCATGATGG	.	5	ESCA
PDZD4	0	.	GRCh37	X	153095904	153095904	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-151C>T	.	.	ENST00000164640	1/8	13	3	10	10	10	0	PDZD4,5_prime_UTR_variant,,ENST00000164640,;PDZD4,upstream_gene_variant,,ENST00000544474,;PDZD4,upstream_gene_variant,,ENST00000393758,;PDZD4,non_coding_transcript_exon_variant,,ENST00000480418,;PDZD4,upstream_gene_variant,,ENST00000475140,;PDZD4,upstream_gene_variant,,ENST00000468491,;PDZD4,upstream_gene_variant,,ENST00000483693,;PDZD4,upstream_gene_variant,,ENST00000480650,;	A	ENSG00000067840	ENST00000164640	Transcript	5_prime_UTR_variant	42	.	.	.	.	.	.	.	-1	PDZD4	HGNC	21167	protein_coding	YES	CCDS14732.1	ENSP00000164640	PDZD4_HUMAN	Q17RL8_HUMAN	UPI0000211CAA	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCCCCGAGGTG	.	4	ESCA
GK	0	.	GRCh37	X	30747192	30747192	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*333C>T	.	.	ENST00000378943	20/20	8	2	6	10	10	0	GK,3_prime_UTR_variant,,ENST00000378945,;GK,3_prime_UTR_variant,,ENST00000378946,;GK,3_prime_UTR_variant,,ENST00000427190,;GK,3_prime_UTR_variant,,ENST00000378943,;GK-AS1,upstream_gene_variant,,ENST00000464659,;GK,3_prime_UTR_variant,,ENST00000481024,;	T	ENSG00000198814	ENST00000378943	Transcript	3_prime_UTR_variant	2174	.	.	.	.	.	.	.	1	GK	HGNC	4289	protein_coding	YES	CCDS48090.1	ENSP00000368226	GLPK_HUMAN	.	UPI000002AA89	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAATCTTCCA	.	2	ESCA
PLP2	0	.	GRCh37	X	49028406	49028406	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>T	p.Ser20Leu	p.S20L	ENST00000376327	1/5	88	24	64	71	71	0	PLP2,missense_variant,p.Ser20Leu,ENST00000376327,;PLP2,missense_variant,p.Ser20Leu,ENST00000376322,;PRICKLE3,downstream_gene_variant,,ENST00000453382,;PRICKLE3,downstream_gene_variant,,ENST00000536904,;PRICKLE3,downstream_gene_variant,,ENST00000540849,;PRICKLE3,downstream_gene_variant,,ENST00000538114,;PRICKLE3,downstream_gene_variant,,ENST00000376317,;MAGIX,downstream_gene_variant,,ENST00000376338,;	T	ENSG00000102007	ENST00000376327	Transcript	missense_variant	134	59	20	S/L	tCg/tTg	.	.	.	1	PLP2	HGNC	9087	protein_coding	YES	CCDS14319.1	ENSP00000365505	PLP2_HUMAN	.	UPI0000117AEB	.	tolerated(0.95)	benign(0.003)	1/5	.	PROSITE_profiles:PS51225,hmmpanther:PTHR22776,hmmpanther:PTHR22776:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTCGCGCA	.	5	ESCA
IGBP1	0	.	GRCh37	X	69353781	69353781	+	5'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FA-01A-11D-A33E-09	TCGA-JY-A6FA-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-17G>T	.	.	ENST00000342206	1/6	232	162	70	77	77	0	IGBP1,5_prime_UTR_variant,,ENST00000342206,;IGBP1,5_prime_UTR_variant,,ENST00000356413,;MTND4P31,upstream_gene_variant,,ENST00000425607,;	T	ENSG00000089289	ENST00000342206	Transcript	5_prime_UTR_variant	483	.	.	.	.	.	.	.	1	IGBP1	HGNC	5461	protein_coding	YES	CCDS14396.1	ENSP00000363661	IGBP1_HUMAN	.	UPI0000119C1E	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGGTTCCT	.	5	ESCA
DNMBP	0	.	GRCh37	10	101658499	101658499	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2720+1G>C	.	p.X907_splice	ENST00000324109	.	31	26	5	39	39	0	DNMBP,splice_donor_variant,,ENST00000422692,;DNMBP,splice_donor_variant,,ENST00000543621,;DNMBP,splice_donor_variant,,ENST00000324109,;DNMBP,splice_donor_variant,,ENST00000342239,;DNMBP,upstream_gene_variant,,ENST00000540316,;	G	ENSG00000107554	ENST00000324109	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	DNMBP	HGNC	30373	protein_coding	YES	CCDS7485.1	ENSP00000315659	DNMBP_HUMAN	B4E0Q3_HUMAN	UPI000013D6C9	.	.	.	.	8/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTTACCATTC	.	4	ESCA
CPN1	0	.	GRCh37	10	101835810	101835810	+	Missense_Mutation	SNP	C	C	T	rs767897122	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.278G>A	p.Arg93His	p.R93H	ENST00000370418	2/9	28	20	7	41	40	0	CPN1,missense_variant,p.Arg93His,ENST00000370418,;	T	ENSG00000120054	ENST00000370418	Transcript	missense_variant	530	278	93	R/H	cGc/cAc	rs767897122,COSM3806263	.	.	-1	CPN1	HGNC	2312	protein_coding	YES	CCDS7486.1	ENSP00000359446	CBPN_HUMAN	B1AP59_HUMAN,B1AP58_HUMAN	UPI00000012AC	.	deleterious(0)	probably_damaging(1)	2/9	.	hmmpanther:PTHR11532:SF7,hmmpanther:PTHR11532,PROSITE_patterns:PS00132,Pfam_domain:PF00246,Gene3D:3.40.630.10,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCTCGCGGCCC	byFrequency	4	ESCA
WNT8B	0	.	GRCh37	10	102241743	102241743	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442G>C	p.Asp148His	p.D148H	ENST00000343737	5/6	29	24	5	48	48	0	WNT8B,missense_variant,p.Asp148His,ENST00000343737,;SEC31B,downstream_gene_variant,,ENST00000370345,;SEC31B,downstream_gene_variant,,ENST00000462434,;SEC31B,downstream_gene_variant,,ENST00000469546,;SEC31B,downstream_gene_variant,,ENST00000479697,;SEC31B,downstream_gene_variant,,ENST00000485800,;SEC31B,downstream_gene_variant,,ENST00000492667,;SEC31B,downstream_gene_variant,,ENST00000482456,;	C	ENSG00000075290	ENST00000343737	Transcript	missense_variant	570	442	148	D/H	Gat/Cat	.	.	.	1	WNT8B	HGNC	12789	protein_coding	YES	CCDS7494.1	ENSP00000340677	WNT8B_HUMAN	.	UPI000013D6C5	.	deleterious(0)	probably_damaging(0.999)	5/6	.	hmmpanther:PTHR12027:SF94,hmmpanther:PTHR12027,Pfam_domain:PF00110,SMART_domains:SM00097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTCGATGCC	.	4	ESCA
COL17A1	0	.	GRCh37	10	105830296	105830296	+	Silent	SNP	G	G	C	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495C>G	p.%3D	p.L165L	ENST00000353479	9/56	73	60	12	67	67	0	COL17A1,synonymous_variant,p.%3D,ENST00000353479,;COL17A1,synonymous_variant,p.%3D,ENST00000369733,;COL17A1,synonymous_variant,p.%3D,ENST00000393211,;COL17A1,non_coding_transcript_exon_variant,,ENST00000483876,;	C	ENSG00000065618	ENST00000353479	Transcript	synonymous_variant	786	495	165	L	ctC/ctG	COSM1504133	.	.	-1	COL17A1	HGNC	2194	protein_coding	YES	CCDS7554.1	ENSP00000340937	COHA1_HUMAN	.	UPI000006DB58	.	.	.	9/56	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTGAGCAA	.	5	ESCA
SORCS3	0	.	GRCh37	10	107024793	107024793	+	3'UTR	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1661T>A	.	.	ENST00000369701	27/27	65	52	13	72	72	0	SORCS3,3_prime_UTR_variant,,ENST00000369701,;	A	ENSG00000156395	ENST00000369701	Transcript	3_prime_UTR_variant	5557	.	.	.	.	.	.	.	1	SORCS3	HGNC	16699	protein_coding	YES	CCDS7558.1	ENSP00000358715	SORC3_HUMAN	B7Z891_HUMAN	UPI0000135CE1	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCTTTTTT	.	5	ESCA
LINC00710	0	.	GRCh37	10	10986282	10986282	+	RNA	SNP	T	T	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.434A>C	.	.	ENST00000428520	5/6	31	22	9	23	23	0	LINC00710,non_coding_transcript_exon_variant,,ENST00000428520,;LINC00710,non_coding_transcript_exon_variant,,ENST00000600516,;LINC00710,downstream_gene_variant,,ENST00000598573,;LINC00710,downstream_gene_variant,,ENST00000596092,;LINC00710,downstream_gene_variant,,ENST00000601050,;LINC00710,downstream_gene_variant,,ENST00000450174,;	G	ENSG00000229240	ENST00000428520	Transcript	non_coding_transcript_exon_variant	434	.	.	.	.	.	.	.	-1	LINC00710	HGNC	27386	lincRNA	YES	.	.	.	.	.	.	.	.	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACATTTTGAC	.	5	ESCA
PNLIPRP1	0	.	GRCh37	10	118354274	118354274	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363C>G	p.Ile121Met	p.I121M	ENST00000528052	5/13	51	41	10	54	54	0	PNLIPRP1,missense_variant,p.Ile121Met,ENST00000534537,;PNLIPRP1,missense_variant,p.Ile121Met,ENST00000471549,;PNLIPRP1,missense_variant,p.Ile121Met,ENST00000531984,;PNLIPRP1,missense_variant,p.Ile121Met,ENST00000358834,;PNLIPRP1,missense_variant,p.Ile121Met,ENST00000528052,;PNLIPRP1,intron_variant,,ENST00000527980,;PNLIPRP1,intron_variant,,ENST00000530319,;PNLIPRP1,downstream_gene_variant,,ENST00000442761,;PNLIPRP1,downstream_gene_variant,,ENST00000525157,;PNLIPRP1,downstream_gene_variant,,ENST00000510125,;PNLIPRP1,downstream_gene_variant,,ENST00000480870,;PNLIPRP1,missense_variant,p.Ile11Met,ENST00000482833,;PNLIPRP1,3_prime_UTR_variant,,ENST00000497792,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000531825,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525820,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000484402,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000526223,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000529584,;PNLIPRP1,downstream_gene_variant,,ENST00000470678,;PNLIPRP1,downstream_gene_variant,,ENST00000530626,;PNLIPRP1,downstream_gene_variant,,ENST00000482159,;PNLIPRP1,upstream_gene_variant,,ENST00000534513,;	G	ENSG00000187021	ENST00000528052	Transcript	missense_variant	434	363	121	I/M	atC/atG	.	.	.	1	PNLIPRP1	HGNC	9156	protein_coding	YES	CCDS7595.1	ENSP00000433933	LIPR1_HUMAN	E9PR20_HUMAN,E9PMA6_HUMAN	UPI000012E6AA	.	deleterious(0)	possibly_damaging(0.795)	5/13	.	hmmpanther:PTHR11610:SF93,hmmpanther:PTHR11610,Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474,Prints_domain:PR00823,Prints_domain:PR00821	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCATCTGCGT	.	5	ESCA
DMBT1	0	.	GRCh37	10	124396806	124396806	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6533C>T	p.Ser2178Leu	p.S2178L	ENST00000368909	51/53	24	20	4	36	36	0	DMBT1,missense_variant,p.Ser1550Leu,ENST00000368956,;DMBT1,missense_variant,p.Ser898Leu,ENST00000359586,;DMBT1,missense_variant,p.Ser1550Leu,ENST00000330163,;DMBT1,missense_variant,p.Ser2168Leu,ENST00000344338,;DMBT1,missense_variant,p.Ser2168Leu,ENST00000368955,;DMBT1,missense_variant,p.Ser2178Leu,ENST00000368909,;DMBT1,missense_variant,p.Ser2178Leu,ENST00000338354,;	T	ENSG00000187908	ENST00000368909	Transcript	missense_variant	6639	6533	2178	S/L	tCa/tTa	.	.	.	1	DMBT1	HGNC	2926	protein_coding	YES	CCDS44490.1	ENSP00000357905	DMBT1_HUMAN	B6V682_HUMAN	UPI000047021C	.	tolerated(0.06)	benign(0.04)	51/53	.	SMART_domains:SM00241,Pfam_domain:PF00100,PROSITE_profiles:PS51034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTACTCAGGCT	.	4	ESCA
DMBT1P1	0	.	GRCh37	10	124516322	124516322	+	RNA	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.113C>T	.	.	ENST00000439464	1/28	40	31	9	52	52	0	DMBT1P1,non_coding_transcript_exon_variant,,ENST00000439464,;	T	ENSG00000176584	ENST00000439464	Transcript	non_coding_transcript_exon_variant	113	.	.	.	.	.	.	.	1	DMBT1P1	HGNC	49497	processed_transcript	YES	.	.	.	.	.	.	.	.	1/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTCTGGGA	.	5	ESCA
CACNB2	0	.	GRCh37	10	18830178	18830178	+	3'Flank	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000324631	.	50	41	9	34	34	0	CACNB2,3_prime_UTR_variant,,ENST00000396576,;CACNB2,downstream_gene_variant,,ENST00000377328,;CACNB2,downstream_gene_variant,,ENST00000377329,;CACNB2,downstream_gene_variant,,ENST00000324631,;CACNB2,downstream_gene_variant,,ENST00000377315,;CACNB2,downstream_gene_variant,,ENST00000282343,;CACNB2,downstream_gene_variant,,ENST00000377331,;NSUN6,downstream_gene_variant,,ENST00000377304,;CACNB2,downstream_gene_variant,,ENST00000352115,;CACNB2,downstream_gene_variant,,ENST00000377319,;RP11-499P20.2,splice_acceptor_variant,,ENST00000425669,;RP11-499P20.2,downstream_gene_variant,,ENST00000436485,;NSUN6,downstream_gene_variant,,ENST00000493816,;	T	ENSG00000165995	ENST00000324631	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	122	1	CACNB2	HGNC	1402	protein_coding	YES	CCDS7125.1	ENSP00000320025	CACB2_HUMAN	.	UPI00001AEA80	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTCTTCAG	.	4	ESCA
ZNF33A	0	.	GRCh37	10	38344263	38344263	+	Missense_Mutation	SNP	A	A	T	rs775518760	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1211A>T	p.Gln404Leu	p.Q404L	ENST00000374618	5/5	70	55	14	60	60	0	ZNF33A,missense_variant,p.Gln410Leu,ENST00000432900,;ZNF33A,missense_variant,p.Gln403Leu,ENST00000307441,;ZNF33A,missense_variant,p.Gln403Leu,ENST00000458705,;ZNF33A,missense_variant,p.Gln404Leu,ENST00000374618,;ZNF33A,intron_variant,,ENST00000469037,;ZNF33A,downstream_gene_variant,,ENST00000478556,;	T	ENSG00000189180	ENST00000374618	Transcript	missense_variant	1389	1211	404	Q/L	cAg/cTg	rs775518760	.	.	1	ZNF33A	HGNC	13096	protein_coding	YES	CCDS44372.1	ENSP00000363747	ZN33A_HUMAN	.	UPI0000161788	.	deleterious(0.05)	probably_damaging(0.999)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF204,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCAGAGAA	.	5	ESCA
AGAP6	0	.	GRCh37	10	51768798	51768798	+	Missense_Mutation	SNP	G	G	A	rs782699081	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.913G>A	p.Val305Ile	p.V305I	ENST00000412531	8/8	258	211	47	284	282	2	AGAP6,missense_variant,p.Val282Ile,ENST00000374056,;AGAP6,missense_variant,p.Val305Ile,ENST00000412531,;	A	ENSG00000204149	ENST00000412531	Transcript	missense_variant	985	913	305	V/I	Gtc/Atc	rs782699081	.	.	1	AGAP6	HGNC	23466	protein_coding	YES	CCDS44397.1	ENSP00000400972	AGAP6_HUMAN	.	UPI00002288AB	.	deleterious(0.03)	probably_damaging(0.984)	8/8	.	Superfamily_domains:SSF50729,SMART_domains:SM00233,Pfam_domain:PF00169,Gene3D:2.30.29.30,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AATACGTCACC	byFrequency	2	ESCA
OIT3	0	.	GRCh37	10	74684045	74684045	+	Missense_Mutation	SNP	C	C	T	rs780471456	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1010C>T	p.Pro337Leu	p.P337L	ENST00000334011	7/9	43	29	13	65	65	0	OIT3,missense_variant,p.Pro337Leu,ENST00000334011,;	T	ENSG00000138315	ENST00000334011	Transcript	missense_variant	1228	1010	337	P/L	cCg/cTg	rs780471456	.	.	1	OIT3	HGNC	29953	protein_coding	YES	CCDS7318.1	ENSP00000333900	OIT3_HUMAN	.	UPI00000389F9	.	deleterious(0)	probably_damaging(0.971)	7/9	.	PROSITE_profiles:PS51034,hmmpanther:PTHR22962,hmmpanther:PTHR22962:SF131,Pfam_domain:PF00100,SMART_domains:SM00241	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCCCGGGGA	byFrequency	5	ESCA
KCNMA1	0	.	GRCh37	10	78778787	78778787	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1999G>T	p.Ala667Ser	p.A667S	ENST00000404857	17/28	55	46	9	47	47	0	KCNMA1,missense_variant,p.Ala667Ser,ENST00000404857,;KCNMA1,missense_variant,p.Ala671Ser,ENST00000406533,;KCNMA1,missense_variant,p.Ala604Ser,ENST00000372408,;KCNMA1,missense_variant,p.Ala618Ser,ENST00000372403,;KCNMA1,missense_variant,p.Ala667Ser,ENST00000372440,;KCNMA1,missense_variant,p.Ala667Ser,ENST00000286628,;KCNMA1,missense_variant,p.Ala532Ser,ENST00000604624,;KCNMA1,missense_variant,p.Ala602Ser,ENST00000372437,;KCNMA1,missense_variant,p.Ala160Ser,ENST00000450795,;KCNMA1,missense_variant,p.Ala151Ser,ENST00000428546,;KCNMA1,missense_variant,p.Ala667Ser,ENST00000354353,;KCNMA1,missense_variant,p.Ala641Ser,ENST00000457953,;KCNMA1,missense_variant,p.Ala667Ser,ENST00000372443,;KCNMA1,missense_variant,p.Ala667Ser,ENST00000286627,;KCNMA1,missense_variant,p.Ala346Ser,ENST00000434208,;KCNMA1,missense_variant,p.Ala667Ser,ENST00000404771,;KCNMA1,missense_variant,p.Ala641Ser,ENST00000372421,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000475352,;	A	ENSG00000156113	ENST00000404857	Transcript	missense_variant	1999	1999	667	A/S	Gcc/Tcc	.	.	.	-1	KCNMA1	HGNC	6284	protein_coding	YES	CCDS53545.1	ENSP00000385806	KCMA1_HUMAN	.	UPI00003519E8	.	tolerated(0.08)	possibly_damaging(0.809)	17/28	.	hmmpanther:PTHR10027:SF18,hmmpanther:PTHR10027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGGCATCAC	.	5	ESCA
SFTPA2	0	.	GRCh37	10	81319210	81319210	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.30C>T	p.%3D	p.L10L	ENST00000372325	3/6	37	27	10	54	54	0	SFTPA2,synonymous_variant,p.%3D,ENST00000372325,;SFTPA2,synonymous_variant,p.%3D,ENST00000492049,;SFTPA2,synonymous_variant,p.%3D,ENST00000372327,;SFTPA2,synonymous_variant,p.%3D,ENST00000417041,;	A	ENSG00000185303	ENST00000372325	Transcript	synonymous_variant	115	30	10	L	ctC/ctT	.	.	.	-1	SFTPA2	HGNC	10799	protein_coding	YES	CCDS41540.1	ENSP00000361400	SFPA2_HUMAN	R4GMN3_HUMAN,B7Z4Y4_HUMAN	UPI000013CAFF	.	.	.	3/6	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24024:SF13,hmmpanther:PTHR24024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATGAGGGT	.	5	ESCA
DYNC2H1	0	.	GRCh37	11	103055753	103055753	+	Missense_Mutation	SNP	G	G	A	rs765701377	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6606G>A	p.Met2202Ile	p.M2202I	ENST00000398093	41/90	76	55	20	59	59	0	DYNC2H1,missense_variant,p.Met2202Ile,ENST00000398093,;DYNC2H1,missense_variant,p.Met2202Ile,ENST00000375735,;DYNC2H1,intron_variant,,ENST00000334267,;	A	ENSG00000187240	ENST00000398093	Transcript	missense_variant	6606	6606	2202	M/I	atG/atA	rs765701377	.	.	1	DYNC2H1	HGNC	2962	protein_coding	YES	CCDS44717.1	ENSP00000381167	DYHC2_HUMAN	.	UPI0000481AC7	.	.	benign(0)	41/90	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATGAAGTC	.	5	ESCA
PCSK7	0	.	GRCh37	11	117098032	117098032	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>A	p.Glu204Lys	p.E204K	ENST00000320934	5/17	31	21	9	28	28	0	PCSK7,missense_variant,p.Glu204Lys,ENST00000320934,;PCSK7,missense_variant,p.Glu204Lys,ENST00000525027,;PCSK7,downstream_gene_variant,,ENST00000532301,;PCSK7,upstream_gene_variant,,ENST00000540028,;PCSK7,downstream_gene_variant,,ENST00000524507,;PCSK7,downstream_gene_variant,,ENST00000530269,;PCSK7,upstream_gene_variant,,ENST00000528217,;PCSK7,upstream_gene_variant,,ENST00000534529,;	T	ENSG00000160613	ENST00000320934	Transcript	missense_variant	1241	610	204	E/K	Gag/Aag	.	.	.	-1	PCSK7	HGNC	8748	protein_coding	YES	CCDS8382.1	ENSP00000325917	PCSK7_HUMAN	E9PMC0_HUMAN,E9PLM0_HUMAN,E9PIW7_HUMAN,B3KUH2_HUMAN	UPI0000070E4E	.	tolerated(0.21)	benign(0.402)	5/17	.	hmmpanther:PTHR10795:SF9,hmmpanther:PTHR10795,Gene3D:3.40.50.200,Pfam_domain:PF00082,Superfamily_domains:SSF52743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCAGGGC	.	5	ESCA
PVRL1	0	.	GRCh37	11	119545303	119545303	+	Intron	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003+566G>A	.	.	ENST00000264025	.	64	49	15	64	64	0	PVRL1,stop_retained_variant,p.%3D,ENST00000340882,;PVRL1,intron_variant,,ENST00000264025,;PVRL1,intron_variant,,ENST00000341398,;PVRL1,downstream_gene_variant,,ENST00000524510,;PVRL1,non_coding_transcript_exon_variant,,ENST00000524429,;PVRL1,downstream_gene_variant,,ENST00000532197,;	T	ENSG00000110400	ENST00000264025	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PVRL1	HGNC	9706	protein_coding	YES	CCDS8426.1	ENSP00000264025	PVRL1_HUMAN	Q6SYC2_HUMAN	UPI000004A2BE	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAGAAC	.	5	ESCA
PVRL1	0	.	GRCh37	11	119545984	119545984	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.888G>C	p.Gln296His	p.Q296H	ENST00000264025	5/6	74	52	21	73	73	0	PVRL1,missense_variant,p.Gln296His,ENST00000340882,;PVRL1,missense_variant,p.Gln296His,ENST00000264025,;PVRL1,missense_variant,p.Gln296His,ENST00000341398,;PVRL1,downstream_gene_variant,,ENST00000524510,;PVRL1,non_coding_transcript_exon_variant,,ENST00000524429,;PVRL1,downstream_gene_variant,,ENST00000532197,;	G	ENSG00000110400	ENST00000264025	Transcript	missense_variant	1419	888	296	Q/H	caG/caC	.	.	.	-1	PVRL1	HGNC	9706	protein_coding	YES	CCDS8426.1	ENSP00000264025	PVRL1_HUMAN	Q6SYC2_HUMAN	UPI000004A2BE	.	deleterious(0.03)	possibly_damaging(0.545)	5/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23277:SF12,hmmpanther:PTHR23277,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTCTGGGC	.	5	ESCA
SLC17A6	0	.	GRCh37	11	22400825	22400825	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1539C>A	.	.	ENST00000263160	12/12	29	23	6	24	24	0	SLC17A6,3_prime_UTR_variant,,ENST00000263160,;	A	ENSG00000091664	ENST00000263160	Transcript	3_prime_UTR_variant	3725	.	.	.	.	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGCTAGTG	.	5	ESCA
OR52I2	0	.	GRCh37	11	4608080	4608080	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38T>C	p.Ile13Thr	p.I13T	ENST00000312614	1/1	38	32	5	33	33	0	OR52I2,missense_variant,p.Ile13Thr,ENST00000312614,;	C	ENSG00000226288	ENST00000312614	Transcript	missense_variant	60	38	13	I/T	aTa/aCa	.	.	.	1	OR52I2	HGNC	15221	protein_coding	YES	CCDS31355.1	ENSP00000308764	O52I2_HUMAN	.	UPI00003B2880	.	deleterious_low_confidence(0.02)	benign(0.007)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCATACATC	.	5	ESCA
SUV420H1	0	.	GRCh37	11	67934523	67934523	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1100G>A	p.Ser367Asn	p.S367N	ENST00000304363	10/11	52	41	10	61	61	0	SUV420H1,missense_variant,p.Ser367Asn,ENST00000402789,;SUV420H1,missense_variant,p.Ser367Asn,ENST00000405515,;SUV420H1,missense_variant,p.Ser367Asn,ENST00000304363,;SUV420H1,missense_variant,p.Ser344Asn,ENST00000402185,;SUV420H1,missense_variant,p.Ser367Asn,ENST00000401547,;SUV420H1,downstream_gene_variant,,ENST00000533271,;SUV420H1,3_prime_UTR_variant,,ENST00000427752,;SUV420H1,3_prime_UTR_variant,,ENST00000441488,;SUV420H1,downstream_gene_variant,,ENST00000524672,;SUV420H1,downstream_gene_variant,,ENST00000323599,;	T	ENSG00000110066	ENST00000304363	Transcript	missense_variant	1454	1100	367	S/N	aGc/aAc	.	.	.	-1	SUV420H1	HGNC	24283	protein_coding	YES	CCDS31623.1	ENSP00000305899	SV421_HUMAN	E9PKD9_HUMAN,C9JP58_HUMAN,C9JFG1_HUMAN,C9J6S5_HUMAN	UPI00001FADE7	.	tolerated(0.07)	benign(0.013)	10/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12977,hmmpanther:PTHR12977:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTGCTGTCA	.	5	ESCA
RELT	0	.	GRCh37	11	73104900	73104900	+	Missense_Mutation	SNP	G	G	A	rs750370305	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.644G>A	p.Arg215Gln	p.R215Q	ENST00000064780	7/11	42	36	5	48	48	0	RELT,missense_variant,p.Arg215Gln,ENST00000064780,;RELT,missense_variant,p.Arg215Gln,ENST00000393580,;RELT,downstream_gene_variant,,ENST00000545687,;RP11-809N8.2,downstream_gene_variant,,ENST00000544674,;RELT,synonymous_variant,p.%3D,ENST00000544075,;RELT,non_coding_transcript_exon_variant,,ENST00000537771,;RELT,non_coding_transcript_exon_variant,,ENST00000545886,;RELT,non_coding_transcript_exon_variant,,ENST00000539134,;	A	ENSG00000054967	ENST00000064780	Transcript	missense_variant	905	644	215	R/Q	cGg/cAg	rs750370305	.	.	1	RELT	HGNC	13764	protein_coding	YES	CCDS8222.1	ENSP00000064780	TR19L_HUMAN	F5H2T5_HUMAN	UPI000003C9E6	.	tolerated(0.56)	possibly_damaging(0.494)	7/11	.	hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTACCGGACTG	.	4	ESCA
C2CD3	0	.	GRCh37	11	73753117	73753117	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5642C>G	p.Ser1881Cys	p.S1881C	ENST00000313663	29/31	51	37	14	48	48	0	C2CD3,missense_variant,p.Ser689Cys,ENST00000414160,;C2CD3,missense_variant,p.Ser1881Cys,ENST00000313663,;C2CD3,missense_variant,p.Ser1881Cys,ENST00000334126,;C2CD3,missense_variant,p.Ser115Cys,ENST00000538361,;C2CD3,non_coding_transcript_exon_variant,,ENST00000540452,;C2CD3,non_coding_transcript_exon_variant,,ENST00000538625,;C2CD3,missense_variant,p.Ser637Cys,ENST00000442398,;	C	ENSG00000168014	ENST00000313663	Transcript	missense_variant	5869	5642	1881	S/C	tCc/tGc	.	.	.	-1	C2CD3	HGNC	24564	protein_coding	YES	CCDS31636.1	ENSP00000323339	C2CD3_HUMAN	.	UPI0000D62650	.	deleterious(0.01)	probably_damaging(0.967)	29/31	.	hmmpanther:PTHR21254,hmmpanther:PTHR21254:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATGGAGGTT	.	5	ESCA
SERPINH1	0	.	GRCh37	11	75274698	75274698	+	5'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-152C>G	.	.	ENST00000524558	1/5	16	12	4	30	30	0	SERPINH1,5_prime_UTR_variant,,ENST00000524558,;SERPINH1,intron_variant,,ENST00000530284,;SERPINH1,intron_variant,,ENST00000528760,;SERPINH1,intron_variant,,ENST00000533449,;SERPINH1,intron_variant,,ENST00000525492,;SERPINH1,intron_variant,,ENST00000528990,;SERPINH1,intron_variant,,ENST00000533603,;SERPINH1,intron_variant,,ENST00000526397,;SERPINH1,intron_variant,,ENST00000532356,;SERPINH1,intron_variant,,ENST00000525611,;SERPINH1,intron_variant,,ENST00000358171,;SERPINH1,intron_variant,,ENST00000526242,;SERPINH1,intron_variant,,ENST00000529643,;SERPINH1,upstream_gene_variant,,ENST00000525876,;	G	ENSG00000149257	ENST00000524558	Transcript	5_prime_UTR_variant	1284	.	.	.	.	.	.	.	1	SERPINH1	HGNC	1546	protein_coding	YES	CCDS8239.1	ENSP00000434412	SERPH_HUMAN	Q9NPA9_HUMAN,E9PRS3_HUMAN,E9PR70_HUMAN,E9PNX1_HUMAN,E9PMI5_HUMAN,E9PKH2_HUMAN,E9PK86_HUMAN,E9PJH8_HUMAN,E9PIG2_HUMAN,B4DN87_HUMAN	UPI00001271B6	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GTGCCCTCTGC	.	4	ESCA
TAS2R30	0	.	GRCh37	12	11286714	11286714	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.130G>C	p.Val44Leu	p.V44L	ENST00000539585	1/1	68	49	18	69	69	0	TAS2R30,missense_variant,p.Val44Leu,ENST00000539585,;TAS2R14,intron_variant,,ENST00000381852,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000546265,;PRR4,intron_variant,,ENST00000541175,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;	G	ENSG00000256188	ENST00000539585	Transcript	missense_variant	530	130	44	V/L	Gtt/Ctt	.	.	.	-1	TAS2R30	HGNC	19112	protein_coding	YES	CCDS53750.1	ENSP00000444736	.	Q50KG7_HUMAN	UPI000006202F	.	deleterious(0.03)	benign(0.061)	1/1	.	hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF48,Pfam_domain:PF05296,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAACAAAGG	.	5	ESCA
PLBD2	0	.	GRCh37	12	113824744	113824744	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1289C>T	p.Ser430Phe	p.S430F	ENST00000280800	10/12	26	16	9	30	30	0	PLBD2,missense_variant,p.Ser430Phe,ENST00000280800,;PLBD2,missense_variant,p.Ser398Phe,ENST00000545182,;	T	ENSG00000151176	ENST00000280800	Transcript	missense_variant	1320	1289	430	S/F	tCc/tTc	.	.	.	1	PLBD2	HGNC	27283	protein_coding	YES	CCDS9168.1	ENSP00000280800	PLBL2_HUMAN	.	UPI000013DC40	.	tolerated(0.23)	benign(0.004)	10/12	.	hmmpanther:PTHR12370:SF3,hmmpanther:PTHR12370,Pfam_domain:PF04916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGTCCTTCG	.	5	ESCA
SLC6A13	0	.	GRCh37	12	369020	369020	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199G>A	p.Gly67Arg	p.G67R	ENST00000343164	2/15	32	29	3	36	36	0	SLC6A13,missense_variant,p.Gly67Arg,ENST00000436453,;SLC6A13,missense_variant,p.Gly67Arg,ENST00000343164,;SLC6A13,missense_variant,p.Gly67Arg,ENST00000546319,;SLC6A13,missense_variant,p.Gly67Arg,ENST00000445055,;RP11-283I3.4,upstream_gene_variant,,ENST00000540868,;SLC6A13,missense_variant,p.Gly67Arg,ENST00000539260,;SLC6A13,non_coding_transcript_exon_variant,,ENST00000536842,;SLC6A13,intron_variant,,ENST00000542272,;	T	ENSG00000010379	ENST00000343164	Transcript	missense_variant	252	199	67	G/R	Gga/Aga	.	.	.	-1	SLC6A13	HGNC	11046	protein_coding	YES	CCDS8502.1	ENSP00000339260	S6A13_HUMAN	.	UPI0000046060	.	deleterious(0)	probably_damaging(0.996)	2/15	.	Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_patterns:PS00610,hmmpanther:PTHR11616:SF111,hmmpanther:PTHR11616,PROSITE_profiles:PS50267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCTCCCCCAT	.	2	ESCA
KMT2D	0	.	GRCh37	12	49422901	49422901	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14194C>T	p.Gln4732Ter	p.Q4732*	ENST00000301067	44/54	25	20	5	56	56	0	KMT2D,stop_gained,p.Gln4732Ter,ENST00000301067,;KMT2D,upstream_gene_variant,,ENST00000526209,;KMT2D,downstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	stop_gained	14194	14194	4732	Q/*	Caa/Taa	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	44/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTGCTCCC	.	5	ESCA
KMT2D	0	.	GRCh37	12	49422902	49422902	+	Missense_Mutation	SNP	C	C	A	rs368920289	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14193G>T	p.Glu4731Asp	p.E4731D	ENST00000301067	44/54	25	20	5	56	56	0	KMT2D,missense_variant,p.Glu4731Asp,ENST00000301067,;KMT2D,upstream_gene_variant,,ENST00000526209,;KMT2D,downstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	missense_variant	14193	14193	4731	E/D	gaG/gaT	rs368920289	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	unknown(0)	44/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	T:0.0008	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTGCTCCCA	byFrequency|byCluster	5	ESCA
ZNF385A	0	.	GRCh37	12	54767829	54767829	+	Missense_Mutation	SNP	C	C	T	rs201286538	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349G>A	p.Val117Ile	p.V117I	ENST00000338010	4/8	58	42	15	76	76	0	ZNF385A,missense_variant,p.Val97Ile,ENST00000546970,;ZNF385A,missense_variant,p.Val60Ile,ENST00000550120,;ZNF385A,missense_variant,p.Val97Ile,ENST00000551771,;ZNF385A,missense_variant,p.Val117Ile,ENST00000338010,;ZNF385A,missense_variant,p.Val80Ile,ENST00000549962,;ZNF385A,missense_variant,p.Val117Ile,ENST00000352268,;ZNF385A,missense_variant,p.Val97Ile,ENST00000550774,;ZNF385A,missense_variant,p.Val79Ile,ENST00000549937,;ZNF385A,missense_variant,p.Val97Ile,ENST00000546919,;ZNF385A,missense_variant,p.Val97Ile,ENST00000547210,;ZNF385A,missense_variant,p.Val97Ile,ENST00000551109,;ZNF385A,missense_variant,p.Val97Ile,ENST00000394313,;RP11-753H16.5,intron_variant,,ENST00000552785,;RP11-753H16.3,intron_variant,,ENST00000550474,;ZNF385A,non_coding_transcript_exon_variant,,ENST00000551864,;ZNF385A,non_coding_transcript_exon_variant,,ENST00000552382,;ZNF385A,missense_variant,p.Val82Ile,ENST00000550779,;	T	ENSG00000161642	ENST00000338010	Transcript	missense_variant	403	349	117	V/I	Gtc/Atc	rs201286538	.	.	-1	ZNF385A	HGNC	17521	protein_coding	YES	CCDS44911.1	ENSP00000338927	Z385A_HUMAN	F8VWV6_HUMAN,F8VSJ1_HUMAN,F8VRY0_HUMAN	UPI00005A791C	.	tolerated(0.18)	benign(0.003)	4/8	.	hmmpanther:PTHR23067:SF13,hmmpanther:PTHR23067	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGACGCCAG	byFrequency|byCluster	5	ESCA
MDM2	0	.	GRCh37	12	69202252	69202252	+	5'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-6C>T	.	.	ENST00000462284	1/11	96	75	21	119	119	0	MDM2,5_prime_UTR_variant,,ENST00000540827,;MDM2,5_prime_UTR_variant,,ENST00000393412,;MDM2,5_prime_UTR_variant,,ENST00000258149,;MDM2,5_prime_UTR_variant,,ENST00000258148,;MDM2,5_prime_UTR_variant,,ENST00000462284,;MDM2,5_prime_UTR_variant,,ENST00000356290,;MDM2,5_prime_UTR_variant,,ENST00000428863,;MDM2,upstream_gene_variant,,ENST00000393415,;MDM2,upstream_gene_variant,,ENST00000393416,;MDM2,upstream_gene_variant,,ENST00000393413,;MDM2,upstream_gene_variant,,ENST00000348801,;MDM2,upstream_gene_variant,,ENST00000517852,;MDM2,upstream_gene_variant,,ENST00000350057,;MDM2,upstream_gene_variant,,ENST00000393410,;MDM2,upstream_gene_variant,,ENST00000299252,;MDM2,upstream_gene_variant,,ENST00000544561,;MDM2,upstream_gene_variant,,ENST00000360430,;MDM2,upstream_gene_variant,,ENST00000545204,;MDM2,upstream_gene_variant,,ENST00000539479,;MDM2,upstream_gene_variant,,ENST00000478070,;MDM2,upstream_gene_variant,,ENST00000543323,;MDM2,upstream_gene_variant,,ENST00000523991,;MDM2,5_prime_UTR_variant,,ENST00000311420,;MDM2,5_prime_UTR_variant,,ENST00000393417,;MDM2,non_coding_transcript_exon_variant,,ENST00000493419,;MDM2,upstream_gene_variant,,ENST00000542502,;MDM2,upstream_gene_variant,,ENST00000546048,;MDM2,upstream_gene_variant,,ENST00000537182,;MDM2,upstream_gene_variant,,ENST00000540352,;MDM2,upstream_gene_variant,,ENST00000496959,;MDM2,upstream_gene_variant,,ENST00000481186,;MDM2,upstream_gene_variant,,ENST00000536089,;RP11-611O2.2,upstream_gene_variant,,ENST00000541551,;	T	ENSG00000135679	ENST00000462284	Transcript	5_prime_UTR_variant	297	.	.	.	.	.	.	.	1	MDM2	HGNC	6973	protein_coding	YES	CCDS8986.2	ENSP00000417281	MDM2_HUMAN	Q546E6_HUMAN,A8WFP2_HUMAN,A7UKY0_HUMAN	UPI00006CA35C	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAACCCCGG	.	5	ESCA
FOXJ2	0	.	GRCh37	12	8201390	8201390	+	Silent	SNP	C	C	T	rs751542947	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1323C>T	p.%3D	p.F441F	ENST00000162391	8/11	34	26	7	28	28	0	FOXJ2,synonymous_variant,p.%3D,ENST00000428177,;FOXJ2,synonymous_variant,p.%3D,ENST00000162391,;FOXJ2,upstream_gene_variant,,ENST00000539192,;	T	ENSG00000065970	ENST00000162391	Transcript	synonymous_variant	2468	1323	441	F	ttC/ttT	rs751542947	.	.	1	FOXJ2	HGNC	24818	protein_coding	YES	CCDS8587.1	ENSP00000162391	FOXJ2_HUMAN	.	UPI000012ADE1	.	.	.	8/11	.	hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATTCTCAGG	byFrequency	5	ESCA
MIPEP	0	.	GRCh37	13	24443488	24443488	+	Missense_Mutation	SNP	C	C	A	rs748903423	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.886G>T	p.Val296Leu	p.V296L	ENST00000382172	7/19	47	37	9	74	74	0	MIPEP,missense_variant,p.Val296Leu,ENST00000382172,;MIPEP,non_coding_transcript_exon_variant,,ENST00000494139,;	A	ENSG00000027001	ENST00000382172	Transcript	missense_variant	985	886	296	V/L	Gtg/Ttg	rs748903423	.	.	-1	MIPEP	HGNC	7104	protein_coding	YES	CCDS9303.1	ENSP00000371607	MIPEP_HUMAN	.	UPI000013C54A	.	tolerated(0.12)	benign(0.147)	7/19	.	hmmpanther:PTHR11804:SF5,hmmpanther:PTHR11804,Gene3D:2o36A02,Pfam_domain:PF01432,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCACCAACT	.	5	ESCA
MAB21L1	0	.	GRCh37	13	36048544	36048544	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*652C>G	.	.	ENST00000379919	1/1	63	46	16	104	104	0	MAB21L1,3_prime_UTR_variant,,ENST00000379919,;NBEA,intron_variant,,ENST00000400445,;NBEA,intron_variant,,ENST00000540320,;NBEA,intron_variant,,ENST00000310336,;NBEA,intron_variant,,ENST00000379939,;NBEA,upstream_gene_variant,,ENST00000537702,;	C	ENSG00000180660	ENST00000379919	Transcript	3_prime_UTR_variant	2289	.	.	.	.	.	.	.	-1	MAB21L1	HGNC	6757	protein_coding	YES	CCDS9353.1	ENSP00000369251	MB211_HUMAN	F1T0A2_HUMAN	UPI0000022CD2	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTAGAAATA	.	5	ESCA
PCDH17	0	.	GRCh37	13	58299063	58299063	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3115C>A	p.Pro1039Thr	p.P1039T	ENST00000377918	4/4	16	12	4	29	29	0	PCDH17,missense_variant,p.Pro1039Thr,ENST00000377918,;PCDH17,3_prime_UTR_variant,,ENST00000484979,;	A	ENSG00000118946	ENST00000377918	Transcript	missense_variant	3141	3115	1039	P/T	Cca/Aca	.	.	.	1	PCDH17	HGNC	14267	protein_coding	YES	CCDS31986.1	ENSP00000367151	PCD17_HUMAN	.	UPI00001FCE5B	.	deleterious_low_confidence(0.01)	possibly_damaging(0.573)	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GCAGCCCAACC	.	2	ESCA
IGHV4-4	0	.	GRCh37	14	106478365	106478365	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.93G>A	p.%3D	p.V31V	ENST00000390596	2/2	71	32	39	87	87	0	IGHV4-4,synonymous_variant,p.%3D,ENST00000390596,;	T	ENSG00000211936	ENST00000390596	Transcript	synonymous_variant	157	93	31	V	gtG/gtA	.	.	.	-1	IGHV4-4	HGNC	5652	IG_V_gene	YES	.	ENSP00000375005	.	.	UPI0000115FF0	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF86,Gene3D:2.60.40.10,Pfam_domain:PF07686,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCACCAG	.	5	ESCA
RNASE2	0	.	GRCh37	14	21424157	21424157	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227C>A	p.Ala76Asp	p.A76D	ENST00000304625	2/2	35	21	14	70	70	0	RNASE2,missense_variant,p.Ala76Asp,ENST00000304625,;	A	ENSG00000169385	ENST00000304625	Transcript	missense_variant	317	227	76	A/D	gCt/gAt	.	.	.	1	RNASE2	HGNC	10045	protein_coding	YES	CCDS9561.1	ENSP00000303276	RNAS2_HUMAN	.	UPI000004D2F8	.	deleterious(0.05)	probably_damaging(0.963)	2/2	.	Prints_domain:PR00794,Superfamily_domains:SSF54076,SMART_domains:SM00092,Pfam_domain:PF00074,Gene3D:3.10.130.10,hmmpanther:PTHR11437,hmmpanther:PTHR11437:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGCTAACG	.	5	ESCA
PRMT5	0	.	GRCh37	14	23392262	23392262	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1483G>A	p.Glu495Lys	p.E495K	ENST00000324366	13/17	30	18	11	35	35	0	PRMT5,missense_variant,p.Glu38Lys,ENST00000454731,;PRMT5,missense_variant,p.Glu495Lys,ENST00000324366,;PRMT5,missense_variant,p.Glu389Lys,ENST00000538452,;PRMT5,missense_variant,p.Glu434Lys,ENST00000216350,;PRMT5,missense_variant,p.Glu324Lys,ENST00000397440,;PRMT5,missense_variant,p.Glu478Lys,ENST00000397441,;PRMT5,missense_variant,p.Glu451Lys,ENST00000553897,;PRMT5,missense_variant,p.Glu94Lys,ENST00000555454,;PRMT5,downstream_gene_variant,,ENST00000421938,;RBM23,upstream_gene_variant,,ENST00000359890,;PRMT5,downstream_gene_variant,,ENST00000554910,;PRMT5,downstream_gene_variant,,ENST00000553502,;RBM23,upstream_gene_variant,,ENST00000554618,;RBM23,upstream_gene_variant,,ENST00000555722,;PRMT5,downstream_gene_variant,,ENST00000556043,;RBM23,upstream_gene_variant,,ENST00000556862,;PRMT5,downstream_gene_variant,,ENST00000554867,;RBM23,upstream_gene_variant,,ENST00000346528,;RBM23,upstream_gene_variant,,ENST00000557227,;PRMT5,downstream_gene_variant,,ENST00000555530,;RBM23,upstream_gene_variant,,ENST00000555676,;RBM23,upstream_gene_variant,,ENST00000555209,;RBM23,upstream_gene_variant,,ENST00000557549,;RBM23,upstream_gene_variant,,ENST00000542016,;RBM23,upstream_gene_variant,,ENST00000399922,;PRMT5,downstream_gene_variant,,ENST00000556616,;PRMT5,downstream_gene_variant,,ENST00000553550,;RBM23,upstream_gene_variant,,ENST00000557403,;PRMT5,upstream_gene_variant,,ENST00000557443,;RBM23,upstream_gene_variant,,ENST00000554256,;RBM23,upstream_gene_variant,,ENST00000557571,;RBM23,upstream_gene_variant,,ENST00000557464,;PRMT5-AS1,non_coding_transcript_exon_variant,,ENST00000609885,;PRMT5-AS1,non_coding_transcript_exon_variant,,ENST00000595662,;PRMT5-AS1,non_coding_transcript_exon_variant,,ENST00000424245,;PRMT5-AS1,non_coding_transcript_exon_variant,,ENST00000587245,;PRMT5-AS1,intron_variant,,ENST00000599580,;PRMT5-AS1,intron_variant,,ENST00000590290,;PRMT5-AS1,intron_variant,,ENST00000457443,;PRMT5,downstream_gene_variant,,ENST00000553641,;RBM23,upstream_gene_variant,,ENST00000556365,;RBM23,upstream_gene_variant,,ENST00000555714,;RBM23,upstream_gene_variant,,ENST00000553920,;PRMT5,downstream_gene_variant,,ENST00000554716,;PRMT5,upstream_gene_variant,,ENST00000476175,;RBM23,upstream_gene_variant,,ENST00000556984,;RBM23,upstream_gene_variant,,ENST00000553777,;PRMT5,splice_region_variant,,ENST00000553915,;PRMT5,upstream_gene_variant,,ENST00000557758,;RBM23,upstream_gene_variant,,ENST00000557667,;PRMT5,downstream_gene_variant,,ENST00000556032,;RBM23,upstream_gene_variant,,ENST00000553902,;RBM23,upstream_gene_variant,,ENST00000307814,;RBM23,upstream_gene_variant,,ENST00000556687,;RBM23,upstream_gene_variant,,ENST00000554955,;PRMT5,downstream_gene_variant,,ENST00000557415,;PRMT5,downstream_gene_variant,,ENST00000553787,;PRMT5,downstream_gene_variant,,ENST00000553417,;	T	ENSG00000100462	ENST00000324366	Transcript	missense_variant	1707	1483	495	E/K	Gag/Aag	.	.	.	-1	PRMT5	HGNC	10894	protein_coding	YES	CCDS9579.1	ENSP00000319169	ANM5_HUMAN	G3V5T6_HUMAN,G3V5L5_HUMAN,B4DV00_HUMAN	UPI000006F09F	.	tolerated(0.33)	possibly_damaging(0.544)	13/17	.	Superfamily_domains:SSF53335,PIRSF_domain:PIRSF015894,Pfam_domain:PF05185,hmmpanther:PTHR10738,PROSITE_profiles:PS51678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCAGGGT	.	5	ESCA
DACT1	0	.	GRCh37	14	59112640	59112641	+	Frame_Shift_Del	DEL	GC	GC	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	GC	GC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1299_1300delGCinsA	p.Leu435CysfsTer72	p.L435Cfs*72	ENST00000335867	4/4	65	35	30	44	44	0	DACT1,frameshift_variant,p.Leu435CysfsTer72,ENST00000335867,;DACT1,frameshift_variant,p.Leu398CysfsTer72,ENST00000395153,;DACT1,frameshift_variant,p.Leu154CysfsTer72,ENST00000556859,;DACT1,frameshift_variant,p.Leu154CysfsTer72,ENST00000541264,;DACT1,downstream_gene_variant,,ENST00000421793,;DACT1,downstream_gene_variant,,ENST00000555845,;	A	ENSG00000165617	ENST00000335867	Transcript	frameshift_variant	1323-1324	1299-1300	433-434	VP/VX	gtGCcc/gtAcc	.	.	.	1	DACT1	HGNC	17748	protein_coding	YES	CCDS9736.1	ENSP00000337439	DACT1_HUMAN	Q5DM88_HUMAN,C9JGV7_HUMAN,B7Z673_HUMAN	UPI000013E4D3	.	.	.	4/4	.	hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF12,Pfam_domain:PF15268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	GAGGGTGCCCCTG	.	5	ESCA
ADCK1	0	.	GRCh37	14	78399710	78399710	+	Silent	SNP	C	C	T	rs746988905	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1548C>T	p.%3D	p.C516C	ENST00000238561	11/11	45	42	3	43	43	0	ADCK1,synonymous_variant,p.%3D,ENST00000238561,;ADCK1,synonymous_variant,p.%3D,ENST00000341211,;ADCK1,non_coding_transcript_exon_variant,,ENST00000556560,;ADCK1,non_coding_transcript_exon_variant,,ENST00000555217,;	T	ENSG00000063761	ENST00000238561	Transcript	synonymous_variant	1647	1548	516	C	tgC/tgT	rs746988905	.	.	1	ADCK1	HGNC	19038	protein_coding	YES	CCDS9869.1	ENSP00000238561	ADCK1_HUMAN	.	UPI000014035F	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATATGCTGGCT	byFrequency	2	ESCA
RPUSD2	0	.	GRCh37	15	40861732	40861732	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196G>C	p.Glu66Gln	p.E66Q	ENST00000315616	1/3	34	27	7	58	58	0	RPUSD2,missense_variant,p.Glu66Gln,ENST00000559271,;RPUSD2,missense_variant,p.Glu66Gln,ENST00000315616,;C15orf57,upstream_gene_variant,,ENST00000560305,;C15orf57,upstream_gene_variant,,ENST00000558871,;C15orf57,upstream_gene_variant,,ENST00000416810,;C15orf57,upstream_gene_variant,,ENST00000558113,;C15orf57,upstream_gene_variant,,ENST00000358005,;C15orf57,upstream_gene_variant,,ENST00000559103,;C15orf57,upstream_gene_variant,,ENST00000558750,;C15orf57,upstream_gene_variant,,ENST00000561011,;C15orf57,upstream_gene_variant,,ENST00000558918,;C15orf57,upstream_gene_variant,,ENST00000559911,;C15orf57,upstream_gene_variant,,ENST00000560109,;C15orf57,upstream_gene_variant,,ENST00000559291,;	C	ENSG00000166133	ENST00000315616	Transcript	missense_variant	234	196	66	E/Q	Gag/Cag	.	.	.	1	RPUSD2	HGNC	24180	protein_coding	YES	CCDS10061.1	ENSP00000323288	RUSD2_HUMAN	B4DWW6_HUMAN	UPI0000163919	.	deleterious_low_confidence(0.05)	benign(0.221)	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTGAGCTG	.	5	ESCA
MYO5A	0	.	GRCh37	15	52676452	52676452	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1820C>T	p.Ser607Leu	p.S607L	ENST00000399231	15/41	69	55	14	79	79	0	MYO5A,missense_variant,p.Ser607Leu,ENST00000358212,;MYO5A,missense_variant,p.Ser607Leu,ENST00000399231,;MYO5A,missense_variant,p.Ser607Leu,ENST00000399233,;MYO5A,missense_variant,p.Ser607Leu,ENST00000356338,;MYO5A,missense_variant,p.Ser607Leu,ENST00000553916,;MYO5A,3_prime_UTR_variant,,ENST00000556196,;MYO5A,downstream_gene_variant,,ENST00000469611,;	A	ENSG00000197535	ENST00000399231	Transcript	missense_variant	2064	1820	607	S/L	tCa/tTa	.	.	.	-1	MYO5A	HGNC	7602	protein_coding	YES	CCDS42037.1	ENSP00000382177	MYO5A_HUMAN	Q9UES4_HUMAN	UPI0000E445E1	.	tolerated(0.08)	benign(0.186)	15/41	.	Superfamily_domains:SSF52540,SMART_domains:SM00242,Pfam_domain:PF00063,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF273,PROSITE_profiles:PS51456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTGAGGAG	.	5	ESCA
ADAM10	0	.	GRCh37	15	58925538	58925538	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1033G>T	p.Glu345Ter	p.E345*	ENST00000260408	9/16	49	37	11	45	45	0	ADAM10,stop_gained,p.Glu44Ter,ENST00000559053,;ADAM10,stop_gained,p.Glu345Ter,ENST00000260408,;ADAM10,stop_gained,p.Glu44Ter,ENST00000396140,;ADAM10,stop_gained,p.Glu44Ter,ENST00000402627,;ADAM10,intron_variant,,ENST00000561288,;ADAM10,upstream_gene_variant,,ENST00000475898,;ADAM10,3_prime_UTR_variant,,ENST00000396136,;	A	ENSG00000137845	ENST00000260408	Transcript	stop_gained	1477	1033	345	E/*	Gaa/Taa	.	.	.	-1	ADAM10	HGNC	188	protein_coding	YES	CCDS10167.1	ENSP00000260408	ADA10_HUMAN	.	UPI00001254C8	.	.	.	9/16	.	PROSITE_profiles:PS50215,hmmpanther:PTHR11905:SF113,hmmpanther:PTHR11905,Gene3D:3.40.390.10,Pfam_domain:PF13574,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCACATA	.	5	ESCA
TLN2	0	.	GRCh37	15	62945485	62945485	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.489G>T	p.Leu163Phe	p.L163F	ENST00000561311	6/58	51	42	9	40	40	0	TLN2,missense_variant,p.Leu163Phe,ENST00000561311,;TLN2,missense_variant,p.Leu163Phe,ENST00000306829,;TLN2,non_coding_transcript_exon_variant,,ENST00000474847,;	T	ENSG00000171914	ENST00000561311	Transcript	missense_variant	719	489	163	L/F	ttG/ttT	.	.	.	1	TLN2	HGNC	15447	protein_coding	YES	CCDS32261.1	ENSP00000453508	TLN2_HUMAN	.	UPI00001FE5FC	.	deleterious(0.04)	probably_damaging(0.995)	6/58	.	SMART_domains:SM00295,Pfam_domain:PF09379,hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF15,PROSITE_profiles:PS50057	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTGAAGGC	.	5	ESCA
PARP16	0	.	GRCh37	15	65553309	65553309	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.747C>G	p.Asp249Glu	p.D249E	ENST00000261888	5/6	33	29	4	49	49	0	PARP16,missense_variant,p.Asp249Glu,ENST00000261888,;PARP16,missense_variant,p.Asp134Glu,ENST00000444347,;PARP16,non_coding_transcript_exon_variant,,ENST00000560149,;PARP16,missense_variant,p.Asp13Glu,ENST00000559805,;	C	ENSG00000138617	ENST00000261888	Transcript	missense_variant	1193	747	249	D/E	gaC/gaG	.	.	.	-1	PARP16	HGNC	26040	protein_coding	YES	CCDS10204.1	ENSP00000261888	PAR16_HUMAN	.	UPI000035079D	.	tolerated(0.37)	benign(0.007)	5/6	.	PROSITE_profiles:PS51059,hmmpanther:PTHR21328,Gene3D:3.90.228.10,Pfam_domain:PF00644,Superfamily_domains:SSF56399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGATGTCTCC	.	4	ESCA
RPP25	0	.	GRCh37	15	75248376	75248376	+	Silent	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549G>C	p.%3D	p.A183A	ENST00000322177	1/1	31	25	6	45	45	0	RPP25,synonymous_variant,p.%3D,ENST00000499788,;RPP25,synonymous_variant,p.%3D,ENST00000322177,;SCAMP5,upstream_gene_variant,,ENST00000568423,;	G	ENSG00000178718	ENST00000322177	Transcript	synonymous_variant	1430	549	183	A	gcG/gcC	.	.	.	-1	RPP25	HGNC	30361	protein_coding	YES	CCDS10274.1	ENSP00000317691	RPP25_HUMAN	.	UPI0000072730	.	.	.	1/1	.	hmmpanther:PTHR13516:SF1,hmmpanther:PTHR13516	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTTCGCGGA	.	5	ESCA
RGMA	0	.	GRCh37	15	93595305	93595305	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.587C>T	p.Pro196Leu	p.P196L	ENST00000557301	3/4	32	22	10	50	50	0	RGMA,missense_variant,p.Pro172Leu,ENST00000556087,;RGMA,missense_variant,p.Pro79Leu,ENST00000538818,;RGMA,missense_variant,p.Pro196Leu,ENST00000557301,;RGMA,missense_variant,p.Pro79Leu,ENST00000556658,;RGMA,missense_variant,p.Pro172Leu,ENST00000425933,;RGMA,missense_variant,p.Pro188Leu,ENST00000329082,;RGMA,missense_variant,p.Pro172Leu,ENST00000542321,;RGMA,missense_variant,p.Pro172Leu,ENST00000543599,;RGMA,intron_variant,,ENST00000557420,;RGMA,downstream_gene_variant,,ENST00000555598,;RGMA,downstream_gene_variant,,ENST00000555584,;RGMA,3_prime_UTR_variant,,ENST00000554387,;	A	ENSG00000182175	ENST00000557301	Transcript	missense_variant	694	587	196	P/L	cCg/cTg	.	.	.	-1	RGMA	HGNC	30308	protein_coding	YES	CCDS53974.1	ENSP00000452126	.	G3V518_HUMAN,G3V4C2_HUMAN,F5H7G2_HUMAN,F5GZU6_HUMAN	UPI0002065681	.	deleterious(0)	probably_damaging(1)	3/4	.	Pfam_domain:PF06535,hmmpanther:PTHR31428,hmmpanther:PTHR31428:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGCGGCCAG	.	5	ESCA
SSTR5	0	.	GRCh37	16	1129139	1129140	+	In_Frame_Ins	INS	-	-	TGT	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.273_274insTTG	p.Leu91dup	p.L91dup	ENST00000293897	1/1	41	30	11	47	47	0	SSTR5,inframe_insertion,p.Leu91dup,ENST00000293897,;SSTR5,inframe_insertion,p.Leu91dup,ENST00000562758,;SSTR5,inframe_insertion,p.Leu91dup,ENST00000397547,;SSTR5-AS1,upstream_gene_variant,,ENST00000569832,;SSTR5-AS1,upstream_gene_variant,,ENST00000566499,;	TGT	ENSG00000162009	ENST00000293897	Transcript	inframe_insertion	359-360	271-272	91	L/LL	ctg/cTGTtg	.	.	.	1	SSTR5	HGNC	11334	protein_coding	YES	CCDS10429.1	ENSP00000293897	SSR5_HUMAN	.	UPI00000015DC	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229:SF20,hmmpanther:PTHR24229,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACATGCTGGGG	.	3	ESCA
KIF22	0	.	GRCh37	16	29808316	29808316	+	Missense_Mutation	SNP	C	C	T	rs150774671	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.173C>T	p.Ala58Val	p.A58V	ENST00000160827	2/14	36	33	3	40	40	0	KIF22,missense_variant,p.Ala58Val,ENST00000160827,;KIF22,5_prime_UTR_variant,,ENST00000561482,;KIF22,5_prime_UTR_variant,,ENST00000400751,;KIF22,5_prime_UTR_variant,,ENST00000569382,;KIF22,5_prime_UTR_variant,,ENST00000400750,;KIF22,5_prime_UTR_variant,,ENST00000569636,;KIF22,upstream_gene_variant,,ENST00000563263,;KIF22,missense_variant,p.Ala58Val,ENST00000570173,;KIF22,non_coding_transcript_exon_variant,,ENST00000563666,;	T	ENSG00000079616	ENST00000160827	Transcript	missense_variant	213	173	58	A/V	gCg/gTg	rs150774671	.	.	1	KIF22	HGNC	6391	protein_coding	YES	CCDS10653.1	ENSP00000160827	KIF22_HUMAN	Q14985_HUMAN,H3BTH5_HUMAN,H3BQB9_HUMAN	UPI00000012C0	.	tolerated(0.26)	benign(0.183)	2/14	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF171,hmmpanther:PTHR24115,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0018	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AACAGCGGGAG	byCluster|by1000G	2	ESCA
CHD9	0	.	GRCh37	16	53243720	53243720	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1779A>C	p.Lys593Asn	p.K593N	ENST00000566029	3/39	10	5	4	11	11	0	CHD9,missense_variant,p.Lys593Asn,ENST00000566029,;CHD9,missense_variant,p.Lys593Asn,ENST00000564845,;CHD9,missense_variant,p.Lys86Asn,ENST00000565442,;CHD9,missense_variant,p.Lys593Asn,ENST00000565832,;CHD9,missense_variant,p.Lys119Asn,ENST00000565803,;CHD9,missense_variant,p.Lys593Asn,ENST00000447540,;CHD9,missense_variant,p.Lys593Asn,ENST00000398510,;CHD9,non_coding_transcript_exon_variant,,ENST00000569794,;CHD9,non_coding_transcript_exon_variant,,ENST00000562791,;CHD9,non_coding_transcript_exon_variant,,ENST00000564255,;	C	ENSG00000177200	ENST00000566029	Transcript	missense_variant	1988	1779	593	K/N	aaA/aaC	.	.	.	1	CHD9	HGNC	25701	protein_coding	YES	CCDS45485.1	ENSP00000457466	CHD9_HUMAN	H3BV31_HUMAN,H3BSP3_HUMAN,H3BRU9_HUMAN	UPI00001FF1A0	.	.	probably_damaging(0.939)	3/39	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACAAAAATTGG	.	3	ESCA
CDH11	0	.	GRCh37	16	65025827	65025827	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.655A>T	p.Thr219Ser	p.T219S	ENST00000268603	6/13	68	53	15	66	66	0	CDH11,missense_variant,p.Thr219Ser,ENST00000567934,;CDH11,missense_variant,p.Thr219Ser,ENST00000394156,;CDH11,missense_variant,p.Thr219Ser,ENST00000268603,;CDH11,missense_variant,p.Thr93Ser,ENST00000566827,;CDH11,non_coding_transcript_exon_variant,,ENST00000569128,;	A	ENSG00000140937	ENST00000268603	Transcript	missense_variant	1271	655	219	T/S	Aca/Tca	.	.	.	-1	CDH11	HGNC	1750	protein_coding	YES	CCDS10803.1	ENSP00000268603	CAD11_HUMAN	H3BUU9_HUMAN,H3BSM4_HUMAN,H3BR78_HUMAN,H3BQH2_HUMAN,H3BQB5_HUMAN,H3BPQ2_HUMAN,H3BP26_HUMAN	UPI000013D7C5	.	deleterious(0)	possibly_damaging(0.504)	6/13	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF85,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGTTCTGA	.	5	ESCA
RLTPR	0	.	GRCh37	16	67682606	67682606	+	Silent	SNP	C	C	T	rs771671329	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1458C>T	p.%3D	p.L486L	ENST00000334583	16/38	19	15	4	30	30	0	RLTPR,synonymous_variant,p.%3D,ENST00000334583,;RLTPR,synonymous_variant,p.%3D,ENST00000545661,;RLTPR,non_coding_transcript_exon_variant,,ENST00000602321,;RLTPR,non_coding_transcript_exon_variant,,ENST00000602562,;RLTPR,downstream_gene_variant,,ENST00000602467,;RLTPR,upstream_gene_variant,,ENST00000602924,;RLTPR,downstream_gene_variant,,ENST00000602563,;RLTPR,upstream_gene_variant,,ENST00000602633,;RLTPR,upstream_gene_variant,,ENST00000602931,;RLTPR,downstream_gene_variant,,ENST00000602742,;	T	ENSG00000159753	ENST00000334583	Transcript	synonymous_variant	1786	1458	486	L	ctC/ctT	rs771671329	.	.	1	RLTPR	HGNC	27089	protein_coding	YES	CCDS45513.1	ENSP00000334958	LR16C_HUMAN	.	UPI00005194F2	.	.	.	16/38	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24112:SF41,hmmpanther:PTHR24112,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCGCGCT	.	4	ESCA
LRRC37BP1	0	.	GRCh37	17	28964385	28964385	+	RNA	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4643G>T	.	.	ENST00000417404	2/2	31	25	6	42	42	0	LRRC37BP1,non_coding_transcript_exon_variant,,ENST00000417404,;AC005562.1,intron_variant,,ENST00000578265,;LRRC37BP1,downstream_gene_variant,,ENST00000412831,;AC005562.1,downstream_gene_variant,,ENST00000431308,;AC005562.1,downstream_gene_variant,,ENST00000398849,;AC005562.1,downstream_gene_variant,,ENST00000440026,;LRRC37BP1,downstream_gene_variant,,ENST00000398851,;	T	ENSG00000250462	ENST00000417404	Transcript	non_coding_transcript_exon_variant	4643	.	.	.	.	.	.	.	1	LRRC37BP1	HGNC	25390	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTGGTTTTT	.	4	ESCA
KRT222	0	.	GRCh37	17	38821286	38821286	+	Missense_Mutation	SNP	C	C	G	rs753712996	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66G>C	p.Gln22His	p.Q22H	ENST00000394052	1/6	35	32	3	38	38	0	KRT222,missense_variant,p.Gln22His,ENST00000394052,;AC073508.1,upstream_gene_variant,,ENST00000607244,;KRT222,missense_variant,p.Gln22His,ENST00000580719,;KRT222,missense_variant,p.Gln22His,ENST00000581564,;KRT222,missense_variant,p.Gln22His,ENST00000476049,;KRT222,missense_variant,p.Gln22His,ENST00000394049,;	G	ENSG00000213424	ENST00000394052	Transcript	missense_variant	108	66	22	Q/H	caG/caC	rs753712996	.	.	-1	KRT222	HGNC	28695	protein_coding	YES	CCDS11371.1	ENSP00000377616	KT222_HUMAN	.	UPI0000072F8A	.	tolerated(0.12)	benign(0.085)	1/6	.	hmmpanther:PTHR23239:SF44,hmmpanther:PTHR23239,Pfam_domain:PF00038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTATCTGATT	.	2	ESCA
NAGS	0	.	GRCh37	17	42084980	42084980	+	Silent	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1290G>C	p.%3D	p.L430L	ENST00000293404	6/7	19	12	6	23	23	0	NAGS,synonymous_variant,p.%3D,ENST00000293404,;NAGS,synonymous_variant,p.%3D,ENST00000589767,;TMEM101,downstream_gene_variant,,ENST00000587529,;PYY,upstream_gene_variant,,ENST00000360085,;TMEM101,downstream_gene_variant,,ENST00000589334,;TMEM101,downstream_gene_variant,,ENST00000542039,;TMEM101,downstream_gene_variant,,ENST00000206380,;NAGS,non_coding_transcript_exon_variant,,ENST00000592915,;	C	ENSG00000161653	ENST00000293404	Transcript	synonymous_variant	1408	1290	430	L	ctG/ctC	.	.	.	1	NAGS	HGNC	17996	protein_coding	YES	CCDS11473.1	ENSP00000293404	NAGS_HUMAN	Q2NKP2_HUMAN	UPI000006E37E	.	.	.	6/7	.	PROSITE_profiles:PS51186,hmmpanther:PTHR23342:SF3,hmmpanther:PTHR23342,Pfam_domain:PF04768,PIRSF_domain:PIRSF036442,Superfamily_domains:SSF55729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTGACCAT	.	5	ESCA
PPM1D	0	.	GRCh37	17	58700916	58700916	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.S169S	ENST00000305921	2/6	66	49	17	49	49	0	PPM1D,synonymous_variant,p.%3D,ENST00000305921,;PPM1D,synonymous_variant,p.%3D,ENST00000590418,;PPM1D,synonymous_variant,p.%3D,ENST00000392995,;	T	ENSG00000170836	ENST00000305921	Transcript	synonymous_variant	739	507	169	S	agC/agT	.	.	.	1	PPM1D	HGNC	9277	protein_coding	YES	CCDS11625.1	ENSP00000306682	PPM1D_HUMAN	.	UPI0000130FE8	.	.	.	2/6	.	hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF231,Gene3D:3.60.40.10,Pfam_domain:PF00481,SMART_domains:SM00332,Superfamily_domains:SSF81606	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTAGCACATC	.	5	ESCA
GNA13	0	.	GRCh37	17	63009618	63009618	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*757C>A	.	.	ENST00000439174	4/4	13	9	4	10	10	0	GNA13,3_prime_UTR_variant,,ENST00000439174,;GNA13,downstream_gene_variant,,ENST00000541118,;	T	ENSG00000120063	ENST00000439174	Transcript	3_prime_UTR_variant	2137	.	.	.	.	.	.	.	-1	GNA13	HGNC	4381	protein_coding	YES	CCDS11661.1	ENSP00000400717	GNA13_HUMAN	F5H1G8_HUMAN	UPI0000073EBA	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TACATGATAAT	.	4	ESCA
DNAI2	0	.	GRCh37	17	72301522	72301522	+	Silent	SNP	C	C	T	rs762652711	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1152C>T	p.%3D	p.G384G	ENST00000446837	8/13	53	38	15	99	99	0	DNAI2,synonymous_variant,p.%3D,ENST00000307504,;DNAI2,synonymous_variant,p.%3D,ENST00000446837,;DNAI2,synonymous_variant,p.%3D,ENST00000582036,;DNAI2,synonymous_variant,p.%3D,ENST00000579490,;DNAI2,synonymous_variant,p.%3D,ENST00000311014,;AC103809.1,downstream_gene_variant,,ENST00000516976,;RP11-647F2.2,downstream_gene_variant,,ENST00000585167,;DNAI2,3_prime_UTR_variant,,ENST00000579055,;	T	ENSG00000171595	ENST00000446837	Transcript	synonymous_variant	1458	1152	384	G	ggC/ggT	rs762652711,COSM4069305	.	.	1	DNAI2	HGNC	18744	protein_coding	YES	CCDS11697.1	ENSP00000400252	DNAI2_HUMAN	.	UPI000013EC1D	.	.	.	8/13	.	PROSITE_profiles:PS50294,hmmpanther:PTHR12442,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGGCGACTG	byFrequency	5	ESCA
TP53	0	.	GRCh37	17	7577022	7577022	+	Nonsense_Mutation	SNP	G	G	A	rs121913344	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	8/11	47	35	12	78	78	0	TP53,stop_gained,p.Arg306Ter,ENST00000420246,;TP53,stop_gained,p.Arg306Ter,ENST00000269305,;TP53,stop_gained,p.Arg174Ter,ENST00000509690,;TP53,stop_gained,p.Arg306Ter,ENST00000359597,;TP53,stop_gained,p.Arg306Ter,ENST00000445888,;TP53,stop_gained,p.Arg306Ter,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	1106	916	306	R/*	Cga/Tga	CM971506,rs121913344,TP53_g.13896del,TP53_g.13896C>T,COSM10663,COSM44631,COSM99947,COSM3388168,COSM1640820	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,0,0,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R306*|c.916C>T|16,SITE|p.R306*|c.916C>T|152,SITE|p.R306*|c.916C>T|24,SITE|p.R306*|c.916C>T|43,CODON|p.0?|c.1_1182del1182|6,BUFFER|p.?|c.919+2T>G|3,BUFFER|p.?|c.919+1G>C|4,BUFFER|p.?|c.919+1G>T|9,BUFFER|p.?|c.919+1G>A|6,BUFFER|p.?|c.919+1G>A|10,BUFFER|p.A307fs*38|c.919delG|4,BUFFER|p.K305N|c.915G>T|3,BUFFER|p.K305*|c.913A>T|16,BUFFER|p.K305*|c.913A>T|3,BUFFER|p.S303N|c.908G>A|3,BUFFER|p.S303T|c.908G>C|3,BUFFER|p.G302E|c.905G>A|3,BUFFER|p.S303fs*42|c.904delG|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTCGCTTAG	.	5	ESCA
TP53	0	.	GRCh37	17	7578439	7578439	+	Frame_Shift_Del	DEL	T	T	-	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.491delA	p.Lys164SerfsTer6	p.K164Sfs*6	ENST00000269305	5/11	39	27	12	34	34	0	TP53,frameshift_variant,p.Lys164SerfsTer?,ENST00000508793,;TP53,frameshift_variant,p.Lys164SerfsTer6,ENST00000413465,;TP53,frameshift_variant,p.Lys164SerfsTer6,ENST00000420246,;TP53,frameshift_variant,p.Lys164SerfsTer6,ENST00000269305,;TP53,frameshift_variant,p.Lys32SerfsTer6,ENST00000509690,;TP53,frameshift_variant,p.Lys164SerfsTer6,ENST00000359597,;TP53,frameshift_variant,p.Lys71SerfsTer6,ENST00000514944,;TP53,frameshift_variant,p.Lys164SerfsTer6,ENST00000445888,;TP53,frameshift_variant,p.Lys164SerfsTer6,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	681	491	164	K/X	aAg/ag	TP53_g.12479A>G,TP53_g.12479A>C,TP53_g.12479A>T,COSM44841,COSM45428,COSM44387	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.Q72*|c.214C>T|6,CODON|p.Q33*|c.97C>T|6,CODON|p.Q165*|c.493C>T|30,CODON|p.Q165*|c.493C>T|6,CODON|p.Q165*|c.493C>T|4,CODON|p.Q165*|c.493C>T|6,CODON|p.Q165*|c.493C>T|4,CODON|p.K164N|c.492G>T|6,BUFFER|p.H75R|c.224A>G|3,BUFFER|p.H168R|c.503A>G|15,BUFFER|p.H168L|c.503A>T|6,BUFFER|p.H168R|c.503A>G|3,BUFFER|p.H168P|c.503A>C|12,BUFFER|p.H168R|c.503A>G|3,BUFFER|p.H168R|c.503A>G|3,BUFFER|p.H168R|c.503A>G|3,BUFFER|p.H36R|c.107A>G|3,BUFFER|p.H168Y|c.502C>T|9,BUFFER|p.Q167fs*13|c.499_500delCA|3,BUFFER|p.Q167Q|c.501G>A|3,BUFFER|p.Q167R|c.500A>G|4,BUFFER|p.Q167L|c.500A>T|3,BUFFER|p.Q167*|c.499C>T|5,BUFFER|p.Q167*|c.499C>T|5,BUFFER|p.Q167*|c.499C>T|26,BUFFER|p.Q35*|c.103C>T|5,BUFFER|p.Q74*|c.220C>T|5,BUFFER|p.Q167fs*14|c.497_498insC|3,BUFFER|p.S166*|c.497C>A|8,BUFFER|p.S166L|c.497C>T|5,BUFFER|p.S166*|c.497C>G|11,BUFFER|p.S166P|c.496T>C|6,BUFFER|p.Q165L|c.494A>T|3,BUFFER|p.K164M|c.491A>T|4,BUFFER|p.K164E|c.490A>G|3,BUFFER|p.K164E|c.490A>G|3,BUFFER|p.K164E|c.490A>G|13,BUFFER|p.K164*|c.490A>T|11,BUFFER|p.K71E|c.211A>G|3,BUFFER|p.K32E|c.94A>G|4,BUFFER|p.Y163*|c.489C>G|5,BUFFER|p.Y163Y|c.489C>T|3,BUFFER|p.Y163*|c.489C>A|3,BUFFER|p.Y163C|c.488A>G|126,BUFFER|p.Y70C|c.209A>G|30,BUFFER|p.Y163S|c.488A>C|5,BUFFER|p.Y31C|c.92A>G|33,BUFFER|p.Y163C|c.488A>G|9,BUFFER|p.Y163C|c.488A>G|13,BUFFER|p.Y163C|c.488A>G|30,BUFFER|p.Y163C|c.488A>G|30,BUFFER|p.Y163H|c.487T>C|19,BUFFER|p.Y70D|c.208T>G|3,BUFFER|p.Y163N|c.487T>A|5,BUFFER|p.Y163N|c.487T>A|5,BUFFER|p.Y163D|c.487T>G|3,BUFFER|p.Y70N|c.208T>A|5,BUFFER|p.Y163N|c.487T>A|22,BUFFER|p.Y163D|c.487T>G|3,BUFFER|p.Y31D|c.91T>G|3,BUFFER|p.Y31N|c.91T>A|5,BUFFER|p.Y163D|c.487T>G|6,BUFFER|p.I162M|c.486C>G|3,BUFFER|p.I162N|c.485T>A|6,BUFFER|p.I162N|c.485T>A|9,BUFFER|p.I162S|c.485T>G|5,BUFFER|p.I69N|c.206T>A|6,BUFFER|p.I162N|c.485T>A|6,BUFFER|p.I30N|c.89T>A|6,BUFFER|p.I162V|c.484A>G|5,BUFFER|p.I162F|c.484A>T|11,BUFFER|p.A161A|c.483C>T|5,BUFFER|p.A161fs*9|c.481delG|3,BUFFER|p.A161V|c.482C>T|9,BUFFER|p.A161D|c.482C>A|9,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A29T|c.85G>A|10,BUFFER|p.A161T|c.481G>A|52,BUFFER|p.A68T|c.202G>A|10,BUFFER|p.A161S|c.481G>T|3,BUFFER|p.M160I|c.480G>T|4,BUFFER|p.M160I|c.480G>A|3	INDELOCATOR*|VARSCANI*|PINDEL	GACTGCTTGTAG	.	3	ESCA
ENGASE	0	.	GRCh37	17	77082217	77082217	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2018C>G	p.Ser673Cys	p.S673C	ENST00000579016	14/14	41	33	8	48	48	0	ENGASE,missense_variant,p.Ser673Cys,ENST00000579016,;RBFOX3,downstream_gene_variant,,ENST00000415831,;ENGASE,downstream_gene_variant,,ENST00000311595,;RBFOX3,downstream_gene_variant,,ENST00000582043,;RBFOX3,downstream_gene_variant,,ENST00000583458,;RBFOX3,downstream_gene_variant,,ENST00000453134,;RBFOX3,downstream_gene_variant,,ENST00000580155,;ENGASE,downstream_gene_variant,,ENST00000539857,;ENGASE,downstream_gene_variant,,ENST00000585160,;ENGASE,downstream_gene_variant,,ENST00000584568,;ENGASE,3_prime_UTR_variant,,ENST00000300682,;ENGASE,non_coding_transcript_exon_variant,,ENST00000579809,;RBFOX3,downstream_gene_variant,,ENST00000581393,;ENGASE,downstream_gene_variant,,ENST00000583041,;ENGASE,downstream_gene_variant,,ENST00000578419,;ENGASE,downstream_gene_variant,,ENST00000577783,;RBFOX3,downstream_gene_variant,,ENST00000578998,;ENGASE,downstream_gene_variant,,ENST00000583646,;	G	ENSG00000167280	ENST00000579016	Transcript	missense_variant	2018	2018	673	S/C	tCt/tGt	COSM3523188	.	.	1	ENGASE	HGNC	24622	protein_coding	YES	CCDS42394.1	ENSP00000462333	ENASE_HUMAN	.	UPI000006CF27	.	deleterious(0.03)	possibly_damaging(0.711)	14/14	.	hmmpanther:PTHR13246:SF0,hmmpanther:PTHR13246	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTCTCCGG	.	5	ESCA
NPLOC4	0	.	GRCh37	17	79564312	79564312	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.952G>A	p.Glu318Lys	p.E318K	ENST00000331134	10/17	49	40	9	47	47	0	NPLOC4,missense_variant,p.Glu318Lys,ENST00000374747,;NPLOC4,missense_variant,p.Glu157Lys,ENST00000539314,;NPLOC4,missense_variant,p.Glu318Lys,ENST00000331134,;NPLOC4,non_coding_transcript_exon_variant,,ENST00000572351,;NPLOC4,3_prime_UTR_variant,,ENST00000574897,;	T	ENSG00000182446	ENST00000331134	Transcript	missense_variant	1168	952	318	E/K	Gaa/Aaa	.	.	.	-1	NPLOC4	HGNC	18261	protein_coding	YES	CCDS45812.1	ENSP00000331487	NPL4_HUMAN	.	UPI0000070BDD	.	tolerated(0.06)	probably_damaging(0.936)	10/17	.	hmmpanther:PTHR12710,Pfam_domain:PF05021,PIRSF_domain:PIRSF010052	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTCTGAGA	.	5	ESCA
AFG3L2	0	.	GRCh37	18	12353077	12353077	+	Silent	SNP	C	C	T	rs777760292	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245G>A	p.%3D	p.K415K	ENST00000269143	10/17	37	31	6	23	23	0	AFG3L2,synonymous_variant,p.%3D,ENST00000269143,;AFG3L2,upstream_gene_variant,,ENST00000588893,;	T	ENSG00000141385	ENST00000269143	Transcript	synonymous_variant	1477	1245	415	K	aaG/aaA	rs777760292,COSM708435	.	.	-1	AFG3L2	HGNC	315	protein_coding	YES	CCDS11859.1	ENSP00000269143	AFG32_HUMAN	D3DUJ0_HUMAN	UPI000013D7FF	.	.	.	10/17	.	HAMAP:MF_01458,hmmpanther:PTHR23076:SF45,hmmpanther:PTHR23076,Gene3D:3.40.50.300,Pfam_domain:PF00004,TIGRFAM_domain:TIGR01241,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTCTTCCT	byFrequency|byCluster	5	ESCA
CCDC178	0	.	GRCh37	18	30803178	30803178	+	Silent	SNP	A	A	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1824T>G	p.%3D	p.L608L	ENST00000383096	18/23	27	22	5	35	35	0	CCDC178,synonymous_variant,p.%3D,ENST00000579947,;CCDC178,synonymous_variant,p.%3D,ENST00000581524,;CCDC178,synonymous_variant,p.%3D,ENST00000406524,;CCDC178,synonymous_variant,p.%3D,ENST00000403303,;CCDC178,synonymous_variant,p.%3D,ENST00000383096,;CCDC178,synonymous_variant,p.%3D,ENST00000402325,;CCDC178,synonymous_variant,p.%3D,ENST00000583930,;CCDC178,intron_variant,,ENST00000579916,;CCDC178,intron_variant,,ENST00000300227,;	C	ENSG00000166960	ENST00000383096	Transcript	synonymous_variant	2007	1824	608	L	ctT/ctG	.	.	.	-1	CCDC178	HGNC	29588	protein_coding	YES	CCDS42424.1	ENSP00000372576	CC178_HUMAN	J3QKU2_HUMAN	UPI000022A700	.	.	.	18/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATTAAGCAT	.	5	ESCA
FBXO15	0	.	GRCh37	18	71803093	71803093	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236C>T	p.Ser79Leu	p.S79L	ENST00000419743	3/10	16	12	4	27	27	0	FBXO15,missense_variant,p.Ser42Leu,ENST00000582526,;FBXO15,missense_variant,p.Ser79Leu,ENST00000419743,;FBXO15,missense_variant,p.Ser3Leu,ENST00000269500,;FBXO15,missense_variant,p.Ser4Leu,ENST00000578399,;FBXO15,3_prime_UTR_variant,,ENST00000583443,;FBXO15,3_prime_UTR_variant,,ENST00000585174,;FBXO15,3_prime_UTR_variant,,ENST00000580552,;FBXO15,3_prime_UTR_variant,,ENST00000581214,;	A	ENSG00000141665	ENST00000419743	Transcript	missense_variant	316	236	79	S/L	tCa/tTa	.	.	.	-1	FBXO15	HGNC	13617	protein_coding	YES	CCDS45884.1	ENSP00000393154	FBX15_HUMAN	J3QRE7_HUMAN	UPI00003CF23D	.	tolerated(0.05)	possibly_damaging(0.876)	3/10	.	Superfamily_domains:SSF81383,SMART_domains:SM00256,Gene3D:1.20.1280.50,Pfam_domain:PF12937,hmmpanther:PTHR20995:SF16,hmmpanther:PTHR20995,PROSITE_profiles:PS50181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTGAAGGC	.	5	ESCA
CNDP2	0	.	GRCh37	18	72186240	72186240	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1267A>G	p.Thr423Ala	p.T423A	ENST00000324262	11/12	32	26	6	59	59	0	CNDP2,missense_variant,p.Thr423Ala,ENST00000579847,;CNDP2,missense_variant,p.Thr423Ala,ENST00000324262,;CNDP2,missense_variant,p.Thr339Ala,ENST00000324301,;CNDP2,intron_variant,,ENST00000579624,;CNDP2,downstream_gene_variant,,ENST00000583695,;CNDP2,non_coding_transcript_exon_variant,,ENST00000584581,;CNDP2,downstream_gene_variant,,ENST00000577409,;CNDP2,downstream_gene_variant,,ENST00000581600,;	G	ENSG00000133313	ENST00000324262	Transcript	missense_variant	1583	1267	423	T/A	Acc/Gcc	.	.	.	1	CNDP2	HGNC	24437	protein_coding	YES	CCDS12006.1	ENSP00000325548	CNDP2_HUMAN	Q9NW02_HUMAN,J3QRD0_HUMAN,J3QR27_HUMAN,J3QQN6_HUMAN,J3QLU1_HUMAN,J3QKT2_HUMAN,J3QKQ0_HUMAN,J3KSV5_HUMAN,J3KSS4_HUMAN,J3KRD5_HUMAN,B4DV28_HUMAN	UPI00000463FE	.	deleterious(0.04)	benign(0.107)	11/12	.	hmmpanther:PTHR11014:SF51,hmmpanther:PTHR11014,Gene3D:3.40.630.10,Pfam_domain:PF01546,PIRSF_domain:PIRSF037242,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTGACCTTT	.	5	ESCA
SBNO2	0	.	GRCh37	19	1108005	1108005	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*214C>T	.	.	ENST00000361757	32/32	18	12	6	37	37	0	SBNO2,3_prime_UTR_variant,,ENST00000438103,;SBNO2,3_prime_UTR_variant,,ENST00000587024,;SBNO2,3_prime_UTR_variant,,ENST00000361757,;GPX4,downstream_gene_variant,,ENST00000585362,;GPX4,downstream_gene_variant,,ENST00000587648,;GPX4,downstream_gene_variant,,ENST00000354171,;GPX4,downstream_gene_variant,,ENST00000589115,;GPX4,downstream_gene_variant,,ENST00000588919,;GPX4,downstream_gene_variant,,ENST00000593032,;SBNO2,downstream_gene_variant,,ENST00000587673,;GPX4,downstream_gene_variant,,ENST00000587932,;SBNO2,downstream_gene_variant,,ENST00000586109,;GPX4,downstream_gene_variant,,ENST00000585480,;GPX4,downstream_gene_variant,,ENST00000592940,;	A	ENSG00000064932	ENST00000361757	Transcript	3_prime_UTR_variant	4553	.	.	.	.	.	.	.	-1	SBNO2	HGNC	29158	protein_coding	YES	CCDS45894.1	ENSP00000354733	SBNO2_HUMAN	K7ERL2_HUMAN,K7ENA9_HUMAN	UPI0000140680	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCACAGAGAGG	.	2	ESCA
GIPC1	0	.	GRCh37	19	14589343	14589343	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.887A>T	p.Asn296Ile	p.N296I	ENST00000393033	9/9	36	29	7	29	29	0	GIPC1,missense_variant,p.Asn199Ile,ENST00000591349,;GIPC1,missense_variant,p.Asn296Ile,ENST00000393033,;GIPC1,missense_variant,p.Asn199Ile,ENST00000393029,;GIPC1,missense_variant,p.Asn199Ile,ENST00000393028,;GIPC1,missense_variant,p.Asn91Ile,ENST00000589631,;GIPC1,missense_variant,p.Asn296Ile,ENST00000345425,;GIPC1,missense_variant,p.Asn296Ile,ENST00000586027,;GIPC1,downstream_gene_variant,,ENST00000591245,;GIPC1,downstream_gene_variant,,ENST00000587210,;PTGER1,upstream_gene_variant,,ENST00000292513,;GIPC1,downstream_gene_variant,,ENST00000587969,;GIPC1,downstream_gene_variant,,ENST00000587934,;GIPC1,3_prime_UTR_variant,,ENST00000589497,;GIPC1,non_coding_transcript_exon_variant,,ENST00000585606,;GIPC1,downstream_gene_variant,,ENST00000587811,;	A	ENSG00000123159	ENST00000393033	Transcript	missense_variant	1157	887	296	N/I	aAc/aTc	.	.	.	-1	GIPC1	HGNC	1226	protein_coding	YES	CCDS12310.1	ENSP00000376753	GIPC1_HUMAN	K7ESN1_HUMAN,K7ELJ2_HUMAN,K7EIT0_HUMAN	UPI000012B4BB	.	deleterious(0)	possibly_damaging(0.896)	9/9	.	hmmpanther:PTHR12259,hmmpanther:PTHR12259:SF4,PIRSF_domain:PIRSF038083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGGTTCCTT	.	5	ESCA
BRD4	0	.	GRCh37	19	15359812	15359812	+	Intron	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2159-4239C>T	.	.	ENST00000263377	.	25	20	4	31	31	0	BRD4,3_prime_UTR_variant,,ENST00000371835,;BRD4,intron_variant,,ENST00000263377,;BRD4,downstream_gene_variant,,ENST00000360016,;BRD4,downstream_gene_variant,,ENST00000595926,;BRD4,upstream_gene_variant,,ENST00000594066,;	A	ENSG00000141867	ENST00000263377	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	BRD4	HGNC	13575	protein_coding	YES	CCDS12328.1	ENSP00000263377	BRD4_HUMAN	Q96HN0_HUMAN,M0R0H4_HUMAN,M0QZD9_HUMAN	UPI0000126ACE	.	.	.	.	11/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAGGACCCC	.	4	ESCA
TLE2	0	.	GRCh37	19	3006510	3006510	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1408C>G	p.Gln470Glu	p.Q470E	ENST00000262953	15/20	55	35	19	111	111	0	TLE2,missense_variant,p.Gln137Glu,ENST00000447365,;TLE2,missense_variant,p.Gln348Glu,ENST00000455444,;TLE2,missense_variant,p.Gln484Glu,ENST00000426948,;TLE2,missense_variant,p.Gln119Glu,ENST00000589364,;TLE2,missense_variant,p.Gln348Glu,ENST00000443826,;TLE2,missense_variant,p.Gln470Glu,ENST00000262953,;TLE2,missense_variant,p.Gln471Glu,ENST00000590536,;TLE2,missense_variant,p.Gln484Glu,ENST00000591529,;TLE2,intron_variant,,ENST00000586422,;TLE2,non_coding_transcript_exon_variant,,ENST00000586492,;TLE2,downstream_gene_variant,,ENST00000589205,;TLE2,downstream_gene_variant,,ENST00000587672,;	C	ENSG00000065717	ENST00000262953	Transcript	missense_variant	1671	1408	470	Q/E	Cag/Gag	.	.	.	-1	TLE2	HGNC	11838	protein_coding	YES	CCDS45911.1	ENSP00000262953	TLE2_HUMAN	.	UPI0000137038	.	deleterious(0)	possibly_damaging(0.519)	15/20	.	PROSITE_profiles:PS50294,hmmpanther:PTHR10814:SF4,hmmpanther:PTHR10814,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCTGTGTGG	.	5	ESCA
CAPN12	0	.	GRCh37	19	39221459	39221459	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*33C>T	.	.	ENST00000328867	21/21	32	25	6	39	39	0	CAPN12,3_prime_UTR_variant,,ENST00000601953,;CAPN12,3_prime_UTR_variant,,ENST00000597987,;ACTN4,3_prime_UTR_variant,,ENST00000252699,;CAPN12,3_prime_UTR_variant,,ENST00000328867,;ACTN4,3_prime_UTR_variant,,ENST00000440400,;CAPN12,3_prime_UTR_variant,,ENST00000595177,;ACTN4,downstream_gene_variant,,ENST00000390009,;ACTN4,downstream_gene_variant,,ENST00000589528,;ACTN4,downstream_gene_variant,,ENST00000424234,;ACTN4,downstream_gene_variant,,ENST00000477174,;ACTN4,downstream_gene_variant,,ENST00000497637,;CAPN12,3_prime_UTR_variant,,ENST00000594552,;CAPN12,non_coding_transcript_exon_variant,,ENST00000597716,;CAPN12,non_coding_transcript_exon_variant,,ENST00000593700,;CAPN12,downstream_gene_variant,,ENST00000594497,;CAPN12,downstream_gene_variant,,ENST00000597354,;CAPN12,downstream_gene_variant,,ENST00000601685,;	A	ENSG00000182472	ENST00000328867	Transcript	3_prime_UTR_variant	2502	.	.	.	.	.	.	.	-1	CAPN12	HGNC	13249	protein_coding	YES	CCDS12519.1	ENSP00000331636	CAN12_HUMAN	M0R3D7_HUMAN	UPI00001C0E17	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTGCCCTG	.	5	ESCA
CAPN12	0	.	GRCh37	19	39221757	39221757	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2064C>T	p.%3D	p.T688T	ENST00000328867	19/21	27	23	4	44	44	0	CAPN12,synonymous_variant,p.%3D,ENST00000601953,;CAPN12,synonymous_variant,p.%3D,ENST00000597987,;CAPN12,synonymous_variant,p.%3D,ENST00000328867,;CAPN12,synonymous_variant,p.%3D,ENST00000595177,;ACTN4,3_prime_UTR_variant,,ENST00000252699,;ACTN4,3_prime_UTR_variant,,ENST00000440400,;ACTN4,downstream_gene_variant,,ENST00000390009,;ACTN4,downstream_gene_variant,,ENST00000589528,;ACTN4,downstream_gene_variant,,ENST00000424234,;ACTN4,downstream_gene_variant,,ENST00000477174,;ACTN4,downstream_gene_variant,,ENST00000497637,;CAPN12,3_prime_UTR_variant,,ENST00000594552,;CAPN12,non_coding_transcript_exon_variant,,ENST00000597716,;CAPN12,non_coding_transcript_exon_variant,,ENST00000593700,;CAPN12,downstream_gene_variant,,ENST00000594497,;CAPN12,downstream_gene_variant,,ENST00000597354,;CAPN12,downstream_gene_variant,,ENST00000601685,;	A	ENSG00000182472	ENST00000328867	Transcript	synonymous_variant	2373	2064	688	T	acC/acT	.	.	.	-1	CAPN12	HGNC	13249	protein_coding	YES	CCDS12519.1	ENSP00000331636	CAN12_HUMAN	M0R3D7_HUMAN	UPI00001C0E17	.	.	.	19/21	.	hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF280,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCAGGTGAG	.	2	ESCA
ZNF526	0	.	GRCh37	19	42731398	42731398	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*830T>C	.	.	ENST00000301215	3/3	38	32	6	51	51	0	ZNF526,3_prime_UTR_variant,,ENST00000301215,;GSK3A,downstream_gene_variant,,ENST00000398249,;GSK3A,downstream_gene_variant,,ENST00000222330,;ZNF526,downstream_gene_variant,,ENST00000597945,;GSK3A,downstream_gene_variant,,ENST00000493059,;GSK3A,downstream_gene_variant,,ENST00000453535,;	C	ENSG00000167625	ENST00000301215	Transcript	3_prime_UTR_variant	3068	.	.	.	.	.	.	.	1	ZNF526	HGNC	29415	protein_coding	YES	CCDS12598.1	ENSP00000301215	ZN526_HUMAN	M0R395_HUMAN,H9ZYJ3_HUMAN	UPI00001C2011	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GAAGGTAGTCC	.	3	ESCA
TMEM145	0	.	GRCh37	19	42821103	42821103	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.888C>G	p.Ile296Met	p.I296M	ENST00000301204	11/15	27	24	3	56	56	0	TMEM145,missense_variant,p.Ile320Met,ENST00000598766,;TMEM145,missense_variant,p.Ile296Met,ENST00000301204,;TMEM145,upstream_gene_variant,,ENST00000601644,;TMEM145,downstream_gene_variant,,ENST00000601020,;TMEM145,downstream_gene_variant,,ENST00000595775,;	G	ENSG00000167619	ENST00000301204	Transcript	missense_variant	929	888	296	I/M	atC/atG	.	.	.	1	TMEM145	HGNC	26912	protein_coding	YES	CCDS12603.1	ENSP00000301204	TM145_HUMAN	.	UPI000013E6E6	.	deleterious(0)	benign(0.403)	11/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23252,hmmpanther:PTHR23252:SF24,Pfam_domain:PF10192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCATCTACGA	.	2	ESCA
PTPRS	0	.	GRCh37	19	5244258	5244258	+	Silent	SNP	G	G	A	rs2230609	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1224C>T	p.%3D	p.I408I	ENST00000357368	11/38	52	41	11	79	79	0	PTPRS,synonymous_variant,p.%3D,ENST00000353284,;PTPRS,synonymous_variant,p.%3D,ENST00000587303,;PTPRS,synonymous_variant,p.%3D,ENST00000372412,;PTPRS,synonymous_variant,p.%3D,ENST00000588012,;PTPRS,synonymous_variant,p.%3D,ENST00000262963,;PTPRS,synonymous_variant,p.%3D,ENST00000357368,;PTPRS,synonymous_variant,p.%3D,ENST00000592099,;PTPRS,synonymous_variant,p.%3D,ENST00000348075,;PTPRS,non_coding_transcript_exon_variant,,ENST00000588552,;	A	ENSG00000105426	ENST00000357368	Transcript	synonymous_variant	1458	1224	408	I	atC/atT	rs2230609	.	.	-1	PTPRS	HGNC	9681	protein_coding	YES	CCDS45930.1	ENSP00000349932	PTPRS_HUMAN	K7ESP0_HUMAN,K7ERX4_HUMAN	UPI000059D63E	.	.	.	11/38	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR19134:SF204,hmmpanther:PTHR19134,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCGATGGA	.	5	ESCA
ZNF611	0	.	GRCh37	19	53207809	53207809	+	3'UTR	SNP	T	T	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*381A>C	.	.	ENST00000543227	6/6	30	25	5	29	29	0	ZNF611,3_prime_UTR_variant,,ENST00000453741,;ZNF611,3_prime_UTR_variant,,ENST00000543227,;ZNF611,3_prime_UTR_variant,,ENST00000319783,;ZNF611,3_prime_UTR_variant,,ENST00000602162,;ZNF611,3_prime_UTR_variant,,ENST00000540744,;ZNF611,downstream_gene_variant,,ENST00000596702,;ZNF611,downstream_gene_variant,,ENST00000600943,;ZNF611,downstream_gene_variant,,ENST00000595798,;ZNF611,downstream_gene_variant,,ENST00000601643,;ZNF611,downstream_gene_variant,,ENST00000602046,;ZNF611,3_prime_UTR_variant,,ENST00000595001,;ZNF611,downstream_gene_variant,,ENST00000601249,;ZNF611,downstream_gene_variant,,ENST00000597343,;ZNF611,downstream_gene_variant,,ENST00000598639,;ZNF611,downstream_gene_variant,,ENST00000598723,;	G	ENSG00000213020	ENST00000543227	Transcript	3_prime_UTR_variant	2774	.	.	.	.	.	.	.	-1	ZNF611	HGNC	28766	protein_coding	YES	CCDS12855.1	ENSP00000437616	ZN611_HUMAN	M0QYR0_HUMAN	UPI00001406C1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGACCTGCAAT	.	3	ESCA
ZNF611	0	.	GRCh37	19	53207811	53207811	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*379G>C	.	.	ENST00000543227	6/6	29	23	6	29	29	0	ZNF611,3_prime_UTR_variant,,ENST00000453741,;ZNF611,3_prime_UTR_variant,,ENST00000543227,;ZNF611,3_prime_UTR_variant,,ENST00000319783,;ZNF611,3_prime_UTR_variant,,ENST00000602162,;ZNF611,3_prime_UTR_variant,,ENST00000540744,;ZNF611,downstream_gene_variant,,ENST00000596702,;ZNF611,downstream_gene_variant,,ENST00000600943,;ZNF611,downstream_gene_variant,,ENST00000595798,;ZNF611,downstream_gene_variant,,ENST00000601643,;ZNF611,downstream_gene_variant,,ENST00000602046,;ZNF611,3_prime_UTR_variant,,ENST00000595001,;ZNF611,downstream_gene_variant,,ENST00000601249,;ZNF611,downstream_gene_variant,,ENST00000597343,;ZNF611,downstream_gene_variant,,ENST00000598639,;ZNF611,downstream_gene_variant,,ENST00000598723,;	G	ENSG00000213020	ENST00000543227	Transcript	3_prime_UTR_variant	2772	.	.	.	.	.	.	.	-1	ZNF611	HGNC	28766	protein_coding	YES	CCDS12855.1	ENSP00000437616	ZN611_HUMAN	M0QYR0_HUMAN	UPI00001406C1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCTGCAATAT	.	3	ESCA
LILRA2	0	.	GRCh37	19	55086220	55086220	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375C>A	p.%3D	p.L125L	ENST00000251377	5/9	153	109	44	248	248	0	LILRA2,synonymous_variant,p.%3D,ENST00000251376,;LILRA2,synonymous_variant,p.%3D,ENST00000391738,;LILRA2,synonymous_variant,p.%3D,ENST00000391737,;LILRA2,synonymous_variant,p.%3D,ENST00000439534,;LILRA2,synonymous_variant,p.%3D,ENST00000251377,;LILRB1,intron_variant,,ENST00000418536,;LILRB1,intron_variant,,ENST00000448689,;LILRB1,intron_variant,,ENST00000396321,;LILRA2,non_coding_transcript_exon_variant,,ENST00000495786,;LILRA2,upstream_gene_variant,,ENST00000472992,;	A	ENSG00000239998	ENST00000251377	Transcript	synonymous_variant	508	375	125	L	ctC/ctA	.	.	.	1	LILRA2	HGNC	6603	protein_coding	YES	CCDS46179.1	ENSP00000251377	LIRA2_HUMAN	E9PDF4_HUMAN	UPI0000034C01	.	.	.	5/9	.	hmmpanther:PTHR11738:SF90,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13927,PIRSF_domain:PIRSF001979,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCTCAGC	.	5	ESCA
ZSCAN5B	0	.	GRCh37	19	56701846	56701846	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838G>C	p.Ala280Pro	p.A280P	ENST00000586855	5/5	97	91	6	103	103	0	ZSCAN5B,missense_variant,p.Ala280Pro,ENST00000586855,;ZSCAN5B,missense_variant,p.Ala280Pro,ENST00000358992,;ZSCAN5B,downstream_gene_variant,,ENST00000587032,;GALP,downstream_gene_variant,,ENST00000440823,;GALP,downstream_gene_variant,,ENST00000357330,;ZSCAN5B,downstream_gene_variant,,ENST00000589938,;	G	ENSG00000197213	ENST00000586855	Transcript	missense_variant	1152	838	280	A/P	Gct/Cct	.	.	.	-1	ZSCAN5B	HGNC	34246	protein_coding	YES	CCDS46203.1	ENSP00000466072	ZSA5B_HUMAN	K7ESD3_HUMAN,K7EJD1_HUMAN	UPI000059D7BA	.	tolerated(0.06)	probably_damaging(0.999)	5/5	.	hmmpanther:PTHR10032:SF163,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAAGCTTCTC	.	2	ESCA
ZNF587B	0	.	GRCh37	19	58352946	58352946	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.904G>C	p.Glu302Gln	p.E302Q	ENST00000442832	3/4	81	56	24	94	94	0	ZNF587B,missense_variant,p.Glu252Gln,ENST00000594328,;ZNF587B,missense_variant,p.Glu302Gln,ENST00000594901,;ZNF587B,missense_variant,p.Glu302Gln,ENST00000442832,;CTD-2583A14.10,intron_variant,,ENST00000598031,;ZNF587B,intron_variant,,ENST00000316462,;CTD-2583A14.10,intron_variant,,ENST00000597134,;CTD-2583A14.10,intron_variant,,ENST00000593873,;CTD-2583A14.10,intron_variant,,ENST00000596498,;CTD-2583A14.10,intron_variant,,ENST00000603271,;CTD-2583A14.10,intron_variant,,ENST00000604231,;	C	ENSG00000269343	ENST00000442832	Transcript	missense_variant	1138	904	302	E/Q	Gaa/Caa	.	.	.	1	ZNF587B	HGNC	37142	protein_coding	YES	CCDS56109.1	ENSP00000392410	Z587B_HUMAN	.	UPI0001AE657B	.	deleterious(0.02)	possibly_damaging(0.864)	3/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF191,hmmpanther:PTHR24387,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAGAATGT	.	5	ESCA
SH2D3A	0	.	GRCh37	19	6752623	6752623	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1712G>A	p.Arg571His	p.R571H	ENST00000245908	10/10	50	33	17	86	86	0	SH2D3A,missense_variant,p.Arg571His,ENST00000245908,;SH2D3A,missense_variant,p.Arg478His,ENST00000437152,;TRIP10,downstream_gene_variant,,ENST00000313285,;SH2D3A,downstream_gene_variant,,ENST00000597687,;TRIP10,downstream_gene_variant,,ENST00000596758,;TRIP10,downstream_gene_variant,,ENST00000600428,;TRIP10,downstream_gene_variant,,ENST00000313244,;CTD-3128G10.6,upstream_gene_variant,,ENST00000594056,;SH2D3A,intron_variant,,ENST00000597168,;SH2D3A,downstream_gene_variant,,ENST00000597254,;SH2D3A,downstream_gene_variant,,ENST00000599563,;TRIP10,downstream_gene_variant,,ENST00000595305,;SH2D3A,downstream_gene_variant,,ENST00000595681,;TRIP10,downstream_gene_variant,,ENST00000598843,;SH2D3A,downstream_gene_variant,,ENST00000595369,;TRIP10,downstream_gene_variant,,ENST00000600677,;	T	ENSG00000125731	ENST00000245908	Transcript	missense_variant	1982	1712	571	R/H	cGc/cAc	.	.	.	-1	SH2D3A	HGNC	16885	protein_coding	YES	CCDS12173.1	ENSP00000245908	SH23A_HUMAN	.	UPI000006FD60	.	deleterious(0.02)	benign(0.035)	10/10	.	hmmpanther:PTHR14247,SMART_domains:SM00147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGCGCTGC	.	5	ESCA
LPPR3	0	.	GRCh37	19	821508	821508	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.52C>T	p.%3D	p.L18L	ENST00000359894	2/7	41	34	6	85	85	0	LPPR3,synonymous_variant,p.%3D,ENST00000519502,;LPPR3,synonymous_variant,p.%3D,ENST00000520876,;LPPR3,synonymous_variant,p.%3D,ENST00000359894,;AZU1,upstream_gene_variant,,ENST00000592205,;	A	ENSG00000129951	ENST00000359894	Transcript	synonymous_variant	116	52	18	L	Ctg/Ttg	.	.	.	-1	LPPR3	Uniprot_gn	.	protein_coding	YES	CCDS12043.1	ENSP00000352962	.	K7ELK5_HUMAN	UPI00000730B6	.	.	.	2/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10165:SF14,hmmpanther:PTHR10165	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCAGAAGCG	.	5	ESCA
COL11A1	0	.	GRCh37	1	103379194	103379194	+	Missense_Mutation	SNP	G	G	T	rs528959090	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4031C>A	p.Pro1344Gln	p.P1344Q	ENST00000370096	53/67	54	44	9	70	70	0	COL11A1,missense_variant,p.Pro1228Gln,ENST00000512756,;COL11A1,missense_variant,p.Pro1305Gln,ENST00000353414,;COL11A1,missense_variant,p.Pro1344Gln,ENST00000370096,;COL11A1,missense_variant,p.Pro1356Gln,ENST00000358392,;	T	ENSG00000060718	ENST00000370096	Transcript	missense_variant	4344	4031	1344	P/Q	cCg/cAg	rs528959090	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	unknown(0)	53/67	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF42,hmmpanther:PTHR24023	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCGGTTGA	by1000G	5	ESCA
PGD	0	.	GRCh37	1	10460539	10460539	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174G>A	p.%3D	p.L58L	ENST00000270776	3/13	39	24	15	45	45	0	PGD,synonymous_variant,p.%3D,ENST00000270776,;PGD,synonymous_variant,p.%3D,ENST00000538557,;PGD,synonymous_variant,p.%3D,ENST00000541529,;PGD,synonymous_variant,p.%3D,ENST00000491493,;PGD,synonymous_variant,p.%3D,ENST00000465632,;PGD,synonymous_variant,p.%3D,ENST00000460189,;PGD,intron_variant,,ENST00000483936,;PGD,stop_retained_variant,p.%3D,ENST00000477958,;PGD,downstream_gene_variant,,ENST00000487775,;	A	ENSG00000142657	ENST00000270776	Transcript	synonymous_variant	212	174	58	L	ctG/ctA	.	.	.	1	PGD	HGNC	8891	protein_coding	YES	CCDS113.1	ENSP00000270776	6PGD_HUMAN	K7EMN2_HUMAN,K7EM49_HUMAN,B4DV68_HUMAN,B4DQJ8_HUMAN	UPI0000169DB9	.	.	.	3/13	.	hmmpanther:PTHR11811,Gene3D:3.40.50.720,TIGRFAM_domain:TIGR00873,Pfam_domain:PF03446,PIRSF_domain:PIRSF000109,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTGAAAGA	.	5	ESCA
OVGP1	0	.	GRCh37	1	111964264	111964264	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640G>T	p.Asp214Tyr	p.D214Y	ENST00000369732	7/11	54	45	9	45	45	0	OVGP1,missense_variant,p.Asp214Tyr,ENST00000369732,;OVGP1,intron_variant,,ENST00000540696,;OVGP1,non_coding_transcript_exon_variant,,ENST00000481495,;OVGP1,upstream_gene_variant,,ENST00000494622,;	A	ENSG00000085465	ENST00000369732	Transcript	missense_variant	696	640	214	D/Y	Gac/Tac	.	.	.	-1	OVGP1	HGNC	8524	protein_coding	YES	CCDS834.1	ENSP00000358747	OVGP1_HUMAN	Q9UJZ3_HUMAN	UPI0000130C53	.	deleterious(0)	probably_damaging(1)	7/11	.	hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF114,Gene3D:3.20.20.80,Pfam_domain:PF00704,SMART_domains:SM00636,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAGTCATAAG	.	4	ESCA
SPAG17	0	.	GRCh37	1	118558800	118558801	+	Frame_Shift_Del	DEL	TT	TT	-	rs781222284	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4074_4075delAA	p.His1360GlnfsTer9	p.H1360Qfs*9	ENST00000336338	29/49	41	33	8	35	35	0	SPAG17,frameshift_variant,p.His1360GlnfsTer9,ENST00000336338,;	-	ENSG00000155761	ENST00000336338	Transcript	frameshift_variant	4140-4141	4074-4075	1358-1359	KS/KX	aaAAgt/aagt	rs781222284	.	.	-1	SPAG17	HGNC	26620	protein_coding	YES	CCDS899.1	ENSP00000337804	SPG17_HUMAN	A7LBF9_HUMAN	UPI00001601FD	.	.	.	29/49	.	hmmpanther:PTHR21963	.	.	.	.	.	.	.	-:0.0002	-:0	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTGACTTTTTCC	.	3	ESCA
ANP32E	0	.	GRCh37	1	150192487	150192487	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*506C>T	.	.	ENST00000314136	7/7	54	43	11	43	43	0	ANP32E,3_prime_UTR_variant,,ENST00000369119,;ANP32E,3_prime_UTR_variant,,ENST00000369116,;ANP32E,3_prime_UTR_variant,,ENST00000314136,;ANP32E,downstream_gene_variant,,ENST00000533654,;ANP32E,downstream_gene_variant,,ENST00000369114,;ANP32E,downstream_gene_variant,,ENST00000534437,;ANP32E,downstream_gene_variant,,ENST00000436748,;ANP32E,downstream_gene_variant,,ENST00000369115,;	A	ENSG00000143401	ENST00000314136	Transcript	3_prime_UTR_variant	1683	.	.	.	.	.	.	.	-1	ANP32E	HGNC	16673	protein_coding	YES	CCDS946.1	ENSP00000324074	AN32E_HUMAN	Q53F20_HUMAN	UPI0000071679	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAGCAACC	.	5	ESCA
HCN3	0	.	GRCh37	1	155258694	155258694	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*440G>A	.	.	ENST00000368358	8/8	43	34	8	57	57	0	HCN3,3_prime_UTR_variant,,ENST00000368358,;PKLR,downstream_gene_variant,,ENST00000342741,;PKLR,downstream_gene_variant,,ENST00000392414,;HCN3,non_coding_transcript_exon_variant,,ENST00000492035,;HCN3,intron_variant,,ENST00000496230,;HCN3,downstream_gene_variant,,ENST00000467204,;	A	ENSG00000143630	ENST00000368358	Transcript	3_prime_UTR_variant	2773	.	.	.	.	.	.	.	1	HCN3	HGNC	19183	protein_coding	YES	CCDS1108.1	ENSP00000357342	HCN3_HUMAN	.	UPI00000559A6	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTGCAGGT	.	5	ESCA
MEF2D	0	.	GRCh37	1	156449079	156449079	+	Intron	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664+3G>T	.	.	ENST00000348159	.	36	24	11	40	40	0	MEF2D,splice_region_variant,,ENST00000348159,;MEF2D,splice_region_variant,,ENST00000353795,;MEF2D,splice_region_variant,,ENST00000360595,;MEF2D,splice_region_variant,,ENST00000464356,;MEF2D,splice_region_variant,,ENST00000340875,;MEF2D,splice_region_variant,,ENST00000368240,;MEF2D,downstream_gene_variant,,ENST00000489057,;Y_RNA,downstream_gene_variant,,ENST00000383924,;MEF2D,splice_region_variant,,ENST00000493077,;MEF2D,splice_region_variant,,ENST00000475587,;	A	ENSG00000116604	ENST00000348159	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	MEF2D	HGNC	6997	protein_coding	YES	CCDS1143.1	ENSP00000271555	MEF2D_HUMAN	.	UPI000012EEB6	.	.	.	.	6/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACTCACCAA	.	4	ESCA
CD1C	0	.	GRCh37	1	158262075	158262075	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530T>A	p.Val177Glu	p.V177E	ENST00000368170	3/6	39	28	11	40	40	0	CD1C,missense_variant,p.Val177Glu,ENST00000368170,;CD1C,missense_variant,p.Val112Glu,ENST00000443761,;	A	ENSG00000158481	ENST00000368170	Transcript	missense_variant	809	530	177	V/E	gTg/gAg	.	.	.	1	CD1C	HGNC	1636	protein_coding	YES	CCDS1175.1	ENSP00000357152	CD1C_HUMAN	B4DP91_HUMAN	UPI000013DF78	.	deleterious(0.04)	benign(0.045)	3/6	.	hmmpanther:PTHR16675:SF155,hmmpanther:PTHR16675,Gene3D:3.30.500.10,Superfamily_domains:SSF54452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAGTGTATA	.	5	ESCA
PPOX	0	.	GRCh37	1	161140274	161140274	+	Nonsense_Mutation	SNP	G	G	T	rs774289225	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1063G>T	p.Glu355Ter	p.E355*	ENST00000367999	10/13	24	19	5	31	31	0	PPOX,stop_gained,p.Glu355Ter,ENST00000367999,;PPOX,stop_gained,p.Glu100Ter,ENST00000432542,;PPOX,stop_gained,p.Glu78Ter,ENST00000537829,;PPOX,stop_gained,p.Glu355Ter,ENST00000352210,;PPOX,stop_gained,p.Glu108Ter,ENST00000537523,;PPOX,intron_variant,,ENST00000544598,;PPOX,intron_variant,,ENST00000535223,;USP21,downstream_gene_variant,,ENST00000289865,;B4GALT3,downstream_gene_variant,,ENST00000367998,;USP21,downstream_gene_variant,,ENST00000368002,;B4GALT3,downstream_gene_variant,,ENST00000319769,;USP21,downstream_gene_variant,,ENST00000368001,;PPOX,non_coding_transcript_exon_variant,,ENST00000466452,;PPOX,non_coding_transcript_exon_variant,,ENST00000495483,;PPOX,intron_variant,,ENST00000497522,;PPOX,intron_variant,,ENST00000462866,;B4GALT3,downstream_gene_variant,,ENST00000496313,;B4GALT3,downstream_gene_variant,,ENST00000470882,;B4GALT3,downstream_gene_variant,,ENST00000465740,;B4GALT3,downstream_gene_variant,,ENST00000493164,;PPOX,downstream_gene_variant,,ENST00000490768,;PPOX,downstream_gene_variant,,ENST00000470607,;PPOX,downstream_gene_variant,,ENST00000494216,;B4GALT3,downstream_gene_variant,,ENST00000486938,;USP21,downstream_gene_variant,,ENST00000493054,;B4GALT3,downstream_gene_variant,,ENST00000466504,;PPOX,downstream_gene_variant,,ENST00000462977,;B4GALT3,downstream_gene_variant,,ENST00000487004,;PPOX,downstream_gene_variant,,ENST00000460611,;PPOX,3_prime_UTR_variant,,ENST00000539753,;PPOX,non_coding_transcript_exon_variant,,ENST00000541818,;PPOX,downstream_gene_variant,,ENST00000468968,;USP21,downstream_gene_variant,,ENST00000485277,;PPOX,downstream_gene_variant,,ENST00000479246,;USP21,downstream_gene_variant,,ENST00000487163,;	T	ENSG00000143224	ENST00000367999	Transcript	stop_gained	1329	1063	355	E/*	Gag/Tag	rs774289225	.	.	1	PPOX	HGNC	9280	protein_coding	YES	CCDS1221.1	ENSP00000356978	PPOX_HUMAN	Q96TC9_HUMAN,Q96SE3_HUMAN	UPI0000000C3C	.	.	.	10/13	.	hmmpanther:PTHR10742:SF16,hmmpanther:PTHR10742,Pfam_domain:PF01593,Gene3D:1sezA02,TIGRFAM_domain:TIGR00562,Superfamily_domains:SSF54373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCTGAGCAG	byFrequency	2	ESCA
DUSP27	0	.	GRCh37	1	167096823	167096823	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2455A>G	p.Thr819Ala	p.T819A	ENST00000361200	6/6	36	25	11	40	40	0	DUSP27,missense_variant,p.Thr819Ala,ENST00000361200,;DUSP27,missense_variant,p.Thr819Ala,ENST00000443333,;DUSP27,missense_variant,p.Thr819Ala,ENST00000271385,;DUSP27,intron_variant,,ENST00000485151,;	G	ENSG00000198842	ENST00000361200	Transcript	missense_variant	2621	2455	819	T/A	Acc/Gcc	.	.	.	1	DUSP27	HGNC	25034	protein_coding	YES	CCDS30932.1	ENSP00000354483	DUS27_HUMAN	.	UPI000040DFF5	.	deleterious(0.02)	benign(0.113)	6/6	.	hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGACCAGC	.	5	ESCA
GABRD	0	.	GRCh37	1	1961759	1961759	+	3'UTR	SNP	C	C	T	rs774210907	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*38C>T	.	.	ENST00000378585	9/9	18	11	7	27	27	0	GABRD,3_prime_UTR_variant,,ENST00000378585,;	T	ENSG00000187730	ENST00000378585	Transcript	3_prime_UTR_variant	1480	.	.	.	.	rs774210907	.	.	1	GABRD	HGNC	4084	protein_coding	YES	CCDS36.1	ENSP00000367848	GBRD_HUMAN	.	UPI0000070D0A	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCCCGGCGG	.	2	ESCA
REN	0	.	GRCh37	1	204131165	204131165	+	Silent	SNP	G	G	A	rs374481579	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.225C>T	p.%3D	p.S75S	ENST00000272190	2/10	51	38	13	63	63	0	REN,synonymous_variant,p.%3D,ENST00000272190,;REN,synonymous_variant,p.%3D,ENST00000367195,;	A	ENSG00000143839	ENST00000272190	Transcript	synonymous_variant	254	225	75	S	tcC/tcT	rs374481579	.	.	-1	REN	HGNC	9958	protein_coding	YES	CCDS30981.1	ENSP00000272190	RENI_HUMAN	Q9UQK5_HUMAN	UPI000000091F	.	.	.	2/10	.	hmmpanther:PTHR13683:SF77,hmmpanther:PTHR13683,Superfamily_domains:SSF50630	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCACGGAGGA	byCluster	5	ESCA
PIK3C2B	0	.	GRCh37	1	204393389	204393389	+	3'UTR	SNP	G	G	T	rs531152790	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*591C>A	.	.	ENST00000367187	34/34	41	23	17	65	65	0	PIK3C2B,3_prime_UTR_variant,,ENST00000367187,;PIK3C2B,3_prime_UTR_variant,,ENST00000424712,;RP11-739N20.2,intron_variant,,ENST00000443515,;	T	ENSG00000133056	ENST00000367187	Transcript	3_prime_UTR_variant	6053	.	.	.	.	rs531152790	.	.	-1	PIK3C2B	HGNC	8972	protein_coding	YES	CCDS1446.1	ENSP00000356155	P3C2B_HUMAN	Q5SW98_HUMAN,Q5SW97_HUMAN,Q4LE65_HUMAN,A2RUF7_HUMAN	UPI00002056D1	.	.	.	34/34	.	.	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGGGCTCT	by1000G	5	ESCA
SLC41A1	0	.	GRCh37	1	205779531	205779531	+	Silent	SNP	C	C	T	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39G>A	p.%3D	p.L13L	ENST00000367137	2/11	27	21	6	41	41	0	SLC41A1,synonymous_variant,p.%3D,ENST00000367137,;SLC41A1,non_coding_transcript_exon_variant,,ENST00000484000,;	T	ENSG00000133065	ENST00000367137	Transcript	synonymous_variant	1054	39	13	L	ctG/ctA	COSM1500760	.	.	-1	SLC41A1	HGNC	19429	protein_coding	YES	CCDS30988.1	ENSP00000356105	S41A1_HUMAN	B2RMP2_HUMAN	UPI000013E1E6	.	.	.	2/11	.	hmmpanther:PTHR16228:SF23,hmmpanther:PTHR16228	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTTCAGTTG	.	5	ESCA
KCTD3	0	.	GRCh37	1	215793669	215793669	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2157G>C	p.Leu719Phe	p.L719F	ENST00000259154	18/18	43	37	6	39	39	0	KCTD3,missense_variant,p.Leu719Phe,ENST00000259154,;USH2A,downstream_gene_variant,,ENST00000366943,;KCTD3,downstream_gene_variant,,ENST00000452413,;USH2A,downstream_gene_variant,,ENST00000307340,;KCTD3,non_coding_transcript_exon_variant,,ENST00000495537,;KCTD3,downstream_gene_variant,,ENST00000465650,;	C	ENSG00000136636	ENST00000259154	Transcript	missense_variant	2451	2157	719	L/F	ttG/ttC	.	.	.	1	KCTD3	HGNC	21305	protein_coding	YES	CCDS1515.1	ENSP00000259154	KCTD3_HUMAN	B4DJX2_HUMAN	UPI0000071A2E	.	tolerated_low_confidence(0.71)	benign(0.019)	18/18	.	hmmpanther:PTHR15859,hmmpanther:PTHR15859:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTGAGAGA	.	5	ESCA
RP11-421L10.1	0	.	GRCh37	1	221507319	221507319	+	RNA	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.443G>C	.	.	ENST00000439004	2/2	32	25	6	51	51	0	RP11-421L10.1,non_coding_transcript_exon_variant,,ENST00000434398,;RP11-421L10.1,non_coding_transcript_exon_variant,,ENST00000439004,;	G	ENSG00000234754	ENST00000439004	Transcript	non_coding_transcript_exon_variant	443	.	.	.	.	.	.	.	-1	RP11-421L10.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATCCTTTGC	.	5	ESCA
OBSCN	0	.	GRCh37	1	228467709	228467709	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8871C>T	p.%3D	p.L2957L	ENST00000570156	33/116	23	18	5	29	29	0	OBSCN,synonymous_variant,p.%3D,ENST00000284548,;OBSCN,synonymous_variant,p.%3D,ENST00000359599,;OBSCN,synonymous_variant,p.%3D,ENST00000366706,;OBSCN,synonymous_variant,p.%3D,ENST00000570156,;OBSCN,synonymous_variant,p.%3D,ENST00000422127,;OBSCN,5_prime_UTR_variant,,ENST00000366707,;OBSCN,5_prime_UTR_variant,,ENST00000366709,;OBSCN,upstream_gene_variant,,ENST00000483539,;RP5-1139B12.3,upstream_gene_variant,,ENST00000602529,;RP5-1139B12.3,upstream_gene_variant,,ENST00000602947,;OBSCN,upstream_gene_variant,,ENST00000366704,;	T	ENSG00000154358	ENST00000570156	Transcript	synonymous_variant	8945	8871	2957	L	ctC/ctT	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	.	33/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCCGGCT	.	5	ESCA
DESI2	0	.	GRCh37	1	244870668	244870668	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1577A>G	.	.	ENST00000302550	5/5	58	39	18	46	46	0	DESI2,3_prime_UTR_variant,,ENST00000302550,;DESI2,downstream_gene_variant,,ENST00000263831,;	G	ENSG00000121644	ENST00000302550	Transcript	3_prime_UTR_variant	2541	.	.	.	.	.	.	.	1	DESI2	HGNC	24264	protein_coding	YES	CCDS1626.1	ENSP00000306528	DESI2_HUMAN	.	UPI0000038D6C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACAATGAAG	.	5	ESCA
MEGF6	0	.	GRCh37	1	3431144	3431144	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.823C>T	p.Gln275Ter	p.Q275*	ENST00000356575	7/37	11	7	4	27	27	0	MEGF6,stop_gained,p.Gln275Ter,ENST00000356575,;MEGF6,stop_gained,p.Gln170Ter,ENST00000294599,;MEGF6,stop_gained,p.Gln282Ter,ENST00000485002,;	A	ENSG00000162591	ENST00000356575	Transcript	stop_gained	1050	823	275	Q/*	Cag/Tag	.	.	.	-1	MEGF6	HGNC	3232	protein_coding	YES	CCDS41237.1	ENSP00000348982	MEGF6_HUMAN	.	UPI0000DACACB	.	.	.	7/37	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24035:SF29,hmmpanther:PTHR24035,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAGCTGATAGC	.	3	ESCA
AGO1	0	.	GRCh37	1	36387714	36387714	+	3'UTR	SNP	C	C	T	rs536462158	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2506C>T	.	.	ENST00000373204	19/19	39	27	11	42	42	0	AGO1,3_prime_UTR_variant,,ENST00000373204,;AGO1,downstream_gene_variant,,ENST00000373206,;	T	ENSG00000092847	ENST00000373204	Transcript	3_prime_UTR_variant	5293	.	.	.	.	rs536462158	.	.	1	AGO1	HGNC	3262	protein_coding	YES	CCDS398.1	ENSP00000362300	AGO1_HUMAN	Q5TA58_HUMAN	UPI000012D07D	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCTACTC	.	5	ESCA
ZCCHC11	0	.	GRCh37	1	52897011	52897011	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4385A>T	p.Gln1462Leu	p.Q1462L	ENST00000257177	28/30	68	48	19	60	60	0	ZCCHC11,missense_variant,p.Gln34Leu,ENST00000494469,;ZCCHC11,missense_variant,p.Gln307Leu,ENST00000474453,;ZCCHC11,missense_variant,p.Gln299Leu,ENST00000531722,;ZCCHC11,missense_variant,p.Gln1462Leu,ENST00000257177,;ZCCHC11,missense_variant,p.Gln1461Leu,ENST00000371544,;ZCCHC11,upstream_gene_variant,,ENST00000471623,;ZCCHC11,upstream_gene_variant,,ENST00000528457,;ZCCHC11,non_coding_transcript_exon_variant,,ENST00000466440,;ZCCHC11,non_coding_transcript_exon_variant,,ENST00000470212,;ZCCHC11,downstream_gene_variant,,ENST00000469810,;ZCCHC11,upstream_gene_variant,,ENST00000527941,;	A	ENSG00000134744	ENST00000257177	Transcript	missense_variant	4530	4385	1462	Q/L	cAg/cTg	.	.	.	-1	ZCCHC11	HGNC	28981	protein_coding	YES	CCDS30715.1	ENSP00000257177	TUT4_HUMAN	H0YEY0_HUMAN,E9PQS7_HUMAN,E9PJN7_HUMAN	UPI00001D7D0C	.	deleterious(0.02)	probably_damaging(0.992)	28/30	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12271,hmmpanther:PTHR12271:SF49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCTGCTGA	.	5	ESCA
TTLL7	0	.	GRCh37	1	84376889	84376889	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1745A>T	p.Asn582Ile	p.N582I	ENST00000260505	15/21	25	18	7	30	30	0	TTLL7,missense_variant,p.Asn582Ile,ENST00000260505,;TTLL7,non_coding_transcript_exon_variant,,ENST00000477524,;TTLL7,non_coding_transcript_exon_variant,,ENST00000472688,;TTLL7,non_coding_transcript_exon_variant,,ENST00000488014,;TTLL7,upstream_gene_variant,,ENST00000464289,;TTLL7,downstream_gene_variant,,ENST00000474702,;TTLL7,missense_variant,p.Asn267Ile,ENST00000474957,;TTLL7,missense_variant,p.Asn582Ile,ENST00000480174,;TTLL7,missense_variant,p.Asn466Ile,ENST00000485638,;	A	ENSG00000137941	ENST00000260505	Transcript	missense_variant	2123	1745	582	N/I	aAt/aTt	.	.	.	-1	TTLL7	HGNC	26242	protein_coding	YES	CCDS690.2	ENSP00000260505	TTLL7_HUMAN	.	UPI000020391D	.	deleterious_low_confidence(0.01)	benign(0.08)	15/21	.	hmmpanther:PTHR12241:SF11,hmmpanther:PTHR12241	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGATTATAT	.	5	ESCA
GBP1	0	.	GRCh37	1	89520389	89520389	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1641G>C	p.Glu547Asp	p.E547D	ENST00000370473	10/11	29	20	9	30	30	0	GBP1,missense_variant,p.Glu547Asp,ENST00000370473,;GBP1,non_coding_transcript_exon_variant,,ENST00000484970,;GBP1,non_coding_transcript_exon_variant,,ENST00000479889,;GBP1,non_coding_transcript_exon_variant,,ENST00000468959,;GBP1,downstream_gene_variant,,ENST00000493139,;GBP1,downstream_gene_variant,,ENST00000495131,;GBP1,downstream_gene_variant,,ENST00000459831,;	G	ENSG00000117228	ENST00000370473	Transcript	missense_variant	1861	1641	547	E/D	gaG/gaC	.	.	.	-1	GBP1	HGNC	4182	protein_coding	YES	CCDS718.1	ENSP00000359504	GBP1_HUMAN	.	UPI000013C9DF	.	tolerated(0.13)	probably_damaging(0.962)	10/11	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10751:SF21,hmmpanther:PTHR10751,Gene3D:1f5nA01,Pfam_domain:PF02841,Superfamily_domains:0037397	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTCTCTTG	.	5	ESCA
FRG1B	0	.	GRCh37	20	29612021	29612021	+	5'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-216C>G	.	.	ENST00000278882	1/9	79	65	14	120	120	0	FRG1B,5_prime_UTR_variant,,ENST00000278882,;FRG1B,5_prime_UTR_variant,,ENST00000439954,;FRG1B,5_prime_UTR_variant,,ENST00000358464,;FRG1B,non_coding_transcript_exon_variant,,ENST00000468180,;FRG1B,upstream_gene_variant,,ENST00000482423,;	G	ENSG00000149531	ENST00000278882	Transcript	5_prime_UTR_variant	165	.	.	.	.	.	.	.	1	FRG1B	HGNC	15792	protein_coding	YES	.	ENSP00000278882	FRG1B_HUMAN	.	UPI000012AC05	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCAGCCTGTCC	.	4	ESCA
ZNF831	0	.	GRCh37	20	57767928	57767928	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1854G>C	p.Glu618Asp	p.E618D	ENST00000371030	1/5	12	7	4	34	34	0	ZNF831,missense_variant,p.Glu618Asp,ENST00000371030,;	C	ENSG00000124203	ENST00000371030	Transcript	missense_variant	1854	1854	618	E/D	gaG/gaC	.	.	.	1	ZNF831	HGNC	16167	protein_coding	YES	CCDS42894.1	ENSP00000360069	ZN831_HUMAN	.	UPI00001D82E4	.	tolerated(0.18)	benign(0.029)	1/5	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGGAGAAGTG	.	3	ESCA
SLC37A1	0	.	GRCh37	21	43955658	43955658	+	Silent	SNP	C	C	A	rs199619177	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348C>A	p.%3D	p.L116L	ENST00000352133	5/20	53	46	7	88	88	0	SLC37A1,synonymous_variant,p.%3D,ENST00000398341,;SLC37A1,synonymous_variant,p.%3D,ENST00000352133,;	A	ENSG00000160190	ENST00000352133	Transcript	synonymous_variant	1330	348	116	L	ctC/ctA	rs199619177	.	.	1	SLC37A1	HGNC	11024	protein_coding	YES	CCDS13689.1	ENSP00000344648	GLPT_HUMAN	.	UPI00001AEB81	.	.	.	5/20	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,PIRSF_domain:PIRSF002808,Pfam_domain:PF07690,Gene3D:1.20.1250.20,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF225,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCTCAGGTA	.	4	ESCA
PDXK	0	.	GRCh37	21	45152521	45152521	+	Intron	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88-1429C>T	.	.	ENST00000291565	.	51	45	5	57	57	0	PDXK,missense_variant,p.Ser88Leu,ENST00000327574,;PDXK,intron_variant,,ENST00000398081,;PDXK,intron_variant,,ENST00000468090,;PDXK,intron_variant,,ENST00000291565,;PDXK,intron_variant,,ENST00000476313,;PDXK,intron_variant,,ENST00000498040,;PDXK,intron_variant,,ENST00000398085,;PDXK,intron_variant,,ENST00000470029,;PDXK,intron_variant,,ENST00000472777,;PDXK,upstream_gene_variant,,ENST00000481512,;PDXK,downstream_gene_variant,,ENST00000438837,;	T	ENSG00000160209	ENST00000291565	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PDXK	HGNC	8819	protein_coding	YES	CCDS13699.1	ENSP00000291565	PDXK_HUMAN	G1UI32_HUMAN	UPI0000131524	.	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTTCACAGT	.	4	ESCA
SLC19A1	0	.	GRCh37	21	46950838	46950838	+	Missense_Mutation	SNP	G	G	A	rs751719682	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.997C>T	p.Arg333Cys	p.R333C	ENST00000311124	4/6	30	21	9	31	31	0	SLC19A1,missense_variant,p.Arg333Cys,ENST00000567670,;SLC19A1,missense_variant,p.Arg333Cys,ENST00000311124,;SLC19A1,missense_variant,p.Arg333Cys,ENST00000380010,;SLC19A1,missense_variant,p.Arg68Cys,ENST00000417954,;SLC19A1,missense_variant,p.Arg293Cys,ENST00000485649,;SLC19A1,downstream_gene_variant,,ENST00000443742,;SLC19A1,downstream_gene_variant,,ENST00000427839,;SLC19A1,downstream_gene_variant,,ENST00000477688,;	A	ENSG00000173638	ENST00000311124	Transcript	missense_variant	1150	997	333	R/C	Cgc/Tgc	rs751719682	.	.	-1	SLC19A1	HGNC	10937	protein_coding	YES	CCDS13725.1	ENSP00000308895	S19A1_HUMAN	E9PIL5_HUMAN,D3DSM6_HUMAN,C9JKP4_HUMAN,C9J8K6_HUMAN	UPI000012AA0F	.	deleterious(0.01)	possibly_damaging(0.532)	4/6	.	hmmpanther:PTHR10686:SF12,hmmpanther:PTHR10686,Gene3D:1.20.1250.20,Pfam_domain:PF01770,TIGRFAM_domain:TIGR00806,PIRSF_domain:PIRSF500793,PIRSF_domain:PIRSF028739,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGCGCCC	.	5	ESCA
HMGXB4	0	.	GRCh37	22	35659857	35659857	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.249C>G	p.Tyr83Ter	p.Y83*	ENST00000216106	4/11	61	48	12	50	50	0	HMGXB4,stop_gained,p.Tyr83Ter,ENST00000216106,;HMGXB4,5_prime_UTR_variant,,ENST00000444518,;HMGXB4,5_prime_UTR_variant,,ENST00000455359,;HMGXB4,5_prime_UTR_variant,,ENST00000420166,;HMGXB4,stop_gained,p.Tyr83Ter,ENST00000418170,;HMGXB4,non_coding_transcript_exon_variant,,ENST00000464480,;HMGXB4,non_coding_transcript_exon_variant,,ENST00000498325,;	G	ENSG00000100281	ENST00000216106	Transcript	stop_gained	377	249	83	Y/*	taC/taG	.	.	.	1	HMGXB4	HGNC	5003	protein_coding	YES	CCDS33641.1	ENSP00000216106	HMGX4_HUMAN	Q7Z641_HUMAN,B0QXZ9_HUMAN,B0QXZ8_HUMAN	UPI00003765B4	.	.	.	4/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTACTACTA	.	5	ESCA
MFNG	0	.	GRCh37	22	37875509	37875509	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435C>T	p.%3D	p.N145N	ENST00000356998	4/8	66	51	14	99	99	0	MFNG,synonymous_variant,p.%3D,ENST00000436341,;MFNG,synonymous_variant,p.%3D,ENST00000442496,;MFNG,synonymous_variant,p.%3D,ENST00000416983,;MFNG,synonymous_variant,p.%3D,ENST00000356998,;MFNG,downstream_gene_variant,,ENST00000424765,;MFNG,upstream_gene_variant,,ENST00000454291,;MFNG,missense_variant,p.Thr129Ile,ENST00000438891,;MFNG,3_prime_UTR_variant,,ENST00000430411,;MFNG,downstream_gene_variant,,ENST00000466943,;	A	ENSG00000100060	ENST00000356998	Transcript	synonymous_variant	659	435	145	N	aaC/aaT	.	.	.	-1	MFNG	HGNC	7038	protein_coding	YES	CCDS13947.1	ENSP00000349490	MFNG_HUMAN	B4DNA5_HUMAN,A9UJQ1_HUMAN,A9UJQ0_HUMAN	UPI000012F045	.	.	.	4/8	.	hmmpanther:PTHR10811,hmmpanther:PTHR10811:SF6,Pfam_domain:PF02434,PIRSF_domain:PIRSF038073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATAGTTGTC	.	5	ESCA
ANAPC1	0	.	GRCh37	2	112529998	112529998	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5639C>G	p.Ser1880Ter	p.S1880*	ENST00000341068	47/48	15	10	5	17	17	0	ANAPC1,stop_gained,p.Ser1880Ter,ENST00000341068,;ANAPC1,stop_gained,p.Ser1415Ter,ENST00000427997,;MIR4771-2,upstream_gene_variant,,ENST00000577758,;ANAPC1,non_coding_transcript_exon_variant,,ENST00000462785,;	C	ENSG00000153107	ENST00000341068	Transcript	stop_gained	6412	5639	1880	S/*	tCa/tGa	.	.	.	-1	ANAPC1	HGNC	19988	protein_coding	YES	CCDS2093.1	ENSP00000339109	APC1_HUMAN	.	UPI000006EC6E	.	.	.	47/48	.	hmmpanther:PTHR12827	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GCTGTGATTCC	.	3	ESCA
TPO	0	.	GRCh37	2	1459852	1459852	+	Missense_Mutation	SNP	G	G	T	rs144088710	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617G>T	p.Arg206Leu	p.R206L	ENST00000345913	7/17	28	15	13	34	34	0	TPO,missense_variant,p.Arg206Leu,ENST00000329066,;TPO,missense_variant,p.Arg206Leu,ENST00000337415,;TPO,missense_variant,p.Arg206Leu,ENST00000382198,;TPO,missense_variant,p.Arg206Leu,ENST00000382201,;TPO,missense_variant,p.Arg206Leu,ENST00000349624,;TPO,missense_variant,p.Arg206Leu,ENST00000346956,;TPO,missense_variant,p.Arg135Leu,ENST00000422464,;TPO,missense_variant,p.Arg206Leu,ENST00000345913,;TPO,downstream_gene_variant,,ENST00000423320,;TPO,intron_variant,,ENST00000497517,;	T	ENSG00000115705	ENST00000345913	Transcript	missense_variant	708	617	206	R/L	cGg/cTg	rs144088710,COSM1305679	.	.	1	TPO	HGNC	12015	protein_coding	YES	CCDS1643.1	ENSP00000318820	PERT_HUMAN	Q53QT2_HUMAN,C9J511_HUMAN	UPI000013D480	.	deleterious(0)	probably_damaging(0.994)	7/17	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF60,Pfam_domain:PF03098,Gene3D:1.10.640.10,Superfamily_domains:SSF48113	.	.	.	.	.	.	.	A:0.0002	A:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCCGGGAGG	byCluster	5	ESCA
CACNB4	0	.	GRCh37	2	152695190	152695190	+	3'UTR	SNP	T	T	C	rs538829019	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*443A>G	.	.	ENST00000539935	14/14	53	45	8	49	49	0	CACNB4,3_prime_UTR_variant,,ENST00000534999,;CACNB4,3_prime_UTR_variant,,ENST00000360283,;CACNB4,3_prime_UTR_variant,,ENST00000539935,;CACNB4,3_prime_UTR_variant,,ENST00000439467,;CACNB4,downstream_gene_variant,,ENST00000427385,;CACNB4,downstream_gene_variant,,ENST00000397327,;CACNB4,downstream_gene_variant,,ENST00000201943,;	C	ENSG00000182389	ENST00000539935	Transcript	3_prime_UTR_variant	2074	.	.	.	.	rs538829019	.	.	-1	CACNB4	HGNC	1404	protein_coding	YES	CCDS46426.1	ENSP00000438949	CACB4_HUMAN	Q9NZA2_HUMAN,Q580I4_HUMAN,Q53S65_HUMAN	UPI0000208F1E	.	.	.	14/14	.	.	C:0.0008	C:0	C:0.0014	.	C:0.002	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTTTCCCCC	byFrequency|by1000G	4	ESCA
FAP	0	.	GRCh37	2	163055274	163055274	+	Silent	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1395C>G	p.%3D	p.V465V	ENST00000188790	16/26	50	42	8	59	59	0	FAP,synonymous_variant,p.%3D,ENST00000443424,;FAP,synonymous_variant,p.%3D,ENST00000188790,;FAP,synonymous_variant,p.%3D,ENST00000422436,;FAP,non_coding_transcript_exon_variant,,ENST00000465088,;FAP,non_coding_transcript_exon_variant,,ENST00000465424,;FAP,upstream_gene_variant,,ENST00000497414,;	C	ENSG00000078098	ENST00000188790	Transcript	synonymous_variant	1603	1395	465	V	gtC/gtG	.	.	.	-1	FAP	HGNC	3590	protein_coding	YES	CCDS33311.1	ENSP00000188790	SEPR_HUMAN	C9J131_HUMAN	UPI00000012A2	.	.	.	16/26	.	hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF111,Gene3D:2.140.10.30,Pfam_domain:PF00930,Superfamily_domains:SSF82171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCAGACAAG	.	5	ESCA
SCN9A	0	.	GRCh37	2	167133514	167133514	+	Silent	SNP	G	G	A	rs764006250	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2820C>T	p.%3D	p.V940V	ENST00000409672	16/27	65	53	12	84	84	0	SCN9A,synonymous_variant,p.%3D,ENST00000409672,;SCN9A,synonymous_variant,p.%3D,ENST00000375387,;SCN9A,synonymous_variant,p.%3D,ENST00000409435,;SCN9A,synonymous_variant,p.%3D,ENST00000303354,;SCN9A,downstream_gene_variant,,ENST00000452182,;SCN9A,downstream_gene_variant,,ENST00000454569,;AC010127.3,intron_variant,,ENST00000447809,;	A	ENSG00000169432	ENST00000409672	Transcript	synonymous_variant	3167	2820	940	V	gtC/gtT	rs764006250	.	.	-1	SCN9A	HGNC	10597	protein_coding	YES	CCDS46441.1	ENSP00000386306	SCN9A_HUMAN	Q53QP0_HUMAN	UPI0000140AC7	.	.	.	16/27	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF28,Pfam_domain:PF00520,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATGACCAT	byFrequency	5	ESCA
DYNC1I2	0	.	GRCh37	2	172584463	172584463	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129G>A	p.Ala377Thr	p.A377T	ENST00000397119	12/18	55	41	13	46	46	0	DYNC1I2,missense_variant,p.Ala351Thr,ENST00000508530,;DYNC1I2,missense_variant,p.Ala351Thr,ENST00000340296,;DYNC1I2,missense_variant,p.Ala351Thr,ENST00000409197,;DYNC1I2,missense_variant,p.Ala377Thr,ENST00000397119,;DYNC1I2,missense_variant,p.Ala377Thr,ENST00000409453,;DYNC1I2,missense_variant,p.Ala371Thr,ENST00000263811,;DYNC1I2,missense_variant,p.Ala377Thr,ENST00000534253,;DYNC1I2,missense_variant,p.Ala369Thr,ENST00000358002,;DYNC1I2,missense_variant,p.Ala371Thr,ENST00000409317,;DYNC1I2,missense_variant,p.Ala369Thr,ENST00000410079,;DYNC1I2,missense_variant,p.Ala377Thr,ENST00000409773,;DYNC1I2,downstream_gene_variant,,ENST00000435234,;DYNC1I2,downstream_gene_variant,,ENST00000425485,;DYNC1I2,downstream_gene_variant,,ENST00000452242,;DYNC1I2,downstream_gene_variant,,ENST00000456808,;DYNC1I2,downstream_gene_variant,,ENST00000438879,;DYNC1I2,downstream_gene_variant,,ENST00000423910,;DYNC1I2,downstream_gene_variant,,ENST00000422646,;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000479806,;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000482454,;DYNC1I2,downstream_gene_variant,,ENST00000470286,;DYNC1I2,downstream_gene_variant,,ENST00000445378,;	A	ENSG00000077380	ENST00000397119	Transcript	missense_variant	1296	1129	377	A/T	Gca/Aca	.	.	.	1	DYNC1I2	HGNC	2964	protein_coding	YES	CCDS46450.1	ENSP00000380308	DC1I2_HUMAN	Q53SA6_HUMAN,E7ERR6_HUMAN	UPI0000129A05	.	tolerated(0.15)	benign(0.074)	12/18	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF36,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCAGCAGCT	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178097394	178097394	+	Intron	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403-83C>T	.	.	ENST00000397062	.	29	26	3	22	22	0	NFE2L2,3_prime_UTR_variant,,ENST00000423513,;NFE2L2,intron_variant,,ENST00000449627,;NFE2L2,intron_variant,,ENST00000397062,;NFE2L2,intron_variant,,ENST00000446151,;NFE2L2,intron_variant,,ENST00000588123,;NFE2L2,intron_variant,,ENST00000586532,;NFE2L2,intron_variant,,ENST00000421929,;NFE2L2,intron_variant,,ENST00000464747,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,intron_variant,,ENST00000448782,;NFE2L2,intron_variant,,ENST00000397063,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,downstream_gene_variant,,ENST00000462023,;NFE2L2,downstream_gene_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	A	ENSG00000116044	ENST00000397062	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAATGGAATC	.	4	ESCA
VSNL1	0	.	GRCh37	2	17837006	17837006	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*345C>G	.	.	ENST00000406397	4/4	58	46	11	52	52	0	VSNL1,3_prime_UTR_variant,,ENST00000404666,;VSNL1,3_prime_UTR_variant,,ENST00000406397,;VSNL1,3_prime_UTR_variant,,ENST00000295156,;	G	ENSG00000163032	ENST00000406397	Transcript	3_prime_UTR_variant	1446	.	.	.	.	.	.	.	1	VSNL1	HGNC	12722	protein_coding	YES	CCDS1689.1	ENSP00000384719	VISL1_HUMAN	Q53RT2_HUMAN,Q4ZFX3_HUMAN,E9PE24_HUMAN,E7ER47_HUMAN	UPI0000001467	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTATCTCCTT	.	5	ESCA
TTN	0	.	GRCh37	2	179443596	179443596	+	Missense_Mutation	SNP	C	C	T	rs374492812	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.68161G>A	p.Glu22721Lys	p.E22721K	ENST00000589042	320/363	34	26	7	30	30	0	TTN,missense_variant,p.Glu13781Lys,ENST00000359218,;TTN,missense_variant,p.Glu21080Lys,ENST00000591111,;TTN,missense_variant,p.Glu22721Lys,ENST00000589042,;TTN,missense_variant,p.Glu13848Lys,ENST00000342175,;TTN,missense_variant,p.Glu20153Lys,ENST00000342992,;TTN,missense_variant,p.Glu13656Lys,ENST00000460472,;RP11-171I2.2,non_coding_transcript_exon_variant,,ENST00000603521,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;RP11-171I2.5,downstream_gene_variant,,ENST00000604215,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	68386	68161	22721	E/K	Gaa/Aaa	rs374492812,COSM1269237,COSM1269236,COSM1269233,COSM1269235,COSM1269234	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	320/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0003	T:0	uncertain_significance	0,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTCGGCAC	byCluster|by1000G	5	ESCA
TTN	0	.	GRCh37	2	179647024	179647024	+	Missense_Mutation	SNP	C	C	T	rs368282893	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3295G>A	p.Val1099Met	p.V1099M	ENST00000589042	20/363	32	20	12	30	30	0	TTN,missense_variant,p.Val1099Met,ENST00000360870,;TTN,missense_variant,p.Val1099Met,ENST00000342992,;TTN,missense_variant,p.Val1053Met,ENST00000342175,;TTN,missense_variant,p.Val1053Met,ENST00000359218,;TTN,missense_variant,p.Val1099Met,ENST00000589042,;TTN,missense_variant,p.Val1099Met,ENST00000591111,;TTN,missense_variant,p.Val1053Met,ENST00000460472,;TTN,downstream_gene_variant,,ENST00000436599,;RP11-88L24.4,downstream_gene_variant,,ENST00000582038,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	3520	3295	1099	V/M	Gtg/Atg	rs368282893	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	20/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	T:0.0002	T:0.0001	uncertain_significance,likely_pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCACGCTCC	byFrequency|byCluster	5	ESCA
ITGAV	0	.	GRCh37	2	187495554	187495554	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554G>A	p.Cys185Tyr	p.C185Y	ENST00000261023	5/30	32	23	9	33	33	0	ITGAV,missense_variant,p.Cys185Tyr,ENST00000261023,;ITGAV,missense_variant,p.Cys139Tyr,ENST00000433736,;ITGAV,intron_variant,,ENST00000374907,;	A	ENSG00000138448	ENST00000261023	Transcript	missense_variant	828	554	185	C/Y	tGt/tAt	.	.	.	1	ITGAV	HGNC	6150	protein_coding	YES	CCDS2292.1	ENSP00000261023	ITAV_HUMAN	L7RXH0_HUMAN	UPI000013D12E	.	deleterious(0)	probably_damaging(0.999)	5/30	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF4,hmmpanther:PTHR23220,Gene3D:3nigC00,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTGTCAAG	.	5	ESCA
GTF3C2	0	.	GRCh37	2	27566340	27566340	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.82C>T	p.Gln28Ter	p.Q28*	ENST00000359541	2/19	29	25	4	42	42	0	GTF3C2,stop_gained,p.Gln28Ter,ENST00000264720,;GTF3C2,stop_gained,p.Gln28Ter,ENST00000457748,;GTF3C2,stop_gained,p.Gln28Ter,ENST00000359541,;GTF3C2,stop_gained,p.Gln28Ter,ENST00000423998,;AC109828.1,downstream_gene_variant,,ENST00000587586,;AC109828.1,downstream_gene_variant,,ENST00000589853,;AC109828.1,downstream_gene_variant,,ENST00000589232,;AC109828.1,downstream_gene_variant,,ENST00000590383,;AC109828.1,downstream_gene_variant,,ENST00000588707,;	A	ENSG00000115207	ENST00000359541	Transcript	stop_gained	512	82	28	Q/*	Caa/Taa	.	.	.	-1	GTF3C2	HGNC	4665	protein_coding	YES	CCDS1749.1	ENSP00000352536	TF3C2_HUMAN	Q53SY8_HUMAN,Q53QN0_HUMAN,C9JQ12_HUMAN,C9JNH7_HUMAN	UPI0000074025	.	.	.	2/19	.	hmmpanther:PTHR15052,hmmpanther:PTHR15052:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCTTGTCCAG	.	3	ESCA
DHX57	0	.	GRCh37	2	39088678	39088678	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874G>A	p.Glu292Lys	p.E292K	ENST00000295373	5/24	34	28	6	29	29	0	DHX57,missense_variant,p.Glu292Lys,ENST00000295373,;DHX57,downstream_gene_variant,,ENST00000417233,;AC018693.6,upstream_gene_variant,,ENST00000442829,;DHX57,non_coding_transcript_exon_variant,,ENST00000479345,;DHX57,upstream_gene_variant,,ENST00000492042,;DHX57,missense_variant,p.Glu190Lys,ENST00000457308,;DHX57,non_coding_transcript_exon_variant,,ENST00000474104,;DHX57,non_coding_transcript_exon_variant,,ENST00000460193,;	T	ENSG00000163214	ENST00000295373	Transcript	missense_variant	1001	874	292	E/K	Gaa/Aaa	.	.	.	-1	DHX57	HGNC	20086	protein_coding	YES	CCDS1800.1	ENSP00000295373	DHX57_HUMAN	C9J207_HUMAN,B4DKW2_HUMAN	UPI0000231C8C	.	tolerated(0.87)	benign(0.008)	5/24	.	hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF106,Pfam_domain:PF05773	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTCTTTTG	.	5	ESCA
FSHR	0	.	GRCh37	2	49381432	49381432	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.125C>T	p.Ser42Phe	p.S42F	ENST00000406846	1/10	24	20	4	48	48	0	FSHR,missense_variant,p.Ser42Phe,ENST00000346173,;FSHR,missense_variant,p.Ser42Phe,ENST00000454032,;FSHR,missense_variant,p.Ser42Phe,ENST00000304421,;FSHR,missense_variant,p.Ser42Phe,ENST00000406846,;FSHR,missense_variant,p.Ser42Phe,ENST00000419927,;	A	ENSG00000170820	ENST00000406846	Transcript	missense_variant	245	125	42	S/F	tCt/tTt	.	.	.	-1	FSHR	HGNC	3969	protein_coding	YES	CCDS1843.1	ENSP00000384708	FSHR_HUMAN	F5GZW2_HUMAN,B6UV82_HUMAN,A5JS81_HUMAN	UPI000013E97A	.	tolerated(0.14)	benign(0.412)	1/10	.	hmmpanther:PTHR24372:SF5,hmmpanther:PTHR24372,Gene3D:3.80.10.10,Pfam_domain:PF01462,SMART_domains:SM00013,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCAGAAGGA	.	4	ESCA
NRXN1	0	.	GRCh37	2	50574483	50574483	+	Intron	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3485-110375C>T	.	.	ENST00000404971	.	101	85	15	140	140	0	NRXN1,5_prime_UTR_variant,,ENST00000342183,;NRXN1,intron_variant,,ENST00000405472,;NRXN1,intron_variant,,ENST00000401710,;NRXN1,intron_variant,,ENST00000404971,;NRXN1,intron_variant,,ENST00000406316,;NRXN1,intron_variant,,ENST00000401669,;NRXN1,intron_variant,,ENST00000406859,;NRXN1,intron_variant,,ENST00000402717,;NRXN1,intron_variant,,ENST00000331040,;	A	ENSG00000179915	ENST00000404971	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NRXN1	HGNC	8008	protein_coding	YES	CCDS46282.1	ENSP00000385142	NRX1A_HUMAN	Q08AH0_HUMAN	UPI00015A218A	.	.	.	.	18/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTGGAAGGT	.	4	ESCA
XPO1	0	.	GRCh37	2	61719279	61719279	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1778A>T	p.Gln593Leu	p.Q593L	ENST00000401558	16/25	42	30	11	35	35	0	XPO1,missense_variant,p.Gln593Leu,ENST00000404992,;XPO1,missense_variant,p.Gln593Leu,ENST00000401558,;XPO1,missense_variant,p.Gln593Leu,ENST00000406957,;XPO1,upstream_gene_variant,,ENST00000494468,;XPO1,3_prime_UTR_variant,,ENST00000428210,;XPO1,non_coding_transcript_exon_variant,,ENST00000481073,;XPO1,downstream_gene_variant,,ENST00000469337,;XPO1,downstream_gene_variant,,ENST00000460037,;XPO1,downstream_gene_variant,,ENST00000475744,;XPO1,downstream_gene_variant,,ENST00000437159,;XPO1,upstream_gene_variant,,ENST00000461407,;	A	ENSG00000082898	ENST00000401558	Transcript	missense_variant	2506	1778	593	Q/L	cAa/cTa	.	.	.	-1	XPO1	HGNC	12825	protein_coding	YES	CCDS33205.1	ENSP00000384863	XPO1_HUMAN	C9JV99_HUMAN,C9JQ02_HUMAN,C9JKM9_HUMAN,C9JF49_HUMAN,C9J673_HUMAN,C9IZS4_HUMAN,C9IYM2_HUMAN,B7ZB16_HUMAN,B3KWD0_HUMAN	UPI0000001C23	.	tolerated(0.11)	benign(0.004)	16/25	.	hmmpanther:PTHR11223,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTTGGGCT	.	5	ESCA
VAX2	0	.	GRCh37	2	71160086	71160086	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626delG	p.Gly209AlafsTer11	p.G209Afs*11	ENST00000234392	3/3	48	35	13	80	80	0	VAX2,frameshift_variant,p.Gly209AlafsTer11,ENST00000234392,;ATP6V1B1,upstream_gene_variant,,ENST00000234396,;ATP6V1B1,upstream_gene_variant,,ENST00000412314,;snoU13,upstream_gene_variant,,ENST00000459218,;ATP6V1B1,upstream_gene_variant,,ENST00000432367,;	-	ENSG00000116035	ENST00000234392	Transcript	frameshift_variant	657	625	209	G/X	Ggc/gc	.	.	.	1	VAX2	HGNC	12661	protein_coding	YES	CCDS1911.1	ENSP00000234392	VAX2_HUMAN	F1T0K5_HUMAN	UPI0000138215	.	.	.	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTGCCAGGCCTA	.	3	ESCA
REG3G	0	.	GRCh37	2	79254209	79254209	+	Missense_Mutation	SNP	G	G	T	rs752083175	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245G>T	p.Gly82Val	p.G82V	ENST00000272324	4/6	41	30	10	67	67	0	REG3G,missense_variant,p.Gly82Val,ENST00000393897,;REG3G,missense_variant,p.Gly82Val,ENST00000272324,;REG3G,intron_variant,,ENST00000409471,;REG3G,non_coding_transcript_exon_variant,,ENST00000490944,;REG3G,downstream_gene_variant,,ENST00000498312,;	T	ENSG00000143954	ENST00000272324	Transcript	missense_variant	429	245	82	G/V	gGg/gTg	rs752083175	.	.	1	REG3G	HGNC	29595	protein_coding	YES	CCDS1962.1	ENSP00000272324	REG3G_HUMAN	.	UPI0000048F1E	.	tolerated(0.08)	benign(0.152)	4/6	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF29,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTGGGGCTG	.	5	ESCA
TMEM45A	0	.	GRCh37	3	100295818	100295818	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.784C>G	p.Leu262Val	p.L262V	ENST00000323523	6/6	46	29	17	24	24	0	TMEM45A,missense_variant,p.Leu278Val,ENST00000403410,;TMEM45A,missense_variant,p.Leu262Val,ENST00000323523,;TMEM45A,non_coding_transcript_exon_variant,,ENST00000488904,;TMEM45A,non_coding_transcript_exon_variant,,ENST00000489060,;	G	ENSG00000181458	ENST00000323523	Transcript	missense_variant	1097	784	262	L/V	Ctg/Gtg	.	.	.	1	TMEM45A	HGNC	25480	protein_coding	YES	CCDS2937.1	ENSP00000319009	TM45A_HUMAN	.	UPI0000039E49	.	deleterious(0.04)	possibly_damaging(0.788)	6/6	.	hmmpanther:PTHR16007:SF10,hmmpanther:PTHR16007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCTGAAA	.	5	ESCA
RPL32	0	.	GRCh37	3	12877607	12877607	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394G>A	p.Glu132Lys	p.E132K	ENST00000429711	4/4	64	45	19	69	69	0	RPL32,missense_variant,p.Glu132Lys,ENST00000396957,;RPL32,missense_variant,p.Glu150Lys,ENST00000273223,;RPL32,missense_variant,p.Glu132Lys,ENST00000457131,;RPL32,missense_variant,p.Glu132Lys,ENST00000429711,;RPL32,missense_variant,p.Glu132Lys,ENST00000435983,;RPL32,missense_variant,p.Glu132Lys,ENST00000396953,;CAND2,intron_variant,,ENST00000454887,;RPL32,downstream_gene_variant,,ENST00000434963,;CAND2,downstream_gene_variant,,ENST00000456430,;CAND2,downstream_gene_variant,,ENST00000295989,;SNORA7A,downstream_gene_variant,,ENST00000384765,;RP11-767C1.2,upstream_gene_variant,,ENST00000606447,;RPL32,downstream_gene_variant,,ENST00000452606,;	T	ENSG00000144713	ENST00000429711	Transcript	missense_variant	494	394	132	E/K	Gaa/Aaa	.	.	.	-1	RPL32	HGNC	10336	protein_coding	YES	CCDS2614.1	ENSP00000416429	RL32_HUMAN	D3YTI8_HUMAN,D3YTB1_HUMAN	UPI0000001684	.	tolerated(0.22)	benign(0.003)	4/4	.	hmmpanther:PTHR23413:SF3,hmmpanther:PTHR23413,Superfamily_domains:0037550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCACTGC	.	5	ESCA
COL6A5	0	.	GRCh37	3	130188024	130188024	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7176G>C	p.Trp2392Cys	p.W2392C	ENST00000265379	38/42	48	40	7	55	55	0	COL6A5,missense_variant,p.Trp2392Cys,ENST00000432398,;COL6A5,missense_variant,p.Trp644Cys,ENST00000512836,;COL6A5,missense_variant,p.Trp227Cys,ENST00000512482,;COL6A5,missense_variant,p.Trp335Cys,ENST00000373157,;COL6A5,missense_variant,p.Trp2392Cys,ENST00000265379,;COL6A5,missense_variant,p.Trp2392Cys,ENST00000312481,;	C	ENSG00000172752	ENST00000265379	Transcript	missense_variant	7670	7176	2392	W/C	tgG/tgC	COSM728489,COSM728490	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	deleterious(0)	probably_damaging(0.999)	38/42	.	PROSITE_profiles:PS50234,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTGGACAAT	.	5	ESCA
COL6A5	0	.	GRCh37	3	130188259	130188259	+	Nonsense_Mutation	SNP	C	C	T	rs753445274	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000265379	38/42	60	46	14	56	56	0	COL6A5,stop_gained,p.Arg2471Ter,ENST00000432398,;COL6A5,stop_gained,p.Arg723Ter,ENST00000512836,;COL6A5,stop_gained,p.Arg306Ter,ENST00000512482,;COL6A5,stop_gained,p.Arg414Ter,ENST00000373157,;COL6A5,stop_gained,p.Arg2471Ter,ENST00000265379,;COL6A5,stop_gained,p.Arg2471Ter,ENST00000312481,;	T	ENSG00000172752	ENST00000265379	Transcript	stop_gained	7905	7411	2471	R/*	Cga/Tga	rs753445274	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	.	.	38/42	.	PROSITE_profiles:PS50234,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R510Q|c.1529G>A|3,BUFFER|p.R2471Q|c.7412G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCCGAACC	byFrequency	5	ESCA
CDV3	0	.	GRCh37	3	133306599	133306599	+	Intron	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.627-141T>A	.	.	ENST00000264993	.	34	24	10	27	27	0	CDV3,3_prime_UTR_variant,,ENST00000420115,;CDV3,intron_variant,,ENST00000508481,;CDV3,intron_variant,,ENST00000264993,;CDV3,intron_variant,,ENST00000503932,;CDV3,intron_variant,,ENST00000515421,;CDV3,downstream_gene_variant,,ENST00000511392,;CDV3,downstream_gene_variant,,ENST00000431519,;CDV3,downstream_gene_variant,,ENST00000507408,;CDV3,downstream_gene_variant,,ENST00000504867,;	A	ENSG00000091527	ENST00000264993	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CDV3	HGNC	26928	protein_coding	YES	CCDS3079.1	ENSP00000264993	CDV3_HUMAN	D6R9V8_HUMAN,D6R973_HUMAN	UPI0000072568	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTGATAAGGA	.	4	ESCA
CNTN6	0	.	GRCh37	3	1367589	1367589	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1037A>T	p.Asn346Ile	p.N346I	ENST00000446702	9/23	35	28	7	33	33	0	CNTN6,missense_variant,p.Asn274Ile,ENST00000539053,;CNTN6,missense_variant,p.Asn346Ile,ENST00000446702,;CNTN6,missense_variant,p.Asn346Ile,ENST00000350110,;CNTN6,3_prime_UTR_variant,,ENST00000397479,;	T	ENSG00000134115	ENST00000446702	Transcript	missense_variant	1664	1037	346	N/I	aAc/aTc	.	.	.	1	CNTN6	HGNC	2176	protein_coding	YES	CCDS2557.1	ENSP00000407822	CNTN6_HUMAN	F5H752_HUMAN	UPI0000072430	.	deleterious(0.03)	benign(0.003)	9/23	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF52,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAAACCCTT	.	5	ESCA
XRN1	0	.	GRCh37	3	142030495	142030495	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4979C>A	p.Ala1660Asp	p.A1660D	ENST00000264951	42/42	81	60	21	62	62	0	XRN1,missense_variant,p.Ala1114Asp,ENST00000498077,;XRN1,missense_variant,p.Ala1648Asp,ENST00000392981,;XRN1,missense_variant,p.Ala1660Asp,ENST00000264951,;	T	ENSG00000114127	ENST00000264951	Transcript	missense_variant	5097	4979	1660	A/D	gCt/gAt	.	.	.	-1	XRN1	HGNC	30654	protein_coding	YES	CCDS3123.1	ENSP00000264951	XRN1_HUMAN	C9JCZ8_HUMAN	UPI0000074113	.	tolerated_low_confidence(0.33)	benign(0.077)	42/42	.	PIRSF_domain:PIRSF006743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGAGCAATC	.	5	ESCA
TRPC1	0	.	GRCh37	3	142525201	142525201	+	3'UTR	DEL	A	A	-	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*127delA	.	.	ENST00000476941	13/13	88	78	10	85	85	0	TRPC1,3_prime_UTR_variant,,ENST00000273482,;TRPC1,3_prime_UTR_variant,,ENST00000476941,;	-	ENSG00000144935	ENST00000476941	Transcript	3_prime_UTR_variant	2992	.	.	.	.	.	.	.	1	TRPC1	HGNC	12333	protein_coding	YES	CCDS58856.1	ENSP00000419313	TRPC1_HUMAN	.	UPI00001374A4	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTTTAAAATA	.	3	ESCA
CPA3	0	.	GRCh37	3	148603919	148603919	+	Missense_Mutation	SNP	C	C	G	rs779939415	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1021C>G	p.Arg341Gly	p.R341G	ENST00000296046	10/11	73	62	11	53	53	0	CPA3,missense_variant,p.Arg341Gly,ENST00000296046,;RP11-680B3.2,intron_variant,,ENST00000488190,;CPA3,non_coding_transcript_exon_variant,,ENST00000477926,;	G	ENSG00000163751	ENST00000296046	Transcript	missense_variant	1073	1021	341	R/G	Cga/Gga	rs779939415	.	.	1	CPA3	HGNC	2298	protein_coding	YES	CCDS3138.1	ENSP00000296046	CBPA3_HUMAN	.	UPI000013E2F4	.	tolerated(0.13)	possibly_damaging(0.66)	10/11	.	hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF65,Pfam_domain:PF00246,Gene3D:3.40.630.10,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCGATAT	byFrequency	5	ESCA
PLCH1	0	.	GRCh37	3	155282725	155282725	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000340059	7/23	52	34	17	40	40	0	PLCH1,missense_variant,p.Glu320Gln,ENST00000334686,;PLCH1,missense_variant,p.Glu320Gln,ENST00000414191,;PLCH1,missense_variant,p.Glu338Gln,ENST00000340059,;PLCH1,missense_variant,p.Glu338Gln,ENST00000447496,;PLCH1,missense_variant,p.Glu320Gln,ENST00000460012,;PLCH1,missense_variant,p.Glu338Gln,ENST00000494598,;	G	ENSG00000114805	ENST00000340059	Transcript	missense_variant	1012	1012	338	E/Q	Gag/Cag	.	.	.	-1	PLCH1	HGNC	29185	protein_coding	YES	CCDS46939.1	ENSP00000345988	PLCH1_HUMAN	.	UPI00001D800E	.	tolerated(0.3)	probably_damaging(0.93)	7/23	.	PROSITE_profiles:PS50007,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF51,Pfam_domain:PF00388,Gene3D:3.20.20.190,SMART_domains:SM00148,Superfamily_domains:SSF51695,Prints_domain:PR00390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCTTGCA	.	5	ESCA
HES1	0	.	GRCh37	3	193854799	193854799	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.254T>C	p.Val85Ala	p.V85A	ENST00000232424	3/4	31	21	10	53	53	0	HES1,missense_variant,p.Val85Ala,ENST00000232424,;HES1,non_coding_transcript_exon_variant,,ENST00000476918,;	C	ENSG00000114315	ENST00000232424	Transcript	missense_variant	490	254	85	V/A	gTg/gCg	.	.	.	1	HES1	HGNC	5192	protein_coding	YES	CCDS3305.1	ENSP00000232424	HES1_HUMAN	Q8IXV0_HUMAN	UPI0000037B01	.	deleterious(0)	probably_damaging(0.996)	3/4	.	PROSITE_profiles:PS50888,hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF19,Gene3D:4.10.280.10,Pfam_domain:PF00010,SMART_domains:SM00353,Superfamily_domains:SSF47459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACAGTGAAGC	.	5	ESCA
MUC20	0	.	GRCh37	3	195452647	195452647	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1173C>T	p.%3D	p.G391G	ENST00000447234	2/4	69	56	12	99	98	1	MUC20,synonymous_variant,p.%3D,ENST00000445522,;MUC20,synonymous_variant,p.%3D,ENST00000447234,;MUC20,synonymous_variant,p.%3D,ENST00000320736,;MUC20,synonymous_variant,p.%3D,ENST00000436408,;MUC20,upstream_gene_variant,,ENST00000423938,;LINC00969,intron_variant,,ENST00000597662,;LINC00969,intron_variant,,ENST00000595086,;LINC00969,intron_variant,,ENST00000600197,;LINC00969,intron_variant,,ENST00000594446,;LINC00969,downstream_gene_variant,,ENST00000599566,;LINC00969,downstream_gene_variant,,ENST00000455807,;LINC00969,downstream_gene_variant,,ENST00000600288,;LINC00969,downstream_gene_variant,,ENST00000432194,;LINC00969,downstream_gene_variant,,ENST00000594976,;MUC20,downstream_gene_variant,,ENST00000485430,;MUC20,downstream_gene_variant,,ENST00000480350,;MUC20,upstream_gene_variant,,ENST00000498018,;	T	ENSG00000176945	ENST00000447234	Transcript	synonymous_variant	1299	1173	391	G	ggC/ggT	.	.	.	1	MUC20	HGNC	23282	protein_coding	YES	CCDS63877.1	ENSP00000414350	MUC20_HUMAN	I0EZ60_HUMAN,I0EZ59_HUMAN,I0CMK3_HUMAN,I0CMJ9_HUMAN	UPI000198CC5A	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G391S|c.1171G>A|3,BUFFER|p.P392L|c.1175C>T|4	RADIA|VARSCANS	GACGGCCCCCA	.	2	ESCA
RYBP	0	.	GRCh37	3	72426821	72426821	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*715T>A	.	.	ENST00000477973	4/4	33	19	14	25	25	0	RYBP,3_prime_UTR_variant,,ENST00000477973,;	T	ENSG00000163602	ENST00000477973	Transcript	3_prime_UTR_variant	1667	.	.	.	.	.	.	.	-1	RYBP	HGNC	10480	protein_coding	YES	.	ENSP00000419494	RYBP_HUMAN	.	UPI0001B794AD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAAAATATA	.	5	ESCA
SLC39A8	0	.	GRCh37	4	103184069	103184069	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*132T>C	.	.	ENST00000394833	8/8	23	18	5	17	17	0	SLC39A8,3_prime_UTR_variant,,ENST00000356736,;SLC39A8,3_prime_UTR_variant,,ENST00000394833,;SLC39A8,intron_variant,,ENST00000424970,;	G	ENSG00000138821	ENST00000394833	Transcript	3_prime_UTR_variant	1992	.	.	.	.	.	.	.	-1	SLC39A8	HGNC	20862	protein_coding	YES	CCDS3656.1	ENSP00000378310	S39A8_HUMAN	.	UPI0000046C4E	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAATAATTAG	.	2	ESCA
DCHS2	0	.	GRCh37	4	155412323	155412323	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.185C>A	p.Ser62Tyr	p.S62Y	ENST00000443500	1/2	23	19	4	53	53	0	DCHS2,missense_variant,p.Ser62Tyr,ENST00000443500,;DCHS2,missense_variant,p.Ser62Tyr,ENST00000339452,;DCHS2,missense_variant,p.Ser55Tyr,ENST00000456341,;	T	ENSG00000197410	ENST00000443500	Transcript	missense_variant	608	185	62	S/Y	tCc/tAc	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	.	CCDS47151.1	ENSP00000395539	.	Q6V1P8_HUMAN,E9PG03_HUMAN	UPI0001881B4E	.	deleterious(0.02)	possibly_damaging(0.653)	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGAGGAGCCC	.	2	ESCA
SLIT2	0	.	GRCh37	4	20552484	20552484	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2524G>A	p.Glu842Lys	p.E842K	ENST00000504154	25/37	31	26	5	28	28	0	SLIT2,missense_variant,p.Glu846Lys,ENST00000273739,;SLIT2,missense_variant,p.Glu842Lys,ENST00000504154,;SLIT2,missense_variant,p.Glu834Lys,ENST00000503823,;SLIT2,missense_variant,p.Glu838Lys,ENST00000503837,;SLIT2,missense_variant,p.Glu43Lys,ENST00000511508,;SLIT2,upstream_gene_variant,,ENST00000509941,;SLIT2,non_coding_transcript_exon_variant,,ENST00000509394,;	A	ENSG00000145147	ENST00000504154	Transcript	missense_variant	2776	2524	842	E/K	Gaa/Aaa	.	.	.	1	SLIT2	HGNC	11086	protein_coding	YES	CCDS3426.1	ENSP00000422591	SLIT2_HUMAN	Q4W5N0_HUMAN,Q4W5K2_HUMAN,B3KNE2_HUMAN	UPI00000747E4	.	deleterious(0.02)	benign(0.245)	25/37	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF107,hmmpanther:PTHR24373,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTGAAGGT	.	5	ESCA
SLIT2	0	.	GRCh37	4	20620418	20620418	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4376G>C	p.Arg1459Thr	p.R1459T	ENST00000504154	37/37	25	20	5	29	29	0	SLIT2,missense_variant,p.Arg1472Thr,ENST00000273739,;SLIT2,missense_variant,p.Arg1459Thr,ENST00000504154,;SLIT2,missense_variant,p.Arg1451Thr,ENST00000503823,;SLIT2,missense_variant,p.Arg1455Thr,ENST00000503837,;SLIT2,intron_variant,,ENST00000512993,;SLIT2,non_coding_transcript_exon_variant,,ENST00000508541,;	C	ENSG00000145147	ENST00000504154	Transcript	missense_variant	4628	4376	1459	R/T	aGa/aCa	.	.	.	1	SLIT2	HGNC	11086	protein_coding	YES	CCDS3426.1	ENSP00000422591	SLIT2_HUMAN	Q4W5N0_HUMAN,Q4W5K2_HUMAN,B3KNE2_HUMAN	UPI00000747E4	.	deleterious(0)	probably_damaging(0.985)	37/37	.	PROSITE_profiles:PS01225,SMART_domains:SM00041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAAGAGATT	.	2	ESCA
ARAP2	0	.	GRCh37	4	36230811	36230811	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298C>T	p.Gln100Ter	p.Q100*	ENST00000303965	2/33	30	23	6	32	32	0	ARAP2,stop_gained,p.Gln100Ter,ENST00000303965,;ARAP2,downstream_gene_variant,,ENST00000506189,;ARAP2,non_coding_transcript_exon_variant,,ENST00000508066,;	A	ENSG00000047365	ENST00000303965	Transcript	stop_gained	788	298	100	Q/*	Cag/Tag	.	.	.	-1	ARAP2	HGNC	16924	protein_coding	YES	CCDS3441.1	ENSP00000302895	ARAP2_HUMAN	D6RAD6_HUMAN	UPI000013E917	.	.	.	2/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTGATCAG	.	5	ESCA
ATP8A1	0	.	GRCh37	4	42627653	42627653	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242T>C	p.Phe81Ser	p.F81S	ENST00000381668	3/37	75	60	15	66	66	0	ATP8A1,missense_variant,p.Phe81Ser,ENST00000381668,;ATP8A1,missense_variant,p.Phe81Ser,ENST00000264449,;ATP8A1,3_prime_UTR_variant,,ENST00000510289,;	G	ENSG00000124406	ENST00000381668	Transcript	missense_variant	474	242	81	F/S	tTt/tCt	.	.	.	-1	ATP8A1	HGNC	13531	protein_coding	YES	CCDS3466.1	ENSP00000371084	AT8A1_HUMAN	H0YAJ4_HUMAN	UPI0000125063	.	deleterious(0)	probably_damaging(0.986)	3/37	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF56,Gene3D:2.70.150.10,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAAAAAAT	.	5	ESCA
HSD17B13	0	.	GRCh37	4	88231439	88231439	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.768G>A	p.Met256Ile	p.M256I	ENST00000328546	6/7	103	81	22	112	112	0	HSD17B13,missense_variant,p.Met220Ile,ENST00000302219,;HSD17B13,missense_variant,p.Met256Ile,ENST00000328546,;	T	ENSG00000170509	ENST00000328546	Transcript	missense_variant	833	768	256	M/I	atG/atA	COSM1431585	.	.	-1	HSD17B13	HGNC	18685	protein_coding	YES	CCDS3618.1	ENSP00000333300	DHB13_HUMAN	.	UPI00000350AE	.	tolerated(0.21)	benign(0.008)	6/7	.	Superfamily_domains:SSF51735,PIRSF_domain:PIRSF000126,hmmpanther:PTHR24316,hmmpanther:PTHR24316:SF247	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCATTTT	.	5	ESCA
MARCH6	0	.	GRCh37	5	10382027	10382027	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306A>G	p.%3D	p.A102A	ENST00000274140	4/26	36	29	6	25	25	0	MARCH6,synonymous_variant,p.%3D,ENST00000274140,;MARCH6,intron_variant,,ENST00000449913,;MARCH6,intron_variant,,ENST00000503788,;MARCH6,non_coding_transcript_exon_variant,,ENST00000507863,;MARCH6,non_coding_transcript_exon_variant,,ENST00000510872,;MARCH6,non_coding_transcript_exon_variant,,ENST00000511802,;MARCH6,intron_variant,,ENST00000502795,;	G	ENSG00000145495	ENST00000274140	Transcript	synonymous_variant	438	306	102	A	gcA/gcG	.	.	.	1	MARCH6	HGNC	30550	protein_coding	YES	CCDS34135.1	ENSP00000274140	MARH6_HUMAN	.	UPI00001B94D6	.	.	.	4/26	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR13145:SF0,hmmpanther:PTHR13145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGCATGGTT	.	5	ESCA
EFNA5	0	.	GRCh37	5	106763018	106763018	+	Silent	SNP	G	G	A	rs779367666	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318C>T	p.%3D	p.H106H	ENST00000333274	2/5	60	47	12	63	63	0	EFNA5,synonymous_variant,p.%3D,ENST00000509503,;EFNA5,synonymous_variant,p.%3D,ENST00000333274,;EFNA5,non_coding_transcript_exon_variant,,ENST00000505499,;EFNA5,non_coding_transcript_exon_variant,,ENST00000504941,;	A	ENSG00000184349	ENST00000333274	Transcript	synonymous_variant	600	318	106	H	caC/caT	rs779367666	.	.	-1	EFNA5	HGNC	3225	protein_coding	YES	CCDS4097.1	ENSP00000328777	EFNA5_HUMAN	.	UPI0000129C93	.	.	.	2/5	.	Superfamily_domains:SSF49503,Gene3D:2.60.40.420,Pfam_domain:PF00812,hmmpanther:PTHR11304,hmmpanther:PTHR11304:SF33,PROSITE_profiles:PS51551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGAGTGAGG	.	5	ESCA
PCDHB17	0	.	GRCh37	5	140537151	140537151	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1575G>A	p.%3D	p.L525L	ENST00000539533	1/1	138	115	23	183	183	0	PCDHB17,synonymous_variant,p.%3D,ENST00000539533,;PCDHB6,downstream_gene_variant,,ENST00000543635,;PCDHB6,downstream_gene_variant,,ENST00000231136,;	A	ENSG00000255622	ENST00000539533	Transcript	synonymous_variant	1575	1575	525	L	ctG/ctA	.	.	.	1	PCDHB17	Uniprot_gn	.	protein_coding	YES	.	ENSP00000438685	.	Q96T98_HUMAN	UPI000006CE19	.	.	.	1/1	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTGCAGGA	.	4	ESCA
PCDHB7	0	.	GRCh37	5	140554584	140554584	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2168G>T	p.Cys723Phe	p.C723F	ENST00000231137	1/1	61	48	13	82	82	0	PCDHB7,missense_variant,p.Cys723Phe,ENST00000231137,;PCDHB8,upstream_gene_variant,,ENST00000239444,;	T	ENSG00000113212	ENST00000231137	Transcript	missense_variant	2342	2168	723	C/F	tGc/tTc	.	.	.	1	PCDHB7	HGNC	8692	protein_coding	YES	CCDS4249.1	ENSP00000231137	PCDB7_HUMAN	.	UPI00001273E3	.	tolerated_low_confidence(0.05)	benign(0.041)	1/1	.	hmmpanther:PTHR24028:SF69,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCTGCTCGG	.	5	ESCA
NR3C1	0	.	GRCh37	5	142659438	142659438	+	3'Flank	SNP	T	T	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000231509	.	19	12	7	24	24	0	NR3C1,3_prime_UTR_variant,,ENST00000394464,;NR3C1,3_prime_UTR_variant,,ENST00000424646,;NR3C1,3_prime_UTR_variant,,ENST00000343796,;NR3C1,intron_variant,,ENST00000415690,;NR3C1,downstream_gene_variant,,ENST00000231509,;NR3C1,downstream_gene_variant,,ENST00000503201,;NR3C1,downstream_gene_variant,,ENST00000504572,;NR3C1,downstream_gene_variant,,ENST00000416954,;NR3C1,downstream_gene_variant,,ENST00000394466,;	G	ENSG00000113580	ENST00000231509	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1289	-1	NR3C1	HGNC	7978	protein_coding	YES	CCDS34258.1	ENSP00000231509	GCR_HUMAN	E5KQF6_HUMAN,Q3MSN4_HUMAN,D6RDA9_HUMAN	UPI000016A246	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGTAAGCA	.	5	ESCA
TCERG1	0	.	GRCh37	5	145834808	145834808	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.249A>G	p.%3D	p.G83G	ENST00000296702	2/22	53	36	16	64	64	0	TCERG1,synonymous_variant,p.%3D,ENST00000296702,;TCERG1,synonymous_variant,p.%3D,ENST00000394421,;TCERG1,synonymous_variant,p.%3D,ENST00000549332,;TCERG1,non_coding_transcript_exon_variant,,ENST00000507175,;TCERG1,upstream_gene_variant,,ENST00000513298,;	G	ENSG00000113649	ENST00000296702	Transcript	synonymous_variant	287	249	83	G	ggA/ggG	.	.	.	1	TCERG1	HGNC	15630	protein_coding	YES	CCDS4282.1	ENSP00000296702	TCRG1_HUMAN	.	UPI000013E374	.	.	.	2/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGAGGGAT	.	5	ESCA
GABRA1	0	.	GRCh37	5	161317974	161317974	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774C>A	p.Tyr258Ter	p.Y258*	ENST00000428797	9/11	38	28	10	43	43	0	GABRA1,stop_gained,p.Tyr258Ter,ENST00000444819,;GABRA1,stop_gained,p.Tyr258Ter,ENST00000420560,;GABRA1,stop_gained,p.Tyr258Ter,ENST00000393943,;GABRA1,stop_gained,p.Tyr258Ter,ENST00000023897,;GABRA1,stop_gained,p.Tyr258Ter,ENST00000437025,;GABRA1,stop_gained,p.Tyr258Ter,ENST00000428797,;GABRA1,non_coding_transcript_exon_variant,,ENST00000519542,;	A	ENSG00000022355	ENST00000428797	Transcript	stop_gained	1129	774	258	Y/*	taC/taA	.	.	.	1	GABRA1	HGNC	4075	protein_coding	YES	CCDS4357.1	ENSP00000393097	GBRA1_HUMAN	E5RK60_HUMAN,E5RJS3_HUMAN	UPI000012AF95	.	.	.	9/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Gene3D:1.20.58.390,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR00253	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATACCTGCC	.	5	ESCA
CREBRF	0	.	GRCh37	5	172550134	172550134	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1733T>C	p.Val578Ala	p.V578A	ENST00000296953	8/9	29	22	7	22	22	0	CREBRF,missense_variant,p.Val580Ala,ENST00000540014,;CREBRF,missense_variant,p.Val578Ala,ENST00000296953,;CREBRF,non_coding_transcript_exon_variant,,ENST00000520464,;	C	ENSG00000164463	ENST00000296953	Transcript	missense_variant	2052	1733	578	V/A	gTa/gCa	.	.	.	1	CREBRF	HGNC	24050	protein_coding	YES	CCDS34293.1	ENSP00000296953	CRERF_HUMAN	E5RI19_HUMAN,B3KV47_HUMAN	UPI000049E01D	.	deleterious(0.05)	probably_damaging(0.99)	8/9	.	hmmpanther:PTHR21552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGGTACAGA	.	5	ESCA
TRIM41	0	.	GRCh37	5	180662142	180662142	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*367C>T	.	.	ENST00000315073	6/6	13	9	4	23	23	0	TRIM41,3_prime_UTR_variant,,ENST00000315073,;TRIM41,intron_variant,,ENST00000351937,;GNB2L1,downstream_gene_variant,,ENST00000511900,;GNB2L1,downstream_gene_variant,,ENST00000509148,;GNB2L1,downstream_gene_variant,,ENST00000504128,;GNB2L1,downstream_gene_variant,,ENST00000456394,;GNB2L1,downstream_gene_variant,,ENST00000503081,;GNB2L1,downstream_gene_variant,,ENST00000513027,;GNB2L1,downstream_gene_variant,,ENST00000504726,;GNB2L1,downstream_gene_variant,,ENST00000514455,;GNB2L1,downstream_gene_variant,,ENST00000512968,;GNB2L1,downstream_gene_variant,,ENST00000502844,;GNB2L1,downstream_gene_variant,,ENST00000502905,;TRIM41,downstream_gene_variant,,ENST00000515499,;GNB2L1,downstream_gene_variant,,ENST00000507756,;GNB2L1,downstream_gene_variant,,ENST00000376817,;GNB2L1,downstream_gene_variant,,ENST00000509535,;GNB2L1,downstream_gene_variant,,ENST00000511566,;GNB2L1,downstream_gene_variant,,ENST00000507000,;GNB2L1,downstream_gene_variant,,ENST00000510199,;GNB2L1,downstream_gene_variant,,ENST00000512805,;CTC-338M12.7,upstream_gene_variant,,ENST00000499096,;TRIM41,downstream_gene_variant,,ENST00000510072,;TRIM41,non_coding_transcript_exon_variant,,ENST00000515223,;TRIM41,non_coding_transcript_exon_variant,,ENST00000508930,;TRIM41,intron_variant,,ENST00000503114,;TRIM41,intron_variant,,ENST00000514219,;GNB2L1,downstream_gene_variant,,ENST00000514183,;GNB2L1,downstream_gene_variant,,ENST00000507273,;GNB2L1,downstream_gene_variant,,ENST00000508682,;GNB2L1,downstream_gene_variant,,ENST00000503494,;GNB2L1,downstream_gene_variant,,ENST00000504325,;GNB2L1,downstream_gene_variant,,ENST00000502548,;TRIM41,downstream_gene_variant,,ENST00000515834,;GNB2L1,downstream_gene_variant,,ENST00000508044,;GNB2L1,downstream_gene_variant,,ENST00000506312,;GNB2L1,downstream_gene_variant,,ENST00000513060,;GNB2L1,downstream_gene_variant,,ENST00000515417,;GNB2L1,downstream_gene_variant,,ENST00000502890,;GNB2L1,downstream_gene_variant,,ENST00000511473,;	T	ENSG00000146063	ENST00000315073	Transcript	3_prime_UTR_variant	2970	.	.	.	.	.	.	.	1	TRIM41	HGNC	19013	protein_coding	YES	CCDS4466.1	ENSP00000320869	TRI41_HUMAN	D6REK2_HUMAN	UPI00001B248B	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCTTCAACCT	.	3	ESCA
TRIM41	0	.	GRCh37	5	180662148	180662148	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*373C>G	.	.	ENST00000315073	6/6	11	7	4	24	24	0	TRIM41,3_prime_UTR_variant,,ENST00000315073,;TRIM41,intron_variant,,ENST00000351937,;GNB2L1,downstream_gene_variant,,ENST00000511900,;GNB2L1,downstream_gene_variant,,ENST00000509148,;GNB2L1,downstream_gene_variant,,ENST00000504128,;GNB2L1,downstream_gene_variant,,ENST00000456394,;GNB2L1,downstream_gene_variant,,ENST00000503081,;GNB2L1,downstream_gene_variant,,ENST00000513027,;GNB2L1,downstream_gene_variant,,ENST00000504726,;GNB2L1,downstream_gene_variant,,ENST00000514455,;GNB2L1,downstream_gene_variant,,ENST00000512968,;GNB2L1,downstream_gene_variant,,ENST00000502844,;GNB2L1,downstream_gene_variant,,ENST00000502905,;TRIM41,downstream_gene_variant,,ENST00000515499,;GNB2L1,downstream_gene_variant,,ENST00000507756,;GNB2L1,downstream_gene_variant,,ENST00000376817,;GNB2L1,downstream_gene_variant,,ENST00000509535,;GNB2L1,downstream_gene_variant,,ENST00000511566,;GNB2L1,downstream_gene_variant,,ENST00000507000,;GNB2L1,downstream_gene_variant,,ENST00000510199,;GNB2L1,downstream_gene_variant,,ENST00000512805,;CTC-338M12.7,upstream_gene_variant,,ENST00000499096,;TRIM41,downstream_gene_variant,,ENST00000510072,;TRIM41,non_coding_transcript_exon_variant,,ENST00000515223,;TRIM41,non_coding_transcript_exon_variant,,ENST00000508930,;TRIM41,intron_variant,,ENST00000503114,;TRIM41,intron_variant,,ENST00000514219,;GNB2L1,downstream_gene_variant,,ENST00000514183,;GNB2L1,downstream_gene_variant,,ENST00000507273,;GNB2L1,downstream_gene_variant,,ENST00000508682,;GNB2L1,downstream_gene_variant,,ENST00000503494,;GNB2L1,downstream_gene_variant,,ENST00000504325,;GNB2L1,downstream_gene_variant,,ENST00000502548,;TRIM41,downstream_gene_variant,,ENST00000515834,;GNB2L1,downstream_gene_variant,,ENST00000508044,;GNB2L1,downstream_gene_variant,,ENST00000506312,;GNB2L1,downstream_gene_variant,,ENST00000513060,;GNB2L1,downstream_gene_variant,,ENST00000515417,;GNB2L1,downstream_gene_variant,,ENST00000502890,;GNB2L1,downstream_gene_variant,,ENST00000511473,;	G	ENSG00000146063	ENST00000315073	Transcript	3_prime_UTR_variant	2976	.	.	.	.	.	.	.	1	TRIM41	HGNC	19013	protein_coding	YES	CCDS4466.1	ENSP00000320869	TRI41_HUMAN	D6REK2_HUMAN	UPI00001B248B	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AACCTCTTTAT	.	3	ESCA
CDH10	0	.	GRCh37	5	24498600	24498600	+	Silent	SNP	A	A	C	rs766154972	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1422T>G	p.%3D	p.A474A	ENST00000264463	9/12	109	99	9	70	70	0	CDH10,synonymous_variant,p.%3D,ENST00000264463,;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,missense_variant,p.Cys429Gly,ENST00000510477,;	C	ENSG00000040731	ENST00000264463	Transcript	synonymous_variant	1930	1422	474	A	gcT/gcG	rs766154972	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	.	.	9/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R472C|c.1414C>T|3	MUTECT|MUSE	AAAACAGCCAC	.	2	ESCA
FCHO2	0	.	GRCh37	5	72285328	72285328	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200G>C	p.Gly67Ala	p.G67A	ENST00000430046	3/26	49	43	6	39	39	0	FCHO2,missense_variant,p.Gly67Ala,ENST00000512348,;FCHO2,missense_variant,p.Gly67Ala,ENST00000287761,;FCHO2,missense_variant,p.Gly67Ala,ENST00000341845,;FCHO2,missense_variant,p.Gly67Ala,ENST00000430046,;FCHO2,intron_variant,,ENST00000507345,;	C	ENSG00000157107	ENST00000430046	Transcript	missense_variant	316	200	67	G/A	gGa/gCa	.	.	.	1	FCHO2	HGNC	25180	protein_coding	YES	CCDS47230.1	ENSP00000393776	FCHO2_HUMAN	B4DEU7_HUMAN	UPI000019971A	.	deleterious(0)	possibly_damaging(0.835)	3/26	.	PROSITE_profiles:PS50133,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF8,Pfam_domain:PF00611,SMART_domains:SM00055,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	ACTTGGGTGAG	.	3	ESCA
TBC1D32	0	.	GRCh37	6	121655552	121655552	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25C>A	p.Gln9Lys	p.Q9K	ENST00000398212	1/32	37	21	15	54	54	0	TBC1D32,missense_variant,p.Gln9Lys,ENST00000422369,;TBC1D32,missense_variant,p.Gln9Lys,ENST00000398212,;TBC1D32,missense_variant,p.Gln9Lys,ENST00000275159,;TBC1D32,missense_variant,p.Gln9Lys,ENST00000464622,;	T	ENSG00000146350	ENST00000398212	Transcript	missense_variant	75	25	9	Q/K	Cag/Aag	.	.	.	-1	TBC1D32	HGNC	21485	protein_coding	YES	CCDS43501.1	ENSP00000381270	BROMI_HUMAN	A2A304_HUMAN	UPI0000E67203	.	deleterious(0)	benign(0.026)	1/32	.	hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTGGTCCT	.	5	ESCA
ENPP3	0	.	GRCh37	6	132068172	132068172	+	3'UTR	SNP	G	G	A	rs544172519	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*76G>A	.	.	ENST00000414305	26/26	50	42	8	42	42	0	ENPP3,3_prime_UTR_variant,,ENST00000357639,;ENPP3,3_prime_UTR_variant,,ENST00000414305,;ENPP3,downstream_gene_variant,,ENST00000358229,;	A	ENSG00000154269	ENST00000414305	Transcript	3_prime_UTR_variant	3032	.	.	.	.	rs544172519	.	.	1	ENPP3	HGNC	3358	protein_coding	YES	CCDS5148.1	ENSP00000406261	ENPP3_HUMAN	Q9UNI4_HUMAN,Q9NQM9_HUMAN,Q9H515_HUMAN,F5GY67_HUMAN	UPI000013DD9F	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAGAATTG	.	5	ESCA
MYB	0	.	GRCh37	6	135521339	135521339	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1824+2T>C	.	p.X608_splice	ENST00000341911	.	90	81	9	58	58	0	MYB,splice_donor_variant,,ENST00000533624,;MYB,splice_donor_variant,,ENST00000527615,;MYB,splice_donor_variant,,ENST00000525369,;MYB,splice_donor_variant,,ENST00000442647,;MYB,splice_donor_variant,,ENST00000528774,;MYB,splice_donor_variant,,ENST00000534044,;MYB,splice_donor_variant,,ENST00000534121,;MYB,splice_donor_variant,,ENST00000316528,;MYB,splice_donor_variant,,ENST00000367814,;MYB,splice_donor_variant,,ENST00000341911,;MYB-AS1,upstream_gene_variant,,ENST00000455534,;MYB,splice_donor_variant,,ENST00000531845,;MYB,upstream_gene_variant,,ENST00000529297,;MYB,splice_donor_variant,,ENST00000533384,;MYB,splice_donor_variant,,ENST00000526320,;MYB,splice_donor_variant,,ENST00000525514,;MYB,splice_donor_variant,,ENST00000367812,;MYB,splice_donor_variant,,ENST00000339290,;MYB,splice_donor_variant,,ENST00000526187,;MYB,splice_donor_variant,,ENST00000529262,;MYB,splice_donor_variant,,ENST00000525002,;MYB,splice_donor_variant,,ENST00000526565,;MYB,splice_donor_variant,,ENST00000528343,;MYB,splice_donor_variant,,ENST00000529586,;MYB,splice_donor_variant,,ENST00000438901,;MYB,splice_donor_variant,,ENST00000533837,;MYB,splice_donor_variant,,ENST00000463282,;MYB,splice_donor_variant,,ENST00000525477,;MYB,splice_donor_variant,,ENST00000524588,;MYB,splice_donor_variant,,ENST00000533808,;MYB,splice_donor_variant,,ENST00000528140,;MYB,splice_donor_variant,,ENST00000525940,;MYB,splice_donor_variant,,ENST00000528345,;MYB,splice_donor_variant,,ENST00000531519,;MYB,splice_donor_variant,,ENST00000528015,;MYB,splice_donor_variant,,ENST00000526889,;MYB,splice_donor_variant,,ENST00000531634,;MYB,splice_donor_variant,,ENST00000531737,;MYB,downstream_gene_variant,,ENST00000534736,;	C	ENSG00000118513	ENST00000341911	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	MYB	HGNC	7545	protein_coding	YES	CCDS47481.1	ENSP00000339992	MYB_HUMAN	Q9UMI7_HUMAN	UPI000002AE9A	.	.	.	.	12/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTAGTAAGTT	.	3	ESCA
CNKSR3	0	.	GRCh37	6	154727685	154727685	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1471C>T	p.Arg491Trp	p.R491W	ENST00000607772	13/13	44	34	9	49	49	0	CNKSR3,missense_variant,p.Arg491Trp,ENST00000607772,;CNKSR3,missense_variant,p.Arg316Trp,ENST00000433165,;CNKSR3,missense_variant,p.Arg411Trp,ENST00000479339,;CNKSR3,downstream_gene_variant,,ENST00000424998,;	A	ENSG00000153721	ENST00000607772	Transcript	missense_variant	2016	1471	491	R/W	Cgg/Tgg	.	.	.	-1	CNKSR3	HGNC	23034	protein_coding	YES	CCDS5246.1	ENSP00000475915	CNKR3_HUMAN	C9JN62_HUMAN,C9IZX4_HUMAN	UPI000020D0EA	.	deleterious(0)	probably_damaging(0.955)	13/13	.	hmmpanther:PTHR12844,hmmpanther:PTHR12844:SF19,Pfam_domain:PF06663	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCCGCTCGG	.	5	ESCA
PACRG	0	.	GRCh37	6	163510422	163510422	+	Missense_Mutation	SNP	A	A	T	rs776149854	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595A>T	p.Ile199Phe	p.I199F	ENST00000337019	5/7	55	35	19	50	50	0	PACRG,missense_variant,p.Ile115Phe,ENST00000534958,;PACRG,missense_variant,p.Ile199Phe,ENST00000366888,;PACRG,missense_variant,p.Ile57Phe,ENST00000542936,;PACRG,missense_variant,p.Ile199Phe,ENST00000337019,;PACRG,missense_variant,p.Ile199Phe,ENST00000366889,;PACRG,non_coding_transcript_exon_variant,,ENST00000545186,;PACRG,3_prime_UTR_variant,,ENST00000541974,;	T	ENSG00000112530	ENST00000337019	Transcript	missense_variant	819	595	199	I/F	Atc/Ttc	rs776149854	.	.	1	PACRG	HGNC	19152	protein_coding	YES	CCDS5284.1	ENSP00000337946	PACRG_HUMAN	.	UPI00001AE671	.	deleterious(0)	possibly_damaging(0.889)	5/7	.	hmmpanther:PTHR21207,Pfam_domain:PF10274	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAACATCTTT	.	5	ESCA
RPS6KA2	0	.	GRCh37	6	166823100	166823100	+	3'Flank	SNP	C	C	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000503859	.	20	14	6	20	20	0	RPS6KA2,3_prime_UTR_variant,,ENST00000265678,;RPS6KA2,3_prime_UTR_variant,,ENST00000510118,;RPS6KA2,downstream_gene_variant,,ENST00000481261,;RPS6KA2,downstream_gene_variant,,ENST00000405189,;RPS6KA2,downstream_gene_variant,,ENST00000503859,;RPS6KA2,downstream_gene_variant,,ENST00000509742,;	G	ENSG00000071242	ENST00000503859	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1620	-1	RPS6KA2	HGNC	10431	protein_coding	YES	CCDS34570.1	ENSP00000427015	KS6A2_HUMAN	D6RHW7_HUMAN,D6RD75_HUMAN,D6R910_HUMAN,B7Z3B5_HUMAN	UPI000020D48C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTCAGCCC	.	5	ESCA
SMOC2	0	.	GRCh37	6	169053824	169053824	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234G>A	p.Asp412Asn	p.D412N	ENST00000354536	11/13	58	51	7	87	87	0	SMOC2,missense_variant,p.Asp401Asn,ENST00000356284,;SMOC2,missense_variant,p.Asp412Asn,ENST00000354536,;SMOC2,missense_variant,p.Asp21Asn,ENST00000417208,;SMOC2,upstream_gene_variant,,ENST00000477998,;SMOC2,missense_variant,p.Asp34Asn,ENST00000392100,;	A	ENSG00000112562	ENST00000354536	Transcript	missense_variant	1454	1234	412	D/N	Gac/Aac	.	.	.	1	SMOC2	HGNC	20323	protein_coding	YES	CCDS5307.1	ENSP00000346537	SMOC2_HUMAN	B4DNB1_HUMAN	UPI0000072A56	.	tolerated(0.09)	benign(0.154)	11/13	.	Superfamily_domains:SSF47473,Gene3D:1.10.238.10,Pfam_domain:PF10591,PROSITE_patterns:PS00018,hmmpanther:PTHR12352:SF11,hmmpanther:PTHR12352,PROSITE_profiles:PS50222	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAATGACAAA	.	4	ESCA
BTN1A1	0	.	GRCh37	6	26506976	26506976	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775C>A	p.Leu259Ile	p.L259I	ENST00000244513	4/7	53	48	5	46	46	0	BTN1A1,missense_variant,p.Leu259Ile,ENST00000244513,;	A	ENSG00000124557	ENST00000244513	Transcript	missense_variant	841	775	259	L/I	Ctt/Att	.	.	.	1	BTN1A1	HGNC	1135	protein_coding	YES	CCDS4614.1	ENSP00000244513	BT1A1_HUMAN	.	UPI000006E521	.	tolerated(0.15)	benign(0.029)	4/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24100:SF53,hmmpanther:PTHR24100	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAGGACTTCTC	.	3	ESCA
TINAG	0	.	GRCh37	6	54212285	54212285	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.869A>G	p.Asp290Gly	p.D290G	ENST00000259782	6/11	47	21	25	63	63	0	TINAG,missense_variant,p.Asp290Gly,ENST00000259782,;	G	ENSG00000137251	ENST00000259782	Transcript	missense_variant	965	869	290	D/G	gAt/gGt	.	.	.	1	TINAG	HGNC	14599	protein_coding	YES	CCDS4955.1	ENSP00000259782	TINAG_HUMAN	B1AQ11_HUMAN	UPI000013D078	.	deleterious(0)	probably_damaging(0.932)	6/11	.	Superfamily_domains:SSF54001,SMART_domains:SM00645,Gene3D:3.90.70.10,Pfam_domain:PF00112,hmmpanther:PTHR12411:SF274,hmmpanther:PTHR12411	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCGATAGGG	.	5	ESCA
DST	0	.	GRCh37	6	56473870	56473870	+	Intron	SNP	T	T	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3672+1355A>T	.	.	ENST00000244364	.	36	17	19	33	33	0	DST,synonymous_variant,p.%3D,ENST00000439203,;DST,synonymous_variant,p.%3D,ENST00000446842,;DST,synonymous_variant,p.%3D,ENST00000370754,;DST,synonymous_variant,p.%3D,ENST00000361203,;DST,synonymous_variant,p.%3D,ENST00000370769,;DST,synonymous_variant,p.%3D,ENST00000312431,;DST,intron_variant,,ENST00000370788,;DST,intron_variant,,ENST00000244364,;DST,intron_variant,,ENST00000421834,;	A	ENSG00000151914	ENST00000244364	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	.	25/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAATTGTGGT	.	5	ESCA
COL12A1	0	.	GRCh37	6	75890711	75890711	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2108C>T	p.Ala703Val	p.A703V	ENST00000322507	11/66	48	40	8	47	47	0	COL12A1,missense_variant,p.Ala703Val,ENST00000416123,;COL12A1,missense_variant,p.Ala703Val,ENST00000322507,;COL12A1,missense_variant,p.Ala703Val,ENST00000483888,;COL12A1,intron_variant,,ENST00000345356,;COL12A1,non_coding_transcript_exon_variant,,ENST00000486533,;	A	ENSG00000111799	ENST00000322507	Transcript	missense_variant	2418	2108	703	A/V	gCg/gTg	COSM1445958	.	.	-1	COL12A1	HGNC	2188	protein_coding	YES	CCDS43482.1	ENSP00000325146	COCA1_HUMAN	.	UPI000045890B	.	.	possibly_damaging(0.804)	11/66	.	PROSITE_profiles:PS50853,hmmpanther:PTHR22992:SF23,hmmpanther:PTHR22992,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCCGCAGTC	.	4	ESCA
NRCAM	0	.	GRCh37	7	107790418	107790418	+	Silent	SNP	C	C	T	rs375886714	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3852G>A	p.%3D	p.P1284P	ENST00000379028	33/33	38	27	11	29	29	0	NRCAM,synonymous_variant,p.%3D,ENST00000351718,;NRCAM,synonymous_variant,p.%3D,ENST00000445634,;NRCAM,synonymous_variant,p.%3D,ENST00000413765,;NRCAM,synonymous_variant,p.%3D,ENST00000379024,;NRCAM,synonymous_variant,p.%3D,ENST00000379028,;NRCAM,synonymous_variant,p.%3D,ENST00000425651,;NRCAM,downstream_gene_variant,,ENST00000379022,;NRCAM,non_coding_transcript_exon_variant,,ENST00000522550,;NRCAM,downstream_gene_variant,,ENST00000415105,;	T	ENSG00000091129	ENST00000379028	Transcript	synonymous_variant	4323	3852	1284	P	ccG/ccA	rs375886714	.	.	-1	NRCAM	HGNC	7994	protein_coding	YES	CCDS47686.1	ENSP00000368314	NRCAM_HUMAN	C9JUR7_HUMAN,C9JF43_HUMAN,B3KRX0_HUMAN	UPI00005E2661	.	.	.	33/33	.	hmmpanther:PTHR10489:SF554,hmmpanther:PTHR10489	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCCGGCTC	byCluster|by1000G	5	ESCA
KCNH2	0	.	GRCh37	7	150642567	150642567	+	Silent	SNP	C	C	T	rs371473271	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3366G>A	p.%3D	p.P1122P	ENST00000262186	15/15	33	26	7	51	51	0	KCNH2,synonymous_variant,p.%3D,ENST00000262186,;KCNH2,synonymous_variant,p.%3D,ENST00000330883,;KCNH2,synonymous_variant,p.%3D,ENST00000392968,;KCNH2,downstream_gene_variant,,ENST00000430723,;KCNH2,downstream_gene_variant,,ENST00000532957,;KCNH2,downstream_gene_variant,,ENST00000473610,;KCNH2,downstream_gene_variant,,ENST00000461280,;	T	ENSG00000055118	ENST00000262186	Transcript	synonymous_variant	3768	3366	1122	P	ccG/ccA	rs371473271	.	.	-1	KCNH2	HGNC	6251	protein_coding	YES	CCDS5910.1	ENSP00000262186	KCNH2_HUMAN	Q75MK9_HUMAN,Q75MK8_HUMAN,Q6U287_HUMAN,Q6U283_HUMAN,Q6U279_HUMAN,Q45QN5_HUMAN	UPI0000062255	.	.	.	15/15	.	.	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	T:0.0005	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCCGGGGG	byFrequency|byCluster|by1000G	5	ESCA
NPC1L1	0	.	GRCh37	7	44561742	44561742	+	Missense_Mutation	SNP	C	C	T	rs756628304	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2737G>A	p.Glu913Lys	p.E913K	ENST00000289547	11/20	74	63	11	51	51	0	NPC1L1,missense_variant,p.Glu867Lys,ENST00000546276,;NPC1L1,missense_variant,p.Glu913Lys,ENST00000381160,;NPC1L1,missense_variant,p.Glu913Lys,ENST00000289547,;	T	ENSG00000015520	ENST00000289547	Transcript	missense_variant	2793	2737	913	E/K	Gag/Aag	rs756628304,COSM1755289	.	.	-1	NPC1L1	HGNC	7898	protein_coding	YES	CCDS5491.1	ENSP00000289547	NPCL1_HUMAN	.	UPI000013DF88	.	tolerated(0.9)	benign(0.001)	11/20	.	hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF89	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCTCGCTGG	.	4	ESCA
NACAD	0	.	GRCh37	7	45125071	45125071	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.708C>T	p.%3D	p.L236L	ENST00000490531	2/8	52	46	6	78	78	0	NACAD,synonymous_variant,p.%3D,ENST00000490531,;NACAD,upstream_gene_variant,,ENST00000460409,;	A	ENSG00000136274	ENST00000490531	Transcript	synonymous_variant	728	708	236	L	ctC/ctT	.	.	.	-1	NACAD	HGNC	22196	protein_coding	YES	CCDS47582.1	ENSP00000420477	NACAD_HUMAN	.	UPI00001D747D	.	.	.	2/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21713:SF1,hmmpanther:PTHR21713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTGAGGGA	.	4	ESCA
SEPT7P2	0	.	GRCh37	7	45797639	45797639	+	Intron	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.531+3C>G	.	.	ENST00000429741	.	111	90	21	111	111	0	SEPT7P2,splice_region_variant,,ENST00000338231,;SEPT7P2,splice_region_variant,,ENST00000428414,;SEPT7P2,splice_region_variant,,ENST00000429741,;SEPT7P2,downstream_gene_variant,,ENST00000450436,;SEPT7P2,non_coding_transcript_exon_variant,,ENST00000428867,;SEPT7P2,splice_region_variant,,ENST00000398921,;SEPT7P2,splice_region_variant,,ENST00000443269,;SEPT7P2,splice_region_variant,,ENST00000417129,;	C	ENSG00000214765	ENST00000429741	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	SEPT7P2	HGNC	32339	processed_transcript	YES	.	.	.	.	.	.	.	.	.	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTGACCCA	.	4	ESCA
CHCHD2	0	.	GRCh37	7	56170694	56170694	+	Missense_Mutation	SNP	C	C	T	rs778377000	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311G>A	p.Gly104Glu	p.G104E	ENST00000395422	3/4	45	36	8	41	41	0	CHCHD2,missense_variant,p.Gly104Glu,ENST00000395422,;snoU13,downstream_gene_variant,,ENST00000458988,;CHCHD2,non_coding_transcript_exon_variant,,ENST00000473095,;	T	ENSG00000106153	ENST00000395422	Transcript	missense_variant	474	311	104	G/E	gGa/gAa	rs778377000,COSM3881912	.	.	-1	CHCHD2	HGNC	21645	protein_coding	YES	CCDS5526.1	ENSP00000378812	CHCH2_HUMAN	.	UPI0000073DC7	.	tolerated(0.12)	benign(0.097)	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13523,hmmpanther:PTHR13523:SF3	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTTCCCTGA	byFrequency	5	ESCA
ZNF733P	0	.	GRCh37	7	62752571	62752571	+	RNA	SNP	T	T	G	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.898A>C	.	.	ENST00000444809	4/4	48	40	8	74	74	0	ZNF733P,non_coding_transcript_exon_variant,,ENST00000331425,;ZNF733P,non_coding_transcript_exon_variant,,ENST00000444809,;	G	ENSG00000185037	ENST00000444809	Transcript	non_coding_transcript_exon_variant	898	.	.	.	.	.	.	.	-1	ZNF733P	HGNC	32473	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TCACATTTGTA	.	2	ESCA
TRIM50	0	.	GRCh37	7	72741936	72741936	+	5'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-52G>A	.	.	ENST00000333149	1/7	21	15	6	30	30	0	TRIM50,5_prime_UTR_variant,,ENST00000333149,;FKBP6,upstream_gene_variant,,ENST00000252037,;FKBP6,upstream_gene_variant,,ENST00000413573,;FKBP6,upstream_gene_variant,,ENST00000431982,;TRIM50,upstream_gene_variant,,ENST00000453152,;FKBP6,upstream_gene_variant,,ENST00000442793,;TRIM50,non_coding_transcript_exon_variant,,ENST00000493498,;FKBP6,upstream_gene_variant,,ENST00000445032,;FKBP6,upstream_gene_variant,,ENST00000437013,;FKBP6,upstream_gene_variant,,ENST00000429879,;	T	ENSG00000146755	ENST00000333149	Transcript	5_prime_UTR_variant	150	.	.	.	.	.	.	.	-1	TRIM50	HGNC	19017	protein_coding	YES	CCDS34654.1	ENSP00000327994	TRI50_HUMAN	.	UPI000015FD8F	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGTGCTCTCT	.	2	ESCA
SUN1	0	.	GRCh37	7	909099	909099	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2094G>A	p.%3D	p.K698K	ENST00000401592	17/19	31	25	6	30	30	0	SUN1,synonymous_variant,p.%3D,ENST00000452783,;SUN1,synonymous_variant,p.%3D,ENST00000456758,;SUN1,synonymous_variant,p.%3D,ENST00000433212,;SUN1,synonymous_variant,p.%3D,ENST00000429178,;SUN1,synonymous_variant,p.%3D,ENST00000405266,;SUN1,synonymous_variant,p.%3D,ENST00000425407,;SUN1,synonymous_variant,p.%3D,ENST00000401592,;SUN1,synonymous_variant,p.%3D,ENST00000413514,;SUN1,synonymous_variant,p.%3D,ENST00000389574,;SUN1,non_coding_transcript_exon_variant,,ENST00000413171,;SUN1,non_coding_transcript_exon_variant,,ENST00000475971,;SUN1,non_coding_transcript_exon_variant,,ENST00000497943,;SUN1,intron_variant,,ENST00000457861,;	A	ENSG00000164828	ENST00000401592	Transcript	synonymous_variant	2118	2094	698	K	aaG/aaA	.	.	.	1	SUN1	HGNC	18587	protein_coding	YES	CCDS47525.1	ENSP00000384015	SUN1_HUMAN	Q5S4N2_HUMAN,C9K051_HUMAN,C9JS54_HUMAN,C9JR15_HUMAN,C9JK55_HUMAN,C9JJU6_HUMAN	UPI000020E965	.	.	.	17/19	.	PROSITE_profiles:PS51469,hmmpanther:PTHR12911:SF18,hmmpanther:PTHR12911,Pfam_domain:PF07738	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTAAGACGCT	.	4	ESCA
PLAG1	0	.	GRCh37	8	57074958	57074959	+	3'UTR	DEL	AC	AC	-	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	AC	AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3843_*3844delGT	.	.	ENST00000316981	5/5	84	68	16	56	56	0	PLAG1,3_prime_UTR_variant,,ENST00000316981,;PLAG1,downstream_gene_variant,,ENST00000423799,;PLAG1,downstream_gene_variant,,ENST00000429357,;PLAG1,downstream_gene_variant,,ENST00000522009,;	-	ENSG00000181690	ENST00000316981	Transcript	3_prime_UTR_variant	5826-5827	.	.	.	.	.	.	.	-1	PLAG1	HGNC	9045	protein_coding	YES	CCDS6165.1	ENSP00000325546	PLAG1_HUMAN	A7IT80_HUMAN,A7IT79_HUMAN	UPI000013FF2F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAAAGACACACA	.	3	ESCA
CYP7B1	0	.	GRCh37	8	65536985	65536985	+	Silent	SNP	A	A	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234T>A	p.%3D	p.G78G	ENST00000310193	2/6	58	50	8	58	58	0	CYP7B1,synonymous_variant,p.%3D,ENST00000310193,;	T	ENSG00000172817	ENST00000310193	Transcript	synonymous_variant	408	234	78	G	ggT/ggA	.	.	.	-1	CYP7B1	HGNC	2652	protein_coding	YES	CCDS6180.1	ENSP00000310721	CP7B1_HUMAN	.	UPI0000128218	.	.	.	2/6	.	hmmpanther:PTHR24304,hmmpanther:PTHR24304:SF0,Pfam_domain:PF00067,Gene3D:1.10.630.10,PIRSF_domain:PIRSF000047,Superfamily_domains:SSF48264,Prints_domain:PR00465	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTCACCATG	.	4	ESCA
STAU2	0	.	GRCh37	8	74332341	74332341	+	3'Flank	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000524300	.	38	28	9	43	43	0	STAU2,downstream_gene_variant,,ENST00000522695,;STAU2,downstream_gene_variant,,ENST00000524300,;STAU2,downstream_gene_variant,,ENST00000523558,;STAU2,downstream_gene_variant,,ENST00000521210,;STAU2-AS1,non_coding_transcript_exon_variant,,ENST00000522703,;STAU2-AS1,non_coding_transcript_exon_variant,,ENST00000517604,;STAU2,downstream_gene_variant,,ENST00000522818,;	C	ENSG00000040341	ENST00000524300	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	265	-1	STAU2	HGNC	11371	protein_coding	YES	CCDS55247.1	ENSP00000428756	.	E5RJN7_HUMAN	UPI000013D271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCGAGCAG	.	5	ESCA
CALB1	0	.	GRCh37	8	91078168	91078168	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.408G>A	p.%3D	p.K136K	ENST00000265431	6/11	57	44	12	46	46	0	CALB1,synonymous_variant,p.%3D,ENST00000520613,;CALB1,synonymous_variant,p.%3D,ENST00000523716,;CALB1,synonymous_variant,p.%3D,ENST00000518457,;CALB1,synonymous_variant,p.%3D,ENST00000265431,;CALB1,downstream_gene_variant,,ENST00000482702,;CALB1,upstream_gene_variant,,ENST00000522070,;CALB1,upstream_gene_variant,,ENST00000497376,;CALB1,upstream_gene_variant,,ENST00000469032,;CALB1,downstream_gene_variant,,ENST00000476853,;	T	ENSG00000104327	ENST00000265431	Transcript	synonymous_variant	590	408	136	K	aaG/aaA	.	.	.	-1	CALB1	HGNC	1434	protein_coding	YES	CCDS6251.1	ENSP00000265431	CALB1_HUMAN	O75552_HUMAN,E5RIZ8_HUMAN,E5RG14_HUMAN,B7Z9J4_HUMAN	UPI000013D620	.	.	.	6/11	.	hmmpanther:PTHR19972,hmmpanther:PTHR19972:SF3,Pfam_domain:PF13499,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGTCTTGTT	.	5	ESCA
C8orf47	0	.	GRCh37	8	99105576	99105576	+	3'UTR	SNP	C	C	T	rs201888178	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*15C>T	.	.	ENST00000318528	3/3	34	25	9	22	22	0	C8orf47,3_prime_UTR_variant,,ENST00000545282,;C8orf47,3_prime_UTR_variant,,ENST00000318528,;	T	ENSG00000177459	ENST00000318528	Transcript	3_prime_UTR_variant	1499	.	.	.	.	rs201888178	.	.	1	C8orf47	HGNC	26823	protein_coding	YES	CCDS34929.1	ENSP00000315614	CH047_HUMAN	.	UPI0000210389	.	.	.	3/3	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0005	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAACCGACAC	byCluster|by1000G	5	ESCA
STK3	0	.	GRCh37	8	99467961	99467961	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*109G>A	.	.	ENST00000523601	13/13	74	63	11	58	58	0	STK3,3_prime_UTR_variant,,ENST00000523601,;STK3,3_prime_UTR_variant,,ENST00000419617,;STK3,intron_variant,,ENST00000517832,;	T	ENSG00000104375	ENST00000523601	Transcript	3_prime_UTR_variant	2069	.	.	.	.	.	.	.	-1	STK3	HGNC	11406	protein_coding	YES	CCDS59108.1	ENSP00000429744	.	B3KYA7_HUMAN	UPI00004FB517	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCTCTGCCT	.	5	ESCA
CDK5RAP2	0	.	GRCh37	9	123182069	123182069	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4174C>G	p.Gln1392Glu	p.Q1392E	ENST00000349780	27/38	53	41	12	51	51	0	CDK5RAP2,missense_variant,p.Gln786Glu,ENST00000416449,;CDK5RAP2,missense_variant,p.Gln1392Glu,ENST00000349780,;CDK5RAP2,missense_variant,p.Gln1360Glu,ENST00000360822,;CDK5RAP2,missense_variant,p.Gln402Glu,ENST00000425647,;CDK5RAP2,missense_variant,p.Gln1392Glu,ENST00000360190,;CDK5RAP2,missense_variant,p.Gln1351Glu,ENST00000359309,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000483412,;	C	ENSG00000136861	ENST00000349780	Transcript	missense_variant	4354	4174	1392	Q/E	Caa/Gaa	COSM3779593	.	.	-1	CDK5RAP2	HGNC	18672	protein_coding	YES	CCDS6823.1	ENSP00000343818	CK5P2_HUMAN	F8WBJ0_HUMAN,C9K0C9_HUMAN	UPI0000367673	.	deleterious(0.04)	benign(0.006)	27/38	.	hmmpanther:PTHR13895,hmmpanther:PTHR13895:SF13	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGAGAAA	.	5	ESCA
CNTRL	0	.	GRCh37	9	123903795	123903795	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2620C>T	p.%3D	p.L874L	ENST00000373855	18/44	52	43	8	48	48	0	CNTRL,synonymous_variant,p.%3D,ENST00000373847,;CNTRL,synonymous_variant,p.%3D,ENST00000373855,;CNTRL,synonymous_variant,p.%3D,ENST00000373850,;CNTRL,synonymous_variant,p.%3D,ENST00000238341,;CNTRL,upstream_gene_variant,,ENST00000431571,;CNTRL,non_coding_transcript_exon_variant,,ENST00000373851,;	T	ENSG00000119397	ENST00000373855	Transcript	synonymous_variant	2880	2620	874	L	Ctg/Ttg	.	.	.	1	CNTRL	HGNC	1858	protein_coding	YES	CCDS35118.1	ENSP00000362962	CNTRL_HUMAN	Q5JVD3_HUMAN,Q5JVD6_HUMAN,Q5JVD1_HUMAN	UPI0000211718	.	.	.	18/44	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18877,hmmpanther:PTHR18877:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCTGCAG	.	5	ESCA
LAMC3	0	.	GRCh37	9	133948140	133948140	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3335G>T	p.Cys1112Phe	p.C1112F	ENST00000361069	19/28	38	29	8	43	43	0	LAMC3,missense_variant,p.Cys1112Phe,ENST00000361069,;LAMC3,intron_variant,,ENST00000480883,;	T	ENSG00000050555	ENST00000361069	Transcript	missense_variant	3468	3335	1112	C/F	tGc/tTc	.	.	.	1	LAMC3	HGNC	6494	protein_coding	YES	CCDS6938.1	ENSP00000354360	LAMC3_HUMAN	Q5JTC4_HUMAN	UPI000013D6D3	.	deleterious(0.03)	probably_damaging(0.999)	19/28	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTGCACCC	.	5	ESCA
BHLHB9	0	.	GRCh37	X	102007031	102007031	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1464G>T	.	.	ENST00000372735	4/4	89	72	16	60	60	0	BHLHB9,3_prime_UTR_variant,,ENST00000448867,;BHLHB9,3_prime_UTR_variant,,ENST00000447531,;BHLHB9,3_prime_UTR_variant,,ENST00000372735,;BHLHB9,3_prime_UTR_variant,,ENST00000457056,;BHLHB9,3_prime_UTR_variant,,ENST00000361229,;BHLHB9,downstream_gene_variant,,ENST00000486988,;BHLHB9,downstream_gene_variant,,ENST00000483294,;	T	ENSG00000198908	ENST00000372735	Transcript	3_prime_UTR_variant	3693	.	.	.	.	.	.	.	1	BHLHB9	HGNC	29353	protein_coding	YES	CCDS14502.1	ENSP00000361820	BHLH9_HUMAN	.	UPI00001C1D50	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTAGACCCA	.	5	ESCA
MID2	0	.	GRCh37	X	107084038	107084038	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143G>A	p.Ser48Asn	p.S48N	ENST00000262843	2/10	32	20	11	39	39	0	MID2,missense_variant,p.Ser28Asn,ENST00000451923,;MID2,missense_variant,p.Ser48Asn,ENST00000262843,;MID2,missense_variant,p.Ser48Asn,ENST00000443968,;	A	ENSG00000080561	ENST00000262843	Transcript	missense_variant	691	143	48	S/N	aGc/aAc	COSM3556490,COSM3556489	.	.	1	MID2	HGNC	7096	protein_coding	YES	CCDS14532.2	ENSP00000262843	TRIM1_HUMAN	A6PVI4_HUMAN	UPI0000D4F411	.	tolerated(0.29)	probably_damaging(0.996)	2/10	.	PROSITE_profiles:PS50089,hmmpanther:PTHR24103:SF319,hmmpanther:PTHR24103,PROSITE_patterns:PS00518,Gene3D:3.30.40.10,Pfam_domain:PF13920,SMART_domains:SM00184,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAGCCTCT	.	5	ESCA
GPR112	0	.	GRCh37	X	135429986	135429987	+	Frame_Shift_Ins	INS	-	-	T	rs748603011	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4127dupT	p.Leu1376PhefsTer4	p.L1376Ffs*4	ENST00000394143	6/26	57	45	12	36	36	0	GPR112,frameshift_variant,p.Leu1313PhefsTer4,ENST00000287534,;GPR112,frameshift_variant,p.Leu1376PhefsTer4,ENST00000370652,;GPR112,frameshift_variant,p.Leu1376PhefsTer4,ENST00000394143,;GPR112,frameshift_variant,p.Leu1171PhefsTer4,ENST00000394141,;GPR112,frameshift_variant,p.Leu1171PhefsTer4,ENST00000412101,;	T	ENSG00000156920	ENST00000394143	Transcript	frameshift_variant	4412-4413	4121-4122	1374	T/TX	act/acTt	rs748603011	.	.	1	GPR112	HGNC	18992	protein_coding	YES	CCDS35409.1	ENSP00000377699	GP112_HUMAN	.	UPI00004CEC5B	.	.	.	6/26	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CACCACTTTTT	.	3	ESCA
GPR112	0	.	GRCh37	X	135430355	135430355	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4490T>C	p.Met1497Thr	p.M1497T	ENST00000394143	6/26	41	35	6	51	51	0	GPR112,missense_variant,p.Met1434Thr,ENST00000287534,;GPR112,missense_variant,p.Met1497Thr,ENST00000370652,;GPR112,missense_variant,p.Met1497Thr,ENST00000394143,;GPR112,missense_variant,p.Met1292Thr,ENST00000394141,;GPR112,missense_variant,p.Met1292Thr,ENST00000412101,;	C	ENSG00000156920	ENST00000394143	Transcript	missense_variant	4781	4490	1497	M/T	aTg/aCg	.	.	.	1	GPR112	HGNC	18992	protein_coding	YES	CCDS35409.1	ENSP00000377699	GP112_HUMAN	.	UPI00004CEC5B	.	tolerated(1)	benign(0)	6/26	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAATGCTTC	.	5	ESCA
HCFC1	0	.	GRCh37	X	153219809	153219809	+	Silent	SNP	A	A	G	rs782457287	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4041T>C	p.%3D	p.G1347G	ENST00000310441	17/26	22	17	4	41	41	0	HCFC1,synonymous_variant,p.%3D,ENST00000369984,;HCFC1,synonymous_variant,p.%3D,ENST00000310441,;HCFC1,synonymous_variant,p.%3D,ENST00000354233,;HCFC1,upstream_gene_variant,,ENST00000444191,;	G	ENSG00000172534	ENST00000310441	Transcript	synonymous_variant	5008	4041	1347	G	ggT/ggC	rs782457287	.	.	-1	HCFC1	HGNC	4839	protein_coding	YES	CCDS44020.1	ENSP00000309555	HCFC1_HUMAN	Q05C05_HUMAN	UPI0000142F1F	.	.	.	17/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCACCCTC	.	5	ESCA
NHS	0	.	GRCh37	X	17752563	17752563	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1979C>T	.	.	ENST00000380060	8/8	43	34	9	40	40	0	NHS,3_prime_UTR_variant,,ENST00000380060,;NHS,3_prime_UTR_variant,,ENST00000398097,;SCML1,upstream_gene_variant,,ENST00000380041,;SCML1,upstream_gene_variant,,ENST00000419185,;SCML1,upstream_gene_variant,,ENST00000380043,;SCML1,upstream_gene_variant,,ENST00000398080,;SCML1,upstream_gene_variant,,ENST00000380045,;SCML1,upstream_gene_variant,,ENST00000427362,;	T	ENSG00000188158	ENST00000380060	Transcript	3_prime_UTR_variant	7210	.	.	.	.	.	.	.	1	NHS	HGNC	7820	protein_coding	YES	CCDS14181.1	ENSP00000369400	NHS_HUMAN	.	UPI00001DFBF3	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGTCATCCT	.	5	ESCA
MXRA5	0	.	GRCh37	X	3261890	3261890	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16C>T	.	.	ENST00000217939	2/7	40	34	6	66	66	0	MXRA5,5_prime_UTR_variant,,ENST00000217939,;	A	ENSG00000101825	ENST00000217939	Transcript	5_prime_UTR_variant	140	.	.	.	.	.	.	.	-1	MXRA5	HGNC	7539	protein_coding	YES	CCDS14124.1	ENSP00000217939	MXRA5_HUMAN	.	UPI000013C73B	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCTGATTCT	.	4	ESCA
BCOR	0	.	GRCh37	X	39910917	39910917	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*445A>G	.	.	ENST00000378444	15/15	57	47	9	66	66	0	BCOR,3_prime_UTR_variant,,ENST00000397354,;BCOR,3_prime_UTR_variant,,ENST00000442018,;BCOR,3_prime_UTR_variant,,ENST00000378444,;BCOR,3_prime_UTR_variant,,ENST00000427012,;BCOR,3_prime_UTR_variant,,ENST00000378455,;BCOR,3_prime_UTR_variant,,ENST00000342274,;BCOR,intron_variant,,ENST00000378463,;BCOR,intron_variant,,ENST00000413905,;	C	ENSG00000183337	ENST00000378444	Transcript	3_prime_UTR_variant	5942	.	.	.	.	.	.	.	-1	BCOR	HGNC	20893	protein_coding	YES	CCDS48093.1	ENSP00000367705	BCOR_HUMAN	H9A532_HUMAN,H7BZ37_HUMAN,C9JHP3_HUMAN,B3KTC2_HUMAN	UPI00002318CF	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGTAAACA	.	5	ESCA
CASK	0	.	GRCh37	X	41524635	41524635	+	Missense_Mutation	SNP	G	G	T	rs762668504	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.603C>A	p.Asp201Glu	p.D201E	ENST00000378166	7/27	41	32	8	44	44	0	CASK,missense_variant,p.Asp201Glu,ENST00000421587,;CASK,missense_variant,p.Asp201Glu,ENST00000442742,;CASK,missense_variant,p.Asp201Glu,ENST00000378166,;CASK,missense_variant,p.Asp201Glu,ENST00000318588,;CASK,missense_variant,p.Asp201Glu,ENST00000378163,;CASK,missense_variant,p.Asp201Glu,ENST00000361962,;CASK,missense_variant,p.Asp201Glu,ENST00000378158,;CASK,missense_variant,p.Asp201Glu,ENST00000378154,;CASK,non_coding_transcript_exon_variant,,ENST00000469265,;CASK,non_coding_transcript_exon_variant,,ENST00000486402,;	T	ENSG00000147044	ENST00000378166	Transcript	missense_variant	630	603	201	D/E	gaC/gaA	rs762668504	.	.	-1	CASK	HGNC	1497	protein_coding	YES	CCDS14257.1	ENSP00000367408	CSKP_HUMAN	.	UPI000013DA91	.	deleterious(0)	probably_damaging(1)	7/27	.	Superfamily_domains:SSF56112,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF40,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGACGTCTAC	.	5	ESCA
JADE3	0	.	GRCh37	X	46917885	46917885	+	Silent	SNP	G	G	A	rs781805711	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1878G>A	p.%3D	p.P626P	ENST00000218343	11/11	32	23	9	35	35	0	JADE3,synonymous_variant,p.%3D,ENST00000218343,;JADE3,synonymous_variant,p.%3D,ENST00000397189,;	A	ENSG00000102221	ENST00000218343	Transcript	synonymous_variant	2176	1878	626	P	ccG/ccA	rs781805711	.	.	1	JADE3	HGNC	22982	protein_coding	YES	CCDS14271.1	ENSP00000218343	JADE3_HUMAN	F2Z3N8_HUMAN,F2Z2B6_HUMAN	UPI0000073DE6	.	.	.	11/11	.	hmmpanther:PTHR13793:SF27,hmmpanther:PTHR13793	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCGTCCTC	byFrequency	5	ESCA
WDR45	0	.	GRCh37	X	48935401	48935401	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136G>T	p.Glu46Ter	p.E46*	ENST00000356463	5/12	28	20	7	48	48	0	WDR45,stop_gained,p.Glu3Ter,ENST00000367375,;WDR45,stop_gained,p.Glu46Ter,ENST00000419567,;WDR45,stop_gained,p.Glu46Ter,ENST00000322995,;WDR45,stop_gained,p.Glu46Ter,ENST00000396681,;WDR45,stop_gained,p.Glu46Ter,ENST00000376372,;WDR45,stop_gained,p.Glu46Ter,ENST00000473974,;WDR45,stop_gained,p.Glu46Ter,ENST00000465382,;WDR45,stop_gained,p.Glu46Ter,ENST00000356463,;WDR45,stop_gained,p.Glu46Ter,ENST00000376368,;WDR45,stop_gained,p.Glu46Ter,ENST00000474053,;WDR45,stop_gained,p.Glu46Ter,ENST00000423215,;WDR45,stop_gained,p.Glu46Ter,ENST00000471338,;AF196779.12,intron_variant,,ENST00000376358,;WDR45,intron_variant,,ENST00000476728,;WDR45,intron_variant,,ENST00000485908,;WDR45,intron_variant,,ENST00000553851,;WDR45,intron_variant,,ENST00000475880,;WDR45,upstream_gene_variant,,ENST00000475977,;WDR45,upstream_gene_variant,,ENST00000486337,;PRAF2,upstream_gene_variant,,ENST00000376390,;PRAF2,upstream_gene_variant,,ENST00000376386,;RNU4-52P,upstream_gene_variant,,ENST00000384209,;WDR45,intron_variant,,ENST00000465431,;WDR45,downstream_gene_variant,,ENST00000460501,;PRAF2,upstream_gene_variant,,ENST00000491199,;WDR45,non_coding_transcript_exon_variant,,ENST00000376357,;WDR45,non_coding_transcript_exon_variant,,ENST00000465806,;WDR45,non_coding_transcript_exon_variant,,ENST00000496803,;WDR45,upstream_gene_variant,,ENST00000480412,;WDR45,upstream_gene_variant,,ENST00000433252,;WDR45,upstream_gene_variant,,ENST00000472654,;	A	ENSG00000196998	ENST00000356463	Transcript	stop_gained	575	136	46	E/*	Gag/Tag	.	.	.	-1	WDR45	HGNC	28912	protein_coding	YES	CCDS14318.1	ENSP00000348848	WIPI4_HUMAN	C9J7Q8_HUMAN	UPI000035B01F	.	.	.	5/12	.	hmmpanther:PTHR11227:SF26,hmmpanther:PTHR11227,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCGTGGT	.	5	ESCA
IQSEC2	0	.	GRCh37	X	53268414	53268414	+	Silent	SNP	G	G	C	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3078C>G	p.%3D	p.P1026P	ENST00000396435	11/15	80	62	18	92	92	0	IQSEC2,synonymous_variant,p.%3D,ENST00000375365,;IQSEC2,synonymous_variant,p.%3D,ENST00000375368,;IQSEC2,synonymous_variant,p.%3D,ENST00000396435,;	C	ENSG00000124313	ENST00000396435	Transcript	synonymous_variant	3279	3078	1026	P	ccC/ccG	.	.	.	-1	IQSEC2	HGNC	29059	protein_coding	YES	CCDS48130.1	ENSP00000379712	IQEC2_HUMAN	C7SDG2_HUMAN	UPI00001C207D	.	.	.	11/15	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF61,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGAGGGGGAA	.	5	ESCA
SPIN4	0	.	GRCh37	X	62570563	62570563	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136C>A	p.Gln46Lys	p.Q46K	ENST00000335144	1/1	42	33	8	50	50	0	SPIN4,missense_variant,p.Gln46Lys,ENST00000335144,;SPIN4,missense_variant,p.Gln28Lys,ENST00000374884,;RP11-357C3.3,intron_variant,,ENST00000610234,;RP11-357C3.3,intron_variant,,ENST00000610088,;SPIN4-AS1,intron_variant,,ENST00000451979,;	T	ENSG00000186767	ENST00000335144	Transcript	missense_variant	656	136	46	Q/K	Caa/Aaa	.	.	.	-1	SPIN4	HGNC	27040	protein_coding	YES	CCDS43964.1	ENSP00000334163	SPIN4_HUMAN	.	UPI000013FD3C	.	tolerated(0.13)	possibly_damaging(0.543)	1/1	.	Pfam_domain:PF02513,hmmpanther:PTHR10405:SF9,hmmpanther:PTHR10405	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTTGAATGC	.	5	ESCA
MED12	0	.	GRCh37	X	70339933	70339933	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.466G>T	p.Ala156Ser	p.A156S	ENST00000374080	4/45	47	38	9	34	34	0	MED12,missense_variant,p.Ala156Ser,ENST00000374102,;MED12,missense_variant,p.Ala156Ser,ENST00000333646,;MED12,missense_variant,p.Ala156Ser,ENST00000374080,;MED12,downstream_gene_variant,,ENST00000429213,;	T	ENSG00000184634	ENST00000374080	Transcript	missense_variant	498	466	156	A/S	Gct/Tct	.	.	.	1	MED12	HGNC	11957	protein_coding	YES	CCDS43970.1	ENSP00000363193	MED12_HUMAN	Q7Z2F4_HUMAN,Q7Z2F1_HUMAN,Q7Z2E0_HUMAN	UPI00004257E2	.	.	benign(0.1)	4/45	.	Pfam_domain:PF09497,hmmpanther:PTHR12796,hmmpanther:PTHR12796:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCGGGCTGCC	.	5	ESCA
NLGN3	0	.	GRCh37	X	70367646	70367646	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.47C>A	p.Pro16His	p.P16H	ENST00000358741	2/8	44	33	10	76	76	0	NLGN3,missense_variant,p.Pro16His,ENST00000358741,;NLGN3,missense_variant,p.Pro16His,ENST00000374051,;NLGN3,missense_variant,p.Pro16His,ENST00000395855,;NLGN3,missense_variant,p.Pro16His,ENST00000536169,;	A	ENSG00000196338	ENST00000358741	Transcript	missense_variant	350	47	16	P/H	cCc/cAc	.	.	.	1	NLGN3	HGNC	14289	protein_coding	YES	CCDS55441.1	ENSP00000351591	NLGN3_HUMAN	.	UPI000006FCBB	.	tolerated_low_confidence(0.06)	benign(0.201)	2/8	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGCCCACGG	.	5	ESCA
ZDHHC15	0	.	GRCh37	X	74644566	74644566	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657G>T	p.%3D	p.V219V	ENST00000373367	8/12	40	24	16	58	58	0	ZDHHC15,missense_variant,p.Trp179Leu,ENST00000373361,;ZDHHC15,synonymous_variant,p.%3D,ENST00000541184,;ZDHHC15,synonymous_variant,p.%3D,ENST00000373367,;	A	ENSG00000102383	ENST00000373367	Transcript	synonymous_variant	888	657	219	V	gtG/gtT	.	.	.	-1	ZDHHC15	HGNC	20342	protein_coding	YES	CCDS14430.1	ENSP00000362465	ZDH15_HUMAN	.	UPI000006DB5A	.	.	.	8/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF6,Pfam_domain:PF01529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGCCACAAA	.	5	ESCA
PCDH19	0	.	GRCh37	X	99661722	99661722	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FD-01A-11D-A33E-09	TCGA-JY-A6FD-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1874G>A	p.Arg625Lys	p.R625K	ENST00000373034	1/6	27	21	5	33	33	0	PCDH19,missense_variant,p.Arg625Lys,ENST00000420881,;PCDH19,missense_variant,p.Arg625Lys,ENST00000255531,;PCDH19,missense_variant,p.Arg625Lys,ENST00000373034,;	T	ENSG00000165194	ENST00000373034	Transcript	missense_variant	3550	1874	625	R/K	aGa/aAa	.	.	.	-1	PCDH19	HGNC	14270	protein_coding	YES	CCDS55462.1	ENSP00000362125	PCD19_HUMAN	.	UPI00001D7BCD	.	tolerated(0.06)	possibly_damaging(0.823)	1/6	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF40,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTTCTGACT	.	5	ESCA
COX15	0	.	GRCh37	10	101473139	101473139	+	3'Flank	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000016171	.	33	11	21	25	25	0	COX15,3_prime_UTR_variant,,ENST00000370483,;COX15,downstream_gene_variant,,ENST00000016171,;CUTC,intron_variant,,ENST00000493385,;COX15,downstream_gene_variant,,ENST00000497381,;	C	ENSG00000014919	ENST00000016171	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	133	-1	COX15	HGNC	2263	protein_coding	YES	CCDS7482.1	ENSP00000016171	COX15_HUMAN	B4DQM2_HUMAN	UPI000006E691	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTATATTAG	.	5	ESCA
PRPF18	0	.	GRCh37	10	13672330	13672330	+	Missense_Mutation	SNP	A	A	G	rs752453925	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1019A>G	p.Asn340Ser	p.N340S	ENST00000378572	10/10	60	34	25	55	55	0	PRPF18,missense_variant,p.Asn340Ser,ENST00000378572,;RP11-295P9.3,intron_variant,,ENST00000601460,;RP11-295P9.3,upstream_gene_variant,,ENST00000440878,;RP11-295P9.3,upstream_gene_variant,,ENST00000601758,;RP11-295P9.3,upstream_gene_variant,,ENST00000599639,;RP11-295P9.3,upstream_gene_variant,,ENST00000601075,;RP11-295P9.3,upstream_gene_variant,,ENST00000596499,;RP11-295P9.3,missense_variant,p.Asn32Ser,ENST00000595538,;RP11-295P9.3,missense_variant,p.Asn16Ser,ENST00000596044,;RP11-295P9.3,upstream_gene_variant,,ENST00000597920,;	G	ENSG00000165630	ENST00000378572	Transcript	missense_variant	1179	1019	340	N/S	aAt/aGt	rs752453925	.	.	1	PRPF18	HGNC	17351	protein_coding	YES	CCDS7100.1	ENSP00000367835	PRP18_HUMAN	M0QXX3_HUMAN	UPI0000070C82	.	tolerated(0.32)	benign(0.045)	10/10	.	hmmpanther:PTHR13007:SF19,hmmpanther:PTHR13007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACAATGCAC	byFrequency	5	ESCA
HERC4	0	.	GRCh37	10	69834989	69834989	+	5'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-197C>A	.	.	ENST00000395198	1/26	79	36	42	78	78	0	HERC4,5_prime_UTR_variant,,ENST00000373700,;HERC4,5_prime_UTR_variant,,ENST00000492996,;HERC4,5_prime_UTR_variant,,ENST00000513996,;HERC4,5_prime_UTR_variant,,ENST00000412272,;HERC4,5_prime_UTR_variant,,ENST00000395198,;HERC4,upstream_gene_variant,,ENST00000506515,;HERC4,upstream_gene_variant,,ENST00000395187,;HERC4,non_coding_transcript_exon_variant,,ENST00000395185,;HERC4,upstream_gene_variant,,ENST00000505760,;HERC4,upstream_gene_variant,,ENST00000515753,;HERC4,5_prime_UTR_variant,,ENST00000473533,;HERC4,upstream_gene_variant,,ENST00000427635,;	T	ENSG00000148634	ENST00000395198	Transcript	5_prime_UTR_variant	52	.	.	.	.	.	.	.	-1	HERC4	HGNC	24521	protein_coding	YES	CCDS41533.1	ENSP00000378624	HERC4_HUMAN	D6RFK9_HUMAN	UPI00004C6F56	.	.	.	1/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACGGGAGGCA	.	5	ESCA
MMP13	0	.	GRCh37	11	102814822	102814822	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*173C>A	.	.	ENST00000260302	10/10	39	22	16	30	30	0	MMP13,3_prime_UTR_variant,,ENST00000260302,;MMP13,downstream_gene_variant,,ENST00000340273,;	T	ENSG00000137745	ENST00000260302	Transcript	3_prime_UTR_variant	1618	.	.	.	.	.	.	.	-1	MMP13	HGNC	7159	protein_coding	YES	CCDS8324.1	ENSP00000260302	MMP13_HUMAN	Q6LBE5_HUMAN	UPI00000422BC	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAATGTGGTT	.	5	ESCA
ZW10	0	.	GRCh37	11	113631036	113631036	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.475T>C	p.%3D	p.L159L	ENST00000200135	5/16	31	19	11	30	30	0	ZW10,synonymous_variant,p.%3D,ENST00000200135,;ZW10,synonymous_variant,p.%3D,ENST00000535142,;ZW10,intron_variant,,ENST00000538209,;	G	ENSG00000086827	ENST00000200135	Transcript	synonymous_variant	620	475	159	L	Ttg/Ctg	.	.	.	-1	ZW10	HGNC	13194	protein_coding	YES	CCDS8363.1	ENSP00000200135	ZW10_HUMAN	B4E1J7_HUMAN,A1A528_HUMAN	UPI000013C491	.	.	.	5/16	.	hmmpanther:PTHR12205:SF0,hmmpanther:PTHR12205,Pfam_domain:PF06248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCAATATTT	.	5	ESCA
HEPACAM	0	.	GRCh37	11	124790261	124790261	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*773A>G	.	.	ENST00000298251	7/7	82	63	19	48	48	0	HEPACAM,3_prime_UTR_variant,,ENST00000298251,;HEPN1,3_prime_UTR_variant,,ENST00000408930,;HEPACAM,downstream_gene_variant,,ENST00000528971,;HEPACAM,downstream_gene_variant,,ENST00000526273,;	C	ENSG00000165478	ENST00000298251	Transcript	3_prime_UTR_variant	2430	.	.	.	.	.	.	.	-1	HEPACAM	HGNC	26361	protein_coding	YES	CCDS8456.1	ENSP00000298251	HECAM_HUMAN	.	UPI000013E4B5	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTTTATTC	.	5	ESCA
QSER1	0	.	GRCh37	11	32987900	32987900	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4637A>G	p.Lys1546Arg	p.K1546R	ENST00000399302	9/13	74	56	18	66	66	0	QSER1,missense_variant,p.Lys1307Arg,ENST00000527788,;QSER1,missense_variant,p.Lys1546Arg,ENST00000399302,;QSER1,missense_variant,p.Lys567Arg,ENST00000524678,;QSER1,intron_variant,,ENST00000528034,;	G	ENSG00000060749	ENST00000399302	Transcript	missense_variant	4972	4637	1546	K/R	aAg/aGg	.	.	.	1	QSER1	HGNC	26154	protein_coding	YES	CCDS41631.1	ENSP00000382241	QSER1_HUMAN	E9PQD3_HUMAN,B3KWV1_HUMAN	UPI0000E467AF	.	tolerated(0.27)	probably_damaging(0.999)	9/13	.	Pfam_domain:PF13926,hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGAAGGAAA	.	5	ESCA
ZFP91	0	.	GRCh37	11	58385599	58385599	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*420A>G	.	.	ENST00000316059	11/11	53	28	25	46	46	0	ZFP91,3_prime_UTR_variant,,ENST00000316059,;CNTF,upstream_gene_variant,,ENST00000361987,;ZFP91-CNTF,intron_variant,,ENST00000389919,;ZFP91-CNTF,intron_variant,,ENST00000422974,;	G	ENSG00000186660	ENST00000316059	Transcript	3_prime_UTR_variant	2304	.	.	.	.	.	.	.	1	ZFP91	HGNC	14983	protein_coding	YES	CCDS31553.1	ENSP00000339030	ZFP91_HUMAN	B4DIN6_HUMAN	UPI0000070D45	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTATGGTT	.	5	ESCA
VPS37C	0	.	GRCh37	11	60899899	60899899	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.461A>C	p.Gln154Pro	p.Q154P	ENST00000301765	5/5	56	51	5	51	51	0	VPS37C,missense_variant,p.Gln154Pro,ENST00000301765,;CD5,downstream_gene_variant,,ENST00000347785,;VPS37C,downstream_gene_variant,,ENST00000538036,;VPS37C,downstream_gene_variant,,ENST00000536000,;	G	ENSG00000167987	ENST00000301765	Transcript	missense_variant	694	461	154	Q/P	cAg/cCg	.	.	.	-1	VPS37C	HGNC	26097	protein_coding	YES	CCDS31573.1	ENSP00000301765	VP37C_HUMAN	F5H4Q5_HUMAN	UPI00001AED12	.	deleterious(0)	probably_damaging(0.998)	5/5	.	PROSITE_profiles:PS51314,hmmpanther:PTHR13678,hmmpanther:PTHR13678:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCCTGGAGC	.	4	ESCA
NPAS4	0	.	GRCh37	11	66190289	66190289	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.575G>C	p.Cys192Ser	p.C192S	ENST00000311034	4/8	25	18	6	23	23	0	NPAS4,missense_variant,p.Cys192Ser,ENST00000311034,;NPAS4,missense_variant,p.Cys192Ser,ENST00000525148,;NPAS4,upstream_gene_variant,,ENST00000524617,;	C	ENSG00000174576	ENST00000311034	Transcript	missense_variant	751	575	192	C/S	tGt/tCt	.	.	.	1	NPAS4	HGNC	18983	protein_coding	YES	CCDS8138.1	ENSP00000311196	NPAS4_HUMAN	.	UPI0000074744	.	deleterious(0.01)	probably_damaging(0.998)	4/8	.	hmmpanther:PTHR23043:SF13,hmmpanther:PTHR23043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTGTGCCC	.	5	ESCA
KIAA1467	0	.	GRCh37	12	13224300	13224300	+	Silent	SNP	C	C	G	rs374898629	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1494C>G	p.%3D	p.A498A	ENST00000197268	10/13	28	13	14	33	33	0	KIAA1467,synonymous_variant,p.%3D,ENST00000197268,;KIAA1467,synonymous_variant,p.%3D,ENST00000537625,;KIAA1467,synonymous_variant,p.%3D,ENST00000416494,;KIAA1467,non_coding_transcript_exon_variant,,ENST00000541950,;KIAA1467,downstream_gene_variant,,ENST00000540455,;	G	ENSG00000084444	ENST00000197268	Transcript	synonymous_variant	1614	1494	498	A	gcC/gcG	rs374898629	.	.	1	KIAA1467	HGNC	29288	protein_coding	YES	CCDS31750.1	ENSP00000197268	K1467_HUMAN	.	UPI00001FB6A1	.	.	.	10/13	.	hmmpanther:PTHR21419,hmmpanther:PTHR21419:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCCGAAGG	byFrequency|byCluster	5	ESCA
CACNB3	0	.	GRCh37	12	49218137	49218143	+	Frame_Shift_Del	DEL	AAACAGG	AAACAGG	-	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	AAACAGG	AAACAGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389_395delAACAGGA	p.Lys130SerfsTer13	p.K130Sfs*13	ENST00000301050	4/13	61	17	44	83	83	0	CACNB3,frameshift_variant,p.Lys130SerfsTer13,ENST00000547392,;CACNB3,frameshift_variant,p.Lys129SerfsTer13,ENST00000548279,;CACNB3,frameshift_variant,p.Lys130SerfsTer13,ENST00000301050,;CACNB3,frameshift_variant,p.Lys129SerfsTer13,ENST00000536187,;CACNB3,frameshift_variant,p.Lys89SerfsTer13,ENST00000547230,;CACNB3,frameshift_variant,p.Lys117SerfsTer13,ENST00000540990,;CACNB3,5_prime_UTR_variant,,ENST00000550064,;CACNB3,5_prime_UTR_variant,,ENST00000547818,;CACNB3,intron_variant,,ENST00000550190,;CACNB3,non_coding_transcript_exon_variant,,ENST00000550168,;CACNB3,non_coding_transcript_exon_variant,,ENST00000552022,;CACNB3,downstream_gene_variant,,ENST00000549971,;CACNB3,frameshift_variant,p.Lys117SerfsTer13,ENST00000550391,;CACNB3,frameshift_variant,p.Lys42SerfsTer13,ENST00000550483,;CACNB3,3_prime_UTR_variant,,ENST00000551544,;CACNB3,non_coding_transcript_exon_variant,,ENST00000549226,;CACNB3,non_coding_transcript_exon_variant,,ENST00000548860,;CACNB3,intron_variant,,ENST00000548874,;CACNB3,upstream_gene_variant,,ENST00000552480,;CACNB3,downstream_gene_variant,,ENST00000551716,;CACNB3,downstream_gene_variant,,ENST00000552812,;CACNB3,downstream_gene_variant,,ENST00000547693,;CACNB3,downstream_gene_variant,,ENST00000550771,;	-	ENSG00000167535	ENST00000301050	Transcript	frameshift_variant	587-593	388-394	130-132	KQE/X	AAACAGGag/ag	.	.	.	1	CACNB3	HGNC	1403	protein_coding	YES	CCDS8769.1	ENSP00000301050	CACB3_HUMAN	F8VUW8_HUMAN,F8VU10_HUMAN	UPI000000D9BA	.	.	.	4/13	.	hmmpanther:PTHR11824,Gene3D:2.30.30.40,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGGCTCAAACAGGAGCAG	.	3	ESCA
LEMD3	0	.	GRCh37	12	65641332	65641332	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1227C>T	.	.	ENST00000308330	13/13	11	8	3	8	8	0	LEMD3,3_prime_UTR_variant,,ENST00000308330,;LEMD3,downstream_gene_variant,,ENST00000544506,;LEMD3,downstream_gene_variant,,ENST00000542032,;LEMD3,downstream_gene_variant,,ENST00000545026,;LEMD3,downstream_gene_variant,,ENST00000539442,;	T	ENSG00000174106	ENST00000308330	Transcript	3_prime_UTR_variant	3989	.	.	.	.	.	.	.	1	LEMD3	HGNC	28887	protein_coding	YES	CCDS8972.1	ENSP00000308369	MAN1_HUMAN	B4DI45_HUMAN	UPI000012EB75	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATTTCAGATA	.	2	ESCA
ATP2B1	0	.	GRCh37	12	89984142	89984142	+	3'UTR	SNP	A	A	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*619T>G	.	.	ENST00000428670	21/21	39	17	22	42	42	0	ATP2B1,3_prime_UTR_variant,,ENST00000428670,;ATP2B1,3_prime_UTR_variant,,ENST00000359142,;ATP2B1,3_prime_UTR_variant,,ENST00000261173,;ATP2B1,3_prime_UTR_variant,,ENST00000348959,;ATP2B1,downstream_gene_variant,,ENST00000550716,;ATP2B1,downstream_gene_variant,,ENST00000393164,;AC068641.1,upstream_gene_variant,,ENST00000585304,;RP11-981P6.1,intron_variant,,ENST00000552778,;	C	ENSG00000070961	ENST00000428670	Transcript	3_prime_UTR_variant	4739	.	.	.	.	.	.	.	-1	ATP2B1	HGNC	814	protein_coding	YES	CCDS9035.1	ENSP00000392043	AT2B1_HUMAN	Q3L582_HUMAN	UPI000002A436	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTAACAAG	.	5	ESCA
NALCN	0	.	GRCh37	13	101755521	101755521	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3057+2T>C	.	p.X1019_splice	ENST00000251127	.	82	76	6	37	37	0	NALCN,splice_donor_variant,,ENST00000251127,;	G	ENSG00000102452	ENST00000251127	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	NALCN	HGNC	19082	protein_coding	YES	CCDS9498.1	ENSP00000251127	NALCN_HUMAN	B3KX53_HUMAN,B3KMK1_HUMAN	UPI000004EBBD	.	.	.	.	26/43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACATACCAAA	.	2	ESCA
MYO16	0	.	GRCh37	13	109617123	109617124	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2176_2177insT	p.Arg726LeufsTer9	p.R726Lfs*9	ENST00000356711	20/35	201	153	48	66	66	0	MYO16,frameshift_variant,p.Arg238LeufsTer9,ENST00000457511,;MYO16,frameshift_variant,p.Arg726LeufsTer9,ENST00000251041,;MYO16,frameshift_variant,p.Arg726LeufsTer9,ENST00000356711,;MYO16,frameshift_variant,p.Arg726LeufsTer9,ENST00000357550,;MYO16,non_coding_transcript_exon_variant,,ENST00000375857,;	T	ENSG00000041515	ENST00000356711	Transcript	frameshift_variant	2302-2303	2176-2177	726	R/LX	cga/cTga	.	.	.	1	MYO16	HGNC	29822	protein_coding	YES	CCDS32008.1	ENSP00000349145	MYO16_HUMAN	.	UPI0000160FF2	.	.	.	20/35	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF345,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAATACGACGA	.	3	ESCA
NUPL1	0	.	GRCh37	13	25910320	25910320	+	Intron	SNP	T	T	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1436-754T>G	.	.	ENST00000381736	.	46	16	30	44	44	0	NUPL1,3_prime_UTR_variant,,ENST00000463407,;NUPL1,intron_variant,,ENST00000381736,;NUPL1,intron_variant,,ENST00000381747,;NUPL1,intron_variant,,ENST00000394327,;NUPL1,intron_variant,,ENST00000381718,;NUPL1,intron_variant,,ENST00000466694,;NUPL1,intron_variant,,ENST00000477876,;	G	ENSG00000139496	ENST00000381736	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NUPL1	HGNC	20261	protein_coding	YES	CCDS9314.1	ENSP00000371155	NUPL1_HUMAN	.	UPI000006D9D4	.	.	.	.	13/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCTTTGTA	.	5	ESCA
MTRF1	0	.	GRCh37	13	41826879	41826879	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.599G>A	p.Cys200Tyr	p.C200Y	ENST00000379480	5/10	51	14	37	43	43	0	MTRF1,missense_variant,p.Cys213Tyr,ENST00000430347,;MTRF1,missense_variant,p.Cys200Tyr,ENST00000379477,;MTRF1,missense_variant,p.Cys200Tyr,ENST00000452359,;MTRF1,missense_variant,p.Cys200Tyr,ENST00000379480,;MTRF1,non_coding_transcript_exon_variant,,ENST00000480434,;MTRF1,non_coding_transcript_exon_variant,,ENST00000239852,;MTRF1,non_coding_transcript_exon_variant,,ENST00000497679,;	T	ENSG00000120662	ENST00000379480	Transcript	missense_variant	700	599	200	C/Y	tGc/tAc	.	.	.	-1	MTRF1	HGNC	7469	protein_coding	YES	CCDS9378.1	ENSP00000368793	RF1M_HUMAN	.	UPI0000035FC6	.	deleterious(0)	probably_damaging(1)	5/10	.	hmmpanther:PTHR11075:SF44,hmmpanther:PTHR11075,Pfam_domain:PF03462,SMART_domains:SM00937,Superfamily_domains:SSF75620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGGCAGATG	.	5	ESCA
SOCS4	0	.	GRCh37	14	55509975	55509975	+	Silent	SNP	A	A	C	rs535547343	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216A>C	p.%3D	p.S72S	ENST00000395472	2/2	52	12	39	52	52	0	SOCS4,synonymous_variant,p.%3D,ENST00000339298,;SOCS4,synonymous_variant,p.%3D,ENST00000395472,;SOCS4,synonymous_variant,p.%3D,ENST00000555846,;	C	ENSG00000180008	ENST00000395472	Transcript	synonymous_variant	548	216	72	S	tcA/tcC	rs535547343	.	.	1	SOCS4	HGNC	19392	protein_coding	YES	CCDS9722.1	ENSP00000378855	SOCS4_HUMAN	Q5H9R6_HUMAN	UPI000000CC33	.	.	.	2/2	.	hmmpanther:PTHR10385,hmmpanther:PTHR10385:SF29,Pfam_domain:PF12610	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCATCCAT	.	5	ESCA
MGA	0	.	GRCh37	15	42057160	42057160	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7824delA	p.Gly2609ValfsTer9	p.G2609Vfs*9	ENST00000219905	23/24	40	36	4	37	37	0	MGA,frameshift_variant,p.Gly2609ValfsTer9,ENST00000219905,;MGA,frameshift_variant,p.Gly2609ValfsTer9,ENST00000570161,;MGA,frameshift_variant,p.Gly2400ValfsTer9,ENST00000545763,;MGA,frameshift_variant,p.Gly2570ValfsTer9,ENST00000389936,;MGA,frameshift_variant,p.Gly2400ValfsTer9,ENST00000566586,;MGA,downstream_gene_variant,,ENST00000564190,;MGA,downstream_gene_variant,,ENST00000568255,;	-	ENSG00000174197	ENST00000219905	Transcript	frameshift_variant	8002	7821	2607	L/X	ctA/ct	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	.	.	23/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CACCCTAAAAGG	.	2	ESCA
NEDD4	0	.	GRCh37	15	56121974	56121974	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*121A>G	.	.	ENST00000338963	22/22	33	10	23	32	32	0	NEDD4,3_prime_UTR_variant,,ENST00000508871,;NEDD4,3_prime_UTR_variant,,ENST00000435532,;NEDD4,3_prime_UTR_variant,,ENST00000338963,;NEDD4,3_prime_UTR_variant,,ENST00000508342,;NEDD4,3_prime_UTR_variant,,ENST00000506154,;NEDD4,3_prime_UTR_variant,,ENST00000503468,;	C	ENSG00000069869	ENST00000338963	Transcript	3_prime_UTR_variant	4165	.	.	.	.	.	.	.	-1	NEDD4	HGNC	7727	protein_coding	YES	CCDS10156.1	ENSP00000345530	NEDD4_HUMAN	.	UPI00001418FE	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGATTTTCT	.	5	ESCA
SEC11A	0	.	GRCh37	15	85213003	85213003	+	3'UTR	SNP	A	A	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247T>G	.	.	ENST00000268220	6/6	49	26	22	23	23	0	SEC11A,3_prime_UTR_variant,,ENST00000560266,;SEC11A,3_prime_UTR_variant,,ENST00000455959,;SEC11A,3_prime_UTR_variant,,ENST00000268220,;SEC11A,3_prime_UTR_variant,,ENST00000558134,;SEC11A,3_prime_UTR_variant,,ENST00000558217,;SEC11A,downstream_gene_variant,,ENST00000559729,;SEC11A,non_coding_transcript_exon_variant,,ENST00000559376,;SEC11A,non_coding_transcript_exon_variant,,ENST00000558924,;SEC11A,downstream_gene_variant,,ENST00000560409,;	C	ENSG00000140612	ENST00000268220	Transcript	3_prime_UTR_variant	1428	.	.	.	.	.	.	.	-1	SEC11A	HGNC	17718	protein_coding	YES	CCDS45340.1	ENSP00000268220	SC11A_HUMAN	H0YNX5_HUMAN,B4DUL4_HUMAN	UPI0000049B6F	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAAAAATTT	.	5	ESCA
BAIAP3	0	.	GRCh37	16	1391467	1391467	+	Silent	SNP	C	C	T	rs147169956	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813C>T	p.%3D	p.P271P	ENST00000324385	8/34	18	4	14	12	12	0	BAIAP3,synonymous_variant,p.%3D,ENST00000426824,;BAIAP3,synonymous_variant,p.%3D,ENST00000562208,;BAIAP3,synonymous_variant,p.%3D,ENST00000421665,;BAIAP3,synonymous_variant,p.%3D,ENST00000568887,;BAIAP3,synonymous_variant,p.%3D,ENST00000397488,;BAIAP3,synonymous_variant,p.%3D,ENST00000324385,;BAIAP3,synonymous_variant,p.%3D,ENST00000397489,;BAIAP3,upstream_gene_variant,,ENST00000561793,;BAIAP3,upstream_gene_variant,,ENST00000566162,;BAIAP3,upstream_gene_variant,,ENST00000564213,;BAIAP3,non_coding_transcript_exon_variant,,ENST00000567825,;BAIAP3,upstream_gene_variant,,ENST00000561602,;BAIAP3,downstream_gene_variant,,ENST00000565665,;BAIAP3,upstream_gene_variant,,ENST00000567203,;BAIAP3,upstream_gene_variant,,ENST00000568198,;	T	ENSG00000007516	ENST00000324385	Transcript	synonymous_variant	971	813	271	P	ccC/ccT	rs147169956	.	.	1	BAIAP3	HGNC	948	protein_coding	YES	CCDS10434.1	ENSP00000324510	BAIP3_HUMAN	.	UPI0000071E58	.	.	.	8/34	.	Superfamily_domains:SSF49562,SMART_domains:SM00239,Gene3D:2.60.40.150,Pfam_domain:PF00168,hmmpanther:PTHR15015,hmmpanther:PTHR15015:SF19,PROSITE_profiles:PS50004	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCCCGTCTG	byCluster	4	ESCA
RNF40	0	.	GRCh37	16	30779971	30779971	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2011C>T	p.%3D	p.L671L	ENST00000324685	14/20	30	6	23	25	25	0	RNF40,synonymous_variant,p.%3D,ENST00000563683,;RNF40,synonymous_variant,p.%3D,ENST00000357890,;RNF40,synonymous_variant,p.%3D,ENST00000324685,;RNF40,synonymous_variant,p.%3D,ENST00000402121,;RNF40,downstream_gene_variant,,ENST00000565995,;RNF40,upstream_gene_variant,,ENST00000567365,;RNF40,non_coding_transcript_exon_variant,,ENST00000493683,;RNF40,downstream_gene_variant,,ENST00000564260,;RNF40,downstream_gene_variant,,ENST00000566703,;	T	ENSG00000103549	ENST00000324685	Transcript	synonymous_variant	2446	2011	671	L	Ctg/Ttg	.	.	.	1	RNF40	HGNC	16867	protein_coding	YES	CCDS10691.1	ENSP00000325677	BRE1B_HUMAN	I3L332_HUMAN,H3BUL6_HUMAN,H3BS50_HUMAN,H3BQ99_HUMAN,B4E313_HUMAN	UPI000013D2CF	.	.	.	14/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23163,hmmpanther:PTHR23163:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAACTGCTG	.	5	ESCA
CREBBP	0	.	GRCh37	16	3820588	3820588	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2863C>T	p.Gln955Ter	p.Q955*	ENST00000262367	14/31	36	6	30	40	40	0	CREBBP,stop_gained,p.Gln955Ter,ENST00000262367,;CREBBP,stop_gained,p.Gln917Ter,ENST00000382070,;CREBBP,upstream_gene_variant,,ENST00000570939,;CREBBP,downstream_gene_variant,,ENST00000572134,;CREBBP,downstream_gene_variant,,ENST00000571826,;CREBBP,non_coding_transcript_exon_variant,,ENST00000573672,;CREBBP,downstream_gene_variant,,ENST00000575237,;	A	ENSG00000005339	ENST00000262367	Transcript	stop_gained	3673	2863	955	Q/*	Cag/Tag	.	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	.	14/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCTGGGCGT	.	5	ESCA
MYLK3	0	.	GRCh37	16	46741550	46741550	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66C>A	.	.	ENST00000394809	13/13	32	21	10	22	22	0	MYLK3,3_prime_UTR_variant,,ENST00000394809,;MYLK3,downstream_gene_variant,,ENST00000536476,;RP11-480G7.1,upstream_gene_variant,,ENST00000562218,;MYLK3,downstream_gene_variant,,ENST00000562104,;MYLK3,downstream_gene_variant,,ENST00000565182,;	T	ENSG00000140795	ENST00000394809	Transcript	3_prime_UTR_variant	2642	.	.	.	.	.	.	.	-1	MYLK3	HGNC	29826	protein_coding	YES	CCDS10723.2	ENSP00000378288	MYLK3_HUMAN	.	UPI000059D380	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGAGTCATC	.	5	ESCA
CTD-2600O9.1	0	.	GRCh37	16	57850795	57850795	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*24G>A	.	.	ENST00000564282	4/4	57	48	9	46	46	0	CTD-2600O9.1,3_prime_UTR_variant,,ENST00000335616,;CTD-2600O9.1,3_prime_UTR_variant,,ENST00000564282,;KIFC3,intron_variant,,ENST00000565684,;KIFC3,intron_variant,,ENST00000563028,;CTD-2600O9.1,downstream_gene_variant,,ENST00000566652,;	A	ENSG00000187185	ENST00000564282	Transcript	3_prime_UTR_variant	1254	.	.	.	.	.	.	.	1	CTD-2600O9.1	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000457453	.	Q86VG7_HUMAN	UPI000018F17A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACCGACCTT	.	4	ESCA
DNAH9	0	.	GRCh37	17	11797759	11797759	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11352G>A	p.%3D	p.T3784T	ENST00000262442	59/69	59	43	15	41	41	0	DNAH9,synonymous_variant,p.%3D,ENST00000454412,;DNAH9,synonymous_variant,p.%3D,ENST00000608377,;DNAH9,synonymous_variant,p.%3D,ENST00000262442,;DNAH9,non_coding_transcript_exon_variant,,ENST00000396001,;DNAH9,non_coding_transcript_exon_variant,,ENST00000581682,;	A	ENSG00000007174	ENST00000262442	Transcript	synonymous_variant	11420	11352	3784	T	acG/acA	.	.	.	1	DNAH9	HGNC	2953	protein_coding	YES	CCDS11160.1	ENSP00000262442	DYH9_HUMAN	Q92865_HUMAN	UPI0000141BA2	.	.	.	59/69	.	hmmpanther:PTHR10676:SF36,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGACGGGCAC	.	5	ESCA
PAFAH1B1	0	.	GRCh37	17	2587317	2587317	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2221G>A	.	.	ENST00000397195	11/11	41	13	28	32	32	0	PAFAH1B1,3_prime_UTR_variant,,ENST00000397195,;PAFAH1B1,downstream_gene_variant,,ENST00000574468,;PAFAH1B1,downstream_gene_variant,,ENST00000451360,;RP11-74E22.6,upstream_gene_variant,,ENST00000608984,;RP11-74E22.5,intron_variant,,ENST00000610120,;RN7SL608P,downstream_gene_variant,,ENST00000492377,;PAFAH1B1,non_coding_transcript_exon_variant,,ENST00000572915,;PAFAH1B1,downstream_gene_variant,,ENST00000397193,;PAFAH1B1,downstream_gene_variant,,ENST00000574213,;PAFAH1B1,downstream_gene_variant,,ENST00000574816,;PAFAH1B1,downstream_gene_variant,,ENST00000610190,;PAFAH1B1,downstream_gene_variant,,ENST00000571495,;	A	ENSG00000007168	ENST00000397195	Transcript	3_prime_UTR_variant	3905	.	.	.	.	.	.	.	1	PAFAH1B1	HGNC	8574	protein_coding	YES	CCDS32528.1	ENSP00000380378	LIS1_HUMAN	I3L495_HUMAN,B4DZN3_HUMAN	UPI0000163BF4	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGCACAC	.	5	ESCA
SSH2	0	.	GRCh37	17	27954662	27954662	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3197G>A	.	.	ENST00000269033	15/15	47	15	31	43	43	0	SSH2,3_prime_UTR_variant,,ENST00000269033,;SSH2,downstream_gene_variant,,ENST00000577991,;CORO6,upstream_gene_variant,,ENST00000584602,;CORO6,upstream_gene_variant,,ENST00000345068,;CORO6,upstream_gene_variant,,ENST00000492276,;SSH2,downstream_gene_variant,,ENST00000540801,;RP11-68I3.2,intron_variant,,ENST00000581474,;CORO6,upstream_gene_variant,,ENST00000577909,;CORO6,upstream_gene_variant,,ENST00000459686,;CORO6,upstream_gene_variant,,ENST00000467534,;	T	ENSG00000141298	ENST00000269033	Transcript	3_prime_UTR_variant	7621	.	.	.	.	.	.	.	-1	SSH2	HGNC	30580	protein_coding	YES	CCDS11253.1	ENSP00000269033	SSH2_HUMAN	J3KSQ9_HUMAN	UPI00001D6272	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATCCCAAA	.	5	ESCA
SKAP1	0	.	GRCh37	17	46265275	46265275	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372T>G	p.Phe124Leu	p.F124L	ENST00000336915	6/13	41	22	18	29	29	0	SKAP1,missense_variant,p.Phe124Leu,ENST00000584924,;SKAP1,missense_variant,p.Phe124Leu,ENST00000336915,;SKAP1,upstream_gene_variant,,ENST00000579336,;RP11-456D7.1,intron_variant,,ENST00000582246,;SKAP1,missense_variant,p.Phe65Leu,ENST00000581400,;SKAP1,3_prime_UTR_variant,,ENST00000581419,;SKAP1,3_prime_UTR_variant,,ENST00000584709,;	C	ENSG00000141293	ENST00000336915	Transcript	missense_variant	442	372	124	F/L	ttT/ttG	.	.	.	-1	SKAP1	HGNC	15605	protein_coding	YES	CCDS32674.1	ENSP00000338171	SKAP1_HUMAN	J3QS38_HUMAN,J3QRG3_HUMAN	UPI0000200EFD	.	tolerated(0.37)	probably_damaging(0.998)	6/13	.	PROSITE_profiles:PS50003,hmmpanther:PTHR15129,hmmpanther:PTHR15129:SF1,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCCAAAGAA	.	5	ESCA
UBE2Z	0	.	GRCh37	17	47006161	47006161	+	3'UTR	SNP	A	A	G	rs778981845	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1665A>G	.	.	ENST00000360943	7/7	34	12	22	41	41	0	UBE2Z,3_prime_UTR_variant,,ENST00000360943,;SNF8,downstream_gene_variant,,ENST00000290330,;SNF8,downstream_gene_variant,,ENST00000502492,;AC091133.1,upstream_gene_variant,,ENST00000435491,;SNF8,downstream_gene_variant,,ENST00000514089,;UBE2Z,non_coding_transcript_exon_variant,,ENST00000513342,;UBE2Z,downstream_gene_variant,,ENST00000506271,;SNF8,downstream_gene_variant,,ENST00000509989,;SNF8,downstream_gene_variant,,ENST00000514929,;SNF8,downstream_gene_variant,,ENST00000504000,;SNF8,downstream_gene_variant,,ENST00000576353,;UBE2Z,downstream_gene_variant,,ENST00000506498,;SNF8,downstream_gene_variant,,ENST00000509995,;SNF8,downstream_gene_variant,,ENST00000573795,;UBE2Z,downstream_gene_variant,,ENST00000504684,;SNF8,downstream_gene_variant,,ENST00000510558,;SNF8,downstream_gene_variant,,ENST00000507302,;SNF8,downstream_gene_variant,,ENST00000515572,;	G	ENSG00000159202	ENST00000360943	Transcript	3_prime_UTR_variant	2865	.	.	.	.	rs778981845	.	.	1	UBE2Z	HGNC	25847	protein_coding	YES	CCDS11540.2	ENSP00000354201	UBE2Z_HUMAN	I3L4C5_HUMAN	UPI00005A774B	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAATGCTC	.	5	ESCA
MED13	0	.	GRCh37	17	60021750	60021750	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2079T>A	.	.	ENST00000397786	30/30	19	15	3	13	13	0	MED13,3_prime_UTR_variant,,ENST00000397786,;	T	ENSG00000108510	ENST00000397786	Transcript	3_prime_UTR_variant	8681	.	.	.	.	.	.	.	-1	MED13	HGNC	22474	protein_coding	YES	CCDS42366.1	ENSP00000380888	MED13_HUMAN	.	UPI0000D7D6F6	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTTAAAGAA	.	3	ESCA
KCNJ16	0	.	GRCh37	17	68129313	68129313	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1085C>A	p.Ser362Tyr	p.S362Y	ENST00000392670	4/4	28	7	21	41	40	1	KCNJ16,missense_variant,p.Ser362Tyr,ENST00000283936,;KCNJ16,missense_variant,p.Ser362Tyr,ENST00000589377,;KCNJ16,missense_variant,p.Ser362Tyr,ENST00000392671,;KCNJ16,missense_variant,p.Ser401Tyr,ENST00000586462,;KCNJ16,missense_variant,p.Ser397Tyr,ENST00000585558,;KCNJ16,missense_variant,p.Ser362Tyr,ENST00000392670,;KCNJ16,downstream_gene_variant,,ENST00000587698,;KCNJ16,downstream_gene_variant,,ENST00000591891,;KCNJ16,downstream_gene_variant,,ENST00000587892,;AC002539.1,upstream_gene_variant,,ENST00000435112,;	A	ENSG00000153822	ENST00000392670	Transcript	missense_variant	1578	1085	362	S/Y	tCc/tAc	.	.	.	1	KCNJ16	HGNC	6262	protein_coding	YES	CCDS11687.1	ENSP00000376438	IRK16_HUMAN	K7ELL5_HUMAN,K7EKJ4_HUMAN	UPI000012D8B3	.	tolerated(0.29)	benign(0.266)	4/4	.	hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF24,PIRSF_domain:PIRSF005465	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGAATCCTGCA	.	4	ESCA
TP53	0	.	GRCh37	17	7578503	7578516	+	Frame_Shift_Del	DEL	CAGGGCAGGTCTTG	CAGGGCAGGTCTTG	-	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	CAGGGCAGGTCTTG	CAGGGCAGGTCTTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.414_427delCAAGACCTGCCCTG	p.Lys139AlafsTer5	p.K139Afs*5	ENST00000269305	5/11	20	3	16	20	20	0	TP53,frameshift_variant,p.Lys139AlafsTer5,ENST00000508793,;TP53,frameshift_variant,p.Lys139AlafsTer5,ENST00000413465,;TP53,frameshift_variant,p.Lys132AlafsTer5,ENST00000604348,;TP53,frameshift_variant,p.Lys139AlafsTer5,ENST00000420246,;TP53,frameshift_variant,p.Lys139AlafsTer5,ENST00000269305,;TP53,frameshift_variant,p.Lys7AlafsTer5,ENST00000509690,;TP53,frameshift_variant,p.Lys139AlafsTer5,ENST00000359597,;TP53,frameshift_variant,p.Lys46AlafsTer5,ENST00000514944,;TP53,frameshift_variant,p.Lys139AlafsTer5,ENST00000445888,;TP53,frameshift_variant,p.Lys139AlafsTer5,ENST00000455263,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	604-617	414-427	138-143	AKTCPV/AX	gcCAAGACCTGCCCTGtg/gctg	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.Q144fs*26|c.430delC|3,CODON|p.Q12*|c.34C>T|10,CODON|p.Q144*|c.430C>T|3,CODON|p.Q144*|c.430C>T|39,CODON|p.Q144*|c.430C>T|10,CODON|p.Q51*|c.151C>T|10,CODON|p.Q144*|c.430C>T|9,CODON|p.Q144*|c.430C>T|3,CODON|p.V11A|c.32T>C|4,CODON|p.V143E|c.428T>A|6,CODON|p.V143A|c.428T>C|3,CODON|p.V143A|c.428T>C|4,CODON|p.V143A|c.428T>C|16,CODON|p.V50A|c.149T>C|4,CODON|p.V143M|c.427G>A|4,CODON|p.V143L|c.427G>T|3,CODON|p.V143M|c.427G>A|3,CODON|p.V143M|c.427G>A|22,CODON|p.V11M|c.31G>A|4,CODON|p.V50M|c.148G>A|4,CODON|p.V143M|c.427G>A|4,CODON|p.P142H|c.425C>A|3,CODON|p.P142L|c.425C>T|8,CODON|p.C141W|c.423C>G|3,CODON|p.C141W|c.423C>G|13,CODON|p.C141*|c.423C>A|12,CODON|p.C48W|c.144C>G|3,CODON|p.C141C|c.423C>T|4,CODON|p.C141W|c.423C>G|3,CODON|p.C9W|c.27C>G|4,CODON|p.C141Y|c.422G>A|3,CODON|p.C141Y|c.422G>A|3,CODON|p.C141Y|c.422G>A|13,CODON|p.C48Y|c.143G>A|13,CODON|p.C141F|c.422G>T|4,CODON|p.C9Y|c.26G>A|13,CODON|p.C141Y|c.422G>A|78,CODON|p.C141Y|c.422G>A|12,CODON|p.C48R|c.142T>C|8,CODON|p.C141G|c.421T>G|3,CODON|p.C141R|c.421T>C|8,CODON|p.C9R|c.25T>C|8,CODON|p.C141R|c.421T>C|22,CODON|p.C141R|c.421T>C|6,CODON|p.C141R|c.421T>C|8,CODON|p.T140T|c.420C>T|6,CODON|p.T140I|c.419C>T|11,CODON|p.K139K|c.417G>A|7,CODON|p.K139N|c.417G>C|6,CODON|p.K139N|c.417G>T|5,CODON|p.K139*|c.415A>T|3,CODON|p.K139*|c.415A>T|5,CODON|p.K7*|c.19A>T|3,CODON|p.K139*|c.415A>T|3,CODON|p.K139E|c.415A>G|4,CODON|p.K46*|c.136A>T|3,BUFFER|p.V147fs*23|c.439delG|7,BUFFER|p.V147I|c.439G>A|6,BUFFER|p.W146*|c.438G>A|5,BUFFER|p.W146*|c.438G>A|4,BUFFER|p.W53*|c.159G>A|5,BUFFER|p.W146*|c.438G>A|34,BUFFER|p.W146*|c.438G>A|3,BUFFER|p.W14*|c.42G>A|5,BUFFER|p.W14*|c.41G>A|9,BUFFER|p.W146*|c.437G>A|3,BUFFER|p.W146*|c.437G>A|9,BUFFER|p.W53*|c.158G>A|9,BUFFER|p.W146*|c.437G>A|7,BUFFER|p.W146*|c.437G>A|9,BUFFER|p.W146*|c.437G>A|43,BUFFER|p.W146R|c.436T>C|4,BUFFER|p.L145L|c.435G>A|3,BUFFER|p.L145R|c.434T>G|7,BUFFER|p.L145P|c.434T>C|17,BUFFER|p.L145Q|c.434T>A|19,BUFFER|p.L145L|c.433C>T|4,BUFFER|p.Q144H|c.432G>C|3,BUFFER|p.Q144R|c.431A>G|5,BUFFER|p.Q144L|c.431A>T|9,BUFFER|p.Q144P|c.431A>C|5,BUFFER|p.A138fs*32|c.412delG|5,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A6V|c.17C>T|4,BUFFER|p.A45V|c.134C>T|4,BUFFER|p.A138V|c.413C>T|21,BUFFER|p.A138P|c.412G>C|14,BUFFER|p.A138T|c.412G>A|5,BUFFER|p.A138fs*11|c.411_412insN|3,BUFFER|p.L137L|c.411G>A|3,BUFFER|p.L137P|c.410T>C|3,BUFFER|p.L137Q|c.410T>A|3,BUFFER|p.Q136H|c.408A>C|5,BUFFER|p.Q136Q|c.408A>G|4,BUFFER|p.Q136P|c.407A>C|3,BUFFER|p.Q136E|c.406C>G|9,BUFFER|p.Q136*|c.406C>T|35,BUFFER|p.Q4*|c.10C>T|5,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q43*|c.127C>T|5,BUFFER|p.Q4E|c.10C>G|6,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q136E|c.406C>G|4,BUFFER|p.Q136E|c.406C>G|5,BUFFER|p.Q43E|c.127C>G|6,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|3,BUFFER|p.C3W|c.9C>G|4,BUFFER|p.C42W|c.126C>G|3,BUFFER|p.C135W|c.405C>G|3,BUFFER|p.C135W|c.405C>G|3,BUFFER|p.C135C|c.405C>T|5,BUFFER|p.C135*|c.405C>A|8,BUFFER|p.C135W|c.405C>G|24,BUFFER|p.C135F|c.404G>T|6,BUFFER|p.C3S|c.8G>C|3,BUFFER|p.C135S|c.404G>C|3,BUFFER|p.C3F|c.8G>T|13,BUFFER|p.C135S|c.404G>C|3,BUFFER|p.C42F|c.125G>T|13,BUFFER|p.C42S|c.125G>C|3,BUFFER|p.C135F|c.404G>T|6,BUFFER|p.C135Y|c.404G>A|8,BUFFER|p.C135Y|c.404G>A|54,BUFFER|p.C135S|c.404G>C|9,BUFFER|p.C135Y|c.404G>A|3,BUFFER|p.C42Y|c.125G>A|8,BUFFER|p.C135Y|c.404G>A|3,BUFFER|p.C135F|c.404G>T|13,BUFFER|p.C135F|c.404G>T|13,BUFFER|p.C135F|c.404G>T|49,BUFFER|p.C135Y|c.404G>A|8,BUFFER|p.C3Y|c.8G>A|8,BUFFER|p.C135fs*35|c.403delT|5,BUFFER|p.C135G|c.403T>G|8,BUFFER|p.C135S|c.403T>A|4,BUFFER|p.C135R|c.403T>C|11	INDELOCATOR|VARSCANI	GCTGCACAGGGCAGGTCTTGGCCAG	.	2	ESCA
WDR45B	0	.	GRCh37	17	80575258	80575258	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.720G>A	p.%3D	p.Q240Q	ENST00000392325	8/10	29	15	13	20	20	0	WDR45B,synonymous_variant,p.%3D,ENST00000392325,;WDR45B,non_coding_transcript_exon_variant,,ENST00000571767,;WDR45B,non_coding_transcript_exon_variant,,ENST00000571835,;FOXK2,intron_variant,,ENST00000574694,;WDR45B,synonymous_variant,p.%3D,ENST00000576517,;WDR45B,3_prime_UTR_variant,,ENST00000573616,;WDR45B,3_prime_UTR_variant,,ENST00000572583,;WDR45B,non_coding_transcript_exon_variant,,ENST00000573656,;WDR45B,non_coding_transcript_exon_variant,,ENST00000577774,;WDR45B,downstream_gene_variant,,ENST00000571817,;	T	ENSG00000141580	ENST00000392325	Transcript	synonymous_variant	915	720	240	Q	caG/caA	.	.	.	-1	WDR45B	HGNC	25072	protein_coding	YES	CCDS11815.2	ENSP00000376139	WIPI3_HUMAN	B4DMI6_HUMAN	UPI000020051D	.	.	.	8/10	.	hmmpanther:PTHR11227,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATCCTGATT	.	5	ESCA
ICAM5	0	.	GRCh37	19	10402942	10402942	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.905G>A	p.Cys302Tyr	p.C302Y	ENST00000221980	4/11	80	71	8	141	141	0	ICAM5,missense_variant,p.Cys302Tyr,ENST00000221980,;ICAM5,downstream_gene_variant,,ENST00000587398,;ICAM4,downstream_gene_variant,,ENST00000393717,;ICAM4,downstream_gene_variant,,ENST00000380770,;ICAM4,downstream_gene_variant,,ENST00000340992,;CTD-2369P2.8,upstream_gene_variant,,ENST00000589379,;ICAM5,downstream_gene_variant,,ENST00000586004,;ICAM5,non_coding_transcript_exon_variant,,ENST00000586480,;ICAM5,downstream_gene_variant,,ENST00000588912,;	A	ENSG00000105376	ENST00000221980	Transcript	missense_variant	968	905	302	C/Y	tGc/tAc	.	.	.	1	ICAM5	HGNC	5348	protein_coding	YES	CCDS12233.1	ENSP00000221980	ICAM5_HUMAN	K7EIL3_HUMAN	UPI000013C7E4	.	deleterious(0)	possibly_damaging(0.711)	4/11	.	hmmpanther:PTHR13771:SF6,hmmpanther:PTHR13771,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V301I|c.901G>A|4	RADIA|MUTECT|MUSE|VARSCANS	GGTCTGCAACG	.	4	ESCA
ASF1B	0	.	GRCh37	19	14231429	14231429	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451A>C	p.Ile151Leu	p.I151L	ENST00000263382	4/4	41	12	28	52	52	0	ASF1B,missense_variant,p.Ile92Leu,ENST00000592798,;ASF1B,missense_variant,p.Ile151Leu,ENST00000263382,;PRKACA,upstream_gene_variant,,ENST00000589284,;PRKACA,upstream_gene_variant,,ENST00000590853,;ASF1B,downstream_gene_variant,,ENST00000474890,;PRKACA,upstream_gene_variant,,ENST00000308677,;CTB-55O6.10,downstream_gene_variant,,ENST00000590715,;ASF1B,3_prime_UTR_variant,,ENST00000589468,;ASF1B,3_prime_UTR_variant,,ENST00000590835,;	G	ENSG00000105011	ENST00000263382	Transcript	missense_variant	951	451	151	I/L	Atc/Ctc	.	.	.	-1	ASF1B	HGNC	20996	protein_coding	YES	CCDS12306.1	ENSP00000263382	ASF1B_HUMAN	B4DXU6_HUMAN	UPI00000437D4	.	deleterious(0)	probably_damaging(0.996)	4/4	.	Superfamily_domains:SSF101546,Gene3D:1rocA00,Pfam_domain:PF04729,hmmpanther:PTHR12040,hmmpanther:PTHR12040:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGATATGGA	.	5	ESCA
TNFAIP8L1	0	.	GRCh37	19	4653043	4653043	+	3'UTR	SNP	C	C	T	rs769855706	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*601C>T	.	.	ENST00000536716	2/2	41	10	30	51	51	0	TNFAIP8L1,3_prime_UTR_variant,,ENST00000536716,;TNFAIP8L1,3_prime_UTR_variant,,ENST00000327473,;C19orf10,intron_variant,,ENST00000599761,;C19orf10,downstream_gene_variant,,ENST00000262947,;AC005339.2,downstream_gene_variant,,ENST00000598070,;	T	ENSG00000185361	ENST00000536716	Transcript	3_prime_UTR_variant	1308	.	.	.	.	rs769855706	.	.	1	TNFAIP8L1	HGNC	28279	protein_coding	YES	CCDS12132.1	ENSP00000444215	TP8L1_HUMAN	.	UPI000013EB11	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGCGCGGT	.	5	ESCA
HIF3A	0	.	GRCh37	19	46832499	46832499	+	Silent	SNP	C	C	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1476C>G	p.%3D	p.P492P	ENST00000377670	12/15	45	12	33	35	35	0	HIF3A,synonymous_variant,p.%3D,ENST00000420102,;HIF3A,synonymous_variant,p.%3D,ENST00000377670,;HIF3A,synonymous_variant,p.%3D,ENST00000300862,;HIF3A,synonymous_variant,p.%3D,ENST00000600383,;HIF3A,synonymous_variant,p.%3D,ENST00000244303,;HIF3A,synonymous_variant,p.%3D,ENST00000339613,;HIF3A,intron_variant,,ENST00000472815,;AC007193.10,intron_variant,,ENST00000596807,;HIF3A,non_coding_transcript_exon_variant,,ENST00000291300,;HIF3A,non_coding_transcript_exon_variant,,ENST00000529542,;HIF3A,non_coding_transcript_exon_variant,,ENST00000244302,;HIF3A,downstream_gene_variant,,ENST00000528563,;	G	ENSG00000124440	ENST00000377670	Transcript	synonymous_variant	1507	1476	492	P	ccC/ccG	.	.	.	1	HIF3A	HGNC	15825	protein_coding	YES	CCDS12681.2	ENSP00000366898	HIF3A_HUMAN	Q9UPH7_HUMAN,O95262_HUMAN,E9PB04_HUMAN	UPI00002026E2	.	.	.	12/15	.	hmmpanther:PTHR23043:SF18,hmmpanther:PTHR23043,Pfam_domain:PF11413	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCCTACAT	.	5	ESCA
NAPSB	0	.	GRCh37	19	50839874	50839875	+	RNA	INS	-	-	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.562dupA	.	.	ENST00000527780	5/9	158	99	59	108	108	0	NR1H2,intron_variant,,ENST00000600355,;NR1H2,intron_variant,,ENST00000542413,;KCNC3,upstream_gene_variant,,ENST00000391818,;KCNC3,upstream_gene_variant,,ENST00000474951,;NAPSB,non_coding_transcript_exon_variant,,ENST00000527780,;NR1H2,intron_variant,,ENST00000600978,;NAPSB,non_coding_transcript_exon_variant,,ENST00000534096,;NAPSB,intron_variant,,ENST00000534789,;NR1H2,intron_variant,,ENST00000593532,;NAPSB,upstream_gene_variant,,ENST00000531692,;NAPSB,downstream_gene_variant,,ENST00000525179,;NAPSB,non_coding_transcript_exon_variant,,ENST00000562112,;	T	ENSG00000131401	ENST00000527780	Transcript	non_coding_transcript_exon_variant	562-563	.	.	.	.	.	.	.	-1	NAPSB	HGNC	13396	processed_transcript	YES	.	.	.	.	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAATATCCCA	.	3	ESCA
KLK15	0	.	GRCh37	19	51329007	51329007	+	3'UTR	DEL	G	G	-	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45delC	.	.	ENST00000598239	5/5	79	50	29	52	52	0	KLK15,3_prime_UTR_variant,,ENST00000326856,;KLK15,3_prime_UTR_variant,,ENST00000598239,;KLK15,3_prime_UTR_variant,,ENST00000301421,;KLK15,3_prime_UTR_variant,,ENST00000416184,;KLK15,downstream_gene_variant,,ENST00000598673,;KLK15,downstream_gene_variant,,ENST00000596931,;KLK1,upstream_gene_variant,,ENST00000301420,;KLK1,upstream_gene_variant,,ENST00000448701,;AC011523.2,upstream_gene_variant,,ENST00000598079,;KLK15,non_coding_transcript_exon_variant,,ENST00000596531,;KLK15,non_coding_transcript_exon_variant,,ENST00000601680,;KLK1,upstream_gene_variant,,ENST00000593859,;KLK1,upstream_gene_variant,,ENST00000593325,;KLK1,upstream_gene_variant,,ENST00000596300,;KLK15,downstream_gene_variant,,ENST00000602114,;	-	ENSG00000174562	ENST00000598239	Transcript	3_prime_UTR_variant	847	.	.	.	.	.	.	.	-1	KLK15	HGNC	20453	protein_coding	YES	CCDS12805.1	ENSP00000469315	KLK15_HUMAN	S5TEP0_HUMAN,M0R2F7_HUMAN	UPI000004CA04	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGCTGTGGGGGC	.	3	ESCA
TPM3P9	0	.	GRCh37	19	53945817	53945817	+	RNA	SNP	A	A	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.814A>T	.	.	ENST00000424846	2/2	87	23	64	60	60	0	TPM3P9,non_coding_transcript_exon_variant,,ENST00000424846,;ZNF761,intron_variant,,ENST00000447129,;ZNF761,intron_variant,,ENST00000454407,;ZNF761,upstream_gene_variant,,ENST00000366293,;ZNF761,upstream_gene_variant,,ENST00000429310,;TPM3P9,non_coding_transcript_exon_variant,,ENST00000492121,;	T	ENSG00000241015	ENST00000424846	Transcript	non_coding_transcript_exon_variant	814	.	.	.	.	.	.	.	1	TPM3P9	HGNC	44142	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACACAAAGGA	.	5	ESCA
SYT5	0	.	GRCh37	19	55685891	55685891	+	Silent	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.954A>G	p.%3D	p.Q318Q	ENST00000354308	8/9	54	38	15	28	28	0	SYT5,synonymous_variant,p.%3D,ENST00000590859,;SYT5,synonymous_variant,p.%3D,ENST00000537500,;SYT5,synonymous_variant,p.%3D,ENST00000354308,;SYT5,synonymous_variant,p.%3D,ENST00000587067,;SYT5,synonymous_variant,p.%3D,ENST00000590851,;SYT5,downstream_gene_variant,,ENST00000589172,;SYT5,downstream_gene_variant,,ENST00000592470,;CTD-2587H24.5,intron_variant,,ENST00000591665,;SYT5,upstream_gene_variant,,ENST00000592935,;SYT5,non_coding_transcript_exon_variant,,ENST00000588305,;SYT5,non_coding_transcript_exon_variant,,ENST00000592956,;SYT5,downstream_gene_variant,,ENST00000585461,;	C	ENSG00000129990	ENST00000354308	Transcript	synonymous_variant	1324	954	318	Q	caA/caG	.	.	.	-1	SYT5	HGNC	11513	protein_coding	YES	CCDS12919.1	ENSP00000346265	SYT5_HUMAN	Q4FD32_HUMAN,Q05BS5_HUMAN,K7EQ59_HUMAN,K7EJS7_HUMAN,K7EJC4_HUMAN	UPI000013C56F	.	.	.	8/9	.	PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF37,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACTTGGTC	.	5	ESCA
C1orf127	0	.	GRCh37	1	11017133	11017133	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725T>C	p.Leu242Pro	p.L242P	ENST00000377004	8/13	63	59	3	52	52	0	C1orf127,missense_variant,p.Leu220Pro,ENST00000520253,;C1orf127,missense_variant,p.Leu242Pro,ENST00000377004,;C1orf127,intron_variant,,ENST00000418570,;C1orf127,intron_variant,,ENST00000377008,;	G	ENSG00000175262	ENST00000377004	Transcript	missense_variant	725	725	242	L/P	cTa/cCa	.	.	.	-1	C1orf127	HGNC	26730	protein_coding	YES	CCDS53267.1	ENSP00000366203	.	G8JLG8_HUMAN,B7ZLG7_HUMAN	UPI0001C0B385	.	deleterious(0)	benign(0.358)	8/13	.	Pfam_domain:PF15094	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCATAGTGGC	.	2	ESCA
COPA	0	.	GRCh37	1	160278920	160278920	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1190delC	p.Pro397LeufsTer20	p.P397Lfs*20	ENST00000368069	13/33	173	134	39	86	86	0	COPA,frameshift_variant,p.Pro397LeufsTer20,ENST00000368069,;COPA,frameshift_variant,p.Pro397LeufsTer20,ENST00000241704,;COPA,non_coding_transcript_exon_variant,,ENST00000481040,;COPA,upstream_gene_variant,,ENST00000481522,;	-	ENSG00000122218	ENST00000368069	Transcript	frameshift_variant	1268	1190	397	P/X	cCt/ct	.	.	.	-1	COPA	HGNC	2230	protein_coding	YES	CCDS41424.1	ENSP00000357048	COPA_HUMAN	.	UPI0000074301	.	.	.	13/33	.	hmmpanther:PTHR19876,Pfam_domain:PF04053,PIRSF_domain:PIRSF003354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTTTAGGGATG	.	3	ESCA
HMCN1	0	.	GRCh37	1	186114919	186114919	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14472C>G	p.Ser4824Arg	p.S4824R	ENST00000271588	93/107	104	68	36	78	78	0	HMCN1,missense_variant,p.Ser4824Arg,ENST00000367492,;HMCN1,missense_variant,p.Ser4824Arg,ENST00000271588,;	G	ENSG00000143341	ENST00000271588	Transcript	missense_variant	14701	14472	4824	S/R	agC/agG	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	benign(0.27)	93/107	.	PROSITE_profiles:PS50092,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGCCAGTG	.	5	ESCA
SOX13	0	.	GRCh37	1	204092273	204092273	+	Missense_Mutation	SNP	G	G	A	rs181852086	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1168G>A	p.Glu390Lys	p.E390K	ENST00000367204	11/14	37	22	15	45	45	0	SOX13,missense_variant,p.Glu390Lys,ENST00000367204,;SOX13,non_coding_transcript_exon_variant,,ENST00000272193,;SOX13,downstream_gene_variant,,ENST00000367203,;SOX13,non_coding_transcript_exon_variant,,ENST00000525258,;SOX13,downstream_gene_variant,,ENST00000480326,;	A	ENSG00000143842	ENST00000367204	Transcript	missense_variant	1277	1168	390	E/K	Gag/Aag	rs181852086	.	.	1	SOX13	HGNC	11192	protein_coding	YES	CCDS44299.1	ENSP00000356172	SOX13_HUMAN	E9PPW0_HUMAN,E9PKD6_HUMAN,B4E3N9_HUMAN	UPI000034ECAB	.	tolerated(0.25)	benign(0.211)	11/14	.	hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF109	A:0.0006	A:0	A:0.0043	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGGAGCGG	byFrequency|byCluster|by1000G	5	ESCA
NFASC	0	.	GRCh37	1	204990510	204990510	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4843C>G	.	.	ENST00000339876	30/30	65	61	4	49	49	0	NFASC,3_prime_UTR_variant,,ENST00000367170,;NFASC,3_prime_UTR_variant,,ENST00000338515,;NFASC,3_prime_UTR_variant,,ENST00000360049,;NFASC,3_prime_UTR_variant,,ENST00000401399,;NFASC,3_prime_UTR_variant,,ENST00000367171,;NFASC,3_prime_UTR_variant,,ENST00000539706,;NFASC,3_prime_UTR_variant,,ENST00000339876,;NFASC,3_prime_UTR_variant,,ENST00000367169,;NFASC,3_prime_UTR_variant,,ENST00000367172,;NFASC,3_prime_UTR_variant,,ENST00000338586,;NFASC,downstream_gene_variant,,ENST00000404076,;NFASC,downstream_gene_variant,,ENST00000447819,;NFASC,downstream_gene_variant,,ENST00000425360,;NFASC,downstream_gene_variant,,ENST00000404907,;NFASC,downstream_gene_variant,,ENST00000413225,;NFASC,downstream_gene_variant,,ENST00000367173,;NFASC,downstream_gene_variant,,ENST00000430393,;NFASC,downstream_gene_variant,,ENST00000513543,;NFASC,non_coding_transcript_exon_variant,,ENST00000495396,;NFASC,downstream_gene_variant,,ENST00000504476,;NFASC,downstream_gene_variant,,ENST00000503221,;	G	ENSG00000163531	ENST00000339876	Transcript	3_prime_UTR_variant	8894	.	.	.	.	.	.	.	1	NFASC	HGNC	29866	protein_coding	YES	CCDS53460.1	ENSP00000344786	NFASC_HUMAN	D6RHX4_HUMAN	UPI0000237208	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTTCCTCCT	.	2	ESCA
YBX1	0	.	GRCh37	1	43167982	43167982	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*362A>G	.	.	ENST00000321358	8/8	34	30	4	32	32	0	YBX1,3_prime_UTR_variant,,ENST00000436427,;YBX1,3_prime_UTR_variant,,ENST00000321358,;	G	ENSG00000065978	ENST00000321358	Transcript	3_prime_UTR_variant	1476	.	.	.	.	.	.	.	1	YBX1	HGNC	8014	protein_coding	YES	CCDS470.1	ENSP00000361626	YBOX1_HUMAN	A0JLU4_HUMAN	UPI0000001C6B	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AGTCAACAAAC	.	2	ESCA
PRDX1	0	.	GRCh37	1	45977030	45977030	+	Missense_Mutation	SNP	T	T	G	rs11544936	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.571A>C	p.Ser191Arg	p.S191R	ENST00000262746	6/6	24	7	16	21	21	0	PRDX1,missense_variant,p.Ser191Arg,ENST00000319248,;PRDX1,missense_variant,p.Ser191Arg,ENST00000262746,;PRDX1,missense_variant,p.Ser89Arg,ENST00000372079,;MMACHC,downstream_gene_variant,,ENST00000401061,;PRDX1,downstream_gene_variant,,ENST00000447184,;PRDX1,downstream_gene_variant,,ENST00000424390,;PRDX1,downstream_gene_variant,,ENST00000483583,;MMACHC,downstream_gene_variant,,ENST00000477188,;	G	ENSG00000117450	ENST00000262746	Transcript	missense_variant	911	571	191	S/R	Agc/Cgc	rs11544936	.	.	-1	PRDX1	HGNC	9352	protein_coding	YES	CCDS522.1	ENSP00000262746	PRDX1_HUMAN	.	UPI000002FC88	.	deleterious(0)	probably_damaging(1)	6/6	.	Superfamily_domains:SSF52833,PIRSF_domain:PIRSF000239,Pfam_domain:PF10417,Gene3D:3.40.30.10,hmmpanther:PTHR10681:SF75,hmmpanther:PTHR10681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCTCTTTT	byHapMap	5	ESCA
PTBP2	0	.	GRCh37	1	97280395	97280395	+	3'Flank	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000426398	.	52	14	38	49	47	1	PTBP2,3_prime_UTR_variant,,ENST00000609116,;PTBP2,downstream_gene_variant,,ENST00000426398,;PTBP2,downstream_gene_variant,,ENST00000370198,;PTBP2,downstream_gene_variant,,ENST00000394184,;PTBP2,downstream_gene_variant,,ENST00000370197,;PTBP2,downstream_gene_variant,,ENST00000541987,;PTBP2,downstream_gene_variant,,ENST00000482253,;PTBP2,downstream_gene_variant,,ENST00000462433,;PTBP2,downstream_gene_variant,,ENST00000476419,;PTBP2,downstream_gene_variant,,ENST00000476783,;PTBP2,downstream_gene_variant,,ENST00000492905,;PTBP2,downstream_gene_variant,,ENST00000459735,;	A	ENSG00000117569	ENST00000426398	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	46	1	PTBP2	HGNC	17662	protein_coding	YES	CCDS754.1	ENSP00000412788	PTBP2_HUMAN	.	UPI000006F5BE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACTCTGCTTAC	.	4	ESCA
OVOL2	0	.	GRCh37	20	18038460	18038460	+	5'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-182G>A	.	.	ENST00000278780	1/4	155	113	42	147	147	0	OVOL2,5_prime_UTR_variant,,ENST00000278780,;RP4-726N1.2,upstream_gene_variant,,ENST00000429853,;OVOL2,intron_variant,,ENST00000483661,;OVOL2,intron_variant,,ENST00000486776,;OVOL2,intron_variant,,ENST00000494030,;	T	ENSG00000125850	ENST00000278780	Transcript	5_prime_UTR_variant	62	.	.	.	.	.	.	.	-1	OVOL2	HGNC	15804	protein_coding	YES	CCDS13132.1	ENSP00000278780	OVOL2_HUMAN	.	UPI000013C360	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTCCCAGCC	.	5	ESCA
EIF2S2	0	.	GRCh37	20	32677149	32677149	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*387T>A	.	.	ENST00000374980	9/9	110	68	42	49	49	0	EIF2S2,3_prime_UTR_variant,,ENST00000374980,;RALY,intron_variant,,ENST00000489384,;	T	ENSG00000125977	ENST00000374980	Transcript	3_prime_UTR_variant	1611	.	.	.	.	.	.	.	-1	EIF2S2	HGNC	3266	protein_coding	YES	CCDS13231.1	ENSP00000364119	IF2B_HUMAN	Q96I16_HUMAN,Q6IBR8_HUMAN	UPI000012D28F	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAGAGCCCG	.	5	ESCA
SALL4	0	.	GRCh37	20	50401201	50401201	+	Missense_Mutation	SNP	G	G	A	rs755288586	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2765C>T	p.Ala922Val	p.A922V	ENST00000217086	4/4	77	40	37	30	30	0	SALL4,missense_variant,p.Ala922Val,ENST00000217086,;SALL4,missense_variant,p.Ala485Val,ENST00000395997,;SALL4,missense_variant,p.Ala145Val,ENST00000371539,;	A	ENSG00000101115	ENST00000217086	Transcript	missense_variant	2877	2765	922	A/V	gCg/gTg	rs755288586,COSM271696	.	.	-1	SALL4	HGNC	15924	protein_coding	YES	CCDS13438.1	ENSP00000217086	SALL4_HUMAN	.	UPI0000135527	.	tolerated(0.64)	benign(0.283)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF19	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCGCCCCG	.	5	ESCA
FERMT1	0	.	GRCh37	20	6065919	6065919	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1387C>G	p.Gln463Glu	p.Q463E	ENST00000217289	12/15	56	44	11	40	40	0	FERMT1,missense_variant,p.Gln206Glu,ENST00000536936,;FERMT1,missense_variant,p.Gln463Glu,ENST00000217289,;FERMT1,non_coding_transcript_exon_variant,,ENST00000478194,;	C	ENSG00000101311	ENST00000217289	Transcript	missense_variant	2176	1387	463	Q/E	Caa/Gaa	.	.	.	-1	FERMT1	HGNC	15889	protein_coding	YES	CCDS13098.1	ENSP00000217289	FERM1_HUMAN	Q5JWV4_HUMAN,G3V1L6_HUMAN	UPI00001285DD	.	tolerated(0.14)	benign(0.009)	12/15	.	PROSITE_profiles:PS50003,hmmpanther:PTHR16160:SF12,hmmpanther:PTHR16160,Pfam_domain:PF00373,Gene3D:2.30.29.30,SMART_domains:SM00233,SMART_domains:SM00295,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATTGGGCGT	.	5	ESCA
GID8	0	.	GRCh37	20	61572954	61572954	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100A>T	p.Met34Leu	p.M34L	ENST00000266069	2/5	110	56	54	53	53	0	GID8,missense_variant,p.Met34Leu,ENST00000266069,;DIDO1,upstream_gene_variant,,ENST00000266070,;DIDO1,upstream_gene_variant,,ENST00000266071,;DIDO1,upstream_gene_variant,,ENST00000395335,;DIDO1,upstream_gene_variant,,ENST00000370371,;GID8,downstream_gene_variant,,ENST00000497101,;	T	ENSG00000101193	ENST00000266069	Transcript	missense_variant	247	100	34	M/L	Atg/Ttg	.	.	.	1	GID8	HGNC	15857	protein_coding	YES	CCDS13510.1	ENSP00000266069	GID8_HUMAN	.	UPI0000034E17	.	deleterious(0.03)	benign(0.21)	2/5	.	PROSITE_profiles:PS50896,hmmpanther:PTHR12864,Pfam_domain:PF08513,SMART_domains:SM00667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATCATGAAC	.	5	ESCA
SLC52A3	0	.	GRCh37	20	744539	744539	+	Missense_Mutation	SNP	G	G	A	rs143511669	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.676C>T	p.Leu226Phe	p.L226F	ENST00000217254	3/5	73	66	7	45	45	0	SLC52A3,missense_variant,p.Leu226Phe,ENST00000381944,;SLC52A3,missense_variant,p.Leu226Phe,ENST00000217254,;SLC52A3,intron_variant,,ENST00000473664,;SLC52A3,downstream_gene_variant,,ENST00000488495,;	A	ENSG00000101276	ENST00000217254	Transcript	missense_variant	918	676	226	L/F	Ctc/Ttc	rs143511669	.	.	-1	SLC52A3	HGNC	16187	protein_coding	YES	CCDS13007.1	ENSP00000217254	S52A3_HUMAN	K0A6P4_HUMAN	UPI000002A74E	.	tolerated(0.83)	benign(0.005)	3/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12929:SF4,hmmpanther:PTHR12929	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGGAGGAGGA	byCluster	4	ESCA
POM121L9P	0	.	GRCh37	22	24657660	24657660	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2078-1G>C	.	.	ENST00000414583	.	60	32	27	86	86	0	POM121L9P,splice_acceptor_variant,,ENST00000414583,;POM121L9P,splice_acceptor_variant,,ENST00000419222,;BCRP1,intron_variant,,ENST00000444246,;	C	ENSG00000128262	ENST00000414583	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	POM121L9P	HGNC	30080	processed_transcript	YES	.	.	.	.	.	.	.	.	.	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCAGGGCTC	.	5	ESCA
RNF185	0	.	GRCh37	22	31556291	31556291	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-49+2T>C	.	.	ENST00000326132	.	10	3	7	17	17	0	RNF185,splice_donor_variant,,ENST00000266252,;RNF185,splice_donor_variant,,ENST00000426256,;RNF185,splice_donor_variant,,ENST00000326132,;MIR3928,upstream_gene_variant,,ENST00000583386,;RNF185,splice_donor_variant,,ENST00000471384,;RNF185,splice_donor_variant,,ENST00000468921,;RNF185,splice_donor_variant,,ENST00000494514,;RNF185,splice_donor_variant,,ENST00000518626,;RP3-412A9.15,upstream_gene_variant,,ENST00000397595,;	C	ENSG00000138942	ENST00000326132	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	RNF185	HGNC	26783	protein_coding	YES	CCDS13890.1	ENSP00000320508	RN185_HUMAN	.	UPI0000036022	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGGTATGTG	.	2	ESCA
LARGE	0	.	GRCh37	22	34046437	34046437	+	Silent	SNP	A	A	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.324T>A	p.%3D	p.T108T	ENST00000354992	4/16	15	3	12	29	29	0	LARGE,synonymous_variant,p.%3D,ENST00000413114,;LARGE,synonymous_variant,p.%3D,ENST00000354992,;LARGE,synonymous_variant,p.%3D,ENST00000437602,;LARGE,synonymous_variant,p.%3D,ENST00000430220,;LARGE,synonymous_variant,p.%3D,ENST00000337431,;LARGE,synonymous_variant,p.%3D,ENST00000402320,;LARGE,synonymous_variant,p.%3D,ENST00000434071,;LARGE,synonymous_variant,p.%3D,ENST00000397394,;LARGE,downstream_gene_variant,,ENST00000423375,;LARGE,downstream_gene_variant,,ENST00000432776,;LARGE,non_coding_transcript_exon_variant,,ENST00000494763,;LARGE,non_coding_transcript_exon_variant,,ENST00000462606,;	T	ENSG00000133424	ENST00000354992	Transcript	synonymous_variant	896	324	108	T	acT/acA	.	.	.	-1	LARGE	HGNC	6511	protein_coding	YES	CCDS13912.1	ENSP00000347088	LARGE_HUMAN	B0QZ02_HUMAN,B0QZ01_HUMAN,B0QZ00_HUMAN,B0QYZ9_HUMAN,B0QYZ8_HUMAN	UPI000012E200	.	.	.	4/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TCTCCAGTGCC	.	4	ESCA
LONRF2	0	.	GRCh37	2	100900818	100900818	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2207T>A	p.Ile736Asn	p.I736N	ENST00000393437	12/12	44	38	6	35	35	0	LONRF2,missense_variant,p.Ile736Asn,ENST00000393437,;LONRF2,missense_variant,p.Ile493Asn,ENST00000409647,;	T	ENSG00000170500	ENST00000393437	Transcript	missense_variant	2847	2207	736	I/N	aTc/aAc	.	.	.	-1	LONRF2	HGNC	24788	protein_coding	YES	CCDS2046.2	ENSP00000377086	LONF2_HUMAN	.	UPI000152B4EF	.	deleterious(0)	possibly_damaging(0.897)	12/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23327,hmmpanther:PTHR23327:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGTGATGATG	.	2	ESCA
MFSD9	0	.	GRCh37	2	103353149	103353149	+	Nonsense_Mutation	SNP	C	C	A	rs754676778	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.121G>T	p.Gly41Ter	p.G41*	ENST00000258436	1/6	82	68	14	67	67	0	MFSD9,stop_gained,p.Gly41Ter,ENST00000258436,;TMEM182,upstream_gene_variant,,ENST00000409528,;TMEM182,upstream_gene_variant,,ENST00000409173,;TMEM182,upstream_gene_variant,,ENST00000454536,;TMEM182,upstream_gene_variant,,ENST00000469971,;TMEM182,upstream_gene_variant,,ENST00000488134,;MFSD9,stop_gained,p.Gly41Ter,ENST00000438943,;MFSD9,stop_gained,p.Gly41Ter,ENST00000421966,;MFSD9,stop_gained,p.Gly41Ter,ENST00000411991,;MFSD9,stop_gained,p.Gly41Ter,ENST00000437075,;MFSD9,non_coding_transcript_exon_variant,,ENST00000462099,;MFSD9,upstream_gene_variant,,ENST00000428085,;	A	ENSG00000135953	ENST00000258436	Transcript	stop_gained	165	121	41	G/*	Gga/Tga	rs754676778	.	.	-1	MFSD9	HGNC	28158	protein_coding	YES	CCDS2063.1	ENSP00000258436	MFSD9_HUMAN	B4DKY6_HUMAN	UPI0000070215	.	.	.	1/6	.	hmmpanther:PTHR24003:SF492,hmmpanther:PTHR24003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTCCGACGG	byFrequency	4	ESCA
LTBP1	0	.	GRCh37	2	33484653	33484653	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2396-2A>C	.	p.X799_splice	ENST00000404816	.	59	45	13	34	34	0	LTBP1,splice_acceptor_variant,,ENST00000407925,;LTBP1,splice_acceptor_variant,,ENST00000468091,;LTBP1,splice_acceptor_variant,,ENST00000354476,;LTBP1,splice_acceptor_variant,,ENST00000418533,;LTBP1,splice_acceptor_variant,,ENST00000413303,;LTBP1,splice_acceptor_variant,,ENST00000390003,;LTBP1,splice_acceptor_variant,,ENST00000404816,;LTBP1,splice_acceptor_variant,,ENST00000402934,;LTBP1,splice_acceptor_variant,,ENST00000404525,;	C	ENSG00000049323	ENST00000404816	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	LTBP1	HGNC	6714	protein_coding	YES	CCDS33177.2	ENSP00000386043	LTBP1_HUMAN	H7C2H7_HUMAN	UPI000173A4A4	.	.	.	.	12/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTAGTGGC	.	5	ESCA
SOX11	0	.	GRCh37	2	5838019	5838019	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3840G>T	.	.	ENST00000322002	1/1	33	9	24	50	50	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	T	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	5221	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTATGTATTT	.	5	ESCA
PRR23A	0	.	GRCh37	3	138724446	138724446	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.665T>C	p.Leu222Pro	p.L222P	ENST00000383163	1/1	126	97	28	117	117	0	PRR23A,missense_variant,p.Leu222Pro,ENST00000383163,;MRPS22,upstream_gene_variant,,ENST00000495075,;	G	ENSG00000206260	ENST00000383163	Transcript	missense_variant	665	665	222	L/P	cTt/cCt	.	.	.	-1	PRR23A	HGNC	37172	protein_coding	YES	CCDS46923.1	ENSP00000372649	PR23A_HUMAN	.	UPI00003671C1	.	deleterious(0)	probably_damaging(0.928)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31813:SF2,hmmpanther:PTHR31813,Pfam_domain:PF10630	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGAAGGCGG	.	5	ESCA
GK5	0	.	GRCh37	3	141923397	141923397	+	Intron	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.411+140A>G	.	.	ENST00000392993	.	91	9	82	56	56	0	GK5,intron_variant,,ENST00000392993,;GK5,intron_variant,,ENST00000544571,;GK5,non_coding_transcript_exon_variant,,ENST00000466685,;GK5,intron_variant,,ENST00000472759,;GK5,3_prime_UTR_variant,,ENST00000487672,;GK5,intron_variant,,ENST00000480757,;GK5,intron_variant,,ENST00000492097,;GK5,intron_variant,,ENST00000460544,;GK5,downstream_gene_variant,,ENST00000489085,;	C	ENSG00000175066	ENST00000392993	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	GK5	HGNC	28635	protein_coding	YES	CCDS33871.1	ENSP00000418001	GLPK5_HUMAN	.	UPI000069B0CB	.	.	.	.	4/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTATTAAAC	.	5	ESCA
EXOSC7	0	.	GRCh37	3	45046822	45046822	+	Silent	SNP	G	G	A	rs773602045	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531G>A	p.%3D	p.S177S	ENST00000265564	6/8	57	21	35	43	43	0	EXOSC7,synonymous_variant,p.%3D,ENST00000265564,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000491476,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000482004,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000468667,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000461361,;EXOSC7,intron_variant,,ENST00000481405,;CLEC3B,intron_variant,,ENST00000490386,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000486727,;EXOSC7,downstream_gene_variant,,ENST00000467846,;	A	ENSG00000075914	ENST00000265564	Transcript	synonymous_variant	579	531	177	S	tcG/tcA	rs773602045	.	.	1	EXOSC7	HGNC	28112	protein_coding	YES	CCDS2725.1	ENSP00000265564	EXOS7_HUMAN	B4DIU0_HUMAN	UPI000020A5E9	.	.	.	6/8	.	hmmpanther:PTHR11097:SF8,hmmpanther:PTHR11097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCGAAGGA	.	5	ESCA
TRIM2	0	.	GRCh37	4	154257196	154257196	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1078T>C	.	.	ENST00000338700	12/12	94	88	5	80	80	0	TRIM2,3_prime_UTR_variant,,ENST00000338700,;TRIM2,3_prime_UTR_variant,,ENST00000437508,;	C	ENSG00000109654	ENST00000338700	Transcript	3_prime_UTR_variant	3459	.	.	.	.	.	.	.	1	TRIM2	HGNC	15974	protein_coding	YES	CCDS3781.2	ENSP00000339659	TRIM2_HUMAN	C9JVI3_HUMAN,C9J084_HUMAN	UPI00005A60C0	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGTTATTTATC	.	2	ESCA
SH3RF1	0	.	GRCh37	4	170077739	170077741	+	In_Frame_Del	DEL	ATG	ATG	-	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	ATG	ATG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483_485delCAT	p.Ile162del	p.I162del	ENST00000284637	3/12	64	24	40	34	34	0	SH3RF1,inframe_deletion,p.Ile162del,ENST00000284637,;SH3RF1,non_coding_transcript_exon_variant,,ENST00000508685,;SH3RF1,inframe_deletion,p.Ile24del,ENST00000511421,;	-	ENSG00000154447	ENST00000284637	Transcript	inframe_deletion	825-827	483-485	161-162	II/I	atCATt/att	.	.	.	-1	SH3RF1	HGNC	17650	protein_coding	YES	CCDS34099.1	ENSP00000284637	SH3R1_HUMAN	D6RHX5_HUMAN,D6RAL3_HUMAN	UPI0000160033	.	.	.	3/12	.	PROSITE_profiles:PS50002,hmmpanther:PTHR10661:SF8,hmmpanther:PTHR10661,Pfam_domain:PF14604,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGCAAAATGATGAT	.	3	ESCA
ATP8A1	0	.	GRCh37	4	42554533	42554533	+	Missense_Mutation	SNP	G	G	A	rs748975781	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1508C>T	p.Ala503Val	p.A503V	ENST00000381668	17/37	39	11	28	36	36	0	ATP8A1,missense_variant,p.Ala503Val,ENST00000381668,;ATP8A1,missense_variant,p.Ala488Val,ENST00000264449,;ATP8A1,downstream_gene_variant,,ENST00000506713,;	A	ENSG00000124406	ENST00000381668	Transcript	missense_variant	1740	1508	503	A/V	gCa/gTa	rs748975781	.	.	-1	ATP8A1	HGNC	13531	protein_coding	YES	CCDS3466.1	ENSP00000371084	AT8A1_HUMAN	H0YAJ4_HUMAN	UPI0000125063	.	deleterious(0)	probably_damaging(0.996)	17/37	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF56,TIGRFAM_domain:TIGR01652,Gene3D:3.40.1110.10,Pfam_domain:PF12710,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGCTTGA	byFrequency	5	ESCA
NFXL1	0	.	GRCh37	4	47849977	47849977	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*203A>G	.	.	ENST00000507489	23/23	36	17	19	55	55	0	NFXL1,3_prime_UTR_variant,,ENST00000381538,;NFXL1,3_prime_UTR_variant,,ENST00000507489,;RP11-121C2.2,upstream_gene_variant,,ENST00000563286,;NFXL1,3_prime_UTR_variant,,ENST00000464756,;NFXL1,non_coding_transcript_exon_variant,,ENST00000502448,;NFXL1,downstream_gene_variant,,ENST00000511452,;NFXL1,downstream_gene_variant,,ENST00000507131,;NFXL1,downstream_gene_variant,,ENST00000508115,;	C	ENSG00000170448	ENST00000507489	Transcript	3_prime_UTR_variant	3116	.	.	.	.	.	.	.	-1	NFXL1	HGNC	18726	protein_coding	YES	CCDS3478.2	ENSP00000422037	NFXL1_HUMAN	.	UPI000020BC5D	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGCCTTCACTT	.	4	ESCA
CNOT6L	0	.	GRCh37	4	78694306	78694306	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329A>G	p.Asn110Ser	p.N110S	ENST00000264903	4/12	129	46	82	149	149	0	CNOT6L,missense_variant,p.Asn110Ser,ENST00000504123,;CNOT6L,missense_variant,p.Asn110Ser,ENST00000264903,;CNOT6L,missense_variant,p.Asn110Ser,ENST00000515441,;CNOT6L,missense_variant,p.Asn139Ser,ENST00000515506,;CNOT6L,missense_variant,p.Asn117Ser,ENST00000512485,;CNOT6L,non_coding_transcript_exon_variant,,ENST00000506166,;CNOT6L,3_prime_UTR_variant,,ENST00000504804,;	C	ENSG00000138767	ENST00000264903	Transcript	missense_variant	411	329	110	N/S	aAt/aGt	.	.	.	-1	CNOT6L	HGNC	18042	protein_coding	YES	CCDS47082.1	ENSP00000264903	CNO6L_HUMAN	D6RGK9_HUMAN	UPI0000E445DF	.	tolerated(0.44)	benign(0.392)	4/12	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51450,hmmpanther:PTHR12121,hmmpanther:PTHR12121:SF35,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTATTTAAA	.	5	ESCA
IBSP	0	.	GRCh37	4	88723664	88723664	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59A>G	p.Lys20Arg	p.K20R	ENST00000226284	3/7	50	16	34	47	47	0	IBSP,missense_variant,p.Lys20Arg,ENST00000226284,;	G	ENSG00000029559	ENST00000226284	Transcript	missense_variant	126	59	20	K/R	aAa/aGa	.	.	.	1	IBSP	HGNC	5341	protein_coding	YES	CCDS3624.1	ENSP00000226284	SIAL_HUMAN	.	UPI000013C899	.	tolerated(0.05)	benign(0.29)	3/7	.	hmmpanther:PTHR10345:SF0,hmmpanther:PTHR10345,Pfam_domain:PF05432	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGAAAAATT	.	5	ESCA
SMARCAD1	0	.	GRCh37	4	95211697	95211697	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1012A>G	.	.	ENST00000359052	24/24	11	2	9	14	14	0	SMARCAD1,3_prime_UTR_variant,,ENST00000457823,;SMARCAD1,3_prime_UTR_variant,,ENST00000354268,;SMARCAD1,3_prime_UTR_variant,,ENST00000359052,;SMARCAD1,downstream_gene_variant,,ENST00000509418,;SMARCAD1,downstream_gene_variant,,ENST00000394961,;	G	ENSG00000163104	ENST00000359052	Transcript	3_prime_UTR_variant	4273	.	.	.	.	.	.	.	1	SMARCAD1	HGNC	18398	protein_coding	YES	CCDS47101.1	ENSP00000351947	SMRCD_HUMAN	.	UPI000020B1CF	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TCAAAATATAT	.	3	ESCA
DNAH5	0	.	GRCh37	5	13766214	13766214	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9972T>G	p.Asp3324Glu	p.D3324E	ENST00000265104	59/79	99	39	59	60	60	0	DNAH5,missense_variant,p.Asp3324Glu,ENST00000265104,;DNAH5,intron_variant,,ENST00000504001,;	C	ENSG00000039139	ENST00000265104	Transcript	missense_variant	10077	9972	3324	D/E	gaT/gaG	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	possibly_damaging(0.739)	59/79	.	Pfam_domain:PF12777,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCAATCCAT	.	5	ESCA
PCDHB17	0	.	GRCh37	5	140537562	140537562	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*222C>A	.	.	ENST00000539533	1/1	50	38	12	86	86	0	PCDHB17,3_prime_UTR_variant,,ENST00000539533,;PCDHB6,downstream_gene_variant,,ENST00000231136,;	A	ENSG00000255622	ENST00000539533	Transcript	3_prime_UTR_variant	1986	.	.	.	.	.	.	.	1	PCDHB17	Uniprot_gn	.	protein_coding	YES	.	ENSP00000438685	.	Q96T98_HUMAN	UPI000006CE19	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTGCTCCTG	.	5	ESCA
PCDHGB6	0	.	GRCh37	5	140789354	140789354	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1585G>A	p.Ala529Thr	p.A529T	ENST00000520790	1/4	32	5	26	35	35	0	PCDHGB6,missense_variant,p.Ala529Thr,ENST00000520790,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGA10,upstream_gene_variant,,ENST00000398610,;	A	ENSG00000253305	ENST00000520790	Transcript	missense_variant	1585	1585	529	A/T	Gcg/Acg	.	.	.	1	PCDHGB6	HGNC	8713	protein_coding	YES	CCDS54929.1	ENSP00000428603	PCDGI_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006EB47	.	deleterious(0)	benign(0.007)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028:SF66,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R526C|c.1576C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCGCGCTC	.	5	ESCA
LTC4S	0	.	GRCh37	5	179221199	179221199	+	Intron	SNP	C	C	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58+60C>A	.	.	ENST00000292596	.	34	10	24	46	46	0	LTC4S,intron_variant,,ENST00000401985,;LTC4S,intron_variant,,ENST00000292596,;MGAT4B,downstream_gene_variant,,ENST00000520875,;MGAT4B,downstream_gene_variant,,ENST00000518778,;MGAT4B,downstream_gene_variant,,ENST00000518867,;MGAT4B,downstream_gene_variant,,ENST00000292591,;MGAT4B,downstream_gene_variant,,ENST00000520969,;MGAT4B,downstream_gene_variant,,ENST00000519836,;MGAT4B,downstream_gene_variant,,ENST00000518980,;MGAT4B,downstream_gene_variant,,ENST00000337755,;MIR1229,downstream_gene_variant,,ENST00000408467,;MAML1,non_coding_transcript_exon_variant,,ENST00000503050,;MGAT4B,downstream_gene_variant,,ENST00000523382,;MGAT4B,downstream_gene_variant,,ENST00000522293,;LTC4S,intron_variant,,ENST00000486713,;LTC4S,intron_variant,,ENST00000505170,;LTC4S,intron_variant,,ENST00000465572,;LTC4S,intron_variant,,ENST00000466071,;LTC4S,upstream_gene_variant,,ENST00000510544,;LTC4S,upstream_gene_variant,,ENST00000509898,;MGAT4B,downstream_gene_variant,,ENST00000522451,;	A	ENSG00000213316	ENST00000292596	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LTC4S	HGNC	6719	protein_coding	YES	CCDS34316.1	ENSP00000292596	LTC4S_HUMAN	B2R523_HUMAN	UPI0000043F83	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTGCCCCCT	.	5	ESCA
IRX1	0	.	GRCh37	5	3601168	3601168	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*14T>C	.	.	ENST00000302006	4/4	52	37	15	36	36	0	IRX1,3_prime_UTR_variant,,ENST00000302006,;CTD-2012M11.3,upstream_gene_variant,,ENST00000559410,;	C	ENSG00000170549	ENST00000302006	Transcript	3_prime_UTR_variant	1509	.	.	.	.	.	.	.	1	IRX1	HGNC	14358	protein_coding	YES	CCDS34132.1	ENSP00000305244	IRX1_HUMAN	.	UPI00001B6455	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTTTTACT	.	5	ESCA
ENPP1	0	.	GRCh37	6	132201052	132201052	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1978G>A	p.Gly660Arg	p.G660R	ENST00000360971	20/25	49	33	15	37	37	0	ENPP1,missense_variant,p.Gly660Arg,ENST00000360971,;ENPP1,3_prime_UTR_variant,,ENST00000513998,;ENPP1,downstream_gene_variant,,ENST00000459624,;	A	ENSG00000197594	ENST00000360971	Transcript	missense_variant	1998	1978	660	G/R	Gga/Aga	.	.	.	1	ENPP1	HGNC	3356	protein_coding	YES	CCDS5150.2	ENSP00000354238	ENPP1_HUMAN	Q9NS95_HUMAN	UPI00001303F0	.	deleterious(0)	benign(0.417)	20/25	.	Gene3D:1g8tA00,hmmpanther:PTHR10151:SF64,hmmpanther:PTHR10151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTATGGAAGA	.	5	ESCA
RGS17	0	.	GRCh37	6	153365046	153365046	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108C>G	p.Cys36Trp	p.C36W	ENST00000367225	1/4	23	12	10	33	33	0	RGS17,missense_variant,p.Cys36Trp,ENST00000367225,;RGS17,missense_variant,p.Cys36Trp,ENST00000206262,;	C	ENSG00000091844	ENST00000367225	Transcript	missense_variant	133	108	36	C/W	tgC/tgG	COSM1441708	.	.	-1	RGS17	HGNC	14088	protein_coding	YES	CCDS5244.1	ENSP00000356194	RGS17_HUMAN	.	UPI000000D76A	.	tolerated(0.16)	probably_damaging(0.995)	1/4	.	hmmpanther:PTHR10845:SF133,hmmpanther:PTHR10845,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTGCAACA	.	5	ESCA
IGF2R	0	.	GRCh37	6	160494796	160494796	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4955G>A	p.Cys1652Tyr	p.C1652Y	ENST00000356956	35/48	25	16	9	26	26	0	IGF2R,missense_variant,p.Cys1652Tyr,ENST00000356956,;IGF2R,non_coding_transcript_exon_variant,,ENST00000487607,;	A	ENSG00000197081	ENST00000356956	Transcript	missense_variant	5103	4955	1652	C/Y	tGt/tAt	.	.	.	1	IGF2R	HGNC	5467	protein_coding	YES	CCDS5273.1	ENSP00000349437	MPRI_HUMAN	A0N9R7_HUMAN,A0N9R6_HUMAN	UPI0000072478	.	deleterious(0)	probably_damaging(1)	35/48	.	hmmpanther:PTHR10439:SF4,hmmpanther:PTHR10439,Pfam_domain:PF00878,Gene3D:2.70.130.10,Superfamily_domains:SSF50911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAATGTTCCG	.	5	ESCA
THBS2	0	.	GRCh37	6	169648945	169648945	+	Missense_Mutation	SNP	C	C	T	rs759210002	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.176G>A	p.Arg59His	p.R59H	ENST00000366787	4/23	40	25	14	47	47	0	THBS2,missense_variant,p.Arg59His,ENST00000435791,;THBS2,missense_variant,p.Arg59His,ENST00000366787,;THBS2,upstream_gene_variant,,ENST00000472733,;	T	ENSG00000186340	ENST00000366787	Transcript	missense_variant	426	176	59	R/H	cGc/cAc	rs759210002,COSM207885	.	.	-1	THBS2	HGNC	11786	protein_coding	YES	CCDS34574.1	ENSP00000355751	TSP2_HUMAN	Q6MZL6_HUMAN,Q5RI53_HUMAN	UPI0000231C7F	.	deleterious(0.02)	probably_damaging(0.999)	4/23	.	hmmpanther:PTHR10199:SF10,hmmpanther:PTHR10199,SMART_domains:SM00210,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGCGCACG	byCluster	5	ESCA
DST	0	.	GRCh37	6	56437732	56437732	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5498C>T	p.Ala1833Val	p.A1833V	ENST00000244364	33/84	149	105	43	38	38	0	DST,missense_variant,p.Ala3921Val,ENST00000446842,;DST,missense_variant,p.Ala2159Val,ENST00000370788,;DST,missense_variant,p.Ala1833Val,ENST00000244364,;DST,missense_variant,p.Ala4425Val,ENST00000370754,;DST,missense_variant,p.Ala4245Val,ENST00000361203,;DST,missense_variant,p.Ala4247Val,ENST00000370769,;DST,missense_variant,p.Ala2159Val,ENST00000421834,;DST,3_prime_UTR_variant,,ENST00000312431,;DST,3_prime_UTR_variant,,ENST00000518398,;	A	ENSG00000151914	ENST00000244364	Transcript	missense_variant	5706	5498	1833	A/V	gCt/gTt	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	benign(0.001)	33/84	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF38,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGAGCAGAC	.	5	ESCA
GJB7	0	.	GRCh37	6	87994440	87994440	+	Missense_Mutation	SNP	C	C	T	rs756299568	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.191G>A	p.Cys64Tyr	p.C64Y	ENST00000525899	3/3	25	19	6	33	33	0	GJB7,missense_variant,p.Cys64Tyr,ENST00000369576,;GJB7,missense_variant,p.Cys64Tyr,ENST00000296882,;GJB7,missense_variant,p.Cys64Tyr,ENST00000525899,;	T	ENSG00000164411	ENST00000525899	Transcript	missense_variant	537	191	64	C/Y	tGt/tAt	rs756299568	.	.	-1	GJB7	HGNC	16690	protein_coding	YES	CCDS5008.1	ENSP00000435355	CXB7_HUMAN	J3KP93_HUMAN	UPI000013E3A1	.	deleterious(0)	probably_damaging(1)	3/3	.	Prints_domain:PR00206,SMART_domains:SM00037,Gene3D:2zw3A00,Pfam_domain:PF00029,hmmpanther:PTHR11984:SF26,hmmpanther:PTHR11984	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAACACACA	.	5	ESCA
PLOD3	0	.	GRCh37	7	100861637	100861637	+	5'Flank	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000223127	.	14	8	6	15	15	0	PLOD3,5_prime_UTR_variant,,ENST00000456079,;ZNHIT1,intron_variant,,ENST00000305105,;PLOD3,upstream_gene_variant,,ENST00000414785,;PLOD3,upstream_gene_variant,,ENST00000223127,;PLOD3,upstream_gene_variant,,ENST00000421736,;ZNHIT1,non_coding_transcript_exon_variant,,ENST00000461205,;ZNHIT1,non_coding_transcript_exon_variant,,ENST00000492315,;PLOD3,non_coding_transcript_exon_variant,,ENST00000481461,;PLOD3,upstream_gene_variant,,ENST00000478264,;ZNHIT1,upstream_gene_variant,,ENST00000485387,;PLOD3,upstream_gene_variant,,ENST00000424135,;PLOD3,upstream_gene_variant,,ENST00000489927,;PLOD3,upstream_gene_variant,,ENST00000478082,;	T	ENSG00000106397	ENST00000223127	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	683	-1	PLOD3	HGNC	9083	protein_coding	YES	CCDS5715.1	ENSP00000223127	PLOD3_HUMAN	C9JIX5_HUMAN	UPI0000046664	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCCTCGAT	.	5	ESCA
PTPRZ1	0	.	GRCh37	7	121679506	121679506	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5503-2A>C	.	p.X1835_splice	ENST00000393386	.	46	31	15	21	21	0	PTPRZ1,splice_acceptor_variant,,ENST00000449182,;PTPRZ1,splice_acceptor_variant,,ENST00000393386,;PTPRZ1,splice_acceptor_variant,,ENST00000470504,;PTPRZ1,downstream_gene_variant,,ENST00000468641,;	C	ENSG00000106278	ENST00000393386	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	PTPRZ1	HGNC	9685	protein_coding	YES	CCDS34740.1	ENSP00000377047	PTPRZ_HUMAN	.	UPI000020F9BB	.	.	.	.	19/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCAGAGAA	.	5	ESCA
CALU	0	.	GRCh37	7	128409582	128409582	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*361A>T	.	.	ENST00000542996	8/8	28	15	13	12	12	0	CALU,3_prime_UTR_variant,,ENST00000449187,;CALU,3_prime_UTR_variant,,ENST00000535623,;CALU,3_prime_UTR_variant,,ENST00000479257,;CALU,3_prime_UTR_variant,,ENST00000538546,;CALU,3_prime_UTR_variant,,ENST00000542996,;CALU,3_prime_UTR_variant,,ENST00000535011,;CALU,3_prime_UTR_variant,,ENST00000249364,;CALU,intron_variant,,ENST00000493278,;OPN1SW,downstream_gene_variant,,ENST00000249389,;	T	ENSG00000128595	ENST00000542996	Transcript	3_prime_UTR_variant	2276	.	.	.	.	.	.	.	1	CALU	HGNC	1458	protein_coding	YES	CCDS56507.1	ENSP00000438248	CALU_HUMAN	.	UPI0001D27CDB	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTATGATT	.	5	ESCA
STYXL1	0	.	GRCh37	7	75659797	75659798	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44dupT	p.Leu16ProfsTer28	p.L16Pfs*28	ENST00000248600	2/9	151	115	36	56	56	0	STYXL1,frameshift_variant,p.Leu16ProfsTer28,ENST00000359697,;STYXL1,frameshift_variant,p.Leu16ProfsTer28,ENST00000431581,;STYXL1,frameshift_variant,p.Leu16ProfsTer28,ENST00000451157,;STYXL1,frameshift_variant,p.Leu16ProfsTer28,ENST00000340062,;STYXL1,frameshift_variant,p.Leu16ProfsTer28,ENST00000248600,;STYXL1,frameshift_variant,p.Leu16ProfsTer28,ENST00000360591,;STYXL1,upstream_gene_variant,,ENST00000454618,;STYXL1,non_coding_transcript_exon_variant,,ENST00000460184,;STYXL1,non_coding_transcript_exon_variant,,ENST00000474328,;STYXL1,upstream_gene_variant,,ENST00000430497,;STYXL1,upstream_gene_variant,,ENST00000438695,;	A	ENSG00000127952	ENST00000248600	Transcript	frameshift_variant	387-388	44-45	15	I/IX	atc/atTc	.	.	.	-1	STYXL1	HGNC	18165	protein_coding	YES	CCDS5580.1	ENSP00000248600	STYL1_HUMAN	.	UPI000012F694	.	.	.	2/9	.	Superfamily_domains:SSF52821,Gene3D:3.40.250.10,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF292	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCAGGATGTT	.	3	ESCA
CD36	0	.	GRCh37	7	80302143	80302143	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1183C>A	p.Pro395Thr	p.P395T	ENST00000435819	15/17	98	45	53	62	62	0	CD36,missense_variant,p.Pro356Thr,ENST00000433696,;CD36,missense_variant,p.Pro395Thr,ENST00000447544,;CD36,missense_variant,p.Pro319Thr,ENST00000534394,;CD36,missense_variant,p.Pro335Thr,ENST00000538969,;CD36,missense_variant,p.Pro395Thr,ENST00000309881,;CD36,missense_variant,p.Pro395Thr,ENST00000435819,;CD36,missense_variant,p.Pro395Thr,ENST00000432207,;CD36,missense_variant,p.Pro395Thr,ENST00000419819,;CD36,missense_variant,p.Pro395Thr,ENST00000394788,;CD36,3_prime_UTR_variant,,ENST00000544133,;CD36,upstream_gene_variant,,ENST00000488048,;CD36,non_coding_transcript_exon_variant,,ENST00000464213,;	A	ENSG00000135218	ENST00000435819	Transcript	missense_variant	1867	1183	395	P/T	Cca/Aca	.	.	.	1	CD36	HGNC	1663	protein_coding	YES	CCDS34673.1	ENSP00000399421	CD36_HUMAN	Q9BZN6_HUMAN,Q9BZN2_HUMAN,Q9BZM9_HUMAN,Q9BQA7_HUMAN,E9PLT1_HUMAN,E9PJX8_HUMAN,E9PC45_HUMAN,E7EX47_HUMAN,E7EWI4_HUMAN,E7EU05_HUMAN,E7ERZ9_HUMAN,A4D1B1_HUMAN	UPI0000000C91	.	deleterious(0)	probably_damaging(0.996)	15/17	.	Pfam_domain:PF01130,hmmpanther:PTHR11923,hmmpanther:PTHR11923:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAGCCATCA	.	5	ESCA
HGF	0	.	GRCh37	7	81372194	81372194	+	Intron	SNP	A	A	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.865+475T>C	.	.	ENST00000222390	.	37	22	14	19	19	0	HGF,3_prime_UTR_variant,,ENST00000453411,;HGF,3_prime_UTR_variant,,ENST00000444829,;HGF,intron_variant,,ENST00000457544,;HGF,intron_variant,,ENST00000222390,;	G	ENSG00000019991	ENST00000222390	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	HGF	HGNC	4893	protein_coding	YES	CCDS5597.1	ENSP00000222390	HGF_HUMAN	C9JS80_HUMAN,C9JDP4_HUMAN	UPI000000D92B	.	.	.	.	7/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTCATTATT	.	5	ESCA
PCLO	0	.	GRCh37	7	82585187	82585187	+	Silent	SNP	G	G	A	rs367988765	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5082C>T	p.%3D	p.D1694D	ENST00000333891	5/25	41	27	14	24	24	0	PCLO,synonymous_variant,p.%3D,ENST00000333891,;PCLO,synonymous_variant,p.%3D,ENST00000423517,;	A	ENSG00000186472	ENST00000333891	Transcript	synonymous_variant	5420	5082	1694	D	gaC/gaT	rs367988765,COSM1092375,COSM1092374,COSM1092376	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	.	5/25	.	hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	A:0.0003	A:0	.	0,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCGTCAAA	byFrequency|byCluster	5	ESCA
GRM3	0	.	GRCh37	7	86274134	86274134	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-195G>A	.	.	ENST00000361669	1/6	50	39	11	38	38	0	GRM3,missense_variant,p.Ala16Thr,ENST00000546348,;GRM3,synonymous_variant,p.%3D,ENST00000536043,;GRM3,synonymous_variant,p.%3D,ENST00000454217,;GRM3,5_prime_UTR_variant,,ENST00000361669,;GRM3,upstream_gene_variant,,ENST00000439827,;GRM3,upstream_gene_variant,,ENST00000421579,;GRM3,upstream_gene_variant,,ENST00000394720,;	A	ENSG00000198822	ENST00000361669	Transcript	5_prime_UTR_variant	905	.	.	.	.	.	.	.	1	GRM3	HGNC	4595	protein_coding	YES	CCDS5600.1	ENSP00000355316	GRM3_HUMAN	C9JUH9_HUMAN,C9JIT1_HUMAN,A4D1D0_HUMAN	UPI0000153EFC	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCGCCGCC	.	5	ESCA
SUN1	0	.	GRCh37	7	889579	889579	+	Intron	SNP	G	G	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659-1442G>C	.	.	ENST00000401592	.	29	23	6	17	17	0	SUN1,missense_variant,p.Lys378Asn,ENST00000456758,;SUN1,missense_variant,p.Lys38Asn,ENST00000433212,;SUN1,missense_variant,p.Lys226Asn,ENST00000405266,;SUN1,missense_variant,p.Lys95Asn,ENST00000419312,;SUN1,intron_variant,,ENST00000429178,;SUN1,intron_variant,,ENST00000425407,;SUN1,intron_variant,,ENST00000401592,;SUN1,intron_variant,,ENST00000452783,;SUN1,intron_variant,,ENST00000450881,;SUN1,intron_variant,,ENST00000389574,;SUN1,intron_variant,,ENST00000413514,;SUN1,non_coding_transcript_exon_variant,,ENST00000464442,;SUN1,non_coding_transcript_exon_variant,,ENST00000480475,;SUN1,non_coding_transcript_exon_variant,,ENST00000413171,;SUN1,non_coding_transcript_exon_variant,,ENST00000340926,;SUN1,downstream_gene_variant,,ENST00000471349,;SUN1,downstream_gene_variant,,ENST00000493681,;SUN1,upstream_gene_variant,,ENST00000457861,;SUN1,upstream_gene_variant,,ENST00000459810,;SUN1,upstream_gene_variant,,ENST00000463848,;SUN1,upstream_gene_variant,,ENST00000488628,;SUN1,upstream_gene_variant,,ENST00000475971,;	C	ENSG00000164828	ENST00000401592	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SUN1	HGNC	18587	protein_coding	YES	CCDS47525.1	ENSP00000384015	SUN1_HUMAN	Q5S4N2_HUMAN,C9K051_HUMAN,C9JS54_HUMAN,C9JR15_HUMAN,C9JK55_HUMAN,C9JJU6_HUMAN	UPI000020E965	.	.	.	.	5/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GGCAAGAGGCA	.	4	ESCA
LRRD1	0	.	GRCh37	7	91793876	91793876	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.641G>C	p.Arg214Thr	p.R214T	ENST00000458448	2/6	55	43	11	47	47	0	LRRD1,missense_variant,p.Arg214Thr,ENST00000458448,;LRRD1,missense_variant,p.Arg214Thr,ENST00000430130,;LRRD1,5_prime_UTR_variant,,ENST00000454089,;LRRD1,intron_variant,,ENST00000343318,;LRRD1,downstream_gene_variant,,ENST00000437357,;CTB-161K23.1,intron_variant,,ENST00000453068,;LRRD1,intron_variant,,ENST00000422722,;	G	ENSG00000240720	ENST00000458448	Transcript	missense_variant	842	641	214	R/T	aGg/aCg	.	.	.	-1	LRRD1	HGNC	34300	protein_coding	YES	CCDS55124.1	ENSP00000405987	LRRD1_HUMAN	C9K0I1_HUMAN	UPI0001662314	.	tolerated(0.17)	benign(0.111)	2/6	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23155:SF452,hmmpanther:PTHR23155,Gene3D:3.80.10.10,Pfam_domain:PF12799,SMART_domains:SM00364,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATCCTTAAA	.	5	ESCA
RAD21	0	.	GRCh37	8	117858714	117858714	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1025A>G	.	.	ENST00000297338	14/14	124	24	100	63	63	0	RAD21,3_prime_UTR_variant,,ENST00000297338,;UTP23,intron_variant,,ENST00000520733,;UTP23,intron_variant,,ENST00000517820,;RAD21,downstream_gene_variant,,ENST00000517749,;RAD21,downstream_gene_variant,,ENST00000518055,;RAD21,downstream_gene_variant,,ENST00000523986,;UTP23,intron_variant,,ENST00000521703,;UTP23,intron_variant,,ENST00000524128,;	C	ENSG00000164754	ENST00000297338	Transcript	3_prime_UTR_variant	3209	.	.	.	.	.	.	.	-1	RAD21	HGNC	9811	protein_coding	YES	CCDS6321.1	ENSP00000297338	RAD21_HUMAN	E5RJW1_HUMAN,E5RJK5_HUMAN,E5RIN7_HUMAN,E5RI01_HUMAN,E5RG18_HUMAN,E5RFZ5_HUMAN,E5RFV8_HUMAN	UPI0000133018	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGATATAGG	.	5	ESCA
ZHX2	0	.	GRCh37	8	123793977	123793977	+	5'UTR	SNP	T	T	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-491T>G	.	.	ENST00000314393	1/4	27	4	22	22	22	0	ZHX2,5_prime_UTR_variant,,ENST00000314393,;RP11-44N11.2,upstream_gene_variant,,ENST00000607710,;RP11-44N11.3,downstream_gene_variant,,ENST00000607393,;	G	ENSG00000178764	ENST00000314393	Transcript	5_prime_UTR_variant	345	.	.	.	.	.	.	.	1	ZHX2	HGNC	18513	protein_coding	YES	CCDS6336.1	ENSP00000314709	ZHX2_HUMAN	H0YKA3_HUMAN	UPI0000073CCB	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATTTTGGCC	.	5	ESCA
WRN	0	.	GRCh37	8	30922442	30922442	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.367G>A	p.Gly123Arg	p.G123R	ENST00000298139	5/35	62	32	29	74	74	0	WRN,missense_variant,p.Gly123Arg,ENST00000298139,;	A	ENSG00000165392	ENST00000298139	Transcript	missense_variant	616	367	123	G/R	Gga/Aga	.	.	.	1	WRN	HGNC	12791	protein_coding	YES	CCDS6082.1	ENSP00000298139	WRN_HUMAN	.	UPI000013E49D	.	deleterious(0.03)	probably_damaging(0.995)	5/35	.	Superfamily_domains:SSF53098,SMART_domains:SM00474,Gene3D:3.30.420.10,Pfam_domain:PF01612,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF80	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAGGGATTA	.	5	ESCA
TACC1	0	.	GRCh37	8	38677795	38677795	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1033C>G	p.Leu345Val	p.L345V	ENST00000317827	3/13	93	64	28	51	51	0	TACC1,missense_variant,p.Leu150Val,ENST00000520615,;TACC1,missense_variant,p.Leu150Val,ENST00000520973,;TACC1,missense_variant,p.Leu345Val,ENST00000317827,;TACC1,missense_variant,p.Leu317Val,ENST00000522904,;TACC1,missense_variant,p.Leu345Val,ENST00000379931,;TACC1,missense_variant,p.Leu361Val,ENST00000443286,;TACC1,missense_variant,p.Leu150Val,ENST00000519416,;TACC1,missense_variant,p.Leu309Val,ENST00000520340,;TACC1,missense_variant,p.Leu300Val,ENST00000518415,;TACC1,missense_variant,p.Leu120Val,ENST00000521866,;TACC1,intron_variant,,ENST00000521050,;TACC1,intron_variant,,ENST00000348567,;TACC1,intron_variant,,ENST00000521642,;TACC1,intron_variant,,ENST00000330691,;TACC1,intron_variant,,ENST00000276520,;TACC1,downstream_gene_variant,,ENST00000521528,;TACC1,downstream_gene_variant,,ENST00000524193,;TACC1,upstream_gene_variant,,ENST00000518809,;TACC1,downstream_gene_variant,,ENST00000524354,;TACC1,upstream_gene_variant,,ENST00000520611,;TACC1,downstream_gene_variant,,ENST00000521935,;TACC1,intron_variant,,ENST00000522752,;TACC1,intron_variant,,ENST00000523239,;TACC1,downstream_gene_variant,,ENST00000522544,;TACC1,upstream_gene_variant,,ENST00000517336,;TACC1,downstream_gene_variant,,ENST00000523834,;TACC1,non_coding_transcript_exon_variant,,ENST00000522955,;TACC1,downstream_gene_variant,,ENST00000521154,;	G	ENSG00000147526	ENST00000317827	Transcript	missense_variant	1412	1033	345	L/V	Ctg/Gtg	COSM3648939,COSM3648940	.	.	1	TACC1	HGNC	11522	protein_coding	YES	CCDS6109.1	ENSP00000321703	TACC1_HUMAN	E5RJU4_HUMAN,E5RJG6_HUMAN,E5RIP3_HUMAN,E5RI10_HUMAN	UPI000013DACE	.	tolerated(0.44)	benign(0.033)	3/13	.	hmmpanther:PTHR13924	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAACTGGGT	.	5	ESCA
ALAD	0	.	GRCh37	9	116155891	116155891	+	5'UTR	SNP	T	T	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-52A>C	.	.	ENST00000409155	2/12	49	28	21	31	31	0	ALAD,5_prime_UTR_variant,,ENST00000452726,;ALAD,5_prime_UTR_variant,,ENST00000448137,;ALAD,5_prime_UTR_variant,,ENST00000277315,;ALAD,5_prime_UTR_variant,,ENST00000445750,;ALAD,5_prime_UTR_variant,,ENST00000409155,;ALAD,upstream_gene_variant,,ENST00000482001,;ALAD,non_coding_transcript_exon_variant,,ENST00000494848,;ALAD,non_coding_transcript_exon_variant,,ENST00000482847,;ALAD,non_coding_transcript_exon_variant,,ENST00000468504,;ALAD,non_coding_transcript_exon_variant,,ENST00000464749,;	G	ENSG00000148218	ENST00000409155	Transcript	5_prime_UTR_variant	146	.	.	.	.	.	.	.	-1	ALAD	HGNC	395	protein_coding	YES	CCDS6794.2	ENSP00000386284	HEM2_HUMAN	.	UPI0000037431	.	.	.	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCTGGGGC	.	5	ESCA
OR5C1	0	.	GRCh37	9	125552143	125552143	+	Missense_Mutation	SNP	G	G	A	rs764398782	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932G>A	p.Arg311Gln	p.R311Q	ENST00000373680	1/1	33	20	13	26	26	0	OR5C1,missense_variant,p.Arg311Gln,ENST00000373680,;	A	ENSG00000148215	ENST00000373680	Transcript	missense_variant	994	932	311	R/Q	cGa/cAa	rs764398782	.	.	1	OR5C1	HGNC	8331	protein_coding	YES	CCDS35131.1	ENSP00000362784	OR5C1_HUMAN	Q6IFM9_HUMAN	UPI0000061E7B	.	deleterious(0.04)	benign(0.277)	1/1	.	hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF119,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGATTCC	byFrequency	5	ESCA
ASS1	0	.	GRCh37	9	133376608	133376608	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*200C>T	.	.	ENST00000372394	16/16	15	7	7	9	9	0	ASS1,3_prime_UTR_variant,,ENST00000372394,;ASS1,3_prime_UTR_variant,,ENST00000352480,;ASS1,3_prime_UTR_variant,,ENST00000372393,;ASS1,downstream_gene_variant,,ENST00000372386,;	T	ENSG00000130707	ENST00000372394	Transcript	3_prime_UTR_variant	1920	.	.	.	.	.	.	.	1	ASS1	HGNC	758	protein_coding	YES	CCDS6933.1	ENSP00000361471	ASSY_HUMAN	Q8NFZ7_HUMAN,Q5T6L6_HUMAN,Q5T6L4_HUMAN	UPI00000015D6	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGCGGTGG	.	5	ESCA
BARHL1	0	.	GRCh37	9	135465513	135465513	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*604G>C	.	.	ENST00000263610	3/3	54	39	15	31	31	0	BARHL1,3_prime_UTR_variant,,ENST00000263610,;DDX31,downstream_gene_variant,,ENST00000372159,;DDX31,downstream_gene_variant,,ENST00000438527,;DDX31,downstream_gene_variant,,ENST00000372153,;BARHL1,downstream_gene_variant,,ENST00000542090,;DDX31,downstream_gene_variant,,ENST00000372155,;	C	ENSG00000125492	ENST00000263610	Transcript	3_prime_UTR_variant	2201	.	.	.	.	.	.	.	1	BARHL1	HGNC	953	protein_coding	YES	CCDS6950.1	ENSP00000263610	BARH1_HUMAN	.	UPI0000126AD2	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCAGGAAGG	.	5	ESCA
CAMSAP1	0	.	GRCh37	9	138719368	138719368	+	Missense_Mutation	SNP	G	G	A	rs765465088	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1108C>T	p.Arg370Cys	p.R370C	ENST00000389532	8/17	75	43	32	40	40	0	CAMSAP1,missense_variant,p.Arg370Cys,ENST00000389532,;CAMSAP1,missense_variant,p.Arg92Cys,ENST00000312405,;CAMSAP1,missense_variant,p.Arg381Cys,ENST00000409386,;CAMSAP1,upstream_gene_variant,,ENST00000483991,;	A	ENSG00000130559	ENST00000389532	Transcript	missense_variant	1173	1108	370	R/C	Cgc/Tgc	rs765465088	.	.	-1	CAMSAP1	HGNC	19946	protein_coding	YES	CCDS35176.2	ENSP00000374183	CAMP1_HUMAN	.	UPI0000EDA283	.	deleterious(0)	possibly_damaging(0.886)	8/17	.	hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGCGTTTGG	.	5	ESCA
RP11-383M4.6	0	.	GRCh37	9	84547572	84547572	+	Intron	SNP	C	C	A	rs781376500	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1040-1263G>T	.	.	ENST00000585776	.	55	49	6	60	60	0	RP11-383M4.6,intron_variant,,ENST00000585776,;RP11-383M4.2,upstream_gene_variant,,ENST00000427387,;SPATA31D4,non_coding_transcript_exon_variant,,ENST00000341875,;SPATA31D4,non_coding_transcript_exon_variant,,ENST00000419782,;	A	ENSG00000267559	ENST00000585776	Transcript	intron_variant	.	.	.	.	.	rs781376500	.	.	-1	RP11-383M4.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TTGAGCAAGAA	byFrequency	2	ESCA
CNGA2	0	.	GRCh37	X	150906969	150906969	+	Missense_Mutation	SNP	C	C	A	rs771830593	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14C>A	p.Thr5Asn	p.T5N	ENST00000329903	1/6	34	20	13	17	17	0	CNGA2,missense_variant,p.Thr5Asn,ENST00000329903,;	A	ENSG00000183862	ENST00000329903	Transcript	missense_variant	47	14	5	T/N	aCc/aAc	rs771830593,COSM1201522	.	.	1	CNGA2	HGNC	2149	protein_coding	YES	CCDS14701.1	ENSP00000328478	CNGA2_HUMAN	.	UPI000003E7AE	.	tolerated_low_confidence(0.18)	benign(0.004)	1/6	.	hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF389	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAACCAATG	.	5	ESCA
FAAH2	0	.	GRCh37	X	57458421	57458421	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FE-01A-11D-A33E-09	TCGA-JY-A6FE-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1067C>G	p.Ser356Cys	p.S356C	ENST00000374900	8/11	81	60	21	14	14	0	FAAH2,missense_variant,p.Ser356Cys,ENST00000374900,;FAAH2,non_coding_transcript_exon_variant,,ENST00000491179,;FAAH2,upstream_gene_variant,,ENST00000465623,;	G	ENSG00000165591	ENST00000374900	Transcript	missense_variant	1187	1067	356	S/C	tCt/tGt	.	.	.	1	FAAH2	HGNC	26440	protein_coding	YES	CCDS14375.1	ENSP00000364035	FAAH2_HUMAN	B2C6G4_HUMAN	UPI000004CC6F	.	deleterious(0)	possibly_damaging(0.616)	8/11	.	Superfamily_domains:SSF75304,Gene3D:3.90.1300.10,Pfam_domain:PF01425,hmmpanther:PTHR11895:SF66,hmmpanther:PTHR11895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACTCTTTTC	.	5	ESCA
PRLHR	0	.	GRCh37	10	120354171	120354171	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586G>A	p.Val196Met	p.V196M	ENST00000239032	2/2	19	13	6	32	32	0	PRLHR,missense_variant,p.Val196Met,ENST00000369169,;PRLHR,missense_variant,p.Val196Met,ENST00000239032,;	T	ENSG00000119973	ENST00000239032	Transcript	missense_variant	725	586	196	V/M	Gtg/Atg	.	.	.	-1	PRLHR	HGNC	4464	protein_coding	YES	CCDS7606.1	ENSP00000239032	PRLHR_HUMAN	.	UPI000013CA6F	.	tolerated(0.14)	benign(0.009)	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF194,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCACGGCGG	.	5	ESCA
MKI67	0	.	GRCh37	10	129910413	129910413	+	Silent	SNP	C	C	T	rs142241283	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1953G>A	p.%3D	p.S651S	ENST00000368654	9/15	72	49	22	33	33	0	MKI67,synonymous_variant,p.%3D,ENST00000368654,;MKI67,synonymous_variant,p.%3D,ENST00000368653,;MKI67,non_coding_transcript_exon_variant,,ENST00000484853,;MKI67,downstream_gene_variant,,ENST00000478293,;	T	ENSG00000148773	ENST00000368654	Transcript	synonymous_variant	2329	1953	651	S	tcG/tcA	rs142241283,COSM916144	.	.	-1	MKI67	HGNC	7107	protein_coding	YES	CCDS7659.1	ENSP00000357643	KI67_HUMAN	.	UPI000013DB54	.	.	.	9/15	.	hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF3	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTCCGAAGC	byCluster	5	ESCA
PWWP2B	0	.	GRCh37	10	134218219	134218219	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.215A>T	p.Glu72Val	p.E72V	ENST00000305233	2/3	21	11	10	24	24	0	PWWP2B,missense_variant,p.Glu72Val,ENST00000305233,;PWWP2B,missense_variant,p.Glu72Val,ENST00000368609,;	T	ENSG00000171813	ENST00000305233	Transcript	missense_variant	274	215	72	E/V	gAg/gTg	.	.	.	1	PWWP2B	HGNC	25150	protein_coding	YES	CCDS7667.2	ENSP00000306324	PWP2B_HUMAN	.	UPI00001D7FE3	.	tolerated(0.1)	benign(0.404)	2/3	.	hmmpanther:PTHR23068,hmmpanther:PTHR23068:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGGAGGGGG	.	5	ESCA
NEBL	0	.	GRCh37	10	21070007	21070007	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4669G>T	.	.	ENST00000377122	28/28	29	17	12	12	12	0	NEBL,3_prime_UTR_variant,,ENST00000377122,;NEBL,downstream_gene_variant,,ENST00000377159,;NEBL,downstream_gene_variant,,ENST00000417816,;	A	ENSG00000078114	ENST00000377122	Transcript	3_prime_UTR_variant	8111	.	.	.	.	.	.	.	-1	NEBL	HGNC	16932	protein_coding	YES	CCDS7134.1	ENSP00000366326	NEBL_HUMAN	B0YJ47_HUMAN	UPI000012FEE8	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTCCTTTGG	.	5	ESCA
ABI1	0	.	GRCh37	10	27040636	27040636	+	Silent	SNP	T	T	G	rs572768904	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1242A>C	p.%3D	p.P414P	ENST00000376142	11/12	50	36	14	48	48	0	ABI1,synonymous_variant,p.%3D,ENST00000359188,;ABI1,synonymous_variant,p.%3D,ENST00000376142,;ABI1,synonymous_variant,p.%3D,ENST00000376137,;ABI1,synonymous_variant,p.%3D,ENST00000376140,;ABI1,synonymous_variant,p.%3D,ENST00000376139,;ABI1,synonymous_variant,p.%3D,ENST00000376160,;ABI1,synonymous_variant,p.%3D,ENST00000536334,;ABI1,synonymous_variant,p.%3D,ENST00000376166,;ABI1,synonymous_variant,p.%3D,ENST00000376138,;ABI1,synonymous_variant,p.%3D,ENST00000376170,;ABI1,synonymous_variant,p.%3D,ENST00000346832,;ABI1,synonymous_variant,p.%3D,ENST00000490841,;ABI1,synonymous_variant,p.%3D,ENST00000376134,;ABI1,synonymous_variant,p.%3D,ENST00000355394,;PDSS1,downstream_gene_variant,,ENST00000376203,;PDSS1,downstream_gene_variant,,ENST00000376215,;PDSS1,downstream_gene_variant,,ENST00000470978,;	G	ENSG00000136754	ENST00000376142	Transcript	synonymous_variant	1314	1242	414	P	ccA/ccC	rs572768904	.	.	-1	ABI1	HGNC	11320	protein_coding	YES	CCDS7150.1	ENSP00000365312	ABI1_HUMAN	.	UPI000006EA57	.	.	.	11/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10460:SF2,hmmpanther:PTHR10460	G:0.0008	G:0	G:0.0058	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGTGGGGG	byFrequency|by1000G	4	ESCA
TMEM72	0	.	GRCh37	10	45430542	45430542	+	Missense_Mutation	SNP	C	C	T	rs374225789	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.788C>T	p.Pro263Leu	p.P263L	ENST00000389583	5/5	23	16	7	31	31	0	TMEM72,missense_variant,p.Pro145Leu,ENST00000544540,;TMEM72,missense_variant,p.Pro263Leu,ENST00000389583,;RP11-285G1.9,upstream_gene_variant,,ENST00000425541,;TMEM72-AS1,intron_variant,,ENST00000450287,;TMEM72,downstream_gene_variant,,ENST00000460364,;	T	ENSG00000187783	ENST00000389583	Transcript	missense_variant	1101	788	263	P/L	cCa/cTa	rs374225789	.	.	1	TMEM72	HGNC	31658	protein_coding	YES	CCDS41504.1	ENSP00000374234	TMM72_HUMAN	.	UPI000036669E	.	deleterious(0.03)	benign(0.085)	5/5	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCCCACTCT	byFrequency|byCluster	2	ESCA
WDFY4	0	.	GRCh37	10	49935564	49935564	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.831C>T	p.%3D	p.D277D	ENST00000325239	6/61	52	36	16	52	52	0	WDFY4,synonymous_variant,p.%3D,ENST00000413659,;WDFY4,synonymous_variant,p.%3D,ENST00000325239,;WDFY4,synonymous_variant,p.%3D,ENST00000360890,;	T	ENSG00000128815	ENST00000325239	Transcript	synonymous_variant	858	831	277	D	gaC/gaT	.	.	.	1	WDFY4	HGNC	29323	protein_coding	YES	CCDS44385.1	ENSP00000320563	WDFY4_HUMAN	Q6PIM1_HUMAN	UPI000176ADB8	.	.	.	6/61	.	hmmpanther:PTHR13743:SF52,hmmpanther:PTHR13743,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGACACTCT	.	5	ESCA
PCDH15	0	.	GRCh37	10	56423942	56423942	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81G>T	p.Gln27His	p.Q27H	ENST00000361849	2/34	55	38	17	43	43	0	PCDH15,missense_variant,p.Gln27His,ENST00000437009,;PCDH15,missense_variant,p.Gln27His,ENST00000395433,;PCDH15,missense_variant,p.Gln27His,ENST00000395445,;PCDH15,missense_variant,p.Gln27His,ENST00000320301,;PCDH15,missense_variant,p.Gln27His,ENST00000395432,;PCDH15,missense_variant,p.Gln27His,ENST00000373955,;PCDH15,missense_variant,p.Gln27His,ENST00000373957,;PCDH15,missense_variant,p.Gln27His,ENST00000395440,;PCDH15,missense_variant,p.Gln27His,ENST00000361849,;PCDH15,missense_variant,p.Gln27His,ENST00000395438,;PCDH15,missense_variant,p.Gln27His,ENST00000395446,;PCDH15,missense_variant,p.Gln27His,ENST00000395442,;PCDH15,missense_variant,p.Gln27His,ENST00000414778,;PCDH15,missense_variant,p.Gln27His,ENST00000458638,;PCDH15,missense_variant,p.Gln27His,ENST00000373965,;PCDH15,missense_variant,p.Gln27His,ENST00000395430,;PCDH15,5_prime_UTR_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Gln27His,ENST00000448885,;PCDH15,missense_variant,p.Gln27His,ENST00000373956,;PCDH15,missense_variant,p.Gln27His,ENST00000414367,;	A	ENSG00000150275	ENST00000361849	Transcript	missense_variant	476	81	27	Q/H	caG/caT	.	.	.	-1	PCDH15	HGNC	14674	protein_coding	YES	CCDS44404.1	ENSP00000354950	.	A2A3E7_HUMAN,A2A3D9_HUMAN	UPI0000EE048B	.	deleterious_low_confidence(0)	probably_damaging(0.968)	2/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATACTGGCC	.	5	ESCA
ANK3	0	.	GRCh37	10	61832903	61832903	+	Missense_Mutation	SNP	C	C	T	rs61732397	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7736G>A	p.Arg2579Lys	p.R2579K	ENST00000280772	37/44	22	14	8	12	12	0	ANK3,missense_variant,p.Arg2579Lys,ENST00000280772,;ANK3,intron_variant,,ENST00000373827,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000355288,;ANK3,intron_variant,,ENST00000511043,;ANK3,intron_variant,,ENST00000503366,;	T	ENSG00000151150	ENST00000280772	Transcript	missense_variant	7928	7736	2579	R/K	aGg/aAg	rs61732397	.	.	-1	ANK3	HGNC	494	protein_coding	YES	CCDS7258.1	ENSP00000280772	ANK3_HUMAN	D6RFK6_HUMAN,D6RBY7_HUMAN,B1AQT1_HUMAN	UPI0000141BA9	.	.	possibly_damaging(0.899)	37/44	.	hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF15	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0.0002	T:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCCTGTCC	byCluster|by1000G	4	ESCA
PALD1	0	.	GRCh37	10	72292493	72292495	+	In_Frame_Del	DEL	GGA	GGA	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	GGA	GGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.755_757delAGG	p.Glu252del	p.E252del	ENST00000263563	6/20	27	19	8	49	49	0	PALD1,inframe_deletion,p.Glu252del,ENST00000263563,;	-	ENSG00000107719	ENST00000263563	Transcript	inframe_deletion	1018-1020	750-752	250-251	TE/T	acGGAg/acg	.	.	.	1	PALD1	HGNC	23530	protein_coding	YES	CCDS31215.1	ENSP00000263563	PALD_HUMAN	.	UPI00001C1EDC	.	.	.	6/20	.	Superfamily_domains:SSF52799,Pfam_domain:PF14566,hmmpanther:PTHR23339:SF34,hmmpanther:PTHR23339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTGACGGAGGAGG	.	3	ESCA
GRID1	0	.	GRCh37	10	87966134	87966134	+	Silent	SNP	G	G	A	rs368572646	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.Y169Y	ENST00000327946	3/16	20	13	7	38	38	0	GRID1,synonymous_variant,p.%3D,ENST00000327946,;GRID1,synonymous_variant,p.%3D,ENST00000464741,;	A	ENSG00000182771	ENST00000327946	Transcript	synonymous_variant	593	507	169	Y	taC/taT	rs368572646,COSM1349374	.	.	-1	GRID1	HGNC	4575	protein_coding	YES	CCDS31236.1	ENSP00000330148	GRID1_HUMAN	B7Z7L0_HUMAN	UPI00001D8051	.	.	.	3/16	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF108,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCGTAGAA	byCluster|by1000G	5	ESCA
C11orf70	0	.	GRCh37	11	101946692	101946692	+	Missense_Mutation	SNP	G	G	A	rs777318658	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524G>A	p.Cys175Tyr	p.C175Y	ENST00000434758	5/7	63	47	16	34	34	0	C11orf70,missense_variant,p.Cys175Tyr,ENST00000526781,;C11orf70,missense_variant,p.Cys67Tyr,ENST00000529204,;C11orf70,missense_variant,p.Cys175Tyr,ENST00000434758,;C11orf70,3_prime_UTR_variant,,ENST00000534360,;C11orf70,non_coding_transcript_exon_variant,,ENST00000530659,;	A	ENSG00000137691	ENST00000434758	Transcript	missense_variant	552	524	175	C/Y	tGc/tAc	rs777318658	.	.	1	C11orf70	HGNC	28188	protein_coding	YES	CCDS8313.2	ENSP00000414390	CK070_HUMAN	.	UPI00001FA24F	.	deleterious(0)	probably_damaging(0.994)	5/7	.	hmmpanther:PTHR31078,hmmpanther:PTHR31078:SF1,Pfam_domain:PF14926	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTGCCTTG	.	5	ESCA
USP28	0	.	GRCh37	11	113700044	113700044	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934A>G	p.Thr312Ala	p.T312A	ENST00000003302	10/25	67	49	17	70	70	0	USP28,missense_variant,p.Thr187Ala,ENST00000545540,;USP28,missense_variant,p.Thr20Ala,ENST00000544967,;USP28,missense_variant,p.Thr211Ala,ENST00000537642,;USP28,missense_variant,p.Thr312Ala,ENST00000003302,;USP28,missense_variant,p.Thr312Ala,ENST00000260188,;USP28,missense_variant,p.Thr312Ala,ENST00000537706,;USP28,missense_variant,p.Thr76Ala,ENST00000538475,;USP28,downstream_gene_variant,,ENST00000542033,;USP28,missense_variant,p.Thr46Ala,ENST00000537490,;USP28,3_prime_UTR_variant,,ENST00000535607,;USP28,3_prime_UTR_variant,,ENST00000545608,;USP28,3_prime_UTR_variant,,ENST00000540438,;	C	ENSG00000048028	ENST00000003302	Transcript	missense_variant	1003	934	312	T/A	Acc/Gcc	.	.	.	-1	USP28	HGNC	12625	protein_coding	YES	CCDS31680.1	ENSP00000003302	UBP28_HUMAN	Q96SV4_HUMAN	UPI0000137A00	.	tolerated(0.26)	probably_damaging(0.976)	10/25	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF110,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGGTCTCAT	.	5	ESCA
HYOU1	0	.	GRCh37	11	118915486	118915486	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*819C>T	.	.	ENST00000404233	26/26	15	10	5	12	12	0	HYOU1,3_prime_UTR_variant,,ENST00000404233,;HYOU1,3_prime_UTR_variant,,ENST00000529972,;HYOU1,downstream_gene_variant,,ENST00000543287,;HYOU1,downstream_gene_variant,,ENST00000525859,;HYOU1,downstream_gene_variant,,ENST00000530473,;RP11-110I1.6,intron_variant,,ENST00000531886,;HYOU1,downstream_gene_variant,,ENST00000532519,;HYOU1,downstream_gene_variant,,ENST00000527738,;HYOU1,downstream_gene_variant,,ENST00000531682,;	A	ENSG00000149428	ENST00000404233	Transcript	3_prime_UTR_variant	3944	.	.	.	.	.	.	.	-1	HYOU1	HGNC	16931	protein_coding	YES	CCDS8408.1	ENSP00000384144	HYOU1_HUMAN	J3QQH7_HUMAN,J3QLE9_HUMAN,J3QL06_HUMAN,J3KTF1_HUMAN,J3KT27_HUMAN,J3KSJ2_HUMAN,E9PJ21_HUMAN	UPI0000130F72	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCAGGCTGC	.	2	ESCA
CBL	0	.	GRCh37	11	119171086	119171086	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*595C>G	.	.	ENST00000264033	16/16	32	18	13	12	12	0	CBL,3_prime_UTR_variant,,ENST00000264033,;	G	ENSG00000110395	ENST00000264033	Transcript	3_prime_UTR_variant	3692	.	.	.	.	.	.	.	1	CBL	HGNC	1541	protein_coding	YES	CCDS8418.1	ENSP00000264033	CBL_HUMAN	.	UPI000013D4A7	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGAACACCTT	.	5	ESCA
PVRL1	0	.	GRCh37	11	119535970	119535970	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041G>A	p.%3D	p.R347R	ENST00000264025	6/6	22	13	8	24	24	0	PVRL1,synonymous_variant,p.%3D,ENST00000264025,;PVRL1,intron_variant,,ENST00000341398,;	T	ENSG00000110400	ENST00000264025	Transcript	synonymous_variant	1572	1041	347	R	cgG/cgA	.	.	.	-1	PVRL1	HGNC	9706	protein_coding	YES	CCDS8426.1	ENSP00000264025	PVRL1_HUMAN	Q6SYC2_HUMAN	UPI000004A2BE	.	.	.	6/6	.	hmmpanther:PTHR23277:SF12,hmmpanther:PTHR23277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCGCGCCGCCC	.	3	ESCA
NCAPD3	0	.	GRCh37	11	134073578	134073578	+	Missense_Mutation	SNP	G	G	A	rs201688313	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439C>T	p.Ser480Leu	p.S480L	ENST00000534548	11/35	59	36	22	59	59	0	NCAPD3,missense_variant,p.Ser480Leu,ENST00000534548,;NCAPD3,missense_variant,p.Ser480Leu,ENST00000525964,;NCAPD3,missense_variant,p.Ser480Leu,ENST00000534532,;	A	ENSG00000151503	ENST00000534548	Transcript	missense_variant	1504	1439	480	S/L	tCg/tTg	rs201688313	.	.	-1	NCAPD3	HGNC	28952	protein_coding	YES	CCDS31723.1	ENSP00000433681	CNDD3_HUMAN	Q96FA6_HUMAN,E9PLE0_HUMAN,E9PL84_HUMAN	UPI00001C1EFE	.	tolerated(0.58)	benign(0.004)	11/35	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF036508,hmmpanther:PTHR14222:SF1,hmmpanther:PTHR14222	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCCGACGCA	byFrequency|byCluster	5	ESCA
ABCC8	0	.	GRCh37	11	17418754	17418754	+	Missense_Mutation	SNP	T	T	G	rs770148379	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3974A>C	p.Tyr1325Ser	p.Y1325S	ENST00000389817	32/39	28	14	13	51	51	0	ABCC8,missense_variant,p.Tyr1325Ser,ENST00000389817,;ABCC8,missense_variant,p.Tyr149Ser,ENST00000528374,;ABCC8,missense_variant,p.Tyr1326Ser,ENST00000302539,;ABCC8,3_prime_UTR_variant,,ENST00000527905,;ABCC8,3_prime_UTR_variant,,ENST00000531891,;ABCC8,non_coding_transcript_exon_variant,,ENST00000531137,;ABCC8,non_coding_transcript_exon_variant,,ENST00000532220,;ABCC8,upstream_gene_variant,,ENST00000526037,;ABCC8,upstream_gene_variant,,ENST00000525022,;ABCC8,upstream_gene_variant,,ENST00000531642,;ABCC8,upstream_gene_variant,,ENST00000526168,;	G	ENSG00000006071	ENST00000389817	Transcript	missense_variant	4043	3974	1325	Y/S	tAc/tCc	rs770148379	.	.	-1	ABCC8	HGNC	59	protein_coding	YES	CCDS31437.1	ENSP00000374467	ABCC8_HUMAN	.	UPI0000DBEF32	.	deleterious(0)	benign(0.013)	32/39	.	hmmpanther:PTHR24223:SF187,hmmpanther:PTHR24223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCGTAGCTC	.	5	ESCA
TPH1	0	.	GRCh37	11	18062306	18062306	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4A>T	p.Ile2Phe	p.I2F	ENST00000250018	1/10	77	39	37	56	56	0	TPH1,missense_variant,p.Ile12Phe,ENST00000528338,;TPH1,missense_variant,p.Ile2Phe,ENST00000250018,;TPH1,missense_variant,p.Ile2Phe,ENST00000341556,;TPH1,missense_variant,p.Ile2Phe,ENST00000417164,;	A	ENSG00000129167	ENST00000250018	Transcript	missense_variant	567	4	2	I/F	Att/Ttt	.	.	.	-1	TPH1	HGNC	12008	protein_coding	YES	CCDS7829.1	ENSP00000250018	TPH1_HUMAN	B3VS10_HUMAN,B3VS05_HUMAN,B3VS00_HUMAN,B3VRZ5_HUMAN,B3VRZ0_HUMAN,B3VRY5_HUMAN,B3VRY0_HUMAN,B3VRX5_HUMAN,B3VRX0_HUMAN,B3VRW5_HUMAN	UPI000013CC9C	.	deleterious(0)	possibly_damaging(0.776)	1/10	.	hmmpanther:PTHR11473,hmmpanther:PTHR11473:SF23,PIRSF_domain:PIRSF000336	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAATCATGA	.	5	ESCA
NAV2	0	.	GRCh37	11	19967974	19967974	+	Missense_Mutation	SNP	G	G	A	rs769722553	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000396087	10/41	68	43	24	73	73	0	NAV2,missense_variant,p.Arg725Gln,ENST00000396085,;NAV2,missense_variant,p.Arg661Gln,ENST00000360655,;NAV2,missense_variant,p.Arg679Gln,ENST00000540292,;NAV2,missense_variant,p.Arg677Gln,ENST00000527559,;NAV2,missense_variant,p.Arg725Gln,ENST00000349880,;NAV2,missense_variant,p.Arg748Gln,ENST00000396087,;	A	ENSG00000166833	ENST00000396087	Transcript	missense_variant	2342	2243	748	R/Q	cGg/cAg	rs769722553	.	.	1	NAV2	HGNC	15997	protein_coding	YES	CCDS58126.1	ENSP00000379396	NAV2_HUMAN	.	UPI00001E0580	.	deleterious(0)	probably_damaging(0.992)	10/41	.	hmmpanther:PTHR12784:SF6,hmmpanther:PTHR12784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCGGACAG	byFrequency	5	ESCA
FJX1	0	.	GRCh37	11	35641852	35641852	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*354T>C	.	.	ENST00000317811	1/1	48	33	14	87	87	0	FJX1,3_prime_UTR_variant,,ENST00000317811,;FJX1,intron_variant,,ENST00000532914,;	C	ENSG00000179431	ENST00000317811	Transcript	3_prime_UTR_variant	2118	.	.	.	.	.	.	.	1	FJX1	HGNC	17166	protein_coding	YES	CCDS44570.1	ENSP00000400223	FJX1_HUMAN	.	UPI0000062321	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCCTCATTC	.	5	ESCA
LRRC56	0	.	GRCh37	11	552588	552588	+	Missense_Mutation	SNP	C	C	T	rs775139825	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1201C>T	p.Pro401Ser	p.P401S	ENST00000270115	13/14	124	89	34	234	234	0	LRRC56,missense_variant,p.Pro401Ser,ENST00000270115,;C11orf35,downstream_gene_variant,,ENST00000329451,;C11orf35,downstream_gene_variant,,ENST00000441853,;C11orf35,downstream_gene_variant,,ENST00000486629,;C11orf35,downstream_gene_variant,,ENST00000469990,;	T	ENSG00000161328	ENST00000270115	Transcript	missense_variant	1701	1201	401	P/S	Ccg/Tcg	rs775139825	.	.	1	LRRC56	HGNC	25430	protein_coding	YES	CCDS7700.1	ENSP00000270115	LRC56_HUMAN	.	UPI000007425F	.	tolerated(0.63)	benign(0.036)	13/14	.	hmmpanther:PTHR22708:SF0,hmmpanther:PTHR22708	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCACCCGGAG	byFrequency	5	ESCA
OR10AG1	0	.	GRCh37	11	55735930	55735930	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10G>T	p.Val4Phe	p.V4F	ENST00000312345	1/1	24	15	9	10	10	0	OR10AG1,missense_variant,p.Val4Phe,ENST00000312345,;	A	ENSG00000174970	ENST00000312345	Transcript	missense_variant	61	10	4	V/F	Gtt/Ttt	.	.	.	-1	OR10AG1	HGNC	19607	protein_coding	YES	CCDS31514.1	ENSP00000311477	O10AG_HUMAN	.	UPI000004B22B	.	deleterious(0.03)	benign(0.117)	1/1	.	hmmpanther:PTHR26453:SF159,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AAGAACAAATT	.	2	ESCA
SMPD1	0	.	GRCh37	11	6413037	6413037	+	Missense_Mutation	SNP	G	G	A	rs200763423	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.742G>A	p.Glu248Lys	p.E248K	ENST00000342245	2/6	16	10	6	26	26	0	SMPD1,missense_variant,p.Glu247Lys,ENST00000527275,;SMPD1,missense_variant,p.Glu248Lys,ENST00000342245,;SMPD1,missense_variant,p.Glu248Lys,ENST00000299397,;SMPD1,missense_variant,p.Glu248Lys,ENST00000356761,;SMPD1,5_prime_UTR_variant,,ENST00000530395,;APBB1,downstream_gene_variant,,ENST00000608704,;APBB1,downstream_gene_variant,,ENST00000608394,;APBB1,downstream_gene_variant,,ENST00000530885,;APBB1,downstream_gene_variant,,ENST00000609360,;APBB1,downstream_gene_variant,,ENST00000299402,;APBB1,downstream_gene_variant,,ENST00000389906,;SMPD1,upstream_gene_variant,,ENST00000526280,;APBB1,downstream_gene_variant,,ENST00000608645,;APBB1,downstream_gene_variant,,ENST00000609331,;APBB1,downstream_gene_variant,,ENST00000311051,;APBB1,downstream_gene_variant,,ENST00000608655,;APBB1,downstream_gene_variant,,ENST00000529519,;SMPD1,intron_variant,,ENST00000533196,;APBB1,downstream_gene_variant,,ENST00000526240,;SMPD1,missense_variant,p.Glu248Lys,ENST00000533123,;SMPD1,missense_variant,p.Glu248Lys,ENST00000534405,;SMPD1,intron_variant,,ENST00000531303,;SMPD1,upstream_gene_variant,,ENST00000532367,;APBB1,downstream_gene_variant,,ENST00000608435,;SMPD1,upstream_gene_variant,,ENST00000531336,;APBB1,downstream_gene_variant,,ENST00000524626,;	A	ENSG00000166311	ENST00000342245	Transcript	missense_variant	910	742	248	E/K	Gaa/Aaa	rs200763423,CM041853	.	.	1	SMPD1	HGNC	11120	protein_coding	YES	CCDS44531.1	ENSP00000340409	ASM_HUMAN	E9PL59_HUMAN	UPI000013E592	.	deleterious(0.01)	probably_damaging(0.922)	2/6	.	hmmpanther:PTHR10340,hmmpanther:PTHR10340:SF13,Gene3D:3.60.21.10,Pfam_domain:PF00149,PIRSF_domain:PIRSF000948,Superfamily_domains:SSF56300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCGAATAC	byCluster	5	ESCA
ATG2A	0	.	GRCh37	11	64658835	64658835	+	3'Flank	SNP	C	C	T	rs754568320	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000377264	.	40	24	15	72	72	0	EHD1,upstream_gene_variant,,ENST00000457202,;ATG2A,downstream_gene_variant,,ENST00000418259,;ATG2A,downstream_gene_variant,,ENST00000421419,;ATG2A,downstream_gene_variant,,ENST00000377264,;MIR194-2,non_coding_transcript_exon_variant,,ENST00000384864,;MIR194-2,downstream_gene_variant,,ENST00000413053,;RP11-665N17.4,upstream_gene_variant,,ENST00000601517,;MIR192,upstream_gene_variant,,ENST00000384915,;AP001187.1,upstream_gene_variant,,ENST00000366222,;	T	ENSG00000110046	ENST00000377264	Transcript	downstream_gene_variant	.	.	.	.	.	rs754568320	.	3183	-1	ATG2A	HGNC	29028	protein_coding	YES	CCDS31602.1	ENSP00000366475	ATG2A_HUMAN	B4DV45_HUMAN	UPI00001C1F21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGCCCC	.	5	ESCA
PPFIBP2	0	.	GRCh37	11	7669640	7669640	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1669C>A	p.Gln557Lys	p.Q557K	ENST00000299492	18/24	30	18	12	25	25	0	PPFIBP2,missense_variant,p.Gln445Lys,ENST00000528883,;PPFIBP2,missense_variant,p.Gln414Lys,ENST00000530181,;PPFIBP2,missense_variant,p.Gln557Lys,ENST00000299492,;PPFIBP2,missense_variant,p.Gln399Lys,ENST00000533792,;PPFIBP2,upstream_gene_variant,,ENST00000534552,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000530582,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000524495,;PPFIBP2,intron_variant,,ENST00000532926,;PPFIBP2,intron_variant,,ENST00000529021,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000532112,;PPFIBP2,upstream_gene_variant,,ENST00000529664,;PPFIBP2,upstream_gene_variant,,ENST00000528929,;	A	ENSG00000166387	ENST00000299492	Transcript	missense_variant	2057	1669	557	Q/K	Cag/Aag	.	.	.	1	PPFIBP2	HGNC	9250	protein_coding	YES	CCDS31419.1	ENSP00000299492	LIPB2_HUMAN	E9PP16_HUMAN,E9PMN3_HUMAN,E9PMH3_HUMAN,E9PK17_HUMAN,E9PJA0_HUMAN,E9PIK8_HUMAN,B3KM46_HUMAN	UPI00001C1EF8	.	tolerated(1)	probably_damaging(0.993)	18/24	.	Superfamily_domains:SSF47769,SMART_domains:SM00454,Gene3D:1.10.150.50,Pfam_domain:PF00536,hmmpanther:PTHR12587:SF18,hmmpanther:PTHR12587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCCCAGTGG	.	5	ESCA
TENM4	0	.	GRCh37	11	78369429	78369429	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7984C>A	p.Arg2662Ser	p.R2662S	ENST00000278550	34/34	33	20	13	39	39	0	TENM4,missense_variant,p.Arg2662Ser,ENST00000278550,;TENM4,intron_variant,,ENST00000530738,;	T	ENSG00000149256	ENST00000278550	Transcript	missense_variant	8447	7984	2662	R/S	Cgc/Agc	.	.	.	-1	TENM4	HGNC	29945	protein_coding	YES	CCDS44688.1	ENSP00000278550	TEN4_HUMAN	G3CAT1_HUMAN	UPI0000DD8112	.	deleterious(0)	probably_damaging(0.965)	34/34	.	hmmpanther:PTHR11219:SF9,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GTAGCGTCTAG	.	4	ESCA
TRIM66	0	.	GRCh37	11	8665968	8665968	+	Intron	SNP	T	T	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664-1295A>C	.	.	ENST00000402157	.	36	24	12	17	17	0	TRIM66,intron_variant,,ENST00000402157,;TRIM66,intron_variant,,ENST00000299550,;TRIM66,non_coding_transcript_exon_variant,,ENST00000531498,;TRIM66,downstream_gene_variant,,ENST00000529057,;TRIM66,intron_variant,,ENST00000481014,;	G	ENSG00000166436	ENST00000402157	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TRIM66	HGNC	29005	protein_coding	YES	.	ENSP00000384876	.	B5MCJ9_HUMAN	UPI00016113E8	.	.	.	.	9/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTATTATCAC	.	5	ESCA
TYR	0	.	GRCh37	11	88961100	88961100	+	Missense_Mutation	SNP	C	C	A	rs104894315	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1146C>A	p.Asn382Lys	p.N382K	ENST00000263321	3/5	54	34	20	47	47	0	TYR,missense_variant,p.Asn382Lys,ENST00000263321,;	A	ENSG00000077498	ENST00000263321	Transcript	missense_variant	1648	1146	382	N/K	aaC/aaA	CM100979,CM920696,rs104894315,RISN_TYR:c.1146C>A	.	.	1	TYR	HGNC	12442	protein_coding	YES	CCDS8284.1	ENSP00000263321	TYRO_HUMAN	Q9UMA2_HUMAN,Q9UMA1_HUMAN,L8B082_HUMAN	UPI000004441A	.	deleterious(0)	probably_damaging(1)	3/5	.	hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF16,Pfam_domain:PF00264,Gene3D:1.10.1280.10,Superfamily_domains:SSF48056,Prints_domain:PR00092	.	.	.	.	.	.	.	T:0	T:0.0001	not_provided,pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAACGATCC	byFrequency|byCluster	5	ESCA
FUT4	0	.	GRCh37	11	94280688	94280688	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1796G>A	.	.	ENST00000358752	1/1	19	12	7	19	19	0	FUT4,3_prime_UTR_variant,,ENST00000358752,;RP11-867G2.8,intron_variant,,ENST00000536540,;RP11-867G2.8,intron_variant,,ENST00000537874,;PIWIL4,intron_variant,,ENST00000543336,;PIWIL4,intron_variant,,ENST00000446230,;	A	ENSG00000196371	ENST00000358752	Transcript	3_prime_UTR_variant	3672	.	.	.	.	.	.	.	1	FUT4	HGNC	4015	protein_coding	YES	CCDS8301.1	ENSP00000351602	FUT4_HUMAN	.	UPI000002CC7E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTGAAAAG	.	5	ESCA
IGF1	0	.	GRCh37	12	102813302	102813302	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387G>T	p.Met129Ile	p.M129I	ENST00000307046	3/4	18	14	4	34	34	0	IGF1,missense_variant,p.Met113Ile,ENST00000424202,;IGF1,missense_variant,p.Met110Ile,ENST00000392905,;IGF1,missense_variant,p.Met129Ile,ENST00000307046,;IGF1,missense_variant,p.Met129Ile,ENST00000456098,;IGF1,missense_variant,p.Met129Ile,ENST00000337514,;IGF1,missense_variant,p.Met129Ile,ENST00000392904,;IGF1,upstream_gene_variant,,ENST00000481539,;	A	ENSG00000017427	ENST00000307046	Transcript	missense_variant	569	387	129	M/I	atG/atT	.	.	.	-1	IGF1	HGNC	5464	protein_coding	YES	CCDS44962.1	ENSP00000302665	IGF1_HUMAN	Q6LD41_HUMAN	UPI0000115ED4	.	tolerated(0.36)	benign(0.126)	3/4	.	hmmpanther:PTHR11454,hmmpanther:PTHR11454:SF4,Prints_domain:PR02005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGGCATGTC	.	4	ESCA
PWP1	0	.	GRCh37	12	108082471	108082471	+	Missense_Mutation	SNP	C	C	T	rs781659412	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211C>T	p.Arg71Cys	p.R71C	ENST00000412830	3/15	44	32	11	31	31	0	PWP1,missense_variant,p.Arg9Cys,ENST00000547995,;PWP1,missense_variant,p.Arg71Cys,ENST00000412830,;PWP1,missense_variant,p.Arg9Cys,ENST00000541166,;PWP1,missense_variant,p.Arg71Cys,ENST00000552760,;PWP1,upstream_gene_variant,,ENST00000547120,;	T	ENSG00000136045	ENST00000412830	Transcript	missense_variant	379	211	71	R/C	Cgc/Tgc	rs781659412,COSM415640	.	.	1	PWP1	HGNC	17015	protein_coding	YES	CCDS9114.1	ENSP00000387365	PWP1_HUMAN	Q86X79_HUMAN,Q05BL3_HUMAN,F8VZ56_HUMAN,B4DJV5_HUMAN	UPI0000132B9C	.	tolerated(0.05)	benign(0.132)	3/15	.	hmmpanther:PTHR14091	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCACGCCCA	byFrequency	5	ESCA
VSIG10	0	.	GRCh37	12	118533516	118533516	+	Silent	SNP	C	C	T	rs117781232	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.183G>A	p.%3D	p.S61S	ENST00000359236	2/9	88	42	45	91	91	0	VSIG10,synonymous_variant,p.%3D,ENST00000359236,;VSIG10,synonymous_variant,p.%3D,ENST00000538357,;VSIG10,non_coding_transcript_exon_variant,,ENST00000542011,;VSIG10,non_coding_transcript_exon_variant,,ENST00000536905,;VSIG10,intron_variant,,ENST00000541855,;	T	ENSG00000176834	ENST00000359236	Transcript	synonymous_variant	460	183	61	S	tcG/tcA	rs117781232,COSM293038	.	.	-1	VSIG10	HGNC	26078	protein_coding	YES	CCDS44992.1	ENSP00000352172	VSI10_HUMAN	.	UPI000007385F	.	.	.	2/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF516,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,SMART_domains:SM00408,SMART_domains:SM00406,Superfamily_domains:SSF48726	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0002	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCCGAGTT	byCluster|by1000G	5	ESCA
PXN	0	.	GRCh37	12	120648834	120648834	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1283C>A	.	.	ENST00000267257	11/11	32	9	23	23	23	0	PXN,3_prime_UTR_variant,,ENST00000228307,;PXN,3_prime_UTR_variant,,ENST00000458477,;PXN,3_prime_UTR_variant,,ENST00000267257,;PXN,3_prime_UTR_variant,,ENST00000424649,;PXN,3_prime_UTR_variant,,ENST00000397506,;PXN,3_prime_UTR_variant,,ENST00000536957,;PXN,downstream_gene_variant,,ENST00000550795,;PXN-AS1,non_coding_transcript_exon_variant,,ENST00000535200,;PXN-AS1,non_coding_transcript_exon_variant,,ENST00000539446,;PXN-AS1,intron_variant,,ENST00000542265,;PXN-AS1,downstream_gene_variant,,ENST00000538804,;PXN-AS1,downstream_gene_variant,,ENST00000542314,;PXN,downstream_gene_variant,,ENST00000538144,;PXN,non_coding_transcript_exon_variant,,ENST00000323871,;	T	ENSG00000089159	ENST00000267257	Transcript	3_prime_UTR_variant	3232	.	.	.	.	.	.	.	-1	PXN	HGNC	9718	protein_coding	YES	CCDS58281.1	ENSP00000267257	PAXI_HUMAN	F8W1E0_HUMAN,F8W0K8_HUMAN,F8W0G0_HUMAN	UPI000013C8CD	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTGATGGC	.	5	ESCA
LRRC43	0	.	GRCh37	12	122676049	122676049	+	Missense_Mutation	SNP	G	G	A	rs756689259	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>A	p.Val342Met	p.V342M	ENST00000339777	6/12	70	31	39	67	67	0	LRRC43,missense_variant,p.Val342Met,ENST00000339777,;LRRC43,missense_variant,p.Val157Met,ENST00000425921,;LRRC43,downstream_gene_variant,,ENST00000537729,;LRRC43,intron_variant,,ENST00000541498,;LRRC43,downstream_gene_variant,,ENST00000538800,;LRRC43,downstream_gene_variant,,ENST00000537113,;	A	ENSG00000158113	ENST00000339777	Transcript	missense_variant	1052	1024	342	V/M	Gtg/Atg	rs756689259	.	.	1	LRRC43	HGNC	28562	protein_coding	YES	CCDS45001.1	ENSP00000344233	LRC43_HUMAN	F5H0N3_HUMAN	UPI00015347BE	.	deleterious(0)	probably_damaging(0.999)	6/12	.	hmmpanther:PTHR10588,hmmpanther:PTHR10588:SF224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTACGTGACC	.	5	ESCA
CACNA1C	0	.	GRCh37	12	2693763	2693763	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2319G>T	p.Lys773Asn	p.K773N	ENST00000347598	16/49	53	28	25	49	49	0	CACNA1C,missense_variant,p.Lys773Asn,ENST00000399644,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399595,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000406454,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399617,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000347598,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000402845,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000327702,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399634,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399641,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399603,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399629,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000480911,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399601,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399597,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399655,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399606,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399637,;CACNA1C,missense_variant,p.Lys798Asn,ENST00000335762,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399621,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399638,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399591,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000344100,;CACNA1C,missense_variant,p.Lys773Asn,ENST00000399649,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000465278,;	T	ENSG00000151067	ENST00000347598	Transcript	missense_variant	2319	2319	773	K/N	aaG/aaT	.	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	tolerated(0.06)	benign(0.211)	16/49	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGGAGAG	.	5	ESCA
OVCH1	0	.	GRCh37	12	29596332	29596332	+	Missense_Mutation	SNP	C	C	T	rs370805015	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3119G>A	p.Arg1040His	p.R1040H	ENST00000318184	25/28	83	57	25	43	43	0	OVCH1,missense_variant,p.Arg1040His,ENST00000318184,;OVCH1,missense_variant,p.Arg65His,ENST00000537054,;OVCH1-AS1,intron_variant,,ENST00000550906,;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,;OVCH1,missense_variant,p.Arg76His,ENST00000539117,;	T	ENSG00000187950	ENST00000318184	Transcript	missense_variant	3119	3119	1040	R/H	cGt/cAt	rs370805015	.	.	-1	OVCH1	HGNC	23080	protein_coding	YES	.	ENSP00000326708	OVCH1_HUMAN	.	UPI000040640A	.	tolerated(0.35)	benign(0)	25/28	.	hmmpanther:PTHR24259,hmmpanther:PTHR24259:SF64,Gene3D:2.60.120.290,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	T:0.0003	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACACGCAGA	byFrequency|byCluster	5	ESCA
TULP3	0	.	GRCh37	12	3000140	3000140	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27T>G	p.Ser9Arg	p.S9R	ENST00000397132	1/12	41	32	9	132	132	0	TULP3,missense_variant,p.Ser9Arg,ENST00000397132,;TULP3,missense_variant,p.Ser9Arg,ENST00000448120,;TULP3,intron_variant,,ENST00000544943,;RHNO1,downstream_gene_variant,,ENST00000461997,;RHNO1,downstream_gene_variant,,ENST00000366285,;RHNO1,downstream_gene_variant,,ENST00000538700,;RHNO1,downstream_gene_variant,,ENST00000538636,;RHNO1,downstream_gene_variant,,ENST00000489288,;RHNO1,downstream_gene_variant,,ENST00000536063,;RHNO1,downstream_gene_variant,,ENST00000464682,;TULP3,missense_variant,p.Ser9Arg,ENST00000538354,;TULP3,missense_variant,p.Ser9Arg,ENST00000545331,;TULP3,intron_variant,,ENST00000540184,;RHNO1,downstream_gene_variant,,ENST00000535978,;	G	ENSG00000078246	ENST00000397132	Transcript	missense_variant	68	27	9	S/R	agT/agG	.	.	.	1	TULP3	HGNC	12425	protein_coding	YES	CCDS53737.1	ENSP00000380321	.	F8WBZ9_HUMAN,F5H7B9_HUMAN	UPI00001FBDC0	.	deleterious_low_confidence(0)	benign(0.048)	1/12	.	hmmpanther:PTHR16517,hmmpanther:PTHR16517:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAGTCCCAG	.	5	ESCA
EFCAB4B	0	.	GRCh37	12	3782646	3782646	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.637G>A	p.Glu213Lys	p.E213K	ENST00000440314	7/20	83	78	5	59	59	0	EFCAB4B,missense_variant,p.Glu213Lys,ENST00000444507,;EFCAB4B,missense_variant,p.Glu213Lys,ENST00000252322,;EFCAB4B,missense_variant,p.Glu213Lys,ENST00000440314,;EFCAB4B,missense_variant,p.Glu16Lys,ENST00000333750,;	T	ENSG00000130038	ENST00000440314	Transcript	missense_variant	1111	637	213	E/K	Gag/Aag	.	.	.	-1	EFCAB4B	HGNC	28657	protein_coding	YES	CCDS44803.1	ENSP00000409382	EFC4B_HUMAN	.	UPI00017A8807	.	tolerated(0.39)	benign(0.009)	7/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22621,hmmpanther:PTHR22621:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCTCATGGG	.	2	ESCA
LRRK2	0	.	GRCh37	12	40693029	40693029	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3466G>C	p.Glu1156Gln	p.E1156Q	ENST00000298910	25/51	67	41	26	60	60	0	LRRK2,missense_variant,p.Glu1156Gln,ENST00000343742,;LRRK2,missense_variant,p.Glu1156Gln,ENST00000298910,;LRRK2,missense_variant,p.Glu171Gln,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,;	C	ENSG00000188906	ENST00000298910	Transcript	missense_variant	3524	3466	1156	E/Q	Gag/Cag	.	.	.	1	LRRK2	HGNC	18618	protein_coding	YES	CCDS31774.1	ENSP00000298910	LRRK2_HUMAN	.	UPI00006C128E	.	deleterious(0)	possibly_damaging(0.756)	25/51	.	hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF417,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTGGAGAGT	.	5	ESCA
GLI1	0	.	GRCh37	12	57860033	57860033	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.773G>A	p.Ser258Asn	p.S258N	ENST00000228682	8/12	46	26	20	58	58	0	GLI1,missense_variant,p.Ser258Asn,ENST00000228682,;GLI1,missense_variant,p.Ser217Asn,ENST00000546141,;GLI1,missense_variant,p.Ser217Asn,ENST00000528467,;GLI1,missense_variant,p.Ser130Asn,ENST00000532291,;GLI1,missense_variant,p.Ser130Asn,ENST00000543426,;GLI1,downstream_gene_variant,,ENST00000528432,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,;	A	ENSG00000111087	ENST00000228682	Transcript	missense_variant	864	773	258	S/N	aGc/aAc	.	.	.	1	GLI1	HGNC	4317	protein_coding	YES	CCDS8940.1	ENSP00000228682	GLI1_HUMAN	F5H6H8_HUMAN,E9PQQ1_HUMAN,E9PIB9_HUMAN,B1Q2M2_HUMAN	UPI000012B607	.	tolerated(1)	probably_damaging(0.939)	8/12	.	PROSITE_profiles:PS50157,hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACAGCGAGC	.	5	ESCA
VWF	0	.	GRCh37	12	6132813	6132813	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3363G>A	p.%3D	p.R1121R	ENST00000261405	25/52	161	106	55	223	223	0	VWF,synonymous_variant,p.%3D,ENST00000261405,;VWF,intron_variant,,ENST00000538635,;VWF,upstream_gene_variant,,ENST00000539641,;	T	ENSG00000110799	ENST00000261405	Transcript	synonymous_variant	3618	3363	1121	R	agG/agA	.	.	.	-1	VWF	HGNC	12726	protein_coding	YES	CCDS8539.1	ENSP00000261405	VWF_HUMAN	H2DLA2_HUMAN	UPI00001AE7EE	.	.	.	25/52	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF259,Pfam_domain:PF08742,PIRSF_domain:PIRSF002495,SMART_domains:SM00832	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGTCCTCCA	.	5	ESCA
C12orf66	0	.	GRCh37	12	64609598	64609598	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381G>A	p.%3D	p.E127E	ENST00000398055	2/3	36	20	16	53	53	0	C12orf66,synonymous_variant,p.%3D,ENST00000544871,;C12orf66,synonymous_variant,p.%3D,ENST00000311915,;C12orf66,synonymous_variant,p.%3D,ENST00000398055,;	T	ENSG00000174206	ENST00000398055	Transcript	synonymous_variant	435	381	127	E	gaG/gaA	.	.	.	-1	C12orf66	HGNC	26517	protein_coding	YES	CCDS41803.1	ENSP00000381132	CL066_HUMAN	.	UPI000013F222	.	.	.	2/3	.	hmmpanther:PTHR31581,hmmpanther:PTHR31581:SF1,Pfam_domain:PF09404,Superfamily_domains:0053959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGCTCTGA	.	5	ESCA
E2F7	0	.	GRCh37	12	77421782	77421783	+	Frame_Shift_Del	DEL	AG	AG	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2020_2021delCT	p.Leu674CysfsTer4	p.L674Cfs*4	ENST00000322886	11/13	41	32	9	48	48	0	E2F7,frameshift_variant,p.Leu674CysfsTer4,ENST00000416496,;E2F7,frameshift_variant,p.Leu674CysfsTer4,ENST00000322886,;E2F7,frameshift_variant,p.Leu674CysfsTer4,ENST00000550669,;	-	ENSG00000165891	ENST00000322886	Transcript	frameshift_variant	2256-2257	2020-2021	674	L/X	CTt/t	.	.	.	-1	E2F7	HGNC	23820	protein_coding	YES	CCDS9016.1	ENSP00000323246	E2F7_HUMAN	F8VXV5_HUMAN,F8VSE7_HUMAN	UPI00001B64A1	.	.	.	11/13	.	hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAACAAGAGAGT	.	3	ESCA
FGF14	0	.	GRCh37	13	102375053	102375053	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128C>G	.	.	ENST00000376131	5/5	25	13	12	28	28	0	FGF14,3_prime_UTR_variant,,ENST00000376131,;ITGBL1,downstream_gene_variant,,ENST00000490242,;FGF14,downstream_gene_variant,,ENST00000376143,;ITGBL1,downstream_gene_variant,,ENST00000545560,;ITGBL1,intron_variant,,ENST00000415285,;	C	ENSG00000102466	ENST00000376131	Transcript	3_prime_UTR_variant	983	.	.	.	.	.	.	.	-1	FGF14	HGNC	3671	protein_coding	YES	CCDS9500.1	ENSP00000365301	FGF14_HUMAN	.	UPI000000D898	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCGGAGACA	.	5	ESCA
MICU2	0	.	GRCh37	13	22067385	22067385	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3A>G	.	.	ENST00000382374	12/12	71	46	25	30	30	0	MICU2,3_prime_UTR_variant,,ENST00000382374,;MICU2,non_coding_transcript_exon_variant,,ENST00000460488,;MICU2,non_coding_transcript_exon_variant,,ENST00000478700,;MICU2,non_coding_transcript_exon_variant,,ENST00000479790,;	C	ENSG00000165487	ENST00000382374	Transcript	3_prime_UTR_variant	1374	.	.	.	.	.	.	.	-1	MICU2	HGNC	31830	protein_coding	YES	CCDS9297.1	ENSP00000371811	MICU2_HUMAN	.	UPI0000035DB8	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTTTATTA	.	5	ESCA
PAN3	0	.	GRCh37	13	28866944	28866944	+	3'Flank	SNP	A	A	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000380958	.	32	17	15	10	10	0	PAN3,3_prime_UTR_variant,,ENST00000399613,;PAN3,3_prime_UTR_variant,,ENST00000282391,;PAN3,downstream_gene_variant,,ENST00000380958,;	T	ENSG00000152520	ENST00000380958	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	268	1	PAN3	HGNC	29991	protein_coding	YES	CCDS9329.2	ENSP00000370345	PAN3_HUMAN	Q6ZMN5_HUMAN	UPI0001BE8112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATATGCAC	.	5	ESCA
FLT1	0	.	GRCh37	13	28897002	28897002	+	Missense_Mutation	SNP	C	C	T	rs554058758	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	21/30	43	24	18	41	41	0	FLT1,missense_variant,p.Val178Ile,ENST00000540678,;FLT1,missense_variant,p.Val960Ile,ENST00000282397,;FLT1,upstream_gene_variant,,ENST00000543394,;	T	ENSG00000102755	ENST00000282397	Transcript	missense_variant	3130	2878	960	V/I	Gtc/Atc	rs554058758,COSM1366224	.	.	-1	FLT1	HGNC	3763	protein_coding	YES	CCDS9330.1	ENSP00000282397	VGFR1_HUMAN	S5U0M6_HUMAN,S5TRK2_HUMAN,L7RSL3_HUMAN,H9N1E8_HUMAN,H9N1E7_HUMAN	UPI000013DCDD	.	tolerated(0.2)	benign(0.034)	21/30	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF126,Pfam_domain:PF07714,SMART_domains:SM00219	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGACGCTAT	byFrequency|byCluster	5	ESCA
MTUS2	0	.	GRCh37	13	29600278	29600278	+	Silent	SNP	G	G	A	rs201515125	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1473G>A	p.%3D	p.T491T	ENST00000431530	1/14	57	26	31	60	60	0	MTUS2,synonymous_variant,p.%3D,ENST00000431530,;	A	ENSG00000132938	ENST00000431530	Transcript	synonymous_variant	1531	1473	491	T	acG/acA	rs201515125	.	.	1	MTUS2	HGNC	20595	protein_coding	YES	CCDS45022.1	ENSP00000392057	.	J3KQA9_HUMAN,B4DWQ4_HUMAN	UPI0000F734AC	.	.	.	1/14	.	hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGACGGAGGT	byCluster|by1000G	5	ESCA
HMGB1	0	.	GRCh37	13	31035081	31035081	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*413G>C	.	.	ENST00000405805	5/5	82	76	6	43	42	1	HMGB1,3_prime_UTR_variant,,ENST00000405805,;HMGB1,3_prime_UTR_variant,,ENST00000339872,;HMGB1,3_prime_UTR_variant,,ENST00000399494,;HMGB1,3_prime_UTR_variant,,ENST00000399489,;HMGB1,3_prime_UTR_variant,,ENST00000341423,;HMGB1,downstream_gene_variant,,ENST00000398908,;HMGB1,downstream_gene_variant,,ENST00000326004,;HMGB1,downstream_gene_variant,,ENST00000490788,;HMGB1,downstream_gene_variant,,ENST00000468384,;	G	ENSG00000189403	ENST00000405805	Transcript	3_prime_UTR_variant	2002	.	.	.	.	.	.	.	-1	HMGB1	HGNC	4983	protein_coding	YES	CCDS9335.1	ENSP00000384678	HMGB1_HUMAN	Q9NYD7_HUMAN,Q5T7C0_HUMAN	UPI00000015ED	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAAACAGCTG	.	2	ESCA
FRY	0	.	GRCh37	13	32869785	32869785	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*188C>G	.	.	ENST00000380250	61/61	24	14	10	22	22	0	FRY,3_prime_UTR_variant,,ENST00000380250,;FRY,downstream_gene_variant,,ENST00000380217,;FRY,downstream_gene_variant,,ENST00000542859,;RP11-37E23.5,upstream_gene_variant,,ENST00000418076,;	G	ENSG00000073910	ENST00000380250	Transcript	3_prime_UTR_variant	9726	.	.	.	.	.	.	.	1	FRY	HGNC	20367	protein_coding	YES	CCDS41875.1	ENSP00000369600	FRY_HUMAN	Q96KW3_HUMAN,F5H4D2_HUMAN	UPI000046FD40	.	.	.	61/61	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAGCTTAGA	.	5	ESCA
MYCBP2	0	.	GRCh37	13	77657220	77657220	+	Silent	SNP	T	T	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10869A>C	p.%3D	p.S3623S	ENST00000544440	63/83	59	32	26	52	52	0	MYCBP2,synonymous_variant,p.%3D,ENST00000429715,;MYCBP2,synonymous_variant,p.%3D,ENST00000544440,;MYCBP2,synonymous_variant,p.%3D,ENST00000357337,;MYCBP2,synonymous_variant,p.%3D,ENST00000407578,;MYCBP2-AS1,non_coding_transcript_exon_variant,,ENST00000422231,;MYCBP2-AS1,intron_variant,,ENST00000450627,;MYCBP2-AS1,intron_variant,,ENST00000593933,;MYCBP2-AS1,intron_variant,,ENST00000448470,;MYCBP2-AS2,upstream_gene_variant,,ENST00000428716,;	G	ENSG00000005810	ENST00000544440	Transcript	synonymous_variant	10887	10869	3623	S	tcA/tcC	.	.	.	-1	MYCBP2	HGNC	23386	protein_coding	YES	.	ENSP00000444596	MYCB2_HUMAN	.	UPI0000212757	.	.	.	63/83	.	hmmpanther:PTHR12846:SF14,hmmpanther:PTHR12846	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTCTGAGAT	.	5	ESCA
PPP1R13B	0	.	GRCh37	14	104220545	104220545	+	Missense_Mutation	SNP	G	G	A	rs776014974	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493C>T	p.Arg165Cys	p.R165C	ENST00000202556	6/17	23	14	9	18	18	0	PPP1R13B,missense_variant,p.Arg165Cys,ENST00000202556,;PPP1R13B,downstream_gene_variant,,ENST00000555734,;PPP1R13B,non_coding_transcript_exon_variant,,ENST00000554106,;PPP1R13B,intron_variant,,ENST00000556325,;PPP1R13B,3_prime_UTR_variant,,ENST00000557082,;	A	ENSG00000088808	ENST00000202556	Transcript	missense_variant	776	493	165	R/C	Cgt/Tgt	rs776014974	.	.	-1	PPP1R13B	HGNC	14950	protein_coding	YES	CCDS41997.1	ENSP00000202556	ASPP1_HUMAN	G3V5J1_HUMAN	UPI000049DDC7	.	deleterious(0.02)	benign(0.021)	6/17	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24131,hmmpanther:PTHR24131:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACGGCGCT	.	5	ESCA
IGHD	0	.	GRCh37	14	106307236	106307236	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801+1G>A	.	p.X267_splice	ENST00000390556	.	57	43	14	78	78	0	IGHD,splice_donor_variant,,ENST00000390556,;	T	ENSG00000211898	ENST00000390556	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	IGHD	HGNC	5480	IG_C_gene	YES	.	ENSP00000374998	.	.	UPI000173A6A0	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCACCGGGT	.	5	ESCA
IGHV7-81	0	.	GRCh37	14	107282902	107282902	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241C>A	p.Gln81Lys	p.Q81K	ENST00000390639	2/2	160	137	23	106	106	0	IGHV7-81,missense_variant,p.Gln81Lys,ENST00000390639,;IGHVIII-82,downstream_gene_variant,,ENST00000522058,;IGHV4-80,upstream_gene_variant,,ENST00000522457,;	T	ENSG00000211979	ENST00000390639	Transcript	missense_variant	295	241	81	Q/K	Cag/Aag	.	.	.	-1	IGHV7-81	HGNC	5669	IG_V_gene	YES	.	ENSP00000375048	.	Q6PIL0_HUMAN	UPI000011AABF	.	tolerated(0.07)	benign(0.253)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF85,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTGGGCAT	.	4	ESCA
MYH7	0	.	GRCh37	14	23894041	23894041	+	Missense_Mutation	SNP	C	C	A	rs746153814	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2616G>T	p.Glu872Asp	p.E872D	ENST00000355349	22/40	21	16	5	30	30	0	MYH7,missense_variant,p.Glu872Asp,ENST00000355349,;	A	ENSG00000092054	ENST00000355349	Transcript	missense_variant	2779	2616	872	E/D	gaG/gaT	rs746153814	.	.	-1	MYH7	HGNC	7577	protein_coding	YES	CCDS9601.1	ENSP00000347507	MYH7_HUMAN	Q59EV3_HUMAN,L0L5E6_HUMAN,A8CLN2_HUMAN,A8CLL2_HUMAN,A6N931_HUMAN,A6N930_HUMAN	UPI000014019B	.	deleterious(0.04)	benign(0.152)	22/40	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF279,hmmpanther:PTHR13140,Gene3D:1.20.5.340,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E875D|c.2625G>C|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGCTCCTT	.	5	ESCA
NFATC4	0	.	GRCh37	14	24839449	24839449	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1034C>T	p.Pro345Leu	p.P345L	ENST00000413692	3/10	45	24	21	89	89	0	NFATC4,missense_variant,p.Pro282Leu,ENST00000554050,;NFATC4,missense_variant,p.Pro270Leu,ENST00000422617,;NFATC4,missense_variant,p.Pro282Leu,ENST00000250373,;NFATC4,missense_variant,p.Pro295Leu,ENST00000555590,;NFATC4,missense_variant,p.Pro270Leu,ENST00000556169,;NFATC4,missense_variant,p.Pro314Leu,ENST00000553469,;NFATC4,missense_variant,p.Pro314Leu,ENST00000539237,;NFATC4,missense_variant,p.Pro212Leu,ENST00000554661,;NFATC4,missense_variant,p.Pro270Leu,ENST00000555453,;NFATC4,missense_variant,p.Pro282Leu,ENST00000553708,;NFATC4,missense_variant,p.Pro212Leu,ENST00000557451,;NFATC4,missense_variant,p.Pro345Leu,ENST00000413692,;NFATC4,missense_variant,p.Pro314Leu,ENST00000556279,;NFATC4,missense_variant,p.Pro212Leu,ENST00000553879,;NFATC4,missense_variant,p.Pro295Leu,ENST00000424781,;NFATC4,missense_variant,p.Pro345Leu,ENST00000554591,;NFATC4,missense_variant,p.Pro295Leu,ENST00000554966,;NFATC4,missense_variant,p.Pro212Leu,ENST00000554344,;NFATC4,intron_variant,,ENST00000554779,;NFATC4,upstream_gene_variant,,ENST00000554473,;NFATC4,upstream_gene_variant,,ENST00000555167,;NFATC4,upstream_gene_variant,,ENST00000557767,;NFATC4,upstream_gene_variant,,ENST00000556759,;NFATC4,downstream_gene_variant,,ENST00000557674,;NFATC4,upstream_gene_variant,,ENST00000555802,;NFATC4,upstream_gene_variant,,ENST00000555393,;NFATC4,downstream_gene_variant,,ENST00000554903,;NFATC4,non_coding_transcript_exon_variant,,ENST00000440487,;NFATC4,non_coding_transcript_exon_variant,,ENST00000556957,;NFATC4,non_coding_transcript_exon_variant,,ENST00000556302,;NFATC4,non_coding_transcript_exon_variant,,ENST00000554655,;NFATC4,intron_variant,,ENST00000557028,;	T	ENSG00000100968	ENST00000413692	Transcript	missense_variant	1178	1034	345	P/L	cCa/cTa	.	.	.	1	NFATC4	HGNC	7778	protein_coding	YES	CCDS45089.1	ENSP00000388910	NFAC4_HUMAN	G3V4K1_HUMAN	UPI00017BD050	.	deleterious(0)	probably_damaging(1)	3/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12533,hmmpanther:PTHR12533:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCCAGCTC	.	5	ESCA
FBXO34	0	.	GRCh37	14	55818294	55818294	+	Missense_Mutation	SNP	G	G	A	rs767666103	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1186G>A	p.Ala396Thr	p.A396T	ENST00000313833	2/2	61	24	36	39	39	0	FBXO34,missense_variant,p.Ala396Thr,ENST00000440021,;FBXO34,missense_variant,p.Ala396Thr,ENST00000313833,;FBXO34,intron_variant,,ENST00000557647,;FBXO34,downstream_gene_variant,,ENST00000555087,;FBXO34,downstream_gene_variant,,ENST00000554940,;FBXO34,missense_variant,p.Ala262Thr,ENST00000555280,;	A	ENSG00000178974	ENST00000313833	Transcript	missense_variant	1431	1186	396	A/T	Gcc/Acc	rs767666103	.	.	1	FBXO34	HGNC	20201	protein_coding	YES	CCDS32086.1	ENSP00000313159	FBX34_HUMAN	G3V2U9_HUMAN	UPI00001FD5AD	.	tolerated(0.53)	benign(0.138)	2/2	.	hmmpanther:PTHR16271:SF11,hmmpanther:PTHR16271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTGCCGTG	.	5	ESCA
C14orf37	0	.	GRCh37	14	58471477	58471477	+	Missense_Mutation	SNP	C	C	A	rs746972575	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2302G>T	p.Asp768Tyr	p.D768Y	ENST00000267485	8/8	95	42	53	36	36	0	C14orf37,missense_variant,p.Asp768Tyr,ENST00000267485,;C14orf37,upstream_gene_variant,,ENST00000556788,;	A	ENSG00000139971	ENST00000267485	Transcript	missense_variant	2497	2302	768	D/Y	Gac/Tac	rs746972575	.	.	-1	C14orf37	HGNC	19846	protein_coding	YES	CCDS32089.1	ENSP00000267485	CN037_HUMAN	.	UPI000000CC37	.	deleterious(0)	probably_damaging(0.963)	8/8	.	hmmpanther:PTHR21585:SF0,hmmpanther:PTHR21585	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGTCGGCTA	byFrequency	5	ESCA
SIX6	0	.	GRCh37	14	60976162	60976162	+	Missense_Mutation	SNP	G	G	T	rs760675929	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.46G>T	p.Gly16Trp	p.G16W	ENST00000327720	1/2	21	13	8	40	40	0	SIX6,missense_variant,p.Gly16Trp,ENST00000327720,;C14orf39,intron_variant,,ENST00000556799,;	T	ENSG00000184302	ENST00000327720	Transcript	missense_variant	494	46	16	G/W	Ggg/Tgg	rs760675929	.	.	1	SIX6	HGNC	10892	protein_coding	YES	CCDS9747.1	ENSP00000328596	SIX6_HUMAN	Q6P051_HUMAN,Q5M8S8_HUMAN	UPI000013E4DB	.	deleterious(0.01)	possibly_damaging(0.785)	1/2	.	hmmpanther:PTHR10390:SF12,hmmpanther:PTHR10390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGGGGTA	.	5	ESCA
FUT8	0	.	GRCh37	14	66188719	66188719	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1062C>T	p.%3D	p.G354G	ENST00000360689	8/11	70	49	21	53	53	0	FUT8,synonymous_variant,p.%3D,ENST00000394585,;FUT8,synonymous_variant,p.%3D,ENST00000557164,;FUT8,synonymous_variant,p.%3D,ENST00000360689,;FUT8,synonymous_variant,p.%3D,ENST00000358307,;FUT8,synonymous_variant,p.%3D,ENST00000394586,;FUT8,intron_variant,,ENST00000417683,;FUT8,downstream_gene_variant,,ENST00000554765,;FUT8,downstream_gene_variant,,ENST00000557536,;FUT8,intron_variant,,ENST00000342677,;	T	ENSG00000033170	ENST00000360689	Transcript	synonymous_variant	2789	1062	354	G	ggC/ggT	.	.	.	1	FUT8	HGNC	4019	protein_coding	YES	CCDS9775.1	ENSP00000353910	FUT8_HUMAN	Q546E0_HUMAN,G3V5Z4_HUMAN,G3V5E3_HUMAN,G3V530_HUMAN,G3V509_HUMAN,G3V4A8_HUMAN	UPI000000DCC9	.	.	.	8/11	.	PROSITE_profiles:PS51659,hmmpanther:PTHR13132,PIRSF_domain:PIRSF000472	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGGCTTCAA	.	5	ESCA
SERPINA9	0	.	GRCh37	14	94935585	94935585	+	Missense_Mutation	SNP	G	G	A	rs575429531	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647C>T	p.Thr216Met	p.T216M	ENST00000337425	2/5	32	15	17	52	52	0	SERPINA9,missense_variant,p.Thr180Met,ENST00000546329,;SERPINA9,missense_variant,p.Thr198Met,ENST00000380365,;SERPINA9,missense_variant,p.Thr118Met,ENST00000448305,;SERPINA9,missense_variant,p.Thr116Met,ENST00000298845,;SERPINA9,missense_variant,p.Thr67Met,ENST00000424550,;SERPINA9,missense_variant,p.Thr216Met,ENST00000337425,;RP11-349I1.2,downstream_gene_variant,,ENST00000536735,;SERPINA9,downstream_gene_variant,,ENST00000539349,;SERPINA9,3_prime_UTR_variant,,ENST00000538527,;	A	ENSG00000170054	ENST00000337425	Transcript	missense_variant	722	647	216	T/M	aCg/aTg	rs575429531	.	.	-1	SERPINA9	HGNC	15995	protein_coding	YES	CCDS41982.1	ENSP00000337133	SPA9_HUMAN	.	UPI000024706E	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR11461:SF40,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:3.30.497.10,SMART_domains:SM00093,Superfamily_domains:SSF56574	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGTCAGA	by1000G	5	ESCA
LRRK1	0	.	GRCh37	15	101606863	101606863	+	Silent	SNP	C	C	T	rs772136882	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5787C>T	p.%3D	p.I1929I	ENST00000388948	33/34	59	37	22	82	82	0	LRRK1,synonymous_variant,p.%3D,ENST00000388948,;LRRK1,synonymous_variant,p.%3D,ENST00000284395,;RP11-505E24.2,intron_variant,,ENST00000559857,;LRRK1,non_coding_transcript_exon_variant,,ENST00000532145,;LRRK1,downstream_gene_variant,,ENST00000525395,;LRRK1,synonymous_variant,p.%3D,ENST00000526457,;LRRK1,3_prime_UTR_variant,,ENST00000531270,;LRRK1,3_prime_UTR_variant,,ENST00000525284,;	T	ENSG00000154237	ENST00000388948	Transcript	synonymous_variant	6146	5787	1929	I	atC/atT	rs772136882	.	.	1	LRRK1	HGNC	18608	protein_coding	YES	CCDS42086.1	ENSP00000373600	LRRK1_HUMAN	E9PMK9_HUMAN,E9PLF8_HUMAN,E9PK39_HUMAN,B3KSX5_HUMAN	UPI0000D4FE63	.	.	.	33/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTATCGTCAT	byFrequency	5	ESCA
SNORD115-27	0	.	GRCh37	15	25467313	25467313	+	3'Flank	SNP	C	C	G	rs746856333	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000364430	.	9	6	3	21	21	0	SNORD115-27,downstream_gene_variant,,ENST00000364430,;SNORD115-31,upstream_gene_variant,,ENST00000365318,;SNORD115-28,upstream_gene_variant,,ENST00000363931,;SNORD115-30,upstream_gene_variant,,ENST00000364117,;SNHG14,downstream_gene_variant,,ENST00000365067,;SNORD115-29,upstream_gene_variant,,ENST00000362834,;SNHG14,non_coding_transcript_exon_variant,,ENST00000453082,;SNHG14,non_coding_transcript_exon_variant,,ENST00000424208,;	G	ENSG00000201300	ENST00000364430	Transcript	downstream_gene_variant	.	.	.	.	.	rs746856333	.	1588	1	SNORD115-27	HGNC	33046	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGACCCTGA	.	2	ESCA
GABRA5	0	.	GRCh37	15	27184654	27184654	+	Intron	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725-418G>T	.	.	ENST00000335625	.	20	6	14	32	31	1	GABRB3,5_prime_UTR_variant,,ENST00000541819,;GABRA5,intron_variant,,ENST00000355395,;GABRA5,intron_variant,,ENST00000400081,;GABRA5,intron_variant,,ENST00000335625,;GABRA5,downstream_gene_variant,,ENST00000555182,;	T	ENSG00000186297	ENST00000335625	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GABRA5	HGNC	4079	protein_coding	YES	CCDS45194.1	ENSP00000335592	GBRA5_HUMAN	G3V408_HUMAN,G3V2Q9_HUMAN,G3V2K2_HUMAN,G3V2G8_HUMAN,G3V296_HUMAN,B4E1A2_HUMAN	UPI000002D731	.	.	.	.	8/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CCCTGGAGCCT	.	2	ESCA
HERC2	0	.	GRCh37	15	28441632	28441632	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8095G>C	p.Val2699Leu	p.V2699L	ENST00000261609	51/93	148	98	50	98	98	0	HERC2,missense_variant,p.Val2699Leu,ENST00000261609,;HERC2,non_coding_transcript_exon_variant,,ENST00000567869,;	G	ENSG00000128731	ENST00000261609	Transcript	missense_variant	8204	8095	2699	V/L	Gta/Cta	.	.	.	-1	HERC2	HGNC	4868	protein_coding	YES	CCDS10021.1	ENSP00000261609	HERC2_HUMAN	.	UPI00004578F7	.	.	benign(0.299)	51/93	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTACCAACT	.	5	ESCA
TMEM62	0	.	GRCh37	15	43476858	43476866	+	3'UTR	DEL	AGCAGGTGG	AGCAGGTGG	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	AGCAGGTGG	AGCAGGTGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*76_*84delCAGGTGGAG	.	.	ENST00000260403	14/14	35	27	8	53	53	0	TMEM62,3_prime_UTR_variant,,ENST00000564494,;TMEM62,3_prime_UTR_variant,,ENST00000260403,;CCNDBP1,upstream_gene_variant,,ENST00000356633,;CCNDBP1,upstream_gene_variant,,ENST00000300213,;RP11-473C18.3,intron_variant,,ENST00000565685,;EPB42,intron_variant,,ENST00000563128,;EPB42,upstream_gene_variant,,ENST00000570199,;TMEM62,downstream_gene_variant,,ENST00000569369,;TMEM62,non_coding_transcript_exon_variant,,ENST00000563859,;CCNDBP1,upstream_gene_variant,,ENST00000568936,;CCNDBP1,upstream_gene_variant,,ENST00000567690,;CCNDBP1,upstream_gene_variant,,ENST00000563065,;CCNDBP1,upstream_gene_variant,,ENST00000569745,;CCNDBP1,upstream_gene_variant,,ENST00000568507,;CCNDBP1,upstream_gene_variant,,ENST00000564630,;CCNDBP1,upstream_gene_variant,,ENST00000566515,;CCNDBP1,upstream_gene_variant,,ENST00000565296,;CCNDBP1,upstream_gene_variant,,ENST00000562553,;TMEM62,downstream_gene_variant,,ENST00000566122,;CCNDBP1,upstream_gene_variant,,ENST00000566833,;CCNDBP1,upstream_gene_variant,,ENST00000444658,;CCNDBP1,upstream_gene_variant,,ENST00000566882,;CCNDBP1,upstream_gene_variant,,ENST00000567434,;	-	ENSG00000137842	ENST00000260403	Transcript	3_prime_UTR_variant	2285-2293	.	.	.	.	.	.	.	1	TMEM62	HGNC	26269	protein_coding	YES	CCDS32210.1	ENSP00000260403	TMM62_HUMAN	H3BTT1_HUMAN,H3BPV2_HUMAN	UPI00004443FD	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCAGTAGCAGGTGGAGGGC	.	3	ESCA
PRTG	0	.	GRCh37	15	55964703	55964703	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1981C>T	p.Gln661Ter	p.Q661*	ENST00000389286	11/20	67	43	24	60	60	0	PRTG,stop_gained,p.Gln661Ter,ENST00000389286,;PRTG,stop_gained,p.Gln196Ter,ENST00000561465,;	A	ENSG00000166450	ENST00000389286	Transcript	stop_gained	2029	1981	661	Q/*	Cag/Tag	.	.	.	-1	PRTG	HGNC	26373	protein_coding	YES	CCDS42040.1	ENSP00000373937	PRTG_HUMAN	H0YKD6_HUMAN	UPI00001555A7	.	.	.	11/20	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,Pfam_domain:PF00041,hmmpanther:PTHR10489:SF20,hmmpanther:PTHR10489,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTGCTGCC	.	5	ESCA
PIF1	0	.	GRCh37	15	65108838	65108838	+	Missense_Mutation	SNP	C	C	T	rs766453021	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1801G>A	p.Val601Ile	p.V601I	ENST00000268043	12/13	60	40	20	92	92	0	PIF1,missense_variant,p.Val601Ile,ENST00000559239,;PIF1,missense_variant,p.Val601Ile,ENST00000333425,;PIF1,missense_variant,p.Val601Ile,ENST00000268043,;PIF1,downstream_gene_variant,,ENST00000559872,;PIF1,downstream_gene_variant,,ENST00000559522,;PIF1,downstream_gene_variant,,ENST00000558380,;PIF1,downstream_gene_variant,,ENST00000560444,;PIF1,downstream_gene_variant,,ENST00000558547,;	T	ENSG00000140451	ENST00000268043	Transcript	missense_variant	1896	1801	601	V/I	Gtt/Att	rs766453021	.	.	-1	PIF1	HGNC	26220	protein_coding	YES	CCDS10195.2	ENSP00000268043	PIF1_HUMAN	B2RPL7_HUMAN	UPI00005EDD9F	.	deleterious(0.02)	benign(0.122)	12/13	.	Superfamily_domains:SSF52540,hmmpanther:PTHR23274,HAMAP:MF_03176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGAACCGCCA	.	5	ESCA
CILP	0	.	GRCh37	15	65499281	65499281	+	Missense_Mutation	SNP	C	C	T	rs376150356	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263G>A	p.Arg88His	p.R88H	ENST00000261883	4/9	49	45	4	80	80	0	CILP,missense_variant,p.Arg88His,ENST00000261883,;	T	ENSG00000138615	ENST00000261883	Transcript	missense_variant	430	263	88	R/H	cGt/cAt	rs376150356,COSM1517265	.	.	-1	CILP	HGNC	1980	protein_coding	YES	CCDS10203.1	ENSP00000261883	CILP1_HUMAN	.	UPI000013D21B	.	deleterious(0.04)	benign(0.017)	4/9	.	hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF3,Pfam_domain:PF13330	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGGACGGGCA	byFrequency|byCluster	3	ESCA
SLC24A1	0	.	GRCh37	15	65916439	65916439	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21G>A	p.Met7Ile	p.M7I	ENST00000261892	2/10	36	24	12	36	36	0	SLC24A1,missense_variant,p.Met7Ile,ENST00000546330,;SLC24A1,missense_variant,p.Met7Ile,ENST00000399033,;SLC24A1,missense_variant,p.Met7Ile,ENST00000544319,;SLC24A1,missense_variant,p.Met7Ile,ENST00000339868,;SLC24A1,missense_variant,p.Met7Ile,ENST00000537259,;SLC24A1,missense_variant,p.Met7Ile,ENST00000261892,;SLC24A1,intron_variant,,ENST00000425561,;SLC24A1,downstream_gene_variant,,ENST00000535950,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000434116,;	A	ENSG00000074621	ENST00000261892	Transcript	missense_variant	308	21	7	M/I	atG/atA	.	.	.	1	SLC24A1	HGNC	10975	protein_coding	YES	CCDS45284.1	ENSP00000261892	NCKX1_HUMAN	.	UPI000013020C	.	.	benign(0)	2/10	.	hmmpanther:PTHR10846,hmmpanther:PTHR10846:SF6,TIGRFAM_domain:TIGR00927	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGGGGCC	.	5	ESCA
CORO2B	0	.	GRCh37	15	69003150	69003150	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.413G>A	p.Arg138Gln	p.R138Q	ENST00000566799	4/12	28	19	8	56	56	0	CORO2B,missense_variant,p.Arg138Gln,ENST00000566799,;CORO2B,missense_variant,p.Arg133Gln,ENST00000540068,;CORO2B,missense_variant,p.Arg133Gln,ENST00000261861,;CORO2B,missense_variant,p.Arg133Gln,ENST00000543950,;	A	ENSG00000103647	ENST00000566799	Transcript	missense_variant	442	413	138	R/Q	cGg/cAg	COSM1749291	.	.	1	CORO2B	HGNC	2256	protein_coding	YES	CCDS10229.2	ENSP00000454783	COR2B_HUMAN	B3KWB4_HUMAN	UPI0000E59C95	.	deleterious(0)	probably_damaging(1)	4/12	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF17,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCGGCGTG	.	5	ESCA
SENP8	0	.	GRCh37	15	72432600	72432600	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.636G>T	p.Lys212Asn	p.K212N	ENST00000544411	3/3	26	18	8	8	8	0	SENP8,missense_variant,p.Lys212Asn,ENST00000544411,;SENP8,missense_variant,p.Lys212Asn,ENST00000340912,;SENP8,missense_variant,p.Lys212Asn,ENST00000542035,;SENP8,missense_variant,p.Lys212Asn,ENST00000544171,;SENP8,downstream_gene_variant,,ENST00000564863,;SENP8,downstream_gene_variant,,ENST00000567794,;SENP8,downstream_gene_variant,,ENST00000564082,;RP11-2I17.4,downstream_gene_variant,,ENST00000568984,;RP11-2I17.1,downstream_gene_variant,,ENST00000478757,;	T	ENSG00000166192	ENST00000544411	Transcript	missense_variant	1123	636	212	K/N	aaG/aaT	.	.	.	1	SENP8	HGNC	22992	protein_coding	YES	CCDS10240.1	ENSP00000441753	SENP8_HUMAN	H3BTK5_HUMAN,H3BTJ8_HUMAN,H3BS71_HUMAN	UPI0000135852	.	deleterious(0.01)	possibly_damaging(0.906)	3/3	.	hmmpanther:PTHR22875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAAAGTAGCT	.	3	ESCA
GRAMD2	0	.	GRCh37	15	72456023	72456023	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.676C>G	p.Pro226Ala	p.P226A	ENST00000309731	9/12	21	16	5	31	31	0	GRAMD2,missense_variant,p.Pro226Ala,ENST00000309731,;GRAMD2,downstream_gene_variant,,ENST00000564129,;GRAMD2,downstream_gene_variant,,ENST00000570275,;GRAMD2,downstream_gene_variant,,ENST00000568594,;GRAMD2,non_coding_transcript_exon_variant,,ENST00000564184,;GRAMD2,non_coding_transcript_exon_variant,,ENST00000565233,;GRAMD2,non_coding_transcript_exon_variant,,ENST00000564773,;GRAMD2,non_coding_transcript_exon_variant,,ENST00000567662,;GRAMD2,non_coding_transcript_exon_variant,,ENST00000567029,;GRAMD2,downstream_gene_variant,,ENST00000567637,;GRAMD2,downstream_gene_variant,,ENST00000562288,;	C	ENSG00000175318	ENST00000309731	Transcript	missense_variant	690	676	226	P/A	Cct/Gct	.	.	.	-1	GRAMD2	HGNC	27287	protein_coding	YES	CCDS32283.1	ENSP00000311657	GRAM2_HUMAN	B4E188_HUMAN	UPI00001FE7DE	.	tolerated(0.08)	benign(0.354)	9/12	.	hmmpanther:PTHR23319:SF7,hmmpanther:PTHR23319	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAAGGGATGT	.	5	ESCA
CD276	0	.	GRCh37	15	74006619	74006619	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1322G>T	.	.	ENST00000318443	10/10	77	46	31	152	152	0	CD276,3_prime_UTR_variant,,ENST00000318443,;CD276,3_prime_UTR_variant,,ENST00000318424,;CD276,downstream_gene_variant,,ENST00000561176,;CD276,downstream_gene_variant,,ENST00000564751,;CD276,downstream_gene_variant,,ENST00000561213,;CD276,downstream_gene_variant,,ENST00000537340,;CD276,3_prime_UTR_variant,,ENST00000559073,;CD276,non_coding_transcript_exon_variant,,ENST00000559465,;CD276,downstream_gene_variant,,ENST00000559978,;CD276,downstream_gene_variant,,ENST00000560928,;	T	ENSG00000103855	ENST00000318443	Transcript	3_prime_UTR_variant	3229	.	.	.	.	.	.	.	1	CD276	HGNC	19137	protein_coding	YES	CCDS32288.1	ENSP00000320084	CD276_HUMAN	H0YN85_HUMAN,H0YLT8_HUMAN,H0YKQ9_HUMAN,H0YK59_HUMAN,H0YK40_HUMAN	UPI0000034C25	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTGCCCCC	.	5	ESCA
TTLL13	0	.	GRCh37	15	90807287	90807287	+	3'Flank	SNP	A	A	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000339615	.	52	32	20	51	51	0	TTLL13,missense_variant,p.Ser733Cys,ENST00000438251,;TTLL13,downstream_gene_variant,,ENST00000339615,;NGRN,upstream_gene_variant,,ENST00000379095,;NGRN,upstream_gene_variant,,ENST00000331497,;RP11-697E2.6,3_prime_UTR_variant,,ENST00000561573,;	T	ENSG00000213471	ENST00000339615	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4967	1	TTLL13	HGNC	32484	protein_coding	YES	.	ENSP00000345294	TTL13_HUMAN	.	UPI00005B2F05	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTAGCCGT	.	5	ESCA
TTLL13	0	.	GRCh37	15	90807288	90807288	+	3'Flank	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000339615	.	51	32	18	51	51	0	TTLL13,missense_variant,p.Ser733Thr,ENST00000438251,;TTLL13,downstream_gene_variant,,ENST00000339615,;NGRN,upstream_gene_variant,,ENST00000379095,;NGRN,upstream_gene_variant,,ENST00000331497,;RP11-697E2.6,splice_region_variant,,ENST00000561573,;	C	ENSG00000213471	ENST00000339615	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4968	1	TTLL13	HGNC	32484	protein_coding	YES	.	ENSP00000345294	TTL13_HUMAN	.	UPI00005B2F05	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTAGCCGTA	.	5	ESCA
ATF7IP2	0	.	GRCh37	16	10575953	10575953	+	Silent	SNP	T	T	A	rs558578447	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1896T>A	p.%3D	p.I632I	ENST00000396560	12/12	65	45	20	28	28	0	ATF7IP2,synonymous_variant,p.%3D,ENST00000396560,;ATF7IP2,synonymous_variant,p.%3D,ENST00000543967,;ATF7IP2,synonymous_variant,p.%3D,ENST00000356427,;ATF7IP2,3_prime_UTR_variant,,ENST00000396559,;ATF7IP2,3_prime_UTR_variant,,ENST00000324570,;ATF7IP2,3_prime_UTR_variant,,ENST00000535850,;ATF7IP2,3_prime_UTR_variant,,ENST00000568027,;ATF7IP2,downstream_gene_variant,,ENST00000565450,;	A	ENSG00000166669	ENST00000396560	Transcript	synonymous_variant	2123	1896	632	I	atT/atA	rs558578447	.	.	1	ATF7IP2	HGNC	20397	protein_coding	YES	CCDS10540.1	ENSP00000379808	MCAF2_HUMAN	H3BUP1_HUMAN,H3BR07_HUMAN,H3BPC9_HUMAN,H3BNE6_HUMAN,B4DKH3_HUMAN	UPI00001FEDD8	.	.	.	12/12	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23210:SF6,hmmpanther:PTHR23210	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATTAAAGC	by1000G	5	ESCA
CLEC16A	0	.	GRCh37	16	11097121	11097121	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1262A>C	p.Glu421Ala	p.E421A	ENST00000409790	11/24	61	43	18	101	101	0	CLEC16A,missense_variant,p.Glu421Ala,ENST00000409790,;CLEC16A,splice_region_variant,,ENST00000409552,;CLEC16A,non_coding_transcript_exon_variant,,ENST00000494853,;	C	ENSG00000038532	ENST00000409790	Transcript	missense_variant	1492	1262	421	E/A	gAg/gCg	.	.	.	1	CLEC16A	HGNC	29013	protein_coding	YES	CCDS45409.1	ENSP00000387122	CL16A_HUMAN	.	UPI0000253BAD	.	tolerated(0.08)	benign(0.146)	11/24	.	hmmpanther:PTHR21481	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAGAGGGTG	.	5	ESCA
IFT140	0	.	GRCh37	16	1621406	1621406	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1652+2T>C	.	p.X551_splice	ENST00000426508	.	85	49	36	95	95	0	IFT140,splice_donor_variant,,ENST00000426508,;IFT140,splice_donor_variant,,ENST00000439987,;IFT140,splice_donor_variant,,ENST00000565298,;IFT140,splice_donor_variant,,ENST00000397417,;	G	ENSG00000187535	ENST00000426508	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	IFT140	HGNC	29077	protein_coding	YES	CCDS10439.1	ENSP00000406012	IF140_HUMAN	Q9UG52_HUMAN,H3BTA5_HUMAN,H3BNC5_HUMAN	UPI0000073C64	.	.	.	.	14/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTACCTTC	.	5	ESCA
USP31	0	.	GRCh37	16	23091494	23091494	+	Splice_Site	SNP	T	T	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1951-2A>C	.	p.X651_splice	ENST00000219689	.	34	23	11	20	20	0	USP31,splice_acceptor_variant,,ENST00000219689,;USP31,splice_acceptor_variant,,ENST00000563525,;	G	ENSG00000103404	ENST00000219689	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	USP31	HGNC	20060	protein_coding	YES	CCDS10607.1	ENSP00000219689	UBP31_HUMAN	.	UPI0000366B06	.	.	.	.	12/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCTGTTGC	.	5	ESCA
ERN2	0	.	GRCh37	16	23713995	23713995	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027A>C	p.Thr343Pro	p.T343P	ENST00000256797	9/22	27	17	10	35	35	0	ERN2,missense_variant,p.Thr295Pro,ENST00000457008,;ERN2,missense_variant,p.Thr343Pro,ENST00000256797,;ERN2,3_prime_UTR_variant,,ENST00000562562,;ERN2,downstream_gene_variant,,ENST00000561478,;ERN2,downstream_gene_variant,,ENST00000566565,;	G	ENSG00000134398	ENST00000256797	Transcript	missense_variant	1196	1027	343	T/P	Act/Cct	.	.	.	-1	ERN2	HGNC	16942	protein_coding	YES	CCDS32407.1	ENSP00000256797	ERN2_HUMAN	.	UPI000041A8F8	.	tolerated(0.19)	benign(0.353)	9/22	.	hmmpanther:PTHR13954:SF9,hmmpanther:PTHR13954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGTTTCAT	.	5	ESCA
NPIPB6	0	.	GRCh37	16	28374090	28374090	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54C>T	p.%3D	p.S18S	ENST00000532254	1/7	175	97	77	209	209	0	NPIPB6,synonymous_variant,p.%3D,ENST00000532254,;RP11-435I10.5,upstream_gene_variant,,ENST00000603787,;	A	ENSG00000198156	ENST00000532254	Transcript	synonymous_variant	740	54	18	S	agC/agT	.	.	.	-1	NPIPB6	HGNC	37454	protein_coding	YES	CCDS61892.1	ENSP00000431871	NPIB6_HUMAN	O60358_HUMAN	UPI000047D9DC	.	.	.	1/7	.	hmmpanther:PTHR15438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGGCTCTG	.	5	ESCA
ADCY9	0	.	GRCh37	16	4016810	4016810	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3028G>A	p.Gly1010Arg	p.G1010R	ENST00000294016	11/11	41	19	21	50	50	0	ADCY9,missense_variant,p.Gly1010Arg,ENST00000294016,;ADCY9,intron_variant,,ENST00000576936,;	T	ENSG00000162104	ENST00000294016	Transcript	missense_variant	3567	3028	1010	G/R	Gga/Aga	.	.	.	-1	ADCY9	HGNC	240	protein_coding	YES	CCDS32382.1	ENSP00000294016	ADCY9_HUMAN	.	UPI000012887F	.	deleterious(0)	benign(0.37)	11/11	.	hmmpanther:PTHR11920:SF272,hmmpanther:PTHR11920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTCCGTGGT	.	5	ESCA
RANBP10	0	.	GRCh37	16	67757912	67757912	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2419C>T	.	.	ENST00000317506	14/14	45	40	5	66	66	0	RANBP10,3_prime_UTR_variant,,ENST00000317506,;GFOD2,upstream_gene_variant,,ENST00000268797,;RANBP10,downstream_gene_variant,,ENST00000536251,;RANBP10,downstream_gene_variant,,ENST00000602677,;RANBP10,downstream_gene_variant,,ENST00000411657,;RANBP10,downstream_gene_variant,,ENST00000448631,;GFOD2,upstream_gene_variant,,ENST00000602855,;GFOD2,upstream_gene_variant,,ENST00000602377,;RANBP10,downstream_gene_variant,,ENST00000602506,;GFOD2,upstream_gene_variant,,ENST00000602496,;	A	ENSG00000141084	ENST00000317506	Transcript	3_prime_UTR_variant	4398	.	.	.	.	.	.	.	-1	RANBP10	HGNC	29285	protein_coding	YES	CCDS32469.1	ENSP00000316589	RBP10_HUMAN	B3KP49_HUMAN	UPI00001C1FA6	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CAGCTGAAACA	.	3	ESCA
PSKH1	0	.	GRCh37	16	67963026	67963026	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1481C>A	.	.	ENST00000291041	3/3	58	37	21	108	108	0	PSKH1,3_prime_UTR_variant,,ENST00000291041,;CTRL,downstream_gene_variant,,ENST00000571605,;CTRL,downstream_gene_variant,,ENST00000574481,;CTRL,downstream_gene_variant,,ENST00000571044,;CTRL,intron_variant,,ENST00000573845,;CTRL,downstream_gene_variant,,ENST00000576408,;CTRL,downstream_gene_variant,,ENST00000575302,;CTC-479C5.12,downstream_gene_variant,,ENST00000575231,;CTRL,downstream_gene_variant,,ENST00000572144,;CTRL,downstream_gene_variant,,ENST00000576915,;CTC-479C5.12,downstream_gene_variant,,ENST00000573493,;	A	ENSG00000159792	ENST00000291041	Transcript	3_prime_UTR_variant	2926	.	.	.	.	.	.	.	1	PSKH1	HGNC	9529	protein_coding	YES	CCDS10851.1	ENSP00000291041	KPSH1_HUMAN	.	UPI000012DFE0	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAACCCAAGC	.	5	ESCA
WDR90	0	.	GRCh37	16	708985	708985	+	Silent	SNP	C	C	A	rs753507061	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2985C>A	p.%3D	p.L995L	ENST00000293879	24/41	58	31	27	87	87	0	WDR90,synonymous_variant,p.%3D,ENST00000549091,;WDR90,synonymous_variant,p.%3D,ENST00000293879,;WDR90,upstream_gene_variant,,ENST00000550739,;LA16c-349E10.1,upstream_gene_variant,,ENST00000573609,;WDR90,non_coding_transcript_exon_variant,,ENST00000548844,;WDR90,upstream_gene_variant,,ENST00000547543,;WDR90,upstream_gene_variant,,ENST00000548603,;WDR90,downstream_gene_variant,,ENST00000552648,;WDR90,synonymous_variant,p.%3D,ENST00000552728,;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,;WDR90,non_coding_transcript_exon_variant,,ENST00000552943,;WDR90,non_coding_transcript_exon_variant,,ENST00000552683,;WDR90,non_coding_transcript_exon_variant,,ENST00000546516,;WDR90,downstream_gene_variant,,ENST00000549648,;WDR90,upstream_gene_variant,,ENST00000549024,;WDR90,downstream_gene_variant,,ENST00000420061,;WDR90,upstream_gene_variant,,ENST00000550902,;WDR90,upstream_gene_variant,,ENST00000546923,;WDR90,downstream_gene_variant,,ENST00000548859,;	A	ENSG00000161996	ENST00000293879	Transcript	synonymous_variant	2985	2985	995	L	ctC/ctA	rs753507061	.	.	1	WDR90	HGNC	26960	protein_coding	YES	CCDS42092.1	ENSP00000293879	WDR90_HUMAN	.	UPI0000D67C48	.	.	.	24/41	.	hmmpanther:PTHR13720:SF10,hmmpanther:PTHR13720,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCTGGGA	byFrequency	5	ESCA
MARVELD3	0	.	GRCh37	16	71674997	71674997	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67G>T	.	.	ENST00000299952	3/3	28	14	14	36	36	0	MARVELD3,3_prime_UTR_variant,,ENST00000299952,;MARVELD3,3_prime_UTR_variant,,ENST00000565261,;PHLPP2,intron_variant,,ENST00000540628,;PHLPP2,downstream_gene_variant,,ENST00000356272,;PHLPP2,downstream_gene_variant,,ENST00000568954,;PHLPP2,downstream_gene_variant,,ENST00000393524,;PHLPP2,downstream_gene_variant,,ENST00000360429,;MARVELD3,downstream_gene_variant,,ENST00000268485,;MARVELD3,intron_variant,,ENST00000561682,;PHLPP2,intron_variant,,ENST00000568004,;PHLPP2,intron_variant,,ENST00000564884,;	T	ENSG00000140832	ENST00000299952	Transcript	3_prime_UTR_variant	1343	.	.	.	.	.	.	.	1	MARVELD3	HGNC	30525	protein_coding	YES	CCDS32478.1	ENSP00000299952	MALD3_HUMAN	.	UPI000013E601	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCCGCATTA	.	5	ESCA
SHISA6	0	.	GRCh37	17	11459150	11459150	+	Missense_Mutation	SNP	C	C	A	rs779639092	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1046C>A	p.Pro349Gln	p.P349Q	ENST00000441885	5/6	53	34	19	52	52	0	SHISA6,missense_variant,p.Pro330Gln,ENST00000432116,;SHISA6,missense_variant,p.Pro298Gln,ENST00000409168,;SHISA6,missense_variant,p.Pro349Gln,ENST00000441885,;	A	ENSG00000188803	ENST00000441885	Transcript	missense_variant	1206	1046	349	P/Q	cCa/cAa	rs779639092	.	.	1	SHISA6	HGNC	34491	protein_coding	YES	CCDS45615.1	ENSP00000390084	SHSA6_HUMAN	.	UPI000183CBD8	.	deleterious(0)	probably_damaging(0.997)	5/6	.	hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCCATCCT	.	5	ESCA
PRPF8	0	.	GRCh37	17	1582171	1582171	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1604G>A	p.Arg535Lys	p.R535K	ENST00000572621	11/42	40	22	17	31	31	0	PRPF8,missense_variant,p.Arg480Lys,ENST00000577001,;PRPF8,missense_variant,p.Arg535Lys,ENST00000572621,;PRPF8,missense_variant,p.Arg535Lys,ENST00000304992,;PRPF8,non_coding_transcript_exon_variant,,ENST00000573716,;PRPF8,downstream_gene_variant,,ENST00000574728,;PRPF8,downstream_gene_variant,,ENST00000571346,;PRPF8,upstream_gene_variant,,ENST00000576407,;PRPF8,upstream_gene_variant,,ENST00000576958,;	T	ENSG00000174231	ENST00000572621	Transcript	missense_variant	1870	1604	535	R/K	aGa/aAa	.	.	.	-1	PRPF8	HGNC	17340	protein_coding	YES	CCDS11010.1	ENSP00000460348	PRP8_HUMAN	.	UPI000006F2DD	.	tolerated(0.05)	probably_damaging(0.999)	11/42	.	hmmpanther:PTHR11140:SF0,hmmpanther:PTHR11140,Pfam_domain:PF08083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCTTTCC	.	5	ESCA
SREBF1	0	.	GRCh37	17	17719808	17719808	+	Silent	SNP	G	G	A	rs776609977	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2100C>T	p.%3D	p.A700A	ENST00000355815	11/20	48	26	21	87	87	0	SREBF1,synonymous_variant,p.%3D,ENST00000338854,;SREBF1,synonymous_variant,p.%3D,ENST00000395757,;SREBF1,synonymous_variant,p.%3D,ENST00000355815,;SREBF1,synonymous_variant,p.%3D,ENST00000261646,;SREBF1,downstream_gene_variant,,ENST00000423161,;SREBF1,upstream_gene_variant,,ENST00000486311,;SREBF1,upstream_gene_variant,,ENST00000478616,;SREBF1,downstream_gene_variant,,ENST00000577897,;SREBF1,downstream_gene_variant,,ENST00000435530,;MIR33B,upstream_gene_variant,,ENST00000385104,;SREBF1,downstream_gene_variant,,ENST00000583732,;SREBF1,3_prime_UTR_variant,,ENST00000395756,;SREBF1,3_prime_UTR_variant,,ENST00000395751,;SREBF1,non_coding_transcript_exon_variant,,ENST00000471445,;SREBF1,upstream_gene_variant,,ENST00000490796,;SREBF1,upstream_gene_variant,,ENST00000581707,;SREBF1,upstream_gene_variant,,ENST00000447641,;SREBF1,downstream_gene_variant,,ENST00000583080,;SREBF1,downstream_gene_variant,,ENST00000487401,;SREBF1,downstream_gene_variant,,ENST00000476994,;SREBF1,upstream_gene_variant,,ENST00000584760,;SREBF1,downstream_gene_variant,,ENST00000469356,;SREBF1,upstream_gene_variant,,ENST00000578469,;SREBF1,upstream_gene_variant,,ENST00000485080,;SREBF1,downstream_gene_variant,,ENST00000580540,;SREBF1,downstream_gene_variant,,ENST00000470247,;	A	ENSG00000072310	ENST00000355815	Transcript	synonymous_variant	2270	2100	700	A	gcC/gcT	rs776609977	.	.	-1	SREBF1	HGNC	11289	protein_coding	YES	CCDS32583.1	ENSP00000348069	SRBP1_HUMAN	J3QLB6_HUMAN,B5MD58_HUMAN	UPI00004432F6	.	.	.	11/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12565,hmmpanther:PTHR12565:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAGGGCTGC	byFrequency|byCluster	5	ESCA
SLC35G3	0	.	GRCh37	17	33520508	33520508	+	Silent	SNP	C	C	T	rs530925246	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.819G>A	p.%3D	p.A273A	ENST00000297307	1/1	124	118	6	197	197	0	SLC35G3,synonymous_variant,p.%3D,ENST00000297307,;UNC45B,downstream_gene_variant,,ENST00000378449,;UNC45B,downstream_gene_variant,,ENST00000433649,;UNC45B,downstream_gene_variant,,ENST00000268876,;UNC45B,downstream_gene_variant,,ENST00000394570,;RP11-799D4.2,downstream_gene_variant,,ENST00000590144,;RP11-799D4.1,downstream_gene_variant,,ENST00000592961,;	T	ENSG00000164729	ENST00000297307	Transcript	synonymous_variant	905	819	273	A	gcG/gcA	rs530925246	.	.	-1	SLC35G3	HGNC	26848	protein_coding	YES	CCDS11293.1	ENSP00000297307	S35G3_HUMAN	.	UPI000006FEAB	.	.	.	1/1	.	hmmpanther:PTHR22911:SF32,hmmpanther:PTHR22911,Pfam_domain:PF00892,Superfamily_domains:0043518	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGACCGCATA	by1000G	2	ESCA
ACACA	0	.	GRCh37	17	35518913	35518913	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5131G>A	p.Gly1711Ser	p.G1711S	ENST00000353139	42/56	53	33	19	31	31	0	ACACA,missense_variant,p.Gly1616Ser,ENST00000360679,;ACACA,missense_variant,p.Gly1596Ser,ENST00000335166,;ACACA,missense_variant,p.Gly125Ser,ENST00000592427,;ACACA,missense_variant,p.Gly326Ser,ENST00000591119,;ACACA,missense_variant,p.Gly1711Ser,ENST00000353139,;ACACA,missense_variant,p.Gly1674Ser,ENST00000394406,;ACACA,upstream_gene_variant,,ENST00000361253,;ACACA,upstream_gene_variant,,ENST00000587233,;RP11-19G24.2,upstream_gene_variant,,ENST00000492524,;	T	ENSG00000132142	ENST00000353139	Transcript	missense_variant	5613	5131	1711	G/S	Ggc/Agc	.	.	.	-1	ACACA	HGNC	84	protein_coding	YES	CCDS42302.1	ENSP00000344789	ACACA_HUMAN	Q7Z5W8_HUMAN,K7EII5_HUMAN,K4DID9_HUMAN,B4DWK9_HUMAN,B4DK31_HUMAN,B4DIW1_HUMAN,B2ZZ90_HUMAN,A8MYL5_HUMAN	UPI00002263AC	.	deleterious(0)	probably_damaging(1)	42/56	.	hmmpanther:PTHR18866:SF89,hmmpanther:PTHR18866,Pfam_domain:PF01039,Gene3D:3.90.226.10,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGCCTTCTG	.	5	ESCA
CTD-2206N4.2	0	.	GRCh37	17	37187981	37187981	+	5'Flank	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000582518	.	76	52	24	49	49	0	CTD-2206N4.2,upstream_gene_variant,,ENST00000582518,;LRRC37A11P,non_coding_transcript_exon_variant,,ENST00000425901,;LRRC37A11P,intron_variant,,ENST00000579258,;CTD-2206N4.1,downstream_gene_variant,,ENST00000584401,;	T	ENSG00000266013	ENST00000582518	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4618	-1	CTD-2206N4.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTGTAGCT	.	5	ESCA
KCNH4	0	.	GRCh37	17	40315780	40315780	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2321C>T	p.Ser774Phe	p.S774F	ENST00000264661	13/17	34	23	11	79	79	0	KCNH4,missense_variant,p.Ser774Phe,ENST00000264661,;KCNH4,missense_variant,p.Ser774Phe,ENST00000607371,;	A	ENSG00000089558	ENST00000264661	Transcript	missense_variant	2654	2321	774	S/F	tCc/tTc	.	.	.	-1	KCNH4	HGNC	6253	protein_coding	YES	CCDS11420.1	ENSP00000264661	KCNH4_HUMAN	.	UPI000012DCA8	.	deleterious(0.03)	probably_damaging(0.998)	13/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF378	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAGGAGACA	.	5	ESCA
TMEM101	0	.	GRCh37	17	42092301	42092301	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20C>A	p.Ser7Ter	p.S7*	ENST00000589334	2/5	24	11	13	49	49	0	TMEM101,stop_gained,p.Ser7Ter,ENST00000587529,;TMEM101,stop_gained,p.Ser7Ter,ENST00000589334,;TMEM101,stop_gained,p.Ser7Ter,ENST00000206380,;TMEM101,5_prime_UTR_variant,,ENST00000586174,;TMEM101,intron_variant,,ENST00000590905,;TMEM101,intron_variant,,ENST00000542039,;TMEM101,intron_variant,,ENST00000585950,;TMEM101,intron_variant,,ENST00000592127,;	T	ENSG00000091947	ENST00000589334	Transcript	stop_gained	336	20	7	S/*	tCg/tAg	.	.	.	-1	TMEM101	HGNC	28653	protein_coding	YES	CCDS11474.1	ENSP00000468025	TM101_HUMAN	K7ERS4_HUMAN,K7EPU9_HUMAN,K7EM72_HUMAN,B4DFS4_HUMAN	UPI000006E158	.	.	.	2/5	.	hmmpanther:PTHR31034,hmmpanther:PTHR31034:SF1,Pfam_domain:PF15111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTCGAACCT	.	5	ESCA
DCAKD	0	.	GRCh37	17	43112365	43112365	+	5'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-112C>A	.	.	ENST00000452796	1/4	17	14	3	18	18	0	DCAKD,splice_region_variant,,ENST00000593094,;DCAKD,splice_region_variant,,ENST00000342350,;DCAKD,splice_region_variant,,ENST00000588499,;DCAKD,splice_region_variant,,ENST00000310604,;DCAKD,5_prime_UTR_variant,,ENST00000452796,;DCAKD,splice_region_variant,,ENST00000588295,;DCAKD,upstream_gene_variant,,ENST00000592902,;	T	ENSG00000172992	ENST00000452796	Transcript	5_prime_UTR_variant	145	.	.	.	.	.	.	.	-1	DCAKD	HGNC	26238	protein_coding	YES	CCDS11493.1	ENSP00000413483	DCAKD_HUMAN	K7ESP4_HUMAN	UPI0000039E6A	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGGACCTG	.	2	ESCA
OSBPL7	0	.	GRCh37	17	45884747	45884747	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*910C>A	.	.	ENST00000007414	23/23	29	20	9	49	49	0	OSBPL7,3_prime_UTR_variant,,ENST00000392507,;OSBPL7,3_prime_UTR_variant,,ENST00000007414,;OSBPL7,3_prime_UTR_variant,,ENST00000579728,;OSBPL7,non_coding_transcript_exon_variant,,ENST00000583167,;OSBPL7,downstream_gene_variant,,ENST00000578461,;	T	ENSG00000006025	ENST00000007414	Transcript	3_prime_UTR_variant	3631	.	.	.	.	.	.	.	-1	OSBPL7	HGNC	16387	protein_coding	YES	CCDS11515.1	ENSP00000007414	OSBL7_HUMAN	J3QLK7_HUMAN	UPI0000130E98	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACAGTCTTT	.	5	ESCA
MTMR4	0	.	GRCh37	17	56582201	56582201	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1238G>A	p.Arg413His	p.R413H	ENST00000323456	12/19	68	63	5	115	115	0	MTMR4,missense_variant,p.Arg413His,ENST00000323456,;MTMR4,missense_variant,p.Arg413His,ENST00000579925,;MTMR4,downstream_gene_variant,,ENST00000583656,;MTMR4,downstream_gene_variant,,ENST00000583966,;MTMR4,downstream_gene_variant,,ENST00000580983,;MTMR4,downstream_gene_variant,,ENST00000582663,;	T	ENSG00000108389	ENST00000323456	Transcript	missense_variant	1363	1238	413	R/H	cGc/cAc	COSM3403052	.	.	-1	MTMR4	HGNC	7452	protein_coding	YES	CCDS11608.1	ENSP00000325285	MTMR4_HUMAN	J3QRJ2_HUMAN	UPI00002010DE	.	deleterious(0)	probably_damaging(1)	12/19	.	PROSITE_profiles:PS51339,PROSITE_profiles:PS50056,hmmpanther:PTHR10807:SF64,hmmpanther:PTHR10807,PROSITE_patterns:PS00383,Pfam_domain:PF06602,Gene3D:3.90.190.10,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGTGCGGTCC	.	2	ESCA
SMG8	0	.	GRCh37	17	57288293	57288293	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.881A>G	p.His294Arg	p.H294R	ENST00000543872	2/5	31	19	12	30	30	0	SMG8,missense_variant,p.His294Arg,ENST00000543872,;SMG8,missense_variant,p.His294Arg,ENST00000578922,;SMG8,missense_variant,p.His294Arg,ENST00000300917,;CTD-2510F5.6,intron_variant,,ENST00000577660,;SMG8,upstream_gene_variant,,ENST00000582469,;SMG8,intron_variant,,ENST00000580498,;SMG8,upstream_gene_variant,,ENST00000580798,;	G	ENSG00000167447	ENST00000543872	Transcript	missense_variant	1145	881	294	H/R	cAt/cGt	.	.	.	1	SMG8	HGNC	25551	protein_coding	YES	CCDS11615.1	ENSP00000438748	SMG8_HUMAN	.	UPI000006CCB5	.	deleterious(0.02)	benign(0.439)	2/5	.	hmmpanther:PTHR13091,hmmpanther:PTHR13091:SF0,Pfam_domain:PF10220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAACATTCTC	.	5	ESCA
ABCA10	0	.	GRCh37	17	67218779	67218780	+	Frame_Shift_Ins	INS	-	-	T	rs760530642	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.93dupA	p.Tyr32IlefsTer3	p.Y32Ifs*3	ENST00000269081	5/40	106	67	39	68	68	0	ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000416101,;ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000432313,;ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000269081,;ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000423818,;ABCA10,downstream_gene_variant,,ENST00000521526,;ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000523512,;ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000523419,;ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000522406,;ABCA10,frameshift_variant,p.Tyr32IlefsTer3,ENST00000518929,;ABCA10,upstream_gene_variant,,ENST00000524273,;	T	ENSG00000154263	ENST00000269081	Transcript	frameshift_variant	1003-1004	93-94	31-32	-/X	-/A	rs760530642	.	.	-1	ABCA10	HGNC	30	protein_coding	YES	CCDS11684.1	ENSP00000269081	ABCAA_HUMAN	K7ERP5_HUMAN	UPI000013D7F6	.	.	.	5/40	.	hmmpanther:PTHR19229:SF120,hmmpanther:PTHR19229,Pfam_domain:PF12698	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATGGTATTTTT	.	2	ESCA
C17orf80	0	.	GRCh37	17	71231802	71231802	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000359042	3/6	59	34	25	37	37	0	C17orf80,missense_variant,p.Asp61Tyr,ENST00000255557,;C17orf80,missense_variant,p.Asp61Tyr,ENST00000535032,;C17orf80,missense_variant,p.Asp61Tyr,ENST00000585109,;C17orf80,missense_variant,p.Asp61Tyr,ENST00000359042,;C17orf80,missense_variant,p.Asp61Tyr,ENST00000582391,;C17orf80,missense_variant,p.Asp61Tyr,ENST00000577615,;C17orf80,missense_variant,p.Asp61Tyr,ENST00000426147,;C17orf80,missense_variant,p.Asp61Tyr,ENST00000268942,;C17orf80,intron_variant,,ENST00000582793,;FAM104A,upstream_gene_variant,,ENST00000403627,;FAM104A,upstream_gene_variant,,ENST00000583024,;FAM104A,upstream_gene_variant,,ENST00000405159,;FAM104A,upstream_gene_variant,,ENST00000581110,;FAM104A,intron_variant,,ENST00000583178,;	T	ENSG00000141219	ENST00000359042	Transcript	missense_variant	375	181	61	D/Y	Gat/Tat	.	.	.	1	C17orf80	HGNC	29601	protein_coding	YES	CCDS11694.1	ENSP00000351937	CQ080_HUMAN	J3QLV1_HUMAN,J3KTJ7_HUMAN,J3KT60_HUMAN	UPI000014128C	.	deleterious(0)	possibly_damaging(0.653)	3/6	.	hmmpanther:PTHR16270:SF5,hmmpanther:PTHR16270	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAAGATTTA	.	5	ESCA
NUP85	0	.	GRCh37	17	73204645	73204645	+	Silent	SNP	G	G	A	rs778531073	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57G>A	p.%3D	p.K19K	ENST00000245544	2/19	86	60	25	66	66	0	NUP85,synonymous_variant,p.%3D,ENST00000245544,;NUP85,synonymous_variant,p.%3D,ENST00000579298,;NUP85,5_prime_UTR_variant,,ENST00000447371,;NUP85,5_prime_UTR_variant,,ENST00000583569,;NUP85,intron_variant,,ENST00000579324,;NUP85,intron_variant,,ENST00000541827,;NUP85,non_coding_transcript_exon_variant,,ENST00000583548,;NUP85,non_coding_transcript_exon_variant,,ENST00000582833,;NUP85,non_coding_transcript_exon_variant,,ENST00000577208,;NUP85,non_coding_transcript_exon_variant,,ENST00000583948,;NUP85,intron_variant,,ENST00000449421,;NUP85,synonymous_variant,p.%3D,ENST00000581104,;	A	ENSG00000125450	ENST00000245544	Transcript	synonymous_variant	128	57	19	K	aaG/aaA	rs778531073	.	.	1	NUP85	HGNC	8734	protein_coding	YES	CCDS32730.1	ENSP00000245544	NUP85_HUMAN	J3QL54_HUMAN,J3KSH3_HUMAN,F5H0W7_HUMAN,B4DMQ3_HUMAN	UPI00000735DC	.	.	.	2/19	.	hmmpanther:PTHR13373:SF21,hmmpanther:PTHR13373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGAAGAA	.	5	ESCA
TP53	0	.	GRCh37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.818G>A	p.Arg273His	p.R273H	ENST00000269305	8/11	32	18	13	34	34	0	TP53,missense_variant,p.Arg273His,ENST00000420246,;TP53,missense_variant,p.Arg273His,ENST00000269305,;TP53,missense_variant,p.Arg141His,ENST00000509690,;TP53,missense_variant,p.Arg273His,ENST00000359597,;TP53,missense_variant,p.Arg273His,ENST00000445888,;TP53,missense_variant,p.Arg273His,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1008	818	273	R/H	cGt/cAt	CM920677,CM010472,rs28934576,CM004342,TP53_g.13798G>C,TP53_g.13798del,TP53_g.13798G>A,TP53_g.13798G>T,COSM10660,COSM43896,COSM44440,COSM10779,COSM318169,COSM99729,COSM165077,COSM3356963,COSM3675521,COSM1640828,COSM1645335,COSM1646808	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.13)	possibly_damaging(0.631)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	T:0.0002	T:0,T:0	T:0,T:0	.	T:0,T:0	T:0.001,T:0.001	T:0,T:0	.	.	pathogenic	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	25105660	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R273H|c.818G>A|116,SITE|p.R273H|c.818G>A|64,SITE|p.R273H|c.818G>A|588,SITE|p.R273H|c.818G>A|83,CODON|p.0?|c.1_1182del1182|6,CODON|p.R273L|c.818G>T|98,CODON|p.R273P|c.818G>C|4,CODON|p.R273L|c.818G>T|5,CODON|p.R273P|c.818G>C|29,CODON|p.R273L|c.818G>T|18,CODON|p.R273L|c.818G>T|12,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3,BUFFER|p.E271Q|c.811G>C|4,BUFFER|p.E271K|c.811G>A|35,BUFFER|p.E271*|c.811G>T|16,BUFFER|p.E271*|c.811G>T|3,BUFFER|p.E271K|c.811G>A|13,BUFFER|p.E271K|c.811G>A|4,BUFFER|p.E271K|c.811G>A|8,BUFFER|p.F270L|c.810T>G|4,BUFFER|p.F270L|c.810T>A|5,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270Y|c.809T>A|5,BUFFER|p.F270C|c.809T>G|16,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270S|c.809T>C|14,BUFFER|p.F270S|c.809T>C|6,BUFFER|p.F270L|c.808T>C|16,BUFFER|p.F270I|c.808T>A|3,BUFFER|p.F270V|c.808T>G|8,BUFFER|p.F270L|c.808T>C|3,BUFFER|p.F270I|c.808T>A|6,BUFFER|p.S269S|c.807C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACACGCACC	byCluster|by1000G	5	ESCA
DNAH17	0	.	GRCh37	17	76423012	76423012	+	Missense_Mutation	SNP	G	G	C	rs147136333	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12835C>G	p.Leu4279Val	p.L4279V	ENST00000389840	78/81	25	17	7	47	47	0	DNAH17,missense_variant,p.Leu4251Val,ENST00000585328,;DNAH17,missense_variant,p.Leu4279Val,ENST00000389840,;PGS1,downstream_gene_variant,,ENST00000329897,;AC061992.1,downstream_gene_variant,,ENST00000600087,;PGS1,downstream_gene_variant,,ENST00000262764,;DNAH17,non_coding_transcript_exon_variant,,ENST00000586052,;DNAH17,non_coding_transcript_exon_variant,,ENST00000586850,;DNAH17,non_coding_transcript_exon_variant,,ENST00000592192,;PGS1,downstream_gene_variant,,ENST00000588281,;PGS1,downstream_gene_variant,,ENST00000586880,;DNAH17,missense_variant,p.Leu1457Val,ENST00000591369,;DNAH17,non_coding_transcript_exon_variant,,ENST00000590227,;PGS1,downstream_gene_variant,,ENST00000589425,;DNAH17,upstream_gene_variant,,ENST00000591647,;PGS1,downstream_gene_variant,,ENST00000589426,;PGS1,downstream_gene_variant,,ENST00000588169,;	C	ENSG00000187775	ENST00000389840	Transcript	missense_variant	12960	12835	4279	L/V	Ctg/Gtg	rs147136333	.	.	-1	DNAH17	HGNC	2946	protein_coding	YES	.	ENSP00000374490	DYH17_HUMAN	.	UPI0001A5EE11	.	.	possibly_damaging(0.868)	78/81	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10676:SF228,hmmpanther:PTHR10676,Pfam_domain:PF03028	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCAGCCCCA	.	5	ESCA
ASPSCR1	0	.	GRCh37	17	79954650	79954650	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.861G>A	p.%3D	p.S287S	ENST00000306729	7/17	98	62	35	196	196	0	ASPSCR1,synonymous_variant,p.%3D,ENST00000581484,;ASPSCR1,synonymous_variant,p.%3D,ENST00000580534,;ASPSCR1,synonymous_variant,p.%3D,ENST00000582355,;ASPSCR1,synonymous_variant,p.%3D,ENST00000306739,;ASPSCR1,synonymous_variant,p.%3D,ENST00000306729,;ASPSCR1,downstream_gene_variant,,ENST00000579684,;ASPSCR1,downstream_gene_variant,,ENST00000581647,;ASPSCR1,synonymous_variant,p.%3D,ENST00000584454,;ASPSCR1,3_prime_UTR_variant,,ENST00000344865,;ASPSCR1,intron_variant,,ENST00000583503,;	A	ENSG00000169696	ENST00000306729	Transcript	synonymous_variant	958	861	287	S	tcG/tcA	.	.	.	1	ASPSCR1	HGNC	13825	protein_coding	YES	CCDS58611.1	ENSP00000306625	ASPC1_HUMAN	.	UPI000007263D	.	.	.	7/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23153:SF33,hmmpanther:PTHR23153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCGGGCCA	.	5	ESCA
PIEZO2	0	.	GRCh37	18	10736690	10736690	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4652A>G	p.Tyr1551Cys	p.Y1551C	ENST00000503781	32/52	37	26	10	29	29	0	PIEZO2,missense_variant,p.Tyr1576Cys,ENST00000580640,;PIEZO2,missense_variant,p.Tyr1551Cys,ENST00000503781,;PIEZO2,missense_variant,p.Tyr1551Cys,ENST00000302079,;PIEZO2,3_prime_UTR_variant,,ENST00000383408,;PIEZO2,downstream_gene_variant,,ENST00000579949,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,;	C	ENSG00000154864	ENST00000503781	Transcript	missense_variant	4652	4652	1551	Y/C	tAt/tGt	.	.	.	-1	PIEZO2	HGNC	26270	protein_coding	YES	.	ENSP00000421377	PIEZ2_HUMAN	J3KSM7_HUMAN	UPI0001B3CB29	.	deleterious(0)	probably_damaging(0.999)	32/52	.	hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAATAATCT	.	5	ESCA
CEP192	0	.	GRCh37	18	13049675	13049675	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2885A>G	p.Asn962Ser	p.N962S	ENST00000506447	16/45	90	54	35	40	40	0	CEP192,missense_variant,p.Asn366Ser,ENST00000325971,;CEP192,missense_variant,p.Asn703Ser,ENST00000589596,;CEP192,missense_variant,p.Asn487Ser,ENST00000430049,;CEP192,missense_variant,p.Asn962Ser,ENST00000506447,;CEP192,missense_variant,p.Asn501Ser,ENST00000511820,;CEP192,missense_variant,p.Asn562Ser,ENST00000510237,;CEP192,3_prime_UTR_variant,,ENST00000513432,;	G	ENSG00000101639	ENST00000506447	Transcript	missense_variant	2965	2885	962	N/S	aAt/aGt	.	.	.	1	CEP192	HGNC	25515	protein_coding	YES	CCDS32792.2	ENSP00000427550	.	E9PF99_HUMAN	UPI0001B09235	.	tolerated(1)	benign(0.008)	16/45	.	hmmpanther:PTHR16029:SF10,hmmpanther:PTHR16029	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAAAATAGTG	.	5	ESCA
MOCOS	0	.	GRCh37	18	33795865	33795865	+	Silent	SNP	C	C	T	rs773100195	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1722C>T	p.%3D	p.V574V	ENST00000261326	8/15	27	20	7	25	25	0	MOCOS,synonymous_variant,p.%3D,ENST00000261326,;	T	ENSG00000075643	ENST00000261326	Transcript	synonymous_variant	1743	1722	574	V	gtC/gtT	rs773100195	.	.	1	MOCOS	HGNC	18234	protein_coding	YES	CCDS11919.1	ENSP00000261326	MOCOS_HUMAN	.	UPI000013D165	.	.	.	8/15	.	hmmpanther:PTHR14237,hmmpanther:PTHR14237:SF19,HAMAP:MF_03050	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGTCCTGGA	.	5	ESCA
C18orf42	0	.	GRCh37	18	5145660	5145660	+	Silent	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111C>G	p.%3D	p.V37V	ENST00000434239	2/2	35	22	13	36	36	0	C18orf42,synonymous_variant,p.%3D,ENST00000434239,;C18orf42,synonymous_variant,p.%3D,ENST00000580650,;	C	ENSG00000231824	ENST00000434239	Transcript	synonymous_variant	283	111	37	V	gtC/gtG	.	.	.	-1	C18orf42	HGNC	28285	protein_coding	YES	CCDS54179.1	ENSP00000399075	CR042_HUMAN	.	UPI0000201977	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15934:SF3,hmmpanther:PTHR15934,Pfam_domain:PF10470	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGAGACTTG	.	5	ESCA
SERPINB8	0	.	GRCh37	18	61637385	61637385	+	5'UTR	SNP	A	A	G	rs55686360	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-30A>G	.	.	ENST00000397985	1/7	18	15	3	40	40	0	SERPINB8,5_prime_UTR_variant,,ENST00000353706,;SERPINB8,5_prime_UTR_variant,,ENST00000397988,;SERPINB8,5_prime_UTR_variant,,ENST00000397985,;SERPINB8,5_prime_UTR_variant,,ENST00000542677,;SERPINB8,upstream_gene_variant,,ENST00000448851,;SERPINB8,upstream_gene_variant,,ENST00000441827,;HMSD,intron_variant,,ENST00000481726,;HMSD,downstream_gene_variant,,ENST00000498680,;	G	ENSG00000166401	ENST00000397985	Transcript	5_prime_UTR_variant	227	.	.	.	.	rs55686360	.	.	1	SERPINB8	HGNC	8952	protein_coding	YES	CCDS11991.1	ENSP00000381072	SPB8_HUMAN	C9JVA8_HUMAN,C9JTJ8_HUMAN,B4DTW2_HUMAN	UPI000013C5F2	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGGCAGCAGC	byFrequency|byCluster|by1000G	2	ESCA
SMIM21	0	.	GRCh37	18	73139414	73139414	+	Missense_Mutation	SNP	C	C	A	rs745449933	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.105G>T	p.Leu35Phe	p.L35F	ENST00000579022	1/3	66	48	17	62	62	0	SMIM21,missense_variant,p.Leu35Phe,ENST00000382638,;SMIM21,missense_variant,p.Leu35Phe,ENST00000584508,;SMIM21,missense_variant,p.Leu35Phe,ENST00000579022,;	A	ENSG00000206026	ENST00000579022	Transcript	missense_variant	245	105	35	L/F	ttG/ttT	rs745449933	.	.	-1	SMIM21	HGNC	27598	protein_coding	YES	CCDS32845.1	ENSP00000462106	SMI21_HUMAN	.	UPI00001B64CE	.	tolerated_low_confidence(0.35)	possibly_damaging(0.765)	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGCAAATT	.	5	ESCA
COL5A3	0	.	GRCh37	19	10070440	10070441	+	3'UTR	INS	-	-	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*646dupG	.	.	ENST00000264828	67/67	82	55	27	129	129	0	COL5A3,3_prime_UTR_variant,,ENST00000264828,;	C	ENSG00000080573	ENST00000264828	Transcript	3_prime_UTR_variant	5970-5971	.	.	.	.	.	.	.	-1	COL5A3	HGNC	14864	protein_coding	YES	CCDS12222.1	ENSP00000264828	CO5A3_HUMAN	.	UPI00002032A3	.	.	.	67/67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GATTCACCCCC	.	2	ESCA
EIF3G	0	.	GRCh37	19	10225804	10225804	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.949C>A	p.Pro317Thr	p.P317T	ENST00000253108	11/11	88	47	41	169	169	0	EIF3G,missense_variant,p.Pro115Thr,ENST00000593054,;EIF3G,missense_variant,p.Pro317Thr,ENST00000253108,;P2RY11,3_prime_UTR_variant,,ENST00000321826,;EIF3G,downstream_gene_variant,,ENST00000589454,;PPAN,downstream_gene_variant,,ENST00000393793,;PPAN,downstream_gene_variant,,ENST00000253107,;EIF3G,downstream_gene_variant,,ENST00000587146,;PPAN-P2RY11,downstream_gene_variant,,ENST00000393796,;PPAN,downstream_gene_variant,,ENST00000446223,;PPAN-P2RY11,downstream_gene_variant,,ENST00000428358,;EIF3G,downstream_gene_variant,,ENST00000588709,;PPAN,downstream_gene_variant,,ENST00000556468,;PPAN,downstream_gene_variant,,ENST00000444703,;P2RY11,downstream_gene_variant,,ENST00000471843,;EIF3G,downstream_gene_variant,,ENST00000587168,;EIF3G,splice_region_variant,,ENST00000590158,;EIF3G,downstream_gene_variant,,ENST00000586151,;EIF3G,downstream_gene_variant,,ENST00000590647,;EIF3G,downstream_gene_variant,,ENST00000587590,;PPAN,downstream_gene_variant,,ENST00000468881,;EIF3G,downstream_gene_variant,,ENST00000590940,;EIF3G,downstream_gene_variant,,ENST00000587681,;EIF3G,downstream_gene_variant,,ENST00000589458,;EIF3G,downstream_gene_variant,,ENST00000589009,;PPAN,downstream_gene_variant,,ENST00000486482,;PPAN,downstream_gene_variant,,ENST00000466025,;EIF3G,downstream_gene_variant,,ENST00000587993,;EIF3G,downstream_gene_variant,,ENST00000593066,;EIF3G,downstream_gene_variant,,ENST00000593095,;EIF3G,downstream_gene_variant,,ENST00000589674,;EIF3G,downstream_gene_variant,,ENST00000592485,;	T	ENSG00000130811	ENST00000253108	Transcript	missense_variant	992	949	317	P/T	Ccg/Acg	.	.	.	-1	EIF3G	HGNC	3274	protein_coding	YES	CCDS12227.1	ENSP00000253108	EIF3G_HUMAN	.	UPI000012D2FE	.	deleterious(0)	probably_damaging(0.995)	11/11	.	HAMAP:MF_03006,PROSITE_profiles:PS50102,hmmpanther:PTHR10352,Gene3D:3.30.70.330,PIRSF_domain:PIRSF037949,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACGGCCTGG	.	5	ESCA
SMARCA4	0	.	GRCh37	19	11143993	11143993	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000429416	27/36	39	20	19	50	50	0	SMARCA4,missense_variant,p.Arg1192Cys,ENST00000450717,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000358026,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000413806,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000444061,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000541122,;SMARCA4,missense_variant,p.Arg37Cys,ENST00000592158,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000590574,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000344626,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000589677,;SMARCA4,missense_variant,p.Arg1192Cys,ENST00000429416,;SMARCA4,upstream_gene_variant,,ENST00000538456,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586892,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,downstream_gene_variant,,ENST00000591545,;	T	ENSG00000127616	ENST00000429416	Transcript	missense_variant	3855	3574	1192	R/C	Cgc/Tgc	COSM1611528,COSM303247,COSM2813735,COSM1611527	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	probably_damaging(1)	27/36	.	Superfamily_domains:SSF52540,SMART_domains:SM00490,Gene3D:3.40.50.300,Pfam_domain:PF00271,hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799,PROSITE_profiles:PS51194	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R1192C|c.3574C>T|3	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCCACCGCATC	.	4	ESCA
ZNF491	0	.	GRCh37	19	11918704	11918704	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*622C>A	.	.	ENST00000323169	3/3	52	35	16	38	38	0	ZNF491,3_prime_UTR_variant,,ENST00000323169,;ZNF491,downstream_gene_variant,,ENST00000450087,;ZNF491,intron_variant,,ENST00000492230,;	A	ENSG00000177599	ENST00000323169	Transcript	3_prime_UTR_variant	2267	.	.	.	.	.	.	.	1	ZNF491	HGNC	23706	protein_coding	YES	CCDS12267.1	ENSP00000313443	ZN491_HUMAN	C9IYV0_HUMAN	UPI000006D12C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTCTGCTG	.	5	ESCA
ATP5D	0	.	GRCh37	19	1244157	1244157	+	Silent	SNP	C	C	A	rs745748653	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.357C>A	p.%3D	p.A119A	ENST00000215375	3/4	86	63	23	167	167	0	ATP5D,synonymous_variant,p.%3D,ENST00000215375,;ATP5D,synonymous_variant,p.%3D,ENST00000395633,;ATP5D,synonymous_variant,p.%3D,ENST00000591660,;MIDN,upstream_gene_variant,,ENST00000300952,;MIDN,upstream_gene_variant,,ENST00000586757,;AC004221.2,downstream_gene_variant,,ENST00000592843,;ATP5D,non_coding_transcript_exon_variant,,ENST00000591249,;ATP5D,non_coding_transcript_exon_variant,,ENST00000588538,;ATP5D,non_coding_transcript_exon_variant,,ENST00000589478,;ATP5D,non_coding_transcript_exon_variant,,ENST00000590265,;ATP5D,downstream_gene_variant,,ENST00000592624,;	A	ENSG00000099624	ENST00000215375	Transcript	synonymous_variant	458	357	119	A	gcC/gcA	rs745748653	.	.	1	ATP5D	HGNC	837	protein_coding	YES	CCDS12058.1	ENSP00000215375	ATPD_HUMAN	.	UPI000004493C	.	.	.	3/4	.	HAMAP:MF_00530,hmmpanther:PTHR13822,Pfam_domain:PF02823,TIGRFAM_domain:TIGR01216,Gene3D:2.60.15.10,Superfamily_domains:SSF51344	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCCGTGAC	byFrequency	5	ESCA
ELL	0	.	GRCh37	19	18557284	18557284	+	Silent	SNP	G	G	A	rs199594269	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1539C>T	p.%3D	p.Y513Y	ENST00000262809	10/12	75	48	26	110	110	0	ELL,synonymous_variant,p.%3D,ENST00000262809,;ELL,synonymous_variant,p.%3D,ENST00000596124,;CTD-3137H5.1,downstream_gene_variant,,ENST00000594590,;ELL,3_prime_UTR_variant,,ENST00000594635,;ELL,non_coding_transcript_exon_variant,,ENST00000608165,;ELL,upstream_gene_variant,,ENST00000610152,;AC010335.1,upstream_gene_variant,,ENST00000541164,;	A	ENSG00000105656	ENST00000262809	Transcript	synonymous_variant	1611	1539	513	Y	taC/taT	rs199594269	.	.	-1	ELL	HGNC	23114	protein_coding	YES	CCDS12380.1	ENSP00000262809	ELL_HUMAN	Q75MS0_HUMAN	UPI0000062324	.	.	.	10/12	.	hmmpanther:PTHR23288:SF9,hmmpanther:PTHR23288,Pfam_domain:PF07303,Superfamily_domains:0053542	A:0.0004	A:0	A:0.0014	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCGTACTT	byFrequency|byCluster|by1000G	5	ESCA
TMEM161A	0	.	GRCh37	19	19243553	19243553	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199G>A	p.Gly67Ser	p.G67S	ENST00000162044	4/12	31	21	9	52	52	0	TMEM161A,missense_variant,p.Gly67Ser,ENST00000162044,;TMEM161A,missense_variant,p.Gly67Ser,ENST00000587583,;TMEM161A,missense_variant,p.Gly67Ser,ENST00000450333,;TMEM161A,missense_variant,p.Gly50Ser,ENST00000587915,;TMEM161A,missense_variant,p.Gly50Ser,ENST00000587096,;TMEM161A,5_prime_UTR_variant,,ENST00000592369,;TMEM161A,upstream_gene_variant,,ENST00000587925,;TMEM161A,non_coding_transcript_exon_variant,,ENST00000592147,;TMEM161A,missense_variant,p.Gly67Ser,ENST00000587985,;TMEM161A,3_prime_UTR_variant,,ENST00000590216,;TMEM161A,non_coding_transcript_exon_variant,,ENST00000587406,;TMEM161A,non_coding_transcript_exon_variant,,ENST00000589448,;TMEM161A,upstream_gene_variant,,ENST00000591031,;TMEM161A,downstream_gene_variant,,ENST00000586357,;	T	ENSG00000064545	ENST00000162044	Transcript	missense_variant	264	199	67	G/S	Ggc/Agc	.	.	.	-1	TMEM161A	HGNC	26020	protein_coding	YES	CCDS12393.1	ENSP00000162044	T161A_HUMAN	K7EQE7_HUMAN,K7EQ34_HUMAN	UPI00000373EF	.	deleterious(0.05)	benign(0.367)	4/12	.	Pfam_domain:PF10268,hmmpanther:PTHR13624:SF4,hmmpanther:PTHR13624	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGCCATTGG	.	5	ESCA
ZNF626	0	.	GRCh37	19	20808178	20808178	+	Missense_Mutation	SNP	C	C	A	rs782429235	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505G>T	p.Gly169Trp	p.G169W	ENST00000601440	4/4	107	72	34	55	54	1	ZNF626,missense_variant,p.Gly169Trp,ENST00000601440,;ZNF626,missense_variant,p.Gly93Trp,ENST00000595405,;CTC-513N18.7,intron_variant,,ENST00000595094,;	A	ENSG00000188171	ENST00000601440	Transcript	missense_variant	652	505	169	G/W	Ggg/Tgg	rs782429235,COSM3531267	.	.	-1	ZNF626	HGNC	30461	protein_coding	YES	CCDS42535.1	ENSP00000469958	ZN626_HUMAN	M0QY39_HUMAN,I0CMK8_HUMAN	UPI000035E843	.	deleterious(0)	probably_damaging(0.981)	4/4	.	hmmpanther:PTHR24384:SF105,hmmpanther:PTHR24384,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCCAGTAT	.	5	ESCA
ZNF714	0	.	GRCh37	19	21300460	21300462	+	Frame_Shift_Del	DEL	TAA	TAA	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	TAA	TAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990_992delTAAinsG	p.His330GlnfsTer13	p.H330Qfs*13	ENST00000596143	5/5	39	25	14	23	23	0	ZNF714,frameshift_variant,p.His330GlnfsTer13,ENST00000596143,;ZNF714,3_prime_UTR_variant,,ENST00000601416,;ZNF714,3_prime_UTR_variant,,ENST00000291770,;ZNF714,intron_variant,,ENST00000596053,;ZNF714,downstream_gene_variant,,ENST00000596367,;ZNF714,downstream_gene_variant,,ENST00000597424,;ZNF714,downstream_gene_variant,,ENST00000597086,;RNA5SP469,upstream_gene_variant,,ENST00000364165,;ZNF714,frameshift_variant,p.His330GlnfsTer13,ENST00000600435,;ZNF714,3_prime_UTR_variant,,ENST00000600770,;AC010620.1,upstream_gene_variant,,ENST00000456283,;	G	ENSG00000160352	ENST00000596143	Transcript	frameshift_variant	1315-1317	990-992	330-331	HK/QX	caTAAa/caGa	.	.	.	1	ZNF714	HGNC	27124	protein_coding	YES	CCDS54239.1	ENSP00000472368	ZN714_HUMAN	M0R2G4_HUMAN,M0QYV9_HUMAN	UPI000059D6C5	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF104,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAACATAAAAGAA	.	3	ESCA
TSHZ3	0	.	GRCh37	19	31770039	31770039	+	Silent	SNP	G	G	A	rs779306559	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660C>T	p.%3D	p.S220S	ENST00000240587	2/2	41	28	13	78	78	0	TSHZ3,synonymous_variant,p.%3D,ENST00000240587,;TSHZ3,downstream_gene_variant,,ENST00000560707,;	A	ENSG00000121297	ENST00000240587	Transcript	synonymous_variant	988	660	220	S	agC/agT	rs779306559	.	.	-1	TSHZ3	HGNC	30700	protein_coding	YES	CCDS12421.2	ENSP00000240587	TSH3_HUMAN	A1L0U7_HUMAN	UPI0000202000	.	.	.	2/2	.	hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5,PROSITE_patterns:PS00028,Pfam_domain:PF12756,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCGCTGCA	byFrequency	5	ESCA
S1PR4	0	.	GRCh37	19	3179168	3179168	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378C>T	p.%3D	p.F126F	ENST00000246115	1/1	10	4	6	25	25	0	S1PR4,synonymous_variant,p.%3D,ENST00000246115,;S1PR4,intron_variant,,ENST00000591346,;	T	ENSG00000125910	ENST00000246115	Transcript	synonymous_variant	433	378	126	F	ttC/ttT	.	.	.	1	S1PR4	HGNC	3170	protein_coding	YES	CCDS12105.1	ENSP00000246115	S1PR4_HUMAN	.	UPI0000050462	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF13,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01523,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCTTCACCGC	.	3	ESCA
TJP3	0	.	GRCh37	19	3734314	3734314	+	Intron	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.905-11T>C	.	.	ENST00000589378	.	59	55	4	113	113	0	TJP3,synonymous_variant,p.%3D,ENST00000382008,;TJP3,synonymous_variant,p.%3D,ENST00000262968,;TJP3,intron_variant,,ENST00000589378,;TJP3,intron_variant,,ENST00000539908,;TJP3,intron_variant,,ENST00000587686,;TJP3,intron_variant,,ENST00000541714,;TJP3,downstream_gene_variant,,ENST00000590545,;TJP3,downstream_gene_variant,,ENST00000587912,;	C	ENSG00000105289	ENST00000589378	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TJP3	HGNC	11829	protein_coding	YES	CCDS59332.1	ENSP00000465419	ZO3_HUMAN	F5H4S9_HUMAN,F5H2X0_HUMAN	UPI00003E3015	.	.	.	.	7/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTCTCCCCC	.	2	ESCA
CATSPERG	0	.	GRCh37	19	38845408	38845408	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1056C>T	p.%3D	p.F352F	ENST00000409235	9/29	62	39	23	68	68	0	CATSPERG,synonymous_variant,p.%3D,ENST00000215069,;CATSPERG,synonymous_variant,p.%3D,ENST00000409235,;CATSPERG,synonymous_variant,p.%3D,ENST00000410018,;CATSPERG,synonymous_variant,p.%3D,ENST00000489693,;CATSPERG,synonymous_variant,p.%3D,ENST00000409410,;CATSPERG,intron_variant,,ENST00000466060,;CATSPERG,missense_variant,p.Ser285Phe,ENST00000312265,;CATSPERG,missense_variant,p.Ser158Phe,ENST00000412458,;CATSPERG,3_prime_UTR_variant,,ENST00000471517,;CATSPERG,upstream_gene_variant,,ENST00000470292,;CATSPERG,upstream_gene_variant,,ENST00000585424,;	T	ENSG00000099338	ENST00000409235	Transcript	synonymous_variant	1171	1056	352	F	ttC/ttT	.	.	.	1	CATSPERG	HGNC	25243	protein_coding	YES	CCDS12514.2	ENSP00000386962	CTSRG_HUMAN	Q32MQ2_HUMAN	UPI000022A813	.	.	.	9/29	.	hmmpanther:PTHR14327,Pfam_domain:PF15064	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTCCATAG	.	5	ESCA
ATCAY	0	.	GRCh37	19	3907828	3907828	+	Missense_Mutation	SNP	G	G	A	rs372708763	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455G>A	p.Arg152His	p.R152H	ENST00000450849	5/13	94	57	36	190	190	0	ATCAY,missense_variant,p.Arg158His,ENST00000398448,;ATCAY,missense_variant,p.Arg152His,ENST00000600960,;ATCAY,missense_variant,p.Arg152His,ENST00000301260,;ATCAY,missense_variant,p.Arg152His,ENST00000450849,;ATCAY,downstream_gene_variant,,ENST00000598136,;ATCAY,3_prime_UTR_variant,,ENST00000597739,;	A	ENSG00000167654	ENST00000450849	Transcript	missense_variant	922	455	152	R/H	cGc/cAc	rs372708763	.	.	1	ATCAY	HGNC	779	protein_coding	YES	CCDS45923.1	ENSP00000390941	ATCAY_HUMAN	M0R197_HUMAN	UPI000006DE3B	.	tolerated(0.17)	probably_damaging(0.996)	5/13	.	Pfam_domain:PF12496,hmmpanther:PTHR12112	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGCGCCTGT	byFrequency|byCluster	5	ESCA
ZNF180	0	.	GRCh37	19	44980661	44980661	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2037T>C	p.%3D	p.H679H	ENST00000221327	5/5	50	34	15	26	26	0	ZNF180,synonymous_variant,p.%3D,ENST00000592529,;ZNF180,synonymous_variant,p.%3D,ENST00000391956,;ZNF180,synonymous_variant,p.%3D,ENST00000221327,;ZNF180,downstream_gene_variant,,ENST00000587047,;ZNF180,downstream_gene_variant,,ENST00000586637,;ZNF180,downstream_gene_variant,,ENST00000591064,;AC069278.4,upstream_gene_variant,,ENST00000591684,;ZNF180,downstream_gene_variant,,ENST00000585514,;ZNF180,3_prime_UTR_variant,,ENST00000592095,;ZNF180,3_prime_UTR_variant,,ENST00000590088,;ZNF285B,downstream_gene_variant,,ENST00000561698,;ZNF285B,downstream_gene_variant,,ENST00000318605,;	G	ENSG00000167384	ENST00000221327	Transcript	synonymous_variant	2319	2037	679	H	caT/caC	.	.	.	-1	ZNF180	HGNC	12970	protein_coding	YES	CCDS12639.1	ENSP00000221327	ZN180_HUMAN	K7EQX9_HUMAN,K7EQP0_HUMAN	UPI000013C7BD	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF27,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGATGCCT	.	5	ESCA
PRR12	0	.	GRCh37	19	50103072	50103072	+	Missense_Mutation	SNP	C	C	A	rs773495179	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4222C>A	p.Pro1408Thr	p.P1408T	ENST00000418929	5/14	40	26	13	84	83	0	PRR12,missense_variant,p.Pro1408Thr,ENST00000418929,;	A	ENSG00000126464	ENST00000418929	Transcript	missense_variant	4234	4222	1408	P/T	Cca/Aca	rs773495179	.	.	1	PRR12	HGNC	29217	protein_coding	YES	CCDS46143.1	ENSP00000394510	PRR12_HUMAN	.	UPI0001596889	.	.	possibly_damaging(0.803)	5/14	.	hmmpanther:PTHR14709:SF1,hmmpanther:PTHR14709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGACCCACCC	.	5	ESCA
CD33	0	.	GRCh37	19	51728475	51728475	+	Silent	SNP	G	G	T	rs143114570	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39G>T	p.%3D	p.G13G	ENST00000262262	2/7	35	23	12	69	69	0	CD33,synonymous_variant,p.%3D,ENST00000262262,;CD33,synonymous_variant,p.%3D,ENST00000391796,;CD33,intron_variant,,ENST00000436584,;CD33,intron_variant,,ENST00000421133,;CD33,non_coding_transcript_exon_variant,,ENST00000601785,;CD33,upstream_gene_variant,,ENST00000598473,;	T	ENSG00000105383	ENST00000262262	Transcript	synonymous_variant	60	39	13	G	ggG/ggT	rs143114570	.	.	1	CD33	HGNC	1659	protein_coding	YES	CCDS33084.1	ENSP00000262262	CD33_HUMAN	Q546G0_HUMAN	UPI000013D285	.	.	.	2/7	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF52	A:0.0054	A:0.0182	A:0.0043	.	A:0	A:0	A:0	A:0.0134	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGGGGCCCT	byFrequency|byCluster|by1000G	5	ESCA
ZNF578	0	.	GRCh37	19	52954490	52954490	+	5'Flank	SNP	C	C	T	rs762159411	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000421239	.	66	37	29	119	119	0	ZNF534,missense_variant,p.Arg108Cys,ENST00000301085,;ZNF534,missense_variant,p.Arg65Cys,ENST00000432303,;ZNF578,upstream_gene_variant,,ENST00000421239,;ZNF578,upstream_gene_variant,,ENST00000596674,;ZNF578,upstream_gene_variant,,ENST00000596382,;ZNF578,upstream_gene_variant,,ENST00000602221,;ZNF578,upstream_gene_variant,,ENST00000594118,;	T	ENSG00000258405	ENST00000421239	Transcript	upstream_gene_variant	.	.	.	.	.	rs762159411,COSM3960400	.	2339	1	ZNF578	HGNC	26449	protein_coding	YES	CCDS54310.1	ENSP00000459216	ZN578_HUMAN	M0QZV4_HUMAN	UPI000048A457	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODIFIER	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGCGCGCG	byFrequency	5	ESCA
ZNF320	0	.	GRCh37	19	53385108	53385108	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271G>A	p.Glu91Lys	p.E91K	ENST00000595635	8/8	101	70	31	53	53	0	ZNF320,missense_variant,p.Glu91Lys,ENST00000595635,;ZNF320,missense_variant,p.Glu77Lys,ENST00000597091,;ZNF320,missense_variant,p.Glu91Lys,ENST00000391781,;ZNF320,missense_variant,p.Glu91Lys,ENST00000593618,;ZNF320,intron_variant,,ENST00000597909,;ZNF320,downstream_gene_variant,,ENST00000594741,;ZNF320,downstream_gene_variant,,ENST00000597265,;ZNF320,intron_variant,,ENST00000600930,;ZNF320,upstream_gene_variant,,ENST00000598199,;	T	ENSG00000182986	ENST00000595635	Transcript	missense_variant	773	271	91	E/K	Gag/Aag	COSM1000680	.	.	-1	ZNF320	HGNC	13842	protein_coding	YES	CCDS33095.1	ENSP00000473091	ZN320_HUMAN	Q6ZP55_HUMAN,M0R2L4_HUMAN,M0R1K6_HUMAN,M0R0Z8_HUMAN,M0QZA2_HUMAN	UPI00004EC06C	.	tolerated(0.38)	benign(0.091)	8/8	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF197	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCAATTT	.	5	ESCA
MYADM	0	.	GRCh37	19	54377604	54377604	+	Missense_Mutation	SNP	C	C	T	rs765254576	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.821C>T	p.Ser274Leu	p.S274L	ENST00000391769	3/3	33	21	12	67	67	0	MYADM,missense_variant,p.Ser274Leu,ENST00000391771,;MYADM,missense_variant,p.Ser274Leu,ENST00000391769,;MYADM,missense_variant,p.Ser274Leu,ENST00000391768,;MYADM,missense_variant,p.Ser274Leu,ENST00000336967,;MYADM,missense_variant,p.Ser274Leu,ENST00000391770,;PRKCG,upstream_gene_variant,,ENST00000479081,;MYADM,downstream_gene_variant,,ENST00000414489,;MYADM,downstream_gene_variant,,ENST00000439000,;MYADM,downstream_gene_variant,,ENST00000448420,;MYADM,downstream_gene_variant,,ENST00000421337,;AC008440.5,downstream_gene_variant,,ENST00000413496,;	T	ENSG00000179820	ENST00000391769	Transcript	missense_variant	1101	821	274	S/L	tCg/tTg	rs765254576	.	.	1	MYADM	HGNC	7544	protein_coding	YES	CCDS12866.1	ENSP00000375649	MYADM_HUMAN	C9JZL8_HUMAN,C9JJV6_HUMAN,C9JC07_HUMAN,C9J5M0_HUMAN	UPI0000001BEF	.	tolerated(0.1)	benign(0.212)	3/3	.	Pfam_domain:PF01284,hmmpanther:PTHR17068:SF3,hmmpanther:PTHR17068,PROSITE_profiles:PS51225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCTCGAGAG	.	5	ESCA
RDH13	0	.	GRCh37	19	55556604	55556604	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.834G>A	p.%3D	p.E278E	ENST00000415061	7/7	59	39	20	112	112	0	RDH13,synonymous_variant,p.%3D,ENST00000396247,;RDH13,synonymous_variant,p.%3D,ENST00000415061,;CTC-550B14.7,intron_variant,,ENST00000593060,;CTC-550B14.7,downstream_gene_variant,,ENST00000586961,;CTC-550B14.7,downstream_gene_variant,,ENST00000586845,;CTC-550B14.6,non_coding_transcript_exon_variant,,ENST00000585492,;RDH13,upstream_gene_variant,,ENST00000591868,;RDH13,downstream_gene_variant,,ENST00000589605,;RDH13,upstream_gene_variant,,ENST00000586331,;RDH13,upstream_gene_variant,,ENST00000592423,;RDH13,3_prime_UTR_variant,,ENST00000592573,;RDH13,3_prime_UTR_variant,,ENST00000291892,;RDH13,intron_variant,,ENST00000591960,;RDH13,downstream_gene_variant,,ENST00000587721,;	T	ENSG00000160439	ENST00000415061	Transcript	synonymous_variant	978	834	278	E	gaG/gaA	.	.	.	-1	RDH13	HGNC	19978	protein_coding	YES	CCDS54320.1	ENSP00000391121	RDH13_HUMAN	K7EQB5_HUMAN,K7EMY5_HUMAN,G8JLA1_HUMAN	UPI000003F042	.	.	.	7/7	.	hmmpanther:PTHR24320:SF38,hmmpanther:PTHR24320,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTCCTCCGC	.	5	ESCA
LONP1	0	.	GRCh37	19	5692046	5692046	+	Silent	SNP	C	C	T	rs150782036	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2877G>A	p.%3D	p.R959R	ENST00000360614	18/18	40	10	30	44	44	0	LONP1,missense_variant,p.Val251Met,ENST00000589473,;LONP1,synonymous_variant,p.%3D,ENST00000590729,;LONP1,synonymous_variant,p.%3D,ENST00000360614,;LONP1,synonymous_variant,p.%3D,ENST00000593119,;LONP1,synonymous_variant,p.%3D,ENST00000540670,;LONP1,synonymous_variant,p.%3D,ENST00000585374,;RPL36,downstream_gene_variant,,ENST00000579649,;RPL36,downstream_gene_variant,,ENST00000347512,;HSD11B1L,downstream_gene_variant,,ENST00000342970,;RPL36,downstream_gene_variant,,ENST00000579446,;HSD11B1L,downstream_gene_variant,,ENST00000577917,;RPL36,downstream_gene_variant,,ENST00000394580,;HSD11B1L,downstream_gene_variant,,ENST00000339423,;HSD11B1L,downstream_gene_variant,,ENST00000578046,;HSD11B1L,downstream_gene_variant,,ENST00000581521,;HSD11B1L,downstream_gene_variant,,ENST00000581893,;HSD11B1L,downstream_gene_variant,,ENST00000583928,;HSD11B1L,downstream_gene_variant,,ENST00000301382,;HSD11B1L,downstream_gene_variant,,ENST00000577257,;LONP1,downstream_gene_variant,,ENST00000590206,;HSD11B1L,downstream_gene_variant,,ENST00000423665,;RPL36,downstream_gene_variant,,ENST00000582463,;HSD11B1L,downstream_gene_variant,,ENST00000579559,;RPL36,downstream_gene_variant,,ENST00000577222,;HSD11B1L,downstream_gene_variant,,ENST00000411793,;HSD11B1L,downstream_gene_variant,,ENST00000581773,;RPL36,downstream_gene_variant,,ENST00000582380,;LONP1,3_prime_UTR_variant,,ENST00000590558,;LONP1,non_coding_transcript_exon_variant,,ENST00000587552,;HSD11B1L,downstream_gene_variant,,ENST00000578832,;HSD11B1L,downstream_gene_variant,,ENST00000579562,;HSD11B1L,downstream_gene_variant,,ENST00000584904,;HSD11B1L,downstream_gene_variant,,ENST00000581423,;HSD11B1L,downstream_gene_variant,,ENST00000577920,;HSD11B1L,downstream_gene_variant,,ENST00000582346,;HSD11B1L,downstream_gene_variant,,ENST00000578167,;RPL36,downstream_gene_variant,,ENST00000590786,;	T	ENSG00000196365	ENST00000360614	Transcript	synonymous_variant	3035	2877	959	R	cgG/cgA	rs150782036	.	.	-1	LONP1	HGNC	9479	protein_coding	YES	CCDS12148.1	ENSP00000353826	LONM_HUMAN	K7EKE6_HUMAN,F5GZ27_HUMAN	UPI000012E7EF	.	.	.	18/18	.	.	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCACCGTTC	byCluster	5	ESCA
ZNF417	0	.	GRCh37	19	58427950	58427950	+	5'Flank	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000312026	.	36	17	19	56	56	0	ZNF417,5_prime_UTR_variant,,ENST00000595559,;ZNF417,5_prime_UTR_variant,,ENST00000599251,;ZNF417,5_prime_UTR_variant,,ENST00000598526,;ZNF417,5_prime_UTR_variant,,ENST00000597515,;ZNF417,upstream_gene_variant,,ENST00000598629,;ZNF417,upstream_gene_variant,,ENST00000594396,;ZNF417,upstream_gene_variant,,ENST00000536263,;ZNF417,upstream_gene_variant,,ENST00000312026,;CTD-2583A14.9,5_prime_UTR_variant,,ENST00000602124,;	A	ENSG00000173480	ENST00000312026	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	6	-1	ZNF417	HGNC	20646	protein_coding	YES	CCDS12965.1	ENSP00000311319	ZN417_HUMAN	M0R2A6_HUMAN,M0R178_HUMAN,M0R0V5_HUMAN,M0R0M6_HUMAN,M0R082_HUMAN,M0QXF5_HUMAN,B4DEU1_HUMAN	UPI000013F249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACACAGCCG	.	5	ESCA
ARHGEF18	0	.	GRCh37	19	7505040	7505040	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214C>T	p.Arg72Cys	p.R72C	ENST00000359920	1/20	67	39	28	101	101	0	ARHGEF18,missense_variant,p.Arg72Cys,ENST00000359920,;ARHGEF18,intron_variant,,ENST00000319670,;CTD-2207O23.3,intron_variant,,ENST00000593531,;ARHGEF18,intron_variant,,ENST00000599752,;ARHGEF18,upstream_gene_variant,,ENST00000595600,;	T	ENSG00000104880	ENST00000359920	Transcript	missense_variant	467	214	72	R/C	Cgc/Tgc	COSM1003208	.	.	1	ARHGEF18	HGNC	17090	protein_coding	YES	CCDS45946.1	ENSP00000352995	ARHGI_HUMAN	M0R125_HUMAN	UPI0000D6170D	.	tolerated_low_confidence(0.07)	benign(0.003)	1/20	.	hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF9	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGCCGCCCC	.	5	ESCA
XAB2	0	.	GRCh37	19	7689248	7689248	+	Silent	SNP	G	G	A	rs201776166	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.906C>T	p.%3D	p.F302F	ENST00000358368	7/19	41	37	4	79	79	0	XAB2,synonymous_variant,p.%3D,ENST00000358368,;XAB2,synonymous_variant,p.%3D,ENST00000534844,;XAB2,non_coding_transcript_exon_variant,,ENST00000595288,;XAB2,upstream_gene_variant,,ENST00000596134,;XAB2,upstream_gene_variant,,ENST00000600230,;	A	ENSG00000076924	ENST00000358368	Transcript	synonymous_variant	944	906	302	F	ttC/ttT	rs201776166,COSM4082856	.	.	-1	XAB2	HGNC	14089	protein_coding	YES	CCDS32892.1	ENSP00000351137	SYF1_HUMAN	Q68CN2_HUMAN,F5H315_HUMAN	UPI0000001BDE	.	.	.	7/19	.	SMART_domains:SM00386,hmmpanther:PTHR11246,hmmpanther:PTHR11246:SF13	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCTCGAACTG	byCluster|by1000G	3	ESCA
MUC16	0	.	GRCh37	19	9085519	9085519	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6296C>A	p.Ser2099Tyr	p.S2099Y	ENST00000397910	1/84	74	51	22	56	56	0	MUC16,missense_variant,p.Ser2099Tyr,ENST00000397910,;	T	ENSG00000181143	ENST00000397910	Transcript	missense_variant	6500	6296	2099	S/Y	tCt/tAt	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	1/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAGATGTG	.	5	ESCA
COL11A1	0	.	GRCh37	1	103355076	103355076	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4399C>G	p.Gln1467Glu	p.Q1467E	ENST00000370096	59/67	119	76	42	82	82	0	COL11A1,missense_variant,p.Gln1351Glu,ENST00000512756,;COL11A1,missense_variant,p.Gln1428Glu,ENST00000353414,;COL11A1,missense_variant,p.Gln1467Glu,ENST00000370096,;COL11A1,missense_variant,p.Gln1479Glu,ENST00000358392,;	C	ENSG00000060718	ENST00000370096	Transcript	missense_variant	4712	4399	1467	Q/E	Caa/Gaa	.	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	unknown(0)	59/67	.	hmmpanther:PTHR24023:SF42,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTGTTCTC	.	5	ESCA
CSDE1	0	.	GRCh37	1	115268876	115268877	+	Frame_Shift_Ins	INS	-	-	AATC	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1730_1733dupGATT	p.Phe578LeufsTer4	p.F578Lfs*4	ENST00000438362	14/20	62	44	18	54	54	0	CSDE1,frameshift_variant,p.Phe547LeufsTer4,ENST00000369530,;CSDE1,frameshift_variant,p.Phe501LeufsTer4,ENST00000261443,;CSDE1,frameshift_variant,p.Phe532LeufsTer4,ENST00000358528,;CSDE1,frameshift_variant,p.Phe501LeufsTer4,ENST00000339438,;CSDE1,frameshift_variant,p.Phe402LeufsTer4,ENST00000530886,;CSDE1,frameshift_variant,p.Phe532LeufsTer4,ENST00000534699,;CSDE1,frameshift_variant,p.Phe578LeufsTer4,ENST00000438362,;Y_RNA,upstream_gene_variant,,ENST00000365030,;CSDE1,non_coding_transcript_exon_variant,,ENST00000483030,;CSDE1,upstream_gene_variant,,ENST00000530784,;	AATC	ENSG00000009307	ENST00000438362	Transcript	frameshift_variant	2112-2113	1733-1734	578	F/LIX	ttt/ttGATTt	.	.	.	-1	CSDE1	HGNC	29905	protein_coding	YES	CCDS55626.1	ENSP00000407724	.	Q9UG93_HUMAN,G5E9Q2_HUMAN,E9PLD4_HUMAN,E9PKN4_HUMAN	UPI0000D99B0F	.	.	.	14/20	.	Superfamily_domains:SSF50249,SMART_domains:SM00357,Pfam_domain:PF00313,Gene3D:2.40.50.140,PROSITE_patterns:PS00352,hmmpanther:PTHR12913,hmmpanther:PTHR12913:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCAATAAATCC	.	3	ESCA
FAM46C	0	.	GRCh37	1	118167490	118167490	+	3'UTR	SNP	G	G	T	rs193170252	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*824G>T	.	.	ENST00000369448	2/2	25	18	7	15	15	0	FAM46C,3_prime_UTR_variant,,ENST00000369448,;	T	ENSG00000183508	ENST00000369448	Transcript	3_prime_UTR_variant	2247	.	.	.	.	rs193170252	.	.	1	FAM46C	HGNC	24712	protein_coding	YES	CCDS896.1	ENSP00000358458	FA46C_HUMAN	.	UPI0000070C6C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAGAATTC	by1000G	5	ESCA
SPAG17	0	.	GRCh37	1	118514619	118514619	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6193G>T	p.Ala2065Ser	p.A2065S	ENST00000336338	45/49	69	43	26	39	39	0	SPAG17,missense_variant,p.Ala545Ser,ENST00000437255,;SPAG17,missense_variant,p.Ala2065Ser,ENST00000336338,;SPAG17,non_coding_transcript_exon_variant,,ENST00000492438,;SPAG17,upstream_gene_variant,,ENST00000469128,;SPAG17,downstream_gene_variant,,ENST00000483383,;	A	ENSG00000155761	ENST00000336338	Transcript	missense_variant	6259	6193	2065	A/S	Gcc/Tcc	.	.	.	-1	SPAG17	HGNC	26620	protein_coding	YES	CCDS899.1	ENSP00000337804	SPG17_HUMAN	A7LBF9_HUMAN	UPI00001601FD	.	tolerated(0.07)	benign(0.343)	45/49	.	hmmpanther:PTHR21963	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGCAGCAG	.	5	ESCA
PDE4DIP	0	.	GRCh37	1	145074926	145074926	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*38T>C	.	.	ENST00000369345	2/2	59	53	5	55	55	0	PDE4DIP,3_prime_UTR_variant,,ENST00000369345,;PDE4DIP,intron_variant,,ENST00000369348,;PDE4DIP,intron_variant,,ENST00000369359,;PDE4DIP,intron_variant,,ENST00000530740,;PDE4DIP,intron_variant,,ENST00000528552,;PDE4DIP,intron_variant,,ENST00000533396,;PDE4DIP,intron_variant,,ENST00000527063,;PDE4DIP,intron_variant,,ENST00000526359,;PDE4DIP,intron_variant,,ENST00000528661,;	G	ENSG00000178104	ENST00000369345	Transcript	3_prime_UTR_variant	583	.	.	.	.	.	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	.	.	ENSP00000358351	.	Q5TB27_HUMAN	UPI0000237213	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACAGATTTTT	.	2	ESCA
PDE4DIP	0	.	GRCh37	1	145075752	145075752	+	Silent	SNP	C	C	T	rs374020871	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111G>A	p.%3D	p.T37T	ENST00000369345	1/2	81	75	6	148	148	0	PDE4DIP,synonymous_variant,p.%3D,ENST00000369345,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369348,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369359,;PDE4DIP,synonymous_variant,p.%3D,ENST00000530740,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000528552,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000533396,;PDE4DIP,synonymous_variant,p.%3D,ENST00000526359,;PDE4DIP,synonymous_variant,p.%3D,ENST00000528661,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000527063,;	T	ENSG00000178104	ENST00000369345	Transcript	synonymous_variant	326	111	37	T	acG/acA	rs374020871,COSM1261772	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	.	.	ENSP00000358351	.	Q5TB27_HUMAN	UPI0000237213	.	.	.	1/2	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.T37T|c.111G>A|3	MUTECT|MUSE	GTTCGCGTCGC	byCluster	2	ESCA
ITGA10	0	.	GRCh37	1	145542801	145542801	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*523G>A	.	.	ENST00000369304	30/30	66	40	25	58	58	0	ITGA10,3_prime_UTR_variant,,ENST00000369304,;ITGA10,downstream_gene_variant,,ENST00000538811,;ITGA10,downstream_gene_variant,,ENST00000539363,;RP11-315I20.3,upstream_gene_variant,,ENST00000415065,;	A	ENSG00000143127	ENST00000369304	Transcript	3_prime_UTR_variant	4202	.	.	.	.	.	.	.	1	ITGA10	HGNC	6135	protein_coding	YES	CCDS918.1	ENSP00000358310	ITA10_HUMAN	.	UPI000013D8D1	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGGGGAGAG	.	5	ESCA
NBPF12	0	.	GRCh37	1	146465946	146465946	+	Missense_Mutation	SNP	C	C	T	rs200985386	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9821C>T	p.Ser3274Leu	p.S3274L	ENST00000442909	82/82	64	19	45	55	55	0	NBPF12,missense_variant,p.Ser3274Leu,ENST00000442909,;NBPF12,3_prime_UTR_variant,,ENST00000309471,;NBPF12,3_prime_UTR_variant,,ENST00000446760,;NBPF12,downstream_gene_variant,,ENST00000446080,;	T	ENSG00000186275	ENST00000442909	Transcript	missense_variant	10657	9821	3274	S/L	tCg/tTg	rs200985386	.	.	1	NBPF12	HGNC	24297	protein_coding	YES	.	ENSP00000391116	NBPFC_HUMAN	S4R3H5_HUMAN,H7BZX4_HUMAN,H7BYX2_HUMAN,F8WEX1_HUMAN,F5GXN6_HUMAN	UPI0001B798CE	.	.	possibly_damaging(0.459)	82/82	.	PROSITE_profiles:PS51316,hmmpanther:PTHR14199:SF16,hmmpanther:PTHR14199,Pfam_domain:PF06758	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATTCGACTC	byCluster	5	ESCA
FLG	0	.	GRCh37	1	152278839	152278841	+	In_Frame_Del	DEL	TGT	TGT	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	TGT	TGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8521_8523delACA	p.Thr2841del	p.T2841del	ENST00000368799	3/3	159	130	29	206	206	0	FLG,inframe_deletion,p.Thr2841del,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	-	ENSG00000143631	ENST00000368799	Transcript	inframe_deletion	8557-8559	8521-8523	2841	T/-	ACA/-	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	.	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATTACGTGTTGTTC	.	3	ESCA
DENND4B	0	.	GRCh37	1	153905768	153905768	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3358G>A	p.Asp1120Asn	p.D1120N	ENST00000361217	21/28	30	18	12	49	49	0	DENND4B,missense_variant,p.Asp1131Asn,ENST00000368646,;DENND4B,missense_variant,p.Asp1120Asn,ENST00000361217,;DENND4B,upstream_gene_variant,,ENST00000474386,;DENND4B,upstream_gene_variant,,ENST00000492898,;DENND4B,upstream_gene_variant,,ENST00000531748,;DENND4B,downstream_gene_variant,,ENST00000477746,;DENND4B,upstream_gene_variant,,ENST00000462423,;DENND4B,upstream_gene_variant,,ENST00000480340,;	T	ENSG00000198837	ENST00000361217	Transcript	missense_variant	3777	3358	1120	D/N	Gac/Aac	.	.	.	-1	DENND4B	HGNC	29044	protein_coding	YES	CCDS44228.1	ENSP00000354597	DEN4B_HUMAN	.	UPI000047EA3E	.	deleterious(0.04)	probably_damaging(0.989)	21/28	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTCCCACT	.	5	ESCA
ADAR	0	.	GRCh37	1	154562755	154562755	+	Missense_Mutation	SNP	G	G	A	rs748161184	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2401C>T	p.Arg801Cys	p.R801C	ENST00000368474	7/15	80	48	32	81	81	0	ADAR,missense_variant,p.Arg844Cys,ENST00000292205,;ADAR,missense_variant,p.Arg796Cys,ENST00000529168,;ADAR,missense_variant,p.Arg506Cys,ENST00000368471,;ADAR,missense_variant,p.Arg801Cys,ENST00000368474,;ADAR,upstream_gene_variant,,ENST00000530954,;ADAR,upstream_gene_variant,,ENST00000534279,;ADAR,upstream_gene_variant,,ENST00000492630,;	A	ENSG00000160710	ENST00000368474	Transcript	missense_variant	2601	2401	801	R/C	Cgc/Tgc	rs748161184	.	.	-1	ADAR	HGNC	225	protein_coding	YES	CCDS1071.1	ENSP00000357459	DSRAD_HUMAN	.	UPI000045626B	.	deleterious(0)	possibly_damaging(0.836)	7/15	.	hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGCGTTCTG	.	5	ESCA
MTX1	0	.	GRCh37	1	155184007	155184007	+	3'Flank	SNP	A	A	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000368376	.	11	8	3	17	17	0	MTX1,downstream_gene_variant,,ENST00000368376,;MTX1,downstream_gene_variant,,ENST00000609421,;MTX1,downstream_gene_variant,,ENST00000316721,;RP11-263K19.6,upstream_gene_variant,,ENST00000455788,;GBAP1,non_coding_transcript_exon_variant,,ENST00000368374,;GBAP1,non_coding_transcript_exon_variant,,ENST00000486869,;MTX1,downstream_gene_variant,,ENST00000495589,;GBAP1,downstream_gene_variant,,ENST00000462587,;GBAP1,non_coding_transcript_exon_variant,,ENST00000486197,;GBAP1,non_coding_transcript_exon_variant,,ENST00000473223,;GBAP1,non_coding_transcript_exon_variant,,ENST00000459805,;MTX1,downstream_gene_variant,,ENST00000481771,;MTX1,downstream_gene_variant,,ENST00000424959,;GBAP1,downstream_gene_variant,,ENST00000463838,;MTX1,downstream_gene_variant,,ENST00000495492,;GBAP1,non_coding_transcript_exon_variant,,ENST00000313929,;GBAP1,downstream_gene_variant,,ENST00000566701,;	C	ENSG00000173171	ENST00000368376	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	393	1	MTX1	HGNC	7504	protein_coding	YES	CCDS1100.1	ENSP00000357360	MTX1_HUMAN	.	UPI0000225CC9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAAAGTGAG	.	2	ESCA
CD244	0	.	GRCh37	1	160811229	160811229	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441C>T	p.%3D	p.D147D	ENST00000368033	3/9	29	19	10	33	33	0	CD244,synonymous_variant,p.%3D,ENST00000368032,;CD244,synonymous_variant,p.%3D,ENST00000368033,;CD244,synonymous_variant,p.%3D,ENST00000368034,;CD244,intron_variant,,ENST00000322302,;CD244,upstream_gene_variant,,ENST00000481677,;CD244,synonymous_variant,p.%3D,ENST00000492063,;	A	ENSG00000122223	ENST00000368033	Transcript	synonymous_variant	524	441	147	D	gaC/gaT	.	.	.	-1	CD244	HGNC	18171	protein_coding	YES	CCDS53399.1	ENSP00000357012	CD244_HUMAN	.	UPI0000367808	.	.	.	3/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF3,Pfam_domain:PF13895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTGTCCAG	.	5	ESCA
F5	0	.	GRCh37	1	169519183	169519183	+	Missense_Mutation	SNP	C	C	A	rs752162680	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1467G>T	p.Glu489Asp	p.E489D	ENST00000367797	10/25	64	36	27	48	48	0	F5,missense_variant,p.Glu489Asp,ENST00000367796,;F5,missense_variant,p.Glu489Asp,ENST00000367797,;F5,3_prime_UTR_variant,,ENST00000546081,;	A	ENSG00000198734	ENST00000367797	Transcript	missense_variant	1669	1467	489	E/D	gaG/gaT	rs752162680	.	.	-1	F5	HGNC	3542	protein_coding	YES	CCDS1281.1	ENSP00000356771	FA5_HUMAN	Q8TD21_HUMAN,Q2HZZ1_HUMAN,Q1L610_HUMAN	UPI0000070F01	.	tolerated(0.12)	benign(0.201)	10/25	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.40.420,Superfamily_domains:SSF49503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAACTCTAA	byFrequency	5	ESCA
FMO6P	0	.	GRCh37	1	171121381	171121381	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1160G>T	p.Trp387Leu	p.W387L	ENST00000236166	6/8	35	26	9	27	27	0	FMO6P,missense_variant,p.Trp387Leu,ENST00000236166,;FMO6P,3_prime_UTR_variant,,ENST00000367754,;	T	ENSG00000117507	ENST00000236166	Transcript	missense_variant	1270	1160	387	W/L	tGg/tTg	.	.	.	1	FMO6P	HGNC	24024	protein_coding	YES	.	ENSP00000236166	FMO6_HUMAN	.	UPI00033351F0	.	deleterious(0.01)	benign(0)	6/8	.	Prints_domain:PR00370,Superfamily_domains:SSF51905,Gene3D:3.50.50.60,Pfam_domain:PF00743,hmmpanther:PTHR23023:SF81,hmmpanther:PTHR23023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCTGGTGGG	.	2	ESCA
RGS8	0	.	GRCh37	1	182617405	182617405	+	Missense_Mutation	SNP	G	G	A	rs759655284	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281C>T	p.Thr94Met	p.T94M	ENST00000258302	5/6	37	23	14	49	47	1	RGS8,missense_variant,p.Thr76Met,ENST00000367557,;RGS8,missense_variant,p.Thr94Met,ENST00000258302,;RGS8,missense_variant,p.Thr76Met,ENST00000367556,;RGS8,missense_variant,p.Thr76Met,ENST00000483095,;RP11-317P15.5,upstream_gene_variant,,ENST00000570153,;	A	ENSG00000135824	ENST00000258302	Transcript	missense_variant	371	281	94	T/M	aCg/aTg	rs759655284	.	.	-1	RGS8	HGNC	16810	protein_coding	YES	CCDS1349.1	ENSP00000258302	RGS8_HUMAN	.	UPI0000038BF1	.	deleterious(0)	probably_damaging(0.997)	5/6	.	PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF147,Gene3D:1.10.196.10,Pfam_domain:PF00615,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACTCCGTCTTC	.	4	ESCA
KLHDC7A	0	.	GRCh37	1	18807852	18807852	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377G>A	p.Arg126Gln	p.R126Q	ENST00000400664	1/1	66	44	22	107	107	0	KLHDC7A,missense_variant,p.Arg126Gln,ENST00000400664,;	A	ENSG00000179023	ENST00000400664	Transcript	missense_variant	429	377	126	R/Q	cGg/cAg	.	.	.	1	KLHDC7A	HGNC	26791	protein_coding	YES	CCDS185.2	ENSP00000383505	KLD7A_HUMAN	A4FU39_HUMAN	UPI0000E0501F	.	tolerated(0.63)	benign(0.001)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGAGCGGGGCG	.	3	ESCA
PKP1	0	.	GRCh37	1	201294233	201294239	+	Frame_Shift_Del	DEL	ATCATCA	ATCATCA	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	ATCATCA	ATCATCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2063_2069delTCATCAA	p.Ile688ThrfsTer45	p.I688Tfs*45	ENST00000263946	12/15	21	9	12	52	52	0	PKP1,frameshift_variant,p.Ile688ThrfsTer45,ENST00000352845,;PKP1,frameshift_variant,p.Ile688ThrfsTer45,ENST00000263946,;PKP1,frameshift_variant,p.Ile667ThrfsTer45,ENST00000367324,;PKP1,upstream_gene_variant,,ENST00000477817,;PKP1,downstream_gene_variant,,ENST00000475988,;	-	ENSG00000081277	ENST00000263946	Transcript	frameshift_variant	2313-2319	2062-2068	688-690	IIN/X	ATCATCAac/ac	.	.	.	1	PKP1	HGNC	9023	protein_coding	YES	CCDS30966.1	ENSP00000263946	PKP1_HUMAN	B4DRX5_HUMAN	UPI0000131B86	.	.	.	12/15	.	hmmpanther:PTHR10372:SF3,hmmpanther:PTHR10372,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R693Q|c.2078G>A|3,BUFFER|p.R672Q|c.2015G>A|3	INDELOCATOR|VARSCANI	AACAACATCATCAACCTG	.	2	ESCA
FLVCR1	0	.	GRCh37	1	213061936	213061936	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1413G>A	p.%3D	p.Q471Q	ENST00000366971	7/10	48	32	16	37	37	0	FLVCR1,synonymous_variant,p.%3D,ENST00000419102,;FLVCR1,synonymous_variant,p.%3D,ENST00000366971,;FLVCR1,splice_region_variant,,ENST00000483790,;FLVCR1,downstream_gene_variant,,ENST00000474693,;	A	ENSG00000162769	ENST00000366971	Transcript	synonymous_variant	1611	1413	471	Q	caG/caA	.	.	.	1	FLVCR1	HGNC	24682	protein_coding	YES	CCDS1510.1	ENSP00000355938	FLVC1_HUMAN	.	UPI000006D3BB	.	.	.	7/10	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,Gene3D:1.20.1250.20,Pfam_domain:PF07690,hmmpanther:PTHR10924:SF2,hmmpanther:PTHR10924,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACAGGTAAA	.	5	ESCA
KDM1A	0	.	GRCh37	1	23357117	23357118	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.508dupG	p.Glu170GlyfsTer37	p.E170Gfs*37	ENST00000400181	2/21	55	43	12	29	29	0	KDM1A,frameshift_variant,p.Glu170GlyfsTer17,ENST00000356634,;KDM1A,frameshift_variant,p.Glu170GlyfsTer37,ENST00000542151,;KDM1A,frameshift_variant,p.Glu170GlyfsTer37,ENST00000400181,;RP1-184J9.2,intron_variant,,ENST00000427154,;	G	ENSG00000004487	ENST00000400181	Transcript	frameshift_variant	611-612	507-508	169-170	-/X	-/G	.	.	.	1	KDM1A	HGNC	29079	protein_coding	YES	CCDS53278.1	ENSP00000383042	KDM1A_HUMAN	.	UPI0000403137	.	.	.	2/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10742:SF245,hmmpanther:PTHR10742,PIRSF_domain:PIRSF038051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTGAAGAACC	.	3	ESCA
AHCTF1	0	.	GRCh37	1	247016531	247016531	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4452G>T	p.Glu1484Asp	p.E1484D	ENST00000326225	32/36	28	15	13	26	26	0	AHCTF1,missense_variant,p.Glu1475Asp,ENST00000391829,;AHCTF1,missense_variant,p.Glu1510Asp,ENST00000366508,;AHCTF1,missense_variant,p.Glu1484Asp,ENST00000326225,;AHCTF1,non_coding_transcript_exon_variant,,ENST00000470300,;AHCTF1,non_coding_transcript_exon_variant,,ENST00000483900,;AHCTF1,upstream_gene_variant,,ENST00000498601,;	A	ENSG00000153207	ENST00000326225	Transcript	missense_variant	4549	4452	1484	E/D	gaG/gaT	.	.	.	-1	AHCTF1	HGNC	24618	protein_coding	YES	CCDS1629.2	ENSP00000355465	ELYS_HUMAN	C9J5C5_HUMAN	UPI0000204034	.	tolerated(0.12)	benign(0.045)	32/36	.	hmmpanther:PTHR21583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCGCTCAGA	.	5	ESCA
RUNX3	0	.	GRCh37	1	25291220	25291220	+	5'UTR	DEL	T	T	-	rs531640124,rs562889237	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-158delA	.	.	ENST00000399916	1/6	23	13	10	22	22	0	RUNX3,5_prime_UTR_variant,,ENST00000399916,;RUNX3,intron_variant,,ENST00000338888,;RP11-84D1.2,downstream_gene_variant,,ENST00000568143,;RP11-84D1.1,downstream_gene_variant,,ENST00000456316,;RUNX3,intron_variant,,ENST00000479341,;	-	ENSG00000020633	ENST00000399916	Transcript	5_prime_UTR_variant	282	.	.	.	.	rs531640124,rs562889237	.	.	-1	RUNX3	HGNC	10473	protein_coding	YES	CCDS30633.1	ENSP00000382800	RUNX3_HUMAN	.	UPI000002B2FF	.	.	.	1/6	.	.	-:0.0048	-:0.0045	-:0.0144	.	-:0	-:0.006	-:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTCTCTTTTTT	byFrequency|byCluster|by1000G	2	ESCA
SLC9A1	0	.	GRCh37	1	27425582	27425582	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1216G>T	.	.	ENST00000263980	12/12	33	19	13	47	47	0	SLC9A1,3_prime_UTR_variant,,ENST00000263980,;SLC9A1,downstream_gene_variant,,ENST00000545949,;SLC9A1,intron_variant,,ENST00000490329,;SLC9A1,non_coding_transcript_exon_variant,,ENST00000374089,;SLC9A1,downstream_gene_variant,,ENST00000447808,;	A	ENSG00000090020	ENST00000263980	Transcript	3_prime_UTR_variant	4240	.	.	.	.	.	.	.	-1	SLC9A1	HGNC	11071	protein_coding	YES	CCDS295.1	ENSP00000263980	SL9A1_HUMAN	B4DTZ6_HUMAN,B1ALD5_HUMAN	UPI000012FD1B	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCTCTGGGG	.	5	ESCA
EPB41	0	.	GRCh37	1	29365939	29365939	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1636+1G>A	.	p.X546_splice	ENST00000343067	.	55	38	16	61	61	0	EPB41,splice_donor_variant,,ENST00000356093,;EPB41,splice_donor_variant,,ENST00000373798,;EPB41,splice_donor_variant,,ENST00000347529,;EPB41,splice_donor_variant,,ENST00000373800,;EPB41,splice_donor_variant,,ENST00000398863,;EPB41,splice_donor_variant,,ENST00000373797,;EPB41,splice_donor_variant,,ENST00000349460,;EPB41,splice_donor_variant,,ENST00000343067,;	A	ENSG00000159023	ENST00000343067	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	EPB41	HGNC	3377	protein_coding	YES	CCDS53288.1	ENSP00000345259	41_HUMAN	.	UPI000014177D	.	.	.	.	11/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGGTTTGT	.	5	ESCA
DLGAP3	0	.	GRCh37	1	35334651	35334651	+	Silent	SNP	G	G	A	rs774076646	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2040C>T	p.%3D	p.G680G	ENST00000373347	9/12	30	17	13	48	48	0	DLGAP3,synonymous_variant,p.%3D,ENST00000373347,;DLGAP3,synonymous_variant,p.%3D,ENST00000235180,;	A	ENSG00000116544	ENST00000373347	Transcript	synonymous_variant	2309	2040	680	G	ggC/ggT	rs774076646	.	.	-1	DLGAP3	HGNC	30368	protein_coding	YES	CCDS30670.1	ENSP00000362444	DLGP3_HUMAN	B4DH33_HUMAN	UPI00003D4D81	.	.	.	9/12	.	hmmpanther:PTHR12353:SF4,hmmpanther:PTHR12353,Pfam_domain:PF03359	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCACGCCAGC	byFrequency	5	ESCA
ZSWIM5	0	.	GRCh37	1	45484252	45484252	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3432G>T	p.Lys1144Asn	p.K1144N	ENST00000359600	14/14	59	41	17	79	79	0	ZSWIM5,missense_variant,p.Lys1144Asn,ENST00000359600,;UROD,downstream_gene_variant,,ENST00000428106,;UROD,downstream_gene_variant,,ENST00000434478,;UROD,downstream_gene_variant,,ENST00000246337,;UROD,downstream_gene_variant,,ENST00000462688,;UROD,downstream_gene_variant,,ENST00000491773,;UROD,downstream_gene_variant,,ENST00000472254,;UROD,downstream_gene_variant,,ENST00000466193,;UROD,downstream_gene_variant,,ENST00000465678,;UROD,downstream_gene_variant,,ENST00000469548,;UROD,downstream_gene_variant,,ENST00000494399,;UROD,downstream_gene_variant,,ENST00000478467,;UROD,downstream_gene_variant,,ENST00000486699,;UROD,downstream_gene_variant,,ENST00000463092,;UROD,downstream_gene_variant,,ENST00000490385,;UROD,downstream_gene_variant,,ENST00000460334,;UROD,downstream_gene_variant,,ENST00000496439,;UROD,downstream_gene_variant,,ENST00000491300,;UROD,downstream_gene_variant,,ENST00000473012,;UROD,downstream_gene_variant,,ENST00000460906,;	A	ENSG00000162415	ENST00000359600	Transcript	missense_variant	3638	3432	1144	K/N	aaG/aaT	.	.	.	-1	ZSWIM5	HGNC	29299	protein_coding	YES	CCDS41319.1	ENSP00000352614	ZSWM5_HUMAN	.	UPI00001C1D76	.	deleterious(0)	unknown(0)	14/14	.	hmmpanther:PTHR22619,hmmpanther:PTHR22619:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGCCTTGCT	.	5	ESCA
EFCAB14	0	.	GRCh37	1	47157529	47157529	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660G>A	p.%3D	p.K220K	ENST00000371933	5/11	55	48	7	40	40	0	EFCAB14,synonymous_variant,p.%3D,ENST00000544071,;EFCAB14,synonymous_variant,p.%3D,ENST00000371933,;EFCAB14-AS1,intron_variant,,ENST00000442839,;EFCAB14-AS1,intron_variant,,ENST00000418985,;EFCAB14,non_coding_transcript_exon_variant,,ENST00000484461,;EFCAB14,upstream_gene_variant,,ENST00000479745,;EFCAB14,upstream_gene_variant,,ENST00000487741,;EFCAB14,upstream_gene_variant,,ENST00000481623,;	T	ENSG00000159658	ENST00000371933	Transcript	synonymous_variant	1637	660	220	K	aaG/aaA	.	.	.	-1	EFCAB14	HGNC	29051	protein_coding	YES	CCDS30706.1	ENSP00000361001	EFC14_HUMAN	.	UPI000003B443	.	.	.	5/11	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15717,hmmpanther:PTHR15717:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTCTTGTG	.	4	ESCA
C1orf177	0	.	GRCh37	1	55307673	55307673	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*127G>T	.	.	ENST00000371273	10/10	50	32	18	60	60	0	C1orf177,3_prime_UTR_variant,,ENST00000358193,;C1orf177,3_prime_UTR_variant,,ENST00000371273,;	T	ENSG00000162398	ENST00000371273	Transcript	3_prime_UTR_variant	1399	.	.	.	.	.	.	.	1	C1orf177	HGNC	26854	protein_coding	YES	CCDS44153.1	ENSP00000360320	CA177_HUMAN	.	UPI0000204405	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGGGAGAGA	.	5	ESCA
NEGR1	0	.	GRCh37	1	71869849	71869849	+	3'UTR	SNP	T	T	A	rs950873	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3280A>T	.	.	ENST00000357731	7/7	87	60	27	57	56	0	NEGR1,3_prime_UTR_variant,,ENST00000306821,;NEGR1,3_prime_UTR_variant,,ENST00000357731,;NEGR1,downstream_gene_variant,,ENST00000434200,;ZRANB2-AS2,intron_variant,,ENST00000583678,;ZRANB2-AS2,intron_variant,,ENST00000594152,;ZRANB2-AS2,intron_variant,,ENST00000600103,;ZRANB2-AS2,intron_variant,,ENST00000599146,;ZRANB2-AS2,intron_variant,,ENST00000430605,;ZRANB2-AS2,intron_variant,,ENST00000608579,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585499,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587306,;ZRANB2-AS2,upstream_gene_variant,,ENST00000586006,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587066,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585415,;ZRANB2-AS2,upstream_gene_variant,,ENST00000590186,;NEGR1,downstream_gene_variant,,ENST00000474357,;	A	ENSG00000172260	ENST00000357731	Transcript	3_prime_UTR_variant	4585	.	.	.	.	rs950873	.	.	-1	NEGR1	HGNC	17302	protein_coding	YES	CCDS661.1	ENSP00000350364	NEGR1_HUMAN	Q8N440_HUMAN,Q68DZ8_HUMAN	UPI00000477EE	.	.	.	7/7	.	.	A:0.0274	A:0.0219	A:0.0648	.	A:0.005	A:0.0219	A:0.0368	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TATATTTTTTT	byFrequency|byCluster|by1000G	3	ESCA
CSRP2BP	0	.	GRCh37	20	18165377	18165377	+	Missense_Mutation	SNP	G	G	A	rs369048963	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2116G>A	p.Val706Ile	p.V706I	ENST00000435364	9/10	24	17	7	20	20	0	CSRP2BP,missense_variant,p.Val705Ile,ENST00000377681,;CSRP2BP,missense_variant,p.Val578Ile,ENST00000489634,;CSRP2BP,missense_variant,p.Val706Ile,ENST00000435364,;	A	ENSG00000149474	ENST00000435364	Transcript	missense_variant	2457	2116	706	V/I	Gtc/Atc	rs369048963	.	.	1	CSRP2BP	HGNC	15904	protein_coding	YES	CCDS13133.1	ENSP00000392318	CSR2B_HUMAN	D6RAU4_HUMAN	UPI000013DB91	.	deleterious(0.02)	probably_damaging(0.984)	9/10	.	Superfamily_domains:SSF55729,Gene3D:3.40.630.30,Pfam_domain:PF00583,hmmpanther:PTHR20916,hmmpanther:PTHR20916:SF0,PROSITE_profiles:PS51186	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCGTCCAC	byFrequency|byCluster	5	ESCA
XRN2	0	.	GRCh37	20	21327129	21327129	+	Missense_Mutation	SNP	C	C	T	rs148676805	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1606C>T	p.Arg536Trp	p.R536W	ENST00000377191	17/30	96	91	5	61	61	0	XRN2,missense_variant,p.Arg482Trp,ENST00000539513,;XRN2,missense_variant,p.Arg460Trp,ENST00000430571,;XRN2,missense_variant,p.Arg536Trp,ENST00000377191,;	T	ENSG00000088930	ENST00000377191	Transcript	missense_variant	1701	1606	536	R/W	Cgg/Tgg	rs148676805	.	.	1	XRN2	HGNC	12836	protein_coding	YES	CCDS13144.1	ENSP00000366396	XRN2_HUMAN	B4DZC3_HUMAN	UPI0000037D02	.	deleterious(0.05)	possibly_damaging(0.586)	17/30	.	hmmpanther:PTHR12341,PIRSF_domain:PIRSF037239	T:0.0010	T:0	T:0	.	T:0.005	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCGTCGGAAA	byFrequency|byCluster|by1000G	2	ESCA
TRIB3	0	.	GRCh37	20	377203	377203	+	Nonsense_Mutation	SNP	C	C	T	rs371072439	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.946C>T	p.Arg316Ter	p.R316*	ENST00000217233	4/4	27	17	10	56	56	0	TRIB3,stop_gained,p.Arg343Ter,ENST00000422053,;TRIB3,stop_gained,p.Arg316Ter,ENST00000217233,;TRIB3,downstream_gene_variant,,ENST00000449710,;	T	ENSG00000101255	ENST00000217233	Transcript	stop_gained	1499	946	316	R/*	Cga/Tga	rs371072439	.	.	1	TRIB3	HGNC	16228	protein_coding	YES	CCDS12997.1	ENSP00000217233	TRIB3_HUMAN	B0QYQ2_HUMAN	UPI000003C950	.	.	.	4/4	.	hmmpanther:PTHR22961,hmmpanther:PTHR22961:SF12,Gene3D:1.10.510.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCTGCGACAG	byCluster	3	ESCA
CHD6	0	.	GRCh37	20	40033753	40033753	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7628C>A	p.Ala2543Glu	p.A2543E	ENST00000373233	37/37	25	16	8	29	29	0	CHD6,missense_variant,p.Ala2543Glu,ENST00000373233,;CHD6,non_coding_transcript_exon_variant,,ENST00000480022,;	T	ENSG00000124177	ENST00000373233	Transcript	missense_variant	7806	7628	2543	A/E	gCa/gAa	.	.	.	-1	CHD6	HGNC	19057	protein_coding	YES	CCDS13317.1	ENSP00000362330	CHD6_HUMAN	.	UPI0000168656	.	tolerated(0.09)	possibly_damaging(0.451)	37/37	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTTGCCATG	.	5	ESCA
HNF4A	0	.	GRCh37	20	43057081	43057081	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1236C>T	p.%3D	p.L412L	ENST00000316099	9/10	31	26	5	46	46	0	HNF4A,synonymous_variant,p.%3D,ENST00000415691,;HNF4A,synonymous_variant,p.%3D,ENST00000316099,;HNF4A,synonymous_variant,p.%3D,ENST00000316673,;HNF4A,synonymous_variant,p.%3D,ENST00000457232,;HNF4A,downstream_gene_variant,,ENST00000443598,;HNF4A,downstream_gene_variant,,ENST00000609795,;AL132772.1,upstream_gene_variant,,ENST00000581483,;HNF4A,3_prime_UTR_variant,,ENST00000372920,;	T	ENSG00000101076	ENST00000316099	Transcript	synonymous_variant	1325	1236	412	L	ctC/ctT	.	.	.	1	HNF4A	HGNC	5024	protein_coding	YES	CCDS13330.1	ENSP00000312987	HNF4A_HUMAN	F1D8T1_HUMAN	UPI000016A0BA	.	.	.	9/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCTCAGCAA	.	4	ESCA
RIMS4	0	.	GRCh37	20	43384310	43384310	+	3'Flank	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000541604	.	76	53	23	132	132	0	RIMS4,3_prime_UTR_variant,,ENST00000372851,;RIMS4,downstream_gene_variant,,ENST00000541604,;KCNK15,downstream_gene_variant,,ENST00000372861,;	A	ENSG00000101098	ENST00000541604	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	242	-1	RIMS4	HGNC	16183	protein_coding	YES	CCDS56191.1	ENSP00000439287	RIMS4_HUMAN	.	UPI0000367043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGCCCCTT	.	5	ESCA
STK4	0	.	GRCh37	20	43607120	43607120	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153G>A	p.%3D	p.E51E	ENST00000372806	3/11	78	46	31	34	34	0	STK4,synonymous_variant,p.%3D,ENST00000499879,;STK4,synonymous_variant,p.%3D,ENST00000372806,;STK4,synonymous_variant,p.%3D,ENST00000372801,;STK4,synonymous_variant,p.%3D,ENST00000396731,;STK4,non_coding_transcript_exon_variant,,ENST00000474717,;STK4,downstream_gene_variant,,ENST00000487587,;STK4,downstream_gene_variant,,ENST00000480745,;	A	ENSG00000101109	ENST00000372806	Transcript	synonymous_variant	248	153	51	E	gaG/gaA	.	.	.	1	STK4	HGNC	11408	protein_coding	YES	CCDS13341.1	ENSP00000361892	STK4_HUMAN	Q9BS84_HUMAN	UPI00001360FF	.	.	.	3/11	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:3.30.200.20,PROSITE_patterns:PS00107,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF275,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGACCGG	.	5	ESCA
ATP9A	0	.	GRCh37	20	50287676	50287676	+	Silent	SNP	C	C	T	rs376405770	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1158G>A	p.%3D	p.S386S	ENST00000338821	12/28	35	21	14	32	32	0	ATP9A,synonymous_variant,p.%3D,ENST00000338821,;ATP9A,synonymous_variant,p.%3D,ENST00000402822,;ATP9A,synonymous_variant,p.%3D,ENST00000311637,;	T	ENSG00000054793	ENST00000338821	Transcript	synonymous_variant	1423	1158	386	S	tcG/tcA	rs376405770	.	.	-1	ATP9A	HGNC	13540	protein_coding	YES	CCDS33489.1	ENSP00000342481	ATP9A_HUMAN	Q2NLD0_HUMAN,B4DR18_HUMAN	UPI000004D334	.	.	.	12/28	.	hmmpanther:PTHR24092:SF49,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,TIGRFAM_domain:TIGR01494,Gene3D:3.40.1110.10,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTACGAAAT	byFrequency|byCluster	5	ESCA
APCDD1L	0	.	GRCh37	20	57088995	57088995	+	Intron	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.49+720G>T	.	.	ENST00000371149	.	43	28	14	53	53	0	APCDD1L,5_prime_UTR_variant,,ENST00000425773,;APCDD1L,5_prime_UTR_variant,,ENST00000439429,;APCDD1L,intron_variant,,ENST00000371149,;APCDD1L-AS1,upstream_gene_variant,,ENST00000420279,;APCDD1L-AS1,upstream_gene_variant,,ENST00000427140,;APCDD1L-AS1,upstream_gene_variant,,ENST00000448374,;APCDD1L-AS1,upstream_gene_variant,,ENST00000439558,;APCDD1L-AS1,upstream_gene_variant,,ENST00000427794,;APCDD1L-AS1,upstream_gene_variant,,ENST00000445984,;APCDD1L-AS1,upstream_gene_variant,,ENST00000447767,;	A	ENSG00000198768	ENST00000371149	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	APCDD1L	HGNC	26892	protein_coding	YES	CCDS13467.1	ENSP00000360191	APCDL_HUMAN	.	UPI000006F69F	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCACACT	.	5	ESCA
GNAS	0	.	GRCh37	20	57484421	57484421	+	Missense_Mutation	SNP	G	G	A	rs121913495	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2531G>A	p.Arg844His	p.R844H	ENST00000371100	8/13	62	34	28	63	63	0	GNAS,missense_variant,p.Arg201His,ENST00000371085,;GNAS,missense_variant,p.Arg187His,ENST00000306090,;GNAS,missense_variant,p.Arg142His,ENST00000604005,;GNAS,missense_variant,p.Arg202His,ENST00000354359,;GNAS,missense_variant,p.Arg187His,ENST00000371095,;GNAS,missense_variant,p.Arg830His,ENST00000371102,;GNAS,missense_variant,p.Arg186His,ENST00000265620,;GNAS,missense_variant,p.Arg844His,ENST00000371100,;GNAS,3_prime_UTR_variant,,ENST00000313949,;GNAS,3_prime_UTR_variant,,ENST00000371075,;GNAS,downstream_gene_variant,,ENST00000419558,;GNAS,downstream_gene_variant,,ENST00000349036,;GNAS,downstream_gene_variant,,ENST00000603546,;GNAS,downstream_gene_variant,,ENST00000450130,;GNAS,non_coding_transcript_exon_variant,,ENST00000477931,;GNAS,non_coding_transcript_exon_variant,,ENST00000481039,;GNAS,non_coding_transcript_exon_variant,,ENST00000482112,;GNAS,non_coding_transcript_exon_variant,,ENST00000467321,;GNAS,non_coding_transcript_exon_variant,,ENST00000480232,;GNAS,non_coding_transcript_exon_variant,,ENST00000472183,;GNAS,non_coding_transcript_exon_variant,,ENST00000464788,;GNAS,non_coding_transcript_exon_variant,,ENST00000488652,;GNAS,non_coding_transcript_exon_variant,,ENST00000493958,;GNAS,non_coding_transcript_exon_variant,,ENST00000488546,;GNAS,non_coding_transcript_exon_variant,,ENST00000470512,;GNAS,non_coding_transcript_exon_variant,,ENST00000492907,;GNAS,non_coding_transcript_exon_variant,,ENST00000468895,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,non_coding_transcript_exon_variant,,ENST00000480975,;GNAS,non_coding_transcript_exon_variant,,ENST00000467227,;GNAS,non_coding_transcript_exon_variant,,ENST00000476935,;GNAS,intron_variant,,ENST00000494081,;GNAS,downstream_gene_variant,,ENST00000485673,;GNAS,downstream_gene_variant,,ENST00000469431,;GNAS,downstream_gene_variant,,ENST00000490374,;GNAS,downstream_gene_variant,,ENST00000478585,;GNAS,non_coding_transcript_exon_variant,,ENST00000479025,;GNAS,non_coding_transcript_exon_variant,,ENST00000487862,;GNAS,non_coding_transcript_exon_variant,,ENST00000476196,;GNAS,non_coding_transcript_exon_variant,,ENST00000487981,;GNAS,non_coding_transcript_exon_variant,,ENST00000496934,;GNAS,upstream_gene_variant,,ENST00000475610,;	A	ENSG00000087460	ENST00000371100	Transcript	missense_variant	3083	2531	844	R/H	cGt/cAt	rs121913495,COSM99221,COSM27895,COSM94388,COSM308279	.	.	1	GNAS	HGNC	4392	protein_coding	YES	CCDS46622.1	ENSP00000360141	GNAS1_HUMAN	S4R3W4_HUMAN,S4R3V9_HUMAN,S4R3F1_HUMAN,S4R3E3_HUMAN,S4R379_HUMAN,B0AZR9_HUMAN	UPI0000E444AE	.	deleterious(0.01)	probably_damaging(1)	8/13	.	hmmpanther:PTHR10218:SF36,hmmpanther:PTHR10218,Gene3D:1.10.400.10,Pfam_domain:PF00503,SMART_domains:SM00275,Superfamily_domains:SSF52540,Superfamily_domains:SSF47895,Prints_domain:PR00318	.	.	.	.	.	.	.	.	.	pathogenic	0,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R844H|c.2531G>A|25,SITE|p.R201H|c.602G>A|306,CODON|p.R844C|c.2530C>T|31,CODON|p.R201S|c.601C>A|15,CODON|p.R201C|c.601C>T|420,CODON|p.R201L|c.602G>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGTGTCC	byFrequency|byCluster	5	ESCA
GMEB2	0	.	GRCh37	20	62250679	62250679	+	Silent	SNP	G	G	A	rs775670456	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72C>T	p.%3D	p.D24D	ENST00000266068	1/9	43	26	17	97	97	0	GMEB2,synonymous_variant,p.%3D,ENST00000266068,;GMEB2,synonymous_variant,p.%3D,ENST00000370077,;	A	ENSG00000101216	ENST00000266068	Transcript	synonymous_variant	551	72	24	D	gaC/gaT	rs775670456,COSM4100451	.	.	-1	GMEB2	HGNC	4371	protein_coding	YES	CCDS13528.1	ENSP00000266068	GMEB2_HUMAN	Q659E7_HUMAN,Q5JTV1_HUMAN	UPI000012B8AD	.	.	.	1/9	.	hmmpanther:PTHR10417,hmmpanther:PTHR10417:SF2	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGTCCAC	.	5	ESCA
PLCB4	0	.	GRCh37	20	9461068	9461068	+	3'UTR	SNP	C	C	T	rs752095719	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1412C>T	.	.	ENST00000378501	36/36	19	13	6	16	16	0	PLCB4,3_prime_UTR_variant,,ENST00000334005,;PLCB4,3_prime_UTR_variant,,ENST00000278655,;PLCB4,3_prime_UTR_variant,,ENST00000378473,;PLCB4,3_prime_UTR_variant,,ENST00000378493,;PLCB4,3_prime_UTR_variant,,ENST00000378501,;PLCB4,downstream_gene_variant,,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;	T	ENSG00000101333	ENST00000378501	Transcript	3_prime_UTR_variant	5012	.	.	.	.	rs752095719	.	.	1	PLCB4	HGNC	9059	protein_coding	YES	CCDS13104.1	ENSP00000367762	PLCB4_HUMAN	B1AJW4_HUMAN,B1AJW3_HUMAN,B1AJW2_HUMAN,B1AJW1_HUMAN	UPI00002069DF	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GATACCATCAA	.	2	ESCA
PAK7	0	.	GRCh37	20	9560912	9560912	+	Silent	SNP	C	C	A	rs149925869	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.870G>T	p.%3D	p.S290S	ENST00000378429	5/11	71	48	23	70	70	0	PAK7,synonymous_variant,p.%3D,ENST00000378423,;PAK7,synonymous_variant,p.%3D,ENST00000378429,;PAK7,synonymous_variant,p.%3D,ENST00000353224,;RP5-986I17.2,downstream_gene_variant,,ENST00000428769,;	A	ENSG00000101349	ENST00000378429	Transcript	synonymous_variant	1417	870	290	S	tcG/tcT	rs149925869	.	.	-1	PAK7	HGNC	15916	protein_coding	YES	CCDS13107.1	ENSP00000367686	PAK7_HUMAN	Q9UJQ0_HUMAN	UPI0000035BAD	.	.	.	5/11	.	hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF183	.	.	.	.	.	.	.	T:0.0009	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E294K|c.880G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCCCGAGCC	byCluster	5	ESCA
NCAM2	0	.	GRCh37	21	22746285	22746285	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147G>T	p.Ala383Ser	p.A383S	ENST00000400546	9/18	37	21	16	53	53	0	NCAM2,missense_variant,p.Ala383Ser,ENST00000400546,;NCAM2,missense_variant,p.Ala241Ser,ENST00000284894,;NCAM2,missense_variant,p.Ala408Ser,ENST00000535285,;	T	ENSG00000154654	ENST00000400546	Transcript	missense_variant	1396	1147	383	A/S	Gca/Tca	.	.	.	1	NCAM2	HGNC	7657	protein_coding	YES	CCDS42910.1	ENSP00000383392	NCAM2_HUMAN	D3DSC5_HUMAN	UPI00001A3703	.	tolerated(1)	benign(0.316)	9/18	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF35,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTGCAAGC	.	5	ESCA
DYRK1A	0	.	GRCh37	21	38845005	38845005	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.30C>A	p.Cys10Ter	p.C10*	ENST00000398960	2/11	42	33	8	37	37	0	DYRK1A,stop_gained,p.Cys10Ter,ENST00000451934,;DYRK1A,stop_gained,p.Cys10Ter,ENST00000339659,;DYRK1A,stop_gained,p.Cys10Ter,ENST00000455097,;DYRK1A,stop_gained,p.Cys10Ter,ENST00000398956,;DYRK1A,stop_gained,p.Cys10Ter,ENST00000398960,;DYRK1A,stop_gained,p.Cys10Ter,ENST00000426672,;DYRK1A,stop_gained,p.Cys10Ter,ENST00000338785,;DYRK1A,stop_gained,p.Cys10Ter,ENST00000321219,;DYRK1A,non_coding_transcript_exon_variant,,ENST00000498351,;DYRK1A,non_coding_transcript_exon_variant,,ENST00000462274,;	A	ENSG00000157540	ENST00000398960	Transcript	stop_gained	105	30	10	C/*	tgC/tgA	.	.	.	1	DYRK1A	HGNC	3091	protein_coding	YES	CCDS42925.1	ENSP00000381932	DYR1A_HUMAN	Q76N25_HUMAN,N0GVR9_HUMAN,F8WAP0_HUMAN,E7EMI5_HUMAN	UPI0000129A31	.	.	.	2/11	.	hmmpanther:PTHR24058:SF28,hmmpanther:PTHR24058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATGCAAACC	.	5	ESCA
LSS	0	.	GRCh37	21	47627461	47627461	+	Missense_Mutation	SNP	C	C	T	rs375698498	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1348G>A	p.Gly450Ser	p.G450S	ENST00000397728	15/22	74	45	29	112	112	0	LSS,missense_variant,p.Gly370Ser,ENST00000457828,;LSS,missense_variant,p.Gly450Ser,ENST00000397728,;LSS,missense_variant,p.Gly439Ser,ENST00000522411,;LSS,missense_variant,p.Gly450Ser,ENST00000356396,;	T	ENSG00000160285	ENST00000397728	Transcript	missense_variant	1427	1348	450	G/S	Ggc/Agc	rs375698498,COSM1414589	.	.	-1	LSS	HGNC	6708	protein_coding	YES	CCDS13733.1	ENSP00000380837	ERG7_HUMAN	.	UPI000012A14D	.	tolerated(0.05)	benign(0.369)	15/22	.	hmmpanther:PTHR11764:SF12,hmmpanther:PTHR11764,Gene3D:1.50.10.20,TIGRFAM_domain:TIGR01787,Superfamily_domains:SSF48239	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCCGCAGT	byCluster|by1000G	5	ESCA
PCNT	0	.	GRCh37	21	47851826	47851826	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8448G>A	p.%3D	p.L2816L	ENST00000359568	38/47	33	15	18	40	40	0	PCNT,synonymous_variant,p.%3D,ENST00000359568,;PCNT,non_coding_transcript_exon_variant,,ENST00000482575,;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,;	A	ENSG00000160299	ENST00000359568	Transcript	synonymous_variant	8555	8448	2816	L	ctG/ctA	.	.	.	1	PCNT	HGNC	16068	protein_coding	YES	CCDS33592.1	ENSP00000352572	PCNT_HUMAN	.	UPI00001AEB88	.	.	.	38/47	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18932:SF11,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTGCATTC	.	5	ESCA
IGLL5	0	.	GRCh37	22	23237782	23237782	+	Missense_Mutation	SNP	G	G	A	rs371694135	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553G>A	p.Glu185Lys	p.E185K	ENST00000526893	3/3	114	102	11	182	182	0	IGLL5,missense_variant,p.Glu186Lys,ENST00000532223,;IGLL5,missense_variant,p.Glu185Lys,ENST00000526893,;IGLL5,3_prime_UTR_variant,,ENST00000531372,;IGLC1,missense_variant,p.Glu77Lys,ENST00000390321,;IGLJ1,downstream_gene_variant,,ENST00000390320,;IGLJ2,upstream_gene_variant,,ENST00000390322,;	A	ENSG00000254709	ENST00000526893	Transcript	missense_variant	827	553	185	E/K	Gag/Aag	rs371694135	.	.	1	IGLL5	HGNC	38476	protein_coding	YES	CCDS54506.1	ENSP00000431254	LAC1_HUMAN,IGLL5_HUMAN	A0M8Q9_HUMAN	UPI0000119C74	.	tolerated_low_confidence(0.11)	benign(0.016)	3/3	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF75,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCCCGAGCAG	byFrequency|byCluster|by1000G	4	ESCA
CRYBB3	0	.	GRCh37	22	25603066	25603066	+	Missense_Mutation	SNP	C	C	T	rs373833533	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523C>T	p.Arg175Trp	p.R175W	ENST00000215855	6/6	122	67	55	217	217	0	CRYBB3,missense_variant,p.Arg175Trp,ENST00000215855,;CRYBB3,3_prime_UTR_variant,,ENST00000404334,;	T	ENSG00000100053	ENST00000215855	Transcript	missense_variant	603	523	175	R/W	Cgg/Tgg	rs373833533	.	.	1	CRYBB3	HGNC	2400	protein_coding	YES	CCDS13830.1	ENSP00000215855	CRBB3_HUMAN	.	UPI000013C6A0	.	tolerated(0.09)	possibly_damaging(0.679)	6/6	.	PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF13,Gene3D:2.60.20.10,Pfam_domain:PF00030,SMART_domains:SM00247,Superfamily_domains:SSF49695,Prints_domain:PR01367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGCGGGGC	byFrequency|byCluster	5	ESCA
CABP7	0	.	GRCh37	22	30126123	30126123	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*565C>A	.	.	ENST00000216144	5/5	26	14	12	37	37	0	CABP7,3_prime_UTR_variant,,ENST00000216144,;ZMAT5,downstream_gene_variant,,ENST00000397781,;ZMAT5,downstream_gene_variant,,ENST00000344318,;	A	ENSG00000100314	ENST00000216144	Transcript	3_prime_UTR_variant	1554	.	.	.	.	.	.	.	1	CABP7	HGNC	20834	protein_coding	YES	CCDS13867.1	ENSP00000216144	CABP7_HUMAN	.	UPI0000004C1D	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACCCTCGTT	.	5	ESCA
OSBP2	0	.	GRCh37	22	31303811	31303811	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1485G>C	.	.	ENST00000332585	14/14	71	50	21	75	75	0	OSBP2,3_prime_UTR_variant,,ENST00000332585,;OSBP2,downstream_gene_variant,,ENST00000431368,;OSBP2,downstream_gene_variant,,ENST00000437268,;OSBP2,downstream_gene_variant,,ENST00000452656,;OSBP2,downstream_gene_variant,,ENST00000401475,;OSBP2,downstream_gene_variant,,ENST00000446658,;OSBP2,downstream_gene_variant,,ENST00000407373,;OSBP2,downstream_gene_variant,,ENST00000382310,;OSBP2,downstream_gene_variant,,ENST00000403222,;OSBP2,downstream_gene_variant,,ENST00000535268,;	C	ENSG00000184792	ENST00000332585	Transcript	3_prime_UTR_variant	4340	.	.	.	.	.	.	.	1	OSBP2	HGNC	8504	protein_coding	YES	CCDS43002.1	ENSP00000332576	OSBP2_HUMAN	C9JS84_HUMAN,C9J7J0_HUMAN	UPI0000161E15	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACTGCCCTG	.	2	ESCA
MAFF	0	.	GRCh37	22	38610952	38610952	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67G>A	.	.	ENST00000338483	3/3	34	26	8	57	57	0	MAFF,3_prime_UTR_variant,,ENST00000407965,;MAFF,3_prime_UTR_variant,,ENST00000338483,;MAFF,3_prime_UTR_variant,,ENST00000426621,;MAFF,3_prime_UTR_variant,,ENST00000538999,;MAFF,3_prime_UTR_variant,,ENST00000538320,;TMEM184B,downstream_gene_variant,,ENST00000361906,;TMEM184B,downstream_gene_variant,,ENST00000361684,;MAFF,downstream_gene_variant,,ENST00000441709,;MAFF,downstream_gene_variant,,ENST00000417948,;TMEM184B,downstream_gene_variant,,ENST00000436674,;	A	ENSG00000185022	ENST00000338483	Transcript	3_prime_UTR_variant	924	.	.	.	.	.	.	.	1	MAFF	HGNC	6780	protein_coding	YES	CCDS13968.1	ENSP00000345393	MAFF_HUMAN	B0QY71_HUMAN,B0QY70_HUMAN	UPI0000062338	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAGCGCCGCC	.	2	ESCA
CSNK1E	0	.	GRCh37	22	38690214	38690214	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1119G>T	p.Glu373Asp	p.E373D	ENST00000396832	9/11	76	47	29	117	117	0	CSNK1E,missense_variant,p.Glu101Asp,ENST00000431632,;CSNK1E,missense_variant,p.Glu373Asp,ENST00000403904,;CSNK1E,missense_variant,p.Glu76Asp,ENST00000366216,;CSNK1E,missense_variant,p.Glu373Asp,ENST00000359867,;CSNK1E,missense_variant,p.Glu373Asp,ENST00000400206,;CSNK1E,missense_variant,p.Glu373Asp,ENST00000396832,;CSNK1E,downstream_gene_variant,,ENST00000405675,;CSNK1E,downstream_gene_variant,,ENST00000451964,;CSNK1E,downstream_gene_variant,,ENST00000413574,;CSNK1E,downstream_gene_variant,,ENST00000498529,;CSNK1E,3_prime_UTR_variant,,ENST00000431611,;CSNK1E,non_coding_transcript_exon_variant,,ENST00000495232,;CSNK1E,non_coding_transcript_exon_variant,,ENST00000494610,;CSNK1E,downstream_gene_variant,,ENST00000442216,;CSNK1E,downstream_gene_variant,,ENST00000467976,;	A	ENSG00000213923	ENST00000396832	Transcript	missense_variant	1380	1119	373	E/D	gaG/gaT	.	.	.	-1	CSNK1E	HGNC	2453	protein_coding	YES	CCDS13970.1	ENSP00000380044	KC1E_HUMAN	Q5U045_HUMAN,B0QY36_HUMAN	UPI000012DC67	.	deleterious_low_confidence(0.04)	benign(0.079)	9/11	.	hmmpanther:PTHR11909:SF74,hmmpanther:PTHR11909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCTCCCG	.	5	ESCA
FAM83F	0	.	GRCh37	22	40391301	40391301	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255C>A	p.%3D	p.G85G	ENST00000333407	1/5	14	7	6	19	19	0	FAM83F,synonymous_variant,p.%3D,ENST00000333407,;FAM83F,upstream_gene_variant,,ENST00000488874,;	A	ENSG00000133477	ENST00000333407	Transcript	synonymous_variant	349	255	85	G	ggC/ggA	.	.	.	1	FAM83F	HGNC	25148	protein_coding	YES	CCDS14000.2	ENSP00000330432	FA83F_HUMAN	.	UPI0000071BF1	.	.	.	1/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16181:SF9,hmmpanther:PTHR16181,Pfam_domain:PF07894	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGGCAAGAG	.	5	ESCA
CELSR1	0	.	GRCh37	22	46787549	46787549	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6129C>T	p.%3D	p.V2043V	ENST00000262738	15/35	50	45	5	89	89	0	CELSR1,synonymous_variant,p.%3D,ENST00000262738,;	A	ENSG00000075275	ENST00000262738	Transcript	synonymous_variant	6129	6129	2043	V	gtC/gtT	.	.	.	-1	CELSR1	HGNC	1850	protein_coding	YES	CCDS14076.1	ENSP00000262738	CELR1_HUMAN	Q8NDT0_HUMAN	UPI0000040648	.	.	.	15/35	.	Superfamily_domains:SSF57196,SMART_domains:SM00180,Gene3D:2.10.25.10,PROSITE_patterns:PS01248,hmmpanther:PTHR24026,PROSITE_profiles:PS50027,PROSITE_profiles:PS50227	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGTGACCTC	.	4	ESCA
MERTK	0	.	GRCh37	2	112786094	112786094	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2653G>T	p.Ala885Ser	p.A885S	ENST00000295408	19/19	55	33	22	50	50	0	MERTK,missense_variant,p.Ala885Ser,ENST00000295408,;MERTK,missense_variant,p.Ala885Ser,ENST00000421804,;MERTK,missense_variant,p.Ala709Ser,ENST00000409780,;MERTK,missense_variant,p.Ala209Ser,ENST00000449344,;MERTK,3_prime_UTR_variant,,ENST00000439966,;	T	ENSG00000153208	ENST00000295408	Transcript	missense_variant	2910	2653	885	A/S	Gcc/Tcc	.	.	.	1	MERTK	HGNC	7027	protein_coding	YES	CCDS2094.1	ENSP00000295408	MERTK_HUMAN	Q96T45_HUMAN,Q53R53_HUMAN,Q53QW0_HUMAN,Q07941_HUMAN,E9PHX8_HUMAN,B4DFQ0_HUMAN	UPI000013E252	.	tolerated(0.07)	benign(0.103)	19/19	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTGGCCCAG	.	5	ESCA
CCDC93	0	.	GRCh37	2	118704391	118704391	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1292A>T	p.Glu431Val	p.E431V	ENST00000376300	16/24	50	33	16	38	38	0	CCDC93,missense_variant,p.Glu431Val,ENST00000376300,;CCDC93,missense_variant,p.Glu430Val,ENST00000319432,;CCDC93,downstream_gene_variant,,ENST00000460781,;CCDC93,missense_variant,p.Glu48Val,ENST00000437999,;CCDC93,downstream_gene_variant,,ENST00000488908,;CCDC93,upstream_gene_variant,,ENST00000466171,;	A	ENSG00000125633	ENST00000376300	Transcript	missense_variant	1430	1292	431	E/V	gAa/gTa	.	.	.	-1	CCDC93	HGNC	25611	protein_coding	YES	CCDS2121.2	ENSP00000365477	CCD93_HUMAN	.	UPI0000207DEC	.	tolerated(0.13)	benign(0.001)	16/24	.	hmmpanther:PTHR16441	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTTCATCT	.	5	ESCA
EN1	0	.	GRCh37	2	119599996	119599996	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*518C>G	.	.	ENST00000295206	2/2	44	31	13	50	50	0	EN1,3_prime_UTR_variant,,ENST00000295206,;EN1,downstream_gene_variant,,ENST00000546667,;	C	ENSG00000163064	ENST00000295206	Transcript	3_prime_UTR_variant	2208	.	.	.	.	.	.	.	-1	EN1	HGNC	3342	protein_coding	YES	CCDS2123.1	ENSP00000295206	HME1_HUMAN	.	UPI000013E21D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCGGCGATG	.	5	ESCA
POTEE	0	.	GRCh37	2	132021653	132021653	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2625C>T	p.%3D	p.T875T	ENST00000356920	15/15	139	104	34	261	261	0	POTEE,synonymous_variant,p.%3D,ENST00000356920,;POTEE,3_prime_UTR_variant,,ENST00000358087,;PLEKHB2,intron_variant,,ENST00000404460,;PLEKHB2,intron_variant,,ENST00000303908,;AC131180.1,non_coding_transcript_exon_variant,,ENST00000514256,;	T	ENSG00000188219	ENST00000356920	Transcript	synonymous_variant	2719	2625	875	T	acC/acT	.	.	.	1	POTEE	HGNC	33895	protein_coding	YES	CCDS46414.1	ENSP00000439189	POTEE_HUMAN	.	UPI0000F58EC8	.	.	.	15/15	.	hmmpanther:PTHR24118:SF46,hmmpanther:PTHR24118,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACCCTGCG	.	5	ESCA
THSD7B	0	.	GRCh37	2	138033559	138033559	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2463C>A	p.%3D	p.G821G	ENST00000272643	11/28	84	47	37	62	62	0	THSD7B,synonymous_variant,p.%3D,ENST00000409968,;THSD7B,synonymous_variant,p.%3D,ENST00000413152,;THSD7B,synonymous_variant,p.%3D,ENST00000272643,;THSD7B,intron_variant,,ENST00000543459,;	A	ENSG00000144229	ENST00000272643	Transcript	synonymous_variant	2463	2463	821	G	ggC/ggA	.	.	.	1	THSD7B	HGNC	29348	protein_coding	YES	.	ENSP00000272643	THS7B_HUMAN	.	UPI00015E0A18	.	.	.	11/28	.	hmmpanther:PTHR11311:SF7,hmmpanther:PTHR11311	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGGCAGCAG	.	5	ESCA
SPOPL	0	.	GRCh37	2	139308582	139308582	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310T>A	p.Phe104Ile	p.F104I	ENST00000280098	4/11	68	46	21	26	26	0	SPOPL,missense_variant,p.Phe104Ile,ENST00000280098,;SPOPL,missense_variant,p.Phe104Ile,ENST00000420679,;SPOPL,3_prime_UTR_variant,,ENST00000430968,;	A	ENSG00000144228	ENST00000280098	Transcript	missense_variant	689	310	104	F/I	Ttt/Att	.	.	.	1	SPOPL	HGNC	27934	protein_coding	YES	CCDS33298.1	ENSP00000280098	SPOPL_HUMAN	B4DEY7_HUMAN	UPI0000208BED	.	deleterious(0.01)	probably_damaging(1)	4/11	.	PROSITE_profiles:PS50144,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF91,Gene3D:2.60.210.10,Pfam_domain:PF00917,SMART_domains:SM00061,Superfamily_domains:SSF49599	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAATTTTCC	.	5	ESCA
LRP1B	0	.	GRCh37	2	140989437	140989437	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1318G>C	.	.	ENST00000389484	91/91	87	50	36	75	75	0	LRP1B,3_prime_UTR_variant,,ENST00000389484,;LRP1B,3_prime_UTR_variant,,ENST00000437977,;	G	ENSG00000168702	ENST00000389484	Transcript	3_prime_UTR_variant	16090	.	.	.	.	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	91/91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATCTTTTG	.	5	ESCA
LRP1B	0	.	GRCh37	2	141299445	141299445	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7290G>A	p.%3D	p.R2430R	ENST00000389484	44/91	59	41	17	56	56	0	LRP1B,synonymous_variant,p.%3D,ENST00000389484,;	T	ENSG00000168702	ENST00000389484	Transcript	synonymous_variant	8262	7290	2430	R	cgG/cgA	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	44/91	.	PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGACCGCAG	.	5	ESCA
FIGN	0	.	GRCh37	2	164468131	164468132	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210dupA	p.Tyr71IlefsTer35	p.Y71Ifs*35	ENST00000333129	3/3	47	32	15	37	37	0	FIGN,frameshift_variant,p.Tyr71IlefsTer35,ENST00000333129,;FIGN,intron_variant,,ENST00000409634,;FIGN,non_coding_transcript_exon_variant,,ENST00000482917,;	T	ENSG00000182263	ENST00000333129	Transcript	frameshift_variant	525-526	210-211	70-71	-/X	-/A	.	.	.	-1	FIGN	HGNC	13285	protein_coding	YES	CCDS2221.2	ENSP00000333836	FIGN_HUMAN	.	UPI000022BD13	.	.	.	3/3	.	hmmpanther:PTHR23074:SF14,hmmpanther:PTHR23074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGCATATTTTT	.	2	ESCA
UBR3	0	.	GRCh37	2	170806482	170806482	+	Missense_Mutation	SNP	G	G	A	rs748028932	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3452G>A	p.Arg1151His	p.R1151H	ENST00000418381	23/39	38	28	10	34	34	0	UBR3,missense_variant,p.Arg1151His,ENST00000418381,;UBR3,missense_variant,p.Arg1151His,ENST00000272793,;UBR3,missense_variant,p.Arg209His,ENST00000392632,;UBR3,missense_variant,p.Arg299His,ENST00000430321,;UBR3,non_coding_transcript_exon_variant,,ENST00000487689,;UBR3,downstream_gene_variant,,ENST00000477461,;	A	ENSG00000144357	ENST00000418381	Transcript	missense_variant	3452	3452	1151	R/H	cGc/cAc	rs748028932,COSM1009391,COSM1009392	.	.	1	UBR3	HGNC	30467	protein_coding	YES	CCDS2238.2	ENSP00000396068	UBR3_HUMAN	Q68DC1_HUMAN	UPI00015FA088	.	tolerated(0.19)	benign(0.007)	23/39	.	hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF25	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAACGCATCA	byFrequency	5	ESCA
WIPF1	0	.	GRCh37	2	175436784	175436784	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.749C>T	p.Pro250Leu	p.P250L	ENST00000392547	5/8	40	29	11	88	88	0	WIPF1,missense_variant,p.Pro250Leu,ENST00000359761,;WIPF1,missense_variant,p.Pro250Leu,ENST00000392547,;WIPF1,missense_variant,p.Pro250Leu,ENST00000409891,;WIPF1,missense_variant,p.Pro250Leu,ENST00000409415,;WIPF1,missense_variant,p.Pro250Leu,ENST00000272746,;WIPF1,missense_variant,p.Pro250Leu,ENST00000392546,;WIPF1,downstream_gene_variant,,ENST00000436221,;WIPF1,downstream_gene_variant,,ENST00000455428,;WIPF1,downstream_gene_variant,,ENST00000410117,;AC018890.6,intron_variant,,ENST00000412835,;AC018890.6,intron_variant,,ENST00000442996,;AC010894.5,upstream_gene_variant,,ENST00000454203,;WIPF1,upstream_gene_variant,,ENST00000467149,;	A	ENSG00000115935	ENST00000392547	Transcript	missense_variant	849	749	250	P/L	cCt/cTt	COSM717692	.	.	-1	WIPF1	HGNC	12736	protein_coding	YES	CCDS2260.1	ENSP00000376330	WIPF1_HUMAN	C9JTB9_HUMAN	UPI000013D4BD	.	deleterious(0)	probably_damaging(0.998)	5/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23202,hmmpanther:PTHR23202:SF30	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGAGGCCGG	.	5	ESCA
TTN	0	.	GRCh37	2	179527477	179527478	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36852dupA	p.Pro12285ThrfsTer10	p.P12285Tfs*10	ENST00000589042	175/363	21	14	7	24	24	0	TTN,frameshift_variant,p.Pro12285ThrfsTer10,ENST00000589042,;TTN,intron_variant,,ENST00000414766,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000342992,;TTN,intron_variant,,ENST00000591111,;TTN,intron_variant,,ENST00000460472,;TTN,downstream_gene_variant,,ENST00000425332,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000589830,;	T	ENSG00000155657	ENST00000589042	Transcript	frameshift_variant	37077-37078	36852-36853	12284-12285	-/X	-/A	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	175/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF02818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTCCGGTTTTT	.	2	ESCA
ZNF804A	0	.	GRCh37	2	185801665	185801665	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1542A>G	p.%3D	p.G514G	ENST00000302277	4/4	55	52	3	31	31	0	ZNF804A,synonymous_variant,p.%3D,ENST00000302277,;	G	ENSG00000170396	ENST00000302277	Transcript	synonymous_variant	2136	1542	514	G	ggA/ggG	.	.	.	1	ZNF804A	HGNC	21711	protein_coding	YES	CCDS2291.1	ENSP00000303252	Z804A_HUMAN	.	UPI00001B4B18	.	.	.	4/4	.	hmmpanther:PTHR17614:SF13,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTGGAAGTAG	.	2	ESCA
FSIP2	0	.	GRCh37	2	186653633	186653633	+	Silent	SNP	G	G	A	rs139442712	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2037G>A	p.%3D	p.T679T	ENST00000343098	16/23	47	27	19	39	39	0	FSIP2,synonymous_variant,p.%3D,ENST00000343098,;FSIP2,synonymous_variant,p.%3D,ENST00000424728,;AC008174.3,non_coding_transcript_exon_variant,,ENST00000436557,;AC008174.3,non_coding_transcript_exon_variant,,ENST00000429929,;	A	ENSG00000188738	ENST00000343098	Transcript	synonymous_variant	2037	2037	679	T	acG/acA	rs139442712	.	.	1	FSIP2	HGNC	21675	protein_coding	YES	CCDS54426.1	ENSP00000344403	.	J3QTJ6_HUMAN	UPI0001D420A1	.	.	.	16/23	.	hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF1	A:0.0008	A:0	A:0	.	A:0	A:0.001	A:0.0031	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACGTCAGT	byFrequency|by1000G	5	ESCA
NABP1	0	.	GRCh37	2	192551686	192551686	+	3'Flank	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000425611	.	22	16	6	11	11	0	NABP1,3_prime_UTR_variant,,ENST00000410026,;NABP1,downstream_gene_variant,,ENST00000425611,;NABP1,downstream_gene_variant,,ENST00000435931,;NABP1,downstream_gene_variant,,ENST00000409510,;NABP1,3_prime_UTR_variant,,ENST00000307849,;NABP1,downstream_gene_variant,,ENST00000451500,;NABP1,downstream_gene_variant,,ENST00000462824,;NABP1,downstream_gene_variant,,ENST00000462712,;NABP1,downstream_gene_variant,,ENST00000491331,;NABP1,downstream_gene_variant,,ENST00000307834,;	C	ENSG00000173559	ENST00000425611	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	12	1	NABP1	HGNC	26232	protein_coding	YES	CCDS33352.1	ENSP00000403683	SOSB2_HUMAN	.	UPI000006F339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTTCAATG	.	5	ESCA
FAM117B	0	.	GRCh37	2	203631961	203631961	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1474G>A	.	.	ENST00000392238	8/8	16	10	5	23	23	0	FAM117B,3_prime_UTR_variant,,ENST00000392238,;FAM117B,3_prime_UTR_variant,,ENST00000303116,;	A	ENSG00000138439	ENST00000392238	Transcript	3_prime_UTR_variant	3244	.	.	.	.	.	.	.	1	FAM117B	HGNC	14440	protein_coding	YES	CCDS33362.2	ENSP00000376071	F117B_HUMAN	.	UPI00015B3B88	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTGCGACC	.	5	ESCA
SLC19A3	0	.	GRCh37	2	228566913	228566913	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.122G>T	p.Gly41Val	p.G41V	ENST00000258403	2/6	57	48	9	36	36	0	SLC19A3,missense_variant,p.Gly41Val,ENST00000419059,;SLC19A3,missense_variant,p.Gly41Val,ENST00000409456,;SLC19A3,missense_variant,p.Gly41Val,ENST00000409287,;SLC19A3,missense_variant,p.Gly41Val,ENST00000258403,;SLC19A3,missense_variant,p.Gly41Val,ENST00000456524,;SLC19A3,5_prime_UTR_variant,,ENST00000541617,;SLC19A3,missense_variant,p.Gly41Val,ENST00000431622,;SLC19A3,missense_variant,p.Gly41Val,ENST00000425817,;SLC19A3,non_coding_transcript_exon_variant,,ENST00000477697,;	A	ENSG00000135917	ENST00000258403	Transcript	missense_variant	194	122	41	G/V	gGa/gTa	COSM574002	.	.	-1	SLC19A3	HGNC	16266	protein_coding	YES	CCDS2468.1	ENSP00000258403	S19A3_HUMAN	C9J4J5_HUMAN,C9IZI1_HUMAN,B8ZZ39_HUMAN	UPI000004DAE9	.	deleterious(0)	possibly_damaging(0.86)	2/6	.	hmmpanther:PTHR10686,hmmpanther:PTHR10686:SF17,Gene3D:1.20.1250.20,Pfam_domain:PF01770,TIGRFAM_domain:TIGR00806,PIRSF_domain:PIRSF028739,PIRSF_domain:PIRSF500795,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGTCCAGAT	.	4	ESCA
SPATA3	0	.	GRCh37	2	231860901	231860901	+	5'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-48G>T	.	.	ENST00000452881	1/9	45	27	17	73	73	0	SPATA3,5_prime_UTR_variant,,ENST00000424440,;SPATA3,5_prime_UTR_variant,,ENST00000452881,;SPATA3,5_prime_UTR_variant,,ENST00000433428,;SPATA3,upstream_gene_variant,,ENST00000423134,;SPATA3,upstream_gene_variant,,ENST00000455816,;SPATA3,upstream_gene_variant,,ENST00000440792,;SPATA3-AS1,upstream_gene_variant,,ENST00000426904,;SPATA3-AS1,upstream_gene_variant,,ENST00000418330,;SPATA3-AS1,upstream_gene_variant,,ENST00000457803,;SPATA3-AS1,upstream_gene_variant,,ENST00000434094,;SPATA3-AS1,upstream_gene_variant,,ENST00000414876,;SPATA3-AS1,upstream_gene_variant,,ENST00000446741,;SPATA3-AS1,upstream_gene_variant,,ENST00000441063,;SPATA3,upstream_gene_variant,,ENST00000409956,;SPATA3,5_prime_UTR_variant,,ENST00000454918,;	T	ENSG00000173699	ENST00000452881	Transcript	5_prime_UTR_variant	61	.	.	.	.	.	.	.	1	SPATA3	HGNC	17884	protein_coding	YES	CCDS2481.1	ENSP00000388895	SPTA3_HUMAN	.	UPI000006E910	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGAGATTAC	.	5	ESCA
ASB18	0	.	GRCh37	2	237150172	237150172	+	Intron	SNP	C	C	T	rs752075953	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.206-127G>A	.	.	ENST00000409749	.	20	10	10	23	23	0	ASB18,5_prime_UTR_variant,,ENST00000330842,;ASB18,intron_variant,,ENST00000409749,;ASB18,intron_variant,,ENST00000430053,;AC079135.1,intron_variant,,ENST00000415226,;	T	ENSG00000182177	ENST00000409749	Transcript	intron_variant	.	.	.	.	.	rs752075953	.	.	-1	ASB18	HGNC	19770	protein_coding	YES	CCDS46548.1	ENSP00000386532	ASB18_HUMAN	.	UPI00015D60A6	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGCCGTCGA	byFrequency	5	ESCA
RNPEPL1	0	.	GRCh37	2	241513671	241513671	+	Silent	SNP	C	C	T	rs749766269	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387C>T	p.%3D	p.F129F	ENST00000270357	5/11	28	17	11	53	53	0	RNPEPL1,synonymous_variant,p.%3D,ENST00000270357,;RNPEPL1,intron_variant,,ENST00000451363,;RNPEPL1,upstream_gene_variant,,ENST00000437406,;RNPEPL1,upstream_gene_variant,,ENST00000464550,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000481757,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000486058,;RNPEPL1,upstream_gene_variant,,ENST00000471657,;RNPEPL1,upstream_gene_variant,,ENST00000498042,;RNPEPL1,upstream_gene_variant,,ENST00000493398,;RNPEPL1,upstream_gene_variant,,ENST00000460884,;	T	ENSG00000142327	ENST00000270357	Transcript	synonymous_variant	980	387	129	F	ttC/ttT	rs749766269	.	.	1	RNPEPL1	HGNC	10079	protein_coding	YES	.	ENSP00000270357	RNPL1_HUMAN	.	UPI000013D885	.	.	.	5/11	.	Prints_domain:PR00756,Superfamily_domains:SSF55486,Pfam_domain:PF01433,hmmpanther:PTHR11533:SF6,hmmpanther:PTHR11533	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTTCGGCAA	byFrequency	5	ESCA
GTF3C2	0	.	GRCh37	2	27551709	27551709	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2127+2T>C	.	p.X709_splice	ENST00000359541	.	45	31	14	37	37	0	GTF3C2,splice_donor_variant,,ENST00000457098,;GTF3C2,splice_donor_variant,,ENST00000264720,;GTF3C2,splice_donor_variant,,ENST00000454704,;GTF3C2,splice_donor_variant,,ENST00000359541,;GTF3C2,upstream_gene_variant,,ENST00000431028,;MPV17,upstream_gene_variant,,ENST00000357186,;GTF3C2,splice_donor_variant,,ENST00000415683,;GTF3C2,splice_donor_variant,,ENST00000484680,;GTF3C2,upstream_gene_variant,,ENST00000495298,;	G	ENSG00000115207	ENST00000359541	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	GTF3C2	HGNC	4665	protein_coding	YES	CCDS1749.1	ENSP00000352536	TF3C2_HUMAN	Q53SY8_HUMAN,Q53QN0_HUMAN,C9JQ12_HUMAN,C9JNH7_HUMAN	UPI0000074025	.	.	.	.	15/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCACCCAA	.	5	ESCA
EHBP1	0	.	GRCh37	2	63272536	63272536	+	Intron	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3606-9G>T	.	.	ENST00000263991	.	55	37	17	68	68	0	EHBP1,intron_variant,,ENST00000263991,;EHBP1,intron_variant,,ENST00000405289,;EHBP1,intron_variant,,ENST00000405015,;EHBP1,intron_variant,,ENST00000431489,;EHBP1,intron_variant,,ENST00000354487,;OTX1,upstream_gene_variant,,ENST00000366671,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000412297,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000413549,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000437346,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000429952,;EHBP1,intron_variant,,ENST00000496857,;EHBP1,intron_variant,,ENST00000471179,;	T	ENSG00000115504	ENST00000263991	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	EHBP1	HGNC	29144	protein_coding	YES	CCDS1872.1	ENSP00000263991	EHBP1_HUMAN	C9K0H9_HUMAN,C9JEP1_HUMAN,C9J268_HUMAN,B3KM32_HUMAN	UPI000013D49A	.	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTGACATC	.	5	ESCA
EHBP1	0	.	GRCh37	2	63272537	63272537	+	Intron	SNP	A	A	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3606-8A>T	.	.	ENST00000263991	.	56	38	17	66	66	0	EHBP1,splice_region_variant,,ENST00000263991,;EHBP1,splice_region_variant,,ENST00000405289,;EHBP1,splice_region_variant,,ENST00000405015,;EHBP1,splice_region_variant,,ENST00000431489,;EHBP1,splice_region_variant,,ENST00000354487,;OTX1,upstream_gene_variant,,ENST00000366671,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000412297,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000413549,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000437346,;AC009501.4,non_coding_transcript_exon_variant,,ENST00000429952,;EHBP1,splice_region_variant,,ENST00000496857,;EHBP1,splice_region_variant,,ENST00000471179,;	T	ENSG00000115504	ENST00000263991	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	EHBP1	HGNC	29144	protein_coding	YES	CCDS1872.1	ENSP00000263991	EHBP1_HUMAN	C9K0H9_HUMAN,C9JEP1_HUMAN,C9J268_HUMAN,B3KM32_HUMAN	UPI000013D49A	.	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGACATCC	.	5	ESCA
ALMS1	0	.	GRCh37	2	73677770	73677770	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4113C>A	p.%3D	p.G1371G	ENST00000264448	8/23	68	43	24	45	45	0	ALMS1,synonymous_variant,p.%3D,ENST00000377715,;ALMS1,synonymous_variant,p.%3D,ENST00000409009,;ALMS1,synonymous_variant,p.%3D,ENST00000264448,;ALMS1,upstream_gene_variant,,ENST00000484298,;ALMS1,upstream_gene_variant,,ENST00000423048,;	A	ENSG00000116127	ENST00000264448	Transcript	synonymous_variant	4224	4113	1371	G	ggC/ggA	.	.	.	1	ALMS1	HGNC	428	protein_coding	YES	CCDS42697.1	ENSP00000264448	ALMS1_HUMAN	A6NMY3_HUMAN	UPI0000212786	.	.	.	8/23	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGGCACACC	.	5	ESCA
KDM3A	0	.	GRCh37	2	86716722	86716722	+	Silent	SNP	A	A	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3513A>T	p.%3D	p.G1171G	ENST00000409556	24/27	33	23	9	25	25	0	KDM3A,synonymous_variant,p.%3D,ENST00000409064,;KDM3A,synonymous_variant,p.%3D,ENST00000542128,;KDM3A,synonymous_variant,p.%3D,ENST00000409556,;KDM3A,synonymous_variant,p.%3D,ENST00000312912,;KDM3A,downstream_gene_variant,,ENST00000462197,;KDM3A,3_prime_UTR_variant,,ENST00000441719,;KDM3A,non_coding_transcript_exon_variant,,ENST00000470160,;KDM3A,non_coding_transcript_exon_variant,,ENST00000483866,;KDM3A,non_coding_transcript_exon_variant,,ENST00000491383,;	T	ENSG00000115548	ENST00000409556	Transcript	synonymous_variant	3878	3513	1171	G	ggA/ggT	.	.	.	1	KDM3A	HGNC	20815	protein_coding	YES	CCDS1990.1	ENSP00000386660	KDM3A_HUMAN	C9JC73_HUMAN,C9J7Q7_HUMAN	UPI0000161FAE	.	.	.	24/27	.	PROSITE_profiles:PS51184,hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF7,Pfam_domain:PF02373,SMART_domains:SM00558,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGAGCACT	.	5	ESCA
FAHD2A	0	.	GRCh37	2	96081612	96081612	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2907A>G	.	.	ENST00000233379	8/8	9	6	3	15	15	0	FAHD2A,3_prime_UTR_variant,,ENST00000233379,;FAHD2A,downstream_gene_variant,,ENST00000447036,;FAHD2A,downstream_gene_variant,,ENST00000470100,;AC009238.6,upstream_gene_variant,,ENST00000512705,;	G	ENSG00000115042	ENST00000233379	Transcript	3_prime_UTR_variant	4005	.	.	.	.	.	.	.	1	FAHD2A	HGNC	24252	protein_coding	YES	CCDS2014.1	ENSP00000233379	FAH2A_HUMAN	C9JGM0_HUMAN,C9J5B6_HUMAN	UPI000006D4CC	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTAACCTCT	.	2	ESCA
NCAPH	0	.	GRCh37	2	97039388	97039388	+	3'UTR	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*299C>G	.	.	ENST00000240423	18/18	45	42	3	17	17	0	NCAPH,3_prime_UTR_variant,,ENST00000455200,;NCAPH,3_prime_UTR_variant,,ENST00000427946,;NCAPH,3_prime_UTR_variant,,ENST00000240423,;NCAPH,downstream_gene_variant,,ENST00000435349,;	G	ENSG00000121152	ENST00000240423	Transcript	3_prime_UTR_variant	2568	.	.	.	.	.	.	.	1	NCAPH	HGNC	1112	protein_coding	YES	CCDS2021.1	ENSP00000240423	CND2_HUMAN	E9PHA2_HUMAN,B4E189_HUMAN	UPI0000163F72	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATATCAATGT	.	2	ESCA
CCDC80	0	.	GRCh37	3	112324432	112324432	+	Silent	SNP	C	C	T	rs768070081	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2685G>A	p.%3D	p.S895S	ENST00000206423	8/8	56	35	21	47	47	0	CCDC80,synonymous_variant,p.%3D,ENST00000479368,;CCDC80,synonymous_variant,p.%3D,ENST00000206423,;CCDC80,synonymous_variant,p.%3D,ENST00000439685,;CCDC80,downstream_gene_variant,,ENST00000461431,;RP11-572C15.6,upstream_gene_variant,,ENST00000610103,;	T	ENSG00000091986	ENST00000206423	Transcript	synonymous_variant	3639	2685	895	S	tcG/tcA	rs768070081	.	.	-1	CCDC80	HGNC	30649	protein_coding	YES	CCDS2968.1	ENSP00000206423	CCD80_HUMAN	.	UPI000004EE7F	.	.	.	8/8	.	Pfam_domain:PF13778,hmmpanther:PTHR19325	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCATCGAATC	.	5	ESCA
FBXO40	0	.	GRCh37	3	121341286	121341286	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1010G>T	p.Gly337Val	p.G337V	ENST00000338040	3/4	34	21	13	20	20	0	FBXO40,missense_variant,p.Gly337Val,ENST00000338040,;	T	ENSG00000163833	ENST00000338040	Transcript	missense_variant	1424	1010	337	G/V	gGc/gTc	COSM1206839	.	.	1	FBXO40	HGNC	29816	protein_coding	YES	CCDS33835.1	ENSP00000337510	FBX40_HUMAN	.	UPI000020A046	.	deleterious(0)	probably_damaging(0.997)	3/4	.	hmmpanther:PTHR15933,hmmpanther:PTHR15933:SF1	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATGGCAAGC	.	5	ESCA
DTX3L	0	.	GRCh37	3	122289345	122289345	+	Missense_Mutation	SNP	G	G	A	rs755071547	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1979G>A	p.Arg660Gln	p.R660Q	ENST00000296161	4/5	62	40	22	33	33	0	DTX3L,missense_variant,p.Arg660Gln,ENST00000296161,;DTX3L,missense_variant,p.Arg148Gln,ENST00000383661,;	A	ENSG00000163840	ENST00000296161	Transcript	missense_variant	2168	1979	660	R/Q	cGa/cAa	rs755071547,COSM1037176	.	.	1	DTX3L	HGNC	30323	protein_coding	YES	CCDS3015.1	ENSP00000296161	DTX3L_HUMAN	.	UPI000000D9D0	.	deleterious(0)	probably_damaging(0.983)	4/5	.	hmmpanther:PTHR12622:SF23,hmmpanther:PTHR12622	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R660Q|c.1979G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCGAACTG	.	5	ESCA
KALRN	0	.	GRCh37	3	124390534	124390534	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000459915	12/13	67	41	26	75	75	0	KALRN,missense_variant,p.Arg335Gln,ENST00000459915,;KALRN,missense_variant,p.Arg546Gln,ENST00000291478,;KALRN,missense_variant,p.Arg584Gln,ENST00000393496,;KALRN,missense_variant,p.Arg2212Gln,ENST00000354186,;KALRN,missense_variant,p.Arg514Gln,ENST00000428018,;KALRN,missense_variant,p.Arg2243Gln,ENST00000360013,;KALRN,upstream_gene_variant,,ENST00000484542,;	A	ENSG00000160145	ENST00000459915	Transcript	missense_variant	1274	1004	335	R/Q	cGg/cAg	.	.	.	1	KALRN	HGNC	4814	protein_coding	.	.	ENSP00000420318	.	E7EUZ8_HUMAN	UPI0001B79837	.	deleterious(0.03)	benign(0.059)	12/13	.	hmmpanther:PTHR22826:SF49,hmmpanther:PTHR22826,Gene3D:2.30.29.30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAACGGAAAG	.	5	ESCA
MUC13	0	.	GRCh37	3	124627023	124627023	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1507C>T	p.His503Tyr	p.H503Y	ENST00000311075	11/12	49	35	13	40	40	0	MUC13,missense_variant,p.His503Tyr,ENST00000311075,;MUC13,downstream_gene_variant,,ENST00000462728,;	A	ENSG00000173702	ENST00000311075	Transcript	missense_variant	1546	1507	503	H/Y	Cac/Tac	.	.	.	-1	MUC13	HGNC	7511	protein_coding	YES	.	ENSP00000312235	MUC13_HUMAN	.	UPI00001AEF8F	.	deleterious(0.01)	benign(0.169)	11/12	.	hmmpanther:PTHR24041,hmmpanther:PTHR24041:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGTGTCTTG	.	5	ESCA
RHO	0	.	GRCh37	3	129251606	129251606	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.927G>A	p.Met309Ile	p.M309I	ENST00000296271	4/5	23	13	10	48	48	0	RHO,missense_variant,p.Met309Ile,ENST00000296271,;	A	ENSG00000163914	ENST00000296271	Transcript	missense_variant	1021	927	309	M/I	atG/atA	.	.	.	1	RHO	HGNC	10012	protein_coding	YES	CCDS3063.1	ENSP00000296271	OPSD_HUMAN	.	UPI0000046CE6	.	deleterious(0)	benign(0.01)	4/5	.	hmmpanther:PTHR24240:SF15,hmmpanther:PTHR24240,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATGAACAA	.	5	ESCA
AMOTL2	0	.	GRCh37	3	134075624	134075624	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*923C>G	.	.	ENST00000249883	10/10	35	22	13	35	35	0	AMOTL2,3_prime_UTR_variant,,ENST00000514516,;AMOTL2,3_prime_UTR_variant,,ENST00000249883,;AMOTL2,3_prime_UTR_variant,,ENST00000422605,;AMOTL2,downstream_gene_variant,,ENST00000513145,;RPL39P5,upstream_gene_variant,,ENST00000273411,;AMOTL2,non_coding_transcript_exon_variant,,ENST00000506326,;RPL39P5,upstream_gene_variant,,ENST00000512505,;	C	ENSG00000114019	ENST00000249883	Transcript	3_prime_UTR_variant	3580	.	.	.	.	.	.	.	-1	AMOTL2	HGNC	17812	protein_coding	YES	CCDS33860.1	ENSP00000249883	AMOL2_HUMAN	D6RJA4_HUMAN,D6RIC7_HUMAN,D6RFG0_HUMAN,D6RF61_HUMAN,D6RCL7_HUMAN,D6RBK2_HUMAN,B3KQD2_HUMAN	UPI00001B216C	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTGACAGG	.	5	ESCA
MRPS25	0	.	GRCh37	3	15106578	15106578	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>A	p.Glu42Lys	p.E42K	ENST00000253686	1/4	54	46	7	124	124	0	MRPS25,missense_variant,p.Glu42Lys,ENST00000449354,;MRPS25,missense_variant,p.Glu42Lys,ENST00000444840,;MRPS25,missense_variant,p.Glu42Lys,ENST00000253686,;MRPS25,missense_variant,p.Glu42Lys,ENST00000420267,;MRPS25,missense_variant,p.Glu42Lys,ENST00000447299,;	T	ENSG00000131368	ENST00000253686	Transcript	missense_variant	265	124	42	E/K	Gag/Aag	.	.	.	-1	MRPS25	HGNC	14511	protein_coding	YES	CCDS2622.1	ENSP00000253686	RT25_HUMAN	Q96Q22_HUMAN,E7EPW2_HUMAN	UPI00001352A0	.	tolerated(0.47)	benign(0.051)	1/4	.	Superfamily_domains:SSF52833,SMART_domains:SM00916,Gene3D:3.40.30.10,hmmpanther:PTHR13274:SF1,hmmpanther:PTHR13274	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGCCCA	.	4	ESCA
GPR149	0	.	GRCh37	3	154139187	154139187	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1264G>A	p.Glu422Lys	p.E422K	ENST00000389740	3/4	17	9	8	11	11	0	GPR149,missense_variant,p.Glu422Lys,ENST00000389740,;	T	ENSG00000174948	ENST00000389740	Transcript	missense_variant	1364	1264	422	E/K	Gaa/Aaa	.	.	.	-1	GPR149	HGNC	23627	protein_coding	YES	CCDS43162.1	ENSP00000374390	GP149_HUMAN	Q2MKA6_HUMAN	UPI00001AEEA9	.	tolerated(0.5)	benign(0.427)	3/4	.	hmmpanther:PTHR24229:SF32,hmmpanther:PTHR24229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCATCAT	.	5	ESCA
IFT80	0	.	GRCh37	3	160037578	160037578	+	Silent	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.927A>G	p.%3D	p.Q309Q	ENST00000326448	9/20	54	36	17	27	27	0	IFT80,synonymous_variant,p.%3D,ENST00000483465,;IFT80,synonymous_variant,p.%3D,ENST00000496589,;IFT80,synonymous_variant,p.%3D,ENST00000326448,;IFT80,downstream_gene_variant,,ENST00000478460,;RP11-432B6.3,synonymous_variant,p.%3D,ENST00000483754,;IFT80,3_prime_UTR_variant,,ENST00000472555,;IFT80,non_coding_transcript_exon_variant,,ENST00000461213,;IFT80,non_coding_transcript_exon_variant,,ENST00000487943,;	C	ENSG00000068885	ENST00000326448	Transcript	synonymous_variant	1360	927	309	Q	caA/caG	.	.	.	-1	IFT80	HGNC	29262	protein_coding	YES	CCDS3188.1	ENSP00000312778	IFT80_HUMAN	C9JUJ1_HUMAN,C9JUI1_HUMAN,C9JSB1_HUMAN,C9J6I5_HUMAN,C9J6G8_HUMAN,C9J627_HUMAN,C9IZR2_HUMAN	UPI0000160F16	.	.	.	9/20	.	hmmpanther:PTHR24098:SF8,hmmpanther:PTHR24098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTACTTGAAA	.	5	ESCA
SMC4	0	.	GRCh37	3	160138588	160138588	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1918C>T	p.%3D	p.L640L	ENST00000357388	13/24	102	67	34	50	50	0	SMC4,synonymous_variant,p.%3D,ENST00000344722,;SMC4,synonymous_variant,p.%3D,ENST00000469762,;SMC4,synonymous_variant,p.%3D,ENST00000462787,;SMC4,synonymous_variant,p.%3D,ENST00000357388,;SMC4,synonymous_variant,p.%3D,ENST00000360111,;SMC4,downstream_gene_variant,,ENST00000487747,;SMC4,3_prime_UTR_variant,,ENST00000469858,;SMC4,non_coding_transcript_exon_variant,,ENST00000497203,;SMC4,non_coding_transcript_exon_variant,,ENST00000462668,;RP11-432B6.3,intron_variant,,ENST00000483754,;SMC4,downstream_gene_variant,,ENST00000493695,;SMC4,downstream_gene_variant,,ENST00000484799,;	T	ENSG00000113810	ENST00000357388	Transcript	synonymous_variant	2369	1918	640	L	Ctg/Ttg	.	.	.	1	SMC4	HGNC	14013	protein_coding	YES	CCDS3189.1	ENSP00000349961	SMC4_HUMAN	C9JWF0_HUMAN,C9JVD8_HUMAN,C9JR83_HUMAN,C9JJ64_HUMAN,C9J9E4_HUMAN,C9J578_HUMAN,C9IYK2_HUMAN	UPI000006DA0A	.	.	.	13/24	.	hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF148,Pfam_domain:PF02463,Pfam_domain:PF06470,PIRSF_domain:PIRSF005719,SMART_domains:SM00968,Superfamily_domains:0038317	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCACTGGAC	.	5	ESCA
SI	0	.	GRCh37	3	164735587	164735587	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3595G>T	p.Gly1199Cys	p.G1199C	ENST00000264382	30/48	53	33	20	41	41	0	SI,missense_variant,p.Gly1199Cys,ENST00000264382,;	A	ENSG00000090402	ENST00000264382	Transcript	missense_variant	3658	3595	1199	G/C	Ggc/Tgc	.	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	deleterious(0)	probably_damaging(0.998)	30/48	.	Superfamily_domains:SSF74650,Pfam_domain:PF01055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCCCAAAA	.	5	ESCA
TBC1D5	0	.	GRCh37	3	17470011	17470011	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98G>T	p.Gly33Val	p.G33V	ENST00000446818	5/24	139	85	53	80	80	0	TBC1D5,missense_variant,p.Gly33Val,ENST00000507877,;TBC1D5,missense_variant,p.Gly33Val,ENST00000415814,;TBC1D5,missense_variant,p.Gly33Val,ENST00000429383,;TBC1D5,missense_variant,p.Gly33Val,ENST00000425944,;TBC1D5,missense_variant,p.Gly33Val,ENST00000428355,;TBC1D5,missense_variant,p.Gly33Val,ENST00000445294,;TBC1D5,missense_variant,p.Gly33Val,ENST00000434420,;TBC1D5,missense_variant,p.Gly33Val,ENST00000446818,;TBC1D5,missense_variant,p.Gly33Val,ENST00000414349,;TBC1D5,missense_variant,p.Gly33Val,ENST00000446863,;TBC1D5,missense_variant,p.Gly33Val,ENST00000253692,;TBC1D5,splice_region_variant,,ENST00000443499,;TBC1D5,splice_region_variant,,ENST00000497531,;TBC1D5,intron_variant,,ENST00000444756,;TBC1D5,intron_variant,,ENST00000414318,;TBC1D5,intron_variant,,ENST00000443386,;TBC1D5,intron_variant,,ENST00000412981,;TBC1D5,intron_variant,,ENST00000452492,;TBC1D5,intron_variant,,ENST00000430169,;	A	ENSG00000131374	ENST00000446818	Transcript	missense_variant	362	98	33	G/V	gGa/gTa	.	.	.	-1	TBC1D5	HGNC	19166	protein_coding	YES	CCDS46770.1	ENSP00000402935	TBCD5_HUMAN	F2Z3C3_HUMAN,C9K0P2_HUMAN,C9JWX0_HUMAN,C9JW04_HUMAN,C9JNM0_HUMAN,C9JMP7_HUMAN,C9JIU4_HUMAN,C9JED7_HUMAN,C9JDR8_HUMAN,C9J397_HUMAN	UPI00017E10F6	.	deleterious_low_confidence(0.03)	benign(0.016)	5/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTCCTGGA	.	5	ESCA
NAALADL2	0	.	GRCh37	3	175165132	175165132	+	Silent	SNP	G	G	A	rs772833242	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1206G>A	p.%3D	p.A402A	ENST00000454872	6/14	40	26	14	29	29	0	NAALADL2,synonymous_variant,p.%3D,ENST00000454872,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000473253,;NAALADL2,intron_variant,,ENST00000489299,;NAALADL2,3_prime_UTR_variant,,ENST00000414826,;	A	ENSG00000177694	ENST00000454872	Transcript	synonymous_variant	1334	1206	402	A	gcG/gcA	rs772833242	.	.	1	NAALADL2	HGNC	23219	protein_coding	YES	CCDS46960.1	ENSP00000404705	NADL2_HUMAN	C9JQ86_HUMAN	UPI0000161608	.	.	.	6/14	.	hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404,Superfamily_domains:SSF52025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCGTGTAG	byFrequency	5	ESCA
PIK3CA	0	.	GRCh37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	T	rs121913279	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	21/21	33	20	13	18	18	0	PIK3CA,missense_variant,p.His1047Leu,ENST00000263967,;RP11-245C23.3,downstream_gene_variant,,ENST00000609807,;	T	ENSG00000121879	ENST00000263967	Transcript	missense_variant	3297	3140	1047	H/L	cAt/cTt	rs121913279,COSM776,COSM775,COSM249874,COSM94987,COSM94986	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	tolerated(0.44)	benign(0.085)	21/21	.	PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	pathogenic	0,1,1,1,1,1	25710561	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H1047L|c.3140A>T|236,SITE|p.H1047L|c.3140A>T|45,CODON|p.H1047Y|c.3139C>T|8,CODON|p.H1047Y|c.3139C>T|54,CODON|p.H1047R|c.3140A>G|1687,CODON|p.H1047R|c.3140A>G|242,BUFFER|p.M1043I|c.3129G>T|4,BUFFER|p.M1043I|c.3129G>A|8,BUFFER|p.M1043I|c.3129G>T|45,BUFFER|p.M1043I|c.3129G>A|22,BUFFER|p.M1043I|c.3129G>C|4,BUFFER|p.M1043I|c.3129G>C|6,BUFFER|p.N1044D|c.3130A>G|4,BUFFER|p.N1044Y|c.3130A>T|3,BUFFER|p.N1044S|c.3131A>G|5,BUFFER|p.N1044S|c.3131A>G|3,BUFFER|p.N1044K|c.3132T>G|5,BUFFER|p.N1044K|c.3132T>A|15,BUFFER|p.N1044K|c.3132T>A|7,BUFFER|p.D1045N|c.3133G>A|6,BUFFER|p.A1046T|c.3136G>A|6,BUFFER|p.A1046E|c.3137C>A|3,BUFFER|p.H1047Q|c.3141T>G|4,BUFFER|p.H1048R|c.3143A>G|6,BUFFER|p.H1048R|c.3143A>G|3,BUFFER|p.G1049S|c.3145G>A|16,BUFFER|p.G1049R|c.3145G>C|29,BUFFER|p.G1049R|c.3145G>C|5,BUFFER|p.G1049A|c.3146G>C|3,BUFFER|p.G1049D|c.3146G>A|4,BUFFER|p.G1049G|c.3147T>C|10,BUFFER|p.G1050S|c.3148G>A|3,BUFFER|p.G1050D|c.3149G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCACATCATG	byFrequency|byCluster	5	ESCA
IGF2BP2	0	.	GRCh37	3	185361542	185361542	+	3'UTR	SNP	A	A	G	rs777833620	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1777T>C	.	.	ENST00000382199	16/16	71	46	25	53	53	0	IGF2BP2,3_prime_UTR_variant,,ENST00000382199,;IGF2BP2,downstream_gene_variant,,ENST00000421047,;IGF2BP2,downstream_gene_variant,,ENST00000457616,;IGF2BP2,downstream_gene_variant,,ENST00000346192,;IGF2BP2,downstream_gene_variant,,ENST00000464166,;	G	ENSG00000073792	ENST00000382199	Transcript	3_prime_UTR_variant	3673	.	.	.	.	rs777833620	.	.	-1	IGF2BP2	HGNC	28867	protein_coding	YES	CCDS3273.2	ENSP00000371634	IF2B2_HUMAN	.	UPI000013C5B6	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGATATATTT	.	5	ESCA
DCLK3	0	.	GRCh37	3	36779064	36779064	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1087G>T	p.Gly363Trp	p.G363W	ENST00000416516	2/5	41	30	10	49	49	0	DCLK3,missense_variant,p.Gly363Trp,ENST00000416516,;	A	ENSG00000163673	ENST00000416516	Transcript	missense_variant	1578	1087	363	G/W	Ggg/Tgg	.	.	.	-1	DCLK3	HGNC	19005	protein_coding	YES	CCDS43064.1	ENSP00000394484	DCLK3_HUMAN	B3KVM3_HUMAN	UPI0000E2657D	.	deleterious(0)	probably_damaging(1)	2/5	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF138,hmmpanther:PTHR24347,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCCCAATGA	.	5	ESCA
CTDSPL	0	.	GRCh37	3	38006108	38006108	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.314G>A	p.Gly105Glu	p.G105E	ENST00000273179	4/8	59	45	14	45	45	0	CTDSPL,missense_variant,p.Gly94Glu,ENST00000443503,;CTDSPL,missense_variant,p.Gly105Glu,ENST00000273179,;CTDSPL,missense_variant,p.Gly14Glu,ENST00000416688,;CTDSPL,upstream_gene_variant,,ENST00000447745,;MIR26A1,upstream_gene_variant,,ENST00000362205,;CTDSPL,non_coding_transcript_exon_variant,,ENST00000486978,;CTDSPL,non_coding_transcript_exon_variant,,ENST00000310189,;	A	ENSG00000144677	ENST00000273179	Transcript	missense_variant	340	314	105	G/E	gGa/gAa	.	.	.	1	CTDSPL	HGNC	16890	protein_coding	YES	CCDS33734.1	ENSP00000273179	CTDSL_HUMAN	.	UPI00001BE8E2	.	deleterious(0.02)	possibly_damaging(0.546)	4/8	.	Superfamily_domains:SSF56784,SMART_domains:SM00577,Gene3D:3.40.50.1000,hmmpanther:PTHR12210:SF43,hmmpanther:PTHR12210,PROSITE_profiles:PS50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATGGAAAGA	.	5	ESCA
LRRN1	0	.	GRCh37	3	3886434	3886434	+	Missense_Mutation	SNP	G	G	A	rs375458276	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.109G>A	p.Val37Ile	p.V37I	ENST00000319331	2/2	72	45	26	51	51	0	LRRN1,missense_variant,p.Val37Ile,ENST00000319331,;SUMF1,intron_variant,,ENST00000534863,;LRRN1,downstream_gene_variant,,ENST00000496115,;SUMF1,intron_variant,,ENST00000448413,;	A	ENSG00000175928	ENST00000319331	Transcript	missense_variant	870	109	37	V/I	Gta/Ata	rs375458276,COSM2987092	.	.	1	LRRN1	HGNC	20980	protein_coding	YES	CCDS33685.1	ENSP00000314901	LRRN1_HUMAN	.	UPI0000034CB8	.	tolerated(0.08)	benign(0.259)	2/2	.	hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF97,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	A:0.0005	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCGTATGT	byFrequency|byCluster	5	ESCA
CX3CR1	0	.	GRCh37	3	39307429	39307429	+	Missense_Mutation	SNP	C	C	T	rs768761417	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668G>A	p.Arg223His	p.R223H	ENST00000358309	2/2	55	37	17	56	56	0	CX3CR1,missense_variant,p.Arg191His,ENST00000542107,;CX3CR1,missense_variant,p.Arg191His,ENST00000399220,;CX3CR1,missense_variant,p.Arg223His,ENST00000358309,;CX3CR1,missense_variant,p.Arg191His,ENST00000541347,;CX3CR1,downstream_gene_variant,,ENST00000435290,;CX3CR1,downstream_gene_variant,,ENST00000412814,;	T	ENSG00000168329	ENST00000358309	Transcript	missense_variant	708	668	223	R/H	cGc/cAc	rs768761417	.	.	-1	CX3CR1	HGNC	2558	protein_coding	YES	CCDS54571.1	ENSP00000351059	CX3C1_HUMAN	C9JN40_HUMAN,C9JLM2_HUMAN	UPI00004570E5	.	tolerated(0.86)	possibly_damaging(0.857)	2/2	.	Prints_domain:PR01562,Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,hmmpanther:PTHR24227:SF9,hmmpanther:PTHR24227,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGCGGAGC	byFrequency	5	ESCA
TMA7	0	.	GRCh37	3	48482033	48482033	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.155C>T	p.Pro52Leu	p.P52L	ENST00000438607	3/4	36	25	10	77	77	0	TMA7,missense_variant,p.Pro52Leu,ENST00000438607,;CCDC51,upstream_gene_variant,,ENST00000447018,;CCDC51,upstream_gene_variant,,ENST00000412398,;CCDC51,upstream_gene_variant,,ENST00000395694,;CCDC51,upstream_gene_variant,,ENST00000438370,;CCDC51,upstream_gene_variant,,ENST00000442740,;CCDC51,upstream_gene_variant,,ENST00000446140,;CCDC51,upstream_gene_variant,,ENST00000395696,;RP11-24C3.2,non_coding_transcript_exon_variant,,ENST00000438872,;RP11-24C3.2,downstream_gene_variant,,ENST00000435578,;TMA7,non_coding_transcript_exon_variant,,ENST00000477624,;TMA7,non_coding_transcript_exon_variant,,ENST00000479126,;	T	ENSG00000232112	ENST00000438607	Transcript	missense_variant	195	155	52	P/L	cCc/cTc	.	.	.	1	TMA7	HGNC	26932	protein_coding	YES	CCDS46823.1	ENSP00000397843	TMA7_HUMAN	.	UPI0000027F8E	.	tolerated(0.06)	unknown(0)	3/4	.	Pfam_domain:PF09072	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCCCTTGG	.	5	ESCA
RHOA	0	.	GRCh37	3	49412922	49412922	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.101A>G	p.Tyr34Cys	p.Y34C	ENST00000418115	2/5	57	44	12	45	45	0	RHOA,missense_variant,p.Tyr34Cys,ENST00000431929,;RHOA,missense_variant,p.Tyr34Cys,ENST00000422781,;RHOA,missense_variant,p.Tyr34Cys,ENST00000454011,;RHOA,missense_variant,p.Tyr34Cys,ENST00000445425,;RHOA,missense_variant,p.Tyr34Cys,ENST00000418115,;	C	ENSG00000067560	ENST00000418115	Transcript	missense_variant	486	101	34	Y/C	tAt/tGt	COSM2849895	.	.	-1	RHOA	HGNC	667	protein_coding	YES	CCDS2795.1	ENSP00000400175	RHOA_HUMAN	Q9BVT0_HUMAN,C9JNR4_HUMAN,B4DKN9_HUMAN	UPI0000046824	.	deleterious(0)	probably_damaging(1)	2/5	.	PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF100,hmmpanther:PTHR24072,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00173,SMART_domains:SM00175,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACATACACC	.	5	ESCA
AMT	0	.	GRCh37	3	49459414	49459414	+	Intron	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258+123G>A	.	.	ENST00000273588	.	26	14	12	33	33	0	AMT,splice_donor_variant,,ENST00000546031,;AMT,intron_variant,,ENST00000430521,;AMT,intron_variant,,ENST00000427987,;AMT,intron_variant,,ENST00000395338,;AMT,intron_variant,,ENST00000458307,;AMT,intron_variant,,ENST00000538581,;AMT,intron_variant,,ENST00000273588,;NICN1,downstream_gene_variant,,ENST00000436744,;NICN1,downstream_gene_variant,,ENST00000273598,;NICN1-AS1,upstream_gene_variant,,ENST00000424915,;AMT,splice_donor_variant,,ENST00000493046,;AMT,splice_donor_variant,,ENST00000462048,;AMT,intron_variant,,ENST00000485108,;AMT,intron_variant,,ENST00000487589,;AMT,intron_variant,,ENST00000476226,;AMT,intron_variant,,ENST00000480957,;NICN1,downstream_gene_variant,,ENST00000422593,;AMT,splice_donor_variant,,ENST00000399379,;AMT,non_coding_transcript_exon_variant,,ENST00000461210,;AMT,non_coding_transcript_exon_variant,,ENST00000498571,;AMT,intron_variant,,ENST00000495436,;AMT,intron_variant,,ENST00000478594,;AMT,upstream_gene_variant,,ENST00000476828,;AMT,upstream_gene_variant,,ENST00000476127,;NICN1,downstream_gene_variant,,ENST00000497742,;NICN1,downstream_gene_variant,,ENST00000423832,;AMT,upstream_gene_variant,,ENST00000473163,;AMT,upstream_gene_variant,,ENST00000465925,;NICN1,downstream_gene_variant,,ENST00000461015,;AMT,upstream_gene_variant,,ENST00000491800,;NICN1,downstream_gene_variant,,ENST00000494057,;	T	ENSG00000145020	ENST00000273588	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AMT	HGNC	473	protein_coding	YES	CCDS2797.1	ENSP00000273588	GCST_HUMAN	B4DGG9_HUMAN,B3KTU4_HUMAN	UPI000012B35E	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGACCTCTA	.	5	ESCA
WDR82	0	.	GRCh37	3	52291334	52291334	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*172G>T	.	.	ENST00000296490	9/9	28	18	10	17	17	0	WDR82,3_prime_UTR_variant,,ENST00000296490,;WDR82,downstream_gene_variant,,ENST00000463624,;WDR82,downstream_gene_variant,,ENST00000469000,;WDR82,non_coding_transcript_exon_variant,,ENST00000487402,;	A	ENSG00000164091	ENST00000296490	Transcript	3_prime_UTR_variant	1396	.	.	.	.	.	.	.	-1	WDR82	HGNC	28826	protein_coding	YES	CCDS2851.2	ENSP00000296490	WDR82_HUMAN	C9JBU3_HUMAN,C9J355_HUMAN	UPI00000EBAC2	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCAAAGT	.	5	ESCA
NEK4	0	.	GRCh37	3	52773550	52773550	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2194C>T	p.Pro732Ser	p.P732S	ENST00000233027	14/16	79	56	23	60	60	0	NEK4,missense_variant,p.Pro732Ser,ENST00000233027,;NEK4,missense_variant,p.Pro643Ser,ENST00000461689,;NEK4,missense_variant,p.Pro686Ser,ENST00000383721,;NEK4,missense_variant,p.Pro643Ser,ENST00000535191,;NEK4,downstream_gene_variant,,ENST00000493199,;RP5-966M1.5,downstream_gene_variant,,ENST00000603259,;	A	ENSG00000114904	ENST00000233027	Transcript	missense_variant	2397	2194	732	P/S	Cca/Tca	.	.	.	-1	NEK4	HGNC	11399	protein_coding	YES	CCDS2863.1	ENSP00000233027	NEK4_HUMAN	.	UPI000013C96A	.	tolerated(0.1)	benign(0.259)	14/16	.	hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGGGTTTG	.	5	ESCA
CACNA2D3	0	.	GRCh37	3	54798316	54798316	+	Missense_Mutation	SNP	C	C	T	rs762550479	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1318C>T	p.Arg440Trp	p.R440W	ENST00000474759	13/38	91	64	27	58	58	0	CACNA2D3,missense_variant,p.Arg440Trp,ENST00000474759,;CACNA2D3,missense_variant,p.Arg440Trp,ENST00000415676,;CACNA2D3,missense_variant,p.Arg346Trp,ENST00000490478,;CACNA2D3,missense_variant,p.Arg440Trp,ENST00000288197,;CACNA2D3,missense_variant,p.Arg346Trp,ENST00000477024,;CACNA2D3,missense_variant,p.Arg346Trp,ENST00000471363,;CACNA2D3,3_prime_UTR_variant,,ENST00000468658,;	T	ENSG00000157445	ENST00000474759	Transcript	missense_variant	1366	1318	440	R/W	Cgg/Tgg	rs762550479	.	.	1	CACNA2D3	HGNC	15460	protein_coding	YES	CCDS54598.1	ENSP00000419101	CA2D3_HUMAN	C9JAV5_HUMAN	UPI000004A7BF	.	deleterious(0)	probably_damaging(0.976)	13/38	.	hmmpanther:PTHR10166:SF25,hmmpanther:PTHR10166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGCCGGCCC	.	5	ESCA
IL17RD	0	.	GRCh37	3	57176535	57176535	+	Intron	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.127-22194G>T	.	.	ENST00000296318	.	47	38	9	69	69	0	IL17RD,intron_variant,,ENST00000320057,;IL17RD,intron_variant,,ENST00000467210,;IL17RD,intron_variant,,ENST00000296318,;IL17RD,upstream_gene_variant,,ENST00000463523,;IL17RD,upstream_gene_variant,,ENST00000427856,;IL17RD,intron_variant,,ENST00000479825,;IL17RD,intron_variant,,ENST00000469841,;	A	ENSG00000144730	ENST00000296318	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	IL17RD	HGNC	17616	protein_coding	YES	CCDS2880.2	ENSP00000296318	I17RD_HUMAN	C9J6R0_HUMAN	UPI0000047CC3	.	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGCATCCCTCC	.	4	ESCA
ASB14	0	.	GRCh37	3	57302616	57302616	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1053C>A	.	.	ENST00000487349	11/11	46	26	20	24	24	0	ASB14,3_prime_UTR_variant,,ENST00000487349,;ASB14,3_prime_UTR_variant,,ENST00000389601,;APPL1,intron_variant,,ENST00000288266,;APPL1,downstream_gene_variant,,ENST00000488530,;APPL1,downstream_gene_variant,,ENST00000482800,;	T	ENSG00000239388	ENST00000487349	Transcript	3_prime_UTR_variant	2938	.	.	.	.	.	.	.	-1	ASB14	HGNC	19766	protein_coding	YES	CCDS46856.2	ENSP00000419199	ASB14_HUMAN	.	UPI0000E5A753	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTGCTTGT	.	5	ESCA
BRPF1	0	.	GRCh37	3	9788006	9788006	+	Missense_Mutation	SNP	G	G	A	rs777944933	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3347G>A	p.Arg1116Gln	p.R1116Q	ENST00000383829	13/14	59	51	8	84	84	0	BRPF1,missense_variant,p.Arg1109Gln,ENST00000424362,;BRPF1,missense_variant,p.Arg1015Gln,ENST00000433861,;BRPF1,missense_variant,p.Arg1110Gln,ENST00000302054,;BRPF1,missense_variant,p.Arg1110Gln,ENST00000457855,;BRPF1,missense_variant,p.Arg1116Gln,ENST00000383829,;OGG1,upstream_gene_variant,,ENST00000349503,;OGG1,upstream_gene_variant,,ENST00000302036,;OGG1,upstream_gene_variant,,ENST00000426518,;OGG1,upstream_gene_variant,,ENST00000449570,;OGG1,upstream_gene_variant,,ENST00000344629,;OGG1,upstream_gene_variant,,ENST00000339511,;OGG1,upstream_gene_variant,,ENST00000302003,;OGG1,upstream_gene_variant,,ENST00000352937,;OGG1,upstream_gene_variant,,ENST00000441094,;OGG1,upstream_gene_variant,,ENST00000302008,;OGG1,upstream_gene_variant,,ENST00000383826,;OGG1,upstream_gene_variant,,ENST00000436092,;BRPF1,downstream_gene_variant,,ENST00000469066,;BRPF1,non_coding_transcript_exon_variant,,ENST00000497565,;OGG1,upstream_gene_variant,,ENST00000429146,;OGG1,upstream_gene_variant,,ENST00000425665,;OGG1,upstream_gene_variant,,ENST00000432857,;	A	ENSG00000156983	ENST00000383829	Transcript	missense_variant	3751	3347	1116	R/Q	cGa/cAa	rs777944933,COSM254572	.	.	1	BRPF1	HGNC	14255	protein_coding	YES	CCDS33692.1	ENSP00000373340	BRPF1_HUMAN	C9JHC0_HUMAN,C9JDK5_HUMAN	UPI00001A9CA3	.	tolerated(0.26)	benign(0.285)	13/14	.	PROSITE_profiles:PS50812,hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF85,Gene3D:2.30.30.160,Pfam_domain:PF00855,SMART_domains:SM00293,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R1116Q|c.3347G>A|3	RADIA|MUTECT|MUSE|VARSCANS	GCCCCGAGAAG	.	4	ESCA
TET2	0	.	GRCh37	4	106159406	106159406	+	Intron	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3409+898G>T	.	.	ENST00000540549	.	28	24	4	14	14	0	TET2,3_prime_UTR_variant,,ENST00000305737,;TET2,3_prime_UTR_variant,,ENST00000394764,;TET2,intron_variant,,ENST00000413648,;TET2,intron_variant,,ENST00000540549,;TET2,intron_variant,,ENST00000380013,;TET2,intron_variant,,ENST00000545826,;TET2,intron_variant,,ENST00000513237,;TET2,downstream_gene_variant,,ENST00000514870,;TET2,intron_variant,,ENST00000265149,;	T	ENSG00000168769	ENST00000540549	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TET2	HGNC	25941	protein_coding	YES	CCDS47120.1	ENSP00000442788	TET2_HUMAN	E7EPB1_HUMAN,D6RE87_HUMAN	UPI00001D75E4	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE	TGATCGCTGTG	.	2	ESCA
NDST3	0	.	GRCh37	4	118975223	118975223	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.158G>A	p.Gly53Asp	p.G53D	ENST00000296499	2/14	37	22	15	31	31	0	NDST3,missense_variant,p.Gly53Asp,ENST00000433996,;NDST3,missense_variant,p.Gly53Asp,ENST00000296499,;NDST3,non_coding_transcript_exon_variant,,ENST00000394488,;	A	ENSG00000164100	ENST00000296499	Transcript	missense_variant	561	158	53	G/D	gGc/gAc	.	.	.	1	NDST3	HGNC	7682	protein_coding	YES	CCDS3708.1	ENSP00000296499	NDST3_HUMAN	.	UPI0000071C44	.	tolerated_low_confidence(0.56)	benign(0.061)	2/14	.	Pfam_domain:PF12062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGGCGACC	.	5	ESCA
ELF2	0	.	GRCh37	4	139981500	139981500	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1099G>A	p.Val367Met	p.V367M	ENST00000394235	9/10	32	22	9	20	20	0	ELF2,missense_variant,p.Val290Met,ENST00000379549,;ELF2,missense_variant,p.Val379Met,ENST00000379550,;ELF2,missense_variant,p.Val367Met,ENST00000265495,;ELF2,missense_variant,p.Val307Met,ENST00000510408,;ELF2,missense_variant,p.Val319Met,ENST00000358635,;ELF2,missense_variant,p.Val367Met,ENST00000394235,;ELF2,downstream_gene_variant,,ENST00000512627,;ELF2,downstream_gene_variant,,ENST00000420916,;RNU6-531P,downstream_gene_variant,,ENST00000516694,;ELF2,non_coding_transcript_exon_variant,,ENST00000515489,;ELF2,downstream_gene_variant,,ENST00000504314,;ELF2,downstream_gene_variant,,ENST00000514577,;	T	ENSG00000109381	ENST00000394235	Transcript	missense_variant	1602	1099	367	V/M	Gtg/Atg	.	.	.	-1	ELF2	HGNC	3317	protein_coding	YES	CCDS3744.1	ENSP00000377782	ELF2_HUMAN	.	UPI0000073EF0	.	tolerated(0.27)	benign(0.015)	9/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11849:SF10,hmmpanther:PTHR11849	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACACAGATG	.	5	ESCA
RP11-542P2.1	0	.	GRCh37	4	141377824	141377825	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.926dupT	p.Leu309PhefsTer15	p.L309Ffs*15	ENST00000503109	9/11	57	36	21	34	34	0	RP11-542P2.1,frameshift_variant,p.Leu36PhefsTer15,ENST00000513018,;RP11-542P2.1,frameshift_variant,p.Leu309PhefsTer15,ENST00000511113,;RP11-542P2.1,frameshift_variant,p.Leu101PhefsTer15,ENST00000515354,;RP11-542P2.1,frameshift_variant,p.Leu309PhefsTer15,ENST00000503109,;RP11-542P2.1,non_coding_transcript_exon_variant,,ENST00000511632,;RP11-542P2.1,3_prime_UTR_variant,,ENST00000515121,;RP11-542P2.1,non_coding_transcript_exon_variant,,ENST00000513106,;	A	ENSG00000205301	ENST00000503109	Transcript	frameshift_variant	926-927	926-927	309	L/FX	tta/ttTa	.	.	.	-1	RP11-542P2.1	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000426225	.	D6RH02_HUMAN	UPI0001D3B874	.	.	.	9/11	.	hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF6,Pfam_domain:PF04666	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACATTAAAAA	.	2	ESCA
IL15	0	.	GRCh37	4	142642320	142642320	+	Intron	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110+601G>T	.	.	ENST00000296545	.	38	24	14	40	40	0	IL15,missense_variant,p.Asp7Tyr,ENST00000514653,;IL15,missense_variant,p.Asp7Tyr,ENST00000394159,;IL15,missense_variant,p.Asp7Tyr,ENST00000477265,;IL15,intron_variant,,ENST00000529613,;IL15,intron_variant,,ENST00000296545,;IL15,intron_variant,,ENST00000320650,;IL15,downstream_gene_variant,,ENST00000505351,;IL15,upstream_gene_variant,,ENST00000509249,;	T	ENSG00000164136	ENST00000296545	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	IL15	HGNC	5977	protein_coding	YES	CCDS3755.1	ENSP00000296545	IL15_HUMAN	.	UPI0000031AC7	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATAGATTTG	.	5	ESCA
NPY1R	0	.	GRCh37	4	164245462	164245462	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*993G>A	.	.	ENST00000296533	3/3	46	29	17	8	8	0	NPY1R,3_prime_UTR_variant,,ENST00000296533,;NPY1R,downstream_gene_variant,,ENST00000511901,;NPY1R,downstream_gene_variant,,ENST00000515701,;NPY1R,downstream_gene_variant,,ENST00000512819,;NPY1R,downstream_gene_variant,,ENST00000504790,;NPY1R,downstream_gene_variant,,ENST00000504391,;NPY1R,downstream_gene_variant,,ENST00000509586,;	T	ENSG00000164128	ENST00000296533	Transcript	3_prime_UTR_variant	2680	.	.	.	.	.	.	.	-1	NPY1R	HGNC	7956	protein_coding	YES	CCDS34089.1	ENSP00000354652	NPY1R_HUMAN	D6RI97_HUMAN,D6RHH6_HUMAN,D6REY0_HUMAN,D6RC44_HUMAN,D6R9D0_HUMAN,B4DKL9_HUMAN	UPI000002D509	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTTCCTTTGA	.	3	ESCA
LINC01098	0	.	GRCh37	4	178896971	178896971	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174G>T	p.Met58Ile	p.M58I	ENST00000507870	5/6	28	16	11	38	38	0	LINC01098,missense_variant,p.Met58Ile,ENST00000507870,;	T	ENSG00000231171	ENST00000507870	Transcript	missense_variant	636	174	58	M/I	atG/atT	.	.	.	1	LINC01098	HGNC	27731	protein_coding	YES	.	ENSP00000421352	.	G5E9X9_HUMAN	UPI0000160C43	.	tolerated_low_confidence(0.37)	benign(0.045)	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATGAGGTC	.	5	ESCA
N4BP2	0	.	GRCh37	4	40144359	40144359	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4852G>A	p.Asp1618Asn	p.D1618N	ENST00000261435	15/18	71	43	28	48	48	0	N4BP2,missense_variant,p.Asp1248Asn,ENST00000513269,;N4BP2,missense_variant,p.Asp1618Asn,ENST00000261435,;N4BP2,3_prime_UTR_variant,,ENST00000511480,;RP11-395I6.1,upstream_gene_variant,,ENST00000507583,;	A	ENSG00000078177	ENST00000261435	Transcript	missense_variant	5268	4852	1618	D/N	Gac/Aac	.	.	.	1	N4BP2	HGNC	29851	protein_coding	YES	CCDS3457.1	ENSP00000261435	N4BP2_HUMAN	D6R9J2_HUMAN	UPI00001A962C	.	tolerated(0.16)	benign(0.167)	15/18	.	hmmpanther:PTHR13308:SF16,hmmpanther:PTHR13308,Pfam_domain:PF08590	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCAGACTAT	.	5	ESCA
DCAF4L1	0	.	GRCh37	4	41984704	41984704	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895C>A	p.Leu299Met	p.L299M	ENST00000333141	1/1	49	33	15	72	72	0	DCAF4L1,missense_variant,p.Leu299Met,ENST00000333141,;	A	ENSG00000182308	ENST00000333141	Transcript	missense_variant	992	895	299	L/M	Ctg/Atg	.	.	.	1	DCAF4L1	HGNC	27723	protein_coding	YES	CCDS33978.1	ENSP00000327796	DC4L1_HUMAN	.	UPI0000160C25	.	deleterious(0.04)	possibly_damaging(0.903)	1/1	.	Superfamily_domains:SSF50978,Gene3D:2.130.10.10,hmmpanther:PTHR22847:SF327,hmmpanther:PTHR22847,PROSITE_profiles:PS50294,PROSITE_profiles:PS50082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGATCTGAGG	.	5	ESCA
LNX1	0	.	GRCh37	4	54362344	54362344	+	Missense_Mutation	SNP	C	C	T	rs769520904	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1196G>A	p.Arg399His	p.R399H	ENST00000263925	6/11	39	27	11	47	47	0	LNX1,missense_variant,p.Arg303His,ENST00000306888,;LNX1,missense_variant,p.Arg399His,ENST00000263925,;FIP1L1,intron_variant,,ENST00000507166,;LNX1-AS1,upstream_gene_variant,,ENST00000502373,;LNX1-AS1,upstream_gene_variant,,ENST00000510785,;LNX1,downstream_gene_variant,,ENST00000511398,;	T	ENSG00000072201	ENST00000263925	Transcript	missense_variant	1511	1196	399	R/H	cGc/cAc	rs769520904	.	.	-1	LNX1	HGNC	6657	protein_coding	YES	CCDS47057.1	ENSP00000263925	LNX1_HUMAN	D6RB76_HUMAN,D6RAH9_HUMAN	UPI000012E7A6	.	deleterious(0.02)	probably_damaging(0.999)	6/11	.	PROSITE_profiles:PS50106,hmmpanther:PTHR19964:SF14,hmmpanther:PTHR19964,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGCGCACC	byFrequency	5	ESCA
FRAS1	0	.	GRCh37	4	79176498	79176498	+	Missense_Mutation	SNP	C	C	T	rs374819478	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572C>T	p.Thr191Ile	p.T191I	ENST00000264895	6/74	56	31	24	49	49	0	FRAS1,missense_variant,p.Thr120Ile,ENST00000502446,;FRAS1,missense_variant,p.Thr191Ile,ENST00000325942,;FRAS1,missense_variant,p.Thr191Ile,ENST00000264899,;FRAS1,missense_variant,p.Thr191Ile,ENST00000264895,;FRAS1,missense_variant,p.Thr34Ile,ENST00000508900,;	T	ENSG00000138759	ENST00000264895	Transcript	missense_variant	1012	572	191	T/I	aCa/aTa	rs374819478	.	.	1	FRAS1	HGNC	19185	protein_coding	YES	CCDS54771.1	ENSP00000264895	FRAS1_HUMAN	Q69YV4_HUMAN,Q4W596_HUMAN	UPI000021D4C2	.	.	benign(0.012)	6/74	.	PROSITE_profiles:PS50184,PROSITE_patterns:PS01208,Pfam_domain:PF00093,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	T:0.001	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCACAGCTC	byFrequency|byCluster|by1000G	5	ESCA
ST8SIA4	0	.	GRCh37	5	100147282	100147282	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*269A>G	.	.	ENST00000231461	5/5	47	33	14	21	21	0	ST8SIA4,3_prime_UTR_variant,,ENST00000231461,;MIR548P,downstream_gene_variant,,ENST00000408336,;	C	ENSG00000113532	ENST00000231461	Transcript	3_prime_UTR_variant	1660	.	.	.	.	.	.	.	-1	ST8SIA4	HGNC	10871	protein_coding	YES	CCDS4091.1	ENSP00000231461	SIA8D_HUMAN	.	UPI0000135973	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGTTGGAT	.	5	ESCA
TSLP	0	.	GRCh37	5	110411672	110411672	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380G>T	p.Arg127Met	p.R127M	ENST00000344895	4/4	35	17	17	26	26	0	TSLP,missense_variant,p.Arg31Met,ENST00000379706,;TSLP,missense_variant,p.Arg127Met,ENST00000420978,;TSLP,missense_variant,p.Arg127Met,ENST00000344895,;CTC-551A13.2,downstream_gene_variant,,ENST00000507269,;	T	ENSG00000145777	ENST00000344895	Transcript	missense_variant	579	380	127	R/M	aGg/aTg	COSM3719285	.	.	1	TSLP	HGNC	30743	protein_coding	YES	CCDS4101.1	ENSP00000339804	TSLP_HUMAN	Q96AU7_HUMAN,G3XAM8_HUMAN	UPI000006DB21	.	deleterious(0.02)	possibly_damaging(0.813)	4/4	.	Low_complexity_(Seg):seg,Pfam_domain:PF15216	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAGGAGAA	.	5	ESCA
MEGF10	0	.	GRCh37	5	126732405	126732405	+	Missense_Mutation	SNP	G	G	C	rs747619946	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594G>C	p.Gln198His	p.Q198H	ENST00000274473	7/26	41	38	3	96	96	0	MEGF10,missense_variant,p.Gln198His,ENST00000508365,;MEGF10,missense_variant,p.Gln198His,ENST00000274473,;MEGF10,missense_variant,p.Gln198His,ENST00000418761,;MEGF10,missense_variant,p.Gln198His,ENST00000503335,;	C	ENSG00000145794	ENST00000274473	Transcript	missense_variant	861	594	198	Q/H	caG/caC	rs747619946	.	.	1	MEGF10	HGNC	29634	protein_coding	YES	CCDS4142.1	ENSP00000274473	MEG10_HUMAN	.	UPI000006F868	.	tolerated(0.51)	benign(0.134)	7/26	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF75,Gene3D:2gy5A03,SMART_domains:SM00180,SMART_domains:SM00181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TGCCAGAATGG	.	2	ESCA
FBN2	0	.	GRCh37	5	127873307	127873307	+	5'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11C>A	.	.	ENST00000508053	7/71	58	39	18	70	70	0	FBN2,5_prime_UTR_variant,,ENST00000262464,;FBN2,5_prime_UTR_variant,,ENST00000508053,;FBN2,5_prime_UTR_variant,,ENST00000502468,;FBN2,5_prime_UTR_variant,,ENST00000508989,;SLC27A6,upstream_gene_variant,,ENST00000508645,;FBN2,non_coding_transcript_exon_variant,,ENST00000514742,;	T	ENSG00000138829	ENST00000508053	Transcript	5_prime_UTR_variant	965	.	.	.	.	.	.	.	-1	FBN2	HGNC	3604	protein_coding	YES	CCDS34222.1	ENSP00000424571	FBN2_HUMAN	.	UPI0000519468	.	.	.	7/71	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCCGAAAGC	.	5	ESCA
SEC24A	0	.	GRCh37	5	134063057	134063057	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2273G>T	.	.	ENST00000398844	23/23	63	34	29	24	24	0	SEC24A,3_prime_UTR_variant,,ENST00000398844,;	T	ENSG00000113615	ENST00000398844	Transcript	3_prime_UTR_variant	5843	.	.	.	.	.	.	.	1	SEC24A	HGNC	10703	protein_coding	YES	CCDS43363.1	ENSP00000381823	SC24A_HUMAN	.	UPI0000185FF9	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAGTACTC	.	5	ESCA
C5orf20	0	.	GRCh37	5	134782217	134782217	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.582G>A	p.Trp194Ter	p.W194*	ENST00000503143	1/1	40	23	16	67	67	0	C5orf20,stop_gained,p.Trp194Ter,ENST00000503143,;TIFAB,3_prime_UTR_variant,,ENST00000537858,;CTB-138E5.1,upstream_gene_variant,,ENST00000510230,;	T	ENSG00000251380	ENST00000503143	Transcript	stop_gained	822	582	194	W/*	tgG/tgA	.	.	.	-1	C5orf20	HGNC	24459	protein_coding	YES	CCDS4186.1	ENSP00000421871	DCNP1_HUMAN	.	UPI000006FF8B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTTCCAGCT	.	5	ESCA
CXXC5	0	.	GRCh37	5	139060532	139060532	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.424G>T	p.Ala142Ser	p.A142S	ENST00000302517	2/3	52	31	21	125	125	0	CXXC5,missense_variant,p.Ala142Ser,ENST00000511457,;CXXC5,missense_variant,p.Ala142Ser,ENST00000504844,;CXXC5,missense_variant,p.Ala142Ser,ENST00000302517,;CXXC5,missense_variant,p.Ala142Ser,ENST00000502716,;CXXC5,missense_variant,p.Ala142Ser,ENST00000511048,;CXXC5,downstream_gene_variant,,ENST00000512816,;CXXC5,downstream_gene_variant,,ENST00000509238,;CXXC5,downstream_gene_variant,,ENST00000503511,;CXXC5,downstream_gene_variant,,ENST00000504944,;CXXC5,downstream_gene_variant,,ENST00000507139,;CXXC5,downstream_gene_variant,,ENST00000511591,;CXXC5,downstream_gene_variant,,ENST00000502295,;CXXC5,downstream_gene_variant,,ENST00000502336,;CXXC5,downstream_gene_variant,,ENST00000520967,;CTB-35F21.1,upstream_gene_variant,,ENST00000515296,;CXXC5,upstream_gene_variant,,ENST00000505812,;CXXC5,upstream_gene_variant,,ENST00000515038,;	T	ENSG00000171604	ENST00000302517	Transcript	missense_variant	1138	424	142	A/S	Gcc/Tcc	.	.	.	1	CXXC5	HGNC	26943	protein_coding	YES	CCDS43370.1	ENSP00000302543	CXXC5_HUMAN	E7EVI8_HUMAN,E7EV55_HUMAN,D6RIR8_HUMAN,D6RHG9_HUMAN,D6RHC6_HUMAN,D6RDY2_HUMAN,D6RCN9_HUMAN,D6RBE0_HUMAN,D6R9V1_HUMAN,D6R966_HUMAN	UPI000003779E	.	tolerated(0.37)	benign(0.031)	2/3	.	hmmpanther:PTHR13419:SF2,hmmpanther:PTHR13419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGGCCAGC	.	5	ESCA
PCDHA7	0	.	GRCh37	5	140215502	140215502	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1534G>A	p.Ala512Thr	p.A512T	ENST00000525929	1/4	186	137	48	329	329	0	PCDHA7,missense_variant,p.Ala512Thr,ENST00000378125,;PCDHA7,missense_variant,p.Ala512Thr,ENST00000525929,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	A	ENSG00000204963	ENST00000525929	Transcript	missense_variant	1534	1534	512	A/T	Gcg/Acg	COSM1541983,COSM1541982	.	.	1	PCDHA7	HGNC	8673	protein_coding	YES	CCDS54918.1	ENSP00000436426	PCDA7_HUMAN	.	UPI00001273CF	.	deleterious_low_confidence(0.01)	possibly_damaging(0.548)	1/4	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACGCGGAG	.	5	ESCA
PCDHB13	0	.	GRCh37	5	140594473	140594473	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778T>C	p.Phe260Leu	p.F260L	ENST00000341948	1/1	96	56	40	90	90	0	PCDHB13,missense_variant,p.Phe260Leu,ENST00000341948,;PCDHB12,downstream_gene_variant,,ENST00000541609,;PCDHB12,downstream_gene_variant,,ENST00000239450,;	C	ENSG00000187372	ENST00000341948	Transcript	missense_variant	965	778	260	F/L	Ttc/Ctc	.	.	.	1	PCDHB13	HGNC	8684	protein_coding	YES	CCDS4255.1	ENSP00000345491	PCDBD_HUMAN	.	UPI0000047816	.	deleterious_low_confidence(0.01)	benign(0.002)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGCTTCCTG	.	5	ESCA
TRIO	0	.	GRCh37	5	14358418	14358418	+	Silent	SNP	C	C	T	rs762757315	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2178C>T	p.%3D	p.N726N	ENST00000344204	12/57	35	24	10	57	57	0	TRIO,synonymous_variant,p.%3D,ENST00000537187,;TRIO,synonymous_variant,p.%3D,ENST00000509967,;TRIO,synonymous_variant,p.%3D,ENST00000344204,;TRIO,synonymous_variant,p.%3D,ENST00000513206,;TRIO,synonymous_variant,p.%3D,ENST00000512070,;TRIO,non_coding_transcript_exon_variant,,ENST00000515144,;	T	ENSG00000038382	ENST00000344204	Transcript	synonymous_variant	2202	2178	726	N	aaC/aaT	rs762757315	.	.	1	TRIO	HGNC	12303	protein_coding	YES	CCDS3883.1	ENSP00000339299	TRIO_HUMAN	.	UPI000034ECE6	.	.	.	12/57	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF46966,SMART_domains:SM00150,Gene3D:1.20.58.60,hmmpanther:PTHR22826:SF104,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAACGTGAT	byFrequency	5	ESCA
ITK	0	.	GRCh37	5	156638349	156638349	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295C>T	p.Arg99Trp	p.R99W	ENST00000422843	3/17	30	24	5	47	47	0	ITK,missense_variant,p.Arg99Trp,ENST00000422843,;ITK,5_prime_UTR_variant,,ENST00000521769,;CTB-4E7.1,intron_variant,,ENST00000519375,;ITK,missense_variant,p.Arg99Trp,ENST00000517779,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,non_coding_transcript_exon_variant,,ENST00000520555,;	T	ENSG00000113263	ENST00000422843	Transcript	missense_variant	447	295	99	R/W	Cgg/Tgg	.	.	.	1	ITK	HGNC	6171	protein_coding	YES	CCDS4336.1	ENSP00000398655	ITK_HUMAN	Q7Z318_HUMAN,E5RFR5_HUMAN	UPI000004CADA	.	deleterious(0)	probably_damaging(0.999)	3/17	.	PROSITE_profiles:PS50003,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGCCGGCAG	.	5	ESCA
TENM2	0	.	GRCh37	5	167689643	167689643	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8153G>A	p.Gly2718Glu	p.G2718E	ENST00000518659	29/29	32	19	12	80	78	1	TENM2,missense_variant,p.Gly2717Glu,ENST00000545108,;TENM2,missense_variant,p.Gly2479Glu,ENST00000520394,;TENM2,missense_variant,p.Gly2597Glu,ENST00000519204,;TENM2,missense_variant,p.Gly2718Glu,ENST00000518659,;TENM2,missense_variant,p.Gly2542Glu,ENST00000403607,;	A	ENSG00000145934	ENST00000518659	Transcript	missense_variant	8192	8153	2718	G/E	gGg/gAg	.	.	.	1	TENM2	HGNC	29943	protein_coding	YES	.	ENSP00000429430	TEN2_HUMAN	G8BLJ6_HUMAN,G3CAS7_HUMAN	UPI0001C48FC2	.	deleterious(0)	probably_damaging(0.95)	29/29	.	hmmpanther:PTHR11219:SF8,hmmpanther:PTHR11219,Pfam_domain:PF15636	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGACGGGAGAG	.	4	ESCA
BTNL9	0	.	GRCh37	5	180480869	180480869	+	Intron	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.886+368C>T	.	.	ENST00000327705	.	35	19	16	90	90	0	BTNL9,3_prime_UTR_variant,,ENST00000515271,;BTNL9,intron_variant,,ENST00000327705,;BTNL9,intron_variant,,ENST00000376841,;BTNL9,intron_variant,,ENST00000376842,;BTNL9,non_coding_transcript_exon_variant,,ENST00000511589,;BTNL9,3_prime_UTR_variant,,ENST00000491209,;BTNL9,non_coding_transcript_exon_variant,,ENST00000506782,;BTNL9,intron_variant,,ENST00000511056,;BTNL9,upstream_gene_variant,,ENST00000512570,;BTNL9,downstream_gene_variant,,ENST00000509395,;	T	ENSG00000165810	ENST00000327705	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	BTNL9	HGNC	24176	protein_coding	YES	CCDS4460.2	ENSP00000330200	BTNL9_HUMAN	Q8N324_HUMAN	UPI000004C620	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCAACATCTC	.	5	ESCA
SKIV2L2	0	.	GRCh37	5	54718789	54718789	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3055C>G	p.Leu1019Val	p.L1019V	ENST00000230640	26/27	57	40	17	22	22	0	SKIV2L2,missense_variant,p.Leu55Val,ENST00000508716,;SKIV2L2,missense_variant,p.Leu918Val,ENST00000545714,;SKIV2L2,missense_variant,p.Leu1019Val,ENST00000230640,;PPAP2A,downstream_gene_variant,,ENST00000264775,;PPAP2A,downstream_gene_variant,,ENST00000307259,;SKIV2L2,3_prime_UTR_variant,,ENST00000506750,;	G	ENSG00000039123	ENST00000230640	Transcript	missense_variant	3309	3055	1019	L/V	Ctg/Gtg	.	.	.	1	SKIV2L2	HGNC	18734	protein_coding	YES	CCDS3967.1	ENSP00000230640	SK2L2_HUMAN	.	UPI000020C772	.	deleterious(0)	probably_damaging(0.988)	26/27	.	hmmpanther:PTHR11752,hmmpanther:PTHR11752:SF54,Pfam_domain:PF08148,PIRSF_domain:PIRSF005198	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGCTGGAA	.	5	ESCA
VCAN	0	.	GRCh37	5	82816578	82816578	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2453C>A	p.Thr818Lys	p.T818K	ENST00000265077	7/15	37	26	10	29	29	0	VCAN,missense_variant,p.Thr818Lys,ENST00000342785,;VCAN,missense_variant,p.Thr818Lys,ENST00000265077,;VCAN,missense_variant,p.Thr770Lys,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000343200,;VCAN,intron_variant,,ENST00000515397,;	A	ENSG00000038427	ENST00000265077	Transcript	missense_variant	3018	2453	818	T/K	aCa/aAa	.	.	.	1	VCAN	HGNC	2464	protein_coding	YES	CCDS4060.1	ENSP00000265077	CSPG2_HUMAN	.	UPI000013178B	.	deleterious(0.01)	probably_damaging(0.972)	7/15	.	hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTACAGAAC	.	5	ESCA
GPR98	0	.	GRCh37	5	89981726	89981726	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6404G>C	p.Gly2135Ala	p.G2135A	ENST00000405460	29/90	54	37	17	34	34	0	GPR98,missense_variant,p.Gly2135Ala,ENST00000405460,;	C	ENSG00000164199	ENST00000405460	Transcript	missense_variant	6500	6404	2135	G/A	gGa/gCa	.	.	.	1	GPR98	HGNC	17416	protein_coding	YES	CCDS47246.1	ENSP00000384582	GPR98_HUMAN	.	UPI00002127A7	.	.	probably_damaging(0.995)	29/90	.	Superfamily_domains:SSF141072,SMART_domains:SM00237,Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTGGACCCA	.	5	ESCA
GRIK2	0	.	GRCh37	6	101847189	101847189	+	Silent	SNP	C	C	A	rs370229898	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36C>A	p.%3D	p.V12V	ENST00000421544	1/16	39	22	17	53	53	0	GRIK2,synonymous_variant,p.%3D,ENST00000369138,;GRIK2,synonymous_variant,p.%3D,ENST00000413795,;GRIK2,synonymous_variant,p.%3D,ENST00000318991,;GRIK2,synonymous_variant,p.%3D,ENST00000421544,;GRIK2,synonymous_variant,p.%3D,ENST00000358361,;GRIK2,synonymous_variant,p.%3D,ENST00000369137,;	A	ENSG00000164418	ENST00000421544	Transcript	synonymous_variant	526	36	12	V	gtC/gtA	rs370229898	.	.	1	GRIK2	HGNC	4580	protein_coding	YES	CCDS5048.1	ENSP00000397026	GRIK2_HUMAN	Q9BZ15_HUMAN,Q6P3V6_HUMAN,H7C2P5_HUMAN,F8WEZ8_HUMAN,D7RWZ8_HUMAN	UPI000012B617	.	.	.	1/16	.	.	G:0.0004	G:0	G:0	.	G:0.002	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R15C|c.43C>T|3,BUFFER|p.R15C|c.43C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGTCTTCAG	byFrequency|byCluster|by1000G	5	ESCA
TFAP2A	0	.	GRCh37	6	10400783	10400783	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.923G>T	p.Cys308Phe	p.C308F	ENST00000379604	6/7	41	31	10	38	38	0	TFAP2A,missense_variant,p.Cys302Phe,ENST00000379608,;TFAP2A,missense_variant,p.Cys310Phe,ENST00000379613,;TFAP2A,missense_variant,p.Cys304Phe,ENST00000319516,;TFAP2A,missense_variant,p.Cys308Phe,ENST00000482890,;TFAP2A,missense_variant,p.Cys308Phe,ENST00000379604,;TFAP2A,intron_variant,,ENST00000461628,;TFAP2A,intron_variant,,ENST00000466073,;TFAP2A,downstream_gene_variant,,ENST00000498450,;TFAP2A,downstream_gene_variant,,ENST00000475264,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000497266,;TFAP2A,downstream_gene_variant,,ENST00000473652,;TFAP2A,downstream_gene_variant,,ENST00000490875,;TFAP2A,3_prime_UTR_variant,,ENST00000488193,;TFAP2A,3_prime_UTR_variant,,ENST00000489805,;TFAP2A,downstream_gene_variant,,ENST00000478375,;	A	ENSG00000137203	ENST00000379604	Transcript	missense_variant	1175	923	308	C/F	tGc/tTc	.	.	.	-1	TFAP2A	HGNC	11742	protein_coding	YES	CCDS4510.1	ENSP00000368924	AP2A_HUMAN	.	UPI0000125BC5	.	deleterious(0)	possibly_damaging(0.878)	6/7	.	hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF8,Pfam_domain:PF03299	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E311K|c.931G>A|3,BUFFER|p.E305K|c.913G>A|3,BUFFER|p.E307K|c.919G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCGCACACG	.	5	ESCA
ZUFSP	0	.	GRCh37	6	116987880	116987880	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.476G>C	p.Cys159Ser	p.C159S	ENST00000368576	2/10	66	45	20	37	36	0	ZUFSP,missense_variant,p.Cys159Ser,ENST00000368576,;ZUFSP,missense_variant,p.Cys159Ser,ENST00000368573,;ZUFSP,non_coding_transcript_exon_variant,,ENST00000471919,;	G	ENSG00000153975	ENST00000368576	Transcript	missense_variant	720	476	159	C/S	tGt/tCt	.	.	.	-1	ZUFSP	HGNC	21224	protein_coding	YES	CCDS5110.1	ENSP00000357565	ZUFSP_HUMAN	.	UPI000006E8C6	.	tolerated(0.05)	probably_damaging(0.95)	2/10	.	SMART_domains:SM00355,hmmpanther:PTHR24382,hmmpanther:PTHR24382:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TTCCACAGAAT	.	4	ESCA
KIAA0408	0	.	GRCh37	6	127767686	127767686	+	Missense_Mutation	SNP	G	G	T	rs756732629	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1778C>A	p.Ser593Tyr	p.S593Y	ENST00000483725	5/6	50	24	26	22	22	0	KIAA0408,missense_variant,p.Ser593Tyr,ENST00000483725,;SOGA3,3_prime_UTR_variant,,ENST00000556132,;KIAA0408,intron_variant,,ENST00000465254,;SOGA3,downstream_gene_variant,,ENST00000368268,;KIAA0408,downstream_gene_variant,,ENST00000487331,;SOGA3,3_prime_UTR_variant,,ENST00000473298,;SOGA3,3_prime_UTR_variant,,ENST00000481848,;KIAA0408,non_coding_transcript_exon_variant,,ENST00000368281,;SOGA3,downstream_gene_variant,,ENST00000464495,;KIAA0408,downstream_gene_variant,,ENST00000472335,;	T	ENSG00000189367	ENST00000483725	Transcript	missense_variant	2115	1778	593	S/Y	tCt/tAt	rs756732629,COSM1440282	.	.	-1	KIAA0408	HGNC	21636	protein_coding	YES	CCDS34531.1	ENSP00000435150	K0408_HUMAN	.	UPI00001C0BD7	.	tolerated(0.05)	benign(0.048)	5/6	.	hmmpanther:PTHR15705	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CATCAGAATTA	.	4	ESCA
PHACTR2	0	.	GRCh37	6	144110003	144110003	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1801C>T	p.Arg601Cys	p.R601C	ENST00000440869	11/13	37	21	15	45	45	0	PHACTR2,missense_variant,p.Arg590Cys,ENST00000427704,;PHACTR2,missense_variant,p.Arg601Cys,ENST00000440869,;PHACTR2,missense_variant,p.Arg510Cys,ENST00000305766,;PHACTR2,missense_variant,p.Arg521Cys,ENST00000367582,;PHACTR2,missense_variant,p.Arg578Cys,ENST00000367584,;PHACTR2,non_coding_transcript_exon_variant,,ENST00000536245,;	T	ENSG00000112419	ENST00000440869	Transcript	missense_variant	2000	1801	601	R/C	Cgc/Tgc	.	.	.	1	PHACTR2	HGNC	20956	protein_coding	YES	CCDS47493.1	ENSP00000417038	PHAR2_HUMAN	.	UPI000020E355	.	deleterious(0)	probably_damaging(0.999)	11/13	.	hmmpanther:PTHR12751:SF5,hmmpanther:PTHR12751	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGACCGCCGA	.	5	ESCA
UTRN	0	.	GRCh37	6	145124230	145124230	+	Nonsense_Mutation	SNP	C	C	T	rs768258957	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9304C>T	p.Arg3102Ter	p.R3102*	ENST00000367545	64/74	90	47	43	40	40	0	UTRN,stop_gained,p.Arg146Ter,ENST00000367524,;UTRN,stop_gained,p.Arg657Ter,ENST00000367526,;UTRN,stop_gained,p.Arg61Ter,ENST00000417142,;UTRN,stop_gained,p.Arg27Ter,ENST00000455022,;UTRN,stop_gained,p.Arg61Ter,ENST00000432686,;UTRN,stop_gained,p.Arg3102Ter,ENST00000367545,;	T	ENSG00000152818	ENST00000367545	Transcript	stop_gained	9304	9304	3102	R/*	Cga/Tga	rs768258957	.	.	1	UTRN	HGNC	12635	protein_coding	YES	CCDS34547.1	ENSP00000356515	UTRO_HUMAN	Q6LBS5_HUMAN,Q5SYY2_HUMAN,Q5JT45_HUMAN	UPI00003673F1	.	.	.	64/74	.	PROSITE_profiles:PS50135,hmmpanther:PTHR11915:SF225,hmmpanther:PTHR11915,Pfam_domain:PF00569,SMART_domains:SM00291,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGTCGAACA	byFrequency	5	ESCA
SYNE1	0	.	GRCh37	6	152680459	152680459	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10434G>C	p.Glu3478Asp	p.E3478D	ENST00000367255	65/146	95	89	5	73	73	0	SYNE1,missense_variant,p.Glu3485Asp,ENST00000448038,;SYNE1,missense_variant,p.Glu3478Asp,ENST00000367255,;SYNE1,missense_variant,p.Glu3485Asp,ENST00000423061,;SYNE1,missense_variant,p.Glu3478Asp,ENST00000265368,;SYNE1,intron_variant,,ENST00000341594,;SYNE1,non_coding_transcript_exon_variant,,ENST00000471834,;	G	ENSG00000131018	ENST00000367255	Transcript	missense_variant	11036	10434	3478	E/D	gaG/gaC	.	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	benign(0.001)	65/146	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCTCTCTTG	.	2	ESCA
MAP3K4	0	.	GRCh37	6	161514016	161514016	+	Silent	SNP	G	G	A	rs369504568	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3276G>A	p.%3D	p.A1092A	ENST00000392142	14/27	94	51	43	52	52	0	MAP3K4,synonymous_variant,p.%3D,ENST00000366920,;MAP3K4,synonymous_variant,p.%3D,ENST00000366919,;MAP3K4,synonymous_variant,p.%3D,ENST00000348824,;MAP3K4,synonymous_variant,p.%3D,ENST00000392142,;MAP3K4,synonymous_variant,p.%3D,ENST00000544041,;MAP3K4,3_prime_UTR_variant,,ENST00000490904,;MAP3K4,upstream_gene_variant,,ENST00000543421,;MAP3K4,upstream_gene_variant,,ENST00000541901,;	A	ENSG00000085511	ENST00000392142	Transcript	synonymous_variant	3424	3276	1092	A	gcG/gcA	rs369504568	.	.	1	MAP3K4	HGNC	6856	protein_coding	YES	CCDS34565.1	ENSP00000375986	M3K4_HUMAN	F5H534_HUMAN	UPI00004574E1	.	.	.	14/27	.	hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF53	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGACTCA	byCluster	5	ESCA
ATXN1	0	.	GRCh37	6	16328464	16328464	+	Silent	SNP	G	G	A	rs370874989	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78C>T	p.%3D	p.S26S	ENST00000244769	8/9	21	16	5	49	49	0	ATXN1,synonymous_variant,p.%3D,ENST00000244769,;ATXN1,synonymous_variant,p.%3D,ENST00000436367,;	A	ENSG00000124788	ENST00000244769	Transcript	synonymous_variant	1015	78	26	S	tcC/tcT	rs370874989	.	.	-1	ATXN1	HGNC	10548	protein_coding	YES	CCDS34342.1	ENSP00000244769	ATX1_HUMAN	.	UPI000013CB8B	.	.	.	8/9	.	hmmpanther:PTHR13392:SF5,hmmpanther:PTHR13392	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCCTCGGAGGA	byFrequency|byCluster	4	ESCA
TCP10	0	.	GRCh37	6	167794750	167794750	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138A>C	p.Arg46Ser	p.R46S	ENST00000397829	3/8	14	8	6	30	30	0	TCP10,missense_variant,p.Arg46Ser,ENST00000366827,;TCP10,missense_variant,p.Arg46Ser,ENST00000485157,;TCP10,missense_variant,p.Arg46Ser,ENST00000397829,;TCP10,missense_variant,p.Arg46Ser,ENST00000476779,;TCP10,intron_variant,,ENST00000460930,;TCP10,non_coding_transcript_exon_variant,,ENST00000491085,;TCP10,non_coding_transcript_exon_variant,,ENST00000463894,;TCP10,non_coding_transcript_exon_variant,,ENST00000508373,;	G	ENSG00000203690	ENST00000397829	Transcript	missense_variant	306	138	46	R/S	agA/agC	.	.	.	-1	TCP10	HGNC	11656	protein_coding	YES	CCDS43527.1	ENSP00000380929	.	D1MPS5_HUMAN	UPI0000D820CE	.	tolerated(0.52)	benign(0.017)	3/8	.	hmmpanther:PTHR10331,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	AGTTTTCTGTG	.	3	ESCA
MLLT4	0	.	GRCh37	6	168323558	168323558	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2910C>T	p.%3D	p.H970H	ENST00000392108	21/30	45	27	17	21	21	0	MLLT4,synonymous_variant,p.%3D,ENST00000351017,;MLLT4,synonymous_variant,p.%3D,ENST00000447894,;MLLT4,synonymous_variant,p.%3D,ENST00000392108,;MLLT4,synonymous_variant,p.%3D,ENST00000392112,;MLLT4,synonymous_variant,p.%3D,ENST00000497596,;MLLT4,synonymous_variant,p.%3D,ENST00000344191,;MLLT4,synonymous_variant,p.%3D,ENST00000400822,;MLLT4,synonymous_variant,p.%3D,ENST00000366806,;MLLT4,non_coding_transcript_exon_variant,,ENST00000366809,;MLLT4,non_coding_transcript_exon_variant,,ENST00000511637,;	T	ENSG00000130396	ENST00000392108	Transcript	synonymous_variant	3052	2910	970	H	caC/caT	.	.	.	1	MLLT4	HGNC	7137	protein_coding	YES	CCDS47517.1	ENSP00000375956	AFAD_HUMAN	.	UPI0000711FD9	.	.	.	21/30	.	hmmpanther:PTHR10398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCACACACG	.	5	ESCA
RBM24	0	.	GRCh37	6	17291124	17291124	+	Intron	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348-863G>T	.	.	ENST00000379052	.	33	20	13	21	21	0	RBM24,splice_region_variant,,ENST00000509686,;RBM24,intron_variant,,ENST00000379052,;RBM24,intron_variant,,ENST00000503965,;RBM24,intron_variant,,ENST00000318204,;RBM24,intron_variant,,ENST00000425446,;RBM24,splice_region_variant,,ENST00000508508,;RBM24,intron_variant,,ENST00000504055,;RBM24,intron_variant,,ENST00000510826,;	T	ENSG00000112183	ENST00000379052	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RBM24	HGNC	21539	protein_coding	YES	CCDS47378.1	ENSP00000368341	RBM24_HUMAN	A8KAI7_HUMAN	UPI000006E912	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACAGGTTTG	.	5	ESCA
HIST1H4E	0	.	GRCh37	6	26204991	26204991	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.119G>C	p.Arg40Pro	p.R40P	ENST00000360441	1/1	70	48	22	88	88	0	HIST1H4E,missense_variant,p.Arg40Pro,ENST00000360441,;HIST1H2BF,downstream_gene_variant,,ENST00000359985,;RP1-34B20.4,downstream_gene_variant,,ENST00000405418,;	C	ENSG00000198518	ENST00000360441	Transcript	missense_variant	134	119	40	R/P	cGt/cCt	.	.	.	1	HIST1H4E	HGNC	4790	protein_coding	YES	CCDS4593.1	ENSP00000353624	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Prints_domain:PR00623,Superfamily_domains:SSF47113,SMART_domains:SM00417,SMART_domains:SM00803,Pfam_domain:PF00125,Gene3D:1.10.20.10,hmmpanther:PTHR10484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTCGTCGCG	.	5	ESCA
HIST1H2AH	0	.	GRCh37	6	27115308	27115308	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*14G>A	.	.	ENST00000377459	1/1	61	36	24	83	83	0	HIST1H2AH,3_prime_UTR_variant,,ENST00000377459,;HIST1H2BK,upstream_gene_variant,,ENST00000356950,;HIST1H2BK,upstream_gene_variant,,ENST00000396891,;MIR3143,upstream_gene_variant,,ENST00000584253,;	A	ENSG00000184825	ENST00000377459	Transcript	3_prime_UTR_variant	448	.	.	.	.	.	.	.	1	HIST1H2AH	HGNC	13671	protein_coding	YES	CCDS4622.1	ENSP00000366679	H2A1H_HUMAN	A3KPC7_HUMAN	UPI0000073C8A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTGAAAAC	.	5	ESCA
MDC1	0	.	GRCh37	6	30672262	30672262	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4698G>C	p.Lys1566Asn	p.K1566N	ENST00000376406	10/15	65	40	24	72	72	0	MDC1,missense_variant,p.Lys1566Asn,ENST00000376406,;MDC1,missense_variant,p.Lys1302Asn,ENST00000376405,;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,downstream_gene_variant,,ENST00000492462,;MDC1,upstream_gene_variant,,ENST00000489540,;	G	ENSG00000137337	ENST00000376406	Transcript	missense_variant	5346	4698	1566	K/N	aaG/aaC	.	.	.	-1	MDC1	HGNC	21163	protein_coding	YES	CCDS34384.1	ENSP00000365588	MDC1_HUMAN	A2AB07_HUMAN,A2AB06_HUMAN,A2AB05_HUMAN,A1Z5I9_HUMAN,A1Z5I7_HUMAN	UPI00001AF453	.	deleterious(0.03)	possibly_damaging(0.871)	10/15	.	hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTCTTGAC	.	5	ESCA
TUBB	0	.	GRCh37	6	30690400	30690401	+	Frame_Shift_Del	DEL	TG	TG	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	TG	TG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147_148delGT	p.Tyr50LeufsTer3	p.Y50Lfs*3	ENST00000327892	2/4	97	66	31	91	91	0	TUBB,frameshift_variant,p.Tyr50LeufsTer3,ENST00000435534,;TUBB,frameshift_variant,p.Tyr50LeufsTer3,ENST00000327892,;TUBB,frameshift_variant,p.Tyr32LeufsTer3,ENST00000396389,;TUBB,5_prime_UTR_variant,,ENST00000396384,;TUBB,5_prime_UTR_variant,,ENST00000330914,;MDC1,upstream_gene_variant,,ENST00000376406,;MDC1,upstream_gene_variant,,ENST00000376405,;XXbac-BPG252P9.9,downstream_gene_variant,,ENST00000607476,;	-	ENSG00000196230	ENST00000327892	Transcript	frameshift_variant	450-451	144-145	48-49	SV/SX	tcTGtg/tctg	.	.	.	1	TUBB	HGNC	20778	protein_coding	YES	CCDS4687.1	ENSP00000339001	TBB5_HUMAN	Q9BUU9_HUMAN,Q96B85_HUMAN,Q6P602_HUMAN,Q5SU16_HUMAN,Q5ST81_HUMAN,A4UCU2_HUMAN	UPI0000001229	.	.	.	2/4	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF61,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01163	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATCTCTGTGTAC	.	3	ESCA
CSNK2B-LY6G5B-1181	0	.	GRCh37	6	31638955	31638955	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.580G>A	p.Val194Met	p.V194M	ENST00000375880	7/8	66	45	21	69	69	0	CSNK2B-LY6G5B-1181,missense_variant,p.Val194Met,ENST00000375880,;LY6G5B,synonymous_variant,p.%3D,ENST00000375864,;CSNK2B-LY6G5B-1181,synonymous_variant,p.%3D,ENST00000409691,;LY6G5B,5_prime_UTR_variant,,ENST00000409525,;CSNK2B,downstream_gene_variant,,ENST00000375866,;GPANK1,upstream_gene_variant,,ENST00000375906,;CSNK2B,downstream_gene_variant,,ENST00000375885,;CSNK2B,downstream_gene_variant,,ENST00000375882,;CSNK2B,downstream_gene_variant,,ENST00000375865,;LY6G5B,upstream_gene_variant,,ENST00000471088,;CSNK2B,downstream_gene_variant,,ENST00000481269,;CSNK2B,downstream_gene_variant,,ENST00000475875,;CSNK2B,downstream_gene_variant,,ENST00000465481,;CSNK2B,downstream_gene_variant,,ENST00000468255,;	A	ENSG00000263020	ENST00000375880	Transcript	missense_variant	698	580	194	V/M	Gtg/Atg	.	.	.	1	CSNK2B-LY6G5B-1181	Uniprot_gn	.	protein_coding	YES	.	ENSP00000365040	.	Q5SRQ3_HUMAN	UPI00004702F4	.	tolerated(0.18)	benign(0)	7/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGACGTGCCA	.	5	ESCA
HLA-DOA	0	.	GRCh37	6	32975251	32975251	+	Silent	SNP	G	G	A	rs756316995	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450C>T	p.%3D	p.N150N	ENST00000229829	3/5	52	32	20	86	86	0	HLA-DOA,synonymous_variant,p.%3D,ENST00000450833,;HLA-DOA,synonymous_variant,p.%3D,ENST00000229829,;HLA-DOA,downstream_gene_variant,,ENST00000374813,;HLA-DOA,non_coding_transcript_exon_variant,,ENST00000495532,;HLA-DOA,downstream_gene_variant,,ENST00000467465,;HLA-DOA,upstream_gene_variant,,ENST00000490305,;HLA-DOA,non_coding_transcript_exon_variant,,ENST00000485901,;	A	ENSG00000204252	ENST00000229829	Transcript	synonymous_variant	526	450	150	N	aaC/aaT	rs756316995,COSM172036	.	.	-1	HLA-DOA	HGNC	4936	protein_coding	YES	CCDS4763.1	ENSP00000229829	DOA_HUMAN	.	UPI0000000CD0	.	.	.	3/5	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19944:SF44,hmmpanther:PTHR19944,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGTTGCG	.	5	ESCA
SLC39A7	0	.	GRCh37	6	33169642	33169642	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.532G>A	p.Gly178Ser	p.G178S	ENST00000374677	2/7	33	19	13	23	22	0	SLC39A7,missense_variant,p.Gly178Ser,ENST00000374675,;SLC39A7,missense_variant,p.Gly88Ser,ENST00000444757,;SLC39A7,missense_variant,p.Gly178Ser,ENST00000374677,;RXRB,upstream_gene_variant,,ENST00000544186,;HSD17B8,upstream_gene_variant,,ENST00000374662,;RXRB,upstream_gene_variant,,ENST00000413614,;RXRB,upstream_gene_variant,,ENST00000374680,;RXRB,upstream_gene_variant,,ENST00000374685,;RNY4P10,downstream_gene_variant,,ENST00000365571,;SLC39A7,upstream_gene_variant,,ENST00000463972,;HSD17B8,upstream_gene_variant,,ENST00000469186,;RXRB,upstream_gene_variant,,ENST00000483281,;RXRB,upstream_gene_variant,,ENST00000481441,;	A	ENSG00000112473	ENST00000374677	Transcript	missense_variant	905	532	178	G/S	Ggt/Agt	.	.	.	1	SLC39A7	HGNC	4927	protein_coding	YES	CCDS43453.1	ENSP00000363809	S39A7_HUMAN	Q29984_HUMAN	UPI0000046C3F	.	deleterious(0)	probably_damaging(1)	2/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR16950,hmmpanther:PTHR16950:SF5,Pfam_domain:PF02535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCCGGTGGG	.	5	ESCA
C6orf222	0	.	GRCh37	6	36291122	36291122	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1419C>A	p.Ser473Arg	p.S473R	ENST00000437635	8/12	33	19	14	74	73	1	C6orf222,missense_variant,p.Ser473Arg,ENST00000437635,;	T	ENSG00000189325	ENST00000437635	Transcript	missense_variant	1597	1419	473	S/R	agC/agA	.	.	.	-1	C6orf222	HGNC	33769	protein_coding	YES	CCDS34439.1	ENSP00000418983	CF222_HUMAN	.	UPI000022CB9B	.	deleterious(0.01)	possibly_damaging(0.883)	8/12	.	hmmpanther:PTHR22435,hmmpanther:PTHR22435:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAAGCTGGG	.	5	ESCA
TBC1D22B	0	.	GRCh37	6	37281657	37281657	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1155C>T	p.%3D	p.S385S	ENST00000373491	10/13	61	57	4	45	45	0	TBC1D22B,synonymous_variant,p.%3D,ENST00000373491,;	T	ENSG00000065491	ENST00000373491	Transcript	synonymous_variant	1301	1155	385	S	agC/agT	.	.	.	1	TBC1D22B	HGNC	21602	protein_coding	YES	CCDS4832.1	ENSP00000362590	TB22B_HUMAN	Q6P4C3_HUMAN,A8KA28_HUMAN	UPI00001C121F	.	.	.	10/13	.	Superfamily_domains:SSF47923,Superfamily_domains:SSF47923,SMART_domains:SM00164,Pfam_domain:PF00566,hmmpanther:PTHR22957:SF239,hmmpanther:PTHR22957,PROSITE_profiles:PS50086	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCAGCCGGAT	.	2	ESCA
GLO1	0	.	GRCh37	6	38670905	38670905	+	5'UTR	SNP	C	C	T	rs541708855	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-75G>A	.	.	ENST00000373365	1/6	17	14	3	44	44	0	GLO1,5_prime_UTR_variant,,ENST00000373365,;	T	ENSG00000124767	ENST00000373365	Transcript	5_prime_UTR_variant	13	.	.	.	.	rs541708855	.	.	-1	GLO1	HGNC	4323	protein_coding	YES	CCDS4837.1	ENSP00000362463	LGUL_HUMAN	.	UPI0000169DF9	.	.	.	1/6	.	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTGCCGCCT	by1000G	4	ESCA
KIF6	0	.	GRCh37	6	39507786	39507786	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1638G>T	p.Lys546Asn	p.K546N	ENST00000287152	13/23	64	40	24	58	58	0	KIF6,missense_variant,p.Lys546Asn,ENST00000287152,;KIF6,missense_variant,p.Lys385Asn,ENST00000373213,;KIF6,missense_variant,p.Lys546Asn,ENST00000373215,;KIF6,missense_variant,p.Lys546Asn,ENST00000373216,;KIF6,missense_variant,p.Lys438Asn,ENST00000458470,;KIF6,intron_variant,,ENST00000538893,;	A	ENSG00000164627	ENST00000287152	Transcript	missense_variant	1733	1638	546	K/N	aaG/aaT	.	.	.	-1	KIF6	HGNC	21202	protein_coding	YES	CCDS4844.1	ENSP00000287152	KIF6_HUMAN	.	UPI0000457436	.	tolerated(0.3)	benign(0.001)	13/23	.	hmmpanther:PTHR24115:SF194,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCTTGTG	.	5	ESCA
HSP90AB1	0	.	GRCh37	6	44217808	44217811	+	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	CAGA	CAGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569_572delCAGA	p.Thr190SerfsTer3	p.T190Sfs*3	ENST00000371554	5/12	41	29	12	37	37	0	HSP90AB1,frameshift_variant,p.Thr190SerfsTer3,ENST00000371646,;HSP90AB1,frameshift_variant,p.Thr190SerfsTer3,ENST00000353801,;HSP90AB1,frameshift_variant,p.Thr190SerfsTer3,ENST00000371554,;SLC35B2,downstream_gene_variant,,ENST00000538577,;SLC35B2,downstream_gene_variant,,ENST00000537814,;SLC35B2,downstream_gene_variant,,ENST00000393810,;SLC35B2,downstream_gene_variant,,ENST00000393812,;MIR4647,downstream_gene_variant,,ENST00000583964,;SLC35B2,downstream_gene_variant,,ENST00000495706,;	-	ENSG00000096384	ENST00000371554	Transcript	frameshift_variant	779-782	565-568	189-190	QT/X	CAGAca/ca	.	.	.	1	HSP90AB1	HGNC	5258	protein_coding	YES	CCDS4909.1	ENSP00000360609	HS90B_HUMAN	A8K3W9_HUMAN	UPI00001411EF	.	.	.	5/12	.	HAMAP:MF_00505,hmmpanther:PTHR11528,Gene3D:3.30.565.10,SMART_domains:SM00387,PIRSF_domain:PIRSF002583,Superfamily_domains:SSF55874,Prints_domain:PR00775	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAGATCAGACAGAG	.	3	ESCA
IL17A	0	.	GRCh37	6	52051228	52051228	+	5'UTR	SNP	C	C	T	rs763918114	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2C>T	.	.	ENST00000340057	1/3	71	48	22	53	53	0	IL17A,5_prime_UTR_variant,,ENST00000340057,;	T	ENSG00000112115	ENST00000340057	Transcript	5_prime_UTR_variant	44	.	.	.	.	rs763918114	.	.	1	IL17A	HGNC	5981	protein_coding	YES	CCDS4937.1	ENSP00000344192	IL17_HUMAN	D9MX03_HUMAN	UPI0000047D95	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAACGATGA	.	5	ESCA
KIAA1586	0	.	GRCh37	6	56918934	56918934	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1637G>A	p.Arg546Lys	p.R546K	ENST00000370733	4/4	50	40	10	38	38	0	KIAA1586,missense_variant,p.Arg546Lys,ENST00000370733,;KIAA1586,missense_variant,p.Arg519Lys,ENST00000545356,;KIAA1586,downstream_gene_variant,,ENST00000488682,;	A	ENSG00000168116	ENST00000370733	Transcript	missense_variant	1844	1637	546	R/K	aGa/aAa	.	.	.	1	KIAA1586	HGNC	21360	protein_coding	YES	CCDS34480.1	ENSP00000359768	K1586_HUMAN	.	UPI0000074573	.	tolerated(0.22)	benign(0.002)	4/4	.	hmmpanther:PTHR11389:SF461,hmmpanther:PTHR11389,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAAGATCAA	.	5	ESCA
PHIP	0	.	GRCh37	6	79692782	79692782	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000275034	23/40	44	27	16	30	30	0	PHIP,stop_gained,p.Gln864Ter,ENST00000275034,;PHIP,upstream_gene_variant,,ENST00000479165,;	A	ENSG00000146247	ENST00000275034	Transcript	stop_gained	2758	2590	864	Q/*	Cag/Tag	.	.	.	-1	PHIP	HGNC	15673	protein_coding	YES	CCDS4987.1	ENSP00000275034	PHIP_HUMAN	.	UPI000013DA40	.	.	.	23/40	.	hmmpanther:PTHR16266:SF4,hmmpanther:PTHR16266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTGCAGAT	.	5	ESCA
PHIP	0	.	GRCh37	6	79692783	79692783	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2589G>T	p.%3D	p.L863L	ENST00000275034	23/40	44	28	16	30	30	0	PHIP,synonymous_variant,p.%3D,ENST00000275034,;PHIP,upstream_gene_variant,,ENST00000479165,;	A	ENSG00000146247	ENST00000275034	Transcript	synonymous_variant	2757	2589	863	L	ctG/ctT	.	.	.	-1	PHIP	HGNC	15673	protein_coding	YES	CCDS4987.1	ENSP00000275034	PHIP_HUMAN	.	UPI000013DA40	.	.	.	23/40	.	hmmpanther:PTHR16266:SF4,hmmpanther:PTHR16266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTGCAGATT	.	5	ESCA
DOPEY1	0	.	GRCh37	6	83832625	83832625	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1264G>T	p.Ala422Ser	p.A422S	ENST00000349129	12/39	91	53	38	70	69	1	DOPEY1,missense_variant,p.Ala16Ser,ENST00000604380,;DOPEY1,missense_variant,p.Ala413Ser,ENST00000237163,;DOPEY1,missense_variant,p.Ala413Ser,ENST00000369739,;DOPEY1,missense_variant,p.Ala422Ser,ENST00000349129,;DOPEY1,downstream_gene_variant,,ENST00000536812,;	T	ENSG00000083097	ENST00000349129	Transcript	missense_variant	1524	1264	422	A/S	Gct/Tct	.	.	.	1	DOPEY1	HGNC	21194	protein_coding	YES	CCDS4996.1	ENSP00000195654	DOP1_HUMAN	.	UPI00001C1574	.	deleterious(0.01)	probably_damaging(0.997)	12/39	.	hmmpanther:PTHR14042:SF22,hmmpanther:PTHR14042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTGCTAAC	.	5	ESCA
HBP1	0	.	GRCh37	7	106829747	106829747	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.776C>T	p.Ser259Phe	p.S259F	ENST00000222574	7/11	80	71	8	55	55	0	HBP1,missense_variant,p.Ser259Phe,ENST00000222574,;HBP1,missense_variant,p.Ser259Phe,ENST00000468410,;HBP1,missense_variant,p.Ser251Phe,ENST00000498408,;HBP1,missense_variant,p.Ser259Phe,ENST00000485846,;CTA-363E19.2,downstream_gene_variant,,ENST00000607036,;HBP1,intron_variant,,ENST00000461963,;HBP1,non_coding_transcript_exon_variant,,ENST00000463202,;HBP1,upstream_gene_variant,,ENST00000483809,;	T	ENSG00000105856	ENST00000222574	Transcript	missense_variant	962	776	259	S/F	tCt/tTt	.	.	.	1	HBP1	HGNC	23200	protein_coding	YES	CCDS5741.1	ENSP00000222574	HBP1_HUMAN	H7C4S2_HUMAN,C9JQU7_HUMAN,C9JPK6_HUMAN,C9JAW1_HUMAN,C9J8V6_HUMAN,C9J5U3_HUMAN,B4DJ36_HUMAN	UPI000006DC04	.	deleterious(0)	probably_damaging(0.948)	7/11	.	PROSITE_profiles:PS51148,hmmpanther:PTHR15499:SF2,hmmpanther:PTHR15499,Pfam_domain:PF08517,SMART_domains:SM00536,Superfamily_domains:0041756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTCTGATG	.	4	ESCA
LRRN3	0	.	GRCh37	7	110765260	110765260	+	3'UTR	DEL	T	T	-	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*312delT	.	.	ENST00000451085	4/4	79	56	23	30	30	0	LRRN3,3_prime_UTR_variant,,ENST00000422987,;LRRN3,3_prime_UTR_variant,,ENST00000451085,;IMMP2L,intron_variant,,ENST00000450877,;IMMP2L,intron_variant,,ENST00000437687,;IMMP2L,intron_variant,,ENST00000415362,;IMMP2L,intron_variant,,ENST00000452895,;IMMP2L,intron_variant,,ENST00000405709,;IMMP2L,intron_variant,,ENST00000447215,;IMMP2L,intron_variant,,ENST00000331762,;LRRN3,downstream_gene_variant,,ENST00000421101,;LRRN3,downstream_gene_variant,,ENST00000308478,;IMMP2L,intron_variant,,ENST00000489381,;	-	ENSG00000173114	ENST00000451085	Transcript	3_prime_UTR_variant	3478	.	.	.	.	.	.	.	1	LRRN3	HGNC	17200	protein_coding	YES	CCDS5754.1	ENSP00000397312	LRRN3_HUMAN	A4D0T1_HUMAN,E7EW58_HUMAN	UPI0000037517	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCTGTATTTTTT	.	2	ESCA
CAV1	0	.	GRCh37	7	116199934	116199934	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*593G>T	.	.	ENST00000341049	3/3	56	36	20	40	40	0	CAV1,3_prime_UTR_variant,,ENST00000341049,;CAV1,3_prime_UTR_variant,,ENST00000393467,;CAV1,3_prime_UTR_variant,,ENST00000405348,;CAV1,downstream_gene_variant,,ENST00000393470,;CAV1,downstream_gene_variant,,ENST00000456473,;CAV1,downstream_gene_variant,,ENST00000393468,;AC006159.4,downstream_gene_variant,,ENST00000421965,;CAV1,downstream_gene_variant,,ENST00000451122,;	T	ENSG00000105974	ENST00000341049	Transcript	3_prime_UTR_variant	1408	.	.	.	.	.	.	.	1	CAV1	HGNC	1527	protein_coding	YES	CCDS5767.1	ENSP00000339191	CAV1_HUMAN	Q2TNI1_HUMAN,C9JKI3_HUMAN	UPI00001270ED	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTGAAATT	.	5	ESCA
CFTR	0	.	GRCh37	7	117246747	117246747	+	Missense_Mutation	SNP	C	C	A	rs776948957	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2928C>A	p.Phe976Leu	p.F976L	ENST00000003084	18/27	59	38	21	35	35	0	CFTR,missense_variant,p.Phe946Leu,ENST00000426809,;CFTR,missense_variant,p.Phe915Leu,ENST00000454343,;CFTR,missense_variant,p.Phe976Leu,ENST00000003084,;CFTR,upstream_gene_variant,,ENST00000468795,;AC000111.6,intron_variant,,ENST00000456270,;	A	ENSG00000001626	ENST00000003084	Transcript	missense_variant	3060	2928	976	F/L	ttC/ttA	rs776948957,COSM1447500	.	.	1	CFTR	HGNC	1884	protein_coding	YES	CCDS5773.1	ENSP00000003084	CFTR_HUMAN	Q9UML7_HUMAN,Q9UJ19_HUMAN,Q99989_HUMAN,Q6KEJ7_HUMAN,Q6KEJ4_HUMAN,Q6KEJ1_HUMAN,Q6KEI8_HUMAN,Q6KEI7_HUMAN,Q6KEI2_HUMAN,Q6KEH8_HUMAN,Q6KEH6_HUMAN,Q6KEH3_HUMAN,Q6KEG9_HUMAN,Q6KEG6_HUMAN,Q6KEG3_HUMAN,Q6KEF9_HUMAN,Q6KEF5_HUMAN,Q6KEE7_HUMAN,Q6KEE3_HUMAN,Q6KED8_HUMAN,Q6KED3_HUMAN,Q6KEC8_HUMAN,Q6KEC3_HUMAN,Q6KEB8_HUMAN,Q6KEB2_HUMAN,Q6KEA5_HUMAN,Q6KEA0_HUMAN,Q6KE95_HUMAN,Q5I6N7_HUMAN,Q5I6N6_HUMAN,Q5I6N5_HUMAN,Q5I6N4_HUMAN,Q5I6F9_HUMAN,C9J6L5_HUMAN,A4L9V0_HUMAN	UPI000013C4D4	.	deleterious(0.01)	probably_damaging(0.958)	18/27	.	PROSITE_profiles:PS50929,hmmpanther:PTHR24223:SF19,hmmpanther:PTHR24223,Pfam_domain:PF00664,TIGRFAM_domain:TIGR01271,Gene3D:2hydA01,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCTCCAA	byFrequency	5	ESCA
PAX4	0	.	GRCh37	7	127251730	127251730	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.748C>A	p.Gln250Lys	p.Q250K	ENST00000341640	8/9	29	18	11	20	20	0	PAX4,missense_variant,p.Gln248Lys,ENST00000463946,;PAX4,missense_variant,p.Ala239Glu,ENST00000338516,;PAX4,missense_variant,p.Gln250Lys,ENST00000378740,;PAX4,missense_variant,p.Gln250Lys,ENST00000341640,;PAX4,3_prime_UTR_variant,,ENST00000483494,;PAX4,downstream_gene_variant,,ENST00000477423,;	T	ENSG00000106331	ENST00000341640	Transcript	missense_variant	954	748	250	Q/K	Cag/Aag	.	.	.	-1	PAX4	HGNC	8618	protein_coding	YES	CCDS5797.1	ENSP00000339906	PAX4_HUMAN	.	UPI000013C824	.	tolerated(0.08)	benign(0.269)	8/9	.	hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTGCTAAA	.	5	ESCA
FLNC	0	.	GRCh37	7	128491646	128491646	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5806C>A	p.His1936Asn	p.H1936N	ENST00000325888	35/48	35	22	13	40	40	0	FLNC,missense_variant,p.His1936Asn,ENST00000325888,;FLNC,missense_variant,p.His1903Asn,ENST00000346177,;RP11-309L24.2,intron_variant,,ENST00000469965,;	A	ENSG00000128591	ENST00000325888	Transcript	missense_variant	6067	5806	1936	H/N	Cac/Aac	.	.	.	1	FLNC	HGNC	3756	protein_coding	YES	CCDS43644.1	ENSP00000327145	FLNC_HUMAN	Q59H94_HUMAN,B3KM41_HUMAN	UPI000006DE6D	.	deleterious(0.04)	benign(0.048)	35/48	.	Superfamily_domains:SSF81296,SMART_domains:SM00557,Pfam_domain:PF00630,Gene3D:2.60.40.10,hmmpanther:PTHR11915:SF173,hmmpanther:PTHR11915,PROSITE_profiles:PS50194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F1932F|c.5796C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAAGCACATC	.	5	ESCA
PTN	0	.	GRCh37	7	136936052	136936052	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376C>A	p.Leu126Met	p.L126M	ENST00000348225	4/5	56	38	17	53	53	0	PTN,missense_variant,p.Leu126Met,ENST00000393083,;PTN,missense_variant,p.Leu126Met,ENST00000348225,;	T	ENSG00000105894	ENST00000348225	Transcript	missense_variant	804	376	126	L/M	Ctg/Atg	.	.	.	-1	PTN	HGNC	9630	protein_coding	YES	CCDS5844.1	ENSP00000341170	PTN_HUMAN	.	UPI000013297B	.	deleterious(0.03)	probably_damaging(0.985)	4/5	.	Prints_domain:PR00269,Superfamily_domains:SSF57288,SMART_domains:SM00193,Gene3D:1mkcA00,Pfam_domain:PF01091,hmmpanther:PTHR13850,hmmpanther:PTHR13850:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCAGGGCTC	.	5	ESCA
ZNF775	0	.	GRCh37	7	150093755	150093755	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186C>T	p.%3D	p.A62A	ENST00000329630	3/3	12	9	3	26	26	0	ZNF775,synonymous_variant,p.%3D,ENST00000478789,;ZNF775,synonymous_variant,p.%3D,ENST00000329630,;ZNF775,synonymous_variant,p.%3D,ENST00000490973,;ZNF775,intron_variant,,ENST00000483664,;ZNF775,intron_variant,,ENST00000486297,;ZNF775,upstream_gene_variant,,ENST00000476489,;	T	ENSG00000196456	ENST00000329630	Transcript	synonymous_variant	293	186	62	A	gcC/gcT	.	.	.	1	ZNF775	HGNC	28501	protein_coding	YES	CCDS43678.1	ENSP00000330838	ZN775_HUMAN	C9JVG2_HUMAN,C9JAM7_HUMAN	UPI00001BDA25	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGAGCCCTGGG	.	2	ESCA
ISPD	0	.	GRCh37	7	16255711	16255711	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1231C>A	p.Leu411Ile	p.L411I	ENST00000407010	9/10	44	29	14	47	47	0	ISPD,missense_variant,p.Leu411Ile,ENST00000407010,;ISPD,missense_variant,p.Leu361Ile,ENST00000399310,;ISPD-AS1,intron_variant,,ENST00000579293,;ISPD-AS1,intron_variant,,ENST00000438573,;ISPD-AS1,intron_variant,,ENST00000457112,;ISPD-AS1,intron_variant,,ENST00000582683,;	T	ENSG00000214960	ENST00000407010	Transcript	missense_variant	1231	1231	411	L/I	Ctt/Att	.	.	.	-1	ISPD	HGNC	37276	protein_coding	YES	.	ENSP00000385478	ISPD_HUMAN	.	UPI00015CFC06	.	tolerated(0.26)	benign(0.088)	9/10	.	hmmpanther:PTHR19136,hmmpanther:PTHR19136:SF79	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGCCCAT	.	5	ESCA
IQCE	0	.	GRCh37	7	2611943	2611943	+	Missense_Mutation	SNP	G	G	A	rs774866500	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377G>A	p.Arg126Lys	p.R126K	ENST00000402050	5/22	25	17	8	46	46	0	IQCE,missense_variant,p.Arg61Lys,ENST00000423395,;IQCE,missense_variant,p.Arg75Lys,ENST00000404984,;IQCE,missense_variant,p.Arg126Lys,ENST00000402050,;IQCE,missense_variant,p.Arg126Lys,ENST00000415271,;IQCE,missense_variant,p.Arg110Lys,ENST00000438376,;IQCE,missense_variant,p.Arg61Lys,ENST00000422276,;IQCE,missense_variant,p.Arg61Lys,ENST00000325979,;IQCE,3_prime_UTR_variant,,ENST00000325997,;IQCE,non_coding_transcript_exon_variant,,ENST00000476665,;IQCE,non_coding_transcript_exon_variant,,ENST00000470731,;	A	ENSG00000106012	ENST00000402050	Transcript	missense_variant	561	377	126	R/K	aGg/aAg	rs774866500	.	.	1	IQCE	HGNC	29171	protein_coding	YES	CCDS43542.1	ENSP00000385597	IQCE_HUMAN	C9JX25_HUMAN,C9JP75_HUMAN	UPI000020E9EF	.	tolerated(0.07)	probably_damaging(0.935)	5/22	.	hmmpanther:PTHR22590	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTCAGGCGCT	.	4	ESCA
HOXA2	0	.	GRCh37	7	27140789	27140789	+	Missense_Mutation	SNP	C	C	G	rs776308114	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.687G>C	p.Glu229Asp	p.E229D	ENST00000222718	2/2	37	33	4	22	22	0	HOXA2,missense_variant,p.Glu229Asp,ENST00000222718,;HOTAIRM1,downstream_gene_variant,,ENST00000593300,;HOTAIRM1,downstream_gene_variant,,ENST00000425358,;HOTAIRM1,downstream_gene_variant,,ENST00000429611,;HOTAIRM1,downstream_gene_variant,,ENST00000428939,;HOTAIRM1,downstream_gene_variant,,ENST00000495032,;HOTAIRM1,downstream_gene_variant,,ENST00000434063,;	G	ENSG00000105996	ENST00000222718	Transcript	missense_variant	998	687	229	E/D	gaG/gaC	rs776308114	.	.	-1	HOXA2	HGNC	5103	protein_coding	YES	CCDS5403.1	ENSP00000222718	HXA2_HUMAN	.	UPI0000049C49	.	tolerated(0.26)	benign(0.006)	2/2	.	hmmpanther:PTHR24326:SF42,hmmpanther:PTHR24326,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTTCTCTTC	.	4	ESCA
ERV3-1	0	.	GRCh37	7	64453295	64453295	+	Missense_Mutation	SNP	G	G	A	rs376520157	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110C>T	p.Ser37Leu	p.S37L	ENST00000394323	2/2	40	31	9	34	34	0	ERV3-1,missense_variant,p.Ser37Leu,ENST00000394323,;ZNF117,upstream_gene_variant,,ENST00000282869,;ZNF117,intron_variant,,ENST00000487644,;	A	ENSG00000213462	ENST00000394323	Transcript	missense_variant	611	110	37	S/L	tCg/tTg	rs376520157,COSM3674965	.	.	-1	ERV3-1	HGNC	3454	protein_coding	YES	CCDS47595.1	ENSP00000391594	ENR1_HUMAN	.	UPI000023FEAF	.	tolerated(0.08)	benign(0.247)	2/2	.	hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF43	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCCCGACCAC	byFrequency|byCluster	3	ESCA
ERV3-1	0	.	GRCh37	7	64453327	64453327	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78G>T	p.Glu26Asp	p.E26D	ENST00000394323	2/2	41	32	9	33	33	0	ERV3-1,missense_variant,p.Glu26Asp,ENST00000394323,;ZNF117,upstream_gene_variant,,ENST00000282869,;ZNF117,intron_variant,,ENST00000487644,;	A	ENSG00000213462	ENST00000394323	Transcript	missense_variant	579	78	26	E/D	gaG/gaT	.	.	.	-1	ERV3-1	HGNC	3454	protein_coding	YES	CCDS47595.1	ENSP00000391594	ENR1_HUMAN	.	UPI000023FEAF	.	tolerated_low_confidence(0.76)	benign(0.388)	2/2	.	hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CATCCCTCCCA	.	3	ESCA
ERV3-1	0	.	GRCh37	7	64453347	64453347	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58T>G	p.Leu20Val	p.L20V	ENST00000394323	2/2	35	25	10	27	27	0	ERV3-1,missense_variant,p.Leu20Val,ENST00000394323,;ZNF117,upstream_gene_variant,,ENST00000282869,;ZNF117,intron_variant,,ENST00000487644,;	C	ENSG00000213462	ENST00000394323	Transcript	missense_variant	559	58	20	L/V	Tta/Gta	.	.	.	-1	ERV3-1	HGNC	3454	protein_coding	YES	CCDS47595.1	ENSP00000391594	ENR1_HUMAN	.	UPI000023FEAF	.	tolerated_low_confidence(1)	unknown(0)	2/2	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTTAACATGG	.	3	ESCA
SEMA3A	0	.	GRCh37	7	83591086	83591086	+	Silent	SNP	T	T	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1917A>G	p.%3D	p.L639L	ENST00000265362	17/17	47	29	18	33	33	0	SEMA3A,synonymous_variant,p.%3D,ENST00000265362,;SEMA3A,synonymous_variant,p.%3D,ENST00000436949,;	C	ENSG00000075213	ENST00000265362	Transcript	synonymous_variant	2232	1917	639	L	ctA/ctG	.	.	.	-1	SEMA3A	HGNC	10723	protein_coding	YES	CCDS5599.1	ENSP00000265362	SEM3A_HUMAN	Q86UJ2_HUMAN,Q75MQ2_HUMAN,C9JD25_HUMAN,C9J9C4_HUMAN	UPI0000135A60	.	.	.	17/17	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11036:SF23,hmmpanther:PTHR11036,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTGTAGACT	.	5	ESCA
FZD1	0	.	GRCh37	7	90895863	90895863	+	Missense_Mutation	SNP	C	C	A	rs779835319	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1668C>A	p.Phe556Leu	p.F556L	ENST00000287934	1/1	25	16	9	41	41	0	FZD1,missense_variant,p.Phe556Leu,ENST00000287934,;	A	ENSG00000157240	ENST00000287934	Transcript	missense_variant	2081	1668	556	F/L	ttC/ttA	rs779835319	.	.	1	FZD1	HGNC	4038	protein_coding	YES	CCDS5620.1	ENSP00000287934	FZD1_HUMAN	.	UPI000005104D	.	tolerated(0.22)	benign(0.267)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309:SF81,hmmpanther:PTHR11309,Pfam_domain:PF01534	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTCTACGA	.	5	ESCA
PILRB	0	.	GRCh37	7	99933888	99933888	+	5'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2345C>T	.	.	ENST00000610247	1/18	100	64	36	184	184	0	PILRB,5_prime_UTR_variant,,ENST00000610247,;STAG3L5P-PVRIG2P-PILRB,non_coding_transcript_exon_variant,,ENST00000444874,;STAG3L5P-PVRIG2P-PILRB,non_coding_transcript_exon_variant,,ENST00000483329,;STAG3L5P,non_coding_transcript_exon_variant,,ENST00000414292,;STAG3L5P-PVRIG2P-PILRB,non_coding_transcript_exon_variant,,ENST00000310771,;STAG3L5P-PVRIG2P-PILRB,non_coding_transcript_exon_variant,,ENST00000470714,;STAG3L5P,intron_variant,,ENST00000422479,;STAG3L5P,upstream_gene_variant,,ENST00000493499,;STAG3L5P,upstream_gene_variant,,ENST00000434211,;STAG3L5P,upstream_gene_variant,,ENST00000488972,;STAG3L5P,intron_variant,,ENST00000473757,;PMS2P1,non_coding_transcript_exon_variant,,ENST00000431037,;PMS2P1,upstream_gene_variant,,ENST00000447708,;STAG3L5P,upstream_gene_variant,,ENST00000443759,;	T	ENSG00000121716	ENST00000610247	Transcript	5_prime_UTR_variant	152	.	.	.	.	.	.	.	1	PILRB	HGNC	18297	protein_coding	YES	CCDS43622.1	ENSP00000477415	.	D6W5V2_HUMAN,C9JNA4_HUMAN,C9J8P3_HUMAN	UPI000006EEBC	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCCACCTG	.	5	ESCA
RGS22	0	.	GRCh37	8	101074951	101074951	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1382T>C	p.Leu461Pro	p.L461P	ENST00000360863	9/28	48	41	7	10	10	0	RGS22,missense_variant,p.Leu280Pro,ENST00000523287,;RGS22,missense_variant,p.Leu449Pro,ENST00000523437,;RGS22,missense_variant,p.Leu461Pro,ENST00000360863,;RGS22,intron_variant,,ENST00000517828,;RGS22,downstream_gene_variant,,ENST00000520117,;RGS22,missense_variant,p.Leu461Pro,ENST00000519725,;RGS22,non_coding_transcript_exon_variant,,ENST00000520923,;	G	ENSG00000132554	ENST00000360863	Transcript	missense_variant	1577	1382	461	L/P	cTa/cCa	.	.	.	-1	RGS22	HGNC	24499	protein_coding	YES	CCDS43758.1	ENSP00000354109	RGS22_HUMAN	E5RHE4_HUMAN,E5RFV6_HUMAN	UPI0000E5AF25	.	deleterious(0)	probably_damaging(0.998)	9/28	.	hmmpanther:PTHR10845:SF132,hmmpanther:PTHR10845,Superfamily_domains:SSF48097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACTAGATAG	.	4	ESCA
FZD6	0	.	GRCh37	8	104341947	104341947	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1606A>G	p.Lys536Glu	p.K536E	ENST00000358755	6/7	118	95	22	28	28	0	FZD6,missense_variant,p.Lys536Glu,ENST00000358755,;FZD6,missense_variant,p.Lys231Glu,ENST00000540287,;FZD6,missense_variant,p.Lys536Glu,ENST00000522566,;FZD6,missense_variant,p.Lys504Glu,ENST00000523739,;FZD6,3_prime_UTR_variant,,ENST00000519011,;FZD6,3_prime_UTR_variant,,ENST00000522484,;FZD6,3_prime_UTR_variant,,ENST00000521195,;FZD6,3_prime_UTR_variant,,ENST00000523933,;	G	ENSG00000164930	ENST00000358755	Transcript	missense_variant	1923	1606	536	K/E	Aaa/Gaa	.	.	.	1	FZD6	HGNC	4044	protein_coding	YES	CCDS6298.1	ENSP00000351605	FZD6_HUMAN	B7ZB79_HUMAN	UPI0000061EB0	.	deleterious_low_confidence(0.02)	benign(0.41)	6/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTAAAGTT	.	5	ESCA
CSMD3	0	.	GRCh37	8	113516192	113516192	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4910C>G	p.Pro1637Arg	p.P1637R	ENST00000297405	30/71	70	61	9	16	16	0	CSMD3,missense_variant,p.Pro1637Arg,ENST00000352409,;CSMD3,missense_variant,p.Pro1533Arg,ENST00000455883,;CSMD3,missense_variant,p.Pro1637Arg,ENST00000297405,;CSMD3,missense_variant,p.Pro977Arg,ENST00000339701,;CSMD3,missense_variant,p.Pro1597Arg,ENST00000343508,;	C	ENSG00000164796	ENST00000297405	Transcript	missense_variant	5155	4910	1637	P/R	cCa/cGa	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	deleterious(0.03)	possibly_damaging(0.582)	30/71	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTTTGGTTCT	.	4	ESCA
CSMD3	0	.	GRCh37	8	113529308	113529308	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4711G>A	p.Val1571Ile	p.V1571I	ENST00000297405	28/71	155	123	31	85	85	0	CSMD3,missense_variant,p.Val1571Ile,ENST00000352409,;CSMD3,missense_variant,p.Val1467Ile,ENST00000455883,;CSMD3,missense_variant,p.Val1571Ile,ENST00000297405,;CSMD3,missense_variant,p.Val911Ile,ENST00000339701,;CSMD3,missense_variant,p.Val1531Ile,ENST00000343508,;	T	ENSG00000164796	ENST00000297405	Transcript	missense_variant	4956	4711	1571	V/I	Gta/Ata	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(1)	probably_damaging(0.936)	28/71	.	PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTACCTGAA	.	4	ESCA
UTP23	0	.	GRCh37	8	117778864	117778864	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22C>T	p.His8Tyr	p.H8Y	ENST00000309822	1/3	52	45	7	46	46	0	UTP23,missense_variant,p.His8Tyr,ENST00000517814,;UTP23,missense_variant,p.His8Tyr,ENST00000309822,;UTP23,missense_variant,p.His8Tyr,ENST00000357148,;UTP23,missense_variant,p.His8Tyr,ENST00000517820,;EIF3H,intron_variant,,ENST00000520813,;EIF3H,upstream_gene_variant,,ENST00000276682,;UTP23,upstream_gene_variant,,ENST00000520733,;UTP23,missense_variant,p.His8Tyr,ENST00000521703,;UTP23,missense_variant,p.His8Tyr,ENST00000521071,;UTP23,non_coding_transcript_exon_variant,,ENST00000519443,;UTP23,upstream_gene_variant,,ENST00000521974,;UTP23,upstream_gene_variant,,ENST00000524128,;	T	ENSG00000147679	ENST00000309822	Transcript	missense_variant	123	22	8	H/Y	Cat/Tat	.	.	.	1	UTP23	HGNC	28224	protein_coding	YES	CCDS6320.1	ENSP00000308332	UTP23_HUMAN	.	UPI000013EF3A	.	deleterious(0.05)	possibly_damaging(0.837)	1/3	.	hmmpanther:PTHR12416,hmmpanther:PTHR12416:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAACATGCC	.	4	ESCA
TBC1D31	0	.	GRCh37	8	124140537	124140537	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1901G>A	p.Arg634Gln	p.R634Q	ENST00000287380	14/22	75	53	22	17	17	0	TBC1D31,missense_variant,p.Arg634Gln,ENST00000309336,;TBC1D31,missense_variant,p.Arg529Gln,ENST00000522420,;TBC1D31,missense_variant,p.Arg529Gln,ENST00000378080,;TBC1D31,missense_variant,p.Arg511Gln,ENST00000521676,;TBC1D31,missense_variant,p.Arg634Gln,ENST00000327098,;TBC1D31,missense_variant,p.Arg634Gln,ENST00000287380,;TBC1D31,intron_variant,,ENST00000518805,;TBC1D31,3_prime_UTR_variant,,ENST00000524307,;TBC1D31,3_prime_UTR_variant,,ENST00000518577,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000518866,;HMGB1P19,downstream_gene_variant,,ENST00000517578,;	A	ENSG00000156787	ENST00000287380	Transcript	missense_variant	1991	1901	634	R/Q	cGg/cAg	.	.	.	1	TBC1D31	HGNC	30888	protein_coding	YES	CCDS6338.1	ENSP00000287380	TBC31_HUMAN	E5RG45_HUMAN	UPI000013DEAB	.	tolerated(0.18)	benign(0.007)	14/22	.	hmmpanther:PTHR19853,hmmpanther:PTHR19853:SF1,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCGGAATA	.	5	ESCA
FAM83A	0	.	GRCh37	8	124221765	124221765	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1837C>T	.	.	ENST00000518448	5/5	132	114	17	63	63	0	FAM83A,missense_variant,p.Thr292Ile,ENST00000522648,;FAM83A,missense_variant,p.Thr292Ile,ENST00000546351,;FAM83A,3_prime_UTR_variant,,ENST00000276699,;FAM83A,3_prime_UTR_variant,,ENST00000518448,;FAM83A,downstream_gene_variant,,ENST00000318462,;FAM83A,downstream_gene_variant,,ENST00000536633,;	T	ENSG00000147689	ENST00000518448	Transcript	3_prime_UTR_variant	5156	.	.	.	.	.	.	.	1	FAM83A	HGNC	28210	protein_coding	YES	CCDS6340.1	ENSP00000428876	FA83A_HUMAN	.	UPI000019275C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACAGCTGACG	.	4	ESCA
GPAA1	0	.	GRCh37	8	145138344	145138344	+	Missense_Mutation	SNP	G	G	A	rs782229443	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.307G>A	p.Val103Ile	p.V103I	ENST00000355091	3/12	116	98	17	100	100	0	GPAA1,missense_variant,p.Val43Ile,ENST00000361036,;GPAA1,missense_variant,p.Val103Ile,ENST00000524418,;GPAA1,missense_variant,p.Val54Ile,ENST00000530258,;GPAA1,missense_variant,p.Val103Ile,ENST00000355091,;GPAA1,intron_variant,,ENST00000525087,;EXOSC4,downstream_gene_variant,,ENST00000525936,;EXOSC4,downstream_gene_variant,,ENST00000316052,;EXOSC4,downstream_gene_variant,,ENST00000527954,;CTD-3065J16.9,upstream_gene_variant,,ENST00000524499,;GPAA1,non_coding_transcript_exon_variant,,ENST00000527144,;GPAA1,non_coding_transcript_exon_variant,,ENST00000526341,;GPAA1,upstream_gene_variant,,ENST00000526233,;GPAA1,missense_variant,p.Val103Ile,ENST00000528073,;GPAA1,non_coding_transcript_exon_variant,,ENST00000532758,;GPAA1,non_coding_transcript_exon_variant,,ENST00000525308,;GPAA1,intron_variant,,ENST00000530633,;GPAA1,intron_variant,,ENST00000529503,;GPAA1,upstream_gene_variant,,ENST00000530796,;GPAA1,upstream_gene_variant,,ENST00000531593,;GPAA1,upstream_gene_variant,,ENST00000527653,;GPAA1,upstream_gene_variant,,ENST00000534072,;GPAA1,upstream_gene_variant,,ENST00000529638,;	A	ENSG00000197858	ENST00000355091	Transcript	missense_variant	428	307	103	V/I	Gtc/Atc	rs782229443	.	.	1	GPAA1	HGNC	4446	protein_coding	YES	CCDS43776.1	ENSP00000347206	GPAA1_HUMAN	E9PLG8_HUMAN	UPI0000073ECC	.	deleterious(0.03)	possibly_damaging(0.829)	3/12	.	hmmpanther:PTHR13304:SF0,hmmpanther:PTHR13304,PIRSF_domain:PIRSF036762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGAGGTCTAC	.	4	ESCA
ZNF251	0	.	GRCh37	8	145947949	145947949	+	Missense_Mutation	SNP	G	G	C	rs552920738	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096C>G	p.Gln366Glu	p.Q366E	ENST00000292562	5/5	91	79	12	27	27	0	ZNF251,missense_variant,p.Gln366Glu,ENST00000292562,;ZNF251,intron_variant,,ENST00000524394,;	C	ENSG00000198169	ENST00000292562	Transcript	missense_variant	1372	1096	366	Q/E	Cag/Gag	rs552920738	.	.	-1	ZNF251	HGNC	13045	protein_coding	YES	CCDS47944.1	ENSP00000292562	ZN251_HUMAN	.	UPI0000160D9A	.	deleterious(0.01)	benign(0.149)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF202,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGAATAA	by1000G	5	ESCA
MTMR7	0	.	GRCh37	8	17159602	17159602	+	Intron	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1620+61C>T	.	.	ENST00000180173	.	25	9	16	20	20	0	MTMR7,3_prime_UTR_variant,,ENST00000521857,;MTMR7,intron_variant,,ENST00000180173,;MTMR7,intron_variant,,ENST00000398099,;VPS37A,downstream_gene_variant,,ENST00000324849,;VPS37A,intron_variant,,ENST00000519515,;MTMR7,downstream_gene_variant,,ENST00000519763,;VPS37A,downstream_gene_variant,,ENST00000521162,;VPS37A,downstream_gene_variant,,ENST00000520997,;VPS37A,downstream_gene_variant,,ENST00000425020,;MTMR7,downstream_gene_variant,,ENST00000519590,;	A	ENSG00000003987	ENST00000180173	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MTMR7	HGNC	7454	protein_coding	YES	CCDS34851.1	ENSP00000180173	MTMR7_HUMAN	I0EZ69_HUMAN,B4E1E5_HUMAN,B4E1B6_HUMAN	UPI00004DFD27	.	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATGAAGCC	.	5	ESCA
PXDNL	0	.	GRCh37	8	52366270	52366270	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058C>A	p.Ala353Asp	p.A353D	ENST00000356297	10/23	57	40	17	44	44	0	PXDNL,missense_variant,p.Ala353Asp,ENST00000543296,;PXDNL,missense_variant,p.Ala353Asp,ENST00000356297,;	T	ENSG00000147485	ENST00000356297	Transcript	missense_variant	1159	1058	353	A/D	gCc/gAc	.	.	.	-1	PXDNL	HGNC	26359	protein_coding	YES	CCDS47855.1	ENSP00000348645	PXDNL_HUMAN	.	UPI0001AE6ED6	.	deleterious(0)	probably_damaging(0.987)	10/23	.	PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGGCCATA	.	5	ESCA
ASPH	0	.	GRCh37	8	62577903	62577903	+	Intron	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.323-11684G>A	.	.	ENST00000379454	.	67	48	19	30	30	0	ASPH,missense_variant,p.Met180Ile,ENST00000522603,;ASPH,missense_variant,p.Met195Ile,ENST00000389204,;ASPH,intron_variant,,ENST00000522349,;ASPH,intron_variant,,ENST00000517856,;ASPH,intron_variant,,ENST00000379454,;ASPH,intron_variant,,ENST00000517903,;ASPH,intron_variant,,ENST00000519234,;ASPH,intron_variant,,ENST00000541428,;ASPH,intron_variant,,ENST00000518068,;ASPH,intron_variant,,ENST00000518306,;ASPH,intron_variant,,ENST00000356457,;ASPH,intron_variant,,ENST00000522835,;ASPH,intron_variant,,ENST00000445642,;ASPH,intron_variant,,ENST00000517847,;ASPH,intron_variant,,ENST00000523927,;ASPH,intron_variant,,ENST00000517928,;	T	ENSG00000198363	ENST00000379454	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ASPH	HGNC	757	protein_coding	YES	CCDS34898.1	ENSP00000368767	ASPH_HUMAN	.	UPI0000161BFE	.	.	.	.	3/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGCCATTTT	.	5	ESCA
JPH1	0	.	GRCh37	8	75171619	75171619	+	Splice_Site	SNP	C	C	T	rs769570203	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1258+1G>A	.	p.X420_splice	ENST00000342232	.	15	8	7	36	36	0	JPH1,splice_donor_variant,,ENST00000342232,;JPH1,splice_donor_variant,,ENST00000519947,;	T	ENSG00000104369	ENST00000342232	Transcript	splice_donor_variant	.	.	.	.	.	rs769570203	.	.	-1	JPH1	HGNC	14201	protein_coding	YES	CCDS6217.1	ENSP00000344488	JPH1_HUMAN	Q7Z682_HUMAN,Q6AHW6_HUMAN,Q4KMX3_HUMAN	UPI000012DAC0	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TTTTACCTGGT	.	2	ESCA
LRRCC1	0	.	GRCh37	8	86019616	86019616	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86T>G	p.Met29Arg	p.M29R	ENST00000360375	1/19	44	32	12	81	81	0	LRRCC1,missense_variant,p.Met29Arg,ENST00000360375,;LRRCC1,upstream_gene_variant,,ENST00000414626,;LRRCC1,missense_variant,p.Met29Arg,ENST00000522770,;LRRCC1,missense_variant,p.Met29Arg,ENST00000517875,;LRRCC1,missense_variant,p.Met29Arg,ENST00000523669,;LRRCC1,missense_variant,p.Met29Arg,ENST00000522567,;	G	ENSG00000133739	ENST00000360375	Transcript	missense_variant	235	86	29	M/R	aTg/aGg	.	.	.	1	LRRCC1	HGNC	29373	protein_coding	YES	CCDS43750.1	ENSP00000353538	LRCC1_HUMAN	.	UPI000021002F	.	deleterious(0)	benign(0.418)	1/19	.	hmmpanther:PTHR10588:SF31,hmmpanther:PTHR10588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCATGGACA	.	5	ESCA
E2F5	0	.	GRCh37	8	86119673	86119673	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564G>A	p.%3D	p.L188L	ENST00000416274	5/8	33	25	8	41	41	0	E2F5,synonymous_variant,p.%3D,ENST00000517476,;E2F5,synonymous_variant,p.%3D,ENST00000256117,;E2F5,synonymous_variant,p.%3D,ENST00000416274,;E2F5,synonymous_variant,p.%3D,ENST00000518234,;E2F5,synonymous_variant,p.%3D,ENST00000418930,;E2F5,synonymous_variant,p.%3D,ENST00000521429,;E2F5,upstream_gene_variant,,ENST00000520225,;E2F5,non_coding_transcript_exon_variant,,ENST00000519128,;E2F5,downstream_gene_variant,,ENST00000521234,;	A	ENSG00000133740	ENST00000416274	Transcript	synonymous_variant	598	564	188	L	ttG/ttA	.	.	.	1	E2F5	HGNC	3119	protein_coding	YES	CCDS47885.1	ENSP00000398124	E2F5_HUMAN	.	UPI000002E057	.	.	.	5/8	.	hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF35,Superfamily_domains:SSF144074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTGGCCAT	.	5	ESCA
CCDC180	0	.	GRCh37	9	100092636	100092636	+	Frame_Shift_Del	DEL	A	A	-	rs749569572	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1998delA	p.Lys666AsnfsTer2	p.K666Nfs*2	ENST00000375202	32/51	59	41	18	37	37	0	CCDC180,frameshift_variant,p.Lys805AsnfsTer2,ENST00000357054,;CCDC180,frameshift_variant,p.Lys666AsnfsTer2,ENST00000375202,;CCDC180,frameshift_variant,p.Lys666AsnfsTer2,ENST00000529487,;CCDC180,frameshift_variant,p.Lys663AsnfsTer2,ENST00000411667,;CCDC180,3_prime_UTR_variant,,ENST00000395220,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000532526,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000375206,;CCDC180,non_coding_transcript_exon_variant,,ENST00000460482,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000534123,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000529787,;CCDC180,upstream_gene_variant,,ENST00000530011,;CCDC180,upstream_gene_variant,,ENST00000528678,;CCDC180,non_coding_transcript_exon_variant,,ENST00000494917,;	-	ENSG00000197816	ENST00000375202	Transcript	frameshift_variant	3345	1993	665	K/X	Aaa/aa	rs749569572	.	.	1	CCDC180	HGNC	29303	protein_coding	YES	CCDS35077.2	ENSP00000364348	CC180_HUMAN	B7ZMG3_HUMAN	UPI00016277C6	.	.	.	32/51	.	hmmpanther:PTHR21444:SF14,hmmpanther:PTHR21444	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAGTGAAAAAA	byFrequency	3	ESCA
ANKS6	0	.	GRCh37	9	101533323	101533323	+	Silent	SNP	G	G	A	rs377000748	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1827C>T	p.%3D	p.P609P	ENST00000353234	10/15	22	13	9	42	42	0	ANKS6,synonymous_variant,p.%3D,ENST00000444472,;ANKS6,synonymous_variant,p.%3D,ENST00000540940,;ANKS6,synonymous_variant,p.%3D,ENST00000375019,;ANKS6,synonymous_variant,p.%3D,ENST00000375018,;ANKS6,synonymous_variant,p.%3D,ENST00000353234,;	A	ENSG00000165138	ENST00000353234	Transcript	synonymous_variant	1875	1827	609	P	ccC/ccT	rs377000748	.	.	-1	ANKS6	HGNC	26724	protein_coding	YES	CCDS43856.1	ENSP00000297837	ANKS6_HUMAN	F5H7X9_HUMAN	UPI0000530317	.	.	.	10/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10627,hmmpanther:PTHR10627:SF2	.	.	.	.	.	.	.	A:0.0003	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTGACGGGTGT	byFrequency|byCluster	4	ESCA
TGFBR1	0	.	GRCh37	9	101907161	101907161	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1121G>A	p.Gly374Glu	p.G374E	ENST00000374994	6/9	59	39	20	47	47	0	TGFBR1,missense_variant,p.Gly305Glu,ENST00000550253,;TGFBR1,missense_variant,p.Gly378Glu,ENST00000552516,;TGFBR1,missense_variant,p.Gly297Glu,ENST00000374990,;TGFBR1,missense_variant,p.Gly374Glu,ENST00000374994,;RNA5SP290,downstream_gene_variant,,ENST00000517133,;TGFBR1,missense_variant,p.Gly378Glu,ENST00000549766,;	A	ENSG00000106799	ENST00000374994	Transcript	missense_variant	1238	1121	374	G/E	gGa/gAa	CM064322	.	.	1	TGFBR1	HGNC	11772	protein_coding	YES	CCDS6738.1	ENSP00000364133	TGFR1_HUMAN	Q5T7S2_HUMAN,F8VVC4_HUMAN,B4DY26_HUMAN	UPI000011D62A	.	deleterious(0)	probably_damaging(1)	6/9	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255:SF61,hmmpanther:PTHR23255,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGGGAACAA	.	5	ESCA
ST6GALNAC6	0	.	GRCh37	9	130656797	130656797	+	Silent	SNP	G	G	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291C>A	p.%3D	p.G97G	ENST00000373146	4/7	49	32	17	88	88	0	ST6GALNAC6,missense_variant,p.Ala33Glu,ENST00000542456,;ST6GALNAC6,synonymous_variant,p.%3D,ENST00000373141,;ST6GALNAC6,synonymous_variant,p.%3D,ENST00000291839,;ST6GALNAC6,synonymous_variant,p.%3D,ENST00000447681,;ST6GALNAC6,synonymous_variant,p.%3D,ENST00000373146,;ST6GALNAC6,synonymous_variant,p.%3D,ENST00000373144,;ST6GALNAC6,synonymous_variant,p.%3D,ENST00000373142,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000494541,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000485320,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000463086,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000480417,;ST6GALNAC6,downstream_gene_variant,,ENST00000494611,;ST6GALNAC6,downstream_gene_variant,,ENST00000478319,;ST6GALNAC6,downstream_gene_variant,,ENST00000481355,;	T	ENSG00000160408	ENST00000373146	Transcript	synonymous_variant	471	291	97	G	ggC/ggA	.	.	.	-1	ST6GALNAC6	HGNC	23364	protein_coding	YES	CCDS6882.1	ENSP00000362239	SIA7F_HUMAN	.	UPI0000073734	.	.	.	4/7	.	Pfam_domain:PF00777,hmmpanther:PTHR13713:SF45,hmmpanther:PTHR13713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTGCCGAG	.	5	ESCA
TPD52L3	0	.	GRCh37	9	6330472	6330472	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1454C>A	.	.	ENST00000344545	1/1	55	33	22	41	41	0	TPD52L3,3_prime_UTR_variant,,ENST00000344545,;TPD52L3,3_prime_UTR_variant,,ENST00000381428,;TPD52L3,intron_variant,,ENST00000314556,;	A	ENSG00000170777	ENST00000344545	Transcript	3_prime_UTR_variant	2124	.	.	.	.	.	.	.	1	TPD52L3	HGNC	23382	protein_coding	YES	CCDS34986.1	ENSP00000341677	TPD55_HUMAN	.	UPI0000367601	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCCTAAGA	.	5	ESCA
KLF9	0	.	GRCh37	9	73001740	73001740	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*952G>T	.	.	ENST00000377126	2/2	20	13	7	9	9	0	KLF9,3_prime_UTR_variant,,ENST00000377126,;	A	ENSG00000119138	ENST00000377126	Transcript	3_prime_UTR_variant	2948	.	.	.	.	.	.	.	-1	KLF9	HGNC	1123	protein_coding	YES	CCDS6633.1	ENSP00000366330	KLF9_HUMAN	.	UPI0000126B0A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCATCTGTTG	.	3	ESCA
GDA	0	.	GRCh37	9	74825650	74825650	+	Silent	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432A>G	p.%3D	p.T144T	ENST00000238018	4/15	38	26	11	21	21	0	GDA,synonymous_variant,p.%3D,ENST00000358399,;GDA,synonymous_variant,p.%3D,ENST00000545168,;GDA,synonymous_variant,p.%3D,ENST00000376986,;GDA,synonymous_variant,p.%3D,ENST00000376989,;GDA,synonymous_variant,p.%3D,ENST00000238018,;GDA,5_prime_UTR_variant,,ENST00000414671,;GDA,non_coding_transcript_exon_variant,,ENST00000477618,;GDA,synonymous_variant,p.%3D,ENST00000475764,;	G	ENSG00000119125	ENST00000238018	Transcript	synonymous_variant	615	432	144	T	acA/acG	.	.	.	1	GDA	HGNC	4212	protein_coding	YES	CCDS56576.1	ENSP00000238018	GUAD_HUMAN	Q5SZC3_HUMAN,B4DIP8_HUMAN,B3KUM3_HUMAN	UPI000015828B	.	.	.	4/15	.	hmmpanther:PTHR11271:SF6,hmmpanther:PTHR11271,Pfam_domain:PF01979,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR02967,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAACAATTCA	.	5	ESCA
C9orf3	0	.	GRCh37	9	97847577	97847577	+	Intron	SNP	C	C	G	rs749058037	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5-1387C>G	.	.	ENST00000375315	.	26	19	7	55	55	0	C9orf3,intron_variant,,ENST00000297979,;C9orf3,intron_variant,,ENST00000428313,;C9orf3,intron_variant,,ENST00000375315,;C9orf3,downstream_gene_variant,,ENST00000424143,;C9orf3,downstream_gene_variant,,ENST00000445181,;C9orf3,downstream_gene_variant,,ENST00000433691,;C9orf3,downstream_gene_variant,,ENST00000425634,;MIR23B,non_coding_transcript_exon_variant,,ENST00000384832,;MIR3074,downstream_gene_variant,,ENST00000384885,;MIR27B,upstream_gene_variant,,ENST00000385129,;C9orf3,intron_variant,,ENST00000471978,;C9orf3,intron_variant,,ENST00000463372,;C9orf3,intron_variant,,ENST00000468164,;C9orf3,downstream_gene_variant,,ENST00000489562,;C9orf3,downstream_gene_variant,,ENST00000479161,;C9orf3,downstream_gene_variant,,ENST00000462125,;C9orf3,intron_variant,,ENST00000478473,;	G	ENSG00000148120	ENST00000375315	Transcript	intron_variant	.	.	.	.	.	rs749058037	.	.	1	C9orf3	HGNC	1361	protein_coding	YES	CCDS55328.1	ENSP00000364464	AMPO_HUMAN	B4DKZ8_HUMAN	UPI0000211ACC	.	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCACGACCT	byFrequency	5	ESCA
GUCY2F	0	.	GRCh37	X	108641818	108641818	+	Silent	SNP	G	G	A	rs772215949	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2235C>T	p.%3D	p.V745V	ENST00000218006	11/20	23	2	21	14	14	0	GUCY2F,synonymous_variant,p.%3D,ENST00000218006,;	A	ENSG00000101890	ENST00000218006	Transcript	synonymous_variant	2527	2235	745	V	gtC/gtT	rs772215949	.	.	-1	GUCY2F	HGNC	4691	protein_coding	YES	CCDS14545.1	ENSP00000218006	GUC2F_HUMAN	.	UPI000013C740	.	.	.	11/20	.	PROSITE_profiles:PS50011,hmmpanther:PTHR11920:SF278,hmmpanther:PTHR11920,Pfam_domain:PF07714,Gene3D:1.10.510.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCGGACCAT	byFrequency	5	ESCA
APLN	0	.	GRCh37	X	128781629	128781629	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*271G>T	.	.	ENST00000307484	3/3	72	13	59	82	82	0	APLN,3_prime_UTR_variant,,ENST00000307484,;APLN,3_prime_UTR_variant,,ENST00000429967,;APLN,downstream_gene_variant,,ENST00000427399,;	A	ENSG00000171388	ENST00000307484	Transcript	3_prime_UTR_variant	831	.	.	.	.	.	.	.	-1	APLN	HGNC	16665	protein_coding	YES	CCDS48165.1	ENSP00000305464	APEL_HUMAN	.	UPI0000125C4A	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGCTTTCT	.	5	ESCA
RAP2C	0	.	GRCh37	X	131338074	131338074	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1576G>T	.	.	ENST00000342983	4/4	32	26	6	14	14	0	RAP2C,3_prime_UTR_variant,,ENST00000342983,;RAP2C,downstream_gene_variant,,ENST00000370874,;RAP2C,downstream_gene_variant,,ENST00000460462,;	A	ENSG00000123728	ENST00000342983	Transcript	3_prime_UTR_variant	2875	.	.	.	.	.	.	.	-1	RAP2C	HGNC	21165	protein_coding	YES	CCDS14632.1	ENSP00000340274	RAP2C_HUMAN	.	UPI00000236AB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	ACCATCACTGC	.	3	ESCA
RP11-1007I13.4	0	.	GRCh37	X	151284037	151284037	+	RNA	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.300G>T	.	.	ENST00000509345	4/4	67	18	49	82	82	0	RP11-1007I13.4,non_coding_transcript_exon_variant,,ENST00000583636,;RP11-1007I13.4,non_coding_transcript_exon_variant,,ENST00000509345,;MAGEA5,non_coding_transcript_exon_variant,,ENST00000427663,;MAGEA5,upstream_gene_variant,,ENST00000446757,;	A	ENSG00000266560	ENST00000509345	Transcript	non_coding_transcript_exon_variant	300	.	.	.	.	.	.	.	-1	RP11-1007I13.4	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGGCAGGAG	.	5	ESCA
BMX	0	.	GRCh37	X	15549481	15549481	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.970T>A	p.Ser324Thr	p.S324T	ENST00000357607	11/19	43	19	24	36	36	0	BMX,missense_variant,p.Ser324Thr,ENST00000348343,;BMX,missense_variant,p.Ser324Thr,ENST00000357607,;BMX,missense_variant,p.Ser324Thr,ENST00000342014,;BMX,non_coding_transcript_exon_variant,,ENST00000489983,;	A	ENSG00000102010	ENST00000357607	Transcript	missense_variant	1158	970	324	S/T	Tcg/Acg	.	.	.	1	BMX	HGNC	1079	protein_coding	YES	CCDS14168.1	ENSP00000350224	BMX_HUMAN	.	UPI0000000DFF	.	deleterious(0)	probably_damaging(0.959)	11/19	.	PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF91,Gene3D:3.30.505.10,Pfam_domain:PF00017,SMART_domains:SM00252,Superfamily_domains:SSF55550,Prints_domain:PR00401	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATTCGAGC	.	5	ESCA
HDX	0	.	GRCh37	X	83724053	83724053	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.678G>T	p.%3D	p.G226G	ENST00000297977	3/10	25	5	20	17	17	0	HDX,synonymous_variant,p.%3D,ENST00000506585,;HDX,synonymous_variant,p.%3D,ENST00000373177,;HDX,synonymous_variant,p.%3D,ENST00000449553,;HDX,synonymous_variant,p.%3D,ENST00000297977,;HDX,non_coding_transcript_exon_variant,,ENST00000472135,;	A	ENSG00000165259	ENST00000297977	Transcript	synonymous_variant	790	678	226	G	ggG/ggT	.	.	.	-1	HDX	HGNC	26411	protein_coding	YES	CCDS35342.1	ENSP00000297977	HDX_HUMAN	E2QRN0_HUMAN	UPI00001A9DA4	.	.	.	3/10	.	hmmpanther:PTHR11636:SF80,hmmpanther:PTHR11636	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCCCAAC	.	5	ESCA
POF1B	0	.	GRCh37	X	84532917	84532917	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1510T>C	.	.	ENST00000262753	17/17	84	18	66	48	48	0	POF1B,3_prime_UTR_variant,,ENST00000262753,;POF1B,downstream_gene_variant,,ENST00000373145,;ZNF711,downstream_gene_variant,,ENST00000373165,;ZNF711,downstream_gene_variant,,ENST00000360700,;ZNF711,downstream_gene_variant,,ENST00000395402,;	G	ENSG00000124429	ENST00000262753	Transcript	3_prime_UTR_variant	3426	.	.	.	.	.	.	.	-1	POF1B	HGNC	13711	protein_coding	YES	CCDS14452.1	ENSP00000262753	POF1B_HUMAN	.	UPI0000212116	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATATATGAAT	.	5	ESCA
PCDH11X	0	.	GRCh37	X	91873637	91873637	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3742C>A	p.Pro1248Thr	p.P1248T	ENST00000373094	7/7	23	8	15	40	40	0	PCDH11X,missense_variant,p.Pro1240Thr,ENST00000406881,;PCDH11X,missense_variant,p.Pro1238Thr,ENST00000373097,;PCDH11X,missense_variant,p.Pro1248Thr,ENST00000373094,;PCDH11X,missense_variant,p.Pro1211Thr,ENST00000373088,;PCDH11X,missense_variant,p.Pro1230Thr,ENST00000361655,;PCDH11X,missense_variant,p.Pro1211Thr,ENST00000298274,;PCDH11X,3_prime_UTR_variant,,ENST00000504220,;	A	ENSG00000102290	ENST00000373094	Transcript	missense_variant	4587	3742	1248	P/T	Cct/Act	.	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	tolerated_low_confidence(0.08)	benign(0.018)	7/7	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCCTTTA	.	5	ESCA
SHROOM2	0	.	GRCh37	X	9905301	9905301	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A6FG-01A-11D-A33E-09	TCGA-JY-A6FG-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3715C>T	p.Pro1239Ser	p.P1239S	ENST00000380913	7/10	29	10	18	59	59	0	SHROOM2,missense_variant,p.Pro1239Ser,ENST00000380913,;SHROOM2,missense_variant,p.Pro74Ser,ENST00000452575,;SHROOM2,missense_variant,p.Pro74Ser,ENST00000418909,;SHROOM2,downstream_gene_variant,,ENST00000493668,;	T	ENSG00000146950	ENST00000380913	Transcript	missense_variant	3805	3715	1239	P/S	Ccc/Tcc	.	.	.	1	SHROOM2	HGNC	630	protein_coding	YES	CCDS14135.1	ENSP00000370299	SHRM2_HUMAN	F5H3B6_HUMAN,C9IZC6_HUMAN	UPI0000125D05	.	tolerated(0.1)	probably_damaging(0.992)	7/10	.	hmmpanther:PTHR15012,hmmpanther:PTHR15012:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGCCCCAC	.	5	ESCA
PDZD7	0	.	GRCh37	10	102789899	102789899	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78C>T	p.%3D	p.S26S	ENST00000370215	2/10	104	65	38	105	105	0	PDZD7,synonymous_variant,p.%3D,ENST00000470414,;PDZD7,synonymous_variant,p.%3D,ENST00000370215,;SFXN3,upstream_gene_variant,,ENST00000393459,;SFXN3,upstream_gene_variant,,ENST00000224807,;PDZD7,synonymous_variant,p.%3D,ENST00000474125,;PDZD7,upstream_gene_variant,,ENST00000476306,;SFXN3,upstream_gene_variant,,ENST00000489434,;	A	ENSG00000186862	ENST00000370215	Transcript	synonymous_variant	304	78	26	S	tcC/tcT	.	.	.	-1	PDZD7	HGNC	26257	protein_coding	YES	CCDS31269.1	ENSP00000359234	PDZD7_HUMAN	S4R3X4_HUMAN	UPI0000072FD2	.	.	.	2/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23116,hmmpanther:PTHR23116:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGAGGAGAG	.	5	ESCA
NOLC1	0	.	GRCh37	10	103912168	103912168	+	Translation_Start_Site	SNP	A	A	T	rs762663571	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1A>T	p.Met1?	p.M1?	ENST00000605788	1/13	55	42	13	59	59	0	NOLC1,start_lost,p.Met1?,ENST00000461421,;NOLC1,start_lost,p.Met1?,ENST00000605788,;NOLC1,start_lost,p.Met1?,ENST00000488254,;NOLC1,start_lost,p.Met1?,ENST00000405356,;NOLC1,5_prime_UTR_variant,,ENST00000603742,;NOLC1,upstream_gene_variant,,ENST00000476468,;PPRC1,downstream_gene_variant,,ENST00000413464,;NOLC1,upstream_gene_variant,,ENST00000370007,;PPRC1,downstream_gene_variant,,ENST00000278070,;PPRC1,downstream_gene_variant,,ENST00000370012,;PPRC1,downstream_gene_variant,,ENST00000495914,;PPRC1,downstream_gene_variant,,ENST00000489648,;NOLC1,start_lost,p.Met1?,ENST00000603946,;NOLC1,start_lost,p.Met1?,ENST00000464969,;	T	ENSG00000166197	ENST00000605788	Transcript	start_lost	236	1	1	M/L	Atg/Ttg	rs762663571	.	.	1	NOLC1	HGNC	15608	protein_coding	YES	CCDS7530.1	ENSP00000474710	NOLC1_HUMAN	Q96J17_HUMAN	UPI000013E575	.	deleterious_low_confidence(0)	possibly_damaging(0.697)	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGATGGCG	.	5	ESCA
INA	0	.	GRCh37	10	105049741	105049741	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1315G>A	.	.	ENST00000369849	3/3	16	11	4	26	26	0	INA,3_prime_UTR_variant,,ENST00000369849,;	A	ENSG00000148798	ENST00000369849	Transcript	3_prime_UTR_variant	2864	.	.	.	.	.	.	.	1	INA	HGNC	6057	protein_coding	YES	CCDS7545.1	ENSP00000358865	AINX_HUMAN	B4DE66_HUMAN	UPI000012573C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CATGCGCCTAC	.	4	ESCA
GPR26	0	.	GRCh37	10	125426291	125426291	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.368C>T	p.Ala123Val	p.A123V	ENST00000284674	1/3	19	10	9	12	12	0	GPR26,missense_variant,p.Ala123Val,ENST00000284674,;	T	ENSG00000154478	ENST00000284674	Transcript	missense_variant	421	368	123	A/V	gCg/gTg	.	.	.	1	GPR26	HGNC	4481	protein_coding	YES	CCDS7636.1	ENSP00000284674	GPR26_HUMAN	.	UPI000006E821	.	deleterious(0)	probably_damaging(0.968)	1/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24245:SF5,hmmpanther:PTHR24245,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGACGCGGCGC	.	5	ESCA
FANK1	0	.	GRCh37	10	127677338	127677338	+	Intron	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.316+94C>T	.	.	ENST00000368693	.	13	7	6	17	17	0	FANK1,missense_variant,p.Thr131Ile,ENST00000449042,;FANK1,intron_variant,,ENST00000445510,;FANK1,intron_variant,,ENST00000417114,;FANK1,intron_variant,,ENST00000368693,;FANK1,intron_variant,,ENST00000368691,;FANK1,intron_variant,,ENST00000368695,;FANK1,intron_variant,,ENST00000368689,;FANK1,intron_variant,,ENST00000492670,;	T	ENSG00000203780	ENST00000368693	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	FANK1	HGNC	23527	protein_coding	YES	CCDS31309.1	ENSP00000357682	FANK1_HUMAN	C9JD80_HUMAN,A6NH44_HUMAN	UPI000046FFD6	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	CCTTACCAGAA	.	3	ESCA
CACNB2	0	.	GRCh37	10	18829711	18829711	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1058G>T	.	.	ENST00000324631	14/14	30	20	10	16	16	0	CACNB2,3_prime_UTR_variant,,ENST00000396576,;CACNB2,3_prime_UTR_variant,,ENST00000377329,;CACNB2,3_prime_UTR_variant,,ENST00000324631,;CACNB2,3_prime_UTR_variant,,ENST00000377315,;CACNB2,3_prime_UTR_variant,,ENST00000282343,;CACNB2,3_prime_UTR_variant,,ENST00000377319,;CACNB2,downstream_gene_variant,,ENST00000377328,;CACNB2,downstream_gene_variant,,ENST00000377331,;NSUN6,downstream_gene_variant,,ENST00000377304,;CACNB2,downstream_gene_variant,,ENST00000352115,;RP11-499P20.2,intron_variant,,ENST00000425669,;RP11-499P20.2,downstream_gene_variant,,ENST00000436485,;	T	ENSG00000165995	ENST00000324631	Transcript	3_prime_UTR_variant	3101	.	.	.	.	.	.	.	1	CACNB2	HGNC	1402	protein_coding	YES	CCDS7125.1	ENSP00000320025	CACB2_HUMAN	.	UPI00001AEA80	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATGCTGAA	.	5	ESCA
RHOBTB1	0	.	GRCh37	10	62631234	62631234	+	3'UTR	SNP	T	T	G	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6A>C	.	.	ENST00000337910	11/11	35	26	9	22	22	0	RHOBTB1,3_prime_UTR_variant,,ENST00000337910,;RHOBTB1,3_prime_UTR_variant,,ENST00000357917,;RHOBTB1,non_coding_transcript_exon_variant,,ENST00000496237,;RHOBTB1,non_coding_transcript_exon_variant,,ENST00000461910,;RHOBTB1,non_coding_transcript_exon_variant,,ENST00000490827,;	G	ENSG00000072422	ENST00000337910	Transcript	3_prime_UTR_variant	2435	.	.	.	.	.	.	.	-1	RHOBTB1	HGNC	18738	protein_coding	YES	CCDS7261.1	ENSP00000338671	RHBT1_HUMAN	Q567T3_HUMAN	UPI000000D9B7	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTCTTCCTCT	.	4	ESCA
PTEN	0	.	GRCh37	10	89717619	89717619	+	Missense_Mutation	SNP	T	T	G	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.644T>G	p.Phe215Cys	p.F215C	ENST00000371953	7/9	80	51	28	69	69	0	PTEN,missense_variant,p.Phe215Cys,ENST00000371953,;PTEN,non_coding_transcript_exon_variant,,ENST00000472832,;	G	ENSG00000171862	ENST00000371953	Transcript	missense_variant	2001	644	215	F/C	tTt/tGt	COSM212632	.	.	1	PTEN	HGNC	9588	protein_coding	YES	CCDS31238.1	ENSP00000361021	PTEN_HUMAN	F6KD01_HUMAN,H6WA51_HUMAN,H6WA46_HUMAN	UPI00001328C5	.	deleterious(0.02)	benign(0.315)	7/9	.	PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Gene3D:1d5rA02,Pfam_domain:PF10409,PIRSF_domain:PIRSF038025,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.0?|c.1_1212del1212|28,BUFFER|p.?|c.635-1G>A|4,BUFFER|p.?|c.635-1G>T|3,BUFFER|p.Q214*|c.640C>T|12,BUFFER|p.Q219*|c.655C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGTTTGTGG	.	5	ESCA
BLNK	0	.	GRCh37	10	97960771	97960771	+	Silent	SNP	G	G	T	rs782086992	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.978C>A	p.%3D	p.P326P	ENST00000224337	14/17	33	24	9	28	28	0	BLNK,synonymous_variant,p.%3D,ENST00000427367,;BLNK,synonymous_variant,p.%3D,ENST00000224337,;BLNK,synonymous_variant,p.%3D,ENST00000371176,;BLNK,synonymous_variant,p.%3D,ENST00000413476,;ZNF518A,intron_variant,,ENST00000442635,;ZNF518A,intron_variant,,ENST00000563195,;BLNK,non_coding_transcript_exon_variant,,ENST00000485193,;BLNK,downstream_gene_variant,,ENST00000467799,;BLNK,downstream_gene_variant,,ENST00000468252,;	T	ENSG00000095585	ENST00000224337	Transcript	synonymous_variant	1120	978	326	P	ccC/ccA	rs782086992,COSM3442233,COSM3442234	.	.	-1	BLNK	HGNC	14211	protein_coding	YES	CCDS7446.1	ENSP00000224337	BLNK_HUMAN	Q2MD56_HUMAN	UPI000006FDD6	.	.	.	14/17	.	hmmpanther:PTHR14098:SF3,hmmpanther:PTHR14098	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTGGGTAG	.	5	ESCA
ZBTB16	0	.	GRCh37	11	113933968	113933968	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-55G>A	.	.	ENST00000335953	2/7	18	9	9	22	22	0	ZBTB16,5_prime_UTR_variant,,ENST00000544220,;ZBTB16,5_prime_UTR_variant,,ENST00000392996,;ZBTB16,5_prime_UTR_variant,,ENST00000535700,;ZBTB16,5_prime_UTR_variant,,ENST00000335953,;ZBTB16,non_coding_transcript_exon_variant,,ENST00000541602,;ZBTB16,upstream_gene_variant,,ENST00000539918,;	A	ENSG00000109906	ENST00000335953	Transcript	5_prime_UTR_variant	326	.	.	.	.	.	.	.	1	ZBTB16	HGNC	12930	protein_coding	YES	CCDS8367.1	ENSP00000338157	ZBT16_HUMAN	Q71UL7_HUMAN,Q71UL6_HUMAN,Q71UL5_HUMAN,F5H6C3_HUMAN,F5H5Y7_HUMAN	UPI000000018E	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGCCACG	.	5	ESCA
KMT2A	0	.	GRCh37	11	118343016	118343017	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147dupG	p.Ala383GlyfsTer6	p.A383Gfs*6	ENST00000534358	3/36	28	19	9	27	27	0	KMT2A,frameshift_variant,p.Ala383GlyfsTer6,ENST00000389506,;KMT2A,frameshift_variant,p.Ala383GlyfsTer6,ENST00000354520,;KMT2A,frameshift_variant,p.Ala383GlyfsTer6,ENST00000534358,;KMT2A,frameshift_variant,p.Ala416GlyfsTer6,ENST00000531904,;KMT2A,intron_variant,,ENST00000527869,;KMT2A,intron_variant,,ENST00000533790,;	G	ENSG00000118058	ENST00000534358	Transcript	frameshift_variant	1165-1166	1142-1143	381	K/KX	aag/aaGg	.	.	.	1	KMT2A	HGNC	7132	protein_coding	YES	CCDS55791.1	ENSP00000436786	KMT2A_HUMAN	Q9UPD0_HUMAN,Q9UM91_HUMAN,Q9HBJ4_HUMAN,B4DIJ7_HUMAN	UPI0001E5E732	.	.	.	3/36	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAAAAGGGGG	.	3	ESCA
KMT2A	0	.	GRCh37	11	118348808	118348808	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3461G>A	p.Arg1154Gln	p.R1154Q	ENST00000534358	5/36	44	26	17	57	57	0	KMT2A,missense_variant,p.Arg1154Gln,ENST00000389506,;KMT2A,missense_variant,p.Arg232Gln,ENST00000533790,;KMT2A,missense_variant,p.Arg1154Gln,ENST00000354520,;KMT2A,missense_variant,p.Arg1154Gln,ENST00000534358,;KMT2A,missense_variant,p.Arg1187Gln,ENST00000531904,;KMT2A,downstream_gene_variant,,ENST00000527869,;KMT2A,upstream_gene_variant,,ENST00000392873,;KMT2A,upstream_gene_variant,,ENST00000420751,;	A	ENSG00000118058	ENST00000534358	Transcript	missense_variant	3484	3461	1154	R/Q	cGg/cAg	COSM3764282,COSM3764281	.	.	1	KMT2A	HGNC	7132	protein_coding	YES	CCDS55791.1	ENSP00000436786	KMT2A_HUMAN	Q9UPD0_HUMAN,Q9UM91_HUMAN,Q9HBJ4_HUMAN,B4DIJ7_HUMAN	UPI0001E5E732	.	.	probably_damaging(0.99)	5/36	.	PROSITE_profiles:PS51058,hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,Pfam_domain:PF02008,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCGGTGTG	.	5	ESCA
COPB1	0	.	GRCh37	11	14498481	14498481	+	Missense_Mutation	SNP	C	C	T	rs754536521	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439G>A	p.Arg480His	p.R480H	ENST00000249923	12/22	33	30	3	25	25	0	COPB1,missense_variant,p.Arg480His,ENST00000439561,;COPB1,missense_variant,p.Arg480His,ENST00000249923,;COPB1,missense_variant,p.Arg480His,ENST00000534234,;RNU7-49P,upstream_gene_variant,,ENST00000516182,;COPB1,upstream_gene_variant,,ENST00000526191,;	T	ENSG00000129083	ENST00000249923	Transcript	missense_variant	1740	1439	480	R/H	cGc/cAc	rs754536521,COSM1352827	.	.	-1	COPB1	HGNC	2231	protein_coding	YES	CCDS7815.1	ENSP00000249923	COPB_HUMAN	E9PP63_HUMAN,E9PKQ1_HUMAN	UPI000000103D	.	deleterious(0)	possibly_damaging(0.908)	12/22	.	hmmpanther:PTHR10635,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF005727,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACCTGCGGATC	byFrequency	2	ESCA
ATHL1	0	.	GRCh37	11	293646	293646	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1533C>T	p.%3D	p.F511F	ENST00000409548	10/14	29	18	11	25	25	0	ATHL1,synonymous_variant,p.%3D,ENST00000409479,;ATHL1,synonymous_variant,p.%3D,ENST00000409548,;ATHL1,intron_variant,,ENST00000409655,;ATHL1,upstream_gene_variant,,ENST00000397660,;IFITM5,downstream_gene_variant,,ENST00000382614,;RP11-326C3.2,downstream_gene_variant,,ENST00000525217,;RP11-326C3.2,downstream_gene_variant,,ENST00000534742,;ATHL1,non_coding_transcript_exon_variant,,ENST00000476372,;ATHL1,non_coding_transcript_exon_variant,,ENST00000474221,;ATHL1,downstream_gene_variant,,ENST00000529087,;ATHL1,downstream_gene_variant,,ENST00000482937,;	T	ENSG00000142102	ENST00000409548	Transcript	synonymous_variant	1648	1533	511	F	ttC/ttT	.	.	.	1	ATHL1	HGNC	26210	protein_coding	YES	CCDS31322.2	ENSP00000387185	ATHL1_HUMAN	.	UPI0000EE80CE	.	.	.	10/14	.	hmmpanther:PTHR11051:SF10,hmmpanther:PTHR11051,Pfam_domain:PF03632,Gene3D:1.50.10.10,Superfamily_domains:SSF48208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTCTCCCT	.	5	ESCA
LRRC4C	0	.	GRCh37	11	40137317	40137317	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526C>T	p.Arg176Ter	p.R176*	ENST00000278198	2/2	36	24	12	29	29	0	LRRC4C,stop_gained,p.Arg176Ter,ENST00000528697,;LRRC4C,stop_gained,p.Arg176Ter,ENST00000278198,;LRRC4C,stop_gained,p.Arg176Ter,ENST00000530763,;LRRC4C,stop_gained,p.Arg176Ter,ENST00000527150,;LRRC4C,downstream_gene_variant,,ENST00000533474,;	A	ENSG00000148948	ENST00000278198	Transcript	stop_gained	2490	526	176	R/*	Cga/Tga	COSM1703826	.	.	-1	LRRC4C	HGNC	29317	protein_coding	YES	CCDS31464.1	ENSP00000278198	LRC4C_HUMAN	E9PLP4_HUMAN	UPI000000D9A7	.	.	.	2/2	.	hmmpanther:PTHR24369:SF8,hmmpanther:PTHR24369,Gene3D:3.80.10.10,Pfam_domain:PF13306,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTCGGCGCA	.	5	ESCA
ACCS	0	.	GRCh37	11	44089274	44089274	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>A	p.Glu33Lys	p.E33K	ENST00000263776	2/15	58	42	16	55	55	0	ACCS,missense_variant,p.Glu33Lys,ENST00000524990,;ACCS,missense_variant,p.Glu33Lys,ENST00000432284,;ACCS,missense_variant,p.Glu33Lys,ENST00000533404,;ACCS,missense_variant,p.Glu33Lys,ENST00000263776,;CTD-2609K8.3,upstream_gene_variant,,ENST00000531268,;ACCS,non_coding_transcript_exon_variant,,ENST00000533208,;ACCS,non_coding_transcript_exon_variant,,ENST00000526577,;ACCS,non_coding_transcript_exon_variant,,ENST00000527603,;	A	ENSG00000110455	ENST00000263776	Transcript	missense_variant	531	97	33	E/K	Gaa/Aaa	.	.	.	1	ACCS	HGNC	23989	protein_coding	YES	CCDS7907.1	ENSP00000263776	1A1L1_HUMAN	E9PS61_HUMAN,E9PRT9_HUMAN	UPI000006D45A	.	tolerated(0.06)	benign(0.034)	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGGAAGGA	.	5	ESCA
LRP4	0	.	GRCh37	11	46895129	46895129	+	Silent	SNP	G	G	A	rs185084650	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4245C>T	p.%3D	p.N1415N	ENST00000378623	29/38	29	18	11	12	12	0	LRP4,synonymous_variant,p.%3D,ENST00000378623,;LRP4-AS1,non_coding_transcript_exon_variant,,ENST00000502049,;LRP4-AS1,downstream_gene_variant,,ENST00000531719,;LRP4,non_coding_transcript_exon_variant,,ENST00000527656,;	A	ENSG00000134569	ENST00000378623	Transcript	synonymous_variant	4488	4245	1415	N	aaC/aaT	rs185084650	.	.	-1	LRP4	HGNC	6696	protein_coding	YES	CCDS31478.1	ENSP00000367888	LRP4_HUMAN	.	UPI0000D625E9	.	.	.	29/38	.	PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF196,Gene3D:2.120.10.30,Pfam_domain:PF00058,SMART_domains:SM00135,Superfamily_domains:SSF63825	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCGTTCAG	byCluster|by1000G	5	ESCA
STIP1	0	.	GRCh37	11	63953731	63953731	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3G>A	.	.	ENST00000305218	1/14	29	18	10	20	20	0	STIP1,5_prime_UTR_variant,,ENST00000543847,;STIP1,5_prime_UTR_variant,,ENST00000305218,;STIP1,5_prime_UTR_variant,,ENST00000538945,;STIP1,intron_variant,,ENST00000358794,;STIP1,upstream_gene_variant,,ENST00000540501,;STIP1,5_prime_UTR_variant,,ENST00000536973,;STIP1,non_coding_transcript_exon_variant,,ENST00000540736,;	A	ENSG00000168439	ENST00000305218	Transcript	5_prime_UTR_variant	145	.	.	.	.	.	.	.	1	STIP1	HGNC	11387	protein_coding	YES	CCDS8058.1	ENSP00000305958	STIP1_HUMAN	.	UPI000012D225	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCGCTATG	.	5	ESCA
OR6A2	0	.	GRCh37	11	6816277	6816277	+	Silent	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.663C>A	p.%3D	p.A221A	ENST00000332601	1/1	21	14	7	19	19	0	OR6A2,synonymous_variant,p.%3D,ENST00000332601,;	T	ENSG00000184933	ENST00000332601	Transcript	synonymous_variant	852	663	221	A	gcC/gcA	.	.	.	-1	OR6A2	HGNC	15301	protein_coding	YES	CCDS7772.1	ENSP00000330384	OR6A2_HUMAN	.	UPI0000061E92	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF234,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGAGGCCCC	.	5	ESCA
ARHGEF17	0	.	GRCh37	11	73021802	73021802	+	Missense_Mutation	SNP	C	C	T	rs369681028	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2119C>T	p.Arg707Cys	p.R707C	ENST00000263674	1/21	52	27	24	40	40	0	ARHGEF17,missense_variant,p.Arg707Cys,ENST00000263674,;ARHGEF17,upstream_gene_variant,,ENST00000544519,;RP11-800A3.7,upstream_gene_variant,,ENST00000546324,;	T	ENSG00000110237	ENST00000263674	Transcript	missense_variant	2469	2119	707	R/C	Cgc/Tgc	rs369681028	.	.	1	ARHGEF17	HGNC	21726	protein_coding	YES	CCDS8221.1	ENSP00000263674	ARHGH_HUMAN	.	UPI000004980B	.	deleterious_low_confidence(0)	probably_damaging(0.996)	1/21	.	hmmpanther:PTHR12877:SF15,hmmpanther:PTHR12877	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCCTCCGCCGA	byFrequency|byCluster	4	ESCA
XRRA1	0	.	GRCh37	11	74559456	74559456	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1408C>T	p.Pro470Ser	p.P470S	ENST00000340360	15/19	33	21	11	27	27	0	XRRA1,missense_variant,p.Pro195Ser,ENST00000321448,;XRRA1,missense_variant,p.Pro383Ser,ENST00000527087,;XRRA1,missense_variant,p.Pro470Ser,ENST00000340360,;RN7SL239P,downstream_gene_variant,,ENST00000490061,;XRRA1,non_coding_transcript_exon_variant,,ENST00000530280,;XRRA1,missense_variant,p.Pro26Ser,ENST00000530562,;XRRA1,3_prime_UTR_variant,,ENST00000531449,;XRRA1,3_prime_UTR_variant,,ENST00000531849,;XRRA1,non_coding_transcript_exon_variant,,ENST00000431210,;XRRA1,downstream_gene_variant,,ENST00000529926,;	A	ENSG00000166435	ENST00000340360	Transcript	missense_variant	1740	1408	470	P/S	Ccg/Tcg	.	.	.	-1	XRRA1	HGNC	18868	protein_coding	YES	CCDS44680.1	ENSP00000339918	XRRA1_HUMAN	E9PJ58_HUMAN	UPI0001572CC6	.	tolerated(0.06)	benign(0.023)	15/19	.	hmmpanther:PTHR22710	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCGGGTGAT	.	5	ESCA
TRIM66	0	.	GRCh37	11	8662484	8662484	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.997C>A	p.Gln333Lys	p.Q333K	ENST00000402157	11/22	31	20	11	22	22	0	TRIM66,missense_variant,p.Gln333Lys,ENST00000402157,;TRIM66,missense_variant,p.Gln335Lys,ENST00000299550,;TRIM66,downstream_gene_variant,,ENST00000529057,;TRIM66,downstream_gene_variant,,ENST00000531498,;TRIM66,non_coding_transcript_exon_variant,,ENST00000481014,;	T	ENSG00000166436	ENST00000402157	Transcript	missense_variant	1438	997	333	Q/K	Cag/Aag	.	.	.	-1	TRIM66	HGNC	29005	protein_coding	YES	.	ENSP00000384876	.	B5MCJ9_HUMAN	UPI00016113E8	.	deleterious(0.02)	benign(0.062)	11/22	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTGGCCTT	.	5	ESCA
GOLGA3	0	.	GRCh37	12	133351713	133351713	+	Intron	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4143+14C>T	.	.	ENST00000204726	.	18	12	6	17	17	0	GOLGA3,missense_variant,p.Ala1386Val,ENST00000456883,;GOLGA3,intron_variant,,ENST00000204726,;GOLGA3,intron_variant,,ENST00000450791,;GOLGA3,non_coding_transcript_exon_variant,,ENST00000541013,;	A	ENSG00000090615	ENST00000204726	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	.	.	.	22/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGACGCGGGC	.	5	ESCA
SLCO1B1	0	.	GRCh37	12	21370110	21370110	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555G>T	p.Ala519Ser	p.A519S	ENST00000256958	12/15	76	58	18	67	67	0	SLCO1B1,missense_variant,p.Ala519Ser,ENST00000256958,;	T	ENSG00000134538	ENST00000256958	Transcript	missense_variant	1651	1555	519	A/S	Gcc/Tcc	.	.	.	1	SLCO1B1	HGNC	10959	protein_coding	YES	CCDS8685.1	ENSP00000256958	SO1B1_HUMAN	K4P403_HUMAN	UPI0000043BED	.	deleterious(0.01)	probably_damaging(0.976)	12/15	.	PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF82,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCAGCCCAT	.	5	ESCA
C2CD5	0	.	GRCh37	12	22601650	22601650	+	3'UTR	SNP	T	T	C	rs528418570	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1044A>G	.	.	ENST00000333957	25/25	16	12	4	14	14	0	C2CD5,3_prime_UTR_variant,,ENST00000333957,;C2CD5,downstream_gene_variant,,ENST00000545552,;C2CD5,downstream_gene_variant,,ENST00000544930,;C2CD5,downstream_gene_variant,,ENST00000542676,;C2CD5,downstream_gene_variant,,ENST00000539615,;C2CD5,downstream_gene_variant,,ENST00000396028,;C2CD5,downstream_gene_variant,,ENST00000446597,;C2CD5,downstream_gene_variant,,ENST00000536386,;	C	ENSG00000111731	ENST00000333957	Transcript	3_prime_UTR_variant	4303	.	.	.	.	rs528418570	.	.	-1	C2CD5	HGNC	29062	protein_coding	YES	CCDS31758.1	ENSP00000334229	C2CD5_HUMAN	.	UPI000000D850	.	.	.	25/25	.	.	C:0.0002	C:0	C:0	.	C:0.001	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTATAAAGA	by1000G	5	ESCA
KMT2D	0	.	GRCh37	12	49425503	49425503	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12985C>T	p.Gln4329Ter	p.Q4329*	ENST00000301067	39/54	57	43	13	49	49	0	KMT2D,stop_gained,p.Gln4329Ter,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	stop_gained	12985	12985	4329	Q/*	Cag/Tag	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	39/54	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAGCTGGGAGC	.	4	ESCA
KRT85	0	.	GRCh37	12	52757174	52757174	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.807C>T	p.%3D	p.A269A	ENST00000257901	5/9	65	40	24	32	32	0	KRT85,synonymous_variant,p.%3D,ENST00000544265,;KRT85,synonymous_variant,p.%3D,ENST00000257901,;KRT85,non_coding_transcript_exon_variant,,ENST00000552537,;	A	ENSG00000135443	ENST00000257901	Transcript	synonymous_variant	883	807	269	A	gcC/gcT	.	.	.	-1	KRT85	HGNC	6462	protein_coding	YES	CCDS8824.1	ENSP00000257901	KRT85_HUMAN	.	UPI000006EB3B	.	.	.	5/9	.	Pfam_domain:PF00038,hmmpanther:PTHR23239:SF92,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGGGCTTG	.	5	ESCA
KRT5	0	.	GRCh37	12	52910941	52910941	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1168A>G	p.Asn390Asp	p.N390D	ENST00000252242	6/9	40	32	7	15	15	0	KRT5,missense_variant,p.Asn98Asp,ENST00000548409,;KRT5,missense_variant,p.Asn390Asp,ENST00000252242,;KRT5,downstream_gene_variant,,ENST00000551275,;KRT5,downstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000549420,;KRT5,downstream_gene_variant,,ENST00000546577,;KRT5,non_coding_transcript_exon_variant,,ENST00000547890,;KRT5,non_coding_transcript_exon_variant,,ENST00000549511,;KRT5,non_coding_transcript_exon_variant,,ENST00000551013,;KRT5,non_coding_transcript_exon_variant,,ENST00000552629,;KRT5,upstream_gene_variant,,ENST00000552952,;	C	ENSG00000186081	ENST00000252242	Transcript	missense_variant	1559	1168	390	N/D	Aac/Gac	.	.	.	-1	KRT5	HGNC	6442	protein_coding	YES	CCDS8830.1	ENSP00000252242	K2C5_HUMAN	Q9UEK9_HUMAN,F8VV57_HUMAN,B4DL32_HUMAN	UPI000013CD4B	.	deleterious(0.03)	possibly_damaging(0.534)	6/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF159,hmmpanther:PTHR23239,Pfam_domain:PF00038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCGGTTCATCT	.	4	ESCA
KRT5	0	.	GRCh37	12	52913949	52913949	+	Silent	SNP	A	A	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132T>G	p.%3D	p.G44G	ENST00000252242	1/9	126	92	33	82	82	0	KRT5,synonymous_variant,p.%3D,ENST00000551275,;KRT5,synonymous_variant,p.%3D,ENST00000252242,;KRT5,synonymous_variant,p.%3D,ENST00000546577,;KRT5,intron_variant,,ENST00000549420,;KRT5,upstream_gene_variant,,ENST00000548409,;KRT5,upstream_gene_variant,,ENST00000551188,;KRT5,non_coding_transcript_exon_variant,,ENST00000552629,;KRT5,upstream_gene_variant,,ENST00000547890,;KRT5,upstream_gene_variant,,ENST00000549511,;KRT5,upstream_gene_variant,,ENST00000551013,;KRT5,upstream_gene_variant,,ENST00000552952,;	C	ENSG00000186081	ENST00000252242	Transcript	synonymous_variant	523	132	44	G	ggT/ggG	.	.	.	-1	KRT5	HGNC	6442	protein_coding	YES	CCDS8830.1	ENSP00000252242	K2C5_HUMAN	Q9UEK9_HUMAN,F8VV57_HUMAN,B4DL32_HUMAN	UPI000013CD4B	.	.	.	1/9	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F46F|c.138C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCCACCACC	.	5	ESCA
LIN7A	0	.	GRCh37	12	81331514	81331514	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13C>T	.	.	ENST00000552864	1/6	80	50	29	63	63	0	LIN7A,5_prime_UTR_variant,,ENST00000552864,;ACSS3,upstream_gene_variant,,ENST00000549175,;LIN7A,upstream_gene_variant,,ENST00000549417,;MIR618,upstream_gene_variant,,ENST00000385287,;LIN7A,5_prime_UTR_variant,,ENST00000261203,;	A	ENSG00000111052	ENST00000552864	Transcript	5_prime_UTR_variant	191	.	.	.	.	.	.	.	-1	LIN7A	HGNC	17787	protein_coding	YES	CCDS9021.1	ENSP00000447488	LIN7A_HUMAN	.	UPI0000073ECD	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTCGTAGTG	.	5	ESCA
PPFIA2	0	.	GRCh37	12	81839369	81839369	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.536C>A	p.Ser179Tyr	p.S179Y	ENST00000549396	6/33	72	56	15	75	75	0	PPFIA2,missense_variant,p.Ser161Tyr,ENST00000333447,;PPFIA2,missense_variant,p.Ser105Tyr,ENST00000407050,;PPFIA2,missense_variant,p.Ser105Tyr,ENST00000443686,;PPFIA2,missense_variant,p.Ser26Tyr,ENST00000550359,;PPFIA2,missense_variant,p.Ser179Tyr,ENST00000549396,;PPFIA2,missense_variant,p.Ser161Tyr,ENST00000549325,;PPFIA2,missense_variant,p.Ser179Tyr,ENST00000548586,;PPFIA2,missense_variant,p.Ser179Tyr,ENST00000550584,;PPFIA2,missense_variant,p.Ser179Tyr,ENST00000552948,;PPFIA2,downstream_gene_variant,,ENST00000551442,;PPFIA2,upstream_gene_variant,,ENST00000548790,;RP11-315E17.1,intron_variant,,ENST00000550272,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000548453,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000545296,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000552020,;	T	ENSG00000139220	ENST00000549396	Transcript	missense_variant	697	536	179	S/Y	tCt/tAt	COSM943919	.	.	-1	PPFIA2	HGNC	9246	protein_coding	YES	CCDS55857.1	ENSP00000450337	LIPA2_HUMAN	H0YHK3_HUMAN,F8W1Y8_HUMAN,F8VU88_HUMAN	UPI0000168655	.	deleterious(0)	probably_damaging(0.984)	6/33	.	hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAAGATTTC	.	5	ESCA
RP11-726G1.1	0	.	GRCh37	12	9728362	9728362	+	RNA	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.7361G>T	.	.	ENST00000520314	12/12	91	61	30	70	70	0	RP11-726G1.1,non_coding_transcript_exon_variant,,ENST00000520314,;RP11-726G1.1,downstream_gene_variant,,ENST00000518709,;	T	ENSG00000214776	ENST00000520314	Transcript	non_coding_transcript_exon_variant	7361	.	.	.	.	.	.	.	1	RP11-726G1.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTAAGAAAAT	.	3	ESCA
RP11-726G1.1	0	.	GRCh37	12	9728368	9728368	+	RNA	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.7367G>A	.	.	ENST00000520314	12/12	86	56	29	69	69	0	RP11-726G1.1,non_coding_transcript_exon_variant,,ENST00000520314,;RP11-726G1.1,downstream_gene_variant,,ENST00000518709,;	A	ENSG00000214776	ENST00000520314	Transcript	non_coding_transcript_exon_variant	7367	.	.	.	.	.	.	.	1	RP11-726G1.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAAATGAAAAC	.	3	ESCA
GJB6	0	.	GRCh37	13	20796579	20796579	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*255G>T	.	.	ENST00000356192	5/5	62	33	28	55	55	0	GJB6,3_prime_UTR_variant,,ENST00000241124,;GJB6,3_prime_UTR_variant,,ENST00000356192,;GJB6,3_prime_UTR_variant,,ENST00000400065,;GJB6,3_prime_UTR_variant,,ENST00000400066,;	A	ENSG00000121742	ENST00000356192	Transcript	3_prime_UTR_variant	1662	.	.	.	.	.	.	.	-1	GJB6	HGNC	4288	protein_coding	YES	CCDS9291.1	ENSP00000348521	CXB6_HUMAN	.	UPI0000074737	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCACTTAAA	.	5	ESCA
XPO4	0	.	GRCh37	13	21355491	21355491	+	3'UTR	SNP	T	T	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2370A>G	.	.	ENST00000255305	23/23	60	57	3	36	35	0	XPO4,3_prime_UTR_variant,,ENST00000255305,;XPO4,3_prime_UTR_variant,,ENST00000400602,;	C	ENSG00000132953	ENST00000255305	Transcript	3_prime_UTR_variant	5898	.	.	.	.	.	.	.	-1	XPO4	HGNC	17796	protein_coding	YES	CCDS41872.1	ENSP00000255305	XPO4_HUMAN	Q8IVQ8_HUMAN,Q0VG75_HUMAN	UPI0000139018	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCCTGAAAA	.	2	ESCA
FREM2	0	.	GRCh37	13	39358714	39358714	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5788C>T	p.Pro1930Ser	p.P1930S	ENST00000280481	6/24	39	35	4	17	17	0	FREM2,missense_variant,p.Pro1930Ser,ENST00000280481,;	T	ENSG00000150893	ENST00000280481	Transcript	missense_variant	6004	5788	1930	P/S	Ccg/Tcg	.	.	.	1	FREM2	HGNC	25396	protein_coding	YES	CCDS31960.1	ENSP00000280481	FREM2_HUMAN	.	UPI00005520B9	.	deleterious(0.04)	benign(0.078)	6/24	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF19,Pfam_domain:PF03160,SMART_domains:SM00237,Superfamily_domains:SSF141072	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTGCCGACT	.	4	ESCA
NHLRC3	0	.	GRCh37	13	39622028	39622028	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009C>T	p.Pro337Ser	p.P337S	ENST00000379600	7/7	19	13	6	18	18	0	NHLRC3,missense_variant,p.Pro337Ser,ENST00000379600,;NHLRC3,missense_variant,p.Pro270Ser,ENST00000379599,;NHLRC3,missense_variant,p.Pro140Ser,ENST00000470258,;NHLRC3,downstream_gene_variant,,ENST00000485407,;	T	ENSG00000188811	ENST00000379600	Transcript	missense_variant	1331	1009	337	P/S	Cct/Tct	.	.	.	1	NHLRC3	HGNC	33751	protein_coding	YES	CCDS31961.1	ENSP00000368920	NHLC3_HUMAN	C9J973_HUMAN	UPI0000251E60	.	deleterious(0)	probably_damaging(0.998)	7/7	.	PROSITE_profiles:PS51125,hmmpanther:PTHR24104,Superfamily_domains:SSF101898	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTCCCTTTG	.	5	ESCA
PCDH20	0	.	GRCh37	13	61987736	61987736	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496G>A	p.Val166Ile	p.V166I	ENST00000409186	5/5	52	34	18	45	45	0	PCDH20,missense_variant,p.Val166Ile,ENST00000409204,;PCDH20,missense_variant,p.Val166Ile,ENST00000409186,;	T	ENSG00000197991	ENST00000409186	Transcript	missense_variant	2602	496	166	V/I	Gtt/Att	.	.	.	-1	PCDH20	HGNC	14257	protein_coding	YES	CCDS9442.2	ENSP00000386653	PCD20_HUMAN	B3KSZ7_HUMAN	UPI000007371F	.	tolerated(0.92)	benign(0)	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF24,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAACGCTGC	.	5	ESCA
ATG14	0	.	GRCh37	14	55833195	55833195	+	3'UTR	SNP	T	T	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3142A>T	.	.	ENST00000247178	10/10	45	31	13	17	17	0	ATG14,3_prime_UTR_variant,,ENST00000247178,;ATG14,non_coding_transcript_exon_variant,,ENST00000558189,;FBXO34,downstream_gene_variant,,ENST00000555280,;	A	ENSG00000126775	ENST00000247178	Transcript	3_prime_UTR_variant	4657	.	.	.	.	.	.	.	-1	ATG14	HGNC	19962	protein_coding	YES	CCDS32087.1	ENSP00000247178	BAKOR_HUMAN	.	UPI00001FD5B2	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAATGGGGA	.	5	ESCA
ATG14	0	.	GRCh37	14	55833227	55833227	+	3'UTR	SNP	G	G	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3110C>G	.	.	ENST00000247178	10/10	23	14	9	12	12	0	ATG14,3_prime_UTR_variant,,ENST00000247178,;ATG14,non_coding_transcript_exon_variant,,ENST00000558189,;FBXO34,downstream_gene_variant,,ENST00000555280,;	C	ENSG00000126775	ENST00000247178	Transcript	3_prime_UTR_variant	4625	.	.	.	.	.	.	.	-1	ATG14	HGNC	19962	protein_coding	YES	CCDS32087.1	ENSP00000247178	BAKOR_HUMAN	.	UPI00001FD5B2	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAGGAGATTCT	.	3	ESCA
UBE3A	0	.	GRCh37	15	25653719	25653719	+	Intron	SNP	T	T	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29+48A>G	.	.	ENST00000397954	.	61	39	22	57	57	0	UBE3A,splice_region_variant,,ENST00000566215,;UBE3A,intron_variant,,ENST00000397954,;UBE3A,intron_variant,,ENST00000428984,;UBE3A,intron_variant,,ENST00000232165,;UBE3A,upstream_gene_variant,,ENST00000438097,;SNHG14,intron_variant,,ENST00000554726,;	C	ENSG00000114062	ENST00000397954	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	UBE3A	HGNC	12496	protein_coding	YES	CCDS45192.1	ENSP00000381045	UBE3A_HUMAN	Q9UBN9_HUMAN,Q9H2G0_HUMAN,Q96GR7_HUMAN	UPI0000161F3B	.	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACTAATCT	.	5	ESCA
GREM1	0	.	GRCh37	15	33010353	33010353	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11G>A	.	.	ENST00000300177	1/2	18	14	4	14	14	0	GREM1,5_prime_UTR_variant,,ENST00000300177,;GREM1,5_prime_UTR_variant,,ENST00000560830,;GREM1,5_prime_UTR_variant,,ENST00000560677,;RP11-758N13.1,non_coding_transcript_exon_variant,,ENST00000560363,;RP11-758N13.1,non_coding_transcript_exon_variant,,ENST00000558441,;	A	ENSG00000166923	ENST00000300177	Transcript	5_prime_UTR_variant	179	.	.	.	.	.	.	.	1	GREM1	HGNC	2001	protein_coding	YES	CCDS10029.1	ENSP00000300177	GREM1_HUMAN	A6XAA7_HUMAN	UPI0000073D48	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|VARSCANS	CCGCCGCACTG	.	2	ESCA
SMAD3	0	.	GRCh37	15	67482843	67482843	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1247C>T	p.Ser416Phe	p.S416F	ENST00000327367	9/9	46	34	12	37	37	0	SMAD3,missense_variant,p.Ser147Phe,ENST00000560424,;SMAD3,missense_variant,p.Ser416Phe,ENST00000327367,;SMAD3,missense_variant,p.Ser221Phe,ENST00000537194,;SMAD3,missense_variant,p.Ser311Phe,ENST00000540846,;SMAD3,missense_variant,p.Ser372Phe,ENST00000439724,;SMAD3,downstream_gene_variant,,ENST00000558894,;SMAD3,non_coding_transcript_exon_variant,,ENST00000558763,;SMAD3,intron_variant,,ENST00000560402,;	T	ENSG00000166949	ENST00000327367	Transcript	missense_variant	1557	1247	416	S/F	tCc/tTc	.	.	.	1	SMAD3	HGNC	6769	protein_coding	YES	CCDS10222.1	ENSP00000332973	SMAD3_HUMAN	Q68DS8_HUMAN,H3BP09_HUMAN,H0YNV1_HUMAN,H0YMP2_HUMAN,H0YL71_HUMAN,H0YKE2_HUMAN	UPI0000023A91	.	deleterious(0)	possibly_damaging(0.807)	9/9	.	Superfamily_domains:SSF49879,Gene3D:2.60.200.10,hmmpanther:PTHR13703:SF25,hmmpanther:PTHR13703,PROSITE_profiles:PS51076	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGGCTCCCCAA	.	4	ESCA
SH3GL3	0	.	GRCh37	15	84237334	84237334	+	Missense_Mutation	SNP	G	G	A	rs764980950	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241G>A	p.Val81Met	p.V81M	ENST00000427482	4/9	43	33	10	34	34	0	SH3GL3,missense_variant,p.Val89Met,ENST00000324537,;SH3GL3,missense_variant,p.Val81Met,ENST00000427482,;SH3GL3,missense_variant,p.Val89Met,ENST00000434347,;SH3GL3,missense_variant,p.Val81Met,ENST00000535412,;SH3GL3,3_prime_UTR_variant,,ENST00000563901,;SH3GL3,downstream_gene_variant,,ENST00000492099,;	A	ENSG00000140600	ENST00000427482	Transcript	missense_variant	547	241	81	V/M	Gtg/Atg	rs764980950	.	.	1	SH3GL3	HGNC	10832	protein_coding	YES	CCDS10325.2	ENSP00000391372	SH3G3_HUMAN	Q9UMB8_HUMAN	UPI0000135935	.	tolerated(0.06)	possibly_damaging(0.87)	4/9	.	PROSITE_profiles:PS51021,hmmpanther:PTHR10661:SF120,hmmpanther:PTHR10661,Pfam_domain:PF03114,Gene3D:1.20.1270.60,SMART_domains:SM00721,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAGGTGAAG	byFrequency	5	ESCA
CRTC3	0	.	GRCh37	15	91181743	91181743	+	Silent	SNP	G	G	A	rs781042347	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1332G>A	p.%3D	p.P444P	ENST00000268184	12/15	40	36	3	19	19	0	CRTC3,synonymous_variant,p.%3D,ENST00000268184,;CRTC3,synonymous_variant,p.%3D,ENST00000420329,;RP11-387D10.2,intron_variant,,ENST00000559531,;CRTC3,non_coding_transcript_exon_variant,,ENST00000558167,;HSPE1P3,downstream_gene_variant,,ENST00000559254,;	A	ENSG00000140577	ENST00000268184	Transcript	synonymous_variant	1336	1332	444	P	ccG/ccA	rs781042347,COSM4057900	.	.	1	CRTC3	HGNC	26148	protein_coding	YES	CCDS32331.1	ENSP00000268184	CRTC3_HUMAN	.	UPI00001FEB98	.	.	.	12/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13589,hmmpanther:PTHR13589:SF4	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TCGCCGCCACC	byFrequency	3	ESCA
CIITA	0	.	GRCh37	16	11001372	11001372	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2023C>T	p.%3D	p.L675L	ENST00000324288	11/20	18	8	10	14	14	0	CIITA,synonymous_variant,p.%3D,ENST00000324288,;CIITA,intron_variant,,ENST00000381835,;CIITA,intron_variant,,ENST00000537380,;CIITA,non_coding_transcript_exon_variant,,ENST00000573309,;CIITA,non_coding_transcript_exon_variant,,ENST00000570546,;CIITA,downstream_gene_variant,,ENST00000571186,;	T	ENSG00000179583	ENST00000324288	Transcript	synonymous_variant	2156	2023	675	L	Cta/Tta	.	.	.	1	CIITA	HGNC	7067	protein_coding	YES	CCDS10544.1	ENSP00000316328	C2TA_HUMAN	I3L2E5_HUMAN	UPI0000456914	.	.	.	11/20	.	PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF104,hmmpanther:PTHR24106,Prints_domain:PR01719	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACCCTACAG	.	5	ESCA
SPSB3	0	.	GRCh37	16	1827862	1827862	+	Missense_Mutation	SNP	G	G	A	rs756651857	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607C>T	p.His203Tyr	p.H203Y	ENST00000566339	6/7	62	41	20	57	57	0	SPSB3,missense_variant,p.His203Tyr,ENST00000301717,;SPSB3,missense_variant,p.His203Tyr,ENST00000566339,;MRPS34,upstream_gene_variant,,ENST00000397375,;SPSB3,downstream_gene_variant,,ENST00000569769,;MRPS34,upstream_gene_variant,,ENST00000177742,;EME2,downstream_gene_variant,,ENST00000568449,;EME2,downstream_gene_variant,,ENST00000307394,;SPSB3,non_coding_transcript_exon_variant,,ENST00000564709,;SPSB3,non_coding_transcript_exon_variant,,ENST00000563668,;SPSB3,non_coding_transcript_exon_variant,,ENST00000563741,;SPSB3,non_coding_transcript_exon_variant,,ENST00000563705,;EME2,non_coding_transcript_exon_variant,,ENST00000570069,;SPSB3,non_coding_transcript_exon_variant,,ENST00000567868,;SPSB3,non_coding_transcript_exon_variant,,ENST00000569380,;EME2,intron_variant,,ENST00000561903,;SPSB3,downstream_gene_variant,,ENST00000564070,;SPSB3,downstream_gene_variant,,ENST00000568416,;EME2,downstream_gene_variant,,ENST00000565326,;EME2,downstream_gene_variant,,ENST00000561564,;SPSB3,downstream_gene_variant,,ENST00000565550,;EME2,downstream_gene_variant,,ENST00000564182,;	A	ENSG00000162032	ENST00000566339	Transcript	missense_variant	938	607	203	H/Y	Cac/Tac	rs756651857	.	.	-1	SPSB3	HGNC	30629	protein_coding	YES	CCDS32365.1	ENSP00000457206	SPSB3_HUMAN	D3DU79_HUMAN,H3BP12_HUMAN	UPI000006FA20	.	deleterious(0)	probably_damaging(1)	6/7	.	PROSITE_profiles:PS50188,hmmpanther:PTHR12245:SF5,hmmpanther:PTHR12245,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTGGTGGA	.	5	ESCA
ECI1	0	.	GRCh37	16	2293218	2293218	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.571G>C	p.Asp191His	p.D191H	ENST00000301729	6/7	85	53	32	68	68	0	ECI1,missense_variant,p.Asp191His,ENST00000301729,;ECI1,missense_variant,p.Asp132His,ENST00000570258,;ECI1,missense_variant,p.Asp174His,ENST00000562238,;ECI1,missense_variant,p.Asp132His,ENST00000566379,;DNASE1L2,downstream_gene_variant,,ENST00000320700,;DNASE1L2,downstream_gene_variant,,ENST00000382437,;DNASE1L2,downstream_gene_variant,,ENST00000564065,;DNASE1L2,downstream_gene_variant,,ENST00000567494,;RP11-304L19.11,downstream_gene_variant,,ENST00000565709,;ECI1,non_coding_transcript_exon_variant,,ENST00000563447,;ECI1,non_coding_transcript_exon_variant,,ENST00000563029,;ECI1,downstream_gene_variant,,ENST00000561688,;	G	ENSG00000167969	ENST00000301729	Transcript	missense_variant	619	571	191	D/H	Gac/Cac	.	.	.	-1	ECI1	HGNC	2703	protein_coding	YES	CCDS10464.1	ENSP00000301729	ECI1_HUMAN	Q96DC0_HUMAN,H3BS70_HUMAN	UPI0000128DAE	.	deleterious(0)	probably_damaging(0.997)	6/7	.	hmmpanther:PTHR11941:SF55,hmmpanther:PTHR11941,Pfam_domain:PF00378,Gene3D:3.90.226.10,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGTCTTTCA	.	5	ESCA
UBN1	0	.	GRCh37	16	4932024	4932024	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1891C>A	.	.	ENST00000396658	17/17	48	37	11	57	57	0	UBN1,3_prime_UTR_variant,,ENST00000262376,;UBN1,3_prime_UTR_variant,,ENST00000545171,;UBN1,3_prime_UTR_variant,,ENST00000396658,;PPL,downstream_gene_variant,,ENST00000592772,;PPL,downstream_gene_variant,,ENST00000590782,;UBN1,downstream_gene_variant,,ENST00000590769,;PPL,downstream_gene_variant,,ENST00000345988,;UBN1,downstream_gene_variant,,ENST00000589191,;UBN1,downstream_gene_variant,,ENST00000586152,;	A	ENSG00000118900	ENST00000396658	Transcript	3_prime_UTR_variant	5999	.	.	.	.	.	.	.	1	UBN1	HGNC	12506	protein_coding	YES	CCDS10525.1	ENSP00000379894	UBN1_HUMAN	K7EQR1_HUMAN	UPI0000071469	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCCTCAGG	.	5	ESCA
NLRC5	0	.	GRCh37	16	57060578	57060581	+	Frame_Shift_Del	DEL	CCCT	CCCT	-	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	CCCT	CCCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1723_1726delCCCT	p.Pro575SerfsTer20	p.P575Sfs*20	ENST00000262510	6/49	15	7	8	33	33	0	NLRC5,frameshift_variant,p.Pro575SerfsTer20,ENST00000308149,;NLRC5,frameshift_variant,p.Pro328SerfsTer20,ENST00000538805,;NLRC5,frameshift_variant,p.Pro82SerfsTer20,ENST00000538110,;NLRC5,frameshift_variant,p.Pro575SerfsTer20,ENST00000539144,;NLRC5,frameshift_variant,p.Pro575SerfsTer20,ENST00000436936,;NLRC5,frameshift_variant,p.Pro575SerfsTer20,ENST00000262510,;NLRC5,upstream_gene_variant,,ENST00000543030,;NLRC5,frameshift_variant,p.Pro575SerfsTer20,ENST00000539881,;NLRC5,frameshift_variant,p.Pro303SerfsTer20,ENST00000545081,;NLRC5,non_coding_transcript_exon_variant,,ENST00000536231,;	-	ENSG00000140853	ENST00000262510	Transcript	frameshift_variant	1948-1951	1723-1726	575-576	PF/X	CCCTtc/tc	.	.	.	1	NLRC5	HGNC	29933	protein_coding	YES	CCDS10773.1	ENSP00000262510	NLRC5_HUMAN	F5H274_HUMAN,F5GYP0_HUMAN	UPI00001AEE94	.	.	.	6/49	.	hmmpanther:PTHR24106:SF69,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F576F|c.1728C>T|3	INDELOCATOR|VARSCANI	TGCCGCCCCTTCCTT	.	2	ESCA
WWP2	0	.	GRCh37	16	69974083	69974083	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*240G>A	.	.	ENST00000359154	24/24	32	25	7	28	28	0	WWP2,3_prime_UTR_variant,,ENST00000356003,;WWP2,3_prime_UTR_variant,,ENST00000448661,;WWP2,3_prime_UTR_variant,,ENST00000359154,;WWP2,3_prime_UTR_variant,,ENST00000568684,;WWP2,downstream_gene_variant,,ENST00000542271,;WWP2,non_coding_transcript_exon_variant,,ENST00000569297,;WWP2,downstream_gene_variant,,ENST00000544162,;WWP2,downstream_gene_variant,,ENST00000567303,;WWP2,downstream_gene_variant,,ENST00000566463,;WWP2,downstream_gene_variant,,ENST00000567161,;	A	ENSG00000198373	ENST00000359154	Transcript	3_prime_UTR_variant	2954	.	.	.	.	.	.	.	1	WWP2	HGNC	16804	protein_coding	YES	CCDS10885.1	ENSP00000352069	WWP2_HUMAN	H3BRX8_HUMAN,H3BPJ8_HUMAN,B4DHF6_HUMAN	UPI000006CD16	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAAGTTCCA	.	5	ESCA
ATXN1L	0	.	GRCh37	16	71887901	71887901	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2188G>A	.	.	ENST00000427980	3/3	20	12	8	21	21	0	ATXN1L,3_prime_UTR_variant,,ENST00000427980,;IST1,intron_variant,,ENST00000568581,;ATXN1L,intron_variant,,ENST00000569119,;	A	ENSG00000224470	ENST00000427980	Transcript	3_prime_UTR_variant	4551	.	.	.	.	.	.	.	1	ATXN1L	HGNC	33279	protein_coding	YES	CCDS45523.1	ENSP00000415822	ATX1L_HUMAN	G1UI23_HUMAN	UPI0000198982	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTGAGGAA	.	5	ESCA
TRIM16L	0	.	GRCh37	17	18638508	18638508	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.782C>T	p.Thr261Met	p.T261M	ENST00000449552	7/7	54	35	19	50	49	1	TRIM16L,missense_variant,p.Thr230Met,ENST00000574042,;TRIM16L,missense_variant,p.Thr261Met,ENST00000395671,;TRIM16L,missense_variant,p.Thr315Met,ENST00000395902,;TRIM16L,missense_variant,p.Thr261Met,ENST00000571708,;TRIM16L,missense_variant,p.Thr261Met,ENST00000395672,;TRIM16L,missense_variant,p.Thr261Met,ENST00000572555,;TRIM16L,missense_variant,p.Thr261Met,ENST00000449552,;TRIM16L,3_prime_UTR_variant,,ENST00000414850,;TRIM16L,downstream_gene_variant,,ENST00000424146,;TRIM16L,downstream_gene_variant,,ENST00000571542,;TRIM16L,downstream_gene_variant,,ENST00000573443,;TRIM16L,downstream_gene_variant,,ENST00000571733,;TRIM16L,downstream_gene_variant,,ENST00000577969,;	T	ENSG00000108448	ENST00000449552	Transcript	missense_variant	2266	782	261	T/M	aCg/aTg	COSM4064544,COSM4064545	.	.	1	TRIM16L	HGNC	32670	protein_coding	YES	CCDS32588.1	ENSP00000461386	TR16L_HUMAN	I3L3K9_HUMAN,I3L2F3_HUMAN,I3L1X9_HUMAN	UPI0000199A7B	.	deleterious(0)	possibly_damaging(0.671)	7/7	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF86,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCACGGCCT	.	5	ESCA
OR1D4	0	.	GRCh37	17	3144529	3144529	+	RNA	SNP	T	T	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.560T>C	.	.	ENST00000525719	1/1	27	12	15	23	23	0	OR1D4,non_coding_transcript_exon_variant,,ENST00000531680,;OR1D4,non_coding_transcript_exon_variant,,ENST00000525719,;	C	ENSG00000255095	ENST00000525719	Transcript	non_coding_transcript_exon_variant	560	.	.	.	.	.	.	.	1	OR1D4	HGNC	8185	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCTGGCAT	.	5	ESCA
KRTAP2-3	0	.	GRCh37	17	39216185	39216185	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118G>A	p.Val40Met	p.V40M	ENST00000391418	1/1	63	38	25	42	42	0	KRTAP2-3,missense_variant,p.Val40Met,ENST00000391418,;KRTAP2-2,upstream_gene_variant,,ENST00000542910,;KRTAP2-2,upstream_gene_variant,,ENST00000398477,;	T	ENSG00000212724	ENST00000391418	Transcript	missense_variant	160	118	40	V/M	Gtg/Atg	.	.	.	-1	KRTAP2-3	HGNC	18906	protein_coding	YES	CCDS54123.1	ENSP00000375237	KRA23_HUMAN	Q9BYS0_HUMAN	UPI000006EB3A	.	deleterious(0)	probably_damaging(0.997)	1/1	.	hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF6,Pfam_domain:PF01500	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GCACACGGTGG	.	3	ESCA
DHX8	0	.	GRCh37	17	41571170	41571170	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1128C>T	p.%3D	p.V376V	ENST00000262415	8/23	68	45	22	49	49	0	DHX8,synonymous_variant,p.%3D,ENST00000540306,;DHX8,synonymous_variant,p.%3D,ENST00000262415,;DHX8,downstream_gene_variant,,ENST00000605777,;DHX8,non_coding_transcript_exon_variant,,ENST00000587044,;DHX8,downstream_gene_variant,,ENST00000592258,;	T	ENSG00000067596	ENST00000262415	Transcript	synonymous_variant	1200	1128	376	V	gtC/gtT	.	.	.	1	DHX8	HGNC	2749	protein_coding	YES	CCDS11464.1	ENSP00000262415	DHX8_HUMAN	.	UPI00001290D9	.	.	.	8/23	.	hmmpanther:PTHR18934:SF85,hmmpanther:PTHR18934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTCAGTGC	.	5	ESCA
ZFP3	0	.	GRCh37	17	4996433	4996433	+	3'UTR	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*125C>A	.	.	ENST00000318833	2/2	75	51	24	66	66	0	ZFP3,3_prime_UTR_variant,,ENST00000318833,;	A	ENSG00000180787	ENST00000318833	Transcript	3_prime_UTR_variant	1970	.	.	.	.	.	.	.	1	ZFP3	HGNC	12861	protein_coding	YES	CCDS11067.1	ENSP00000320347	ZFP3_HUMAN	.	UPI0000070244	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCCACTGA	.	5	ESCA
RNF43	0	.	GRCh37	17	56432304	56432316	+	Frame_Shift_Del	DEL	TCACACAGCCTGT	TCACACAGCCTGT	-	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	TCACACAGCCTGT	TCACACAGCCTGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2340_2352delACAGGCTGTGTGA	p.Gln781Met	p.Q781M	ENST00000584437	9/9	42	29	13	24	24	0	RNF43,frameshift_variant,p.Gln781Met,ENST00000407977,;RNF43,frameshift_variant,p.Gln781Met,ENST00000584437,;RNF43,frameshift_variant,p.Gln740Met,ENST00000583753,;RNF43,frameshift_variant,p.Gln781Met,ENST00000577716,;RNF43,frameshift_variant,p.Gln740Met,ENST00000500597,;RNF43,frameshift_variant,p.Gln654Met,ENST00000577625,;SUPT4H1,upstream_gene_variant,,ENST00000580947,;SUPT4H1,upstream_gene_variant,,ENST00000577396,;SUPT4H1,upstream_gene_variant,,ENST00000581540,;RNF43,downstream_gene_variant,,ENST00000581868,;SUPT4H1,upstream_gene_variant,,ENST00000225504,;BZRAP1-AS1,intron_variant,,ENST00000583841,;BZRAP1-AS1,downstream_gene_variant,,ENST00000578334,;BZRAP1-AS1,downstream_gene_variant,,ENST00000583826,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580515,;BZRAP1-AS1,downstream_gene_variant,,ENST00000579527,;BZRAP1-AS1,downstream_gene_variant,,ENST00000578025,;BZRAP1-AS1,downstream_gene_variant,,ENST00000582348,;BZRAP1-AS1,downstream_gene_variant,,ENST00000585236,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580633,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580022,;BZRAP1-AS1,downstream_gene_variant,,ENST00000579859,;SUPT4H1,upstream_gene_variant,,ENST00000579289,;SUPT4H1,upstream_gene_variant,,ENST00000581166,;	-	ENSG00000108375	ENST00000584437	Transcript	frameshift_variant	4296-4308	2340-2352	780-784	EQAV*/X	gaACAGGCTGTGTGA/ga	.	.	.	-1	RNF43	HGNC	18505	protein_coding	YES	CCDS11607.1	ENSP00000463069	RNF43_HUMAN	.	UPI000022A469	.	.	.	9/9	.	hmmpanther:PTHR16200,hmmpanther:PTHR16200:SF2,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACATCTCACACAGCCTGTTCACA	.	2	ESCA
TBX2	0	.	GRCh37	17	59486690	59486690	+	3'UTR	SNP	A	A	G	rs539363382	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*823A>G	.	.	ENST00000240328	7/7	26	19	7	24	24	0	TBX2,3_prime_UTR_variant,,ENST00000240328,;C17orf82,upstream_gene_variant,,ENST00000335108,;RP11-332H18.4,intron_variant,,ENST00000592009,;TBX2,non_coding_transcript_exon_variant,,ENST00000586986,;TBX2,3_prime_UTR_variant,,ENST00000419047,;TBX2,downstream_gene_variant,,ENST00000477081,;	G	ENSG00000121068	ENST00000240328	Transcript	3_prime_UTR_variant	3243	.	.	.	.	rs539363382	.	.	1	TBX2	HGNC	11597	protein_coding	YES	CCDS11627.2	ENSP00000240328	TBX2_HUMAN	.	UPI000020116F	.	.	.	7/7	.	.	G:0.0004	G:0	G:0	.	G:0.002	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCGACCCCT	byFrequency|by1000G	5	ESCA
C17orf58	0	.	GRCh37	17	65989137	65989137	+	Intron	SNP	G	G	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103+23C>G	.	.	ENST00000449250	.	45	31	13	43	42	0	C17orf58,missense_variant,p.Asp42Glu,ENST00000334461,;C17orf58,missense_variant,p.Asp42Glu,ENST00000536693,;C17orf58,intron_variant,,ENST00000449250,;RP11-855A2.5,downstream_gene_variant,,ENST00000580729,;	C	ENSG00000186665	ENST00000449250	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	C17orf58	HGNC	27568	protein_coding	YES	CCDS45765.1	ENSP00000402020	CQ058_HUMAN	.	UPI0000160F31	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCAGCGTCATT	.	4	ESCA
SYNGR2	0	.	GRCh37	17	76168023	76168023	+	3'UTR	SNP	G	G	A	rs750367286	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6G>A	.	.	ENST00000225777	4/4	42	26	15	33	33	0	SYNGR2,missense_variant,p.Arg257Gln,ENST00000588282,;SYNGR2,splice_region_variant,,ENST00000585591,;SYNGR2,3_prime_UTR_variant,,ENST00000225777,;SYNGR2,3_prime_UTR_variant,,ENST00000589168,;SYNGR2,3_prime_UTR_variant,,ENST00000589711,;SYNGR2,3_prime_UTR_variant,,ENST00000590201,;TK1,downstream_gene_variant,,ENST00000590862,;TK1,downstream_gene_variant,,ENST00000586613,;TK1,downstream_gene_variant,,ENST00000590430,;TK1,downstream_gene_variant,,ENST00000405273,;TK1,downstream_gene_variant,,ENST00000301634,;TK1,downstream_gene_variant,,ENST00000588734,;SYNGR2,non_coding_transcript_exon_variant,,ENST00000592456,;SYNGR2,3_prime_UTR_variant,,ENST00000589183,;SYNGR2,downstream_gene_variant,,ENST00000591770,;TK1,downstream_gene_variant,,ENST00000592126,;	A	ENSG00000108639	ENST00000225777	Transcript	3_prime_UTR_variant	740	.	.	.	.	rs750367286	.	.	1	SYNGR2	HGNC	11499	protein_coding	YES	CCDS11753.1	ENSP00000225777	SNG2_HUMAN	K7EJ35_HUMAN	UPI00000012DD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGCGGTTAG	byFrequency	5	ESCA
CYTH1	0	.	GRCh37	17	76672223	76672223	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147G>A	p.Glu383Lys	p.E383K	ENST00000361101	13/13	35	24	11	22	22	0	CYTH1,missense_variant,p.Glu383Lys,ENST00000361101,;CYTH1,missense_variant,p.Glu324Lys,ENST00000589297,;CYTH1,missense_variant,p.Glu383Lys,ENST00000446868,;CYTH1,missense_variant,p.Glu382Lys,ENST00000591455,;CYTH1,missense_variant,p.Glu324Lys,ENST00000585509,;CYTH1,intron_variant,,ENST00000589296,;CYTH1,non_coding_transcript_exon_variant,,ENST00000586175,;CYTH1,non_coding_transcript_exon_variant,,ENST00000590775,;CYTH1,3_prime_UTR_variant,,ENST00000591574,;CYTH1,non_coding_transcript_exon_variant,,ENST00000586299,;CYTH1,non_coding_transcript_exon_variant,,ENST00000586430,;	T	ENSG00000108669	ENST00000361101	Transcript	missense_variant	1218	1147	383	E/K	Gaa/Aaa	COSM1710857	.	.	-1	CYTH1	HGNC	9501	protein_coding	YES	CCDS42392.2	ENSP00000354398	CYH1_HUMAN	K7ENH6_HUMAN,K7EKA2_HUMAN,B7Z1T4_HUMAN	UPI000000009A	.	deleterious(0)	benign(0.195)	13/13	.	hmmpanther:PTHR10663:SF113,hmmpanther:PTHR10663	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTCGTAGA	.	5	ESCA
RTTN	0	.	GRCh37	18	67869157	67869157	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460C>A	p.Gln154Lys	p.Q154K	ENST00000255674	4/49	66	38	27	68	68	0	RTTN,missense_variant,p.Gln154Lys,ENST00000255674,;RTTN,missense_variant,p.Gln154Lys,ENST00000454359,;RTTN,missense_variant,p.Gln154Lys,ENST00000437017,;RTTN,missense_variant,p.Gln154Lys,ENST00000581161,;RTTN,non_coding_transcript_exon_variant,,ENST00000581583,;RTTN,upstream_gene_variant,,ENST00000583043,;	T	ENSG00000176225	ENST00000255674	Transcript	missense_variant	747	460	154	Q/K	Cag/Aag	.	.	.	-1	RTTN	HGNC	18654	protein_coding	YES	CCDS42443.1	ENSP00000255674	RTTN_HUMAN	.	UPI0000201E92	.	tolerated(0.07)	benign(0.195)	4/49	.	hmmpanther:PTHR31691:SF1,hmmpanther:PTHR31691	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTGCTGGA	.	5	ESCA
ADNP2	0	.	GRCh37	18	77895502	77895502	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2206G>C	p.Ala736Pro	p.A736P	ENST00000262198	4/4	45	35	10	38	38	0	ADNP2,missense_variant,p.Ala736Pro,ENST00000262198,;ADNP2,intron_variant,,ENST00000561195,;ADNP2,downstream_gene_variant,,ENST00000559951,;ADNP2,downstream_gene_variant,,ENST00000560561,;ADNP2,downstream_gene_variant,,ENST00000560752,;	C	ENSG00000101544	ENST00000262198	Transcript	missense_variant	2661	2206	736	A/P	Gca/Cca	.	.	.	1	ADNP2	HGNC	23803	protein_coding	YES	CCDS32853.1	ENSP00000262198	ADNP2_HUMAN	H0YLN6_HUMAN	UPI0000071DEA	.	deleterious(0)	probably_damaging(0.999)	4/4	.	hmmpanther:PTHR15740:SF2,hmmpanther:PTHR15740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGTGTGCACCA	.	4	ESCA
SMARCA4	0	.	GRCh37	19	11132513	11132513	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2729C>T	p.Thr910Met	p.T910M	ENST00000429416	20/36	34	25	9	28	28	0	SMARCA4,missense_variant,p.Thr910Met,ENST00000450717,;SMARCA4,missense_variant,p.Thr910Met,ENST00000358026,;SMARCA4,missense_variant,p.Thr910Met,ENST00000413806,;SMARCA4,missense_variant,p.Thr910Met,ENST00000590574,;SMARCA4,missense_variant,p.Thr910Met,ENST00000444061,;SMARCA4,missense_variant,p.Thr910Met,ENST00000344626,;SMARCA4,missense_variant,p.Thr910Met,ENST00000541122,;SMARCA4,missense_variant,p.Thr910Met,ENST00000429416,;SMARCA4,missense_variant,p.Thr910Met,ENST00000589677,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586122,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000587988,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;	T	ENSG00000127616	ENST00000429416	Transcript	missense_variant	3010	2729	910	T/M	aCg/aTg	COSM88025,COSM1226753	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	probably_damaging(0.99)	20/36	.	Superfamily_domains:SSF52540,SMART_domains:SM00487,Pfam_domain:PF00176,Gene3D:3.40.50.300,hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.T910M|c.2729C>T|13,SITE|p.T910M|c.2729C>T|7	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGACGGGCA	.	5	ESCA
APC2	0	.	GRCh37	19	1457140	1457140	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1105C>G	p.Arg369Gly	p.R369G	ENST00000535453	8/14	9	5	4	16	16	0	APC2,missense_variant,p.Arg369Gly,ENST00000233607,;APC2,missense_variant,p.Arg369Gly,ENST00000590469,;APC2,missense_variant,p.Arg369Gly,ENST00000535453,;APC2,intron_variant,,ENST00000238483,;APC2,downstream_gene_variant,,ENST00000587149,;C19orf25,downstream_gene_variant,,ENST00000588427,;APC2,downstream_gene_variant,,ENST00000587869,;APC2,downstream_gene_variant,,ENST00000590877,;CTB-25B13.12,downstream_gene_variant,,ENST00000588225,;APC2,non_coding_transcript_exon_variant,,ENST00000593146,;CTB-25B13.12,downstream_gene_variant,,ENST00000591252,;	G	ENSG00000115266	ENST00000535453	Transcript	missense_variant	2818	1105	369	R/G	Cgc/Ggc	.	.	.	1	APC2	HGNC	24036	protein_coding	YES	CCDS12068.1	ENSP00000442954	APC2_HUMAN	K7ELQ3_HUMAN,K7EN62_HUMAN	UPI0000073D85	.	.	probably_damaging(0.999)	8/14	.	Superfamily_domains:SSF48371,hmmpanther:PTHR12607:SF3,hmmpanther:PTHR12607	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AGATGCGCGTC	.	2	ESCA
NOTCH3	0	.	GRCh37	19	15281251	15281251	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5005C>T	p.Arg1669Cys	p.R1669C	ENST00000263388	27/33	31	18	12	23	23	0	NOTCH3,missense_variant,p.Arg1669Cys,ENST00000263388,;NOTCH3,upstream_gene_variant,,ENST00000597756,;NOTCH3,upstream_gene_variant,,ENST00000595514,;	A	ENSG00000074181	ENST00000263388	Transcript	missense_variant	5081	5005	1669	R/C	Cgc/Tgc	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	deleterious(0)	probably_damaging(0.999)	27/33	.	PIRSF_domain:PIRSF002279,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.R1669R|c.5007C>T|3,CODON|p.R1669R|c.5007C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGCGCTTGC	.	5	ESCA
RYR1	0	.	GRCh37	19	39028578	39028578	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11667G>T	p.Leu3889Phe	p.L3889F	ENST00000359596	84/106	57	36	20	40	40	0	RYR1,missense_variant,p.Leu3884Phe,ENST00000355481,;RYR1,missense_variant,p.Leu3889Phe,ENST00000359596,;RYR1,missense_variant,p.Leu3884Phe,ENST00000360985,;RYR1,missense_variant,p.Leu126Phe,ENST00000596431,;RYR1,downstream_gene_variant,,ENST00000599547,;RYR1,downstream_gene_variant,,ENST00000601514,;AC067969.2,upstream_gene_variant,,ENST00000595853,;RYR1,3_prime_UTR_variant,,ENST00000593322,;RYR1,3_prime_UTR_variant,,ENST00000594335,;	T	ENSG00000196218	ENST00000359596	Transcript	missense_variant	11667	11667	3889	L/F	ttG/ttT	.	.	.	1	RYR1	HGNC	10483	protein_coding	YES	CCDS33011.1	ENSP00000352608	RYR1_HUMAN	O75591_HUMAN,B4DET7_HUMAN	UPI0000D7E62F	.	.	possibly_damaging(0.667)	84/106	.	hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF08454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATTGCTCTG	.	5	ESCA
C2CD4C	0	.	GRCh37	19	407400	407400	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.962G>A	p.Arg321His	p.R321H	ENST00000332235	2/2	10	6	4	15	15	0	C2CD4C,missense_variant,p.Arg321His,ENST00000332235,;	T	ENSG00000183186	ENST00000332235	Transcript	missense_variant	1136	962	321	R/H	cGc/cAc	.	.	.	-1	C2CD4C	HGNC	29417	protein_coding	YES	CCDS45890.1	ENSP00000328677	C2C4C_HUMAN	.	UPI00001C2016	.	deleterious(0)	probably_damaging(0.994)	2/2	.	PROSITE_profiles:PS50004,hmmpanther:PTHR10024:SF116,hmmpanther:PTHR10024,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCAGGCGGGCC	.	3	ESCA
FSD1	0	.	GRCh37	19	4323073	4323073	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1130G>T	p.Ser377Ile	p.S377I	ENST00000221856	11/13	54	39	14	53	53	0	FSD1,missense_variant,p.Ser60Ile,ENST00000601006,;FSD1,missense_variant,p.Ser15Ile,ENST00000594438,;FSD1,missense_variant,p.Ser377Ile,ENST00000597590,;FSD1,missense_variant,p.Ser377Ile,ENST00000221856,;FSD1,intron_variant,,ENST00000597480,;STAP2,downstream_gene_variant,,ENST00000594605,;STAP2,downstream_gene_variant,,ENST00000601956,;STAP2,downstream_gene_variant,,ENST00000600324,;STAP2,downstream_gene_variant,,ENST00000601482,;STAP2,downstream_gene_variant,,ENST00000598443,;STAP2,downstream_gene_variant,,ENST00000597593,;FSD1,downstream_gene_variant,,ENST00000598010,;FSD1,non_coding_transcript_exon_variant,,ENST00000598179,;STAP2,downstream_gene_variant,,ENST00000596242,;STAP2,downstream_gene_variant,,ENST00000599736,;STAP2,downstream_gene_variant,,ENST00000602007,;STAP2,downstream_gene_variant,,ENST00000601179,;	T	ENSG00000105255	ENST00000221856	Transcript	missense_variant	1277	1130	377	S/I	aGc/aTc	.	.	.	1	FSD1	HGNC	13745	protein_coding	YES	CCDS12127.1	ENSP00000221856	FSD1_HUMAN	.	UPI000007168A	.	deleterious(0)	possibly_damaging(0.548)	11/13	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24099,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCAGCCTGG	.	5	ESCA
XRCC1	0	.	GRCh37	19	44058864	44058864	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348G>A	p.%3D	p.L116L	ENST00000262887	4/17	57	36	21	59	59	0	XRCC1,synonymous_variant,p.%3D,ENST00000594107,;XRCC1,synonymous_variant,p.%3D,ENST00000599693,;L34079.2,synonymous_variant,p.%3D,ENST00000594374,;XRCC1,synonymous_variant,p.%3D,ENST00000262887,;XRCC1,synonymous_variant,p.%3D,ENST00000543982,;XRCC1,synonymous_variant,p.%3D,ENST00000598165,;L34079.3,intron_variant,,ENST00000597119,;XRCC1,synonymous_variant,p.%3D,ENST00000597811,;XRCC1,non_coding_transcript_exon_variant,,ENST00000595789,;XRCC1,upstream_gene_variant,,ENST00000598422,;	T	ENSG00000073050	ENST00000262887	Transcript	synonymous_variant	896	348	116	L	ctG/ctA	.	.	.	-1	XRCC1	HGNC	12828	protein_coding	YES	CCDS12624.1	ENSP00000262887	XRCC1_HUMAN	M4WFF9_HUMAN	UPI000013D351	.	.	.	4/17	.	hmmpanther:PTHR11370,hmmpanther:PTHR11370:SF1,Gene3D:2.60.120.260,Pfam_domain:PF01834,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGACCAGCTT	.	5	ESCA
GEMIN7	0	.	GRCh37	19	45593410	45593410	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38G>A	p.Arg13Gln	p.R13Q	ENST00000270257	3/3	80	47	33	80	80	0	GEMIN7,missense_variant,p.Arg13Gln,ENST00000591747,;GEMIN7,missense_variant,p.Arg13Gln,ENST00000591607,;GEMIN7,missense_variant,p.Arg13Gln,ENST00000270257,;GEMIN7,missense_variant,p.Arg13Gln,ENST00000391951,;MARK4,intron_variant,,ENST00000587566,;PPP1R37,upstream_gene_variant,,ENST00000544069,;PPP1R37,upstream_gene_variant,,ENST00000221462,;PPP1R37,upstream_gene_variant,,ENST00000421905,;CTB-179K24.3,non_coding_transcript_exon_variant,,ENST00000586744,;CTB-179K24.3,non_coding_transcript_exon_variant,,ENST00000586556,;PPP1R37,upstream_gene_variant,,ENST00000496125,;PPP1R37,upstream_gene_variant,,ENST00000542809,;PPP1R37,upstream_gene_variant,,ENST00000593240,;GEMIN7,downstream_gene_variant,,ENST00000592351,;	A	ENSG00000142252	ENST00000270257	Transcript	missense_variant	285	38	13	R/Q	cGg/cAg	.	.	.	1	GEMIN7	HGNC	20045	protein_coding	YES	CCDS12654.1	ENSP00000270257	GEMI7_HUMAN	.	UPI000006E0B4	.	tolerated(0.06)	benign(0.018)	3/3	.	hmmpanther:PTHR14679	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCGGCTGC	.	5	ESCA
CCDC9	0	.	GRCh37	19	47761647	47761647	+	5'UTR	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11C>A	.	.	ENST00000221922	2/12	44	27	16	40	40	0	CCDC9,5_prime_UTR_variant,,ENST00000595659,;CCDC9,5_prime_UTR_variant,,ENST00000596938,;CCDC9,5_prime_UTR_variant,,ENST00000599398,;CCDC9,5_prime_UTR_variant,,ENST00000221922,;CCDC9,downstream_gene_variant,,ENST00000601154,;	A	ENSG00000105321	ENST00000221922	Transcript	5_prime_UTR_variant	212	.	.	.	.	.	.	.	1	CCDC9	HGNC	24560	protein_coding	YES	CCDS12698.1	ENSP00000221922	CCDC9_HUMAN	M0R2W0_HUMAN,M0QZR0_HUMAN,M0QYB4_HUMAN	UPI0000073E41	.	.	.	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACGCAGCCA	.	5	ESCA
SSC5D	0	.	GRCh37	19	56012123	56012123	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2569G>T	p.Gly857Trp	p.G857W	ENST00000389623	11/14	37	18	19	34	34	0	SSC5D,missense_variant,p.Gly857Trp,ENST00000389623,;SSC5D,missense_variant,p.Gly857Trp,ENST00000587166,;SSC5D,downstream_gene_variant,,ENST00000589020,;	T	ENSG00000179954	ENST00000389623	Transcript	missense_variant	2592	2569	857	G/W	Ggg/Tgg	.	.	.	1	SSC5D	HGNC	26641	protein_coding	YES	CCDS46196.1	ENSP00000374274	SRCRL_HUMAN	M0QZ17_HUMAN	UPI000192952A	.	.	probably_damaging(1)	11/14	.	PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF21,Pfam_domain:PF00530,Gene3D:3.10.250.10,SMART_domains:SM00202,Superfamily_domains:SSF56487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGGGGGAAG	.	5	ESCA
ZNF581	0	.	GRCh37	19	56156448	56156448	+	Missense_Mutation	SNP	C	C	T	rs201594382	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.511C>T	p.Arg171Cys	p.R171C	ENST00000587252	2/2	100	72	28	73	73	0	ZNF581,missense_variant,p.Arg171Cys,ENST00000588537,;ZNF581,missense_variant,p.Arg171Cys,ENST00000270451,;ZNF581,missense_variant,p.Arg171Cys,ENST00000587252,;CCDC106,intron_variant,,ENST00000592996,;ZNF580,downstream_gene_variant,,ENST00000592881,;ZNF580,downstream_gene_variant,,ENST00000325333,;CCDC106,upstream_gene_variant,,ENST00000591241,;ZNF580,downstream_gene_variant,,ENST00000592461,;ZNF580,downstream_gene_variant,,ENST00000545125,;ZNF580,downstream_gene_variant,,ENST00000543039,;CCDC106,upstream_gene_variant,,ENST00000308964,;CCDC106,upstream_gene_variant,,ENST00000591578,;CCDC106,upstream_gene_variant,,ENST00000588740,;ZNF581,downstream_gene_variant,,ENST00000585995,;ZNF580,downstream_gene_variant,,ENST00000590190,;CCDC106,upstream_gene_variant,,ENST00000586790,;CCDC106,upstream_gene_variant,,ENST00000593069,;CCDC106,upstream_gene_variant,,ENST00000587213,;CCDC106,upstream_gene_variant,,ENST00000586864,;	T	ENSG00000171425	ENST00000587252	Transcript	missense_variant	784	511	171	R/C	Cgc/Tgc	rs201594382,COSM1234302	.	.	1	ZNF581	HGNC	25017	protein_coding	YES	CCDS12932.1	ENSP00000466047	ZN581_HUMAN	K7EM32_HUMAN	UPI0000070E84	.	deleterious(0)	probably_damaging(0.997)	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF110,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAACGCCCG	byCluster	5	ESCA
ZNF667	0	.	GRCh37	19	56952917	56952917	+	Silent	SNP	G	G	T	rs776553770	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1447C>A	p.%3D	p.R483R	ENST00000504904	7/7	61	42	18	34	34	0	ZNF667,synonymous_variant,p.%3D,ENST00000342634,;ZNF667,synonymous_variant,p.%3D,ENST00000292069,;ZNF667,synonymous_variant,p.%3D,ENST00000504904,;ZNF667,3_prime_UTR_variant,,ENST00000591790,;ZNF667,downstream_gene_variant,,ENST00000587555,;ZNF667,3_prime_UTR_variant,,ENST00000592189,;	T	ENSG00000198046	ENST00000504904	Transcript	synonymous_variant	2167	1447	483	R	Cga/Aga	rs776553770	.	.	-1	ZNF667	HGNC	28854	protein_coding	YES	CCDS12944.1	ENSP00000439402	ZN667_HUMAN	K7ERY5_HUMAN,K7EIE0_HUMAN	UPI0000202CEE	.	.	.	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTCGGTGGC	.	5	ESCA
ZNF134	0	.	GRCh37	19	58132263	58132263	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.776C>T	p.Pro259Leu	p.P259L	ENST00000396161	3/3	40	25	14	28	28	0	ZNF134,missense_variant,p.Pro259Leu,ENST00000396161,;ZNF134,downstream_gene_variant,,ENST00000600883,;ZNF134,downstream_gene_variant,,ENST00000600344,;AC003682.16,upstream_gene_variant,,ENST00000599190,;ZNF134,downstream_gene_variant,,ENST00000597975,;	T	ENSG00000213762	ENST00000396161	Transcript	missense_variant	1086	776	259	P/L	cCt/cTt	.	.	.	1	ZNF134	HGNC	12918	protein_coding	YES	CCDS42638.1	ENSP00000379464	ZN134_HUMAN	M0QXC7_HUMAN	UPI0000071FFE	.	deleterious(0.01)	probably_damaging(1)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24399:SF4,hmmpanther:PTHR24399,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AATGCCTTATA	.	4	ESCA
CELF3	0	.	GRCh37	1	151689182	151689182	+	5'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-686C>T	.	.	ENST00000290583	1/13	15	10	5	19	19	0	CELF3,5_prime_UTR_variant,,ENST00000290583,;CELF3,intron_variant,,ENST00000420342,;RIIAD1,intron_variant,,ENST00000326413,;AL589765.1,intron_variant,,ENST00000442233,;RIIAD1,upstream_gene_variant,,ENST00000479191,;CELF3,upstream_gene_variant,,ENST00000290585,;CELF3,intron_variant,,ENST00000478829,;CELF3,upstream_gene_variant,,ENST00000479893,;	A	ENSG00000159409	ENST00000290583	Transcript	5_prime_UTR_variant	109	.	.	.	.	.	.	.	-1	CELF3	HGNC	11967	protein_coding	YES	CCDS1002.1	ENSP00000290583	CELF3_HUMAN	Q8IZ97_HUMAN	UPI000013F059	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCTGGGCTGCT	.	3	ESCA
TDRKH	0	.	GRCh37	1	151748932	151748932	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027C>A	p.His343Asn	p.H343N	ENST00000368822	7/14	47	31	16	36	36	0	TDRKH,missense_variant,p.His343Asn,ENST00000368827,;TDRKH,missense_variant,p.His339Asn,ENST00000368823,;TDRKH,missense_variant,p.His119Asn,ENST00000440583,;TDRKH,missense_variant,p.His343Asn,ENST00000368824,;TDRKH,missense_variant,p.His343Asn,ENST00000458431,;TDRKH,missense_variant,p.His343Asn,ENST00000368822,;TDRKH,missense_variant,p.His298Asn,ENST00000368825,;TDRKH,downstream_gene_variant,,ENST00000526378,;TDRKH,downstream_gene_variant,,ENST00000484421,;TDRKH,3_prime_UTR_variant,,ENST00000525790,;TDRKH,3_prime_UTR_variant,,ENST00000526413,;TDRKH,downstream_gene_variant,,ENST00000530202,;TDRKH,downstream_gene_variant,,ENST00000494725,;TDRKH,downstream_gene_variant,,ENST00000486986,;	T	ENSG00000182134	ENST00000368822	Transcript	missense_variant	1661	1027	343	H/N	Cac/Aac	.	.	.	-1	TDRKH	HGNC	11713	protein_coding	YES	CCDS41394.1	ENSP00000357812	TDRKH_HUMAN	Q9NYV3_HUMAN,E9PKN8_HUMAN,B4DJ68_HUMAN	UPI0000204267	.	tolerated(0.11)	possibly_damaging(0.723)	7/14	.	hmmpanther:PTHR22948:SF13,hmmpanther:PTHR22948,Pfam_domain:PF00567,Gene3D:2.30.30.140,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGTGCTGGG	.	5	ESCA
ARID1A	0	.	GRCh37	1	27097621	27097622	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3216dupA	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	12/20	71	53	18	50	50	0	ARID1A,frameshift_variant,p.Trp1073MetfsTer32,ENST00000457599,;ARID1A,frameshift_variant,p.Trp1073MetfsTer32,ENST00000324856,;ARID1A,frameshift_variant,p.Trp690MetfsTer32,ENST00000374152,;ARID1A,upstream_gene_variant,,ENST00000540690,;ARID1A,upstream_gene_variant,,ENST00000430799,;ARID1A,upstream_gene_variant,,ENST00000466382,;ARID1A,downstream_gene_variant,,ENST00000430291,;ARID1A,upstream_gene_variant,,ENST00000532781,;	A	ENSG00000117713	ENST00000324856	Transcript	frameshift_variant	3581-3582	3210-3211	1070-1071	-/X	-/A	.	.	.	1	ARID1A	HGNC	11110	protein_coding	YES	CCDS285.1	ENSP00000320485	ARI1A_HUMAN	Q96T01_HUMAN,Q96SY8_HUMAN,Q96SM7_HUMAN,E9PQW6_HUMAN,C1KEN7_HUMAN,A4FU79_HUMAN	UPI0000167B91	.	.	.	12/20	.	PROSITE_profiles:PS51011,hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12,Pfam_domain:PF01388,Gene3D:1.10.150.60,SMART_domains:SM01014,SMART_domains:SM00501,Superfamily_domains:SSF46774	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGAACAAAAA	.	3	ESCA
DFFB	0	.	GRCh37	1	3782553	3782553	+	Missense_Mutation	SNP	C	C	T	rs773522402	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.419C>T	p.Pro140Leu	p.P140L	ENST00000378209	3/7	122	78	44	125	125	0	DFFB,missense_variant,p.Pro140Leu,ENST00000378209,;DFFB,missense_variant,p.Pro140Leu,ENST00000338895,;DFFB,downstream_gene_variant,,ENST00000378212,;DFFB,missense_variant,p.Pro140Leu,ENST00000491998,;DFFB,3_prime_UTR_variant,,ENST00000477548,;DFFB,3_prime_UTR_variant,,ENST00000475969,;DFFB,3_prime_UTR_variant,,ENST00000378206,;DFFB,3_prime_UTR_variant,,ENST00000468793,;DFFB,3_prime_UTR_variant,,ENST00000339350,;DFFB,upstream_gene_variant,,ENST00000481945,;	T	ENSG00000169598	ENST00000378209	Transcript	missense_variant	742	419	140	P/L	cCg/cTg	rs773522402	.	.	1	DFFB	HGNC	2773	protein_coding	YES	CCDS52.1	ENSP00000367454	DFFB_HUMAN	Q96P72_HUMAN	UPI000006230F	.	tolerated(0.13)	benign(0.02)	3/7	.	Superfamily_domains:SSF54060,Pfam_domain:PF09230,hmmpanther:PTHR13067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGCCGTGGT	byFrequency	5	ESCA
ZC3H12A	0	.	GRCh37	1	37947279	37947279	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.661G>T	p.Val221Leu	p.V221L	ENST00000373087	4/6	42	23	19	47	47	0	ZC3H12A,missense_variant,p.Val221Leu,ENST00000373087,;ZC3H12A,upstream_gene_variant,,ENST00000471012,;ZC3H12A,non_coding_transcript_exon_variant,,ENST00000472312,;	T	ENSG00000163874	ENST00000373087	Transcript	missense_variant	777	661	221	V/L	Gtg/Ttg	.	.	.	1	ZC3H12A	HGNC	26259	protein_coding	YES	CCDS417.1	ENSP00000362179	ZC12A_HUMAN	C0LED9_HUMAN	UPI000004D30E	.	deleterious(0.03)	possibly_damaging(0.9)	4/6	.	Pfam_domain:PF11977,hmmpanther:PTHR12876:SF10,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCGGGTGGTG	.	5	ESCA
ZNF644	0	.	GRCh37	1	91381005	91381005	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1350C>A	.	.	ENST00000370440	6/6	51	40	11	49	49	0	ZNF644,3_prime_UTR_variant,,ENST00000347275,;ZNF644,3_prime_UTR_variant,,ENST00000370440,;ZNF644,3_prime_UTR_variant,,ENST00000337393,;ZNF644,downstream_gene_variant,,ENST00000361321,;ZNF644,downstream_gene_variant,,ENST00000482709,;ZNF644,downstream_gene_variant,,ENST00000479798,;ZNF644,downstream_gene_variant,,ENST00000467231,;	T	ENSG00000122482	ENST00000370440	Transcript	3_prime_UTR_variant	5552	.	.	.	.	.	.	.	-1	ZNF644	HGNC	29222	protein_coding	YES	CCDS731.1	ENSP00000359469	ZN644_HUMAN	Q9NVH8_HUMAN,Q9H8J8_HUMAN,Q8NEI6_HUMAN	UPI000004A010	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGAAGCAAAG	.	5	ESCA
TOP1	0	.	GRCh37	20	39709878	39709880	+	In_Frame_Del	DEL	GAG	GAG	-	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	GAG	GAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.506_507+1delAGG	.	.	ENST00000361337	7/21	29	21	8	43	43	0	TOP1,inframe_deletion,,ENST00000361337,;	-	ENSG00000198900	ENST00000361337	Transcript	inframe_deletion	755-757	505-507	169	E/-	GAG/-	.	.	.	1	TOP1	HGNC	11986	protein_coding	YES	CCDS13312.1	ENSP00000354522	TOP1_HUMAN	Q9BVT2_HUMAN	UPI000004F0B1	.	.	.	7/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10290,hmmpanther:PTHR10290:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAGAAGAGGTTAG	.	3	ESCA
SLC5A3	0	.	GRCh37	21	35478299	35478299	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8645A>G	.	.	ENST00000608209	2/2	59	56	3	59	59	0	SLC5A3,3_prime_UTR_variant,,ENST00000608209,;SLC5A3,3_prime_UTR_variant,,ENST00000381151,;MRPS6,intron_variant,,ENST00000399312,;MRPS6,intron_variant,,ENST00000477091,;MRPS6,intron_variant,,ENST00000488492,;AP000320.7,intron_variant,,ENST00000362077,;	G	ENSG00000272962	ENST00000608209	Transcript	3_prime_UTR_variant	11314	.	.	.	.	.	.	.	1	SLC5A3	Uniprot_gn	11038	protein_coding	YES	CCDS33549.1	ENSP00000477068	.	.	UPI00001359F3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTTAAAAAA	.	2	ESCA
TRAPPC10	0	.	GRCh37	21	45524557	45524557	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1145G>T	.	.	ENST00000291574	23/23	42	35	7	43	43	0	TRAPPC10,3_prime_UTR_variant,,ENST00000291574,;PWP2,upstream_gene_variant,,ENST00000456705,;PWP2,upstream_gene_variant,,ENST00000291576,;TRAPPC10,3_prime_UTR_variant,,ENST00000422875,;TRAPPC10,non_coding_transcript_exon_variant,,ENST00000459741,;TRAPPC10,non_coding_transcript_exon_variant,,ENST00000468864,;	T	ENSG00000160218	ENST00000291574	Transcript	3_prime_UTR_variant	5100	.	.	.	.	.	.	.	1	TRAPPC10	HGNC	11868	protein_coding	YES	CCDS13704.1	ENSP00000291574	TPC10_HUMAN	Q76NH5_HUMAN	UPI0000129E26	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGTGAAAGT	.	5	ESCA
SH3BP1	0	.	GRCh37	22	38051980	38051980	+	3'UTR	SNP	G	G	A	rs766207269	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*289G>A	.	.	ENST00000357436	18/18	71	50	21	69	69	0	SH3BP1,3_prime_UTR_variant,,ENST00000357436,;SH3BP1,intron_variant,,ENST00000599616,;PDXP,upstream_gene_variant,,ENST00000215904,;Z83844.1,intron_variant,,ENST00000456099,;SH3BP1,3_prime_UTR_variant,,ENST00000417536,;SH3BP1,non_coding_transcript_exon_variant,,ENST00000469947,;SH3BP1,intron_variant,,ENST00000451997,;	A	ENSG00000100092	ENST00000357436	Transcript	3_prime_UTR_variant	2708	.	.	.	.	rs766207269	.	.	1	SH3BP1	HGNC	10824	protein_coding	YES	CCDS13952.2	ENSP00000350018	3BP1_HUMAN	F8WEQ3_HUMAN	UPI000004EE00	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTACGGGACT	byFrequency	5	ESCA
PKP4	0	.	GRCh37	2	159488428	159488428	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1317G>A	p.%3D	p.Q439Q	ENST00000389759	8/22	63	42	20	33	33	0	PKP4,synonymous_variant,p.%3D,ENST00000389759,;PKP4,synonymous_variant,p.%3D,ENST00000389757,;PKP4,upstream_gene_variant,,ENST00000494945,;PKP4,3_prime_UTR_variant,,ENST00000426248,;PKP4,3_prime_UTR_variant,,ENST00000481115,;PKP4,3_prime_UTR_variant,,ENST00000452162,;PKP4,3_prime_UTR_variant,,ENST00000421462,;	A	ENSG00000144283	ENST00000389759	Transcript	synonymous_variant	1429	1317	439	Q	caG/caA	.	.	.	1	PKP4	HGNC	9026	protein_coding	YES	CCDS33305.1	ENSP00000374409	PKP4_HUMAN	Q53TM5_HUMAN	UPI000044D379	.	.	.	8/22	.	hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCAGACGGC	.	5	ESCA
NHEJ1	0	.	GRCh37	2	219940992	219940992	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*111G>A	.	.	ENST00000356853	8/8	25	17	8	17	17	0	NHEJ1,3_prime_UTR_variant,,ENST00000356853,;NHEJ1,3_prime_UTR_variant,,ENST00000409720,;NHEJ1,downstream_gene_variant,,ENST00000426304,;NHEJ1,downstream_gene_variant,,ENST00000457600,;NHEJ1,downstream_gene_variant,,ENST00000491159,;NHEJ1,downstream_gene_variant,,ENST00000494211,;NHEJ1,downstream_gene_variant,,ENST00000483627,;NHEJ1,3_prime_UTR_variant,,ENST00000418099,;SLC23A3,3_prime_UTR_variant,,ENST00000318673,;SLC23A3,non_coding_transcript_exon_variant,,ENST00000498327,;	T	ENSG00000187736	ENST00000356853	Transcript	3_prime_UTR_variant	1145	.	.	.	.	.	.	.	-1	NHEJ1	HGNC	25737	protein_coding	YES	CCDS2432.1	ENSP00000349313	NHEJ1_HUMAN	C9JWV4_HUMAN	UPI000006D9F7	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGCCTCTG	.	5	ESCA
HDLBP	0	.	GRCh37	2	242170211	242170211	+	Missense_Mutation	SNP	C	C	T	rs768699303	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3437G>A	p.Arg1146His	p.R1146H	ENST00000391975	25/28	50	42	8	56	56	0	HDLBP,missense_variant,p.Arg1146His,ENST00000310931,;HDLBP,missense_variant,p.Arg1113His,ENST00000427183,;HDLBP,missense_variant,p.Arg10His,ENST00000442730,;HDLBP,missense_variant,p.Arg1146His,ENST00000391976,;HDLBP,missense_variant,p.Arg1146His,ENST00000391975,;HDLBP,intron_variant,,ENST00000373292,;AC104841.2,downstream_gene_variant,,ENST00000601871,;HDLBP,non_coding_transcript_exon_variant,,ENST00000470482,;HDLBP,non_coding_transcript_exon_variant,,ENST00000484412,;HDLBP,downstream_gene_variant,,ENST00000483086,;HDLBP,non_coding_transcript_exon_variant,,ENST00000488013,;HDLBP,non_coding_transcript_exon_variant,,ENST00000487169,;HDLBP,upstream_gene_variant,,ENST00000494862,;HDLBP,downstream_gene_variant,,ENST00000479894,;	T	ENSG00000115677	ENST00000391975	Transcript	missense_variant	3665	3437	1146	R/H	cGc/cAc	rs768699303	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	tolerated(0.11)	benign(0.364)	25/28	.	PROSITE_profiles:PS50084,hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCGCGGGCA	.	4	ESCA
DRC1	0	.	GRCh37	2	26672862	26672862	+	Splice_Site	SNP	A	A	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1510-2A>T	.	p.X504_splice	ENST00000288710	.	49	28	20	44	44	0	DRC1,splice_acceptor_variant,,ENST00000288710,;DRC1,splice_acceptor_variant,,ENST00000439066,;	T	ENSG00000157856	ENST00000288710	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	DRC1	HGNC	24245	protein_coding	YES	CCDS1723.1	ENSP00000288710	DRC1_HUMAN	.	UPI000013DF36	.	.	.	.	11/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCAGGGGT	.	5	ESCA
FAM98A	0	.	GRCh37	2	33808901	33808901	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*942C>T	.	.	ENST00000238823	8/8	32	18	14	33	33	0	FAM98A,3_prime_UTR_variant,,ENST00000403368,;FAM98A,3_prime_UTR_variant,,ENST00000238823,;FAM98A,downstream_gene_variant,,ENST00000441530,;FAM98A,downstream_gene_variant,,ENST00000498340,;FAM98A,non_coding_transcript_exon_variant,,ENST00000474985,;FAM98A,downstream_gene_variant,,ENST00000492649,;FAM98A,downstream_gene_variant,,ENST00000475122,;	A	ENSG00000119812	ENST00000238823	Transcript	3_prime_UTR_variant	2640	.	.	.	.	.	.	.	-1	FAM98A	HGNC	24520	protein_coding	YES	CCDS33179.1	ENSP00000238823	FA98A_HUMAN	C9J3G8_HUMAN,B4DT23_HUMAN	UPI000013F15A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTGCAGCA	.	5	ESCA
VAX2	0	.	GRCh37	2	71160034	71160034	+	Silent	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.573G>T	p.%3D	p.L191L	ENST00000234392	3/3	69	44	25	68	68	0	VAX2,synonymous_variant,p.%3D,ENST00000234392,;ATP6V1B1,upstream_gene_variant,,ENST00000234396,;ATP6V1B1,upstream_gene_variant,,ENST00000412314,;snoU13,upstream_gene_variant,,ENST00000459218,;ATP6V1B1,upstream_gene_variant,,ENST00000432367,;	T	ENSG00000116035	ENST00000234392	Transcript	synonymous_variant	605	573	191	L	ctG/ctT	.	.	.	1	VAX2	HGNC	12661	protein_coding	YES	CCDS1911.1	ENSP00000234392	VAX2_HUMAN	F1T0K5_HUMAN	UPI0000138215	.	.	.	3/3	.	hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCTGCTCTC	.	5	ESCA
DNAH6	0	.	GRCh37	2	85046562	85046562	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*30C>T	.	.	ENST00000389394	77/77	39	30	9	17	17	0	DNAH6,3_prime_UTR_variant,,ENST00000237449,;DNAH6,3_prime_UTR_variant,,ENST00000389394,;TRABD2A,downstream_gene_variant,,ENST00000335459,;TRABD2A,downstream_gene_variant,,ENST00000409520,;TRABD2A,downstream_gene_variant,,ENST00000496500,;TRABD2A,downstream_gene_variant,,ENST00000479944,;	T	ENSG00000115423	ENST00000389394	Transcript	3_prime_UTR_variant	12644	.	.	.	.	.	.	.	1	DNAH6	HGNC	2951	protein_coding	YES	CCDS46348.1	ENSP00000374045	DYH6_HUMAN	B0I1R8_HUMAN	UPI000163AC9D	.	.	.	77/77	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAACCAGGC	.	5	ESCA
IGKV1D-16	0	.	GRCh37	2	90139101	90139101	+	5'UTR	SNP	C	C	G	rs747504769	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4C>G	.	.	ENST00000492446	1/2	264	226	37	195	195	0	IGKV1D-16,5_prime_UTR_variant,,ENST00000492446,;AC073416.1,upstream_gene_variant,,ENST00000323194,;	G	ENSG00000241244	ENST00000492446	Transcript	5_prime_UTR_variant	24	.	.	.	.	rs747504769	.	.	1	IGKV1D-16	HGNC	5748	IG_V_gene	YES	.	ENSP00000418200	.	.	UPI0000116772	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGACACAGCAT	byFrequency	3	ESCA
STXBP5L	0	.	GRCh37	3	121126164	121126164	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2734C>T	p.Pro912Ser	p.P912S	ENST00000273666	24/28	34	25	8	21	21	0	STXBP5L,missense_variant,p.Pro855Ser,ENST00000471262,;STXBP5L,missense_variant,p.Pro888Ser,ENST00000472879,;STXBP5L,missense_variant,p.Pro912Ser,ENST00000273666,;STXBP5L,missense_variant,p.Pro888Ser,ENST00000471454,;STXBP5L,missense_variant,p.Pro912Ser,ENST00000492541,;STXBP5L,missense_variant,p.Pro886Ser,ENST00000497029,;	T	ENSG00000145087	ENST00000273666	Transcript	missense_variant	3005	2734	912	P/S	Cca/Tca	.	.	.	1	STXBP5L	HGNC	30757	protein_coding	YES	CCDS43137.1	ENSP00000273666	STB5L_HUMAN	C9JUZ7_HUMAN	UPI00001C1DEA	.	tolerated(0.84)	probably_damaging(1)	24/28	.	hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Pfam_domain:PF08596	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCGCCATAT	.	5	ESCA
TGFBR2	0	.	GRCh37	3	30732976	30732976	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1664C>T	p.Thr555Ile	p.T555I	ENST00000359013	8/8	47	27	19	45	45	0	TGFBR2,missense_variant,p.Thr530Ile,ENST00000295754,;TGFBR2,missense_variant,p.Thr555Ile,ENST00000359013,;	T	ENSG00000163513	ENST00000359013	Transcript	missense_variant	1947	1664	555	T/I	aCa/aTa	CM093626	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	deleterious(0)	probably_damaging(1)	8/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037393,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R528C|c.1582C>T|4,BUFFER|p.R528H|c.1583G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCACAGCCC	.	5	ESCA
ELP6	0	.	GRCh37	3	47545863	47545863	+	Missense_Mutation	SNP	C	C	T	rs759438726	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280G>A	p.Val94Ile	p.V94I	ENST00000296149	4/7	48	30	18	36	36	0	ELP6,missense_variant,p.Val21Ile,ENST00000446787,;ELP6,missense_variant,p.Val21Ile,ENST00000414236,;ELP6,missense_variant,p.Val21Ile,ENST00000449409,;ELP6,missense_variant,p.Val21Ile,ENST00000439305,;ELP6,missense_variant,p.Val21Ile,ENST00000444760,;ELP6,missense_variant,p.Val21Ile,ENST00000425291,;ELP6,missense_variant,p.Val94Ile,ENST00000296149,;ELP6,missense_variant,p.Val21Ile,ENST00000412761,;Y_RNA,downstream_gene_variant,,ENST00000607813,;RP11-708J19.2,downstream_gene_variant,,ENST00000604904,;ELP6,missense_variant,p.Val21Ile,ENST00000445044,;ELP6,3_prime_UTR_variant,,ENST00000442215,;ELP6,non_coding_transcript_exon_variant,,ENST00000485029,;ELP6,non_coding_transcript_exon_variant,,ENST00000494161,;ELP6,non_coding_transcript_exon_variant,,ENST00000461208,;RP11-708J19.2,downstream_gene_variant,,ENST00000603861,;	T	ENSG00000163832	ENST00000296149	Transcript	missense_variant	451	280	94	V/I	Gtc/Atc	rs759438726,COSM1734690	.	.	-1	ELP6	HGNC	25976	protein_coding	YES	CCDS43082.1	ENSP00000296149	ELP6_HUMAN	C9JLH5_HUMAN,C9JA82_HUMAN,C9J9N8_HUMAN,C9IYN7_HUMAN	UPI000020A684	.	tolerated(0.21)	benign(0.002)	4/7	.	hmmpanther:PTHR16184,hmmpanther:PTHR16184:SF6,Pfam_domain:PF09807	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGACGACGT	byFrequency	5	ESCA
RYBP	0	.	GRCh37	3	72427500	72427500	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*36G>A	.	.	ENST00000477973	4/4	50	33	17	31	31	0	RYBP,3_prime_UTR_variant,,ENST00000477973,;	T	ENSG00000163602	ENST00000477973	Transcript	3_prime_UTR_variant	988	.	.	.	.	.	.	.	-1	RYBP	HGNC	10480	protein_coding	YES	.	ENSP00000419494	RYBP_HUMAN	.	UPI0001B794AD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATACCCTGA	.	5	ESCA
ELOVL6	0	.	GRCh37	4	110972735	110972735	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.557C>A	p.Ala186Glu	p.A186E	ENST00000394607	5/5	49	29	19	47	47	0	ELOVL6,missense_variant,p.Ala186Glu,ENST00000394607,;ELOVL6,missense_variant,p.Ala186Glu,ENST00000302274,;ELOVL6,downstream_gene_variant,,ENST00000506625,;ELOVL6,downstream_gene_variant,,ENST00000507451,;ELOVL6,downstream_gene_variant,,ENST00000514184,;	T	ENSG00000170522	ENST00000394607	Transcript	missense_variant	721	557	186	A/E	gCa/gAa	.	.	.	-1	ELOVL6	HGNC	15829	protein_coding	YES	CCDS3690.1	ENSP00000378105	ELOV6_HUMAN	D6RHI2_HUMAN,D6RCU0_HUMAN	UPI00000343F5	.	deleterious(0)	probably_damaging(0.958)	5/5	.	hmmpanther:PTHR11157:SF34,hmmpanther:PTHR11157,Pfam_domain:PF01151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCTGCCGCC	.	5	ESCA
KIAA1109	0	.	GRCh37	4	123147861	123147861	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2794-1G>A	.	p.X932_splice	ENST00000264501	.	48	25	23	42	42	0	KIAA1109,splice_acceptor_variant,,ENST00000424425,;KIAA1109,splice_acceptor_variant,,ENST00000455637,;KIAA1109,splice_acceptor_variant,,ENST00000264501,;KIAA1109,splice_acceptor_variant,,ENST00000388738,;KIAA1109,intron_variant,,ENST00000449251,;KIAA1109,splice_acceptor_variant,,ENST00000495260,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000482114,;	A	ENSG00000138688	ENST00000264501	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	KIAA1109	HGNC	26953	protein_coding	YES	CCDS43267.1	ENSP00000264501	K1109_HUMAN	B3KN93_HUMAN	UPI0000DD87B4	.	.	.	.	23/85	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTAGCTGGC	.	5	ESCA
GNPDA2	0	.	GRCh37	4	44704975	44704975	+	3'UTR	SNP	C	C	T	rs762902700	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*123G>A	.	.	ENST00000295448	7/7	28	13	15	28	28	0	GNPDA2,3_prime_UTR_variant,,ENST00000295448,;GNPDA2,3_prime_UTR_variant,,ENST00000507534,;GNPDA2,3_prime_UTR_variant,,ENST00000507917,;GNPDA2,intron_variant,,ENST00000608855,;GNPDA2,intron_variant,,ENST00000609092,;GNPDA2,downstream_gene_variant,,ENST00000509756,;GUF1,downstream_gene_variant,,ENST00000281543,;RP11-700J17.2,upstream_gene_variant,,ENST00000610267,;GUF1,downstream_gene_variant,,ENST00000511493,;GNPDA2,downstream_gene_variant,,ENST00000511187,;GUF1,downstream_gene_variant,,ENST00000506793,;	T	ENSG00000163281	ENST00000295448	Transcript	3_prime_UTR_variant	1111	.	.	.	.	rs762902700	.	.	-1	GNPDA2	HGNC	21526	protein_coding	YES	CCDS3469.1	ENSP00000295448	GNPI2_HUMAN	.	UPI000004D013	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACTCGAATG	.	5	ESCA
DGKQ	0	.	GRCh37	4	956346	956346	+	Silent	SNP	C	C	T	rs770688103	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2091G>A	p.%3D	p.P697P	ENST00000273814	18/23	46	38	8	36	36	0	DGKQ,synonymous_variant,p.%3D,ENST00000273814,;DGKQ,synonymous_variant,p.%3D,ENST00000509465,;TMEM175,downstream_gene_variant,,ENST00000510493,;TMEM175,downstream_gene_variant,,ENST00000264771,;DGKQ,upstream_gene_variant,,ENST00000515182,;TMEM175,downstream_gene_variant,,ENST00000515492,;TMEM175,downstream_gene_variant,,ENST00000508204,;TMEM175,downstream_gene_variant,,ENST00000515740,;DGKQ,downstream_gene_variant,,ENST00000502309,;TMEM175,downstream_gene_variant,,ENST00000438836,;TMEM175,downstream_gene_variant,,ENST00000513952,;	T	ENSG00000145214	ENST00000273814	Transcript	synonymous_variant	2165	2091	697	P	ccG/ccA	rs770688103	.	.	-1	DGKQ	HGNC	2856	protein_coding	YES	CCDS3342.1	ENSP00000273814	DGKQ_HUMAN	.	UPI00001AE9B4	.	.	.	18/23	.	PROSITE_profiles:PS50146,hmmpanther:PTHR11255:SF8,hmmpanther:PTHR11255,Pfam_domain:PF00781,SMART_domains:SM00046,Superfamily_domains:SSF111331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGAACGGGTC	byFrequency	4	ESCA
SNCAIP	0	.	GRCh37	5	121786488	121786488	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1946C>T	p.Ser649Phe	p.S649F	ENST00000261368	10/11	47	29	17	36	36	0	SNCAIP,missense_variant,p.Ser589Phe,ENST00000379536,;SNCAIP,missense_variant,p.Ser589Phe,ENST00000509154,;SNCAIP,missense_variant,p.Ser649Phe,ENST00000261368,;SNCAIP,missense_variant,p.Ser283Phe,ENST00000379538,;SNCAIP,missense_variant,p.Ser207Phe,ENST00000542191,;SNCAIP,missense_variant,p.Ser696Phe,ENST00000379533,;SNCAIP,missense_variant,p.Ser251Phe,ENST00000414317,;SNCAIP,missense_variant,p.Ser696Phe,ENST00000261367,;SNCAIP,3_prime_UTR_variant,,ENST00000503116,;SNCAIP,3_prime_UTR_variant,,ENST00000504884,;CTC-210G5.1,intron_variant,,ENST00000510972,;CTC-210G5.1,intron_variant,,ENST00000505546,;CTC-210G5.1,intron_variant,,ENST00000503529,;CTC-210G5.1,intron_variant,,ENST00000506053,;CTC-210G5.1,intron_variant,,ENST00000509993,;SNCAIP,3_prime_UTR_variant,,ENST00000508017,;SNCAIP,3_prime_UTR_variant,,ENST00000395466,;SNCAIP,3_prime_UTR_variant,,ENST00000512146,;SNCAIP,3_prime_UTR_variant,,ENST00000512385,;SNCAIP,3_prime_UTR_variant,,ENST00000395469,;SNCAIP,3_prime_UTR_variant,,ENST00000510658,;SNCAIP,3_prime_UTR_variant,,ENST00000509023,;SNCAIP,3_prime_UTR_variant,,ENST00000515215,;SNCAIP,non_coding_transcript_exon_variant,,ENST00000513719,;	T	ENSG00000064692	ENST00000261368	Transcript	missense_variant	2208	1946	649	S/F	tCt/tTt	.	.	.	1	SNCAIP	HGNC	11139	protein_coding	YES	CCDS4131.1	ENSP00000261368	SNCAP_HUMAN	D6RD29_HUMAN,D6RBR2_HUMAN,B7Z616_HUMAN	UPI000006D872	.	deleterious(0)	possibly_damaging(0.864)	10/11	.	hmmpanther:PTHR22882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTAGAA	.	5	ESCA
ZNF608	0	.	GRCh37	5	124080411	124080411	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272C>T	p.Ser91Phe	p.S91F	ENST00000306315	1/9	59	39	20	50	50	0	ZNF608,missense_variant,p.Ser91Phe,ENST00000513986,;ZNF608,missense_variant,p.Ser91Phe,ENST00000509799,;ZNF608,missense_variant,p.Ser91Phe,ENST00000306315,;ZNF608,upstream_gene_variant,,ENST00000504926,;ZNF608,non_coding_transcript_exon_variant,,ENST00000512940,;ZNF608,upstream_gene_variant,,ENST00000503896,;ZNF608,missense_variant,p.Ser91Phe,ENST00000505686,;	A	ENSG00000168916	ENST00000306315	Transcript	missense_variant	708	272	91	S/F	tCt/tTt	COSM448514	.	.	-1	ZNF608	HGNC	29238	protein_coding	YES	CCDS34219.1	ENSP00000307746	ZN608_HUMAN	Q9UFL4_HUMAN,B3KPE6_HUMAN	UPI000013EB23	.	deleterious(0)	possibly_damaging(0.549)	1/9	.	hmmpanther:PTHR21564,hmmpanther:PTHR21564:SF4	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCAGAGGCC	.	5	ESCA
DNAH5	0	.	GRCh37	5	13692122	13692122	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13846G>A	p.Gly4616Arg	p.G4616R	ENST00000265104	79/79	52	34	17	35	35	0	DNAH5,missense_variant,p.Gly4616Arg,ENST00000265104,;	T	ENSG00000039139	ENST00000265104	Transcript	missense_variant	13951	13846	4616	G/R	Ggg/Agg	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	probably_damaging(0.988)	79/79	.	Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCCCACGGA	.	5	ESCA
KDM3B	0	.	GRCh37	5	137759943	137759943	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4152G>C	p.Trp1384Cys	p.W1384C	ENST00000314358	16/24	85	51	34	51	51	0	KDM3B,missense_variant,p.Trp416Cys,ENST00000542866,;KDM3B,missense_variant,p.Trp1384Cys,ENST00000314358,;KDM3B,missense_variant,p.Trp1040Cys,ENST00000394866,;KDM3B,downstream_gene_variant,,ENST00000508386,;KDM3B,3_prime_UTR_variant,,ENST00000507996,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,non_coding_transcript_exon_variant,,ENST00000505756,;KDM3B,upstream_gene_variant,,ENST00000509468,;	C	ENSG00000120733	ENST00000314358	Transcript	missense_variant	4352	4152	1384	W/C	tgG/tgC	.	.	.	1	KDM3B	HGNC	1337	protein_coding	YES	CCDS34242.1	ENSP00000326563	KDM3B_HUMAN	F5H275_HUMAN	UPI000020C6A8	.	deleterious(0)	probably_damaging(0.999)	16/24	.	hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGGCTTTG	.	5	ESCA
PROB1	0	.	GRCh37	5	138729895	138729895	+	Silent	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.876G>T	p.%3D	p.L292L	ENST00000434752	1/1	182	113	68	155	155	0	PROB1,synonymous_variant,p.%3D,ENST00000434752,;MZB1,upstream_gene_variant,,ENST00000412103,;SPATA24,downstream_gene_variant,,ENST00000512761,;SPATA24,downstream_gene_variant,,ENST00000514983,;SPATA24,downstream_gene_variant,,ENST00000450845,;SPATA24,downstream_gene_variant,,ENST00000302091,;MZB1,upstream_gene_variant,,ENST00000302125,;MZB1,upstream_gene_variant,,ENST00000457570,;MZB1,upstream_gene_variant,,ENST00000509591,;MZB1,upstream_gene_variant,,ENST00000503351,;MZB1,upstream_gene_variant,,ENST00000513389,;MZB1,upstream_gene_variant,,ENST00000417694,;MZB1,upstream_gene_variant,,ENST00000503481,;MZB1,upstream_gene_variant,,ENST00000503120,;	A	ENSG00000228672	ENST00000434752	Transcript	synonymous_variant	991	876	292	L	ctG/ctT	.	.	.	-1	PROB1	HGNC	41906	protein_coding	YES	CCDS54909.1	ENSP00000416033	PROB1_HUMAN	.	UPI00001974A9	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCCAGGAC	.	5	ESCA
BASP1	0	.	GRCh37	5	17275448	17275448	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123G>T	p.Glu41Asp	p.E41D	ENST00000322611	2/2	23	13	9	21	21	0	BASP1,missense_variant,p.Glu41Asp,ENST00000606445,;BASP1,missense_variant,p.Glu41Asp,ENST00000322611,;	T	ENSG00000176788	ENST00000322611	Transcript	missense_variant	383	123	41	E/D	gaG/gaT	.	.	.	1	BASP1	HGNC	957	protein_coding	YES	CCDS3888.1	ENSP00000319281	BASP1_HUMAN	U3KQP0_HUMAN	UPI0000140E98	.	deleterious(0.04)	unknown(0)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23212:SF0,hmmpanther:PTHR23212,Pfam_domain:PF05466	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGAGCCCCA	.	5	ESCA
KIAA1191	0	.	GRCh37	5	175775305	175775305	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514G>T	p.Ala172Ser	p.A172S	ENST00000298569	7/9	70	60	9	68	68	0	KIAA1191,missense_variant,p.Ser28Ile,ENST00000533553,;KIAA1191,missense_variant,p.Ala153Ser,ENST00000393725,;KIAA1191,missense_variant,p.Ala172Ser,ENST00000510164,;KIAA1191,missense_variant,p.Ala172Ser,ENST00000298569,;KIAA1191,downstream_gene_variant,,ENST00000504688,;KIAA1191,downstream_gene_variant,,ENST00000506983,;SIMC1,downstream_gene_variant,,ENST00000443967,;SIMC1,downstream_gene_variant,,ENST00000430704,;SIMC1,downstream_gene_variant,,ENST00000332772,;SIMC1,downstream_gene_variant,,ENST00000341199,;KIAA1191,downstream_gene_variant,,ENST00000503082,;RP11-843P14.2,intron_variant,,ENST00000508187,;KIAA1191,non_coding_transcript_exon_variant,,ENST00000393728,;KIAA1191,downstream_gene_variant,,ENST00000506668,;	A	ENSG00000122203	ENST00000298569	Transcript	missense_variant	1048	514	172	A/S	Gcc/Tcc	.	.	.	-1	KIAA1191	HGNC	29209	protein_coding	YES	CCDS4399.1	ENSP00000298569	P33MX_HUMAN	D6RF63_HUMAN,D6RCE3_HUMAN,D6RAJ7_HUMAN	UPI0000070560	.	tolerated(0.06)	benign(0.015)	7/9	.	Low_complexity_(Seg):seg,Pfam_domain:PF15302	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGGCTGATG	.	4	ESCA
NSD1	0	.	GRCh37	5	176694593	176694593	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5177C>T	p.Pro1726Leu	p.P1726L	ENST00000439151	15/23	37	17	19	24	24	0	NSD1,missense_variant,p.Pro1623Leu,ENST00000361032,;NSD1,missense_variant,p.Pro1457Leu,ENST00000354179,;NSD1,missense_variant,p.Pro1726Leu,ENST00000439151,;NSD1,missense_variant,p.Pro1457Leu,ENST00000347982,;NSD1,5_prime_UTR_variant,,ENST00000503056,;NSD1,5_prime_UTR_variant,,ENST00000508029,;NSD1,5_prime_UTR_variant,,ENST00000505395,;NSD1,5_prime_UTR_variant,,ENST00000515735,;NSD1,5_prime_UTR_variant,,ENST00000504457,;CTD-2301A4.3,downstream_gene_variant,,ENST00000460608,;CTD-2301A4.5,upstream_gene_variant,,ENST00000604252,;	T	ENSG00000165671	ENST00000439151	Transcript	missense_variant	5222	5177	1726	P/L	cCt/cTt	CM033420,COSM124865	.	.	1	NSD1	HGNC	14234	protein_coding	YES	CCDS4412.1	ENSP00000395929	NSD1_HUMAN	Q9H6H8_HUMAN,Q9H6B5_HUMAN,Q96MN8_HUMAN,Q96DQ7_HUMAN,Q658U6_HUMAN,D6RE14_HUMAN,D6RBP3_HUMAN,D6RA90_HUMAN	UPI000006F9C6	.	deleterious(0)	probably_damaging(1)	15/23	.	PROSITE_profiles:PS50016,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312,PROSITE_patterns:PS01359,Pfam_domain:PF00628,Gene3D:3.30.40.10,SMART_domains:SM00249,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCCCTGCTG	.	5	ESCA
NSD1	0	.	GRCh37	5	176709465	176709465	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5893-1G>A	.	p.X1965_splice	ENST00000439151	.	65	44	21	40	40	0	NSD1,splice_acceptor_variant,,ENST00000361032,;NSD1,splice_acceptor_variant,,ENST00000354179,;NSD1,splice_acceptor_variant,,ENST00000439151,;NSD1,splice_acceptor_variant,,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000503056,;	A	ENSG00000165671	ENST00000439151	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	NSD1	HGNC	14234	protein_coding	YES	CCDS4412.1	ENSP00000395929	NSD1_HUMAN	Q9H6H8_HUMAN,Q9H6B5_HUMAN,Q96MN8_HUMAN,Q96DQ7_HUMAN,Q658U6_HUMAN,D6RE14_HUMAN,D6RBP3_HUMAN,D6RA90_HUMAN	UPI000006F9C6	.	.	.	.	18/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTAGGGTGA	.	5	ESCA
PDZD2	0	.	GRCh37	5	32098533	32098533	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8011C>T	p.Leu2671Phe	p.L2671F	ENST00000438447	23/25	60	40	20	34	33	0	PDZD2,missense_variant,p.Leu2671Phe,ENST00000438447,;PDZD2,missense_variant,p.Leu2671Phe,ENST00000282493,;PDZD2,upstream_gene_variant,,ENST00000515115,;PDZD2,upstream_gene_variant,,ENST00000513490,;PDZD2,upstream_gene_variant,,ENST00000397559,;	T	ENSG00000133401	ENST00000438447	Transcript	missense_variant	8399	8011	2671	L/F	Ctt/Ttt	.	.	.	1	PDZD2	HGNC	18486	protein_coding	YES	CCDS34137.1	ENSP00000402033	PDZD2_HUMAN	B4DGS3_HUMAN	UPI000069648B	.	deleterious(0)	probably_damaging(1)	23/25	.	PROSITE_profiles:PS50106,hmmpanther:PTHR11324:SF16,hmmpanther:PTHR11324,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCCTTCTG	.	5	ESCA
SPEF2	0	.	GRCh37	5	35814614	35814614	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5428G>A	p.Gly1810Arg	p.G1810R	ENST00000356031	37/37	41	24	16	42	42	0	SPEF2,missense_variant,p.Gly607Arg,ENST00000303129,;SPEF2,missense_variant,p.Gly1810Arg,ENST00000356031,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,3_prime_UTR_variant,,ENST00000513078,;SPEF2,3_prime_UTR_variant,,ENST00000506526,;	A	ENSG00000152582	ENST00000356031	Transcript	missense_variant	5582	5428	1810	G/R	Gga/Aga	.	.	.	1	SPEF2	HGNC	26293	protein_coding	YES	CCDS43309.1	ENSP00000348314	SPEF2_HUMAN	.	UPI0001505B9F	.	tolerated(0.07)	benign(0.362)	37/37	.	hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGATGGAGAG	.	5	ESCA
ERBB2IP	0	.	GRCh37	5	65338949	65338949	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351G>A	p.Glu451Lys	p.E451K	ENST00000506030	16/26	80	54	25	60	60	0	ERBB2IP,missense_variant,p.Glu451Lys,ENST00000380935,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000511297,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000284037,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000508515,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000380943,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000380938,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000380936,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000506030,;ERBB2IP,missense_variant,p.Glu451Lys,ENST00000380939,;ERBB2IP,intron_variant,,ENST00000416865,;	A	ENSG00000112851	ENST00000506030	Transcript	missense_variant	1442	1351	451	E/K	Gag/Aag	.	.	.	1	ERBB2IP	HGNC	15842	protein_coding	YES	CCDS58952.1	ENSP00000426632	LAP2_HUMAN	.	UPI0001D3B314	.	deleterious(0)	probably_damaging(0.998)	16/26	.	hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF421	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGGGAGGAA	.	5	ESCA
ARSB	0	.	GRCh37	5	78135223	78135223	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1169A>T	p.Glu390Val	p.E390V	ENST00000264914	6/8	46	32	14	33	33	0	ARSB,missense_variant,p.Glu390Val,ENST00000264914,;ARSB,missense_variant,p.Glu390Val,ENST00000396151,;ARSB,missense_variant,p.Glu390Val,ENST00000565165,;	A	ENSG00000113273	ENST00000264914	Transcript	missense_variant	1706	1169	390	E/V	gAg/gTg	.	.	.	-1	ARSB	HGNC	714	protein_coding	YES	CCDS4043.1	ENSP00000264914	ARSB_HUMAN	E5RHC4_HUMAN	UPI00001260A3	.	deleterious(0.04)	probably_damaging(0.912)	6/8	.	hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF206,Gene3D:3.30.1120.10,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCTCAATT	.	5	ESCA
ROS1	0	.	GRCh37	6	117658466	117658466	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5117G>T	p.Cys1706Phe	p.C1706F	ENST00000368508	31/43	53	39	13	60	59	1	ROS1,missense_variant,p.Cys1700Phe,ENST00000368507,;ROS1,missense_variant,p.Cys1706Phe,ENST00000368508,;ROS1,missense_variant,p.Cys13Phe,ENST00000403284,;GOPC,intron_variant,,ENST00000467125,;	A	ENSG00000047936	ENST00000368508	Transcript	missense_variant	5316	5117	1706	C/F	tGc/tTc	.	.	.	-1	ROS1	HGNC	10261	protein_coding	YES	CCDS5116.1	ENSP00000357494	ROS1_HUMAN	.	UPI000013D467	.	deleterious(0)	probably_damaging(1)	31/43	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF304,hmmpanther:PTHR24416,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGCTGCATGAA	.	4	ESCA
IFNGR1	0	.	GRCh37	6	137522074	137522074	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805delT	p.Tyr269IlefsTer8	p.Y269Ifs*8	ENST00000367739	6/7	68	46	22	45	45	0	IFNGR1,frameshift_variant,p.Tyr241IlefsTer8,ENST00000543628,;IFNGR1,frameshift_variant,p.Tyr269IlefsTer8,ENST00000367739,;IFNGR1,downstream_gene_variant,,ENST00000458076,;IFNGR1,downstream_gene_variant,,ENST00000367735,;IFNGR1,downstream_gene_variant,,ENST00000414770,;	-	ENSG00000027697	ENST00000367739	Transcript	frameshift_variant	927	805	269	Y/X	Tat/at	.	.	.	-1	IFNGR1	HGNC	5439	protein_coding	YES	CCDS5185.1	ENSP00000356713	INGR1_HUMAN	Q7Z687_HUMAN,Q14936_HUMAN,E5QBZ2_HUMAN,A1Z2M9_HUMAN	UPI000002CE40	.	.	.	6/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR20859:SF5,hmmpanther:PTHR20859,Pfam_domain:PF07140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAATATAAAAAC	.	3	ESCA
DTNBP1	0	.	GRCh37	6	15533520	15533520	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.618C>T	p.%3D	p.D206D	ENST00000344537	8/10	67	45	22	45	45	0	DTNBP1,synonymous_variant,p.%3D,ENST00000462989,;DTNBP1,synonymous_variant,p.%3D,ENST00000344537,;DTNBP1,synonymous_variant,p.%3D,ENST00000355917,;DTNBP1,synonymous_variant,p.%3D,ENST00000509674,;DTNBP1,synonymous_variant,p.%3D,ENST00000511762,;DTNBP1,synonymous_variant,p.%3D,ENST00000338950,;DTNBP1,synonymous_variant,p.%3D,ENST00000515875,;DTNBP1,3_prime_UTR_variant,,ENST00000506844,;DTNBP1,3_prime_UTR_variant,,ENST00000510395,;DTNBP1,3_prime_UTR_variant,,ENST00000513680,;DTNBP1,non_coding_transcript_exon_variant,,ENST00000514651,;	A	ENSG00000047579	ENST00000344537	Transcript	synonymous_variant	791	618	206	D	gaC/gaT	.	.	.	-1	DTNBP1	HGNC	17328	protein_coding	YES	CCDS4534.1	ENSP00000341680	DTBP1_HUMAN	D6RAR7_HUMAN	UPI000006F968	.	.	.	8/10	.	hmmpanther:PTHR16294,hmmpanther:PTHR16294:SF5,Pfam_domain:PF04440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATGTCCTG	.	5	ESCA
ZNF184	0	.	GRCh37	6	27419848	27419848	+	Missense_Mutation	SNP	G	G	A	rs759048815	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1490C>T	p.Thr497Met	p.T497M	ENST00000211936	6/6	65	39	25	56	56	0	ZNF184,missense_variant,p.Thr497Met,ENST00000211936,;ZNF184,missense_variant,p.Thr497Met,ENST00000377419,;	A	ENSG00000096654	ENST00000211936	Transcript	missense_variant	1775	1490	497	T/M	aCg/aTg	rs759048815	.	.	-1	ZNF184	HGNC	12975	protein_coding	YES	CCDS4624.1	ENSP00000211936	ZN184_HUMAN	.	UPI000013C311	.	deleterious(0)	probably_damaging(0.999)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF108,hmmpanther:PTHR24375,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTCGTGTGA	byFrequency	5	ESCA
PPP1R18	0	.	GRCh37	6	30653411	30653411	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385A>G	p.Met129Val	p.M129V	ENST00000274853	1/3	51	29	22	45	45	0	PPP1R18,missense_variant,p.Met129Val,ENST00000399199,;PPP1R18,missense_variant,p.Met129Val,ENST00000274853,;NRM,downstream_gene_variant,,ENST00000376420,;NRM,downstream_gene_variant,,ENST00000376421,;NRM,downstream_gene_variant,,ENST00000444096,;NRM,downstream_gene_variant,,ENST00000259953,;PPP1R18,intron_variant,,ENST00000467662,;PPP1R18,intron_variant,,ENST00000488324,;NRM,downstream_gene_variant,,ENST00000462857,;NRM,downstream_gene_variant,,ENST00000482141,;NRM,downstream_gene_variant,,ENST00000474864,;NRM,downstream_gene_variant,,ENST00000470733,;NRM,downstream_gene_variant,,ENST00000495946,;	C	ENSG00000146112	ENST00000274853	Transcript	missense_variant	2262	385	129	M/V	Atg/Gtg	.	.	.	-1	PPP1R18	HGNC	29413	protein_coding	YES	CCDS43444.1	ENSP00000274853	PPR18_HUMAN	.	UPI00001C1E5E	.	tolerated_low_confidence(0.55)	benign(0.004)	1/3	.	hmmpanther:PTHR21685	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCATCTCCC	.	5	ESCA
FLOT1	0	.	GRCh37	6	30695880	30695880	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13C>T	.	.	ENST00000376389	13/13	52	38	14	43	43	0	FLOT1,3_prime_UTR_variant,,ENST00000376389,;FLOT1,3_prime_UTR_variant,,ENST00000456573,;TUBB,downstream_gene_variant,,ENST00000435534,;FLOT1,downstream_gene_variant,,ENST00000438162,;TUBB,downstream_gene_variant,,ENST00000396384,;TUBB,downstream_gene_variant,,ENST00000330914,;FLOT1,downstream_gene_variant,,ENST00000413165,;TUBB,downstream_gene_variant,,ENST00000327892,;TUBB,downstream_gene_variant,,ENST00000396389,;XXbac-BPG252P9.9,upstream_gene_variant,,ENST00000607476,;FLOT1,non_coding_transcript_exon_variant,,ENST00000487376,;FLOT1,downstream_gene_variant,,ENST00000476729,;	A	ENSG00000137312	ENST00000376389	Transcript	3_prime_UTR_variant	1518	.	.	.	.	.	.	.	-1	FLOT1	HGNC	3757	protein_coding	YES	CCDS4688.1	ENSP00000365569	FLOT1_HUMAN	Q5ST80_HUMAN,A2AB13_HUMAN,A2AB12_HUMAN,A2AB10_HUMAN	UPI000000D73F	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGTGAGGGC	.	5	ESCA
HLA-B	0	.	GRCh37	6	31323325	31323325	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664G>T	p.Glu222Ter	p.E222*	ENST00000412585	4/8	103	75	28	88	88	0	HLA-B,stop_gained,p.Glu222Ter,ENST00000412585,;HLA-B,stop_gained,p.Glu233Ter,ENST00000434333,;HLA-B,non_coding_transcript_exon_variant,,ENST00000463574,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,non_coding_transcript_exon_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000497377,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,;	A	ENSG00000234745	ENST00000412585	Transcript	stop_gained	693	664	222	E/*	Gag/Tag	.	.	.	-1	HLA-B	HGNC	4932	protein_coding	YES	CCDS34394.1	ENSP00000399168	1B73_HUMAN,1B07_HUMAN,1B42_HUMAN,1B67_HUMAN,1B81_HUMAN,1B48_HUMAN	T1R372_HUMAN,R4QQU0_HUMAN,N0A4A9_HUMAN,N0A0K3_HUMAN,M9XMA8_HUMAN,M9PAL2_HUMAN,M9P9U8_HUMAN,M9P9C4_HUMAN,M9P9A4_HUMAN,M9P990_HUMAN,M9P8G8_HUMAN,M1FXF1_HUMAN,M1FWX2_HUMAN,M1F4D0_HUMAN,E5FQ95_HUMAN,Q9UIP1_HUMAN,Q9TQC5_HUMAN,Q9TQC2_HUMAN,Q9TPU4_HUMAN,Q9GIM0_HUMAN,Q95IE1_HUMAN,Q95HL7_HUMAN,Q8SP64_HUMAN,Q8HWQ3_HUMAN,Q861E5_HUMAN,Q861D6_HUMAN,Q861D4_HUMAN,Q7YP17_HUMAN,Q7YNX2_HUMAN,Q7JGR7_HUMAN,Q710M8_HUMAN,Q710M7_HUMAN,Q70HJ6_HUMAN,Q709M5_HUMAN,Q6ZXT6_HUMAN,Q5QR88_HUMAN,Q5QR87_HUMAN,Q5QR86_HUMAN,Q5QR85_HUMAN,Q5QR84_HUMAN,Q5QR83_HUMAN,Q5QR76_HUMAN,Q5QR73_HUMAN,Q5QR69_HUMAN,Q5QR62_HUMAN,Q5QR60_HUMAN,Q5QR59_HUMAN,Q5QR58_HUMAN,Q5QR57_HUMAN,Q5QR48_HUMAN,Q5QR47_HUMAN,Q5QR46_HUMAN,Q5QR36_HUMAN,Q5QR34_HUMAN,Q5QR33_HUMAN,Q5QR31_HUMAN,Q5F311_HUMAN,Q53ZP0_HUMAN,Q29923_HUMAN,Q29843_HUMAN,Q256S0_HUMAN,O19782_HUMAN,O19746_HUMAN,O19644_HUMAN,O19638_HUMAN,O19563_HUMAN,L0RH50_HUMAN,L0BXM2_HUMAN,K9LCN4_HUMAN,K9L8E6_HUMAN,K7QT39_HUMAN,K7P5R9_HUMAN,K4JQY2_HUMAN,J9UP90_HUMAN,J9PWQ9_HUMAN,J9PW07_HUMAN,J7K017_HUMAN,J7F682_HUMAN,J7F577_HUMAN,I7A4E3_HUMAN,I6TRW4_HUMAN,I6RCX9_HUMAN,I6NXG0_HUMAN,I6NWI0_HUMAN,I6NVS4_HUMAN,I4EC43_HUMAN,I3VZ13_HUMAN,I3UI65_HUMAN,I3QHR8_HUMAN,I2B2Z4_HUMAN,I2B2W6_HUMAN,H9C5J4_HUMAN,H9BQ86_HUMAN,H9BQ83_HUMAN,H9BQ82_HUMAN,G9I2L1_HUMAN,G3D6I7_HUMAN,G1EPU3_HUMAN,G1EPN0_HUMAN,G1EPJ1_HUMAN,G1ENJ6_HUMAN,G1ENJ0_HUMAN,G1EMP0_HUMAN,G1EMK6_HUMAN,G0ZMJ0_HUMAN,G0ZMH5_HUMAN,G0Z8C9_HUMAN,G0WVB6_HUMAN,F8SKV9_HUMAN,F8RHF3_HUMAN,F6KRS1_HUMAN,F6KRR7_HUMAN,F6KRQ7_HUMAN,F4YU56_HUMAN,F4YTC4_HUMAN,F4NBP2_HUMAN,F4NBP0_HUMAN,F2X5W5_HUMAN,F2X5T3_HUMAN,F2VNN2_HUMAN,E9LY38_HUMAN,E7BYA5_HUMAN,E3SWI1_HUMAN,E3SWH9_HUMAN,E2GJN0_HUMAN,E2DH92_HUMAN,E2D5Q2_HUMAN,E2D5P9_HUMAN,E2D5N8_HUMAN,D9U3G7_HUMAN,D7NSR4_HUMAN,D5L9C9_HUMAN,D5FWA6_HUMAN,D5FI14_HUMAN,D5FHY1_HUMAN,D5FHV8_HUMAN,D5FHU6_HUMAN,D4HPL2_HUMAN,D4HPB9_HUMAN,D4HPB2_HUMAN,D4HP81_HUMAN,D3Y5Y4_HUMAN,D3U4B8_HUMAN,D2DL25_HUMAN,D2DKQ8_HUMAN,D2DKN8_HUMAN,D2DKN6_HUMAN,D2DKF7_HUMAN,D2DKF6_HUMAN,C9WEP9_HUMAN,C9WEN6_HUMAN,C9WD06_HUMAN,C9WCZ5_HUMAN,C9WCQ2_HUMAN,C9E1H2_HUMAN,C8CH80_HUMAN,C8CAX9_HUMAN,C7FDQ9_HUMAN,C6L830_HUMAN,C5JA70_HUMAN,C3VIU8_HUMAN,B9VWB1_HUMAN,B4DUK6_HUMAN,B2YG95_HUMAN,A7E1C3_HUMAN,A5PHP5_HUMAN,A2VC07_HUMAN	UPI0000000B17	.	.	.	4/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF157,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCCTCATGGT	.	3	ESCA
TBC1D22B	0	.	GRCh37	6	37300161	37300161	+	3'UTR	SNP	G	G	A	rs573512856	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1213G>A	.	.	ENST00000373491	13/13	67	39	28	69	69	0	TBC1D22B,3_prime_UTR_variant,,ENST00000373491,;	A	ENSG00000065491	ENST00000373491	Transcript	3_prime_UTR_variant	2877	.	.	.	.	rs573512856	.	.	1	TBC1D22B	HGNC	21602	protein_coding	YES	CCDS4832.1	ENSP00000362590	TB22B_HUMAN	Q6P4C3_HUMAN,A8KA28_HUMAN	UPI00001C121F	.	.	.	13/13	.	.	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCGGAATC	byFrequency|by1000G	5	ESCA
FAXC	0	.	GRCh37	6	99729215	99729215	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1055G>A	p.Ser352Asn	p.S352N	ENST00000389677	6/6	35	32	3	15	15	0	FAXC,missense_variant,p.Ser72Asn,ENST00000538471,;FAXC,missense_variant,p.Ser352Asn,ENST00000389677,;FAXC,non_coding_transcript_exon_variant,,ENST00000461803,;	T	ENSG00000146267	ENST00000389677	Transcript	missense_variant	1338	1055	352	S/N	aGc/aAc	.	.	.	-1	FAXC	HGNC	20742	protein_coding	YES	CCDS34500.1	ENSP00000374328	FAXC_HUMAN	Q9BR58_HUMAN	UPI000006FEA4	.	deleterious_low_confidence(0.04)	possibly_damaging(0.549)	6/6	.	hmmpanther:PTHR12289:SF27,hmmpanther:PTHR12289	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTGCTGCCT	.	2	ESCA
MUC17	0	.	GRCh37	7	100676006	100676006	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1309G>T	p.Ala437Ser	p.A437S	ENST00000306151	3/13	97	81	16	46	46	0	MUC17,missense_variant,p.Ala437Ser,ENST00000306151,;MUC17,missense_variant,p.Ala437Ser,ENST00000379439,;	T	ENSG00000169876	ENST00000306151	Transcript	missense_variant	1373	1309	437	A/S	Gct/Tct	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	possibly_damaging(0.804)	3/13	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACTGCTGAA	.	4	ESCA
DOCK4	0	.	GRCh37	7	111367457	111367457	+	3'Flank	SNP	T	T	G	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000437633	.	39	28	10	37	37	0	DOCK4,3_prime_UTR_variant,,ENST00000428084,;DOCK4,3_prime_UTR_variant,,ENST00000423057,;DOCK4,downstream_gene_variant,,ENST00000445943,;DOCK4,downstream_gene_variant,,ENST00000494651,;DOCK4,downstream_gene_variant,,ENST00000437633,;DOCK4,downstream_gene_variant,,ENST00000494769,;DOCK4,non_coding_transcript_exon_variant,,ENST00000486186,;	G	ENSG00000128512	ENST00000437633	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	819	-1	DOCK4	HGNC	19192	protein_coding	YES	CCDS47688.1	ENSP00000404179	DOCK4_HUMAN	Q75MU6_HUMAN	UPI0000D5BB0D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGTATTGA	.	5	ESCA
KIAA1549	0	.	GRCh37	7	138603524	138603524	+	Nonsense_Mutation	SNP	A	A	T	rs752375544	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.848T>A	p.Leu283Ter	p.L283*	ENST00000422774	2/20	27	16	10	18	18	0	KIAA1549,stop_gained,p.Leu283Ter,ENST00000422774,;KIAA1549,stop_gained,p.Leu233Ter,ENST00000242365,;KIAA1549,stop_gained,p.Leu283Ter,ENST00000440172,;	T	ENSG00000122778	ENST00000422774	Transcript	stop_gained	897	848	283	L/*	tTa/tAa	rs752375544,COSM1239242,COSM2860437,COSM1239241,COSM2860436	.	.	-1	KIAA1549	HGNC	22219	protein_coding	YES	CCDS56513.1	ENSP00000416040	K1549_HUMAN	.	UPI0001837EBD	.	.	.	2/20	.	hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF4	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTAAAAAA	.	5	ESCA
RP11-1220K2.2	0	.	GRCh37	7	141831824	141831824	+	Missense_Mutation	SNP	G	G	A	rs568239061	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514G>A	p.Val172Met	p.V172M	ENST00000550469	6/13	66	44	21	51	51	0	RP11-1220K2.2,missense_variant,p.Val172Met,ENST00000477922,;RP11-1220K2.2,missense_variant,p.Val172Met,ENST00000550469,;	A	ENSG00000257743	ENST00000550469	Transcript	missense_variant	573	514	172	V/M	Gtg/Atg	rs568239061	.	.	1	RP11-1220K2.2	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000447431	MGAL2_HUMAN	.	UPI00001411D7	.	deleterious(0.02)	benign(0.073)	6/13	.	hmmpanther:PTHR22762:SF55,hmmpanther:PTHR22762,Superfamily_domains:SSF74650	A:0.0006	A:0	A:0	.	A:0	A:0	A:0.0031	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTACGTGGAG	byFrequency|by1000G	5	ESCA
ZNF467	0	.	GRCh37	7	149474801	149474801	+	5'Flank	SNP	C	C	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000302017	.	67	42	25	67	67	0	ZNF467,upstream_gene_variant,,ENST00000302017,;ZNF467,upstream_gene_variant,,ENST00000484747,;SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000262089,;SSPO,intron_variant,,ENST00000486824,;SSPO,upstream_gene_variant,,ENST00000465080,;	A	ENSG00000181444	ENST00000302017	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4233	-1	ZNF467	HGNC	23154	protein_coding	YES	CCDS5899.1	ENSP00000304769	ZN467_HUMAN	.	UPI0000160B41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGGCTTCCA	.	5	ESCA
NUB1	0	.	GRCh37	7	151065005	151065005	+	Missense_Mutation	SNP	G	G	A	rs373576077	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000568733	10/15	47	33	14	30	30	0	NUB1,missense_variant,p.Arg349Gln,ENST00000355851,;NUB1,missense_variant,p.Arg349Gln,ENST00000566856,;NUB1,missense_variant,p.Arg373Gln,ENST00000568733,;NUB1,missense_variant,p.Arg373Gln,ENST00000413040,;NUB1,upstream_gene_variant,,ENST00000460712,;NUB1,upstream_gene_variant,,ENST00000480714,;NUB1,non_coding_transcript_exon_variant,,ENST00000480907,;NUB1,non_coding_transcript_exon_variant,,ENST00000497987,;	A	ENSG00000013374	ENST00000568733	Transcript	missense_variant	1184	1118	373	R/Q	cGa/cAa	rs373576077,COSM206162	.	.	1	NUB1	HGNC	17623	protein_coding	YES	CCDS59089.1	ENSP00000454264	.	H3BM74_HUMAN,C9JRT6_HUMAN,C9J7X7_HUMAN	UPI00021CF908	.	tolerated(0.33)	benign(0.014)	10/15	.	hmmpanther:PTHR12948,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	A:0.0003	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCCGAAACT	byFrequency|byCluster	5	ESCA
GALNTL5	0	.	GRCh37	7	151716773	151716773	+	Missense_Mutation	SNP	T	T	C	rs779333636	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1219T>C	p.Tyr407His	p.Y407H	ENST00000392800	9/9	54	46	7	36	36	0	GALNTL5,missense_variant,p.Tyr407His,ENST00000431418,;GALNTL5,missense_variant,p.Tyr407His,ENST00000392800,;GALNTL5,3_prime_UTR_variant,,ENST00000426341,;GALNTL5,3_prime_UTR_variant,,ENST00000416062,;GALNTL5,3_prime_UTR_variant,,ENST00000448366,;GALNTL5,3_prime_UTR_variant,,ENST00000414073,;GALNTL5,3_prime_UTR_variant,,ENST00000416269,;	C	ENSG00000106648	ENST00000392800	Transcript	missense_variant	1473	1219	407	Y/H	Tac/Cac	rs779333636	.	.	1	GALNTL5	HGNC	21725	protein_coding	YES	CCDS5929.1	ENSP00000376548	GLTL5_HUMAN	.	UPI000013C82E	.	deleterious(0)	probably_damaging(0.976)	9/9	.	Superfamily_domains:SSF53448,hmmpanther:PTHR11675:SF17,hmmpanther:PTHR11675	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACCTACGGA	byFrequency	4	ESCA
NCALD	0	.	GRCh37	8	102698799	102698799	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2738G>A	.	.	ENST00000395923	6/6	19	12	7	17	17	0	NCALD,3_prime_UTR_variant,,ENST00000311028,;NCALD,3_prime_UTR_variant,,ENST00000395923,;NCALD,downstream_gene_variant,,ENST00000521599,;NCALD,downstream_gene_variant,,ENST00000519508,;NCALD,downstream_gene_variant,,ENST00000220931,;NCALD,downstream_gene_variant,,ENST00000522448,;NCALD,downstream_gene_variant,,ENST00000522951,;KB-1107E3.1,non_coding_transcript_exon_variant,,ENST00000518749,;NCALD,downstream_gene_variant,,ENST00000522754,;	T	ENSG00000104490	ENST00000395923	Transcript	3_prime_UTR_variant	3780	.	.	.	.	.	.	.	-1	NCALD	HGNC	7655	protein_coding	YES	CCDS6292.1	ENSP00000379256	NCALD_HUMAN	E5RK89_HUMAN,E5RJT1_HUMAN,E5RJJ6_HUMAN,E5RIZ1_HUMAN,E5RIX3_HUMAN,E5RIG4_HUMAN,E5RI95_HUMAN,E5RI78_HUMAN,E5RHE8_HUMAN,E5RHC8_HUMAN,E5RGZ0_HUMAN,E5RFL9_HUMAN,B2RB70_HUMAN	UPI0000004090	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAATGCCAGGC	.	2	ESCA
SLC25A32	0	.	GRCh37	8	104427088	104427088	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78G>A	p.%3D	p.L26L	ENST00000297578	1/7	80	63	17	56	56	0	SLC25A32,synonymous_variant,p.%3D,ENST00000297578,;DCAF13,5_prime_UTR_variant,,ENST00000297579,;SLC25A32,5_prime_UTR_variant,,ENST00000543107,;DCAF13,upstream_gene_variant,,ENST00000521971,;DCAF13,upstream_gene_variant,,ENST00000519682,;DCAF13,upstream_gene_variant,,ENST00000521716,;DCAF13,upstream_gene_variant,,ENST00000521999,;SLC25A32,synonymous_variant,p.%3D,ENST00000521645,;SLC25A32,synonymous_variant,p.%3D,ENST00000523256,;SLC25A32,synonymous_variant,p.%3D,ENST00000523866,;DCAF13,upstream_gene_variant,,ENST00000518554,;	T	ENSG00000164933	ENST00000297578	Transcript	synonymous_variant	245	78	26	L	ctG/ctA	.	.	.	-1	SLC25A32	HGNC	29683	protein_coding	YES	CCDS6300.1	ENSP00000297578	MFTC_HUMAN	B4DUQ5_HUMAN	UPI0000040C0F	.	.	.	1/7	.	PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF62,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTATCAGGTT	.	5	ESCA
COL22A1	0	.	GRCh37	8	139601151	139601151	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*345C>T	.	.	ENST00000303045	65/65	38	27	10	21	21	0	COL22A1,3_prime_UTR_variant,,ENST00000303045,;COL22A1,3_prime_UTR_variant,,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,;	A	ENSG00000169436	ENST00000303045	Transcript	3_prime_UTR_variant	5673	.	.	.	.	.	.	.	-1	COL22A1	HGNC	22989	protein_coding	YES	CCDS6376.1	ENSP00000303153	COMA1_HUMAN	.	UPI00001C1EA1	.	.	.	65/65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACGCGTCAGA	.	5	ESCA
BAI1	0	.	GRCh37	8	143623556	143623556	+	Missense_Mutation	SNP	G	G	A	rs774828542	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3961G>A	p.Gly1321Ser	p.G1321S	ENST00000517894	28/31	120	87	33	69	69	0	BAI1,missense_variant,p.Gly1321Ser,ENST00000323289,;BAI1,missense_variant,p.Gly1321Ser,ENST00000517894,;BAI1,3_prime_UTR_variant,,ENST00000521208,;BAI1,upstream_gene_variant,,ENST00000518812,;BAI1,downstream_gene_variant,,ENST00000518820,;	A	ENSG00000181790	ENST00000517894	Transcript	missense_variant	4855	3961	1321	G/S	Ggt/Agt	rs774828542,COSM1096844	.	.	1	BAI1	HGNC	943	protein_coding	YES	CCDS64985.1	ENSP00000430945	BAI1_HUMAN	.	UPI00002109E8	.	tolerated(0.36)	possibly_damaging(0.862)	28/31	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTCGGTGAC	byFrequency	5	ESCA
ELP3	0	.	GRCh37	8	28047324	28047324	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*82G>T	.	.	ENST00000256398	15/15	14	7	7	10	10	0	ELP3,3_prime_UTR_variant,,ENST00000380353,;ELP3,3_prime_UTR_variant,,ENST00000537665,;ELP3,3_prime_UTR_variant,,ENST00000521015,;ELP3,3_prime_UTR_variant,,ENST00000523357,;ELP3,3_prime_UTR_variant,,ENST00000542181,;ELP3,3_prime_UTR_variant,,ENST00000524103,;ELP3,3_prime_UTR_variant,,ENST00000256398,;ELP3,3_prime_UTR_variant,,ENST00000517975,;ELP3,3_prime_UTR_variant,,ENST00000523687,;ELP3,3_prime_UTR_variant,,ENST00000518112,;ELP3,3_prime_UTR_variant,,ENST00000519261,;	T	ENSG00000134014	ENST00000256398	Transcript	3_prime_UTR_variant	2103	.	.	.	.	.	.	.	1	ELP3	HGNC	20696	protein_coding	YES	CCDS6065.1	ENSP00000256398	ELP3_HUMAN	E5RIZ7_HUMAN,E5RIC0_HUMAN,E5RHY2_HUMAN,E5RHR2_HUMAN,B4DKA4_HUMAN,B4DIG1_HUMAN	UPI000006F0B5	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGAGGCTGA	.	2	ESCA
NRG1	0	.	GRCh37	8	32621513	32621513	+	Missense_Mutation	SNP	G	G	A	rs376858256	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1531G>A	p.Ala511Thr	p.A511T	ENST00000356819	13/13	86	65	21	43	43	0	NRG1,missense_variant,p.Ala514Thr,ENST00000338921,;NRG1,missense_variant,p.Ala503Thr,ENST00000287842,;NRG1,missense_variant,p.Ala349Thr,ENST00000539990,;NRG1,missense_variant,p.Ala456Thr,ENST00000519301,;NRG1,missense_variant,p.Ala511Thr,ENST00000356819,;NRG1,missense_variant,p.Ala473Thr,ENST00000518104,;NRG1,missense_variant,p.Ala579Thr,ENST00000523534,;NRG1,missense_variant,p.Ala506Thr,ENST00000405005,;NRG1,missense_variant,p.Ala477Thr,ENST00000287845,;NRG1,3_prime_UTR_variant,,ENST00000521670,;NRG1,3_prime_UTR_variant,,ENST00000341377,;NRG1,downstream_gene_variant,,ENST00000523079,;RP11-1002K11.1,upstream_gene_variant,,ENST00000607314,;	A	ENSG00000157168	ENST00000356819	Transcript	missense_variant	2048	1531	511	A/T	Gcg/Acg	rs376858256	.	.	1	NRG1	HGNC	7997	protein_coding	YES	CCDS6083.1	ENSP00000349275	NRG1_HUMAN	Q7RTW5_HUMAN,B7Z168_HUMAN	UPI000013DED7	.	tolerated(0.51)	benign(0.02)	13/13	.	Pfam_domain:PF02158,hmmpanther:PTHR11100,hmmpanther:PTHR11100:SF7	A:0.0004	A:0.0008	A:0	.	A:0	A:0	A:0.001	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCCGCGCAT	byFrequency|byCluster|by1000G	5	ESCA
SNAI2	0	.	GRCh37	8	49831433	49831433	+	Missense_Mutation	SNP	G	G	A	rs376627182	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740C>T	p.Ser247Phe	p.S247F	ENST00000396822	4/4	115	83	32	81	81	0	SNAI2,missense_variant,p.Ser247Phe,ENST00000020945,;SNAI2,missense_variant,p.Ser247Phe,ENST00000396822,;RP11-22C8.1,downstream_gene_variant,,ENST00000438521,;RP11-22C8.1,downstream_gene_variant,,ENST00000522657,;	A	ENSG00000019549	ENST00000396822	Transcript	missense_variant	1098	740	247	S/F	tCc/tTc	rs376627182	.	.	-1	SNAI2	HGNC	11094	protein_coding	YES	CCDS6146.1	ENSP00000380034	SNAI2_HUMAN	.	UPI0000135A3A	.	tolerated(0.06)	benign(0.126)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR11389:SF400,hmmpanther:PTHR11389,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	C:0.0002	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGGAGCAG	.	5	ESCA
TOX	0	.	GRCh37	8	60031650	60031650	+	5'UTR	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-104C>A	.	.	ENST00000361421	1/9	21	15	6	12	12	0	TOX,5_prime_UTR_variant,,ENST00000361421,;RP11-25K19.1,non_coding_transcript_exon_variant,,ENST00000523683,;RP11-25K19.1,upstream_gene_variant,,ENST00000518993,;RP11-25K19.1,upstream_gene_variant,,ENST00000517898,;	T	ENSG00000198846	ENST00000361421	Transcript	5_prime_UTR_variant	118	.	.	.	.	.	.	.	-1	TOX	HGNC	18988	protein_coding	YES	CCDS34897.1	ENSP00000354842	TOX_HUMAN	B4DYA1_HUMAN	UPI0000070A73	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGAGTAAAA	.	5	ESCA
KCNB2	0	.	GRCh37	8	73480515	73480515	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.546G>T	p.Leu182Phe	p.L182F	ENST00000523207	2/3	68	50	18	36	36	0	KCNB2,missense_variant,p.Leu182Phe,ENST00000523207,;	T	ENSG00000182674	ENST00000523207	Transcript	missense_variant	1134	546	182	L/F	ttG/ttT	.	.	.	1	KCNB2	HGNC	6232	protein_coding	YES	CCDS6209.1	ENSP00000430846	KCNB2_HUMAN	.	UPI000012DC85	.	deleterious(0.01)	benign(0.234)	2/3	.	hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF110,Prints_domain:PR01495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTGCTGGA	.	5	ESCA
IL7	0	.	GRCh37	8	79710313	79710313	+	Silent	SNP	T	T	C	rs764670407	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141A>G	p.%3D	p.Q47Q	ENST00000263851	2/6	34	27	7	21	21	0	IL7,synonymous_variant,p.%3D,ENST00000520269,;IL7,synonymous_variant,p.%3D,ENST00000379113,;IL7,synonymous_variant,p.%3D,ENST00000263851,;IL7,synonymous_variant,p.%3D,ENST00000518982,;IL7,non_coding_transcript_exon_variant,,ENST00000521323,;IL7,intron_variant,,ENST00000520215,;IL7,intron_variant,,ENST00000520317,;	C	ENSG00000104432	ENST00000263851	Transcript	synonymous_variant	742	141	47	Q	caA/caG	rs764670407	.	.	-1	IL7	HGNC	6023	protein_coding	YES	CCDS6224.1	ENSP00000263851	IL7_HUMAN	Q5FBY8_HUMAN,D0EYG7_HUMAN	UPI00000622F3	.	.	.	2/6	.	hmmpanther:PTHR10526,Pfam_domain:PF01415,PIRSF_domain:PIRSF001942,SMART_domains:SM00127,Prints_domain:PR00435	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATAATTGATC	.	5	ESCA
REXO1L1P	0	.	GRCh37	8	86573768	86573768	+	Missense_Mutation	SNP	C	C	A	rs768103286	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1959G>T	p.Lys653Asn	p.K653N	ENST00000379010	1/1	794	769	24	446	446	0	REXO1L1P,missense_variant,p.Lys653Asn,ENST00000379010,;	A	ENSG00000205176	ENST00000379010	Transcript	missense_variant	1959	1959	653	K/N	aaG/aaT	rs768103286,COSM360451	.	.	-1	REXO1L1P	HGNC	24660	protein_coding	YES	.	ENSP00000368295	GOR_HUMAN	.	UPI000057A11F	.	deleterious(0.01)	possibly_damaging(0.609)	1/1	.	Superfamily_domains:SSF53098,SMART_domains:SM00479,Gene3D:3.30.420.10,hmmpanther:PTHR12801:SF22,hmmpanther:PTHR12801	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGACCTTCCA	byFrequency	2	ESCA
NBN	0	.	GRCh37	8	90949256	90949256	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2232delT	p.Phe744LeufsTer7	p.F744Lfs*7	ENST00000265433	15/16	65	55	10	37	37	0	NBN,frameshift_variant,p.Phe744LeufsTer7,ENST00000265433,;NBN,frameshift_variant,p.Phe662LeufsTer7,ENST00000409330,;NBN,splice_region_variant,,ENST00000396252,;NBN,splice_region_variant,,ENST00000474821,;	-	ENSG00000104320	ENST00000265433	Transcript	frameshift_variant	2387	2232	744	F/X	ttT/tt	.	.	.	-1	NBN	HGNC	7652	protein_coding	YES	CCDS6249.1	ENSP00000265433	NBN_HUMAN	E5RGR7_HUMAN,E5RGN7_HUMAN	UPI0000073BF4	.	.	.	15/16	.	hmmpanther:PTHR12162,Pfam_domain:PF08599,PIRSF_domain:PIRSF011869	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTACCTAAAAAG	.	3	ESCA
TGFBR1	0	.	GRCh37	9	101912644	101912644	+	3'UTR	SNP	A	A	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1057A>C	.	.	ENST00000374994	9/9	53	35	17	53	53	0	TGFBR1,3_prime_UTR_variant,,ENST00000552516,;TGFBR1,3_prime_UTR_variant,,ENST00000374990,;TGFBR1,3_prime_UTR_variant,,ENST00000374994,;TGFBR1,downstream_gene_variant,,ENST00000550253,;RNA5SP290,upstream_gene_variant,,ENST00000517133,;TGFBR1,downstream_gene_variant,,ENST00000549766,;	C	ENSG00000106799	ENST00000374994	Transcript	3_prime_UTR_variant	2686	.	.	.	.	.	.	.	1	TGFBR1	HGNC	11772	protein_coding	YES	CCDS6738.1	ENSP00000364133	TGFR1_HUMAN	Q5T7S2_HUMAN,F8VVC4_HUMAN,B4DY26_HUMAN	UPI000011D62A	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAAAGTTAT	.	5	ESCA
ABCA1	0	.	GRCh37	9	107543308	107543308	+	3'UTR	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3288G>A	.	.	ENST00000374736	50/50	69	50	19	46	46	0	ABCA1,3_prime_UTR_variant,,ENST00000374736,;NIPSNAP3B,downstream_gene_variant,,ENST00000460936,;	T	ENSG00000165029	ENST00000374736	Transcript	3_prime_UTR_variant	10469	.	.	.	.	.	.	.	-1	ABCA1	HGNC	29	protein_coding	YES	CCDS6762.1	ENSP00000363868	ABCA1_HUMAN	Q9NS76_HUMAN,Q9NP93_HUMAN,Q9H002_HUMAN	UPI000013E441	.	.	.	50/50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCACAGCTT	.	5	ESCA
C9orf9	0	.	GRCh37	9	135763819	135763819	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490C>T	p.Gln164Ter	p.Q164*	ENST00000350499	4/5	75	56	19	60	60	0	C9orf9,stop_gained,p.Gln164Ter,ENST00000372136,;C9orf9,stop_gained,p.Gln164Ter,ENST00000350499,;C9orf9,stop_gained,p.Gln164Ter,ENST00000356311,;TSC1,downstream_gene_variant,,ENST00000298552,;TSC1,downstream_gene_variant,,ENST00000545250,;TSC1,downstream_gene_variant,,ENST00000440111,;	T	ENSG00000165698	ENST00000350499	Transcript	stop_gained	644	490	164	Q/*	Cag/Tag	.	.	.	1	C9orf9	HGNC	1367	protein_coding	YES	CCDS6955.1	ENSP00000298546	CI009_HUMAN	.	UPI0000049CA1	.	.	.	4/5	.	hmmpanther:PTHR32455	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGCAGCAC	.	5	ESCA
TMEM252	0	.	GRCh37	9	71155464	71155464	+	Silent	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267C>T	p.%3D	p.A89A	ENST00000377311	1/2	19	12	6	19	19	0	TMEM252,synonymous_variant,p.%3D,ENST00000377311,;RP11-274B18.2,downstream_gene_variant,,ENST00000446290,;RP11-274B18.4,upstream_gene_variant,,ENST00000413269,;RP11-274B18.2,downstream_gene_variant,,ENST00000432148,;	A	ENSG00000181778	ENST00000377311	Transcript	synonymous_variant	320	267	89	A	gcC/gcT	.	.	.	-1	TMEM252	HGNC	28537	protein_coding	YES	CCDS35040.1	ENSP00000366528	TM252_HUMAN	.	UPI000006D6CF	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTGGCCAC	.	5	ESCA
GCNT1	0	.	GRCh37	9	79120659	79120659	+	3'UTR	SNP	A	A	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2075A>T	.	.	ENST00000442371	3/3	27	15	12	28	28	0	GCNT1,3_prime_UTR_variant,,ENST00000376730,;GCNT1,3_prime_UTR_variant,,ENST00000442371,;GCNT1,3_prime_UTR_variant,,ENST00000444201,;GCNT1,downstream_gene_variant,,ENST00000536223,;GCNT1,downstream_gene_variant,,ENST00000488136,;GCNT1,downstream_gene_variant,,ENST00000480311,;	T	ENSG00000187210	ENST00000442371	Transcript	3_prime_UTR_variant	4301	.	.	.	.	.	.	.	1	GCNT1	HGNC	4203	protein_coding	YES	CCDS6653.1	ENSP00000415454	GCNT1_HUMAN	.	UPI000013CF63	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTAAAAAT	.	5	ESCA
IRS4	0	.	GRCh37	X	107976167	107976167	+	Silent	SNP	C	C	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3408G>A	p.%3D	p.A1136A	ENST00000372129	1/1	44	33	11	41	41	0	IRS4,synonymous_variant,p.%3D,ENST00000372129,;RP6-24A23.6,upstream_gene_variant,,ENST00000563887,;RP6-24A23.3,upstream_gene_variant,,ENST00000608811,;RP6-24A23.3,upstream_gene_variant,,ENST00000436013,;	T	ENSG00000133124	ENST00000372129	Transcript	synonymous_variant	3485	3408	1136	A	gcG/gcA	.	.	.	-1	IRS4	HGNC	6128	protein_coding	YES	CCDS14544.1	ENSP00000361202	IRS4_HUMAN	.	UPI0000073FE7	.	.	.	1/1	.	hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF2,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCCGCAGC	.	5	ESCA
KLHL13	0	.	GRCh37	X	117031945	117031945	+	3'UTR	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*926C>A	.	.	ENST00000539496	8/8	74	43	31	53	53	0	KLHL13,3_prime_UTR_variant,,ENST00000540167,;KLHL13,3_prime_UTR_variant,,ENST00000371876,;KLHL13,3_prime_UTR_variant,,ENST00000539496,;KLHL13,3_prime_UTR_variant,,ENST00000371878,;KLHL13,3_prime_UTR_variant,,ENST00000545703,;KLHL13,3_prime_UTR_variant,,ENST00000371882,;KLHL13,3_prime_UTR_variant,,ENST00000541812,;KLHL13,3_prime_UTR_variant,,ENST00000447671,;KLHL13,3_prime_UTR_variant,,ENST00000262820,;KLHL13,downstream_gene_variant,,ENST00000469946,;	T	ENSG00000003096	ENST00000539496	Transcript	3_prime_UTR_variant	2903	.	.	.	.	.	.	.	-1	KLHL13	HGNC	22931	protein_coding	YES	CCDS55480.1	ENSP00000443191	KLH13_HUMAN	Q96HC9_HUMAN,C9JTS9_HUMAN	UPI0001914B0F	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGGAGTAG	.	5	ESCA
SH2D1A	0	.	GRCh37	X	123505580	123505581	+	3'UTR	INS	-	-	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*344dupT	.	.	ENST00000371139	4/4	182	147	35	102	102	0	SH2D1A,3_prime_UTR_variant,,ENST00000371139,;SH2D1A,downstream_gene_variant,,ENST00000360027,;TENM1,downstream_gene_variant,,ENST00000422452,;SH2D1A,downstream_gene_variant,,ENST00000477673,;TENM1,downstream_gene_variant,,ENST00000371130,;STAG2,intron_variant,,ENST00000469481,;SH2D1A,downstream_gene_variant,,ENST00000494073,;SH2D1A,downstream_gene_variant,,ENST00000491950,;	T	ENSG00000183918	ENST00000371139	Transcript	3_prime_UTR_variant	1025-1026	.	.	.	.	.	.	.	1	SH2D1A	HGNC	10820	protein_coding	YES	CCDS14608.1	ENSP00000360181	SH21A_HUMAN	.	UPI0000000D0B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTCCATTTTT	.	3	ESCA
SLC9A6	0	.	GRCh37	X	135128288	135128289	+	3'UTR	INS	-	-	T	rs781849116	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1413dupT	.	.	ENST00000370695	16/16	58	36	22	48	47	0	SLC9A6,3_prime_UTR_variant,,ENST00000370695,;SLC9A6,3_prime_UTR_variant,,ENST00000370698,;SLC9A6,3_prime_UTR_variant,,ENST00000370701,;	T	ENSG00000198689	ENST00000370695	Transcript	3_prime_UTR_variant	3546-3547	.	.	.	.	rs781849116	.	.	1	SLC9A6	HGNC	11079	protein_coding	YES	CCDS44003.1	ENSP00000359729	SL9A6_HUMAN	Q8WYK8_HUMAN,B4DLY9_HUMAN,B4DK83_HUMAN	UPI0000062320	.	.	.	16/16	.	.	T:0.0003	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTGGATTTTT	by1000G	2	ESCA
FGF13	0	.	GRCh37	X	137714268	137714268	+	3'Flank	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000370603	.	87	58	28	70	70	0	FGF13,3_prime_UTR_variant,,ENST00000441825,;FGF13,3_prime_UTR_variant,,ENST00000315930,;FGF13,3_prime_UTR_variant,,ENST00000305414,;FGF13,downstream_gene_variant,,ENST00000541469,;FGF13,downstream_gene_variant,,ENST00000436198,;FGF13,downstream_gene_variant,,ENST00000370603,;FGF13,downstream_gene_variant,,ENST00000455663,;RP6-27P15.2,downstream_gene_variant,,ENST00000411940,;	T	ENSG00000129682	ENST00000370603	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	743	-1	FGF13	HGNC	3670	protein_coding	YES	CCDS55513.1	ENSP00000359635	FGF13_HUMAN	Q9Y643_HUMAN,B1B1H9_HUMAN,B1AK17_HUMAN	UPI00001484B4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGGTTGAC	.	5	ESCA
MAGEC1	0	.	GRCh37	X	140993740	140993740	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550G>T	p.Glu184Ter	p.E184*	ENST00000285879	4/4	249	192	57	144	144	0	MAGEC1,stop_gained,p.Glu184Ter,ENST00000285879,;MAGEC1,intron_variant,,ENST00000406005,;	T	ENSG00000155495	ENST00000285879	Transcript	stop_gained	836	550	184	E/*	Gag/Tag	.	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S185R|c.555T>A|3,BUFFER|p.Q187Q|c.561A>G|4	RADIA|MUTECT|MUSE|VARSCANS	CCCCTGAGAGT	.	4	ESCA
SLITRK2	0	.	GRCh37	X	144907271	144907271	+	3'UTR	SNP	A	A	G	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*790A>G	.	.	ENST00000370490	1/1	93	60	32	82	82	0	SLITRK2,3_prime_UTR_variant,,ENST00000370490,;SLITRK2,3_prime_UTR_variant,,ENST00000434188,;SLITRK2,3_prime_UTR_variant,,ENST00000428560,;SLITRK2,3_prime_UTR_variant,,ENST00000413937,;SLITRK2,3_prime_UTR_variant,,ENST00000447897,;TMEM257,upstream_gene_variant,,ENST00000408967,;SLITRK2,downstream_gene_variant,,ENST00000335565,;	G	ENSG00000185985	ENST00000370490	Transcript	3_prime_UTR_variant	7583	.	.	.	.	.	.	.	1	SLITRK2	HGNC	13449	protein_coding	YES	CCDS14680.1	ENSP00000359521	SLIK2_HUMAN	B3KTY4_HUMAN	UPI000004E64B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTAAGTCAA	.	5	ESCA
BCAP31	0	.	GRCh37	X	152967491	152967491	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874C>T	p.Arg292Cys	p.R292C	ENST00000458587	7/8	100	66	33	71	71	0	BCAP31,missense_variant,p.Arg292Cys,ENST00000458587,;BCAP31,missense_variant,p.Arg225Cys,ENST00000441714,;BCAP31,missense_variant,p.Arg225Cys,ENST00000345046,;BCAP31,downstream_gene_variant,,ENST00000430088,;BCAP31,downstream_gene_variant,,ENST00000423827,;BCAP31,downstream_gene_variant,,ENST00000429550,;BCAP31,downstream_gene_variant,,ENST00000442093,;BCAP31,downstream_gene_variant,,ENST00000416815,;	A	ENSG00000185825	ENST00000458587	Transcript	missense_variant	1304	874	292	R/C	Cgc/Tgc	.	.	.	-1	BCAP31	HGNC	16695	protein_coding	YES	CCDS48191.1	ENSP00000392330	BAP31_HUMAN	C9JSP1_HUMAN,C9JQ75_HUMAN,C9JMD7_HUMAN,C9JM14_HUMAN,C9J0M4_HUMAN	UPI00001A8439	.	deleterious(0)	probably_damaging(0.996)	7/8	.	hmmpanther:PTHR12701:SF15,hmmpanther:PTHR12701,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGCGGTCGT	.	5	ESCA
MECP2	0	.	GRCh37	X	153295833	153295833	+	Silent	SNP	G	G	A	rs76895094	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1482C>T	p.%3D	p.T494T	ENST00000453960	3/3	71	47	24	51	51	0	MECP2,synonymous_variant,p.%3D,ENST00000303391,;MECP2,synonymous_variant,p.%3D,ENST00000453960,;MECP2,downstream_gene_variant,,ENST00000407218,;MECP2,downstream_gene_variant,,ENST00000415944,;MECP2,downstream_gene_variant,,ENST00000488293,;MECP2,downstream_gene_variant,,ENST00000460227,;MECP2,downstream_gene_variant,,ENST00000486506,;MECP2,downstream_gene_variant,,ENST00000496908,;MECP2,downstream_gene_variant,,ENST00000481807,;MECP2,downstream_gene_variant,,ENST00000463644,;MECP2,downstream_gene_variant,,ENST00000369957,;	A	ENSG00000169057	ENST00000453960	Transcript	synonymous_variant	1537	1482	494	T	acC/acT	rs76895094,RettBASE_c.1446C>T	.	.	-1	MECP2	HGNC	6990	protein_coding	YES	CCDS48193.1	ENSP00000395535	MECP2_HUMAN	.	UPI0000253F1B	.	.	.	3/3	.	hmmpanther:PTHR15074:SF1,hmmpanther:PTHR15074,PIRSF_domain:PIRSF038006	.	.	.	.	.	.	.	.	.	benign	.	.	.	.	.	.	LOW	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCGGTCAC	byFrequency|byCluster	5	ESCA
CHST7	0	.	GRCh37	X	46434207	46434207	+	Silent	SNP	A	A	C	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841A>C	p.%3D	p.R281R	ENST00000276055	1/2	27	21	6	14	14	0	CHST7,synonymous_variant,p.%3D,ENST00000276055,;	C	ENSG00000147119	ENST00000276055	Transcript	synonymous_variant	989	841	281	R	Agg/Cgg	.	.	.	1	CHST7	HGNC	13817	protein_coding	YES	CCDS14268.1	ENSP00000276055	CHST7_HUMAN	.	UPI000000DADD	.	.	.	1/2	.	hmmpanther:PTHR10704:SF5,hmmpanther:PTHR10704,Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCGAGGGCG	.	5	ESCA
AMER1	0	.	GRCh37	X	63405112	63405112	+	3'UTR	SNP	G	G	A	novel	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4647C>T	.	.	ENST00000330258	2/2	61	29	31	32	32	0	AMER1,3_prime_UTR_variant,,ENST00000374869,;AMER1,3_prime_UTR_variant,,ENST00000330258,;AMER1,downstream_gene_variant,,ENST00000403336,;	A	ENSG00000184675	ENST00000330258	Transcript	3_prime_UTR_variant	8328	.	.	.	.	.	.	.	-1	AMER1	HGNC	26837	protein_coding	YES	CCDS14377.2	ENSP00000329117	AMER1_HUMAN	.	UPI0000EDA0FC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGTGGAGAG	.	5	ESCA
ZCCHC13	0	.	GRCh37	X	73524760	73524760	+	3'UTR	DEL	A	A	-	rs200377931	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*166delA	.	.	ENST00000339534	1/1	100	60	40	68	68	0	ZCCHC13,3_prime_UTR_variant,,ENST00000339534,;	-	ENSG00000187969	ENST00000339534	Transcript	3_prime_UTR_variant	736	.	.	.	.	rs200377931	.	.	1	ZCCHC13	HGNC	31749	protein_coding	YES	CCDS14425.1	ENSP00000345633	ZCH13_HUMAN	.	UPI0000070721	.	.	.	1/1	.	.	-:0.0021	-:0.0061	-:0	.	-:0	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGCTAGAAAAAA	byFrequency|byCluster|by1000G	2	ESCA
KIAA2022	0	.	GRCh37	X	73960195	73960195	+	Missense_Mutation	SNP	G	G	T	rs774480770	.	TCGA-JY-A93F-01A-21D-A37C-09	TCGA-JY-A93F-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4197C>A	p.Ser1399Arg	p.S1399R	ENST00000055682	3/4	68	43	24	37	37	0	KIAA2022,missense_variant,p.Ser1399Arg,ENST00000055682,;KIAA2022,coding_sequence_variant,p.%3D,ENST00000424929,;	T	ENSG00000050030	ENST00000055682	Transcript	missense_variant	4809	4197	1399	S/R	agC/agA	rs774480770	.	.	-1	KIAA2022	HGNC	29433	protein_coding	YES	CCDS35337.1	ENSP00000055682	K2022_HUMAN	.	UPI00001C207B	.	deleterious(0.02)	benign(0.299)	3/4	.	hmmpanther:PTHR10322:SF2,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTGCTCAC	byFrequency	5	ESCA
AP2A2	0	.	GRCh37	11	1010963	1010963	+	3'UTR	SNP	G	G	A	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*338G>A	.	.	ENST00000448903	22/22	130	124	6	117	117	0	AP2A2,3_prime_UTR_variant,,ENST00000448903,;MUC6,downstream_gene_variant,,ENST00000421673,;AP2A2,downstream_gene_variant,,ENST00000534328,;MUC6,downstream_gene_variant,,ENST00000532016,;AP2A2,downstream_gene_variant,,ENST00000332231,;AP2A2,downstream_gene_variant,,ENST00000529438,;AP2A2,downstream_gene_variant,,ENST00000525891,;AP2A2,downstream_gene_variant,,ENST00000529427,;AP2A2,downstream_gene_variant,,ENST00000528815,;AP2A2,downstream_gene_variant,,ENST00000528816,;AP2A2,downstream_gene_variant,,ENST00000526401,;AP2A2,downstream_gene_variant,,ENST00000531497,;AP2A2,downstream_gene_variant,,ENST00000526376,;	A	ENSG00000183020	ENST00000448903	Transcript	3_prime_UTR_variant	3299	.	.	.	.	.	.	.	1	AP2A2	HGNC	562	protein_coding	YES	CCDS44512.1	ENSP00000413234	AP2A2_HUMAN	Q9UFK5_HUMAN,E9PS94_HUMAN,E9PQP4_HUMAN,E9PPZ3_HUMAN,E9PNC4_HUMAN	UPI0000124FF5	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATGGCCCGT	.	2	ESCA
AP2A2	0	.	GRCh37	11	1010964	1010964	+	3'UTR	SNP	C	C	T	rs752047868	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*339C>T	.	.	ENST00000448903	22/22	129	123	6	116	116	0	AP2A2,3_prime_UTR_variant,,ENST00000448903,;MUC6,downstream_gene_variant,,ENST00000421673,;AP2A2,downstream_gene_variant,,ENST00000534328,;MUC6,downstream_gene_variant,,ENST00000532016,;AP2A2,downstream_gene_variant,,ENST00000332231,;AP2A2,downstream_gene_variant,,ENST00000529438,;AP2A2,downstream_gene_variant,,ENST00000525891,;AP2A2,downstream_gene_variant,,ENST00000529427,;AP2A2,downstream_gene_variant,,ENST00000528815,;AP2A2,downstream_gene_variant,,ENST00000528816,;AP2A2,downstream_gene_variant,,ENST00000526401,;AP2A2,downstream_gene_variant,,ENST00000531497,;AP2A2,downstream_gene_variant,,ENST00000526376,;	T	ENSG00000183020	ENST00000448903	Transcript	3_prime_UTR_variant	3300	.	.	.	.	rs752047868	.	.	1	AP2A2	HGNC	562	protein_coding	YES	CCDS44512.1	ENSP00000413234	AP2A2_HUMAN	Q9UFK5_HUMAN,E9PS94_HUMAN,E9PQP4_HUMAN,E9PPZ3_HUMAN,E9PNC4_HUMAN	UPI0000124FF5	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGGCCCGTG	.	2	ESCA
SLC17A6	0	.	GRCh37	11	22399084	22399084	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1547G>T	p.Cys516Phe	p.C516F	ENST00000263160	12/12	33	29	4	39	39	0	SLC17A6,missense_variant,p.Cys516Phe,ENST00000263160,;	T	ENSG00000091664	ENST00000263160	Transcript	missense_variant	1984	1547	516	C/F	tGt/tTt	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	deleterious(0.03)	benign(0.197)	12/12	.	hmmpanther:PTHR11662:SF201,hmmpanther:PTHR11662	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAATGTGGAT	.	4	ESCA
KMT2D	0	.	GRCh37	12	49427264	49427264	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11224C>T	p.Gln3742Ter	p.Q3742*	ENST00000301067	39/54	50	41	8	46	46	0	KMT2D,stop_gained,p.Gln3742Ter,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	stop_gained	11224	11224	3742	Q/*	Cag/Tag	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	39/54	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTGTTGCT	.	4	ESCA
RNF31	0	.	GRCh37	14	24626751	24626751	+	Silent	SNP	G	G	A	rs201794587	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2631G>A	p.%3D	p.S877S	ENST00000324103	16/21	50	46	4	44	44	0	RNF31,synonymous_variant,p.%3D,ENST00000559719,;RNF31,synonymous_variant,p.%3D,ENST00000324103,;RNF31,synonymous_variant,p.%3D,ENST00000382687,;RNF31,synonymous_variant,p.%3D,ENST00000560787,;RNF31,synonymous_variant,p.%3D,ENST00000559275,;IRF9,upstream_gene_variant,,ENST00000396864,;IRF9,upstream_gene_variant,,ENST00000559284,;IRF9,upstream_gene_variant,,ENST00000560275,;RNF31,downstream_gene_variant,,ENST00000560754,;IRF9,upstream_gene_variant,,ENST00000557894,;RNA5SP383,upstream_gene_variant,,ENST00000362934,;RP11-468E2.4,synonymous_variant,p.%3D,ENST00000558468,;RNF31,synonymous_variant,p.%3D,ENST00000559449,;RNF31,synonymous_variant,p.%3D,ENST00000483895,;RNF31,3_prime_UTR_variant,,ENST00000491351,;RNF31,non_coding_transcript_exon_variant,,ENST00000559071,;RNF31,non_coding_transcript_exon_variant,,ENST00000558452,;IRF9,upstream_gene_variant,,ENST00000561412,;IRF9,upstream_gene_variant,,ENST00000560365,;IRF9,upstream_gene_variant,,ENST00000560852,;RNF31,upstream_gene_variant,,ENST00000560631,;IRF9,upstream_gene_variant,,ENST00000561009,;RNF31,upstream_gene_variant,,ENST00000559491,;IRF9,upstream_gene_variant,,ENST00000561415,;IRF9,upstream_gene_variant,,ENST00000561342,;	A	ENSG00000092098	ENST00000324103	Transcript	synonymous_variant	2951	2631	877	S	tcG/tcA	rs201794587	.	.	1	RNF31	HGNC	16031	protein_coding	YES	CCDS41931.1	ENSP00000315112	RNF31_HUMAN	H0YNK5_HUMAN,H0YNJ0_HUMAN,H0YNC1_HUMAN,H0YMK6_HUMAN,H0YM83_HUMAN,H0YM57_HUMAN,H0YM13_HUMAN	UPI0000072F93	.	.	.	16/21	.	hmmpanther:PTHR16004,hmmpanther:PTHR16004:SF1,SMART_domains:SM00647,Superfamily_domains:SSF57850	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCTCGTACGC	byCluster|by1000G	3	ESCA
LYSMD4	0	.	GRCh37	15	100272100	100272100	+	Missense_Mutation	SNP	C	C	T	rs370472215	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17G>A	p.Arg6Gln	p.R6Q	ENST00000344791	3/6	78	74	4	78	78	0	LYSMD4,missense_variant,p.Arg6Gln,ENST00000344791,;LYSMD4,missense_variant,p.Arg6Gln,ENST00000450512,;LYSMD4,synonymous_variant,p.%3D,ENST00000409796,;LYSMD4,synonymous_variant,p.%3D,ENST00000332728,;LYSMD4,5_prime_UTR_variant,,ENST00000545021,;LYSMD4,intron_variant,,ENST00000484050,;LYSMD4,intron_variant,,ENST00000604213,;LYSMD4,intron_variant,,ENST00000496108,;LYSMD4,non_coding_transcript_exon_variant,,ENST00000493256,;LYSMD4,non_coding_transcript_exon_variant,,ENST00000479791,;	T	ENSG00000183060	ENST00000344791	Transcript	missense_variant	290	17	6	R/Q	cGg/cAg	rs370472215	.	.	-1	LYSMD4	HGNC	26571	protein_coding	YES	CCDS10381.1	ENSP00000342840	LYSM4_HUMAN	B3KWE4_HUMAN	UPI000021D1F8	.	tolerated_low_confidence(0.21)	benign(0.002)	3/6	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCCCGAGTC	byFrequency|byCluster	2	ESCA
IGF2BP1	0	.	GRCh37	17	47128344	47128344	+	3'UTR	SNP	G	G	A	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1538G>A	.	.	ENST00000290341	15/15	81	76	4	57	57	0	IGF2BP1,3_prime_UTR_variant,,ENST00000290341,;IGF2BP1,downstream_gene_variant,,ENST00000431824,;AC105030.1,downstream_gene_variant,,ENST00000578722,;	A	ENSG00000159217	ENST00000290341	Transcript	3_prime_UTR_variant	3606	.	.	.	.	.	.	.	1	IGF2BP1	HGNC	28866	protein_coding	YES	CCDS11543.1	ENSP00000290341	IF2B1_HUMAN	D3DTW3_HUMAN	UPI0000117170	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATGCGTGGAG	.	2	ESCA
SETBP1	0	.	GRCh37	18	42643239	42643239	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4367G>A	p.Arg1456His	p.R1456H	ENST00000282030	6/6	22	18	4	10	10	0	SETBP1,missense_variant,p.Arg1456His,ENST00000282030,;	A	ENSG00000152217	ENST00000282030	Transcript	missense_variant	4663	4367	1456	R/H	cGt/cAt	COSM3388443	.	.	1	SETBP1	HGNC	15573	protein_coding	YES	CCDS11923.2	ENSP00000282030	SETBP_HUMAN	K7ES17_HUMAN	UPI0000201C54	.	deleterious(0)	probably_damaging(0.996)	6/6	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF322,SMART_domains:SM00384	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGGCGTCCCA	.	4	ESCA
AC139100.2	0	.	GRCh37	18	77920429	77920429	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.127G>T	p.Gly43Cys	p.G43C	ENST00000586421	2/3	28	24	4	35	35	0	AC139100.2,missense_variant,p.Gly43Cys,ENST00000586421,;AC139100.2,missense_variant,p.Gly43Cys,ENST00000587254,;AC139100.2,intron_variant,,ENST00000585422,;PARD6G,intron_variant,,ENST00000353265,;AC139100.2,intron_variant,,ENST00000589574,;	T	ENSG00000267270	ENST00000586421	Transcript	missense_variant	361	127	43	G/C	Ggc/Tgc	.	.	.	1	AC139100.2	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000467155	.	K7ENZ4_HUMAN	UPI000195170D	.	.	probably_damaging(0.992)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CACCCGGCCTC	.	2	ESCA
PRTN3	0	.	GRCh37	19	847929	847929	+	Missense_Mutation	SNP	G	G	T	rs369029250	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731G>T	p.Arg244Leu	p.R244L	ENST00000234347	5/5	27	24	3	13	13	0	PRTN3,missense_variant,p.Arg203Leu,ENST00000544537,;PRTN3,missense_variant,p.Arg244Leu,ENST00000234347,;ELANE,upstream_gene_variant,,ENST00000263621,;ELANE,upstream_gene_variant,,ENST00000590230,;	T	ENSG00000196415	ENST00000234347	Transcript	missense_variant	777	731	244	R/L	cGt/cTt	rs369029250	.	.	1	PRTN3	HGNC	9495	protein_coding	YES	CCDS32860.1	ENSP00000234347	PRTN3_HUMAN	U3KPS2_HUMAN	UPI0000132263	.	deleterious(0.01)	benign(0.011)	5/5	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24257:SF15,hmmpanther:PTHR24257,Gene3D:2.40.10.10,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GATCCGTTCCA	byFrequency|byCluster	2	ESCA
MFN2	0	.	GRCh37	1	12061834	12061834	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.979C>G	p.Leu327Val	p.L327V	ENST00000235329	10/19	36	33	3	23	23	0	MFN2,missense_variant,p.Leu327Val,ENST00000235329,;MFN2,missense_variant,p.Leu327Val,ENST00000444836,;	G	ENSG00000116688	ENST00000235329	Transcript	missense_variant	1301	979	327	L/V	Ctc/Gtc	.	.	.	1	MFN2	HGNC	16877	protein_coding	YES	CCDS30587.1	ENSP00000235329	MFN2_HUMAN	Q5JXC5_HUMAN	UPI0000039854	.	tolerated(0.05)	possibly_damaging(0.721)	10/19	.	PROSITE_profiles:PS51718,hmmpanther:PTHR10465,hmmpanther:PTHR10465:SF1,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCTCTCGCA	.	2	ESCA
CNTN2	0	.	GRCh37	1	205033529	205033529	+	Silent	SNP	C	C	T	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1320C>T	p.%3D	p.C440C	ENST00000331830	11/23	38	35	3	33	33	0	CNTN2,synonymous_variant,p.%3D,ENST00000331830,;AL583832.1,downstream_gene_variant,,ENST00000515887,;CNTN2,non_coding_transcript_exon_variant,,ENST00000527340,;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,;CNTN2,downstream_gene_variant,,ENST00000530117,;CNTN2,upstream_gene_variant,,ENST00000530594,;	T	ENSG00000184144	ENST00000331830	Transcript	synonymous_variant	1604	1320	440	C	tgC/tgT	.	.	.	1	CNTN2	HGNC	2172	protein_coding	YES	CCDS1449.1	ENSP00000330633	CNTN2_HUMAN	.	UPI00001266A5	.	.	.	11/23	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Pfam_domain:PF07679,Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF50,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CCCTGCCAGCC	.	2	ESCA
ASXL1	0	.	GRCh37	20	31022346	31022346	+	Missense_Mutation	SNP	G	G	A	rs372418554	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1831G>A	p.Ala611Thr	p.A611T	ENST00000375687	13/13	147	140	7	80	79	1	ASXL1,missense_variant,p.Ala611Thr,ENST00000375687,;ASXL1,missense_variant,p.Ala606Thr,ENST00000306058,;ASXL1,downstream_gene_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000470145,;ASXL1,downstream_gene_variant,,ENST00000555564,;	A	ENSG00000171456	ENST00000375687	Transcript	missense_variant	2255	1831	611	A/T	Gcc/Acc	rs372418554	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	deleterious(0.05)	benign(0.017)	13/13	.	hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.G605G|c.1815C>T|4,CODON|p.G610G|c.1830C>T|7	MUTECT|MUSE	CTGGCGCCAGG	byFrequency|byCluster	2	ESCA
HEG1	0	.	GRCh37	3	124729390	124729390	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2966G>C	p.Cys989Ser	p.C989S	ENST00000311127	7/17	44	38	6	27	27	0	HEG1,missense_variant,p.Cys989Ser,ENST00000311127,;HEG1,downstream_gene_variant,,ENST00000477536,;HEG1,non_coding_transcript_exon_variant,,ENST00000488654,;	G	ENSG00000173706	ENST00000311127	Transcript	missense_variant	3034	2966	989	C/S	tGt/tCt	.	.	.	-1	HEG1	HGNC	29227	protein_coding	YES	CCDS46898.1	ENSP00000311502	HEG1_HUMAN	.	UPI00006C069B	.	deleterious(0.01)	probably_damaging(1)	7/17	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50026,hmmpanther:PTHR24037:SF2,hmmpanther:PTHR24037,Pfam_domain:PF00008,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCACAGCTG	.	4	ESCA
FRYL	0	.	GRCh37	4	48525101	48525101	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7338C>A	p.Phe2446Leu	p.F2446L	ENST00000358350	54/64	16	12	4	20	20	0	FRYL,missense_variant,p.Phe2446Leu,ENST00000358350,;FRYL,missense_variant,p.Phe1316Leu,ENST00000514617,;FRYL,missense_variant,p.Phe2446Leu,ENST00000503238,;FRYL,missense_variant,p.Phe2446Leu,ENST00000537810,;FRYL,5_prime_UTR_variant,,ENST00000507873,;FRYL,5_prime_UTR_variant,,ENST00000264319,;FRYL,upstream_gene_variant,,ENST00000512810,;FRYL,non_coding_transcript_exon_variant,,ENST00000513401,;	T	ENSG00000075539	ENST00000358350	Transcript	missense_variant	7943	7338	2446	F/L	ttC/ttA	COSM3604292	.	.	-1	FRYL	HGNC	29127	protein_coding	YES	CCDS43227.1	ENSP00000351113	FRYL_HUMAN	.	UPI0000EBC149	.	deleterious(0)	benign(0.129)	54/64	.	hmmpanther:PTHR12295:SF9,hmmpanther:PTHR12295	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V2450G|c.7349T>G|4	RADIA|SOMATICSNIPER|MUSE	CAGTTGAAATT	.	3	ESCA
MARCH3	0	.	GRCh37	5	126206168	126206168	+	3'UTR	SNP	C	C	T	rs551765745	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*157G>A	.	.	ENST00000308660	5/5	67	58	9	46	46	0	MARCH3,3_prime_UTR_variant,,ENST00000308660,;MARCH3,non_coding_transcript_exon_variant,,ENST00000506088,;	T	ENSG00000173926	ENST00000308660	Transcript	3_prime_UTR_variant	1434	.	.	.	.	rs551765745	.	.	-1	MARCH3	HGNC	28728	protein_coding	YES	CCDS4141.1	ENSP00000309141	MARH3_HUMAN	.	UPI000000DC16	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGGCGGAGG	.	4	ESCA
PCDHB11	0	.	GRCh37	5	140580114	140580114	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767T>C	p.Ile256Thr	p.I256T	ENST00000354757	1/1	59	54	5	55	55	0	PCDHB11,missense_variant,p.Ile256Thr,ENST00000354757,;PCDHB11,5_prime_UTR_variant,,ENST00000536699,;PCDHB10,downstream_gene_variant,,ENST00000239446,;	C	ENSG00000197479	ENST00000354757	Transcript	missense_variant	767	767	256	I/T	aTc/aCc	.	.	.	1	PCDHB11	HGNC	8682	protein_coding	YES	CCDS4253.1	ENSP00000346802	PCDBB_HUMAN	B4DSF7_HUMAN	UPI00001273E6	.	deleterious_low_confidence(0.02)	benign(0.005)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF91,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAGCATCCTTG	.	3	ESCA
NSD1	0	.	GRCh37	5	176721258	176721258	+	Missense_Mutation	SNP	A	A	G	rs757698935	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6889A>G	p.Arg2297Gly	p.R2297G	ENST00000439151	23/23	41	37	4	43	43	0	NSD1,missense_variant,p.Arg2194Gly,ENST00000361032,;NSD1,missense_variant,p.Arg2028Gly,ENST00000354179,;NSD1,missense_variant,p.Arg2297Gly,ENST00000439151,;NSD1,missense_variant,p.Arg2028Gly,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000513736,;	G	ENSG00000165671	ENST00000439151	Transcript	missense_variant	6934	6889	2297	R/G	Aga/Gga	rs757698935	.	.	1	NSD1	HGNC	14234	protein_coding	YES	CCDS4412.1	ENSP00000395929	NSD1_HUMAN	Q9H6H8_HUMAN,Q9H6B5_HUMAN,Q96MN8_HUMAN,Q96DQ7_HUMAN,Q658U6_HUMAN,D6RE14_HUMAN,D6RBP3_HUMAN,D6RA90_HUMAN	UPI000006F9C6	.	deleterious_low_confidence(0.01)	benign(0.357)	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGTCAGAGAC	byFrequency	3	ESCA
C6orf48	0	.	GRCh37	6	31802728	31802728	+	5'UTR	SNP	A	A	C	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-384A>C	.	.	ENST00000375640	1/4	117	100	17	96	96	0	C6orf48,5_prime_UTR_variant,,ENST00000375638,;C6orf48,5_prime_UTR_variant,,ENST00000375635,;C6orf48,5_prime_UTR_variant,,ENST00000375640,;C6orf48,5_prime_UTR_variant,,ENST00000395789,;C6orf48,5_prime_UTR_variant,,ENST00000375639,;C6orf48,5_prime_UTR_variant,,ENST00000375642,;C6orf48,intron_variant,,ENST00000375641,;C6orf48,upstream_gene_variant,,ENST00000395788,;HSPA1B,downstream_gene_variant,,ENST00000375650,;C6orf48,upstream_gene_variant,,ENST00000375633,;SNORD52,upstream_gene_variant,,ENST00000364884,;SNORD48,upstream_gene_variant,,ENST00000364953,;	C	ENSG00000204387	ENST00000375640	Transcript	5_prime_UTR_variant	344	.	.	.	.	.	.	.	1	C6orf48	HGNC	19078	protein_coding	YES	CCDS34416.1	ENSP00000364791	G8_HUMAN	.	UPI0000070B70	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTATGAGAGTT	.	4	ESCA
TMEM63B	0	.	GRCh37	6	44122676	44122676	+	3'UTR	SNP	G	G	C	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*56G>C	.	.	ENST00000259746	24/24	52	42	10	44	44	0	TMEM63B,3_prime_UTR_variant,,ENST00000371893,;TMEM63B,3_prime_UTR_variant,,ENST00000323267,;TMEM63B,3_prime_UTR_variant,,ENST00000259746,;CAPN11,upstream_gene_variant,,ENST00000398776,;CAPN11,upstream_gene_variant,,ENST00000532171,;CAPN11,upstream_gene_variant,,ENST00000542245,;TMEM63B,3_prime_UTR_variant,,ENST00000533121,;CAPN11,upstream_gene_variant,,ENST00000526118,;	C	ENSG00000137216	ENST00000259746	Transcript	3_prime_UTR_variant	2738	.	.	.	.	.	.	.	1	TMEM63B	HGNC	17735	protein_coding	YES	CCDS34461.1	ENSP00000259746	TM63B_HUMAN	E9PNG1_HUMAN	UPI000020DDEE	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACGGACAC	.	5	ESCA
F13A1	0	.	GRCh37	6	6174842	6174842	+	Missense_Mutation	SNP	G	G	A	rs113599940	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1718C>T	p.Thr573Met	p.T573M	ENST00000264870	12/15	108	93	15	86	86	0	F13A1,missense_variant,p.Thr573Met,ENST00000264870,;	A	ENSG00000124491	ENST00000264870	Transcript	missense_variant	1984	1718	573	T/M	aCg/aTg	rs113599940,COSM3411230	.	.	-1	F13A1	HGNC	3531	protein_coding	YES	CCDS4496.1	ENSP00000264870	F13A_HUMAN	Q9NQP5_HUMAN	UPI000013D585	.	deleterious(0.01)	benign(0.414)	12/15	.	hmmpanther:PTHR11590:SF42,hmmpanther:PTHR11590,Pfam_domain:PF00927,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000459,Superfamily_domains:SSF49309	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAACGTCTCC	.	4	ESCA
RREB1	0	.	GRCh37	6	7246768	7246768	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4085G>T	p.Gly1362Val	p.G1362V	ENST00000379938	12/13	25	21	3	25	25	0	RREB1,missense_variant,p.Gly1307Val,ENST00000349384,;RREB1,missense_variant,p.Gly1362Val,ENST00000379938,;RREB1,missense_variant,p.Gly1307Val,ENST00000379933,;RREB1,intron_variant,,ENST00000334984,;	T	ENSG00000124782	ENST00000379938	Transcript	missense_variant	4622	4085	1362	G/V	gGg/gTg	.	.	.	1	RREB1	HGNC	10449	protein_coding	YES	CCDS34335.1	ENSP00000369270	RREB1_HUMAN	C9JU34_HUMAN,C9JPJ6_HUMAN,C9JE09_HUMAN	UPI000020E496	.	tolerated(0.14)	benign(0.047)	12/13	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CGCAGGGGATG	.	2	ESCA
PRRT4	0	.	GRCh37	7	127999678	127999678	+	Missense_Mutation	SNP	C	C	T	rs573263452	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.368G>A	p.Arg123Gln	p.R123Q	ENST00000446477	3/6	48	43	5	53	53	0	PRRT4,missense_variant,p.Arg123Gln,ENST00000489517,;PRRT4,missense_variant,p.Arg123Gln,ENST00000489835,;PRRT4,missense_variant,p.Arg123Gln,ENST00000535159,;PRRT4,missense_variant,p.Arg5Gln,ENST00000480290,;PRRT4,missense_variant,p.Arg123Gln,ENST00000446477,;PRRT4,missense_variant,p.Arg123Gln,ENST00000495931,;PRRT4,missense_variant,p.Arg123Gln,ENST00000435512,;PRRT4,missense_variant,p.Arg123Gln,ENST00000464607,;	T	ENSG00000224940	ENST00000446477	Transcript	missense_variant	682	368	123	R/Q	cGg/cAg	rs573263452,COSM1085231	.	.	-1	PRRT4	HGNC	37280	protein_coding	YES	CCDS55160.1	ENSP00000415026	PRRT4_HUMAN	C9JWH6_HUMAN,C9JVX5_HUMAN,C9JQT1_HUMAN	UPI0000DD7E1D	.	tolerated_low_confidence(0.12)	unknown(0)	3/6	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCCGGGGC	by1000G	4	ESCA
AC009365.3	0	.	GRCh37	7	132412309	132412309	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161T>C	p.Leu54Pro	p.L54P	ENST00000332558	5/5	41	37	4	26	26	0	AC009365.3,missense_variant,p.Leu54Pro,ENST00000332558,;	C	ENSG00000183470	ENST00000332558	Transcript	missense_variant	779	161	54	L/P	cTg/cCg	.	.	.	1	AC009365.3	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000331939	YG018_HUMAN	.	UPI0000140A0D	.	deleterious_low_confidence(0)	benign(0)	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGCTGCTGC	.	4	ESCA
NOTCH1	0	.	GRCh37	9	139397632	139397632	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5167+2T>C	.	p.X1723_splice	ENST00000277541	.	128	111	16	77	77	0	NOTCH1,splice_donor_variant,,ENST00000277541,;NOTCH1,splice_donor_variant,,ENST00000494783,;	G	ENSG00000148400	ENST00000277541	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	.	27/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V1721M|c.5161G>A|3	RADIA|MUTECT|MUSE|VARSCANS	CACTTACTCTG	.	4	ESCA
DPH7	0	.	GRCh37	9	140473264	140473264	+	5'UTR	SNP	G	G	C	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-35C>G	.	.	ENST00000277540	1/9	38	34	3	42	42	0	DPH7,5_prime_UTR_variant,,ENST00000277540,;ZMYND19,downstream_gene_variant,,ENST00000298585,;DPH7,non_coding_transcript_exon_variant,,ENST00000472113,;DPH7,non_coding_transcript_exon_variant,,ENST00000467768,;DPH7,non_coding_transcript_exon_variant,,ENST00000479650,;DPH7,non_coding_transcript_exon_variant,,ENST00000491359,;DPH7,non_coding_transcript_exon_variant,,ENST00000476303,;DPH7,non_coding_transcript_exon_variant,,ENST00000475100,;DPH7,upstream_gene_variant,,ENST00000481839,;DPH7,upstream_gene_variant,,ENST00000470855,;DPH7,upstream_gene_variant,,ENST00000460572,;DPH7,upstream_gene_variant,,ENST00000485189,;DPH7,upstream_gene_variant,,ENST00000477690,;	C	ENSG00000148399	ENST00000277540	Transcript	5_prime_UTR_variant	124	.	.	.	.	.	.	.	-1	DPH7	HGNC	25199	protein_coding	YES	CCDS7047.1	ENSP00000277540	DPH7_HUMAN	.	UPI000006F34E	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CAGTAGAGGCG	.	2	ESCA
DLG3	0	.	GRCh37	X	69722994	69722994	+	3'UTR	SNP	C	C	T	novel	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*875C>T	.	.	ENST00000374360	19/19	17	12	5	14	14	0	DLG3,3_prime_UTR_variant,,ENST00000542398,;DLG3,3_prime_UTR_variant,,ENST00000374355,;DLG3,3_prime_UTR_variant,,ENST00000194900,;DLG3,3_prime_UTR_variant,,ENST00000374360,;DLG3,downstream_gene_variant,,ENST00000489733,;DLG3,downstream_gene_variant,,ENST00000466140,;DLG3,downstream_gene_variant,,ENST00000461646,;DLG3,non_coding_transcript_exon_variant,,ENST00000463252,;DLG3,downstream_gene_variant,,ENST00000496931,;	T	ENSG00000082458	ENST00000374360	Transcript	3_prime_UTR_variant	3562	.	.	.	.	.	.	.	1	DLG3	HGNC	2902	protein_coding	YES	CCDS14403.1	ENSP00000363480	DLG3_HUMAN	Q59FY1_HUMAN	UPI000013C60C	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GTGTGCGGACA	.	4	ESCA
RGAG4	0	.	GRCh37	X	71349976	71349976	+	Missense_Mutation	SNP	G	G	C	rs770843646	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1415C>G	p.Pro472Arg	p.P472R	ENST00000545866	1/2	33	29	4	30	30	0	RGAG4,missense_variant,p.Pro472Arg,ENST00000609883,;RGAG4,missense_variant,p.Pro472Arg,ENST00000545866,;NHSL2,intron_variant,,ENST00000540800,;NHSL2,upstream_gene_variant,,ENST00000373677,;NHSL2,upstream_gene_variant,,ENST00000510661,;NHSL2,upstream_gene_variant,,ENST00000535692,;RGAG4,missense_variant,p.Pro472Arg,ENST00000479991,;RP11-262D11.1,upstream_gene_variant,,ENST00000513469,;	C	ENSG00000242732	ENST00000545866	Transcript	missense_variant	1783	1415	472	P/R	cCg/cGg	rs770843646	.	.	-1	RGAG4	HGNC	29430	protein_coding	YES	CCDS55446.1	ENSP00000441366	RGAG4_HUMAN	.	UPI00001C2079	.	deleterious_low_confidence(0)	unknown(0)	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15503:SF2,hmmpanther:PTHR15503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTCGGCTCC	byFrequency	2	ESCA
TSPAN6	0	.	GRCh37	X	99887533	99887533	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-KH-A6WC-01A-11D-A33E-09	TCGA-KH-A6WC-10B-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.618G>C	p.Glu206Asp	p.E206D	ENST00000373020	6/8	64	60	4	93	93	0	TSPAN6,missense_variant,p.Glu206Asp,ENST00000373020,;TSPAN6,downstream_gene_variant,,ENST00000496771,;TSPAN6,downstream_gene_variant,,ENST00000494424,;	G	ENSG00000000003	ENST00000373020	Transcript	missense_variant	730	618	206	E/D	gaG/gaC	COSM176505	.	.	-1	TSPAN6	HGNC	11858	protein_coding	YES	CCDS14470.1	ENSP00000362111	TSN6_HUMAN	.	UPI0000049052	.	tolerated(0.08)	benign(0.021)	6/8	.	hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF169,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Superfamily_domains:0037997	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGACTCTAT	.	2	ESCA
C10orf76	0	.	GRCh37	10	103771512	103771512	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.799C>A	p.Gln267Lys	p.Q267K	ENST00000370033	11/26	16	12	3	34	34	0	C10orf76,missense_variant,p.Gln267Lys,ENST00000370033,;	T	ENSG00000120029	ENST00000370033	Transcript	missense_variant	919	799	267	Q/K	Caa/Aaa	COSM914081	.	.	-1	C10orf76	HGNC	25788	protein_coding	YES	CCDS41563.1	ENSP00000359050	CJ076_HUMAN	.	UPI000047005B	.	tolerated(0.32)	benign(0.01)	11/26	.	hmmpanther:PTHR13608:SF3,hmmpanther:PTHR13608,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTGGTGTT	.	5	ESCA
SUFU	0	.	GRCh37	10	104386980	104386980	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1345G>T	p.Asp449Tyr	p.D449Y	ENST00000369902	11/12	28	24	4	12	12	0	SUFU,missense_variant,p.Asp449Tyr,ENST00000369902,;	T	ENSG00000107882	ENST00000369902	Transcript	missense_variant	1511	1345	449	D/Y	Gat/Tat	.	.	.	1	SUFU	HGNC	16466	protein_coding	YES	CCDS7537.1	ENSP00000358918	SUFU_HUMAN	.	UPI0000073C79	.	tolerated(1)	benign(0.163)	11/12	.	hmmpanther:PTHR10928:SF2,hmmpanther:PTHR10928,Pfam_domain:PF12470,PIRSF_domain:PIRSF011844	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE	TAGAAGATTTG	.	2	ESCA
PDCD11	0	.	GRCh37	10	105204417	105204417	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5422C>A	p.His1808Asn	p.H1808N	ENST00000369797	35/36	28	17	11	19	19	0	PDCD11,missense_variant,p.His1808Asn,ENST00000369797,;CALHM2,downstream_gene_variant,,ENST00000369788,;CALHM2,downstream_gene_variant,,ENST00000393235,;CALHM2,downstream_gene_variant,,ENST00000260743,;CALHM2,downstream_gene_variant,,ENST00000494180,;PDCD11,non_coding_transcript_exon_variant,,ENST00000478543,;	A	ENSG00000148843	ENST00000369797	Transcript	missense_variant	5516	5422	1808	H/N	Cac/Aac	.	.	.	1	PDCD11	HGNC	13408	protein_coding	YES	CCDS31276.1	ENSP00000358812	RRP5_HUMAN	.	UPI00001C1ED1	.	deleterious(0)	benign(0.137)	35/36	.	hmmpanther:PTHR23270,hmmpanther:PTHR23270:SF5,Gene3D:1.25.40.10,Pfam_domain:PF05843,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAAGCACGGC	.	5	ESCA
DCLRE1C	0	.	GRCh37	10	14995953	14995953	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57C>T	p.%3D	p.F19F	ENST00000378278	1/14	83	78	4	95	95	0	DCLRE1C,synonymous_variant,p.%3D,ENST00000378278,;DCLRE1C,synonymous_variant,p.%3D,ENST00000378289,;DCLRE1C,5_prime_UTR_variant,,ENST00000396817,;DCLRE1C,5_prime_UTR_variant,,ENST00000378258,;DCLRE1C,5_prime_UTR_variant,,ENST00000378241,;DCLRE1C,5_prime_UTR_variant,,ENST00000378254,;DCLRE1C,5_prime_UTR_variant,,ENST00000418843,;DCLRE1C,5_prime_UTR_variant,,ENST00000378246,;DCLRE1C,5_prime_UTR_variant,,ENST00000378255,;DCLRE1C,5_prime_UTR_variant,,ENST00000378249,;DCLRE1C,5_prime_UTR_variant,,ENST00000456122,;DCLRE1C,5_prime_UTR_variant,,ENST00000357717,;DCLRE1C,5_prime_UTR_variant,,ENST00000453695,;	A	ENSG00000152457	ENST00000378278	Transcript	synonymous_variant	95	57	19	F	ttC/ttT	.	.	.	-1	DCLRE1C	HGNC	17642	protein_coding	YES	CCDS31149.1	ENSP00000367527	DCR1C_HUMAN	B3KSJ7_HUMAN	UPI000013EEDC	.	.	.	1/14	.	hmmpanther:PTHR23240,hmmpanther:PTHR23240:SF8,Gene3D:3.60.15.10,Superfamily_domains:SSF56281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTATCGAAGCG	.	2	ESCA
SYNPO2L	0	.	GRCh37	10	75413174	75413174	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495C>T	p.%3D	p.P165P	ENST00000394810	3/4	47	28	18	29	29	0	SYNPO2L,synonymous_variant,p.%3D,ENST00000394810,;SYNPO2L,synonymous_variant,p.%3D,ENST00000606523,;SYNPO2L,upstream_gene_variant,,ENST00000372873,;RP11-464F9.21,upstream_gene_variant,,ENST00000607450,;RP11-464F9.21,upstream_gene_variant,,ENST00000606726,;	A	ENSG00000166317	ENST00000394810	Transcript	synonymous_variant	645	495	165	P	ccC/ccT	.	.	.	-1	SYNPO2L	HGNC	23532	protein_coding	YES	CCDS44438.1	ENSP00000378289	SYP2L_HUMAN	U3KQD0_HUMAN	UPI000042704D	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24217:SF10,hmmpanther:PTHR24217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTGGGCCT	.	5	ESCA
RRP12	0	.	GRCh37	10	99160097	99160097	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334C>T	p.Arg112Cys	p.R112C	ENST00000370992	2/34	31	28	3	22	22	0	RRP12,missense_variant,p.Arg112Cys,ENST00000414986,;RRP12,missense_variant,p.Arg112Cys,ENST00000315563,;RRP12,missense_variant,p.Arg112Cys,ENST00000370992,;RP11-452K12.7,upstream_gene_variant,,ENST00000422848,;	A	ENSG00000052749	ENST00000370992	Transcript	missense_variant	446	334	112	R/C	Cgc/Tgc	.	.	.	-1	RRP12	HGNC	29100	protein_coding	YES	CCDS7457.1	ENSP00000360031	RRP12_HUMAN	.	UPI000013E51C	.	deleterious(0)	probably_damaging(0.962)	2/34	.	hmmpanther:PTHR21576:SF2,hmmpanther:PTHR21576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAAGCGCTGTA	.	3	ESCA
KRTAP5-3	0	.	GRCh37	11	1628947	1628947	+	Silent	SNP	G	G	A	rs544320132,rs747926844	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.669C>T	p.%3D	p.S223S	ENST00000399685	1/1	76	63	13	134	134	0	KRTAP5-3,synonymous_variant,p.%3D,ENST00000399685,;	A	ENSG00000196224	ENST00000399685	Transcript	synonymous_variant	747	669	223	S	tcC/tcT	rs544320132,rs747926844	.	.	-1	KRTAP5-3	HGNC	23598	protein_coding	YES	CCDS41591.1	ENSP00000382592	KRA53_HUMAN	.	UPI000037605E	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF16	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGGGAGGAGCA	byFrequency|by1000G	3	ESCA
KRTAP5-3	0	.	GRCh37	11	1628956	1628956	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660G>A	p.%3D	p.K220K	ENST00000399685	1/1	76	63	12	143	143	0	KRTAP5-3,synonymous_variant,p.%3D,ENST00000399685,;	T	ENSG00000196224	ENST00000399685	Transcript	synonymous_variant	738	660	220	K	aaG/aaA	.	.	.	-1	KRTAP5-3	HGNC	23598	protein_coding	YES	CCDS41591.1	ENSP00000382592	KRA53_HUMAN	.	UPI000037605E	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGGGCTTGCA	.	3	ESCA
ARHGEF17	0	.	GRCh37	11	73080017	73080017	+	3'UTR	SNP	G	G	C	rs537983274	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1192G>C	.	.	ENST00000263674	21/21	14	11	3	18	18	0	ARHGEF17,3_prime_UTR_variant,,ENST00000263674,;ARHGEF17,downstream_gene_variant,,ENST00000543530,;ARHGEF17,downstream_gene_variant,,ENST00000536481,;	C	ENSG00000110237	ENST00000263674	Transcript	3_prime_UTR_variant	7734	.	.	.	.	rs537983274	.	.	1	ARHGEF17	HGNC	21726	protein_coding	YES	CCDS8221.1	ENSP00000263674	ARHGH_HUMAN	.	UPI000004980B	.	.	.	21/21	.	.	C:0.0004	C:0	C:0.0014	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTGGGGTGG	byFrequency|byCluster|by1000G	2	ESCA
ARRB1	0	.	GRCh37	11	74995295	74995295	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141T>A	p.Tyr47Ter	p.Y47*	ENST00000420843	4/16	50	31	19	28	28	0	ARRB1,stop_gained,p.Tyr42Ter,ENST00000532525,;ARRB1,stop_gained,p.Tyr47Ter,ENST00000360025,;ARRB1,stop_gained,p.Tyr47Ter,ENST00000420843,;ARRB1,stop_gained,p.Tyr47Ter,ENST00000393505,;ARRB1,missense_variant,p.Ile65Asn,ENST00000527385,;ARRB1,missense_variant,p.Ile62Asn,ENST00000524400,;ARRB1,3_prime_UTR_variant,,ENST00000533609,;ARRB1,non_coding_transcript_exon_variant,,ENST00000529280,;ARRB1,non_coding_transcript_exon_variant,,ENST00000533255,;ARRB1,upstream_gene_variant,,ENST00000530086,;	T	ENSG00000137486	ENST00000420843	Transcript	stop_gained	239	141	47	Y/*	taT/taA	.	.	.	-1	ARRB1	HGNC	711	protein_coding	YES	CCDS44684.1	ENSP00000409581	ARRB1_HUMAN	.	UPI0000126076	.	.	.	4/16	.	hmmpanther:PTHR11792:SF22,hmmpanther:PTHR11792,Gene3D:1g4mA01,Pfam_domain:PF00339,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGATACTC	.	5	ESCA
KLRK1	0	.	GRCh37	12	10530782	10530782	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482C>A	p.Pro161Gln	p.P161Q	ENST00000240618	7/8	56	26	29	21	21	0	KLRK1,missense_variant,p.Pro161Gln,ENST00000540818,;KLRK1,missense_variant,p.Pro161Gln,ENST00000240618,;RP11-277P12.20,intron_variant,,ENST00000500682,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000591546,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000586581,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000543572,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000590131,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000543812,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000539300,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000588263,;KLRC4-KLRK1,3_prime_UTR_variant,,ENST00000585711,;KLRK1,3_prime_UTR_variant,,ENST00000396451,;KLRK1,non_coding_transcript_exon_variant,,ENST00000544449,;KLRK1,non_coding_transcript_exon_variant,,ENST00000540267,;KLRC4-KLRK1,downstream_gene_variant,,ENST00000585507,;KLRC4-KLRK1,downstream_gene_variant,,ENST00000539370,;KLRC4-KLRK1,downstream_gene_variant,,ENST00000588447,;KLRC4-KLRK1,downstream_gene_variant,,ENST00000591937,;KLRC4-KLRK1,downstream_gene_variant,,ENST00000590323,;	T	ENSG00000213809	ENST00000240618	Transcript	missense_variant	623	482	161	P/Q	cCa/cAa	.	.	.	-1	KLRK1	HGNC	18788	protein_coding	YES	CCDS8623.1	ENSP00000240618	NKG2D_HUMAN	Q8WZ67_HUMAN	UPI000013CAB1	.	tolerated(0.32)	benign(0.003)	7/8	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22800:SF14,hmmpanther:PTHR22800,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTGGAATG	.	5	ESCA
PDE3A	0	.	GRCh37	12	20807069	20807069	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3114C>T	p.%3D	p.D1038D	ENST00000359062	15/16	58	45	13	23	23	0	PDE3A,synonymous_variant,p.%3D,ENST00000359062,;PDE3A,non_coding_transcript_exon_variant,,ENST00000544307,;	T	ENSG00000172572	ENST00000359062	Transcript	synonymous_variant	3154	3114	1038	D	gaC/gaT	.	.	.	1	PDE3A	HGNC	8778	protein_coding	YES	CCDS31754.1	ENSP00000351957	PDE3A_HUMAN	.	UPI000014175F	.	.	.	15/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11347:SF104,hmmpanther:PTHR11347,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGACCCAGA	.	5	ESCA
CNTN1	0	.	GRCh37	12	41323615	41323615	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514T>C	p.Trp172Arg	p.W172R	ENST00000551295	7/24	44	35	8	27	27	0	CNTN1,missense_variant,p.Trp172Arg,ENST00000360099,;CNTN1,missense_variant,p.Trp172Arg,ENST00000551295,;CNTN1,missense_variant,p.Trp172Arg,ENST00000347616,;CNTN1,missense_variant,p.Trp161Arg,ENST00000348761,;CNTN1,missense_variant,p.Trp172Arg,ENST00000547849,;CNTN1,missense_variant,p.Trp172Arg,ENST00000547702,;	C	ENSG00000018236	ENST00000551295	Transcript	missense_variant	631	514	172	W/R	Tgg/Cgg	.	.	.	1	CNTN1	HGNC	2171	protein_coding	YES	CCDS8737.1	ENSP00000447006	CNTN1_HUMAN	F8VX96_HUMAN,F8VUI9_HUMAN,F8VUI8_HUMAN,F8VQW3_HUMAN	UPI0000127EBA	.	deleterious(0)	probably_damaging(1)	7/24	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF531,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGCTGGCTT	.	5	ESCA
ESPL1	0	.	GRCh37	12	53663505	53663505	+	Missense_Mutation	SNP	G	G	A	rs761300540	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.779G>A	p.Arg260His	p.R260H	ENST00000257934	3/31	27	23	4	21	21	0	ESPL1,missense_variant,p.Arg260His,ENST00000257934,;ESPL1,missense_variant,p.Arg260His,ENST00000552462,;ESPL1,downstream_gene_variant,,ENST00000553219,;ESPL1,upstream_gene_variant,,ENST00000550026,;ESPL1,3_prime_UTR_variant,,ENST00000552671,;	A	ENSG00000135476	ENST00000257934	Transcript	missense_variant	870	779	260	R/H	cGt/cAt	rs761300540	.	.	1	ESPL1	HGNC	16856	protein_coding	YES	CCDS8852.1	ENSP00000257934	ESPL1_HUMAN	H3BRX7_HUMAN	UPI00003668C3	.	deleterious(0)	probably_damaging(0.978)	3/31	.	hmmpanther:PTHR12792	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCCGTCGCT	byFrequency	4	ESCA
R3HDM2	0	.	GRCh37	12	57647802	57647802	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*754C>T	.	.	ENST00000347140	24/24	26	23	3	25	25	0	R3HDM2,3_prime_UTR_variant,,ENST00000402412,;R3HDM2,3_prime_UTR_variant,,ENST00000347140,;R3HDM2,3_prime_UTR_variant,,ENST00000358907,;R3HDM2,intron_variant,,ENST00000413953,;R3HDM2,downstream_gene_variant,,ENST00000429355,;STAC3,upstream_gene_variant,,ENST00000332782,;STAC3,upstream_gene_variant,,ENST00000546246,;STAC3,upstream_gene_variant,,ENST00000553489,;STAC3,upstream_gene_variant,,ENST00000554578,;R3HDM2,downstream_gene_variant,,ENST00000403821,;R3HDM2,downstream_gene_variant,,ENST00000548161,;R3HDM2,downstream_gene_variant,,ENST00000441731,;R3HDM2,downstream_gene_variant,,ENST00000546843,;R3HDM2,non_coding_transcript_exon_variant,,ENST00000393811,;RP11-123K3.4,intron_variant,,ENST00000548184,;STAC3,upstream_gene_variant,,ENST00000553294,;STAC3,upstream_gene_variant,,ENST00000557176,;	A	ENSG00000179912	ENST00000347140	Transcript	3_prime_UTR_variant	4076	.	.	.	.	.	.	.	-1	R3HDM2	HGNC	29167	protein_coding	YES	CCDS8937.2	ENSP00000317903	R3HD2_HUMAN	C9J7N6_HUMAN	UPI00005A60D3	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGAGAGAAT	.	2	ESCA
SRGAP1	0	.	GRCh37	12	64491124	64491124	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1782G>T	p.Lys594Asn	p.K594N	ENST00000355086	15/22	39	32	7	22	21	0	SRGAP1,missense_variant,p.Lys531Asn,ENST00000543397,;SRGAP1,missense_variant,p.Lys571Asn,ENST00000357825,;SRGAP1,missense_variant,p.Lys594Asn,ENST00000355086,;RP11-196H14.2,intron_variant,,ENST00000535594,;	T	ENSG00000196935	ENST00000355086	Transcript	missense_variant	2306	1782	594	K/N	aaG/aaT	.	.	.	1	SRGAP1	HGNC	17382	protein_coding	YES	CCDS8967.1	ENSP00000347198	SRGP1_HUMAN	.	UPI00001A9CB9	.	tolerated(0.06)	possibly_damaging(0.783)	15/22	.	PROSITE_profiles:PS50238,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF15,Pfam_domain:PF00620,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTAAGGAAAG	.	5	ESCA
SRGAP1	0	.	GRCh37	12	64536104	64536104	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2910G>A	p.%3D	p.L970L	ENST00000355086	22/22	25	20	5	11	11	0	SRGAP1,synonymous_variant,p.%3D,ENST00000543397,;SRGAP1,synonymous_variant,p.%3D,ENST00000357825,;SRGAP1,synonymous_variant,p.%3D,ENST00000355086,;RP11-196H14.3,downstream_gene_variant,,ENST00000536455,;SRGAP1,non_coding_transcript_exon_variant,,ENST00000542841,;	A	ENSG00000196935	ENST00000355086	Transcript	synonymous_variant	3434	2910	970	L	ttG/ttA	.	.	.	1	SRGAP1	HGNC	17382	protein_coding	YES	CCDS8967.1	ENSP00000347198	SRGP1_HUMAN	.	UPI00001A9CB9	.	.	.	22/22	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTGAATGA	.	5	ESCA
CPSF6	0	.	GRCh37	12	69663599	69663599	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*311C>G	.	.	ENST00000435070	10/10	46	37	8	25	25	0	CPSF6,3_prime_UTR_variant,,ENST00000266679,;CPSF6,3_prime_UTR_variant,,ENST00000435070,;CPSF6,3_prime_UTR_variant,,ENST00000456847,;CPSF6,downstream_gene_variant,,ENST00000551516,;	G	ENSG00000111605	ENST00000435070	Transcript	3_prime_UTR_variant	2077	.	.	.	.	.	.	.	1	CPSF6	HGNC	13871	protein_coding	YES	CCDS8988.1	ENSP00000391774	CPSF6_HUMAN	.	UPI00001FC746	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGTCAAGTA	.	5	ESCA
NDFIP2	0	.	GRCh37	13	80117762	80117762	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785A>G	p.Tyr262Cys	p.Y262C	ENST00000218652	5/8	78	57	21	48	48	0	NDFIP2,missense_variant,p.Tyr262Cys,ENST00000218652,;NDFIP2,missense_variant,p.Tyr159Cys,ENST00000487865,;NDFIP2,intron_variant,,ENST00000465762,;	G	ENSG00000102471	ENST00000218652	Transcript	missense_variant	837	785	262	Y/C	tAt/tGt	.	.	.	1	NDFIP2	HGNC	18537	protein_coding	YES	CCDS31998.1	ENSP00000218652	NFIP2_HUMAN	.	UPI000015F962	.	deleterious(0.03)	probably_damaging(0.999)	5/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR13396,hmmpanther:PTHR13396:SF4,Pfam_domain:PF10176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGTATGGTG	.	5	ESCA
ARHGAP5	0	.	GRCh37	14	32560528	32560528	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.653A>G	p.Asn218Ser	p.N218S	ENST00000345122	2/7	27	21	5	13	13	0	ARHGAP5,missense_variant,p.Asn218Ser,ENST00000432921,;ARHGAP5,missense_variant,p.Asn218Ser,ENST00000539826,;ARHGAP5,missense_variant,p.Asn218Ser,ENST00000345122,;ARHGAP5,missense_variant,p.Asn218Ser,ENST00000556611,;ARHGAP5,intron_variant,,ENST00000554090,;ARHGAP5,intron_variant,,ENST00000396582,;ARHGAP5,intron_variant,,ENST00000433497,;ARHGAP5,downstream_gene_variant,,ENST00000556191,;ARHGAP5,downstream_gene_variant,,ENST00000555814,;ARHGAP5,upstream_gene_variant,,ENST00000557643,;	G	ENSG00000100852	ENST00000345122	Transcript	missense_variant	968	653	218	N/S	aAt/aGt	.	.	.	1	ARHGAP5	HGNC	675	protein_coding	YES	CCDS32062.1	ENSP00000371897	RHG05_HUMAN	G3V5I7_HUMAN,G3V444_HUMAN,G3V360_HUMAN	UPI000057B85C	.	tolerated(1)	benign(0.015)	2/7	.	hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF4,Pfam_domain:PF00071,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAAATAAAA	.	5	ESCA
NAA30	0	.	GRCh37	14	57866569	57866569	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.919A>G	p.Ile307Val	p.I307V	ENST00000556492	4/5	33	22	11	27	27	0	NAA30,missense_variant,p.Ile119Val,ENST00000298406,;NAA30,missense_variant,p.Ile49Val,ENST00000555166,;NAA30,missense_variant,p.Ile307Val,ENST00000556492,;NAA30,intron_variant,,ENST00000554703,;	G	ENSG00000139977	ENST00000556492	Transcript	missense_variant	1073	919	307	I/V	Ata/Gta	.	.	.	1	NAA30	HGNC	19844	protein_coding	YES	CCDS32088.1	ENSP00000452521	NAA30_HUMAN	B4DK34_HUMAN	UPI0000161013	.	deleterious(0)	possibly_damaging(0.627)	4/5	.	PROSITE_profiles:PS51186,hmmpanther:PTHR23091,hmmpanther:PTHR23091:SF209,Gene3D:3.40.630.30,Pfam_domain:PF00583,Superfamily_domains:SSF55729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTATATAT	.	5	ESCA
MAN2C1	0	.	GRCh37	15	75656447	75656447	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683C>T	p.Pro228Leu	p.P228L	ENST00000565683	6/26	48	40	7	36	36	0	MAN2C1,missense_variant,p.Pro228Leu,ENST00000565683,;MAN2C1,missense_variant,p.Pro228Leu,ENST00000267978,;MAN2C1,missense_variant,p.Pro228Leu,ENST00000569482,;MAN2C1,intron_variant,,ENST00000563622,;MAN2C1,downstream_gene_variant,,ENST00000566256,;MAN2C1,downstream_gene_variant,,ENST00000561615,;MAN2C1,downstream_gene_variant,,ENST00000568374,;RP11-817O13.8,upstream_gene_variant,,ENST00000563278,;MAN2C1,intron_variant,,ENST00000563539,;MAN2C1,upstream_gene_variant,,ENST00000566253,;MAN2C1,missense_variant,p.Pro111Leu,ENST00000570257,;MAN2C1,3_prime_UTR_variant,,ENST00000565784,;MAN2C1,3_prime_UTR_variant,,ENST00000569355,;MAN2C1,3_prime_UTR_variant,,ENST00000566634,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000565699,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563441,;MAN2C1,intron_variant,,ENST00000421803,;MAN2C1,upstream_gene_variant,,ENST00000563794,;MAN2C1,downstream_gene_variant,,ENST00000569069,;MAN2C1,upstream_gene_variant,,ENST00000563058,;MAN2C1,upstream_gene_variant,,ENST00000566013,;MAN2C1,downstream_gene_variant,,ENST00000562071,;MAN2C1,upstream_gene_variant,,ENST00000562461,;MAN2C1,upstream_gene_variant,,ENST00000568944,;MAN2C1,upstream_gene_variant,,ENST00000565801,;MAN2C1,upstream_gene_variant,,ENST00000564570,;MAN2C1,upstream_gene_variant,,ENST00000563596,;MAN2C1,downstream_gene_variant,,ENST00000565534,;MAN2C1,upstream_gene_variant,,ENST00000563013,;MAN2C1,downstream_gene_variant,,ENST00000565652,;MAN2C1,upstream_gene_variant,,ENST00000564785,;MAN2C1,upstream_gene_variant,,ENST00000567163,;MAN2C1,upstream_gene_variant,,ENST00000563368,;MAN2C1,upstream_gene_variant,,ENST00000565953,;MAN2C1,upstream_gene_variant,,ENST00000562228,;MAN2C1,upstream_gene_variant,,ENST00000569176,;	A	ENSG00000140400	ENST00000565683	Transcript	missense_variant	695	683	228	P/L	cCc/cTc	.	.	.	-1	MAN2C1	HGNC	6827	protein_coding	YES	CCDS58391.1	ENSP00000457788	MA2C1_HUMAN	H3BRV3_HUMAN	UPI0000229CBC	.	deleterious(0.03)	benign(0.118)	6/26	.	hmmpanther:PTHR11607:SF15,hmmpanther:PTHR11607,Gene3D:3.20.110.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCGGGCTGG	.	5	ESCA
UBE2Q2	0	.	GRCh37	15	76192832	76192832	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1033A>G	.	.	ENST00000267938	13/13	42	30	11	39	39	0	UBE2Q2,3_prime_UTR_variant,,ENST00000338677,;UBE2Q2,3_prime_UTR_variant,,ENST00000569423,;UBE2Q2,3_prime_UTR_variant,,ENST00000426727,;UBE2Q2,3_prime_UTR_variant,,ENST00000267938,;FBXO22,upstream_gene_variant,,ENST00000308275,;FBXO22,upstream_gene_variant,,ENST00000540507,;UBE2Q2,downstream_gene_variant,,ENST00000561851,;FBXO22,upstream_gene_variant,,ENST00000569054,;FBXO22,upstream_gene_variant,,ENST00000453211,;FBXO22,upstream_gene_variant,,ENST00000565036,;UBE2Q2,downstream_gene_variant,,ENST00000563966,;FBXO22,upstream_gene_variant,,ENST00000565131,;UBE2Q2,downstream_gene_variant,,ENST00000567921,;FBXO22,upstream_gene_variant,,ENST00000569022,;FBXO22,upstream_gene_variant,,ENST00000569749,;UBE2Q2,downstream_gene_variant,,ENST00000561723,;	G	ENSG00000140367	ENST00000267938	Transcript	3_prime_UTR_variant	2543	.	.	.	.	.	.	.	1	UBE2Q2	HGNC	19248	protein_coding	YES	CCDS10286.1	ENSP00000267938	UB2Q2_HUMAN	B4DFQ2_HUMAN	UPI0000073AF9	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATCAGTCCT	.	5	ESCA
CREBBP	0	.	GRCh37	16	3786138	3786138	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4627G>C	p.Asp1543His	p.D1543H	ENST00000262367	28/31	74	55	18	59	59	0	CREBBP,missense_variant,p.Asp1505His,ENST00000382070,;CREBBP,missense_variant,p.Asp1543His,ENST00000262367,;CREBBP,downstream_gene_variant,,ENST00000573517,;CREBBP,downstream_gene_variant,,ENST00000570939,;CREBBP,non_coding_transcript_exon_variant,,ENST00000576720,;CREBBP,non_coding_transcript_exon_variant,,ENST00000571763,;CREBBP,downstream_gene_variant,,ENST00000574740,;CREBBP,downstream_gene_variant,,ENST00000572569,;	G	ENSG00000005339	ENST00000262367	Transcript	missense_variant	5437	4627	1543	D/H	Gat/Cat	CM065107,COSM460549,COSM3957565	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	unknown(0)	28/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5,Pfam_domain:PF08214	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAATCACCTT	.	5	ESCA
ITFG1	0	.	GRCh37	16	47345168	47345168	+	Silent	SNP	T	T	C	rs370897829	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1053A>G	p.%3D	p.L351L	ENST00000320640	10/18	41	21	20	30	30	0	ITFG1,synonymous_variant,p.%3D,ENST00000320640,;ITFG1,synonymous_variant,p.%3D,ENST00000544001,;RP11-474B12.1,intron_variant,,ENST00000564739,;Y_RNA,downstream_gene_variant,,ENST00000410835,;ITFG1,non_coding_transcript_exon_variant,,ENST00000537184,;ITFG1,non_coding_transcript_exon_variant,,ENST00000542691,;ITFG1,non_coding_transcript_exon_variant,,ENST00000568047,;	C	ENSG00000129636	ENST00000320640	Transcript	synonymous_variant	1282	1053	351	L	ctA/ctG	rs370897829	.	.	-1	ITFG1	HGNC	30697	protein_coding	YES	CCDS10728.1	ENSP00000319918	TIP_HUMAN	H3BQ64_HUMAN,B4DSA2_HUMAN,B4DHQ9_HUMAN	UPI0000039EB3	.	.	.	10/18	.	hmmpanther:PTHR13412:SF0,hmmpanther:PTHR13412,Gene3D:3nigC00,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTTAGTAT	byFrequency|byCluster	5	ESCA
OSGIN1	0	.	GRCh37	16	83992949	83992949	+	Missense_Mutation	SNP	C	C	A	rs755464394	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.152C>A	p.Pro51His	p.P51H	ENST00000361711	3/6	21	17	4	11	11	0	OSGIN1,missense_variant,p.Pro51His,ENST00000361711,;OSGIN1,missense_variant,p.Pro51His,ENST00000565123,;OSGIN1,missense_variant,p.Pro134His,ENST00000343939,;OSGIN1,missense_variant,p.Pro51His,ENST00000393306,;OSGIN1,missense_variant,p.Pro51His,ENST00000567707,;OSGIN1,downstream_gene_variant,,ENST00000561552,;OSGIN1,downstream_gene_variant,,ENST00000563543,;	A	ENSG00000140961	ENST00000361711	Transcript	missense_variant	624	152	51	P/H	cCc/cAc	rs755464394	.	.	1	OSGIN1	HGNC	30093	protein_coding	YES	CCDS10939.1	ENSP00000355374	OSGI1_HUMAN	J3KRK7_HUMAN,H3BTF9_HUMAN	UPI000006CF29	.	deleterious(0.04)	benign(0.349)	3/6	.	hmmpanther:PTHR15192,hmmpanther:PTHR15192:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACCCCCTGC	byFrequency	4	ESCA
TUSC5	0	.	GRCh37	17	1198846	1198846	+	Missense_Mutation	SNP	G	G	A	rs751457450	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.449G>A	p.Arg150Gln	p.R150Q	ENST00000333813	2/3	56	48	7	34	34	0	TUSC5,missense_variant,p.Arg150Gln,ENST00000333813,;	A	ENSG00000184811	ENST00000333813	Transcript	missense_variant	788	449	150	R/Q	cGg/cAg	rs751457450	.	.	1	TUSC5	HGNC	29592	protein_coding	YES	CCDS42225.1	ENSP00000329548	TUSC5_HUMAN	.	UPI0000200566	.	deleterious(0.04)	benign(0.158)	2/3	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR14948,hmmpanther:PTHR14948:SF1,Pfam_domain:PF04505	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTCGGCTGC	.	4	ESCA
SDF2	0	.	GRCh37	17	26976284	26976284	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359C>T	p.Ala120Val	p.A120V	ENST00000247020	3/3	45	41	4	27	27	0	SDF2,missense_variant,p.Ala120Val,ENST00000247020,;SDF2,intron_variant,,ENST00000587788,;KIAA0100,upstream_gene_variant,,ENST00000544884,;KIAA0100,upstream_gene_variant,,ENST00000389003,;KIAA0100,upstream_gene_variant,,ENST00000528896,;SDF2,non_coding_transcript_exon_variant,,ENST00000592250,;SDF2,non_coding_transcript_exon_variant,,ENST00000585749,;SDF2,non_coding_transcript_exon_variant,,ENST00000587629,;SDF2,non_coding_transcript_exon_variant,,ENST00000587338,;SDF2,intron_variant,,ENST00000588472,;SDF2,3_prime_UTR_variant,,ENST00000591903,;SDF2,non_coding_transcript_exon_variant,,ENST00000589788,;KIAA0100,upstream_gene_variant,,ENST00000580882,;KIAA0100,upstream_gene_variant,,ENST00000583403,;KIAA0100,upstream_gene_variant,,ENST00000577417,;	A	ENSG00000132581	ENST00000247020	Transcript	missense_variant	658	359	120	A/V	gCt/gTt	.	.	.	-1	SDF2	HGNC	10675	protein_coding	YES	CCDS11238.1	ENSP00000247020	SDF2_HUMAN	Q6IBU4_HUMAN	UPI000013CC0C	.	deleterious(0)	probably_damaging(0.97)	3/3	.	PROSITE_profiles:PS50919,hmmpanther:PTHR10050:SF10,hmmpanther:PTHR10050,Gene3D:2.80.10.50,Pfam_domain:PF02815,SMART_domains:SM00472,Superfamily_domains:SSF82109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CAAAAGCACTC	.	2	ESCA
FBXL20	0	.	GRCh37	17	37437666	37437666	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672G>A	p.%3D	p.V224V	ENST00000264658	9/15	19	14	5	10	10	0	FBXL20,synonymous_variant,p.%3D,ENST00000394294,;FBXL20,synonymous_variant,p.%3D,ENST00000264658,;FBXL20,synonymous_variant,p.%3D,ENST00000583610,;FBXL20,synonymous_variant,p.%3D,ENST00000577399,;	T	ENSG00000108306	ENST00000264658	Transcript	synonymous_variant	933	672	224	V	gtG/gtA	.	.	.	-1	FBXL20	HGNC	24679	protein_coding	YES	CCDS32640.1	ENSP00000264658	FXL20_HUMAN	.	UPI000000D932	.	.	.	9/15	.	hmmpanther:PTHR23125,hmmpanther:PTHR23125:SF209,Gene3D:3.80.10.10,Pfam_domain:PF13516,SMART_domains:SM00367,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGTCACCAG	.	5	ESCA
CSF3	0	.	GRCh37	17	38171850	38171850	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40+83C>T	.	.	ENST00000225474	.	62	58	4	49	49	0	CSF3,5_prime_UTR_variant,,ENST00000577675,;CSF3,5_prime_UTR_variant,,ENST00000331769,;CSF3,intron_variant,,ENST00000225474,;CSF3,intron_variant,,ENST00000394149,;CSF3,intron_variant,,ENST00000394148,;CSF3,intron_variant,,ENST00000583218,;MED24,downstream_gene_variant,,ENST00000422942,;MED24,downstream_gene_variant,,ENST00000501516,;MED24,downstream_gene_variant,,ENST00000356271,;MED24,downstream_gene_variant,,ENST00000394128,;MED24,downstream_gene_variant,,ENST00000394126,;MED24,downstream_gene_variant,,ENST00000394127,;RP11-387H17.6,upstream_gene_variant,,ENST00000583462,;RP11-387H17.6,upstream_gene_variant,,ENST00000584649,;MED24,downstream_gene_variant,,ENST00000470126,;CSF3,non_coding_transcript_exon_variant,,ENST00000479880,;CSF3,intron_variant,,ENST00000579852,;CSF3,intron_variant,,ENST00000582798,;MED24,downstream_gene_variant,,ENST00000579364,;MED24,downstream_gene_variant,,ENST00000535508,;MED24,downstream_gene_variant,,ENST00000491466,;	T	ENSG00000108342	ENST00000225474	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CSF3	HGNC	2438	protein_coding	YES	CCDS11357.1	ENSP00000225474	CSF3_HUMAN	.	UPI0000128525	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCCCGTTCT	.	2	ESCA
SDK2	0	.	GRCh37	17	71426704	71426704	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1529G>C	p.Gly510Ala	p.G510A	ENST00000392650	12/45	23	18	5	27	27	0	SDK2,missense_variant,p.Gly510Ala,ENST00000388726,;SDK2,missense_variant,p.Gly510Ala,ENST00000392650,;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,;	G	ENSG00000069188	ENST00000392650	Transcript	missense_variant	1530	1529	510	G/A	gGc/gCc	.	.	.	-1	SDK2	HGNC	19308	protein_coding	YES	CCDS45769.1	ENSP00000376421	SDK2_HUMAN	.	UPI0000E5A088	.	deleterious(0)	probably_damaging(1)	12/45	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF37,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGGTGCCCTTG	.	4	ESCA
CD68	0	.	GRCh37	17	7483026	7483026	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31C>T	p.%3D	p.L11L	ENST00000250092	1/6	44	30	13	48	48	0	CD68,synonymous_variant,p.%3D,ENST00000250092,;CD68,synonymous_variant,p.%3D,ENST00000584502,;CD68,synonymous_variant,p.%3D,ENST00000380498,;EIF4A1,downstream_gene_variant,,ENST00000584784,;EIF4A1,downstream_gene_variant,,ENST00000583802,;CD68,upstream_gene_variant,,ENST00000584180,;MPDU1,upstream_gene_variant,,ENST00000396501,;EIF4A1,downstream_gene_variant,,ENST00000380512,;EIF4A1,downstream_gene_variant,,ENST00000577929,;MPDU1,upstream_gene_variant,,ENST00000250124,;EIF4A1,downstream_gene_variant,,ENST00000584860,;MPDU1,upstream_gene_variant,,ENST00000579445,;EIF4A1,downstream_gene_variant,,ENST00000582169,;EIF4A1,downstream_gene_variant,,ENST00000578495,;EIF4A1,downstream_gene_variant,,ENST00000578754,;EIF4A1,downstream_gene_variant,,ENST00000293831,;EIF4A1,downstream_gene_variant,,ENST00000581770,;MPDU1,upstream_gene_variant,,ENST00000581380,;MPDU1,upstream_gene_variant,,ENST00000582151,;MPDU1,upstream_gene_variant,,ENST00000584378,;MPDU1,upstream_gene_variant,,ENST00000585217,;EIF4A1,downstream_gene_variant,,ENST00000581384,;EIF4A1,downstream_gene_variant,,ENST00000585024,;MPDU1,upstream_gene_variant,,ENST00000423172,;EIF4A1,downstream_gene_variant,,ENST00000582746,;EIF4A1,downstream_gene_variant,,ENST00000577269,;EIF4A1,downstream_gene_variant,,ENST00000583389,;SNORD10,downstream_gene_variant,,ENST00000459579,;SNORA48,downstream_gene_variant,,ENST00000386847,;SNORA67,downstream_gene_variant,,ENST00000384423,;AC113189.5,downstream_gene_variant,,ENST00000417897,;AC113189.5,downstream_gene_variant,,ENST00000572046,;AC113189.5,downstream_gene_variant,,ENST00000415124,;AC113189.5,downstream_gene_variant,,ENST00000573187,;SNORA67,non_coding_transcript_exon_variant,,ENST00000581621,;SENP3-EIF4A1,downstream_gene_variant,,ENST00000579777,;EIF4A1,downstream_gene_variant,,ENST00000581808,;EIF4A1,downstream_gene_variant,,ENST00000577738,;EIF4A1,downstream_gene_variant,,ENST00000582213,;MPDU1,upstream_gene_variant,,ENST00000575256,;MPDU1,upstream_gene_variant,,ENST00000580834,;EIF4A1,downstream_gene_variant,,ENST00000577731,;EIF4A1,downstream_gene_variant,,ENST00000580461,;EIF4A1,downstream_gene_variant,,ENST00000578324,;EIF4A1,downstream_gene_variant,,ENST00000581841,;MPDU1,upstream_gene_variant,,ENST00000585188,;EIF4A1,downstream_gene_variant,,ENST00000584901,;EIF4A1,downstream_gene_variant,,ENST00000581544,;MPDU1,upstream_gene_variant,,ENST00000574558,;MPDU1,upstream_gene_variant,,ENST00000572836,;MPDU1,upstream_gene_variant,,ENST00000571391,;EIF4A1,downstream_gene_variant,,ENST00000583899,;MPDU1,upstream_gene_variant,,ENST00000570458,;EIF4A1,downstream_gene_variant,,ENST00000584798,;MPDU1,upstream_gene_variant,,ENST00000571822,;MPDU1,upstream_gene_variant,,ENST00000576066,;EIF4A1,downstream_gene_variant,,ENST00000580888,;MPDU1,upstream_gene_variant,,ENST00000584479,;EIF4A1,downstream_gene_variant,,ENST00000578476,;EIF4A1,downstream_gene_variant,,ENST00000583217,;MPDU1,upstream_gene_variant,,ENST00000577088,;EIF4A1,downstream_gene_variant,,ENST00000580886,;EIF4A1,downstream_gene_variant,,ENST00000582848,;MPDU1,upstream_gene_variant,,ENST00000576272,;EIF4A1,downstream_gene_variant,,ENST00000584054,;MPDU1,upstream_gene_variant,,ENST00000572719,;EIF4A1,downstream_gene_variant,,ENST00000584712,;MPDU1,upstream_gene_variant,,ENST00000580708,;MPDU1,upstream_gene_variant,,ENST00000581886,;EIF4A1,downstream_gene_variant,,ENST00000396527,;EIF4A1,downstream_gene_variant,,ENST00000579085,;EIF4A1,downstream_gene_variant,,ENST00000578569,;MPDU1,upstream_gene_variant,,ENST00000359822,;EIF4A1,downstream_gene_variant,,ENST00000579139,;MPDU1,upstream_gene_variant,,ENST00000578267,;EIF4A1,downstream_gene_variant,,ENST00000582050,;MPDU1,upstream_gene_variant,,ENST00000572936,;	T	ENSG00000129226	ENST00000250092	Transcript	synonymous_variant	242	31	11	L	Ctg/Ttg	.	.	.	1	CD68	HGNC	1693	protein_coding	YES	CCDS11114.1	ENSP00000250092	CD68_HUMAN	B4DNT7_HUMAN	UPI000013CCA1	.	.	.	1/6	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11506:SF2,hmmpanther:PTHR11506	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCCTGCTG	.	5	ESCA
TP53	0	.	GRCh37	17	7578526	7578527	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403dupT	p.Cys135LeufsTer14	p.C135Lfs*14	ENST00000269305	5/11	51	33	18	21	21	0	TP53,frameshift_variant,p.Cys135LeufsTer14,ENST00000508793,;TP53,frameshift_variant,p.Cys135LeufsTer14,ENST00000413465,;TP53,frameshift_variant,p.Cys128LeufsTer14,ENST00000604348,;TP53,frameshift_variant,p.Cys135LeufsTer14,ENST00000420246,;TP53,frameshift_variant,p.Cys135LeufsTer14,ENST00000269305,;TP53,frameshift_variant,p.Cys3LeufsTer14,ENST00000509690,;TP53,frameshift_variant,p.Cys135LeufsTer14,ENST00000359597,;TP53,frameshift_variant,p.Cys42LeufsTer14,ENST00000514944,;TP53,frameshift_variant,p.Cys135LeufsTer14,ENST00000445888,;TP53,frameshift_variant,p.Cys135LeufsTer14,ENST00000455263,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	593-594	403-404	135	C/LX	tgc/tTgc	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.C3W|c.9C>G|4,CODON|p.C42W|c.126C>G|3,CODON|p.C135W|c.405C>G|3,CODON|p.C135W|c.405C>G|3,CODON|p.C135C|c.405C>T|5,CODON|p.C135*|c.405C>A|8,CODON|p.C135W|c.405C>G|24,CODON|p.C135F|c.404G>T|6,CODON|p.C3S|c.8G>C|3,CODON|p.C135S|c.404G>C|3,CODON|p.C3F|c.8G>T|13,CODON|p.C135S|c.404G>C|3,CODON|p.C42F|c.125G>T|13,CODON|p.C42S|c.125G>C|3,CODON|p.C135F|c.404G>T|6,CODON|p.C135Y|c.404G>A|8,CODON|p.C135Y|c.404G>A|54,CODON|p.C135S|c.404G>C|9,CODON|p.C135Y|c.404G>A|3,CODON|p.C42Y|c.125G>A|8,CODON|p.C135Y|c.404G>A|3,CODON|p.C135F|c.404G>T|13,CODON|p.C135F|c.404G>T|13,CODON|p.C135F|c.404G>T|49,CODON|p.C135Y|c.404G>A|8,CODON|p.C3Y|c.8G>A|8,CODON|p.C135fs*35|c.403delT|5,BUFFER|p.K139*|c.415A>T|3,BUFFER|p.K139*|c.415A>T|5,BUFFER|p.K7*|c.19A>T|3,BUFFER|p.K139*|c.415A>T|3,BUFFER|p.K139E|c.415A>G|4,BUFFER|p.K46*|c.136A>T|3,BUFFER|p.A138fs*32|c.412delG|5,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A6V|c.17C>T|4,BUFFER|p.A45V|c.134C>T|4,BUFFER|p.A138V|c.413C>T|21,BUFFER|p.A138P|c.412G>C|14,BUFFER|p.A138T|c.412G>A|5,BUFFER|p.A138fs*11|c.411_412insN|3,BUFFER|p.L137L|c.411G>A|3,BUFFER|p.L137P|c.410T>C|3,BUFFER|p.L137Q|c.410T>A|3,BUFFER|p.Q136H|c.408A>C|5,BUFFER|p.Q136Q|c.408A>G|4,BUFFER|p.Q136P|c.407A>C|3,BUFFER|p.Q136E|c.406C>G|9,BUFFER|p.Q136*|c.406C>T|35,BUFFER|p.Q4*|c.10C>T|5,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q43*|c.127C>T|5,BUFFER|p.Q4E|c.10C>G|6,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q136E|c.406C>G|4,BUFFER|p.Q136E|c.406C>G|5,BUFFER|p.Q43E|c.127C>G|6,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|3,BUFFER|p.C135G|c.403T>G|8,BUFFER|p.C135S|c.403T>A|4,BUFFER|p.C135R|c.403T>C|11,BUFFER|p.C135fs*35|c.400delT|6,BUFFER|p.F134S|c.401T>C|4,BUFFER|p.F134C|c.401T>G|9,BUFFER|p.F134V|c.400T>G|11,BUFFER|p.F41L|c.121T>C|4,BUFFER|p.F134L|c.400T>C|3,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F2L|c.4T>C|4,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F134L|c.400T>C|18,BUFFER|p.M133T|c.398T>C|5,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M40T|c.119T>C|3,BUFFER|p.M1T|c.2T>C|3,BUFFER|p.M1R|c.2T>G|3,BUFFER|p.M133R|c.398T>G|7,BUFFER|p.M133K|c.398T>A|12,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M40R|c.119T>G|3,BUFFER|p.Y126_K132delYSPALNK|c.376_396del21|6,BUFFER|p.K132N|c.396G>C|29,BUFFER|p.K132N|c.396G>T|3,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>C|5,BUFFER|p.K132N|c.396G>T|24,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>T|6,BUFFER|p.N131delN|c.393_395delCAA|4,BUFFER|p.K132R|c.395A>G|5,BUFFER|p.K132T|c.395A>C|7,BUFFER|p.K39T|c.116A>C|3,BUFFER|p.K132R|c.395A>G|39,BUFFER|p.K132M|c.395A>T|10,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K39R|c.116A>G|7,BUFFER|p.K132Q|c.394A>C|13,BUFFER|p.K39E|c.115A>G|3,BUFFER|p.K132*|c.394A>T|5,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|19,BUFFER|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.N131delN|c.391_393delAAC|8	INDELOCATOR*|VARSCANI*|PINDEL	GTTGGCAAAAC	.	3	ESCA
TCF4	0	.	GRCh37	18	52891704	52891704	+	3'Flank	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000398339	.	23	18	5	25	25	0	TCF4,3_prime_UTR_variant,,ENST00000354452,;TCF4,3_prime_UTR_variant,,ENST00000356073,;TCF4,downstream_gene_variant,,ENST00000570177,;TCF4,downstream_gene_variant,,ENST00000568740,;TCF4,downstream_gene_variant,,ENST00000565018,;TCF4,downstream_gene_variant,,ENST00000566279,;TCF4,downstream_gene_variant,,ENST00000568673,;TCF4,downstream_gene_variant,,ENST00000537578,;TCF4,downstream_gene_variant,,ENST00000544241,;TCF4,downstream_gene_variant,,ENST00000398339,;TCF4,downstream_gene_variant,,ENST00000564403,;TCF4,downstream_gene_variant,,ENST00000570287,;TCF4,downstream_gene_variant,,ENST00000543082,;TCF4,downstream_gene_variant,,ENST00000566286,;TCF4,downstream_gene_variant,,ENST00000567880,;TCF4,downstream_gene_variant,,ENST00000564228,;TCF4,downstream_gene_variant,,ENST00000537856,;TCF4,downstream_gene_variant,,ENST00000540999,;TCF4,downstream_gene_variant,,ENST00000561831,;TCF4,downstream_gene_variant,,ENST00000564999,;TCF4,downstream_gene_variant,,ENST00000457482,;TCF4,downstream_gene_variant,,ENST00000561992,;TCF4,downstream_gene_variant,,ENST00000562680,;	T	ENSG00000196628	ENST00000398339	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3463	-1	TCF4	HGNC	11634	protein_coding	YES	CCDS58631.1	ENSP00000381382	.	K7ERJ0_HUMAN,H3BUQ3_HUMAN,H3BTM9_HUMAN,H3BTC3_HUMAN,H3BT24_HUMAN,H3BSX3_HUMAN,H3BRF7_HUMAN,H3BPG3_HUMAN,H3BP59_HUMAN,H3BNZ2_HUMAN,H3BNI2_HUMAN,H3BME8_HUMAN,H3BMC8_HUMAN,G0LNT8_HUMAN,G0LNT7_HUMAN,G0LNT4_HUMAN,G0LNT3_HUMAN,E9PH57_HUMAN	UPI000059D58C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTGTGCTT	.	5	ESCA
NOTCH3	0	.	GRCh37	19	15292541	15292541	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2638G>A	p.Ala880Thr	p.A880T	ENST00000263388	17/33	119	110	8	93	93	0	NOTCH3,missense_variant,p.Ala880Thr,ENST00000263388,;NOTCH3,missense_variant,p.Ala827Thr,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,;	T	ENSG00000074181	ENST00000263388	Transcript	missense_variant	2714	2638	880	A/T	Gcc/Acc	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	tolerated(0.71)	benign(0.009)	17/33	.	Superfamily_domains:SSF57184,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Gene3D:2gy5A03,Pfam_domain:PF00008,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCCGGCGAAAC	.	2	ESCA
THOP1	0	.	GRCh37	19	2790452	2790452	+	Missense_Mutation	SNP	C	C	T	rs200100559	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50C>T	p.Pro17Leu	p.P17L	ENST00000307741	2/13	36	32	3	13	13	0	THOP1,missense_variant,p.Pro7Leu,ENST00000585338,;THOP1,missense_variant,p.Pro17Leu,ENST00000307741,;THOP1,non_coding_transcript_exon_variant,,ENST00000586780,;THOP1,non_coding_transcript_exon_variant,,ENST00000585673,;	T	ENSG00000172009	ENST00000307741	Transcript	missense_variant	253	50	17	P/L	cCg/cTg	rs200100559	.	.	1	THOP1	HGNC	11793	protein_coding	YES	CCDS12095.1	ENSP00000304467	THOP1_HUMAN	Q9BW75_HUMAN,K7EKB6_HUMAN,K7EIK4_HUMAN	UPI0000000C3E	.	deleterious(0.01)	benign(0.2)	2/13	.	hmmpanther:PTHR11804:SF34,hmmpanther:PTHR11804	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTCCGTGCT	byCluster|by1000G	4	ESCA
GPI	0	.	GRCh37	19	34890655	34890655	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1539C>T	p.%3D	p.G513G	ENST00000415930	17/18	80	57	23	45	45	0	GPI,synonymous_variant,p.%3D,ENST00000415930,;GPI,synonymous_variant,p.%3D,ENST00000588991,;GPI,synonymous_variant,p.%3D,ENST00000356487,;RP11-618P17.4,intron_variant,,ENST00000592740,;GPI,intron_variant,,ENST00000586425,;RP11-618P17.4,upstream_gene_variant,,ENST00000606020,;PDCD2L,upstream_gene_variant,,ENST00000246535,;GPI,non_coding_transcript_exon_variant,,ENST00000586077,;GPI,non_coding_transcript_exon_variant,,ENST00000586392,;GPI,downstream_gene_variant,,ENST00000589985,;PDCD2L,upstream_gene_variant,,ENST00000587385,;	T	ENSG00000105220	ENST00000415930	Transcript	synonymous_variant	1709	1539	513	G	ggC/ggT	.	.	.	1	GPI	HGNC	4458	protein_coding	YES	CCDS54246.1	ENSP00000405573	G6PI_HUMAN	K7EPY4_HUMAN,K7ERK8_HUMAN,K7ELR7_HUMAN,K7EIL4_HUMAN,B4DE36_HUMAN	UPI00017A6DE4	.	.	.	17/18	.	hmmpanther:PTHR11469,hmmpanther:PTHR11469:SF4,HAMAP:MF_00473,PROSITE_profiles:PS51463,Prints_domain:PR00662,Prints_domain:PR00662,Superfamily_domains:SSF53697,Pfam_domain:PF00342,Gene3D:3.40.50.10490,PROSITE_patterns:PS00174	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCATCAT	.	5	ESCA
SUPT5H	0	.	GRCh37	19	39959492	39959492	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1134G>T	p.Met378Ile	p.M378I	ENST00000599117	15/31	14	9	5	17	17	0	SUPT5H,missense_variant,p.Met378Ile,ENST00000432763,;SUPT5H,missense_variant,p.Met378Ile,ENST00000598725,;SUPT5H,missense_variant,p.Met374Ile,ENST00000402194,;SUPT5H,missense_variant,p.Met378Ile,ENST00000599117,;SUPT5H,missense_variant,p.Met374Ile,ENST00000359191,;SUPT5H,downstream_gene_variant,,ENST00000593727,;SUPT5H,non_coding_transcript_exon_variant,,ENST00000599335,;SUPT5H,downstream_gene_variant,,ENST00000598520,;SUPT5H,upstream_gene_variant,,ENST00000596208,;SUPT5H,downstream_gene_variant,,ENST00000599907,;SUPT5H,upstream_gene_variant,,ENST00000598117,;	T	ENSG00000196235	ENST00000599117	Transcript	missense_variant	1501	1134	378	M/I	atG/atT	.	.	.	1	SUPT5H	HGNC	11469	protein_coding	YES	CCDS12536.1	ENSP00000470252	SPT5H_HUMAN	M0R2M5_HUMAN,M0R105_HUMAN,B4E0Q4_HUMAN,B4DZJ7_HUMAN	UPI000006D81A	.	tolerated(0.53)	benign(0.023)	15/31	.	hmmpanther:PTHR11125,PIRSF_domain:PIRSF036945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATGTCTGC	.	5	ESCA
PSMC4	0	.	GRCh37	19	40480482	40480482	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.521A>T	p.Lys174Met	p.K174M	ENST00000157812	5/11	17	12	5	13	13	0	PSMC4,missense_variant,p.Lys174Met,ENST00000157812,;PSMC4,missense_variant,p.Lys143Met,ENST00000455878,;PSMC4,non_coding_transcript_exon_variant,,ENST00000593455,;PSMC4,non_coding_transcript_exon_variant,,ENST00000596386,;PSMC4,non_coding_transcript_exon_variant,,ENST00000601697,;PSMC4,upstream_gene_variant,,ENST00000601194,;	T	ENSG00000013275	ENST00000157812	Transcript	missense_variant	719	521	174	K/M	aAg/aTg	.	.	.	1	PSMC4	HGNC	9551	protein_coding	YES	CCDS12547.1	ENSP00000157812	PRS6B_HUMAN	A8K2M0_HUMAN	UPI0000132373	.	tolerated(0.09)	probably_damaging(0.989)	5/11	.	hmmpanther:PTHR23073:SF8,hmmpanther:PTHR23073,TIGRFAM_domain:TIGR01242,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGAAGCAGG	.	5	ESCA
IRGQ	0	.	GRCh37	19	44097061	44097061	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.989G>A	p.Arg330His	p.R330H	ENST00000422989	3/3	46	35	11	41	41	0	IRGQ,missense_variant,p.Arg330His,ENST00000422989,;IRGQ,missense_variant,p.Arg330His,ENST00000602269,;L34079.2,missense_variant,p.Ala44Thr,ENST00000594374,;ZNF576,upstream_gene_variant,,ENST00000525771,;ZNF576,upstream_gene_variant,,ENST00000528387,;SRRM5,upstream_gene_variant,,ENST00000607544,;ZNF576,upstream_gene_variant,,ENST00000391965,;ZNF576,upstream_gene_variant,,ENST00000336564,;SRRM5,upstream_gene_variant,,ENST00000526798,;ZNF576,upstream_gene_variant,,ENST00000529930,;IRGQ,downstream_gene_variant,,ENST00000598324,;ZNF576,upstream_gene_variant,,ENST00000533118,;IRGQ,non_coding_transcript_exon_variant,,ENST00000601520,;IRGQ,upstream_gene_variant,,ENST00000596409,;ZNF576,upstream_gene_variant,,ENST00000595041,;	T	ENSG00000167378	ENST00000422989	Transcript	missense_variant	1145	989	330	R/H	cGc/cAc	COSM1564381	.	.	-1	IRGQ	HGNC	24868	protein_coding	YES	CCDS33040.1	ENSP00000387535	IRGQ_HUMAN	M0QZP8_HUMAN	UPI000003FDB6	.	deleterious(0.02)	probably_damaging(0.999)	3/3	.	PROSITE_profiles:PS51716,hmmpanther:PTHR19364,hmmpanther:PTHR19364:SF2	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G333G|c.999C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGCGCACG	.	5	ESCA
ZNF229	0	.	GRCh37	19	44946800	44946800	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40C>T	p.His14Tyr	p.H14Y	ENST00000588931	4/6	58	44	13	42	42	0	ZNF229,missense_variant,p.His14Tyr,ENST00000588931,;ZNF229,missense_variant,p.His14Tyr,ENST00000291187,;ZNF229,5_prime_UTR_variant,,ENST00000592308,;CTC-512J12.4,non_coding_transcript_exon_variant,,ENST00000588655,;ZNF229,non_coding_transcript_exon_variant,,ENST00000591289,;ZNF229,missense_variant,p.His14Tyr,ENST00000591604,;	A	ENSG00000167383	ENST00000588931	Transcript	missense_variant	474	40	14	H/Y	Cat/Tat	.	.	.	-1	ZNF229	HGNC	13022	protein_coding	YES	CCDS42574.1	ENSP00000466519	ZN229_HUMAN	.	UPI00001D8174	.	tolerated(0.87)	benign(0.097)	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAATGAAGAG	.	5	ESCA
SIGLEC10	0	.	GRCh37	19	51918195	51918195	+	Missense_Mutation	SNP	C	C	T	rs554914804	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498G>A	p.Gly500Arg	p.G500R	ENST00000356298	8/12	51	41	9	68	68	0	SIGLEC10,missense_variant,p.Gly500Arg,ENST00000339313,;SIGLEC10,missense_variant,p.Gly500Arg,ENST00000356298,;SIGLEC10,missense_variant,p.Gly442Arg,ENST00000439889,;SIGLEC10,intron_variant,,ENST00000436984,;SIGLEC10,intron_variant,,ENST00000525998,;SIGLEC10,intron_variant,,ENST00000432469,;SIGLEC10,intron_variant,,ENST00000442846,;SIGLEC10,intron_variant,,ENST00000353836,;SIGLEC10,intron_variant,,ENST00000441969,;SIGLEC10,downstream_gene_variant,,ENST00000530476,;SIGLEC10,downstream_gene_variant,,ENST00000529627,;CTD-2616J11.3,non_coding_transcript_exon_variant,,ENST00000532473,;CTD-2616J11.2,upstream_gene_variant,,ENST00000532688,;CTD-2616J11.2,upstream_gene_variant,,ENST00000526996,;SIGLEC10,non_coding_transcript_exon_variant,,ENST00000357375,;SIGLEC10,downstream_gene_variant,,ENST00000524527,;	T	ENSG00000142512	ENST00000356298	Transcript	missense_variant	1615	1498	500	G/R	Ggg/Agg	rs554914804,COSM3537627,COSM3537628	.	.	-1	SIGLEC10	HGNC	15620	protein_coding	YES	CCDS12832.1	ENSP00000348646	SIG10_HUMAN	.	UPI0000047E1A	.	deleterious(0.01)	possibly_damaging(0.874)	8/12	.	hmmpanther:PTHR12035:SF13,hmmpanther:PTHR12035,Superfamily_domains:SSF48726	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCCGGCTG	by1000G	5	ESCA
ZNF766	0	.	GRCh37	19	52794164	52794164	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1120C>T	p.Gln374Ter	p.Q374*	ENST00000439461	4/4	25	22	3	14	14	0	ZNF766,stop_gained,p.Gln389Ter,ENST00000359102,;ZNF766,stop_gained,p.Gln389Ter,ENST00000593612,;ZNF766,stop_gained,p.Gln374Ter,ENST00000439461,;ZNF766,3_prime_UTR_variant,,ENST00000599581,;ZNF766,downstream_gene_variant,,ENST00000593703,;ZNF766,downstream_gene_variant,,ENST00000600821,;ZNF766,downstream_gene_variant,,ENST00000595149,;ZNF766,downstream_gene_variant,,ENST00000595000,;CTD-2525I3.5,intron_variant,,ENST00000594865,;	T	ENSG00000196214	ENST00000439461	Transcript	stop_gained	1163	1120	374	Q/*	Cag/Tag	.	.	.	1	ZNF766	HGNC	28063	protein_coding	YES	CCDS46163.1	ENSP00000409652	ZN766_HUMAN	M0R1P9_HUMAN,M0R139_HUMAN,M0QXI4_HUMAN	UPI0000202AF7	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF5,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCATCAGAGA	.	4	ESCA
LILRA3	0	.	GRCh37	19	54802107	54802107	+	Missense_Mutation	SNP	C	C	A	rs774359959	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1081G>T	p.Gly361Trp	p.G361W	ENST00000251390	6/7	78	72	6	90	90	0	LILRA3,missense_variant,p.Gly378Trp,ENST00000391745,;LILRA3,missense_variant,p.Gly361Trp,ENST00000251390,;LILRA3,missense_variant,p.Gly297Trp,ENST00000391744,;AC010518.3,upstream_gene_variant,,ENST00000417373,;	A	ENSG00000170866	ENST00000251390	Transcript	missense_variant	1173	1081	361	G/W	Ggg/Tgg	rs774359959	.	.	-1	LILRA3	HGNC	6604	protein_coding	YES	CCDS12887.1	ENSP00000251390	LIRA3_HUMAN	.	UPI0000116F1D	.	deleterious(0)	probably_damaging(0.998)	6/7	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF89,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,PIRSF_domain:PIRSF001979,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCCCCTCCT	.	2	ESCA
ZNF606	0	.	GRCh37	19	58491630	58491630	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418G>T	p.Glu140Ter	p.E140*	ENST00000341164	7/7	48	42	6	20	20	0	ZNF606,stop_gained,p.Glu50Ter,ENST00000536132,;ZNF606,stop_gained,p.Glu140Ter,ENST00000551380,;ZNF606,stop_gained,p.Glu140Ter,ENST00000341164,;ZNF606,3_prime_UTR_variant,,ENST00000550599,;	A	ENSG00000166704	ENST00000341164	Transcript	stop_gained	1039	418	140	E/*	Gaa/Taa	.	.	.	-1	ZNF606	HGNC	25879	protein_coding	YES	CCDS12968.1	ENSP00000343617	ZN606_HUMAN	Q9H7U2_HUMAN,F8W1C8_HUMAN,F5H208_HUMAN	UPI000013C35B	.	.	.	7/7	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF278	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTTCAAGAT	.	4	ESCA
ARHGEF2	0	.	GRCh37	1	155922445	155922445	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000361247	15/22	45	29	15	23	23	0	ARHGEF2,missense_variant,p.Arg653Gln,ENST00000361247,;ARHGEF2,missense_variant,p.Arg654Gln,ENST00000368315,;ARHGEF2,missense_variant,p.Arg625Gln,ENST00000313695,;ARHGEF2,missense_variant,p.Arg625Gln,ENST00000368316,;ARHGEF2,missense_variant,p.Arg652Gln,ENST00000313667,;ARHGEF2,missense_variant,p.Arg698Gln,ENST00000462460,;ARHGEF2,upstream_gene_variant,,ENST00000470541,;ARHGEF2,intron_variant,,ENST00000477754,;ARHGEF2,downstream_gene_variant,,ENST00000474428,;ARHGEF2,downstream_gene_variant,,ENST00000470975,;	T	ENSG00000116584	ENST00000361247	Transcript	missense_variant	2058	1958	653	R/Q	cGg/cAg	.	.	.	-1	ARHGEF2	HGNC	682	protein_coding	YES	CCDS53376.1	ENSP00000354837	ARHG2_HUMAN	.	UPI000045892C	.	tolerated(0.22)	possibly_damaging(0.466)	15/22	.	hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCCGCTCG	.	5	ESCA
OR10Z1	0	.	GRCh37	1	158577071	158577071	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843G>A	p.%3D	p.V281V	ENST00000361284	1/1	54	45	9	30	30	0	OR10Z1,synonymous_variant,p.%3D,ENST00000361284,;SPTA1,downstream_gene_variant,,ENST00000368147,;SPTA1,downstream_gene_variant,,ENST00000485680,;	A	ENSG00000198967	ENST00000361284	Transcript	synonymous_variant	843	843	281	V	gtG/gtA	.	.	.	1	OR10Z1	HGNC	14996	protein_coding	YES	CCDS30901.1	ENSP00000354707	O10Z1_HUMAN	.	UPI000004CA23	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGTGACCCC	.	5	ESCA
FCGR2B	0	.	GRCh37	1	161641285	161641285	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237C>T	p.%3D	p.S79S	ENST00000358671	3/8	110	89	20	75	75	0	FCGR2B,synonymous_variant,p.%3D,ENST00000403078,;FCGR2B,synonymous_variant,p.%3D,ENST00000367960,;FCGR2B,synonymous_variant,p.%3D,ENST00000236937,;FCGR2B,synonymous_variant,p.%3D,ENST00000428605,;FCGR2B,synonymous_variant,p.%3D,ENST00000367962,;FCGR2B,synonymous_variant,p.%3D,ENST00000358671,;FCGR2B,synonymous_variant,p.%3D,ENST00000367961,;RP11-25K21.1,downstream_gene_variant,,ENST00000453111,;FCGR2B,non_coding_transcript_exon_variant,,ENST00000485778,;FCGR2B,non_coding_transcript_exon_variant,,ENST00000480308,;	T	ENSG00000072694	ENST00000358671	Transcript	synonymous_variant	318	237	79	S	agC/agT	.	.	.	1	FCGR2B	HGNC	3618	protein_coding	YES	CCDS30924.1	ENSP00000351497	FCG2B_HUMAN	Q8NIA0_HUMAN,Q8NI89_HUMAN,Q8IZV7_HUMAN,Q8IU79_HUMAN	UPI0000001600	.	.	.	3/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF51,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGCGACTC	.	5	ESCA
PIGR	0	.	GRCh37	1	207109009	207109009	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1200C>A	p.Asp400Glu	p.D400E	ENST00000356495	5/11	82	66	16	52	52	0	PIGR,missense_variant,p.Asp400Glu,ENST00000356495,;PIGR,downstream_gene_variant,,ENST00000491503,;PIGR,upstream_gene_variant,,ENST00000487208,;	T	ENSG00000162896	ENST00000356495	Transcript	missense_variant	1384	1200	400	D/E	gaC/gaA	.	.	.	-1	PIGR	HGNC	8968	protein_coding	YES	CCDS1474.1	ENSP00000348888	PIGR_HUMAN	.	UPI000007407E	.	tolerated(1)	benign(0.001)	5/11	.	hmmpanther:PTHR11860:SF44,hmmpanther:PTHR11860,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCTGTCCAC	.	5	ESCA
GALNT2	0	.	GRCh37	1	230410227	230410227	+	Missense_Mutation	SNP	A	A	T	rs774570005	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1477A>T	p.Met493Leu	p.M493L	ENST00000366672	15/16	75	63	11	46	46	0	GALNT2,missense_variant,p.Met455Leu,ENST00000543760,;GALNT2,missense_variant,p.Met493Leu,ENST00000366672,;GALNT2,3_prime_UTR_variant,,ENST00000541865,;GALNT2,non_coding_transcript_exon_variant,,ENST00000485438,;	T	ENSG00000143641	ENST00000366672	Transcript	missense_variant	1549	1477	493	M/L	Atg/Ttg	rs774570005	.	.	1	GALNT2	HGNC	4124	protein_coding	YES	CCDS1582.1	ENSP00000355632	GALT2_HUMAN	.	UPI0000074053	.	tolerated(0.43)	benign(0.001)	15/16	.	PROSITE_profiles:PS50231,hmmpanther:PTHR11675:SF24,hmmpanther:PTHR11675,Pfam_domain:PF00652,Gene3D:2.80.10.50,SMART_domains:SM00458,Superfamily_domains:SSF50370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCACATGGAT	byFrequency	5	ESCA
ASXL1	0	.	GRCh37	20	30956919	30956919	+	Missense_Mutation	SNP	C	C	T	rs769697612	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245C>T	p.Thr82Met	p.T82M	ENST00000375687	4/13	72	66	6	29	29	0	ASXL1,missense_variant,p.Thr71Met,ENST00000497249,;ASXL1,missense_variant,p.Thr82Met,ENST00000375687,;ASXL1,missense_variant,p.Thr77Met,ENST00000306058,;ASXL1,missense_variant,p.Thr81Met,ENST00000542461,;ASXL1,missense_variant,p.Thr78Met,ENST00000375689,;ASXL1,non_coding_transcript_exon_variant,,ENST00000470145,;ASXL1,non_coding_transcript_exon_variant,,ENST00000555343,;	T	ENSG00000171456	ENST00000375687	Transcript	missense_variant	669	245	82	T/M	aCg/aTg	rs769697612	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	deleterious(0)	possibly_damaging(0.785)	4/13	.	Pfam_domain:PF05066,hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTCACGCTCA	.	3	ESCA
AAR2	0	.	GRCh37	20	34828331	34828331	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.541T>C	p.Cys181Arg	p.C181R	ENST00000373932	2/4	44	39	5	22	22	0	AAR2,missense_variant,p.Cys181Arg,ENST00000320849,;AAR2,missense_variant,p.Cys181Arg,ENST00000373932,;AAR2,missense_variant,p.Cys181Arg,ENST00000397286,;	C	ENSG00000131043	ENST00000373932	Transcript	missense_variant	887	541	181	C/R	Tgt/Cgt	.	.	.	1	AAR2	HGNC	15886	protein_coding	YES	CCDS13273.1	ENSP00000363043	AAR2_HUMAN	.	UPI00001285C6	.	tolerated(0.35)	benign(0.116)	2/4	.	hmmpanther:PTHR12689,Pfam_domain:PF05282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCGCTGTGGC	.	4	ESCA
PROKR2	0	.	GRCh37	20	5282783	5282783	+	Missense_Mutation	SNP	C	C	T	rs576243101	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058G>A	p.Arg353His	p.R353H	ENST00000546004	3/3	77	56	21	47	47	0	PROKR2,missense_variant,p.Arg353His,ENST00000546004,;PROKR2,missense_variant,p.Arg353His,ENST00000217270,;	T	ENSG00000101292	ENST00000546004	Transcript	missense_variant	1305	1058	353	R/H	cGt/cAt	rs576243101,COSM117279	.	.	-1	PROKR2	HGNC	15836	protein_coding	YES	CCDS13089.1	ENSP00000440790	PKR2_HUMAN	.	UPI000003BCC6	.	tolerated(0.16)	benign(0.004)	3/3	.	hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF189,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R353H|c.1058G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGACGCCAG	by1000G	5	ESCA
ZNF831	0	.	GRCh37	20	57768323	57768323	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2249C>T	p.Ser750Phe	p.S750F	ENST00000371030	1/5	37	33	4	44	44	0	ZNF831,missense_variant,p.Ser750Phe,ENST00000371030,;	T	ENSG00000124203	ENST00000371030	Transcript	missense_variant	2249	2249	750	S/F	tCt/tTt	.	.	.	1	ZNF831	HGNC	16167	protein_coding	YES	CCDS42894.1	ENSP00000360069	ZN831_HUMAN	.	UPI00001D82E4	.	deleterious(0.01)	possibly_damaging(0.556)	1/5	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCTCTCCAA	.	4	ESCA
MED15	0	.	GRCh37	22	20909285	20909285	+	Missense_Mutation	SNP	A	A	G	rs148919404	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301A>G	p.Met101Val	p.M101V	ENST00000263205	5/18	60	55	5	48	48	0	MED15,missense_variant,p.Met75Val,ENST00000414658,;MED15,missense_variant,p.Met54Val,ENST00000424287,;MED15,missense_variant,p.Met101Val,ENST00000263205,;MED15,missense_variant,p.Met101Val,ENST00000292733,;MED15,missense_variant,p.Met75Val,ENST00000451058,;MED15,missense_variant,p.Met75Val,ENST00000406969,;MED15,missense_variant,p.Met75Val,ENST00000445987,;MED15,missense_variant,p.Met75Val,ENST00000445189,;MED15,missense_variant,p.Met62Val,ENST00000457322,;MED15,missense_variant,p.Met75Val,ENST00000541476,;MED15,splice_region_variant,,ENST00000423862,;MED15,intron_variant,,ENST00000542773,;MED15,intron_variant,,ENST00000432052,;MED15,intron_variant,,ENST00000382974,;MED15,intron_variant,,ENST00000428629,;MED15,intron_variant,,ENST00000425759,;MED15,non_coding_transcript_exon_variant,,ENST00000473028,;MED15,non_coding_transcript_exon_variant,,ENST00000477824,;MED15,non_coding_transcript_exon_variant,,ENST00000487550,;MED15,3_prime_UTR_variant,,ENST00000444094,;MED15,3_prime_UTR_variant,,ENST00000433831,;MED15,3_prime_UTR_variant,,ENST00000420849,;MED15,3_prime_UTR_variant,,ENST00000441501,;MED15,non_coding_transcript_exon_variant,,ENST00000476767,;MED15,non_coding_transcript_exon_variant,,ENST00000492381,;MED15,downstream_gene_variant,,ENST00000486656,;	G	ENSG00000099917	ENST00000263205	Transcript	missense_variant	370	301	101	M/V	Atg/Gtg	rs148919404	.	.	1	MED15	HGNC	14248	protein_coding	YES	CCDS33602.1	ENSP00000263205	MED15_HUMAN	Q69YK5_HUMAN,C9JZV5_HUMAN,C9JM58_HUMAN,C9JGN2_HUMAN,C9J1I1_HUMAN,B4DM43_HUMAN,B3KWF1_HUMAN	UPI00001313C4	.	deleterious(0.01)	unknown(0)	5/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31804,Pfam_domain:PF09606	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGCATGCCT	byFrequency|byCluster	2	ESCA
IGLL5	0	.	GRCh37	22	23235889	23235889	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216C>T	p.%3D	p.L72L	ENST00000526893	2/3	50	43	7	33	33	0	IGLL5,synonymous_variant,p.%3D,ENST00000532223,;IGLL5,synonymous_variant,p.%3D,ENST00000526893,;IGLL5,intron_variant,,ENST00000531372,;IGLJ1,synonymous_variant,p.%3D,ENST00000390320,;IGLC1,upstream_gene_variant,,ENST00000390321,;	T	ENSG00000254709	ENST00000526893	Transcript	synonymous_variant	490	216	72	L	ctC/ctT	.	.	.	1	IGLL5	HGNC	38476	protein_coding	YES	CCDS54506.1	ENSP00000431254	LAC1_HUMAN,IGLL5_HUMAN	A0M8Q9_HUMAN	UPI0000119C74	.	.	.	2/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTCCAGCC	.	4	ESCA
RHBDD3	0	.	GRCh37	22	29661510	29661510	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.106G>A	p.Gly36Ser	p.G36S	ENST00000216085	3/7	48	42	5	28	28	0	RHBDD3,missense_variant,p.Gly36Ser,ENST00000406335,;RHBDD3,missense_variant,p.Gly36Ser,ENST00000216085,;RHBDD3,missense_variant,p.Gly36Ser,ENST00000414672,;EWSR1,upstream_gene_variant,,ENST00000406548,;EWSR1,upstream_gene_variant,,ENST00000397938,;EWSR1,upstream_gene_variant,,ENST00000332035,;EWSR1,upstream_gene_variant,,ENST00000415761,;EWSR1,upstream_gene_variant,,ENST00000447973,;EWSR1,upstream_gene_variant,,ENST00000444626,;EWSR1,upstream_gene_variant,,ENST00000414183,;EWSR1,upstream_gene_variant,,ENST00000332050,;EWSR1,upstream_gene_variant,,ENST00000436425,;EWSR1,upstream_gene_variant,,ENST00000455726,;EWSR1,upstream_gene_variant,,ENST00000333395,;EWSR1,upstream_gene_variant,,ENST00000331029,;EWSR1,upstream_gene_variant,,ENST00000437155,;CTA-984G1.5,downstream_gene_variant,,ENST00000433125,;RHBDD3,missense_variant,p.Gly36Ser,ENST00000413137,;RHBDD3,non_coding_transcript_exon_variant,,ENST00000493894,;RHBDD3,non_coding_transcript_exon_variant,,ENST00000488106,;EWSR1,upstream_gene_variant,,ENST00000485037,;RHBDD3,upstream_gene_variant,,ENST00000496342,;EWSR1,upstream_gene_variant,,ENST00000493426,;EWSR1,upstream_gene_variant,,ENST00000483415,;	T	ENSG00000100263	ENST00000216085	Transcript	missense_variant	531	106	36	G/S	Ggc/Agc	.	.	.	-1	RHBDD3	HGNC	1308	protein_coding	YES	CCDS13850.1	ENSP00000216085	RHBD3_HUMAN	B0QYJ2_HUMAN,B0QYJ1_HUMAN	UPI0000128721	.	tolerated(1)	benign(0)	3/7	.	hmmpanther:PTHR22790,hmmpanther:PTHR22790:SF32,Superfamily_domains:SSF144091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGCCGGGGC	.	4	ESCA
TNRC6B	0	.	GRCh37	22	40731027	40731028	+	3'UTR	INS	-	-	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11792dupT	.	.	ENST00000454349	23/23	34	26	8	19	19	0	TNRC6B,3_prime_UTR_variant,,ENST00000454349,;TNRC6B,3_prime_UTR_variant,,ENST00000301923,;TNRC6B,3_prime_UTR_variant,,ENST00000335727,;	T	ENSG00000100354	ENST00000454349	Transcript	3_prime_UTR_variant	17495-17496	.	.	.	.	.	.	.	1	TNRC6B	HGNC	29190	protein_coding	YES	CCDS54533.1	ENSP00000401946	TNR6B_HUMAN	.	UPI00017A6F19	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAAGTGTTTTT	.	2	ESCA
ARFGAP3	0	.	GRCh37	22	43219704	43219704	+	Silent	SNP	T	T	A	rs368201919	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630A>T	p.%3D	p.V210V	ENST00000263245	8/16	31	24	7	24	24	0	ARFGAP3,synonymous_variant,p.%3D,ENST00000453516,;ARFGAP3,synonymous_variant,p.%3D,ENST00000437119,;ARFGAP3,synonymous_variant,p.%3D,ENST00000454099,;ARFGAP3,synonymous_variant,p.%3D,ENST00000263245,;ARFGAP3,synonymous_variant,p.%3D,ENST00000429508,;	A	ENSG00000242247	ENST00000263245	Transcript	synonymous_variant	850	630	210	V	gtA/gtT	rs368201919	.	.	-1	ARFGAP3	HGNC	661	protein_coding	YES	CCDS14042.1	ENSP00000263245	ARFG3_HUMAN	.	UPI0000125DF8	.	.	.	8/16	.	hmmpanther:PTHR23180:SF208,hmmpanther:PTHR23180	.	.	.	.	.	.	.	C:0.0002	C:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGATACCTC	byCluster	5	ESCA
EIF5B	0	.	GRCh37	2	100006805	100006805	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2527C>G	p.Gln843Glu	p.Q843E	ENST00000289371	16/24	36	23	13	25	25	0	EIF5B,missense_variant,p.Gln843Glu,ENST00000289371,;EIF5B,non_coding_transcript_exon_variant,,ENST00000470868,;EIF5B,upstream_gene_variant,,ENST00000494190,;	G	ENSG00000158417	ENST00000289371	Transcript	missense_variant	2729	2527	843	Q/E	Cag/Gag	.	.	.	1	EIF5B	HGNC	30793	protein_coding	YES	CCDS42721.1	ENSP00000289371	IF2P_HUMAN	D3DVI5_HUMAN	UPI0000207EC7	.	.	possibly_damaging(0.557)	16/24	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF99	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTCAGACC	.	5	ESCA
AFF3	0	.	GRCh37	2	100182070	100182070	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3073A>G	p.Lys1025Glu	p.K1025E	ENST00000356421	19/24	46	43	3	26	26	0	AFF3,missense_variant,p.Lys1025Glu,ENST00000409579,;AFF3,missense_variant,p.Lys1025Glu,ENST00000356421,;AFF3,missense_variant,p.Lys1000Glu,ENST00000317233,;AFF3,missense_variant,p.Lys1000Glu,ENST00000409236,;AFF3,missense_variant,p.Lys42Glu,ENST00000445815,;	C	ENSG00000144218	ENST00000356421	Transcript	missense_variant	3217	3073	1025	K/E	Aag/Gag	.	.	.	-1	AFF3	HGNC	6473	protein_coding	YES	CCDS33258.1	ENSP00000348793	AFF3_HUMAN	.	UPI000041098C	.	deleterious(0)	probably_damaging(0.992)	19/24	.	hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCTTTCCAA	.	2	ESCA
LYPD6	0	.	GRCh37	2	150325190	150325190	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.249G>A	p.Met83Ile	p.M83I	ENST00000334166	4/5	29	19	10	29	29	0	LYPD6,missense_variant,p.Met83Ile,ENST00000409381,;LYPD6,missense_variant,p.Met83Ile,ENST00000334166,;LYPD6,3_prime_UTR_variant,,ENST00000392854,;LYPD6,3_prime_UTR_variant,,ENST00000418762,;	A	ENSG00000187123	ENST00000334166	Transcript	missense_variant	506	249	83	M/I	atG/atA	.	.	.	1	LYPD6	HGNC	28751	protein_coding	YES	CCDS2188.1	ENSP00000334463	LYPD6_HUMAN	C9IYE7_HUMAN	UPI000000DB99	.	deleterious(0.03)	benign(0.306)	4/5	.	hmmpanther:PTHR31171:SF0,hmmpanther:PTHR31171,Gene3D:2.10.60.10,Superfamily_domains:SSF57302	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATGGAAGT	.	5	ESCA
FZD7	0	.	GRCh37	2	202900692	202900692	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1322T>A	p.Leu441Gln	p.L441Q	ENST00000286201	1/1	62	53	9	52	52	0	FZD7,missense_variant,p.Leu441Gln,ENST00000286201,;RP11-107N15.1,upstream_gene_variant,,ENST00000608741,;	A	ENSG00000155760	ENST00000286201	Transcript	missense_variant	1383	1322	441	L/Q	cTg/cAg	.	.	.	1	FZD7	HGNC	4045	protein_coding	YES	CCDS2351.1	ENSP00000286201	FZD7_HUMAN	.	UPI0000051051	.	deleterious(0)	probably_damaging(0.994)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF31,Pfam_domain:PF01534,Prints_domain:PR00489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCTGGCCG	.	5	ESCA
CARF	0	.	GRCh37	2	203847041	203847041	+	Missense_Mutation	SNP	G	G	T	rs772628105	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1936G>T	p.Asp646Tyr	p.D646Y	ENST00000402905	15/16	24	14	9	22	22	0	CARF,missense_variant,p.Asp646Tyr,ENST00000320443,;CARF,missense_variant,p.Asp558Tyr,ENST00000545253,;CARF,missense_variant,p.Asp646Tyr,ENST00000438828,;CARF,missense_variant,p.Asp570Tyr,ENST00000428585,;CARF,missense_variant,p.Asp646Tyr,ENST00000402905,;CARF,missense_variant,p.Asp544Tyr,ENST00000414439,;CARF,missense_variant,p.Asp570Tyr,ENST00000545262,;WDR12,intron_variant,,ENST00000477723,;	T	ENSG00000138380	ENST00000402905	Transcript	missense_variant	2257	1936	646	D/Y	Gac/Tac	rs772628105	.	.	1	CARF	HGNC	14435	protein_coding	YES	CCDS42801.1	ENSP00000384006	CARTF_HUMAN	C9JT99_HUMAN,C9JZI6_HUMAN,C9JZ91_HUMAN,C9JSN4_HUMAN,C9JL40_HUMAN,C9JI92_HUMAN,C9JCD6_HUMAN,C9JBK9_HUMAN	UPI000007284D	.	deleterious_low_confidence(0.03)	probably_damaging(0.922)	15/16	.	hmmpanther:PTHR14694,hmmpanther:PTHR14694:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATGGACGAG	.	5	ESCA
SP110	0	.	GRCh37	2	231065665	231065665	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1065T>C	p.%3D	p.T355T	ENST00000258381	10/19	41	35	6	40	40	0	SP110,synonymous_variant,p.%3D,ENST00000338556,;SP110,synonymous_variant,p.%3D,ENST00000392048,;SP110,synonymous_variant,p.%3D,ENST00000358662,;SP110,synonymous_variant,p.%3D,ENST00000258381,;SP110,synonymous_variant,p.%3D,ENST00000258382,;SP110,synonymous_variant,p.%3D,ENST00000540870,;SP140,upstream_gene_variant,,ENST00000456542,;SP110,downstream_gene_variant,,ENST00000486146,;SP140,upstream_gene_variant,,ENST00000441657,;SP110,non_coding_transcript_exon_variant,,ENST00000490880,;	G	ENSG00000135899	ENST00000258381	Transcript	synonymous_variant	1143	1065	355	T	acT/acC	.	.	.	-1	SP110	HGNC	5401	protein_coding	YES	CCDS2475.1	ENSP00000258381	SP110_HUMAN	Q2I9M3_HUMAN,Q2I9M2_HUMAN,Q2I9M1_HUMAN,Q2I9M0_HUMAN,Q2I9L9_HUMAN,E9PHK4_HUMAN,E7EM70_HUMAN,C9JZQ4_HUMAN	UPI000013CFC9	.	.	.	10/19	.	hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGAAGTGCC	.	5	ESCA
THADA	0	.	GRCh37	2	43818024	43818024	+	Missense_Mutation	SNP	T	T	C	rs768333408	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241A>G	p.Ile81Val	p.I81V	ENST00000405006	4/38	68	38	29	31	31	0	THADA,missense_variant,p.Ile81Val,ENST00000404790,;THADA,missense_variant,p.Ile81Val,ENST00000402360,;THADA,missense_variant,p.Ile81Val,ENST00000403856,;THADA,missense_variant,p.Ile81Val,ENST00000405006,;THADA,missense_variant,p.Ile81Val,ENST00000405975,;THADA,5_prime_UTR_variant,,ENST00000415080,;THADA,missense_variant,p.Ile81Val,ENST00000408045,;THADA,missense_variant,p.Ile81Val,ENST00000398653,;THADA,missense_variant,p.Ile81Val,ENST00000474159,;	C	ENSG00000115970	ENST00000405006	Transcript	missense_variant	593	241	81	I/V	Atc/Gtc	rs768333408	.	.	-1	THADA	HGNC	19217	protein_coding	YES	CCDS46268.1	ENSP00000385995	THADA_HUMAN	Q6YHU4_HUMAN	UPI00001C0473	.	tolerated(0.27)	benign(0.004)	4/38	.	hmmpanther:PTHR14387:SF0,hmmpanther:PTHR14387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGATATCCA	byFrequency	5	ESCA
LRPPRC	0	.	GRCh37	2	44177716	44177716	+	Missense_Mutation	SNP	C	C	T	rs771987532	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1673G>A	p.Ser558Asn	p.S558N	ENST00000260665	15/38	74	69	5	35	35	0	LRPPRC,missense_variant,p.Ser558Asn,ENST00000260665,;LRPPRC,non_coding_transcript_exon_variant,,ENST00000467058,;	T	ENSG00000138095	ENST00000260665	Transcript	missense_variant	1731	1673	558	S/N	aGc/aAc	rs771987532	.	.	-1	LRPPRC	HGNC	15714	protein_coding	YES	CCDS33189.1	ENSP00000260665	LPPRC_HUMAN	E5KNY5_HUMAN	UPI000019B4D2	.	tolerated(0.17)	benign(0.036)	15/38	.	hmmpanther:PTHR24015:SF0,hmmpanther:PTHR24015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCGCTCCAA	.	2	ESCA
ZNF638	0	.	GRCh37	2	71653884	71653884	+	Missense_Mutation	SNP	G	G	A	rs759199913	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4885G>A	p.Glu1629Lys	p.E1629K	ENST00000409544	24/28	20	12	8	14	14	0	ZNF638,missense_variant,p.Glu569Lys,ENST00000409407,;ZNF638,missense_variant,p.Glu1629Lys,ENST00000409544,;ZNF638,missense_variant,p.Glu1629Lys,ENST00000264447,;ZNF638,3_prime_UTR_variant,,ENST00000355812,;ZNF638,non_coding_transcript_exon_variant,,ENST00000483421,;ZNF638,upstream_gene_variant,,ENST00000493576,;ZNF638,upstream_gene_variant,,ENST00000472758,;ZNF638,upstream_gene_variant,,ENST00000492262,;ZNF638,upstream_gene_variant,,ENST00000460310,;ZNF638,upstream_gene_variant,,ENST00000488126,;ZNF638,upstream_gene_variant,,ENST00000461991,;ZNF638,non_coding_transcript_exon_variant,,ENST00000487638,;ZNF638,downstream_gene_variant,,ENST00000494241,;	A	ENSG00000075292	ENST00000409544	Transcript	missense_variant	5515	4885	1629	E/K	Gaa/Aaa	rs759199913	.	.	1	ZNF638	HGNC	17894	protein_coding	YES	CCDS1917.1	ENSP00000386433	ZN638_HUMAN	Q57Z90_HUMAN,C9JWN0_HUMAN,C9JSD0_HUMAN,C9JMR2_HUMAN,C9JHV0_HUMAN,A8K583_HUMAN	UPI000013D51B	.	deleterious(0.01)	possibly_damaging(0.619)	24/28	.	hmmpanther:PTHR15592:SF1,hmmpanther:PTHR15592	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAGAACTA	.	5	ESCA
KIDINS220	0	.	GRCh37	2	8946498	8946498	+	Missense_Mutation	SNP	T	T	C	rs780568354	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.506A>G	p.Tyr169Cys	p.Y169C	ENST00000256707	7/30	32	28	4	26	26	0	KIDINS220,missense_variant,p.Tyr169Cys,ENST00000427284,;KIDINS220,missense_variant,p.Tyr170Cys,ENST00000489024,;KIDINS220,missense_variant,p.Tyr127Cys,ENST00000418530,;KIDINS220,missense_variant,p.Tyr169Cys,ENST00000473731,;KIDINS220,missense_variant,p.Tyr170Cys,ENST00000319688,;KIDINS220,missense_variant,p.Tyr169Cys,ENST00000256707,;KIDINS220,upstream_gene_variant,,ENST00000496383,;KIDINS220,splice_region_variant,,ENST00000488729,;KIDINS220,non_coding_transcript_exon_variant,,ENST00000471275,;	C	ENSG00000134313	ENST00000256707	Transcript	missense_variant	688	506	169	Y/C	tAt/tGt	rs780568354	.	.	-1	KIDINS220	HGNC	29508	protein_coding	YES	CCDS42650.1	ENSP00000256707	KDIS_HUMAN	F8WAY8_HUMAN	UPI0000208E08	.	deleterious(0)	probably_damaging(0.981)	7/30	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCATACTAT	.	2	ESCA
CCDC14	0	.	GRCh37	3	123634433	123634433	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1932T>C	p.%3D	p.P644P	ENST00000433542	12/12	90	85	5	28	28	0	CCDC14,synonymous_variant,p.%3D,ENST00000310351,;CCDC14,synonymous_variant,p.%3D,ENST00000485727,;CCDC14,synonymous_variant,p.%3D,ENST00000409697,;CCDC14,synonymous_variant,p.%3D,ENST00000488653,;CCDC14,synonymous_variant,p.%3D,ENST00000433542,;CCDC14,synonymous_variant,p.%3D,ENST00000489746,;CCDC14,intron_variant,,ENST00000419247,;CCDC14,intron_variant,,ENST00000479903,;CCDC14,intron_variant,,ENST00000463996,;CCDC14,intron_variant,,ENST00000483247,;CCDC14,3_prime_UTR_variant,,ENST00000409657,;CCDC14,intron_variant,,ENST00000495381,;	G	ENSG00000175455	ENST00000433542	Transcript	synonymous_variant	2332	1932	644	P	ccT/ccC	.	.	.	-1	CCDC14	HGNC	25766	protein_coding	YES	CCDS3025.2	ENSP00000395706	CCD14_HUMAN	C9JWZ1_HUMAN	UPI00016632FB	.	.	.	12/12	.	hmmpanther:PTHR22367,hmmpanther:PTHR22367:SF1,Pfam_domain:PF15254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAGCAGGAGC	.	2	ESCA
ACKR4	0	.	GRCh37	3	132320087	132320087	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.846C>T	p.%3D	p.D282D	ENST00000249887	2/2	90	85	4	36	36	0	ACKR4,synonymous_variant,p.%3D,ENST00000249887,;ACAD11,intron_variant,,ENST00000264990,;ACAD11,intron_variant,,ENST00000545291,;ACAD11,intron_variant,,ENST00000355458,;ACAD11,intron_variant,,ENST00000507705,;NPHP3,intron_variant,,ENST00000471702,;ACAD11,intron_variant,,ENST00000496418,;ACAD11,intron_variant,,ENST00000477604,;ACAD11,intron_variant,,ENST00000487024,;ACAD11,intron_variant,,ENST00000485198,;ACAD11,intron_variant,,ENST00000469042,;ACAD11,intron_variant,,ENST00000510100,;ACKR4,upstream_gene_variant,,ENST00000509820,;	T	ENSG00000129048	ENST00000249887	Transcript	synonymous_variant	942	846	282	D	gaC/gaT	.	.	.	1	ACKR4	HGNC	1611	protein_coding	YES	CCDS3075.1	ENSP00000249887	ACKR4_HUMAN	H0Y9Z2_HUMAN	UPI0000039DBA	.	.	.	2/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24227:SF35,hmmpanther:PTHR24227,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGACATCGC	.	2	ESCA
MED12L	0	.	GRCh37	3	151102876	151102876	+	Missense_Mutation	SNP	T	T	C	rs61740424	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4880T>C	p.Leu1627Ser	p.L1627S	ENST00000474524	34/43	47	41	6	23	23	0	MED12L,missense_variant,p.Leu1627Ser,ENST00000474524,;MED12L,missense_variant,p.Leu1487Ser,ENST00000273432,;P2RY12,upstream_gene_variant,,ENST00000302632,;	C	ENSG00000144893	ENST00000474524	Transcript	missense_variant	4918	4880	1627	L/S	tTg/tCg	rs61740424,COSM4114482	.	.	1	MED12L	HGNC	16050	protein_coding	YES	CCDS33876.1	ENSP00000417235	MD12L_HUMAN	.	UPI000020A46B	.	deleterious(0)	probably_damaging(0.937)	34/43	.	hmmpanther:PTHR12796,hmmpanther:PTHR12796:SF5	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTTTGCCGA	byFrequency	4	ESCA
LEKR1	0	.	GRCh37	3	156544566	156544574	+	5'UTR	DEL	AGTCTTAGG	AGTCTTAGG	-	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	AGTCTTAGG	AGTCTTAGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-376_-368delGTCTTAGGA	.	.	ENST00000491763	1/5	105	58	47	64	64	0	LEKR1,5_prime_UTR_variant,,ENST00000491763,;LEKR1,intron_variant,,ENST00000470811,;LEKR1,intron_variant,,ENST00000498839,;LEKR1,intron_variant,,ENST00000477399,;LEKR1,intron_variant,,ENST00000356539,;LEKR1,intron_variant,,ENST00000483177,;LEKR1,non_coding_transcript_exon_variant,,ENST00000485017,;LEKR1,intron_variant,,ENST00000489350,;LEKR1,intron_variant,,ENST00000465728,;LEKR1,intron_variant,,ENST00000467376,;	-	ENSG00000197980	ENST00000491763	Transcript	5_prime_UTR_variant	419-427	.	.	.	.	.	.	.	1	LEKR1	HGNC	33765	protein_coding	YES	CCDS54660.1	ENSP00000474182	.	D3DNK7_HUMAN	UPI00006C06BC	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGAAAGTCTTAGGATGTG	.	3	ESCA
GPR160	0	.	GRCh37	3	169802652	169802652	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.892A>C	p.Lys298Gln	p.K298Q	ENST00000355897	4/4	91	74	17	33	32	1	GPR160,missense_variant,p.Lys298Gln,ENST00000355897,;GPR160,downstream_gene_variant,,ENST00000473675,;PHC3,downstream_gene_variant,,ENST00000484068,;GPR160,downstream_gene_variant,,ENST00000482710,;GPR160,downstream_gene_variant,,ENST00000492492,;GPR160,downstream_gene_variant,,ENST00000485735,;PHC3,downstream_gene_variant,,ENST00000495893,;RP11-379K17.12,upstream_gene_variant,,ENST00000599781,;	C	ENSG00000173890	ENST00000355897	Transcript	missense_variant	1500	892	298	K/Q	Aag/Cag	.	.	.	1	GPR160	HGNC	23693	protein_coding	YES	CCDS3211.1	ENSP00000348161	GP160_HUMAN	C9JUZ9_HUMAN,C9JTZ7_HUMAN,C9JBW1_HUMAN,C9J0J1_HUMAN	UPI0000033731	.	tolerated(0.15)	probably_damaging(0.925)	4/4	.	hmmpanther:PTHR15573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTCACAAGCTT	.	2	ESCA
DNAJC19	0	.	GRCh37	3	180707422	180707422	+	5'UTR	SNP	G	G	A	rs756805866	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-32C>T	.	.	ENST00000382564	1/6	67	63	4	35	35	0	DNAJC19,5_prime_UTR_variant,,ENST00000486355,;DNAJC19,5_prime_UTR_variant,,ENST00000491873,;DNAJC19,5_prime_UTR_variant,,ENST00000382564,;DNAJC19,upstream_gene_variant,,ENST00000479269,;SOX2-OT,upstream_gene_variant,,ENST00000487240,;SOX2-OT,upstream_gene_variant,,ENST00000461063,;DNAJC19,5_prime_UTR_variant,,ENST00000469657,;DNAJC19,non_coding_transcript_exon_variant,,ENST00000478723,;DNAJC19,non_coding_transcript_exon_variant,,ENST00000472504,;DNAJC19,non_coding_transcript_exon_variant,,ENST00000485675,;DNAJC19,non_coding_transcript_exon_variant,,ENST00000482363,;	A	ENSG00000205981	ENST00000382564	Transcript	5_prime_UTR_variant	140	.	.	.	.	rs756805866	.	.	-1	DNAJC19	HGNC	30528	protein_coding	YES	CCDS33895.1	ENSP00000372005	TIM14_HUMAN	.	UPI000006CD5D	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCGGGAGCAC	byFrequency	2	ESCA
SENP2	0	.	GRCh37	3	185347597	185347597	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735A>T	p.Met579Leu	p.M579L	ENST00000296257	17/17	71	61	10	18	18	0	SENP2,missense_variant,p.Met569Leu,ENST00000545472,;SENP2,missense_variant,p.Met403Leu,ENST00000427465,;SENP2,missense_variant,p.Met579Leu,ENST00000296257,;SENP2,downstream_gene_variant,,ENST00000444509,;SENP2,3_prime_UTR_variant,,ENST00000413407,;	T	ENSG00000163904	ENST00000296257	Transcript	missense_variant	1975	1735	579	M/L	Atg/Ttg	.	.	.	1	SENP2	HGNC	23116	protein_coding	YES	CCDS33902.1	ENSP00000296257	SENP2_HUMAN	J3KQD2_HUMAN,B4E2S4_HUMAN	UPI000007452F	.	deleterious(0)	probably_damaging(0.987)	17/17	.	hmmpanther:PTHR12606,hmmpanther:PTHR12606:SF11,Pfam_domain:PF02902,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGATGGTG	.	5	ESCA
DLG1	0	.	GRCh37	3	196863514	196863514	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1018C>G	p.Gln340Glu	p.Q340E	ENST00000346964	11/26	38	15	22	21	21	0	DLG1,missense_variant,p.Gln224Glu,ENST00000452595,;DLG1,missense_variant,p.Gln307Glu,ENST00000450955,;DLG1,missense_variant,p.Gln307Glu,ENST00000392382,;DLG1,missense_variant,p.Gln307Glu,ENST00000357674,;DLG1,missense_variant,p.Gln289Glu,ENST00000422288,;DLG1,missense_variant,p.Gln340Glu,ENST00000448528,;DLG1,missense_variant,p.Gln340Glu,ENST00000346964,;DLG1,missense_variant,p.Gln224Glu,ENST00000443183,;DLG1,missense_variant,p.Gln340Glu,ENST00000419354,;DLG1,missense_variant,p.Gln149Glu,ENST00000447466,;DLG1,missense_variant,p.Gln289Glu,ENST00000314062,;DLG1,downstream_gene_variant,,ENST00000453607,;DLG1,missense_variant,p.Gln340Glu,ENST00000392381,;DLG1,missense_variant,p.Gln289Glu,ENST00000419227,;DLG1,non_coding_transcript_exon_variant,,ENST00000471733,;DLG1,non_coding_transcript_exon_variant,,ENST00000477312,;	C	ENSG00000075711	ENST00000346964	Transcript	missense_variant	1208	1018	340	Q/E	Cag/Gag	COSM1694039,COSM1694040	.	.	-1	DLG1	HGNC	2900	protein_coding	YES	CCDS3327.1	ENSP00000345731	DLG1_HUMAN	F2Z2L0_HUMAN,C9JUA9_HUMAN,C9JN61_HUMAN,C9J110_HUMAN,A8MUT6_HUMAN	UPI000013CD24	.	tolerated(0.19)	benign(0.129)	11/26	.	PROSITE_profiles:PS50106,hmmpanther:PTHR23119,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,PIRSF_domain:PIRSF001741,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCTGATTTC	.	5	ESCA
PRSS42	0	.	GRCh37	3	46875457	46875457	+	Silent	SNP	G	G	A	rs761630852	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129C>T	p.%3D	p.G43G	ENST00000429665	1/5	54	50	4	48	48	0	PRSS42,synonymous_variant,p.%3D,ENST00000429665,;PRSS42,upstream_gene_variant,,ENST00000447340,;	A	ENSG00000178055	ENST00000429665	Transcript	synonymous_variant	129	129	43	G	ggC/ggT	rs761630852	.	.	-1	PRSS42	HGNC	30716	protein_coding	YES	CCDS46816.1	ENSP00000401701	PRS42_HUMAN	.	UPI00001B2328	.	.	.	1/5	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCTCGCCGCC	.	3	ESCA
SH3RF1	0	.	GRCh37	4	170077752	170077752	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472G>T	p.Gly158Cys	p.G158C	ENST00000284637	3/12	36	33	3	27	27	0	SH3RF1,missense_variant,p.Gly158Cys,ENST00000284637,;SH3RF1,non_coding_transcript_exon_variant,,ENST00000508685,;SH3RF1,missense_variant,p.Gly20Cys,ENST00000511421,;	A	ENSG00000154447	ENST00000284637	Transcript	missense_variant	814	472	158	G/C	Ggt/Tgt	.	.	.	-1	SH3RF1	HGNC	17650	protein_coding	YES	CCDS34099.1	ENSP00000284637	SH3R1_HUMAN	D6RHX5_HUMAN,D6RAL3_HUMAN	UPI0000160033	.	deleterious(0)	probably_damaging(1)	3/12	.	PROSITE_profiles:PS50002,hmmpanther:PTHR10661:SF8,hmmpanther:PTHR10661,Pfam_domain:PF14604,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCACCTTTGC	.	2	ESCA
ATP10D	0	.	GRCh37	4	47517556	47517556	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.354C>G	p.Phe118Leu	p.F118L	ENST00000273859	3/23	45	34	11	29	29	0	ATP10D,missense_variant,p.Phe118Leu,ENST00000504445,;ATP10D,missense_variant,p.Phe118Leu,ENST00000273859,;ATP10D,downstream_gene_variant,,ENST00000507889,;	G	ENSG00000145246	ENST00000273859	Transcript	missense_variant	623	354	118	F/L	ttC/ttG	COSM1540335	.	.	1	ATP10D	HGNC	13549	protein_coding	YES	CCDS3476.1	ENSP00000273859	AT10D_HUMAN	.	UPI00001AE9B7	.	deleterious(0)	probably_damaging(0.999)	3/23	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF61,Gene3D:2.70.150.10,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCCAAAA	.	5	ESCA
SDAD1	0	.	GRCh37	4	76902592	76902592	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227A>G	p.Asn76Ser	p.N76S	ENST00000356260	3/22	37	27	10	18	18	0	SDAD1,missense_variant,p.Asn76Ser,ENST00000395711,;SDAD1,missense_variant,p.Asn76Ser,ENST00000356260,;RP11-630D6.5,intron_variant,,ENST00000501239,;SDAD1,non_coding_transcript_exon_variant,,ENST00000504975,;SDAD1,upstream_gene_variant,,ENST00000515836,;SDAD1,3_prime_UTR_variant,,ENST00000514710,;SDAD1,3_prime_UTR_variant,,ENST00000503411,;SDAD1,3_prime_UTR_variant,,ENST00000395710,;	C	ENSG00000198301	ENST00000356260	Transcript	missense_variant	346	227	76	N/S	aAt/aGt	.	.	.	-1	SDAD1	HGNC	25537	protein_coding	YES	CCDS3573.2	ENSP00000348596	SDA1_HUMAN	.	UPI000020B02A	.	tolerated(0.8)	benign(0.004)	3/22	.	hmmpanther:PTHR12730,hmmpanther:PTHR12730:SF0,Pfam_domain:PF08158,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAATTACTT	.	5	ESCA
CNOT6L	0	.	GRCh37	4	78638339	78638339	+	3'UTR	SNP	A	A	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3246T>G	.	.	ENST00000264903	12/12	41	31	10	23	23	0	CNOT6L,3_prime_UTR_variant,,ENST00000504123,;CNOT6L,3_prime_UTR_variant,,ENST00000264903,;CNOT6L,downstream_gene_variant,,ENST00000515506,;CNOT6L,downstream_gene_variant,,ENST00000512485,;CNOT6L,downstream_gene_variant,,ENST00000504804,;	C	ENSG00000138767	ENST00000264903	Transcript	3_prime_UTR_variant	4996	.	.	.	.	.	.	.	-1	CNOT6L	HGNC	18042	protein_coding	YES	CCDS47082.1	ENSP00000264903	CNO6L_HUMAN	D6RGK9_HUMAN	UPI0000E445DF	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTAAAACAA	.	5	ESCA
PCDHA6	0	.	GRCh37	5	140209869	140209869	+	Silent	SNP	G	G	A	rs536478075	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2193G>A	p.%3D	p.A731A	ENST00000529310	1/4	45	36	8	60	60	0	PCDHA6,synonymous_variant,p.%3D,ENST00000529310,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA7,upstream_gene_variant,,ENST00000378125,;PCDHA7,upstream_gene_variant,,ENST00000525929,;	A	ENSG00000081842	ENST00000529310	Transcript	synonymous_variant	2307	2193	731	A	gcG/gcA	rs536478075,COSM46463,COSM736243,COSM166727,COSM736242	.	.	1	PCDHA6	HGNC	8672	protein_coding	YES	CCDS47281.1	ENSP00000433378	PCDA6_HUMAN	.	UPI00001273CE	.	.	.	1/4	.	hmmpanther:PTHR24028:SF83,hmmpanther:PTHR24028	C:0.0002	C:0	C:0.0014	.	C:0	C:0	C:0	.	.	.	0,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A731T|c.2191G>A|3,BUFFER|p.A731T|c.2191G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGCGTGCAC	by1000G	5	ESCA
TCERG1	0	.	GRCh37	5	145834757	145834757	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198C>G	p.%3D	p.P66P	ENST00000296702	2/22	44	39	5	32	32	0	TCERG1,synonymous_variant,p.%3D,ENST00000296702,;TCERG1,synonymous_variant,p.%3D,ENST00000394421,;TCERG1,synonymous_variant,p.%3D,ENST00000549332,;TCERG1,non_coding_transcript_exon_variant,,ENST00000507175,;TCERG1,upstream_gene_variant,,ENST00000513298,;	G	ENSG00000113649	ENST00000296702	Transcript	synonymous_variant	236	198	66	P	ccC/ccG	.	.	.	1	TCERG1	HGNC	15630	protein_coding	YES	CCDS4282.1	ENSP00000296702	TCRG1_HUMAN	.	UPI000013E374	.	.	.	2/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCCCTTTGG	.	4	ESCA
CLK4	0	.	GRCh37	5	178040553	178040553	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.747C>A	p.Phe249Leu	p.F249L	ENST00000316308	7/13	38	30	7	21	21	0	CLK4,missense_variant,p.Phe249Leu,ENST00000316308,;CLK4,downstream_gene_variant,,ENST00000522749,;CLK4,3_prime_UTR_variant,,ENST00000522136,;CLK4,3_prime_UTR_variant,,ENST00000521621,;CLK4,non_coding_transcript_exon_variant,,ENST00000520878,;CLK4,non_coding_transcript_exon_variant,,ENST00000519132,;CLK4,non_coding_transcript_exon_variant,,ENST00000519583,;CLK4,downstream_gene_variant,,ENST00000520126,;CLK4,downstream_gene_variant,,ENST00000520909,;CLK4,downstream_gene_variant,,ENST00000520199,;	T	ENSG00000113240	ENST00000316308	Transcript	missense_variant	916	747	249	F/L	ttC/ttA	.	.	.	-1	CLK4	HGNC	13659	protein_coding	YES	CCDS4437.1	ENSP00000316948	CLK4_HUMAN	Q68D95_HUMAN	UPI000007065C	.	deleterious(0.01)	probably_damaging(0.985)	7/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24058:SF25,hmmpanther:PTHR24058,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTAATGAAATC	.	3	ESCA
SQSTM1	0	.	GRCh37	5	179260710	179260710	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1093A>T	p.Ser365Cys	p.S365C	ENST00000389805	7/8	25	22	3	12	12	0	SQSTM1,missense_variant,p.Ser365Cys,ENST00000389805,;SQSTM1,missense_variant,p.Ser281Cys,ENST00000376929,;SQSTM1,missense_variant,p.Ser281Cys,ENST00000402874,;SQSTM1,missense_variant,p.Ser281Cys,ENST00000360718,;SQSTM1,intron_variant,,ENST00000510187,;C5orf45,downstream_gene_variant,,ENST00000520698,;C5orf45,downstream_gene_variant,,ENST00000292586,;C5orf45,downstream_gene_variant,,ENST00000518219,;C5orf45,downstream_gene_variant,,ENST00000376931,;C5orf45,downstream_gene_variant,,ENST00000521333,;C5orf45,downstream_gene_variant,,ENST00000523084,;C5orf45,downstream_gene_variant,,ENST00000403396,;C5orf45,downstream_gene_variant,,ENST00000518235,;C5orf45,downstream_gene_variant,,ENST00000523267,;SQSTM1,downstream_gene_variant,,ENST00000466342,;C5orf45,downstream_gene_variant,,ENST00000522663,;C5orf45,downstream_gene_variant,,ENST00000521299,;C5orf45,downstream_gene_variant,,ENST00000518950,;	T	ENSG00000161011	ENST00000389805	Transcript	missense_variant	1271	1093	365	S/C	Agc/Tgc	.	.	.	1	SQSTM1	HGNC	11280	protein_coding	YES	CCDS34317.1	ENSP00000374455	SQSTM_HUMAN	E9PFW8_HUMAN,C9JRJ8_HUMAN	UPI0000071099	.	tolerated(0.12)	benign(0.005)	7/8	.	hmmpanther:PTHR15090	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGCCAAGCTCT	.	2	ESCA
GOLPH3	0	.	GRCh37	5	32143866	32143866	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.346T>C	p.%3D	p.L116L	ENST00000265070	2/4	45	39	5	21	21	0	GOLPH3,synonymous_variant,p.%3D,ENST00000265070,;GOLPH3,intron_variant,,ENST00000512668,;GOLPH3,3_prime_UTR_variant,,ENST00000503610,;	G	ENSG00000113384	ENST00000265070	Transcript	synonymous_variant	662	346	116	L	Tta/Cta	.	.	.	-1	GOLPH3	HGNC	15452	protein_coding	YES	CCDS3896.1	ENSP00000265070	GOLP3_HUMAN	B3KQJ9_HUMAN,B3KS18_HUMAN,B3KQ71_HUMAN	UPI000006EEF4	.	.	.	2/4	.	Pfam_domain:PF05719,Gene3D:2zihB00,hmmpanther:PTHR12704:SF3,hmmpanther:PTHR12704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTTAATAGAC	.	4	ESCA
PRLR	0	.	GRCh37	5	35072680	35072680	+	Nonsense_Mutation	SNP	C	C	T	rs776871201	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.540G>A	p.Trp180Ter	p.W180*	ENST00000382002	6/10	51	36	15	18	18	0	PRLR,stop_gained,p.Trp180Ter,ENST00000310101,;PRLR,stop_gained,p.Trp180Ter,ENST00000382002,;PRLR,stop_gained,p.Trp180Ter,ENST00000348262,;PRLR,stop_gained,p.Trp79Ter,ENST00000342362,;PRLR,stop_gained,p.Trp79Ter,ENST00000511486,;PRLR,stop_gained,p.Trp109Ter,ENST00000397391,;PRLR,stop_gained,p.Trp180Ter,ENST00000542609,;PRLR,stop_gained,p.Trp180Ter,ENST00000231423,;PRLR,stop_gained,p.Trp180Ter,ENST00000513753,;PRLR,non_coding_transcript_exon_variant,,ENST00000509934,;PRLR,3_prime_UTR_variant,,ENST00000509140,;PRLR,3_prime_UTR_variant,,ENST00000514088,;PRLR,intron_variant,,ENST00000508107,;	T	ENSG00000113494	ENST00000382002	Transcript	stop_gained	967	540	180	W/*	tgG/tgA	rs776871201	.	.	-1	PRLR	HGNC	9446	protein_coding	YES	CCDS3909.1	ENSP00000371432	PRLR_HUMAN	D6RD41_HUMAN,D6RC67_HUMAN,D6RAN9_HUMAN,D6R9V7_HUMAN,D6R9P5_HUMAN	UPI0000132234	.	.	.	6/10	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,PROSITE_patterns:PS01352,hmmpanther:PTHR23036:SF86,hmmpanther:PTHR23036,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTCCCACTC	.	5	ESCA
KIF2A	0	.	GRCh37	5	61661149	61661149	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1547C>G	p.Ser516Cys	p.S516C	ENST00000407818	15/21	78	72	6	24	24	0	KIF2A,missense_variant,p.Ser516Cys,ENST00000401507,;KIF2A,missense_variant,p.Ser470Cys,ENST00000506857,;KIF2A,missense_variant,p.Ser516Cys,ENST00000407818,;KIF2A,missense_variant,p.Ser496Cys,ENST00000381103,;KIF2A,intron_variant,,ENST00000512006,;KIF2A,downstream_gene_variant,,ENST00000514082,;KIF2A,intron_variant,,ENST00000509663,;KIF2A,downstream_gene_variant,,ENST00000509624,;	G	ENSG00000068796	ENST00000407818	Transcript	missense_variant	1568	1547	516	S/C	tCt/tGt	.	.	.	1	KIF2A	HGNC	6318	protein_coding	YES	CCDS47216.1	ENSP00000385000	KIF2A_HUMAN	D6RD93_HUMAN	UPI0001533DB2	.	deleterious(0)	benign(0.222)	15/21	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF378,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	AGATTCTTTCA	.	3	ESCA
MEF2C	0	.	GRCh37	5	88027681	88027681	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729G>A	p.%3D	p.L243L	ENST00000340208	9/12	63	52	11	36	36	0	MEF2C,synonymous_variant,p.%3D,ENST00000504921,;MEF2C,synonymous_variant,p.%3D,ENST00000510942,;MEF2C,synonymous_variant,p.%3D,ENST00000514028,;MEF2C,synonymous_variant,p.%3D,ENST00000514015,;MEF2C,synonymous_variant,p.%3D,ENST00000506554,;MEF2C,synonymous_variant,p.%3D,ENST00000340208,;MEF2C,synonymous_variant,p.%3D,ENST00000424173,;MEF2C,synonymous_variant,p.%3D,ENST00000437473,;MEF2C,synonymous_variant,p.%3D,ENST00000508569,;MEF2C,synonymous_variant,p.%3D,ENST00000513252,;MEF2C,synonymous_variant,p.%3D,ENST00000539796,;MEF2C,synonymous_variant,p.%3D,ENST00000506716,;MEF2C,downstream_gene_variant,,ENST00000503554,;MEF2C,non_coding_transcript_exon_variant,,ENST00000515715,;MEF2C,upstream_gene_variant,,ENST00000510980,;	T	ENSG00000081189	ENST00000340208	Transcript	synonymous_variant	1135	729	243	L	ctG/ctA	.	.	.	-1	MEF2C	HGNC	6996	protein_coding	YES	CCDS54878.1	ENSP00000340874	MEF2C_HUMAN	H0YNI2_HUMAN,D6RJA7_HUMAN,D6RJ95_HUMAN,D6RG14_HUMAN	UPI0000D9B539	.	.	.	9/12	.	hmmpanther:PTHR11945:SF25,hmmpanther:PTHR11945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAGCAGACC	.	5	ESCA
CHD1	0	.	GRCh37	5	98232051	98232051	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1589A>G	p.Tyr530Cys	p.Y530C	ENST00000284049	11/35	40	34	6	16	16	0	CHD1,missense_variant,p.Tyr530Cys,ENST00000284049,;	C	ENSG00000153922	ENST00000284049	Transcript	missense_variant	1739	1589	530	Y/C	tAt/tGt	.	.	.	-1	CHD1	HGNC	1915	protein_coding	YES	CCDS34204.1	ENSP00000284049	CHD1_HUMAN	.	UPI000013DD75	.	deleterious(0)	possibly_damaging(0.841)	11/35	.	Superfamily_domains:SSF52540,SMART_domains:SM00487,Gene3D:3.40.50.300,Pfam_domain:PF00176,hmmpanther:PTHR10799:SF535,hmmpanther:PTHR10799,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCATATAAT	.	5	ESCA
TFAP2A	0	.	GRCh37	6	10402728	10402728	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880G>T	p.Glu294Ter	p.E294*	ENST00000379604	5/7	42	23	18	25	25	0	TFAP2A,stop_gained,p.Glu69Ter,ENST00000461628,;TFAP2A,stop_gained,p.Glu296Ter,ENST00000379613,;TFAP2A,stop_gained,p.Glu294Ter,ENST00000482890,;TFAP2A,stop_gained,p.Glu294Ter,ENST00000379604,;TFAP2A,stop_gained,p.Glu199Ter,ENST00000475264,;TFAP2A,stop_gained,p.Glu288Ter,ENST00000379608,;TFAP2A,stop_gained,p.Glu294Ter,ENST00000466073,;TFAP2A,stop_gained,p.Glu290Ter,ENST00000319516,;TFAP2A,downstream_gene_variant,,ENST00000498450,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000497266,;TFAP2A,downstream_gene_variant,,ENST00000462727,;TFAP2A,downstream_gene_variant,,ENST00000473652,;TFAP2A,downstream_gene_variant,,ENST00000490875,;TFAP2A,3_prime_UTR_variant,,ENST00000488193,;TFAP2A,3_prime_UTR_variant,,ENST00000489805,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000478375,;TFAP2A,downstream_gene_variant,,ENST00000474952,;	A	ENSG00000137203	ENST00000379604	Transcript	stop_gained	1132	880	294	E/*	Gag/Tag	.	.	.	-1	TFAP2A	HGNC	11742	protein_coding	YES	CCDS4510.1	ENSP00000368924	AP2A_HUMAN	.	UPI0000125BC5	.	.	.	5/7	.	hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF8,Pfam_domain:PF03299,Prints_domain:PR01748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCTACTA	.	5	ESCA
VNN3	0	.	GRCh37	6	133044729	133044729	+	Intron	SNP	A	A	G	rs763714937	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*461+144T>C	.	.	ENST00000427187	.	12	8	4	8	8	0	VNN3,3_prime_UTR_variant,,ENST00000509351,;VNN3,intron_variant,,ENST00000414302,;VNN3,intron_variant,,ENST00000275223,;VNN3,intron_variant,,ENST00000427187,;VNN3,intron_variant,,ENST00000367927,;VNN3,intron_variant,,ENST00000392393,;VNN3,intron_variant,,ENST00000519686,;VNN3,intron_variant,,ENST00000207771,;VNN3,intron_variant,,ENST00000423615,;VNN3,intron_variant,,ENST00000425515,;VNN3,intron_variant,,ENST00000417437,;VNN3,downstream_gene_variant,,ENST00000450865,;VNN3,downstream_gene_variant,,ENST00000544102,;	G	ENSG00000093134	ENST00000427187	Transcript	intron_variant	.	.	.	.	.	rs763714937	.	.	-1	VNN3	HGNC	16431	protein_coding	YES	.	ENSP00000444491	VNN3_HUMAN	A0AUL5_HUMAN	UPI0001737A7C	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCATATCATA	.	2	ESCA
KDM1B	0	.	GRCh37	6	18215356	18215357	+	Frame_Shift_Ins	INS	-	-	GC	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1533_1534dupGC	p.Gln512ArgfsTer28	p.Q512Rfs*28	ENST00000297792	16/18	33	21	12	26	26	0	KDM1B,frameshift_variant,p.Gln35ArgfsTer28,ENST00000546309,;KDM1B,frameshift_variant,p.Gln745ArgfsTer28,ENST00000388870,;KDM1B,frameshift_variant,p.Gln513ArgfsTer28,ENST00000397244,;KDM1B,frameshift_variant,p.Gln562ArgfsTer28,ENST00000449850,;KDM1B,frameshift_variant,p.Gln512ArgfsTer28,ENST00000297792,;	GC	ENSG00000165097	ENST00000297792	Transcript	frameshift_variant	1709-1710	1532-1533	511	E/EX	gag/gaGCg	.	.	.	1	KDM1B	HGNC	21577	protein_coding	YES	CCDS34343.1	ENSP00000297792	KDM1B_HUMAN	Q08EI0_HUMAN	UPI000023739E	.	.	.	16/18	.	hmmpanther:PTHR10742:SF241,hmmpanther:PTHR10742,Gene3D:3.90.660.10,Pfam_domain:PF01593,Superfamily_domains:SSF54373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAAGGAGCAGG	.	3	ESCA
C6orf136	0	.	GRCh37	6	30615096	30615096	+	Missense_Mutation	SNP	G	G	C	rs551438712	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88G>C	p.Glu30Gln	p.E30Q	ENST00000293604	1/6	38	18	20	36	36	0	C6orf136,missense_variant,p.Glu30Gln,ENST00000293604,;C6orf136,intron_variant,,ENST00000376473,;C6orf136,intron_variant,,ENST00000376471,;ATAT1,downstream_gene_variant,,ENST00000318999,;C6orf136,upstream_gene_variant,,ENST00000467801,;C6orf136,upstream_gene_variant,,ENST00000528347,;ATAT1,downstream_gene_variant,,ENST00000376485,;C6orf136,upstream_gene_variant,,ENST00000465699,;ATAT1,downstream_gene_variant,,ENST00000376478,;ATAT1,downstream_gene_variant,,ENST00000330083,;ATAT1,downstream_gene_variant,,ENST00000329992,;C6orf136,upstream_gene_variant,,ENST00000446773,;C6orf136,upstream_gene_variant,,ENST00000468785,;ATAT1,downstream_gene_variant,,ENST00000376483,;ATAT1,downstream_gene_variant,,ENST00000319027,;AL662800.2,upstream_gene_variant,,ENST00000583820,;C6orf136,intron_variant,,ENST00000493705,;ATAT1,downstream_gene_variant,,ENST00000462304,;ATAT1,downstream_gene_variant,,ENST00000468713,;C6orf136,intron_variant,,ENST00000463794,;C6orf136,intron_variant,,ENST00000484551,;C6orf136,intron_variant,,ENST00000488383,;ATAT1,downstream_gene_variant,,ENST00000479562,;C6orf136,upstream_gene_variant,,ENST00000487873,;ATAT1,downstream_gene_variant,,ENST00000471782,;	C	ENSG00000204564	ENST00000293604	Transcript	missense_variant	281	88	30	E/Q	Gag/Cag	rs551438712	.	.	1	C6orf136	HGNC	21301	protein_coding	YES	CCDS54979.1	ENSP00000293604	CF136_HUMAN	Q0P5T2_HUMAN,H7C5B5_HUMAN,H7C4Z6_HUMAN	UPI0001A51C32	.	deleterious_low_confidence(0.05)	benign(0)	1/6	.	Low_complexity_(Seg):seg	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGAGGGA	by1000G	5	ESCA
PACSIN1	0	.	GRCh37	6	34500722	34500722	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*415G>T	.	.	ENST00000538621	10/10	19	15	4	14	14	0	PACSIN1,3_prime_UTR_variant,,ENST00000538621,;PACSIN1,3_prime_UTR_variant,,ENST00000244458,;PACSIN1,3_prime_UTR_variant,,ENST00000374043,;SPDEF,downstream_gene_variant,,ENST00000374037,;PACSIN1,downstream_gene_variant,,ENST00000486120,;	T	ENSG00000124507	ENST00000538621	Transcript	3_prime_UTR_variant	1995	.	.	.	.	.	.	.	1	PACSIN1	HGNC	8570	protein_coding	YES	CCDS4793.1	ENSP00000439639	PACN1_HUMAN	Q5TZC3_HUMAN,F6U236_HUMAN	UPI000000D983	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CCCCTGCCCTG	.	3	ESCA
LCA5	0	.	GRCh37	6	80196741	80196741	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2074G>A	p.Glu692Lys	p.E692K	ENST00000392959	9/9	55	32	22	30	30	0	LCA5,missense_variant,p.Glu692Lys,ENST00000369846,;LCA5,missense_variant,p.Glu692Lys,ENST00000392959,;LCA5,downstream_gene_variant,,ENST00000467898,;	T	ENSG00000135338	ENST00000392959	Transcript	missense_variant	2686	2074	692	E/K	Gaa/Aaa	.	.	.	-1	LCA5	HGNC	31923	protein_coding	YES	CCDS4990.1	ENSP00000376686	LCA5_HUMAN	A7X9N5_HUMAN	UPI000007144D	.	deleterious(0)	probably_damaging(1)	9/9	.	hmmpanther:PTHR16650:SF8,hmmpanther:PTHR16650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCAATTT	.	5	ESCA
LYRM2	0	.	GRCh37	6	90346865	90346865	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*127G>C	.	.	ENST00000523377	3/3	17	9	7	9	9	0	LYRM2,3_prime_UTR_variant,,ENST00000520318,;LYRM2,3_prime_UTR_variant,,ENST00000523377,;LYRM2,intron_variant,,ENST00000520441,;ANKRD6,downstream_gene_variant,,ENST00000369408,;LYRM2,non_coding_transcript_exon_variant,,ENST00000524153,;LYRM2,non_coding_transcript_exon_variant,,ENST00000521961,;LYRM2,non_coding_transcript_exon_variant,,ENST00000523075,;LYRM2,non_coding_transcript_exon_variant,,ENST00000517396,;LYRM2,intron_variant,,ENST00000520897,;LYRM2,intron_variant,,ENST00000523793,;LYRM2,intron_variant,,ENST00000412237,;ANKRD6,downstream_gene_variant,,ENST00000415924,;	G	ENSG00000083099	ENST00000523377	Transcript	3_prime_UTR_variant	431	.	.	.	.	.	.	.	-1	LYRM2	HGNC	25229	protein_coding	YES	CCDS5023.1	ENSP00000430025	LYRM2_HUMAN	.	UPI00000703DA	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTCCTTTG	.	2	ESCA
ANKMY2	0	.	GRCh37	7	16655488	16655488	+	Nonsense_Mutation	SNP	G	G	A	rs768646683	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.412C>T	p.Arg138Ter	p.R138*	ENST00000306999	5/10	34	19	15	18	18	0	ANKMY2,stop_gained,p.Arg138Ter,ENST00000306999,;ANKMY2,stop_gained,p.Arg138Ter,ENST00000447802,;	A	ENSG00000106524	ENST00000306999	Transcript	stop_gained	656	412	138	R/*	Cga/Tga	rs768646683	.	.	-1	ANKMY2	HGNC	25370	protein_coding	YES	CCDS5361.1	ENSP00000303570	ANKY2_HUMAN	.	UPI0000035D93	.	.	.	5/10	.	hmmpanther:PTHR24150,SMART_domains:SM00248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCGAGGAA	byFrequency	5	ESCA
SNX13	0	.	GRCh37	7	17832652	17832652	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1017C>T	.	.	ENST00000428135	26/26	33	24	9	19	19	0	SNX13,3_prime_UTR_variant,,ENST00000428135,;SNX13,3_prime_UTR_variant,,ENST00000409389,;SNX13,downstream_gene_variant,,ENST00000496855,;SNX13,downstream_gene_variant,,ENST00000409076,;	A	ENSG00000071189	ENST00000428135	Transcript	3_prime_UTR_variant	4090	.	.	.	.	.	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATAGAATTA	.	5	ESCA
SNX13	0	.	GRCh37	7	17833516	17833516	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*153C>G	.	.	ENST00000428135	26/26	12	7	5	10	10	0	SNX13,3_prime_UTR_variant,,ENST00000428135,;SNX13,3_prime_UTR_variant,,ENST00000409389,;SNX13,non_coding_transcript_exon_variant,,ENST00000496855,;SNX13,3_prime_UTR_variant,,ENST00000409076,;	C	ENSG00000071189	ENST00000428135	Transcript	3_prime_UTR_variant	3226	.	.	.	.	.	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGAATGAGAAG	.	3	ESCA
SNX13	0	.	GRCh37	7	17833695	17833695	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2848C>G	p.Gln950Glu	p.Q950E	ENST00000428135	26/26	39	27	12	29	29	0	SNX13,missense_variant,p.Gln950Glu,ENST00000428135,;SNX13,3_prime_UTR_variant,,ENST00000409389,;SNX13,non_coding_transcript_exon_variant,,ENST00000496855,;SNX13,3_prime_UTR_variant,,ENST00000409076,;	C	ENSG00000071189	ENST00000428135	Transcript	missense_variant	3047	2848	950	Q/E	Caa/Gaa	.	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	tolerated_low_confidence(0.06)	benign(0.008)	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTTGAGTAG	.	5	ESCA
IQCE	0	.	GRCh37	7	2645633	2645633	+	Splice_Site	SNP	T	T	C	.	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1865+2T>C	.	p.X622_splice	ENST00000402050	.	102	89	13	90	90	0	IQCE,splice_donor_variant,,ENST00000404984,;IQCE,splice_donor_variant,,ENST00000402050,;IQCE,splice_donor_variant,,ENST00000438376,;IQCE,splice_donor_variant,,ENST00000325979,;IQCE,splice_donor_variant,,ENST00000423196,;IQCE,splice_donor_variant,,ENST00000486730,;IQCE,splice_donor_variant,,ENST00000476665,;IQCE,splice_donor_variant,,ENST00000325997,;IQCE,downstream_gene_variant,,ENST00000470731,;	C	ENSG00000106012	ENST00000402050	Transcript	splice_donor_variant	.	.	.	.	.	COSM485237	.	.	1	IQCE	HGNC	29171	protein_coding	YES	CCDS43542.1	ENSP00000385597	IQCE_HUMAN	C9JX25_HUMAN,C9JP75_HUMAN	UPI000020E9EF	.	.	.	.	20/21	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAGGTGAGTC	.	4	ESCA
RADIL	0	.	GRCh37	7	4917679	4917679	+	Missense_Mutation	SNP	G	G	A	rs772766287	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92C>T	p.Thr31Met	p.T31M	ENST00000399583	2/15	36	27	9	39	39	0	RADIL,missense_variant,p.Thr31Met,ENST00000457174,;RADIL,missense_variant,p.Thr31Met,ENST00000399583,;RADIL,missense_variant,p.Thr31Met,ENST00000536091,;RADIL,missense_variant,p.Thr31Met,ENST00000445392,;	A	ENSG00000157927	ENST00000399583	Transcript	missense_variant	280	92	31	T/M	aCg/aTg	rs772766287,COSM1090548	.	.	-1	RADIL	HGNC	22226	protein_coding	YES	CCDS43544.1	ENSP00000382492	RADIL_HUMAN	F5H6X3_HUMAN,C9J7G0_HUMAN	UPI0000E0A787	.	deleterious(0)	probably_damaging(0.999)	2/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF3	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCGTCCGG	byFrequency	5	ESCA
AUTS2	0	.	GRCh37	7	70256405	70256405	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*423T>C	.	.	ENST00000342771	19/19	33	27	6	16	16	0	AUTS2,3_prime_UTR_variant,,ENST00000342771,;AUTS2,3_prime_UTR_variant,,ENST00000406775,;AUTS2,downstream_gene_variant,,ENST00000418686,;AUTS2,downstream_gene_variant,,ENST00000449547,;	C	ENSG00000158321	ENST00000342771	Transcript	3_prime_UTR_variant	4524	.	.	.	.	.	.	.	1	AUTS2	HGNC	14262	protein_coding	YES	CCDS5539.1	ENSP00000344087	AUTS2_HUMAN	Q75MQ7_HUMAN,Q75MQ4_HUMAN,Q75MQ3_HUMAN,Q75MD7_HUMAN	UPI0000126665	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGTTCATA	.	5	ESCA
SEMA3A	0	.	GRCh37	7	83675741	83675741	+	Missense_Mutation	SNP	C	C	A	rs778827801	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.566G>T	p.Gly189Val	p.G189V	ENST00000265362	6/17	45	37	8	22	22	0	SEMA3A,missense_variant,p.Gly189Val,ENST00000265362,;SEMA3A,missense_variant,p.Gly189Val,ENST00000436949,;	A	ENSG00000075213	ENST00000265362	Transcript	missense_variant	881	566	189	G/V	gGa/gTa	rs778827801	.	.	-1	SEMA3A	HGNC	10723	protein_coding	YES	CCDS5599.1	ENSP00000265362	SEM3A_HUMAN	Q86UJ2_HUMAN,Q75MQ2_HUMAN,C9JD25_HUMAN,C9J9C4_HUMAN	UPI0000135A60	.	deleterious(0)	probably_damaging(1)	6/17	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF23,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTTCCAGAG	.	5	ESCA
FZD1	0	.	GRCh37	7	90895458	90895459	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1264dupA	p.Ile422AsnfsTer61	p.I422Nfs*61	ENST00000287934	1/1	78	58	20	49	49	0	FZD1,frameshift_variant,p.Ile422AsnfsTer61,ENST00000287934,;	A	ENSG00000157240	ENST00000287934	Transcript	frameshift_variant	1676-1677	1263-1264	421-422	-/X	-/A	.	.	.	1	FZD1	HGNC	4038	protein_coding	YES	CCDS5620.1	ENSP00000287934	FZD1_HUMAN	.	UPI000005104D	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309:SF81,hmmpanther:PTHR11309,Pfam_domain:PF01534,Prints_domain:PR00489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGGTGATCCT	.	3	ESCA
USP17L2	0	.	GRCh37	8	11996082	11996082	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188C>T	p.Ala63Val	p.A63V	ENST00000333796	1/1	77	64	13	58	58	0	USP17L2,missense_variant,p.Ala63Val,ENST00000333796,;FAM66D,intron_variant,,ENST00000434078,;USP17L7,upstream_gene_variant,,ENST00000530447,;USP17L7,upstream_gene_variant,,ENST00000416902,;	A	ENSG00000223443	ENST00000333796	Transcript	missense_variant	505	188	63	A/V	gCt/gTt	.	.	.	-1	USP17L2	HGNC	34434	protein_coding	YES	CCDS43713.1	ENSP00000333329	U17L2_HUMAN	.	UPI0000198137	.	tolerated(0.08)	benign(0.045)	1/1	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF382	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGGGAGCAAGC	.	3	ESCA
SLC52A2	0	.	GRCh37	8	145584272	145584272	+	Missense_Mutation	SNP	C	C	T	rs531845498	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024C>T	p.Leu342Phe	p.L342F	ENST00000532887	4/5	33	23	10	27	27	0	SLC52A2,missense_variant,p.Leu342Phe,ENST00000532887,;SLC52A2,missense_variant,p.Leu342Phe,ENST00000527078,;SLC52A2,missense_variant,p.Leu342Phe,ENST00000530047,;SLC52A2,missense_variant,p.Leu254Phe,ENST00000540505,;SLC52A2,missense_variant,p.Leu342Phe,ENST00000402965,;SLC52A2,missense_variant,p.Leu342Phe,ENST00000329994,;SLC52A2,intron_variant,,ENST00000526752,;FBXL6,upstream_gene_variant,,ENST00000331890,;SLC52A2,downstream_gene_variant,,ENST00000526338,;FBXL6,upstream_gene_variant,,ENST00000455319,;SLC52A2,downstream_gene_variant,,ENST00000524541,;SLC52A2,downstream_gene_variant,,ENST00000534725,;SLC52A2,downstream_gene_variant,,ENST00000532815,;FBXL6,upstream_gene_variant,,ENST00000530687,;FBXL6,upstream_gene_variant,,ENST00000524909,;FBXL6,upstream_gene_variant,,ENST00000526524,;FBXL6,upstream_gene_variant,,ENST00000527000,;SLC52A2,downstream_gene_variant,,ENST00000526891,;SLC52A2,3_prime_UTR_variant,,ENST00000526779,;SLC52A2,downstream_gene_variant,,ENST00000533662,;FBXL6,upstream_gene_variant,,ENST00000530142,;FBXL6,upstream_gene_variant,,ENST00000529279,;FBXL6,upstream_gene_variant,,ENST00000524492,;	T	ENSG00000185803	ENST00000532887	Transcript	missense_variant	1607	1024	342	L/F	Ctc/Ttc	rs531845498	.	.	1	SLC52A2	HGNC	30224	protein_coding	YES	CCDS6423.1	ENSP00000436768	S52A2_HUMAN	F5GXA8_HUMAN,E9PRC3_HUMAN,E9PIX2_HUMAN	UPI000004470A	.	deleterious(0.01)	benign(0.202)	4/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12929,hmmpanther:PTHR12929:SF5,Pfam_domain:PF06237	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGCCTCTCT	byFrequency|by1000G	5	ESCA
ZNF250	0	.	GRCh37	8	146107894	146107894	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.689G>A	p.Ser230Asn	p.S230N	ENST00000292579	6/6	63	57	6	45	45	0	ZNF250,missense_variant,p.Ser230Asn,ENST00000292579,;ZNF250,missense_variant,p.Ser225Asn,ENST00000417550,;ZNF250,intron_variant,,ENST00000342660,;ZNF250,intron_variant,,ENST00000543949,;ZNF250,downstream_gene_variant,,ENST00000533622,;ZNF250,downstream_gene_variant,,ENST00000533221,;ZNF250,downstream_gene_variant,,ENST00000525694,;ZNF250,intron_variant,,ENST00000529780,;ZNF250,intron_variant,,ENST00000528258,;ZNF250,intron_variant,,ENST00000533543,;	T	ENSG00000196150	ENST00000292579	Transcript	missense_variant	806	689	230	S/N	aGt/aAt	.	.	.	-1	ZNF250	HGNC	13044	protein_coding	YES	CCDS34972.1	ENSP00000292579	ZN250_HUMAN	.	UPI0000197F51	.	tolerated(0.98)	benign(0.006)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF112,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATACACTGCAC	.	4	ESCA
CSMD1	0	.	GRCh37	8	3015451	3015451	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5882G>T	p.Arg1961Leu	p.R1961L	ENST00000537824	39/70	21	17	4	12	12	0	CSMD1,missense_variant,p.Arg1962Leu,ENST00000400186,;CSMD1,missense_variant,p.Arg1961Leu,ENST00000542608,;CSMD1,missense_variant,p.Arg1962Leu,ENST00000602723,;CSMD1,missense_variant,p.Arg1442Leu,ENST00000335551,;CSMD1,missense_variant,p.Arg1961Leu,ENST00000537824,;CSMD1,missense_variant,p.Arg1962Leu,ENST00000520002,;CSMD1,missense_variant,p.Arg1961Leu,ENST00000539096,;CSMD1,missense_variant,p.Arg1962Leu,ENST00000602557,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523387,;CSMD1,non_coding_transcript_exon_variant,,ENST00000520451,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,;	A	ENSG00000183117	ENST00000537824	Transcript	missense_variant	5882	5882	1961	R/L	cGc/cTc	.	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	possibly_damaging(0.864)	39/70	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF323,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACGGCGAACG	.	4	ESCA
SGK223	0	.	GRCh37	8	8185259	8185259	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3033C>A	p.Cys1011Ter	p.C1011*	ENST00000520004	5/6	35	28	7	31	31	0	SGK223,stop_gained,p.Cys1011Ter,ENST00000520004,;SGK223,stop_gained,p.Cys1011Ter,ENST00000330777,;	T	ENSG00000182319	ENST00000520004	Transcript	stop_gained	3298	3033	1011	C/*	tgC/tgA	.	.	.	-1	SGK223	Uniprot_gn	.	protein_coding	YES	CCDS43706.1	ENSP00000428054	SG223_HUMAN	.	UPI00001D82A6	.	.	.	5/6	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972,SMART_domains:SM00220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGAGCAGGT	.	5	ESCA
OTUD6B	0	.	GRCh37	8	92090650	92090650	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472A>G	p.Thr158Ala	p.T158A	ENST00000285420	4/7	21	15	5	22	22	0	OTUD6B,missense_variant,p.Thr27Ala,ENST00000404789,;OTUD6B,missense_variant,p.Thr158Ala,ENST00000285420,;OTUD6B,3_prime_UTR_variant,,ENST00000522894,;OTUD6B,non_coding_transcript_exon_variant,,ENST00000524027,;	G	ENSG00000155100	ENST00000285420	Transcript	missense_variant	571	472	158	T/A	Aca/Gca	.	.	.	1	OTUD6B	HGNC	24281	protein_coding	YES	CCDS6253.2	ENSP00000285420	OTU6B_HUMAN	.	UPI0000E5AF0F	.	tolerated(1)	benign(0.005)	4/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12419:SF1,hmmpanther:PTHR12419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTAACAGGA	.	5	ESCA
LAPTM4B	0	.	GRCh37	8	98837299	98837299	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.794G>A	p.Ser265Asn	p.S265N	ENST00000445593	6/7	47	34	13	32	32	0	LAPTM4B,missense_variant,p.Ser265Asn,ENST00000445593,;LAPTM4B,missense_variant,p.Ser174Asn,ENST00000521545,;	A	ENSG00000104341	ENST00000445593	Transcript	missense_variant	1474	794	265	S/N	aGc/aAc	.	.	.	1	LAPTM4B	HGNC	13646	protein_coding	YES	CCDS6275.1	ENSP00000402301	LAP4B_HUMAN	Q86SJ0_HUMAN	UPI000018F5E2	.	tolerated(0.51)	benign(0.199)	6/7	.	Transmembrane_helices:TMhelix,Pfam_domain:PF03821,hmmpanther:PTHR12479,hmmpanther:PTHR12479:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTAGCTGTG	.	5	ESCA
NR4A3	0	.	GRCh37	9	102627890	102627890	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1741G>C	.	.	ENST00000330847	7/7	51	30	20	35	35	0	NR4A3,3_prime_UTR_variant,,ENST00000330847,;NR4A3,downstream_gene_variant,,ENST00000395097,;	C	ENSG00000119508	ENST00000330847	Transcript	3_prime_UTR_variant	3699	.	.	.	.	.	.	.	1	NR4A3	HGNC	7982	protein_coding	YES	CCDS6742.1	ENSP00000333122	NR4A3_HUMAN	.	UPI0000160FE4	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTAGTTTTT	.	5	ESCA
RABL6	0	.	GRCh37	9	139733890	139733891	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1713_1714insT	p.Asp572Ter	p.D572*	ENST00000371663	12/15	49	43	6	61	61	0	RABL6,frameshift_variant,p.Asp572Ter,ENST00000371663,;RABL6,frameshift_variant,p.Asp365Ter,ENST00000435930,;RABL6,frameshift_variant,p.Asp456Ter,ENST00000371675,;RABL6,frameshift_variant,p.Asp571Ter,ENST00000311502,;RABL6,3_prime_UTR_variant,,ENST00000432842,;RABL6,intron_variant,,ENST00000357466,;C9orf172,upstream_gene_variant,,ENST00000436881,;RABL6,downstream_gene_variant,,ENST00000461992,;RABL6,downstream_gene_variant,,ENST00000466096,;RABL6,frameshift_variant,p.Trp457CysfsTer161,ENST00000484471,;RABL6,3_prime_UTR_variant,,ENST00000464941,;	T	ENSG00000196642	ENST00000371663	Transcript	frameshift_variant	1988-1989	1713-1714	571-572	-/X	-/T	.	.	.	1	RABL6	HGNC	24703	protein_coding	YES	CCDS55352.1	ENSP00000360727	RABL6_HUMAN	.	UPI0000E0C208	.	.	.	12/15	.	hmmpanther:PTHR14932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCATGGATGA	.	3	ESCA
FOXD4L5	0	.	GRCh37	9	70177178	70177178	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806G>A	p.Arg269His	p.R269H	ENST00000377420	1/1	42	37	5	55	55	0	FOXD4L5,missense_variant,p.Arg269His,ENST00000377420,;RP11-15J10.1,downstream_gene_variant,,ENST00000445695,;	T	ENSG00000204779	ENST00000377420	Transcript	missense_variant	1638	806	269	R/H	cGc/cAc	.	.	.	-1	FOXD4L5	HGNC	18522	protein_coding	YES	CCDS47977.1	ENSP00000366637	FX4L5_HUMAN	Q8WTR0_HUMAN	UPI0000458A33	.	deleterious(0.02)	probably_damaging(0.964)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11829:SF149,hmmpanther:PTHR11829	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GGTAGCGAAGA	.	2	ESCA
TRPM6	0	.	GRCh37	9	77377816	77377816	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3771C>T	p.%3D	p.I1257I	ENST00000360774	26/39	30	18	11	28	28	0	TRPM6,synonymous_variant,p.%3D,ENST00000451710,;TRPM6,synonymous_variant,p.%3D,ENST00000449912,;TRPM6,synonymous_variant,p.%3D,ENST00000361255,;TRPM6,synonymous_variant,p.%3D,ENST00000376864,;TRPM6,synonymous_variant,p.%3D,ENST00000360774,;TRPM6,intron_variant,,ENST00000376871,;TRPM6,intron_variant,,ENST00000376872,;	A	ENSG00000119121	ENST00000360774	Transcript	synonymous_variant	4009	3771	1257	I	atC/atT	.	.	.	-1	TRPM6	HGNC	17995	protein_coding	YES	CCDS6647.1	ENSP00000354006	TRPM6_HUMAN	.	UPI000006E041	.	.	.	26/39	.	hmmpanther:PTHR13800:SF15,hmmpanther:PTHR13800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACAGATGAC	.	5	ESCA
ZNF185	0	.	GRCh37	X	152101493	152101493	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096G>T	p.Asp366Tyr	p.D366Y	ENST00000535861	14/24	34	17	16	17	17	0	ZNF185,missense_variant,p.Asp307Tyr,ENST00000318504,;ZNF185,missense_variant,p.Asp366Tyr,ENST00000370270,;ZNF185,missense_variant,p.Asp367Tyr,ENST00000449285,;ZNF185,missense_variant,p.Asp366Tyr,ENST00000370268,;ZNF185,missense_variant,p.Asp145Tyr,ENST00000318529,;ZNF185,missense_variant,p.Asp337Tyr,ENST00000539731,;ZNF185,missense_variant,p.Asp366Tyr,ENST00000535861,;ZNF185,missense_variant,p.Asp125Tyr,ENST00000426821,;ZNF185,intron_variant,,ENST00000324823,;ZNF185,intron_variant,,ENST00000447792,;ZNF185,missense_variant,p.Asp337Tyr,ENST00000436731,;	T	ENSG00000147394	ENST00000535861	Transcript	missense_variant	1144	1096	366	D/Y	Gac/Tac	.	.	.	1	ZNF185	HGNC	12976	protein_coding	YES	CCDS55529.1	ENSP00000440847	ZN185_HUMAN	H7BZT5_HUMAN,B3KPM4_HUMAN	UPI0001D27F7E	.	deleterious(0.02)	benign(0.132)	14/24	.	hmmpanther:PTHR15468:SF2,hmmpanther:PTHR15468	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTAGACATC	.	5	ESCA
WASH6P	0	.	GRCh37	X	155253891	155253891	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2807G>A	.	.	ENST00000461007	2/2	72	48	24	53	53	0	WASH6P,non_coding_transcript_exon_variant,,ENST00000340131,;AJ271736.10,non_coding_transcript_exon_variant,,ENST00000285718,;WASH6P,non_coding_transcript_exon_variant,,ENST00000464205,;WASH6P,non_coding_transcript_exon_variant,,ENST00000484415,;WASH6P,non_coding_transcript_exon_variant,,ENST00000492963,;WASH6P,non_coding_transcript_exon_variant,,ENST00000461007,;WASH6P,non_coding_transcript_exon_variant,,ENST00000483286,;WASH6P,non_coding_transcript_exon_variant,,ENST00000460206,;WASH6P,non_coding_transcript_exon_variant,,ENST00000496301,;WASH6P,downstream_gene_variant,,ENST00000476066,;WASH6P,downstream_gene_variant,,ENST00000475594,;WASH6P,downstream_gene_variant,,ENST00000482170,;WASH6P,downstream_gene_variant,,ENST00000469624,;WASH6P,downstream_gene_variant,,ENST00000479401,;WASH6P,downstream_gene_variant,,ENST00000496011,;WASH6P,downstream_gene_variant,,ENST00000483079,;AJ271736.10,downstream_gene_variant,,ENST00000483543,;WASH6P,non_coding_transcript_exon_variant,,ENST00000359512,;DDX11L16,downstream_gene_variant,,ENST00000445777,;DDX11L16,downstream_gene_variant,,ENST00000507418,;	A	ENSG00000182484	ENST00000461007	Transcript	non_coding_transcript_exon_variant	2807	.	.	.	.	.	.	.	1	WASH6P	HGNC	31685	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	AGCATGAAGGA	.	3	ESCA
AWAT2	0	.	GRCh37	X	69262136	69262136	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.748C>T	p.Gln250Ter	p.Q250*	ENST00000276101	6/8	26	23	3	18	18	0	AWAT2,stop_gained,p.Gln250Ter,ENST00000276101,;EDA,downstream_gene_variant,,ENST00000374553,;EDA,downstream_gene_variant,,ENST00000374552,;AWAT2,3_prime_UTR_variant,,ENST00000440401,;AWAT2,downstream_gene_variant,,ENST00000443056,;	A	ENSG00000147160	ENST00000276101	Transcript	stop_gained	754	748	250	Q/*	Cag/Tag	.	.	.	-1	AWAT2	HGNC	23251	protein_coding	YES	CCDS35320.1	ENSP00000421172	AWAT2_HUMAN	.	UPI00001D7BE0	.	.	.	6/8	.	hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF12,Pfam_domain:PF03982	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTCTGGAACC	.	3	ESCA
GPR174	0	.	GRCh37	X	78427641	78427641	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43H-01A-11D-A247-09	TCGA-L5-A43H-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*135C>T	.	.	ENST00000276077	1/1	26	23	3	14	14	0	GPR174,3_prime_UTR_variant,,ENST00000276077,;	T	ENSG00000147138	ENST00000276077	Transcript	3_prime_UTR_variant	1173	.	.	.	.	.	.	.	1	GPR174	HGNC	30245	protein_coding	YES	CCDS14443.1	ENSP00000276077	GP174_HUMAN	.	UPI0000050477	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GAATTCACTTC	.	3	ESCA
PYROXD2	0	.	GRCh37	10	100170525	100170525	+	Intron	SNP	G	G	A	rs767395272	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147+171C>T	.	.	ENST00000370575	.	14	5	9	10	10	0	PYROXD2,intron_variant,,ENST00000370575,;PYROXD2,non_coding_transcript_exon_variant,,ENST00000483923,;PYROXD2,downstream_gene_variant,,ENST00000462874,;PYROXD2,downstream_gene_variant,,ENST00000494941,;	A	ENSG00000119943	ENST00000370575	Transcript	intron_variant	.	.	.	.	.	rs767395272	.	.	-1	PYROXD2	HGNC	23517	protein_coding	YES	CCDS7474.1	ENSP00000359607	PYRD2_HUMAN	B4DIN5_HUMAN	UPI000013CA6A	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGAGCATTC	.	2	ESCA
PYROXD2	0	.	GRCh37	10	100170526	100170526	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147+170G>A	.	.	ENST00000370575	.	14	5	9	10	10	0	PYROXD2,intron_variant,,ENST00000370575,;PYROXD2,non_coding_transcript_exon_variant,,ENST00000483923,;PYROXD2,downstream_gene_variant,,ENST00000462874,;PYROXD2,downstream_gene_variant,,ENST00000494941,;	T	ENSG00000119943	ENST00000370575	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PYROXD2	HGNC	23517	protein_coding	YES	CCDS7474.1	ENSP00000359607	PYRD2_HUMAN	B4DIN5_HUMAN	UPI000013CA6A	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGAGCATTCG	.	2	ESCA
ERLIN1	0	.	GRCh37	10	101911766	101911766	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*122C>T	.	.	ENST00000421367	11/11	36	23	12	24	24	0	ERLIN1,3_prime_UTR_variant,,ENST00000421367,;ERLIN1,3_prime_UTR_variant,,ENST00000407654,;ERLIN1,downstream_gene_variant,,ENST00000370408,;	A	ENSG00000107566	ENST00000421367	Transcript	3_prime_UTR_variant	3877	.	.	.	.	.	.	.	-1	ERLIN1	HGNC	16947	protein_coding	YES	CCDS7487.2	ENSP00000410964	ERLN1_HUMAN	D3DR65_HUMAN,B0QZ43_HUMAN	UPI0000155AF8	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATCGCAGGA	.	5	ESCA
SCD	0	.	GRCh37	10	102124254	102124254	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3564G>A	.	.	ENST00000370355	6/6	25	13	12	24	24	0	SCD,3_prime_UTR_variant,,ENST00000370355,;AL139819.1,downstream_gene_variant,,ENST00000537595,;	A	ENSG00000099194	ENST00000370355	Transcript	3_prime_UTR_variant	5025	.	.	.	.	.	.	.	1	SCD	HGNC	10571	protein_coding	YES	CCDS7493.1	ENSP00000359380	ACOD_HUMAN	.	UPI00001252D2	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATAGGAATG	.	5	ESCA
BTRC	0	.	GRCh37	10	103285773	103285773	+	Missense_Mutation	SNP	G	G	A	rs747705989	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560G>A	p.Arg187Gln	p.R187Q	ENST00000370187	6/15	72	53	18	57	57	0	BTRC,missense_variant,p.Arg151Gln,ENST00000408038,;BTRC,missense_variant,p.Arg169Gln,ENST00000370183,;BTRC,missense_variant,p.Arg187Gln,ENST00000370187,;BTRC,missense_variant,p.Arg146Gln,ENST00000393441,;BTRC,non_coding_transcript_exon_variant,,ENST00000465182,;BTRC,downstream_gene_variant,,ENST00000475200,;	A	ENSG00000166167	ENST00000370187	Transcript	missense_variant	678	560	187	R/Q	cGg/cAg	rs747705989	.	.	1	BTRC	HGNC	1144	protein_coding	YES	CCDS7512.1	ENSP00000359206	FBW1A_HUMAN	Q5T1W7_HUMAN	UPI00000012B5	.	tolerated(0.7)	benign(0.003)	6/15	.	hmmpanther:PTHR22844:SF143,hmmpanther:PTHR22844,Gene3D:1.20.1280.50,Superfamily_domains:SSF81383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTCGGGGAT	byFrequency	5	ESCA
PSD	0	.	GRCh37	10	104172212	104172212	+	Silent	SNP	C	C	T	rs200243712	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1674G>A	p.%3D	p.A558A	ENST00000020673	6/17	74	47	27	28	28	0	PSD,synonymous_variant,p.%3D,ENST00000020673,;PSD,synonymous_variant,p.%3D,ENST00000406432,;PSD,upstream_gene_variant,,ENST00000488194,;PSD,downstream_gene_variant,,ENST00000492902,;PSD,downstream_gene_variant,,ENST00000472685,;PSD,upstream_gene_variant,,ENST00000461698,;	T	ENSG00000059915	ENST00000020673	Transcript	synonymous_variant	2201	1674	558	A	gcG/gcA	rs200243712	.	.	-1	PSD	HGNC	9507	protein_coding	YES	CCDS31272.1	ENSP00000020673	PSD1_HUMAN	.	UPI0000404928	.	.	.	6/17	.	PROSITE_profiles:PS50190,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF115,Pfam_domain:PF01369,SMART_domains:SM00222,Superfamily_domains:SSF48425	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTGCGCAGC	byCluster|by1000G	5	ESCA
SUFU	0	.	GRCh37	10	104353466	104353466	+	Missense_Mutation	SNP	G	G	A	rs199673680	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.671G>A	p.Arg224Gln	p.R224Q	ENST00000369902	5/12	38	21	17	13	13	0	SUFU,missense_variant,p.Arg224Gln,ENST00000369899,;SUFU,missense_variant,p.Arg224Gln,ENST00000369902,;SUFU,missense_variant,p.Arg224Gln,ENST00000423559,;RNU6-43P,downstream_gene_variant,,ENST00000384302,;SUFU,non_coding_transcript_exon_variant,,ENST00000471000,;	A	ENSG00000107882	ENST00000369902	Transcript	missense_variant	837	671	224	R/Q	cGg/cAg	rs199673680,COSM682393	.	.	1	SUFU	HGNC	16466	protein_coding	YES	CCDS7537.1	ENSP00000358918	SUFU_HUMAN	.	UPI0000073C79	.	tolerated(0.16)	benign(0.264)	5/12	.	hmmpanther:PTHR10928:SF2,hmmpanther:PTHR10928,Pfam_domain:PF05076,PIRSF_domain:PIRSF011844,Superfamily_domains:0040736	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCGGACAG	byCluster|by1000G	4	ESCA
RPEL1	0	.	GRCh37	10	105006854	105006855	+	3'UTR	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*420dupT	.	.	ENST00000441178	1/1	54	47	7	36	36	0	RPEL1,3_prime_UTR_variant,,ENST00000441178,;	T	ENSG00000235376	ENST00000441178	Transcript	3_prime_UTR_variant	1211-1212	.	.	.	.	.	.	.	1	RPEL1	HGNC	45241	protein_coding	YES	CCDS65929.1	ENSP00000476672	.	Q2QD12_HUMAN	UPI00001C1ED0	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TATGGCTTTTT	.	2	ESCA
PCGF6	0	.	GRCh37	10	105063538	105063538	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*124delT	.	.	ENST00000369847	10/10	73	55	18	47	47	0	PCGF6,3_prime_UTR_variant,,ENST00000369847,;PCGF6,3_prime_UTR_variant,,ENST00000337211,;PCGF6,non_coding_transcript_exon_variant,,ENST00000490296,;	-	ENSG00000156374	ENST00000369847	Transcript	3_prime_UTR_variant	1245	.	.	.	.	.	.	.	-1	PCGF6	HGNC	21156	protein_coding	YES	CCDS31275.1	ENSP00000358862	PCGF6_HUMAN	.	UPI00001F9669	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTGCTAAAAAT	.	3	ESCA
SORCS1	0	.	GRCh37	10	108923947	108923947	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.338C>T	p.Ala113Val	p.A113V	ENST00000344440	1/27	34	22	11	19	19	0	SORCS1,missense_variant,p.Ala113Val,ENST00000263054,;SORCS1,missense_variant,p.Ala113Val,ENST00000344440,;	A	ENSG00000108018	ENST00000344440	Transcript	missense_variant	338	338	113	A/V	gCg/gTg	COSM1227132,COSM1227131	.	.	-1	SORCS1	HGNC	16697	protein_coding	YES	CCDS31283.1	ENSP00000345964	SORC1_HUMAN	B3KVZ0_HUMAN	UPI000036671B	.	tolerated_low_confidence(0.32)	benign(0.011)	1/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12106:SF8,hmmpanther:PTHR12106	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCCGCTCCG	.	5	ESCA
VTI1A	0	.	GRCh37	10	114220329	114220329	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141A>C	p.Glu47Asp	p.E47D	ENST00000393077	2/8	17	14	3	15	15	0	VTI1A,missense_variant,p.Glu47Asp,ENST00000432306,;VTI1A,missense_variant,p.Glu47Asp,ENST00000393077,;VTI1A,non_coding_transcript_exon_variant,,ENST00000494728,;VTI1A,non_coding_transcript_exon_variant,,ENST00000480057,;VTI1A,non_coding_transcript_exon_variant,,ENST00000489357,;VTI1A,non_coding_transcript_exon_variant,,ENST00000496445,;VTI1A,non_coding_transcript_exon_variant,,ENST00000489142,;	C	ENSG00000151532	ENST00000393077	Transcript	missense_variant	257	141	47	E/D	gaA/gaC	.	.	.	1	VTI1A	HGNC	17792	protein_coding	YES	CCDS7575.2	ENSP00000376792	VTI1A_HUMAN	.	UPI0000DD7870	.	tolerated(0.05)	probably_damaging(0.999)	2/8	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21230,hmmpanther:PTHR21230:SF26,Gene3D:1vcsA00,Pfam_domain:PF05008,Superfamily_domains:SSF47661	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GAAGAAGCGAA	.	3	ESCA
USP6NL	0	.	GRCh37	10	11504795	11504795	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2183C>T	p.Ser728Leu	p.S728L	ENST00000277575	14/14	23	8	15	29	29	0	USP6NL,missense_variant,p.Ser711Leu,ENST00000609104,;USP6NL,missense_variant,p.Ser734Leu,ENST00000379237,;USP6NL,missense_variant,p.Ser728Leu,ENST00000277575,;	A	ENSG00000148429	ENST00000277575	Transcript	missense_variant	2226	2183	728	S/L	tCg/tTg	.	.	.	-1	USP6NL	HGNC	16858	protein_coding	YES	CCDS44357.1	ENSP00000277575	US6NL_HUMAN	.	UPI0000251ED1	.	tolerated_low_confidence(0.22)	benign(0.006)	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGAATAT	.	5	ESCA
TDRD1	0	.	GRCh37	10	115986880	115986880	+	Frame_Shift_Del	DEL	A	A	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3230delA	p.Asn1077IlefsTer4	p.N1077Ifs*4	ENST00000251864	23/26	81	58	23	46	46	0	TDRD1,frameshift_variant,p.Asn963IlefsTer4,ENST00000369281,;TDRD1,frameshift_variant,p.Asn1077IlefsTer4,ENST00000251864,;TDRD1,intron_variant,,ENST00000369282,;TDRD1,intron_variant,,ENST00000369280,;TDRD1,intron_variant,,ENST00000422662,;	-	ENSG00000095627	ENST00000251864	Transcript	frameshift_variant	3378	3225	1075	L/X	ttA/tt	COSM201884	.	.	1	TDRD1	HGNC	11712	protein_coding	YES	CCDS7588.1	ENSP00000251864	TDRD1_HUMAN	.	UPI00001F9753	.	.	.	23/26	.	hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF4	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	5	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTATTAAAAAA	.	3	ESCA
ABLIM1	0	.	GRCh37	10	116203872	116203872	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1849T>C	p.%3D	p.L617L	ENST00000277895	17/23	45	31	14	39	39	0	ABLIM1,synonymous_variant,p.%3D,ENST00000369253,;ABLIM1,synonymous_variant,p.%3D,ENST00000369266,;ABLIM1,synonymous_variant,p.%3D,ENST00000533213,;ABLIM1,synonymous_variant,p.%3D,ENST00000277895,;ABLIM1,synonymous_variant,p.%3D,ENST00000392952,;ABLIM1,synonymous_variant,p.%3D,ENST00000369252,;ABLIM1,synonymous_variant,p.%3D,ENST00000392955,;ABLIM1,synonymous_variant,p.%3D,ENST00000369256,;ABLIM1,upstream_gene_variant,,ENST00000485570,;	G	ENSG00000099204	ENST00000277895	Transcript	synonymous_variant	1947	1849	617	L	Ttg/Ctg	.	.	.	-1	ABLIM1	HGNC	78	protein_coding	YES	CCDS7590.1	ENSP00000277895	ABLM1_HUMAN	.	UPI0000418D06	.	.	.	17/23	.	hmmpanther:PTHR24213:SF18,hmmpanther:PTHR24213	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCAACTGTC	.	5	ESCA
ATRNL1	0	.	GRCh37	10	117061383	117061383	+	Missense_Mutation	SNP	C	C	T	rs140372621	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2648C>T	p.Ala883Val	p.A883V	ENST00000355044	17/29	54	40	14	34	34	0	ATRNL1,missense_variant,p.Ala13Val,ENST00000526373,;ATRNL1,missense_variant,p.Ala883Val,ENST00000355044,;ATRNL1,5_prime_UTR_variant,,ENST00000423111,;ATRNL1,upstream_gene_variant,,ENST00000303745,;ATRNL1,upstream_gene_variant,,ENST00000534530,;	T	ENSG00000107518	ENST00000355044	Transcript	missense_variant	2774	2648	883	A/V	gCg/gTg	rs140372621,COSM3396925	.	.	1	ATRNL1	HGNC	29063	protein_coding	YES	CCDS7592.1	ENSP00000347152	ATRN1_HUMAN	.	UPI000021CCF8	.	tolerated(0.29)	benign(0.011)	17/29	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF224	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATGCGAGGC	byCluster|by1000G	5	ESCA
PNLIPRP3	0	.	GRCh37	10	118187509	118187510	+	5'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-10dupA	.	.	ENST00000369230	1/12	38	25	13	17	17	0	PNLIPRP3,5_prime_UTR_variant,,ENST00000369230,;	A	ENSG00000203837	ENST00000369230	Transcript	5_prime_UTR_variant	131-132	.	.	.	.	.	.	.	1	PNLIPRP3	HGNC	23492	protein_coding	YES	CCDS31292.1	ENSP00000358232	LIPR3_HUMAN	.	UPI000013DB40	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGATTTAAAAA	.	2	ESCA
HSPA12A	0	.	GRCh37	10	118464786	118464786	+	Missense_Mutation	SNP	C	C	T	rs782810800	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.130G>A	p.Asp44Asn	p.D44N	ENST00000369209	3/12	87	58	29	37	37	0	HSPA12A,missense_variant,p.Asp44Asn,ENST00000369209,;HSPA12A,missense_variant,p.Asp37Asn,ENST00000468935,;HSPA12A,upstream_gene_variant,,ENST00000481291,;	T	ENSG00000165868	ENST00000369209	Transcript	missense_variant	235	130	44	D/N	Gac/Aac	rs782810800	.	.	-1	HSPA12A	HGNC	19022	protein_coding	YES	CCDS41569.1	ENSP00000358211	HS12A_HUMAN	.	UPI00001B3DE3	.	tolerated_low_confidence(0.34)	benign(0.003)	3/12	.	hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGTCGTTCT	.	5	ESCA
UPF2	0	.	GRCh37	10	12070974	12070974	+	Silent	SNP	G	G	C	rs759777920	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915C>G	p.%3D	p.V305V	ENST00000356352	2/21	25	10	14	20	20	0	UPF2,synonymous_variant,p.%3D,ENST00000357604,;UPF2,synonymous_variant,p.%3D,ENST00000356352,;UPF2,synonymous_variant,p.%3D,ENST00000397053,;	C	ENSG00000151461	ENST00000356352	Transcript	synonymous_variant	1389	915	305	V	gtC/gtG	rs759777920	.	.	-1	UPF2	HGNC	17854	protein_coding	YES	CCDS7086.1	ENSP00000348708	RENT2_HUMAN	B4DHP3_HUMAN	UPI0000070D5E	.	.	.	2/21	.	hmmpanther:PTHR12839,Gene3D:1.25.40.180,Pfam_domain:PF02854,SMART_domains:SM00543,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGAGACATG	.	5	ESCA
DOCK1	0	.	GRCh37	10	128841421	128841421	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2131G>A	p.Ala711Thr	p.A711T	ENST00000280333	21/52	40	23	16	31	31	0	DOCK1,missense_variant,p.Ala711Thr,ENST00000280333,;	A	ENSG00000150760	ENST00000280333	Transcript	missense_variant	2240	2131	711	A/T	Gcc/Acc	.	.	.	1	DOCK1	HGNC	2987	protein_coding	YES	.	ENSP00000280333	DOCK1_HUMAN	.	UPI0000246CA1	.	deleterious(0)	benign(0.003)	21/52	.	hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF79,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTTAGCCTAC	.	5	ESCA
DOCK1	0	.	GRCh37	10	129242473	129242473	+	Silent	SNP	G	G	A	rs190104158	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5280G>A	p.%3D	p.S1760S	ENST00000280333	50/52	57	46	11	29	29	0	DOCK1,synonymous_variant,p.%3D,ENST00000280333,;	A	ENSG00000150760	ENST00000280333	Transcript	synonymous_variant	5389	5280	1760	S	tcG/tcA	rs190104158	.	.	1	DOCK1	HGNC	2987	protein_coding	YES	.	ENSP00000280333	DOCK1_HUMAN	.	UPI0000246CA1	.	.	.	50/52	.	Low_complexity_(Seg):seg	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	A:0.0031	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTCGTCACC	byFrequency|byCluster|by1000G	5	ESCA
TTC40	0	.	GRCh37	10	134682866	134682866	+	Missense_Mutation	SNP	C	C	T	rs779226172	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4522G>A	p.Ala1508Thr	p.A1508T	ENST00000368586	33/58	30	19	11	17	17	0	TTC40,missense_variant,p.Ala1508Thr,ENST00000368586,;TTC40,downstream_gene_variant,,ENST00000368582,;TTC40,downstream_gene_variant,,ENST00000417862,;	T	ENSG00000171811	ENST00000368586	Transcript	missense_variant	4623	4522	1508	A/T	Gcg/Acg	rs779226172	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	tolerated(0.27)	benign(0.057)	33/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCACGCGTGGG	.	3	ESCA
ARL5B	0	.	GRCh37	10	18965171	18965171	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1031delA	.	.	ENST00000377275	6/6	45	28	17	31	31	0	ARL5B,3_prime_UTR_variant,,ENST00000377275,;	-	ENSG00000165997	ENST00000377275	Transcript	3_prime_UTR_variant	1799	.	.	.	.	.	.	.	1	ARL5B	HGNC	23052	protein_coding	YES	CCDS7131.1	ENSP00000366487	ARL5B_HUMAN	B0YIW9_HUMAN	UPI000006F7A5	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTACTTAAAAAA	.	3	ESCA
PIP4K2A	0	.	GRCh37	10	22830827	22830828	+	Frame_Shift_Ins	INS	-	-	G	rs755454854	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941dupC	p.Asp315ArgfsTer2	p.D315Rfs*2	ENST00000376573	8/10	20	6	13	12	12	0	PIP4K2A,frameshift_variant,p.Asp315ArgfsTer2,ENST00000376573,;PIP4K2A,frameshift_variant,p.Asp256ArgfsTer2,ENST00000545335,;PIP4K2A,frameshift_variant,p.Asp175ArgfsTer2,ENST00000323883,;PIP4K2A,downstream_gene_variant,,ENST00000604912,;PIP4K2A,upstream_gene_variant,,ENST00000474335,;	G	ENSG00000150867	ENST00000376573	Transcript	frameshift_variant	1170-1171	941-942	314	P/PX	cca/ccCa	rs755454854,COSM1347246	.	.	-1	PIP4K2A	HGNC	8997	protein_coding	YES	CCDS7141.1	ENSP00000365757	PI42A_HUMAN	S4R320_HUMAN,B4DGX2_HUMAN	UPI0000001052	.	.	.	8/10	.	PROSITE_profiles:PS51455,hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF21,Gene3D:1bo1A02,Pfam_domain:PF01504,SMART_domains:SM00330,Superfamily_domains:SSF56104	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	insertion	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	CTATCTGGGGG	.	2	ESCA
ARHGAP21	0	.	GRCh37	10	24886394	24886394	+	Missense_Mutation	SNP	T	T	C	rs199641044	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3316A>G	p.Arg1106Gly	p.R1106G	ENST00000396432	16/26	36	16	20	37	37	0	ARHGAP21,missense_variant,p.Arg1106Gly,ENST00000446003,;ARHGAP21,missense_variant,p.Arg893Gly,ENST00000320481,;ARHGAP21,missense_variant,p.Arg1106Gly,ENST00000396432,;ARHGAP21,missense_variant,p.Arg1096Gly,ENST00000376410,;ARHGAP21,upstream_gene_variant,,ENST00000418325,;ARHGAP21,upstream_gene_variant,,ENST00000418033,;ARHGAP21,downstream_gene_variant,,ENST00000493154,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000486374,;ARHGAP21,upstream_gene_variant,,ENST00000482792,;	C	ENSG00000107863	ENST00000396432	Transcript	missense_variant	3803	3316	1106	R/G	Agg/Ggg	rs199641044	.	.	-1	ARHGAP21	HGNC	23725	protein_coding	YES	CCDS7144.2	ENSP00000379709	RHG21_HUMAN	E7ESW5_HUMAN	UPI0001639C78	.	deleterious(0)	probably_damaging(0.996)	16/26	.	hmmpanther:PTHR23175:SF16,hmmpanther:PTHR23175	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCTTTCCG	byCluster	5	ESCA
ANKRD26	0	.	GRCh37	10	27332391	27332391	+	Missense_Mutation	SNP	T	T	C	rs370486658	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2125A>G	p.Met709Val	p.M709V	ENST00000376087	20/34	27	7	20	31	31	0	ANKRD26,missense_variant,p.Met709Val,ENST00000376087,;ANKRD26,missense_variant,p.Met266Val,ENST00000376070,;ANKRD26,missense_variant,p.Met725Val,ENST00000436985,;ANKRD26,non_coding_transcript_exon_variant,,ENST00000490015,;	C	ENSG00000107890	ENST00000376087	Transcript	missense_variant	2291	2125	709	M/V	Atg/Gtg	rs370486658	.	.	-1	ANKRD26	HGNC	29186	protein_coding	YES	CCDS41499.1	ENSP00000365255	ANR26_HUMAN	.	UPI000006FC41	.	tolerated(0.33)	benign(0.002)	20/34	.	hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF17	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACATAAAAT	.	5	ESCA
ZEB1	0	.	GRCh37	10	31810288	31810288	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2028A>G	p.%3D	p.V676V	ENST00000361642	7/9	14	7	7	18	18	0	ZEB1,synonymous_variant,p.%3D,ENST00000560721,;ZEB1,synonymous_variant,p.%3D,ENST00000446923,;ZEB1,synonymous_variant,p.%3D,ENST00000361642,;ZEB1,synonymous_variant,p.%3D,ENST00000320985,;ZEB1,synonymous_variant,p.%3D,ENST00000542815,;ZEB1,downstream_gene_variant,,ENST00000424869,;ZEB1,downstream_gene_variant,,ENST00000558440,;ZEB1,downstream_gene_variant,,ENST00000559476,;ZEB1,downstream_gene_variant,,ENST00000561212,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558655,;ZEB1,downstream_gene_variant,,ENST00000558863,;	G	ENSG00000148516	ENST00000361642	Transcript	synonymous_variant	2091	2028	676	V	gtA/gtG	.	.	.	1	ZEB1	HGNC	11642	protein_coding	YES	CCDS53505.1	ENSP00000354487	ZEB1_HUMAN	F6TDF5_HUMAN	UPI000068F51D	.	.	.	7/9	.	hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	ACAGTAAATCT	.	4	ESCA
CREM	0	.	GRCh37	10	35500810	35500810	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*79G>A	.	.	ENST00000345491	8/8	39	15	23	33	33	0	CREM,3_prime_UTR_variant,,ENST00000429130,;CREM,3_prime_UTR_variant,,ENST00000488328,;CREM,3_prime_UTR_variant,,ENST00000474362,;CREM,3_prime_UTR_variant,,ENST00000374728,;CREM,3_prime_UTR_variant,,ENST00000345491,;CREM,3_prime_UTR_variant,,ENST00000374721,;CREM,3_prime_UTR_variant,,ENST00000344351,;CREM,3_prime_UTR_variant,,ENST00000333809,;CREM,3_prime_UTR_variant,,ENST00000460270,;CREM,3_prime_UTR_variant,,ENST00000348787,;CREM,3_prime_UTR_variant,,ENST00000439705,;CREM,3_prime_UTR_variant,,ENST00000473940,;CREM,3_prime_UTR_variant,,ENST00000342105,;CREM,3_prime_UTR_variant,,ENST00000356917,;CREM,3_prime_UTR_variant,,ENST00000463314,;CREM,3_prime_UTR_variant,,ENST00000354759,;CREM,3_prime_UTR_variant,,ENST00000395895,;CREM,3_prime_UTR_variant,,ENST00000361599,;CREM,downstream_gene_variant,,ENST00000487763,;CREM,downstream_gene_variant,,ENST00000474931,;CREM,downstream_gene_variant,,ENST00000463960,;CREM,downstream_gene_variant,,ENST00000494479,;CREM,downstream_gene_variant,,ENST00000484283,;CREM,downstream_gene_variant,,ENST00000374734,;CREM,downstream_gene_variant,,ENST00000395887,;CREM,downstream_gene_variant,,ENST00000468236,;CREM,downstream_gene_variant,,ENST00000487132,;CREM,downstream_gene_variant,,ENST00000490511,;CREM,downstream_gene_variant,,ENST00000479070,;CREM,downstream_gene_variant,,ENST00000488741,;CREM,downstream_gene_variant,,ENST00000337656,;RP11-324I22.3,downstream_gene_variant,,ENST00000602435,;CREM,downstream_gene_variant,,ENST00000469517,;CREM,downstream_gene_variant,,ENST00000461968,;CREM,downstream_gene_variant,,ENST00000466251,;CREM,downstream_gene_variant,,ENST00000495960,;CREM,downstream_gene_variant,,ENST00000490460,;CREM,downstream_gene_variant,,ENST00000464475,;	A	ENSG00000095794	ENST00000345491	Transcript	3_prime_UTR_variant	1144	.	.	.	.	.	.	.	1	CREM	HGNC	2352	protein_coding	YES	CCDS7180.1	ENSP00000265372	CREM_HUMAN	E9PBM5_HUMAN,E9PB41_HUMAN,C9J5A7_HUMAN,C9J2J0_HUMAN	UPI00001BDF4F	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGGCTTCT	.	5	ESCA
RBP3	0	.	GRCh37	10	48390416	48390416	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462C>T	p.%3D	p.H154H	ENST00000224600	1/4	34	28	6	20	20	0	RBP3,synonymous_variant,p.%3D,ENST00000224600,;AL731561.2,downstream_gene_variant,,ENST00000581861,;	A	ENSG00000107618	ENST00000224600	Transcript	synonymous_variant	576	462	154	H	caC/caT	.	.	.	-1	RBP3	HGNC	9921	protein_coding	YES	CCDS7218.1	ENSP00000224600	RET3_HUMAN	.	UPI000012D87A	.	.	.	1/4	.	hmmpanther:PTHR11261,hmmpanther:PTHR11261:SF1,Pfam_domain:PF03572,Gene3D:3.90.226.10,SMART_domains:SM00245,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACGTGGGC	.	5	ESCA
GLUD1P2	0	.	GRCh37	10	48980252	48980252	+	RNA	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.915C>G	.	.	ENST00000594520	5/5	38	27	11	14	14	0	GLUD1P2,non_coding_transcript_exon_variant,,ENST00000594520,;GLUD1P2,non_coding_transcript_exon_variant,,ENST00000598412,;GLUD1P2,non_coding_transcript_exon_variant,,ENST00000601214,;CTSLP3,non_coding_transcript_exon_variant,,ENST00000458206,;	G	ENSG00000227781	ENST00000594520	Transcript	non_coding_transcript_exon_variant	915	.	.	.	.	.	.	.	1	GLUD1P2	HGNC	4337	processed_transcript	YES	.	.	.	.	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TTCCCCTTCCT	.	3	ESCA
ERCC6-PGBD3	0	.	GRCh37	10	50740752	50740752	+	Missense_Mutation	SNP	C	C	T	rs755721992	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259G>A	p.Ala87Thr	p.A87T	ENST00000515869	2/6	80	48	31	52	52	0	ERCC6-PGBD3,missense_variant,p.Ala87Thr,ENST00000515869,;ERCC6,missense_variant,p.Ala87Thr,ENST00000462247,;ERCC6,missense_variant,p.Ala87Thr,ENST00000355832,;ERCC6-PGBD3,missense_variant,p.Ala87Thr,ENST00000447839,;PGBD3,missense_variant,p.Ala87Thr,ENST00000603152,;ERCC6,upstream_gene_variant,,ENST00000479652,;	T	ENSG00000258838	ENST00000515869	Transcript	missense_variant	380	259	87	A/T	Gcc/Acc	rs755721992	.	.	-1	ERCC6-PGBD3	HGNC	48347	protein_coding	YES	CCDS60529.1	ENSP00000423550	.	E7EV46_HUMAN,D6R9X7_HUMAN	UPI00001F98BA	.	deleterious_low_confidence(0)	probably_damaging(0.943)	2/6	.	hmmpanther:PTHR10799:SF49,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGCGCTAG	byFrequency	5	ESCA
CSTF2T	0	.	GRCh37	10	53457615	53457615	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1695G>A	p.%3D	p.G565G	ENST00000331173	1/1	56	44	12	47	46	0	CSTF2T,synonymous_variant,p.%3D,ENST00000331173,;PRKG1,intron_variant,,ENST00000373976,;PRKG1,intron_variant,,ENST00000401604,;PRKG1,intron_variant,,ENST00000373985,;PRKG1,intron_variant,,ENST00000373980,;	T	ENSG00000177613	ENST00000331173	Transcript	synonymous_variant	1741	1695	565	G	ggG/ggA	.	.	.	-1	CSTF2T	HGNC	17086	protein_coding	YES	CCDS7245.1	ENSP00000332444	CSTFT_HUMAN	.	UPI0000073CA9	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23139,hmmpanther:PTHR23139:SF55	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGCCCAGG	.	5	ESCA
CSTF2T	0	.	GRCh37	10	53459077	53459077	+	Missense_Mutation	SNP	T	T	C	rs376475408	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.233A>G	p.Asn78Ser	p.N78S	ENST00000331173	1/1	44	29	14	31	31	0	CSTF2T,missense_variant,p.Asn78Ser,ENST00000331173,;PRKG1,intron_variant,,ENST00000373976,;PRKG1,intron_variant,,ENST00000401604,;PRKG1,intron_variant,,ENST00000373985,;PRKG1,intron_variant,,ENST00000373980,;	C	ENSG00000177613	ENST00000331173	Transcript	missense_variant	279	233	78	N/S	aAt/aGt	rs376475408	.	.	-1	CSTF2T	HGNC	17086	protein_coding	YES	CCDS7245.1	ENSP00000332444	CSTFT_HUMAN	.	UPI0000073CA9	.	deleterious(0.03)	probably_damaging(0.911)	1/1	.	PROSITE_profiles:PS50102,hmmpanther:PTHR23139,hmmpanther:PTHR23139:SF55,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	C:0	C:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCATTGAGG	byFrequency|byCluster	5	ESCA
RHOBTB1	0	.	GRCh37	10	62647970	62647970	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1456G>T	p.Asp486Tyr	p.D486Y	ENST00000337910	6/11	41	20	20	35	35	0	RHOBTB1,missense_variant,p.Asp486Tyr,ENST00000337910,;RHOBTB1,missense_variant,p.Asp486Tyr,ENST00000357917,;RHOBTB1,splice_region_variant,,ENST00000483488,;	A	ENSG00000072422	ENST00000337910	Transcript	missense_variant	1794	1456	486	D/Y	Gac/Tac	.	.	.	-1	RHOBTB1	HGNC	18738	protein_coding	YES	CCDS7261.1	ENSP00000338671	RHBT1_HUMAN	Q567T3_HUMAN	UPI000000D9B7	.	deleterious(0)	probably_damaging(0.933)	6/11	.	PROSITE_profiles:PS50097,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACCCGAGA	.	5	ESCA
TET1	0	.	GRCh37	10	70453114	70453114	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1543C>T	.	.	ENST00000373644	12/12	27	23	4	20	20	0	TET1,3_prime_UTR_variant,,ENST00000373644,;	T	ENSG00000138336	ENST00000373644	Transcript	3_prime_UTR_variant	8163	.	.	.	.	.	.	.	1	TET1	HGNC	29484	protein_coding	YES	CCDS7281.1	ENSP00000362748	TET1_HUMAN	.	UPI000013D114	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTGCTTCTC	.	4	ESCA
USP54	0	.	GRCh37	10	75277223	75277225	+	In_Frame_Del	DEL	ATG	ATG	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	ATG	ATG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2959_2961delCAT	p.His987del	p.H987del	ENST00000339859	19/23	76	60	16	44	44	0	USP54,inframe_deletion,p.His837del,ENST00000428547,;USP54,inframe_deletion,p.His987del,ENST00000339859,;USP54,inframe_deletion,p.His987del,ENST00000408019,;USP54,inframe_deletion,p.His169del,ENST00000422491,;USP54,inframe_deletion,p.His75del,ENST00000394811,;RP11-137L10.6,intron_variant,,ENST00000600206,;RP11-137L10.6,intron_variant,,ENST00000597958,;RP11-137L10.6,intron_variant,,ENST00000595069,;RP11-137L10.6,intron_variant,,ENST00000593790,;RP11-137L10.6,downstream_gene_variant,,ENST00000600607,;USP54,non_coding_transcript_exon_variant,,ENST00000497106,;USP54,3_prime_UTR_variant,,ENST00000418501,;USP54,3_prime_UTR_variant,,ENST00000466048,;USP54,3_prime_UTR_variant,,ENST00000424265,;USP54,downstream_gene_variant,,ENST00000498143,;	-	ENSG00000166348	ENST00000339859	Transcript	inframe_deletion	3060-3062	2959-2961	987	H/-	CAT/-	.	.	.	-1	USP54	HGNC	23513	protein_coding	YES	CCDS7329.2	ENSP00000345216	UBP54_HUMAN	.	UPI0000DFF136	.	.	.	19/23	.	hmmpanther:PTHR22975,hmmpanther:PTHR22975:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAACTATGATGAG	.	3	ESCA
RP11-464F9.1	0	.	GRCh37	10	75487193	75487193	+	RNA	SNP	C	C	T	rs778587289	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.285G>A	.	.	ENST00000399449	3/19	95	79	16	81	81	0	RP11-464F9.1,non_coding_transcript_exon_variant,,ENST00000449532,;BMS1P4,non_coding_transcript_exon_variant,,ENST00000584747,;RP11-574K11.28,non_coding_transcript_exon_variant,,ENST00000580790,;RP11-464F9.1,non_coding_transcript_exon_variant,,ENST00000399449,;GLUD1P3,upstream_gene_variant,,ENST00000507952,;BMS1P4,non_coding_transcript_exon_variant,,ENST00000441263,;DUSP8P5,upstream_gene_variant,,ENST00000422884,;GLUD1P3,upstream_gene_variant,,ENST00000508551,;	T	ENSG00000242288	ENST00000399449	Transcript	non_coding_transcript_exon_variant	285	.	.	.	.	rs778587289	.	.	-1	RP11-464F9.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	3/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTCGATCA	.	5	ESCA
KAT6B	0	.	GRCh37	10	76780447	76780447	+	Missense_Mutation	SNP	T	T	C	rs771809008	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2737T>C	p.Tyr913His	p.Y913H	ENST00000287239	14/18	37	11	26	10	10	0	KAT6B,missense_variant,p.Tyr621His,ENST00000372714,;KAT6B,missense_variant,p.Tyr621His,ENST00000372725,;KAT6B,missense_variant,p.Tyr621His,ENST00000372724,;KAT6B,missense_variant,p.Tyr913His,ENST00000287239,;KAT6B,missense_variant,p.Tyr730His,ENST00000372711,;RP11-77G23.2,intron_variant,,ENST00000413431,;RP11-77G23.5,downstream_gene_variant,,ENST00000436608,;KAT6B,non_coding_transcript_exon_variant,,ENST00000490365,;	C	ENSG00000156650	ENST00000287239	Transcript	missense_variant	3226	2737	913	Y/H	Tat/Cat	rs771809008	.	.	1	KAT6B	HGNC	17582	protein_coding	YES	CCDS7345.1	ENSP00000287239	KAT6B_HUMAN	.	UPI000013DEA0	.	.	possibly_damaging(0.62)	14/18	.	hmmpanther:PTHR10615:SF73,hmmpanther:PTHR10615,Pfam_domain:PF01853,Gene3D:3.40.630.30,Superfamily_domains:SSF55729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGTATCTC	.	5	ESCA
DUPD1	0	.	GRCh37	10	76803696	76803696	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280G>A	p.Val94Met	p.V94M	ENST00000338487	2/3	66	53	13	25	25	0	DUPD1,missense_variant,p.Val94Met,ENST00000338487,;	T	ENSG00000188716	ENST00000338487	Transcript	missense_variant	280	280	94	V/M	Gtg/Atg	.	.	.	-1	DUPD1	HGNC	23481	protein_coding	YES	CCDS31223.1	ENSP00000340609	DUPD1_HUMAN	.	UPI000003E897	.	deleterious(0)	probably_damaging(0.987)	2/3	.	PROSITE_profiles:PS50054,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF114,Pfam_domain:PF00782,Gene3D:3.90.190.10,SMART_domains:SM00195,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCACGTTCC	.	5	ESCA
KCNMA1	0	.	GRCh37	10	78870005	78870005	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057G>A	p.Val353Ile	p.V353I	ENST00000404857	8/28	59	43	15	55	55	0	KCNMA1,missense_variant,p.Val353Ile,ENST00000404857,;KCNMA1,missense_variant,p.Val214Ile,ENST00000604624,;KCNMA1,missense_variant,p.Val288Ile,ENST00000372437,;KCNMA1,missense_variant,p.Val353Ile,ENST00000406533,;KCNMA1,missense_variant,p.Val353Ile,ENST00000354353,;KCNMA1,missense_variant,p.Val327Ile,ENST00000457953,;KCNMA1,missense_variant,p.Val290Ile,ENST00000372408,;KCNMA1,missense_variant,p.Val353Ile,ENST00000372443,;KCNMA1,missense_variant,p.Val304Ile,ENST00000372403,;KCNMA1,missense_variant,p.Val353Ile,ENST00000286627,;KCNMA1,missense_variant,p.Val32Ile,ENST00000434208,;KCNMA1,missense_variant,p.Val353Ile,ENST00000404771,;KCNMA1,missense_variant,p.Val353Ile,ENST00000372440,;KCNMA1,missense_variant,p.Val327Ile,ENST00000372421,;KCNMA1,missense_variant,p.Val353Ile,ENST00000286628,;	T	ENSG00000156113	ENST00000404857	Transcript	missense_variant	1057	1057	353	V/I	Gtt/Att	COSM920645,COSM1349227,COSM1349228,COSM920646	.	.	-1	KCNMA1	HGNC	6284	protein_coding	YES	CCDS53545.1	ENSP00000385806	KCMA1_HUMAN	.	UPI00003519E8	.	deleterious(0)	probably_damaging(0.999)	8/28	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10027:SF18,hmmpanther:PTHR10027,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324,Prints_domain:PR00169	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAACGGTGG	.	5	ESCA
DLG5	0	.	GRCh37	10	79579660	79579660	+	Silent	SNP	C	C	T	rs374398523	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3519G>A	p.%3D	p.P1173P	ENST00000372391	16/32	40	34	5	35	35	0	DLG5,synonymous_variant,p.%3D,ENST00000424842,;DLG5,synonymous_variant,p.%3D,ENST00000372388,;DLG5,synonymous_variant,p.%3D,ENST00000372391,;DLG5,non_coding_transcript_exon_variant,,ENST00000459739,;DLG5,3_prime_UTR_variant,,ENST00000468332,;DLG5,non_coding_transcript_exon_variant,,ENST00000463362,;DLG5,non_coding_transcript_exon_variant,,ENST00000475613,;DLG5,non_coding_transcript_exon_variant,,ENST00000476354,;DLG5,downstream_gene_variant,,ENST00000466198,;	T	ENSG00000151208	ENST00000372391	Transcript	synonymous_variant	3525	3519	1173	P	ccG/ccA	rs374398523	.	.	-1	DLG5	HGNC	2904	protein_coding	YES	CCDS7353.2	ENSP00000361467	DLG5_HUMAN	.	UPI0000470041	.	.	.	16/32	.	hmmpanther:PTHR13865	.	.	.	.	.	.	.	T:0.0007	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAGACGGCCT	byFrequency|byCluster	4	ESCA
WAPAL	0	.	GRCh37	10	88195258	88195260	+	3'UTR	DEL	GTT	GTT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GTT	GTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2040_*2042delAAC	.	.	ENST00000298767	19/19	47	36	11	38	38	0	WAPAL,3_prime_UTR_variant,,ENST00000298767,;WAPAL,downstream_gene_variant,,ENST00000372075,;WAPAL,downstream_gene_variant,,ENST00000263070,;WAPAL,non_coding_transcript_exon_variant,,ENST00000484070,;	-	ENSG00000062650	ENST00000298767	Transcript	3_prime_UTR_variant	6086-6088	.	.	.	.	.	.	.	-1	WAPAL	HGNC	23293	protein_coding	YES	CCDS7375.1	ENSP00000298767	WAPL_HUMAN	B3Y1W2_HUMAN,B2RTX8_HUMAN	UPI00001AE41A	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTTTAGTTAAGTC	.	3	ESCA
ADIRF	0	.	GRCh37	10	88730275	88730275	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.167A>G	p.Lys56Arg	p.K56R	ENST00000372013	3/3	38	18	20	27	26	0	ADIRF,missense_variant,p.Lys56Arg,ENST00000372013,;ADIRF,missense_variant,p.Lys35Arg,ENST00000416348,;MMRN2,upstream_gene_variant,,ENST00000474994,;MMRN2,upstream_gene_variant,,ENST00000609457,;RP11-96C23.15,non_coding_transcript_exon_variant,,ENST00000609363,;ADIRF-AS1,non_coding_transcript_exon_variant,,ENST00000609111,;ADIRF-AS1,non_coding_transcript_exon_variant,,ENST00000418273,;ADIRF-AS1,upstream_gene_variant,,ENST00000440490,;RP11-96C23.5,upstream_gene_variant,,ENST00000433214,;ADIRF,missense_variant,p.Lys56Arg,ENST00000561504,;ADIRF-AS1,upstream_gene_variant,,ENST00000609170,;	G	ENSG00000148671	ENST00000372013	Transcript	missense_variant	520	167	56	K/R	aAg/aGg	.	.	.	1	ADIRF	HGNC	24043	protein_coding	YES	CCDS7381.1	ENSP00000361083	ADIRF_HUMAN	Q5TBU5_HUMAN	UPI0000000C61	.	deleterious(0.01)	benign(0.025)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGACAAGACTG	.	5	ESCA
IFIT5	0	.	GRCh37	10	91177806	91177806	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.850T>C	p.Phe284Leu	p.F284L	ENST00000371795	2/2	35	21	13	21	21	0	IFIT5,missense_variant,p.Phe284Leu,ENST00000371795,;IFIT5,missense_variant,p.Phe236Leu,ENST00000416601,;LIPA,upstream_gene_variant,,ENST00000371837,;	C	ENSG00000152778	ENST00000371795	Transcript	missense_variant	1063	850	284	F/L	Ttc/Ctc	.	.	.	1	IFIT5	HGNC	13328	protein_coding	YES	CCDS7403.1	ENSP00000360860	IFIT5_HUMAN	.	UPI000012D3E6	.	tolerated(0.12)	probably_damaging(0.997)	2/2	.	Superfamily_domains:SSF48452,Gene3D:1.25.40.10,hmmpanther:PTHR10271:SF5,hmmpanther:PTHR10271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTTTCCTG	.	5	ESCA
KIF20B	0	.	GRCh37	10	91518600	91518600	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4521T>G	p.Ile1507Met	p.I1507M	ENST00000260753	27/33	24	13	11	27	27	0	KIF20B,missense_variant,p.Ile1547Met,ENST00000371728,;KIF20B,missense_variant,p.Ile1577Met,ENST00000416354,;KIF20B,missense_variant,p.Ile1507Met,ENST00000260753,;KIF20B,missense_variant,p.Ile1547Met,ENST00000394289,;KIF20B,non_coding_transcript_exon_variant,,ENST00000478929,;	G	ENSG00000138182	ENST00000260753	Transcript	missense_variant	4593	4521	1507	I/M	atT/atG	.	.	.	1	KIF20B	HGNC	7212	protein_coding	YES	CCDS7407.1	ENSP00000260753	KI20B_HUMAN	.	UPI00001F9377	.	deleterious(0)	probably_damaging(0.999)	27/33	.	hmmpanther:PTHR23165	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAATTGAACA	.	5	ESCA
SORBS1	0	.	GRCh37	10	97096993	97096993	+	Missense_Mutation	SNP	C	C	T	rs376968108	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2924G>A	p.Arg975Gln	p.R975Q	ENST00000371247	30/33	38	28	10	26	26	0	SORBS1,missense_variant,p.Arg929Gln,ENST00000371227,;SORBS1,missense_variant,p.Arg975Gln,ENST00000371247,;SORBS1,missense_variant,p.Arg975Gln,ENST00000361941,;SORBS1,intron_variant,,ENST00000371239,;SORBS1,intron_variant,,ENST00000607232,;SORBS1,intron_variant,,ENST00000353505,;SORBS1,intron_variant,,ENST00000371241,;SORBS1,intron_variant,,ENST00000371245,;SORBS1,intron_variant,,ENST00000306402,;SORBS1,intron_variant,,ENST00000347291,;SORBS1,intron_variant,,ENST00000277982,;SORBS1,intron_variant,,ENST00000393949,;SORBS1,intron_variant,,ENST00000354106,;SORBS1,intron_variant,,ENST00000371249,;SORBS1,intron_variant,,ENST00000371246,;SORBS1,downstream_gene_variant,,ENST00000371228,;SORBS1,downstream_gene_variant,,ENST00000474353,;	T	ENSG00000095637	ENST00000371247	Transcript	missense_variant	3114	2924	975	R/Q	cGa/cAa	rs376968108	.	.	-1	SORBS1	HGNC	14565	protein_coding	YES	CCDS31255.1	ENSP00000360293	SRBS1_HUMAN	.	UPI000013D6B7	.	tolerated(0.11)	benign(0.002)	30/33	.	hmmpanther:PTHR10661,hmmpanther:PTHR10661:SF4	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTCGGCGG	byFrequency|byCluster	5	ESCA
TLL2	0	.	GRCh37	10	98170377	98170377	+	Intron	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1049-146T>C	.	.	ENST00000357947	.	59	41	18	27	27	0	TLL2,intron_variant,,ENST00000357947,;TLL2,non_coding_transcript_exon_variant,,ENST00000469598,;	G	ENSG00000095587	ENST00000357947	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TLL2	HGNC	11844	protein_coding	YES	CCDS7449.1	ENSP00000350630	TLL2_HUMAN	.	UPI0000073AEE	.	.	.	.	8/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTGATGTTT	.	5	ESCA
TM9SF3	0	.	GRCh37	10	98281178	98281178	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*842delT	.	.	ENST00000371142	15/15	41	33	8	20	20	0	TM9SF3,3_prime_UTR_variant,,ENST00000371142,;TM9SF3,downstream_gene_variant,,ENST00000485093,;	-	ENSG00000077147	ENST00000371142	Transcript	3_prime_UTR_variant	2829	.	.	.	.	.	.	.	-1	TM9SF3	HGNC	21529	protein_coding	YES	CCDS7450.1	ENSP00000360184	TM9S3_HUMAN	Q96K55_HUMAN,Q96JZ5_HUMAN,Q8WUB5_HUMAN,Q5TB53_HUMAN	UPI000013684E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GGGGGGAAAAAA	.	2	ESCA
ZDHHC16	0	.	GRCh37	10	99215505	99215507	+	In_Frame_Del	DEL	AAG	AAG	-	rs756458996	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AAG	AAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916_918delAAG	p.Lys306del	p.K306del	ENST00000393760	10/12	54	41	13	46	46	0	ZDHHC16,inframe_deletion,p.Lys225del,ENST00000345745,;ZDHHC16,inframe_deletion,p.Lys230del,ENST00000417044,;ZDHHC16,inframe_deletion,p.Lys290del,ENST00000352634,;ZDHHC16,inframe_deletion,p.Lys241del,ENST00000433086,;ZDHHC16,inframe_deletion,p.Lys290del,ENST00000370842,;ZDHHC16,inframe_deletion,p.Lys306del,ENST00000370854,;ZDHHC16,inframe_deletion,p.Lys236del,ENST00000370846,;ZDHHC16,inframe_deletion,p.Lys306del,ENST00000393760,;ZDHHC16,inframe_deletion,p.Lys267del,ENST00000353979,;ZDHHC16,inframe_deletion,p.Lys248del,ENST00000420089,;MMS19,downstream_gene_variant,,ENST00000370782,;MMS19,downstream_gene_variant,,ENST00000327238,;MMS19,downstream_gene_variant,,ENST00000438925,;MMS19,downstream_gene_variant,,ENST00000327277,;ZDHHC16,downstream_gene_variant,,ENST00000414567,;MMS19,downstream_gene_variant,,ENST00000355839,;MMS19,downstream_gene_variant,,ENST00000444411,;MMS19,downstream_gene_variant,,ENST00000434538,;ZDHHC16,non_coding_transcript_exon_variant,,ENST00000492733,;ZDHHC16,non_coding_transcript_exon_variant,,ENST00000462924,;ZDHHC16,non_coding_transcript_exon_variant,,ENST00000487315,;ZDHHC16,non_coding_transcript_exon_variant,,ENST00000459777,;ZDHHC16,non_coding_transcript_exon_variant,,ENST00000495735,;ZDHHC16,non_coding_transcript_exon_variant,,ENST00000466895,;ZDHHC16,downstream_gene_variant,,ENST00000492610,;MMS19,downstream_gene_variant,,ENST00000415383,;MMS19,downstream_gene_variant,,ENST00000480108,;MMS19,downstream_gene_variant,,ENST00000485400,;MMS19,downstream_gene_variant,,ENST00000495415,;	-	ENSG00000171307	ENST00000393760	Transcript	inframe_deletion	1262-1264	913-915	305	K/-	AAG/-	rs756458996,COSM922024	.	.	1	ZDHHC16	HGNC	20714	protein_coding	YES	CCDS7460.1	ENSP00000377357	ZDH16_HUMAN	B4DNL2_HUMAN,B1AMU5_HUMAN	UPI0000073C8D	.	.	.	10/12	.	hmmpanther:PTHR12246:SF11,hmmpanther:PTHR12246	.	.	.	.	.	.	.	-:0.0002	-:0	.	0,1	.	.	.	.	.	MODERATE	.	deletion	.	3	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATCAACAAGAAGGA	byFrequency	3	ESCA
GRIA4	0	.	GRCh37	11	105852024	105852024	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1558G>A	.	.	ENST00000282499	17/17	71	57	13	57	57	0	GRIA4,3_prime_UTR_variant,,ENST00000282499,;GRIA4,3_prime_UTR_variant,,ENST00000530497,;GRIA4,3_prime_UTR_variant,,ENST00000393127,;GRIA4,downstream_gene_variant,,ENST00000525187,;GRIA4,downstream_gene_variant,,ENST00000533094,;	A	ENSG00000152578	ENST00000282499	Transcript	3_prime_UTR_variant	4713	.	.	.	.	.	.	.	1	GRIA4	HGNC	4574	protein_coding	YES	CCDS8333.1	ENSP00000282499	GRIA4_HUMAN	E9PJZ5_HUMAN	UPI000013DCE6	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGGCCTTG	.	5	ESCA
ACAT1	0	.	GRCh37	11	108004588	108004588	+	Frame_Shift_Del	DEL	T	T	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.167delT	p.Leu56Ter	p.L56*	ENST00000265838	3/12	112	89	23	67	67	0	ACAT1,frameshift_variant,p.Leu56Ter,ENST00000265838,;ACAT1,frameshift_variant,p.Leu56Ter,ENST00000299355,;ACAT1,5_prime_UTR_variant,,ENST00000527942,;ACAT1,upstream_gene_variant,,ENST00000528370,;ACAT1,non_coding_transcript_exon_variant,,ENST00000531853,;ACAT1,downstream_gene_variant,,ENST00000526119,;ACAT1,frameshift_variant,p.Leu56Ter,ENST00000531813,;ACAT1,non_coding_transcript_exon_variant,,ENST00000524833,;ACAT1,upstream_gene_variant,,ENST00000534773,;	-	ENSG00000075239	ENST00000265838	Transcript	frameshift_variant	253	162	54	S/X	tcT/tc	COSM1350693	.	.	1	ACAT1	HGNC	93	protein_coding	YES	CCDS8339.1	ENSP00000265838	THIL_HUMAN	E9PKF3_HUMAN	UPI0000136E41	.	.	.	3/12	.	Superfamily_domains:SSF53901,PIRSF_domain:PIRSF000429,TIGRFAM_domain:TIGR01930,Pfam_domain:PF00108,Gene3D:3.40.47.10,hmmpanther:PTHR18919:SF79,hmmpanther:PTHR18919	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	5	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGATCTTTTTT	.	3	ESCA
C11orf87	0	.	GRCh37	11	109295860	109295860	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*907T>C	.	.	ENST00000327419	2/2	117	53	64	71	71	0	C11orf87,3_prime_UTR_variant,,ENST00000327419,;RP11-708B6.2,intron_variant,,ENST00000532929,;RP11-708B6.2,intron_variant,,ENST00000532992,;	C	ENSG00000185742	ENST00000327419	Transcript	3_prime_UTR_variant	1904	.	.	.	.	.	.	.	1	C11orf87	HGNC	33788	protein_coding	YES	CCDS31672.1	ENSP00000331581	CK087_HUMAN	.	UPI000013E5BC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGATTACTT	.	5	ESCA
ARHGAP20	0	.	GRCh37	11	110451806	110451806	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1864G>A	p.Asp622Asn	p.D622N	ENST00000260283	16/16	45	26	18	32	32	0	ARHGAP20,missense_variant,p.Asp622Asn,ENST00000260283,;ARHGAP20,missense_variant,p.Asp165Asn,ENST00000529591,;ARHGAP20,missense_variant,p.Asp586Asn,ENST00000527598,;ARHGAP20,missense_variant,p.Asp586Asn,ENST00000528829,;ARHGAP20,missense_variant,p.Asp596Asn,ENST00000357139,;ARHGAP20,missense_variant,p.Asp596Asn,ENST00000533353,;ARHGAP20,missense_variant,p.Asp599Asn,ENST00000524756,;	T	ENSG00000137727	ENST00000260283	Transcript	missense_variant	2149	1864	622	D/N	Gac/Aac	.	.	.	-1	ARHGAP20	HGNC	18357	protein_coding	YES	CCDS31673.1	ENSP00000260283	RHG20_HUMAN	.	UPI000013D0BA	.	deleterious(0.01)	probably_damaging(0.989)	16/16	.	hmmpanther:PTHR23179,hmmpanther:PTHR23179:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGTCACTGA	.	5	ESCA
TMPRSS5	0	.	GRCh37	11	113560988	113560988	+	Missense_Mutation	SNP	C	C	T	rs201422387	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1171G>A	p.Ala391Thr	p.A391T	ENST00000299882	11/13	19	6	12	13	13	0	TMPRSS5,missense_variant,p.Ala278Thr,ENST00000544476,;TMPRSS5,missense_variant,p.Ala347Thr,ENST00000538955,;TMPRSS5,missense_variant,p.Ala132Thr,ENST00000540540,;TMPRSS5,missense_variant,p.Ala322Thr,ENST00000544634,;TMPRSS5,missense_variant,p.Ala132Thr,ENST00000536856,;TMPRSS5,missense_variant,p.Ala382Thr,ENST00000545579,;TMPRSS5,missense_variant,p.Ala391Thr,ENST00000299882,;TMPRSS5,downstream_gene_variant,,ENST00000539732,;TMPRSS5,downstream_gene_variant,,ENST00000538770,;TMPRSS5,non_coding_transcript_exon_variant,,ENST00000545265,;TMPRSS5,downstream_gene_variant,,ENST00000545412,;	T	ENSG00000166682	ENST00000299882	Transcript	missense_variant	1320	1171	391	A/T	Gct/Act	rs201422387	.	.	-1	TMPRSS5	HGNC	14908	protein_coding	YES	CCDS44735.1	ENSP00000299882	TMPS5_HUMAN	G5EA43_HUMAN,F5H2M3_HUMAN,B0YJB1_HUMAN	UPI00001FA3AA	.	deleterious(0)	probably_damaging(1)	11/13	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF18,hmmpanther:PTHR24256,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0.0002	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGCGCAAA	byCluster|by1000G	5	ESCA
ZW10	0	.	GRCh37	11	113639628	113639628	+	Missense_Mutation	SNP	G	G	A	rs201149106	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.167C>T	p.Ala56Val	p.A56V	ENST00000200135	2/16	53	30	22	28	28	0	ZW10,missense_variant,p.Ala56Val,ENST00000200135,;RP11-667M19.2,downstream_gene_variant,,ENST00000543486,;ZW10,missense_variant,p.Ala56Val,ENST00000535142,;ZW10,missense_variant,p.Ala56Val,ENST00000538209,;RP11-667M19.4,upstream_gene_variant,,ENST00000397185,;	A	ENSG00000086827	ENST00000200135	Transcript	missense_variant	312	167	56	A/V	gCg/gTg	rs201149106	.	.	-1	ZW10	HGNC	13194	protein_coding	YES	CCDS8363.1	ENSP00000200135	ZW10_HUMAN	B4E1J7_HUMAN,A1A528_HUMAN	UPI000013C491	.	tolerated(0.17)	possibly_damaging(0.802)	2/16	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12205:SF0,hmmpanther:PTHR12205,Pfam_domain:PF06248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCGCGCTC	byCluster	5	ESCA
ATF4P4	0	.	GRCh37	11	113660924	113660924	+	RNA	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.977delC	.	.	ENST00000393544	1/1	96	75	21	56	56	0	ATF4P4,non_coding_transcript_exon_variant,,ENST00000393544,;ATF4P4,upstream_gene_variant,,ENST00000438498,;RP11-667M19.5,downstream_gene_variant,,ENST00000544730,;LRRC37A13P,upstream_gene_variant,,ENST00000546055,;	-	ENSG00000256167	ENST00000393544	Transcript	non_coding_transcript_exon_variant	972	.	.	.	.	.	.	.	1	ATF4P4	HGNC	787	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCGGCACCCCCC	.	3	ESCA
SIDT2	0	.	GRCh37	11	117067147	117067147	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*365G>A	.	.	ENST00000324225	26/26	23	17	6	15	15	0	SIDT2,3_prime_UTR_variant,,ENST00000532062,;SIDT2,3_prime_UTR_variant,,ENST00000324225,;SIDT2,3_prime_UTR_variant,,ENST00000525478,;SIDT2,3_prime_UTR_variant,,ENST00000431081,;SIDT2,intron_variant,,ENST00000278951,;TAGLN,upstream_gene_variant,,ENST00000525531,;TAGLN,upstream_gene_variant,,ENST00000278968,;TAGLN,upstream_gene_variant,,ENST00000529792,;TAGLN,upstream_gene_variant,,ENST00000392951,;SIDT2,downstream_gene_variant,,ENST00000525339,;SIDT2,downstream_gene_variant,,ENST00000529484,;SIDT2,downstream_gene_variant,,ENST00000525065,;SIDT2,downstream_gene_variant,,ENST00000529441,;TAGLN,upstream_gene_variant,,ENST00000533863,;SIDT2,downstream_gene_variant,,ENST00000526813,;	A	ENSG00000149577	ENST00000324225	Transcript	3_prime_UTR_variant	3395	.	.	.	.	.	.	.	1	SIDT2	HGNC	24272	protein_coding	YES	CCDS31682.1	ENSP00000314023	SIDT2_HUMAN	G3V172_HUMAN,E9PPN9_HUMAN,E9PME7_HUMAN,E9PMC3_HUMAN	UPI000004BA68	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGTCCTC	.	5	ESCA
KMT2A	0	.	GRCh37	11	118343390	118343390	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516A>G	p.Thr506Ala	p.T506A	ENST00000534358	3/36	23	18	5	12	12	0	KMT2A,missense_variant,p.Thr506Ala,ENST00000389506,;KMT2A,missense_variant,p.Thr506Ala,ENST00000354520,;KMT2A,missense_variant,p.Thr506Ala,ENST00000534358,;KMT2A,missense_variant,p.Thr539Ala,ENST00000531904,;KMT2A,intron_variant,,ENST00000527869,;KMT2A,intron_variant,,ENST00000533790,;	G	ENSG00000118058	ENST00000534358	Transcript	missense_variant	1539	1516	506	T/A	Acc/Gcc	.	.	.	1	KMT2A	HGNC	7132	protein_coding	YES	CCDS55791.1	ENSP00000436786	KMT2A_HUMAN	Q9UPD0_HUMAN,Q9UM91_HUMAN,Q9HBJ4_HUMAN,B4DIJ7_HUMAN	UPI0001E5E732	.	.	benign(0.001)	3/36	.	hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGATACCCCT	.	5	ESCA
PHLDB1	0	.	GRCh37	11	118499019	118499019	+	Missense_Mutation	SNP	C	C	T	rs782496270	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1480C>T	p.Arg494Cys	p.R494C	ENST00000361417	7/24	40	19	20	20	20	0	PHLDB1,missense_variant,p.Arg494Cys,ENST00000361417,;PHLDB1,missense_variant,p.Arg494Cys,ENST00000356063,;PHLDB1,intron_variant,,ENST00000530708,;PHLDB1,upstream_gene_variant,,ENST00000534140,;PHLDB1,downstream_gene_variant,,ENST00000526670,;PHLDB1,downstream_gene_variant,,ENST00000526374,;PHLDB1,downstream_gene_variant,,ENST00000532639,;PHLDB1,upstream_gene_variant,,ENST00000534672,;PHLDB1,downstream_gene_variant,,ENST00000527259,;PHLDB1,missense_variant,p.Arg494Cys,ENST00000530994,;PHLDB1,missense_variant,p.Arg494Cys,ENST00000528594,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000532517,;PHLDB1,upstream_gene_variant,,ENST00000525698,;PHLDB1,upstream_gene_variant,,ENST00000531862,;	T	ENSG00000019144	ENST00000361417	Transcript	missense_variant	1891	1480	494	R/C	Cgc/Tgc	rs782496270	.	.	1	PHLDB1	HGNC	23697	protein_coding	YES	CCDS8401.1	ENSP00000354498	PHLB1_HUMAN	.	UPI0000192101	.	deleterious(0)	probably_damaging(0.972)	7/24	.	hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGGCGCTGG	.	5	ESCA
BCL9L	0	.	GRCh37	11	118769840	118769840	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3784C>G	p.Pro1262Ala	p.P1262A	ENST00000334801	8/8	12	9	3	8	8	0	BCL9L,missense_variant,p.Pro1262Ala,ENST00000334801,;CXCR5,downstream_gene_variant,,ENST00000292174,;BCL9L,non_coding_transcript_exon_variant,,ENST00000526143,;BCL9L,downstream_gene_variant,,ENST00000527266,;BCL9L,downstream_gene_variant,,ENST00000526514,;BCL9L,downstream_gene_variant,,ENST00000530293,;	C	ENSG00000186174	ENST00000334801	Transcript	missense_variant	4749	3784	1262	P/A	Cct/Gct	.	.	.	-1	BCL9L	HGNC	23688	protein_coding	YES	CCDS8403.1	ENSP00000335320	BCL9L_HUMAN	E9PNR0_HUMAN	UPI0000192102	.	.	possibly_damaging(0.543)	8/8	.	hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAGGCAGGG	.	2	ESCA
BCL9L	0	.	GRCh37	11	118772427	118772427	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2025T>C	p.%3D	p.R675R	ENST00000334801	6/8	46	25	20	24	24	0	BCL9L,synonymous_variant,p.%3D,ENST00000334801,;CXCR5,downstream_gene_variant,,ENST00000292174,;BCL9L,non_coding_transcript_exon_variant,,ENST00000526143,;BCL9L,intron_variant,,ENST00000526514,;BCL9L,intron_variant,,ENST00000530293,;BCL9L,downstream_gene_variant,,ENST00000527266,;	G	ENSG00000186174	ENST00000334801	Transcript	synonymous_variant	2990	2025	675	R	cgT/cgC	.	.	.	-1	BCL9L	HGNC	23688	protein_coding	YES	CCDS8403.1	ENSP00000335320	BCL9L_HUMAN	E9PNR0_HUMAN	UPI0000192102	.	.	.	6/8	.	hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCACGGAC	.	5	ESCA
BCL9L	0	.	GRCh37	11	118779083	118779083	+	Missense_Mutation	SNP	G	G	T	rs761712435	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.308C>A	p.Pro103His	p.P103H	ENST00000334801	2/8	47	28	19	26	26	0	BCL9L,missense_variant,p.Pro103His,ENST00000334801,;BCL9L,missense_variant,p.Pro103His,ENST00000532899,;MIR4492,upstream_gene_variant,,ENST00000581627,;BCL9L,non_coding_transcript_exon_variant,,ENST00000527266,;BCL9L,non_coding_transcript_exon_variant,,ENST00000526514,;BCL9L,non_coding_transcript_exon_variant,,ENST00000526143,;BCL9L,intron_variant,,ENST00000530293,;	T	ENSG00000186174	ENST00000334801	Transcript	missense_variant	1273	308	103	P/H	cCt/cAt	rs761712435	.	.	-1	BCL9L	HGNC	23688	protein_coding	YES	CCDS8403.1	ENSP00000335320	BCL9L_HUMAN	E9PNR0_HUMAN	UPI0000192102	.	.	probably_damaging(0.953)	2/8	.	hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAAGGGGGC	.	5	ESCA
NLRX1	0	.	GRCh37	11	119054391	119054391	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*243C>A	.	.	ENST00000409109	10/10	85	58	26	71	71	0	NLRX1,3_prime_UTR_variant,,ENST00000292199,;NLRX1,3_prime_UTR_variant,,ENST00000409991,;NLRX1,3_prime_UTR_variant,,ENST00000409109,;NLRX1,intron_variant,,ENST00000409265,;NLRX1,intron_variant,,ENST00000525863,;PDZD3,upstream_gene_variant,,ENST00000525131,;PDZD3,upstream_gene_variant,,ENST00000392817,;PDZD3,upstream_gene_variant,,ENST00000322712,;PDZD3,upstream_gene_variant,,ENST00000355547,;PDZD3,upstream_gene_variant,,ENST00000531114,;NLRX1,downstream_gene_variant,,ENST00000469103,;PDZD3,upstream_gene_variant,,ENST00000526279,;PDZD3,upstream_gene_variant,,ENST00000527308,;PDZD3,upstream_gene_variant,,ENST00000529573,;PDZD3,upstream_gene_variant,,ENST00000526836,;PDZD3,upstream_gene_variant,,ENST00000529098,;PDZD3,upstream_gene_variant,,ENST00000527028,;PDZD3,upstream_gene_variant,,ENST00000527951,;PDZD3,upstream_gene_variant,,ENST00000528730,;PDZD3,upstream_gene_variant,,ENST00000534790,;NLRX1,downstream_gene_variant,,ENST00000481860,;PDZD3,upstream_gene_variant,,ENST00000533688,;	A	ENSG00000160703	ENST00000409109	Transcript	3_prime_UTR_variant	3758	.	.	.	.	.	.	.	1	NLRX1	HGNC	29890	protein_coding	YES	CCDS8416.1	ENSP00000387334	NLRX1_HUMAN	C9JQE9_HUMAN,C9JLK8_HUMAN,C9J0R6_HUMAN,B7Z889_HUMAN	UPI0000161217	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTCAGCTA	.	5	ESCA
ZNF202	0	.	GRCh37	11	123596704	123596704	+	3'UTR	SNP	G	G	A	rs771827999	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1C>T	.	.	ENST00000336139	8/8	36	32	4	42	42	0	ZNF202,3_prime_UTR_variant,,ENST00000529691,;ZNF202,3_prime_UTR_variant,,ENST00000336139,;ZNF202,3_prime_UTR_variant,,ENST00000530393,;ZNF202,downstream_gene_variant,,ENST00000528306,;ZNF202,downstream_gene_variant,,ENST00000533463,;ZNF202,downstream_gene_variant,,ENST00000526252,;ZNF202,downstream_gene_variant,,ENST00000529250,;ZNF202,downstream_gene_variant,,ENST00000530944,;	A	ENSG00000166261	ENST00000336139	Transcript	3_prime_UTR_variant	2311	.	.	.	.	rs771827999	.	.	-1	ZNF202	HGNC	12994	protein_coding	YES	CCDS8443.1	ENSP00000337724	ZN202_HUMAN	E9PM99_HUMAN,E9PJL4_HUMAN	UPI000013E581	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTAGCTAGG	byFrequency	4	ESCA
OR4D5	0	.	GRCh37	11	123810341	123810341	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18T>C	p.%3D	p.H6H	ENST00000307033	1/1	85	40	45	60	60	0	OR4D5,synonymous_variant,p.%3D,ENST00000307033,;OR6T1,downstream_gene_variant,,ENST00000321252,;	C	ENSG00000171014	ENST00000307033	Transcript	synonymous_variant	92	18	6	H	caT/caC	.	.	.	1	OR4D5	HGNC	14852	protein_coding	YES	CCDS31699.1	ENSP00000305970	OR4D5_HUMAN	.	UPI000003F227	.	.	.	1/1	.	hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF73,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCATTCCCA	.	5	ESCA
OR8G1	0	.	GRCh37	11	124120778	124120778	+	Missense_Mutation	SNP	C	C	T	rs747754834	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.356C>T	p.Ala119Val	p.A119V	ENST00000341493	1/3	166	128	38	135	135	0	OR8G1,missense_variant,p.Ala119Val,ENST00000341493,;OR8G1,missense_variant,p.Ala119Val,ENST00000534473,;	T	ENSG00000197849	ENST00000341493	Transcript	missense_variant	356	356	119	A/V	gCg/gTg	rs747754834	.	.	1	OR8G1	HGNC	8484	protein_coding	YES	.	ENSP00000476313	.	.	UPI00004565A2	.	deleterious_low_confidence(0)	probably_damaging(0.994)	1/3	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,PROSITE_patterns:PS00237,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF73,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGCGTATG	.	5	ESCA
MUC5B	0	.	GRCh37	11	1252187	1252187	+	Missense_Mutation	SNP	G	G	A	rs368620070	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1492G>A	p.Gly498Ser	p.G498S	ENST00000529681	13/49	25	18	7	21	21	0	MUC5B,missense_variant,p.Gly498Ser,ENST00000529681,;MUC5B,missense_variant,p.Gly501Ser,ENST00000447027,;MUC5B,downstream_gene_variant,,ENST00000531082,;MUC5B,non_coding_transcript_exon_variant,,ENST00000525715,;	A	ENSG00000117983	ENST00000529681	Transcript	missense_variant	1550	1492	498	G/S	Ggc/Agc	rs368620070	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	unknown(0)	13/49	.	PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237,Pfam_domain:PF00094,SMART_domains:SM00216	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGACGGCGGC	byCluster|by1000G	5	ESCA
FEZ1	0	.	GRCh37	11	125330507	125330509	+	In_Frame_Del	DEL	TCT	TCT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TCT	TCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552_554delAGA	p.Glu186del	p.E186del	ENST00000278919	5/10	48	16	32	50	50	0	FEZ1,inframe_deletion,p.Glu186del,ENST00000278919,;FEZ1,inframe_deletion,p.Glu119del,ENST00000577924,;FEZ1,intron_variant,,ENST00000527350,;FEZ1,non_coding_transcript_exon_variant,,ENST00000534022,;FEZ1,non_coding_transcript_exon_variant,,ENST00000533294,;FEZ1,non_coding_transcript_exon_variant,,ENST00000392709,;FEZ1,downstream_gene_variant,,ENST00000532981,;FEZ1,upstream_gene_variant,,ENST00000524427,;	-	ENSG00000149557	ENST00000278919	Transcript	inframe_deletion	787-789	552-554	184-185	EE/E	gaAGAg/gag	.	.	.	-1	FEZ1	HGNC	3659	protein_coding	YES	CCDS31716.1	ENSP00000278919	FEZ1_HUMAN	E9PNH2_HUMAN	UPI000012A6FE	.	.	.	5/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12394:SF4,hmmpanther:PTHR12394,Pfam_domain:PF07763	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCTCCTCTTCTTC	.	3	ESCA
EI24	0	.	GRCh37	11	125454387	125454387	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*809G>T	.	.	ENST00000278903	12/12	44	20	23	34	34	0	EI24,3_prime_UTR_variant,,ENST00000343678,;EI24,3_prime_UTR_variant,,ENST00000278903,;STT3A-AS1,intron_variant,,ENST00000532714,;STT3A-AS1,intron_variant,,ENST00000530526,;EI24,non_coding_transcript_exon_variant,,ENST00000530985,;EI24,downstream_gene_variant,,ENST00000527628,;EI24,downstream_gene_variant,,ENST00000527675,;EI24,downstream_gene_variant,,ENST00000531350,;EI24,downstream_gene_variant,,ENST00000534430,;EI24,downstream_gene_variant,,ENST00000535422,;EI24,downstream_gene_variant,,ENST00000530540,;EI24,downstream_gene_variant,,ENST00000525737,;EI24,downstream_gene_variant,,ENST00000534546,;	T	ENSG00000149547	ENST00000278903	Transcript	3_prime_UTR_variant	2071	.	.	.	.	.	.	.	1	EI24	HGNC	13276	protein_coding	YES	.	ENSP00000278903	EI24_HUMAN	E9PM05_HUMAN,E9PL33_HUMAN	UPI00015E00C2	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTGGCCAC	.	5	ESCA
PATE1	0	.	GRCh37	11	125616592	125616592	+	Splice_Site	SNP	G	G	A	rs186985607	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88+1G>A	.	p.X30_splice	ENST00000305738	.	33	16	17	39	39	0	PATE1,splice_donor_variant,,ENST00000437148,;PATE1,splice_donor_variant,,ENST00000305738,;PATE1,splice_donor_variant,,ENST00000525969,;	A	ENSG00000171053	ENST00000305738	Transcript	splice_donor_variant	.	.	.	.	.	rs186985607	.	.	1	PATE1	HGNC	24664	protein_coding	YES	CCDS8464.1	ENSP00000307164	PATE1_HUMAN	.	UPI0000071A6F	.	.	.	.	2/4	.	A:0.0004	A:0	A:0.0014	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGGTGAGT	byFrequency|byCluster|by1000G	5	ESCA
MUC5B	0	.	GRCh37	11	1282626	1282626	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17077G>A	p.Ala5693Thr	p.A5693T	ENST00000529681	49/49	95	63	32	69	69	0	MUC5B,missense_variant,p.Ala5693Thr,ENST00000529681,;MUC5B,missense_variant,p.Ala5696Thr,ENST00000447027,;MUC5B,intron_variant,,ENST00000526859,;MUC5B,downstream_gene_variant,,ENST00000527802,;	A	ENSG00000117983	ENST00000529681	Transcript	missense_variant	17135	17077	5693	A/T	Gca/Aca	.	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	unknown(0)	49/49	.	PROSITE_profiles:PS01225,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237,SMART_domains:SM00041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCAGCAGAG	.	5	ESCA
NFRKB	0	.	GRCh37	11	129762692	129762692	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92G>T	p.Gly31Val	p.G31V	ENST00000524794	1/25	21	14	7	17	17	0	NFRKB,missense_variant,p.Gly18Val,ENST00000532225,;NFRKB,missense_variant,p.Gly18Val,ENST00000531318,;NFRKB,missense_variant,p.Gly31Val,ENST00000524794,;NFRKB,missense_variant,p.Gly18Val,ENST00000526940,;NFRKB,missense_variant,p.Gly18Val,ENST00000446488,;NFRKB,missense_variant,p.Gly18Val,ENST00000524746,;NFRKB,missense_variant,p.Gly18Val,ENST00000304521,;NFRKB,missense_variant,p.Gly18Val,ENST00000529319,;NFRKB,missense_variant,p.Gly18Val,ENST00000531755,;NFRKB,missense_variant,p.Gly18Val,ENST00000526884,;NFRKB,missense_variant,p.Gly18Val,ENST00000530278,;	A	ENSG00000170322	ENST00000524794	Transcript	missense_variant	213	92	31	G/V	gGa/gTa	.	.	.	-1	NFRKB	HGNC	7802	protein_coding	YES	CCDS8483.1	ENSP00000436926	NFRKB_HUMAN	E9PM88_HUMAN,E9PJU3_HUMAN,E9PJG2_HUMAN	UPI000006E542	.	tolerated_low_confidence(0.08)	unknown(0)	1/25	.	hmmpanther:PTHR13052	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCCACAC	.	5	ESCA
PRDM10	0	.	GRCh37	11	129812346	129812346	+	Frame_Shift_Del	DEL	T	T	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941delA	p.Asn314MetfsTer8	p.N314Mfs*8	ENST00000358825	7/22	108	74	34	57	57	0	PRDM10,frameshift_variant,p.Asn228MetfsTer8,ENST00000526082,;PRDM10,frameshift_variant,p.Asn314MetfsTer8,ENST00000360871,;PRDM10,frameshift_variant,p.Asn288MetfsTer8,ENST00000528746,;PRDM10,frameshift_variant,p.Asn314MetfsTer8,ENST00000358825,;PRDM10,frameshift_variant,p.Asn31MetfsTer8,ENST00000533431,;PRDM10,frameshift_variant,p.Asn228MetfsTer8,ENST00000423662,;PRDM10,frameshift_variant,p.Asn228MetfsTer8,ENST00000304538,;PRDM10,downstream_gene_variant,,ENST00000527581,;	-	ENSG00000170325	ENST00000358825	Transcript	frameshift_variant	1173	941	314	N/X	aAt/at	COSM213347	.	.	-1	PRDM10	HGNC	13995	protein_coding	YES	CCDS44771.1	ENSP00000351686	PRD10_HUMAN	.	UPI00002371B3	.	.	.	7/22	.	Superfamily_domains:SSF82199,Gene3D:2.170.270.10,hmmpanther:PTHR11389:SF415,hmmpanther:PTHR11389,PROSITE_profiles:PS50280	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCACATTTTTT	.	3	ESCA
ADAMTS15	0	.	GRCh37	11	130343039	130343039	+	Missense_Mutation	SNP	C	C	A	rs766558119	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2176C>A	p.Leu726Met	p.L726M	ENST00000299164	8/8	54	39	14	24	24	0	ADAMTS15,missense_variant,p.Leu726Met,ENST00000299164,;	A	ENSG00000166106	ENST00000299164	Transcript	missense_variant	2176	2176	726	L/M	Ctg/Atg	rs766558119,COSM541675	.	.	1	ADAMTS15	HGNC	16305	protein_coding	YES	CCDS8488.1	ENSP00000299164	ATS15_HUMAN	.	UPI000004F277	.	deleterious(0)	probably_damaging(0.995)	8/8	.	hmmpanther:PTHR13723:SF39,hmmpanther:PTHR13723,Pfam_domain:PF05986	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTACCTGGCT	byFrequency	5	ESCA
SNX19	0	.	GRCh37	11	130775936	130775936	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2355delA	p.Asp786IlefsTer35	p.D786Ifs*35	ENST00000265909	7/11	50	42	8	41	41	0	SNX19,frameshift_variant,p.Asp769IlefsTer49,ENST00000533214,;SNX19,frameshift_variant,p.Asp26IlefsTer35,ENST00000534726,;SNX19,frameshift_variant,p.Asp166IlefsTer35,ENST00000528555,;SNX19,frameshift_variant,p.Asp229IlefsTer35,ENST00000539184,;SNX19,frameshift_variant,p.Asp786IlefsTer35,ENST00000265909,;SNX19,frameshift_variant,p.Asp26IlefsTer35,ENST00000545537,;SNX19,frameshift_variant,p.Asp166IlefsTer35,ENST00000530356,;SNX19,non_coding_transcript_exon_variant,,ENST00000524460,;SNX19,non_coding_transcript_exon_variant,,ENST00000533318,;SNX19,upstream_gene_variant,,ENST00000526579,;SNX19,non_coding_transcript_exon_variant,,ENST00000527451,;SNX19,downstream_gene_variant,,ENST00000531608,;	-	ENSG00000120451	ENST00000265909	Transcript	frameshift_variant	2925	2355	785	K/X	aaA/aa	.	.	.	-1	SNX19	HGNC	21532	protein_coding	YES	CCDS31721.1	ENSP00000265909	SNX19_HUMAN	E9PLV3_HUMAN,E9PJV7_HUMAN	UPI000013D6A5	.	.	.	7/11	.	hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGATCTTTTTC	.	3	ESCA
NTM	0	.	GRCh37	11	132206082	132206083	+	3'Flank	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000425719	.	28	18	10	23	23	0	NTM,3_prime_UTR_variant,,ENST00000374791,;NTM,3_prime_UTR_variant,,ENST00000374786,;NTM,downstream_gene_variant,,ENST00000457381,;NTM,downstream_gene_variant,,ENST00000539799,;NTM,downstream_gene_variant,,ENST00000425719,;NTM,downstream_gene_variant,,ENST00000427481,;NTM,non_coding_transcript_exon_variant,,ENST00000474900,;NTM,downstream_gene_variant,,ENST00000496094,;NTM,downstream_gene_variant,,ENST00000483174,;NTM,downstream_gene_variant,,ENST00000496198,;	T	ENSG00000182667	ENST00000425719	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	523	1	NTM	HGNC	17941	protein_coding	YES	CCDS44777.1	ENSP00000396722	NTRI_HUMAN	.	UPI00001A58B9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CATATATTTTT	.	2	ESCA
ARNTL	0	.	GRCh37	11	13399889	13399889	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1417C>A	p.Pro473Thr	p.P473T	ENST00000389707	17/20	32	7	25	25	25	0	ARNTL,missense_variant,p.Pro430Thr,ENST00000403510,;ARNTL,missense_variant,p.Pro356Thr,ENST00000361003,;ARNTL,missense_variant,p.Pro474Thr,ENST00000403290,;ARNTL,missense_variant,p.Pro473Thr,ENST00000396441,;ARNTL,missense_variant,p.Pro431Thr,ENST00000401424,;ARNTL,missense_variant,p.Pro472Thr,ENST00000403482,;ARNTL,missense_variant,p.Pro473Thr,ENST00000389707,;ARNTL,synonymous_variant,p.%3D,ENST00000389708,;ARNTL,synonymous_variant,p.%3D,ENST00000524392,;ARNTL,non_coding_transcript_exon_variant,,ENST00000472842,;ARNTL,downstream_gene_variant,,ENST00000529390,;	A	ENSG00000133794	ENST00000389707	Transcript	missense_variant	1805	1417	473	P/T	Cca/Aca	.	.	.	1	ARNTL	HGNC	701	protein_coding	YES	CCDS31430.1	ENSP00000374357	BMAL1_HUMAN	E9PSD2_HUMAN,E9PL54_HUMAN,E9PKN1_HUMAN,E9PKG7_HUMAN,E9PKF0_HUMAN	UPI00001D70A3	.	tolerated(0.76)	benign(0.001)	17/20	.	hmmpanther:PTHR23042,hmmpanther:PTHR23042:SF52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCCCAAAG	.	5	ESCA
KCNC1	0	.	GRCh37	11	17799295	17799295	+	Intron	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1505-1700delT	.	.	ENST00000265969	.	58	47	11	38	38	0	KCNC1,3_prime_UTR_variant,,ENST00000379472,;KCNC1,intron_variant,,ENST00000265969,;KCNC1,intron_variant,,ENST00000525802,;KCNC1,upstream_gene_variant,,ENST00000526029,;	-	ENSG00000129159	ENST00000265969	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KCNC1	HGNC	6233	protein_coding	YES	CCDS44547.1	ENSP00000265969	.	K4DI87_HUMAN	UPI0000E2291F	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAGACTTTTTT	.	2	ESCA
SAAL1	0	.	GRCh37	11	18103046	18103046	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1244C>T	p.Thr415Met	p.T415M	ENST00000524803	11/12	21	18	3	12	12	0	SAAL1,missense_variant,p.Thr417Met,ENST00000529318,;SAAL1,missense_variant,p.Thr74Met,ENST00000532452,;SAAL1,missense_variant,p.Thr414Met,ENST00000300013,;SAAL1,missense_variant,p.Thr415Met,ENST00000524803,;SAAL1,synonymous_variant,p.%3D,ENST00000530436,;SAAL1,synonymous_variant,p.%3D,ENST00000531751,;SAAL1,non_coding_transcript_exon_variant,,ENST00000534721,;SAAL1,upstream_gene_variant,,ENST00000532403,;SAAL1,3_prime_UTR_variant,,ENST00000531581,;SAAL1,non_coding_transcript_exon_variant,,ENST00000530237,;SAAL1,downstream_gene_variant,,ENST00000531216,;	A	ENSG00000166788	ENST00000524803	Transcript	missense_variant	1294	1244	415	T/M	aCg/aTg	COSM4031885	.	.	-1	SAAL1	HGNC	25158	protein_coding	YES	CCDS31439.1	ENSP00000432487	SAAL1_HUMAN	G1UCX3_HUMAN	UPI00001F9E3B	.	tolerated(0.07)	benign(0.033)	11/12	.	hmmpanther:PTHR23424:SF4,hmmpanther:PTHR23424	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACCGTCTCC	.	2	ESCA
SLC17A6	0	.	GRCh37	11	22400904	22400905	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1628dupA	.	.	ENST00000263160	12/12	36	27	9	38	38	0	SLC17A6,3_prime_UTR_variant,,ENST00000263160,;	A	ENSG00000091664	ENST00000263160	Transcript	3_prime_UTR_variant	3804-3805	.	.	.	.	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTAAGAAAAA	.	2	ESCA
CARS	0	.	GRCh37	11	3062148	3062148	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433G>A	p.Ala145Thr	p.A145T	ENST00000380525	4/23	17	13	4	25	25	0	CARS,missense_variant,p.Ala62Thr,ENST00000278224,;CARS,missense_variant,p.Ala62Thr,ENST00000397111,;CARS,missense_variant,p.Ala145Thr,ENST00000380525,;CARS,missense_variant,p.Ala52Thr,ENST00000397114,;CARS,missense_variant,p.Ala75Thr,ENST00000401769,;CARS-AS1,non_coding_transcript_exon_variant,,ENST00000499962,;CARS,non_coding_transcript_exon_variant,,ENST00000524825,;CARS,non_coding_transcript_exon_variant,,ENST00000465331,;CARS,missense_variant,p.Ala62Thr,ENST00000527330,;CARS,3_prime_UTR_variant,,ENST00000529772,;CARS,3_prime_UTR_variant,,ENST00000439280,;CARS,3_prime_UTR_variant,,ENST00000531387,;CARS,non_coding_transcript_exon_variant,,ENST00000526890,;CARS,upstream_gene_variant,,ENST00000465207,;	T	ENSG00000110619	ENST00000380525	Transcript	missense_variant	503	433	145	A/T	Gca/Aca	.	.	.	-1	CARS	HGNC	1493	protein_coding	YES	CCDS41600.1	ENSP00000369897	SYCC_HUMAN	.	UPI00004C4152	.	deleterious(0)	possibly_damaging(0.746)	4/23	.	HAMAP:MF_00041,hmmpanther:PTHR10890,hmmpanther:PTHR10890:SF3,Pfam_domain:PF01406,Gene3D:3.40.50.620,TIGRFAM_domain:TIGR00435,Superfamily_domains:SSF52374,Prints_domain:PR00983	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGATGCGTCAT	.	3	ESCA
KIAA1549L	0	.	GRCh37	11	33677558	33677558	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4870G>T	p.Ala1624Ser	p.A1624S	ENST00000321505	17/20	77	52	24	43	43	0	KIAA1549L,missense_variant,p.Ala1624Ser,ENST00000321505,;KIAA1549L,missense_variant,p.Ala1630Ser,ENST00000389726,;	T	ENSG00000110427	ENST00000321505	Transcript	missense_variant	5050	4870	1624	A/S	Gct/Tct	.	.	.	1	KIAA1549L	HGNC	24836	protein_coding	YES	CCDS44565.2	ENSP00000315295	K154L_HUMAN	.	UPI0000E59322	.	tolerated(0.07)	benign(0.111)	17/20	.	hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAGGCTTAC	.	5	ESCA
EHF	0	.	GRCh37	11	34680734	34680734	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*263delT	.	.	ENST00000531794	9/9	65	48	17	69	69	0	EHF,3_prime_UTR_variant,,ENST00000257831,;EHF,3_prime_UTR_variant,,ENST00000531794,;EHF,3_prime_UTR_variant,,ENST00000450654,;EHF,3_prime_UTR_variant,,ENST00000533754,;EHF,downstream_gene_variant,,ENST00000530286,;EHF,downstream_gene_variant,,ENST00000529527,;	-	ENSG00000135373	ENST00000531794	Transcript	3_prime_UTR_variant	1351	.	.	.	.	.	.	.	1	EHF	HGNC	3246	protein_coding	YES	CCDS55752.1	ENSP00000435835	EHF_HUMAN	E9PQX0_HUMAN,E9PQR6_HUMAN	UPI0001892666	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTGTGATTTTTT	.	2	ESCA
TRAF6	0	.	GRCh37	11	36522834	36522834	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.232C>T	p.Arg78Ter	p.R78*	ENST00000526995	2/7	54	33	21	37	37	0	TRAF6,stop_gained,p.Arg78Ter,ENST00000348124,;TRAF6,stop_gained,p.Arg78Ter,ENST00000526995,;TRAF6,upstream_gene_variant,,ENST00000529150,;	A	ENSG00000175104	ENST00000526995	Transcript	stop_gained	479	232	78	R/*	Cga/Tga	.	.	.	-1	TRAF6	HGNC	12036	protein_coding	YES	CCDS7901.1	ENSP00000433623	TRAF6_HUMAN	.	UPI000000D924	.	.	.	2/7	.	PROSITE_profiles:PS50089,hmmpanther:PTHR10131,hmmpanther:PTHR10131:SF52,Gene3D:3.30.40.10,Pfam_domain:PF13923,PIRSF_domain:PIRSF015614,SMART_domains:SM00184,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCGTAATG	.	5	ESCA
RAG1	0	.	GRCh37	11	36599907	36599907	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1927delT	.	.	ENST00000299440	2/2	28	13	15	31	31	0	RAG1,3_prime_UTR_variant,,ENST00000299440,;RAG2,intron_variant,,ENST00000524423,;RAG1,intron_variant,,ENST00000534663,;	-	ENSG00000166349	ENST00000299440	Transcript	3_prime_UTR_variant	5165	.	.	.	.	.	.	.	1	RAG1	HGNC	9831	protein_coding	YES	CCDS7902.1	ENSP00000299440	RAG1_HUMAN	.	UPI000013E5A0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CATTAGTTTTTT	.	2	ESCA
CHST1	0	.	GRCh37	11	45671131	45671131	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*107G>A	.	.	ENST00000308064	4/4	47	40	7	36	36	0	CHST1,3_prime_UTR_variant,,ENST00000308064,;RP11-495O11.1,upstream_gene_variant,,ENST00000525563,;CHST1,non_coding_transcript_exon_variant,,ENST00000533673,;CHST1,downstream_gene_variant,,ENST00000531322,;	T	ENSG00000175264	ENST00000308064	Transcript	3_prime_UTR_variant	2014	.	.	.	.	.	.	.	-1	CHST1	HGNC	1969	protein_coding	YES	CCDS7913.1	ENSP00000309270	CHST1_HUMAN	.	UPI0000073EA0	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACACGAAGA	.	5	ESCA
OR51E1	0	.	GRCh37	11	4676602	4676602	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1889G>C	.	.	ENST00000396952	2/2	32	27	4	26	26	0	OR51E1,3_prime_UTR_variant,,ENST00000396952,;OR51E1,downstream_gene_variant,,ENST00000530215,;	C	ENSG00000180785	ENST00000396952	Transcript	3_prime_UTR_variant	3496	.	.	.	.	.	.	.	1	OR51E1	HGNC	15194	protein_coding	YES	CCDS31358.2	ENSP00000380155	O51E1_HUMAN	.	UPI000003ACE2	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCCTGGATTTC	.	3	ESCA
OR4A47	0	.	GRCh37	11	48510904	48510904	+	Missense_Mutation	SNP	G	G	A	rs572867266	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560G>A	p.Cys187Tyr	p.C187Y	ENST00000446524	1/1	64	54	10	51	51	0	OR4A47,missense_variant,p.Cys187Tyr,ENST00000446524,;OR4R1P,upstream_gene_variant,,ENST00000529879,;OR4A48P,upstream_gene_variant,,ENST00000531359,;	A	ENSG00000237388	ENST00000446524	Transcript	missense_variant	636	560	187	C/Y	tGc/tAc	rs572867266	.	.	1	OR4A47	HGNC	31266	protein_coding	YES	CCDS31490.1	ENSP00000412752	O4A47_HUMAN	.	UPI00001971E5	.	deleterious_low_confidence(0.01)	benign(0.424)	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26451:SF87,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTGCACTG	byCluster|by1000G	5	ESCA
OR4C46	0	.	GRCh37	11	51515970	51515970	+	Missense_Mutation	SNP	C	C	T	rs763006450	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.689C>T	p.Ala230Val	p.A230V	ENST00000328188	1/1	144	127	17	120	120	0	OR4C46,missense_variant,p.Ala230Val,ENST00000328188,;	T	ENSG00000185926	ENST00000328188	Transcript	missense_variant	689	689	230	A/V	gCa/gTa	rs763006450	.	.	1	OR4C46	HGNC	31271	protein_coding	YES	CCDS31498.1	ENSP00000329056	O4C46_HUMAN	.	UPI000013F6F8	.	deleterious_low_confidence(0.04)	benign(0.021)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF284,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGGCAAGGC	.	4	ESCA
TNKS1BP1	0	.	GRCh37	11	57087989	57087989	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292C>T	p.Pro98Ser	p.P98S	ENST00000532437	2/11	76	29	46	38	38	0	TNKS1BP1,missense_variant,p.Pro98Ser,ENST00000532437,;TNKS1BP1,missense_variant,p.Pro98Ser,ENST00000358252,;TNKS1BP1,missense_variant,p.Pro98Ser,ENST00000527207,;TNKS1BP1,missense_variant,p.Pro98Ser,ENST00000528882,;	A	ENSG00000149115	ENST00000532437	Transcript	missense_variant	604	292	98	P/S	Ccc/Tcc	.	.	.	-1	TNKS1BP1	HGNC	19081	protein_coding	YES	CCDS7951.1	ENSP00000437271	TB182_HUMAN	E9PKK0_HUMAN,E9PKE7_HUMAN	UPI000013DB72	.	tolerated(0.12)	probably_damaging(0.956)	2/11	.	hmmpanther:PTHR22042:SF2,hmmpanther:PTHR22042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGGGAAGGG	.	5	ESCA
PRG2	0	.	GRCh37	11	57155247	57155247	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590G>A	p.Cys197Tyr	p.C197Y	ENST00000311862	5/6	74	68	6	55	55	0	PRG2,missense_variant,p.Cys186Tyr,ENST00000533605,;PRG2,missense_variant,p.Cys197Tyr,ENST00000311862,;PRG2,missense_variant,p.Cys197Tyr,ENST00000525955,;RP11-872D17.8,downstream_gene_variant,,ENST00000529411,;RP11-872D17.8,non_coding_transcript_exon_variant,,ENST00000534081,;PRG2,non_coding_transcript_exon_variant,,ENST00000530105,;RP11-872D17.8,downstream_gene_variant,,ENST00000528835,;	T	ENSG00000186652	ENST00000311862	Transcript	missense_variant	664	590	197	C/Y	tGc/tAc	.	.	.	-1	PRG2	HGNC	9362	protein_coding	YES	CCDS7955.1	ENSP00000312134	PRG2_HUMAN	.	UPI000013CF50	.	deleterious(0)	probably_damaging(1)	5/6	.	PROSITE_profiles:PS50041,hmmpanther:PTHR10068:SF7,hmmpanther:PTHR10068,PROSITE_patterns:PS00615,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR00770	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACGCAGTGA	.	2	ESCA
OSBP	0	.	GRCh37	11	59341932	59341932	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2118delT	.	.	ENST00000263847	14/14	27	10	17	18	18	0	OSBP,3_prime_UTR_variant,,ENST00000263847,;OSBP,downstream_gene_variant,,ENST00000525357,;	-	ENSG00000110048	ENST00000263847	Transcript	3_prime_UTR_variant	5022	.	.	.	.	.	.	.	-1	OSBP	HGNC	8503	protein_coding	YES	CCDS7974.1	ENSP00000263847	OSBP1_HUMAN	B4DR25_HUMAN	UPI0000130EAF	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAAGGCAAAAAA	.	2	ESCA
PATL1	0	.	GRCh37	11	59425146	59425146	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.478delC	p.Gln160ArgfsTer33	p.Q160Rfs*33	ENST00000300146	5/19	51	38	13	27	27	0	PATL1,frameshift_variant,p.Gln160ArgfsTer33,ENST00000300146,;	-	ENSG00000166889	ENST00000300146	Transcript	frameshift_variant	563	478	160	Q/X	Cag/ag	.	.	.	-1	PATL1	HGNC	26721	protein_coding	YES	CCDS44613.1	ENSP00000300146	PATL1_HUMAN	B3KXN0_HUMAN	UPI00001FA7D8	.	.	.	5/19	.	hmmpanther:PTHR21551,hmmpanther:PTHR21551:SF2,Pfam_domain:PF09770	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GACCCTGGGGGG	.	3	ESCA
MS4A6A	0	.	GRCh37	11	59947419	59947419	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.251G>C	p.Gly84Ala	p.G84A	ENST00000412309	3/6	50	29	20	43	43	0	MS4A6A,missense_variant,p.Gly56Ala,ENST00000528851,;MS4A6A,missense_variant,p.Gly84Ala,ENST00000534596,;MS4A6A,missense_variant,p.Gly84Ala,ENST00000529054,;MS4A6A,missense_variant,p.Gly56Ala,ENST00000420732,;MS4A6A,missense_variant,p.Gly56Ala,ENST00000323961,;MS4A6A,missense_variant,p.Gly56Ala,ENST00000532169,;MS4A6A,missense_variant,p.Gly56Ala,ENST00000530839,;MS4A6A,missense_variant,p.Gly84Ala,ENST00000412309,;MS4A6A,intron_variant,,ENST00000533023,;MS4A6A,intron_variant,,ENST00000533989,;MS4A6A,intron_variant,,ENST00000426738,;MS4A6A,downstream_gene_variant,,ENST00000531531,;MS4A6A,downstream_gene_variant,,ENST00000533409,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000529906,;MS4A6A,downstream_gene_variant,,ENST00000528925,;MS4A6A,missense_variant,p.Gly56Ala,ENST00000527254,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000530179,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000526677,;MS4A6A,intron_variant,,ENST00000525549,;MS4A6A,upstream_gene_variant,,ENST00000531914,;MS4A6A,downstream_gene_variant,,ENST00000533660,;MS4A6A,downstream_gene_variant,,ENST00000526697,;	G	ENSG00000110077	ENST00000412309	Transcript	missense_variant	269	251	84	G/A	gGc/gCc	.	.	.	-1	MS4A6A	HGNC	13375	protein_coding	YES	CCDS58134.1	ENSP00000403212	.	F8W9K1_HUMAN,E9PNG6_HUMAN,E9PMN8_HUMAN,E9PL03_HUMAN	UPI0001F77AB4	.	tolerated(0.13)	possibly_damaging(0.778)	3/6	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF53,Pfam_domain:PF04103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCATGCCACAC	.	3	ESCA
MS4A6A	0	.	GRCh37	11	59947431	59947431	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239A>G	p.Gln80Arg	p.Q80R	ENST00000412309	3/6	46	27	19	45	45	0	MS4A6A,missense_variant,p.Gln52Arg,ENST00000528851,;MS4A6A,missense_variant,p.Gln80Arg,ENST00000534596,;MS4A6A,missense_variant,p.Gln80Arg,ENST00000529054,;MS4A6A,missense_variant,p.Gln52Arg,ENST00000420732,;MS4A6A,missense_variant,p.Gln52Arg,ENST00000323961,;MS4A6A,missense_variant,p.Gln52Arg,ENST00000532169,;MS4A6A,missense_variant,p.Gln52Arg,ENST00000530839,;MS4A6A,missense_variant,p.Gln80Arg,ENST00000412309,;MS4A6A,intron_variant,,ENST00000533023,;MS4A6A,intron_variant,,ENST00000533989,;MS4A6A,intron_variant,,ENST00000426738,;MS4A6A,downstream_gene_variant,,ENST00000531531,;MS4A6A,downstream_gene_variant,,ENST00000533409,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000529906,;MS4A6A,downstream_gene_variant,,ENST00000528925,;MS4A6A,missense_variant,p.Gln52Arg,ENST00000527254,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000530179,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000526677,;MS4A6A,intron_variant,,ENST00000525549,;MS4A6A,upstream_gene_variant,,ENST00000531914,;MS4A6A,downstream_gene_variant,,ENST00000533660,;MS4A6A,downstream_gene_variant,,ENST00000526697,;	C	ENSG00000110077	ENST00000412309	Transcript	missense_variant	257	239	80	Q/R	cAg/cGg	.	.	.	-1	MS4A6A	HGNC	13375	protein_coding	YES	CCDS58134.1	ENSP00000403212	.	F8W9K1_HUMAN,E9PNG6_HUMAN,E9PMN8_HUMAN,E9PL03_HUMAN	UPI0001F77AB4	.	deleterious(0)	probably_damaging(0.999)	3/6	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF53,Pfam_domain:PF04103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGATCTGGATA	.	3	ESCA
CYB561A3	0	.	GRCh37	11	61124145	61124145	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92G>A	p.Gly31Glu	p.G31E	ENST00000426130	4/8	36	26	10	31	31	0	CYB561A3,missense_variant,p.Gly14Glu,ENST00000537364,;CYB561A3,missense_variant,p.Gly31Glu,ENST00000426130,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000545361,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000294072,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000546151,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000537680,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000542361,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000536915,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000539128,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000447532,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000539890,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000544118,;DAK,downstream_gene_variant,,ENST00000534084,;CYB561A3,upstream_gene_variant,,ENST00000540139,;CYB561A3,non_coding_transcript_exon_variant,,ENST00000538263,;CYB561A3,non_coding_transcript_exon_variant,,ENST00000536687,;CYB561A3,intron_variant,,ENST00000540317,;CYB561A3,downstream_gene_variant,,ENST00000535152,;CYB561A3,missense_variant,p.Gly14Glu,ENST00000540755,;CYB561A3,non_coding_transcript_exon_variant,,ENST00000535177,;CYB561A3,non_coding_transcript_exon_variant,,ENST00000542411,;	T	ENSG00000162144	ENST00000426130	Transcript	missense_variant	872	92	31	G/E	gGg/gAg	.	.	.	-1	CYB561A3	HGNC	23014	protein_coding	YES	CCDS53639.1	ENSP00000398979	CYAC3_HUMAN	F5H684_HUMAN,F5H5Y9_HUMAN,F5H5L0_HUMAN,F5H121_HUMAN,F5H0P5_HUMAN,F5GX87_HUMAN	UPI0000EE44D0	.	tolerated(0.12)	possibly_damaging(0.687)	4/8	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10106,hmmpanther:PTHR10106:SF2,PROSITE_profiles:PS50939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGACCCCAGC	.	5	ESCA
RARRES3	0	.	GRCh37	11	63313709	63313709	+	Frame_Shift_Del	DEL	A	A	-	rs547099153,rs745860467	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483delA	p.Ala162ArgfsTer56	p.A162Rfs*56	ENST00000255688	4/4	71	39	32	43	43	0	RARRES3,frameshift_variant,p.Ala162ArgfsTer56,ENST00000354445,;RARRES3,frameshift_variant,p.Ala162ArgfsTer56,ENST00000255688,;RARRES3,downstream_gene_variant,,ENST00000439013,;RARRES3,non_coding_transcript_exon_variant,,ENST00000544107,;RARRES3,non_coding_transcript_exon_variant,,ENST00000537871,;	-	ENSG00000133321	ENST00000255688	Transcript	frameshift_variant	524	476	159	Q/X	cAa/ca	rs547099153,rs745860467,COSM1355555	.	.	1	RARRES3	HGNC	9869	protein_coding	YES	CCDS41662.1	ENSP00000255688	HRSL4_HUMAN	.	UPI0000136F56	.	.	.	4/4	.	hmmpanther:PTHR13943,hmmpanther:PTHR13943:SF36	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	deletion	.	7	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.A162fs*>3|c.476delA|4	INDELOCATOR|VARSCANI	GATACCAAAAAA	by1000G	2	ESCA
FLRT1	0	.	GRCh37	11	63886077	63886079	+	3'UTR	DEL	TTC	TTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TTC	TTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*313_*315delTTC	.	.	ENST00000246841	2/2	51	36	15	38	38	0	FLRT1,3_prime_UTR_variant,,ENST00000246841,;MACROD1,intron_variant,,ENST00000255681,;RP11-21A7A.3,non_coding_transcript_exon_variant,,ENST00000543817,;MACROD1,intron_variant,,ENST00000543422,;MACROD1,intron_variant,,ENST00000542359,;MACROD1,intron_variant,,ENST00000545464,;	-	ENSG00000126500	ENST00000246841	Transcript	3_prime_UTR_variant	3381-3383	.	.	.	.	.	.	.	1	FLRT1	HGNC	3760	protein_coding	YES	CCDS8057.1	ENSP00000246841	FLRT1_HUMAN	O43408_HUMAN	UPI0000039F94	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTTTTTCCCCCC	.	3	ESCA
SF1	0	.	GRCh37	11	64536544	64536545	+	Frame_Shift_Del	DEL	AC	AC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AC	AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1211_1212delGT	p.Cys404TyrfsTer14	p.C404Yfs*14	ENST00000377387	8/13	112	78	34	37	37	0	SF1,frameshift_variant,p.Cys279TyrfsTer14,ENST00000227503,;SF1,frameshift_variant,p.Cys279TyrfsTer14,ENST00000377390,;SF1,frameshift_variant,p.Cys164TyrfsTer14,ENST00000422298,;SF1,frameshift_variant,p.Cys279TyrfsTer14,ENST00000377394,;SF1,frameshift_variant,p.Cys279TyrfsTer14,ENST00000334944,;SF1,frameshift_variant,p.Cys404TyrfsTer14,ENST00000377387,;SF1,frameshift_variant,p.Cys253TyrfsTer14,ENST00000433274,;SF1,upstream_gene_variant,,ENST00000443908,;SF1,downstream_gene_variant,,ENST00000432725,;SF1,upstream_gene_variant,,ENST00000486867,;SF1,upstream_gene_variant,,ENST00000413725,;SF1,non_coding_transcript_exon_variant,,ENST00000489544,;SF1,downstream_gene_variant,,ENST00000496969,;SF1,3_prime_UTR_variant,,ENST00000448404,;SF1,upstream_gene_variant,,ENST00000477596,;SF1,downstream_gene_variant,,ENST00000486960,;SF1,downstream_gene_variant,,ENST00000482693,;SF1,downstream_gene_variant,,ENST00000413951,;	-	ENSG00000168066	ENST00000377387	Transcript	frameshift_variant	1288-1289	1211-1212	404	C/X	tGT/t	.	.	.	-1	SF1	HGNC	12950	protein_coding	YES	CCDS53661.1	ENSP00000366604	SF01_HUMAN	Q14821_HUMAN,C9J792_HUMAN,B4DX42_HUMAN	UPI0000074300	.	.	.	8/13	.	PROSITE_profiles:PS50158,hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF45,Pfam_domain:PF00098,Gene3D:4.10.60.10,SMART_domains:SM00343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTGGTACACACT	.	3	ESCA
HPX	0	.	GRCh37	11	6461701	6461701	+	Frame_Shift_Del	DEL	A	A	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210delT	p.Phe70LeufsTer16	p.F70Lfs*16	ENST00000265983	3/10	49	32	17	23	23	0	HPX,frameshift_variant,p.Phe70LeufsTer16,ENST00000265983,;HPX,non_coding_transcript_exon_variant,,ENST00000534800,;HPX,non_coding_transcript_exon_variant,,ENST00000525057,;HPX,non_coding_transcript_exon_variant,,ENST00000533561,;HPX,downstream_gene_variant,,ENST00000527105,;HPX,upstream_gene_variant,,ENST00000534429,;HPX,non_coding_transcript_exon_variant,,ENST00000533856,;HPX,non_coding_transcript_exon_variant,,ENST00000528348,;HPX,non_coding_transcript_exon_variant,,ENST00000533369,;HPX,upstream_gene_variant,,ENST00000529775,;HPX,upstream_gene_variant,,ENST00000527556,;	-	ENSG00000110169	ENST00000265983	Transcript	frameshift_variant	311	210	70	F/X	ttT/tt	COSM1355746	.	.	-1	HPX	HGNC	5171	protein_coding	YES	CCDS7763.1	ENSP00000265983	HEMO_HUMAN	.	UPI000012C5AF	.	.	.	3/10	.	Superfamily_domains:SSF50923,PIRSF_domain:PIRSF002551,SMART_domains:SM00120,Pfam_domain:PF00045,Gene3D:2.110.10.10,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF136,PROSITE_profiles:PS51642	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCTTTAAAAAA	.	3	ESCA
MAP3K11	0	.	GRCh37	11	65374944	65374944	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1286G>A	p.Arg429His	p.R429H	ENST00000309100	5/10	55	49	6	10	10	0	MAP3K11,missense_variant,p.Arg429His,ENST00000309100,;MAP3K11,missense_variant,p.Arg172His,ENST00000530153,;MAP3K11,downstream_gene_variant,,ENST00000526293,;MAP3K11,upstream_gene_variant,,ENST00000532507,;MAP3K11,downstream_gene_variant,,ENST00000529839,;MAP3K11,upstream_gene_variant,,ENST00000534432,;MAP3K11,synonymous_variant,p.%3D,ENST00000524848,;MAP3K11,non_coding_transcript_exon_variant,,ENST00000524856,;MAP3K11,non_coding_transcript_exon_variant,,ENST00000533032,;MAP3K11,downstream_gene_variant,,ENST00000534110,;MAP3K11,downstream_gene_variant,,ENST00000527304,;MAP3K11,upstream_gene_variant,,ENST00000526647,;MAP3K11,downstream_gene_variant,,ENST00000530949,;	T	ENSG00000173327	ENST00000309100	Transcript	missense_variant	1772	1286	429	R/H	cGc/cAc	.	.	.	-1	MAP3K11	HGNC	6850	protein_coding	YES	CCDS8107.1	ENSP00000309597	M3K11_HUMAN	E9PLB1_HUMAN,E9PID4_HUMAN,B4DS76_HUMAN	UPI0000049BF7	.	deleterious(0.03)	possibly_damaging(0.512)	5/10	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF329,PIRSF_domain:PIRSF000556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCGCGCGCC	.	2	ESCA
SF3B2	0	.	GRCh37	11	65827296	65827296	+	Missense_Mutation	SNP	C	C	T	rs751434640	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1445C>T	p.Ala482Val	p.A482V	ENST00000322535	13/22	101	89	11	33	33	0	SF3B2,missense_variant,p.Ala482Val,ENST00000322535,;SF3B2,missense_variant,p.Ala465Val,ENST00000528302,;SF3B2,upstream_gene_variant,,ENST00000530981,;SF3B2,downstream_gene_variant,,ENST00000524475,;SF3B2,downstream_gene_variant,,ENST00000530322,;SF3B2,downstream_gene_variant,,ENST00000524627,;SF3B2,downstream_gene_variant,,ENST00000533595,;SF3B2,downstream_gene_variant,,ENST00000533421,;SF3B2,non_coding_transcript_exon_variant,,ENST00000529994,;SF3B2,upstream_gene_variant,,ENST00000534765,;SF3B2,downstream_gene_variant,,ENST00000526653,;SF3B2,downstream_gene_variant,,ENST00000525207,;SF3B2,downstream_gene_variant,,ENST00000531589,;	T	ENSG00000087365	ENST00000322535	Transcript	missense_variant	1494	1445	482	A/V	gCg/gTg	rs751434640	.	.	1	SF3B2	HGNC	10769	protein_coding	YES	CCDS31612.1	ENSP00000318861	SF3B2_HUMAN	E9PIL8_HUMAN	UPI00001C1F20	.	deleterious(0.01)	possibly_damaging(0.804)	13/22	.	hmmpanther:PTHR12785,hmmpanther:PTHR12785:SF6,Pfam_domain:PF04037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACAGCGCAGG	.	4	ESCA
RAB1B	0	.	GRCh37	11	66039143	66039143	+	Intron	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15-116delA	.	.	ENST00000311481	.	65	34	31	11	11	0	RAB1B,intron_variant,,ENST00000311481,;RAB1B,intron_variant,,ENST00000527397,;KLC2,downstream_gene_variant,,ENST00000316924,;KLC2,downstream_gene_variant,,ENST00000394078,;KLC2,downstream_gene_variant,,ENST00000417856,;KLC2,downstream_gene_variant,,ENST00000394066,;KLC2,downstream_gene_variant,,ENST00000394067,;KLC2,downstream_gene_variant,,ENST00000394065,;KLC2,downstream_gene_variant,,ENST00000421552,;RP11-867G23.3,non_coding_transcript_exon_variant,,ENST00000501708,;RP11-867G23.2,upstream_gene_variant,,ENST00000533287,;	-	ENSG00000174903	ENST00000311481	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RAB1B	HGNC	18370	protein_coding	YES	CCDS31613.1	ENSP00000310226	RAB1B_HUMAN	Q92927_HUMAN	UPI0000037B58	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTGCTAAAAAA	.	2	ESCA
DCHS1	0	.	GRCh37	11	6655411	6655411	+	Missense_Mutation	SNP	G	G	A	rs374740842	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1924C>T	p.Arg642Trp	p.R642W	ENST00000299441	3/21	64	28	36	27	27	0	DCHS1,missense_variant,p.Arg642Trp,ENST00000299441,;RP11-732A19.6,intron_variant,,ENST00000526633,;	A	ENSG00000166341	ENST00000299441	Transcript	missense_variant	2336	1924	642	R/W	Cgg/Tgg	rs374740842	.	.	-1	DCHS1	HGNC	13681	protein_coding	YES	CCDS7771.1	ENSP00000299441	PCD16_HUMAN	.	UPI00001313B6	.	deleterious(0.02)	possibly_damaging(0.773)	3/21	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24027:SF294,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCCGGGTTG	byCluster	5	ESCA
RPS6KB2	0	.	GRCh37	11	67202050	67202050	+	Intron	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1156-3C>A	.	.	ENST00000312629	.	156	119	36	38	38	0	RPS6KB2,splice_region_variant,,ENST00000312629,;RPS6KB2,downstream_gene_variant,,ENST00000524934,;CORO1B,downstream_gene_variant,,ENST00000341356,;CORO1B,downstream_gene_variant,,ENST00000393893,;RPS6KB2,downstream_gene_variant,,ENST00000539188,;PTPRCAP,downstream_gene_variant,,ENST00000326294,;AP003419.16,intron_variant,,ENST00000535922,;RPS6KB2,downstream_gene_variant,,ENST00000524814,;CORO1B,downstream_gene_variant,,ENST00000539724,;RPS6KB2,splice_region_variant,,ENST00000526268,;RPS6KB2,splice_region_variant,,ENST00000525088,;RPS6KB2,splice_region_variant,,ENST00000528964,;RPS6KB2,splice_region_variant,,ENST00000525996,;RPS6KB2,non_coding_transcript_exon_variant,,ENST00000531765,;RPS6KB2,downstream_gene_variant,,ENST00000420069,;RPS6KB2,downstream_gene_variant,,ENST00000525726,;CORO1B,downstream_gene_variant,,ENST00000537042,;RPS6KB2,downstream_gene_variant,,ENST00000530623,;RPS6KB2,downstream_gene_variant,,ENST00000556575,;	A	ENSG00000175634	ENST00000312629	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	RPS6KB2	HGNC	10437	protein_coding	YES	CCDS41677.1	ENSP00000308413	KS6B2_HUMAN	.	UPI00001FAD74	.	.	.	.	13/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCCCAGGGC	.	4	ESCA
CORO1B	0	.	GRCh37	11	67209168	67209169	+	Intron	DEL	GG	GG	-	rs764793065	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GG	GG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454+35_454+36delCC	.	.	ENST00000393893	.	57	27	30	17	17	0	CORO1B,frameshift_variant,p.His164ArgfsTer15,ENST00000545016,;CORO1B,intron_variant,,ENST00000341356,;CORO1B,intron_variant,,ENST00000453768,;CORO1B,intron_variant,,ENST00000393893,;PTPRCAP,upstream_gene_variant,,ENST00000326294,;CORO1B,upstream_gene_variant,,ENST00000539970,;CORO1B,downstream_gene_variant,,ENST00000537010,;CORO1B,downstream_gene_variant,,ENST00000545736,;CORO1B,upstream_gene_variant,,ENST00000539724,;CORO1B,intron_variant,,ENST00000537042,;	-	ENSG00000172725	ENST00000393893	Transcript	intron_variant	.	.	.	.	.	rs764793065	.	.	-1	CORO1B	HGNC	2253	protein_coding	YES	CCDS8164.1	ENSP00000377471	COR1B_HUMAN	.	UPI0000127C42	.	.	.	.	5/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTCCGTGGGGGGG	.	2	ESCA
UNC93B1	0	.	GRCh37	11	67766770	67766770	+	Missense_Mutation	SNP	G	G	A	rs754100504	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560C>T	p.Ala187Val	p.A187V	ENST00000227471	5/12	67	49	18	33	33	0	UNC93B1,missense_variant,p.Ala116Val,ENST00000528423,;UNC93B1,missense_variant,p.Ala187Val,ENST00000227471,;UNC93B1,non_coding_transcript_exon_variant,,ENST00000530331,;UNC93B1,upstream_gene_variant,,ENST00000533966,;UNC93B1,synonymous_variant,p.%3D,ENST00000524455,;UNC93B1,non_coding_transcript_exon_variant,,ENST00000533424,;UNC93B1,non_coding_transcript_exon_variant,,ENST00000528096,;UNC93B1,non_coding_transcript_exon_variant,,ENST00000525743,;UNC93B1,downstream_gene_variant,,ENST00000530138,;UNC93B1,upstream_gene_variant,,ENST00000525368,;UNC93B1,downstream_gene_variant,,ENST00000531152,;	A	ENSG00000110057	ENST00000227471	Transcript	missense_variant	640	560	187	A/V	gCg/gTg	rs754100504,COSM4036061	.	.	-1	UNC93B1	HGNC	13481	protein_coding	YES	.	ENSP00000227471	UN93B_HUMAN	E9PNE5_HUMAN	UPI000013C8B8	.	deleterious(0.01)	possibly_damaging(0.718)	5/12	.	Pfam_domain:PF05978,hmmpanther:PTHR19444:SF3,hmmpanther:PTHR19444	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCGCCATC	.	5	ESCA
SUV420H1	0	.	GRCh37	11	67924860	67924860	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*295C>T	.	.	ENST00000304363	11/11	29	19	10	23	23	0	SUV420H1,3_prime_UTR_variant,,ENST00000304363,;SUV420H1,downstream_gene_variant,,ENST00000427752,;SUV420H1,downstream_gene_variant,,ENST00000441488,;	A	ENSG00000110066	ENST00000304363	Transcript	3_prime_UTR_variant	3307	.	.	.	.	.	.	.	-1	SUV420H1	HGNC	24283	protein_coding	YES	CCDS31623.1	ENSP00000305899	SV421_HUMAN	E9PKD9_HUMAN,C9JP58_HUMAN,C9JFG1_HUMAN,C9J6S5_HUMAN	UPI00001FADE7	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAACGTCCTG	.	5	ESCA
MTL5	0	.	GRCh37	11	68517736	68517736	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393G>A	p.%3D	p.A131A	ENST00000255087	2/10	74	60	14	28	28	0	MTL5,synonymous_variant,p.%3D,ENST00000255087,;MTL5,synonymous_variant,p.%3D,ENST00000544963,;MTL5,synonymous_variant,p.%3D,ENST00000443940,;CPT1A,downstream_gene_variant,,ENST00000265641,;CPT1A,downstream_gene_variant,,ENST00000540367,;CPT1A,downstream_gene_variant,,ENST00000376618,;MTL5,non_coding_transcript_exon_variant,,ENST00000432435,;MTL5,upstream_gene_variant,,ENST00000540869,;MTL5,upstream_gene_variant,,ENST00000538944,;	T	ENSG00000132749	ENST00000255087	Transcript	synonymous_variant	577	393	131	A	gcG/gcA	.	.	.	-1	MTL5	HGNC	7446	protein_coding	YES	CCDS8184.1	ENSP00000255087	MTL5_HUMAN	.	UPI00001FAE07	.	.	.	2/10	.	hmmpanther:PTHR12446:SF20,hmmpanther:PTHR12446	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGTGCGCGGG	.	5	ESCA
CPT1A	0	.	GRCh37	11	68522887	68522887	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2225delA	.	.	ENST00000265641	19/19	59	34	25	23	23	0	CPT1A,3_prime_UTR_variant,,ENST00000265641,;CPT1A,intron_variant,,ENST00000540367,;CPT1A,intron_variant,,ENST00000376618,;MTL5,upstream_gene_variant,,ENST00000255087,;CPT1A,downstream_gene_variant,,ENST00000539743,;MTL5,upstream_gene_variant,,ENST00000544963,;MTL5,upstream_gene_variant,,ENST00000443940,;MTL5,upstream_gene_variant,,ENST00000432435,;	-	ENSG00000110090	ENST00000265641	Transcript	3_prime_UTR_variant	4702	.	.	.	.	.	.	.	-1	CPT1A	HGNC	2328	protein_coding	YES	CCDS8185.1	ENSP00000265641	CPT1A_HUMAN	Q8WZ48_HUMAN,H3BUV7_HUMAN,H3BUJ0_HUMAN,H3BP22_HUMAN	UPI000013D658	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTTGCTTTTTT	.	2	ESCA
OR10A2	0	.	GRCh37	11	6891852	6891852	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.867C>G	p.Ser289Arg	p.S289R	ENST00000307322	1/1	51	37	14	40	40	0	OR10A2,missense_variant,p.Ser289Arg,ENST00000307322,;	G	ENSG00000170790	ENST00000307322	Transcript	missense_variant	929	867	289	S/R	agC/agG	.	.	.	1	OR10A2	HGNC	8161	protein_coding	YES	CCDS31415.1	ENSP00000303862	O10A2_HUMAN	.	UPI000015F21C	.	tolerated(1)	benign(0)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF90	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGCAGGAC	.	5	ESCA
SHANK2	0	.	GRCh37	11	70644566	70644566	+	Missense_Mutation	SNP	G	G	A	rs149996975	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1762C>T	p.Pro588Ser	p.P588S	ENST00000338508	20/33	83	51	32	47	47	0	SHANK2,missense_variant,p.Pro218Ser,ENST00000294018,;SHANK2,missense_variant,p.Pro588Ser,ENST00000338508,;SHANK2,missense_variant,p.Pro208Ser,ENST00000423696,;SHANK2,non_coding_transcript_exon_variant,,ENST00000460048,;SHANK2,non_coding_transcript_exon_variant,,ENST00000468619,;SHANK2,non_coding_transcript_exon_variant,,ENST00000470759,;SHANK2,non_coding_transcript_exon_variant,,ENST00000498519,;	A	ENSG00000162105	ENST00000338508	Transcript	missense_variant	1762	1762	588	P/S	Ccc/Tcc	rs149996975	.	.	-1	SHANK2	HGNC	14295	protein_coding	YES	.	ENSP00000345193	.	C9JFP8_HUMAN,A6NHU9_HUMAN	UPI00020653A9	.	tolerated(0.89)	benign(0.015)	20/33	.	hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17,Gene3D:2.30.30.40,Superfamily_domains:SSF50044	A:0.0006	A:0	A:0.0029	.	A:0	A:0.001	A:0	A:0	A:0.0009	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGGCTTAC	byFrequency|byCluster|by1000G	5	ESCA
EPS8L2	0	.	GRCh37	11	709356	709356	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-52C>T	.	.	ENST00000533256	3/22	36	15	21	22	22	0	EPS8L2,5_prime_UTR_variant,,ENST00000527199,;EPS8L2,5_prime_UTR_variant,,ENST00000318562,;EPS8L2,5_prime_UTR_variant,,ENST00000530636,;EPS8L2,5_prime_UTR_variant,,ENST00000534755,;EPS8L2,5_prime_UTR_variant,,ENST00000533500,;EPS8L2,5_prime_UTR_variant,,ENST00000531348,;EPS8L2,5_prime_UTR_variant,,ENST00000524763,;EPS8L2,5_prime_UTR_variant,,ENST00000533256,;TMEM80,downstream_gene_variant,,ENST00000526170,;EPS8L2,upstream_gene_variant,,ENST00000526198,;AP006621.9,intron_variant,,ENST00000527021,;DEAF1,upstream_gene_variant,,ENST00000525626,;DEAF1,upstream_gene_variant,,ENST00000526857,;EPS8L2,5_prime_UTR_variant,,ENST00000526909,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000529680,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000530093,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000527807,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000529346,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000526380,;EPS8L2,upstream_gene_variant,,ENST00000530118,;	T	ENSG00000177106	ENST00000533256	Transcript	5_prime_UTR_variant	324	.	.	.	.	.	.	.	1	EPS8L2	HGNC	21296	protein_coding	YES	CCDS31328.1	ENSP00000435585	ES8L2_HUMAN	E9PNY4_HUMAN,E9PNT0_HUMAN,E9PN68_HUMAN,E9PLN2_HUMAN,E9PLH1_HUMAN	UPI000006226C	.	.	.	3/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGACCGGGGC	.	5	ESCA
KRTAP5-8	0	.	GRCh37	11	71250101	71250101	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*436C>T	.	.	ENST00000398534	1/1	55	42	13	37	37	0	KRTAP5-8,3_prime_UTR_variant,,ENST00000398534,;	T	ENSG00000241233	ENST00000398534	Transcript	3_prime_UTR_variant	1031	.	.	.	.	.	.	.	1	KRTAP5-8	HGNC	23603	protein_coding	YES	CCDS41683.1	ENSP00000420723	KRA58_HUMAN	.	UPI000013ECDA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGACTCAGA	.	5	ESCA
ANAPC15	0	.	GRCh37	11	71822269	71822269	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54T>C	p.%3D	p.F18F	ENST00000227618	3/6	89	60	29	54	54	0	ANAPC15,synonymous_variant,p.%3D,ENST00000537644,;ANAPC15,synonymous_variant,p.%3D,ENST00000227618,;ANAPC15,synonymous_variant,p.%3D,ENST00000545944,;ANAPC15,synonymous_variant,p.%3D,ENST00000543587,;ANAPC15,synonymous_variant,p.%3D,ENST00000543050,;ANAPC15,synonymous_variant,p.%3D,ENST00000545680,;ANAPC15,synonymous_variant,p.%3D,ENST00000438939,;ANAPC15,synonymous_variant,p.%3D,ENST00000535503,;ANAPC15,synonymous_variant,p.%3D,ENST00000542531,;ANAPC15,synonymous_variant,p.%3D,ENST00000538393,;ANAPC15,synonymous_variant,p.%3D,ENST00000535234,;ANAPC15,synonymous_variant,p.%3D,ENST00000545333,;ANAPC15,synonymous_variant,p.%3D,ENST00000539395,;ANAPC15,synonymous_variant,p.%3D,ENST00000538919,;ANAPC15,intron_variant,,ENST00000502597,;LRTOMT,downstream_gene_variant,,ENST00000439209,;LRTOMT,downstream_gene_variant,,ENST00000435085,;LRTOMT,downstream_gene_variant,,ENST00000307198,;LRTOMT,downstream_gene_variant,,ENST00000419228,;ANAPC15,upstream_gene_variant,,ENST00000543015,;ANAPC15,synonymous_variant,p.%3D,ENST00000538117,;FOLR3,upstream_gene_variant,,ENST00000542161,;LRTOMT,downstream_gene_variant,,ENST00000544409,;LRTOMT,downstream_gene_variant,,ENST00000427369,;LRTOMT,downstream_gene_variant,,ENST00000541899,;	G	ENSG00000110200	ENST00000227618	Transcript	synonymous_variant	280	54	18	F	ttT/ttC	.	.	.	-1	ANAPC15	HGNC	24531	protein_coding	YES	CCDS8210.1	ENSP00000227618	APC15_HUMAN	F5H2T3_HUMAN,F5GXB9_HUMAN	UPI000002356F	.	.	.	3/6	.	Pfam_domain:PF15243,hmmpanther:PTHR22526	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTAAACCA	.	5	ESCA
FOLR1	0	.	GRCh37	11	71906681	71906681	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383G>T	p.Arg128Leu	p.R128L	ENST00000393679	4/5	112	64	48	74	74	0	FOLR1,missense_variant,p.Arg128Leu,ENST00000393679,;FOLR1,missense_variant,p.Arg128Leu,ENST00000393676,;FOLR1,missense_variant,p.Arg128Leu,ENST00000312293,;FOLR1,missense_variant,p.Arg128Leu,ENST00000393681,;RP11-807H22.7,intron_variant,,ENST00000378140,;	T	ENSG00000110195	ENST00000393679	Transcript	missense_variant	819	383	128	R/L	cGg/cTg	.	.	.	1	FOLR1	HGNC	3791	protein_coding	YES	CCDS8211.1	ENSP00000377284	FOLR1_HUMAN	Q9NP04_HUMAN,Q96QD1_HUMAN,Q6LDL1_HUMAN	UPI0000000C4C	.	deleterious(0)	possibly_damaging(0.693)	4/5	.	hmmpanther:PTHR10517:SF15,hmmpanther:PTHR10517,Pfam_domain:PF03024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGCGGGTAC	.	5	ESCA
CHRDL2	0	.	GRCh37	11	74415621	74415621	+	Missense_Mutation	SNP	C	C	T	rs200667288	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.661G>A	p.Ala221Thr	p.A221T	ENST00000263671	7/12	61	39	22	24	24	0	CHRDL2,missense_variant,p.Ala221Thr,ENST00000263671,;CHRDL2,missense_variant,p.Ala221Thr,ENST00000528789,;CHRDL2,missense_variant,p.Ala21Thr,ENST00000525413,;CHRDL2,missense_variant,p.Ala221Thr,ENST00000376332,;CHRDL2,non_coding_transcript_exon_variant,,ENST00000534159,;CHRDL2,3_prime_UTR_variant,,ENST00000528471,;CHRDL2,3_prime_UTR_variant,,ENST00000534276,;CHRDL2,3_prime_UTR_variant,,ENST00000376324,;	T	ENSG00000054938	ENST00000263671	Transcript	missense_variant	948	661	221	A/T	Gcc/Acc	rs200667288	.	.	-1	CHRDL2	HGNC	24168	protein_coding	YES	CCDS8234.1	ENSP00000263671	CRDL2_HUMAN	.	UPI0000034E41	.	tolerated(0.1)	benign(0.009)	7/12	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF226	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGCGCTGA	byCluster|by1000G	5	ESCA
C11orf30	0	.	GRCh37	11	76256924	76256924	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3357A>G	p.Ile1119Met	p.I1119M	ENST00000529032	19/20	33	20	13	32	32	0	C11orf30,missense_variant,p.Ile1028Met,ENST00000533248,;C11orf30,missense_variant,p.Ile1134Met,ENST00000524767,;C11orf30,missense_variant,p.Ile1021Met,ENST00000524490,;C11orf30,missense_variant,p.Ile1119Met,ENST00000334736,;C11orf30,missense_variant,p.Ile1120Met,ENST00000525919,;C11orf30,missense_variant,p.Ile1120Met,ENST00000525038,;C11orf30,missense_variant,p.Ile1119Met,ENST00000529032,;C11orf30,intron_variant,,ENST00000532719,;C11orf30,intron_variant,,ENST00000343878,;C11orf30,upstream_gene_variant,,ENST00000531793,;C11orf30,downstream_gene_variant,,ENST00000524451,;C11orf30,downstream_gene_variant,,ENST00000531641,;C11orf30,downstream_gene_variant,,ENST00000534573,;	G	ENSG00000158636	ENST00000529032	Transcript	missense_variant	3357	3357	1119	I/M	atA/atG	.	.	.	1	C11orf30	HGNC	18071	protein_coding	YES	CCDS8244.1	ENSP00000432327	EMSY_HUMAN	.	UPI0000071307	.	deleterious_low_confidence(0.03)	benign(0.307)	19/20	.	hmmpanther:PTHR16500:SF2,hmmpanther:PTHR16500	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATAACTGG	.	5	ESCA
LRRC32	0	.	GRCh37	11	76371703	76371703	+	Missense_Mutation	SNP	G	G	A	rs143082901	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934C>T	p.Arg312Cys	p.R312C	ENST00000407242	3/3	67	38	29	31	31	0	LRRC32,missense_variant,p.Arg312Cys,ENST00000260061,;LRRC32,missense_variant,p.Arg312Cys,ENST00000407242,;LRRC32,missense_variant,p.Arg312Cys,ENST00000404995,;LRRC32,downstream_gene_variant,,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,;	A	ENSG00000137507	ENST00000407242	Transcript	missense_variant	1177	934	312	R/C	Cgc/Tgc	rs143082901	.	.	-1	LRRC32	HGNC	4161	protein_coding	YES	CCDS8245.1	ENSP00000384126	LRC32_HUMAN	C9JYU3_HUMAN	UPI000012B0DF	.	tolerated(0.18)	benign(0.044)	3/3	.	Superfamily_domains:SSF52058,hmmpanther:PTHR24365:SF237,hmmpanther:PTHR24365	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0	A:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGGCCGC	byCluster|by1000G	5	ESCA
MYO7A	0	.	GRCh37	11	76901898	76901898	+	Missense_Mutation	SNP	A	A	G	rs762713039	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3907A>G	p.Ile1303Val	p.I1303V	ENST00000409709	30/49	55	35	19	22	22	0	MYO7A,missense_variant,p.Ile484Val,ENST00000458169,;MYO7A,missense_variant,p.Ile1292Val,ENST00000409619,;MYO7A,missense_variant,p.Ile1303Val,ENST00000409709,;MYO7A,missense_variant,p.Ile1303Val,ENST00000458637,;MYO7A,non_coding_transcript_exon_variant,,ENST00000481328,;MYO7A,non_coding_transcript_exon_variant,,ENST00000467137,;	G	ENSG00000137474	ENST00000409709	Transcript	missense_variant	4179	3907	1303	I/V	Att/Gtt	rs762713039	.	.	1	MYO7A	HGNC	7606	protein_coding	YES	CCDS53683.1	ENSP00000386331	MYO7A_HUMAN	.	UPI00001FAFE6	.	tolerated(0.57)	probably_damaging(0.982)	30/49	.	PROSITE_profiles:PS50057,Pfam_domain:PF09379,SMART_domains:SM00295,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTACATTGCC	byFrequency	5	ESCA
AQP11	0	.	GRCh37	11	77320575	77320575	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*161delA	.	.	ENST00000313578	3/3	35	20	14	16	16	0	AQP11,3_prime_UTR_variant,,ENST00000313578,;CLNS1A,downstream_gene_variant,,ENST00000525428,;AQP11,non_coding_transcript_exon_variant,,ENST00000528638,;CLNS1A,downstream_gene_variant,,ENST00000533957,;CLNS1A,intron_variant,,ENST00000526761,;	-	ENSG00000178301	ENST00000313578	Transcript	3_prime_UTR_variant	1327	.	.	.	.	.	.	.	1	AQP11	HGNC	19940	protein_coding	YES	CCDS8251.1	ENSP00000318770	AQP11_HUMAN	.	UPI000003B106	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GACTTTAAAAAA	.	2	ESCA
USP35	0	.	GRCh37	11	77911710	77911710	+	Frame_Shift_Del	DEL	C	C	-	rs765009852,rs778695044	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059delC	p.Met354TrpfsTer119	p.M354Wfs*119	ENST00000529308	6/11	105	64	41	31	31	0	USP35,frameshift_variant,p.Met110TrpfsTer119,ENST00000528910,;USP35,frameshift_variant,p.Met354TrpfsTer119,ENST00000529308,;USP35,frameshift_variant,p.Met85TrpfsTer119,ENST00000526425,;USP35,5_prime_UTR_variant,,ENST00000441408,;USP35,intron_variant,,ENST00000530267,;USP35,intron_variant,,ENST00000530535,;USP35,3_prime_UTR_variant,,ENST00000530546,;	-	ENSG00000118369	ENST00000529308	Transcript	frameshift_variant	1314	1053	351	I/X	atC/at	rs765009852,rs778695044,COSM1357162,COSM1357161	.	.	1	USP35	HGNC	20061	protein_coding	YES	CCDS41693.1	ENSP00000431876	UBP35_HUMAN	E9PRM2_HUMAN,E9PK78_HUMAN	UPI0000456553	.	.	.	6/11	.	hmmpanther:PTHR24006:SF343,hmmpanther:PTHR24006,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	-:0.0005	-:0.0035	.	0,0,1,1	.	.	.	.	.	HIGH	.	deletion	.	6	0,0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCACATCCCCCC	byFrequency	3	ESCA
OR5P2	0	.	GRCh37	11	7818170	7818170	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320A>T	p.Glu107Val	p.E107V	ENST00000329434	1/1	51	31	19	38	38	0	OR5P2,missense_variant,p.Glu107Val,ENST00000329434,;RP11-35J10.5,intron_variant,,ENST00000527565,;RP11-494M8.4,intron_variant,,ENST00000529488,;	A	ENSG00000183303	ENST00000329434	Transcript	missense_variant	351	320	107	E/V	gAa/gTa	.	.	.	-1	OR5P2	HGNC	14783	protein_coding	YES	CCDS7782.1	ENSP00000331823	OR5P2_HUMAN	Q6IFE0_HUMAN	UPI00000015AC	.	deleterious(0)	possibly_damaging(0.5)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF114,hmmpanther:PTHR26452,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCATTCGACT	.	5	ESCA
OR5P2	0	.	GRCh37	11	7818171	7818171	+	Nonsense_Mutation	SNP	C	C	A	rs147652902	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319G>T	p.Glu107Ter	p.E107*	ENST00000329434	1/1	52	32	19	36	36	0	OR5P2,stop_gained,p.Glu107Ter,ENST00000329434,;RP11-35J10.5,intron_variant,,ENST00000527565,;RP11-494M8.4,intron_variant,,ENST00000529488,;	A	ENSG00000183303	ENST00000329434	Transcript	stop_gained	350	319	107	E/*	Gaa/Taa	rs147652902,COSM72012	.	.	-1	OR5P2	HGNC	14783	protein_coding	YES	CCDS7782.1	ENSP00000331823	OR5P2_HUMAN	Q6IFE0_HUMAN	UPI00000015AC	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF114,hmmpanther:PTHR26452,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	T:0.0005	T:0	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTCGACTG	byCluster	5	ESCA
TUB	0	.	GRCh37	11	8060205	8060205	+	5'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-216G>T	.	.	ENST00000305253	1/13	12	5	7	18	18	0	TUB,5_prime_UTR_variant,,ENST00000305253,;TUB,intron_variant,,ENST00000534099,;RP11-236J17.6,non_coding_transcript_exon_variant,,ENST00000528151,;RP11-236J17.6,intron_variant,,ENST00000526646,;	T	ENSG00000166402	ENST00000305253	Transcript	5_prime_UTR_variant	26	.	.	.	.	.	.	.	1	TUB	HGNC	12406	protein_coding	YES	CCDS7786.1	ENSP00000305426	TUB_HUMAN	Q9H4D2_HUMAN	UPI000013EA27	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGAAGGGTTT	.	3	ESCA
RIC3	0	.	GRCh37	11	8132633	8132633	+	Missense_Mutation	SNP	C	C	T	rs575742410	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.722G>A	p.Arg241His	p.R241H	ENST00000309737	6/6	30	23	6	31	31	0	RIC3,missense_variant,p.Arg160His,ENST00000425599,;RIC3,missense_variant,p.Arg192His,ENST00000539720,;RIC3,missense_variant,p.Arg79His,ENST00000396677,;RIC3,missense_variant,p.Arg269His,ENST00000531450,;RIC3,missense_variant,p.Arg241His,ENST00000309737,;RIC3,missense_variant,p.Arg59His,ENST00000335425,;RIC3,missense_variant,p.Arg240His,ENST00000343202,;TUB,downstream_gene_variant,,ENST00000305253,;RIC3,non_coding_transcript_exon_variant,,ENST00000524799,;RIC3,non_coding_transcript_exon_variant,,ENST00000530060,;RIC3,3_prime_UTR_variant,,ENST00000526962,;RIC3,3_prime_UTR_variant,,ENST00000528463,;	T	ENSG00000166405	ENST00000309737	Transcript	missense_variant	722	722	241	R/H	cGt/cAt	rs575742410	.	.	-1	RIC3	HGNC	30338	protein_coding	YES	CCDS55742.1	ENSP00000308820	RIC3_HUMAN	F5GZ89_HUMAN	UPI00001B3DB4	.	tolerated(0.52)	benign(0.016)	6/6	.	hmmpanther:PTHR21723:SF0,hmmpanther:PTHR21723	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTACGCTTG	byFrequency|byCluster	5	ESCA
ANKRD42	0	.	GRCh37	11	82935967	82935967	+	Silent	SNP	G	G	A	rs145591736	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.573G>A	p.%3D	p.T191T	ENST00000393392	6/10	31	23	8	26	26	0	ANKRD42,synonymous_variant,p.%3D,ENST00000260047,;ANKRD42,synonymous_variant,p.%3D,ENST00000531895,;ANKRD42,synonymous_variant,p.%3D,ENST00000533342,;ANKRD42,synonymous_variant,p.%3D,ENST00000393392,;ANKRD42,upstream_gene_variant,,ENST00000531815,;	A	ENSG00000137494	ENST00000393392	Transcript	synonymous_variant	735	573	191	T	acG/acA	rs145591736,COSM197205	.	.	1	ANKRD42	HGNC	26752	protein_coding	YES	CCDS8265.1	ENSP00000377051	ANR42_HUMAN	.	UPI000013D0A8	.	.	.	6/10	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24201,hmmpanther:PTHR24201:SF2,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0002	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGACGCAAGT	byCluster|by1000G	5	ESCA
DLG2	0	.	GRCh37	11	84996271	84996271	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179C>T	p.Ser60Phe	p.S60F	ENST00000376104	4/28	85	50	34	55	55	0	DLG2,missense_variant,p.Ser60Phe,ENST00000543673,;DLG2,missense_variant,p.Ser60Phe,ENST00000376104,;	A	ENSG00000150672	ENST00000376104	Transcript	missense_variant	491	179	60	S/F	tCt/tTt	.	.	.	-1	DLG2	HGNC	2901	protein_coding	YES	CCDS44690.1	ENSP00000365272	DLG2_HUMAN	F8W750_HUMAN,E9PQT9_HUMAN	UPI0000E59399	.	tolerated_low_confidence(0.07)	benign(0.01)	4/28	.	PIRSF_domain:PIRSF001741,hmmpanther:PTHR23119:SF6,hmmpanther:PTHR23119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAGATTTT	.	5	ESCA
CTSC	0	.	GRCh37	11	88068234	88068234	+	Frame_Shift_Del	DEL	T	T	-	rs758958232,rs774553369	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189delA	p.Val64Ter	p.V64*	ENST00000227266	2/7	27	18	9	19	19	0	CTSC,frameshift_variant,p.Val64Ter,ENST00000524463,;CTSC,frameshift_variant,p.Val21Ter,ENST00000527018,;CTSC,frameshift_variant,p.Val64Ter,ENST00000529974,;CTSC,frameshift_variant,p.Val64Ter,ENST00000227266,;CTSC,non_coding_transcript_exon_variant,,ENST00000393301,;CTSC,non_coding_transcript_exon_variant,,ENST00000533865,;CTSC,non_coding_transcript_exon_variant,,ENST00000534131,;	-	ENSG00000109861	ENST00000227266	Transcript	frameshift_variant	304	189	63	K/X	aaA/aa	rs758958232,rs774553369,COSM1357598,COSM1357599	.	.	-1	CTSC	HGNC	2528	protein_coding	YES	CCDS8282.1	ENSP00000227266	CATC_HUMAN	I3V9T0_HUMAN	UPI000006D22D	.	.	.	2/7	.	Superfamily_domains:SSF75001,Gene3D:2djfA00,Pfam_domain:PF08773,hmmpanther:PTHR12411:SF314,hmmpanther:PTHR12411	.	.	.	.	.	.	.	.	.	.	0,0,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.V64fs*1|c.189delA|3,SITE|p.V64fs*1|c.189delA|3	INDELOCATOR|VARSCANI	CACTACTTTTTT	.	2	ESCA
SCUBE2	0	.	GRCh37	11	9090982	9090982	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578G>T	p.Arg193Met	p.R193M	ENST00000520467	5/22	33	19	13	20	20	0	SCUBE2,missense_variant,p.Arg193Met,ENST00000457346,;SCUBE2,missense_variant,p.Arg193Met,ENST00000450649,;SCUBE2,missense_variant,p.Arg193Met,ENST00000309263,;SCUBE2,missense_variant,p.Arg193Met,ENST00000520467,;SCUBE2,upstream_gene_variant,,ENST00000531429,;SCUBE2,upstream_gene_variant,,ENST00000519788,;RP11-467K18.2,downstream_gene_variant,,ENST00000521394,;	A	ENSG00000175356	ENST00000520467	Transcript	missense_variant	649	578	193	R/M	aGg/aTg	.	.	.	-1	SCUBE2	HGNC	30425	protein_coding	YES	CCDS7797.2	ENSP00000429969	SCUB2_HUMAN	.	UPI0001E5E848	.	tolerated(0.07)	possibly_damaging(0.819)	5/22	.	hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF3,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCCTTGGG	.	5	ESCA
DENND5A	0	.	GRCh37	11	9164987	9164987	+	Missense_Mutation	SNP	T	T	C	rs767982228	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3350A>G	p.Asn1117Ser	p.N1117S	ENST00000328194	20/23	31	13	18	24	24	0	DENND5A,missense_variant,p.Asn1117Ser,ENST00000530044,;DENND5A,missense_variant,p.Asn460Ser,ENST00000527700,;DENND5A,missense_variant,p.Asn1117Ser,ENST00000328194,;DENND5A,missense_variant,p.Asn5Ser,ENST00000533737,;DENND5A,intron_variant,,ENST00000525784,;DENND5A,intron_variant,,ENST00000528725,;DENND5A,downstream_gene_variant,,ENST00000524446,;DENND5A,3_prime_UTR_variant,,ENST00000531747,;DENND5A,non_coding_transcript_exon_variant,,ENST00000529977,;DENND5A,downstream_gene_variant,,ENST00000531580,;DENND5A,downstream_gene_variant,,ENST00000526707,;	C	ENSG00000184014	ENST00000328194	Transcript	missense_variant	3671	3350	1117	N/S	aAt/aGt	rs767982228	.	.	-1	DENND5A	HGNC	19344	protein_coding	YES	CCDS31423.1	ENSP00000328524	DEN5A_HUMAN	B3KWN5_HUMAN	UPI00001C1F29	.	deleterious(0)	probably_damaging(0.977)	20/23	.	hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF45,Superfamily_domains:0052343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCATTGACT	.	5	ESCA
MED17	0	.	GRCh37	11	93521196	93521196	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280C>T	p.Pro94Ser	p.P94S	ENST00000251871	2/12	44	26	18	52	52	0	MED17,missense_variant,p.Pro94Ser,ENST00000533359,;MED17,missense_variant,p.Pro94Ser,ENST00000530819,;MED17,missense_variant,p.Pro94Ser,ENST00000251871,;MED17,5_prime_UTR_variant,,ENST00000528786,;TAF1D,upstream_gene_variant,,ENST00000527690,;MED17,missense_variant,p.Pro94Ser,ENST00000533133,;MED17,upstream_gene_variant,,ENST00000525026,;	T	ENSG00000042429	ENST00000251871	Transcript	missense_variant	567	280	94	P/S	Cct/Tct	.	.	.	1	MED17	HGNC	2375	protein_coding	YES	CCDS8295.1	ENSP00000251871	MED17_HUMAN	E9PJZ4_HUMAN	UPI000013CD1D	.	deleterious(0)	possibly_damaging(0.729)	2/12	.	Pfam_domain:PF10156,hmmpanther:PTHR13114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGGCCTTGG	.	5	ESCA
HEPHL1	0	.	GRCh37	11	93796775	93796775	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.517G>A	p.Ala173Thr	p.A173T	ENST00000315765	3/20	78	54	24	35	35	0	HEPHL1,missense_variant,p.Ala173Thr,ENST00000315765,;	A	ENSG00000181333	ENST00000315765	Transcript	missense_variant	525	517	173	A/T	Gca/Aca	.	.	.	1	HEPHL1	HGNC	30477	protein_coding	YES	CCDS44710.1	ENSP00000313699	HPHL1_HUMAN	.	UPI0000237563	.	deleterious(0)	probably_damaging(0.938)	3/20	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF615,Pfam_domain:PF07732,Gene3D:2.60.40.420,Superfamily_domains:SSF49503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATGCACCT	.	5	ESCA
SRSF8	0	.	GRCh37	11	94802335	94802336	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1101dupA	.	.	ENST00000529911	1/1	20	10	10	13	13	0	SRSF8,3_prime_UTR_variant,,ENST00000529911,;SRSF8,non_coding_transcript_exon_variant,,ENST00000446101,;	A	ENSG00000271885	ENST00000529911	Transcript	3_prime_UTR_variant	1975-1976	.	.	.	.	.	.	.	1	SRSF8	Clone_based_vega_gene	16988	polymorphic_pseudogene	YES	.	ENSP00000475842	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTGAGAAAAT	.	2	ESCA
CCDC82	0	.	GRCh37	11	96117597	96117597	+	Silent	SNP	G	G	A	rs774545821	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315C>T	p.%3D	p.N105N	ENST00000278520	3/9	145	85	60	87	87	0	CCDC82,synonymous_variant,p.%3D,ENST00000542662,;CCDC82,synonymous_variant,p.%3D,ENST00000538597,;CCDC82,synonymous_variant,p.%3D,ENST00000278520,;CCDC82,synonymous_variant,p.%3D,ENST00000423339,;CCDC82,downstream_gene_variant,,ENST00000530203,;CCDC82,downstream_gene_variant,,ENST00000524836,;CCDC82,downstream_gene_variant,,ENST00000525786,;CCDC82,non_coding_transcript_exon_variant,,ENST00000530106,;	A	ENSG00000149231	ENST00000278520	Transcript	synonymous_variant	744	315	105	N	aaC/aaT	rs774545821,COSM933666	.	.	-1	CCDC82	HGNC	26282	protein_coding	YES	CCDS8307.1	ENSP00000278520	CCD82_HUMAN	F5H777_HUMAN,E9PMD6_HUMAN	UPI000007367A	.	.	.	3/9	.	Pfam_domain:PF13846,hmmpanther:PTHR14689,hmmpanther:PTHR14689:SF1	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACCGTTGCC	byFrequency	5	ESCA
NT5DC3	0	.	GRCh37	12	104187260	104187260	+	Missense_Mutation	SNP	C	C	T	rs200566738	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.845G>A	p.Arg282His	p.R282H	ENST00000392876	8/14	48	37	11	27	27	0	NT5DC3,missense_variant,p.Arg282His,ENST00000392876,;NT5DC3,upstream_gene_variant,,ENST00000474268,;NT5DC3,downstream_gene_variant,,ENST00000465502,;NT5DC3,upstream_gene_variant,,ENST00000415849,;	T	ENSG00000111696	ENST00000392876	Transcript	missense_variant	886	845	282	R/H	cGc/cAc	rs200566738	.	.	-1	NT5DC3	HGNC	30826	protein_coding	YES	CCDS41824.1	ENSP00000376615	NT5D3_HUMAN	.	UPI0000192759	.	tolerated(0.6)	benign(0.006)	8/14	.	Superfamily_domains:SSF56784,PIRSF_domain:PIRSF017434,Pfam_domain:PF05761,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR02244,hmmpanther:PTHR12103,hmmpanther:PTHR12103:SF11	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCGCGGGTC	byFrequency|byCluster	5	ESCA
HSP90B1	0	.	GRCh37	12	104341424	104341424	+	Frame_Shift_Del	DEL	A	A	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2400delA	p.Asp801MetfsTer56	p.D801Mfs*56	ENST00000299767	18/18	91	54	37	49	49	0	HSP90B1,frameshift_variant,p.Asp801MetfsTer56,ENST00000299767,;HSP90B1,intron_variant,,ENST00000550595,;C12orf73,downstream_gene_variant,,ENST00000553183,;C12orf73,downstream_gene_variant,,ENST00000549478,;C12orf73,downstream_gene_variant,,ENST00000547945,;C12orf73,downstream_gene_variant,,ENST00000547975,;C12orf73,downstream_gene_variant,,ENST00000552940,;C12orf73,downstream_gene_variant,,ENST00000378090,;C12orf73,downstream_gene_variant,,ENST00000543740,;HSP90B1,non_coding_transcript_exon_variant,,ENST00000548462,;C12orf73,downstream_gene_variant,,ENST00000552460,;C12orf73,downstream_gene_variant,,ENST00000549960,;HSP90B1,downstream_gene_variant,,ENST00000552051,;HSP90B1,downstream_gene_variant,,ENST00000551983,;	-	ENSG00000166598	ENST00000299767	Transcript	frameshift_variant	2578	2396	799	E/X	gAa/ga	COSM934202	.	.	1	HSP90B1	HGNC	12028	protein_coding	YES	CCDS9094.1	ENSP00000299767	ENPL_HUMAN	Q5CAQ5_HUMAN,F8W026_HUMAN,B4DHT9_HUMAN	UPI0000129FBA	.	.	.	18/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11528,hmmpanther:PTHR11528:SF44	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	4	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGCTGAAAAAG	.	3	ESCA
NUAK1	0	.	GRCh37	12	106457424	106457424	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3156delT	.	.	ENST00000261402	7/7	19	11	8	18	18	0	NUAK1,3_prime_UTR_variant,,ENST00000261402,;NUAK1,downstream_gene_variant,,ENST00000548902,;NUAK1,downstream_gene_variant,,ENST00000553094,;NUAK1,downstream_gene_variant,,ENST00000549704,;	-	ENSG00000074590	ENST00000261402	Transcript	3_prime_UTR_variant	6522	.	.	.	.	.	.	.	-1	NUAK1	HGNC	14311	protein_coding	YES	CCDS31892.1	ENSP00000261402	NUAK1_HUMAN	F8VZ96_HUMAN,F8VXF0_HUMAN,F8VSH4_HUMAN	UPI00000403BC	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTACCAAAAAA	.	2	ESCA
POLR3B	0	.	GRCh37	12	106751627	106751630	+	5'UTR	DEL	TCTA	TCTA	-	rs767199959	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TCTA	TCTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-28_-25delATCT	.	.	ENST00000228347	1/28	71	61	10	31	31	0	POLR3B,5_prime_UTR_variant,,ENST00000228347,;POLR3B,upstream_gene_variant,,ENST00000539066,;	-	ENSG00000013503	ENST00000228347	Transcript	5_prime_UTR_variant	192-195	.	.	.	.	rs767199959	.	.	1	POLR3B	HGNC	30348	protein_coding	YES	CCDS9105.1	ENSP00000228347	RPC2_HUMAN	F8VRU2_HUMAN,B3KRQ8_HUMAN	UPI000000DB67	.	.	.	1/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAGGTTCTATCTGT	byFrequency	3	ESCA
POLR3B	0	.	GRCh37	12	106890645	106890645	+	Missense_Mutation	SNP	G	G	A	rs117293015	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2933G>A	p.Arg978His	p.R978H	ENST00000228347	25/28	107	84	22	86	86	0	POLR3B,missense_variant,p.Arg920His,ENST00000539066,;POLR3B,missense_variant,p.Arg978His,ENST00000228347,;RP11-144F15.1,intron_variant,,ENST00000551505,;RP11-144F15.1,intron_variant,,ENST00000549203,;	A	ENSG00000013503	ENST00000228347	Transcript	missense_variant	3155	2933	978	R/H	cGc/cAc	rs117293015,COSM934414	.	.	1	POLR3B	HGNC	30348	protein_coding	YES	CCDS9105.1	ENSP00000228347	RPC2_HUMAN	F8VRU2_HUMAN,B3KRQ8_HUMAN	UPI000000DB67	.	tolerated(0.05)	possibly_damaging(0.671)	25/28	.	hmmpanther:PTHR20856,hmmpanther:PTHR20856:SF8,Gene3D:2a6hC01,Pfam_domain:PF00562,Superfamily_domains:SSF64484	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0	A:0.0003	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTTCGCCATG	byCluster|by1000G	5	ESCA
TCHP	0	.	GRCh37	12	110350842	110350842	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1099C>T	p.Arg367Ter	p.R367*	ENST00000312777	10/13	50	37	13	25	25	0	TCHP,stop_gained,p.Arg367Ter,ENST00000312777,;TCHP,stop_gained,p.Arg367Ter,ENST00000405876,;TCHP,stop_gained,p.Arg367Ter,ENST00000544838,;TCHP,non_coding_transcript_exon_variant,,ENST00000551627,;TCHP,non_coding_transcript_exon_variant,,ENST00000549550,;TCHP,upstream_gene_variant,,ENST00000537880,;	T	ENSG00000139437	ENST00000312777	Transcript	stop_gained	1313	1099	367	R/*	Cga/Tga	.	.	.	1	TCHP	HGNC	28135	protein_coding	YES	CCDS9137.1	ENSP00000324404	TCHP_HUMAN	F5GWH6_HUMAN	UPI000006E329	.	.	.	10/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31183,hmmpanther:PTHR31183:SF2,Pfam_domain:PF13868	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCCGAGAG	.	5	ESCA
TCHP	0	.	GRCh37	12	110353217	110353217	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1330C>T	p.Arg444Cys	p.R444C	ENST00000312777	12/13	45	21	23	32	32	0	TCHP,missense_variant,p.Arg444Cys,ENST00000312777,;TCHP,missense_variant,p.Arg444Cys,ENST00000405876,;TCHP,missense_variant,p.Arg444Cys,ENST00000544838,;TCHP,non_coding_transcript_exon_variant,,ENST00000551627,;TCHP,non_coding_transcript_exon_variant,,ENST00000537880,;TCHP,downstream_gene_variant,,ENST00000549550,;	T	ENSG00000139437	ENST00000312777	Transcript	missense_variant	1544	1330	444	R/C	Cgc/Tgc	COSM934886	.	.	1	TCHP	HGNC	28135	protein_coding	YES	CCDS9137.1	ENSP00000324404	TCHP_HUMAN	F5GWH6_HUMAN	UPI000006E329	.	deleterious(0.01)	benign(0.159)	12/13	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31183,hmmpanther:PTHR31183:SF2,Pfam_domain:PF13868	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGCGCCGG	.	5	ESCA
ATP2A2	0	.	GRCh37	12	110777173	110777173	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1507C>T	p.Pro503Ser	p.P503S	ENST00000539276	12/20	30	10	20	23	23	0	ATP2A2,missense_variant,p.Pro394Ser,ENST00000548169,;ATP2A2,missense_variant,p.Pro503Ser,ENST00000308664,;ATP2A2,missense_variant,p.Pro476Ser,ENST00000395494,;ATP2A2,missense_variant,p.Pro503Ser,ENST00000539276,;ATP2A2,3_prime_UTR_variant,,ENST00000377685,;ATP2A2,upstream_gene_variant,,ENST00000547792,;	T	ENSG00000174437	ENST00000539276	Transcript	missense_variant	1616	1507	503	P/S	Cca/Tca	.	.	.	1	ATP2A2	HGNC	812	protein_coding	YES	CCDS9144.1	ENSP00000440045	AT2A2_HUMAN	.	UPI0000001C3A	.	tolerated(0.35)	benign(0.006)	12/20	.	hmmpanther:PTHR24093:SF234,hmmpanther:PTHR24093,Pfam_domain:PF13246,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01116,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAAACCAAGC	.	5	ESCA
CUX2	0	.	GRCh37	12	111748477	111748477	+	Missense_Mutation	SNP	C	C	T	rs761088744	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1891C>T	p.Arg631Trp	p.R631W	ENST00000261726	15/22	21	15	5	12	12	0	CUX2,missense_variant,p.Arg631Trp,ENST00000261726,;	T	ENSG00000111249	ENST00000261726	Transcript	missense_variant	2045	1891	631	R/W	Cgg/Tgg	rs761088744	.	.	1	CUX2	HGNC	19347	protein_coding	YES	CCDS41837.1	ENSP00000261726	CUX2_HUMAN	Q9BZX3_HUMAN,Q9BZV4_HUMAN	UPI00001FBB07	.	deleterious(0)	probably_damaging(0.999)	15/22	.	PROSITE_profiles:PS51042,hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTGCGGCAG	.	5	ESCA
HECTD4	0	.	GRCh37	12	112630932	112630932	+	Missense_Mutation	SNP	C	C	T	rs374889610	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8581G>A	p.Val2861Met	p.V2861M	ENST00000550722	58/76	44	35	9	46	46	0	HECTD4,missense_variant,p.Val2585Met,ENST00000430131,;HECTD4,missense_variant,p.Val2861Met,ENST00000550722,;HECTD4,missense_variant,p.Val2835Met,ENST00000377560,;HECTD4,downstream_gene_variant,,ENST00000548896,;	T	ENSG00000173064	ENST00000550722	Transcript	missense_variant	8977	8581	2861	V/M	Gtg/Atg	rs374889610	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	probably_damaging(0.975)	58/76	.	hmmpanther:PTHR11254:SF286,hmmpanther:PTHR11254	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCACGTCCA	byFrequency|byCluster	5	ESCA
SDS	0	.	GRCh37	12	113831717	113831717	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758C>T	p.Ala253Val	p.A253V	ENST00000257549	7/8	26	14	12	12	12	0	SDS,missense_variant,p.Ala253Val,ENST00000257549,;PLBD2,downstream_gene_variant,,ENST00000280800,;PLBD2,downstream_gene_variant,,ENST00000545182,;SDS,downstream_gene_variant,,ENST00000547342,;SDS,downstream_gene_variant,,ENST00000552280,;SDS,downstream_gene_variant,,ENST00000546639,;SDS,downstream_gene_variant,,ENST00000553112,;	A	ENSG00000135094	ENST00000257549	Transcript	missense_variant	881	758	253	A/V	gCc/gTc	.	.	.	-1	SDS	HGNC	10691	protein_coding	YES	CCDS9169.1	ENSP00000257549	SDHL_HUMAN	.	UPI000013CF6B	.	tolerated(0.29)	benign(0.022)	7/8	.	hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF73,Pfam_domain:PF00291,Gene3D:3.40.50.1100,Superfamily_domains:SSF53686	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCGGCCACA	.	5	ESCA
MED13L	0	.	GRCh37	12	116418612	116418612	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5307A>G	p.%3D	p.K1769K	ENST00000281928	23/31	39	19	20	33	33	0	MED13L,synonymous_variant,p.%3D,ENST00000552340,;MED13L,synonymous_variant,p.%3D,ENST00000281928,;MED13L,downstream_gene_variant,,ENST00000549786,;MED13L,non_coding_transcript_exon_variant,,ENST00000548694,;	C	ENSG00000123066	ENST00000281928	Transcript	synonymous_variant	5514	5307	1769	K	aaA/aaG	.	.	.	-1	MED13L	HGNC	22962	protein_coding	YES	CCDS9177.1	ENSP00000281928	MD13L_HUMAN	Q9H6Z7_HUMAN	UPI0000241C1E	.	.	.	23/31	.	Pfam_domain:PF06333,hmmpanther:PTHR12950,hmmpanther:PTHR12950:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGATTTAAT	.	5	ESCA
NOS1	0	.	GRCh37	12	117768638	117768638	+	Silent	SNP	G	G	A	rs201853230	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237C>T	p.%3D	p.S79S	ENST00000338101	1/29	40	19	21	18	18	0	NOS1,synonymous_variant,p.%3D,ENST00000344089,;NOS1,synonymous_variant,p.%3D,ENST00000317775,;NOS1,synonymous_variant,p.%3D,ENST00000338101,;NOS1,downstream_gene_variant,,ENST00000549189,;	A	ENSG00000089250	ENST00000338101	Transcript	synonymous_variant	242	237	79	S	agC/agT	rs201853230	.	.	-1	NOS1	HGNC	7872	protein_coding	YES	CCDS55890.1	ENSP00000337459	NOS1_HUMAN	A0PJJ7_HUMAN	UPI00001FBC10	.	.	.	1/29	.	Superfamily_domains:SSF50156,SMART_domains:SM00228,PIRSF_domain:PIRSF000333,Pfam_domain:PF00595,Gene3D:2.30.42.10,PROSITE_profiles:PS50106	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGCGCTGTC	byFrequency|byCluster|by1000G	5	ESCA
PXN	0	.	GRCh37	12	120652715	120652715	+	Silent	SNP	G	G	A	rs746357371	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1233C>T	p.%3D	p.F411F	ENST00000267257	8/11	94	43	51	59	59	0	PXN,synonymous_variant,p.%3D,ENST00000228307,;PXN,synonymous_variant,p.%3D,ENST00000458477,;PXN,synonymous_variant,p.%3D,ENST00000267257,;PXN,synonymous_variant,p.%3D,ENST00000424649,;PXN,synonymous_variant,p.%3D,ENST00000550795,;PXN,synonymous_variant,p.%3D,ENST00000397506,;PXN,synonymous_variant,p.%3D,ENST00000536957,;PXN-AS1,downstream_gene_variant,,ENST00000535200,;PXN-AS1,downstream_gene_variant,,ENST00000539446,;PXN-AS1,downstream_gene_variant,,ENST00000538804,;PXN-AS1,downstream_gene_variant,,ENST00000542314,;PXN-AS1,downstream_gene_variant,,ENST00000542265,;PXN,non_coding_transcript_exon_variant,,ENST00000538144,;PXN,non_coding_transcript_exon_variant,,ENST00000323871,;	A	ENSG00000089159	ENST00000267257	Transcript	synonymous_variant	1364	1233	411	F	ttC/ttT	rs746357371	.	.	-1	PXN	HGNC	9718	protein_coding	YES	CCDS58281.1	ENSP00000267257	PAXI_HUMAN	F8W1E0_HUMAN,F8W0K8_HUMAN,F8W0G0_HUMAN	UPI000013C8CD	.	.	.	8/11	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24216,hmmpanther:PTHR24216:SF11,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTCGAAGAA	.	5	ESCA
MSI1	0	.	GRCh37	12	120779262	120779262	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1668delT	.	.	ENST00000257552	15/15	25	15	10	16	15	0	MSI1,3_prime_UTR_variant,,ENST00000257552,;MSI1,downstream_gene_variant,,ENST00000546985,;	-	ENSG00000135097	ENST00000257552	Transcript	3_prime_UTR_variant	2846	.	.	.	.	.	.	.	-1	MSI1	HGNC	7330	protein_coding	YES	CCDS9196.1	ENSP00000257552	MSI1H_HUMAN	B3KN16_HUMAN	UPI0000073DD8	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CATCTTAAAAAA	.	2	ESCA
RNF10	0	.	GRCh37	12	120984267	120984267	+	Frame_Shift_Del	DEL	A	A	-	rs757634356	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221delA	p.Asn74MetfsTer46	p.N74Mfs*46	ENST00000325954	2/17	35	25	10	26	26	0	RNF10,frameshift_variant,p.Asn74MetfsTer46,ENST00000413266,;RNF10,frameshift_variant,p.Asn74MetfsTer46,ENST00000325954,;RNF10,frameshift_variant,p.Asn24MetfsTer46,ENST00000537997,;RNF10,intron_variant,,ENST00000542438,;RNF10,non_coding_transcript_exon_variant,,ENST00000543578,;RNF10,non_coding_transcript_exon_variant,,ENST00000551139,;RNF10,frameshift_variant,p.Asn54MetfsTer?,ENST00000536869,;RNF10,3_prime_UTR_variant,,ENST00000538796,;	-	ENSG00000022840	ENST00000325954	Transcript	frameshift_variant	678	217	73	K/X	Aaa/aa	rs757634356	.	.	1	RNF10	HGNC	10055	protein_coding	YES	CCDS9201.1	ENSP00000322242	RNF10_HUMAN	F5H3A4_HUMAN	UPI000006D77E	.	.	.	2/17	.	hmmpanther:PTHR12983	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TACCCCAAAAAT	byFrequency	3	ESCA
MLEC	0	.	GRCh37	12	121138085	121138085	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3737C>A	.	.	ENST00000228506	5/5	99	57	41	56	56	0	MLEC,3_prime_UTR_variant,,ENST00000228506,;MLEC,downstream_gene_variant,,ENST00000412616,;MLEC,downstream_gene_variant,,ENST00000535656,;MLEC,downstream_gene_variant,,ENST00000545525,;RP11-173P15.3,upstream_gene_variant,,ENST00000541383,;RP11-173P15.3,upstream_gene_variant,,ENST00000535720,;MLEC,intron_variant,,ENST00000535413,;	A	ENSG00000110917	ENST00000228506	Transcript	3_prime_UTR_variant	5044	.	.	.	.	.	.	.	1	MLEC	HGNC	28973	protein_coding	YES	CCDS9206.1	ENSP00000228506	MLEC_HUMAN	F5H1S8_HUMAN	UPI000013938A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCCCTTCC	.	5	ESCA
HNF1A	0	.	GRCh37	12	121437180	121437180	+	Silent	SNP	G	G	A	rs199511735	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1611G>A	p.%3D	p.T537T	ENST00000257555	8/10	107	84	22	46	46	0	HNF1A,synonymous_variant,p.%3D,ENST00000544413,;HNF1A,synonymous_variant,p.%3D,ENST00000541395,;HNF1A,synonymous_variant,p.%3D,ENST00000257555,;C12orf43,downstream_gene_variant,,ENST00000538296,;C12orf43,downstream_gene_variant,,ENST00000288757,;HNF1A,downstream_gene_variant,,ENST00000400024,;HNF1A,downstream_gene_variant,,ENST00000402929,;C12orf43,downstream_gene_variant,,ENST00000546272,;C12orf43,downstream_gene_variant,,ENST00000536407,;C12orf43,downstream_gene_variant,,ENST00000539736,;C12orf43,downstream_gene_variant,,ENST00000445832,;C12orf43,downstream_gene_variant,,ENST00000535367,;HNF1A,downstream_gene_variant,,ENST00000538626,;C12orf43,downstream_gene_variant,,ENST00000366211,;HNF1A,downstream_gene_variant,,ENST00000543427,;C12orf43,downstream_gene_variant,,ENST00000537817,;HNF1A,downstream_gene_variant,,ENST00000535955,;RP11-216P16.2,downstream_gene_variant,,ENST00000606238,;HNF1A,3_prime_UTR_variant,,ENST00000560968,;HNF1A,3_prime_UTR_variant,,ENST00000540108,;C12orf43,downstream_gene_variant,,ENST00000502891,;HNF1A,downstream_gene_variant,,ENST00000544574,;HNF1A,downstream_gene_variant,,ENST00000541924,;C12orf43,downstream_gene_variant,,ENST00000539088,;HNF1A,downstream_gene_variant,,ENST00000543255,;HNF1A,downstream_gene_variant,,ENST00000538646,;	A	ENSG00000135100	ENST00000257555	Transcript	synonymous_variant	1837	1611	537	T	acG/acA	rs199511735,CD083317,COSM269326	.	.	1	HNF1A	HGNC	11621	protein_coding	YES	CCDS9209.1	ENSP00000257555	.	E0YMJ2_HUMAN,E0YMJ1_HUMAN,B8YNW1_HUMAN,B8YNU9_HUMAN	UPI000013CF6C	.	.	.	8/10	.	hmmpanther:PTHR11568:SF4,hmmpanther:PTHR11568,Pfam_domain:PF04812	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACGCCCAC	byCluster|by1000G	5	ESCA
B3GNT4	0	.	GRCh37	12	122691380	122691380	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.582G>A	p.%3D	p.T194T	ENST00000324189	3/3	47	22	24	32	32	0	B3GNT4,synonymous_variant,p.%3D,ENST00000535274,;B3GNT4,synonymous_variant,p.%3D,ENST00000546192,;B3GNT4,synonymous_variant,p.%3D,ENST00000324189,;DIABLO,downstream_gene_variant,,ENST00000540535,;DIABLO,downstream_gene_variant,,ENST00000474004,;DIABLO,downstream_gene_variant,,ENST00000541656,;DIABLO,downstream_gene_variant,,ENST00000353548,;DIABLO,downstream_gene_variant,,ENST00000464942,;DIABLO,downstream_gene_variant,,ENST00000413918,;DIABLO,downstream_gene_variant,,ENST00000541273,;DIABLO,downstream_gene_variant,,ENST00000446652,;DIABLO,downstream_gene_variant,,ENST00000439489,;DIABLO,downstream_gene_variant,,ENST00000267169,;LRRC43,downstream_gene_variant,,ENST00000425921,;LRRC43,downstream_gene_variant,,ENST00000339777,;DIABLO,downstream_gene_variant,,ENST00000443649,;B3GNT4,non_coding_transcript_exon_variant,,ENST00000538257,;B3GNT4,non_coding_transcript_exon_variant,,ENST00000537991,;B3GNT4,intron_variant,,ENST00000545141,;LRRC43,downstream_gene_variant,,ENST00000537733,;DIABLO,downstream_gene_variant,,ENST00000342392,;RP11-512M8.5,downstream_gene_variant,,ENST00000535844,;	A	ENSG00000176383	ENST00000324189	Transcript	synonymous_variant	938	582	194	T	acG/acA	.	.	.	1	B3GNT4	HGNC	15683	protein_coding	YES	CCDS9227.1	ENSP00000319636	B3GN4_HUMAN	.	UPI0000051E30	.	.	.	3/3	.	hmmpanther:PTHR11214:SF27,hmmpanther:PTHR11214,Pfam_domain:PF01762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACGCTCAA	.	5	ESCA
CLIP1	0	.	GRCh37	12	122756484	122756484	+	3'Flank	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000540338	.	33	25	8	42	42	0	CLIP1,3_prime_UTR_variant,,ENST00000302528,;CLIP1,3_prime_UTR_variant,,ENST00000361654,;CLIP1,3_prime_UTR_variant,,ENST00000545889,;CLIP1,3_prime_UTR_variant,,ENST00000358808,;CLIP1,downstream_gene_variant,,ENST00000537178,;CLIP1,downstream_gene_variant,,ENST00000540539,;CLIP1,downstream_gene_variant,,ENST00000540338,;CLIP1,downstream_gene_variant,,ENST00000536634,;CLIP1,downstream_gene_variant,,ENST00000501271,;CLIP1,downstream_gene_variant,,ENST00000538120,;	-	ENSG00000130779	ENST00000540338	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	897	-1	CLIP1	HGNC	10461	protein_coding	YES	CCDS58285.1	ENSP00000439093	CLIP1_HUMAN	F5H367_HUMAN,F5H270_HUMAN	UPI0000E00D4E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAAGGAAAAAA	.	2	ESCA
KNTC1	0	.	GRCh37	12	123036051	123036051	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1177G>A	p.Glu393Lys	p.E393K	ENST00000333479	15/64	46	35	10	39	39	0	KNTC1,missense_variant,p.Glu356Lys,ENST00000450485,;KNTC1,missense_variant,p.Glu393Lys,ENST00000333479,;	A	ENSG00000184445	ENST00000333479	Transcript	missense_variant	1354	1177	393	E/K	Gaa/Aaa	.	.	.	1	KNTC1	HGNC	17255	protein_coding	YES	CCDS45002.1	ENSP00000328236	KNTC1_HUMAN	J3KQF2_HUMAN,F5H5V0_HUMAN	UPI0000047FD6	.	deleterious(0.02)	probably_damaging(0.956)	15/64	.	hmmpanther:PTHR15688:SF1,hmmpanther:PTHR15688	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACGGAAGCT	.	5	ESCA
DNAH10	0	.	GRCh37	12	124417966	124417966	+	Missense_Mutation	SNP	G	G	A	rs755986415,rs765072673	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13031G>A	p.Arg4344Gln	p.R4344Q	ENST00000409039	76/78	75	31	44	42	42	0	DNAH10,missense_variant,p.Arg4344Gln,ENST00000409039,;DNAH10OS,intron_variant,,ENST00000514254,;CCDC92,downstream_gene_variant,,ENST00000545135,;CCDC92,downstream_gene_variant,,ENST00000539551,;CCDC92,downstream_gene_variant,,ENST00000238156,;CCDC92,downstream_gene_variant,,ENST00000539761,;CCDC92,downstream_gene_variant,,ENST00000545891,;CCDC92,downstream_gene_variant,,ENST00000535556,;RP11-380L11.3,downstream_gene_variant,,ENST00000602292,;DNAH10,non_coding_transcript_exon_variant,,ENST00000538983,;CCDC92,intron_variant,,ENST00000544798,;CCDC92,intron_variant,,ENST00000542348,;DNAH10,non_coding_transcript_exon_variant,,ENST00000492261,;DNAH10,downstream_gene_variant,,ENST00000545078,;	A	ENSG00000197653	ENST00000409039	Transcript	missense_variant	13056	13031	4344	R/Q	cGg/cAg	rs755986415,rs765072673,COSM430652,COSM430653	.	.	1	DNAH10	HGNC	2941	protein_coding	YES	CCDS9255.2	ENSP00000386770	DYH10_HUMAN	.	UPI00014F7B89	.	.	probably_damaging(0.999)	76/78	.	hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF03028	.	.	.	.	.	.	.	-:0.0003	-:0.001	.	0,0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCGGAAGA	byFrequency|byCluster	5	ESCA
NCOR2	0	.	GRCh37	12	124862853	124862853	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2097G>A	p.%3D	p.V699V	ENST00000405201	18/47	75	64	11	42	42	0	NCOR2,synonymous_variant,p.%3D,ENST00000356219,;NCOR2,synonymous_variant,p.%3D,ENST00000458234,;NCOR2,synonymous_variant,p.%3D,ENST00000404121,;NCOR2,synonymous_variant,p.%3D,ENST00000429285,;NCOR2,synonymous_variant,p.%3D,ENST00000405201,;NCOR2,synonymous_variant,p.%3D,ENST00000404621,;NCOR2,synonymous_variant,p.%3D,ENST00000448614,;NCOR2,synonymous_variant,p.%3D,ENST00000397355,;	T	ENSG00000196498	ENST00000405201	Transcript	synonymous_variant	2098	2097	699	V	gtG/gtA	.	.	.	-1	NCOR2	HGNC	7673	protein_coding	YES	CCDS41858.2	ENSP00000384018	.	C9JFD3_HUMAN,C9J330_HUMAN	UPI000013D737	.	.	.	18/47	.	hmmpanther:PTHR13992:SF21,hmmpanther:PTHR13992	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCACCACGGG	.	4	ESCA
TMEM132B	0	.	GRCh37	12	126138243	126138243	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2224G>A	p.Glu742Lys	p.E742K	ENST00000299308	9/9	61	43	18	63	63	0	TMEM132B,missense_variant,p.Glu254Lys,ENST00000535886,;TMEM132B,missense_variant,p.Glu742Lys,ENST00000299308,;	A	ENSG00000139364	ENST00000299308	Transcript	missense_variant	2232	2224	742	E/K	Gag/Aag	.	.	.	1	TMEM132B	HGNC	29397	protein_coding	YES	CCDS41859.1	ENSP00000299308	T132B_HUMAN	.	UPI00006BFF58	.	tolerated(0.83)	benign(0.018)	9/9	.	hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGAGTCC	.	5	ESCA
TMEM132C	0	.	GRCh37	12	128899918	128899918	+	Missense_Mutation	SNP	G	G	A	rs544445512	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.727G>A	p.Gly243Arg	p.G243R	ENST00000435159	2/9	54	27	26	21	21	0	TMEM132C,missense_variant,p.Gly243Arg,ENST00000435159,;	A	ENSG00000181234	ENST00000435159	Transcript	missense_variant	727	727	243	G/R	Ggg/Agg	rs544445512	.	.	1	TMEM132C	HGNC	25436	protein_coding	YES	.	ENSP00000410852	T132C_HUMAN	F5H439_HUMAN,E9PC33_HUMAN	UPI0001C0B37C	.	tolerated(0.45)	benign(0.014)	2/9	.	hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCCGGGGGT	.	5	ESCA
RIMBP2	0	.	GRCh37	12	130898732	130898732	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2590A>G	p.Met864Val	p.M864V	ENST00000261655	14/19	54	32	22	36	36	0	RIMBP2,start_lost,p.Met1?,ENST00000536632,;RIMBP2,missense_variant,p.Met864Val,ENST00000261655,;	C	ENSG00000060709	ENST00000261655	Transcript	missense_variant	2754	2590	864	M/V	Atg/Gtg	.	.	.	-1	RIMBP2	HGNC	30339	protein_coding	YES	CCDS31925.1	ENSP00000261655	RIMB2_HUMAN	F5H3X3_HUMAN	UPI00001C1F42	.	deleterious(0)	possibly_damaging(0.883)	14/19	.	PROSITE_profiles:PS50002,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18,Pfam_domain:PF07653,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACATGGTGA	.	5	ESCA
KIAA1467	0	.	GRCh37	12	13232776	13232776	+	Missense_Mutation	SNP	C	C	T	rs756086154	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1696C>T	p.Pro566Ser	p.P566S	ENST00000197268	12/13	91	51	40	52	52	0	KIAA1467,missense_variant,p.Pro566Ser,ENST00000197268,;KIAA1467,intron_variant,,ENST00000537625,;GSG1,downstream_gene_variant,,ENST00000396310,;GSG1,downstream_gene_variant,,ENST00000432710,;GSG1,downstream_gene_variant,,ENST00000324458,;GSG1,downstream_gene_variant,,ENST00000351606,;GSG1,downstream_gene_variant,,ENST00000396302,;GSG1,downstream_gene_variant,,ENST00000537302,;GSG1,downstream_gene_variant,,ENST00000337630,;GSG1,downstream_gene_variant,,ENST00000457134,;KIAA1467,missense_variant,p.Pro566Ser,ENST00000416494,;KIAA1467,non_coding_transcript_exon_variant,,ENST00000541950,;	T	ENSG00000084444	ENST00000197268	Transcript	missense_variant	1816	1696	566	P/S	Cca/Tca	rs756086154	.	.	1	KIAA1467	HGNC	29288	protein_coding	YES	CCDS31750.1	ENSP00000197268	K1467_HUMAN	.	UPI00001FB6A1	.	deleterious(0.01)	possibly_damaging(0.522)	12/13	.	hmmpanther:PTHR21419,hmmpanther:PTHR21419:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S568T|c.1702T>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCCAAGC	.	5	ESCA
LMO3	0	.	GRCh37	12	16713448	16713448	+	Silent	SNP	G	G	A	rs149014326	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297C>T	p.%3D	p.C99C	ENST00000540445	5/6	28	22	5	14	14	0	LMO3,synonymous_variant,p.%3D,ENST00000354662,;LMO3,synonymous_variant,p.%3D,ENST00000447609,;LMO3,synonymous_variant,p.%3D,ENST00000545436,;LMO3,synonymous_variant,p.%3D,ENST00000541846,;LMO3,synonymous_variant,p.%3D,ENST00000541295,;LMO3,synonymous_variant,p.%3D,ENST00000546279,;LMO3,synonymous_variant,p.%3D,ENST00000540848,;LMO3,synonymous_variant,p.%3D,ENST00000540445,;LMO3,synonymous_variant,p.%3D,ENST00000534946,;LMO3,synonymous_variant,p.%3D,ENST00000539534,;LMO3,synonymous_variant,p.%3D,ENST00000537304,;LMO3,synonymous_variant,p.%3D,ENST00000546281,;LMO3,synonymous_variant,p.%3D,ENST00000320122,;LMO3,synonymous_variant,p.%3D,ENST00000441439,;LMO3,synonymous_variant,p.%3D,ENST00000538051,;LMO3,synonymous_variant,p.%3D,ENST00000535535,;LMO3,synonymous_variant,p.%3D,ENST00000537757,;LMO3,synonymous_variant,p.%3D,ENST00000540590,;LMO3,synonymous_variant,p.%3D,ENST00000261169,;LMO3,non_coding_transcript_exon_variant,,ENST00000332914,;LMO3,non_coding_transcript_exon_variant,,ENST00000536509,;MGST1,intron_variant,,ENST00000538857,;MGST1,intron_variant,,ENST00000539036,;LMO3,missense_variant,p.Arg58Cys,ENST00000536172,;LMO3,missense_variant,p.Arg58Cys,ENST00000453727,;LMO3,missense_variant,p.Arg58Cys,ENST00000541589,;LMO3,missense_variant,p.Arg58Cys,ENST00000539232,;LMO3,3_prime_UTR_variant,,ENST00000544754,;LMO3,3_prime_UTR_variant,,ENST00000424192,;LMO3,3_prime_UTR_variant,,ENST00000396205,;LMO3,3_prime_UTR_variant,,ENST00000541764,;	A	ENSG00000048540	ENST00000540445	Transcript	synonymous_variant	522	297	99	C	tgC/tgT	rs149014326,COSM4040624	.	.	-1	LMO3	HGNC	6643	protein_coding	YES	CCDS58210.1	ENSP00000442786	LMO3_HUMAN	.	UPI00017A6FD2	.	.	.	5/6	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	A:0	A:0.0005	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCGCAGTT	byCluster	4	ESCA
RECQL	0	.	GRCh37	12	21623237	21623237	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1841delA	p.Lys614ArgfsTer46	p.K614Rfs*46	ENST00000444129	15/15	80	56	24	51	51	0	RECQL,frameshift_variant,p.Lys614ArgfsTer46,ENST00000444129,;RECQL,frameshift_variant,p.Lys614ArgfsTer46,ENST00000421138,;PYROXD1,3_prime_UTR_variant,,ENST00000240651,;PYROXD1,3_prime_UTR_variant,,ENST00000538582,;PYROXD1,downstream_gene_variant,,ENST00000536851,;PYROXD1,downstream_gene_variant,,ENST00000375266,;PYROXD1,downstream_gene_variant,,ENST00000544970,;PYROXD1,downstream_gene_variant,,ENST00000538615,;	-	ENSG00000004700	ENST00000444129	Transcript	frameshift_variant	2310	1841	614	K/X	aAg/ag	.	.	.	-1	RECQL	HGNC	9948	protein_coding	YES	CCDS31756.1	ENSP00000416739	RECQ1_HUMAN	F8WD97_HUMAN,F8WA66_HUMAN,F5H4P4_HUMAN,F5H3W0_HUMAN,F5H2L2_HUMAN,F5GYB7_HUMAN	UPI0000167E2F	.	.	.	15/15	.	hmmpanther:PTHR13710:SF72,hmmpanther:PTHR13710	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCATCTTTTTA	.	3	ESCA
GYS2	0	.	GRCh37	12	21715887	21715887	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027C>G	p.Leu343Val	p.L343V	ENST00000261195	7/16	85	46	39	65	65	0	GYS2,missense_variant,p.Leu343Val,ENST00000261195,;	C	ENSG00000111713	ENST00000261195	Transcript	missense_variant	1282	1027	343	L/V	Cta/Gta	.	.	.	-1	GYS2	HGNC	4707	protein_coding	YES	CCDS8690.1	ENSP00000261195	GYS2_HUMAN	.	UPI000013D13D	.	deleterious(0.03)	possibly_damaging(0.566)	7/16	.	Superfamily_domains:SSF53756,Pfam_domain:PF05693,hmmpanther:PTHR10176:SF1,hmmpanther:PTHR10176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTAGGAAGA	.	5	ESCA
BHLHE41	0	.	GRCh37	12	26273790	26273790	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1209T>A	.	.	ENST00000242728	5/5	131	77	54	74	74	0	BHLHE41,3_prime_UTR_variant,,ENST00000242728,;SSPN,upstream_gene_variant,,ENST00000538142,;RP11-283G6.3,downstream_gene_variant,,ENST00000545819,;RP11-283G6.3,downstream_gene_variant,,ENST00000535914,;SSPN,upstream_gene_variant,,ENST00000534829,;BHLHE41,downstream_gene_variant,,ENST00000394326,;BHLHE41,downstream_gene_variant,,ENST00000541271,;	T	ENSG00000123095	ENST00000242728	Transcript	3_prime_UTR_variant	3006	.	.	.	.	.	.	.	-1	BHLHE41	HGNC	16617	protein_coding	YES	CCDS8706.1	ENSP00000242728	BHE41_HUMAN	.	UPI0000052B52	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATTAAAAAA	.	5	ESCA
CACNA1C	0	.	GRCh37	12	2693755	2693757	+	In_Frame_Del	DEL	GAG	GAG	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GAG	GAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2314_2316delGAG	p.Glu772del	p.E772del	ENST00000347598	16/49	56	32	23	20	20	0	CACNA1C,inframe_deletion,p.Glu772del,ENST00000399644,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399595,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000406454,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399617,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000347598,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000402845,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000327702,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399634,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399641,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399603,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399629,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000480911,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399601,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399597,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399655,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399606,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399637,;CACNA1C,inframe_deletion,p.Glu797del,ENST00000335762,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399621,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399638,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399591,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000344100,;CACNA1C,inframe_deletion,p.Glu772del,ENST00000399649,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000465278,;	-	ENSG00000151067	ENST00000347598	Transcript	inframe_deletion	2311-2313	2311-2313	771	E/-	GAG/-	.	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	.	.	16/49	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGGAAGAGGAGAA	.	2	ESCA
NRIP2	0	.	GRCh37	12	2943918	2943918	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.232C>A	p.His78Asn	p.H78N	ENST00000337508	1/6	109	71	38	46	46	0	NRIP2,missense_variant,p.His28Asn,ENST00000542386,;NRIP2,missense_variant,p.His28Asn,ENST00000542990,;NRIP2,missense_variant,p.His78Asn,ENST00000337508,;ITFG2,downstream_gene_variant,,ENST00000542548,;ITFG2,intron_variant,,ENST00000552005,;ITFG2,upstream_gene_variant,,ENST00000537710,;ITFG2,downstream_gene_variant,,ENST00000538822,;ITFG2,downstream_gene_variant,,ENST00000540929,;	T	ENSG00000053702	ENST00000337508	Transcript	missense_variant	273	232	78	H/N	Cac/Aac	.	.	.	-1	NRIP2	HGNC	23078	protein_coding	YES	CCDS8514.1	ENSP00000337501	NRIP2_HUMAN	F5H2G5_HUMAN,F5H065_HUMAN,A2RRE3_HUMAN	UPI000006E2A1	.	tolerated(0.62)	benign(0.09)	1/6	.	hmmpanther:PTHR12917:SF3,hmmpanther:PTHR12917	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGTGGGCTC	.	5	ESCA
FOXM1	0	.	GRCh37	12	2968282	2968282	+	Missense_Mutation	SNP	G	G	A	rs199632659	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1928C>T	p.Thr643Met	p.T643M	ENST00000342628	10/10	44	26	17	30	30	0	FOXM1,missense_variant,p.Thr590Met,ENST00000361953,;FOXM1,missense_variant,p.Thr643Met,ENST00000342628,;FOXM1,missense_variant,p.Thr605Met,ENST00000359843,;FOXM1,downstream_gene_variant,,ENST00000535350,;AC005841.1,upstream_gene_variant,,ENST00000382678,;Y_RNA,upstream_gene_variant,,ENST00000410561,;ITFG2,intron_variant,,ENST00000537710,;ITFG2,intron_variant,,ENST00000545509,;ITFG2,downstream_gene_variant,,ENST00000540300,;FOXM1,non_coding_transcript_exon_variant,,ENST00000536066,;FOXM1,downstream_gene_variant,,ENST00000366362,;	A	ENSG00000111206	ENST00000342628	Transcript	missense_variant	2042	1928	643	T/M	aCg/aTg	rs199632659,COSM938596	.	.	-1	FOXM1	HGNC	3818	protein_coding	YES	CCDS8516.1	ENSP00000342307	FOXM1_HUMAN	.	UPI000016B22B	.	tolerated(0.29)	benign(0.064)	10/10	.	.	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0.0014	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGTTTCC	byCluster|by1000G	5	ESCA
DDX11	0	.	GRCh37	12	31256314	31256314	+	Missense_Mutation	SNP	G	G	A	rs755347093	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2516G>A	p.Arg839His	p.R839H	ENST00000407793	25/27	114	78	36	63	63	0	DDX11,missense_variant,p.Val791Ile,ENST00000350437,;DDX11,missense_variant,p.Val107Ile,ENST00000539702,;DDX11,missense_variant,p.Val841Ile,ENST00000542838,;DDX11,missense_variant,p.Arg839His,ENST00000545668,;DDX11,missense_variant,p.Val815Ile,ENST00000228264,;DDX11,missense_variant,p.Arg839His,ENST00000407793,;DDX11,3_prime_UTR_variant,,ENST00000251758,;DDX11,downstream_gene_variant,,ENST00000539673,;DDX11,3_prime_UTR_variant,,ENST00000435753,;DDX11,3_prime_UTR_variant,,ENST00000538345,;DDX11,non_coding_transcript_exon_variant,,ENST00000536265,;DDX11,intron_variant,,ENST00000545115,;DDX11,intron_variant,,ENST00000539049,;DDX11,downstream_gene_variant,,ENST00000542661,;DDX11,downstream_gene_variant,,ENST00000542777,;DDX11,downstream_gene_variant,,ENST00000537136,;DDX11,downstream_gene_variant,,ENST00000539699,;DDX11,downstream_gene_variant,,ENST00000538740,;RP11-551L14.7,downstream_gene_variant,,ENST00000605711,;	A	ENSG00000013573	ENST00000407793	Transcript	missense_variant	2767	2516	839	R/H	cGt/cAt	rs755347093	.	.	1	DDX11	HGNC	2736	protein_coding	YES	CCDS44856.1	ENSP00000384703	DDX11_HUMAN	F5GXJ8_HUMAN	UPI000006F88F	.	tolerated_low_confidence(0.17)	benign(0.16)	25/27	.	SMART_domains:SM00491	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCGTCAAC	byFrequency	5	ESCA
SLC6A13	0	.	GRCh37	12	369121	369121	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98G>A	p.Gly33Glu	p.G33E	ENST00000343164	2/15	119	69	50	59	59	0	SLC6A13,missense_variant,p.Gly33Glu,ENST00000436453,;SLC6A13,missense_variant,p.Gly33Glu,ENST00000343164,;SLC6A13,missense_variant,p.Gly33Glu,ENST00000546319,;SLC6A13,missense_variant,p.Gly33Glu,ENST00000445055,;RP11-283I3.4,upstream_gene_variant,,ENST00000540868,;SLC6A13,missense_variant,p.Gly33Glu,ENST00000539260,;SLC6A13,non_coding_transcript_exon_variant,,ENST00000536842,;SLC6A13,intron_variant,,ENST00000542272,;	T	ENSG00000010379	ENST00000343164	Transcript	missense_variant	151	98	33	G/E	gGg/gAg	.	.	.	-1	SLC6A13	HGNC	11046	protein_coding	YES	CCDS8502.1	ENSP00000339260	S6A13_HUMAN	.	UPI0000046060	.	tolerated(0.61)	benign(0.099)	2/15	.	Superfamily_domains:0053687,Pfam_domain:PF00209,hmmpanther:PTHR11616:SF111,hmmpanther:PTHR11616,PROSITE_profiles:PS50267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGCCCCCGC	.	5	ESCA
KDM5A	0	.	GRCh37	12	392715	392715	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1907delA	.	.	ENST00000399788	28/28	49	33	15	28	28	0	KDM5A,3_prime_UTR_variant,,ENST00000399788,;KDM5A,downstream_gene_variant,,ENST00000382815,;KDM5A,downstream_gene_variant,,ENST00000540838,;	-	ENSG00000073614	ENST00000399788	Transcript	3_prime_UTR_variant	7343	.	.	.	.	.	.	.	-1	KDM5A	HGNC	9886	protein_coding	YES	CCDS41736.1	ENSP00000382688	KDM5A_HUMAN	.	UPI0000DB2E73	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACATCTTTTTT	.	2	ESCA
KDM5A	0	.	GRCh37	12	393805	393805	+	3'UTR	DEL	T	T	-	rs79783495	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*817delA	.	.	ENST00000399788	28/28	25	13	12	24	24	0	KDM5A,3_prime_UTR_variant,,ENST00000399788,;KDM5A,downstream_gene_variant,,ENST00000382815,;KDM5A,downstream_gene_variant,,ENST00000540838,;	-	ENSG00000073614	ENST00000399788	Transcript	3_prime_UTR_variant	6253	.	.	.	.	rs79783495	.	.	-1	KDM5A	HGNC	9886	protein_coding	YES	CCDS41736.1	ENSP00000382688	KDM5A_HUMAN	.	UPI0000DB2E73	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTCTCTTTTTT	.	2	ESCA
ABCD2	0	.	GRCh37	12	39947725	39947725	+	Missense_Mutation	SNP	C	C	T	rs572444310	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2212G>A	p.Glu738Lys	p.E738K	ENST00000308666	10/10	35	15	20	45	45	0	ABCD2,missense_variant,p.Glu738Lys,ENST00000308666,;	T	ENSG00000173208	ENST00000308666	Transcript	missense_variant	2348	2212	738	E/K	Gag/Aag	rs572444310	.	.	-1	ABCD2	HGNC	66	protein_coding	YES	CCDS8734.1	ENSP00000310688	ABCD2_HUMAN	.	UPI000004C4C6	.	tolerated_low_confidence(0.3)	benign(0.001)	10/10	.	hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTCATCTT	byCluster	5	ESCA
LRRK2	0	.	GRCh37	12	40699629	40699629	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3820G>A	p.Asp1274Asn	p.D1274N	ENST00000298910	28/51	44	26	17	45	45	0	LRRK2,missense_variant,p.Asp1274Asn,ENST00000298910,;LRRK2,downstream_gene_variant,,ENST00000343742,;LRRK2,3_prime_UTR_variant,,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,;	A	ENSG00000188906	ENST00000298910	Transcript	missense_variant	3878	3820	1274	D/N	Gat/Aat	.	.	.	1	LRRK2	HGNC	18618	protein_coding	YES	CCDS31774.1	ENSP00000298910	LRRK2_HUMAN	.	UPI00006C128E	.	tolerated(0.05)	probably_damaging(0.993)	28/51	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF417,Gene3D:3.80.10.10,Pfam_domain:PF12799,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGGATGTC	.	5	ESCA
GXYLT1	0	.	GRCh37	12	42481529	42481529	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*59G>T	.	.	ENST00000398675	8/8	39	31	8	46	46	0	GXYLT1,3_prime_UTR_variant,,ENST00000280876,;GXYLT1,3_prime_UTR_variant,,ENST00000398675,;	A	ENSG00000151233	ENST00000398675	Transcript	3_prime_UTR_variant	1615	.	.	.	.	.	.	.	-1	GXYLT1	HGNC	27482	protein_coding	YES	CCDS41772.1	ENSP00000381666	GXLT1_HUMAN	.	UPI0000237587	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTCCTTCAC	.	5	ESCA
CCND2	0	.	GRCh37	12	4411083	4411083	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1918delT	.	.	ENST00000261254	5/5	64	34	30	27	27	0	CCND2,3_prime_UTR_variant,,ENST00000261254,;CCND2,downstream_gene_variant,,ENST00000536537,;	-	ENSG00000118971	ENST00000261254	Transcript	3_prime_UTR_variant	3047	.	.	.	.	.	.	.	1	CCND2	HGNC	1583	protein_coding	YES	CCDS8524.1	ENSP00000261254	CCND2_HUMAN	.	UPI00001275C5	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGGTTGTTTTTT	.	2	ESCA
TMEM117	0	.	GRCh37	12	44783452	44783452	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*997T>C	.	.	ENST00000266534	8/8	23	9	14	20	20	0	TMEM117,3_prime_UTR_variant,,ENST00000551577,;TMEM117,3_prime_UTR_variant,,ENST00000266534,;TMEM117,downstream_gene_variant,,ENST00000550495,;TMEM117,downstream_gene_variant,,ENST00000536799,;TMEM117,non_coding_transcript_exon_variant,,ENST00000546978,;TMEM117,3_prime_UTR_variant,,ENST00000546868,;	C	ENSG00000139173	ENST00000266534	Transcript	3_prime_UTR_variant	2669	.	.	.	.	.	.	.	1	TMEM117	HGNC	25308	protein_coding	YES	CCDS8745.1	ENSP00000266534	TM117_HUMAN	H0YI63_HUMAN	UPI0000037D18	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAATTTGTTT	.	5	ESCA
FGF23	0	.	GRCh37	12	4479741	4479741	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524G>A	p.Arg175Gln	p.R175Q	ENST00000237837	3/3	67	44	23	20	20	0	FGF23,missense_variant,p.Arg175Gln,ENST00000237837,;	T	ENSG00000118972	ENST00000237837	Transcript	missense_variant	670	524	175	R/Q	cGg/cAg	.	.	.	-1	FGF23	HGNC	3680	protein_coding	YES	CCDS8526.1	ENSP00000237837	FGF23_HUMAN	.	UPI000003ED58	.	tolerated(0.1)	possibly_damaging(0.734)	3/3	.	hmmpanther:PTHR11486:SF69,hmmpanther:PTHR11486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R176Q|c.527G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCCGTGGT	.	5	ESCA
CCNT1	0	.	GRCh37	12	49087795	49087795	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1202C>T	p.Ala401Val	p.A401V	ENST00000261900	9/9	61	48	13	57	57	0	CCNT1,missense_variant,p.Ala401Val,ENST00000261900,;CCNT1,3_prime_UTR_variant,,ENST00000417344,;CCNT1,non_coding_transcript_exon_variant,,ENST00000551989,;	A	ENSG00000129315	ENST00000261900	Transcript	missense_variant	1425	1202	401	A/V	gCt/gTt	.	.	.	-1	CCNT1	HGNC	1599	protein_coding	YES	CCDS8766.1	ENSP00000261900	CCNT1_HUMAN	.	UPI0000044259	.	deleterious(0.01)	probably_damaging(0.971)	9/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10026,hmmpanther:PTHR10026:SF42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCAGCCAAT	.	5	ESCA
KCNA6	0	.	GRCh37	12	4919431	4919431	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224G>A	p.Arg75His	p.R75H	ENST00000433855	1/2	158	82	75	80	80	0	KCNA6,missense_variant,p.Arg75His,ENST00000433855,;KCNA6,missense_variant,p.Arg75His,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,;	A	ENSG00000151079	ENST00000433855	Transcript	missense_variant	1090	224	75	R/H	cGc/cAc	.	.	.	1	KCNA6	HGNC	6225	protein_coding	YES	CCDS8534.1	ENSP00000408321	KCNA6_HUMAN	.	UPI00001279AD	.	deleterious(0.05)	benign(0.016)	1/2	.	Prints_domain:PR01496,Superfamily_domains:SSF54695,SMART_domains:SM00225,Pfam_domain:PF02214,Gene3D:3.30.710.10,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCCGCTTCT	.	5	ESCA
DDX23	0	.	GRCh37	12	49226301	49226301	+	Missense_Mutation	SNP	T	T	C	rs766593969	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1859A>G	p.Tyr620Cys	p.Y620C	ENST00000308025	14/17	37	34	3	15	15	0	DDX23,missense_variant,p.Tyr620Cys,ENST00000308025,;DDX23,intron_variant,,ENST00000550834,;CACNB3,downstream_gene_variant,,ENST00000547392,;CACNB3,downstream_gene_variant,,ENST00000301050,;CACNB3,downstream_gene_variant,,ENST00000536187,;CACNB3,downstream_gene_variant,,ENST00000550190,;CACNB3,downstream_gene_variant,,ENST00000547230,;CACNB3,downstream_gene_variant,,ENST00000540990,;DDX23,downstream_gene_variant,,ENST00000553182,;DDX23,3_prime_UTR_variant,,ENST00000552802,;DDX23,non_coding_transcript_exon_variant,,ENST00000551331,;DDX23,non_coding_transcript_exon_variant,,ENST00000547842,;DDX23,non_coding_transcript_exon_variant,,ENST00000547290,;DDX23,non_coding_transcript_exon_variant,,ENST00000549795,;CACNB3,downstream_gene_variant,,ENST00000552480,;DDX23,downstream_gene_variant,,ENST00000551189,;DDX23,downstream_gene_variant,,ENST00000552069,;DDX23,downstream_gene_variant,,ENST00000547135,;CACNB3,downstream_gene_variant,,ENST00000548860,;DDX23,downstream_gene_variant,,ENST00000547165,;CACNB3,downstream_gene_variant,,ENST00000551544,;DDX23,downstream_gene_variant,,ENST00000553065,;	C	ENSG00000174243	ENST00000308025	Transcript	missense_variant	1939	1859	620	Y/C	tAt/tGt	rs766593969	.	.	-1	DDX23	HGNC	17347	protein_coding	YES	CCDS8770.1	ENSP00000310723	DDX23_HUMAN	F8W1J5_HUMAN,F8VVA2_HUMAN,B3KY11_HUMAN	UPI0000073875	.	deleterious(0)	probably_damaging(0.968)	14/17	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF23,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGATAGCTC	.	4	ESCA
KMT2D	0	.	GRCh37	12	49420213	49420213	+	Missense_Mutation	SNP	C	C	T	rs267607237	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	48/54	30	21	9	17	17	0	KMT2D,missense_variant,p.Arg5179His,ENST00000301067,;KMT2D,upstream_gene_variant,,ENST00000526209,;KMT2D,downstream_gene_variant,,ENST00000552391,;	T	ENSG00000167548	ENST00000301067	Transcript	missense_variant	15536	15536	5179	R/H	cGt/cAt	CM105472,rs267607237,COSM3356316,COSM693720,COSM693719,COSM3356315	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	unknown(0)	48/54	.	PROSITE_profiles:PS51542,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	pathogenic	0,0,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACACGGAAC	.	5	ESCA
KRT1	0	.	GRCh37	12	53073764	53073764	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369C>T	p.%3D	p.G123G	ENST00000252244	1/9	125	64	60	62	62	0	KRT1,synonymous_variant,p.%3D,ENST00000252244,;KRT1,upstream_gene_variant,,ENST00000548765,;	A	ENSG00000167768	ENST00000252244	Transcript	synonymous_variant	428	369	123	G	ggC/ggT	.	.	.	-1	KRT1	HGNC	6412	protein_coding	YES	CCDS8836.1	ENSP00000252244	K2C1_HUMAN	H6VRG1_HUMAN	UPI000013CD4D	.	.	.	1/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF95,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTGCCAAA	.	5	ESCA
SP1	0	.	GRCh37	12	53809428	53809428	+	3'Flank	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000327443	.	56	46	10	56	56	0	SP1,3_prime_UTR_variant,,ENST00000426431,;SP1,downstream_gene_variant,,ENST00000327443,;	G	ENSG00000185591	ENST00000327443	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4014	1	SP1	HGNC	11205	protein_coding	YES	CCDS8857.1	ENSP00000329357	SP1_HUMAN	G5E9M8_HUMAN,Q9NR52_HUMAN,H3BVI2_HUMAN,C4PGM0_HUMAN	UPI0000135D4E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GAAAAAAAAAA	.	2	ESCA
CALCOCO1	0	.	GRCh37	12	54105819	54105819	+	Missense_Mutation	SNP	C	C	T	rs775292722	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1985G>A	p.Arg662His	p.R662H	ENST00000550804	15/15	68	35	32	58	58	0	CALCOCO1,missense_variant,p.Arg661His,ENST00000262059,;CALCOCO1,missense_variant,p.Arg577His,ENST00000430117,;CALCOCO1,missense_variant,p.Arg203His,ENST00000546443,;CALCOCO1,missense_variant,p.Arg662His,ENST00000550804,;CALCOCO1,3_prime_UTR_variant,,ENST00000548263,;CALCOCO1,downstream_gene_variant,,ENST00000549935,;CALCOCO1,downstream_gene_variant,,ENST00000552282,;CALCOCO1,downstream_gene_variant,,ENST00000549613,;	T	ENSG00000012822	ENST00000550804	Transcript	missense_variant	2046	1985	662	R/H	cGc/cAc	rs775292722	.	.	-1	CALCOCO1	HGNC	29306	protein_coding	YES	CCDS8864.1	ENSP00000449960	CACO1_HUMAN	F8W0X2_HUMAN,F8VZI3_HUMAN,F8VWP8_HUMAN,F8VUB3_HUMAN,F8VRQ9_HUMAN,F8VQE3_HUMAN,F8VPN1_HUMAN	UPI0000037D7A	.	tolerated_low_confidence(0.08)	benign(0.008)	15/15	.	hmmpanther:PTHR31915,hmmpanther:PTHR31915:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGCGCTCC	byFrequency	5	ESCA
RPS26	0	.	GRCh37	12	56436335	56436336	+	Frame_Shift_Del	DEL	AT	AT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AT	AT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.131_132delTA	p.Ile44SerfsTer11	p.I44Sfs*11	ENST00000356464	2/4	135	100	35	47	47	0	RPS26,frameshift_variant,p.Ile44SerfsTer11,ENST00000356464,;RPS26,frameshift_variant,p.Ile44SerfsTer11,ENST00000552361,;IKZF4,downstream_gene_variant,,ENST00000262032,;RP11-603J24.4,upstream_gene_variant,,ENST00000551846,;RPS26,non_coding_transcript_exon_variant,,ENST00000548590,;IKZF4,downstream_gene_variant,,ENST00000551124,;	-	ENSG00000197728	ENST00000356464	Transcript	frameshift_variant	444-445	130-131	44	I/X	ATa/a	.	.	.	1	RPS26	HGNC	10414	protein_coding	YES	CCDS31832.1	ENSP00000348849	RS26_HUMAN	Q76N57_HUMAN,Q76N56_HUMAN	UPI0000001687	.	.	.	2/4	.	hmmpanther:PTHR12538,Pfam_domain:PF01283	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGAAACATAGTGG	.	3	ESCA
RPL41	0	.	GRCh37	12	56510435	56510435	+	5'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-131delT	.	.	ENST00000546591	1/3	39	31	8	24	24	0	RPL41,5_prime_UTR_variant,,ENST00000546591,;RPL41,5_prime_UTR_variant,,ENST00000501597,;ZC3H10,upstream_gene_variant,,ENST00000257940,;ZC3H10,upstream_gene_variant,,ENST00000546903,;PA2G4,downstream_gene_variant,,ENST00000552766,;ZC3H10,upstream_gene_variant,,ENST00000551880,;PA2G4,downstream_gene_variant,,ENST00000303305,;ESYT1,upstream_gene_variant,,ENST00000551790,;ZC3H10,upstream_gene_variant,,ENST00000552345,;RP11-603J24.5,downstream_gene_variant,,ENST00000549438,;RP11-603J24.5,downstream_gene_variant,,ENST00000550947,;RP11-603J24.6,downstream_gene_variant,,ENST00000550840,;RP11-603J24.17,upstream_gene_variant,,ENST00000548595,;RPL41,non_coding_transcript_exon_variant,,ENST00000358888,;RPL41,non_coding_transcript_exon_variant,,ENST00000546485,;RPL41,upstream_gene_variant,,ENST00000546654,;ZC3H10,upstream_gene_variant,,ENST00000549973,;RPL41,upstream_gene_variant,,ENST00000552314,;	-	ENSG00000229117	ENST00000546591	Transcript	5_prime_UTR_variant	66	.	.	.	.	.	.	.	1	RPL41	HGNC	10354	protein_coding	YES	CCDS44919.1	ENSP00000449026	RL41_HUMAN	.	UPI0000000DDF	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCGCCATTTTTT	.	3	ESCA
LRP1	0	.	GRCh37	12	57579515	57579515	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6665C>T	p.Ala2222Val	p.A2222V	ENST00000243077	41/89	50	31	19	34	34	0	LRP1,missense_variant,p.Ala2222Val,ENST00000243077,;LRP1,upstream_gene_variant,,ENST00000554118,;	T	ENSG00000123384	ENST00000243077	Transcript	missense_variant	7131	6665	2222	A/V	gCg/gTg	.	.	.	1	LRP1	HGNC	6692	protein_coding	YES	CCDS8932.1	ENSP00000243077	LRP1_HUMAN	Q6LBN5_HUMAN,Q6LAF4_HUMAN	UPI00001B044F	.	.	benign(0.341)	41/89	.	hmmpanther:PTHR10529:SF100,hmmpanther:PTHR10529,Gene3D:2.120.10.30,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATGCGCCCG	.	5	ESCA
LRP1	0	.	GRCh37	12	57589915	57589915	+	Missense_Mutation	SNP	G	G	A	rs199825634	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8747G>A	p.Arg2916His	p.R2916H	ENST00000243077	55/89	74	56	17	27	27	0	LRP1,missense_variant,p.Arg2916His,ENST00000243077,;LRP1,upstream_gene_variant,,ENST00000555124,;LRP1,downstream_gene_variant,,ENST00000554118,;MIR1228,downstream_gene_variant,,ENST00000408438,;LRP1,upstream_gene_variant,,ENST00000555941,;	A	ENSG00000123384	ENST00000243077	Transcript	missense_variant	9213	8747	2916	R/H	cGc/cAc	rs199825634	.	.	1	LRP1	HGNC	6692	protein_coding	YES	CCDS8932.1	ENSP00000243077	LRP1_HUMAN	Q6LBN5_HUMAN,Q6LAF4_HUMAN	UPI00001B044F	.	.	possibly_damaging(0.602)	55/89	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529:SF100,hmmpanther:PTHR10529,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGCGCTGTG	byCluster|by1000G	5	ESCA
ARHGAP9	0	.	GRCh37	12	57871263	57871263	+	Silent	SNP	C	C	T	rs548695816	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.735G>A	p.%3D	p.P245P	ENST00000393791	4/18	51	31	20	26	26	0	ARHGAP9,synonymous_variant,p.%3D,ENST00000552604,;ARHGAP9,synonymous_variant,p.%3D,ENST00000430041,;ARHGAP9,synonymous_variant,p.%3D,ENST00000551452,;ARHGAP9,synonymous_variant,p.%3D,ENST00000356411,;ARHGAP9,synonymous_variant,p.%3D,ENST00000393791,;ARHGAP9,synonymous_variant,p.%3D,ENST00000550288,;ARHGAP9,synonymous_variant,p.%3D,ENST00000549602,;ARHGAP9,synonymous_variant,p.%3D,ENST00000548139,;ARHGAP9,synonymous_variant,p.%3D,ENST00000552066,;ARHGAP9,synonymous_variant,p.%3D,ENST00000393797,;ARHGAP9,synonymous_variant,p.%3D,ENST00000424809,;ARHGAP9,upstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000552249,;ARHGAP9,upstream_gene_variant,,ENST00000550130,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000550454,;MARS,intron_variant,,ENST00000549133,;ARHGAP9,upstream_gene_variant,,ENST00000547200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000551000,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000552420,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000546200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000551574,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000547216,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000548148,;ARHGAP9,upstream_gene_variant,,ENST00000550440,;ARHGAP9,upstream_gene_variant,,ENST00000546704,;ARHGAP9,upstream_gene_variant,,ENST00000552953,;	T	ENSG00000123329	ENST00000393791	Transcript	synonymous_variant	874	735	245	P	ccG/ccA	rs548695816,COSM942054	.	.	-1	ARHGAP9	HGNC	14130	protein_coding	YES	CCDS8941.2	ENSP00000377380	RHG09_HUMAN	F8VW89_HUMAN,F8VSD0_HUMAN,F8VR90_HUMAN,F8VQY5_HUMAN	UPI000007131B	.	.	.	4/18	.	PROSITE_profiles:PS50020,hmmpanther:PTHR23181,hmmpanther:PTHR23181:SF4,Gene3D:2.20.70.10,Superfamily_domains:SSF51045	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCGCGGGGG	by1000G	5	ESCA
OS9	0	.	GRCh37	12	58112063	58112063	+	Silent	SNP	G	G	A	rs759549472	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269G>A	p.%3D	p.E423E	ENST00000315970	11/15	53	23	30	20	20	0	OS9,synonymous_variant,p.%3D,ENST00000413095,;OS9,synonymous_variant,p.%3D,ENST00000257966,;OS9,synonymous_variant,p.%3D,ENST00000435406,;OS9,synonymous_variant,p.%3D,ENST00000551035,;OS9,synonymous_variant,p.%3D,ENST00000315970,;OS9,synonymous_variant,p.%3D,ENST00000552285,;OS9,synonymous_variant,p.%3D,ENST00000389142,;OS9,synonymous_variant,p.%3D,ENST00000389146,;OS9,synonymous_variant,p.%3D,ENST00000439210,;OS9,intron_variant,,ENST00000547079,;OS9,downstream_gene_variant,,ENST00000550372,;RP11-571M6.7,intron_variant,,ENST00000549477,;OS9,non_coding_transcript_exon_variant,,ENST00000549307,;OS9,non_coding_transcript_exon_variant,,ENST00000550202,;OS9,downstream_gene_variant,,ENST00000552787,;OS9,downstream_gene_variant,,ENST00000550699,;OS9,downstream_gene_variant,,ENST00000550438,;OS9,downstream_gene_variant,,ENST00000553208,;OS9,upstream_gene_variant,,ENST00000546916,;	A	ENSG00000135506	ENST00000315970	Transcript	synonymous_variant	1310	1269	423	E	gaG/gaA	rs759549472	.	.	1	OS9	HGNC	16994	protein_coding	YES	CCDS31843.1	ENSP00000318165	OS9_HUMAN	Q9BR60_HUMAN	UPI0000130EAC	.	.	.	11/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15414,hmmpanther:PTHR15414:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAGGATGA	.	5	ESCA
LRIG3	0	.	GRCh37	12	59270334	59270334	+	Missense_Mutation	SNP	G	G	A	rs760319879	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2588C>T	p.Thr863Met	p.T863M	ENST00000320743	16/19	49	39	10	34	34	0	LRIG3,missense_variant,p.Thr803Met,ENST00000379141,;LRIG3,missense_variant,p.Thr863Met,ENST00000320743,;LRIG3,upstream_gene_variant,,ENST00000550825,;LRIG3,3_prime_UTR_variant,,ENST00000433272,;LRIG3,non_coding_transcript_exon_variant,,ENST00000552646,;LRIG3,downstream_gene_variant,,ENST00000547329,;	A	ENSG00000139263	ENST00000320743	Transcript	missense_variant	2875	2588	863	T/M	aCg/aTg	rs760319879	.	.	-1	LRIG3	HGNC	30991	protein_coding	YES	CCDS8960.1	ENSP00000326759	LRIG3_HUMAN	F8VYZ5_HUMAN	UPI0000035BB5	.	deleterious(0)	possibly_damaging(0.76)	16/19	.	hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF242	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAACGTTCCC	byFrequency	5	ESCA
SLC16A7	0	.	GRCh37	12	60175138	60175138	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1685delT	.	.	ENST00000261187	5/5	51	41	9	47	47	0	SLC16A7,3_prime_UTR_variant,,ENST00000261187,;SLC16A7,downstream_gene_variant,,ENST00000543448,;SLC16A7,downstream_gene_variant,,ENST00000552432,;SLC16A7,downstream_gene_variant,,ENST00000548610,;SLC16A7,downstream_gene_variant,,ENST00000547379,;SLC16A7,downstream_gene_variant,,ENST00000552024,;SLC16A7,downstream_gene_variant,,ENST00000549033,;SLC16A7,downstream_gene_variant,,ENST00000549928,;	-	ENSG00000118596	ENST00000261187	Transcript	3_prime_UTR_variant	3279	.	.	.	.	.	.	.	1	SLC16A7	HGNC	10928	protein_coding	YES	CCDS8961.1	ENSP00000261187	MOT2_HUMAN	F8W0N3_HUMAN,F8VS95_HUMAN,F5H843_HUMAN	UPI00000722FD	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAGCCATTTTTT	.	2	ESCA
TBC1D30	0	.	GRCh37	12	65269009	65269009	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1727T>C	p.Met576Thr	p.M576T	ENST00000539867	12/12	37	21	15	17	17	0	TBC1D30,missense_variant,p.Met576Thr,ENST00000539867,;TBC1D30,missense_variant,p.Met739Thr,ENST00000229088,;TBC1D30,missense_variant,p.Met462Thr,ENST00000542120,;	C	ENSG00000111490	ENST00000539867	Transcript	missense_variant	2035	1727	576	M/T	aTg/aCg	.	.	.	1	TBC1D30	HGNC	29164	protein_coding	YES	CCDS53813.1	ENSP00000440207	TBC30_HUMAN	F8VZ81_HUMAN,F5H7L7_HUMAN	UPI000013F308	.	tolerated_low_confidence(0.2)	benign(0.002)	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACATGCCAA	.	5	ESCA
GRIP1	0	.	GRCh37	12	66990679	66990679	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84C>T	p.%3D	p.S28S	ENST00000398016	2/24	32	20	12	31	31	0	GRIP1,synonymous_variant,p.%3D,ENST00000541947,;GRIP1,synonymous_variant,p.%3D,ENST00000538211,;GRIP1,synonymous_variant,p.%3D,ENST00000286445,;GRIP1,synonymous_variant,p.%3D,ENST00000398016,;GRIP1,synonymous_variant,p.%3D,ENST00000359742,;GRIP1,5_prime_UTR_variant,,ENST00000539540,;GRIP1,5_prime_UTR_variant,,ENST00000538373,;GRIP1,5_prime_UTR_variant,,ENST00000542309,;GRIP1,intron_variant,,ENST00000545666,;GRIP1,intron_variant,,ENST00000540433,;	A	ENSG00000155974	ENST00000398016	Transcript	synonymous_variant	153	84	28	S	agC/agT	.	.	.	-1	GRIP1	HGNC	18708	protein_coding	YES	CCDS41807.1	ENSP00000381098	GRIP1_HUMAN	F5H5I0_HUMAN,F5H4P8_HUMAN,F5H424_HUMAN	UPI0000DD8148	.	.	.	2/24	.	hmmpanther:PTHR10316:SF39,hmmpanther:PTHR10316	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGGCTGGC	.	5	ESCA
DYRK2	0	.	GRCh37	12	68053151	68053151	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*658C>T	.	.	ENST00000344096	3/3	56	27	29	42	42	0	DYRK2,3_prime_UTR_variant,,ENST00000344096,;DYRK2,downstream_gene_variant,,ENST00000393555,;DYRK2,downstream_gene_variant,,ENST00000319833,;DYRK2,downstream_gene_variant,,ENST00000543747,;DYRK2,downstream_gene_variant,,ENST00000542503,;RP11-335O4.3,non_coding_transcript_exon_variant,,ENST00000425371,;	T	ENSG00000127334	ENST00000344096	Transcript	3_prime_UTR_variant	2877	.	.	.	.	.	.	.	1	DYRK2	HGNC	3093	protein_coding	YES	CCDS8978.1	ENSP00000342105	DYRK2_HUMAN	G8JLB4_HUMAN,F5GXG1_HUMAN	UPI000006E92B	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAACGTGTG	.	5	ESCA
LEPREL2	0	.	GRCh37	12	6939693	6939693	+	Frame_Shift_Del	DEL	G	G	-	rs782672632	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.830delG	p.Gly277AlafsTer42	p.G277Afs*42	ENST00000396725	4/16	97	72	25	23	23	0	LEPREL2,frameshift_variant,p.Gly93AlafsTer42,ENST00000251761,;LEPREL2,frameshift_variant,p.Gly277AlafsTer42,ENST00000396725,;GPR162,downstream_gene_variant,,ENST00000545321,;GPR162,downstream_gene_variant,,ENST00000428545,;GPR162,downstream_gene_variant,,ENST00000382315,;GPR162,downstream_gene_variant,,ENST00000311268,;LEPREL2,non_coding_transcript_exon_variant,,ENST00000538102,;LEPREL2,non_coding_transcript_exon_variant,,ENST00000544813,;GPR162,downstream_gene_variant,,ENST00000542330,;LEPREL2,non_coding_transcript_exon_variant,,ENST00000290510,;LEPREL2,non_coding_transcript_exon_variant,,ENST00000536140,;LEPREL2,upstream_gene_variant,,ENST00000544949,;LEPREL2,upstream_gene_variant,,ENST00000541956,;LEPREL2,upstream_gene_variant,,ENST00000544200,;LEPREL2,upstream_gene_variant,,ENST00000545596,;LEPREL2,upstream_gene_variant,,ENST00000540406,;LEPREL2,upstream_gene_variant,,ENST00000542976,;LEPREL2,frameshift_variant,p.Ala278ProfsTer?,ENST00000606935,;	-	ENSG00000110811	ENST00000396725	Transcript	frameshift_variant	859	825	275	Q/X	caG/ca	rs782672632,COSM1363912,COSM1363911	.	.	1	LEPREL2	HGNC	19318	protein_coding	YES	.	ENSP00000379951	.	G8JLI6_HUMAN	UPI00001AF55A	.	.	.	4/16	.	hmmpanther:PTHR14049:SF14,hmmpanther:PTHR14049,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	deletion	.	5	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAGCCAGGGGGG	.	3	ESCA
MYRFL	0	.	GRCh37	12	70321513	70321514	+	5'Flank	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000535034	.	21	15	6	19	19	0	MYRFL,frameshift_variant,p.Asn73LysfsTer15,ENST00000548892,;MYRFL,frameshift_variant,p.Asn608LysfsTer15,ENST00000552032,;MYRFL,frameshift_variant,p.Asn608LysfsTer15,ENST00000547771,;MYRFL,5_prime_UTR_variant,,ENST00000299350,;MYRFL,upstream_gene_variant,,ENST00000535034,;RP11-611E13.2,intron_variant,,ENST00000549419,;	A	ENSG00000166268	ENST00000535034	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4802	1	MYRFL	HGNC	26316	protein_coding	YES	.	ENSP00000440626	.	F5GYH9_HUMAN	UPI00020654F3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTTCATAAAAA	.	2	ESCA
KCNMB4	0	.	GRCh37	12	70824403	70824403	+	Silent	SNP	G	G	A	rs765167113	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.603G>A	p.%3D	p.A201A	ENST00000258111	3/3	50	38	11	25	25	0	KCNMB4,synonymous_variant,p.%3D,ENST00000258111,;KCNMB4,3_prime_UTR_variant,,ENST00000531884,;	A	ENSG00000135643	ENST00000258111	Transcript	synonymous_variant	1062	603	201	A	gcG/gcA	rs765167113	.	.	1	KCNMB4	HGNC	6289	protein_coding	YES	CCDS8997.1	ENSP00000258111	KCMB4_HUMAN	.	UPI0000073E0E	.	.	.	3/3	.	Pfam_domain:PF03185,hmmpanther:PTHR10258,hmmpanther:PTHR10258:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCGGAAGC	byFrequency	5	ESCA
KCNC2	0	.	GRCh37	12	75601161	75601161	+	Silent	SNP	G	G	A	rs200758140	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.603C>T	p.%3D	p.P201P	ENST00000549446	2/5	127	54	72	51	51	0	KCNC2,synonymous_variant,p.%3D,ENST00000341669,;KCNC2,synonymous_variant,p.%3D,ENST00000393288,;KCNC2,synonymous_variant,p.%3D,ENST00000540018,;KCNC2,synonymous_variant,p.%3D,ENST00000548513,;KCNC2,synonymous_variant,p.%3D,ENST00000550433,;KCNC2,synonymous_variant,p.%3D,ENST00000298972,;KCNC2,synonymous_variant,p.%3D,ENST00000549446,;KCNC2,synonymous_variant,p.%3D,ENST00000350228,;	A	ENSG00000166006	ENST00000549446	Transcript	synonymous_variant	1284	603	201	P	ccC/ccT	rs200758140	.	.	-1	KCNC2	HGNC	6234	protein_coding	YES	CCDS9007.1	ENSP00000449253	KCNC2_HUMAN	.	UPI000004DB9B	.	.	.	2/5	.	hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF48	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTCGGGGCC	byFrequency|byCluster	5	ESCA
CD163	0	.	GRCh37	12	7635292	7635292	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3194delT	p.Phe1065SerfsTer7	p.F1065Sfs*7	ENST00000359156	14/17	67	51	16	30	30	0	CD163,frameshift_variant,p.Phe1053SerfsTer7,ENST00000541972,;CD163,frameshift_variant,p.Phe1065SerfsTer7,ENST00000359156,;CD163,frameshift_variant,p.Phe1098SerfsTer7,ENST00000396620,;CD163,frameshift_variant,p.Phe78SerfsTer7,ENST00000537626,;CD163,frameshift_variant,p.Phe1065SerfsTer7,ENST00000432237,;CD163,intron_variant,,ENST00000542280,;CD163L1,upstream_gene_variant,,ENST00000543276,;CD163,downstream_gene_variant,,ENST00000539632,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,;CD163,downstream_gene_variant,,ENST00000538840,;	-	ENSG00000177575	ENST00000359156	Transcript	frameshift_variant	3397	3194	1065	F/X	tTc/tc	.	.	.	-1	CD163	HGNC	1631	protein_coding	YES	CCDS8578.1	ENSP00000352071	C163A_HUMAN	.	UPI00004565CC	.	.	.	14/17	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR19331:SF268,hmmpanther:PTHR19331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.F1065F|c.3195C>T|4,CODON|p.F1098F|c.3294C>T|4	INDELOCATOR*|VARSCANI*|PINDEL	GCGACGAAAATG	.	3	ESCA
FOXJ2	0	.	GRCh37	12	8207110	8207110	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1670delT	.	.	ENST00000162391	11/11	20	12	7	10	10	0	FOXJ2,3_prime_UTR_variant,,ENST00000162391,;FOXJ2,downstream_gene_variant,,ENST00000428177,;C3AR1,downstream_gene_variant,,ENST00000307637,;FOXJ2,downstream_gene_variant,,ENST00000539192,;	-	ENSG00000065970	ENST00000162391	Transcript	3_prime_UTR_variant	4534	.	.	.	.	.	.	.	1	FOXJ2	HGNC	24818	protein_coding	YES	CCDS8587.1	ENSP00000162391	FOXJ2_HUMAN	.	UPI000012ADE1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTTCCTTTTTT	.	2	ESCA
LINC00937	0	.	GRCh37	12	8543091	8543091	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.856C>T	.	.	ENST00000544461	2/5	22	8	14	10	10	0	LINC00937,non_coding_transcript_exon_variant,,ENST00000538304,;LINC00937,non_coding_transcript_exon_variant,,ENST00000420040,;LINC00937,non_coding_transcript_exon_variant,,ENST00000544461,;LINC00937,upstream_gene_variant,,ENST00000536539,;LINC00937,upstream_gene_variant,,ENST00000536560,;LINC00937,upstream_gene_variant,,ENST00000539348,;	A	ENSG00000226091	ENST00000544461	Transcript	non_coding_transcript_exon_variant	856	.	.	.	.	.	.	.	-1	LINC00937	HGNC	48629	lincRNA	YES	.	.	.	.	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCGGGGGC	.	5	ESCA
CCER1	0	.	GRCh37	12	91348469	91348469	+	Silent	SNP	A	A	G	rs761676354	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51T>C	p.%3D	p.G17G	ENST00000358859	1/1	48	38	10	25	25	0	CCER1,synonymous_variant,p.%3D,ENST00000358859,;CCER1,intron_variant,,ENST00000548187,;CCER1,upstream_gene_variant,,ENST00000549707,;	G	ENSG00000197651	ENST00000358859	Transcript	synonymous_variant	485	51	17	G	ggT/ggC	rs761676354	.	.	-1	CCER1	HGNC	28373	protein_coding	YES	CCDS9036.1	ENSP00000351727	CCER1_HUMAN	.	UPI000006EE70	.	.	.	1/1	.	Low_complexity_(Seg):seg,Pfam_domain:PF15482	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCCACCGCC	byFrequency	5	ESCA
A2M	0	.	GRCh37	12	9252079	9252079	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1599C>T	p.%3D	p.D533D	ENST00000318602	14/36	38	27	11	26	26	0	A2M,synonymous_variant,p.%3D,ENST00000318602,;A2M,intron_variant,,ENST00000545828,;A2M,synonymous_variant,p.%3D,ENST00000546069,;A2M,non_coding_transcript_exon_variant,,ENST00000472360,;	A	ENSG00000175899	ENST00000318602	Transcript	synonymous_variant	1907	1599	533	D	gaC/gaT	.	.	.	-1	A2M	HGNC	7	protein_coding	YES	CCDS44827.1	ENSP00000323929	A2MG_HUMAN	Q9BQ22_HUMAN,F8W7L3_HUMAN,F5H1E8_HUMAN	UPI000014038F	.	.	.	14/36	.	hmmpanther:PTHR11412:SF75,hmmpanther:PTHR11412,Pfam_domain:PF07703	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAATGTCTGA	.	5	ESCA
CLECL1	0	.	GRCh37	12	9875256	9875256	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470A>G	p.Gln157Arg	p.Q157R	ENST00000327839	2/2	51	36	14	47	47	0	CLECL1,start_lost,p.Gln1?,ENST00000540988,;CLECL1,missense_variant,p.Gln109Arg,ENST00000542530,;CLECL1,missense_variant,p.Gln157Arg,ENST00000327839,;	C	ENSG00000184293	ENST00000327839	Transcript	missense_variant	505	470	157	Q/R	cAa/cGa	.	.	.	-1	CLECL1	HGNC	24462	protein_coding	YES	CCDS8603.1	ENSP00000331766	CLCL1_HUMAN	.	UPI00000740B2	.	tolerated(0.23)	benign(0.084)	2/2	.	hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF132,Gene3D:3.10.100.10,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTTGAATC	.	5	ESCA
KDELC1	0	.	GRCh37	13	103443722	103443722	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731delA	p.Lys244ArgfsTer23	p.K244Rfs*23	ENST00000376004	5/10	105	61	44	61	61	0	KDELC1,frameshift_variant,p.Lys244ArgfsTer23,ENST00000376004,;KDELC1,non_coding_transcript_exon_variant,,ENST00000460338,;KDELC1,downstream_gene_variant,,ENST00000486540,;KDELC1,upstream_gene_variant,,ENST00000484943,;	-	ENSG00000134901	ENST00000376004	Transcript	frameshift_variant	1068	731	244	K/X	aAg/ag	.	.	.	-1	KDELC1	HGNC	19350	protein_coding	YES	CCDS9504.1	ENSP00000365172	KDEL1_HUMAN	.	UPI000004C663	.	.	.	5/10	.	hmmpanther:PTHR12203:SF21,hmmpanther:PTHR12203,Pfam_domain:PF05686,SMART_domains:SM00672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATTTCTTTTTT	.	3	ESCA
ANKRD20A19P	0	.	GRCh37	13	24515468	24515468	+	RNA	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1289delA	.	.	ENST00000442969	3/4	159	134	25	96	96	0	ANKRD20A19P,non_coding_transcript_exon_variant,,ENST00000420143,;ANKRD20A19P,non_coding_transcript_exon_variant,,ENST00000442969,;ANKRD20A19P,non_coding_transcript_exon_variant,,ENST00000602724,;	-	ENSG00000196593	ENST00000442969	Transcript	non_coding_transcript_exon_variant	1289	.	.	.	.	.	.	.	-1	ANKRD20A19P	HGNC	42737	processed_transcript	YES	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGCAGTTTTTT	.	3	ESCA
SPATA13	0	.	GRCh37	13	24798196	24798196	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129G>A	p.Gly377Arg	p.G377R	ENST00000424834	4/15	44	27	17	30	30	0	SPATA13,missense_variant,p.Gly377Arg,ENST00000382108,;SPATA13,missense_variant,p.Gly377Arg,ENST00000424834,;SPATA13,intron_variant,,ENST00000382095,;SPATA13,upstream_gene_variant,,ENST00000474317,;RP11-307N16.6,missense_variant,p.Gly377Arg,ENST00000382141,;SPATA13,non_coding_transcript_exon_variant,,ENST00000466831,;	A	ENSG00000182957	ENST00000424834	Transcript	missense_variant	1602	1129	377	G/R	Ggg/Agg	.	.	.	1	SPATA13	HGNC	23222	protein_coding	YES	CCDS53857.1	ENSP00000398560	.	J3KQH2_HUMAN	UPI000165C148	.	tolerated_low_confidence(0.55)	benign(0.078)	4/15	.	hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGGGGCG	.	5	ESCA
CDK8	0	.	GRCh37	13	26978124	26978124	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1301C>A	p.Pro434His	p.P434H	ENST00000381527	13/13	35	21	14	26	26	0	CDK8,missense_variant,p.Pro434His,ENST00000381527,;CDK8,3_prime_UTR_variant,,ENST00000536792,;CDK8,non_coding_transcript_exon_variant,,ENST00000480323,;CDK8,non_coding_transcript_exon_variant,,ENST00000477277,;CDK8,downstream_gene_variant,,ENST00000465820,;CDK8,downstream_gene_variant,,ENST00000477290,;	A	ENSG00000132964	ENST00000381527	Transcript	missense_variant	1804	1301	434	P/H	cCt/cAt	.	.	.	1	CDK8	HGNC	1779	protein_coding	YES	CCDS9317.1	ENSP00000370938	CDK8_HUMAN	B4DL75_HUMAN	UPI000002E531	.	deleterious_low_confidence(0.03)	benign(0.219)	13/13	.	hmmpanther:PTHR24056:SF162,hmmpanther:PTHR24056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACCCTGGAC	.	5	ESCA
WASF3	0	.	GRCh37	13	27256953	27256953	+	Missense_Mutation	SNP	C	C	T	rs373519573	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1193C>T	p.Pro398Leu	p.P398L	ENST00000335327	9/10	20	10	9	12	12	0	WASF3,missense_variant,p.Pro395Leu,ENST00000361042,;WASF3,missense_variant,p.Pro398Leu,ENST00000335327,;	T	ENSG00000132970	ENST00000335327	Transcript	missense_variant	1371	1193	398	P/L	cCg/cTg	rs373519573	.	.	1	WASF3	HGNC	12734	protein_coding	YES	CCDS9318.1	ENSP00000335055	WASF3_HUMAN	Q5T8P4_HUMAN,B4DGR1_HUMAN	UPI000013CEA7	.	deleterious(0.05)	probably_damaging(0.998)	9/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12902:SF7,hmmpanther:PTHR12902	T:0.0006	T:0	T:0.0014	.	T:0.001	T:0	T:0.001	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCCGGGCC	byFrequency|byCluster|by1000G	5	ESCA
PDX1	0	.	GRCh37	13	28498619	28498619	+	Silent	SNP	C	C	T	rs776932903	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633C>T	p.%3D	p.G211G	ENST00000381033	2/2	30	26	3	11	11	0	PDX1,synonymous_variant,p.%3D,ENST00000381033,;PDX1-AS1,upstream_gene_variant,,ENST00000499662,;	T	ENSG00000139515	ENST00000381033	Transcript	synonymous_variant	752	633	211	G	ggC/ggT	rs776932903	.	.	1	PDX1	HGNC	6107	protein_coding	YES	CCDS9327.1	ENSP00000370421	PDX1_HUMAN	.	UPI000012D7D9	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCGGCGGGAC	.	4	ESCA
FLT3	0	.	GRCh37	13	28636205	28636205	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.167T>C	p.Val56Ala	p.V56A	ENST00000241453	3/24	16	13	3	12	12	0	FLT3,missense_variant,p.Val56Ala,ENST00000241453,;FLT3,missense_variant,p.Val56Ala,ENST00000537084,;FLT3,missense_variant,p.Val56Ala,ENST00000380982,;FLT3,missense_variant,p.Val56Ala,ENST00000380987,;	G	ENSG00000122025	ENST00000241453	Transcript	missense_variant	249	167	56	V/A	gTa/gCa	.	.	.	-1	FLT3	HGNC	3765	protein_coding	YES	CCDS31953.1	ENSP00000241453	FLT3_HUMAN	.	UPI00001FC90B	.	tolerated_low_confidence(0.4)	benign(0.001)	3/24	.	PIRSF_domain:PIRSF000615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGATACCTAC	.	2	ESCA
POMP	0	.	GRCh37	13	29238658	29238658	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114G>T	p.%3D	p.V38V	ENST00000380842	3/6	42	24	17	29	29	0	POMP,synonymous_variant,p.%3D,ENST00000380842,;POMP,non_coding_transcript_exon_variant,,ENST00000460403,;	T	ENSG00000132963	ENST00000380842	Transcript	synonymous_variant	195	114	38	V	gtG/gtT	.	.	.	1	POMP	HGNC	20330	protein_coding	YES	CCDS9331.1	ENSP00000370222	POMP_HUMAN	.	UPI000006E3C4	.	.	.	3/6	.	hmmpanther:PTHR12828:SF3,hmmpanther:PTHR12828,Pfam_domain:PF05348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTGAAAAA	.	5	ESCA
KATNAL1	0	.	GRCh37	13	30829644	30829644	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432G>T	p.Lys144Asn	p.K144N	ENST00000380615	4/11	73	39	34	62	62	0	KATNAL1,missense_variant,p.Lys144Asn,ENST00000414289,;KATNAL1,missense_variant,p.Lys144Asn,ENST00000380617,;KATNAL1,missense_variant,p.Lys144Asn,ENST00000441394,;KATNAL1,missense_variant,p.Lys144Asn,ENST00000380615,;	A	ENSG00000102781	ENST00000380615	Transcript	missense_variant	600	432	144	K/N	aaG/aaT	.	.	.	-1	KATNAL1	HGNC	28361	protein_coding	YES	CCDS31956.1	ENSP00000369989	KATL1_HUMAN	Q5T558_HUMAN,A2A3H2_HUMAN	UPI000006F05B	.	tolerated(0.3)	benign(0.005)	4/11	.	HAMAP:MF_03023,HAMAP:MF_03024,hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTCTTTGA	.	5	ESCA
FRY	0	.	GRCh37	13	32709319	32709319	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076T>C	p.Leu359Ser	p.L359S	ENST00000380250	10/61	31	15	15	33	33	0	FRY,missense_variant,p.Leu359Ser,ENST00000380250,;	C	ENSG00000073910	ENST00000380250	Transcript	missense_variant	1572	1076	359	L/S	tTg/tCg	.	.	.	1	FRY	HGNC	20367	protein_coding	YES	CCDS41875.1	ENSP00000369600	FRY_HUMAN	Q96KW3_HUMAN,F5H4D2_HUMAN	UPI000046FD40	.	deleterious(0.03)	probably_damaging(0.999)	10/61	.	Pfam_domain:PF14222,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTTGGTTA	.	5	ESCA
BRCA2	0	.	GRCh37	13	32913836	32913837	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5351dupA	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000544455	11/28	34	26	8	32	32	0	BRCA2,frameshift_variant,p.Asn1784LysfsTer3,ENST00000544455,;BRCA2,frameshift_variant,p.Asn1784LysfsTer3,ENST00000380152,;	A	ENSG00000139618	ENST00000544455	Transcript	frameshift_variant	5571-5572	5344-5345	1782	Q/QX	caa/cAaa	.	.	.	1	BRCA2	HGNC	1101	protein_coding	YES	CCDS9344.1	ENSP00000439902	BRCA2_HUMAN	Q9H4L3_HUMAN,Q8IU82_HUMAN,Q8IU77_HUMAN,Q8IU64_HUMAN,K4K7W0_HUMAN,K4JXT6_HUMAN,K4JTT2_HUMAN,E9PIQ1_HUMAN	UPI00001FCBCC	.	.	.	11/28	.	hmmpanther:PTHR11289:SF0,hmmpanther:PTHR11289,PIRSF_domain:PIRSF002397	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAGATCAAAAA	.	2	ESCA
RFC3	0	.	GRCh37	13	34410549	34410549	+	3'UTR	SNP	G	G	A	rs556832657	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*117G>A	.	.	ENST00000380071	9/9	10	5	5	10	10	0	RFC3,3_prime_UTR_variant,,ENST00000380071,;RFC3,intron_variant,,ENST00000434425,;	A	ENSG00000133119	ENST00000380071	Transcript	3_prime_UTR_variant	1318	.	.	.	.	rs556832657	.	.	1	RFC3	HGNC	9971	protein_coding	YES	CCDS9352.1	ENSP00000369411	RFC3_HUMAN	.	UPI0000125168	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTTGGTAATA	.	3	ESCA
RFXAP	0	.	GRCh37	13	37401948	37401948	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*64delT	.	.	ENST00000255476	3/3	38	33	5	33	33	0	RFXAP,3_prime_UTR_variant,,ENST00000255476,;RFXAP,intron_variant,,ENST00000472888,;	-	ENSG00000133111	ENST00000255476	Transcript	3_prime_UTR_variant	1011	.	.	.	.	.	.	.	1	RFXAP	HGNC	9988	protein_coding	YES	CCDS9359.1	ENSP00000255476	RFXAP_HUMAN	.	UPI0000133812	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGCATATTTTTT	.	3	ESCA
EXOSC8	0	.	GRCh37	13	37580070	37580070	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.252T>A	p.Asp84Glu	p.D84E	ENST00000389704	6/11	55	31	23	44	44	0	EXOSC8,missense_variant,p.Asp84Glu,ENST00000389704,;SUPT20H,downstream_gene_variant,,ENST00000360252,;SUPT20H,downstream_gene_variant,,ENST00000356185,;SUPT20H,downstream_gene_variant,,ENST00000469488,;SUPT20H,downstream_gene_variant,,ENST00000350612,;EXOSC8,upstream_gene_variant,,ENST00000481013,;SUPT20H,downstream_gene_variant,,ENST00000464744,;SUPT20H,downstream_gene_variant,,ENST00000475892,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000489088,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000488779,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000474661,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000464235,;EXOSC8,downstream_gene_variant,,ENST00000488108,;EXOSC8,downstream_gene_variant,,ENST00000470423,;EXOSC8,3_prime_UTR_variant,,ENST00000239893,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000495092,;EXOSC8,intron_variant,,ENST00000490537,;SUPT20H,downstream_gene_variant,,ENST00000473871,;SUPT20H,downstream_gene_variant,,ENST00000484078,;SUPT20H,downstream_gene_variant,,ENST00000490716,;SUPT20H,downstream_gene_variant,,ENST00000495071,;SUPT20H,downstream_gene_variant,,ENST00000472948,;	A	ENSG00000120699	ENST00000389704	Transcript	missense_variant	517	252	84	D/E	gaT/gaA	.	.	.	1	EXOSC8	HGNC	17035	protein_coding	YES	CCDS31958.1	ENSP00000374354	EXOS8_HUMAN	.	UPI000004A07D	.	tolerated(0.64)	benign(0.005)	6/11	.	hmmpanther:PTHR11097:SF9,hmmpanther:PTHR11097,Pfam_domain:PF01138,Gene3D:1e3hA01,Superfamily_domains:SSF54211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGATCTACC	.	5	ESCA
FOXO1	0	.	GRCh37	13	41133062	41133062	+	3'UTR	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*124A>C	.	.	ENST00000379561	3/3	28	21	7	23	23	0	FOXO1,3_prime_UTR_variant,,ENST00000379561,;FOXO1,downstream_gene_variant,,ENST00000473775,;	G	ENSG00000150907	ENST00000379561	Transcript	3_prime_UTR_variant	2477	.	.	.	.	.	.	.	-1	FOXO1	HGNC	3819	protein_coding	YES	CCDS9371.1	ENSP00000368880	FOXO1_HUMAN	.	UPI000013DC20	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TTTTTTTGTTT	.	2	ESCA
LRRC63	0	.	GRCh37	13	46840913	46840913	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360delC	p.His454MetfsTer4	p.H454Mfs*4	ENST00000595396	8/9	56	40	16	38	38	0	LRRC63,frameshift_variant,p.His454MetfsTer4,ENST00000446175,;LRRC63,frameshift_variant,p.His454MetfsTer4,ENST00000595396,;LRRC63,frameshift_variant,p.His454MetfsTer4,ENST00000378805,;FAM206BP,upstream_gene_variant,,ENST00000510179,;	-	ENSG00000173988	ENST00000595396	Transcript	frameshift_variant	1356	1356	452	F/X	ttC/tt	.	.	.	1	LRRC63	HGNC	34296	protein_coding	YES	CCDS61325.1	ENSP00000469337	.	M0QXR7_HUMAN	UPI0002742DC2	.	.	.	8/9	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF416,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTTTCCCCCA	.	3	ESCA
UTP14C	0	.	GRCh37	13	52604834	52604834	+	Missense_Mutation	SNP	G	G	A	rs770374423	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1894G>A	p.Glu632Lys	p.E632K	ENST00000521776	2/2	57	36	21	40	40	0	UTP14C,missense_variant,p.Glu632Lys,ENST00000521776,;ALG11,downstream_gene_variant,,ENST00000523764,;ALG11,downstream_gene_variant,,ENST00000521508,;ALG11,downstream_gene_variant,,ENST00000519151,;	A	ENSG00000253797	ENST00000521776	Transcript	missense_variant	2627	1894	632	E/K	Gag/Aag	rs770374423,COSM1232144	.	.	1	UTP14C	HGNC	20321	protein_coding	YES	CCDS31978.1	ENSP00000428619	UT14C_HUMAN	.	UPI000006DB4B	.	tolerated(0.06)	benign(0.117)	2/2	.	Pfam_domain:PF04615,hmmpanther:PTHR14150:SF16,hmmpanther:PTHR14150	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGAGTGG	byFrequency	5	ESCA
RP11-248G5.8	0	.	GRCh37	13	52854009	52854009	+	RNA	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.529G>A	.	.	ENST00000451298	6/22	75	58	17	67	67	0	TPTE2P2,non_coding_transcript_exon_variant,,ENST00000605924,;RP11-248G5.8,non_coding_transcript_exon_variant,,ENST00000451298,;TPTE2P2,non_coding_transcript_exon_variant,,ENST00000403471,;	T	ENSG00000217576	ENST00000451298	Transcript	non_coding_transcript_exon_variant	529	.	.	.	.	.	.	.	-1	RP11-248G5.8	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	6/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCCCGAAGA	.	5	ESCA
PCDH17	0	.	GRCh37	13	58206843	58206843	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163G>A	p.Gly55Ser	p.G55S	ENST00000377918	1/4	8	2	6	13	13	0	PCDH17,missense_variant,p.Gly55Ser,ENST00000377918,;PCDH17,missense_variant,p.Gly55Ser,ENST00000484979,;	A	ENSG00000118946	ENST00000377918	Transcript	missense_variant	189	163	55	G/S	Ggc/Agc	.	.	.	1	PCDH17	HGNC	14267	protein_coding	YES	CCDS31986.1	ENSP00000367151	PCD17_HUMAN	.	UPI00001FCE5B	.	tolerated(0.88)	benign(0.109)	1/4	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF41,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGGCGGCGGA	.	2	ESCA
PCDH17	0	.	GRCh37	13	58302171	58302171	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2743T>A	.	.	ENST00000377918	4/4	51	33	18	42	42	0	PCDH17,3_prime_UTR_variant,,ENST00000377918,;PCDH17,downstream_gene_variant,,ENST00000484979,;	A	ENSG00000118946	ENST00000377918	Transcript	3_prime_UTR_variant	6249	.	.	.	.	.	.	.	1	PCDH17	HGNC	14267	protein_coding	YES	CCDS31986.1	ENSP00000367151	PCD17_HUMAN	.	UPI00001FCE5B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAGTGATTT	.	5	ESCA
TDRD3	0	.	GRCh37	13	61109341	61109341	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2092A>G	p.Ile698Val	p.I698V	ENST00000535286	12/14	57	30	26	39	39	0	TDRD3,missense_variant,p.Ile605Val,ENST00000377894,;TDRD3,missense_variant,p.Ile605Val,ENST00000196169,;TDRD3,missense_variant,p.Ile605Val,ENST00000377881,;TDRD3,missense_variant,p.Ile698Val,ENST00000535286,;TDRD3,non_coding_transcript_exon_variant,,ENST00000471710,;	G	ENSG00000083544	ENST00000535286	Transcript	missense_variant	2164	2092	698	I/V	Atc/Gtc	.	.	.	1	TDRD3	HGNC	20612	protein_coding	YES	CCDS53872.1	ENSP00000440190	TDRD3_HUMAN	B1AMN9_HUMAN	UPI000174200C	.	deleterious(0.05)	benign(0.046)	12/14	.	PROSITE_profiles:PS50304,hmmpanther:PTHR13681,Pfam_domain:PF00567,Gene3D:2.30.30.140,SMART_domains:SM00333,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCAATATCAAG	.	3	ESCA
PCDH20	0	.	GRCh37	13	61986976	61986976	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1256T>C	p.Val419Ala	p.V419A	ENST00000409186	5/5	20	11	8	24	24	0	PCDH20,missense_variant,p.Val419Ala,ENST00000409204,;PCDH20,missense_variant,p.Val419Ala,ENST00000409186,;	G	ENSG00000197991	ENST00000409186	Transcript	missense_variant	3362	1256	419	V/A	gTt/gCt	.	.	.	-1	PCDH20	HGNC	14257	protein_coding	YES	CCDS9442.2	ENSP00000386653	PCD20_HUMAN	B3KSZ7_HUMAN	UPI000007371F	.	deleterious(0)	benign(0.029)	5/5	.	SMART_domains:SM00112,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF24,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATAACTTTA	.	5	ESCA
PCDH9	0	.	GRCh37	13	66877245	66877245	+	3'UTR	DEL	T	T	-	rs137921427	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1542delA	.	.	ENST00000544246	5/5	28	14	14	26	26	0	PCDH9,3_prime_UTR_variant,,ENST00000544246,;PCDH9,3_prime_UTR_variant,,ENST00000377865,;PCDH9,downstream_gene_variant,,ENST00000328454,;PCDH9,downstream_gene_variant,,ENST00000456367,;PCDH9-AS1,upstream_gene_variant,,ENST00000430861,;	-	ENSG00000184226	ENST00000544246	Transcript	3_prime_UTR_variant	5948	.	.	.	.	rs137921427	.	.	-1	PCDH9	HGNC	8661	protein_coding	YES	CCDS9444.1	ENSP00000442186	PCDH9_HUMAN	.	UPI00001FCE90	.	.	.	5/5	.	.	G:0.0016	G:0.0015	G:0.0029	.	G:0.001	G:0.002	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTTTGTTTTTT	byFrequency|byCluster|by1000G	2	ESCA
MZT1	0	.	GRCh37	13	73284242	73284242	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*218delT	.	.	ENST00000377818	3/3	49	39	10	43	43	0	MZT1,3_prime_UTR_variant,,ENST00000377818,;RNU6-80P,upstream_gene_variant,,ENST00000384195,;	-	ENSG00000204899	ENST00000377818	Transcript	3_prime_UTR_variant	552	.	.	.	.	.	.	.	-1	MZT1	HGNC	33830	protein_coding	YES	CCDS31990.1	ENSP00000367049	MZT1_HUMAN	.	UPI000013D73A	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTGTTAAAAAA	.	3	ESCA
PIBF1	0	.	GRCh37	13	73505320	73505320	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1748G>C	p.Arg583Thr	p.R583T	ENST00000326291	14/18	13	6	6	17	17	0	PIBF1,missense_variant,p.Arg583Thr,ENST00000326291,;	C	ENSG00000083535	ENST00000326291	Transcript	missense_variant	2086	1748	583	R/T	aGa/aCa	.	.	.	1	PIBF1	HGNC	23352	protein_coding	YES	CCDS31991.1	ENSP00000317144	PIBF1_HUMAN	.	UPI00001418B9	.	deleterious(0)	probably_damaging(0.99)	14/18	.	hmmpanther:PTHR18950:SF0,hmmpanther:PTHR18950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AAGAAGAGTGC	.	4	ESCA
LMO7	0	.	GRCh37	13	76374862	76374862	+	5'UTR	SNP	A	A	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-195A>C	.	.	ENST00000465261	4/27	52	37	15	58	58	0	LMO7,missense_variant,p.Ser221Arg,ENST00000357063,;LMO7,missense_variant,p.Ser130Arg,ENST00000526202,;LMO7,missense_variant,p.Ser221Arg,ENST00000341547,;LMO7,missense_variant,p.Ser221Arg,ENST00000377534,;LMO7,missense_variant,p.Ser169Arg,ENST00000377499,;LMO7,5_prime_UTR_variant,,ENST00000534657,;LMO7,5_prime_UTR_variant,,ENST00000465261,;LMO7,5_prime_UTR_variant,,ENST00000497947,;LMO7,5_prime_UTR_variant,,ENST00000321797,;LMO7,upstream_gene_variant,,ENST00000526371,;LMO7,upstream_gene_variant,,ENST00000489941,;LMO7,upstream_gene_variant,,ENST00000526528,;LMO7,upstream_gene_variant,,ENST00000525373,;LMO7,upstream_gene_variant,,ENST00000447038,;LMO7,non_coding_transcript_exon_variant,,ENST00000533305,;RP11-29G8.3,non_coding_transcript_exon_variant,,ENST00000563635,;LMO7,non_coding_transcript_exon_variant,,ENST00000465309,;	C	ENSG00000136153	ENST00000465261	Transcript	5_prime_UTR_variant	566	.	.	.	.	.	.	.	1	LMO7	HGNC	6646	protein_coding	YES	CCDS53876.1	ENSP00000433352	.	E9PRJ0_HUMAN,E9PLH4_HUMAN	UPI0001929501	.	.	.	4/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGACAGTGGC	.	5	ESCA
KCTD12	0	.	GRCh37	13	77454950	77454951	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4355dupT	.	.	ENST00000377474	1/1	33	17	15	36	36	0	KCTD12,3_prime_UTR_variant,,ENST00000377474,;KCTD12,downstream_gene_variant,,ENST00000317765,;	A	ENSG00000178695	ENST00000377474	Transcript	3_prime_UTR_variant	5575-5576	.	.	.	.	.	.	.	-1	KCTD12	HGNC	14678	protein_coding	YES	CCDS9455.1	ENSP00000366694	KCD12_HUMAN	.	UPI0000073DDF	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAATTTAAAAA	.	2	ESCA
SLAIN1	0	.	GRCh37	13	78337494	78337494	+	3'Flank	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000488699	.	60	30	30	39	39	0	SLAIN1,3_prime_UTR_variant,,ENST00000466548,;SLAIN1,3_prime_UTR_variant,,ENST00000314070,;SLAIN1,3_prime_UTR_variant,,ENST00000351546,;SLAIN1,3_prime_UTR_variant,,ENST00000358679,;SLAIN1,3_prime_UTR_variant,,ENST00000267219,;SLAIN1,3_prime_UTR_variant,,ENST00000418532,;SLAIN1,downstream_gene_variant,,ENST00000441784,;SLAIN1,downstream_gene_variant,,ENST00000488699,;	T	ENSG00000139737	ENST00000488699	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2	1	SLAIN1	HGNC	26387	protein_coding	YES	CCDS31995.2	ENSP00000418707	SLAI1_HUMAN	Q5T6P2_HUMAN,C9JUW9_HUMAN,C9JP03_HUMAN	UPI0001914D54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATGGACCAG	.	5	ESCA
SLITRK1	0	.	GRCh37	13	84452663	84452664	+	3'UTR	INS	-	-	A	rs200663563	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*888dupT	.	.	ENST00000377084	1/1	24	17	6	18	18	0	SLITRK1,3_prime_UTR_variant,,ENST00000377084,;	A	ENSG00000178235	ENST00000377084	Transcript	3_prime_UTR_variant	3865-3866	.	.	.	.	rs200663563	.	.	-1	SLITRK1	HGNC	20297	protein_coding	YES	CCDS9464.1	ENSP00000366288	SLIK1_HUMAN	.	UPI0000035971	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTATTAAAAA	byCluster|by1000G	2	ESCA
IPO5	0	.	GRCh37	13	98655251	98655251	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1511T>C	p.Val504Ala	p.V504A	ENST00000261574	16/29	31	25	6	20	20	0	IPO5,missense_variant,p.Val504Ala,ENST00000261574,;IPO5,missense_variant,p.Val488Ala,ENST00000469360,;IPO5,missense_variant,p.Val486Ala,ENST00000490680,;IPO5,missense_variant,p.Val486Ala,ENST00000357602,;IPO5,missense_variant,p.Val361Ala,ENST00000539640,;IPO5,upstream_gene_variant,,ENST00000493492,;IPO5,non_coding_transcript_exon_variant,,ENST00000479736,;IPO5,non_coding_transcript_exon_variant,,ENST00000491555,;IPO5,downstream_gene_variant,,ENST00000470493,;	C	ENSG00000065150	ENST00000261574	Transcript	missense_variant	1691	1511	504	V/A	gTg/gCg	.	.	.	1	IPO5	HGNC	6402	protein_coding	YES	CCDS31999.1	ENSP00000261574	IPO5_HUMAN	Q9BVS9_HUMAN,E7EX05_HUMAN,E7EWK4_HUMAN,E7ETV3_HUMAN,E7ESZ1_HUMAN,E7ESA1_HUMAN,C9JZD8_HUMAN,C9JZ53_HUMAN,C9JXE0_HUMAN,C9JQT6_HUMAN,C9J875_HUMAN,B3KWG6_HUMAN	UPI0000163C1C	.	tolerated(0.3)	benign(0.138)	16/29	.	hmmpanther:PTHR10527:SF22,hmmpanther:PTHR10527,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGGTGAAAC	.	5	ESCA
RCOR1	0	.	GRCh37	14	103194510	103194510	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1675delT	.	.	ENST00000262241	12/12	14	7	7	8	8	0	RCOR1,3_prime_UTR_variant,,ENST00000262241,;RCOR1,3_prime_UTR_variant,,ENST00000570597,;RCOR1,downstream_gene_variant,,ENST00000560472,;	-	ENSG00000089902	ENST00000262241	Transcript	3_prime_UTR_variant	3351	.	.	.	.	.	.	.	1	RCOR1	HGNC	17441	protein_coding	YES	CCDS9974.2	ENSP00000262241	.	J3KN32_HUMAN	UPI0000D6A053	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTAAATTTTTT	.	2	ESCA
TNFAIP2	0	.	GRCh37	14	103598087	103598087	+	Silent	SNP	T	T	C	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1410T>C	p.%3D	p.H470H	ENST00000560869	8/12	100	71	28	26	26	0	TNFAIP2,synonymous_variant,p.%3D,ENST00000560670,;TNFAIP2,synonymous_variant,p.%3D,ENST00000333007,;TNFAIP2,synonymous_variant,p.%3D,ENST00000451723,;TNFAIP2,synonymous_variant,p.%3D,ENST00000560869,;TNFAIP2,upstream_gene_variant,,ENST00000559255,;TNFAIP2,upstream_gene_variant,,ENST00000538222,;TNFAIP2,upstream_gene_variant,,ENST00000561217,;TNFAIP2,downstream_gene_variant,,ENST00000559195,;TNFAIP2,synonymous_variant,p.%3D,ENST00000561156,;TNFAIP2,3_prime_UTR_variant,,ENST00000560562,;TNFAIP2,3_prime_UTR_variant,,ENST00000559406,;TNFAIP2,non_coding_transcript_exon_variant,,ENST00000560428,;	C	ENSG00000185215	ENST00000560869	Transcript	synonymous_variant	2049	1410	470	H	caT/caC	COSM4049257	.	.	1	TNFAIP2	HGNC	11895	protein_coding	YES	CCDS9979.1	ENSP00000452634	TNAP2_HUMAN	H0YL88_HUMAN,E7EWH2_HUMAN,B7ZB31_HUMAN	UPI0000164A41	.	.	.	8/12	.	hmmpanther:PTHR21292:SF4,hmmpanther:PTHR21292,Pfam_domain:PF06046	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCATGAGGA	.	5	ESCA
INF2	0	.	GRCh37	14	105180705	105180705	+	Missense_Mutation	SNP	C	C	T	rs376139171	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3206C>T	p.Pro1069Leu	p.P1069L	ENST00000392634	21/23	85	12	73	32	32	0	INF2,missense_variant,p.Pro537Leu,ENST00000252527,;INF2,missense_variant,p.Pro1069Leu,ENST00000330634,;INF2,missense_variant,p.Pro1069Leu,ENST00000392634,;INF2,upstream_gene_variant,,ENST00000481338,;INF2,downstream_gene_variant,,ENST00000474229,;INF2,downstream_gene_variant,,ENST00000477497,;INF2,downstream_gene_variant,,ENST00000480763,;	T	ENSG00000203485	ENST00000392634	Transcript	missense_variant	3318	3206	1069	P/L	cCa/cTa	rs376139171	.	.	1	INF2	HGNC	23791	protein_coding	YES	CCDS9989.2	ENSP00000376410	INF2_HUMAN	.	UPI000156D0FB	.	tolerated_low_confidence(0.08)	unknown(0)	21/23	.	hmmpanther:PTHR23213:SF5,hmmpanther:PTHR23213	.	.	.	.	.	.	.	T:0	T:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTCCACGGC	byFrequency|byCluster	5	ESCA
AKT1	0	.	GRCh37	14	105246502	105246502	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98G>A	p.Gly33Asp	p.G33D	ENST00000554581	2/13	105	95	10	38	38	0	AKT1,missense_variant,p.Gly33Asp,ENST00000407796,;AKT1,missense_variant,p.Gly33Asp,ENST00000555926,;AKT1,missense_variant,p.Gly33Asp,ENST00000554581,;AKT1,missense_variant,p.Gly33Asp,ENST00000402615,;AKT1,missense_variant,p.Gly33Asp,ENST00000349310,;AKT1,missense_variant,p.Gly33Asp,ENST00000555528,;AKT1,missense_variant,p.Gly33Asp,ENST00000554848,;AKT1,5_prime_UTR_variant,,ENST00000555380,;AKT1,upstream_gene_variant,,ENST00000544168,;AKT1,upstream_gene_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000557552,;AKT1,upstream_gene_variant,,ENST00000556836,;	T	ENSG00000142208	ENST00000554581	Transcript	missense_variant	1579	98	33	G/D	gGc/gAc	.	.	.	-1	AKT1	HGNC	391	protein_coding	YES	CCDS9994.1	ENSP00000451828	AKT1_HUMAN	B0LPE5_HUMAN,Q9BV07_HUMAN,G3V4I6_HUMAN,G3V3K5_HUMAN,B7Z5R1_HUMAN,B3KXD7_HUMAN	UPI0000070813	.	deleterious(0)	probably_damaging(0.99)	2/13	.	PROSITE_profiles:PS50003,hmmpanther:PTHR24352,hmmpanther:PTHR24352:SF30,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGTGCCATCA	.	4	ESCA
CEP170B	0	.	GRCh37	14	105353130	105353130	+	Missense_Mutation	SNP	C	C	T	rs758162711	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2554C>T	p.Arg852Trp	p.R852W	ENST00000414716	12/19	54	40	13	23	23	0	CEP170B,missense_variant,p.Arg852Trp,ENST00000414716,;CEP170B,missense_variant,p.Arg782Trp,ENST00000556508,;CEP170B,missense_variant,p.Arg782Trp,ENST00000418279,;CEP170B,missense_variant,p.Arg853Trp,ENST00000453495,;	T	ENSG00000099814	ENST00000414716	Transcript	missense_variant	2782	2554	852	R/W	Cgg/Tgg	rs758162711	.	.	1	CEP170B	HGNC	20362	protein_coding	YES	CCDS45175.1	ENSP00000404151	C170B_HUMAN	E9PFC1_HUMAN	UPI00001FDCF7	.	deleterious(0.03)	benign(0.008)	12/19	.	hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF18,Pfam_domain:PF15308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGACGGTCC	byFrequency	5	ESCA
AHNAK2	0	.	GRCh37	14	105411968	105411968	+	Missense_Mutation	SNP	T	T	C	rs772239379	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9820A>G	p.Met3274Val	p.M3274V	ENST00000333244	7/7	194	182	12	73	73	0	AHNAK2,missense_variant,p.Met3274Val,ENST00000333244,;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;	C	ENSG00000185567	ENST00000333244	Transcript	missense_variant	9940	9820	3274	M/V	Atg/Gtg	rs772239379	.	.	-1	AHNAK2	HGNC	20125	protein_coding	YES	CCDS45177.1	ENSP00000353114	AHNK2_HUMAN	.	UPI00015BB2CA	.	.	benign(0.001)	7/7	.	hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCATGCTGG	byFrequency	2	ESCA
AHNAK2	0	.	GRCh37	14	105411976	105411976	+	Missense_Mutation	SNP	T	T	A	rs777007026	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9812A>T	p.Gln3271Leu	p.Q3271L	ENST00000333244	7/7	187	176	10	67	67	0	AHNAK2,missense_variant,p.Gln3271Leu,ENST00000333244,;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;	A	ENSG00000185567	ENST00000333244	Transcript	missense_variant	9932	9812	3271	Q/L	cAg/cTg	rs777007026	.	.	-1	AHNAK2	HGNC	20125	protein_coding	YES	CCDS45177.1	ENSP00000353114	AHNK2_HUMAN	.	UPI00015BB2CA	.	.	benign(0.001)	7/7	.	hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGGCTGAGAC	byFrequency	2	ESCA
POTEM	0	.	GRCh37	14	20002279	20002279	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1143G>T	p.%3D	p.L381L	ENST00000551509	7/11	186	147	38	80	80	0	POTEM,synonymous_variant,p.%3D,ENST00000551509,;RP11-244H18.1,upstream_gene_variant,,ENST00000547584,;POTEM,synonymous_variant,p.%3D,ENST00000547848,;POTEM,3_prime_UTR_variant,,ENST00000547722,;CTD-2311B13.8,downstream_gene_variant,,ENST00000547150,;	A	ENSG00000187537	ENST00000551509	Transcript	synonymous_variant	1195	1143	381	L	ctG/ctT	.	.	.	-1	POTEM	HGNC	37096	protein_coding	YES	CCDS45076.1	ENSP00000452296	POTEM_HUMAN	.	UPI00006C1407	.	.	.	7/11	.	hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GATGTCAGCTT	.	2	ESCA
TEP1	0	.	GRCh37	14	20845785	20845785	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5849G>T	p.Gly1950Val	p.G1950V	ENST00000262715	40/55	39	19	20	23	23	0	TEP1,missense_variant,p.Gly288Val,ENST00000545983,;TEP1,missense_variant,p.Gly1842Val,ENST00000556935,;TEP1,missense_variant,p.Gly1950Val,ENST00000262715,;TEP1,upstream_gene_variant,,ENST00000553984,;TEP1,missense_variant,p.Ala51Ser,ENST00000471684,;TEP1,missense_variant,p.Ala75Ser,ENST00000556488,;TEP1,missense_variant,p.Gly1293Val,ENST00000555008,;TEP1,3_prime_UTR_variant,,ENST00000555727,;TEP1,3_prime_UTR_variant,,ENST00000557314,;TEP1,upstream_gene_variant,,ENST00000553365,;	A	ENSG00000129566	ENST00000262715	Transcript	missense_variant	5890	5849	1950	G/V	gGc/gTc	COSM954221	.	.	-1	TEP1	HGNC	11726	protein_coding	YES	CCDS9548.1	ENSP00000262715	TEP1_HUMAN	G3V591_HUMAN	UPI000013D30B	.	deleterious(0)	probably_damaging(0.997)	40/55	.	Superfamily_domains:SSF50978,Superfamily_domains:SSF63829,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF402,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATGCCATCC	.	5	ESCA
TMEM55B	0	.	GRCh37	14	20926824	20926824	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.749T>G	p.Ile250Ser	p.I250S	ENST00000398020	7/7	77	50	26	24	24	0	TMEM55B,missense_variant,p.Ile76Ser,ENST00000554028,;TMEM55B,missense_variant,p.Ile250Ser,ENST00000398020,;TMEM55B,missense_variant,p.Ile83Ser,ENST00000553460,;TMEM55B,missense_variant,p.Ile243Ser,ENST00000250489,;APEX1,downstream_gene_variant,,ENST00000557054,;APEX1,downstream_gene_variant,,ENST00000438886,;APEX1,downstream_gene_variant,,ENST00000556054,;APEX1,downstream_gene_variant,,ENST00000557150,;APEX1,downstream_gene_variant,,ENST00000557344,;APEX1,downstream_gene_variant,,ENST00000398030,;APEX1,downstream_gene_variant,,ENST00000553368,;APEX1,downstream_gene_variant,,ENST00000555414,;OSGEP,upstream_gene_variant,,ENST00000206542,;APEX1,downstream_gene_variant,,ENST00000553681,;APEX1,downstream_gene_variant,,ENST00000555839,;APEX1,downstream_gene_variant,,ENST00000557181,;APEX1,downstream_gene_variant,,ENST00000216714,;OSGEP,upstream_gene_variant,,ENST00000488532,;TMEM55B,downstream_gene_variant,,ENST00000556093,;APEX1,downstream_gene_variant,,ENST00000557592,;OSGEP,upstream_gene_variant,,ENST00000553640,;OSGEP,upstream_gene_variant,,ENST00000556252,;APEX1,downstream_gene_variant,,ENST00000556296,;OSGEP,upstream_gene_variant,,ENST00000554699,;APEX1,downstream_gene_variant,,ENST00000557365,;APEX1,downstream_gene_variant,,ENST00000554813,;TMEM55B,non_coding_transcript_exon_variant,,ENST00000557041,;TMEM55B,non_coding_transcript_exon_variant,,ENST00000553602,;APEX1,downstream_gene_variant,,ENST00000553555,;OSGEP,upstream_gene_variant,,ENST00000556439,;APEX1,downstream_gene_variant,,ENST00000555306,;APEX1,downstream_gene_variant,,ENST00000554325,;APEX1,downstream_gene_variant,,ENST00000557159,;	C	ENSG00000165782	ENST00000398020	Transcript	missense_variant	889	749	250	I/S	aTc/aGc	.	.	.	-1	TMEM55B	HGNC	19299	protein_coding	YES	CCDS41911.1	ENSP00000381102	TM55B_HUMAN	G3V5T5_HUMAN,G3V3P3_HUMAN	UPI00001B3DC8	.	deleterious(0)	possibly_damaging(0.787)	7/7	.	hmmpanther:PTHR21014:SF3,hmmpanther:PTHR21014,Pfam_domain:PF09788	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAGATGCCT	.	5	ESCA
HNRNPC	0	.	GRCh37	14	21678705	21678705	+	3'UTR	DEL	T	T	-	rs557994808	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*677delA	.	.	ENST00000320084	8/8	39	30	9	17	17	0	HNRNPC,3_prime_UTR_variant,,ENST00000554969,;HNRNPC,3_prime_UTR_variant,,ENST00000336053,;HNRNPC,3_prime_UTR_variant,,ENST00000556142,;HNRNPC,3_prime_UTR_variant,,ENST00000320084,;HNRNPC,3_prime_UTR_variant,,ENST00000449098,;HNRNPC,downstream_gene_variant,,ENST00000555883,;HNRNPC,downstream_gene_variant,,ENST00000556628,;HNRNPC,downstream_gene_variant,,ENST00000554539,;HNRNPC,downstream_gene_variant,,ENST00000556513,;HNRNPC,downstream_gene_variant,,ENST00000553753,;HNRNPC,downstream_gene_variant,,ENST00000556897,;HNRNPC,downstream_gene_variant,,ENST00000553300,;HNRNPC,downstream_gene_variant,,ENST00000555309,;HNRNPC,downstream_gene_variant,,ENST00000554383,;HNRNPC,downstream_gene_variant,,ENST00000555137,;HNRNPC,downstream_gene_variant,,ENST00000554455,;HNRNPC,downstream_gene_variant,,ENST00000554891,;HNRNPC,downstream_gene_variant,,ENST00000555914,;HNRNPC,downstream_gene_variant,,ENST00000557201,;HNRNPC,downstream_gene_variant,,ENST00000557157,;HNRNPC,downstream_gene_variant,,ENST00000420743,;HNRNPC,downstream_gene_variant,,ENST00000555215,;HNRNPC,downstream_gene_variant,,ENST00000430246,;LINC00641,upstream_gene_variant,,ENST00000555688,;HNRNPC,downstream_gene_variant,,ENST00000553444,;HNRNPC,downstream_gene_variant,,ENST00000554417,;HNRNPC,downstream_gene_variant,,ENST00000557442,;HNRNPC,downstream_gene_variant,,ENST00000555585,;	-	ENSG00000092199	ENST00000320084	Transcript	3_prime_UTR_variant	1838	.	.	.	.	rs557994808	.	.	-1	HNRNPC	HGNC	5035	protein_coding	YES	CCDS41915.1	ENSP00000319690	HNRPC_HUMAN	G3V575_HUMAN,G3V555_HUMAN,G3V4M8_HUMAN,G3V2H6_HUMAN	UPI000013C6E4	.	.	.	8/8	.	.	G:0.0010	G:0	G:0.0014	.	G:0	G:0.004	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCAGGGTTTTTT	byFrequency|by1000G	2	ESCA
RAB2B	0	.	GRCh37	14	21936607	21936607	+	Missense_Mutation	SNP	G	G	A	rs773591681	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271C>T	p.Arg91Cys	p.R91C	ENST00000397762	5/8	47	25	22	23	23	0	RAB2B,missense_variant,p.Arg91Cys,ENST00000397762,;RAB2B,splice_region_variant,,ENST00000461909,;RAB2B,intron_variant,,ENST00000417141,;	A	ENSG00000129472	ENST00000397762	Transcript	missense_variant	372	271	91	R/C	Cgt/Tgt	rs773591681	.	.	-1	RAB2B	HGNC	20246	protein_coding	YES	CCDS9570.1	ENSP00000380869	RAB2B_HUMAN	Q9UL31_HUMAN,E9PE37_HUMAN,B4DUD4_HUMAN	UPI000013316C	.	deleterious(0)	probably_damaging(0.999)	5/8	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF359,hmmpanther:PTHR24073,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCACGCCTAC	byFrequency	5	ESCA
METTL3	0	.	GRCh37	14	21969886	21969886	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.883C>T	p.Arg295Cys	p.R295C	ENST00000298717	4/11	119	96	23	61	61	0	METTL3,missense_variant,p.Arg295Cys,ENST00000298717,;METTL3,3_prime_UTR_variant,,ENST00000538267,;TOX4,downstream_gene_variant,,ENST00000405508,;METTL3,downstream_gene_variant,,ENST00000377543,;TOX4,downstream_gene_variant,,ENST00000448790,;TOX4,downstream_gene_variant,,ENST00000262709,;METTL3,missense_variant,p.Arg245Cys,ENST00000539760,;METTL3,3_prime_UTR_variant,,ENST00000537163,;METTL3,3_prime_UTR_variant,,ENST00000543235,;METTL3,non_coding_transcript_exon_variant,,ENST00000544500,;METTL3,non_coding_transcript_exon_variant,,ENST00000536201,;METTL3,non_coding_transcript_exon_variant,,ENST00000542054,;METTL3,intron_variant,,ENST00000396522,;METTL3,intron_variant,,ENST00000544248,;METTL3,downstream_gene_variant,,ENST00000539910,;TOX4,downstream_gene_variant,,ENST00000455393,;	A	ENSG00000165819	ENST00000298717	Transcript	missense_variant	1035	883	295	R/C	Cgc/Tgc	.	.	.	-1	METTL3	HGNC	17563	protein_coding	YES	CCDS32044.1	ENSP00000298717	MTA70_HUMAN	B3KSH0_HUMAN	UPI000006CD69	.	deleterious(0.05)	possibly_damaging(0.608)	4/11	.	PROSITE_profiles:PS51563,hmmpanther:PTHR12829	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCGACAGG	.	5	ESCA
MYH6	0	.	GRCh37	14	23859332	23859334	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3664_3666delGAG	p.Glu1222del	p.E1222del	ENST00000405093	26/39	208	186	22	100	100	0	MYH6,inframe_deletion,p.Glu1222del,ENST00000405093,;MYH6,inframe_deletion,p.Glu1222del,ENST00000356287,;MIR208A,upstream_gene_variant,,ENST00000362287,;	-	ENSG00000197616	ENST00000405093	Transcript	inframe_deletion	3735-3737	3664-3666	1222	E/-	GAG/-	.	.	.	-1	MYH6	HGNC	7576	protein_coding	YES	CCDS9600.1	ENSP00000386041	MYH6_HUMAN	Q9UQV1_HUMAN,A8CLL2_HUMAN	UPI0000160969	.	.	.	26/39	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF260,hmmpanther:PTHR13140,Pfam_domain:PF01576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTCTTCTCCTTCT	.	3	ESCA
MYH7	0	.	GRCh37	14	23889279	23889279	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3501C>T	p.%3D	p.R1167R	ENST00000355349	27/40	38	33	5	18	18	0	MYH7,synonymous_variant,p.%3D,ENST00000355349,;MIR208B,upstream_gene_variant,,ENST00000401172,;CTD-2201G16.1,downstream_gene_variant,,ENST00000557368,;	A	ENSG00000092054	ENST00000355349	Transcript	synonymous_variant	3664	3501	1167	R	cgC/cgT	.	.	.	-1	MYH7	HGNC	7577	protein_coding	YES	CCDS9601.1	ENSP00000347507	MYH7_HUMAN	Q59EV3_HUMAN,L0L5E6_HUMAN,A8CLN2_HUMAN,A8CLL2_HUMAN,A6N931_HUMAN,A6N930_HUMAN	UPI000014019B	.	.	.	27/40	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF279,hmmpanther:PTHR13140,Pfam_domain:PF01576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GCCTCGCGCTT	.	2	ESCA
AP1G2	0	.	GRCh37	14	24037239	24037239	+	5'UTR	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-716delG	.	.	ENST00000308724	1/21	84	74	9	32	32	0	AP1G2,5_prime_UTR_variant,,ENST00000308724,;AP1G2,upstream_gene_variant,,ENST00000556843,;JPH4,downstream_gene_variant,,ENST00000544177,;JPH4,downstream_gene_variant,,ENST00000397118,;AP1G2,upstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000397120,;JPH4,downstream_gene_variant,,ENST00000356300,;RP11-66N24.3,non_coding_transcript_exon_variant,,ENST00000555968,;AP1G2,upstream_gene_variant,,ENST00000555118,;AP1G2,upstream_gene_variant,,ENST00000555510,;AP1G2,upstream_gene_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000556943,;AP1G2,upstream_gene_variant,,ENST00000556741,;AP1G2,upstream_gene_variant,,ENST00000554069,;AP1G2,upstream_gene_variant,,ENST00000555789,;AP1G2,upstream_gene_variant,,ENST00000554312,;AP1G2,upstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000556743,;AP1G2,upstream_gene_variant,,ENST00000535852,;AP1G2,upstream_gene_variant,,ENST00000460049,;AP1G2,upstream_gene_variant,,ENST00000554816,;AP1G2,upstream_gene_variant,,ENST00000557132,;AP1G2,upstream_gene_variant,,ENST00000553756,;AP1G2,upstream_gene_variant,,ENST00000557162,;AP1G2,upstream_gene_variant,,ENST00000555974,;AP1G2,upstream_gene_variant,,ENST00000557619,;AP1G2,upstream_gene_variant,,ENST00000554977,;AP1G2,upstream_gene_variant,,ENST00000554554,;AP1G2,upstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000555896,;AP1G2,upstream_gene_variant,,ENST00000556152,;AP1G2,upstream_gene_variant,,ENST00000554982,;AP1G2,upstream_gene_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000465445,;	-	ENSG00000213983	ENST00000308724	Transcript	5_prime_UTR_variant	41	.	.	.	.	.	.	.	-1	AP1G2	HGNC	556	protein_coding	YES	CCDS9602.1	ENSP00000312442	AP1G2_HUMAN	Q86U41_HUMAN,Q86U03_HUMAN,G3V532_HUMAN,G3V3Z2_HUMAN,G3V2V9_HUMAN	UPI0000124FE8	.	.	.	1/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GACAATCCCCCC	.	2	ESCA
PSME2	0	.	GRCh37	14	24615778	24615778	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13T>C	p.Cys5Arg	p.C5R	ENST00000216802	1/11	40	37	3	25	25	0	PSME2,missense_variant,p.Cys5Arg,ENST00000216802,;PSME2,missense_variant,p.Cys5Arg,ENST00000560410,;RNF31,upstream_gene_variant,,ENST00000557991,;RNF31,upstream_gene_variant,,ENST00000559533,;PSME2,upstream_gene_variant,,ENST00000559056,;RNF31,upstream_gene_variant,,ENST00000560787,;RNF31,upstream_gene_variant,,ENST00000560071,;RNF31,upstream_gene_variant,,ENST00000560875,;EMC9,upstream_gene_variant,,ENST00000216799,;EMC9,upstream_gene_variant,,ENST00000560403,;RNF31,upstream_gene_variant,,ENST00000324103,;RNF31,upstream_gene_variant,,ENST00000382687,;EMC9,upstream_gene_variant,,ENST00000419198,;RNF31,upstream_gene_variant,,ENST00000559308,;RNF31,upstream_gene_variant,,ENST00000559275,;RNF31,upstream_gene_variant,,ENST00000559260,;PSME2,non_coding_transcript_exon_variant,,ENST00000471700,;PSME2,non_coding_transcript_exon_variant,,ENST00000559613,;RNF31,upstream_gene_variant,,ENST00000558634,;RNF31,upstream_gene_variant,,ENST00000559438,;PSME2,downstream_gene_variant,,ENST00000561103,;RNF31,upstream_gene_variant,,ENST00000559882,;RNF31,upstream_gene_variant,,ENST00000559583,;RNF31,upstream_gene_variant,,ENST00000557878,;PSME2,missense_variant,p.Cys5Arg,ENST00000560370,;PSME2,missense_variant,p.Cys5Arg,ENST00000558273,;PSME2,non_coding_transcript_exon_variant,,ENST00000560788,;PSME2,non_coding_transcript_exon_variant,,ENST00000559493,;PSME2,non_coding_transcript_exon_variant,,ENST00000558931,;PSME2,non_coding_transcript_exon_variant,,ENST00000560592,;PSME2,upstream_gene_variant,,ENST00000559042,;RNF31,upstream_gene_variant,,ENST00000491351,;PSME2,upstream_gene_variant,,ENST00000559005,;PSME2,upstream_gene_variant,,ENST00000559359,;RNF31,upstream_gene_variant,,ENST00000558907,;RP11-468E2.4,upstream_gene_variant,,ENST00000558468,;RNF31,upstream_gene_variant,,ENST00000559071,;PSME2,upstream_gene_variant,,ENST00000559453,;RNF31,upstream_gene_variant,,ENST00000560342,;	G	ENSG00000100911	ENST00000216802	Transcript	missense_variant	653	13	5	C/R	Tgt/Cgt	.	.	.	-1	PSME2	HGNC	9569	protein_coding	YES	CCDS9614.1	ENSP00000216802	PSME2_HUMAN	Q86SZ7_HUMAN,H0YKU2_HUMAN	UPI000000CC17	.	tolerated(0.12)	benign(0.094)	1/11	.	hmmpanther:PTHR10660:SF6,hmmpanther:PTHR10660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCACACGGCT	.	2	ESCA
RNF31	0	.	GRCh37	14	24621199	24621199	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2128C>T	p.Arg710Trp	p.R710W	ENST00000324103	11/21	65	55	10	33	33	0	RNF31,missense_variant,p.Arg710Trp,ENST00000324103,;RNF31,missense_variant,p.Arg559Trp,ENST00000382687,;RNF31,missense_variant,p.Arg555Trp,ENST00000560787,;RNF31,missense_variant,p.Arg559Trp,ENST00000559275,;RNF31,downstream_gene_variant,,ENST00000560875,;RNF31,downstream_gene_variant,,ENST00000557991,;RNF31,upstream_gene_variant,,ENST00000560754,;RNF31,downstream_gene_variant,,ENST00000559533,;PSME2,upstream_gene_variant,,ENST00000216802,;RNF31,downstream_gene_variant,,ENST00000559308,;RNF31,downstream_gene_variant,,ENST00000560071,;RNF31,downstream_gene_variant,,ENST00000559260,;PSME2,upstream_gene_variant,,ENST00000561103,;RNF31,downstream_gene_variant,,ENST00000559882,;RNF31,downstream_gene_variant,,ENST00000559583,;RNF31,downstream_gene_variant,,ENST00000557878,;RNF31,downstream_gene_variant,,ENST00000558634,;RNF31,downstream_gene_variant,,ENST00000559438,;RP11-468E2.4,missense_variant,p.Arg185Trp,ENST00000558468,;RNF31,splice_region_variant,,ENST00000559071,;RNF31,splice_region_variant,,ENST00000491351,;PSME2,upstream_gene_variant,,ENST00000558273,;RNF31,upstream_gene_variant,,ENST00000559449,;RNF31,upstream_gene_variant,,ENST00000558452,;RNF31,downstream_gene_variant,,ENST00000560342,;PSME2,upstream_gene_variant,,ENST00000558931,;RNF31,downstream_gene_variant,,ENST00000558907,;	T	ENSG00000092098	ENST00000324103	Transcript	missense_variant	2448	2128	710	R/W	Cgg/Tgg	.	.	.	1	RNF31	HGNC	16031	protein_coding	YES	CCDS41931.1	ENSP00000315112	RNF31_HUMAN	H0YNK5_HUMAN,H0YNJ0_HUMAN,H0YNC1_HUMAN,H0YMK6_HUMAN,H0YM83_HUMAN,H0YM57_HUMAN,H0YM13_HUMAN	UPI0000072F93	.	deleterious(0)	possibly_damaging(0.582)	11/21	.	hmmpanther:PTHR16004,hmmpanther:PTHR16004:SF1,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAACCGGGTA	.	5	ESCA
IRF9	0	.	GRCh37	14	24632612	24632612	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390A>G	p.%3D	p.P130P	ENST00000396864	4/9	102	55	47	75	75	0	IRF9,synonymous_variant,p.%3D,ENST00000396864,;IRF9,synonymous_variant,p.%3D,ENST00000559284,;IRF9,synonymous_variant,p.%3D,ENST00000560275,;IRF9,synonymous_variant,p.%3D,ENST00000557894,;IRF9,synonymous_variant,p.%3D,ENST00000324076,;RNF31,downstream_gene_variant,,ENST00000559719,;RNF31,downstream_gene_variant,,ENST00000324103,;RNF31,downstream_gene_variant,,ENST00000382687,;RNF31,downstream_gene_variant,,ENST00000560787,;RNF31,downstream_gene_variant,,ENST00000559275,;RNA5SP383,downstream_gene_variant,,ENST00000362934,;RP11-468E2.4,3_prime_UTR_variant,,ENST00000558468,;IRF9,3_prime_UTR_variant,,ENST00000560852,;IRF9,3_prime_UTR_variant,,ENST00000561342,;IRF9,non_coding_transcript_exon_variant,,ENST00000560365,;IRF9,non_coding_transcript_exon_variant,,ENST00000561415,;IRF9,downstream_gene_variant,,ENST00000561412,;RNF31,downstream_gene_variant,,ENST00000559071,;RNF31,downstream_gene_variant,,ENST00000559449,;RNF31,downstream_gene_variant,,ENST00000491351,;IRF9,upstream_gene_variant,,ENST00000560542,;RNF31,downstream_gene_variant,,ENST00000483895,;RNF31,downstream_gene_variant,,ENST00000560631,;IRF9,downstream_gene_variant,,ENST00000561009,;IRF9,upstream_gene_variant,,ENST00000559863,;IRF9,upstream_gene_variant,,ENST00000559229,;RNF31,downstream_gene_variant,,ENST00000559491,;IRF9,upstream_gene_variant,,ENST00000560311,;	G	ENSG00000213928	ENST00000396864	Transcript	synonymous_variant	677	390	130	P	ccA/ccG	.	.	.	1	IRF9	HGNC	6131	protein_coding	YES	CCDS9615.1	ENSP00000380073	IRF9_HUMAN	.	UPI000012D8C2	.	.	.	4/9	.	hmmpanther:PTHR11949:SF21,hmmpanther:PTHR11949	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACCATCAAA	.	5	ESCA
KHNYN	0	.	GRCh37	14	24902031	24902031	+	Missense_Mutation	SNP	C	C	T	rs200900567	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1453C>T	p.Arg485Cys	p.R485C	ENST00000251343	4/8	87	41	46	30	30	0	KHNYN,missense_variant,p.Arg485Cys,ENST00000251343,;KHNYN,missense_variant,p.Arg485Cys,ENST00000556842,;KHNYN,missense_variant,p.Arg485Cys,ENST00000553935,;KHNYN,5_prime_UTR_variant,,ENST00000554268,;CBLN3,upstream_gene_variant,,ENST00000555436,;CBLN3,upstream_gene_variant,,ENST00000267406,;KHNYN,downstream_gene_variant,,ENST00000556510,;KHNYN,upstream_gene_variant,,ENST00000556255,;	T	ENSG00000100441	ENST00000251343	Transcript	missense_variant	1592	1453	485	R/C	Cgc/Tgc	rs200900567	.	.	1	KHNYN	HGNC	20166	protein_coding	YES	CCDS32058.1	ENSP00000251343	KHNYN_HUMAN	G3V3G3_HUMAN,G3V331_HUMAN	UPI000000CC1F	.	deleterious(0)	probably_damaging(0.999)	4/8	.	hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF28,Pfam_domain:PF11977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGGCGCTTC	byCluster	5	ESCA
BAZ1A	0	.	GRCh37	14	35222381	35222381	+	3'UTR	DEL	A	A	-	rs56071390	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*333delT	.	.	ENST00000360310	27/27	31	12	19	22	22	0	BAZ1A,3_prime_UTR_variant,,ENST00000358716,;BAZ1A,3_prime_UTR_variant,,ENST00000360310,;BAZ1A,3_prime_UTR_variant,,ENST00000382422,;BAZ1A,downstream_gene_variant,,ENST00000555331,;	-	ENSG00000198604	ENST00000360310	Transcript	3_prime_UTR_variant	5572	.	.	.	.	rs56071390	.	.	-1	BAZ1A	HGNC	960	protein_coding	YES	CCDS9651.1	ENSP00000353458	BAZ1A_HUMAN	D3DS96_HUMAN	UPI00001584D3	.	.	.	27/27	.	.	T:0.0064	T:0.0242	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CACTTTAAAAAA	byFrequency|byCluster|by1000G	2	ESCA
MIA2	0	.	GRCh37	14	39703161	39703161	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-158G>A	.	.	ENST00000280082	1/6	14	4	10	9	9	0	RP11-407N17.3,5_prime_UTR_variant,,ENST00000553728,;MIA2,5_prime_UTR_variant,,ENST00000280082,;MIA2,5_prime_UTR_variant,,ENST00000555143,;MIA2,intron_variant,,ENST00000557148,;MIA2,upstream_gene_variant,,ENST00000556784,;	A	ENSG00000150526	ENST00000280082	Transcript	5_prime_UTR_variant	42	.	.	.	.	.	.	.	1	MIA2	HGNC	18432	protein_coding	YES	CCDS9672.1	ENSP00000280082	MIA2_HUMAN	G3V4M1_HUMAN,B2RA73_HUMAN	UPI0000351D6B	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGCCGATAGA	.	3	ESCA
LRFN5	0	.	GRCh37	14	42356300	42356300	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472A>G	p.Asn158Asp	p.N158D	ENST00000298119	3/6	67	49	17	31	31	0	LRFN5,missense_variant,p.Asn158Asp,ENST00000298119,;LRFN5,missense_variant,p.Asn158Asp,ENST00000554120,;LRFN5,missense_variant,p.Asn158Asp,ENST00000554171,;	G	ENSG00000165379	ENST00000298119	Transcript	missense_variant	1661	472	158	N/D	Aat/Gat	COSM397482	.	.	1	LRFN5	HGNC	20360	protein_coding	YES	CCDS9678.1	ENSP00000298119	LRFN5_HUMAN	.	UPI000000DA1E	.	deleterious(0)	probably_damaging(0.999)	3/6	.	Superfamily_domains:SSF52058,SMART_domains:SM00369,Gene3D:3.80.10.10,Pfam_domain:PF13306,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAATAATCTA	.	5	ESCA
DDHD1	0	.	GRCh37	14	53513450	53513480	+	3'UTR	DEL	AATCAGTTTTAGGCCATTCATGTCCTTCAAG	AATCAGTTTTAGGCCATTCATGTCCTTCAAG	TCAGTTTTAGGCCATTCATGTCCTTCA	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AATCAGTTTTAGGCCATTCATGTCCTTCAAG	AATCAGTTTTAGGCCATTCATGTCCTTCAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6_*36delCTTGAAGGACATGAATGGCCTAAAACTGATTinsTGAAGGACATGAATGGCCTAAAACTGA	.	.	ENST00000323669	13/13	59	54	5	33	33	0	DDHD1,3_prime_UTR_variant,,ENST00000395606,;DDHD1,3_prime_UTR_variant,,ENST00000323669,;DDHD1,3_prime_UTR_variant,,ENST00000357758,;DDHD1,downstream_gene_variant,,ENST00000555621,;DDHD1,non_coding_transcript_exon_variant,,ENST00000556027,;	TCAGTTTTAGGCCATTCATGTCCTTCA	ENSG00000100523	ENST00000323669	Transcript	3_prime_UTR_variant	2709-2739	.	.	.	.	.	.	.	-1	DDHD1	HGNC	19714	protein_coding	YES	CCDS53895.1	ENSP00000327104	DDHD1_HUMAN	G3V2P6_HUMAN	UPI00001D7B55	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	AAAAAAAATCAGTTTTAGGCCATTCATGTCCTTCAAGAGAGT	.	2	ESCA
DAAM1	0	.	GRCh37	14	59835592	59835592	+	3'UTR	DEL	T	T	-	rs772529255	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*22delT	.	.	ENST00000395125	25/25	43	11	31	37	37	0	DAAM1,3_prime_UTR_variant,,ENST00000351081,;DAAM1,3_prime_UTR_variant,,ENST00000395125,;DAAM1,3_prime_UTR_variant,,ENST00000360909,;DAAM1,non_coding_transcript_exon_variant,,ENST00000553966,;DAAM1,downstream_gene_variant,,ENST00000557029,;DAAM1,non_coding_transcript_exon_variant,,ENST00000555651,;DAAM1,non_coding_transcript_exon_variant,,ENST00000553307,;DAAM1,downstream_gene_variant,,ENST00000553472,;DAAM1,downstream_gene_variant,,ENST00000557628,;	-	ENSG00000100592	ENST00000395125	Transcript	3_prime_UTR_variant	3275	.	.	.	.	rs772529255	.	.	1	DAAM1	HGNC	18142	protein_coding	YES	CCDS9737.1	ENSP00000378557	DAAM1_HUMAN	.	UPI0000161FAA	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAATACTTTTTT	.	2	ESCA
JKAMP	0	.	GRCh37	14	59965486	59965486	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.500T>C	p.Leu167Ser	p.L167S	ENST00000261247	5/7	50	24	26	21	21	0	JKAMP,missense_variant,p.Leu161Ser,ENST00000425728,;JKAMP,missense_variant,p.Leu167Ser,ENST00000261247,;JKAMP,missense_variant,p.Leu175Ser,ENST00000356057,;JKAMP,missense_variant,p.Leu181Ser,ENST00000554271,;JKAMP,missense_variant,p.Leu175Ser,ENST00000554795,;JKAMP,downstream_gene_variant,,ENST00000556985,;JKAMP,non_coding_transcript_exon_variant,,ENST00000554754,;RP11-701B16.2,intron_variant,,ENST00000554253,;JKAMP,downstream_gene_variant,,ENST00000557560,;JKAMP,synonymous_variant,p.%3D,ENST00000555491,;JKAMP,non_coding_transcript_exon_variant,,ENST00000553941,;JKAMP,non_coding_transcript_exon_variant,,ENST00000602482,;JKAMP,non_coding_transcript_exon_variant,,ENST00000554721,;JKAMP,upstream_gene_variant,,ENST00000553647,;	C	ENSG00000050130	ENST00000261247	Transcript	missense_variant	647	500	167	L/S	tTa/tCa	.	.	.	1	JKAMP	HGNC	20184	protein_coding	YES	CCDS45116.1	ENSP00000261247	JKAMP_HUMAN	G3V372_HUMAN	UPI00000377AB	.	tolerated(0.16)	possibly_damaging(0.742)	5/7	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Pfam_domain:PF05571,hmmpanther:PTHR12740,hmmpanther:PTHR12740:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTATTAATGA	.	5	ESCA
HIF1A	0	.	GRCh37	14	62214347	62214347	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*551delT	.	.	ENST00000539097	15/15	42	34	8	30	30	0	HIF1A,3_prime_UTR_variant,,ENST00000539097,;HIF1A,3_prime_UTR_variant,,ENST00000337138,;HIF1A,3_prime_UTR_variant,,ENST00000323441,;HIF1A,3_prime_UTR_variant,,ENST00000557538,;HIF1A,3_prime_UTR_variant,,ENST00000394997,;HIF1A-AS2,intron_variant,,ENST00000554254,;RP11-618G20.1,intron_variant,,ENST00000555937,;HIF1A,downstream_gene_variant,,ENST00000556827,;	-	ENSG00000100644	ENST00000539097	Transcript	3_prime_UTR_variant	3326	.	.	.	.	.	.	.	1	HIF1A	HGNC	4910	protein_coding	YES	CCDS58324.1	ENSP00000437955	HIF1A_HUMAN	F8W9L0_HUMAN,B4E2U7_HUMAN	UPI0001982748	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAGAAATTTTTT	.	2	ESCA
RHOJ	0	.	GRCh37	14	63671516	63671516	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-72C>T	.	.	ENST00000316754	1/5	14	3	10	11	11	0	RHOJ,5_prime_UTR_variant,,ENST00000316754,;RHOJ,upstream_gene_variant,,ENST00000555125,;RHOJ,non_coding_transcript_exon_variant,,ENST00000557133,;RHOJ,5_prime_UTR_variant,,ENST00000557447,;	T	ENSG00000126785	ENST00000316754	Transcript	5_prime_UTR_variant	391	.	.	.	.	.	.	.	1	RHOJ	HGNC	688	protein_coding	YES	CCDS9757.1	ENSP00000316729	RHOJ_HUMAN	.	UPI0000133894	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TTCTGCCGCTT	.	4	ESCA
ADAM21P1	0	.	GRCh37	14	70714016	70714016	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.503C>T	.	.	ENST00000530196	1/1	43	6	36	20	20	0	ADAM21P1,non_coding_transcript_exon_variant,,ENST00000530196,;ADAM21P1,non_coding_transcript_exon_variant,,ENST00000529267,;	A	ENSG00000235812	ENST00000530196	Transcript	non_coding_transcript_exon_variant	503	.	.	.	.	.	.	.	-1	ADAM21P1	HGNC	19822	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGAGACTCA	.	5	ESCA
NRXN3	0	.	GRCh37	14	79270068	79270068	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000554719	6/17	83	17	66	41	41	0	NRXN3,missense_variant,p.Arg344Gln,ENST00000554719,;NRXN3,missense_variant,p.Arg344Gln,ENST00000335750,;NRXN3,missense_variant,p.Arg715Gln,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,;	A	ENSG00000021645	ENST00000554719	Transcript	missense_variant	1522	1031	344	R/Q	cGa/cAa	.	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	deleterious(0.02)	probably_damaging(0.997)	6/17	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF405,hmmpanther:PTHR10127,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGAGCTT	.	5	ESCA
NRXN3	0	.	GRCh37	14	80328899	80328899	+	3'Flank	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000554719	.	102	58	44	38	38	0	NRXN3,3_prime_UTR_variant,,ENST00000281127,;NRXN3,3_prime_UTR_variant,,ENST00000428277,;NRXN3,downstream_gene_variant,,ENST00000554719,;NRXN3,downstream_gene_variant,,ENST00000557594,;NRXN3,downstream_gene_variant,,ENST00000335750,;NRXN3,downstream_gene_variant,,ENST00000556003,;NRXN3,downstream_gene_variant,,ENST00000555387,;NRXN3,downstream_gene_variant,,ENST00000554738,;	-	ENSG00000021645	ENST00000554719	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	113	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAGGGGAAAAAT	.	3	ESCA
FLRT2	0	.	GRCh37	14	86092478	86092478	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2637C>A	.	.	ENST00000330753	2/2	52	44	8	31	31	0	FLRT2,3_prime_UTR_variant,,ENST00000330753,;FLRT2,downstream_gene_variant,,ENST00000554746,;FLRT2,non_coding_transcript_exon_variant,,ENST00000553650,;	A	ENSG00000185070	ENST00000330753	Transcript	3_prime_UTR_variant	5387	.	.	.	.	.	.	.	1	FLRT2	HGNC	3761	protein_coding	YES	CCDS9877.1	ENSP00000332879	FLRT2_HUMAN	B4DM15_HUMAN	UPI0000049E10	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCCATTTG	.	5	ESCA
FLRT2	0	.	GRCh37	14	86092634	86092634	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2793C>A	.	.	ENST00000330753	2/2	75	47	28	33	33	0	FLRT2,3_prime_UTR_variant,,ENST00000330753,;FLRT2,downstream_gene_variant,,ENST00000554746,;FLRT2,downstream_gene_variant,,ENST00000553650,;	A	ENSG00000185070	ENST00000330753	Transcript	3_prime_UTR_variant	5543	.	.	.	.	.	.	.	1	FLRT2	HGNC	3761	protein_coding	YES	CCDS9877.1	ENSP00000332879	FLRT2_HUMAN	B4DM15_HUMAN	UPI0000049E10	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTGCTCTGT	.	5	ESCA
FLRT2	0	.	GRCh37	14	86092726	86092726	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2891delA	.	.	ENST00000330753	2/2	71	63	8	24	24	0	FLRT2,3_prime_UTR_variant,,ENST00000330753,;FLRT2,downstream_gene_variant,,ENST00000554746,;FLRT2,downstream_gene_variant,,ENST00000553650,;	-	ENSG00000185070	ENST00000330753	Transcript	3_prime_UTR_variant	5635	.	.	.	.	.	.	.	1	FLRT2	HGNC	3761	protein_coding	YES	CCDS9877.1	ENSP00000332879	FLRT2_HUMAN	B4DM15_HUMAN	UPI0000049E10	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATGGGAAAAAA	.	3	ESCA
FOXN3	0	.	GRCh37	14	89626912	89626912	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1846A>G	.	.	ENST00000345097	7/7	80	66	13	37	37	0	FOXN3,3_prime_UTR_variant,,ENST00000345097,;FOXN3,3_prime_UTR_variant,,ENST00000261302,;FOXN3,intron_variant,,ENST00000557572,;FOXN3,downstream_gene_variant,,ENST00000553840,;FOXN3,downstream_gene_variant,,ENST00000555353,;FOXN3,downstream_gene_variant,,ENST00000557258,;	C	ENSG00000053254	ENST00000345097	Transcript	3_prime_UTR_variant	3436	.	.	.	.	.	.	.	-1	FOXN3	HGNC	1928	protein_coding	YES	CCDS41977.1	ENSP00000343288	FOXN3_HUMAN	G3V5C7_HUMAN,G3V4N5_HUMAN,G3V3A7_HUMAN	UPI000003B451	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGTAATGA	.	5	ESCA
RPS6KA5	0	.	GRCh37	14	91366489	91366489	+	Frame_Shift_Del	DEL	T	T	-	rs771092000	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1342delA	p.Ser448ValfsTer9	p.S448Vfs*9	ENST00000261991	11/17	164	94	70	29	29	0	RPS6KA5,frameshift_variant,p.Ser448ValfsTer9,ENST00000261991,;RPS6KA5,frameshift_variant,p.Ser448ValfsTer9,ENST00000418736,;RPS6KA5,frameshift_variant,p.Ser369ValfsTer9,ENST00000536315,;RPS6KA5,3_prime_UTR_variant,,ENST00000556178,;RPS6KA5,downstream_gene_variant,,ENST00000554206,;	-	ENSG00000100784	ENST00000261991	Transcript	frameshift_variant	1516	1342	448	S/X	Agt/gt	rs771092000	.	.	-1	RPS6KA5	HGNC	10434	protein_coding	YES	CCDS9893.1	ENSP00000261991	KS6A5_HUMAN	Q9UG98_HUMAN,B7Z2Y5_HUMAN	UPI0000031C30	.	.	.	11/17	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,PIRSF_domain:PIRSF000606,Pfam_domain:PF00069,Gene3D:3.30.200.20,PROSITE_patterns:PS00107,hmmpanther:PTHR24351:SF42,hmmpanther:PTHR24351,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTTACTTTTTT	byFrequency	3	ESCA
SLC24A4	0	.	GRCh37	14	92962394	92962394	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2422G>A	.	.	ENST00000532405	17/17	18	6	12	12	12	0	SLC24A4,3_prime_UTR_variant,,ENST00000531433,;SLC24A4,3_prime_UTR_variant,,ENST00000525557,;SLC24A4,3_prime_UTR_variant,,ENST00000393265,;SLC24A4,3_prime_UTR_variant,,ENST00000351924,;SLC24A4,3_prime_UTR_variant,,ENST00000298877,;SLC24A4,3_prime_UTR_variant,,ENST00000532405,;SLC24A4,non_coding_transcript_exon_variant,,ENST00000526482,;SLC24A4,downstream_gene_variant,,ENST00000554925,;	A	ENSG00000140090	ENST00000532405	Transcript	3_prime_UTR_variant	4517	.	.	.	.	.	.	.	1	SLC24A4	HGNC	10978	protein_coding	YES	CCDS9903.2	ENSP00000431840	NCKX4_HUMAN	G3V505_HUMAN,B4DHR5_HUMAN	UPI000044C5DE	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACGTATCC	.	5	ESCA
BTBD7	0	.	GRCh37	14	93708433	93708433	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*186delT	.	.	ENST00000334746	11/11	31	17	13	19	19	0	BTBD7,3_prime_UTR_variant,,ENST00000393170,;BTBD7,3_prime_UTR_variant,,ENST00000553975,;BTBD7,3_prime_UTR_variant,,ENST00000334746,;BTBD7,3_prime_UTR_variant,,ENST00000554565,;BTBD7,3_prime_UTR_variant,,ENST00000355125,;RP11-85G20.2,upstream_gene_variant,,ENST00000492041,;	-	ENSG00000011114	ENST00000334746	Transcript	3_prime_UTR_variant	3893	.	.	.	.	.	.	.	-1	BTBD7	HGNC	18269	protein_coding	YES	CCDS32146.1	ENSP00000335615	BTBD7_HUMAN	G3V2J4_HUMAN	UPI00001FDA78	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACATTAAAAAA	.	2	ESCA
VRK1	0	.	GRCh37	14	97319255	97319255	+	Silent	SNP	C	C	G	rs757654085	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462C>G	p.%3D	p.V154V	ENST00000216639	6/13	77	57	20	35	35	0	VRK1,synonymous_variant,p.%3D,ENST00000216639,;VRK1,synonymous_variant,p.%3D,ENST00000557222,;VRK1,upstream_gene_variant,,ENST00000557352,;VRK1,non_coding_transcript_exon_variant,,ENST00000555351,;	G	ENSG00000100749	ENST00000216639	Transcript	synonymous_variant	611	462	154	V	gtC/gtG	rs757654085	.	.	1	VRK1	HGNC	12718	protein_coding	YES	CCDS9947.1	ENSP00000216639	VRK1_HUMAN	.	UPI0000073867	.	.	.	6/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF78,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTCTTGCA	.	5	ESCA
LRRK1	0	.	GRCh37	15	101549153	101549153	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874A>G	p.Thr292Ala	p.T292A	ENST00000388948	7/34	54	14	40	23	23	0	LRRK1,missense_variant,p.Thr292Ala,ENST00000388948,;LRRK1,missense_variant,p.Thr289Ala,ENST00000284395,;LRRK1,missense_variant,p.Thr292Ala,ENST00000531270,;LRRK1,missense_variant,p.Thr292Ala,ENST00000525284,;	G	ENSG00000154237	ENST00000388948	Transcript	missense_variant	1233	874	292	T/A	Acc/Gcc	.	.	.	1	LRRK1	HGNC	18608	protein_coding	YES	CCDS42086.1	ENSP00000373600	LRRK1_HUMAN	E9PMK9_HUMAN,E9PLF8_HUMAN,E9PK39_HUMAN,B3KSX5_HUMAN	UPI0000D4FE63	.	tolerated(0.19)	benign(0.001)	7/34	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF239,Gene3D:3.80.10.10,SMART_domains:SM00364,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCGACCCTC	.	5	ESCA
IGHV1OR15-9	0	.	GRCh37	15	20170075	20170075	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.197G>A	p.Trp66Ter	p.W66*	ENST00000338912	2/2	140	37	103	98	98	0	IGHV1OR15-9,stop_gained,p.Trp66Ter,ENST00000338912,;SLC20A1P3,downstream_gene_variant,,ENST00000555979,;	T	ENSG00000188403	ENST00000338912	Transcript	stop_gained	197	197	66	W/*	tGg/tAg	.	.	.	-1	IGHV1OR15-9	HGNC	5569	IG_V_gene	YES	.	ENSP00000474639	.	.	UPI0000113A94	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266:SF73,hmmpanther:PTHR23266,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCACTCA	.	5	ESCA
NPAP1	0	.	GRCh37	15	24927892	24927892	+	3'UTR	DEL	A	A	-	rs564867798	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3416delA	.	.	ENST00000329468	1/1	29	15	13	23	23	0	NPAP1,3_prime_UTR_variant,,ENST00000329468,;	-	ENSG00000185823	ENST00000329468	Transcript	3_prime_UTR_variant	7352	.	.	.	.	rs564867798	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCCCATAAAAAA	.	2	ESCA
SNORD115-42	0	.	GRCh37	15	25492540	25492540	+	RNA	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.53delA	.	.	ENST00000364273	1/1	144	85	59	55	55	0	SNORD115-42,non_coding_transcript_exon_variant,,ENST00000364273,;SNORD115-40,downstream_gene_variant,,ENST00000606510,;SNORD115-44,upstream_gene_variant,,ENST00000365391,;SNORD115-43,upstream_gene_variant,,ENST00000365503,;SNORD115-41,downstream_gene_variant,,ENST00000363608,;SNHG14,upstream_gene_variant,,ENST00000452731,;SNHG14,downstream_gene_variant,,ENST00000453082,;	-	ENSG00000201143	ENST00000364273	Transcript	non_coding_transcript_exon_variant	49	.	.	.	.	.	.	.	1	SNORD115-42	HGNC	33061	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGACTTAAAAAT	.	3	ESCA
WHAMMP2	0	.	GRCh37	15	28996727	28996727	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.199G>A	.	.	ENST00000512149	2/4	29	10	19	23	23	0	WHAMMP2,non_coding_transcript_exon_variant,,ENST00000508764,;WHAMMP2,non_coding_transcript_exon_variant,,ENST00000512149,;WHAMMP2,downstream_gene_variant,,ENST00000515318,;WHAMMP2,non_coding_transcript_exon_variant,,ENST00000563942,;	A	ENSG00000248334	ENST00000512149	Transcript	non_coding_transcript_exon_variant	199	.	.	.	.	.	.	.	1	WHAMMP2	HGNC	32360	processed_transcript	YES	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	AATTCGGAAGT	.	3	ESCA
APBA2	0	.	GRCh37	15	29410179	29410179	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*843A>G	.	.	ENST00000558402	16/16	18	1	17	12	12	0	APBA2,3_prime_UTR_variant,,ENST00000558259,;APBA2,3_prime_UTR_variant,,ENST00000558402,;APBA2,3_prime_UTR_variant,,ENST00000411764,;FAM189A1,downstream_gene_variant,,ENST00000261275,;APBA2,downstream_gene_variant,,ENST00000561069,;APBA2,downstream_gene_variant,,ENST00000558330,;	G	ENSG00000034053	ENST00000558402	Transcript	3_prime_UTR_variant	3692	.	.	.	.	.	.	.	1	APBA2	HGNC	579	protein_coding	YES	CCDS10022.1	ENSP00000453293	APBA2_HUMAN	H0YNG7_HUMAN,H0YNE8_HUMAN,H0YMS0_HUMAN,H0YL28_HUMAN	UPI0000046798	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACTCTAGAAAA	.	4	ESCA
FMN1	0	.	GRCh37	15	33443448	33443448	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11delT	.	.	ENST00000320930	5/5	52	29	23	37	37	0	FMN1,3_prime_UTR_variant,,ENST00000320930,;FMN1,intron_variant,,ENST00000559047,;FMN1,intron_variant,,ENST00000561249,;	-	ENSG00000248905	ENST00000320930	Transcript	3_prime_UTR_variant	2467	.	.	.	.	.	.	.	-1	FMN1	HGNC	3768	protein_coding	.	CCDS61582.1	ENSP00000325166	FMN1_HUMAN	.	UPI00006C150E	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATATCAAAAAA	.	3	ESCA
MEIS2	0	.	GRCh37	15	37391811	37391811	+	5'UTR	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-144delC	.	.	ENST00000561208	1/12	15	11	4	14	14	0	MEIS2,5_prime_UTR_variant,,ENST00000424352,;MEIS2,5_prime_UTR_variant,,ENST00000559561,;MEIS2,5_prime_UTR_variant,,ENST00000444725,;MEIS2,5_prime_UTR_variant,,ENST00000382766,;MEIS2,5_prime_UTR_variant,,ENST00000561208,;MEIS2,intron_variant,,ENST00000558313,;MEIS2,intron_variant,,ENST00000338564,;MEIS2,intron_variant,,ENST00000340545,;MEIS2,upstream_gene_variant,,ENST00000219869,;MEIS2,upstream_gene_variant,,ENST00000560697,;MEIS2,upstream_gene_variant,,ENST00000397620,;MEIS2,upstream_gene_variant,,ENST00000560617,;MEIS2,upstream_gene_variant,,ENST00000607277,;MEIS2,upstream_gene_variant,,ENST00000397624,;MEIS2,upstream_gene_variant,,ENST00000559085,;MEIS2,upstream_gene_variant,,ENST00000557796,;RP11-128A17.1,intron_variant,,ENST00000559509,;MEIS2,5_prime_UTR_variant,,ENST00000314177,;MEIS2,upstream_gene_variant,,ENST00000561163,;MEIS2,upstream_gene_variant,,ENST00000560570,;MEIS2,upstream_gene_variant,,ENST00000559129,;	-	ENSG00000134138	ENST00000561208	Transcript	5_prime_UTR_variant	276	.	.	.	.	.	.	.	-1	MEIS2	HGNC	7001	protein_coding	YES	CCDS10044.1	ENSP00000453793	MEIS2_HUMAN	H0YKN2_HUMAN,H0YKE5_HUMAN	UPI000012EEBC	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TTTTTAGGGGGG	.	2	ESCA
C15orf62	0	.	GRCh37	15	41064413	41064413	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1192C>T	.	.	ENST00000344320	1/1	37	5	32	26	26	0	C15orf62,3_prime_UTR_variant,,ENST00000344320,;DNAJC17,intron_variant,,ENST00000220496,;GCHFR,downstream_gene_variant,,ENST00000260447,;GCHFR,downstream_gene_variant,,ENST00000559445,;GCHFR,downstream_gene_variant,,ENST00000558467,;GCHFR,downstream_gene_variant,,ENST00000559932,;GCHFR,downstream_gene_variant,,ENST00000558670,;DNAJC17,upstream_gene_variant,,ENST00000558727,;DNAJC17,intron_variant,,ENST00000561110,;DNAJC17,intron_variant,,ENST00000559238,;DNAJC17,downstream_gene_variant,,ENST00000560065,;DNAJC17,downstream_gene_variant,,ENST00000560645,;DNAJC17,downstream_gene_variant,,ENST00000560301,;DNAJC17,downstream_gene_variant,,ENST00000561018,;DNAJC17,downstream_gene_variant,,ENST00000559310,;DNAJC17,downstream_gene_variant,,ENST00000558769,;	T	ENSG00000188277	ENST00000344320	Transcript	3_prime_UTR_variant	2255	.	.	.	.	.	.	.	1	C15orf62	HGNC	34489	protein_coding	YES	CCDS45229.1	ENSP00000341178	CO062_HUMAN	.	UPI00001FE27C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGCTGTGC	.	5	ESCA
SPTBN5	0	.	GRCh37	15	42160632	42160632	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6021G>A	p.%3D	p.Q2007Q	ENST00000320955	33/68	63	16	47	44	44	0	SPTBN5,synonymous_variant,p.%3D,ENST00000320955,;MIR4310,upstream_gene_variant,,ENST00000582950,;	T	ENSG00000137877	ENST00000320955	Transcript	synonymous_variant	6249	6021	2007	Q	caG/caA	.	.	.	-1	SPTBN5	HGNC	15680	protein_coding	YES	CCDS61599.1	ENSP00000317790	SPTN5_HUMAN	.	UPI0000E59BE4	.	.	.	33/68	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF249,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGCTGCCC	.	5	ESCA
MAP1A	0	.	GRCh37	15	43817459	43817459	+	Missense_Mutation	SNP	C	C	T	rs774871578	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3788C>T	p.Ala1263Val	p.A1263V	ENST00000300231	4/6	30	8	22	15	15	0	MAP1A,missense_variant,p.Ala1263Val,ENST00000399453,;MAP1A,missense_variant,p.Ala1263Val,ENST00000300231,;MAP1A,missense_variant,p.Ala1501Val,ENST00000382031,;	T	ENSG00000166963	ENST00000300231	Transcript	missense_variant	4238	3788	1263	A/V	gCg/gTg	rs774871578	.	.	1	MAP1A	HGNC	6835	protein_coding	YES	CCDS42031.1	ENSP00000300231	MAP1A_HUMAN	.	UPI000013E63C	.	.	benign(0.001)	4/6	.	hmmpanther:PTHR13843:SF6,hmmpanther:PTHR13843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAGCGTCAC	.	5	ESCA
PRTG	0	.	GRCh37	15	55965576	55965576	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1845C>T	p.%3D	p.S615S	ENST00000389286	10/20	35	18	16	24	24	0	PRTG,synonymous_variant,p.%3D,ENST00000389286,;PRTG,synonymous_variant,p.%3D,ENST00000561465,;PRTG,downstream_gene_variant,,ENST00000559842,;	A	ENSG00000166450	ENST00000389286	Transcript	synonymous_variant	1893	1845	615	S	agC/agT	COSM276924	.	.	-1	PRTG	HGNC	26373	protein_coding	YES	CCDS42040.1	ENSP00000373937	PRTG_HUMAN	H0YKD6_HUMAN	UPI00001555A7	.	.	.	10/20	.	hmmpanther:PTHR10489:SF20,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCACGCTTGT	.	5	ESCA
VPS13C	0	.	GRCh37	15	62202414	62202414	+	Nonsense_Mutation	SNP	G	G	A	rs148074630	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8806C>T	p.Arg2936Ter	p.R2936*	ENST00000261517	64/85	16	1	15	19	19	0	VPS13C,stop_gained,p.Arg2936Ter,ENST00000261517,;VPS13C,stop_gained,p.Arg2936Ter,ENST00000395896,;VPS13C,stop_gained,p.Arg2893Ter,ENST00000249837,;VPS13C,stop_gained,p.Arg2893Ter,ENST00000395898,;RN7SL613P,upstream_gene_variant,,ENST00000584412,;VPS13C,non_coding_transcript_exon_variant,,ENST00000558338,;	A	ENSG00000129003	ENST00000261517	Transcript	stop_gained	8880	8806	2936	R/*	Cga/Tga	rs148074630	.	.	-1	VPS13C	HGNC	23594	protein_coding	YES	CCDS32257.1	ENSP00000261517	VP13C_HUMAN	B4E2S9_HUMAN,B3KW10_HUMAN	UPI000023B7D3	.	.	.	64/85	.	hmmpanther:PTHR16166:SF69,hmmpanther:PTHR16166,Pfam_domain:PF06650	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CTGTCGGTTAT	byCluster	3	ESCA
TLN2	0	.	GRCh37	15	63133188	63133189	+	3'UTR	INS	-	-	A	rs548516251	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*386dupA	.	.	ENST00000561311	58/58	49	40	9	36	36	0	TLN2,3_prime_UTR_variant,,ENST00000494733,;TLN2,3_prime_UTR_variant,,ENST00000561311,;TLN2,3_prime_UTR_variant,,ENST00000306829,;RP11-1069G10.1,intron_variant,,ENST00000558404,;RP11-1069G10.1,downstream_gene_variant,,ENST00000560963,;RP11-1069G10.1,downstream_gene_variant,,ENST00000557994,;TLN2,non_coding_transcript_exon_variant,,ENST00000489129,;TLN2,downstream_gene_variant,,ENST00000559174,;	A	ENSG00000171914	ENST00000561311	Transcript	3_prime_UTR_variant	8238-8239	.	.	.	.	rs548516251	.	.	1	TLN2	HGNC	15447	protein_coding	YES	CCDS32261.1	ENSP00000453508	TLN2_HUMAN	.	UPI00001FE5FC	.	.	.	58/58	.	.	A:0.0012	A:0.0045	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATAGGGAAAAA	byFrequency|by1000G	2	ESCA
CSNK1G1	0	.	GRCh37	15	64463359	64463359	+	3'UTR	DEL	T	T	-	rs553594662	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*771delA	.	.	ENST00000303052	12/12	36	14	22	37	37	0	CSNK1G1,3_prime_UTR_variant,,ENST00000303052,;CSNK1G1,intron_variant,,ENST00000607537,;CSNK1G1,downstream_gene_variant,,ENST00000606225,;	-	ENSG00000169118	ENST00000303052	Transcript	3_prime_UTR_variant	2464	.	.	.	.	rs553594662	.	.	-1	CSNK1G1	HGNC	2454	protein_coding	YES	CCDS10192.2	ENSP00000305777	KC1G1_HUMAN	U3KQP7_HUMAN	UPI000003F575	.	.	.	12/12	.	.	-:0.0030	-:0.0113	-:0	.	-:0	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTTTGTTTTTT	byFrequency|by1000G	2	ESCA
IGDCC3	0	.	GRCh37	15	65628266	65628266	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438G>T	p.Gln146His	p.Q146H	ENST00000327987	3/14	68	21	46	38	38	0	IGDCC3,missense_variant,p.Gln9His,ENST00000558354,;IGDCC3,missense_variant,p.Gln146His,ENST00000327987,;IGDCC3,missense_variant,p.Gln23His,ENST00000559058,;IGDCC3,upstream_gene_variant,,ENST00000559231,;	A	ENSG00000174498	ENST00000327987	Transcript	missense_variant	690	438	146	Q/H	caG/caT	.	.	.	-1	IGDCC3	HGNC	9700	protein_coding	YES	CCDS10205.1	ENSP00000332773	IGDC3_HUMAN	H0YNQ1_HUMAN	UPI000019908F	.	tolerated(0.05)	probably_damaging(0.968)	3/14	.	hmmpanther:PTHR10489:SF106,hmmpanther:PTHR10489,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCCTGGGG	.	5	ESCA
IGDCC4	0	.	GRCh37	15	65702608	65702608	+	Silent	SNP	G	G	A	rs777293264	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471C>T	p.%3D	p.N157N	ENST00000352385	3/20	33	7	26	27	27	0	IGDCC4,synonymous_variant,p.%3D,ENST00000352385,;IGDCC4,downstream_gene_variant,,ENST00000558819,;	A	ENSG00000103742	ENST00000352385	Transcript	synonymous_variant	681	471	157	N	aaC/aaT	rs777293264,COSM4056304	.	.	-1	IGDCC4	HGNC	13770	protein_coding	YES	CCDS10206.1	ENSP00000319623	IGDC4_HUMAN	.	UPI000006F31C	.	.	.	3/20	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCGTTCTC	byFrequency	5	ESCA
MAP2K1	0	.	GRCh37	15	66777404	66777404	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.770C>T	p.Ala257Val	p.A257V	ENST00000307102	7/11	62	11	50	42	42	0	MAP2K1,missense_variant,p.Ala257Val,ENST00000307102,;MAP2K1,missense_variant,p.Ala81Val,ENST00000566326,;CTD-3185P2.1,downstream_gene_variant,,ENST00000565387,;CTD-3185P2.2,downstream_gene_variant,,ENST00000602360,;	T	ENSG00000169032	ENST00000307102	Transcript	missense_variant	1301	770	257	A/V	gCg/gTg	.	.	.	1	MAP2K1	HGNC	6840	protein_coding	YES	CCDS10216.1	ENSP00000302486	MP2K1_HUMAN	A4QPA9_HUMAN	UPI000013EBC9	.	tolerated(0.11)	benign(0.119)	7/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF15,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGGCGGTTG	.	5	ESCA
PML	0	.	GRCh37	15	74335396	74335396	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1777C>A	p.Leu593Ile	p.L593I	ENST00000268058	8/9	35	16	19	18	18	0	PML,missense_variant,p.Leu593Ile,ENST00000395135,;PML,missense_variant,p.Leu593Ile,ENST00000268058,;PML,missense_variant,p.Leu545Ile,ENST00000564428,;PML,missense_variant,p.Leu545Ile,ENST00000565898,;PML,3_prime_UTR_variant,,ENST00000569965,;PML,3_prime_UTR_variant,,ENST00000359928,;PML,non_coding_transcript_exon_variant,,ENST00000565317,;	A	ENSG00000140464	ENST00000268058	Transcript	missense_variant	1873	1777	593	L/I	Ctc/Atc	.	.	.	1	PML	HGNC	9113	protein_coding	YES	CCDS10255.1	ENSP00000268058	PML_HUMAN	Q9UE85_HUMAN,Q05835_HUMAN	UPI000013D78F	.	deleterious(0.03)	possibly_damaging(0.839)	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCCTCAGG	.	5	ESCA
CCDC33	0	.	GRCh37	15	74623335	74623337	+	In_Frame_Del	DEL	AGA	AGA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AGA	AGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1561_1563delAAG	p.Lys521del	p.K521del	ENST00000398814	14/19	25	3	22	29	29	0	CCDC33,inframe_deletion,p.Lys114del,ENST00000268082,;CCDC33,inframe_deletion,p.Lys114del,ENST00000558821,;CCDC33,inframe_deletion,p.Lys724del,ENST00000321288,;CCDC33,inframe_deletion,p.Lys402del,ENST00000558659,;CCDC33,inframe_deletion,p.Lys521del,ENST00000398814,;CCDC33,inframe_deletion,p.Lys114del,ENST00000321374,;CCDC33,non_coding_transcript_exon_variant,,ENST00000560565,;	-	ENSG00000140481	ENST00000398814	Transcript	inframe_deletion	1990-1992	1559-1561	520-521	EK/E	gAGAag/gag	.	.	.	1	CCDC33	HGNC	26552	protein_coding	YES	CCDS42058.1	ENSP00000381795	CCD33_HUMAN	.	UPI0000E671FE	.	.	.	14/19	.	hmmpanther:PTHR21623,hmmpanther:PTHR21623:SF2,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATCGAGAGAAGGAG	.	3	ESCA
CSPG4	0	.	GRCh37	15	75983102	75983103	+	Frame_Shift_Del	DEL	TC	TC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TC	TC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303_304delGA	p.Glu101AspfsTer5	p.E101Dfs*5	ENST00000308508	3/10	159	122	37	90	90	0	CSPG4,frameshift_variant,p.Glu101AspfsTer5,ENST00000308508,;	-	ENSG00000173546	ENST00000308508	Transcript	frameshift_variant	396-397	303-304	101-102	ET/DX	gaGAcg/gacg	.	.	.	-1	CSPG4	HGNC	2466	protein_coding	YES	CCDS10284.1	ENSP00000312506	CSPG4_HUMAN	.	UPI00001AEEB6	.	.	.	3/10	.	Superfamily_domains:SSF49899,SMART_domains:SM00282,Gene3D:2.60.120.200,Pfam_domain:PF00054,hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF11,PROSITE_profiles:PS50025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCAGCGTCTCTGC	.	3	ESCA
C15orf27	0	.	GRCh37	15	76496546	76496546	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1486T>A	p.Phe496Ile	p.F496I	ENST00000388942	11/11	35	10	25	26	26	0	C15orf27,missense_variant,p.Phe496Ile,ENST00000388942,;C15orf27,3_prime_UTR_variant,,ENST00000484722,;C15orf27,non_coding_transcript_exon_variant,,ENST00000558249,;C15orf27,intron_variant,,ENST00000561302,;	A	ENSG00000169758	ENST00000388942	Transcript	missense_variant	1762	1486	496	F/I	Ttt/Att	.	.	.	1	C15orf27	HGNC	26763	protein_coding	YES	CCDS10289.2	ENSP00000373594	CO027_HUMAN	.	UPI0000DBEE67	.	deleterious_low_confidence(0.03)	benign(0.089)	11/11	.	hmmpanther:PTHR12305:SF45,hmmpanther:PTHR12305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCTTTCAG	.	5	ESCA
KLHL25	0	.	GRCh37	15	86312008	86312008	+	Missense_Mutation	SNP	G	G	A	rs748049897	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1034C>T	p.Thr345Met	p.T345M	ENST00000337975	2/3	66	15	51	49	49	0	KLHL25,missense_variant,p.Thr345Met,ENST00000536947,;KLHL25,missense_variant,p.Thr345Met,ENST00000337975,;MIR1276,downstream_gene_variant,,ENST00000408707,;KLHL25,intron_variant,,ENST00000559131,;RP11-158M2.6,upstream_gene_variant,,ENST00000559631,;	A	ENSG00000183655	ENST00000337975	Transcript	missense_variant	1309	1034	345	T/M	aCg/aTg	rs748049897	.	.	-1	KLHL25	HGNC	25732	protein_coding	YES	CCDS10339.1	ENSP00000336800	KLH25_HUMAN	.	UPI0000037CB1	.	deleterious(0.03)	probably_damaging(0.999)	2/3	.	hmmpanther:PTHR24410,hmmpanther:PTHR24410:SF6,Pfam_domain:PF01344,Gene3D:1zgkA00,SMART_domains:SM00612,PIRSF_domain:PIRSF037037,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCCGTCACA	byFrequency	5	ESCA
MAN2A2	0	.	GRCh37	15	91453522	91453522	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1577G>A	p.Arg526Gln	p.R526Q	ENST00000360468	9/22	37	12	25	24	23	1	MAN2A2,missense_variant,p.Arg169Gln,ENST00000557865,;MAN2A2,missense_variant,p.Arg526Gln,ENST00000360468,;MAN2A2,missense_variant,p.Arg47Gln,ENST00000558171,;MAN2A2,missense_variant,p.Arg526Gln,ENST00000559717,;MAN2A2,intron_variant,,ENST00000560616,;MAN2A2,intron_variant,,ENST00000431652,;MAN2A2,upstream_gene_variant,,ENST00000560147,;MAN2A2,downstream_gene_variant,,ENST00000559965,;MAN2A2,downstream_gene_variant,,ENST00000559999,;MAN2A2,upstream_gene_variant,,ENST00000557990,;MAN2A2,upstream_gene_variant,,ENST00000430376,;MAN2A2,downstream_gene_variant,,ENST00000558290,;MAN2A2,downstream_gene_variant,,ENST00000559132,;MAN2A2,downstream_gene_variant,,ENST00000558640,;MAN2A2,upstream_gene_variant,,ENST00000561240,;MAN2A2,missense_variant,p.Arg526Gln,ENST00000558161,;MAN2A2,missense_variant,p.Arg526Gln,ENST00000560451,;MAN2A2,splice_region_variant,,ENST00000560192,;MAN2A2,upstream_gene_variant,,ENST00000560505,;MAN2A2,upstream_gene_variant,,ENST00000561448,;MAN2A2,upstream_gene_variant,,ENST00000561047,;MAN2A2,upstream_gene_variant,,ENST00000559374,;MAN2A2,downstream_gene_variant,,ENST00000561046,;	A	ENSG00000196547	ENST00000360468	Transcript	missense_variant	1595	1577	526	R/Q	cGg/cAg	COSM1608839	.	.	1	MAN2A2	HGNC	6825	protein_coding	YES	CCDS32332.1	ENSP00000353655	MA2A2_HUMAN	H0YNC8_HUMAN,H0YMU0_HUMAN,H0YL67_HUMAN,H0YK77_HUMAN,B7ZA35_HUMAN	UPI0000408EF0	.	deleterious(0)	probably_damaging(0.991)	9/22	.	Superfamily_domains:SSF88688,SMART_domains:SM00872,Pfam_domain:PF09261,Gene3D:3bvxA02,hmmpanther:PTHR11607:SF24,hmmpanther:PTHR11607	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CCTGCGGTGAG	.	2	ESCA
SLCO3A1	0	.	GRCh37	15	92459375	92459375	+	Silent	SNP	C	C	T	rs760273166	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333C>T	p.%3D	p.C111C	ENST00000318445	2/10	26	18	7	16	16	0	SLCO3A1,synonymous_variant,p.%3D,ENST00000318445,;SLCO3A1,synonymous_variant,p.%3D,ENST00000424469,;SLCO3A1,synonymous_variant,p.%3D,ENST00000553304,;SLCO3A1,non_coding_transcript_exon_variant,,ENST00000555769,;SLCO3A1,non_coding_transcript_exon_variant,,ENST00000553653,;	T	ENSG00000176463	ENST00000318445	Transcript	synonymous_variant	547	333	111	C	tgC/tgT	rs760273166,COSM1629747	.	.	1	SLCO3A1	HGNC	10952	protein_coding	YES	CCDS10371.1	ENSP00000320634	SO3A1_HUMAN	.	UPI00001AF1F7	.	.	.	2/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF9,Gene3D:1.20.1250.20,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGCGGCGG	byFrequency	5	ESCA
MCTP2	0	.	GRCh37	15	94858854	94858854	+	Nonsense_Mutation	SNP	C	C	T	rs200389318	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.625C>T	p.Arg209Ter	p.R209*	ENST00000357742	3/22	153	48	105	86	86	0	MCTP2,stop_gained,p.Arg209Ter,ENST00000357742,;MCTP2,stop_gained,p.Arg209Ter,ENST00000451018,;MCTP2,stop_gained,p.Arg209Ter,ENST00000543482,;MCTP2,5_prime_UTR_variant,,ENST00000331706,;MCTP2,downstream_gene_variant,,ENST00000561608,;MCTP2,3_prime_UTR_variant,,ENST00000456504,;MCTP2,non_coding_transcript_exon_variant,,ENST00000556363,;	T	ENSG00000140563	ENST00000357742	Transcript	stop_gained	625	625	209	R/*	Cga/Tga	rs200389318	.	.	1	MCTP2	HGNC	25636	protein_coding	YES	CCDS32338.1	ENSP00000350377	MCTP2_HUMAN	Q9NPN6_HUMAN	UPI0000D613A2	.	.	.	3/22	.	PROSITE_profiles:PS50004,hmmpanther:PTHR16122,hmmpanther:PTHR16122:SF5,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTCCGAGAT	byCluster|by1000G	5	ESCA
TEKT5	0	.	GRCh37	16	10788423	10788423	+	Missense_Mutation	SNP	C	C	T	rs201724934	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.308G>A	p.Arg103His	p.R103H	ENST00000283025	1/7	81	43	38	49	49	0	TEKT5,missense_variant,p.Arg103His,ENST00000283025,;TEKT5,upstream_gene_variant,,ENST00000576638,;RP11-109M19.1,downstream_gene_variant,,ENST00000576710,;	T	ENSG00000153060	ENST00000283025	Transcript	missense_variant	380	308	103	R/H	cGt/cAt	rs201724934	.	.	-1	TEKT5	HGNC	26554	protein_coding	YES	CCDS10542.1	ENSP00000283025	TEKT5_HUMAN	I3L1F7_HUMAN	UPI000006D1A0	.	deleterious(0.04)	benign(0.035)	1/7	.	hmmpanther:PTHR19960:SF23,hmmpanther:PTHR19960,Pfam_domain:PF03148	T:0.0010	T:0	T:0	.	T:0.005	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCACGCACC	byFrequency|byCluster|by1000G	5	ESCA
CLEC16A	0	.	GRCh37	16	11272324	11272324	+	Missense_Mutation	SNP	C	C	T	rs764039952	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2939C>T	p.Ser980Phe	p.S980F	ENST00000409790	24/24	54	43	11	19	19	0	CLEC16A,missense_variant,p.Ser980Phe,ENST00000409790,;CLEC16A,missense_variant,p.Ser67Phe,ENST00000381822,;CLEC16A,3_prime_UTR_variant,,ENST00000261657,;	T	ENSG00000038532	ENST00000409790	Transcript	missense_variant	3169	2939	980	S/F	tCc/tTc	rs764039952	.	.	1	CLEC16A	HGNC	29013	protein_coding	YES	CCDS45409.1	ENSP00000387122	CL16A_HUMAN	.	UPI0000253BAD	.	deleterious_low_confidence(0)	possibly_damaging(0.555)	24/24	.	hmmpanther:PTHR21481	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGTCCCCCA	.	5	ESCA
MKL2	0	.	GRCh37	16	14351991	14351991	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2587C>G	p.Leu863Val	p.L863V	ENST00000318282	15/16	37	30	7	34	34	0	MKL2,missense_variant,p.Leu863Val,ENST00000318282,;MKL2,missense_variant,p.Leu902Val,ENST00000341243,;MKL2,missense_variant,p.Leu913Val,ENST00000571589,;MKL2,missense_variant,p.Leu863Val,ENST00000574045,;MKL2,missense_variant,p.Leu5Val,ENST00000571770,;MKL2,non_coding_transcript_exon_variant,,ENST00000572588,;	G	ENSG00000186260	ENST00000318282	Transcript	missense_variant	2717	2587	863	L/V	Ctc/Gtc	.	.	.	1	MKL2	HGNC	29819	protein_coding	YES	CCDS32391.1	ENSP00000339086	MKL2_HUMAN	I3L0U1_HUMAN	UPI0000225CCB	.	deleterious(0)	probably_damaging(0.999)	15/16	.	hmmpanther:PTHR22793:SF5,hmmpanther:PTHR22793	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACCTCTTT	.	5	ESCA
CLCN7	0	.	GRCh37	16	1497455	1497455	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2188G>A	p.Glu730Lys	p.E730K	ENST00000382745	23/25	69	50	19	32	32	0	CLCN7,missense_variant,p.Glu706Lys,ENST00000448525,;CLCN7,missense_variant,p.Glu706Lys,ENST00000262318,;CLCN7,missense_variant,p.Glu730Lys,ENST00000382745,;CCDC154,upstream_gene_variant,,ENST00000389176,;CCDC154,upstream_gene_variant,,ENST00000409671,;LA16c-390E6.5,downstream_gene_variant,,ENST00000566287,;LA16c-390E6.4,upstream_gene_variant,,ENST00000563610,;CLCN7,non_coding_transcript_exon_variant,,ENST00000565092,;CLCN7,non_coding_transcript_exon_variant,,ENST00000563642,;CLCN7,non_coding_transcript_exon_variant,,ENST00000567836,;CLCN7,downstream_gene_variant,,ENST00000567789,;	T	ENSG00000103249	ENST00000382745	Transcript	missense_variant	2794	2188	730	E/K	Gag/Aag	CM099584	.	.	-1	CLCN7	HGNC	2025	protein_coding	YES	CCDS32361.1	ENSP00000372193	CLCN7_HUMAN	Q9BSM4_HUMAN,Q96RY8_HUMAN,I3L470_HUMAN,B3KXZ3_HUMAN	UPI000004904C	.	tolerated(0.13)	possibly_damaging(0.459)	23/25	.	hmmpanther:PTHR11689:SF14,hmmpanther:PTHR11689,Gene3D:3.10.580.10,Superfamily_domains:SSF54631	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCTCGTCCT	.	5	ESCA
NTAN1	0	.	GRCh37	16	15132457	15132457	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.727C>T	p.His243Tyr	p.H243Y	ENST00000287706	9/10	72	52	20	53	53	0	NTAN1,missense_variant,p.His216Tyr,ENST00000566419,;NTAN1,missense_variant,p.His138Tyr,ENST00000568320,;NTAN1,missense_variant,p.His243Tyr,ENST00000287706,;PDXDC1,intron_variant,,ENST00000535621,;PDXDC1,downstream_gene_variant,,ENST00000569715,;PDXDC1,downstream_gene_variant,,ENST00000325823,;PDXDC1,downstream_gene_variant,,ENST00000447912,;PDXDC1,downstream_gene_variant,,ENST00000563679,;PDXDC1,downstream_gene_variant,,ENST00000396410,;PDXDC1,downstream_gene_variant,,ENST00000450288,;NTAN1,3_prime_UTR_variant,,ENST00000565187,;NTAN1,3_prime_UTR_variant,,ENST00000568738,;NTAN1,non_coding_transcript_exon_variant,,ENST00000566542,;NTAN1,downstream_gene_variant,,ENST00000570292,;NTAN1,downstream_gene_variant,,ENST00000563940,;PDXDC1,downstream_gene_variant,,ENST00000562119,;PDXDC1,downstream_gene_variant,,ENST00000570001,;PDXDC1,downstream_gene_variant,,ENST00000565986,;	A	ENSG00000157045	ENST00000287706	Transcript	missense_variant	820	727	243	H/Y	Cac/Tac	.	.	.	-1	NTAN1	HGNC	29909	protein_coding	YES	CCDS10558.1	ENSP00000287706	NTAN1_HUMAN	Q658S0_HUMAN,H3BPN7_HUMAN	UPI0000071024	.	deleterious(0.01)	benign(0.013)	9/10	.	hmmpanther:PTHR12498,hmmpanther:PTHR12498:SF0,Pfam_domain:PF14736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGTGCAACC	.	5	ESCA
RP11-1186N24.5	0	.	GRCh37	16	15225202	15225202	+	RNA	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.257T>C	.	.	ENST00000605794	1/18	129	64	65	96	96	0	PDXDC1,intron_variant,,ENST00000535621,;RP11-1186N24.5,non_coding_transcript_exon_variant,,ENST00000605794,;PKD1P6,non_coding_transcript_exon_variant,,ENST00000424133,;PKD1P6,downstream_gene_variant,,ENST00000540075,;PKD1P6,downstream_gene_variant,,ENST00000540502,;PKD1P6,downstream_gene_variant,,ENST00000538100,;PKD1P6,downstream_gene_variant,,ENST00000546358,;PKD1P6,non_coding_transcript_exon_variant,,ENST00000343738,;NPIPP1,non_coding_transcript_exon_variant,,ENST00000448014,;NPIPP1,non_coding_transcript_exon_variant,,ENST00000358815,;	G	ENSG00000270580	ENST00000605794	Transcript	non_coding_transcript_exon_variant	257	.	.	.	.	.	.	.	-1	RP11-1186N24.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGTAGTTGC	.	5	ESCA
RP11-1186N24.5	0	.	GRCh37	16	15225392	15225392	+	RNA	SNP	G	G	A	rs574820691	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.67C>T	.	.	ENST00000605794	1/18	145	128	17	112	112	0	PDXDC1,intron_variant,,ENST00000535621,;RP11-1186N24.5,non_coding_transcript_exon_variant,,ENST00000605794,;PKD1P6,downstream_gene_variant,,ENST00000540075,;PKD1P6,upstream_gene_variant,,ENST00000424133,;PKD1P6,downstream_gene_variant,,ENST00000540502,;PKD1P6,downstream_gene_variant,,ENST00000538100,;PKD1P6,downstream_gene_variant,,ENST00000546358,;PKD1P6,non_coding_transcript_exon_variant,,ENST00000343738,;NPIPP1,non_coding_transcript_exon_variant,,ENST00000448014,;NPIPP1,non_coding_transcript_exon_variant,,ENST00000358815,;	A	ENSG00000270580	ENST00000605794	Transcript	non_coding_transcript_exon_variant	67	.	.	.	.	rs574820691	.	.	-1	RP11-1186N24.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/18	.	.	A:0.0008	A:0.0008	A:0.0029	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TCCTCGCCCGC	byFrequency|by1000G	2	ESCA
TELO2	0	.	GRCh37	16	1550422	1550422	+	Silent	SNP	C	C	T	rs375335497	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1077C>T	p.%3D	p.H359H	ENST00000262319	8/21	33	26	7	20	20	0	TELO2,synonymous_variant,p.%3D,ENST00000262319,;TELO2,upstream_gene_variant,,ENST00000567423,;TELO2,upstream_gene_variant,,ENST00000564507,;TELO2,upstream_gene_variant,,ENST00000567427,;TELO2,synonymous_variant,p.%3D,ENST00000497339,;TELO2,upstream_gene_variant,,ENST00000569744,;	T	ENSG00000100726	ENST00000262319	Transcript	synonymous_variant	1356	1077	359	H	caC/caT	rs375335497	.	.	1	TELO2	HGNC	29099	protein_coding	YES	CCDS32363.1	ENSP00000262319	TELO2_HUMAN	.	UPI000016961D	.	.	.	8/21	.	hmmpanther:PTHR15830,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCACGTCAG	byFrequency|byCluster	5	ESCA
UMOD	0	.	GRCh37	16	20352508	20352508	+	Silent	SNP	G	G	A	rs776537437	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1482C>T	p.%3D	p.G494G	ENST00000570689	7/11	67	34	32	32	32	0	UMOD,synonymous_variant,p.%3D,ENST00000570689,;UMOD,synonymous_variant,p.%3D,ENST00000396142,;UMOD,synonymous_variant,p.%3D,ENST00000396134,;UMOD,synonymous_variant,p.%3D,ENST00000302509,;UMOD,synonymous_variant,p.%3D,ENST00000424589,;UMOD,synonymous_variant,p.%3D,ENST00000396138,;UMOD,non_coding_transcript_exon_variant,,ENST00000570331,;	A	ENSG00000169344	ENST00000570689	Transcript	synonymous_variant	1629	1482	494	G	ggC/ggT	rs776537437	.	.	-1	UMOD	HGNC	12559	protein_coding	YES	CCDS10583.1	ENSP00000460548	UROM_HUMAN	Q8NHW8_HUMAN,I3L4Y6_HUMAN,I3L4B0_HUMAN,I3L2J2_HUMAN,I3L1M3_HUMAN,I3L1A9_HUMAN,B3KXM9_HUMAN	UPI0000137E1A	.	.	.	7/11	.	PROSITE_profiles:PS51034,hmmpanther:PTHR22962,hmmpanther:PTHR22962:SF12,PROSITE_patterns:PS00682,Pfam_domain:PF00100,SMART_domains:SM00241	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTCGCCCCC	.	5	ESCA
ACSM2A	0	.	GRCh37	16	20491948	20491948	+	Silent	SNP	A	A	C	rs749990598	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1335A>C	p.%3D	p.G445G	ENST00000573854	11/14	84	30	53	56	56	0	ACSM2A,synonymous_variant,p.%3D,ENST00000575690,;ACSM2A,synonymous_variant,p.%3D,ENST00000573854,;ACSM2A,synonymous_variant,p.%3D,ENST00000536134,;ACSM2A,synonymous_variant,p.%3D,ENST00000219054,;ACSM2A,synonymous_variant,p.%3D,ENST00000417235,;ACSM2A,synonymous_variant,p.%3D,ENST00000396104,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000575558,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000570698,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000572843,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000576101,;ACSM2A,upstream_gene_variant,,ENST00000576119,;	C	ENSG00000183747	ENST00000573854	Transcript	synonymous_variant	1449	1335	445	G	ggA/ggC	rs749990598	.	.	1	ACSM2A	HGNC	32017	protein_coding	YES	CCDS32401.1	ENSP00000459451	ACS2A_HUMAN	I3L438_HUMAN,I3L339_HUMAN,I3L2Y5_HUMAN,F5GWL3_HUMAN	UPI0000251E27	.	.	.	11/14	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF140,Gene3D:2.30.38.10,Pfam_domain:PF00501,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGAGACCG	.	5	ESCA
TSC2	0	.	GRCh37	16	2131769	2131769	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3784A>G	p.Lys1262Glu	p.K1262E	ENST00000219476	31/42	108	88	19	68	68	0	TSC2,missense_variant,p.Lys1182Glu,ENST00000439673,;TSC2,missense_variant,p.Lys1262Glu,ENST00000219476,;TSC2,missense_variant,p.Lys1219Glu,ENST00000353929,;TSC2,missense_variant,p.Lys1262Glu,ENST00000350773,;TSC2,missense_variant,p.Lys1229Glu,ENST00000568454,;TSC2,missense_variant,p.Lys1170Glu,ENST00000382538,;TSC2,missense_variant,p.Lys1218Glu,ENST00000401874,;TSC2,upstream_gene_variant,,ENST00000569110,;TSC2,downstream_gene_variant,,ENST00000568366,;TSC2,3_prime_UTR_variant,,ENST00000439117,;TSC2,non_coding_transcript_exon_variant,,ENST00000497886,;TSC2,downstream_gene_variant,,ENST00000561695,;TSC2,upstream_gene_variant,,ENST00000569930,;TSC2,downstream_gene_variant,,ENST00000471143,;TSC2,downstream_gene_variant,,ENST00000483020,;	G	ENSG00000103197	ENST00000219476	Transcript	missense_variant	4414	3784	1262	K/E	Aaa/Gaa	.	.	.	1	TSC2	HGNC	12363	protein_coding	YES	CCDS10458.1	ENSP00000219476	TSC2_HUMAN	.	UPI000013C781	.	tolerated_low_confidence(0.14)	benign(0.144)	31/42	.	hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCAAACCC	.	5	ESCA
CACNG3	0	.	GRCh37	16	24372735	24372735	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499C>T	p.Arg167Cys	p.R167C	ENST00000005284	4/4	46	17	29	34	34	0	CACNG3,missense_variant,p.Arg167Cys,ENST00000005284,;	T	ENSG00000006116	ENST00000005284	Transcript	missense_variant	1701	499	167	R/C	Cgt/Tgt	COSM4059473	.	.	1	CACNG3	HGNC	1407	protein_coding	YES	CCDS10620.1	ENSP00000005284	CCG3_HUMAN	.	UPI000000D979	.	deleterious(0.03)	possibly_damaging(0.505)	4/4	.	Pfam_domain:PF00822,hmmpanther:PTHR12107:SF5,hmmpanther:PTHR12107	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGCGTGAC	.	5	ESCA
PDPK1	0	.	GRCh37	16	2647921	2647922	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*161dupA	.	.	ENST00000342085	14/14	28	17	11	19	19	0	PDPK1,3_prime_UTR_variant,,ENST00000389224,;PDPK1,3_prime_UTR_variant,,ENST00000342085,;PDPK1,3_prime_UTR_variant,,ENST00000268673,;PDPK1,downstream_gene_variant,,ENST00000354836,;PDPK1,downstream_gene_variant,,ENST00000441549,;CTD-3126B10.1,non_coding_transcript_exon_variant,,ENST00000562166,;PDPK1,upstream_gene_variant,,ENST00000561962,;PDPK1,upstream_gene_variant,,ENST00000569721,;	A	ENSG00000140992	ENST00000342085	Transcript	3_prime_UTR_variant	1973-1974	.	.	.	.	.	.	.	1	PDPK1	HGNC	8816	protein_coding	YES	CCDS10472.1	ENSP00000344220	PDPK1_HUMAN	Q9UPJ8_HUMAN,Q9UPJ7_HUMAN,H3BQ10_HUMAN,E9PER6_HUMAN	UPI00001314D4	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAGAAGAAAAA	.	2	ESCA
GTF3C1	0	.	GRCh37	16	27506096	27506096	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2766A>T	p.Gln922His	p.Q922H	ENST00000356183	16/37	37	23	14	25	25	0	GTF3C1,missense_variant,p.Gln922His,ENST00000561623,;GTF3C1,missense_variant,p.Gln922His,ENST00000356183,;GTF3C1,intron_variant,,ENST00000569653,;	A	ENSG00000077235	ENST00000356183	Transcript	missense_variant	2782	2766	922	Q/H	caA/caT	.	.	.	-1	GTF3C1	HGNC	4664	protein_coding	YES	CCDS32414.1	ENSP00000348510	TF3C1_HUMAN	Q7Z7H4_HUMAN,I3L1Z3_HUMAN	UPI00001FF123	.	deleterious(0)	probably_damaging(0.94)	16/37	.	hmmpanther:PTHR15180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACTTGCAC	.	5	ESCA
SRRM2	0	.	GRCh37	16	2812095	2812095	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1566G>T	p.Trp522Cys	p.W522C	ENST00000301740	11/15	31	27	4	24	24	0	SRRM2,missense_variant,p.Trp522Cys,ENST00000576924,;SRRM2,missense_variant,p.Trp426Cys,ENST00000571378,;SRRM2,missense_variant,p.Trp522Cys,ENST00000301740,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000574340,;SRRM2,downstream_gene_variant,,ENST00000576415,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,non_coding_transcript_exon_variant,,ENST00000572952,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,downstream_gene_variant,,ENST00000575701,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,downstream_gene_variant,,ENST00000573451,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000571372,;	T	ENSG00000167978	ENST00000301740	Transcript	missense_variant	2115	1566	522	W/C	tgG/tgT	.	.	.	1	SRRM2	HGNC	16639	protein_coding	YES	CCDS32373.1	ENSP00000301740	SRRM2_HUMAN	I3L4D8_HUMAN,I3L1I8_HUMAN,I3L1C0_HUMAN,I3L182_HUMAN,I3L0N7_HUMAN	UPI000049DDFC	.	.	unknown(0)	11/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTGGGGAAG	.	2	ESCA
TCEB2	0	.	GRCh37	16	2821468	2821468	+	3'UTR	SNP	C	C	T	rs772677442	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5G>A	.	.	ENST00000262306	5/5	79	61	18	39	39	0	TCEB2,3_prime_UTR_variant,,ENST00000409477,;TCEB2,3_prime_UTR_variant,,ENST00000262306,;TCEB2,3_prime_UTR_variant,,ENST00000409906,;TCEB2,downstream_gene_variant,,ENST00000494946,;SRRM2,downstream_gene_variant,,ENST00000570539,;TCEB2,downstream_gene_variant,,ENST00000572954,;SRRM2,downstream_gene_variant,,ENST00000301740,;AC092117.2,downstream_gene_variant,,ENST00000581119,;SRRM2,non_coding_transcript_exon_variant,,ENST00000573583,;SRRM2,downstream_gene_variant,,ENST00000572721,;SRRM2,downstream_gene_variant,,ENST00000574866,;SRRM2,downstream_gene_variant,,ENST00000574593,;SRRM2,downstream_gene_variant,,ENST00000572883,;SRRM2,downstream_gene_variant,,ENST00000573692,;SRRM2,downstream_gene_variant,,ENST00000576878,;SRRM2,downstream_gene_variant,,ENST00000571041,;SRRM2,downstream_gene_variant,,ENST00000573311,;SRRM2,downstream_gene_variant,,ENST00000574331,;SRRM2,downstream_gene_variant,,ENST00000570705,;	T	ENSG00000103363	ENST00000262306	Transcript	3_prime_UTR_variant	529	.	.	.	.	rs772677442	.	.	-1	TCEB2	HGNC	11619	protein_coding	YES	CCDS32374.1	ENSP00000262306	ELOB_HUMAN	.	UPI0000353500	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTCCGTGAT	byFrequency	5	ESCA
NFATC2IP	0	.	GRCh37	16	28967541	28967541	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729A>T	p.Gln243His	p.Q243H	ENST00000320805	5/8	34	22	12	28	28	0	NFATC2IP,missense_variant,p.Gln243His,ENST00000320805,;NFATC2IP,intron_variant,,ENST00000564978,;NFATC2IP,upstream_gene_variant,,ENST00000568148,;MIR4517,upstream_gene_variant,,ENST00000578855,;RP11-264B17.2,downstream_gene_variant,,ENST00000569974,;RP11-264B17.2,downstream_gene_variant,,ENST00000568057,;NFATC2IP,intron_variant,,ENST00000562977,;NFATC2IP,non_coding_transcript_exon_variant,,ENST00000568998,;NFATC2IP,downstream_gene_variant,,ENST00000565919,;NFATC2IP,downstream_gene_variant,,ENST00000565752,;	T	ENSG00000176953	ENST00000320805	Transcript	missense_variant	804	729	243	Q/H	caA/caT	.	.	.	1	NFATC2IP	HGNC	25906	protein_coding	YES	CCDS10645.1	ENSP00000324792	NF2IP_HUMAN	.	UPI00000316E2	.	tolerated(0.55)	benign(0)	5/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10562,hmmpanther:PTHR10562:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCAACAGGG	.	5	ESCA
SPN	0	.	GRCh37	16	29678366	29678366	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2114C>T	.	.	ENST00000360121	2/2	28	20	8	15	15	0	SPN,3_prime_UTR_variant,,ENST00000360121,;QPRT,intron_variant,,ENST00000449759,;SPN,downstream_gene_variant,,ENST00000436527,;SPN,downstream_gene_variant,,ENST00000395389,;SPN,intron_variant,,ENST00000563039,;SPN,upstream_gene_variant,,ENST00000561857,;	T	ENSG00000197471	ENST00000360121	Transcript	3_prime_UTR_variant	3409	.	.	.	.	.	.	.	1	SPN	HGNC	11249	protein_coding	YES	CCDS10650.1	ENSP00000353238	LEUK_HUMAN	C9JUK7_HUMAN,A8K9B1_HUMAN	UPI000012E5AA	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTGCAGTGG	.	5	ESCA
MAZ	0	.	GRCh37	16	29821568	29821568	+	3'UTR	SNP	C	C	T	rs571424053	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*193C>T	.	.	ENST00000219782	6/6	18	13	5	25	25	0	MAZ,missense_variant,p.Ala138Val,ENST00000566906,;MAZ,missense_variant,p.Ala140Val,ENST00000563402,;MAZ,3_prime_UTR_variant,,ENST00000545521,;MAZ,3_prime_UTR_variant,,ENST00000568544,;MAZ,3_prime_UTR_variant,,ENST00000563012,;MAZ,3_prime_UTR_variant,,ENST00000568282,;MAZ,3_prime_UTR_variant,,ENST00000322945,;MAZ,3_prime_UTR_variant,,ENST00000219782,;MAZ,3_prime_UTR_variant,,ENST00000562337,;MAZ,intron_variant,,ENST00000562594,;MAZ,intron_variant,,ENST00000568411,;KIF22,downstream_gene_variant,,ENST00000569382,;MAZ,downstream_gene_variant,,ENST00000569978,;KIF22,downstream_gene_variant,,ENST00000561482,;KIF22,downstream_gene_variant,,ENST00000400751,;PRRT2,upstream_gene_variant,,ENST00000300797,;KIF22,downstream_gene_variant,,ENST00000160827,;MAZ,downstream_gene_variant,,ENST00000567444,;PRRT2,upstream_gene_variant,,ENST00000358758,;PRRT2,upstream_gene_variant,,ENST00000562148,;PRRT2,upstream_gene_variant,,ENST00000567659,;MAZ,downstream_gene_variant,,ENST00000562557,;PRRT2,upstream_gene_variant,,ENST00000572820,;AC009133.14,non_coding_transcript_exon_variant,,ENST00000569981,;AC009133.20,intron_variant,,ENST00000569039,;AC009133.15,upstream_gene_variant,,ENST00000566537,;AC009133.14,upstream_gene_variant,,ENST00000563806,;PRRT2,upstream_gene_variant,,ENST00000567551,;MAZ,upstream_gene_variant,,ENST00000568516,;MAZ,3_prime_UTR_variant,,ENST00000561855,;MAZ,non_coding_transcript_exon_variant,,ENST00000565777,;KIF22,downstream_gene_variant,,ENST00000565736,;KIF22,downstream_gene_variant,,ENST00000568312,;	T	ENSG00000103495	ENST00000219782	Transcript	3_prime_UTR_variant	1781	.	.	.	.	rs571424053	.	.	1	MAZ	HGNC	6914	protein_coding	YES	CCDS42144.1	ENSP00000219782	MAZ_HUMAN	Q9UJ31_HUMAN,Q8IUI2_HUMAN,I3L4Y2_HUMAN,I3L0M3_HUMAN	UPI00001AE621	.	.	.	6/6	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGTTGCGGGGG	by1000G	4	ESCA
KCTD13	0	.	GRCh37	16	29918228	29918228	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.955C>T	p.Arg319Cys	p.R319C	ENST00000568000	6/6	34	28	6	24	24	0	KCTD13,missense_variant,p.Arg319Cys,ENST00000568000,;KCTD13,intron_variant,,ENST00000568995,;ASPHD1,downstream_gene_variant,,ENST00000308748,;ASPHD1,downstream_gene_variant,,ENST00000483405,;ASPHD1,downstream_gene_variant,,ENST00000563177,;KCTD13,downstream_gene_variant,,ENST00000563264,;KCTD13,missense_variant,p.Arg319Cys,ENST00000308768,;KCTD13,3_prime_UTR_variant,,ENST00000566842,;ASPHD1,intron_variant,,ENST00000414952,;ASPHD1,intron_variant,,ENST00000566693,;KCTD13,downstream_gene_variant,,ENST00000563955,;	A	ENSG00000174943	ENST00000568000	Transcript	missense_variant	1957	955	319	R/C	Cgt/Tgt	.	.	.	-1	KCTD13	HGNC	22234	protein_coding	YES	CCDS10661.1	ENSP00000455785	BACD1_HUMAN	.	UPI0000073C51	.	deleterious_low_confidence(0)	probably_damaging(0.998)	6/6	.	hmmpanther:PTHR11145,hmmpanther:PTHR11145:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGACGCTCGT	.	4	ESCA
CORO1A	0	.	GRCh37	16	30198370	30198370	+	Silent	SNP	C	C	T	rs762370414	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462C>T	p.%3D	p.N154N	ENST00000219150	5/11	79	40	38	54	54	0	CORO1A,synonymous_variant,p.%3D,ENST00000219150,;CORO1A,synonymous_variant,p.%3D,ENST00000569970,;CORO1A,synonymous_variant,p.%3D,ENST00000565497,;CORO1A,synonymous_variant,p.%3D,ENST00000563778,;CORO1A,synonymous_variant,p.%3D,ENST00000570244,;CORO1A,synonymous_variant,p.%3D,ENST00000561815,;CORO1A,synonymous_variant,p.%3D,ENST00000570045,;CORO1A,downstream_gene_variant,,ENST00000569203,;RP11-455F5.5,upstream_gene_variant,,ENST00000566144,;RP11-455F5.5,upstream_gene_variant,,ENST00000568506,;RP11-455F5.5,upstream_gene_variant,,ENST00000567153,;CORO1A,non_coding_transcript_exon_variant,,ENST00000569469,;CORO1A,downstream_gene_variant,,ENST00000564446,;CORO1A,downstream_gene_variant,,ENST00000566619,;CORO1A,non_coding_transcript_exon_variant,,ENST00000567034,;CORO1A,non_coding_transcript_exon_variant,,ENST00000568982,;CORO1A,non_coding_transcript_exon_variant,,ENST00000568763,;CORO1A,non_coding_transcript_exon_variant,,ENST00000564768,;CORO1A,downstream_gene_variant,,ENST00000561849,;CORO1A,upstream_gene_variant,,ENST00000562129,;	T	ENSG00000102879	ENST00000219150	Transcript	synonymous_variant	767	462	154	N	aaC/aaT	rs762370414,COSM969794	.	.	1	CORO1A	HGNC	2252	protein_coding	YES	CCDS10673.1	ENSP00000219150	COR1A_HUMAN	H3BU76_HUMAN,H3BRJ0_HUMAN,H3BNA2_HUMAN	UPI00000413AE	.	.	.	5/11	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF18,PROSITE_patterns:PS00678,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACAACGTGAT	.	5	ESCA
ZNF629	0	.	GRCh37	16	30794962	30794962	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.687G>A	p.%3D	p.T229T	ENST00000262525	3/3	94	65	29	52	52	0	ZNF629,synonymous_variant,p.%3D,ENST00000262525,;RP11-2C24.6,downstream_gene_variant,,ENST00000575562,;	T	ENSG00000102870	ENST00000262525	Transcript	synonymous_variant	895	687	229	T	acG/acA	.	.	.	-1	ZNF629	HGNC	29008	protein_coding	YES	CCDS45463.1	ENSP00000262525	ZN629_HUMAN	.	UPI00001C1FA5	.	.	.	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF286,hmmpanther:PTHR24377,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCCGTGTG	.	5	ESCA
PRSS36	0	.	GRCh37	16	31150582	31150582	+	Silent	SNP	G	G	T	rs780793903	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2445C>A	p.%3D	p.P815P	ENST00000268281	15/15	37	27	10	19	19	0	PRSS36,synonymous_variant,p.%3D,ENST00000418068,;PRSS36,synonymous_variant,p.%3D,ENST00000268281,;PRSS36,synonymous_variant,p.%3D,ENST00000569305,;PRSS8,upstream_gene_variant,,ENST00000568261,;PRSS8,upstream_gene_variant,,ENST00000567797,;PRSS8,upstream_gene_variant,,ENST00000317508,;PRSS8,upstream_gene_variant,,ENST00000567531,;PRSS36,3_prime_UTR_variant,,ENST00000571878,;PRSS36,non_coding_transcript_exon_variant,,ENST00000562368,;PRSS36,downstream_gene_variant,,ENST00000563693,;PRSS8,upstream_gene_variant,,ENST00000567833,;PRSS8,upstream_gene_variant,,ENST00000564025,;	T	ENSG00000178226	ENST00000268281	Transcript	synonymous_variant	2504	2445	815	P	ccC/ccA	TMP_ESP_16_31150582_31150582,rs780793903	.	.	-1	PRSS36	HGNC	26906	protein_coding	YES	CCDS32436.1	ENSP00000268281	POLS2_HUMAN	B4DNP1_HUMAN	UPI00001FFF6A	.	.	.	15/15	.	PIRSF_domain:PIRSF037933	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTGGGGGG	.	5	ESCA
ITFG3	0	.	GRCh37	16	315060	315060	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39C>T	.	.	ENST00000399932	13/13	45	18	27	18	18	0	ITFG3,3_prime_UTR_variant,,ENST00000301678,;ITFG3,3_prime_UTR_variant,,ENST00000399932,;ITFG3,3_prime_UTR_variant,,ENST00000424016,;ITFG3,intron_variant,,ENST00000442458,;ITFG3,intron_variant,,ENST00000600536,;ITFG3,intron_variant,,ENST00000301679,;ITFG3,intron_variant,,ENST00000450082,;RGS11,downstream_gene_variant,,ENST00000397770,;ITFG3,downstream_gene_variant,,ENST00000420046,;ITFG3,downstream_gene_variant,,ENST00000421000,;ITFG3,downstream_gene_variant,,ENST00000453430,;ARHGDIG,upstream_gene_variant,,ENST00000435035,;ARHGDIG,upstream_gene_variant,,ENST00000412541,;RGS11,downstream_gene_variant,,ENST00000316163,;RGS11,downstream_gene_variant,,ENST00000359740,;ITFG3,downstream_gene_variant,,ENST00000449945,;ARHGDIG,upstream_gene_variant,,ENST00000464609,;RGS11,downstream_gene_variant,,ENST00000168869,;RGS11,downstream_gene_variant,,ENST00000477143,;ITFG3,downstream_gene_variant,,ENST00000468354,;	T	ENSG00000167930	ENST00000399932	Transcript	3_prime_UTR_variant	2149	.	.	.	.	.	.	.	1	ITFG3	HGNC	14163	protein_coding	YES	CCDS10402.1	ENSP00000382814	ITFG3_HUMAN	C9JR71_HUMAN,C9JJN3_HUMAN,C9J8V3_HUMAN,C9J3Y6_HUMAN,C9J1M4_HUMAN,C9IYB9_HUMAN	UPI000006DF0D	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGCTGACA	.	5	ESCA
ZNF263	0	.	GRCh37	16	3340414	3340414	+	Silent	SNP	C	C	T	rs754419593	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1908C>T	p.%3D	p.C636C	ENST00000219069	6/6	25	20	5	31	31	0	ZNF263,synonymous_variant,p.%3D,ENST00000538765,;ZNF263,synonymous_variant,p.%3D,ENST00000574674,;ZNF263,synonymous_variant,p.%3D,ENST00000219069,;ZNF263,synonymous_variant,p.%3D,ENST00000575332,;ZNF263,downstream_gene_variant,,ENST00000573578,;ZNF263,downstream_gene_variant,,ENST00000572748,;ZNF263,downstream_gene_variant,,ENST00000574253,;ZNF263,downstream_gene_variant,,ENST00000575823,;	T	ENSG00000006194	ENST00000219069	Transcript	synonymous_variant	2784	1908	636	C	tgC/tgT	rs754419593	.	.	1	ZNF263	HGNC	13056	protein_coding	YES	CCDS10499.1	ENSP00000219069	ZN263_HUMAN	B4DI05_HUMAN	UPI000013C33A	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23226:SF50,hmmpanther:PTHR23226,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGTGCGGAGA	.	4	ESCA
CREBBP	0	.	GRCh37	16	3820601	3820601	+	Silent	SNP	C	C	T	rs141651423	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2850G>A	p.%3D	p.T950T	ENST00000262367	14/31	43	21	22	20	20	0	CREBBP,synonymous_variant,p.%3D,ENST00000262367,;CREBBP,synonymous_variant,p.%3D,ENST00000382070,;CREBBP,upstream_gene_variant,,ENST00000570939,;CREBBP,downstream_gene_variant,,ENST00000572134,;CREBBP,downstream_gene_variant,,ENST00000571826,;CREBBP,non_coding_transcript_exon_variant,,ENST00000573672,;CREBBP,downstream_gene_variant,,ENST00000575237,;	T	ENSG00000005339	ENST00000262367	Transcript	synonymous_variant	3660	2850	950	T	acG/acA	rs141651423	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	.	14/31	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5	T:0.0008	T:0.003	T:0	.	T:0	T:0	T:0	T:0.0016	T:0	uncertain_significance	.	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	ACAGGCGTCGG	byFrequency|byCluster|by1000G	3	ESCA
NME4	0	.	GRCh37	16	450578	450579	+	3'UTR	INS	-	-	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*245dupG	.	.	ENST00000219479	5/5	35	20	15	27	27	0	NME4,3_prime_UTR_variant,,ENST00000433358,;NME4,3_prime_UTR_variant,,ENST00000397722,;NME4,3_prime_UTR_variant,,ENST00000219479,;DECR2,upstream_gene_variant,,ENST00000397710,;NME4,downstream_gene_variant,,ENST00000382940,;NME4,downstream_gene_variant,,ENST00000454619,;NME4,downstream_gene_variant,,ENST00000450036,;DECR2,upstream_gene_variant,,ENST00000424398,;DECR2,upstream_gene_variant,,ENST00000219481,;DECR2,upstream_gene_variant,,ENST00000461802,;NME4,3_prime_UTR_variant,,ENST00000448828,;NME4,non_coding_transcript_exon_variant,,ENST00000468031,;NME4,non_coding_transcript_exon_variant,,ENST00000460297,;NME4,intron_variant,,ENST00000444498,;DECR2,upstream_gene_variant,,ENST00000437024,;DECR2,upstream_gene_variant,,ENST00000445291,;DECR2,upstream_gene_variant,,ENST00000439661,;	G	ENSG00000103202	ENST00000219479	Transcript	3_prime_UTR_variant	814-815	.	.	.	.	.	.	.	1	NME4	HGNC	7852	protein_coding	YES	CCDS10408.1	ENSP00000219479	NDKM_HUMAN	A2IDD0_HUMAN,A2IDC9_HUMAN	UPI000012FE96	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTGGTGGGGG	.	2	ESCA
MGRN1	0	.	GRCh37	16	4740935	4740935	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2030delT	.	.	ENST00000262370	17/17	28	20	8	15	15	0	MGRN1,3_prime_UTR_variant,,ENST00000415496,;MGRN1,3_prime_UTR_variant,,ENST00000262370,;MGRN1,3_prime_UTR_variant,,ENST00000399577,;NUDT16L1,upstream_gene_variant,,ENST00000590460,;NUDT16L1,upstream_gene_variant,,ENST00000586536,;MGRN1,downstream_gene_variant,,ENST00000588994,;NUDT16L1,upstream_gene_variant,,ENST00000586252,;NUDT16L1,upstream_gene_variant,,ENST00000405142,;MGRN1,downstream_gene_variant,,ENST00000587747,;MGRN1,downstream_gene_variant,,ENST00000586183,;NUDT16L1,upstream_gene_variant,,ENST00000304301,;MGRN1,downstream_gene_variant,,ENST00000536343,;	-	ENSG00000102858	ENST00000262370	Transcript	3_prime_UTR_variant	3928	.	.	.	.	.	.	.	1	MGRN1	HGNC	20254	protein_coding	YES	CCDS42115.1	ENSP00000262370	MGRN1_HUMAN	K7ERA1_HUMAN	UPI000018CE7F	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGTTCGTTTTTA	.	2	ESCA
ABCC11	0	.	GRCh37	16	48218359	48218359	+	Missense_Mutation	SNP	C	C	T	rs553813897	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3250G>A	p.Val1084Met	p.V1084M	ENST00000394747	22/29	51	40	10	34	34	0	ABCC11,missense_variant,p.Val1084Met,ENST00000394747,;ABCC11,missense_variant,p.Val1084Met,ENST00000394748,;ABCC11,missense_variant,p.Val1084Met,ENST00000353782,;ABCC11,missense_variant,p.Val1084Met,ENST00000356608,;ABCC11,downstream_gene_variant,,ENST00000537808,;ABCC11,non_coding_transcript_exon_variant,,ENST00000565329,;ABCC11,downstream_gene_variant,,ENST00000569172,;	T	ENSG00000121270	ENST00000394747	Transcript	missense_variant	3600	3250	1084	V/M	Gtg/Atg	rs553813897,COSM3937074	.	.	-1	ABCC11	HGNC	14639	protein_coding	YES	CCDS10732.1	ENSP00000378230	ABCCB_HUMAN	H3BRJ2_HUMAN	UPI0000052711	.	deleterious(0.03)	benign(0.418)	22/29	.	hmmpanther:PTHR24223:SF168,hmmpanther:PTHR24223,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123	T:0.0004	T:0	T:0	.	T:0.002	T:0	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCACGATGT	byFrequency|by1000G	5	ESCA
LONP2	0	.	GRCh37	16	48295365	48295365	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.754A>G	p.Thr252Ala	p.T252A	ENST00000285737	5/15	60	34	26	36	36	0	LONP2,missense_variant,p.Thr208Ala,ENST00000535754,;LONP2,missense_variant,p.Thr252Ala,ENST00000285737,;LONP2,missense_variant,p.Thr208Ala,ENST00000416006,;LONP2,missense_variant,p.Thr252Ala,ENST00000566755,;LONP2,upstream_gene_variant,,ENST00000570174,;	G	ENSG00000102910	ENST00000285737	Transcript	missense_variant	847	754	252	T/A	Aca/Gca	.	.	.	1	LONP2	HGNC	20598	protein_coding	YES	CCDS10734.1	ENSP00000285737	LONP2_HUMAN	Q9BU35_HUMAN	UPI000000DCD1	.	tolerated(0.43)	benign(0)	5/15	.	HAMAP:MF_03121,hmmpanther:PTHR10046,hmmpanther:PTHR10046:SF24,TIGRFAM_domain:TIGR00763,PIRSF_domain:PIRSF001174	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTACACAT	.	5	ESCA
LONP2	0	.	GRCh37	16	48381516	48381516	+	Silent	SNP	C	C	T	rs768589313	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2037C>T	p.%3D	p.G679G	ENST00000285737	13/15	92	63	29	50	50	0	LONP2,synonymous_variant,p.%3D,ENST00000535754,;LONP2,synonymous_variant,p.%3D,ENST00000285737,;LONP2,synonymous_variant,p.%3D,ENST00000565867,;LONP2,upstream_gene_variant,,ENST00000564259,;LONP2,3_prime_UTR_variant,,ENST00000416006,;LONP2,3_prime_UTR_variant,,ENST00000566755,;	T	ENSG00000102910	ENST00000285737	Transcript	synonymous_variant	2130	2037	679	G	ggC/ggT	rs768589313,COSM2833148	.	.	1	LONP2	HGNC	20598	protein_coding	YES	CCDS10734.1	ENSP00000285737	LONP2_HUMAN	Q9BU35_HUMAN	UPI000000DCD1	.	.	.	13/15	.	HAMAP:MF_03121,hmmpanther:PTHR10046,hmmpanther:PTHR10046:SF24,Gene3D:3.30.230.10,TIGRFAM_domain:TIGR00763,Pfam_domain:PF05362,PIRSF_domain:PIRSF001174,Superfamily_domains:SSF54211	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGGCGAGGG	byFrequency	5	ESCA
PAPD5	0	.	GRCh37	16	50263455	50263455	+	3'UTR	DEL	A	A	-	rs369429144	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*223delA	.	.	ENST00000436909	13/13	39	18	21	18	18	0	PAPD5,3_prime_UTR_variant,,ENST00000561678,;PAPD5,3_prime_UTR_variant,,ENST00000436909,;PAPD5,3_prime_UTR_variant,,ENST00000357464,;PAPD5,non_coding_transcript_exon_variant,,ENST00000573002,;PAPD5,intron_variant,,ENST00000562717,;	-	ENSG00000121274	ENST00000436909	Transcript	3_prime_UTR_variant	2348	.	.	.	.	rs369429144	.	.	1	PAPD5	HGNC	30758	protein_coding	YES	CCDS54006.1	ENSP00000396995	PAPD5_HUMAN	Q5EBM7_HUMAN,G4U4J3_HUMAN,B7ZLC1_HUMAN,B4DRJ7_HUMAN	UPI00017A7DC6	.	.	.	13/13	.	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAGGGAAAAAA	byCluster|by1000G	2	ESCA
SEC14L5	0	.	GRCh37	16	5061151	5061152	+	Frame_Shift_Ins	INS	-	-	C	rs764657044	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1863dupC	p.Ser622GlnfsTer31	p.S622Qfs*31	ENST00000251170	15/16	99	74	25	44	44	0	SEC14L5,frameshift_variant,p.Ser622GlnfsTer31,ENST00000251170,;RP11-165E7.1,non_coding_transcript_exon_variant,,ENST00000588778,;	C	ENSG00000103184	ENST00000251170	Transcript	frameshift_variant	2036-2037	1856-1857	619	S/SX	agc/agCc	rs764657044	.	.	1	SEC14L5	HGNC	29032	protein_coding	YES	CCDS45403.1	ENSP00000251170	S14L5_HUMAN	K7ERV2_HUMAN	UPI00001C1FA3	.	.	.	15/16	.	PROSITE_profiles:PS50866,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF39,Superfamily_domains:0041713	.	.	.	.	.	.	.	C:0.0044	C:0.001	.	.	.	.	.	.	.	HIGH	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCACAGCCCCC	byFrequency	2	ESCA
NKD1	0	.	GRCh37	16	50667134	50667135	+	Frame_Shift_Ins	INS	-	-	C	rs772439983	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.862dupC	p.Arg288ProfsTer12	p.R288Pfs*12	ENST00000268459	10/10	59	37	22	22	22	0	NKD1,frameshift_variant,p.Arg288ProfsTer12,ENST00000268459,;NKD1,downstream_gene_variant,,ENST00000566396,;	C	ENSG00000140807	ENST00000268459	Transcript	frameshift_variant	1079-1080	855-856	285-286	-/X	-/C	rs772439983,COSM1378196	.	.	1	NKD1	HGNC	17045	protein_coding	YES	CCDS10743.1	ENSP00000268459	NKD1_HUMAN	.	UPI0000073F02	.	.	.	10/10	.	hmmpanther:PTHR22611,hmmpanther:PTHR22611:SF2	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	insertion	.	7	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAACTGCCCCC	.	2	ESCA
SNX20	0	.	GRCh37	16	50707525	50707525	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743C>T	p.Ala248Val	p.A248V	ENST00000330943	4/4	47	26	21	18	18	0	SNX20,missense_variant,p.Ala248Val,ENST00000330943,;SNX20,intron_variant,,ENST00000423026,;SNX20,intron_variant,,ENST00000300590,;RP11-401P9.5,downstream_gene_variant,,ENST00000570167,;RP11-401P9.5,downstream_gene_variant,,ENST00000570241,;SNX20,intron_variant,,ENST00000568993,;	A	ENSG00000167208	ENST00000330943	Transcript	missense_variant	915	743	248	A/V	gCg/gTg	.	.	.	-1	SNX20	HGNC	30390	protein_coding	YES	CCDS10745.1	ENSP00000332062	SNX20_HUMAN	.	UPI000004348D	.	tolerated(0.18)	possibly_damaging(0.857)	4/4	.	hmmpanther:PTHR20939:SF1,hmmpanther:PTHR20939,Gene3D:1.25.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCGCGAAG	.	5	ESCA
NOD2	0	.	GRCh37	16	50745137	50745137	+	Missense_Mutation	SNP	C	C	T	rs375201229	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315C>T	p.Arg439Cys	p.R439C	ENST00000300589	4/12	29	19	10	16	16	0	NOD2,missense_variant,p.Arg439Cys,ENST00000300589,;NOD2,upstream_gene_variant,,ENST00000534057,;RP11-327F22.6,upstream_gene_variant,,ENST00000602304,;NOD2,downstream_gene_variant,,ENST00000532206,;NOD2,downstream_gene_variant,,ENST00000526417,;NOD2,downstream_gene_variant,,ENST00000527070,;NOD2,upstream_gene_variant,,ENST00000524712,;NOD2,upstream_gene_variant,,ENST00000529633,;NOD2,upstream_gene_variant,,ENST00000527052,;NOD2,upstream_gene_variant,,ENST00000534067,;	T	ENSG00000167207	ENST00000300589	Transcript	missense_variant	1420	1315	439	R/C	Cgc/Tgc	rs375201229	.	.	1	NOD2	HGNC	5331	protein_coding	YES	CCDS10746.1	ENSP00000300589	NOD2_HUMAN	Q7Z597_HUMAN,Q7Z596_HUMAN,Q6TDC3_HUMAN,E9PK30_HUMAN,D9N2T7_HUMAN,D6CHF9_HUMAN,B5B2Z6_HUMAN,B5B2Z5_HUMAN,B5B2Z4_HUMAN,B5A7D5_HUMAN,A7KZR0_HUMAN,A7KZQ9_HUMAN,A7J384_HUMAN,A3FA72_HUMAN	UPI000005027A	.	tolerated(0.08)	benign(0.036)	4/12	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF64,Pfam_domain:PF05729,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCCGCACC	byFrequency|byCluster	5	ESCA
AKTIP	0	.	GRCh37	16	53525747	53525748	+	3'UTR	INS	-	-	A	rs576554175	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*576dupT	.	.	ENST00000394657	10/10	71	33	37	45	45	0	AKTIP,3_prime_UTR_variant,,ENST00000300245,;AKTIP,3_prime_UTR_variant,,ENST00000394657,;AKTIP,downstream_gene_variant,,ENST00000565408,;AKTIP,downstream_gene_variant,,ENST00000563928,;RBL2,downstream_gene_variant,,ENST00000544545,;AKTIP,downstream_gene_variant,,ENST00000568022,;AKTIP,downstream_gene_variant,,ENST00000568596,;RBL2,downstream_gene_variant,,ENST00000262133,;AKTIP,downstream_gene_variant,,ENST00000570004,;RBL2,downstream_gene_variant,,ENST00000379935,;AKTIP,non_coding_transcript_exon_variant,,ENST00000571523,;AKTIP,downstream_gene_variant,,ENST00000563108,;AKTIP,downstream_gene_variant,,ENST00000561799,;AKTIP,downstream_gene_variant,,ENST00000566045,;AKTIP,downstream_gene_variant,,ENST00000565431,;	A	ENSG00000166971	ENST00000394657	Transcript	3_prime_UTR_variant	1630-1631	.	.	.	.	rs576554175	.	.	-1	AKTIP	HGNC	16710	protein_coding	YES	CCDS10749.1	ENSP00000378152	AKTIP_HUMAN	Q659E0_HUMAN,H3BVH0_HUMAN,H3BSX7_HUMAN,H3BRV2_HUMAN,H3BNB8_HUMAN	UPI0000073A64	.	.	.	10/10	.	.	A:0.0012	A:0.0023	A:0.0014	.	A:0.001	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTGCTTAAAAA	byFrequency|by1000G	2	ESCA
RP11-441F2.5	0	.	GRCh37	16	56390360	56390361	+	5'Flank	INS	-	-	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000606772	.	22	11	11	9	9	0	GNAO1,3_prime_UTR_variant,,ENST00000262493,;GNAO1,downstream_gene_variant,,ENST00000564727,;RP11-441F2.5,upstream_gene_variant,,ENST00000606772,;GNAO1,downstream_gene_variant,,ENST00000568375,;	G	ENSG00000272372	ENST00000606772	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2924	-1	RP11-441F2.5	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCTGCTGGGGG	.	2	ESCA
AMFR	0	.	GRCh37	16	56390939	56390939	+	3'Flank	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000290649	.	30	12	18	14	14	0	GNAO1,3_prime_UTR_variant,,ENST00000262493,;GNAO1,downstream_gene_variant,,ENST00000564727,;AMFR,downstream_gene_variant,,ENST00000290649,;AMFR,downstream_gene_variant,,ENST00000492830,;RP11-441F2.5,upstream_gene_variant,,ENST00000606772,;GNAO1,downstream_gene_variant,,ENST00000568375,;AMFR,downstream_gene_variant,,ENST00000568325,;AMFR,downstream_gene_variant,,ENST00000566757,;	-	ENSG00000159461	ENST00000290649	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4425	-1	AMFR	HGNC	463	protein_coding	YES	CCDS10758.1	ENSP00000290649	AMFR_HUMAN	Q6PGR1_HUMAN,Q1RN03_HUMAN,H3BSK3_HUMAN,H3BQM3_HUMAN	UPI000013EDCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAGAACAAAAAA	.	2	ESCA
MT1A	0	.	GRCh37	16	56673953	56673953	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*98delT	.	.	ENST00000290705	3/3	43	25	18	13	13	0	MT1A,3_prime_UTR_variant,,ENST00000290705,;MT1JP,downstream_gene_variant,,ENST00000564564,;MT1DP,upstream_gene_variant,,ENST00000463480,;MT1JP,downstream_gene_variant,,ENST00000563395,;MT1DP,upstream_gene_variant,,ENST00000486551,;MT1JP,downstream_gene_variant,,ENST00000444023,;	-	ENSG00000205362	ENST00000290705	Transcript	3_prime_UTR_variant	350	.	.	.	.	.	.	.	1	MT1A	HGNC	7393	protein_coding	YES	CCDS32454.1	ENSP00000290705	MT1A_HUMAN	.	UPI000000D79B	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACTGTATTTTTT	.	2	ESCA
MT1H	0	.	GRCh37	16	56704965	56704994	+	3'UTR	ONP	TCTACAACTCCGACTCATTTGCTACATTCC	TCTACAACTCCGACTCATTTGCTACATTCC	CTACAACCCCGACTCATTTGCTACATTCCT	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TCTACAACTCCGACTCATTTGCTACATTCC	TCTACAACTCCGACTCATTTGCTACATTCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63_*93delTTCTACAACTCCGACTCATTTGCTACATTCCinsTCTACAACCCCGACTCATTTGCTACATTCCT	.	.	ENST00000332374	3/3	76	59	17	38	38	0	MT1H,3_prime_UTR_variant,,ENST00000332374,;MT1H,3_prime_UTR_variant,,ENST00000569155,;MT1G,upstream_gene_variant,,ENST00000379811,;MT1G,upstream_gene_variant,,ENST00000444837,;MT1G,upstream_gene_variant,,ENST00000568675,;MT1G,upstream_gene_variant,,ENST00000569500,;	TCTACAACCCCGACTCATTTGCTACATTCCT	ENSG00000205358	ENST00000332374	Transcript	3_prime_UTR_variant	320-350	.	.	.	.	.	.	.	1	MT1H	HGNC	7400	protein_coding	YES	CCDS10767.1	ENSP00000330587	MT1H_HUMAN	.	UPI000012F6DC	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TTTTTTTCTACAACTCCGACTCATTTGCTACATTCCTTTTT	.	2	ESCA
NLRC5	0	.	GRCh37	16	57113482	57113482	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5262C>T	p.%3D	p.N1754N	ENST00000262510	46/49	61	54	7	19	19	0	NLRC5,synonymous_variant,p.%3D,ENST00000308149,;NLRC5,synonymous_variant,p.%3D,ENST00000539144,;NLRC5,synonymous_variant,p.%3D,ENST00000262510,;NLRC5,3_prime_UTR_variant,,ENST00000436936,;NLRC5,3_prime_UTR_variant,,ENST00000537056,;NLRC5,3_prime_UTR_variant,,ENST00000540182,;NLRC5,3_prime_UTR_variant,,ENST00000545081,;NLRC5,3_prime_UTR_variant,,ENST00000538453,;NLRC5,non_coding_transcript_exon_variant,,ENST00000534927,;NLRC5,downstream_gene_variant,,ENST00000545349,;NLRC5,downstream_gene_variant,,ENST00000544189,;NLRC5,upstream_gene_variant,,ENST00000543103,;NLRC5,upstream_gene_variant,,ENST00000543049,;	T	ENSG00000140853	ENST00000262510	Transcript	synonymous_variant	5487	5262	1754	N	aaC/aaT	.	.	.	1	NLRC5	HGNC	29933	protein_coding	YES	CCDS10773.1	ENSP00000262510	NLRC5_HUMAN	F5H274_HUMAN,F5GYP0_HUMAN	UPI00001AEE94	.	.	.	46/49	.	hmmpanther:PTHR24106:SF69,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACAACCAGAC	.	3	ESCA
CNGB1	0	.	GRCh37	16	57918169	57918169	+	Missense_Mutation	SNP	C	C	T	rs773308978	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3655G>A	p.Glu1219Lys	p.E1219K	ENST00000251102	33/33	49	40	9	15	15	0	CNGB1,missense_variant,p.Glu1213Lys,ENST00000564448,;CNGB1,missense_variant,p.Glu1219Lys,ENST00000251102,;CNGB1,downstream_gene_variant,,ENST00000565942,;	T	ENSG00000070729	ENST00000251102	Transcript	missense_variant	3716	3655	1219	E/K	Gaa/Aaa	rs773308978	.	.	-1	CNGB1	HGNC	2151	protein_coding	YES	CCDS42169.1	ENSP00000251102	CNGB1_HUMAN	H3BQC3_HUMAN	UPI000013CCDF	.	tolerated(0.27)	benign(0.114)	33/33	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCGGGCT	byFrequency	5	ESCA
ZNF319	0	.	GRCh37	16	58029381	58029381	+	3'UTR	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1040delC	.	.	ENST00000299237	2/2	68	46	21	20	20	0	ZNF319,3_prime_UTR_variant,,ENST00000299237,;ZNF319,downstream_gene_variant,,ENST00000562909,;USB1,upstream_gene_variant,,ENST00000561743,;	-	ENSG00000166188	ENST00000299237	Transcript	3_prime_UTR_variant	3412	.	.	.	.	.	.	.	-1	ZNF319	HGNC	13644	protein_coding	YES	CCDS32462.1	ENSP00000299237	ZN319_HUMAN	H3BT69_HUMAN	UPI000013C357	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGTACTGGGGGG	.	2	ESCA
CDH11	0	.	GRCh37	16	64984778	64984778	+	Missense_Mutation	SNP	C	C	T	rs374274441	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1786G>A	p.Asp596Asn	p.D596N	ENST00000268603	12/13	101	74	26	24	24	0	CDH11,missense_variant,p.Asp596Asn,ENST00000394156,;CDH11,missense_variant,p.Asp596Asn,ENST00000268603,;CDH11,missense_variant,p.Asp470Asn,ENST00000566827,;	T	ENSG00000140937	ENST00000268603	Transcript	missense_variant	2402	1786	596	D/N	Gac/Aac	rs374274441	.	.	-1	CDH11	HGNC	1750	protein_coding	YES	CCDS10803.1	ENSP00000268603	CAD11_HUMAN	H3BUU9_HUMAN,H3BSM4_HUMAN,H3BR78_HUMAN,H3BQH2_HUMAN,H3BQB5_HUMAN,H3BPQ2_HUMAN,H3BP26_HUMAN	UPI000013D7C5	.	deleterious(0.05)	benign(0.005)	12/13	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF85,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM00112	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.N598N|c.1794C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACGTCGCACC	byFrequency|byCluster	5	ESCA
CDH11	0	.	GRCh37	16	64984913	64984913	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1651G>A	p.Ala551Thr	p.A551T	ENST00000268603	12/13	68	59	9	24	24	0	CDH11,missense_variant,p.Ala551Thr,ENST00000394156,;CDH11,missense_variant,p.Ala551Thr,ENST00000268603,;CDH11,missense_variant,p.Ala425Thr,ENST00000566827,;	T	ENSG00000140937	ENST00000268603	Transcript	missense_variant	2267	1651	551	A/T	Gca/Aca	.	.	.	-1	CDH11	HGNC	1750	protein_coding	YES	CCDS10803.1	ENSP00000268603	CAD11_HUMAN	H3BUU9_HUMAN,H3BSM4_HUMAN,H3BR78_HUMAN,H3BQH2_HUMAN,H3BQB5_HUMAN,H3BPQ2_HUMAN,H3BP26_HUMAN	UPI000013D7C5	.	deleterious(0)	benign(0.172)	12/13	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF85,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTGCTGTGT	.	4	ESCA
PLEKHG4	0	.	GRCh37	16	67320198	67320198	+	Missense_Mutation	SNP	G	G	A	rs763999027	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2464G>A	p.Ala822Thr	p.A822T	ENST00000360461	14/21	163	70	92	65	65	0	PLEKHG4,missense_variant,p.Ala822Thr,ENST00000360461,;PLEKHG4,missense_variant,p.Ala822Thr,ENST00000379344,;PLEKHG4,missense_variant,p.Ala822Thr,ENST00000427155,;PLEKHG4,missense_variant,p.Ala741Thr,ENST00000450733,;KCTD19,downstream_gene_variant,,ENST00000304372,;PLEKHG4,upstream_gene_variant,,ENST00000569875,;KCTD19,downstream_gene_variant,,ENST00000562841,;PLEKHG4,3_prime_UTR_variant,,ENST00000563969,;PLEKHG4,intron_variant,,ENST00000393966,;KCTD19,downstream_gene_variant,,ENST00000570049,;KCTD19,downstream_gene_variant,,ENST00000566392,;PLEKHG4,upstream_gene_variant,,ENST00000567136,;PLEKHG4,upstream_gene_variant,,ENST00000562289,;KCTD19,downstream_gene_variant,,ENST00000569333,;	A	ENSG00000196155	ENST00000360461	Transcript	missense_variant	4999	2464	822	A/T	Gcg/Acg	rs763999027	.	.	1	PLEKHG4	HGNC	24501	protein_coding	YES	CCDS32466.1	ENSP00000353646	PKHG4_HUMAN	H3BSU4_HUMAN,H3BQP9_HUMAN,H3BQE6_HUMAN,H3BPQ5_HUMAN,H3BME5_HUMAN,C5IFI8_HUMAN	UPI000013C774	.	deleterious(0)	probably_damaging(0.999)	14/21	.	Superfamily_domains:SSF48065,SMART_domains:SM00325,Gene3D:1.20.900.10,Pfam_domain:PF00621,hmmpanther:PTHR22826:SF110,hmmpanther:PTHR22826,PROSITE_profiles:PS50010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTACGCGCTC	.	5	ESCA
RANBP10	0	.	GRCh37	16	67757025	67757025	+	3'UTR	DEL	T	T	-	rs543994390	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3306delA	.	.	ENST00000317506	14/14	75	27	48	36	36	0	RANBP10,3_prime_UTR_variant,,ENST00000317506,;GFOD2,upstream_gene_variant,,ENST00000268797,;RANBP10,downstream_gene_variant,,ENST00000536251,;RANBP10,downstream_gene_variant,,ENST00000602677,;RANBP10,downstream_gene_variant,,ENST00000411657,;RANBP10,downstream_gene_variant,,ENST00000448631,;GFOD2,upstream_gene_variant,,ENST00000602855,;GFOD2,upstream_gene_variant,,ENST00000602377,;RANBP10,downstream_gene_variant,,ENST00000602506,;GFOD2,upstream_gene_variant,,ENST00000602496,;	-	ENSG00000141084	ENST00000317506	Transcript	3_prime_UTR_variant	5285	.	.	.	.	rs543994390	.	.	-1	RANBP10	HGNC	29285	protein_coding	YES	CCDS32469.1	ENSP00000316589	RBP10_HUMAN	B3KP49_HUMAN	UPI00001C1FA6	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACAGAGTTTTTT	.	2	ESCA
EDC4	0	.	GRCh37	16	67916729	67916729	+	Missense_Mutation	SNP	G	G	A	rs543342658	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3590G>A	p.Arg1197His	p.R1197H	ENST00000358933	26/29	129	115	14	39	39	0	EDC4,missense_variant,p.Arg99His,ENST00000577105,;EDC4,missense_variant,p.Arg1197His,ENST00000358933,;EDC4,missense_variant,p.Arg16His,ENST00000575033,;EDC4,intron_variant,,ENST00000573985,;NRN1L,upstream_gene_variant,,ENST00000576147,;NRN1L,upstream_gene_variant,,ENST00000339176,;NRN1L,upstream_gene_variant,,ENST00000576758,;CTC-479C5.10,non_coding_transcript_exon_variant,,ENST00000572067,;EDC4,downstream_gene_variant,,ENST00000574770,;EDC4,non_coding_transcript_exon_variant,,ENST00000575507,;EDC4,non_coding_transcript_exon_variant,,ENST00000573992,;EDC4,non_coding_transcript_exon_variant,,ENST00000572221,;EDC4,downstream_gene_variant,,ENST00000577028,;EDC4,downstream_gene_variant,,ENST00000576972,;EDC4,downstream_gene_variant,,ENST00000536072,;EDC4,downstream_gene_variant,,ENST00000572031,;EDC4,downstream_gene_variant,,ENST00000572724,;EDC4,downstream_gene_variant,,ENST00000575514,;	A	ENSG00000038358	ENST00000358933	Transcript	missense_variant	3829	3590	1197	R/H	cGt/cAt	rs543342658,COSM1740284	.	.	1	EDC4	HGNC	17157	protein_coding	YES	CCDS10849.1	ENSP00000351811	EDC4_HUMAN	.	UPI0000141377	.	tolerated(0.24)	benign(0.004)	26/29	.	hmmpanther:PTHR15598	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTTCGTGCTG	byFrequency|byCluster	4	ESCA
DDX28	0	.	GRCh37	16	68056444	68056444	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662C>A	p.Ala221Asp	p.A221D	ENST00000332395	1/1	98	39	58	38	38	0	DDX28,missense_variant,p.Ala221Asp,ENST00000332395,;DUS2,intron_variant,,ENST00000571081,;DUS2,intron_variant,,ENST00000570709,;DUS2,intron_variant,,ENST00000566306,;DUS2,intron_variant,,ENST00000575677,;DUS2,intron_variant,,ENST00000576994,;DUS2,upstream_gene_variant,,ENST00000569289,;DUS2,upstream_gene_variant,,ENST00000567100,;DUS2,upstream_gene_variant,,ENST00000432752,;DUS2,upstream_gene_variant,,ENST00000568099,;DUS2,upstream_gene_variant,,ENST00000565263,;DUS2,upstream_gene_variant,,ENST00000564781,;DUS2,upstream_gene_variant,,ENST00000358896,;RNU6-359P,upstream_gene_variant,,ENST00000365466,;DUS2,upstream_gene_variant,,ENST00000564975,;	T	ENSG00000182810	ENST00000332395	Transcript	missense_variant	1327	662	221	A/D	gCt/gAt	.	.	.	-1	DDX28	HGNC	17330	protein_coding	YES	CCDS10858.1	ENSP00000332340	DDX28_HUMAN	.	UPI000006D6C8	.	deleterious(0.05)	benign(0.238)	1/1	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF35,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAGCCCGC	.	5	ESCA
DUS2	0	.	GRCh37	16	68088489	68088489	+	Missense_Mutation	SNP	G	G	A	rs756355529	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277G>A	p.Ala93Thr	p.A93T	ENST00000565263	6/17	228	199	29	88	88	0	DUS2,missense_variant,p.Ala93Thr,ENST00000562246,;DUS2,missense_variant,p.Ala93Thr,ENST00000570709,;DUS2,missense_variant,p.Ala93Thr,ENST00000566306,;DUS2,missense_variant,p.Ala93Thr,ENST00000568099,;DUS2,missense_variant,p.Ala93Thr,ENST00000565263,;DUS2,missense_variant,p.Ala93Thr,ENST00000575677,;DUS2,missense_variant,p.Ala93Thr,ENST00000358896,;DUS2,intron_variant,,ENST00000432752,;DUS2,downstream_gene_variant,,ENST00000571081,;DUS2,downstream_gene_variant,,ENST00000567100,;DUS2,downstream_gene_variant,,ENST00000576994,;AC130462.1,downstream_gene_variant,,ENST00000408862,;DUS2,synonymous_variant,p.%3D,ENST00000561965,;DUS2,downstream_gene_variant,,ENST00000564975,;	A	ENSG00000167264	ENST00000565263	Transcript	missense_variant	771	277	93	A/T	Gca/Aca	rs756355529	.	.	1	DUS2	HGNC	26014	protein_coding	YES	CCDS10859.1	ENSP00000455229	DUS2L_HUMAN	J3QLD5_HUMAN,I3L4Y9_HUMAN,I3L4H0_HUMAN,I3L1K5_HUMAN,I3L0K0_HUMAN,H3BSF3_HUMAN,H3BRI6_HUMAN,H3BQX4_HUMAN,H3BMK6_HUMAN,H3BM64_HUMAN	UPI0000036040	.	deleterious(0.03)	probably_damaging(0.934)	6/17	.	hmmpanther:PTHR11082,hmmpanther:PTHR11082:SF4,Pfam_domain:PF01207,Gene3D:3.20.20.70,Superfamily_domains:SSF51395	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGACGCAGAG	.	4	ESCA
NFAT5	0	.	GRCh37	16	69732200	69732200	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1952delT	.	.	ENST00000432919	15/15	168	111	57	43	43	0	NFAT5,3_prime_UTR_variant,,ENST00000432919,;NFAT5,3_prime_UTR_variant,,ENST00000354436,;NFAT5,3_prime_UTR_variant,,ENST00000393742,;NFAT5,3_prime_UTR_variant,,ENST00000349945,;NFAT5,downstream_gene_variant,,ENST00000567239,;NFAT5,downstream_gene_variant,,ENST00000565301,;NFAT5,downstream_gene_variant,,ENST00000566899,;RP11-311C24.1,upstream_gene_variant,,ENST00000561622,;NFAT5,3_prime_UTR_variant,,ENST00000426654,;	-	ENSG00000102908	ENST00000432919	Transcript	3_prime_UTR_variant	7804	.	.	.	.	.	.	.	1	NFAT5	HGNC	7774	protein_coding	YES	CCDS45518.1	ENSP00000396538	NFAT5_HUMAN	.	UPI000049DE1B	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTTCATTTTTT	.	3	ESCA
WWP2	0	.	GRCh37	16	69820935	69820935	+	Missense_Mutation	SNP	C	C	T	rs142617495	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22C>T	p.Arg8Trp	p.R8W	ENST00000359154	2/24	35	21	14	23	23	0	WWP2,missense_variant,p.Arg8Trp,ENST00000356003,;WWP2,missense_variant,p.Arg8Trp,ENST00000448661,;WWP2,missense_variant,p.Arg8Trp,ENST00000561780,;WWP2,missense_variant,p.Arg8Trp,ENST00000563659,;WWP2,missense_variant,p.Arg8Trp,ENST00000569174,;WWP2,missense_variant,p.Arg8Trp,ENST00000359154,;SNORA62,upstream_gene_variant,,ENST00000516634,;WWP2,non_coding_transcript_exon_variant,,ENST00000568845,;WWP2,missense_variant,p.Arg8Trp,ENST00000569620,;WWP2,non_coding_transcript_exon_variant,,ENST00000569658,;	T	ENSG00000198373	ENST00000359154	Transcript	missense_variant	123	22	8	R/W	Cgg/Tgg	rs142617495	.	.	1	WWP2	HGNC	16804	protein_coding	YES	CCDS10885.1	ENSP00000352069	WWP2_HUMAN	H3BRX8_HUMAN,H3BPJ8_HUMAN,B4DHF6_HUMAN	UPI000006CD16	.	deleterious_low_confidence(0.04)	possibly_damaging(0.635)	2/24	.	PIRSF_domain:PIRSF001569	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAGCCGGGCA	byCluster	5	ESCA
DDX19B	0	.	GRCh37	16	70351424	70351425	+	Frame_Shift_Del	DEL	TA	TA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.323_324delAT	p.Tyr108CysfsTer21	p.Y108Cfs*21	ENST00000288071	5/12	126	92	34	45	45	0	DDX19B,frameshift_variant,p.Tyr108CysfsTer21,ENST00000288071,;DDX19B,frameshift_variant,p.Tyr95CysfsTer21,ENST00000566216,;RP11-529K1.3,frameshift_variant,p.Tyr108CysfsTer21,ENST00000567706,;DDX19B,frameshift_variant,p.Tyr113CysfsTer21,ENST00000563206,;DDX19B,5_prime_UTR_variant,,ENST00000393657,;DDX19B,5_prime_UTR_variant,,ENST00000568625,;DDX19B,5_prime_UTR_variant,,ENST00000563392,;DDX19B,intron_variant,,ENST00000451014,;DDX19B,intron_variant,,ENST00000355992,;RP11-529K1.2,intron_variant,,ENST00000562077,;DDX19B,non_coding_transcript_exon_variant,,ENST00000570055,;DDX19B,downstream_gene_variant,,ENST00000569099,;DDX19B,3_prime_UTR_variant,,ENST00000562912,;DDX19B,3_prime_UTR_variant,,ENST00000568460,;DDX19B,non_coding_transcript_exon_variant,,ENST00000569224,;DDX19B,intron_variant,,ENST00000562519,;DDX19B,intron_variant,,ENST00000568408,;DDX19B,intron_variant,,ENST00000568008,;RP11-529K1.3,intron_variant,,ENST00000565116,;	-	ENSG00000157349	ENST00000288071	Transcript	frameshift_variant	567-568	322-323	108	Y/X	TAt/t	.	.	.	1	DDX19B	HGNC	2742	protein_coding	YES	CCDS10888.1	ENSP00000288071	DD19B_HUMAN	Q2NL95_HUMAN,H3BN59_HUMAN,B4DL69_HUMAN	UPI000012907F	.	.	.	5/12	.	PROSITE_profiles:PS51195,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF194,Gene3D:3.40.50.300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAGTCTATGCCA	.	3	ESCA
SF3B3	0	.	GRCh37	16	70590170	70590170	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1799A>T	p.Gln600Leu	p.Q600L	ENST00000302516	14/26	92	50	42	47	47	0	SF3B3,missense_variant,p.Gln600Leu,ENST00000302516,;SF3B3,non_coding_transcript_exon_variant,,ENST00000568291,;SF3B3,non_coding_transcript_exon_variant,,ENST00000567250,;SF3B3,downstream_gene_variant,,ENST00000567635,;SF3B3,upstream_gene_variant,,ENST00000568539,;	T	ENSG00000189091	ENST00000302516	Transcript	missense_variant	2010	1799	600	Q/L	cAg/cTg	.	.	.	1	SF3B3	HGNC	10770	protein_coding	YES	CCDS10894.1	ENSP00000305790	SF3B3_HUMAN	J3QRB2_HUMAN,J3QL37_HUMAN,I3L4G7_HUMAN,H3BMB0_HUMAN,B3KM77_HUMAN	UPI0000167878	.	tolerated(0.84)	benign(0.005)	14/26	.	hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF1,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGCAGCGGT	.	5	ESCA
IL34	0	.	GRCh37	16	70690943	70690943	+	Silent	SNP	C	C	T	rs368553371	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321C>T	p.%3D	p.D107D	ENST00000429149	5/7	64	43	21	32	32	0	IL34,synonymous_variant,p.%3D,ENST00000288098,;IL34,synonymous_variant,p.%3D,ENST00000429149,;IL34,synonymous_variant,p.%3D,ENST00000566361,;IL34,downstream_gene_variant,,ENST00000563721,;FLJ00418,upstream_gene_variant,,ENST00000597002,;MTSS1L,downstream_gene_variant,,ENST00000338779,;IL34,downstream_gene_variant,,ENST00000569641,;IL34,non_coding_transcript_exon_variant,,ENST00000574181,;	T	ENSG00000157368	ENST00000429149	Transcript	synonymous_variant	876	321	107	D	gaC/gaT	rs368553371	.	.	1	IL34	HGNC	28529	protein_coding	YES	CCDS10895.1	ENSP00000397863	IL34_HUMAN	J3QQT3_HUMAN,H3BPB7_HUMAN	UPI000004C5C6	.	.	.	5/7	.	Pfam_domain:PF15036,Prints_domain:PR01938	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGACGTGCT	byFrequency|byCluster|by1000G	5	ESCA
MTSS1L	0	.	GRCh37	16	70708260	70708260	+	Silent	SNP	G	G	A	rs769290285	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1002C>T	p.%3D	p.D334D	ENST00000338779	11/15	215	112	102	107	107	0	MTSS1L,synonymous_variant,p.%3D,ENST00000338779,;MTSS1L,synonymous_variant,p.%3D,ENST00000562883,;MTSS1L,downstream_gene_variant,,ENST00000576338,;	A	ENSG00000132613	ENST00000338779	Transcript	synonymous_variant	1277	1002	334	D	gaC/gaT	rs769290285,COSM4062393	.	.	-1	MTSS1L	HGNC	25094	protein_coding	YES	CCDS32476.1	ENSP00000341171	MTSSL_HUMAN	.	UPI00001D627C	.	.	.	11/15	.	hmmpanther:PTHR15708:SF8,hmmpanther:PTHR15708	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCGTCCTG	byFrequency	5	ESCA
WDR90	0	.	GRCh37	16	717616	717616	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*27C>T	.	.	ENST00000293879	41/41	41	27	14	31	31	0	WDR90,missense_variant,p.Ala61Val,ENST00000546896,;WDR90,3_prime_UTR_variant,,ENST00000547944,;WDR90,3_prime_UTR_variant,,ENST00000551100,;WDR90,3_prime_UTR_variant,,ENST00000315764,;WDR90,3_prime_UTR_variant,,ENST00000549091,;WDR90,3_prime_UTR_variant,,ENST00000293879,;RHOT2,upstream_gene_variant,,ENST00000315082,;RHOT2,upstream_gene_variant,,ENST00000563134,;RHOT2,upstream_gene_variant,,ENST00000561929,;RHOT2,upstream_gene_variant,,ENST00000569943,;WDR90,downstream_gene_variant,,ENST00000548603,;WDR90,downstream_gene_variant,,ENST00000547543,;WDR90,3_prime_UTR_variant,,ENST00000552728,;WDR90,non_coding_transcript_exon_variant,,ENST00000553080,;WDR90,non_coding_transcript_exon_variant,,ENST00000549024,;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,;RHOT2,upstream_gene_variant,,ENST00000569358,;RHOT2,upstream_gene_variant,,ENST00000568950,;WDR90,downstream_gene_variant,,ENST00000548448,;RHOT2,upstream_gene_variant,,ENST00000566214,;RHOT2,upstream_gene_variant,,ENST00000570092,;WDR90,downstream_gene_variant,,ENST00000546923,;RHOT2,upstream_gene_variant,,ENST00000569706,;RHOT2,upstream_gene_variant,,ENST00000569675,;WDR90,downstream_gene_variant,,ENST00000552683,;RHOT2,upstream_gene_variant,,ENST00000602564,;RHOT2,upstream_gene_variant,,ENST00000570280,;RHOT2,upstream_gene_variant,,ENST00000562333,;RHOT2,upstream_gene_variant,,ENST00000562708,;RHOT2,upstream_gene_variant,,ENST00000567017,;RHOT2,upstream_gene_variant,,ENST00000567589,;RHOT2,upstream_gene_variant,,ENST00000566965,;RHOT2,upstream_gene_variant,,ENST00000563776,;RHOT2,upstream_gene_variant,,ENST00000561983,;RHOT2,upstream_gene_variant,,ENST00000568636,;RHOT2,upstream_gene_variant,,ENST00000563637,;WDR90,downstream_gene_variant,,ENST00000546516,;RHOT2,upstream_gene_variant,,ENST00000562598,;RHOT2,upstream_gene_variant,,ENST00000565004,;RHOT2,upstream_gene_variant,,ENST00000561711,;	T	ENSG00000161996	ENST00000293879	Transcript	3_prime_UTR_variant	5274	.	.	.	.	.	.	.	1	WDR90	HGNC	26960	protein_coding	YES	CCDS42092.1	ENSP00000293879	WDR90_HUMAN	.	UPI0000D67C48	.	.	.	41/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGGCATCAC	.	5	ESCA
RHBDL1	0	.	GRCh37	16	727386	727386	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.881C>T	p.Ala294Val	p.A294V	ENST00000219551	4/7	54	27	27	40	40	0	RHBDL1,missense_variant,p.Ala229Val,ENST00000352681,;RHBDL1,missense_variant,p.Ala154Val,ENST00000561556,;RHBDL1,missense_variant,p.Ala294Val,ENST00000219551,;STUB1,upstream_gene_variant,,ENST00000565677,;RHOT2,downstream_gene_variant,,ENST00000569197,;JMJD8,downstream_gene_variant,,ENST00000609261,;STUB1,upstream_gene_variant,,ENST00000567173,;RHOT2,downstream_gene_variant,,ENST00000315082,;JMJD8,downstream_gene_variant,,ENST00000454700,;STUB1,upstream_gene_variant,,ENST00000219548,;STUB1,upstream_gene_variant,,ENST00000564316,;JMJD8,downstream_gene_variant,,ENST00000293882,;STUB1,upstream_gene_variant,,ENST00000564370,;STUB1,upstream_gene_variant,,ENST00000566408,;JMJD8,downstream_gene_variant,,ENST00000412368,;LA16c-313D11.9,downstream_gene_variant,,ENST00000571933,;LA16c-313D11.9,downstream_gene_variant,,ENST00000567091,;STUB1,upstream_gene_variant,,ENST00000566181,;RHBDL1,splice_region_variant,,ENST00000450775,;JMJD8,downstream_gene_variant,,ENST00000565302,;STUB1,upstream_gene_variant,,ENST00000569248,;JMJD8,downstream_gene_variant,,ENST00000568689,;RHOT2,downstream_gene_variant,,ENST00000569358,;RHOT2,downstream_gene_variant,,ENST00000569675,;RHOT2,downstream_gene_variant,,ENST00000602564,;RHOT2,downstream_gene_variant,,ENST00000564659,;JMJD8,downstream_gene_variant,,ENST00000567120,;STUB1,upstream_gene_variant,,ENST00000563505,;JMJD8,downstream_gene_variant,,ENST00000568313,;RHOT2,downstream_gene_variant,,ENST00000568636,;RHOT2,downstream_gene_variant,,ENST00000562957,;STUB1,upstream_gene_variant,,ENST00000567790,;RHOT2,downstream_gene_variant,,ENST00000565004,;RHOT2,downstream_gene_variant,,ENST00000561711,;	T	ENSG00000103269	ENST00000219551	Transcript	missense_variant	908	881	294	A/V	gCa/gTa	.	.	.	1	RHBDL1	HGNC	10007	protein_coding	YES	.	ENSP00000219551	RHBL1_HUMAN	.	UPI0000048DB3	.	deleterious(0)	probably_damaging(0.996)	4/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22936:SF7,hmmpanther:PTHR22936,Gene3D:2xovA00,Pfam_domain:PF01694,PIRSF_domain:PIRSF037470,Superfamily_domains:SSF144091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGGCAGGTG	.	5	ESCA
ZFHX3	0	.	GRCh37	16	72845811	72845811	+	Missense_Mutation	SNP	G	G	A	rs776155336	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3656C>T	p.Pro1219Leu	p.P1219L	ENST00000268489	6/10	37	21	15	29	29	0	ZFHX3,missense_variant,p.Pro305Leu,ENST00000397992,;ZFHX3,missense_variant,p.Pro1219Leu,ENST00000268489,;RP5-991G20.2,downstream_gene_variant,,ENST00000558618,;	A	ENSG00000140836	ENST00000268489	Transcript	missense_variant	4329	3656	1219	P/L	cCg/cTg	rs776155336	.	.	-1	ZFHX3	HGNC	777	protein_coding	YES	CCDS10908.1	ENSP00000268489	ZFHX3_HUMAN	Q6TCJ2_HUMAN	UPI00001AE937	.	.	benign(0.026)	6/10	.	hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCGGTTTG	.	5	ESCA
GLG1	0	.	GRCh37	16	74526855	74526855	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234G>C	p.Gly412Arg	p.G412R	ENST00000205061	7/27	33	18	15	30	30	0	GLG1,missense_variant,p.Gly401Arg,ENST00000447066,;GLG1,missense_variant,p.Gly412Arg,ENST00000422840,;GLG1,missense_variant,p.Gly412Arg,ENST00000205061,;GLG1,downstream_gene_variant,,ENST00000565474,;GLG1,missense_variant,p.Gly412Arg,ENST00000562090,;GLG1,intron_variant,,ENST00000567951,;	G	ENSG00000090863	ENST00000205061	Transcript	missense_variant	1254	1234	412	G/R	Ggg/Cgg	.	.	.	-1	GLG1	HGNC	4316	protein_coding	YES	CCDS32485.1	ENSP00000205061	GSLG1_HUMAN	Q6ZMF1_HUMAN,H3BQT1_HUMAN	UPI00001FFBD9	.	deleterious(0.03)	benign(0.303)	7/27	.	PROSITE_profiles:PS51289,hmmpanther:PTHR11884,hmmpanther:PTHR11884:SF1,Pfam_domain:PF00839	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTACCTCTGT	.	5	ESCA
LDHD	0	.	GRCh37	16	75147877	75147877	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.885C>T	p.%3D	p.P295P	ENST00000300051	6/11	39	31	7	22	22	0	LDHD,synonymous_variant,p.%3D,ENST00000300051,;LDHD,synonymous_variant,p.%3D,ENST00000450168,;ZNRF1,downstream_gene_variant,,ENST00000335325,;RP11-252E2.1,upstream_gene_variant,,ENST00000499110,;LDHD,downstream_gene_variant,,ENST00000569876,;ZNRF1,downstream_gene_variant,,ENST00000568844,;LDHD,downstream_gene_variant,,ENST00000568164,;	A	ENSG00000166816	ENST00000300051	Transcript	synonymous_variant	932	885	295	P	ccC/ccT	.	.	.	-1	LDHD	HGNC	19708	protein_coding	YES	CCDS10913.1	ENSP00000300051	LDHD_HUMAN	.	UPI0000062302	.	.	.	6/11	.	hmmpanther:PTHR11748:SF72,hmmpanther:PTHR11748,Pfam_domain:PF02913,Superfamily_domains:SSF55103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTACGGGCAC	.	5	ESCA
ZFP1	0	.	GRCh37	16	75203737	75203737	+	Silent	SNP	G	G	A	rs753659921	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729G>A	p.%3D	p.P243P	ENST00000393430	4/4	35	23	11	34	34	0	ZFP1,synonymous_variant,p.%3D,ENST00000332307,;ZFP1,synonymous_variant,p.%3D,ENST00000393430,;ZFP1,synonymous_variant,p.%3D,ENST00000570010,;ZFP1,3_prime_UTR_variant,,ENST00000464850,;ZFP1,3_prime_UTR_variant,,ENST00000568079,;ZFP1,downstream_gene_variant,,ENST00000567481,;ZFP1,downstream_gene_variant,,ENST00000563356,;	A	ENSG00000184517	ENST00000393430	Transcript	synonymous_variant	853	729	243	P	ccG/ccA	rs753659921	.	.	1	ZFP1	HGNC	23328	protein_coding	YES	CCDS10914.2	ENSP00000377080	ZFP1_HUMAN	Q29RW8_HUMAN,J3KNQ1_HUMAN	UPI00001FFC12	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF248,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCCGGAATG	byFrequency	5	ESCA
RBFOX1	0	.	GRCh37	16	7761452	7761453	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*713dupA	.	.	ENST00000311745	13/13	36	21	14	25	25	0	RBFOX1,3_prime_UTR_variant,,ENST00000355637,;RBFOX1,3_prime_UTR_variant,,ENST00000340209,;RBFOX1,3_prime_UTR_variant,,ENST00000311745,;RBFOX1,3_prime_UTR_variant,,ENST00000547372,;RBFOX1,downstream_gene_variant,,ENST00000553186,;RBFOX1,downstream_gene_variant,,ENST00000535565,;RBFOX1,downstream_gene_variant,,ENST00000552089,;RBFOX1,downstream_gene_variant,,ENST00000567470,;RBFOX1,downstream_gene_variant,,ENST00000547338,;RBFOX1,downstream_gene_variant,,ENST00000436368,;RBFOX1,downstream_gene_variant,,ENST00000422070,;RBFOX1,downstream_gene_variant,,ENST00000550418,;RBFOX1,downstream_gene_variant,,ENST00000570188,;	A	ENSG00000078328	ENST00000311745	Transcript	3_prime_UTR_variant	2214-2215	.	.	.	.	.	.	.	1	RBFOX1	HGNC	18222	protein_coding	YES	CCDS10531.1	ENSP00000309117	RFOX1_HUMAN	.	UPI000006E29E	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTAGGAAAAA	.	2	ESCA
RBFOX1	0	.	GRCh37	16	7762401	7762402	+	3'UTR	INS	-	-	A	rs199500912	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1663dupA	.	.	ENST00000311745	13/13	40	24	16	37	37	0	RBFOX1,3_prime_UTR_variant,,ENST00000355637,;RBFOX1,3_prime_UTR_variant,,ENST00000340209,;RBFOX1,3_prime_UTR_variant,,ENST00000311745,;RBFOX1,downstream_gene_variant,,ENST00000553186,;RBFOX1,downstream_gene_variant,,ENST00000535565,;RBFOX1,downstream_gene_variant,,ENST00000552089,;RBFOX1,downstream_gene_variant,,ENST00000567470,;RBFOX1,downstream_gene_variant,,ENST00000547338,;RBFOX1,downstream_gene_variant,,ENST00000436368,;RBFOX1,downstream_gene_variant,,ENST00000422070,;RBFOX1,downstream_gene_variant,,ENST00000550418,;RBFOX1,downstream_gene_variant,,ENST00000547372,;RBFOX1,downstream_gene_variant,,ENST00000570188,;	A	ENSG00000078328	ENST00000311745	Transcript	3_prime_UTR_variant	3163-3164	.	.	.	.	rs199500912	.	.	1	RBFOX1	HGNC	18222	protein_coding	YES	CCDS10531.1	ENSP00000309117	RFOX1_HUMAN	.	UPI000006E29E	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACTTTAAAAA	by1000G	2	ESCA
BCMO1	0	.	GRCh37	16	81304016	81304016	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096G>A	p.Asp366Asn	p.D366N	ENST00000258168	7/11	39	26	13	17	17	0	BCMO1,missense_variant,p.Asp297Asn,ENST00000425577,;BCMO1,missense_variant,p.Asp366Asn,ENST00000258168,;BCMO1,3_prime_UTR_variant,,ENST00000563804,;	A	ENSG00000135697	ENST00000258168	Transcript	missense_variant	1557	1096	366	D/N	Gac/Aac	.	.	.	1	BCMO1	HGNC	13815	protein_coding	YES	CCDS10934.1	ENSP00000258168	BCDO1_HUMAN	.	UPI0000049CF7	.	tolerated(0.13)	benign(0.062)	7/11	.	hmmpanther:PTHR10543:SF22,hmmpanther:PTHR10543,Pfam_domain:PF03055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTGGACAAG	.	5	ESCA
GAN	0	.	GRCh37	16	81410849	81410849	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1528T>C	p.%3D	p.L510L	ENST00000568107	10/11	206	122	83	117	117	0	GAN,synonymous_variant,p.%3D,ENST00000568107,;	C	ENSG00000261609	ENST00000568107	Transcript	synonymous_variant	1690	1528	510	L	Tta/Cta	.	.	.	1	GAN	HGNC	4137	protein_coding	YES	CCDS10935.1	ENSP00000476795	GAN_HUMAN	.	UPI000000DAB6	.	.	.	10/11	.	hmmpanther:PTHR24412:SF167,hmmpanther:PTHR24412,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAATTTATGC	.	5	ESCA
KLHL36	0	.	GRCh37	16	84695293	84695293	+	Missense_Mutation	SNP	C	C	T	rs770567702	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1405C>T	p.Arg469Trp	p.R469W	ENST00000564996	5/5	49	25	23	27	27	0	KLHL36,missense_variant,p.Arg406Trp,ENST00000258157,;KLHL36,missense_variant,p.Arg469Trp,ENST00000564996,;KLHL36,downstream_gene_variant,,ENST00000565743,;KLHL36,downstream_gene_variant,,ENST00000567410,;KLHL36,downstream_gene_variant,,ENST00000569472,;KLHL36,non_coding_transcript_exon_variant,,ENST00000564159,;KLHL36,non_coding_transcript_exon_variant,,ENST00000325279,;	T	ENSG00000135686	ENST00000564996	Transcript	missense_variant	1546	1405	469	R/W	Cgg/Tgg	rs770567702	.	.	1	KLHL36	HGNC	17844	protein_coding	YES	CCDS10948.1	ENSP00000456743	KLH36_HUMAN	H3BQW5_HUMAN,H3BQE9_HUMAN,H3BPB9_HUMAN	UPI000006F9CF	.	deleterious(0.02)	possibly_damaging(0.908)	5/5	.	Superfamily_domains:0052715,SMART_domains:SM00612,PIRSF_domain:PIRSF037037,Gene3D:1k3iA02,hmmpanther:PTHR24412:SF161,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACCGGACA	.	5	ESCA
MTHFSD	0	.	GRCh37	16	86585831	86585831	+	Intron	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124-79T>C	.	.	ENST00000360900	.	42	28	13	19	19	0	MTHFSD,missense_variant,p.Val44Ala,ENST00000564364,;MTHFSD,missense_variant,p.Val64Ala,ENST00000381214,;MTHFSD,missense_variant,p.Val63Ala,ENST00000543303,;MTHFSD,5_prime_UTR_variant,,ENST00000546093,;MTHFSD,intron_variant,,ENST00000562940,;MTHFSD,intron_variant,,ENST00000565482,;MTHFSD,intron_variant,,ENST00000566469,;MTHFSD,intron_variant,,ENST00000561522,;MTHFSD,intron_variant,,ENST00000562994,;MTHFSD,intron_variant,,ENST00000561989,;MTHFSD,intron_variant,,ENST00000569000,;MTHFSD,intron_variant,,ENST00000360900,;MTHFSD,intron_variant,,ENST00000322911,;MTHFSD,non_coding_transcript_exon_variant,,ENST00000568037,;MTHFSD,intron_variant,,ENST00000561848,;MTHFSD,intron_variant,,ENST00000567539,;MTHFSD,intron_variant,,ENST00000568798,;MTHFSD,intron_variant,,ENST00000566050,;	G	ENSG00000103248	ENST00000360900	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MTHFSD	HGNC	25778	protein_coding	YES	CCDS54047.1	ENSP00000354152	MTHSD_HUMAN	H3BUU0_HUMAN,F5H0M7_HUMAN	UPI000059D3CD	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTACTTTA	.	5	ESCA
JPH3	0	.	GRCh37	16	87677966	87677966	+	Missense_Mutation	SNP	C	C	T	rs763624700	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.485C>T	p.Thr162Met	p.T162M	ENST00000284262	2/5	125	81	43	60	60	0	JPH3,missense_variant,p.Thr162Met,ENST00000284262,;JPH3,non_coding_transcript_exon_variant,,ENST00000537256,;	T	ENSG00000154118	ENST00000284262	Transcript	missense_variant	727	485	162	T/M	aCg/aTg	rs763624700	.	.	1	JPH3	HGNC	14203	protein_coding	YES	CCDS10962.1	ENSP00000284262	JPH3_HUMAN	B4DLY6_HUMAN,B4DIC1_HUMAN,B3KP13_HUMAN	UPI000012DAC4	.	deleterious(0)	probably_damaging(0.915)	2/5	.	PIRSF_domain:PIRSF037387,hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGACGTCCA	byFrequency	5	ESCA
JPH3	0	.	GRCh37	16	87678537	87678537	+	Frame_Shift_Del	DEL	C	C	-	rs563154923	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1060delC	p.Leu354CysfsTer117	p.L354Cfs*117	ENST00000284262	2/5	88	62	26	28	28	0	JPH3,frameshift_variant,p.Leu354CysfsTer117,ENST00000284262,;JPH3,non_coding_transcript_exon_variant,,ENST00000537256,;	-	ENSG00000154118	ENST00000284262	Transcript	frameshift_variant	1298	1056	352	I/X	atC/at	rs563154923	.	.	1	JPH3	HGNC	14203	protein_coding	YES	CCDS10962.1	ENSP00000284262	JPH3_HUMAN	B4DLY6_HUMAN,B4DIC1_HUMAN,B3KP13_HUMAN	UPI000012DAC4	.	.	.	2/5	.	PIRSF_domain:PIRSF037387,hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF7	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTCATCCCCCT	by1000G	3	ESCA
RPL13	0	.	GRCh37	16	89629407	89629407	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.593delG	p.Arg198LysfsTer60	p.R198Kfs*60	ENST00000393099	5/5	39	32	7	21	21	0	RPL13,frameshift_variant,p.Arg198LysfsTer?,ENST00000567815,;RPL13,frameshift_variant,p.Arg151LysfsTer60,ENST00000452368,;RPL13,frameshift_variant,p.Arg198LysfsTer60,ENST00000393099,;RPL13,frameshift_variant,p.Arg44LysfsTer?,ENST00000563270,;RPL13,frameshift_variant,p.Arg65LysfsTer60,ENST00000472354,;RPL13,frameshift_variant,p.Arg198LysfsTer60,ENST00000311528,;RPL13,downstream_gene_variant,,ENST00000467736,;SNORD68,downstream_gene_variant,,ENST00000363214,;RPL13,3_prime_UTR_variant,,ENST00000562879,;RPL13,non_coding_transcript_exon_variant,,ENST00000570149,;RPL13,non_coding_transcript_exon_variant,,ENST00000484610,;RPL13,non_coding_transcript_exon_variant,,ENST00000563749,;RPL13,non_coding_transcript_exon_variant,,ENST00000399461,;RPL13,downstream_gene_variant,,ENST00000487034,;RPL13,downstream_gene_variant,,ENST00000491523,;RPL13,downstream_gene_variant,,ENST00000565571,;	-	ENSG00000167526	ENST00000393099	Transcript	frameshift_variant	842	593	198	R/X	aGa/aa	.	.	.	1	RPL13	HGNC	10303	protein_coding	YES	CCDS10979.1	ENSP00000376811	RL13_HUMAN	O60250_HUMAN,J3QSB4_HUMAN,H3BUK8_HUMAN,A8K4C8_HUMAN	UPI0000001228	.	.	.	5/5	.	hmmpanther:PTHR11722,hmmpanther:PTHR11722:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAAAAAGAGCCA	.	3	ESCA
VPS9D1	0	.	GRCh37	16	89777228	89777228	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>A	p.Ala342Thr	p.A342T	ENST00000389386	10/15	29	15	13	15	15	0	VPS9D1,missense_variant,p.Ala342Thr,ENST00000389386,;VPS9D1,missense_variant,p.Ala272Thr,ENST00000561976,;VPS9D1,upstream_gene_variant,,ENST00000565023,;VPS9D1-AS1,upstream_gene_variant,,ENST00000562866,;VPS9D1,downstream_gene_variant,,ENST00000565452,;VPS9D1,downstream_gene_variant,,ENST00000567379,;VPS9D1,downstream_gene_variant,,ENST00000568691,;VPS9D1,downstream_gene_variant,,ENST00000563798,;	T	ENSG00000075399	ENST00000389386	Transcript	missense_variant	1149	1024	342	A/T	Gca/Aca	.	.	.	-1	VPS9D1	HGNC	13526	protein_coding	YES	CCDS42220.1	ENSP00000374037	VP9D1_HUMAN	H3BM58_HUMAN	UPI00001FF749	.	tolerated(0.73)	benign(0.002)	10/15	.	hmmpanther:PTHR23101:SF25,hmmpanther:PTHR23101	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGCGCTGG	.	5	ESCA
USP7	0	.	GRCh37	16	8997206	8997206	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1758A>T	p.Glu586Asp	p.E586D	ENST00000344836	16/31	30	20	10	22	22	0	USP7,missense_variant,p.Glu487Asp,ENST00000563085,;USP7,missense_variant,p.Glu487Asp,ENST00000535863,;USP7,missense_variant,p.Glu586Asp,ENST00000344836,;USP7,missense_variant,p.Glu570Asp,ENST00000381886,;USP7,3_prime_UTR_variant,,ENST00000542333,;USP7,3_prime_UTR_variant,,ENST00000565455,;USP7,3_prime_UTR_variant,,ENST00000563961,;USP7,non_coding_transcript_exon_variant,,ENST00000567329,;USP7,non_coding_transcript_exon_variant,,ENST00000570256,;USP7,upstream_gene_variant,,ENST00000566131,;USP7,upstream_gene_variant,,ENST00000567692,;USP7,upstream_gene_variant,,ENST00000569448,;USP7,upstream_gene_variant,,ENST00000565883,;USP7,upstream_gene_variant,,ENST00000562615,;USP7,upstream_gene_variant,,ENST00000563043,;USP7,upstream_gene_variant,,ENST00000562051,;	A	ENSG00000187555	ENST00000344836	Transcript	missense_variant	1957	1758	586	E/D	gaA/gaT	.	.	.	-1	USP7	HGNC	12630	protein_coding	YES	CCDS32385.1	ENSP00000343535	UBP7_HUMAN	H3BUV0_HUMAN,H3BTM1_HUMAN,H3BRA2_HUMAN,H3BND8_HUMAN,F5H8E5_HUMAN	UPI000013F0BE	.	tolerated(0.54)	benign(0.005)	16/31	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF89	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCTTCATC	.	5	ESCA
TCF25	0	.	GRCh37	16	89972642	89972642	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1669C>T	p.Arg557Cys	p.R557C	ENST00000263346	15/18	75	59	15	38	38	0	TCF25,missense_variant,p.Arg322Cys,ENST00000263347,;TCF25,missense_variant,p.Arg557Cys,ENST00000263346,;TCF25,missense_variant,p.Arg419Cys,ENST00000562256,;TCF25,downstream_gene_variant,,ENST00000562193,;TCF25,downstream_gene_variant,,ENST00000568409,;TCF25,upstream_gene_variant,,ENST00000566283,;TCF25,upstream_gene_variant,,ENST00000564957,;TCF25,upstream_gene_variant,,ENST00000565860,;TCF25,non_coding_transcript_exon_variant,,ENST00000563484,;RP11-566K11.7,non_coding_transcript_exon_variant,,ENST00000570217,;TCF25,non_coding_transcript_exon_variant,,ENST00000570116,;TCF25,upstream_gene_variant,,ENST00000567171,;	T	ENSG00000141002	ENST00000263346	Transcript	missense_variant	1725	1669	557	R/C	Cgc/Tgc	.	.	.	1	TCF25	HGNC	29181	protein_coding	YES	CCDS10987.1	ENSP00000263346	TCF25_HUMAN	.	UPI000012A80B	.	deleterious(0)	probably_damaging(1)	15/18	.	hmmpanther:PTHR22684:SF0,hmmpanther:PTHR22684,Pfam_domain:PF04910	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACCGCCAT	.	5	ESCA
MYO1C	0	.	GRCh37	17	1367847	1367847	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1173T>C	.	.	ENST00000359786	32/32	115	66	49	35	35	0	MYO1C,3_prime_UTR_variant,,ENST00000438665,;MYO1C,3_prime_UTR_variant,,ENST00000361007,;MYO1C,3_prime_UTR_variant,,ENST00000575158,;MYO1C,3_prime_UTR_variant,,ENST00000359786,;MYO1C,downstream_gene_variant,,ENST00000545534,;CRK,upstream_gene_variant,,ENST00000572145,;MYO1C,downstream_gene_variant,,ENST00000572615,;MYO1C,downstream_gene_variant,,ENST00000574341,;MYO1C,downstream_gene_variant,,ENST00000574308,;	G	ENSG00000197879	ENST00000359786	Transcript	3_prime_UTR_variant	4690	.	.	.	.	.	.	.	-1	MYO1C	HGNC	7597	protein_coding	YES	CCDS42226.1	ENSP00000352834	MYO1C_HUMAN	I3L4D4_HUMAN,I3L3Y6_HUMAN,I3L3F5_HUMAN,I3L204_HUMAN,I3L168_HUMAN	UPI0000200579	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATGATGTGG	.	5	ESCA
COX10	0	.	GRCh37	17	14095522	14095522	+	Silent	SNP	G	G	A	rs762702842	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912G>A	p.%3D	p.T304T	ENST00000261643	6/7	104	93	10	73	73	0	COX10,synonymous_variant,p.%3D,ENST00000261643,;COX10,synonymous_variant,p.%3D,ENST00000537334,;COX10,synonymous_variant,p.%3D,ENST00000536205,;COX10,3_prime_UTR_variant,,ENST00000580561,;COX10,3_prime_UTR_variant,,ENST00000581931,;	A	ENSG00000006695	ENST00000261643	Transcript	synonymous_variant	989	912	304	T	acG/acA	rs762702842	.	.	1	COX10	HGNC	2260	protein_coding	YES	CCDS11166.1	ENSP00000261643	COX10_HUMAN	B4DFR1_HUMAN	UPI000013D1C8	.	.	.	6/7	.	Transmembrane_helices:TMhelix,HAMAP:MF_00154,hmmpanther:PTHR11048,hmmpanther:PTHR11048:SF3,Pfam_domain:PF01040,TIGRFAM_domain:TIGR01473,PIRSF_domain:PIRSF001773	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCCACGGGCAG	.	3	ESCA
WDR81	0	.	GRCh37	17	1628919	1628919	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.666G>T	p.Glu222Asp	p.E222D	ENST00000409644	1/10	26	16	10	23	23	0	WDR81,missense_variant,p.Glu222Asp,ENST00000409644,;WDR81,intron_variant,,ENST00000468539,;WDR81,intron_variant,,ENST00000419248,;WDR81,intron_variant,,ENST00000309182,;WDR81,intron_variant,,ENST00000437219,;WDR81,intron_variant,,ENST00000446363,;WDR81,intron_variant,,ENST00000455636,;WDR81,intron_variant,,ENST00000418841,;WDR81,upstream_gene_variant,,ENST00000575206,;WDR81,upstream_gene_variant,,ENST00000545662,;RP11-961A15.1,downstream_gene_variant,,ENST00000576540,;WDR81,intron_variant,,ENST00000492901,;WDR81,upstream_gene_variant,,ENST00000479966,;WDR81,upstream_gene_variant,,ENST00000464528,;WDR81,upstream_gene_variant,,ENST00000474958,;	T	ENSG00000167716	ENST00000409644	Transcript	missense_variant	666	666	222	E/D	gaG/gaT	.	.	.	1	WDR81	HGNC	26600	protein_coding	YES	CCDS54062.1	ENSP00000386609	WDR81_HUMAN	E9PDG3_HUMAN,C9JD20_HUMAN	UPI0001881A85	.	tolerated(0.29)	benign(0.129)	1/10	.	Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGAGGCCTT	.	5	ESCA
GID4	0	.	GRCh37	17	17968960	17968960	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*403C>A	.	.	ENST00000268719	6/6	81	44	36	39	39	0	GID4,3_prime_UTR_variant,,ENST00000268719,;GID4,downstream_gene_variant,,ENST00000481836,;GID4,downstream_gene_variant,,ENST00000459843,;GID4,upstream_gene_variant,,ENST00000579871,;	A	ENSG00000141034	ENST00000268719	Transcript	3_prime_UTR_variant	1479	.	.	.	.	.	.	.	1	GID4	HGNC	28453	protein_coding	YES	CCDS11190.1	ENSP00000268719	GID4_HUMAN	K7ELH7_HUMAN,B3KXL6_HUMAN	UPI00000745B4	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCCCCGCC	.	5	ESCA
RTN4RL1	0	.	GRCh37	17	1839548	1839548	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*242G>A	.	.	ENST00000331238	2/2	38	26	12	20	20	0	RTN4RL1,3_prime_UTR_variant,,ENST00000331238,;	T	ENSG00000185924	ENST00000331238	Transcript	3_prime_UTR_variant	2048	.	.	.	.	.	.	.	-1	RTN4RL1	HGNC	21329	protein_coding	YES	CCDS45569.1	ENSP00000330631	R4RL1_HUMAN	.	UPI000018CD23	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCCGTGGG	.	5	ESCA
TVP23B	0	.	GRCh37	17	18694321	18694323	+	In_Frame_Del	DEL	TTG	TTG	-	rs771479580	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TTG	TTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.215_217delTGT	p.Leu72del	p.L72del	ENST00000307767	3/7	104	71	33	75	75	0	TVP23B,inframe_deletion,p.Leu8del,ENST00000575261,;TVP23B,inframe_deletion,p.Leu72del,ENST00000307767,;TVP23B,inframe_deletion,p.Leu72del,ENST00000574226,;TVP23B,inframe_deletion,p.Leu8del,ENST00000581733,;TVP23B,inframe_deletion,p.Leu8del,ENST00000476139,;TVP23B,intron_variant,,ENST00000572845,;TVP23B,intron_variant,,ENST00000571018,;TVP23B,intron_variant,,ENST00000574294,;TVP23B,upstream_gene_variant,,ENST00000482741,;TVP23B,downstream_gene_variant,,ENST00000582288,;	-	ENSG00000171928	ENST00000307767	Transcript	inframe_deletion	507-509	208-210	70	L/-	TTG/-	rs771479580	.	.	1	TVP23B	HGNC	20399	protein_coding	YES	CCDS42274.1	ENSP00000305654	TV23B_HUMAN	K7ENL4_HUMAN,J3QL63_HUMAN,I3L376_HUMAN	UPI00000713C4	.	.	.	3/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR13019,hmmpanther:PTHR13019:SF9,Pfam_domain:PF05832	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTATCTTGTTGTT	byFrequency	2	ESCA
SLC5A10	0	.	GRCh37	17	18916758	18916758	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1066C>T	p.Arg356Trp	p.R356W	ENST00000395647	10/15	100	56	43	32	32	0	SLC5A10,missense_variant,p.Arg340Trp,ENST00000395645,;SLC5A10,missense_variant,p.Arg273Trp,ENST00000317977,;SLC5A10,missense_variant,p.Arg356Trp,ENST00000395647,;SLC5A10,missense_variant,p.Arg313Trp,ENST00000395643,;SLC5A10,missense_variant,p.Arg273Trp,ENST00000395642,;SLC5A10,intron_variant,,ENST00000417251,;SLC5A10,upstream_gene_variant,,ENST00000584658,;	T	ENSG00000154025	ENST00000395647	Transcript	missense_variant	1107	1066	356	R/W	Cgg/Tgg	.	.	.	1	SLC5A10	HGNC	23155	protein_coding	YES	CCDS11201.2	ENSP00000379008	SC5AA_HUMAN	.	UPI00001401D2	.	deleterious(0)	probably_damaging(0.994)	10/15	.	PROSITE_profiles:PS50283,hmmpanther:PTHR11819:SF57,hmmpanther:PTHR11819,Pfam_domain:PF00474,TIGRFAM_domain:TIGR00813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGCGGGCC	.	5	ESCA
KCNJ12	0	.	GRCh37	17	21319498	21319498	+	Missense_Mutation	SNP	G	G	A	rs782257483	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844G>A	p.Gly282Ser	p.G282S	ENST00000583088	3/3	145	116	28	89	89	0	KCNJ12,missense_variant,p.Gly282Ser,ENST00000331718,;KCNJ12,missense_variant,p.Gly282Ser,ENST00000583088,;	A	ENSG00000184185	ENST00000583088	Transcript	missense_variant	1739	844	282	G/S	Ggc/Agc	rs782257483	.	.	1	KCNJ12	HGNC	6258	protein_coding	YES	CCDS11219.1	ENSP00000463778	IRK12_HUMAN	.	UPI00000725C7	.	tolerated(0.38)	benign(0.064)	3/3	.	Superfamily_domains:SSF81296,PIRSF_domain:PIRSF005465,Gene3D:2.60.40.1400,Pfam_domain:PF01007,hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S278S|c.834C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTCGGCATC	byFrequency	5	ESCA
LGALS9	0	.	GRCh37	17	25969367	25969367	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437G>A	p.Ser146Asn	p.S146N	ENST00000395473	4/11	106	90	15	82	82	0	LGALS9,missense_variant,p.Ser89Asn,ENST00000413914,;LGALS9,missense_variant,p.Ser146Asn,ENST00000577392,;LGALS9,missense_variant,p.Ser146Asn,ENST00000395473,;LGALS9,missense_variant,p.Ser56Asn,ENST00000584661,;LGALS9,missense_variant,p.Ser146Asn,ENST00000313648,;LGALS9,missense_variant,p.Ser49Asn,ENST00000581710,;LGALS9,missense_variant,p.Ser146Asn,ENST00000302228,;LGALS9,missense_variant,p.Ser146Asn,ENST00000310394,;LGALS9,upstream_gene_variant,,ENST00000578944,;LGALS9,downstream_gene_variant,,ENST00000448970,;LGALS9,3_prime_UTR_variant,,ENST00000580779,;LGALS9,3_prime_UTR_variant,,ENST00000467111,;LGALS9,non_coding_transcript_exon_variant,,ENST00000584386,;LGALS9,non_coding_transcript_exon_variant,,ENST00000579930,;LGALS9,non_coding_transcript_exon_variant,,ENST00000583671,;AC015688.3,downstream_gene_variant,,ENST00000584605,;LGALS9,downstream_gene_variant,,ENST00000579402,;LGALS9,upstream_gene_variant,,ENST00000486774,;LGALS9,upstream_gene_variant,,ENST00000481514,;AC015688.3,downstream_gene_variant,,ENST00000579290,;	A	ENSG00000168961	ENST00000395473	Transcript	missense_variant	1905	437	146	S/N	aGc/aAc	.	.	.	1	LGALS9	HGNC	6570	protein_coding	YES	CCDS11222.1	ENSP00000378856	LEG9_HUMAN	K7EPS0_HUMAN	UPI000012E437	.	tolerated(0.17)	benign(0.014)	4/11	.	PROSITE_profiles:PS51304,hmmpanther:PTHR11346:SF91,hmmpanther:PTHR11346,Gene3D:2.60.120.200,Pfam_domain:PF00337,SMART_domains:SM00908,SMART_domains:SM00276,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCAGCTTCC	.	4	ESCA
FLOT2	0	.	GRCh37	17	27211323	27211323	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142G>T	p.Glu48Ter	p.E48*	ENST00000394908	3/11	36	33	3	12	12	0	FLOT2,stop_gained,p.Glu103Ter,ENST00000394906,;FLOT2,stop_gained,p.Glu48Ter,ENST00000394908,;FLOT2,intron_variant,,ENST00000585169,;FLOT2,intron_variant,,ENST00000465427,;FLOT2,intron_variant,,ENST00000577789,;FLOT2,upstream_gene_variant,,ENST00000584569,;FLOT2,missense_variant,p.Arg78Ile,ENST00000580805,;FLOT2,non_coding_transcript_exon_variant,,ENST00000581509,;FLOT2,non_coding_transcript_exon_variant,,ENST00000580313,;FLOT2,intron_variant,,ENST00000582174,;FLOT2,intron_variant,,ENST00000593158,;FLOT2,intron_variant,,ENST00000586827,;	A	ENSG00000132589	ENST00000394908	Transcript	stop_gained	247	142	48	E/*	Gag/Tag	.	.	.	-1	FLOT2	HGNC	3758	protein_coding	YES	CCDS11245.2	ENSP00000378368	FLOT2_HUMAN	Q6FG43_HUMAN	UPI00001AE777	.	.	.	3/11	.	hmmpanther:PTHR13806,hmmpanther:PTHR13806:SF17,Pfam_domain:PF01145,Superfamily_domains:0050593	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCTCTAGGG	.	2	ESCA
PHF12	0	.	GRCh37	17	27234682	27234682	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2467A>T	p.Met823Leu	p.M823L	ENST00000332830	13/15	74	43	30	34	34	0	PHF12,missense_variant,p.Met823Leu,ENST00000332830,;PHF12,3_prime_UTR_variant,,ENST00000577226,;PHF12,downstream_gene_variant,,ENST00000579036,;DHRS13,upstream_gene_variant,,ENST00000426464,;PHF12,downstream_gene_variant,,ENST00000268756,;DHRS13,upstream_gene_variant,,ENST00000394901,;DHRS13,upstream_gene_variant,,ENST00000378895,;PHF12,downstream_gene_variant,,ENST00000579563,;PHF12,downstream_gene_variant,,ENST00000582655,;PHF12,3_prime_UTR_variant,,ENST00000589176,;PHF12,downstream_gene_variant,,ENST00000582436,;PHF12,downstream_gene_variant,,ENST00000378879,;	A	ENSG00000109118	ENST00000332830	Transcript	missense_variant	3278	2467	823	M/L	Atg/Ttg	.	.	.	-1	PHF12	HGNC	20816	protein_coding	YES	CCDS32598.1	ENSP00000329933	PHF12_HUMAN	K7ERZ4_HUMAN,K7ENU0_HUMAN,K7EMX6_HUMAN	UPI0000197E05	.	deleterious(0.02)	probably_damaging(0.97)	13/15	.	PROSITE_profiles:PS50006,hmmpanther:PTHR24102:SF16,hmmpanther:PTHR24102,Gene3D:2.60.200.20,Superfamily_domains:SSF49879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCATGTCAG	.	5	ESCA
MYO18A	0	.	GRCh37	17	27424355	27424355	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4116G>A	p.%3D	p.R1372R	ENST00000527372	27/42	72	56	15	43	43	0	MYO18A,synonymous_variant,p.%3D,ENST00000354329,;MYO18A,synonymous_variant,p.%3D,ENST00000527372,;MYO18A,synonymous_variant,p.%3D,ENST00000533112,;MYO18A,synonymous_variant,p.%3D,ENST00000531253,;MYO18A,3_prime_UTR_variant,,ENST00000530254,;MYO18A,non_coding_transcript_exon_variant,,ENST00000533652,;MYO18A,non_coding_transcript_exon_variant,,ENST00000530557,;MYO18A,downstream_gene_variant,,ENST00000532143,;	T	ENSG00000196535	ENST00000527372	Transcript	synonymous_variant	4297	4116	1372	R	cgG/cgA	.	.	.	-1	MYO18A	HGNC	31104	protein_coding	YES	CCDS45642.1	ENSP00000437073	MY18A_HUMAN	.	UPI0000167F32	.	.	.	27/42	.	Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF293	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAGCCGCCA	.	5	ESCA
ADAP2	0	.	GRCh37	17	29261308	29261308	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.503A>C	p.Lys168Thr	p.K168T	ENST00000330889	5/11	51	21	30	35	35	0	ADAP2,missense_variant,p.Lys168Thr,ENST00000581285,;ADAP2,missense_variant,p.Lys46Thr,ENST00000581548,;ADAP2,missense_variant,p.Lys168Thr,ENST00000330889,;ADAP2,missense_variant,p.Lys174Thr,ENST00000580525,;ADAP2,3_prime_UTR_variant,,ENST00000585130,;ADAP2,3_prime_UTR_variant,,ENST00000580526,;	C	ENSG00000184060	ENST00000330889	Transcript	missense_variant	838	503	168	K/T	aAg/aCg	COSM1679691	.	.	1	ADAP2	HGNC	16487	protein_coding	YES	CCDS11261.1	ENSP00000329468	ADAP2_HUMAN	K7ENT1_HUMAN,J3QRA6_HUMAN	UPI0000127487	.	deleterious(0)	probably_damaging(1)	5/11	.	PROSITE_profiles:PS50003,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF196,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAAAGGAAC	.	5	ESCA
MYO1D	0	.	GRCh37	17	30986155	30986155	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2323G>T	p.Ala775Ser	p.A775S	ENST00000318217	17/22	79	63	16	63	63	0	MYO1D,missense_variant,p.Ala775Ser,ENST00000318217,;MYO1D,missense_variant,p.Ala775Ser,ENST00000579584,;MYO1D,missense_variant,p.Ala687Ser,ENST00000394649,;RP11-220C2.1,intron_variant,,ENST00000582272,;MYO1D,non_coding_transcript_exon_variant,,ENST00000581059,;MYO1D,non_coding_transcript_exon_variant,,ENST00000582217,;MYO1D,non_coding_transcript_exon_variant,,ENST00000577352,;MYO1D,non_coding_transcript_exon_variant,,ENST00000585094,;	A	ENSG00000176658	ENST00000318217	Transcript	missense_variant	2628	2323	775	A/S	Gcc/Tcc	.	.	.	-1	MYO1D	HGNC	7598	protein_coding	YES	CCDS32615.1	ENSP00000324527	MYO1D_HUMAN	Q8N618_HUMAN,K7EIG7_HUMAN	UPI0000186004	.	tolerated(0.82)	benign(0.004)	17/22	.	hmmpanther:PTHR13140:SF333,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCCTCCT	.	5	ESCA
LIG3	0	.	GRCh37	17	33323122	33323122	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1655delG	p.Gly552AlafsTer4	p.G552Afs*4	ENST00000378526	10/20	56	38	18	23	23	0	LIG3,frameshift_variant,p.Gly552AlafsTer4,ENST00000378526,;LIG3,frameshift_variant,p.Gly552AlafsTer4,ENST00000262327,;LIG3,downstream_gene_variant,,ENST00000585740,;LIG3,downstream_gene_variant,,ENST00000585941,;LIG3,non_coding_transcript_exon_variant,,ENST00000588713,;LIG3,non_coding_transcript_exon_variant,,ENST00000590630,;LIG3,non_coding_transcript_exon_variant,,ENST00000586058,;LIG3,upstream_gene_variant,,ENST00000586119,;LIG3,downstream_gene_variant,,ENST00000586435,;LIG3,upstream_gene_variant,,ENST00000585370,;LIG3,upstream_gene_variant,,ENST00000593099,;	-	ENSG00000005156	ENST00000378526	Transcript	frameshift_variant	1784	1651	551	G/X	Ggg/gg	.	.	.	1	LIG3	HGNC	6600	protein_coding	YES	CCDS11284.2	ENSP00000367787	DNLI3_HUMAN	E5KLB5_HUMAN,K7EQB6_HUMAN,K7ENR9_HUMAN,C4B7Q3_HUMAN,B7Z6I3_HUMAN	UPI0000350B71	.	.	.	10/20	.	hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF11,Pfam_domain:PF01068,Gene3D:3.30.470.30,TIGRFAM_domain:TIGR00574,Superfamily_domains:SSF56091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTCCTGGGGGC	.	3	ESCA
FNDC8	0	.	GRCh37	17	33457310	33457310	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>A	p.Leu278Met	p.L278M	ENST00000158009	4/4	27	22	4	38	38	0	FNDC8,missense_variant,p.Leu278Met,ENST00000158009,;NLE1,3_prime_UTR_variant,,ENST00000586869,;NLE1,downstream_gene_variant,,ENST00000442241,;NLE1,downstream_gene_variant,,ENST00000360831,;NLE1,downstream_gene_variant,,ENST00000588019,;	A	ENSG00000073598	ENST00000158009	Transcript	missense_variant	947	832	278	L/M	Ctg/Atg	.	.	.	1	FNDC8	HGNC	25286	protein_coding	YES	CCDS11290.1	ENSP00000158009	FNDC8_HUMAN	.	UPI000006D671	.	tolerated_low_confidence(0.14)	benign(0.013)	4/4	.	PROSITE_profiles:PS50853,hmmpanther:PTHR32430,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAACCCTGGCC	.	3	ESCA
SLFN14	0	.	GRCh37	17	33879871	33879871	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1782delT	p.Pro595GlnfsTer8	p.P595Qfs*8	ENST00000415846	3/4	30	26	4	21	21	0	SLFN14,frameshift_variant,p.Pro595GlnfsTer8,ENST00000415846,;RP11-1094M14.12,upstream_gene_variant,,ENST00000588445,;	-	ENSG00000236320	ENST00000415846	Transcript	frameshift_variant	1818	1782	594	F/X	ttT/tt	.	.	.	-1	SLFN14	HGNC	32689	protein_coding	YES	CCDS45650.1	ENSP00000391101	SLN14_HUMAN	.	UPI000041A9FB	.	.	.	3/4	.	hmmpanther:PTHR12155,hmmpanther:PTHR12155:SF22,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCTGGAAAGCA	.	3	ESCA
CCL14	0	.	GRCh37	17	34311431	34311431	+	Missense_Mutation	SNP	C	C	T	rs144903710	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.185G>A	p.Arg62His	p.R62H	ENST00000536149	7/8	71	33	37	45	45	0	CCL14,missense_variant,p.Arg68His,ENST00000480944,;CCL14,missense_variant,p.Arg46His,ENST00000394509,;CCL14,missense_variant,p.Arg46His,ENST00000586216,;CCL14,missense_variant,p.Arg62His,ENST00000435911,;CCL14,missense_variant,p.Arg62His,ENST00000536149,;CCL16,upstream_gene_variant,,ENST00000293275,;CTB-186H2.3,upstream_gene_variant,,ENST00000591669,;CTB-186H2.3,intron_variant,,ENST00000593057,;CCL15-CCL14,3_prime_UTR_variant,,ENST00000481427,;CCL15-CCL14,3_prime_UTR_variant,,ENST00000495214,;CCL16,upstream_gene_variant,,ENST00000586567,;	T	ENSG00000213494	ENST00000536149	Transcript	missense_variant	1197	185	62	R/H	cGt/cAt	rs144903710	.	.	-1	CCL14	HGNC	10612	protein_coding	YES	CCDS45652.1	ENSP00000441771	CCL14_HUMAN	.	UPI000002B47E	.	tolerated(0.14)	benign(0.059)	7/8	.	Superfamily_domains:SSF54117,SMART_domains:SM00199,Pfam_domain:PF00048,Gene3D:2.40.50.40,PROSITE_patterns:PS00472,hmmpanther:PTHR12015:SF75,hmmpanther:PTHR12015	.	.	.	.	.	.	.	T:0.0002	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGACGCGGG	byCluster	5	ESCA
TAX1BP3	0	.	GRCh37	17	3566992	3566992	+	3'UTR	SNP	C	C	T	rs373420100	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50G>A	.	.	ENST00000225525	4/4	47	38	9	16	16	0	TAX1BP3,3_prime_UTR_variant,,ENST00000225525,;CTNS,downstream_gene_variant,,ENST00000046640,;CTNS,downstream_gene_variant,,ENST00000441220,;CTNS,downstream_gene_variant,,ENST00000381870,;CTNS,downstream_gene_variant,,ENST00000414524,;P2RX5-TAX1BP3,3_prime_UTR_variant,,ENST00000550383,;RP11-48B14.1,upstream_gene_variant,,ENST00000486753,;	T	ENSG00000213977	ENST00000225525	Transcript	3_prime_UTR_variant	581	.	.	.	.	rs373420100	.	.	-1	TAX1BP3	HGNC	30684	protein_coding	YES	CCDS11032.1	ENSP00000225525	TX1B3_HUMAN	.	UPI000006E07B	.	.	.	4/4	.	.	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGTGGCGTTAC	byCluster|by1000G	4	ESCA
SRCIN1	0	.	GRCh37	17	36699355	36699355	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3417+703C>T	.	.	ENST00000264659	.	46	27	19	13	13	0	SRCIN1,3_prime_UTR_variant,,ENST00000542707,;SRCIN1,intron_variant,,ENST00000264659,;SRCIN1,intron_variant,,ENST00000578925,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000398579,;SRCIN1,downstream_gene_variant,,ENST00000581656,;SRCIN1,downstream_gene_variant,,ENST00000584491,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000577193,;	A	ENSG00000017373	ENST00000264659	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SRCIN1	HGNC	29506	protein_coding	YES	CCDS45660.1	ENSP00000264659	SRCN1_HUMAN	.	UPI0000E27F82	.	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCCGCGCCT	.	5	ESCA
FBXO47	0	.	GRCh37	17	37093481	37093483	+	In_Frame_Del	DEL	TAG	TAG	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TAG	TAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1304_1306delCTA	p.Ala435_Asn436delinsAsp	p.A435_N436delinsD	ENST00000378079	11/11	39	24	15	21	21	0	FBXO47,inframe_deletion,p.Ala435_Asn436delinsAsp,ENST00000378079,;	-	ENSG00000204952	ENST00000378079	Transcript	inframe_deletion	1504-1506	1304-1306	435-436	AN/D	gCTAac/gac	.	.	.	-1	FBXO47	HGNC	31969	protein_coding	YES	CCDS32639.1	ENSP00000367319	FBX47_HUMAN	.	UPI00004DDAF1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAAGTTAGCCTGA	.	3	ESCA
CDK12	0	.	GRCh37	17	37667792	37667795	+	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	ACAA	ACAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2682_2685delCAAA	p.Asn894LysfsTer14	p.N894Kfs*14	ENST00000447079	8/14	28	15	13	32	32	0	CDK12,frameshift_variant,p.Asn894LysfsTer14,ENST00000447079,;CDK12,frameshift_variant,p.Asn893LysfsTer14,ENST00000584632,;CDK12,frameshift_variant,p.Asn894LysfsTer14,ENST00000430627,;	-	ENSG00000167258	ENST00000447079	Transcript	frameshift_variant	2710-2713	2677-2680	893-894	TN/X	ACAAac/ac	.	.	.	1	CDK12	HGNC	24224	protein_coding	YES	CCDS11337.1	ENSP00000398880	CDK12_HUMAN	.	UPI000013E688	.	.	.	8/14	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24056:SF126,hmmpanther:PTHR24056,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R890H|c.2669G>A|5	INDELOCATOR*|VARSCANI*|PINDEL	CCTTACACAAACAAA	.	3	ESCA
CSF3	0	.	GRCh37	17	38171995	38171995	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97delC	p.Leu33TrpfsTer16	p.L33Wfs*16	ENST00000225474	2/5	51	42	9	26	26	0	CSF3,frameshift_variant,p.Leu33TrpfsTer16,ENST00000225474,;CSF3,frameshift_variant,p.Leu29TrpfsTer16,ENST00000577675,;CSF3,frameshift_variant,p.Leu29TrpfsTer16,ENST00000331769,;CSF3,frameshift_variant,p.Leu33TrpfsTer16,ENST00000394149,;CSF3,frameshift_variant,p.Leu33TrpfsTer16,ENST00000394148,;CSF3,frameshift_variant,p.Leu33TrpfsTer16,ENST00000583218,;MED24,downstream_gene_variant,,ENST00000422942,;MED24,downstream_gene_variant,,ENST00000501516,;MED24,downstream_gene_variant,,ENST00000356271,;MED24,downstream_gene_variant,,ENST00000394128,;MED24,downstream_gene_variant,,ENST00000394126,;MED24,downstream_gene_variant,,ENST00000394127,;RP11-387H17.6,upstream_gene_variant,,ENST00000583462,;RP11-387H17.6,upstream_gene_variant,,ENST00000584649,;MED24,downstream_gene_variant,,ENST00000470126,;CSF3,non_coding_transcript_exon_variant,,ENST00000479880,;CSF3,non_coding_transcript_exon_variant,,ENST00000582798,;CSF3,intron_variant,,ENST00000579852,;MED24,downstream_gene_variant,,ENST00000579364,;MED24,downstream_gene_variant,,ENST00000535508,;MED24,downstream_gene_variant,,ENST00000491466,;	-	ENSG00000108342	ENST00000225474	Transcript	frameshift_variant	123	92	31	T/X	aCc/ac	.	.	.	1	CSF3	HGNC	2438	protein_coding	YES	CCDS11357.1	ENSP00000225474	CSF3_HUMAN	.	UPI0000128525	.	.	.	2/5	.	hmmpanther:PTHR10511,Gene3D:1.20.1250.10,PIRSF_domain:PIRSF001935	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGCCACCCCCC	.	3	ESCA
KRT25	0	.	GRCh37	17	38911154	38911154	+	Missense_Mutation	SNP	G	G	A	rs370147296	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370C>T	p.Arg124Cys	p.R124C	ENST00000312150	1/8	59	31	27	41	41	0	KRT25,missense_variant,p.Arg124Cys,ENST00000312150,;	A	ENSG00000204897	ENST00000312150	Transcript	missense_variant	431	370	124	R/C	Cgt/Tgt	rs370147296	.	.	-1	KRT25	HGNC	30839	protein_coding	YES	CCDS11373.1	ENSP00000310573	K1C25_HUMAN	.	UPI000019B3C3	.	deleterious(0.01)	benign(0.344)	1/8	.	Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF160	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACGGCAAG	byCluster	5	ESCA
KRTAP4-6	0	.	GRCh37	17	39296576	39296576	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.164G>A	p.Cys55Tyr	p.C55Y	ENST00000345847	1/1	216	166	49	125	125	0	KRTAP4-6,missense_variant,p.Cys55Tyr,ENST00000345847,;	T	ENSG00000198090	ENST00000345847	Transcript	missense_variant	164	164	55	C/Y	tGc/tAc	.	.	.	-1	KRTAP4-6	HGNC	18909	protein_coding	YES	CCDS54125.1	ENSP00000328270	KRA46_HUMAN	.	UPI00006C17B9	.	deleterious(0)	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGCACACA	.	5	ESCA
ZZEF1	0	.	GRCh37	17	3936179	3936179	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6702A>G	p.%3D	p.P2234P	ENST00000381638	41/55	58	42	16	29	29	0	ZZEF1,synonymous_variant,p.%3D,ENST00000573183,;ZZEF1,synonymous_variant,p.%3D,ENST00000381638,;ZZEF1,3_prime_UTR_variant,,ENST00000571436,;ZZEF1,non_coding_transcript_exon_variant,,ENST00000573606,;ZZEF1,downstream_gene_variant,,ENST00000572426,;	C	ENSG00000074755	ENST00000381638	Transcript	synonymous_variant	6827	6702	2234	P	ccA/ccG	.	.	.	-1	ZZEF1	HGNC	29027	protein_coding	YES	CCDS11043.1	ENSP00000371051	ZZEF1_HUMAN	.	UPI00004569F7	.	.	.	41/55	.	hmmpanther:PTHR22772,hmmpanther:PTHR22772:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAATGGCAG	.	5	ESCA
KRT35	0	.	GRCh37	17	39633867	39633867	+	Missense_Mutation	SNP	G	G	A	rs780375339	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1123C>T	p.Arg375Trp	p.R375W	ENST00000393989	6/8	71	53	17	50	50	0	KRT35,missense_variant,p.Arg345Trp,ENST00000246639,;KRT35,missense_variant,p.Arg375Trp,ENST00000393989,;	A	ENSG00000197079	ENST00000393989	Transcript	missense_variant	1166	1123	375	R/W	Cgg/Tgg	rs780375339,COSM560782	.	.	-1	KRT35	HGNC	6453	protein_coding	YES	CCDS11394.2	ENSP00000377558	KRT35_HUMAN	C4AM86_HUMAN	UPI0000D74C4B	.	deleterious(0.02)	probably_damaging(1)	6/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF109,Gene3D:1.20.5.170,Pfam_domain:PF00038,Superfamily_domains:SSF64593	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCGCTCCA	byFrequency	5	ESCA
KRT17	0	.	GRCh37	17	39785135	39785135	+	5'Flank	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000311208	.	138	112	25	106	106	0	JUP,intron_variant,,ENST00000540235,;KRT17,upstream_gene_variant,,ENST00000577817,;KRT17,upstream_gene_variant,,ENST00000311208,;KRT17,upstream_gene_variant,,ENST00000463128,;KRT42P,non_coding_transcript_exon_variant,,ENST00000438131,;KRT42P,intron_variant,,ENST00000398469,;KRT42P,downstream_gene_variant,,ENST00000587390,;KRT42P,downstream_gene_variant,,ENST00000589633,;KRT42P,upstream_gene_variant,,ENST00000587335,;KRT17,upstream_gene_variant,,ENST00000491673,;KRT17,upstream_gene_variant,,ENST00000493253,;KRT42P,intron_variant,,ENST00000458343,;	G	ENSG00000128422	ENST00000311208	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4306	-1	KRT17	HGNC	6427	protein_coding	YES	CCDS11402.1	ENSP00000308452	K1C17_HUMAN	K7ESE1_HUMAN,B4E2P9_HUMAN	UPI0000148FD6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCACAGTGAA	.	5	ESCA
KAT2A	0	.	GRCh37	17	40270397	40270399	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096_1098delGAG	p.Glu366del	p.E366del	ENST00000225916	7/18	34	28	6	27	27	0	KAT2A,inframe_deletion,p.Glu366del,ENST00000225916,;HSPB9,upstream_gene_variant,,ENST00000355067,;CTD-2132N18.3,downstream_gene_variant,,ENST00000592574,;KAT2A,3_prime_UTR_variant,,ENST00000465682,;CTD-2132N18.3,downstream_gene_variant,,ENST00000592248,;CTD-2132N18.3,downstream_gene_variant,,ENST00000585562,;KAT2A,upstream_gene_variant,,ENST00000588759,;KAT2A,upstream_gene_variant,,ENST00000586972,;KAT2A,upstream_gene_variant,,ENST00000592310,;	-	ENSG00000108773	ENST00000225916	Transcript	inframe_deletion	1150-1152	1096-1098	366	E/-	GAG/-	.	.	.	-1	KAT2A	HGNC	4201	protein_coding	YES	CCDS11417.1	ENSP00000225916	KAT2A_HUMAN	K7ERS6_HUMAN	UPI000000D978	.	.	.	7/18	.	hmmpanther:PTHR22880:SF124,hmmpanther:PTHR22880,PIRSF_domain:PIRSF003048	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATAGATCTCCTCCT	.	2	ESCA
KCNH4	0	.	GRCh37	17	40315711	40315711	+	Missense_Mutation	SNP	C	C	G	rs770748876	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2390G>C	p.Gly797Ala	p.G797A	ENST00000264661	13/17	35	15	19	21	21	0	KCNH4,missense_variant,p.Gly797Ala,ENST00000264661,;KCNH4,missense_variant,p.Gly797Ala,ENST00000607371,;	G	ENSG00000089558	ENST00000264661	Transcript	missense_variant	2723	2390	797	G/A	gGc/gCc	rs770748876	.	.	-1	KCNH4	HGNC	6253	protein_coding	YES	CCDS11420.1	ENSP00000264661	KCNH4_HUMAN	.	UPI000012DCA8	.	tolerated(0.86)	benign(0.001)	13/17	.	hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF378	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGCCGTGA	byFrequency	5	ESCA
ETV4	0	.	GRCh37	17	41605290	41605290	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*597C>T	.	.	ENST00000319349	13/13	24	18	6	21	21	0	ETV4,3_prime_UTR_variant,,ENST00000319349,;ETV4,3_prime_UTR_variant,,ENST00000393664,;DHX8,intron_variant,,ENST00000589898,;DHX8,downstream_gene_variant,,ENST00000540306,;DHX8,downstream_gene_variant,,ENST00000262415,;ETV4,downstream_gene_variant,,ENST00000591713,;ETV4,downstream_gene_variant,,ENST00000586826,;ETV4,downstream_gene_variant,,ENST00000545954,;DHX8,downstream_gene_variant,,ENST00000587574,;ETV4,downstream_gene_variant,,ENST00000545089,;ETV4,downstream_gene_variant,,ENST00000538265,;DHX8,downstream_gene_variant,,ENST00000587044,;	A	ENSG00000175832	ENST00000319349	Transcript	3_prime_UTR_variant	2351	.	.	.	.	.	.	.	-1	ETV4	HGNC	3493	protein_coding	YES	CCDS11465.1	ENSP00000321835	ETV4_HUMAN	K7EMW0_HUMAN	UPI0000000236	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTAGGAAAGG	.	5	ESCA
MPP2	0	.	GRCh37	17	41958085	41958085	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1124C>T	p.Pro375Leu	p.P375L	ENST00000269095	10/13	31	23	8	26	26	0	MPP2,missense_variant,p.Pro420Leu,ENST00000518766,;MPP2,missense_variant,p.Pro375Leu,ENST00000269095,;MPP2,missense_variant,p.Pro364Leu,ENST00000536246,;MPP2,missense_variant,p.Pro236Leu,ENST00000520305,;MPP2,missense_variant,p.Pro399Leu,ENST00000461854,;MPP2,missense_variant,p.Pro392Leu,ENST00000377184,;MPP2,missense_variant,p.Pro364Leu,ENST00000523501,;MPP2,downstream_gene_variant,,ENST00000520406,;MPP2,downstream_gene_variant,,ENST00000521178,;MPP2,downstream_gene_variant,,ENST00000523762,;MPP2,downstream_gene_variant,,ENST00000522172,;MPP2,downstream_gene_variant,,ENST00000523934,;MPP2,downstream_gene_variant,,ENST00000520241,;MPP2,downstream_gene_variant,,ENST00000523220,;MPP2,downstream_gene_variant,,ENST00000473246,;MPP2,downstream_gene_variant,,ENST00000524294,;MPP2,downstream_gene_variant,,ENST00000520319,;	A	ENSG00000108852	ENST00000269095	Transcript	missense_variant	1429	1124	375	P/L	cCa/cTa	.	.	.	-1	MPP2	HGNC	7220	protein_coding	YES	CCDS11471.1	ENSP00000269095	MPP2_HUMAN	E7EX01_HUMAN,E7EV91_HUMAN,E5RK50_HUMAN,E5RJK0_HUMAN,E5RIU3_HUMAN,E5RIM9_HUMAN,E5RI32_HUMAN,E5RFN8_HUMAN	UPI000013D7F7	.	deleterious(0)	possibly_damaging(0.608)	10/13	.	PROSITE_profiles:PS50052,hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF38,Gene3D:3.40.50.300,Pfam_domain:PF00625,SMART_domains:SM00072,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTGGATCC	.	5	ESCA
ASB16	0	.	GRCh37	17	42249535	42249535	+	Silent	SNP	C	C	T	rs373603799	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.423C>T	p.%3D	p.V141V	ENST00000293414	2/5	50	36	14	27	27	0	ASB16,synonymous_variant,p.%3D,ENST00000293414,;ASB16,synonymous_variant,p.%3D,ENST00000591700,;ASB16-AS1,downstream_gene_variant,,ENST00000585457,;ASB16-AS1,downstream_gene_variant,,ENST00000588785,;ASB16-AS1,downstream_gene_variant,,ENST00000591166,;ASB16,synonymous_variant,p.%3D,ENST00000589618,;	T	ENSG00000161664	ENST00000293414	Transcript	synonymous_variant	507	423	141	V	gtC/gtT	rs373603799	.	.	1	ASB16	HGNC	19768	protein_coding	YES	CCDS11478.1	ENSP00000293414	ASB16_HUMAN	K7EM41_HUMAN	UPI000013E105	.	.	.	2/5	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24188,hmmpanther:PTHR24188:SF2,Gene3D:1.25.40.20,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGTCGGGGG	byCluster	5	ESCA
SP2	0	.	GRCh37	17	46000463	46000463	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1199delA	p.Lys400SerfsTer25	p.K400Sfs*25	ENST00000376741	4/7	47	34	13	25	25	0	SP2,frameshift_variant,p.Lys400SerfsTer25,ENST00000376741,;AC003665.1,intron_variant,,ENST00000411573,;AC003665.1,intron_variant,,ENST00000433001,;AC003665.1,intron_variant,,ENST00000451140,;AC003665.1,intron_variant,,ENST00000585280,;	-	ENSG00000167182	ENST00000376741	Transcript	frameshift_variant	1332	1195	399	K/X	Aaa/aa	.	.	.	1	SP2	HGNC	11207	protein_coding	YES	CCDS11521.2	ENSP00000365931	SP2_HUMAN	.	UPI00005A7765	.	.	.	4/7	.	hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCAGCAAAAAG	.	3	ESCA
SP2	0	.	GRCh37	17	46005405	46005405	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*215C>T	.	.	ENST00000376741	7/7	27	19	8	10	10	0	SP2,3_prime_UTR_variant,,ENST00000376741,;AC003665.1,intron_variant,,ENST00000411573,;AC003665.1,intron_variant,,ENST00000433001,;AC003665.1,intron_variant,,ENST00000451140,;AC003665.1,intron_variant,,ENST00000585280,;RP11-6N17.3,downstream_gene_variant,,ENST00000584276,;	T	ENSG00000167182	ENST00000376741	Transcript	3_prime_UTR_variant	2194	.	.	.	.	.	.	.	1	SP2	HGNC	11207	protein_coding	YES	CCDS11521.2	ENSP00000365931	SP2_HUMAN	.	UPI00005A7765	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCGGCCT	.	5	ESCA
HOXB3	0	.	GRCh37	17	46628044	46628044	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.948C>T	p.%3D	p.G316G	ENST00000470495	2/2	63	47	16	35	35	0	HOXB3,synonymous_variant,p.%3D,ENST00000476342,;HOXB3,synonymous_variant,p.%3D,ENST00000460160,;HOXB3,synonymous_variant,p.%3D,ENST00000498678,;HOXB3,synonymous_variant,p.%3D,ENST00000485909,;HOXB3,synonymous_variant,p.%3D,ENST00000470495,;HOXB3,synonymous_variant,p.%3D,ENST00000472863,;HOXB3,synonymous_variant,p.%3D,ENST00000489475,;HOXB3,synonymous_variant,p.%3D,ENST00000490677,;HOXB3,synonymous_variant,p.%3D,ENST00000311626,;HOXB2,upstream_gene_variant,,ENST00000330070,;HOXB3,downstream_gene_variant,,ENST00000465120,;HOXB3,downstream_gene_variant,,ENST00000471459,;HOXB-AS1,intron_variant,,ENST00000508688,;HOXB-AS1,intron_variant,,ENST00000502764,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS1,intron_variant,,ENST00000435312,;HOXB-AS1,downstream_gene_variant,,ENST00000504972,;HOXB3,downstream_gene_variant,,ENST00000478644,;	A	ENSG00000120093	ENST00000470495	Transcript	synonymous_variant	2396	948	316	G	ggC/ggT	.	.	.	-1	HOXB3	HGNC	5114	protein_coding	YES	CCDS11528.1	ENSP00000417207	HXB3_HUMAN	C9J2I3_HUMAN,B7ZAD0_HUMAN,B7Z5N8_HUMAN	UPI00001AEFBF	.	.	.	2/2	.	hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGCCGCA	.	5	ESCA
PLD2	0	.	GRCh37	17	4711646	4711646	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321delT	p.Gln108ArgfsTer8	p.Q108Rfs*8	ENST00000263088	4/25	60	42	18	22	22	0	PLD2,frameshift_variant,p.Gln108ArgfsTer8,ENST00000575316,;PLD2,frameshift_variant,p.Gln108ArgfsTer8,ENST00000263088,;PLD2,frameshift_variant,p.Gln108ArgfsTer8,ENST00000572940,;RP11-81A22.5,upstream_gene_variant,,ENST00000571067,;PLD2,frameshift_variant,p.Gln108ArgfsTer8,ENST00000575246,;PLD2,non_coding_transcript_exon_variant,,ENST00000574268,;PLD2,upstream_gene_variant,,ENST00000575813,;	-	ENSG00000129219	ENST00000263088	Transcript	frameshift_variant	449	318	106	H/X	caT/ca	.	.	.	1	PLD2	HGNC	9068	protein_coding	YES	CCDS11057.1	ENSP00000263088	PLD2_HUMAN	I3L222_HUMAN,I3L1F3_HUMAN	UPI0000131BDE	.	.	.	4/25	.	PROSITE_profiles:PS50195,hmmpanther:PTHR18896,hmmpanther:PTHR18896:SF7,Pfam_domain:PF00787,Gene3D:3.30.1520.10,PIRSF_domain:PIRSF009376,SMART_domains:SM00312,Superfamily_domains:SSF64268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCGTCATTTTCA	.	2	ESCA
C17orf107	0	.	GRCh37	17	4803451	4803451	+	Intron	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.276+16delG	.	.	ENST00000381365	.	31	22	9	8	8	0	C17orf107,frameshift_variant,p.Ala98LeufsTer124,ENST00000521575,;CHRNE,intron_variant,,ENST00000293780,;C17orf107,intron_variant,,ENST00000381365,;MINK1,downstream_gene_variant,,ENST00000355280,;MINK1,downstream_gene_variant,,ENST00000347992,;MINK1,downstream_gene_variant,,ENST00000576037,;MINK1,downstream_gene_variant,,ENST00000453408,;CHRNE,downstream_gene_variant,,ENST00000575637,;CHRNE,intron_variant,,ENST00000572438,;MINK1,downstream_gene_variant,,ENST00000575511,;MINK1,downstream_gene_variant,,ENST00000572330,;MINK1,downstream_gene_variant,,ENST00000574453,;MINK1,downstream_gene_variant,,ENST00000571207,;MINK1,downstream_gene_variant,,ENST00000574871,;	-	ENSG00000205710	ENST00000381365	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C17orf107	HGNC	37238	protein_coding	YES	CCDS45591.1	ENSP00000370770	CQ107_HUMAN	.	UPI00001C0FE1	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGTACTGGGGGG	.	2	ESCA
TOB1	0	.	GRCh37	17	48940076	48940076	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*265delT	.	.	ENST00000499247	2/2	30	13	16	26	26	0	TOB1,3_prime_UTR_variant,,ENST00000499247,;TOB1,downstream_gene_variant,,ENST00000268957,;TOB1-AS1,upstream_gene_variant,,ENST00000416263,;TOB1-AS1,upstream_gene_variant,,ENST00000514358,;TOB1-AS1,upstream_gene_variant,,ENST00000523470,;TOB1,downstream_gene_variant,,ENST00000509385,;	-	ENSG00000141232	ENST00000499247	Transcript	3_prime_UTR_variant	1737	.	.	.	.	.	.	.	-1	TOB1	HGNC	11979	protein_coding	YES	CCDS11576.1	ENSP00000427695	TOB1_HUMAN	.	UPI00001370FB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTTATAAAAAA	.	2	ESCA
ZFP3	0	.	GRCh37	17	4996726	4996728	+	3'UTR	DEL	CTC	CTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*422_*424delTCC	.	.	ENST00000318833	2/2	100	62	38	64	64	0	ZFP3,3_prime_UTR_variant,,ENST00000318833,;	-	ENSG00000180787	ENST00000318833	Transcript	3_prime_UTR_variant	2263-2265	.	.	.	.	.	.	.	1	ZFP3	HGNC	12861	protein_coding	YES	CCDS11067.1	ENSP00000320347	ZFP3_HUMAN	.	UPI0000070244	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCCTTCTCCTCCC	.	3	ESCA
COX11	0	.	GRCh37	17	53039053	53039053	+	3'UTR	SNP	A	A	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1041T>G	.	.	ENST00000299335	4/4	37	28	9	32	32	0	COX11,3_prime_UTR_variant,,ENST00000299335,;TOM1L1,3_prime_UTR_variant,,ENST00000445275,;TOM1L1,3_prime_UTR_variant,,ENST00000348161,;TOM1L1,3_prime_UTR_variant,,ENST00000575882,;TOM1L1,downstream_gene_variant,,ENST00000574318,;COX11,downstream_gene_variant,,ENST00000571584,;TOM1L1,downstream_gene_variant,,ENST00000540336,;TOM1L1,downstream_gene_variant,,ENST00000536554,;TOM1L1,downstream_gene_variant,,ENST00000572158,;COX11,upstream_gene_variant,,ENST00000573912,;COX11,upstream_gene_variant,,ENST00000574989,;COX11,3_prime_UTR_variant,,ENST00000576370,;COX11,intron_variant,,ENST00000574821,;COX11,intron_variant,,ENST00000572558,;TOM1L1,downstream_gene_variant,,ENST00000574653,;TOM1L1,downstream_gene_variant,,ENST00000571319,;	C	ENSG00000166260	ENST00000299335	Transcript	3_prime_UTR_variant	2011	.	.	.	.	.	.	.	-1	COX11	HGNC	2261	protein_coding	YES	CCDS11583.1	ENSP00000299335	COX11_HUMAN	B4DEY8_HUMAN	UPI000013E580	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAAAGTCAA	.	5	ESCA
HLF	0	.	GRCh37	17	53400189	53400189	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1949A>T	.	.	ENST00000226067	4/4	14	9	5	16	16	0	HLF,3_prime_UTR_variant,,ENST00000573945,;HLF,3_prime_UTR_variant,,ENST00000575345,;HLF,3_prime_UTR_variant,,ENST00000226067,;HLF,downstream_gene_variant,,ENST00000572002,;HLF,downstream_gene_variant,,ENST00000430986,;RP11-515O17.3,downstream_gene_variant,,ENST00000576751,;HLF,downstream_gene_variant,,ENST00000575868,;HLF,downstream_gene_variant,,ENST00000575307,;HLF,downstream_gene_variant,,ENST00000573422,;HLF,downstream_gene_variant,,ENST00000570962,;	T	ENSG00000108924	ENST00000226067	Transcript	3_prime_UTR_variant	3310	.	.	.	.	.	.	.	1	HLF	HGNC	4977	protein_coding	YES	CCDS11585.1	ENSP00000226067	HLF_HUMAN	Q6FHS9_HUMAN,A8K1X8_HUMAN	UPI0000001C51	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATGAGGTTG	.	5	ESCA
TRIM25	0	.	GRCh37	17	54968084	54968085	+	3'UTR	DEL	AG	AG	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*976_*977delCT	.	.	ENST00000316881	9/9	59	33	26	37	37	0	TRIM25,3_prime_UTR_variant,,ENST00000316881,;TRIM25,downstream_gene_variant,,ENST00000537230,;MIR3614,downstream_gene_variant,,ENST00000581261,;RP11-670E13.5,intron_variant,,ENST00000574826,;TRIM25,non_coding_transcript_exon_variant,,ENST00000573108,;TRIM25,downstream_gene_variant,,ENST00000574234,;TRIM25,downstream_gene_variant,,ENST00000572021,;	-	ENSG00000121060	ENST00000316881	Transcript	3_prime_UTR_variant	2919-2920	.	.	.	.	.	.	.	-1	TRIM25	HGNC	12932	protein_coding	YES	CCDS11591.1	ENSP00000323889	TRI25_HUMAN	.	UPI00001AE6B8	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGGAAGAGAGG	.	3	ESCA
SCPEP1	0	.	GRCh37	17	55058513	55058513	+	Silent	SNP	C	C	A	rs376140010	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147C>A	p.%3D	p.A49A	ENST00000262288	2/13	76	43	32	48	48	0	SCPEP1,synonymous_variant,p.%3D,ENST00000572710,;SCPEP1,synonymous_variant,p.%3D,ENST00000262288,;SCPEP1,intron_variant,,ENST00000575395,;RP5-1107A17.4,upstream_gene_variant,,ENST00000572877,;SCPEP1,non_coding_transcript_exon_variant,,ENST00000573823,;SCPEP1,non_coding_transcript_exon_variant,,ENST00000571345,;SCPEP1,non_coding_transcript_exon_variant,,ENST00000571898,;SCPEP1,missense_variant,p.Leu38Ile,ENST00000575423,;SCPEP1,synonymous_variant,p.%3D,ENST00000576154,;SCPEP1,synonymous_variant,p.%3D,ENST00000572591,;	A	ENSG00000121064	ENST00000262288	Transcript	synonymous_variant	202	147	49	A	gcC/gcA	rs376140010,COSM473082	.	.	1	SCPEP1	HGNC	29507	protein_coding	YES	CCDS11593.1	ENSP00000262288	RISC_HUMAN	I3L506_HUMAN	UPI0000038BD2	.	.	.	2/13	.	hmmpanther:PTHR11802:SF3,hmmpanther:PTHR11802,Gene3D:3.40.50.1820,Pfam_domain:PF00450,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGCCTACAT	byCluster	5	ESCA
RNF43	0	.	GRCh37	17	56440667	56440667	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.551T>C	p.Val184Ala	p.V184A	ENST00000584437	4/9	60	44	15	31	31	0	RNF43,missense_variant,p.Val184Ala,ENST00000407977,;RNF43,missense_variant,p.Val143Ala,ENST00000583753,;RNF43,missense_variant,p.Val184Ala,ENST00000584437,;RNF43,missense_variant,p.Val143Ala,ENST00000500597,;RNF43,missense_variant,p.Val184Ala,ENST00000577716,;RNF43,missense_variant,p.Val57Ala,ENST00000577625,;RNF43,missense_variant,p.Val57Ala,ENST00000581868,;BZRAP1-AS1,intron_variant,,ENST00000583841,;RNF43,non_coding_transcript_exon_variant,,ENST00000582293,;	G	ENSG00000108375	ENST00000584437	Transcript	missense_variant	2507	551	184	V/A	gTg/gCg	.	.	.	-1	RNF43	HGNC	18505	protein_coding	YES	CCDS11607.1	ENSP00000463069	RNF43_HUMAN	.	UPI000022A469	.	tolerated(0.26)	probably_damaging(0.997)	4/9	.	hmmpanther:PTHR16200,hmmpanther:PTHR16200:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCACATGG	.	5	ESCA
VMP1	0	.	GRCh37	17	57917896	57917896	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*624T>C	.	.	ENST00000262291	12/12	43	35	8	22	22	0	VMP1,3_prime_UTR_variant,,ENST00000262291,;VMP1,downstream_gene_variant,,ENST00000536180,;VMP1,downstream_gene_variant,,ENST00000545362,;VMP1,downstream_gene_variant,,ENST00000591877,;VMP1,downstream_gene_variant,,ENST00000537567,;VMP1,downstream_gene_variant,,ENST00000539763,;MIR21,upstream_gene_variant,,ENST00000362134,;VMP1,downstream_gene_variant,,ENST00000591782,;VMP1,downstream_gene_variant,,ENST00000588617,;VMP1,non_coding_transcript_exon_variant,,ENST00000592790,;VMP1,downstream_gene_variant,,ENST00000592619,;VMP1,downstream_gene_variant,,ENST00000587470,;	C	ENSG00000062716	ENST00000262291	Transcript	3_prime_UTR_variant	2155	.	.	.	.	.	.	.	1	VMP1	HGNC	29559	protein_coding	YES	CCDS11619.1	ENSP00000262291	VMP1_HUMAN	K7ENU2_HUMAN,K7EMI0_HUMAN,K7EM96_HUMAN,K7EK01_HUMAN,D3DU01_HUMAN,B4DVV9_HUMAN	UPI0000037791	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGTGTATT	.	5	ESCA
C17orf64	0	.	GRCh37	17	58512851	58512851	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000269127	.	24	18	6	16	16	0	C17orf64,downstream_gene_variant,,ENST00000269127,;RPL12P38,non_coding_transcript_exon_variant,,ENST00000588627,;RPL12P38,upstream_gene_variant,,ENST00000471280,;	A	ENSG00000141371	ENST00000269127	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4069	1	C17orf64	HGNC	26990	protein_coding	YES	CCDS32698.2	ENSP00000269127	CQ064_HUMAN	K7EQ24_HUMAN	UPI0000161125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCGGCGCG	.	2	ESCA
SMARCD2	0	.	GRCh37	17	61910074	61910076	+	3'UTR	DEL	GAG	GAG	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GAG	GAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*222_*224delCTC	.	.	ENST00000448276	13/13	27	22	5	22	22	0	SMARCD2,3_prime_UTR_variant,,ENST00000450364,;SMARCD2,3_prime_UTR_variant,,ENST00000323347,;SMARCD2,3_prime_UTR_variant,,ENST00000448276,;SMARCD2,3_prime_UTR_variant,,ENST00000225742,;PSMC5,downstream_gene_variant,,ENST00000581882,;PSMC5,downstream_gene_variant,,ENST00000579708,;PSMC5,downstream_gene_variant,,ENST00000375812,;PSMC5,downstream_gene_variant,,ENST00000580864,;PSMC5,downstream_gene_variant,,ENST00000581842,;PSMC5,downstream_gene_variant,,ENST00000585123,;PSMC5,downstream_gene_variant,,ENST00000584320,;PSMC5,downstream_gene_variant,,ENST00000310144,;PSMC5,downstream_gene_variant,,ENST00000582130,;FTSJ3,upstream_gene_variant,,ENST00000580295,;PSMC5,downstream_gene_variant,,ENST00000582420,;SMARCD2,downstream_gene_variant,,ENST00000584483,;PSMC5,downstream_gene_variant,,ENST00000583283,;PSMC5,downstream_gene_variant,,ENST00000584657,;PSMC5,downstream_gene_variant,,ENST00000580265,;PSMC5,downstream_gene_variant,,ENST00000578570,;PSMC5,downstream_gene_variant,,ENST00000584536,;SMARCD2,downstream_gene_variant,,ENST00000578234,;PSMC5,downstream_gene_variant,,ENST00000580063,;PSMC5,downstream_gene_variant,,ENST00000579031,;PSMC5,downstream_gene_variant,,ENST00000581764,;SMARCD2,downstream_gene_variant,,ENST00000580054,;SMARCD2,downstream_gene_variant,,ENST00000581832,;PSMC5,downstream_gene_variant,,ENST00000584880,;SMARCD2,downstream_gene_variant,,ENST00000584400,;SMARCD2,downstream_gene_variant,,ENST00000577686,;PSMC5,downstream_gene_variant,,ENST00000579147,;PSMC5,downstream_gene_variant,,ENST00000585242,;	-	ENSG00000108604	ENST00000448276	Transcript	3_prime_UTR_variant	2084-2086	.	.	.	.	.	.	.	-1	SMARCD2	HGNC	11107	protein_coding	YES	CCDS45756.1	ENSP00000392617	SMRD2_HUMAN	J3KT18_HUMAN,J3KMX2_HUMAN	UPI0000D695F8	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGGGCAGAGGAGGC	.	3	ESCA
SMARCD2	0	.	GRCh37	17	61911556	61911556	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1054T>C	p.Tyr352His	p.Y352H	ENST00000448276	8/13	20	12	7	12	12	0	SMARCD2,missense_variant,p.Tyr93His,ENST00000450364,;SMARCD2,missense_variant,p.Tyr304His,ENST00000323347,;SMARCD2,missense_variant,p.Tyr352His,ENST00000448276,;SMARCD2,missense_variant,p.Tyr277His,ENST00000225742,;PSMC5,downstream_gene_variant,,ENST00000581882,;PSMC5,downstream_gene_variant,,ENST00000579708,;PSMC5,downstream_gene_variant,,ENST00000580864,;PSMC5,downstream_gene_variant,,ENST00000375812,;PSMC5,downstream_gene_variant,,ENST00000581842,;PSMC5,downstream_gene_variant,,ENST00000585123,;PSMC5,downstream_gene_variant,,ENST00000584320,;PSMC5,downstream_gene_variant,,ENST00000310144,;PSMC5,downstream_gene_variant,,ENST00000582130,;FTSJ3,upstream_gene_variant,,ENST00000580295,;SMARCD2,3_prime_UTR_variant,,ENST00000584400,;SMARCD2,non_coding_transcript_exon_variant,,ENST00000584483,;SMARCD2,non_coding_transcript_exon_variant,,ENST00000578234,;PSMC5,downstream_gene_variant,,ENST00000583283,;PSMC5,downstream_gene_variant,,ENST00000584657,;PSMC5,downstream_gene_variant,,ENST00000578570,;PSMC5,downstream_gene_variant,,ENST00000584536,;PSMC5,downstream_gene_variant,,ENST00000580063,;PSMC5,downstream_gene_variant,,ENST00000579031,;PSMC5,downstream_gene_variant,,ENST00000581764,;SMARCD2,downstream_gene_variant,,ENST00000580054,;SMARCD2,downstream_gene_variant,,ENST00000581832,;PSMC5,downstream_gene_variant,,ENST00000584880,;SMARCD2,downstream_gene_variant,,ENST00000577686,;PSMC5,downstream_gene_variant,,ENST00000579147,;PSMC5,downstream_gene_variant,,ENST00000585242,;	G	ENSG00000108604	ENST00000448276	Transcript	missense_variant	1320	1054	352	Y/H	Tac/Cac	.	.	.	-1	SMARCD2	HGNC	11107	protein_coding	YES	CCDS45756.1	ENSP00000392617	SMRD2_HUMAN	J3KT18_HUMAN,J3KMX2_HUMAN	UPI0000D695F8	.	tolerated(0.1)	benign(0.018)	8/13	.	hmmpanther:PTHR13844,hmmpanther:PTHR13844:SF2,Pfam_domain:PF02201,Gene3D:1.10.245.10,SMART_domains:SM00151,Superfamily_domains:SSF47592	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGTACTCCC	.	5	ESCA
APOH	0	.	GRCh37	17	64224221	64224221	+	Missense_Mutation	SNP	G	G	A	rs371962881	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.158C>T	p.Pro53Leu	p.P53L	ENST00000205948	2/8	66	30	35	61	61	0	APOH,missense_variant,p.Pro53Leu,ENST00000205948,;APOH,missense_variant,p.Pro53Leu,ENST00000577982,;APOH,5_prime_UTR_variant,,ENST00000581797,;	A	ENSG00000091583	ENST00000205948	Transcript	missense_variant	196	158	53	P/L	cCg/cTg	rs371962881	.	.	-1	APOH	HGNC	616	protein_coding	YES	CCDS11663.1	ENSP00000205948	APOH_HUMAN	J3QRN2_HUMAN,J3QLI0_HUMAN,D9IWP9_HUMAN	UPI0000125CAA	.	deleterious(0)	probably_damaging(0.916)	2/8	.	Superfamily_domains:SSF57535,SMART_domains:SM00032,Pfam_domain:PF00084,Gene3D:2.10.70.10,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF46,PROSITE_profiles:PS50923	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCGGCTTG	byFrequency|byCluster	5	ESCA
PSMD12	0	.	GRCh37	17	65337163	65337163	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1167C>T	p.%3D	p.S389S	ENST00000356126	11/11	26	18	8	30	30	0	PSMD12,synonymous_variant,p.%3D,ENST00000357146,;PSMD12,synonymous_variant,p.%3D,ENST00000356126,;PSMD12,3_prime_UTR_variant,,ENST00000584008,;PSMD12,non_coding_transcript_exon_variant,,ENST00000577724,;PSMD12,downstream_gene_variant,,ENST00000584289,;	A	ENSG00000197170	ENST00000356126	Transcript	synonymous_variant	1275	1167	389	S	tcC/tcT	COSM983251	.	.	-1	PSMD12	HGNC	9557	protein_coding	YES	CCDS11669.1	ENSP00000348442	PSD12_HUMAN	.	UPI0000132792	.	.	.	11/11	.	hmmpanther:PTHR10855:SF1,hmmpanther:PTHR10855,Pfam_domain:PF01399,Gene3D:1.10.10.10,SMART_domains:SM00088,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTCGGACTC	.	5	ESCA
TTYH2	0	.	GRCh37	17	72248476	72248476	+	Missense_Mutation	SNP	T	T	C	rs367606811	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1220T>C	p.Ile407Thr	p.I407T	ENST00000269346	11/14	56	30	25	46	46	0	TTYH2,missense_variant,p.Ile407Thr,ENST00000269346,;TTYH2,missense_variant,p.Ile86Thr,ENST00000441391,;TTYH2,missense_variant,p.Ile386Thr,ENST00000529107,;CTD-2514K5.4,downstream_gene_variant,,ENST00000583018,;TTYH2,downstream_gene_variant,,ENST00000534346,;TTYH2,3_prime_UTR_variant,,ENST00000526858,;TTYH2,non_coding_transcript_exon_variant,,ENST00000528152,;TTYH2,downstream_gene_variant,,ENST00000534039,;TTYH2,downstream_gene_variant,,ENST00000528128,;	C	ENSG00000141540	ENST00000269346	Transcript	missense_variant	1294	1220	407	I/T	aTc/aCc	rs367606811	.	.	1	TTYH2	HGNC	13877	protein_coding	YES	CCDS32717.1	ENSP00000269346	TTYH2_HUMAN	.	UPI00002001AA	.	deleterious(0.04)	benign(0.05)	11/14	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12424:SF6,hmmpanther:PTHR12424,Pfam_domain:PF04906	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGATCTGTG	byCluster	5	ESCA
GPR142	0	.	GRCh37	17	72363813	72363813	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.169A>G	p.Arg57Gly	p.R57G	ENST00000335666	1/4	47	18	29	30	30	0	GPR142,missense_variant,p.Arg57Gly,ENST00000335666,;GPR142,missense_variant,p.Arg57Gly,ENST00000585308,;GPR142,missense_variant,p.Arg57Gly,ENST00000582579,;	G	ENSG00000257008	ENST00000335666	Transcript	missense_variant	217	169	57	R/G	Agg/Ggg	.	.	.	1	GPR142	HGNC	20088	protein_coding	YES	CCDS11698.1	ENSP00000335158	GP142_HUMAN	.	UPI00001AA7F1	.	deleterious_low_confidence(0)	possibly_damaging(0.587)	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGAGGTCT	.	5	ESCA
TMEM256-PLSCR3	0	.	GRCh37	17	7293585	7293585	+	3'UTR	DEL	C	C	-	rs558397818	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*119delG	.	.	ENST00000535512	11/11	34	18	16	15	15	0	TMEM256-PLSCR3,3_prime_UTR_variant,,ENST00000535512,;TMEM256-PLSCR3,3_prime_UTR_variant,,ENST00000576201,;TMEM256-PLSCR3,3_prime_UTR_variant,,ENST00000574401,;TMEM256-PLSCR3,3_prime_UTR_variant,,ENST00000575434,;TMEM256-PLSCR3,3_prime_UTR_variant,,ENST00000576362,;TMEM256-PLSCR3,3_prime_UTR_variant,,ENST00000324822,;TMEM256-PLSCR3,downstream_gene_variant,,ENST00000573213,;TMEM256-PLSCR3,downstream_gene_variant,,ENST00000571802,;TMEM256-PLSCR3,downstream_gene_variant,,ENST00000571078,;TNK1,downstream_gene_variant,,ENST00000576812,;TNK1,downstream_gene_variant,,ENST00000311668,;TNK1,downstream_gene_variant,,ENST00000570896,;TNK1,downstream_gene_variant,,ENST00000576716,;TMEM256-PLSCR3,3_prime_UTR_variant,,ENST00000573070,;C17orf61-PLSCR3,3_prime_UTR_variant,,ENST00000573331,;C17orf61-PLSCR3,3_prime_UTR_variant,,ENST00000570600,;TMEM256-PLSCR3,non_coding_transcript_exon_variant,,ENST00000571541,;TMEM256-PLSCR3,non_coding_transcript_exon_variant,,ENST00000575543,;TMEM256-PLSCR3,non_coding_transcript_exon_variant,,ENST00000573774,;TNK1,downstream_gene_variant,,ENST00000576136,;TNK1,downstream_gene_variant,,ENST00000577009,;C17orf61-PLSCR3,downstream_gene_variant,,ENST00000571125,;C17orf61-PLSCR3,downstream_gene_variant,,ENST00000570569,;	-	ENSG00000187838	ENST00000535512	Transcript	3_prime_UTR_variant	2025	.	.	.	.	rs558397818	.	.	-1	TMEM256-PLSCR3	HGNC	49186	protein_coding	YES	CCDS42253.1	ENSP00000438547	PLS3_HUMAN	I3L4F5_HUMAN	UPI000006FF67	.	.	.	11/11	.	.	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATGGGGCCCCCC	byFrequency|by1000G	2	ESCA
GGA3	0	.	GRCh37	17	73234468	73234470	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2062_2064delGAG	p.Glu688del	p.E688del	ENST00000245541	17/17	40	22	18	23	23	0	GGA3,inframe_deletion,p.Glu616del,ENST00000582717,;GGA3,inframe_deletion,p.Glu688del,ENST00000245541,;GGA3,inframe_deletion,p.Glu655del,ENST00000351904,;GGA3,inframe_deletion,p.Glu566del,ENST00000538886,;GGA3,3_prime_UTR_variant,,ENST00000578208,;GGA3,intron_variant,,ENST00000578348,;GGA3,intron_variant,,ENST00000582486,;GGA3,intron_variant,,ENST00000583282,;NUP85,downstream_gene_variant,,ENST00000245544,;NUP85,downstream_gene_variant,,ENST00000579324,;GGA3,downstream_gene_variant,,ENST00000537686,;NUP85,downstream_gene_variant,,ENST00000579298,;NUP85,downstream_gene_variant,,ENST00000540768,;NUP85,downstream_gene_variant,,ENST00000579900,;NUP85,downstream_gene_variant,,ENST00000583070,;NUP85,downstream_gene_variant,,ENST00000447371,;GGA3,downstream_gene_variant,,ENST00000580799,;NUP85,downstream_gene_variant,,ENST00000579838,;NUP85,downstream_gene_variant,,ENST00000541827,;GGA3,splice_region_variant,,ENST00000582200,;GGA3,splice_region_variant,,ENST00000578275,;GGA3,splice_region_variant,,ENST00000584550,;GGA3,splice_region_variant,,ENST00000578773,;GGA3,splice_region_variant,,ENST00000584978,;GGA3,splice_region_variant,,ENST00000537584,;GGA3,intron_variant,,ENST00000580646,;NUP85,downstream_gene_variant,,ENST00000584155,;GGA3,downstream_gene_variant,,ENST00000583667,;GGA3,downstream_gene_variant,,ENST00000582376,;GGA3,downstream_gene_variant,,ENST00000582821,;NUP85,downstream_gene_variant,,ENST00000578987,;NUP85,downstream_gene_variant,,ENST00000578294,;GGA3,downstream_gene_variant,,ENST00000578896,;GGA3,downstream_gene_variant,,ENST00000582232,;GGA3,downstream_gene_variant,,ENST00000584243,;NUP85,downstream_gene_variant,,ENST00000581104,;GGA3,downstream_gene_variant,,ENST00000577435,;	-	ENSG00000125447	ENST00000245541	Transcript	inframe_deletion	2279-2281	2062-2064	688	E/-	GAG/-	.	.	.	-1	GGA3	HGNC	17079	protein_coding	YES	CCDS11717.1	ENSP00000245541	GGA3_HUMAN	J3KSG3_HUMAN,B7Z456_HUMAN	UPI000012B3DF	.	.	.	17/17	.	Superfamily_domains:SSF49348,SMART_domains:SM00809,Pfam_domain:PF02883,Gene3D:2.60.40.1230,hmmpanther:PTHR13856:SF34,hmmpanther:PTHR13856,PROSITE_profiles:PS50180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CACCTTCTCCTGTG	.	2	ESCA
KIAA0195	0	.	GRCh37	17	73487189	73487189	+	Silent	SNP	G	G	A	rs142602580	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1188G>A	p.%3D	p.T396T	ENST00000314256	12/32	75	51	23	55	55	0	KIAA0195,synonymous_variant,p.%3D,ENST00000580918,;KIAA0195,synonymous_variant,p.%3D,ENST00000579208,;KIAA0195,synonymous_variant,p.%3D,ENST00000314256,;KIAA0195,synonymous_variant,p.%3D,ENST00000581252,;KIAA0195,synonymous_variant,p.%3D,ENST00000375248,;KIAA0195,upstream_gene_variant,,ENST00000578853,;KIAA0195,downstream_gene_variant,,ENST00000577380,;KIAA0195,downstream_gene_variant,,ENST00000582186,;KIAA0195,downstream_gene_variant,,ENST00000581519,;KIAA0195,downstream_gene_variant,,ENST00000580416,;KIAA0195,downstream_gene_variant,,ENST00000583795,;KIAA0195,non_coding_transcript_exon_variant,,ENST00000585105,;KIAA0195,non_coding_transcript_exon_variant,,ENST00000579241,;KIAA0195,non_coding_transcript_exon_variant,,ENST00000581085,;KIAA0195,downstream_gene_variant,,ENST00000580849,;KIAA0195,upstream_gene_variant,,ENST00000579898,;KIAA0195,upstream_gene_variant,,ENST00000583071,;KIAA0195,upstream_gene_variant,,ENST00000583296,;KIAA0195,upstream_gene_variant,,ENST00000581723,;KIAA0195,downstream_gene_variant,,ENST00000579707,;KIAA0195,downstream_gene_variant,,ENST00000580441,;KIAA0195,upstream_gene_variant,,ENST00000581867,;KIAA0195,downstream_gene_variant,,ENST00000584383,;KIAA0195,upstream_gene_variant,,ENST00000578624,;KIAA0195,upstream_gene_variant,,ENST00000582843,;	A	ENSG00000177728	ENST00000314256	Transcript	synonymous_variant	1582	1188	396	T	acG/acA	rs142602580	.	.	1	KIAA0195	HGNC	28983	protein_coding	YES	CCDS32732.1	ENSP00000313885	K0195_HUMAN	J3QS17_HUMAN,J3QRT3_HUMAN,J3QLM7_HUMAN,J3KT63_HUMAN,J3KRU7_HUMAN	UPI0000139439	.	.	.	12/32	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13219:SF6,hmmpanther:PTHR13219	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAACGCTGAG	byCluster	5	ESCA
RECQL5	0	.	GRCh37	17	73623721	73623723	+	In_Frame_Del	DEL	TCT	TCT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TCT	TCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2855_2857delAGA	p.Lys952del	p.K952del	ENST00000317905	19/20	34	22	12	10	10	0	RECQL5,inframe_deletion,p.Lys925del,ENST00000423245,;RECQL5,inframe_deletion,p.Lys952del,ENST00000317905,;RECQL5,intron_variant,,ENST00000581825,;RECQL5,downstream_gene_variant,,ENST00000578201,;RECQL5,downstream_gene_variant,,ENST00000580707,;RECQL5,downstream_gene_variant,,ENST00000582548,;RECQL5,non_coding_transcript_exon_variant,,ENST00000443199,;MYO15B,downstream_gene_variant,,ENST00000577948,;MYO15B,downstream_gene_variant,,ENST00000580262,;RECQL5,downstream_gene_variant,,ENST00000583673,;MYO15B,downstream_gene_variant,,ENST00000580096,;MYO15B,downstream_gene_variant,,ENST00000580414,;MYO15B,downstream_gene_variant,,ENST00000578382,;MYO15B,downstream_gene_variant,,ENST00000578220,;RECQL5,non_coding_transcript_exon_variant,,ENST00000578865,;MYO15B,downstream_gene_variant,,ENST00000577986,;RECQL5,downstream_gene_variant,,ENST00000585205,;RECQL5,downstream_gene_variant,,ENST00000582464,;RECQL5,downstream_gene_variant,,ENST00000579265,;	-	ENSG00000108469	ENST00000317905	Transcript	inframe_deletion	3015-3017	2855-2857	952-953	KT/T	aAGAcc/acc	.	.	.	-1	RECQL5	HGNC	9950	protein_coding	YES	CCDS42380.1	ENSP00000317636	RECQ5_HUMAN	Q9BW80_HUMAN,Q9BSD6_HUMAN,J3QLU0_HUMAN,J3KTQ2_HUMAN	UPI0000133477	.	.	.	19/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGAGGTCTTCTGA	.	2	ESCA
ZBTB4	0	.	GRCh37	17	7369187	7369187	+	Missense_Mutation	SNP	C	C	T	rs770942130	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934G>A	p.Ala312Thr	p.A312T	ENST00000311403	3/4	113	93	20	43	43	0	ZBTB4,missense_variant,p.Ala312Thr,ENST00000311403,;ZBTB4,missense_variant,p.Ala312Thr,ENST00000380599,;	T	ENSG00000174282	ENST00000311403	Transcript	missense_variant	1274	934	312	A/T	Gcg/Acg	rs770942130	.	.	-1	ZBTB4	HGNC	23847	protein_coding	YES	CCDS11107.1	ENSP00000307858	ZBTB4_HUMAN	B3KVD4_HUMAN	UPI00001A9C9A	.	.	possibly_damaging(0.821)	3/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24397,hmmpanther:PTHR24397:SF0,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCGCGCACA	byFrequency	5	ESCA
PRCD	0	.	GRCh37	17	74540281	74540281	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000586148	.	17	12	5	13	13	0	CYGB,intron_variant,,ENST00000589145,;PRCD,downstream_gene_variant,,ENST00000592014,;PRCD,downstream_gene_variant,,ENST00000586148,;RP11-666A8.8,downstream_gene_variant,,ENST00000589963,;PRCD,non_coding_transcript_exon_variant,,ENST00000591317,;PRCD,non_coding_transcript_exon_variant,,ENST00000465808,;PRCD,non_coding_transcript_exon_variant,,ENST00000397633,;PRCD,non_coding_transcript_exon_variant,,ENST00000592432,;PRCD,intron_variant,,ENST00000587289,;PRCD,intron_variant,,ENST00000592340,;PRCD,intron_variant,,ENST00000587813,;PRCD,upstream_gene_variant,,ENST00000593023,;PRCD,downstream_gene_variant,,ENST00000590555,;PRCD,upstream_gene_variant,,ENST00000587063,;PRCD,non_coding_transcript_exon_variant,,ENST00000397630,;	A	ENSG00000214140	ENST00000586148	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	812	1	PRCD	HGNC	32528	protein_coding	YES	CCDS42382.1	ENSP00000465932	PRCD_HUMAN	.	UPI000047DE08	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCCCGTGCCT	.	2	ESCA
CD68	0	.	GRCh37	17	7482902	7482903	+	5'UTR	DEL	TT	TT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-93_-92delTT	.	.	ENST00000250092	1/6	94	67	27	40	40	0	CD68,5_prime_UTR_variant,,ENST00000250092,;CD68,5_prime_UTR_variant,,ENST00000380498,;EIF4A1,downstream_gene_variant,,ENST00000584784,;EIF4A1,downstream_gene_variant,,ENST00000583802,;CD68,upstream_gene_variant,,ENST00000584180,;MPDU1,upstream_gene_variant,,ENST00000396501,;EIF4A1,downstream_gene_variant,,ENST00000380512,;EIF4A1,downstream_gene_variant,,ENST00000577929,;MPDU1,upstream_gene_variant,,ENST00000250124,;EIF4A1,downstream_gene_variant,,ENST00000584860,;MPDU1,upstream_gene_variant,,ENST00000579445,;EIF4A1,downstream_gene_variant,,ENST00000582169,;EIF4A1,downstream_gene_variant,,ENST00000578495,;EIF4A1,downstream_gene_variant,,ENST00000578754,;EIF4A1,downstream_gene_variant,,ENST00000293831,;CD68,upstream_gene_variant,,ENST00000584502,;EIF4A1,downstream_gene_variant,,ENST00000581770,;MPDU1,upstream_gene_variant,,ENST00000581380,;MPDU1,upstream_gene_variant,,ENST00000582151,;MPDU1,upstream_gene_variant,,ENST00000584378,;MPDU1,upstream_gene_variant,,ENST00000585217,;EIF4A1,downstream_gene_variant,,ENST00000581384,;EIF4A1,downstream_gene_variant,,ENST00000585024,;MPDU1,upstream_gene_variant,,ENST00000423172,;EIF4A1,downstream_gene_variant,,ENST00000582746,;EIF4A1,downstream_gene_variant,,ENST00000577269,;EIF4A1,downstream_gene_variant,,ENST00000583389,;SNORD10,downstream_gene_variant,,ENST00000459579,;SNORA48,downstream_gene_variant,,ENST00000386847,;SNORA67,downstream_gene_variant,,ENST00000384423,;AC113189.5,downstream_gene_variant,,ENST00000417897,;AC113189.5,downstream_gene_variant,,ENST00000572046,;AC113189.5,downstream_gene_variant,,ENST00000415124,;AC113189.5,downstream_gene_variant,,ENST00000573187,;SNORA67,non_coding_transcript_exon_variant,,ENST00000581621,;SENP3-EIF4A1,downstream_gene_variant,,ENST00000579777,;EIF4A1,downstream_gene_variant,,ENST00000581808,;EIF4A1,downstream_gene_variant,,ENST00000577738,;EIF4A1,downstream_gene_variant,,ENST00000582213,;MPDU1,upstream_gene_variant,,ENST00000575256,;MPDU1,upstream_gene_variant,,ENST00000580834,;EIF4A1,downstream_gene_variant,,ENST00000577731,;EIF4A1,downstream_gene_variant,,ENST00000580461,;EIF4A1,downstream_gene_variant,,ENST00000578324,;EIF4A1,downstream_gene_variant,,ENST00000581841,;MPDU1,upstream_gene_variant,,ENST00000585188,;EIF4A1,downstream_gene_variant,,ENST00000584901,;EIF4A1,downstream_gene_variant,,ENST00000581544,;MPDU1,upstream_gene_variant,,ENST00000574558,;MPDU1,upstream_gene_variant,,ENST00000572836,;MPDU1,upstream_gene_variant,,ENST00000571391,;EIF4A1,downstream_gene_variant,,ENST00000583899,;MPDU1,upstream_gene_variant,,ENST00000570458,;EIF4A1,downstream_gene_variant,,ENST00000584798,;MPDU1,upstream_gene_variant,,ENST00000571822,;MPDU1,upstream_gene_variant,,ENST00000576066,;EIF4A1,downstream_gene_variant,,ENST00000580888,;MPDU1,upstream_gene_variant,,ENST00000584479,;EIF4A1,downstream_gene_variant,,ENST00000578476,;EIF4A1,downstream_gene_variant,,ENST00000583217,;MPDU1,upstream_gene_variant,,ENST00000577088,;EIF4A1,downstream_gene_variant,,ENST00000580886,;EIF4A1,downstream_gene_variant,,ENST00000582848,;MPDU1,upstream_gene_variant,,ENST00000576272,;EIF4A1,downstream_gene_variant,,ENST00000584054,;MPDU1,upstream_gene_variant,,ENST00000572719,;EIF4A1,downstream_gene_variant,,ENST00000584712,;MPDU1,upstream_gene_variant,,ENST00000580708,;MPDU1,upstream_gene_variant,,ENST00000581886,;EIF4A1,downstream_gene_variant,,ENST00000396527,;EIF4A1,downstream_gene_variant,,ENST00000579085,;EIF4A1,downstream_gene_variant,,ENST00000578569,;MPDU1,upstream_gene_variant,,ENST00000359822,;EIF4A1,downstream_gene_variant,,ENST00000579139,;MPDU1,upstream_gene_variant,,ENST00000578267,;EIF4A1,downstream_gene_variant,,ENST00000582050,;MPDU1,upstream_gene_variant,,ENST00000572936,;	-	ENSG00000129226	ENST00000250092	Transcript	5_prime_UTR_variant	118-119	.	.	.	.	.	.	.	1	CD68	HGNC	1693	protein_coding	YES	CCDS11114.1	ENSP00000250092	CD68_HUMAN	B4DNT7_HUMAN	UPI000013CCA1	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGAGACTTTCATT	.	3	ESCA
SEC14L1	0	.	GRCh37	17	75208083	75208083	+	Missense_Mutation	SNP	G	G	A	rs777176254	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1663G>A	p.Val555Met	p.V555M	ENST00000392476	17/20	34	27	7	26	26	0	SEC14L1,missense_variant,p.Val79Met,ENST00000588488,;SEC14L1,missense_variant,p.Val555Met,ENST00000436233,;SEC14L1,missense_variant,p.Val521Met,ENST00000591437,;SEC14L1,missense_variant,p.Val555Met,ENST00000585618,;SEC14L1,missense_variant,p.Val555Met,ENST00000413679,;SEC14L1,missense_variant,p.Val555Met,ENST00000392476,;SEC14L1,missense_variant,p.Val555Met,ENST00000443798,;SEC14L1,missense_variant,p.Val555Met,ENST00000430767,;SEC14L1,missense_variant,p.Val521Met,ENST00000431431,;SEC14L1,upstream_gene_variant,,ENST00000588721,;SEC14L1,non_coding_transcript_exon_variant,,ENST00000591413,;SEC14L1,non_coding_transcript_exon_variant,,ENST00000587491,;	A	ENSG00000129657	ENST00000392476	Transcript	missense_variant	2222	1663	555	V/M	Gtg/Atg	rs777176254,COSM1522216	.	.	1	SEC14L1	HGNC	10698	protein_coding	YES	CCDS42385.1	ENSP00000376268	S14L1_HUMAN	K7EQK4_HUMAN,K7ELU0_HUMAN,K7ELM0_HUMAN,K7EJ08_HUMAN,B4E0D1_HUMAN,B4DEZ7_HUMAN	UPI00006AB82A	.	deleterious(0.01)	benign(0.446)	17/20	.	Superfamily_domains:0041713,Gene3D:3.40.525.10,hmmpanther:PTHR23324:SF51,hmmpanther:PTHR23324,PROSITE_profiles:PS50866	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGACGTGTGC	.	5	ESCA
TP53	0	.	GRCh37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	rs28934574	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	8/11	55	32	22	36	36	0	TP53,missense_variant,p.Arg282Trp,ENST00000420246,;TP53,missense_variant,p.Arg282Trp,ENST00000269305,;TP53,missense_variant,p.Arg150Trp,ENST00000509690,;TP53,missense_variant,p.Arg282Trp,ENST00000359597,;TP53,missense_variant,p.Arg282Trp,ENST00000445888,;TP53,missense_variant,p.Arg282Trp,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1034	844	282	R/W	Cgg/Tgg	CM920678,CM056413,rs28934574,TP53_g.13824C>A,TP53_g.13824C>G,TP53_g.13824C>T,TP53_g.13824del,COSM43813,COSM10704,COSM10992,COSM44918,COSM99925,COSM99934,COSM3378339,COSM3675520,COSM1725698,COSM1636702	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.997)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	likely_benign,pathogenic	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1	25105660,25404506,22536362	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R282W|c.844C>T|49,SITE|p.R282W|c.844C>T|86,SITE|p.R282W|c.844C>T|450,SITE|p.R282W|c.844C>T|58,CODON|p.0?|c.1_1182del1182|6,CODON|p.R282R|c.846G>A|4,CODON|p.R282Q|c.845G>A|5,CODON|p.R282Q|c.845G>A|26,CODON|p.R282L|c.845G>T|3,CODON|p.R282Q|c.845G>A|3,CODON|p.R282P|c.845G>C|17,CODON|p.R282W|c.843_844CC>TT|10,BUFFER|p.E285E|c.855G>A|3,BUFFER|p.E285V|c.854A>T|3,BUFFER|p.E285G|c.854A>G|4,BUFFER|p.E285V|c.854A>T|17,BUFFER|p.E285V|c.854A>T|4,BUFFER|p.E285K|c.853G>A|19,BUFFER|p.E285*|c.853G>T|5,BUFFER|p.E285K|c.853G>A|114,BUFFER|p.E285*|c.853G>T|9,BUFFER|p.E285Q|c.853G>C|4,BUFFER|p.E285*|c.853G>T|25,BUFFER|p.E285K|c.853G>A|5,BUFFER|p.E285K|c.853G>A|9,BUFFER|p.T284T|c.852A>T|3,BUFFER|p.T284A|c.850A>G|3,BUFFER|p.T284P|c.850A>C|8,BUFFER|p.R283fs*62|c.847delC|3,BUFFER|p.R283P|c.848G>C|4,BUFFER|p.R283H|c.848G>A|12,BUFFER|p.R283L|c.848G>T|4,BUFFER|p.R283P|c.848G>C|24,BUFFER|p.R283C|c.847C>T|19,BUFFER|p.R282G|c.844C>G|5,BUFFER|p.R282G|c.844C>G|3,BUFFER|p.R282R|c.844C>A|3,BUFFER|p.R282G|c.844C>G|29,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12,BUFFER|p.D281V|c.842A>T|5,BUFFER|p.D281G|c.842A>G|10,BUFFER|p.D281H|c.841G>C|6,BUFFER|p.D281H|c.841G>C|28,BUFFER|p.D281H|c.841G>C|3,BUFFER|p.D281H|c.841G>C|4,BUFFER|p.D281Y|c.841G>T|7,BUFFER|p.D281N|c.841G>A|7,BUFFER|p.D281N|c.841G>A|3,BUFFER|p.D281Y|c.841G>T|13,BUFFER|p.D281Y|c.841G>T|4,BUFFER|p.D281N|c.841G>A|27,BUFFER|p.R280R|c.840A>G|3,BUFFER|p.R280S|c.840A>T|11,BUFFER|p.R280S|c.840A>C|6,BUFFER|p.R280T|c.839G>C|63,BUFFER|p.R280T|c.839G>C|4,BUFFER|p.R280I|c.839G>T|17,BUFFER|p.R280K|c.839G>A|17,BUFFER|p.R280K|c.839G>A|6,BUFFER|p.R280I|c.839G>T|4,BUFFER|p.R280K|c.839G>A|57,BUFFER|p.R280I|c.839G>T|3,BUFFER|p.R280T|c.839G>C|10,BUFFER|p.R280K|c.839G>A|11,BUFFER|p.R280*|c.838A>T|12,BUFFER|p.R280G|c.838A>G|6,BUFFER|p.R280G|c.838A>G|3,BUFFER|p.R280G|c.838A>G|23,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279E|c.836G>A|4,BUFFER|p.G279E|c.836G>A|34,BUFFER|p.G279V|c.836G>T|3,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278fs*67|c.833delC|3,BUFFER|p.P278F|c.832_833CC>TT|3,BUFFER|p.P278H|c.833C>A|15,BUFFER|p.P278R|c.833C>G|5,BUFFER|p.P278R|c.833C>G|30,BUFFER|p.P278R|c.833C>G|3,BUFFER|p.P278H|c.833C>A|3,BUFFER|p.P278L|c.833C>T|3,BUFFER|p.P278L|c.833C>T|11,BUFFER|p.P278L|c.833C>T|65,BUFFER|p.P278L|c.833C>T|8,BUFFER|p.P278fs*67|c.832delC|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCCGGTCTC	byFrequency|byCluster	5	ESCA
TP53	0	.	GRCh37	17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	rs121912666	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	6/11	78	43	34	25	25	0	TP53,missense_variant,p.Tyr220Cys,ENST00000413465,;TP53,missense_variant,p.Tyr220Cys,ENST00000420246,;TP53,missense_variant,p.Tyr220Cys,ENST00000269305,;TP53,missense_variant,p.Tyr88Cys,ENST00000509690,;TP53,missense_variant,p.Tyr220Cys,ENST00000359597,;TP53,missense_variant,p.Tyr127Cys,ENST00000514944,;TP53,missense_variant,p.Tyr220Cys,ENST00000445888,;TP53,missense_variant,p.Tyr220Cys,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	849	659	220	Y/C	tAt/tGt	CM015378,CM951227,rs121912666,TP53_g.12728A>T,TP53_g.12728A>C,TP53_g.12728A>G,COSM10758,COSM43850,COSM1564197,COSM99720,COSM251427,COSM1564198,COSM251426,COSM99718,COSM1564199,COSM3355993,COSM3675523,COSM1644277,COSM3675522,COSM99719,COSM251428,COSM1564200	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Y220C|c.659A>G|264,SITE|p.Y220C|c.659A>G|63,SITE|p.Y127C|c.380A>G|63,SITE|p.Y220C|c.659A>G|25,SITE|p.Y220C|c.659A>G|61,SITE|p.Y220C|c.659A>G|33,CODON|p.0?|c.1_1182del1182|6,CODON|p.Y220*|c.660T>G|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y127S|c.380A>C|4,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y220S|c.659A>C|13,BUFFER|p.E224K|c.670G>A|4,BUFFER|p.E224*|c.670G>T|5,BUFFER|p.P223L|c.668C>T|3,BUFFER|p.P222P|c.666G>C|3,BUFFER|p.P222L|c.665C>T|4,BUFFER|p.P222T|c.664C>A|3,BUFFER|p.E221G|c.662A>G|3,BUFFER|p.E221fs*4|c.660_661insN|3,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E128*|c.382G>T|6,BUFFER|p.E221*|c.661G>T|10,BUFFER|p.?|c.252+10T>A|3,BUFFER|p.Y220N|c.658T>A|16,BUFFER|p.?|c.252+10T>C|4,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220H|c.658T>C|13,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.Y127H|c.379T>C|4,BUFFER|p.Y127N|c.379T>A|3,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.P219P|c.657C>T|3,BUFFER|p.Y220fs*27|c.655delC|4,BUFFER|p.V218delV|c.652_654delGTG|3,BUFFER|p.P219S|c.655C>T|4,BUFFER|p.V218G|c.653T>G|6,BUFFER|p.V218A|c.653T>C|3,BUFFER|p.V218E|c.653T>A|8,BUFFER|p.V218M|c.652G>A|7,BUFFER|p.V217A|c.650T>C|5,BUFFER|p.V217G|c.650T>G|4,BUFFER|p.V217E|c.650T>A|3,BUFFER|p.V218delV|c.646_648delGTG|8	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCATAGGGC	byFrequency|byCluster	5	ESCA
TNRC6C	0	.	GRCh37	17	76100682	76100682	+	Missense_Mutation	SNP	C	C	T	rs181099354	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4937C>T	p.Ala1646Val	p.A1646V	ENST00000335749	21/21	34	25	9	18	18	0	TNRC6C,missense_variant,p.Ala1610Val,ENST00000301624,;TNRC6C,missense_variant,p.Ala1646Val,ENST00000544502,;TNRC6C,missense_variant,p.Ala1610Val,ENST00000588061,;TNRC6C,missense_variant,p.Ala1646Val,ENST00000588847,;TNRC6C,missense_variant,p.Ala1646Val,ENST00000335749,;TNRC6C,missense_variant,p.Ala1610Val,ENST00000541771,;TNRC6C-AS1,downstream_gene_variant,,ENST00000589217,;TNRC6C-AS1,downstream_gene_variant,,ENST00000374976,;TNRC6C-AS1,downstream_gene_variant,,ENST00000592939,;TNRC6C,downstream_gene_variant,,ENST00000592566,;AC021593.1,upstream_gene_variant,,ENST00000544529,;	T	ENSG00000078687	ENST00000335749	Transcript	missense_variant	5506	4937	1646	A/V	gCg/gTg	rs181099354	.	.	1	TNRC6C	HGNC	29318	protein_coding	YES	CCDS45799.1	ENSP00000336783	.	K7ELY5_HUMAN,K7EKN9_HUMAN,G3XAB8_HUMAN	UPI0000EE5F80	.	deleterious(0.02)	benign(0.294)	21/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF9	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCGCGTCCA	byCluster|by1000G	5	ESCA
TMC8	0	.	GRCh37	17	76127679	76127679	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10C>T	p.Pro4Ser	p.P4S	ENST00000318430	2/16	15	11	3	9	9	0	TMC8,missense_variant,p.Pro4Ser,ENST00000318430,;TMC8,missense_variant,p.Pro4Ser,ENST00000590799,;TMC6,intron_variant,,ENST00000322914,;TMC8,intron_variant,,ENST00000589691,;TMC6,upstream_gene_variant,,ENST00000592063,;TMC6,upstream_gene_variant,,ENST00000592594,;TMC8,downstream_gene_variant,,ENST00000590426,;TMC6,upstream_gene_variant,,ENST00000306591,;TMC6,upstream_gene_variant,,ENST00000392467,;TMC6,upstream_gene_variant,,ENST00000590602,;TMC6,upstream_gene_variant,,ENST00000589553,;TMC6,upstream_gene_variant,,ENST00000322933,;TMC6,upstream_gene_variant,,ENST00000589271,;TMC6,downstream_gene_variant,,ENST00000587480,;TMC8,upstream_gene_variant,,ENST00000590184,;TMC8,upstream_gene_variant,,ENST00000592399,;TMC6,upstream_gene_variant,,ENST00000586126,;TMC8,upstream_gene_variant,,ENST00000591983,;TMC6,upstream_gene_variant,,ENST00000591594,;TMC6,upstream_gene_variant,,ENST00000593044,;TMC6,upstream_gene_variant,,ENST00000588087,;TMC6,upstream_gene_variant,,ENST00000586697,;TMC6,upstream_gene_variant,,ENST00000590162,;TMC6,upstream_gene_variant,,ENST00000588792,;	T	ENSG00000167895	ENST00000318430	Transcript	missense_variant	384	10	4	P/S	Ccg/Tcg	.	.	.	1	TMC8	HGNC	20474	protein_coding	YES	CCDS32749.1	ENSP00000325561	TMC8_HUMAN	B3KXZ8_HUMAN	UPI00000747D3	.	tolerated_low_confidence(0.35)	benign(0)	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|VARSCANS	TGCTGCCGCGG	.	3	ESCA
ENPP7	0	.	GRCh37	17	77710926	77710926	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1113T>C	p.%3D	p.P371P	ENST00000328313	4/6	54	35	19	26	26	0	ENPP7,synonymous_variant,p.%3D,ENST00000328313,;ENPP7,synonymous_variant,p.%3D,ENST00000576512,;	C	ENSG00000182156	ENST00000328313	Transcript	synonymous_variant	1334	1113	371	P	ccT/ccC	.	.	.	1	ENPP7	HGNC	23764	protein_coding	YES	CCDS11763.1	ENSP00000332656	ENPP7_HUMAN	I3L3G5_HUMAN	UPI00001983C8	.	.	.	4/6	.	hmmpanther:PTHR10151:SF63,hmmpanther:PTHR10151,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F373L|c.1119C>A|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCTAGCTT	.	5	ESCA
CCDC40	0	.	GRCh37	17	78032417	78032417	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1284G>C	p.Glu428Asp	p.E428D	ENST00000397545	8/20	61	30	30	22	22	0	CCDC40,missense_variant,p.Glu428Asp,ENST00000397545,;CCDC40,missense_variant,p.Glu428Asp,ENST00000374876,;CCDC40,missense_variant,p.Glu428Asp,ENST00000269318,;CCDC40,missense_variant,p.Glu428Asp,ENST00000374877,;CCDC40,upstream_gene_variant,,ENST00000571028,;CCDC40,non_coding_transcript_exon_variant,,ENST00000574799,;	C	ENSG00000141519	ENST00000397545	Transcript	missense_variant	1311	1284	428	E/D	gaG/gaC	.	.	.	1	CCDC40	HGNC	26090	protein_coding	YES	CCDS42395.1	ENSP00000380679	CCD40_HUMAN	I3L2X6_HUMAN,I3L292_HUMAN	UPI0000201739	.	tolerated(0.14)	benign(0.029)	8/20	.	hmmpanther:PTHR16275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGGAGAGGAT	.	5	ESCA
GAA	0	.	GRCh37	17	78085835	78085835	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1690T>C	p.Phe564Leu	p.F564L	ENST00000302262	12/20	49	35	14	24	24	0	GAA,missense_variant,p.Phe564Leu,ENST00000390015,;GAA,missense_variant,p.Phe564Leu,ENST00000302262,;GAA,downstream_gene_variant,,ENST00000570803,;GAA,missense_variant,p.Phe27Leu,ENST00000572080,;GAA,non_coding_transcript_exon_variant,,ENST00000572803,;GAA,upstream_gene_variant,,ENST00000570716,;GAA,upstream_gene_variant,,ENST00000573556,;	C	ENSG00000171298	ENST00000302262	Transcript	missense_variant	1909	1690	564	F/L	Ttt/Ctt	.	.	.	1	GAA	HGNC	4065	protein_coding	YES	CCDS32760.1	ENSP00000305692	LYAG_HUMAN	I3L3L3_HUMAN,I3L0S5_HUMAN	UPI00000744FF	.	tolerated(0.26)	benign(0.014)	12/20	.	hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF48,Pfam_domain:PF01055,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAGTTTCTC	.	5	ESCA
RNF213	0	.	GRCh37	17	78360569	78360569	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14800C>A	p.Leu4934Ile	p.L4934I	ENST00000582970	63/68	41	32	9	21	21	0	RNF213,missense_variant,p.Leu3007Ile,ENST00000336301,;RNF213,missense_variant,p.Leu4934Ile,ENST00000582970,;RNF213,missense_variant,p.Leu4983Ile,ENST00000508628,;CTD-2047H16.4,intron_variant,,ENST00000572151,;CTD-2047H16.4,intron_variant,,ENST00000575034,;CTD-2047H16.4,intron_variant,,ENST00000573394,;RNF213,non_coding_transcript_exon_variant,,ENST00000427003,;RNF213,non_coding_transcript_exon_variant,,ENST00000560083,;RNF213,non_coding_transcript_exon_variant,,ENST00000411702,;RNF213,upstream_gene_variant,,ENST00000573919,;RNF213,downstream_gene_variant,,ENST00000558116,;RNF213,downstream_gene_variant,,ENST00000570776,;	A	ENSG00000173821	ENST00000582970	Transcript	missense_variant	14943	14800	4934	L/I	Ctc/Atc	.	.	.	1	RNF213	HGNC	14539	protein_coding	YES	CCDS58606.1	ENSP00000464087	RN213_HUMAN	H3BLU6_HUMAN	UPI0001D3BDB1	.	.	possibly_damaging(0.788)	63/68	.	hmmpanther:PTHR22605,hmmpanther:PTHR22605:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTCTCTCC	.	5	ESCA
ALOX12B	0	.	GRCh37	17	7979514	7979514	+	Missense_Mutation	SNP	G	G	A	rs141010860	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	11/15	47	23	24	26	26	0	ALOX12B,missense_variant,p.Ala504Val,ENST00000319144,;AC129492.6,upstream_gene_variant,,ENST00000399413,;ALOX12B,non_coding_transcript_exon_variant,,ENST00000577351,;ALOX12B,downstream_gene_variant,,ENST00000584116,;ALOX12B,downstream_gene_variant,,ENST00000583276,;	A	ENSG00000179477	ENST00000319144	Transcript	missense_variant	1772	1511	504	A/V	gCg/gTg	rs141010860	.	.	-1	ALOX12B	HGNC	430	protein_coding	YES	CCDS11129.1	ENSP00000315167	LX12B_HUMAN	.	UPI000000D996	.	deleterious(0.01)	possibly_damaging(0.785)	11/15	.	PROSITE_profiles:PS51393,hmmpanther:PTHR11771:SF41,hmmpanther:PTHR11771,Pfam_domain:PF00305,Gene3D:1.20.245.10,Superfamily_domains:SSF48484	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCGCCAAG	byCluster	5	ESCA
SIRT7	0	.	GRCh37	17	79872373	79872373	+	Missense_Mutation	SNP	C	C	T	rs771395879	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.613G>A	p.Val205Met	p.V205M	ENST00000328666	7/10	60	30	29	24	24	0	SIRT7,missense_variant,p.Val205Met,ENST00000328666,;SIRT7,missense_variant,p.Val56Met,ENST00000572902,;PCYT2,upstream_gene_variant,,ENST00000576343,;PCYT2,upstream_gene_variant,,ENST00000570391,;PCYT2,upstream_gene_variant,,ENST00000572473,;PCYT2,upstream_gene_variant,,ENST00000331285,;PCYT2,upstream_gene_variant,,ENST00000538936,;PCYT2,upstream_gene_variant,,ENST00000573927,;PCYT2,upstream_gene_variant,,ENST00000571105,;PCYT2,upstream_gene_variant,,ENST00000538721,;MAFG,downstream_gene_variant,,ENST00000357736,;PCYT2,upstream_gene_variant,,ENST00000572157,;PCYT2,upstream_gene_variant,,ENST00000573636,;PCYT2,upstream_gene_variant,,ENST00000570388,;SIRT7,3_prime_UTR_variant,,ENST00000575360,;SIRT7,non_coding_transcript_exon_variant,,ENST00000571233,;SIRT7,non_coding_transcript_exon_variant,,ENST00000571915,;SIRT7,non_coding_transcript_exon_variant,,ENST00000573367,;SIRT7,non_coding_transcript_exon_variant,,ENST00000574992,;SIRT7,non_coding_transcript_exon_variant,,ENST00000572350,;SIRT7,non_coding_transcript_exon_variant,,ENST00000574495,;SIRT7,non_coding_transcript_exon_variant,,ENST00000536038,;SIRT7,non_coding_transcript_exon_variant,,ENST00000572976,;SIRT7,non_coding_transcript_exon_variant,,ENST00000576156,;SIRT7,non_coding_transcript_exon_variant,,ENST00000577065,;SIRT7,non_coding_transcript_exon_variant,,ENST00000571832,;PCYT2,upstream_gene_variant,,ENST00000571581,;SIRT7,downstream_gene_variant,,ENST00000573576,;SIRT7,downstream_gene_variant,,ENST00000571213,;SIRT7,downstream_gene_variant,,ENST00000572671,;PCYT2,upstream_gene_variant,,ENST00000573401,;SIRT7,downstream_gene_variant,,ENST00000570367,;SIRT7,downstream_gene_variant,,ENST00000575244,;SIRT7,downstream_gene_variant,,ENST00000574915,;SIRT7,upstream_gene_variant,,ENST00000574153,;	T	ENSG00000187531	ENST00000328666	Transcript	missense_variant	676	613	205	V/M	Gtg/Atg	rs771395879,COSM3523707,COSM1610986	.	.	-1	SIRT7	HGNC	14935	protein_coding	YES	CCDS11792.1	ENSP00000329466	SIR7_HUMAN	I3L480_HUMAN	UPI0000072CE1	.	deleterious(0.05)	benign(0.166)	7/10	.	PROSITE_profiles:PS50305,hmmpanther:PTHR11085:SF1,hmmpanther:PTHR11085,Pfam_domain:PF02146,Superfamily_domains:SSF52467	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCACGTACT	.	5	ESCA
FASN	0	.	GRCh37	17	80046083	80046083	+	Silent	SNP	C	C	T	rs373471307	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2694G>A	p.%3D	p.T898T	ENST00000306749	17/43	67	52	15	37	37	0	FASN,synonymous_variant,p.%3D,ENST00000306749,;FASN,upstream_gene_variant,,ENST00000579758,;FASN,upstream_gene_variant,,ENST00000579410,;	T	ENSG00000169710	ENST00000306749	Transcript	synonymous_variant	2913	2694	898	T	acG/acA	rs373471307	.	.	-1	FASN	HGNC	3594	protein_coding	YES	CCDS11801.1	ENSP00000304592	FAS_HUMAN	.	UPI000013EB82	.	.	.	17/43	.	hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF227,Pfam_domain:PF14765,SMART_domains:SM00826	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGCGTCTT	byFrequency|byCluster|by1000G	5	ESCA
HEXDC	0	.	GRCh37	17	80397532	80397532	+	Missense_Mutation	SNP	G	G	A	rs375964079	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.925G>A	p.Glu309Lys	p.E309K	ENST00000337014	9/12	175	87	88	93	93	0	HEXDC,missense_variant,p.Glu78Lys,ENST00000578130,;HEXDC,missense_variant,p.Glu309Lys,ENST00000577944,;HEXDC,missense_variant,p.Glu309Lys,ENST00000337014,;HEXDC,missense_variant,p.Glu309Lys,ENST00000327949,;C17orf62,downstream_gene_variant,,ENST00000577732,;C17orf62,downstream_gene_variant,,ENST00000585080,;HEXDC,downstream_gene_variant,,ENST00000580235,;C17orf62,downstream_gene_variant,,ENST00000577436,;C17orf62,downstream_gene_variant,,ENST00000577471,;C17orf62,downstream_gene_variant,,ENST00000434650,;C17orf62,downstream_gene_variant,,ENST00000336995,;C17orf62,downstream_gene_variant,,ENST00000342572,;C17orf62,downstream_gene_variant,,ENST00000577696,;C17orf62,downstream_gene_variant,,ENST00000437807,;C17orf62,downstream_gene_variant,,ENST00000579751,;C17orf62,downstream_gene_variant,,ENST00000577834,;C17orf62,downstream_gene_variant,,ENST00000306645,;C17orf62,downstream_gene_variant,,ENST00000578919,;C17orf62,downstream_gene_variant,,ENST00000583617,;C17orf62,downstream_gene_variant,,ENST00000582438,;C17orf62,downstream_gene_variant,,ENST00000578913,;C17orf62,downstream_gene_variant,,ENST00000585064,;C17orf62,downstream_gene_variant,,ENST00000584891,;C17orf62,downstream_gene_variant,,ENST00000580560,;C17orf62,downstream_gene_variant,,ENST00000581196,;C17orf62,downstream_gene_variant,,ENST00000584503,;HEXDC,missense_variant,p.Glu59Lys,ENST00000578616,;HEXDC,missense_variant,p.Glu168Lys,ENST00000582429,;HEXDC,non_coding_transcript_exon_variant,,ENST00000585077,;HEXDC,upstream_gene_variant,,ENST00000582131,;C17orf62,downstream_gene_variant,,ENST00000585044,;C17orf62,downstream_gene_variant,,ENST00000582725,;C17orf62,downstream_gene_variant,,ENST00000579444,;HEXDC,downstream_gene_variant,,ENST00000578775,;C17orf62,downstream_gene_variant,,ENST00000577888,;HEXDC,downstream_gene_variant,,ENST00000582315,;C17orf62,downstream_gene_variant,,ENST00000584408,;HEXDC,downstream_gene_variant,,ENST00000581482,;HEXDC,upstream_gene_variant,,ENST00000583354,;C17orf62,downstream_gene_variant,,ENST00000584024,;C17orf62,downstream_gene_variant,,ENST00000578895,;C17orf62,downstream_gene_variant,,ENST00000536759,;C17orf62,downstream_gene_variant,,ENST00000577707,;	A	ENSG00000169660	ENST00000337014	Transcript	missense_variant	1399	925	309	E/K	Gag/Aag	rs375964079	.	.	1	HEXDC	HGNC	26307	protein_coding	YES	CCDS42402.1	ENSP00000337854	HEXDC_HUMAN	J3QLN1_HUMAN,J3KT84_HUMAN	UPI00001AF695	.	deleterious(0)	probably_damaging(0.996)	9/12	.	hmmpanther:PTHR21040:SF6,hmmpanther:PTHR21040,Gene3D:3.20.20.80,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCGAGCTG	byFrequency|byCluster	5	ESCA
HEXDC	0	.	GRCh37	17	80400297	80400298	+	Frame_Shift_Ins	INS	-	-	G	rs751615819	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594dupG	p.Ala532GlyfsTer31	p.A532Gfs*31	ENST00000337014	12/12	43	22	21	18	18	0	HEXDC,frameshift_variant,p.Leu505AlafsTer55,ENST00000577944,;HEXDC,frameshift_variant,p.Ala532GlyfsTer31,ENST00000337014,;HEXDC,3_prime_UTR_variant,,ENST00000578130,;HEXDC,3_prime_UTR_variant,,ENST00000327949,;C17orf62,downstream_gene_variant,,ENST00000577732,;C17orf62,downstream_gene_variant,,ENST00000585080,;C17orf62,downstream_gene_variant,,ENST00000577436,;C17orf62,downstream_gene_variant,,ENST00000577471,;C17orf62,downstream_gene_variant,,ENST00000434650,;C17orf62,downstream_gene_variant,,ENST00000336995,;C17orf62,downstream_gene_variant,,ENST00000342572,;C17orf62,downstream_gene_variant,,ENST00000582545,;C17orf62,downstream_gene_variant,,ENST00000577696,;C17orf62,downstream_gene_variant,,ENST00000437807,;C17orf62,downstream_gene_variant,,ENST00000579751,;C17orf62,downstream_gene_variant,,ENST00000577834,;C17orf62,downstream_gene_variant,,ENST00000306645,;C17orf62,downstream_gene_variant,,ENST00000578919,;C17orf62,downstream_gene_variant,,ENST00000583617,;C17orf62,downstream_gene_variant,,ENST00000582438,;C17orf62,downstream_gene_variant,,ENST00000578913,;C17orf62,downstream_gene_variant,,ENST00000585064,;C17orf62,downstream_gene_variant,,ENST00000584891,;C17orf62,downstream_gene_variant,,ENST00000580560,;C17orf62,downstream_gene_variant,,ENST00000581196,;C17orf62,downstream_gene_variant,,ENST00000583359,;C17orf62,downstream_gene_variant,,ENST00000584503,;HEXDC,3_prime_UTR_variant,,ENST00000582429,;HEXDC,downstream_gene_variant,,ENST00000582131,;C17orf62,downstream_gene_variant,,ENST00000582395,;C17orf62,downstream_gene_variant,,ENST00000585044,;HEXDC,downstream_gene_variant,,ENST00000578616,;C17orf62,downstream_gene_variant,,ENST00000582608,;C17orf62,downstream_gene_variant,,ENST00000582725,;C17orf62,downstream_gene_variant,,ENST00000579444,;C17orf62,downstream_gene_variant,,ENST00000578064,;C17orf62,downstream_gene_variant,,ENST00000577888,;HEXDC,downstream_gene_variant,,ENST00000585077,;C17orf62,downstream_gene_variant,,ENST00000584408,;HEXDC,downstream_gene_variant,,ENST00000583354,;C17orf62,downstream_gene_variant,,ENST00000584024,;C17orf62,downstream_gene_variant,,ENST00000578895,;C17orf62,downstream_gene_variant,,ENST00000536759,;C17orf62,downstream_gene_variant,,ENST00000577707,;C17orf62,downstream_gene_variant,,ENST00000578941,;	G	ENSG00000169660	ENST00000337014	Transcript	frameshift_variant	2061-2062	1587-1588	529-530	-/X	-/G	rs751615819	.	.	1	HEXDC	HGNC	26307	protein_coding	YES	CCDS42402.1	ENSP00000337854	HEXDC_HUMAN	J3QLN1_HUMAN,J3KT84_HUMAN	UPI00001AF695	.	.	.	12/12	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.A532fs*41|c.1588delG|3	INDELOCATOR|VARSCANI	GAGGCTGGGGG	.	2	ESCA
PER1	0	.	GRCh37	17	8053368	8053368	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450G>A	p.%3D	p.P150P	ENST00000317276	4/23	35	31	4	18	18	0	PER1,synonymous_variant,p.%3D,ENST00000317276,;PER1,synonymous_variant,p.%3D,ENST00000581082,;PER1,synonymous_variant,p.%3D,ENST00000354903,;PER1,synonymous_variant,p.%3D,ENST00000577253,;PER1,synonymous_variant,p.%3D,ENST00000581703,;PER1,downstream_gene_variant,,ENST00000584202,;PER1,upstream_gene_variant,,ENST00000583559,;RP11-599B13.6,downstream_gene_variant,,ENST00000498285,;PER1,upstream_gene_variant,,ENST00000578089,;PER1,synonymous_variant,p.%3D,ENST00000581395,;PER1,synonymous_variant,p.%3D,ENST00000582719,;PER1,non_coding_transcript_exon_variant,,ENST00000579065,;PER1,upstream_gene_variant,,ENST00000577424,;PER1,upstream_gene_variant,,ENST00000578950,;PER1,upstream_gene_variant,,ENST00000579203,;PER1,upstream_gene_variant,,ENST00000585095,;PER1,upstream_gene_variant,,ENST00000578223,;	T	ENSG00000179094	ENST00000317276	Transcript	synonymous_variant	688	450	150	P	ccG/ccA	.	.	.	-1	PER1	HGNC	8845	protein_coding	YES	CCDS11131.1	ENSP00000314420	PER1_HUMAN	J3QLQ5_HUMAN,A2I2P6_HUMAN	UPI000013FFF5	.	.	.	4/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11269,hmmpanther:PTHR11269:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGGCGGCAG	.	4	ESCA
TBCD	0	.	GRCh37	17	80895806	80895806	+	Intron	SNP	G	G	A	rs535183295	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3282-119G>A	.	.	ENST00000355528	.	68	35	33	53	53	0	TBCD,synonymous_variant,p.%3D,ENST00000539345,;TBCD,intron_variant,,ENST00000355528,;TBCD,intron_variant,,ENST00000577051,;TBCD,upstream_gene_variant,,ENST00000572794,;TBCD,non_coding_transcript_exon_variant,,ENST00000576691,;TBCD,intron_variant,,ENST00000576603,;B3GNTL1,downstream_gene_variant,,ENST00000572267,;TBCD,intron_variant,,ENST00000576677,;TBCD,intron_variant,,ENST00000575132,;TBCD,intron_variant,,ENST00000576432,;TBCD,downstream_gene_variant,,ENST00000573364,;TBCD,upstream_gene_variant,,ENST00000572389,;B3GNTL1,downstream_gene_variant,,ENST00000572977,;	A	ENSG00000141556	ENST00000355528	Transcript	intron_variant	.	.	.	.	.	rs535183295	.	.	1	TBCD	HGNC	11581	protein_coding	YES	CCDS45818.1	ENSP00000347719	TBCD_HUMAN	I3L4D2_HUMAN,I3L439_HUMAN,I3L3H4_HUMAN,I3L1S3_HUMAN,I3L163_HUMAN,I3L131_HUMAN	UPI000020053F	.	.	.	.	35/38	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCGCACTG	by1000G	5	ESCA
CCDC42	0	.	GRCh37	17	8638830	8638830	+	Missense_Mutation	SNP	G	G	A	rs752677099	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592C>T	p.Arg198Cys	p.R198C	ENST00000293845	5/7	54	30	24	23	23	0	CCDC42,missense_variant,p.Arg198Cys,ENST00000293845,;CCDC42,intron_variant,,ENST00000539522,;	A	ENSG00000161973	ENST00000293845	Transcript	missense_variant	819	592	198	R/C	Cgc/Tgc	rs752677099	.	.	-1	CCDC42	HGNC	26528	protein_coding	YES	CCDS11145.1	ENSP00000293845	CCD42_HUMAN	.	UPI000013E127	.	deleterious(0)	benign(0.425)	5/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21683:SF4,hmmpanther:PTHR21683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGCGCTCAA	byFrequency	5	ESCA
ABR	0	.	GRCh37	17	910416	910416	+	Missense_Mutation	SNP	C	C	T	rs111816976	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2479G>A	p.Val827Ile	p.V827I	ENST00000302538	22/23	50	26	23	24	24	0	ABR,missense_variant,p.Val157Ile,ENST00000573559,;ABR,missense_variant,p.Val790Ile,ENST00000291107,;ABR,missense_variant,p.Val781Ile,ENST00000574437,;ABR,missense_variant,p.Val152Ile,ENST00000571797,;ABR,missense_variant,p.Val278Ile,ENST00000543210,;ABR,missense_variant,p.Val781Ile,ENST00000544583,;ABR,missense_variant,p.Val609Ile,ENST00000536794,;ABR,missense_variant,p.Val827Ile,ENST00000302538,;ABR,intron_variant,,ENST00000572441,;TIMM22,downstream_gene_variant,,ENST00000327158,;ABR,downstream_gene_variant,,ENST00000571383,;ABR,downstream_gene_variant,,ENST00000577052,;ABR,downstream_gene_variant,,ENST00000571120,;ABR,downstream_gene_variant,,ENST00000571022,;ABR,non_coding_transcript_exon_variant,,ENST00000572585,;ABR,downstream_gene_variant,,ENST00000570688,;ABR,downstream_gene_variant,,ENST00000572650,;ABR,downstream_gene_variant,,ENST00000572152,;	T	ENSG00000159842	ENST00000302538	Transcript	missense_variant	2626	2479	827	V/I	Gtc/Atc	rs111816976	.	.	-1	ABR	HGNC	81	protein_coding	YES	CCDS10999.1	ENSP00000303909	ABR_HUMAN	I3L4Y1_HUMAN,I3L2P5_HUMAN,I3L2L3_HUMAN,I3L259_HUMAN,B7Z2X0_HUMAN	UPI00001AED3D	.	deleterious(0)	probably_damaging(0.986)	22/23	.	PROSITE_profiles:PS50238,hmmpanther:PTHR23182:SF5,hmmpanther:PTHR23182,SMART_domains:SM00324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGACGTCAT	.	5	ESCA
USP43	0	.	GRCh37	17	9578294	9578294	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827A>G	p.Gln276Arg	p.Q276R	ENST00000285199	4/15	113	64	49	63	63	0	USP43,missense_variant,p.Gln63Arg,ENST00000574408,;USP43,missense_variant,p.Gln276Arg,ENST00000570475,;USP43,missense_variant,p.Gln276Arg,ENST00000285199,;USP43,non_coding_transcript_exon_variant,,ENST00000570827,;USP43,non_coding_transcript_exon_variant,,ENST00000575346,;	G	ENSG00000154914	ENST00000285199	Transcript	missense_variant	923	827	276	Q/R	cAg/cGg	.	.	.	1	USP43	HGNC	20072	protein_coding	YES	CCDS45610.1	ENSP00000285199	UBP43_HUMAN	.	UPI0000047AFB	.	deleterious(0.01)	possibly_damaging(0.542)	4/15	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF408,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCCAGACGA	.	5	ESCA
PIEZO2	0	.	GRCh37	18	10699097	10699097	+	Missense_Mutation	SNP	C	C	T	rs754406783	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6181G>A	p.Gly2061Ser	p.G2061S	ENST00000503781	40/52	35	21	14	27	27	0	PIEZO2,missense_variant,p.Gly2086Ser,ENST00000580640,;PIEZO2,missense_variant,p.Gly2061Ser,ENST00000503781,;PIEZO2,missense_variant,p.Gly18Ser,ENST00000538948,;PIEZO2,missense_variant,p.Gly2061Ser,ENST00000302079,;PIEZO2,5_prime_UTR_variant,,ENST00000285141,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,;	T	ENSG00000154864	ENST00000503781	Transcript	missense_variant	6181	6181	2061	G/S	Ggt/Agt	rs754406783	.	.	-1	PIEZO2	HGNC	26270	protein_coding	YES	.	ENSP00000421377	PIEZ2_HUMAN	J3KSM7_HUMAN	UPI0001B3CB29	.	tolerated(0.92)	benign(0)	40/52	.	hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACCGAGGG	.	5	ESCA
CIDEA	0	.	GRCh37	18	12277160	12277160	+	Missense_Mutation	SNP	C	C	T	rs374773954	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.551C>T	p.Thr184Met	p.T184M	ENST00000320477	5/5	98	57	40	42	42	0	CIDEA,missense_variant,p.Thr184Met,ENST00000320477,;CIDEA,non_coding_transcript_exon_variant,,ENST00000520620,;CIDEA,non_coding_transcript_exon_variant,,ENST00000521296,;CIDEA,3_prime_UTR_variant,,ENST00000522713,;	T	ENSG00000176194	ENST00000320477	Transcript	missense_variant	616	551	184	T/M	aCg/aTg	rs374773954	.	.	1	CIDEA	HGNC	1976	protein_coding	YES	CCDS11856.1	ENSP00000320209	CIDEA_HUMAN	.	UPI0000049059	.	deleterious(0.02)	probably_damaging(0.968)	5/5	.	hmmpanther:PTHR12306:SF8,hmmpanther:PTHR12306	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGACGGGAC	byFrequency|byCluster	5	ESCA
ESCO1	0	.	GRCh37	18	19153489	19153489	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1316delT	p.Leu439Ter	p.L439*	ENST00000269214	4/12	53	45	8	27	27	0	ESCO1,frameshift_variant,p.Leu439Ter,ENST00000269214,;ESCO1,frameshift_variant,p.Leu439Ter,ENST00000383276,;	-	ENSG00000141446	ENST00000269214	Transcript	frameshift_variant	2254	1316	439	L/X	tTa/ta	.	.	.	-1	ESCO1	HGNC	24645	protein_coding	YES	CCDS32800.1	ENSP00000269214	ESCO1_HUMAN	.	UPI00001C1FF4	.	.	.	4/12	.	hmmpanther:PTHR11076:SF26,hmmpanther:PTHR11076	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCCCTAAAAAC	.	3	ESCA
ABHD3	0	.	GRCh37	18	19231211	19231211	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*341delT	.	.	ENST00000289119	9/9	55	44	11	33	33	0	ABHD3,3_prime_UTR_variant,,ENST00000580981,;ABHD3,3_prime_UTR_variant,,ENST00000289119,;ABHD3,3_prime_UTR_variant,,ENST00000578270,;ABHD3,downstream_gene_variant,,ENST00000580477,;ABHD3,downstream_gene_variant,,ENST00000577564,;	-	ENSG00000158201	ENST00000289119	Transcript	3_prime_UTR_variant	1711	.	.	.	.	.	.	.	-1	ABHD3	HGNC	18718	protein_coding	YES	CCDS32802.1	ENSP00000289119	ABHD3_HUMAN	.	UPI0000163938	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAATCTAAAAAA	.	3	ESCA
DLGAP1	0	.	GRCh37	18	3534565	3534565	+	Silent	SNP	G	G	A	rs373443663	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2106C>T	p.%3D	p.A702A	ENST00000315677	10/13	26	12	14	11	11	0	DLGAP1,synonymous_variant,p.%3D,ENST00000581527,;DLGAP1,synonymous_variant,p.%3D,ENST00000315677,;DLGAP1,synonymous_variant,p.%3D,ENST00000400149,;DLGAP1,synonymous_variant,p.%3D,ENST00000584874,;DLGAP1,synonymous_variant,p.%3D,ENST00000400145,;DLGAP1,synonymous_variant,p.%3D,ENST00000400150,;DLGAP1,synonymous_variant,p.%3D,ENST00000400155,;DLGAP1,synonymous_variant,p.%3D,ENST00000400147,;DLGAP1,synonymous_variant,p.%3D,ENST00000539435,;DLGAP1,synonymous_variant,p.%3D,ENST00000515196,;DLGAP1,synonymous_variant,p.%3D,ENST00000534970,;DLGAP1,synonymous_variant,p.%3D,ENST00000581699,;	A	ENSG00000170579	ENST00000315677	Transcript	synonymous_variant	2702	2106	702	A	gcC/gcT	rs373443663	.	.	-1	DLGAP1	HGNC	2905	protein_coding	YES	CCDS11836.1	ENSP00000316377	DLGP1_HUMAN	.	UPI0000129490	.	.	.	10/13	.	hmmpanther:PTHR12353:SF7,hmmpanther:PTHR12353,Pfam_domain:PF03359	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTCGGCCTG	byFrequency|byCluster	5	ESCA
SLC14A2	0	.	GRCh37	18	43248420	43248420	+	Missense_Mutation	SNP	G	G	A	rs145938404	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2014G>A	p.Val672Ile	p.V672I	ENST00000255226	15/20	92	73	19	80	80	0	SLC14A2,missense_variant,p.Val149Ile,ENST00000589658,;SLC14A2,missense_variant,p.Val672Ile,ENST00000255226,;SLC14A2,missense_variant,p.Val672Ile,ENST00000586448,;RP11-116O18.3,downstream_gene_variant,,ENST00000589510,;	A	ENSG00000132874	ENST00000255226	Transcript	missense_variant	2830	2014	672	V/I	Gtc/Atc	rs145938404	.	.	1	SLC14A2	HGNC	10919	protein_coding	YES	CCDS11924.1	ENSP00000255226	UT2_HUMAN	.	UPI000013CE99	.	tolerated(0.07)	benign(0.038)	15/20	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10464,hmmpanther:PTHR10464:SF2,Gene3D:1.10.3430.10,Pfam_domain:PF03253	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCCGTCATC	byFrequency	5	ESCA
EPG5	0	.	GRCh37	18	43459143	43459143	+	Frame_Shift_Del	DEL	A	A	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5704delT	p.Tyr1902IlefsTer26	p.Y1902Ifs*26	ENST00000282041	33/44	32	26	6	27	27	0	EPG5,frameshift_variant,p.Tyr1902IlefsTer26,ENST00000282041,;EPG5,non_coding_transcript_exon_variant,,ENST00000585906,;EPG5,frameshift_variant,p.Tyr777IlefsTer26,ENST00000592272,;EPG5,3_prime_UTR_variant,,ENST00000587884,;EPG5,3_prime_UTR_variant,,ENST00000590884,;	-	ENSG00000152223	ENST00000282041	Transcript	frameshift_variant	5739	5704	1902	Y/X	Tat/at	COSM1388765	.	.	-1	EPG5	HGNC	29331	protein_coding	YES	CCDS11926.2	ENSP00000282041	EPG5_HUMAN	Q9BYJ3_HUMAN,Q9BTI0_HUMAN	UPI00004F6F8A	.	.	.	33/44	.	hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GCTTATAAAAAA	.	2	ESCA
C18orf25	0	.	GRCh37	18	43844099	43844099	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1026delA	.	.	ENST00000282059	5/5	15	9	6	14	14	0	C18orf25,3_prime_UTR_variant,,ENST00000321319,;C18orf25,3_prime_UTR_variant,,ENST00000282059,;	-	ENSG00000152242	ENST00000282059	Transcript	3_prime_UTR_variant	2604	.	.	.	.	.	.	.	1	C18orf25	HGNC	28172	protein_coding	YES	CCDS42430.1	ENSP00000282059	CR025_HUMAN	Q5BIX2_HUMAN,K7ER64_HUMAN,K7EQH1_HUMAN	UPI000013DCB6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCTTCTAAAAAA	.	2	ESCA
C18orf25	0	.	GRCh37	18	43844672	43844674	+	3'UTR	DEL	TTC	TTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TTC	TTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1606_*1608delTTC	.	.	ENST00000282059	5/5	14	7	7	13	13	0	C18orf25,3_prime_UTR_variant,,ENST00000321319,;C18orf25,3_prime_UTR_variant,,ENST00000282059,;	-	ENSG00000152242	ENST00000282059	Transcript	3_prime_UTR_variant	3177-3179	.	.	.	.	.	.	.	1	C18orf25	HGNC	28172	protein_coding	YES	CCDS42430.1	ENSP00000282059	CR025_HUMAN	Q5BIX2_HUMAN,K7ER64_HUMAN,K7EQH1_HUMAN	UPI000013DCB6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	15	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGCCTGTTCTTCTT	.	2	ESCA
SMAD7	0	.	GRCh37	18	46447624	46447624	+	3'UTR	DEL	A	A	-	rs536375171	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*118delT	.	.	ENST00000262158	4/4	18	7	11	12	12	0	SMAD7,3_prime_UTR_variant,,ENST00000591805,;SMAD7,3_prime_UTR_variant,,ENST00000262158,;SMAD7,downstream_gene_variant,,ENST00000586093,;SMAD7,downstream_gene_variant,,ENST00000589634,;SMAD7,downstream_gene_variant,,ENST00000585986,;SMAD7,downstream_gene_variant,,ENST00000588190,;SMAD7,downstream_gene_variant,,ENST00000587336,;SMAD7,non_coding_transcript_exon_variant,,ENST00000545051,;	-	ENSG00000101665	ENST00000262158	Transcript	3_prime_UTR_variant	1686	.	.	.	.	rs536375171	.	.	-1	SMAD7	HGNC	6773	protein_coding	YES	CCDS11936.1	ENSP00000262158	SMAD7_HUMAN	K7EKF0_HUMAN	UPI0000135A83	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACAAACAAAAAA	.	2	ESCA
MBD1	0	.	GRCh37	18	47802303	47802304	+	Frame_Shift_Del	DEL	CA	CA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564_565delTG	p.Cys188TrpfsTer13	p.C188Wfs*13	ENST00000590208	7/16	53	44	9	21	21	0	MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000588937,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000587605,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000269471,;MBD1,frameshift_variant,p.Cys56TrpfsTer13,ENST00000589733,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000585595,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000347968,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000269468,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000591535,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000398495,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000590208,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000339998,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000398493,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000457839,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000436910,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000349085,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000382948,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000591416,;MBD1,frameshift_variant,p.Cys188TrpfsTer13,ENST00000398488,;MBD1,frameshift_variant,p.Cys214TrpfsTer13,ENST00000424334,;MBD1,intron_variant,,ENST00000592060,;MBD1,intron_variant,,ENST00000585672,;MBD1,intron_variant,,ENST00000353909,;MBD1,upstream_gene_variant,,ENST00000589541,;MBD1,non_coding_transcript_exon_variant,,ENST00000586679,;MBD1,non_coding_transcript_exon_variant,,ENST00000591661,;MBD1,non_coding_transcript_exon_variant,,ENST00000586118,;MBD1,downstream_gene_variant,,ENST00000589867,;MBD1,upstream_gene_variant,,ENST00000586884,;MBD1,downstream_gene_variant,,ENST00000589758,;MBD1,downstream_gene_variant,,ENST00000590215,;	-	ENSG00000141644	ENST00000590208	Transcript	frameshift_variant	911-912	564-565	188-189	CG/WX	tgTGgg/tggg	.	.	.	-1	MBD1	HGNC	6916	protein_coding	YES	CCDS59320.1	ENSP00000468785	.	K7ESN0_HUMAN	UPI0001F995B6	.	.	.	7/16	.	PROSITE_profiles:PS51058,hmmpanther:PTHR12396,hmmpanther:PTHR12396:SF4,Pfam_domain:PF02008	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGCCCCACAGTC	.	3	ESCA
DCC	0	.	GRCh37	18	50589808	50589808	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1119T>C	p.%3D	p.P373P	ENST00000442544	6/29	106	80	26	99	99	0	DCC,synonymous_variant,p.%3D,ENST00000581580,;DCC,synonymous_variant,p.%3D,ENST00000578949,;DCC,synonymous_variant,p.%3D,ENST00000442544,;DCC,synonymous_variant,p.%3D,ENST00000412726,;DCC,non_coding_transcript_exon_variant,,ENST00000580146,;DCC,synonymous_variant,p.%3D,ENST00000304775,;DCC,non_coding_transcript_exon_variant,,ENST00000579883,;	C	ENSG00000187323	ENST00000442544	Transcript	synonymous_variant	1735	1119	373	P	ccT/ccC	.	.	.	1	DCC	HGNC	2701	protein_coding	YES	CCDS11952.1	ENSP00000389140	DCC_HUMAN	J3QQJ6_HUMAN	UPI00001AEDC6	.	.	.	6/29	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF68,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCCTAGTGA	.	5	ESCA
DCC	0	.	GRCh37	18	50592505	50592505	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1230G>T	p.Gln410His	p.Q410H	ENST00000442544	7/29	56	45	11	74	74	0	DCC,missense_variant,p.Gln65His,ENST00000581580,;DCC,missense_variant,p.Gln65His,ENST00000578949,;DCC,missense_variant,p.Gln410His,ENST00000442544,;DCC,missense_variant,p.Gln258His,ENST00000412726,;DCC,non_coding_transcript_exon_variant,,ENST00000580146,;DCC,missense_variant,p.Gln344His,ENST00000304775,;DCC,downstream_gene_variant,,ENST00000579883,;	T	ENSG00000187323	ENST00000442544	Transcript	missense_variant	1846	1230	410	Q/H	caG/caT	.	.	.	1	DCC	HGNC	2701	protein_coding	YES	CCDS11952.1	ENSP00000389140	DCC_HUMAN	J3QQJ6_HUMAN	UPI00001AEDC6	.	deleterious(0.02)	possibly_damaging(0.907)	7/29	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF68,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCAGACCAG	.	5	ESCA
WDR7	0	.	GRCh37	18	54348614	54348614	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337G>A	p.Gly113Ser	p.G113S	ENST00000254442	4/28	47	37	10	34	34	0	WDR7,missense_variant,p.Gly113Ser,ENST00000254442,;WDR7,missense_variant,p.Gly113Ser,ENST00000593058,;WDR7,missense_variant,p.Gly113Ser,ENST00000357574,;WDR7,intron_variant,,ENST00000589935,;	A	ENSG00000091157	ENST00000254442	Transcript	missense_variant	548	337	113	G/S	Ggc/Agc	.	.	.	1	WDR7	HGNC	13490	protein_coding	YES	CCDS11962.1	ENSP00000254442	WDR7_HUMAN	K7ERP9_HUMAN,K7EPQ4_HUMAN,K7EMB8_HUMAN,K7ELZ4_HUMAN	UPI000013CE33	.	tolerated(0.45)	benign(0.376)	4/28	.	hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF48,Gene3D:2.130.10.10,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTGGCATA	.	5	ESCA
ONECUT2	0	.	GRCh37	18	55153929	55153929	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9980delT	.	.	ENST00000491143	2/2	83	55	28	50	50	0	ONECUT2,3_prime_UTR_variant,,ENST00000491143,;	-	ENSG00000119547	ENST00000491143	Transcript	3_prime_UTR_variant	11521	.	.	.	.	.	.	.	1	ONECUT2	HGNC	8139	protein_coding	YES	CCDS42440.1	ENSP00000419185	ONEC2_HUMAN	.	UPI0000201DC1	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTATGTTTTTT	.	3	ESCA
KIAA1468	0	.	GRCh37	18	59922664	59922664	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1849C>T	p.Arg617Ter	p.R617*	ENST00000398130	13/29	17	8	9	15	14	0	KIAA1468,stop_gained,p.Arg617Ter,ENST00000256858,;KIAA1468,stop_gained,p.Arg617Ter,ENST00000398130,;KIAA1468,downstream_gene_variant,,ENST00000591227,;KIAA1468,stop_gained,p.Arg617Ter,ENST00000587725,;	T	ENSG00000134444	ENST00000398130	Transcript	stop_gained	2081	1849	617	R/*	Cga/Tga	.	.	.	1	KIAA1468	HGNC	29289	protein_coding	YES	CCDS11979.2	ENSP00000381198	K1468_HUMAN	Q96ES0_HUMAN	UPI0000DA5AF7	.	.	.	13/29	.	hmmpanther:PTHR32059,hmmpanther:PTHR32059:SF0,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AAAGACGACTG	.	4	ESCA
SERPINB8	0	.	GRCh37	18	61637382	61637382	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-33G>A	.	.	ENST00000397985	1/7	24	17	7	14	14	0	SERPINB8,5_prime_UTR_variant,,ENST00000353706,;SERPINB8,5_prime_UTR_variant,,ENST00000397988,;SERPINB8,5_prime_UTR_variant,,ENST00000397985,;SERPINB8,5_prime_UTR_variant,,ENST00000542677,;SERPINB8,upstream_gene_variant,,ENST00000448851,;SERPINB8,upstream_gene_variant,,ENST00000441827,;HMSD,intron_variant,,ENST00000481726,;HMSD,downstream_gene_variant,,ENST00000498680,;	A	ENSG00000166401	ENST00000397985	Transcript	5_prime_UTR_variant	224	.	.	.	.	.	.	.	1	SERPINB8	HGNC	8952	protein_coding	YES	CCDS11991.1	ENSP00000381072	SPB8_HUMAN	C9JVA8_HUMAN,C9JTJ8_HUMAN,B4DTW2_HUMAN	UPI000013C5F2	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GCGGCGGCAGC	.	4	ESCA
LAMA1	0	.	GRCh37	18	6975948	6975948	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6477T>C	p.%3D	p.G2159G	ENST00000389658	45/63	25	15	10	14	14	0	LAMA1,synonymous_variant,p.%3D,ENST00000389658,;RN7SL537P,upstream_gene_variant,,ENST00000584392,;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,upstream_gene_variant,,ENST00000484335,;	G	ENSG00000101680	ENST00000389658	Transcript	synonymous_variant	6571	6477	2159	G	ggT/ggC	.	.	.	-1	LAMA1	HGNC	6481	protein_coding	YES	CCDS32787.1	ENSP00000374309	LAMA1_HUMAN	Q7Z5W6_HUMAN,Q6P6D3_HUMAN	UPI00001C1FF9	.	.	.	45/63	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10574:SF38,hmmpanther:PTHR10574,Gene3D:2.60.120.200,Pfam_domain:PF00054,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTACCGAG	.	4	ESCA
FBXO15	0	.	GRCh37	18	71749238	71749238	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1187delA	p.Asn396IlefsTer25	p.N396Ifs*25	ENST00000419743	9/10	72	45	27	43	43	0	FBXO15,frameshift_variant,p.Asn396IlefsTer25,ENST00000419743,;FBXO15,frameshift_variant,p.Asn320IlefsTer25,ENST00000269500,;FBXO15,frameshift_variant,p.Asn65IlefsTer25,ENST00000580088,;FBXO15,non_coding_transcript_exon_variant,,ENST00000580806,;FBXO15,non_coding_transcript_exon_variant,,ENST00000577575,;FBXO15,upstream_gene_variant,,ENST00000579108,;FBXO15,3_prime_UTR_variant,,ENST00000583443,;FBXO15,3_prime_UTR_variant,,ENST00000578399,;FBXO15,3_prime_UTR_variant,,ENST00000581214,;FBXO15,non_coding_transcript_exon_variant,,ENST00000584425,;	-	ENSG00000141665	ENST00000419743	Transcript	frameshift_variant	1267	1187	396	N/X	aAt/at	.	.	.	-1	FBXO15	HGNC	13617	protein_coding	YES	CCDS45884.1	ENSP00000393154	FBX15_HUMAN	J3QRE7_HUMAN	UPI00003CF23D	.	.	.	9/10	.	hmmpanther:PTHR20995:SF16,hmmpanther:PTHR20995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTGTTATTTTTT	.	3	ESCA
ZNF407	0	.	GRCh37	18	72343072	72343072	+	Missense_Mutation	SNP	G	G	A	rs747714506	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>A	p.Gly33Ser	p.G33S	ENST00000299687	1/8	41	24	17	43	43	0	ZNF407,missense_variant,p.Gly33Ser,ENST00000309902,;ZNF407,missense_variant,p.Gly33Ser,ENST00000299687,;ZNF407,missense_variant,p.Gly33Ser,ENST00000582337,;ZNF407,missense_variant,p.Gly33Ser,ENST00000577538,;	A	ENSG00000215421	ENST00000299687	Transcript	missense_variant	97	97	33	G/S	Ggt/Agt	rs747714506	.	.	1	ZNF407	HGNC	19904	protein_coding	YES	CCDS45885.1	ENSP00000299687	ZN407_HUMAN	.	UPI0000F58ED1	.	tolerated_low_confidence(0.46)	benign(0)	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AAGACGGTGGG	byFrequency	4	ESCA
CTDP1	0	.	GRCh37	18	77474867	77474867	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1407C>T	p.%3D	p.S469S	ENST00000299543	8/13	31	23	8	9	9	0	CTDP1,synonymous_variant,p.%3D,ENST00000591598,;CTDP1,synonymous_variant,p.%3D,ENST00000075430,;CTDP1,synonymous_variant,p.%3D,ENST00000299543,;	T	ENSG00000060069	ENST00000299543	Transcript	synonymous_variant	1554	1407	469	S	tcC/tcT	.	.	.	1	CTDP1	HGNC	2498	protein_coding	YES	CCDS12017.1	ENSP00000299543	CTDP1_HUMAN	K7EPW4_HUMAN	UPI000013C57B	.	.	.	8/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23081:SF0,hmmpanther:PTHR23081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGTCCTCCTC	.	3	ESCA
ICAM5	0	.	GRCh37	19	10403406	10403406	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1080G>A	p.%3D	p.A360A	ENST00000221980	5/11	51	30	20	16	16	0	ICAM5,synonymous_variant,p.%3D,ENST00000221980,;ICAM5,downstream_gene_variant,,ENST00000587398,;ICAM4,downstream_gene_variant,,ENST00000393717,;ICAM4,downstream_gene_variant,,ENST00000380770,;ICAM4,downstream_gene_variant,,ENST00000340992,;CTD-2369P2.8,upstream_gene_variant,,ENST00000589379,;ICAM5,downstream_gene_variant,,ENST00000586004,;ICAM5,non_coding_transcript_exon_variant,,ENST00000586480,;ICAM5,downstream_gene_variant,,ENST00000588912,;	A	ENSG00000105376	ENST00000221980	Transcript	synonymous_variant	1143	1080	360	A	gcG/gcA	.	.	.	1	ICAM5	HGNC	5348	protein_coding	YES	CCDS12233.1	ENSP00000221980	ICAM5_HUMAN	K7EIL3_HUMAN	UPI000013C7E4	.	.	.	5/11	.	hmmpanther:PTHR13771:SF6,hmmpanther:PTHR13771,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCGGTCCC	.	5	ESCA
KEAP1	0	.	GRCh37	19	10602788	10602788	+	Missense_Mutation	SNP	C	C	T	rs755995530	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.790G>A	p.Val264Ile	p.V264I	ENST00000171111	3/6	89	56	33	34	34	0	KEAP1,missense_variant,p.Val264Ile,ENST00000393623,;KEAP1,missense_variant,p.Val264Ile,ENST00000592055,;KEAP1,missense_variant,p.Val264Ile,ENST00000171111,;KEAP1,upstream_gene_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000591419,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,non_coding_transcript_exon_variant,,ENST00000588024,;KEAP1,3_prime_UTR_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,;KEAP1,upstream_gene_variant,,ENST00000590593,;	T	ENSG00000079999	ENST00000171111	Transcript	missense_variant	1338	790	264	V/I	Gtc/Atc	rs755995530	.	.	-1	KEAP1	HGNC	23177	protein_coding	YES	CCDS12239.1	ENSP00000171111	KEAP1_HUMAN	K7ESE0_HUMAN,K7EJD8_HUMAN,K7EJ49_HUMAN	UPI000007139C	.	tolerated(0.19)	benign(0.005)	3/6	.	hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF07707,SMART_domains:SM00875,PIRSF_domain:PIRSF037037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGACGTAGA	.	5	ESCA
CARM1	0	.	GRCh37	19	11032872	11032872	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*445delT	.	.	ENST00000327064	16/16	121	87	34	34	34	0	CARM1,3_prime_UTR_variant,,ENST00000327064,;CARM1,3_prime_UTR_variant,,ENST00000344150,;YIPF2,downstream_gene_variant,,ENST00000585858,;YIPF2,downstream_gene_variant,,ENST00000586575,;YIPF2,downstream_gene_variant,,ENST00000586748,;YIPF2,downstream_gene_variant,,ENST00000591872,;YIPF2,downstream_gene_variant,,ENST00000589971,;YIPF2,downstream_gene_variant,,ENST00000587943,;YIPF2,downstream_gene_variant,,ENST00000588347,;YIPF2,downstream_gene_variant,,ENST00000253031,;YIPF2,downstream_gene_variant,,ENST00000590329,;CARM1,downstream_gene_variant,,ENST00000586298,;YIPF2,downstream_gene_variant,,ENST00000592646,;CARM1,3_prime_UTR_variant,,ENST00000586221,;YIPF2,downstream_gene_variant,,ENST00000588962,;CARM1,downstream_gene_variant,,ENST00000592516,;CARM1,downstream_gene_variant,,ENST00000590699,;CARM1,downstream_gene_variant,,ENST00000586508,;	-	ENSG00000142453	ENST00000327064	Transcript	3_prime_UTR_variant	2456	.	.	.	.	.	.	.	1	CARM1	HGNC	23393	protein_coding	YES	CCDS12250.1	ENSP00000325690	CARM1_HUMAN	.	UPI000004B825	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCTGCTTTTTT	.	3	ESCA
CARM1	0	.	GRCh37	19	11033024	11033024	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*591delT	.	.	ENST00000327064	16/16	116	89	27	40	40	0	CARM1,3_prime_UTR_variant,,ENST00000327064,;CARM1,3_prime_UTR_variant,,ENST00000344150,;YIPF2,downstream_gene_variant,,ENST00000585858,;YIPF2,downstream_gene_variant,,ENST00000586575,;YIPF2,downstream_gene_variant,,ENST00000586748,;YIPF2,downstream_gene_variant,,ENST00000591872,;YIPF2,downstream_gene_variant,,ENST00000589971,;YIPF2,downstream_gene_variant,,ENST00000587943,;YIPF2,downstream_gene_variant,,ENST00000588347,;YIPF2,downstream_gene_variant,,ENST00000253031,;YIPF2,downstream_gene_variant,,ENST00000590329,;CARM1,downstream_gene_variant,,ENST00000586298,;YIPF2,downstream_gene_variant,,ENST00000592646,;CARM1,3_prime_UTR_variant,,ENST00000586221,;YIPF2,downstream_gene_variant,,ENST00000588962,;CARM1,downstream_gene_variant,,ENST00000592516,;CARM1,downstream_gene_variant,,ENST00000590699,;CARM1,downstream_gene_variant,,ENST00000586508,;	-	ENSG00000142453	ENST00000327064	Transcript	3_prime_UTR_variant	2608	.	.	.	.	.	.	.	1	CARM1	HGNC	23393	protein_coding	YES	CCDS12250.1	ENSP00000325690	CARM1_HUMAN	.	UPI000004B825	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCCCCTCCCCA	.	3	ESCA
SMARCA4	0	.	GRCh37	19	11123691	11123691	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2341A>G	p.Met781Val	p.M781V	ENST00000429416	17/36	57	54	3	37	36	1	SMARCA4,missense_variant,p.Met781Val,ENST00000450717,;SMARCA4,missense_variant,p.Met781Val,ENST00000358026,;SMARCA4,missense_variant,p.Met781Val,ENST00000413806,;SMARCA4,missense_variant,p.Met781Val,ENST00000590574,;SMARCA4,missense_variant,p.Met781Val,ENST00000444061,;SMARCA4,missense_variant,p.Met781Val,ENST00000344626,;SMARCA4,missense_variant,p.Met781Val,ENST00000541122,;SMARCA4,missense_variant,p.Met781Val,ENST00000429416,;SMARCA4,missense_variant,p.Met781Val,ENST00000589677,;CTC-215O4.4,intron_variant,,ENST00000587831,;RN7SL192P,downstream_gene_variant,,ENST00000584303,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;	G	ENSG00000127616	ENST00000429416	Transcript	missense_variant	2622	2341	781	M/V	Atg/Gtg	.	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	possibly_damaging(0.9)	17/36	.	Superfamily_domains:SSF52540,SMART_domains:SM00487,Pfam_domain:PF00176,Gene3D:3.40.50.300,hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACGAGATGGGC	.	2	ESCA
SBNO2	0	.	GRCh37	19	1122525	1122525	+	Missense_Mutation	SNP	G	G	A	rs745855080	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.947C>T	p.Ala316Val	p.A316V	ENST00000361757	10/32	13	8	5	12	12	0	SBNO2,missense_variant,p.Ala259Val,ENST00000438103,;SBNO2,missense_variant,p.Ala316Val,ENST00000587024,;SBNO2,missense_variant,p.Ala316Val,ENST00000361757,;SBNO2,non_coding_transcript_exon_variant,,ENST00000592222,;SBNO2,upstream_gene_variant,,ENST00000590446,;	A	ENSG00000064932	ENST00000361757	Transcript	missense_variant	1185	947	316	A/V	gCg/gTg	rs745855080	.	.	-1	SBNO2	HGNC	29158	protein_coding	YES	CCDS45894.1	ENSP00000354733	SBNO2_HUMAN	K7ERL2_HUMAN,K7ENA9_HUMAN	UPI0000140680	.	deleterious(0.03)	probably_damaging(0.995)	10/32	.	hmmpanther:PTHR12706:SF5,hmmpanther:PTHR12706,Gene3D:3.40.50.300,Pfam_domain:PF13872,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT	GCTCCGCATCG	byFrequency	3	ESCA
ELAVL3	0	.	GRCh37	19	11564773	11564773	+	3'UTR	DEL	T	T	-	rs559068480	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*568delA	.	.	ENST00000359227	7/7	46	28	18	22	22	0	ELAVL3,3_prime_UTR_variant,,ENST00000359227,;ELAVL3,downstream_gene_variant,,ENST00000438662,;PRKCSH,downstream_gene_variant,,ENST00000587327,;PRKCSH,downstream_gene_variant,,ENST00000589838,;PRKCSH,downstream_gene_variant,,ENST00000412601,;PRKCSH,downstream_gene_variant,,ENST00000591462,;PRKCSH,downstream_gene_variant,,ENST00000592741,;PRKCSH,downstream_gene_variant,,ENST00000252455,;PRKCSH,downstream_gene_variant,,ENST00000591510,;PRKCSH,downstream_gene_variant,,ENST00000586486,;PRKCSH,downstream_gene_variant,,ENST00000587290,;PRKCSH,downstream_gene_variant,,ENST00000592435,;PRKCSH,downstream_gene_variant,,ENST00000590098,;	-	ENSG00000196361	ENST00000359227	Transcript	3_prime_UTR_variant	2097	.	.	.	.	rs559068480	.	.	-1	ELAVL3	HGNC	3314	protein_coding	YES	CCDS32912.1	ENSP00000352162	ELAV3_HUMAN	Q96J71_HUMAN	UPI0000129E75	.	.	.	7/7	.	.	C:0.0008	C:0.0008	C:0.0029	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCCCCCTTTTTT	byFrequency|by1000G	2	ESCA
ZNF491	0	.	GRCh37	19	11918803	11918803	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*721G>T	.	.	ENST00000323169	3/3	106	87	19	80	80	0	ZNF491,3_prime_UTR_variant,,ENST00000323169,;ZNF491,downstream_gene_variant,,ENST00000450087,;ZNF491,intron_variant,,ENST00000492230,;	T	ENSG00000177599	ENST00000323169	Transcript	3_prime_UTR_variant	2366	.	.	.	.	.	.	.	1	ZNF491	HGNC	23706	protein_coding	YES	CCDS12267.1	ENSP00000313443	ZN491_HUMAN	C9IYV0_HUMAN	UPI000006D12C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAGGAGAA	.	5	ESCA
ZNF878	0	.	GRCh37	19	12157236	12157236	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138delA	p.Lys46AsnfsTer18	p.K46Nfs*18	ENST00000547628	3/4	93	74	19	57	57	0	ZNF878,frameshift_variant,p.Lys46AsnfsTer18,ENST00000547628,;ZNF878,frameshift_variant,p.Lys93AsnfsTer18,ENST00000602107,;CTD-2006C1.2,downstream_gene_variant,,ENST00000591898,;CTD-2006C1.2,downstream_gene_variant,,ENST00000476474,;CTD-2006C1.2,downstream_gene_variant,,ENST00000591838,;CTD-2006C1.10,frameshift_variant,p.Lys46AsnfsTer18,ENST00000547473,;	-	ENSG00000257446	ENST00000547628	Transcript	frameshift_variant	276	138	46	K/X	aaA/aa	.	.	.	-1	ZNF878	HGNC	37246	protein_coding	YES	CCDS45984.2	ENSP00000447931	ZN878_HUMAN	.	UPI00001D8268	.	.	.	3/4	.	Superfamily_domains:0044637,SMART_domains:SM00349,hmmpanther:PTHR24379,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTCCATTTTTT	.	3	ESCA
STK11	0	.	GRCh37	19	1220393	1220393	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486C>T	p.%3D	p.D162D	ENST00000326873	4/10	74	51	23	29	29	0	STK11,synonymous_variant,p.%3D,ENST00000326873,;STK11,synonymous_variant,p.%3D,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000586243,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,3_prime_UTR_variant,,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,upstream_gene_variant,,ENST00000585465,;	T	ENSG00000118046	ENST00000326873	Transcript	synonymous_variant	1659	486	162	D	gaC/gaT	.	.	.	1	STK11	HGNC	11389	protein_coding	YES	CCDS45896.1	ENSP00000324856	STK11_HUMAN	Q9NS52_HUMAN	UPI0000136105	.	.	.	4/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF1,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.0?|c.1_1302del1302|16,CODON|p.?|c.1_378del378|3,CODON|p.Y156fs*87|c.465_597del133|4,BUFFER|p.Q159*|c.475C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGACGGCCT	.	5	ESCA
GADD45GIP1	0	.	GRCh37	19	13065136	13065138	+	In_Frame_Del	DEL	CTT	CTT	-	rs777674072	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553_555delAAG	p.Lys185del	p.K185del	ENST00000316939	2/2	110	69	41	52	52	0	GADD45GIP1,inframe_deletion,p.Lys185del,ENST00000316939,;RAD23A,downstream_gene_variant,,ENST00000541222,;RAD23A,downstream_gene_variant,,ENST00000316856,;RAD23A,downstream_gene_variant,,ENST00000592268,;RAD23A,downstream_gene_variant,,ENST00000586534,;RAD23A,downstream_gene_variant,,ENST00000590881,;AC092069.1,upstream_gene_variant,,ENST00000410560,;RAD23A,downstream_gene_variant,,ENST00000588826,;RAD23A,downstream_gene_variant,,ENST00000593114,;RAD23A,downstream_gene_variant,,ENST00000591467,;RAD23A,downstream_gene_variant,,ENST00000591499,;RAD23A,downstream_gene_variant,,ENST00000586375,;	-	ENSG00000179271	ENST00000316939	Transcript	inframe_deletion	577-579	553-555	185	K/-	AAG/-	rs777674072,COSM1390697	.	.	-1	GADD45GIP1	HGNC	29996	protein_coding	YES	CCDS12290.1	ENSP00000323065	G45IP_HUMAN	Q7LAX7_HUMAN	UPI000006E725	.	.	.	2/2	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31761:SF1,hmmpanther:PTHR31761,Pfam_domain:PF10147	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCGCTCCTTCTTCT	.	3	ESCA
CCDC130	0	.	GRCh37	19	13873201	13873201	+	Missense_Mutation	SNP	C	C	T	rs377239448	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662C>T	p.Thr221Met	p.T221M	ENST00000586600	10/11	55	33	21	24	24	0	CCDC130,missense_variant,p.Thr221Met,ENST00000221554,;CCDC130,missense_variant,p.Thr84Met,ENST00000585844,;CCDC130,missense_variant,p.Thr221Met,ENST00000586600,;CCDC130,missense_variant,p.Thr172Met,ENST00000586666,;CCDC130,5_prime_UTR_variant,,ENST00000589669,;MRI1,upstream_gene_variant,,ENST00000040663,;CCDC130,downstream_gene_variant,,ENST00000589096,;MRI1,upstream_gene_variant,,ENST00000319545,;CCDC130,downstream_gene_variant,,ENST00000588809,;MRI1,upstream_gene_variant,,ENST00000593245,;CCDC130,non_coding_transcript_exon_variant,,ENST00000587019,;CCDC130,non_coding_transcript_exon_variant,,ENST00000593174,;MRI1,upstream_gene_variant,,ENST00000588526,;MRI1,upstream_gene_variant,,ENST00000589290,;CCDC130,downstream_gene_variant,,ENST00000588071,;MRI1,upstream_gene_variant,,ENST00000591688,;CCDC130,downstream_gene_variant,,ENST00000540216,;	T	ENSG00000104957	ENST00000586600	Transcript	missense_variant	1165	662	221	T/M	aCg/aTg	rs377239448	.	.	1	CCDC130	HGNC	28118	protein_coding	YES	CCDS12296.1	ENSP00000465776	CC130_HUMAN	K7EPA5_HUMAN,K7ELI4_HUMAN	UPI0000071AFB	.	deleterious(0.01)	possibly_damaging(0.788)	10/11	.	hmmpanther:PTHR12111:SF2,hmmpanther:PTHR12111,Pfam_domain:PF04502	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGACGGAAG	byFrequency|byCluster	5	ESCA
PRKACA	0	.	GRCh37	19	14208488	14208488	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547-2A>G	.	p.X183_splice	ENST00000308677	.	61	37	24	31	31	0	PRKACA,splice_acceptor_variant,,ENST00000593092,;PRKACA,splice_acceptor_variant,,ENST00000308677,;PRKACA,splice_acceptor_variant,,ENST00000587372,;PRKACA,splice_acceptor_variant,,ENST00000589994,;PRKACA,intron_variant,,ENST00000590853,;PRKACA,splice_acceptor_variant,,ENST00000350356,;PRKACA,splice_acceptor_variant,,ENST00000588209,;PRKACA,splice_acceptor_variant,,ENST00000536649,;PRKACA,non_coding_transcript_exon_variant,,ENST00000587533,;	C	ENSG00000072062	ENST00000308677	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	PRKACA	HGNC	9380	protein_coding	YES	CCDS12304.1	ENSP00000309591	KAPCA_HUMAN	K7EMV1_HUMAN	UPI0000001C8D	.	.	.	.	6/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCTGTGGG	.	5	ESCA
DAZAP1	0	.	GRCh37	19	1434830	1434830	+	Frame_Shift_Del	DEL	G	G	-	rs368917206,rs771328337	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1148delG	p.Gly383AlafsTer46	p.G383Afs*46	ENST00000233078	12/12	104	66	38	29	29	0	DAZAP1,frameshift_variant,p.Gly383AlafsTer46,ENST00000233078,;DAZAP1,frameshift_variant,p.Gly182AlafsTer46,ENST00000587079,;DAZAP1,3_prime_UTR_variant,,ENST00000336761,;DAZAP1,3_prime_UTR_variant,,ENST00000591999,;RPS15,upstream_gene_variant,,ENST00000591804,;RPS15,upstream_gene_variant,,ENST00000593052,;RPS15,upstream_gene_variant,,ENST00000233609,;RPS15,upstream_gene_variant,,ENST00000586686,;DAZAP1,downstream_gene_variant,,ENST00000592453,;RPS15,upstream_gene_variant,,ENST00000589656,;RPS15,upstream_gene_variant,,ENST00000591032,;RPS15,upstream_gene_variant,,ENST00000586656,;RPS15,upstream_gene_variant,,ENST00000586096,;RPS15,upstream_gene_variant,,ENST00000585665,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000585485,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000589874,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000589484,;RPS15,upstream_gene_variant,,ENST00000592623,;RPS15,upstream_gene_variant,,ENST00000592588,;RPS15,upstream_gene_variant,,ENST00000592700,;	-	ENSG00000071626	ENST00000233078	Transcript	frameshift_variant	1304	1143	381	S/X	tcG/tc	rs368917206,rs771328337	.	.	1	DAZAP1	HGNC	2683	protein_coding	YES	CCDS12065.1	ENSP00000233078	DAZP1_HUMAN	Q5IRM7_HUMAN,B3KS63_HUMAN	UPI00000728D6	.	.	.	12/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF259	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G383A|c.1148G>C|4	INDELOCATOR*|VARSCANI*|PINDEL	AGGGTCGGGGGG	byCluster|by1000G	3	ESCA
NDUFB7	0	.	GRCh37	19	14677646	14677646	+	Missense_Mutation	SNP	C	C	T	rs778158600	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212G>A	p.Arg71His	p.R71H	ENST00000215565	2/3	58	48	10	33	33	0	NDUFB7,missense_variant,p.Arg71His,ENST00000215565,;TECR,downstream_gene_variant,,ENST00000596073,;TECR,downstream_gene_variant,,ENST00000594545,;TECR,downstream_gene_variant,,ENST00000601187,;TECR,downstream_gene_variant,,ENST00000436007,;TECR,downstream_gene_variant,,ENST00000598715,;TECR,downstream_gene_variant,,ENST00000600083,;TECR,downstream_gene_variant,,ENST00000215567,;TECR,downstream_gene_variant,,ENST00000598298,;TECR,downstream_gene_variant,,ENST00000596164,;NDUFB7,synonymous_variant,p.%3D,ENST00000593353,;TECR,downstream_gene_variant,,ENST00000601461,;TECR,downstream_gene_variant,,ENST00000598918,;TECR,downstream_gene_variant,,ENST00000594958,;TECR,downstream_gene_variant,,ENST00000598408,;TECR,downstream_gene_variant,,ENST00000600076,;TECR,downstream_gene_variant,,ENST00000600395,;TECR,downstream_gene_variant,,ENST00000599101,;TECR,downstream_gene_variant,,ENST00000593637,;TECR,downstream_gene_variant,,ENST00000601350,;TECR,downstream_gene_variant,,ENST00000598333,;TECR,downstream_gene_variant,,ENST00000593775,;TECR,downstream_gene_variant,,ENST00000597607,;TECR,downstream_gene_variant,,ENST00000596953,;TECR,downstream_gene_variant,,ENST00000601652,;TECR,downstream_gene_variant,,ENST00000598987,;TECR,downstream_gene_variant,,ENST00000594807,;	T	ENSG00000099795	ENST00000215565	Transcript	missense_variant	274	212	71	R/H	cGt/cAt	rs778158600	.	.	-1	NDUFB7	HGNC	7702	protein_coding	YES	CCDS12314.1	ENSP00000215565	NDUB7_HUMAN	.	UPI000013C68C	.	deleterious(0.02)	possibly_damaging(0.698)	2/3	.	hmmpanther:PTHR20900,hmmpanther:PTHR20900:SF0,Pfam_domain:PF05676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCACGCTTG	.	4	ESCA
SYDE1	0	.	GRCh37	19	15222161	15222161	+	Missense_Mutation	SNP	T	T	C	rs771589119	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1328T>C	p.Val443Ala	p.V443A	ENST00000342784	5/8	95	69	25	69	69	0	SYDE1,missense_variant,p.Val376Ala,ENST00000600440,;SYDE1,missense_variant,p.Val65Ala,ENST00000602203,;SYDE1,missense_variant,p.Val100Ala,ENST00000600252,;SYDE1,missense_variant,p.Val443Ala,ENST00000342784,;ILVBL,downstream_gene_variant,,ENST00000598709,;ILVBL,downstream_gene_variant,,ENST00000534378,;ILVBL,downstream_gene_variant,,ENST00000263383,;SYDE1,downstream_gene_variant,,ENST00000597977,;ILVBL,downstream_gene_variant,,ENST00000534806,;ILVBL,downstream_gene_variant,,ENST00000533086,;ILVBL,downstream_gene_variant,,ENST00000596093,;ILVBL,downstream_gene_variant,,ENST00000524779,;ILVBL,downstream_gene_variant,,ENST00000525880,;	C	ENSG00000105137	ENST00000342784	Transcript	missense_variant	1359	1328	443	V/A	gTg/gCg	rs771589119	.	.	1	SYDE1	HGNC	25824	protein_coding	YES	CCDS12324.1	ENSP00000341489	SYDE1_HUMAN	.	UPI00001C092C	.	deleterious(0.03)	possibly_damaging(0.73)	5/8	.	PROSITE_profiles:PS50238,hmmpanther:PTHR23178:SF22,hmmpanther:PTHR23178,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGTGAAGA	byFrequency	5	ESCA
CYP4F3	0	.	GRCh37	19	15769134	15769134	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1176T>C	p.%3D	p.H392H	ENST00000221307	10/13	85	51	34	51	51	0	CYP4F3,synonymous_variant,p.%3D,ENST00000221307,;CYP4F3,synonymous_variant,p.%3D,ENST00000591058,;CYP4F3,synonymous_variant,p.%3D,ENST00000585846,;CYP4F3,synonymous_variant,p.%3D,ENST00000586182,;CYP4F3,upstream_gene_variant,,ENST00000588886,;CYP4F3,non_coding_transcript_exon_variant,,ENST00000592279,;CYP4F3,downstream_gene_variant,,ENST00000592424,;	C	ENSG00000186529	ENST00000221307	Transcript	synonymous_variant	1223	1176	392	H	caT/caC	.	.	.	1	CYP4F3	HGNC	2646	protein_coding	YES	CCDS12332.1	ENSP00000221307	CP4F3_HUMAN	B7Z5A8_HUMAN	UPI0000052BE3	.	.	.	10/13	.	hmmpanther:PTHR24290:SF46,hmmpanther:PTHR24290,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCATCCCCC	.	5	ESCA
AP1M1	0	.	GRCh37	19	16345014	16345014	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1214G>A	p.Arg405His	p.R405H	ENST00000444449	12/13	110	67	42	54	54	0	AP1M1,missense_variant,p.Arg340His,ENST00000429941,;AP1M1,missense_variant,p.Arg393His,ENST00000291439,;AP1M1,missense_variant,p.Arg321His,ENST00000590756,;AP1M1,missense_variant,p.Arg405His,ENST00000444449,;AP1M1,missense_variant,p.Arg321His,ENST00000541844,;AP1M1,intron_variant,,ENST00000586543,;AP1M1,non_coding_transcript_exon_variant,,ENST00000592703,;	A	ENSG00000072958	ENST00000444449	Transcript	missense_variant	1307	1214	405	R/H	cGc/cAc	COSM992439	.	.	1	AP1M1	HGNC	13667	protein_coding	YES	CCDS46008.1	ENSP00000388996	AP1M1_HUMAN	Q59EK3_HUMAN,K7ER75_HUMAN,K7EQ90_HUMAN,K7EPJ8_HUMAN,K7ENA7_HUMAN	UPI000051DDEE	.	deleterious(0)	benign(0.344)	12/13	.	PROSITE_profiles:PS51072,hmmpanther:PTHR11998,hmmpanther:PTHR11998:SF22,Pfam_domain:PF00928,PIRSF_domain:PIRSF005992,Superfamily_domains:0038852	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGCGCTACC	.	5	ESCA
TMEM38A	0	.	GRCh37	19	16799143	16799143	+	Silent	SNP	C	C	T	rs199670971	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.861C>T	p.%3D	p.S287S	ENST00000187762	6/6	34	19	15	15	15	0	TMEM38A,synonymous_variant,p.%3D,ENST00000187762,;TMEM38A,intron_variant,,ENST00000599479,;	T	ENSG00000072954	ENST00000187762	Transcript	synonymous_variant	952	861	287	S	agC/agT	rs199670971	.	.	1	TMEM38A	HGNC	28462	protein_coding	YES	CCDS12349.1	ENSP00000187762	TM38A_HUMAN	.	UPI000006E0B9	.	.	.	6/6	.	hmmpanther:PTHR12454:SF3,hmmpanther:PTHR12454	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0003	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGCGAGGG	byCluster|by1000G	5	ESCA
ATP8B3	0	.	GRCh37	19	1796768	1796768	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1695G>T	p.Trp565Cys	p.W565C	ENST00000310127	16/29	43	27	16	16	16	0	ATP8B3,missense_variant,p.Trp565Cys,ENST00000310127,;ATP8B3,missense_variant,p.Trp565Cys,ENST00000539485,;ATP8B3,missense_variant,p.Trp518Cys,ENST00000525591,;ATP8B3,downstream_gene_variant,,ENST00000526092,;ATP8B3,3_prime_UTR_variant,,ENST00000531925,;ATP8B3,downstream_gene_variant,,ENST00000533107,;	A	ENSG00000130270	ENST00000310127	Transcript	missense_variant	1934	1695	565	W/C	tgG/tgT	.	.	.	-1	ATP8B3	HGNC	13535	protein_coding	YES	CCDS45901.1	ENSP00000311336	AT8B3_HUMAN	.	UPI0000074660	.	deleterious(0.01)	benign(0.316)	16/29	.	hmmpanther:PTHR24092:SF44,hmmpanther:PTHR24092,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01652,Pfam_domain:PF12710,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCGCCAGAA	.	5	ESCA
RPL18A	0	.	GRCh37	19	17972276	17972276	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193G>T	p.Gly65Trp	p.G65W	ENST00000222247	2/5	16	10	5	11	11	0	RPL18A,missense_variant,p.Gly36Trp,ENST00000597648,;RPL18A,missense_variant,p.Gly36Trp,ENST00000599870,;RPL18A,missense_variant,p.Gly65Trp,ENST00000600147,;RPL18A,missense_variant,p.Gly26Trp,ENST00000599898,;RPL18A,missense_variant,p.Gly65Trp,ENST00000222247,;SNORA68,upstream_gene_variant,,ENST00000384437,;RPL18A,non_coding_transcript_exon_variant,,ENST00000600238,;RPL18A,non_coding_transcript_exon_variant,,ENST00000602216,;	T	ENSG00000105640	ENST00000222247	Transcript	missense_variant	274	193	65	G/W	Ggg/Tgg	.	.	.	1	RPL18A	HGNC	10311	protein_coding	YES	CCDS12367.1	ENSP00000222247	RL18A_HUMAN	Q76N54_HUMAN,M0R3D6_HUMAN,M0R1A7_HUMAN,B4DUV3_HUMAN	UPI0000133CD9	.	deleterious(0)	probably_damaging(0.928)	2/5	.	HAMAP:MF_00273,hmmpanther:PTHR10052:SF6,hmmpanther:PTHR10052,Pfam_domain:PF01775,PIRSF_domain:PIRSF002190	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTGGGCAG	.	5	ESCA
KCNN1	0	.	GRCh37	19	18100628	18100628	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1274G>A	p.Arg425His	p.R425H	ENST00000222249	8/11	59	37	22	44	44	0	KCNN1,missense_variant,p.Arg425His,ENST00000222249,;	A	ENSG00000105642	ENST00000222249	Transcript	missense_variant	1593	1274	425	R/H	cGt/cAt	COSM3099295,COSM3099294	.	.	1	KCNN1	HGNC	6290	protein_coding	YES	CCDS67611.1	ENSP00000476519	KCNN1_HUMAN	.	UPI00001649F9	.	deleterious(0)	probably_damaging(0.987)	8/11	.	hmmpanther:PTHR10153:SF8,hmmpanther:PTHR10153,Pfam_domain:PF02888,Gene3D:1.10.287.70,SMART_domains:SM01053,Superfamily_domains:SSF81327	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGTAAGT	.	5	ESCA
PIK3R2	0	.	GRCh37	19	18266584	18266584	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-106C>T	.	.	ENST00000222254	2/16	64	50	14	40	40	0	PIK3R2,5_prime_UTR_variant,,ENST00000222254,;MAST3,downstream_gene_variant,,ENST00000262811,;AC007192.6,upstream_gene_variant,,ENST00000600364,;PIK3R2,5_prime_UTR_variant,,ENST00000593731,;PIK3R2,5_prime_UTR_variant,,ENST00000426902,;	T	ENSG00000105647	ENST00000222254	Transcript	5_prime_UTR_variant	495	.	.	.	.	.	.	.	1	PIK3R2	HGNC	8980	protein_coding	YES	CCDS12371.1	ENSP00000222254	P85B_HUMAN	Q96CK7_HUMAN,M0QYU3_HUMAN	UPI000006EF95	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCACCCCAA	.	5	ESCA
UPF1	0	.	GRCh37	19	18967000	18967000	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1715C>A	p.Pro572His	p.P572H	ENST00000262803	13/24	52	19	33	52	52	0	UPF1,missense_variant,p.Pro583His,ENST00000599848,;UPF1,missense_variant,p.Pro572His,ENST00000262803,;UPF1,downstream_gene_variant,,ENST00000598209,;UPF1,downstream_gene_variant,,ENST00000600310,;UPF1,downstream_gene_variant,,ENST00000600868,;UPF1,downstream_gene_variant,,ENST00000600012,;UPF1,downstream_gene_variant,,ENST00000598471,;UPF1,downstream_gene_variant,,ENST00000594243,;UPF1,downstream_gene_variant,,ENST00000601689,;UPF1,upstream_gene_variant,,ENST00000596842,;	A	ENSG00000005007	ENST00000262803	Transcript	missense_variant	1987	1715	572	P/H	cCt/cAt	.	.	.	1	UPF1	HGNC	9962	protein_coding	YES	CCDS12386.1	ENSP00000262803	RENT1_HUMAN	B3KY55_HUMAN	UPI0000001C89	.	tolerated(0.06)	benign(0.017)	13/24	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF340,Gene3D:3.40.50.300,Pfam_domain:PF13086,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGCCTGAGC	.	5	ESCA
ARMC6	0	.	GRCh37	19	19145003	19145003	+	5'UTR	SNP	T	T	C	rs763291625	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16T>C	.	.	ENST00000535612	2/9	42	10	32	35	35	0	ARMC6,splice_region_variant,,ENST00000541725,;ARMC6,5_prime_UTR_variant,,ENST00000392336,;ARMC6,5_prime_UTR_variant,,ENST00000543877,;ARMC6,5_prime_UTR_variant,,ENST00000540792,;ARMC6,5_prime_UTR_variant,,ENST00000535612,;ARMC6,intron_variant,,ENST00000540707,;ARMC6,intron_variant,,ENST00000537263,;ARMC6,intron_variant,,ENST00000546344,;ARMC6,intron_variant,,ENST00000536098,;ARMC6,intron_variant,,ENST00000392335,;ARMC6,intron_variant,,ENST00000535288,;ARMC6,intron_variant,,ENST00000538663,;ARMC6,intron_variant,,ENST00000269932,;ARMC6,intron_variant,,ENST00000541898,;SUGP2,upstream_gene_variant,,ENST00000601879,;SUGP2,upstream_gene_variant,,ENST00000600377,;SUGP2,upstream_gene_variant,,ENST00000594445,;SUGP2,upstream_gene_variant,,ENST00000452918,;SUGP2,upstream_gene_variant,,ENST00000337018,;SUGP2,upstream_gene_variant,,ENST00000456085,;SUGP2,upstream_gene_variant,,ENST00000598202,;ARMC6,5_prime_UTR_variant,,ENST00000539985,;ARMC6,intron_variant,,ENST00000545091,;ARMC6,upstream_gene_variant,,ENST00000535758,;SUGP2,upstream_gene_variant,,ENST00000330854,;SUGP2,upstream_gene_variant,,ENST00000600239,;SUGP2,upstream_gene_variant,,ENST00000598240,;SUGP2,upstream_gene_variant,,ENST00000594773,;	C	ENSG00000105676	ENST00000535612	Transcript	5_prime_UTR_variant	417	.	.	.	.	rs763291625	.	.	1	ARMC6	HGNC	25049	protein_coding	YES	CCDS56089.1	ENSP00000444156	ARMC6_HUMAN	F5H7V0_HUMAN,F5H6J3_HUMAN,F5H4P3_HUMAN,F5H3X1_HUMAN,F5H2X2_HUMAN,F5H2K4_HUMAN,F5H052_HUMAN,F5GWV0_HUMAN,B4E1N1_HUMAN	UPI0000D4C04D	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGCTACAGG	byFrequency	5	ESCA
CSNK1G2	0	.	GRCh37	19	1954193	1954193	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-266+12776C>T	.	.	ENST00000255641	.	65	38	27	33	33	0	CSNK1G2,intron_variant,,ENST00000255641,;CSNK1G2,intron_variant,,ENST00000591752,;CSNK1G2,upstream_gene_variant,,ENST00000589350,;CSNK1G2-AS1,non_coding_transcript_exon_variant,,ENST00000586395,;CSNK1G2-AS1,non_coding_transcript_exon_variant,,ENST00000314315,;CSNK1G2,downstream_gene_variant,,ENST00000587123,;	T	ENSG00000133275	ENST00000255641	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CSNK1G2	HGNC	2455	protein_coding	YES	CCDS12077.1	ENSP00000255641	KC1G2_HUMAN	.	UPI00000015E2	.	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGCGCCCCTCC	.	4	ESCA
MKNK2	0	.	GRCh37	19	2038031	2038031	+	3'UTR	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1581delG	.	.	ENST00000250896	14/14	44	36	8	30	30	0	MKNK2,3_prime_UTR_variant,,ENST00000591601,;MKNK2,3_prime_UTR_variant,,ENST00000250896,;MKNK2,intron_variant,,ENST00000589441,;MKNK2,intron_variant,,ENST00000309340,;MKNK2,intron_variant,,ENST00000591142,;MKNK2,downstream_gene_variant,,ENST00000541165,;MKNK2,downstream_gene_variant,,ENST00000588014,;MKNK2,downstream_gene_variant,,ENST00000591588,;BTBD2,upstream_gene_variant,,ENST00000590646,;BTBD2,upstream_gene_variant,,ENST00000587742,;BTBD2,upstream_gene_variant,,ENST00000588395,;MKNK2,non_coding_transcript_exon_variant,,ENST00000587416,;MKNK2,downstream_gene_variant,,ENST00000588346,;MKNK2,downstream_gene_variant,,ENST00000586620,;MKNK2,downstream_gene_variant,,ENST00000586828,;MKNK2,downstream_gene_variant,,ENST00000585667,;	-	ENSG00000099875	ENST00000250896	Transcript	3_prime_UTR_variant	3224	.	.	.	.	.	.	.	-1	MKNK2	HGNC	7111	protein_coding	YES	CCDS12080.1	ENSP00000250896	MKNK2_HUMAN	K7EIN7_HUMAN,B4DEQ4_HUMAN,B3KS07_HUMAN,A4CYL7_HUMAN	UPI000006E9B4	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCCCCACCCCCC	.	2	ESCA
LMNB2	0	.	GRCh37	19	2432415	2432415	+	Missense_Mutation	SNP	G	G	A	rs771054060	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1589C>T	p.Thr530Met	p.T530M	ENST00000325327	9/12	76	19	56	62	62	0	LMNB2,missense_variant,p.Thr510Met,ENST00000582871,;LMNB2,missense_variant,p.Thr530Met,ENST00000325327,;TIMM13,upstream_gene_variant,,ENST00000215570,;TIMM13,upstream_gene_variant,,ENST00000591871,;LMNB2,splice_region_variant,,ENST00000532465,;LMNB2,downstream_gene_variant,,ENST00000527409,;LMNB2,downstream_gene_variant,,ENST00000534495,;LMNB2,upstream_gene_variant,,ENST00000475819,;LMNB2,downstream_gene_variant,,ENST00000490554,;	A	ENSG00000176619	ENST00000325327	Transcript	missense_variant	1652	1589	530	T/M	aCg/aTg	rs771054060,COSM1197300	.	.	-1	LMNB2	HGNC	6638	protein_coding	YES	CCDS12090.2	ENSP00000327054	.	J9JID7_HUMAN	UPI000059D625	.	deleterious(0.01)	probably_damaging(0.995)	9/12	.	hmmpanther:PTHR23239:SF152,hmmpanther:PTHR23239,Pfam_domain:PF00932,Gene3D:2.60.40.1260,Superfamily_domains:SSF74853	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACCGTGACC	byFrequency	5	ESCA
USF2	0	.	GRCh37	19	35770659	35770659	+	3'UTR	DEL	A	A	-	rs551671278	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*509delA	.	.	ENST00000222305	10/10	19	11	7	28	27	1	USF2,3_prime_UTR_variant,,ENST00000222305,;USF2,3_prime_UTR_variant,,ENST00000343550,;USF2,3_prime_UTR_variant,,ENST00000595068,;HAMP,upstream_gene_variant,,ENST00000598398,;USF2,downstream_gene_variant,,ENST00000594064,;USF2,downstream_gene_variant,,ENST00000379134,;USF2,downstream_gene_variant,,ENST00000599471,;USF2,downstream_gene_variant,,ENST00000599625,;USF2,downstream_gene_variant,,ENST00000596380,;HAMP,upstream_gene_variant,,ENST00000222304,;USF2,non_coding_transcript_exon_variant,,ENST00000600341,;USF2,non_coding_transcript_exon_variant,,ENST00000607959,;USF2,non_coding_transcript_exon_variant,,ENST00000594264,;HAMP,upstream_gene_variant,,ENST00000593580,;USF2,downstream_gene_variant,,ENST00000600898,;USF2,downstream_gene_variant,,ENST00000597671,;	-	ENSG00000105698	ENST00000222305	Transcript	3_prime_UTR_variant	1578	.	.	.	.	rs551671278	.	.	1	USF2	HGNC	12594	protein_coding	YES	CCDS12452.1	ENSP00000222305	USF2_HUMAN	.	UPI0000137E4A	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTGACAAAAAA	.	2	ESCA
CD22	0	.	GRCh37	19	35828664	35828664	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725C>T	p.Pro242Leu	p.P242L	ENST00000085219	5/14	10	4	6	16	16	0	CD22,missense_variant,p.Pro242Leu,ENST00000544992,;CD22,missense_variant,p.Pro122Leu,ENST00000270311,;CD22,missense_variant,p.Pro242Leu,ENST00000085219,;CD22,missense_variant,p.Pro242Leu,ENST00000536635,;CD22,missense_variant,p.Pro70Leu,ENST00000419549,;CD22,intron_variant,,ENST00000600424,;CD22,intron_variant,,ENST00000341773,;CD22,intron_variant,,ENST00000594250,;CD22,intron_variant,,ENST00000599811,;CD22,downstream_gene_variant,,ENST00000595780,;CD22,downstream_gene_variant,,ENST00000598537,;CD22,downstream_gene_variant,,ENST00000600131,;CD22,downstream_gene_variant,,ENST00000593867,;CD22,downstream_gene_variant,,ENST00000597916,;CD22,non_coding_transcript_exon_variant,,ENST00000601329,;CD22,non_coding_transcript_exon_variant,,ENST00000598028,;CD22,non_coding_transcript_exon_variant,,ENST00000601732,;CD22,intron_variant,,ENST00000597433,;CD22,intron_variant,,ENST00000598815,;CD22,downstream_gene_variant,,ENST00000595419,;CD22,downstream_gene_variant,,ENST00000598138,;CD22,downstream_gene_variant,,ENST00000601414,;CD22,downstream_gene_variant,,ENST00000600905,;CD22,3_prime_UTR_variant,,ENST00000601769,;CD22,3_prime_UTR_variant,,ENST00000594349,;CD22,intron_variant,,ENST00000600655,;CD22,upstream_gene_variant,,ENST00000594125,;CD22,upstream_gene_variant,,ENST00000602123,;CD22,downstream_gene_variant,,ENST00000602224,;CD22,downstream_gene_variant,,ENST00000599717,;CD22,downstream_gene_variant,,ENST00000596492,;	T	ENSG00000012124	ENST00000085219	Transcript	missense_variant	791	725	242	P/L	cCg/cTg	.	.	.	1	CD22	HGNC	1643	protein_coding	YES	CCDS12457.1	ENSP00000085219	CD22_HUMAN	Q0EAF5_HUMAN,Q9UQB2_HUMAN,Q9UQB1_HUMAN,M0R3H1_HUMAN,M0R2M0_HUMAN,M0R1M2_HUMAN,M0QYP4_HUMAN	UPI000012733D	.	deleterious(0)	probably_damaging(1)	5/14	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF39,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CACCCCGAAGT	.	3	ESCA
RYR1	0	.	GRCh37	19	38937180	38937180	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.700C>A	p.Pro234Thr	p.P234T	ENST00000359596	8/106	34	19	15	38	38	0	RYR1,missense_variant,p.Pro234Thr,ENST00000355481,;RYR1,missense_variant,p.Pro234Thr,ENST00000360985,;RYR1,missense_variant,p.Pro234Thr,ENST00000359596,;	A	ENSG00000196218	ENST00000359596	Transcript	missense_variant	700	700	234	P/T	Cct/Act	COSM3533374	.	.	1	RYR1	HGNC	10483	protein_coding	YES	CCDS33011.1	ENSP00000352608	RYR1_HUMAN	O75591_HUMAN,B4DET7_HUMAN	UPI0000D7E62F	.	.	benign(0.18)	8/106	.	PROSITE_profiles:PS50919,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF02815,Gene3D:2.80.10.50,SMART_domains:SM00472,Superfamily_domains:SSF82109	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCCCTGCT	.	5	ESCA
RYR1	0	.	GRCh37	19	38968461	38968461	+	Missense_Mutation	SNP	C	C	T	rs200546266	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4405C>T	p.Arg1469Trp	p.R1469W	ENST00000359596	30/106	20	4	16	19	19	0	RYR1,missense_variant,p.Arg1469Trp,ENST00000355481,;RYR1,missense_variant,p.Arg1469Trp,ENST00000360985,;RYR1,missense_variant,p.Arg1469Trp,ENST00000359596,;	T	ENSG00000196218	ENST00000359596	Transcript	missense_variant	4405	4405	1469	R/W	Cgg/Tgg	rs200546266,CM105854,COSM1564447	.	.	1	RYR1	HGNC	10483	protein_coding	YES	CCDS33011.1	ENSP00000352608	RYR1_HUMAN	O75591_HUMAN,B4DET7_HUMAN	UPI0000D7E62F	.	.	probably_damaging(0.994)	30/106	.	PROSITE_profiles:PS50188,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF00622,SMART_domains:SM00449	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0001	uncertain_significance	0,0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTCCGGGTC	byCluster|by1000G	5	ESCA
EEF2	0	.	GRCh37	19	3984216	3984216	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136A>G	p.Ile46Val	p.I46V	ENST00000309311	2/15	105	43	62	81	81	0	EEF2,missense_variant,p.Ile46Val,ENST00000309311,;SNORD37,upstream_gene_variant,,ENST00000384048,;EEF2,non_coding_transcript_exon_variant,,ENST00000600720,;EEF2,non_coding_transcript_exon_variant,,ENST00000594885,;EEF2,upstream_gene_variant,,ENST00000598436,;EEF2,upstream_gene_variant,,ENST00000598182,;EEF2,upstream_gene_variant,,ENST00000596417,;	C	ENSG00000167658	ENST00000309311	Transcript	missense_variant	225	136	46	I/V	Atc/Gtc	.	.	.	-1	EEF2	HGNC	3214	protein_coding	YES	CCDS12117.1	ENSP00000307940	EF2_HUMAN	Q8TA90_HUMAN,B4DMC6_HUMAN	UPI00001649F3	.	deleterious(0.05)	benign(0.039)	2/15	.	hmmpanther:PTHR23115:SF103,hmmpanther:PTHR23115,Gene3D:3.40.50.300,Pfam_domain:PF00009,TIGRFAM_domain:TIGR00231,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGATGATGC	.	5	ESCA
FCGBP	0	.	GRCh37	19	40392611	40392611	+	Silent	SNP	C	C	T	rs781896995	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7893G>A	p.%3D	p.P2631P	ENST00000221347	16/36	95	69	26	104	104	0	FCGBP,synonymous_variant,p.%3D,ENST00000221347,;FCGBP,intron_variant,,ENST00000601713,;	T	ENSG00000090920	ENST00000221347	Transcript	synonymous_variant	7901	7893	2631	P	ccG/ccA	rs781896995	.	.	-1	FCGBP	HGNC	13572	protein_coding	YES	CCDS12546.1	ENSP00000221347	FCGBP_HUMAN	.	UPI00001B0455	.	.	.	16/36	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF244,hmmpanther:PTHR11339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGGCGGCAG	byFrequency	5	ESCA
FCGBP	0	.	GRCh37	19	40396087	40396087	+	Missense_Mutation	SNP	C	C	T	rs782342257	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7310G>A	p.Arg2437Gln	p.R2437Q	ENST00000221347	15/36	81	56	25	49	49	0	FCGBP,missense_variant,p.Arg2437Gln,ENST00000221347,;FCGBP,intron_variant,,ENST00000601713,;	T	ENSG00000090920	ENST00000221347	Transcript	missense_variant	7318	7310	2437	R/Q	cGg/cAg	rs782342257	.	.	-1	FCGBP	HGNC	13572	protein_coding	YES	CCDS12546.1	ENSP00000221347	FCGBP_HUMAN	.	UPI00001B0455	.	.	possibly_damaging(0.553)	15/36	.	hmmpanther:PTHR11339:SF244,hmmpanther:PTHR11339,Pfam_domain:PF12714,SMART_domains:SM00215,SMART_domains:SM00214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	ATGGCCGGCAG	.	2	ESCA
ITPKC	0	.	GRCh37	19	41223790	41223791	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756dupA	p.Gln253ThrfsTer4	p.Q253Tfs*4	ENST00000263370	1/7	34	24	10	24	24	0	ITPKC,frameshift_variant,p.Gln253ThrfsTer4,ENST00000263370,;ADCK4,intron_variant,,ENST00000594084,;ADCK4,upstream_gene_variant,,ENST00000593723,;ADCK4,upstream_gene_variant,,ENST00000243583,;ADCK4,upstream_gene_variant,,ENST00000595254,;ADCK4,upstream_gene_variant,,ENST00000600707,;ADCK4,upstream_gene_variant,,ENST00000450541,;ADCK4,upstream_gene_variant,,ENST00000594720,;ADCK4,upstream_gene_variant,,ENST00000600080,;ADCK4,upstream_gene_variant,,ENST00000594490,;ADCK4,upstream_gene_variant,,ENST00000324464,;ADCK4,upstream_gene_variant,,ENST00000601967,;ADCK4,upstream_gene_variant,,ENST00000596357,;ADCK4,upstream_gene_variant,,ENST00000599643,;ADCK4,upstream_gene_variant,,ENST00000596455,;ADCK4,upstream_gene_variant,,ENST00000601451,;ADCK4,upstream_gene_variant,,ENST00000601304,;ADCK4,upstream_gene_variant,,ENST00000593544,;	A	ENSG00000086544	ENST00000263370	Transcript	frameshift_variant	783-784	750-751	250-251	-/X	-/A	.	.	.	1	ITPKC	HGNC	14897	protein_coding	YES	CCDS12563.1	ENSP00000263370	IP3KC_HUMAN	.	UPI000006E1AC	.	.	.	1/7	.	hmmpanther:PTHR12400,hmmpanther:PTHR12400:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCCAGAAAAA	.	3	ESCA
RTN2	0	.	GRCh37	19	45996513	45996513	+	Frame_Shift_Del	DEL	G	G	-	rs748397131	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938delC	p.Pro313LeufsTer9	p.P313Lfs*9	ENST00000245923	5/11	34	23	11	30	30	0	RTN2,frameshift_variant,p.Pro39LeufsTer9,ENST00000590526,;RTN2,frameshift_variant,p.Pro313LeufsTer9,ENST00000245923,;RTN2,5_prime_UTR_variant,,ENST00000430715,;RTN2,intron_variant,,ENST00000344680,;PPM1N,intron_variant,,ENST00000401705,;PPM1N,upstream_gene_variant,,ENST00000456399,;PPM1N,upstream_gene_variant,,ENST00000396737,;RTN2,upstream_gene_variant,,ENST00000590746,;RTN2,downstream_gene_variant,,ENST00000589384,;RTN2,upstream_gene_variant,,ENST00000588036,;RTN2,frameshift_variant,p.Pro313LeufsTer9,ENST00000587597,;RTN2,intron_variant,,ENST00000591286,;RTN2,upstream_gene_variant,,ENST00000593129,;RTN2,upstream_gene_variant,,ENST00000591789,;RTN2,downstream_gene_variant,,ENST00000592064,;RTN2,upstream_gene_variant,,ENST00000589628,;RTN2,upstream_gene_variant,,ENST00000593187,;	-	ENSG00000125744	ENST00000245923	Transcript	frameshift_variant	1174	938	313	P/X	cCt/ct	rs748397131	.	.	-1	RTN2	HGNC	10468	protein_coding	YES	CCDS12665.1	ENSP00000245923	RTN2_HUMAN	K7EMR7_HUMAN	UPI00001352DC	.	.	.	5/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10994:SF66,hmmpanther:PTHR10994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAGTAGGGGGG	.	3	ESCA
VASP	0	.	GRCh37	19	46029855	46029855	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*420A>T	.	.	ENST00000245932	13/13	12	5	6	17	17	0	VASP,3_prime_UTR_variant,,ENST00000245932,;VASP,downstream_gene_variant,,ENST00000590603,;VASP,downstream_gene_variant,,ENST00000592139,;OPA3,downstream_gene_variant,,ENST00000323060,;VASP,downstream_gene_variant,,ENST00000586619,;VASP,3_prime_UTR_variant,,ENST00000586014,;VASP,downstream_gene_variant,,ENST00000590459,;VASP,downstream_gene_variant,,ENST00000588482,;VASP,downstream_gene_variant,,ENST00000587444,;VASP,downstream_gene_variant,,ENST00000588273,;VASP,downstream_gene_variant,,ENST00000588463,;	T	ENSG00000125753	ENST00000245932	Transcript	3_prime_UTR_variant	1919	.	.	.	.	.	.	.	1	VASP	HGNC	12652	protein_coding	YES	CCDS33051.1	ENSP00000245932	VASP_HUMAN	K7ENR7_HUMAN	UPI0000001C69	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	GGGAAATTTTT	.	4	ESCA
SYMPK	0	.	GRCh37	19	46328449	46328449	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2470C>T	p.%3D	p.L824L	ENST00000245934	18/27	104	38	65	49	49	0	SYMPK,synonymous_variant,p.%3D,ENST00000245934,;AC092301.3,upstream_gene_variant,,ENST00000601618,;SYMPK,upstream_gene_variant,,ENST00000598155,;SYMPK,3_prime_UTR_variant,,ENST00000600237,;SYMPK,non_coding_transcript_exon_variant,,ENST00000599460,;SYMPK,non_coding_transcript_exon_variant,,ENST00000599814,;SYMPK,non_coding_transcript_exon_variant,,ENST00000593504,;SYMPK,upstream_gene_variant,,ENST00000598329,;	A	ENSG00000125755	ENST00000245934	Transcript	synonymous_variant	2715	2470	824	L	Ctg/Ttg	.	.	.	-1	SYMPK	HGNC	22935	protein_coding	YES	CCDS12676.2	ENSP00000245934	SYMPK_HUMAN	M0R1C2_HUMAN,M0R180_HUMAN,M0R039_HUMAN,M0QXP5_HUMAN	UPI00002026C0	.	.	.	18/27	.	hmmpanther:PTHR15245,hmmpanther:PTHR15245:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCAGCACCG	.	5	ESCA
CCDC8	0	.	GRCh37	19	46914706	46914706	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1362T>C	p.%3D	p.A454A	ENST00000307522	1/1	54	44	10	20	20	0	CCDC8,synonymous_variant,p.%3D,ENST00000307522,;	G	ENSG00000169515	ENST00000307522	Transcript	synonymous_variant	2136	1362	454	A	gcT/gcC	.	.	.	-1	CCDC8	HGNC	25367	protein_coding	YES	CCDS12685.1	ENSP00000303158	CCDC8_HUMAN	.	UPI00000730F2	.	.	.	1/1	.	hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTTCAGCTTC	.	4	ESCA
ARHGAP35	0	.	GRCh37	19	47423886	47423886	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1954C>T	p.Gln652Ter	p.Q652*	ENST00000404338	1/6	21	6	15	19	19	0	ARHGAP35,stop_gained,p.Gln652Ter,ENST00000404338,;	T	ENSG00000160007	ENST00000404338	Transcript	stop_gained	1954	1954	652	Q/*	Cag/Tag	.	.	.	1	ARHGAP35	HGNC	4591	protein_coding	YES	CCDS46127.1	ENSP00000385720	RHG35_HUMAN	.	UPI0000163F71	.	.	.	1/6	.	hmmpanther:PTHR23178,hmmpanther:PTHR23178:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTCCAGACG	.	5	ESCA
FEM1A	0	.	GRCh37	19	4794097	4794097	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*221C>T	.	.	ENST00000269856	1/1	70	34	36	48	48	0	FEM1A,3_prime_UTR_variant,,ENST00000269856,;AC005523.3,upstream_gene_variant,,ENST00000598782,;AC005523.2,non_coding_transcript_exon_variant,,ENST00000601192,;AC005523.2,downstream_gene_variant,,ENST00000596170,;	T	ENSG00000141965	ENST00000269856	Transcript	3_prime_UTR_variant	2370	.	.	.	.	.	.	.	1	FEM1A	HGNC	16934	protein_coding	YES	CCDS12135.1	ENSP00000269856	FEM1A_HUMAN	.	UPI0000073096	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCCGGGAG	.	5	ESCA
PTOV1	0	.	GRCh37	19	50363638	50363639	+	3'UTR	INS	-	-	G	rs577978306	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*110dupG	.	.	ENST00000391842	12/12	21	14	6	17	17	0	PTOV1,3_prime_UTR_variant,,ENST00000391842,;PTOV1,3_prime_UTR_variant,,ENST00000221557,;PTOV1,intron_variant,,ENST00000601675,;PTOV1,intron_variant,,ENST00000599732,;PTOV1,intron_variant,,ENST00000600603,;PTOV1,intron_variant,,ENST00000597730,;PTOV1,intron_variant,,ENST00000601638,;PTOV1,intron_variant,,ENST00000601093,;PNKP,downstream_gene_variant,,ENST00000600910,;PNKP,downstream_gene_variant,,ENST00000597965,;PNKP,downstream_gene_variant,,ENST00000596014,;PNKP,downstream_gene_variant,,ENST00000600573,;PNKP,downstream_gene_variant,,ENST00000322344,;PTOV1,downstream_gene_variant,,ENST00000600793,;PTOV1,downstream_gene_variant,,ENST00000594151,;AC018766.4,non_coding_transcript_exon_variant,,ENST00000596624,;AC018766.5,upstream_gene_variant,,ENST00000593654,;AC018766.5,upstream_gene_variant,,ENST00000599259,;AC018766.5,upstream_gene_variant,,ENST00000601893,;PTOV1,intron_variant,,ENST00000598325,;PTOV1,downstream_gene_variant,,ENST00000600105,;PTOV1,downstream_gene_variant,,ENST00000594165,;PTOV1,intron_variant,,ENST00000597793,;PTOV1,intron_variant,,ENST00000601612,;PNKP,downstream_gene_variant,,ENST00000599454,;PNKP,downstream_gene_variant,,ENST00000595081,;PNKP,downstream_gene_variant,,ENST00000593706,;PNKP,downstream_gene_variant,,ENST00000594661,;PNKP,downstream_gene_variant,,ENST00000593946,;PTOV1,downstream_gene_variant,,ENST00000595934,;PTOV1,downstream_gene_variant,,ENST00000596424,;PNKP,downstream_gene_variant,,ENST00000601816,;PTOV1,downstream_gene_variant,,ENST00000598632,;PNKP,downstream_gene_variant,,ENST00000598020,;	G	ENSG00000104960	ENST00000391842	Transcript	3_prime_UTR_variant	1523-1524	.	.	.	.	rs577978306	.	.	1	PTOV1	HGNC	9632	protein_coding	YES	CCDS12782.1	ENSP00000375717	PTOV1_HUMAN	.	UPI000000DA02	.	.	.	12/12	.	.	G:0.0124	G:0.0356	G:0.0043	.	G:0.002	G:0.001	G:0.0092	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCATGTGGGGG	byFrequency|by1000G	2	ESCA
MADCAM1	0	.	GRCh37	19	504772	504772	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956C>T	p.Pro319Leu	p.P319L	ENST00000215637	5/5	67	31	35	30	30	0	MADCAM1,missense_variant,p.Pro100Leu,ENST00000587541,;MADCAM1,missense_variant,p.Pro137Leu,ENST00000382683,;MADCAM1,missense_variant,p.Pro319Leu,ENST00000215637,;MADCAM1,missense_variant,p.Pro232Leu,ENST00000346144,;TPGS1,upstream_gene_variant,,ENST00000359315,;AC005775.2,intron_variant,,ENST00000592413,;TPGS1,upstream_gene_variant,,ENST00000588278,;	T	ENSG00000099866	ENST00000215637	Transcript	missense_variant	1002	956	319	P/L	cCc/cTc	.	.	.	1	MADCAM1	HGNC	6765	protein_coding	YES	CCDS12028.1	ENSP00000215637	MADCA_HUMAN	B9EGE2_HUMAN	UPI000013C68F	.	deleterious(0.01)	possibly_damaging(0.713)	5/5	.	hmmpanther:PTHR14162,hmmpanther:PTHR14162:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCCCGCGG	.	5	ESCA
KCNC3	0	.	GRCh37	19	50824036	50824036	+	Missense_Mutation	SNP	G	G	A	rs748735877	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1984C>T	p.Arg662Cys	p.R662C	ENST00000477616	3/5	132	29	103	74	74	0	KCNC3,missense_variant,p.Arg662Cys,ENST00000477616,;KCNC3,missense_variant,p.Arg662Cys,ENST00000376959,;KCNC3,5_prime_UTR_variant,,ENST00000474951,;KCNC3,5_prime_UTR_variant,,ENST00000391818,;	A	ENSG00000131398	ENST00000477616	Transcript	missense_variant	2279	1984	662	R/C	Cgc/Tgc	rs748735877	.	.	-1	KCNC3	HGNC	6235	protein_coding	YES	CCDS12793.1	ENSP00000434241	KCNC3_HUMAN	.	UPI000013EA5D	.	deleterious_low_confidence(0)	possibly_damaging(0.689)	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGAGGAT	byFrequency	5	ESCA
SHANK1	0	.	GRCh37	19	51165133	51165133	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*89C>T	.	.	ENST00000293441	23/23	21	10	11	33	33	0	SHANK1,3_prime_UTR_variant,,ENST00000391813,;SHANK1,3_prime_UTR_variant,,ENST00000293441,;SYT3,intron_variant,,ENST00000544769,;C19orf81,downstream_gene_variant,,ENST00000458538,;SHANK1,downstream_gene_variant,,ENST00000391814,;C19orf81,downstream_gene_variant,,ENST00000425202,;SHANK1,downstream_gene_variant,,ENST00000359082,;SHANK1,downstream_gene_variant,,ENST00000483981,;C19orf81,downstream_gene_variant,,ENST00000490451,;SHANK1,downstream_gene_variant,,ENST00000468654,;	A	ENSG00000161681	ENST00000293441	Transcript	3_prime_UTR_variant	6594	.	.	.	.	.	.	.	-1	SHANK1	HGNC	15474	protein_coding	YES	CCDS12799.1	ENSP00000293441	SHAN1_HUMAN	.	UPI000013E109	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCGGGGAG	.	5	ESCA
GPR32	0	.	GRCh37	19	51274615	51274615	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758G>A	p.Arg253Gln	p.R253Q	ENST00000270590	1/1	71	25	46	63	63	0	GPR32,missense_variant,p.Arg253Gln,ENST00000270590,;CTD-2568A17.1,downstream_gene_variant,,ENST00000563228,;	A	ENSG00000142511	ENST00000270590	Transcript	missense_variant	895	758	253	R/Q	cGg/cAg	.	.	.	1	GPR32	HGNC	4487	protein_coding	YES	CCDS12801.1	ENSP00000270590	GPR32_HUMAN	H9NIL6_HUMAN	UPI000005045C	.	tolerated(0.29)	benign(0.274)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF27,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00526	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACCGGCCCA	.	5	ESCA
KLKP1	0	.	GRCh37	19	51391542	51391543	+	RNA	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.375dupA	.	.	ENST00000600104	1/2	119	67	52	65	65	0	KLKP1,non_coding_transcript_exon_variant,,ENST00000600104,;KLKP1,intron_variant,,ENST00000597246,;KLKP1,upstream_gene_variant,,ENST00000595979,;KLKP1,upstream_gene_variant,,ENST00000358534,;	T	ENSG00000197588	ENST00000600104	Transcript	non_coding_transcript_exon_variant	375-376	.	.	.	.	.	.	.	-1	KLKP1	HGNC	21260	processed_transcript	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAGCAGTTTTT	.	3	ESCA
ZNF845	0	.	GRCh37	19	53854383	53854383	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455A>G	p.His152Arg	p.H152R	ENST00000458035	4/4	63	47	15	59	59	0	ZNF845,missense_variant,p.His152Arg,ENST00000595091,;ZNF845,missense_variant,p.His152Arg,ENST00000458035,;ZNF845,downstream_gene_variant,,ENST00000601857,;	G	ENSG00000213799	ENST00000458035	Transcript	missense_variant	572	455	152	H/R	cAc/cGc	.	.	.	1	ZNF845	HGNC	25112	protein_coding	YES	CCDS46170.1	ENSP00000388311	ZN845_HUMAN	M0R2N3_HUMAN,M0R0Z8_HUMAN	UPI0001662BAC	.	tolerated(0.15)	probably_damaging(0.989)	4/4	.	hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCACATGT	.	5	ESCA
NLRP12	0	.	GRCh37	19	54313232	54313232	+	Missense_Mutation	SNP	G	G	A	rs747435135	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1681C>T	p.Arg561Cys	p.R561C	ENST00000324134	3/10	22	11	11	20	20	0	NLRP12,missense_variant,p.Arg561Cys,ENST00000535162,;NLRP12,missense_variant,p.Arg561Cys,ENST00000391775,;NLRP12,missense_variant,p.Arg561Cys,ENST00000354278,;NLRP12,missense_variant,p.Arg561Cys,ENST00000391773,;NLRP12,missense_variant,p.Arg561Cys,ENST00000324134,;NLRP12,missense_variant,p.Arg561Cys,ENST00000391772,;NLRP12,missense_variant,p.Arg561Cys,ENST00000345770,;NLRP12,missense_variant,p.Arg561Cys,ENST00000351894,;NLRP12,upstream_gene_variant,,ENST00000492915,;	A	ENSG00000142405	ENST00000324134	Transcript	missense_variant	1850	1681	561	R/C	Cgc/Tgc	rs747435135	.	.	-1	NLRP12	HGNC	22938	protein_coding	YES	CCDS12864.1	ENSP00000319377	NAL12_HUMAN	.	UPI00001412CE	.	deleterious(0)	probably_damaging(0.961)	3/10	.	hmmpanther:PTHR24106:SF6,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCGGCTGG	.	5	ESCA
MYADM	0	.	GRCh37	19	54379518	54379518	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1766A>T	.	.	ENST00000391769	3/3	20	12	8	16	16	0	MYADM,3_prime_UTR_variant,,ENST00000391771,;MYADM,3_prime_UTR_variant,,ENST00000391769,;MYADM,3_prime_UTR_variant,,ENST00000336967,;MYADM,3_prime_UTR_variant,,ENST00000391770,;PRKCG,upstream_gene_variant,,ENST00000479081,;MYADM,downstream_gene_variant,,ENST00000414489,;MYADM,downstream_gene_variant,,ENST00000391768,;MYADM,downstream_gene_variant,,ENST00000439000,;MYADM,downstream_gene_variant,,ENST00000448420,;MYADM,downstream_gene_variant,,ENST00000421337,;AC008440.5,upstream_gene_variant,,ENST00000413496,;	T	ENSG00000179820	ENST00000391769	Transcript	3_prime_UTR_variant	3015	.	.	.	.	.	.	.	1	MYADM	HGNC	7544	protein_coding	YES	CCDS12866.1	ENSP00000375649	MYADM_HUMAN	C9JZL8_HUMAN,C9JJV6_HUMAN,C9JC07_HUMAN,C9J5M0_HUMAN	UPI0000001BEF	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTGATATATAT	.	2	ESCA
MYADM	0	.	GRCh37	19	54379520	54379520	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1768A>G	.	.	ENST00000391769	3/3	17	9	8	15	15	0	MYADM,3_prime_UTR_variant,,ENST00000391771,;MYADM,3_prime_UTR_variant,,ENST00000391769,;MYADM,3_prime_UTR_variant,,ENST00000336967,;MYADM,3_prime_UTR_variant,,ENST00000391770,;PRKCG,upstream_gene_variant,,ENST00000479081,;MYADM,downstream_gene_variant,,ENST00000414489,;MYADM,downstream_gene_variant,,ENST00000391768,;MYADM,downstream_gene_variant,,ENST00000439000,;MYADM,downstream_gene_variant,,ENST00000448420,;MYADM,downstream_gene_variant,,ENST00000421337,;AC008440.5,upstream_gene_variant,,ENST00000413496,;	G	ENSG00000179820	ENST00000391769	Transcript	3_prime_UTR_variant	3017	.	.	.	.	.	.	.	1	MYADM	HGNC	7544	protein_coding	YES	CCDS12866.1	ENSP00000375649	MYADM_HUMAN	C9JZL8_HUMAN,C9JJV6_HUMAN,C9JC07_HUMAN,C9J5M0_HUMAN	UPI0000001BEF	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GATATATATAT	.	2	ESCA
CNOT3	0	.	GRCh37	19	54656009	54656009	+	Missense_Mutation	SNP	C	C	T	rs764340197	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1652C>T	p.Ala551Val	p.A551V	ENST00000406403	13/17	45	14	31	41	41	0	CNOT3,missense_variant,p.Ala83Val,ENST00000457463,;CNOT3,missense_variant,p.Ala370Val,ENST00000358389,;CNOT3,missense_variant,p.Ala551Val,ENST00000406403,;CNOT3,missense_variant,p.Ala551Val,ENST00000221232,;LENG1,downstream_gene_variant,,ENST00000222224,;CNOT3,downstream_gene_variant,,ENST00000440571,;CNOT3,upstream_gene_variant,,ENST00000471126,;CNOT3,non_coding_transcript_exon_variant,,ENST00000496327,;CNOT3,3_prime_UTR_variant,,ENST00000447684,;CNOT3,non_coding_transcript_exon_variant,,ENST00000482247,;CNOT3,upstream_gene_variant,,ENST00000489953,;	T	ENSG00000088038	ENST00000406403	Transcript	missense_variant	3255	1652	551	A/V	gCc/gTc	rs764340197	.	.	1	CNOT3	HGNC	7879	protein_coding	YES	CCDS12880.1	ENSP00000383954	CNOT3_HUMAN	.	UPI00000729AD	.	tolerated(0.1)	possibly_damaging(0.483)	13/17	.	PIRSF_domain:PIRSF005290,hmmpanther:PTHR23326,hmmpanther:PTHR23326:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGCCATCA	.	5	ESCA
KIR2DL3	0	.	GRCh37	19	55263121	55263121	+	Missense_Mutation	SNP	G	G	A	rs767421124	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736G>A	p.Val246Ile	p.V246I	ENST00000342376	6/8	139	121	17	160	160	0	KIR2DL3,missense_variant,p.Val246Ile,ENST00000342376,;KIR2DL4,intron_variant,,ENST00000396284,;KIR3DL1,intron_variant,,ENST00000541392,;KIR3DL1,intron_variant,,ENST00000538269,;KIR3DL1,intron_variant,,ENST00000402254,;KIR2DL3,intron_variant,,ENST00000434419,;CTB-61M7.1,intron_variant,,ENST00000400864,;KIR2DP1,upstream_gene_variant,,ENST00000415311,;	A	ENSG00000243772	ENST00000342376	Transcript	missense_variant	767	736	246	V/I	Gtt/Att	rs767421124	.	.	1	KIR2DL3	HGNC	6331	protein_coding	YES	CCDS33107.1	ENSP00000342215	KI2L3_HUMAN	M4NBK9_HUMAN,M4N692_HUMAN,E3NZD8_HUMAN,Q9UPI8_HUMAN,C6EVR7_HUMAN	UPI000012DB1C	.	tolerated(0.77)	benign(0.006)	6/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGCATGTTCTG	byFrequency	3	ESCA
KIR3DL2	0	.	GRCh37	19	55361941	55361941	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11C>T	p.Thr4Met	p.T4M	ENST00000326321	1/9	84	20	64	34	34	0	KIR3DL2,missense_variant,p.Thr4Met,ENST00000270442,;KIR3DL2,missense_variant,p.Thr4Met,ENST00000326321,;KIR3DL1,intron_variant,,ENST00000402254,;KIR2DS4,downstream_gene_variant,,ENST00000391729,;KIR2DS4,downstream_gene_variant,,ENST00000339924,;	T	ENSG00000240403	ENST00000326321	Transcript	missense_variant	44	11	4	T/M	aCg/aTg	.	.	.	1	KIR3DL2	HGNC	6339	protein_coding	YES	CCDS12906.1	ENSP00000325525	KI3L2_HUMAN	O78200_HUMAN,E4W3V6_HUMAN,A7YL13_HUMAN	UPI000012DB25	.	tolerated(0.65)	benign(0.003)	1/9	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11738:SF19,hmmpanther:PTHR11738	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCACGGTCG	.	5	ESCA
FAM71E2	0	.	GRCh37	19	55874319	55874319	+	Missense_Mutation	SNP	C	C	T	rs775529719	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116G>A	p.Arg39His	p.R39H	ENST00000424985	1/11	43	25	17	47	47	0	FAM71E2,missense_variant,p.Arg39His,ENST00000424985,;IL11,downstream_gene_variant,,ENST00000264563,;IL11,downstream_gene_variant,,ENST00000585513,;IL11,downstream_gene_variant,,ENST00000590625,;FAM71E2,intron_variant,,ENST00000585734,;CTD-2105E13.6,upstream_gene_variant,,ENST00000591954,;	T	ENSG00000180043	ENST00000424985	Transcript	missense_variant	310	116	39	R/H	cGt/cAt	rs775529719,COSM1396570,COSM1396571	.	.	-1	FAM71E2	HGNC	25278	protein_coding	YES	.	ENSP00000398617	F71E2_HUMAN	.	UPI0001949ABA	.	deleterious(0.04)	possibly_damaging(0.491)	1/11	.	hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF1	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGACGGAGG	byFrequency	5	ESCA
ZNF579	0	.	GRCh37	19	56089076	56089076	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*241delA	.	.	ENST00000325421	2/2	172	89	83	53	53	0	ZNF579,3_prime_UTR_variant,,ENST00000325421,;ZNF579,downstream_gene_variant,,ENST00000592239,;CTD-2537I9.5,upstream_gene_variant,,ENST00000589396,;	-	ENSG00000218891	ENST00000325421	Transcript	3_prime_UTR_variant	1959	.	.	.	.	.	.	.	-1	ZNF579	HGNC	26646	protein_coding	YES	CCDS12927.1	ENSP00000320188	ZN579_HUMAN	.	UPI0000141657	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCGCCTTTTTT	.	3	ESCA
NLRP9	0	.	GRCh37	19	56249721	56249722	+	Frame_Shift_Ins	INS	-	-	A	rs568593996	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19dupT	p.Ser7PhefsTer21	p.S7Ffs*21	ENST00000332836	1/9	42	21	21	41	41	0	NLRP9,frameshift_variant,p.Ser7PhefsTer21,ENST00000332836,;NLRP9,frameshift_variant,p.Ser7PhefsTer21,ENST00000590200,;RN7SKP109,downstream_gene_variant,,ENST00000410592,;	A	ENSG00000185792	ENST00000332836	Transcript	frameshift_variant	47-48	19-20	7	S/FX	tcg/tTcg	rs568593996,COSM1396684	.	.	-1	NLRP9	HGNC	22941	protein_coding	YES	CCDS12934.1	ENSP00000331857	NALP9_HUMAN	.	UPI00001B6B39	.	.	.	1/9	.	PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:1.10.533.10,Superfamily_domains:SSF47986	A:0.0014	.	.	.	.	.	.	A:0.0026	A:0.001	.	0,1	.	.	.	.	.	HIGH	.	insertion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.S7fs*9|c.19delT|3	INDELOCATOR|VARSCANI	AATCCGAAAAA	byFrequency|byCluster|by1000G	2	ESCA
SAFB	0	.	GRCh37	19	5653399	5653399	+	Silent	SNP	C	C	T	rs749049469	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1494C>T	p.%3D	p.D498D	ENST00000588852	11/21	22	13	8	14	14	0	SAFB,synonymous_variant,p.%3D,ENST00000588852,;SAFB,synonymous_variant,p.%3D,ENST00000454510,;SAFB,synonymous_variant,p.%3D,ENST00000292123,;SAFB,synonymous_variant,p.%3D,ENST00000538656,;SAFB,synonymous_variant,p.%3D,ENST00000433404,;SAFB,synonymous_variant,p.%3D,ENST00000592224,;SAFB,upstream_gene_variant,,ENST00000589006,;SAFB,downstream_gene_variant,,ENST00000586934,;SAFB,3_prime_UTR_variant,,ENST00000589863,;SAFB,non_coding_transcript_exon_variant,,ENST00000592396,;SAFB,downstream_gene_variant,,ENST00000590485,;SAFB,downstream_gene_variant,,ENST00000592707,;	T	ENSG00000160633	ENST00000588852	Transcript	synonymous_variant	1547	1494	498	D	gaC/gaT	rs749049469	.	.	1	SAFB	HGNC	10520	protein_coding	YES	CCDS59339.1	ENSP00000467423	SAFB1_HUMAN	Q68DW3_HUMAN,F5GZU3_HUMAN	UPI0000E5BE82	.	.	.	11/21	.	hmmpanther:PTHR15683:SF6,hmmpanther:PTHR15683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGACGGGAA	byFrequency	5	ESCA
ZNF667-AS1	0	.	GRCh37	19	57006425	57006425	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1145G>A	.	.	ENST00000585445	2/2	53	16	37	63	63	0	ZNF667-AS1,non_coding_transcript_exon_variant,,ENST00000592146,;ZNF667-AS1,non_coding_transcript_exon_variant,,ENST00000299997,;ZNF667-AS1,non_coding_transcript_exon_variant,,ENST00000585445,;ZNF667-AS1,non_coding_transcript_exon_variant,,ENST00000586091,;ZNF667-AS1,intron_variant,,ENST00000588158,;ZNF667-AS1,downstream_gene_variant,,ENST00000601875,;ZNF667-AS1,downstream_gene_variant,,ENST00000594783,;ZNF667-AS1,downstream_gene_variant,,ENST00000591797,;ZNF667-AS1,downstream_gene_variant,,ENST00000586822,;	A	ENSG00000166770	ENST00000585445	Transcript	non_coding_transcript_exon_variant	1145	.	.	.	.	.	.	.	1	ZNF667-AS1	HGNC	44321	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAACGTTGGA	.	5	ESCA
FUT5	0	.	GRCh37	19	5866418	5866418	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*194C>A	.	.	ENST00000252675	5/5	52	27	24	32	32	0	FUT5,3_prime_UTR_variant,,ENST00000252675,;FUT5,3_prime_UTR_variant,,ENST00000588525,;AC024592.12,downstream_gene_variant,,ENST00000585661,;AC024592.12,downstream_gene_variant,,ENST00000586349,;AC024592.12,3_prime_UTR_variant,,ENST00000592091,;	T	ENSG00000130383	ENST00000252675	Transcript	3_prime_UTR_variant	1882	.	.	.	.	.	.	.	-1	FUT5	HGNC	4016	protein_coding	YES	CCDS12154.1	ENSP00000252675	FUT5_HUMAN	K7ENC0_HUMAN	UPI000013CD7B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGTGAAATC	.	5	ESCA
ACSBG2	0	.	GRCh37	19	6151730	6151730	+	Missense_Mutation	SNP	C	C	T	rs182356930	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310C>T	p.Arg104Cys	p.R104C	ENST00000586696	4/15	134	85	48	87	87	0	ACSBG2,missense_variant,p.Arg104Cys,ENST00000586696,;ACSBG2,missense_variant,p.Arg104Cys,ENST00000591403,;ACSBG2,missense_variant,p.Arg104Cys,ENST00000591738,;ACSBG2,missense_variant,p.Arg104Cys,ENST00000252669,;ACSBG2,missense_variant,p.Arg54Cys,ENST00000588304,;ACSBG2,missense_variant,p.Arg104Cys,ENST00000588722,;ACSBG2,5_prime_UTR_variant,,ENST00000588485,;RFX2,intron_variant,,ENST00000592883,;ACSBG2,downstream_gene_variant,,ENST00000589401,;ACSBG2,missense_variant,p.Arg104Cys,ENST00000587617,;ACSBG2,missense_variant,p.Arg104Cys,ENST00000592677,;ACSBG2,upstream_gene_variant,,ENST00000587227,;	T	ENSG00000130377	ENST00000586696	Transcript	missense_variant	586	310	104	R/C	Cgt/Tgt	rs182356930	.	.	1	ACSBG2	HGNC	24174	protein_coding	YES	CCDS12159.1	ENSP00000465589	ACBG2_HUMAN	K7ESC8_HUMAN,K7ERT0_HUMAN,K7EL11_HUMAN	UPI00001414E6	.	deleterious(0.02)	benign(0.175)	4/15	.	hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF129,Pfam_domain:PF00501,Gene3D:3.40.50.980,Superfamily_domains:SSF56801	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGCGTTTC	byCluster|by1000G	5	ESCA
MLLT1	0	.	GRCh37	19	6210417	6210418	+	3'Flank	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000252674	.	33	24	9	16	16	0	MLLT1,downstream_gene_variant,,ENST00000252674,;CTC-503J8.6,non_coding_transcript_exon_variant,,ENST00000586154,;CTC-503J8.6,downstream_gene_variant,,ENST00000587473,;MLLT1,downstream_gene_variant,,ENST00000585588,;	T	ENSG00000130382	ENST00000252674	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2548	-1	MLLT1	HGNC	7134	protein_coding	YES	CCDS12160.1	ENSP00000252674	ENL_HUMAN	.	UPI000006F7B3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTCACTTTTT	.	2	ESCA
POLRMT	0	.	GRCh37	19	621120	621120	+	Missense_Mutation	SNP	G	G	A	rs779119991	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2578C>T	p.Arg860Cys	p.R860C	ENST00000588649	10/21	88	52	36	34	34	0	POLRMT,missense_variant,p.Arg860Cys,ENST00000588649,;HCN2,downstream_gene_variant,,ENST00000251287,;POLRMT,upstream_gene_variant,,ENST00000590336,;POLRMT,downstream_gene_variant,,ENST00000590573,;LLNLR-299G3.1,upstream_gene_variant,,ENST00000607288,;AC005559.2,upstream_gene_variant,,ENST00000591847,;POLRMT,downstream_gene_variant,,ENST00000588630,;POLRMT,upstream_gene_variant,,ENST00000592633,;POLRMT,upstream_gene_variant,,ENST00000589961,;POLRMT,downstream_gene_variant,,ENST00000586384,;POLRMT,upstream_gene_variant,,ENST00000587057,;POLRMT,downstream_gene_variant,,ENST00000590709,;	A	ENSG00000099821	ENST00000588649	Transcript	missense_variant	2663	2578	860	R/C	Cgc/Tgc	rs779119991	.	.	-1	POLRMT	HGNC	9200	protein_coding	YES	CCDS12036.1	ENSP00000465759	RPOM_HUMAN	.	UPI000013C68E	.	deleterious(0)	probably_damaging(0.96)	10/21	.	hmmpanther:PTHR10102:SF0,hmmpanther:PTHR10102,Gene3D:1mswD04,Pfam_domain:PF00940,Superfamily_domains:SSF56672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGCGCTTCC	byFrequency	5	ESCA
KHSRP	0	.	GRCh37	19	6413424	6413425	+	3'UTR	INS	-	-	T	rs780848156	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*698dupA	.	.	ENST00000398148	20/20	44	36	8	19	19	0	KHSRP,3_prime_UTR_variant,,ENST00000398148,;KHSRP,3_prime_UTR_variant,,ENST00000594745,;KHSRP,downstream_gene_variant,,ENST00000599395,;KHSRP,downstream_gene_variant,,ENST00000600480,;KHSRP,downstream_gene_variant,,ENST00000595548,;KHSRP,downstream_gene_variant,,ENST00000594496,;KHSRP,downstream_gene_variant,,ENST00000597656,;KHSRP,downstream_gene_variant,,ENST00000595223,;CTB-180A7.8,downstream_gene_variant,,ENST00000596254,;CTB-180A7.8,downstream_gene_variant,,ENST00000593563,;CTB-180A7.8,downstream_gene_variant,,ENST00000398173,;MIR3940,downstream_gene_variant,,ENST00000579148,;KHSRP,downstream_gene_variant,,ENST00000595112,;KHSRP,downstream_gene_variant,,ENST00000599642,;	T	ENSG00000088247	ENST00000398148	Transcript	3_prime_UTR_variant	2927-2928	.	.	.	.	rs780848156	.	.	-1	KHSRP	HGNC	6316	protein_coding	YES	CCDS45936.1	ENSP00000381216	FUBP2_HUMAN	M0QYH3_HUMAN,M0QXW7_HUMAN	UPI000049DE96	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATACAATTTTT	.	2	ESCA
DENND1C	0	.	GRCh37	19	6475732	6475732	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.810C>T	p.%3D	p.H270H	ENST00000381480	12/23	54	30	24	16	16	0	DENND1C,synonymous_variant,p.%3D,ENST00000381480,;DENND1C,synonymous_variant,p.%3D,ENST00000543576,;DENND1C,downstream_gene_variant,,ENST00000590173,;DENND1C,downstream_gene_variant,,ENST00000588421,;DENND1C,downstream_gene_variant,,ENST00000590473,;DENND1C,downstream_gene_variant,,ENST00000591030,;DENND1C,non_coding_transcript_exon_variant,,ENST00000590818,;DENND1C,intron_variant,,ENST00000590867,;DENND1C,intron_variant,,ENST00000590444,;DENND1C,downstream_gene_variant,,ENST00000586046,;DENND1C,downstream_gene_variant,,ENST00000589491,;DENND1C,downstream_gene_variant,,ENST00000588988,;DENND1C,downstream_gene_variant,,ENST00000592543,;	A	ENSG00000205744	ENST00000381480	Transcript	synonymous_variant	923	810	270	H	caC/caT	.	.	.	-1	DENND1C	HGNC	26225	protein_coding	YES	CCDS45938.1	ENSP00000370889	DEN1C_HUMAN	K7ENM0_HUMAN,K7EMN9_HUMAN,K7EM80_HUMAN,K7EKL5_HUMAN,B3KP66_HUMAN	UPI000007469C	.	.	.	12/23	.	PROSITE_profiles:PS50211,hmmpanther:PTHR13196:SF21,hmmpanther:PTHR13196,Pfam_domain:PF02141,SMART_domains:SM00799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGCGTGCAC	.	5	ESCA
PRAM1	0	.	GRCh37	19	8563644	8563644	+	Missense_Mutation	SNP	G	G	A	rs369144041	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1048C>T	p.Arg350Cys	p.R350C	ENST00000423345	2/10	64	42	22	44	44	0	PRAM1,missense_variant,p.Arg350Cys,ENST00000255612,;PRAM1,missense_variant,p.Arg350Cys,ENST00000423345,;PRAM1,downstream_gene_variant,,ENST00000600262,;	A	ENSG00000133246	ENST00000423345	Transcript	missense_variant	1569	1048	350	R/C	Cgc/Tgc	rs369144041	.	.	-1	PRAM1	HGNC	30091	protein_coding	YES	CCDS45954.2	ENSP00000408342	PRAM_HUMAN	.	UPI00001AE786	.	tolerated(0.2)	benign(0.002)	2/10	.	hmmpanther:PTHR16830:SF6,hmmpanther:PTHR16830	.	.	.	.	.	.	.	T:0	T:0.0004	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGCGCTCCG	byFrequency|byCluster	5	ESCA
MUC16	0	.	GRCh37	19	8971684	8971684	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42908A>G	p.His14303Arg	p.H14303R	ENST00000397910	78/84	55	46	8	52	52	0	MUC16,missense_variant,p.His944Arg,ENST00000380951,;MUC16,missense_variant,p.His14303Arg,ENST00000397910,;MUC16,missense_variant,p.His1126Arg,ENST00000599436,;MUC16,downstream_gene_variant,,ENST00000596956,;MUC16,missense_variant,p.His1121Arg,ENST00000601404,;MUC16,3_prime_UTR_variant,,ENST00000596768,;	C	ENSG00000181143	ENST00000397910	Transcript	missense_variant	43112	42908	14303	H/R	cAt/cGt	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	possibly_damaging(0.903)	78/84	.	Superfamily_domains:0047452,hmmpanther:PTHR14672,hmmpanther:PTHR14672:SF0,PROSITE_profiles:PS50024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACATGGATG	.	4	ESCA
ZNF317	0	.	GRCh37	19	9271738	9271738	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1417C>T	p.Arg473Cys	p.R473C	ENST00000247956	7/7	26	23	3	20	20	0	ZNF317,missense_variant,p.Arg441Cys,ENST00000360385,;ZNF317,missense_variant,p.Arg473Cys,ENST00000247956,;ZNF317,intron_variant,,ENST00000591508,;ZNF317,3_prime_UTR_variant,,ENST00000591278,;ZNF317,non_coding_transcript_exon_variant,,ENST00000590152,;ZNF317,downstream_gene_variant,,ENST00000419608,;	T	ENSG00000130803	ENST00000247956	Transcript	missense_variant	1722	1417	473	R/C	Cgc/Tgc	.	.	.	1	ZNF317	HGNC	13507	protein_coding	YES	CCDS12210.1	ENSP00000247956	ZN317_HUMAN	.	UPI0000366D00	.	deleterious(0.03)	benign(0.017)	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF22,hmmpanther:PTHR24377,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGACGCTAC	.	2	ESCA
OR7D2	0	.	GRCh37	19	9296772	9296773	+	Frame_Shift_Ins	INS	-	-	T	rs771661883	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321dupT	p.Pro108SerfsTer14	p.P108Sfs*14	ENST00000344248	1/1	132	94	38	77	77	0	OR7D2,frameshift_variant,p.Pro108SerfsTer14,ENST00000344248,;TCEB1P29,upstream_gene_variant,,ENST00000588193,;	T	ENSG00000188000	ENST00000344248	Transcript	frameshift_variant	494-495	315-316	105-106	-/X	-/T	rs771661883	.	.	1	OR7D2	HGNC	8378	protein_coding	YES	CCDS32900.1	ENSP00000345563	OR7D2_HUMAN	.	UPI0000041C0C	.	.	.	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451:SF157,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P108S|c.322C>T|3	INDELOCATOR*|VARSCANI*|PINDEL	TCCATGTTTTT	byFrequency	3	ESCA
ZNF560	0	.	GRCh37	19	9578028	9578028	+	Missense_Mutation	SNP	C	C	T	rs141562027	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1595G>A	p.Arg532His	p.R532H	ENST00000301480	10/10	82	49	33	63	63	0	ZNF560,missense_variant,p.Arg532His,ENST00000301480,;ZNF560,downstream_gene_variant,,ENST00000585974,;	T	ENSG00000198028	ENST00000301480	Transcript	missense_variant	1809	1595	532	R/H	cGt/cAt	rs141562027	.	.	-1	ZNF560	HGNC	26484	protein_coding	YES	CCDS12214.1	ENSP00000301480	ZN560_HUMAN	.	UPI000013E720	.	tolerated(0.16)	benign(0)	10/10	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF44,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	T:0.0014	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATACGAAGA	byFrequency|byCluster|by1000G	5	ESCA
AGL	0	.	GRCh37	1	100378027	100378028	+	Frame_Shift_Ins	INS	-	-	A	rs772172553	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3911dupA	p.Asn1304LysfsTer7	p.N1304Kfs*7	ENST00000294724	29/34	57	29	28	51	51	0	AGL,frameshift_variant,p.Asn1304LysfsTer7,ENST00000370163,;AGL,frameshift_variant,p.Asn1288LysfsTer7,ENST00000361302,;AGL,frameshift_variant,p.Asn1304LysfsTer7,ENST00000294724,;AGL,frameshift_variant,p.Asn1304LysfsTer7,ENST00000370165,;AGL,frameshift_variant,p.Asn1287LysfsTer7,ENST00000361522,;AGL,frameshift_variant,p.Asn1288LysfsTer7,ENST00000370161,;AGL,frameshift_variant,p.Asn1304LysfsTer7,ENST00000361915,;	A	ENSG00000162688	ENST00000294724	Transcript	frameshift_variant	4381-4382	3903-3904	1301-1302	-/X	-/A	rs772172553,COSM1244644	.	.	1	AGL	HGNC	321	protein_coding	YES	CCDS759.1	ENSP00000294724	GDE_HUMAN	G1UI17_HUMAN	UPI00001694CB	.	.	.	29/34	.	hmmpanther:PTHR10569,Pfam_domain:PF06202,TIGRFAM_domain:TIGR01531,Superfamily_domains:SSF48208	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	0,1	.	.	.	.	.	HIGH	.	insertion	.	8	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.N1304fs*7|c.3903_3904insA|3	INDELOCATOR|VARSCANI	TTATCCAAAAA	.	2	ESCA
HIAT1	0	.	GRCh37	1	100547662	100547662	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1370G>T	p.Arg457Met	p.R457M	ENST00000370152	12/12	23	14	9	25	25	0	HIAT1,missense_variant,p.Arg457Met,ENST00000370152,;SASS6,downstream_gene_variant,,ENST00000535161,;SASS6,downstream_gene_variant,,ENST00000287482,;RP4-714D9.2,intron_variant,,ENST00000432294,;SASS6,downstream_gene_variant,,ENST00000462159,;	T	ENSG00000156875	ENST00000370152	Transcript	missense_variant	1506	1370	457	R/M	aGg/aTg	.	.	.	1	HIAT1	HGNC	23363	protein_coding	YES	CCDS763.1	ENSP00000359171	HIAT1_HUMAN	.	UPI0000049F99	.	deleterious(0.02)	benign(0.36)	12/12	.	hmmpanther:PTHR24003:SF367,hmmpanther:PTHR24003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTAAGGTCCA	.	5	ESCA
VCAM1	0	.	GRCh37	1	101194932	101194932	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1198C>A	p.Leu400Ile	p.L400I	ENST00000294728	5/9	48	26	21	35	35	0	VCAM1,missense_variant,p.Leu400Ile,ENST00000294728,;VCAM1,missense_variant,p.Leu338Ile,ENST00000370119,;VCAM1,intron_variant,,ENST00000347652,;VCAM1,intron_variant,,ENST00000370115,;	A	ENSG00000162692	ENST00000294728	Transcript	missense_variant	1299	1198	400	L/I	Ctc/Atc	.	.	.	1	VCAM1	HGNC	12663	protein_coding	YES	CCDS773.1	ENSP00000294728	VCAM1_HUMAN	Q68DC4_HUMAN,G0ZI12_HUMAN,G0ZFQ0_HUMAN,F8UV74_HUMAN,F8UU18_HUMAN,F2YYR6_HUMAN	UPI0000000E06	.	tolerated(0.43)	possibly_damaging(0.724)	5/9	.	hmmpanther:PTHR10489,SMART_domains:SM00409,Superfamily_domains:SSF48726,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGCTCTAC	.	5	ESCA
C1orf159	0	.	GRCh37	1	1019361	1019361	+	Intron	SNP	G	G	A	rs147871493	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502+372C>T	.	.	ENST00000421241	.	170	93	77	106	106	0	C1orf159,missense_variant,p.Arg328Cys,ENST00000379339,;C1orf159,missense_variant,p.Arg292Cys,ENST00000294576,;C1orf159,missense_variant,p.Arg328Cys,ENST00000448924,;C1orf159,missense_variant,p.Arg292Cys,ENST00000379320,;C1orf159,missense_variant,p.Pro178Leu,ENST00000434641,;C1orf159,intron_variant,,ENST00000379319,;C1orf159,intron_variant,,ENST00000421241,;C1orf159,downstream_gene_variant,,ENST00000442117,;C1orf159,downstream_gene_variant,,ENST00000475119,;C1orf159,downstream_gene_variant,,ENST00000462097,;C1orf159,downstream_gene_variant,,ENST00000437760,;C1orf159,non_coding_transcript_exon_variant,,ENST00000482816,;C1orf159,non_coding_transcript_exon_variant,,ENST00000464905,;C1orf159,3_prime_UTR_variant,,ENST00000467751,;C1orf159,3_prime_UTR_variant,,ENST00000477196,;C1orf159,3_prime_UTR_variant,,ENST00000379325,;C1orf159,non_coding_transcript_exon_variant,,ENST00000487177,;C1orf159,intron_variant,,ENST00000465822,;C1orf159,downstream_gene_variant,,ENST00000473600,;	A	ENSG00000131591	ENST00000421241	Transcript	intron_variant	.	.	.	.	.	rs147871493	.	.	-1	C1orf159	HGNC	26062	protein_coding	YES	CCDS7.2	ENSP00000400736	CA159_HUMAN	J3QRL0_HUMAN,J3KSJ6_HUMAN,B2REC4_HUMAN	UPI0000049DAC	.	.	.	.	9/9	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGCGGAGGC	by1000G	5	ESCA
AMY2A	0	.	GRCh37	1	104162312	104162312	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650T>C	p.Met217Thr	p.M217T	ENST00000414303	4/10	281	236	44	274	274	0	AMY2A,missense_variant,p.Met217Thr,ENST00000414303,;AMY2A,intron_variant,,ENST00000423678,;AMY2A,upstream_gene_variant,,ENST00000497748,;	C	ENSG00000243480	ENST00000414303	Transcript	missense_variant	714	650	217	M/T	aTg/aCg	.	.	.	1	AMY2A	HGNC	477	protein_coding	YES	CCDS783.1	ENSP00000397582	AMYP_HUMAN	.	UPI0000000C80	.	deleterious(0.01)	probably_damaging(0.959)	4/10	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Pfam_domain:PF00128,Gene3D:3.20.20.80,SMART_domains:SM00642,Superfamily_domains:SSF51445,Prints_domain:PR00110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCACATGTGGC	.	3	ESCA
AMY1C	0	.	GRCh37	1	104297180	104297180	+	Missense_Mutation	SNP	A	A	T	rs200267405	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938A>T	p.Asn313Ile	p.N313I	ENST00000370079	6/10	271	239	32	190	190	0	AMY1C,missense_variant,p.Asn313Ile,ENST00000370079,;	T	ENSG00000187733	ENST00000370079	Transcript	missense_variant	1002	938	313	N/I	aAc/aTc	rs200267405,COSM3676647	.	.	1	AMY1C	HGNC	476	protein_coding	YES	CCDS30784.1	ENSP00000359096	AMY1_HUMAN	Q5T085_HUMAN,Q5T084_HUMAN	UPI0000125AA9	.	deleterious(0)	probably_damaging(1)	6/10	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Pfam_domain:PF00128,Gene3D:3.20.20.80,SMART_domains:SM00642,Superfamily_domains:SSF51445,Prints_domain:PR00110	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATAACCATG	.	4	ESCA
CASZ1	0	.	GRCh37	1	10725151	10725151	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.494G>T	p.Arg165Met	p.R165M	ENST00000377022	5/21	52	38	14	31	31	0	CASZ1,missense_variant,p.Arg165Met,ENST00000344008,;CASZ1,missense_variant,p.Arg165Met,ENST00000377022,;CASZ1,non_coding_transcript_exon_variant,,ENST00000478728,;CASZ1,non_coding_transcript_exon_variant,,ENST00000496432,;CASZ1,upstream_gene_variant,,ENST00000492173,;	A	ENSG00000130940	ENST00000377022	Transcript	missense_variant	812	494	165	R/M	aGg/aTg	.	.	.	-1	CASZ1	HGNC	26002	protein_coding	YES	CCDS41246.1	ENSP00000366221	CASZ1_HUMAN	.	UPI0000EBB7D6	.	deleterious_low_confidence(0.01)	benign(0.028)	5/21	.	hmmpanther:PTHR12451	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCCTGGTG	.	5	ESCA
CELSR2	0	.	GRCh37	1	109811737	109811737	+	Frame_Shift_Del	DEL	C	C	-	rs775221918	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6642delC	p.Val2215TrpfsTer26	p.V2215Wfs*26	ENST00000271332	20/34	49	30	19	18	18	0	CELSR2,frameshift_variant,p.Val2215TrpfsTer26,ENST00000271332,;CELSR2,upstream_gene_variant,,ENST00000489018,;CELSR2,upstream_gene_variant,,ENST00000498157,;CELSR2,downstream_gene_variant,,ENST00000459940,;	-	ENSG00000143126	ENST00000271332	Transcript	frameshift_variant	6698	6637	2213	P/X	Ccc/cc	rs775221918,COSM1242118	.	.	1	CELSR2	HGNC	3231	protein_coding	YES	CCDS796.1	ENSP00000271332	CELR2_HUMAN	.	UPI00000015B6	.	.	.	20/34	.	hmmpanther:PTHR24026:SF32,hmmpanther:PTHR24026,Pfam_domain:PF12003	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	5	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V2215fs*26|c.6637delC|3	INDELOCATOR|VARSCANI	GAGACGCCCCCC	byFrequency	2	ESCA
C1orf127	0	.	GRCh37	1	11008750	11008750	+	Missense_Mutation	SNP	G	G	A	rs777328651	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1442C>T	p.Thr481Met	p.T481M	ENST00000377004	12/13	70	59	11	48	48	0	C1orf127,missense_variant,p.Thr433Met,ENST00000520253,;C1orf127,missense_variant,p.Thr481Met,ENST00000377004,;C1orf127,missense_variant,p.Thr316Met,ENST00000418570,;C1orf127,missense_variant,p.Thr314Met,ENST00000377008,;C1orf127,upstream_gene_variant,,ENST00000468348,;C1orf127,non_coding_transcript_exon_variant,,ENST00000476357,;	A	ENSG00000175262	ENST00000377004	Transcript	missense_variant	1442	1442	481	T/M	aCg/aTg	rs777328651	.	.	-1	C1orf127	HGNC	26730	protein_coding	YES	CCDS53267.1	ENSP00000366203	.	G8JLG8_HUMAN,B7ZLG7_HUMAN	UPI0001C0B385	.	tolerated(0.11)	probably_damaging(0.996)	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCGTGGCT	byFrequency	5	ESCA
AMPD2	0	.	GRCh37	1	110163442	110163443	+	5'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-193dupA	.	.	ENST00000256578	1/18	107	84	23	46	46	0	AMPD2,5_prime_UTR_variant,,ENST00000256578,;AMPD2,intron_variant,,ENST00000469039,;AMPD2,intron_variant,,ENST00000528667,;AMPD2,intron_variant,,ENST00000474459,;AMPD2,intron_variant,,ENST00000342115,;AMPD2,intron_variant,,ENST00000531203,;AMPD2,intron_variant,,ENST00000531734,;AMPD2,upstream_gene_variant,,ENST00000528454,;AMPD2,upstream_gene_variant,,ENST00000358729,;AMPD2,upstream_gene_variant,,ENST00000527846,;AMPD2,upstream_gene_variant,,ENST00000369840,;AMPD2,upstream_gene_variant,,ENST00000393688,;AMPD2,intron_variant,,ENST00000526301,;AMPD2,upstream_gene_variant,,ENST00000459643,;AMPD2,upstream_gene_variant,,ENST00000486282,;AMPD2,upstream_gene_variant,,ENST00000528270,;	A	ENSG00000116337	ENST00000256578	Transcript	5_prime_UTR_variant	167-168	.	.	.	.	.	.	.	1	AMPD2	HGNC	469	protein_coding	YES	CCDS805.1	ENSP00000256578	AMPD2_HUMAN	E9PIJ1_HUMAN	UPI0000125956	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCATGATGGG	.	3	ESCA
CTTNBP2NL	0	.	GRCh37	1	112999148	112999148	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1034A>G	p.Tyr345Cys	p.Y345C	ENST00000271277	6/6	21	7	14	17	17	0	CTTNBP2NL,missense_variant,p.Tyr345Cys,ENST00000271277,;CTTNBP2NL,downstream_gene_variant,,ENST00000441739,;CTTNBP2NL,upstream_gene_variant,,ENST00000607039,;	G	ENSG00000143079	ENST00000271277	Transcript	missense_variant	1259	1034	345	Y/C	tAt/tGt	.	.	.	1	CTTNBP2NL	HGNC	25330	protein_coding	YES	CCDS845.1	ENSP00000271277	CT2NL_HUMAN	B1AMN7_HUMAN	UPI000006ED23	.	tolerated(0.17)	benign(0.009)	6/6	.	hmmpanther:PTHR23166,hmmpanther:PTHR23166:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATATGCAA	.	5	ESCA
MOV10	0	.	GRCh37	1	113239426	113239426	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2156G>A	p.Gly719Asp	p.G719D	ENST00000413052	14/21	40	28	11	33	33	0	MOV10,missense_variant,p.Gly663Asp,ENST00000369644,;MOV10,missense_variant,p.Gly719Asp,ENST00000369645,;MOV10,missense_variant,p.Gly719Asp,ENST00000357443,;MOV10,missense_variant,p.Gly719Asp,ENST00000413052,;RHOC,downstream_gene_variant,,ENST00000369633,;RHOC,downstream_gene_variant,,ENST00000425265,;RHOC,downstream_gene_variant,,ENST00000369632,;RHOC,downstream_gene_variant,,ENST00000285735,;RHOC,downstream_gene_variant,,ENST00000534717,;RHOC,downstream_gene_variant,,ENST00000339083,;RHOC,downstream_gene_variant,,ENST00000369642,;RHOC,downstream_gene_variant,,ENST00000369638,;RHOC,downstream_gene_variant,,ENST00000369636,;RHOC,downstream_gene_variant,,ENST00000369637,;RP11-426L16.3,upstream_gene_variant,,ENST00000421943,;MOV10,non_coding_transcript_exon_variant,,ENST00000488160,;MOV10,non_coding_transcript_exon_variant,,ENST00000468624,;MOV10,non_coding_transcript_exon_variant,,ENST00000496577,;MOV10,downstream_gene_variant,,ENST00000479858,;MOV10,upstream_gene_variant,,ENST00000490413,;MOV10,upstream_gene_variant,,ENST00000471160,;MOV10,upstream_gene_variant,,ENST00000481711,;MOV10,upstream_gene_variant,,ENST00000495374,;MOV10,upstream_gene_variant,,ENST00000482545,;MOV10,upstream_gene_variant,,ENST00000494319,;RHOC,downstream_gene_variant,,ENST00000468093,;RHOC,downstream_gene_variant,,ENST00000484280,;RHOC,downstream_gene_variant,,ENST00000473074,;	A	ENSG00000155363	ENST00000413052	Transcript	missense_variant	2546	2156	719	G/D	gGc/gAc	.	.	.	1	MOV10	HGNC	7200	protein_coding	YES	CCDS853.1	ENSP00000399797	MOV10_HUMAN	Q5JR04_HUMAN,B3KQ43_HUMAN	UPI000012FA84	.	tolerated(0.1)	benign(0.161)	14/21	.	hmmpanther:PTHR10887:SF326,hmmpanther:PTHR10887,Gene3D:3.40.50.300,Pfam_domain:PF13087,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATGGCTATG	.	5	ESCA
TRIM33	0	.	GRCh37	1	115007001	115007001	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.536T>G	p.Ile179Arg	p.I179R	ENST00000358465	2/20	26	21	5	16	16	0	TRIM33,missense_variant,p.Ile179Arg,ENST00000369543,;TRIM33,missense_variant,p.Ile179Arg,ENST00000358465,;TRIM33,upstream_gene_variant,,ENST00000448034,;TRIM33,upstream_gene_variant,,ENST00000450349,;EIF2S2P5,upstream_gene_variant,,ENST00000457635,;RP4-591B8.2,downstream_gene_variant,,ENST00000427409,;	C	ENSG00000197323	ENST00000358465	Transcript	missense_variant	620	536	179	I/R	aTa/aGa	.	.	.	-1	TRIM33	HGNC	16290	protein_coding	YES	CCDS872.1	ENSP00000351250	TRI33_HUMAN	.	UPI000013D8CD	.	deleterious(0)	possibly_damaging(0.879)	2/20	.	PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF118,Gene3D:3.30.40.10,Pfam_domain:PF13639,SMART_domains:SM00249,SMART_domains:SM00184,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGTATTACA	.	5	ESCA
DENND2C	0	.	GRCh37	1	115168367	115168367	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239G>A	p.Gly80Asp	p.G80D	ENST00000393274	4/21	63	34	28	50	50	0	DENND2C,missense_variant,p.Gly80Asp,ENST00000393274,;DENND2C,missense_variant,p.Gly80Asp,ENST00000393277,;DENND2C,missense_variant,p.Gly80Asp,ENST00000393276,;DENND2C,non_coding_transcript_exon_variant,,ENST00000493549,;DENND2C,upstream_gene_variant,,ENST00000481894,;	T	ENSG00000175984	ENST00000393274	Transcript	missense_variant	865	239	80	G/D	gGt/gAt	.	.	.	-1	DENND2C	HGNC	24748	protein_coding	YES	CCDS58018.1	ENSP00000376955	DEN2C_HUMAN	.	UPI000048AF71	.	tolerated(0.09)	benign(0.007)	4/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAGACCCACA	.	5	ESCA
VANGL1	0	.	GRCh37	1	116234551	116234551	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*556delA	.	.	ENST00000355485	8/8	134	92	42	76	76	0	VANGL1,3_prime_UTR_variant,,ENST00000355485,;VANGL1,3_prime_UTR_variant,,ENST00000369510,;VANGL1,downstream_gene_variant,,ENST00000369509,;VANGL1,downstream_gene_variant,,ENST00000310260,;	-	ENSG00000173218	ENST00000355485	Transcript	3_prime_UTR_variant	2397	.	.	.	.	.	.	.	1	VANGL1	HGNC	15512	protein_coding	YES	CCDS883.1	ENSP00000347672	VANG1_HUMAN	.	UPI0000070B72	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CACAACAAAAAA	.	3	ESCA
CPSF3L	0	.	GRCh37	1	1248015	1248015	+	Missense_Mutation	SNP	C	C	T	rs759048878	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1378G>A	p.Val460Ile	p.V460I	ENST00000540437	15/19	37	27	10	26	26	0	CPSF3L,missense_variant,p.Val353Ile,ENST00000419704,;CPSF3L,missense_variant,p.Val432Ile,ENST00000450926,;CPSF3L,missense_variant,p.Val425Ile,ENST00000545578,;CPSF3L,missense_variant,p.Val454Ile,ENST00000435064,;CPSF3L,missense_variant,p.Val196Ile,ENST00000421495,;CPSF3L,missense_variant,p.Val460Ile,ENST00000540437,;CPSF3L,missense_variant,p.Val356Ile,ENST00000411962,;CPSF3L,downstream_gene_variant,,ENST00000434694,;CPSF3L,downstream_gene_variant,,ENST00000527719,;ACAP3,upstream_gene_variant,,ENST00000354700,;CPSF3L,downstream_gene_variant,,ENST00000530031,;CPSF3L,downstream_gene_variant,,ENST00000526332,;ACAP3,upstream_gene_variant,,ENST00000353662,;PUSL1,downstream_gene_variant,,ENST00000379031,;PUSL1,downstream_gene_variant,,ENST00000467712,;RP5-890O3.9,downstream_gene_variant,,ENST00000444968,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000462432,;PUSL1,downstream_gene_variant,,ENST00000470520,;ACAP3,upstream_gene_variant,,ENST00000438966,;CPSF3L,3_prime_UTR_variant,,ENST00000532772,;CPSF3L,3_prime_UTR_variant,,ENST00000528879,;CPSF3L,3_prime_UTR_variant,,ENST00000458452,;CPSF3L,3_prime_UTR_variant,,ENST00000527098,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000323275,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000470030,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000478641,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000497304,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000461514,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000485710,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000525164,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000525769,;CPSF3L,downstream_gene_variant,,ENST00000531377,;CPSF3L,downstream_gene_variant,,ENST00000531292,;CPSF3L,downstream_gene_variant,,ENST00000533916,;CPSF3L,downstream_gene_variant,,ENST00000430786,;CPSF3L,downstream_gene_variant,,ENST00000488042,;CPSF3L,downstream_gene_variant,,ENST00000531020,;PUSL1,downstream_gene_variant,,ENST00000493657,;CPSF3L,downstream_gene_variant,,ENST00000467408,;ACAP3,upstream_gene_variant,,ENST00000479108,;CPSF3L,downstream_gene_variant,,ENST00000526904,;CPSF3L,downstream_gene_variant,,ENST00000525603,;ACAP3,upstream_gene_variant,,ENST00000354980,;CPSF3L,downstream_gene_variant,,ENST00000526797,;PUSL1,downstream_gene_variant,,ENST00000463758,;CPSF3L,downstream_gene_variant,,ENST00000526113,;CPSF3L,downstream_gene_variant,,ENST00000527383,;ACAP3,upstream_gene_variant,,ENST00000472541,;	T	ENSG00000127054	ENST00000540437	Transcript	missense_variant	1834	1378	460	V/I	Gta/Ata	rs759048878	.	.	-1	CPSF3L	HGNC	26052	protein_coding	YES	CCDS57960.1	ENSP00000445001	INT11_HUMAN	J3QRY6_HUMAN,E9PNH9_HUMAN,E9PI75_HUMAN	UPI0000EE7E27	.	tolerated(0.64)	benign(0.064)	15/19	.	hmmpanther:PTHR11203,hmmpanther:PTHR11203:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTACGGGGA	.	5	ESCA
NBPF20	0	.	GRCh37	1	148346596	148346596	+	Missense_Mutation	SNP	T	T	C	rs587753227	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161A>G	p.Gln54Arg	p.Q54R	ENST00000369202	2/111	104	95	9	94	93	0	NBPF20,missense_variant,p.Gln54Arg,ENST00000414710,;NBPF20,missense_variant,p.Gln54Arg,ENST00000369188,;NBPF20,missense_variant,p.Gln54Arg,ENST00000369202,;NBPF20,synonymous_variant,p.%3D,ENST00000369189,;PFN1P3,upstream_gene_variant,,ENST00000443612,;	C	ENSG00000203832	ENST00000369202	Transcript	missense_variant	359	161	54	Q/R	cAg/cGg	rs587753227	.	.	-1	NBPF20	HGNC	32000	protein_coding	YES	.	ENSP00000358203	.	S4R3H5_HUMAN,I0CMK7_HUMAN,H7BY69_HUMAN,F5H1Q5_HUMAN,A2BH96_HUMAN	UPI000066DA61	.	.	benign(0.001)	2/111	.	.	C:0.0020	C:0	C:0	.	C:0.0079	C:0.002	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TCTGCTGGTTG	.	2	ESCA
HIST2H2BF	0	.	GRCh37	1	149783804	149783806	+	In_Frame_Del	DEL	CTT	CTT	-	rs782079686	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73_75delAAG	p.Lys25del	p.K25del	ENST00000545683	1/2	135	99	36	81	81	0	HIST2H2BF,inframe_deletion,p.Lys25del,ENST00000545683,;HIST2H2BF,inframe_deletion,p.Lys25del,ENST00000369167,;HIST2H2BF,inframe_deletion,p.Lys25del,ENST00000427880,;HIST2H3D,downstream_gene_variant,,ENST00000331491,;RP11-196G18.21,upstream_gene_variant,,ENST00000420462,;HIST2H2BF,non_coding_transcript_exon_variant,,ENST00000469483,;	-	ENSG00000203814	ENST00000545683	Transcript	inframe_deletion	123-125	73-75	25	K/-	AAG/-	rs782079686	.	.	-1	HIST2H2BF	HGNC	24700	protein_coding	YES	CCDS53359.1	ENSP00000445831	H2B2F_HUMAN	.	UPI00017A7443	.	.	.	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23428,Gene3D:1.10.20.10,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GCCGTCCTTCTTCT	.	2	ESCA
SETDB1	0	.	GRCh37	1	150931756	150931756	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2433G>A	p.%3D	p.Q811Q	ENST00000271640	15/22	96	65	31	84	84	0	SETDB1,synonymous_variant,p.%3D,ENST00000498193,;SETDB1,synonymous_variant,p.%3D,ENST00000271640,;SETDB1,synonymous_variant,p.%3D,ENST00000368969,;CERS2,downstream_gene_variant,,ENST00000561294,;SETDB1,intron_variant,,ENST00000459773,;SETDB1,upstream_gene_variant,,ENST00000533529,;SETDB1,upstream_gene_variant,,ENST00000497314,;CERS2,downstream_gene_variant,,ENST00000482825,;SETDB1,upstream_gene_variant,,ENST00000528749,;	A	ENSG00000143379	ENST00000271640	Transcript	synonymous_variant	2623	2433	811	Q	caG/caA	.	.	.	1	SETDB1	HGNC	10761	protein_coding	YES	CCDS44217.1	ENSP00000271640	SETB1_HUMAN	E9PS59_HUMAN,B0QZE6_HUMAN	UPI0000135897	.	.	.	15/22	.	PROSITE_profiles:PS51573,PROSITE_profiles:PS50280,hmmpanther:PTHR22884:SF323,hmmpanther:PTHR22884,Gene3D:2.170.270.10,SMART_domains:SM00317,Superfamily_domains:SSF82199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACAGAACAA	.	5	ESCA
PIP5K1A	0	.	GRCh37	1	151220636	151220636	+	3'Flank	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000368888	.	20	13	7	11	11	0	PIP5K1A,3_prime_UTR_variant,,ENST00000368890,;PIP5K1A,3_prime_UTR_variant,,ENST00000414290,;PIP5K1A,3_prime_UTR_variant,,ENST00000409426,;PIP5K1A,3_prime_UTR_variant,,ENST00000349792,;PIP5K1A,downstream_gene_variant,,ENST00000441902,;PIP5K1A,downstream_gene_variant,,ENST00000368888,;PIP5K1A,non_coding_transcript_exon_variant,,ENST00000489625,;	-	ENSG00000143398	ENST00000368888	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	272	1	PIP5K1A	HGNC	8994	protein_coding	YES	CCDS44219.1	ENSP00000357883	PI51A_HUMAN	P78517_HUMAN,A6PW58_HUMAN	UPI000006F821	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTGAATTTTTT	.	2	ESCA
POGZ	0	.	GRCh37	1	151377009	151377009	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*269delT	.	.	ENST00000271715	19/19	17	5	12	20	20	0	POGZ,3_prime_UTR_variant,,ENST00000271715,;POGZ,3_prime_UTR_variant,,ENST00000392723,;POGZ,3_prime_UTR_variant,,ENST00000409503,;POGZ,3_prime_UTR_variant,,ENST00000361398,;POGZ,3_prime_UTR_variant,,ENST00000531094,;POGZ,3_prime_UTR_variant,,ENST00000368863,;POGZ,downstream_gene_variant,,ENST00000529669,;PSMB4,downstream_gene_variant,,ENST00000290541,;POGZ,downstream_gene_variant,,ENST00000540984,;POGZ,downstream_gene_variant,,ENST00000491586,;POGZ,non_coding_transcript_exon_variant,,ENST00000358476,;PSMB4,downstream_gene_variant,,ENST00000495288,;POGZ,downstream_gene_variant,,ENST00000497787,;POGZ,downstream_gene_variant,,ENST00000492528,;PSMB4,downstream_gene_variant,,ENST00000476467,;PSMB4,downstream_gene_variant,,ENST00000495805,;PSMB4,downstream_gene_variant,,ENST00000466425,;PSMB4,downstream_gene_variant,,ENST00000493673,;PSMB4,downstream_gene_variant,,ENST00000474100,;	-	ENSG00000143442	ENST00000271715	Transcript	3_prime_UTR_variant	4817	.	.	.	.	.	.	.	-1	POGZ	HGNC	18801	protein_coding	YES	CCDS997.1	ENSP00000271715	POGZ_HUMAN	F5H8H4_HUMAN,E9PJY9_HUMAN,E9PIR8_HUMAN	UPI000035895F	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAATTTAAAAAA	.	2	ESCA
HRNR	0	.	GRCh37	1	152187979	152187979	+	Silent	SNP	G	G	A	rs773303607	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6126C>T	p.%3D	p.H2042H	ENST00000368801	3/3	140	123	17	135	135	0	HRNR,synonymous_variant,p.%3D,ENST00000368801,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	A	ENSG00000197915	ENST00000368801	Transcript	synonymous_variant	6202	6126	2042	H	caC/caT	rs773303607	.	.	-1	HRNR	HGNC	20846	protein_coding	YES	CCDS30859.1	ENSP00000357791	HORN_HUMAN	Q5W8V9_HUMAN	UPI00001D7CAD	.	.	.	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGACCGTGGCT	byFrequency	2	ESCA
KAZN	0	.	GRCh37	1	15287271	15287271	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318G>A	p.%3D	p.S106S	ENST00000376030	2/15	30	13	17	23	23	0	KAZN,synonymous_variant,p.%3D,ENST00000400797,;KAZN,synonymous_variant,p.%3D,ENST00000361144,;KAZN,synonymous_variant,p.%3D,ENST00000376030,;KAZN,synonymous_variant,p.%3D,ENST00000422387,;KAZN,synonymous_variant,p.%3D,ENST00000376028,;KAZN,synonymous_variant,p.%3D,ENST00000503743,;KAZN,synonymous_variant,p.%3D,ENST00000400798,;KAZN,non_coding_transcript_exon_variant,,ENST00000491547,;	A	ENSG00000189337	ENST00000376030	Transcript	synonymous_variant	612	318	106	S	tcG/tcA	.	.	.	1	KAZN	HGNC	29173	protein_coding	YES	CCDS152.2	ENSP00000365198	KAZRN_HUMAN	B4DEV2_HUMAN,B0QYQ6_HUMAN	UPI0000E1E68A	.	.	.	2/15	.	hmmpanther:PTHR12776	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCGCAGGG	.	5	ESCA
DENND4B	0	.	GRCh37	1	153914345	153914345	+	Missense_Mutation	SNP	G	G	A	rs766715207	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1055C>T	p.Ala352Val	p.A352V	ENST00000361217	6/28	63	42	21	34	34	0	DENND4B,missense_variant,p.Ala363Val,ENST00000368646,;DENND4B,missense_variant,p.Ala352Val,ENST00000361217,;DENND4B,downstream_gene_variant,,ENST00000472932,;DENND4B,splice_region_variant,,ENST00000483561,;DENND4B,downstream_gene_variant,,ENST00000464048,;DENND4B,upstream_gene_variant,,ENST00000494683,;DENND4B,upstream_gene_variant,,ENST00000485359,;	A	ENSG00000198837	ENST00000361217	Transcript	missense_variant	1474	1055	352	A/V	gCg/gTg	rs766715207	.	.	-1	DENND4B	HGNC	29044	protein_coding	YES	CCDS44228.1	ENSP00000354597	DEN4B_HUMAN	.	UPI000047EA3E	.	deleterious(0)	benign(0.059)	6/28	.	PROSITE_profiles:PS50211,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF18,Pfam_domain:PF02141,SMART_domains:SM00799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACGCTTCC	.	5	ESCA
DENND4B	0	.	GRCh37	1	153914758	153914758	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715C>T	p.Pro239Ser	p.P239S	ENST00000361217	5/28	55	31	24	22	22	0	DENND4B,missense_variant,p.Pro250Ser,ENST00000368646,;DENND4B,missense_variant,p.Pro239Ser,ENST00000361217,;DENND4B,intron_variant,,ENST00000472932,;DENND4B,non_coding_transcript_exon_variant,,ENST00000464048,;DENND4B,upstream_gene_variant,,ENST00000483561,;DENND4B,upstream_gene_variant,,ENST00000494683,;DENND4B,upstream_gene_variant,,ENST00000485359,;	A	ENSG00000198837	ENST00000361217	Transcript	missense_variant	1134	715	239	P/S	Ccc/Tcc	.	.	.	-1	DENND4B	HGNC	29044	protein_coding	YES	CCDS44228.1	ENSP00000354597	DEN4B_HUMAN	.	UPI000047EA3E	.	deleterious(0)	probably_damaging(0.999)	5/28	.	PROSITE_profiles:PS50946,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF18,Pfam_domain:PF03456,SMART_domains:SM00800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGGCAGGC	.	5	ESCA
DCST1	0	.	GRCh37	1	155007018	155007018	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174delG	p.Leu59SerfsTer4	p.L59Sfs*4	ENST00000295542	3/17	89	68	21	45	45	0	DCST1,frameshift_variant,p.Leu59SerfsTer4,ENST00000423025,;DCST1,frameshift_variant,p.Leu59SerfsTer4,ENST00000392480,;DCST1,frameshift_variant,p.Leu59SerfsTer4,ENST00000295542,;DCST1,frameshift_variant,p.Leu59SerfsTer4,ENST00000368419,;DCST2,upstream_gene_variant,,ENST00000295536,;DCST2,upstream_gene_variant,,ENST00000368424,;DCST1,frameshift_variant,p.Leu84SerfsTer4,ENST00000525273,;DCST1,non_coding_transcript_exon_variant,,ENST00000368420,;DCST2,upstream_gene_variant,,ENST00000485982,;DCST2,upstream_gene_variant,,ENST00000368423,;	-	ENSG00000163357	ENST00000295542	Transcript	frameshift_variant	265	169	57	G/X	Ggg/gg	.	.	.	1	DCST1	HGNC	26539	protein_coding	YES	CCDS1083.1	ENSP00000295542	DCST1_HUMAN	.	UPI000013E269	.	.	.	3/17	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR21041:SF5,hmmpanther:PTHR21041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCGCTGGGGGG	.	3	ESCA
EFNA1	0	.	GRCh37	1	155100484	155100484	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31C>A	p.Leu11Met	p.L11M	ENST00000368407	1/5	67	48	18	48	48	0	EFNA1,missense_variant,p.Leu11Met,ENST00000368407,;EFNA1,missense_variant,p.Leu11Met,ENST00000368406,;EFNA1,non_coding_transcript_exon_variant,,ENST00000469878,;EFNA1,upstream_gene_variant,,ENST00000474413,;EFNA1,upstream_gene_variant,,ENST00000497282,;	A	ENSG00000169242	ENST00000368407	Transcript	missense_variant	549	31	11	L/M	Ctg/Atg	.	.	.	1	EFNA1	HGNC	3221	protein_coding	YES	CCDS1091.1	ENSP00000357392	EFNA1_HUMAN	.	UPI00000495C7	.	tolerated(0.11)	possibly_damaging(0.714)	1/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11304,hmmpanther:PTHR11304:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTCTGTGC	.	5	ESCA
GON4L	0	.	GRCh37	1	155734981	155734981	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4283delC	p.Pro1428GlnfsTer70	p.P1428Qfs*70	ENST00000437809	21/32	63	52	11	49	49	0	GON4L,frameshift_variant,p.Pro1428GlnfsTer70,ENST00000437809,;GON4L,frameshift_variant,p.Pro1428GlnfsTer65,ENST00000361040,;GON4L,frameshift_variant,p.Pro1428GlnfsTer70,ENST00000368331,;GON4L,frameshift_variant,p.Pro1428GlnfsTer70,ENST00000271883,;GON4L,non_coding_transcript_exon_variant,,ENST00000471341,;GON4L,downstream_gene_variant,,ENST00000496021,;GON4L,downstream_gene_variant,,ENST00000490801,;GON4L,downstream_gene_variant,,ENST00000497369,;	-	ENSG00000116580	ENST00000437809	Transcript	frameshift_variant	4406	4283	1428	P/X	cCa/ca	.	.	.	-1	GON4L	HGNC	25973	protein_coding	YES	CCDS44242.1	ENSP00000396117	GON4L_HUMAN	Q9NXJ9_HUMAN	UPI0000603C24	.	.	.	21/32	.	hmmpanther:PTHR16088,hmmpanther:PTHR16088:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCCCTGGGGGG	.	3	ESCA
KIAA0907	0	.	GRCh37	1	155903598	155903598	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81C>A	p.%3D	p.L27L	ENST00000368321	2/14	35	19	15	22	22	0	KIAA0907,synonymous_variant,p.%3D,ENST00000368320,;KIAA0907,synonymous_variant,p.%3D,ENST00000368319,;KIAA0907,synonymous_variant,p.%3D,ENST00000368321,;KIAA0907,non_coding_transcript_exon_variant,,ENST00000491599,;KIAA0907,non_coding_transcript_exon_variant,,ENST00000482337,;KIAA0907,non_coding_transcript_exon_variant,,ENST00000466713,;	T	ENSG00000132680	ENST00000368321	Transcript	synonymous_variant	105	81	27	L	ctC/ctA	.	.	.	-1	KIAA0907	HGNC	29145	protein_coding	YES	CCDS30885.1	ENSP00000357304	K0907_HUMAN	.	UPI00001A36E0	.	.	.	2/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15744,hmmpanther:PTHR15744:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGAGAAG	.	5	ESCA
MEF2D	0	.	GRCh37	1	156436230	156436230	+	3'UTR	SNP	C	C	T	rs191700727	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1207G>A	.	.	ENST00000348159	12/12	76	36	40	53	53	0	MEF2D,3_prime_UTR_variant,,ENST00000464356,;MEF2D,3_prime_UTR_variant,,ENST00000340875,;MEF2D,3_prime_UTR_variant,,ENST00000348159,;MEF2D,3_prime_UTR_variant,,ENST00000353795,;MEF2D,3_prime_UTR_variant,,ENST00000368240,;MEF2D,3_prime_UTR_variant,,ENST00000360595,;MEF2D,downstream_gene_variant,,ENST00000475587,;	T	ENSG00000116604	ENST00000348159	Transcript	3_prime_UTR_variant	3254	.	.	.	.	rs191700727	.	.	-1	MEF2D	HGNC	6997	protein_coding	YES	CCDS1143.1	ENSP00000271555	MEF2D_HUMAN	.	UPI000012EEB6	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGCGCCAA	by1000G	5	ESCA
CD1A	0	.	GRCh37	1	158226752	158226752	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.781T>C	p.Tyr261His	p.Y261H	ENST00000289429	4/6	72	56	16	47	47	0	CD1A,missense_variant,p.Tyr261His,ENST00000289429,;	C	ENSG00000158477	ENST00000289429	Transcript	missense_variant	1314	781	261	Y/H	Tat/Cat	COSM1200244	.	.	1	CD1A	HGNC	1634	protein_coding	YES	CCDS1174.1	ENSP00000289429	CD1A_HUMAN	.	UPI0000161A54	.	deleterious(0.05)	benign(0.081)	4/6	.	Superfamily_domains:SSF48726,SMART_domains:SM00407,Pfam_domain:PF07654,Gene3D:2.60.40.10,hmmpanther:PTHR16675:SF160,hmmpanther:PTHR16675,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R263R|c.789C>T|3,BUFFER|p.A264T|c.790G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGTATCTC	.	5	ESCA
PEA15	0	.	GRCh37	1	160183258	160183258	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375C>A	p.%3D	p.P125P	ENST00000360472	4/4	16	10	6	13	12	0	PEA15,synonymous_variant,p.%3D,ENST00000360472,;PEA15,synonymous_variant,p.%3D,ENST00000368077,;PEA15,synonymous_variant,p.%3D,ENST00000368076,;DCAF8,downstream_gene_variant,,ENST00000473382,;DCAF8,downstream_gene_variant,,ENST00000556710,;DCAF8,downstream_gene_variant,,ENST00000326837,;DCAF8,downstream_gene_variant,,ENST00000608310,;DCAF8,downstream_gene_variant,,ENST00000368073,;DCAF8,downstream_gene_variant,,ENST00000368074,;DCAF8,downstream_gene_variant,,ENST00000477163,;RP11-536C5.7,upstream_gene_variant,,ENST00000418602,;PEA15,non_coding_transcript_exon_variant,,ENST00000488858,;DCAF8,downstream_gene_variant,,ENST00000497354,;DCAF8,downstream_gene_variant,,ENST00000476033,;DCAF8,downstream_gene_variant,,ENST00000490368,;DCAF8,downstream_gene_variant,,ENST00000461888,;DCAF8,downstream_gene_variant,,ENST00000481831,;	A	ENSG00000162734	ENST00000360472	Transcript	synonymous_variant	563	375	125	P	ccC/ccA	.	.	.	1	PEA15	HGNC	8822	protein_coding	YES	CCDS1199.1	ENSP00000353660	PEA15_HUMAN	B1AKZ4_HUMAN	UPI000006E972	.	.	.	4/4	.	Superfamily_domains:SSF47986,Gene3D:1.10.533.10,hmmpanther:PTHR15094:SF0,hmmpanther:PTHR15094	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTCCCCCACC	.	3	ESCA
NDUFS2	0	.	GRCh37	1	161179901	161179901	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703G>T	p.Asp235Tyr	p.D235Y	ENST00000367993	8/15	50	37	12	43	43	0	NDUFS2,missense_variant,p.Asp137Tyr,ENST00000476409,;NDUFS2,missense_variant,p.Asp235Tyr,ENST00000392179,;NDUFS2,missense_variant,p.Asp235Tyr,ENST00000367993,;NDUFS2,splice_region_variant,,ENST00000480762,;NDUFS2,splice_region_variant,,ENST00000478866,;NDUFS2,splice_region_variant,,ENST00000483804,;NDUFS2,splice_region_variant,,ENST00000465923,;NDUFS2,splice_region_variant,,ENST00000467295,;NDUFS2,upstream_gene_variant,,ENST00000493849,;NDUFS2,downstream_gene_variant,,ENST00000496133,;NDUFS2,upstream_gene_variant,,ENST00000468828,;NDUFS2,downstream_gene_variant,,ENST00000473321,;NDUFS2,upstream_gene_variant,,ENST00000492153,;NDUFS2,downstream_gene_variant,,ENST00000496553,;NDUFS2,downstream_gene_variant,,ENST00000479948,;	T	ENSG00000158864	ENST00000367993	Transcript	missense_variant	1151	703	235	D/Y	Gac/Tac	.	.	.	1	NDUFS2	HGNC	7708	protein_coding	YES	CCDS1224.1	ENSP00000356972	NDUS2_HUMAN	Q9HC12_HUMAN,Q9HC11_HUMAN,B7Z9L2_HUMAN	UPI00001308D2	.	deleterious(0)	probably_damaging(0.999)	8/15	.	HAMAP:MF_01358,hmmpanther:PTHR11993,hmmpanther:PTHR11993:SF10,TIGRFAM_domain:TIGR01962,Pfam_domain:PF00346,Gene3D:1.10.645.10,Superfamily_domains:SSF56762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTAGGACCTA	.	5	ESCA
CLCNKB	0	.	GRCh37	1	16375608	16375608	+	Intron	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.656-3delC	.	.	ENST00000375679	.	123	66	57	56	56	0	CLCNKB,frameshift_variant,p.Pro49GlnfsTer131,ENST00000375667,;CLCNKB,splice_region_variant,,ENST00000375679,;CLCNKB,upstream_gene_variant,,ENST00000431772,;	-	ENSG00000184908	ENST00000375679	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	CLCNKB	HGNC	2027	protein_coding	YES	CCDS168.1	ENSP00000364831	CLCKB_HUMAN	.	UPI000040E261	.	.	.	.	7/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGTCGCCCCCA	.	3	ESCA
EPHA2	0	.	GRCh37	1	16451577	16451577	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*133A>T	.	.	ENST00000358432	17/17	41	14	26	30	30	0	EPHA2,3_prime_UTR_variant,,ENST00000358432,;	A	ENSG00000142627	ENST00000358432	Transcript	3_prime_UTR_variant	3219	.	.	.	.	.	.	.	-1	EPHA2	HGNC	3386	protein_coding	YES	CCDS169.1	ENSP00000351209	EPHA2_HUMAN	Q96HF4_HUMAN,Q8IZL0_HUMAN	UPI00000731AB	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCTCAGCG	.	5	ESCA
POGK	0	.	GRCh37	1	166818617	166818617	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801C>T	p.%3D	p.A267A	ENST00000367875	5/5	29	22	7	14	14	0	POGK,synonymous_variant,p.%3D,ENST00000367876,;POGK,synonymous_variant,p.%3D,ENST00000536514,;POGK,synonymous_variant,p.%3D,ENST00000537173,;POGK,synonymous_variant,p.%3D,ENST00000367875,;POGK,downstream_gene_variant,,ENST00000449930,;	T	ENSG00000143157	ENST00000367875	Transcript	synonymous_variant	1161	801	267	A	gcC/gcT	.	.	.	1	POGK	HGNC	18800	protein_coding	YES	CCDS1254.1	ENSP00000356849	POGK_HUMAN	Q5TIJ2_HUMAN	UPI0000167816	.	.	.	5/5	.	PROSITE_profiles:PS51253,hmmpanther:PTHR19303:SF21,hmmpanther:PTHR19303,Gene3D:1.10.10.60,Pfam_domain:PF03221,SMART_domains:SM00674,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCCGAATA	.	5	ESCA
MPZL1	0	.	GRCh37	1	167734970	167734970	+	Missense_Mutation	SNP	C	C	G	rs757960465	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242C>G	p.Ala81Gly	p.A81G	ENST00000359523	2/6	34	28	6	30	30	0	MPZL1,missense_variant,p.Ala81Gly,ENST00000359523,;MPZL1,missense_variant,p.Ala81Gly,ENST00000474859,;MPZL1,missense_variant,p.Ala55Gly,ENST00000367853,;MPZL1,missense_variant,p.Ala81Gly,ENST00000392121,;MPZL1,missense_variant,p.Ala81Gly,ENST00000448405,;MPZL1,non_coding_transcript_exon_variant,,ENST00000465787,;MPZL1,non_coding_transcript_exon_variant,,ENST00000474729,;MPZL1,non_coding_transcript_exon_variant,,ENST00000464954,;	G	ENSG00000197965	ENST00000359523	Transcript	missense_variant	444	242	81	A/G	gCc/gGc	rs757960465	.	.	1	MPZL1	HGNC	7226	protein_coding	YES	CCDS1264.1	ENSP00000352513	MPZL1_HUMAN	A8K5D4_HUMAN	UPI000004BA6A	.	tolerated(0.27)	benign(0.009)	2/6	.	Prints_domain:PR00213,Superfamily_domains:SSF48726,SMART_domains:SM00406,SMART_domains:SM00409,Pfam_domain:PF07686,Gene3D:2.60.40.10,hmmpanther:PTHR13869:SF19,hmmpanther:PTHR13869,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGCCGACA	.	5	ESCA
NADK	0	.	GRCh37	1	1683486	1683486	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*857C>T	.	.	ENST00000344463	14/14	30	23	7	18	18	0	NADK,3_prime_UTR_variant,,ENST00000378625,;NADK,3_prime_UTR_variant,,ENST00000344463,;NADK,3_prime_UTR_variant,,ENST00000341991,;NADK,3_prime_UTR_variant,,ENST00000341426,;NADK,downstream_gene_variant,,ENST00000469045,;NADK,downstream_gene_variant,,ENST00000400922,;NADK,downstream_gene_variant,,ENST00000342348,;NADK,downstream_gene_variant,,ENST00000492768,;NADK,downstream_gene_variant,,ENST00000460602,;NADK,downstream_gene_variant,,ENST00000477235,;NADK,downstream_gene_variant,,ENST00000480499,;NADK,downstream_gene_variant,,ENST00000497186,;NADK,downstream_gene_variant,,ENST00000498806,;NADK,downstream_gene_variant,,ENST00000492845,;NADK,downstream_gene_variant,,ENST00000497615,;NADK,downstream_gene_variant,,ENST00000489538,;NADK,downstream_gene_variant,,ENST00000497747,;	A	ENSG00000008130	ENST00000344463	Transcript	3_prime_UTR_variant	2855	.	.	.	.	.	.	.	-1	NADK	HGNC	29831	protein_coding	YES	CCDS55562.1	ENSP00000340925	NADK_HUMAN	.	UPI000013CBEB	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGATCGCACTG	.	2	ESCA
NME7	0	.	GRCh37	1	169101823	169101823	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*200T>C	.	.	ENST00000367811	12/12	22	12	10	10	10	0	NME7,3_prime_UTR_variant,,ENST00000367811,;ATP1B1,3_prime_UTR_variant,,ENST00000367816,;NME7,3_prime_UTR_variant,,ENST00000472647,;ATP1B1,downstream_gene_variant,,ENST00000367813,;ATP1B1,downstream_gene_variant,,ENST00000499679,;ATP1B1,downstream_gene_variant,,ENST00000367815,;NME7,non_coding_transcript_exon_variant,,ENST00000493481,;NME7,non_coding_transcript_exon_variant,,ENST00000530739,;NME7,3_prime_UTR_variant,,ENST00000525440,;	G	ENSG00000143156	ENST00000367811	Transcript	3_prime_UTR_variant	1588	.	.	.	.	.	.	.	-1	NME7	HGNC	20461	protein_coding	YES	CCDS1277.1	ENSP00000356785	NDK7_HUMAN	.	UPI000012FE8C	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCATAGAC	.	5	ESCA
RP5-1182A14.5	0	.	GRCh37	1	16945454	16945454	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000607700	.	108	99	8	69	69	0	CROCCP2,non_coding_transcript_exon_variant,,ENST00000540383,;CROCCP2,non_coding_transcript_exon_variant,,ENST00000412962,;RP5-1182A14.5,downstream_gene_variant,,ENST00000607700,;	A	ENSG00000271732	ENST00000607700	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1230	1	RP5-1182A14.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGACGGCAGGC	.	2	ESCA
CROCC	0	.	GRCh37	1	17248507	17248507	+	5'UTR	DEL	C	C	-	rs778769958	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1delC	.	.	ENST00000375541	1/37	61	28	33	36	36	0	CROCC,5_prime_UTR_variant,,ENST00000375541,;CROCC,upstream_gene_variant,,ENST00000445545,;CROCC,intron_variant,,ENST00000466256,;CROCC,upstream_gene_variant,,ENST00000467938,;	-	ENSG00000058453	ENST00000375541	Transcript	5_prime_UTR_variant	63	.	.	.	.	rs778769958,TMP_ESP_1_17248507_17248507	.	.	1	CROCC	HGNC	21299	protein_coding	YES	CCDS30616.1	ENSP00000364691	CROCC_HUMAN	.	UPI00001AE5A0	.	.	.	1/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGCCTCCCCCC	.	3	ESCA
SLC9C2	0	.	GRCh37	1	173526482	173526482	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1212A>G	p.%3D	p.Q404Q	ENST00000367714	10/28	35	15	20	23	23	0	SLC9C2,synonymous_variant,p.%3D,ENST00000367714,;SLC9C2,synonymous_variant,p.%3D,ENST00000536496,;RP3-436N22.3,intron_variant,,ENST00000431459,;SLC9C2,non_coding_transcript_exon_variant,,ENST00000466087,;	C	ENSG00000162753	ENST00000367714	Transcript	synonymous_variant	1635	1212	404	Q	caA/caG	.	.	.	-1	SLC9C2	HGNC	28664	protein_coding	YES	CCDS1308.1	ENSP00000356687	SL9C2_HUMAN	F5H342_HUMAN	UPI0000197379	.	.	.	10/28	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10110:SF91,hmmpanther:PTHR10110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATTTGTGG	.	5	ESCA
KLHL20	0	.	GRCh37	1	173703092	173703092	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264C>A	p.%3D	p.A88A	ENST00000209884	3/12	93	45	48	83	83	0	KLHL20,synonymous_variant,p.%3D,ENST00000209884,;KLHL20,intron_variant,,ENST00000546011,;KLHL20,non_coding_transcript_exon_variant,,ENST00000493170,;KLHL20,non_coding_transcript_exon_variant,,ENST00000483154,;KLHL20,downstream_gene_variant,,ENST00000479505,;	A	ENSG00000076321	ENST00000209884	Transcript	synonymous_variant	400	264	88	A	gcC/gcA	.	.	.	1	KLHL20	HGNC	25056	protein_coding	YES	CCDS1310.1	ENSP00000209884	KLH20_HUMAN	.	UPI0000227E1A	.	.	.	3/12	.	Superfamily_domains:SSF54695,PIRSF_domain:PIRSF037037,SMART_domains:SM00225,Pfam_domain:PF00651,Gene3D:3.30.710.10,hmmpanther:PTHR24412:SF177,hmmpanther:PTHR24412,PROSITE_profiles:PS50097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P91L|c.272C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCCTGTAG	.	5	ESCA
RC3H1	0	.	GRCh37	1	173907542	173907542	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*317delA	.	.	ENST00000367696	20/20	25	15	9	17	17	0	RC3H1,3_prime_UTR_variant,,ENST00000258349,;RC3H1,3_prime_UTR_variant,,ENST00000367696,;RC3H1,downstream_gene_variant,,ENST00000367694,;RC3H1,downstream_gene_variant,,ENST00000479099,;	-	ENSG00000135870	ENST00000367696	Transcript	3_prime_UTR_variant	4071	.	.	.	.	.	.	.	-1	RC3H1	HGNC	29434	protein_coding	YES	CCDS30940.1	ENSP00000356669	RC3H1_HUMAN	B9EGU6_HUMAN	UPI00001D7DA8	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AATATCTTTTTT	.	2	ESCA
TNN	0	.	GRCh37	1	175097224	175097224	+	Silent	SNP	C	C	T	rs528565931	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3102C>T	p.%3D	p.G1034G	ENST00000239462	14/19	65	32	32	37	37	0	TNN,synonymous_variant,p.%3D,ENST00000239462,;	T	ENSG00000120332	ENST00000239462	Transcript	synonymous_variant	3215	3102	1034	G	ggC/ggT	rs528565931,COSM899911	.	.	1	TNN	HGNC	22942	protein_coding	YES	CCDS30943.1	ENSP00000239462	TENN_HUMAN	.	UPI00001D7DA9	.	.	.	14/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF167,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CAAGGCGCCAC	byFrequency|by1000G	4	ESCA
TNR	0	.	GRCh37	1	175360447	175360447	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1484delC	p.Pro495LeufsTer42	p.P495Lfs*42	ENST00000367674	7/23	75	45	30	34	34	0	TNR,frameshift_variant,p.Pro495LeufsTer42,ENST00000367674,;TNR,frameshift_variant,p.Pro495LeufsTer42,ENST00000263525,;TNR,downstream_gene_variant,,ENST00000422274,;	-	ENSG00000116147	ENST00000367674	Transcript	frameshift_variant	2193	1484	495	P/X	cCt/ct	COSM1689250	.	.	-1	TNR	HGNC	11953	protein_coding	YES	CCDS1318.1	ENSP00000356646	TENR_HUMAN	A1L306_HUMAN	UPI000013D41C	.	.	.	7/23	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF39,hmmpanther:PTHR19143,Pfam_domain:PF00041,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAGGTAGGGGGG	.	3	ESCA
PAPPA2	0	.	GRCh37	1	176526097	176526097	+	Silent	SNP	C	C	T	rs371392086	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639C>T	p.%3D	p.S213S	ENST00000367662	2/23	30	20	10	29	29	0	PAPPA2,synonymous_variant,p.%3D,ENST00000367661,;PAPPA2,synonymous_variant,p.%3D,ENST00000367662,;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,;	T	ENSG00000116183	ENST00000367662	Transcript	synonymous_variant	1803	639	213	S	tcC/tcT	rs371392086	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	.	.	2/23	.	Superfamily_domains:SSF49899	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0003	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTCCGGTAT	byCluster|by1000G	5	ESCA
FAM20B	0	.	GRCh37	1	179041052	179041052	+	Missense_Mutation	SNP	C	C	T	rs756589376	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003C>T	p.Arg335Trp	p.R335W	ENST00000263733	8/8	33	21	12	26	26	0	FAM20B,missense_variant,p.Arg335Trp,ENST00000263733,;	T	ENSG00000116199	ENST00000263733	Transcript	missense_variant	1339	1003	335	R/W	Cgg/Tgg	rs756589376	.	.	1	FAM20B	HGNC	23017	protein_coding	YES	CCDS1328.1	ENSP00000263733	XYLK_HUMAN	.	UPI000000DB7F	.	deleterious(0)	probably_damaging(1)	8/8	.	hmmpanther:PTHR12450,Pfam_domain:PF06702	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCATTCGGGTG	.	4	ESCA
TDRD5	0	.	GRCh37	1	179638527	179638527	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2848C>T	p.Pro950Ser	p.P950S	ENST00000444136	17/18	87	54	33	99	99	0	TDRD5,missense_variant,p.Pro896Ser,ENST00000367614,;TDRD5,missense_variant,p.Pro406Ser,ENST00000417329,;TDRD5,missense_variant,p.Pro950Ser,ENST00000444136,;TDRD5,missense_variant,p.Pro896Ser,ENST00000294848,;	T	ENSG00000162782	ENST00000444136	Transcript	missense_variant	3098	2848	950	P/S	Ccc/Tcc	.	.	.	1	TDRD5	HGNC	20614	protein_coding	YES	CCDS55663.1	ENSP00000406052	TDRD5_HUMAN	.	UPI000022AC96	.	tolerated(0.48)	benign(0.004)	17/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAGCCCTCT	.	5	ESCA
CACNA1E	0	.	GRCh37	1	181769317	181769317	+	3'Flank	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000367573	.	32	26	6	25	25	0	CACNA1E,3_prime_UTR_variant,,ENST00000358338,;CACNA1E,3_prime_UTR_variant,,ENST00000367567,;CACNA1E,3_prime_UTR_variant,,ENST00000357570,;CACNA1E,3_prime_UTR_variant,,ENST00000526775,;CACNA1E,3_prime_UTR_variant,,ENST00000367570,;CACNA1E,downstream_gene_variant,,ENST00000360108,;CACNA1E,downstream_gene_variant,,ENST00000367573,;	A	ENSG00000198216	ENST00000367573	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1222	1	CACNA1E	HGNC	1392	protein_coding	YES	CCDS55664.1	ENSP00000356545	CAC1E_HUMAN	Q9UN68_HUMAN,Q9NYZ6_HUMAN,Q9NY05_HUMAN,E9PIE8_HUMAN	UPI00004588C2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGATGCTTTAA	.	3	ESCA
ARPC5	0	.	GRCh37	1	183599769	183599769	+	Missense_Mutation	SNP	G	G	A	rs369978826	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.229C>T	p.Arg77Trp	p.R77W	ENST00000294742	3/4	24	19	5	22	22	0	ARPC5,missense_variant,p.Arg77Trp,ENST00000294742,;ARPC5,missense_variant,p.Arg74Trp,ENST00000359856,;ARPC5,missense_variant,p.Arg74Trp,ENST00000367534,;ARPC5,non_coding_transcript_exon_variant,,ENST00000462965,;ARPC5,non_coding_transcript_exon_variant,,ENST00000602490,;	A	ENSG00000162704	ENST00000294742	Transcript	missense_variant	327	229	77	R/W	Cgg/Tgg	rs369978826	.	.	-1	ARPC5	HGNC	708	protein_coding	YES	CCDS58050.1	ENSP00000294742	ARPC5_HUMAN	.	UPI00001CE02C	.	deleterious(0)	possibly_damaging(0.782)	3/4	.	hmmpanther:PTHR12644:SF1,hmmpanther:PTHR12644,Pfam_domain:PF04699,Gene3D:1k8kG00,Superfamily_domains:0047762	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGGTCCT	byCluster	5	ESCA
RNF2	0	.	GRCh37	1	185070204	185070204	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*778delT	.	.	ENST00000367510	7/7	47	24	23	38	38	0	RNF2,3_prime_UTR_variant,,ENST00000367510,;RNF2,downstream_gene_variant,,ENST00000453650,;RNF2,downstream_gene_variant,,ENST00000367509,;	-	ENSG00000121481	ENST00000367510	Transcript	3_prime_UTR_variant	2070	.	.	.	.	.	.	.	1	RNF2	HGNC	10061	protein_coding	YES	CCDS1365.1	ENSP00000356480	RING2_HUMAN	.	UPI000007131D	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGTGCTTTTTT	.	2	ESCA
SWT1	0	.	GRCh37	1	185151134	185151134	+	Silent	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1083T>A	p.%3D	p.P361P	ENST00000367500	7/19	42	35	7	28	28	0	SWT1,synonymous_variant,p.%3D,ENST00000367501,;SWT1,synonymous_variant,p.%3D,ENST00000367500,;	A	ENSG00000116668	ENST00000367500	Transcript	synonymous_variant	1248	1083	361	P	ccT/ccA	.	.	.	1	SWT1	HGNC	16785	protein_coding	YES	CCDS1367.1	ENSP00000356470	SWT1_HUMAN	Q5TC96_HUMAN,B3KSB6_HUMAN	UPI000013D4C5	.	.	.	7/19	.	hmmpanther:PTHR16161,hmmpanther:PTHR16161:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACCTGGAGA	.	5	ESCA
UBR4	0	.	GRCh37	1	19441999	19441999	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10956G>T	p.Gln3652His	p.Q3652H	ENST00000375254	74/106	41	14	26	27	27	0	UBR4,missense_variant,p.Gln67His,ENST00000375218,;UBR4,missense_variant,p.Gln3652His,ENST00000375254,;UBR4,missense_variant,p.Gln3645His,ENST00000375217,;UBR4,missense_variant,p.Gln3652His,ENST00000375267,;UBR4,missense_variant,p.Gln3628His,ENST00000375226,;UBR4,upstream_gene_variant,,ENST00000494503,;UBR4,upstream_gene_variant,,ENST00000466969,;	A	ENSG00000127481	ENST00000375254	Transcript	missense_variant	10984	10956	3652	Q/H	caG/caT	.	.	.	-1	UBR4	HGNC	30313	protein_coding	YES	CCDS189.1	ENSP00000364403	UBR4_HUMAN	Q96HY5_HUMAN	UPI000021276F	.	.	probably_damaging(0.948)	74/106	.	hmmpanther:PTHR21725	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGCCTGGTA	.	5	ESCA
KCNT2	0	.	GRCh37	1	196392230	196392230	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135G>A	p.Glu379Lys	p.E379K	ENST00000294725	12/28	48	21	27	39	39	0	KCNT2,missense_variant,p.Glu379Lys,ENST00000294725,;KCNT2,missense_variant,p.Glu379Lys,ENST00000367433,;KCNT2,missense_variant,p.Glu379Lys,ENST00000367431,;KCNT2,missense_variant,p.Glu379Lys,ENST00000609185,;KCNT2,intron_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,;KCNT2,missense_variant,p.Glu86Lys,ENST00000466914,;	T	ENSG00000162687	ENST00000294725	Transcript	missense_variant	2051	1135	379	E/K	Gag/Aag	.	.	.	-1	KCNT2	HGNC	18866	protein_coding	YES	CCDS1384.1	ENSP00000294725	KCNT2_HUMAN	A9LNM6_HUMAN	UPI00001E0966	.	tolerated(0.09)	probably_damaging(0.991)	12/28	.	hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCAGCGT	.	5	ESCA
NR5A2	0	.	GRCh37	1	200145299	200145299	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1961C>T	.	.	ENST00000367362	8/8	52	34	17	45	45	0	NR5A2,3_prime_UTR_variant,,ENST00000367362,;NR5A2,downstream_gene_variant,,ENST00000544748,;NR5A2,downstream_gene_variant,,ENST00000236914,;	T	ENSG00000116833	ENST00000367362	Transcript	3_prime_UTR_variant	3833	.	.	.	.	.	.	.	1	NR5A2	HGNC	7984	protein_coding	YES	CCDS1401.1	ENSP00000356331	NR5A2_HUMAN	Q8WY08_HUMAN,B4E2P3_HUMAN	UPI0000130482	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGACTTGTA	.	5	ESCA
C1orf106	0	.	GRCh37	1	200870139	200870141	+	In_Frame_Del	DEL	GGA	GGA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GGA	GGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376_378delGAG	p.Glu126del	p.E126del	ENST00000413687	5/10	39	16	23	28	28	0	C1orf106,inframe_deletion,p.Glu211del,ENST00000367342,;C1orf106,inframe_deletion,p.Glu126del,ENST00000413687,;C1orf106,downstream_gene_variant,,ENST00000532631,;C1orf106,downstream_gene_variant,,ENST00000451872,;C1orf106,upstream_gene_variant,,ENST00000531649,;	-	ENSG00000163362	ENST00000413687	Transcript	inframe_deletion	733-735	372-374	124-125	LE/L	ctGGAg/ctg	.	.	.	1	C1orf106	HGNC	25599	protein_coding	YES	CCDS44292.1	ENSP00000392105	CA106_HUMAN	E9PK29_HUMAN,C9JAT8_HUMAN	UPI0000204714	.	.	.	5/10	.	hmmpanther:PTHR16093:SF4,hmmpanther:PTHR16093,Pfam_domain:PF11819	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGCCTGGAGGAGA	.	3	ESCA
PPP1R12B	0	.	GRCh37	1	202560952	202560952	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11264A>G	.	.	ENST00000608999	24/24	35	15	20	29	29	0	PPP1R12B,3_prime_UTR_variant,,ENST00000608999,;SYT2,3_prime_UTR_variant,,ENST00000367267,;SYT2,3_prime_UTR_variant,,ENST00000367268,;PPP1R12B,downstream_gene_variant,,ENST00000391959,;PPP1R12B,downstream_gene_variant,,ENST00000336894,;PPP1R12B,downstream_gene_variant,,ENST00000367270,;	G	ENSG00000077157	ENST00000608999	Transcript	3_prime_UTR_variant	14366	.	.	.	.	.	.	.	1	PPP1R12B	HGNC	7619	protein_coding	YES	CCDS1426.1	ENSP00000476755	.	.	UPI0000458A57	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCCACAGGG	.	5	ESCA
SYT2	0	.	GRCh37	1	202574790	202574790	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111G>A	p.%3D	p.G37G	ENST00000367267	2/9	161	87	73	99	99	0	SYT2,synonymous_variant,p.%3D,ENST00000367267,;SYT2,synonymous_variant,p.%3D,ENST00000367268,;RP11-569A11.1,downstream_gene_variant,,ENST00000428573,;	T	ENSG00000143858	ENST00000367267	Transcript	synonymous_variant	304	111	37	G	ggG/ggA	.	.	.	-1	SYT2	HGNC	11510	protein_coding	YES	CCDS1427.1	ENSP00000356236	SYT2_HUMAN	.	UPI000006E8FC	.	.	.	2/9	.	hmmpanther:PTHR10024:SF208,hmmpanther:PTHR10024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCTCCCCAGC	.	3	ESCA
PPFIA4	0	.	GRCh37	1	203008166	203008166	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34delG	p.Asp12ThrfsTer18	p.D12Tfs*18	ENST00000367240	2/29	37	27	10	21	21	0	PPFIA4,frameshift_variant,p.Asp12ThrfsTer18,ENST00000367240,;PPFIA4,frameshift_variant,p.Asp12ThrfsTer18,ENST00000447715,;PPFIA4,5_prime_UTR_variant,,ENST00000295706,;	-	ENSG00000143847	ENST00000367240	Transcript	frameshift_variant	557	30	10	E/X	gaG/ga	.	.	.	1	PPFIA4	HGNC	9248	protein_coding	.	.	ENSP00000356209	.	B1APN9_HUMAN	UPI0001881B39	.	.	.	2/29	.	hmmpanther:PTHR12587:SF5,hmmpanther:PTHR12587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAATGAGGGGGA	.	2	ESCA
FMOD	0	.	GRCh37	1	203316470	203316470	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.929delC	p.Pro310GlnfsTer31	p.P310Qfs*31	ENST00000354955	2/3	37	30	7	29	29	0	FMOD,frameshift_variant,p.Pro310GlnfsTer31,ENST00000354955,;FMOD,intron_variant,,ENST00000493296,;FMOD,intron_variant,,ENST00000461936,;	-	ENSG00000122176	ENST00000354955	Transcript	frameshift_variant	1393	929	310	P/X	cCa/ca	COSM1337988,COSM77725	.	.	-1	FMOD	HGNC	3774	protein_coding	YES	CCDS30976.1	ENSP00000347041	FMOD_HUMAN	Q12833_HUMAN,B4E1J3_HUMAN	UPI00000746A2	.	.	.	2/3	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24371:SF11,hmmpanther:PTHR24371,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	deletion	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTGACTGGGGGG	.	3	ESCA
ZC3H11A	0	.	GRCh37	1	203770937	203770946	+	5'UTR	DEL	TGGTTTTGAT	TGGTTTTGAT	GGTTTTGA	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TGGTTTTGAT	TGGTTTTGAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1353_-1344delTGGTTTTGATinsGGTTTTGA	.	.	ENST00000545588	1/17	80	70	10	62	62	0	ZC3H11A,5_prime_UTR_variant,,ENST00000545588,;ZC3H11A,intron_variant,,ENST00000367212,;ZC3H11A,intron_variant,,ENST00000453771,;ZC3H11A,intron_variant,,ENST00000367214,;ZC3H11A,intron_variant,,ENST00000432282,;ZC3H11A,intron_variant,,ENST00000332127,;ZBED6,downstream_gene_variant,,ENST00000550078,;ZC3H11A,non_coding_transcript_exon_variant,,ENST00000461980,;ZC3H11A,non_coding_transcript_exon_variant,,ENST00000466470,;ZC3H11A,5_prime_UTR_variant,,ENST00000495527,;RP11-397P13.6,downstream_gene_variant,,ENST00000432760,;	GGTTTTGA	ENSG00000058673	ENST00000545588	Transcript	5_prime_UTR_variant	2475-2484	.	.	.	.	.	.	.	1	ZC3H11A	HGNC	29093	protein_coding	YES	CCDS30978.1	ENSP00000438527	ZC11A_HUMAN	E9PBY7_HUMAN,C9J0L0_HUMAN,B4DLG2_HUMAN	UPI000006F3FD	.	.	.	1/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTTTTGGTTTTGATTTTTT	.	3	ESCA
RBBP5	0	.	GRCh37	1	205056864	205056865	+	3'UTR	INS	-	-	A	rs780962739	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1050dupT	.	.	ENST00000264515	14/14	33	24	9	42	42	0	RBBP5,3_prime_UTR_variant,,ENST00000264515,;RBBP5,3_prime_UTR_variant,,ENST00000367164,;TMEM81,upstream_gene_variant,,ENST00000367167,;RP11-536L3.4,upstream_gene_variant,,ENST00000603227,;	A	ENSG00000117222	ENST00000264515	Transcript	3_prime_UTR_variant	2809-2810	.	.	.	.	rs780962739	.	.	-1	RBBP5	HGNC	9888	protein_coding	YES	CCDS30983.1	ENSP00000264515	RBBP5_HUMAN	.	UPI00001A9CA5	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AATGTCAAAAA	.	2	ESCA
RASSF5	0	.	GRCh37	1	206762574	206762574	+	3'Flank	DEL	A	A	-	rs571671993	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000355294	.	62	46	16	60	60	0	RASSF5,3_prime_UTR_variant,,ENST00000304534,;EIF2D,downstream_gene_variant,,ENST00000367114,;RASSF5,downstream_gene_variant,,ENST00000367117,;RASSF5,downstream_gene_variant,,ENST00000355294,;EIF2D,downstream_gene_variant,,ENST00000271764,;RASSF5,non_coding_transcript_exon_variant,,ENST00000491368,;RASSF5,non_coding_transcript_exon_variant,,ENST00000481486,;EIF2D,intron_variant,,ENST00000472709,;	-	ENSG00000136653	ENST00000355294	Transcript	downstream_gene_variant	.	.	.	.	.	rs571671993	.	1530	1	RASSF5	HGNC	17609	protein_coding	YES	CCDS30998.1	ENSP00000347443	RASF5_HUMAN	.	UPI0000072CF5	.	.	.	.	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGTTTTAAAAAA	by1000G	2	ESCA
PINK1	0	.	GRCh37	1	20977076	20977076	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1638G>T	p.Glu546Asp	p.E546D	ENST00000321556	8/8	30	9	20	26	26	0	PINK1,missense_variant,p.Glu546Asp,ENST00000321556,;DDOST,downstream_gene_variant,,ENST00000464364,;DDOST,downstream_gene_variant,,ENST00000375048,;DDOST,downstream_gene_variant,,ENST00000415136,;DDOST,downstream_gene_variant,,ENST00000602624,;PINK1,non_coding_transcript_exon_variant,,ENST00000492302,;PINK1,non_coding_transcript_exon_variant,,ENST00000400490,;DDOST,downstream_gene_variant,,ENST00000475210,;PINK1-AS,non_coding_transcript_exon_variant,,ENST00000451424,;AL391357.1,non_coding_transcript_exon_variant,,ENST00000535128,;	T	ENSG00000158828	ENST00000321556	Transcript	missense_variant	1732	1638	546	E/D	gaG/gaT	COSM903283	.	.	1	PINK1	HGNC	14581	protein_coding	YES	CCDS211.1	ENSP00000364204	PINK1_HUMAN	.	UPI0000035BA9	.	tolerated(0.46)	benign(0.005)	8/8	.	hmmpanther:PTHR22972	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGAGAAGTG	.	5	ESCA
HSD11B1	0	.	GRCh37	1	209880402	209880402	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.446delT	p.Val149AlafsTer2	p.V149Afs*2	ENST00000367028	5/7	17	8	8	19	19	0	HSD11B1,frameshift_variant,p.Val149AlafsTer2,ENST00000367027,;HSD11B1,frameshift_variant,p.Val149AlafsTer2,ENST00000261465,;HSD11B1,frameshift_variant,p.Val149AlafsTer2,ENST00000367028,;RP1-28O10.1,intron_variant,,ENST00000441672,;	-	ENSG00000117594	ENST00000367028	Transcript	frameshift_variant	615	446	149	V/X	gTc/gc	.	.	.	1	HSD11B1	HGNC	5208	protein_coding	YES	CCDS1489.1	ENSP00000355995	DHI1_HUMAN	.	UPI000004C796	.	.	.	5/7	.	hmmpanther:PTHR24322:SF249,hmmpanther:PTHR24322,Pfam_domain:PF00106,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACGTGGTCCTGA	.	2	ESCA
TRAF5	0	.	GRCh37	1	211526639	211526639	+	Missense_Mutation	SNP	G	G	A	rs148579195	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>A	p.Gly20Ser	p.G20S	ENST00000261464	2/11	24	18	6	25	25	0	TRAF5,missense_variant,p.Gly20Ser,ENST00000367004,;TRAF5,missense_variant,p.Gly20Ser,ENST00000261464,;TRAF5,missense_variant,p.Gly20Ser,ENST00000427925,;TRAF5,missense_variant,p.Gly20Ser,ENST00000336184,;TRAF5,non_coding_transcript_exon_variant,,ENST00000462410,;TRAF5,non_coding_transcript_exon_variant,,ENST00000488428,;TRAF5,non_coding_transcript_exon_variant,,ENST00000494355,;	A	ENSG00000082512	ENST00000261464	Transcript	missense_variant	112	58	20	G/S	Ggc/Agc	rs148579195,COSM1501144	.	.	1	TRAF5	HGNC	12035	protein_coding	YES	CCDS1497.1	ENSP00000261464	TRAF5_HUMAN	D3DT93_HUMAN,B4E0A2_HUMAN,B3KX26_HUMAN	UPI0000070955	.	tolerated(0.61)	benign(0.003)	2/11	.	hmmpanther:PTHR10131:SF66,hmmpanther:PTHR10131,PIRSF_domain:PIRSF015614	A:0.0016	A:0.0038	A:0	.	A:0.002	A:0.001	A:0	A:0.0016	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	ATTCCGGCAAC	byFrequency|byCluster|by1000G	4	ESCA
RAB3GAP2	0	.	GRCh37	1	220327392	220327392	+	Frame_Shift_Del	DEL	T	T	-	rs749173523	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3563delA	p.Asn1188MetfsTer7	p.N1188Mfs*7	ENST00000358951	32/35	58	45	13	28	28	0	RAB3GAP2,frameshift_variant,p.Asn1188MetfsTer7,ENST00000358951,;RAB3GAP2,non_coding_transcript_exon_variant,,ENST00000491305,;RAB3GAP2,non_coding_transcript_exon_variant,,ENST00000491005,;RAB3GAP2,upstream_gene_variant,,ENST00000474966,;	-	ENSG00000118873	ENST00000358951	Transcript	frameshift_variant	3680	3563	1188	N/X	aAt/at	rs749173523	.	.	-1	RAB3GAP2	HGNC	17168	protein_coding	YES	CCDS31028.1	ENSP00000351832	RBGPR_HUMAN	.	UPI0000072269	.	.	.	32/35	.	Pfam_domain:PF14656,hmmpanther:PTHR12472	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATGCATTTTTT	byFrequency	3	ESCA
MARK1	0	.	GRCh37	1	220837142	220837175	+	3'Flank	DEL	ATGTGTAGCCCCTTTTTAACCTAGTGTTCATTCA	ATGTGTAGCCCCTTTTTAACCTAGTGTTCATTCA	TGTGTAGCCCCTTTTTAACCTAGTGTTCATTC	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	ATGTGTAGCCCCTTTTTAACCTAGTGTTCATTCA	ATGTGTAGCCCCTTTTTAACCTAGTGTTCATTCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000366917	.	32	25	7	23	23	0	MARK1,3_prime_UTR_variant,,ENST00000366918,;MARK1,3_prime_UTR_variant,,ENST00000402574,;MARK1,downstream_gene_variant,,ENST00000366917,;RP11-322F10.2,upstream_gene_variant,,ENST00000446040,;	TGTGTAGCCCCTTTTTAACCTAGTGTTCATTC	ENSG00000116141	ENST00000366917	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1342	1	MARK1	HGNC	6896	protein_coding	YES	CCDS31029.2	ENSP00000355884	MARK1_HUMAN	B4DIB3_HUMAN	UPI0000048D8B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	AAAAAAATGTGTAGCCCCTTTTTAACCTAGTGTTCATTCAAAAAA	.	2	ESCA
MARK1	0	.	GRCh37	1	220837175	220837175	+	3'Flank	DEL	A	A	-	rs766747788	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000366917	.	19	13	6	26	26	0	MARK1,3_prime_UTR_variant,,ENST00000366918,;MARK1,3_prime_UTR_variant,,ENST00000402574,;MARK1,downstream_gene_variant,,ENST00000366917,;RP11-322F10.2,upstream_gene_variant,,ENST00000446040,;	-	ENSG00000116141	ENST00000366917	Transcript	downstream_gene_variant	.	.	.	.	.	rs766747788	.	1375	1	MARK1	HGNC	6896	protein_coding	YES	CCDS31029.2	ENSP00000355884	MARK1_HUMAN	B4DIB3_HUMAN	UPI0000048D8B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCATTCAAAAAA	.	2	ESCA
RP4-559A3.7	0	.	GRCh37	1	226075158	226075158	+	Missense_Mutation	SNP	C	C	T	rs145906534	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003G>A	p.Ala335Thr	p.A335T	ENST00000432920	7/8	25	19	6	23	23	0	RP4-559A3.7,missense_variant,p.Ala335Thr,ENST00000432920,;LEFTY1,synonymous_variant,p.%3D,ENST00000272134,;LEFTY1,downstream_gene_variant,,ENST00000492457,;	T	ENSG00000255835	ENST00000432920	Transcript	missense_variant	1171	1003	335	A/T	Gcc/Acc	rs145906534	.	.	-1	RP4-559A3.7	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000414068	.	J3KR12_HUMAN	UPI0001AE79EB	.	.	unknown(0)	7/8	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCTGGCGCCCC	byCluster	4	ESCA
GUK1	0	.	GRCh37	1	228333720	228333720	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.176-7C>T	.	.	ENST00000366728	.	66	27	39	43	43	0	GUK1,splice_region_variant,,ENST00000453943,;GUK1,splice_region_variant,,ENST00000435153,;GUK1,splice_region_variant,,ENST00000412265,;GUK1,splice_region_variant,,ENST00000391865,;GUK1,splice_region_variant,,ENST00000366722,;GUK1,splice_region_variant,,ENST00000366726,;GUK1,splice_region_variant,,ENST00000366718,;GUK1,splice_region_variant,,ENST00000366716,;GUK1,splice_region_variant,,ENST00000366728,;GUK1,splice_region_variant,,ENST00000312726,;GUK1,splice_region_variant,,ENST00000366721,;GUK1,splice_region_variant,,ENST00000366730,;GUK1,splice_region_variant,,ENST00000366723,;GJC2,upstream_gene_variant,,ENST00000366714,;GUK1,splice_region_variant,,ENST00000498092,;GUK1,splice_region_variant,,ENST00000485859,;GUK1,splice_region_variant,,ENST00000472939,;GUK1,splice_region_variant,,ENST00000493138,;GUK1,splice_region_variant,,ENST00000478725,;GUK1,splice_region_variant,,ENST00000485838,;GUK1,splice_region_variant,,ENST00000462807,;GUK1,splice_region_variant,,ENST00000486668,;GUK1,splice_region_variant,,ENST00000492871,;GUK1,splice_region_variant,,ENST00000493209,;GUK1,splice_region_variant,,ENST00000485733,;GUK1,splice_region_variant,,ENST00000484953,;GUK1,non_coding_transcript_exon_variant,,ENST00000464858,;GUK1,non_coding_transcript_exon_variant,,ENST00000460224,;GUK1,non_coding_transcript_exon_variant,,ENST00000485168,;GUK1,non_coding_transcript_exon_variant,,ENST00000485083,;GUK1,non_coding_transcript_exon_variant,,ENST00000470040,;GUK1,non_coding_transcript_exon_variant,,ENST00000495999,;GUK1,upstream_gene_variant,,ENST00000470155,;GUK1,upstream_gene_variant,,ENST00000465025,;GUK1,downstream_gene_variant,,ENST00000491613,;GUK1,downstream_gene_variant,,ENST00000469973,;GUK1,upstream_gene_variant,,ENST00000498115,;GUK1,upstream_gene_variant,,ENST00000480056,;GUK1,upstream_gene_variant,,ENST00000481341,;GUK1,upstream_gene_variant,,ENST00000477206,;GUK1,upstream_gene_variant,,ENST00000471270,;	T	ENSG00000143774	ENST00000366728	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	GUK1	HGNC	4693	protein_coding	YES	CCDS55689.1	ENSP00000355689	KGUA_HUMAN	.	UPI000046FFA0	.	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCTGCTA	.	5	ESCA
OBSCN	0	.	GRCh37	1	228496835	228496835	+	Missense_Mutation	SNP	G	G	A	rs560506912	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15646G>A	p.Val5216Met	p.V5216M	ENST00000570156	59/116	31	24	6	22	22	0	OBSCN,missense_variant,p.Val1893Met,ENST00000366707,;OBSCN,missense_variant,p.Val1378Met,ENST00000366709,;OBSCN,missense_variant,p.Val4259Met,ENST00000284548,;OBSCN,missense_variant,p.Val4259Met,ENST00000422127,;OBSCN,missense_variant,p.Val5216Met,ENST00000570156,;OBSCN,downstream_gene_variant,,ENST00000483539,;OBSCN,downstream_gene_variant,,ENST00000359599,;OBSCN,downstream_gene_variant,,ENST00000602832,;	A	ENSG00000154358	ENST00000570156	Transcript	missense_variant	15720	15646	5216	V/M	Gtg/Atg	rs560506912	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	benign(0.304)	59/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGACGTGCAG	byFrequency|byCluster	5	ESCA
EPHA8	0	.	GRCh37	1	22903132	22903133	+	Frame_Shift_Ins	INS	-	-	CT	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590_591dupTC	p.Arg198SerfsTer22	p.R198Sfs*22	ENST00000166244	3/17	60	46	14	44	44	0	EPHA8,frameshift_variant,p.Arg198SerfsTer22,ENST00000374644,;EPHA8,frameshift_variant,p.Arg198SerfsTer22,ENST00000538803,;EPHA8,frameshift_variant,p.Arg198SerfsTer22,ENST00000166244,;	CT	ENSG00000070886	ENST00000166244	Transcript	frameshift_variant	654-655	582-583	194-195	-/X	-/CT	.	.	.	1	EPHA8	HGNC	3391	protein_coding	YES	CCDS225.1	ENSP00000166244	EPHA8_HUMAN	.	UPI000012A07B	.	.	.	3/17	.	Superfamily_domains:SSF49785,SMART_domains:SM00615,PIRSF_domain:PIRSF000666,Pfam_domain:PF01404,Gene3D:2.60.120.260,PROSITE_patterns:PS00790,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF274,PROSITE_profiles:PS51550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCCATCCTCTC	.	2	ESCA
EPHA8	0	.	GRCh37	1	22913109	22913109	+	Silent	SNP	G	G	A	rs201432613	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.960G>A	p.%3D	p.P320P	ENST00000166244	4/17	76	23	52	53	53	0	EPHA8,synonymous_variant,p.%3D,ENST00000374644,;EPHA8,synonymous_variant,p.%3D,ENST00000538803,;EPHA8,synonymous_variant,p.%3D,ENST00000166244,;	A	ENSG00000070886	ENST00000166244	Transcript	synonymous_variant	1032	960	320	P	ccG/ccA	rs201432613,COSM464103,COSM464104	.	.	1	EPHA8	HGNC	3391	protein_coding	YES	CCDS225.1	ENSP00000166244	EPHA8_HUMAN	.	UPI000012A07B	.	.	.	4/17	.	PIRSF_domain:PIRSF000666,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF274	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCCGCCGTC	byCluster|by1000G	5	ESCA
NID1	0	.	GRCh37	1	236141179	236141179	+	Silent	SNP	G	G	A	rs772051661	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3732C>T	p.%3D	p.I1244I	ENST00000264187	20/20	37	26	11	22	22	0	NID1,synonymous_variant,p.%3D,ENST00000264187,;NID1,synonymous_variant,p.%3D,ENST00000366595,;	A	ENSG00000116962	ENST00000264187	Transcript	synonymous_variant	3815	3732	1244	I	atC/atT	rs772051661,COSM210427	.	.	-1	NID1	HGNC	7821	protein_coding	YES	CCDS1608.1	ENSP00000264187	NID1_HUMAN	.	UPI000013D4D9	.	.	.	20/20	.	hmmpanther:PTHR10529:SF107,hmmpanther:PTHR10529,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTCGATACA	byFrequency	5	ESCA
ERO1LB	0	.	GRCh37	1	236399648	236399648	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556C>T	p.Arg186Cys	p.R186C	ENST00000354619	7/16	62	55	7	37	37	0	ERO1LB,missense_variant,p.Arg67Cys,ENST00000366589,;ERO1LB,missense_variant,p.Arg186Cys,ENST00000354619,;ERO1LB,3_prime_UTR_variant,,ENST00000327333,;	A	ENSG00000086619	ENST00000354619	Transcript	missense_variant	758	556	186	R/C	Cgt/Tgt	.	.	.	-1	ERO1LB	HGNC	14355	protein_coding	YES	CCDS31064.1	ENSP00000346635	ERO1B_HUMAN	Q5TAE8_HUMAN,Q5T1H5_HUMAN	UPI00004700B5	.	deleterious(0)	probably_damaging(0.998)	7/16	.	Superfamily_domains:0043331,PIRSF_domain:PIRSF017205,Pfam_domain:PF04137,hmmpanther:PTHR12613,hmmpanther:PTHR12613:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAACGCTCTG	.	4	ESCA
FMN2	0	.	GRCh37	1	240638313	240638313	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*859C>T	.	.	ENST00000319653	18/18	49	30	19	40	40	0	FMN2,3_prime_UTR_variant,,ENST00000319653,;AL646016.1,intron_variant,,ENST00000596886,;FMN2,downstream_gene_variant,,ENST00000545751,;FMN2,downstream_gene_variant,,ENST00000543681,;FMN2,downstream_gene_variant,,ENST00000496950,;	T	ENSG00000155816	ENST00000319653	Transcript	3_prime_UTR_variant	6258	.	.	.	.	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTCCTGTCC	.	5	ESCA
OR13G1	0	.	GRCh37	1	247836052	247836052	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292C>G	p.Leu98Val	p.L98V	ENST00000359688	1/1	47	39	7	32	32	0	OR13G1,missense_variant,p.Leu98Val,ENST00000359688,;RP11-634B7.4,intron_variant,,ENST00000449298,;OR3D1P,downstream_gene_variant,,ENST00000438288,;	C	ENSG00000197437	ENST00000359688	Transcript	missense_variant	314	292	98	L/V	Ctc/Gtc	.	.	.	-1	OR13G1	HGNC	14999	protein_coding	YES	CCDS31094.1	ENSP00000352717	O13G1_HUMAN	.	UPI0000061E5B	.	tolerated(0.14)	probably_damaging(0.991)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF237,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGAGCTGGG	.	5	ESCA
PTPRU	0	.	GRCh37	1	29641996	29641996	+	Missense_Mutation	SNP	C	C	A	rs780002847	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3370C>A	p.Arg1124Ser	p.R1124S	ENST00000345512	24/31	55	16	38	44	44	0	PTPRU,missense_variant,p.Arg1114Ser,ENST00000373779,;PTPRU,missense_variant,p.Arg1111Ser,ENST00000428026,;PTPRU,missense_variant,p.Arg1120Ser,ENST00000460170,;PTPRU,missense_variant,p.Arg1120Ser,ENST00000323874,;PTPRU,missense_variant,p.Arg1120Ser,ENST00000356870,;PTPRU,missense_variant,p.Arg1124Ser,ENST00000345512,;PTPRU,downstream_gene_variant,,ENST00000415600,;PTPRU,upstream_gene_variant,,ENST00000493601,;PTPRU,upstream_gene_variant,,ENST00000465525,;PTPRU,downstream_gene_variant,,ENST00000526080,;	A	ENSG00000060656	ENST00000345512	Transcript	missense_variant	3499	3370	1124	R/S	Cgt/Agt	rs780002847	.	.	1	PTPRU	HGNC	9683	protein_coding	YES	CCDS334.1	ENSP00000334941	PTPRU_HUMAN	B3KT29_HUMAN	UPI000013C57E	.	deleterious(0)	probably_damaging(1)	24/31	.	PROSITE_profiles:PS50056,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF207,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00404,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGGCGTGTC	.	5	ESCA
KIAA1522	0	.	GRCh37	1	33240337	33240339	+	3'UTR	DEL	CTT	CTT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1852_*1854delCTT	.	.	ENST00000401073	7/7	70	43	27	49	49	0	KIAA1522,3_prime_UTR_variant,,ENST00000373481,;KIAA1522,3_prime_UTR_variant,,ENST00000373480,;KIAA1522,3_prime_UTR_variant,,ENST00000401073,;YARS,downstream_gene_variant,,ENST00000373477,;KIAA1522,downstream_gene_variant,,ENST00000294521,;YARS,downstream_gene_variant,,ENST00000469100,;YARS,downstream_gene_variant,,ENST00000490826,;YARS,downstream_gene_variant,,ENST00000487404,;YARS,downstream_gene_variant,,ENST00000478828,;	-	ENSG00000162522	ENST00000401073	Transcript	3_prime_UTR_variant	5204-5206	.	.	.	.	.	.	.	1	KIAA1522	HGNC	29301	protein_coding	YES	CCDS41298.1	ENSP00000383851	K1522_HUMAN	.	UPI000022ACD0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCAGCCCTTCTTTG	.	3	ESCA
ADC	0	.	GRCh37	1	33562406	33562406	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852C>T	p.%3D	p.A284A	ENST00000294517	9/12	85	52	33	34	34	0	ADC,synonymous_variant,p.%3D,ENST00000373443,;ADC,synonymous_variant,p.%3D,ENST00000373440,;ADC,synonymous_variant,p.%3D,ENST00000294517,;ADC,synonymous_variant,p.%3D,ENST00000373441,;ADC,synonymous_variant,p.%3D,ENST00000358680,;ADC,synonymous_variant,p.%3D,ENST00000398167,;ADC,non_coding_transcript_exon_variant,,ENST00000492521,;ADC,non_coding_transcript_exon_variant,,ENST00000484656,;ADC,non_coding_transcript_exon_variant,,ENST00000475935,;ADC,non_coding_transcript_exon_variant,,ENST00000473089,;ADC,non_coding_transcript_exon_variant,,ENST00000481886,;ADC,non_coding_transcript_exon_variant,,ENST00000471119,;ADC,non_coding_transcript_exon_variant,,ENST00000478204,;ADC,non_coding_transcript_exon_variant,,ENST00000477570,;ADC,downstream_gene_variant,,ENST00000497710,;ADC,downstream_gene_variant,,ENST00000483027,;ADC,downstream_gene_variant,,ENST00000492420,;ADC,downstream_gene_variant,,ENST00000478635,;ADC,downstream_gene_variant,,ENST00000462920,;ADC,downstream_gene_variant,,ENST00000497280,;	T	ENSG00000142920	ENST00000294517	Transcript	synonymous_variant	1439	852	284	A	gcC/gcT	.	.	.	1	ADC	HGNC	29957	protein_coding	YES	CCDS375.1	ENSP00000294517	ADC_HUMAN	D3DPR0_HUMAN,B3KV62_HUMAN	UPI0000047152	.	.	.	9/12	.	Prints_domain:PR01179,Superfamily_domains:SSF51419,Superfamily_domains:SSF50621,Gene3D:2.40.37.10,hmmpanther:PTHR11482,hmmpanther:PTHR11482:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGCCTTCAC	.	5	ESCA
MEGF6	0	.	GRCh37	1	3424356	3424356	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1789+3G>A	.	.	ENST00000356575	.	39	30	9	23	23	0	MEGF6,splice_region_variant,,ENST00000356575,;MEGF6,splice_region_variant,,ENST00000294599,;MEGF6,splice_region_variant,,ENST00000485002,;	T	ENSG00000162591	ENST00000356575	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	MEGF6	HGNC	3232	protein_coding	YES	CCDS41237.1	ENSP00000348982	MEGF6_HUMAN	.	UPI0000DACACB	.	.	.	.	14/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACGCACCAT	.	4	ESCA
MEGF6	0	.	GRCh37	1	3519090	3519090	+	Missense_Mutation	SNP	G	G	A	rs373558942	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.206C>T	p.Thr69Met	p.T69M	ENST00000356575	2/37	100	76	23	82	82	0	MEGF6,missense_variant,p.Thr69Met,ENST00000356575,;MEGF6,missense_variant,p.Thr69Met,ENST00000485002,;	A	ENSG00000162591	ENST00000356575	Transcript	missense_variant	433	206	69	T/M	aCg/aTg	rs373558942,COSM177714	.	.	-1	MEGF6	HGNC	3232	protein_coding	YES	CCDS41237.1	ENSP00000348982	MEGF6_HUMAN	.	UPI0000DACACB	.	tolerated(1)	benign(0.003)	2/37	.	PROSITE_profiles:PS51041	.	.	.	.	.	.	.	A:0	A:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCGTGTGG	byFrequency|byCluster	5	ESCA
MAP7D1	0	.	GRCh37	1	36642154	36642154	+	Missense_Mutation	SNP	C	C	T	rs780310575	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1205C>T	p.Pro402Leu	p.P402L	ENST00000373151	7/17	26	9	17	21	21	0	MAP7D1,missense_variant,p.Pro402Leu,ENST00000373151,;MAP7D1,missense_variant,p.Pro370Leu,ENST00000373150,;MAP7D1,missense_variant,p.Pro365Leu,ENST00000316156,;MAP7D1,upstream_gene_variant,,ENST00000373148,;MAP7D1,upstream_gene_variant,,ENST00000530975,;MAP7D1,downstream_gene_variant,,ENST00000530729,;MAP7D1,downstream_gene_variant,,ENST00000429533,;MAP7D1,non_coding_transcript_exon_variant,,ENST00000474796,;MAP7D1,upstream_gene_variant,,ENST00000487131,;MAP7D1,upstream_gene_variant,,ENST00000532131,;MAP7D1,upstream_gene_variant,,ENST00000487114,;MAP7D1,downstream_gene_variant,,ENST00000527764,;MAP7D1,downstream_gene_variant,,ENST00000462118,;	T	ENSG00000116871	ENST00000373151	Transcript	missense_variant	1421	1205	402	P/L	cCg/cTg	rs780310575,COSM4007452	.	.	1	MAP7D1	HGNC	25514	protein_coding	YES	CCDS30673.1	ENSP00000362244	MA7D1_HUMAN	E9PLH3_HUMAN,D3DPS3_HUMAN,C9JIR3_HUMAN	UPI00005C3036	.	.	benign(0.001)	7/17	.	hmmpanther:PTHR15073:SF2,hmmpanther:PTHR15073	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTCCGGTGC	byFrequency	5	ESCA
MACF1	0	.	GRCh37	1	39789902	39789902	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4289A>G	p.Lys1430Arg	p.K1430R	ENST00000545844	34/94	40	26	13	41	41	0	MACF1,missense_variant,p.Lys564Arg,ENST00000372925,;MACF1,missense_variant,p.Lys1430Arg,ENST00000361689,;MACF1,missense_variant,p.Lys1425Arg,ENST00000564288,;MACF1,missense_variant,p.Lys1579Arg,ENST00000530262,;MACF1,missense_variant,p.Lys1430Arg,ENST00000539005,;MACF1,missense_variant,p.Lys1430Arg,ENST00000372915,;MACF1,missense_variant,p.Lys1430Arg,ENST00000317713,;MACF1,missense_variant,p.Lys1462Arg,ENST00000567887,;MACF1,missense_variant,p.Lys1430Arg,ENST00000545844,;MACF1,downstream_gene_variant,,ENST00000524432,;MACF1,non_coding_transcript_exon_variant,,ENST00000476350,;MACF1,upstream_gene_variant,,ENST00000528611,;MACF1,3_prime_UTR_variant,,ENST00000496804,;	G	ENSG00000127603	ENST00000545844	Transcript	missense_variant	4397	4289	1430	K/R	aAg/aGg	.	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	benign(0.171)	34/94	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF46966,SMART_domains:SM00150,hmmpanther:PTHR11915:SF37,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGAAGGTTA	.	5	ESCA
MACF1	0	.	GRCh37	1	39951776	39951776	+	3'UTR	SNP	G	G	A	rs778915106	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*310G>A	.	.	ENST00000545844	94/94	41	35	6	33	33	0	MACF1,3_prime_UTR_variant,,ENST00000372925,;MACF1,3_prime_UTR_variant,,ENST00000446276,;MACF1,3_prime_UTR_variant,,ENST00000361689,;MACF1,3_prime_UTR_variant,,ENST00000289893,;MACF1,3_prime_UTR_variant,,ENST00000564288,;MACF1,3_prime_UTR_variant,,ENST00000539005,;MACF1,3_prime_UTR_variant,,ENST00000372915,;MACF1,3_prime_UTR_variant,,ENST00000317713,;MACF1,3_prime_UTR_variant,,ENST00000567887,;MACF1,3_prime_UTR_variant,,ENST00000545844,;MACF1,3_prime_UTR_variant,,ENST00000360115,;MACF1,3_prime_UTR_variant,,ENST00000442046,;MACF1,non_coding_transcript_exon_variant,,ENST00000496360,;MACF1,non_coding_transcript_exon_variant,,ENST00000497807,;	A	ENSG00000127603	ENST00000545844	Transcript	3_prime_UTR_variant	16711	.	.	.	.	rs778915106	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	.	94/94	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCGCGGTG	.	5	ESCA
KCNQ4	0	.	GRCh37	1	41282938	41282938	+	Frame_Shift_Del	DEL	T	T	-	rs189892658	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320delT	p.Leu107CysfsTer32	p.L107Cfs*32	ENST00000347132	2/14	164	97	67	70	70	0	KCNQ4,frameshift_variant,p.Leu107CysfsTer32,ENST00000509682,;KCNQ4,frameshift_variant,p.Leu3CysfsTer32,ENST00000443478,;KCNQ4,frameshift_variant,p.Leu107CysfsTer32,ENST00000347132,;KCNQ4,upstream_gene_variant,,ENST00000506017,;	-	ENSG00000117013	ENST00000347132	Transcript	frameshift_variant	398	316	106	F/X	Ttt/tt	rs189892658	.	.	1	KCNQ4	HGNC	6298	protein_coding	YES	CCDS456.1	ENSP00000262916	KCNQ4_HUMAN	.	UPI000013D35B	.	.	.	2/14	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF4,Gene3D:1.10.287.70,Superfamily_domains:SSF81324	G:0.0004	G:0	G:0	.	G:0.002	G:0	G:0	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCAGATTTTTG	byFrequency|byCluster|by1000G	3	ESCA
PTPRF	0	.	GRCh37	1	44054632	44054632	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.910C>T	p.%3D	p.L304L	ENST00000359947	8/34	88	66	22	36	36	0	PTPRF,synonymous_variant,p.%3D,ENST00000438120,;PTPRF,synonymous_variant,p.%3D,ENST00000359947,;PTPRF,synonymous_variant,p.%3D,ENST00000372413,;PTPRF,synonymous_variant,p.%3D,ENST00000372414,;PTPRF,upstream_gene_variant,,ENST00000412568,;PTPRF,upstream_gene_variant,,ENST00000414879,;PTPRF,upstream_gene_variant,,ENST00000429895,;PTPRF,upstream_gene_variant,,ENST00000422171,;PTPRF,non_coding_transcript_exon_variant,,ENST00000467464,;	T	ENSG00000142949	ENST00000359947	Transcript	synonymous_variant	1250	910	304	L	Ctg/Ttg	.	.	.	1	PTPRF	HGNC	9670	protein_coding	YES	CCDS489.2	ENSP00000353030	PTPRF_HUMAN	G1UI20_HUMAN	UPI0000470154	.	.	.	8/34	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF07679,hmmpanther:PTHR19134:SF203,hmmpanther:PTHR19134,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCGCTGGGC	.	5	ESCA
IPO13	0	.	GRCh37	1	44432189	44432189	+	Intron	DEL	G	G	-	rs768909814	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2398-52delG	.	.	ENST00000372343	.	54	40	14	21	21	0	IPO13,5_prime_UTR_variant,,ENST00000372339,;IPO13,intron_variant,,ENST00000372343,;DPH2,upstream_gene_variant,,ENST00000396758,;DPH2,upstream_gene_variant,,ENST00000459879,;DPH2,upstream_gene_variant,,ENST00000255108,;DPH2,upstream_gene_variant,,ENST00000412950,;IPO13,upstream_gene_variant,,ENST00000486876,;DPH2,upstream_gene_variant,,ENST00000471934,;DPH2,upstream_gene_variant,,ENST00000477294,;DPH2,upstream_gene_variant,,ENST00000529729,;DPH2,upstream_gene_variant,,ENST00000534655,;DPH2,upstream_gene_variant,,ENST00000532140,;DPH2,upstream_gene_variant,,ENST00000490861,;DPH2,upstream_gene_variant,,ENST00000534786,;DPH2,upstream_gene_variant,,ENST00000527319,;DPH2,upstream_gene_variant,,ENST00000524776,;DPH2,upstream_gene_variant,,ENST00000492306,;DPH2,upstream_gene_variant,,ENST00000476260,;DPH2,upstream_gene_variant,,ENST00000530988,;DPH2,upstream_gene_variant,,ENST00000527567,;DPH2,upstream_gene_variant,,ENST00000495421,;	-	ENSG00000117408	ENST00000372343	Transcript	intron_variant	.	.	.	.	.	rs768909814	.	.	1	IPO13	HGNC	16853	protein_coding	YES	CCDS503.1	ENSP00000361418	IPO13_HUMAN	.	UPI0000073F11	.	.	.	.	15/19	.	.	.	.	.	.	.	.	-:0.0012	-:0.0004	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGAGTGGGGGG	.	3	ESCA
TMEM53	0	.	GRCh37	1	45120337	45120337	+	Missense_Mutation	SNP	C	C	T	rs150431791	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.728G>A	p.Arg243His	p.R243H	ENST00000372237	3/3	37	27	10	39	39	0	TMEM53,missense_variant,p.Arg213His,ENST00000372235,;TMEM53,missense_variant,p.Arg243His,ENST00000372237,;TMEM53,intron_variant,,ENST00000372244,;TMEM53,intron_variant,,ENST00000372242,;TMEM53,intron_variant,,ENST00000372243,;RNF220,downstream_gene_variant,,ENST00000440132,;RNF220,downstream_gene_variant,,ENST00000361799,;RNF220,downstream_gene_variant,,ENST00000335497,;RNF220,downstream_gene_variant,,ENST00000443020,;RNF220,downstream_gene_variant,,ENST00000355387,;RNF220,downstream_gene_variant,,ENST00000372247,;TMEM53,downstream_gene_variant,,ENST00000420706,;TMEM53,non_coding_transcript_exon_variant,,ENST00000468117,;TMEM53,non_coding_transcript_exon_variant,,ENST00000476724,;TMEM53,intron_variant,,ENST00000495630,;RNF220,downstream_gene_variant,,ENST00000474394,;RNF220,downstream_gene_variant,,ENST00000474956,;RNF220,downstream_gene_variant,,ENST00000484745,;RNF220,downstream_gene_variant,,ENST00000480686,;RNF220,downstream_gene_variant,,ENST00000475378,;RNF220,downstream_gene_variant,,ENST00000474064,;	T	ENSG00000126106	ENST00000372237	Transcript	missense_variant	892	728	243	R/H	cGt/cAt	rs150431791	.	.	-1	TMEM53	HGNC	26186	protein_coding	YES	CCDS511.1	ENSP00000361311	TMM53_HUMAN	B4DI10_HUMAN	UPI000013E157	.	tolerated(0.1)	benign(0.022)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12265:SF0,hmmpanther:PTHR12265,Gene3D:3.40.50.1820,Pfam_domain:PF05705,Superfamily_domains:SSF53474	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAACGCGCC	byCluster|by1000G	5	ESCA
MAST2	0	.	GRCh37	1	46499903	46499903	+	Missense_Mutation	SNP	A	A	G	rs748102570	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3833A>G	p.Gln1278Arg	p.Q1278R	ENST00000361297	28/29	18	14	4	23	23	0	MAST2,missense_variant,p.Gln1278Arg,ENST00000361297,;MAST2,missense_variant,p.Gln1185Arg,ENST00000372009,;MAST2,downstream_gene_variant,,ENST00000372008,;MAST2,non_coding_transcript_exon_variant,,ENST00000492813,;MAST2,downstream_gene_variant,,ENST00000477968,;	G	ENSG00000086015	ENST00000361297	Transcript	missense_variant	4116	3833	1278	Q/R	cAa/cGa	rs748102570	.	.	1	MAST2	HGNC	19035	protein_coding	YES	CCDS41326.1	ENSP00000354671	MAST2_HUMAN	Q9NT11_HUMAN	UPI0000458AEB	.	tolerated_low_confidence(0.41)	benign(0.14)	28/29	.	hmmpanther:PTHR24356:SF136,hmmpanther:PTHR24356	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CACTCAAGGCT	.	3	ESCA
MAST2	0	.	GRCh37	1	46501229	46501229	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4888C>A	p.Leu1630Ile	p.L1630I	ENST00000361297	29/29	28	23	5	20	20	0	MAST2,missense_variant,p.Leu1630Ile,ENST00000361297,;MAST2,missense_variant,p.Leu1440Ile,ENST00000372009,;PIK3R3,downstream_gene_variant,,ENST00000372006,;PIK3R3,downstream_gene_variant,,ENST00000420542,;PIK3R3,downstream_gene_variant,,ENST00000262741,;PIK3R3,downstream_gene_variant,,ENST00000340332,;MAST2,downstream_gene_variant,,ENST00000372008,;PIK3R3,downstream_gene_variant,,ENST00000354242,;MAST2,downstream_gene_variant,,ENST00000492813,;	A	ENSG00000086015	ENST00000361297	Transcript	missense_variant	5171	4888	1630	L/I	Ctt/Att	.	.	.	1	MAST2	HGNC	19035	protein_coding	YES	CCDS41326.1	ENSP00000354671	MAST2_HUMAN	Q9NT11_HUMAN	UPI0000458AEB	.	deleterious_low_confidence(0)	probably_damaging(0.992)	29/29	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCACTTTCT	.	5	ESCA
POMGNT1	0	.	GRCh37	1	46659217	46659217	+	Intron	DEL	C	C	-	rs777318600	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1026+19delG	.	.	ENST00000371992	.	29	22	7	14	14	0	POMGNT1,3_prime_UTR_variant,,ENST00000396420,;POMGNT1,intron_variant,,ENST00000371992,;POMGNT1,intron_variant,,ENST00000535522,;POMGNT1,intron_variant,,ENST00000371986,;POMGNT1,intron_variant,,ENST00000371984,;POMGNT1,non_coding_transcript_exon_variant,,ENST00000485714,;POMGNT1,non_coding_transcript_exon_variant,,ENST00000477114,;POMGNT1,upstream_gene_variant,,ENST00000475642,;POMGNT1,downstream_gene_variant,,ENST00000489985,;POMGNT1,downstream_gene_variant,,ENST00000497439,;POMGNT1,upstream_gene_variant,,ENST00000463030,;POMGNT1,upstream_gene_variant,,ENST00000480972,;	-	ENSG00000085998	ENST00000371992	Transcript	intron_variant	.	.	.	.	.	rs777318600	.	.	-1	POMGNT1	HGNC	19139	protein_coding	YES	CCDS57995.1	ENSP00000361060	.	Q5VST3_HUMAN	UPI0000458AF4	.	.	.	.	11/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGGCACCCCCC	.	2	ESCA
ATPAF1	0	.	GRCh37	1	47100598	47100598	+	3'UTR	DEL	A	A	-	rs546203289	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*850delT	.	.	ENST00000576409	9/9	32	12	20	26	26	0	ATPAF1,3_prime_UTR_variant,,ENST00000371937,;ATPAF1,3_prime_UTR_variant,,ENST00000574428,;ATPAF1,3_prime_UTR_variant,,ENST00000576409,;ATPAF1,intron_variant,,ENST00000492233,;ATPAF1,downstream_gene_variant,,ENST00000534216,;ATPAF1,downstream_gene_variant,,ENST00000542495,;ATPAF1,downstream_gene_variant,,ENST00000532925,;ATPAF1,downstream_gene_variant,,ENST00000329231,;ATPAF1,downstream_gene_variant,,ENST00000526821,;ATPAF1,downstream_gene_variant,,ENST00000529214,;	-	ENSG00000123472	ENST00000576409	Transcript	3_prime_UTR_variant	1969	.	.	.	.	rs546203289	.	.	-1	ATPAF1	HGNC	18803	protein_coding	YES	CCDS541.2	ENSP00000460964	.	I3L448_HUMAN	UPI000222BB4E	.	.	.	9/9	.	.	-:0.0010	-:0.0015	-:0	.	-:0.001	-:0	-:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGACTTAAAAAA	byFrequency|by1000G	2	ESCA
EFCAB14	0	.	GRCh37	1	47142712	47142712	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1421delA	.	.	ENST00000371933	11/11	67	43	24	51	51	0	EFCAB14,3_prime_UTR_variant,,ENST00000371933,;EFCAB14,intron_variant,,ENST00000544071,;TEX38,downstream_gene_variant,,ENST00000564373,;TEX38,downstream_gene_variant,,ENST00000415500,;TEX38,downstream_gene_variant,,ENST00000564071,;TEX38,downstream_gene_variant,,ENST00000569393,;TEX38,downstream_gene_variant,,ENST00000334122,;EFCAB14-AS1,intron_variant,,ENST00000442839,;EFCAB14-AS1,intron_variant,,ENST00000418985,;EFCAB14,downstream_gene_variant,,ENST00000479745,;ATPAF1,upstream_gene_variant,,ENST00000525633,;EFCAB14,downstream_gene_variant,,ENST00000487741,;EFCAB14,downstream_gene_variant,,ENST00000481623,;	-	ENSG00000159658	ENST00000371933	Transcript	3_prime_UTR_variant	3886	.	.	.	.	.	.	.	-1	EFCAB14	HGNC	29051	protein_coding	YES	CCDS30706.1	ENSP00000361001	EFC14_HUMAN	.	UPI000003B443	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTGTAGTTTTTT	.	2	ESCA
CYP4Z1	0	.	GRCh37	1	47550552	47550552	+	Missense_Mutation	SNP	G	G	A	rs778352142	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.674G>A	p.Arg225His	p.R225H	ENST00000334194	6/12	25	16	9	21	21	0	CYP4Z1,missense_variant,p.Arg225His,ENST00000334194,;	A	ENSG00000186160	ENST00000334194	Transcript	missense_variant	677	674	225	R/H	cGc/cAc	rs778352142	.	.	1	CYP4Z1	HGNC	20583	protein_coding	YES	CCDS545.1	ENSP00000334246	CP4Z1_HUMAN	.	UPI00000477F8	.	deleterious(0.02)	probably_damaging(0.954)	6/12	.	Superfamily_domains:SSF48264,Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24290,hmmpanther:PTHR24290:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CCAGCGCATGA	byFrequency	2	ESCA
FAF1	0	.	GRCh37	1	51210386	51210386	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429delA	p.Gly144AlafsTer13	p.G144Afs*13	ENST00000396153	5/19	74	49	25	51	51	0	FAF1,frameshift_variant,p.Gly144AlafsTer13,ENST00000371778,;FAF1,frameshift_variant,p.Gly144AlafsTer13,ENST00000396153,;FAF1,non_coding_transcript_exon_variant,,ENST00000487898,;	-	ENSG00000185104	ENST00000396153	Transcript	frameshift_variant	881	429	143	K/X	aaA/aa	.	.	.	-1	FAF1	HGNC	3578	protein_coding	YES	CCDS554.1	ENSP00000379457	FAF1_HUMAN	.	UPI0000032C67	.	.	.	5/19	.	hmmpanther:PTHR23322,hmmpanther:PTHR23322:SF1,Gene3D:3.10.20.90,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAGCCTTTTAA	.	3	ESCA
USP24	0	.	GRCh37	1	55591178	55591178	+	Missense_Mutation	SNP	C	C	T	rs761278282	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3775G>A	p.Asp1259Asn	p.D1259N	ENST00000294383	34/68	50	26	23	47	47	0	USP24,missense_variant,p.Asp1099Asn,ENST00000407756,;USP24,missense_variant,p.Asp1259Asn,ENST00000294383,;	T	ENSG00000162402	ENST00000294383	Transcript	missense_variant	3775	3775	1259	D/N	Gac/Aac	rs761278282,COSM1503084,COSM1503083	.	.	-1	USP24	HGNC	12623	protein_coding	YES	CCDS44154.2	ENSP00000294383	UBP24_HUMAN	.	UPI000059CFDE	.	tolerated(0.13)	benign(0.051)	34/68	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF349	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGTCTTCAT	.	5	ESCA
KCNAB2	0	.	GRCh37	1	6158455	6158455	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1159-90G>A	.	.	ENST00000378083	.	17	11	6	22	22	0	KCNAB2,3_prime_UTR_variant,,ENST00000602612,;KCNAB2,intron_variant,,ENST00000378083,;KCNAB2,intron_variant,,ENST00000164247,;KCNAB2,intron_variant,,ENST00000378097,;KCNAB2,intron_variant,,ENST00000378087,;KCNAB2,intron_variant,,ENST00000341524,;KCNAB2,intron_variant,,ENST00000352527,;KCNAB2,intron_variant,,ENST00000458166,;KCNAB2,intron_variant,,ENST00000378092,;KCNAB2,intron_variant,,ENST00000378111,;KCNAB2,downstream_gene_variant,,ENST00000389632,;CHD5,downstream_gene_variant,,ENST00000262450,;CHD5,downstream_gene_variant,,ENST00000378021,;KCNAB2,downstream_gene_variant,,ENST00000428161,;KCNAB2,intron_variant,,ENST00000481789,;	A	ENSG00000069424	ENST00000378083	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KCNAB2	HGNC	6229	protein_coding	YES	CCDS55570.1	ENSP00000367323	KCAB2_HUMAN	.	UPI000035E741	.	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCCGACCAT	.	5	ESCA
RPL22	0	.	GRCh37	1	6257785	6257785	+	Frame_Shift_Del	DEL	T	T	-	rs759765382	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44delA	p.Lys15ArgfsTer5	p.K15Rfs*5	ENST00000234875	2/4	22	11	10	23	23	0	RPL22,frameshift_variant,p.Lys15ArgfsTer5,ENST00000234875,;RPL22,5_prime_UTR_variant,,ENST00000465387,;RPL22,5_prime_UTR_variant,,ENST00000497965,;RPL22,5_prime_UTR_variant,,ENST00000462296,;RPL22,5_prime_UTR_variant,,ENST00000471204,;RPL22,5_prime_UTR_variant,,ENST00000484532,;RPL22,5_prime_UTR_variant,,ENST00000465335,;RPL22,non_coding_transcript_exon_variant,,ENST00000480661,;	-	ENSG00000116251	ENST00000234875	Transcript	frameshift_variant	83	44	15	K/X	aAg/ag	rs759765382,COSM179404	.	.	-1	RPL22	HGNC	10315	protein_coding	YES	CCDS58.1	ENSP00000346088	RL22_HUMAN	Q8WYP0_HUMAN,K7ERI7_HUMAN,K7EP65_HUMAN,K7EMH1_HUMAN,K7ELC4_HUMAN,K7EJT5_HUMAN	UPI000015A487	.	.	.	2/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10064:SF2,hmmpanther:PTHR10064,Pfam_domain:PF01776	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.K15fs*5|c.44delA|6	INDELOCATOR|VARSCANI	TGCTTCTTTTTT	.	2	ESCA
GPR153	0	.	GRCh37	1	6311533	6311533	+	Missense_Mutation	SNP	C	C	T	rs777963528	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844G>A	p.Val282Met	p.V282M	ENST00000377893	4/6	29	16	12	15	15	0	GPR153,missense_variant,p.Val282Met,ENST00000377893,;	T	ENSG00000158292	ENST00000377893	Transcript	missense_variant	1104	844	282	V/M	Gtg/Atg	rs777963528,COSM220661	.	.	-1	GPR153	HGNC	23618	protein_coding	YES	CCDS64.1	ENSP00000367125	GP153_HUMAN	.	UPI000040E9D7	.	deleterious(0.02)	probably_damaging(1)	4/6	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR16518,hmmpanther:PTHR16518:SF5,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01991	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCACGCAGA	.	5	ESCA
JAK1	0	.	GRCh37	1	65306997	65306997	+	Frame_Shift_Del	DEL	T	T	-	rs202179869	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2580delA	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	19/25	50	37	13	41	41	0	JAK1,frameshift_variant,p.Lys860AsnfsTer16,ENST00000342505,;JAK1,upstream_gene_variant,,ENST00000481702,;JAK1,downstream_gene_variant,,ENST00000471473,;JAK1,downstream_gene_variant,,ENST00000465376,;	-	ENSG00000162434	ENST00000342505	Transcript	frameshift_variant	2829	2580	860	K/X	aaA/aa	rs202179869,COSM1343905	.	.	-1	JAK1	HGNC	6190	protein_coding	YES	CCDS41346.1	ENSP00000343204	JAK1_HUMAN	.	UPI0000054C7D	.	.	.	19/25	.	hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF67,PIRSF_domain:PIRSF000636	G:0.0002	G:0	G:0.0014	.	G:0	G:0	G:0	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGCTGGTTTTTT	byCluster|by1000G	2	ESCA
LEPR	0	.	GRCh37	1	66098886	66098886	+	Intron	SNP	G	G	A	rs756643733	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2674-2988G>A	.	.	ENST00000349533	.	28	21	6	42	42	0	LEPR,3_prime_UTR_variant,,ENST00000371060,;LEPR,intron_variant,,ENST00000349533,;LEPR,intron_variant,,ENST00000406510,;LEPR,downstream_gene_variant,,ENST00000371059,;	A	ENSG00000116678	ENST00000349533	Transcript	intron_variant	.	.	.	.	.	rs756643733	.	.	1	LEPR	HGNC	6554	protein_coding	YES	CCDS631.1	ENSP00000330393	LEPR_HUMAN	L0I9J6_HUMAN,A2RRQ4_HUMAN	UPI000014C37B	.	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAATGTGCCA	.	5	ESCA
THAP3	0	.	GRCh37	1	6694120	6694120	+	3'Flank	SNP	G	G	A	rs762900711	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000054650	.	28	24	4	25	25	0	THAP3,missense_variant,p.Arg167His,ENST00000377627,;DNAJC11,downstream_gene_variant,,ENST00000377573,;THAP3,downstream_gene_variant,,ENST00000307896,;THAP3,downstream_gene_variant,,ENST00000054650,;DNAJC11,downstream_gene_variant,,ENST00000294401,;DNAJC11,downstream_gene_variant,,ENST00000349363,;THAP3,downstream_gene_variant,,ENST00000472925,;DNAJC11,downstream_gene_variant,,ENST00000377577,;DNAJC11,downstream_gene_variant,,ENST00000542246,;DNAJC11,downstream_gene_variant,,ENST00000451196,;DNAJC11,downstream_gene_variant,,ENST00000472414,;THAP3,downstream_gene_variant,,ENST00000484669,;DNAJC11,downstream_gene_variant,,ENST00000465508,;THAP3,downstream_gene_variant,,ENST00000480647,;THAP3,downstream_gene_variant,,ENST00000487819,;	A	ENSG00000041988	ENST00000054650	Transcript	downstream_gene_variant	.	.	.	.	.	rs762900711	.	495	1	THAP3	HGNC	20855	protein_coding	YES	CCDS55572.1	ENSP00000054650	THAP3_HUMAN	.	UPI000006CFCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCACGTGAAG	byFrequency	2	ESCA
FPGT-TNNI3K	0	.	GRCh37	1	74930383	74930383	+	Intron	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2463+1149A>G	.	.	ENST00000557284	.	126	64	62	102	102	0	FPGT-TNNI3K,missense_variant,p.Asn830Ser,ENST00000370899,;TNNI3K,intron_variant,,ENST00000370891,;FPGT-TNNI3K,intron_variant,,ENST00000557284,;TNNI3K,intron_variant,,ENST00000326637,;RP4-650F12.2,upstream_gene_variant,,ENST00000442876,;RP4-650F12.2,upstream_gene_variant,,ENST00000411417,;TNNI3K,downstream_gene_variant,,ENST00000370889,;	G	ENSG00000259030	ENST00000557284	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	FPGT-TNNI3K	HGNC	42952	protein_coding	YES	CCDS44161.2	ENSP00000450895	.	A6NHC7_HUMAN	UPI0001EECC26	.	.	.	.	23/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAAATGAAG	.	5	ESCA
PER3	0	.	GRCh37	1	7846785	7846785	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279C>T	p.%3D	p.N93N	ENST00000361923	3/21	58	45	13	47	47	0	PER3,synonymous_variant,p.%3D,ENST00000377541,;PER3,synonymous_variant,p.%3D,ENST00000377532,;PER3,synonymous_variant,p.%3D,ENST00000361923,;PER3,non_coding_transcript_exon_variant,,ENST00000473653,;PER3,upstream_gene_variant,,ENST00000602883,;	T	ENSG00000049246	ENST00000361923	Transcript	synonymous_variant	454	279	93	N	aaC/aaT	.	.	.	1	PER3	HGNC	8847	protein_coding	YES	CCDS89.1	ENSP00000355031	PER3_HUMAN	Q8TAR6_HUMAN,B4DR65_HUMAN,A2I2N5_HUMAN	UPI0000167B1D	.	.	.	3/21	.	hmmpanther:PTHR11269,hmmpanther:PTHR11269:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAACAGTGA	.	5	ESCA
IFI44	0	.	GRCh37	1	79129487	79129487	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1332delA	p.Lys444AsnfsTer17	p.K444Nfs*17	ENST00000370747	9/9	75	57	18	42	42	0	IFI44,frameshift_variant,p.Lys444AsnfsTer17,ENST00000370747,;IFI44,frameshift_variant,p.Lys76AsnfsTer17,ENST00000446486,;IFI44,downstream_gene_variant,,ENST00000438486,;IFI44,downstream_gene_variant,,ENST00000545124,;IFI44,non_coding_transcript_exon_variant,,ENST00000472152,;IFI44,non_coding_transcript_exon_variant,,ENST00000495254,;IFI44,non_coding_transcript_exon_variant,,ENST00000485662,;IFI44,non_coding_transcript_exon_variant,,ENST00000476911,;IFI44,downstream_gene_variant,,ENST00000470323,;RP4-641G12.3,upstream_gene_variant,,ENST00000427236,;	-	ENSG00000137965	ENST00000370747	Transcript	frameshift_variant	1411	1326	442	G/X	ggA/gg	.	.	.	1	IFI44	HGNC	16938	protein_coding	YES	CCDS688.1	ENSP00000359783	IFI44_HUMAN	C9JUM8_HUMAN	UPI000013D0E5	.	.	.	9/9	.	hmmpanther:PTHR14241:SF3,hmmpanther:PTHR14241	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAAGGAAAAAA	.	3	ESCA
SPATA1	0	.	GRCh37	1	84991635	84991635	+	RNA	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.688T>C	.	.	ENST00000263717	6/15	59	48	11	35	35	0	SPATA1,non_coding_transcript_exon_variant,,ENST00000473108,;SPATA1,non_coding_transcript_exon_variant,,ENST00000370638,;SPATA1,non_coding_transcript_exon_variant,,ENST00000431031,;SPATA1,non_coding_transcript_exon_variant,,ENST00000485121,;SPATA1,non_coding_transcript_exon_variant,,ENST00000490879,;SPATA1,non_coding_transcript_exon_variant,,ENST00000554297,;SPATA1,non_coding_transcript_exon_variant,,ENST00000263717,;	C	ENSG00000122432	ENST00000263717	Transcript	non_coding_transcript_exon_variant	688	.	.	.	.	.	.	.	1	SPATA1	HGNC	14682	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	6/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTAATGAGGC	.	4	ESCA
SSX2IP	0	.	GRCh37	1	85112953	85112953	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*163A>G	.	.	ENST00000342203	14/14	50	42	7	55	55	0	SSX2IP,3_prime_UTR_variant,,ENST00000342203,;SSX2IP,3_prime_UTR_variant,,ENST00000437941,;SSX2IP,downstream_gene_variant,,ENST00000370612,;SSX2IP,downstream_gene_variant,,ENST00000603677,;SSX2IP,downstream_gene_variant,,ENST00000605755,;SSX2IP,downstream_gene_variant,,ENST00000481102,;SSX2IP,downstream_gene_variant,,ENST00000476905,;SSX2IP,downstream_gene_variant,,ENST00000490476,;	C	ENSG00000117155	ENST00000342203	Transcript	3_prime_UTR_variant	2272	.	.	.	.	.	.	.	-1	SSX2IP	HGNC	16509	protein_coding	YES	CCDS699.1	ENSP00000340279	ADIP_HUMAN	C9JIX7_HUMAN	UPI00000728CA	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAATAGATT	.	5	ESCA
NOC2L	0	.	GRCh37	1	889215	889215	+	Missense_Mutation	SNP	C	C	T	rs772311539	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835G>A	p.Val279Met	p.V279M	ENST00000327044	8/19	27	18	9	23	23	0	NOC2L,missense_variant,p.Val279Met,ENST00000327044,;NOC2L,downstream_gene_variant,,ENST00000487214,;NOC2L,non_coding_transcript_exon_variant,,ENST00000477976,;NOC2L,downstream_gene_variant,,ENST00000469563,;	T	ENSG00000188976	ENST00000327044	Transcript	missense_variant	885	835	279	V/M	Gtg/Atg	rs772311539	.	.	-1	NOC2L	HGNC	24517	protein_coding	YES	CCDS3.1	ENSP00000317992	NOC2L_HUMAN	.	UPI000041820C	.	tolerated(0.23)	benign(0.223)	8/19	.	hmmpanther:PTHR12687:SF4,hmmpanther:PTHR12687,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCACGCTGA	byFrequency	5	ESCA
ENO1	0	.	GRCh37	1	8928104	8928104	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.253A>G	p.Thr85Ala	p.T85A	ENST00000234590	5/12	45	18	27	37	37	0	ENO1,missense_variant,p.Thr85Ala,ENST00000497492,;ENO1,missense_variant,p.Thr85Ala,ENST00000234590,;ENO1,non_coding_transcript_exon_variant,,ENST00000464920,;ENO1,downstream_gene_variant,,ENST00000486051,;ENO1,downstream_gene_variant,,ENST00000492343,;	C	ENSG00000074800	ENST00000234590	Transcript	missense_variant	373	253	85	T/A	Aca/Gca	.	.	.	-1	ENO1	HGNC	3350	protein_coding	YES	CCDS97.1	ENSP00000234590	ENOA_HUMAN	Q9BT62_HUMAN,Q96GV1_HUMAN,K7EM90_HUMAN,E2DRY6_HUMAN,A4UCS8_HUMAN	UPI000013C9AF	.	tolerated_low_confidence(0.12)	benign(0)	5/12	.	Coiled-coils_(Ncoils):Coil,HAMAP:MF_00318,hmmpanther:PTHR11902,TIGRFAM_domain:TIGR01060,Gene3D:3.30.390.10,Pfam_domain:PF03952,PIRSF_domain:PIRSF001400,Superfamily_domains:SSF54826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGTGACGT	.	5	ESCA
ZNF644	0	.	GRCh37	1	91381965	91381965	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*390T>A	.	.	ENST00000370440	6/6	31	18	13	28	28	0	ZNF644,3_prime_UTR_variant,,ENST00000347275,;ZNF644,3_prime_UTR_variant,,ENST00000370440,;ZNF644,3_prime_UTR_variant,,ENST00000337393,;ZNF644,3_prime_UTR_variant,,ENST00000361321,;ZNF644,non_coding_transcript_exon_variant,,ENST00000467231,;ZNF644,downstream_gene_variant,,ENST00000482709,;ZNF644,downstream_gene_variant,,ENST00000479798,;	T	ENSG00000122482	ENST00000370440	Transcript	3_prime_UTR_variant	4592	.	.	.	.	.	.	.	-1	ZNF644	HGNC	29222	protein_coding	YES	CCDS731.1	ENSP00000359469	ZN644_HUMAN	Q9NVH8_HUMAN,Q9H8J8_HUMAN,Q8NEI6_HUMAN	UPI000004A010	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAATATCTTA	.	5	ESCA
CCDC18	0	.	GRCh37	1	93682272	93682273	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1963dupA	p.Asn655LysfsTer13	p.N655Kfs*13	ENST00000370276	13/29	61	50	11	36	36	0	CCDC18,frameshift_variant,p.Asn321LysfsTer11,ENST00000455267,;CCDC18,frameshift_variant,p.Asn720LysfsTer13,ENST00000557479,;CCDC18,frameshift_variant,p.Asn602LysfsTer13,ENST00000401026,;CCDC18,frameshift_variant,p.Asn601LysfsTer13,ENST00000343253,;CCDC18,frameshift_variant,p.Asn401LysfsTer11,ENST00000338949,;CCDC18,frameshift_variant,p.Asn655LysfsTer13,ENST00000370276,;CCDC18,5_prime_UTR_variant,,ENST00000334652,;CCDC18,upstream_gene_variant,,ENST00000421014,;CCDC18,downstream_gene_variant,,ENST00000481180,;	A	ENSG00000122483	ENST00000370276	Transcript	frameshift_variant	1957-1958	1958-1959	653	A/AX	gca/gcAa	.	.	.	1	CCDC18	HGNC	30370	protein_coding	YES	.	ENSP00000359299	.	.	UPI0001F78148	.	.	.	13/29	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18875:SF4,hmmpanther:PTHR18875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCTGCAAAAA	.	3	ESCA
FNBP1L	0	.	GRCh37	1	94019461	94019461	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1488C>T	.	.	ENST00000271234	17/17	82	59	22	46	46	0	FNBP1L,3_prime_UTR_variant,,ENST00000370253,;FNBP1L,3_prime_UTR_variant,,ENST00000271234,;FNBP1L,3_prime_UTR_variant,,ENST00000260506,;FNBP1L,3_prime_UTR_variant,,ENST00000370256,;FNBP1L,downstream_gene_variant,,ENST00000604705,;FNBP1L,downstream_gene_variant,,ENST00000424449,;FNBP1L,downstream_gene_variant,,ENST00000603526,;	T	ENSG00000137942	ENST00000271234	Transcript	3_prime_UTR_variant	3457	.	.	.	.	.	.	.	1	FNBP1L	HGNC	20851	protein_coding	YES	CCDS53343.1	ENSP00000271234	.	J3QSS4_HUMAN,B4DSW1_HUMAN,B4DSI7_HUMAN,B4DKY5_HUMAN	UPI0001B25604	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AAGAACGTGAA	.	4	ESCA
ABCA4	0	.	GRCh37	1	94506867	94506867	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3420C>A	p.Cys1140Ter	p.C1140*	ENST00000370225	23/50	94	39	55	68	68	0	ABCA4,stop_gained,p.Cys1140Ter,ENST00000370225,;ABCA4,downstream_gene_variant,,ENST00000535735,;	T	ENSG00000198691	ENST00000370225	Transcript	stop_gained	3507	3420	1140	C/*	tgC/tgA	.	.	.	-1	ABCA4	HGNC	34	protein_coding	YES	CCDS747.1	ENSP00000359245	ABCA4_HUMAN	Q86V62_HUMAN,Q0QD48_HUMAN,F5H5R2_HUMAN	UPI000012511C	.	.	.	23/50	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF97,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR01257,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGAGCAGTA	.	5	ESCA
SLC25A33	0	.	GRCh37	1	9642760	9642760	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*209delT	.	.	ENST00000302692	7/7	20	11	9	19	19	0	SLC25A33,3_prime_UTR_variant,,ENST00000302692,;	-	ENSG00000171612	ENST00000302692	Transcript	3_prime_UTR_variant	1377	.	.	.	.	.	.	.	1	SLC25A33	HGNC	29681	protein_coding	YES	CCDS103.1	ENSP00000306328	S2533_HUMAN	.	UPI000004D33B	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TATAACTTTTTT	.	2	ESCA
CLSTN1	0	.	GRCh37	1	9795218	9795219	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1897dupG	p.Ala633GlyfsTer37	p.A633Gfs*37	ENST00000377298	14/19	42	36	6	33	33	0	CLSTN1,frameshift_variant,p.Ala434GlyfsTer37,ENST00000435891,;CLSTN1,frameshift_variant,p.Ala633GlyfsTer37,ENST00000377298,;CLSTN1,frameshift_variant,p.Ala614GlyfsTer37,ENST00000377288,;CLSTN1,frameshift_variant,p.Ala623GlyfsTer37,ENST00000361311,;CLSTN1,upstream_gene_variant,,ENST00000477264,;	C	ENSG00000171603	ENST00000377298	Transcript	frameshift_variant	2690-2691	1897-1898	633	A/GX	gcc/gGcc	.	.	.	-1	CLSTN1	HGNC	17447	protein_coding	YES	CCDS30580.1	ENSP00000366513	CSTN1_HUMAN	.	UPI0000127B95	.	.	.	14/19	.	hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGTGGCCTCG	.	3	ESCA
SDCBP2	0	.	GRCh37	20	1293248	1293248	+	Silent	SNP	G	G	A	rs151023134	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543C>T	p.%3D	p.V181V	ENST00000360779	6/9	127	58	68	43	43	0	SDCBP2,synonymous_variant,p.%3D,ENST00000381812,;SDCBP2,synonymous_variant,p.%3D,ENST00000381808,;SDCBP2,synonymous_variant,p.%3D,ENST00000339987,;SDCBP2,synonymous_variant,p.%3D,ENST00000360779,;SNPH,downstream_gene_variant,,ENST00000381873,;SNPH,downstream_gene_variant,,ENST00000381867,;SDCBP2,upstream_gene_variant,,ENST00000467129,;	A	ENSG00000125775	ENST00000360779	Transcript	synonymous_variant	717	543	181	V	gtC/gtT	rs151023134	.	.	-1	SDCBP2	HGNC	15756	protein_coding	YES	CCDS42848.1	ENSP00000354013	SDCB2_HUMAN	.	UPI0000135710	.	.	.	6/9	.	PROSITE_profiles:PS50106,hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF13,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V97M|c.289G>A|4,BUFFER|p.V182M|c.544G>A|3,BUFFER|p.V182M|c.544G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACGACAAT	.	5	ESCA
NAA20	0	.	GRCh37	20	20013995	20013995	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*164G>C	.	.	ENST00000334982	6/6	95	88	7	49	49	0	NAA20,3_prime_UTR_variant,,ENST00000310450,;NAA20,3_prime_UTR_variant,,ENST00000398602,;NAA20,3_prime_UTR_variant,,ENST00000334982,;CRNKL1,downstream_gene_variant,,ENST00000377327,;CRNKL1,downstream_gene_variant,,ENST00000377340,;CRNKL1,downstream_gene_variant,,ENST00000536226,;NAA20,non_coding_transcript_exon_variant,,ENST00000480550,;NAA20,non_coding_transcript_exon_variant,,ENST00000463154,;NAA20,non_coding_transcript_exon_variant,,ENST00000484480,;CRNKL1,downstream_gene_variant,,ENST00000521379,;CRNKL1,downstream_gene_variant,,ENST00000490910,;CRNKL1,downstream_gene_variant,,ENST00000496549,;CRNKL1,downstream_gene_variant,,ENST00000490258,;	C	ENSG00000173418	ENST00000334982	Transcript	3_prime_UTR_variant	982	.	.	.	.	.	.	.	1	NAA20	HGNC	15908	protein_coding	YES	CCDS13141.1	ENSP00000335636	NAA20_HUMAN	.	UPI0000029838	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCAGTTAGC	.	2	ESCA
CRNKL1	0	.	GRCh37	20	20024273	20024273	+	Missense_Mutation	SNP	G	G	T	rs778511962	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1318C>A	p.Leu440Met	p.L440M	ENST00000377340	8/15	76	60	15	36	35	1	CRNKL1,missense_variant,p.Leu440Met,ENST00000377340,;CRNKL1,missense_variant,p.Leu428Met,ENST00000377327,;CRNKL1,missense_variant,p.Leu279Met,ENST00000536226,;CRNKL1,3_prime_UTR_variant,,ENST00000496549,;CRNKL1,3_prime_UTR_variant,,ENST00000490910,;	T	ENSG00000101343	ENST00000377340	Transcript	missense_variant	1350	1318	440	L/M	Ctg/Atg	rs778511962	.	.	-1	CRNKL1	HGNC	15762	protein_coding	YES	CCDS33446.1	ENSP00000366557	CRNL1_HUMAN	.	UPI00004A39A7	.	deleterious(0.01)	probably_damaging(0.989)	8/15	.	Superfamily_domains:SSF48452,SMART_domains:SM00386,Gene3D:1.25.40.10,hmmpanther:PTHR11246,hmmpanther:PTHR11246:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTCCAGGGCAT	.	4	ESCA
INSM1	0	.	GRCh37	20	20351323	20351323	+	3'UTR	SNP	C	C	T	rs576055079	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*879C>T	.	.	ENST00000310227	1/1	94	63	30	39	39	0	INSM1,3_prime_UTR_variant,,ENST00000310227,;	T	ENSG00000173404	ENST00000310227	Transcript	3_prime_UTR_variant	2559	.	.	.	.	rs576055079	.	.	1	INSM1	HGNC	6090	protein_coding	YES	CCDS13143.1	ENSP00000312631	INSM1_HUMAN	.	UPI0000046C2F	.	.	.	1/1	.	.	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCACTGTGC	by1000G	5	ESCA
GZF1	0	.	GRCh37	20	23350283	23350283	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1690C>T	p.Arg564Cys	p.R564C	ENST00000338121	5/6	43	28	15	15	15	0	GZF1,missense_variant,p.Arg564Cys,ENST00000377051,;GZF1,missense_variant,p.Arg88Cys,ENST00000544236,;GZF1,missense_variant,p.Arg73Cys,ENST00000542987,;GZF1,missense_variant,p.Arg564Cys,ENST00000338121,;NAPB,downstream_gene_variant,,ENST00000377026,;NAPB,downstream_gene_variant,,ENST00000398425,;GZF1,intron_variant,,ENST00000477239,;GZF1,downstream_gene_variant,,ENST00000461789,;	T	ENSG00000125812	ENST00000338121	Transcript	missense_variant	1767	1690	564	R/C	Cgc/Tgc	.	.	.	1	GZF1	HGNC	15808	protein_coding	YES	CCDS13151.1	ENSP00000338290	GZF1_HUMAN	Q5JXG1_HUMAN,F5H2R0_HUMAN,B4DF58_HUMAN	UPI000013C35D	.	deleterious(0)	probably_damaging(0.982)	5/6	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24402:SF170,hmmpanther:PTHR24402,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGCGCCAC	.	5	ESCA
GZF1	0	.	GRCh37	20	23352852	23352852	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1780delA	.	.	ENST00000338121	6/6	52	43	9	18	18	0	GZF1,3_prime_UTR_variant,,ENST00000377051,;GZF1,3_prime_UTR_variant,,ENST00000338121,;GZF1,downstream_gene_variant,,ENST00000544236,;NAPB,downstream_gene_variant,,ENST00000377026,;GZF1,downstream_gene_variant,,ENST00000542987,;NAPB,downstream_gene_variant,,ENST00000398425,;NAPB,downstream_gene_variant,,ENST00000432543,;GZF1,downstream_gene_variant,,ENST00000477239,;GZF1,downstream_gene_variant,,ENST00000461789,;	-	ENSG00000125812	ENST00000338121	Transcript	3_prime_UTR_variant	3987	.	.	.	.	.	.	.	1	GZF1	HGNC	15808	protein_coding	YES	CCDS13151.1	ENSP00000338290	GZF1_HUMAN	Q5JXG1_HUMAN,F5H2R0_HUMAN,B4DF58_HUMAN	UPI000013C35D	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTCTACAAAAAA	.	2	ESCA
XKR7	0	.	GRCh37	20	30584487	30584487	+	Missense_Mutation	SNP	G	G	A	rs781133344	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967G>A	p.Val323Ile	p.V323I	ENST00000562532	3/3	72	28	43	41	41	0	XKR7,missense_variant,p.Val323Ile,ENST00000562532,;	A	ENSG00000260903	ENST00000562532	Transcript	missense_variant	1141	967	323	V/I	Gtc/Atc	rs781133344,COSM352956,COSM3963453	.	.	1	XKR7	HGNC	23062	protein_coding	YES	CCDS33459.1	ENSP00000477059	XKR7_HUMAN	.	UPI00004C7A9E	.	tolerated(0.32)	possibly_damaging(0.903)	3/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF9,Pfam_domain:PF09815	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGTCTAC	.	5	ESCA
PLAGL2	0	.	GRCh37	20	30776958	30776958	+	3'Flank	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000246229	.	23	15	8	9	9	0	PLAGL2,downstream_gene_variant,,ENST00000246229,;TSPY26P,non_coding_transcript_exon_variant,,ENST00000565928,;TSPY26P,downstream_gene_variant,,ENST00000476365,;TSPY26P,downstream_gene_variant,,ENST00000400643,;	G	ENSG00000126003	ENST00000246229	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3348	-1	PLAGL2	HGNC	9047	protein_coding	YES	CCDS13197.1	ENSP00000246229	PLAL2_HUMAN	.	UPI0000001C1D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCGTAGGAGG	.	3	ESCA
PLAGL2	0	.	GRCh37	20	30783233	30783233	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1022G>A	.	.	ENST00000246229	3/3	69	30	39	35	35	0	PLAGL2,3_prime_UTR_variant,,ENST00000246229,;TSPY26P,upstream_gene_variant,,ENST00000476365,;	T	ENSG00000126003	ENST00000246229	Transcript	3_prime_UTR_variant	2778	.	.	.	.	.	.	.	-1	PLAGL2	HGNC	9047	protein_coding	YES	CCDS13197.1	ENSP00000246229	PLAL2_HUMAN	.	UPI0000001C1D	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGACGGACG	.	5	ESCA
ASXL1	0	.	GRCh37	20	30954215	30954215	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86T>C	p.Met29Thr	p.M29T	ENST00000375687	2/13	112	62	50	55	55	0	ASXL1,missense_variant,p.Met18Thr,ENST00000497249,;ASXL1,missense_variant,p.Met29Thr,ENST00000375687,;ASXL1,missense_variant,p.Met25Thr,ENST00000306058,;ASXL1,missense_variant,p.Met29Thr,ENST00000542461,;ASXL1,missense_variant,p.Met25Thr,ENST00000375689,;ASXL1,non_coding_transcript_exon_variant,,ENST00000470145,;ASXL1,non_coding_transcript_exon_variant,,ENST00000555343,;	C	ENSG00000171456	ENST00000375687	Transcript	missense_variant	510	86	29	M/T	aTg/aCg	.	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	deleterious(0)	probably_damaging(0.972)	2/13	.	Pfam_domain:PF05066,hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAATGACAC	.	5	ESCA
ASXL1	0	.	GRCh37	20	31022442	31022442	+	Frame_Shift_Del	DEL	G	G	-	rs773395454,rs781077343	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1934delG	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	13/13	87	62	24	46	46	0	ASXL1,frameshift_variant,p.Gly645ValfsTer58,ENST00000375687,;ASXL1,frameshift_variant,p.Gly640ValfsTer58,ENST00000306058,;ASXL1,downstream_gene_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000470145,;ASXL1,downstream_gene_variant,,ENST00000555564,;	-	ENSG00000171456	ENST00000375687	Transcript	frameshift_variant	2351	1927	643	G/X	Ggg/gg	TMP_ESP_20_31022442_31022442,rs773395454,rs781077343,COSM1180918	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	.	.	13/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	.	.	.	0,0,0,1	.	.	.	.	.	HIGH	.	deletion	.	7	0,0,0,1	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.E635fs*15|c.1902_1924del23|7,BUFFER|p.E635fs*15|c.1899_1921del23|3,BUFFER|p.E635fs*15|c.1900_1922del23|41,BUFFER|p.G645fs*58|c.1927delG|3,BUFFER|p.G643fs*15|c.1927_1928insA|3,BUFFER|p.G645fs*58|c.1934_1934delG|5,BUFFER|p.G646fs*12|c.1934_1935insG|325	INDELOCATOR|VARSCANI	ATCGGAGGGGGG	.	2	ESCA
BPIFB1	0	.	GRCh37	20	31876669	31876669	+	Missense_Mutation	SNP	G	G	A	rs374640604	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.238G>A	p.Val80Ile	p.V80I	ENST00000253354	3/16	58	32	25	33	33	0	BPIFB1,missense_variant,p.Val80Ile,ENST00000423645,;BPIFB1,missense_variant,p.Val80Ile,ENST00000253354,;	A	ENSG00000125999	ENST00000253354	Transcript	missense_variant	399	238	80	V/I	Gtc/Atc	rs374640604,COSM724031	.	.	1	BPIFB1	HGNC	16108	protein_coding	YES	CCDS13218.1	ENSP00000253354	BPIB1_HUMAN	A2A2R0_HUMAN	UPI000006EEF9	.	tolerated(1)	benign(0.007)	3/16	.	hmmpanther:PTHR10504:SF21,hmmpanther:PTHR10504,Pfam_domain:PF01273,SMART_domains:SM00328,PIRSF_domain:PIRSF037186,Superfamily_domains:SSF55394	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCGTCCTG	byCluster|by1000G	5	ESCA
RALY	0	.	GRCh37	20	32660107	32660107	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227A>G	p.Asn76Ser	p.N76S	ENST00000246194	3/10	54	43	11	15	15	0	RALY,missense_variant,p.Asn76Ser,ENST00000375114,;RALY,missense_variant,p.Asn76Ser,ENST00000246194,;RALY,missense_variant,p.Asn76Ser,ENST00000448364,;RALY,missense_variant,p.Asn76Ser,ENST00000413297,;RALY,missense_variant,p.Asn76Ser,ENST00000442805,;RALY,intron_variant,,ENST00000333552,;RALY,intron_variant,,ENST00000493399,;RALY,upstream_gene_variant,,ENST00000489384,;RALY,upstream_gene_variant,,ENST00000488227,;RALY,upstream_gene_variant,,ENST00000481580,;	G	ENSG00000125970	ENST00000246194	Transcript	missense_variant	729	227	76	N/S	aAt/aGt	.	.	.	1	RALY	HGNC	15921	protein_coding	YES	CCDS13230.1	ENSP00000246194	RALY_HUMAN	Q5QPM2_HUMAN,Q5QPM1_HUMAN,Q53GL6_HUMAN,B4DSJ1_HUMAN	UPI00000467E6	.	deleterious(0.01)	probably_damaging(0.999)	3/10	.	PROSITE_profiles:PS50102,hmmpanther:PTHR13968:SF6,hmmpanther:PTHR13968,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,PIRSF_domain:PIRSF037992,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAATGGGC	.	5	ESCA
NCOA6	0	.	GRCh37	20	33346694	33346694	+	Frame_Shift_Del	DEL	G	G	-	rs769546399	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.557delC	p.Pro186ArgfsTer9	p.P186Rfs*9	ENST00000374796	7/16	41	31	10	18	18	0	NCOA6,frameshift_variant,p.Pro186ArgfsTer9,ENST00000374796,;NCOA6,frameshift_variant,p.Pro186ArgfsTer9,ENST00000359003,;	-	ENSG00000198646	ENST00000374796	Transcript	frameshift_variant	3128	557	186	P/X	cCg/cg	rs769546399	.	.	-1	NCOA6	HGNC	15936	protein_coding	YES	CCDS13241.1	ENSP00000363929	NCOA6_HUMAN	.	UPI000013C634	.	.	.	7/16	.	hmmpanther:PTHR15690:SF0,hmmpanther:PTHR15690,Pfam_domain:PF13820	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCACCCGGGGGT	byFrequency	2	ESCA
GGT7	0	.	GRCh37	20	33451230	33451230	+	Silent	SNP	C	C	T	rs781413741	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291G>A	p.%3D	p.A97A	ENST00000336431	2/15	71	31	39	28	28	0	GGT7,synonymous_variant,p.%3D,ENST00000427420,;GGT7,synonymous_variant,p.%3D,ENST00000336431,;	T	ENSG00000131067	ENST00000336431	Transcript	synonymous_variant	336	291	97	A	gcG/gcA	rs781413741	.	.	-1	GGT7	HGNC	4259	protein_coding	YES	CCDS13242.2	ENSP00000338964	GGT7_HUMAN	A4FU32_HUMAN,A0PJJ9_HUMAN	UPI000004C2AB	.	.	.	2/15	.	hmmpanther:PTHR11686:SF18,hmmpanther:PTHR11686	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGCCGCTGC	byFrequency	5	ESCA
GSS	0	.	GRCh37	20	33530434	33530435	+	Intron	INS	-	-	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.352-5dupC	.	.	ENST00000216951	.	63	56	7	21	21	0	GSS,splice_region_variant,,ENST00000216951,;GSS,5_prime_UTR_variant,,ENST00000541098,;GSS,intron_variant,,ENST00000451957,;	G	ENSG00000100983	ENST00000216951	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	GSS	HGNC	4624	protein_coding	YES	CCDS13245.1	ENSP00000216951	GSHB_HUMAN	B7Z514_HUMAN,B7Z1C5_HUMAN	UPI0000111B5F	.	.	.	.	4/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCTGTGGGGA	.	3	ESCA
MYH7B	0	.	GRCh37	20	33565839	33565839	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.157G>A	p.Ala53Thr	p.A53T	ENST00000262873	3/43	88	64	24	37	37	0	MYH7B,missense_variant,p.Ala53Thr,ENST00000262873,;MYH7B,upstream_gene_variant,,ENST00000481922,;MYH7B,non_coding_transcript_exon_variant,,ENST00000470929,;	A	ENSG00000078814	ENST00000262873	Transcript	missense_variant	249	157	53	A/T	Gcc/Acc	.	.	.	1	MYH7B	HGNC	15906	protein_coding	YES	CCDS42869.1	ENSP00000262873	MYH7B_HUMAN	.	UPI0000253BD4	.	.	possibly_damaging(0.776)	3/43	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF310	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTGCCCGC	.	5	ESCA
MYH7B	0	.	GRCh37	20	33577720	33577720	+	Missense_Mutation	SNP	G	G	A	rs571377722	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1891G>A	p.Val631Met	p.V631M	ENST00000262873	18/43	71	60	11	37	37	0	MYH7B,missense_variant,p.Val631Met,ENST00000262873,;MIR499A,upstream_gene_variant,,ENST00000384903,;	A	ENSG00000078814	ENST00000262873	Transcript	missense_variant	1983	1891	631	V/M	Gtg/Atg	rs571377722	.	.	1	MYH7B	HGNC	15906	protein_coding	YES	CCDS42869.1	ENSP00000262873	MYH7B_HUMAN	.	UPI0000253BD4	.	.	probably_damaging(0.959)	18/43	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF310,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGCGTGGTA	byFrequency|byCluster	4	ESCA
CNBD2	0	.	GRCh37	20	34568534	34568534	+	Missense_Mutation	SNP	C	C	T	rs146293825	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397C>T	p.Arg133Cys	p.R133C	ENST00000349339	4/12	44	23	20	19	19	0	CNBD2,missense_variant,p.Arg133Cys,ENST00000373973,;CNBD2,missense_variant,p.Arg133Cys,ENST00000538900,;CNBD2,missense_variant,p.Arg133Cys,ENST00000349339,;CNBD2,missense_variant,p.Arg133Cys,ENST00000463258,;	T	ENSG00000149646	ENST00000349339	Transcript	missense_variant	553	397	133	R/C	Cgc/Tgc	rs146293825	.	.	1	CNBD2	HGNC	16145	protein_coding	YES	CCDS13270.1	ENSP00000340954	CNBD2_HUMAN	.	UPI0000367038	.	deleterious(0.01)	possibly_damaging(0.659)	4/12	.	PROSITE_profiles:PS50042,hmmpanther:PTHR23011:SF1,hmmpanther:PTHR23011,Gene3D:2.60.120.10,SMART_domains:SM00100,Superfamily_domains:SSF51206	T:0.0008	T:0.003	T:0	.	T:0	T:0	T:0	T:0.0005	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATGCGCTTT	byFrequency|byCluster|by1000G	5	ESCA
TGIF2	0	.	GRCh37	20	35220206	35220206	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*372T>C	.	.	ENST00000373874	3/3	78	38	40	42	42	0	TGIF2,3_prime_UTR_variant,,ENST00000561398,;TGIF2,3_prime_UTR_variant,,ENST00000558465,;TGIF2,3_prime_UTR_variant,,ENST00000557885,;TGIF2,3_prime_UTR_variant,,ENST00000373872,;TGIF2,3_prime_UTR_variant,,ENST00000373874,;TGIF2-C20orf24,intron_variant,,ENST00000558530,;TGIF2,downstream_gene_variant,,ENST00000560025,;TGIF2,downstream_gene_variant,,ENST00000558028,;RP5-977B1.11,intron_variant,,ENST00000561134,;	C	ENSG00000118707	ENST00000373874	Transcript	3_prime_UTR_variant	1285	.	.	.	.	.	.	.	1	TGIF2	HGNC	15764	protein_coding	YES	CCDS13278.1	ENSP00000362981	TGIF2_HUMAN	H0YKN5_HUMAN	UPI0000136CC1	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCTGTGCT	.	5	ESCA
ATRN	0	.	GRCh37	20	3631609	3631609	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4120delT	.	.	ENST00000262919	29/29	79	51	28	22	22	0	ATRN,3_prime_UTR_variant,,ENST00000262919,;	-	ENSG00000088812	ENST00000262919	Transcript	3_prime_UTR_variant	8473	.	.	.	.	.	.	.	1	ATRN	HGNC	885	protein_coding	YES	CCDS13053.1	ENSP00000262919	ATRN_HUMAN	.	UPI000012661C	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTGGTATTTTTT	.	3	ESCA
MAVS	0	.	GRCh37	20	3845276	3845276	+	Silent	SNP	T	T	C	rs374618610	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.999T>C	p.%3D	p.P333P	ENST00000428216	6/7	64	43	21	28	28	0	MAVS,synonymous_variant,p.%3D,ENST00000416600,;MAVS,synonymous_variant,p.%3D,ENST00000428216,;MAVS,3_prime_UTR_variant,,ENST00000358134,;	C	ENSG00000088888	ENST00000428216	Transcript	synonymous_variant	1127	999	333	P	ccT/ccC	rs374618610	.	.	1	MAVS	HGNC	29233	protein_coding	YES	CCDS33437.1	ENSP00000401980	MAVS_HUMAN	M1P2Z0_HUMAN	UPI000015F983	.	.	.	6/7	.	hmmpanther:PTHR21446:SF3,hmmpanther:PTHR21446	.	.	.	.	.	.	.	C:0.0002	C:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCCTGGTGC	.	5	ESCA
PANK2	0	.	GRCh37	20	3888689	3888689	+	Missense_Mutation	SNP	C	C	T	rs747490823	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.745C>T	p.Arg249Trp	p.R249W	ENST00000316562	2/7	42	29	13	25	25	0	PANK2,missense_variant,p.Arg126Trp,ENST00000610179,;PANK2,missense_variant,p.Arg249Trp,ENST00000316562,;PANK2,5_prime_UTR_variant,,ENST00000497424,;PANK2,5_prime_UTR_variant,,ENST00000495692,;PANK2,non_coding_transcript_exon_variant,,ENST00000471830,;PANK2,upstream_gene_variant,,ENST00000464452,;PANK2,missense_variant,p.Arg126Trp,ENST00000336066,;	T	ENSG00000125779	ENST00000316562	Transcript	missense_variant	751	745	249	R/W	Cgg/Tgg	rs747490823	.	.	1	PANK2	HGNC	15894	protein_coding	YES	CCDS13071.2	ENSP00000313377	PANK2_HUMAN	Q52M85_HUMAN,D3DVZ1_HUMAN,A4FU43_HUMAN	UPI000036701A	.	deleterious(0.01)	benign(0.38)	2/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12280:SF25,hmmpanther:PTHR12280,TIGRFAM_domain:TIGR00555,Pfam_domain:PF03630,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTCGGAAG	byFrequency	5	ESCA
RBPJL	0	.	GRCh37	20	43945485	43945485	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1440C>A	p.Ser480Arg	p.S480R	ENST00000343694	12/12	131	72	58	49	49	0	RBPJL,missense_variant,p.Ser480Arg,ENST00000343694,;RBPJL,missense_variant,p.Ser479Arg,ENST00000372743,;RBPJL,3_prime_UTR_variant,,ENST00000372741,;RBPJL,non_coding_transcript_exon_variant,,ENST00000464504,;	A	ENSG00000124232	ENST00000343694	Transcript	missense_variant	1512	1440	480	S/R	agC/agA	COSM1027214	.	.	1	RBPJL	HGNC	13761	protein_coding	YES	CCDS13349.1	ENSP00000341243	RBPJL_HUMAN	.	UPI0000047297	.	tolerated(0.1)	benign(0.422)	12/12	.	hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAGCGTGCG	.	5	ESCA
WFDC2	0	.	GRCh37	20	44108503	44108503	+	Intron	DEL	G	G	-	rs150529863	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224-73delG	.	.	ENST00000372676	.	53	35	17	9	9	0	WFDC2,5_prime_UTR_variant,,ENST00000342873,;WFDC2,intron_variant,,ENST00000372676,;WFDC2,intron_variant,,ENST00000339946,;WFDC2,downstream_gene_variant,,ENST00000217425,;AL031663.1,upstream_gene_variant,,ENST00000599747,;WFDC2,intron_variant,,ENST00000488143,;WFDC2,intron_variant,,ENST00000462062,;WFDC2,intron_variant,,ENST00000447118,;	-	ENSG00000101443	ENST00000372676	Transcript	intron_variant	.	.	.	.	.	rs150529863	.	.	1	WFDC2	HGNC	15939	protein_coding	YES	CCDS35501.1	ENSP00000361761	WFDC2_HUMAN	.	UPI000000D8F6	.	.	.	.	2/3	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGCAGTGGGGGG	by1000G	2	ESCA
MMP9	0	.	GRCh37	20	44639804	44639804	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672C>T	p.%3D	p.N224N	ENST00000372330	5/13	86	53	32	37	37	0	MMP9,synonymous_variant,p.%3D,ENST00000372330,;RP11-465L10.10,downstream_gene_variant,,ENST00000535913,;AL162458.1,upstream_gene_variant,,ENST00000366171,;	T	ENSG00000100985	ENST00000372330	Transcript	synonymous_variant	691	672	224	N	aaC/aaT	.	.	.	1	MMP9	HGNC	7176	protein_coding	YES	CCDS13390.1	ENSP00000361405	MMP9_HUMAN	.	UPI000013C712	.	.	.	5/13	.	hmmpanther:PTHR10201:SF30,hmmpanther:PTHR10201,Pfam_domain:PF00413,Gene3D:2.10.10.10,SMART_domains:SM00235,SMART_domains:SM00059,Superfamily_domains:SSF57440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAACGCAGA	.	5	ESCA
ELMO2	0	.	GRCh37	20	45000560	45000560	+	Missense_Mutation	SNP	G	G	T	rs747312721	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1465C>A	p.Pro489Thr	p.P489T	ENST00000290246	17/22	60	50	10	28	28	0	ELMO2,missense_variant,p.Pro221Thr,ENST00000454865,;ELMO2,missense_variant,p.Pro306Thr,ENST00000445496,;ELMO2,missense_variant,p.Pro501Thr,ENST00000439931,;ELMO2,missense_variant,p.Pro401Thr,ENST00000372176,;ELMO2,missense_variant,p.Pro489Thr,ENST00000290246,;ELMO2,missense_variant,p.Pro56Thr,ENST00000452857,;ELMO2,missense_variant,p.Pro489Thr,ENST00000396391,;ELMO2,missense_variant,p.Pro487Thr,ENST00000352077,;ELMO2,downstream_gene_variant,,ENST00000425546,;ELMO2,downstream_gene_variant,,ENST00000450812,;ELMO2,non_coding_transcript_exon_variant,,ENST00000464448,;ELMO2,downstream_gene_variant,,ENST00000481852,;ELMO2,downstream_gene_variant,,ENST00000488853,;ELMO2,downstream_gene_variant,,ENST00000462491,;ELMO2,missense_variant,p.Pro214Thr,ENST00000467800,;	T	ENSG00000062598	ENST00000290246	Transcript	missense_variant	1660	1465	489	P/T	Ccc/Acc	rs747312721	.	.	-1	ELMO2	HGNC	17233	protein_coding	YES	CCDS13398.1	ENSP00000290246	ELMO2_HUMAN	Q7Z5G9_HUMAN,Q5JVZ4_HUMAN,Q5BLP5_HUMAN,F5GZP8_HUMAN	UPI000013F6C4	.	deleterious(0)	probably_damaging(0.98)	17/22	.	hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGGGTTTGG	.	5	ESCA
PRNP	0	.	GRCh37	20	4679939	4679939	+	Missense_Mutation	SNP	C	C	T	rs751211144	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73C>T	p.Arg25Cys	p.R25C	ENST00000379440	2/2	50	40	10	18	18	0	PRNP,missense_variant,p.Arg25Cys,ENST00000424424,;PRNP,missense_variant,p.Arg25Cys,ENST00000430350,;PRNP,missense_variant,p.Arg25Cys,ENST00000379440,;PRNP,missense_variant,p.Arg25Cys,ENST00000457586,;	T	ENSG00000171867	ENST00000379440	Transcript	missense_variant	360	73	25	R/C	Cgc/Tgc	rs751211144	.	.	1	PRNP	HGNC	9449	protein_coding	YES	CCDS13080.1	ENSP00000368752	PRIO_HUMAN	Q86XR1_HUMAN,Q6SES1_HUMAN,Q53YK7_HUMAN,O75942_HUMAN,A2A2V1_HUMAN	UPI0000033C27	.	deleterious(0)	probably_damaging(0.967)	2/2	.	SMART_domains:SM00157,Pfam_domain:PF11587,hmmpanther:PTHR11522:SF0,hmmpanther:PTHR11522	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGCGCCCG	byFrequency	5	ESCA
PRND	0	.	GRCh37	20	4708726	4708726	+	3'UTR	SNP	G	G	A	rs761088828	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2998G>A	.	.	ENST00000305817	2/2	70	60	9	29	29	0	PRND,3_prime_UTR_variant,,ENST00000305817,;PRNT,downstream_gene_variant,,ENST00000418528,;PRNT,downstream_gene_variant,,ENST00000423718,;PRNT,downstream_gene_variant,,ENST00000326539,;	A	ENSG00000171864	ENST00000305817	Transcript	3_prime_UTR_variant	3600	.	.	.	.	rs761088828	.	.	1	PRND	HGNC	15748	protein_coding	YES	CCDS13081.1	ENSP00000306900	PRND_HUMAN	.	UPI000003E880	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCACGCCCTG	.	4	ESCA
CSNK2A1	0	.	GRCh37	20	485835	485835	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.140G>A	p.Arg47Gln	p.R47Q	ENST00000217244	4/14	49	39	10	65	65	0	CSNK2A1,missense_variant,p.Arg47Gln,ENST00000349736,;CSNK2A1,missense_variant,p.Arg47Gln,ENST00000400227,;CSNK2A1,missense_variant,p.Arg47Gln,ENST00000609525,;CSNK2A1,missense_variant,p.Arg47Gln,ENST00000608066,;CSNK2A1,missense_variant,p.Arg47Gln,ENST00000217244,;CSNK2A1,5_prime_UTR_variant,,ENST00000460062,;CSNK2A1,5_prime_UTR_variant,,ENST00000400217,;CSNK2A1,non_coding_transcript_exon_variant,,ENST00000609606,;CSNK2A1,non_coding_transcript_exon_variant,,ENST00000608490,;	T	ENSG00000101266	ENST00000217244	Transcript	missense_variant	516	140	47	R/Q	cGa/cAa	.	.	.	-1	CSNK2A1	HGNC	2457	protein_coding	YES	CCDS13003.1	ENSP00000217244	CSK21_HUMAN	.	UPI0000000CB5	.	deleterious(0.01)	possibly_damaging(0.87)	4/14	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24054:SF28,hmmpanther:PTHR24054,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCTCGGCCT	.	5	ESCA
SLC23A2	0	.	GRCh37	20	4913279	4913279	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-71C>T	.	.	ENST00000379333	3/17	26	18	8	12	12	0	SLC23A2,5_prime_UTR_variant,,ENST00000379333,;SLC23A2,5_prime_UTR_variant,,ENST00000424750,;SLC23A2,5_prime_UTR_variant,,ENST00000338244,;SLC23A2,non_coding_transcript_exon_variant,,ENST00000468355,;	A	ENSG00000089057	ENST00000379333	Transcript	5_prime_UTR_variant	323	.	.	.	.	.	.	.	-1	SLC23A2	HGNC	10973	protein_coding	YES	CCDS13085.1	ENSP00000368637	S23A2_HUMAN	Q4ZGM1_HUMAN	UPI0000136292	.	.	.	3/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGGAGCCCAG	.	2	ESCA
ADNP	0	.	GRCh37	20	49508204	49508204	+	Frame_Shift_Del	DEL	T	T	-	rs766989352	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3047delA	p.Lys1016ArgfsTer11	p.K1016Rfs*11	ENST00000396029	5/5	91	46	45	69	69	0	ADNP,frameshift_variant,p.Lys1016ArgfsTer11,ENST00000396032,;ADNP,frameshift_variant,p.Lys1016ArgfsTer11,ENST00000396029,;ADNP,frameshift_variant,p.Lys1016ArgfsTer11,ENST00000349014,;ADNP,frameshift_variant,p.Lys1016ArgfsTer11,ENST00000371602,;ADNP,downstream_gene_variant,,ENST00000534467,;	-	ENSG00000101126	ENST00000396029	Transcript	frameshift_variant	3615	3047	1016	K/X	aAg/ag	rs766989352,COSM1163731	.	.	-1	ADNP	HGNC	15766	protein_coding	YES	CCDS13433.1	ENSP00000379346	ADNP_HUMAN	E9PQK8_HUMAN	UPI00000375B9	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15740:SF1,hmmpanther:PTHR15740	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.K1016fs*11|c.3047delA|14	INDELOCATOR|VARSCANI	GTAGCCTTTTTT	.	2	ESCA
NFATC2	0	.	GRCh37	20	50140068	50140068	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712G>A	p.Val238Met	p.V238M	ENST00000396009	2/10	112	55	56	27	27	0	NFATC2,missense_variant,p.Val238Met,ENST00000396009,;NFATC2,missense_variant,p.Val218Met,ENST00000609943,;NFATC2,missense_variant,p.Val238Met,ENST00000371564,;NFATC2,missense_variant,p.Val19Met,ENST00000609507,;NFATC2,missense_variant,p.Val19Met,ENST00000610033,;NFATC2,missense_variant,p.Val218Met,ENST00000414705,;	T	ENSG00000101096	ENST00000396009	Transcript	missense_variant	932	712	238	V/M	Gtg/Atg	COSM317681	.	.	-1	NFATC2	HGNC	7776	protein_coding	YES	CCDS13437.1	ENSP00000379330	NFAC2_HUMAN	B5B2P4_HUMAN,B5B2P3_HUMAN	UPI0000167D0F	.	tolerated(0.19)	possibly_damaging(0.514)	2/10	.	hmmpanther:PTHR12533:SF4,hmmpanther:PTHR12533,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCACGGGCG	.	5	ESCA
ZNF217	0	.	GRCh37	20	52184372	52184372	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1455delT	.	.	ENST00000371471	6/6	30	24	6	19	19	0	ZNF217,3_prime_UTR_variant,,ENST00000302342,;ZNF217,3_prime_UTR_variant,,ENST00000371471,;ZNF217,downstream_gene_variant,,ENST00000437222,;RP4-724E16.2,intron_variant,,ENST00000424252,;	-	ENSG00000171940	ENST00000371471	Transcript	3_prime_UTR_variant	5028	.	.	.	.	.	.	.	-1	ZNF217	HGNC	13009	protein_coding	YES	CCDS13443.1	ENSP00000360526	ZN217_HUMAN	A2A326_HUMAN	UPI000013C323	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAATTTAAAAAA	.	2	ESCA
SS18L1	0	.	GRCh37	20	60737811	60737811	+	Missense_Mutation	SNP	C	C	T	rs751601438	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380C>T	p.Pro127Leu	p.P127L	ENST00000331758	5/11	99	48	50	27	27	0	SS18L1,missense_variant,p.Pro127Leu,ENST00000421564,;SS18L1,missense_variant,p.Pro130Leu,ENST00000370848,;SS18L1,missense_variant,p.Pro127Leu,ENST00000331758,;SS18L1,downstream_gene_variant,,ENST00000450482,;SS18L1,non_coding_transcript_exon_variant,,ENST00000491916,;SS18L1,upstream_gene_variant,,ENST00000492466,;	T	ENSG00000184402	ENST00000331758	Transcript	missense_variant	406	380	127	P/L	cCg/cTg	rs751601438	.	.	1	SS18L1	HGNC	15592	protein_coding	YES	CCDS13491.1	ENSP00000333012	CREST_HUMAN	.	UPI000013543D	.	deleterious_low_confidence(0)	probably_damaging(0.999)	5/11	.	hmmpanther:PTHR23107,hmmpanther:PTHR23107:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGCCGAGCC	byFrequency	5	ESCA
TCFL5	0	.	GRCh37	20	61488860	61488860	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125T>C	p.%3D	p.A375A	ENST00000335351	4/6	82	39	42	38	38	0	TCFL5,synonymous_variant,p.%3D,ENST00000217162,;TCFL5,synonymous_variant,p.%3D,ENST00000335351,;	G	ENSG00000101190	ENST00000335351	Transcript	synonymous_variant	1218	1125	375	A	gcT/gcC	.	.	.	-1	TCFL5	HGNC	11646	protein_coding	YES	CCDS13506.1	ENSP00000334294	TCFL5_HUMAN	.	UPI0000206389	.	.	.	4/6	.	hmmpanther:PTHR15402,hmmpanther:PTHR15402:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAAGCGCC	.	5	ESCA
DIDO1	0	.	GRCh37	20	61524253	61524253	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3163A>G	p.Thr1055Ala	p.T1055A	ENST00000266070	13/16	62	40	22	49	49	0	DIDO1,missense_variant,p.Thr1055Ala,ENST00000266070,;DIDO1,missense_variant,p.Thr1055Ala,ENST00000395335,;DIDO1,missense_variant,p.Thr1055Ala,ENST00000395340,;DIDO1,missense_variant,p.Thr1055Ala,ENST00000395343,;	C	ENSG00000101191	ENST00000266070	Transcript	missense_variant	3489	3163	1055	T/A	Acc/Gcc	.	.	.	-1	DIDO1	HGNC	2680	protein_coding	YES	CCDS33506.1	ENSP00000266070	DIDO1_HUMAN	.	UPI0000206380	.	.	benign(0.06)	13/16	.	hmmpanther:PTHR14914:SF7,hmmpanther:PTHR14914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGTGCTGA	.	5	ESCA
YTHDF1	0	.	GRCh37	20	61827084	61827084	+	3'UTR	SNP	G	G	A	rs112508567	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*976C>T	.	.	ENST00000370339	5/5	21	17	4	10	10	0	YTHDF1,3_prime_UTR_variant,,ENST00000370339,;YTHDF1,downstream_gene_variant,,ENST00000370334,;YTHDF1,downstream_gene_variant,,ENST00000370333,;	A	ENSG00000149658	ENST00000370339	Transcript	3_prime_UTR_variant	2998	.	.	.	.	rs112508567	.	.	-1	YTHDF1	HGNC	15867	protein_coding	YES	CCDS13511.1	ENSP00000359364	YTHD1_HUMAN	F8W840_HUMAN	UPI0000128DD9	.	.	.	5/5	.	.	A:0.0076	A:0.0287	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TCAACGGTCCC	byFrequency|byCluster|by1000G	3	ESCA
KCNQ2	0	.	GRCh37	20	62055548	62055548	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1229delC	p.Pro410ArgfsTer30	p.P410Rfs*30	ENST00000359125	11/17	45	33	12	12	12	0	KCNQ2,frameshift_variant,p.Pro410ArgfsTer30,ENST00000359689,;KCNQ2,frameshift_variant,p.Pro410ArgfsTer30,ENST00000359125,;KCNQ2,frameshift_variant,p.Pro400ArgfsTer12,ENST00000354587,;KCNQ2,frameshift_variant,p.Pro400ArgfsTer12,ENST00000370224,;KCNQ2,frameshift_variant,p.Pro400ArgfsTer12,ENST00000360480,;KCNQ2,frameshift_variant,p.Pro410ArgfsTer12,ENST00000357249,;KCNQ2,frameshift_variant,p.Pro410ArgfsTer24,ENST00000344462,;KCNQ2,non_coding_transcript_exon_variant,,ENST00000370221,;	-	ENSG00000075043	ENST00000359125	Transcript	frameshift_variant	1404	1229	410	P/X	cCg/cg	CD094786	.	.	-1	KCNQ2	HGNC	6296	protein_coding	YES	CCDS13520.1	ENSP00000352035	KCNQ2_HUMAN	.	UPI00001279ED	.	.	.	11/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11537:SF6,hmmpanther:PTHR11537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TCCGGCGGGGGG	.	2	ESCA
HELZ2	0	.	GRCh37	20	62193250	62193251	+	Frame_Shift_Ins	INS	-	-	G	rs776302757	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6616dupC	p.Arg2206ProfsTer42	p.R2206Pfs*42	ENST00000467148	11/19	36	28	8	14	14	0	HELZ2,frameshift_variant,p.Arg2206ProfsTer42,ENST00000467148,;HELZ2,frameshift_variant,p.Arg1637ProfsTer42,ENST00000427522,;HELZ2,upstream_gene_variant,,ENST00000478861,;	G	ENSG00000130589	ENST00000467148	Transcript	frameshift_variant	6686-6687	6616-6617	2206	R/PX	cgt/cCgt	rs776302757,COSM1413134	.	.	-1	HELZ2	HGNC	30021	protein_coding	YES	CCDS33508.1	ENSP00000417401	HELZ2_HUMAN	Q3C1U4_HUMAN	UPI0000246BF7	.	.	.	11/19	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF332,Gene3D:3.40.50.300,Pfam_domain:PF13086,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	insertion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCCCACGGGGG	.	2	ESCA
HELZ2	0	.	GRCh37	20	62195615	62195615	+	Silent	SNP	C	C	T	rs749599121	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4560G>A	p.%3D	p.A1520A	ENST00000467148	8/19	72	46	25	21	21	0	HELZ2,synonymous_variant,p.%3D,ENST00000467148,;HELZ2,synonymous_variant,p.%3D,ENST00000427522,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,upstream_gene_variant,,ENST00000478861,;	T	ENSG00000130589	ENST00000467148	Transcript	synonymous_variant	4630	4560	1520	A	gcG/gcA	rs749599121,COSM1615866	.	.	-1	HELZ2	HGNC	30021	protein_coding	YES	CCDS33508.1	ENSP00000417401	HELZ2_HUMAN	Q3C1U4_HUMAN	UPI0000246BF7	.	.	.	8/19	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF332,Pfam_domain:PF00773,SMART_domains:SM00955,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGCCGCGCG	.	5	ESCA
ABHD16B	0	.	GRCh37	20	62494101	62494101	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1208C>T	p.Ala403Val	p.A403V	ENST00000369916	1/1	42	36	6	27	27	0	ABHD16B,missense_variant,p.Ala403Val,ENST00000369916,;TPD52L2,upstream_gene_variant,,ENST00000369927,;C20ORF135,upstream_gene_variant,,ENST00000601296,;TPD52L2,upstream_gene_variant,,ENST00000217121,;TPD52L2,upstream_gene_variant,,ENST00000351424,;TPD52L2,upstream_gene_variant,,ENST00000348257,;TPD52L2,upstream_gene_variant,,ENST00000358548,;TPD52L2,upstream_gene_variant,,ENST00000352482,;TPD52L2,upstream_gene_variant,,ENST00000346249,;	T	ENSG00000183260	ENST00000369916	Transcript	missense_variant	1536	1208	403	A/V	gCa/gTa	.	.	.	1	ABHD16B	HGNC	16128	protein_coding	YES	CCDS13539.1	ENSP00000358932	ABHGB_HUMAN	.	UPI000012860E	.	tolerated(0.05)	benign(0.03)	1/1	.	hmmpanther:PTHR12277:SF37,hmmpanther:PTHR12277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGTGCACGCT	.	2	ESCA
PLCB4	0	.	GRCh37	20	9460648	9460648	+	3'UTR	SNP	A	A	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*992A>C	.	.	ENST00000378501	36/36	27	24	3	13	13	0	PLCB4,3_prime_UTR_variant,,ENST00000334005,;PLCB4,3_prime_UTR_variant,,ENST00000278655,;PLCB4,3_prime_UTR_variant,,ENST00000378473,;PLCB4,3_prime_UTR_variant,,ENST00000378493,;PLCB4,3_prime_UTR_variant,,ENST00000378501,;PLCB4,downstream_gene_variant,,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;	C	ENSG00000101333	ENST00000378501	Transcript	3_prime_UTR_variant	4592	.	.	.	.	.	.	.	1	PLCB4	HGNC	9059	protein_coding	YES	CCDS13104.1	ENSP00000367762	PLCB4_HUMAN	B1AJW4_HUMAN,B1AJW3_HUMAN,B1AJW2_HUMAN,B1AJW1_HUMAN	UPI00002069DF	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GAAAAACCCTC	.	2	ESCA
PLCB4	0	.	GRCh37	20	9460657	9460658	+	3'UTR	INS	-	-	TA	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1011_*1012dupAT	.	.	ENST00000378501	36/36	29	13	16	15	15	0	PLCB4,3_prime_UTR_variant,,ENST00000334005,;PLCB4,3_prime_UTR_variant,,ENST00000278655,;PLCB4,3_prime_UTR_variant,,ENST00000378473,;PLCB4,3_prime_UTR_variant,,ENST00000378493,;PLCB4,3_prime_UTR_variant,,ENST00000378501,;PLCB4,downstream_gene_variant,,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;	TA	ENSG00000101333	ENST00000378501	Transcript	3_prime_UTR_variant	4601-4602	.	.	.	.	.	.	.	1	PLCB4	HGNC	9059	protein_coding	YES	CCDS13104.1	ENSP00000367762	PLCB4_HUMAN	B1AJW4_HUMAN,B1AJW3_HUMAN,B1AJW2_HUMAN,B1AJW1_HUMAN	UPI00002069DF	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	11	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TCTCTCTATAT	.	2	ESCA
KRTAP24-1	0	.	GRCh37	21	31655068	31655068	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.183C>T	p.%3D	p.C61C	ENST00000340345	1/1	49	15	34	36	36	0	KRTAP24-1,synonymous_variant,p.%3D,ENST00000340345,;	A	ENSG00000188694	ENST00000340345	Transcript	synonymous_variant	209	183	61	C	tgC/tgT	COSM3550136,COSM1307709	.	.	-1	KRTAP24-1	HGNC	33902	protein_coding	YES	CCDS42915.1	ENSP00000339238	KR241_HUMAN	.	UPI00005C50F3	.	.	.	1/1	.	hmmpanther:PTHR23260:SF2,hmmpanther:PTHR23260,Pfam_domain:PF05287	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTGGCAGTA	.	5	ESCA
SLC5A3	0	.	GRCh37	21	35476637	35476639	+	3'UTR	DEL	TTC	TTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TTC	TTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6987_*6989delTCT	.	.	ENST00000608209	2/2	46	20	26	41	41	0	SLC5A3,3_prime_UTR_variant,,ENST00000608209,;SLC5A3,3_prime_UTR_variant,,ENST00000381151,;MRPS6,intron_variant,,ENST00000399312,;MRPS6,intron_variant,,ENST00000477091,;MRPS6,intron_variant,,ENST00000488492,;AP000320.7,intron_variant,,ENST00000362077,;	-	ENSG00000272962	ENST00000608209	Transcript	3_prime_UTR_variant	9652-9654	.	.	.	.	.	.	.	1	SLC5A3	Uniprot_gn	11038	protein_coding	YES	CCDS33549.1	ENSP00000477068	.	.	UPI00001359F3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGTATGTTCTTCTA	.	3	ESCA
RUNX1	0	.	GRCh37	21	36206863	36206863	+	Missense_Mutation	SNP	C	C	T	rs749004431	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.649G>A	p.Gly217Arg	p.G217R	ENST00000300305	6/8	68	45	23	45	45	0	RUNX1,missense_variant,p.Gly205Arg,ENST00000399237,;RUNX1,missense_variant,p.Gly190Arg,ENST00000358356,;RUNX1,missense_variant,p.Gly205Arg,ENST00000325074,;RUNX1,missense_variant,p.Gly190Arg,ENST00000344691,;RUNX1,missense_variant,p.Gly217Arg,ENST00000300305,;RUNX1,missense_variant,p.Gly217Arg,ENST00000437180,;RUNX1,intron_variant,,ENST00000399240,;RUNX1,upstream_gene_variant,,ENST00000479325,;RUNX1,3_prime_UTR_variant,,ENST00000482318,;RUNX1,non_coding_transcript_exon_variant,,ENST00000469087,;	T	ENSG00000159216	ENST00000300305	Transcript	missense_variant	1094	649	217	G/R	Ggg/Agg	rs749004431,CM107646	.	.	-1	RUNX1	HGNC	10471	protein_coding	YES	CCDS13639.1	ENSP00000300305	RUNX1_HUMAN	.	UPI000015FE6A	.	deleterious(0.02)	probably_damaging(0.948)	6/8	.	hmmpanther:PTHR11950,PIRSF_domain:PIRSF009374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCGGGCT	byFrequency	5	ESCA
SIK1	0	.	GRCh37	21	44839827	44839827	+	Missense_Mutation	SNP	C	C	T	rs778543025	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000270162	9/14	34	22	11	29	29	0	SIK1,missense_variant,p.Arg344Gln,ENST00000270162,;SIK1,downstream_gene_variant,,ENST00000478426,;	T	ENSG00000142178	ENST00000270162	Transcript	missense_variant	1164	1031	344	R/Q	cGg/cAg	rs778543025	.	.	-1	SIK1	HGNC	11142	protein_coding	YES	CCDS33575.1	ENSP00000270162	SIK1_HUMAN	.	UPI0000206F2B	.	deleterious(0.01)	probably_damaging(0.978)	9/14	.	PIRSF_domain:PIRSF037014,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF0,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGCCGCTCA	.	5	ESCA
TSPEAR	0	.	GRCh37	21	45947292	45947292	+	Silent	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032A>C	p.%3D	p.T344T	ENST00000323084	7/12	31	7	24	32	32	0	TSPEAR,synonymous_variant,p.%3D,ENST00000397916,;TSPEAR,synonymous_variant,p.%3D,ENST00000323084,;C21orf90,downstream_gene_variant,,ENST00000465978,;	G	ENSG00000175894	ENST00000323084	Transcript	synonymous_variant	1098	1032	344	T	acA/acC	.	.	.	-1	TSPEAR	HGNC	1268	protein_coding	YES	CCDS13712.1	ENSP00000321987	TSEAR_HUMAN	.	UPI0000137746	.	.	.	7/12	.	hmmpanther:PTHR15261,PROSITE_profiles:PS50912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCTGTGGC	.	5	ESCA
PCNT	0	.	GRCh37	21	47858171	47858173	+	In_Frame_Del	DEL	AGA	AGA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AGA	AGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9196_9198delAAG	p.Lys3066del	p.K3066del	ENST00000359568	41/47	41	14	27	28	28	0	PCNT,inframe_deletion,p.Lys3066del,ENST00000359568,;PCNT,inframe_deletion,p.Lys47del,ENST00000418394,;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,;PCNT,upstream_gene_variant,,ENST00000465356,;	-	ENSG00000160299	ENST00000359568	Transcript	inframe_deletion	9301-9303	9194-9196	3065-3066	EK/E	gAGAag/gag	.	.	.	1	PCNT	HGNC	16068	protein_coding	YES	CCDS33592.1	ENSP00000352572	PCNT_HUMAN	.	UPI00001AEB88	.	.	.	41/47	.	hmmpanther:PTHR18932:SF11,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCAGGAGAAGCTG	.	3	ESCA
POTEH	0	.	GRCh37	22	16256520	16256520	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*159delA	.	.	ENST00000343518	11/11	1027	897	130	425	425	0	POTEH,3_prime_UTR_variant,,ENST00000343518,;POTEH,3_prime_UTR_variant,,ENST00000452800,;LA16c-3G11.7,upstream_gene_variant,,ENST00000417657,;LA16c-3G11.7,upstream_gene_variant,,ENST00000339523,;	-	ENSG00000198062	ENST00000343518	Transcript	3_prime_UTR_variant	1849	.	.	.	.	.	.	.	-1	POTEH	HGNC	133	protein_coding	YES	CCDS46658.1	ENSP00000340610	POTEH_HUMAN	.	UPI0000E5A425	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCATTCTTTTTT	.	3	ESCA
MICAL3	0	.	GRCh37	22	18300311	18300311	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5116C>T	p.Arg1706Cys	p.R1706C	ENST00000441493	26/32	37	21	16	16	16	0	MICAL3,missense_variant,p.Arg1706Cys,ENST00000441493,;MICAL3,upstream_gene_variant,,ENST00000579997,;MICAL3,upstream_gene_variant,,ENST00000577821,;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000580469,;	A	ENSG00000243156	ENST00000441493	Transcript	missense_variant	5469	5116	1706	R/C	Cgc/Tgc	.	.	.	-1	MICAL3	HGNC	24694	protein_coding	YES	CCDS46659.1	ENSP00000416015	MICA3_HUMAN	C9J922_HUMAN,A8K0E1_HUMAN	UPI0001823FDE	.	.	benign(0.009)	26/32	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCGGGGGG	.	5	ESCA
MICAL3	0	.	GRCh37	22	18376579	18376579	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1541G>A	p.Arg514His	p.R514H	ENST00000441493	11/32	24	19	5	16	16	0	MICAL3,missense_variant,p.Arg514His,ENST00000207726,;MICAL3,missense_variant,p.Arg514His,ENST00000444520,;MICAL3,missense_variant,p.Arg514His,ENST00000383094,;MICAL3,missense_variant,p.Arg514His,ENST00000414725,;MICAL3,missense_variant,p.Arg33His,ENST00000461307,;MICAL3,missense_variant,p.Arg514His,ENST00000585038,;MICAL3,missense_variant,p.Arg514His,ENST00000429452,;MICAL3,missense_variant,p.Arg514His,ENST00000441493,;MICAL3,missense_variant,p.Arg514His,ENST00000400561,;MICAL3,3_prime_UTR_variant,,ENST00000495076,;	T	ENSG00000243156	ENST00000441493	Transcript	missense_variant	1894	1541	514	R/H	cGc/cAc	.	.	.	-1	MICAL3	HGNC	24694	protein_coding	YES	CCDS46659.1	ENSP00000416015	MICA3_HUMAN	C9J922_HUMAN,A8K0E1_HUMAN	UPI0001823FDE	.	.	probably_damaging(0.985)	11/32	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF218,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTGCGAGTC	.	5	ESCA
ARVCF	0	.	GRCh37	22	19961708	19961708	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2015C>T	p.Thr672Met	p.T672M	ENST00000263207	12/20	55	28	26	37	37	0	ARVCF,missense_variant,p.Thr672Met,ENST00000263207,;ARVCF,missense_variant,p.Thr603Met,ENST00000406522,;ARVCF,missense_variant,p.Thr609Met,ENST00000344269,;ARVCF,missense_variant,p.Thr666Met,ENST00000406259,;ARVCF,missense_variant,p.Thr609Met,ENST00000401994,;COMT,downstream_gene_variant,,ENST00000361682,;COMT,downstream_gene_variant,,ENST00000449653,;ARVCF,non_coding_transcript_exon_variant,,ENST00000480792,;ARVCF,non_coding_transcript_exon_variant,,ENST00000495096,;	A	ENSG00000099889	ENST00000263207	Transcript	missense_variant	2307	2015	672	T/M	aCg/aTg	.	.	.	-1	ARVCF	HGNC	728	protein_coding	YES	CCDS13771.1	ENSP00000263207	ARVC_HUMAN	.	UPI00001260C8	.	deleterious(0.01)	probably_damaging(0.987)	12/20	.	hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF5,Pfam_domain:PF00514,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCGTGAGG	.	5	ESCA
DGCR8	0	.	GRCh37	22	20077689	20077689	+	Missense_Mutation	SNP	C	C	T	rs560910865	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1214C>T	p.Pro405Leu	p.P405L	ENST00000351989	5/14	30	14	16	12	12	0	DGCR8,missense_variant,p.Pro405Leu,ENST00000351989,;DGCR8,missense_variant,p.Pro405Leu,ENST00000383024,;DGCR8,missense_variant,p.Pro405Leu,ENST00000407755,;DGCR8,downstream_gene_variant,,ENST00000457069,;MIR1306,downstream_gene_variant,,ENST00000408439,;MIR3618,downstream_gene_variant,,ENST00000580330,;DGCR8,non_coding_transcript_exon_variant,,ENST00000495826,;DGCR8,non_coding_transcript_exon_variant,,ENST00000498171,;DGCR8,upstream_gene_variant,,ENST00000491892,;	T	ENSG00000128191	ENST00000351989	Transcript	missense_variant	1643	1214	405	P/L	cCg/cTg	rs560910865	.	.	1	DGCR8	HGNC	2847	protein_coding	YES	CCDS13773.1	ENSP00000263209	DGCR8_HUMAN	C9JSD5_HUMAN	UPI0000129225	.	tolerated(0.46)	benign(0)	5/14	.	hmmpanther:PTHR13482,hmmpanther:PTHR13482:SF2	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCCGGACG	by1000G	5	ESCA
DGCR6L	0	.	GRCh37	22	20303643	20303643	+	Missense_Mutation	SNP	T	T	A	rs575784275	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.371A>T	p.Glu124Val	p.E124V	ENST00000248879	3/5	121	81	40	73	73	0	DGCR6L,missense_variant,p.Glu124Val,ENST00000248879,;DGCR6L,intron_variant,,ENST00000405465,;XXbac-B444P24.14,upstream_gene_variant,,ENST00000609632,;XXbac-B444P24.13,downstream_gene_variant,,ENST00000608275,;DGCR6L,intron_variant,,ENST00000443409,;XXbac-B444P24.10,downstream_gene_variant,,ENST00000438948,;	A	ENSG00000128185	ENST00000248879	Transcript	missense_variant	463	371	124	E/V	gAg/gTg	rs575784275	.	.	-1	DGCR6L	HGNC	18551	protein_coding	YES	CCDS13778.1	ENSP00000248879	DGC6L_HUMAN	.	UPI0000129216	.	deleterious(0.01)	possibly_damaging(0.697)	3/5	.	Coiled-coils_(Ncoils):Coil,Pfam_domain:PF07324,hmmpanther:PTHR13054:SF4,hmmpanther:PTHR13054	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACCTCTAGT	by1000G	5	ESCA
PI4KA	0	.	GRCh37	22	21147531	21147531	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2278G>A	p.Ala760Thr	p.A760T	ENST00000255882	19/55	23	17	5	20	20	0	PI4KA,missense_variant,p.Ala702Thr,ENST00000572273,;PI4KA,missense_variant,p.Ala760Thr,ENST00000255882,;PI4KA,splice_region_variant,,ENST00000466162,;PI4KA,splice_region_variant,,ENST00000490873,;PI4KA,splice_region_variant,,ENST00000484220,;	T	ENSG00000241973	ENST00000255882	Transcript	missense_variant	2365	2278	760	A/T	Gct/Act	.	.	.	-1	PI4KA	HGNC	8983	protein_coding	YES	CCDS33603.2	ENSP00000255882	.	Q4LE69_HUMAN,J3KN10_HUMAN,C9JLI1_HUMAN	UPI0000E06BD6	.	tolerated(0.06)	possibly_damaging(0.677)	19/55	.	Superfamily_domains:SSF48371,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGCCTAGA	.	5	ESCA
LZTR1	0	.	GRCh37	22	21347194	21347194	+	Splice_Site	SNP	G	G	A	rs143868364	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1260+1G>A	.	p.X420_splice	ENST00000215739	.	58	33	24	22	22	0	LZTR1,splice_donor_variant,,ENST00000215739,;LZTR1,splice_donor_variant,,ENST00000389355,;LZTR1,upstream_gene_variant,,ENST00000415817,;LZTR1,splice_donor_variant,,ENST00000479606,;LZTR1,downstream_gene_variant,,ENST00000497716,;LZTR1,downstream_gene_variant,,ENST00000480895,;LZTR1,splice_region_variant,,ENST00000492480,;LZTR1,upstream_gene_variant,,ENST00000464807,;LZTR1,upstream_gene_variant,,ENST00000452988,;LZTR1,upstream_gene_variant,,ENST00000498649,;LZTR1,upstream_gene_variant,,ENST00000491432,;LZTR1,upstream_gene_variant,,ENST00000463909,;LZTR1,upstream_gene_variant,,ENST00000439171,;LZTR1,upstream_gene_variant,,ENST00000495142,;LZTR1,downstream_gene_variant,,ENST00000461510,;LZTR1,downstream_gene_variant,,ENST00000414985,;LZTR1,upstream_gene_variant,,ENST00000415354,;LZTR1,downstream_gene_variant,,ENST00000443265,;	A	ENSG00000099949	ENST00000215739	Transcript	splice_donor_variant	.	.	.	.	.	rs143868364	.	.	1	LZTR1	HGNC	6742	protein_coding	YES	CCDS33606.1	ENSP00000215739	LZTR1_HUMAN	B2R8T5_HUMAN	UPI000013C695	.	.	.	.	11/20	.	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGGTGTGG	byFrequency|byCluster|by1000G	5	ESCA
HIC2	0	.	GRCh37	22	21803715	21803715	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2691delA	.	.	ENST00000443632	2/2	44	35	9	37	37	0	HIC2,3_prime_UTR_variant,,ENST00000443632,;HIC2,3_prime_UTR_variant,,ENST00000407598,;HIC2,3_prime_UTR_variant,,ENST00000407464,;	-	ENSG00000169635	ENST00000443632	Transcript	3_prime_UTR_variant	4903	.	.	.	.	.	.	.	1	HIC2	HGNC	18595	protein_coding	YES	CCDS13789.1	ENSP00000387757	HIC2_HUMAN	.	UPI000012C71C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAAAGAAAAAA	.	2	ESCA
PPM1F	0	.	GRCh37	22	22287853	22287853	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657C>T	p.%3D	p.R219R	ENST00000263212	5/8	45	23	22	20	20	0	PPM1F,synonymous_variant,p.%3D,ENST00000445205,;PPM1F,synonymous_variant,p.%3D,ENST00000538191,;PPM1F,synonymous_variant,p.%3D,ENST00000407142,;PPM1F,synonymous_variant,p.%3D,ENST00000263212,;PPM1F,synonymous_variant,p.%3D,ENST00000397495,;PPM1F,downstream_gene_variant,,ENST00000424647,;LL22NC03-86G7.1,upstream_gene_variant,,ENST00000538634,;LL22NC03-86G7.1,upstream_gene_variant,,ENST00000458178,;PPM1F,upstream_gene_variant,,ENST00000484588,;PPM1F,downstream_gene_variant,,ENST00000486259,;	A	ENSG00000100034	ENST00000263212	Transcript	synonymous_variant	763	657	219	R	cgC/cgT	.	.	.	-1	PPM1F	HGNC	19388	protein_coding	YES	CCDS13796.1	ENSP00000263212	PPM1F_HUMAN	Q6IPC0_HUMAN,Q0VGL7_HUMAN,C9J2F3_HUMAN,B5MCT7_HUMAN,A0M8Q2_HUMAN	UPI000012A61C	.	.	.	5/8	.	hmmpanther:PTHR13832:SF233,hmmpanther:PTHR13832,Gene3D:3.60.40.10,Pfam_domain:PF00481,SMART_domains:SM00331,SMART_domains:SM00332,Superfamily_domains:SSF81606	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGGCGGGC	.	5	ESCA
RGL4	0	.	GRCh37	22	24041155	24041155	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*85G>C	.	.	ENST00000290691	11/11	63	40	23	28	28	0	RGL4,missense_variant,p.Arg533Thr,ENST00000423392,;RGL4,3_prime_UTR_variant,,ENST00000452208,;RGL4,3_prime_UTR_variant,,ENST00000290691,;RGL4,3_prime_UTR_variant,,ENST00000401461,;GUSBP11,intron_variant,,ENST00000452737,;GUSBP11,intron_variant,,ENST00000445682,;KB-1572G7.2,intron_variant,,ENST00000421064,;GUSBP11,intron_variant,,ENST00000451837,;GUSBP11,intron_variant,,ENST00000422506,;AP000347.2,downstream_gene_variant,,ENST00000432595,;RGL4,downstream_gene_variant,,ENST00000460167,;RGL4,3_prime_UTR_variant,,ENST00000441897,;RGL4,non_coding_transcript_exon_variant,,ENST00000460003,;RGL4,non_coding_transcript_exon_variant,,ENST00000467354,;AP000347.2,intron_variant,,ENST00000435868,;	C	ENSG00000159496	ENST00000290691	Transcript	3_prime_UTR_variant	2677	.	.	.	.	.	.	.	1	RGL4	HGNC	31911	protein_coding	YES	CCDS13811.1	ENSP00000290691	RGDSR_HUMAN	B5MCW5_HUMAN	UPI00000740FE	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTAGACACC	.	5	ESCA
FAM211B	0	.	GRCh37	22	24984229	24984229	+	Silent	SNP	C	C	T	rs776835009	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375G>A	p.%3D	p.S125S	ENST00000318753	3/4	114	66	48	57	57	0	FAM211B,synonymous_variant,p.%3D,ENST00000318753,;GGT1,intron_variant,,ENST00000248923,;FAM211B,downstream_gene_variant,,ENST00000495297,;FAM211B,downstream_gene_variant,,ENST00000464490,;FAM211B,3_prime_UTR_variant,,ENST00000446942,;FAM211B,3_prime_UTR_variant,,ENST00000404045,;FAM211B,non_coding_transcript_exon_variant,,ENST00000491910,;FAM211B,non_coding_transcript_exon_variant,,ENST00000460524,;SNRPD3,intron_variant,,ENST00000404603,;SNRPD3,intron_variant,,ENST00000439775,;FAM211B,downstream_gene_variant,,ENST00000465334,;	T	ENSG00000178026	ENST00000318753	Transcript	synonymous_variant	399	375	125	S	tcG/tcA	rs776835009	.	.	-1	FAM211B	HGNC	33155	protein_coding	YES	CCDS42991.1	ENSP00000320520	F211B_HUMAN	.	UPI00002073C9	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCGAGTG	byFrequency	5	ESCA
MYO18B	0	.	GRCh37	22	26224901	26224901	+	Missense_Mutation	SNP	G	G	A	rs759388866	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2945G>A	p.Arg982Gln	p.R982Q	ENST00000335473	15/44	68	37	31	36	36	0	MYO18B,missense_variant,p.Arg982Gln,ENST00000335473,;MYO18B,missense_variant,p.Arg982Gln,ENST00000407587,;MYO18B,missense_variant,p.Arg982Gln,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,;	A	ENSG00000133454	ENST00000335473	Transcript	missense_variant	3195	2945	982	R/Q	cGg/cAg	rs759388866	.	.	1	MYO18B	HGNC	18150	protein_coding	YES	CCDS54507.1	ENSP00000334563	.	Q8N903_HUMAN	UPI0000207402	.	deleterious(0.03)	benign(0.16)	15/44	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF254,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGGACCT	byFrequency	5	ESCA
SRRD	0	.	GRCh37	22	26884176	26884176	+	Silent	SNP	C	C	T	rs748081893	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432C>T	p.%3D	p.Y144Y	ENST00000215917	3/7	31	18	12	19	19	0	SRRD,synonymous_variant,p.%3D,ENST00000215917,;TFIP11,downstream_gene_variant,,ENST00000407148,;TFIP11,downstream_gene_variant,,ENST00000405938,;HPS4,upstream_gene_variant,,ENST00000398145,;TFIP11,downstream_gene_variant,,ENST00000407431,;HPS4,upstream_gene_variant,,ENST00000336873,;HPS4,upstream_gene_variant,,ENST00000422379,;TFIP11,downstream_gene_variant,,ENST00000407690,;HPS4,upstream_gene_variant,,ENST00000473782,;HPS4,upstream_gene_variant,,ENST00000479064,;HPS4,upstream_gene_variant,,ENST00000483631,;SRRD,non_coding_transcript_exon_variant,,ENST00000477945,;HPS4,upstream_gene_variant,,ENST00000466781,;SRRD,upstream_gene_variant,,ENST00000471799,;HPS4,upstream_gene_variant,,ENST00000439453,;TFIP11,downstream_gene_variant,,ENST00000492137,;	T	ENSG00000100104	ENST00000215917	Transcript	synonymous_variant	446	432	144	Y	taC/taT	rs748081893	.	.	1	SRRD	HGNC	33910	protein_coding	YES	CCDS42995.1	ENSP00000215917	SRR1L_HUMAN	.	UPI00000723CF	.	.	.	3/7	.	Pfam_domain:PF07985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTACGGCAT	byFrequency	5	ESCA
ZNRF3	0	.	GRCh37	22	29451191	29451191	+	3'UTR	DEL	T	T	-	rs552661003	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1588delT	.	.	ENST00000544604	9/9	21	11	10	12	12	0	ZNRF3,3_prime_UTR_variant,,ENST00000332811,;ZNRF3,3_prime_UTR_variant,,ENST00000544604,;C22orf31,downstream_gene_variant,,ENST00000216071,;ZNRF3,downstream_gene_variant,,ENST00000406323,;ZNRF3,downstream_gene_variant,,ENST00000402174,;	-	ENSG00000183579	ENST00000544604	Transcript	3_prime_UTR_variant	4567	.	.	.	.	rs552661003	.	.	1	ZNRF3	HGNC	18126	protein_coding	YES	CCDS56225.1	ENSP00000443824	ZNRF3_HUMAN	.	UPI0000EE5944	.	.	.	9/9	.	.	A:0.0004	A:0.0008	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAAAATTTTTT	byFrequency|by1000G	2	ESCA
EWSR1	0	.	GRCh37	22	29693886	29693886	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1382delG	p.Gly461ValfsTer170	p.G461Vfs*170	ENST00000414183	14/18	58	49	9	21	21	0	EWSR1,frameshift_variant,p.Gly455ValfsTer170,ENST00000406548,;EWSR1,frameshift_variant,p.Gly461ValfsTer170,ENST00000414183,;EWSR1,frameshift_variant,p.Gly383ValfsTer170,ENST00000332050,;EWSR1,frameshift_variant,p.Gly456ValfsTer170,ENST00000397938,;EWSR1,frameshift_variant,p.Gly400ValfsTer170,ENST00000332035,;EWSR1,frameshift_variant,p.Gly418ValfsTer170,ENST00000331029,;EWSR1,frameshift_variant,p.Gly112ValfsTer81,ENST00000360091,;EWSR1,non_coding_transcript_exon_variant,,ENST00000490315,;EWSR1,non_coding_transcript_exon_variant,,ENST00000483629,;EWSR1,non_coding_transcript_exon_variant,,ENST00000469669,;EWSR1,non_coding_transcript_exon_variant,,ENST00000479135,;	-	ENSG00000182944	ENST00000414183	Transcript	frameshift_variant	1400	1379	460	R/X	cGg/cg	.	.	.	1	EWSR1	HGNC	3508	protein_coding	YES	CCDS13852.2	ENSP00000400142	EWS_HUMAN	.	UPI000006DE88	.	.	.	14/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23238:SF3,hmmpanther:PTHR23238,Gene3D:3.30.70.330,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTATGCGGGGTG	.	3	ESCA
EWSR1	0	.	GRCh37	22	29694848	29694848	+	Missense_Mutation	SNP	G	G	A	rs535564625	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1558G>A	p.Val520Ile	p.V520I	ENST00000414183	15/18	27	15	12	16	16	0	EWSR1,missense_variant,p.Val514Ile,ENST00000406548,;EWSR1,missense_variant,p.Val520Ile,ENST00000414183,;EWSR1,missense_variant,p.Val442Ile,ENST00000332050,;EWSR1,missense_variant,p.Val515Ile,ENST00000397938,;EWSR1,missense_variant,p.Val459Ile,ENST00000332035,;EWSR1,missense_variant,p.Val477Ile,ENST00000331029,;EWSR1,missense_variant,p.Val171Ile,ENST00000360091,;EWSR1,non_coding_transcript_exon_variant,,ENST00000490315,;EWSR1,non_coding_transcript_exon_variant,,ENST00000483629,;EWSR1,non_coding_transcript_exon_variant,,ENST00000469669,;EWSR1,non_coding_transcript_exon_variant,,ENST00000479135,;	A	ENSG00000182944	ENST00000414183	Transcript	missense_variant	1579	1558	520	V/I	Gtc/Atc	rs535564625	.	.	1	EWSR1	HGNC	3508	protein_coding	YES	CCDS13852.2	ENSP00000400142	EWS_HUMAN	.	UPI000006DE88	.	tolerated(0.27)	unknown(0)	15/18	.	hmmpanther:PTHR23238:SF3,hmmpanther:PTHR23238,Gene3D:1n0zA00,Superfamily_domains:SSF90209	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GAAACGTCCAG	by1000G	3	ESCA
TCN2	0	.	GRCh37	22	31011717	31011717	+	Missense_Mutation	SNP	G	G	A	rs770684965	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.883G>A	p.Val295Ile	p.V295I	ENST00000215838	6/9	51	33	18	27	27	0	TCN2,missense_variant,p.Val268Ile,ENST00000407817,;TCN2,missense_variant,p.Val291Ile,ENST00000405742,;TCN2,missense_variant,p.Val295Ile,ENST00000215838,;TCN2,downstream_gene_variant,,ENST00000423350,;TCN2,3_prime_UTR_variant,,ENST00000450638,;TCN2,non_coding_transcript_exon_variant,,ENST00000493542,;TCN2,non_coding_transcript_exon_variant,,ENST00000471659,;	A	ENSG00000185339	ENST00000215838	Transcript	missense_variant	1377	883	295	V/I	Gtt/Att	rs770684965,COSM4103473	.	.	1	TCN2	HGNC	11653	protein_coding	YES	CCDS13881.1	ENSP00000215838	TCO2_HUMAN	.	UPI0000167BDB	.	tolerated(0.13)	benign(0.365)	6/9	.	hmmpanther:PTHR10559,hmmpanther:PTHR10559:SF14,Pfam_domain:PF01122	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGTTCTG	byFrequency	5	ESCA
RASD2	0	.	GRCh37	22	35949225	35949225	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1146G>A	.	.	ENST00000216127	3/3	9	4	5	17	17	0	RASD2,3_prime_UTR_variant,,ENST00000216127,;	A	ENSG00000100302	ENST00000216127	Transcript	3_prime_UTR_variant	2589	.	.	.	.	.	.	.	1	RASD2	HGNC	18229	protein_coding	YES	CCDS13916.1	ENSP00000216127	RHES_HUMAN	.	UPI000004980A	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGGGTCCCC	.	2	ESCA
MYH9	0	.	GRCh37	22	36684430	36684430	+	Silent	SNP	G	G	A	rs201223994	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4800C>T	p.%3D	p.D1600D	ENST00000216181	34/41	73	61	11	18	18	0	MYH9,synonymous_variant,p.%3D,ENST00000216181,;MYH9,upstream_gene_variant,,ENST00000475726,;MYH9,upstream_gene_variant,,ENST00000486218,;	A	ENSG00000100345	ENST00000216181	Transcript	synonymous_variant	5031	4800	1600	D	gaC/gaT	rs201223994,COSM3149572	.	.	-1	MYH9	HGNC	7579	protein_coding	YES	CCDS13927.1	ENSP00000216181	MYH9_HUMAN	Q9UMJ0_HUMAN,B1AH99_HUMAN	UPI000012FB80	.	.	.	34/41	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF317,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCGTCCTC	byFrequency|byCluster|by1000G	5	ESCA
CACNG2	0	.	GRCh37	22	36960232	36960233	+	3'UTR	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*165dupA	.	.	ENST00000300105	4/4	69	59	10	39	39	0	CACNG2,3_prime_UTR_variant,,ENST00000300105,;RP5-1119A7.17,upstream_gene_variant,,ENST00000562756,;	T	ENSG00000166862	ENST00000300105	Transcript	3_prime_UTR_variant	2119-2120	.	.	.	.	.	.	.	-1	CACNG2	HGNC	1406	protein_coding	YES	CCDS13931.1	ENSP00000300105	CCG2_HUMAN	.	UPI00001272AC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTCTCTTTTT	.	2	ESCA
SOX10	0	.	GRCh37	22	38373971	38373971	+	Silent	SNP	G	G	A	rs143057951	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600C>T	p.%3D	p.T200T	ENST00000396884	3/4	54	39	15	34	34	0	SOX10,synonymous_variant,p.%3D,ENST00000427770,;SOX10,synonymous_variant,p.%3D,ENST00000360880,;SOX10,synonymous_variant,p.%3D,ENST00000396884,;SOX10,synonymous_variant,p.%3D,ENST00000446929,;POLR2F,intron_variant,,ENST00000407936,;POLR2F,intron_variant,,ENST00000405557,;SOX10,downstream_gene_variant,,ENST00000470555,;POLR2F,intron_variant,,ENST00000443002,;	A	ENSG00000100146	ENST00000396884	Transcript	synonymous_variant	883	600	200	T	acC/acT	rs143057951,COSM1266482	.	.	-1	SOX10	HGNC	11190	protein_coding	YES	CCDS13964.1	ENSP00000380093	SOX10_HUMAN	A6PVD3_HUMAN	UPI00001362AA	.	.	.	3/4	.	hmmpanther:PTHR10270:SF106,hmmpanther:PTHR10270	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGCGGTCCC	byFrequency|byCluster	5	ESCA
SLC16A8	0	.	GRCh37	22	38474461	38474461	+	Silent	SNP	G	G	A	rs377373294	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1449C>T	p.%3D	p.S483S	ENST00000320521	5/5	51	40	11	18	18	0	SLC16A8,synonymous_variant,p.%3D,ENST00000320521,;SLC16A8,downstream_gene_variant,,ENST00000427592,;PICK1,downstream_gene_variant,,ENST00000404072,;PICK1,downstream_gene_variant,,ENST00000356976,;RP5-1039K5.13,upstream_gene_variant,,ENST00000445483,;SLC16A8,non_coding_transcript_exon_variant,,ENST00000469516,;PICK1,downstream_gene_variant,,ENST00000484021,;	A	ENSG00000100156	ENST00000320521	Transcript	synonymous_variant	1558	1449	483	S	agC/agT	rs377373294	.	.	-1	SLC16A8	HGNC	16270	protein_coding	YES	CCDS13966.1	ENSP00000321735	MOT3_HUMAN	B0QYL4_HUMAN	UPI000012F3C8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	T:0.0018	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGCGCTGAG	byFrequency|byCluster	5	ESCA
TOMM22	0	.	GRCh37	22	39078977	39078977	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330A>G	p.%3D	p.Q110Q	ENST00000216034	3/4	107	85	22	54	54	0	TOMM22,synonymous_variant,p.%3D,ENST00000216034,;JOSD1,downstream_gene_variant,,ENST00000545590,;JOSD1,downstream_gene_variant,,ENST00000216039,;RP3-508I15.9,upstream_gene_variant,,ENST00000444381,;RP3-508I15.9,upstream_gene_variant,,ENST00000431924,;RP3-508I15.9,upstream_gene_variant,,ENST00000412067,;TOMM22,non_coding_transcript_exon_variant,,ENST00000492561,;JOSD1,downstream_gene_variant,,ENST00000482442,;	G	ENSG00000100216	ENST00000216034	Transcript	synonymous_variant	361	330	110	Q	caA/caG	.	.	.	1	TOMM22	HGNC	18002	protein_coding	YES	CCDS13975.1	ENSP00000216034	TOM22_HUMAN	Q549C5_HUMAN	UPI0000040C1F	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12504,hmmpanther:PTHR12504:SF0,Pfam_domain:PF04281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCAACAGCA	.	5	ESCA
NPTXR	0	.	GRCh37	22	39218069	39218069	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*545C>G	.	.	ENST00000333039	5/5	147	112	35	59	57	1	NPTXR,3_prime_UTR_variant,,ENST00000333039,;	C	ENSG00000221890	ENST00000333039	Transcript	3_prime_UTR_variant	2172	.	.	.	.	.	.	.	-1	NPTXR	HGNC	7954	protein_coding	YES	CCDS33647.1	ENSP00000327545	NPTXR_HUMAN	.	UPI00001B0258	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTGGGGGGGGG	.	2	ESCA
TNRC6B	0	.	GRCh37	22	40722032	40722032	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2796delA	.	.	ENST00000454349	23/23	21	11	10	11	11	0	TNRC6B,3_prime_UTR_variant,,ENST00000454349,;TNRC6B,3_prime_UTR_variant,,ENST00000301923,;TNRC6B,3_prime_UTR_variant,,ENST00000335727,;TNRC6B,downstream_gene_variant,,ENST00000446273,;TNRC6B,downstream_gene_variant,,ENST00000402203,;	-	ENSG00000100354	ENST00000454349	Transcript	3_prime_UTR_variant	8500	.	.	.	.	.	.	.	1	TNRC6B	HGNC	29190	protein_coding	YES	CCDS54533.1	ENSP00000401946	TNR6B_HUMAN	.	UPI00017A6F19	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACTTTAAAAAA	.	2	ESCA
TCF20	0	.	GRCh37	22	42608248	42608248	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3064C>T	p.Arg1022Trp	p.R1022W	ENST00000359486	1/5	63	55	8	36	36	0	TCF20,missense_variant,p.Arg1022Trp,ENST00000335626,;TCF20,missense_variant,p.Arg1022Trp,ENST00000359486,;TCF20,upstream_gene_variant,,ENST00000404876,;TCF20,downstream_gene_variant,,ENST00000515426,;	A	ENSG00000100207	ENST00000359486	Transcript	missense_variant	3201	3064	1022	R/W	Cgg/Tgg	COSM4104557	.	.	-1	TCF20	HGNC	11631	protein_coding	YES	CCDS14033.1	ENSP00000352463	TCF20_HUMAN	I3L1M7_HUMAN	UPI00001A95D9	.	.	probably_damaging(0.999)	1/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14955,hmmpanther:PTHR14955:SF7	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCCGCCCAG	.	2	ESCA
NFAM1	0	.	GRCh37	22	42776810	42776811	+	3'UTR	INS	-	-	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4356_*4357insC	.	.	ENST00000329021	6/6	30	15	15	15	15	0	NFAM1,3_prime_UTR_variant,,ENST00000329021,;	G	ENSG00000235568	ENST00000329021	Transcript	3_prime_UTR_variant	5207-5208	.	.	.	.	.	.	.	-1	NFAM1	HGNC	29872	protein_coding	YES	CCDS14034.1	ENSP00000333680	NFAM1_HUMAN	.	UPI00000701BF	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAAAAAGAGA	.	2	ESCA
RRP7A	0	.	GRCh37	22	42910203	42910203	+	Silent	SNP	G	G	A	rs748642666	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.666C>T	p.%3D	p.S222S	ENST00000323013	6/7	86	60	25	41	41	0	RRP7A,synonymous_variant,p.%3D,ENST00000323013,;SERHL,downstream_gene_variant,,ENST00000359906,;SERHL,downstream_gene_variant,,ENST00000421475,;RRP7A,downstream_gene_variant,,ENST00000483303,;RRP7A,downstream_gene_variant,,ENST00000416699,;SERHL,downstream_gene_variant,,ENST00000455578,;	A	ENSG00000189306	ENST00000323013	Transcript	synonymous_variant	682	666	222	S	agC/agT	rs748642666,COSM1327196	.	.	-1	RRP7A	HGNC	24286	protein_coding	YES	CCDS14036.1	ENSP00000321449	RRP7A_HUMAN	.	UPI000013C6B7	.	.	.	6/7	.	Low_complexity_(Seg):seg,Pfam_domain:PF12923,hmmpanther:PTHR13191	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R224W|c.670C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCAAGCTGGC	.	5	ESCA
TTLL12	0	.	GRCh37	22	43570300	43570300	+	Missense_Mutation	SNP	C	C	G	rs778703258	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1144G>C	p.Glu382Gln	p.E382Q	ENST00000216129	8/14	48	29	19	14	14	0	TTLL12,missense_variant,p.Glu382Gln,ENST00000216129,;TTLL12,upstream_gene_variant,,ENST00000494035,;TTLL12,non_coding_transcript_exon_variant,,ENST00000484118,;TTLL12,upstream_gene_variant,,ENST00000484711,;	G	ENSG00000100304	ENST00000216129	Transcript	missense_variant	1208	1144	382	E/Q	Gag/Cag	rs778703258	.	.	-1	TTLL12	HGNC	28974	protein_coding	YES	CCDS14047.1	ENSP00000216129	TTL12_HUMAN	.	UPI000013938D	.	tolerated(0.28)	benign(0.069)	8/14	.	PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF13,Pfam_domain:PF03133	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGGGGC	.	5	ESCA
PHF21B	0	.	GRCh37	22	45312251	45312251	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473G>A	p.Ser158Asn	p.S158N	ENST00000313237	4/13	43	30	13	25	25	0	PHF21B,missense_variant,p.Ser146Asn,ENST00000420689,;PHF21B,missense_variant,p.Ser146Asn,ENST00000447824,;PHF21B,missense_variant,p.Ser158Asn,ENST00000396103,;PHF21B,missense_variant,p.Ser158Asn,ENST00000313237,;PHF21B,missense_variant,p.Ser146Asn,ENST00000404079,;PHF21B,5_prime_UTR_variant,,ENST00000414269,;PHF21B,5_prime_UTR_variant,,ENST00000403565,;PHF21B,non_coding_transcript_exon_variant,,ENST00000490679,;PHF21B,downstream_gene_variant,,ENST00000460507,;PHF21B,downstream_gene_variant,,ENST00000474327,;	T	ENSG00000056487	ENST00000313237	Transcript	missense_variant	624	473	158	S/N	aGc/aAc	.	.	.	-1	PHF21B	HGNC	25161	protein_coding	YES	CCDS14061.1	ENSP00000324403	PF21B_HUMAN	B3KTL5_HUMAN	UPI0000072111	.	tolerated_low_confidence(0.13)	possibly_damaging(0.488)	4/13	.	hmmpanther:PTHR24102:SF1,hmmpanther:PTHR24102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A160A|c.480C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTGCTGGGG	.	5	ESCA
PKDREJ	0	.	GRCh37	22	46655330	46655330	+	Missense_Mutation	SNP	C	C	T	rs558518913	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3890G>A	p.Arg1297His	p.R1297H	ENST00000253255	1/1	52	31	21	54	54	0	PKDREJ,missense_variant,p.Arg1297His,ENST00000253255,;	T	ENSG00000130943	ENST00000253255	Transcript	missense_variant	3890	3890	1297	R/H	cGt/cAt	rs558518913	.	.	-1	PKDREJ	HGNC	9015	protein_coding	YES	CCDS14073.1	ENSP00000253255	PKDRE_HUMAN	A6MW40_HUMAN	UPI0000031D01	.	deleterious(0.05)	possibly_damaging(0.8)	1/1	.	PROSITE_profiles:PS50095,hmmpanther:PTHR10877:SF113,hmmpanther:PTHR10877,Gene3D:2.60.60.20,Pfam_domain:PF01477,SMART_domains:SM00308,Superfamily_domains:SSF49723	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACACGGATG	by1000G	5	ESCA
CELSR1	0	.	GRCh37	22	46931227	46931227	+	Frame_Shift_Del	DEL	C	C	-	rs746621407	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1841delG	p.Gly614AlafsTer54	p.G614Afs*54	ENST00000262738	1/35	114	76	38	24	24	0	CELSR1,frameshift_variant,p.Gly614AlafsTer54,ENST00000262738,;CELSR1,frameshift_variant,p.Gly614AlafsTer54,ENST00000395964,;CELSR1,upstream_gene_variant,,ENST00000454637,;CELSR1,upstream_gene_variant,,ENST00000497509,;	-	ENSG00000075275	ENST00000262738	Transcript	frameshift_variant	1841	1841	614	G/X	gGc/gc	rs746621407,COSM1416908	.	.	-1	CELSR1	HGNC	1850	protein_coding	YES	CCDS14076.1	ENSP00000262738	CELR1_HUMAN	Q8NDT0_HUMAN	UPI0000040648	.	.	.	1/35	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24026,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G614fs*54|c.1841delG|4	INDELOCATOR*|VARSCANI*|PINDEL	CTGCCGCCCCCC	.	3	ESCA
GRAMD4	0	.	GRCh37	22	47062721	47062721	+	Splice_Site	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813delG	p.Trp272GlyfsTer22	p.X271_splice	ENST00000406902	.	72	54	18	30	30	0	GRAMD4,splice_acceptor_variant,p.Trp95GlyfsTer22,ENST00000456069,;GRAMD4,splice_acceptor_variant,p.Trp272GlyfsTer22,ENST00000406902,;GRAMD4,splice_acceptor_variant,p.Trp272GlyfsTer22,ENST00000361034,;	-	ENSG00000075240	ENST00000406902	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	GRAMD4	HGNC	29113	protein_coding	YES	CCDS33672.1	ENSP00000385689	GRAM4_HUMAN	.	UPI0000161A59	.	.	.	.	9/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCGCCAGGGGGT	.	3	ESCA
WI2-81516E3.1	0	.	GRCh37	22	49290904	49290904	+	RNA	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.792delG	.	.	ENST00000380981	3/4	67	45	22	32	32	0	WI2-81516E3.1,non_coding_transcript_exon_variant,,ENST00000380981,;	-	ENSG00000205632	ENST00000380981	Transcript	non_coding_transcript_exon_variant	786	.	.	.	.	.	.	.	1	WI2-81516E3.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGATTGGGGGG	.	3	ESCA
ZBED4	0	.	GRCh37	22	50278015	50278017	+	In_Frame_Del	DEL	CTC	CTC	-	rs759236299	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.708_710delCTC	p.Ser237del	p.S237del	ENST00000216268	2/2	62	54	7	18	18	0	ZBED4,inframe_deletion,p.Ser237del,ENST00000216268,;	-	ENSG00000100426	ENST00000216268	Transcript	inframe_deletion	1182-1184	705-707	235-236	IS/I	atCTCc/atc	rs759236299	.	.	1	ZBED4	HGNC	20721	protein_coding	YES	CCDS33677.1	ENSP00000216268	ZBED4_HUMAN	.	UPI000013C6DB	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23272,hmmpanther:PTHR23272:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAAATCTCCTCTG	byFrequency	2	ESCA
ZBED4	0	.	GRCh37	22	50281996	50281996	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1170A>G	.	.	ENST00000216268	2/2	71	50	21	40	40	0	ZBED4,3_prime_UTR_variant,,ENST00000216268,;	G	ENSG00000100426	ENST00000216268	Transcript	3_prime_UTR_variant	5163	.	.	.	.	.	.	.	1	ZBED4	HGNC	20721	protein_coding	YES	CCDS33677.1	ENSP00000216268	ZBED4_HUMAN	.	UPI000013C6DB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTACGTAC	.	5	ESCA
TUBGCP6	0	.	GRCh37	22	50656444	50656444	+	Frame_Shift_Del	DEL	C	C	-	rs769880509	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5271delG	p.Pro1759LeufsTer33	p.P1759Lfs*33	ENST00000248846	24/25	56	34	22	24	24	0	TUBGCP6,frameshift_variant,p.Pro428LeufsTer33,ENST00000425018,;TUBGCP6,frameshift_variant,p.Pro1759LeufsTer33,ENST00000248846,;TUBGCP6,3_prime_UTR_variant,,ENST00000439308,;SELO,downstream_gene_variant,,ENST00000380903,;TUBGCP6,non_coding_transcript_exon_variant,,ENST00000491449,;SELO,downstream_gene_variant,,ENST00000492092,;TUBGCP6,downstream_gene_variant,,ENST00000473946,;TUBGCP6,downstream_gene_variant,,ENST00000489511,;TUBGCP6,non_coding_transcript_exon_variant,,ENST00000498611,;	-	ENSG00000128159	ENST00000248846	Transcript	frameshift_variant	5376	5271	1757	G/X	ggG/gg	rs769880509,COSM1566393	.	.	-1	TUBGCP6	HGNC	18127	protein_coding	YES	CCDS14087.1	ENSP00000248846	GCP6_HUMAN	.	UPI000013CC55	.	.	.	24/25	.	hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF32	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGGGGCCCCCA	.	3	ESCA
LMF2	0	.	GRCh37	22	50944625	50944625	+	Missense_Mutation	SNP	C	C	T	rs202067766	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.613G>A	p.Glu205Lys	p.E205K	ENST00000474879	5/14	97	66	30	60	60	0	LMF2,missense_variant,p.Glu180Lys,ENST00000216080,;LMF2,missense_variant,p.Glu205Lys,ENST00000380796,;LMF2,missense_variant,p.Glu205Lys,ENST00000474879,;NCAPH2,upstream_gene_variant,,ENST00000523045,;NCAPH2,upstream_gene_variant,,ENST00000395701,;NCAPH2,upstream_gene_variant,,ENST00000420993,;NCAPH2,upstream_gene_variant,,ENST00000299821,;NCAPH2,upstream_gene_variant,,ENST00000395698,;LMF2,non_coding_transcript_exon_variant,,ENST00000505981,;LMF2,non_coding_transcript_exon_variant,,ENST00000514938,;LMF2,downstream_gene_variant,,ENST00000507607,;NCAPH2,upstream_gene_variant,,ENST00000418794,;NCAPH2,upstream_gene_variant,,ENST00000518394,;LMF2,upstream_gene_variant,,ENST00000504717,;	T	ENSG00000100258	ENST00000474879	Transcript	missense_variant	629	613	205	E/K	Gag/Aag	rs202067766	.	.	-1	LMF2	HGNC	25096	protein_coding	YES	CCDS14093.2	ENSP00000424381	LMF2_HUMAN	.	UPI0000071DF9	.	deleterious(0)	probably_damaging(0.973)	5/14	.	hmmpanther:PTHR14463,hmmpanther:PTHR14463:SF5,Pfam_domain:PF06762	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	G:0	G:0.0004	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCGTAGT	byCluster|by1000G	5	ESCA
SHANK3	0	.	GRCh37	22	51171214	51171214	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1484delA	.	.	ENST00000262795	23/23	51	36	15	28	28	0	SHANK3,3_prime_UTR_variant,,ENST00000262795,;SHANK3,3_prime_UTR_variant,,ENST00000445220,;SHANK3,3_prime_UTR_variant,,ENST00000414786,;AC000036.4,downstream_gene_variant,,ENST00000449652,;	-	ENSG00000251322	ENST00000262795	Transcript	3_prime_UTR_variant	6718	.	.	.	.	.	.	.	1	SHANK3	HGNC	14294	protein_coding	YES	.	ENSP00000442518	.	F8TCV3_HUMAN,F2Z3L0_HUMAN	UPI0000DD85FB	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAAAATAAAAAA	.	2	ESCA
NPAS2	0	.	GRCh37	2	101598834	101598834	+	Missense_Mutation	SNP	G	G	A	rs756916445	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1624G>A	p.Val542Ile	p.V542I	ENST00000335681	16/21	36	19	16	23	23	0	NPAS2,missense_variant,p.Val41Ile,ENST00000433408,;NPAS2,missense_variant,p.Val542Ile,ENST00000335681,;NPAS2,missense_variant,p.Val607Ile,ENST00000542504,;NPAS2,missense_variant,p.Val141Ile,ENST00000450763,;NPAS2,non_coding_transcript_exon_variant,,ENST00000471974,;NPAS2,non_coding_transcript_exon_variant,,ENST00000474550,;	A	ENSG00000170485	ENST00000335681	Transcript	missense_variant	1909	1624	542	V/I	Gtc/Atc	rs756916445	.	.	1	NPAS2	HGNC	7895	protein_coding	YES	CCDS2048.1	ENSP00000338283	NPAS2_HUMAN	A2I2P5_HUMAN	UPI0000163B27	.	tolerated(0.39)	benign(0.005)	16/21	.	hmmpanther:PTHR23042:SF4,hmmpanther:PTHR23042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAACGTCCAG	.	5	ESCA
MAP4K4	0	.	GRCh37	2	102456423	102456423	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916A>G	p.Ile306Val	p.I306V	ENST00000347699	10/30	54	33	21	40	40	0	MAP4K4,missense_variant,p.Ile306Val,ENST00000347699,;MAP4K4,missense_variant,p.Ile306Val,ENST00000425019,;MAP4K4,missense_variant,p.Ile306Val,ENST00000350198,;MAP4K4,missense_variant,p.Ile306Val,ENST00000413150,;MAP4K4,missense_variant,p.Ile46Val,ENST00000421882,;MAP4K4,missense_variant,p.Ile286Val,ENST00000350878,;MAP4K4,missense_variant,p.Ile268Val,ENST00000417294,;MAP4K4,missense_variant,p.Ile306Val,ENST00000324219,;MAP4K4,intron_variant,,ENST00000456652,;MAP4K4,intron_variant,,ENST00000302217,;MAP4K4,non_coding_transcript_exon_variant,,ENST00000476609,;	G	ENSG00000071054	ENST00000347699	Transcript	missense_variant	916	916	306	I/V	Ata/Gta	.	.	.	1	MAP4K4	HGNC	6866	protein_coding	YES	CCDS56130.1	ENSP00000314363	M4K4_HUMAN	Q53TW0_HUMAN,E7ETN6_HUMAN	UPI00000747E2	.	deleterious_low_confidence(0)	unknown(0)	10/30	.	hmmpanther:PTHR24361:SF225,hmmpanther:PTHR24361,Gene3D:1.10.510.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATATAGAT	.	5	ESCA
ATP6V1C2	0	.	GRCh37	2	10923488	10923488	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99A>T	.	.	ENST00000272238	14/14	31	20	11	21	21	0	ATP6V1C2,3_prime_UTR_variant,,ENST00000381661,;ATP6V1C2,3_prime_UTR_variant,,ENST00000272238,;PDIA6,downstream_gene_variant,,ENST00000404371,;PDIA6,downstream_gene_variant,,ENST00000272227,;PDIA6,downstream_gene_variant,,ENST00000540494,;PDIA6,downstream_gene_variant,,ENST00000404824,;PDIA6,downstream_gene_variant,,ENST00000381611,;ATP6V1C2,downstream_gene_variant,,ENST00000480289,;	T	ENSG00000143882	ENST00000272238	Transcript	3_prime_UTR_variant	1492	.	.	.	.	.	.	.	1	ATP6V1C2	HGNC	18264	protein_coding	YES	CCDS42653.1	ENSP00000272238	VATC2_HUMAN	.	UPI0000208E71	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTAAGATCTTT	.	2	ESCA
MARCO	0	.	GRCh37	2	119739053	119739053	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835A>G	p.Lys279Glu	p.K279E	ENST00000327097	9/17	34	28	6	19	19	0	MARCO,missense_variant,p.Lys279Glu,ENST00000327097,;MARCO,missense_variant,p.Lys201Glu,ENST00000541757,;	G	ENSG00000019169	ENST00000327097	Transcript	missense_variant	970	835	279	K/E	Aaa/Gaa	.	.	.	1	MARCO	HGNC	6895	protein_coding	YES	CCDS2124.1	ENSP00000318916	MARCO_HUMAN	Q4ZG40_HUMAN,C9JKT8_HUMAN,B4DW79_HUMAN,B4DLJ6_HUMAN	UPI0000000DF8	.	deleterious(0.01)	probably_damaging(0.973)	9/17	.	hmmpanther:PTHR24021:SF16,hmmpanther:PTHR24021,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F282F|c.846C>T|3	RADIA|MUTECT|MUSE	GGAGTAAAGGT	.	3	ESCA
RALB	0	.	GRCh37	2	121052255	121052255	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1427delT	.	.	ENST00000272519	5/5	47	31	16	48	48	0	RALB,3_prime_UTR_variant,,ENST00000404963,;RALB,3_prime_UTR_variant,,ENST00000272519,;RALB,downstream_gene_variant,,ENST00000420510,;RALB,downstream_gene_variant,,ENST00000447591,;RALB,downstream_gene_variant,,ENST00000412383,;RALB,downstream_gene_variant,,ENST00000474855,;RALB,downstream_gene_variant,,ENST00000470417,;RALB,downstream_gene_variant,,ENST00000431732,;	-	ENSG00000144118	ENST00000272519	Transcript	3_prime_UTR_variant	2310	.	.	.	.	.	.	.	1	RALB	HGNC	9840	protein_coding	YES	CCDS2131.1	ENSP00000272519	RALB_HUMAN	C9JYR1_HUMAN,C9J6B1_HUMAN	UPI000000124F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATGGGCTTTTTT	.	2	ESCA
CLASP1	0	.	GRCh37	2	122125240	122125240	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3810A>G	p.%3D	p.S1270S	ENST00000263710	35/40	118	79	38	62	62	0	CLASP1,synonymous_variant,p.%3D,ENST00000397587,;CLASP1,synonymous_variant,p.%3D,ENST00000263710,;CLASP1,synonymous_variant,p.%3D,ENST00000541859,;CLASP1,synonymous_variant,p.%3D,ENST00000455322,;CLASP1,synonymous_variant,p.%3D,ENST00000541377,;CLASP1,synonymous_variant,p.%3D,ENST00000545861,;CLASP1,synonymous_variant,p.%3D,ENST00000409078,;CLASP1,3_prime_UTR_variant,,ENST00000452274,;CLASP1,non_coding_transcript_exon_variant,,ENST00000472776,;	C	ENSG00000074054	ENST00000263710	Transcript	synonymous_variant	4200	3810	1270	S	tcA/tcG	.	.	.	-1	CLASP1	HGNC	17088	protein_coding	YES	.	ENSP00000263710	CLAP1_HUMAN	C9JP76_HUMAN,C9J151_HUMAN	UPI00001A8BFF	.	.	.	35/40	.	hmmpanther:PTHR21567:SF28,hmmpanther:PTHR21567,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A1272S|c.3814G>T|10	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCTGAGTA	.	5	ESCA
CNTNAP5	0	.	GRCh37	2	125547549	125547549	+	Missense_Mutation	SNP	G	G	A	rs780606060	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2820G>A	p.Met940Ile	p.M940I	ENST00000431078	18/24	42	32	9	42	42	0	CNTNAP5,missense_variant,p.Met940Ile,ENST00000431078,;	A	ENSG00000155052	ENST00000431078	Transcript	missense_variant	3184	2820	940	M/I	atG/atA	rs780606060	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	deleterious(0.04)	benign(0)	18/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Gene3D:2.60.120.200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATGGACCT	.	5	ESCA
BIN1	0	.	GRCh37	2	127825800	127825801	+	Frame_Shift_Ins	INS	-	-	G	rs746044582	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550dupC	p.Gln184ProfsTer16	p.Q184Pfs*16	ENST00000316724	7/19	58	33	24	19	19	0	BIN1,frameshift_variant,p.Gln184ProfsTer16,ENST00000351659,;BIN1,frameshift_variant,p.Gln184ProfsTer16,ENST00000316724,;BIN1,frameshift_variant,p.Gln184ProfsTer16,ENST00000357970,;BIN1,intron_variant,,ENST00000393041,;BIN1,intron_variant,,ENST00000393040,;BIN1,intron_variant,,ENST00000348750,;BIN1,intron_variant,,ENST00000346226,;BIN1,intron_variant,,ENST00000409400,;BIN1,intron_variant,,ENST00000259238,;BIN1,intron_variant,,ENST00000352848,;BIN1,intron_variant,,ENST00000376113,;BIN1,upstream_gene_variant,,ENST00000484253,;BIN1,upstream_gene_variant,,ENST00000466111,;	G	ENSG00000136717	ENST00000316724	Transcript	frameshift_variant	962-963	550-551	184	Q/PX	cag/cCag	rs746044582	.	.	-1	BIN1	HGNC	1052	protein_coding	YES	CCDS2138.1	ENSP00000316779	BIN1_HUMAN	.	UPI0000001303	.	.	.	7/19	.	PROSITE_profiles:PS51021,hmmpanther:PTHR10321:SF24,hmmpanther:PTHR10321,Pfam_domain:PF03114,SMART_domains:SM00721	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACCACTGGGGG	byFrequency	2	ESCA
MAP3K2	0	.	GRCh37	2	128088010	128088017	+	Frame_Shift_Del	DEL	CATATGAA	CATATGAA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CATATGAA	CATATGAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329_336delTTCATATG	p.Ile110LysfsTer17	p.I110Kfs*17	ENST00000409947	6/17	51	30	21	40	40	0	MAP3K2,frameshift_variant,p.Ile110LysfsTer17,ENST00000409947,;MAP3K2,frameshift_variant,p.Ile110LysfsTer17,ENST00000344908,;	-	ENSG00000169967	ENST00000409947	Transcript	frameshift_variant	612-619	329-336	110-112	IHM/X	aTTCATATG/a	.	.	.	-1	MAP3K2	HGNC	6854	protein_coding	YES	CCDS46404.1	ENSP00000387246	M3K2_HUMAN	Q96K88_HUMAN,F8W6K3_HUMAN	UPI0000208C78	.	.	.	6/17	.	hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF37,Gene3D:3.10.20.240,Pfam_domain:PF00564,SMART_domains:SM00666,Superfamily_domains:SSF54277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTCTTCATATGAATACTA	.	3	ESCA
TRIB2	0	.	GRCh37	2	12881399	12881399	+	3'UTR	DEL	A	A	-	rs535207032	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*488delA	.	.	ENST00000155926	3/3	41	28	12	20	20	0	TRIB2,3_prime_UTR_variant,,ENST00000381465,;TRIB2,3_prime_UTR_variant,,ENST00000155926,;MIR3125,downstream_gene_variant,,ENST00000579927,;	-	ENSG00000071575	ENST00000155926	Transcript	3_prime_UTR_variant	2930	.	.	.	.	rs535207032	.	.	1	TRIB2	HGNC	30809	protein_coding	YES	CCDS1683.1	ENSP00000155926	TRIB2_HUMAN	F8WA18_HUMAN	UPI0000051C55	.	.	.	3/3	.	.	-:0.0032	-:0.0121	-:0	.	-:0	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCACTTAAAAAA	byFrequency|byCluster|by1000G	2	ESCA
UGGT1	0	.	GRCh37	2	128900742	128900742	+	Silent	SNP	G	G	A	rs548464056	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1794G>A	p.%3D	p.P598P	ENST00000259253	17/41	93	67	26	65	65	0	UGGT1,synonymous_variant,p.%3D,ENST00000259253,;UGGT1,synonymous_variant,p.%3D,ENST00000375990,;UGGT1,3_prime_UTR_variant,,ENST00000376723,;UGGT1,3_prime_UTR_variant,,ENST00000438277,;UGGT1,upstream_gene_variant,,ENST00000488439,;AC108059.4,upstream_gene_variant,,ENST00000411629,;	A	ENSG00000136731	ENST00000259253	Transcript	synonymous_variant	1841	1794	598	P	ccG/ccA	rs548464056	.	.	1	UGGT1	HGNC	15663	protein_coding	YES	CCDS2154.1	ENSP00000259253	UGGG1_HUMAN	.	UPI00000707D8	.	.	.	17/41	.	hmmpanther:PTHR11226:SF3,hmmpanther:PTHR11226	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCCGTATGT	by1000G	5	ESCA
RAB6C	0	.	GRCh37	2	130737406	130737406	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-283G>A	.	.	ENST00000410061	1/1	109	85	24	34	34	0	RAB6C,5_prime_UTR_variant,,ENST00000410061,;RAB6C-AS1,intron_variant,,ENST00000412425,;	A	ENSG00000222014	ENST00000410061	Transcript	5_prime_UTR_variant	172	.	.	.	.	.	.	.	1	RAB6C	HGNC	16525	protein_coding	YES	CCDS46408.1	ENSP00000387307	RAB6C_HUMAN	.	UPI00001AF8C6	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAAGCACAC	.	5	ESCA
TUBA3D	0	.	GRCh37	2	132236889	132236889	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235C>T	p.Arg79Cys	p.R79C	ENST00000321253	3/5	66	56	9	40	40	0	TUBA3D,missense_variant,p.Arg79Cys,ENST00000321253,;MZT2A,downstream_gene_variant,,ENST00000309451,;TUBA3D,non_coding_transcript_exon_variant,,ENST00000409047,;MZT2A,downstream_gene_variant,,ENST00000410036,;MZT2A,intron_variant,,ENST00000445782,;MZT2A,intron_variant,,ENST00000427024,;	T	ENSG00000075886	ENST00000321253	Transcript	missense_variant	342	235	79	R/C	Cgc/Tgc	.	.	.	1	TUBA3D	HGNC	24071	protein_coding	YES	CCDS33290.1	ENSP00000326042	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	deleterious_low_confidence(0.02)	benign(0.019)	3/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AAGTGCGCACA	.	3	ESCA
NCKAP5	0	.	GRCh37	2	133489420	133489420	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5333A>C	p.Asp1778Ala	p.D1778A	ENST00000409261	17/20	77	51	26	35	35	0	NCKAP5,missense_variant,p.Asp459Ala,ENST00000409213,;NCKAP5,missense_variant,p.Asp1778Ala,ENST00000409261,;NCKAP5,missense_variant,p.Asp459Ala,ENST00000405974,;NCKAP5,missense_variant,p.Asp1778Ala,ENST00000317721,;NCKAP5,downstream_gene_variant,,ENST00000473859,;	G	ENSG00000176771	ENST00000409261	Transcript	missense_variant	5707	5333	1778	D/A	gAc/gCc	.	.	.	-1	NCKAP5	HGNC	29847	protein_coding	YES	CCDS46418.1	ENSP00000387128	NCKP5_HUMAN	C9JYL7_HUMAN	UPI0000E07A3F	.	deleterious(0.03)	probably_damaging(0.917)	17/20	.	hmmpanther:PTHR21740:SF0,hmmpanther:PTHR21740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCGTCTGTG	.	5	ESCA
NCKAP5	0	.	GRCh37	2	133539753	133539753	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4631A>T	p.Asn1544Ile	p.N1544I	ENST00000409261	14/20	35	30	5	31	31	0	NCKAP5,missense_variant,p.Asn1544Ile,ENST00000409261,;NCKAP5,missense_variant,p.Asn1544Ile,ENST00000317721,;NCKAP5,intron_variant,,ENST00000409213,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,upstream_gene_variant,,ENST00000473859,;	A	ENSG00000176771	ENST00000409261	Transcript	missense_variant	5005	4631	1544	N/I	aAc/aTc	.	.	.	-1	NCKAP5	HGNC	29847	protein_coding	YES	CCDS46418.1	ENSP00000387128	NCKP5_HUMAN	C9JYL7_HUMAN	UPI0000E07A3F	.	tolerated(0.34)	probably_damaging(0.967)	14/20	.	hmmpanther:PTHR21740:SF0,hmmpanther:PTHR21740,Pfam_domain:PF15246	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTGTTTCCA	.	4	ESCA
NCKAP5	0	.	GRCh37	2	133540491	133540491	+	Missense_Mutation	SNP	C	C	T	rs545006757	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3893G>A	p.Arg1298His	p.R1298H	ENST00000409261	14/20	79	62	17	66	66	0	NCKAP5,missense_variant,p.Arg1298His,ENST00000409261,;NCKAP5,missense_variant,p.Arg1298His,ENST00000317721,;NCKAP5,intron_variant,,ENST00000409213,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,upstream_gene_variant,,ENST00000473859,;	T	ENSG00000176771	ENST00000409261	Transcript	missense_variant	4267	3893	1298	R/H	cGc/cAc	rs545006757	.	.	-1	NCKAP5	HGNC	29847	protein_coding	YES	CCDS46418.1	ENSP00000387128	NCKP5_HUMAN	C9JYL7_HUMAN	UPI0000E07A3F	.	deleterious(0)	probably_damaging(1)	14/20	.	hmmpanther:PTHR21740:SF0,hmmpanther:PTHR21740	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTGCGGACT	byCluster|by1000G	5	ESCA
MAP3K19	0	.	GRCh37	2	135763096	135763096	+	Silent	SNP	G	G	A	rs749805940	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144C>T	p.%3D	p.F48F	ENST00000375845	3/10	76	43	33	52	52	0	MAP3K19,synonymous_variant,p.%3D,ENST00000392917,;MAP3K19,synonymous_variant,p.%3D,ENST00000425952,;MAP3K19,synonymous_variant,p.%3D,ENST00000375844,;MAP3K19,synonymous_variant,p.%3D,ENST00000414343,;MAP3K19,synonymous_variant,p.%3D,ENST00000375845,;MAP3K19,synonymous_variant,p.%3D,ENST00000392918,;MAP3K19,synonymous_variant,p.%3D,ENST00000392915,;MAP3K19,synonymous_variant,p.%3D,ENST00000358371,;MAP3K19,5_prime_UTR_variant,,ENST00000315513,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000468155,;	A	ENSG00000176601	ENST00000375845	Transcript	synonymous_variant	175	144	48	F	ttC/ttT	rs749805940,COSM1006778	.	.	-1	MAP3K19	HGNC	26249	protein_coding	YES	CCDS2176.2	ENSP00000365005	M3K19_HUMAN	H7C041_HUMAN,C9JGQ2_HUMAN,C9JEJ9_HUMAN	UPI00004F77F2	.	.	.	3/10	.	hmmpanther:PTHR24361:SF129,hmmpanther:PTHR24361	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTCGAACTC	.	5	ESCA
R3HDM1	0	.	GRCh37	2	136437868	136437868	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2328T>C	p.%3D	p.I776I	ENST00000264160	20/26	44	36	8	33	33	0	R3HDM1,synonymous_variant,p.%3D,ENST00000429703,;R3HDM1,synonymous_variant,p.%3D,ENST00000264160,;R3HDM1,synonymous_variant,p.%3D,ENST00000410054,;R3HDM1,synonymous_variant,p.%3D,ENST00000409606,;R3HDM1,synonymous_variant,p.%3D,ENST00000329971,;R3HDM1,synonymous_variant,p.%3D,ENST00000409478,;R3HDM1,synonymous_variant,p.%3D,ENST00000445855,;	C	ENSG00000048991	ENST00000264160	Transcript	synonymous_variant	2698	2328	776	I	atT/atC	.	.	.	1	R3HDM1	HGNC	9757	protein_coding	YES	CCDS2177.1	ENSP00000264160	R3HD1_HUMAN	Q53SQ1_HUMAN,Q4ZG59_HUMAN	UPI000007456C	.	.	.	20/26	.	hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATTCCACC	.	5	ESCA
SPOPL	0	.	GRCh37	2	139329588	139329588	+	3'UTR	SNP	C	C	T	rs528927025	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2938C>T	.	.	ENST00000280098	11/11	21	12	8	9	9	0	SPOPL,3_prime_UTR_variant,,ENST00000280098,;AC092620.2,intron_variant,,ENST00000458007,;AC092620.2,downstream_gene_variant,,ENST00000449869,;SPOPL,downstream_gene_variant,,ENST00000420679,;	T	ENSG00000144228	ENST00000280098	Transcript	3_prime_UTR_variant	4496	.	.	.	.	rs528927025	.	.	1	SPOPL	HGNC	27934	protein_coding	YES	CCDS33298.1	ENSP00000280098	SPOPL_HUMAN	B4DEY7_HUMAN	UPI0000208BED	.	.	.	11/11	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTATGCGCGTG	by1000G	3	ESCA
ZEB2	0	.	GRCh37	2	145156467	145156467	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2287C>T	p.Pro763Ser	p.P763S	ENST00000558170	8/10	46	27	19	41	41	0	ZEB2,missense_variant,p.Pro739Ser,ENST00000539609,;ZEB2,missense_variant,p.Pro763Ser,ENST00000409487,;ZEB2,missense_variant,p.Pro763Ser,ENST00000303660,;ZEB2,missense_variant,p.Pro763Ser,ENST00000558170,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000427902,;ZEB2,downstream_gene_variant,,ENST00000392861,;	A	ENSG00000169554	ENST00000558170	Transcript	missense_variant	3472	2287	763	P/S	Cct/Tct	.	.	.	-1	ZEB2	HGNC	14881	protein_coding	YES	CCDS2186.1	ENSP00000454157	ZEB2_HUMAN	U3KPV5_HUMAN,Q53TG0_HUMAN,Q53TD9_HUMAN,E7EUW9_HUMAN,E7ESP8_HUMAN,C9JUQ1_HUMAN,C9JU62_HUMAN,A0JP08_HUMAN	UPI00001359A2	.	tolerated(0.63)	benign(0)	8/10	.	hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGGTTTTG	.	5	ESCA
ACVR2A	0	.	GRCh37	2	148677866	148677866	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1030G>A	p.Ala344Thr	p.A344T	ENST00000241416	8/11	25	17	8	18	18	0	ACVR2A,missense_variant,p.Ala344Thr,ENST00000241416,;ACVR2A,missense_variant,p.Ala344Thr,ENST00000404590,;ACVR2A,missense_variant,p.Ala236Thr,ENST00000535787,;	A	ENSG00000121989	ENST00000241416	Transcript	missense_variant	1666	1030	344	A/T	Gcc/Acc	.	.	.	1	ACVR2A	HGNC	173	protein_coding	YES	CCDS33301.1	ENSP00000241416	AVR2A_HUMAN	B4DWQ2_HUMAN	UPI0000126673	.	deleterious(0)	probably_damaging(1)	8/11	.	Prints_domain:PR00653,Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF64,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTGGCCTTA	.	5	ESCA
ACVR2A	0	.	GRCh37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	A	-	rs764719749	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1310delA	p.Lys437ArgfsTer5	p.K437Rfs*5	ENST00000241416	10/11	65	44	21	41	41	0	ACVR2A,frameshift_variant,p.Lys437ArgfsTer5,ENST00000241416,;ACVR2A,frameshift_variant,p.Lys437ArgfsTer5,ENST00000404590,;ACVR2A,frameshift_variant,p.Lys329ArgfsTer5,ENST00000535787,;ORC4,downstream_gene_variant,,ENST00000392857,;ACVR2A,non_coding_transcript_exon_variant,,ENST00000495775,;	-	ENSG00000121989	ENST00000241416	Transcript	frameshift_variant	1939	1303	435	K/X	Aaa/aa	rs764719749,COSM252949	.	.	1	ACVR2A	HGNC	173	protein_coding	YES	CCDS33301.1	ENSP00000241416	AVR2A_HUMAN	B4DWQ2_HUMAN	UPI0000126673	.	.	.	10/11	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF64,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	7	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.K437fs*5|c.1310delA|5,BUFFER|p.K437fs*5|c.1303delA|21	INDELOCATOR|VARSCANI	GTGCATAAAAAA	.	2	ESCA
KIF5C	0	.	GRCh37	2	149854978	149854978	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2165G>A	p.Arg722Gln	p.R722Q	ENST00000435030	19/26	68	39	28	30	30	0	KIF5C,missense_variant,p.Arg490Gln,ENST00000397413,;KIF5C,missense_variant,p.Arg722Gln,ENST00000435030,;KIF5C,missense_variant,p.Arg627Gln,ENST00000414838,;KIF5C,non_coding_transcript_exon_variant,,ENST00000464066,;KIF5C,non_coding_transcript_exon_variant,,ENST00000460377,;KIF5C,upstream_gene_variant,,ENST00000482151,;	A	ENSG00000168280	ENST00000435030	Transcript	missense_variant	2533	2165	722	R/Q	cGa/cAa	.	.	.	1	KIF5C	HGNC	6325	protein_coding	YES	.	ENSP00000393379	KIF5C_HUMAN	Q9UFW7_HUMAN,Q57Z91_HUMAN,Q57YV6_HUMAN,Q57YV5_HUMAN,Q53QT4_HUMAN,C9JWB9_HUMAN	UPI000012DDB7	.	deleterious(0.02)	probably_damaging(1)	19/26	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF365	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E724K|c.2170G>A|3,BUFFER|p.E627K|c.1879G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCGAGACG	.	5	ESCA
LYPD6B	0	.	GRCh37	2	150071273	150071273	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53delA	.	.	ENST00000409642	7/7	39	21	18	24	24	0	LYPD6B,3_prime_UTR_variant,,ENST00000280115,;LYPD6B,3_prime_UTR_variant,,ENST00000409029,;LYPD6B,3_prime_UTR_variant,,ENST00000409876,;LYPD6B,3_prime_UTR_variant,,ENST00000409642,;LYPD6B,non_coding_transcript_exon_variant,,ENST00000498249,;	-	ENSG00000150556	ENST00000409642	Transcript	3_prime_UTR_variant	1074	.	.	.	.	.	.	.	1	LYPD6B	HGNC	27018	protein_coding	YES	CCDS46423.1	ENSP00000387077	LPD6B_HUMAN	.	UPI00001BDB14	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAAGCCAAAAAC	.	2	ESCA
RIF1	0	.	GRCh37	2	152293790	152293790	+	Frame_Shift_Del	DEL	T	T	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1414delT	p.Ser472ProfsTer34	p.S472Pfs*34	ENST00000243326	12/35	80	56	24	37	37	0	RIF1,frameshift_variant,p.Ser464ProfsTer34,ENST00000414861,;RIF1,frameshift_variant,p.Ser472ProfsTer34,ENST00000444746,;RIF1,frameshift_variant,p.Ser472ProfsTer34,ENST00000453091,;RIF1,frameshift_variant,p.Ser472ProfsTer34,ENST00000428287,;RIF1,frameshift_variant,p.Ser472ProfsTer34,ENST00000243326,;RIF1,frameshift_variant,p.Ser472ProfsTer34,ENST00000430328,;RIF1,3_prime_UTR_variant,,ENST00000433166,;	-	ENSG00000080345	ENST00000243326	Transcript	frameshift_variant	1891	1408	470	F/X	Ttt/tt	COSM1399899	.	.	1	RIF1	HGNC	23207	protein_coding	YES	CCDS2194.1	ENSP00000243326	RIF1_HUMAN	C9J1D6_HUMAN,B4DRJ4_HUMAN	UPI000023729F	.	.	.	12/35	.	hmmpanther:PTHR22928	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	6	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S472fs*34|c.1408delT|3	INDELOCATOR*|VARSCANI*|PINDEL	CCTTCCTTTTTT	.	3	ESCA
NEB	0	.	GRCh37	2	152410372	152410372	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19596C>T	p.%3D	p.H6532H	ENST00000397345	126/182	61	44	17	26	26	0	NEB,synonymous_variant,p.%3D,ENST00000603639,;NEB,synonymous_variant,p.%3D,ENST00000172853,;NEB,synonymous_variant,p.%3D,ENST00000427231,;NEB,synonymous_variant,p.%3D,ENST00000397345,;NEB,synonymous_variant,p.%3D,ENST00000604864,;NEB,synonymous_variant,p.%3D,ENST00000413693,;NEB,synonymous_variant,p.%3D,ENST00000409198,;	A	ENSG00000183091	ENST00000397345	Transcript	synonymous_variant	19799	19596	6532	H	caC/caT	.	.	.	-1	NEB	HGNC	7720	protein_coding	YES	CCDS54407.1	ENSP00000380505	.	H7C2D0_HUMAN,F8WCL5_HUMAN	UPI0002065BA0	.	.	.	126/182	.	PROSITE_profiles:PS51216,hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTGACGTGATC	.	4	ESCA
TPO	0	.	GRCh37	2	1544474	1544474	+	Silent	SNP	C	C	A	rs765076528	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2727C>A	p.%3D	p.A909A	ENST00000345913	16/17	70	39	30	40	40	0	TPO,synonymous_variant,p.%3D,ENST00000329066,;TPO,synonymous_variant,p.%3D,ENST00000382198,;TPO,synonymous_variant,p.%3D,ENST00000382201,;TPO,synonymous_variant,p.%3D,ENST00000349624,;TPO,synonymous_variant,p.%3D,ENST00000425083,;TPO,synonymous_variant,p.%3D,ENST00000346956,;TPO,synonymous_variant,p.%3D,ENST00000469607,;TPO,synonymous_variant,p.%3D,ENST00000422464,;TPO,synonymous_variant,p.%3D,ENST00000345913,;TPO,intron_variant,,ENST00000337415,;TPO,intron_variant,,ENST00000446278,;TPO,intron_variant,,ENST00000479902,;TPO,intron_variant,,ENST00000497517,;	A	ENSG00000115705	ENST00000345913	Transcript	synonymous_variant	2818	2727	909	A	gcC/gcA	rs765076528	.	.	1	TPO	HGNC	12015	protein_coding	YES	CCDS1643.1	ENSP00000318820	PERT_HUMAN	Q53QT2_HUMAN,C9J511_HUMAN	UPI000013D480	.	.	.	16/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.A910T|c.2728G>A|3,BUFFER|p.R908W|c.2722C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGCCGCAGC	byFrequency	5	ESCA
GPD2	0	.	GRCh37	2	157407142	157407142	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855T>C	p.%3D	p.C285C	ENST00000310454	8/17	37	21	16	30	30	0	GPD2,synonymous_variant,p.%3D,ENST00000310454,;GPD2,synonymous_variant,p.%3D,ENST00000409674,;GPD2,synonymous_variant,p.%3D,ENST00000438166,;GPD2,synonymous_variant,p.%3D,ENST00000540309,;GPD2,synonymous_variant,p.%3D,ENST00000409125,;GPD2,synonymous_variant,p.%3D,ENST00000409861,;	C	ENSG00000115159	ENST00000310454	Transcript	synonymous_variant	1227	855	285	C	tgT/tgC	.	.	.	1	GPD2	HGNC	4456	protein_coding	YES	CCDS2202.1	ENSP00000308610	GPDM_HUMAN	Q53T76_HUMAN,Q53RD0_HUMAN,F8W6E4_HUMAN,F5GYK7_HUMAN,E7EM56_HUMAN	UPI000013F012	.	.	.	8/17	.	hmmpanther:PTHR11985:SF1,hmmpanther:PTHR11985,Pfam_domain:PF01266,Gene3D:3.50.50.60,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATGTGTTAT	.	5	ESCA
CCDC148	0	.	GRCh37	2	159035476	159035476	+	Missense_Mutation	SNP	C	C	T	rs748550649	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1403G>A	p.Arg468His	p.R468H	ENST00000283233	12/14	61	43	18	41	41	0	CCDC148,missense_variant,p.Arg477His,ENST00000409187,;CCDC148,missense_variant,p.Arg468His,ENST00000283233,;CCDC148-AS1,intron_variant,,ENST00000412781,;CCDC148,3_prime_UTR_variant,,ENST00000448656,;CCDC148,3_prime_UTR_variant,,ENST00000454257,;	T	ENSG00000153237	ENST00000283233	Transcript	missense_variant	1717	1403	468	R/H	cGt/cAt	rs748550649	.	.	-1	CCDC148	HGNC	25191	protein_coding	YES	CCDS33304.1	ENSP00000283233	CC148_HUMAN	.	UPI0000208F63	.	deleterious(0.02)	probably_damaging(0.923)	12/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21549:SF1,hmmpanther:PTHR21549	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAAACGCCTT	byFrequency	5	ESCA
PKP4	0	.	GRCh37	2	159537313	159537313	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*133delT	.	.	ENST00000389759	22/22	33	17	16	30	30	0	PKP4,3_prime_UTR_variant,,ENST00000389759,;PKP4,3_prime_UTR_variant,,ENST00000389757,;AC005042.4,intron_variant,,ENST00000442666,;AC005042.4,intron_variant,,ENST00000342892,;PKP4,3_prime_UTR_variant,,ENST00000426248,;PKP4,non_coding_transcript_exon_variant,,ENST00000480171,;PKP4,downstream_gene_variant,,ENST00000486254,;	-	ENSG00000144283	ENST00000389759	Transcript	3_prime_UTR_variant	3815	.	.	.	.	.	.	.	1	PKP4	HGNC	9026	protein_coding	YES	CCDS33305.1	ENSP00000374409	PKP4_HUMAN	Q53TM5_HUMAN	UPI000044D379	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGTGTGTTTTTT	.	2	ESCA
TANC1	0	.	GRCh37	2	160050800	160050800	+	Silent	SNP	C	C	T	rs768318459	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2775C>T	p.%3D	p.N925N	ENST00000263635	17/27	68	52	16	32	32	0	TANC1,synonymous_variant,p.%3D,ENST00000263635,;TANC1,synonymous_variant,p.%3D,ENST00000454300,;TANC1,upstream_gene_variant,,ENST00000470074,;	T	ENSG00000115183	ENST00000263635	Transcript	synonymous_variant	3012	2775	925	N	aaC/aaT	rs768318459	.	.	1	TANC1	HGNC	29364	protein_coding	YES	CCDS42766.1	ENSP00000263635	TANC1_HUMAN	.	UPI0000421D80	.	.	.	17/27	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,Gene3D:1.25.40.20,Pfam_domain:PF12796,hmmpanther:PTHR24166:SF23,hmmpanther:PTHR24166,PROSITE_profiles:PS50297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAACGTGAA	.	5	ESCA
FAP	0	.	GRCh37	2	163055317	163055317	+	Missense_Mutation	SNP	T	T	C	rs772231311	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1352A>G	p.Tyr451Cys	p.Y451C	ENST00000188790	16/26	73	51	21	55	55	0	FAP,missense_variant,p.Tyr426Cys,ENST00000443424,;FAP,missense_variant,p.Tyr451Cys,ENST00000188790,;FAP,missense_variant,p.Tyr7Cys,ENST00000422436,;FAP,non_coding_transcript_exon_variant,,ENST00000465088,;FAP,non_coding_transcript_exon_variant,,ENST00000465424,;FAP,upstream_gene_variant,,ENST00000497414,;	C	ENSG00000078098	ENST00000188790	Transcript	missense_variant	1560	1352	451	Y/C	tAc/tGc	rs772231311	.	.	-1	FAP	HGNC	3590	protein_coding	YES	CCDS33311.1	ENSP00000188790	SEPR_HUMAN	C9J131_HUMAN	UPI00000012A2	.	tolerated(0.07)	probably_damaging(1)	16/26	.	hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF111,Gene3D:2.140.10.30,Pfam_domain:PF00930,Superfamily_domains:SSF82171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGTAATAT	.	5	ESCA
FIGN	0	.	GRCh37	2	164465713	164465713	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*349G>A	.	.	ENST00000333129	3/3	14	11	3	8	8	0	FIGN,3_prime_UTR_variant,,ENST00000333129,;FIGN,intron_variant,,ENST00000409634,;FIGN,downstream_gene_variant,,ENST00000482917,;	T	ENSG00000182263	ENST00000333129	Transcript	3_prime_UTR_variant	2944	.	.	.	.	.	.	.	-1	FIGN	HGNC	13285	protein_coding	YES	CCDS2221.2	ENSP00000333836	FIGN_HUMAN	.	UPI000022BD13	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCACTTGAC	.	2	ESCA
TTC21B	0	.	GRCh37	2	166731124	166731124	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*141A>G	.	.	ENST00000243344	29/29	31	24	7	23	23	0	TTC21B,3_prime_UTR_variant,,ENST00000243344,;TTC21B,intron_variant,,ENST00000536175,;TTC21B,upstream_gene_variant,,ENST00000489714,;TTC21B,intron_variant,,ENST00000392695,;TTC21B,upstream_gene_variant,,ENST00000486672,;	C	ENSG00000123607	ENST00000243344	Transcript	3_prime_UTR_variant	4230	.	.	.	.	.	.	.	-1	TTC21B	HGNC	25660	protein_coding	YES	CCDS33315.1	ENSP00000243344	TT21B_HUMAN	B3KU32_HUMAN	UPI000020900A	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATGTACAGC	.	5	ESCA
TTC21B	0	.	GRCh37	2	166781085	166781085	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1490T>A	p.Leu497Gln	p.L497Q	ENST00000243344	12/29	60	36	24	32	32	0	TTC21B,missense_variant,p.Leu497Gln,ENST00000243344,;TTC21B,downstream_gene_variant,,ENST00000464374,;	T	ENSG00000123607	ENST00000243344	Transcript	missense_variant	1628	1490	497	L/Q	cTa/cAa	.	.	.	-1	TTC21B	HGNC	25660	protein_coding	YES	CCDS33315.1	ENSP00000243344	TT21B_HUMAN	B3KU32_HUMAN	UPI000020900A	.	tolerated(0.05)	probably_damaging(0.982)	12/29	.	PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF1,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATTAGGAAG	.	5	ESCA
XIRP2	0	.	GRCh37	2	168107566	168107566	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9664C>T	p.Arg3222Cys	p.R3222C	ENST00000409195	9/11	19	15	4	11	11	0	XIRP2,missense_variant,p.Arg3000Cys,ENST00000409273,;XIRP2,missense_variant,p.Arg3222Cys,ENST00000409195,;XIRP2,missense_variant,p.Arg3222Cys,ENST00000295237,;XIRP2,intron_variant,,ENST00000409605,;XIRP2,intron_variant,,ENST00000420519,;XIRP2,intron_variant,,ENST00000409756,;XIRP2,intron_variant,,ENST00000409043,;XIRP2,intron_variant,,ENST00000409728,;	T	ENSG00000163092	ENST00000409195	Transcript	missense_variant	9753	9664	3222	R/C	Cgt/Tgt	COSM1400961	.	.	1	XIRP2	HGNC	14303	protein_coding	YES	CCDS42769.1	ENSP00000386840	.	J3KNB1_HUMAN	UPI0000E9BBED	.	.	probably_damaging(1)	9/11	.	hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCGTCGT	.	5	ESCA
PHOSPHO2	0	.	GRCh37	2	170551051	170551051	+	5'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-312A>G	.	.	ENST00000359744	1/4	16	10	6	9	9	0	PHOSPHO2,5_prime_UTR_variant,,ENST00000449906,;PHOSPHO2,5_prime_UTR_variant,,ENST00000438838,;KLHL23,5_prime_UTR_variant,,ENST00000272797,;KLHL23,5_prime_UTR_variant,,ENST00000498202,;PHOSPHO2,5_prime_UTR_variant,,ENST00000438710,;PHOSPHO2,5_prime_UTR_variant,,ENST00000359744,;CCDC173,upstream_gene_variant,,ENST00000421028,;KLHL23,upstream_gene_variant,,ENST00000602521,;CCDC173,upstream_gene_variant,,ENST00000447353,;PHOSPHO2,upstream_gene_variant,,ENST00000476919,;	G	ENSG00000144362	ENST00000359744	Transcript	5_prime_UTR_variant	77	.	.	.	.	.	.	.	1	PHOSPHO2	HGNC	28316	protein_coding	YES	CCDS33319.1	ENSP00000352782	PHOP2_HUMAN	C9JZQ7_HUMAN,C9JD35_HUMAN,C9J4G2_HUMAN	UPI000006D7F5	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGAGAGGGCA	.	2	ESCA
MYO3B	0	.	GRCh37	2	171371459	171371459	+	Silent	SNP	A	A	G	rs753401956	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3399A>G	p.%3D	p.P1133P	ENST00000408978	29/35	44	26	18	26	26	0	MYO3B,synonymous_variant,p.%3D,ENST00000408978,;MYO3B,synonymous_variant,p.%3D,ENST00000334231,;MYO3B,synonymous_variant,p.%3D,ENST00000409044,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,synonymous_variant,p.%3D,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,;	G	ENSG00000071909	ENST00000408978	Transcript	synonymous_variant	3542	3399	1133	P	ccA/ccG	rs753401956	.	.	1	MYO3B	HGNC	15576	protein_coding	YES	CCDS42773.1	ENSP00000386213	MYO3B_HUMAN	.	UPI000020907B	.	.	.	29/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCACATTC	.	5	ESCA
ITGA6	0	.	GRCh37	2	173335732	173335733	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681dupT	p.Asp228Ter	p.D228*	ENST00000409080	5/25	67	52	15	33	33	0	ITGA6,frameshift_variant,p.Asp114Ter,ENST00000412899,;ITGA6,frameshift_variant,p.Asp228Ter,ENST00000442250,;ITGA6,frameshift_variant,p.Asp228Ter,ENST00000264106,;ITGA6,frameshift_variant,p.Asp228Ter,ENST00000375221,;ITGA6,frameshift_variant,p.Asp228Ter,ENST00000264107,;ITGA6,frameshift_variant,p.Asp228Ter,ENST00000409080,;ITGA6,intron_variant,,ENST00000458358,;ITGA6,intron_variant,,ENST00000343713,;ITGA6,intron_variant,,ENST00000409532,;AC078883.3,upstream_gene_variant,,ENST00000417539,;AC078883.3,upstream_gene_variant,,ENST00000458314,;ITGA6,non_coding_transcript_exon_variant,,ENST00000497107,;	T	ENSG00000091409	ENST00000409080	Transcript	frameshift_variant	674-675	674-675	225	T/TX	act/acTt	.	.	.	1	ITGA6	HGNC	6142	protein_coding	YES	CCDS46451.1	ENSP00000386896	ITA6_HUMAN	C9JXX7_HUMAN	UPI0000EA87E5	.	.	.	5/25	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF9,hmmpanther:PTHR23220,Gene3D:3nigC00,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAACACTTTTT	.	2	ESCA
HOXD10	0	.	GRCh37	2	176984427	176984427	+	3'UTR	DEL	A	A	-	rs532592274	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*477delA	.	.	ENST00000249501	2/2	31	18	13	20	20	0	HOXD10,3_prime_UTR_variant,,ENST00000249501,;HOXD9,upstream_gene_variant,,ENST00000249499,;HOXD-AS2,downstream_gene_variant,,ENST00000440016,;HOXD10,downstream_gene_variant,,ENST00000549469,;HOXD10,downstream_gene_variant,,ENST00000490088,;	-	ENSG00000128710	ENST00000249501	Transcript	3_prime_UTR_variant	1746	.	.	.	.	rs532592274	.	.	1	HOXD10	HGNC	5133	protein_coding	YES	CCDS2266.1	ENSP00000249501	HXD10_HUMAN	.	UPI000013CC87	.	.	.	2/2	.	.	T:0.0006	T:0.0008	T:0.0014	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATATTTAAAAAA	byFrequency|by1000G	2	ESCA
NFE2L2	0	.	GRCh37	2	178095075	178095075	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*438delT	.	.	ENST00000397062	5/5	22	15	7	17	17	0	NFE2L2,3_prime_UTR_variant,,ENST00000397062,;NFE2L2,3_prime_UTR_variant,,ENST00000446151,;NFE2L2,3_prime_UTR_variant,,ENST00000464747,;NFE2L2,3_prime_UTR_variant,,ENST00000397063,;NFE2L2,intron_variant,,ENST00000458603,;NFE2L2,downstream_gene_variant,,ENST00000449627,;NFE2L2,downstream_gene_variant,,ENST00000423513,;NFE2L2,downstream_gene_variant,,ENST00000588123,;NFE2L2,downstream_gene_variant,,ENST00000586532,;NFE2L2,downstream_gene_variant,,ENST00000421929,;NFE2L2,downstream_gene_variant,,ENST00000430047,;NFE2L2,downstream_gene_variant,,ENST00000448782,;NFE2L2,downstream_gene_variant,,ENST00000462023,;NFE2L2,downstream_gene_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	-	ENSG00000116044	ENST00000397062	Transcript	3_prime_UTR_variant	2811	.	.	.	.	.	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCTCTTAAAATT	.	2	ESCA
TTN	0	.	GRCh37	2	179445156	179445156	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66950C>T	p.Thr22317Ile	p.T22317I	ENST00000589042	317/363	55	33	21	31	31	0	TTN,missense_variant,p.Thr13377Ile,ENST00000359218,;TTN,missense_variant,p.Thr20676Ile,ENST00000591111,;TTN,missense_variant,p.Thr22317Ile,ENST00000589042,;TTN,missense_variant,p.Thr13444Ile,ENST00000342175,;TTN,missense_variant,p.Thr19749Ile,ENST00000342992,;TTN,missense_variant,p.Thr13252Ile,ENST00000460472,;RP11-171I2.2,non_coding_transcript_exon_variant,,ENST00000603521,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,upstream_gene_variant,,ENST00000590743,;RP11-171I2.5,downstream_gene_variant,,ENST00000604215,;TTN-AS1,upstream_gene_variant,,ENST00000589907,;	A	ENSG00000155657	ENST00000589042	Transcript	missense_variant	67175	66950	22317	T/I	aCt/aTt	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	317/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAAGTGTCA	.	5	ESCA
TTN	0	.	GRCh37	2	179584079	179584079	+	Missense_Mutation	SNP	G	G	A	rs773761640	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.24038C>T	p.Pro8013Leu	p.P8013L	ENST00000589042	83/363	42	19	22	45	45	0	TTN,missense_variant,p.Pro6769Leu,ENST00000342992,;TTN,missense_variant,p.Pro7696Leu,ENST00000591111,;TTN,missense_variant,p.Pro8013Leu,ENST00000589042,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000585451,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,;	A	ENSG00000155657	ENST00000589042	Transcript	missense_variant	24263	24038	8013	P/L	cCg/cTg	rs773761640	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	83/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S6771L|c.20312C>T|4,BUFFER|p.S6771L|c.20312C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATCGGGGCT	.	5	ESCA
NUP35	0	.	GRCh37	2	184023093	184023093	+	Frame_Shift_Del	DEL	T	T	-	rs201358343	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696delT	p.Phe232LeufsTer6	p.F232Lfs*6	ENST00000295119	7/9	99	86	13	31	31	0	NUP35,frameshift_variant,p.Phe97LeufsTer6,ENST00000541912,;NUP35,frameshift_variant,p.Phe232LeufsTer6,ENST00000295119,;NUP35,frameshift_variant,p.Phe215LeufsTer6,ENST00000409798,;NUP35,3_prime_UTR_variant,,ENST00000374930,;NUP35,non_coding_transcript_exon_variant,,ENST00000479162,;	-	ENSG00000163002	ENST00000295119	Transcript	frameshift_variant	795	692	231	I/X	aTt/at	rs201358343	.	.	1	NUP35	HGNC	29797	protein_coding	YES	CCDS2290.1	ENSP00000295119	NUP53_HUMAN	C9JWU7_HUMAN,C9JIY9_HUMAN,C9IYQ7_HUMAN,B4DYB4_HUMAN,B4DP57_HUMAN	UPI000000DBA2	.	.	.	7/9	.	PROSITE_profiles:PS51472,hmmpanther:PTHR21527,Pfam_domain:PF05172,PIRSF_domain:PIRSF038119,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAGGATTTTTG	by1000G	3	ESCA
FSIP2	0	.	GRCh37	2	186671157	186671157	+	Frame_Shift_Del	DEL	C	C	-	rs776643141	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17396delC	p.Pro5799GlnfsTer6	p.P5799Qfs*6	ENST00000343098	17/23	70	48	22	43	43	0	FSIP2,frameshift_variant,p.Pro5799GlnfsTer6,ENST00000343098,;FSIP2,frameshift_variant,p.Pro5710GlnfsTer6,ENST00000424728,;FSIP2,intron_variant,,ENST00000415915,;	-	ENSG00000188738	ENST00000343098	Transcript	frameshift_variant	17391	17391	5797	S/X	agC/ag	rs776643141	.	.	1	FSIP2	HGNC	21675	protein_coding	YES	CCDS54426.1	ENSP00000344403	.	J3QTJ6_HUMAN	UPI0001D420A1	.	.	.	17/23	.	hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAAAGCCCCCC	byFrequency	3	ESCA
ITGAV	0	.	GRCh37	2	187521085	187521085	+	Frame_Shift_Del	DEL	G	G	-	rs567294324	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1682delG	p.Gly561AspfsTer2	p.G561Dfs*2	ENST00000261023	17/30	30	21	9	19	19	0	ITGAV,frameshift_variant,p.Gly525AspfsTer2,ENST00000374907,;ITGAV,frameshift_variant,p.Gly561AspfsTer2,ENST00000261023,;ITGAV,frameshift_variant,p.Gly515AspfsTer2,ENST00000433736,;AC017101.10,intron_variant,,ENST00000453665,;	-	ENSG00000138448	ENST00000261023	Transcript	frameshift_variant	1950	1676	559	R/X	aGg/ag	rs567294324,COSM1403929	.	.	1	ITGAV	HGNC	6150	protein_coding	YES	CCDS2292.1	ENSP00000261023	ITAV_HUMAN	L7RXH0_HUMAN	UPI000013D12E	.	.	.	17/30	.	hmmpanther:PTHR23220:SF4,hmmpanther:PTHR23220,Gene3D:1jv2A02,Pfam_domain:PF08441,Superfamily_domains:SSF69179	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	6	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTCAAGGGGGG	by1000G	2	ESCA
ITGAV	0	.	GRCh37	2	187545514	187545514	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3495T>A	.	.	ENST00000261023	30/30	32	22	9	34	34	0	ITGAV,3_prime_UTR_variant,,ENST00000374907,;ITGAV,3_prime_UTR_variant,,ENST00000261023,;ITGAV,downstream_gene_variant,,ENST00000430709,;ITGAV,downstream_gene_variant,,ENST00000433736,;AC017101.10,intron_variant,,ENST00000453665,;	A	ENSG00000138448	ENST00000261023	Transcript	3_prime_UTR_variant	6916	.	.	.	.	.	.	.	1	ITGAV	HGNC	6150	protein_coding	YES	CCDS2292.1	ENSP00000261023	ITAV_HUMAN	L7RXH0_HUMAN	UPI000013D12E	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTTCTAAA	.	5	ESCA
NT5C1B	0	.	GRCh37	2	18764147	18764147	+	Silent	SNP	G	G	A	rs780305599	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1188C>T	p.%3D	p.S396S	ENST00000359846	7/10	46	24	22	24	24	0	NT5C1B,synonymous_variant,p.%3D,ENST00000359846,;NT5C1B,synonymous_variant,p.%3D,ENST00000304081,;NT5C1B,synonymous_variant,p.%3D,ENST00000600945,;NT5C1B-RDH14,synonymous_variant,p.%3D,ENST00000532967,;NT5C1B,synonymous_variant,p.%3D,ENST00000418427,;NT5C1B-RDH14,synonymous_variant,p.%3D,ENST00000444297,;NT5C1B,downstream_gene_variant,,ENST00000416783,;RNU6-1215P,downstream_gene_variant,,ENST00000384441,;NT5C1B,downstream_gene_variant,,ENST00000460052,;NT5C1B,3_prime_UTR_variant,,ENST00000406971,;NT5C1B,downstream_gene_variant,,ENST00000490687,;	A	ENSG00000185013	ENST00000359846	Transcript	synonymous_variant	1266	1188	396	S	agC/agT	rs780305599	.	.	-1	NT5C1B	HGNC	17818	protein_coding	YES	CCDS33150.1	ENSP00000352904	5NT1B_HUMAN	B4DZ86_HUMAN	UPI000035B1B0	.	.	.	7/10	.	hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0,Pfam_domain:PF06189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGACGCTGTT	byFrequency	5	ESCA
OSGEPL1	0	.	GRCh37	2	190626331	190626331	+	Frame_Shift_Del	DEL	A	A	-	rs750679212	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36delT	p.Phe12LeufsTer12	p.F12Lfs*12	ENST00000264151	2/9	26	14	11	24	24	0	OSGEPL1,frameshift_variant,p.Phe12LeufsTer12,ENST00000521630,;OSGEPL1,frameshift_variant,p.Phe12LeufsTer12,ENST00000519810,;OSGEPL1,frameshift_variant,p.Phe12LeufsTer12,ENST00000264151,;OSGEPL1,frameshift_variant,p.Phe12LeufsTer12,ENST00000517895,;OSGEPL1,frameshift_variant,p.Phe12LeufsTer12,ENST00000522700,;OSGEPL1,intron_variant,,ENST00000520350,;OSGEPL1-AS1,upstream_gene_variant,,ENST00000523895,;RP11-455J20.3,downstream_gene_variant,,ENST00000608680,;OSGEPL1-AS1,upstream_gene_variant,,ENST00000520651,;OSGEPL1-AS1,upstream_gene_variant,,ENST00000521819,;OSGEPL1,non_coding_transcript_exon_variant,,ENST00000518114,;OSGEPL1,non_coding_transcript_exon_variant,,ENST00000524043,;ANKAR,downstream_gene_variant,,ENST00000441800,;	-	ENSG00000128694	ENST00000264151	Transcript	frameshift_variant	139	36	12	F/X	ttT/tt	rs750679212,COSM267089	.	.	-1	OSGEPL1	HGNC	23075	protein_coding	YES	CCDS46472.1	ENSP00000264151	OSGP2_HUMAN	E7EVL7_HUMAN,E5RIL9_HUMAN,E5RGZ1_HUMAN	UPI000006D878	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGGTTTAAAAAA	.	2	ESCA
GTF3C3	0	.	GRCh37	2	197653994	197653994	+	Missense_Mutation	SNP	C	C	T	rs768859221	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827G>A	p.Arg276His	p.R276H	ENST00000263956	6/18	65	61	4	43	43	0	GTF3C3,missense_variant,p.Arg276His,ENST00000409364,;GTF3C3,missense_variant,p.Arg276His,ENST00000263956,;GTF3C3,upstream_gene_variant,,ENST00000448087,;GTF3C3,non_coding_transcript_exon_variant,,ENST00000470386,;GTF3C3,downstream_gene_variant,,ENST00000448539,;GTF3C3,downstream_gene_variant,,ENST00000451088,;GTF3C3,downstream_gene_variant,,ENST00000455546,;	T	ENSG00000119041	ENST00000263956	Transcript	missense_variant	917	827	276	R/H	cGt/cAt	rs768859221,COSM1404247	.	.	-1	GTF3C3	HGNC	4666	protein_coding	YES	CCDS2316.1	ENSP00000263956	TF3C3_HUMAN	.	UPI0000070C01	.	tolerated(0.1)	benign(0.133)	6/18	.	PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR23082,Pfam_domain:PF13414,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATACGCCTA	byFrequency	2	ESCA
MYT1L	0	.	GRCh37	2	1983001	1983001	+	Splice_Site	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90-2A>C	.	p.X30_splice	ENST00000428368	.	34	28	5	20	20	0	MYT1L,splice_acceptor_variant,,ENST00000399161,;MYT1L,splice_acceptor_variant,,ENST00000428368,;MYT1L,splice_acceptor_variant,,ENST00000485348,;	G	ENSG00000186487	ENST00000428368	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	MYT1L	HGNC	7623	protein_coding	YES	CCDS46222.1	ENSP00000396103	MYT1L_HUMAN	.	UPI00004E55EA	.	.	.	.	7/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCTGCAAC	.	5	ESCA
ICA1L	0	.	GRCh37	2	203684413	203684413	+	Intron	SNP	C	C	T	rs781474166	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558+11G>A	.	.	ENST00000392237	.	25	13	12	34	34	0	ICA1L,3_prime_UTR_variant,,ENST00000425178,;ICA1L,intron_variant,,ENST00000420558,;ICA1L,intron_variant,,ENST00000392237,;ICA1L,intron_variant,,ENST00000358299,;ICA1L,downstream_gene_variant,,ENST00000441547,;ICA1L,downstream_gene_variant,,ENST00000435143,;ICA1L,downstream_gene_variant,,ENST00000454326,;ICA1L,downstream_gene_variant,,ENST00000416760,;ICA1L,downstream_gene_variant,,ENST00000450143,;ICA1L,downstream_gene_variant,,ENST00000457524,;ICA1L,downstream_gene_variant,,ENST00000432273,;ICA1L,downstream_gene_variant,,ENST00000412210,;ICA1L,downstream_gene_variant,,ENST00000418208,;ICA1L,downstream_gene_variant,,ENST00000419460,;ICA1L,non_coding_transcript_exon_variant,,ENST00000476602,;ICA1L,intron_variant,,ENST00000494560,;ICA1L,intron_variant,,ENST00000438804,;ICA1L,downstream_gene_variant,,ENST00000437978,;	T	ENSG00000163596	ENST00000392237	Transcript	intron_variant	.	.	.	.	.	rs781474166	.	.	-1	ICA1L	HGNC	14442	protein_coding	YES	CCDS2354.1	ENSP00000376070	ICA1L_HUMAN	C9JRB6_HUMAN,C9JP49_HUMAN,C9JEP0_HUMAN,C9JEN4_HUMAN,C9JDM8_HUMAN,C9JDK6_HUMAN,C9JAQ4_HUMAN,C9J9Z8_HUMAN,C9J5Z0_HUMAN,C9J1M7_HUMAN	UPI000007263F	.	.	.	.	6/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATACGTTTT	.	5	ESCA
ZDBF2	0	.	GRCh37	2	207174428	207174428	+	Frame_Shift_Del	DEL	A	A	-	rs745875253	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5184delA	p.Lys1728AsnfsTer5	p.K1728Nfs*5	ENST00000374423	5/5	18	9	9	14	14	0	ZDBF2,frameshift_variant,p.Lys1728AsnfsTer5,ENST00000374423,;	-	ENSG00000204186	ENST00000374423	Transcript	frameshift_variant	5562	5176	1726	K/X	Aaa/aa	rs745875253,COSM1404812,COSM1404811	.	.	1	ZDBF2	HGNC	29313	protein_coding	YES	CCDS46501.1	ENSP00000363545	ZDBF2_HUMAN	N0DVB2_HUMAN	UPI000022BDE3	.	.	.	5/5	.	hmmpanther:PTHR21639:SF2,hmmpanther:PTHR21639	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	deletion	.	8	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.K1728fs*5|c.5176delA|6,BUFFER|p.K1728fs*5|c.5176delA|6	INDELOCATOR|VARSCANI	GCTGATAAAAAA	.	2	ESCA
MAP2	0	.	GRCh37	2	210561667	210561667	+	Frame_Shift_Del	DEL	A	A	-	rs752185114	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4420delA	p.Thr1474GlnfsTer14	p.T1474Qfs*14	ENST00000360351	9/15	50	45	5	27	27	0	MAP2,frameshift_variant,p.Thr1470GlnfsTer14,ENST00000447185,;MAP2,frameshift_variant,p.Thr1474GlnfsTer14,ENST00000360351,;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000199940,;MAP2,intron_variant,,ENST00000392194,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000475600,;MAP2,intron_variant,,ENST00000471619,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,;MAP2,downstream_gene_variant,,ENST00000482864,;	-	ENSG00000078018	ENST00000360351	Transcript	frameshift_variant	4920	4414	1472	K/X	Aaa/aa	rs752185114,COSM272920	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	.	.	9/15	.	hmmpanther:PTHR11501:SF15,hmmpanther:PTHR11501,Pfam_domain:PF08377	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	6	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CTTGCTAAAAAA	.	2	ESCA
MAP2	0	.	GRCh37	2	210595271	210595271	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*155delA	.	.	ENST00000360351	15/15	22	14	7	16	16	0	MAP2,3_prime_UTR_variant,,ENST00000360351,;MAP2,3_prime_UTR_variant,,ENST00000392194,;MAP2,downstream_gene_variant,,ENST00000447185,;MAP2,downstream_gene_variant,,ENST00000199940,;MAP2,downstream_gene_variant,,ENST00000361559,;MAP2,downstream_gene_variant,,ENST00000475600,;	-	ENSG00000078018	ENST00000360351	Transcript	3_prime_UTR_variant	6140	.	.	.	.	.	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTATTTAAAAAA	.	2	ESCA
ERBB4	0	.	GRCh37	2	212248355	212248355	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3912delG	p.Asn1305IlefsTer57	p.N1305Ifs*57	ENST00000342788	28/28	49	39	10	29	29	0	ERBB4,frameshift_variant,p.Asn1295IlefsTer?,ENST00000402597,;ERBB4,frameshift_variant,p.Asn1289IlefsTer57,ENST00000436443,;ERBB4,frameshift_variant,p.Asn1305IlefsTer57,ENST00000342788,;	-	ENSG00000178568	ENST00000342788	Transcript	frameshift_variant	4223	3912	1304	R/X	cgG/cg	.	.	.	-1	ERBB4	HGNC	3432	protein_coding	YES	CCDS2394.1	ENSP00000342235	ERBB4_HUMAN	Q580Q7_HUMAN,Q53T57_HUMAN,Q53R48_HUMAN,Q53R25_HUMAN,Q53QS8_HUMAN,Q4ZG14_HUMAN,E9PDR1_HUMAN	UPI00000499DF	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTATTCCGGTG	.	3	ESCA
APOB	0	.	GRCh37	2	21234423	21234425	+	In_Frame_Del	DEL	TGT	TGT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TGT	TGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5315_5317delACA	p.Asn1772del	p.N1772del	ENST00000233242	26/29	63	55	8	42	42	0	APOB,inframe_deletion,p.Asn1772del,ENST00000233242,;	-	ENSG00000084674	ENST00000233242	Transcript	inframe_deletion	5443-5445	5315-5317	1772-1773	NI/I	aACAtt/att	.	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	.	26/29	.	hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTAAATGTTGTCA	.	3	ESCA
APOB	0	.	GRCh37	2	21260129	21260129	+	Splice_Site	SNP	T	T	C	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538-2A>G	.	p.X180_splice	ENST00000233242	.	107	52	54	53	53	0	APOB,splice_acceptor_variant,,ENST00000233242,;APOB,splice_acceptor_variant,,ENST00000399256,;	C	ENSG00000084674	ENST00000233242	Transcript	splice_acceptor_variant	.	.	.	.	.	COSM1183240	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	.	.	5/28	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCCTATGGA	.	5	ESCA
MARCH4	0	.	GRCh37	2	217234779	217234779	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205delC	p.Gln69SerfsTer90	p.Q69Sfs*90	ENST00000273067	1/4	31	14	17	17	17	0	MARCH4,frameshift_variant,p.Gln69SerfsTer90,ENST00000273067,;	-	ENSG00000144583	ENST00000273067	Transcript	frameshift_variant	1972	205	69	Q/X	Cag/ag	.	.	.	-1	MARCH4	HGNC	29269	protein_coding	YES	CCDS33376.1	ENSP00000273067	MARH4_HUMAN	.	UPI00001C1DB9	.	.	.	1/4	.	hmmpanther:PTHR23012:SF51,hmmpanther:PTHR23012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGGGCTGGGGGT	.	2	ESCA
SMARCAL1	0	.	GRCh37	2	217300166	217300168	+	In_Frame_Del	DEL	CTT	CTT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594_1596delCTT	p.Leu532del	p.L532del	ENST00000357276	9/18	66	37	29	46	46	0	SMARCAL1,inframe_deletion,p.Leu532del,ENST00000357276,;SMARCAL1,inframe_deletion,p.Leu90del,ENST00000445153,;SMARCAL1,inframe_deletion,p.Leu396del,ENST00000392128,;SMARCAL1,inframe_deletion,p.Leu532del,ENST00000358207,;SMARCAL1,downstream_gene_variant,,ENST00000479008,;	-	ENSG00000138375	ENST00000357276	Transcript	inframe_deletion	1921-1923	1591-1593	531	L/-	CTT/-	.	.	.	1	SMARCAL1	HGNC	11102	protein_coding	YES	CCDS2403.1	ENSP00000349823	SMAL1_HUMAN	C9JP32_HUMAN,C9JHQ1_HUMAN,C9J8F8_HUMAN,C9J6I8_HUMAN	UPI000000DA30	.	.	.	9/18	.	PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF571,hmmpanther:PTHR10799,Pfam_domain:PF00176,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTGACCTTCTTAG	.	3	ESCA
CXCR2	0	.	GRCh37	2	219000454	219000454	+	Frame_Shift_Del	DEL	C	C	-	rs544347825	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934delC	p.Leu312SerfsTer18	p.L312Sfs*18	ENST00000318507	3/3	87	58	29	22	22	0	CXCR2,frameshift_variant,p.Leu312SerfsTer18,ENST00000318507,;CXCR2,downstream_gene_variant,,ENST00000418878,;CXCR2,downstream_gene_variant,,ENST00000428565,;CXCR2,downstream_gene_variant,,ENST00000415392,;CXCR2,downstream_gene_variant,,ENST00000454148,;CXCR2,downstream_gene_variant,,ENST00000449014,;CXCR2,downstream_gene_variant,,ENST00000453237,;	-	ENSG00000180871	ENST00000318507	Transcript	frameshift_variant	1357	930	310	N/X	aaC/aa	rs544347825	.	.	1	CXCR2	HGNC	6027	protein_coding	YES	CCDS2408.1	ENSP00000319635	CXCR2_HUMAN	Q53PC4_HUMAN,C9JW47_HUMAN,C9JG19_HUMAN,C9J2F9_HUMAN,C9J1J7_HUMAN	UPI000004358A	.	.	.	3/3	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24227:SF63,hmmpanther:PTHR24227,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTCAACCCCCT	by1000G	3	ESCA
PNKD	0	.	GRCh37	2	219135295	219135296	+	Frame_Shift_Ins	INS	-	-	G	rs777779692	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43dupG	p.Ala15GlyfsTer17	p.A15Gfs*17	ENST00000273077	1/10	34	25	8	9	9	0	PNKD,frameshift_variant,p.Ala15GlyfsTer17,ENST00000248451,;PNKD,frameshift_variant,p.Ala15GlyfsTer17,ENST00000273077,;AAMP,upstream_gene_variant,,ENST00000422731,;TMBIM1,downstream_gene_variant,,ENST00000444881,;TMBIM1,downstream_gene_variant,,ENST00000396809,;TMBIM1,downstream_gene_variant,,ENST00000258412,;AAMP,upstream_gene_variant,,ENST00000420660,;TMBIM1,downstream_gene_variant,,ENST00000445635,;AAMP,upstream_gene_variant,,ENST00000444053,;AAMP,upstream_gene_variant,,ENST00000248450,;AAMP,upstream_gene_variant,,ENST00000447885,;PNKD,upstream_gene_variant,,ENST00000472650,;PNKD,non_coding_transcript_exon_variant,,ENST00000469689,;AAMP,upstream_gene_variant,,ENST00000465442,;AAMP,upstream_gene_variant,,ENST00000475678,;AAMP,upstream_gene_variant,,ENST00000461911,;AAMP,upstream_gene_variant,,ENST00000489767,;AAMP,upstream_gene_variant,,ENST00000494720,;TMBIM1,downstream_gene_variant,,ENST00000465082,;TMBIM1,downstream_gene_variant,,ENST00000437694,;	G	ENSG00000127838	ENST00000273077	Transcript	frameshift_variant	88-89	37-38	13	R/RX	cgg/cGgg	rs777779692,COSM1287268,COSM1287269	.	.	1	PNKD	HGNC	9153	protein_coding	YES	CCDS2411.1	ENSP00000273077	PNKD_HUMAN	.	UPI0000246C7E	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	insertion	.	6	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGGGCCGGGGG	.	2	ESCA
C2orf62	0	.	GRCh37	2	219222406	219222406	+	Missense_Mutation	SNP	G	G	A	rs759205178	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268G>A	p.Ala90Thr	p.A90T	ENST00000289388	3/10	53	40	13	52	52	0	C2orf62,missense_variant,p.Ala90Thr,ENST00000289388,;AC021016.8,intron_variant,,ENST00000411433,;C2orf62,upstream_gene_variant,,ENST00000481940,;C2orf62,non_coding_transcript_exon_variant,,ENST00000480532,;C2orf62,non_coding_transcript_exon_variant,,ENST00000495773,;AC021016.7,downstream_gene_variant,,ENST00000414167,;	A	ENSG00000158428	ENST00000289388	Transcript	missense_variant	297	268	90	A/T	Gcc/Acc	rs759205178	.	.	1	C2orf62	HGNC	25062	protein_coding	YES	CCDS2414.1	ENSP00000289388	CB062_HUMAN	.	UPI000019B2D3	.	deleterious(0)	probably_damaging(0.965)	3/10	.	hmmpanther:PTHR15505,hmmpanther:PTHR15505:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCATGCCTCT	.	5	ESCA
CYP27A1	0	.	GRCh37	2	219674399	219674399	+	Missense_Mutation	SNP	C	C	T	rs369294392,rs587778793	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355C>T	p.Arg119Trp	p.R119W	ENST00000258415	2/9	67	41	25	30	30	0	CYP27A1,missense_variant,p.Arg25Trp,ENST00000411688,;CYP27A1,missense_variant,p.Arg119Trp,ENST00000258415,;CYP27A1,non_coding_transcript_exon_variant,,ENST00000494263,;CYP27A1,intron_variant,,ENST00000466602,;CYP27A1,intron_variant,,ENST00000445971,;	T	ENSG00000135929	ENST00000258415	Transcript	missense_variant	782	355	119	R/W	Cgg/Tgg	rs369294392,CD941659,rs587778793	.	.	1	CYP27A1	HGNC	2605	protein_coding	YES	CCDS2423.1	ENSP00000258415	CP27A_HUMAN	C9J1K5_HUMAN	UPI00001281BD	.	deleterious(0)	probably_damaging(1)	2/9	.	hmmpanther:PTHR24291:SF6,hmmpanther:PTHR24291,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0001	pathogenic	.	20301583,7977352	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGATGCGGCAA	byCluster|by1000G	4	ESCA
SPEG	0	.	GRCh37	2	220333698	220333698	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3419A>T	p.Asn1140Ile	p.N1140I	ENST00000312358	12/41	80	49	31	43	43	0	SPEG,missense_variant,p.Asn1140Ile,ENST00000312358,;SPEG,downstream_gene_variant,,ENST00000396695,;SPEG,downstream_gene_variant,,ENST00000396688,;SPEG,downstream_gene_variant,,ENST00000396686,;SPEG,downstream_gene_variant,,ENST00000396689,;SPEG,downstream_gene_variant,,ENST00000396698,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,downstream_gene_variant,,ENST00000498378,;SPEG,downstream_gene_variant,,ENST00000496786,;SPEG,downstream_gene_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000464989,;SPEG,downstream_gene_variant,,ENST00000475921,;SPEG,upstream_gene_variant,,ENST00000485069,;	T	ENSG00000072195	ENST00000312358	Transcript	missense_variant	3551	3419	1140	N/I	aAc/aTc	.	.	.	1	SPEG	HGNC	16901	protein_coding	YES	CCDS42824.1	ENSP00000311684	SPEG_HUMAN	B9A038_HUMAN	UPI000066D99E	.	.	probably_damaging(0.976)	12/41	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF156,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTAACACCC	.	5	ESCA
TMEM198	0	.	GRCh37	2	220415144	220415144	+	3'UTR	DEL	G	G	-	rs374252677	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*574delG	.	.	ENST00000344458	6/6	78	51	27	22	22	0	TMEM198,3_prime_UTR_variant,,ENST00000373883,;TMEM198,3_prime_UTR_variant,,ENST00000344458,;OBSL1,downstream_gene_variant,,ENST00000603926,;TMEM198,downstream_gene_variant,,ENST00000421791,;OBSL1,downstream_gene_variant,,ENST00000373876,;TMEM198,downstream_gene_variant,,ENST00000451952,;OBSL1,downstream_gene_variant,,ENST00000265317,;OBSL1,downstream_gene_variant,,ENST00000265318,;OBSL1,downstream_gene_variant,,ENST00000404537,;MIR3132,upstream_gene_variant,,ENST00000581997,;RP11-256I23.1,upstream_gene_variant,,ENST00000596829,;OBSL1,downstream_gene_variant,,ENST00000465149,;OBSL1,downstream_gene_variant,,ENST00000462534,;OBSL1,downstream_gene_variant,,ENST00000489804,;OBSL1,downstream_gene_variant,,ENST00000596474,;	-	ENSG00000188760	ENST00000344458	Transcript	3_prime_UTR_variant	2236	.	.	.	.	rs374252677	.	.	1	TMEM198	HGNC	33704	protein_coding	YES	CCDS33385.1	ENSP00000343507	TM198_HUMAN	C9JXI5_HUMAN,B4DYC9_HUMAN,B3KVR4_HUMAN	UPI0000160257	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGGGGTGGGGGG	.	3	ESCA
AP1S3	0	.	GRCh37	2	224623241	224623241	+	3'UTR	DEL	T	T	-	rs529498764,rs533058835	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*191delA	.	.	ENST00000396654	5/5	61	42	19	35	35	0	AP1S3,3_prime_UTR_variant,,ENST00000396654,;AP1S3,intron_variant,,ENST00000443700,;AP1S3,3_prime_UTR_variant,,ENST00000334271,;AP1S3,3_prime_UTR_variant,,ENST00000415298,;	-	ENSG00000152056	ENST00000396654	Transcript	3_prime_UTR_variant	788	.	.	.	.	rs529498764,rs533058835	.	.	-1	AP1S3	HGNC	18971	protein_coding	YES	CCDS42827.1	ENSP00000379891	AP1S3_HUMAN	Q53R44_HUMAN	UPI00003D357B	.	.	.	5/5	.	.	-:0.0032,A:0.0002	-:0.0091,A:0.0008	-:0.0043,A:0	.	-:0,A:0	-:0,A:0	-:0.001,A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACATAATTTTTT	byFrequency|by1000G	2	ESCA
COL4A3	0	.	GRCh37	2	228131180	228131180	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1363G>T	p.Gly455Cys	p.G455C	ENST00000396578	22/52	58	32	25	43	43	0	COL4A3,missense_variant,p.Gly455Cys,ENST00000396578,;AC097662.2,intron_variant,,ENST00000396588,;AC097662.2,intron_variant,,ENST00000439598,;AC097662.2,downstream_gene_variant,,ENST00000433324,;AC097662.2,upstream_gene_variant,,ENST00000437673,;	T	ENSG00000169031	ENST00000396578	Transcript	missense_variant	1525	1363	455	G/C	Ggc/Tgc	.	.	.	1	COL4A3	HGNC	2204	protein_coding	YES	CCDS42829.1	ENSP00000379823	CO4A3_HUMAN	Q548X1_HUMAN,A9QVI3_HUMAN	UPI000013E9F3	.	.	probably_damaging(1)	22/52	.	hmmpanther:PTHR24023:SF417,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCCAGGCTAT	.	3	ESCA
SPHKAP	0	.	GRCh37	2	228884465	228884465	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1105G>A	p.Gly369Arg	p.G369R	ENST00000392056	7/12	100	66	34	58	58	0	SPHKAP,missense_variant,p.Gly369Arg,ENST00000344657,;SPHKAP,missense_variant,p.Gly369Arg,ENST00000392056,;	T	ENSG00000153820	ENST00000392056	Transcript	missense_variant	1152	1105	369	G/R	Gga/Aga	.	.	.	-1	SPHKAP	HGNC	30619	protein_coding	YES	CCDS46537.1	ENSP00000375909	SPKAP_HUMAN	.	UPI0000411D7E	.	tolerated(0.47)	benign(0.062)	7/12	.	hmmpanther:PTHR10226,hmmpanther:PTHR10226:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTCCTGGGT	.	5	ESCA
DNER	0	.	GRCh37	2	230222652	230222652	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*604G>A	.	.	ENST00000341772	13/13	19	14	5	14	14	0	DNER,3_prime_UTR_variant,,ENST00000341772,;	T	ENSG00000187957	ENST00000341772	Transcript	3_prime_UTR_variant	2953	.	.	.	.	.	.	.	-1	DNER	HGNC	24456	protein_coding	YES	CCDS33390.1	ENSP00000345229	DNER_HUMAN	B4E399_HUMAN	UPI0000048EB8	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTTCGACGA	.	5	ESCA
PSMD1	0	.	GRCh37	2	231931656	231931656	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.341A>G	p.Glu114Gly	p.E114G	ENST00000308696	5/25	23	16	7	22	22	0	PSMD1,missense_variant,p.Glu14Gly,ENST00000444007,;PSMD1,missense_variant,p.Glu114Gly,ENST00000409643,;PSMD1,missense_variant,p.Glu120Gly,ENST00000440838,;PSMD1,missense_variant,p.Glu114Gly,ENST00000373635,;PSMD1,missense_variant,p.Glu114Gly,ENST00000308696,;PSMD1,3_prime_UTR_variant,,ENST00000431051,;	G	ENSG00000173692	ENST00000308696	Transcript	missense_variant	503	341	114	E/G	gAa/gGa	.	.	.	1	PSMD1	HGNC	9554	protein_coding	YES	CCDS2482.1	ENSP00000309474	PSMD1_HUMAN	.	UPI00001678A2	.	tolerated(0.2)	benign(0.003)	5/25	.	hmmpanther:PTHR10943,PIRSF_domain:PIRSF015947	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGGAAAATG	.	5	ESCA
NCL	0	.	GRCh37	2	232326385	232326393	+	In_Frame_Del	DEL	TCATCCTCC	TCATCCTCC	-	rs766445200	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TCATCCTCC	TCATCCTCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471_479delGGAGGATGA	p.Glu157_Asp159del	p.E157_D159del	ENST00000322723	3/14	288	205	83	168	168	0	NCL,inframe_deletion,p.Glu141_Asp143del,ENST00000454824,;NCL,inframe_deletion,p.Glu141_Asp143del,ENST00000417652,;NCL,inframe_deletion,p.Glu157_Asp159del,ENST00000322723,;NCL,inframe_deletion,p.Glu141_Asp143del,ENST00000453992,;NCL,coding_sequence_variant,,ENST00000436894,;NCL,upstream_gene_variant,,ENST00000356936,;SNORD82,upstream_gene_variant,,ENST00000365530,;NCL,non_coding_transcript_exon_variant,,ENST00000461347,;NCL,downstream_gene_variant,,ENST00000484328,;NCL,upstream_gene_variant,,ENST00000494618,;NCL,upstream_gene_variant,,ENST00000466274,;	-	ENSG00000115053	ENST00000322723	Transcript	inframe_deletion	712-720	471-479	157-160	EEDD/D	gaGGAGGATGAc/gac	rs766445200	.	.	-1	NCL	HGNC	7667	protein_coding	YES	CCDS33397.1	ENSP00000318195	NUCL_HUMAN	C9JYW2_HUMAN,C9JWL1_HUMAN,C9JLB1_HUMAN,C9J1H7_HUMAN,B3KM80_HUMAN	UPI0000456F25	.	.	.	3/14	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	-:0.0005	-:0.0004	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCCTCGTCATCCTCCTCATC	.	2	ESCA
ALPP	0	.	GRCh37	2	233245388	233245388	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.921C>T	p.%3D	p.D307D	ENST00000392027	8/11	122	98	24	74	74	0	ALPP,synonymous_variant,p.%3D,ENST00000392027,;AC068134.8,intron_variant,,ENST00000439072,;AC068134.8,intron_variant,,ENST00000441266,;ALPP,downstream_gene_variant,,ENST00000474529,;ALPP,upstream_gene_variant,,ENST00000485563,;	T	ENSG00000163283	ENST00000392027	Transcript	synonymous_variant	1190	921	307	D	gaC/gaT	.	.	.	1	ALPP	HGNC	439	protein_coding	YES	CCDS2490.1	ENSP00000375881	PPB1_HUMAN	.	UPI0000131FF9	.	.	.	8/11	.	hmmpanther:PTHR11596,hmmpanther:PTHR11596:SF31,Gene3D:3.40.720.10,Pfam_domain:PF00245,SMART_domains:SM00098,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGACCCCTC	.	4	ESCA
CHRND	0	.	GRCh37	2	233393037	233393037	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.314delC	p.Pro105ArgfsTer77	p.P105Rfs*77	ENST00000258385	4/12	49	37	12	17	17	0	CHRND,frameshift_variant,p.Pro105ArgfsTer?,ENST00000536614,;CHRND,frameshift_variant,p.Arg15GlyfsTer15,ENST00000457943,;CHRND,frameshift_variant,p.Pro105ArgfsTer77,ENST00000258385,;CHRND,frameshift_variant,p.Pro90ArgfsTer77,ENST00000449596,;CHRND,frameshift_variant,p.Pro90ArgfsTer77,ENST00000543200,;PRSS56,downstream_gene_variant,,ENST00000449534,;CHRND,frameshift_variant,p.Pro105ArgfsTer?,ENST00000412233,;CHRND,frameshift_variant,p.Pro105ArgfsTer377,ENST00000441621,;CHRND,frameshift_variant,p.Pro105ArgfsTer403,ENST00000446616,;PRSS56,downstream_gene_variant,,ENST00000602410,;	-	ENSG00000135902	ENST00000258385	Transcript	frameshift_variant	341	309	103	L/X	ctC/ct	.	.	.	1	CHRND	HGNC	1965	protein_coding	YES	CCDS2494.1	ENSP00000258385	ACHD_HUMAN	.	UPI000012525E	.	.	.	4/12	.	hmmpanther:PTHR18945:SF61,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02931,Gene3D:2.70.170.10,Superfamily_domains:0038932,Prints_domain:PR00254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCGCCTCCCCCC	.	2	ESCA
ARL4C	0	.	GRCh37	2	235402410	235402410	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2242delA	.	.	ENST00000390645	1/1	20	13	7	17	17	0	ARL4C,3_prime_UTR_variant,,ENST00000390645,;ARL4C,3_prime_UTR_variant,,ENST00000339728,;	-	ENSG00000188042	ENST00000390645	Transcript	3_prime_UTR_variant	3288	.	.	.	.	.	.	.	-1	ARL4C	HGNC	698	protein_coding	YES	CCDS2512.1	ENSP00000375057	ARL4C_HUMAN	.	UPI0000004144	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GATGGATTTTTT	.	2	ESCA
IQCA1	0	.	GRCh37	2	237240170	237240170	+	Silent	SNP	C	C	T	rs377472762	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2205G>A	p.%3D	p.A735A	ENST00000409907	18/19	55	36	18	31	31	0	IQCA1,synonymous_variant,p.%3D,ENST00000309507,;IQCA1,synonymous_variant,p.%3D,ENST00000409907,;IQCA1,synonymous_variant,p.%3D,ENST00000431676,;IQCA1,non_coding_transcript_exon_variant,,ENST00000409100,;IQCA1,3_prime_UTR_variant,,ENST00000254653,;IQCA1,non_coding_transcript_exon_variant,,ENST00000479783,;IQCA1,non_coding_transcript_exon_variant,,ENST00000479471,;	T	ENSG00000132321	ENST00000409907	Transcript	synonymous_variant	2480	2205	735	A	gcG/gcA	rs377472762	.	.	-1	IQCA1	HGNC	26195	protein_coding	YES	CCDS46549.1	ENSP00000387347	IQCA1_HUMAN	Q53SG8_HUMAN	UPI000000DA5B	.	.	.	18/19	.	hmmpanther:PTHR14690,hmmpanther:PTHR14690:SF2,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCGCCAG	byFrequency|byCluster	5	ESCA
COL6A3	0	.	GRCh37	2	238232746	238232747	+	3'UTR	DEL	CA	CA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*670_*671delTG	.	.	ENST00000295550	44/44	74	60	14	26	26	0	COL6A3,3_prime_UTR_variant,,ENST00000472056,;COL6A3,3_prime_UTR_variant,,ENST00000295550,;COL6A3,3_prime_UTR_variant,,ENST00000347401,;COL6A3,3_prime_UTR_variant,,ENST00000353578,;COL6A3,downstream_gene_variant,,ENST00000409809,;COL6A3,downstream_gene_variant,,ENST00000346358,;COL6A3,non_coding_transcript_exon_variant,,ENST00000473258,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;	-	ENSG00000163359	ENST00000295550	Transcript	3_prime_UTR_variant	10657-10658	.	.	.	.	.	.	.	-1	COL6A3	HGNC	2213	protein_coding	YES	CCDS33412.1	ENSP00000295550	CO6A3_HUMAN	Q8N4Z1_HUMAN,D9ZGF2_HUMAN	UPI0000456F39	.	.	.	44/44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CTCCAGCACACAC	.	2	ESCA
KLHL30	0	.	GRCh37	2	239049639	239049639	+	Missense_Mutation	SNP	G	G	A	rs751497973	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244G>A	p.Ala82Thr	p.A82T	ENST00000409223	2/8	53	27	25	38	38	0	KLHL30,missense_variant,p.Ala64Thr,ENST00000305959,;KLHL30,missense_variant,p.Ala82Thr,ENST00000409223,;	A	ENSG00000168427	ENST00000409223	Transcript	missense_variant	351	244	82	A/T	Gcc/Acc	rs751497973,COSM3782156,COSM3782155	.	.	1	KLHL30	HGNC	24770	protein_coding	YES	CCDS46555.2	ENSP00000386389	KLH30_HUMAN	J3KND5_HUMAN	UPI00001D7DA5	.	tolerated(0.53)	benign(0.311)	2/8	.	PROSITE_profiles:PS50097,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF9,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,PIRSF_domain:PIRSF037037,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCGCCGTG	byFrequency	5	ESCA
HDAC4	0	.	GRCh37	2	240002800	240002800	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2726C>T	p.Ala909Val	p.A909V	ENST00000345617	22/27	72	46	26	32	32	0	HDAC4,missense_variant,p.Ala493Val,ENST00000543185,;HDAC4,missense_variant,p.Ala909Val,ENST00000345617,;MIR4441,downstream_gene_variant,,ENST00000582623,;AC017028.8,downstream_gene_variant,,ENST00000582701,;HDAC4,non_coding_transcript_exon_variant,,ENST00000494800,;HDAC4,non_coding_transcript_exon_variant,,ENST00000487617,;	A	ENSG00000068024	ENST00000345617	Transcript	missense_variant	3518	2726	909	A/V	gCg/gTg	COSM4092777	.	.	-1	HDAC4	HGNC	14063	protein_coding	YES	CCDS2529.1	ENSP00000264606	HDAC4_HUMAN	Q53SM2_HUMAN,Q53SB4_HUMAN,F5H0B1_HUMAN,F5GX36_HUMAN,C9J0X4_HUMAN	UPI000013D541	.	deleterious(0.03)	possibly_damaging(0.835)	22/27	.	hmmpanther:PTHR10625:SF100,hmmpanther:PTHR10625,Pfam_domain:PF00850,Gene3D:3.40.800.20,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCGCCAAG	.	5	ESCA
HDAC4	0	.	GRCh37	2	240036830	240036830	+	Silent	SNP	G	G	A	rs141268656	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1695C>T	p.%3D	p.S565S	ENST00000345617	13/27	137	118	19	69	69	0	HDAC4,synonymous_variant,p.%3D,ENST00000541256,;HDAC4,synonymous_variant,p.%3D,ENST00000543185,;HDAC4,synonymous_variant,p.%3D,ENST00000345617,;HDAC4,non_coding_transcript_exon_variant,,ENST00000535493,;HDAC4,non_coding_transcript_exon_variant,,ENST00000463007,;HDAC4,non_coding_transcript_exon_variant,,ENST00000493582,;	A	ENSG00000068024	ENST00000345617	Transcript	synonymous_variant	2487	1695	565	S	agC/agT	rs141268656	.	.	-1	HDAC4	HGNC	14063	protein_coding	YES	CCDS2529.1	ENSP00000264606	HDAC4_HUMAN	Q53SM2_HUMAN,Q53SB4_HUMAN,F5H0B1_HUMAN,F5GX36_HUMAN,C9J0X4_HUMAN	UPI000013D541	.	.	.	13/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10625:SF100,hmmpanther:PTHR10625,PIRSF_domain:PIRSF037911	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATCGCTCTC	byCluster|by1000G	4	ESCA
MTERFD2	0	.	GRCh37	2	242035595	242035595	+	Missense_Mutation	SNP	G	G	A	rs376613445	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964C>T	p.Arg322Trp	p.R322W	ENST00000391980	4/4	108	64	44	77	77	0	MTERFD2,missense_variant,p.Arg175Trp,ENST00000439144,;MTERFD2,missense_variant,p.Arg322Trp,ENST00000391980,;MTERFD2,missense_variant,p.Arg134Trp,ENST00000406593,;MTERFD2,intron_variant,,ENST00000495694,;MTERFD2,intron_variant,,ENST00000401626,;MTERFD2,intron_variant,,ENST00000414146,;MTERFD2,downstream_gene_variant,,ENST00000407095,;SNED1,downstream_gene_variant,,ENST00000342631,;MTERFD2,downstream_gene_variant,,ENST00000434791,;SNED1,downstream_gene_variant,,ENST00000405547,;MTERFD2,downstream_gene_variant,,ENST00000424798,;MTERFD2,upstream_gene_variant,,ENST00000449133,;SNED1,downstream_gene_variant,,ENST00000310397,;MTERFD2,intron_variant,,ENST00000480298,;MTERFD2,intron_variant,,ENST00000455202,;MTERFD2,intron_variant,,ENST00000464344,;MTERFD2,intron_variant,,ENST00000493169,;MTERFD2,upstream_gene_variant,,ENST00000479205,;MTERFD2,upstream_gene_variant,,ENST00000488567,;MTERFD2,missense_variant,p.Arg322Trp,ENST00000241527,;MTERFD2,intron_variant,,ENST00000476564,;MTERFD2,upstream_gene_variant,,ENST00000496878,;MTERFD2,downstream_gene_variant,,ENST00000475860,;MTERFD2,downstream_gene_variant,,ENST00000460915,;SNED1,downstream_gene_variant,,ENST00000466618,;	A	ENSG00000122085	ENST00000391980	Transcript	missense_variant	1023	964	322	R/W	Cgg/Tgg	rs376613445	.	.	-1	MTERFD2	HGNC	28785	protein_coding	YES	CCDS2544.1	ENSP00000375840	MTER2_HUMAN	C9JX74_HUMAN,B4DFP7_HUMAN	UPI0000209875	.	deleterious(0.01)	probably_damaging(0.998)	4/4	.	hmmpanther:PTHR13068,hmmpanther:PTHR13068:SF11	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCGAGCCA	byFrequency|byCluster	5	ESCA
CXXC11	0	.	GRCh37	2	242814375	242814375	+	Frame_Shift_Del	DEL	C	C	-	rs758733313,rs35989328	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.674delC	p.Pro225LeufsTer8	p.P225Lfs*8	ENST00000343216	2/2	94	62	32	29	29	0	CXXC11,frameshift_variant,p.Pro225LeufsTer8,ENST00000343216,;CXXC11,3_prime_UTR_variant,,ENST00000419912,;	-	ENSG00000188011	ENST00000343216	Transcript	frameshift_variant	696	668	223	A/X	gCc/gc	rs758733313,rs35989328	.	.	1	CXXC11	HGNC	26585	protein_coding	YES	CCDS42843.1	ENSP00000345374	CB085_HUMAN	.	UPI000014050F	.	.	.	2/2	.	hmmpanther:PTHR14402,hmmpanther:PTHR14402:SF2,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCCTGCCCCCC	byFrequency	3	ESCA
AC093642.5	0	.	GRCh37	2	243056848	243056848	+	RNA	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.375delA	.	.	ENST00000456398	3/8	59	44	15	38	38	0	AC093642.5,non_coding_transcript_exon_variant,,ENST00000442213,;AC093642.5,non_coding_transcript_exon_variant,,ENST00000456398,;AC093642.5,non_coding_transcript_exon_variant,,ENST00000431796,;AC093642.5,intron_variant,,ENST00000403324,;AC093642.5,non_coding_transcript_exon_variant,,ENST00000444990,;AC093642.5,non_coding_transcript_exon_variant,,ENST00000453598,;AC093642.5,non_coding_transcript_exon_variant,,ENST00000416103,;	-	ENSG00000220804	ENST00000456398	Transcript	non_coding_transcript_exon_variant	369	.	.	.	.	.	.	.	1	AC093642.5	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	3/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCATCCAAAAAA	.	3	ESCA
NCOA1	0	.	GRCh37	2	24991841	24991841	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*587delT	.	.	ENST00000406961	23/23	78	55	23	30	30	0	NCOA1,3_prime_UTR_variant,,ENST00000348332,;NCOA1,3_prime_UTR_variant,,ENST00000288599,;NCOA1,3_prime_UTR_variant,,ENST00000406961,;NCOA1,3_prime_UTR_variant,,ENST00000395856,;NCOA1,3_prime_UTR_variant,,ENST00000405141,;NCOA1,downstream_gene_variant,,ENST00000407230,;NCOA1,downstream_gene_variant,,ENST00000538539,;NCOA1,downstream_gene_variant,,ENST00000493773,;	-	ENSG00000084676	ENST00000406961	Transcript	3_prime_UTR_variant	5559	.	.	.	.	.	.	.	1	NCOA1	HGNC	7668	protein_coding	YES	CCDS1712.1	ENSP00000385216	NCOA1_HUMAN	.	UPI000006E1F7	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTCCTTTTTT	.	3	ESCA
ASXL2	0	.	GRCh37	2	26101215	26101215	+	5'UTR	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-124delC	.	.	ENST00000435504	1/13	38	28	9	20	20	0	ASXL2,5_prime_UTR_variant,,ENST00000272341,;ASXL2,5_prime_UTR_variant,,ENST00000336112,;ASXL2,5_prime_UTR_variant,,ENST00000435504,;	-	ENSG00000143970	ENST00000435504	Transcript	5_prime_UTR_variant	171	.	.	.	.	.	.	.	-1	ASXL2	HGNC	23805	protein_coding	YES	.	ENSP00000391447	ASXL2_HUMAN	.	UPI00001DFBE8	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAGACCGGGGGG	.	2	ESCA
GPR113	0	.	GRCh37	2	26535919	26535919	+	Silent	SNP	C	C	T	rs749656962	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1545G>A	p.%3D	p.A515A	ENST00000311519	10/13	70	45	24	36	36	0	GPR113,synonymous_variant,p.%3D,ENST00000541401,;GPR113,synonymous_variant,p.%3D,ENST00000333478,;GPR113,synonymous_variant,p.%3D,ENST00000311519,;GPR113,synonymous_variant,p.%3D,ENST00000421160,;EPT1,intron_variant,,ENST00000442141,;GPR113,downstream_gene_variant,,ENST00000433584,;GPR113,non_coding_transcript_exon_variant,,ENST00000459892,;GPR113,downstream_gene_variant,,ENST00000487878,;GPR113,synonymous_variant,p.%3D,ENST00000447444,;GPR113,3_prime_UTR_variant,,ENST00000435303,;	T	ENSG00000173567	ENST00000311519	Transcript	synonymous_variant	1545	1545	515	A	gcG/gcA	rs749656962,COSM184110	.	.	-1	GPR113	HGNC	18989	protein_coding	YES	CCDS46239.1	ENSP00000307831	GP113_HUMAN	.	UPI000007411E	.	.	.	10/13	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF214,Pfam_domain:PF12003	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCCGCCTG	byFrequency	5	ESCA
OTOF	0	.	GRCh37	2	26684619	26684619	+	Silent	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5478G>A	p.%3D	p.A1826A	ENST00000272371	43/47	74	49	25	31	31	0	OTOF,synonymous_variant,p.%3D,ENST00000403946,;OTOF,synonymous_variant,p.%3D,ENST00000338581,;OTOF,synonymous_variant,p.%3D,ENST00000272371,;OTOF,synonymous_variant,p.%3D,ENST00000339598,;OTOF,synonymous_variant,p.%3D,ENST00000402415,;OTOF,downstream_gene_variant,,ENST00000464574,;	T	ENSG00000115155	ENST00000272371	Transcript	synonymous_variant	5605	5478	1826	A	gcG/gcA	COSM1614694,COSM1614696,COSM1614695	.	.	-1	OTOF	HGNC	8515	protein_coding	YES	CCDS1725.1	ENSP00000272371	OTOF_HUMAN	.	UPI000013D94D	.	.	.	43/47	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGCGCGGG	.	5	ESCA
GPN1	0	.	GRCh37	2	27858031	27858031	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496A>G	p.Ile166Val	p.I166V	ENST00000264718	7/14	188	107	81	105	105	0	GPN1,missense_variant,p.Ile73Val,ENST00000424214,;GPN1,missense_variant,p.Ile166Val,ENST00000264718,;GPN1,missense_variant,p.Ile140Val,ENST00000407583,;GPN1,missense_variant,p.Ile152Val,ENST00000610189,;GPN1,missense_variant,p.Ile57Val,ENST00000458167,;GPN1,missense_variant,p.Ile57Val,ENST00000503738,;GPN1,missense_variant,p.Ile73Val,ENST00000515877,;ZNF512,3_prime_UTR_variant,,ENST00000556601,;RP11-158I13.2,non_coding_transcript_exon_variant,,ENST00000505973,;GPN1,non_coding_transcript_exon_variant,,ENST00000461249,;GPN1,3_prime_UTR_variant,,ENST00000436280,;GPN1,downstream_gene_variant,,ENST00000478484,;	G	ENSG00000198522	ENST00000264718	Transcript	missense_variant	517	496	166	I/V	Atc/Gtc	.	.	.	1	GPN1	HGNC	17030	protein_coding	YES	CCDS1760.2	ENSP00000264718	.	Q53RZ9_HUMAN,B4DQM4_HUMAN	UPI00017A77BC	.	tolerated(0.83)	benign(0.009)	7/14	.	hmmpanther:PTHR21231,hmmpanther:PTHR21231:SF7,Pfam_domain:PF03029,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTCATCTAT	.	5	ESCA
SLC4A1AP	0	.	GRCh37	2	27917513	27917513	+	Missense_Mutation	SNP	A	A	G	rs762687983	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2354A>G	p.Asp785Gly	p.D785G	ENST00000326019	14/14	62	44	18	52	52	0	SLC4A1AP,missense_variant,p.Asp785Gly,ENST00000326019,;SLC4A1AP,non_coding_transcript_exon_variant,,ENST00000492196,;	G	ENSG00000163798	ENST00000326019	Transcript	missense_variant	2636	2354	785	D/G	gAt/gGt	rs762687983	.	.	1	SLC4A1AP	HGNC	13813	protein_coding	YES	CCDS33166.1	ENSP00000323837	NADAP_HUMAN	B4DV74_HUMAN	UPI000006F66B	.	deleterious(0)	possibly_damaging(0.735)	14/14	.	hmmpanther:PTHR23308:SF2,hmmpanther:PTHR23308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGATGGCA	.	5	ESCA
YPEL5	0	.	GRCh37	2	30382103	30382103	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*403delT	.	.	ENST00000379520	5/5	36	23	13	29	29	0	YPEL5,3_prime_UTR_variant,,ENST00000402003,;YPEL5,3_prime_UTR_variant,,ENST00000379519,;YPEL5,3_prime_UTR_variant,,ENST00000379520,;YPEL5,3_prime_UTR_variant,,ENST00000402708,;YPEL5,3_prime_UTR_variant,,ENST00000261353,;YPEL5,downstream_gene_variant,,ENST00000492439,;YPEL5,downstream_gene_variant,,ENST00000470120,;YPEL5,downstream_gene_variant,,ENST00000495673,;YPEL5,downstream_gene_variant,,ENST00000490211,;	-	ENSG00000119801	ENST00000379520	Transcript	3_prime_UTR_variant	1264	.	.	.	.	.	.	.	1	YPEL5	HGNC	18329	protein_coding	YES	CCDS1771.1	ENSP00000368835	YPEL5_HUMAN	.	UPI000000407C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTAAACTTTTTT	.	2	ESCA
TRAPPC12	0	.	GRCh37	2	3464042	3464042	+	Missense_Mutation	SNP	C	C	T	rs547696140	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1612C>T	p.Arg538Trp	p.R538W	ENST00000324266	8/12	143	91	52	56	56	0	TRAPPC12,missense_variant,p.Arg538Trp,ENST00000324266,;TRAPPC12,missense_variant,p.Arg218Trp,ENST00000441983,;TRAPPC12,missense_variant,p.Arg538Trp,ENST00000382110,;TRAPPC12,missense_variant,p.Arg36Trp,ENST00000415624,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000473348,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000462983,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000469147,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000479955,;TRAPPC12,missense_variant,p.Arg150Trp,ENST00000417243,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000461577,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000497597,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000479897,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000433382,;TRAPPC12,downstream_gene_variant,,ENST00000441099,;TRAPPC12,upstream_gene_variant,,ENST00000437733,;TRAPPC12,upstream_gene_variant,,ENST00000489032,;	T	ENSG00000171853	ENST00000324266	Transcript	missense_variant	1807	1612	538	R/W	Cgg/Tgg	rs547696140	.	.	1	TRAPPC12	HGNC	24284	protein_coding	YES	CCDS1652.1	ENSP00000324318	TPC12_HUMAN	Q53S18_HUMAN,Q53QD4_HUMAN	UPI000014132D	.	deleterious(0)	possibly_damaging(0.676)	8/12	.	hmmpanther:PTHR21581:SF1,hmmpanther:PTHR21581,Gene3D:1.25.40.10	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATCCGGCTG	by1000G	5	ESCA
EML4	0	.	GRCh37	2	42490438	42490438	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633T>C	p.%3D	p.T211T	ENST00000318522	5/23	95	67	28	65	65	0	EML4,synonymous_variant,p.%3D,ENST00000401738,;EML4,synonymous_variant,p.%3D,ENST00000318522,;EML4,synonymous_variant,p.%3D,ENST00000402711,;EML4,downstream_gene_variant,,ENST00000409040,;	C	ENSG00000143924	ENST00000318522	Transcript	synonymous_variant	895	633	211	T	acT/acC	.	.	.	1	EML4	HGNC	1316	protein_coding	YES	CCDS1807.1	ENSP00000320663	EMAL4_HUMAN	F2Z2B5_HUMAN	UPI0000140350	.	.	.	5/23	.	hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAACTGCAGA	.	5	ESCA
EML4	0	.	GRCh37	2	42557121	42557121	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2720A>G	p.Asn907Ser	p.N907S	ENST00000318522	23/23	29	14	14	24	24	0	EML4,missense_variant,p.Asn918Ser,ENST00000401738,;EML4,missense_variant,p.Asn907Ser,ENST00000318522,;EML4,missense_variant,p.Asn171Ser,ENST00000453191,;EML4,missense_variant,p.Asn849Ser,ENST00000402711,;COX7A2L,downstream_gene_variant,,ENST00000468711,;EML4,non_coding_transcript_exon_variant,,ENST00000406175,;	G	ENSG00000143924	ENST00000318522	Transcript	missense_variant	2982	2720	907	N/S	aAt/aGt	.	.	.	1	EML4	HGNC	1316	protein_coding	YES	CCDS1807.1	ENSP00000320663	EMAL4_HUMAN	F2Z2B5_HUMAN	UPI0000140350	.	tolerated_low_confidence(0.66)	benign(0.001)	23/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTAAATGAGA	.	5	ESCA
KCNG3	0	.	GRCh37	2	42671596	42671596	+	Silent	SNP	C	C	T	rs367799233	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.789G>A	p.%3D	p.T263T	ENST00000306078	2/2	33	27	5	15	15	0	KCNG3,synonymous_variant,p.%3D,ENST00000306078,;KCNG3,synonymous_variant,p.%3D,ENST00000394973,;SNORD75,downstream_gene_variant,,ENST00000408373,;	T	ENSG00000171126	ENST00000306078	Transcript	synonymous_variant	1385	789	263	T	acG/acA	rs367799233	.	.	-1	KCNG3	HGNC	18306	protein_coding	YES	CCDS1809.1	ENSP00000304127	KCNG3_HUMAN	.	UPI00000557D9	.	.	.	2/2	.	Transmembrane_helices:TMhelix,Prints_domain:PR00169,Superfamily_domains:SSF81324,Pfam_domain:PF00520,Gene3D:1.20.120.350,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF91	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACGGCGTGAT	byFrequency|byCluster	4	ESCA
SIX3	0	.	GRCh37	2	45171872	45171872	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972C>T	p.%3D	p.T324T	ENST00000260653	2/2	53	30	23	13	13	0	SIX3,synonymous_variant,p.%3D,ENST00000260653,;SIX3-AS1,upstream_gene_variant,,ENST00000456467,;SIX3-AS1,upstream_gene_variant,,ENST00000419364,;	T	ENSG00000138083	ENST00000260653	Transcript	synonymous_variant	1314	972	324	T	acC/acT	.	.	.	1	SIX3	HGNC	10889	protein_coding	YES	CCDS1821.1	ENSP00000260653	SIX3_HUMAN	Q9NSJ2_HUMAN,A0PJI2_HUMAN	UPI00001359C4	.	.	.	2/2	.	hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAACCTCCAG	.	5	ESCA
PRKCE	0	.	GRCh37	2	46414855	46414855	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2846delA	.	.	ENST00000306156	15/15	56	35	21	30	30	0	PRKCE,3_prime_UTR_variant,,ENST00000306156,;	-	ENSG00000171132	ENST00000306156	Transcript	3_prime_UTR_variant	5376	.	.	.	.	.	.	.	1	PRKCE	HGNC	9401	protein_coding	YES	CCDS1824.1	ENSP00000306124	KPCE_HUMAN	Q53RT0_HUMAN,L7RTI5_HUMAN,C9JR22_HUMAN	UPI000012DF6B	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	11	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGCTTTAAAAAA	.	2	ESCA
SOCS5	0	.	GRCh37	2	46986468	46986468	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.799A>G	p.Arg267Gly	p.R267G	ENST00000306503	2/2	56	28	27	47	47	0	SOCS5,missense_variant,p.Arg267Gly,ENST00000394861,;SOCS5,missense_variant,p.Arg267Gly,ENST00000306503,;	G	ENSG00000171150	ENST00000306503	Transcript	missense_variant	971	799	267	R/G	Aga/Gga	.	.	.	1	SOCS5	HGNC	16852	protein_coding	YES	CCDS1830.1	ENSP00000305133	SOCS5_HUMAN	B4DL10_HUMAN	UPI0000135B69	.	tolerated(0.09)	possibly_damaging(0.533)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10385,hmmpanther:PTHR10385:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGAGAAGG	.	5	ESCA
PPP1R21	0	.	GRCh37	2	48686995	48686995	+	Missense_Mutation	SNP	G	G	A	rs142054593	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.478G>A	p.Gly160Ser	p.G160S	ENST00000294952	5/22	60	50	9	23	23	0	PPP1R21,missense_variant,p.Gly160Ser,ENST00000449090,;PPP1R21,missense_variant,p.Gly160Ser,ENST00000281394,;PPP1R21,missense_variant,p.Gly160Ser,ENST00000294952,;PPP1R21,3_prime_UTR_variant,,ENST00000416913,;PPP1R21,3_prime_UTR_variant,,ENST00000431614,;	A	ENSG00000162869	ENST00000294952	Transcript	missense_variant	635	478	160	G/S	Ggt/Agt	rs142054593,COSM1212714,COSM1212713	.	.	1	PPP1R21	HGNC	30595	protein_coding	YES	CCDS46278.1	ENSP00000294952	PPR21_HUMAN	F8W7E1_HUMAN	UPI000015C523	.	tolerated(0.47)	benign(0.02)	5/22	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21448	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGACGGTCTC	byCluster	5	ESCA
TSPYL6	0	.	GRCh37	2	54483060	54483060	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.229G>A	p.Ala77Thr	p.A77T	ENST00000317802	1/1	54	44	10	13	13	0	TSPYL6,missense_variant,p.Ala77Thr,ENST00000317802,;ACYP2,intron_variant,,ENST00000394666,;ACYP2,intron_variant,,ENST00000303536,;ACYP2,intron_variant,,ENST00000606865,;ACYP2,intron_variant,,ENST00000607452,;ACYP2,intron_variant,,ENST00000494922,;	T	ENSG00000178021	ENST00000317802	Transcript	missense_variant	350	229	77	A/T	Gcg/Acg	.	.	.	-1	TSPYL6	HGNC	14521	protein_coding	YES	CCDS42682.1	ENSP00000417919	TSYL6_HUMAN	.	UPI000006CF77	.	tolerated(0.05)	benign(0.085)	1/1	.	hmmpanther:PTHR11875:SF29,hmmpanther:PTHR11875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCGCATCGA	.	5	ESCA
RTN4	0	.	GRCh37	2	55252408	55252408	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2827T>C	p.Ser943Pro	p.S943P	ENST00000337526	3/9	47	42	5	39	39	0	RTN4,missense_variant,p.Ser737Pro,ENST00000404909,;RTN4,missense_variant,p.Ser737Pro,ENST00000405240,;RTN4,missense_variant,p.Ser711Pro,ENST00000354474,;RTN4,missense_variant,p.Ser943Pro,ENST00000337526,;RTN4,missense_variant,p.Ser737Pro,ENST00000357376,;RTN4,missense_variant,p.Ser737Pro,ENST00000394611,;RTN4,intron_variant,,ENST00000402434,;RTN4,intron_variant,,ENST00000357732,;RTN4,intron_variant,,ENST00000438462,;RTN4,intron_variant,,ENST00000317610,;RTN4,downstream_gene_variant,,ENST00000427710,;	G	ENSG00000115310	ENST00000337526	Transcript	missense_variant	3071	2827	943	S/P	Tct/Cct	.	.	.	-1	RTN4	HGNC	14085	protein_coding	YES	CCDS42684.1	ENSP00000337838	RTN4_HUMAN	Q53SY1_HUMAN,Q53RF4_HUMAN,Q53R94_HUMAN,C9J685_HUMAN	UPI000000D81D	.	tolerated(0.46)	benign(0.003)	3/9	.	hmmpanther:PTHR10994:SF25,hmmpanther:PTHR10994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGCAGACCCAT	.	3	ESCA
SOX11	0	.	GRCh37	2	5838410	5838410	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4239delT	.	.	ENST00000322002	1/1	38	26	11	28	28	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	-	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	5612	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AATTGATTTTTT	.	2	ESCA
BCL11A	0	.	GRCh37	2	60684502	60684502	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3037delT	.	.	ENST00000335712	4/4	53	27	26	16	16	0	BCL11A,3_prime_UTR_variant,,ENST00000335712,;BCL11A,intron_variant,,ENST00000538214,;BCL11A,intron_variant,,ENST00000359629,;BCL11A,intron_variant,,ENST00000356842,;BCL11A,intron_variant,,ENST00000537768,;BCL11A,downstream_gene_variant,,ENST00000358510,;BCL11A,intron_variant,,ENST00000479026,;BCL11A,intron_variant,,ENST00000489516,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,downstream_gene_variant,,ENST00000477659,;	-	ENSG00000119866	ENST00000335712	Transcript	3_prime_UTR_variant	5773	.	.	.	.	.	.	.	-1	BCL11A	HGNC	13221	protein_coding	YES	CCDS1862.1	ENSP00000338774	BC11A_HUMAN	D6W5D9_HUMAN,Q53TS1_HUMAN,Q53TE8_HUMAN	UPI000013DC00	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTAAATAAAAAA	.	2	ESCA
AHSA2	0	.	GRCh37	2	61406203	61406203	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-204C>T	.	.	ENST00000394457	1/6	61	40	20	29	29	0	AHSA2,5_prime_UTR_variant,,ENST00000394457,;AHSA2,5_prime_UTR_variant,,ENST00000357022,;AHSA2,non_coding_transcript_exon_variant,,ENST00000463681,;AHSA2,non_coding_transcript_exon_variant,,ENST00000489653,;AHSA2,upstream_gene_variant,,ENST00000493310,;AHSA2,upstream_gene_variant,,ENST00000493628,;AHSA2,non_coding_transcript_exon_variant,,ENST00000471542,;AHSA2,upstream_gene_variant,,ENST00000484217,;AHSA2,upstream_gene_variant,,ENST00000487904,;	T	ENSG00000173209	ENST00000394457	Transcript	5_prime_UTR_variant	1540	.	.	.	.	.	.	.	1	AHSA2	HGNC	20437	protein_coding	YES	CCDS1868.1	ENSP00000377970	AHSA2_HUMAN	.	UPI000006DEC9	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCGGCGAGAT	.	5	ESCA
USP34	0	.	GRCh37	2	61462997	61462998	+	Frame_Shift_Del	DEL	TA	TA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7014_7015delTA	p.Asn2338LysfsTer6	p.N2338Kfs*6	ENST00000398571	57/80	33	29	4	21	21	0	USP34,frameshift_variant,p.Asn98LysfsTer6,ENST00000411912,;USP34,frameshift_variant,p.Asn616LysfsTer6,ENST00000453734,;USP34,frameshift_variant,p.Asn2338LysfsTer6,ENST00000398571,;USP34,intron_variant,,ENST00000472706,;USP34,non_coding_transcript_exon_variant,,ENST00000463046,;	-	ENSG00000115464	ENST00000398571	Transcript	frameshift_variant	7091-7092	7014-7015	2338-2339	NS/KX	aaTAgt/aagt	.	.	.	-1	USP34	HGNC	20066	protein_coding	YES	CCDS42686.1	ENSP00000381577	UBP34_HUMAN	.	UPI0000410E09	.	.	.	57/80	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF97	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCTGACTATTATT	.	2	ESCA
MXD1	0	.	GRCh37	2	70166271	70166271	+	3'UTR	DEL	T	T	-	rs777568921	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*860delT	.	.	ENST00000264444	6/6	48	26	22	28	28	0	MXD1,3_prime_UTR_variant,,ENST00000264444,;MXD1,downstream_gene_variant,,ENST00000540449,;MXD1,downstream_gene_variant,,ENST00000435990,;MXD1,intron_variant,,ENST00000465446,;MXD1,downstream_gene_variant,,ENST00000409442,;	-	ENSG00000059728	ENST00000264444	Transcript	3_prime_UTR_variant	1781	.	.	.	.	rs777568921	.	.	1	MXD1	HGNC	6761	protein_coding	YES	CCDS1896.1	ENSP00000264444	MAD1_HUMAN	C9JBE8_HUMAN,B7ZLI7_HUMAN	UPI0000035C7D	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTATCCTTTTTT	byCluster	3	ESCA
C2orf42	0	.	GRCh37	2	70387883	70387883	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1390C>T	p.Arg464Ter	p.R464*	ENST00000264434	9/10	75	43	32	56	56	0	C2orf42,stop_gained,p.Arg464Ter,ENST00000420306,;C2orf42,stop_gained,p.Arg464Ter,ENST00000264434,;	A	ENSG00000115998	ENST00000264434	Transcript	stop_gained	1770	1390	464	R/*	Cga/Tga	.	.	.	-1	C2orf42	HGNC	26056	protein_coding	YES	CCDS1899.1	ENSP00000264434	CB042_HUMAN	C9JZF3_HUMAN,C9JV10_HUMAN,C9JS43_HUMAN,C9JKD5_HUMAN,C9JK51_HUMAN,C9JJF4_HUMAN,C9J5U1_HUMAN,C9J4L7_HUMAN	UPI0000037CF2	.	.	.	9/10	.	hmmpanther:PTHR13518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCGGTTCT	.	5	ESCA
TIA1	0	.	GRCh37	2	70442603	70442603	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.788C>T	p.Ala263Val	p.A263V	ENST00000433529	11/13	51	30	20	44	44	0	TIA1,missense_variant,p.Ala263Val,ENST00000433529,;TIA1,missense_variant,p.Ala34Val,ENST00000454815,;TIA1,missense_variant,p.Ala252Val,ENST00000415783,;TIA1,missense_variant,p.Ala263Val,ENST00000282574,;TIA1,intron_variant,,ENST00000445587,;TIA1,downstream_gene_variant,,ENST00000416149,;TIA1,non_coding_transcript_exon_variant,,ENST00000482876,;TIA1,non_coding_transcript_exon_variant,,ENST00000468787,;C2orf42,intron_variant,,ENST00000470096,;TIA1,non_coding_transcript_exon_variant,,ENST00000495774,;TIA1,downstream_gene_variant,,ENST00000477415,;TIA1,downstream_gene_variant,,ENST00000496096,;TIA1,downstream_gene_variant,,ENST00000484065,;TIA1,upstream_gene_variant,,ENST00000486392,;TIA1,downstream_gene_variant,,ENST00000474699,;TIA1,downstream_gene_variant,,ENST00000474809,;TIA1,downstream_gene_variant,,ENST00000497672,;	A	ENSG00000116001	ENST00000433529	Transcript	missense_variant	999	788	263	A/V	gCa/gTa	.	.	.	-1	TIA1	HGNC	11802	protein_coding	YES	CCDS1901.1	ENSP00000401371	TIA1_HUMAN	F8WE16_HUMAN	UPI0000410EF5	.	deleterious(0.02)	probably_damaging(0.934)	11/13	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF271,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00361,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGTGCTGCA	.	5	ESCA
TGFA	0	.	GRCh37	2	70674501	70674501	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3490A>T	.	.	ENST00000295400	6/6	42	24	18	28	28	0	TGFA,3_prime_UTR_variant,,ENST00000295400,;TGFA,downstream_gene_variant,,ENST00000419940,;TGFA,downstream_gene_variant,,ENST00000444975,;TGFA,downstream_gene_variant,,ENST00000445399,;TGFA,downstream_gene_variant,,ENST00000450929,;TGFA,downstream_gene_variant,,ENST00000418333,;	A	ENSG00000163235	ENST00000295400	Transcript	3_prime_UTR_variant	4221	.	.	.	.	.	.	.	-1	TGFA	HGNC	11765	protein_coding	YES	CCDS1905.1	ENSP00000295400	TGFA_HUMAN	Q9UQ91_HUMAN,Q9UIS3_HUMAN,Q6QBS1_HUMAN	UPI0000006BEF	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAATTGCGT	.	5	ESCA
VAX2	0	.	GRCh37	2	71160174	71160174	+	Frame_Shift_Del	DEL	C	C	-	rs555134830,rs782563368	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.719delC	p.Pro240HisfsTer36	p.P240Hfs*36	ENST00000234392	3/3	71	45	26	23	23	0	VAX2,frameshift_variant,p.Pro240HisfsTer36,ENST00000234392,;ATP6V1B1,upstream_gene_variant,,ENST00000234396,;ATP6V1B1,upstream_gene_variant,,ENST00000412314,;snoU13,upstream_gene_variant,,ENST00000459218,;ATP6V1B1,upstream_gene_variant,,ENST00000432367,;	-	ENSG00000116035	ENST00000234392	Transcript	frameshift_variant	745	713	238	S/X	tCc/tc	rs555134830,rs782563368	.	.	1	VAX2	HGNC	12661	protein_coding	YES	CCDS1911.1	ENSP00000234392	VAX2_HUMAN	F1T0K5_HUMAN	UPI0000138215	.	.	.	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF23	G:0.0006	G:0	G:0	.	G:0.003	G:0	G:0	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAGCGTCCCCCC	byFrequency|by1000G	2	ESCA
CCT7	0	.	GRCh37	2	73461425	73461425	+	5'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-82T>C	.	.	ENST00000258091	1/12	102	62	39	62	62	0	CCT7,5_prime_UTR_variant,,ENST00000540468,;CCT7,5_prime_UTR_variant,,ENST00000258091,;CCT7,5_prime_UTR_variant,,ENST00000539919,;CCT7,upstream_gene_variant,,ENST00000399032,;CCT7,upstream_gene_variant,,ENST00000538797,;PRADC1,upstream_gene_variant,,ENST00000258083,;CCT7,upstream_gene_variant,,ENST00000398422,;CCT7,upstream_gene_variant,,ENST00000537131,;CCT7,intron_variant,,ENST00000471927,;CCT7,intron_variant,,ENST00000473197,;CCT7,intron_variant,,ENST00000492253,;CCT7,intron_variant,,ENST00000469844,;PRADC1,upstream_gene_variant,,ENST00000480093,;CCT7,upstream_gene_variant,,ENST00000482064,;CCT7,upstream_gene_variant,,ENST00000473786,;CCT7,non_coding_transcript_exon_variant,,ENST00000461290,;CCT7,upstream_gene_variant,,ENST00000409924,;PRADC1,upstream_gene_variant,,ENST00000470391,;CCT7,upstream_gene_variant,,ENST00000464397,;CCT7,upstream_gene_variant,,ENST00000480489,;	C	ENSG00000135624	ENST00000258091	Transcript	5_prime_UTR_variant	60	.	.	.	.	.	.	.	1	CCT7	HGNC	1622	protein_coding	YES	CCDS46336.1	ENSP00000258091	TCPH_HUMAN	F8WAM2_HUMAN	UPI0000136B06	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTATTGCGC	.	5	ESCA
CCT7	0	.	GRCh37	2	73477474	73477474	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1111A>G	p.Thr371Ala	p.T371A	ENST00000258091	10/12	99	56	42	45	45	0	CCT7,missense_variant,p.Thr284Ala,ENST00000540468,;CCT7,missense_variant,p.Thr371Ala,ENST00000258091,;CCT7,missense_variant,p.Thr243Ala,ENST00000538797,;CCT7,missense_variant,p.Thr167Ala,ENST00000398422,;CCT7,missense_variant,p.Thr327Ala,ENST00000539919,;CCT7,missense_variant,p.Thr271Ala,ENST00000537131,;FBXO41,downstream_gene_variant,,ENST00000295133,;FBXO41,downstream_gene_variant,,ENST00000521871,;CCT7,downstream_gene_variant,,ENST00000473786,;CCT7,downstream_gene_variant,,ENST00000488856,;CCT7,downstream_gene_variant,,ENST00000409924,;	G	ENSG00000135624	ENST00000258091	Transcript	missense_variant	1252	1111	371	T/A	Acc/Gcc	.	.	.	1	CCT7	HGNC	1622	protein_coding	YES	CCDS46336.1	ENSP00000258091	TCPH_HUMAN	F8WAM2_HUMAN	UPI0000136B06	.	deleterious(0)	probably_damaging(0.989)	10/12	.	Prints_domain:PR00304,Superfamily_domains:SSF52029,Superfamily_domains:SSF54849,Gene3D:3.50.7.10,Pfam_domain:PF00118,TIGRFAM_domain:TIGR02345,hmmpanther:PTHR11353:SF22,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGCACCTTC	.	5	ESCA
CCT7	0	.	GRCh37	2	73478542	73478542	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1392G>A	p.%3D	p.L464L	ENST00000258091	11/12	88	55	32	28	28	0	CCT7,synonymous_variant,p.%3D,ENST00000540468,;CCT7,synonymous_variant,p.%3D,ENST00000258091,;CCT7,synonymous_variant,p.%3D,ENST00000538797,;CCT7,synonymous_variant,p.%3D,ENST00000398422,;CCT7,synonymous_variant,p.%3D,ENST00000539919,;CCT7,synonymous_variant,p.%3D,ENST00000537131,;FBXO41,downstream_gene_variant,,ENST00000295133,;FBXO41,downstream_gene_variant,,ENST00000521871,;CCT7,downstream_gene_variant,,ENST00000473786,;CCT7,downstream_gene_variant,,ENST00000488856,;CCT7,downstream_gene_variant,,ENST00000409924,;	A	ENSG00000135624	ENST00000258091	Transcript	synonymous_variant	1533	1392	464	L	ctG/ctA	.	.	.	1	CCT7	HGNC	1622	protein_coding	YES	CCDS46336.1	ENSP00000258091	TCPH_HUMAN	F8WAM2_HUMAN	UPI0000136B06	.	.	.	11/12	.	Superfamily_domains:SSF48592,Pfam_domain:PF00118,Gene3D:1.10.560.10,TIGRFAM_domain:TIGR02345,hmmpanther:PTHR11353:SF22,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTGCGGGC	.	5	ESCA
TET3	0	.	GRCh37	2	74326650	74326652	+	In_Frame_Del	DEL	AGA	AGA	-	rs745864343	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AGA	AGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3119_3121delAGA	p.Lys1040del	p.K1040del	ENST00000409262	8/9	57	33	24	24	24	0	TET3,inframe_deletion,p.Lys1040del,ENST00000409262,;	-	ENSG00000187605	ENST00000409262	Transcript	inframe_deletion	3110-3112	3110-3112	1037-1038	EK/E	gAGAag/gag	rs745864343	.	.	1	TET3	HGNC	28313	protein_coding	YES	CCDS46339.1	ENSP00000386869	TET3_HUMAN	K9JJH7_HUMAN	UPI0000DD79F5	.	.	.	8/9	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF4,Pfam_domain:PF12851	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAGCCGAGAAGAAG	.	2	ESCA
TET3	0	.	GRCh37	2	74328621	74328621	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4301C>T	p.Ala1434Val	p.A1434V	ENST00000409262	9/9	94	77	17	45	45	0	TET3,missense_variant,p.Ala1434Val,ENST00000409262,;	T	ENSG00000187605	ENST00000409262	Transcript	missense_variant	4301	4301	1434	A/V	gCc/gTc	.	.	.	1	TET3	HGNC	28313	protein_coding	YES	CCDS46339.1	ENSP00000386869	TET3_HUMAN	K9JJH7_HUMAN	UPI0000DD79F5	.	tolerated(0.05)	benign(0.077)	9/9	.	hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF4,Pfam_domain:PF12851	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGCCGCAG	.	5	ESCA
MTHFD2	0	.	GRCh37	2	74437167	74437167	+	Missense_Mutation	SNP	C	C	T	rs751985540	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.661C>T	p.Arg221Cys	p.R221C	ENST00000394053	5/8	65	46	19	52	52	0	MTHFD2,missense_variant,p.Arg180Cys,ENST00000409601,;MTHFD2,missense_variant,p.Arg221Cys,ENST00000394053,;MTHFD2,missense_variant,p.Arg119Cys,ENST00000264090,;MTHFD2,missense_variant,p.Arg57Cys,ENST00000394050,;MTHFD2,intron_variant,,ENST00000409804,;MTHFD2,non_coding_transcript_exon_variant,,ENST00000462026,;MTHFD2,downstream_gene_variant,,ENST00000477455,;MTHFD2,downstream_gene_variant,,ENST00000488086,;MTHFD2,3_prime_UTR_variant,,ENST00000470592,;MTHFD2,3_prime_UTR_variant,,ENST00000489041,;RP11-287D1.3,downstream_gene_variant,,ENST00000451608,;	T	ENSG00000065911	ENST00000394053	Transcript	missense_variant	741	661	221	R/C	Cgt/Tgt	rs751985540	.	.	1	MTHFD2	HGNC	7434	protein_coding	YES	CCDS1935.2	ENSP00000377617	MTDC_HUMAN	Q7Z650_HUMAN,B4DY35_HUMAN,B2R7W0_HUMAN	UPI0000208708	.	tolerated(0.1)	benign(0.052)	5/8	.	HAMAP:MF_01576,hmmpanther:PTHR10025:SF29,hmmpanther:PTHR10025,Gene3D:3.40.50.720,Pfam_domain:PF02882,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAACGTCCC	.	5	ESCA
DOK1	0	.	GRCh37	2	74782459	74782459	+	Frame_Shift_Del	DEL	C	C	-	rs200525020	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245delC	p.Pro82LeufsTer76	p.P82Lfs*76	ENST00000233668	2/5	183	123	60	42	42	0	DOK1,frameshift_variant,p.Pro82LeufsTer76,ENST00000233668,;DOK1,frameshift_variant,p.Pro82LeufsTer339,ENST00000340004,;DOK1,5_prime_UTR_variant,,ENST00000409429,;LOXL3,intron_variant,,ENST00000413469,;M1AP,downstream_gene_variant,,ENST00000290536,;M1AP,downstream_gene_variant,,ENST00000536235,;LOXL3,upstream_gene_variant,,ENST00000264094,;LOXL3,upstream_gene_variant,,ENST00000409986,;M1AP,downstream_gene_variant,,ENST00000409585,;LOXL3,upstream_gene_variant,,ENST00000409249,;M1AP,downstream_gene_variant,,ENST00000358434,;LOXL3,upstream_gene_variant,,ENST00000409549,;LOXL3,upstream_gene_variant,,ENST00000393937,;DOK1,non_coding_transcript_exon_variant,,ENST00000480318,;DOK1,non_coding_transcript_exon_variant,,ENST00000489958,;DOK1,non_coding_transcript_exon_variant,,ENST00000485132,;DOK1,intron_variant,,ENST00000496966,;DOK1,downstream_gene_variant,,ENST00000488613,;M1AP,downstream_gene_variant,,ENST00000485997,;LOXL3,upstream_gene_variant,,ENST00000484369,;M1AP,downstream_gene_variant,,ENST00000464686,;DOK1,frameshift_variant,p.Pro45LeufsTer50,ENST00000429631,;DOK1,non_coding_transcript_exon_variant,,ENST00000475191,;DOK1,non_coding_transcript_exon_variant,,ENST00000464613,;DOK1,non_coding_transcript_exon_variant,,ENST00000474924,;DOK1,non_coding_transcript_exon_variant,,ENST00000482206,;	-	ENSG00000115325	ENST00000233668	Transcript	frameshift_variant	908	239	80	T/X	aCc/ac	rs200525020	.	.	1	DOK1	HGNC	2990	protein_coding	YES	CCDS1954.1	ENSP00000233668	DOK1_HUMAN	Q2TA81_HUMAN	UPI00001296A9	.	.	.	2/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF46,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGAGACCCCCC	byCluster|by1000G	3	ESCA
LRRTM1	0	.	GRCh37	2	80530816	80530816	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129C>T	p.%3D	p.C43C	ENST00000295057	2/2	28	22	6	11	11	0	LRRTM1,synonymous_variant,p.%3D,ENST00000415098,;LRRTM1,synonymous_variant,p.%3D,ENST00000452811,;LRRTM1,synonymous_variant,p.%3D,ENST00000295057,;LRRTM1,synonymous_variant,p.%3D,ENST00000409148,;LRRTM1,synonymous_variant,p.%3D,ENST00000416268,;CTNNA2,intron_variant,,ENST00000496558,;CTNNA2,intron_variant,,ENST00000361291,;CTNNA2,intron_variant,,ENST00000541047,;CTNNA2,intron_variant,,ENST00000540488,;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000402739,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,synonymous_variant,p.%3D,ENST00000417012,;LRRTM1,synonymous_variant,p.%3D,ENST00000433224,;	A	ENSG00000162951	ENST00000295057	Transcript	synonymous_variant	786	129	43	C	tgC/tgT	.	.	.	-1	LRRTM1	HGNC	19408	protein_coding	YES	CCDS1966.1	ENSP00000295057	LRRT1_HUMAN	C9JPM9_HUMAN,C9JF97_HUMAN,C9JEE2_HUMAN	UPI000013E1FE	.	.	.	2/2	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCGGCACAG	.	5	ESCA
CTNNA2	0	.	GRCh37	2	80875615	80875615	+	3'UTR	DEL	T	T	-	rs535237092	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*624delT	.	.	ENST00000466387	22/22	117	64	53	44	44	0	CTNNA2,3_prime_UTR_variant,,ENST00000496558,;CTNNA2,3_prime_UTR_variant,,ENST00000466387,;CTNNA2,3_prime_UTR_variant,,ENST00000541047,;CTNNA2,3_prime_UTR_variant,,ENST00000343114,;CTNNA2,3_prime_UTR_variant,,ENST00000402739,;CTNNA2,downstream_gene_variant,,ENST00000540488,;CTNNA2,downstream_gene_variant,,ENST00000361291,;	-	ENSG00000066032	ENST00000466387	Transcript	3_prime_UTR_variant	4060	.	.	.	.	rs535237092	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	.	.	22/22	.	.	-:0.0010	-:0	-:0.0014	.	-:0.001	-:0.001	-:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATCATGTTTTTT	byFrequency|by1000G	3	ESCA
ANKRD36BP2	0	.	GRCh37	2	89103911	89103911	+	RNA	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4385T>G	.	.	ENST00000393525	13/15	152	112	39	112	112	0	ANKRD36BP2,non_coding_transcript_exon_variant,,ENST00000393525,;ANKRD36BP2,non_coding_transcript_exon_variant,,ENST00000393515,;ANKRD36BP2,non_coding_transcript_exon_variant,,ENST00000454490,;ANKRD36BP2,non_coding_transcript_exon_variant,,ENST00000575193,;	G	ENSG00000230006	ENST00000393525	Transcript	non_coding_transcript_exon_variant	4385	.	.	.	.	.	.	.	1	ANKRD36BP2	HGNC	33607	processed_transcript	YES	.	.	.	.	.	.	.	.	13/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGATCAACT	.	5	ESCA
ASAP2	0	.	GRCh37	2	9491025	9491025	+	Splice_Site	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1111+1G>A	.	p.X371_splice	ENST00000281419	.	42	21	20	33	33	0	ASAP2,splice_donor_variant,,ENST00000281419,;ASAP2,splice_donor_variant,,ENST00000315273,;ASAP2,splice_donor_variant,,ENST00000471687,;	A	ENSG00000151693	ENST00000281419	Transcript	splice_donor_variant	.	.	.	.	.	COSM4096246	.	.	1	ASAP2	HGNC	2721	protein_coding	YES	CCDS1661.1	ENSP00000281419	ASAP2_HUMAN	Q53RT9_HUMAN,Q53RS3_HUMAN,Q53R39_HUMAN	UPI0000073459	.	.	.	.	12/27	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCACGTAAGG	.	5	ESCA
CNNM4	0	.	GRCh37	2	97475532	97475532	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*285delT	.	.	ENST00000377075	7/7	54	46	8	30	30	0	CNNM4,3_prime_UTR_variant,,ENST00000377075,;CNNM4,downstream_gene_variant,,ENST00000540067,;RP11-353K11.1,downstream_gene_variant,,ENST00000608609,;CNNM4,downstream_gene_variant,,ENST00000496186,;	-	ENSG00000158158	ENST00000377075	Transcript	3_prime_UTR_variant	2704	.	.	.	.	.	.	.	1	CNNM4	HGNC	105	protein_coding	YES	CCDS2024.2	ENSP00000366275	CNNM4_HUMAN	.	UPI0000207C95	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CATCACTTTTTT	.	2	ESCA
TSGA10	0	.	GRCh37	2	99695219	99695219	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785C>A	p.Thr262Asn	p.T262N	ENST00000393483	12/21	55	32	23	37	37	0	TSGA10,missense_variant,p.Thr262Asn,ENST00000410001,;TSGA10,missense_variant,p.Thr262Asn,ENST00000542655,;TSGA10,missense_variant,p.Thr262Asn,ENST00000409564,;TSGA10,missense_variant,p.Thr262Asn,ENST00000539964,;TSGA10,missense_variant,p.Thr262Asn,ENST00000355053,;TSGA10,missense_variant,p.Thr262Asn,ENST00000393483,;TSGA10,missense_variant,p.Thr262Asn,ENST00000393482,;TSGA10,non_coding_transcript_exon_variant,,ENST00000488960,;TSGA10,non_coding_transcript_exon_variant,,ENST00000489546,;TSGA10,intron_variant,,ENST00000478090,;	T	ENSG00000135951	ENST00000393483	Transcript	missense_variant	1630	785	262	T/N	aCc/aAc	.	.	.	-1	TSGA10	HGNC	14927	protein_coding	YES	CCDS2037.1	ENSP00000377123	TSG10_HUMAN	F8WA32_HUMAN	UPI0000072CE3	.	deleterious(0.01)	possibly_damaging(0.777)	12/21	.	hmmpanther:PTHR23159:SF9,hmmpanther:PTHR23159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGGGTTCCA	.	5	ESCA
C2ORF15	0	.	GRCh37	2	99758247	99758247	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-337C>A	.	.	ENST00000302513	1/4	24	19	5	13	13	0	C2ORF15,5_prime_UTR_variant,,ENST00000302513,;C2ORF15,5_prime_UTR_variant,,ENST00000409684,;TSGA10,intron_variant,,ENST00000393483,;TSGA10,upstream_gene_variant,,ENST00000355053,;TSGA10,upstream_gene_variant,,ENST00000542655,;TSGA10,upstream_gene_variant,,ENST00000539964,;TSGA10,upstream_gene_variant,,ENST00000393482,;TSGA10,intron_variant,,ENST00000471174,;TSGA10,intron_variant,,ENST00000476849,;TSGA10,upstream_gene_variant,,ENST00000494483,;TSGA10,upstream_gene_variant,,ENST00000489926,;TSGA10,upstream_gene_variant,,ENST00000497915,;C2orf15,5_prime_UTR_variant,,ENST00000424491,;TSGA10,upstream_gene_variant,,ENST00000464459,;C2ORF15,upstream_gene_variant,,ENST00000496794,;TSGA10,upstream_gene_variant,,ENST00000462782,;	A	ENSG00000273045	ENST00000302513	Transcript	5_prime_UTR_variant	300	.	.	.	.	.	.	.	1	C2ORF15	Uniprot_gn	.	protein_coding	YES	CCDS2038.1	ENSP00000302202	CB015_HUMAN	.	UPI000006E239	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGGCTTGGG	.	2	ESCA
PCNP	0	.	GRCh37	3	101311692	101311692	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*103delT	.	.	ENST00000265260	5/5	34	26	8	28	28	0	PCNP,3_prime_UTR_variant,,ENST00000296024,;PCNP,3_prime_UTR_variant,,ENST00000265260,;PCNP,3_prime_UTR_variant,,ENST00000469941,;PCNP,non_coding_transcript_exon_variant,,ENST00000486406,;PCNP,downstream_gene_variant,,ENST00000470490,;PCNP,3_prime_UTR_variant,,ENST00000460231,;PCNP,non_coding_transcript_exon_variant,,ENST00000465366,;PCNP,downstream_gene_variant,,ENST00000498274,;	-	ENSG00000081154	ENST00000265260	Transcript	3_prime_UTR_variant	753	.	.	.	.	.	.	.	1	PCNP	HGNC	30023	protein_coding	YES	CCDS2942.1	ENSP00000265260	PCNP_HUMAN	.	UPI0000070241	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGCCGCTTTTTT	.	2	ESCA
PCNP	0	.	GRCh37	3	101312475	101312476	+	3'UTR	DEL	AA	AA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AA	AA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*886_*887delAA	.	.	ENST00000265260	5/5	44	22	22	20	20	0	PCNP,3_prime_UTR_variant,,ENST00000296024,;PCNP,3_prime_UTR_variant,,ENST00000265260,;PCNP,3_prime_UTR_variant,,ENST00000469941,;PCNP,downstream_gene_variant,,ENST00000470490,;PCNP,downstream_gene_variant,,ENST00000486406,;PCNP,3_prime_UTR_variant,,ENST00000460231,;PCNP,downstream_gene_variant,,ENST00000498274,;PCNP,downstream_gene_variant,,ENST00000465366,;	-	ENSG00000081154	ENST00000265260	Transcript	3_prime_UTR_variant	1536-1537	.	.	.	.	.	.	.	1	PCNP	HGNC	30023	protein_coding	YES	CCDS2942.1	ENSP00000265260	PCNP_HUMAN	.	UPI0000070241	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACACCAAAAAAA	.	2	ESCA
CEP97	0	.	GRCh37	3	101484459	101484459	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*71delT	.	.	ENST00000341893	11/11	88	58	30	56	56	0	CEP97,3_prime_UTR_variant,,ENST00000494050,;CEP97,3_prime_UTR_variant,,ENST00000327230,;CEP97,3_prime_UTR_variant,,ENST00000341893,;CEP97,downstream_gene_variant,,ENST00000467655,;	-	ENSG00000182504	ENST00000341893	Transcript	3_prime_UTR_variant	3414	.	.	.	.	.	.	.	1	CEP97	HGNC	26244	protein_coding	YES	CCDS2944.1	ENSP00000342510	CEP97_HUMAN	.	UPI0000074569	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTTGCTTTTTT	.	2	ESCA
ATP2B2	0	.	GRCh37	3	10369568	10369568	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*930C>T	.	.	ENST00000360273	23/23	36	14	22	46	46	0	ATP2B2,3_prime_UTR_variant,,ENST00000343816,;ATP2B2,3_prime_UTR_variant,,ENST00000383800,;ATP2B2,3_prime_UTR_variant,,ENST00000397077,;ATP2B2,3_prime_UTR_variant,,ENST00000352432,;ATP2B2,3_prime_UTR_variant,,ENST00000360273,;ATP2B2,downstream_gene_variant,,ENST00000452124,;MIR378B,upstream_gene_variant,,ENST00000578876,;ATP2B2,downstream_gene_variant,,ENST00000467702,;ATP2B2,downstream_gene_variant,,ENST00000468426,;ATP2B2,3_prime_UTR_variant,,ENST00000460129,;	A	ENSG00000157087	ENST00000360273	Transcript	3_prime_UTR_variant	5101	.	.	.	.	.	.	.	-1	ATP2B2	HGNC	815	protein_coding	YES	CCDS33701.1	ENSP00000353414	AT2B2_HUMAN	Q4J699_HUMAN,Q4J696_HUMAN	UPI00001261EF	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATGGCTATC	.	5	ESCA
CCDC80	0	.	GRCh37	3	112358576	112358576	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177C>T	p.%3D	p.R59R	ENST00000206423	2/8	90	58	32	45	45	0	CCDC80,synonymous_variant,p.%3D,ENST00000206423,;CCDC80,synonymous_variant,p.%3D,ENST00000439685,;CCDC80,upstream_gene_variant,,ENST00000461431,;CCDC80,non_coding_transcript_exon_variant,,ENST00000475181,;CCDC80,downstream_gene_variant,,ENST00000473959,;CCDC80,downstream_gene_variant,,ENST00000469554,;CCDC80,downstream_gene_variant,,ENST00000480275,;	A	ENSG00000091986	ENST00000206423	Transcript	synonymous_variant	1131	177	59	R	cgC/cgT	.	.	.	-1	CCDC80	HGNC	30649	protein_coding	YES	CCDS2968.1	ENSP00000206423	CCD80_HUMAN	.	UPI000004EE7F	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCCGCGAGA	.	5	ESCA
CD200R1	0	.	GRCh37	3	112693701	112693701	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4C>A	p.Leu2Ile	p.L2I	ENST00000308611	1/8	44	31	13	16	16	0	CD200R1,missense_variant,p.Leu2Ile,ENST00000440122,;CD200R1,missense_variant,p.Leu2Ile,ENST00000490004,;CD200R1,missense_variant,p.Leu2Ile,ENST00000295863,;CD200R1,missense_variant,p.Leu2Ile,ENST00000308611,;CD200R1,missense_variant,p.Leu2Ile,ENST00000471858,;	T	ENSG00000163606	ENST00000308611	Transcript	missense_variant	269	4	2	L/I	Ctc/Atc	.	.	.	-1	CD200R1	HGNC	24235	protein_coding	YES	CCDS2969.1	ENSP00000311035	MO2R1_HUMAN	.	UPI000013E2BD	.	tolerated(0.39)	benign(0.125)	1/8	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGAGCATTT	.	5	ESCA
KIAA2018	0	.	GRCh37	3	113368347	113368347	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5444delA	.	.	ENST00000316407	7/7	32	20	12	34	34	0	KIAA2018,3_prime_UTR_variant,,ENST00000491165,;KIAA2018,3_prime_UTR_variant,,ENST00000316407,;KIAA2018,downstream_gene_variant,,ENST00000478658,;KIAA2018,downstream_gene_variant,,ENST00000496826,;	-	ENSG00000176542	ENST00000316407	Transcript	3_prime_UTR_variant	12593	.	.	.	.	.	.	.	-1	KIAA2018	HGNC	30494	protein_coding	YES	CCDS43133.1	ENSP00000320794	K2018_HUMAN	.	UPI00004800D8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACTAGGTTTTTT	.	2	ESCA
RP11-71H17.7	0	.	GRCh37	3	124438073	124438073	+	5'Flank	SNP	G	G	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000568966	.	33	21	12	25	25	0	KALRN,missense_variant,p.Gly1209Ala,ENST00000291478,;KALRN,missense_variant,p.Gly2875Ala,ENST00000354186,;KALRN,missense_variant,p.Gly1177Ala,ENST00000428018,;KALRN,missense_variant,p.Gly2906Ala,ENST00000360013,;RP11-71H17.7,upstream_gene_variant,,ENST00000568966,;	C	ENSG00000260391	ENST00000568966	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4562	1	RP11-71H17.7	Clone_based_vega_gene	.	sense_overlapping	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGGTGTGA	.	5	ESCA
HEG1	0	.	GRCh37	3	124733606	124733606	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1589-772C>T	.	.	ENST00000311127	.	43	28	14	20	20	0	HEG1,intron_variant,,ENST00000311127,;HEG1,non_coding_transcript_exon_variant,,ENST00000477536,;HEG1,upstream_gene_variant,,ENST00000488654,;	A	ENSG00000173706	ENST00000311127	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	HEG1	HGNC	29227	protein_coding	YES	CCDS46898.1	ENSP00000311502	HEG1_HUMAN	.	UPI00006C069B	.	.	.	.	5/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCGTCCGT	.	5	ESCA
ALG1L	0	.	GRCh37	3	125647977	125647977	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000340333	.	24	12	11	19	19	0	ALG1L,downstream_gene_variant,,ENST00000340333,;FAM86JP,non_coding_transcript_exon_variant,,ENST00000485843,;FAM86JP,non_coding_transcript_exon_variant,,ENST00000467239,;FAM86JP,non_coding_transcript_exon_variant,,ENST00000486431,;FAM86JP,downstream_gene_variant,,ENST00000484500,;	A	ENSG00000189366	ENST00000340333	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	141	-1	ALG1L	HGNC	33721	protein_coding	YES	CCDS33840.1	ENSP00000340009	ALG1L_HUMAN	.	UPI000020A11A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAACGCAGGA	.	5	ESCA
KLF15	0	.	GRCh37	3	126071107	126071107	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659T>C	p.Leu220Ser	p.L220S	ENST00000296233	2/3	46	26	20	18	18	0	KLF15,missense_variant,p.Leu220Ser,ENST00000296233,;KLF15,downstream_gene_variant,,ENST00000509675,;	G	ENSG00000163884	ENST00000296233	Transcript	missense_variant	890	659	220	L/S	tTg/tCg	.	.	.	-1	KLF15	HGNC	14536	protein_coding	YES	CCDS3036.1	ENSP00000296233	KLF15_HUMAN	.	UPI0000001659	.	deleterious(0)	probably_damaging(0.964)	2/3	.	hmmpanther:PTHR23223:SF146,hmmpanther:PTHR23223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCAACACT	.	5	ESCA
RAF1	0	.	GRCh37	3	12625385	12625385	+	3'UTR	SNP	C	C	T	rs374944110	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*628G>A	.	.	ENST00000251849	17/17	34	21	12	43	43	0	RAF1,3_prime_UTR_variant,,ENST00000442415,;RAF1,3_prime_UTR_variant,,ENST00000251849,;RAF1,downstream_gene_variant,,ENST00000432427,;MKRN2,downstream_gene_variant,,ENST00000411987,;MKRN2,downstream_gene_variant,,ENST00000170447,;RAF1,downstream_gene_variant,,ENST00000534997,;MKRN2,downstream_gene_variant,,ENST00000448482,;RAF1,downstream_gene_variant,,ENST00000542177,;RAF1,downstream_gene_variant,,ENST00000471449,;RAF1,downstream_gene_variant,,ENST00000475353,;RAF1,downstream_gene_variant,,ENST00000494557,;RAF1,downstream_gene_variant,,ENST00000423275,;RAF1,downstream_gene_variant,,ENST00000465826,;	T	ENSG00000132155	ENST00000251849	Transcript	3_prime_UTR_variant	3015	.	.	.	.	rs374944110	.	.	-1	RAF1	HGNC	9829	protein_coding	YES	CCDS2612.1	ENSP00000251849	RAF1_HUMAN	L7RRS6_HUMAN	UPI0000049CFC	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGCGGATT	byCluster	5	ESCA
TOPBP1	0	.	GRCh37	3	133379900	133379900	+	Frame_Shift_Del	DEL	A	A	-	rs778900877,rs142462088	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72delT	p.Phe24LeufsTer7	p.F24Lfs*7	ENST00000260810	2/28	92	61	31	39	39	0	TOPBP1,frameshift_variant,p.Phe24LeufsTer7,ENST00000260810,;TOPBP1,upstream_gene_variant,,ENST00000508524,;RNU6-678P,upstream_gene_variant,,ENST00000516832,;TFP1,upstream_gene_variant,,ENST00000460564,;TOPBP1,upstream_gene_variant,,ENST00000511439,;TFP1,upstream_gene_variant,,ENST00000490470,;TFP1,upstream_gene_variant,,ENST00000497521,;	-	ENSG00000163781	ENST00000260810	Transcript	frameshift_variant	204	72	24	F/X	ttT/tt	rs778900877,rs142462088,COSM1419183	.	.	-1	TOPBP1	HGNC	17008	protein_coding	YES	CCDS46919.1	ENSP00000260810	TOPB1_HUMAN	A0AV47_HUMAN	UPI000020A292	.	.	.	2/28	.	hmmpanther:PTHR13561:SF25,hmmpanther:PTHR13561	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.F24fs*7|c.72delT|3	INDELOCATOR*|VARSCANI*|PINDEL	AGCTTTAAAAAA	.	3	ESCA
AMOTL2	0	.	GRCh37	3	134076011	134076011	+	3'UTR	DEL	A	A	-	rs74910485	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*536delT	.	.	ENST00000249883	10/10	24	13	11	17	17	0	AMOTL2,3_prime_UTR_variant,,ENST00000514516,;AMOTL2,3_prime_UTR_variant,,ENST00000249883,;AMOTL2,3_prime_UTR_variant,,ENST00000422605,;AMOTL2,downstream_gene_variant,,ENST00000513145,;RPL39P5,upstream_gene_variant,,ENST00000273411,;AMOTL2,non_coding_transcript_exon_variant,,ENST00000506326,;	-	ENSG00000114019	ENST00000249883	Transcript	3_prime_UTR_variant	3193	.	.	.	.	rs74910485	.	.	-1	AMOTL2	HGNC	17812	protein_coding	YES	CCDS33860.1	ENSP00000249883	AMOL2_HUMAN	D6RJA4_HUMAN,D6RIC7_HUMAN,D6RFG0_HUMAN,D6RF61_HUMAN,D6RCL7_HUMAN,D6RBK2_HUMAN,B3KQD2_HUMAN	UPI00001B216C	.	.	.	10/10	.	.	C:0.0405	C:0.1422	C:0.0173	.	C:0	C:0.003	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTCCCCAAAAAA	byFrequency|byCluster|by1000G	2	ESCA
EPHB1	0	.	GRCh37	3	134978479	134978479	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*517A>G	.	.	ENST00000398015	16/16	34	25	9	23	23	0	EPHB1,3_prime_UTR_variant,,ENST00000398015,;EPHB1,downstream_gene_variant,,ENST00000493838,;	G	ENSG00000154928	ENST00000398015	Transcript	3_prime_UTR_variant	3842	.	.	.	.	.	.	.	1	EPHB1	HGNC	3392	protein_coding	YES	CCDS46921.1	ENSP00000381097	EPHB1_HUMAN	C9K090_HUMAN,C9JB88_HUMAN,C9J6S4_HUMAN,C9J466_HUMAN,B3KTB2_HUMAN	UPI000012A07E	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGAGTCTC	.	5	ESCA
FBLN2	0	.	GRCh37	3	13679189	13679189	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3466G>A	p.Ala1156Thr	p.A1156T	ENST00000404922	18/18	32	8	24	17	17	0	FBLN2,missense_variant,p.Ala1109Thr,ENST00000295760,;FBLN2,missense_variant,p.Ala1156Thr,ENST00000492059,;FBLN2,missense_variant,p.Ala1156Thr,ENST00000404922,;FBLN2,missense_variant,p.Ala1135Thr,ENST00000535798,;FBLN2,intron_variant,,ENST00000295761,;FBLN2,intron_variant,,ENST00000421373,;	A	ENSG00000163520	ENST00000404922	Transcript	missense_variant	3585	3466	1156	A/T	Gcg/Acg	COSM244456,COSM244455	.	.	1	FBLN2	HGNC	3601	protein_coding	YES	CCDS46761.1	ENSP00000384169	FBLN2_HUMAN	Q9Y3V7_HUMAN,C9JQS6_HUMAN	UPI000042B0C1	.	tolerated(0.08)	benign(0.3)	18/18	.	hmmpanther:PTHR24048,hmmpanther:PTHR24048:SF72	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A1156T|c.3466G>A|3,BUFFER|p.A575T|c.1723G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCGCGCCA	.	5	ESCA
DZIP1L	0	.	GRCh37	3	137811298	137811299	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.796dupG	p.Glu266GlyfsTer4	p.E266Gfs*4	ENST00000327532	5/16	55	42	13	30	30	0	DZIP1L,frameshift_variant,p.Glu266GlyfsTer4,ENST00000469243,;DZIP1L,frameshift_variant,p.Glu266GlyfsTer4,ENST00000327532,;DZIP1L,non_coding_transcript_exon_variant,,ENST00000488595,;DZIP1L,non_coding_transcript_exon_variant,,ENST00000490472,;DZIP1L,upstream_gene_variant,,ENST00000473850,;	C	ENSG00000158163	ENST00000327532	Transcript	frameshift_variant	1159-1160	796-797	266	E/GX	gaa/gGaa	.	.	.	-1	DZIP1L	HGNC	26551	protein_coding	YES	CCDS3096.1	ENSP00000332148	DZI1L_HUMAN	C9JRW2_HUMAN,C9JD19_HUMAN	UPI0000161A66	.	.	.	5/16	.	hmmpanther:PTHR21502:SF8,hmmpanther:PTHR21502	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTATTTCCCCA	.	3	ESCA
ARMC8	0	.	GRCh37	3	137965245	137965246	+	Intron	INS	-	-	AT	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1092+1229_1092+1230dupAT	.	.	ENST00000481646	.	68	47	21	43	43	0	ARMC8,3_prime_UTR_variant,,ENST00000358441,;ARMC8,3_prime_UTR_variant,,ENST00000471453,;ARMC8,intron_variant,,ENST00000469044,;ARMC8,intron_variant,,ENST00000538260,;ARMC8,intron_variant,,ENST00000485396,;ARMC8,intron_variant,,ENST00000463485,;ARMC8,intron_variant,,ENST00000393058,;ARMC8,intron_variant,,ENST00000481646,;ARMC8,intron_variant,,ENST00000461822,;ARMC8,intron_variant,,ENST00000491704,;ARMC8,downstream_gene_variant,,ENST00000489213,;ARMC8,downstream_gene_variant,,ENST00000469860,;ARMC8,downstream_gene_variant,,ENST00000470821,;ARMC8,non_coding_transcript_exon_variant,,ENST00000486832,;ARMC8,intron_variant,,ENST00000460495,;ARMC8,downstream_gene_variant,,ENST00000470549,;	AT	ENSG00000114098	ENST00000481646	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ARMC8	HGNC	24999	protein_coding	YES	CCDS54646.1	ENSP00000420333	ARMC8_HUMAN	C9J8P8_HUMAN,C9J625_HUMAN,B7Z979_HUMAN	UPI000007471D	.	.	.	.	13/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTAGTGATATA	.	2	ESCA
SLC6A6	0	.	GRCh37	3	14530420	14530420	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3916delT	.	.	ENST00000454876	15/15	33	19	14	23	22	0	SLC6A6,3_prime_UTR_variant,,ENST00000454876,;SLC6A6,3_prime_UTR_variant,,ENST00000360861,;SLC6A6,downstream_gene_variant,,ENST00000452151,;GRIP2,downstream_gene_variant,,ENST00000273083,;GRIP2,downstream_gene_variant,,ENST00000430219,;GRIP2,downstream_gene_variant,,ENST00000443613,;GRIP2,downstream_gene_variant,,ENST00000507975,;SLC6A6,3_prime_UTR_variant,,ENST00000458124,;	-	ENSG00000131389	ENST00000454876	Transcript	3_prime_UTR_variant	6097	.	.	.	.	.	.	.	1	SLC6A6	HGNC	11052	protein_coding	YES	CCDS33705.1	ENSP00000398063	SC6A6_HUMAN	C9JPV1_HUMAN	UPI000013549A	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	11	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCTTCATTTTTT	.	2	ESCA
PLSCR1	0	.	GRCh37	3	146239638	146239640	+	In_Frame_Del	DEL	ACA	ACA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	ACA	ACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556_558delTGT	p.Cys186del	p.C186del	ENST00000342435	6/9	84	69	15	34	34	0	PLSCR1,inframe_deletion,p.Cys162del,ENST00000462666,;PLSCR1,inframe_deletion,p.Cys179del,ENST00000487389,;PLSCR1,inframe_deletion,p.Cys186del,ENST00000472349,;PLSCR1,inframe_deletion,p.Cys105del,ENST00000486631,;PLSCR1,inframe_deletion,p.Cys105del,ENST00000448787,;PLSCR1,inframe_deletion,p.Cys186del,ENST00000342435,;PLSCR1,intron_variant,,ENST00000483300,;PLSCR1,intron_variant,,ENST00000448205,;PLSCR1,upstream_gene_variant,,ENST00000484560,;PLSCR1,upstream_gene_variant,,ENST00000470496,;PLSCR1,3_prime_UTR_variant,,ENST00000489775,;PLSCR1,3_prime_UTR_variant,,ENST00000468985,;PLSCR1,3_prime_UTR_variant,,ENST00000478267,;PLSCR1,non_coding_transcript_exon_variant,,ENST00000494568,;PLSCR1,intron_variant,,ENST00000463777,;PLSCR1,intron_variant,,ENST00000493432,;PLSCR1,intron_variant,,ENST00000488253,;PLSCR1,downstream_gene_variant,,ENST00000490745,;	-	ENSG00000188313	ENST00000342435	Transcript	inframe_deletion	967-969	556-558	186	C/-	TGT/-	.	.	.	-1	PLSCR1	HGNC	9092	protein_coding	YES	CCDS3135.1	ENSP00000345494	PLS1_HUMAN	C9JSI9_HUMAN,C9JE06_HUMAN,C9J7K9_HUMAN	UPI0000001627	.	.	.	6/9	.	Low_complexity_(Seg):seg,Pfam_domain:PF03803,hmmpanther:PTHR23248,hmmpanther:PTHR23248:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCAGGGACAACAAC	.	3	ESCA
ZIC1	0	.	GRCh37	3	147132838	147132838	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1500C>T	.	.	ENST00000282928	3/3	46	36	9	28	28	0	ZIC1,3_prime_UTR_variant,,ENST00000282928,;ZIC1,downstream_gene_variant,,ENST00000488404,;ZIC1,intron_variant,,ENST00000472523,;	T	ENSG00000152977	ENST00000282928	Transcript	3_prime_UTR_variant	3573	.	.	.	.	.	.	.	1	ZIC1	HGNC	12872	protein_coding	YES	CCDS3136.1	ENSP00000282928	ZIC1_HUMAN	.	UPI000013DD09	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGTCGATGC	.	5	ESCA
MED12L	0	.	GRCh37	3	151150682	151150682	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*96delT	.	.	ENST00000474524	43/43	66	59	7	44	44	0	MED12L,3_prime_UTR_variant,,ENST00000474524,;MED12L,3_prime_UTR_variant,,ENST00000273432,;IGSF10,intron_variant,,ENST00000489791,;IGSF10,downstream_gene_variant,,ENST00000282466,;IGSF10,intron_variant,,ENST00000497472,;MED12L,downstream_gene_variant,,ENST00000488092,;IGSF10,downstream_gene_variant,,ENST00000495443,;IGSF10,downstream_gene_variant,,ENST00000493841,;	-	ENSG00000144893	ENST00000474524	Transcript	3_prime_UTR_variant	6566	.	.	.	.	.	.	.	1	MED12L	HGNC	16050	protein_coding	YES	CCDS33876.1	ENSP00000417235	MD12L_HUMAN	.	UPI000020A46B	.	.	.	43/43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTCCCTTTTTT	.	3	ESCA
PTX3	0	.	GRCh37	3	157161191	157161191	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*430delA	.	.	ENST00000295927	3/3	85	52	33	60	60	0	PTX3,3_prime_UTR_variant,,ENST00000295927,;VEPH1,intron_variant,,ENST00000362010,;VEPH1,intron_variant,,ENST00000392833,;VEPH1,intron_variant,,ENST00000392832,;VEPH1,intron_variant,,ENST00000543418,;VEPH1,intron_variant,,ENST00000479987,;	-	ENSG00000163661	ENST00000295927	Transcript	3_prime_UTR_variant	1714	.	.	.	.	.	.	.	1	PTX3	HGNC	9692	protein_coding	YES	CCDS3180.1	ENSP00000295927	PTX3_HUMAN	.	UPI000013E2D6	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TATTACAAAAAA	.	2	ESCA
ANKRD28	0	.	GRCh37	3	15765962	15765962	+	Missense_Mutation	SNP	T	T	C	rs748420293	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.620A>G	p.Tyr207Cys	p.Y207C	ENST00000399451	7/28	27	8	19	29	29	0	ANKRD28,missense_variant,p.Tyr207Cys,ENST00000399451,;ANKRD28,missense_variant,p.Tyr240Cys,ENST00000383777,;ANKRD28,non_coding_transcript_exon_variant,,ENST00000460278,;ANKRD28,non_coding_transcript_exon_variant,,ENST00000497037,;ANKRD28,non_coding_transcript_exon_variant,,ENST00000476472,;ANKRD28,upstream_gene_variant,,ENST00000492895,;ANKRD28,missense_variant,p.Tyr207Cys,ENST00000412318,;ANKRD28,missense_variant,p.Tyr151Cys,ENST00000451422,;ANKRD28,non_coding_transcript_exon_variant,,ENST00000498524,;	C	ENSG00000206560	ENST00000399451	Transcript	missense_variant	988	620	207	Y/C	tAt/tGt	rs748420293	.	.	-1	ANKRD28	HGNC	29024	protein_coding	YES	CCDS46769.1	ENSP00000382379	ANR28_HUMAN	.	UPI00004120FF	.	deleterious(0.01)	probably_damaging(0.996)	7/28	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24158:SF22,hmmpanther:PTHR24158,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTATAAGAC	.	5	ESCA
PRKCI	0	.	GRCh37	3	169988209	169988209	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451C>T	p.Arg151Cys	p.R151C	ENST00000295797	6/18	34	24	10	20	20	0	PRKCI,missense_variant,p.Arg151Cys,ENST00000295797,;	T	ENSG00000163558	ENST00000295797	Transcript	missense_variant	756	451	151	R/C	Cgt/Tgt	.	.	.	1	PRKCI	HGNC	9404	protein_coding	YES	CCDS3212.2	ENSP00000295797	KPCI_HUMAN	.	UPI000020A798	.	deleterious(0.04)	probably_damaging(0.938)	6/18	.	Prints_domain:PR00008,Superfamily_domains:SSF57889,PIRSF_domain:PIRSF000554,SMART_domains:SM00109,Gene3D:3.30.60.20,Pfam_domain:PF00130,PROSITE_patterns:PS00479,hmmpanther:PTHR24357:SF60,hmmpanther:PTHR24357,PROSITE_profiles:PS50081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAGCGTGCT	.	5	ESCA
EIF5A2	0	.	GRCh37	3	170606437	170606437	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4712A>G	.	.	ENST00000295822	5/5	56	37	19	33	33	0	EIF5A2,3_prime_UTR_variant,,ENST00000295822,;EIF5A2,downstream_gene_variant,,ENST00000474096,;EIF5A2,downstream_gene_variant,,ENST00000487522,;EIF5A2,downstream_gene_variant,,ENST00000460117,;	C	ENSG00000163577	ENST00000295822	Transcript	3_prime_UTR_variant	5360	.	.	.	.	.	.	.	-1	EIF5A2	HGNC	3301	protein_coding	YES	CCDS3214.1	ENSP00000295822	IF5A2_HUMAN	C9J4W5_HUMAN	UPI0000035FC3	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGTTTCTGC	.	5	ESCA
FNDC3B	0	.	GRCh37	3	172096210	172096210	+	Frame_Shift_Del	DEL	C	C	-	rs772258822,rs776920749	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3165delC	p.Thr1056ProfsTer7	p.T1056Pfs*7	ENST00000336824	24/26	111	81	30	40	40	0	FNDC3B,frameshift_variant,p.Thr1056ProfsTer7,ENST00000416957,;FNDC3B,frameshift_variant,p.Thr1056ProfsTer7,ENST00000415807,;FNDC3B,frameshift_variant,p.Thr1056ProfsTer7,ENST00000336824,;	-	ENSG00000075420	ENST00000336824	Transcript	frameshift_variant	3258	3159	1053	V/X	gtC/gt	rs772258822,rs776920749	.	.	1	FNDC3B	HGNC	24670	protein_coding	YES	CCDS3217.1	ENSP00000338523	FND3B_HUMAN	.	UPI00001AE8B2	.	.	.	24/26	.	hmmpanther:PTHR19900,hmmpanther:PTHR19900:SF54,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	AAGTGTCCCCCC	byFrequency	2	ESCA
FNDC3B	0	.	GRCh37	3	172098807	172098807	+	Missense_Mutation	SNP	C	C	T	rs752282685	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3227C>T	p.Thr1076Met	p.T1076M	ENST00000336824	25/26	91	82	9	33	33	0	FNDC3B,missense_variant,p.Thr1076Met,ENST00000416957,;FNDC3B,missense_variant,p.Thr1076Met,ENST00000415807,;FNDC3B,missense_variant,p.Thr1076Met,ENST00000336824,;	T	ENSG00000075420	ENST00000336824	Transcript	missense_variant	3326	3227	1076	T/M	aCg/aTg	rs752282685,COSM582580	.	.	1	FNDC3B	HGNC	24670	protein_coding	YES	CCDS3217.1	ENSP00000338523	FND3B_HUMAN	.	UPI00001AE8B2	.	tolerated(0.21)	benign(0.105)	25/26	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19900,hmmpanther:PTHR19900:SF54,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	GGAGACGGTAC	.	2	ESCA
TBL1XR1	0	.	GRCh37	3	176740814	176740814	+	3'UTR	DEL	A	A	-	rs373608516	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2472delT	.	.	ENST00000430069	16/16	26	16	10	17	16	0	TBL1XR1,3_prime_UTR_variant,,ENST00000430069,;TBL1XR1,downstream_gene_variant,,ENST00000457928,;TBL1XR1,non_coding_transcript_exon_variant,,ENST00000474363,;	-	ENSG00000177565	ENST00000430069	Transcript	3_prime_UTR_variant	4277	.	.	.	.	rs373608516	.	.	-1	TBL1XR1	HGNC	29529	protein_coding	YES	CCDS46961.1	ENSP00000405574	TBL1R_HUMAN	C9JY82_HUMAN,C9JTW8_HUMAN,C9JLJ1_HUMAN,C9JEC9_HUMAN,C9JCW4_HUMAN,C9JCK0_HUMAN,C9JBN1_HUMAN,C9J903_HUMAN,C9J7E1_HUMAN,C9J3H2_HUMAN,C9IYU9_HUMAN	UPI0000136A71	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAAAGAAAAAA	byCluster	2	ESCA
DNAJC19	0	.	GRCh37	3	180705810	180705810	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129+1G>A	.	p.X43_splice	ENST00000382564	.	52	40	12	20	20	0	DNAJC19,splice_donor_variant,,ENST00000486355,;DNAJC19,splice_donor_variant,,ENST00000491873,;DNAJC19,splice_donor_variant,,ENST00000382564,;DNAJC19,splice_donor_variant,,ENST00000479269,;SOX2-OT,upstream_gene_variant,,ENST00000487240,;SOX2-OT,upstream_gene_variant,,ENST00000461063,;DNAJC19,splice_donor_variant,,ENST00000469657,;DNAJC19,splice_donor_variant,,ENST00000478723,;DNAJC19,non_coding_transcript_exon_variant,,ENST00000472504,;DNAJC19,non_coding_transcript_exon_variant,,ENST00000485675,;DNAJC19,non_coding_transcript_exon_variant,,ENST00000482363,;	T	ENSG00000205981	ENST00000382564	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	DNAJC19	HGNC	30528	protein_coding	YES	CCDS33895.1	ENSP00000372005	TIM14_HUMAN	.	UPI000006CD5D	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTACAGATT	.	5	ESCA
ATP11B	0	.	GRCh37	3	182635844	182635844	+	Silent	SNP	C	C	T	rs372790774	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3486C>T	p.%3D	p.N1162N	ENST00000323116	30/30	107	96	10	58	58	0	ATP11B,synonymous_variant,p.%3D,ENST00000323116,;ATP11B,3_prime_UTR_variant,,ENST00000498086,;ATP11B,downstream_gene_variant,,ENST00000484691,;ATP11B,downstream_gene_variant,,ENST00000491699,;RP11-531F16.4,downstream_gene_variant,,ENST00000608000,;ATP11B,downstream_gene_variant,,ENST00000475636,;ATP11B,3_prime_UTR_variant,,ENST00000466758,;ATP11B,downstream_gene_variant,,ENST00000490303,;	T	ENSG00000058063	ENST00000323116	Transcript	synonymous_variant	3746	3486	1162	N	aaC/aaT	rs372790774,COSM243109	.	.	1	ATP11B	HGNC	13553	protein_coding	YES	CCDS33896.1	ENSP00000321195	AT11B_HUMAN	B4E3T1_HUMAN	UPI000004124E	.	.	.	30/30	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF57	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCAACGACAG	byCluster	4	ESCA
DCUN1D1	0	.	GRCh37	3	182661936	182661936	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*946delT	.	.	ENST00000292782	7/7	44	32	12	16	16	0	DCUN1D1,3_prime_UTR_variant,,ENST00000292782,;DCUN1D1,downstream_gene_variant,,ENST00000469954,;DCUN1D1,downstream_gene_variant,,ENST00000492563,;	-	ENSG00000043093	ENST00000292782	Transcript	3_prime_UTR_variant	1880	.	.	.	.	.	.	.	-1	DCUN1D1	HGNC	18184	protein_coding	YES	CCDS3240.1	ENSP00000292782	DCNL1_HUMAN	C9JVE2_HUMAN,C9JUW4_HUMAN,C9JRU6_HUMAN,C9J8R4_HUMAN,C9J0B2_HUMAN	UPI0000073D68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GATGACAAAAAA	.	2	ESCA
B3GNT5	0	.	GRCh37	3	182989418	182989418	+	3'UTR	DEL	T	T	-	rs200010970	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*703delT	.	.	ENST00000326505	2/2	59	43	16	31	31	0	B3GNT5,3_prime_UTR_variant,,ENST00000460419,;B3GNT5,3_prime_UTR_variant,,ENST00000326505,;MCF2L2,intron_variant,,ENST00000328913,;MCF2L2,intron_variant,,ENST00000473233,;MCF2L2,intron_variant,,ENST00000447025,;B3GNT5,downstream_gene_variant,,ENST00000481531,;MCF2L2,downstream_gene_variant,,ENST00000414362,;B3GNT5,downstream_gene_variant,,ENST00000464191,;B3GNT5,downstream_gene_variant,,ENST00000464923,;B3GNT5,downstream_gene_variant,,ENST00000465010,;B3GNT5,intron_variant,,ENST00000480551,;B3GNT5,downstream_gene_variant,,ENST00000496270,;B3GNT5,downstream_gene_variant,,ENST00000493370,;B3GNT5,downstream_gene_variant,,ENST00000488301,;B3GNT5,downstream_gene_variant,,ENST00000477699,;MCF2L2,intron_variant,,ENST00000488149,;	-	ENSG00000176597	ENST00000326505	Transcript	3_prime_UTR_variant	2362	.	.	.	.	rs200010970	.	.	1	B3GNT5	HGNC	15684	protein_coding	YES	CCDS3244.1	ENSP00000316173	B3GN5_HUMAN	C9J5K2_HUMAN,C9J368_HUMAN,C9IYY0_HUMAN	UPI000003D75E	.	.	.	2/2	.	.	-:0.0098	-:0.0318	-:0.0014	.	-:0.001	-:0.002	-:0.0031	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AATGGATTTTTT	byFrequency|byCluster|by1000G	2	ESCA
EIF2B5	0	.	GRCh37	3	183854553	183854553	+	Intron	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320+31delT	.	.	ENST00000273783	.	29	22	6	17	17	0	EIF2B5,3_prime_UTR_variant,,ENST00000432569,;EIF2B5,intron_variant,,ENST00000273783,;EIF2B5,intron_variant,,ENST00000444495,;RP11-778D9.13,upstream_gene_variant,,ENST00000609288,;RP11-778D9.12,upstream_gene_variant,,ENST00000608232,;RP11-778D9.12,upstream_gene_variant,,ENST00000608135,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000471832,;EIF2B5,intron_variant,,ENST00000498831,;EIF2B5,upstream_gene_variant,,ENST00000492773,;EIF2B5,upstream_gene_variant,,ENST00000479833,;EIF2B5,intron_variant,,ENST00000432982,;EIF2B5,intron_variant,,ENST00000481054,;EIF2B5,intron_variant,,ENST00000491144,;EIF2B5,upstream_gene_variant,,ENST00000491008,;EIF2B5,upstream_gene_variant,,ENST00000493740,;EIF2B5,upstream_gene_variant,,ENST00000468748,;	-	ENSG00000145191	ENST00000273783	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	EIF2B5	HGNC	3261	protein_coding	YES	CCDS3252.1	ENSP00000273783	EI2BE_HUMAN	C9JRD9_HUMAN	UPI000013D9CF	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCCATGTTTCGC	.	2	ESCA
SATB1	0	.	GRCh37	3	18390354	18390354	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*308delT	.	.	ENST00000417717	12/12	27	8	19	38	38	0	SATB1,3_prime_UTR_variant,,ENST00000454909,;SATB1,3_prime_UTR_variant,,ENST00000417717,;SATB1,3_prime_UTR_variant,,ENST00000338745,;TBC1D5,intron_variant,,ENST00000414318,;SATB1,downstream_gene_variant,,ENST00000476178,;SATB1,downstream_gene_variant,,ENST00000467628,;SATB1,downstream_gene_variant,,ENST00000606296,;	-	ENSG00000182568	ENST00000417717	Transcript	3_prime_UTR_variant	3667	.	.	.	.	.	.	.	-1	SATB1	HGNC	10541	protein_coding	YES	CCDS56242.1	ENSP00000399518	SATB1_HUMAN	C9JP21_HUMAN,C9JLL5_HUMAN,C9JGL9_HUMAN,C9J7F3_HUMAN,C9J3I0_HUMAN	UPI0000E1FB67	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAACTAAAAAA	.	2	ESCA
CLCN2	0	.	GRCh37	3	184064408	184064408	+	Missense_Mutation	SNP	C	C	T	rs150751460	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2683G>A	p.Asp895Asn	p.D895N	ENST00000265593	24/24	58	46	12	21	21	0	CLCN2,missense_variant,p.Asp851Asn,ENST00000434054,;CLCN2,missense_variant,p.Asp895Asn,ENST00000265593,;CLCN2,missense_variant,p.Asp878Asn,ENST00000344937,;CLCN2,missense_variant,p.Asp866Asn,ENST00000457512,;CLCN2,3_prime_UTR_variant,,ENST00000423355,;EIF2B5,intron_variant,,ENST00000444495,;FAM131A,downstream_gene_variant,,ENST00000340957,;FAM131A,downstream_gene_variant,,ENST00000418768,;FAM131A,downstream_gene_variant,,ENST00000453072,;FAM131A,downstream_gene_variant,,ENST00000383847,;FAM131A,downstream_gene_variant,,ENST00000433578,;FAM131A,downstream_gene_variant,,ENST00000310585,;FAM131A,downstream_gene_variant,,ENST00000418281,;FAM131A,downstream_gene_variant,,ENST00000450976,;FAM131A,downstream_gene_variant,,ENST00000487702,;CLCN2,3_prime_UTR_variant,,ENST00000430397,;	T	ENSG00000114859	ENST00000265593	Transcript	missense_variant	2855	2683	895	D/N	Gac/Aac	rs150751460	.	.	-1	CLCN2	HGNC	2020	protein_coding	YES	CCDS3263.1	ENSP00000265593	CLCN2_HUMAN	.	UPI000013D645	.	deleterious(0.04)	benign(0.041)	24/24	.	.	T:0.0010	T:0.0038	T:0	.	T:0	T:0	T:0	T:0.0025	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCGTCGC	byFrequency|byCluster|by1000G	5	ESCA
IGF2BP2	0	.	GRCh37	3	185361566	185361566	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1753A>G	.	.	ENST00000382199	16/16	71	62	9	36	36	0	IGF2BP2,3_prime_UTR_variant,,ENST00000382199,;IGF2BP2,downstream_gene_variant,,ENST00000421047,;IGF2BP2,downstream_gene_variant,,ENST00000457616,;IGF2BP2,downstream_gene_variant,,ENST00000346192,;IGF2BP2,downstream_gene_variant,,ENST00000464166,;	C	ENSG00000073792	ENST00000382199	Transcript	3_prime_UTR_variant	3649	.	.	.	.	.	.	.	-1	IGF2BP2	HGNC	28867	protein_coding	YES	CCDS3273.2	ENSP00000371634	IF2B2_HUMAN	.	UPI000013C5B6	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTTTCTTTT	.	3	ESCA
TRA2B	0	.	GRCh37	3	185635349	185635349	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*154C>A	.	.	ENST00000453386	9/9	33	23	10	35	35	0	TRA2B,3_prime_UTR_variant,,ENST00000259043,;TRA2B,3_prime_UTR_variant,,ENST00000453386,;TRA2B,3_prime_UTR_variant,,ENST00000414862,;TRA2B,downstream_gene_variant,,ENST00000382191,;TRA2B,downstream_gene_variant,,ENST00000465245,;TRA2B,3_prime_UTR_variant,,ENST00000456380,;TRA2B,non_coding_transcript_exon_variant,,ENST00000463328,;TRA2B,non_coding_transcript_exon_variant,,ENST00000487615,;TRA2B,non_coding_transcript_exon_variant,,ENST00000492417,;TRA2B,non_coding_transcript_exon_variant,,ENST00000466832,;	T	ENSG00000136527	ENST00000453386	Transcript	3_prime_UTR_variant	1297	.	.	.	.	.	.	.	-1	TRA2B	HGNC	10781	protein_coding	YES	CCDS33905.1	ENSP00000416959	TRA2B_HUMAN	.	UPI00000040A0	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACAGCATTT	.	5	ESCA
ETV5	0	.	GRCh37	3	185823652	185823652	+	Silent	SNP	G	G	A	rs200588942	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6C>T	p.%3D	p.D2D	ENST00000306376	2/13	45	38	6	27	27	0	ETV5,synonymous_variant,p.%3D,ENST00000413301,;ETV5,synonymous_variant,p.%3D,ENST00000421809,;ETV5,synonymous_variant,p.%3D,ENST00000422039,;ETV5,synonymous_variant,p.%3D,ENST00000440773,;ETV5,synonymous_variant,p.%3D,ENST00000434744,;ETV5,synonymous_variant,p.%3D,ENST00000537818,;ETV5,synonymous_variant,p.%3D,ENST00000306376,;DGKG,non_coding_transcript_exon_variant,,ENST00000447054,;ETV5,non_coding_transcript_exon_variant,,ENST00000476890,;ETV5,non_coding_transcript_exon_variant,,ENST00000472868,;ETV5,upstream_gene_variant,,ENST00000475484,;ETV5,upstream_gene_variant,,ENST00000495808,;	A	ENSG00000244405	ENST00000306376	Transcript	synonymous_variant	253	6	2	D	gaC/gaT	rs200588942	.	.	-1	ETV5	HGNC	3494	protein_coding	YES	CCDS33906.1	ENSP00000306894	ETV5_HUMAN	C9JMF0_HUMAN,C9J5A5_HUMAN,C9J0Z2_HUMAN	UPI000012A175	.	.	.	2/13	.	hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF166,Pfam_domain:PF04621	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACCCGTCCAT	byCluster|by1000G	4	ESCA
TP63	0	.	GRCh37	3	189614077	189614077	+	3'UTR	DEL	T	T	-	rs550984911	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1795delT	.	.	ENST00000264731	14/14	63	50	13	23	23	0	TP63,3_prime_UTR_variant,,ENST00000354600,;TP63,3_prime_UTR_variant,,ENST00000264731,;TP63,3_prime_UTR_variant,,ENST00000382063,;TP63,downstream_gene_variant,,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000456148,;TP63,downstream_gene_variant,,ENST00000392460,;TP63,downstream_gene_variant,,ENST00000320472,;TP63,downstream_gene_variant,,ENST00000440651,;TP63,downstream_gene_variant,,ENST00000449992,;TP63,downstream_gene_variant,,ENST00000392463,;	-	ENSG00000073282	ENST00000264731	Transcript	3_prime_UTR_variant	3918	.	.	.	.	rs550984911	.	.	1	TP63	HGNC	15979	protein_coding	YES	CCDS3293.1	ENSP00000264731	P63_HUMAN	.	UPI0000073CF2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGATTATTTTTT	.	2	ESCA
TFRC	0	.	GRCh37	3	195778941	195778941	+	Missense_Mutation	SNP	G	G	A	rs764730449	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2155C>T	p.Arg719Cys	p.R719C	ENST00000360110	19/19	75	66	9	34	34	0	TFRC,missense_variant,p.Arg719Cys,ENST00000360110,;TFRC,missense_variant,p.Arg719Cys,ENST00000392396,;TFRC,missense_variant,p.Arg638Cys,ENST00000420415,;TFRC,missense_variant,p.Arg437Cys,ENST00000535031,;TFRC,3_prime_UTR_variant,,ENST00000540528,;TFRC,intron_variant,,ENST00000426789,;TFRC,downstream_gene_variant,,ENST00000463047,;TFRC,downstream_gene_variant,,ENST00000475593,;TFRC,downstream_gene_variant,,ENST00000483983,;	A	ENSG00000072274	ENST00000360110	Transcript	missense_variant	2325	2155	719	R/C	Cgt/Tgt	rs764730449	.	.	-1	TFRC	HGNC	11763	protein_coding	YES	CCDS3312.1	ENSP00000353224	TFR1_HUMAN	G3V0E5_HUMAN,F5H6B1_HUMAN	UPI0000049ADE	.	tolerated(0.14)	probably_damaging(0.973)	19/19	.	hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF26,Gene3D:3kasA03,Pfam_domain:PF04253,Superfamily_domains:SSF47672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTACGCAGTT	byFrequency	2	ESCA
ZNF385D	0	.	GRCh37	3	22413997	22413997	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.127C>T	.	.	ENST00000494118	1/7	37	16	20	30	30	0	ZNF385D,non_coding_transcript_exon_variant,,ENST00000494118,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494108,;ZNF385D,intron_variant,,ENST00000466511,;	A	ENSG00000151789	ENST00000494118	Transcript	non_coding_transcript_exon_variant	127	.	.	.	.	.	.	.	-1	ZNF385D	HGNC	26191	processed_transcript	.	.	.	.	.	.	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCGAGCTC	.	5	ESCA
UBE2E1	0	.	GRCh37	3	23848848	23848850	+	In_Frame_Del	DEL	AAG	AAG	-	rs781155886	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AAG	AAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94_96delAAG	p.Lys32del	p.K32del	ENST00000306627	2/6	40	15	25	45	45	0	UBE2E1,inframe_deletion,p.Lys32del,ENST00000442670,;UBE2E1,inframe_deletion,p.Lys32del,ENST00000306627,;UBE2E1,inframe_deletion,p.Lys32del,ENST00000346855,;UBE2E1,upstream_gene_variant,,ENST00000424381,;UBE2E1,upstream_gene_variant,,ENST00000467766,;UBE2E1,upstream_gene_variant,,ENST00000452012,;UBE2E1-AS1,upstream_gene_variant,,ENST00000426702,;UBE2E1,non_coding_transcript_exon_variant,,ENST00000481622,;UBE2E1,upstream_gene_variant,,ENST00000475680,;UBE2E1,non_coding_transcript_exon_variant,,ENST00000495141,;UBE2E1,non_coding_transcript_exon_variant,,ENST00000484048,;	-	ENSG00000170142	ENST00000306627	Transcript	inframe_deletion	307-309	88-90	30	K/-	AAG/-	rs781155886,COSM1422160	.	.	1	UBE2E1	HGNC	12477	protein_coding	YES	CCDS2638.1	ENSP00000303709	UB2E1_HUMAN	C9J2P0_HUMAN	UPI0000137964	.	.	.	2/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24068,hmmpanther:PTHR24068:SF23,Gene3D:3.10.110.10	.	.	.	.	.	.	.	-:0	-:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	deletion	.	6	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCCCCAAGAAGAA	.	3	ESCA
CMC1	0	.	GRCh37	3	28283209	28283209	+	5'UTR	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-76C>G	.	.	ENST00000466830	1/4	20	10	10	16	16	0	CMC1,5_prime_UTR_variant,,ENST00000466830,;CMC1,5_prime_UTR_variant,,ENST00000423894,;CMC1,5_prime_UTR_variant,,ENST00000334841,;CMC1,non_coding_transcript_exon_variant,,ENST00000477739,;	G	ENSG00000187118	ENST00000466830	Transcript	5_prime_UTR_variant	124	.	.	.	.	.	.	.	1	CMC1	HGNC	28783	protein_coding	YES	CCDS33722.1	ENSP00000418348	COXM1_HUMAN	.	UPI0000161ABD	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GAGCCCAAGCC	.	4	ESCA
TRIM71	0	.	GRCh37	3	32933735	32933735	+	3'UTR	DEL	A	A	-	rs77419892	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*440delA	.	.	ENST00000383763	4/4	39	21	17	39	39	0	TRIM71,3_prime_UTR_variant,,ENST00000383763,;	-	ENSG00000206557	ENST00000383763	Transcript	3_prime_UTR_variant	3102	.	.	.	.	rs77419892	.	.	1	TRIM71	HGNC	32669	protein_coding	YES	CCDS43060.1	ENSP00000373272	LIN41_HUMAN	.	UPI000067CB89	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAACACAAAAAA	.	2	ESCA
FAM198A	0	.	GRCh37	3	43074481	43074481	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726T>C	p.%3D	p.C242C	ENST00000430121	2/5	38	14	24	20	20	0	FAM198A,synonymous_variant,p.%3D,ENST00000430121,;FAM198A,intron_variant,,ENST00000488863,;KRBOX1,downstream_gene_variant,,ENST00000446977,;KRBOX1,downstream_gene_variant,,ENST00000451200,;KRBOX1,downstream_gene_variant,,ENST00000418093,;FAM198A,synonymous_variant,p.%3D,ENST00000273146,;FAM198A,non_coding_transcript_exon_variant,,ENST00000434206,;FAM198A,intron_variant,,ENST00000492161,;KRBOX1,intron_variant,,ENST00000443313,;RP11-136C24.1,upstream_gene_variant,,ENST00000417304,;	C	ENSG00000144649	ENST00000430121	Transcript	synonymous_variant	821	726	242	C	tgT/tgC	.	.	.	1	FAM198A	HGNC	24485	protein_coding	YES	CCDS46808.1	ENSP00000407301	F198A_HUMAN	.	UPI000016146E	.	.	.	2/5	.	hmmpanther:PTHR15905,hmmpanther:PTHR15905:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGTGATGC	.	5	ESCA
CCR3	0	.	GRCh37	3	46307343	46307343	+	Frame_Shift_Del	DEL	A	A	-	rs775866199	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.764delA	p.Lys255SerfsTer52	p.K255Sfs*52	ENST00000545097	3/3	16	6	10	25	25	0	CCR3,frameshift_variant,p.Lys255SerfsTer52,ENST00000545097,;CCR3,frameshift_variant,p.Lys234SerfsTer52,ENST00000395940,;CCR3,frameshift_variant,p.Lys234SerfsTer52,ENST00000395942,;CCR3,frameshift_variant,p.Lys234SerfsTer52,ENST00000357422,;CCR3,frameshift_variant,p.Lys234SerfsTer52,ENST00000541018,;CCR3,downstream_gene_variant,,ENST00000452454,;CCR3,downstream_gene_variant,,ENST00000457243,;CCR3,downstream_gene_variant,,ENST00000484025,;CCR3,downstream_gene_variant,,ENST00000475150,;	-	ENSG00000183625	ENST00000545097	Transcript	frameshift_variant	932	757	253	K/X	Aaa/aa	rs775866199	.	.	1	CCR3	HGNC	1604	protein_coding	YES	CCDS54574.1	ENSP00000441600	CCR3_HUMAN	Q96T97_HUMAN,Q96T96_HUMAN,Q8TDP8_HUMAN,Q8TDP5_HUMAN,Q8TDP4_HUMAN	UPI000020A60F	.	.	.	3/3	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24227,hmmpanther:PTHR24227:SF13,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01108	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCCAGTAAAAAA	.	2	ESCA
KLHDC8B	0	.	GRCh37	3	49210244	49210244	+	Frame_Shift_Del	DEL	C	C	-	rs201475255,rs764592621	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.48delC	p.Met17CysfsTer59	p.M17Cfs*59	ENST00000332780	2/6	84	62	22	39	39	0	KLHDC8B,frameshift_variant,p.Met17CysfsTer59,ENST00000332780,;C3orf84,downstream_gene_variant,,ENST00000545770,;C3orf84,downstream_gene_variant,,ENST00000432035,;KLHDC8B,non_coding_transcript_exon_variant,,ENST00000476495,;KLHDC8B,intron_variant,,ENST00000459846,;KLHDC8B,upstream_gene_variant,,ENST00000462582,;C3orf84,downstream_gene_variant,,ENST00000443990,;KLHDC8B,upstream_gene_variant,,ENST00000471811,;	-	ENSG00000185909	ENST00000332780	Transcript	frameshift_variant	251	42	14	F/X	ttC/tt	rs201475255,rs764592621	.	.	1	KLHDC8B	HGNC	28557	protein_coding	YES	CCDS2791.1	ENSP00000327468	KLD8B_HUMAN	.	UPI000004EE01	.	.	.	2/6	.	hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF152,Gene3D:1zgkA00,Superfamily_domains:0052715	T:0.0006	T:0	T:0	.	T:0.002	T:0	T:0.001	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTGTTCCCCCC	byFrequency|byCluster|by1000G	3	ESCA
MST1	0	.	GRCh37	3	49721799	49721799	+	Missense_Mutation	SNP	C	C	T	rs749446082	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000449682	17/18	22	4	18	23	23	0	MST1,missense_variant,p.Arg655Gln,ENST00000449682,;MST1,missense_variant,p.Arg125Gln,ENST00000448220,;APEH,downstream_gene_variant,,ENST00000296456,;MST1,downstream_gene_variant,,ENST00000383728,;APEH,downstream_gene_variant,,ENST00000438011,;MST1,downstream_gene_variant,,ENST00000545762,;MST1,downstream_gene_variant,,ENST00000491943,;MST1,downstream_gene_variant,,ENST00000494828,;MST1,non_coding_transcript_exon_variant,,ENST00000479115,;MST1,non_coding_transcript_exon_variant,,ENST00000488350,;MST1,non_coding_transcript_exon_variant,,ENST00000484144,;MST1,non_coding_transcript_exon_variant,,ENST00000493836,;MST1,non_coding_transcript_exon_variant,,ENST00000492329,;MST1,downstream_gene_variant,,ENST00000498021,;MST1,downstream_gene_variant,,ENST00000494809,;MST1,downstream_gene_variant,,ENST00000484269,;MST1,downstream_gene_variant,,ENST00000489007,;APEH,downstream_gene_variant,,ENST00000446089,;MST1,downstream_gene_variant,,ENST00000497359,;APEH,downstream_gene_variant,,ENST00000480772,;APEH,downstream_gene_variant,,ENST00000469362,;MST1,downstream_gene_variant,,ENST00000481930,;MST1,downstream_gene_variant,,ENST00000468847,;MST1,downstream_gene_variant,,ENST00000492370,;MST1,downstream_gene_variant,,ENST00000490966,;APEH,downstream_gene_variant,,ENST00000447436,;AC099668.5,downstream_gene_variant,,ENST00000563780,;MST1,downstream_gene_variant,,ENST00000484673,;MST1,downstream_gene_variant,,ENST00000480268,;APEH,downstream_gene_variant,,ENST00000482301,;MST1,downstream_gene_variant,,ENST00000481055,;	T	ENSG00000173531	ENST00000449682	Transcript	missense_variant	2326	1964	655	R/Q	cGg/cAg	rs749446082	.	.	-1	MST1	HGNC	7380	protein_coding	YES	CCDS33757.2	ENSP00000414287	.	G3XAK1_HUMAN	UPI0000EE2A31	.	tolerated(0.39)	benign(0.004)	17/18	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24272,hmmpanther:PTHR24272:SF43,Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001152,SMART_domains:SM00020,PIRSF_domain:PIRSF500185,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCCGCACA	byFrequency	5	ESCA
SEMA3F	0	.	GRCh37	3	50222192	50222192	+	Silent	SNP	C	C	T	rs139236502	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1401C>T	p.%3D	p.A467A	ENST00000002829	13/19	56	24	31	65	65	0	SEMA3F,synonymous_variant,p.%3D,ENST00000413852,;SEMA3F,synonymous_variant,p.%3D,ENST00000434342,;SEMA3F,synonymous_variant,p.%3D,ENST00000002829,;SEMA3F,downstream_gene_variant,,ENST00000414301,;SEMA3F,downstream_gene_variant,,ENST00000450338,;SEMA3F,non_coding_transcript_exon_variant,,ENST00000470737,;SEMA3F,downstream_gene_variant,,ENST00000493743,;	T	ENSG00000001617	ENST00000002829	Transcript	synonymous_variant	1885	1401	467	A	gcC/gcT	rs139236502	.	.	1	SEMA3F	HGNC	10728	protein_coding	YES	CCDS2811.1	ENSP00000002829	SEM3F_HUMAN	.	UPI0000135A69	.	.	.	13/19	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF27,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGCCGTGGA	byCluster	5	ESCA
HYAL3	0	.	GRCh37	3	50332292	50332292	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.742C>T	p.Pro248Ser	p.P248S	ENST00000336307	2/4	80	52	28	49	49	0	HYAL3,missense_variant,p.Pro248Ser,ENST00000450982,;HYAL3,missense_variant,p.Pro248Ser,ENST00000336307,;HYAL3,missense_variant,p.Pro248Ser,ENST00000359051,;HYAL3,splice_region_variant,,ENST00000415204,;HYAL3,splice_region_variant,,ENST00000513170,;NAT6,downstream_gene_variant,,ENST00000417393,;NAT6,downstream_gene_variant,,ENST00000443842,;HYAL3,downstream_gene_variant,,ENST00000435141,;IFRD2,upstream_gene_variant,,ENST00000429673,;NAT6,downstream_gene_variant,,ENST00000443094,;NAT6,downstream_gene_variant,,ENST00000442620,;NAT6,downstream_gene_variant,,ENST00000354862,;IFRD2,upstream_gene_variant,,ENST00000336089,;NAT6,downstream_gene_variant,,ENST00000450489,;IFRD2,upstream_gene_variant,,ENST00000417626,;NAT6,downstream_gene_variant,,ENST00000452674,;IFRD2,upstream_gene_variant,,ENST00000436390,;IFRD2,upstream_gene_variant,,ENST00000484043,;IFRD2,upstream_gene_variant,,ENST00000468737,;IFRD2,upstream_gene_variant,,ENST00000414734,;IFRD2,upstream_gene_variant,,ENST00000474556,;IFRD2,upstream_gene_variant,,ENST00000462001,;IFRD2,upstream_gene_variant,,ENST00000483071,;IFRD2,upstream_gene_variant,,ENST00000438296,;IFRD2,upstream_gene_variant,,ENST00000489569,;	A	ENSG00000186792	ENST00000336307	Transcript	missense_variant	1015	742	248	P/S	Cca/Tca	.	.	.	-1	HYAL3	HGNC	5322	protein_coding	YES	CCDS2815.1	ENSP00000337425	HYAL3_HUMAN	C9JB51_HUMAN	UPI000006E0AC	.	tolerated(0.1)	probably_damaging(0.999)	2/4	.	hmmpanther:PTHR11769:SF19,hmmpanther:PTHR11769,Gene3D:3.20.20.70,Pfam_domain:PF01630,PIRSF_domain:PIRSF500776,PIRSF_domain:PIRSF038193,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTGGGAGGT	.	5	ESCA
TUSC2	0	.	GRCh37	3	50362462	50362462	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1090delT	.	.	ENST00000232496	3/3	24	17	7	28	28	0	TUSC2,3_prime_UTR_variant,,ENST00000232496,;HYAL2,upstream_gene_variant,,ENST00000426286,;HYAL2,upstream_gene_variant,,ENST00000424190,;HYAL2,upstream_gene_variant,,ENST00000442581,;RASSF1,downstream_gene_variant,,ENST00000357043,;RASSF1,downstream_gene_variant,,ENST00000395126,;RASSF1,downstream_gene_variant,,ENST00000327761,;HYAL2,upstream_gene_variant,,ENST00000447092,;HYAL2,upstream_gene_variant,,ENST00000458018,;RASSF1,downstream_gene_variant,,ENST00000359365,;HYAL2,upstream_gene_variant,,ENST00000357750,;HYAL2,upstream_gene_variant,,ENST00000395139,;HYAL2,upstream_gene_variant,,ENST00000428028,;HYAL2,upstream_gene_variant,,ENST00000415028,;TUSC2,intron_variant,,ENST00000462137,;TUSC2,downstream_gene_variant,,ENST00000463304,;TUSC2,downstream_gene_variant,,ENST00000421918,;TUSC2,downstream_gene_variant,,ENST00000417867,;RASSF1,downstream_gene_variant,,ENST00000482447,;RASSF1,downstream_gene_variant,,ENST00000395117,;TUSC2,downstream_gene_variant,,ENST00000454201,;HYAL2,upstream_gene_variant,,ENST00000481597,;	-	ENSG00000114383	ENST00000232496	Transcript	3_prime_UTR_variant	1567	.	.	.	.	.	.	.	-1	TUSC2	HGNC	17034	protein_coding	YES	CCDS2819.1	ENSP00000232496	TUSC2_HUMAN	.	UPI000012AD8D	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTACTTAAAAAA	.	2	ESCA
PARP3	0	.	GRCh37	3	51980259	51980259	+	Silent	SNP	C	C	T	rs370560805	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1197C>T	p.%3D	p.A399A	ENST00000398755	9/11	16	9	6	16	16	0	PARP3,synonymous_variant,p.%3D,ENST00000417220,;PARP3,synonymous_variant,p.%3D,ENST00000398755,;PARP3,synonymous_variant,p.%3D,ENST00000431474,;PARP3,downstream_gene_variant,,ENST00000498510,;RRP9,upstream_gene_variant,,ENST00000232888,;PARP3,upstream_gene_variant,,ENST00000486510,;PARP3,3_prime_UTR_variant,,ENST00000471971,;PARP3,non_coding_transcript_exon_variant,,ENST00000475782,;PARP3,downstream_gene_variant,,ENST00000470601,;PARP3,downstream_gene_variant,,ENST00000470749,;	T	ENSG00000041880	ENST00000398755	Transcript	synonymous_variant	1528	1197	399	A	gcC/gcT	rs370560805	.	.	1	PARP3	HGNC	273	protein_coding	YES	CCDS46839.1	ENSP00000381740	PARP3_HUMAN	C9J9C7_HUMAN	UPI00015E16A5	.	.	.	9/11	.	PROSITE_profiles:PS51059,hmmpanther:PTHR15447:SF9,hmmpanther:PTHR15447,Pfam_domain:PF00644,Gene3D:3.90.228.10,Superfamily_domains:SSF56399	.	.	.	.	.	.	.	T:0.0002	T:0.0005	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCCGCCAT	byFrequency|byCluster	5	ESCA
TLR9	0	.	GRCh37	3	52257989	52257989	+	Missense_Mutation	SNP	C	C	T	rs184563116	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.803G>A	p.Glu269Lys	p.E269K	ENST00000494383	5/5	132	122	9	100	100	0	TLR9,missense_variant,p.Glu269Lys,ENST00000494383,;TLR9,missense_variant,p.Glu139Lys,ENST00000597542,;TLR9,missense_variant,p.Glu115Lys,ENST00000360658,;TWF2,downstream_gene_variant,,ENST00000499914,;TWF2,downstream_gene_variant,,ENST00000305533,;TLR9,3_prime_UTR_variant,,ENST00000478201,;	T	ENSG00000173366	ENST00000494383	Transcript	missense_variant	803	805	269	E/K	Gag/Aag	rs184563116	.	.	-1	TLR9	Uniprot_gn	15633	protein_coding	YES	.	ENSP00000417517	.	C3W5P5_HUMAN	UPI0001B795AC	.	deleterious(0.02)	possibly_damaging(0.715)	5/5	.	hmmpanther:PTHR24373:SF37,hmmpanther:PTHR24373,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCTCGATGG	byCluster|by1000G	2	ESCA
DNAH1	0	.	GRCh37	3	52397145	52397145	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5229G>T	p.Glu1743Asp	p.E1743D	ENST00000420323	32/78	42	23	19	40	40	0	DNAH1,missense_variant,p.Glu1743Asp,ENST00000420323,;DNAH1,downstream_gene_variant,,ENST00000466628,;DNAH1,non_coding_transcript_exon_variant,,ENST00000486752,;	T	ENSG00000114841	ENST00000420323	Transcript	missense_variant	5490	5229	1743	E/D	gaG/gaT	.	.	.	1	DNAH1	HGNC	2940	protein_coding	YES	CCDS46842.1	ENSP00000401514	DYH1_HUMAN	.	UPI0001AE79D6	.	.	probably_damaging(0.999)	32/78	.	Superfamily_domains:SSF52540,Pfam_domain:PF12774,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGAGCAGCT	.	5	ESCA
SELK	0	.	GRCh37	3	53920927	53920927	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.145delA	p.Arg49GlufsTer51	p.R49Efs*51	ENST00000495461	3/5	36	22	14	31	31	0	SELK,frameshift_variant,p.Arg49GlufsTer51,ENST00000541726,;SELK,frameshift_variant,p.Arg49GlufsTer51,ENST00000495461,;ACTR8,upstream_gene_variant,,ENST00000335754,;AC012467.1,upstream_gene_variant,,ENST00000410956,;SELK,downstream_gene_variant,,ENST00000485414,;SELK,frameshift_variant,p.Arg49GlufsTer41,ENST00000488746,;SELK,downstream_gene_variant,,ENST00000487571,;	-	ENSG00000113811	ENST00000495461	Transcript	frameshift_variant	345	145	49	R/X	Aga/ga	.	.	.	-1	SELK	Uniprot_gn	.	protein_coding	YES	CCDS54597.1	ENSP00000418813	SELK_HUMAN	A8K0M9_HUMAN	UPI0000163E13	.	.	.	3/5	.	Pfam_domain:PF10961,hmmpanther:PTHR16875:SF0,hmmpanther:PTHR16875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTTCTTTTTT	.	3	ESCA
APPL1	0	.	GRCh37	3	57293965	57293965	+	Missense_Mutation	SNP	C	C	T	rs769152501	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1576C>T	p.Arg526Cys	p.R526C	ENST00000288266	17/22	35	12	22	44	44	0	APPL1,missense_variant,p.Arg526Cys,ENST00000288266,;APPL1,non_coding_transcript_exon_variant,,ENST00000492501,;APPL1,non_coding_transcript_exon_variant,,ENST00000488530,;APPL1,non_coding_transcript_exon_variant,,ENST00000464446,;APPL1,non_coding_transcript_exon_variant,,ENST00000482800,;	T	ENSG00000157500	ENST00000288266	Transcript	missense_variant	1723	1576	526	R/C	Cgc/Tgc	rs769152501	.	.	1	APPL1	HGNC	24035	protein_coding	YES	CCDS2882.1	ENSP00000288266	DP13A_HUMAN	.	UPI00000712DA	.	deleterious(0)	probably_damaging(1)	17/22	.	PROSITE_profiles:PS01179,Gene3D:2.30.29.30,Pfam_domain:PF00640,SMART_domains:SM00462,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATGCGCCAA	.	5	ESCA
FAM19A1	0	.	GRCh37	3	68055751	68055751	+	Intron	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3-16C>A	.	.	ENST00000478136	.	37	7	30	47	47	0	FAM19A1,5_prime_UTR_variant,,ENST00000496687,;FAM19A1,intron_variant,,ENST00000478136,;	A	ENSG00000183662	ENST00000478136	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	FAM19A1	HGNC	21587	protein_coding	YES	CCDS54606.1	ENSP00000418575	F19A1_HUMAN	.	UPI00001B3DB2	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGTCGAATG	.	5	ESCA
TMF1	0	.	GRCh37	3	69072373	69072373	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3237G>A	p.Met1079Ile	p.M1079I	ENST00000398559	17/17	29	14	14	49	49	0	TMF1,missense_variant,p.Met1079Ile,ENST00000398559,;TMF1,missense_variant,p.Met1082Ile,ENST00000543976,;CTD-2013N24.2,intron_variant,,ENST00000596523,;CTD-2013N24.2,intron_variant,,ENST00000601511,;CTD-2013N24.2,intron_variant,,ENST00000597950,;CTD-2013N24.2,intron_variant,,ENST00000596732,;CTD-2013N24.2,intron_variant,,ENST00000599467,;CTD-2013N24.2,intron_variant,,ENST00000598783,;CTD-2013N24.2,intron_variant,,ENST00000597366,;CTD-2013N24.2,intron_variant,,ENST00000601735,;CTD-2013N24.2,intron_variant,,ENST00000595925,;CTD-2013N24.2,intron_variant,,ENST00000482368,;TMF1,downstream_gene_variant,,ENST00000489370,;TMF1,3_prime_UTR_variant,,ENST00000488010,;	T	ENSG00000144747	ENST00000398559	Transcript	missense_variant	3454	3237	1079	M/I	atG/atA	.	.	.	-1	TMF1	HGNC	11870	protein_coding	YES	CCDS43105.1	ENSP00000381567	TMF1_HUMAN	.	UPI000013D9A7	.	deleterious(0)	probably_damaging(0.999)	17/17	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF285,Pfam_domain:PF12325	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTACATATT	.	5	ESCA
VGLL3	0	.	GRCh37	3	86990336	86990336	+	3'UTR	DEL	A	A	-	rs72417699	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5838delT	.	.	ENST00000398399	4/4	23	9	14	26	26	0	VGLL3,3_prime_UTR_variant,,ENST00000398399,;	-	ENSG00000206538	ENST00000398399	Transcript	3_prime_UTR_variant	7183	.	.	.	.	rs72417699	.	.	-1	VGLL3	HGNC	24327	protein_coding	YES	CCDS43110.1	ENSP00000381436	VGLL3_HUMAN	.	UPI0000197E88	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTCCTGAAAAAA	.	2	ESCA
ZNF654	0	.	GRCh37	3	88192557	88192557	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1762delA	.	.	ENST00000309495	2/2	23	11	12	34	34	0	ZNF654,3_prime_UTR_variant,,ENST00000309495,;CGGBP1,intron_variant,,ENST00000462901,;CGGBP1,intron_variant,,ENST00000467332,;RP11-159G9.5,downstream_gene_variant,,ENST00000498458,;	-	ENSG00000175105	ENST00000309495	Transcript	3_prime_UTR_variant	3708	.	.	.	.	.	.	.	1	ZNF654	HGNC	25612	protein_coding	YES	CCDS46874.1	ENSP00000312141	ZN654_HUMAN	.	UPI0000DD0307	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCAGCTAAAAAA	.	2	ESCA
ARL13B	0	.	GRCh37	3	93772140	93772140	+	3'UTR	SNP	G	G	A	rs753533317	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*33G>A	.	.	ENST00000394222	10/10	25	20	5	20	20	0	ARL13B,3_prime_UTR_variant,,ENST00000394222,;ARL13B,3_prime_UTR_variant,,ENST00000303097,;ARL13B,3_prime_UTR_variant,,ENST00000535334,;ARL13B,3_prime_UTR_variant,,ENST00000471138,;ARL13B,3_prime_UTR_variant,,ENST00000539730,;DHFRL1,downstream_gene_variant,,ENST00000314636,;DHFRL1,downstream_gene_variant,,ENST00000394221,;DHFRL1,intron_variant,,ENST00000481631,;ARL13B,3_prime_UTR_variant,,ENST00000335438,;ARL13B,3_prime_UTR_variant,,ENST00000460371,;	A	ENSG00000169379	ENST00000394222	Transcript	3_prime_UTR_variant	1595	.	.	.	.	rs753533317	.	.	1	ARL13B	HGNC	25419	protein_coding	YES	CCDS2925.1	ENSP00000377769	AR13B_HUMAN	B4DRI8_HUMAN	UPI00001B94DF	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCAGCAAGG	.	5	ESCA
BRPF1	0	.	GRCh37	3	9785476	9785476	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2526G>A	p.%3D	p.R842R	ENST00000383829	8/14	58	43	15	35	35	0	BRPF1,synonymous_variant,p.%3D,ENST00000433861,;BRPF1,synonymous_variant,p.%3D,ENST00000457855,;BRPF1,synonymous_variant,p.%3D,ENST00000383829,;BRPF1,synonymous_variant,p.%3D,ENST00000302054,;BRPF1,synonymous_variant,p.%3D,ENST00000424362,;BRPF1,non_coding_transcript_exon_variant,,ENST00000469066,;BRPF1,upstream_gene_variant,,ENST00000497565,;	A	ENSG00000156983	ENST00000383829	Transcript	synonymous_variant	2930	2526	842	R	cgG/cgA	COSM371404	.	.	1	BRPF1	HGNC	14255	protein_coding	YES	CCDS33692.1	ENSP00000373340	BRPF1_HUMAN	C9JHC0_HUMAN,C9JDK5_HUMAN	UPI00001A9CA3	.	.	.	8/14	.	hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF85	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCGGCATGG	.	5	ESCA
DCBLD2	0	.	GRCh37	3	98516120	98516120	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2096delT	.	.	ENST00000326840	16/16	15	3	12	12	12	0	DCBLD2,3_prime_UTR_variant,,ENST00000326840,;ST3GAL6,downstream_gene_variant,,ENST00000394162,;ST3GAL6,downstream_gene_variant,,ENST00000483910,;DCBLD2,downstream_gene_variant,,ENST00000326857,;ST3GAL6,downstream_gene_variant,,ENST00000265261,;ST3GAL6,intron_variant,,ENST00000491912,;ST3GAL6,downstream_gene_variant,,ENST00000474595,;ST3GAL6,upstream_gene_variant,,ENST00000495502,;ST3GAL6,downstream_gene_variant,,ENST00000462152,;DCBLD2,downstream_gene_variant,,ENST00000494614,;ST3GAL6,downstream_gene_variant,,ENST00000497621,;ST3GAL6,downstream_gene_variant,,ENST00000469105,;ST3GAL6,downstream_gene_variant,,ENST00000486249,;DCBLD2,downstream_gene_variant,,ENST00000496736,;	-	ENSG00000057019	ENST00000326840	Transcript	3_prime_UTR_variant	4787	.	.	.	.	.	.	.	-1	DCBLD2	HGNC	24627	protein_coding	YES	CCDS46878.1	ENSP00000321573	DCBD2_HUMAN	B7Z7Y3_HUMAN	UPI0000072ABB	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCTCTTAAAAAA	.	2	ESCA
ADH7	0	.	GRCh37	4	100340170	100340170	+	Missense_Mutation	SNP	G	G	A	rs367907552	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.994C>T	p.Arg332Cys	p.R332C	ENST00000476959	7/9	37	26	11	48	48	0	ADH7,missense_variant,p.Arg324Cys,ENST00000209665,;ADH7,missense_variant,p.Arg255Cys,ENST00000482593,;ADH7,missense_variant,p.Arg332Cys,ENST00000476959,;ADH7,missense_variant,p.Arg312Cys,ENST00000437033,;ADH7,upstream_gene_variant,,ENST00000485660,;	A	ENSG00000196344	ENST00000476959	Transcript	missense_variant	1024	994	332	R/C	Cgc/Tgc	rs367907552	.	.	-1	ADH7	HGNC	256	protein_coding	YES	CCDS54781.1	ENSP00000420269	ADH7_HUMAN	E9PFG0_HUMAN,C9JP14_HUMAN,B4DWS1_HUMAN	UPI00017A81B5	.	deleterious(0.03)	benign(0.017)	7/9	.	hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF406,Gene3D:3.40.50.720,Pfam_domain:PF00107,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCGTCCAG	byCluster	5	ESCA
CENPE	0	.	GRCh37	4	104115550	104115550	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608C>T	p.Ser203Phe	p.S203F	ENST00000265148	7/49	18	5	13	36	36	0	CENPE,missense_variant,p.Ser203Phe,ENST00000503705,;CENPE,missense_variant,p.Ser203Phe,ENST00000380026,;CENPE,missense_variant,p.Ser203Phe,ENST00000265148,;CENPE,missense_variant,p.Ser163Phe,ENST00000514974,;	A	ENSG00000138778	ENST00000265148	Transcript	missense_variant	698	608	203	S/F	tCt/tTt	.	.	.	-1	CENPE	HGNC	1856	protein_coding	YES	CCDS34042.1	ENSP00000265148	CENPE_HUMAN	D6RBW0_HUMAN	UPI000020B28A	.	.	probably_damaging(1)	7/49	.	Prints_domain:PR00380,Superfamily_domains:SSF52540,SMART_domains:SM00129,Pfam_domain:PF00225,Gene3D:3.40.850.10,hmmpanther:PTHR24115:SF384,hmmpanther:PTHR24115,PROSITE_profiles:PS50067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGAGAACGA	.	5	ESCA
CFI	0	.	GRCh37	4	110670692	110670692	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1007G>A	p.Arg336Gln	p.R336Q	ENST00000394634	9/13	27	17	10	23	23	0	CFI,missense_variant,p.Arg336Gln,ENST00000394634,;CFI,missense_variant,p.Arg329Gln,ENST00000512148,;CFI,missense_variant,p.Arg344Gln,ENST00000394635,;CFI,non_coding_transcript_exon_variant,,ENST00000504853,;CFI,upstream_gene_variant,,ENST00000515512,;	T	ENSG00000205403	ENST00000394634	Transcript	missense_variant	1215	1007	336	R/Q	cGa/cAa	.	.	.	-1	CFI	HGNC	5394	protein_coding	YES	CCDS34049.1	ENSP00000378130	CFAI_HUMAN	Q6LAM0_HUMAN,D6R9Z8_HUMAN	UPI0000D615A9	.	deleterious(0)	probably_damaging(0.922)	9/13	.	Superfamily_domains:SSF50494,hmmpanther:PTHR24265,hmmpanther:PTHR24265:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.R336*|c.1006C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCGAATG	.	5	ESCA
C4orf21	0	.	GRCh37	4	113539992	113539992	+	Silent	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1206A>T	p.%3D	p.V402V	ENST00000505019	6/28	26	18	8	36	36	0	C4orf21,synonymous_variant,p.%3D,ENST00000309071,;C4orf21,synonymous_variant,p.%3D,ENST00000505019,;C4orf21,synonymous_variant,p.%3D,ENST00000445203,;C4orf21,downstream_gene_variant,,ENST00000503172,;C4orf21,synonymous_variant,p.%3D,ENST00000473015,;C4orf21,3_prime_UTR_variant,,ENST00000514770,;C4orf21,non_coding_transcript_exon_variant,,ENST00000264370,;C4orf21,downstream_gene_variant,,ENST00000502805,;C4orf21,downstream_gene_variant,,ENST00000512075,;	A	ENSG00000138658	ENST00000505019	Transcript	synonymous_variant	1332	1206	402	V	gtA/gtT	.	.	.	-1	C4orf21	HGNC	25654	protein_coding	YES	CCDS3700.2	ENSP00000424737	CD021_HUMAN	I3L0G6_HUMAN,D6REN9_HUMAN	UPI0000EE2F8F	.	.	.	6/28	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF325	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTTACTTC	.	5	ESCA
ANK2	0	.	GRCh37	4	114293761	114293761	+	Intron	SNP	C	C	T	rs190818207	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11611-485C>T	.	.	ENST00000357077	.	32	26	5	30	30	0	ANK2,missense_variant,p.Arg812Cys,ENST00000514960,;ANK2,missense_variant,p.Arg462Cys,ENST00000510275,;ANK2,intron_variant,,ENST00000264366,;ANK2,intron_variant,,ENST00000394537,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000506722,;ANK2,intron_variant,,ENST00000357077,;ANK2,intron_variant,,ENST00000505342,;ANK2,upstream_gene_variant,,ENST00000506344,;ANK2,upstream_gene_variant,,ENST00000514167,;	T	ENSG00000145362	ENST00000357077	Transcript	intron_variant	.	.	.	.	.	rs190818207	.	.	1	ANK2	HGNC	493	protein_coding	YES	CCDS3702.1	ENSP00000349588	ANK2_HUMAN	D6RHC5_HUMAN	UPI0000441EF3	.	.	.	.	43/45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTCCGCCGG	by1000G	5	ESCA
PDE5A	0	.	GRCh37	4	120484001	120484001	+	Missense_Mutation	SNP	T	T	C	rs148453628	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118A>G	p.Asp373Gly	p.D373G	ENST00000354960	6/21	50	39	10	54	54	0	PDE5A,missense_variant,p.Asp373Gly,ENST00000354960,;PDE5A,missense_variant,p.Asp331Gly,ENST00000264805,;PDE5A,missense_variant,p.Asp321Gly,ENST00000394439,;PDE5A,non_coding_transcript_exon_variant,,ENST00000508914,;	C	ENSG00000138735	ENST00000354960	Transcript	missense_variant	1438	1118	373	D/G	gAt/gGt	rs148453628	.	.	-1	PDE5A	HGNC	8784	protein_coding	YES	CCDS3713.1	ENSP00000347046	PDE5A_HUMAN	Q9P0K6_HUMAN,Q9P0K4_HUMAN,Q4W5L4_HUMAN,G5E9C5_HUMAN,C9JGT3_HUMAN	UPI000013D571	.	deleterious(0.03)	probably_damaging(0.963)	6/21	.	hmmpanther:PTHR11347:SF21,hmmpanther:PTHR11347,Gene3D:3.30.450.40,Pfam_domain:PF01590,SMART_domains:SM00065,Superfamily_domains:SSF55781	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCATCCACT	byCluster|by1000G	5	ESCA
BBS7	0	.	GRCh37	4	122746918	122746918	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*97A>G	.	.	ENST00000264499	19/19	21	13	8	21	21	0	BBS7,3_prime_UTR_variant,,ENST00000264499,;BBS7,intron_variant,,ENST00000507814,;BBS7,downstream_gene_variant,,ENST00000506636,;CCNA2,upstream_gene_variant,,ENST00000274026,;	C	ENSG00000138686	ENST00000264499	Transcript	3_prime_UTR_variant	2429	.	.	.	.	.	.	.	-1	BBS7	HGNC	18758	protein_coding	YES	CCDS3724.1	ENSP00000264499	BBS7_HUMAN	H0Y973_HUMAN	UPI00001684D7	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCATTTGAA	.	5	ESCA
KIAA1109	0	.	GRCh37	4	123131023	123131023	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1982A>T	p.Asp661Val	p.D661V	ENST00000264501	19/86	33	21	12	56	56	0	KIAA1109,missense_variant,p.Asp494Val,ENST00000424425,;KIAA1109,missense_variant,p.Asp661Val,ENST00000455637,;KIAA1109,missense_variant,p.Asp661Val,ENST00000264501,;KIAA1109,missense_variant,p.Asp661Val,ENST00000388738,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000495260,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000482114,;	T	ENSG00000138688	ENST00000264501	Transcript	missense_variant	2355	1982	661	D/V	gAt/gTt	.	.	.	1	KIAA1109	HGNC	26953	protein_coding	YES	CCDS43267.1	ENSP00000264501	K1109_HUMAN	B3KN93_HUMAN	UPI0000DD87B4	.	.	possibly_damaging(0.821)	19/86	.	hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTGATTATA	.	5	ESCA
ADAD1	0	.	GRCh37	4	123342535	123342535	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1607A>G	p.His536Arg	p.H536R	ENST00000296513	12/13	22	15	6	33	33	0	ADAD1,missense_variant,p.His525Arg,ENST00000388724,;ADAD1,missense_variant,p.His536Arg,ENST00000296513,;ADAD1,missense_variant,p.His518Arg,ENST00000388725,;	G	ENSG00000164113	ENST00000296513	Transcript	missense_variant	1792	1607	536	H/R	cAt/cGt	.	.	.	1	ADAD1	HGNC	30713	protein_coding	YES	CCDS34058.1	ENSP00000296513	ADAD1_HUMAN	C9JGM6_HUMAN,C9JAT9_HUMAN	UPI000006DF76	.	tolerated(0.52)	benign(0.05)	12/13	.	PROSITE_profiles:PS50141,hmmpanther:PTHR10910:SF44,hmmpanther:PTHR10910,Pfam_domain:PF02137,SMART_domains:SM00552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATCATGCAG	.	5	ESCA
SPATA5	0	.	GRCh37	4	123855285	123855285	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.539A>G	p.Tyr180Cys	p.Y180C	ENST00000274008	5/16	46	31	15	41	41	0	SPATA5,missense_variant,p.Tyr180Cys,ENST00000274008,;SPATA5,non_coding_transcript_exon_variant,,ENST00000422835,;	G	ENSG00000145375	ENST00000274008	Transcript	missense_variant	608	539	180	Y/C	tAt/tGt	.	.	.	1	SPATA5	HGNC	18119	protein_coding	YES	CCDS3730.1	ENSP00000274008	SPAT5_HUMAN	.	UPI000013D9E6	.	tolerated(0.16)	possibly_damaging(0.765)	5/16	.	hmmpanther:PTHR23077:SF27,hmmpanther:PTHR23077	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTATTGTA	.	5	ESCA
C4orf29	0	.	GRCh37	4	128949844	128949844	+	Missense_Mutation	SNP	G	G	A	rs767049484	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.914G>A	p.Arg305His	p.R305H	ENST00000398965	10/11	16	11	5	18	18	0	C4orf29,missense_variant,p.Arg257His,ENST00000388795,;C4orf29,missense_variant,p.Arg305His,ENST00000444616,;C4orf29,missense_variant,p.Arg305His,ENST00000398965,;C4orf29,3_prime_UTR_variant,,ENST00000473040,;	A	ENSG00000164074	ENST00000398965	Transcript	missense_variant	1232	914	305	R/H	cGc/cAc	rs767049484	.	.	1	C4orf29	HGNC	26111	protein_coding	YES	CCDS47131.1	ENSP00000381937	CD029_HUMAN	D6RGX5_HUMAN	UPI00006C511D	.	tolerated(0.15)	benign(0.116)	10/11	.	hmmpanther:PTHR13617,Pfam_domain:PF09752,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCGCTTCA	byFrequency|byCluster	5	ESCA
MAEA	0	.	GRCh37	4	1332301	1332301	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.991G>A	p.Ala331Thr	p.A331T	ENST00000303400	8/9	111	60	50	47	47	0	MAEA,missense_variant,p.Ala283Thr,ENST00000505839,;MAEA,missense_variant,p.Ala263Thr,ENST00000514708,;MAEA,missense_variant,p.Ala369Thr,ENST00000505177,;MAEA,missense_variant,p.Ala330Thr,ENST00000510794,;MAEA,missense_variant,p.Ala331Thr,ENST00000303400,;MAEA,missense_variant,p.Ala252Thr,ENST00000452175,;MAEA,missense_variant,p.Ala290Thr,ENST00000264750,;MAEA,downstream_gene_variant,,ENST00000503653,;MAEA,non_coding_transcript_exon_variant,,ENST00000512289,;MAEA,3_prime_UTR_variant,,ENST00000509531,;MAEA,non_coding_transcript_exon_variant,,ENST00000506530,;MAEA,non_coding_transcript_exon_variant,,ENST00000515766,;MAEA,non_coding_transcript_exon_variant,,ENST00000503162,;	A	ENSG00000090316	ENST00000303400	Transcript	missense_variant	1054	991	331	A/T	Gcc/Acc	COSM4122257	.	.	1	MAEA	HGNC	13731	protein_coding	YES	CCDS33936.1	ENSP00000302830	MAEA_HUMAN	D6RID6_HUMAN,D3DVP1_HUMAN,B4DQT1_HUMAN,B3KXS8_HUMAN	UPI00000343F4	.	deleterious(0)	probably_damaging(0.985)	8/9	.	hmmpanther:PTHR12170:SF2,hmmpanther:PTHR12170	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGGCCCAC	.	5	ESCA
BOD1L1	0	.	GRCh37	4	13606084	13606084	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2440A>G	p.Ile814Val	p.I814V	ENST00000040738	10/26	42	13	29	44	44	0	BOD1L1,missense_variant,p.Ile814Val,ENST00000040738,;	C	ENSG00000038219	ENST00000040738	Transcript	missense_variant	2576	2440	814	I/V	Ata/Gta	.	.	.	-1	BOD1L1	HGNC	31792	protein_coding	YES	CCDS3411.2	ENSP00000040738	BD1L1_HUMAN	.	UPI000066D9E3	.	.	possibly_damaging(0.729)	10/26	.	hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTATAATAT	.	5	ESCA
CRIPAK	0	.	GRCh37	4	1388569	1388569	+	Silent	SNP	C	C	T	rs550621315	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.270C>T	p.%3D	p.A90A	ENST00000324803	1/1	414	344	69	164	164	0	CRIPAK,synonymous_variant,p.%3D,ENST00000324803,;	T	ENSG00000179979	ENST00000324803	Transcript	synonymous_variant	3230	270	90	A	gcC/gcT	rs550621315	.	.	1	CRIPAK	HGNC	26619	protein_coding	YES	CCDS3349.1	ENSP00000323978	CRPAK_HUMAN	.	UPI0000070390	.	.	.	1/1	.	.	T:0.0010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTGCCGATGT	byFrequency|byCluster|by1000G	4	ESCA
ELF2	0	.	GRCh37	4	139979169	139979169	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*968T>C	.	.	ENST00000394235	10/10	26	12	13	14	14	0	ELF2,3_prime_UTR_variant,,ENST00000379549,;ELF2,3_prime_UTR_variant,,ENST00000379550,;ELF2,3_prime_UTR_variant,,ENST00000265495,;ELF2,3_prime_UTR_variant,,ENST00000358635,;ELF2,3_prime_UTR_variant,,ENST00000394235,;ELF2,downstream_gene_variant,,ENST00000510408,;ELF2,downstream_gene_variant,,ENST00000512627,;ELF2,downstream_gene_variant,,ENST00000420916,;RNU6-531P,downstream_gene_variant,,ENST00000516694,;ELF2,intron_variant,,ENST00000515489,;ELF2,downstream_gene_variant,,ENST00000504314,;ELF2,downstream_gene_variant,,ENST00000514577,;	G	ENSG00000109381	ENST00000394235	Transcript	3_prime_UTR_variant	3217	.	.	.	.	.	.	.	-1	ELF2	HGNC	3317	protein_coding	YES	CCDS3744.1	ENSP00000377782	ELF2_HUMAN	.	UPI0000073EF0	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAAGAAAA	.	5	ESCA
ELF2	0	.	GRCh37	4	139979170	139979170	+	3'UTR	SNP	G	G	A	rs11556074	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*967C>T	.	.	ENST00000394235	10/10	28	11	16	14	14	0	ELF2,3_prime_UTR_variant,,ENST00000379549,;ELF2,3_prime_UTR_variant,,ENST00000379550,;ELF2,3_prime_UTR_variant,,ENST00000265495,;ELF2,3_prime_UTR_variant,,ENST00000358635,;ELF2,3_prime_UTR_variant,,ENST00000394235,;ELF2,downstream_gene_variant,,ENST00000510408,;ELF2,downstream_gene_variant,,ENST00000512627,;ELF2,downstream_gene_variant,,ENST00000420916,;RNU6-531P,downstream_gene_variant,,ENST00000516694,;ELF2,intron_variant,,ENST00000515489,;ELF2,downstream_gene_variant,,ENST00000504314,;ELF2,downstream_gene_variant,,ENST00000514577,;	A	ENSG00000109381	ENST00000394235	Transcript	3_prime_UTR_variant	3216	.	.	.	.	rs11556074	.	.	-1	ELF2	HGNC	3317	protein_coding	YES	CCDS3744.1	ENSP00000377782	ELF2_HUMAN	.	UPI0000073EF0	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAGAAAAA	byCluster	4	ESCA
SCOC	0	.	GRCh37	4	141302186	141302186	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.408A>G	p.%3D	p.G136G	ENST00000608372	4/4	36	27	8	30	30	0	SCOC,synonymous_variant,p.%3D,ENST00000510586,;SCOC,synonymous_variant,p.%3D,ENST00000394203,;SCOC,synonymous_variant,p.%3D,ENST00000506597,;SCOC,synonymous_variant,p.%3D,ENST00000506322,;SCOC,synonymous_variant,p.%3D,ENST00000394205,;SCOC,synonymous_variant,p.%3D,ENST00000502535,;SCOC,synonymous_variant,p.%3D,ENST00000512749,;SCOC,synonymous_variant,p.%3D,ENST00000394201,;SCOC,synonymous_variant,p.%3D,ENST00000608372,;SCOC,synonymous_variant,p.%3D,ENST00000338517,;	G	ENSG00000153130	ENST00000608372	Transcript	synonymous_variant	435	408	136	G	ggA/ggG	.	.	.	1	SCOC	HGNC	20335	protein_coding	YES	CCDS54806.1	ENSP00000477352	.	.	UPI0000E5AC43	.	.	.	4/4	.	hmmpanther:PTHR21614,Pfam_domain:PF10224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGACAATA	.	5	ESCA
HHIP	0	.	GRCh37	4	145580090	145580090	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.621G>T	p.Glu207Asp	p.E207D	ENST00000296575	3/13	21	15	6	36	36	0	HHIP,missense_variant,p.Glu207Asp,ENST00000296575,;HHIP,missense_variant,p.Glu207Asp,ENST00000434550,;HHIP-AS1,intron_variant,,ENST00000512359,;HHIP,non_coding_transcript_exon_variant,,ENST00000511314,;HHIP,non_coding_transcript_exon_variant,,ENST00000509630,;HHIP,non_coding_transcript_exon_variant,,ENST00000505891,;HHIP,downstream_gene_variant,,ENST00000515080,;	T	ENSG00000164161	ENST00000296575	Transcript	missense_variant	1276	621	207	E/D	gaG/gaT	.	.	.	1	HHIP	HGNC	14866	protein_coding	YES	CCDS3762.1	ENSP00000296575	HHIP_HUMAN	.	UPI0000071302	.	tolerated(0.46)	benign(0.007)	3/13	.	Pfam_domain:PF03024,hmmpanther:PTHR19328,hmmpanther:PTHR19328:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GAAGAGATCAG	.	4	ESCA
CPEB2	0	.	GRCh37	4	15060881	15060881	+	Missense_Mutation	SNP	G	G	A	rs374594133	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2651G>A	p.Arg884Gln	p.R884Q	ENST00000538197	10/12	80	63	16	47	47	0	CPEB2,missense_variant,p.Arg439Gln,ENST00000507071,;CPEB2,missense_variant,p.Arg876Gln,ENST00000541112,;CPEB2,missense_variant,p.Arg417Gln,ENST00000382395,;CPEB2,missense_variant,p.Arg409Gln,ENST00000345451,;CPEB2,missense_variant,p.Arg447Gln,ENST00000259997,;CPEB2,missense_variant,p.Arg92Gln,ENST00000509684,;CPEB2,missense_variant,p.Arg412Gln,ENST00000382401,;CPEB2,missense_variant,p.Arg884Gln,ENST00000538197,;CPEB2,missense_variant,p.Arg857Gln,ENST00000442003,;RP11-665G4.1,intron_variant,,ENST00000502344,;RP11-665G4.1,intron_variant,,ENST00000513384,;	A	ENSG00000137449	ENST00000538197	Transcript	missense_variant	2651	2651	884	R/Q	cGa/cAa	rs374594133	.	.	1	CPEB2	HGNC	21745	protein_coding	YES	CCDS56325.1	ENSP00000443985	.	J3KN18_HUMAN,H0Y9D9_HUMAN,F5H160_HUMAN	UPI0001D0434B	.	deleterious_low_confidence(0.01)	probably_damaging(0.993)	10/12	.	hmmpanther:PTHR12566,Gene3D:3.30.70.330,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCGAAAAA	.	5	ESCA
DCHS2	0	.	GRCh37	4	155253834	155253834	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2029A>G	p.Thr677Ala	p.T677A	ENST00000357232	9/25	32	24	8	47	47	0	DCHS2,missense_variant,p.Thr1176Ala,ENST00000339452,;DCHS2,missense_variant,p.Thr677Ala,ENST00000357232,;DCHS2,downstream_gene_variant,,ENST00000507542,;DCHS2,downstream_gene_variant,,ENST00000504580,;	C	ENSG00000197410	ENST00000357232	Transcript	missense_variant	2029	2029	677	T/A	Aca/Gca	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	YES	CCDS3785.1	ENSP00000349768	PCD23_HUMAN	B3KT73_HUMAN	UPI000035B018	.	tolerated(0.17)	benign(0.001)	9/25	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF257,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTGTAGTGC	.	5	ESCA
FGG	0	.	GRCh37	4	155525918	155525918	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*68delT	.	.	ENST00000336098	9/9	37	26	11	24	24	0	FGG,3_prime_UTR_variant,,ENST00000407946,;FGG,3_prime_UTR_variant,,ENST00000336098,;FGG,intron_variant,,ENST00000404648,;FGG,intron_variant,,ENST00000405164,;FGG,downstream_gene_variant,,ENST00000443553,;FGG,downstream_gene_variant,,ENST00000393846,;FGG,non_coding_transcript_exon_variant,,ENST00000465913,;FGG,intron_variant,,ENST00000492082,;	-	ENSG00000171557	ENST00000336098	Transcript	3_prime_UTR_variant	1469	.	.	.	.	.	.	.	-1	FGG	HGNC	3694	protein_coding	YES	CCDS3788.1	ENSP00000336829	FIBG_HUMAN	C9JU00_HUMAN,C9JPQ9_HUMAN	UPI000012A78D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAAGAGAAAAAA	.	3	ESCA
MAP9	0	.	GRCh37	4	156281335	156281335	+	Silent	SNP	T	T	G	rs776150288	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1035A>C	p.%3D	p.A345A	ENST00000311277	7/14	45	31	13	59	59	0	MAP9,synonymous_variant,p.%3D,ENST00000311277,;MAP9,synonymous_variant,p.%3D,ENST00000433024,;MAP9,synonymous_variant,p.%3D,ENST00000515654,;AC097467.2,intron_variant,,ENST00000598890,;AC097467.2,intron_variant,,ENST00000594666,;AC097467.2,intron_variant,,ENST00000597831,;AC097467.2,intron_variant,,ENST00000594492,;AC097467.2,intron_variant,,ENST00000598252,;AC097467.2,intron_variant,,ENST00000417474,;AC097467.2,intron_variant,,ENST00000596165,;AC097467.2,intron_variant,,ENST00000608406,;AC097467.2,intron_variant,,ENST00000600928,;AC097467.2,intron_variant,,ENST00000609254,;AC097467.2,intron_variant,,ENST00000609716,;AC097467.2,intron_variant,,ENST00000608544,;AC097467.2,intron_variant,,ENST00000608762,;AC097467.2,intron_variant,,ENST00000596754,;AC097467.2,downstream_gene_variant,,ENST00000601977,;AC097467.2,downstream_gene_variant,,ENST00000609486,;AC097467.2,downstream_gene_variant,,ENST00000608092,;AC097467.2,downstream_gene_variant,,ENST00000593387,;AC097467.2,downstream_gene_variant,,ENST00000608463,;MAP9,synonymous_variant,p.%3D,ENST00000424373,;	G	ENSG00000164114	ENST00000311277	Transcript	synonymous_variant	1299	1035	345	A	gcA/gcC	rs776150288	.	.	-1	MAP9	HGNC	26118	protein_coding	YES	CCDS35493.1	ENSP00000310593	MAP9_HUMAN	C9JXH8_HUMAN,A2VCT0_HUMAN	UPI000020B618	.	.	.	7/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14739	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGTTGCACT	.	5	ESCA
RXFP1	0	.	GRCh37	4	159554592	159554592	+	Missense_Mutation	SNP	C	C	T	rs200427299	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.935C>T	p.Pro312Leu	p.P312L	ENST00000307765	12/18	57	41	16	66	66	0	RXFP1,missense_variant,p.Pro207Leu,ENST00000448688,;RXFP1,missense_variant,p.Pro279Leu,ENST00000470033,;RXFP1,missense_variant,p.Pro312Leu,ENST00000307765,;RXFP1,missense_variant,p.Pro231Leu,ENST00000460056,;RXFP1,intron_variant,,ENST00000343542,;RXFP1,3_prime_UTR_variant,,ENST00000471616,;RXFP1,3_prime_UTR_variant,,ENST00000342048,;	T	ENSG00000171509	ENST00000307765	Transcript	missense_variant	1186	935	312	P/L	cCg/cTg	rs200427299	.	.	1	RXFP1	HGNC	19718	protein_coding	YES	CCDS43276.1	ENSP00000303248	RXFP1_HUMAN	Q4W5D9_HUMAN,E9PCA3_HUMAN	UPI000013EC4B	.	deleterious(0.03)	benign(0.004)	12/18	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF18,Gene3D:3.80.10.10,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACCGCTTA	byFrequency|byCluster	5	ESCA
RAPGEF2	0	.	GRCh37	4	160260486	160260486	+	Silent	SNP	C	C	T	rs751558601	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2031C>T	p.%3D	p.D677D	ENST00000264431	13/24	26	20	6	31	31	0	RAPGEF2,synonymous_variant,p.%3D,ENST00000264431,;RAPGEF2,upstream_gene_variant,,ENST00000502485,;	T	ENSG00000109756	ENST00000264431	Transcript	synonymous_variant	2450	2031	677	D	gaC/gaT	rs751558601	.	.	1	RAPGEF2	HGNC	16854	protein_coding	YES	CCDS43277.1	ENSP00000264431	RPGF2_HUMAN	Q9UFT5_HUMAN,Q4W5Q4_HUMAN,Q17RH5_HUMAN,D6REY8_HUMAN,B4DG82_HUMAN	UPI0000033783	.	.	.	13/24	.	PROSITE_profiles:PS50200,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF202,Pfam_domain:PF00788,SMART_domains:SM00314,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGACAGAAT	byFrequency	5	ESCA
FAM218A	0	.	GRCh37	4	165878447	165878447	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.273C>A	p.%3D	p.R91R	ENST00000513876	1/1	33	16	17	24	24	0	FAM218A,synonymous_variant,p.%3D,ENST00000513876,;TRIM61,intron_variant,,ENST00000329314,;RP11-366M4.8,intron_variant,,ENST00000596751,;	A	ENSG00000250486	ENST00000513876	Transcript	synonymous_variant	348	273	91	R	cgC/cgA	.	.	.	1	FAM218A	HGNC	26466	protein_coding	YES	CCDS3807.1	ENSP00000427428	F218A_HUMAN	.	UPI000006D0F5	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGCTCATG	.	5	ESCA
NEK1	0	.	GRCh37	4	170315420	170315420	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*241A>G	.	.	ENST00000507142	36/36	37	28	9	32	32	0	NEK1,3_prime_UTR_variant,,ENST00000510533,;NEK1,3_prime_UTR_variant,,ENST00000511633,;NEK1,3_prime_UTR_variant,,ENST00000439128,;NEK1,3_prime_UTR_variant,,ENST00000512193,;NEK1,3_prime_UTR_variant,,ENST00000507142,;	C	ENSG00000137601	ENST00000507142	Transcript	3_prime_UTR_variant	4682	.	.	.	.	.	.	.	-1	NEK1	HGNC	7744	protein_coding	YES	CCDS56351.1	ENSP00000424757	NEK1_HUMAN	Q5JXL9_HUMAN	UPI00001D76CA	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGATTTAAT	.	5	ESCA
GALNTL6	0	.	GRCh37	4	173150833	173150833	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165G>A	p.%3D	p.G55G	ENST00000506823	3/13	74	47	27	64	64	0	GALNTL6,synonymous_variant,p.%3D,ENST00000508122,;GALNTL6,synonymous_variant,p.%3D,ENST00000506823,;	A	ENSG00000174473	ENST00000506823	Transcript	synonymous_variant	822	165	55	G	ggG/ggA	.	.	.	1	GALNTL6	HGNC	33844	protein_coding	YES	CCDS34104.1	ENSP00000423313	GLTL6_HUMAN	E5D8G0_HUMAN	UPI000058EB5C	.	.	.	3/13	.	hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGGGCAATT	.	5	ESCA
GPM6A	0	.	GRCh37	4	176555452	176555453	+	3'UTR	DEL	TT	TT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*603_*604delAA	.	.	ENST00000280187	8/8	31	24	6	27	27	0	GPM6A,3_prime_UTR_variant,,ENST00000280187,;GPM6A,3_prime_UTR_variant,,ENST00000506894,;GPM6A,3_prime_UTR_variant,,ENST00000393658,;GPM6A,downstream_gene_variant,,ENST00000515090,;GPM6A,downstream_gene_variant,,ENST00000506219,;GPM6A,downstream_gene_variant,,ENST00000508323,;GPM6A,non_coding_transcript_exon_variant,,ENST00000507080,;	-	ENSG00000150625	ENST00000280187	Transcript	3_prime_UTR_variant	1486-1487	.	.	.	.	.	.	.	-1	GPM6A	HGNC	4460	protein_coding	YES	CCDS3824.1	ENSP00000280187	GPM6A_HUMAN	Q49AH3_HUMAN,D6RIF4_HUMAN,D6RFZ3_HUMAN,D6RFY0_HUMAN,D6REJ8_HUMAN,D6RD95_HUMAN,D6RBM6_HUMAN,D6RBH3_HUMAN,D6RAE4_HUMAN,D6R9T7_HUMAN	UPI000012EAE1	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAGCACTTTTTTT	.	2	ESCA
VEGFC	0	.	GRCh37	4	177632776	177632777	+	Frame_Shift_Ins	INS	-	-	GA	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.579_580dupTC	p.Gln194LeufsTer7	p.Q194Lfs*7	ENST00000280193	4/7	48	34	14	41	41	0	VEGFC,frameshift_variant,p.Gln194LeufsTer7,ENST00000280193,;VEGFC,non_coding_transcript_exon_variant,,ENST00000507638,;	GA	ENSG00000150630	ENST00000280193	Transcript	frameshift_variant	996-997	580-581	194	Q/LX	caa/cTCaa	.	.	.	-1	VEGFC	HGNC	12682	protein_coding	YES	CCDS43285.1	ENSP00000280193	VEGFC_HUMAN	.	UPI000020B749	.	.	.	4/7	.	PROSITE_profiles:PS50278,hmmpanther:PTHR12025,hmmpanther:PTHR12025:SF3,Pfam_domain:PF00341,Gene3D:2.10.90.10,SMART_domains:SM00141,Superfamily_domains:SSF57501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	GGCCTTGAGAG	.	2	ESCA
SNX25	0	.	GRCh37	4	186244914	186244914	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1221delA	p.Lys407AsnfsTer6	p.K407Nfs*6	ENST00000504273	9/19	55	44	11	49	49	0	SNX25,frameshift_variant,p.Lys407AsnfsTer6,ENST00000504273,;SNX25,frameshift_variant,p.Lys407AsnfsTer6,ENST00000264694,;SNX25,non_coding_transcript_exon_variant,,ENST00000512853,;SNX25,frameshift_variant,p.Lys86AsnfsTer6,ENST00000504959,;	-	ENSG00000109762	ENST00000504273	Transcript	frameshift_variant	1511	1217	406	E/X	gAa/ga	.	.	.	1	SNX25	HGNC	21883	protein_coding	YES	CCDS34116.1	ENSP00000426255	SNX25_HUMAN	B3KTI8_HUMAN	UPI000020B7BB	.	.	.	9/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22775:SF6,hmmpanther:PTHR22775	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGAAGAAAAAC	.	3	ESCA
CCDC110	0	.	GRCh37	4	186380035	186380035	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1706T>C	p.Ile569Thr	p.I569T	ENST00000307588	6/7	60	39	20	79	79	0	CCDC110,missense_variant,p.Ile569Thr,ENST00000510617,;CCDC110,missense_variant,p.Ile569Thr,ENST00000307588,;CCDC110,missense_variant,p.Ile532Thr,ENST00000393540,;CCDC110,downstream_gene_variant,,ENST00000506876,;CCDC110,downstream_gene_variant,,ENST00000506962,;CCDC110,downstream_gene_variant,,ENST00000507501,;CCDC110,downstream_gene_variant,,ENST00000510481,;CCDC110,upstream_gene_variant,,ENST00000508538,;CCDC110,downstream_gene_variant,,ENST00000504020,;	G	ENSG00000168491	ENST00000307588	Transcript	missense_variant	1782	1706	569	I/T	aTa/aCa	.	.	.	-1	CCDC110	HGNC	28504	protein_coding	YES	CCDS3843.1	ENSP00000306776	CC110_HUMAN	.	UPI0000070BFC	.	tolerated(0.18)	benign(0.062)	6/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTATACTC	.	5	ESCA
SORBS2	0	.	GRCh37	4	186541266	186541266	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2843A>G	p.Asp948Gly	p.D948G	ENST00000355634	17/24	70	57	12	61	61	0	SORBS2,missense_variant,p.Asp848Gly,ENST00000431808,;SORBS2,missense_variant,p.Asp439Gly,ENST00000319454,;SORBS2,missense_variant,p.Asp948Gly,ENST00000355634,;SORBS2,missense_variant,p.Asp848Gly,ENST00000284776,;SORBS2,missense_variant,p.Asp752Gly,ENST00000418609,;SORBS2,missense_variant,p.Asp414Gly,ENST00000393528,;SORBS2,missense_variant,p.Asp409Gly,ENST00000448662,;SORBS2,missense_variant,p.Asp392Gly,ENST00000449407,;SORBS2,missense_variant,p.Asp572Gly,ENST00000437304,;SORBS2,missense_variant,p.Asp197Gly,ENST00000451974,;SORBS2,missense_variant,p.Asp265Gly,ENST00000438278,;SORBS2,missense_variant,p.Asp479Gly,ENST00000319471,;SORBS2,non_coding_transcript_exon_variant,,ENST00000498125,;SORBS2,downstream_gene_variant,,ENST00000487184,;SORBS2,upstream_gene_variant,,ENST00000480146,;	C	ENSG00000154556	ENST00000355634	Transcript	missense_variant	3557	2843	948	D/G	gAc/gGc	.	.	.	-1	SORBS2	HGNC	24098	protein_coding	YES	CCDS59482.1	ENSP00000347852	SRBS2_HUMAN	C9JZ60_HUMAN,C9JN77_HUMAN,C9JL62_HUMAN,C9JI79_HUMAN,C9JDX2_HUMAN,C9JBR8_HUMAN,C9JBB0_HUMAN,C9J8E3_HUMAN,C9J7Q5_HUMAN,C9J4Z9_HUMAN,C9J4K2_HUMAN,C9J3W4_HUMAN,C9J372_HUMAN,C9IZT7_HUMAN,C9IZ89_HUMAN	UPI000198C7F0	.	deleterious(0.01)	benign(0.01)	17/24	.	hmmpanther:PTHR10661,hmmpanther:PTHR10661:SF122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGTCAGTC	.	5	ESCA
GPR125	0	.	GRCh37	4	22414846	22414846	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2191A>G	p.Thr731Ala	p.T731A	ENST00000334304	14/19	80	68	12	58	58	0	GPR125,missense_variant,p.Thr731Ala,ENST00000334304,;GPR125,downstream_gene_variant,,ENST00000508133,;GPR125,non_coding_transcript_exon_variant,,ENST00000506155,;GPR125,non_coding_transcript_exon_variant,,ENST00000504617,;GPR125,non_coding_transcript_exon_variant,,ENST00000282943,;	C	ENSG00000152990	ENST00000334304	Transcript	missense_variant	2461	2191	731	T/A	Acg/Gcg	.	.	.	-1	GPR125	HGNC	13839	protein_coding	YES	CCDS33964.1	ENSP00000334952	GP125_HUMAN	Q6JN45_HUMAN,D6RER4_HUMAN,D6RDX4_HUMAN	UPI00001D7735	.	tolerated(0.11)	benign(0.02)	14/19	.	SMART_domains:SM00303,Pfam_domain:PF01825,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF35,PROSITE_profiles:PS50221	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.T731T|c.2193G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCGTAGTGA	.	5	ESCA
MXD4	0	.	GRCh37	4	2251851	2251854	+	3'UTR	DEL	CCTT	CCTT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CCTT	CCTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*417_*420delAAGG	.	.	ENST00000337190	6/6	81	40	41	46	46	0	MXD4,3_prime_UTR_variant,,ENST00000337190,;MIR4800,mature_miRNA_variant,,ENST00000537353,;MXD4,downstream_gene_variant,,ENST00000515378,;MXD4,non_coding_transcript_exon_variant,,ENST00000513372,;MXD4,downstream_gene_variant,,ENST00000513380,;	-	ENSG00000123933	ENST00000337190	Transcript	3_prime_UTR_variant	1361-1364	.	.	.	.	.	.	.	-1	MXD4	HGNC	13906	protein_coding	YES	CCDS3361.1	ENSP00000337889	MAD4_HUMAN	D3DVQ5_HUMAN	UPI000012EB1A	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCCTTGCCTTCCTTC	.	2	ESCA
PPARGC1A	0	.	GRCh37	4	23796668	23796668	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*777delT	.	.	ENST00000264867	13/13	23	16	7	18	17	0	PPARGC1A,3_prime_UTR_variant,,ENST00000264867,;PPARGC1A,intron_variant,,ENST00000509702,;PPARGC1A,downstream_gene_variant,,ENST00000506055,;	-	ENSG00000109819	ENST00000264867	Transcript	3_prime_UTR_variant	3294	.	.	.	.	.	.	.	-1	PPARGC1A	HGNC	9237	protein_coding	YES	CCDS3429.1	ENSP00000264867	PRGC1_HUMAN	G8DM16_HUMAN	UPI000004D072	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	AAAAAGAAAAAA	.	2	ESCA
RGS12	0	.	GRCh37	4	3432792	3432792	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4114+110C>T	.	.	ENST00000344733	.	41	7	34	8	8	0	RGS12,3_prime_UTR_variant,,ENST00000538395,;RGS12,3_prime_UTR_variant,,ENST00000336727,;RGS12,3_prime_UTR_variant,,ENST00000382788,;RGS12,intron_variant,,ENST00000344733,;RGS12,intron_variant,,ENST00000338806,;RGS12,downstream_gene_variant,,ENST00000306648,;RGS12,intron_variant,,ENST00000509772,;RGS12,downstream_gene_variant,,ENST00000508158,;RGS12,downstream_gene_variant,,ENST00000507246,;RGS12,downstream_gene_variant,,ENST00000515521,;RGS12,intron_variant,,ENST00000504194,;RGS12,downstream_gene_variant,,ENST00000513991,;RGS12,downstream_gene_variant,,ENST00000507041,;	T	ENSG00000159788	ENST00000344733	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RGS12	HGNC	9994	protein_coding	YES	CCDS3366.1	ENSP00000339381	RGS12_HUMAN	Q69YN1_HUMAN,Q56A82_HUMAN,E9PBG5_HUMAN	UPI0000133830	.	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCTCCGTGAC	.	3	ESCA
LINC00955	0	.	GRCh37	4	3589709	3589709	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77G>T	p.Trp26Leu	p.W26L	ENST00000514422	2/3	151	105	45	95	95	0	LINC00955,missense_variant,p.Trp26Leu,ENST00000514422,;LINC00955,intron_variant,,ENST00000502775,;	T	ENSG00000216560	ENST00000514422	Transcript	missense_variant	363	77	26	W/L	tGg/tTg	.	.	.	1	LINC00955	HGNC	26644	protein_coding	YES	.	ENSP00000427553	.	E7ETJ0_HUMAN	UPI0000160C3E	.	tolerated_low_confidence(0.23)	possibly_damaging(0.514)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTCTTGGTTCA	.	4	ESCA
WDR19	0	.	GRCh37	4	39230210	39230212	+	In_Frame_Del	DEL	AAC	AAC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AAC	AAC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1886_1888delACA	p.Asn629del	p.N629del	ENST00000399820	17/37	80	68	12	36	36	0	WDR19,inframe_deletion,p.Asn469del,ENST00000288634,;WDR19,inframe_deletion,p.Asn629del,ENST00000399820,;WDR19,non_coding_transcript_exon_variant,,ENST00000515631,;WDR19,non_coding_transcript_exon_variant,,ENST00000511729,;WDR19,inframe_deletion,p.Asn22del,ENST00000507228,;WDR19,3_prime_UTR_variant,,ENST00000506869,;WDR19,non_coding_transcript_exon_variant,,ENST00000512095,;	-	ENSG00000157796	ENST00000399820	Transcript	inframe_deletion	2036-2038	1882-1884	628	N/-	AAC/-	.	.	.	1	WDR19	HGNC	18340	protein_coding	YES	CCDS47042.1	ENSP00000382717	WDR19_HUMAN	D6RE75_HUMAN,B4DGR6_HUMAN	UPI000004CC24	.	.	.	17/37	.	hmmpanther:PTHR14920,hmmpanther:PTHR14920:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAGTAAACAACAT	.	3	ESCA
UGDH	0	.	GRCh37	4	39501756	39501756	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7C>T	.	.	ENST00000316423	12/12	75	66	8	40	40	0	UGDH,3_prime_UTR_variant,,ENST00000501493,;UGDH,3_prime_UTR_variant,,ENST00000316423,;UGDH,3_prime_UTR_variant,,ENST00000507089,;UGDH,3_prime_UTR_variant,,ENST00000506179,;	A	ENSG00000109814	ENST00000316423	Transcript	3_prime_UTR_variant	1835	.	.	.	.	.	.	.	-1	UGDH	HGNC	12525	protein_coding	YES	CCDS3455.1	ENSP00000319501	UGDH_HUMAN	Q9NY20_HUMAN,Q9NQ83_HUMAN,Q9NQ82_HUMAN,Q9NQ81_HUMAN,E7ETF4_HUMAN,E7ER95_HUMAN,E7ER83_HUMAN,D6RHF4_HUMAN	UPI0000001075	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATGGCAATC	.	4	ESCA
TMEM128	0	.	GRCh37	4	4237303	4237303	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*690delT	.	.	ENST00000254742	5/5	28	13	15	12	12	0	TMEM128,3_prime_UTR_variant,,ENST00000382753,;TMEM128,3_prime_UTR_variant,,ENST00000254742,;TMEM128,downstream_gene_variant,,ENST00000540397,;TMEM128,downstream_gene_variant,,ENST00000538516,;	-	ENSG00000132406	ENST00000254742	Transcript	3_prime_UTR_variant	1703	.	.	.	.	.	.	.	-1	TMEM128	HGNC	28201	protein_coding	YES	CCDS3373.1	ENSP00000254742	TM128_HUMAN	.	UPI0000073696	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATACAGAAAAAA	.	2	ESCA
ZNF721	0	.	GRCh37	4	435768	435768	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2488A>G	p.Ile830Val	p.I830V	ENST00000511833	3/3	66	32	33	38	38	0	ZNF721,missense_variant,p.Ile818Val,ENST00000338977,;ZNF721,missense_variant,p.Ile830Val,ENST00000511833,;ZNF721,intron_variant,,ENST00000506646,;ZNF721,downstream_gene_variant,,ENST00000505900,;ZNF721,intron_variant,,ENST00000507078,;ABCA11P,intron_variant,,ENST00000514396,;ABCA11P,intron_variant,,ENST00000451020,;ABCA11P,intron_variant,,ENST00000507854,;ZNF721,intron_variant,,ENST00000515578,;	C	ENSG00000182903	ENST00000511833	Transcript	missense_variant	2682	2488	830	I/V	Att/Gtt	.	.	.	-1	ZNF721	HGNC	29425	protein_coding	YES	CCDS46991.1	ENSP00000428878	ZN721_HUMAN	.	UPI0000E9B4A9	.	tolerated(0.16)	benign(0.401)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24376,hmmpanther:PTHR24376:SF16,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAATTCTCC	.	5	ESCA
GUF1	0	.	GRCh37	4	44690095	44690095	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1010T>C	p.Leu337Ser	p.L337S	ENST00000281543	9/17	78	65	13	55	55	0	GUF1,missense_variant,p.Leu337Ser,ENST00000281543,;GNPDA2,intron_variant,,ENST00000609092,;GNPDA2,intron_variant,,ENST00000608855,;GUF1,non_coding_transcript_exon_variant,,ENST00000506793,;GUF1,3_prime_UTR_variant,,ENST00000513775,;	C	ENSG00000151806	ENST00000281543	Transcript	missense_variant	1204	1010	337	L/S	tTa/tCa	.	.	.	1	GUF1	HGNC	25799	protein_coding	YES	CCDS3468.1	ENSP00000281543	GUF1_HUMAN	.	UPI000006FFEC	.	deleterious(0)	probably_damaging(0.979)	9/17	.	Superfamily_domains:SSF50447,Gene3D:2.40.30.10,Pfam_domain:PF03144,TIGRFAM_domain:TIGR01393,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF97,HAMAP:MF_00071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACATTATGTT	.	5	ESCA
KIT	0	.	GRCh37	4	55606777	55606777	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2054G>A	.	.	ENST00000288135	21/21	70	30	40	52	52	0	KIT,3_prime_UTR_variant,,ENST00000288135,;KIT,downstream_gene_variant,,ENST00000412167,;	A	ENSG00000157404	ENST00000288135	Transcript	3_prime_UTR_variant	5082	.	.	.	.	.	.	.	1	KIT	HGNC	6342	protein_coding	YES	CCDS3496.1	ENSP00000288135	KIT_HUMAN	Q8TCG9_HUMAN	UPI000003F17D	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCGGCGTAA	.	5	ESCA
SRP72	0	.	GRCh37	4	57333820	57333820	+	Frame_Shift_Del	DEL	G	G	-	rs17524437	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25delG	p.Val9CysfsTer10	p.V9Cfs*10	ENST00000342756	1/19	32	13	19	14	14	0	SRP72,frameshift_variant,p.Val9CysfsTer10,ENST00000504757,;SRP72,frameshift_variant,p.Val9CysfsTer10,ENST00000510663,;SRP72,frameshift_variant,p.Val9CysfsTer10,ENST00000342756,;RP11-393M11.2,downstream_gene_variant,,ENST00000602434,;	-	ENSG00000174780	ENST00000342756	Transcript	frameshift_variant	740	19	7	G/X	Ggg/gg	rs17524437	.	.	1	SRP72	HGNC	11303	protein_coding	YES	CCDS3506.1	ENSP00000342181	SRP72_HUMAN	Q86X80_HUMAN	UPI000013EEB0	.	.	.	1/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14094:SF9,hmmpanther:PTHR14094,PIRSF_domain:PIRSF038922	T:0.0126	T:0	T:0	.	T:0.0615	T:0	T:0.001	C:0	C:0.0002	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.G7G|c.21G>T|3	INDELOCATOR|VARSCANI	GGCAGCGGGGGG	byFrequency|byCluster|by1000G	2	ESCA
CRMP1	0	.	GRCh37	4	5857915	5857915	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775T>C	p.Tyr259His	p.Y259H	ENST00000324989	4/14	74	23	51	58	58	0	CRMP1,missense_variant,p.Tyr143His,ENST00000512574,;CRMP1,missense_variant,p.Tyr259His,ENST00000324989,;CRMP1,missense_variant,p.Tyr145His,ENST00000397890,;CRMP1,non_coding_transcript_exon_variant,,ENST00000511535,;CRMP1,non_coding_transcript_exon_variant,,ENST00000506216,;	G	ENSG00000072832	ENST00000324989	Transcript	missense_variant	864	775	259	Y/H	Tac/Cac	.	.	.	-1	CRMP1	HGNC	2365	protein_coding	YES	CCDS33950.1	ENSP00000321606	DPYL1_HUMAN	Q96I11_HUMAN,B3KT07_HUMAN	UPI000020BA92	.	tolerated(0.7)	benign(0.021)	4/14	.	hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF54,Gene3D:3.20.20.140,Pfam_domain:PF01979,TIGRFAM_domain:TIGR02033,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGTACCAGC	.	5	ESCA
LPHN3	0	.	GRCh37	4	62937514	62937514	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*888A>G	.	.	ENST00000514591	25/25	26	10	15	28	28	0	LPHN3,3_prime_UTR_variant,,ENST00000502815,;LPHN3,3_prime_UTR_variant,,ENST00000545650,;LPHN3,3_prime_UTR_variant,,ENST00000514591,;LPHN3,3_prime_UTR_variant,,ENST00000512091,;LPHN3,downstream_gene_variant,,ENST00000507625,;LPHN3,downstream_gene_variant,,ENST00000508946,;LPHN3,downstream_gene_variant,,ENST00000506700,;LPHN3,downstream_gene_variant,,ENST00000509896,;LPHN3,downstream_gene_variant,,ENST00000511324,;LPHN3,downstream_gene_variant,,ENST00000506720,;LPHN3,downstream_gene_variant,,ENST00000504896,;LPHN3,downstream_gene_variant,,ENST00000508693,;LPHN3,downstream_gene_variant,,ENST00000506746,;LPHN3,downstream_gene_variant,,ENST00000514996,;LPHN3,downstream_gene_variant,,ENST00000514157,;LPHN3,downstream_gene_variant,,ENST00000507164,;RP11-84A1.3,intron_variant,,ENST00000504135,;RP11-84A1.3,intron_variant,,ENST00000506704,;RP11-84A1.3,downstream_gene_variant,,ENST00000509461,;	G	ENSG00000150471	ENST00000514591	Transcript	3_prime_UTR_variant	5627	.	.	.	.	.	.	.	1	LPHN3	HGNC	20974	protein_coding	YES	CCDS54768.1	ENSP00000422533	.	Q4W5J9_HUMAN,E9PE04_HUMAN	UPI00016278EF	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAATAAATGG	.	5	ESCA
PPP2R2C	0	.	GRCh37	4	6323275	6323275	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1754T>C	.	.	ENST00000335585	9/9	37	32	5	19	19	0	PPP2R2C,3_prime_UTR_variant,,ENST00000335585,;PPP2R2C,downstream_gene_variant,,ENST00000382599,;PPP2R2C,downstream_gene_variant,,ENST00000515571,;PPP2R2C,downstream_gene_variant,,ENST00000507294,;PPP2R2C,downstream_gene_variant,,ENST00000506140,;	G	ENSG00000074211	ENST00000335585	Transcript	3_prime_UTR_variant	3122	.	.	.	.	.	.	.	-1	PPP2R2C	HGNC	9306	protein_coding	YES	CCDS3388.1	ENSP00000335083	2ABG_HUMAN	.	UPI0000140CE7	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGTACACAT	.	4	ESCA
UBA6	0	.	GRCh37	4	68499110	68499110	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2095T>C	p.Cys699Arg	p.C699R	ENST00000322244	23/33	39	29	9	30	30	0	UBA6,missense_variant,p.Cys699Arg,ENST00000322244,;UBA6,intron_variant,,ENST00000505673,;RP11-17P16.2,upstream_gene_variant,,ENST00000604441,;	G	ENSG00000033178	ENST00000322244	Transcript	missense_variant	2155	2095	699	C/R	Tgt/Cgt	.	.	.	-1	UBA6	HGNC	25581	protein_coding	YES	CCDS3516.1	ENSP00000313454	UBA6_HUMAN	B3KSS1_HUMAN	UPI000004A4F7	.	deleterious(0)	probably_damaging(1)	23/33	.	hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF141,Gene3D:1y8qD02,TIGRFAM_domain:TIGR01408,Superfamily_domains:SSF69572,Prints_domain:PR01849	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACACACTGGG	.	5	ESCA
UGT2B10	0	.	GRCh37	4	69696698	69696698	+	3'UTR	DEL	A	A	-	rs74464983	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*109delA	.	.	ENST00000265403	6/6	23	10	13	20	20	0	UGT2B10,3_prime_UTR_variant,,ENST00000265403,;UGT2B10,downstream_gene_variant,,ENST00000458688,;RP11-468N14.3,downstream_gene_variant,,ENST00000512503,;	-	ENSG00000109181	ENST00000265403	Transcript	3_prime_UTR_variant	1715	.	.	.	.	rs74464983	.	.	1	UGT2B10	HGNC	12544	protein_coding	YES	.	ENSP00000265403	UDB10_HUMAN	.	UPI0000137A96	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTGACAAAAAA	.	2	ESCA
RASGEF1B	0	.	GRCh37	4	82348573	82348574	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*348dupT	.	.	ENST00000264400	14/14	17	9	7	28	28	0	RASGEF1B,3_prime_UTR_variant,,ENST00000509081,;RASGEF1B,3_prime_UTR_variant,,ENST00000264400,;RASGEF1B,downstream_gene_variant,,ENST00000335927,;	A	ENSG00000138670	ENST00000264400	Transcript	3_prime_UTR_variant	1922-1923	.	.	.	.	.	.	.	-1	RASGEF1B	HGNC	24881	protein_coding	YES	CCDS34022.1	ENSP00000264400	RGF1B_HUMAN	D6RE71_HUMAN,B4E121_HUMAN	UPI0000044685	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAAATTAAAAA	.	2	ESCA
ACOX3	0	.	GRCh37	4	8398737	8398737	+	Missense_Mutation	SNP	C	C	T	rs528832606	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.983G>A	p.Arg328His	p.R328H	ENST00000356406	9/18	81	32	49	51	51	0	ACOX3,missense_variant,p.Arg328His,ENST00000356406,;ACOX3,missense_variant,p.Arg328His,ENST00000413009,;ACOX3,missense_variant,p.Arg328His,ENST00000503233,;RNA5SP152,downstream_gene_variant,,ENST00000365184,;ACOX3,upstream_gene_variant,,ENST00000508302,;ACOX3,non_coding_transcript_exon_variant,,ENST00000510365,;	T	ENSG00000087008	ENST00000356406	Transcript	missense_variant	1061	983	328	R/H	cGc/cAc	rs528832606,COSM1058236	.	.	-1	ACOX3	HGNC	121	protein_coding	YES	CCDS3401.1	ENSP00000348775	ACOX3_HUMAN	D6RJ89_HUMAN	UPI000013EEE2	.	deleterious(0)	probably_damaging(0.997)	9/18	.	hmmpanther:PTHR10909:SF11,hmmpanther:PTHR10909,Gene3D:1.20.140.10,Pfam_domain:PF00441,PIRSF_domain:PIRSF000168,Superfamily_domains:SSF47203	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGCGAAGA	byFrequency|byCluster	5	ESCA
WDFY3	0	.	GRCh37	4	85658516	85658516	+	Missense_Mutation	SNP	C	C	T	rs766567564	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6578G>A	p.Arg2193His	p.R2193H	ENST00000295888	41/68	10	4	6	22	22	0	WDFY3,missense_variant,p.Arg2193His,ENST00000295888,;WDFY3,missense_variant,p.Arg2193His,ENST00000322366,;WDFY3,upstream_gene_variant,,ENST00000514711,;WDFY3,non_coding_transcript_exon_variant,,ENST00000504839,;	T	ENSG00000163625	ENST00000295888	Transcript	missense_variant	6986	6578	2193	R/H	cGt/cAt	rs766567564,COSM1058360	.	.	-1	WDFY3	HGNC	20751	protein_coding	YES	CCDS3609.1	ENSP00000295888	WDFY3_HUMAN	D6RJE4_HUMAN,A7E1Z6_HUMAN	UPI000013E2C7	.	tolerated(0.37)	benign(0.008)	41/68	.	hmmpanther:PTHR13743:SF55,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTGACGCCCT	byFrequency	3	ESCA
DSPP	0	.	GRCh37	4	88537661	88537666	+	In_Frame_Del	DEL	AGTGAC	AGTGAC	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AGTGAC	AGTGAC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3864_3869delCAGTGA	p.Asp1288_Ser1289del	p.D1288_S1289del	ENST00000399271	5/5	25	17	8	52	52	0	DSPP,inframe_deletion,p.Asp1288_Ser1289del,ENST00000282478,;DSPP,inframe_deletion,p.Asp1288_Ser1289del,ENST00000399271,;RP11-742B18.1,intron_variant,,ENST00000506480,;	-	ENSG00000152591	ENST00000399271	Transcript	inframe_deletion	3967-3972	3847-3852	1283-1284	SD/-	AGTGAC/-	TMP_ESP_4_88537661_88537666	.	.	1	DSPP	HGNC	3054	protein_coding	YES	CCDS43248.1	ENSP00000382213	DSPP_HUMAN	B7SEZ4_HUMAN,B7SEY4_HUMAN	UPI00006BFF57	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32093	.	.	.	.	.	.	.	-:0	-:0.0005	.	.	.	.	.	.	.	MODERATE	.	deletion	.	17	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	AATGGAAGTGACAGTGA	.	2	ESCA
HERC3	0	.	GRCh37	4	89628197	89628197	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*92delT	.	.	ENST00000402738	26/26	21	15	6	21	21	0	HERC3,3_prime_UTR_variant,,ENST00000402738,;HERC3,3_prime_UTR_variant,,ENST00000543130,;HERC3,3_prime_UTR_variant,,ENST00000264345,;FAM13A-AS1,upstream_gene_variant,,ENST00000500765,;	-	ENSG00000138641	ENST00000402738	Transcript	3_prime_UTR_variant	3478	.	.	.	.	.	.	.	1	HERC3	HGNC	4876	protein_coding	YES	CCDS34028.1	ENSP00000385684	HERC3_HUMAN	Q4W5H5_HUMAN,F5GWU0_HUMAN,D6RAT5_HUMAN,C9JKA7_HUMAN,C9JFL2_HUMAN,C9J8E7_HUMAN,C9J6Z1_HUMAN,B4DK41_HUMAN	UPI000012C614	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTCTATTTTTT	.	3	ESCA
GPRIN3	0	.	GRCh37	4	90169281	90169281	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1981G>T	p.Gly661Ter	p.G661*	ENST00000609438	2/2	43	23	20	52	52	0	GPRIN3,stop_gained,p.Gly661Ter,ENST00000609438,;GPRIN3,stop_gained,p.Gly661Ter,ENST00000333209,;	A	ENSG00000185477	ENST00000609438	Transcript	stop_gained	2500	1981	661	G/*	Gga/Tga	.	.	.	-1	GPRIN3	HGNC	27733	protein_coding	YES	CCDS34030.1	ENSP00000476603	.	.	UPI00001C1E20	.	.	.	2/2	.	hmmpanther:PTHR15718:SF2,hmmpanther:PTHR15718,Pfam_domain:PF15235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCCTGGAG	.	5	ESCA
CCSER1	0	.	GRCh37	4	91701607	91701607	+	Intron	SNP	G	G	T	rs756999993	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2011-35306G>T	.	.	ENST00000509176	.	13	6	6	34	34	0	CCSER1,missense_variant,p.Arg675Ser,ENST00000432775,;CCSER1,intron_variant,,ENST00000509176,;CCSER1,intron_variant,,ENST00000503421,;CCSER1,intron_variant,,ENST00000333691,;CCSER1,non_coding_transcript_exon_variant,,ENST00000504150,;CCSER1,3_prime_UTR_variant,,ENST00000510519,;CCSER1,intron_variant,,ENST00000505073,;CCSER1,intron_variant,,ENST00000513522,;CCSER1,intron_variant,,ENST00000509109,;	T	ENSG00000184305	ENST00000509176	Transcript	intron_variant	.	.	.	.	.	rs756999993	.	.	1	CCSER1	HGNC	29349	protein_coding	YES	CCDS47099.1	ENSP00000425040	CCSE1_HUMAN	.	UPI00005A6104	.	.	.	.	7/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CCTAGGGAATT	.	4	ESCA
ST8SIA4	0	.	GRCh37	5	100146435	100146435	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1116delA	.	.	ENST00000231461	5/5	18	7	11	23	23	0	ST8SIA4,3_prime_UTR_variant,,ENST00000231461,;	-	ENSG00000113532	ENST00000231461	Transcript	3_prime_UTR_variant	2507	.	.	.	.	.	.	.	-1	ST8SIA4	HGNC	10871	protein_coding	YES	CCDS4091.1	ENSP00000231461	SIA8D_HUMAN	.	UPI0000135973	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAAAGATTTTTT	.	2	ESCA
SLCO6A1	0	.	GRCh37	5	101834246	101834246	+	Nonsense_Mutation	SNP	A	A	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303T>A	p.Cys101Ter	p.C101*	ENST00000506729	1/14	31	10	21	25	25	0	SLCO6A1,stop_gained,p.Cys101Ter,ENST00000379807,;SLCO6A1,stop_gained,p.Cys101Ter,ENST00000513675,;SLCO6A1,stop_gained,p.Cys101Ter,ENST00000379810,;SLCO6A1,stop_gained,p.Cys101Ter,ENST00000506729,;SLCO6A1,stop_gained,p.Cys101Ter,ENST00000389019,;RP11-58B2.1,upstream_gene_variant,,ENST00000502494,;SLCO6A1,non_coding_transcript_exon_variant,,ENST00000505407,;SLCO6A1,non_coding_transcript_exon_variant,,ENST00000514551,;	T	ENSG00000205359	ENST00000506729	Transcript	stop_gained	475	303	101	C/*	tgT/tgA	COSM3607346	.	.	-1	SLCO6A1	HGNC	23613	protein_coding	YES	CCDS34206.1	ENSP00000421339	SO6A1_HUMAN	H0Y8R6_HUMAN,D3DSZ4_HUMAN	UPI000020C392	.	.	.	1/14	.	hmmpanther:PTHR11388:SF3,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCAACACTC	.	5	ESCA
SLC12A7	0	.	GRCh37	5	1085510	1085510	+	Missense_Mutation	SNP	G	G	A	rs762241589	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.754C>T	p.Arg252Cys	p.R252C	ENST00000264930	7/24	116	107	8	25	25	0	SLC12A7,missense_variant,p.Arg252Cys,ENST00000264930,;SLC12A7,upstream_gene_variant,,ENST00000510943,;	A	ENSG00000113504	ENST00000264930	Transcript	missense_variant	798	754	252	R/C	Cgt/Tgt	rs762241589	.	.	-1	SLC12A7	HGNC	10915	protein_coding	YES	CCDS34129.1	ENSP00000264930	S12A7_HUMAN	.	UPI0000141815	.	deleterious(0)	probably_damaging(1)	7/24	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11827:SF47,hmmpanther:PTHR11827,Pfam_domain:PF00324,TIGRFAM_domain:TIGR00930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACACGCATGT	.	2	ESCA
TRIM36	0	.	GRCh37	5	114499432	114499432	+	Silent	SNP	G	G	A	rs763230187	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81C>T	p.%3D	p.I27I	ENST00000282369	2/10	13	3	10	26	26	0	TRIM36,synonymous_variant,p.%3D,ENST00000508894,;TRIM36,synonymous_variant,p.%3D,ENST00000282369,;TRIM36,synonymous_variant,p.%3D,ENST00000513154,;TRIM36,intron_variant,,ENST00000514154,;TRIM36,non_coding_transcript_exon_variant,,ENST00000515104,;TRIM36,intron_variant,,ENST00000510222,;	A	ENSG00000152503	ENST00000282369	Transcript	synonymous_variant	203	81	27	I	atC/atT	rs763230187	.	.	-1	TRIM36	HGNC	16280	protein_coding	YES	CCDS4115.1	ENSP00000282369	TRI36_HUMAN	E9PBG3_HUMAN	UPI000013DCD9	.	.	.	2/10	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF29,Gene3D:3.30.40.10,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CTTTCGATATT	.	4	ESCA
SLC12A2	0	.	GRCh37	5	127523673	127523673	+	3'UTR	SNP	G	G	A	rs187398964	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1350G>A	.	.	ENST00000262461	27/27	15	2	12	9	9	0	SLC12A2,3_prime_UTR_variant,,ENST00000343225,;SLC12A2,3_prime_UTR_variant,,ENST00000262461,;SLC12A2,downstream_gene_variant,,ENST00000507791,;SLC12A2,downstream_gene_variant,,ENST00000509205,;	A	ENSG00000064651	ENST00000262461	Transcript	3_prime_UTR_variant	5178	.	.	.	.	rs187398964	.	.	1	SLC12A2	HGNC	10911	protein_coding	YES	CCDS4144.1	ENSP00000262461	S12A2_HUMAN	Q53ZR1_HUMAN	UPI000013541A	.	.	.	27/27	.	.	A:0.0010	A:0.0038	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTGTGTATAT	byFrequency|by1000G	3	ESCA
FNIP1	0	.	GRCh37	5	130979570	130979570	+	3'Flank	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000510461	.	22	2	20	23	23	0	FNIP1,3_prime_UTR_variant,,ENST00000307968,;FNIP1,3_prime_UTR_variant,,ENST00000307954,;CTC-432M15.3,intron_variant,,ENST00000514667,;FNIP1,downstream_gene_variant,,ENST00000510461,;	C	ENSG00000217128	ENST00000510461	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	560	-1	FNIP1	HGNC	29418	protein_coding	YES	CCDS34227.1	ENSP00000421985	FNIP1_HUMAN	B3KX44_HUMAN	UPI00001AEE81	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTTATAAG	.	5	ESCA
SOWAHA	0	.	GRCh37	5	132150631	132150631	+	Missense_Mutation	SNP	G	G	A	rs746186847	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1318G>A	p.Asp440Asn	p.D440N	ENST00000378693	1/1	15	10	5	11	11	0	SOWAHA,missense_variant,p.Asp440Asn,ENST00000378693,;AC004775.5,downstream_gene_variant,,ENST00000607389,;	A	ENSG00000198944	ENST00000378693	Transcript	missense_variant	1599	1318	440	D/N	Gat/Aat	rs746186847	.	.	1	SOWAHA	HGNC	27033	protein_coding	YES	CCDS43361.1	ENSP00000367965	SWAHA_HUMAN	.	UPI0000413F35	.	deleterious(0)	probably_damaging(0.997)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14491:SF2,hmmpanther:PTHR14491,Gene3D:1.25.40.20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCGATCCA	.	5	ESCA
GDF9	0	.	GRCh37	5	132198210	132198210	+	Missense_Mutation	SNP	G	G	A	rs76349024	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436C>T	p.Arg146Cys	p.R146C	ENST00000378673	3/3	24	5	19	20	20	0	GDF9,missense_variant,p.Arg146Cys,ENST00000296875,;GDF9,missense_variant,p.Arg146Cys,ENST00000378673,;UQCRQ,upstream_gene_variant,,ENST00000378667,;UQCRQ,upstream_gene_variant,,ENST00000378670,;UQCRQ,upstream_gene_variant,,ENST00000378665,;GDF9,non_coding_transcript_exon_variant,,ENST00000472320,;GDF9,non_coding_transcript_exon_variant,,ENST00000464378,;UQCRQ,upstream_gene_variant,,ENST00000496429,;UQCRQ,upstream_gene_variant,,ENST00000480372,;UQCRQ,upstream_gene_variant,,ENST00000498309,;	A	ENSG00000164404	ENST00000378673	Transcript	missense_variant	1303	436	146	R/C	Cgc/Tgc	rs76349024	.	.	-1	GDF9	HGNC	4224	protein_coding	YES	CCDS4162.1	ENSP00000367942	GDF9_HUMAN	B4DXG3_HUMAN	UPI000012B396	.	tolerated(0.05)	benign(0.046)	3/3	.	hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF19	A:0.0014	A:0	A:0	.	A:0.0069	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AATGCGATCCA	byFrequency|byCluster|by1000G	3	ESCA
JADE2	0	.	GRCh37	5	133915409	133915409	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*402C>A	.	.	ENST00000395003	11/11	31	27	4	17	17	0	JADE2,3_prime_UTR_variant,,ENST00000395003,;JADE2,3_prime_UTR_variant,,ENST00000361895,;JADE2,downstream_gene_variant,,ENST00000282605,;JADE2,downstream_gene_variant,,ENST00000402835,;JADE2,downstream_gene_variant,,ENST00000470876,;JADE2,downstream_gene_variant,,ENST00000430087,;	A	ENSG00000043143	ENST00000395003	Transcript	3_prime_UTR_variant	2954	.	.	.	.	.	.	.	1	JADE2	HGNC	22984	protein_coding	YES	CCDS4176.1	ENSP00000378451	JADE2_HUMAN	D6R9B8_HUMAN,C9J929_HUMAN	UPI00002331C9	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCGCCTTGCC	.	3	ESCA
SPOCK1	0	.	GRCh37	5	136312360	136312360	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1983delT	.	.	ENST00000394945	11/11	17	8	9	17	16	0	SPOCK1,3_prime_UTR_variant,,ENST00000394945,;SPOCK1,downstream_gene_variant,,ENST00000282223,;SPOCK1,downstream_gene_variant,,ENST00000509978,;SPOCK1,downstream_gene_variant,,ENST00000515091,;	-	ENSG00000152377	ENST00000394945	Transcript	3_prime_UTR_variant	3473	.	.	.	.	.	.	.	-1	SPOCK1	HGNC	11251	protein_coding	YES	CCDS4191.1	ENSP00000378401	TICN1_HUMAN	D6RB21_HUMAN,D6RAM7_HUMAN,D3DQB3_HUMAN	UPI0000136F50	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAGAGAAAAAA	.	2	ESCA
KLHL3	0	.	GRCh37	5	136983320	136983320	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.904-7654G>A	.	.	ENST00000309755	.	58	28	29	26	26	0	KLHL3,intron_variant,,ENST00000506491,;KLHL3,intron_variant,,ENST00000541417,;KLHL3,intron_variant,,ENST00000309755,;KLHL3,intron_variant,,ENST00000505853,;KLHL3,intron_variant,,ENST00000508657,;MIR874,non_coding_transcript_exon_variant,,ENST00000401190,;KLHL3,intron_variant,,ENST00000506873,;KLHL3,intron_variant,,ENST00000502381,;KLHL3,intron_variant,,ENST00000504208,;	T	ENSG00000146021	ENST00000309755	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KLHL3	HGNC	6354	protein_coding	YES	CCDS4192.1	ENSP00000312397	KLHL3_HUMAN	Q8N4I8_HUMAN,Q49A42_HUMAN	UPI000012DE05	.	.	.	.	8/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGCGTGGG	.	5	ESCA
DNAH5	0	.	GRCh37	5	13839629	13839629	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5718G>A	p.Met1906Ile	p.M1906I	ENST00000265104	35/79	58	51	6	17	17	0	DNAH5,missense_variant,p.Met1906Ile,ENST00000265104,;	T	ENSG00000039139	ENST00000265104	Transcript	missense_variant	5823	5718	1906	M/I	atG/atA	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.019)	35/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATGCATATG	.	4	ESCA
TMEM173	0	.	GRCh37	5	138858042	138858042	+	Missense_Mutation	SNP	C	C	T	rs750561744	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572G>A	p.Arg191Gln	p.R191Q	ENST00000330794	6/8	71	41	30	46	46	0	TMEM173,missense_variant,p.Arg191Gln,ENST00000510817,;TMEM173,missense_variant,p.Arg191Gln,ENST00000330794,;TMEM173,non_coding_transcript_exon_variant,,ENST00000512606,;TMEM173,non_coding_transcript_exon_variant,,ENST00000511886,;TMEM173,non_coding_transcript_exon_variant,,ENST00000515507,;TMEM173,downstream_gene_variant,,ENST00000514542,;TMEM173,downstream_gene_variant,,ENST00000511850,;TMEM173,non_coding_transcript_exon_variant,,ENST00000509573,;TMEM173,non_coding_transcript_exon_variant,,ENST00000514119,;TMEM173,non_coding_transcript_exon_variant,,ENST00000502825,;TMEM173,non_coding_transcript_exon_variant,,ENST00000507297,;TMEM173,non_coding_transcript_exon_variant,,ENST00000503287,;TMEM173,downstream_gene_variant,,ENST00000503838,;TMEM173,downstream_gene_variant,,ENST00000514348,;TMEM173,downstream_gene_variant,,ENST00000502362,;	T	ENSG00000184584	ENST00000330794	Transcript	missense_variant	906	572	191	R/Q	cGg/cAg	rs750561744	.	.	-1	TMEM173	HGNC	27962	protein_coding	YES	CCDS4215.1	ENSP00000331288	STING_HUMAN	J3QTB1_HUMAN	UPI000000DC5E	.	tolerated(0.59)	benign(0.016)	6/8	.	Pfam_domain:PF15009	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCCGTAGC	byFrequency	5	ESCA
PCDHA2	0	.	GRCh37	5	140176199	140176199	+	Silent	SNP	G	G	A	rs544759315	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1650G>A	p.%3D	p.T550T	ENST00000526136	1/4	196	135	61	94	94	0	PCDHA2,synonymous_variant,p.%3D,ENST00000378132,;PCDHA2,synonymous_variant,p.%3D,ENST00000526136,;PCDHA2,synonymous_variant,p.%3D,ENST00000520672,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,upstream_gene_variant,,ENST00000532566,;PCDHA3,upstream_gene_variant,,ENST00000522353,;	A	ENSG00000204969	ENST00000526136	Transcript	synonymous_variant	1650	1650	550	T	acG/acA	rs544759315	.	.	1	PCDHA2	HGNC	8668	protein_coding	YES	CCDS54914.1	ENSP00000431748	PCDA2_HUMAN	.	UPI00001273C9	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGACGCTGCA	by1000G	5	ESCA
PCDHA13	0	.	GRCh37	5	140262129	140262129	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.276C>T	p.%3D	p.R92R	ENST00000289272	1/4	122	62	59	58	58	0	PCDHA13,synonymous_variant,p.%3D,ENST00000289272,;PCDHA13,synonymous_variant,p.%3D,ENST00000409494,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;	T	ENSG00000239389	ENST00000289272	Transcript	synonymous_variant	276	276	92	R	cgC/cgT	.	.	.	1	PCDHA13	HGNC	8667	protein_coding	YES	CCDS4240.1	ENSP00000289272	PCDAD_HUMAN	.	UPI00001273D6	.	.	.	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF08266,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D91N|c.271G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCGCGAGGA	.	5	ESCA
PCDHB3	0	.	GRCh37	5	140480982	140480982	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.749C>T	p.Ala250Val	p.A250V	ENST00000231130	1/1	20	5	15	20	20	0	PCDHB3,missense_variant,p.Ala250Val,ENST00000231130,;PCDHB2,downstream_gene_variant,,ENST00000194155,;AC005754.7,intron_variant,,ENST00000607216,;	T	ENSG00000113205	ENST00000231130	Transcript	missense_variant	749	749	250	A/V	gCa/gTa	.	.	.	1	PCDHB3	HGNC	8688	protein_coding	YES	CCDS4245.1	ENSP00000231130	PCDB3_HUMAN	.	UPI00001273DD	.	deleterious_low_confidence(0)	benign(0.001)	1/1	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028:SF19,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTGCAGTTC	.	5	ESCA
PCDHB16	0	.	GRCh37	5	140563150	140563150	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1016A>G	p.Asp339Gly	p.D339G	ENST00000361016	1/1	33	25	8	25	25	0	PCDHB16,missense_variant,p.Asp339Gly,ENST00000361016,;PCDHB8,downstream_gene_variant,,ENST00000239444,;PCDHB9,upstream_gene_variant,,ENST00000316105,;	G	ENSG00000196963	ENST00000361016	Transcript	missense_variant	2171	1016	339	D/G	gAc/gGc	.	.	.	1	PCDHB16	HGNC	14546	protein_coding	YES	CCDS4251.1	ENSP00000354293	PCDBG_HUMAN	.	UPI000006D372	.	deleterious_low_confidence(0)	probably_damaging(0.999)	1/1	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,PROSITE_patterns:PS00232,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF71,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGGACGTGA	.	5	ESCA
PCDHB16	0	.	GRCh37	5	140563850	140563850	+	Silent	SNP	C	C	T	rs568748617	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1716C>T	p.%3D	p.C572C	ENST00000361016	1/1	169	130	38	42	42	0	PCDHB16,synonymous_variant,p.%3D,ENST00000361016,;PCDHB8,downstream_gene_variant,,ENST00000239444,;PCDHB9,upstream_gene_variant,,ENST00000316105,;	T	ENSG00000196963	ENST00000361016	Transcript	synonymous_variant	2871	1716	572	C	tgC/tgT	rs568748617,COSM3994033	.	.	1	PCDHB16	HGNC	14546	protein_coding	YES	CCDS4251.1	ENSP00000354293	PCDBG_HUMAN	.	UPI000006D372	.	.	.	1/1	.	Superfamily_domains:SSF49313,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF71	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T573T|c.1719T>C|4	RADIA|MUTECT|MUSE|VARSCANS	CCCTGCACTGA	by1000G	4	ESCA
PCDHB10	0	.	GRCh37	5	140574675	140574675	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*153delT	.	.	ENST00000239446	1/1	50	43	7	27	27	0	PCDHB10,3_prime_UTR_variant,,ENST00000239446,;PCDHB11,upstream_gene_variant,,ENST00000536699,;PCDHB11,upstream_gene_variant,,ENST00000354757,;PCDHB9,downstream_gene_variant,,ENST00000316105,;	-	ENSG00000120324	ENST00000239446	Transcript	3_prime_UTR_variant	2734	.	.	.	.	.	.	.	1	PCDHB10	HGNC	8681	protein_coding	YES	CCDS4252.1	ENSP00000239446	PCDBA_HUMAN	O95883_HUMAN	UPI0000048F2E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCATCATTTTTT	.	3	ESCA
PCDHB15	0	.	GRCh37	5	140626827	140626827	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1681G>A	p.Val561Met	p.V561M	ENST00000231173	1/1	171	56	115	92	92	0	PCDHB15,missense_variant,p.Val561Met,ENST00000231173,;PCDHB19P,downstream_gene_variant,,ENST00000570871,;	A	ENSG00000113248	ENST00000231173	Transcript	missense_variant	1681	1681	561	V/M	Gtg/Atg	COSM1062875	.	.	1	PCDHB15	HGNC	8686	protein_coding	YES	CCDS4257.1	ENSP00000231173	PCDBF_HUMAN	.	UPI00001273E8	.	deleterious_low_confidence(0)	possibly_damaging(0.873)	1/1	.	Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Gene3D:2.60.40.60,hmmpanther:PTHR24028:SF97,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.F560F|c.1680C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCGTGCTG	.	5	ESCA
PCDHGB2	0	.	GRCh37	5	140741195	140741195	+	Missense_Mutation	SNP	C	C	T	rs751712279	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1493C>T	p.Pro498Leu	p.P498L	ENST00000522605	1/4	50	12	38	40	40	0	PCDHGB2,missense_variant,p.Pro498Leu,ENST00000522605,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA5,upstream_gene_variant,,ENST00000518069,;	T	ENSG00000253910	ENST00000522605	Transcript	missense_variant	1493	1493	498	P/L	cCg/cTg	rs751712279	.	.	1	PCDHGB2	HGNC	8709	protein_coding	YES	CCDS54924.1	ENSP00000429018	PCDGE_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006EE67	.	tolerated(0.11)	benign(0.146)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF102,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCCGCGGG	byFrequency	5	ESCA
PCDHGB4	0	.	GRCh37	5	140768214	140768214	+	Missense_Mutation	SNP	G	G	A	rs778996768	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763G>A	p.Val255Met	p.V255M	ENST00000519479	1/4	53	38	15	19	19	0	PCDHGB4,missense_variant,p.Val255Met,ENST00000519479,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGA8,upstream_gene_variant,,ENST00000398604,;	A	ENSG00000253953	ENST00000519479	Transcript	missense_variant	763	763	255	V/M	Gtg/Atg	rs778996768	.	.	1	PCDHGB4	HGNC	8711	protein_coding	YES	CCDS54928.1	ENSP00000428288	PCDGG_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006F773	.	tolerated(0.11)	benign(0.393)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF73,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAACGTGTAC	byFrequency	5	ESCA
DIAPH1	0	.	GRCh37	5	140894715	140894716	+	3'UTR	INS	-	-	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1702_*1703insG	.	.	ENST00000398557	28/28	15	3	12	13	13	0	DIAPH1,3_prime_UTR_variant,,ENST00000389057,;DIAPH1,3_prime_UTR_variant,,ENST00000253811,;DIAPH1,3_prime_UTR_variant,,ENST00000398557,;DIAPH1,3_prime_UTR_variant,,ENST00000398566,;DIAPH1,3_prime_UTR_variant,,ENST00000520569,;DIAPH1,3_prime_UTR_variant,,ENST00000398562,;DIAPH1,3_prime_UTR_variant,,ENST00000389054,;PCDHGB6,downstream_gene_variant,,ENST00000520790,;PCDHGA1,downstream_gene_variant,,ENST00000517417,;PCDHGB1,downstream_gene_variant,,ENST00000523390,;PCDHGB3,downstream_gene_variant,,ENST00000576222,;PCDHGA4,downstream_gene_variant,,ENST00000571252,;PCDHGA2,downstream_gene_variant,,ENST00000394576,;DIAPH1,downstream_gene_variant,,ENST00000448451,;PCDHGB4,downstream_gene_variant,,ENST00000519479,;PCDHGB7,downstream_gene_variant,,ENST00000398594,;PCDHGA9,downstream_gene_variant,,ENST00000573521,;PCDHGB2,downstream_gene_variant,,ENST00000522605,;PCDHGA3,downstream_gene_variant,,ENST00000253812,;PCDHGA7,downstream_gene_variant,,ENST00000518325,;PCDHGA10,downstream_gene_variant,,ENST00000398610,;PCDHGA5,downstream_gene_variant,,ENST00000518069,;PCDHGA11,downstream_gene_variant,,ENST00000398587,;PCDHGA12,downstream_gene_variant,,ENST00000252085,;PCDHGA8,downstream_gene_variant,,ENST00000398604,;PCDHGC3,downstream_gene_variant,,ENST00000308177,;DIAPH1,downstream_gene_variant,,ENST00000518047,;PCDHGA11,downstream_gene_variant,,ENST00000518882,;PCDHGC4,downstream_gene_variant,,ENST00000306593,;PCDHGA6,downstream_gene_variant,,ENST00000517434,;PCDHGC5,downstream_gene_variant,,ENST00000252087,;DIAPH1,downstream_gene_variant,,ENST00000468119,;DIAPH1,non_coding_transcript_exon_variant,,ENST00000476339,;DIAPH1,downstream_gene_variant,,ENST00000521457,;	C	ENSG00000131504	ENST00000398557	Transcript	3_prime_UTR_variant	5662-5663	.	.	.	.	.	.	.	-1	DIAPH1	HGNC	2876	protein_coding	YES	CCDS43374.1	ENSP00000381565	DIAP1_HUMAN	Q96IL1_HUMAN,Q7KZJ7_HUMAN,Q6UUU0_HUMAN,E5RJ79_HUMAN,B4DVR3_HUMAN,A0RZB7_HUMAN	UPI0000EA87E6	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	CTCTCTTTTTT	.	2	ESCA
PCDH1	0	.	GRCh37	5	141243507	141243507	+	Missense_Mutation	SNP	G	G	A	rs143703336	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2389C>T	p.Arg797Cys	p.R797C	ENST00000287008	3/5	27	3	24	19	19	0	PCDH1,missense_variant,p.Arg775Cys,ENST00000536585,;PCDH1,missense_variant,p.Arg785Cys,ENST00000456271,;PCDH1,missense_variant,p.Arg797Cys,ENST00000287008,;PCDH1,missense_variant,p.Arg797Cys,ENST00000394536,;PCDH1,missense_variant,p.Arg808Cys,ENST00000357517,;PCDH1,intron_variant,,ENST00000503492,;PCDH1,non_coding_transcript_exon_variant,,ENST00000511044,;PCDH1,3_prime_UTR_variant,,ENST00000515351,;PCDH1,downstream_gene_variant,,ENST00000505937,;	A	ENSG00000156453	ENST00000287008	Transcript	missense_variant	2537	2389	797	R/C	Cgc/Tgc	rs143703336,COSM1219424	.	.	-1	PCDH1	HGNC	8655	protein_coding	YES	CCDS4267.1	ENSP00000287008	PCDH1_HUMAN	D6RBG2_HUMAN	UPI000016158F	.	deleterious(0.01)	possibly_damaging(0.886)	3/5	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24027:SF30,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	A:0.0005	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCGGTCAC	byFrequency|byCluster|by1000G	5	ESCA
FAM105B	0	.	GRCh37	5	14693294	14693294	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*137G>T	.	.	ENST00000284274	7/7	24	16	8	9	9	0	FAM105B,3_prime_UTR_variant,,ENST00000284274,;FAM105B,3_prime_UTR_variant,,ENST00000506417,;FAM105B,downstream_gene_variant,,ENST00000503023,;FAM105B,downstream_gene_variant,,ENST00000514913,;	T	ENSG00000154124	ENST00000284274	Transcript	3_prime_UTR_variant	1274	.	.	.	.	.	.	.	1	FAM105B	HGNC	25118	protein_coding	YES	CCDS43302.1	ENSP00000284274	OTUL_HUMAN	.	UPI0000374C00	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACAGGATGTC	.	2	ESCA
ANKH	0	.	GRCh37	5	14758594	14758594	+	Missense_Mutation	SNP	C	C	T	rs772363889	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427G>A	p.Ala143Thr	p.A143T	ENST00000284268	3/12	118	101	17	23	23	0	ANKH,missense_variant,p.Ala143Thr,ENST00000284268,;ANKH,upstream_gene_variant,,ENST00000503939,;	T	ENSG00000154122	ENST00000284268	Transcript	missense_variant	758	427	143	A/T	Gca/Aca	rs772363889,COSM3852547	.	.	-1	ANKH	HGNC	15492	protein_coding	YES	CCDS3885.1	ENSP00000284268	ANKH_HUMAN	B3KMG4_HUMAN	UPI000003F535	.	deleterious(0.01)	probably_damaging(0.999)	3/12	.	Transmembrane_helices:TMhelix,Pfam_domain:PF07260	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTGCGTCCA	.	4	ESCA
CSF1R	0	.	GRCh37	5	149432909	149432912	+	3'UTR	DEL	GTTA	GTTA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GTTA	GTTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*720_*723delTAAC	.	.	ENST00000286301	22/22	68	52	16	38	38	0	CSF1R,3_prime_UTR_variant,,ENST00000286301,;HMGXB3,downstream_gene_variant,,ENST00000502717,;HMGXB3,downstream_gene_variant,,ENST00000503427,;CSF1R,3_prime_UTR_variant,,ENST00000504875,;CSF1R,downstream_gene_variant,,ENST00000509861,;CSF1R,downstream_gene_variant,,ENST00000515068,;HMGXB3,downstream_gene_variant,,ENST00000510472,;	-	ENSG00000182578	ENST00000286301	Transcript	3_prime_UTR_variant	3931-3934	.	.	.	.	.	.	.	-1	CSF1R	HGNC	2433	protein_coding	YES	CCDS4302.1	ENSP00000286301	CSF1R_HUMAN	Q6LEI2_HUMAN,D6RGW1_HUMAN	UPI000004984A	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGACTGTTAGTTAG	.	3	ESCA
ARSI	0	.	GRCh37	5	149677873	149677873	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614G>A	p.Gly205Asp	p.G205D	ENST00000328668	2/2	46	12	34	16	16	0	ARSI,missense_variant,p.Gly62Asp,ENST00000509146,;ARSI,missense_variant,p.Gly62Asp,ENST00000515301,;ARSI,missense_variant,p.Gly205Asp,ENST00000328668,;	T	ENSG00000183876	ENST00000328668	Transcript	missense_variant	1194	614	205	G/D	gGc/gAc	.	.	.	-1	ARSI	HGNC	32521	protein_coding	YES	CCDS34275.1	ENSP00000333395	ARSI_HUMAN	D6RDH0_HUMAN	UPI000003FD83	.	deleterious(0.01)	probably_damaging(1)	2/2	.	hmmpanther:PTHR10342:SF68,hmmpanther:PTHR10342,Pfam_domain:PF00884,Gene3D:3.40.720.10,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGGCCGCTG	.	5	ESCA
ZNF300	0	.	GRCh37	5	150275828	150275828	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1021T>C	p.Tyr341His	p.Y341H	ENST00000446148	7/7	45	35	10	44	44	0	ZNF300,missense_variant,p.Tyr289His,ENST00000418587,;ZNF300,missense_variant,p.Tyr325His,ENST00000274599,;ZNF300,missense_variant,p.Tyr325His,ENST00000394226,;ZNF300,missense_variant,p.Tyr341His,ENST00000446148,;ZNF300,3_prime_UTR_variant,,ENST00000427179,;IRGM,intron_variant,,ENST00000520549,;	G	ENSG00000145908	ENST00000446148	Transcript	missense_variant	1449	1021	341	Y/H	Tat/Cat	.	.	.	-1	ZNF300	HGNC	13091	protein_coding	YES	CCDS54940.1	ENSP00000397178	.	J3KQF6_HUMAN	UPI0001AE74AD	.	tolerated(0.08)	probably_damaging(1)	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF288,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATAAGGTT	.	5	ESCA
FAT2	0	.	GRCh37	5	150922881	150922882	+	Frame_Shift_Del	DEL	GA	GA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GA	GA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7806_7807delTC	p.Pro2603GlyfsTer8	p.P2603Gfs*8	ENST00000261800	9/23	201	111	90	105	105	0	FAT2,frameshift_variant,p.Pro2603GlyfsTer8,ENST00000261800,;	-	ENSG00000086570	ENST00000261800	Transcript	frameshift_variant	7819-7820	7806-7807	2602-2603	SP/SX	tcTCcg/tccg	.	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	.	9/23	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAACCGGAGAGTC	.	3	ESCA
PLEKHG4B	0	.	GRCh37	5	156905	156905	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1298C>T	p.Ala433Val	p.A433V	ENST00000283426	9/18	108	88	20	18	18	0	PLEKHG4B,missense_variant,p.Ala347Val,ENST00000502646,;PLEKHG4B,missense_variant,p.Ala433Val,ENST00000283426,;	T	ENSG00000153404	ENST00000283426	Transcript	missense_variant	1348	1298	433	A/V	gCc/gTc	.	.	.	1	PLEKHG4B	HGNC	29399	protein_coding	YES	CCDS34124.1	ENSP00000283426	PKH4B_HUMAN	.	UPI0000D615EE	.	tolerated(0.45)	benign(0.038)	9/18	.	hmmpanther:PTHR22826:SF119,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCGCCACAA	.	5	ESCA
ADAM19	0	.	GRCh37	5	156946869	156946869	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578A>G	p.Gln193Arg	p.Q193R	ENST00000257527	6/23	63	48	14	45	45	0	ADAM19,missense_variant,p.Gln195Arg,ENST00000394020,;ADAM19,missense_variant,p.Gln193Arg,ENST00000517905,;ADAM19,missense_variant,p.Gln193Arg,ENST00000257527,;ADAM19,5_prime_UTR_variant,,ENST00000430702,;ADAM19,missense_variant,p.Gln193Arg,ENST00000517951,;	C	ENSG00000135074	ENST00000257527	Transcript	missense_variant	657	578	193	Q/R	cAg/cGg	.	.	.	-1	ADAM19	HGNC	197	protein_coding	YES	CCDS4338.1	ENSP00000257527	ADA19_HUMAN	.	UPI000013CF6A	.	tolerated(0.54)	benign(0.008)	6/23	.	hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTCTGTTGT	.	5	ESCA
FBXL7	0	.	GRCh37	5	15928463	15928463	+	Missense_Mutation	SNP	C	C	T	rs369795247	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592C>T	p.Arg198Trp	p.R198W	ENST00000504595	3/4	139	122	17	48	48	0	FBXL7,missense_variant,p.Arg186Trp,ENST00000329673,;FBXL7,missense_variant,p.Arg151Trp,ENST00000510662,;FBXL7,missense_variant,p.Arg198Trp,ENST00000504595,;	T	ENSG00000183580	ENST00000504595	Transcript	missense_variant	1073	592	198	R/W	Cgg/Tgg	rs369795247	.	.	1	FBXL7	HGNC	13604	protein_coding	YES	CCDS54833.1	ENSP00000423630	FBXL7_HUMAN	J3KNM9_HUMAN,D6RDY7_HUMAN	UPI00000724E0	.	deleterious(0.02)	possibly_damaging(0.898)	3/4	.	hmmpanther:PTHR23125:SF70,hmmpanther:PTHR23125,Gene3D:3.80.10.10,SMART_domains:SM00367,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGGCGGCTC	byFrequency|byCluster	4	ESCA
TENM2	0	.	GRCh37	5	167674984	167674984	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7040A>G	p.Tyr2347Cys	p.Y2347C	ENST00000518659	27/29	29	5	24	31	31	0	TENM2,missense_variant,p.Tyr2346Cys,ENST00000545108,;TENM2,missense_variant,p.Tyr2108Cys,ENST00000520394,;TENM2,missense_variant,p.Tyr2226Cys,ENST00000519204,;TENM2,missense_variant,p.Tyr2347Cys,ENST00000518659,;TENM2,missense_variant,p.Tyr2171Cys,ENST00000403607,;	G	ENSG00000145934	ENST00000518659	Transcript	missense_variant	7079	7040	2347	Y/C	tAc/tGc	.	.	.	1	TENM2	HGNC	29943	protein_coding	YES	.	ENSP00000429430	TEN2_HUMAN	G8BLJ6_HUMAN,G3CAS7_HUMAN	UPI0001C48FC2	.	deleterious(0)	probably_damaging(0.999)	27/29	.	hmmpanther:PTHR11219:SF8,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTACTACG	.	5	ESCA
PLEKHG4B	0	.	GRCh37	5	171525	171525	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2948A>G	p.Asp983Gly	p.D983G	ENST00000283426	14/18	80	61	19	11	11	0	PLEKHG4B,missense_variant,p.Asp983Gly,ENST00000283426,;PLEKHG4B,non_coding_transcript_exon_variant,,ENST00000504041,;	G	ENSG00000153404	ENST00000283426	Transcript	missense_variant	2998	2948	983	D/G	gAc/gGc	.	.	.	1	PLEKHG4B	HGNC	29399	protein_coding	YES	CCDS34124.1	ENSP00000283426	PKH4B_HUMAN	.	UPI0000D615EE	.	deleterious(0)	probably_damaging(0.987)	14/18	.	PROSITE_profiles:PS50010,hmmpanther:PTHR22826:SF119,hmmpanther:PTHR22826,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATGACCTGC	.	5	ESCA
SH3PXD2B	0	.	GRCh37	5	171809111	171809111	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330delC	p.Tyr111ThrfsTer19	p.Y111Tfs*19	ENST00000311601	5/13	40	7	33	15	15	0	SH3PXD2B,frameshift_variant,p.Tyr111ThrfsTer19,ENST00000519643,;SH3PXD2B,frameshift_variant,p.Tyr111ThrfsTer19,ENST00000311601,;	-	ENSG00000174705	ENST00000311601	Transcript	frameshift_variant	501	330	110	P/X	ccC/cc	.	.	.	-1	SH3PXD2B	HGNC	29242	protein_coding	YES	CCDS34291.1	ENSP00000309714	SPD2B_HUMAN	.	UPI000020C12E	.	.	.	5/13	.	PROSITE_profiles:PS50195,hmmpanther:PTHR15706:SF8,hmmpanther:PTHR15706,Pfam_domain:PF00787,Gene3D:3.30.1520.10,SMART_domains:SM00312,Superfamily_domains:SSF64268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	GATGTAGGGGGG	.	2	ESCA
FAM153B	0	.	GRCh37	5	175516516	175516516	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-6G>A	.	.	ENST00000515817	2/20	17	6	11	13	13	0	FAM153B,missense_variant,p.Val76Ile,ENST00000253490,;FAM153B,5_prime_UTR_variant,,ENST00000503724,;FAM153B,5_prime_UTR_variant,,ENST00000512862,;FAM153B,5_prime_UTR_variant,,ENST00000515817,;FAM153B,5_prime_UTR_variant,,ENST00000510151,;FAM153B,non_coding_transcript_exon_variant,,ENST00000393522,;FAM153B,non_coding_transcript_exon_variant,,ENST00000503533,;FAM153B,5_prime_UTR_variant,,ENST00000508296,;FAM153B,non_coding_transcript_exon_variant,,ENST00000513938,;FAM153B,non_coding_transcript_exon_variant,,ENST00000511680,;FAM153B,non_coding_transcript_exon_variant,,ENST00000514235,;FAM153B,non_coding_transcript_exon_variant,,ENST00000507409,;	A	ENSG00000182230	ENST00000515817	Transcript	5_prime_UTR_variant	279	.	.	.	.	.	.	.	1	FAM153B	HGNC	27323	protein_coding	YES	CCDS43401.2	ENSP00000427684	.	H0YL08_HUMAN,D6RF84_HUMAN,D6RA46_HUMAN	UPI00001D7EF3	.	.	.	2/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TGGGCGTTCAT	.	2	ESCA
GRK6	0	.	GRCh37	5	176869086	176869086	+	3'UTR	SNP	C	C	T	rs139039774	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*258C>T	.	.	ENST00000528793	16/16	37	12	24	22	22	0	GRK6,3_prime_UTR_variant,,ENST00000355472,;GRK6,3_prime_UTR_variant,,ENST00000528793,;GRK6,3_prime_UTR_variant,,ENST00000393576,;PRR7,upstream_gene_variant,,ENST00000323249,;GRK6,downstream_gene_variant,,ENST00000355958,;PRR7,upstream_gene_variant,,ENST00000502922,;PRR7,upstream_gene_variant,,ENST00000507881,;PRR7-AS1,intron_variant,,ENST00000425316,;PRR7-AS1,downstream_gene_variant,,ENST00000506465,;PRR7-AS1,downstream_gene_variant,,ENST00000511565,;PRR7-AS1,downstream_gene_variant,,ENST00000514846,;GRK6,downstream_gene_variant,,ENST00000515666,;	T	ENSG00000198055	ENST00000528793	Transcript	3_prime_UTR_variant	2031	.	.	.	.	rs139039774	.	.	1	GRK6	HGNC	4545	protein_coding	YES	CCDS47348.1	ENSP00000433511	GRK6_HUMAN	D6RHC7_HUMAN,D6RDA3_HUMAN,D6R9V4_HUMAN	UPI000002AAC9	.	.	.	16/16	.	.	T:0.0048	T:0.0121	T:0.0072	.	T:0	T:0.003	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCCCGCCGC	byFrequency|byCluster|by1000G	5	ESCA
PDLIM7	0	.	GRCh37	5	176910724	176910724	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1295A>C	p.Gln432Pro	p.Q432P	ENST00000355841	13/13	52	9	43	28	28	0	PDLIM7,missense_variant,p.Gln398Pro,ENST00000359895,;PDLIM7,missense_variant,p.Gln432Pro,ENST00000355841,;PDLIM7,3_prime_UTR_variant,,ENST00000356618,;PDLIM7,downstream_gene_variant,,ENST00000393551,;PDLIM7,downstream_gene_variant,,ENST00000505746,;PDLIM7,3_prime_UTR_variant,,ENST00000486828,;PDLIM7,3_prime_UTR_variant,,ENST00000493815,;PDLIM7,non_coding_transcript_exon_variant,,ENST00000504380,;	G	ENSG00000196923	ENST00000355841	Transcript	missense_variant	1362	1295	432	Q/P	cAg/cCg	.	.	.	-1	PDLIM7	HGNC	22958	protein_coding	YES	CCDS4422.1	ENSP00000348099	PDLI7_HUMAN	D6RF83_HUMAN,D6RAN1_HUMAN	UPI0000073DEF	.	tolerated(0.14)	probably_damaging(0.99)	13/13	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24214,PROSITE_patterns:PS00478,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATCTGACAT	.	5	ESCA
CANX	0	.	GRCh37	5	179156974	179156974	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1337delT	.	.	ENST00000247461	15/15	62	32	30	48	48	0	CANX,3_prime_UTR_variant,,ENST00000247461,;CANX,3_prime_UTR_variant,,ENST00000452673,;CANX,downstream_gene_variant,,ENST00000415618,;CANX,downstream_gene_variant,,ENST00000504734,;CANX,downstream_gene_variant,,ENST00000512607,;MAML1,upstream_gene_variant,,ENST00000292599,;CANX,downstream_gene_variant,,ENST00000503303,;MAML1,upstream_gene_variant,,ENST00000503050,;CANX,downstream_gene_variant,,ENST00000514032,;CANX,downstream_gene_variant,,ENST00000505090,;	-	ENSG00000127022	ENST00000247461	Transcript	3_prime_UTR_variant	3308	.	.	.	.	.	.	.	1	CANX	HGNC	1473	protein_coding	YES	CCDS4447.1	ENSP00000247461	CALX_HUMAN	D6RHJ3_HUMAN,D6RFW4_HUMAN,D6RFL1_HUMAN,D6RDP7_HUMAN,D6RB85_HUMAN,D6RAU8_HUMAN,D6RAQ8_HUMAN,B4E2T8_HUMAN	UPI000000D9F9	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTCAAATTTTTT	.	2	ESCA
TBC1D9B	0	.	GRCh37	5	179306764	179306764	+	Missense_Mutation	SNP	G	G	A	rs770831310	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1280C>T	p.Ser427Leu	p.S427L	ENST00000356834	8/22	40	10	30	20	20	0	TBC1D9B,missense_variant,p.Ser427Leu,ENST00000355235,;TBC1D9B,missense_variant,p.Ser427Leu,ENST00000356834,;TBC1D9B,intron_variant,,ENST00000524222,;TBC1D9B,upstream_gene_variant,,ENST00000522472,;TBC1D9B,downstream_gene_variant,,ENST00000522029,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000518115,;TBC1D9B,upstream_gene_variant,,ENST00000518459,;	A	ENSG00000197226	ENST00000356834	Transcript	missense_variant	1318	1280	427	S/L	tCg/tTg	rs770831310	.	.	-1	TBC1D9B	HGNC	29097	protein_coding	YES	CCDS43408.1	ENSP00000349291	TBC9B_HUMAN	.	UPI000034ECFF	.	tolerated(0.26)	benign(0.003)	8/22	.	hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCGACCCC	.	5	ESCA
CNOT6	0	.	GRCh37	5	180002824	180002824	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1631delA	.	.	ENST00000393356	14/14	29	9	20	31	31	0	CNOT6,3_prime_UTR_variant,,ENST00000393356,;CNOT6,3_prime_UTR_variant,,ENST00000261951,;	-	ENSG00000113300	ENST00000393356	Transcript	3_prime_UTR_variant	3722	.	.	.	.	.	.	.	1	CNOT6	HGNC	14099	protein_coding	YES	CCDS4455.1	ENSP00000377024	CNOT6_HUMAN	.	UPI000013D22B	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTAGGAAAAAA	.	2	ESCA
CDH6	0	.	GRCh37	5	31323493	31323493	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*78G>A	.	.	ENST00000265071	12/12	33	29	4	11	11	0	CDH6,3_prime_UTR_variant,,ENST00000265071,;CDH6,downstream_gene_variant,,ENST00000504835,;	A	ENSG00000113361	ENST00000265071	Transcript	3_prime_UTR_variant	2716	.	.	.	.	.	.	.	1	CDH6	HGNC	1765	protein_coding	YES	CCDS3894.1	ENSP00000265071	CADH6_HUMAN	.	UPI0000126D9B	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCCGTGAAG	.	4	ESCA
DROSHA	0	.	GRCh37	5	31431690	31431690	+	Silent	SNP	C	C	T	rs768254802	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3138G>A	p.%3D	p.A1046A	ENST00000511367	25/35	64	59	5	28	28	0	DROSHA,synonymous_variant,p.%3D,ENST00000442743,;DROSHA,synonymous_variant,p.%3D,ENST00000511367,;DROSHA,synonymous_variant,p.%3D,ENST00000513349,;DROSHA,synonymous_variant,p.%3D,ENST00000344624,;DROSHA,upstream_gene_variant,,ENST00000510178,;DROSHA,non_coding_transcript_exon_variant,,ENST00000504133,;	T	ENSG00000113360	ENST00000511367	Transcript	synonymous_variant	3383	3138	1046	A	gcG/gcA	rs768254802	.	.	-1	DROSHA	HGNC	17904	protein_coding	YES	CCDS47195.1	ENSP00000425979	RNC_HUMAN	E5RHD1_HUMAN	UPI0000134351	.	.	.	25/35	.	Superfamily_domains:SSF69065,SMART_domains:SM00535,Pfam_domain:PF14622,Gene3D:1.10.1520.10,hmmpanther:PTHR11207,PROSITE_profiles:PS50142	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ATTAACGCTTC	byFrequency	2	ESCA
PDZD2	0	.	GRCh37	5	32087827	32087827	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4273A>G	p.Thr1425Ala	p.T1425A	ENST00000438447	20/25	100	83	16	28	28	0	PDZD2,missense_variant,p.Thr1425Ala,ENST00000438447,;PDZD2,missense_variant,p.Thr1425Ala,ENST00000282493,;PDZD2,downstream_gene_variant,,ENST00000503961,;	G	ENSG00000133401	ENST00000438447	Transcript	missense_variant	4661	4273	1425	T/A	Acg/Gcg	.	.	.	1	PDZD2	HGNC	18486	protein_coding	YES	CCDS34137.1	ENSP00000402033	PDZD2_HUMAN	B4DGS3_HUMAN	UPI000069648B	.	deleterious(0.03)	benign(0.037)	20/25	.	hmmpanther:PTHR11324:SF16,hmmpanther:PTHR11324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGACGGAC	.	5	ESCA
PDZD2	0	.	GRCh37	5	32108783	32108783	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*548delA	.	.	ENST00000438447	25/25	98	90	8	42	42	0	PDZD2,3_prime_UTR_variant,,ENST00000438447,;PDZD2,3_prime_UTR_variant,,ENST00000282493,;CTD-2152M20.2,intron_variant,,ENST00000503441,;PDZD2,non_coding_transcript_exon_variant,,ENST00000513490,;PDZD2,non_coding_transcript_exon_variant,,ENST00000397559,;PDZD2,downstream_gene_variant,,ENST00000510285,;PDZD2,downstream_gene_variant,,ENST00000515115,;	-	ENSG00000133401	ENST00000438447	Transcript	3_prime_UTR_variant	9450	.	.	.	.	.	.	.	1	PDZD2	HGNC	18486	protein_coding	YES	CCDS34137.1	ENSP00000402033	PDZD2_HUMAN	B4DGS3_HUMAN	UPI000069648B	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	TTACTTAAAAAA	.	2	ESCA
GOLPH3	0	.	GRCh37	5	32143921	32143922	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.290dupT	p.Leu97PhefsTer17	p.L97Ffs*17	ENST00000265070	2/4	129	111	18	52	52	0	GOLPH3,frameshift_variant,p.Leu97PhefsTer17,ENST00000265070,;GOLPH3,intron_variant,,ENST00000512668,;GOLPH3,3_prime_UTR_variant,,ENST00000503610,;	A	ENSG00000113384	ENST00000265070	Transcript	frameshift_variant	606-607	290-291	97	L/FX	tta/ttTa	.	.	.	-1	GOLPH3	HGNC	15452	protein_coding	YES	CCDS3896.1	ENSP00000265070	GOLP3_HUMAN	B3KQJ9_HUMAN,B3KS18_HUMAN,B3KQ71_HUMAN	UPI000006EEF4	.	.	.	2/4	.	Pfam_domain:PF05719,Gene3D:2zihB00,hmmpanther:PTHR12704:SF3,hmmpanther:PTHR12704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATGCTAATTC	.	3	ESCA
TARS	0	.	GRCh37	5	33441106	33441106	+	5'UTR	SNP	G	G	A	rs543938072	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-87G>A	.	.	ENST00000455217	1/20	100	73	27	23	23	0	TARS,5_prime_UTR_variant,,ENST00000265112,;TARS,5_prime_UTR_variant,,ENST00000541634,;TARS,5_prime_UTR_variant,,ENST00000455217,;TARS,5_prime_UTR_variant,,ENST00000414361,;TARS,intron_variant,,ENST00000514259,;TARS,intron_variant,,ENST00000502553,;TARS,upstream_gene_variant,,ENST00000506040,;CTD-2203K17.1,upstream_gene_variant,,ENST00000507251,;TARS,non_coding_transcript_exon_variant,,ENST00000502508,;TARS,5_prime_UTR_variant,,ENST00000509731,;TARS,5_prime_UTR_variant,,ENST00000507716,;TARS,5_prime_UTR_variant,,ENST00000513066,;TARS,5_prime_UTR_variant,,ENST00000505012,;TARS,5_prime_UTR_variant,,ENST00000508361,;	A	ENSG00000113407	ENST00000455217	Transcript	5_prime_UTR_variant	36	.	.	.	.	rs543938072	.	.	1	TARS	HGNC	11572	protein_coding	YES	CCDS58943.1	ENSP00000387710	SYTC_HUMAN	D6RBR8_HUMAN	UPI00017A6D60	.	.	.	1/20	.	.	C:0.0006	C:0	C:0	.	C:0	C:0.003	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCGGGCGC	byFrequency|byCluster|by1000G	5	ESCA
SLC1A3	0	.	GRCh37	5	36686403	36686403	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*32A>G	.	.	ENST00000265113	10/10	88	81	7	30	30	0	SLC1A3,3_prime_UTR_variant,,ENST00000265113,;SLC1A3,3_prime_UTR_variant,,ENST00000381918,;CTD-2353F22.1,intron_variant,,ENST00000510740,;SLC1A3,downstream_gene_variant,,ENST00000506178,;	G	ENSG00000079215	ENST00000265113	Transcript	3_prime_UTR_variant	2137	.	.	.	.	.	.	.	1	SLC1A3	HGNC	10941	protein_coding	YES	CCDS3919.1	ENSP00000265113	EAA1_HUMAN	E7EUV6_HUMAN,E7EUS7_HUMAN	UPI0000129B0F	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GCACCAGGTGT	.	3	ESCA
NIPBL	0	.	GRCh37	5	37065247	37065247	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*260delA	.	.	ENST00000282516	47/47	52	40	12	17	17	0	NIPBL,3_prime_UTR_variant,,ENST00000282516,;NIPBL,downstream_gene_variant,,ENST00000448238,;NIPBL,downstream_gene_variant,,ENST00000513819,;NIPBL,non_coding_transcript_exon_variant,,ENST00000514335,;	-	ENSG00000164190	ENST00000282516	Transcript	3_prime_UTR_variant	9167	.	.	.	.	.	.	.	1	NIPBL	HGNC	28862	protein_coding	YES	CCDS3920.1	ENSP00000282516	NIPBL_HUMAN	A2RRA7_HUMAN	UPI00003761B5	.	.	.	47/47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TCTTGGAAAAAA	.	2	ESCA
C5orf42	0	.	GRCh37	5	37198930	37198931	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3545dupA	p.Asn1182LysfsTer2	p.N1182Kfs*2	ENST00000425232	20/52	68	61	7	22	22	0	C5orf42,frameshift_variant,p.Asn63LysfsTer2,ENST00000274258,;C5orf42,frameshift_variant,p.Asn1182LysfsTer2,ENST00000508244,;C5orf42,frameshift_variant,p.Asn1182LysfsTer2,ENST00000425232,;C5orf42,frameshift_variant,p.Asn230LysfsTer2,ENST00000514429,;C5orf42,frameshift_variant,p.Asn187LysfsTer2,ENST00000509849,;	T	ENSG00000197603	ENST00000425232	Transcript	frameshift_variant	3776-3777	3545-3546	1182	N/KX	aat/aaAt	.	.	.	-1	C5orf42	HGNC	25801	protein_coding	YES	CCDS34146.2	ENSP00000389014	CE042_HUMAN	.	UPI0001AAB3EA	.	.	.	20/52	.	hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	CGATTATTTTT	.	2	ESCA
EGFLAM	0	.	GRCh37	5	38258799	38258799	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-58G>A	.	.	ENST00000354891	1/23	58	45	13	13	13	0	EGFLAM,5_prime_UTR_variant,,ENST00000354891,;EGFLAM,5_prime_UTR_variant,,ENST00000322350,;EGFLAM,5_prime_UTR_variant,,ENST00000504709,;	A	ENSG00000164318	ENST00000354891	Transcript	5_prime_UTR_variant	289	.	.	.	.	.	.	.	1	EGFLAM	HGNC	26810	protein_coding	YES	CCDS56363.1	ENSP00000346964	EGFLA_HUMAN	D6RJD2_HUMAN	UPI000022C806	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGAGACGCC	.	5	ESCA
EGFLAM	0	.	GRCh37	5	38438444	38438444	+	Missense_Mutation	SNP	C	C	T	rs200259259	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2351C>T	p.Ala784Val	p.A784V	ENST00000354891	17/23	107	79	27	37	37	0	EGFLAM,missense_variant,p.Ala550Val,ENST00000336740,;EGFLAM,missense_variant,p.Ala784Val,ENST00000354891,;EGFLAM,missense_variant,p.Ala150Val,ENST00000397202,;EGFLAM,missense_variant,p.Ala784Val,ENST00000322350,;	T	ENSG00000164318	ENST00000354891	Transcript	missense_variant	2697	2351	784	A/V	gCg/gTg	rs200259259,COSM2688899,COSM2688898	.	.	1	EGFLAM	HGNC	26810	protein_coding	YES	CCDS56363.1	ENSP00000346964	EGFLA_HUMAN	D6RJD2_HUMAN	UPI000022C806	.	deleterious(0.02)	possibly_damaging(0.604)	17/23	.	PROSITE_profiles:PS50025,PROSITE_profiles:PS50026,hmmpanther:PTHR10574:SF202,hmmpanther:PTHR10574,Gene3D:2.60.120.200	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATGCGGCCC	byCluster	5	ESCA
C9	0	.	GRCh37	5	39285145	39285145	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*156T>C	.	.	ENST00000263408	11/11	21	18	3	13	13	0	C9,3_prime_UTR_variant,,ENST00000263408,;	G	ENSG00000113600	ENST00000263408	Transcript	3_prime_UTR_variant	1932	.	.	.	.	.	.	.	-1	C9	HGNC	1358	protein_coding	YES	CCDS3929.1	ENSP00000263408	CO9_HUMAN	Q9UGI4_HUMAN	UPI0000001065	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AAAAAAAAATT	.	2	ESCA
HCN1	0	.	GRCh37	5	45259630	45259630	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2393delA	.	.	ENST00000303230	8/8	69	60	9	29	29	0	HCN1,3_prime_UTR_variant,,ENST00000303230,;	-	ENSG00000164588	ENST00000303230	Transcript	3_prime_UTR_variant	5124	.	.	.	.	.	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	GAGTCATTTTTT	.	2	ESCA
PDE4D	0	.	GRCh37	5	58271490	58271490	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2007delA	p.Lys669AsnfsTer7	p.K669Nfs*7	ENST00000340635	14/15	85	47	38	45	45	0	PDE4D,frameshift_variant,p.Lys367AsnfsTer7,ENST00000505453,;PDE4D,frameshift_variant,p.Lys539AsnfsTer7,ENST00000503258,;PDE4D,frameshift_variant,p.Lys608AsnfsTer7,ENST00000546160,;PDE4D,frameshift_variant,p.Lys533AsnfsTer7,ENST00000360047,;PDE4D,frameshift_variant,p.Lys669AsnfsTer7,ENST00000340635,;PDE4D,frameshift_variant,p.Lys547AsnfsTer7,ENST00000405755,;PDE4D,frameshift_variant,p.Lys605AsnfsTer7,ENST00000507116,;PDE4D,frameshift_variant,p.Lys367AsnfsTer7,ENST00000358923,;PDE4D,frameshift_variant,p.Lys608AsnfsTer7,ENST00000502484,;PDE4D,frameshift_variant,p.Lys378AsnfsTer7,ENST00000317118,;PDE4D,3_prime_UTR_variant,,ENST00000309641,;PDE4D,non_coding_transcript_exon_variant,,ENST00000515011,;	-	ENSG00000113448	ENST00000340635	Transcript	frameshift_variant	2183	2007	669	K/X	aaA/aa	.	.	.	-1	PDE4D	HGNC	8783	protein_coding	YES	CCDS47213.1	ENSP00000345502	PDE4D_HUMAN	D6RHE0_HUMAN	UPI0000050EB1	.	.	.	14/15	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF91,Gene3D:1.10.1300.10,Pfam_domain:PF00233,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTGTGATTTTTC	.	3	ESCA
DEPDC1B	0	.	GRCh37	5	59893478	59893478	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*102delA	.	.	ENST00000265036	11/11	14	9	5	10	10	0	DEPDC1B,3_prime_UTR_variant,,ENST00000453022,;DEPDC1B,3_prime_UTR_variant,,ENST00000265036,;DEPDC1B,downstream_gene_variant,,ENST00000545085,;DEPDC1B,downstream_gene_variant,,ENST00000512078,;	-	ENSG00000035499	ENST00000265036	Transcript	3_prime_UTR_variant	1760	.	.	.	.	.	.	.	-1	DEPDC1B	HGNC	24902	protein_coding	YES	CCDS3977.1	ENSP00000265036	DEP1B_HUMAN	.	UPI000020C7D4	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCTTTGTTTTAT	.	2	ESCA
PAPD7	0	.	GRCh37	5	6755215	6755215	+	3'UTR	SNP	G	G	A	rs768809578	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*157G>A	.	.	ENST00000230859	13/13	133	109	23	43	43	0	PAPD7,3_prime_UTR_variant,,ENST00000230859,;PAPD7,non_coding_transcript_exon_variant,,ENST00000514697,;PAPD7,downstream_gene_variant,,ENST00000514410,;PAPD7,downstream_gene_variant,,ENST00000505457,;	A	ENSG00000112941	ENST00000230859	Transcript	3_prime_UTR_variant	1915	.	.	.	.	rs768809578	.	.	1	PAPD7	HGNC	16705	protein_coding	YES	CCDS3871.1	ENSP00000230859	PAPD7_HUMAN	M1JCE6_HUMAN,D6RJD0_HUMAN,B7ZLL4_HUMAN,B4E0T3_HUMAN	UPI0000071E30	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCGCGTCCAT	.	5	ESCA
PAPD7	0	.	GRCh37	5	6755440	6755440	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*382G>A	.	.	ENST00000230859	13/13	200	184	16	56	56	0	PAPD7,3_prime_UTR_variant,,ENST00000230859,;PAPD7,non_coding_transcript_exon_variant,,ENST00000514697,;PAPD7,downstream_gene_variant,,ENST00000514410,;PAPD7,downstream_gene_variant,,ENST00000505457,;	A	ENSG00000112941	ENST00000230859	Transcript	3_prime_UTR_variant	2140	.	.	.	.	.	.	.	1	PAPD7	HGNC	16705	protein_coding	YES	CCDS3871.1	ENSP00000230859	PAPD7_HUMAN	M1JCE6_HUMAN,D6RJD0_HUMAN,B7ZLL4_HUMAN,B4E0T3_HUMAN	UPI0000071E30	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCCCGTTCGT	.	2	ESCA
ENC1	0	.	GRCh37	5	73931058	73931058	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1253A>G	p.Asp418Gly	p.D418G	ENST00000302351	2/3	12	5	7	17	17	0	ENC1,missense_variant,p.Asp345Gly,ENST00000510316,;ENC1,missense_variant,p.Asp418Gly,ENST00000537006,;ENC1,missense_variant,p.Asp418Gly,ENST00000302351,;HEXB,upstream_gene_variant,,ENST00000511181,;ENC1,downstream_gene_variant,,ENST00000508331,;ENC1,downstream_gene_variant,,ENST00000509127,;ENC1,upstream_gene_variant,,ENST00000509284,;	C	ENSG00000171617	ENST00000302351	Transcript	missense_variant	2384	1253	418	D/G	gAc/gGc	.	.	.	-1	ENC1	HGNC	3345	protein_coding	YES	CCDS4021.1	ENSP00000306356	ENC1_HUMAN	Q53XS2_HUMAN,D6R9D7_HUMAN,B4DS90_HUMAN	UPI0000129EBB	.	deleterious(0.01)	possibly_damaging(0.802)	2/3	.	hmmpanther:PTHR24410,hmmpanther:PTHR24410:SF5,Gene3D:1zgkA00,Pfam_domain:PF01344,SMART_domains:SM00612,PIRSF_domain:PIRSF037037,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGGGGTCATAA	.	3	ESCA
EDIL3	0	.	GRCh37	5	83239319	83239319	+	Silent	SNP	T	T	C	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1362A>G	p.%3D	p.R454R	ENST00000296591	11/11	44	32	12	67	67	0	EDIL3,synonymous_variant,p.%3D,ENST00000296591,;EDIL3,synonymous_variant,p.%3D,ENST00000380138,;	C	ENSG00000164176	ENST00000296591	Transcript	synonymous_variant	1781	1362	454	R	cgA/cgG	COSM3856730	.	.	-1	EDIL3	HGNC	3173	protein_coding	YES	CCDS4062.1	ENSP00000296591	EDIL3_HUMAN	.	UPI000004D126	.	.	.	11/11	.	Superfamily_domains:SSF49785,SMART_domains:SM00231,Pfam_domain:PF00754,Gene3D:2.60.120.260,hmmpanther:PTHR10127:SF29,hmmpanther:PTHR10127,PROSITE_profiles:PS50022	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTGTCGTGC	.	5	ESCA
BRD9	0	.	GRCh37	5	876321	876321	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1278G>T	p.Gln426His	p.Q426H	ENST00000467963	12/16	74	65	8	18	18	0	BRD9,missense_variant,p.Gln426His,ENST00000467963,;BRD9,missense_variant,p.Gln330His,ENST00000323510,;BRD9,missense_variant,p.Gln310His,ENST00000388890,;BRD9,missense_variant,p.Gln373His,ENST00000483173,;BRD9,3_prime_UTR_variant,,ENST00000435709,;BRD9,non_coding_transcript_exon_variant,,ENST00000519838,;BRD9,downstream_gene_variant,,ENST00000494422,;BRD9,missense_variant,p.Gln47His,ENST00000519112,;BRD9,missense_variant,p.Gln31His,ENST00000518251,;BRD9,3_prime_UTR_variant,,ENST00000489816,;BRD9,3_prime_UTR_variant,,ENST00000495265,;BRD9,3_prime_UTR_variant,,ENST00000466684,;BRD9,3_prime_UTR_variant,,ENST00000490814,;BRD9,non_coding_transcript_exon_variant,,ENST00000483234,;BRD9,non_coding_transcript_exon_variant,,ENST00000495794,;BRD9,non_coding_transcript_exon_variant,,ENST00000475706,;BRD9,intron_variant,,ENST00000493082,;BRD9,upstream_gene_variant,,ENST00000523139,;	A	ENSG00000028310	ENST00000467963	Transcript	missense_variant	1445	1278	426	Q/H	caG/caT	.	.	.	-1	BRD9	HGNC	25818	protein_coding	YES	CCDS34127.2	ENSP00000419765	BRD9_HUMAN	.	UPI000020BEBE	.	tolerated(0.55)	probably_damaging(1)	12/16	.	Pfam_domain:PF12024,hmmpanther:PTHR22881,hmmpanther:PTHR22881:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTCCTGCAG	.	4	ESCA
MEF2C	0	.	GRCh37	5	88017128	88017129	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1292dupT	.	.	ENST00000340208	12/12	35	24	11	31	31	0	MEF2C,3_prime_UTR_variant,,ENST00000504921,;MEF2C,3_prime_UTR_variant,,ENST00000510942,;MEF2C,3_prime_UTR_variant,,ENST00000514028,;MEF2C,3_prime_UTR_variant,,ENST00000506554,;MEF2C,3_prime_UTR_variant,,ENST00000340208,;MEF2C,3_prime_UTR_variant,,ENST00000424173,;MEF2C,3_prime_UTR_variant,,ENST00000437473,;MEF2C,downstream_gene_variant,,ENST00000514015,;MEF2C,downstream_gene_variant,,ENST00000508569,;MEF2C,downstream_gene_variant,,ENST00000539796,;CTC-467M3.1,intron_variant,,ENST00000510274,;MEF2C,downstream_gene_variant,,ENST00000510980,;	A	ENSG00000081189	ENST00000340208	Transcript	3_prime_UTR_variant	3150-3151	.	.	.	.	.	.	.	-1	MEF2C	HGNC	6996	protein_coding	YES	CCDS54878.1	ENSP00000340874	MEF2C_HUMAN	H0YNI2_HUMAN,D6RJA7_HUMAN,D6RJ95_HUMAN,D6RG14_HUMAN	UPI0000D9B539	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAATGCAAAAA	.	3	ESCA
MEF2C	0	.	GRCh37	5	88017644	88017644	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*777delT	.	.	ENST00000340208	12/12	54	34	20	40	40	0	MEF2C,3_prime_UTR_variant,,ENST00000504921,;MEF2C,3_prime_UTR_variant,,ENST00000510942,;MEF2C,3_prime_UTR_variant,,ENST00000514028,;MEF2C,3_prime_UTR_variant,,ENST00000506554,;MEF2C,3_prime_UTR_variant,,ENST00000340208,;MEF2C,3_prime_UTR_variant,,ENST00000424173,;MEF2C,3_prime_UTR_variant,,ENST00000437473,;MEF2C,downstream_gene_variant,,ENST00000514015,;MEF2C,downstream_gene_variant,,ENST00000508569,;MEF2C,downstream_gene_variant,,ENST00000539796,;CTC-467M3.1,intron_variant,,ENST00000510274,;MEF2C,downstream_gene_variant,,ENST00000510980,;	-	ENSG00000081189	ENST00000340208	Transcript	3_prime_UTR_variant	2635	.	.	.	.	.	.	.	-1	MEF2C	HGNC	6996	protein_coding	YES	CCDS54878.1	ENSP00000340874	MEF2C_HUMAN	H0YNI2_HUMAN,D6RJA7_HUMAN,D6RJ95_HUMAN,D6RG14_HUMAN	UPI0000D9B539	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGGGGAAAAAA	.	3	ESCA
POU5F2	0	.	GRCh37	5	93076993	93076993	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277C>T	p.Arg93Ter	p.R93*	ENST00000510627	1/1	26	6	19	21	21	0	POU5F2,stop_gained,p.Arg93Ter,ENST00000510627,;FAM172A,intron_variant,,ENST00000509739,;FAM172A,intron_variant,,ENST00000505869,;FAM172A,intron_variant,,ENST00000509163,;FAM172A,intron_variant,,ENST00000395965,;RP11-185E12.2,upstream_gene_variant,,ENST00000606528,;POU5F2,upstream_gene_variant,,ENST00000606183,;FAM172A,intron_variant,,ENST00000502503,;	A	ENSG00000248483	ENST00000510627	Transcript	stop_gained	351	277	93	R/*	Cga/Tga	COSM1439152	.	.	-1	POU5F2	HGNC	26367	protein_coding	YES	CCDS59489.1	ENSP00000464890	PO5F2_HUMAN	.	UPI0000135E4C	.	.	.	1/1	.	hmmpanther:PTHR11636:SF14,hmmpanther:PTHR11636	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGTCGCAACC	.	5	ESCA
ERAP1	0	.	GRCh37	5	96126302	96126302	+	Silent	SNP	G	G	A	rs202098147	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1365C>T	p.%3D	p.D455D	ENST00000296754	9/20	13	5	7	31	31	0	ERAP1,synonymous_variant,p.%3D,ENST00000443439,;ERAP1,synonymous_variant,p.%3D,ENST00000296754,;CTD-2260A17.1,downstream_gene_variant,,ENST00000602972,;CTD-2260A17.1,downstream_gene_variant,,ENST00000512856,;ERAP1,upstream_gene_variant,,ENST00000514604,;ERAP1,non_coding_transcript_exon_variant,,ENST00000503311,;ERAP1,non_coding_transcript_exon_variant,,ENST00000507859,;	A	ENSG00000164307	ENST00000296754	Transcript	synonymous_variant	1623	1365	455	D	gaC/gaT	rs202098147	.	.	-1	ERAP1	HGNC	18173	protein_coding	YES	CCDS4085.1	ENSP00000296754	ERAP1_HUMAN	D6RAL9_HUMAN	UPI000045731D	.	.	.	9/20	.	hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF156,Gene3D:1.10.390.10,Superfamily_domains:SSF55486	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AATGCGTCAGC	byCluster|by1000G	4	ESCA
TFAP2A	0	.	GRCh37	6	10407037	10407038	+	Frame_Shift_Del	DEL	AC	AC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AC	AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520_521delGT	p.Val174AsnfsTer2	p.V174Nfs*2	ENST00000379604	3/7	54	40	14	43	43	0	TFAP2A,frameshift_variant,p.Val31AsnfsTer2,ENST00000498450,;TFAP2A,frameshift_variant,p.Val176AsnfsTer2,ENST00000379613,;TFAP2A,frameshift_variant,p.Val174AsnfsTer2,ENST00000482890,;TFAP2A,frameshift_variant,p.Val174AsnfsTer2,ENST00000379604,;TFAP2A,frameshift_variant,p.Val79AsnfsTer2,ENST00000475264,;TFAP2A,frameshift_variant,p.Val168AsnfsTer2,ENST00000379608,;TFAP2A,frameshift_variant,p.Val174AsnfsTer2,ENST00000466073,;TFAP2A,frameshift_variant,p.Val170AsnfsTer2,ENST00000319516,;TFAP2A,downstream_gene_variant,,ENST00000465858,;TFAP2A,upstream_gene_variant,,ENST00000461628,;TFAP2A-AS1,upstream_gene_variant,,ENST00000420777,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000462727,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000497266,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000473652,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000490875,;TFAP2A,3_prime_UTR_variant,,ENST00000488193,;TFAP2A,3_prime_UTR_variant,,ENST00000489805,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000478375,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000474952,;TFAP2A,downstream_gene_variant,,ENST00000464323,;	-	ENSG00000137203	ENST00000379604	Transcript	frameshift_variant	772-773	520-521	174	V/X	GTa/a	.	.	.	-1	TFAP2A	HGNC	11742	protein_coding	YES	CCDS4510.1	ENSP00000368924	AP2A_HUMAN	.	UPI0000125BC5	.	.	.	3/7	.	hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTAATTACAGTTT	.	3	ESCA
HACE1	0	.	GRCh37	6	105192413	105192413	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2416T>C	p.Tyr806His	p.Y806H	ENST00000262903	21/24	44	30	14	34	34	0	HACE1,missense_variant,p.Tyr245His,ENST00000518503,;HACE1,missense_variant,p.Tyr806His,ENST00000262903,;HACE1,missense_variant,p.Tyr591His,ENST00000369125,;HACE1,missense_variant,p.Tyr197His,ENST00000518402,;HACE1,non_coding_transcript_exon_variant,,ENST00000517995,;HACE1,3_prime_UTR_variant,,ENST00000517424,;HACE1,3_prime_UTR_variant,,ENST00000416605,;HACE1,non_coding_transcript_exon_variant,,ENST00000369127,;	G	ENSG00000085382	ENST00000262903	Transcript	missense_variant	2693	2416	806	Y/H	Tat/Cat	.	.	.	-1	HACE1	HGNC	21033	protein_coding	YES	CCDS5050.1	ENSP00000262903	HACE1_HUMAN	E5RFX0_HUMAN,E3W983_HUMAN	UPI00001602DC	.	deleterious(0)	probably_damaging(0.984)	21/24	.	PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF278,hmmpanther:PTHR11254,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATAGCCAC	.	5	ESCA
PRDM1	0	.	GRCh37	6	106553730	106553730	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1695G>A	p.%3D	p.P565P	ENST00000369096	5/7	26	17	8	15	15	0	PRDM1,synonymous_variant,p.%3D,ENST00000369096,;PRDM1,synonymous_variant,p.%3D,ENST00000369091,;PRDM1,synonymous_variant,p.%3D,ENST00000369089,;PRDM1,downstream_gene_variant,,ENST00000450060,;	A	ENSG00000057657	ENST00000369096	Transcript	synonymous_variant	1929	1695	565	P	ccG/ccA	.	.	.	1	PRDM1	HGNC	9346	protein_coding	YES	CCDS5054.2	ENSP00000358092	PRDM1_HUMAN	Q5T4E8_HUMAN,B2REA5_HUMAN	UPI0000D49069	.	.	.	5/7	.	hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF339,PIRSF_domain:PIRSF013212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCCGCTGAA	.	5	ESCA
ARMC2	0	.	GRCh37	6	109215690	109215690	+	Missense_Mutation	SNP	C	C	T	rs200206972	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.692C>T	p.Ala231Val	p.A231V	ENST00000392644	6/18	32	25	7	23	23	0	ARMC2,missense_variant,p.Ala66Val,ENST00000368972,;ARMC2,missense_variant,p.Ala231Val,ENST00000392644,;	T	ENSG00000118690	ENST00000392644	Transcript	missense_variant	860	692	231	A/V	gCg/gTg	rs200206972,COSM1487099	.	.	1	ARMC2	HGNC	23045	protein_coding	YES	CCDS5069.2	ENSP00000376417	ARMC2_HUMAN	G5E993_HUMAN,B0QZC1_HUMAN	UPI000022CC80	.	tolerated(0.5)	benign(0.001)	6/18	.	hmmpanther:PTHR21356	T:0.0004	T:0.0008	T:0	.	T:0.001	T:0	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATGCGAGGG	byFrequency|byCluster|by1000G	5	ESCA
SMPD2	0	.	GRCh37	6	109764847	109764847	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1011C>G	p.%3D	p.L337L	ENST00000258052	10/10	53	29	24	43	43	0	SMPD2,synonymous_variant,p.%3D,ENST00000258052,;PPIL6,upstream_gene_variant,,ENST00000440797,;PPIL6,upstream_gene_variant,,ENST00000521072,;PPIL6,upstream_gene_variant,,ENST00000424445,;PPIL6,upstream_gene_variant,,ENST00000520723,;MICAL1,downstream_gene_variant,,ENST00000358807,;SMPD2,downstream_gene_variant,,ENST00000458487,;PPIL6,upstream_gene_variant,,ENST00000417394,;PPIL6,upstream_gene_variant,,ENST00000518648,;MICAL1,downstream_gene_variant,,ENST00000433205,;MICAL1,downstream_gene_variant,,ENST00000358577,;MICAL1,downstream_gene_variant,,ENST00000368952,;PPIL6,upstream_gene_variant,,ENST00000447468,;MICAL1,downstream_gene_variant,,ENST00000456101,;MICAL1,downstream_gene_variant,,ENST00000465904,;SMPD2,downstream_gene_variant,,ENST00000439615,;	G	ENSG00000135587	ENST00000258052	Transcript	synonymous_variant	1370	1011	337	L	ctC/ctG	.	.	.	1	SMPD2	HGNC	11121	protein_coding	YES	CCDS5075.1	ENSP00000258052	NSMA_HUMAN	.	UPI000013CFAC	.	.	.	10/10	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCCTGGC	.	5	ESCA
CDC40	0	.	GRCh37	6	110530394	110530394	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598G>T	p.Val200Leu	p.V200L	ENST00000368932	6/16	43	37	6	41	41	0	CDC40,missense_variant,p.Val200Leu,ENST00000307731,;CDC40,missense_variant,p.Val200Leu,ENST00000368932,;CDC40,missense_variant,p.Val200Leu,ENST00000368930,;CDC40,downstream_gene_variant,,ENST00000453107,;CDC40,non_coding_transcript_exon_variant,,ENST00000431461,;CDC40,non_coding_transcript_exon_variant,,ENST00000606893,;	T	ENSG00000168438	ENST00000368932	Transcript	missense_variant	699	598	200	V/L	Gtg/Ttg	.	.	.	1	CDC40	HGNC	17350	protein_coding	YES	CCDS5081.1	ENSP00000357928	PRP17_HUMAN	Q5SRM9_HUMAN	UPI0000132145	.	tolerated(0.29)	benign(0.064)	6/16	.	hmmpanther:PTHR19852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATATGTGGAT	.	4	ESCA
CDK19	0	.	GRCh37	6	110953273	110953273	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606A>G	p.%3D	p.P202P	ENST00000368911	6/13	42	28	14	36	36	0	CDK19,synonymous_variant,p.%3D,ENST00000413605,;CDK19,synonymous_variant,p.%3D,ENST00000457688,;CDK19,synonymous_variant,p.%3D,ENST00000323817,;CDK19,synonymous_variant,p.%3D,ENST00000368911,;CDK19,3_prime_UTR_variant,,ENST00000463016,;	C	ENSG00000155111	ENST00000368911	Transcript	synonymous_variant	786	606	202	P	ccA/ccG	.	.	.	-1	CDK19	HGNC	19338	protein_coding	YES	CCDS5085.1	ENSP00000357907	CDK19_HUMAN	Q5JQZ9_HUMAN	UPI0000070643	.	.	.	6/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF131,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTCTGGAGC	.	5	ESCA
CDK19	0	.	GRCh37	6	110988756	110988756	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337G>A	p.Ala113Thr	p.A113T	ENST00000368911	4/13	20	10	10	15	15	0	CDK19,missense_variant,p.Ala53Thr,ENST00000457688,;CDK19,missense_variant,p.Ala53Thr,ENST00000323817,;CDK19,missense_variant,p.Ala113Thr,ENST00000368911,;CDK19,non_coding_transcript_exon_variant,,ENST00000460913,;CDK19,missense_variant,p.Ala71Thr,ENST00000463016,;	T	ENSG00000155111	ENST00000368911	Transcript	missense_variant	517	337	113	A/T	Gca/Aca	.	.	.	-1	CDK19	HGNC	19338	protein_coding	YES	CCDS5085.1	ENSP00000357907	CDK19_HUMAN	Q5JQZ9_HUMAN	UPI0000070643	.	tolerated(0.24)	benign(0.052)	4/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:3.30.200.20,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF131,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATGCACGGT	.	5	ESCA
REV3L	0	.	GRCh37	6	111694984	111694984	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4574C>G	p.Ser1525Cys	p.S1525C	ENST00000358835	14/33	76	55	21	60	60	0	REV3L,missense_variant,p.Ser1447Cys,ENST00000435970,;REV3L,missense_variant,p.Ser1525Cys,ENST00000358835,;REV3L,missense_variant,p.Ser1525Cys,ENST00000368802,;REV3L,missense_variant,p.Ser1525Cys,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000434009,;REV3L,3_prime_UTR_variant,,ENST00000422377,;	C	ENSG00000009413	ENST00000358835	Transcript	missense_variant	5029	4574	1525	S/C	tCt/tGt	COSM1487126,COSM1487125	.	.	-1	REV3L	HGNC	9968	protein_coding	YES	CCDS5091.2	ENSP00000351697	DPOLZ_HUMAN	Q9UID5_HUMAN,C4TNX2_HUMAN,C4TNX1_HUMAN,C4TNX0_HUMAN,C4B7Q4_HUMAN	UPI0000140023	.	deleterious(0)	probably_damaging(0.999)	14/33	.	hmmpanther:PTHR10322:SF16,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCAGACTGT	.	5	ESCA
FAM26F	0	.	GRCh37	6	116783245	116783245	+	Silent	SNP	C	C	T	rs541870005	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153C>T	p.%3D	p.Y51Y	ENST00000368605	2/3	19	13	5	18	18	0	FAM26F,synonymous_variant,p.%3D,ENST00000368605,;FAM26F,intron_variant,,ENST00000368606,;FAM26F,upstream_gene_variant,,ENST00000368604,;Z84488.1,upstream_gene_variant,,ENST00000584665,;RP1-93H18.6,intron_variant,,ENST00000476099,;KRT18P22,upstream_gene_variant,,ENST00000402024,;	T	ENSG00000188820	ENST00000368605	Transcript	synonymous_variant	248	153	51	Y	taC/taT	rs541870005	.	.	1	FAM26F	HGNC	33391	protein_coding	YES	CCDS34519.1	ENSP00000357594	FA26F_HUMAN	.	UPI0000161884	.	.	.	2/3	.	Transmembrane_helices:TMhelix,Pfam_domain:PF14798,hmmpanther:PTHR32261,hmmpanther:PTHR32261:SF6	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTACGGCCT	by1000G	5	ESCA
CEP85L	0	.	GRCh37	6	118887391	118887391	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330C>T	p.%3D	p.S110S	ENST00000368488	4/14	38	23	15	36	36	0	CEP85L,synonymous_variant,p.%3D,ENST00000360290,;CEP85L,synonymous_variant,p.%3D,ENST00000419517,;CEP85L,synonymous_variant,p.%3D,ENST00000368488,;CEP85L,synonymous_variant,p.%3D,ENST00000434604,;CEP85L,synonymous_variant,p.%3D,ENST00000392500,;CEP85L,synonymous_variant,p.%3D,ENST00000368491,;CEP85L,non_coding_transcript_exon_variant,,ENST00000462101,;CEP85L,non_coding_transcript_exon_variant,,ENST00000476150,;CEP85L,non_coding_transcript_exon_variant,,ENST00000472713,;CEP85L,non_coding_transcript_exon_variant,,ENST00000483035,;	A	ENSG00000111860	ENST00000368488	Transcript	synonymous_variant	397	330	110	S	tcC/tcT	.	.	.	-1	CEP85L	HGNC	21638	protein_coding	YES	CCDS55052.1	ENSP00000357474	CE85L_HUMAN	A2A3P3_HUMAN	UPI0001D1E40A	.	.	.	4/14	.	hmmpanther:PTHR31075,hmmpanther:PTHR31075:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCTGGAATT	.	5	ESCA
TRDN	0	.	GRCh37	6	123786066	123786066	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916T>G	p.Ser306Ala	p.S306A	ENST00000398178	10/41	31	25	5	19	19	0	TRDN,missense_variant,p.Ser306Ala,ENST00000398178,;TRDN,missense_variant,p.Ser306Ala,ENST00000334268,;TRDN,missense_variant,p.Ser286Ala,ENST00000546248,;RP11-532N4.2,intron_variant,,ENST00000427828,;RP11-532N4.2,intron_variant,,ENST00000589182,;RP11-532N4.2,intron_variant,,ENST00000587106,;RP11-532N4.2,intron_variant,,ENST00000418467,;RP11-532N4.2,intron_variant,,ENST00000434768,;RP11-532N4.2,downstream_gene_variant,,ENST00000587049,;	C	ENSG00000186439	ENST00000398178	Transcript	missense_variant	938	916	306	S/A	Tca/Gca	.	.	.	-1	TRDN	HGNC	12261	protein_coding	YES	CCDS55053.1	ENSP00000381240	TRDN_HUMAN	.	UPI0000D820CC	.	tolerated_low_confidence(0.15)	benign(0.188)	10/41	.	hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGATGCCG	.	5	ESCA
RP11-510H23.1	0	.	GRCh37	6	125232172	125232172	+	RNA	SNP	C	C	T	rs372298254	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2574G>A	.	.	ENST00000439075	7/7	22	9	13	19	19	0	RP11-510H23.1,non_coding_transcript_exon_variant,,ENST00000439075,;	T	ENSG00000236548	ENST00000439075	Transcript	non_coding_transcript_exon_variant	2574	.	.	.	.	rs372298254	.	.	-1	RP11-510H23.1	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	7/7	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0017	T:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CAGGGCGGTCT	byCluster|by1000G	4	ESCA
HEY2	0	.	GRCh37	6	126080617	126080617	+	Missense_Mutation	SNP	C	C	T	rs761904411	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683C>T	p.Thr228Met	p.T228M	ENST00000368364	5/5	31	15	15	15	15	0	HEY2,missense_variant,p.Thr182Met,ENST00000368365,;HEY2,missense_variant,p.Thr228Met,ENST00000368364,;	T	ENSG00000135547	ENST00000368364	Transcript	missense_variant	880	683	228	T/M	aCg/aTg	rs761904411,COSM1662133	.	.	1	HEY2	HGNC	4881	protein_coding	YES	CCDS5131.1	ENSP00000357348	HEY2_HUMAN	Q5TF93_HUMAN,B4E1L3_HUMAN	UPI0000037AFE	.	deleterious(0.01)	possibly_damaging(0.899)	5/5	.	hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF79	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCACGGCCA	.	5	ESCA
TAAR9	0	.	GRCh37	6	132860174	132860174	+	Missense_Mutation	SNP	T	T	C	rs765695223	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.746T>C	p.Val249Ala	p.V249A	ENST00000434551	1/1	33	25	8	38	38	0	TAAR9,missense_variant,p.Val249Ala,ENST00000434551,;	C	ENSG00000237110	ENST00000434551	Transcript	missense_variant	746	746	249	V/A	gTa/gCa	rs765695223	.	.	1	TAAR9	HGNC	20977	polymorphic_pseudogene	YES	.	ENSP00000424607	.	.	.	.	tolerated(0.17)	probably_damaging(0.994)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAGTAGCAA	.	5	ESCA
ESR1	0	.	GRCh37	6	152422515	152422515	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2422delA	.	.	ENST00000440973	10/10	17	11	6	11	11	0	ESR1,3_prime_UTR_variant,,ENST00000440973,;ESR1,3_prime_UTR_variant,,ENST00000443427,;ESR1,3_prime_UTR_variant,,ENST00000456483,;ESR1,3_prime_UTR_variant,,ENST00000206249,;ESR1,intron_variant,,ENST00000427531,;ESR1,downstream_gene_variant,,ENST00000338799,;ESR1,downstream_gene_variant,,ENST00000406599,;	-	ENSG00000091831	ENST00000440973	Transcript	3_prime_UTR_variant	4572	.	.	.	.	.	.	.	1	ESR1	HGNC	3467	protein_coding	YES	CCDS5234.1	ENSP00000405330	ESR1_HUMAN	Q9UE35_HUMAN,Q9UBT1_HUMAN,Q5T5H8_HUMAN,K7R989_HUMAN,K4Q331_HUMAN,K4PXX0_HUMAN,K4PX46_HUMAN,G4XH65_HUMAN,E3WH18_HUMAN,C8CJL0_HUMAN,C7FFR5_HUMAN,B6DU67_HUMAN	UPI000004A328	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAAAACAAAAAA	.	2	ESCA
LPA	0	.	GRCh37	6	160958928	160958928	+	Missense_Mutation	SNP	G	G	T	rs553481085	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5801C>A	p.Ala1934Asp	p.A1934D	ENST00000447678	38/40	59	37	22	83	83	0	LPA,missense_variant,p.Ala1934Asp,ENST00000316300,;LPA,missense_variant,p.Ala1934Asp,ENST00000447678,;	T	ENSG00000198670	ENST00000447678	Transcript	missense_variant	5922	5801	1934	A/D	gCc/gAc	rs553481085	.	.	-1	LPA	HGNC	6667	protein_coding	YES	CCDS43523.1	ENSP00000395608	APOA_HUMAN	Q9UKJ7_HUMAN,Q9UIR8_HUMAN,Q9UIR6_HUMAN,Q9UIR5_HUMAN	UPI0000458AC9	.	tolerated(1)	benign(0.19)	38/40	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24261,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGGCGGTG	byCluster	5	ESCA
MAP3K4	0	.	GRCh37	6	161455391	161455391	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258delC	p.Ser87AlafsTer6	p.S87Afs*6	ENST00000392142	2/27	67	48	19	40	40	0	MAP3K4,frameshift_variant,p.Ser87AlafsTer6,ENST00000366920,;MAP3K4,frameshift_variant,p.Ser87AlafsTer6,ENST00000366919,;MAP3K4,frameshift_variant,p.Ser87AlafsTer6,ENST00000348824,;MAP3K4,frameshift_variant,p.Ser87AlafsTer6,ENST00000392142,;MAP3K4,5_prime_UTR_variant,,ENST00000448119,;MAP3K4,non_coding_transcript_exon_variant,,ENST00000446500,;MAP3K4,frameshift_variant,p.Ser87AlafsTer6,ENST00000544041,;MAP3K4,frameshift_variant,p.Ser87AlafsTer6,ENST00000490904,;MAP3K4,intron_variant,,ENST00000542952,;	-	ENSG00000085511	ENST00000392142	Transcript	frameshift_variant	401	253	85	P/X	Ccc/cc	.	.	.	1	MAP3K4	HGNC	6856	protein_coding	YES	CCDS34565.1	ENSP00000375986	M3K4_HUMAN	F5H534_HUMAN	UPI00004574E1	.	.	.	2/27	.	hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCTCTCCCCCC	.	3	ESCA
C6orf118	0	.	GRCh37	6	165715153	165715153	+	Missense_Mutation	SNP	G	G	A	rs140500230	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658C>T	p.Arg220Cys	p.R220C	ENST00000230301	2/9	30	14	15	21	21	0	C6orf118,missense_variant,p.Arg116Cys,ENST00000543069,;C6orf118,missense_variant,p.Arg220Cys,ENST00000230301,;	A	ENSG00000112539	ENST00000230301	Transcript	missense_variant	679	658	220	R/C	Cgt/Tgt	rs140500230	.	.	-1	C6orf118	HGNC	21233	protein_coding	YES	CCDS5288.1	ENSP00000230301	CF118_HUMAN	.	UPI0000367401	.	tolerated(0.15)	benign(0.006)	2/9	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAACGCAGGA	byCluster	5	ESCA
RP3-470B24.5	0	.	GRCh37	6	168376899	168376900	+	RNA	INS	-	-	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.720dupC	.	.	ENST00000538528	1/1	44	31	13	24	24	0	MLLT4,downstream_gene_variant,,ENST00000400822,;MLLT4,downstream_gene_variant,,ENST00000392112,;MLLT4,downstream_gene_variant,,ENST00000366806,;RP3-470B24.5,non_coding_transcript_exon_variant,,ENST00000538528,;RP3-470B24.5,downstream_gene_variant,,ENST00000441716,;	G	ENSG00000235994	ENST00000538528	Transcript	non_coding_transcript_exon_variant	720-721	.	.	.	.	.	.	.	-1	RP3-470B24.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGCAGTGGGGG	.	2	ESCA
DLL1	0	.	GRCh37	6	170591889	170591889	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*73A>G	.	.	ENST00000366756	11/11	33	12	20	24	24	0	DLL1,3_prime_UTR_variant,,ENST00000366756,;RP5-894D12.3,downstream_gene_variant,,ENST00000438622,;RP5-894D12.3,downstream_gene_variant,,ENST00000607074,;RP5-894D12.3,downstream_gene_variant,,ENST00000422894,;	C	ENSG00000198719	ENST00000366756	Transcript	3_prime_UTR_variant	2579	.	.	.	.	.	.	.	-1	DLL1	HGNC	2908	protein_coding	YES	CCDS5313.1	ENSP00000355718	DLL1_HUMAN	.	UPI000004C656	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCATTCGTT	.	5	ESCA
CAP2	0	.	GRCh37	6	17507510	17507510	+	Silent	SNP	C	C	T	rs556554484	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.411C>T	p.%3D	p.S137S	ENST00000229922	5/13	49	35	14	64	64	0	CAP2,synonymous_variant,p.%3D,ENST00000465994,;CAP2,synonymous_variant,p.%3D,ENST00000378990,;CAP2,synonymous_variant,p.%3D,ENST00000229922,;CAP2,intron_variant,,ENST00000489374,;CAP2,intron_variant,,ENST00000493172,;CAP2,synonymous_variant,p.%3D,ENST00000479291,;CAP2,3_prime_UTR_variant,,ENST00000476263,;	T	ENSG00000112186	ENST00000229922	Transcript	synonymous_variant	943	411	137	S	agC/agT	rs556554484,COSM1076260	.	.	1	CAP2	HGNC	20039	protein_coding	YES	CCDS4539.1	ENSP00000229922	CAP2_HUMAN	.	UPI0000126EC6	.	.	.	5/13	.	hmmpanther:PTHR10652,hmmpanther:PTHR10652:SF2,Pfam_domain:PF01213,Superfamily_domains:0043456	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V136I|c.406G>A|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAGCGAAAG	by1000G	5	ESCA
HDGFL1	0	.	GRCh37	6	22569743	22569743	+	5'Flank	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000510882	.	9	4	5	14	14	0	HDGFL1,5_prime_UTR_variant,,ENST00000230012,;HDGFL1,upstream_gene_variant,,ENST00000510882,;	T	ENSG00000112273	ENST00000510882	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	52	1	HDGFL1	HGNC	21095	protein_coding	YES	CCDS34347.1	ENSP00000442129	HDGL1_HUMAN	.	UPI0000039B1A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACTGCGCGCG	.	3	ESCA
LRRC16A	0	.	GRCh37	6	25495432	25495432	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1314T>C	p.%3D	p.P438P	ENST00000329474	16/37	25	19	6	32	32	0	LRRC16A,synonymous_variant,p.%3D,ENST00000329474,;	C	ENSG00000079691	ENST00000329474	Transcript	synonymous_variant	1682	1314	438	P	ccT/ccC	.	.	.	1	LRRC16A	HGNC	21581	protein_coding	YES	CCDS54973.1	ENSP00000331983	LR16A_HUMAN	.	UPI00004588AB	.	.	.	16/37	.	hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF39,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCTGAGCC	.	5	ESCA
HIST1H3I	0	.	GRCh37	6	27839733	27839733	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361A>T	p.Met121Leu	p.M121L	ENST00000328488	1/1	54	30	24	41	41	0	HIST1H3I,missense_variant,p.Met121Leu,ENST00000328488,;HIST1H1B,upstream_gene_variant,,ENST00000331442,;HIST1H4L,downstream_gene_variant,,ENST00000355981,;	A	ENSG00000182572	ENST00000328488	Transcript	missense_variant	367	361	121	M/L	Atg/Ttg	.	.	.	-1	HIST1H3I	HGNC	4771	protein_coding	YES	CCDS4636.1	ENSP00000329554	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0.02)	benign(0.004)	1/1	.	Prints_domain:PR00622,Superfamily_domains:SSF47113,SMART_domains:SM00428,Gene3D:1.10.20.10,Pfam_domain:PF00125,hmmpanther:PTHR11426	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCATAATAG	.	5	ESCA
NKAPL	0	.	GRCh37	6	28227519	28227520	+	Frame_Shift_Del	DEL	GA	GA	-	rs780859004	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GA	GA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.379_380delAG	p.Arg127AspfsTer8	p.R127Dfs*8	ENST00000343684	1/1	29	23	6	25	25	0	NKAPL,frameshift_variant,p.Arg127AspfsTer8,ENST00000343684,;ZKSCAN4,upstream_gene_variant,,ENST00000423974,;	-	ENSG00000189134	ENST00000343684	Transcript	frameshift_variant	422-423	370-371	124	E/X	GAg/g	rs780859004,COSM1442798	.	.	1	NKAPL	HGNC	21584	protein_coding	YES	CCDS34353.1	ENSP00000345716	NKAPL_HUMAN	.	UPI0000072A86	.	.	.	1/1	.	hmmpanther:PTHR13087,hmmpanther:PTHR13087:SF3	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	9	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R127fs*8|c.370_371delGA|3	INDELOCATOR|VARSCANI	CTGAAGGAGAGAG	.	2	ESCA
HLA-G	0	.	GRCh37	6	29797635	29797635	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938C>T	p.Ala313Val	p.A313V	ENST00000428701	6/8	118	80	37	91	91	0	HLA-G,missense_variant,p.Ala318Val,ENST00000376828,;HLA-G,missense_variant,p.Ala313Val,ENST00000360323,;HLA-G,missense_variant,p.Ala313Val,ENST00000428701,;HLA-G,missense_variant,p.Ala129Val,ENST00000376815,;HLA-G,missense_variant,p.Ala221Val,ENST00000376818,;HLA-G,missense_variant,p.Ala221Val,ENST00000478519,;HLA-G,non_coding_transcript_exon_variant,,ENST00000478355,;HCG4P8,upstream_gene_variant,,ENST00000443049,;	T	ENSG00000204632	ENST00000428701	Transcript	missense_variant	1116	938	313	A/V	gCt/gTt	.	.	.	1	HLA-G	HGNC	4964	protein_coding	YES	CCDS4668.1	ENSP00000412927	HLAG_HUMAN	Q6DU14_HUMAN,M9TK49_HUMAN,Q9UM45_HUMAN,Q9TP14_HUMAN,Q9TP13_HUMAN,Q9TP12_HUMAN,Q9TP11_HUMAN,Q9TP10_HUMAN,Q95356_HUMAN,Q7JFN0_HUMAN,Q6DL89_HUMAN,Q6DL88_HUMAN,Q6DL87_HUMAN,Q6DL86_HUMAN,Q6DL85_HUMAN,Q6B9Y6_HUMAN,Q6B9Y4_HUMAN,Q6B9Y3_HUMAN,Q6B9Y2_HUMAN,Q6B9Y1_HUMAN,Q6B845_HUMAN,Q68YS4_HUMAN,Q68YS3_HUMAN,Q68YS2_HUMAN,Q68YS1_HUMAN,Q68YS0_HUMAN,Q68YR9_HUMAN,Q68YR8_HUMAN,Q30182_HUMAN,O78136_HUMAN,O78135_HUMAN,O78134_HUMAN,O78133_HUMAN,O78131_HUMAN,O19809_HUMAN,O19807_HUMAN,O19806_HUMAN,O19805_HUMAN,O19768_HUMAN,O19767_HUMAN,O19766_HUMAN,O19745_HUMAN,O19684_HUMAN,O19659_HUMAN,O19658_HUMAN,O02928_HUMAN,O02927_HUMAN,O02926_HUMAN,O02923_HUMAN,J3JRT1_HUMAN,C7SJ32_HUMAN,C0JTC7_HUMAN,C0JT30_HUMAN,C0JT28_HUMAN,C0JSV3_HUMAN,C0JSV2_HUMAN,B5LFX9_HUMAN,B1P198_HUMAN,A5HSK0_HUMAN	UPI000000166E	.	tolerated_low_confidence(0.31)	benign(0.005)	6/8	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR16675:SF149,hmmpanther:PTHR16675	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTTGCTGGCC	.	5	ESCA
MUC21	0	.	GRCh37	6	30956125	30956125	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*154A>G	.	.	ENST00000376296	3/3	17	9	8	28	28	0	MUC21,3_prime_UTR_variant,,ENST00000376296,;MUC21,3_prime_UTR_variant,,ENST00000486149,;	G	ENSG00000204544	ENST00000376296	Transcript	3_prime_UTR_variant	2096	.	.	.	.	.	.	.	1	MUC21	HGNC	21661	protein_coding	YES	CCDS34388.1	ENSP00000365473	MUC21_HUMAN	.	UPI000047030C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CCTTTACCAGA	.	4	ESCA
POU5F1	0	.	GRCh37	6	31132322	31132324	+	3'UTR	DEL	TTC	TTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TTC	TTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*54_*56delGAA	.	.	ENST00000259915	5/5	29	19	10	46	46	0	POU5F1,3_prime_UTR_variant,,ENST00000441888,;POU5F1,3_prime_UTR_variant,,ENST00000471529,;POU5F1,3_prime_UTR_variant,,ENST00000259915,;POU5F1,3_prime_UTR_variant,,ENST00000513407,;POU5F1,3_prime_UTR_variant,,ENST00000512818,;POU5F1,3_prime_UTR_variant,,ENST00000606567,;TCF19,intron_variant,,ENST00000542218,;TCF19,downstream_gene_variant,,ENST00000376257,;TCF19,downstream_gene_variant,,ENST00000376255,;TCF19,downstream_gene_variant,,ENST00000496421,;POU5F1,downstream_gene_variant,,ENST00000461401,;	-	ENSG00000204531	ENST00000259915	Transcript	3_prime_UTR_variant	1210-1212	.	.	.	.	.	.	.	-1	POU5F1	HGNC	9221	protein_coding	YES	CCDS34391.1	ENSP00000259915	PO5F1_HUMAN	U3KQH6_HUMAN,F2Z381_HUMAN,D2IYK3_HUMAN,B5B8Q4_HUMAN,B5B8Q2_HUMAN,B5B8Q1_HUMAN,B5B8Q0_HUMAN,B5B8P9_HUMAN,B5B8P8_HUMAN,B5B8P7_HUMAN,B5B8P6_HUMAN,B5B8P4_HUMAN,B5B8P3_HUMAN,B5B8P2_HUMAN,B5B8P1_HUMAN,B5B8P0_HUMAN,B5B8N9_HUMAN,B5B8N8_HUMAN,B5B8N7_HUMAN	UPI0000049CDE	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	CAGGTTTTCTTTCC	.	2	ESCA
TNXB	0	.	GRCh37	6	32032631	32032631	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6808C>T	p.Arg2270Cys	p.R2270C	ENST00000375247	19/44	36	31	5	26	26	0	TNXB,missense_variant,p.Arg2270Cys,ENST00000375247,;TNXB,missense_variant,p.Arg2270Cys,ENST00000375244,;	A	ENSG00000168477	ENST00000375247	Transcript	missense_variant	7010	6808	2270	R/C	Cgc/Tgc	.	.	.	-1	TNXB	HGNC	11976	protein_coding	.	.	ENSP00000364396	TENX_HUMAN	Q9NPK8_HUMAN,Q9NPK7_HUMAN,B6RHJ5_HUMAN	UPI000174F11D	.	.	probably_damaging(0.997)	19/44	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,hmmpanther:PTHR19143:SF190,hmmpanther:PTHR19143,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACGCGCTGGC	.	2	ESCA
AGPAT1	0	.	GRCh37	6	32138784	32138784	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264G>T	p.%3D	p.G88G	ENST00000395499	3/7	28	19	9	27	27	0	AGPAT1,synonymous_variant,p.%3D,ENST00000395496,;AGPAT1,synonymous_variant,p.%3D,ENST00000375107,;AGPAT1,synonymous_variant,p.%3D,ENST00000395499,;AGPAT1,synonymous_variant,p.%3D,ENST00000375104,;AGPAT1,synonymous_variant,p.%3D,ENST00000395497,;AGPAT1,synonymous_variant,p.%3D,ENST00000336984,;AGPAT1,intron_variant,,ENST00000412465,;EGFL8,downstream_gene_variant,,ENST00000395512,;EGFL8,downstream_gene_variant,,ENST00000333845,;EGFL8,downstream_gene_variant,,ENST00000432129,;PPT2,downstream_gene_variant,,ENST00000445576,;PPT2,downstream_gene_variant,,ENST00000437001,;AGPAT1,non_coding_transcript_exon_variant,,ENST00000476663,;AGPAT1,intron_variant,,ENST00000490711,;PPT2-EGFL8,downstream_gene_variant,,ENST00000453656,;EGFL8,downstream_gene_variant,,ENST00000489721,;PPT2-EGFL8,3_prime_UTR_variant,,ENST00000422437,;EGFL8,downstream_gene_variant,,ENST00000482938,;PPT2-EGFL8,downstream_gene_variant,,ENST00000585246,;PPT2-EGFL8,downstream_gene_variant,,ENST00000428388,;PPT2-EGFL8,downstream_gene_variant,,ENST00000479001,;PPT2-EGFL8,downstream_gene_variant,,ENST00000421600,;EGFL8,downstream_gene_variant,,ENST00000466239,;PPT2-EGFL8,downstream_gene_variant,,ENST00000583227,;	A	ENSG00000204310	ENST00000395499	Transcript	synonymous_variant	844	264	88	G	ggG/ggT	.	.	.	-1	AGPAT1	HGNC	324	protein_coding	YES	CCDS4744.1	ENSP00000378877	PLCA_HUMAN	Q9HBM8_HUMAN,Q71VH6_HUMAN	UPI0000131BD2	.	.	.	3/7	.	hmmpanther:PTHR10434,hmmpanther:PTHR10434:SF1,Pfam_domain:PF01553,Gene3D:1iuqA02,TIGRFAM_domain:TIGR00530,Superfamily_domains:0039877	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGCCCCTCG	.	5	ESCA
PHF1	0	.	GRCh37	6	33382566	33382566	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1013delC	p.Pro338LeufsTer39	p.P338Lfs*39	ENST00000374516	11/15	31	25	6	22	22	0	PHF1,frameshift_variant,p.Pro338LeufsTer39,ENST00000374516,;PHF1,frameshift_variant,p.Pro338LeufsTer114,ENST00000374512,;CUTA,downstream_gene_variant,,ENST00000607266,;CUTA,downstream_gene_variant,,ENST00000494751,;CUTA,downstream_gene_variant,,ENST00000374500,;CUTA,downstream_gene_variant,,ENST00000488034,;PHF1,upstream_gene_variant,,ENST00000427826,;PHF1,downstream_gene_variant,,ENST00000427004,;KIFC1,downstream_gene_variant,,ENST00000428849,;CUTA,downstream_gene_variant,,ENST00000374496,;CUTA,downstream_gene_variant,,ENST00000440279,;CUTA,downstream_gene_variant,,ENST00000488478,;PHF1,downstream_gene_variant,,ENST00000428274,;PHF1,downstream_gene_variant,,ENST00000459809,;CUTA,downstream_gene_variant,,ENST00000492510,;PHF1,frameshift_variant,p.Pro338LeufsTer39,ENST00000487667,;PHF1,frameshift_variant,p.Pro338LeufsTer?,ENST00000495509,;PHF1,non_coding_transcript_exon_variant,,ENST00000486845,;CUTA,downstream_gene_variant,,ENST00000374484,;PHF1,upstream_gene_variant,,ENST00000479029,;CUTA,downstream_gene_variant,,ENST00000462802,;CUTA,downstream_gene_variant,,ENST00000482684,;CUTA,downstream_gene_variant,,ENST00000465956,;CUTA,downstream_gene_variant,,ENST00000479249,;PHF1,downstream_gene_variant,,ENST00000488767,;CUTA,downstream_gene_variant,,ENST00000487637,;	-	ENSG00000112511	ENST00000374516	Transcript	frameshift_variant	1280	1009	337	P/X	Ccc/cc	.	.	.	1	PHF1	HGNC	8919	protein_coding	YES	CCDS4777.1	ENSP00000363640	PHF1_HUMAN	A2AB23_HUMAN,A2AB22_HUMAN	UPI0000457421	.	.	.	11/15	.	hmmpanther:PTHR12628,hmmpanther:PTHR12628:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	ATGCCTCCCCCT	.	2	ESCA
BAK1	0	.	GRCh37	6	33540814	33540814	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*766C>A	.	.	ENST00000374467	6/6	17	14	3	30	30	0	BAK1,3_prime_UTR_variant,,ENST00000374467,;BAK1,3_prime_UTR_variant,,ENST00000442998,;BAK1,downstream_gene_variant,,ENST00000360661,;	T	ENSG00000030110	ENST00000374467	Transcript	3_prime_UTR_variant	1651	.	.	.	.	.	.	.	-1	BAK1	HGNC	949	protein_coding	YES	CCDS4781.1	ENSP00000363591	BAK_HUMAN	Q8NFF3_HUMAN,Q5HCI0_HUMAN,B3KRK7_HUMAN	UPI0000126777	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAAGTGTCT	.	2	ESCA
SRPK1	0	.	GRCh37	6	35838144	35838145	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.904dupA	p.Arg302LysfsTer13	p.R302Kfs*13	ENST00000373825	10/16	52	43	9	47	47	0	SRPK1,frameshift_variant,p.Arg286LysfsTer13,ENST00000423325,;SRPK1,frameshift_variant,p.Arg40LysfsTer13,ENST00000510290,;SRPK1,frameshift_variant,p.Arg318LysfsTer13,ENST00000361690,;SRPK1,frameshift_variant,p.Arg195LysfsTer13,ENST00000373822,;SRPK1,frameshift_variant,p.Arg302LysfsTer13,ENST00000373825,;SRPK1,downstream_gene_variant,,ENST00000373821,;SRPK1,non_coding_transcript_exon_variant,,ENST00000346162,;SRPK1,intron_variant,,ENST00000502969,;SRPK1,upstream_gene_variant,,ENST00000507292,;	T	ENSG00000096063	ENST00000373825	Transcript	frameshift_variant	1190-1191	904-905	302	R/KX	aga/aAga	.	.	.	-1	SRPK1	HGNC	11305	protein_coding	YES	CCDS47415.1	ENSP00000362931	SRPK1_HUMAN	D6RBF8_HUMAN	UPI000020DBDD	.	.	.	10/16	.	SMART_domains:SM00220,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF101,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTGGTCTTTTT	.	3	ESCA
SLC26A8	0	.	GRCh37	6	35944996	35944996	+	Silent	SNP	A	A	G	rs770658057	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1158T>C	p.%3D	p.S386S	ENST00000490799	9/20	28	19	8	33	33	0	SLC26A8,synonymous_variant,p.%3D,ENST00000490799,;SLC26A8,synonymous_variant,p.%3D,ENST00000355574,;SLC26A8,synonymous_variant,p.%3D,ENST00000394602,;SLC26A8,non_coding_transcript_exon_variant,,ENST00000486155,;	G	ENSG00000112053	ENST00000490799	Transcript	synonymous_variant	1512	1158	386	S	agT/agC	rs770658057	.	.	-1	SLC26A8	HGNC	14468	protein_coding	YES	CCDS4813.1	ENSP00000417638	S26A8_HUMAN	.	UPI00000739C0	.	.	.	9/20	.	hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF11,Pfam_domain:PF00916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGACACTGTA	.	5	ESCA
MDGA1	0	.	GRCh37	6	37619877	37619877	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1222A>G	p.Ser408Gly	p.S408G	ENST00000434837	7/17	33	24	9	37	37	0	MDGA1,missense_variant,p.Ser408Gly,ENST00000297153,;MDGA1,missense_variant,p.Ser408Gly,ENST00000505425,;MDGA1,missense_variant,p.Ser408Gly,ENST00000434837,;MDGA1,downstream_gene_variant,,ENST00000508399,;MDGA1,downstream_gene_variant,,ENST00000515437,;MDGA1,upstream_gene_variant,,ENST00000510077,;MDGA1,non_coding_transcript_exon_variant,,ENST00000478143,;MDGA1,upstream_gene_variant,,ENST00000502298,;	C	ENSG00000112139	ENST00000434837	Transcript	missense_variant	2401	1222	408	S/G	Agt/Ggt	.	.	.	-1	MDGA1	HGNC	19267	protein_coding	YES	CCDS47417.1	ENSP00000402584	MDGA1_HUMAN	D6RHU8_HUMAN,D6RFG6_HUMAN	UPI0000071D28	.	deleterious(0.02)	benign(0.252)	7/17	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Pfam_domain:PF07679,Gene3D:2.60.40.10,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF66,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCACTGAAGT	.	2	ESCA
ZFAND3	0	.	GRCh37	6	38122150	38122150	+	3'UTR	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1992delG	.	.	ENST00000287218	6/6	23	8	15	13	13	0	ZFAND3,3_prime_UTR_variant,,ENST00000373391,;ZFAND3,3_prime_UTR_variant,,ENST00000287218,;ZFAND3,downstream_gene_variant,,ENST00000463847,;ZFAND3,downstream_gene_variant,,ENST00000440482,;	-	ENSG00000156639	ENST00000287218	Transcript	3_prime_UTR_variant	3116	.	.	.	.	.	.	.	1	ZFAND3	HGNC	18019	protein_coding	YES	CCDS4836.1	ENSP00000287218	ZFAN3_HUMAN	.	UPI000006E3A4	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAGCTGGGGGG	.	2	ESCA
BTBD9	0	.	GRCh37	6	38561994	38561994	+	Missense_Mutation	SNP	G	G	A	rs150015110	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295C>T	p.Arg99Trp	p.R99W	ENST00000481247	3/11	34	21	13	34	34	0	BTBD9,missense_variant,p.Arg40Trp,ENST00000419706,;BTBD9,missense_variant,p.Arg31Trp,ENST00000314100,;BTBD9,missense_variant,p.Arg31Trp,ENST00000497373,;BTBD9,missense_variant,p.Arg99Trp,ENST00000481247,;BTBD9,missense_variant,p.Arg31Trp,ENST00000408958,;BTBD9,missense_variant,p.Arg99Trp,ENST00000403056,;BTBD9,downstream_gene_variant,,ENST00000498633,;BTBD9,missense_variant,p.Arg31Trp,ENST00000328403,;	A	ENSG00000183826	ENST00000481247	Transcript	missense_variant	447	295	99	R/W	Cgg/Tgg	rs150015110,COSM1329713,COSM1329712	.	.	-1	BTBD9	HGNC	21228	protein_coding	YES	CCDS47418.1	ENSP00000418751	BTBD9_HUMAN	Q8N299_HUMAN,C9JVC1_HUMAN,C9J8E4_HUMAN	UPI00001C040E	.	deleterious(0.02)	unknown(0)	3/11	.	PROSITE_profiles:PS50097,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF101,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGCCCAG	by1000G	5	ESCA
NFYA	0	.	GRCh37	6	41059278	41059279	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562dupT	p.Ser188PhefsTer74	p.S188Ffs*74	ENST00000341376	7/10	32	20	12	26	26	0	NFYA,frameshift_variant,p.Ser188PhefsTer74,ENST00000341376,;NFYA,frameshift_variant,p.Ser159PhefsTer74,ENST00000353205,;OARD1,intron_variant,,ENST00000488238,;OARD1,intron_variant,,ENST00000480585,;	T	ENSG00000001167	ENST00000341376	Transcript	frameshift_variant	760-761	559-560	187	V/VX	gtt/gTtt	.	.	.	1	NFYA	HGNC	7804	protein_coding	YES	CCDS4849.1	ENSP00000345702	NFYA_HUMAN	K9JA49_HUMAN	UPI000012717C	.	.	.	7/10	.	hmmpanther:PTHR12632	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCCTGTTTCA	.	3	ESCA
TFEB	0	.	GRCh37	6	41651898	41651898	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*439A>T	.	.	ENST00000230323	10/10	25	20	5	11	11	0	TFEB,3_prime_UTR_variant,,ENST00000373033,;TFEB,3_prime_UTR_variant,,ENST00000403298,;TFEB,3_prime_UTR_variant,,ENST00000358871,;TFEB,3_prime_UTR_variant,,ENST00000420312,;TFEB,3_prime_UTR_variant,,ENST00000406563,;TFEB,3_prime_UTR_variant,,ENST00000343317,;TFEB,3_prime_UTR_variant,,ENST00000230323,;TFEB,downstream_gene_variant,,ENST00000416140,;TFEB,downstream_gene_variant,,ENST00000394283,;AL035588.1,upstream_gene_variant,,ENST00000597468,;TFEB,downstream_gene_variant,,ENST00000419396,;TFEB,downstream_gene_variant,,ENST00000419574,;TFEB,downstream_gene_variant,,ENST00000494822,;	A	ENSG00000112561	ENST00000230323	Transcript	3_prime_UTR_variant	2172	.	.	.	.	.	.	.	-1	TFEB	HGNC	11753	protein_coding	YES	CCDS4858.1	ENSP00000230323	TFEB_HUMAN	Q86WB1_HUMAN,Q709A9_HUMAN,Q709A8_HUMAN,B1AKB4_HUMAN,B1AKB2_HUMAN,B1AKB1_HUMAN,B1AKA9_HUMAN	UPI0000001615	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACCTCCTGC	.	5	ESCA
RPL7L1	0	.	GRCh37	6	42857242	42857242	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3040A>G	.	.	ENST00000493763	6/6	40	33	6	56	56	0	RPL7L1,3_prime_UTR_variant,,ENST00000493763,;RPL7L1,3_prime_UTR_variant,,ENST00000304734,;RPL7L1,downstream_gene_variant,,ENST00000602561,;RPL7L1,downstream_gene_variant,,ENST00000424341,;C6orf226,downstream_gene_variant,,ENST00000408925,;RPL7L1,downstream_gene_variant,,ENST00000483998,;RPL7L1,downstream_gene_variant,,ENST00000397415,;RPL7L1,downstream_gene_variant,,ENST00000462348,;RPL7L1,downstream_gene_variant,,ENST00000459829,;	G	ENSG00000146223	ENST00000493763	Transcript	3_prime_UTR_variant	4084	.	.	.	.	.	.	.	1	RPL7L1	HGNC	21370	protein_coding	YES	CCDS4873.1	ENSP00000418221	RL7L_HUMAN	B7Z4G0_HUMAN,A8K5J5_HUMAN	UPI00001D81E1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGTAACCTGC	.	4	ESCA
POLR1C	0	.	GRCh37	6	43488100	43488102	+	In_Frame_Del	DEL	TCC	TCC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TCC	TCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592_594delCTC	p.Leu198del	p.L198del	ENST00000372389	6/9	35	26	9	34	34	0	POLR1C,inframe_deletion,p.Leu198del,ENST00000372389,;POLR1C,inframe_deletion,p.Leu198del,ENST00000372344,;POLR1C,inframe_deletion,p.Leu198del,ENST00000304004,;XPO5,downstream_gene_variant,,ENST00000265351,;XPO5,downstream_gene_variant,,ENST00000455285,;YIPF3,upstream_gene_variant,,ENST00000506469,;YIPF3,upstream_gene_variant,,ENST00000503972,;YIPF3,upstream_gene_variant,,ENST00000372422,;YIPF3,upstream_gene_variant,,ENST00000500090,;POLR1C,downstream_gene_variant,,ENST00000423780,;POLR1C,downstream_gene_variant,,ENST00000428025,;YIPF3,upstream_gene_variant,,ENST00000511831,;RP3-337H4.9,upstream_gene_variant,,ENST00000607571,;POLR1C,non_coding_transcript_exon_variant,,ENST00000455605,;POLR1C,non_coding_transcript_exon_variant,,ENST00000488601,;POLR1C,non_coding_transcript_exon_variant,,ENST00000481352,;YIPF3,upstream_gene_variant,,ENST00000488966,;YIPF3,upstream_gene_variant,,ENST00000460903,;YIPF3,upstream_gene_variant,,ENST00000502714,;YIPF3,upstream_gene_variant,,ENST00000490447,;YIPF3,upstream_gene_variant,,ENST00000510102,;XPO5,downstream_gene_variant,,ENST00000486936,;XPO5,downstream_gene_variant,,ENST00000488195,;POLR1C,downstream_gene_variant,,ENST00000512472,;XPO5,downstream_gene_variant,,ENST00000455854,;YIPF3,upstream_gene_variant,,ENST00000455768,;YIPF3,upstream_gene_variant,,ENST00000416380,;YIPF3,upstream_gene_variant,,ENST00000460547,;	-	ENSG00000171453	ENST00000372389	Transcript	inframe_deletion	678-680	590-592	197-198	IL/I	aTCCtc/atc	.	.	.	1	POLR1C	HGNC	20194	protein_coding	YES	CCDS4901.1	ENSP00000361465	RPAC1_HUMAN	Q96HT3_HUMAN,D6RDJ3_HUMAN	UPI00001345BC	.	.	.	6/9	.	hmmpanther:PTHR11800:SF13,hmmpanther:PTHR11800,Pfam_domain:PF01000,Pfam_domain:PF01193,Gene3D:2.170.120.12,SMART_domains:SM00662,Superfamily_domains:SSF56553	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V193V|c.579G>T|4,BUFFER|p.V193V|c.579G>T|4	INDELOCATOR*|VARSCANI*|PINDEL	ATGATATCCTCATC	.	3	ESCA
GTPBP2	0	.	GRCh37	6	43596716	43596717	+	Frame_Shift_Ins	INS	-	-	G	rs756968780	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.183dupC	p.Glu62ArgfsTer3	p.E62Rfs*3	ENST00000307126	1/12	81	61	20	46	46	0	GTPBP2,frameshift_variant,p.Glu62ArgfsTer3,ENST00000452781,;GTPBP2,frameshift_variant,p.Glu62ArgfsTer3,ENST00000307126,;MAD2L1BP,upstream_gene_variant,,ENST00000451025,;GTPBP2,upstream_gene_variant,,ENST00000442748,;GTPBP2,upstream_gene_variant,,ENST00000307114,;GTPBP2,upstream_gene_variant,,ENST00000480263,;GTPBP2,upstream_gene_variant,,ENST00000476510,;	G	ENSG00000172432	ENST00000307126	Transcript	frameshift_variant	183-184	183-184	61-62	-/X	-/C	rs756968780	.	.	-1	GTPBP2	HGNC	4670	protein_coding	YES	CCDS4903.1	ENSP00000303997	GTPB2_HUMAN	.	UPI0000070C45	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CACCTCGGGGG	byFrequency	3	ESCA
SLC29A1	0	.	GRCh37	6	44201262	44201262	+	Silent	SNP	G	G	A	rs749985533	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1368G>A	p.%3D	p.V456V	ENST00000393841	14/14	45	31	14	30	30	0	SLC29A1,synonymous_variant,p.%3D,ENST00000371740,;SLC29A1,synonymous_variant,p.%3D,ENST00000371731,;SLC29A1,synonymous_variant,p.%3D,ENST00000313248,;SLC29A1,synonymous_variant,p.%3D,ENST00000371713,;SLC29A1,synonymous_variant,p.%3D,ENST00000371755,;SLC29A1,synonymous_variant,p.%3D,ENST00000393844,;SLC29A1,synonymous_variant,p.%3D,ENST00000371724,;SLC29A1,synonymous_variant,p.%3D,ENST00000393841,;SLC29A1,synonymous_variant,p.%3D,ENST00000427851,;SLC29A1,synonymous_variant,p.%3D,ENST00000371708,;SLC29A1,downstream_gene_variant,,ENST00000472176,;	A	ENSG00000112759	ENST00000393841	Transcript	synonymous_variant	1859	1368	456	V	gtG/gtA	rs749985533	.	.	1	SLC29A1	HGNC	11003	protein_coding	YES	CCDS4908.1	ENSP00000377424	S29A1_HUMAN	C8KHU2_HUMAN,C8KHU1_HUMAN	UPI0000001BCC	.	.	.	14/14	.	hmmpanther:PTHR10332,hmmpanther:PTHR10332:SF9,TIGRFAM_domain:TIGR00939,PIRSF_domain:PIRSF016379	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTGTGACA	byFrequency	5	ESCA
CLIC5	0	.	GRCh37	6	45870934	45870934	+	Missense_Mutation	SNP	C	C	T	rs372300556	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1124G>A	p.Arg375Gln	p.R375Q	ENST00000185206	6/6	32	20	11	34	34	0	CLIC5,missense_variant,p.Arg375Gln,ENST00000185206,;CLIC5,missense_variant,p.Arg216Gln,ENST00000339561,;CLIC5,non_coding_transcript_exon_variant,,ENST00000484572,;CLIC5,upstream_gene_variant,,ENST00000487396,;	T	ENSG00000112782	ENST00000185206	Transcript	missense_variant	1277	1124	375	R/Q	cGg/cAg	rs372300556	.	.	-1	CLIC5	HGNC	13517	protein_coding	YES	CCDS47438.1	ENSP00000185206	CLIC5_HUMAN	.	UPI000013C5ED	.	deleterious(0.04)	possibly_damaging(0.823)	6/6	.	PROSITE_profiles:PS50405,hmmpanther:PTHR11260:SF152,hmmpanther:PTHR11260,TIGRFAM_domain:TIGR00862,Gene3D:1.20.1050.10,Superfamily_domains:SSF47616	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTACCGCCAC	byFrequency|byCluster	5	ESCA
TDRD6	0	.	GRCh37	6	46656650	46656650	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785C>A	p.Pro262His	p.P262H	ENST00000316081	1/4	58	40	17	65	65	0	TDRD6,missense_variant,p.Pro262His,ENST00000316081,;TDRD6,missense_variant,p.Pro262His,ENST00000544460,;RP11-446F17.3,upstream_gene_variant,,ENST00000422284,;RP11-446F17.3,upstream_gene_variant,,ENST00000571590,;RP11-446F17.3,upstream_gene_variant,,ENST00000434329,;	A	ENSG00000180113	ENST00000316081	Transcript	missense_variant	785	785	262	P/H	cCc/cAc	.	.	.	1	TDRD6	HGNC	21339	protein_coding	YES	CCDS34470.1	ENSP00000346065	TDRD6_HUMAN	.	UPI0000251E8A	.	deleterious(0)	probably_damaging(1)	1/4	.	Pfam_domain:PF00567,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCCCACC	.	5	ESCA
TFAP2B	0	.	GRCh37	6	50814901	50814901	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3805delA	.	.	ENST00000393655	7/7	18	8	10	14	14	0	TFAP2B,3_prime_UTR_variant,,ENST00000393655,;TFAP2B,3_prime_UTR_variant,,ENST00000263046,;	-	ENSG00000008196	ENST00000393655	Transcript	3_prime_UTR_variant	5348	.	.	.	.	.	.	.	1	TFAP2B	HGNC	11743	protein_coding	YES	CCDS4934.2	ENSP00000377265	AP2B_HUMAN	A8K557_HUMAN	UPI000020DE90	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGGCTTAAAAAA	.	2	ESCA
DST	0	.	GRCh37	6	56335022	56335022	+	Silent	SNP	G	G	A	rs545772116	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14511C>T	p.%3D	p.G4837G	ENST00000244364	77/84	29	24	5	35	35	0	DST,synonymous_variant,p.%3D,ENST00000446842,;DST,synonymous_variant,p.%3D,ENST00000370788,;DST,synonymous_variant,p.%3D,ENST00000244364,;DST,synonymous_variant,p.%3D,ENST00000361203,;DST,synonymous_variant,p.%3D,ENST00000370754,;DST,synonymous_variant,p.%3D,ENST00000370769,;DST,synonymous_variant,p.%3D,ENST00000421834,;DST,3_prime_UTR_variant,,ENST00000312431,;DST,downstream_gene_variant,,ENST00000523943,;DST,upstream_gene_variant,,ENST00000523292,;DST,upstream_gene_variant,,ENST00000523597,;DST,upstream_gene_variant,,ENST00000482156,;DST,downstream_gene_variant,,ENST00000492944,;DST,upstream_gene_variant,,ENST00000524216,;	A	ENSG00000151914	ENST00000244364	Transcript	synonymous_variant	14719	14511	4837	G	ggC/ggT	rs545772116,COSM1445274,COSM1445275	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	77/84	.	PROSITE_profiles:PS50222,PROSITE_patterns:PS00018,Pfam_domain:PF13499,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATCGCCATC	by1000G	4	ESCA
BAI3	0	.	GRCh37	6	70048831	70048831	+	Missense_Mutation	SNP	G	G	T	rs766550347	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3212G>T	p.Gly1071Val	p.G1071V	ENST00000370598	25/32	38	32	6	32	32	0	BAI3,missense_variant,p.Gly35Val,ENST00000546190,;BAI3,missense_variant,p.Gly277Val,ENST00000238918,;BAI3,missense_variant,p.Gly1071Val,ENST00000370598,;	T	ENSG00000135298	ENST00000370598	Transcript	missense_variant	4033	3212	1071	G/V	gGt/gTt	rs766550347	.	.	1	BAI3	HGNC	945	protein_coding	YES	CCDS4968.1	ENSP00000359630	BAI3_HUMAN	S4R3D0_HUMAN,B7Z1K0_HUMAN	UPI00001AE6A9	.	deleterious(0.02)	probably_damaging(0.999)	25/32	.	PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF40,hmmpanther:PTHR12011,Pfam_domain:PF00002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S1070S|c.3210C>T|3,BUFFER|p.T1073M|c.3218C>T|4	RADIA|MUTECT|MUSE|VARSCANS	TAGCGGTTTGA	.	4	ESCA
RIOK1	0	.	GRCh37	6	7404247	7404247	+	Missense_Mutation	SNP	G	G	T	rs751208156	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841G>T	p.Gly281Cys	p.G281C	ENST00000379834	9/17	42	29	12	61	61	0	RIOK1,missense_variant,p.Gly281Cys,ENST00000379834,;RIOK1,non_coding_transcript_exon_variant,,ENST00000264874,;RIOK1,non_coding_transcript_exon_variant,,ENST00000484626,;RIOK1,downstream_gene_variant,,ENST00000475351,;	T	ENSG00000124784	ENST00000379834	Transcript	missense_variant	1348	841	281	G/C	Ggt/Tgt	rs751208156	.	.	1	RIOK1	HGNC	18656	protein_coding	YES	CCDS4500.1	ENSP00000369162	RIOK1_HUMAN	Q9H2L9_HUMAN	UPI000003FDCE	.	deleterious(0.01)	probably_damaging(0.99)	9/17	.	Superfamily_domains:SSF56112,SMART_domains:SM00090,PIRSF_domain:PIRSF038147,Gene3D:3.30.200.20,Pfam_domain:PF01163,hmmpanther:PTHR10593:SF23,hmmpanther:PTHR10593	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATCGGTAAA	byFrequency	5	ESCA
KHDC3L	0	.	GRCh37	6	74073483	74073483	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554C>T	p.Ala185Val	p.A185V	ENST00000370367	3/3	93	44	49	52	52	0	KHDC3L,missense_variant,p.Ala185Val,ENST00000370367,;OOEP,downstream_gene_variant,,ENST00000370359,;OOEP,downstream_gene_variant,,ENST00000370363,;	T	ENSG00000203908	ENST00000370367	Transcript	missense_variant	607	554	185	A/V	gCt/gTt	.	.	.	1	KHDC3L	HGNC	33699	protein_coding	YES	CCDS34484.1	ENSP00000359392	KHD3L_HUMAN	.	UPI00001D8131	.	tolerated(0.1)	probably_damaging(0.936)	3/3	.	hmmpanther:PTHR19447:SF5,hmmpanther:PTHR19447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGCTGCCA	.	5	ESCA
COL12A1	0	.	GRCh37	6	75836149	75836149	+	Silent	SNP	G	G	A	rs371734128	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6378C>T	p.%3D	p.D2126D	ENST00000322507	39/66	30	13	16	26	26	0	COL12A1,synonymous_variant,p.%3D,ENST00000416123,;COL12A1,synonymous_variant,p.%3D,ENST00000322507,;COL12A1,synonymous_variant,p.%3D,ENST00000483888,;COL12A1,synonymous_variant,p.%3D,ENST00000345356,;	A	ENSG00000111799	ENST00000322507	Transcript	synonymous_variant	6688	6378	2126	D	gaC/gaT	rs371734128	.	.	-1	COL12A1	HGNC	2188	protein_coding	YES	CCDS43482.1	ENSP00000325146	COCA1_HUMAN	.	UPI000045890B	.	.	.	39/66	.	PROSITE_profiles:PS50853,hmmpanther:PTHR22992:SF23,hmmpanther:PTHR22992,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTCGTCAGA	byCluster	5	ESCA
HTR1B	0	.	GRCh37	6	78172236	78172236	+	Silent	SNP	G	G	A	rs777408306	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.885C>T	p.%3D	p.S295S	ENST00000369947	1/1	28	22	6	23	23	0	HTR1B,synonymous_variant,p.%3D,ENST00000369947,;	A	ENSG00000135312	ENST00000369947	Transcript	synonymous_variant	1255	885	295	S	tcC/tcT	rs777408306,COSM1081813	.	.	-1	HTR1B	HGNC	5287	protein_coding	YES	CCDS4986.1	ENSP00000358963	5HT1B_HUMAN	.	UPI00000007CB	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF16,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00513	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGTCGGAGAC	.	5	ESCA
DOPEY1	0	.	GRCh37	6	83819909	83819909	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560delG	p.Gly187ValfsTer21	p.G187Vfs*21	ENST00000349129	6/39	64	34	30	46	46	0	DOPEY1,frameshift_variant,p.Gly187ValfsTer21,ENST00000536812,;DOPEY1,frameshift_variant,p.Gly187ValfsTer21,ENST00000237163,;DOPEY1,frameshift_variant,p.Gly187ValfsTer21,ENST00000369739,;DOPEY1,frameshift_variant,p.Gly187ValfsTer21,ENST00000349129,;	-	ENSG00000083097	ENST00000349129	Transcript	frameshift_variant	817	557	186	W/X	tGg/tg	.	.	.	1	DOPEY1	HGNC	21194	protein_coding	YES	CCDS4996.1	ENSP00000195654	DOP1_HUMAN	.	UPI00001C1574	.	.	.	6/39	.	hmmpanther:PTHR14042:SF22,hmmpanther:PTHR14042,Pfam_domain:PF04118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCCTGTGGGGTA	.	2	ESCA
HTR1E	0	.	GRCh37	6	87726135	87726135	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1083C>T	p.%3D	p.C361C	ENST00000305344	2/2	61	37	24	62	62	0	HTR1E,synonymous_variant,p.%3D,ENST00000305344,;	T	ENSG00000168830	ENST00000305344	Transcript	synonymous_variant	1786	1083	361	C	tgC/tgT	.	.	.	1	HTR1E	HGNC	5291	protein_coding	YES	CCDS5006.1	ENSP00000307766	5HT1E_HUMAN	.	UPI000000126D	.	.	.	2/2	.	hmmpanther:PTHR24247:SF33,hmmpanther:PTHR24247,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGCCGAGA	.	5	ESCA
FUT9	0	.	GRCh37	6	96654644	96654644	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2540delT	.	.	ENST00000302103	3/3	15	8	7	17	17	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	-	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	3939	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CACCTGTTTTTT	.	2	ESCA
POU3F2	0	.	GRCh37	6	99283509	99283509	+	Missense_Mutation	SNP	G	G	A	rs773452318	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.760G>A	p.Ala254Thr	p.A254T	ENST00000328345	1/1	27	16	11	19	19	0	POU3F2,missense_variant,p.Ala254Thr,ENST00000328345,;	A	ENSG00000184486	ENST00000328345	Transcript	missense_variant	930	760	254	A/T	Gcg/Acg	rs773452318	.	.	1	POU3F2	HGNC	9215	protein_coding	YES	CCDS5040.1	ENSP00000329170	PO3F2_HUMAN	.	UPI000016A1E7	.	tolerated(0.26)	benign(0.041)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11636:SF79,hmmpanther:PTHR11636,PIRSF_domain:PIRSF002629	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGCGCGCAC	byFrequency	2	ESCA
POU3F2	0	.	GRCh37	6	99285654	99285654	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1573C>A	.	.	ENST00000328345	1/1	11	7	4	10	10	0	POU3F2,3_prime_UTR_variant,,ENST00000328345,;	A	ENSG00000184486	ENST00000328345	Transcript	3_prime_UTR_variant	3075	.	.	.	.	.	.	.	1	POU3F2	HGNC	9215	protein_coding	YES	CCDS5040.1	ENSP00000329170	PO3F2_HUMAN	.	UPI000016A1E7	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACTCCAAAC	.	2	ESCA
NYAP1	0	.	GRCh37	7	100092415	100092415	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*889A>G	.	.	ENST00000300179	7/7	29	21	7	17	17	0	NYAP1,3_prime_UTR_variant,,ENST00000423930,;NYAP1,3_prime_UTR_variant,,ENST00000300179,;NYAP1,downstream_gene_variant,,ENST00000454988,;NYAP1,downstream_gene_variant,,ENST00000489641,;NYAP1,downstream_gene_variant,,ENST00000496985,;	G	ENSG00000166924	ENST00000300179	Transcript	3_prime_UTR_variant	3574	.	.	.	.	.	.	.	1	NYAP1	HGNC	22009	protein_coding	YES	CCDS5696.1	ENSP00000300179	NYAP1_HUMAN	.	UPI00001C0A2E	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTCATGATC	.	5	ESCA
MUC17	0	.	GRCh37	7	100677782	100677782	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3085G>A	p.Gly1029Ser	p.G1029S	ENST00000306151	3/13	134	82	52	77	77	0	MUC17,missense_variant,p.Gly1029Ser,ENST00000306151,;MUC17,missense_variant,p.Gly1029Ser,ENST00000379439,;	A	ENSG00000169876	ENST00000306151	Transcript	missense_variant	3149	3085	1029	G/S	Ggt/Agt	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	benign(0.003)	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAGGTACC	.	5	ESCA
CUX1	0	.	GRCh37	7	101845168	101845168	+	Missense_Mutation	SNP	G	G	T	rs748035791	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2624G>T	p.Arg875Leu	p.R875L	ENST00000360264	18/24	95	57	37	38	38	0	CUX1,missense_variant,p.Arg762Leu,ENST00000546411,;CUX1,missense_variant,p.Arg706Leu,ENST00000556210,;CUX1,missense_variant,p.Arg842Leu,ENST00000549414,;CUX1,missense_variant,p.Arg875Leu,ENST00000360264,;CUX1,missense_variant,p.Arg864Leu,ENST00000292535,;CUX1,missense_variant,p.Arg808Leu,ENST00000550008,;CUX1,intron_variant,,ENST00000437600,;CUX1,intron_variant,,ENST00000547394,;CUX1,intron_variant,,ENST00000292538,;CUX1,intron_variant,,ENST00000425244,;CUX1,intron_variant,,ENST00000393824,;CUX1,intron_variant,,ENST00000560541,;CUX1,intron_variant,,ENST00000558836,;	T	ENSG00000257923	ENST00000360264	Transcript	missense_variant	2644	2624	875	R/L	cGg/cTg	rs748035791	.	.	1	CUX1	HGNC	2557	protein_coding	YES	CCDS56498.1	ENSP00000353401	CUX1_HUMAN	.	UPI00001AEB98	.	deleterious(0.01)	unknown(0)	18/24	.	hmmpanther:PTHR14043:SF4,hmmpanther:PTHR14043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCGGGCCG	byFrequency|byCluster	5	ESCA
DNAJC2	0	.	GRCh37	7	102964992	102964992	+	Frame_Shift_Del	DEL	T	T	-	rs772726513	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590delA	p.Asn197MetfsTer8	p.N197Mfs*8	ENST00000379263	6/17	37	25	12	13	13	0	DNAJC2,frameshift_variant,p.Asn197MetfsTer8,ENST00000249270,;DNAJC2,frameshift_variant,p.Asn197MetfsTer8,ENST00000379263,;DNAJC2,frameshift_variant,p.Asn123MetfsTer8,ENST00000454277,;DNAJC2,intron_variant,,ENST00000426036,;PMPCB,intron_variant,,ENST00000420236,;DNAJC2,3_prime_UTR_variant,,ENST00000379257,;DNAJC2,non_coding_transcript_exon_variant,,ENST00000483637,;DNAJC2,non_coding_transcript_exon_variant,,ENST00000464253,;DNAJC2,non_coding_transcript_exon_variant,,ENST00000475065,;PMPCB,intron_variant,,ENST00000444457,;DNAJC2,upstream_gene_variant,,ENST00000475090,;	-	ENSG00000105821	ENST00000379263	Transcript	frameshift_variant	841	590	197	N/X	aAt/at	rs772726513,COSM1181029,COSM1181030	.	.	-1	DNAJC2	HGNC	13192	protein_coding	YES	CCDS43628.1	ENSP00000368565	DNJC2_HUMAN	Q08AR5_HUMAN,C9IZ83_HUMAN	UPI000020F858	.	.	.	6/17	.	hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF67	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.N197fs*8|c.590delA|3,SITE|p.N197fs*8|c.590delA|3	INDELOCATOR|VARSCANI	GGAACATTTTTT	.	2	ESCA
LHFPL3	0	.	GRCh37	7	104548840	104548840	+	3'UTR	DEL	A	A	-	rs550279684,rs139211927	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2187delA	.	.	ENST00000535008	5/5	29	21	8	11	11	0	LHFPL3,3_prime_UTR_variant,,ENST00000535008,;LHFPL3,downstream_gene_variant,,ENST00000401970,;LHFPL3,downstream_gene_variant,,ENST00000424859,;LHFPL3,downstream_gene_variant,,ENST00000543266,;RN7SL8P,upstream_gene_variant,,ENST00000461771,;	-	ENSG00000187416	ENST00000535008	Transcript	3_prime_UTR_variant	3013	.	.	.	.	rs550279684,rs139211927	.	.	1	LHFPL3	HGNC	6589	protein_coding	YES	.	ENSP00000444350	.	F5GZM2_HUMAN	UPI0002065540	.	.	.	5/5	.	.	T:0.0004	T:0.0008	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTTTTAAAAAA	byFrequency|byCluster|by1000G	2	ESCA
KMT2E	0	.	GRCh37	7	104731836	104731836	+	Intron	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1722+75G>T	.	.	ENST00000311117	.	195	146	49	80	80	0	KMT2E,missense_variant,p.Trp599Cys,ENST00000476671,;KMT2E,intron_variant,,ENST00000334914,;KMT2E,intron_variant,,ENST00000257745,;KMT2E,intron_variant,,ENST00000311117,;KMT2E,intron_variant,,ENST00000334877,;KMT2E,downstream_gene_variant,,ENST00000478990,;KMT2E,intron_variant,,ENST00000334884,;KMT2E,downstream_gene_variant,,ENST00000482560,;	T	ENSG00000005483	ENST00000311117	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KMT2E	HGNC	18541	protein_coding	YES	CCDS34723.1	ENSP00000312379	KMT2E_HUMAN	O95038_HUMAN,C9JQ68_HUMAN,C9JNE1_HUMAN	UPI0000074133	.	.	.	.	15/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATGGGCTTT	.	5	ESCA
DLD	0	.	GRCh37	7	107557313	107557313	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.950C>A	p.Pro317His	p.P317H	ENST00000205402	10/14	144	113	31	51	51	0	DLD,missense_variant,p.Pro317His,ENST00000205402,;DLD,missense_variant,p.Pro269His,ENST00000437604,;DLD,missense_variant,p.Pro294His,ENST00000440410,;DLD,missense_variant,p.Pro218His,ENST00000537148,;DLD,missense_variant,p.Pro317His,ENST00000417551,;DLD,3_prime_UTR_variant,,ENST00000415325,;DLD,downstream_gene_variant,,ENST00000451081,;	A	ENSG00000091140	ENST00000205402	Transcript	missense_variant	1231	950	317	P/H	cCc/cAc	.	.	.	1	DLD	HGNC	2898	protein_coding	YES	CCDS5749.1	ENSP00000205402	DLDH_HUMAN	B4DHG0_HUMAN	UPI0000072725	.	deleterious(0)	probably_damaging(0.999)	10/14	.	Prints_domain:PR00411,Prints_domain:PR00368,Superfamily_domains:SSF51905,Gene3D:3.50.50.60,TIGRFAM_domain:TIGR01350,Pfam_domain:PF07992,hmmpanther:PTHR22912:SF20,hmmpanther:PTHR22912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGACCCTTTA	.	5	ESCA
C7orf60	0	.	GRCh37	7	112460529	112460529	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1270delT	.	.	ENST00000297145	5/5	30	22	8	25	25	0	C7orf60,3_prime_UTR_variant,,ENST00000297145,;C7orf60,downstream_gene_variant,,ENST00000432572,;C7orf60,downstream_gene_variant,,ENST00000485446,;	-	ENSG00000164603	ENST00000297145	Transcript	3_prime_UTR_variant	2654	.	.	.	.	.	.	.	-1	C7orf60	HGNC	26475	protein_coding	YES	CCDS43634.1	ENSP00000297145	BMT2_HUMAN	.	UPI000020F946	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CACTTGAAAAAA	.	2	ESCA
GPER1	0	.	GRCh37	7	1131884	1131884	+	Missense_Mutation	SNP	G	G	A	rs775268794	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520G>A	p.Ala174Thr	p.A174T	ENST00000397092	3/3	66	46	20	33	33	0	GPER1,missense_variant,p.Ala174Thr,ENST00000297469,;GPER1,missense_variant,p.Ala174Thr,ENST00000397092,;GPER1,missense_variant,p.Ala174Thr,ENST00000397088,;GPER1,missense_variant,p.Ala174Thr,ENST00000401670,;C7orf50,intron_variant,,ENST00000397100,;C7orf50,intron_variant,,ENST00000357429,;C7orf50,intron_variant,,ENST00000397098,;C7orf50,intron_variant,,ENST00000491163,;GPER1,downstream_gene_variant,,ENST00000413368,;C7orf50,intron_variant,,ENST00000488073,;	A	ENSG00000164850	ENST00000397092	Transcript	missense_variant	1404	520	174	A/T	Gcc/Acc	rs775268794	.	.	1	GPER1	HGNC	4485	protein_coding	YES	CCDS5322.1	ENSP00000380281	GPER1_HUMAN	C9J3W2_HUMAN	UPI00000503F2	.	deleterious(0.03)	possibly_damaging(0.899)	3/3	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF00001,hmmpanther:PTHR24226,hmmpanther:PTHR24226:SF2,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACCACGCCCGG	byFrequency	4	ESCA
MET	0	.	GRCh37	7	116340117	116340117	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.979G>A	p.Ala327Thr	p.A327T	ENST00000318493	2/21	57	35	21	40	40	0	MET,missense_variant,p.Ala327Thr,ENST00000318493,;MET,missense_variant,p.Ala327Thr,ENST00000397752,;MET,missense_variant,p.Ala327Thr,ENST00000436117,;MET,downstream_gene_variant,,ENST00000456159,;	A	ENSG00000105976	ENST00000318493	Transcript	missense_variant	1166	979	327	A/T	Gcc/Acc	.	.	.	1	MET	HGNC	7029	protein_coding	YES	CCDS47689.1	ENSP00000317272	MET_HUMAN	Q9UEJ3_HUMAN,B4DPY6_HUMAN	UPI000014033E	.	tolerated(0.11)	benign(0.021)	2/21	.	PROSITE_profiles:PS51004,Gene3D:2.130.10.10,Pfam_domain:PF01403,PIRSF_domain:PIRSF000617,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGGCCCAG	.	5	ESCA
GPR37	0	.	GRCh37	7	124386623	124386623	+	Missense_Mutation	SNP	G	G	A	rs200937236	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1798C>T	p.Arg600Cys	p.R600C	ENST00000303921	2/2	33	17	16	28	28	0	GPR37,missense_variant,p.Arg600Cys,ENST00000303921,;	A	ENSG00000170775	ENST00000303921	Transcript	missense_variant	2449	1798	600	R/C	Cgc/Tgc	rs200937236,COSM2767913	.	.	-1	GPR37	HGNC	4494	protein_coding	YES	CCDS5792.1	ENSP00000306449	GPR37_HUMAN	.	UPI0000001C92	.	deleterious(0.01)	benign(0.363)	2/2	.	hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF32	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGGCGTATGG	byCluster	5	ESCA
ARL4A	0	.	GRCh37	7	12727191	12727191	+	5'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-252A>G	.	.	ENST00000396663	1/2	30	25	5	22	22	0	ARL4A,5_prime_UTR_variant,,ENST00000396663,;ARL4A,5_prime_UTR_variant,,ENST00000439721,;ARL4A,intron_variant,,ENST00000396664,;ARL4A,intron_variant,,ENST00000396662,;ARL4A,intron_variant,,ENST00000356797,;ARL4A,upstream_gene_variant,,ENST00000404894,;CTD-2320J21.1,downstream_gene_variant,,ENST00000604949,;	G	ENSG00000122644	ENST00000396663	Transcript	5_prime_UTR_variant	231	.	.	.	.	.	.	.	1	ARL4A	HGNC	695	protein_coding	YES	CCDS5359.1	ENSP00000379898	ARL4A_HUMAN	C9J7Q9_HUMAN	UPI000005273E	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATCATGAGT	.	4	ESCA
LRRC4	0	.	GRCh37	7	127668233	127668233	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*499delA	.	.	ENST00000249363	2/2	45	31	14	25	25	0	LRRC4,3_prime_UTR_variant,,ENST00000249363,;SND1,intron_variant,,ENST00000354725,;SND1,intron_variant,,ENST00000486037,;LRRC4,downstream_gene_variant,,ENST00000494115,;LRRC4,downstream_gene_variant,,ENST00000478726,;LRRC4,downstream_gene_variant,,ENST00000476782,;SND1,intron_variant,,ENST00000484767,;SND1,intron_variant,,ENST00000470723,;	-	ENSG00000128594	ENST00000249363	Transcript	3_prime_UTR_variant	2719	.	.	.	.	.	.	.	-1	LRRC4	HGNC	15586	protein_coding	YES	CCDS5799.1	ENSP00000249363	LRRC4_HUMAN	C9JA92_HUMAN,C9J7V8_HUMAN,C9J7K7_HUMAN	UPI0000049DF3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGGTGCTTTTTT	.	2	ESCA
FLNC	0	.	GRCh37	7	128498203	128498203	+	Missense_Mutation	SNP	G	G	A	rs760857362	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7922G>A	p.Arg2641Gln	p.R2641Q	ENST00000325888	47/48	118	77	41	55	55	0	FLNC,missense_variant,p.Arg2641Gln,ENST00000325888,;FLNC,missense_variant,p.Arg2608Gln,ENST00000346177,;ATP6V1F,upstream_gene_variant,,ENST00000492758,;ATP6V1F,upstream_gene_variant,,ENST00000249289,;RP11-309L24.2,intron_variant,,ENST00000469965,;KCP,downstream_gene_variant,,ENST00000492679,;	A	ENSG00000128591	ENST00000325888	Transcript	missense_variant	8183	7922	2641	R/Q	cGg/cAg	rs760857362	.	.	1	FLNC	HGNC	3756	protein_coding	YES	CCDS43644.1	ENSP00000327145	FLNC_HUMAN	Q59H94_HUMAN,B3KM41_HUMAN	UPI000006DE6D	.	tolerated(0.07)	possibly_damaging(0.768)	47/48	.	Superfamily_domains:SSF81296,SMART_domains:SM00557,Gene3D:2.60.40.10,Pfam_domain:PF00630,hmmpanther:PTHR11915:SF173,hmmpanther:PTHR11915,PROSITE_profiles:PS50194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTCGGGGCC	byFrequency	5	ESCA
SLC35B4	0	.	GRCh37	7	133977009	133977009	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2576delA	.	.	ENST00000378509	10/10	14	4	10	13	13	0	SLC35B4,3_prime_UTR_variant,,ENST00000378509,;SLC35B4,downstream_gene_variant,,ENST00000466599,;SLC35B4,downstream_gene_variant,,ENST00000416907,;	-	ENSG00000205060	ENST00000378509	Transcript	3_prime_UTR_variant	3872	.	.	.	.	.	.	.	-1	SLC35B4	HGNC	20584	protein_coding	YES	CCDS34756.1	ENSP00000367770	S35B4_HUMAN	.	UPI00000377B5	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACGTATTTTTT	.	2	ESCA
ZC3HAV1	0	.	GRCh37	7	138749694	138749695	+	Frame_Shift_Del	DEL	AG	AG	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1923_1924delCT	p.Tyr642SerfsTer18	p.Y642Sfs*18	ENST00000242351	8/13	49	41	8	29	29	0	ZC3HAV1,frameshift_variant,p.Tyr642SerfsTer18,ENST00000471652,;ZC3HAV1,frameshift_variant,p.Tyr764SerfsTer18,ENST00000464606,;ZC3HAV1,frameshift_variant,p.Tyr207SerfsTer18,ENST00000460845,;ZC3HAV1,frameshift_variant,p.Tyr642SerfsTer18,ENST00000242351,;	-	ENSG00000105939	ENST00000242351	Transcript	frameshift_variant	2240-2241	1923-1924	641-642	LY/LX	ctCTat/ctat	.	.	.	-1	ZC3HAV1	HGNC	23721	protein_coding	YES	CCDS5851.1	ENSP00000242351	ZCCHV_HUMAN	.	UPI00001612AE	.	.	.	8/13	.	PROSITE_profiles:PS50918,hmmpanther:PTHR14453,hmmpanther:PTHR14453:SF49,Superfamily_domains:SSF117839	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	ATTGATAGAGAGA	.	2	ESCA
TRBV6-4	0	.	GRCh37	7	142250828	142250828	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.219C>T	p.%3D	p.T73T	ENST00000390360	2/2	37	23	13	28	28	0	TRBV6-4,synonymous_variant,p.%3D,ENST00000390360,;TRBV7-3,upstream_gene_variant,,ENST00000390361,;	A	ENSG00000211713	ENST00000390360	Transcript	synonymous_variant	240	219	73	T	acC/acT	.	.	.	-1	TRBV6-4	HGNC	12229	TR_V_gene	YES	.	ENSP00000374883	.	A0A542_HUMAN	UPI00001140DC	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23268:SF18,hmmpanther:PTHR23268,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTGGTACC	.	5	ESCA
TRBC2	0	.	GRCh37	7	142499034	142499034	+	Missense_Mutation	SNP	C	C	T	rs549814570,rs61732509	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310C>T	p.Ser104Leu	p.S104L	ENST00000466254	1/4	85	67	17	44	44	0	TRBC2,missense_variant,p.Ser104Leu,ENST00000466254,;TRBJ2-4,downstream_gene_variant,,ENST00000390416,;TRBJ2-5,downstream_gene_variant,,ENST00000390417,;TRBJ2-2P,downstream_gene_variant,,ENST00000390414,;TRBJ2-3,downstream_gene_variant,,ENST00000390415,;TRBJ2-7,downstream_gene_variant,,ENST00000390419,;TRBJ2-6,downstream_gene_variant,,ENST00000390418,;TRBJ2-2,downstream_gene_variant,,ENST00000390413,;TRBJ2-1,downstream_gene_variant,,ENST00000390412,;	T	ENSG00000211772	ENST00000466254	Transcript	missense_variant	310	311	104	S/L	tCg/tTg	rs549814570,rs61732509	.	.	1	TRBC2	HGNC	12157	TR_C_gene	YES	.	ENSP00000417300	TRBC2_HUMAN	.	UPI0000F30372	.	deleterious_low_confidence(0.01)	benign(0.217)	1/4	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23268,hmmpanther:PTHR23268:SF15,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726	T:0.0004	T:0,T:0	T:0,T:0	.	T:0.001,T:0.001	T:0.001,T:0.001	T:0,T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTCGGAGA	by1000G	5	ESCA
OR2F1	0	.	GRCh37	7	143657236	143657236	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.173C>T	p.Pro58Leu	p.P58L	ENST00000392899	1/1	185	112	73	97	97	0	OR2F1,missense_variant,p.Pro58Leu,ENST00000392899,;RP4-669B10.3,intron_variant,,ENST00000470988,;RP4-669B10.3,downstream_gene_variant,,ENST00000466281,;	T	ENSG00000213215	ENST00000392899	Transcript	missense_variant	210	173	58	P/L	cCc/cTc	.	.	.	1	OR2F1	HGNC	8246	protein_coding	YES	CCDS5887.1	ENSP00000376633	OR2F1_HUMAN	.	UPI000003FF87	.	deleterious(0)	probably_damaging(1)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF116,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCCCATGT	.	5	ESCA
ZNF746	0	.	GRCh37	7	149172342	149172342	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1071T>C	p.%3D	p.G357G	ENST00000458143	7/7	88	58	30	37	37	0	ZNF746,synonymous_variant,p.%3D,ENST00000340622,;ZNF746,synonymous_variant,p.%3D,ENST00000458143,;ZNF746,downstream_gene_variant,,ENST00000471735,;	G	ENSG00000181220	ENST00000458143	Transcript	synonymous_variant	1342	1071	357	G	ggT/ggC	.	.	.	-1	ZNF746	HGNC	21948	protein_coding	YES	CCDS55180.1	ENSP00000395007	ZN746_HUMAN	Q96N48_HUMAN	UPI00015DA840	.	.	.	7/7	.	hmmpanther:PTHR24402:SF13,hmmpanther:PTHR24402	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTCACCCAT	.	5	ESCA
KRBA1	0	.	GRCh37	7	149421922	149421922	+	Missense_Mutation	SNP	T	T	C	rs777640969	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1108T>C	p.Trp370Arg	p.W370R	ENST00000255992	9/18	73	51	22	52	52	0	KRBA1,missense_variant,p.Trp370Arg,ENST00000485033,;KRBA1,missense_variant,p.Trp370Arg,ENST00000319551,;KRBA1,missense_variant,p.Trp370Arg,ENST00000255992,;KRBA1,downstream_gene_variant,,ENST00000486744,;KRBA1,downstream_gene_variant,,ENST00000497895,;KRBA1,downstream_gene_variant,,ENST00000467333,;KRBA1,non_coding_transcript_exon_variant,,ENST00000479560,;KRBA1,non_coding_transcript_exon_variant,,ENST00000466546,;KRBA1,missense_variant,p.Trp327Arg,ENST00000496259,;KRBA1,non_coding_transcript_exon_variant,,ENST00000496080,;	C	ENSG00000133619	ENST00000255992	Transcript	missense_variant	1507	1108	370	W/R	Tgg/Cgg	rs777640969	.	.	1	KRBA1	HGNC	22228	protein_coding	YES	.	ENSP00000255992	.	C9J5U6_HUMAN,C4P1W5_HUMAN	UPI000049E0A4	.	deleterious(0)	benign(0.183)	9/18	.	hmmpanther:PTHR22740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCTGGGGC	byFrequency	5	ESCA
NOS3	0	.	GRCh37	7	150707781	150707783	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2785_2787delCTC	p.Leu929del	p.L929del	ENST00000297494	22/27	81	55	26	26	26	0	NOS3,inframe_deletion,p.Leu723del,ENST00000461406,;NOS3,inframe_deletion,p.Leu929del,ENST00000297494,;NOS3,inframe_deletion,p.Leu223del,ENST00000475017,;ATG9B,downstream_gene_variant,,ENST00000444312,;ATG9B,downstream_gene_variant,,ENST00000605938,;ATG9B,downstream_gene_variant,,ENST00000377974,;NOS3,non_coding_transcript_exon_variant,,ENST00000477227,;NOS3,non_coding_transcript_exon_variant,,ENST00000468293,;ATG9B,downstream_gene_variant,,ENST00000476282,;ATG9B,downstream_gene_variant,,ENST00000498521,;ATG9B,downstream_gene_variant,,ENST00000464855,;ATG9B,downstream_gene_variant,,ENST00000494791,;ATG9B,downstream_gene_variant,,ENST00000473698,;NOS3,downstream_gene_variant,,ENST00000473057,;ATG9B,downstream_gene_variant,,ENST00000486407,;ATG9B,downstream_gene_variant,,ENST00000471797,;ATG9B,downstream_gene_variant,,ENST00000404733,;NOS3,upstream_gene_variant,,ENST00000475454,;ATG9B,downstream_gene_variant,,ENST00000469530,;	-	ENSG00000164867	ENST00000297494	Transcript	inframe_deletion	3139-3141	2782-2784	928	L/-	CTC/-	.	.	.	1	NOS3	HGNC	7876	protein_coding	YES	CCDS5912.1	ENSP00000297494	NOS3_HUMAN	Q96P37_HUMAN,Q96J98_HUMAN,O14937_HUMAN,E7ESA7_HUMAN	UPI000013E417	.	.	.	22/27	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF66,Pfam_domain:PF00667,Gene3D:1.20.990.10,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF63380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCACTGCTCCTCAC	.	3	ESCA
AC005631.1	0	.	GRCh37	7	152139920	152139920	+	3'Flank	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000408527	.	43	23	20	20	20	0	AC005631.1,downstream_gene_variant,,ENST00000408527,;FABP5P3,non_coding_transcript_exon_variant,,ENST00000477993,;FABP5P3,non_coding_transcript_exon_variant,,ENST00000437960,;CCT8L1P,upstream_gene_variant,,ENST00000465400,;CCT8L1P,upstream_gene_variant,,ENST00000021776,;	G	ENSG00000221454	ENST00000408527	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3527	1	AC005631.1	Clone_based_ensembl_gene	.	miRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCAGGAGT	.	5	ESCA
MEOX2	0	.	GRCh37	7	15652021	15652021	+	Silent	SNP	C	C	T	rs777058351	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.906G>A	p.%3D	p.A302A	ENST00000262041	3/3	96	88	8	58	58	0	MEOX2,synonymous_variant,p.%3D,ENST00000262041,;	T	ENSG00000106511	ENST00000262041	Transcript	synonymous_variant	1316	906	302	A	gcG/gcA	rs777058351,COSM181641	.	.	-1	MEOX2	HGNC	7014	protein_coding	YES	CCDS34605.1	ENSP00000262041	MEOX2_HUMAN	Q6FHY5_HUMAN,A4D127_HUMAN	UPI000013D247	.	.	.	3/3	.	hmmpanther:PTHR24328:SF1,hmmpanther:PTHR24328	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A302A|c.906G>A|3	MUTECT|MUSE|VARSCANS	AAGTGCGCATG	.	3	ESCA
TMEM184A	0	.	GRCh37	7	1582758	1582758	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3830T>C	.	.	ENST00000297477	9/9	43	15	27	28	28	0	TMEM184A,3_prime_UTR_variant,,ENST00000297477,;MAFK,downstream_gene_variant,,ENST00000343242,;MAFK,downstream_gene_variant,,ENST00000406174,;TMEM184A,downstream_gene_variant,,ENST00000449955,;TMEM184A,downstream_gene_variant,,ENST00000421996,;TMEM184A,downstream_gene_variant,,ENST00000319018,;TMEM184A,downstream_gene_variant,,ENST00000468535,;MAFK,downstream_gene_variant,,ENST00000403150,;AC093734.1,downstream_gene_variant,,ENST00000540816,;	G	ENSG00000164855	ENST00000297477	Transcript	3_prime_UTR_variant	5389	.	.	.	.	.	.	.	-1	TMEM184A	HGNC	28797	protein_coding	YES	CCDS43537.1	ENSP00000297477	T184A_HUMAN	C9JKG9_HUMAN,C9JDD9_HUMAN,C9J4I0_HUMAN	UPI000013E413	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGACCCTG	.	5	ESCA
HDAC9	0	.	GRCh37	7	18674336	18674336	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.883T>C	p.Ser295Pro	p.S295P	ENST00000441542	7/25	124	102	22	76	76	0	HDAC9,missense_variant,p.Ser251Pro,ENST00000401921,;HDAC9,missense_variant,p.Ser292Pro,ENST00000405010,;HDAC9,missense_variant,p.Ser248Pro,ENST00000428307,;HDAC9,missense_variant,p.Ser295Pro,ENST00000441542,;HDAC9,missense_variant,p.Ser290Pro,ENST00000417496,;HDAC9,missense_variant,p.Ser279Pro,ENST00000406072,;HDAC9,missense_variant,p.Ser292Pro,ENST00000406451,;HDAC9,missense_variant,p.Ser264Pro,ENST00000456174,;HDAC9,missense_variant,p.Ser292Pro,ENST00000432645,;HDAC9,missense_variant,p.Ser215Pro,ENST00000524023,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;	C	ENSG00000048052	ENST00000441542	Transcript	missense_variant	883	883	295	S/P	Tcg/Ccg	.	.	.	1	HDAC9	HGNC	14065	protein_coding	YES	CCDS47553.1	ENSP00000408617	HDAC9_HUMAN	Q8N926_HUMAN,Q75N15_HUMAN,Q75N14_HUMAN,Q75N10_HUMAN,C9JLX1_HUMAN,C9J835_HUMAN,C9J1W4_HUMAN,C9IZS0_HUMAN	UPI000019AB75	.	tolerated(0.31)	benign(0.001)	7/25	.	hmmpanther:PTHR10625:SF116,hmmpanther:PTHR10625,PIRSF_domain:PIRSF037911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTTCGGTT	.	5	ESCA
ITGB8	0	.	GRCh37	7	20451644	20451644	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2032delT	.	.	ENST00000222573	14/14	33	27	6	21	21	0	ITGB8,3_prime_UTR_variant,,ENST00000222573,;ITGB8,downstream_gene_variant,,ENST00000537992,;	-	ENSG00000105855	ENST00000222573	Transcript	3_prime_UTR_variant	5018	.	.	.	.	.	.	.	1	ITGB8	HGNC	6163	protein_coding	YES	CCDS5370.1	ENSP00000222573	ITB8_HUMAN	B4DHD4_HUMAN	UPI000012DA14	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AATATCTTTTTT	.	2	ESCA
EIF3B	0	.	GRCh37	7	2419847	2419847	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*23C>A	.	.	ENST00000360876	19/19	22	14	7	13	13	0	EIF3B,3_prime_UTR_variant,,ENST00000360876,;EIF3B,intron_variant,,ENST00000397011,;AC004840.8,upstream_gene_variant,,ENST00000443103,;EIF3B,non_coding_transcript_exon_variant,,ENST00000465670,;EIF3B,non_coding_transcript_exon_variant,,ENST00000475415,;EIF3B,intron_variant,,ENST00000468611,;EIF3B,downstream_gene_variant,,ENST00000494658,;	A	ENSG00000106263	ENST00000360876	Transcript	3_prime_UTR_variant	2524	.	.	.	.	.	.	.	1	EIF3B	HGNC	3280	protein_coding	YES	CCDS5332.1	ENSP00000354125	EIF3B_HUMAN	Q86UM1_HUMAN,C9JQN7_HUMAN	UPI000013F934	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGGACTCCGC	.	2	ESCA
CHST12	0	.	GRCh37	7	2474043	2474043	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*524C>A	.	.	ENST00000258711	2/2	75	62	12	30	30	0	CHST12,3_prime_UTR_variant,,ENST00000258711,;CHST12,downstream_gene_variant,,ENST00000432336,;AC004840.9,upstream_gene_variant,,ENST00000313156,;	A	ENSG00000136213	ENST00000258711	Transcript	3_prime_UTR_variant	1904	.	.	.	.	.	.	.	1	CHST12	HGNC	17423	protein_coding	YES	CCDS5333.1	ENSP00000258711	CHSTC_HUMAN	C9J991_HUMAN	UPI000004C65C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCTAGGA	.	5	ESCA
AC005013.5	0	.	GRCh37	7	28996482	28996482	+	5'Flank	DEL	G	G	-	rs761449491	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000436594	.	99	74	25	20	20	0	AC005013.5,upstream_gene_variant,,ENST00000436594,;TRIL,non_coding_transcript_exon_variant,,ENST00000322982,;AC005013.1,non_coding_transcript_exon_variant,,ENST00000539664,;	-	ENSG00000228421	ENST00000436594	Transcript	upstream_gene_variant	.	.	.	.	.	rs761449491	.	801	1	AC005013.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGGCCGGGGGG	byFrequency	3	ESCA
KBTBD2	0	.	GRCh37	7	32914666	32914666	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274G>A	p.Gly92Ser	p.G92S	ENST00000304056	3/4	119	72	47	83	83	0	KBTBD2,missense_variant,p.Gly92Ser,ENST00000304056,;AVL9,intron_variant,,ENST00000404479,;KBTBD2,downstream_gene_variant,,ENST00000423022,;KBTBD2,downstream_gene_variant,,ENST00000452926,;KBTBD2,downstream_gene_variant,,ENST00000453627,;KBTBD2,downstream_gene_variant,,ENST00000424468,;KBTBD2,non_coding_transcript_exon_variant,,ENST00000485611,;KBTBD2,non_coding_transcript_exon_variant,,ENST00000477129,;	T	ENSG00000170852	ENST00000304056	Transcript	missense_variant	974	274	92	G/S	Ggt/Agt	.	.	.	-1	KBTBD2	HGNC	21751	protein_coding	YES	CCDS34614.1	ENSP00000302586	KBTB2_HUMAN	C9JZ29_HUMAN,C9JI11_HUMAN	UPI0000036156	.	tolerated(0.86)	benign(0.138)	3/4	.	PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF124,hmmpanther:PTHR24412,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,PIRSF_domain:PIRSF037037,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTACCCGTGT	.	5	ESCA
EEPD1	0	.	GRCh37	7	36194797	36194797	+	Silent	SNP	A	A	G	rs369820285	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864A>G	p.%3D	p.T288T	ENST00000242108	2/8	35	30	5	20	20	0	EEPD1,synonymous_variant,p.%3D,ENST00000242108,;EEPD1,synonymous_variant,p.%3D,ENST00000534978,;	G	ENSG00000122547	ENST00000242108	Transcript	synonymous_variant	1582	864	288	T	acA/acG	rs369820285	.	.	1	EEPD1	HGNC	22223	protein_coding	YES	CCDS34619.1	ENSP00000242108	EEPD1_HUMAN	.	UPI000020ED9D	.	.	.	2/8	.	Superfamily_domains:SSF56219,Gene3D:3.60.10.10,Pfam_domain:PF03372,hmmpanther:PTHR21180,hmmpanther:PTHR21180:SF32	.	.	.	.	.	.	.	G:0.0005	G:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGACACTCCT	byFrequency|byCluster	4	ESCA
ELMO1	0	.	GRCh37	7	36894043	36894043	+	3'UTR	DEL	A	A	-	rs193274930	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1113delT	.	.	ENST00000310758	22/22	30	19	11	19	19	0	ELMO1,3_prime_UTR_variant,,ENST00000396045,;ELMO1,3_prime_UTR_variant,,ENST00000310758,;ELMO1,3_prime_UTR_variant,,ENST00000341056,;ELMO1,downstream_gene_variant,,ENST00000442504,;ELMO1,downstream_gene_variant,,ENST00000396040,;ELMO1,downstream_gene_variant,,ENST00000448602,;ELMO1,downstream_gene_variant,,ENST00000487843,;ELMO1,downstream_gene_variant,,ENST00000497024,;	-	ENSG00000155849	ENST00000310758	Transcript	3_prime_UTR_variant	3945	.	.	.	.	rs193274930	.	.	-1	ELMO1	HGNC	16286	protein_coding	YES	CCDS5449.1	ENSP00000312185	ELMO1_HUMAN	C9JIW2_HUMAN,C9JB20_HUMAN,C9J5X3_HUMAN,B4DJV6_HUMAN,A4D1X5_HUMAN	UPI000006F687	.	.	.	22/22	.	.	T:0.0014	T:0	T:0.0029	.	T:0	T:0.003	T:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATAATTAAAAAA	byFrequency|by1000G	2	ESCA
GPR141	0	.	GRCh37	7	37780310	37780310	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315C>G	p.Phe105Leu	p.F105L	ENST00000447769	4/4	66	41	25	35	35	0	GPR141,missense_variant,p.Phe105Leu,ENST00000334425,;GPR141,missense_variant,p.Phe105Leu,ENST00000447769,;EPDR1,intron_variant,,ENST00000476620,;GPR141,downstream_gene_variant,,ENST00000450180,;GPR141,intron_variant,,ENST00000461610,;	G	ENSG00000187037	ENST00000447769	Transcript	missense_variant	604	315	105	F/L	ttC/ttG	.	.	.	1	GPR141	HGNC	19997	protein_coding	YES	CCDS5451.1	ENSP00000390410	GP141_HUMAN	C9JDP7_HUMAN	UPI000004B92B	.	deleterious(0.01)	possibly_damaging(0.841)	4/4	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF0,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATTCTATGT	.	5	ESCA
RALA	0	.	GRCh37	7	39745913	39745913	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69G>T	.	.	ENST00000005257	5/5	33	28	5	28	28	0	RALA,3_prime_UTR_variant,,ENST00000005257,;AC004837.5,upstream_gene_variant,,ENST00000435766,;RALA,non_coding_transcript_exon_variant,,ENST00000468201,;RALA,downstream_gene_variant,,ENST00000466491,;RALA,downstream_gene_variant,,ENST00000434466,;	T	ENSG00000006451	ENST00000005257	Transcript	3_prime_UTR_variant	1070	.	.	.	.	.	.	.	1	RALA	HGNC	9839	protein_coding	YES	CCDS5460.1	ENSP00000005257	RALA_HUMAN	C9JPE8_HUMAN	UPI0000001C8F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGAAGGCTTA	.	2	ESCA
GLI3	0	.	GRCh37	7	42085011	42085011	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.798C>T	p.%3D	p.I266I	ENST00000395925	6/15	96	63	33	50	50	0	GLI3,synonymous_variant,p.%3D,ENST00000395925,;GLI3,downstream_gene_variant,,ENST00000448703,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,;	A	ENSG00000106571	ENST00000395925	Transcript	synonymous_variant	883	798	266	I	atC/atT	.	.	.	-1	GLI3	HGNC	4319	protein_coding	YES	CCDS5465.1	ENSP00000379258	GLI3_HUMAN	C9J9N4_HUMAN	UPI000020EE4C	.	.	.	6/15	.	hmmpanther:PTHR19818:SF5,hmmpanther:PTHR19818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTGGATGGC	.	5	ESCA
STK17A	0	.	GRCh37	7	43647973	43647973	+	Missense_Mutation	SNP	C	C	T	rs770356144	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538C>T	p.Arg180Cys	p.R180C	ENST00000319357	3/7	61	39	22	40	40	0	STK17A,missense_variant,p.Arg180Cys,ENST00000319357,;STK17A,non_coding_transcript_exon_variant,,ENST00000462448,;COA1,downstream_gene_variant,,ENST00000415076,;COA1,downstream_gene_variant,,ENST00000446564,;COA1,downstream_gene_variant,,ENST00000446330,;	T	ENSG00000164543	ENST00000319357	Transcript	missense_variant	717	538	180	R/C	Cgt/Tgt	rs770356144	.	.	1	STK17A	HGNC	11395	protein_coding	YES	CCDS5470.1	ENSP00000319192	ST17A_HUMAN	Q86UI9_HUMAN,Q75MK4_HUMAN	UPI00001405A1	.	tolerated(0.08)	benign(0)	3/7	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24342,hmmpanther:PTHR24342:SF6,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACTCGTGAT	byFrequency	5	ESCA
BLVRA	0	.	GRCh37	7	43846645	43846645	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.702G>T	p.Lys234Asn	p.K234N	ENST00000402924	9/9	44	27	16	37	37	0	BLVRA,missense_variant,p.Lys234Asn,ENST00000265523,;BLVRA,missense_variant,p.Lys234Asn,ENST00000402924,;BLVRA,downstream_gene_variant,,ENST00000486984,;	T	ENSG00000106605	ENST00000402924	Transcript	missense_variant	865	702	234	K/N	aaG/aaT	.	.	.	1	BLVRA	HGNC	1062	protein_coding	YES	CCDS5472.1	ENSP00000385757	BIEA_HUMAN	C9J1E1_HUMAN	UPI0000126937	.	tolerated(0.06)	possibly_damaging(0.639)	9/9	.	hmmpanther:PTHR22604:SF14,hmmpanther:PTHR22604,Gene3D:3.30.360.10,Pfam_domain:PF09166,PIRSF_domain:PIRSF037032,Superfamily_domains:SSF55347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAAGTCTGG	.	5	ESCA
DBNL	0	.	GRCh37	7	44101106	44101106	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*591G>A	.	.	ENST00000468694	13/13	77	42	34	34	34	0	DBNL,3_prime_UTR_variant,,ENST00000432854,;DBNL,3_prime_UTR_variant,,ENST00000494774,;DBNL,3_prime_UTR_variant,,ENST00000468694,;DBNL,downstream_gene_variant,,ENST00000448521,;DBNL,downstream_gene_variant,,ENST00000452661,;PGAM2,downstream_gene_variant,,ENST00000297283,;DBNL,downstream_gene_variant,,ENST00000456905,;DBNL,downstream_gene_variant,,ENST00000452943,;DBNL,downstream_gene_variant,,ENST00000490734,;DBNL,downstream_gene_variant,,ENST00000440166,;AC017116.11,upstream_gene_variant,,ENST00000425727,;AC017116.11,upstream_gene_variant,,ENST00000445938,;DBNL,non_coding_transcript_exon_variant,,ENST00000497184,;DBNL,3_prime_UTR_variant,,ENST00000441840,;DBNL,non_coding_transcript_exon_variant,,ENST00000449997,;DBNL,downstream_gene_variant,,ENST00000464762,;DBNL,downstream_gene_variant,,ENST00000458579,;DBNL,downstream_gene_variant,,ENST00000485932,;DBNL,downstream_gene_variant,,ENST00000441904,;DBNL,downstream_gene_variant,,ENST00000498733,;DBNL,downstream_gene_variant,,ENST00000423561,;DBNL,downstream_gene_variant,,ENST00000429716,;DBNL,downstream_gene_variant,,ENST00000411855,;DBNL,downstream_gene_variant,,ENST00000439815,;	A	ENSG00000136279	ENST00000468694	Transcript	3_prime_UTR_variant	1938	.	.	.	.	.	.	.	1	DBNL	HGNC	2696	protein_coding	YES	CCDS47579.1	ENSP00000417653	DBNL_HUMAN	F2Z2V3_HUMAN	UPI000007147D	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGGCCAAG	.	5	ESCA
NUDCD3	0	.	GRCh37	7	44432048	44432048	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.823G>A	p.Ala275Thr	p.A275T	ENST00000355451	5/6	107	78	29	53	53	0	NUDCD3,missense_variant,p.Ala275Thr,ENST00000355451,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000338427,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000460110,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000472246,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000493613,;NUDCD3,intron_variant,,ENST00000487118,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000475952,;	T	ENSG00000015676	ENST00000355451	Transcript	missense_variant	1103	823	275	A/T	Gcc/Acc	COSM3881239	.	.	-1	NUDCD3	HGNC	22208	protein_coding	YES	CCDS5490.2	ENSP00000347626	NUDC3_HUMAN	A4D2J8_HUMAN	UPI000020EEEB	.	deleterious(0)	benign(0.07)	5/6	.	PROSITE_profiles:PS51203,hmmpanther:PTHR12356:SF16,hmmpanther:PTHR12356,Gene3D:2.60.40.790,Superfamily_domains:SSF49764	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGGCGTTCC	.	5	ESCA
NPC1L1	0	.	GRCh37	7	44578910	44578910	+	Silent	SNP	C	C	T	rs201987651	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1086G>A	p.%3D	p.P362P	ENST00000289547	2/20	38	23	15	23	23	0	NPC1L1,synonymous_variant,p.%3D,ENST00000546276,;NPC1L1,synonymous_variant,p.%3D,ENST00000381160,;NPC1L1,synonymous_variant,p.%3D,ENST00000423141,;NPC1L1,synonymous_variant,p.%3D,ENST00000289547,;	T	ENSG00000015520	ENST00000289547	Transcript	synonymous_variant	1142	1086	362	P	ccG/ccA	rs201987651	.	.	-1	NPC1L1	HGNC	7898	protein_coding	YES	CCDS5491.1	ENSP00000289547	NPCL1_HUMAN	.	UPI000013DF88	.	.	.	2/20	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF89	T:0.0004	T:0.0008	T:0	.	T:0.001	T:0	T:0	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACCGGGAT	byFrequency|byCluster|by1000G	5	ESCA
PKD1L1	0	.	GRCh37	7	47925456	47925456	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3033G>T	p.Glu1011Asp	p.E1011D	ENST00000289672	18/57	71	50	20	19	19	0	PKD1L1,missense_variant,p.Glu1011Asp,ENST00000289672,;HUS1,intron_variant,,ENST00000436444,;	A	ENSG00000158683	ENST00000289672	Transcript	missense_variant	3084	3033	1011	E/D	gaG/gaT	.	.	.	-1	PKD1L1	HGNC	18053	protein_coding	YES	CCDS34633.1	ENSP00000289672	PK1L1_HUMAN	.	UPI0000130FA9	.	tolerated(0.22)	possibly_damaging(0.831)	18/57	.	Pfam_domain:PF02010,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF32,PROSITE_profiles:PS51111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGGCTCTGT	.	5	ESCA
GRB10	0	.	GRCh37	7	50737427	50737427	+	Missense_Mutation	SNP	C	C	T	rs761493243	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496G>A	p.Ala166Thr	p.A166T	ENST00000398812	4/16	64	49	15	45	45	0	GRB10,missense_variant,p.Ala108Thr,ENST00000406641,;GRB10,missense_variant,p.Ala166Thr,ENST00000398812,;GRB10,missense_variant,p.Ala108Thr,ENST00000398810,;GRB10,missense_variant,p.Ala166Thr,ENST00000401949,;GRB10,missense_variant,p.Ala166Thr,ENST00000357271,;GRB10,missense_variant,p.Ala160Thr,ENST00000403097,;GRB10,missense_variant,p.Ala108Thr,ENST00000407526,;GRB10,missense_variant,p.Ala108Thr,ENST00000402578,;GRB10,missense_variant,p.Ala160Thr,ENST00000439599,;GRB10,missense_variant,p.Ala108Thr,ENST00000402497,;GRB10,missense_variant,p.Ala108Thr,ENST00000335866,;GRB10,downstream_gene_variant,,ENST00000439044,;	T	ENSG00000106070	ENST00000398812	Transcript	missense_variant	527	496	166	A/T	Gca/Aca	rs761493243,COSM1208836,COSM1208837	.	.	-1	GRB10	HGNC	4564	protein_coding	YES	CCDS43582.1	ENSP00000381793	GRB10_HUMAN	Q75MT1_HUMAN,Q75M93_HUMAN	UPI000012BA84	.	tolerated(0.6)	benign(0.001)	4/16	.	Superfamily_domains:SSF54236,SMART_domains:SM00314,Gene3D:3.10.20.90,hmmpanther:PTHR11243:SF4,hmmpanther:PTHR11243,PROSITE_profiles:PS50200	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTGCGGCGG	byFrequency	5	ESCA
POM121L12	0	.	GRCh37	7	53104354	53104354	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99C>T	.	.	ENST00000408890	1/1	44	31	13	18	18	0	POM121L12,3_prime_UTR_variant,,ENST00000408890,;	T	ENSG00000221900	ENST00000408890	Transcript	3_prime_UTR_variant	1006	.	.	.	.	.	.	.	1	POM121L12	HGNC	25369	protein_coding	YES	CCDS43584.1	ENSP00000386133	P1L12_HUMAN	.	UPI00001B6540	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCACGTTAT	.	5	ESCA
TNRC18	0	.	GRCh37	7	5410103	5410103	+	Silent	SNP	G	G	A	rs201136741	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4122C>T	p.%3D	p.A1374A	ENST00000430969	11/30	37	21	15	16	16	0	TNRC18,synonymous_variant,p.%3D,ENST00000430969,;TNRC18,synonymous_variant,p.%3D,ENST00000399537,;	A	ENSG00000182095	ENST00000430969	Transcript	synonymous_variant	4471	4122	1374	A	gcC/gcT	rs201136741	.	.	-1	TNRC18	HGNC	11962	protein_coding	YES	CCDS47534.1	ENSP00000395538	TNC18_HUMAN	H7C3U5_HUMAN,C9J9K1_HUMAN	UPI00016632FD	.	.	.	11/30	.	hmmpanther:PTHR12505:SF21,hmmpanther:PTHR12505	A:0.0004	A:0	A:0.0029	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCGGCTGC	byFrequency|byCluster|by1000G	5	ESCA
VSTM2A	0	.	GRCh37	7	54617880	54617880	+	Intron	SNP	C	C	T	rs778072086	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.634+17C>T	.	.	ENST00000407838	.	22	18	4	11	11	0	VSTM2A,synonymous_variant,p.%3D,ENST00000402026,;VSTM2A,synonymous_variant,p.%3D,ENST00000302287,;VSTM2A,intron_variant,,ENST00000402613,;VSTM2A,intron_variant,,ENST00000404951,;VSTM2A,intron_variant,,ENST00000407838,;VSTM2A,intron_variant,,ENST00000466888,;VSTM2A,intron_variant,,ENST00000498834,;VSTM2A,intron_variant,,ENST00000469952,;VSTM2A,downstream_gene_variant,,ENST00000495904,;	T	ENSG00000170419	ENST00000407838	Transcript	intron_variant	.	.	.	.	.	rs778072086	.	.	1	VSTM2A	HGNC	28499	protein_coding	YES	CCDS5512.2	ENSP00000384967	VTM2A_HUMAN	.	UPI0000EE7EC1	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTCGAGCC	byFrequency	2	ESCA
EGFR	0	.	GRCh37	7	55231514	55231514	+	Missense_Mutation	SNP	C	C	T	rs760471492	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1720C>T	p.Arg574Trp	p.R574W	ENST00000275493	14/28	22	15	7	11	11	0	EGFR,missense_variant,p.Arg521Trp,ENST00000454757,;EGFR,missense_variant,p.Arg574Trp,ENST00000344576,;EGFR,missense_variant,p.Arg574Trp,ENST00000342916,;EGFR,missense_variant,p.Arg574Trp,ENST00000275493,;EGFR,missense_variant,p.Arg529Trp,ENST00000455089,;EGFR,missense_variant,p.Arg574Trp,ENST00000442591,;	T	ENSG00000146648	ENST00000275493	Transcript	missense_variant	1897	1720	574	R/W	Cgg/Tgg	rs760471492	.	.	1	EGFR	HGNC	3236	protein_coding	YES	CCDS5514.1	ENSP00000275493	EGFR_HUMAN	Q75MF2_HUMAN,I3WA73_HUMAN,I3WA72_HUMAN,G9MC81_HUMAN,F1JTL6_HUMAN,E9PFD7_HUMAN,C9JYS6_HUMAN,A7VN06_HUMAN	UPI000003E750	.	deleterious(0)	possibly_damaging(0.472)	14/28	.	Superfamily_domains:SSF57184,PIRSF_domain:PIRSF000619,SMART_domains:SM00261,Gene3D:2.10.220.10,Pfam_domain:PF14843,hmmpanther:PTHR24416:SF91,hmmpanther:PTHR24416	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGACGGGTA	byFrequency	5	ESCA
MIR3147	0	.	GRCh37	7	57472766	57472766	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.36G>A	.	.	ENST00000577811	1/1	69	52	17	36	36	0	MIR3147,non_coding_transcript_exon_variant,,ENST00000577811,;	A	ENSG00000266168	ENST00000577811	Transcript	non_coding_transcript_exon_variant	36	.	.	.	.	.	.	.	1	MIR3147	HGNC	38300	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCGAAGTG	.	5	ESCA
AIMP2	0	.	GRCh37	7	6062967	6062967	+	Missense_Mutation	SNP	C	C	T	rs766467029	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608C>T	p.Thr203Met	p.T203M	ENST00000223029	4/4	98	60	38	62	62	0	AIMP2,missense_variant,p.Thr134Met,ENST00000395236,;AIMP2,missense_variant,p.Thr125Met,ENST00000400479,;AIMP2,missense_variant,p.Thr203Met,ENST00000223029,;EIF2AK1,3_prime_UTR_variant,,ENST00000422786,;EIF2AK1,3_prime_UTR_variant,,ENST00000199389,;EIF2AK1,downstream_gene_variant,,ENST00000536084,;EIF2AK1,downstream_gene_variant,,ENST00000490523,;	T	ENSG00000106305	ENST00000223029	Transcript	missense_variant	727	608	203	T/M	aCg/aTg	rs766467029	.	.	1	AIMP2	HGNC	20609	protein_coding	YES	CCDS5344.1	ENSP00000223029	AIMP2_HUMAN	A8MU58_HUMAN	UPI000012ED59	.	tolerated(0.14)	benign(0.143)	4/4	.	hmmpanther:PTHR13438,hmmpanther:PTHR13438:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGACGATGT	byFrequency	5	ESCA
USP42	0	.	GRCh37	7	6200309	6200309	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*168delT	.	.	ENST00000306177	18/18	39	28	11	26	26	0	USP42,3_prime_UTR_variant,,ENST00000306177,;CYTH3,downstream_gene_variant,,ENST00000396741,;CYTH3,downstream_gene_variant,,ENST00000350796,;CYTH3,downstream_gene_variant,,ENST00000465320,;CYTH3,downstream_gene_variant,,ENST00000461891,;USP42,downstream_gene_variant,,ENST00000521713,;USP42,downstream_gene_variant,,ENST00000479544,;CYTH3,downstream_gene_variant,,ENST00000495176,;	-	ENSG00000106346	ENST00000306177	Transcript	3_prime_UTR_variant	4269	.	.	.	.	.	.	.	1	USP42	HGNC	20068	protein_coding	YES	CCDS47535.1	ENSP00000301962	UBP42_HUMAN	E5RJP3_HUMAN,C9JPC9_HUMAN	UPI0000416754	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGAACTTTTTT	.	2	ESCA
ZNF733P	0	.	GRCh37	7	62752759	62752759	+	RNA	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.710A>G	.	.	ENST00000444809	4/4	38	29	9	42	42	0	ZNF733P,non_coding_transcript_exon_variant,,ENST00000331425,;ZNF733P,non_coding_transcript_exon_variant,,ENST00000444809,;	C	ENSG00000185037	ENST00000444809	Transcript	non_coding_transcript_exon_variant	710	.	.	.	.	.	.	.	-1	ZNF733P	HGNC	32473	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGTATGAA	.	4	ESCA
RAC1	0	.	GRCh37	7	6443115	6443115	+	3'Flank	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000356142	.	67	59	8	28	28	0	RAC1,3_prime_UTR_variant,,ENST00000348035,;RAC1,downstream_gene_variant,,ENST00000356142,;RAC1,downstream_gene_variant,,ENST00000488373,;RAC1,downstream_gene_variant,,ENST00000497741,;RAC1,downstream_gene_variant,,ENST00000495499,;RAC1,downstream_gene_variant,,ENST00000473564,;	-	ENSG00000136238	ENST00000356142	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	964	1	RAC1	HGNC	9801	protein_coding	YES	CCDS5349.1	ENSP00000348461	RAC1_HUMAN	A4D2P0_HUMAN	UPI000002B20E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAAGGTTTTTT	.	3	ESCA
LAT2	0	.	GRCh37	7	73639016	73639018	+	In_Frame_Del	DEL	GAG	GAG	-	rs782098274	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	GAG	GAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681_683delGGA	p.Glu227del	p.E227del	ENST00000460943	13/14	73	33	40	55	55	0	LAT2,inframe_deletion,p.Glu227del,ENST00000460943,;LAT2,inframe_deletion,p.Glu227del,ENST00000398475,;LAT2,inframe_deletion,p.Glu227del,ENST00000344995,;LAT2,inframe_deletion,p.Glu227del,ENST00000275635,;LAT2,downstream_gene_variant,,ENST00000361082,;LAT2,downstream_gene_variant,,ENST00000475494,;LAT2,downstream_gene_variant,,ENST00000470709,;LAT2,downstream_gene_variant,,ENST00000465116,;LAT2,3_prime_UTR_variant,,ENST00000488266,;LAT2,non_coding_transcript_exon_variant,,ENST00000490586,;	-	ENSG00000086730	ENST00000460943	Transcript	inframe_deletion	1565-1567	676-678	226	E/-	GAG/-	rs782098274	.	.	1	LAT2	HGNC	12749	protein_coding	YES	CCDS5566.2	ENSP00000420494	NTAL_HUMAN	F8W947_HUMAN,C9JDY7_HUMAN,C9JA24_HUMAN	UPI0000037782	.	.	.	13/14	.	hmmpanther:PTHR15646	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAGACGAGGAGGA	.	3	ESCA
CLIP2	0	.	GRCh37	7	73770923	73770923	+	Silent	SNP	C	C	T	rs199730295	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.987C>T	p.%3D	p.S329S	ENST00000223398	5/17	60	40	19	34	34	0	CLIP2,synonymous_variant,p.%3D,ENST00000395060,;CLIP2,synonymous_variant,p.%3D,ENST00000361545,;CLIP2,synonymous_variant,p.%3D,ENST00000223398,;	T	ENSG00000106665	ENST00000223398	Transcript	synonymous_variant	1314	987	329	S	tcC/tcT	rs199730295	.	.	1	CLIP2	HGNC	2586	protein_coding	YES	CCDS5569.1	ENSP00000223398	CLIP2_HUMAN	Q7Z5B7_HUMAN	UPI000007061E	.	.	.	5/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR18916:SF10,hmmpanther:PTHR18916,Superfamily_domains:SSF74924	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCCGTGGG	byCluster	5	ESCA
POR	0	.	GRCh37	7	75609955	75609955	+	Intron	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.516+152delC	.	.	ENST00000461988	.	43	31	12	22	22	0	POR,frameshift_variant,p.Pro196GlnfsTer27,ENST00000447222,;POR,frameshift_variant,p.Pro44GlnfsTer27,ENST00000450476,;POR,intron_variant,,ENST00000394893,;POR,intron_variant,,ENST00000461988,;POR,intron_variant,,ENST00000439963,;POR,intron_variant,,ENST00000545601,;POR,intron_variant,,ENST00000419840,;POR,downstream_gene_variant,,ENST00000439297,;POR,downstream_gene_variant,,ENST00000432753,;POR,downstream_gene_variant,,ENST00000414186,;POR,downstream_gene_variant,,ENST00000453773,;POR,downstream_gene_variant,,ENST00000426184,;POR,downstream_gene_variant,,ENST00000412521,;POR,upstream_gene_variant,,ENST00000439269,;POR,downstream_gene_variant,,ENST00000475509,;POR,3_prime_UTR_variant,,ENST00000448410,;POR,intron_variant,,ENST00000454934,;POR,intron_variant,,ENST00000412064,;POR,upstream_gene_variant,,ENST00000487247,;POR,upstream_gene_variant,,ENST00000495770,;POR,downstream_gene_variant,,ENST00000471238,;POR,upstream_gene_variant,,ENST00000460892,;POR,upstream_gene_variant,,ENST00000493973,;POR,upstream_gene_variant,,ENST00000496888,;	-	ENSG00000127948	ENST00000461988	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	POR	HGNC	9208	protein_coding	YES	CCDS5579.1	ENSP00000419970	NCPR_HUMAN	Q59ED7_HUMAN,E7EMD0_HUMAN,C9JQ78_HUMAN	UPI000013D5F4	.	.	.	.	5/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTCTGCCCCAG	.	3	ESCA
DTX2	0	.	GRCh37	7	76131626	76131626	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1242C>T	p.%3D	p.I414I	ENST00000324432	9/12	97	62	34	50	50	0	DTX2,synonymous_variant,p.%3D,ENST00000446600,;DTX2,synonymous_variant,p.%3D,ENST00000307569,;DTX2,synonymous_variant,p.%3D,ENST00000324432,;DTX2,synonymous_variant,p.%3D,ENST00000430490,;DTX2,synonymous_variant,p.%3D,ENST00000413936,;DTX2,synonymous_variant,p.%3D,ENST00000446820,;DTX2,missense_variant,p.Ser74Phe,ENST00000435251,;DTX2,non_coding_transcript_exon_variant,,ENST00000467729,;DTX2,non_coding_transcript_exon_variant,,ENST00000479915,;DTX2,non_coding_transcript_exon_variant,,ENST00000468546,;DTX2,upstream_gene_variant,,ENST00000465488,;	T	ENSG00000091073	ENST00000324432	Transcript	synonymous_variant	1752	1242	414	I	atC/atT	.	.	.	1	DTX2	HGNC	15973	protein_coding	YES	CCDS5587.1	ENSP00000322885	DTX2_HUMAN	Q75MM6_HUMAN,Q4FEB2_HUMAN,E7ET89_HUMAN,C9JY61_HUMAN,C9JVC8_HUMAN,C9JS11_HUMAN,C9JLU8_HUMAN,C9JII1_HUMAN,C9JF39_HUMAN,C9JEH4_HUMAN	UPI00001413A2	.	.	.	9/12	.	Superfamily_domains:SSF57850,SMART_domains:SM00184,Gene3D:3.30.40.10,Pfam_domain:PF00097,hmmpanther:PTHR12622,hmmpanther:PTHR12622:SF21,PROSITE_profiles:PS50089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATCTGCAT	.	5	ESCA
RSBN1L	0	.	GRCh37	7	77408706	77408706	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*229delA	.	.	ENST00000334955	8/8	20	10	10	17	17	0	RSBN1L,3_prime_UTR_variant,,ENST00000334955,;RSBN1L,3_prime_UTR_variant,,ENST00000445288,;RSBN1L,downstream_gene_variant,,ENST00000441514,;RSBN1L,downstream_gene_variant,,ENST00000445512,;	-	ENSG00000187257	ENST00000334955	Transcript	3_prime_UTR_variant	2789	.	.	.	.	.	.	.	1	RSBN1L	HGNC	24765	protein_coding	YES	CCDS43607.1	ENSP00000334040	RSBNL_HUMAN	C9JM20_HUMAN	UPI000020F469	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTCTTTAAAAAA	.	2	ESCA
PHTF2	0	.	GRCh37	7	77569845	77569845	+	Nonsense_Mutation	SNP	C	C	T	rs774201076	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1639C>T	p.Arg547Ter	p.R547*	ENST00000416283	13/18	52	41	11	39	39	0	PHTF2,stop_gained,p.Arg547Ter,ENST00000416283,;PHTF2,stop_gained,p.Arg547Ter,ENST00000422959,;PHTF2,stop_gained,p.Arg581Ter,ENST00000248550,;PHTF2,stop_gained,p.Arg543Ter,ENST00000307305,;PHTF2,stop_gained,p.Arg543Ter,ENST00000275575,;PHTF2,downstream_gene_variant,,ENST00000424760,;PHTF2,intron_variant,,ENST00000470215,;PHTF2,downstream_gene_variant,,ENST00000454592,;PHTF2,downstream_gene_variant,,ENST00000479515,;	T	ENSG00000006576	ENST00000416283	Transcript	stop_gained	1765	1639	547	R/*	Cga/Tga	rs774201076	.	.	1	PHTF2	HGNC	13411	protein_coding	YES	CCDS47621.1	ENSP00000400958	PHTF2_HUMAN	.	UPI0000E674D3	.	.	.	13/18	.	hmmpanther:PTHR12680:SF2,hmmpanther:PTHR12680	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAGCGATTA	.	5	ESCA
ABCB1	0	.	GRCh37	7	87214954	87214954	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.160G>A	p.Gly54Arg	p.G54R	ENST00000265724	5/29	24	18	5	34	34	0	ABCB1,missense_variant,p.Gly54Arg,ENST00000265724,;ABCB1,missense_variant,p.Gly54Arg,ENST00000543898,;ABCB1,downstream_gene_variant,,ENST00000416177,;	T	ENSG00000085563	ENST00000265724	Transcript	missense_variant	578	160	54	G/R	Gga/Aga	.	.	.	-1	ABCB1	HGNC	40	protein_coding	YES	CCDS5608.1	ENSP00000265724	MDR1_HUMAN	Q6TBL4_HUMAN,E7EWT8_HUMAN,B5U2G4_HUMAN,A4D1D2_HUMAN	UPI000013D66C	.	deleterious(0)	probably_damaging(1)	5/29	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTCCCACCA	.	5	ESCA
ZNF804B	0	.	GRCh37	7	88956723	88956724	+	Frame_Shift_Ins	INS	-	-	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321dupA	p.Gln108ThrfsTer6	p.Q108Tfs*6	ENST00000333190	3/4	49	38	11	34	34	0	ZNF804B,frameshift_variant,p.Gln108ThrfsTer6,ENST00000333190,;	A	ENSG00000182348	ENST00000333190	Transcript	frameshift_variant	924-925	315-316	105-106	-/X	-/A	COSM1452646	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	.	.	3/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	insertion	.	6	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATGAGAAAAA	.	3	ESCA
TECPR1	0	.	GRCh37	7	97860399	97860399	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2156delG	p.Ser719ThrfsTer24	p.S719Tfs*24	ENST00000447648	15/26	99	69	30	42	42	0	TECPR1,frameshift_variant,p.Ser719ThrfsTer24,ENST00000447648,;TECPR1,frameshift_variant,p.Ser649ThrfsTer24,ENST00000542604,;TECPR1,frameshift_variant,p.Ser720ThrfsTer24,ENST00000379795,;TECPR1,non_coding_transcript_exon_variant,,ENST00000479911,;TECPR1,upstream_gene_variant,,ENST00000479975,;TECPR1,upstream_gene_variant,,ENST00000476659,;TECPR1,downstream_gene_variant,,ENST00000471397,;TECPR1,non_coding_transcript_exon_variant,,ENST00000490842,;TECPR1,non_coding_transcript_exon_variant,,ENST00000483740,;	-	ENSG00000205356	ENST00000447648	Transcript	frameshift_variant	2456	2156	719	S/X	aGc/ac	.	.	.	-1	TECPR1	HGNC	22214	protein_coding	YES	CCDS47648.1	ENSP00000404923	TCPR1_HUMAN	C9JUV4_HUMAN	UPI0000161940	.	.	.	15/26	.	hmmpanther:PTHR23250,hmmpanther:PTHR23250:SF1,Gene3D:2.30.29.30,SMART_domains:SM00706,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCCGGCTCTCG	.	3	ESCA
TRRAP	0	.	GRCh37	7	98552779	98552779	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5768C>T	p.Ala1923Val	p.A1923V	ENST00000359863	40/72	38	20	18	19	19	0	TRRAP,missense_variant,p.Ala1905Val,ENST00000355540,;TRRAP,missense_variant,p.Ala1904Val,ENST00000446306,;TRRAP,missense_variant,p.Ala1645Val,ENST00000456197,;TRRAP,missense_variant,p.Ala1923Val,ENST00000359863,;	T	ENSG00000196367	ENST00000359863	Transcript	missense_variant	5977	5768	1923	A/V	gCg/gTg	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	probably_damaging(0.98)	40/72	.	hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGCGATGG	.	5	ESCA
PILRB	0	.	GRCh37	7	99956488	99956490	+	In_Frame_Del	DEL	CTT	CTT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242_244delTCT	p.Phe81del	p.F81del	ENST00000610247	16/18	79	61	18	55	55	0	PILRB,inframe_deletion,p.Phe81del,ENST00000444073,;PILRB,inframe_deletion,p.Phe81del,ENST00000419749,;PILRB,inframe_deletion,p.Phe81del,ENST00000610247,;PILRB,inframe_deletion,p.Phe81del,ENST00000452089,;PILRB,inframe_deletion,p.Phe81del,ENST00000457519,;PILRB,inframe_deletion,p.Phe81del,ENST00000609309,;PILRB,inframe_deletion,p.Phe81del,ENST00000422808,;PILRB,inframe_deletion,p.Phe81del,ENST00000608825,;PILRB,inframe_deletion,p.Phe81del,ENST00000443526,;PILRB,inframe_deletion,p.Phe81del,ENST00000438231,;PILRB,intron_variant,,ENST00000438028,;PILRB,intron_variant,,ENST00000431140,;PILRB,intron_variant,,ENST00000448382,;PILRB,downstream_gene_variant,,ENST00000455145,;STAG3L5P-PVRIG2P-PILRB,non_coding_transcript_exon_variant,,ENST00000310771,;STAG3L5P-PVRIG2P-PILRB,intron_variant,,ENST00000444874,;STAG3L5P-PVRIG2P-PILRB,downstream_gene_variant,,ENST00000472646,;PILRB,downstream_gene_variant,,ENST00000493091,;	-	ENSG00000121716	ENST00000610247	Transcript	inframe_deletion	2736-2738	240-242	80-81	SF/S	tcCTTc/tcc	.	.	.	1	PILRB	HGNC	18297	protein_coding	YES	CCDS43622.1	ENSP00000477415	.	D6W5V2_HUMAN,C9JNA4_HUMAN,C9J8P3_HUMAN	UPI000006EEBC	.	.	.	16/18	.	PROSITE_profiles:PS50835,hmmpanther:PTHR15549:SF1,hmmpanther:PTHR15549,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCAGTCCTTCTACA	.	3	ESCA
GRHL2	0	.	GRCh37	8	102504783	102504783	+	5'UTR	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-212delG	.	.	ENST00000251808	1/16	129	112	17	32	32	0	GRHL2,5_prime_UTR_variant,,ENST00000251808,;GRHL2,5_prime_UTR_variant,,ENST00000521085,;GRHL2,upstream_gene_variant,,ENST00000395927,;KB-1562D12.1,upstream_gene_variant,,ENST00000520268,;GRHL2,non_coding_transcript_exon_variant,,ENST00000472106,;	-	ENSG00000083307	ENST00000251808	Transcript	5_prime_UTR_variant	124	.	.	.	.	.	.	.	1	GRHL2	HGNC	2799	protein_coding	YES	CCDS34931.1	ENSP00000251808	GRHL2_HUMAN	.	UPI000013CD16	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGTGAGGGGCC	.	3	ESCA
UBR5	0	.	GRCh37	8	103289349	103289349	+	Frame_Shift_Del	DEL	T	T	-	rs763652408,rs775007886	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6360delA	p.Glu2121LysfsTer28	p.E2121Kfs*28	ENST00000520539	45/59	238	181	57	96	96	0	UBR5,frameshift_variant,p.Glu2121LysfsTer28,ENST00000520539,;UBR5,frameshift_variant,p.Glu2121LysfsTer28,ENST00000220959,;UBR5,frameshift_variant,p.Glu2115LysfsTer28,ENST00000521922,;UBR5,upstream_gene_variant,,ENST00000521566,;UBR5,upstream_gene_variant,,ENST00000518205,;	-	ENSG00000104517	ENST00000520539	Transcript	frameshift_variant	6967	6360	2120	K/X	aaA/aa	rs763652408,rs775007886,COSM214501	.	.	-1	UBR5	HGNC	16806	protein_coding	YES	CCDS34933.1	ENSP00000429084	UBR5_HUMAN	Q49A65_HUMAN,E5RFK7_HUMAN,B3KML2_HUMAN	UPI0000129BCB	.	.	.	45/59	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11254:SF77,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E2121fs*28|c.6360delA|20	INDELOCATOR|VARSCANI	CCCTTCTTTTTT	byFrequency	2	ESCA
FZD6	0	.	GRCh37	8	104343649	104343649	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2033G>A	p.Ser678Asn	p.S678N	ENST00000358755	7/7	135	121	14	59	59	0	FZD6,missense_variant,p.Ser678Asn,ENST00000358755,;FZD6,missense_variant,p.Ser373Asn,ENST00000540287,;FZD6,missense_variant,p.Ser678Asn,ENST00000522566,;FZD6,missense_variant,p.Ser646Asn,ENST00000523739,;FZD6,3_prime_UTR_variant,,ENST00000519011,;FZD6,3_prime_UTR_variant,,ENST00000522484,;FZD6,3_prime_UTR_variant,,ENST00000521195,;FZD6,downstream_gene_variant,,ENST00000523933,;	A	ENSG00000164930	ENST00000358755	Transcript	missense_variant	2350	2033	678	S/N	aGc/aAc	COSM3395019	.	.	1	FZD6	HGNC	4044	protein_coding	YES	CCDS6298.1	ENSP00000351605	FZD6_HUMAN	B7ZB79_HUMAN	UPI0000061EB0	.	tolerated_low_confidence(0.29)	benign(0.001)	7/7	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCAAGCAGCC	.	4	ESCA
ZFPM2	0	.	GRCh37	8	106816399	106816399	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*633G>T	.	.	ENST00000407775	8/8	62	47	15	20	20	0	ZFPM2,3_prime_UTR_variant,,ENST00000407775,;ZFPM2,downstream_gene_variant,,ENST00000517361,;ZFPM2,downstream_gene_variant,,ENST00000378472,;ZFPM2,downstream_gene_variant,,ENST00000520492,;RP11-152P17.2,intron_variant,,ENST00000524045,;RP11-152P17.2,intron_variant,,ENST00000509144,;RP11-152P17.2,intron_variant,,ENST00000521622,;RP11-152P17.2,intron_variant,,ENST00000520594,;RP11-152P17.2,intron_variant,,ENST00000520433,;RP11-152P17.2,intron_variant,,ENST00000518932,;ZFPM2,downstream_gene_variant,,ENST00000522296,;RP11-152P17.2,intron_variant,,ENST00000520078,;	T	ENSG00000169946	ENST00000407775	Transcript	3_prime_UTR_variant	4339	.	.	.	.	.	.	.	1	ZFPM2	HGNC	16700	protein_coding	YES	CCDS47908.1	ENSP00000384179	FOG2_HUMAN	Q9NPQ0_HUMAN,F5H542_HUMAN,E7ET52_HUMAN,E5RJX0_HUMAN	UPI000057A0B4	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGGCAATT	.	5	ESCA
CSMD3	0	.	GRCh37	8	113301669	113301669	+	Missense_Mutation	SNP	G	G	A	rs775065918	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9073C>T	p.Arg3025Cys	p.R3025C	ENST00000297405	57/71	57	46	11	30	30	0	CSMD3,missense_variant,p.Arg2955Cys,ENST00000352409,;CSMD3,missense_variant,p.Arg2856Cys,ENST00000455883,;CSMD3,missense_variant,p.Arg3025Cys,ENST00000297405,;CSMD3,missense_variant,p.Arg2295Cys,ENST00000339701,;CSMD3,missense_variant,p.Arg2985Cys,ENST00000343508,;	A	ENSG00000164796	ENST00000297405	Transcript	missense_variant	9318	9073	3025	R/C	Cgt/Tgt	rs775065918,COSM3382049,COSM3382050	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	deleterious(0.01)	probably_damaging(0.967)	57/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R2985C|c.8953C>T|4,SITE|p.R3025C|c.9073C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAACGCTTTC	byFrequency	5	ESCA
CSMD3	0	.	GRCh37	8	113308228	113308228	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8448T>A	p.His2816Gln	p.H2816Q	ENST00000297405	54/71	103	55	47	50	50	0	CSMD3,missense_variant,p.His2746Gln,ENST00000352409,;CSMD3,missense_variant,p.His2647Gln,ENST00000455883,;CSMD3,missense_variant,p.His2816Gln,ENST00000297405,;CSMD3,missense_variant,p.His2086Gln,ENST00000339701,;CSMD3,missense_variant,p.His2776Gln,ENST00000343508,;	T	ENSG00000164796	ENST00000297405	Transcript	missense_variant	8693	8448	2816	H/Q	caT/caA	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	deleterious(0)	probably_damaging(0.953)	54/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Gene3D:2.10.70.10,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAATGACC	.	5	ESCA
CSMD3	0	.	GRCh37	8	113529438	113529438	+	Silent	SNP	C	C	T	rs563110439	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4581G>A	p.%3D	p.A1527A	ENST00000297405	28/71	116	103	12	41	41	0	CSMD3,synonymous_variant,p.%3D,ENST00000352409,;CSMD3,synonymous_variant,p.%3D,ENST00000455883,;CSMD3,synonymous_variant,p.%3D,ENST00000297405,;CSMD3,synonymous_variant,p.%3D,ENST00000339701,;CSMD3,synonymous_variant,p.%3D,ENST00000343508,;	T	ENSG00000164796	ENST00000297405	Transcript	synonymous_variant	4826	4581	1527	A	gcG/gcA	rs563110439	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	.	.	28/71	.	PROSITE_profiles:PS50923,Gene3D:2.10.70.10,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R1529H|c.4586G>A|4,BUFFER|p.R1489H|c.4466G>A|3	RADIA|MUTECT|MUSE|VARSCANS	CGACACGCAGT	byFrequency|byCluster	4	ESCA
RAD21	0	.	GRCh37	8	117858533	117858533	+	3'UTR	DEL	T	T	-	rs16918579,rs189612341	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1206delA	.	.	ENST00000297338	14/14	63	46	17	29	29	0	RAD21,3_prime_UTR_variant,,ENST00000297338,;UTP23,intron_variant,,ENST00000520733,;UTP23,intron_variant,,ENST00000517820,;RAD21,downstream_gene_variant,,ENST00000517749,;RAD21,downstream_gene_variant,,ENST00000518055,;RAD21,downstream_gene_variant,,ENST00000523986,;UTP23,intron_variant,,ENST00000521703,;UTP23,intron_variant,,ENST00000524128,;	-	ENSG00000164754	ENST00000297338	Transcript	3_prime_UTR_variant	3390	.	.	.	.	rs16918579,rs189612341	.	.	-1	RAD21	HGNC	9811	protein_coding	YES	CCDS6321.1	ENSP00000297338	RAD21_HUMAN	E5RJW1_HUMAN,E5RJK5_HUMAN,E5RIN7_HUMAN,E5RI01_HUMAN,E5RG18_HUMAN,E5RFZ5_HUMAN,E5RFV8_HUMAN	UPI0000133018	.	.	.	14/14	.	.	-:0.0306,A:0.0008	-:0.1051,A:0	-:0.0101,A:0	.	-:0.002,A:0.004	-:0.001,A:0	-:0.0041,A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	AAGTGATTTTTT	byFrequency|suspect|byCluster|by1000G	2	ESCA
ZHX2	0	.	GRCh37	8	123793943	123793943	+	5'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-517delT	.	.	ENST00000314393	1/4	74	56	18	17	17	0	ZHX2,5_prime_UTR_variant,,ENST00000314393,;RP11-44N11.2,upstream_gene_variant,,ENST00000607710,;RP11-44N11.3,downstream_gene_variant,,ENST00000607393,;	-	ENSG00000178764	ENST00000314393	Transcript	5_prime_UTR_variant	311	.	.	.	.	.	.	.	1	ZHX2	HGNC	18513	protein_coding	YES	CCDS6336.1	ENSP00000314709	ZHX2_HUMAN	H0YKA3_HUMAN	UPI0000073CCB	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTCCCTTTTTT	.	2	ESCA
SQLE	0	.	GRCh37	8	126017779	126017779	+	Missense_Mutation	SNP	G	G	T	rs764717217	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.557G>T	p.Gly186Val	p.G186V	ENST00000265896	3/11	128	106	22	37	37	0	SQLE,missense_variant,p.Gly128Val,ENST00000521232,;SQLE,missense_variant,p.Gly186Val,ENST00000265896,;SQLE,missense_variant,p.Gly91Val,ENST00000523430,;SQLE,upstream_gene_variant,,ENST00000518931,;	T	ENSG00000104549	ENST00000265896	Transcript	missense_variant	1455	557	186	G/V	gGt/gTt	rs764717217	.	.	1	SQLE	HGNC	11279	protein_coding	YES	CCDS47918.1	ENSP00000265896	ERG1_HUMAN	Q9UNR6_HUMAN,H0YBN7_HUMAN,B4DHX0_HUMAN	UPI0000073EEE	.	deleterious(0)	possibly_damaging(0.813)	3/11	.	Superfamily_domains:SSF51905,Gene3D:3.50.50.60,hmmpanther:PTHR10835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGGTCTTG	.	5	ESCA
FAM84B	0	.	GRCh37	8	127569172	127569172	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.463C>A	p.Leu155Met	p.L155M	ENST00000304916	2/2	112	97	14	15	15	0	FAM84B,missense_variant,p.Leu155Met,ENST00000304916,;RP11-103H7.5,non_coding_transcript_exon_variant,,ENST00000524320,;RP11-89K10.1,upstream_gene_variant,,ENST00000520512,;RP11-89K10.1,upstream_gene_variant,,ENST00000519880,;RP11-89K10.1,upstream_gene_variant,,ENST00000517773,;FAM84B,upstream_gene_variant,,ENST00000517458,;	T	ENSG00000168672	ENST00000304916	Transcript	missense_variant	919	463	155	L/M	Ctg/Atg	.	.	.	-1	FAM84B	HGNC	24166	protein_coding	YES	CCDS6358.1	ENSP00000302578	FA84B_HUMAN	.	UPI00000710F2	.	deleterious(0.04)	possibly_damaging(0.49)	2/2	.	hmmpanther:PTHR13943,hmmpanther:PTHR13943:SF39,Gene3D:3.90.1720.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTCAGGAAGC	.	4	ESCA
KIAA1456	0	.	GRCh37	8	12879900	12879900	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*347T>C	.	.	ENST00000524591	5/5	16	6	9	26	26	0	KIAA1456,3_prime_UTR_variant,,ENST00000524591,;KIAA1456,intron_variant,,ENST00000447063,;KIAA1456,non_coding_transcript_exon_variant,,ENST00000529978,;KIAA1456,downstream_gene_variant,,ENST00000529706,;	C	ENSG00000250305	ENST00000524591	Transcript	3_prime_UTR_variant	2201	.	.	.	.	.	.	.	1	KIAA1456	HGNC	26725	protein_coding	YES	CCDS47808.1	ENSP00000432695	K1456_HUMAN	E9PK20_HUMAN	UPI0001596892	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGCTGTTAA	.	5	ESCA
DLC1	0	.	GRCh37	8	12957055	12957055	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2791G>A	p.Gly931Arg	p.G931R	ENST00000276297	9/18	60	20	39	47	47	0	DLC1,missense_variant,p.Gly494Arg,ENST00000358919,;DLC1,missense_variant,p.Gly528Arg,ENST00000512044,;DLC1,missense_variant,p.Gly931Arg,ENST00000276297,;DLC1,missense_variant,p.Gly420Arg,ENST00000520226,;DLC1,downstream_gene_variant,,ENST00000503161,;DLC1,downstream_gene_variant,,ENST00000515225,;DLC1,downstream_gene_variant,,ENST00000509922,;DLC1,upstream_gene_variant,,ENST00000510318,;DLC1,upstream_gene_variant,,ENST00000513883,;DLC1,non_coding_transcript_exon_variant,,ENST00000510250,;	T	ENSG00000164741	ENST00000276297	Transcript	missense_variant	3201	2791	931	G/R	Gga/Aga	.	.	.	-1	DLC1	HGNC	2897	protein_coding	YES	CCDS5989.1	ENSP00000276297	RHG07_HUMAN	.	UPI0000210275	.	deleterious(0.04)	probably_damaging(0.972)	9/18	.	hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCCCTCAT	.	5	ESCA
TG	0	.	GRCh37	8	133913767	133913767	+	Silent	SNP	G	G	A	rs750765107	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3603G>A	p.%3D	p.T1201T	ENST00000220616	16/48	66	32	34	16	16	0	TG,synonymous_variant,p.%3D,ENST00000220616,;TG,synonymous_variant,p.%3D,ENST00000377869,;TG,synonymous_variant,p.%3D,ENST00000518505,;TG,intron_variant,,ENST00000523756,;TG,downstream_gene_variant,,ENST00000518097,;	A	ENSG00000042832	ENST00000220616	Transcript	synonymous_variant	3643	3603	1201	T	acG/acA	rs750765107	.	.	1	TG	HGNC	11764	protein_coding	YES	CCDS34944.1	ENSP00000220616	THYG_HUMAN	Q9NYM1_HUMAN,Q9NYD9_HUMAN,E5RG33_HUMAN	UPI000013C79F	.	.	.	16/48	.	Superfamily_domains:SSF57610,PIRSF_domain:PIRSF001831,SMART_domains:SM00211,Pfam_domain:PF00086,Gene3D:4.10.800.10,PROSITE_profiles:PS51162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGACGCGCGT	.	5	ESCA
TG	0	.	GRCh37	8	133978910	133978910	+	Frame_Shift_Del	DEL	C	C	-	rs757483872	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5654delC	p.Ser1885Ter	p.S1885*	ENST00000220616	30/48	64	56	8	13	13	0	TG,frameshift_variant,p.Ser1885Ter,ENST00000220616,;TG,frameshift_variant,p.Ser255Ter,ENST00000542445,;TG,frameshift_variant,p.Ser1828Ter,ENST00000377869,;TG,frameshift_variant,p.Ser39Ter,ENST00000519543,;TG,frameshift_variant,p.Ser341Ter,ENST00000519178,;TG,intron_variant,,ENST00000518058,;TG,upstream_gene_variant,,ENST00000520197,;TG,3_prime_UTR_variant,,ENST00000523756,;TG,upstream_gene_variant,,ENST00000520089,;	-	ENSG00000042832	ENST00000220616	Transcript	frameshift_variant	5694	5654	1885	S/X	tCa/ta	rs757483872	.	.	1	TG	HGNC	11764	protein_coding	YES	CCDS34944.1	ENSP00000220616	THYG_HUMAN	Q9NYM1_HUMAN,Q9NYD9_HUMAN,E5RG33_HUMAN	UPI000013C79F	.	.	.	30/48	.	PIRSF_domain:PIRSF001831	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TGTTTTCAGCCC	.	2	ESCA
TRAPPC9	0	.	GRCh37	8	141294067	141294067	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2329C>T	p.Pro777Ser	p.P777S	ENST00000389328	14/23	76	68	8	28	28	0	TRAPPC9,missense_variant,p.Pro523Ser,ENST00000520857,;TRAPPC9,missense_variant,p.Pro670Ser,ENST00000389327,;TRAPPC9,missense_variant,p.Pro777Ser,ENST00000389328,;TRAPPC9,missense_variant,p.Pro679Ser,ENST00000438773,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000521667,;TRAPPC9,downstream_gene_variant,,ENST00000521167,;	A	ENSG00000167632	ENST00000389328	Transcript	missense_variant	2344	2329	777	P/S	Ccg/Tcg	.	.	.	-1	TRAPPC9	HGNC	30832	protein_coding	YES	CCDS34946.1	ENSP00000373979	TPPC9_HUMAN	.	UPI0000DBEF2B	.	tolerated(0.19)	probably_damaging(0.994)	14/23	.	Pfam_domain:PF08626,hmmpanther:PTHR21512,hmmpanther:PTHR21512:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCGGCAGGT	.	4	ESCA
DENND3	0	.	GRCh37	8	142161921	142161921	+	Silent	SNP	C	C	T	rs778157810	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.819C>T	p.%3D	p.F273F	ENST00000262585	7/23	175	165	10	56	56	0	DENND3,synonymous_variant,p.%3D,ENST00000519811,;DENND3,synonymous_variant,p.%3D,ENST00000424248,;DENND3,synonymous_variant,p.%3D,ENST00000262585,;DENND3,synonymous_variant,p.%3D,ENST00000518668,;DENND3,synonymous_variant,p.%3D,ENST00000520986,;DENND3,downstream_gene_variant,,ENST00000523058,;DENND3,upstream_gene_variant,,ENST00000521477,;DENND3,downstream_gene_variant,,ENST00000523015,;	T	ENSG00000105339	ENST00000262585	Transcript	synonymous_variant	1097	819	273	F	ttC/ttT	rs778157810	.	.	1	DENND3	HGNC	29134	protein_coding	YES	CCDS34947.1	ENSP00000262585	DEND3_HUMAN	B3KRG7_HUMAN	UPI00003CEFBA	.	.	.	7/23	.	SMART_domains:SM00799,Pfam_domain:PF02141,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF3,PROSITE_profiles:PS50211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACTTCGAAGA	byFrequency	2	ESCA
ARC	0	.	GRCh37	8	143694918	143694918	+	Missense_Mutation	SNP	G	G	T	rs770890443	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715C>A	p.Leu239Met	p.L239M	ENST00000356613	1/3	210	180	30	66	66	0	ARC,missense_variant,p.Leu239Met,ENST00000356613,;ARC,upstream_gene_variant,,ENST00000581404,;	T	ENSG00000198576	ENST00000356613	Transcript	missense_variant	1916	715	239	L/M	Ctg/Atg	rs770890443	.	.	-1	ARC	HGNC	648	protein_coding	YES	CCDS34950.1	ENSP00000349022	ARC_HUMAN	.	UPI0000163B0F	.	deleterious(0.01)	probably_damaging(0.998)	1/3	.	hmmpanther:PTHR15962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGACAGCCAGT	.	4	ESCA
EPPK1	0	.	GRCh37	8	144940504	144940504	+	Silent	SNP	G	G	A	rs555448234	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6918C>T	p.%3D	p.A2306A	ENST00000525985	2/2	661	633	28	144	144	0	EPPK1,synonymous_variant,p.%3D,ENST00000525985,;	A	ENSG00000227184	ENST00000525985	Transcript	synonymous_variant	6990	6918	2306	A	gcC/gcT	rs555448234,COSM3412812	.	.	-1	EPPK1	HGNC	15577	protein_coding	YES	.	ENSP00000436337	.	E9PPU0_HUMAN	UPI00006C0DF1	.	.	.	2/2	.	Superfamily_domains:SSF75399,SMART_domains:SM00250,Gene3D:3.90.1290.10,hmmpanther:PTHR11915:SF252,hmmpanther:PTHR11915	A:0.0006	A:0	A:0	.	A:0.001	A:0	A:0.002	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGACGGCGCG	byFrequency|by1000G	2	ESCA
EPPK1	0	.	GRCh37	8	144947011	144947011	+	Silent	SNP	G	G	A	rs549982161	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.411C>T	p.%3D	p.I137I	ENST00000525985	2/2	155	110	45	33	33	0	EPPK1,synonymous_variant,p.%3D,ENST00000525985,;	A	ENSG00000227184	ENST00000525985	Transcript	synonymous_variant	483	411	137	I	atC/atT	rs549982161	.	.	-1	EPPK1	HGNC	15577	protein_coding	YES	.	ENSP00000436337	.	E9PPU0_HUMAN	UPI00006C0DF1	.	.	.	2/2	.	Superfamily_domains:SSF75399,SMART_domains:SM00250,Gene3D:3.90.1290.10	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCGATGGC	by1000G	5	ESCA
PLEC	0	.	GRCh37	8	145008493	145008493	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1573T>C	p.Phe525Leu	p.F525L	ENST00000322810	11/32	151	106	45	38	38	0	PLEC,missense_variant,p.Phe525Leu,ENST00000322810,;PLEC,missense_variant,p.Phe411Leu,ENST00000527096,;PLEC,missense_variant,p.Phe388Leu,ENST00000345136,;PLEC,missense_variant,p.Phe392Leu,ENST00000357649,;PLEC,missense_variant,p.Phe356Leu,ENST00000398774,;PLEC,missense_variant,p.Phe432Leu,ENST00000528025,;PLEC,missense_variant,p.Phe388Leu,ENST00000354589,;PLEC,missense_variant,p.Phe374Leu,ENST00000356346,;PLEC,missense_variant,p.Phe415Leu,ENST00000436759,;PLEC,missense_variant,p.Phe366Leu,ENST00000354958,;PLEC,downstream_gene_variant,,ENST00000527816,;PLEC,downstream_gene_variant,,ENST00000526416,;PLEC,downstream_gene_variant,,ENST00000528131,;PLEC,downstream_gene_variant,,ENST00000532346,;	G	ENSG00000178209	ENST00000322810	Transcript	missense_variant	1743	1573	525	F/L	Ttt/Ctt	.	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	unknown(0)	11/32	.	Superfamily_domains:SSF46966,hmmpanther:PTHR11915:SF247,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAAACTCGC	.	5	ESCA
GPAA1	0	.	GRCh37	8	145138709	145138710	+	Frame_Shift_Del	DEL	CT	CT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CT	CT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.461_462delCT	p.Ser154TyrfsTer34	p.S154Yfs*34	ENST00000355091	4/12	159	119	40	23	23	0	GPAA1,frameshift_variant,p.Ser94TyrfsTer34,ENST00000361036,;GPAA1,frameshift_variant,p.Ser154TyrfsTer20,ENST00000524418,;GPAA1,frameshift_variant,p.Ser154TyrfsTer34,ENST00000355091,;GPAA1,intron_variant,,ENST00000525087,;EXOSC4,downstream_gene_variant,,ENST00000525936,;GPAA1,downstream_gene_variant,,ENST00000530258,;EXOSC4,downstream_gene_variant,,ENST00000316052,;EXOSC4,downstream_gene_variant,,ENST00000527954,;CTD-3065J16.9,upstream_gene_variant,,ENST00000524499,;GPAA1,non_coding_transcript_exon_variant,,ENST00000527144,;GPAA1,upstream_gene_variant,,ENST00000526233,;GPAA1,downstream_gene_variant,,ENST00000526341,;GPAA1,frameshift_variant,p.Ser154TyrfsTer34,ENST00000528073,;GPAA1,frameshift_variant,p.Leu69ThrfsTer?,ENST00000530633,;GPAA1,frameshift_variant,p.Leu129ThrfsTer?,ENST00000529503,;GPAA1,non_coding_transcript_exon_variant,,ENST00000532758,;GPAA1,non_coding_transcript_exon_variant,,ENST00000525308,;GPAA1,upstream_gene_variant,,ENST00000530796,;GPAA1,upstream_gene_variant,,ENST00000531593,;GPAA1,upstream_gene_variant,,ENST00000527653,;GPAA1,upstream_gene_variant,,ENST00000534072,;GPAA1,upstream_gene_variant,,ENST00000529638,;	-	ENSG00000197858	ENST00000355091	Transcript	frameshift_variant	580-581	459-460	153-154	DS/DX	gaCTct/gact	.	.	.	1	GPAA1	HGNC	4446	protein_coding	YES	CCDS43776.1	ENSP00000347206	GPAA1_HUMAN	E9PLG8_HUMAN	UPI0000073ECC	.	.	.	4/12	.	hmmpanther:PTHR13304:SF0,hmmpanther:PTHR13304,Pfam_domain:PF04114,PIRSF_domain:PIRSF036762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCTGACTCTACC	.	3	ESCA
MROH1	0	.	GRCh37	8	145267982	145267982	+	Intron	SNP	G	G	A	rs373393781	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1142-7521G>A	.	.	ENST00000528919	.	90	82	8	32	32	0	MROH1,synonymous_variant,p.%3D,ENST00000423230,;MROH1,intron_variant,,ENST00000534366,;MROH1,intron_variant,,ENST00000398656,;MROH1,intron_variant,,ENST00000528919,;MROH1,intron_variant,,ENST00000326134,;MROH1,intron_variant,,ENST00000527071,;MROH1,intron_variant,,ENST00000532255,;MROH1,intron_variant,,ENST00000527552,;	A	ENSG00000179832	ENST00000528919	Transcript	intron_variant	.	.	.	.	.	rs373393781	.	.	1	MROH1	HGNC	26958	protein_coding	YES	CCDS47938.1	ENSP00000435565	MROH1_HUMAN	.	UPI0001AE6FA6	.	.	.	.	11/42	.	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCCGCAGCC	byFrequency|byCluster	2	ESCA
SCRT1	0	.	GRCh37	8	145554612	145554612	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2235G>A	.	.	ENST00000332135	2/2	106	78	27	28	28	0	SCRT1,3_prime_UTR_variant,,ENST00000332135,;DGAT1,upstream_gene_variant,,ENST00000332324,;DGAT1,upstream_gene_variant,,ENST00000531896,;DGAT1,upstream_gene_variant,,ENST00000525371,;	T	ENSG00000170616	ENST00000332135	Transcript	3_prime_UTR_variant	3394	.	.	.	.	.	.	.	-1	SCRT1	HGNC	15950	protein_coding	YES	CCDS6421.1	ENSP00000331692	SCRT1_HUMAN	.	UPI0000071337	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCACGGCGG	.	5	ESCA
CPSF1	0	.	GRCh37	8	145625613	145625613	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.884delC	p.Pro295ArgfsTer53	p.P295Rfs*53	ENST00000349769	9/38	95	84	11	23	23	0	CPSF1,frameshift_variant,p.Pro295ArgfsTer53,ENST00000349769,;CPSF1,downstream_gene_variant,,ENST00000531042,;MIR1234,upstream_gene_variant,,ENST00000408875,;CPSF1,non_coding_transcript_exon_variant,,ENST00000532560,;CPSF1,non_coding_transcript_exon_variant,,ENST00000531683,;CPSF1,upstream_gene_variant,,ENST00000533492,;CPSF1,upstream_gene_variant,,ENST00000529288,;CPSF1,upstream_gene_variant,,ENST00000527916,;CPSF1,upstream_gene_variant,,ENST00000527827,;	-	ENSG00000071894	ENST00000349769	Transcript	frameshift_variant	979	884	295	P/X	cCg/cg	.	.	.	-1	CPSF1	HGNC	2324	protein_coding	YES	CCDS34966.1	ENSP00000339353	CPSF1_HUMAN	Q9C0J6_HUMAN,E9PIM1_HUMAN,D3DWL9_HUMAN	UPI00001282EE	.	.	.	9/38	.	hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF2,Pfam_domain:PF10433	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	CCATACGGGGGG	.	2	ESCA
GPT	0	.	GRCh37	8	145732306	145732306	+	Frame_Shift_Del	DEL	C	C	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1419delC	p.Leu474TrpfsTer11	p.L474Wfs*11	ENST00000394955	11/11	141	109	32	30	30	0	GPT,frameshift_variant,p.Leu474TrpfsTer11,ENST00000528431,;GPT,frameshift_variant,p.Leu474TrpfsTer11,ENST00000394955,;MFSD3,upstream_gene_variant,,ENST00000301327,;PPP1R16A,downstream_gene_variant,,ENST00000528430,;PPP1R16A,downstream_gene_variant,,ENST00000435887,;PPP1R16A,downstream_gene_variant,,ENST00000292539,;RECQL4,downstream_gene_variant,,ENST00000428558,;CTD-2517M22.14,upstream_gene_variant,,ENST00000527086,;RECQL4,downstream_gene_variant,,ENST00000532237,;RECQL4,downstream_gene_variant,,ENST00000531875,;RECQL4,downstream_gene_variant,,ENST00000529424,;RECQL4,downstream_gene_variant,,ENST00000532269,;PPP1R16A,downstream_gene_variant,,ENST00000526183,;GPT,downstream_gene_variant,,ENST00000527165,;RECQL4,downstream_gene_variant,,ENST00000301323,;GPT,downstream_gene_variant,,ENST00000354769,;GPT,downstream_gene_variant,,ENST00000531330,;CTD-2517M22.14,upstream_gene_variant,,ENST00000528690,;MFSD3,upstream_gene_variant,,ENST00000534427,;MFSD3,upstream_gene_variant,,ENST00000528047,;GPT,downstream_gene_variant,,ENST00000534702,;MFSD3,upstream_gene_variant,,ENST00000526749,;GPT,downstream_gene_variant,,ENST00000527961,;	-	ENSG00000167701	ENST00000394955	Transcript	frameshift_variant	1637	1414	472	P/X	Ccc/cc	COSM1674341	.	.	1	GPT	HGNC	4552	protein_coding	YES	CCDS6430.1	ENSP00000378408	ALAT1_HUMAN	.	UPI0000001054	.	.	.	11/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11751,hmmpanther:PTHR11751:SF308,Pfam_domain:PF00155,Gene3D:3.90.1150.10,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	5	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATTCTGCCCCCC	.	3	ESCA
ARHGAP39	0	.	GRCh37	8	145773078	145773078	+	Silent	SNP	C	C	T	rs758000654	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1392G>A	p.%3D	p.P464P	ENST00000377307	4/11	199	176	23	43	43	0	ARHGAP39,synonymous_variant,p.%3D,ENST00000540274,;ARHGAP39,synonymous_variant,p.%3D,ENST00000276826,;ARHGAP39,synonymous_variant,p.%3D,ENST00000377307,;ARHGAP39,upstream_gene_variant,,ENST00000528810,;AC084125.1,upstream_gene_variant,,ENST00000536320,;	T	ENSG00000147799	ENST00000377307	Transcript	synonymous_variant	1477	1392	464	P	ccG/ccA	rs758000654,COSM398382	.	.	-1	ARHGAP39	HGNC	29351	protein_coding	YES	CCDS34971.1	ENSP00000366522	RHG39_HUMAN	B3KS00_HUMAN	UPI000021015B	.	.	.	4/11	.	hmmpanther:PTHR23177:SF9,hmmpanther:PTHR23177	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCAGCGGCGT	byFrequency	4	ESCA
ZNF7	0	.	GRCh37	8	146063679	146063679	+	Intron	SNP	C	C	T	rs568673197	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247+787C>T	.	.	ENST00000528372	.	28	22	6	10	10	0	ZNF7,3_prime_UTR_variant,,ENST00000528130,;ZNF7,intron_variant,,ENST00000528372,;ZNF7,intron_variant,,ENST00000533314,;ZNF7,intron_variant,,ENST00000446747,;ZNF7,intron_variant,,ENST00000325217,;ZNF7,intron_variant,,ENST00000325241,;ZNF7,intron_variant,,ENST00000532777,;ZNF7,intron_variant,,ENST00000525266,;ZNF7,intron_variant,,ENST00000544249,;ZNF7,intron_variant,,ENST00000529819,;ZNF7,intron_variant,,ENST00000527218,;ZNF7,intron_variant,,ENST00000530776,;ZNF7,intron_variant,,ENST00000532051,;ZNF7,intron_variant,,ENST00000532393,;ZNF7,intron_variant,,ENST00000529767,;ZNF7,intron_variant,,ENST00000528017,;ZNF7,intron_variant,,ENST00000532382,;ZNF7,intron_variant,,ENST00000530082,;COMMD5,downstream_gene_variant,,ENST00000530332,;	T	ENSG00000147789	ENST00000528372	Transcript	intron_variant	.	.	.	.	.	rs568673197	.	.	1	ZNF7	HGNC	13139	protein_coding	YES	CCDS6435.1	ENSP00000432724	ZNF7_HUMAN	Q7KZ25_HUMAN,F5H290_HUMAN,E9PPK0_HUMAN	UPI000013C3F8	.	.	.	.	4/4	.	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTGCAACGA	by1000G	5	ESCA
MTMR7	0	.	GRCh37	8	17161980	17161980	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1401G>A	p.%3D	p.R467R	ENST00000180173	12/14	55	16	38	70	70	0	MTMR7,synonymous_variant,p.%3D,ENST00000521857,;MTMR7,synonymous_variant,p.%3D,ENST00000180173,;MTMR7,synonymous_variant,p.%3D,ENST00000398099,;MTMR7,non_coding_transcript_exon_variant,,ENST00000519763,;VPS37A,downstream_gene_variant,,ENST00000521162,;VPS37A,downstream_gene_variant,,ENST00000519515,;VPS37A,downstream_gene_variant,,ENST00000520997,;MTMR7,non_coding_transcript_exon_variant,,ENST00000519590,;	T	ENSG00000003987	ENST00000180173	Transcript	synonymous_variant	1436	1401	467	R	cgG/cgA	.	.	.	-1	MTMR7	HGNC	7454	protein_coding	YES	CCDS34851.1	ENSP00000180173	MTMR7_HUMAN	I0EZ69_HUMAN,B4E1E5_HUMAN,B4E1B6_HUMAN	UPI00004DFD27	.	.	.	12/14	.	PROSITE_profiles:PS51339,hmmpanther:PTHR10807:SF35,hmmpanther:PTHR10807,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGCCCGATT	.	5	ESCA
DMTN	0	.	GRCh37	8	21926552	21926552	+	Frame_Shift_Del	DEL	C	C	-	rs377647942	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281delC	p.Pro94HisfsTer137	p.P94Hfs*137	ENST00000523266	5/16	34	21	13	24	24	0	DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000265800,;DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000381470,;DMTN,frameshift_variant,p.Pro94HisfsTer?,ENST00000517804,;DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000415253,;DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000432128,;DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000519907,;DMTN,frameshift_variant,p.Pro69HisfsTer?,ENST00000520174,;DMTN,frameshift_variant,p.Pro69HisfsTer?,ENST00000522148,;DMTN,frameshift_variant,p.Pro69HisfsTer137,ENST00000443491,;DMTN,frameshift_variant,p.Pro94HisfsTer?,ENST00000519850,;DMTN,frameshift_variant,p.Pro69HisfsTer?,ENST00000523300,;DMTN,frameshift_variant,p.Pro69HisfsTer?,ENST00000523623,;DMTN,frameshift_variant,p.Pro69HisfsTer137,ENST00000523782,;DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000523266,;DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000358242,;DMTN,frameshift_variant,p.Pro94HisfsTer?,ENST00000517418,;DMTN,intron_variant,,ENST00000517600,;DMTN,frameshift_variant,p.Pro94HisfsTer137,ENST00000517305,;DMTN,non_coding_transcript_exon_variant,,ENST00000519333,;DMTN,non_coding_transcript_exon_variant,,ENST00000520856,;DMTN,non_coding_transcript_exon_variant,,ENST00000518816,;DMTN,downstream_gene_variant,,ENST00000522340,;DMTN,downstream_gene_variant,,ENST00000519959,;	-	ENSG00000158856	ENST00000523266	Transcript	frameshift_variant	737	275	92	S/X	tCc/tc	rs377647942,COSM1456022	.	.	1	DMTN	HGNC	3382	protein_coding	YES	CCDS6020.1	ENSP00000427866	DEMA_HUMAN	E5RJ61_HUMAN	UPI0000129189	.	.	.	5/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24213	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	6	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCACATCCCCCC	.	3	ESCA
PIWIL2	0	.	GRCh37	8	22211817	22211817	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2691G>A	p.%3D	p.R897R	ENST00000356766	22/23	47	14	32	59	59	0	PIWIL2,synonymous_variant,p.%3D,ENST00000454009,;PIWIL2,synonymous_variant,p.%3D,ENST00000356766,;PIWIL2,intron_variant,,ENST00000521356,;PIWIL2,non_coding_transcript_exon_variant,,ENST00000519884,;	A	ENSG00000197181	ENST00000356766	Transcript	synonymous_variant	2839	2691	897	R	cgG/cgA	.	.	.	1	PIWIL2	HGNC	17644	protein_coding	YES	CCDS6029.1	ENSP00000349208	PIWL2_HUMAN	.	UPI000006E98E	.	.	.	22/23	.	Superfamily_domains:SSF53098,SMART_domains:SM00950,Gene3D:3.30.420.10,Pfam_domain:PF02171,hmmpanther:PTHR22892:SF30,hmmpanther:PTHR22892,PROSITE_profiles:PS50822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACGGCAGGG	.	5	ESCA
STC1	0	.	GRCh37	8	23700815	23700815	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1468delA	.	.	ENST00000290271	4/4	18	6	11	20	20	0	STC1,3_prime_UTR_variant,,ENST00000290271,;STC1,downstream_gene_variant,,ENST00000524323,;	-	ENSG00000159167	ENST00000290271	Transcript	3_prime_UTR_variant	2496	.	.	.	.	.	.	.	-1	STC1	HGNC	11373	protein_coding	YES	CCDS6043.1	ENSP00000290271	STC1_HUMAN	Q71UE5_HUMAN,B4DN22_HUMAN	UPI00001360B4	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCTTTCTTTTTT	.	2	ESCA
STMN4	0	.	GRCh37	8	27097501	27097501	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578G>A	p.Arg193Gln	p.R193Q	ENST00000350889	6/7	59	21	38	71	70	0	STMN4,missense_variant,p.Arg166Gln,ENST00000519614,;STMN4,missense_variant,p.Arg193Gln,ENST00000523048,;STMN4,missense_variant,p.Arg193Gln,ENST00000350889,;STMN4,missense_variant,p.Arg166Gln,ENST00000265770,;STMN4,missense_variant,p.Arg157Gln,ENST00000519997,;STMN4,missense_variant,p.Arg193Gln,ENST00000522908,;STMN4,downstream_gene_variant,,ENST00000522750,;	T	ENSG00000015592	ENST00000350889	Transcript	missense_variant	692	578	193	R/Q	cGg/cAg	.	.	.	-1	STMN4	HGNC	16078	protein_coding	YES	CCDS6055.1	ENSP00000342538	STMN4_HUMAN	.	UPI000002B451	.	deleterious(0.02)	probably_damaging(0.995)	6/7	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51663,hmmpanther:PTHR10104:SF6,hmmpanther:PTHR10104,Pfam_domain:PF00836,PIRSF_domain:PIRSF002285,Superfamily_domains:0043535,Prints_domain:PR00345	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCCGTTCC	.	5	ESCA
GSR	0	.	GRCh37	8	30546820	30546820	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.899delA	p.Lys300ArgfsTer21	p.K300Rfs*21	ENST00000221130	9/13	39	24	15	26	26	0	GSR,frameshift_variant,p.Lys257ArgfsTer21,ENST00000414019,;GSR,frameshift_variant,p.Lys300ArgfsTer21,ENST00000221130,;GSR,frameshift_variant,p.Lys254ArgfsTer21,ENST00000520888,;GSR,frameshift_variant,p.Lys271ArgfsTer21,ENST00000546342,;GSR,intron_variant,,ENST00000541648,;GSR,intron_variant,,ENST00000537535,;GSR,3_prime_UTR_variant,,ENST00000523295,;	-	ENSG00000104687	ENST00000221130	Transcript	frameshift_variant	990	899	300	K/X	aAg/ag	.	.	.	-1	GSR	HGNC	4623	protein_coding	YES	CCDS34877.1	ENSP00000221130	GSHR_HUMAN	E5RI06_HUMAN	UPI000012BBFF	.	.	.	9/13	.	hmmpanther:PTHR22912:SF106,hmmpanther:PTHR22912,Pfam_domain:PF00070,TIGRFAM_domain:TIGR01421,Pfam_domain:PF07992,Gene3D:3.50.50.60,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAGTCTTTTTA	.	3	ESCA
CSMD1	0	.	GRCh37	8	3059147	3059147	+	Silent	SNP	C	C	A	rs376908643	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5085G>T	p.%3D	p.S1695S	ENST00000537824	32/70	40	8	31	37	37	0	CSMD1,synonymous_variant,p.%3D,ENST00000400186,;CSMD1,synonymous_variant,p.%3D,ENST00000542608,;CSMD1,synonymous_variant,p.%3D,ENST00000602723,;CSMD1,synonymous_variant,p.%3D,ENST00000335551,;CSMD1,synonymous_variant,p.%3D,ENST00000537824,;CSMD1,synonymous_variant,p.%3D,ENST00000520002,;CSMD1,synonymous_variant,p.%3D,ENST00000539096,;CSMD1,synonymous_variant,p.%3D,ENST00000602557,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523387,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,;	A	ENSG00000183117	ENST00000537824	Transcript	synonymous_variant	5085	5085	1695	S	tcG/tcT	rs376908643	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	.	32/70	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS01180,hmmpanther:PTHR19325:SF323,hmmpanther:PTHR19325,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	T:0.0006	T:0.0015	T:0	.	T:0	T:0.001	T:0	T:0.0008	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCCCGAGAG	byFrequency|byCluster|by1000G	5	ESCA
WRN	0	.	GRCh37	8	30921934	30921934	+	Silent	SNP	C	C	T	rs374898432	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339C>T	p.%3D	p.H113H	ENST00000298139	4/35	87	65	22	85	85	0	WRN,synonymous_variant,p.%3D,ENST00000298139,;	T	ENSG00000165392	ENST00000298139	Transcript	synonymous_variant	588	339	113	H	caC/caT	rs374898432	.	.	1	WRN	HGNC	12791	protein_coding	YES	CCDS6082.1	ENSP00000298139	WRN_HUMAN	.	UPI000013E49D	.	.	.	4/35	.	Superfamily_domains:SSF53098,SMART_domains:SM00474,Gene3D:3.30.420.10,Pfam_domain:PF01612,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF80	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCACGTTTC	byFrequency|byCluster	5	ESCA
DUSP26	0	.	GRCh37	8	33449611	33449611	+	Nonsense_Mutation	SNP	G	G	A	rs750549145	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556C>T	p.Arg186Ter	p.R186*	ENST00000256261	4/4	52	20	31	41	41	0	DUSP26,stop_gained,p.Arg186Ter,ENST00000523956,;DUSP26,stop_gained,p.Arg186Ter,ENST00000256261,;DUSP26,downstream_gene_variant,,ENST00000522982,;	A	ENSG00000133878	ENST00000256261	Transcript	stop_gained	1074	556	186	R/*	Cga/Tga	rs750549145	.	.	-1	DUSP26	HGNC	28161	protein_coding	YES	CCDS6092.1	ENSP00000256261	DUS26_HUMAN	E5RHD0_HUMAN	UPI000003E899	.	.	.	4/4	.	Superfamily_domains:SSF52799,SMART_domains:SM00195,Gene3D:3.90.190.10,Pfam_domain:PF00782,hmmpanther:PTHR10159:SF112,hmmpanther:PTHR10159,PROSITE_profiles:PS50056,PROSITE_profiles:PS50054	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCGGTGGT	.	5	ESCA
THAP1	0	.	GRCh37	8	42692825	42692825	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*280delT	.	.	ENST00000254250	3/3	44	17	27	34	34	0	THAP1,3_prime_UTR_variant,,ENST00000345117,;THAP1,3_prime_UTR_variant,,ENST00000254250,;THAP1,downstream_gene_variant,,ENST00000529779,;THAP1,downstream_gene_variant,,ENST00000532093,;	-	ENSG00000131931	ENST00000254250	Transcript	3_prime_UTR_variant	1153	.	.	.	.	.	.	.	-1	THAP1	HGNC	20856	protein_coding	YES	CCDS6136.1	ENSP00000254250	THAP1_HUMAN	.	UPI000007035E	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	AATACTAAAAAA	.	2	ESCA
TDRP	0	.	GRCh37	8	442324	442324	+	Intron	SNP	G	G	A	rs779642900	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.498+135C>T	.	.	ENST00000523656	.	24	6	17	38	38	0	TDRP,3_prime_UTR_variant,,ENST00000324079,;TDRP,intron_variant,,ENST00000523656,;TDRP,intron_variant,,ENST00000427263,;TDRP,downstream_gene_variant,,ENST00000524229,;	A	ENSG00000180190	ENST00000523656	Transcript	intron_variant	.	.	.	.	.	rs779642900	.	.	-1	TDRP	HGNC	26951	protein_coding	YES	CCDS59090.1	ENSP00000430325	TDRP_HUMAN	.	UPI000183D60A	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACGCGGAAAA	.	5	ESCA
PRKDC	0	.	GRCh37	8	48805866	48805866	+	Frame_Shift_Del	DEL	C	C	-	rs767959125	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3680delG	p.Gly1227ValfsTer49	p.G1227Vfs*49	ENST00000314191	31/87	239	206	33	47	47	0	PRKDC,frameshift_variant,p.Gly1227ValfsTer49,ENST00000338368,;PRKDC,frameshift_variant,p.Gly1227ValfsTer49,ENST00000314191,;AC103686.1,downstream_gene_variant,,ENST00000390136,;PRKDC,non_coding_transcript_exon_variant,,ENST00000518216,;PRKDC,non_coding_transcript_exon_variant,,ENST00000523565,;	-	ENSG00000253729	ENST00000314191	Transcript	frameshift_variant	3737	3680	1227	G/X	gGt/gt	rs767959125	.	.	-1	PRKDC	HGNC	9413	protein_coding	YES	.	ENSP00000313420	PRKDC_HUMAN	F5GX40_HUMAN	UPI000045790C	.	.	.	31/87	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF54,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGCCACCCCCC	.	3	ESCA
SNAI2	0	.	GRCh37	8	49831235	49831235	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*131A>G	.	.	ENST00000396822	4/4	33	19	14	17	17	0	SNAI2,3_prime_UTR_variant,,ENST00000020945,;SNAI2,3_prime_UTR_variant,,ENST00000396822,;RP11-22C8.1,downstream_gene_variant,,ENST00000438521,;RP11-22C8.1,downstream_gene_variant,,ENST00000522657,;	C	ENSG00000019549	ENST00000396822	Transcript	3_prime_UTR_variant	1296	.	.	.	.	.	.	.	-1	SNAI2	HGNC	11094	protein_coding	YES	CCDS6146.1	ENSP00000380034	SNAI2_HUMAN	.	UPI0000135A3A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTGTGTGCATA	.	4	ESCA
ST18	0	.	GRCh37	8	53055599	53055599	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2059C>A	p.Pro687Thr	p.P687T	ENST00000276480	17/26	126	90	36	36	36	0	ST18,missense_variant,p.Pro687Thr,ENST00000276480,;ST18,3_prime_UTR_variant,,ENST00000521824,;ST18,3_prime_UTR_variant,,ENST00000522251,;ST18,3_prime_UTR_variant,,ENST00000521582,;	T	ENSG00000147488	ENST00000276480	Transcript	missense_variant	2743	2059	687	P/T	Cca/Aca	COSM1457466	.	.	-1	ST18	HGNC	18695	protein_coding	YES	CCDS6149.1	ENSP00000276480	ST18_HUMAN	E5RHS3_HUMAN	UPI0000046C30	.	tolerated(0.28)	benign(0.008)	17/26	.	hmmpanther:PTHR10816:SF9,hmmpanther:PTHR10816,Pfam_domain:PF08474	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGGGTCTT	.	5	ESCA
PLAG1	0	.	GRCh37	8	57076593	57076593	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2209A>G	.	.	ENST00000316981	5/5	49	42	7	26	26	0	PLAG1,3_prime_UTR_variant,,ENST00000316981,;PLAG1,downstream_gene_variant,,ENST00000423799,;PLAG1,downstream_gene_variant,,ENST00000429357,;PLAG1,downstream_gene_variant,,ENST00000522009,;	C	ENSG00000181690	ENST00000316981	Transcript	3_prime_UTR_variant	4192	.	.	.	.	.	.	.	-1	PLAG1	HGNC	9045	protein_coding	YES	CCDS6165.1	ENSP00000325546	PLAG1_HUMAN	A7IT80_HUMAN,A7IT79_HUMAN	UPI000013FF2F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AGCAGTAATGA	.	2	ESCA
PLAG1	0	.	GRCh37	8	57077121	57077122	+	3'UTR	INS	-	-	T	rs199621845	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1680dupA	.	.	ENST00000316981	5/5	69	52	17	22	22	0	PLAG1,3_prime_UTR_variant,,ENST00000316981,;PLAG1,downstream_gene_variant,,ENST00000423799,;PLAG1,downstream_gene_variant,,ENST00000429357,;PLAG1,downstream_gene_variant,,ENST00000522009,;	T	ENSG00000181690	ENST00000316981	Transcript	3_prime_UTR_variant	3663-3664	.	.	.	.	rs199621845	.	.	-1	PLAG1	HGNC	9045	protein_coding	YES	CCDS6165.1	ENSP00000325546	PLAG1_HUMAN	A7IT80_HUMAN,A7IT79_HUMAN	UPI000013FF2F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TTTCTGTTTTT	by1000G	2	ESCA
ASPH	0	.	GRCh37	8	62537887	62537887	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.935-6309G>A	.	.	ENST00000379454	.	28	17	10	8	8	0	ASPH,3_prime_UTR_variant,,ENST00000519234,;ASPH,3_prime_UTR_variant,,ENST00000356457,;ASPH,3_prime_UTR_variant,,ENST00000517847,;ASPH,3_prime_UTR_variant,,ENST00000517903,;ASPH,3_prime_UTR_variant,,ENST00000518068,;ASPH,3_prime_UTR_variant,,ENST00000445642,;ASPH,intron_variant,,ENST00000522349,;ASPH,intron_variant,,ENST00000522919,;ASPH,intron_variant,,ENST00000379454,;ASPH,intron_variant,,ENST00000541428,;ASPH,downstream_gene_variant,,ENST00000522835,;ASPH,intron_variant,,ENST00000523927,;ASPH,intron_variant,,ENST00000523897,;ASPH,intron_variant,,ENST00000524173,;ASPH,downstream_gene_variant,,ENST00000519678,;ASPH,intron_variant,,ENST00000521499,;ASPH,downstream_gene_variant,,ENST00000518441,;	T	ENSG00000198363	ENST00000379454	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ASPH	HGNC	757	protein_coding	YES	CCDS34898.1	ENSP00000368767	ASPH_HUMAN	.	UPI0000161BFE	.	.	.	.	13/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAACCCAGCT	.	3	ESCA
MYBL1	0	.	GRCh37	8	67488453	67488453	+	Frame_Shift_Del	DEL	T	T	-	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1259delA	p.Asn420ThrfsTer13	p.N420Tfs*13	ENST00000522677	10/16	212	162	50	71	71	0	MYBL1,frameshift_variant,p.Asn420ThrfsTer13,ENST00000522677,;MYBL1,frameshift_variant,p.Asn420ThrfsTer13,ENST00000524176,;MYBL1,intron_variant,,ENST00000517885,;	-	ENSG00000185697	ENST00000522677	Transcript	frameshift_variant	1670	1259	420	N/X	aAc/ac	COSM1457861	.	.	-1	MYBL1	HGNC	7547	protein_coding	YES	CCDS47867.1	ENSP00000429633	MYBA_HUMAN	Q6LD85_HUMAN	UPI000012FADE	.	.	.	10/16	.	hmmpanther:PTHR10641:SF153,hmmpanther:PTHR10641	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.N420fs*13|c.1259delA|5,CODON|p.N420fs*4|c.1259_1260insA|5	INDELOCATOR|VARSCANI	CAAGTGTTTTTT	.	2	ESCA
CSPP1	0	.	GRCh37	8	68107929	68107929	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*107delT	.	.	ENST00000262210	29/29	89	59	30	24	24	0	CSPP1,3_prime_UTR_variant,,ENST00000262210,;CSPP1,3_prime_UTR_variant,,ENST00000412460,;ARFGEF1,intron_variant,,ENST00000520381,;ARFGEF1,downstream_gene_variant,,ENST00000518230,;ARFGEF1,downstream_gene_variant,,ENST00000518789,;ARFGEF1,downstream_gene_variant,,ENST00000262215,;CSPP1,downstream_gene_variant,,ENST00000519668,;ARFGEF1,intron_variant,,ENST00000522878,;ARFGEF1,downstream_gene_variant,,ENST00000517955,;CSPP1,downstream_gene_variant,,ENST00000521168,;CSPP1,downstream_gene_variant,,ENST00000521324,;ARFGEF1,downstream_gene_variant,,ENST00000518290,;	-	ENSG00000104218	ENST00000262210	Transcript	3_prime_UTR_variant	3798	.	.	.	.	.	.	.	1	CSPP1	HGNC	26193	protein_coding	YES	CCDS43744.1	ENSP00000262210	CSPP1_HUMAN	.	UPI00005A95D7	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTTACTTTTTT	.	3	ESCA
EYA1	0	.	GRCh37	8	72128937	72128938	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1349dupA	p.Asn450LysfsTer2	p.N450Kfs*2	ENST00000340726	14/18	98	79	19	36	36	0	EYA1,frameshift_variant,p.Asn416LysfsTer2,ENST00000388741,;EYA1,frameshift_variant,p.Asn415LysfsTer2,ENST00000419131,;EYA1,frameshift_variant,p.Asn450LysfsTer2,ENST00000388742,;EYA1,frameshift_variant,p.Asn450LysfsTer2,ENST00000340726,;EYA1,frameshift_variant,p.Asn417LysfsTer2,ENST00000388740,;EYA1,frameshift_variant,p.Asn449LysfsTer2,ENST00000388743,;EYA1,frameshift_variant,p.Asn444LysfsTer2,ENST00000303824,;EYA1,3_prime_UTR_variant,,ENST00000465115,;EYA1,3_prime_UTR_variant,,ENST00000493349,;EYA1,non_coding_transcript_exon_variant,,ENST00000496494,;	T	ENSG00000104313	ENST00000340726	Transcript	frameshift_variant	1989-1990	1349-1350	450	N/KX	aat/aaAt	.	.	.	-1	EYA1	HGNC	3519	protein_coding	YES	CCDS34906.1	ENSP00000342626	EYA1_HUMAN	Q4A4D0_HUMAN	UPI000012A3B3	.	.	.	14/18	.	TIGRFAM_domain:TIGR01658,hmmpanther:PTHR10190:SF11,hmmpanther:PTHR10190	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACATTATTTTT	.	3	ESCA
RP11-383H13.1	0	.	GRCh37	8	72965086	72965086	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*513C>T	.	.	ENST00000537896	5/5	19	4	14	9	9	0	RP11-383H13.1,3_prime_UTR_variant,,ENST00000537896,;TRPA1,intron_variant,,ENST00000523582,;TRPA1,intron_variant,,ENST00000262209,;RP11-383H13.1,downstream_gene_variant,,ENST00000524152,;RP11-383H13.1,non_coding_transcript_exon_variant,,ENST00000457356,;RP11-383H13.1,non_coding_transcript_exon_variant,,ENST00000512290,;RP11-383H13.1,intron_variant,,ENST00000518916,;RP11-383H13.1,downstream_gene_variant,,ENST00000519751,;RP11-383H13.1,3_prime_UTR_variant,,ENST00000522519,;RP11-383H13.1,intron_variant,,ENST00000519068,;TRPA1,downstream_gene_variant,,ENST00000520788,;	T	ENSG00000235531	ENST00000537896	Transcript	3_prime_UTR_variant	1332	.	.	.	.	.	.	.	1	RP11-383H13.1	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000440866	.	B7Z945_HUMAN	UPI000191533B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTAGCGACAC	.	3	ESCA
HNF4G	0	.	GRCh37	8	76459907	76459907	+	Frame_Shift_Del	DEL	A	A	-	rs763345258	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348delA	p.Glu117LysfsTer10	p.E117Kfs*10	ENST00000396423	3/10	108	78	30	58	58	0	HNF4G,frameshift_variant,p.Glu117LysfsTer10,ENST00000396423,;HNF4G,frameshift_variant,p.Glu80LysfsTer10,ENST00000354370,;HNF4G,non_coding_transcript_exon_variant,,ENST00000396419,;	-	ENSG00000164749	ENST00000396423	Transcript	frameshift_variant	467	343	115	K/X	Aaa/aa	rs763345258	.	.	1	HNF4G	HGNC	5026	protein_coding	YES	CCDS6220.2	ENSP00000379701	HNF4G_HUMAN	F1D8Q4_HUMAN	UPI0000D47E07	.	.	.	3/10	.	PROSITE_profiles:PS51030,hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Pfam_domain:PF00105,SMART_domains:SM00399,Superfamily_domains:SSF57716,Superfamily_domains:SSF48508,Prints_domain:PR00398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAATGAAAAAA	.	3	ESCA
RALYL	0	.	GRCh37	8	85774569	85774569	+	Missense_Mutation	SNP	G	G	A	rs766785304	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.491G>A	p.Arg164His	p.R164H	ENST00000517638	6/9	77	50	26	32	32	0	RALYL,missense_variant,p.Arg62His,ENST00000521376,;RALYL,missense_variant,p.Arg78His,ENST00000523850,;RALYL,missense_variant,p.Arg151His,ENST00000521695,;RALYL,missense_variant,p.Arg151His,ENST00000521268,;RALYL,missense_variant,p.Arg140His,ENST00000518566,;RALYL,missense_variant,p.Arg151His,ENST00000522455,;RALYL,missense_variant,p.Arg164His,ENST00000517638,;RP11-98H4.4,downstream_gene_variant,,ENST00000521595,;	A	ENSG00000184672	ENST00000517638	Transcript	missense_variant	615	491	164	R/H	cGt/cAt	rs766785304,COSM1159073,COSM1159074	.	.	1	RALYL	HGNC	27036	protein_coding	YES	CCDS55252.1	ENSP00000430128	.	G3V129_HUMAN,E5RIX9_HUMAN,E5RG71_HUMAN	UPI00002108E6	.	deleterious(0.02)	probably_damaging(0.962)	6/9	.	hmmpanther:PTHR13968,PIRSF_domain:PIRSF037992	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R151H|c.452G>A|3,SITE|p.R151H|c.452G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCGTGCAG	byFrequency	5	ESCA
MMP16	0	.	GRCh37	8	89051307	89051307	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2382T>C	.	.	ENST00000286614	10/10	69	64	5	36	36	0	MMP16,3_prime_UTR_variant,,ENST00000286614,;	G	ENSG00000156103	ENST00000286614	Transcript	3_prime_UTR_variant	4488	.	.	.	.	.	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTATAAATAT	.	2	ESCA
TMEM64	0	.	GRCh37	8	91637754	91637754	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*145delT	.	.	ENST00000458549	3/3	36	17	19	15	15	0	TMEM64,3_prime_UTR_variant,,ENST00000418210,;TMEM64,3_prime_UTR_variant,,ENST00000422900,;TMEM64,3_prime_UTR_variant,,ENST00000458549,;TMEM64,downstream_gene_variant,,ENST00000519519,;	-	ENSG00000180694	ENST00000458549	Transcript	3_prime_UTR_variant	1466	.	.	.	.	.	.	.	-1	TMEM64	HGNC	25441	protein_coding	YES	CCDS34920.2	ENSP00000414786	TMM64_HUMAN	B3KW24_HUMAN	UPI0000DBEF28	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGCTTTAAAAAA	.	2	ESCA
NECAB1	0	.	GRCh37	8	91952986	91952986	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.748-28G>A	.	.	ENST00000417640	.	61	55	5	23	23	0	NECAB1,5_prime_UTR_variant,,ENST00000521366,;NECAB1,intron_variant,,ENST00000522820,;NECAB1,intron_variant,,ENST00000417640,;	A	ENSG00000123119	ENST00000417640	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NECAB1	HGNC	20983	protein_coding	YES	CCDS47889.1	ENSP00000387380	NECA1_HUMAN	.	UPI0000070EEA	.	.	.	.	9/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCAACGCAGTG	.	3	ESCA
RUNX1T1	0	.	GRCh37	8	92988144	92988144	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1370G>T	p.Trp457Leu	p.W457L	ENST00000436581	9/11	64	19	45	25	25	0	RUNX1T1,missense_variant,p.Trp457Leu,ENST00000436581,;RUNX1T1,missense_variant,p.Trp446Leu,ENST00000265814,;RUNX1T1,missense_variant,p.Trp419Leu,ENST00000518844,;RUNX1T1,missense_variant,p.Trp446Leu,ENST00000523629,;RUNX1T1,missense_variant,p.Trp409Leu,ENST00000360348,;RUNX1T1,missense_variant,p.Trp409Leu,ENST00000520724,;RUNX1T1,missense_variant,p.Trp419Leu,ENST00000396218,;RUNX1T1,missense_variant,p.Trp409Leu,ENST00000422361,;GS1-5L10.1,non_coding_transcript_exon_variant,,ENST00000522980,;RUNX1T1,3_prime_UTR_variant,,ENST00000521751,;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,upstream_gene_variant,,ENST00000521078,;	A	ENSG00000079102	ENST00000436581	Transcript	missense_variant	1381	1370	457	W/L	tGg/tTg	.	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	tolerated(0.12)	benign(0.41)	9/11	.	hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTCCAGATC	.	5	ESCA
RBM12B	0	.	GRCh37	8	94744119	94744119	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1514delA	.	.	ENST00000399300	3/3	66	41	25	24	23	0	RBM12B,3_prime_UTR_variant,,ENST00000399300,;RBM12B,3_prime_UTR_variant,,ENST00000517700,;RBM12B,downstream_gene_variant,,ENST00000519109,;FAM92A1,downstream_gene_variant,,ENST00000518322,;FAM92A1,downstream_gene_variant,,ENST00000517718,;RBM12B,downstream_gene_variant,,ENST00000518597,;RBM12B,downstream_gene_variant,,ENST00000521947,;FAM92A1,downstream_gene_variant,,ENST00000423990,;FAM92A1,downstream_gene_variant,,ENST00000521641,;RBM12B,downstream_gene_variant,,ENST00000520560,;RP11-10N23.4,upstream_gene_variant,,ENST00000517998,;RBM12B,intron_variant,,ENST00000520961,;FAM92A1,downstream_gene_variant,,ENST00000520363,;FAM92A1,downstream_gene_variant,,ENST00000359421,;FAM92A1,downstream_gene_variant,,ENST00000523577,;FAM92A1,downstream_gene_variant,,ENST00000518116,;FAM92A1,downstream_gene_variant,,ENST00000452913,;	-	ENSG00000183808	ENST00000399300	Transcript	3_prime_UTR_variant	4734	.	.	.	.	.	.	.	-1	RBM12B	HGNC	32310	protein_coding	YES	CCDS43755.1	ENSP00000382239	RB12B_HUMAN	E5RJW8_HUMAN,E5RJV8_HUMAN,E5RJ83_HUMAN,E5RHG1_HUMAN	UPI0000E9B14C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCACTCTTTTTT	.	2	ESCA
RBM12B	0	.	GRCh37	8	94746149	94746149	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2490C>A	p.%3D	p.P830P	ENST00000399300	3/3	78	44	34	35	35	0	RBM12B,synonymous_variant,p.%3D,ENST00000399300,;RBM12B,synonymous_variant,p.%3D,ENST00000517700,;RBM12B,downstream_gene_variant,,ENST00000519109,;FAM92A1,downstream_gene_variant,,ENST00000518322,;RBM12B,downstream_gene_variant,,ENST00000520560,;RBM12B,downstream_gene_variant,,ENST00000518597,;RBM12B,downstream_gene_variant,,ENST00000521947,;RP11-10N23.4,non_coding_transcript_exon_variant,,ENST00000517998,;RBM12B,intron_variant,,ENST00000520961,;FAM92A1,downstream_gene_variant,,ENST00000518116,;FAM92A1,downstream_gene_variant,,ENST00000523577,;	T	ENSG00000183808	ENST00000399300	Transcript	synonymous_variant	2704	2490	830	P	ccC/ccA	.	.	.	-1	RBM12B	HGNC	32310	protein_coding	YES	CCDS43755.1	ENSP00000382239	RB12B_HUMAN	E5RJW8_HUMAN,E5RJV8_HUMAN,E5RJ83_HUMAN,E5RHG1_HUMAN	UPI0000E9B14C	.	.	.	3/3	.	hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGGGGGCT	.	5	ESCA
RBM12B-AS1	0	.	GRCh37	8	94752472	94752472	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-9C>T	.	.	ENST00000391680	1/1	81	50	31	23	23	0	RBM12B-AS1,5_prime_UTR_variant,,ENST00000391680,;RBM12B,intron_variant,,ENST00000519109,;RBM12B,intron_variant,,ENST00000399300,;RBM12B,intron_variant,,ENST00000517700,;RBM12B,intron_variant,,ENST00000518597,;RBM12B,intron_variant,,ENST00000520560,;RBM12B,intron_variant,,ENST00000521947,;RP11-10N23.5,upstream_gene_variant,,ENST00000523945,;RBM12B,upstream_gene_variant,,ENST00000520961,;	T	ENSG00000212998	ENST00000391680	Transcript	5_prime_UTR_variant	124	.	.	.	.	.	.	.	1	RBM12B-AS1	HGNC	28818	protein_coding	YES	.	ENSP00000375562	RBAS1_HUMAN	.	UPI000013EA3C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGACGAATC	.	5	ESCA
GEM	0	.	GRCh37	8	95262531	95262532	+	3'UTR	INS	-	-	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6dupC	.	.	ENST00000297596	5/5	151	112	39	46	46	0	GEM,3_prime_UTR_variant,,ENST00000297596,;GEM,3_prime_UTR_variant,,ENST00000396194,;	G	ENSG00000164949	ENST00000297596	Transcript	3_prime_UTR_variant	1162-1163	.	.	.	.	.	.	.	-1	GEM	HGNC	4234	protein_coding	YES	CCDS6261.1	ENSP00000297596	GEM_HUMAN	E5RJF9_HUMAN	UPI000012B3BC	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GACCCTGGGTT	.	3	ESCA
TP53INP1	0	.	GRCh37	8	95941247	95941247	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1460T>C	.	.	ENST00000342697	4/4	87	56	31	29	29	0	TP53INP1,3_prime_UTR_variant,,ENST00000342697,;TP53INP1,3_prime_UTR_variant,,ENST00000448464,;NDUFAF6,intron_variant,,ENST00000519136,;NDUFAF6,intron_variant,,ENST00000396113,;NDUFAF6,intron_variant,,ENST00000523378,;TP53INP1,downstream_gene_variant,,ENST00000378776,;	G	ENSG00000164938	ENST00000342697	Transcript	3_prime_UTR_variant	2591	.	.	.	.	.	.	.	-1	TP53INP1	HGNC	18022	protein_coding	YES	CCDS6265.1	ENSP00000344215	T53I1_HUMAN	.	UPI00000725F8	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAAACCCAT	.	5	ESCA
KCNS2	0	.	GRCh37	8	99441109	99441109	+	Missense_Mutation	SNP	G	G	A	rs745687970	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.902G>A	p.Arg301Gln	p.R301Q	ENST00000287042	2/2	71	63	7	27	27	0	KCNS2,missense_variant,p.Arg301Gln,ENST00000287042,;KCNS2,missense_variant,p.Arg301Gln,ENST00000521839,;STK3,intron_variant,,ENST00000517832,;	A	ENSG00000156486	ENST00000287042	Transcript	missense_variant	1252	902	301	R/Q	cGg/cAg	rs745687970	.	.	1	KCNS2	HGNC	6301	protein_coding	YES	CCDS6279.1	ENSP00000287042	KCNS2_HUMAN	.	UPI0000001653	.	deleterious(0)	probably_damaging(0.992)	2/2	.	Prints_domain:PR00169,Superfamily_domains:SSF81324,Pfam_domain:PF00520,Gene3D:1.20.120.350,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATGCGGATCT	byFrequency	4	ESCA
STK3	0	.	GRCh37	8	99467038	99467038	+	3'UTR	DEL	T	T	-	rs545434912	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1032delA	.	.	ENST00000523601	13/13	57	34	22	15	15	0	STK3,3_prime_UTR_variant,,ENST00000523601,;STK3,3_prime_UTR_variant,,ENST00000419617,;STK3,intron_variant,,ENST00000517832,;	-	ENSG00000104375	ENST00000523601	Transcript	3_prime_UTR_variant	2992	.	.	.	.	rs545434912	.	.	-1	STK3	HGNC	11406	protein_coding	YES	CCDS59108.1	ENSP00000429744	.	B3KYA7_HUMAN	UPI00004FB517	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTAATCTTTTTT	byCluster	2	ESCA
CCDC180	0	.	GRCh37	9	100085126	100085126	+	Missense_Mutation	SNP	G	G	A	rs142121305	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1303G>A	p.Val435Met	p.V435M	ENST00000375202	26/51	107	78	29	70	70	0	CCDC180,missense_variant,p.Val574Met,ENST00000357054,;CCDC180,missense_variant,p.Val435Met,ENST00000375202,;CCDC180,missense_variant,p.Val435Met,ENST00000529487,;CCDC180,missense_variant,p.Val534Met,ENST00000395220,;CCDC180,missense_variant,p.Val432Met,ENST00000411667,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000532526,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000375206,;CCDC180,non_coding_transcript_exon_variant,,ENST00000460482,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000534123,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000529787,;CCDC180,non_coding_transcript_exon_variant,,ENST00000494917,;	A	ENSG00000197816	ENST00000375202	Transcript	missense_variant	2655	1303	435	V/M	Gtg/Atg	rs142121305	.	.	1	CCDC180	HGNC	29303	protein_coding	YES	CCDS35077.2	ENSP00000364348	CC180_HUMAN	B7ZMG3_HUMAN	UPI00016277C6	.	tolerated(1)	benign(0.062)	26/51	.	hmmpanther:PTHR21444:SF14,hmmpanther:PTHR21444,Pfam_domain:PF14643	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACGTGGAC	byCluster	5	ESCA
ALDOB	0	.	GRCh37	9	104189797	104189797	+	Silent	SNP	G	G	A	rs746351347	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.N169N	ENST00000374855	5/9	63	47	16	24	24	0	ALDOB,synonymous_variant,p.%3D,ENST00000374855,;ALDOB,intron_variant,,ENST00000468981,;	A	ENSG00000136872	ENST00000374855	Transcript	synonymous_variant	632	507	169	N	aaC/aaT	rs746351347	.	.	-1	ALDOB	HGNC	417	protein_coding	YES	CCDS6756.1	ENSP00000363988	ALDOB_HUMAN	.	UPI000016A4A9	.	.	.	5/9	.	Superfamily_domains:SSF51569,Gene3D:3.20.20.70,Pfam_domain:PF00274,hmmpanther:PTHR11627,hmmpanther:PTHR11627:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGCGTTGGC	byFrequency	5	ESCA
SLC44A1	0	.	GRCh37	9	108151462	108151463	+	3'UTR	DEL	AC	AC	-	rs373188354	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AC	AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*136_*137delCA	.	.	ENST00000374720	16/16	74	49	25	68	68	0	SLC44A1,3_prime_UTR_variant,,ENST00000374720,;SLC44A1,intron_variant,,ENST00000374724,;SLC44A1,intron_variant,,ENST00000343170,;SLC44A1,intron_variant,,ENST00000374723,;SLC44A1,intron_variant,,ENST00000436716,;SLC44A1,splice_region_variant,,ENST00000470972,;	-	ENSG00000070214	ENST00000374720	Transcript	3_prime_UTR_variant	2346-2347	.	.	.	.	rs373188354	.	.	1	SLC44A1	HGNC	18798	protein_coding	YES	CCDS6763.1	ENSP00000363852	CTL1_HUMAN	B3KMS7_HUMAN	UPI0000062328	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	11	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTATATACACACA	.	2	ESCA
FAM206A	0	.	GRCh37	9	111698645	111698645	+	Silent	SNP	T	T	C	rs767557342	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189T>C	p.%3D	p.I63I	ENST00000322940	3/6	33	25	8	26	26	0	FAM206A,synonymous_variant,p.%3D,ENST00000445175,;FAM206A,synonymous_variant,p.%3D,ENST00000322940,;FAM206A,synonymous_variant,p.%3D,ENST00000374624,;IKBKAP,upstream_gene_variant,,ENST00000537196,;IKBKAP,upstream_gene_variant,,ENST00000374647,;FAM206A,downstream_gene_variant,,ENST00000466200,;	C	ENSG00000119328	ENST00000322940	Transcript	synonymous_variant	495	189	63	I	atT/atC	rs767557342	.	.	1	FAM206A	HGNC	1364	protein_coding	YES	CCDS6774.1	ENSP00000363753	F206A_HUMAN	.	UPI0000072779	.	.	.	3/6	.	Superfamily_domains:SSF51230,hmmpanther:PTHR13651,hmmpanther:PTHR13651:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATTAAAAG	byFrequency|byCluster	5	ESCA
TMEM245	0	.	GRCh37	9	111849505	111849505	+	Missense_Mutation	SNP	G	G	A	rs565558586	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1268C>T	p.Ala423Val	p.A423V	ENST00000374586	6/18	37	27	10	30	30	0	TMEM245,missense_variant,p.Ala423Val,ENST00000374586,;TMEM245,missense_variant,p.Ala24Val,ENST00000413712,;TMEM245,missense_variant,p.Ala173Val,ENST00000491854,;	A	ENSG00000106771	ENST00000374586	Transcript	missense_variant	1300	1268	423	A/V	gCg/gTg	rs565558586	.	.	-1	TMEM245	HGNC	1363	protein_coding	YES	CCDS43858.1	ENSP00000363714	TM245_HUMAN	.	UPI000013C833	.	tolerated(0.85)	benign(0.064)	6/18	.	hmmpanther:PTHR21716,hmmpanther:PTHR21716:SF1	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCGCGAGA	by1000G	5	ESCA
SVEP1	0	.	GRCh37	9	113208246	113208246	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4334T>C	p.Leu1445Pro	p.L1445P	ENST00000401783	26/48	38	26	12	21	21	0	SVEP1,missense_variant,p.Leu1445Pro,ENST00000401783,;SVEP1,missense_variant,p.Leu1422Pro,ENST00000374469,;SVEP1,missense_variant,p.Leu1445Pro,ENST00000302728,;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,;	G	ENSG00000165124	ENST00000401783	Transcript	missense_variant	4671	4334	1445	L/P	cTc/cCc	.	.	.	-1	SVEP1	HGNC	15985	protein_coding	YES	CCDS48004.1	ENSP00000384917	SVEP1_HUMAN	.	UPI000153DA74	.	.	probably_damaging(0.982)	26/48	.	Superfamily_domains:SSF49899,SMART_domains:SM00159,Gene3D:2.60.120.200,Pfam_domain:PF00354,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.M1444L|c.4330A>C|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGGAGCATG	.	5	ESCA
SVEP1	0	.	GRCh37	9	113219572	113219572	+	Missense_Mutation	SNP	G	G	A	rs185467075	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3637C>T	p.Arg1213Cys	p.R1213C	ENST00000401783	21/48	31	16	15	35	35	0	SVEP1,missense_variant,p.Arg1213Cys,ENST00000401783,;SVEP1,missense_variant,p.Arg1190Cys,ENST00000374469,;SVEP1,missense_variant,p.Arg1213Cys,ENST00000302728,;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,;	A	ENSG00000165124	ENST00000401783	Transcript	missense_variant	3974	3637	1213	R/C	Cgt/Tgt	rs185467075,COSM1228064	.	.	-1	SVEP1	HGNC	15985	protein_coding	YES	CCDS48004.1	ENSP00000384917	SVEP1_HUMAN	.	UPI000153DA74	.	.	possibly_damaging(0.67)	21/48	.	Superfamily_domains:SSF57196,SMART_domains:SM00179,SMART_domains:SM00181,Gene3D:2.10.25.10,Pfam_domain:PF00008,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,PROSITE_profiles:PS50026	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACGCCCAA	byCluster|by1000G	5	ESCA
MUSK	0	.	GRCh37	9	113457777	113457777	+	Silent	SNP	A	A	G	rs373961420	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453A>G	p.%3D	p.S151S	ENST00000374448	4/15	29	21	8	36	36	0	MUSK,synonymous_variant,p.%3D,ENST00000374440,;MUSK,synonymous_variant,p.%3D,ENST00000374448,;MUSK,synonymous_variant,p.%3D,ENST00000374439,;MUSK,synonymous_variant,p.%3D,ENST00000189978,;MUSK,synonymous_variant,p.%3D,ENST00000416899,;	G	ENSG00000030304	ENST00000374448	Transcript	synonymous_variant	587	453	151	S	tcA/tcG	rs373961420	.	.	1	MUSK	HGNC	7525	protein_coding	YES	CCDS48005.1	ENSP00000363571	MUSK_HUMAN	.	UPI000006D2F7	.	.	.	4/15	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00408,Pfam_domain:PF07679,Gene3D:2.60.40.10,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF63,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCAGTGTC	byFrequency|byCluster	5	ESCA
PTBP3	0	.	GRCh37	9	114981366	114981366	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4765C>T	.	.	ENST00000458258	14/14	19	13	5	11	11	0	PTBP3,3_prime_UTR_variant,,ENST00000374257,;PTBP3,3_prime_UTR_variant,,ENST00000334318,;PTBP3,3_prime_UTR_variant,,ENST00000458258,;PTBP3,downstream_gene_variant,,ENST00000343327,;PTBP3,downstream_gene_variant,,ENST00000374255,;	A	ENSG00000119314	ENST00000458258	Transcript	3_prime_UTR_variant	6442	.	.	.	.	.	.	.	-1	PTBP3	HGNC	10253	protein_coding	YES	CCDS59141.1	ENSP00000414921	PTBP3_HUMAN	.	UPI000000DA96	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCGCTCTG	.	5	ESCA
PTBP3	0	.	GRCh37	9	114982433	114982433	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3698delT	.	.	ENST00000458258	14/14	35	26	9	20	20	0	PTBP3,3_prime_UTR_variant,,ENST00000374257,;PTBP3,3_prime_UTR_variant,,ENST00000334318,;PTBP3,3_prime_UTR_variant,,ENST00000458258,;PTBP3,downstream_gene_variant,,ENST00000343327,;PTBP3,downstream_gene_variant,,ENST00000374255,;	-	ENSG00000119314	ENST00000458258	Transcript	3_prime_UTR_variant	5375	.	.	.	.	.	.	.	-1	PTBP3	HGNC	10253	protein_coding	YES	CCDS59141.1	ENSP00000414921	PTBP3_HUMAN	.	UPI000000DA96	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGGGGAAAAAC	.	3	ESCA
ZNF618	0	.	GRCh37	9	116818309	116818311	+	3'UTR	DEL	TGT	TGT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TGT	TGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5865_*5867delTGT	.	.	ENST00000288466	14/14	58	39	19	43	43	0	ZNF618,3_prime_UTR_variant,,ENST00000288466,;AMBP,downstream_gene_variant,,ENST00000466610,;AMBP,downstream_gene_variant,,ENST00000265132,;AMBP,downstream_gene_variant,,ENST00000540645,;	-	ENSG00000157657	ENST00000288466	Transcript	3_prime_UTR_variant	8547-8549	.	.	.	.	.	.	.	1	ZNF618	HGNC	29416	protein_coding	YES	CCDS48008.1	ENSP00000288466	ZN618_HUMAN	.	UPI0000D4BD81	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAAGATGTTGTGT	.	3	ESCA
CBWD1	0	.	GRCh37	9	121272	121272	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*195C>T	.	.	ENST00000356521	15/15	61	47	14	50	50	0	CBWD1,3_prime_UTR_variant,,ENST00000377400,;CBWD1,3_prime_UTR_variant,,ENST00000356521,;CBWD1,downstream_gene_variant,,ENST00000382447,;CBWD1,downstream_gene_variant,,ENST00000314367,;FOXD4,upstream_gene_variant,,ENST00000382500,;CBWD1,non_coding_transcript_exon_variant,,ENST00000475990,;CBWD1,downstream_gene_variant,,ENST00000475411,;CBWD1,downstream_gene_variant,,ENST00000465014,;CBWD1,downstream_gene_variant,,ENST00000487575,;CBWD1,downstream_gene_variant,,ENST00000464198,;CBWD1,downstream_gene_variant,,ENST00000462513,;CBWD1,downstream_gene_variant,,ENST00000495302,;	A	ENSG00000172785	ENST00000356521	Transcript	3_prime_UTR_variant	1472	.	.	.	.	.	.	.	-1	CBWD1	HGNC	17134	protein_coding	YES	CCDS6438.1	ENSP00000348915	CBWD1_HUMAN	.	UPI000006EFDF	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAAAGGATAT	.	4	ESCA
MEGF9	0	.	GRCh37	9	123366682	123366682	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*786delA	.	.	ENST00000373930	6/6	36	24	12	11	11	0	MEGF9,3_prime_UTR_variant,,ENST00000426959,;MEGF9,3_prime_UTR_variant,,ENST00000373930,;	-	ENSG00000106780	ENST00000373930	Transcript	3_prime_UTR_variant	2707	.	.	.	.	.	.	.	-1	MEGF9	HGNC	3234	protein_coding	YES	CCDS48010.2	ENSP00000363040	MEGF9_HUMAN	.	UPI000045779F	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACATGATTTTTT	.	2	ESCA
ZBTB34	0	.	GRCh37	9	129645443	129645443	+	3'UTR	DEL	T	T	-	rs375804188	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2258delT	.	.	ENST00000373452	1/1	17	8	9	11	10	0	ZBTB34,3_prime_UTR_variant,,ENST00000319119,;ZBTB34,3_prime_UTR_variant,,ENST00000373452,;	-	ENSG00000177125	ENST00000373452	Transcript	3_prime_UTR_variant	3817	.	.	.	.	rs375804188	.	.	1	ZBTB34	HGNC	31446	protein_coding	YES	CCDS48023.1	ENSP00000362551	ZBT34_HUMAN	.	UPI00004031FA	.	.	.	1/1	.	.	-:0.0355	-:0	-:0.0029	.	-:0.1052	-:0.001	-:0.0706	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTGGGTTTTTT	byFrequency|byCluster|by1000G	2	ESCA
ZBTB34	0	.	GRCh37	9	129646127	129646127	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2934C>A	.	.	ENST00000373452	1/1	48	29	19	17	17	0	ZBTB34,3_prime_UTR_variant,,ENST00000319119,;ZBTB34,3_prime_UTR_variant,,ENST00000373452,;	A	ENSG00000177125	ENST00000373452	Transcript	3_prime_UTR_variant	4501	.	.	.	.	.	.	.	1	ZBTB34	HGNC	31446	protein_coding	YES	CCDS48023.1	ENSP00000362551	ZBT34_HUMAN	.	UPI00004031FA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTCCATTC	.	5	ESCA
ZBTB34	0	.	GRCh37	9	129647021	129647022	+	3'UTR	INS	-	-	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3834dupG	.	.	ENST00000373452	1/1	24	13	11	19	19	0	ZBTB34,3_prime_UTR_variant,,ENST00000319119,;ZBTB34,3_prime_UTR_variant,,ENST00000373452,;	G	ENSG00000177125	ENST00000373452	Transcript	3_prime_UTR_variant	5395-5396	.	.	.	.	.	.	.	1	ZBTB34	HGNC	31446	protein_coding	YES	CCDS48023.1	ENSP00000362551	ZBT34_HUMAN	.	UPI00004031FA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGGGCTGGGGG	.	2	ESCA
MPDZ	0	.	GRCh37	9	13106846	13106846	+	3'UTR	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*118delG	.	.	ENST00000541718	46/46	71	53	18	26	26	0	MPDZ,3_prime_UTR_variant,,ENST00000438511,;MPDZ,3_prime_UTR_variant,,ENST00000381022,;MPDZ,3_prime_UTR_variant,,ENST00000545857,;MPDZ,3_prime_UTR_variant,,ENST00000541093,;MPDZ,3_prime_UTR_variant,,ENST00000319217,;MPDZ,3_prime_UTR_variant,,ENST00000538841,;MPDZ,3_prime_UTR_variant,,ENST00000541718,;MPDZ,downstream_gene_variant,,ENST00000447879,;MPDZ,downstream_gene_variant,,ENST00000546205,;MPDZ,downstream_gene_variant,,ENST00000381015,;MPDZ,downstream_gene_variant,,ENST00000536827,;MPDZ,non_coding_transcript_exon_variant,,ENST00000381017,;MPDZ,non_coding_transcript_exon_variant,,ENST00000319198,;MPDZ,non_coding_transcript_exon_variant,,ENST00000539508,;MPDZ,downstream_gene_variant,,ENST00000542806,;	-	ENSG00000107186	ENST00000541718	Transcript	3_prime_UTR_variant	6466	.	.	.	.	.	.	.	-1	MPDZ	HGNC	7208	protein_coding	YES	CCDS47951.1	ENSP00000439807	MPDZ_HUMAN	.	UPI00015367D3	.	.	.	46/46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTATTTCCCCCC	.	3	ESCA
PKN3	0	.	GRCh37	9	131482844	131482844	+	Missense_Mutation	SNP	C	C	T	rs754968087	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2629C>T	p.Arg877Trp	p.R877W	ENST00000291906	22/22	60	18	42	22	22	0	PKN3,missense_variant,p.Arg877Trp,ENST00000291906,;ZDHHC12,downstream_gene_variant,,ENST00000372667,;ZDHHC12,downstream_gene_variant,,ENST00000406904,;ZDHHC12,downstream_gene_variant,,ENST00000372672,;ZDHHC12,downstream_gene_variant,,ENST00000372663,;ZDHHC12,downstream_gene_variant,,ENST00000452105,;RP11-545E17.3,upstream_gene_variant,,ENST00000443631,;PKN3,non_coding_transcript_exon_variant,,ENST00000483521,;ZDHHC12,downstream_gene_variant,,ENST00000467312,;PKN3,downstream_gene_variant,,ENST00000485301,;	T	ENSG00000160447	ENST00000291906	Transcript	missense_variant	3022	2629	877	R/W	Cgg/Tgg	rs754968087	.	.	1	PKN3	HGNC	17999	protein_coding	YES	CCDS6908.1	ENSP00000291906	PKN3_HUMAN	Q05BU1_HUMAN	UPI000013E087	.	deleterious(0.01)	benign(0.017)	22/22	.	SMART_domains:SM00133,Pfam_domain:PF00433,hmmpanther:PTHR24357:SF53,hmmpanther:PTHR24357,PROSITE_profiles:PS51285	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCCGGGAC	byFrequency	5	ESCA
CRAT	0	.	GRCh37	9	131864814	131864814	+	Frame_Shift_Del	DEL	C	C	-	rs766774245,rs773396880	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495delG	p.Lys166SerfsTer5	p.K166Sfs*5	ENST00000318080	5/14	121	81	40	43	43	0	CRAT,frameshift_variant,p.Lys166SerfsTer5,ENST00000318080,;CRAT,upstream_gene_variant,,ENST00000455396,;CRAT,downstream_gene_variant,,ENST00000393384,;AL158151.2,downstream_gene_variant,,ENST00000408594,;RP11-247A12.1,downstream_gene_variant,,ENST00000434250,;CRAT,non_coding_transcript_exon_variant,,ENST00000464290,;CRAT,upstream_gene_variant,,ENST00000467343,;CRAT,3_prime_UTR_variant,,ENST00000415948,;CRAT,3_prime_UTR_variant,,ENST00000458362,;CRAT,downstream_gene_variant,,ENST00000441796,;	-	ENSG00000095321	ENST00000318080	Transcript	frameshift_variant	790	495	165	G/X	ggG/gg	rs766774245,rs773396880,COSM1460391	.	.	-1	CRAT	HGNC	2342	protein_coding	YES	CCDS6919.1	ENSP00000315013	CACP_HUMAN	.	UPI000014021A	.	.	.	5/14	.	hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF50,Pfam_domain:PF00755,Superfamily_domains:SSF52777	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGCTTCCCCCC	byFrequency	3	ESCA
TTF1	0	.	GRCh37	9	135277540	135277541	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668dupA	p.Lys224GlufsTer5	p.K224Efs*5	ENST00000334270	2/11	55	38	17	22	22	0	TTF1,frameshift_variant,p.Lys224GlufsTer5,ENST00000334270,;	T	ENSG00000125482	ENST00000334270	Transcript	frameshift_variant	708-709	668-669	223	K/KX	aag/aaAg	.	.	.	-1	TTF1	HGNC	12397	protein_coding	YES	CCDS6948.1	ENSP00000333920	TTF1_HUMAN	.	UPI00001B55A7	.	.	.	2/11	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S226F|c.677C>T|3	INDELOCATOR|VARSCANI	TTTTTCTTTTT	.	2	ESCA
SURF1	0	.	GRCh37	9	136218825	136218826	+	Frame_Shift_Del	DEL	AG	AG	-	rs782316919	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.845_846delCT	p.Ser282CysfsTer9	p.S282Cfs*9	ENST00000371974	9/9	68	53	15	34	34	0	SURF1,frameshift_variant,p.Ser282CysfsTer9,ENST00000371974,;SURF2,upstream_gene_variant,,ENST00000371964,;MED22,upstream_gene_variant,,ENST00000476080,;MED22,upstream_gene_variant,,ENST00000344469,;RPL7A,downstream_gene_variant,,ENST00000426651,;RPL7A,downstream_gene_variant,,ENST00000315731,;MED22,upstream_gene_variant,,ENST00000491289,;MED22,upstream_gene_variant,,ENST00000343730,;MED22,upstream_gene_variant,,ENST00000494177,;RPL7A,downstream_gene_variant,,ENST00000323345,;MED22,upstream_gene_variant,,ENST00000446777,;MED22,upstream_gene_variant,,ENST00000371999,;MED22,upstream_gene_variant,,ENST00000457204,;SNORD36C,downstream_gene_variant,,ENST00000516733,;SNORD24,downstream_gene_variant,,ENST00000383884,;SNORD36A,downstream_gene_variant,,ENST00000362874,;SNORD36B,downstream_gene_variant,,ENST00000363961,;SURF1,non_coding_transcript_exon_variant,,ENST00000495952,;RPL7A,downstream_gene_variant,,ENST00000496554,;RPL7A,downstream_gene_variant,,ENST00000468019,;RPL7A,downstream_gene_variant,,ENST00000485706,;RPL7A,downstream_gene_variant,,ENST00000489392,;SURF2,upstream_gene_variant,,ENST00000495524,;MED22,upstream_gene_variant,,ENST00000471524,;RPL7A,downstream_gene_variant,,ENST00000463740,;SURF1,downstream_gene_variant,,ENST00000463965,;RPL7A,downstream_gene_variant,,ENST00000492798,;SURF1,non_coding_transcript_exon_variant,,ENST00000437995,;MED22,upstream_gene_variant,,ENST00000482295,;	-	ENSG00000148290	ENST00000371974	Transcript	frameshift_variant	877-878	845-846	282	S/X	tCT/t	rs782316919	.	.	-1	SURF1	HGNC	11474	protein_coding	YES	CCDS6966.1	ENSP00000361042	SURF1_HUMAN	E5KRX5_HUMAN,Q9UE08_HUMAN	UPI000013622E	.	.	.	9/9	.	PROSITE_profiles:PS50895,hmmpanther:PTHR23427:SF2,hmmpanther:PTHR23427,Pfam_domain:PF02104	.	.	.	.	.	.	.	-:0.0033	-:0.0052	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGCTGCAGAGAGT	.	3	ESCA
SLC2A6	0	.	GRCh37	9	136339152	136339152	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.986C>T	p.Ala329Val	p.A329V	ENST00000371899	7/10	124	84	39	59	59	0	SLC2A6,missense_variant,p.Ala329Val,ENST00000371899,;SLC2A6,missense_variant,p.Ala329Val,ENST00000371897,;SLC2A6,downstream_gene_variant,,ENST00000414172,;CACFD1,downstream_gene_variant,,ENST00000542192,;SLC2A6,downstream_gene_variant,,ENST00000432868,;CACFD1,downstream_gene_variant,,ENST00000316948,;CACFD1,downstream_gene_variant,,ENST00000291722,;SLC2A6,non_coding_transcript_exon_variant,,ENST00000485978,;	A	ENSG00000160326	ENST00000371899	Transcript	missense_variant	1064	986	329	A/V	gCc/gTc	.	.	.	-1	SLC2A6	HGNC	11011	protein_coding	YES	CCDS6975.1	ENSP00000360966	GTR6_HUMAN	.	UPI0000001BE8	.	deleterious(0)	probably_damaging(0.992)	7/10	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24063,hmmpanther:PTHR24063:SF47,PROSITE_patterns:PS00216,TIGRFAM_domain:TIGR00879,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCGGCGATC	.	5	ESCA
VAV2	0	.	GRCh37	9	136726534	136726534	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342G>A	p.%3D	p.R114R	ENST00000371850	3/30	27	17	10	21	21	0	VAV2,synonymous_variant,p.%3D,ENST00000371850,;VAV2,synonymous_variant,p.%3D,ENST00000406606,;VAV2,synonymous_variant,p.%3D,ENST00000371851,;VAV2,non_coding_transcript_exon_variant,,ENST00000486113,;	T	ENSG00000160293	ENST00000371850	Transcript	synonymous_variant	374	342	114	R	agG/agA	.	.	.	-1	VAV2	HGNC	12658	protein_coding	YES	CCDS48053.1	ENSP00000360916	VAV2_HUMAN	.	UPI000013E06E	.	.	.	3/30	.	PROSITE_profiles:PS50021,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF95,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGCCTCGA	.	5	ESCA
BRD3	0	.	GRCh37	9	136897975	136897978	+	3'UTR	DEL	TTTA	TTTA	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TTTA	TTTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*734_*737delTAAA	.	.	ENST00000303407	12/12	35	21	14	12	12	0	BRD3,3_prime_UTR_variant,,ENST00000303407,;BRD3,downstream_gene_variant,,ENST00000371834,;BRD3,downstream_gene_variant,,ENST00000357885,;LINC00094,intron_variant,,ENST00000605164,;LINC00094,downstream_gene_variant,,ENST00000552018,;LINC00094,downstream_gene_variant,,ENST00000603928,;LINC00094,downstream_gene_variant,,ENST00000550853,;LINC00094,downstream_gene_variant,,ENST00000432807,;LINC00094,downstream_gene_variant,,ENST00000430633,;LINC00094,downstream_gene_variant,,ENST00000599836,;BRD3,downstream_gene_variant,,ENST00000473349,;	-	ENSG00000169925	ENST00000303407	Transcript	3_prime_UTR_variant	3101-3104	.	.	.	.	.	.	.	-1	BRD3	HGNC	1104	protein_coding	YES	CCDS6980.1	ENSP00000305918	BRD3_HUMAN	B4DS09_HUMAN,A9J575_HUMAN,A9J571_HUMAN	UPI0000126ACD	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTTTTTTTAAATCT	.	2	ESCA
COL5A1	0	.	GRCh37	9	137645711	137645711	+	Missense_Mutation	SNP	G	G	A	rs770761070	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735G>A	p.Gly579Arg	p.G579R	ENST00000371817	15/66	62	56	6	45	45	0	COL5A1,missense_variant,p.Gly579Arg,ENST00000371817,;	A	ENSG00000130635	ENST00000371817	Transcript	missense_variant	2149	1735	579	G/R	Gga/Aga	rs770761070	.	.	1	COL5A1	HGNC	2209	protein_coding	YES	CCDS6982.1	ENSP00000360882	CO5A1_HUMAN	Q9UML4_HUMAN,Q96HC0_HUMAN,Q59EE7_HUMAN	UPI0000210EE3	.	.	probably_damaging(1)	15/66	.	Low_complexity_(Seg):seg,Pfam_domain:PF01391,hmmpanther:PTHR24023:SF387,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGAGCGGAGGT	byFrequency	3	ESCA
DNLZ	0	.	GRCh37	9	139256417	139256419	+	3'UTR	DEL	CCT	CCT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CCT	CCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45_*47delAGG	.	.	ENST00000371738	3/3	63	51	12	33	33	0	DNLZ,3_prime_UTR_variant,,ENST00000371739,;DNLZ,3_prime_UTR_variant,,ENST00000371738,;GPSM1,downstream_gene_variant,,ENST00000291775,;GPSM1,downstream_gene_variant,,ENST00000392944,;GPSM1,downstream_gene_variant,,ENST00000429455,;CARD9,downstream_gene_variant,,ENST00000371732,;CARD9,downstream_gene_variant,,ENST00000371734,;GPSM1,downstream_gene_variant,,ENST00000440944,;GPSM1,downstream_gene_variant,,ENST00000354753,;CARD9,downstream_gene_variant,,ENST00000460290,;CARD9,non_coding_transcript_exon_variant,,ENST00000481053,;CARD9,downstream_gene_variant,,ENST00000489932,;CARD9,downstream_gene_variant,,ENST00000485975,;	-	ENSG00000213221	ENST00000371738	Transcript	3_prime_UTR_variant	657-659	.	.	.	.	.	.	.	-1	DNLZ	HGNC	33879	protein_coding	YES	CCDS35179.1	ENSP00000360803	DNLZ_HUMAN	.	UPI00001612A7	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAAAACCTCCTTC	.	3	ESCA
NOTCH1	0	.	GRCh37	9	139399786	139399789	+	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	CAGT	CAGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4559_4562delACTG	p.Asp1520AlafsTer59	p.D1520Afs*59	ENST00000277541	25/34	36	17	19	17	17	0	NOTCH1,frameshift_variant,p.Asp1520AlafsTer59,ENST00000277541,;NOTCH1,upstream_gene_variant,,ENST00000494783,;	-	ENSG00000148400	ENST00000277541	Transcript	frameshift_variant	4635-4638	4559-4562	1520-1521	DC/X	gACTGc/gc	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	25/34	.	PROSITE_profiles:PS50258,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,Pfam_domain:PF00066,PIRSF_domain:PIRSF002279,SMART_domains:SM00004,Superfamily_domains:0042228,Prints_domain:PR01452,Prints_domain:PR01983	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CGCTGGCAGTCAAAG	.	2	ESCA
NOTCH1	0	.	GRCh37	9	139401189	139401189	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3880G>T	p.Glu1294Ter	p.E1294*	ENST00000277541	23/34	82	13	69	36	36	0	NOTCH1,stop_gained,p.Glu1294Ter,ENST00000277541,;NOTCH1,upstream_gene_variant,,ENST00000494783,;	A	ENSG00000148400	ENST00000277541	Transcript	stop_gained	3956	3880	1294	E/*	Gag/Tag	COSM3727820	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	23/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACTCGCAGT	.	5	ESCA
PTGDS	0	.	GRCh37	9	139873716	139873716	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296C>T	p.Ala99Val	p.A99V	ENST00000371625	3/7	88	54	33	41	41	0	PTGDS,missense_variant,p.Ala99Val,ENST00000371623,;PTGDS,missense_variant,p.Ala99Val,ENST00000224167,;PTGDS,missense_variant,p.Ala122Val,ENST00000446677,;PTGDS,missense_variant,p.Ala99Val,ENST00000457950,;PTGDS,missense_variant,p.Ala99Val,ENST00000371625,;PTGDS,upstream_gene_variant,,ENST00000444903,;LCNL1,upstream_gene_variant,,ENST00000408973,;PTGDS,non_coding_transcript_exon_variant,,ENST00000460340,;PTGDS,non_coding_transcript_exon_variant,,ENST00000492068,;PTGDS,upstream_gene_variant,,ENST00000462514,;LCNL1,upstream_gene_variant,,ENST00000432827,;RP11-229P13.19,downstream_gene_variant,,ENST00000413913,;PTGDS,upstream_gene_variant,,ENST00000467871,;PTGDS,missense_variant,p.Ala99Val,ENST00000471521,;LCNL1,upstream_gene_variant,,ENST00000460177,;LCNL1,upstream_gene_variant,,ENST00000482657,;	T	ENSG00000107317	ENST00000371625	Transcript	missense_variant	370	296	99	A/V	gCg/gTg	.	.	.	1	PTGDS	HGNC	9592	protein_coding	YES	CCDS7019.1	ENSP00000360687	PTGDS_HUMAN	.	UPI00001317A4	.	deleterious(0.04)	benign(0.193)	3/7	.	hmmpanther:PTHR11430:SF64,hmmpanther:PTHR11430,Pfam_domain:PF00061,Gene3D:2.40.128.20,Superfamily_domains:SSF50814	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCGCGGGGT	.	5	ESCA
LCNL1	0	.	GRCh37	9	139877796	139877796	+	5'UTR	SNP	C	C	G	rs756979805	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-243C>G	.	.	ENST00000408973	1/3	56	15	41	25	25	0	LCNL1,5_prime_UTR_variant,,ENST00000408973,;PTGDS,downstream_gene_variant,,ENST00000224167,;PTGDS,downstream_gene_variant,,ENST00000444903,;PTGDS,downstream_gene_variant,,ENST00000446677,;PTGDS,downstream_gene_variant,,ENST00000457950,;PTGDS,downstream_gene_variant,,ENST00000371625,;PTGDS,downstream_gene_variant,,ENST00000371623,;PTGDS,downstream_gene_variant,,ENST00000462514,;PTGDS,downstream_gene_variant,,ENST00000492068,;PTGDS,downstream_gene_variant,,ENST00000467871,;PTGDS,downstream_gene_variant,,ENST00000460340,;LCNL1,upstream_gene_variant,,ENST00000432827,;LCNL1,5_prime_UTR_variant,,ENST00000482657,;LCNL1,5_prime_UTR_variant,,ENST00000460177,;PTGDS,intron_variant,,ENST00000471521,;	G	ENSG00000214402	ENST00000408973	Transcript	5_prime_UTR_variant	352	.	.	.	.	rs756979805	.	.	1	LCNL1	HGNC	34436	protein_coding	YES	CCDS43908.1	ENSP00000386162	LCNL1_HUMAN	Q6ZSQ0_HUMAN,F2Z3E7_HUMAN	UPI0000251FB0	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCATCCAGCC	.	5	ESCA
GRIN1	0	.	GRCh37	9	140059553	140059553	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2653-85C>T	.	.	ENST00000371553	.	52	29	23	30	30	0	GRIN1,3_prime_UTR_variant,,ENST00000350902,;GRIN1,intron_variant,,ENST00000371555,;GRIN1,intron_variant,,ENST00000371561,;GRIN1,intron_variant,,ENST00000371546,;GRIN1,intron_variant,,ENST00000315048,;GRIN1,intron_variant,,ENST00000371550,;GRIN1,intron_variant,,ENST00000371559,;GRIN1,intron_variant,,ENST00000371553,;GRIN1,intron_variant,,ENST00000371560,;LRRC26,downstream_gene_variant,,ENST00000371542,;MIR3621,downstream_gene_variant,,ENST00000580529,;GRIN1,non_coding_transcript_exon_variant,,ENST00000471122,;GRIN1,upstream_gene_variant,,ENST00000473811,;GRIN1,upstream_gene_variant,,ENST00000462584,;GRIN1,downstream_gene_variant,,ENST00000460273,;RP11-350O14.18,downstream_gene_variant,,ENST00000568665,;	T	ENSG00000176884	ENST00000371553	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GRIN1	HGNC	4584	protein_coding	YES	CCDS55354.1	ENSP00000360608	NMDZ1_HUMAN	.	UPI000014AF8E	.	.	.	.	19/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCAGGCTGGGC	.	4	ESCA
ZMYND19	0	.	GRCh37	9	140481423	140481423	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355C>T	p.Gln119Ter	p.Q119*	ENST00000298585	4/6	50	27	22	26	26	0	ZMYND19,stop_gained,p.Gln119Ter,ENST00000298585,;ZMYND19,downstream_gene_variant,,ENST00000471957,;	A	ENSG00000165724	ENST00000298585	Transcript	stop_gained	582	355	119	Q/*	Cag/Tag	.	.	.	-1	ZMYND19	HGNC	21146	protein_coding	YES	CCDS7048.1	ENSP00000298585	ZMY19_HUMAN	.	UPI0000022A7D	.	.	.	4/6	.	hmmpanther:PTHR13244:SF5,hmmpanther:PTHR13244	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTGCTTGC	.	5	ESCA
CACNA1B	0	.	GRCh37	9	140941361	140941361	+	Missense_Mutation	SNP	G	G	A	rs756199654	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3419G>A	p.Arg1140His	p.R1140H	ENST00000371372	22/47	83	65	17	43	43	0	CACNA1B,missense_variant,p.Arg166His,ENST00000545473,;CACNA1B,missense_variant,p.Arg1141His,ENST00000371355,;CACNA1B,missense_variant,p.Arg1141His,ENST00000371357,;CACNA1B,missense_variant,p.Arg332His,ENST00000277549,;CACNA1B,missense_variant,p.Arg1140His,ENST00000277551,;CACNA1B,missense_variant,p.Arg1140His,ENST00000371363,;CACNA1B,missense_variant,p.Arg1140His,ENST00000371372,;	A	ENSG00000148408	ENST00000371372	Transcript	missense_variant	3564	3419	1140	R/H	cGc/cAc	rs756199654	.	.	1	CACNA1B	HGNC	1389	protein_coding	YES	CCDS59522.1	ENSP00000360423	CAC1B_HUMAN	Q9HBI3_HUMAN,Q9HBH4_HUMAN,Q9HBG3_HUMAN,Q9HBG2_HUMAN,Q9HAT5_HUMAN,Q9HAT4_HUMAN	UPI0000127267	.	deleterious(0)	possibly_damaging(0.777)	22/47	.	hmmpanther:PTHR10037:SF161,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCTCCGCCGCT	byFrequency	4	ESCA
BNC2	0	.	GRCh37	9	16412328	16412328	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6659delT	.	.	ENST00000380672	7/7	28	16	12	28	28	0	BNC2,3_prime_UTR_variant,,ENST00000380672,;	-	ENSG00000173068	ENST00000380672	Transcript	3_prime_UTR_variant	10017	.	.	.	.	.	.	.	-1	BNC2	HGNC	30988	protein_coding	YES	CCDS6482.2	ENSP00000370047	BNC2_HUMAN	S4R351_HUMAN,Q06HC7_HUMAN,Q06HC2_HUMAN,Q06HB9_HUMAN,D3DRJ1_HUMAN	UPI000035E7B0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GATAAGAAAAAA	.	2	ESCA
FOCAD	0	.	GRCh37	9	20995670	20995670	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45delA	.	.	ENST00000380249	46/46	69	36	33	32	32	0	FOCAD,3_prime_UTR_variant,,ENST00000380249,;FOCAD,3_prime_UTR_variant,,ENST00000605086,;FOCAD,3_prime_UTR_variant,,ENST00000338382,;PTPLAD2,3_prime_UTR_variant,,ENST00000513293,;PTPLAD2,downstream_gene_variant,,ENST00000495827,;	-	ENSG00000188352	ENST00000380249	Transcript	3_prime_UTR_variant	5812	.	.	.	.	.	.	.	1	FOCAD	HGNC	23377	protein_coding	YES	CCDS34993.1	ENSP00000369599	FOCAD_HUMAN	S4R450_HUMAN,S4R400_HUMAN,S4R3S9_HUMAN	UPI00002111D4	.	.	.	46/46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGAGGAAAACC	.	3	ESCA
ELAVL2	0	.	GRCh37	9	23704941	23704941	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462T>C	p.%3D	p.S154S	ENST00000397312	4/7	23	14	9	15	15	0	ELAVL2,synonymous_variant,p.%3D,ENST00000423281,;ELAVL2,synonymous_variant,p.%3D,ENST00000440102,;ELAVL2,synonymous_variant,p.%3D,ENST00000380117,;ELAVL2,synonymous_variant,p.%3D,ENST00000380110,;ELAVL2,synonymous_variant,p.%3D,ENST00000397312,;ELAVL2,synonymous_variant,p.%3D,ENST00000223951,;ELAVL2,synonymous_variant,p.%3D,ENST00000544538,;	G	ENSG00000107105	ENST00000397312	Transcript	synonymous_variant	737	462	154	S	tcT/tcC	.	.	.	-1	ELAVL2	HGNC	3313	protein_coding	YES	CCDS6515.1	ENSP00000380479	ELAV2_HUMAN	C9JB16_HUMAN,B1AM48_HUMAN	UPI000013C83F	.	.	.	4/7	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011:SF199,hmmpanther:PTHR24011,TIGRFAM_domain:TIGR01661,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928,Prints_domain:PR00961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R155C|c.463C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACGAGAAGT	.	5	ESCA
AQP3	0	.	GRCh37	9	33441446	33441447	+	3'UTR	INS	-	-	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*594dupA	.	.	ENST00000297991	6/6	45	37	8	25	25	0	AQP3,3_prime_UTR_variant,,ENST00000297991,;AQP3,non_coding_transcript_exon_variant,,ENST00000493581,;AQP3,non_coding_transcript_exon_variant,,ENST00000494313,;AQP3,downstream_gene_variant,,ENST00000463983,;AQP3,downstream_gene_variant,,ENST00000473153,;	T	ENSG00000165272	ENST00000297991	Transcript	3_prime_UTR_variant	1554-1555	.	.	.	.	.	.	.	-1	AQP3	HGNC	636	protein_coding	YES	CCDS6542.1	ENSP00000297991	AQP3_HUMAN	.	UPI0000125D1C	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCCCCTCCTC	.	3	ESCA
UBE2R2	0	.	GRCh37	9	33918993	33918997	+	3'UTR	DEL	TGGTC	TGGTC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TGGTC	TGGTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1762_*1766delCTGGT	.	.	ENST00000263228	5/5	35	28	7	17	17	0	UBE2R2,3_prime_UTR_variant,,ENST00000263228,;UBAP2,downstream_gene_variant,,ENST00000379238,;UBAP2,downstream_gene_variant,,ENST00000379239,;UBAP2,downstream_gene_variant,,ENST00000379235,;UBAP2,downstream_gene_variant,,ENST00000449054,;UBAP2,downstream_gene_variant,,ENST00000539807,;UBAP2,downstream_gene_variant,,ENST00000360802,;UBAP2,downstream_gene_variant,,ENST00000474372,;	-	ENSG00000107341	ENST00000263228	Transcript	3_prime_UTR_variant	2666-2670	.	.	.	.	.	.	.	1	UBE2R2	HGNC	19907	protein_coding	YES	CCDS6546.1	ENSP00000263228	UB2R2_HUMAN	.	UPI0000000C64	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAGTTTGGTCTGGTA	.	2	ESCA
UBAP2	0	.	GRCh37	9	33956118	33956118	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.825C>A	p.%3D	p.A275A	ENST00000379238	11/29	56	36	20	55	55	0	UBAP2,synonymous_variant,p.%3D,ENST00000379238,;UBAP2,synonymous_variant,p.%3D,ENST00000418786,;UBAP2,synonymous_variant,p.%3D,ENST00000421278,;UBAP2,synonymous_variant,p.%3D,ENST00000449054,;UBAP2,synonymous_variant,p.%3D,ENST00000412543,;UBAP2,synonymous_variant,p.%3D,ENST00000539807,;UBAP2,synonymous_variant,p.%3D,ENST00000360802,;UBAP2,intron_variant,,ENST00000379239,;SNORD121A,upstream_gene_variant,,ENST00000459386,;UBAP2,intron_variant,,ENST00000462799,;	T	ENSG00000137073	ENST00000379238	Transcript	synonymous_variant	943	825	275	A	gcC/gcA	.	.	.	-1	UBAP2	HGNC	14185	protein_coding	YES	CCDS6547.1	ENSP00000368540	UBAP2_HUMAN	Q5JV03_HUMAN	UPI0000140784	.	.	.	11/29	.	hmmpanther:PTHR16308,hmmpanther:PTHR16308:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAGGCAGT	.	5	ESCA
UBAP1	0	.	GRCh37	9	34241819	34241819	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.988C>A	p.Leu330Met	p.L330M	ENST00000545103	3/6	51	25	26	38	38	0	UBAP1,missense_variant,p.Leu302Met,ENST00000543944,;UBAP1,missense_variant,p.Leu266Met,ENST00000540348,;UBAP1,missense_variant,p.Leu266Met,ENST00000359544,;UBAP1,missense_variant,p.Leu266Met,ENST00000379186,;UBAP1,missense_variant,p.Leu330Met,ENST00000545103,;UBAP1,missense_variant,p.Leu266Met,ENST00000297661,;UBAP1,missense_variant,p.Leu266Met,ENST00000536252,;	A	ENSG00000165006	ENST00000545103	Transcript	missense_variant	998	988	330	L/M	Ctg/Atg	.	.	.	1	UBAP1	HGNC	12461	protein_coding	YES	CCDS55303.1	ENSP00000441024	UBAP1_HUMAN	.	UPI0001C2BF9D	.	deleterious(0)	probably_damaging(1)	3/6	.	hmmpanther:PTHR15960:SF2,hmmpanther:PTHR15960	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCCCTGTCT	.	5	ESCA
FAM205A	0	.	GRCh37	9	34724675	34724676	+	Frame_Shift_Del	DEL	TT	TT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2561_2562delAA	p.Lys854ArgfsTer25	p.K854Rfs*25	ENST00000378788	4/4	237	157	80	122	122	0	FAM205A,frameshift_variant,p.Lys854ArgfsTer25,ENST00000378788,;	-	ENSG00000205108	ENST00000378788	Transcript	frameshift_variant	2601-2602	2561-2562	854	K/X	aAA/a	.	.	.	-1	FAM205A	HGNC	41911	protein_coding	YES	CCDS55305.1	ENSP00000417711	F205A_HUMAN	.	UPI00017EE92B	.	.	.	4/4	.	hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAACTCTTTTGCA	.	3	ESCA
C9orf131	0	.	GRCh37	9	35044004	35044005	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1382dupA	p.Asn461LysfsTer33	p.N461Kfs*33	ENST00000312292	2/2	23	12	11	10	10	0	C9orf131,frameshift_variant,p.Asn413LysfsTer33,ENST00000421362,;C9orf131,frameshift_variant,p.Asn461LysfsTer33,ENST00000312292,;C9orf131,frameshift_variant,p.Asn388LysfsTer33,ENST00000354479,;FLJ00273,upstream_gene_variant,,ENST00000595331,;C9orf131,downstream_gene_variant,,ENST00000534880,;C9orf131,downstream_gene_variant,,ENST00000537671,;C9orf131,downstream_gene_variant,,ENST00000378745,;C9orf131,downstream_gene_variant,,ENST00000416537,;	A	ENSG00000174038	ENST00000312292	Transcript	frameshift_variant	1425-1426	1378-1379	460	E/EX	gaa/gAaa	.	.	.	1	C9orf131	HGNC	31418	protein_coding	YES	CCDS6572.2	ENSP00000308279	CI131_HUMAN	.	UPI00001605AC	.	.	.	2/2	.	hmmpanther:PTHR21777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTAGAGAAAAT	.	2	ESCA
UNC13B	0	.	GRCh37	9	35404969	35404970	+	3'UTR	DEL	TC	TC	-	rs778563152	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TC	TC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*951_*952delTC	.	.	ENST00000378495	39/39	31	22	9	16	16	0	UNC13B,3_prime_UTR_variant,,ENST00000378495,;UNC13B,downstream_gene_variant,,ENST00000396787,;UNC13B,downstream_gene_variant,,ENST00000378496,;ATP8B5P,upstream_gene_variant,,ENST00000439972,;ATP8B5P,upstream_gene_variant,,ENST00000329395,;ATP8B5P,upstream_gene_variant,,ENST00000430846,;ATP8B5P,upstream_gene_variant,,ENST00000417941,;	-	ENSG00000198722	ENST00000378495	Transcript	3_prime_UTR_variant	5937-5938	.	.	.	.	rs778563152	.	.	1	UNC13B	HGNC	12566	protein_coding	YES	CCDS6579.1	ENSP00000367756	UN13B_HUMAN	.	UPI0000211336	.	.	.	39/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	12	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTTGGTCTCTCT	byCluster	2	ESCA
CREB3	0	.	GRCh37	9	35733097	35733097	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234C>T	p.%3D	p.D78D	ENST00000353704	2/9	45	36	9	38	38	0	CREB3,synonymous_variant,p.%3D,ENST00000353704,;GBA2,downstream_gene_variant,,ENST00000378088,;GBA2,downstream_gene_variant,,ENST00000378094,;TLN1,upstream_gene_variant,,ENST00000540444,;TLN1,upstream_gene_variant,,ENST00000314888,;GBA2,downstream_gene_variant,,ENST00000378103,;GBA2,downstream_gene_variant,,ENST00000545786,;CREB3,non_coding_transcript_exon_variant,,ENST00000486056,;GBA2,downstream_gene_variant,,ENST00000486797,;GBA2,downstream_gene_variant,,ENST00000467252,;TLN1,upstream_gene_variant,,ENST00000378192,;	T	ENSG00000107175	ENST00000353704	Transcript	synonymous_variant	672	234	78	D	gaC/gaT	.	.	.	1	CREB3	HGNC	2347	protein_coding	YES	CCDS6588.1	ENSP00000342136	CREB3_HUMAN	B4DSK1_HUMAN	UPI0000073728	.	.	.	2/9	.	hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF100	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGACCACAC	.	5	ESCA
FBXO10	0	.	GRCh37	9	37537267	37537267	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1259C>T	p.Ala420Val	p.A420V	ENST00000432825	3/11	47	27	19	8	8	0	FBXO10,missense_variant,p.Ala420Val,ENST00000432825,;FBXO10,intron_variant,,ENST00000541829,;FBXO10,downstream_gene_variant,,ENST00000541607,;RP11-613M10.8,non_coding_transcript_exon_variant,,ENST00000544475,;RP11-613M10.8,intron_variant,,ENST00000541804,;FBXO10,upstream_gene_variant,,ENST00000543968,;FBXO10,missense_variant,p.Ala420Val,ENST00000276960,;RP11-613M10.8,downstream_gene_variant,,ENST00000537239,;	A	ENSG00000147912	ENST00000432825	Transcript	missense_variant	1308	1259	420	A/V	gCc/gTc	.	.	.	-1	FBXO10	HGNC	13589	protein_coding	YES	CCDS47966.1	ENSP00000403802	FBX10_HUMAN	Q08AL4_HUMAN,F5GXN9_HUMAN	UPI00001C1EC6	.	tolerated(0.16)	possibly_damaging(0.553)	3/11	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22990,SMART_domains:SM00722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCATGGCCTCC	.	3	ESCA
RP11-204M4.2	0	.	GRCh37	9	41962084	41962084	+	RNA	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1421T>C	.	.	ENST00000454645	3/3	40	27	13	32	31	1	RP11-204M4.2,non_coding_transcript_exon_variant,,ENST00000454645,;	G	ENSG00000204837	ENST00000454645	Transcript	non_coding_transcript_exon_variant	1421	.	.	.	.	.	.	.	-1	RP11-204M4.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTCCATAGTT	.	3	ESCA
JAK2	0	.	GRCh37	9	5044449	5044449	+	Silent	SNP	C	C	A	rs371826393	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397C>A	p.%3D	p.R133R	ENST00000381652	5/25	46	33	13	39	39	0	JAK2,synonymous_variant,p.%3D,ENST00000539801,;JAK2,synonymous_variant,p.%3D,ENST00000381652,;JAK2,5_prime_UTR_variant,,ENST00000544510,;RP11-39K24.2,downstream_gene_variant,,ENST00000442675,;	A	ENSG00000096968	ENST00000381652	Transcript	synonymous_variant	891	397	133	R	Cgg/Agg	rs371826393	.	.	1	JAK2	HGNC	6192	protein_coding	YES	CCDS6457.1	ENSP00000371067	JAK2_HUMAN	Q8IXP2_HUMAN,F5H5U8_HUMAN	UPI000012DA9E	.	.	.	5/25	.	PROSITE_profiles:PS50057,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF179,PIRSF_domain:PIRSF000636,SMART_domains:SM00295,Prints_domain:PR01825	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATCGGCAT	byFrequency|byCluster	5	ESCA
KIAA2026	0	.	GRCh37	9	5919250	5919251	+	3'UTR	DEL	TT	TT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*433_*434delAA	.	.	ENST00000399933	8/8	30	12	18	26	26	0	KIAA2026,3_prime_UTR_variant,,ENST00000381461,;KIAA2026,3_prime_UTR_variant,,ENST00000399933,;KIAA2026,intron_variant,,ENST00000436015,;KIAA2026,downstream_gene_variant,,ENST00000540714,;	-	ENSG00000183354	ENST00000399933	Transcript	3_prime_UTR_variant	6745-6746	.	.	.	.	.	.	.	-1	KIAA2026	HGNC	23378	protein_coding	YES	.	ENSP00000382815	K2026_HUMAN	.	UPI0001533DB0	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TATGTATTTTTTT	.	2	ESCA
PGM5	0	.	GRCh37	9	71094403	71094403	+	Missense_Mutation	SNP	G	G	A	rs782232692	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1229G>A	p.Arg410Gln	p.R410Q	ENST00000396396	8/11	54	11	43	39	39	0	PGM5,missense_variant,p.Arg410Gln,ENST00000396396,;PGM5,non_coding_transcript_exon_variant,,ENST00000472639,;	A	ENSG00000154330	ENST00000396396	Transcript	missense_variant	1458	1229	410	R/Q	cGg/cAg	rs782232692,COSM85162	.	.	1	PGM5	HGNC	8908	protein_coding	YES	CCDS6622.2	ENSP00000379678	PGM5_HUMAN	.	UPI0000210ABF	.	tolerated(0.06)	possibly_damaging(0.857)	8/11	.	hmmpanther:PTHR22573,hmmpanther:PTHR22573:SF27,Gene3D:3.40.120.10,Pfam_domain:PF02880,Superfamily_domains:SSF53738	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGGAAGC	byFrequency	5	ESCA
TRPM3	0	.	GRCh37	9	73151058	73151058	+	Silent	SNP	C	C	A	rs146678870	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4935G>T	p.%3D	p.A1645A	ENST00000377110	25/25	96	72	23	63	62	0	TRPM3,synonymous_variant,p.%3D,ENST00000377106,;TRPM3,synonymous_variant,p.%3D,ENST00000360823,;TRPM3,synonymous_variant,p.%3D,ENST00000358082,;TRPM3,synonymous_variant,p.%3D,ENST00000396292,;TRPM3,synonymous_variant,p.%3D,ENST00000396280,;TRPM3,synonymous_variant,p.%3D,ENST00000423814,;TRPM3,synonymous_variant,p.%3D,ENST00000408909,;TRPM3,synonymous_variant,p.%3D,ENST00000357533,;TRPM3,synonymous_variant,p.%3D,ENST00000377110,;TRPM3,synonymous_variant,p.%3D,ENST00000377105,;TRPM3,synonymous_variant,p.%3D,ENST00000396285,;TRPM3,intron_variant,,ENST00000377111,;	A	ENSG00000083067	ENST00000377110	Transcript	synonymous_variant	5179	4935	1645	A	gcG/gcT	rs146678870	.	.	-1	TRPM3	HGNC	17992	protein_coding	YES	CCDS43835.1	ENSP00000366314	TRPM3_HUMAN	.	UPI0001596895	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGCGCACT	byFrequency|byCluster	4	ESCA
C9orf40	0	.	GRCh37	9	77562916	77562917	+	3'UTR	DEL	AG	AG	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*47_*48delCT	.	.	ENST00000376854	2/2	51	31	20	29	29	0	C9orf40,3_prime_UTR_variant,,ENST00000376854,;RP11-197P3.4,upstream_gene_variant,,ENST00000455609,;	-	ENSG00000135045	ENST00000376854	Transcript	3_prime_UTR_variant	907-908	.	.	.	.	.	.	.	-1	C9orf40	HGNC	23433	protein_coding	YES	CCDS6648.1	ENSP00000366050	CI040_HUMAN	.	UPI0000074360	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCACTTAGAGACA	.	3	ESCA
FOXB2	0	.	GRCh37	9	79634851	79634851	+	Missense_Mutation	SNP	G	G	T	rs774683505	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281G>T	p.Gly94Val	p.G94V	ENST00000376708	1/1	37	13	24	19	19	0	FOXB2,missense_variant,p.Gly94Val,ENST00000376708,;	T	ENSG00000204612	ENST00000376708	Transcript	missense_variant	281	281	94	G/V	gGg/gTg	rs774683505	.	.	1	FOXB2	HGNC	23315	protein_coding	YES	CCDS35045.1	ENSP00000365898	FOXB2_HUMAN	.	UPI00004588EE	.	deleterious(0)	unknown(0)	1/1	.	PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF76,hmmpanther:PTHR11829,Gene3D:1.10.10.10,Pfam_domain:PF00250,SMART_domains:SM00339,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCGGGGACA	.	5	ESCA
VPS13A	0	.	GRCh37	9	79827940	79827940	+	Missense_Mutation	SNP	G	G	A	rs756091546	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.611G>A	p.Arg204His	p.R204H	ENST00000360280	8/72	101	27	74	87	86	0	VPS13A,missense_variant,p.Arg204His,ENST00000357409,;VPS13A,missense_variant,p.Arg204His,ENST00000376634,;VPS13A,missense_variant,p.Arg204His,ENST00000376636,;VPS13A,missense_variant,p.Arg204His,ENST00000360280,;VPS13A,downstream_gene_variant,,ENST00000471439,;	A	ENSG00000197969	ENST00000360280	Transcript	missense_variant	871	611	204	R/H	cGt/cAt	rs756091546	.	.	1	VPS13A	HGNC	1908	protein_coding	YES	CCDS6655.1	ENSP00000353422	VP13A_HUMAN	.	UPI0000210B7A	.	tolerated(0.28)	benign(0.001)	8/72	.	hmmpanther:PTHR16166,hmmpanther:PTHR16166:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCGTAAGG	byFrequency	5	ESCA
HNRNPK	0	.	GRCh37	9	86586596	86586596	+	Silent	SNP	G	G	A	rs774149530	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.999C>T	p.%3D	p.Y333Y	ENST00000376263	12/17	50	23	27	52	52	0	HNRNPK,synonymous_variant,p.%3D,ENST00000376264,;HNRNPK,synonymous_variant,p.%3D,ENST00000351839,;HNRNPK,synonymous_variant,p.%3D,ENST00000376263,;HNRNPK,synonymous_variant,p.%3D,ENST00000457156,;HNRNPK,synonymous_variant,p.%3D,ENST00000376281,;HNRNPK,synonymous_variant,p.%3D,ENST00000360384,;HNRNPK,upstream_gene_variant,,ENST00000481820,;MIR7-1,upstream_gene_variant,,ENST00000384871,;RP11-575L7.8,upstream_gene_variant,,ENST00000448389,;HNRNPK,upstream_gene_variant,,ENST00000493362,;HNRNPK,downstream_gene_variant,,ENST00000483135,;HNRNPK,downstream_gene_variant,,ENST00000472778,;HNRNPK,downstream_gene_variant,,ENST00000376256,;HNRNPK,upstream_gene_variant,,ENST00000492865,;	A	ENSG00000165119	ENST00000376263	Transcript	synonymous_variant	1223	999	333	Y	taC/taT	rs774149530	.	.	-1	HNRNPK	HGNC	5044	protein_coding	YES	CCDS6668.1	ENSP00000365439	HNRPK_HUMAN	Q6IBN1_HUMAN	UPI0000021C42	.	.	.	12/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTCGTAACG	.	5	ESCA
CDK20	0	.	GRCh37	9	90582463	90582463	+	Frame_Shift_Del	DEL	G	G	-	rs151084868,rs67862915	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.955delC	p.His319ThrfsTer16	p.H319Tfs*16	ENST00000325303	8/8	27	16	11	25	25	0	CDK20,frameshift_variant,p.His311ThrfsTer16,ENST00000336654,;CDK20,frameshift_variant,p.His319ThrfsTer16,ENST00000325303,;CDK20,frameshift_variant,p.His298ThrfsTer16,ENST00000375883,;CDK20,3_prime_UTR_variant,,ENST00000375871,;CDK20,3_prime_UTR_variant,,ENST00000605159,;CDK20,non_coding_transcript_exon_variant,,ENST00000486228,;CDK20,non_coding_transcript_exon_variant,,ENST00000459720,;CDK20,non_coding_transcript_exon_variant,,ENST00000603475,;CDK20,downstream_gene_variant,,ENST00000605591,;CDK20,downstream_gene_variant,,ENST00000604175,;	-	ENSG00000156345	ENST00000325303	Transcript	frameshift_variant	1261	955	319	H/X	Cac/ac	rs151084868,rs67862915,COSM1463487,COSM1463488	.	.	-1	CDK20	HGNC	21420	protein_coding	YES	CCDS35060.1	ENSP00000322343	CDK20_HUMAN	A8K6P8_HUMAN	UPI00000740E8	.	.	.	8/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF171	C:0.0006	C:0.0023	C:0	.	C:0	C:0	C:0	C:0.0005,-:0.0053	C:0,-:0.0056	.	0,0,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGATGTGGGGGG	byFrequency|byCluster|by1000G	2	ESCA
DMRT1	0	.	GRCh37	9	968375	968375	+	3'UTR	DEL	T	T	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*242delT	.	.	ENST00000382276	5/5	89	53	36	35	35	0	DMRT1,3_prime_UTR_variant,,ENST00000382276,;DMRT1,3_prime_UTR_variant,,ENST00000569227,;	-	ENSG00000137090	ENST00000382276	Transcript	3_prime_UTR_variant	1507	.	.	.	.	.	.	.	1	DMRT1	HGNC	2934	protein_coding	YES	CCDS6442.1	ENSP00000371711	DMRT1_HUMAN	H3BN61_HUMAN	UPI00000008AC	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTTCATTTTTT	.	3	ESCA
PTCH1	0	.	GRCh37	9	98211549	98211549	+	Frame_Shift_Del	DEL	G	G	-	rs138240178	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3606delC	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	22/24	56	46	10	38	38	0	PTCH1,frameshift_variant,p.Ser1202AlafsTer52,ENST00000375274,;PTCH1,frameshift_variant,p.Ser1203AlafsTer52,ENST00000331920,;PTCH1,frameshift_variant,p.Ser1137AlafsTer52,ENST00000430669,;PTCH1,frameshift_variant,p.Ser1052AlafsTer52,ENST00000418258,;PTCH1,frameshift_variant,p.Ser1052AlafsTer52,ENST00000429896,;PTCH1,frameshift_variant,p.Ser1052AlafsTer52,ENST00000421141,;PTCH1,frameshift_variant,p.Ser1137AlafsTer52,ENST00000437951,;PTCH1,3_prime_UTR_variant,,ENST00000375290,;PTCH1,non_coding_transcript_exon_variant,,ENST00000546744,;	-	ENSG00000185920	ENST00000331920	Transcript	frameshift_variant	3906	3606	1202	P/X	ccC/cc	rs138240178,COSM198969,COSM198970,COSM198971	.	.	-1	PTCH1	HGNC	9585	protein_coding	YES	CCDS6714.1	ENSP00000332353	PTC1_HUMAN	Q6TKQ0_HUMAN,F8VXL8_HUMAN,F8VQS6_HUMAN	UPI00001AFF9C	.	.	.	22/24	.	TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796:SF61,hmmpanther:PTHR10796,Low_complexity_(Seg):seg	A:0.0082	A:0.0287	A:0.0043	.	A:0	A:0	A:0	A:0.0318	A:0.0001	.	0,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CACGCTGGGGGG	byFrequency|byCluster|by1000G	3	ESCA
DCX	0	.	GRCh37	X	110542237	110542237	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2678G>T	.	.	ENST00000338081	7/7	16	7	9	9	9	0	DCX,3_prime_UTR_variant,,ENST00000371993,;DCX,3_prime_UTR_variant,,ENST00000338081,;DCX,3_prime_UTR_variant,,ENST00000358070,;DCX,3_prime_UTR_variant,,ENST00000356915,;DCX,downstream_gene_variant,,ENST00000356220,;DCX,downstream_gene_variant,,ENST00000488120,;	A	ENSG00000077279	ENST00000338081	Transcript	3_prime_UTR_variant	4176	.	.	.	.	.	.	.	-1	DCX	HGNC	2714	protein_coding	YES	CCDS14556.1	ENSP00000337697	DCX_HUMAN	E7EU50_HUMAN	UPI000013D33F	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGGCAAATG	.	2	ESCA
HCCS	0	.	GRCh37	X	11135400	11135400	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.266A>T	p.Asn89Ile	p.N89I	ENST00000321143	4/7	24	7	17	24	24	0	HCCS,missense_variant,p.Asn89Ile,ENST00000380763,;HCCS,missense_variant,p.Asn89Ile,ENST00000380762,;HCCS,missense_variant,p.Asn89Ile,ENST00000321143,;ARHGAP6,downstream_gene_variant,,ENST00000534860,;Y_RNA,upstream_gene_variant,,ENST00000384422,;	T	ENSG00000004961	ENST00000321143	Transcript	missense_variant	468	266	89	N/I	aAt/aTt	.	.	.	1	HCCS	HGNC	4837	protein_coding	YES	CCDS14139.1	ENSP00000326579	CCHL_HUMAN	.	UPI00001272B7	.	deleterious(0)	probably_damaging(0.994)	4/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12743,Pfam_domain:PF01265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAAATCAAA	.	5	ESCA
ENOX2	0	.	GRCh37	X	129804065	129804065	+	Missense_Mutation	SNP	G	G	A	rs762779115	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.655C>T	p.Arg219Cys	p.R219C	ENST00000338144	8/16	90	20	70	29	29	0	ENOX2,missense_variant,p.Arg219Cys,ENST00000370927,;ENOX2,missense_variant,p.Arg190Cys,ENST00000432489,;ENOX2,missense_variant,p.Arg219Cys,ENST00000338144,;ENOX2,missense_variant,p.Arg190Cys,ENST00000394363,;ENOX2,missense_variant,p.Arg190Cys,ENST00000370935,;	A	ENSG00000165675	ENST00000338144	Transcript	missense_variant	1073	655	219	R/C	Cgt/Tgt	rs762779115,COSM1115160	.	.	-1	ENOX2	HGNC	2259	protein_coding	YES	CCDS14626.1	ENSP00000337146	ENOX2_HUMAN	B1AKF7_HUMAN	UPI00000729D5	.	deleterious(0)	probably_damaging(0.998)	8/16	.	hmmpanther:PTHR16001,hmmpanther:PTHR16001:SF7	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A222V|c.665C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATACGCTGTT	byFrequency	5	ESCA
ZIC3	0	.	GRCh37	X	136653275	136653275	+	3'UTR	SNP	T	T	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1046T>G	.	.	ENST00000287538	3/3	17	2	15	14	14	0	ZIC3,3_prime_UTR_variant,,ENST00000287538,;ZIC3,intron_variant,,ENST00000370606,;ZIC3,downstream_gene_variant,,ENST00000478471,;	G	ENSG00000156925	ENST00000287538	Transcript	3_prime_UTR_variant	3000	.	.	.	.	.	.	.	1	ZIC3	HGNC	12874	protein_coding	YES	CCDS14663.1	ENSP00000287538	ZIC3_HUMAN	.	UPI000013C3DD	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGATCAATT	.	5	ESCA
ATP11C	0	.	GRCh37	X	138809668	138809669	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1456dupT	.	.	ENST00000327569	30/30	16	4	12	20	20	0	ATP11C,3_prime_UTR_variant,,ENST00000361648,;ATP11C,3_prime_UTR_variant,,ENST00000450801,;ATP11C,3_prime_UTR_variant,,ENST00000327569,;ATP11C,3_prime_UTR_variant,,ENST00000433868,;ATP11C,3_prime_UTR_variant,,ENST00000370557,;ATP11C,downstream_gene_variant,,ENST00000370543,;ATP11C,downstream_gene_variant,,ENST00000460773,;	A	ENSG00000101974	ENST00000327569	Transcript	3_prime_UTR_variant	4954-4955	.	.	.	.	.	.	.	-1	ATP11C	HGNC	13554	protein_coding	YES	CCDS14668.1	ENSP00000332756	AT11C_HUMAN	.	UPI000036777E	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTTAGAAAAA	.	2	ESCA
SLITRK4	0	.	GRCh37	X	142717789	142717789	+	Missense_Mutation	SNP	G	G	A	rs782089060	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1136C>T	p.Ala379Val	p.A379V	ENST00000381779	2/2	30	6	24	29	29	0	SLITRK4,missense_variant,p.Ala379Val,ENST00000381779,;SLITRK4,missense_variant,p.Ala379Val,ENST00000338017,;SLITRK4,missense_variant,p.Ala379Val,ENST00000356928,;	A	ENSG00000179542	ENST00000381779	Transcript	missense_variant	1362	1136	379	A/V	gCg/gTg	rs782089060	.	.	-1	SLITRK4	HGNC	23502	protein_coding	YES	CCDS14679.1	ENSP00000371198	SLIK4_HUMAN	.	UPI000004E650	.	deleterious(0)	benign(0.278)	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTCGCATTT	.	5	ESCA
PLXNB3	0	.	GRCh37	X	153044130	153044130	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5694+1G>A	.	p.X1898_splice	ENST00000538966	.	27	5	22	18	18	0	PLXNB3,splice_donor_variant,,ENST00000538966,;SRPK3,splice_donor_variant,,ENST00000489426,;PLXNB3,splice_donor_variant,,ENST00000538776,;PLXNB3,splice_donor_variant,,ENST00000361971,;PLXNB3,downstream_gene_variant,,ENST00000411613,;SRPK3,upstream_gene_variant,,ENST00000370108,;SRPK3,upstream_gene_variant,,ENST00000370100,;PLXNB3,downstream_gene_variant,,ENST00000455214,;PLXNB3,downstream_gene_variant,,ENST00000448847,;SRPK3,upstream_gene_variant,,ENST00000430541,;SRPK3,upstream_gene_variant,,ENST00000393786,;PLXNB3,downstream_gene_variant,,ENST00000538282,;SRPK3,upstream_gene_variant,,ENST00000370104,;SRPK3,upstream_gene_variant,,ENST00000370101,;PLXNB3,splice_donor_variant,,ENST00000472415,;PLXNB3,splice_donor_variant,,ENST00000469190,;PLXNB3,downstream_gene_variant,,ENST00000485980,;PLXNB3,downstream_gene_variant,,ENST00000482654,;	A	ENSG00000198753	ENST00000538966	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	PLXNB3	HGNC	9105	protein_coding	YES	CCDS55536.1	ENSP00000442736	PLXB3_HUMAN	.	UPI0001AFF680	.	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAGGTGAGG	.	5	ESCA
IRAK1	0	.	GRCh37	X	153277192	153277192	+	3'UTR	SNP	G	G	A	rs782327366	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*118C>T	.	.	ENST00000369980	14/14	57	12	45	23	23	0	IRAK1,synonymous_variant,p.%3D,ENST00000455690,;IRAK1,3_prime_UTR_variant,,ENST00000369980,;IRAK1,3_prime_UTR_variant,,ENST00000369974,;IRAK1,3_prime_UTR_variant,,ENST00000393682,;IRAK1,3_prime_UTR_variant,,ENST00000444254,;IRAK1,intron_variant,,ENST00000444230,;IRAK1,downstream_gene_variant,,ENST00000443220,;IRAK1,downstream_gene_variant,,ENST00000429936,;IRAK1,downstream_gene_variant,,ENST00000393687,;IRAK1,downstream_gene_variant,,ENST00000437278,;IRAK1,intron_variant,,ENST00000477274,;IRAK1,downstream_gene_variant,,ENST00000467236,;IRAK1,3_prime_UTR_variant,,ENST00000369973,;	A	ENSG00000184216	ENST00000369980	Transcript	3_prime_UTR_variant	2425	.	.	.	.	rs782327366	.	.	-1	IRAK1	HGNC	6112	protein_coding	YES	CCDS14740.1	ENSP00000358997	IRAK1_HUMAN	.	UPI000012D873	.	.	.	14/14	.	.	A:0.0003	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCCGCGGGC	by1000G	5	ESCA
DCAF8L2	0	.	GRCh37	X	27765039	27765039	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27C>T	p.%3D	p.D9D	ENST00000451261	5/5	16	2	14	9	9	0	DCAF8L2,synonymous_variant,p.%3D,ENST00000451261,;DCAF8L2,synonymous_variant,p.%3D,ENST00000431122,;DCAF8L2,downstream_gene_variant,,ENST00000583068,;AC107613.1,non_coding_transcript_exon_variant,,ENST00000545306,;	T	ENSG00000189186	ENST00000451261	Transcript	synonymous_variant	426	27	9	D	gaC/gaT	.	.	.	1	DCAF8L2	HGNC	31811	protein_coding	YES	CCDS59162.1	ENSP00000462745	DC8L2_HUMAN	J3QRI4_HUMAN	UPI000183CBD9	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	ACAGACGGCTT	.	4	ESCA
MAOB	0	.	GRCh37	X	43741511	43741511	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35delG	p.Gly12AlafsTer17	p.G12Afs*17	ENST00000378069	1/15	63	28	35	23	23	0	MAOB,frameshift_variant,p.Gly12AlafsTer17,ENST00000378069,;MAOB,5_prime_UTR_variant,,ENST00000536181,;MAOB,non_coding_transcript_exon_variant,,ENST00000468431,;MAOB,non_coding_transcript_exon_variant,,ENST00000487544,;	-	ENSG00000069535	ENST00000378069	Transcript	frameshift_variant	183	35	12	G/X	gGc/gc	.	.	.	-1	MAOB	HGNC	6834	protein_coding	YES	CCDS14261.1	ENSP00000367309	AOFB_HUMAN	H0YCD8_HUMAN,B7Z242_HUMAN	UPI0000049071	.	.	.	1/15	.	hmmpanther:PTHR10742,hmmpanther:PTHR10742:SF219,Gene3D:3.50.50.60,Superfamily_domains:SSF51905,Prints_domain:PR00757	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGCCGCCCCCC	.	3	ESCA
CXorf36	0	.	GRCh37	X	45051221	45051221	+	Silent	SNP	G	G	A	rs141296501	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.273C>T	p.%3D	p.P91P	ENST00000398000	2/5	33	9	24	28	28	0	CXorf36,synonymous_variant,p.%3D,ENST00000377934,;CXorf36,synonymous_variant,p.%3D,ENST00000398000,;RP11-342D14.1,intron_variant,,ENST00000438181,;RP11-342D14.1,intron_variant,,ENST00000450527,;CXorf36,upstream_gene_variant,,ENST00000477281,;CXorf36,upstream_gene_variant,,ENST00000492138,;	A	ENSG00000147113	ENST00000398000	Transcript	synonymous_variant	348	273	91	P	ccC/ccT	rs141296501	.	.	-1	CXorf36	HGNC	25866	protein_coding	YES	CCDS48096.1	ENSP00000381086	DIA1R_HUMAN	B7Z295_HUMAN	UPI000059DAFE	.	.	.	2/5	.	hmmpanther:PTHR32073:SF8,hmmpanther:PTHR32073	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATCGGGAGG	byFrequency|byCluster	5	ESCA
ZNF41	0	.	GRCh37	X	47307383	47307383	+	Missense_Mutation	SNP	C	C	T	rs555581955	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1786G>A	p.Val596Met	p.V596M	ENST00000377065	5/5	19	5	14	18	18	0	ZNF41,missense_variant,p.Val596Met,ENST00000313116,;ZNF41,missense_variant,p.Val606Met,ENST00000397050,;ZNF41,missense_variant,p.Val596Met,ENST00000377065,;ZNF41,downstream_gene_variant,,ENST00000432977,;ZNF41,downstream_gene_variant,,ENST00000465311,;	T	ENSG00000147124	ENST00000377065	Transcript	missense_variant	2426	1786	596	V/M	Gtg/Atg	rs555581955,COSM189851	.	.	-1	ZNF41	HGNC	13107	protein_coding	YES	CCDS14279.1	ENSP00000366265	ZNF41_HUMAN	.	UPI0000001C0E	.	tolerated(0.5)	benign(0.159)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF82,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCACGCTTA	.	5	ESCA
GLOD5	0	.	GRCh37	X	48631890	48631890	+	3'UTR	SNP	C	C	T	rs781850276	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39C>T	.	.	ENST00000303227	4/4	14	11	3	14	14	0	GLOD5,3_prime_UTR_variant,,ENST00000445229,;GLOD5,3_prime_UTR_variant,,ENST00000303227,;RNU6-29P,downstream_gene_variant,,ENST00000384637,;GLOD5,non_coding_transcript_exon_variant,,ENST00000470676,;AC115617.2,downstream_gene_variant,,ENST00000419045,;	T	ENSG00000171433	ENST00000303227	Transcript	3_prime_UTR_variant	563	.	.	.	.	rs781850276	.	.	1	GLOD5	HGNC	33358	protein_coding	YES	CCDS55410.1	ENSP00000302552	GLOD5_HUMAN	.	UPI00003D5F30	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGTCGCCCT	byFrequency	2	ESCA
FOXP3	0	.	GRCh37	X	49108166	49108166	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1105C>T	p.Arg369Cys	p.R369C	ENST00000376207	11/12	32	6	25	21	21	0	FOXP3,missense_variant,p.Arg334Cys,ENST00000557224,;FOXP3,missense_variant,p.Arg334Cys,ENST00000376199,;FOXP3,missense_variant,p.Arg319Cys,ENST00000376197,;FOXP3,missense_variant,p.Arg369Cys,ENST00000376207,;FOXP3,missense_variant,p.Arg334Cys,ENST00000518685,;FOXP3,missense_variant,p.Arg342Cys,ENST00000455775,;CCDC22,downstream_gene_variant,,ENST00000376227,;	A	ENSG00000049768	ENST00000376207	Transcript	missense_variant	1293	1105	369	R/C	Cgc/Tgc	.	.	.	-1	FOXP3	HGNC	6106	protein_coding	YES	CCDS14323.1	ENSP00000365380	FOXP3_HUMAN	B7ZLG1_HUMAN	UPI000012ADED	.	deleterious(0)	possibly_damaging(0.893)	11/12	.	PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF115,hmmpanther:PTHR11829,Pfam_domain:PF00250,Gene3D:1.10.10.10,SMART_domains:SM00339,Superfamily_domains:SSF46785,Prints_domain:PR00053	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGCGTGTGA	.	5	ESCA
MAGED1	0	.	GRCh37	X	51639754	51639754	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1171C>T	p.Pro391Ser	p.P391S	ENST00000375695	5/14	49	12	36	32	32	0	MAGED1,missense_variant,p.Pro335Ser,ENST00000326587,;MAGED1,missense_variant,p.Pro335Ser,ENST00000375722,;MAGED1,missense_variant,p.Pro391Ser,ENST00000375695,;MAGED1,missense_variant,p.Pro335Ser,ENST00000375772,;MAGED1,non_coding_transcript_exon_variant,,ENST00000494718,;MAGED1,non_coding_transcript_exon_variant,,ENST00000485420,;MAGED1,downstream_gene_variant,,ENST00000482188,;MAGED1,downstream_gene_variant,,ENST00000470461,;MAGED1,upstream_gene_variant,,ENST00000473931,;MAGED1,downstream_gene_variant,,ENST00000482599,;	T	ENSG00000179222	ENST00000375695	Transcript	missense_variant	1324	1171	391	P/S	Cca/Tca	.	.	.	1	MAGED1	HGNC	6813	protein_coding	YES	CCDS35279.1	ENSP00000364847	MAGD1_HUMAN	.	UPI0000074161	.	tolerated_low_confidence(0.06)	unknown(0)	5/14	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACCCAGTC	.	5	ESCA
HUWE1	0	.	GRCh37	X	53576405	53576405	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9550G>A	p.Glu3184Lys	p.E3184K	ENST00000342160	66/83	19	8	11	18	18	0	HUWE1,missense_variant,p.Glu3184Lys,ENST00000342160,;HUWE1,missense_variant,p.Glu3184Lys,ENST00000262854,;HUWE1,missense_variant,p.Glu2218Lys,ENST00000427052,;HUWE1,missense_variant,p.Glu22Lys,ENST00000426907,;HUWE1,upstream_gene_variant,,ENST00000474288,;HUWE1,upstream_gene_variant,,ENST00000468322,;	T	ENSG00000086758	ENST00000342160	Transcript	missense_variant	10008	9550	3184	E/K	Gaa/Aaa	.	.	.	-1	HUWE1	HGNC	30892	protein_coding	YES	CCDS35301.1	ENSP00000340648	HUWE1_HUMAN	Q5H963_HUMAN	UPI00004A0DAC	.	.	benign(0.305)	66/83	.	hmmpanther:PTHR11254:SF67,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCGTGGT	.	5	ESCA
PHF8	0	.	GRCh37	X	53963903	53963906	+	3'UTR	DEL	AAAT	AAAT	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AAAT	AAAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1685_*1688delATTT	.	.	ENST00000357988	22/22	32	7	25	14	14	0	PHF8,3_prime_UTR_variant,,ENST00000357988,;PHF8,3_prime_UTR_variant,,ENST00000338154,;PHF8,3_prime_UTR_variant,,ENST00000338946,;PHF8,downstream_gene_variant,,ENST00000396282,;PHF8,downstream_gene_variant,,ENST00000470103,;	-	ENSG00000172943	ENST00000357988	Transcript	3_prime_UTR_variant	5227-5230	.	.	.	.	.	.	.	-1	PHF8	HGNC	20672	protein_coding	YES	CCDS55420.1	ENSP00000350676	PHF8_HUMAN	Q5JPR8_HUMAN,B3KMV4_HUMAN,B0QZZ4_HUMAN,B0QZZ3_HUMAN,B0QZZ2_HUMAN,B0QZE1_HUMAN	UPI00001C2071	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCCCCAAAATAAGCA	.	2	ESCA
WNK3	0	.	GRCh37	X	54360201	54360201	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-95G>A	.	.	ENST00000354646	2/24	24	4	20	17	17	0	WNK3,5_prime_UTR_variant,,ENST00000458404,;WNK3,5_prime_UTR_variant,,ENST00000354646,;WNK3,5_prime_UTR_variant,,ENST00000375169,;WNK3,upstream_gene_variant,,ENST00000375159,;	T	ENSG00000196632	ENST00000354646	Transcript	5_prime_UTR_variant	345	.	.	.	.	.	.	.	-1	WNK3	HGNC	14543	protein_coding	YES	CCDS14357.1	ENSP00000346667	WNK3_HUMAN	B1AQN8_HUMAN	UPI00001AF003	.	.	.	2/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGCGTGGT	.	5	ESCA
UBQLN2	0	.	GRCh37	X	56593362	56593362	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1186delA	.	.	ENST00000338222	1/1	28	8	20	17	17	0	UBQLN2,3_prime_UTR_variant,,ENST00000338222,;	-	ENSG00000188021	ENST00000338222	Transcript	3_prime_UTR_variant	3337	.	.	.	.	.	.	.	1	UBQLN2	HGNC	12509	protein_coding	YES	CCDS14374.1	ENSP00000345195	UBQL2_HUMAN	.	UPI000004A059	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAAAATAAAAAA	.	2	ESCA
FAAH2	0	.	GRCh37	X	57318978	57318978	+	Silent	SNP	C	C	T	.	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240C>T	p.%3D	p.D80D	ENST00000374900	2/11	20	4	16	11	11	0	FAAH2,synonymous_variant,p.%3D,ENST00000374900,;	T	ENSG00000165591	ENST00000374900	Transcript	synonymous_variant	360	240	80	D	gaC/gaT	COSM613331	.	.	1	FAAH2	HGNC	26440	protein_coding	YES	CCDS14375.1	ENSP00000364035	FAAH2_HUMAN	B2C6G4_HUMAN	UPI000004CC6F	.	.	.	2/11	.	Superfamily_domains:SSF75304,Gene3D:3.90.1300.10,Pfam_domain:PF01425,hmmpanther:PTHR11895:SF66,hmmpanther:PTHR11895	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGACGTGAA	.	5	ESCA
IL2RG	0	.	GRCh37	X	70330527	70330527	+	Missense_Mutation	SNP	G	G	A	rs775704953	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281C>T	p.Ser94Leu	p.S94L	ENST00000374202	3/8	24	8	16	22	22	0	IL2RG,missense_variant,p.Ser50Leu,ENST00000464642,;IL2RG,missense_variant,p.Ser73Leu,ENST00000473378,;IL2RG,missense_variant,p.Ser82Leu,ENST00000487883,;IL2RG,missense_variant,p.Ser94Leu,ENST00000374202,;IL2RG,intron_variant,,ENST00000456850,;CXorf65,upstream_gene_variant,,ENST00000374251,;IL2RG,upstream_gene_variant,,ENST00000374188,;IL2RG,upstream_gene_variant,,ENST00000482750,;IL2RG,non_coding_transcript_exon_variant,,ENST00000512747,;IL2RG,non_coding_transcript_exon_variant,,ENST00000276110,;CXorf65,upstream_gene_variant,,ENST00000483257,;CXorf65,upstream_gene_variant,,ENST00000438526,;	A	ENSG00000147168	ENST00000374202	Transcript	missense_variant	373	281	94	S/L	tCg/tTg	rs775704953	.	.	-1	IL2RG	HGNC	6010	protein_coding	YES	CCDS14406.1	ENSP00000363318	IL2RG_HUMAN	Q6LER1_HUMAN,D6RDW9_HUMAN	UPI0000000DEA	.	deleterious(0.05)	benign(0.013)	3/8	.	hmmpanther:PTHR23036:SF92,hmmpanther:PTHR23036,Gene3D:2.60.40.10,Pfam_domain:PF09240,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCCGAGTTC	byFrequency	5	ESCA
OGT	0	.	GRCh37	X	70795640	70795641	+	3'UTR	INS	-	-	TC	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1996_*1997insTC	.	.	ENST00000373719	22/22	60	35	25	35	35	0	OGT,3_prime_UTR_variant,,ENST00000373719,;ACRC,upstream_gene_variant,,ENST00000373695,;OGT,downstream_gene_variant,,ENST00000373701,;ACRC,upstream_gene_variant,,ENST00000373696,;OGT,downstream_gene_variant,,ENST00000488174,;	TC	ENSG00000147162	ENST00000373719	Transcript	3_prime_UTR_variant	5354-5355	.	.	.	.	.	.	.	1	OGT	HGNC	8127	protein_coding	YES	CCDS14414.1	ENSP00000362824	OGT1_HUMAN	C9JZL3_HUMAN	UPI0000073C9F	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTTTCTATT	.	3	ESCA
XIST	0	.	GRCh37	X	73068387	73068387	+	RNA	SNP	C	C	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4202G>C	.	.	ENST00000429829	1/6	18	10	7	11	11	0	XIST,non_coding_transcript_exon_variant,,ENST00000429829,;	G	ENSG00000229807	ENST00000429829	Transcript	non_coding_transcript_exon_variant	4202	.	.	.	.	.	.	.	-1	XIST	HGNC	12810	lincRNA	YES	.	.	.	.	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCACATTGT	.	5	ESCA
KIAA2022	0	.	GRCh37	X	73958693	73958694	+	3'UTR	DEL	AC	AC	-	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	AC	AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*546_*547delGT	.	.	ENST00000055682	4/4	22	5	17	15	15	0	KIAA2022,3_prime_UTR_variant,,ENST00000055682,;KIAA2022,intron_variant,,ENST00000424929,;	-	ENSG00000050030	ENST00000055682	Transcript	3_prime_UTR_variant	5709-5710	.	.	.	.	.	.	.	-1	KIAA2022	HGNC	29433	protein_coding	YES	CCDS35337.1	ENSP00000055682	K2022_HUMAN	.	UPI00001C207B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATATATACACACA	.	2	ESCA
ATRX	0	.	GRCh37	X	76761749	76761749	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2080T>C	.	.	ENST00000373344	35/35	31	18	13	13	13	0	ATRX,3_prime_UTR_variant,,ENST00000395603,;ATRX,3_prime_UTR_variant,,ENST00000373344,;ATRX,non_coding_transcript_exon_variant,,ENST00000480283,;	G	ENSG00000085224	ENST00000373344	Transcript	3_prime_UTR_variant	9774	.	.	.	.	.	.	.	-1	ATRX	HGNC	886	protein_coding	YES	CCDS14434.1	ENSP00000362441	ATRX_HUMAN	B4DLE1_HUMAN	UPI0000161F78	.	.	.	35/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AAAGTACATAT	.	4	ESCA
BRWD3	0	.	GRCh37	X	79932174	79932174	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5343A>G	p.%3D	p.R1781R	ENST00000373275	41/41	28	8	19	11	11	0	BRWD3,synonymous_variant,p.%3D,ENST00000373275,;BRWD3,downstream_gene_variant,,ENST00000473691,;	C	ENSG00000165288	ENST00000373275	Transcript	synonymous_variant	5560	5343	1781	R	agA/agG	.	.	.	-1	BRWD3	HGNC	17342	protein_coding	YES	CCDS14447.1	ENSP00000362372	BRWD3_HUMAN	.	UPI000045785B	.	.	.	41/41	.	hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGATCTGGA	.	5	ESCA
POU3F4	0	.	GRCh37	X	82763400	82763400	+	Missense_Mutation	SNP	C	C	T	rs779536644	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.68C>T	p.Ala23Val	p.A23V	ENST00000373200	1/1	44	22	22	21	21	0	POU3F4,missense_variant,p.Ala23Val,ENST00000373200,;RP3-326L13.3,upstream_gene_variant,,ENST00000607789,;RP3-326L13.2,non_coding_transcript_exon_variant,,ENST00000607095,;	T	ENSG00000196767	ENST00000373200	Transcript	missense_variant	132	68	23	A/V	gCg/gTg	rs779536644,COSM1472310,COSM1472309	.	.	1	POU3F4	HGNC	9217	protein_coding	YES	CCDS14450.1	ENSP00000362296	PO3F4_HUMAN	.	UPI000045785D	.	tolerated_low_confidence(0.11)	benign(0.001)	1/1	.	hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF66,PIRSF_domain:PIRSF002629	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTCTGCGGGCA	byFrequency	4	ESCA
PCDH11X	0	.	GRCh37	X	91091004	91091004	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A43J-01A-12D-A247-09	TCGA-L5-A43J-11A-11D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501C>T	p.%3D	p.D167D	ENST00000373094	1/7	42	8	33	36	36	0	PCDH11X,synonymous_variant,p.%3D,ENST00000373088,;PCDH11X,synonymous_variant,p.%3D,ENST00000361724,;PCDH11X,synonymous_variant,p.%3D,ENST00000395337,;PCDH11X,synonymous_variant,p.%3D,ENST00000298274,;PCDH11X,synonymous_variant,p.%3D,ENST00000504220,;PCDH11X,synonymous_variant,p.%3D,ENST00000406881,;PCDH11X,synonymous_variant,p.%3D,ENST00000373094,;PCDH11X,synonymous_variant,p.%3D,ENST00000373097,;PCDH11X,synonymous_variant,p.%3D,ENST00000361655,;	T	ENSG00000102290	ENST00000373094	Transcript	synonymous_variant	1346	501	167	D	gaC/gaT	.	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	.	.	1/7	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF15,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGACGTAGG	.	5	ESCA
SLC39A12	0	.	GRCh37	10	18292265	18292265	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1925T>C	p.Leu642Ser	p.L642S	ENST00000377369	12/13	141	116	24	135	135	0	SLC39A12,missense_variant,p.Leu642Ser,ENST00000377369,;SLC39A12,missense_variant,p.Leu508Ser,ENST00000539911,;SLC39A12,missense_variant,p.Leu641Ser,ENST00000377371,;SLC39A12,missense_variant,p.Leu605Ser,ENST00000377374,;SLC39A12-AS1,non_coding_transcript_exon_variant,,ENST00000445287,;SLC39A12-AS1,non_coding_transcript_exon_variant,,ENST00000439319,;	C	ENSG00000148482	ENST00000377369	Transcript	missense_variant	2198	1925	642	L/S	tTa/tCa	.	.	.	1	SLC39A12	HGNC	20860	protein_coding	YES	CCDS44362.1	ENSP00000366586	S39AC_HUMAN	F5GX72_HUMAN	UPI00004044FC	.	deleterious(0)	probably_damaging(0.999)	12/13	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191,Pfam_domain:PF02535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTTATATT	.	5	ESCA
MLLT10	0	.	GRCh37	10	22031223	22031223	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*311T>C	.	.	ENST00000307729	23/23	21	17	4	15	15	0	MLLT10,3_prime_UTR_variant,,ENST00000446906,;MLLT10,3_prime_UTR_variant,,ENST00000377059,;MLLT10,3_prime_UTR_variant,,ENST00000307729,;MLLT10,3_prime_UTR_variant,,ENST00000377072,;	C	ENSG00000078403	ENST00000307729	Transcript	3_prime_UTR_variant	3696	.	.	.	.	.	.	.	1	MLLT10	HGNC	16063	protein_coding	YES	CCDS55708.1	ENSP00000307411	AF10_HUMAN	Q71UR7_HUMAN,B4DVS6_HUMAN	UPI00001F8FF7	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGTTGGTAC	.	4	ESCA
WDFY4	0	.	GRCh37	10	49951516	49951516	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2382G>A	p.%3D	p.P794P	ENST00000325239	11/61	20	11	9	31	31	0	WDFY4,synonymous_variant,p.%3D,ENST00000413659,;WDFY4,synonymous_variant,p.%3D,ENST00000325239,;RP11-534L6.3,downstream_gene_variant,,ENST00000434320,;	A	ENSG00000128815	ENST00000325239	Transcript	synonymous_variant	2409	2382	794	P	ccG/ccA	.	.	.	1	WDFY4	HGNC	29323	protein_coding	YES	CCDS44385.1	ENSP00000320563	WDFY4_HUMAN	Q6PIM1_HUMAN	UPI000176ADB8	.	.	.	11/61	.	hmmpanther:PTHR13743:SF52,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCGGTTGT	.	5	ESCA
C10orf53	0	.	GRCh37	10	50902828	50902828	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217+889G>A	.	.	ENST00000374112	.	17	12	5	13	13	0	C10orf53,3_prime_UTR_variant,,ENST00000374111,;C10orf53,3_prime_UTR_variant,,ENST00000374113,;C10orf53,intron_variant,,ENST00000374112,;C10orf53,intron_variant,,ENST00000535836,;CHAT,downstream_gene_variant,,ENST00000455728,;	A	ENSG00000178645	ENST00000374112	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C10orf53	HGNC	27421	protein_coding	YES	CCDS31202.1	ENSP00000363226	CJ053_HUMAN	.	UPI00001406B3	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGAGCCCAC	.	5	ESCA
PRR5L	0	.	GRCh37	11	36422705	36422705	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34G>A	p.Glu12Lys	p.E12K	ENST00000378867	3/10	49	28	20	42	42	0	PRR5L,missense_variant,p.Glu12Lys,ENST00000526682,;PRR5L,missense_variant,p.Glu12Lys,ENST00000532121,;PRR5L,missense_variant,p.Glu12Lys,ENST00000530639,;PRR5L,missense_variant,p.Glu12Lys,ENST00000530050,;PRR5L,missense_variant,p.Glu12Lys,ENST00000526728,;PRR5L,missense_variant,p.Glu12Lys,ENST00000527487,;PRR5L,missense_variant,p.Glu12Lys,ENST00000530252,;PRR5L,missense_variant,p.Glu12Lys,ENST00000524380,;PRR5L,missense_variant,p.Glu12Lys,ENST00000526679,;PRR5L,missense_variant,p.Glu12Lys,ENST00000527172,;PRR5L,missense_variant,p.Glu12Lys,ENST00000378867,;PRR5L,5_prime_UTR_variant,,ENST00000311599,;PRR5L,non_coding_transcript_exon_variant,,ENST00000529034,;PRR5L,intron_variant,,ENST00000389693,;PRR5L,downstream_gene_variant,,ENST00000527751,;	A	ENSG00000135362	ENST00000378867	Transcript	missense_variant	389	34	12	E/K	Gag/Aag	.	.	.	1	PRR5L	HGNC	25878	protein_coding	YES	CCDS31463.1	ENSP00000368144	PRR5L_HUMAN	E9PS02_HUMAN,E9PP62_HUMAN,E9PP25_HUMAN,E9PLJ6_HUMAN,E9PL62_HUMAN,E9PKK6_HUMAN,E9PJV4_HUMAN,E9PIU0_HUMAN	UPI0000DBEF36	.	tolerated_low_confidence(0.07)	benign(0.054)	3/10	.	hmmpanther:PTHR32428,hmmpanther:PTHR32428:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTCGAGTTC	.	5	ESCA
API5	0	.	GRCh37	11	43364101	43364101	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*41A>G	.	.	ENST00000531273	14/14	49	29	20	31	31	0	API5,missense_variant,p.Ile90Met,ENST00000534695,;API5,3_prime_UTR_variant,,ENST00000455725,;API5,3_prime_UTR_variant,,ENST00000378852,;API5,3_prime_UTR_variant,,ENST00000420461,;API5,3_prime_UTR_variant,,ENST00000531273,;RP11-484D2.2,intron_variant,,ENST00000526220,;API5,downstream_gene_variant,,ENST00000529334,;	G	ENSG00000166181	ENST00000531273	Transcript	3_prime_UTR_variant	1755	.	.	.	.	.	.	.	1	API5	HGNC	594	protein_coding	YES	CCDS44572.1	ENSP00000431391	API5_HUMAN	.	UPI0000E229DE	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATATACTT	.	5	ESCA
OR4C46	0	.	GRCh37	11	51515594	51515594	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313T>C	p.Phe105Leu	p.F105L	ENST00000328188	1/1	108	82	26	101	101	0	OR4C46,missense_variant,p.Phe105Leu,ENST00000328188,;	C	ENSG00000185926	ENST00000328188	Transcript	missense_variant	313	313	105	F/L	Ttc/Ctc	.	.	.	1	OR4C46	HGNC	31271	protein_coding	YES	CCDS31498.1	ENSP00000329056	O4C46_HUMAN	.	UPI000013F6F8	.	tolerated_low_confidence(0.16)	benign(0.02)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF284,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCTTCGGA	.	5	ESCA
CDHR5	0	.	GRCh37	11	621243	621243	+	Missense_Mutation	SNP	G	G	A	rs774600340	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626C>T	p.Pro209Leu	p.P209L	ENST00000358353	8/16	96	80	16	86	86	0	CDHR5,missense_variant,p.Pro209Leu,ENST00000397542,;CDHR5,missense_variant,p.Pro209Leu,ENST00000349570,;CDHR5,missense_variant,p.Pro209Leu,ENST00000358353,;CDHR5,synonymous_variant,p.%3D,ENST00000526077,;CDHR5,downstream_gene_variant,,ENST00000531088,;CDHR5,downstream_gene_variant,,ENST00000534311,;CDHR5,downstream_gene_variant,,ENST00000529337,;CDHR5,upstream_gene_variant,,ENST00000532949,;CDHR5,3_prime_UTR_variant,,ENST00000531177,;CDHR5,non_coding_transcript_exon_variant,,ENST00000531899,;	A	ENSG00000099834	ENST00000358353	Transcript	missense_variant	949	626	209	P/L	cCg/cTg	rs774600340	.	.	-1	CDHR5	HGNC	7521	protein_coding	YES	CCDS7707.1	ENSP00000351118	CDHR5_HUMAN	.	UPI0000456444	.	tolerated(0.32)	benign(0.209)	8/16	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,hmmpanther:PTHR24027:SF121,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCCCGGAGTG	byFrequency	4	ESCA
MTA2	0	.	GRCh37	11	62362771	62362771	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1448A>G	p.Tyr483Cys	p.Y483C	ENST00000278823	14/18	33	23	10	37	37	0	MTA2,missense_variant,p.Tyr310Cys,ENST00000524902,;MTA2,missense_variant,p.Tyr310Cys,ENST00000527204,;MTA2,missense_variant,p.Tyr483Cys,ENST00000278823,;TUT1,upstream_gene_variant,,ENST00000476907,;TUT1,upstream_gene_variant,,ENST00000278279,;TUT1,upstream_gene_variant,,ENST00000308436,;TUT1,upstream_gene_variant,,ENST00000494385,;MTA2,downstream_gene_variant,,ENST00000532239,;MTA2,downstream_gene_variant,,ENST00000531261,;MTA2,downstream_gene_variant,,ENST00000526844,;MTA2,downstream_gene_variant,,ENST00000531179,;MIR3654,upstream_gene_variant,,ENST00000496634,;TUT1,upstream_gene_variant,,ENST00000478537,;	C	ENSG00000149480	ENST00000278823	Transcript	missense_variant	1838	1448	483	Y/C	tAt/tGt	.	.	.	-1	MTA2	HGNC	7411	protein_coding	YES	CCDS8022.1	ENSP00000278823	MTA2_HUMAN	Q68DB1_HUMAN	UPI000012F743	.	tolerated(0.07)	possibly_damaging(0.781)	14/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10865:SF4,hmmpanther:PTHR10865	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCATAAGGC	.	5	ESCA
CDC42BPG	0	.	GRCh37	11	64606671	64606671	+	Missense_Mutation	SNP	T	T	A	rs760928514	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.710A>T	p.Tyr237Phe	p.Y237F	ENST00000342711	7/37	24	17	6	28	28	0	CDC42BPG,missense_variant,p.Tyr237Phe,ENST00000342711,;	A	ENSG00000171219	ENST00000342711	Transcript	missense_variant	710	710	237	Y/F	tAt/tTt	rs760928514	.	.	-1	CDC42BPG	HGNC	29829	protein_coding	YES	CCDS31601.1	ENSP00000345133	MRCKG_HUMAN	.	UPI000047C9E2	.	deleterious(0)	probably_damaging(0.999)	7/37	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF22,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGATATAGTCC	byFrequency	4	ESCA
OR2AG2	0	.	GRCh37	11	6789646	6789646	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543C>T	p.%3D	p.I181I	ENST00000338569	1/1	73	42	30	39	39	0	OR2AG2,synonymous_variant,p.%3D,ENST00000338569,;	A	ENSG00000188124	ENST00000338569	Transcript	synonymous_variant	641	543	181	I	atC/atT	.	.	.	-1	OR2AG2	HGNC	15143	protein_coding	YES	CCDS31413.1	ENSP00000342697	O2AG2_HUMAN	.	UPI0000041C10	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF107,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGGATCTC	.	5	ESCA
HECTD4	0	.	GRCh37	12	112717042	112717042	+	Silent	SNP	T	T	C	rs373751710	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245A>G	p.%3D	p.S415S	ENST00000550722	9/76	30	19	11	33	33	0	HECTD4,synonymous_variant,p.%3D,ENST00000430131,;HECTD4,synonymous_variant,p.%3D,ENST00000550722,;HECTD4,synonymous_variant,p.%3D,ENST00000377560,;HECTD4,intron_variant,,ENST00000550724,;	C	ENSG00000173064	ENST00000550722	Transcript	synonymous_variant	1641	1245	415	S	tcA/tcG	rs373751710,COSM1511140,COSM1511141	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	.	9/76	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	C:0.0003	C:0	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGATGACAA	byCluster	5	ESCA
ZNF385A	0	.	GRCh37	12	54764422	54764422	+	Silent	SNP	G	G	A	rs752247719	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.918C>T	p.%3D	p.A306A	ENST00000338010	7/8	18	12	5	16	16	0	ZNF385A,synonymous_variant,p.%3D,ENST00000546970,;ZNF385A,synonymous_variant,p.%3D,ENST00000551771,;ZNF385A,synonymous_variant,p.%3D,ENST00000338010,;ZNF385A,synonymous_variant,p.%3D,ENST00000352268,;ZNF385A,synonymous_variant,p.%3D,ENST00000551109,;ZNF385A,synonymous_variant,p.%3D,ENST00000394313,;ZNF385A,downstream_gene_variant,,ENST00000550120,;ZNF385A,downstream_gene_variant,,ENST00000549962,;ZNF385A,downstream_gene_variant,,ENST00000550774,;ZNF385A,downstream_gene_variant,,ENST00000549937,;ZNF385A,downstream_gene_variant,,ENST00000546919,;ZNF385A,downstream_gene_variant,,ENST00000547210,;RP11-753H16.5,intron_variant,,ENST00000552785,;RP11-753H16.3,intron_variant,,ENST00000550474,;ZNF385A,non_coding_transcript_exon_variant,,ENST00000552382,;ZNF385A,downstream_gene_variant,,ENST00000551864,;ZNF385A,3_prime_UTR_variant,,ENST00000550779,;	A	ENSG00000161642	ENST00000338010	Transcript	synonymous_variant	972	918	306	A	gcC/gcT	rs752247719	.	.	-1	ZNF385A	HGNC	17521	protein_coding	YES	CCDS44911.1	ENSP00000338927	Z385A_HUMAN	F8VWV6_HUMAN,F8VSJ1_HUMAN,F8VRY0_HUMAN	UPI00005A791C	.	.	.	7/8	.	hmmpanther:PTHR23067:SF13,hmmpanther:PTHR23067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCGGCGCC	byFrequency	5	ESCA
LIN7A	0	.	GRCh37	12	81205437	81205437	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.509A>C	p.Lys170Thr	p.K170T	ENST00000552864	5/6	54	31	23	44	44	0	LIN7A,missense_variant,p.Lys170Thr,ENST00000552864,;LIN7A,3_prime_UTR_variant,,ENST00000261203,;	G	ENSG00000111052	ENST00000552864	Transcript	missense_variant	712	509	170	K/T	aAa/aCa	.	.	.	-1	LIN7A	HGNC	17787	protein_coding	YES	CCDS9021.1	ENSP00000447488	LIN7A_HUMAN	.	UPI0000073ECD	.	deleterious(0)	benign(0.185)	5/6	.	PROSITE_profiles:PS50106,hmmpanther:PTHR14063,hmmpanther:PTHR14063:SF4,Gene3D:2.30.42.10,Pfam_domain:PF00595,PIRSF_domain:PIRSF038039,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTTTCTCA	.	5	ESCA
AMER2	0	.	GRCh37	13	25744194	25744194	+	Missense_Mutation	SNP	C	C	T	rs745945541	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1564G>A	p.Glu522Lys	p.E522K	ENST00000515384	1/1	39	28	11	44	44	0	AMER2,missense_variant,p.Glu522Lys,ENST00000515384,;AMER2,missense_variant,p.Glu403Lys,ENST00000357816,;AMER2,missense_variant,p.Glu403Lys,ENST00000381853,;AMER2-AS1,downstream_gene_variant,,ENST00000413501,;	T	ENSG00000165566	ENST00000515384	Transcript	missense_variant	2232	1564	522	E/K	Gag/Aag	rs745945541,COSM550982,COSM550981	.	.	-1	AMER2	HGNC	26360	protein_coding	YES	CCDS53859.1	ENSP00000426528	AMER2_HUMAN	Q8N785_HUMAN	UPI0000231C76	.	deleterious(0.01)	possibly_damaging(0.741)	1/1	.	Pfam_domain:PF09422,hmmpanther:PTHR22237:SF1,hmmpanther:PTHR22237	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCGTCGC	byFrequency	5	ESCA
MTUS2	0	.	GRCh37	13	29675026	29675026	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2593G>A	p.Val865Ile	p.V865I	ENST00000431530	3/14	61	51	10	81	81	0	MTUS2,missense_variant,p.Val865Ile,ENST00000431530,;MTUS2,non_coding_transcript_exon_variant,,ENST00000255289,;	A	ENSG00000132938	ENST00000431530	Transcript	missense_variant	2651	2593	865	V/I	Gtc/Atc	.	.	.	1	MTUS2	HGNC	20595	protein_coding	YES	CCDS45022.1	ENSP00000392057	.	J3KQA9_HUMAN,B4DWQ4_HUMAN	UPI0000F734AC	.	tolerated(0.05)	possibly_damaging(0.467)	3/14	.	hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTTGTCCGG	.	4	ESCA
TRIM13	0	.	GRCh37	13	50591278	50591278	+	3'Flank	SNP	A	A	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000356017	.	43	28	15	35	35	0	TRIM13,3_prime_UTR_variant,,ENST00000378182,;KCNRG,intron_variant,,ENST00000360473,;KCNRG,intron_variant,,ENST00000312942,;TRIM13,downstream_gene_variant,,ENST00000378183,;TRIM13,downstream_gene_variant,,ENST00000420995,;TRIM13,downstream_gene_variant,,ENST00000356017,;TRIM13,downstream_gene_variant,,ENST00000457662,;TRIM13,downstream_gene_variant,,ENST00000442421,;TRIM13,downstream_gene_variant,,ENST00000298772,;TRIM13,intron_variant,,ENST00000478111,;TRIM13,intron_variant,,ENST00000474805,;	G	ENSG00000204977	ENST00000356017	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3962	1	TRIM13	HGNC	9976	protein_coding	YES	CCDS41888.1	ENSP00000348299	TRI13_HUMAN	.	UPI00001FCDDE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTATCTTT	.	5	ESCA
ZFYVE21	0	.	GRCh37	14	104199926	104199926	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*571C>T	.	.	ENST00000216602	8/8	51	33	18	59	59	0	ZFYVE21,3_prime_UTR_variant,,ENST00000311141,;ZFYVE21,3_prime_UTR_variant,,ENST00000216602,;ZFYVE21,downstream_gene_variant,,ENST00000555163,;PPP1R13B,downstream_gene_variant,,ENST00000423488,;PPP1R13B,downstream_gene_variant,,ENST00000202556,;PPP1R13B,downstream_gene_variant,,ENST00000555391,;ZFYVE21,non_coding_transcript_exon_variant,,ENST00000555501,;ZFYVE21,non_coding_transcript_exon_variant,,ENST00000554757,;ZFYVE21,downstream_gene_variant,,ENST00000556610,;PPP1R13B,downstream_gene_variant,,ENST00000557082,;PPP1R13B,downstream_gene_variant,,ENST00000557587,;ZFYVE21,downstream_gene_variant,,ENST00000556795,;ZFYVE21,downstream_gene_variant,,ENST00000554630,;ZFYVE21,downstream_gene_variant,,ENST00000553724,;PPP1R13B,downstream_gene_variant,,ENST00000555825,;PPP1R13B,downstream_gene_variant,,ENST00000556597,;PPP1R13B,downstream_gene_variant,,ENST00000556334,;ZFYVE21,downstream_gene_variant,,ENST00000602552,;ZFYVE21,downstream_gene_variant,,ENST00000553512,;PPP1R13B,downstream_gene_variant,,ENST00000554432,;	T	ENSG00000100711	ENST00000216602	Transcript	3_prime_UTR_variant	1442	.	.	.	.	.	.	.	1	ZFYVE21	HGNC	20760	protein_coding	YES	CCDS55948.1	ENSP00000216602	ZFY21_HUMAN	.	UPI000006E373	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTCACTAT	.	5	ESCA
RTN1	0	.	GRCh37	14	60212843	60212843	+	Missense_Mutation	SNP	T	T	G	rs767482992	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598A>C	p.Thr200Pro	p.T200P	ENST00000267484	2/9	37	21	16	55	55	0	RTN1,missense_variant,p.Thr200Pro,ENST00000267484,;	G	ENSG00000139970	ENST00000267484	Transcript	missense_variant	934	598	200	T/P	Acc/Ccc	rs767482992	.	.	-1	RTN1	HGNC	10467	protein_coding	YES	CCDS9740.1	ENSP00000267484	RTN1_HUMAN	Q2NKQ5_HUMAN,Q2L7A7_HUMAN	UPI00001352DA	.	deleterious(0.01)	benign(0.265)	2/9	.	hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGGTTATGT	byFrequency	5	ESCA
ALDH6A1	0	.	GRCh37	14	74551066	74551066	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.32G>A	p.Arg11Gln	p.R11Q	ENST00000553458	1/12	61	54	7	90	90	0	ALDH6A1,missense_variant,p.Arg11Gln,ENST00000553458,;ALDH6A1,missense_variant,p.Arg11Gln,ENST00000350259,;LIN52,upstream_gene_variant,,ENST00000554938,;LIN52,upstream_gene_variant,,ENST00000555028,;CCDC176,downstream_gene_variant,,ENST00000553773,;ALDH6A1,non_coding_transcript_exon_variant,,ENST00000553814,;ALDH6A1,non_coding_transcript_exon_variant,,ENST00000556852,;LIN52,upstream_gene_variant,,ENST00000554076,;AC005484.5,downstream_gene_variant,,ENST00000492026,;ALDH6A1,non_coding_transcript_exon_variant,,ENST00000554231,;ALDH6A1,non_coding_transcript_exon_variant,,ENST00000554501,;LIN52,upstream_gene_variant,,ENST00000554289,;LIN52,upstream_gene_variant,,ENST00000553404,;	T	ENSG00000119711	ENST00000553458	Transcript	missense_variant	131	32	11	R/Q	cGa/cAa	.	.	.	-1	ALDH6A1	HGNC	7179	protein_coding	YES	CCDS9826.1	ENSP00000450436	MMSA_HUMAN	G3V4Z4_HUMAN	UPI0000001610	.	tolerated(0.1)	unknown(0)	1/12	.	hmmpanther:PTHR11699:SF27,hmmpanther:PTHR11699,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGCTCGCACT	.	4	ESCA
PROX2	0	.	GRCh37	14	75320932	75320932	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*903T>A	.	.	ENST00000556084	3/3	52	33	19	61	61	0	PROX2,3_prime_UTR_variant,,ENST00000556489,;PROX2,3_prime_UTR_variant,,ENST00000556084,;YLPM1,intron_variant,,ENST00000554107,;PROX2,downstream_gene_variant,,ENST00000445876,;RP11-316E14.6,intron_variant,,ENST00000553381,;	T	ENSG00000119608	ENST00000556084	Transcript	3_prime_UTR_variant	2001	.	.	.	.	.	.	.	-1	PROX2	HGNC	26715	protein_coding	YES	CCDS45136.2	ENSP00000451463	PROX2_HUMAN	.	UPI00002522F9	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATTATCCAG	.	5	ESCA
PGF	0	.	GRCh37	14	75413456	75413456	+	Intron	SNP	G	G	T	rs746891062	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393-345C>A	.	.	ENST00000555567	.	85	66	18	85	85	0	PGF,missense_variant,p.Asn196Lys,ENST00000405431,;PGF,intron_variant,,ENST00000553716,;PGF,intron_variant,,ENST00000238607,;PGF,intron_variant,,ENST00000555567,;PGF,non_coding_transcript_exon_variant,,ENST00000555253,;PGF,intron_variant,,ENST00000557748,;PGF,downstream_gene_variant,,ENST00000555234,;PGF,downstream_gene_variant,,ENST00000556939,;	T	ENSG00000119630	ENST00000555567	Transcript	intron_variant	.	.	.	.	.	rs746891062	.	.	-1	PGF	HGNC	8893	protein_coding	YES	CCDS9835.1	ENSP00000451040	PLGF_HUMAN	Q53XY6_HUMAN	UPI000002B14D	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCGTTCCT	byFrequency	5	ESCA
ZSCAN29	0	.	GRCh37	15	43654034	43654034	+	Missense_Mutation	SNP	C	C	A	rs141880595	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1796G>T	p.Arg599Leu	p.R599L	ENST00000396976	5/5	34	24	10	49	49	0	ZSCAN29,missense_variant,p.Arg210Leu,ENST00000396972,;ZSCAN29,missense_variant,p.Arg209Leu,ENST00000568898,;ZSCAN29,missense_variant,p.Gly528Cys,ENST00000562072,;ZSCAN29,missense_variant,p.Arg599Leu,ENST00000396976,;ZSCAN29,downstream_gene_variant,,ENST00000570181,;ZSCAN29,3_prime_UTR_variant,,ENST00000566849,;	A	ENSG00000140265	ENST00000396976	Transcript	missense_variant	1931	1796	599	R/L	cGg/cTg	TMP_ESP_15_43654034_43654034,rs141880595,COSM109671	.	.	-1	ZSCAN29	HGNC	26673	protein_coding	YES	CCDS10095.2	ENSP00000380174	ZSC29_HUMAN	Q96AG1_HUMAN,H3BVH1_HUMAN	UPI0000DA5AF5	.	tolerated(0.14)	benign(0.039)	5/5	.	hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF209	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0011	T:0	not_provided	0,1,1	21499247	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R599Q|c.1796G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATACCGGGGA	byCluster|by1000G	5	ESCA
AP3B2	0	.	GRCh37	15	83333651	83333653	+	In_Frame_Del	DEL	CTC	CTC	-	rs765815539	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2014_2016delGAG	p.Glu672del	p.E672del	ENST00000261722	17/26	64	37	27	61	61	0	AP3B2,inframe_deletion,p.Glu640del,ENST00000535348,;AP3B2,inframe_deletion,p.Glu691del,ENST00000535359,;AP3B2,inframe_deletion,p.Glu672del,ENST00000261722,;RP11-752G15.3,intron_variant,,ENST00000560650,;AP3B2,non_coding_transcript_exon_variant,,ENST00000543938,;AP3B2,upstream_gene_variant,,ENST00000538592,;AP3B2,upstream_gene_variant,,ENST00000537735,;AP3B2,upstream_gene_variant,,ENST00000545315,;	-	ENSG00000103723	ENST00000261722	Transcript	inframe_deletion	2222-2224	2014-2016	672	E/-	GAG/-	rs765815539	.	.	-1	AP3B2	HGNC	567	protein_coding	YES	CCDS45331.1	ENSP00000261722	AP3B2_HUMAN	F5GWU4_HUMAN	UPI0000125030	.	.	.	17/26	.	hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF11,PIRSF_domain:PIRSF037096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCCTTCTCCTTTC	byFrequency	3	ESCA
SULT1A1	0	.	GRCh37	16	28617218	28617218	+	Missense_Mutation	SNP	G	G	A	rs767993186	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.812C>T	p.Ala271Val	p.A271V	ENST00000395609	10/10	39	32	7	48	48	0	SULT1A1,missense_variant,p.Ala271Val,ENST00000569554,;SULT1A1,missense_variant,p.Ala271Val,ENST00000395607,;SULT1A1,missense_variant,p.Ala271Val,ENST00000566189,;SULT1A1,missense_variant,p.Ala271Val,ENST00000314752,;SULT1A1,missense_variant,p.Ala271Val,ENST00000395609,;SULT1A1,missense_variant,p.Ala193Val,ENST00000350842,;SULT1A1,downstream_gene_variant,,ENST00000567512,;SULT1A1,3_prime_UTR_variant,,ENST00000564818,;SULT1A1,3_prime_UTR_variant,,ENST00000562058,;SULT1A1,3_prime_UTR_variant,,ENST00000563493,;SULT1A1,non_coding_transcript_exon_variant,,ENST00000567998,;	A	ENSG00000196502	ENST00000395609	Transcript	missense_variant	1571	812	271	A/V	gCg/gTg	rs767993186	.	.	-1	SULT1A1	HGNC	11453	protein_coding	YES	CCDS32420.1	ENSP00000378972	ST1A1_HUMAN	Q9UMT9_HUMAN,H3BRY5_HUMAN	UPI000013EA41	.	deleterious(0.03)	benign(0.133)	10/10	.	hmmpanther:PTHR11783:SF42,hmmpanther:PTHR11783,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TCTGCGCCACG	byFrequency	3	ESCA
KCTD19	0	.	GRCh37	16	67354649	67354649	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143C>T	p.Ser48Phe	p.S48F	ENST00000304372	2/16	54	46	7	49	49	0	KCTD19,missense_variant,p.Ser43Phe,ENST00000567976,;KCTD19,missense_variant,p.Ser48Phe,ENST00000304372,;KCTD19,missense_variant,p.Ser43Phe,ENST00000566295,;RN7SKP118,downstream_gene_variant,,ENST00000364331,;KCTD19,non_coding_transcript_exon_variant,,ENST00000562860,;KCTD19,non_coding_transcript_exon_variant,,ENST00000561625,;KCTD19,3_prime_UTR_variant,,ENST00000562721,;KCTD19,non_coding_transcript_exon_variant,,ENST00000570049,;KCTD19,non_coding_transcript_exon_variant,,ENST00000566392,;KCTD19,non_coding_transcript_exon_variant,,ENST00000568736,;KCTD19,non_coding_transcript_exon_variant,,ENST00000569333,;	A	ENSG00000168676	ENST00000304372	Transcript	missense_variant	199	143	48	S/F	tCt/tTt	.	.	.	-1	KCTD19	HGNC	24753	protein_coding	YES	CCDS42179.1	ENSP00000305702	KCD19_HUMAN	J3KSZ9_HUMAN,H3BVC0_HUMAN	UPI00001D7875	.	deleterious(0.04)	benign(0.409)	2/16	.	hmmpanther:PTHR14499:SF20,hmmpanther:PTHR14499,Pfam_domain:PF02214,Gene3D:3.30.710.10,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGAAGAGGTC	.	4	ESCA
FAM83G	0	.	GRCh37	17	18874806	18874806	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2338C>T	p.Pro780Ser	p.P780S	ENST00000388995	6/6	122	116	6	134	134	0	FAM83G,missense_variant,p.Pro780Ser,ENST00000585154,;FAM83G,missense_variant,p.Pro780Ser,ENST00000388995,;FAM83G,missense_variant,p.Pro780Ser,ENST00000345041,;SLC5A10,intron_variant,,ENST00000417251,;SLC5A10,intron_variant,,ENST00000395647,;SLC5A10,intron_variant,,ENST00000395643,;SLC5A10,intron_variant,,ENST00000395642,;SLC5A10,intron_variant,,ENST00000395645,;SLC5A10,intron_variant,,ENST00000317977,;FAM83G,downstream_gene_variant,,ENST00000399096,;	A	ENSG00000188522	ENST00000388995	Transcript	missense_variant	2562	2338	780	P/S	Ccg/Tcg	COSM3514995	.	.	-1	FAM83G	HGNC	32554	protein_coding	YES	CCDS42276.1	ENSP00000373647	FA83G_HUMAN	.	UPI0000E03260	.	tolerated(0.63)	benign(0.004)	6/6	.	hmmpanther:PTHR16181:SF5,hmmpanther:PTHR16181	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTCGGATGCT	.	2	ESCA
ANKRD40	0	.	GRCh37	17	48774476	48774476	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785T>G	p.Val262Gly	p.V262G	ENST00000285243	4/5	44	33	10	41	41	0	ANKRD40,missense_variant,p.Val262Gly,ENST00000285243,;ANKRD40,downstream_gene_variant,,ENST00000513072,;ABCC3,downstream_gene_variant,,ENST00000285238,;RP11-294J22.6,downstream_gene_variant,,ENST00000574246,;Y_RNA,downstream_gene_variant,,ENST00000364470,;ANKRD40,downstream_gene_variant,,ENST00000507114,;	C	ENSG00000154945	ENST00000285243	Transcript	missense_variant	1055	785	262	V/G	gTa/gGa	.	.	.	-1	ANKRD40	HGNC	28233	protein_coding	YES	CCDS11572.1	ENSP00000285243	ANR40_HUMAN	K7ERW4_HUMAN,A8IK34_HUMAN	UPI000006F76F	.	deleterious(0)	probably_damaging(0.997)	4/5	.	hmmpanther:PTHR24192,hmmpanther:PTHR24192:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGTACCAGC	.	5	ESCA
PRKAR1A	0	.	GRCh37	17	66527600	66527600	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1010A>T	.	.	ENST00000589228	11/11	17	12	4	10	10	0	PRKAR1A,3_prime_UTR_variant,,ENST00000392711,;PRKAR1A,3_prime_UTR_variant,,ENST00000358598,;PRKAR1A,3_prime_UTR_variant,,ENST00000536854,;PRKAR1A,3_prime_UTR_variant,,ENST00000589228,;PRKAR1A,intron_variant,,ENST00000588188,;PRKAR1A,downstream_gene_variant,,ENST00000586397,;PRKAR1A,downstream_gene_variant,,ENST00000585981,;PRKAR1A,downstream_gene_variant,,ENST00000592800,;FAM20A,downstream_gene_variant,,ENST00000226094,;PRKAR1A,3_prime_UTR_variant,,ENST00000392710,;PRKAR1A,downstream_gene_variant,,ENST00000585907,;PRKAR1A,downstream_gene_variant,,ENST00000586541,;	T	ENSG00000108946	ENST00000589228	Transcript	3_prime_UTR_variant	2284	.	.	.	.	.	.	.	1	PRKAR1A	HGNC	9388	protein_coding	YES	CCDS11678.1	ENSP00000464977	KAP0_HUMAN	Q96P62_HUMAN,K7EQK3_HUMAN,K7EPR5_HUMAN,K7EPB2_HUMAN,K7ENR3_HUMAN,K7EMU2_HUMAN,K7EK41_HUMAN,K7EJ40_HUMAN,K7EIE5_HUMAN,K7EID3_HUMAN,B2R5T5_HUMAN	UPI0000001C57	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTAAAGGGAG	.	5	ESCA
TP53	0	.	GRCh37	17	7578370	7578370	+	Splice_Site	SNP	C	C	T	.	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559+1G>A	.	p.X187_splice	ENST00000269305	.	432	85	347	353	353	0	TP53,splice_donor_variant,,ENST00000413465,;TP53,splice_donor_variant,,ENST00000420246,;TP53,splice_donor_variant,,ENST00000269305,;TP53,splice_donor_variant,,ENST00000509690,;TP53,splice_donor_variant,,ENST00000359597,;TP53,splice_donor_variant,,ENST00000514944,;TP53,splice_donor_variant,,ENST00000445888,;TP53,splice_donor_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,splice_donor_variant,,ENST00000574684,;TP53,splice_donor_variant,,ENST00000504937,;TP53,splice_donor_variant,,ENST00000505014,;TP53,splice_donor_variant,,ENST00000504290,;TP53,splice_donor_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	splice_donor_variant	.	.	.	.	.	TP53_g.12548G>C,TP53_g.12548G>T,TP53_g.12548G>A,COSM6901,COSM44268,COSM33648,COSM131534,COSM437533,COSM254992,COSM131535,COSM254991,COSM437534,COSM437536,COSM131537,COSM254993,COSM3388354,COSM3932745,COSM1756958,COSM2744800,COSM1649387,COSM131536,COSM254994,COSM437535	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	5/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.559+1G>A|4,SITE|p.?|c.559+1G>A|11,SITE|p.?|c.559+1G>A|25,SITE|p.?|c.559+1G>A|4,SITE|p.?|c.163+1G>A|11,SITE|p.?|c.559+1G>A|11,SITE|p.?|c.280+1G>A|11,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.?|c.559+2T>G|5,BUFFER|p.?|c.163+1G>C|3,BUFFER|p.?|c.559+1G>C|3,BUFFER|p.?|c.280+1G>C|3,BUFFER|p.?|c.559+1G>T|7,BUFFER|p.?|c.559+1G>C|3,BUFFER|p.?|c.559+1G>C|4,BUFFER|p.?|c.163+1G>T|3,BUFFER|p.G187S|c.559G>A|3,BUFFER|p.G187S|c.559G>A|17,BUFFER|p.G55S|c.163G>A|3,BUFFER|p.G94S|c.280G>A|3,BUFFER|p.G187S|c.559G>A|3,BUFFER|p.D186fs*61|c.556delG|3,BUFFER|p.D186G|c.557A>G|4,BUFFER|p.D54G|c.161A>G|4,BUFFER|p.D186G|c.557A>G|4,BUFFER|p.D186G|c.557A>G|5,BUFFER|p.D93G|c.278A>G|4,BUFFER|p.D186N|c.556G>A|5,BUFFER|p.D186H|c.556G>C|4,BUFFER|p.S185R|c.555C>A|4,BUFFER|p.S185S|c.555C>T|3,BUFFER|p.D184H|c.550G>C|6,BUFFER|p.D184N|c.550G>A|14,BUFFER|p.D184Y|c.550G>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCACCATCG	.	5	ESCA
FASN	0	.	GRCh37	17	80037129	80037129	+	Missense_Mutation	SNP	C	C	T	rs1140623	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7426G>A	p.Val2476Ile	p.V2476I	ENST00000306749	43/43	49	40	9	54	54	0	FASN,missense_variant,p.Val2476Ile,ENST00000306749,;FASN,downstream_gene_variant,,ENST00000579758,;FASN,3_prime_UTR_variant,,ENST00000580382,;FASN,non_coding_transcript_exon_variant,,ENST00000584610,;FASN,downstream_gene_variant,,ENST00000578424,;	T	ENSG00000169710	ENST00000306749	Transcript	missense_variant	7645	7426	2476	V/I	Gtc/Atc	rs1140623	.	.	-1	FASN	HGNC	3594	protein_coding	YES	CCDS11801.1	ENSP00000304592	FAS_HUMAN	.	UPI000013EB82	.	tolerated(0.29)	benign(0.004)	43/43	.	hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF227,Gene3D:3.40.50.1820,Pfam_domain:PF00975,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGACGTGGA	.	5	ESCA
ROCK1	0	.	GRCh37	18	18530348	18530348	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*997C>T	.	.	ENST00000399799	33/33	49	34	14	36	36	0	ROCK1,3_prime_UTR_variant,,ENST00000399799,;ROCK1,downstream_gene_variant,,ENST00000578051,;ROCK1,downstream_gene_variant,,ENST00000584687,;	A	ENSG00000067900	ENST00000399799	Transcript	3_prime_UTR_variant	6003	.	.	.	.	.	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTGAAAAT	.	5	ESCA
ROCK1	0	.	GRCh37	18	18530962	18530962	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*383C>G	.	.	ENST00000399799	33/33	27	19	8	20	20	0	ROCK1,3_prime_UTR_variant,,ENST00000399799,;ROCK1,downstream_gene_variant,,ENST00000578051,;ROCK1,downstream_gene_variant,,ENST00000584687,;	C	ENSG00000067900	ENST00000399799	Transcript	3_prime_UTR_variant	5389	.	.	.	.	.	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATCTTGATAGT	.	3	ESCA
ROCK1	0	.	GRCh37	18	18530984	18530984	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*361C>T	.	.	ENST00000399799	33/33	31	24	7	18	18	0	ROCK1,3_prime_UTR_variant,,ENST00000399799,;ROCK1,downstream_gene_variant,,ENST00000578051,;ROCK1,downstream_gene_variant,,ENST00000584687,;	A	ENSG00000067900	ENST00000399799	Transcript	3_prime_UTR_variant	5367	.	.	.	.	.	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CACTTGAAAGT	.	3	ESCA
MIB1	0	.	GRCh37	18	19429195	19429195	+	Missense_Mutation	SNP	A	A	T	rs757717286	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2432A>T	p.Asn811Ile	p.N811I	ENST00000261537	17/21	43	30	12	28	28	0	MIB1,missense_variant,p.Asn811Ile,ENST00000261537,;MIB1,non_coding_transcript_exon_variant,,ENST00000578646,;	T	ENSG00000101752	ENST00000261537	Transcript	missense_variant	2696	2432	811	N/I	aAt/aTt	rs757717286	.	.	1	MIB1	HGNC	21086	protein_coding	YES	CCDS11871.1	ENSP00000261537	MIB1_HUMAN	B3KRA8_HUMAN	UPI000000D833	.	tolerated(0.11)	benign(0.004)	17/21	.	hmmpanther:PTHR24202,hmmpanther:PTHR24202:SF52,Gene3D:3.30.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTAATGATT	byFrequency	5	ESCA
CCDC68	0	.	GRCh37	18	52571492	52571492	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*97T>A	.	.	ENST00000591504	12/12	12	7	5	12	12	0	CCDC68,3_prime_UTR_variant,,ENST00000591504,;CCDC68,3_prime_UTR_variant,,ENST00000432185,;CCDC68,3_prime_UTR_variant,,ENST00000337363,;CCDC68,intron_variant,,ENST00000592040,;	T	ENSG00000166510	ENST00000591504	Transcript	3_prime_UTR_variant	1380	.	.	.	.	.	.	.	-1	CCDC68	HGNC	24350	protein_coding	YES	CCDS11959.1	ENSP00000466690	CCD68_HUMAN	.	UPI00000435F1	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAATAATGGCA	.	3	ESCA
NCAN	0	.	GRCh37	19	19330103	19330103	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453C>A	p.Asp151Glu	p.D151E	ENST00000252575	3/15	47	41	6	41	41	0	NCAN,missense_variant,p.Asp151Glu,ENST00000252575,;	A	ENSG00000130287	ENST00000252575	Transcript	missense_variant	552	453	151	D/E	gaC/gaA	.	.	.	1	NCAN	HGNC	2465	protein_coding	YES	CCDS12397.1	ENSP00000252575	NCAN_HUMAN	Q4LE67_HUMAN,F5H7X3_HUMAN	UPI000013CD70	.	deleterious(0)	probably_damaging(0.998)	3/15	.	PROSITE_profiles:PS50835,hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF24,SMART_domains:SM00409,Superfamily_domains:SSF48726,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGACCTGGT	.	4	ESCA
ZNF208	0	.	GRCh37	19	22155555	22155555	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2281T>C	p.Ser761Pro	p.S761P	ENST00000397126	4/4	51	30	21	36	36	0	ZNF208,missense_variant,p.Ser761Pro,ENST00000397126,;ZNF208,intron_variant,,ENST00000601773,;ZNF208,intron_variant,,ENST00000599916,;	G	ENSG00000160321	ENST00000397126	Transcript	missense_variant	2430	2281	761	S/P	Tcc/Ccc	.	.	.	-1	ZNF208	HGNC	12999	protein_coding	YES	CCDS54240.1	ENSP00000380315	ZN208_HUMAN	.	UPI0001B23C28	.	tolerated(0.18)	benign(0)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGGACCACT	.	5	ESCA
PPP1R15A	0	.	GRCh37	19	49377829	49377829	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1339G>T	p.Asp447Tyr	p.D447Y	ENST00000200453	2/3	34	25	9	31	31	0	PPP1R15A,missense_variant,p.Asp86Tyr,ENST00000600406,;PPP1R15A,missense_variant,p.Asp447Tyr,ENST00000200453,;	T	ENSG00000087074	ENST00000200453	Transcript	missense_variant	1608	1339	447	D/Y	Gat/Tat	.	.	.	1	PPP1R15A	HGNC	14375	protein_coding	YES	CCDS12738.1	ENSP00000200453	PR15A_HUMAN	.	UPI000006F652	.	deleterious(0.01)	probably_damaging(0.99)	2/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16489,hmmpanther:PTHR16489:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAGGATGTG	.	5	ESCA
SIGLEC6	0	.	GRCh37	19	52034113	52034113	+	Silent	SNP	C	C	T	rs758976882	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528G>A	p.%3D	p.T176T	ENST00000425629	3/8	39	27	11	43	43	0	SIGLEC6,synonymous_variant,p.%3D,ENST00000436458,;SIGLEC6,synonymous_variant,p.%3D,ENST00000391797,;SIGLEC6,synonymous_variant,p.%3D,ENST00000359982,;SIGLEC6,synonymous_variant,p.%3D,ENST00000425629,;SIGLEC6,synonymous_variant,p.%3D,ENST00000343300,;SIGLEC6,synonymous_variant,p.%3D,ENST00000346477,;SIGLEC6,upstream_gene_variant,,ENST00000474054,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000489837,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000496422,;	T	ENSG00000105492	ENST00000425629	Transcript	synonymous_variant	683	528	176	T	acG/acA	rs758976882	.	.	-1	SIGLEC6	HGNC	10875	protein_coding	YES	CCDS12834.3	ENSP00000401502	SIGL6_HUMAN	.	UPI0000223FFD	.	.	.	3/8	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF00047,Gene3D:2.60.40.10,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF41,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGCGTCCC	byFrequency	5	ESCA
LILRB3	0	.	GRCh37	19	54720935	54720935	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*27C>T	.	.	ENST00000245620	13/13	69	64	5	76	76	0	LILRB3,3_prime_UTR_variant,,ENST00000424807,;LILRB3,3_prime_UTR_variant,,ENST00000407860,;LILRA6,3_prime_UTR_variant,,ENST00000270464,;LILRB3,3_prime_UTR_variant,,ENST00000391750,;LILRA6,3_prime_UTR_variant,,ENST00000391735,;LILRA6,3_prime_UTR_variant,,ENST00000440558,;LILRA6,3_prime_UTR_variant,,ENST00000419410,;LILRB3,3_prime_UTR_variant,,ENST00000245620,;LILRB3,3_prime_UTR_variant,,ENST00000346401,;LILRB3,downstream_gene_variant,,ENST00000445347,;LILRB3,downstream_gene_variant,,ENST00000469273,;LILRB3,3_prime_UTR_variant,,ENST00000414379,;RPS9,intron_variant,,ENST00000448962,;LILRB3,downstream_gene_variant,,ENST00000436504,;LILRB3,downstream_gene_variant,,ENST00000468668,;LILRB3,downstream_gene_variant,,ENST00000460208,;	A	ENSG00000204577	ENST00000245620	Transcript	3_prime_UTR_variant	1928	.	.	.	.	.	.	.	-1	LILRB3	HGNC	6607	protein_coding	YES	CCDS46175.1	ENSP00000245620	LIRB3_HUMAN	C9JWL8_HUMAN	UPI0000E04BFA	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCTGAGTGT	.	2	ESCA
ZNF697	0	.	GRCh37	1	120165681	120165681	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1285C>T	p.Arg429Cys	p.R429C	ENST00000421812	3/3	31	20	11	33	33	0	ZNF697,missense_variant,p.Arg429Cys,ENST00000421812,;	A	ENSG00000143067	ENST00000421812	Transcript	missense_variant	1405	1285	429	R/C	Cgc/Tgc	COSM3399604,COSM3399603	.	.	-1	ZNF697	HGNC	32034	protein_coding	YES	CCDS44202.1	ENSP00000396857	ZN697_HUMAN	Q8N508_HUMAN	UPI0000DD78D7	.	deleterious(0)	probably_damaging(0.999)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF55,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGTGCGCTTGT	.	4	ESCA
YY1AP1	0	.	GRCh37	1	155630265	155630265	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1850C>G	p.Ser617Cys	p.S617C	ENST00000368339	10/10	66	43	22	44	44	0	YY1AP1,missense_variant,p.Ser479Cys,ENST00000355499,;YY1AP1,missense_variant,p.Ser448Cys,ENST00000311573,;YY1AP1,missense_variant,p.Ser325Cys,ENST00000535662,;YY1AP1,missense_variant,p.Ser617Cys,ENST00000368339,;YY1AP1,missense_variant,p.Ser525Cys,ENST00000295566,;YY1AP1,missense_variant,p.Ser479Cys,ENST00000347088,;YY1AP1,missense_variant,p.Ser468Cys,ENST00000361831,;YY1AP1,missense_variant,p.Ser597Cys,ENST00000368340,;YY1AP1,missense_variant,p.Ser448Cys,ENST00000407221,;YY1AP1,missense_variant,p.Ser459Cys,ENST00000404643,;YY1AP1,missense_variant,p.Ser468Cys,ENST00000359205,;YY1AP1,missense_variant,p.Ser479Cys,ENST00000368330,;MSTO1,intron_variant,,ENST00000538143,;MSTO1,intron_variant,,ENST00000452804,;YY1AP1,downstream_gene_variant,,ENST00000405763,;YY1AP1,downstream_gene_variant,,ENST00000488784,;YY1AP1,downstream_gene_variant,,ENST00000493625,;YY1AP1,downstream_gene_variant,,ENST00000477470,;YY1AP1,3_prime_UTR_variant,,ENST00000361140,;YY1AP1,3_prime_UTR_variant,,ENST00000436865,;YY1AP1,3_prime_UTR_variant,,ENST00000354691,;YY1AP1,non_coding_transcript_exon_variant,,ENST00000442834,;MSTO2P,intron_variant,,ENST00000538914,;RP11-29H23.5,upstream_gene_variant,,ENST00000500626,;	C	ENSG00000163374	ENST00000368339	Transcript	missense_variant	1855	1850	617	S/C	tCt/tGt	.	.	.	-1	YY1AP1	HGNC	30935	protein_coding	YES	CCDS55645.1	ENSP00000357323	YYAP1_HUMAN	A3KFK2_HUMAN,A3KFK1_HUMAN	UPI0001AE792F	.	tolerated_low_confidence(0.14)	benign(0.067)	10/10	.	hmmpanther:PTHR16088,hmmpanther:PTHR16088:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGAGACTCA	.	5	ESCA
NHLH1	0	.	GRCh37	1	160341717	160341717	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*794G>A	.	.	ENST00000302101	2/2	28	22	6	25	25	0	NHLH1,3_prime_UTR_variant,,ENST00000302101,;	A	ENSG00000171786	ENST00000302101	Transcript	3_prime_UTR_variant	1642	.	.	.	.	.	.	.	1	NHLH1	HGNC	7817	protein_coding	YES	CCDS1204.1	ENSP00000302189	HEN1_HUMAN	Q5T203_HUMAN	UPI000012C5FE	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGGGATGAC	.	5	ESCA
COLGALT2	0	.	GRCh37	1	183909716	183909716	+	Missense_Mutation	SNP	C	C	A	rs759172474	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1603G>T	p.Val535Leu	p.V535L	ENST00000361927	11/12	46	32	14	42	42	0	COLGALT2,missense_variant,p.Val272Leu,ENST00000367520,;COLGALT2,missense_variant,p.Val535Leu,ENST00000361927,;COLGALT2,missense_variant,p.Val143Leu,ENST00000367521,;COLGALT2,missense_variant,p.Val535Phe,ENST00000546159,;COLGALT2,splice_region_variant,,ENST00000486375,;	A	ENSG00000198756	ENST00000361927	Transcript	missense_variant	1975	1603	535	V/L	Gta/Tta	rs759172474	.	.	-1	COLGALT2	HGNC	16790	protein_coding	YES	CCDS1360.1	ENSP00000354960	GT252_HUMAN	Q5SXQ5_HUMAN,B3KT92_HUMAN	UPI000007423A	.	tolerated(0.29)	benign(0.04)	11/12	.	hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCACACGGGAT	byFrequency	4	ESCA
C1orf27	0	.	GRCh37	1	186388404	186388404	+	3'UTR	SNP	G	G	A	rs186485557	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*196G>A	.	.	ENST00000287859	14/14	10	6	4	8	8	0	C1orf27,3_prime_UTR_variant,,ENST00000419367,;C1orf27,3_prime_UTR_variant,,ENST00000367470,;C1orf27,3_prime_UTR_variant,,ENST00000287859,;C1orf27,downstream_gene_variant,,ENST00000432021,;C1orf27,downstream_gene_variant,,ENST00000461662,;	A	ENSG00000157181	ENST00000287859	Transcript	3_prime_UTR_variant	1686	.	.	.	.	rs186485557	.	.	1	C1orf27	HGNC	24299	protein_coding	YES	CCDS53448.1	ENSP00000287859	ODR4_HUMAN	.	UPI00003744FF	.	.	.	14/14	.	.	A:0.0010	A:0	A:0.0014	.	A:0	A:0.001	A:0.0031	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCCGCATTT	byFrequency|byCluster|by1000G	2	ESCA
FBXO28	0	.	GRCh37	1	224345198	224345198	+	Missense_Mutation	SNP	G	G	A	rs754206716	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.857G>A	p.Arg286His	p.R286H	ENST00000366862	5/5	40	37	3	26	26	0	FBXO28,missense_variant,p.Arg286His,ENST00000366862,;FBXO28,3_prime_UTR_variant,,ENST00000424254,;FBXO28,3_prime_UTR_variant,,ENST00000523990,;	A	ENSG00000143756	ENST00000366862	Transcript	missense_variant	900	857	286	R/H	cGc/cAc	rs754206716	.	.	1	FBXO28	HGNC	29046	protein_coding	YES	CCDS1539.1	ENSP00000355827	FBX28_HUMAN	B4E0H5_HUMAN	UPI000006F1C1	.	deleterious(0.05)	benign(0.079)	5/5	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13252	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTCGCACCA	byFrequency	2	ESCA
H3F3A	0	.	GRCh37	1	226252079	226252079	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27C>T	p.%3D	p.R9R	ENST00000366813	1/3	135	119	15	72	72	0	H3F3A,synonymous_variant,p.%3D,ENST00000366813,;H3F3A,synonymous_variant,p.%3D,ENST00000366814,;H3F3A,synonymous_variant,p.%3D,ENST00000366816,;H3F3A,synonymous_variant,p.%3D,ENST00000366815,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,;	T	ENSG00000163041	ENST00000366813	Transcript	synonymous_variant	402	27	9	R	cgC/cgT	.	.	.	1	H3F3A	HGNC	4764	protein_coding	YES	CCDS1550.1	ENSP00000355778	H33_HUMAN	K7EK07_HUMAN,B4E380_HUMAN,B2R4P9_HUMAN	UPI00000007B0	.	.	.	1/3	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCGCAAATC	.	4	ESCA
OR11L1	0	.	GRCh37	1	248005147	248005147	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.52C>T	p.Gln18Ter	p.Q18*	ENST00000355784	1/1	30	18	12	12	12	0	OR11L1,stop_gained,p.Gln18Ter,ENST00000355784,;	A	ENSG00000197591	ENST00000355784	Transcript	stop_gained	108	52	18	Q/*	Cag/Tag	.	.	.	-1	OR11L1	HGNC	14998	protein_coding	YES	CCDS31098.1	ENSP00000348033	O11L1_HUMAN	.	UPI0000061EBC	.	.	.	1/1	.	hmmpanther:PTHR26452:SF12,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTGGAATC	.	5	ESCA
SH3BP5L	0	.	GRCh37	1	249107261	249107261	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.638A>T	p.Lys213Met	p.K213M	ENST00000366472	6/7	59	47	11	34	34	0	SH3BP5L,missense_variant,p.Lys181Met,ENST00000411742,;SH3BP5L,missense_variant,p.Lys213Met,ENST00000366472,;SH3BP5L,non_coding_transcript_exon_variant,,ENST00000475978,;SH3BP5L,non_coding_transcript_exon_variant,,ENST00000484202,;SH3BP5L,downstream_gene_variant,,ENST00000494837,;	A	ENSG00000175137	ENST00000366472	Transcript	missense_variant	1868	638	213	K/M	aAg/aTg	.	.	.	-1	SH3BP5L	HGNC	29360	protein_coding	YES	CCDS31126.1	ENSP00000355428	3BP5L_HUMAN	Q96MW4_HUMAN,Q96ET3_HUMAN	UPI000003F53A	.	deleterious(0)	probably_damaging(0.995)	6/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19423,Pfam_domain:PF05276	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCTTCTGC	.	5	ESCA
CLSTN1	0	.	GRCh37	1	9793590	9793590	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2296G>A	p.Ala766Thr	p.A766T	ENST00000377298	16/19	53	50	3	54	54	0	CLSTN1,missense_variant,p.Ala567Thr,ENST00000435891,;CLSTN1,missense_variant,p.Ala766Thr,ENST00000377298,;CLSTN1,missense_variant,p.Ala747Thr,ENST00000377288,;CLSTN1,missense_variant,p.Ala756Thr,ENST00000361311,;PIK3CD,downstream_gene_variant,,ENST00000536656,;PIK3CD,downstream_gene_variant,,ENST00000377346,;CLSTN1,upstream_gene_variant,,ENST00000477264,;	T	ENSG00000171603	ENST00000377298	Transcript	missense_variant	3089	2296	766	A/T	Gcc/Acc	.	.	.	-1	CLSTN1	HGNC	17447	protein_coding	YES	CCDS30580.1	ENSP00000366513	CSTN1_HUMAN	.	UPI0000127B95	.	tolerated(0.23)	benign(0.371)	16/19	.	hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGGCCATGG	.	2	ESCA
ZNF512B	0	.	GRCh37	20	62594469	62594469	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1947G>A	p.%3D	p.V649V	ENST00000450537	12/17	34	26	8	28	28	0	ZNF512B,synonymous_variant,p.%3D,ENST00000450537,;ZNF512B,synonymous_variant,p.%3D,ENST00000217130,;ZNF512B,synonymous_variant,p.%3D,ENST00000369888,;	T	ENSG00000196700	ENST00000450537	Transcript	synonymous_variant	2008	1947	649	V	gtG/gtA	.	.	.	-1	ZNF512B	HGNC	29212	protein_coding	YES	CCDS13548.1	ENSP00000393795	Z512B_HUMAN	.	UPI000013A290	.	.	.	12/17	.	PROSITE_profiles:PS50157,hmmpanther:PTHR22979,hmmpanther:PTHR22979:SF3,PROSITE_patterns:PS00028,Pfam_domain:PF13894,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCGCACGTG	.	5	ESCA
MICAL3	0	.	GRCh37	22	18383650	18383650	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805A>G	p.Ile269Val	p.I269V	ENST00000441493	6/32	67	51	16	61	61	0	MICAL3,missense_variant,p.Ile269Val,ENST00000207726,;MICAL3,missense_variant,p.Ile269Val,ENST00000444520,;MICAL3,missense_variant,p.Ile269Val,ENST00000383094,;MICAL3,missense_variant,p.Ile269Val,ENST00000414725,;MICAL3,missense_variant,p.Ile269Val,ENST00000429452,;MICAL3,missense_variant,p.Ile269Val,ENST00000585038,;MICAL3,missense_variant,p.Ile269Val,ENST00000441493,;MICAL3,missense_variant,p.Ile269Val,ENST00000400561,;MICAL3,downstream_gene_variant,,ENST00000424046,;MICAL3,missense_variant,p.Ile269Val,ENST00000495076,;	C	ENSG00000243156	ENST00000441493	Transcript	missense_variant	1158	805	269	I/V	Ata/Gta	.	.	.	-1	MICAL3	HGNC	24694	protein_coding	YES	CCDS46659.1	ENSP00000416015	MICA3_HUMAN	C9J922_HUMAN,A8K0E1_HUMAN	UPI0001823FDE	.	.	benign(0.158)	6/32	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATATAAAAG	.	5	ESCA
BCR	0	.	GRCh37	22	23658925	23658925	+	3'UTR	SNP	G	G	A	rs550338960	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1216G>A	.	.	ENST00000305877	23/23	54	42	12	44	44	0	BCR,3_prime_UTR_variant,,ENST00000305877,;BCR,downstream_gene_variant,,ENST00000359540,;BCR,non_coding_transcript_exon_variant,,ENST00000436990,;BCR,downstream_gene_variant,,ENST00000458056,;BCR,downstream_gene_variant,,ENST00000475025,;	A	ENSG00000186716	ENST00000305877	Transcript	3_prime_UTR_variant	5783	.	.	.	.	rs550338960	.	.	1	BCR	HGNC	1014	protein_coding	YES	CCDS13806.1	ENSP00000303507	BCR_HUMAN	.	UPI000016A088	.	.	.	23/23	.	.	C:0.0046	C:0.0174	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTCCCGGAGCA	byFrequency|by1000G	2	ESCA
NCKAP5	0	.	GRCh37	2	133618079	133618079	+	Missense_Mutation	SNP	C	C	T	rs375710595	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.793G>A	p.Asp265Asn	p.D265N	ENST00000409261	11/20	64	61	3	48	48	0	NCKAP5,missense_variant,p.Asp265Asn,ENST00000409213,;NCKAP5,missense_variant,p.Asp265Asn,ENST00000409261,;NCKAP5,missense_variant,p.Asp265Asn,ENST00000405974,;NCKAP5,missense_variant,p.Asp265Asn,ENST00000317721,;	T	ENSG00000176771	ENST00000409261	Transcript	missense_variant	1167	793	265	D/N	Gat/Aat	rs375710595	.	.	-1	NCKAP5	HGNC	29847	protein_coding	YES	CCDS46418.1	ENSP00000387128	NCKP5_HUMAN	C9JYL7_HUMAN	UPI0000E07A3F	.	deleterious(0.01)	possibly_damaging(0.907)	11/20	.	hmmpanther:PTHR21740:SF0,hmmpanther:PTHR21740	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0008	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATCAGAAG	byCluster|by1000G	2	ESCA
LY75-CD302	0	.	GRCh37	2	160664960	160664960	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4822G>C	p.Asp1608His	p.D1608H	ENST00000504764	33/39	66	46	20	41	41	0	LY75-CD302,missense_variant,p.Asp1608His,ENST00000504764,;LY75,missense_variant,p.Asp1608His,ENST00000553424,;LY75,missense_variant,p.Asp1608His,ENST00000554112,;LY75,missense_variant,p.Asp1608His,ENST00000263636,;LY75-CD302,missense_variant,p.Asp1608His,ENST00000505052,;AC009961.5,downstream_gene_variant,,ENST00000435771,;	G	ENSG00000248672	ENST00000504764	Transcript	missense_variant	4850	4822	1608	D/H	Gac/Cac	.	.	.	-1	LY75-CD302	HGNC	38828	protein_coding	YES	CCDS56141.1	ENSP00000423463	.	.	UPI00018817E3	.	deleterious(0.01)	benign(0.15)	33/39	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22803:SF65,hmmpanther:PTHR22803,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTACCAACAG	.	5	ESCA
SCN2A	0	.	GRCh37	2	166153528	166153528	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.269C>A	p.Thr90Lys	p.T90K	ENST00000357398	3/27	66	36	29	70	70	0	SCN2A,missense_variant,p.Thr90Lys,ENST00000283256,;SCN2A,missense_variant,p.Thr90Lys,ENST00000375437,;SCN2A,missense_variant,p.Thr90Lys,ENST00000424833,;SCN2A,missense_variant,p.Thr90Lys,ENST00000375427,;SCN2A,missense_variant,p.Thr90Lys,ENST00000357398,;SCN2A,splice_region_variant,,ENST00000480032,;	A	ENSG00000136531	ENST00000357398	Transcript	missense_variant	559	269	90	T/K	aCg/aAg	.	.	.	1	SCN2A	HGNC	10588	protein_coding	YES	CCDS33313.1	ENSP00000349973	SCN2A_HUMAN	F8T7W7_HUMAN	UPI000002A663	.	deleterious(0)	possibly_damaging(0.82)	3/27	.	hmmpanther:PTHR10037:SF133,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGACGTTTA	.	5	ESCA
SCN1A	0	.	GRCh37	2	166847217	166847217	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*538C>A	.	.	ENST00000303395	26/26	17	13	4	8	8	0	SCN1A,3_prime_UTR_variant,,ENST00000423058,;SCN1A,3_prime_UTR_variant,,ENST00000303395,;SCN1A,3_prime_UTR_variant,,ENST00000375405,;SCN1A,downstream_gene_variant,,ENST00000409050,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000597623,;	T	ENSG00000144285	ENST00000303395	Transcript	3_prime_UTR_variant	6568	.	.	.	.	.	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAGCTGGGAGG	.	3	ESCA
OLA1	0	.	GRCh37	2	174940204	174940204	+	Missense_Mutation	SNP	C	C	T	rs761407656	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1141G>A	p.Asp381Asn	p.D381N	ENST00000284719	11/11	112	62	49	76	76	0	OLA1,missense_variant,p.Asp381Asn,ENST00000284719,;OLA1,missense_variant,p.Asp223Asn,ENST00000344357,;OLA1,missense_variant,p.Asp401Asn,ENST00000409546,;OLA1,synonymous_variant,p.%3D,ENST00000428402,;OLA1,non_coding_transcript_exon_variant,,ENST00000392560,;OLA1,non_coding_transcript_exon_variant,,ENST00000497760,;	T	ENSG00000138430	ENST00000284719	Transcript	missense_variant	1388	1141	381	D/N	Gat/Aat	rs761407656	.	.	-1	OLA1	HGNC	28833	protein_coding	YES	CCDS2255.1	ENSP00000284719	OLA1_HUMAN	Q53SW9_HUMAN,Q53SQ6_HUMAN,C9JTK6_HUMAN,C9JCJ9_HUMAN	UPI00001328C1	.	deleterious(0.01)	probably_damaging(0.997)	11/11	.	HAMAP:MF_00944,hmmpanther:PTHR23305,Pfam_domain:PF06071,TIGRFAM_domain:TIGR00092,Gene3D:3.10.20.30,PIRSF_domain:PIRSF006641,Superfamily_domains:SSF81271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATCTCCAT	byFrequency	5	ESCA
TTN	0	.	GRCh37	2	179593015	179593015	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19536T>C	p.%3D	p.A6512A	ENST00000589042	67/363	22	10	12	12	12	0	TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,upstream_gene_variant,,ENST00000582847,;RP11-171I2.1,downstream_gene_variant,,ENST00000590024,;	G	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	19761	19536	6512	A	gcT/gcC	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	67/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGAGCACT	.	5	ESCA
RAPH1	0	.	GRCh37	2	204306703	204306703	+	Intron	SNP	G	G	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1777-567C>A	.	.	ENST00000319170	.	22	12	10	21	21	0	RAPH1,3_prime_UTR_variant,,ENST00000374488,;RAPH1,3_prime_UTR_variant,,ENST00000374489,;ABI2,3_prime_UTR_variant,,ENST00000295851,;RAPH1,3_prime_UTR_variant,,ENST00000308091,;RAPH1,intron_variant,,ENST00000374493,;RAPH1,intron_variant,,ENST00000457812,;RAPH1,intron_variant,,ENST00000319170,;RAPH1,downstream_gene_variant,,ENST00000418114,;RAPH1,downstream_gene_variant,,ENST00000423104,;RAPH1,downstream_gene_variant,,ENST00000419464,;RAPH1,downstream_gene_variant,,ENST00000439222,;RAPH1,downstream_gene_variant,,ENST00000453034,;	T	ENSG00000173166	ENST00000319170	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RAPH1	HGNC	14436	protein_coding	YES	CCDS2359.1	ENSP00000316543	RAPH1_HUMAN	C9JLG4_HUMAN	UPI000020940F	.	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAAGCTTGA	.	5	ESCA
RAPH1	0	.	GRCh37	2	204306704	204306704	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1777-568G>A	.	.	ENST00000319170	.	22	12	10	21	21	0	RAPH1,3_prime_UTR_variant,,ENST00000374488,;RAPH1,3_prime_UTR_variant,,ENST00000374489,;ABI2,3_prime_UTR_variant,,ENST00000295851,;RAPH1,3_prime_UTR_variant,,ENST00000308091,;RAPH1,intron_variant,,ENST00000374493,;RAPH1,intron_variant,,ENST00000457812,;RAPH1,intron_variant,,ENST00000319170,;RAPH1,downstream_gene_variant,,ENST00000418114,;RAPH1,downstream_gene_variant,,ENST00000423104,;RAPH1,downstream_gene_variant,,ENST00000419464,;RAPH1,downstream_gene_variant,,ENST00000439222,;RAPH1,downstream_gene_variant,,ENST00000453034,;	T	ENSG00000173166	ENST00000319170	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RAPH1	HGNC	14436	protein_coding	YES	CCDS2359.1	ENSP00000316543	RAPH1_HUMAN	C9JLG4_HUMAN	UPI000020940F	.	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAGCTTGAC	.	5	ESCA
CCDC108	0	.	GRCh37	2	219894879	219894879	+	Missense_Mutation	SNP	G	G	T	rs766238595	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213C>A	p.Gln405Lys	p.Q405K	ENST00000341552	10/35	31	25	5	28	28	0	CCDC108,missense_variant,p.Gln340Lys,ENST00000410037,;CCDC108,missense_variant,p.Gln405Lys,ENST00000441968,;CCDC108,missense_variant,p.Gln405Lys,ENST00000453220,;CCDC108,missense_variant,p.Gln394Lys,ENST00000409865,;CCDC108,missense_variant,p.Gln405Lys,ENST00000341552,;CCDC108,downstream_gene_variant,,ENST00000436631,;CCDC108,downstream_gene_variant,,ENST00000457968,;CCDC108,downstream_gene_variant,,ENST00000295729,;CCDC108,non_coding_transcript_exon_variant,,ENST00000462848,;CCDC108,non_coding_transcript_exon_variant,,ENST00000463683,;CCDC108,upstream_gene_variant,,ENST00000474601,;	T	ENSG00000181378	ENST00000341552	Transcript	missense_variant	1297	1213	405	Q/K	Cag/Aag	rs766238595	.	.	-1	CCDC108	HGNC	25325	protein_coding	YES	CCDS2430.2	ENSP00000340776	CC108_HUMAN	C9JLP9_HUMAN,C9JIV0_HUMAN	UPI0000609097	.	tolerated(0.18)	benign(0.138)	10/35	.	hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTGGTCTT	byFrequency	5	ESCA
BIRC6	0	.	GRCh37	2	32735596	32735596	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10241T>C	p.Leu3414Ser	p.L3414S	ENST00000421745	53/74	39	36	3	36	36	0	BIRC6,missense_variant,p.Leu3414Ser,ENST00000421745,;BIRC6,non_coding_transcript_exon_variant,,ENST00000496555,;	C	ENSG00000115760	ENST00000421745	Transcript	missense_variant	10375	10241	3414	L/S	tTg/tCg	.	.	.	1	BIRC6	HGNC	13516	protein_coding	YES	CCDS33175.2	ENSP00000393596	BIRC6_HUMAN	.	UPI0001611442	.	.	benign(0.35)	53/74	.	hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATTTGAATA	.	2	ESCA
SOCS5	0	.	GRCh37	2	46989846	46989846	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2566G>A	.	.	ENST00000306503	2/2	90	81	9	57	57	0	SOCS5,3_prime_UTR_variant,,ENST00000306503,;SOCS5,downstream_gene_variant,,ENST00000394861,;	A	ENSG00000171150	ENST00000306503	Transcript	3_prime_UTR_variant	4349	.	.	.	.	.	.	.	1	SOCS5	HGNC	16852	protein_coding	YES	CCDS1830.1	ENSP00000305133	SOCS5_HUMAN	B4DL10_HUMAN	UPI0000135B69	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCATTGTAGCC	.	3	ESCA
TCF7L1	0	.	GRCh37	2	85529698	85529698	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617C>A	p.Ser206Tyr	p.S206Y	ENST00000282111	5/12	64	38	25	29	29	0	TCF7L1,missense_variant,p.Ser206Tyr,ENST00000282111,;TCF7L1,downstream_gene_variant,,ENST00000442813,;AC093162.1,downstream_gene_variant,,ENST00000408652,;TCF7L1,upstream_gene_variant,,ENST00000490744,;	A	ENSG00000152284	ENST00000282111	Transcript	missense_variant	892	617	206	S/Y	tCc/tAc	.	.	.	1	TCF7L1	HGNC	11640	protein_coding	YES	CCDS1971.1	ENSP00000282111	TF7L1_HUMAN	Q53T87_HUMAN,C9JPE3_HUMAN	UPI0000136846	.	deleterious(0)	probably_damaging(0.914)	5/12	.	hmmpanther:PTHR10373,hmmpanther:PTHR10373:SF25,Pfam_domain:PF08347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCTCCCCTC	.	5	ESCA
TMEM127	0	.	GRCh37	2	96919649	96919649	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614A>G	p.Glu205Gly	p.E205G	ENST00000258439	4/4	62	42	19	36	36	0	TMEM127,missense_variant,p.Glu121Gly,ENST00000435268,;TMEM127,missense_variant,p.Glu205Gly,ENST00000258439,;TMEM127,missense_variant,p.Glu205Gly,ENST00000432959,;	C	ENSG00000135956	ENST00000258439	Transcript	missense_variant	871	614	205	E/G	gAg/gGg	.	.	.	-1	TMEM127	HGNC	26038	protein_coding	YES	CCDS2018.1	ENSP00000258439	TM127_HUMAN	C9J4H2_HUMAN	UPI000000D96F	.	deleterious(0.01)	benign(0.16)	4/4	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTGCTCCTCT	.	3	ESCA
ZBTB20	0	.	GRCh37	3	114099155	114099155	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108G>A	p.%3D	p.L36L	ENST00000474710	3/5	60	55	5	49	49	0	ZBTB20,synonymous_variant,p.%3D,ENST00000474710,;ZBTB20,5_prime_UTR_variant,,ENST00000481632,;ZBTB20,5_prime_UTR_variant,,ENST00000462705,;ZBTB20,5_prime_UTR_variant,,ENST00000471418,;ZBTB20,5_prime_UTR_variant,,ENST00000470311,;ZBTB20,5_prime_UTR_variant,,ENST00000357258,;ZBTB20,5_prime_UTR_variant,,ENST00000393785,;ZBTB20,5_prime_UTR_variant,,ENST00000464560,;ZBTB20,downstream_gene_variant,,ENST00000482689,;ZBTB20-AS1,intron_variant,,ENST00000475939,;ZBTB20-AS1,downstream_gene_variant,,ENST00000460210,;ZBTB20,non_coding_transcript_exon_variant,,ENST00000479879,;ZBTB20,downstream_gene_variant,,ENST00000463890,;	T	ENSG00000181722	ENST00000474710	Transcript	synonymous_variant	287	108	36	L	ctG/ctA	.	.	.	-1	ZBTB20	HGNC	13503	protein_coding	YES	CCDS54626.1	ENSP00000419153	ZBT20_HUMAN	C9JCX0_HUMAN	UPI0000141957	.	.	.	3/5	.	hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF351	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGTTCAGGCA	.	3	ESCA
MUC13	0	.	GRCh37	3	124653576	124653576	+	5'UTR	SNP	T	T	C	rs779178488	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-20A>G	.	.	ENST00000311075	1/12	115	105	10	58	58	0	MUC13,5_prime_UTR_variant,,ENST00000478191,;MUC13,5_prime_UTR_variant,,ENST00000311075,;MUC13,intron_variant,,ENST00000497378,;	C	ENSG00000173702	ENST00000311075	Transcript	5_prime_UTR_variant	20	.	.	.	.	rs779178488	.	.	-1	MUC13	HGNC	7511	protein_coding	YES	.	ENSP00000312235	MUC13_HUMAN	.	UPI00001AEF8F	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGGTAATCT	.	2	ESCA
EEFSEC	0	.	GRCh37	3	128060142	128060142	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.853C>T	p.Arg285Trp	p.R285W	ENST00000254730	5/7	73	62	10	53	53	0	EEFSEC,missense_variant,p.Arg230Trp,ENST00000483457,;EEFSEC,missense_variant,p.Arg285Trp,ENST00000254730,;EEFSEC,non_coding_transcript_exon_variant,,ENST00000483569,;EEFSEC,non_coding_transcript_exon_variant,,ENST00000484438,;	T	ENSG00000132394	ENST00000254730	Transcript	missense_variant	907	853	285	R/W	Cgg/Tgg	.	.	.	1	EEFSEC	HGNC	24614	protein_coding	YES	CCDS33849.1	ENSP00000254730	SELB_HUMAN	.	UPI000013CE58	.	deleterious(0)	probably_damaging(1)	5/7	.	hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF106,Pfam_domain:PF03144,Gene3D:2.40.30.10,Superfamily_domains:SSF50447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACCGGCTG	.	5	ESCA
MUC4	0	.	GRCh37	3	195513156	195513156	+	Silent	SNP	G	G	A	rs573701105	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5295C>T	p.%3D	p.D1765D	ENST00000463781	2/25	605	551	54	261	261	0	MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000477086,;MUC4,synonymous_variant,p.%3D,ENST00000466475,;MUC4,synonymous_variant,p.%3D,ENST00000478156,;MUC4,synonymous_variant,p.%3D,ENST00000470451,;MUC4,synonymous_variant,p.%3D,ENST00000479406,;MUC4,synonymous_variant,p.%3D,ENST00000477756,;MUC4,synonymous_variant,p.%3D,ENST00000462323,;MUC4,synonymous_variant,p.%3D,ENST00000480843,;	A	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	5755	5295	1765	D	gaC/gaT	rs573701105	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAAGTGTCGGT	by1000G	3	ESCA
ZNF445	0	.	GRCh37	3	44489304	44489304	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1859C>T	p.Thr620Ile	p.T620I	ENST00000425708	7/7	36	31	5	55	55	0	ZNF445,missense_variant,p.Thr620Ile,ENST00000425708,;ZNF445,missense_variant,p.Thr620Ile,ENST00000396077,;ZNF445,downstream_gene_variant,,ENST00000460529,;	A	ENSG00000185219	ENST00000425708	Transcript	missense_variant	2201	1859	620	T/I	aCc/aTc	.	.	.	-1	ZNF445	HGNC	21018	protein_coding	YES	CCDS2713.1	ENSP00000413073	ZN445_HUMAN	B7ZKX2_HUMAN	UPI000019AD12	.	deleterious(0)	benign(0.001)	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24385:SF48,hmmpanther:PTHR24385,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGGGTGTGA	.	4	ESCA
LARS2	0	.	GRCh37	3	45557698	45557698	+	Silent	SNP	G	G	A	rs189078355	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1974G>A	p.%3D	p.G658G	ENST00000415258	16/21	37	18	18	61	61	0	LARS2,synonymous_variant,p.%3D,ENST00000414984,;LARS2,synonymous_variant,p.%3D,ENST00000265537,;LARS2,synonymous_variant,p.%3D,ENST00000415258,;LARS2,non_coding_transcript_exon_variant,,ENST00000467936,;LARS2,upstream_gene_variant,,ENST00000485461,;	A	ENSG00000011376	ENST00000415258	Transcript	synonymous_variant	2115	1974	658	G	ggG/ggA	rs189078355	.	.	1	LARS2	HGNC	17095	protein_coding	YES	CCDS2728.1	ENSP00000408576	SYLM_HUMAN	Q9BQR0_HUMAN,C9JYR8_HUMAN	UPI0000001297	.	.	.	16/21	.	hmmpanther:PTHR11946:SF7,hmmpanther:PTHR11946,TIGRFAM_domain:TIGR00396,Gene3D:3.40.50.620,Pfam_domain:PF00133,Superfamily_domains:SSF52374	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGGATCGA	byCluster|by1000G	5	ESCA
GNL3	0	.	GRCh37	3	52724786	52724786	+	Intron	DEL	A	A	-	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.654+69delA	.	.	ENST00000418458	.	46	27	19	47	47	0	GNL3,intron_variant,,ENST00000394799,;GNL3,intron_variant,,ENST00000418458,;GNL3,downstream_gene_variant,,ENST00000474423,;GNL3,downstream_gene_variant,,ENST00000479230,;GLT8D1,downstream_gene_variant,,ENST00000491606,;PBRM1,upstream_gene_variant,,ENST00000450271,;PBRM1,upstream_gene_variant,,ENST00000431678,;PBRM1,upstream_gene_variant,,ENST00000420148,;GLT8D1,downstream_gene_variant,,ENST00000394783,;GLT8D1,downstream_gene_variant,,ENST00000407584,;GLT8D1,downstream_gene_variant,,ENST00000478968,;PBRM1,upstream_gene_variant,,ENST00000394830,;PBRM1,upstream_gene_variant,,ENST00000424867,;PBRM1,upstream_gene_variant,,ENST00000458294,;GLT8D1,downstream_gene_variant,,ENST00000266014,;SNORD19B,non_coding_transcript_exon_variant,,ENST00000459623,;SNORD19B,downstream_gene_variant,,ENST00000516978,;SNORD69,upstream_gene_variant,,ENST00000391150,;SNORD19,downstream_gene_variant,,ENST00000391191,;SNORD19,upstream_gene_variant,,ENST00000410413,;GLT8D1,downstream_gene_variant,,ENST00000463827,;GNL3,downstream_gene_variant,,ENST00000460073,;GNL3,downstream_gene_variant,,ENST00000468146,;GNL3,non_coding_transcript_exon_variant,,ENST00000496254,;GNL3,intron_variant,,ENST00000484022,;GLT8D1,downstream_gene_variant,,ENST00000481643,;GLT8D1,downstream_gene_variant,,ENST00000484163,;GLT8D1,downstream_gene_variant,,ENST00000480080,;GNL3,downstream_gene_variant,,ENST00000492349,;GNL3,downstream_gene_variant,,ENST00000462550,;GNL3,downstream_gene_variant,,ENST00000468885,;GNL3,upstream_gene_variant,,ENST00000497356,;	-	ENSG00000163938	ENST00000418458	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GNL3	HGNC	29931	protein_coding	YES	CCDS2861.1	ENSP00000395772	GNL3_HUMAN	C9JZT7_HUMAN,C9JYH9_HUMAN	UPI000003C48A	.	.	.	.	7/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGTACAAAATC	.	3	ESCA
ADH6	0	.	GRCh37	4	100128630	100128630	+	Missense_Mutation	SNP	G	G	A	rs778701583	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937C>T	p.Arg313Cys	p.R313C	ENST00000394899	7/9	63	49	13	53	53	0	ADH6,missense_variant,p.Arg313Cys,ENST00000237653,;ADH6,missense_variant,p.Arg104Cys,ENST00000407820,;ADH6,missense_variant,p.Arg313Cys,ENST00000394899,;ADH6,missense_variant,p.Arg249Cys,ENST00000508558,;ADH6,intron_variant,,ENST00000394897,;RP11-696N14.1,intron_variant,,ENST00000500358,;RP11-696N14.1,intron_variant,,ENST00000506160,;RP11-696N14.1,intron_variant,,ENST00000506454,;ADH6,downstream_gene_variant,,ENST00000504257,;ADH6,3_prime_UTR_variant,,ENST00000507484,;ADH6,intron_variant,,ENST00000512708,;	A	ENSG00000172955	ENST00000394899	Transcript	missense_variant	1031	937	313	R/C	Cgt/Tgt	rs778701583,COSM2155313,COSM2155312	.	.	-1	ADH6	HGNC	255	protein_coding	YES	CCDS43255.1	ENSP00000378359	ADH6_HUMAN	Q9H1A0_HUMAN,B7ZAL1_HUMAN,B4DPD8_HUMAN	UPI000013CA1E	.	deleterious(0.01)	probably_damaging(0.999)	7/9	.	hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF307,Pfam_domain:PF00107,Gene3D:3.40.50.720,SMART_domains:SM00829,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAACGTCCTG	.	5	ESCA
TBCK	0	.	GRCh37	4	107037369	107037369	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2402A>G	p.Asn801Ser	p.N801S	ENST00000273980	25/27	99	65	34	122	122	0	TBCK,missense_variant,p.Asn738Ser,ENST00000361687,;TBCK,missense_variant,p.Asn801Ser,ENST00000273980,;TBCK,missense_variant,p.Asn801Ser,ENST00000394708,;TBCK,missense_variant,p.Asn801Ser,ENST00000432496,;TBCK,missense_variant,p.Asn762Ser,ENST00000394706,;TBCK,non_coding_transcript_exon_variant,,ENST00000514689,;TBCK,downstream_gene_variant,,ENST00000515705,;TBCK,3_prime_UTR_variant,,ENST00000467183,;TBCK,non_coding_transcript_exon_variant,,ENST00000510927,;	C	ENSG00000145348	ENST00000273980	Transcript	missense_variant	2850	2402	801	N/S	aAt/aGt	.	.	.	-1	TBCK	HGNC	28261	protein_coding	YES	CCDS54788.1	ENSP00000273980	TBCK_HUMAN	D6RDY5_HUMAN,D6RDG2_HUMAN,D6RC61_HUMAN,D6R950_HUMAN	UPI000013EF70	.	tolerated(0.77)	benign(0.004)	25/27	.	PROSITE_profiles:PS50206,hmmpanther:PTHR22957:SF22,hmmpanther:PTHR22957,Gene3D:3.40.250.10,Pfam_domain:PF00581,SMART_domains:SM00450,Superfamily_domains:SSF52821	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTATTCCGG	.	5	ESCA
RP11-384K6.6	0	.	GRCh37	4	119554298	119554298	+	RNA	SNP	A	A	G	rs35102067	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3809A>G	.	.	ENST00000567913	10/10	18	8	10	9	9	0	RP11-384K6.6,non_coding_transcript_exon_variant,,ENST00000567913,;RP11-384K6.2,non_coding_transcript_exon_variant,,ENST00000426314,;CICP16,downstream_gene_variant,,ENST00000502609,;CICP16,downstream_gene_variant,,ENST00000401754,;	G	ENSG00000260404	ENST00000567913	Transcript	non_coding_transcript_exon_variant	3809	.	.	.	.	rs35102067	.	.	1	RP11-384K6.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	10/10	.	.	G:0.1823	G:0.025	G:0.2061	.	G:0.1815	G:0.326	G:0.2311	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CTTTCAGCCCA	byFrequency|byCluster|by1000G	3	ESCA
CLGN	0	.	GRCh37	4	141321590	141321590	+	Silent	SNP	G	G	A	rs749787516	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615C>T	p.%3D	p.F205F	ENST00000325617	7/15	40	26	13	40	40	0	CLGN,synonymous_variant,p.%3D,ENST00000414773,;CLGN,synonymous_variant,p.%3D,ENST00000325617,;CLGN,synonymous_variant,p.%3D,ENST00000537281,;CLGN,downstream_gene_variant,,ENST00000509477,;	A	ENSG00000153132	ENST00000325617	Transcript	synonymous_variant	1056	615	205	F	ttC/ttT	rs749787516,COSM3428193	.	.	-1	CLGN	HGNC	2060	protein_coding	YES	CCDS3751.1	ENSP00000326699	CLGN_HUMAN	D6RAZ4_HUMAN,B4DRG2_HUMAN	UPI0000126E4A	.	.	.	7/15	.	Superfamily_domains:SSF49899,Gene3D:2.60.120.200,Pfam_domain:PF00262,hmmpanther:PTHR11073,hmmpanther:PTHR11073:SF7	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCGAAAAC	.	5	ESCA
HTT	0	.	GRCh37	4	3133112	3133112	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2086G>A	p.Gly696Arg	p.G696R	ENST00000355072	15/67	59	50	8	93	93	0	HTT,missense_variant,p.Gly696Arg,ENST00000355072,;HTT,non_coding_transcript_exon_variant,,ENST00000510626,;	A	ENSG00000197386	ENST00000355072	Transcript	missense_variant	2231	2086	696	G/R	Ggg/Agg	.	.	.	1	HTT	HGNC	4851	protein_coding	YES	CCDS43206.1	ENSP00000347184	HD_HUMAN	D3DVR8_HUMAN,D2CTD8_HUMAN,D2CTD7_HUMAN,D2CTD4_HUMAN,D2CTD2_HUMAN	UPI000013D567	.	.	possibly_damaging(0.883)	15/67	.	hmmpanther:PTHR10170:SF10,hmmpanther:PTHR10170,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAACAGGGGGA	.	5	ESCA
ATP10D	0	.	GRCh37	4	47594268	47594268	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*870A>T	.	.	ENST00000273859	23/23	49	23	26	34	34	0	ATP10D,3_prime_UTR_variant,,ENST00000273859,;CORIN,downstream_gene_variant,,ENST00000502252,;CORIN,downstream_gene_variant,,ENST00000505909,;CORIN,downstream_gene_variant,,ENST00000273857,;CORIN,downstream_gene_variant,,ENST00000508498,;ATP10D,downstream_gene_variant,,ENST00000505277,;ATP10D,downstream_gene_variant,,ENST00000505476,;ATP10D,3_prime_UTR_variant,,ENST00000503288,;	T	ENSG00000145246	ENST00000273859	Transcript	3_prime_UTR_variant	5420	.	.	.	.	.	.	.	1	ATP10D	HGNC	13549	protein_coding	YES	CCDS3476.1	ENSP00000273859	AT10D_HUMAN	.	UPI00001AE9B7	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCAAAGTGA	.	5	ESCA
FEM1C	0	.	GRCh37	5	114860452	114860452	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1407A>G	p.Ile469Met	p.I469M	ENST00000274457	3/3	44	15	28	58	58	0	FEM1C,missense_variant,p.Ile469Met,ENST00000274457,;	C	ENSG00000145780	ENST00000274457	Transcript	missense_variant	1969	1407	469	I/M	atA/atG	.	.	.	-1	FEM1C	HGNC	16933	protein_coding	YES	CCDS4118.1	ENSP00000274457	FEM1C_HUMAN	.	UPI0000046A79	.	deleterious(0.03)	possibly_damaging(0.885)	3/3	.	hmmpanther:PTHR24173:SF14,hmmpanther:PTHR24173,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTATATAGT	.	5	ESCA
TCOF1	0	.	GRCh37	5	149772327	149772327	+	Missense_Mutation	SNP	G	G	A	rs751297952	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3574G>A	p.Glu1192Lys	p.E1192K	ENST00000504761	22/26	33	26	7	72	72	0	TCOF1,missense_variant,p.Glu1154Lys,ENST00000427724,;TCOF1,missense_variant,p.Glu1192Lys,ENST00000513346,;TCOF1,missense_variant,p.Glu1155Lys,ENST00000439160,;TCOF1,missense_variant,p.Glu1193Lys,ENST00000377797,;TCOF1,missense_variant,p.Glu1229Lys,ENST00000451292,;TCOF1,missense_variant,p.Glu1116Lys,ENST00000445265,;TCOF1,missense_variant,p.Glu1115Lys,ENST00000323668,;TCOF1,missense_variant,p.Glu1192Lys,ENST00000504761,;TCOF1,intron_variant,,ENST00000515516,;TCOF1,non_coding_transcript_exon_variant,,ENST00000506630,;TCOF1,non_coding_transcript_exon_variant,,ENST00000514442,;TCOF1,downstream_gene_variant,,ENST00000506767,;	A	ENSG00000070814	ENST00000504761	Transcript	missense_variant	3574	3574	1192	E/K	Gag/Aag	rs751297952,COSM737223,COSM737222	.	.	1	TCOF1	HGNC	11654	protein_coding	YES	CCDS54936.1	ENSP00000421655	TCOF_HUMAN	Q9UFD4_HUMAN	UPI0000EE3736	.	deleterious(0)	probably_damaging(0.911)	22/26	.	hmmpanther:PTHR20787	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCGAGGAT	byFrequency	5	ESCA
TARS	0	.	GRCh37	5	33458676	33458676	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089A>T	p.Gln363His	p.Q363H	ENST00000455217	11/20	41	34	7	31	31	0	TARS,missense_variant,p.Gln330His,ENST00000502553,;TARS,missense_variant,p.Gln330His,ENST00000265112,;TARS,missense_variant,p.Gln226His,ENST00000541634,;TARS,missense_variant,p.Gln363His,ENST00000455217,;TARS,missense_variant,p.Gln209His,ENST00000414361,;TARS,upstream_gene_variant,,ENST00000509410,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,3_prime_UTR_variant,,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,non_coding_transcript_exon_variant,,ENST00000504698,;TARS,downstream_gene_variant,,ENST00000505012,;	T	ENSG00000113407	ENST00000455217	Transcript	missense_variant	1211	1089	363	Q/H	caA/caT	.	.	.	1	TARS	HGNC	11572	protein_coding	YES	CCDS58943.1	ENSP00000387710	SYTC_HUMAN	D6RBR8_HUMAN	UPI00017A6D60	.	deleterious(0)	benign(0.249)	11/20	.	Superfamily_domains:SSF55681,Gene3D:3.30.930.10,TIGRFAM_domain:TIGR00418,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF23,HAMAP:MF_00184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GACCAAGAACT	.	3	ESCA
PDE4D	0	.	GRCh37	5	58571194	58571194	+	Intron	SNP	G	G	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.456-59400C>A	.	.	ENST00000340635	.	18	14	4	35	35	0	PDE4D,missense_variant,p.Thr12Lys,ENST00000503258,;PDE4D,intron_variant,,ENST00000505453,;PDE4D,intron_variant,,ENST00000546160,;PDE4D,intron_variant,,ENST00000360047,;PDE4D,intron_variant,,ENST00000340635,;PDE4D,intron_variant,,ENST00000405755,;PDE4D,intron_variant,,ENST00000507116,;PDE4D,intron_variant,,ENST00000502575,;PDE4D,intron_variant,,ENST00000502484,;PDE4D,intron_variant,,ENST00000405053,;PDE4D,intron_variant,,ENST00000309641,;PDE4D,intron_variant,,ENST00000514231,;	T	ENSG00000113448	ENST00000340635	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PDE4D	HGNC	8783	protein_coding	YES	CCDS47213.1	ENSP00000345502	PDE4D_HUMAN	D6RHE0_HUMAN	UPI0000050EB1	.	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	AACTTGTAGAT	.	3	ESCA
ZDHHC11	0	.	GRCh37	5	801230	801230	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1231G>C	p.Glu411Gln	p.E411Q	ENST00000283441	12/13	146	140	5	103	103	0	ZDHHC11,missense_variant,p.Glu411Gln,ENST00000283441,;ZDHHC11,missense_variant,p.Glu411Gln,ENST00000424784,;ZDHHC11,non_coding_transcript_exon_variant,,ENST00000503758,;ZDHHC11,3_prime_UTR_variant,,ENST00000507800,;	G	ENSG00000188818	ENST00000283441	Transcript	missense_variant	1615	1231	411	E/Q	Gaa/Caa	.	.	.	-1	ZDHHC11	HGNC	19158	protein_coding	YES	CCDS3857.1	ENSP00000283441	ZDH11_HUMAN	.	UPI000013C384	.	tolerated_low_confidence(0.56)	benign(0.403)	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCTTCACTTT	.	2	ESCA
ATG5	0	.	GRCh37	6	106649888	106649888	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650A>T	p.Asp217Val	p.D217V	ENST00000369076	7/8	46	30	16	52	52	0	ATG5,missense_variant,p.Asp217Val,ENST00000343245,;ATG5,missense_variant,p.Asp139Val,ENST00000369070,;ATG5,missense_variant,p.Asp217Val,ENST00000369076,;ATG5,3_prime_UTR_variant,,ENST00000360666,;ATG5,non_coding_transcript_exon_variant,,ENST00000475645,;ATG5,non_coding_transcript_exon_variant,,ENST00000476518,;	A	ENSG00000057663	ENST00000369076	Transcript	missense_variant	974	650	217	D/V	gAt/gTt	.	.	.	-1	ATG5	HGNC	589	protein_coding	YES	CCDS5055.1	ENSP00000358072	ATG5_HUMAN	A9UGY9_HUMAN	UPI0000125C62	.	deleterious(0)	probably_damaging(0.991)	7/8	.	hmmpanther:PTHR13040:SF2,hmmpanther:PTHR13040,Pfam_domain:PF04106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGATCTCCT	.	5	ESCA
HIST1H3B	0	.	GRCh37	6	26032136	26032136	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153G>C	p.Glu51Asp	p.E51D	ENST00000244661	1/1	80	67	12	68	68	0	HIST1H3B,missense_variant,p.Glu51Asp,ENST00000244661,;HIST1H2AB,downstream_gene_variant,,ENST00000259791,;HIST1H4B,upstream_gene_variant,,ENST00000377364,;	G	ENSG00000124693	ENST00000244661	Transcript	missense_variant	153	153	51	E/D	gaG/gaC	COSM1487522	.	.	-1	HIST1H3B	HGNC	4776	protein_coding	YES	CCDS4573.1	ENSP00000244661	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0.03)	possibly_damaging(0.858)	1/1	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGATCTCGCG	.	5	ESCA
PLA2G7	0	.	GRCh37	6	46684165	46684165	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.332T>C	p.Leu111Pro	p.L111P	ENST00000274793	4/12	59	48	11	45	45	0	PLA2G7,missense_variant,p.Leu66Pro,ENST00000538237,;PLA2G7,missense_variant,p.Leu111Pro,ENST00000537365,;PLA2G7,missense_variant,p.Leu111Pro,ENST00000274793,;PLA2G7,intron_variant,,ENST00000541026,;	G	ENSG00000146070	ENST00000274793	Transcript	missense_variant	529	332	111	L/P	cTt/cCt	.	.	.	-1	PLA2G7	HGNC	9040	protein_coding	YES	CCDS4917.1	ENSP00000274793	PAFA_HUMAN	.	UPI000002FED1	.	deleterious(0)	probably_damaging(0.99)	4/12	.	hmmpanther:PTHR10272,hmmpanther:PTHR10272:SF9,Pfam_domain:PF03403,PIRSF_domain:PIRSF018169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCAAGAAAT	.	5	ESCA
FUT9	0	.	GRCh37	6	96661992	96661992	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9881C>A	.	.	ENST00000302103	3/3	20	10	10	26	26	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	A	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	11287	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCCCAAAA	.	5	ESCA
POM121	0	.	GRCh37	7	72417074	72417074	+	Intron	SNP	C	C	T	rs191099053	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2857+827C>T	.	.	ENST00000395270	.	39	34	4	25	25	0	POM121,3_prime_UTR_variant,,ENST00000257622,;POM121,3_prime_UTR_variant,,ENST00000358357,;POM121,intron_variant,,ENST00000446813,;POM121,intron_variant,,ENST00000395270,;POM121,downstream_gene_variant,,ENST00000434423,;NSUN5P2,downstream_gene_variant,,ENST00000388955,;NSUN5P2,downstream_gene_variant,,ENST00000602348,;NSUN5P2,downstream_gene_variant,,ENST00000444583,;NSUN5P2,downstream_gene_variant,,ENST00000485741,;NSUN5P2,downstream_gene_variant,,ENST00000457352,;	T	ENSG00000196313	ENST00000395270	Transcript	intron_variant	.	.	.	.	.	rs191099053	.	.	1	POM121	HGNC	19702	protein_coding	YES	CCDS59059.1	ENSP00000378687	P121A_HUMAN	A8MY32_HUMAN	UPI000013DA6B	.	.	.	.	15/15	.	T:0.0006	T:0.0015	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTCCCGCTTA	byFrequency|by1000G	2	ESCA
DBF4	0	.	GRCh37	7	87536898	87536898	+	Missense_Mutation	SNP	A	A	G	rs373255355	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1445A>G	p.Tyr482Cys	p.Y482C	ENST00000265728	12/12	112	91	20	58	58	0	DBF4,missense_variant,p.Tyr482Cys,ENST00000265728,;DBF4,3_prime_UTR_variant,,ENST00000431138,;DBF4,3_prime_UTR_variant,,ENST00000413643,;DBF4,downstream_gene_variant,,ENST00000430279,;DBF4,downstream_gene_variant,,ENST00000498144,;	G	ENSG00000006634	ENST00000265728	Transcript	missense_variant	1949	1445	482	Y/C	tAt/tGt	rs373255355	.	.	1	DBF4	HGNC	17364	protein_coding	YES	CCDS5611.1	ENSP00000265728	DBF4A_HUMAN	B7Z8C6_HUMAN,B3KMY2_HUMAN	UPI000000DC33	.	tolerated(0.31)	benign(0)	12/12	.	hmmpanther:PTHR15375,hmmpanther:PTHR15375:SF21	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTATAAAT	.	5	ESCA
COL14A1	0	.	GRCh37	8	121384017	121384017	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*547A>G	.	.	ENST00000297848	48/48	66	35	31	58	58	0	COL14A1,3_prime_UTR_variant,,ENST00000247781,;COL14A1,3_prime_UTR_variant,,ENST00000297848,;COL14A1,downstream_gene_variant,,ENST00000309791,;COL14A1,downstream_gene_variant,,ENST00000440844,;	G	ENSG00000187955	ENST00000297848	Transcript	3_prime_UTR_variant	6208	.	.	.	.	.	.	.	1	COL14A1	HGNC	2191	protein_coding	YES	CCDS34938.1	ENSP00000297848	COEA1_HUMAN	.	UPI000046D377	.	.	.	48/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAAATCAGC	.	5	ESCA
RAPGEF1	0	.	GRCh37	9	134525617	134525617	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217A>G	p.Arg73Gly	p.R73G	ENST00000372190	3/24	49	35	14	43	43	0	RAPGEF1,missense_variant,p.Arg73Gly,ENST00000372190,;RAPGEF1,missense_variant,p.Arg73Gly,ENST00000427994,;RAPGEF1,missense_variant,p.Arg72Gly,ENST00000372195,;RAPGEF1,missense_variant,p.Arg55Gly,ENST00000372189,;RAPGEF1,intron_variant,,ENST00000438647,;	C	ENSG00000107263	ENST00000372190	Transcript	missense_variant	376	217	73	R/G	Aga/Gga	.	.	.	-1	RAPGEF1	HGNC	4568	protein_coding	YES	CCDS48048.1	ENSP00000361264	RPGF1_HUMAN	Q5JUE5_HUMAN	UPI0000074689	.	tolerated_low_confidence(0.07)	benign(0.185)	3/24	.	hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATCTGTCTG	.	5	ESCA
KIAA0020	0	.	GRCh37	9	2829813	2829813	+	Silent	SNP	C	C	A	rs200827106	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813G>T	p.%3D	p.L271L	ENST00000397885	8/18	64	57	6	53	53	0	KIAA0020,synonymous_variant,p.%3D,ENST00000397885,;KIAA0020,non_coding_transcript_exon_variant,,ENST00000469168,;	A	ENSG00000080608	ENST00000397885	Transcript	synonymous_variant	1020	813	271	L	ctG/ctT	rs200827106	.	.	-1	KIAA0020	HGNC	29676	protein_coding	YES	CCDS6448.2	ENSP00000380982	K0020_HUMAN	S4R3K8_HUMAN	UPI000013D67E	.	.	.	8/18	.	Superfamily_domains:SSF48371,SMART_domains:SM00025,Gene3D:1.25.10.10,hmmpanther:PTHR13389,PROSITE_profiles:PS50303	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCGTCAGCAT	by1000G	4	ESCA
KIAA0020	0	.	GRCh37	9	2829936	2829936	+	Silent	SNP	C	C	T	.	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.690G>A	p.%3D	p.Q230Q	ENST00000397885	8/18	60	57	3	53	53	0	KIAA0020,synonymous_variant,p.%3D,ENST00000397885,;KIAA0020,upstream_gene_variant,,ENST00000469168,;	T	ENSG00000080608	ENST00000397885	Transcript	synonymous_variant	897	690	230	Q	caG/caA	COSM282122	.	.	-1	KIAA0020	HGNC	29676	protein_coding	YES	CCDS6448.2	ENSP00000380982	K0020_HUMAN	S4R3K8_HUMAN	UPI000013D67E	.	.	.	8/18	.	Superfamily_domains:SSF48371,SMART_domains:SM00025,Gene3D:1.25.10.10,hmmpanther:PTHR13389,PROSITE_profiles:PS50302,PROSITE_profiles:PS50303	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAATCTGTGG	.	2	ESCA
KIAA0020	0	.	GRCh37	9	2834111	2834111	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.360G>A	p.%3D	p.L120L	ENST00000397885	4/18	62	50	11	61	61	0	KIAA0020,synonymous_variant,p.%3D,ENST00000397885,;KIAA0020,upstream_gene_variant,,ENST00000469168,;	T	ENSG00000080608	ENST00000397885	Transcript	synonymous_variant	567	360	120	L	ctG/ctA	.	.	.	-1	KIAA0020	HGNC	29676	protein_coding	YES	CCDS6448.2	ENSP00000380982	K0020_HUMAN	S4R3K8_HUMAN	UPI000013D67E	.	.	.	4/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTCAGTTC	.	5	ESCA
KIAA0020	0	.	GRCh37	9	2837324	2837324	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.160G>A	p.Glu54Lys	p.E54K	ENST00000397885	3/18	69	52	16	70	70	0	KIAA0020,missense_variant,p.Glu54Lys,ENST00000397885,;	T	ENSG00000080608	ENST00000397885	Transcript	missense_variant	367	160	54	E/K	Gag/Aag	.	.	.	-1	KIAA0020	HGNC	29676	protein_coding	YES	CCDS6448.2	ENSP00000380982	K0020_HUMAN	S4R3K8_HUMAN	UPI000013D67E	.	tolerated(0.5)	benign(0.016)	3/18	.	hmmpanther:PTHR13389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCAAAGT	.	5	ESCA
PTPRD	0	.	GRCh37	9	8521445	8521445	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.793C>A	p.Pro265Thr	p.P265T	ENST00000381196	17/43	39	8	31	28	28	0	PTPRD,missense_variant,p.Pro255Thr,ENST00000397617,;PTPRD,missense_variant,p.Pro265Thr,ENST00000486161,;PTPRD,missense_variant,p.Pro252Thr,ENST00000358503,;PTPRD,missense_variant,p.Pro252Thr,ENST00000360074,;PTPRD,missense_variant,p.Pro265Thr,ENST00000381196,;PTPRD,missense_variant,p.Pro255Thr,ENST00000397606,;PTPRD,missense_variant,p.Pro265Thr,ENST00000356435,;PTPRD,missense_variant,p.Pro265Thr,ENST00000355233,;PTPRD,missense_variant,p.Pro262Thr,ENST00000397611,;PTPRD,missense_variant,p.Pro265Thr,ENST00000540109,;PTPRD,missense_variant,p.Pro262Thr,ENST00000537002,;PTPRD,downstream_gene_variant,,ENST00000488774,;	T	ENSG00000153707	ENST00000381196	Transcript	missense_variant	1337	793	265	P/T	Cct/Act	.	.	.	-1	PTPRD	HGNC	9668	protein_coding	YES	CCDS43786.1	ENSP00000370593	PTPRD_HUMAN	C9J6E4_HUMAN,B4DK48_HUMAN	UPI0000132990	.	deleterious(0)	probably_damaging(0.999)	17/43	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Pfam_domain:PF07679,Gene3D:2.60.40.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAGGCATTG	.	5	ESCA
KIAA1210	0	.	GRCh37	X	118219376	118219376	+	Silent	SNP	G	G	T	rs371643117	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4818C>A	p.%3D	p.A1606A	ENST00000402510	12/14	130	82	48	135	135	0	KIAA1210,synonymous_variant,p.%3D,ENST00000402510,;	T	ENSG00000250423	ENST00000402510	Transcript	synonymous_variant	4818	4818	1606	A	gcC/gcA	rs371643117	.	.	-1	KIAA1210	HGNC	29218	protein_coding	YES	CCDS48156.1	ENSP00000384670	K1210_HUMAN	.	UPI0001596C4C	.	.	.	12/14	.	.	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATCGGCTCC	byFrequency|byCluster	5	ESCA
GLUD2	0	.	GRCh37	X	120181834	120181834	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296G>A	p.Arg99Gln	p.R99Q	ENST00000328078	1/1	63	50	13	52	52	0	GLUD2,missense_variant,p.Arg99Gln,ENST00000328078,;	A	ENSG00000182890	ENST00000328078	Transcript	missense_variant	373	296	99	R/Q	cGg/cAg	.	.	.	1	GLUD2	HGNC	4336	protein_coding	YES	CCDS14603.1	ENSP00000327589	DHE4_HUMAN	Q9BSD0_HUMAN	UPI0000129301	.	tolerated(0.22)	benign(0.006)	1/1	.	hmmpanther:PTHR11606:SF10,hmmpanther:PTHR11606,Gene3D:3mw9A01,Superfamily_domains:SSF53223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGCGGAACC	.	5	ESCA
CXorf64	0	.	GRCh37	X	125955211	125955211	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590C>A	p.Pro197His	p.P197H	ENST00000371125	2/2	42	27	15	54	54	0	CXorf64,missense_variant,p.Pro197His,ENST00000371125,;	A	ENSG00000183631	ENST00000371125	Transcript	missense_variant	670	590	197	P/H	cCc/cAc	.	.	.	1	CXorf64	HGNC	34498	protein_coding	YES	CCDS48163.1	ENSP00000360166	CX064_HUMAN	.	UPI00004A3B00	.	deleterious(0.01)	possibly_damaging(0.746)	2/2	.	Pfam_domain:PF15488	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G198R|c.592G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCCCGGAA	.	5	ESCA
IRAK1	0	.	GRCh37	X	153276107	153276107	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1203G>A	.	.	ENST00000369980	14/14	32	26	6	28	28	0	IRAK1,3_prime_UTR_variant,,ENST00000369980,;IRAK1,3_prime_UTR_variant,,ENST00000369974,;IRAK1,3_prime_UTR_variant,,ENST00000444230,;IRAK1,3_prime_UTR_variant,,ENST00000393682,;IRAK1,downstream_gene_variant,,ENST00000443220,;IRAK1,downstream_gene_variant,,ENST00000429936,;IRAK1,downstream_gene_variant,,ENST00000393687,;IRAK1,downstream_gene_variant,,ENST00000455690,;IRAK1,downstream_gene_variant,,ENST00000444254,;IRAK1,downstream_gene_variant,,ENST00000437278,;IRAK1,downstream_gene_variant,,ENST00000477274,;IRAK1,downstream_gene_variant,,ENST00000467236,;IRAK1,downstream_gene_variant,,ENST00000369973,;	T	ENSG00000184216	ENST00000369980	Transcript	3_prime_UTR_variant	3510	.	.	.	.	.	.	.	-1	IRAK1	HGNC	6112	protein_coding	YES	CCDS14740.1	ENSP00000358997	IRAK1_HUMAN	.	UPI000012D873	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGGACACTCG	.	2	ESCA
CLCN5	0	.	GRCh37	X	49859648	49859648	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2772G>A	.	.	ENST00000376088	15/15	50	45	5	52	52	0	CLCN5,3_prime_UTR_variant,,ENST00000376088,;CLCN5,downstream_gene_variant,,ENST00000307367,;CLCN5,downstream_gene_variant,,ENST00000376091,;CLCN5,downstream_gene_variant,,ENST00000376108,;	A	ENSG00000171365	ENST00000376088	Transcript	3_prime_UTR_variant	5864	.	.	.	.	.	.	.	1	CLCN5	HGNC	2023	protein_coding	YES	CCDS48115.1	ENSP00000365256	CLCN5_HUMAN	.	UPI0000212052	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAGGACTGT	.	2	ESCA
PJA1	0	.	GRCh37	X	68382750	68382750	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A4OM-01A-11D-A27G-09	TCGA-L5-A4OM-11A-11D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.332G>T	p.Arg111Ile	p.R111I	ENST00000361478	2/2	55	35	20	53	53	0	PJA1,missense_variant,p.Arg56Ile,ENST00000374571,;PJA1,missense_variant,p.Arg111Ile,ENST00000361478,;PJA1,missense_variant,p.Arg111Ile,ENST00000590146,;PJA1,missense_variant,p.Arg111Ile,ENST00000374583,;PJA1,intron_variant,,ENST00000374584,;PJA1,upstream_gene_variant,,ENST00000471141,;PJA1,non_coding_transcript_exon_variant,,ENST00000477231,;	A	ENSG00000181191	ENST00000361478	Transcript	missense_variant	710	332	111	R/I	aGa/aTa	COSM3845230	.	.	-1	PJA1	HGNC	16648	protein_coding	YES	CCDS14393.1	ENSP00000355014	PJA1_HUMAN	K7EPI8_HUMAN,B4DDN5_HUMAN	UPI000006D00A	.	deleterious(0)	possibly_damaging(0.885)	2/2	.	hmmpanther:PTHR15710:SF2,hmmpanther:PTHR15710	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCTTCTG	.	5	ESCA
PSD	0	.	GRCh37	10	104173823	104173823	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1256C>G	p.Ser419Cys	p.S419C	ENST00000020673	5/17	134	106	28	127	127	0	PSD,missense_variant,p.Ser419Cys,ENST00000020673,;PSD,missense_variant,p.Ser419Cys,ENST00000406432,;PSD,upstream_gene_variant,,ENST00000488194,;PSD,downstream_gene_variant,,ENST00000492902,;PSD,downstream_gene_variant,,ENST00000472685,;PSD,upstream_gene_variant,,ENST00000461698,;	C	ENSG00000059915	ENST00000020673	Transcript	missense_variant	1783	1256	419	S/C	tCc/tGc	.	.	.	-1	PSD	HGNC	9507	protein_coding	YES	CCDS31272.1	ENSP00000020673	PSD1_HUMAN	.	UPI0000404928	.	tolerated(0.08)	probably_damaging(0.997)	5/17	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAGGAGGTG	.	5	ESCA
SFXN2	0	.	GRCh37	10	104489519	104489519	+	Missense_Mutation	SNP	G	G	A	rs376492604	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547G>A	p.Ala183Thr	p.A183T	ENST00000369893	6/12	55	42	12	52	52	0	SFXN2,missense_variant,p.Ala183Thr,ENST00000369893,;SFXN2,downstream_gene_variant,,ENST00000602764,;SFXN2,downstream_gene_variant,,ENST00000602831,;SFXN2,downstream_gene_variant,,ENST00000602439,;SFXN2,downstream_gene_variant,,ENST00000602868,;SFXN2,downstream_gene_variant,,ENST00000602647,;SFXN2,downstream_gene_variant,,ENST00000602785,;SFXN2,synonymous_variant,p.%3D,ENST00000459894,;SFXN2,intron_variant,,ENST00000480358,;SFXN2,downstream_gene_variant,,ENST00000602670,;SFXN2,downstream_gene_variant,,ENST00000602287,;SFXN2,downstream_gene_variant,,ENST00000602660,;SFXN2,downstream_gene_variant,,ENST00000602544,;	A	ENSG00000156398	ENST00000369893	Transcript	missense_variant	714	547	183	A/T	Gct/Act	rs376492604	.	.	1	SFXN2	HGNC	16086	protein_coding	YES	CCDS7539.1	ENSP00000358909	SFXN2_HUMAN	R4GN74_HUMAN,R4GMW0_HUMAN	UPI0000001241	.	deleterious(0)	probably_damaging(0.939)	6/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11153,hmmpanther:PTHR11153:SF14,TIGRFAM_domain:TIGR00798,Pfam_domain:PF03820	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCGCTGTG	byFrequency|byCluster	5	ESCA
EIF5AL1	0	.	GRCh37	10	81275734	81275734	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2864C>A	.	.	ENST00000520547	1/1	52	41	10	57	57	0	EIF5AL1,3_prime_UTR_variant,,ENST00000520547,;	A	ENSG00000253626	ENST00000520547	Transcript	3_prime_UTR_variant	3378	.	.	.	.	.	.	.	1	EIF5AL1	HGNC	17419	protein_coding	YES	CCDS53546.1	ENSP00000430706	IF5AL_HUMAN	.	UPI00001972AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCGCATGCG	.	5	ESCA
KIF11	0	.	GRCh37	10	94373310	94373310	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.966T>A	p.Asp322Glu	p.D322E	ENST00000260731	8/22	102	85	17	105	105	0	KIF11,missense_variant,p.Asp322Glu,ENST00000260731,;	A	ENSG00000138160	ENST00000260731	Transcript	missense_variant	1056	966	322	D/E	gaT/gaA	.	.	.	1	KIF11	HGNC	6388	protein_coding	YES	CCDS7422.1	ENSP00000260731	KIF11_HUMAN	.	UPI000013D0FC	.	deleterious(0)	possibly_damaging(0.766)	8/22	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF105,hmmpanther:PTHR24115,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGATTCTCT	.	5	ESCA
ANKRD2	0	.	GRCh37	10	99338349	99338349	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524A>G	p.Asp175Gly	p.D175G	ENST00000307518	4/9	58	55	3	51	51	0	ANKRD2,missense_variant,p.Asp175Gly,ENST00000307518,;ANKRD2,missense_variant,p.Asp148Gly,ENST00000370655,;ANKRD2,missense_variant,p.Asp175Gly,ENST00000298808,;ANKRD2,missense_variant,p.Asp148Gly,ENST00000455090,;	G	ENSG00000165887	ENST00000307518	Transcript	missense_variant	791	524	175	D/G	gAc/gGc	.	.	.	1	ANKRD2	HGNC	495	protein_coding	YES	CCDS7466.1	ENSP00000306163	ANKR2_HUMAN	.	UPI0000231C90	.	deleterious(0.01)	probably_damaging(1)	4/9	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24126,hmmpanther:PTHR24126:SF3,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCGACACGT	.	2	ESCA
DCDC1	0	.	GRCh37	11	30902766	30902766	+	Silent	SNP	G	G	A	rs532651593	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5163C>T	p.%3D	p.D1721D	ENST00000597505	35/36	46	30	16	78	78	0	DCDC1,synonymous_variant,p.%3D,ENST00000597505,;DCDC1,downstream_gene_variant,,ENST00000406071,;DCDC1,synonymous_variant,p.%3D,ENST00000444572,;DCDC1,3_prime_UTR_variant,,ENST00000303697,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,;	A	ENSG00000170959	ENST00000597505	Transcript	synonymous_variant	5163	5163	1721	D	gaC/gaT	rs532651593	.	.	-1	DCDC1	HGNC	20625	protein_coding	.	.	ENSP00000472625	.	M0R2J8_HUMAN	UPI0002A47319	.	.	.	35/36	.	Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCGTCCCA	by1000G	5	ESCA
HBE1	0	.	GRCh37	11	5290891	5290891	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108C>A	p.Tyr36Ter	p.Y36*	ENST00000380237	4/5	40	29	10	55	55	0	HBE1,stop_gained,p.Tyr36Ter,ENST00000396895,;HBE1,stop_gained,p.Tyr36Ter,ENST00000380237,;HBE1,stop_gained,p.Tyr36Ter,ENST00000292896,;HBG2,intron_variant,,ENST00000380252,;HBG2,intron_variant,,ENST00000380259,;	T	ENSG00000213931	ENST00000380237	Transcript	stop_gained	453	108	36	Y/*	taC/taA	.	.	.	-1	HBE1	HGNC	4830	protein_coding	YES	CCDS7756.1	ENSP00000369586	HBE_HUMAN	D9YZU7_HUMAN,A8MUF7_HUMAN	UPI00000004B9	.	.	.	4/5	.	Prints_domain:PR00814,Superfamily_domains:SSF46458,Gene3D:1.10.490.10,Pfam_domain:PF00042,hmmpanther:PTHR11442,hmmpanther:PTHR11442:SF7,PROSITE_profiles:PS01033	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGGTAAAC	.	5	ESCA
GIF	0	.	GRCh37	11	59604768	59604768	+	Silent	SNP	C	C	T	rs377432418	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.750G>A	p.%3D	p.T250T	ENST00000257248	6/9	93	77	16	80	80	0	GIF,synonymous_variant,p.%3D,ENST00000257248,;GIF,synonymous_variant,p.%3D,ENST00000541311,;GIF,3_prime_UTR_variant,,ENST00000525058,;GIF,non_coding_transcript_exon_variant,,ENST00000533847,;GIF,upstream_gene_variant,,ENST00000533067,;	T	ENSG00000134812	ENST00000257248	Transcript	synonymous_variant	798	750	250	T	acG/acA	rs377432418,COSM3450327	.	.	-1	GIF	HGNC	4268	protein_coding	YES	CCDS7977.1	ENSP00000257248	IF_HUMAN	.	UPI0000001C67	.	.	.	6/9	.	hmmpanther:PTHR10559,hmmpanther:PTHR10559:SF15,Pfam_domain:PF01122	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATCCGTAGT	byCluster|by1000G	4	ESCA
MS4A10	0	.	GRCh37	11	60565933	60565933	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668C>T	p.Pro223Leu	p.P223L	ENST00000308287	7/8	62	48	13	66	66	0	MS4A10,missense_variant,p.Pro223Leu,ENST00000308287,;	T	ENSG00000172689	ENST00000308287	Transcript	missense_variant	764	668	223	P/L	cCg/cTg	COSM358551	.	.	1	MS4A10	HGNC	13368	protein_coding	YES	CCDS7992.1	ENSP00000311862	M4A10_HUMAN	.	UPI000023754A	.	tolerated(0.08)	benign(0.38)	7/8	.	hmmpanther:PTHR23320:SF5,hmmpanther:PTHR23320	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCCGCCAT	.	5	ESCA
DDB1	0	.	GRCh37	11	61067602	61067602	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6G>T	.	.	ENST00000301764	27/27	71	58	13	76	76	0	DDB1,3_prime_UTR_variant,,ENST00000451943,;DDB1,3_prime_UTR_variant,,ENST00000301764,;DDB1,3_prime_UTR_variant,,ENST00000450997,;DDB1,3_prime_UTR_variant,,ENST00000538470,;VWCE,upstream_gene_variant,,ENST00000335613,;DDB1,downstream_gene_variant,,ENST00000539332,;DDB1,3_prime_UTR_variant,,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000545894,;	A	ENSG00000167986	ENST00000301764	Transcript	3_prime_UTR_variant	3827	.	.	.	.	.	.	.	-1	DDB1	HGNC	2717	protein_coding	YES	CCDS31576.1	ENSP00000301764	DDB1_HUMAN	F8WF81_HUMAN,F5H775_HUMAN,F5H6C5_HUMAN,F5H581_HUMAN,F5H2L3_HUMAN,F5H0Y5_HUMAN,F5GZY8_HUMAN,F5GZ34_HUMAN,F5GYG8_HUMAN	UPI0000000CB7	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCCCTTGG	.	5	ESCA
OR2AG2	0	.	GRCh37	11	6790090	6790090	+	Silent	SNP	G	G	T	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99C>A	p.%3D	p.I33I	ENST00000338569	1/1	58	34	23	78	78	0	OR2AG2,synonymous_variant,p.%3D,ENST00000338569,;	T	ENSG00000188124	ENST00000338569	Transcript	synonymous_variant	197	99	33	I	atC/atA	COSM3452406	.	.	-1	OR2AG2	HGNC	15143	protein_coding	YES	CCDS31413.1	ENSP00000342697	O2AG2_HUMAN	.	UPI0000041C10	.	.	.	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF107,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAGGATTGT	.	5	ESCA
SUV420H1	0	.	GRCh37	11	67926519	67926519	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1294A>G	p.Ile432Val	p.I432V	ENST00000304363	11/11	46	42	4	23	23	0	SUV420H1,missense_variant,p.Ile432Val,ENST00000304363,;SUV420H1,3_prime_UTR_variant,,ENST00000427752,;SUV420H1,3_prime_UTR_variant,,ENST00000441488,;	C	ENSG00000110066	ENST00000304363	Transcript	missense_variant	1648	1294	432	I/V	Ata/Gta	.	.	.	-1	SUV420H1	HGNC	24283	protein_coding	YES	CCDS31623.1	ENSP00000305899	SV421_HUMAN	E9PKD9_HUMAN,C9JP58_HUMAN,C9JFG1_HUMAN,C9J6S5_HUMAN	UPI00001FADE7	.	tolerated(1)	benign(0.001)	11/11	.	hmmpanther:PTHR12977,hmmpanther:PTHR12977:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTTATATGAG	.	4	ESCA
LRP5	0	.	GRCh37	11	68157387	68157387	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1451T>C	p.Ile484Thr	p.I484T	ENST00000294304	7/23	60	45	15	54	54	0	LRP5,missense_variant,p.Ile484Thr,ENST00000294304,;LRP5,intron_variant,,ENST00000529993,;	C	ENSG00000162337	ENST00000294304	Transcript	missense_variant	1557	1451	484	I/T	aTc/aCc	.	.	.	1	LRP5	HGNC	6697	protein_coding	YES	CCDS8181.1	ENSP00000294304	LRP5_HUMAN	E9PHY1_HUMAN	UPI0000073246	.	deleterious(0)	probably_damaging(0.995)	7/23	.	Superfamily_domains:SSF63825,PIRSF_domain:PIRSF036314,SMART_domains:SM00135,Pfam_domain:PF00058,Gene3D:2.120.10.30,hmmpanther:PTHR10529:SF202,hmmpanther:PTHR10529,PROSITE_profiles:PS51120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAATCGAGT	.	5	ESCA
FAT3	0	.	GRCh37	11	92531258	92531258	+	Missense_Mutation	SNP	C	C	G	rs771454774	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5079C>G	p.Ile1693Met	p.I1693M	ENST00000298047	9/27	28	23	5	36	36	0	FAT3,missense_variant,p.Ile1693Met,ENST00000298047,;FAT3,missense_variant,p.Ile1693Met,ENST00000409404,;FAT3,missense_variant,p.Ile1543Met,ENST00000525166,;	G	ENSG00000165323	ENST00000298047	Transcript	missense_variant	5096	5079	1693	I/M	atC/atG	rs771454774	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	possibly_damaging(0.595)	9/27	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTAATCTCTGC	.	4	ESCA
JRKL	0	.	GRCh37	11	96126565	96126565	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1177T>A	.	.	ENST00000458427	1/1	125	103	22	131	131	0	JRKL,3_prime_UTR_variant,,ENST00000458427,;CCDC82,upstream_gene_variant,,ENST00000542662,;CCDC82,upstream_gene_variant,,ENST00000538597,;JRKL,downstream_gene_variant,,ENST00000332349,;JRKL,intron_variant,,ENST00000546177,;CCDC82,upstream_gene_variant,,ENST00000524836,;CCDC82,upstream_gene_variant,,ENST00000525786,;	A	ENSG00000183340	ENST00000458427	Transcript	3_prime_UTR_variant	3408	.	.	.	.	.	.	.	1	JRKL	HGNC	6200	protein_coding	YES	CCDS8308.1	ENSP00000389989	JERKL_HUMAN	.	UPI0000167818	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGATAAATT	.	5	ESCA
NUAK1	0	.	GRCh37	12	106460744	106460744	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1822C>T	p.Leu608Phe	p.L608F	ENST00000261402	7/7	80	64	16	77	77	0	NUAK1,missense_variant,p.Leu608Phe,ENST00000261402,;NUAK1,downstream_gene_variant,,ENST00000548902,;NUAK1,downstream_gene_variant,,ENST00000553094,;NUAK1,downstream_gene_variant,,ENST00000549704,;	A	ENSG00000074590	ENST00000261402	Transcript	missense_variant	3202	1822	608	L/F	Ctc/Ttc	.	.	.	-1	NUAK1	HGNC	14311	protein_coding	YES	CCDS31892.1	ENSP00000261402	NUAK1_HUMAN	F8VZ96_HUMAN,F8VXF0_HUMAN,F8VSH4_HUMAN	UPI00000403BC	.	deleterious(0)	probably_damaging(0.999)	7/7	.	hmmpanther:PTHR24343:SF79,hmmpanther:PTHR24343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAGGAAGT	.	5	ESCA
DDX54	0	.	GRCh37	12	113617119	113617119	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393G>C	p.Leu131Phe	p.L131F	ENST00000314045	4/20	32	28	3	40	40	0	DDX54,missense_variant,p.Leu131Phe,ENST00000306014,;DDX54,missense_variant,p.Leu48Phe,ENST00000552375,;DDX54,missense_variant,p.Leu131Phe,ENST00000314045,;Y_RNA,upstream_gene_variant,,ENST00000364338,;DDX54,3_prime_UTR_variant,,ENST00000551344,;DDX54,upstream_gene_variant,,ENST00000546869,;	G	ENSG00000123064	ENST00000314045	Transcript	missense_variant	421	393	131	L/F	ttG/ttC	.	.	.	-1	DDX54	HGNC	20084	protein_coding	YES	CCDS44984.1	ENSP00000323858	DDX54_HUMAN	F8VRX4_HUMAN	UPI000006F3A5	.	deleterious(0)	probably_damaging(0.984)	4/20	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031:SF71,hmmpanther:PTHR24031,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATCCAAGAT	.	4	ESCA
ULK1	0	.	GRCh37	12	132405711	132405711	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3028G>T	p.Ala1010Ser	p.A1010S	ENST00000321867	27/28	19	15	4	17	17	0	ULK1,missense_variant,p.Ala255Ser,ENST00000540647,;ULK1,missense_variant,p.Ala1010Ser,ENST00000321867,;ULK1,downstream_gene_variant,,ENST00000541761,;RP11-417L19.4,downstream_gene_variant,,ENST00000539078,;ULK1,non_coding_transcript_exon_variant,,ENST00000544718,;ULK1,non_coding_transcript_exon_variant,,ENST00000540568,;	T	ENSG00000177169	ENST00000321867	Transcript	missense_variant	3379	3028	1010	A/S	Gcc/Tcc	COSM401399	.	.	1	ULK1	HGNC	12558	protein_coding	YES	CCDS9274.1	ENSP00000324560	ULK1_HUMAN	F5H4E9_HUMAN,F5H1S7_HUMAN,F5GZQ0_HUMAN	UPI00001FB0D9	.	deleterious(0.01)	probably_damaging(0.999)	27/28	.	hmmpanther:PTHR24348:SF19,hmmpanther:PTHR24348,Pfam_domain:PF12063,PIRSF_domain:PIRSF000580	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAGGCCCTG	.	5	ESCA
ULK1	0	.	GRCh37	12	132405712	132405712	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3029C>T	p.Ala1010Val	p.A1010V	ENST00000321867	27/28	20	15	4	16	16	0	ULK1,missense_variant,p.Ala255Val,ENST00000540647,;ULK1,missense_variant,p.Ala1010Val,ENST00000321867,;ULK1,downstream_gene_variant,,ENST00000541761,;RP11-417L19.4,downstream_gene_variant,,ENST00000539078,;ULK1,non_coding_transcript_exon_variant,,ENST00000544718,;ULK1,non_coding_transcript_exon_variant,,ENST00000540568,;	T	ENSG00000177169	ENST00000321867	Transcript	missense_variant	3380	3029	1010	A/V	gCc/gTc	.	.	.	1	ULK1	HGNC	12558	protein_coding	YES	CCDS9274.1	ENSP00000324560	ULK1_HUMAN	F5H4E9_HUMAN,F5H1S7_HUMAN,F5GZQ0_HUMAN	UPI00001FB0D9	.	deleterious(0)	probably_damaging(0.999)	27/28	.	hmmpanther:PTHR24348:SF19,hmmpanther:PTHR24348,Pfam_domain:PF12063,PIRSF_domain:PIRSF000580	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGGCCCTGC	.	5	ESCA
PRMT8	0	.	GRCh37	12	3702913	3702913	+	3'UTR	SNP	C	C	T	rs151272255	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*565C>T	.	.	ENST00000382622	10/10	59	53	5	52	52	0	PRMT8,3_prime_UTR_variant,,ENST00000382622,;PRMT8,downstream_gene_variant,,ENST00000452611,;PRMT8,non_coding_transcript_exon_variant,,ENST00000261252,;PRMT8,non_coding_transcript_exon_variant,,ENST00000543701,;	T	ENSG00000111218	ENST00000382622	Transcript	3_prime_UTR_variant	2140	.	.	.	.	rs151272255	.	.	1	PRMT8	HGNC	5188	protein_coding	YES	CCDS8521.2	ENSP00000372067	ANM8_HUMAN	.	UPI00005B2E00	.	.	.	10/10	.	.	T:0.0022	T:0.0008	T:0.0058	.	T:0	T:0.006	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCGTGCGCGTG	byFrequency|byCluster|by1000G	3	ESCA
FGF23	0	.	GRCh37	12	4479523	4479523	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.742G>A	p.Ala248Thr	p.A248T	ENST00000237837	3/3	58	50	8	62	62	0	FGF23,missense_variant,p.Ala248Thr,ENST00000237837,;	T	ENSG00000118972	ENST00000237837	Transcript	missense_variant	888	742	248	A/T	Gcc/Acc	.	.	.	-1	FGF23	HGNC	3680	protein_coding	YES	CCDS8526.1	ENSP00000237837	FGF23_HUMAN	.	UPI000003ED58	.	deleterious_low_confidence(0.01)	benign(0.002)	3/3	.	hmmpanther:PTHR11486:SF69,hmmpanther:PTHR11486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTGGCGAAGG	.	4	ESCA
ACVR1B	0	.	GRCh37	12	52385743	52385743	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1481G>A	p.Arg494His	p.R494H	ENST00000541224	9/10	76	57	19	85	84	0	ACVR1B,missense_variant,p.Arg453His,ENST00000426655,;ACVR1B,missense_variant,p.Arg494His,ENST00000541224,;ACVR1B,missense_variant,p.Arg453His,ENST00000257963,;ACVR1B,missense_variant,p.Arg401His,ENST00000542485,;ACVR1B,downstream_gene_variant,,ENST00000415850,;RNU6-574P,downstream_gene_variant,,ENST00000384265,;ACVR1B,non_coding_transcript_exon_variant,,ENST00000563121,;	A	ENSG00000135503	ENST00000541224	Transcript	missense_variant	1524	1481	494	R/H	cGt/cAt	COSM4042768	.	.	1	ACVR1B	HGNC	172	protein_coding	YES	CCDS44894.2	ENSP00000442656	ACV1B_HUMAN	F5H5Q2_HUMAN	UPI0001915052	.	deleterious(0)	possibly_damaging(0.891)	9/10	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR23255:SF22,hmmpanther:PTHR23255,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCGTCCCA	.	5	ESCA
ZNF384	0	.	GRCh37	12	6778331	6778331	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1198G>C	p.Asp400His	p.D400H	ENST00000396801	10/11	92	79	12	87	86	1	ZNF384,missense_variant,p.Asp284His,ENST00000355772,;ZNF384,missense_variant,p.Asp339His,ENST00000396795,;ZNF384,missense_variant,p.Asp400His,ENST00000361959,;ZNF384,missense_variant,p.Asp400His,ENST00000396801,;ZNF384,missense_variant,p.Asp323His,ENST00000319770,;ZNF384,missense_variant,p.Asp339His,ENST00000396799,;ZNF384,downstream_gene_variant,,ENST00000417772,;ZNF384,downstream_gene_variant,,ENST00000436774,;ZNF384,upstream_gene_variant,,ENST00000545946,;RP4-761J14.8,intron_variant,,ENST00000586338,;RP4-761J14.8,downstream_gene_variant,,ENST00000589924,;ZNF384,downstream_gene_variant,,ENST00000542519,;ZNF384,downstream_gene_variant,,ENST00000537383,;	G	ENSG00000126746	ENST00000396801	Transcript	missense_variant	1406	1198	400	D/H	Gat/Cat	.	.	.	-1	ZNF384	HGNC	11955	protein_coding	YES	CCDS44817.1	ENSP00000380019	ZN384_HUMAN	F5H3Z9_HUMAN,F5H105_HUMAN,F5H0D6_HUMAN,F5GYZ1_HUMAN,D3DUR9_HUMAN,B4DQU6_HUMAN,A9X425_HUMAN	UPI00001AE6F8	.	deleterious(0)	probably_damaging(0.998)	10/11	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,Gene3D:3.30.160.60,hmmpanther:PTHR11389:SF332,hmmpanther:PTHR11389,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TTTATCTTTGT	.	3	ESCA
C1R	0	.	GRCh37	12	7242061	7242061	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.593C>T	p.Thr198Met	p.T198M	ENST00000542285	5/11	33	30	3	37	37	0	C1R,missense_variant,p.Thr213Met,ENST00000536053,;C1R,missense_variant,p.Thr198Met,ENST00000542285,;C1R,missense_variant,p.Thr199Met,ENST00000542220,;C1R,missense_variant,p.Thr165Met,ENST00000535233,;C1R,incomplete_terminal_codon_variant,p.%3D,ENST00000540610,;C1R,downstream_gene_variant,,ENST00000540242,;C1RL,downstream_gene_variant,,ENST00000545280,;C1R,downstream_gene_variant,,ENST00000538050,;C1R,downstream_gene_variant,,ENST00000543835,;C1R,downstream_gene_variant,,ENST00000541042,;C1R,upstream_gene_variant,,ENST00000602298,;C1R,3_prime_UTR_variant,,ENST00000543362,;C1R,non_coding_transcript_exon_variant,,ENST00000540394,;C1R,downstream_gene_variant,,ENST00000536092,;C1R,downstream_gene_variant,,ENST00000545466,;C1R,downstream_gene_variant,,ENST00000543851,;C1RL,downstream_gene_variant,,ENST00000539803,;	A	ENSG00000159403	ENST00000542285	Transcript	missense_variant	743	593	198	T/M	aCg/aTg	.	.	.	-1	C1R	HGNC	1246	protein_coding	YES	.	ENSP00000438615	.	H0YFH3_HUMAN,F5H3A3_HUMAN,F5H1N6_HUMAN,F5GWL0_HUMAN	UPI00020653A8	.	deleterious(0.01)	probably_damaging(1)	5/11	.	PROSITE_profiles:PS01180,hmmpanther:PTHR24265:SF78,hmmpanther:PTHR24265,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,PIRSF_domain:PIRSF001155,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCCGTGTAC	.	2	ESCA
LRRIQ1	0	.	GRCh37	12	85546923	85546923	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4541G>T	p.Arg1514Ile	p.R1514I	ENST00000393217	21/27	71	54	17	93	93	0	LRRIQ1,missense_variant,p.Arg1514Ile,ENST00000393217,;	T	ENSG00000133640	ENST00000393217	Transcript	missense_variant	4602	4541	1514	R/I	aGa/aTa	.	.	.	1	LRRIQ1	HGNC	25708	protein_coding	YES	CCDS41816.1	ENSP00000376910	LRIQ1_HUMAN	A8MY60_HUMAN	UPI0000ED4E82	.	deleterious(0)	probably_damaging(0.921)	21/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCAGGTAAG	.	5	ESCA
TMTC4	0	.	GRCh37	13	101256470	101256470	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*778G>A	.	.	ENST00000342624	19/19	90	55	34	117	117	0	TMTC4,3_prime_UTR_variant,,ENST00000376234,;TMTC4,3_prime_UTR_variant,,ENST00000342624,;TMTC4,downstream_gene_variant,,ENST00000328767,;	T	ENSG00000125247	ENST00000342624	Transcript	3_prime_UTR_variant	3320	.	.	.	.	.	.	.	-1	TMTC4	HGNC	25904	protein_coding	YES	CCDS9497.2	ENSP00000343871	TMTC4_HUMAN	C9K0R2_HUMAN	UPI000004B63E	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCTTCAC	.	5	ESCA
TBC1D4	0	.	GRCh37	13	76055775	76055775	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129delG	p.Ser44ArgfsTer39	p.S44Rfs*39	ENST00000377636	1/21	46	30	16	36	36	0	TBC1D4,frameshift_variant,p.Ser44ArgfsTer39,ENST00000377625,;TBC1D4,frameshift_variant,p.Ser44ArgfsTer39,ENST00000431480,;TBC1D4,frameshift_variant,p.Ser44ArgfsTer39,ENST00000377636,;TBC1D4,5_prime_UTR_variant,,ENST00000425511,;	-	ENSG00000136111	ENST00000377636	Transcript	frameshift_variant	476	129	43	G/X	ggG/gg	.	.	.	-1	TBC1D4	HGNC	19165	protein_coding	YES	CCDS41901.1	ENSP00000366863	TBCD4_HUMAN	.	UPI00001AE7B3	.	.	.	1/21	.	Gene3D:2.30.29.30,SMART_domains:SM00462,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCACGACCCCCC	.	3	ESCA
RTL1	0	.	GRCh37	14	101349583	101349583	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1543G>A	p.Glu515Lys	p.E515K	ENST00000534062	1/1	75	61	13	58	58	0	RTL1,missense_variant,p.Glu515Lys,ENST00000534062,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,downstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,;MIR127,downstream_gene_variant,,ENST00000384876,;MIR431,downstream_gene_variant,,ENST00000385266,;	T	ENSG00000254656	ENST00000534062	Transcript	missense_variant	1602	1543	515	E/K	Gaa/Aaa	COSM3814243	.	.	-1	RTL1	HGNC	14665	protein_coding	YES	CCDS53910.1	ENSP00000435342	RTL1_HUMAN	.	UPI00001D7B9E	.	tolerated(0.07)	benign(0.05)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCGGGGG	.	5	ESCA
MIR409	0	.	GRCh37	14	101531679	101531679	+	RNA	SNP	C	C	T	rs773414152	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.43C>T	.	.	ENST00000362237	1/1	50	38	12	83	83	0	MIR409,non_coding_transcript_exon_variant,,ENST00000362237,;MIR541,downstream_gene_variant,,ENST00000401360,;MIR656,upstream_gene_variant,,ENST00000385224,;MEG9,upstream_gene_variant,,ENST00000429368,;MIR412,upstream_gene_variant,,ENST00000362142,;MIR369,upstream_gene_variant,,ENST00000362155,;MIR410,upstream_gene_variant,,ENST00000362222,;MIR496,downstream_gene_variant,,ENST00000385226,;MIR377,downstream_gene_variant,,ENST00000362145,;	T	ENSG00000199107	ENST00000362237	Transcript	non_coding_transcript_exon_variant	43	.	.	.	.	rs773414152	.	.	1	MIR409	HGNC	32055	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGACGACGA	byFrequency	5	ESCA
TEP1	0	.	GRCh37	14	20844365	20844365	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6147A>G	p.%3D	p.E2049E	ENST00000262715	42/55	37	30	7	33	33	0	TEP1,synonymous_variant,p.%3D,ENST00000545983,;TEP1,synonymous_variant,p.%3D,ENST00000556935,;TEP1,synonymous_variant,p.%3D,ENST00000262715,;TEP1,upstream_gene_variant,,ENST00000553984,;TEP1,synonymous_variant,p.%3D,ENST00000555008,;TEP1,3_prime_UTR_variant,,ENST00000555727,;TEP1,3_prime_UTR_variant,,ENST00000471684,;TEP1,3_prime_UTR_variant,,ENST00000557314,;TEP1,3_prime_UTR_variant,,ENST00000556488,;TEP1,upstream_gene_variant,,ENST00000553365,;	C	ENSG00000129566	ENST00000262715	Transcript	synonymous_variant	6188	6147	2049	E	gaA/gaG	.	.	.	-1	TEP1	HGNC	11726	protein_coding	YES	CCDS9548.1	ENSP00000262715	TEP1_HUMAN	G3V591_HUMAN	UPI000013D30B	.	.	.	42/55	.	Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF402,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCTTCTGC	.	5	ESCA
THSD4	0	.	GRCh37	15	72063512	72063512	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2879A>G	p.Glu960Gly	p.E960G	ENST00000355327	17/18	109	82	26	103	103	0	THSD4,missense_variant,p.Glu960Gly,ENST00000355327,;THSD4,missense_variant,p.Glu600Gly,ENST00000357769,;THSD4,missense_variant,p.Glu960Gly,ENST00000261862,;THSD4,downstream_gene_variant,,ENST00000567838,;	G	ENSG00000187720	ENST00000355327	Transcript	missense_variant	3013	2879	960	E/G	gAa/gGa	.	.	.	1	THSD4	HGNC	25835	protein_coding	YES	CCDS10238.2	ENSP00000347484	THSD4_HUMAN	.	UPI00001A797D	.	deleterious(0)	probably_damaging(0.968)	17/18	.	PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF16,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGAATCTT	.	5	ESCA
CACNA1H	0	.	GRCh37	16	1270643	1270643	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6711C>A	p.%3D	p.G2237G	ENST00000348261	35/35	31	22	8	24	24	0	CACNA1H,synonymous_variant,p.%3D,ENST00000562079,;CACNA1H,synonymous_variant,p.%3D,ENST00000348261,;CACNA1H,synonymous_variant,p.%3D,ENST00000564231,;CACNA1H,synonymous_variant,p.%3D,ENST00000565831,;CACNA1H,synonymous_variant,p.%3D,ENST00000358590,;CACNA1H,synonymous_variant,p.%3D,ENST00000564927,;CACNA1H,synonymous_variant,p.%3D,ENST00000569107,;TPSG1,downstream_gene_variant,,ENST00000234798,;TPSG1,downstream_gene_variant,,ENST00000564684,;	A	ENSG00000196557	ENST00000348261	Transcript	synonymous_variant	6959	6711	2237	G	ggC/ggA	.	.	.	1	CACNA1H	HGNC	1395	protein_coding	YES	CCDS45375.1	ENSP00000334198	CAC1H_HUMAN	Q9NYY7_HUMAN,Q9NYY6_HUMAN	UPI000012727B	.	.	.	35/35	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGGCTCAGG	.	5	ESCA
NSMCE1	0	.	GRCh37	16	27237089	27237089	+	Missense_Mutation	SNP	G	G	A	rs753831018	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679C>T	p.Arg227Cys	p.R227C	ENST00000361439	7/8	97	75	22	72	72	0	NSMCE1,missense_variant,p.Arg227Cys,ENST00000361439,;NSMCE1,intron_variant,,ENST00000562039,;KDM8,downstream_gene_variant,,ENST00000441782,;KDM8,downstream_gene_variant,,ENST00000380948,;KDM8,downstream_gene_variant,,ENST00000568965,;NSMCE1,downstream_gene_variant,,ENST00000563273,;KDM8,downstream_gene_variant,,ENST00000286096,;KDM8,downstream_gene_variant,,ENST00000567735,;NSMCE1,non_coding_transcript_exon_variant,,ENST00000565384,;KDM8,downstream_gene_variant,,ENST00000567785,;NSMCE1,3_prime_UTR_variant,,ENST00000569236,;NSMCE1,non_coding_transcript_exon_variant,,ENST00000565070,;NSMCE1,downstream_gene_variant,,ENST00000566087,;KDM8,downstream_gene_variant,,ENST00000569592,;	A	ENSG00000169189	ENST00000361439	Transcript	missense_variant	779	679	227	R/C	Cgc/Tgc	rs753831018,COSM3690879	.	.	-1	NSMCE1	HGNC	29897	protein_coding	YES	CCDS10628.2	ENSP00000355077	NSE1_HUMAN	H3BSL0_HUMAN,H3BR73_HUMAN,H3BN81_HUMAN	UPI0000035D91	.	deleterious(0.05)	possibly_damaging(0.868)	7/8	.	PROSITE_profiles:PS50089,PROSITE_profiles:PS50081,hmmpanther:PTHR20973:SF0,hmmpanther:PTHR20973,Pfam_domain:PF08746,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGCGGTT	byFrequency	5	ESCA
HCFC1R1	0	.	GRCh37	16	3073311	3073311	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204C>T	p.%3D	p.F68F	ENST00000248089	3/4	35	25	9	29	29	0	HCFC1R1,synonymous_variant,p.%3D,ENST00000574980,;HCFC1R1,synonymous_variant,p.%3D,ENST00000354679,;HCFC1R1,synonymous_variant,p.%3D,ENST00000396916,;HCFC1R1,synonymous_variant,p.%3D,ENST00000573842,;HCFC1R1,synonymous_variant,p.%3D,ENST00000574151,;HCFC1R1,synonymous_variant,p.%3D,ENST00000248089,;HCFC1R1,synonymous_variant,p.%3D,ENST00000572355,;THOC6,upstream_gene_variant,,ENST00000575576,;THOC6,upstream_gene_variant,,ENST00000574549,;TNFRSF12A,downstream_gene_variant,,ENST00000575124,;CCDC64B,downstream_gene_variant,,ENST00000573514,;CLDN6,upstream_gene_variant,,ENST00000396925,;TNFRSF12A,downstream_gene_variant,,ENST00000341627,;TNFRSF12A,downstream_gene_variant,,ENST00000326577,;TNFRSF12A,downstream_gene_variant,,ENST00000573001,;CCDC64B,downstream_gene_variant,,ENST00000572449,;THOC6,upstream_gene_variant,,ENST00000326266,;TNFRSF12A,downstream_gene_variant,,ENST00000575836,;THOC6,upstream_gene_variant,,ENST00000253952,;CCDC64B,downstream_gene_variant,,ENST00000389347,;HCFC1R1,non_coding_transcript_exon_variant,,ENST00000573095,;HCFC1R1,non_coding_transcript_exon_variant,,ENST00000575214,;HCFC1R1,non_coding_transcript_exon_variant,,ENST00000576921,;TNFRSF12A,downstream_gene_variant,,ENST00000571351,;THOC6,upstream_gene_variant,,ENST00000571046,;TNFRSF12A,downstream_gene_variant,,ENST00000574699,;THOC6,upstream_gene_variant,,ENST00000576143,;THOC6,upstream_gene_variant,,ENST00000573704,;THOC6,upstream_gene_variant,,ENST00000574498,;CCDC64B,downstream_gene_variant,,ENST00000572240,;THOC6,upstream_gene_variant,,ENST00000571057,;THOC6,upstream_gene_variant,,ENST00000574957,;	A	ENSG00000103145	ENST00000248089	Transcript	synonymous_variant	509	204	68	F	ttC/ttT	.	.	.	-1	HCFC1R1	HGNC	21198	protein_coding	YES	CCDS10490.1	ENSP00000248089	HPIP_HUMAN	I3L1N5_HUMAN,I3L174_HUMAN	UPI000000D826	.	.	.	3/4	.	hmmpanther:PTHR16246,hmmpanther:PTHR16246:SF2,Pfam_domain:PF15226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGAGAAGTG	.	5	ESCA
LINC00922	0	.	GRCh37	16	65319330	65319330	+	RNA	SNP	G	G	A	rs375252980	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.832C>T	.	.	ENST00000569736	9/9	29	20	9	36	36	0	LINC00922,non_coding_transcript_exon_variant,,ENST00000564041,;LINC00922,non_coding_transcript_exon_variant,,ENST00000569736,;LINC00922,non_coding_transcript_exon_variant,,ENST00000568492,;RP11-256I9.3,intron_variant,,ENST00000562656,;	A	ENSG00000261742	ENST00000569736	Transcript	non_coding_transcript_exon_variant	832	.	.	.	.	rs375252980	.	.	-1	LINC00922	HGNC	27545	lincRNA	YES	.	.	.	.	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTGGCGGTCTT	byFrequency|byCluster	4	ESCA
BEAN1	0	.	GRCh37	16	66514909	66514909	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*81C>G	.	.	ENST00000536005	5/5	12	9	3	11	11	0	BEAN1,3_prime_UTR_variant,,ENST00000536005,;BEAN1,3_prime_UTR_variant,,ENST00000299694,;BEAN1,intron_variant,,ENST00000564819,;BEAN1,intron_variant,,ENST00000561796,;BEAN1,intron_variant,,ENST00000562146,;AC132186.1,downstream_gene_variant,,ENST00000544589,;CTD-2258A20.5,intron_variant,,ENST00000569125,;CTD-2258A20.5,upstream_gene_variant,,ENST00000567528,;BEAN1,intron_variant,,ENST00000563075,;BEAN1,upstream_gene_variant,,ENST00000566654,;BEAN1,3_prime_UTR_variant,,ENST00000562849,;RP11-403P17.5,intron_variant,,ENST00000561527,;RP11-403P17.5,intron_variant,,ENST00000561728,;	G	ENSG00000166546	ENST00000536005	Transcript	3_prime_UTR_variant	1078	.	.	.	.	.	.	.	1	BEAN1	HGNC	24160	protein_coding	YES	CCDS54015.1	ENSP00000442793	BEAN1_HUMAN	.	UPI000164284B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACACACAGAGA	.	2	ESCA
AP1G1	0	.	GRCh37	16	71765676	71765676	+	3'Flank	SNP	G	G	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000393512	.	79	58	21	72	72	0	AP1G1,3_prime_UTR_variant,,ENST00000423132,;AP1G1,3_prime_UTR_variant,,ENST00000299980,;AP1G1,downstream_gene_variant,,ENST00000569748,;AP1G1,downstream_gene_variant,,ENST00000564155,;AP1G1,downstream_gene_variant,,ENST00000393512,;AP1G1,downstream_gene_variant,,ENST00000433195,;RP11-432I5.4,downstream_gene_variant,,ENST00000563557,;AP1G1,downstream_gene_variant,,ENST00000570052,;	C	ENSG00000166747	ENST00000393512	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	612	-1	AP1G1	HGNC	555	protein_coding	YES	CCDS45522.1	ENSP00000377148	AP1G1_HUMAN	H3BV30_HUMAN,H3BS13_HUMAN,H3BRM7_HUMAN,H3BR36_HUMAN,H3BPN9_HUMAN,H3BN75_HUMAN,H3BN71_HUMAN,B3KNW1_HUMAN	UPI000016A4AD	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTGAGGAA	.	5	ESCA
PKD1L3	0	.	GRCh37	16	71976822	71976822	+	RNA	SNP	A	A	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3961T>A	.	.	ENST00000534738	24/30	122	79	42	121	121	0	PKD1L3,non_coding_transcript_exon_variant,,ENST00000534738,;PKD1L3,non_coding_transcript_exon_variant,,ENST00000335106,;	T	ENSG00000187008	ENST00000534738	Transcript	non_coding_transcript_exon_variant	3961	.	.	.	.	.	.	.	-1	PKD1L3	HGNC	21716	processed_transcript	YES	.	.	.	.	.	.	.	.	24/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGAGAACTGG	.	5	ESCA
CTU2	0	.	GRCh37	16	88779139	88779139	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.563T>C	p.Leu188Pro	p.L188P	ENST00000453996	7/15	37	33	4	46	46	0	CTU2,missense_variant,p.Leu188Pro,ENST00000312060,;CTU2,missense_variant,p.Leu101Pro,ENST00000378384,;CTU2,missense_variant,p.Leu259Pro,ENST00000567949,;CTU2,missense_variant,p.Leu188Pro,ENST00000453996,;PIEZO1,downstream_gene_variant,,ENST00000518793,;CTU2,downstream_gene_variant,,ENST00000564921,;CTU2,upstream_gene_variant,,ENST00000567316,;PIEZO1,downstream_gene_variant,,ENST00000327397,;PIEZO1,downstream_gene_variant,,ENST00000301015,;PIEZO1,downstream_gene_variant,,ENST00000466823,;MIR4722,downstream_gene_variant,,ENST00000578292,;CTU2,3_prime_UTR_variant,,ENST00000564105,;CTU2,non_coding_transcript_exon_variant,,ENST00000566637,;PIEZO1,downstream_gene_variant,,ENST00000419505,;CTU2,upstream_gene_variant,,ENST00000562011,;PIEZO1,downstream_gene_variant,,ENST00000472168,;CTU2,upstream_gene_variant,,ENST00000564584,;PIEZO1,downstream_gene_variant,,ENST00000484567,;PIEZO1,downstream_gene_variant,,ENST00000521877,;CTU2,downstream_gene_variant,,ENST00000565071,;PIEZO1,downstream_gene_variant,,ENST00000495568,;	C	ENSG00000174177	ENST00000453996	Transcript	missense_variant	631	563	188	L/P	cTg/cCg	.	.	.	1	CTU2	HGNC	28005	protein_coding	YES	CCDS45545.1	ENSP00000388320	CTU2_HUMAN	H3BNU5_HUMAN,B4DS10_HUMAN	UPI0000251EAE	.	tolerated(0.3)	benign(0.013)	7/15	.	Low_complexity_(Seg):seg,HAMAP:MF_03054,hmmpanther:PTHR20882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTGCTGGGGG	.	4	ESCA
SPIRE2	0	.	GRCh37	16	89924827	89924827	+	Missense_Mutation	SNP	A	A	G	rs766337569	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1184A>G	p.Asp395Gly	p.D395G	ENST00000378247	8/15	87	74	12	81	81	0	SPIRE2,missense_variant,p.Asp395Gly,ENST00000378247,;SPIRE2,missense_variant,p.Asp395Gly,ENST00000393062,;SPIRE2,3_prime_UTR_variant,,ENST00000566337,;SPIRE2,non_coding_transcript_exon_variant,,ENST00000569108,;SPIRE2,upstream_gene_variant,,ENST00000562029,;SPIRE2,downstream_gene_variant,,ENST00000561883,;	G	ENSG00000204991	ENST00000378247	Transcript	missense_variant	1227	1184	395	D/G	gAt/gGt	rs766337569	.	.	1	SPIRE2	HGNC	30623	protein_coding	YES	CCDS32516.1	ENSP00000367494	SPIR2_HUMAN	B3KT42_HUMAN	UPI00001C1FA8	.	tolerated(0.3)	benign(0.008)	8/15	.	hmmpanther:PTHR21345:SF5,hmmpanther:PTHR21345	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAGATGCTG	.	5	ESCA
MYH1	0	.	GRCh37	17	10415473	10415473	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1184C>G	p.Ser395Cys	p.S395C	ENST00000226207	13/40	108	89	18	90	90	0	MYH1,missense_variant,p.Ser395Cys,ENST00000226207,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	C	ENSG00000109061	ENST00000226207	Transcript	missense_variant	1279	1184	395	S/C	tCt/tGt	.	.	.	-1	MYH1	HGNC	7567	protein_coding	YES	CCDS11155.1	ENSP00000226207	MYH1_HUMAN	.	UPI000013C891	.	deleterious(0)	possibly_damaging(0.906)	13/40	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF264,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGAGTTC	.	5	ESCA
MYH2	0	.	GRCh37	17	10426976	10426976	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5309T>A	p.Met1770Lys	p.M1770K	ENST00000245503	37/40	100	60	39	102	102	0	MYH2,missense_variant,p.Met1770Lys,ENST00000245503,;MYH2,missense_variant,p.Met1770Lys,ENST00000397183,;MYH2,intron_variant,,ENST00000532183,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	T	ENSG00000125414	ENST00000245503	Transcript	missense_variant	5694	5309	1770	M/K	aTg/aAg	.	.	.	-1	MYH2	HGNC	7572	protein_coding	YES	CCDS11156.1	ENSP00000245503	MYH2_HUMAN	J3QLR0_HUMAN,E7EX84_HUMAN,C9JIX4_HUMAN	UPI000012FB6C	.	deleterious(0.02)	benign(0.305)	37/40	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF57997,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF314	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCATGGCG	.	5	ESCA
MYO15A	0	.	GRCh37	17	18023165	18023165	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1051G>A	p.Ala351Thr	p.A351T	ENST00000205890	2/66	97	71	26	86	86	0	MYO15A,missense_variant,p.Ala351Thr,ENST00000205890,;MYO15A,non_coding_transcript_exon_variant,,ENST00000583079,;	A	ENSG00000091536	ENST00000205890	Transcript	missense_variant	1389	1051	351	A/T	Gcg/Acg	COSM976192	.	.	1	MYO15A	HGNC	7594	protein_coding	YES	CCDS42271.1	ENSP00000205890	MYO15_HUMAN	K7EQV1_HUMAN,G3V4G3_HUMAN	UPI0000E59E6E	.	.	possibly_damaging(0.499)	2/66	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGACGCGCCA	.	5	ESCA
CDK5R1	0	.	GRCh37	17	30816093	30816093	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*531G>A	.	.	ENST00000313401	2/2	46	25	20	29	29	0	CDK5R1,3_prime_UTR_variant,,ENST00000313401,;MYO1D,downstream_gene_variant,,ENST00000394649,;MYO1D,downstream_gene_variant,,ENST00000318217,;CDK5R1,downstream_gene_variant,,ENST00000584792,;CDK5R1,intron_variant,,ENST00000584716,;	A	ENSG00000176749	ENST00000313401	Transcript	3_prime_UTR_variant	2144	.	.	.	.	.	.	.	1	CDK5R1	HGNC	1775	protein_coding	YES	CCDS11273.1	ENSP00000318486	CD5R1_HUMAN	.	UPI000012738E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGGGTCTAG	.	5	ESCA
MYO1D	0	.	GRCh37	17	30921477	30921477	+	Intron	SNP	G	G	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2864+10628C>G	.	.	ENST00000318217	.	40	32	8	38	38	0	MYO1D,3_prime_UTR_variant,,ENST00000579584,;MYO1D,intron_variant,,ENST00000394649,;MYO1D,intron_variant,,ENST00000318217,;MYO1D,non_coding_transcript_exon_variant,,ENST00000580547,;MYO1D,intron_variant,,ENST00000577352,;	C	ENSG00000176658	ENST00000318217	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MYO1D	HGNC	7598	protein_coding	YES	CCDS32615.1	ENSP00000324527	MYO1D_HUMAN	Q8N618_HUMAN,K7EIG7_HUMAN	UPI0000186004	.	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTGTTTCT	.	5	ESCA
PCGF2	0	.	GRCh37	17	36891292	36891292	+	3'UTR	SNP	T	T	C	rs756894383	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*184A>G	.	.	ENST00000580830	12/12	230	185	45	215	215	0	PCGF2,3_prime_UTR_variant,,ENST00000581345,;PCGF2,3_prime_UTR_variant,,ENST00000360797,;PCGF2,3_prime_UTR_variant,,ENST00000580830,;PCGF2,intron_variant,,ENST00000578487,;PCGF2,downstream_gene_variant,,ENST00000578109,;PCGF2,downstream_gene_variant,,ENST00000579882,;PCGF2,downstream_gene_variant,,ENST00000585100,;CISD3,downstream_gene_variant,,ENST00000439660,;RNA5SP440,upstream_gene_variant,,ENST00000363245,;CISD3,non_coding_transcript_exon_variant,,ENST00000578573,;CISD3,downstream_gene_variant,,ENST00000581668,;	C	ENSG00000056661	ENST00000580830	Transcript	3_prime_UTR_variant	1921	.	.	.	.	rs756894383	.	.	-1	PCGF2	HGNC	12929	protein_coding	YES	CCDS32638.1	ENSP00000461961	PCGF2_HUMAN	.	UPI0000001279	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCATAGAAA	.	5	ESCA
TP53	0	.	GRCh37	17	7576897	7576897	+	Nonsense_Mutation	SNP	G	G	A	rs764735889	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	9/11	85	46	38	96	95	0	TP53,stop_gained,p.Gln317Ter,ENST00000420246,;TP53,stop_gained,p.Gln317Ter,ENST00000269305,;TP53,stop_gained,p.Gln4Ter,ENST00000576024,;TP53,stop_gained,p.Gln185Ter,ENST00000509690,;TP53,stop_gained,p.Gln317Ter,ENST00000359597,;TP53,stop_gained,p.Gln317Ter,ENST00000445888,;TP53,stop_gained,p.Gln317Ter,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	1139	949	317	Q/*	Cag/Tag	rs764735889,TP53_g.14021del,TP53_g.14021C>T,TP53_g.14021C>A,COSM10786,COSM43769,COSM43573,COSM165085,COSM1630410,COSM3388166,COSM1709728,COSM1735382	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	9/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Q317*|c.949C>T|7,SITE|p.Q317*|c.949C>T|16,SITE|p.Q317*|c.949C>T|36,SITE|p.Q317*|c.949C>T|10,CODON|p.0?|c.1_1182del1182|6,CODON|p.Q317R|c.950A>G|3,CODON|p.Q317fs*28|c.949delC|3,BUFFER|p.K320N|c.960G>C|4,BUFFER|p.K320*|c.958A>T|3,BUFFER|p.K319*|c.955A>T|6,BUFFER|p.Q317K|c.949C>A|3,BUFFER|p.S315P|c.943T>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTGGGGAG	byFrequency	5	ESCA
ANKRD29	0	.	GRCh37	18	21180238	21180238	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*952T>C	.	.	ENST00000592179	10/10	12	8	4	13	13	0	ANKRD29,3_prime_UTR_variant,,ENST00000284207,;ANKRD29,3_prime_UTR_variant,,ENST00000592179,;ANKRD29,downstream_gene_variant,,ENST00000322980,;ANKRD29,non_coding_transcript_exon_variant,,ENST00000591280,;ANKRD29,downstream_gene_variant,,ENST00000591617,;ANKRD29,downstream_gene_variant,,ENST00000587763,;	G	ENSG00000154065	ENST00000592179	Transcript	3_prime_UTR_variant	2013	.	.	.	.	.	.	.	-1	ANKRD29	HGNC	27110	protein_coding	YES	CCDS11879.1	ENSP00000468354	ANR29_HUMAN	.	UPI00001618ED	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGCAATAGTA	.	3	ESCA
ALPK2	0	.	GRCh37	18	56202529	56202529	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4890T>C	p.%3D	p.P1630P	ENST00000361673	5/13	95	86	9	95	95	0	ALPK2,synonymous_variant,p.%3D,ENST00000361673,;RP11-1151B14.4,upstream_gene_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,;	G	ENSG00000198796	ENST00000361673	Transcript	synonymous_variant	5104	4890	1630	P	ccT/ccC	.	.	.	-1	ALPK2	HGNC	20565	protein_coding	YES	CCDS11966.2	ENSP00000354991	ALPK2_HUMAN	.	UPI000022A768	.	.	.	5/13	.	hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTTTAGGTTC	.	3	ESCA
KMT2B	0	.	GRCh37	19	36218097	36218097	+	Silent	SNP	C	C	T	rs761407686	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4044C>T	p.%3D	p.N1348N	ENST00000222270	15/37	46	34	12	46	46	0	KMT2B,synonymous_variant,p.%3D,ENST00000420124,;KMT2B,synonymous_variant,p.%3D,ENST00000222270,;KMT2B,non_coding_transcript_exon_variant,,ENST00000607650,;	T	ENSG00000272333	ENST00000222270	Transcript	synonymous_variant	4044	4044	1348	N	aaC/aaT	rs761407686	.	.	1	KMT2B	Uniprot_gn	15840	protein_coding	YES	CCDS46055.1	ENSP00000222270	KMT2B_HUMAN	.	UPI00001376B5	.	.	.	15/37	.	PROSITE_profiles:PS50016,hmmpanther:PTHR22884:SF280,hmmpanther:PTHR22884,Pfam_domain:PF00628,Gene3D:3.30.40.10,PIRSF_domain:PIRSF010354,SMART_domains:SM00249,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACAACGACTA	byFrequency	5	ESCA
ZNF570	0	.	GRCh37	19	37958719	37958719	+	5'Flank	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000330173	.	44	28	15	58	58	0	ZNF570,5_prime_UTR_variant,,ENST00000586475,;ZNF569,intron_variant,,ENST00000448051,;ZNF569,upstream_gene_variant,,ENST00000591710,;ZNF569,upstream_gene_variant,,ENST00000316950,;ZNF570,upstream_gene_variant,,ENST00000330173,;ZNF569,upstream_gene_variant,,ENST00000592490,;ZNF569,upstream_gene_variant,,ENST00000392149,;ZNF570,upstream_gene_variant,,ENST00000388801,;ZNF570,upstream_gene_variant,,ENST00000589725,;ZNF569,intron_variant,,ENST00000591073,;ZNF570,upstream_gene_variant,,ENST00000591380,;ZNF570,5_prime_UTR_variant,,ENST00000587363,;ZNF570,upstream_gene_variant,,ENST00000590664,;ZNF570,upstream_gene_variant,,ENST00000588644,;	A	ENSG00000171827	ENST00000330173	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1263	1	ZNF570	HGNC	26416	protein_coding	YES	CCDS12504.1	ENSP00000331540	ZN570_HUMAN	K7EP64_HUMAN,K7ENX9_HUMAN,K7EMF5_HUMAN,B4DMP1_HUMAN	UPI000006DC96	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGACCTTTTG	.	5	ESCA
LIG1	0	.	GRCh37	19	48630558	48630558	+	Silent	SNP	G	G	A	rs774839059	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1980C>T	p.%3D	p.F660F	ENST00000263274	21/28	65	32	33	46	46	0	LIG1,synonymous_variant,p.%3D,ENST00000536218,;LIG1,synonymous_variant,p.%3D,ENST00000427526,;LIG1,synonymous_variant,p.%3D,ENST00000263274,;CTC-453G23.5,non_coding_transcript_exon_variant,,ENST00000596839,;CTC-453G23.5,non_coding_transcript_exon_variant,,ENST00000596563,;LIG1,synonymous_variant,p.%3D,ENST00000594759,;LIG1,synonymous_variant,p.%3D,ENST00000601091,;LIG1,3_prime_UTR_variant,,ENST00000596672,;LIG1,non_coding_transcript_exon_variant,,ENST00000594067,;LIG1,non_coding_transcript_exon_variant,,ENST00000596457,;LIG1,upstream_gene_variant,,ENST00000596332,;	A	ENSG00000105486	ENST00000263274	Transcript	synonymous_variant	2400	1980	660	F	ttC/ttT	rs774839059	.	.	-1	LIG1	HGNC	6598	protein_coding	YES	CCDS12711.1	ENSP00000263274	DNLI1_HUMAN	Q76GR4_HUMAN,M0R1S4_HUMAN,M0QY71_HUMAN	UPI0000129656	.	.	.	21/28	.	PROSITE_profiles:PS50160,hmmpanther:PTHR10459:SF10,hmmpanther:PTHR10459,Gene3D:3.30.470.30,Pfam_domain:PF01068,TIGRFAM_domain:TIGR00574,Superfamily_domains:SSF56091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTCGAAGGC	.	5	ESCA
MED25	0	.	GRCh37	19	50331715	50331715	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315C>T	p.%3D	p.G105G	ENST00000312865	4/18	74	69	5	66	65	1	MED25,synonymous_variant,p.%3D,ENST00000595185,;MED25,synonymous_variant,p.%3D,ENST00000312865,;MED25,intron_variant,,ENST00000538643,;MED25,upstream_gene_variant,,ENST00000594998,;MED25,upstream_gene_variant,,ENST00000599722,;	T	ENSG00000104973	ENST00000312865	Transcript	synonymous_variant	368	315	105	G	ggC/ggT	.	.	.	1	MED25	HGNC	28845	protein_coding	YES	CCDS33075.1	ENSP00000326767	MED25_HUMAN	.	UPI00002029A3	.	.	.	4/18	.	hmmpanther:PTHR12433,hmmpanther:PTHR12433:SF10,Pfam_domain:PF11265,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ATGGGCGGGGG	.	2	ESCA
KDM4B	0	.	GRCh37	19	5144079	5144079	+	Silent	SNP	C	C	T	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2652C>T	p.%3D	p.H884H	ENST00000159111	19/23	75	65	9	65	65	0	KDM4B,synonymous_variant,p.%3D,ENST00000536461,;KDM4B,synonymous_variant,p.%3D,ENST00000159111,;KDM4B,downstream_gene_variant,,ENST00000588361,;KDM4B,non_coding_transcript_exon_variant,,ENST00000589104,;	T	ENSG00000127663	ENST00000159111	Transcript	synonymous_variant	2870	2652	884	H	caC/caT	COSM4080524	.	.	1	KDM4B	HGNC	29136	protein_coding	YES	CCDS12138.1	ENSP00000159111	KDM4B_HUMAN	K7ES23_HUMAN	UPI00001C202B	.	.	.	19/23	.	hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30,Pfam_domain:PF13832,SMART_domains:SM00249	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCACGCCGC	.	4	ESCA
LILRA6	0	.	GRCh37	19	54743803	54743803	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1283C>T	p.Pro428Leu	p.P428L	ENST00000396365	7/8	62	31	31	52	52	0	LILRA6,missense_variant,p.Pro428Leu,ENST00000396365,;LILRA6,missense_variant,p.Pro428Leu,ENST00000419410,;LILRA6,3_prime_UTR_variant,,ENST00000391735,;LILRA6,intron_variant,,ENST00000245621,;LILRB3,intron_variant,,ENST00000407860,;LILRA6,intron_variant,,ENST00000270464,;LILRA6,intron_variant,,ENST00000440558,;LILRA6,3_prime_UTR_variant,,ENST00000430421,;RPS9,intron_variant,,ENST00000448962,;LILRA6,downstream_gene_variant,,ENST00000474697,;	A	ENSG00000244482	ENST00000396365	Transcript	missense_variant	1323	1283	428	P/L	cCa/cTa	.	.	.	-1	LILRA6	HGNC	15495	protein_coding	YES	CCDS42610.1	ENSP00000379651	LIRA6_HUMAN	.	UPI000022A9CA	.	tolerated(0.05)	benign(0.039)	7/8	.	Low_complexity_(Seg):seg,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738:SF99,hmmpanther:PTHR11738	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTGGGAGG	.	5	ESCA
NOTCH2	0	.	GRCh37	1	120512304	120512304	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938G>A	p.Gly313Asp	p.G313D	ENST00000256646	6/34	54	42	12	71	71	0	NOTCH2,missense_variant,p.Gly313Asp,ENST00000256646,;NOTCH2,non_coding_transcript_exon_variant,,ENST00000479412,;	T	ENSG00000134250	ENST00000256646	Transcript	missense_variant	1158	938	313	G/D	gGc/gAc	.	.	.	-1	NOTCH2	HGNC	7882	protein_coding	YES	CCDS908.1	ENSP00000256646	NOTC2_HUMAN	Q9UFD5_HUMAN,Q13560_HUMAN	UPI000013CF1D	.	deleterious(0)	probably_damaging(1)	6/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF4,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,PIRSF_domain:PIRSF002279,SMART_domains:SM00181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGCCCCCA	.	5	ESCA
HRNR	0	.	GRCh37	1	152188455	152188455	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5650T>A	p.Tyr1884Asn	p.Y1884N	ENST00000368801	3/3	735	707	28	709	709	0	HRNR,missense_variant,p.Tyr1884Asn,ENST00000368801,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	T	ENSG00000197915	ENST00000368801	Transcript	missense_variant	5726	5650	1884	Y/N	Tac/Aac	COSM4022368	.	.	-1	HRNR	HGNC	20846	protein_coding	YES	CCDS30859.1	ENSP00000357791	HORN_HUMAN	Q5W8V9_HUMAN	UPI00001D7CAD	.	.	unknown(0)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF23,hmmpanther:PTHR22571	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGTAACCAG	.	2	ESCA
EFNA4	0	.	GRCh37	1	155041931	155041943	+	3'UTR	DEL	GGACTCTTCATGA	GGACTCTTCATGA	-	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	GGACTCTTCATGA	GGACTCTTCATGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*284_*296delACTCTTCATGAGG	.	.	ENST00000427683	4/4	41	33	8	62	62	0	EFNA4,3_prime_UTR_variant,,ENST00000368409,;EFNA4,3_prime_UTR_variant,,ENST00000427683,;EFNA4,3_prime_UTR_variant,,ENST00000359751,;EFNA3,intron_variant,,ENST00000556931,;EFNA3,intron_variant,,ENST00000505139,;	-	ENSG00000243364	ENST00000427683	Transcript	3_prime_UTR_variant	969-981	.	.	.	.	.	.	.	1	EFNA4	HGNC	3224	protein_coding	YES	CCDS44237.1	ENSP00000414378	EFNA4_HUMAN	.	UPI00001B5785	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GAAGACGGACTCTTCATGAGGTTG	.	2	ESCA
MPZL1	0	.	GRCh37	1	167741701	167741701	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448A>T	p.Ile150Phe	p.I150F	ENST00000359523	3/6	55	51	4	44	44	0	MPZL1,missense_variant,p.Ile150Phe,ENST00000359523,;MPZL1,missense_variant,p.Ile150Phe,ENST00000474859,;MPZL1,missense_variant,p.Ile124Phe,ENST00000367853,;MPZL1,intron_variant,,ENST00000392121,;MPZL1,upstream_gene_variant,,ENST00000403379,;MPZL1,non_coding_transcript_exon_variant,,ENST00000465787,;MPZL1,non_coding_transcript_exon_variant,,ENST00000474729,;MPZL1,intron_variant,,ENST00000448405,;	T	ENSG00000197965	ENST00000359523	Transcript	missense_variant	650	448	150	I/F	Att/Ttt	.	.	.	1	MPZL1	HGNC	7226	protein_coding	YES	CCDS1264.1	ENSP00000352513	MPZL1_HUMAN	A8K5D4_HUMAN	UPI000004BA6A	.	deleterious(0)	probably_damaging(0.998)	3/6	.	Prints_domain:PR00213,Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF07686,Gene3D:2.60.40.10,hmmpanther:PTHR13869:SF19,hmmpanther:PTHR13869	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACACATTAGG	.	2	ESCA
ASPM	0	.	GRCh37	1	197097636	197097636	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2920T>G	p.Cys974Gly	p.C974G	ENST00000367409	10/28	133	122	11	105	105	0	ASPM,missense_variant,p.Cys974Gly,ENST00000367409,;ASPM,missense_variant,p.Cys224Gly,ENST00000367408,;ASPM,missense_variant,p.Cys974Gly,ENST00000294732,;	C	ENSG00000066279	ENST00000367409	Transcript	missense_variant	3177	2920	974	C/G	Tgt/Ggt	.	.	.	-1	ASPM	HGNC	19048	protein_coding	YES	CCDS1389.1	ENSP00000356379	ASPM_HUMAN	.	UPI0000458904	.	deleterious(0)	probably_damaging(0.994)	10/28	.	PROSITE_profiles:PS50021,hmmpanther:PTHR25069:SF115,hmmpanther:PTHR25069,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCACATTGCA	.	3	ESCA
IGFN1	0	.	GRCh37	1	201196257	201196257	+	Silent	SNP	G	G	A	rs749503568	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11034G>A	p.%3D	p.P3678P	ENST00000335211	23/24	75	60	14	61	61	0	IGFN1,synonymous_variant,p.%3D,ENST00000412892,;IGFN1,synonymous_variant,p.%3D,ENST00000335211,;IGFN1,3_prime_UTR_variant,,ENST00000295591,;RP11-567E21.3,upstream_gene_variant,,ENST00000453155,;IGFN1,3_prime_UTR_variant,,ENST00000437879,;IGFN1,non_coding_transcript_exon_variant,,ENST00000473483,;	A	ENSG00000163395	ENST00000335211	Transcript	synonymous_variant	11164	11034	3678	P	ccG/ccA	rs749503568	.	.	1	IGFN1	HGNC	24607	protein_coding	YES	CCDS53455.1	ENSP00000334714	IGFN1_HUMAN	.	UPI0001B300F4	.	.	.	23/24	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Pfam_domain:PF07679,Gene3D:2.60.40.10,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF145,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCGAAGGA	byFrequency	5	ESCA
PLXNA2	0	.	GRCh37	1	208227883	208227883	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2739G>T	p.Gln913His	p.Q913H	ENST00000367033	14/32	57	46	10	72	72	0	PLXNA2,missense_variant,p.Gln913His,ENST00000367033,;	A	ENSG00000076356	ENST00000367033	Transcript	missense_variant	3497	2739	913	Q/H	caG/caT	.	.	.	-1	PLXNA2	HGNC	9100	protein_coding	YES	CCDS31013.1	ENSP00000356000	PLXA2_HUMAN	.	UPI000022B239	.	deleterious(0)	possibly_damaging(0.606)	14/32	.	hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625,Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATCCTGGG	.	5	ESCA
LIN9	0	.	GRCh37	1	226475417	226475417	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394C>T	p.Pro132Ser	p.P132S	ENST00000328205	5/15	71	54	17	84	84	0	LIN9,missense_variant,p.Pro92Ser,ENST00000460719,;LIN9,missense_variant,p.Pro97Ser,ENST00000481685,;LIN9,missense_variant,p.Pro132Ser,ENST00000328205,;LIN9,missense_variant,p.Pro64Ser,ENST00000359525,;LIN9,missense_variant,p.Pro187Ser,ENST00000366808,;LIN9,missense_variant,p.Pro81Ser,ENST00000366801,;	A	ENSG00000183814	ENST00000328205	Transcript	missense_variant	940	394	132	P/S	Cct/Tct	.	.	.	-1	LIN9	HGNC	30830	protein_coding	YES	CCDS1553.1	ENSP00000329102	LIN9_HUMAN	B1B047_HUMAN	UPI00001B2F3C	.	deleterious(0)	probably_damaging(0.925)	5/15	.	hmmpanther:PTHR21689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAGGAAGCT	.	5	ESCA
OR2T3	0	.	GRCh37	1	248636827	248636827	+	Missense_Mutation	SNP	G	G	A	rs757364328	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.176G>A	p.Arg59His	p.R59H	ENST00000359594	1/1	47	37	10	44	44	0	OR2T3,missense_variant,p.Arg59His,ENST00000359594,;	A	ENSG00000196539	ENST00000359594	Transcript	missense_variant	201	176	59	R/H	cGc/cAc	rs757364328	.	.	1	OR2T3	HGNC	14727	protein_coding	YES	CCDS31117.1	ENSP00000352604	OR2T3_HUMAN	.	UPI00001D7CA5	.	tolerated(0.61)	benign(0.001)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF4,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GCCCCGCCTCC	.	3	ESCA
NCDN	0	.	GRCh37	1	36028933	36028933	+	Missense_Mutation	SNP	G	G	A	rs768006525	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516G>A	p.Asp506Asn	p.D506N	ENST00000373243	5/7	43	26	16	34	34	0	NCDN,missense_variant,p.Asp100Asn,ENST00000423723,;NCDN,missense_variant,p.Asp489Asn,ENST00000373253,;NCDN,missense_variant,p.Asp506Asn,ENST00000373243,;NCDN,missense_variant,p.Asp506Asn,ENST00000356090,;NCDN,downstream_gene_variant,,ENST00000437806,;NCDN,downstream_gene_variant,,ENST00000459931,;	A	ENSG00000020129	ENST00000373243	Transcript	missense_variant	1899	1516	506	D/N	Gac/Aac	rs768006525	.	.	1	NCDN	HGNC	17597	protein_coding	YES	CCDS392.1	ENSP00000362340	NCDN_HUMAN	C9J5H8_HUMAN,B4DJ92_HUMAN	UPI000007147C	.	tolerated(0.46)	benign(0.219)	5/7	.	hmmpanther:PTHR13109,Pfam_domain:PF05536	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCACGACACC	.	5	ESCA
ZC3H12A	0	.	GRCh37	1	37948688	37948688	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1276G>C	p.Asp426His	p.D426H	ENST00000373087	6/6	133	124	9	165	165	0	ZC3H12A,missense_variant,p.Asp426His,ENST00000373087,;ZC3H12A,downstream_gene_variant,,ENST00000471012,;ZC3H12A,downstream_gene_variant,,ENST00000472312,;	C	ENSG00000163874	ENST00000373087	Transcript	missense_variant	1392	1276	426	D/H	Gac/Cac	.	.	.	1	ZC3H12A	HGNC	26259	protein_coding	YES	CCDS417.1	ENSP00000362179	ZC12A_HUMAN	C0LED9_HUMAN	UPI000004D30E	.	deleterious(0.04)	benign(0.049)	6/6	.	hmmpanther:PTHR12876:SF10,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCTGGACTCA	.	2	ESCA
OSBPL9	0	.	GRCh37	1	52253063	52253063	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2069A>C	p.Asp690Ala	p.D690A	ENST00000447887	23/24	48	36	11	55	55	0	OSBPL9,missense_variant,p.Asp680Ala,ENST00000428468,;OSBPL9,missense_variant,p.Asp698Ala,ENST00000371710,;OSBPL9,missense_variant,p.Asp690Ala,ENST00000447887,;OSBPL9,missense_variant,p.Asp502Ala,ENST00000486942,;OSBPL9,missense_variant,p.Asp685Ala,ENST00000337809,;OSBPL9,missense_variant,p.Asp515Ala,ENST00000435686,;OSBPL9,missense_variant,p.Asp667Ala,ENST00000371714,;OSBPL9,missense_variant,p.Asp570Ala,ENST00000361556,;OSBPL9,missense_variant,p.Asp599Ala,ENST00000530544,;OSBPL9,missense_variant,p.Asp515Ala,ENST00000531828,;OSBPL9,missense_variant,p.Asp663Ala,ENST00000453295,;OSBPL9,missense_variant,p.Asp502Ala,ENST00000462759,;NRD1,downstream_gene_variant,,ENST00000440943,;NRD1,downstream_gene_variant,,ENST00000354831,;NRD1,downstream_gene_variant,,ENST00000352171,;NRD1,downstream_gene_variant,,ENST00000539524,;NRD1,downstream_gene_variant,,ENST00000485608,;NRD1,downstream_gene_variant,,ENST00000464385,;OSBPL9,3_prime_UTR_variant,,ENST00000495776,;OSBPL9,3_prime_UTR_variant,,ENST00000435274,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000531819,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000475697,;	C	ENSG00000117859	ENST00000447887	Transcript	missense_variant	2088	2069	690	D/A	gAc/gCc	.	.	.	1	OSBPL9	HGNC	16386	protein_coding	YES	CCDS44145.1	ENSP00000412733	OSBL9_HUMAN	Q9BRN2_HUMAN,E9PNR1_HUMAN,B3KW33_HUMAN	UPI0000167BAD	.	deleterious(0)	probably_damaging(0.999)	23/24	.	hmmpanther:PTHR10972:SF27,hmmpanther:PTHR10972,Pfam_domain:PF01237,Superfamily_domains:0051579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGACATTG	.	5	ESCA
SLX4IP	0	.	GRCh37	20	10579382	10579382	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298A>G	p.Arg100Gly	p.R100G	ENST00000334534	5/8	74	62	12	56	56	0	SLX4IP,missense_variant,p.Arg100Gly,ENST00000334534,;SLX4IP,missense_variant,p.Arg21Gly,ENST00000488816,;	G	ENSG00000149346	ENST00000334534	Transcript	missense_variant	478	298	100	R/G	Agg/Ggg	.	.	.	1	SLX4IP	HGNC	16225	protein_coding	YES	CCDS33439.1	ENSP00000335557	SLX4I_HUMAN	.	UPI00001D8318	.	tolerated(0.43)	benign(0.002)	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCAGGAGC	.	5	ESCA
KIF16B	0	.	GRCh37	20	16474995	16474995	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1243G>A	p.Val415Ile	p.V415I	ENST00000408042	12/23	112	95	17	75	75	0	KIF16B,missense_variant,p.Val415Ile,ENST00000408042,;KIF16B,missense_variant,p.Val415Ile,ENST00000354981,;KIF16B,missense_variant,p.Val415Ile,ENST00000355755,;KIF16B,splice_region_variant,,ENST00000378003,;	T	ENSG00000089177	ENST00000408042	Transcript	missense_variant	1401	1243	415	V/I	Gtt/Att	.	.	.	-1	KIF16B	HGNC	15869	protein_coding	YES	CCDS56178.1	ENSP00000384164	KI16B_HUMAN	.	UPI00003BF77C	.	tolerated(0.19)	probably_damaging(0.998)	12/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF400,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAACCTGAA	.	4	ESCA
CRNKL1	0	.	GRCh37	20	20019078	20019078	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2045A>G	p.Tyr682Cys	p.Y682C	ENST00000377340	13/15	115	94	20	78	78	0	CRNKL1,missense_variant,p.Tyr670Cys,ENST00000377327,;CRNKL1,missense_variant,p.Tyr682Cys,ENST00000377340,;CRNKL1,missense_variant,p.Tyr521Cys,ENST00000536226,;NAA20,downstream_gene_variant,,ENST00000310450,;NAA20,downstream_gene_variant,,ENST00000398602,;NAA20,downstream_gene_variant,,ENST00000334982,;CRNKL1,non_coding_transcript_exon_variant,,ENST00000521379,;NAA20,downstream_gene_variant,,ENST00000480550,;NAA20,downstream_gene_variant,,ENST00000463154,;NAA20,downstream_gene_variant,,ENST00000484480,;CRNKL1,3_prime_UTR_variant,,ENST00000490910,;CRNKL1,3_prime_UTR_variant,,ENST00000496549,;CRNKL1,non_coding_transcript_exon_variant,,ENST00000490258,;	C	ENSG00000101343	ENST00000377340	Transcript	missense_variant	2077	2045	682	Y/C	tAt/tGt	.	.	.	-1	CRNKL1	HGNC	15762	protein_coding	YES	CCDS33446.1	ENSP00000366557	CRNL1_HUMAN	.	UPI00004A39A7	.	deleterious(0.02)	possibly_damaging(0.844)	13/15	.	Superfamily_domains:SSF48452,SMART_domains:SM00386,hmmpanther:PTHR11246,hmmpanther:PTHR11246:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATATATGAT	.	5	ESCA
CD93	0	.	GRCh37	20	23066170	23066170	+	Silent	SNP	C	C	T	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660G>A	p.%3D	p.A220A	ENST00000246006	1/2	76	60	15	53	53	0	CD93,synonymous_variant,p.%3D,ENST00000246006,;AL118508.1,upstream_gene_variant,,ENST00000539654,;	T	ENSG00000125810	ENST00000246006	Transcript	synonymous_variant	808	660	220	A	gcG/gcA	COSM1247736	.	.	-1	CD93	HGNC	15855	protein_coding	YES	CCDS13149.1	ENSP00000246006	C1QR1_HUMAN	.	UPI00001273BC	.	.	.	1/2	.	hmmpanther:PTHR24838,hmmpanther:PTHR24838:SF261,PIRSF_domain:PIRSF001775	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.A220V|c.659C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCCGCAGA	.	5	ESCA
DIDO1	0	.	GRCh37	20	61542393	61542393	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572A>T	p.Lys191Met	p.K191M	ENST00000266070	3/16	30	26	4	24	24	0	DIDO1,missense_variant,p.Lys191Met,ENST00000354665,;DIDO1,missense_variant,p.Lys191Met,ENST00000395340,;DIDO1,missense_variant,p.Lys191Met,ENST00000370371,;DIDO1,missense_variant,p.Lys191Met,ENST00000395343,;DIDO1,missense_variant,p.Lys191Met,ENST00000266070,;DIDO1,missense_variant,p.Lys191Met,ENST00000370368,;DIDO1,missense_variant,p.Lys191Met,ENST00000266071,;DIDO1,missense_variant,p.Lys191Met,ENST00000395335,;DIDO1,missense_variant,p.Lys191Met,ENST00000370366,;	A	ENSG00000101191	ENST00000266070	Transcript	missense_variant	898	572	191	K/M	aAg/aTg	.	.	.	-1	DIDO1	HGNC	2680	protein_coding	YES	CCDS33506.1	ENSP00000266070	DIDO1_HUMAN	.	UPI0000206380	.	.	possibly_damaging(0.838)	3/16	.	hmmpanther:PTHR14914:SF7,hmmpanther:PTHR14914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCGCTTCTTC	.	4	ESCA
PLCB4	0	.	GRCh37	20	9404406	9404406	+	Silent	SNP	G	G	A	rs147575829	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2295G>A	p.%3D	p.P765P	ENST00000378501	24/36	86	69	17	64	64	0	PLCB4,synonymous_variant,p.%3D,ENST00000334005,;PLCB4,synonymous_variant,p.%3D,ENST00000414679,;PLCB4,synonymous_variant,p.%3D,ENST00000278655,;PLCB4,synonymous_variant,p.%3D,ENST00000378473,;PLCB4,synonymous_variant,p.%3D,ENST00000378493,;PLCB4,synonymous_variant,p.%3D,ENST00000378501,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;	A	ENSG00000101333	ENST00000378501	Transcript	synonymous_variant	2310	2295	765	P	ccG/ccA	rs147575829	.	.	1	PLCB4	HGNC	9059	protein_coding	YES	CCDS13104.1	ENSP00000367762	PLCB4_HUMAN	B1AJW4_HUMAN,B1AJW3_HUMAN,B1AJW2_HUMAN,B1AJW1_HUMAN	UPI00002069DF	.	.	.	24/36	.	PROSITE_profiles:PS50004,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF78,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,PIRSF_domain:PIRSF000956,Superfamily_domains:SSF49562	C:0.0004	C:0	C:0	.	C:0	C:0	C:0.002	C:0.0005	C:0.0006	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCGGACCT	byFrequency|byCluster|by1000G	5	ESCA
GRIK1-AS2	0	.	GRCh37	21	31002955	31002955	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*526C>T	.	.	ENST00000333765	3/3	31	27	4	16	16	0	BACH1,3_prime_UTR_variant,,ENST00000468059,;BACH1,3_prime_UTR_variant,,ENST00000422809,;GRIK1-AS2,3_prime_UTR_variant,,ENST00000333765,;GRIK1,intron_variant,,ENST00000327783,;GRIK1,intron_variant,,ENST00000389124,;GRIK1,intron_variant,,ENST00000399914,;GRIK1,intron_variant,,ENST00000535441,;GRIK1,intron_variant,,ENST00000399907,;GRIK1,intron_variant,,ENST00000399909,;GRIK1,intron_variant,,ENST00000399913,;GRIK1,intron_variant,,ENST00000309434,;GRIK1,intron_variant,,ENST00000389125,;BACH1,non_coding_transcript_exon_variant,,ENST00000462262,;GRIK1,intron_variant,,ENST00000472429,;	T	ENSG00000183653	ENST00000333765	Transcript	3_prime_UTR_variant	961	.	.	.	.	.	.	.	1	GRIK1-AS2	HGNC	1282	protein_coding	YES	.	ENSP00000330087	.	.	UPI0000072D97	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AGCAGCCCCAG	.	2	ESCA
C21orf119	0	.	GRCh37	21	33765484	33765484	+	5'UTR	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-48T>C	.	.	ENST00000534991	1/1	185	147	38	244	244	0	C21orf119,5_prime_UTR_variant,,ENST00000534991,;URB1,upstream_gene_variant,,ENST00000382751,;	C	ENSG00000256073	ENST00000534991	Transcript	5_prime_UTR_variant	46	.	.	.	.	.	.	.	1	C21orf119	HGNC	23128	protein_coding	YES	.	ENSP00000442411	CU119_HUMAN	.	UPI000006CE1E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGTCTTGG	.	5	ESCA
KREMEN1	0	.	GRCh37	22	29533368	29533368	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670T>G	p.Ser224Ala	p.S224A	ENST00000327813	6/10	62	47	15	50	50	0	KREMEN1,missense_variant,p.Ser224Ala,ENST00000327813,;KREMEN1,missense_variant,p.Ser224Ala,ENST00000400338,;KREMEN1,missense_variant,p.Ser224Ala,ENST00000400335,;KREMEN1,missense_variant,p.Ser222Ala,ENST00000407188,;RNU6-810P,downstream_gene_variant,,ENST00000364001,;KREMEN1,upstream_gene_variant,,ENST00000479755,;KREMEN1,non_coding_transcript_exon_variant,,ENST00000474001,;KREMEN1,intron_variant,,ENST00000453585,;	G	ENSG00000183762	ENST00000327813	Transcript	missense_variant	683	670	224	S/A	Tct/Gct	.	.	.	1	KREMEN1	HGNC	17550	protein_coding	YES	CCDS13849.1	ENSP00000331242	KREM1_HUMAN	.	UPI000002AD01	.	tolerated(0.17)	benign(0.005)	6/10	.	PROSITE_profiles:PS01180,hmmpanther:PTHR24269:SF13,hmmpanther:PTHR24269,Pfam_domain:PF00431,Gene3D:2.60.120.290,PIRSF_domain:PIRSF036961,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGTCTTCT	.	5	ESCA
RANBP2	0	.	GRCh37	2	109367786	109367786	+	Missense_Mutation	SNP	T	T	C	rs539147212	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1340T>C	p.Leu447Ser	p.L447S	ENST00000283195	10/29	398	311	86	426	426	0	RANBP2,missense_variant,p.Leu447Ser,ENST00000283195,;RANBP2,upstream_gene_variant,,ENST00000495506,;	C	ENSG00000153201	ENST00000283195	Transcript	missense_variant	1466	1340	447	L/S	tTg/tCg	rs539147212	.	.	1	RANBP2	HGNC	9848	protein_coding	YES	CCDS2079.1	ENSP00000283195	RBP2_HUMAN	I1Z9D1_HUMAN	UPI0000207FB9	.	tolerated(0.21)	benign(0.006)	10/29	.	hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF8	C:0.0004	C:0.0015	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATTGCCTG	byFrequency|by1000G	5	ESCA
DBI	0	.	GRCh37	2	120125868	120125868	+	Silent	SNP	C	C	A	rs755716082	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297C>A	p.%3D	p.G99G	ENST00000542275	2/4	39	29	9	39	39	0	DBI,synonymous_variant,p.%3D,ENST00000542275,;DBI,synonymous_variant,p.%3D,ENST00000311521,;DBI,synonymous_variant,p.%3D,ENST00000393103,;DBI,synonymous_variant,p.%3D,ENST00000535617,;DBI,synonymous_variant,p.%3D,ENST00000355857,;DBI,synonymous_variant,p.%3D,ENST00000409094,;DBI,synonymous_variant,p.%3D,ENST00000535757,;C2orf76,upstream_gene_variant,,ENST00000409523,;C2orf76,upstream_gene_variant,,ENST00000409877,;C2orf76,upstream_gene_variant,,ENST00000414534,;C2orf76,upstream_gene_variant,,ENST00000334816,;C2orf76,upstream_gene_variant,,ENST00000409466,;DBI,non_coding_transcript_exon_variant,,ENST00000460901,;C2orf76,upstream_gene_variant,,ENST00000498049,;DBI,non_coding_transcript_exon_variant,,ENST00000492375,;DBI,upstream_gene_variant,,ENST00000475783,;	A	ENSG00000155368	ENST00000542275	Transcript	synonymous_variant	381	297	99	G	ggC/ggA	rs755716082	.	.	1	DBI	HGNC	2690	protein_coding	YES	CCDS54391.1	ENSP00000440698	ACBP_HUMAN	B8ZWD8_HUMAN	UPI00018E1AD6	.	.	.	2/4	.	PROSITE_profiles:PS51228,hmmpanther:PTHR23310,hmmpanther:PTHR23310:SF54,PROSITE_patterns:PS00880,Gene3D:1.20.80.10,Pfam_domain:PF00887,Superfamily_domains:SSF47027,Prints_domain:PR00689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGGCGACAT	byFrequency	5	ESCA
ACVR1C	0	.	GRCh37	2	158397600	158397600	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1225+2T>C	.	p.X409_splice	ENST00000243349	.	126	106	20	130	130	0	ACVR1C,splice_donor_variant,,ENST00000348328,;ACVR1C,splice_donor_variant,,ENST00000409680,;ACVR1C,splice_donor_variant,,ENST00000243349,;ACVR1C,splice_donor_variant,,ENST00000335450,;	G	ENSG00000123612	ENST00000243349	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	ACVR1C	HGNC	18123	protein_coding	YES	CCDS2205.1	ENSP00000243349	ACV1C_HUMAN	Q53SF5_HUMAN	UPI000006CFAE	.	.	.	.	7/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTACCTCC	.	5	ESCA
COBLL1	0	.	GRCh37	2	165552272	165552272	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1744A>G	p.Ile582Val	p.I582V	ENST00000342193	12/14	84	70	14	75	75	0	COBLL1,missense_variant,p.Ile544Val,ENST00000375458,;COBLL1,missense_variant,p.Ile582Val,ENST00000409184,;COBLL1,missense_variant,p.Ile582Val,ENST00000342193,;COBLL1,missense_variant,p.Ile620Val,ENST00000392717,;COBLL1,missense_variant,p.Ile649Val,ENST00000194871,;COBLL1,upstream_gene_variant,,ENST00000493713,;COBLL1,upstream_gene_variant,,ENST00000495084,;COBLL1,downstream_gene_variant,,ENST00000491126,;COBLL1,non_coding_transcript_exon_variant,,ENST00000493868,;COBLL1,non_coding_transcript_exon_variant,,ENST00000489955,;COBLL1,downstream_gene_variant,,ENST00000460238,;COBLL1,downstream_gene_variant,,ENST00000456171,;	C	ENSG00000082438	ENST00000342193	Transcript	missense_variant	1960	1744	582	I/V	Atc/Gtc	.	.	.	-1	COBLL1	HGNC	23571	protein_coding	YES	CCDS2223.2	ENSP00000341360	COBL1_HUMAN	C9JWZ0_HUMAN,C9JAU3_HUMAN,B3KMG7_HUMAN	UPI000007132B	.	tolerated(0.13)	benign(0.114)	12/14	.	hmmpanther:PTHR21557:SF2,hmmpanther:PTHR21557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGATTTCTG	.	5	ESCA
PLCL1	0	.	GRCh37	2	199011706	199011706	+	3'UTR	SNP	G	G	A	rs374739063	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*20G>A	.	.	ENST00000428675	6/6	128	85	43	130	130	0	PLCL1,3_prime_UTR_variant,,ENST00000428675,;PLCL1,3_prime_UTR_variant,,ENST00000437704,;PLCL1,downstream_gene_variant,,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,;	A	ENSG00000115896	ENST00000428675	Transcript	3_prime_UTR_variant	3706	.	.	.	.	rs374739063	.	.	1	PLCL1	HGNC	9063	protein_coding	YES	CCDS2326.2	ENSP00000402861	PLCL1_HUMAN	.	UPI000165BCF5	.	.	.	6/6	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACACGTTCAC	byCluster|by1000G	5	ESCA
PPIL3	0	.	GRCh37	2	201753762	201753762	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-154G>T	.	.	ENST00000286175	1/7	51	43	7	42	42	0	PPIL3,5_prime_UTR_variant,,ENST00000409361,;PPIL3,5_prime_UTR_variant,,ENST00000286175,;PPIL3,5_prime_UTR_variant,,ENST00000392283,;PPIL3,intron_variant,,ENST00000409449,;PPIL3,intron_variant,,ENST00000443398,;NIF3L1,upstream_gene_variant,,ENST00000409020,;NIF3L1,upstream_gene_variant,,ENST00000409357,;PPIL3,upstream_gene_variant,,ENST00000457063,;PPIL3,upstream_gene_variant,,ENST00000409264,;NIF3L1,upstream_gene_variant,,ENST00000416651,;NIF3L1,upstream_gene_variant,,ENST00000454952,;NIF3L1,upstream_gene_variant,,ENST00000409588,;NIF3L1,upstream_gene_variant,,ENST00000409129,;NIF3L1,upstream_gene_variant,,ENST00000426253,;NIF3L1,upstream_gene_variant,,ENST00000359683,;PPIL3,non_coding_transcript_exon_variant,,ENST00000465823,;PPIL3,non_coding_transcript_exon_variant,,ENST00000492074,;PPIL3,non_coding_transcript_exon_variant,,ENST00000497263,;PPIL3,intron_variant,,ENST00000497501,;PPIL3,non_coding_transcript_exon_variant,,ENST00000470442,;PPIL3,non_coding_transcript_exon_variant,,ENST00000487879,;PPIL3,upstream_gene_variant,,ENST00000415562,;	A	ENSG00000240344	ENST00000286175	Transcript	5_prime_UTR_variant	231	.	.	.	.	.	.	.	-1	PPIL3	HGNC	9262	protein_coding	YES	CCDS2332.1	ENSP00000286175	PPIL3_HUMAN	.	UPI000006E160	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTCAAAAT	.	4	ESCA
SLC16A14	0	.	GRCh37	2	230902054	230902054	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*42G>A	.	.	ENST00000295190	5/5	38	21	16	50	49	0	SLC16A14,3_prime_UTR_variant,,ENST00000295190,;	T	ENSG00000163053	ENST00000295190	Transcript	3_prime_UTR_variant	2034	.	.	.	.	.	.	.	-1	SLC16A14	HGNC	26417	protein_coding	YES	CCDS2473.1	ENSP00000295190	MOT14_HUMAN	C9JME4_HUMAN,C9JIV1_HUMAN,B3KNY7_HUMAN	UPI000004EE99	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGGCATGAG	.	5	ESCA
SFXN5	0	.	GRCh37	2	73215400	73215400	+	Silent	SNP	C	C	T	rs148672407	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612G>A	p.%3D	p.P204P	ENST00000272433	10/14	49	37	12	57	57	0	SFXN5,synonymous_variant,p.%3D,ENST00000272433,;SFXN5,synonymous_variant,p.%3D,ENST00000411783,;SFXN5,synonymous_variant,p.%3D,ENST00000410065,;SFXN5,non_coding_transcript_exon_variant,,ENST00000482289,;SFXN5,non_coding_transcript_exon_variant,,ENST00000416579,;SFXN5,non_coding_transcript_exon_variant,,ENST00000463277,;SFXN5,non_coding_transcript_exon_variant,,ENST00000482542,;SFXN5,non_coding_transcript_exon_variant,,ENST00000474528,;SFXN5,intron_variant,,ENST00000461352,;SFXN5,downstream_gene_variant,,ENST00000464825,;	T	ENSG00000144040	ENST00000272433	Transcript	synonymous_variant	743	612	204	P	ccG/ccA	rs148672407	.	.	-1	SFXN5	HGNC	16073	protein_coding	YES	CCDS1922.1	ENSP00000272433	SFXN5_HUMAN	.	UPI000006D292	.	.	.	10/14	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11153,hmmpanther:PTHR11153:SF17,TIGRFAM_domain:TIGR00798,Pfam_domain:PF03820	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAACGGCAC	byFrequency|byCluster	5	ESCA
TOPBP1	0	.	GRCh37	3	133320154	133320154	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4509A>T	p.Leu1503Phe	p.L1503F	ENST00000260810	28/28	91	70	21	89	89	0	TOPBP1,missense_variant,p.Leu1503Phe,ENST00000260810,;TOPBP1,intron_variant,,ENST00000503464,;TOPBP1,intron_variant,,ENST00000503338,;	A	ENSG00000163781	ENST00000260810	Transcript	missense_variant	4641	4509	1503	L/F	ttA/ttT	.	.	.	-1	TOPBP1	HGNC	17008	protein_coding	YES	CCDS46919.1	ENSP00000260810	TOPB1_HUMAN	A0AV47_HUMAN	UPI000020A292	.	tolerated(0.26)	benign(0.019)	28/28	.	hmmpanther:PTHR13561:SF25,hmmpanther:PTHR13561	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGATAATCC	.	5	ESCA
SLC7A14	0	.	GRCh37	3	170198523	170198523	+	Missense_Mutation	SNP	C	C	T	rs115446306	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1548G>A	p.Met516Ile	p.M516I	ENST00000231706	7/8	336	316	20	37	37	0	SLC7A14,missense_variant,p.Met516Ile,ENST00000231706,;CLDN11,intron_variant,,ENST00000486975,;CLDN11,intron_variant,,ENST00000451576,;CLDN11,intron_variant,,ENST00000480067,;CLDN11,intron_variant,,ENST00000471373,;	T	ENSG00000013293	ENST00000231706	Transcript	missense_variant	1864	1548	516	M/I	atG/atA	rs115446306	.	.	-1	SLC7A14	HGNC	29326	protein_coding	YES	CCDS33892.1	ENSP00000231706	S7A14_HUMAN	.	UPI0000051F6B	.	tolerated(0.28)	benign(0.001)	7/8	.	hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF250	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	G:0.0005	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGTCATGTC	byCluster|by1000G	2	ESCA
HTR3E	0	.	GRCh37	3	183823112	183823112	+	Missense_Mutation	SNP	G	G	A	rs145547998	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.695G>A	p.Arg232Gln	p.R232Q	ENST00000440596	4/7	58	48	10	29	29	0	HTR3E,missense_variant,p.Arg191Gln,ENST00000425359,;HTR3E,missense_variant,p.Arg232Gln,ENST00000440596,;HTR3E,missense_variant,p.Arg135Gln,ENST00000431041,;HTR3E,missense_variant,p.Arg221Gln,ENST00000335304,;HTR3E,missense_variant,p.Arg206Gln,ENST00000436361,;HTR3E,missense_variant,p.Arg206Gln,ENST00000415389,;HTR3E-AS1,upstream_gene_variant,,ENST00000431427,;	A	ENSG00000186038	ENST00000440596	Transcript	missense_variant	695	695	232	R/Q	cGg/cAg	rs145547998,COSM4115641	.	.	1	HTR3E	HGNC	24005	protein_coding	YES	CCDS58871.1	ENSP00000406050	5HT3E_HUMAN	.	UPI000198CB5D	.	tolerated(0.5)	benign(0.005)	4/7	.	hmmpanther:PTHR18945:SF378,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932	A:0.0018	A:0.0068	A:0	.	A:0	A:0	A:0	A:0.0034	A:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCCGGAACA	byFrequency|byCluster|by1000G	5	ESCA
BRPF1	0	.	GRCh37	3	9789298	9789298	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*265C>T	.	.	ENST00000383829	14/14	25	13	12	38	38	0	BRPF1,3_prime_UTR_variant,,ENST00000424362,;BRPF1,3_prime_UTR_variant,,ENST00000433861,;BRPF1,3_prime_UTR_variant,,ENST00000302054,;BRPF1,3_prime_UTR_variant,,ENST00000457855,;BRPF1,3_prime_UTR_variant,,ENST00000383829,;OGG1,upstream_gene_variant,,ENST00000349503,;OGG1,upstream_gene_variant,,ENST00000416333,;OGG1,upstream_gene_variant,,ENST00000302036,;OGG1,upstream_gene_variant,,ENST00000426518,;OGG1,upstream_gene_variant,,ENST00000449570,;OGG1,upstream_gene_variant,,ENST00000344629,;OGG1,upstream_gene_variant,,ENST00000339511,;OGG1,upstream_gene_variant,,ENST00000302003,;OGG1,upstream_gene_variant,,ENST00000352937,;OGG1,upstream_gene_variant,,ENST00000441094,;OGG1,upstream_gene_variant,,ENST00000302008,;OGG1,upstream_gene_variant,,ENST00000383826,;OGG1,upstream_gene_variant,,ENST00000383825,;OGG1,upstream_gene_variant,,ENST00000436092,;BRPF1,downstream_gene_variant,,ENST00000469066,;OGG1,upstream_gene_variant,,ENST00000429146,;BRPF1,downstream_gene_variant,,ENST00000497565,;OGG1,upstream_gene_variant,,ENST00000425665,;OGG1,upstream_gene_variant,,ENST00000432857,;	T	ENSG00000156983	ENST00000383829	Transcript	3_prime_UTR_variant	4332	.	.	.	.	.	.	.	1	BRPF1	HGNC	14255	protein_coding	YES	CCDS33692.1	ENSP00000373340	BRPF1_HUMAN	C9JHC0_HUMAN,C9JDK5_HUMAN	UPI00001A9CA3	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGGCGGGGT	.	5	ESCA
EGF	0	.	GRCh37	4	110901176	110901176	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2102A>G	p.Asp701Gly	p.D701G	ENST00000265171	14/24	66	42	23	64	64	0	EGF,missense_variant,p.Asp701Gly,ENST00000503392,;EGF,missense_variant,p.Asp701Gly,ENST00000265171,;EGF,missense_variant,p.Asp659Gly,ENST00000509793,;EGF,downstream_gene_variant,,ENST00000541061,;EGF,upstream_gene_variant,,ENST00000509996,;EGF,upstream_gene_variant,,ENST00000511228,;EGF,downstream_gene_variant,,ENST00000502579,;	G	ENSG00000138798	ENST00000265171	Transcript	missense_variant	2547	2102	701	D/G	gAt/gGt	.	.	.	1	EGF	HGNC	3229	protein_coding	YES	CCDS3689.1	ENSP00000265171	EGF_HUMAN	Q6QBS2_HUMAN	UPI000013D5C8	.	deleterious(0.01)	probably_damaging(0.984)	14/24	.	Superfamily_domains:SSF63825,PIRSF_domain:PIRSF001778,SMART_domains:SM00135,Gene3D:2.120.10.30,hmmpanther:PTHR10529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGATTGGG	.	5	ESCA
NDST4	0	.	GRCh37	4	115997643	115997643	+	Missense_Mutation	SNP	G	G	T	rs564044682	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550C>A	p.Leu184Ile	p.L184I	ENST00000264363	2/14	49	41	7	69	69	0	NDST4,missense_variant,p.Leu184Ile,ENST00000264363,;NDST4,intron_variant,,ENST00000504854,;NDST4,intron_variant,,ENST00000514570,;	T	ENSG00000138653	ENST00000264363	Transcript	missense_variant	1229	550	184	L/I	Ctt/Att	rs564044682,COSM1216903,COSM307720	.	.	-1	NDST4	HGNC	20779	protein_coding	YES	CCDS3706.1	ENSP00000264363	NDST4_HUMAN	.	UPI000006CED7	.	tolerated(0.33)	benign(0.145)	2/14	.	Pfam_domain:PF12062,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF29	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAAGGTTTA	by1000G	5	ESCA
FAT1	0	.	GRCh37	4	187629096	187629096	+	Frame_Shift_Del	DEL	G	G	-	rs776913986	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1886delC	p.Ser629CysfsTer2	p.S629Cfs*2	ENST00000441802	2/27	82	68	14	69	69	0	FAT1,frameshift_variant,p.Ser629CysfsTer2,ENST00000441802,;FAT1,downstream_gene_variant,,ENST00000509647,;	-	ENSG00000083857	ENST00000441802	Transcript	frameshift_variant	2096	1886	629	S/X	tCg/tg	rs776913986	.	.	-1	FAT1	HGNC	3595	protein_coding	YES	CCDS47177.1	ENSP00000406229	FAT1_HUMAN	D6RCE4_HUMAN	UPI000051946B	.	.	.	2/27	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATTAGCGATCGC	byFrequency	3	ESCA
EPHA5	0	.	GRCh37	4	66189849	66189849	+	Missense_Mutation	SNP	C	C	T	rs139793674	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3097G>A	p.Gly1033Arg	p.G1033R	ENST00000273854	18/18	44	31	13	45	45	0	EPHA5,missense_variant,p.Gly1033Arg,ENST00000273854,;EPHA5,missense_variant,p.Gly870Arg,ENST00000432638,;EPHA5,missense_variant,p.Gly1011Arg,ENST00000354839,;	T	ENSG00000145242	ENST00000273854	Transcript	missense_variant	3698	3097	1033	G/R	Gga/Aga	rs139793674,COSM1580851	.	.	-1	EPHA5	HGNC	3389	protein_coding	YES	CCDS3513.1	ENSP00000273854	EPHA5_HUMAN	.	UPI000013D9D9	.	tolerated(0.57)	benign(0.436)	18/18	.	hmmpanther:PTHR24416:SF17,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0.0002	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G1033R|c.3097G>A|3,BUFFER|p.N1032S|c.3095A>G|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTCCGTTTA	byCluster|by1000G	5	ESCA
AGPAT9	0	.	GRCh37	4	84526805	84526805	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*885C>A	.	.	ENST00000395226	13/13	65	58	7	60	59	1	AGPAT9,3_prime_UTR_variant,,ENST00000395226,;AGPAT9,3_prime_UTR_variant,,ENST00000264409,;AGPAT9,downstream_gene_variant,,ENST00000509044,;	A	ENSG00000138678	ENST00000395226	Transcript	3_prime_UTR_variant	2408	.	.	.	.	.	.	.	1	AGPAT9	HGNC	28157	protein_coding	YES	CCDS3606.1	ENSP00000378651	GPAT3_HUMAN	.	UPI000004B62F	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCCCAGTCT	.	4	ESCA
CCNI2	0	.	GRCh37	5	132088631	132088631	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1079G>A	p.Cys360Tyr	p.C360Y	ENST00000378731	6/6	48	39	8	41	41	0	CCNI2,missense_variant,p.Cys360Tyr,ENST00000378731,;SEPT8,intron_variant,,ENST00000378719,;SEPT8,downstream_gene_variant,,ENST00000378706,;SEPT8,downstream_gene_variant,,ENST00000448933,;SEPT8,downstream_gene_variant,,ENST00000378721,;SEPT8,downstream_gene_variant,,ENST00000296873,;SEPT8,intron_variant,,ENST00000481030,;CCNI2,downstream_gene_variant,,ENST00000468733,;CCNI2,downstream_gene_variant,,ENST00000492179,;	A	ENSG00000205089	ENST00000378731	Transcript	missense_variant	1130	1079	360	C/Y	tGc/tAc	.	.	.	1	CCNI2	HGNC	33869	protein_coding	YES	CCDS34236.1	ENSP00000368005	CCNI2_HUMAN	B7ZMB8_HUMAN,B7ZMB7_HUMAN	UPI0000160A91	.	tolerated(0.96)	benign(0.314)	6/6	.	hmmpanther:PTHR10177,hmmpanther:PTHR10177:SF57	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTGCACAG	.	5	ESCA
SPOCK1	0	.	GRCh37	5	136312100	136312100	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2243C>A	.	.	ENST00000394945	11/11	37	28	8	44	44	0	SPOCK1,3_prime_UTR_variant,,ENST00000394945,;SPOCK1,downstream_gene_variant,,ENST00000282223,;SPOCK1,downstream_gene_variant,,ENST00000509978,;SPOCK1,downstream_gene_variant,,ENST00000515091,;	T	ENSG00000152377	ENST00000394945	Transcript	3_prime_UTR_variant	3733	.	.	.	.	.	.	.	-1	SPOCK1	HGNC	11251	protein_coding	YES	CCDS4191.1	ENSP00000378401	TICN1_HUMAN	D6RB21_HUMAN,D6RAM7_HUMAN,D3DQB3_HUMAN	UPI0000136F50	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTGATACT	.	5	ESCA
PCDHA10	0	.	GRCh37	5	140235896	140235896	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263G>A	p.Arg88Gln	p.R88Q	ENST00000307360	1/4	177	138	39	155	155	0	PCDHA10,missense_variant,p.Arg88Gln,ENST00000506939,;PCDHA10,missense_variant,p.Arg88Gln,ENST00000307360,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA9,intron_variant,,ENST00000532602,;AC005609.1,downstream_gene_variant,,ENST00000502505,;PCDHA9,downstream_gene_variant,,ENST00000378122,;PCDHA14,upstream_gene_variant,,ENST00000506751,;	A	ENSG00000250120	ENST00000307360	Transcript	missense_variant	263	263	88	R/Q	cGg/cAg	.	.	.	1	PCDHA10	HGNC	8664	protein_coding	YES	CCDS54921.1	ENSP00000304234	PCDAA_HUMAN	.	UPI00001273D3	.	deleterious_low_confidence(0.02)	probably_damaging(0.996)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF08266,hmmpanther:PTHR24028:SF76,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCGGATTG	.	5	ESCA
PCDHB12	0	.	GRCh37	5	140589663	140589663	+	Missense_Mutation	SNP	C	C	T	rs781796244	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1184C>T	p.Ser395Phe	p.S395F	ENST00000239450	1/1	116	88	28	143	143	0	PCDHB12,missense_variant,p.Ser58Phe,ENST00000541609,;PCDHB12,missense_variant,p.Ser395Phe,ENST00000239450,;PCDHB13,upstream_gene_variant,,ENST00000341948,;	T	ENSG00000120328	ENST00000239450	Transcript	missense_variant	1373	1184	395	S/F	tCt/tTt	rs781796244,COSM3429046,COSM3610891	.	.	1	PCDHB12	HGNC	8683	protein_coding	YES	CCDS4254.1	ENSP00000239450	PCDBC_HUMAN	B4DDU1_HUMAN	UPI000000DAFD	.	deleterious_low_confidence(0)	possibly_damaging(0.726)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V392M|c.1174G>A|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCTTCGG	byFrequency	5	ESCA
PCDH1	0	.	GRCh37	5	141233235	141233235	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*372C>T	.	.	ENST00000287008	5/5	49	35	14	40	40	0	PCDH1,3_prime_UTR_variant,,ENST00000503492,;PCDH1,3_prime_UTR_variant,,ENST00000287008,;	A	ENSG00000156453	ENST00000287008	Transcript	3_prime_UTR_variant	4234	.	.	.	.	.	.	.	-1	PCDH1	HGNC	8655	protein_coding	YES	CCDS4267.1	ENSP00000287008	PCDH1_HUMAN	D6RBG2_HUMAN	UPI000016158F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTCGGCCAT	.	5	ESCA
PCDH12	0	.	GRCh37	5	141335614	141335614	+	Silent	SNP	C	C	T	rs769053658	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1803G>A	p.%3D	p.A601A	ENST00000231484	1/4	135	105	29	91	91	0	PCDH12,synonymous_variant,p.%3D,ENST00000231484,;RNF14,upstream_gene_variant,,ENST00000506822,;RNF14,upstream_gene_variant,,ENST00000511961,;PCDH12,downstream_gene_variant,,ENST00000510041,;AC005740.6,downstream_gene_variant,,ENST00000607378,;PCDH12,downstream_gene_variant,,ENST00000512221,;	T	ENSG00000113555	ENST00000231484	Transcript	synonymous_variant	3014	1803	601	A	gcG/gcA	rs769053658	.	.	-1	PCDH12	HGNC	8657	protein_coding	YES	CCDS4269.1	ENSP00000231484	PCD12_HUMAN	E5RJD4_HUMAN	UPI00001313B4	.	.	.	1/4	.	Gene3D:2.60.40.60,hmmpanther:PTHR24028:SF42,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCCCGCTGG	.	5	ESCA
PDZD2	0	.	GRCh37	5	32057775	32057775	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1915G>C	p.Asp639His	p.D639H	ENST00000438447	11/25	60	55	5	44	44	0	PDZD2,missense_variant,p.Asp639His,ENST00000438447,;PDZD2,missense_variant,p.Asp639His,ENST00000282493,;PDZD2,upstream_gene_variant,,ENST00000513184,;PDZD2,non_coding_transcript_exon_variant,,ENST00000502489,;PDZD2,non_coding_transcript_exon_variant,,ENST00000509256,;	C	ENSG00000133401	ENST00000438447	Transcript	missense_variant	2303	1915	639	D/H	Gat/Cat	.	.	.	1	PDZD2	HGNC	18486	protein_coding	YES	CCDS34137.1	ENSP00000402033	PDZD2_HUMAN	B4DGS3_HUMAN	UPI000069648B	.	deleterious(0)	probably_damaging(1)	11/25	.	PROSITE_profiles:PS50106,hmmpanther:PTHR11324:SF16,hmmpanther:PTHR11324,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCTAGATGTA	.	3	ESCA
IL6ST	0	.	GRCh37	5	55256372	55256372	+	Silent	SNP	T	T	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.831A>T	p.%3D	p.T277T	ENST00000381298	8/17	56	43	12	47	47	0	IL6ST,synonymous_variant,p.%3D,ENST00000522633,;IL6ST,synonymous_variant,p.%3D,ENST00000381287,;IL6ST,synonymous_variant,p.%3D,ENST00000381293,;IL6ST,synonymous_variant,p.%3D,ENST00000336909,;IL6ST,synonymous_variant,p.%3D,ENST00000381298,;IL6ST,synonymous_variant,p.%3D,ENST00000536319,;IL6ST,synonymous_variant,p.%3D,ENST00000381294,;IL6ST,synonymous_variant,p.%3D,ENST00000502326,;IL6ST,intron_variant,,ENST00000381286,;IL6ST,downstream_gene_variant,,ENST00000396816,;IL6ST,downstream_gene_variant,,ENST00000577363,;IL6ST,synonymous_variant,p.%3D,ENST00000503773,;IL6ST,upstream_gene_variant,,ENST00000506241,;	A	ENSG00000134352	ENST00000381298	Transcript	synonymous_variant	1144	831	277	T	acA/acT	.	.	.	-1	IL6ST	HGNC	6021	protein_coding	YES	CCDS3971.1	ENSP00000370698	IL6RB_HUMAN	.	UPI000013CF29	.	.	.	8/17	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF25,hmmpanther:PTHR23036,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGCTGTGTC	.	5	ESCA
POC5	0	.	GRCh37	5	75001600	75001601	+	Frame_Shift_Ins	INS	-	-	CA	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234_235dupTG	p.Glu79ValfsTer3	p.E79Vfs*3	ENST00000428202	4/12	115	104	11	117	117	0	POC5,frameshift_variant,p.Glu54ValfsTer3,ENST00000446329,;POC5,frameshift_variant,p.Glu79ValfsTer3,ENST00000428202,;POC5,5_prime_UTR_variant,,ENST00000380475,;POC5,5_prime_UTR_variant,,ENST00000506164,;POC5,5_prime_UTR_variant,,ENST00000502826,;POC5,5_prime_UTR_variant,,ENST00000510798,;POC5,5_prime_UTR_variant,,ENST00000503835,;POC5,intron_variant,,ENST00000514838,;RNU6-680P,downstream_gene_variant,,ENST00000384603,;POC5,non_coding_transcript_exon_variant,,ENST00000504862,;POC5,3_prime_UTR_variant,,ENST00000515285,;POC5,non_coding_transcript_exon_variant,,ENST00000512125,;POC5,non_coding_transcript_exon_variant,,ENST00000508467,;POC5,downstream_gene_variant,,ENST00000507421,;	CA	ENSG00000152359	ENST00000428202	Transcript	frameshift_variant	425-426	235-236	79	E/VX	gaa/gTGaa	.	.	.	-1	POC5	HGNC	26658	protein_coding	YES	CCDS47236.1	ENSP00000410216	POC5_HUMAN	D6RJ06_HUMAN,D6REA5_HUMAN,D6RBC1_HUMAN	UPI000020CB20	.	.	.	4/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTACTTCAGAG	.	3	ESCA
CLVS2	0	.	GRCh37	6	123319130	123319130	+	Missense_Mutation	SNP	C	C	T	rs766143997	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.208C>T	p.Arg70Cys	p.R70C	ENST00000275162	2/6	61	54	7	40	40	0	CLVS2,missense_variant,p.Arg70Cys,ENST00000275162,;CLVS2,intron_variant,,ENST00000368438,;	T	ENSG00000146352	ENST00000275162	Transcript	missense_variant	1543	208	70	R/C	Cgc/Tgc	rs766143997	.	.	1	CLVS2	HGNC	23046	protein_coding	YES	CCDS34525.1	ENSP00000275162	CLVS2_HUMAN	.	UPI000013DA49	.	deleterious(0.01)	probably_damaging(0.964)	2/6	.	hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF73,Pfam_domain:PF03765,Gene3D:3.40.525.10,SMART_domains:SM01100,Superfamily_domains:SSF46938,Prints_domain:PR00180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CCTTCCGCCTC	.	3	ESCA
FNDC1	0	.	GRCh37	6	159621085	159621085	+	Missense_Mutation	SNP	G	G	A	rs780310956	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.362G>A	p.Arg121His	p.R121H	ENST00000297267	3/23	90	73	16	92	92	0	FNDC1,missense_variant,p.Arg121His,ENST00000340366,;FNDC1,missense_variant,p.Arg121His,ENST00000297267,;FNDC1,missense_variant,p.Arg80His,ENST00000329629,;	A	ENSG00000164694	ENST00000297267	Transcript	missense_variant	562	362	121	R/H	cGt/cAt	rs780310956	.	.	1	FNDC1	HGNC	21184	protein_coding	YES	CCDS47512.1	ENSP00000297267	FNDC1_HUMAN	.	UPI0000579B80	.	deleterious(0.04)	unknown(0)	3/23	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23197:SF8,hmmpanther:PTHR23197,Pfam_domain:PF00041,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCCGTCCTG	byFrequency	5	ESCA
TNXB	0	.	GRCh37	6	32024678	32024678	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7828G>T	p.Asp2610Tyr	p.D2610Y	ENST00000375247	23/44	78	65	13	83	83	0	TNXB,missense_variant,p.Asp2610Tyr,ENST00000375247,;TNXB,missense_variant,p.Asp2610Tyr,ENST00000375244,;	A	ENSG00000168477	ENST00000375247	Transcript	missense_variant	8030	7828	2610	D/Y	Gat/Tat	.	.	.	-1	TNXB	HGNC	11976	protein_coding	.	.	ENSP00000364396	TENX_HUMAN	Q9NPK8_HUMAN,Q9NPK7_HUMAN,B6RHJ5_HUMAN	UPI000174F11D	.	.	benign(0.264)	23/44	.	Gene3D:2.60.40.10,hmmpanther:PTHR19143:SF190,hmmpanther:PTHR19143,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCATCCTCTG	.	4	ESCA
FUT9	0	.	GRCh37	6	96651510	96651510	+	Missense_Mutation	SNP	G	G	A	rs763326668	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479G>A	p.Arg160His	p.R160H	ENST00000302103	3/3	45	39	6	46	46	0	FUT9,missense_variant,p.Arg160His,ENST00000302103,;	A	ENSG00000172461	ENST00000302103	Transcript	missense_variant	805	479	160	R/H	cGt/cAt	rs763326668	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	tolerated(0.05)	possibly_damaging(0.531)	3/3	.	hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF10,Pfam_domain:PF00852,Superfamily_domains:SSF53756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCCGTGATT	.	4	ESCA
HBP1	0	.	GRCh37	7	106822898	106822898	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250C>A	p.Gln84Lys	p.Q84K	ENST00000222574	3/11	54	36	18	80	80	0	HBP1,missense_variant,p.Gln84Lys,ENST00000468410,;HBP1,missense_variant,p.Gln84Lys,ENST00000464009,;HBP1,missense_variant,p.Gln84Lys,ENST00000222574,;HBP1,missense_variant,p.Gln84Lys,ENST00000479011,;HBP1,missense_variant,p.Gln76Lys,ENST00000498408,;HBP1,missense_variant,p.Gln84Lys,ENST00000485846,;HBP1,missense_variant,p.Gln84Lys,ENST00000497535,;HBP1,downstream_gene_variant,,ENST00000468401,;HBP1,downstream_gene_variant,,ENST00000478930,;HBP1,upstream_gene_variant,,ENST00000461963,;HBP1,non_coding_transcript_exon_variant,,ENST00000463202,;	A	ENSG00000105856	ENST00000222574	Transcript	missense_variant	436	250	84	Q/K	Caa/Aaa	.	.	.	1	HBP1	HGNC	23200	protein_coding	YES	CCDS5741.1	ENSP00000222574	HBP1_HUMAN	H7C4S2_HUMAN,C9JQU7_HUMAN,C9JPK6_HUMAN,C9JAW1_HUMAN,C9J8V6_HUMAN,C9J5U3_HUMAN,B4DJ36_HUMAN	UPI000006DC04	.	deleterious(0.01)	possibly_damaging(0.638)	3/11	.	hmmpanther:PTHR15499:SF2,hmmpanther:PTHR15499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATCAAGAA	.	5	ESCA
LAMB1	0	.	GRCh37	7	107570010	107570010	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4592T>C	p.Met1531Thr	p.M1531T	ENST00000222399	30/34	31	16	14	32	32	0	LAMB1,missense_variant,p.Met1555Thr,ENST00000393561,;LAMB1,missense_variant,p.Met1531Thr,ENST00000222399,;LAMB1,non_coding_transcript_exon_variant,,ENST00000474380,;LAMB1,downstream_gene_variant,,ENST00000468518,;LAMB1,non_coding_transcript_exon_variant,,ENST00000472714,;DLD,intron_variant,,ENST00000417551,;	G	ENSG00000091136	ENST00000222399	Transcript	missense_variant	4823	4592	1531	M/T	aTg/aCg	.	.	.	-1	LAMB1	HGNC	6486	protein_coding	YES	CCDS5750.1	ENSP00000222399	LAMB1_HUMAN	Q75MC8_HUMAN,E9PCS6_HUMAN	UPI00001AE63F	.	deleterious(0)	possibly_damaging(0.722)	30/34	.	hmmpanther:PTHR10574:SF233,hmmpanther:PTHR10574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCATTTTC	.	5	ESCA
IQUB	0	.	GRCh37	7	123150076	123150076	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.411T>C	p.%3D	p.L137L	ENST00000466202	3/13	122	85	37	140	140	0	IQUB,synonymous_variant,p.%3D,ENST00000324698,;IQUB,synonymous_variant,p.%3D,ENST00000466202,;IQUB,synonymous_variant,p.%3D,ENST00000434450,;IQUB,intron_variant,,ENST00000488987,;IQUB,synonymous_variant,p.%3D,ENST00000484508,;IQUB,synonymous_variant,p.%3D,ENST00000469057,;IQUB,non_coding_transcript_exon_variant,,ENST00000483567,;	G	ENSG00000164675	ENST00000466202	Transcript	synonymous_variant	988	411	137	L	ctT/ctC	.	.	.	-1	IQUB	HGNC	21995	protein_coding	YES	CCDS5787.1	ENSP00000417769	IQUB_HUMAN	.	UPI000013E3DF	.	.	.	3/13	.	PROSITE_profiles:PS50053,hmmpanther:PTHR21074:SF0,hmmpanther:PTHR21074,Gene3D:3.10.20.90,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAATAAGTAC	.	5	ESCA
SEMA3A	0	.	GRCh37	7	83634710	83634710	+	Silent	SNP	G	G	C	rs771477479	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1305C>G	p.%3D	p.V435V	ENST00000265362	11/17	113	76	37	79	79	0	SEMA3A,synonymous_variant,p.%3D,ENST00000265362,;SEMA3A,synonymous_variant,p.%3D,ENST00000436949,;	C	ENSG00000075213	ENST00000265362	Transcript	synonymous_variant	1620	1305	435	V	gtC/gtG	rs771477479	.	.	-1	SEMA3A	HGNC	10723	protein_coding	YES	CCDS5599.1	ENSP00000265362	SEM3A_HUMAN	Q86UJ2_HUMAN,Q75MQ2_HUMAN,C9JD25_HUMAN,C9J9C4_HUMAN	UPI0000135A60	.	.	.	11/17	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF23,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTACGACAAT	.	5	ESCA
ZNF804B	0	.	GRCh37	7	88963404	88963404	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1108C>A	p.Pro370Thr	p.P370T	ENST00000333190	4/4	63	57	6	36	36	0	ZNF804B,missense_variant,p.Pro370Thr,ENST00000333190,;	A	ENSG00000182348	ENST00000333190	Transcript	missense_variant	1717	1108	370	P/T	Cca/Aca	COSM341504	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	tolerated(0.39)	benign(0.017)	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCCACCAAAC	.	3	ESCA
AKAP9	0	.	GRCh37	7	91714250	91714250	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8828T>A	p.Ile2943Lys	p.I2943K	ENST00000356239	35/50	97	62	34	28	28	0	AKAP9,missense_variant,p.Ile2943Lys,ENST00000356239,;AKAP9,missense_variant,p.Ile2947Lys,ENST00000359028,;AKAP9,missense_variant,p.Ile88Lys,ENST00000435423,;AKAP9,missense_variant,p.Ile789Lys,ENST00000394534,;AKAP9,intron_variant,,ENST00000358100,;	A	ENSG00000127914	ENST00000356239	Transcript	missense_variant	9061	8828	2943	I/K	aTa/aAa	.	.	.	1	AKAP9	HGNC	379	protein_coding	YES	CCDS5622.1	ENSP00000348573	AKAP9_HUMAN	Q8IW64_HUMAN	UPI000002A38D	.	.	probably_damaging(0.999)	35/50	.	hmmpanther:PTHR18932:SF10,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAATAAAGG	.	5	ESCA
KPNA7	0	.	GRCh37	7	98805040	98805040	+	Missense_Mutation	SNP	C	C	T	rs746388880	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50G>A	p.Arg17Gln	p.R17Q	ENST00000327442	1/10	228	206	22	51	51	0	KPNA7,missense_variant,p.Arg17Gln,ENST00000327442,;	T	ENSG00000185467	ENST00000327442	Transcript	missense_variant	90	50	17	R/Q	cGa/cAa	rs746388880,COSM3735896	.	.	-1	KPNA7	HGNC	21839	protein_coding	YES	CCDS47651.1	ENSP00000330878	IMA8_HUMAN	.	UPI00004193B5	.	deleterious(0.03)	probably_damaging(0.921)	1/10	.	PROSITE_profiles:PS51214,hmmpanther:PTHR23316:SF11,hmmpanther:PTHR23316,Gene3D:1.25.10.10,Pfam_domain:PF01749,PIRSF_domain:PIRSF005673,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCTCGGTAC	.	4	ESCA
PABPC1	0	.	GRCh37	8	101734271	101734271	+	5'UTR	SNP	G	G	C	rs531848744	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-460C>G	.	.	ENST00000318607	1/15	31	23	7	44	44	0	PABPC1,5_prime_UTR_variant,,ENST00000520142,;PABPC1,5_prime_UTR_variant,,ENST00000519004,;PABPC1,5_prime_UTR_variant,,ENST00000318607,;PABPC1,intron_variant,,ENST00000521067,;PABPC1,intron_variant,,ENST00000522720,;PABPC1,intron_variant,,ENST00000519363,;PABPC1,intron_variant,,ENST00000521865,;PABPC1,intron_variant,,ENST00000520804,;PABPC1,upstream_gene_variant,,ENST00000519100,;PABPC1,upstream_gene_variant,,ENST00000522387,;PABPC1,upstream_gene_variant,,ENST00000523555,;PABPC1,upstream_gene_variant,,ENST00000518196,;PABPC1,upstream_gene_variant,,ENST00000517921,;	C	ENSG00000070756	ENST00000318607	Transcript	5_prime_UTR_variant	670	.	.	.	.	rs531848744	.	.	-1	PABPC1	HGNC	8554	protein_coding	YES	CCDS6289.1	ENSP00000313007	PABP1_HUMAN	H0YB75_HUMAN,E7EQV3_HUMAN,E5RJM8_HUMAN,E5RJB9_HUMAN,E5RHG7_HUMAN,E5RH24_HUMAN,E5RGH3_HUMAN,E5RGC4_HUMAN,E5RFD8_HUMAN	UPI0000000BC4	.	.	.	1/15	.	.	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCGGAGCAC	by1000G	5	ESCA
SGCZ	0	.	GRCh37	8	14412433	14412433	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42G>C	p.Met14Ile	p.M14I	ENST00000382080	2/8	67	53	14	62	62	0	SGCZ,start_lost,p.Met1?,ENST00000421524,;SGCZ,missense_variant,p.Met14Ile,ENST00000382080,;	G	ENSG00000185053	ENST00000382080	Transcript	missense_variant	758	42	14	M/I	atG/atC	.	.	.	-1	SGCZ	HGNC	14075	protein_coding	YES	CCDS5992.2	ENSP00000371512	SGCZ_HUMAN	.	UPI00002339F6	.	tolerated(0.13)	benign(0.005)	2/8	.	hmmpanther:PTHR12939,hmmpanther:PTHR12939:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGTCATCTG	.	5	ESCA
TUBBP1	0	.	GRCh37	8	30210335	30210335	+	RNA	SNP	C	C	T	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.947C>T	.	.	ENST00000518096	1/1	64	45	19	67	66	1	TUBBP1,non_coding_transcript_exon_variant,,ENST00000518096,;TUBBP1,non_coding_transcript_exon_variant,,ENST00000248151,;CTD-3107M8.2,upstream_gene_variant,,ENST00000519658,;	T	ENSG00000127589	ENST00000518096	Transcript	non_coding_transcript_exon_variant	947	.	.	.	.	.	.	.	1	TUBBP1	HGNC	12414	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTGCCCCTC	.	5	ESCA
KAT6A	0	.	GRCh37	8	41836223	41836223	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.980T>C	p.Ile327Thr	p.I327T	ENST00000396930	7/18	108	86	22	67	67	0	KAT6A,missense_variant,p.Ile327Thr,ENST00000396930,;KAT6A,missense_variant,p.Ile327Thr,ENST00000406337,;KAT6A,missense_variant,p.Ile327Thr,ENST00000485568,;KAT6A,missense_variant,p.Ile327Thr,ENST00000265713,;KAT6A,upstream_gene_variant,,ENST00000463961,;KAT6A,upstream_gene_variant,,ENST00000470574,;	G	ENSG00000083168	ENST00000396930	Transcript	missense_variant	1524	980	327	I/T	aTa/aCa	.	.	.	-1	KAT6A	HGNC	13013	protein_coding	YES	CCDS6124.1	ENSP00000380136	KAT6A_HUMAN	A5PKX7_HUMAN	UPI000013D666	.	.	probably_damaging(0.968)	7/18	.	hmmpanther:PTHR10615:SF26,hmmpanther:PTHR10615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTATCTGT	.	5	ESCA
SGK3	0	.	GRCh37	8	67716673	67716673	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244T>A	p.Phe82Ile	p.F82I	ENST00000396596	4/17	198	154	44	185	185	0	SGK3,missense_variant,p.Phe82Ile,ENST00000522398,;SGK3,missense_variant,p.Phe82Ile,ENST00000522629,;SGK3,missense_variant,p.Phe15Ile,ENST00000521960,;C8orf44-SGK3,missense_variant,p.Phe82Ile,ENST00000519289,;SGK3,missense_variant,p.Phe82Ile,ENST00000521198,;SGK3,missense_variant,p.Phe82Ile,ENST00000520976,;SGK3,missense_variant,p.Phe82Ile,ENST00000345714,;SGK3,missense_variant,p.Phe82Ile,ENST00000518388,;SGK3,missense_variant,p.Phe15Ile,ENST00000521152,;SGK3,missense_variant,p.Phe82Ile,ENST00000396596,;SGK3,5_prime_UTR_variant,,ENST00000519396,;SGK3,non_coding_transcript_exon_variant,,ENST00000523401,;	A	ENSG00000104205	ENST00000396596	Transcript	missense_variant	458	244	82	F/I	Ttt/Att	.	.	.	1	SGK3	HGNC	10812	protein_coding	YES	CCDS6195.1	ENSP00000379842	SGK3_HUMAN	Q6FHV7_HUMAN,E5RK28_HUMAN,E5RJV7_HUMAN,E5RHR8_HUMAN	UPI000013591F	.	deleterious(0.01)	probably_damaging(0.999)	4/17	.	PROSITE_profiles:PS50195,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF121,Pfam_domain:PF00787,Gene3D:3.30.1520.10,SMART_domains:SM00312,Superfamily_domains:SSF64268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAATTTTGAT	.	5	ESCA
PKIA	0	.	GRCh37	8	79514046	79514046	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221C>A	p.Ser74Tyr	p.S74Y	ENST00000396418	4/4	78	63	15	92	92	0	PKIA,missense_variant,p.Ser74Tyr,ENST00000396418,;PKIA,missense_variant,p.Ser74Tyr,ENST00000518467,;PKIA,missense_variant,p.Ser74Tyr,ENST00000352966,;RP11-594N15.3,upstream_gene_variant,,ENST00000565862,;	A	ENSG00000171033	ENST00000396418	Transcript	missense_variant	707	221	74	S/Y	tCt/tAt	COSM3925618	.	.	1	PKIA	HGNC	9017	protein_coding	YES	CCDS6222.1	ENSP00000379696	IPKA_HUMAN	.	UPI0000000298	.	deleterious(0.03)	benign(0.14)	4/4	.	hmmpanther:PTHR15416:SF2,hmmpanther:PTHR15416,Pfam_domain:PF02827,PIRSF_domain:PIRSF001667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCTGAAA	.	5	ESCA
TMEM64	0	.	GRCh37	8	91636035	91636035	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1864G>C	.	.	ENST00000458549	3/3	28	20	8	34	34	0	TMEM64,3_prime_UTR_variant,,ENST00000418210,;TMEM64,3_prime_UTR_variant,,ENST00000458549,;TMEM64,downstream_gene_variant,,ENST00000519519,;TMEM64,downstream_gene_variant,,ENST00000422900,;AB015752.3,upstream_gene_variant,,ENST00000521975,;	G	ENSG00000180694	ENST00000458549	Transcript	3_prime_UTR_variant	3185	.	.	.	.	.	.	.	-1	TMEM64	HGNC	25441	protein_coding	YES	CCDS34920.2	ENSP00000414786	TMM64_HUMAN	B3KW24_HUMAN	UPI0000DBEF28	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAACTAACC	.	5	ESCA
IL1RAPL2	0	.	GRCh37	X	105011645	105011645	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2052T>G	p.Asp684Glu	p.D684E	ENST00000372582	11/11	13	7	5	10	10	0	IL1RAPL2,missense_variant,p.Asp684Glu,ENST00000344799,;IL1RAPL2,missense_variant,p.Asp684Glu,ENST00000372582,;IL1RAPL2,downstream_gene_variant,,ENST00000485671,;	G	ENSG00000189108	ENST00000372582	Transcript	missense_variant	2808	2052	684	D/E	gaT/gaG	.	.	.	1	IL1RAPL2	HGNC	5997	protein_coding	YES	CCDS14517.1	ENSP00000361663	IRPL2_HUMAN	.	UPI0000073DF7	.	tolerated_low_confidence(0.69)	probably_damaging(0.991)	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AGTGATATTTG	.	4	ESCA
RBMX2	0	.	GRCh37	X	129536265	129536265	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42T>C	p.%3D	p.N14N	ENST00000305536	2/6	37	23	14	66	66	0	RBMX2,synonymous_variant,p.%3D,ENST00000370947,;RBMX2,synonymous_variant,p.%3D,ENST00000305536,;RBMX2,non_coding_transcript_exon_variant,,ENST00000469953,;	C	ENSG00000134597	ENST00000305536	Transcript	synonymous_variant	106	42	14	N	aaT/aaC	.	.	.	1	RBMX2	HGNC	24282	protein_coding	YES	CCDS43993.1	ENSP00000339090	RBMX2_HUMAN	Q5JY83_HUMAN	UPI00000704DB	.	.	.	2/6	.	hmmpanther:PTHR23139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAATGAACG	.	5	ESCA
SLITRK2	0	.	GRCh37	X	144907135	144907135	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*654G>C	.	.	ENST00000370490	1/1	74	56	17	95	95	0	SLITRK2,3_prime_UTR_variant,,ENST00000370490,;SLITRK2,3_prime_UTR_variant,,ENST00000434188,;SLITRK2,3_prime_UTR_variant,,ENST00000428560,;SLITRK2,3_prime_UTR_variant,,ENST00000413937,;SLITRK2,3_prime_UTR_variant,,ENST00000447897,;TMEM257,upstream_gene_variant,,ENST00000408967,;SLITRK2,downstream_gene_variant,,ENST00000335565,;	C	ENSG00000185985	ENST00000370490	Transcript	3_prime_UTR_variant	7447	.	.	.	.	.	.	.	1	SLITRK2	HGNC	13449	protein_coding	YES	CCDS14680.1	ENSP00000359521	SLIK2_HUMAN	B3KTY4_HUMAN	UPI000004E64B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGTGTCAGC	.	5	ESCA
PRICKLE3	0	.	GRCh37	X	49033352	49033352	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88S-01A-11D-A36J-09	TCGA-L5-A88S-11A-21D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1155C>T	p.%3D	p.G385G	ENST00000376317	8/9	44	16	28	41	41	0	PRICKLE3,synonymous_variant,p.%3D,ENST00000453382,;PRICKLE3,synonymous_variant,p.%3D,ENST00000536904,;PRICKLE3,synonymous_variant,p.%3D,ENST00000540849,;PRICKLE3,synonymous_variant,p.%3D,ENST00000376317,;PRICKLE3,intron_variant,,ENST00000538114,;PLP2,downstream_gene_variant,,ENST00000376327,;PRICKLE3,downstream_gene_variant,,ENST00000376310,;PRICKLE3,downstream_gene_variant,,ENST00000432913,;PLP2,downstream_gene_variant,,ENST00000376322,;	A	ENSG00000012211	ENST00000376317	Transcript	synonymous_variant	1250	1155	385	G	ggC/ggT	.	.	.	-1	PRICKLE3	HGNC	6645	protein_coding	YES	CCDS14320.1	ENSP00000365494	PRIC3_HUMAN	F5H4N2_HUMAN	UPI000004B120	.	.	.	8/9	.	hmmpanther:PTHR24218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGGCCGGC	.	5	ESCA
SORCS3	0	.	GRCh37	10	106907465	106907465	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1393G>A	p.Asp465Asn	p.D465N	ENST00000369701	9/27	106	69	37	135	135	0	SORCS3,missense_variant,p.Asp465Asn,ENST00000369701,;	A	ENSG00000156395	ENST00000369701	Transcript	missense_variant	1620	1393	465	D/N	Gac/Aac	.	.	.	1	SORCS3	HGNC	16699	protein_coding	YES	CCDS7558.1	ENSP00000358715	SORC3_HUMAN	B7Z891_HUMAN	UPI0000135CE1	.	deleterious(0)	benign(0.356)	9/27	.	hmmpanther:PTHR12106:SF10,hmmpanther:PTHR12106,Gene3D:2.130.10.140,SMART_domains:SM00602,Superfamily_domains:SSF110296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCAGACACG	.	5	ESCA
ITIH2	0	.	GRCh37	10	7780587	7780587	+	Frame_Shift_Del	DEL	C	C	-	rs184798502	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1963delC	p.Leu655CysfsTer23	p.L655Cfs*23	ENST00000358415	16/21	113	78	35	64	64	0	ITIH2,frameshift_variant,p.Leu644CysfsTer23,ENST00000379587,;ITIH2,frameshift_variant,p.Leu655CysfsTer23,ENST00000358415,;	-	ENSG00000151655	ENST00000358415	Transcript	frameshift_variant	2127	1961	654	A/X	gCc/gc	rs184798502	.	.	1	ITIH2	HGNC	6167	protein_coding	YES	CCDS31141.1	ENSP00000351190	ITIH2_HUMAN	.	UPI000036665E	.	.	.	16/21	.	hmmpanther:PTHR10338:SF14,hmmpanther:PTHR10338	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGGGCCCTGT	byCluster|by1000G	3	ESCA
ZCCHC24	0	.	GRCh37	10	81145972	81145972	+	3'UTR	SNP	C	C	T	rs757455894	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*129G>A	.	.	ENST00000372336	4/4	15	8	7	9	9	0	ZCCHC24,missense_variant,p.Gly226Arg,ENST00000372333,;ZCCHC24,3_prime_UTR_variant,,ENST00000372336,;RP11-342M3.5,intron_variant,,ENST00000438554,;	T	ENSG00000165424	ENST00000372336	Transcript	3_prime_UTR_variant	1042	.	.	.	.	rs757455894	.	.	-1	ZCCHC24	HGNC	26911	protein_coding	YES	CCDS7359.1	ENSP00000361411	ZCH24_HUMAN	.	UPI000006F100	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCCCCGGCCC	byFrequency	3	ESCA
TMEM254	0	.	GRCh37	10	81841630	81841630	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.121C>G	p.Gln41Glu	p.Q41E	ENST00000372281	2/4	40	22	17	53	53	0	TMEM254,missense_variant,p.Gln19Glu,ENST00000450179,;TMEM254,missense_variant,p.Gln41Glu,ENST00000372277,;TMEM254,missense_variant,p.Gln41Glu,ENST00000372274,;TMEM254,missense_variant,p.Gln41Glu,ENST00000372275,;TMEM254,missense_variant,p.Gln62Glu,ENST00000372273,;TMEM254,missense_variant,p.Gln41Glu,ENST00000372281,;TMEM254-AS1,upstream_gene_variant,,ENST00000432070,;TMEM254-AS1,upstream_gene_variant,,ENST00000448729,;TMEM254-AS1,upstream_gene_variant,,ENST00000412298,;TMEM254,non_coding_transcript_exon_variant,,ENST00000472622,;TMEM254,non_coding_transcript_exon_variant,,ENST00000476173,;TMEM254,non_coding_transcript_exon_variant,,ENST00000463209,;TMEM254,non_coding_transcript_exon_variant,,ENST00000467529,;TMEM254,non_coding_transcript_exon_variant,,ENST00000483732,;TMEM254,non_coding_transcript_exon_variant,,ENST00000463029,;	G	ENSG00000133678	ENST00000372281	Transcript	missense_variant	151	121	41	Q/E	Cag/Gag	.	.	.	1	TMEM254	HGNC	25804	protein_coding	YES	CCDS7363.1	ENSP00000361355	TM254_HUMAN	.	UPI0000072C96	.	tolerated(0.33)	benign(0.137)	2/4	.	Pfam_domain:PF14934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTATCAGAAC	.	5	ESCA
KIF20B	0	.	GRCh37	10	91528563	91528563	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5040C>A	p.Asn1680Lys	p.N1680K	ENST00000260753	31/33	94	64	30	89	89	0	KIF20B,missense_variant,p.Asn1720Lys,ENST00000371728,;KIF20B,missense_variant,p.Asn1750Lys,ENST00000416354,;KIF20B,missense_variant,p.Asn1680Lys,ENST00000260753,;KIF20B,downstream_gene_variant,,ENST00000394289,;KIF20B,non_coding_transcript_exon_variant,,ENST00000478929,;	A	ENSG00000138182	ENST00000260753	Transcript	missense_variant	5112	5040	1680	N/K	aaC/aaA	.	.	.	1	KIF20B	HGNC	7212	protein_coding	YES	CCDS7407.1	ENSP00000260753	KI20B_HUMAN	.	UPI00001F9377	.	tolerated(0.91)	benign(0.331)	31/33	.	hmmpanther:PTHR23165	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAACCTGGC	.	5	ESCA
KBTBD3	0	.	GRCh37	11	105929763	105929763	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.62C>G	p.Pro21Arg	p.P21R	ENST00000526793	2/3	66	47	19	78	78	0	KBTBD3,missense_variant,p.Pro21Arg,ENST00000531482,;KBTBD3,missense_variant,p.Pro21Arg,ENST00000531837,;KBTBD3,missense_variant,p.Pro21Arg,ENST00000526793,;KBTBD3,intron_variant,,ENST00000532662,;KBTBD3,intron_variant,,ENST00000534815,;KBTBD3,non_coding_transcript_exon_variant,,ENST00000528483,;	C	ENSG00000182359	ENST00000526793	Transcript	missense_variant	222	62	21	P/R	cCa/cGa	.	.	.	-1	KBTBD3	HGNC	22934	protein_coding	YES	CCDS8334.1	ENSP00000436262	KBTB3_HUMAN	G3V161_HUMAN,E9PKJ3_HUMAN	UPI00001BDB79	.	deleterious_low_confidence(0)	benign(0.063)	2/3	.	PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATGGAATT	.	5	ESCA
BCL9L	0	.	GRCh37	11	118773129	118773129	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1323G>A	p.%3D	p.G441G	ENST00000334801	6/8	13	8	5	12	12	0	BCL9L,synonymous_variant,p.%3D,ENST00000334801,;CXCR5,downstream_gene_variant,,ENST00000292174,;BCL9L,non_coding_transcript_exon_variant,,ENST00000526143,;BCL9L,intron_variant,,ENST00000526514,;BCL9L,intron_variant,,ENST00000530293,;BCL9L,downstream_gene_variant,,ENST00000527266,;	T	ENSG00000186174	ENST00000334801	Transcript	synonymous_variant	2288	1323	441	G	ggG/ggA	.	.	.	-1	BCL9L	HGNC	23688	protein_coding	YES	CCDS8403.1	ENSP00000335320	BCL9L_HUMAN	E9PNR0_HUMAN	UPI0000192102	.	.	.	6/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGCCCCCCTC	.	3	ESCA
USP47	0	.	GRCh37	11	11974404	11974404	+	Missense_Mutation	SNP	G	G	A	rs752493697	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3496G>A	p.Glu1166Lys	p.E1166K	ENST00000339865	24/27	137	81	56	152	152	0	USP47,missense_variant,p.Glu1234Lys,ENST00000527733,;USP47,missense_variant,p.Glu1166Lys,ENST00000339865,;USP47,missense_variant,p.Glu1254Lys,ENST00000399455,;USP47,missense_variant,p.Glu36Lys,ENST00000539466,;USP47,non_coding_transcript_exon_variant,,ENST00000305481,;USP47,downstream_gene_variant,,ENST00000530041,;USP47,non_coding_transcript_exon_variant,,ENST00000529813,;USP47,downstream_gene_variant,,ENST00000531513,;USP47,downstream_gene_variant,,ENST00000530369,;	A	ENSG00000170242	ENST00000339865	Transcript	missense_variant	4259	3496	1166	E/K	Gaa/Aaa	rs752493697	.	.	1	USP47	HGNC	20076	protein_coding	YES	CCDS41619.1	ENSP00000339957	UBP47_HUMAN	.	UPI00001F9D69	.	deleterious(0.02)	probably_damaging(0.922)	24/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACGAATTG	.	5	ESCA
OR8D2	0	.	GRCh37	11	124189277	124189277	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817G>C	p.Val273Leu	p.V273L	ENST00000357438	1/1	82	48	33	77	77	0	OR8D2,missense_variant,p.Val273Leu,ENST00000357438,;	G	ENSG00000197263	ENST00000357438	Transcript	missense_variant	908	817	273	V/L	Gtg/Ctg	.	.	.	-1	OR8D2	HGNC	8482	protein_coding	YES	CCDS31707.1	ENSP00000350022	OR8D2_HUMAN	.	UPI0000041D8E	.	deleterious(0.02)	benign(0.377)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF278,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGACACCTTCT	.	3	ESCA
SLC37A2	0	.	GRCh37	11	124958032	124958032	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*47G>C	.	.	ENST00000308074	19/19	47	34	13	67	67	0	SLC37A2,3_prime_UTR_variant,,ENST00000308074,;SLC37A2,3_prime_UTR_variant,,ENST00000403796,;SLC37A2,3_prime_UTR_variant,,ENST00000298280,;SLC37A2,downstream_gene_variant,,ENST00000407458,;SLC37A2,downstream_gene_variant,,ENST00000525837,;SLC37A2,non_coding_transcript_exon_variant,,ENST00000526405,;AP001007.1,upstream_gene_variant,,ENST00000354617,;	C	ENSG00000134955	ENST00000308074	Transcript	3_prime_UTR_variant	1597	.	.	.	.	.	.	.	1	SLC37A2	HGNC	20644	protein_coding	YES	CCDS31714.1	ENSP00000311833	SPX2_HUMAN	E9PRJ4_HUMAN,B7Z480_HUMAN	UPI000019AB60	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAGGCCCCA	.	5	ESCA
LGR4	0	.	GRCh37	11	27389347	27389347	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67C>T	.	.	ENST00000379214	18/18	59	41	17	90	90	0	LGR4,3_prime_UTR_variant,,ENST00000389858,;LGR4,3_prime_UTR_variant,,ENST00000379214,;CCDC34,upstream_gene_variant,,ENST00000328697,;CCDC34,upstream_gene_variant,,ENST00000317945,;	A	ENSG00000205213	ENST00000379214	Transcript	3_prime_UTR_variant	3367	.	.	.	.	.	.	.	-1	LGR4	HGNC	13299	protein_coding	YES	CCDS31449.1	ENSP00000368516	LGR4_HUMAN	Q59ER8_HUMAN	UPI00000373E7	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATGAGAAT	.	5	ESCA
FBXO3	0	.	GRCh37	11	33763561	33763561	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1309G>C	p.Asp437His	p.D437H	ENST00000265651	11/11	27	16	11	34	34	0	FBXO3,missense_variant,p.Asp124His,ENST00000532057,;FBXO3,missense_variant,p.Asp324His,ENST00000526785,;FBXO3,missense_variant,p.Asp437His,ENST00000265651,;FBXO3,missense_variant,p.Asp124His,ENST00000531080,;FBXO3,3_prime_UTR_variant,,ENST00000530401,;FBXO3,downstream_gene_variant,,ENST00000448981,;FBXO3,downstream_gene_variant,,ENST00000534136,;FBXO3,downstream_gene_variant,,ENST00000527772,;FBXO3,non_coding_transcript_exon_variant,,ENST00000530013,;	G	ENSG00000110429	ENST00000265651	Transcript	missense_variant	1328	1309	437	D/H	Gat/Cat	.	.	.	-1	FBXO3	HGNC	13582	protein_coding	YES	CCDS7887.1	ENSP00000265651	FBX3_HUMAN	Q49AF1_HUMAN,G3V1E0_HUMAN	UPI000000DB30	.	tolerated_low_confidence(0.54)	unknown(0)	11/11	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14289:SF15,hmmpanther:PTHR14289	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATCATCCT	.	5	ESCA
C11orf74	0	.	GRCh37	11	36669570	36669570	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363G>T	p.Leu121Phe	p.L121F	ENST00000532470	6/7	98	71	27	90	90	0	C11orf74,missense_variant,p.Leu47Phe,ENST00000347206,;C11orf74,missense_variant,p.Leu47Phe,ENST00000534635,;C11orf74,missense_variant,p.Leu47Phe,ENST00000527108,;C11orf74,missense_variant,p.Leu121Phe,ENST00000531554,;C11orf74,missense_variant,p.Leu121Phe,ENST00000532470,;C11orf74,missense_variant,p.Leu121Phe,ENST00000446510,;C11orf74,missense_variant,p.Leu121Phe,ENST00000334307,;C11orf74,missense_variant,p.Cys99Phe,ENST00000528092,;C11orf74,non_coding_transcript_exon_variant,,ENST00000524539,;	T	ENSG00000166352	ENST00000532470	Transcript	missense_variant	539	363	121	L/F	ttG/ttT	.	.	.	1	C11orf74	HGNC	25142	protein_coding	YES	CCDS7904.1	ENSP00000431374	CK074_HUMAN	E9PPH4_HUMAN,E9PL16_HUMAN	UPI000018D54E	.	tolerated(0.29)	benign(0.072)	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTGCTGCT	.	5	ESCA
PSMC3	0	.	GRCh37	11	47444219	47444219	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.790G>T	p.Gly264Cys	p.G264C	ENST00000298852	8/12	69	41	28	74	74	0	PSMC3,missense_variant,p.Gly229Cys,ENST00000531051,;PSMC3,missense_variant,p.Gly225Cys,ENST00000524447,;PSMC3,missense_variant,p.Gly248Cys,ENST00000602866,;PSMC3,missense_variant,p.Gly264Cys,ENST00000298852,;PSMC3,missense_variant,p.Gly271Cys,ENST00000530651,;PSMC3,missense_variant,p.Gly222Cys,ENST00000530912,;PSMC3,downstream_gene_variant,,ENST00000526993,;PSMC3,3_prime_UTR_variant,,ENST00000530887,;PSMC3,downstream_gene_variant,,ENST00000528362,;PSMC3,downstream_gene_variant,,ENST00000527906,;PSMC3,downstream_gene_variant,,ENST00000529500,;PSMC3,downstream_gene_variant,,ENST00000531653,;	A	ENSG00000165916	ENST00000298852	Transcript	missense_variant	948	790	264	G/C	Ggt/Tgt	COSM4033185	.	.	-1	PSMC3	HGNC	9549	protein_coding	YES	CCDS7935.1	ENSP00000298852	PRS6A_HUMAN	R4GNH3_HUMAN	UPI0000132389	.	deleterious(0)	probably_damaging(1)	8/12	.	hmmpanther:PTHR23073,hmmpanther:PTHR23073:SF7,TIGRFAM_domain:TIGR01242,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCACCATCTC	.	5	ESCA
OR5AS1	0	.	GRCh37	11	55798042	55798042	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148A>G	p.Asn50Asp	p.N50D	ENST00000313555	1/1	72	48	23	78	78	0	OR5AS1,missense_variant,p.Asn50Asp,ENST00000313555,;	G	ENSG00000181785	ENST00000313555	Transcript	missense_variant	148	148	50	N/D	Aat/Gat	.	.	.	1	OR5AS1	HGNC	15261	protein_coding	YES	CCDS31516.1	ENSP00000324111	O5AS1_HUMAN	.	UPI000004B1FB	.	tolerated(0.18)	benign(0.081)	1/1	.	Low_complexity_(Seg):seg,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF153,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTTAATATT	.	5	ESCA
HPX	0	.	GRCh37	11	6459607	6459607	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.469G>A	p.Glu157Lys	p.E157K	ENST00000265983	5/10	84	56	28	95	94	0	HPX,missense_variant,p.Glu157Lys,ENST00000265983,;HPX,non_coding_transcript_exon_variant,,ENST00000525057,;HPX,intron_variant,,ENST00000533561,;HPX,downstream_gene_variant,,ENST00000527105,;HPX,upstream_gene_variant,,ENST00000534429,;HPX,downstream_gene_variant,,ENST00000534800,;HPX,non_coding_transcript_exon_variant,,ENST00000533369,;HPX,upstream_gene_variant,,ENST00000529775,;HPX,downstream_gene_variant,,ENST00000533856,;HPX,upstream_gene_variant,,ENST00000527556,;HPX,downstream_gene_variant,,ENST00000528348,;	T	ENSG00000110169	ENST00000265983	Transcript	missense_variant	570	469	157	E/K	Gaa/Aaa	.	.	.	-1	HPX	HGNC	5171	protein_coding	YES	CCDS7763.1	ENSP00000265983	HEMO_HUMAN	.	UPI000012C5AF	.	deleterious(0.01)	benign(0.404)	5/10	.	Superfamily_domains:SSF50923,PIRSF_domain:PIRSF002551,Gene3D:2.110.10.10,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF136,PROSITE_profiles:PS51642	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCAGCTT	.	5	ESCA
NAALADL1	0	.	GRCh37	11	64815123	64815123	+	Missense_Mutation	SNP	G	G	A	rs202090288	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1504C>T	p.Pro502Ser	p.P502S	ENST00000358658	12/18	55	36	18	51	51	0	NAALADL1,missense_variant,p.Pro502Ser,ENST00000339885,;NAALADL1,missense_variant,p.Pro502Ser,ENST00000355369,;NAALADL1,missense_variant,p.Pro553Ser,ENST00000340252,;NAALADL1,missense_variant,p.Pro467Ser,ENST00000356632,;NAALADL1,missense_variant,p.Pro502Ser,ENST00000358658,;NAALADL1,missense_variant,p.Pro461Ser,ENST00000355721,;NAALADL1,5_prime_UTR_variant,,ENST00000526516,;NAALADL1,5_prime_UTR_variant,,ENST00000532802,;NAALADL1,5_prime_UTR_variant,,ENST00000533340,;NAALADL1,5_prime_UTR_variant,,ENST00000526799,;NAALADL1,5_prime_UTR_variant,,ENST00000530995,;NAALADL1,5_prime_UTR_variant,,ENST00000533842,;NAALADL1,5_prime_UTR_variant,,ENST00000528884,;NAALADL1,5_prime_UTR_variant,,ENST00000530139,;SAC3D1,downstream_gene_variant,,ENST00000531072,;SAC3D1,downstream_gene_variant,,ENST00000398846,;SAC3D1,downstream_gene_variant,,ENST00000529996,;NAALADL1,upstream_gene_variant,,ENST00000533753,;RN7SL114P,downstream_gene_variant,,ENST00000582042,;SAC3D1,downstream_gene_variant,,ENST00000533017,;SAC3D1,downstream_gene_variant,,ENST00000530213,;SAC3D1,downstream_gene_variant,,ENST00000528109,;NAALADL1,missense_variant,p.Pro28Ser,ENST00000532450,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000528977,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000529685,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000524445,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000531746,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000531174,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000529274,;NAALADL1,upstream_gene_variant,,ENST00000534568,;NAALADL1,downstream_gene_variant,,ENST00000532432,;	A	ENSG00000168060	ENST00000358658	Transcript	missense_variant	1532	1504	502	P/S	Ccc/Tcc	rs202090288	.	.	-1	NAALADL1	HGNC	23536	protein_coding	YES	CCDS31604.1	ENSP00000351484	NALDL_HUMAN	E9PRC7_HUMAN,E9PLR8_HUMAN,E9PKW7_HUMAN,E9PKG8_HUMAN,E9PJQ1_HUMAN,E9PIU1_HUMAN,E9PII9_HUMAN	UPI000013E761	.	deleterious(0)	possibly_damaging(0.612)	12/18	.	hmmpanther:PTHR10404:SF40,hmmpanther:PTHR10404,Gene3D:3.40.630.10,Pfam_domain:PF04389,Superfamily_domains:SSF53187	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGGGACCA	byCluster|by1000G	5	ESCA
LTBP3	0	.	GRCh37	11	65315164	65315164	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1975G>A	p.Val659Met	p.V659M	ENST00000301873	13/28	75	44	31	67	67	0	LTBP3,missense_variant,p.Val310Met,ENST00000526927,;LTBP3,missense_variant,p.Val659Met,ENST00000301873,;LTBP3,missense_variant,p.Val570Met,ENST00000530866,;LTBP3,missense_variant,p.Val659Met,ENST00000322147,;LTBP3,missense_variant,p.Val285Met,ENST00000536982,;LTBP3,missense_variant,p.Val89Met,ENST00000532932,;LTBP3,upstream_gene_variant,,ENST00000527339,;LTBP3,upstream_gene_variant,,ENST00000530785,;LTBP3,downstream_gene_variant,,ENST00000530426,;LTBP3,upstream_gene_variant,,ENST00000529189,;LTBP3,3_prime_UTR_variant,,ENST00000528516,;LTBP3,downstream_gene_variant,,ENST00000524798,;LTBP3,downstream_gene_variant,,ENST00000526825,;LTBP3,downstream_gene_variant,,ENST00000527792,;LTBP3,upstream_gene_variant,,ENST00000525443,;LTBP3,downstream_gene_variant,,ENST00000529764,;LTBP3,downstream_gene_variant,,ENST00000528966,;	T	ENSG00000168056	ENST00000301873	Transcript	missense_variant	2244	1975	659	V/M	Gtg/Atg	.	.	.	-1	LTBP3	HGNC	6716	protein_coding	YES	CCDS44647.1	ENSP00000301873	LTBP3_HUMAN	Q9P0Z7_HUMAN,E9PR84_HUMAN,E9PKW1_HUMAN	UPI00003667EB	.	tolerated(0.05)	benign(0.085)	13/28	.	hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF35,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCACGCACG	.	5	ESCA
CAPN5	0	.	GRCh37	11	76804733	76804733	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.171C>G	p.Ile57Met	p.I57M	ENST00000278559	3/13	40	24	16	53	53	0	CAPN5,missense_variant,p.Ile57Met,ENST00000529629,;CAPN5,missense_variant,p.Ile97Met,ENST00000456580,;CAPN5,missense_variant,p.Ile57Met,ENST00000527066,;CAPN5,missense_variant,p.Ile57Met,ENST00000278559,;CAPN5,intron_variant,,ENST00000531028,;CAPN5,non_coding_transcript_exon_variant,,ENST00000533889,;	G	ENSG00000149260	ENST00000278559	Transcript	missense_variant	360	171	57	I/M	atC/atG	.	.	.	1	CAPN5	HGNC	1482	protein_coding	YES	CCDS8248.1	ENSP00000278559	CAN5_HUMAN	E9PS73_HUMAN	UPI0000126E9F	.	deleterious(0.01)	possibly_damaging(0.553)	3/13	.	Prints_domain:PR00704,Superfamily_domains:SSF54001,SMART_domains:SM00230,Pfam_domain:PF00648,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF138,PROSITE_profiles:PS50203	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCATCTGCGA	.	2	ESCA
PIDD	0	.	GRCh37	11	801462	801462	+	Missense_Mutation	SNP	G	G	C	rs771694039	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1465C>G	p.Arg489Gly	p.R489G	ENST00000347755	8/16	50	38	11	58	58	0	PIDD,missense_variant,p.Arg489Gly,ENST00000347755,;PIDD,missense_variant,p.Arg489Gly,ENST00000411829,;SLC25A22,upstream_gene_variant,,ENST00000532484,;SLC25A22,upstream_gene_variant,,ENST00000531214,;SLC25A22,upstream_gene_variant,,ENST00000531514,;SLC25A22,upstream_gene_variant,,ENST00000531437,;PIDD,non_coding_transcript_exon_variant,,ENST00000527812,;PIDD,downstream_gene_variant,,ENST00000528122,;PIDD,downstream_gene_variant,,ENST00000530911,;PIDD,downstream_gene_variant,,ENST00000534649,;PIDD,missense_variant,p.Arg206Gly,ENST00000531286,;PIDD,3_prime_UTR_variant,,ENST00000525028,;PIDD,3_prime_UTR_variant,,ENST00000524486,;PIDD,non_coding_transcript_exon_variant,,ENST00000534525,;PIDD,non_coding_transcript_exon_variant,,ENST00000527357,;SLC25A22,upstream_gene_variant,,ENST00000529351,;	C	ENSG00000177595	ENST00000347755	Transcript	missense_variant	1607	1465	489	R/G	Cgt/Ggt	rs771694039	.	.	-1	PIDD	HGNC	16491	protein_coding	YES	CCDS7716.1	ENSP00000337797	PIDD_HUMAN	.	UPI000045644A	.	deleterious(0.01)	possibly_damaging(0.842)	8/16	.	PROSITE_profiles:PS51145,Pfam_domain:PF00791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGACGAGGCT	byFrequency	5	ESCA
FAT3	0	.	GRCh37	11	92532140	92532140	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5961T>C	p.%3D	p.Y1987Y	ENST00000298047	9/27	61	40	20	89	89	0	FAT3,synonymous_variant,p.%3D,ENST00000298047,;FAT3,synonymous_variant,p.%3D,ENST00000409404,;FAT3,synonymous_variant,p.%3D,ENST00000525166,;	C	ENSG00000165323	ENST00000298047	Transcript	synonymous_variant	5978	5961	1987	Y	taT/taC	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	.	9/27	.	Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTCTATTCCAC	.	3	ESCA
FAT3	0	.	GRCh37	11	92532150	92532150	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5971A>G	p.Ile1991Val	p.I1991V	ENST00000298047	9/27	57	40	16	91	91	0	FAT3,missense_variant,p.Ile1991Val,ENST00000298047,;FAT3,missense_variant,p.Ile1991Val,ENST00000409404,;FAT3,missense_variant,p.Ile1841Val,ENST00000525166,;	G	ENSG00000165323	ENST00000298047	Transcript	missense_variant	5988	5971	1991	I/V	Atc/Gtc	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	probably_damaging(0.999)	9/27	.	Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCAATCTCA	.	3	ESCA
ANO4	0	.	GRCh37	12	101188629	101188629	+	5'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-317A>G	.	.	ENST00000392979	1/27	12	8	4	12	12	0	ANO4,5_prime_UTR_variant,,ENST00000546991,;ANO4,5_prime_UTR_variant,,ENST00000392979,;ANO4,intron_variant,,ENST00000538618,;ANO4,upstream_gene_variant,,ENST00000299222,;ANO4,upstream_gene_variant,,ENST00000392977,;ANO4,non_coding_transcript_exon_variant,,ENST00000551148,;ANO4,intron_variant,,ENST00000549155,;	G	ENSG00000151572	ENST00000392979	Transcript	5_prime_UTR_variant	45	.	.	.	.	.	.	.	1	ANO4	HGNC	23837	protein_coding	YES	CCDS31884.1	ENSP00000376705	ANO4_HUMAN	.	UPI0000198E2E	.	.	.	1/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCATACGGCC	.	3	ESCA
PARPBP	0	.	GRCh37	12	102591245	102591245	+	3'Flank	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000358383	.	59	36	22	60	60	0	PARPBP,3_prime_UTR_variant,,ENST00000378128,;PARPBP,3_prime_UTR_variant,,ENST00000327680,;PMCH,intron_variant,,ENST00000329406,;PARPBP,downstream_gene_variant,,ENST00000358383,;PARPBP,downstream_gene_variant,,ENST00000543784,;PARPBP,downstream_gene_variant,,ENST00000541394,;PARPBP,downstream_gene_variant,,ENST00000417507,;PARPBP,downstream_gene_variant,,ENST00000392911,;PARPBP,downstream_gene_variant,,ENST00000412715,;PARPBP,downstream_gene_variant,,ENST00000535811,;PARPBP,downstream_gene_variant,,ENST00000457614,;	T	ENSG00000185480	ENST00000358383	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	875	1	PARPBP	HGNC	26074	protein_coding	YES	CCDS9090.2	ENSP00000351153	PARI_HUMAN	.	UPI000004A06B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTGTAAGA	.	5	ESCA
TCTN1	0	.	GRCh37	12	111078278	111078278	+	Missense_Mutation	SNP	G	G	A	rs118057448	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934G>A	p.Val312Ile	p.V312I	ENST00000397659	8/15	89	62	27	110	109	1	TCTN1,missense_variant,p.Val134Ile,ENST00000377654,;TCTN1,missense_variant,p.Val298Ile,ENST00000397655,;TCTN1,missense_variant,p.Val312Ile,ENST00000397659,;TCTN1,missense_variant,p.Val312Ile,ENST00000551590,;HVCN1,intron_variant,,ENST00000548312,;TCTN1,upstream_gene_variant,,ENST00000549123,;TCTN1,non_coding_transcript_exon_variant,,ENST00000551555,;TCTN1,missense_variant,p.Val10Ile,ENST00000547461,;TCTN1,3_prime_UTR_variant,,ENST00000397656,;TCTN1,3_prime_UTR_variant,,ENST00000495659,;TCTN1,3_prime_UTR_variant,,ENST00000490514,;TCTN1,3_prime_UTR_variant,,ENST00000480648,;TCTN1,3_prime_UTR_variant,,ENST00000464809,;TCTN1,non_coding_transcript_exon_variant,,ENST00000463313,;TCTN1,non_coding_transcript_exon_variant,,ENST00000482281,;TCTN1,upstream_gene_variant,,ENST00000460357,;TCTN1,upstream_gene_variant,,ENST00000485445,;TCTN1,upstream_gene_variant,,ENST00000491068,;TCTN1,upstream_gene_variant,,ENST00000552038,;	A	ENSG00000204852	ENST00000397659	Transcript	missense_variant	953	934	312	V/I	Gtc/Atc	rs118057448,COSM1228804	.	.	1	TCTN1	HGNC	26113	protein_coding	YES	CCDS41834.1	ENSP00000380779	TECT1_HUMAN	.	UPI00006E225F	.	tolerated(0.28)	benign(0.008)	8/15	.	hmmpanther:PTHR14611:SF1,hmmpanther:PTHR14611,Pfam_domain:PF07773	A:0.0008	A:0.0008	A:0	.	A:0	A:0.003	A:0	A:0.0012	A:0.0005	uncertain_significance	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCGTCAAC	byFrequency|byCluster|by1000G	5	ESCA
GTF2H3	0	.	GRCh37	12	124144761	124144761	+	Missense_Mutation	SNP	G	G	T	rs755944714	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.906G>T	p.Lys302Asn	p.K302N	ENST00000543341	13/13	47	30	17	50	50	0	GTF2H3,missense_variant,p.Lys188Asn,ENST00000543154,;GTF2H3,missense_variant,p.Lys261Asn,ENST00000228955,;GTF2H3,missense_variant,p.Lys302Asn,ENST00000543341,;GTF2H3,downstream_gene_variant,,ENST00000538845,;GTF2H3,downstream_gene_variant,,ENST00000538533,;GTF2H3,downstream_gene_variant,,ENST00000536375,;GTF2H3,3_prime_UTR_variant,,ENST00000543415,;GTF2H3,non_coding_transcript_exon_variant,,ENST00000539429,;GTF2H3,downstream_gene_variant,,ENST00000542279,;	T	ENSG00000111358	ENST00000543341	Transcript	missense_variant	937	906	302	K/N	aaG/aaT	rs755944714	.	.	1	GTF2H3	HGNC	4657	protein_coding	YES	CCDS9252.1	ENSP00000445162	TF2H3_HUMAN	B4DNZ6_HUMAN	UPI00000622FE	.	deleterious(0)	unknown(0)	13/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12831:SF0,hmmpanther:PTHR12831	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAGAAACT	.	5	ESCA
NRIP2	0	.	GRCh37	12	2939666	2939666	+	Intron	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495+208T>C	.	.	ENST00000337508	.	9	6	3	12	12	0	ITFG2,3_prime_UTR_variant,,ENST00000542548,;NRIP2,intron_variant,,ENST00000542386,;NRIP2,intron_variant,,ENST00000542990,;NRIP2,intron_variant,,ENST00000337508,;ITFG2,non_coding_transcript_exon_variant,,ENST00000552005,;ITFG2,3_prime_UTR_variant,,ENST00000540929,;ITFG2,intron_variant,,ENST00000538822,;	G	ENSG00000053702	ENST00000337508	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NRIP2	HGNC	23078	protein_coding	YES	CCDS8514.1	ENSP00000337501	NRIP2_HUMAN	F5H2G5_HUMAN,F5H065_HUMAN,A2RRE3_HUMAN	UPI000006E2A1	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GAGTAATGGTG	.	2	ESCA
SLC6A12	0	.	GRCh37	12	306029	306029	+	Silent	SNP	G	G	A	rs771756771	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1095C>T	p.%3D	p.I365I	ENST00000428720	11/16	52	26	26	47	47	0	SLC6A12,synonymous_variant,p.%3D,ENST00000536824,;SLC6A12,synonymous_variant,p.%3D,ENST00000359674,;SLC6A12,synonymous_variant,p.%3D,ENST00000397296,;SLC6A12,synonymous_variant,p.%3D,ENST00000428720,;SLC6A12,synonymous_variant,p.%3D,ENST00000424061,;RP11-283I3.1,downstream_gene_variant,,ENST00000544067,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000535498,;SLC6A12,downstream_gene_variant,,ENST00000538272,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000542825,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000544782,;SLC6A12,intron_variant,,ENST00000545058,;SLC6A12,downstream_gene_variant,,ENST00000538580,;SLC6A12,downstream_gene_variant,,ENST00000540094,;	A	ENSG00000111181	ENST00000428720	Transcript	synonymous_variant	1839	1095	365	I	atC/atT	rs771756771,COSM3460069	.	.	-1	SLC6A12	HGNC	11045	protein_coding	YES	CCDS8501.1	ENSP00000388184	S6A12_HUMAN	F5H2T6_HUMAN,B3KTU1_HUMAN	UPI000013C8DB	.	.	.	11/16	.	PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF118,Pfam_domain:PF00209,Superfamily_domains:0053687	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCGATGAA	byFrequency	5	ESCA
KMT2D	0	.	GRCh37	12	49420423	49420423	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15326G>T	p.Cys5109Phe	p.C5109F	ENST00000301067	48/54	30	17	13	29	29	0	KMT2D,missense_variant,p.Cys5109Phe,ENST00000301067,;KMT2D,upstream_gene_variant,,ENST00000526209,;KMT2D,downstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	missense_variant	15326	15326	5109	C/F	tGc/tTc	CM105471,COSM1128578,COSM1128577	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	unknown(0)	48/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324,Pfam_domain:PF13771,SMART_domains:SM00249,SMART_domains:SM00184	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R5106H|c.15317G>A|3,BUFFER|p.R4836H|c.14507G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGGCAACGC	.	5	ESCA
KMT2D	0	.	GRCh37	12	49441854	49441854	+	Splice_Site	SNP	T	T	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4132-2A>C	.	p.X1378_splice	ENST00000301067	.	36	20	16	59	59	0	KMT2D,splice_acceptor_variant,,ENST00000301067,;KMT2D,upstream_gene_variant,,ENST00000550356,;	G	ENSG00000167548	ENST00000301067	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	.	13/53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCCTGGGGA	.	5	ESCA
MFSD5	0	.	GRCh37	12	53646627	53646627	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329T>C	p.Val110Ala	p.V110A	ENST00000534842	2/2	34	29	5	51	50	0	MFSD5,missense_variant,p.Val3Ala,ENST00000329548,;MFSD5,missense_variant,p.Val110Ala,ENST00000534842,;MFSD5,missense_variant,p.Val110Ala,ENST00000551660,;MFSD5,non_coding_transcript_exon_variant,,ENST00000552097,;MFSD5,downstream_gene_variant,,ENST00000546655,;	C	ENSG00000182544	ENST00000534842	Transcript	missense_variant	476	329	110	V/A	gTg/gCg	.	.	.	1	MFSD5	HGNC	28156	protein_coding	YES	CCDS53796.1	ENSP00000442688	MFSD5_HUMAN	F8VV69_HUMAN	UPI0000EE2648	.	deleterious(0.03)	possibly_damaging(0.6)	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24003:SF500,hmmpanther:PTHR24003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTGGTGACTG	.	3	ESCA
SP7	0	.	GRCh37	12	53723184	53723184	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42C>T	p.%3D	p.S14S	ENST00000536324	3/3	31	21	10	45	45	0	SP7,synonymous_variant,p.%3D,ENST00000536324,;SP7,synonymous_variant,p.%3D,ENST00000303846,;SP7,5_prime_UTR_variant,,ENST00000537210,;SP7,5_prime_UTR_variant,,ENST00000547755,;AAAS,upstream_gene_variant,,ENST00000550286,;AAAS,upstream_gene_variant,,ENST00000548258,;AAAS,upstream_gene_variant,,ENST00000551724,;	A	ENSG00000170374	ENST00000536324	Transcript	synonymous_variant	326	42	14	S	tcC/tcT	.	.	.	-1	SP7	HGNC	17321	protein_coding	YES	CCDS44897.1	ENSP00000443827	SP7_HUMAN	F8VV67_HUMAN	UPI000000D7AE	.	.	.	3/3	.	hmmpanther:PTHR23223,hmmpanther:PTHR23223:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTGGAGCC	.	5	ESCA
FRS2	0	.	GRCh37	12	69970560	69970560	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1825A>G	.	.	ENST00000299293	10/10	12	8	4	29	29	0	FRS2,3_prime_UTR_variant,,ENST00000550389,;FRS2,3_prime_UTR_variant,,ENST00000397997,;FRS2,3_prime_UTR_variant,,ENST00000299293,;FRS2,downstream_gene_variant,,ENST00000551325,;FRS2,downstream_gene_variant,,ENST00000549921,;	G	ENSG00000166225	ENST00000299293	Transcript	3_prime_UTR_variant	3862	.	.	.	.	.	.	.	1	FRS2	HGNC	16971	protein_coding	YES	CCDS41809.1	ENSP00000299293	FRS2_HUMAN	L7RTG7_HUMAN,F8VZI4_HUMAN,F8VZ12_HUMAN,F8VYZ7_HUMAN,F8VX65_HUMAN,F8VW66_HUMAN,F8VS98_HUMAN	UPI000003F143	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCATAGCAGA	.	3	ESCA
ZFC3H1	0	.	GRCh37	12	72021557	72021558	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4103dupC	p.Tyr1369ValfsTer8	p.Y1369Vfs*8	ENST00000378743	21/35	95	76	19	86	86	0	ZFC3H1,frameshift_variant,p.Tyr1369ValfsTer8,ENST00000378743,;ZFC3H1,frameshift_variant,p.Tyr1369ValfsTer8,ENST00000552994,;ZFC3H1,downstream_gene_variant,,ENST00000546606,;	G	ENSG00000133858	ENST00000378743	Transcript	frameshift_variant	4462-4463	4103-4104	1368	A/AX	gcg/gcCg	.	.	.	-1	ZFC3H1	HGNC	28328	protein_coding	YES	CCDS41813.1	ENSP00000368017	ZC3H1_HUMAN	.	UPI00003668E9	.	.	.	21/35	.	PROSITE_profiles:PS50293,hmmpanther:PTHR21563,Gene3D:1.25.40.120,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTGTACGCAAG	.	3	ESCA
TBC1D15	0	.	GRCh37	12	72316853	72316862	+	Frame_Shift_Del	DEL	GTCATGACTC	GTCATGACTC	-	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	GTCATGACTC	GTCATGACTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1945_1954delGTCATGACTC	p.Val649LeufsTer37	p.V649Lfs*37	ENST00000550746	18/18	61	45	16	64	64	0	TBC1D15,frameshift_variant,p.Val632LeufsTer37,ENST00000485960,;TBC1D15,frameshift_variant,p.Val640LeufsTer37,ENST00000319106,;TBC1D15,frameshift_variant,p.Val649LeufsTer37,ENST00000550746,;TBC1D15,frameshift_variant,p.Val403LeufsTer37,ENST00000393309,;TBC1D15,downstream_gene_variant,,ENST00000548679,;TBC1D15,3_prime_UTR_variant,,ENST00000462788,;TBC1D15,non_coding_transcript_exon_variant,,ENST00000546450,;	-	ENSG00000121749	ENST00000550746	Transcript	frameshift_variant	2009-2018	1945-1954	649-652	VMTP/X	GTCATGACTCct/ct	.	.	.	1	TBC1D15	HGNC	25694	protein_coding	YES	CCDS31858.1	ENSP00000448182	TBC15_HUMAN	Q9NSR4_HUMAN,F8VV61_HUMAN,A8K8E1_HUMAN	UPI000049DD7C	.	.	.	18/18	.	hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATGTTGTCATGACTCCTTGT	.	3	ESCA
CCDC41	0	.	GRCh37	12	94702581	94702581	+	3'UTR	SNP	C	C	T	rs202111595	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8G>A	.	.	ENST00000397809	17/17	28	18	10	38	38	0	CCDC41,3_prime_UTR_variant,,ENST00000397809,;CCDC41,3_prime_UTR_variant,,ENST00000339839,;CCDC41,3_prime_UTR_variant,,ENST00000552632,;PLXNC1,downstream_gene_variant,,ENST00000545312,;PLXNC1,downstream_gene_variant,,ENST00000547057,;PLXNC1,downstream_gene_variant,,ENST00000258526,;CCDC41,downstream_gene_variant,,ENST00000546783,;PLXNC1,downstream_gene_variant,,ENST00000549217,;CCDC41,downstream_gene_variant,,ENST00000547232,;	T	ENSG00000173588	ENST00000397809	Transcript	3_prime_UTR_variant	2664	.	.	.	.	rs202111595	.	.	-1	CCDC41	HGNC	17966	protein_coding	YES	CCDS41820.1	ENSP00000380911	.	J3KNW7_HUMAN,H0YHH5_HUMAN	UPI0000D4BD6F	.	.	.	17/17	.	.	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	T:0	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCCAAGAA	byFrequency|byCluster|by1000G	5	ESCA
TPTE2	0	.	GRCh37	13	20012288	20012288	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.979A>T	p.Thr327Ser	p.T327S	ENST00000400230	14/20	101	70	30	122	122	0	TPTE2,missense_variant,p.Thr327Ser,ENST00000382977,;TPTE2,missense_variant,p.Thr250Ser,ENST00000255310,;TPTE2,missense_variant,p.Thr216Ser,ENST00000457266,;TPTE2,missense_variant,p.Thr287Ser,ENST00000382975,;TPTE2,missense_variant,p.Thr287Ser,ENST00000382978,;TPTE2,missense_variant,p.Thr250Ser,ENST00000390680,;TPTE2,missense_variant,p.Thr216Ser,ENST00000400103,;TPTE2,missense_variant,p.Thr327Ser,ENST00000400230,;TPTE2,missense_variant,p.Thr196Ser,ENST00000462409,;	A	ENSG00000132958	ENST00000400230	Transcript	missense_variant	1024	979	327	T/S	Acc/Tcc	.	.	.	-1	TPTE2	HGNC	17299	protein_coding	YES	CCDS45014.1	ENSP00000383089	TPTE2_HUMAN	.	UPI000040738D	.	deleterious(0.04)	possibly_damaging(0.882)	14/20	.	PROSITE_profiles:PS51181,hmmpanther:PTHR12305,PROSITE_patterns:PS00383,Gene3D:3.90.190.10,Pfam_domain:PF00782,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGGTTCTTC	.	5	ESCA
SACS	0	.	GRCh37	13	23913886	23913886	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4129A>T	p.Thr1377Ser	p.T1377S	ENST00000382298	10/10	52	38	14	79	78	0	SACS,missense_variant,p.Thr1377Ser,ENST00000382292,;SACS,missense_variant,p.Thr627Ser,ENST00000402364,;SACS,missense_variant,p.Thr1377Ser,ENST00000382298,;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,;	A	ENSG00000151835	ENST00000382298	Transcript	missense_variant	4718	4129	1377	T/S	Aca/Tca	.	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	benign(0.27)	10/10	.	hmmpanther:PTHR15600:SF26,hmmpanther:PTHR15600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGTGTTGG	.	5	ESCA
WASF3	0	.	GRCh37	13	27255248	27255248	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774G>T	p.%3D	p.L258L	ENST00000335327	8/10	161	113	47	174	174	0	WASF3,synonymous_variant,p.%3D,ENST00000361042,;WASF3,synonymous_variant,p.%3D,ENST00000335327,;WASF3,downstream_gene_variant,,ENST00000496788,;	T	ENSG00000132970	ENST00000335327	Transcript	synonymous_variant	952	774	258	L	ctG/ctT	.	.	.	1	WASF3	HGNC	12734	protein_coding	YES	CCDS9318.1	ENSP00000335055	WASF3_HUMAN	Q5T8P4_HUMAN,B4DGR1_HUMAN	UPI000013CEA7	.	.	.	8/10	.	hmmpanther:PTHR12902:SF7,hmmpanther:PTHR12902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTGCACCC	.	5	ESCA
FREM2	0	.	GRCh37	13	39261662	39261662	+	Missense_Mutation	SNP	G	G	A	rs553605556	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181G>A	p.Ala61Thr	p.A61T	ENST00000280481	1/24	54	39	14	59	59	0	FREM2,missense_variant,p.Ala61Thr,ENST00000280481,;	A	ENSG00000150893	ENST00000280481	Transcript	missense_variant	397	181	61	A/T	Gcg/Acg	rs553605556	.	.	1	FREM2	HGNC	25396	protein_coding	YES	CCDS31960.1	ENSP00000280481	FREM2_HUMAN	.	UPI00005520B9	.	tolerated_low_confidence(0.54)	benign(0.012)	1/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF19	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTCGCGGGG	by1000G	5	ESCA
FNDC3A	0	.	GRCh37	13	49781580	49781580	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*49C>G	.	.	ENST00000492622	26/26	16	11	5	18	18	0	FNDC3A,3_prime_UTR_variant,,ENST00000541916,;FNDC3A,3_prime_UTR_variant,,ENST00000492622,;FNDC3A,3_prime_UTR_variant,,ENST00000398316,;FNDC3A,3_prime_UTR_variant,,ENST00000484074,;FNDC3A,downstream_gene_variant,,ENST00000497644,;OGFOD1P1,downstream_gene_variant,,ENST00000447552,;	G	ENSG00000102531	ENST00000492622	Transcript	3_prime_UTR_variant	3951	.	.	.	.	.	.	.	1	FNDC3A	HGNC	20296	protein_coding	YES	CCDS41886.1	ENSP00000417257	FND3A_HUMAN	.	UPI0000229601	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTACTAAAA	.	5	ESCA
ARHGAP5	0	.	GRCh37	14	32625839	32625839	+	3'UTR	SNP	A	A	T	rs45596831	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1685A>T	.	.	ENST00000345122	7/7	41	30	10	40	40	0	ARHGAP5,3_prime_UTR_variant,,ENST00000432921,;ARHGAP5,3_prime_UTR_variant,,ENST00000396582,;ARHGAP5,3_prime_UTR_variant,,ENST00000433497,;ARHGAP5,3_prime_UTR_variant,,ENST00000345122,;ARHGAP5,downstream_gene_variant,,ENST00000554090,;ARHGAP5,downstream_gene_variant,,ENST00000539826,;ARHGAP5,downstream_gene_variant,,ENST00000556611,;ARHGAP5,non_coding_transcript_exon_variant,,ENST00000216743,;ARHGAP5,downstream_gene_variant,,ENST00000557643,;	T	ENSG00000100852	ENST00000345122	Transcript	3_prime_UTR_variant	6509	.	.	.	.	rs45596831	.	.	1	ARHGAP5	HGNC	675	protein_coding	YES	CCDS32062.1	ENSP00000371897	RHG05_HUMAN	G3V5I7_HUMAN,G3V444_HUMAN,G3V360_HUMAN	UPI000057B85C	.	.	.	7/7	.	.	T:0.0044	T:0.0015	T:0.0029	.	T:0.003	T:0.0099	T:0.0051	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTAAAAAA	byFrequency|by1000G	5	ESCA
DICER1	0	.	GRCh37	14	95569749	95569749	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3984C>T	p.%3D	p.T1328T	ENST00000526495	23/29	52	39	13	46	46	0	DICER1,synonymous_variant,p.%3D,ENST00000343455,;DICER1,synonymous_variant,p.%3D,ENST00000541352,;DICER1,synonymous_variant,p.%3D,ENST00000527414,;DICER1,synonymous_variant,p.%3D,ENST00000526495,;DICER1,synonymous_variant,p.%3D,ENST00000532939,;DICER1,synonymous_variant,p.%3D,ENST00000556045,;DICER1,synonymous_variant,p.%3D,ENST00000393063,;DICER1,downstream_gene_variant,,ENST00000556681,;DICER1,downstream_gene_variant,,ENST00000554367,;	A	ENSG00000100697	ENST00000526495	Transcript	synonymous_variant	4276	3984	1328	T	acC/acT	.	.	.	-1	DICER1	HGNC	17098	protein_coding	YES	CCDS9931.1	ENSP00000437256	DICER_HUMAN	Q5D0K5_HUMAN,B3KMJ0_HUMAN	UPI0000168662	.	.	.	23/29	.	PROSITE_profiles:PS50142,hmmpanther:PTHR14950:SF3,hmmpanther:PTHR14950,Gene3D:1.10.1520.10,Pfam_domain:PF00636,SMART_domains:SM00535,Superfamily_domains:SSF69065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGTGGTGAT	.	5	ESCA
MGA	0	.	GRCh37	15	42003256	42003256	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2793T>A	p.His931Gln	p.H931Q	ENST00000219905	8/24	71	44	27	77	77	0	MGA,missense_variant,p.His931Gln,ENST00000219905,;MGA,missense_variant,p.His931Gln,ENST00000563576,;MGA,missense_variant,p.His931Gln,ENST00000570161,;MGA,missense_variant,p.His931Gln,ENST00000545763,;MGA,missense_variant,p.His931Gln,ENST00000389936,;MGA,missense_variant,p.His931Gln,ENST00000566718,;MGA,missense_variant,p.His931Gln,ENST00000566586,;	A	ENSG00000174197	ENST00000219905	Transcript	missense_variant	2974	2793	931	H/Q	caT/caA	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	tolerated(0.46)	benign(0.002)	8/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCATGTGAT	.	5	ESCA
TGM5	0	.	GRCh37	15	43525478	43525478	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2074G>A	p.Gly692Arg	p.G692R	ENST00000220420	13/13	56	32	23	59	58	1	TGM5,missense_variant,p.Gly692Arg,ENST00000220420,;TGM5,missense_variant,p.Gly610Arg,ENST00000349114,;TGM5,non_coding_transcript_exon_variant,,ENST00000396996,;	T	ENSG00000104055	ENST00000220420	Transcript	missense_variant	2082	2074	692	G/R	Gga/Aga	.	.	.	-1	TGM5	HGNC	11781	protein_coding	YES	CCDS32212.1	ENSP00000220420	TGM5_HUMAN	.	UPI0000136CCF	.	deleterious(0.01)	probably_damaging(1)	13/13	.	Superfamily_domains:SSF49309,PIRSF_domain:PIRSF000459,Pfam_domain:PF00927,Gene3D:2.60.40.10,hmmpanther:PTHR11590:SF38,hmmpanther:PTHR11590	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTCCACTCT	.	5	ESCA
SYNM	0	.	GRCh37	15	99671376	99671376	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2808G>A	p.Met936Ile	p.M936I	ENST00000336292	5/5	45	25	20	36	36	0	SYNM,missense_variant,p.Met936Ile,ENST00000328642,;SYNM,missense_variant,p.Met936Ile,ENST00000336292,;SYNM,missense_variant,p.Met651Ile,ENST00000560674,;RP11-6O2.4,non_coding_transcript_exon_variant,,ENST00000566974,;SYNM,non_coding_transcript_exon_variant,,ENST00000558420,;SYNM,non_coding_transcript_exon_variant,,ENST00000561323,;SYNM,intron_variant,,ENST00000561306,;	A	ENSG00000182253	ENST00000336292	Transcript	missense_variant	2928	2808	936	M/I	atG/atA	.	.	.	1	SYNM	HGNC	24466	protein_coding	YES	.	ENSP00000336775	SYNEM_HUMAN	.	UPI00001B03B3	.	tolerated(1)	benign(0.001)	5/5	.	hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATGAAGGG	.	5	ESCA
IFT140	0	.	GRCh37	16	1568310	1568310	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4089C>T	p.%3D	p.L1363L	ENST00000426508	30/31	39	27	12	41	41	0	IFT140,synonymous_variant,p.%3D,ENST00000568837,;IFT140,synonymous_variant,p.%3D,ENST00000361339,;IFT140,synonymous_variant,p.%3D,ENST00000426508,;LA16c-385E7.1,downstream_gene_variant,,ENST00000566922,;IFT140,3_prime_UTR_variant,,ENST00000397417,;IFT140,non_coding_transcript_exon_variant,,ENST00000565298,;	A	ENSG00000187535	ENST00000426508	Transcript	synonymous_variant	4453	4089	1363	L	ctC/ctT	.	.	.	-1	IFT140	HGNC	29077	protein_coding	YES	CCDS10439.1	ENSP00000406012	IF140_HUMAN	Q9UG52_HUMAN,H3BTA5_HUMAN,H3BNC5_HUMAN	UPI0000073C64	.	.	.	30/31	.	hmmpanther:PTHR15722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGGAGCAG	.	5	ESCA
IL27	0	.	GRCh37	16	28511194	28511194	+	Silent	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510G>A	p.%3D	p.E170E	ENST00000356897	5/5	33	30	3	41	41	0	IL27,synonymous_variant,p.%3D,ENST00000356897,;APOBR,downstream_gene_variant,,ENST00000328423,;APOBR,downstream_gene_variant,,ENST00000431282,;APOBR,downstream_gene_variant,,ENST00000564831,;IL27,downstream_gene_variant,,ENST00000568075,;CLN3,upstream_gene_variant,,ENST00000569430,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000567160,;	T	ENSG00000197272	ENST00000356897	Transcript	synonymous_variant	533	510	170	E	gaG/gaA	COSM3817696	.	.	-1	IL27	HGNC	19157	protein_coding	YES	CCDS10633.1	ENSP00000349365	IL27A_HUMAN	H3BQY2_HUMAN	UPI0000141330	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR20879:SF0,hmmpanther:PTHR20879	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTCCTCTTC	.	2	ESCA
MGRN1	0	.	GRCh37	16	4730035	4730035	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1068T>G	p.Cys356Trp	p.C356W	ENST00000262370	12/17	189	178	11	152	152	0	MGRN1,missense_variant,p.Cys321Trp,ENST00000590790,;MGRN1,missense_variant,p.Cys356Trp,ENST00000262370,;MGRN1,missense_variant,p.Cys395Trp,ENST00000587747,;MGRN1,missense_variant,p.Cys356Trp,ENST00000399577,;MGRN1,intron_variant,,ENST00000588994,;MGRN1,intron_variant,,ENST00000415496,;MGRN1,intron_variant,,ENST00000586183,;MGRN1,splice_region_variant,,ENST00000591673,;MGRN1,downstream_gene_variant,,ENST00000588015,;MGRN1,upstream_gene_variant,,ENST00000588111,;MGRN1,upstream_gene_variant,,ENST00000592256,;MGRN1,intron_variant,,ENST00000536343,;MGRN1,upstream_gene_variant,,ENST00000585676,;	G	ENSG00000102858	ENST00000262370	Transcript	missense_variant	1239	1068	356	C/W	tgT/tgG	.	.	.	1	MGRN1	HGNC	20254	protein_coding	YES	CCDS42115.1	ENSP00000262370	MGRN1_HUMAN	K7ERA1_HUMAN	UPI000018CE7F	.	deleterious_low_confidence(0.01)	possibly_damaging(0.789)	12/17	.	hmmpanther:PTHR22996,hmmpanther:PTHR22996:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGTGTCCCTT	.	2	ESCA
ADCY7	0	.	GRCh37	16	50335099	50335099	+	Missense_Mutation	SNP	C	C	T	rs367758610	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1342C>T	p.Arg448Cys	p.R448C	ENST00000394697	10/26	211	150	60	202	202	0	ADCY7,missense_variant,p.Arg448Cys,ENST00000254235,;ADCY7,missense_variant,p.Arg448Cys,ENST00000538642,;ADCY7,missense_variant,p.Arg448Cys,ENST00000394697,;ADCY7,missense_variant,p.Arg448Cys,ENST00000566433,;ADCY7,intron_variant,,ENST00000537579,;ADCY7,non_coding_transcript_exon_variant,,ENST00000568731,;ADCY7,downstream_gene_variant,,ENST00000563677,;ADCY7,downstream_gene_variant,,ENST00000564044,;ADCY7,missense_variant,p.Arg448Cys,ENST00000567277,;ADCY7,upstream_gene_variant,,ENST00000570187,;	T	ENSG00000121281	ENST00000394697	Transcript	missense_variant	1682	1342	448	R/C	Cgc/Tgc	rs367758610	.	.	1	ADCY7	HGNC	238	protein_coding	YES	CCDS10741.1	ENSP00000378187	ADCY7_HUMAN	I3L3Q5_HUMAN	UPI000004C5DB	.	deleterious(0.01)	probably_damaging(0.912)	10/26	.	Gene3D:3.30.70.1230,hmmpanther:PTHR11920:SF273,hmmpanther:PTHR11920	.	.	.	.	.	.	.	T:0.0002	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCCGCACC	byFrequency|byCluster	5	ESCA
CYLD	0	.	GRCh37	16	50818239	50818239	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1827-1G>T	.	p.X609_splice	ENST00000427738	.	110	84	26	91	91	0	CYLD,splice_acceptor_variant,,ENST00000568704,;CYLD,splice_acceptor_variant,,ENST00000564326,;CYLD,splice_acceptor_variant,,ENST00000569418,;CYLD,splice_acceptor_variant,,ENST00000566206,;CYLD,splice_acceptor_variant,,ENST00000540145,;CYLD,splice_acceptor_variant,,ENST00000427738,;CYLD,splice_acceptor_variant,,ENST00000398568,;CYLD,splice_acceptor_variant,,ENST00000311559,;RP11-327F22.4,intron_variant,,ENST00000564510,;RP11-327F22.4,intron_variant,,ENST00000575917,;CYLD,splice_acceptor_variant,,ENST00000563629,;CYLD,splice_acceptor_variant,,ENST00000569891,;	T	ENSG00000083799	ENST00000427738	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	CYLD	HGNC	2584	protein_coding	YES	CCDS45482.1	ENSP00000392025	CYLD_HUMAN	H3BTB8_HUMAN,H3BSW9_HUMAN,H3BPZ5_HUMAN	UPI0000073A15	.	.	.	.	10/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAGCTTAT	.	5	ESCA
RPGRIP1L	0	.	GRCh37	16	53634205	53634205	+	3'Flank	SNP	A	A	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000379925	.	103	68	35	106	106	0	RPGRIP1L,3_prime_UTR_variant,,ENST00000262135,;RPGRIP1L,downstream_gene_variant,,ENST00000563746,;RPGRIP1L,downstream_gene_variant,,ENST00000379925,;	C	ENSG00000103494	ENST00000379925	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	485	-1	RPGRIP1L	HGNC	29168	protein_coding	YES	CCDS32447.1	ENSP00000369257	FTM_HUMAN	J3QLR9_HUMAN,I3L2P2_HUMAN,H3BPF5_HUMAN	UPI000047DAF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAAAAAATG	.	5	ESCA
CPNE2	0	.	GRCh37	16	57180262	57180262	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1539+29C>T	.	.	ENST00000535318	.	45	42	3	57	56	1	CPNE2,intron_variant,,ENST00000565874,;CPNE2,intron_variant,,ENST00000535318,;CPNE2,intron_variant,,ENST00000290776,;CPNE2,intron_variant,,ENST00000537605,;CPNE2,non_coding_transcript_exon_variant,,ENST00000565951,;CPNE2,intron_variant,,ENST00000566910,;CPNE2,intron_variant,,ENST00000567011,;CPNE2,intron_variant,,ENST00000566042,;	T	ENSG00000140848	ENST00000535318	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CPNE2	HGNC	2315	protein_coding	YES	CCDS10774.1	ENSP00000439018	CPNE2_HUMAN	Q719H8_HUMAN,H3BQQ3_HUMAN,H3BPR8_HUMAN	UPI000017DA4F	.	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGGCGGTTA	.	2	ESCA
THAP11	0	.	GRCh37	16	67877021	67877021	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564C>T	p.%3D	p.I188I	ENST00000303596	1/1	44	24	20	50	50	0	THAP11,synonymous_variant,p.%3D,ENST00000303596,;CENPT,5_prime_UTR_variant,,ENST00000567985,;CENPT,intron_variant,,ENST00000561593,;CENPT,intron_variant,,ENST00000562787,;CENPT,intron_variant,,ENST00000565114,;NUTF2,upstream_gene_variant,,ENST00000219169,;NUTF2,upstream_gene_variant,,ENST00000568396,;NUTF2,upstream_gene_variant,,ENST00000569436,;NUTF2,upstream_gene_variant,,ENST00000567105,;CENPT,non_coding_transcript_exon_variant,,ENST00000564144,;CENPT,non_coding_transcript_exon_variant,,ENST00000567482,;CENPT,non_coding_transcript_exon_variant,,ENST00000565385,;CENPT,non_coding_transcript_exon_variant,,ENST00000569019,;CENPT,intron_variant,,ENST00000568652,;CENPT,intron_variant,,ENST00000565132,;CENPT,intron_variant,,ENST00000568765,;CENPT,intron_variant,,ENST00000569094,;CENPT,upstream_gene_variant,,ENST00000564346,;CENPT,upstream_gene_variant,,ENST00000565436,;NUTF2,upstream_gene_variant,,ENST00000568390,;NUTF2,upstream_gene_variant,,ENST00000570026,;NUTF2,upstream_gene_variant,,ENST00000568233,;	T	ENSG00000168286	ENST00000303596	Transcript	synonymous_variant	809	564	188	I	atC/atT	.	.	.	1	THAP11	HGNC	23194	protein_coding	YES	CCDS10847.1	ENSP00000304689	THA11_HUMAN	B5APZ3_HUMAN	UPI000013E8BD	.	.	.	1/1	.	hmmpanther:PTHR22794	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCCATCGATCT	.	4	ESCA
NARFL	0	.	GRCh37	16	784156	784156	+	Intron	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693+73G>C	.	.	ENST00000251588	.	57	33	23	62	62	0	NARFL,intron_variant,,ENST00000301694,;NARFL,intron_variant,,ENST00000568545,;NARFL,intron_variant,,ENST00000251588,;NARFL,intron_variant,,ENST00000540986,;NARFL,intron_variant,,ENST00000562421,;HAGHL,downstream_gene_variant,,ENST00000564537,;NARFL,downstream_gene_variant,,ENST00000567403,;HAGHL,downstream_gene_variant,,ENST00000341413,;HAGHL,downstream_gene_variant,,ENST00000389703,;HAGHL,downstream_gene_variant,,ENST00000549114,;NARFL,downstream_gene_variant,,ENST00000566614,;HAGHL,downstream_gene_variant,,ENST00000561546,;HAGHL,non_coding_transcript_exon_variant,,ENST00000569604,;NARFL,non_coding_transcript_exon_variant,,ENST00000562862,;NARFL,non_coding_transcript_exon_variant,,ENST00000569759,;NARFL,downstream_gene_variant,,ENST00000565693,;NARFL,downstream_gene_variant,,ENST00000567455,;NARFL,downstream_gene_variant,,ENST00000563534,;HAGHL,downstream_gene_variant,,ENST00000563156,;NARFL,non_coding_transcript_exon_variant,,ENST00000562752,;NARFL,non_coding_transcript_exon_variant,,ENST00000565341,;NARFL,intron_variant,,ENST00000565425,;HAGHL,downstream_gene_variant,,ENST00000569385,;NARFL,downstream_gene_variant,,ENST00000570289,;HAGHL,downstream_gene_variant,,ENST00000567696,;NARFL,downstream_gene_variant,,ENST00000565065,;HAGHL,downstream_gene_variant,,ENST00000389701,;NARFL,upstream_gene_variant,,ENST00000566650,;NARFL,upstream_gene_variant,,ENST00000563051,;NARFL,upstream_gene_variant,,ENST00000564285,;NARFL,downstream_gene_variant,,ENST00000570066,;	G	ENSG00000103245	ENST00000251588	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NARFL	HGNC	14179	protein_coding	YES	CCDS10425.1	ENSP00000251588	NARFL_HUMAN	I3L2A3_HUMAN,H3BSJ7_HUMAN,H3BSH2_HUMAN	UPI0000070186	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCATGGC	.	5	ESCA
GAN	0	.	GRCh37	16	81412137	81412137	+	3'UTR	SNP	C	C	T	rs552774303	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*936C>T	.	.	ENST00000568107	11/11	14	9	5	14	14	0	GAN,3_prime_UTR_variant,,ENST00000568107,;	T	ENSG00000261609	ENST00000568107	Transcript	3_prime_UTR_variant	2892	.	.	.	.	rs552774303	.	.	1	GAN	HGNC	4137	protein_coding	YES	CCDS10935.1	ENSP00000476795	GAN_HUMAN	.	UPI000000DAB6	.	.	.	11/11	.	.	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATACATAGG	by1000G	5	ESCA
PLCG2	0	.	GRCh37	16	81942086	81942086	+	Silent	SNP	G	G	A	rs772797149	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1623G>A	p.%3D	p.T541T	ENST00000359376	17/33	95	65	29	107	107	0	PLCG2,synonymous_variant,p.%3D,ENST00000359376,;PLCG2,non_coding_transcript_exon_variant,,ENST00000567980,;PLCG2,downstream_gene_variant,,ENST00000563375,;PLCG2,downstream_gene_variant,,ENST00000570198,;	A	ENSG00000197943	ENST00000359376	Transcript	synonymous_variant	1837	1623	541	T	acG/acA	rs772797149,COSM1324241,COSM1324240	.	.	1	PLCG2	HGNC	9066	protein_coding	YES	CCDS42204.1	ENSP00000352336	PLCG2_HUMAN	H3BQV5_HUMAN	UPI00001411F7	.	.	.	17/33	.	Superfamily_domains:SSF55550,PIRSF_domain:PIRSF000952,SMART_domains:SM00252,Pfam_domain:PF00017,Gene3D:3.30.505.10,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF25,PROSITE_profiles:PS50001	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGACGAGTGC	byFrequency	5	ESCA
PLD6	0	.	GRCh37	17	17106063	17106063	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*18C>T	.	.	ENST00000321560	2/2	39	36	3	47	47	0	PLD6,3_prime_UTR_variant,,ENST00000321560,;MPRIP,intron_variant,,ENST00000578209,;RP11-45M22.4,3_prime_UTR_variant,,ENST00000427497,;	A	ENSG00000179598	ENST00000321560	Transcript	3_prime_UTR_variant	806	.	.	.	.	.	.	.	-1	PLD6	HGNC	30447	protein_coding	YES	CCDS11182.1	ENSP00000317177	PLD6_HUMAN	.	UPI000006EEE7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GGAGGGCTCAG	.	2	ESCA
TSR1	0	.	GRCh37	17	2236267	2236267	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1293G>A	p.%3D	p.E431E	ENST00000301364	7/15	57	39	18	68	68	0	TSR1,synonymous_variant,p.%3D,ENST00000301364,;SGSM2,upstream_gene_variant,,ENST00000268989,;SGSM2,upstream_gene_variant,,ENST00000426855,;SGSM2,upstream_gene_variant,,ENST00000574563,;TSR1,downstream_gene_variant,,ENST00000576112,;SNORD91B,upstream_gene_variant,,ENST00000391250,;SNORD91A,upstream_gene_variant,,ENST00000390861,;SNORD91A,upstream_gene_variant,,ENST00000609620,;SNORD91B,upstream_gene_variant,,ENST00000608459,;TSR1,downstream_gene_variant,,ENST00000576202,;TSR1,downstream_gene_variant,,ENST00000571806,;SGSM2,upstream_gene_variant,,ENST00000572875,;SGSM2,upstream_gene_variant,,ENST00000573062,;TSR1,upstream_gene_variant,,ENST00000575049,;	T	ENSG00000167721	ENST00000301364	Transcript	synonymous_variant	2373	1293	431	E	gaG/gaA	.	.	.	-1	TSR1	HGNC	25542	protein_coding	YES	CCDS32525.1	ENSP00000301364	TSR1_HUMAN	.	UPI00002005DF	.	.	.	7/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12858	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCCTCCAT	.	5	ESCA
SPAG5	0	.	GRCh37	17	26905265	26905265	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3400G>A	p.Glu1134Lys	p.E1134K	ENST00000321765	22/24	25	14	11	33	33	0	SPAG5,missense_variant,p.Glu1134Lys,ENST00000321765,;SPAG5,missense_variant,p.Glu147Lys,ENST00000582076,;ALDOC,upstream_gene_variant,,ENST00000226253,;RP11-192H23.4,downstream_gene_variant,,ENST00000531839,;ALDOC,upstream_gene_variant,,ENST00000581807,;ALDOC,upstream_gene_variant,,ENST00000578590,;ALDOC,upstream_gene_variant,,ENST00000395319,;ALDOC,upstream_gene_variant,,ENST00000460201,;ALDOC,upstream_gene_variant,,ENST00000584086,;ALDOC,upstream_gene_variant,,ENST00000435638,;ALDOC,upstream_gene_variant,,ENST00000395321,;RP11-192H23.5,downstream_gene_variant,,ENST00000585189,;SPAG5,non_coding_transcript_exon_variant,,ENST00000582175,;SPAG5,non_coding_transcript_exon_variant,,ENST00000580676,;SPAG5,non_coding_transcript_exon_variant,,ENST00000580377,;RP11-192H23.4,intron_variant,,ENST00000481916,;SPAG5,downstream_gene_variant,,ENST00000581133,;SPAG5,downstream_gene_variant,,ENST00000578230,;SPAG5,downstream_gene_variant,,ENST00000580406,;SPAG5,downstream_gene_variant,,ENST00000577259,;ALDOC,upstream_gene_variant,,ENST00000582381,;SPAG5,downstream_gene_variant,,ENST00000378976,;SPAG5,downstream_gene_variant,,ENST00000580083,;SPAG5,downstream_gene_variant,,ENST00000580682,;	T	ENSG00000076382	ENST00000321765	Transcript	missense_variant	3733	3400	1134	E/K	Gaa/Aaa	.	.	.	-1	SPAG5	HGNC	13452	protein_coding	YES	CCDS32594.1	ENSP00000323300	SPAG5_HUMAN	.	UPI0000073414	.	tolerated(0.22)	benign(0.117)	22/24	.	hmmpanther:PTHR15347,hmmpanther:PTHR15347:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCCTTCT	.	5	ESCA
RNF135	0	.	GRCh37	17	29326185	29326185	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1275G>A	p.%3D	p.L425L	ENST00000328381	5/5	57	33	24	42	41	1	RNF135,synonymous_variant,p.%3D,ENST00000328381,;RNF135,3_prime_UTR_variant,,ENST00000324689,;RNF135,3_prime_UTR_variant,,ENST00000443677,;RNF135,3_prime_UTR_variant,,ENST00000535306,;RNF135,downstream_gene_variant,,ENST00000434242,;RNF135,downstream_gene_variant,,ENST00000580444,;	A	ENSG00000181481	ENST00000328381	Transcript	synonymous_variant	2148	1275	425	L	ctG/ctA	.	.	.	1	RNF135	HGNC	21158	protein_coding	YES	CCDS11262.1	ENSP00000328340	RN135_HUMAN	B3KV69_HUMAN	UPI00001AF795	.	.	.	5/5	.	SMART_domains:SM00449,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF200,PROSITE_profiles:PS50188	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TACCTGATAAT	.	4	ESCA
CCL11	0	.	GRCh37	17	32612701	32612701	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-127C>T	.	.	ENST00000305869	1/3	38	25	13	34	34	0	CCL11,5_prime_UTR_variant,,ENST00000305869,;	T	ENSG00000172156	ENST00000305869	Transcript	5_prime_UTR_variant	15	.	.	.	.	.	.	.	1	CCL11	HGNC	10610	protein_coding	YES	CCDS11279.1	ENSP00000302234	CCL11_HUMAN	Q6I9T4_HUMAN	UPI0000050AFD	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTTCCCTGG	.	2	ESCA
GPR179	0	.	GRCh37	17	36483702	36483702	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5750G>C	p.Arg1917Thr	p.R1917T	ENST00000342292	11/11	58	43	15	72	72	0	GPR179,missense_variant,p.Arg1917Thr,ENST00000342292,;MRPL45,downstream_gene_variant,,ENST00000312513,;GPR179,intron_variant,,ENST00000584976,;MRPL45,downstream_gene_variant,,ENST00000579911,;	G	ENSG00000188888	ENST00000342292	Transcript	missense_variant	5771	5750	1917	R/T	aGa/aCa	COSM261156	.	.	-1	GPR179	HGNC	31371	protein_coding	YES	CCDS42308.1	ENSP00000345060	GP179_HUMAN	.	UPI000041A9C2	.	tolerated(0.58)	benign(0.01)	11/11	.	hmmpanther:PTHR32546:SF7,hmmpanther:PTHR32546	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGTCTCAGG	.	5	ESCA
KANSL1	0	.	GRCh37	17	44248467	44248467	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000262419	2/15	71	38	33	78	78	0	KANSL1,missense_variant,p.Arg348Gln,ENST00000575318,;KANSL1,missense_variant,p.Arg348Gln,ENST00000574590,;KANSL1,missense_variant,p.Arg348Gln,ENST00000432791,;KANSL1,missense_variant,p.Arg348Gln,ENST00000262419,;KANSL1,missense_variant,p.Arg348Gln,ENST00000572904,;KANSL1,5_prime_UTR_variant,,ENST00000393476,;KANSL1,downstream_gene_variant,,ENST00000576739,;KANSL1,downstream_gene_variant,,ENST00000574655,;KANSL1,downstream_gene_variant,,ENST00000571698,;KANSL1,non_coding_transcript_exon_variant,,ENST00000576248,;KANSL1,upstream_gene_variant,,ENST00000577114,;	T	ENSG00000120071	ENST00000262419	Transcript	missense_variant	1514	1043	348	R/Q	cGa/cAa	.	.	.	-1	KANSL1	HGNC	24565	protein_coding	YES	CCDS11503.1	ENSP00000262419	KANL1_HUMAN	I3L243_HUMAN,I3L233_HUMAN	UPI0001AE66EA	.	deleterious(0.03)	probably_damaging(0.995)	2/15	.	hmmpanther:PTHR22443:SF14,hmmpanther:PTHR22443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTCGAGTC	.	5	ESCA
SPOP	0	.	GRCh37	17	47699360	47699360	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148G>A	p.Glu50Lys	p.E50K	ENST00000393331	5/12	74	54	19	101	101	0	SPOP,missense_variant,p.Glu50Lys,ENST00000514121,;SPOP,missense_variant,p.Glu50Lys,ENST00000393331,;SPOP,missense_variant,p.Glu50Lys,ENST00000504102,;SPOP,missense_variant,p.Glu50Lys,ENST00000509079,;SPOP,missense_variant,p.Glu50Lys,ENST00000393328,;SPOP,missense_variant,p.Glu50Lys,ENST00000507970,;SPOP,missense_variant,p.Glu50Lys,ENST00000347630,;SPOP,missense_variant,p.Glu50Lys,ENST00000505581,;SPOP,missense_variant,p.Glu50Lys,ENST00000515508,;SPOP,missense_variant,p.Glu50Lys,ENST00000503676,;SPOP,missense_variant,p.Glu50Lys,ENST00000510476,;SPOP,downstream_gene_variant,,ENST00000451526,;SPOP,downstream_gene_variant,,ENST00000508805,;SPOP,non_coding_transcript_exon_variant,,ENST00000513080,;SPOP,downstream_gene_variant,,ENST00000502385,;SPOP,3_prime_UTR_variant,,ENST00000504212,;SPOP,3_prime_UTR_variant,,ENST00000506399,;SPOP,downstream_gene_variant,,ENST00000509765,;SPOP,upstream_gene_variant,,ENST00000509869,;	T	ENSG00000121067	ENST00000393331	Transcript	missense_variant	619	148	50	E/K	Gaa/Aaa	COSM980818	.	.	-1	SPOP	HGNC	11254	protein_coding	YES	CCDS11551.1	ENSP00000377004	SPOP_HUMAN	D6RIS7_HUMAN,D6RGZ4_HUMAN,D6RFL7_HUMAN,D6RDV6_HUMAN,D6RDG8_HUMAN,D6RD94_HUMAN,D6RBH6_HUMAN,D6RA79_HUMAN,B4DUE7_HUMAN,B4DEE4_HUMAN	UPI0000003F5C	.	tolerated(0.06)	possibly_damaging(0.883)	5/12	.	PROSITE_profiles:PS50144,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF97,Pfam_domain:PF00917,Gene3D:2.60.210.10,SMART_domains:SM00061,Superfamily_domains:SSF49599	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E50K|c.148G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCACCCA	.	5	ESCA
TANC2	0	.	GRCh37	17	61497497	61497497	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4154C>T	p.Pro1385Leu	p.P1385L	ENST00000424789	25/25	44	29	14	44	44	0	TANC2,missense_variant,p.Pro1395Leu,ENST00000389520,;TANC2,missense_variant,p.Pro1385Leu,ENST00000424789,;TANC2,3_prime_UTR_variant,,ENST00000583356,;RP11-269G24.3,intron_variant,,ENST00000583552,;TANC2,downstream_gene_variant,,ENST00000579541,;	T	ENSG00000170921	ENST00000424789	Transcript	missense_variant	4158	4154	1385	P/L	cCg/cTg	.	.	.	1	TANC2	HGNC	30212	protein_coding	YES	CCDS45754.1	ENSP00000387593	TANC2_HUMAN	.	UPI00015D57DF	.	tolerated(0.66)	benign(0.011)	25/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24166:SF21,hmmpanther:PTHR24166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCACCGCAGC	.	5	ESCA
ABCA10	0	.	GRCh37	17	67160217	67160217	+	Missense_Mutation	SNP	T	T	C	rs753945392	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3361A>G	p.Ile1121Val	p.I1121V	ENST00000269081	28/40	46	34	11	62	62	0	ABCA10,missense_variant,p.Ile1121Val,ENST00000269081,;ABCA10,splice_region_variant,,ENST00000416101,;ABCA10,splice_region_variant,,ENST00000519732,;ABCA10,missense_variant,p.Ile1121Val,ENST00000523419,;ABCA10,splice_region_variant,,ENST00000522406,;ABCA10,splice_region_variant,,ENST00000518929,;	C	ENSG00000154263	ENST00000269081	Transcript	missense_variant	4271	3361	1121	I/V	Ata/Gta	rs753945392	.	.	-1	ABCA10	HGNC	30	protein_coding	YES	CCDS11684.1	ENSP00000269081	ABCAA_HUMAN	K7ERP5_HUMAN	UPI000013D7F6	.	tolerated(0.07)	benign(0.158)	28/40	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR19229:SF120,hmmpanther:PTHR19229,Pfam_domain:PF12698	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACTATTAAGG	.	3	ESCA
ARHGEF15	0	.	GRCh37	17	8222159	8222159	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1964C>T	p.Ser655Leu	p.S655L	ENST00000361926	12/16	20	15	5	28	28	0	ARHGEF15,missense_variant,p.Ser655Leu,ENST00000361926,;ARHGEF15,missense_variant,p.Ser655Leu,ENST00000421050,;AC135178.7,upstream_gene_variant,,ENST00000458568,;ARHGEF15,non_coding_transcript_exon_variant,,ENST00000582060,;ARHGEF15,downstream_gene_variant,,ENST00000581809,;ARHGEF15,downstream_gene_variant,,ENST00000455564,;ARHGEF15,downstream_gene_variant,,ENST00000578286,;	T	ENSG00000198844	ENST00000361926	Transcript	missense_variant	2074	1964	655	S/L	tCg/tTg	COSM3796267	.	.	1	ARHGEF15	HGNC	15590	protein_coding	YES	CCDS11139.1	ENSP00000355026	ARHGF_HUMAN	J3QS60_HUMAN,J3KT46_HUMAN	UPI000013D2C0	.	tolerated(0.2)	benign(0.077)	12/16	.	Superfamily_domains:SSF50729,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF7	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCGCGCC	.	5	ESCA
CCDC42	0	.	GRCh37	17	8633412	8633412	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*36G>T	.	.	ENST00000293845	7/7	34	21	13	31	31	0	CCDC42,3_prime_UTR_variant,,ENST00000539522,;CCDC42,3_prime_UTR_variant,,ENST00000293845,;	A	ENSG00000161973	ENST00000293845	Transcript	3_prime_UTR_variant	1214	.	.	.	.	.	.	.	-1	CCDC42	HGNC	26528	protein_coding	YES	CCDS11145.1	ENSP00000293845	CCD42_HUMAN	.	UPI000013E127	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGATCTCTGT	.	5	ESCA
WDR16	0	.	GRCh37	17	9497542	9497542	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.440C>G	p.Ala147Gly	p.A147G	ENST00000352665	4/14	55	31	24	59	59	0	WDR16,missense_variant,p.Ala157Gly,ENST00000299764,;WDR16,missense_variant,p.Ala147Gly,ENST00000352665,;WDR16,missense_variant,p.Ala79Gly,ENST00000396219,;WDR16,3_prime_UTR_variant,,ENST00000576499,;WDR16,3_prime_UTR_variant,,ENST00000572333,;WDR16,3_prime_UTR_variant,,ENST00000575247,;WDR16,3_prime_UTR_variant,,ENST00000576630,;WDR16,non_coding_transcript_exon_variant,,ENST00000576320,;WDR16,intron_variant,,ENST00000574937,;RPL19P18,upstream_gene_variant,,ENST00000466869,;	G	ENSG00000166596	ENST00000352665	Transcript	missense_variant	509	440	147	A/G	gCc/gGc	.	.	.	1	WDR16	HGNC	16053	protein_coding	YES	CCDS11149.2	ENSP00000339449	WDR16_HUMAN	.	UPI00001AECC1	.	deleterious(0.02)	possibly_damaging(0.589)	4/14	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13720:SF14,hmmpanther:PTHR13720,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGCCATCT	.	5	ESCA
ROCK1	0	.	GRCh37	18	18608786	18608786	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1162G>A	p.Val388Ile	p.V388I	ENST00000399799	10/33	104	99	5	88	88	0	ROCK1,missense_variant,p.Val388Ile,ENST00000399799,;	T	ENSG00000067900	ENST00000399799	Transcript	missense_variant	2103	1162	388	V/I	Gtt/Att	COSM986897	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	tolerated(0.11)	benign(0.23)	10/33	.	PROSITE_profiles:PS51285,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF28,Pfam_domain:PF00433,PIRSF_domain:PIRSF037568,SMART_domains:SM00133,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAACGAAAG	.	2	ESCA
COLEC12	0	.	GRCh37	18	334825	334825	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1733G>C	p.Gly578Ala	p.G578A	ENST00000400256	6/10	50	31	18	52	52	0	COLEC12,missense_variant,p.Gly578Ala,ENST00000400256,;COLEC12,non_coding_transcript_exon_variant,,ENST00000582147,;	G	ENSG00000158270	ENST00000400256	Transcript	missense_variant	1941	1733	578	G/A	gGc/gCc	.	.	.	-1	COLEC12	HGNC	16016	protein_coding	YES	CCDS32782.1	ENSP00000383115	COL12_HUMAN	.	UPI00002018EC	.	tolerated(0.08)	unknown(0)	6/10	.	Pfam_domain:PF01391,hmmpanther:PTHR24021,hmmpanther:PTHR24021:SF19,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGCCCTTG	.	5	ESCA
CD226	0	.	GRCh37	18	67531489	67531489	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*61T>C	.	.	ENST00000280200	7/7	41	27	14	41	41	0	CD226,3_prime_UTR_variant,,ENST00000280200,;CD226,3_prime_UTR_variant,,ENST00000581982,;CD226,3_prime_UTR_variant,,ENST00000577287,;CD226,downstream_gene_variant,,ENST00000582621,;CD226,intron_variant,,ENST00000578928,;	G	ENSG00000150637	ENST00000280200	Transcript	3_prime_UTR_variant	1341	.	.	.	.	.	.	.	-1	CD226	HGNC	16961	protein_coding	YES	CCDS11997.1	ENSP00000280200	CD226_HUMAN	J3QRQ4_HUMAN,J3QR77_HUMAN,J3QQW1_HUMAN,J3QL19_HUMAN,J3QKM7_HUMAN	UPI000013DC05	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGCATAAAG	.	5	ESCA
ZNF516	0	.	GRCh37	18	74153320	74153320	+	Missense_Mutation	SNP	G	G	A	rs569947953	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1691C>T	p.Ser564Leu	p.S564L	ENST00000443185	3/8	11	6	5	11	11	0	ZNF516,missense_variant,p.Ser564Leu,ENST00000443185,;ZNF516,downstream_gene_variant,,ENST00000532857,;ZNF516,non_coding_transcript_exon_variant,,ENST00000524431,;	A	ENSG00000101493	ENST00000443185	Transcript	missense_variant	2009	1691	564	S/L	tCg/tTg	rs569947953	.	.	-1	ZNF516	HGNC	28990	protein_coding	YES	.	ENSP00000394757	ZN516_HUMAN	F5H2K2_HUMAN	UPI00001394A1	.	deleterious(0)	benign(0.171)	3/8	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF3	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCCGAGTCA	by1000G	2	ESCA
SMARCA4	0	.	GRCh37	19	11132513	11132513	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2729C>T	p.Thr910Met	p.T910M	ENST00000429416	20/36	54	34	20	35	35	0	SMARCA4,missense_variant,p.Thr910Met,ENST00000450717,;SMARCA4,missense_variant,p.Thr910Met,ENST00000358026,;SMARCA4,missense_variant,p.Thr910Met,ENST00000413806,;SMARCA4,missense_variant,p.Thr910Met,ENST00000590574,;SMARCA4,missense_variant,p.Thr910Met,ENST00000444061,;SMARCA4,missense_variant,p.Thr910Met,ENST00000344626,;SMARCA4,missense_variant,p.Thr910Met,ENST00000541122,;SMARCA4,missense_variant,p.Thr910Met,ENST00000429416,;SMARCA4,missense_variant,p.Thr910Met,ENST00000589677,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586122,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000587988,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;	T	ENSG00000127616	ENST00000429416	Transcript	missense_variant	3010	2729	910	T/M	aCg/aTg	COSM88025,COSM1226753	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	probably_damaging(0.99)	20/36	.	Superfamily_domains:SSF52540,SMART_domains:SM00487,Pfam_domain:PF00176,Gene3D:3.40.50.300,hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.T910M|c.2729C>T|13,SITE|p.T910M|c.2729C>T|7	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGACGGGCA	.	5	ESCA
EMR2	0	.	GRCh37	19	14846768	14846768	+	3'UTR	SNP	A	A	G	rs779591944	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*280T>C	.	.	ENST00000315576	21/21	10	5	5	15	15	0	EMR2,3_prime_UTR_variant,,ENST00000346057,;EMR2,3_prime_UTR_variant,,ENST00000353005,;EMR2,3_prime_UTR_variant,,ENST00000353876,;EMR2,3_prime_UTR_variant,,ENST00000315576,;EMR2,3_prime_UTR_variant,,ENST00000392967,;EMR2,downstream_gene_variant,,ENST00000594076,;EMR2,downstream_gene_variant,,ENST00000594294,;EMR2,downstream_gene_variant,,ENST00000595839,;EMR2,downstream_gene_variant,,ENST00000392965,;ZNF333,downstream_gene_variant,,ENST00000540689,;EMR2,downstream_gene_variant,,ENST00000596991,;EMR2,non_coding_transcript_exon_variant,,ENST00000360222,;	G	ENSG00000127507	ENST00000315576	Transcript	3_prime_UTR_variant	3204	.	.	.	.	rs779591944	.	.	-1	EMR2	HGNC	3337	protein_coding	YES	CCDS32935.1	ENSP00000319883	EMR2_HUMAN	.	UPI000016393A	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTTCTATAGCT	.	3	ESCA
TPM4	0	.	GRCh37	19	16186866	16186866	+	Missense_Mutation	SNP	G	G	C	rs755151675	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>C	p.Glu42Gln	p.E42Q	ENST00000538887	2/10	64	47	17	85	85	0	TPM4,missense_variant,p.Glu26Gln,ENST00000586499,;TPM4,missense_variant,p.Glu42Gln,ENST00000344824,;TPM4,missense_variant,p.Glu5Gln,ENST00000586833,;TPM4,missense_variant,p.Glu42Gln,ENST00000589897,;TPM4,missense_variant,p.Glu42Gln,ENST00000538887,;TPM4,upstream_gene_variant,,ENST00000300933,;TPM4,upstream_gene_variant,,ENST00000588410,;TPM4,upstream_gene_variant,,ENST00000588507,;TPM4,upstream_gene_variant,,ENST00000588483,;TPM4,upstream_gene_variant,,ENST00000590180,;TPM4,upstream_gene_variant,,ENST00000587201,;	C	ENSG00000167460	ENST00000538887	Transcript	missense_variant	211	124	42	E/Q	Gag/Cag	rs755151675	.	.	1	TPM4	HGNC	12013	protein_coding	YES	CCDS46007.1	ENSP00000439135	TPM4_HUMAN	K7EPV9_HUMAN,K7EMU5_HUMAN,K7ELP0_HUMAN	UPI000002B5B9	.	tolerated(0.05)	possibly_damaging(0.484)	2/10	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19269:SF40,hmmpanther:PTHR19269,Gene3D:1.20.5.340,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AGGAGGAGCTG	.	3	ESCA
TPM4	0	.	GRCh37	19	16186908	16186908	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166G>A	p.Glu56Lys	p.E56K	ENST00000538887	2/10	93	62	31	116	116	0	TPM4,missense_variant,p.Glu40Lys,ENST00000586499,;TPM4,missense_variant,p.Glu56Lys,ENST00000344824,;TPM4,missense_variant,p.Glu19Lys,ENST00000586833,;TPM4,missense_variant,p.Glu56Lys,ENST00000589897,;TPM4,missense_variant,p.Glu56Lys,ENST00000538887,;TPM4,upstream_gene_variant,,ENST00000300933,;TPM4,upstream_gene_variant,,ENST00000588410,;TPM4,upstream_gene_variant,,ENST00000588507,;TPM4,upstream_gene_variant,,ENST00000588483,;TPM4,upstream_gene_variant,,ENST00000590180,;TPM4,upstream_gene_variant,,ENST00000587201,;	A	ENSG00000167460	ENST00000538887	Transcript	missense_variant	253	166	56	E/K	Gag/Aag	.	.	.	1	TPM4	HGNC	12013	protein_coding	YES	CCDS46007.1	ENSP00000439135	TPM4_HUMAN	K7EPV9_HUMAN,K7EMU5_HUMAN,K7ELP0_HUMAN	UPI000002B5B9	.	deleterious(0.02)	benign(0.004)	2/10	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19269:SF40,hmmpanther:PTHR19269,Pfam_domain:PF00261,Gene3D:1.20.5.340,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AGGACGAGCTG	.	3	ESCA
UNC13A	0	.	GRCh37	19	17740954	17740954	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3669G>T	p.Lys1223Asn	p.K1223N	ENST00000519716	30/44	63	40	22	73	73	0	UNC13A,missense_variant,p.Lys1223Asn,ENST00000252773,;UNC13A,missense_variant,p.Lys1223Asn,ENST00000519716,;UNC13A,missense_variant,p.Lys1221Asn,ENST00000550896,;UNC13A,missense_variant,p.Lys1223Asn,ENST00000552293,;UNC13A,missense_variant,p.Lys1223Asn,ENST00000551649,;UNC13A,missense_variant,p.Lys1311Asn,ENST00000428389,;UNC13A,upstream_gene_variant,,ENST00000601528,;	A	ENSG00000130477	ENST00000519716	Transcript	missense_variant	3669	3669	1223	K/N	aaG/aaT	.	.	.	-1	UNC13A	HGNC	23150	protein_coding	YES	CCDS46013.2	ENSP00000429562	UN13A_HUMAN	.	UPI00006C19A7	.	deleterious(0)	probably_damaging(0.982)	30/44	.	PROSITE_profiles:PS51258,hmmpanther:PTHR10480	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACCTTGGC	.	5	ESCA
ZNF430	0	.	GRCh37	19	21203604	21203604	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3G>A	.	.	ENST00000261560	1/5	135	89	45	129	129	0	ZNF430,5_prime_UTR_variant,,ENST00000595401,;ZNF430,5_prime_UTR_variant,,ENST00000594110,;ZNF430,5_prime_UTR_variant,,ENST00000599548,;ZNF430,5_prime_UTR_variant,,ENST00000261560,;ZNF430,non_coding_transcript_exon_variant,,ENST00000595833,;	A	ENSG00000118620	ENST00000261560	Transcript	5_prime_UTR_variant	179	.	.	.	.	.	.	.	1	ZNF430	HGNC	20808	protein_coding	YES	CCDS32978.1	ENSP00000261560	ZN430_HUMAN	Q69YQ2_HUMAN,Q2NKJ9_HUMAN	UPI000020389E	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTAGAAATG	.	5	ESCA
SF3A2	0	.	GRCh37	19	2243467	2243469	+	In_Frame_Del	DEL	CCT	CCT	-	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	CCT	CCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58_60delTCC	p.Ser20del	p.S20del	ENST00000221494	2/9	65	44	21	62	62	0	SF3A2,inframe_deletion,p.Ser20del,ENST00000221494,;SF3A2,inframe_deletion,p.Ser20del,ENST00000586396,;SF3A2,non_coding_transcript_exon_variant,,ENST00000590034,;SF3A2,non_coding_transcript_exon_variant,,ENST00000592839,;SF3A2,non_coding_transcript_exon_variant,,ENST00000592314,;SF3A2,non_coding_transcript_exon_variant,,ENST00000591121,;SF3A2,upstream_gene_variant,,ENST00000587637,;SF3A2,upstream_gene_variant,,ENST00000589118,;	-	ENSG00000104897	ENST00000221494	Transcript	inframe_deletion	468-470	50-52	17-18	AS/A	gCCTcc/gcc	.	.	.	1	SF3A2	HGNC	10766	protein_coding	YES	CCDS12084.1	ENSP00000221494	SF3A2_HUMAN	K7EP23_HUMAN	UPI0000135468	.	.	.	2/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23205:SF0,hmmpanther:PTHR23205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCGTGGCCTCCTCC	.	2	ESCA
ZNF492	0	.	GRCh37	19	22847630	22847630	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1159C>T	p.His387Tyr	p.H387Y	ENST00000456783	4/4	85	66	19	87	87	0	ZNF492,missense_variant,p.His387Tyr,ENST00000456783,;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,;	T	ENSG00000229676	ENST00000456783	Transcript	missense_variant	1403	1159	387	H/Y	Cat/Tat	.	.	.	1	ZNF492	HGNC	23707	protein_coding	YES	CCDS46032.1	ENSP00000413660	ZN492_HUMAN	.	UPI00001C200B	.	deleterious(0.01)	possibly_damaging(0.514)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF108,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATTCATACT	.	5	ESCA
DIRAS1	0	.	GRCh37	19	2716404	2716404	+	3'UTR	SNP	G	G	T	rs144939018	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*804C>A	.	.	ENST00000323469	2/2	16	11	4	19	19	0	DIRAS1,3_prime_UTR_variant,,ENST00000323469,;AC006538.4,downstream_gene_variant,,ENST00000586572,;DIRAS1,downstream_gene_variant,,ENST00000588128,;DIRAS1,downstream_gene_variant,,ENST00000585334,;	T	ENSG00000176490	ENST00000323469	Transcript	3_prime_UTR_variant	1585	.	.	.	.	rs144939018	.	.	-1	DIRAS1	HGNC	19127	protein_coding	YES	CCDS12092.1	ENSP00000325836	DIRA1_HUMAN	K7EN06_HUMAN	UPI000000D876	.	.	.	2/2	.	.	A:0.0060	A:0.0227	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCGCCATG	byFrequency|byCluster|by1000G	4	ESCA
C19orf55	0	.	GRCh37	19	36253035	36253035	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427C>G	p.Gln143Glu	p.Q143E	ENST00000544099	4/11	72	37	35	100	100	0	C19orf55,missense_variant,p.Gln43Glu,ENST00000421853,;C19orf55,missense_variant,p.Gln75Glu,ENST00000542134,;C19orf55,missense_variant,p.Gln143Glu,ENST00000301165,;C19orf55,missense_variant,p.Gln143Glu,ENST00000537459,;C19orf55,missense_variant,p.Gln143Glu,ENST00000544099,;C19orf55,missense_variant,p.Gln143Glu,ENST00000396908,;C19orf55,missense_variant,p.Gln58Glu,ENST00000444637,;C19orf55,missense_variant,p.Gln143Glu,ENST00000536950,;C19orf55,missense_variant,p.Gln58Glu,ENST00000545674,;HSPB6,upstream_gene_variant,,ENST00000592984,;C19orf55,intron_variant,,ENST00000544876,;C19orf55,upstream_gene_variant,,ENST00000542591,;C19orf55,missense_variant,p.Gln116Glu,ENST00000601095,;C19orf55,missense_variant,p.Gln143Glu,ENST00000535581,;C19orf55,3_prime_UTR_variant,,ENST00000539771,;C19orf55,non_coding_transcript_exon_variant,,ENST00000600988,;	G	ENSG00000167595	ENST00000544099	Transcript	missense_variant	490	427	143	Q/E	Caa/Gaa	.	.	.	1	C19orf55	HGNC	25204	protein_coding	YES	.	ENSP00000467267	.	K7EP81_HUMAN	UPI00006CA356	.	tolerated(0.13)	benign(0.039)	4/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22045	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTCAAAGT	.	5	ESCA
ARHGAP33	0	.	GRCh37	19	36279303	36279303	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3353C>T	p.Ser1118Phe	p.S1118F	ENST00000314737	21/21	55	31	23	50	50	0	ARHGAP33,missense_variant,p.Ser1279Phe,ENST00000007510,;ARHGAP33,missense_variant,p.Ser1115Phe,ENST00000378944,;ARHGAP33,missense_variant,p.Ser855Phe,ENST00000587447,;ARHGAP33,missense_variant,p.Ser1118Phe,ENST00000314737,;ARHGAP33,intron_variant,,ENST00000588248,;AC002398.5,downstream_gene_variant,,ENST00000564335,;AC002398.5,downstream_gene_variant,,ENST00000433059,;AC002398.5,downstream_gene_variant,,ENST00000567313,;ARHGAP33,downstream_gene_variant,,ENST00000591438,;ARHGAP33,downstream_gene_variant,,ENST00000593034,;ARHGAP33,downstream_gene_variant,,ENST00000587984,;ARHGAP33,downstream_gene_variant,,ENST00000601474,;	T	ENSG00000004777	ENST00000314737	Transcript	missense_variant	3437	3353	1118	S/F	tCt/tTt	COSM1304457	.	.	1	ARHGAP33	HGNC	23085	protein_coding	YES	CCDS12477.1	ENSP00000320038	RHG33_HUMAN	.	UPI000013F8F9	.	deleterious_low_confidence(0)	probably_damaging(0.953)	21/21	.	hmmpanther:PTHR15729,hmmpanther:PTHR15729:SF8	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTCTGAGG	.	5	ESCA
ARHGAP33	0	.	GRCh37	19	36279603	36279603	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*272C>G	.	.	ENST00000314737	21/21	67	45	22	68	68	0	ARHGAP33,splice_region_variant,,ENST00000588248,;ARHGAP33,3_prime_UTR_variant,,ENST00000007510,;ARHGAP33,3_prime_UTR_variant,,ENST00000378944,;ARHGAP33,3_prime_UTR_variant,,ENST00000587447,;ARHGAP33,3_prime_UTR_variant,,ENST00000314737,;AC002398.5,downstream_gene_variant,,ENST00000564335,;AC002398.5,downstream_gene_variant,,ENST00000433059,;AC002398.5,downstream_gene_variant,,ENST00000567313,;ARHGAP33,downstream_gene_variant,,ENST00000591438,;ARHGAP33,downstream_gene_variant,,ENST00000593034,;ARHGAP33,downstream_gene_variant,,ENST00000587984,;ARHGAP33,downstream_gene_variant,,ENST00000601474,;	G	ENSG00000004777	ENST00000314737	Transcript	3_prime_UTR_variant	3737	.	.	.	.	.	.	.	1	ARHGAP33	HGNC	23085	protein_coding	YES	CCDS12477.1	ENSP00000320038	RHG33_HUMAN	.	UPI000013F8F9	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTCCAGGA	.	5	ESCA
SAMD4B	0	.	GRCh37	19	39870719	39870719	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1644G>A	p.%3D	p.Q548Q	ENST00000314471	12/16	56	34	22	85	85	0	SAMD4B,synonymous_variant,p.%3D,ENST00000598913,;SAMD4B,synonymous_variant,p.%3D,ENST00000314471,;SAMD4B,intron_variant,,ENST00000596368,;SAMD4B,upstream_gene_variant,,ENST00000598605,;SAMD4B,downstream_gene_variant,,ENST00000600018,;SAMD4B,non_coding_transcript_exon_variant,,ENST00000595476,;SAMD4B,downstream_gene_variant,,ENST00000596319,;	A	ENSG00000179134	ENST00000314471	Transcript	synonymous_variant	2679	1644	548	Q	caG/caA	.	.	.	1	SAMD4B	HGNC	25492	protein_coding	YES	CCDS33020.1	ENSP00000317224	SMAG2_HUMAN	M0QY61_HUMAN,M0QXV2_HUMAN	UPI00001D8165	.	.	.	12/16	.	hmmpanther:PTHR12515,hmmpanther:PTHR12515:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCAGAAAGG	.	5	ESCA
ZNF780B	0	.	GRCh37	19	40539193	40539193	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1071G>C	.	.	ENST00000434248	5/5	26	19	7	24	24	0	ZNF780B,3_prime_UTR_variant,,ENST00000434248,;ZNF780B,downstream_gene_variant,,ENST00000598845,;ZNF780B,downstream_gene_variant,,ENST00000221355,;ZNF780B,downstream_gene_variant,,ENST00000595995,;	G	ENSG00000128000	ENST00000434248	Transcript	3_prime_UTR_variant	3639	.	.	.	.	.	.	.	-1	ZNF780B	HGNC	33109	protein_coding	YES	CCDS46077.1	ENSP00000391641	Z780B_HUMAN	M0R0W9_HUMAN,C9JTJ1_HUMAN	UPI000007137F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATTCACTGC	.	5	ESCA
PSG6	0	.	GRCh37	19	43411757	43411757	+	Missense_Mutation	SNP	C	C	T	rs148457672	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956G>A	p.Arg319His	p.R319H	ENST00000292125	4/6	265	181	83	272	272	0	PSG6,missense_variant,p.Arg319His,ENST00000187910,;PSG6,missense_variant,p.Arg319His,ENST00000292125,;PSG6,intron_variant,,ENST00000402603,;PSG6,downstream_gene_variant,,ENST00000594375,;PSG6,3_prime_UTR_variant,,ENST00000599753,;PSG6,intron_variant,,ENST00000595062,;PSG6,downstream_gene_variant,,ENST00000402456,;PSG6,downstream_gene_variant,,ENST00000484292,;	T	ENSG00000170848	ENST00000292125	Transcript	missense_variant	1001	956	319	R/H	cGc/cAc	rs148457672	.	.	-1	PSG6	HGNC	9523	protein_coding	YES	CCDS12613.1	ENSP00000292125	PSG6_HUMAN	.	UPI00001327A1	.	tolerated(0.38)	benign(0.009)	4/6	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR19955:SF126,hmmpanther:PTHR19955,PROSITE_profiles:PS50835	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	T:0.0005	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTGCGGATG	byCluster|by1000G	5	ESCA
SNRPD2	0	.	GRCh37	19	46195207	46195207	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-61C>T	.	.	ENST00000342669	1/3	56	43	13	83	83	0	SNRPD2,5_prime_UTR_variant,,ENST00000588301,;SNRPD2,5_prime_UTR_variant,,ENST00000342669,;QPCTL,upstream_gene_variant,,ENST00000366382,;QPCTL,upstream_gene_variant,,ENST00000012049,;SNRPD2,upstream_gene_variant,,ENST00000587367,;SNRPD2,upstream_gene_variant,,ENST00000391932,;SNRPD2,upstream_gene_variant,,ENST00000585392,;SNRPD2,upstream_gene_variant,,ENST00000588599,;SNRPD2,upstream_gene_variant,,ENST00000590212,;SNRPD2,downstream_gene_variant,,ENST00000587579,;QPCTL,upstream_gene_variant,,ENST00000591606,;	A	ENSG00000125743	ENST00000342669	Transcript	5_prime_UTR_variant	385	.	.	.	.	.	.	.	-1	SNRPD2	HGNC	11159	protein_coding	YES	CCDS33053.1	ENSP00000342374	SMD2_HUMAN	K7EJB5_HUMAN	UPI0000028222	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGAGAGAGG	.	5	ESCA
ETFB	0	.	GRCh37	19	51857574	51857574	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319C>T	p.Pro107Ser	p.P107S	ENST00000354232	1/5	46	33	12	44	44	0	ETFB,missense_variant,p.Pro107Ser,ENST00000354232,;ETFB,intron_variant,,ENST00000596253,;ETFB,intron_variant,,ENST00000309244,;CTD-2616J11.9,downstream_gene_variant,,ENST00000600974,;ETFB,intron_variant,,ENST00000593992,;CTD-2616J11.11,intron_variant,,ENST00000600067,;	A	ENSG00000105379	ENST00000354232	Transcript	missense_variant	2787	319	107	P/S	Cct/Tct	.	.	.	-1	ETFB	HGNC	3482	protein_coding	YES	CCDS33085.1	ENSP00000346173	ETFB_HUMAN	.	UPI00001A8223	.	deleterious_low_confidence(0)	benign(0.07)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGGAGGGG	.	5	ESCA
ZNF480	0	.	GRCh37	19	52825738	52825738	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1235C>G	p.Ser412Ter	p.S412*	ENST00000595962	5/5	64	43	20	70	70	0	ZNF480,stop_gained,p.Ser369Ter,ENST00000334564,;ZNF480,stop_gained,p.Ser335Ter,ENST00000335090,;ZNF480,stop_gained,p.Ser412Ter,ENST00000595962,;ZNF480,3_prime_UTR_variant,,ENST00000490272,;ZNF480,downstream_gene_variant,,ENST00000598016,;CTD-2525I3.6,intron_variant,,ENST00000594379,;ZNF480,stop_gained,p.Ser412Ter,ENST00000468240,;	G	ENSG00000198464	ENST00000595962	Transcript	stop_gained	1301	1235	412	S/*	tCa/tGa	.	.	.	1	ZNF480	HGNC	23305	protein_coding	YES	CCDS12850.2	ENSP00000471754	ZN480_HUMAN	.	UPI0000202AEF	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF12,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTCAAATC	.	5	ESCA
ZNF765	0	.	GRCh37	19	53913101	53913102	+	3'UTR	INS	-	-	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*722dupT	.	.	ENST00000396408	4/4	99	79	20	70	70	0	ZNF765,3_prime_UTR_variant,,ENST00000396408,;ZNF765,intron_variant,,ENST00000594030,;ZNF765,downstream_gene_variant,,ENST00000505866,;ZNF765,intron_variant,,ENST00000504146,;ZNF765,intron_variant,,ENST00000507045,;ZNF765,intron_variant,,ENST00000504235,;RPL39P36,upstream_gene_variant,,ENST00000490784,;	T	ENSG00000196417	ENST00000396408	Transcript	3_prime_UTR_variant	2410-2411	.	.	.	.	.	.	.	1	ZNF765	HGNC	25092	protein_coding	YES	CCDS46171.1	ENSP00000379689	ZN765_HUMAN	D6RF03_HUMAN	UPI000040C508	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACTTCATACTG	.	3	ESCA
TPM3P9	0	.	GRCh37	19	53945524	53945524	+	RNA	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.521A>G	.	.	ENST00000424846	2/2	52	34	18	76	76	0	TPM3P9,non_coding_transcript_exon_variant,,ENST00000424846,;ZNF761,intron_variant,,ENST00000447129,;ZNF761,intron_variant,,ENST00000454407,;ZNF761,upstream_gene_variant,,ENST00000366293,;ZNF761,upstream_gene_variant,,ENST00000429310,;TPM3P9,non_coding_transcript_exon_variant,,ENST00000492121,;	G	ENSG00000241015	ENST00000424846	Transcript	non_coding_transcript_exon_variant	521	.	.	.	.	.	.	.	1	TPM3P9	HGNC	44142	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGAAGGAGA	.	5	ESCA
TNNI3	0	.	GRCh37	19	55668465	55668465	+	Missense_Mutation	SNP	G	G	A	rs267607128	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61C>T	p.Arg21Cys	p.R21C	ENST00000344887	3/8	117	76	41	112	112	0	TNNI3,missense_variant,p.Arg21Cys,ENST00000344887,;DNAAF3,downstream_gene_variant,,ENST00000391720,;DNAAF3,downstream_gene_variant,,ENST00000524407,;DNAAF3,downstream_gene_variant,,ENST00000455045,;DNAAF3,downstream_gene_variant,,ENST00000588076,;TNNI3,upstream_gene_variant,,ENST00000586858,;TNNI3,upstream_gene_variant,,ENST00000588882,;DNAAF3,downstream_gene_variant,,ENST00000527223,;CTD-2587H24.5,upstream_gene_variant,,ENST00000591665,;TNNI3,non_coding_transcript_exon_variant,,ENST00000590463,;TNNI3,non_coding_transcript_exon_variant,,ENST00000586669,;DNAAF3,downstream_gene_variant,,ENST00000587789,;DNAAF3,downstream_gene_variant,,ENST00000527166,;DNAAF3,downstream_gene_variant,,ENST00000527292,;CTD-2587H24.4,3_prime_UTR_variant,,ENST00000587871,;TNNI3,non_coding_transcript_exon_variant,,ENST00000586446,;TNNI3,non_coding_transcript_exon_variant,,ENST00000587176,;DNAAF3,downstream_gene_variant,,ENST00000526959,;TNNI3,upstream_gene_variant,,ENST00000585806,;DNAAF3,downstream_gene_variant,,ENST00000533527,;TNNI3,upstream_gene_variant,,ENST00000589864,;DNAAF3,downstream_gene_variant,,ENST00000528412,;	A	ENSG00000129991	ENST00000344887	Transcript	missense_variant	204	61	21	R/C	Cgc/Tgc	rs267607128,CM034574	.	.	-1	TNNI3	HGNC	11947	protein_coding	YES	CCDS42628.1	ENSP00000341838	TNNI3_HUMAN	Q6FGX2_HUMAN,A9UD06_HUMAN,A8CN18_HUMAN,A8CLQ8_HUMAN	UPI0000155A10	.	deleterious(0)	unknown(0)	3/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13738,hmmpanther:PTHR13738:SF4,Pfam_domain:PF11636	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGCGTCTGA	.	5	ESCA
CCDC106	0	.	GRCh37	19	56162854	56162854	+	Missense_Mutation	SNP	G	G	T	rs148442107	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.519G>T	p.Arg173Ser	p.R173S	ENST00000586790	4/5	24	17	7	29	29	0	CCDC106,missense_variant,p.Arg173Ser,ENST00000591578,;CCDC106,missense_variant,p.Arg173Ser,ENST00000588740,;CCDC106,missense_variant,p.Arg138Ser,ENST00000591241,;CCDC106,missense_variant,p.Arg173Ser,ENST00000586790,;CCDC106,missense_variant,p.Arg173Ser,ENST00000308964,;U2AF2,upstream_gene_variant,,ENST00000308924,;CCDC106,downstream_gene_variant,,ENST00000592996,;U2AF2,upstream_gene_variant,,ENST00000450554,;CCDC106,downstream_gene_variant,,ENST00000593069,;CCDC106,downstream_gene_variant,,ENST00000587213,;CCDC106,downstream_gene_variant,,ENST00000586864,;U2AF2,upstream_gene_variant,,ENST00000587196,;U2AF2,upstream_gene_variant,,ENST00000588850,;	T	ENSG00000173581	ENST00000586790	Transcript	missense_variant	1423	519	173	R/S	agG/agT	rs148442107	.	.	1	CCDC106	HGNC	30181	protein_coding	YES	CCDS33118.1	ENSP00000465757	CC106_HUMAN	K7ES29_HUMAN,K7ER22_HUMAN,K7EMP7_HUMAN	UPI0000072074	.	deleterious(0)	probably_damaging(0.997)	4/5	.	hmmpanther:PTHR16477,hmmpanther:PTHR16477:SF1	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	A:0.0007	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAGGCAGCG	byFrequency|byCluster|by1000G	5	ESCA
SAFB2	0	.	GRCh37	19	5622770	5622770	+	5'UTR	SNP	G	G	A	rs540292495	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-44C>T	.	.	ENST00000252542	1/21	48	32	16	34	34	0	SAFB2,5_prime_UTR_variant,,ENST00000252542,;SAFB2,intron_variant,,ENST00000590262,;SAFB,upstream_gene_variant,,ENST00000588852,;SAFB,upstream_gene_variant,,ENST00000454510,;SAFB,upstream_gene_variant,,ENST00000292123,;SAFB,upstream_gene_variant,,ENST00000538656,;SAFB,upstream_gene_variant,,ENST00000433404,;SAFB,upstream_gene_variant,,ENST00000592224,;SAFB,upstream_gene_variant,,ENST00000586934,;SAFB2,5_prime_UTR_variant,,ENST00000591120,;SAFB,upstream_gene_variant,,ENST00000589863,;SAFB,upstream_gene_variant,,ENST00000591666,;	A	ENSG00000130254	ENST00000252542	Transcript	5_prime_UTR_variant	222	.	.	.	.	rs540292495	.	.	-1	SAFB2	HGNC	21605	protein_coding	YES	CCDS32879.1	ENSP00000252542	SAFB2_HUMAN	.	UPI0000071DB7	.	.	.	1/21	.	.	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCCGGCAGC	by1000G	5	ESCA
NLRP4	0	.	GRCh37	19	56369442	56369442	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683T>G	p.Phe228Cys	p.F228C	ENST00000301295	3/10	63	41	21	66	66	0	NLRP4,missense_variant,p.Phe228Cys,ENST00000301295,;NLRP4,missense_variant,p.Phe228Cys,ENST00000346986,;NLRP4,missense_variant,p.Phe153Cys,ENST00000587891,;NLRP4,upstream_gene_variant,,ENST00000589437,;NLRP4,downstream_gene_variant,,ENST00000587464,;	G	ENSG00000160505	ENST00000301295	Transcript	missense_variant	1105	683	228	F/C	tTc/tGc	.	.	.	1	NLRP4	HGNC	22943	protein_coding	YES	CCDS12936.1	ENSP00000301295	NALP4_HUMAN	K7ES09_HUMAN	UPI000013E6FD	.	deleterious(0)	probably_damaging(1)	3/10	.	PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106,Pfam_domain:PF05729,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGTTCGTCA	.	5	ESCA
S1PR1	0	.	GRCh37	1	101705189	101705189	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.649A>G	p.Ile217Val	p.I217V	ENST00000305352	2/2	17	12	5	18	18	0	S1PR1,missense_variant,p.Ile217Val,ENST00000305352,;RP4-575N6.5,upstream_gene_variant,,ENST00000561748,;RP4-575N6.4,upstream_gene_variant,,ENST00000432195,;S1PR1,downstream_gene_variant,,ENST00000475821,;S1PR1,downstream_gene_variant,,ENST00000475289,;	G	ENSG00000170989	ENST00000305352	Transcript	missense_variant	1024	649	217	I/V	Atc/Gtc	.	.	.	1	S1PR1	HGNC	3165	protein_coding	YES	CCDS777.1	ENSP00000305416	S1PR1_HUMAN	Q7L853_HUMAN	UPI0000050421	.	deleterious(0)	probably_damaging(0.98)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF16,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCATCGTC	.	5	ESCA
COL11A1	0	.	GRCh37	1	103467522	103467522	+	Missense_Mutation	SNP	G	G	A	rs771448295	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2101C>T	p.Leu701Phe	p.L701F	ENST00000370096	24/67	113	81	32	116	116	0	COL11A1,missense_variant,p.Leu585Phe,ENST00000512756,;COL11A1,missense_variant,p.Leu662Phe,ENST00000353414,;COL11A1,missense_variant,p.Leu701Phe,ENST00000370096,;COL11A1,missense_variant,p.Leu713Phe,ENST00000358392,;COL11A1,non_coding_transcript_exon_variant,,ENST00000461720,;COL11A1,non_coding_transcript_exon_variant,,ENST00000475980,;	A	ENSG00000060718	ENST00000370096	Transcript	missense_variant	2414	2101	701	L/F	Ctt/Ttt	rs771448295	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	unknown(0)	24/67	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF42,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAGACCCT	.	5	ESCA
AMY1C	0	.	GRCh37	1	104297202	104297202	+	Silent	SNP	T	T	C	rs756303606	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.960T>C	p.%3D	p.H320H	ENST00000370079	6/10	295	248	46	375	375	0	AMY1C,synonymous_variant,p.%3D,ENST00000370079,;	C	ENSG00000187733	ENST00000370079	Transcript	synonymous_variant	1024	960	320	H	caT/caC	rs756303606	.	.	1	AMY1C	HGNC	476	protein_coding	YES	CCDS30784.1	ENSP00000359096	AMY1_HUMAN	Q5T085_HUMAN,Q5T084_HUMAN	UPI0000125AA9	.	.	.	6/10	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Pfam_domain:PF00128,Gene3D:3.20.20.80,SMART_domains:SM00642,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGACATGGCGC	.	4	ESCA
NTNG1	0	.	GRCh37	1	108023343	108023343	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501C>T	p.Arg501Trp	p.R501W	ENST00000370068	8/8	35	32	3	42	42	0	NTNG1,missense_variant,p.Arg400Trp,ENST00000370074,;NTNG1,missense_variant,p.Arg422Trp,ENST00000370070,;NTNG1,missense_variant,p.Arg442Trp,ENST00000370071,;NTNG1,missense_variant,p.Arg456Trp,ENST00000370072,;NTNG1,missense_variant,p.Arg422Trp,ENST00000370067,;NTNG1,missense_variant,p.Arg501Trp,ENST00000370073,;NTNG1,missense_variant,p.Arg467Trp,ENST00000370061,;NTNG1,missense_variant,p.Arg501Trp,ENST00000542803,;NTNG1,missense_variant,p.Arg501Trp,ENST00000370068,;NTNG1,missense_variant,p.Arg442Trp,ENST00000370066,;NTNG1,missense_variant,p.Arg456Trp,ENST00000370065,;	T	ENSG00000162631	ENST00000370068	Transcript	missense_variant	2347	1501	501	R/W	Cgg/Tgg	.	.	.	1	NTNG1	HGNC	23319	protein_coding	YES	CCDS44180.1	ENSP00000359085	NTNG1_HUMAN	Q5IEC8_HUMAN	UPI0000458A3E	.	deleterious(0.01)	probably_damaging(0.918)	8/8	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGCTGCGGTGC	.	3	ESCA
MTOR	0	.	GRCh37	1	11187803	11187803	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6094G>A	p.Glu2032Lys	p.E2032K	ENST00000361445	44/58	35	19	15	51	51	0	MTOR,missense_variant,p.Glu2032Lys,ENST00000361445,;MTOR,missense_variant,p.Glu237Lys,ENST00000376838,;MTOR,downstream_gene_variant,,ENST00000495435,;	T	ENSG00000198793	ENST00000361445	Transcript	missense_variant	6171	6094	2032	E/K	Gaa/Aaa	.	.	.	-1	MTOR	HGNC	3942	protein_coding	YES	CCDS127.1	ENSP00000354558	MTOR_HUMAN	Q96QW8_HUMAN,B1AKQ2_HUMAN,B1AKP8_HUMAN	UPI000012ABD3	.	deleterious(0)	probably_damaging(0.994)	44/58	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF63,Gene3D:3fapB00,Pfam_domain:PF08771,Superfamily_domains:0045511	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCCAGGC	.	5	ESCA
CD101	0	.	GRCh37	1	117568494	117568494	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2792C>T	p.Ser931Leu	p.S931L	ENST00000256652	8/10	30	22	8	29	29	0	CD101,missense_variant,p.Ser931Leu,ENST00000369470,;CD101,missense_variant,p.Ser931Leu,ENST00000256652,;RP11-27K13.3,non_coding_transcript_exon_variant,,ENST00000445523,;RP11-27K13.3,downstream_gene_variant,,ENST00000421254,;	T	ENSG00000134256	ENST00000256652	Transcript	missense_variant	2850	2792	931	S/L	tCa/tTa	.	.	.	1	CD101	HGNC	5949	protein_coding	YES	CCDS891.1	ENSP00000256652	IGSF2_HUMAN	.	UPI000013CF1F	.	deleterious(0)	possibly_damaging(0.814)	8/10	.	hmmpanther:PTHR12207:SF20,hmmpanther:PTHR12207,Gene3D:2.60.40.10,SMART_domains:SM00409	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAGTCACAGC	.	2	ESCA
PRAMEF10	0	.	GRCh37	1	12954550	12954550	+	Missense_Mutation	SNP	G	G	A	rs757290180	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.733C>T	p.Arg245Cys	p.R245C	ENST00000235347	3/4	262	165	97	309	309	0	PRAMEF10,missense_variant,p.Arg245Cys,ENST00000235347,;	A	ENSG00000187545	ENST00000235347	Transcript	missense_variant	813	733	245	R/C	Cgt/Tgt	rs757290180,COSM4021498	.	.	-1	PRAMEF10	HGNC	27997	protein_coding	YES	CCDS41255.1	ENSP00000235347	PRA10_HUMAN	.	UPI0000199949	.	tolerated(0.08)	benign(0.001)	3/4	.	Superfamily_domains:SSF52047,PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224:SF16,hmmpanther:PTHR14224	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACGCTCAT	byFrequency	5	ESCA
PDE4DIP	0	.	GRCh37	1	144859760	144859760	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6324A>C	p.Gln2108His	p.Q2108H	ENST00000369356	38/44	46	41	5	56	56	0	PDE4DIP,missense_variant,p.Gln2108His,ENST00000369356,;PDE4DIP,missense_variant,p.Gln2108His,ENST00000369354,;PDE4DIP,missense_variant,p.Gln2244His,ENST00000369359,;PDE4DIP,missense_variant,p.Gln2193His,ENST00000530740,;PDE4DIP,missense_variant,p.Gln2002His,ENST00000313382,;PDE4DIP,intron_variant,,ENST00000530130,;RP4-791M13.4,intron_variant,,ENST00000532137,;PDE4DIP,splice_region_variant,,ENST00000524974,;PDE4DIP,intron_variant,,ENST00000526664,;PDE4DIP,upstream_gene_variant,,ENST00000525630,;PDE4DIP,splice_region_variant,,ENST00000534466,;PDE4DIP,intron_variant,,ENST00000530062,;PDE4DIP,downstream_gene_variant,,ENST00000525886,;PDE4DIP,upstream_gene_variant,,ENST00000534367,;PDE4DIP,downstream_gene_variant,,ENST00000479369,;PDE4DIP,upstream_gene_variant,,ENST00000533768,;PDE4DIP,downstream_gene_variant,,ENST00000481227,;PDE4DIP,downstream_gene_variant,,ENST00000527901,;	G	ENSG00000178104	ENST00000369356	Transcript	missense_variant	6615	6324	2108	Q/H	caA/caC	.	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	MYOME_HUMAN	I1VE15_HUMAN	UPI0000458A81	.	tolerated(0.17)	possibly_damaging(0.834)	38/44	.	hmmpanther:PTHR13895:SF2,hmmpanther:PTHR13895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTACCTTGGAG	.	4	ESCA
PIP5K1A	0	.	GRCh37	1	151219428	151219428	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1673C>T	p.Ser558Leu	p.S558L	ENST00000368888	15/16	53	31	22	55	55	0	PIP5K1A,stop_gained,p.Gln167Ter,ENST00000414290,;PIP5K1A,missense_variant,p.Ser518Leu,ENST00000441902,;PIP5K1A,missense_variant,p.Ser496Leu,ENST00000368890,;PIP5K1A,missense_variant,p.Ser546Leu,ENST00000409426,;PIP5K1A,missense_variant,p.Ser545Leu,ENST00000349792,;PIP5K1A,missense_variant,p.Ser558Leu,ENST00000368888,;PIP5K1A,non_coding_transcript_exon_variant,,ENST00000489625,;	T	ENSG00000143398	ENST00000368888	Transcript	missense_variant	2095	1673	558	S/L	tCa/tTa	COSM1472598	.	.	1	PIP5K1A	HGNC	8994	protein_coding	YES	CCDS44219.1	ENSP00000357883	PI51A_HUMAN	P78517_HUMAN,A6PW58_HUMAN	UPI000006F821	.	deleterious_low_confidence(0)	benign(0.149)	15/16	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGTCAGAGT	.	5	ESCA
SELENBP1	0	.	GRCh37	1	151338111	151338111	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972C>T	p.%3D	p.F324F	ENST00000368868	9/12	36	24	11	30	30	0	SELENBP1,synonymous_variant,p.%3D,ENST00000424475,;SELENBP1,synonymous_variant,p.%3D,ENST00000368868,;SELENBP1,synonymous_variant,p.%3D,ENST00000435071,;SELENBP1,synonymous_variant,p.%3D,ENST00000447402,;SELENBP1,synonymous_variant,p.%3D,ENST00000426705,;SELENBP1,downstream_gene_variant,,ENST00000427867,;SELENBP1,downstream_gene_variant,,ENST00000458566,;SELENBP1,downstream_gene_variant,,ENST00000473693,;SELENBP1,downstream_gene_variant,,ENST00000498494,;SELENBP1,3_prime_UTR_variant,,ENST00000455397,;SELENBP1,3_prime_UTR_variant,,ENST00000423070,;SELENBP1,3_prime_UTR_variant,,ENST00000443708,;SELENBP1,3_prime_UTR_variant,,ENST00000427977,;SELENBP1,non_coding_transcript_exon_variant,,ENST00000470345,;SELENBP1,non_coding_transcript_exon_variant,,ENST00000474352,;SELENBP1,non_coding_transcript_exon_variant,,ENST00000493560,;SELENBP1,non_coding_transcript_exon_variant,,ENST00000463664,;SELENBP1,downstream_gene_variant,,ENST00000492643,;SELENBP1,downstream_gene_variant,,ENST00000465273,;SELENBP1,downstream_gene_variant,,ENST00000455839,;	A	ENSG00000143416	ENST00000368868	Transcript	synonymous_variant	1064	972	324	F	ttC/ttT	.	.	.	-1	SELENBP1	HGNC	10719	protein_coding	YES	CCDS995.1	ENSP00000357861	SBP1_HUMAN	C9JVL0_HUMAN	UPI000007300D	.	.	.	9/12	.	hmmpanther:PTHR23300,Pfam_domain:PF05694,Gene3D:2.130.10.10,Superfamily_domains:0047643	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCTGAAGTA	.	5	ESCA
CELA2A	0	.	GRCh37	1	15788089	15788089	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163T>C	p.Tyr55His	p.Y55H	ENST00000359621	3/8	79	48	30	100	100	0	CELA2A,missense_variant,p.Tyr55His,ENST00000359621,;CELA2A,non_coding_transcript_exon_variant,,ENST00000459653,;CELA2A,downstream_gene_variant,,ENST00000497590,;CELA2B,upstream_gene_variant,,ENST00000494280,;	C	ENSG00000142615	ENST00000359621	Transcript	missense_variant	188	163	55	Y/H	Tac/Cac	.	.	.	1	CELA2A	HGNC	24609	protein_coding	YES	CCDS157.1	ENSP00000352639	CEL2A_HUMAN	.	UPI0000129E36	.	tolerated(0.38)	benign(0.068)	3/8	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24257,hmmpanther:PTHR24257:SF13,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGGTACCAC	.	5	ESCA
EPHA2	0	.	GRCh37	1	16459852	16459852	+	Nonsense_Mutation	SNP	C	C	A	rs772510492	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1876G>T	p.Glu626Ter	p.E626*	ENST00000358432	11/17	33	23	10	41	41	0	EPHA2,stop_gained,p.Glu626Ter,ENST00000358432,;EPHA2,non_coding_transcript_exon_variant,,ENST00000462805,;EPHA2,downstream_gene_variant,,ENST00000480202,;	A	ENSG00000142627	ENST00000358432	Transcript	stop_gained	2031	1876	626	E/*	Gag/Tag	rs772510492	.	.	-1	EPHA2	HGNC	3386	protein_coding	YES	CCDS169.1	ENSP00000351209	EPHA2_HUMAN	Q96HF4_HUMAN,Q8IZL0_HUMAN	UPI00000731AB	.	.	.	11/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF306,hmmpanther:PTHR24416,PROSITE_patterns:PS00107,Pfam_domain:PF07714,Gene3D:3.30.200.20,SMART_domains:SM00219,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTCCCCAA	byFrequency	5	ESCA
TBX19	0	.	GRCh37	1	168283399	168283399	+	3'UTR	SNP	G	G	T	rs530015294	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1159G>T	.	.	ENST00000367821	8/8	13	10	3	19	19	0	TBX19,3_prime_UTR_variant,,ENST00000431969,;TBX19,3_prime_UTR_variant,,ENST00000367821,;TBX19,downstream_gene_variant,,ENST00000441464,;TBX19,non_coding_transcript_exon_variant,,ENST00000465440,;	T	ENSG00000143178	ENST00000367821	Transcript	3_prime_UTR_variant	2557	.	.	.	.	rs530015294	.	.	1	TBX19	HGNC	11596	protein_coding	YES	CCDS1272.1	ENSP00000356795	TBX19_HUMAN	.	UPI000003176C	.	.	.	8/8	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTGGCTGAA	by1000G	2	ESCA
RABGAP1L	0	.	GRCh37	1	174652677	174652677	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1842T>G	p.Asp614Glu	p.D614E	ENST00000251507	15/21	102	70	32	102	102	0	RABGAP1L,missense_variant,p.Asp614Glu,ENST00000251507,;RABGAP1L,non_coding_transcript_exon_variant,,ENST00000474375,;	G	ENSG00000152061	ENST00000251507	Transcript	missense_variant	2016	1842	614	D/E	gaT/gaG	.	.	.	1	RABGAP1L	HGNC	24663	protein_coding	YES	CCDS1314.1	ENSP00000251507	RBG1L_HUMAN	F1LJ00_HUMAN	UPI0000458A9F	.	deleterious(0)	probably_damaging(0.993)	15/21	.	Superfamily_domains:SSF47923,SMART_domains:SM00164,Gene3D:2qq8A02,Pfam_domain:PF00566,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF205,PROSITE_profiles:PS50086	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGATGAAGA	.	5	ESCA
TOR1AIP1	0	.	GRCh37	1	179887823	179887823	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*449G>A	.	.	ENST00000606911	10/10	14	8	6	25	25	0	TOR1AIP1,3_prime_UTR_variant,,ENST00000606911,;TOR1AIP1,3_prime_UTR_variant,,ENST00000528443,;TOR1AIP1,3_prime_UTR_variant,,ENST00000435319,;TOR1AIP1,3_prime_UTR_variant,,ENST00000271583,;TOR1AIP1,downstream_gene_variant,,ENST00000447964,;TOR1AIP1,downstream_gene_variant,,ENST00000527391,;TOR1AIP1,downstream_gene_variant,,ENST00000531630,;TOR1AIP1,downstream_gene_variant,,ENST00000474875,;	A	ENSG00000143337	ENST00000606911	Transcript	3_prime_UTR_variant	2392	.	.	.	.	.	.	.	1	TOR1AIP1	HGNC	29456	protein_coding	YES	CCDS1335.1	ENSP00000476687	.	.	UPI0000203C95	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGAGTTCCT	.	5	ESCA
EIF2D	0	.	GRCh37	1	206776495	206776495	+	Silent	SNP	G	G	C	rs782300669	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>G	p.%3D	p.L198L	ENST00000271764	6/15	67	46	21	66	66	0	EIF2D,synonymous_variant,p.%3D,ENST00000271764,;EIF2D,synonymous_variant,p.%3D,ENST00000437518,;EIF2D,intron_variant,,ENST00000367114,;EIF2D,non_coding_transcript_exon_variant,,ENST00000461334,;EIF2D,upstream_gene_variant,,ENST00000484492,;EIF2D,upstream_gene_variant,,ENST00000468891,;	C	ENSG00000143486	ENST00000271764	Transcript	synonymous_variant	803	594	198	L	ctC/ctG	rs782300669	.	.	-1	EIF2D	HGNC	6583	protein_coding	YES	CCDS1465.1	ENSP00000271764	EIF2D_HUMAN	.	UPI00000710E1	.	.	.	6/15	.	hmmpanther:PTHR12217:SF4,hmmpanther:PTHR12217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTGAGATC	byFrequency	5	ESCA
PRKCZ	0	.	GRCh37	1	2113342	2113342	+	Intron	SNP	C	C	T	rs780392269	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1576-2680C>T	.	.	ENST00000378567	.	88	58	29	63	63	0	PRKCZ,intron_variant,,ENST00000400921,;PRKCZ,intron_variant,,ENST00000461106,;PRKCZ,intron_variant,,ENST00000378567,;PRKCZ,intron_variant,,ENST00000400920,;C1orf86,downstream_gene_variant,,ENST00000400919,;C1orf86,downstream_gene_variant,,ENST00000400918,;RP11-181G12.2,non_coding_transcript_exon_variant,,ENST00000333854,;RP11-181G12.2,non_coding_transcript_exon_variant,,ENST00000536678,;RP11-181G12.2,downstream_gene_variant,,ENST00000444529,;PRKCZ,intron_variant,,ENST00000479263,;C1orf86,downstream_gene_variant,,ENST00000469733,;PRKCZ,3_prime_UTR_variant,,ENST00000478770,;PRKCZ,intron_variant,,ENST00000505322,;C1orf86,downstream_gene_variant,,ENST00000414253,;C1orf86,downstream_gene_variant,,ENST00000428120,;	T	ENSG00000067606	ENST00000378567	Transcript	intron_variant	.	.	.	.	.	rs780392269	.	.	1	PRKCZ	HGNC	9412	protein_coding	YES	CCDS37.1	ENSP00000367830	KPCZ_HUMAN	J3KRP7_HUMAN,F2Z2H9_HUMAN,D6RGG1_HUMAN,D6RG01_HUMAN,D6REZ8_HUMAN,D6RDM0_HUMAN,D6RD31_HUMAN,D6RCN4_HUMAN,D6RC84_HUMAN,D6RBD4_HUMAN,D6RAU1_HUMAN,D6RAN5_HUMAN	UPI0000169EB7	.	.	.	.	16/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGCGCACA	.	5	ESCA
LDLRAD2	0	.	GRCh37	1	22148718	22148718	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10C>G	.	.	ENST00000344642	5/5	94	65	29	134	134	0	LDLRAD2,3_prime_UTR_variant,,ENST00000344642,;LDLRAD2,3_prime_UTR_variant,,ENST00000543870,;HSPG2,downstream_gene_variant,,ENST00000374695,;LDLRAD2,non_coding_transcript_exon_variant,,ENST00000484271,;HSPG2,downstream_gene_variant,,ENST00000486901,;HSPG2,downstream_gene_variant,,ENST00000481644,;	G	ENSG00000187942	ENST00000344642	Transcript	3_prime_UTR_variant	1016	.	.	.	.	.	.	.	1	LDLRAD2	HGNC	32071	protein_coding	YES	CCDS30624.1	ENSP00000340988	LRAD2_HUMAN	.	UPI0000470177	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATCAAAGA	.	5	ESCA
ENAH	0	.	GRCh37	1	225684578	225684578	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*899C>T	.	.	ENST00000366844	15/15	94	55	38	85	85	0	ENAH,3_prime_UTR_variant,,ENST00000366844,;ENAH,downstream_gene_variant,,ENST00000366843,;ENAH,downstream_gene_variant,,ENST00000284563,;ENAH,intron_variant,,ENST00000488523,;ENAH,non_coding_transcript_exon_variant,,ENST00000358675,;ENAH,downstream_gene_variant,,ENST00000498108,;ENAH,downstream_gene_variant,,ENST00000483952,;	A	ENSG00000154380	ENST00000366844	Transcript	3_prime_UTR_variant	3127	.	.	.	.	.	.	.	-1	ENAH	HGNC	18271	protein_coding	YES	CCDS31041.1	ENSP00000355809	ENAH_HUMAN	.	UPI0000203FDB	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGTGTGACA	.	5	ESCA
LUZP1	0	.	GRCh37	1	23412009	23412009	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3379G>T	.	.	ENST00000302291	5/5	59	39	19	47	47	0	LUZP1,3_prime_UTR_variant,,ENST00000374623,;LUZP1,3_prime_UTR_variant,,ENST00000418342,;LUZP1,3_prime_UTR_variant,,ENST00000302291,;KDM1A,downstream_gene_variant,,ENST00000542151,;LUZP1,downstream_gene_variant,,ENST00000314174,;KDM1A,downstream_gene_variant,,ENST00000356634,;KDM1A,downstream_gene_variant,,ENST00000494920,;KDM1A,downstream_gene_variant,,ENST00000400181,;RP1-184J9.2,intron_variant,,ENST00000427154,;KDM1A,downstream_gene_variant,,ENST00000602503,;	A	ENSG00000169641	ENST00000302291	Transcript	3_prime_UTR_variant	7412	.	.	.	.	.	.	.	-1	LUZP1	HGNC	14985	protein_coding	YES	CCDS30628.1	ENSP00000303758	LUZP1_HUMAN	E5RHU7_HUMAN,E5RFK8_HUMAN	UPI000020466A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCTCATAAC	.	5	ESCA
AGO1	0	.	GRCh37	1	36379442	36379442	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1583-1G>A	.	p.X528_splice	ENST00000373204	.	61	43	17	57	57	0	AGO1,splice_acceptor_variant,,ENST00000373204,;AGO1,splice_acceptor_variant,,ENST00000373206,;	A	ENSG00000092847	ENST00000373204	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	AGO1	HGNC	3262	protein_coding	YES	CCDS398.1	ENSP00000362300	AGO1_HUMAN	Q5TA58_HUMAN	UPI000012D07D	.	.	.	.	12/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTAGCTGAG	.	5	ESCA
NPHP4	0	.	GRCh37	1	5925321	5925321	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3657G>T	p.%3D	p.L1219L	ENST00000378156	27/30	70	45	24	72	72	0	NPHP4,synonymous_variant,p.%3D,ENST00000378156,;MIR4689,upstream_gene_variant,,ENST00000582517,;NPHP4,non_coding_transcript_exon_variant,,ENST00000478423,;NPHP4,3_prime_UTR_variant,,ENST00000378169,;NPHP4,3_prime_UTR_variant,,ENST00000489180,;NPHP4,non_coding_transcript_exon_variant,,ENST00000378161,;NPHP4,non_coding_transcript_exon_variant,,ENST00000460696,;NPHP4,downstream_gene_variant,,ENST00000468253,;	A	ENSG00000131697	ENST00000378156	Transcript	synonymous_variant	3923	3657	1219	L	ctG/ctT	.	.	.	-1	NPHP4	HGNC	19104	protein_coding	YES	CCDS44052.1	ENSP00000367398	NPHP4_HUMAN	.	UPI00001303E5	.	.	.	27/30	.	hmmpanther:PTHR31043:SF3,hmmpanther:PTHR31043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCGCCAGCCA	.	5	ESCA
IL23R	0	.	GRCh37	1	67724812	67724812	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1A>G	.	.	ENST00000347310	11/11	43	21	22	47	47	0	IL23R,3_prime_UTR_variant,,ENST00000425614,;IL23R,3_prime_UTR_variant,,ENST00000347310,;IL23R,3_prime_UTR_variant,,ENST00000395227,;IL23R,3_prime_UTR_variant,,ENST00000371002,;IL23R,non_coding_transcript_exon_variant,,ENST00000473881,;	G	ENSG00000162594	ENST00000347310	Transcript	3_prime_UTR_variant	2062	.	.	.	.	.	.	.	1	IL23R	HGNC	19100	protein_coding	YES	CCDS637.1	ENSP00000321345	IL23R_HUMAN	D9N2T9_HUMAN,B6HY80_HUMAN	UPI000004CACD	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTAGAGCTGT	.	5	ESCA
LPPR4	0	.	GRCh37	1	99774777	99774777	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2211T>A	.	.	ENST00000370185	7/7	50	34	16	69	69	0	LPPR4,3_prime_UTR_variant,,ENST00000370185,;LPPR4,3_prime_UTR_variant,,ENST00000457765,;LPPR4,3_prime_UTR_variant,,ENST00000370184,;	A	ENSG00000117600	ENST00000370185	Transcript	3_prime_UTR_variant	5000	.	.	.	.	.	.	.	1	LPPR4	Uniprot_gn	.	protein_coding	YES	CCDS757.1	ENSP00000359204	LPPR4_HUMAN	.	UPI0000161229	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAATTTGTT	.	5	ESCA
FER1L4	0	.	GRCh37	20	34192495	34192495	+	RNA	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.374G>T	.	.	ENST00000431615	5/45	51	36	15	58	58	0	FER1L4,non_coding_transcript_exon_variant,,ENST00000430275,;FER1L4,non_coding_transcript_exon_variant,,ENST00000426117,;FER1L4,non_coding_transcript_exon_variant,,ENST00000325076,;FER1L4,non_coding_transcript_exon_variant,,ENST00000434843,;FER1L4,upstream_gene_variant,,ENST00000400461,;FER1L4,upstream_gene_variant,,ENST00000412452,;FER1L4,non_coding_transcript_exon_variant,,ENST00000431615,;	A	ENSG00000088340	ENST00000431615	Transcript	non_coding_transcript_exon_variant	374	.	.	.	.	.	.	.	-1	FER1L4	HGNC	15801	unitary_pseudogene	YES	.	.	.	.	.	.	.	.	5/45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCCAGTAG	.	5	ESCA
SLC9A8	0	.	GRCh37	20	48471998	48471998	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.641C>A	p.Ser214Tyr	p.S214Y	ENST00000417961	8/16	93	60	32	108	108	0	SLC9A8,missense_variant,p.Ser214Tyr,ENST00000417961,;SLC9A8,missense_variant,p.Ser198Tyr,ENST00000361573,;SLC9A8,5_prime_UTR_variant,,ENST00000541138,;SLC9A8,5_prime_UTR_variant,,ENST00000539601,;	A	ENSG00000197818	ENST00000417961	Transcript	missense_variant	851	641	214	S/Y	tCt/tAt	.	.	.	1	SLC9A8	HGNC	20728	protein_coding	YES	CCDS58774.1	ENSP00000416418	SL9A8_HUMAN	B7Z3B1_HUMAN,B4DIV9_HUMAN	UPI00017A7E08	.	deleterious(0)	probably_damaging(0.999)	8/16	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999,Prints_domain:PR01084	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCTGCTG	.	5	ESCA
GNAS	0	.	GRCh37	20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2530C>T	p.Arg844Cys	p.R844C	ENST00000371100	8/13	90	66	24	93	93	0	GNAS,missense_variant,p.Arg201Cys,ENST00000371085,;GNAS,missense_variant,p.Arg187Cys,ENST00000306090,;GNAS,missense_variant,p.Arg142Cys,ENST00000604005,;GNAS,missense_variant,p.Arg202Cys,ENST00000354359,;GNAS,missense_variant,p.Arg187Cys,ENST00000371095,;GNAS,missense_variant,p.Arg830Cys,ENST00000371102,;GNAS,missense_variant,p.Arg186Cys,ENST00000265620,;GNAS,missense_variant,p.Arg844Cys,ENST00000371100,;GNAS,3_prime_UTR_variant,,ENST00000313949,;GNAS,3_prime_UTR_variant,,ENST00000371075,;GNAS,downstream_gene_variant,,ENST00000419558,;GNAS,downstream_gene_variant,,ENST00000349036,;GNAS,downstream_gene_variant,,ENST00000603546,;GNAS,downstream_gene_variant,,ENST00000450130,;GNAS,non_coding_transcript_exon_variant,,ENST00000477931,;GNAS,non_coding_transcript_exon_variant,,ENST00000481039,;GNAS,non_coding_transcript_exon_variant,,ENST00000482112,;GNAS,non_coding_transcript_exon_variant,,ENST00000467321,;GNAS,non_coding_transcript_exon_variant,,ENST00000480232,;GNAS,non_coding_transcript_exon_variant,,ENST00000472183,;GNAS,non_coding_transcript_exon_variant,,ENST00000464788,;GNAS,non_coding_transcript_exon_variant,,ENST00000488652,;GNAS,non_coding_transcript_exon_variant,,ENST00000493958,;GNAS,non_coding_transcript_exon_variant,,ENST00000488546,;GNAS,non_coding_transcript_exon_variant,,ENST00000470512,;GNAS,non_coding_transcript_exon_variant,,ENST00000492907,;GNAS,non_coding_transcript_exon_variant,,ENST00000468895,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,non_coding_transcript_exon_variant,,ENST00000480975,;GNAS,non_coding_transcript_exon_variant,,ENST00000467227,;GNAS,non_coding_transcript_exon_variant,,ENST00000476935,;GNAS,intron_variant,,ENST00000494081,;GNAS,downstream_gene_variant,,ENST00000485673,;GNAS,downstream_gene_variant,,ENST00000469431,;GNAS,downstream_gene_variant,,ENST00000490374,;GNAS,downstream_gene_variant,,ENST00000478585,;GNAS,non_coding_transcript_exon_variant,,ENST00000479025,;GNAS,non_coding_transcript_exon_variant,,ENST00000487862,;GNAS,non_coding_transcript_exon_variant,,ENST00000476196,;GNAS,non_coding_transcript_exon_variant,,ENST00000487981,;GNAS,non_coding_transcript_exon_variant,,ENST00000496934,;GNAS,upstream_gene_variant,,ENST00000475610,;	T	ENSG00000087460	ENST00000371100	Transcript	missense_variant	3082	2530	844	R/C	Cgt/Tgt	COSM27899,COSM1757313,COSM27887,COSM1566192,COSM123397	.	.	1	GNAS	HGNC	4392	protein_coding	YES	CCDS46622.1	ENSP00000360141	GNAS1_HUMAN	S4R3W4_HUMAN,S4R3V9_HUMAN,S4R3F1_HUMAN,S4R3E3_HUMAN,S4R379_HUMAN,B0AZR9_HUMAN	UPI0000E444AE	.	deleterious(0.01)	probably_damaging(1)	8/13	.	hmmpanther:PTHR10218:SF36,hmmpanther:PTHR10218,Gene3D:1.10.400.10,Pfam_domain:PF00503,SMART_domains:SM00275,Superfamily_domains:SSF52540,Superfamily_domains:SSF47895,Prints_domain:PR00318	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R844C|c.2530C>T|31,SITE|p.R201C|c.601C>T|420,BUFFER|p.R201S|c.601C>A|15,BUFFER|p.R844H|c.2531G>A|25,BUFFER|p.R201L|c.602G>T|3,BUFFER|p.R201H|c.602G>A|306	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCCGTGTC	.	5	ESCA
SYCP2	0	.	GRCh37	20	58441562	58441562	+	Missense_Mutation	SNP	C	C	T	rs760667527	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4208G>A	p.Ser1403Asn	p.S1403N	ENST00000357552	40/45	122	75	47	96	96	0	SYCP2,missense_variant,p.Ser89Asn,ENST00000412613,;SYCP2,missense_variant,p.Ser1403Asn,ENST00000357552,;SYCP2,missense_variant,p.Ser1403Asn,ENST00000371001,;	T	ENSG00000196074	ENST00000357552	Transcript	missense_variant	4434	4208	1403	S/N	aGt/aAt	rs760667527	.	.	-1	SYCP2	HGNC	11490	protein_coding	YES	CCDS13482.1	ENSP00000350162	SYCP2_HUMAN	A2A341_HUMAN	UPI0000135683	.	deleterious(0)	benign(0.093)	40/45	.	hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGACTTTGA	.	5	ESCA
LAMA5	0	.	GRCh37	20	60886979	60886979	+	Missense_Mutation	SNP	G	G	A	rs763726733	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9632C>T	p.Thr3211Met	p.T3211M	ENST00000252999	70/80	175	111	64	190	190	0	LAMA5,missense_variant,p.Thr3211Met,ENST00000252999,;ADRM1,downstream_gene_variant,,ENST00000253003,;LAMA5,upstream_gene_variant,,ENST00000492698,;LAMA5,missense_variant,p.Thr376Met,ENST00000370691,;LAMA5,non_coding_transcript_exon_variant,,ENST00000462415,;LAMA5,upstream_gene_variant,,ENST00000495695,;LAMA5,downstream_gene_variant,,ENST00000491036,;LAMA5,downstream_gene_variant,,ENST00000468786,;LAMA5,downstream_gene_variant,,ENST00000471042,;	A	ENSG00000130702	ENST00000252999	Transcript	missense_variant	9699	9632	3211	T/M	aCg/aTg	rs763726733	.	.	-1	LAMA5	HGNC	6485	protein_coding	YES	CCDS33502.1	ENSP00000252999	LAMA5_HUMAN	O75079_HUMAN	UPI0000161FDC	.	.	benign(0.091)	70/80	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10574:SF261,hmmpanther:PTHR10574,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCGTGGCA	byFrequency	5	ESCA
MYT1	0	.	GRCh37	20	62844938	62844938	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1569G>A	p.%3D	p.E523E	ENST00000328439	10/23	45	34	11	60	60	0	MYT1,synonymous_variant,p.%3D,ENST00000536311,;MYT1,synonymous_variant,p.%3D,ENST00000360149,;MYT1,synonymous_variant,p.%3D,ENST00000328439,;	A	ENSG00000196132	ENST00000328439	Transcript	synonymous_variant	1933	1569	523	E	gaG/gaA	.	.	.	1	MYT1	HGNC	7622	protein_coding	YES	CCDS13558.1	ENSP00000327465	MYT1_HUMAN	.	UPI000012FBFA	.	.	.	10/23	.	hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGAGAAGCA	.	5	ESCA
PLCB1	0	.	GRCh37	20	8707959	8707959	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1682G>C	p.Arg561Thr	p.R561T	ENST00000338037	17/32	23	11	12	32	32	0	PLCB1,missense_variant,p.Arg561Thr,ENST00000378641,;PLCB1,missense_variant,p.Arg561Thr,ENST00000338037,;PLCB1,missense_variant,p.Arg561Thr,ENST00000378637,;PLCB1,non_coding_transcript_exon_variant,,ENST00000494924,;PLCB1,missense_variant,p.Arg302Thr,ENST00000487210,;	C	ENSG00000182621	ENST00000338037	Transcript	missense_variant	1709	1682	561	R/T	aGa/aCa	COSM3549408,COSM3549409	.	.	1	PLCB1	HGNC	15917	protein_coding	YES	CCDS13102.1	ENSP00000338185	PLCB1_HUMAN	.	UPI0000131A8F	.	tolerated(0.06)	possibly_damaging(0.573)	17/32	.	PROSITE_profiles:PS50008,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF12,Pfam_domain:PF00387,Gene3D:3.20.20.190,PIRSF_domain:PIRSF000956,SMART_domains:SM00149,Superfamily_domains:SSF51695	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAAGAAATA	.	5	ESCA
DONSON	0	.	GRCh37	21	34951684	34951718	+	Frame_Shift_Del	DEL	CAGATGTTAAATACAGCAGTTGGCTCGTGTGGATA	CAGATGTTAAATACAGCAGTTGGCTCGTGTGGATA	-	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	CAGATGTTAAATACAGCAGTTGGCTCGTGTGGATA	CAGATGTTAAATACAGCAGTTGGCTCGTGTGGATA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501_1535delTATCCACACGAGCCAACTGCTGTATTTAACATCTG	p.Tyr501ProfsTer8	p.Y501Pfs*8	ENST00000303071	9/10	98	77	21	112	112	0	DONSON,frameshift_variant,p.Tyr487ProfsTer8,ENST00000303113,;DONSON,frameshift_variant,p.Tyr501ProfsTer8,ENST00000303071,;DONSON,frameshift_variant,p.Ile453LeufsTer55,ENST00000453626,;DONSON,frameshift_variant,p.Tyr472ProfsTer8,ENST00000437395,;DONSON,intron_variant,,ENST00000432378,;SON,downstream_gene_variant,,ENST00000436227,;DONSON,downstream_gene_variant,,ENST00000440810,;SON,downstream_gene_variant,,ENST00000381692,;AP000304.1,upstream_gene_variant,,ENST00000595468,;SON,downstream_gene_variant,,ENST00000290239,;SON,downstream_gene_variant,,ENST00000356577,;SON,downstream_gene_variant,,ENST00000473102,;SON,downstream_gene_variant,,ENST00000470533,;SON,downstream_gene_variant,,ENST00000467616,;SON,downstream_gene_variant,,ENST00000484294,;DONSON,3_prime_UTR_variant,,ENST00000457359,;DONSON,3_prime_UTR_variant,,ENST00000442660,;DONSON,3_prime_UTR_variant,,ENST00000417871,;DONSON,3_prime_UTR_variant,,ENST00000444517,;DONSON,non_coding_transcript_exon_variant,,ENST00000460557,;SON,downstream_gene_variant,,ENST00000478183,;DONSON,upstream_gene_variant,,ENST00000439593,;DONSON,downstream_gene_variant,,ENST00000462566,;SON,downstream_gene_variant,,ENST00000455528,;SON,downstream_gene_variant,,ENST00000465834,;SON,downstream_gene_variant,,ENST00000491794,;SON,downstream_gene_variant,,ENST00000477419,;SON,downstream_gene_variant,,ENST00000457208,;	-	ENSG00000159147	ENST00000303071	Transcript	frameshift_variant	1568-1602	1501-1535	501-512	YPHEPTAVFNIC/X	TATCCACACGAGCCAACTGCTGTATTTAACATCTGc/c	.	.	.	-1	DONSON	HGNC	2993	protein_coding	YES	CCDS13632.1	ENSP00000307143	DONS_HUMAN	.	UPI00001296AD	.	.	.	9/10	.	hmmpanther:PTHR12972	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCAGGCAGATGTTAAATACAGCAGTTGGCTCGTGTGGATACAGTA	.	3	ESCA
DYRK1A	0	.	GRCh37	21	38865336	38865336	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.969G>C	p.Gln323His	p.Q323H	ENST00000398960	7/11	79	51	28	70	70	0	DYRK1A,missense_variant,p.Gln323His,ENST00000451934,;DYRK1A,missense_variant,p.Gln314His,ENST00000339659,;DYRK1A,missense_variant,p.Gln95His,ENST00000455387,;DYRK1A,missense_variant,p.Gln323His,ENST00000398956,;DYRK1A,missense_variant,p.Gln323His,ENST00000398960,;DYRK1A,missense_variant,p.Gln323His,ENST00000338785,;DYRK1A,missense_variant,p.Gln323His,ENST00000321219,;	C	ENSG00000157540	ENST00000398960	Transcript	missense_variant	1044	969	323	Q/H	caG/caC	.	.	.	1	DYRK1A	HGNC	3091	protein_coding	YES	CCDS42925.1	ENSP00000381932	DYR1A_HUMAN	Q76N25_HUMAN,N0GVR9_HUMAN,F8WAP0_HUMAN,E7EMI5_HUMAN	UPI0000129A31	.	deleterious(0)	probably_damaging(0.999)	7/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24058:SF28,hmmpanther:PTHR24058,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCAGAGTCG	.	5	ESCA
DSCAM	0	.	GRCh37	21	41424027	41424027	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5043C>A	p.%3D	p.R1681R	ENST00000400454	30/33	71	50	21	77	77	0	DSCAM,synonymous_variant,p.%3D,ENST00000404019,;DSCAM,synonymous_variant,p.%3D,ENST00000400454,;	T	ENSG00000171587	ENST00000400454	Transcript	synonymous_variant	5521	5043	1681	R	cgC/cgA	.	.	.	-1	DSCAM	HGNC	3039	protein_coding	YES	CCDS42929.1	ENSP00000383303	DSCAM_HUMAN	.	UPI00000422DF	.	.	.	30/33	.	hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R1681C|c.5041C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAGCGATC	.	5	ESCA
PPM1F	0	.	GRCh37	22	22273962	22273962	+	3'UTR	SNP	C	C	T	rs760094772	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3503G>A	.	.	ENST00000263212	8/8	19	9	10	22	22	0	PPM1F,3_prime_UTR_variant,,ENST00000407142,;PPM1F,3_prime_UTR_variant,,ENST00000263212,;PPM1F,downstream_gene_variant,,ENST00000538191,;PPM1F,downstream_gene_variant,,ENST00000496143,;	T	ENSG00000100034	ENST00000263212	Transcript	3_prime_UTR_variant	4974	.	.	.	.	rs760094772	.	.	-1	PPM1F	HGNC	19388	protein_coding	YES	CCDS13796.1	ENSP00000263212	PPM1F_HUMAN	Q6IPC0_HUMAN,Q0VGL7_HUMAN,C9J2F3_HUMAN,B5MCT7_HUMAN,A0M8Q2_HUMAN	UPI000012A61C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCACCGAGAC	.	5	ESCA
SLC16A8	0	.	GRCh37	22	38478026	38478026	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228C>A	p.Ser76Arg	p.S76R	ENST00000320521	3/5	106	66	40	105	105	0	SLC16A8,missense_variant,p.Ser76Arg,ENST00000320521,;SLC16A8,missense_variant,p.Ser76Arg,ENST00000427592,;BAIAP2L2,downstream_gene_variant,,ENST00000428572,;BAIAP2L2,downstream_gene_variant,,ENST00000381669,;SLC16A8,intron_variant,,ENST00000469516,;	T	ENSG00000100156	ENST00000320521	Transcript	missense_variant	337	228	76	S/R	agC/agA	.	.	.	-1	SLC16A8	HGNC	16270	protein_coding	YES	CCDS13966.1	ENSP00000321735	MOT3_HUMAN	B0QYL4_HUMAN	UPI000012F3C8	.	deleterious(0)	probably_damaging(0.998)	3/5	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11360:SF26,hmmpanther:PTHR11360,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00892,Pfam_domain:PF07690,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGCTGGA	.	5	ESCA
RPL3	0	.	GRCh37	22	39710147	39710147	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916G>A	p.Asp306Asn	p.D306N	ENST00000216146	7/10	44	28	16	47	47	0	RPL3,missense_variant,p.Asp254Asn,ENST00000401609,;RPL3,missense_variant,p.Asp306Asn,ENST00000216146,;RPL3,missense_variant,p.Asp254Asn,ENST00000402527,;RPL3,downstream_gene_variant,,ENST00000453303,;RPL3,downstream_gene_variant,,ENST00000427905,;SNORD83A,downstream_gene_variant,,ENST00000386747,;SNORD83B,upstream_gene_variant,,ENST00000386745,;SNORD43,downstream_gene_variant,,ENST00000583861,;RPL3,non_coding_transcript_exon_variant,,ENST00000465618,;RPL3,downstream_gene_variant,,ENST00000471290,;RPL3,downstream_gene_variant,,ENST00000459859,;RPL3,non_coding_transcript_exon_variant,,ENST00000481985,;RPL3,non_coding_transcript_exon_variant,,ENST00000467105,;RPL3,downstream_gene_variant,,ENST00000498462,;RPL3,upstream_gene_variant,,ENST00000464182,;RPL3,downstream_gene_variant,,ENST00000420536,;RPL3,upstream_gene_variant,,ENST00000473638,;RPL3,downstream_gene_variant,,ENST00000484358,;RPL3,downstream_gene_variant,,ENST00000460589,;RPL3,downstream_gene_variant,,ENST00000484615,;RPL3,downstream_gene_variant,,ENST00000461967,;	T	ENSG00000100316	ENST00000216146	Transcript	missense_variant	1090	916	306	D/N	Gac/Aac	.	.	.	-1	RPL3	HGNC	10332	protein_coding	YES	CCDS13988.1	ENSP00000346001	RL3_HUMAN	Q9NY85_HUMAN,Q9BT63_HUMAN,Q8TBW1_HUMAN,Q49AJ9_HUMAN,G5E9G0_HUMAN,B5MCW2_HUMAN,B4DN06_HUMAN	UPI0000167B7E	.	tolerated(0.13)	benign(0.136)	7/10	.	hmmpanther:PTHR11363,Gene3D:2.40.30.10,Pfam_domain:PF00297,Superfamily_domains:SSF50447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGTCAGTGG	.	5	ESCA
PPP6R2	0	.	GRCh37	22	50882849	50882849	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000395741	.	30	21	8	39	39	0	PPP6R2,3_prime_UTR_variant,,ENST00000359139,;PPP6R2,downstream_gene_variant,,ENST00000395741,;SBF1,downstream_gene_variant,,ENST00000418590,;SBF1,downstream_gene_variant,,ENST00000390679,;SBF1,downstream_gene_variant,,ENST00000348911,;PPP6R2,downstream_gene_variant,,ENST00000401672,;PPP6R2,downstream_gene_variant,,ENST00000427222,;SBF1,downstream_gene_variant,,ENST00000380817,;PPP6R2,downstream_gene_variant,,ENST00000395744,;PPP6R2,downstream_gene_variant,,ENST00000216061,;PPP6R2,downstream_gene_variant,,ENST00000473283,;PPP6R2,downstream_gene_variant,,ENST00000470046,;SBF1,downstream_gene_variant,,ENST00000473724,;SBF1,downstream_gene_variant,,ENST00000470434,;	A	ENSG00000100239	ENST00000395741	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	46	1	PPP6R2	HGNC	19253	protein_coding	YES	CCDS56235.1	ENSP00000379090	PP6R2_HUMAN	.	UPI0000453B02	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTGCCTGA	.	5	ESCA
AC140481.2	0	.	GRCh37	2	131331896	131331896	+	5'UTR	SNP	C	C	A	rs768231768	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-30C>A	.	.	ENST00000409982	2/3	59	48	11	56	56	0	AC140481.2,5_prime_UTR_variant,,ENST00000409982,;AC140481.2,5_prime_UTR_variant,,ENST00000409793,;AC140481.2,upstream_gene_variant,,ENST00000440359,;AC140481.2,intron_variant,,ENST00000414595,;AC140481.2,intron_variant,,ENST00000419965,;	A	ENSG00000183292	ENST00000409982	Transcript	5_prime_UTR_variant	142	.	.	.	.	rs768231768	.	.	1	AC140481.2	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000387081	.	B9A030_HUMAN	UPI000188179A	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACCAGCAAAGC	.	2	ESCA
NEB	0	.	GRCh37	2	152436107	152436107	+	Silent	SNP	G	G	A	rs546992311	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16449C>T	p.%3D	p.S5483S	ENST00000397345	105/182	28	23	5	34	34	0	NEB,synonymous_variant,p.%3D,ENST00000603639,;NEB,synonymous_variant,p.%3D,ENST00000427231,;NEB,synonymous_variant,p.%3D,ENST00000397345,;NEB,synonymous_variant,p.%3D,ENST00000604864,;NEB,synonymous_variant,p.%3D,ENST00000413693,;NEB,intron_variant,,ENST00000172853,;NEB,intron_variant,,ENST00000409198,;	A	ENSG00000183091	ENST00000397345	Transcript	synonymous_variant	16652	16449	5483	S	agC/agT	rs546992311	.	.	-1	NEB	HGNC	7720	protein_coding	YES	CCDS54407.1	ENSP00000380505	.	H7C2D0_HUMAN,F8WCL5_HUMAN	UPI0002065BA0	.	.	.	105/182	.	PROSITE_profiles:PS51216,hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227	A:0.0126	A:0	A:0.0159	.	A:0.0446	A:0	A:0.0072	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TTGGCGCTGCG	byFrequency|by1000G	2	ESCA
LRP2	0	.	GRCh37	2	170063036	170063036	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7194G>C	p.Leu2398Phe	p.L2398F	ENST00000263816	39/79	87	53	34	79	79	0	LRP2,missense_variant,p.Leu2398Phe,ENST00000263816,;	G	ENSG00000081479	ENST00000263816	Transcript	missense_variant	7480	7194	2398	L/F	ttG/ttC	.	.	.	-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	LRP2_HUMAN	Q9NP34_HUMAN,Q53TL0_HUMAN,Q4ZG84_HUMAN	UPI0000141BA5	.	.	possibly_damaging(0.846)	39/79	.	hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF220,Gene3D:2.120.10.30,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S2395S|c.7185T>C|4,BUFFER|p.S2395P|c.7183T>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCAAGGA	.	5	ESCA
SATB2	0	.	GRCh37	2	200136399	200136400	+	3'UTR	INS	-	-	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*534dupA	.	.	ENST00000417098	11/11	108	77	31	138	138	0	SATB2,3_prime_UTR_variant,,ENST00000260926,;SATB2,3_prime_UTR_variant,,ENST00000443023,;SATB2,3_prime_UTR_variant,,ENST00000417098,;SATB2,downstream_gene_variant,,ENST00000428695,;SATB2,downstream_gene_variant,,ENST00000457245,;	T	ENSG00000119042	ENST00000417098	Transcript	3_prime_UTR_variant	3553-3554	.	.	.	.	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAGTGGTTTTT	.	2	ESCA
NBEAL1	0	.	GRCh37	2	204058577	204058577	+	Silent	SNP	C	C	T	rs765999889	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6894C>T	p.%3D	p.D2298D	ENST00000449802	46/55	71	44	26	89	89	0	NBEAL1,synonymous_variant,p.%3D,ENST00000449802,;NBEAL1,synonymous_variant,p.%3D,ENST00000414576,;NBEAL1,downstream_gene_variant,,ENST00000460355,;AC011737.2,downstream_gene_variant,,ENST00000431098,;AC011737.2,downstream_gene_variant,,ENST00000314394,;	T	ENSG00000144426	ENST00000449802	Transcript	synonymous_variant	7227	6894	2298	D	gaC/gaT	rs765999889	.	.	1	NBEAL1	HGNC	20681	protein_coding	YES	CCDS46495.1	ENSP00000399903	NBEL1_HUMAN	.	UPI000194EC27	.	.	.	46/55	.	hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGACACTTC	.	5	ESCA
KLHL29	0	.	GRCh37	2	23914666	23914666	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1202C>T	p.Ser401Leu	p.S401L	ENST00000486442	7/14	65	41	24	60	60	0	KLHL29,missense_variant,p.Ser241Leu,ENST00000288548,;KLHL29,missense_variant,p.Ser401Leu,ENST00000486442,;KLHL29,non_coding_transcript_exon_variant,,ENST00000471654,;	T	ENSG00000119771	ENST00000486442	Transcript	missense_variant	1919	1202	401	S/L	tCg/tTg	.	.	.	1	KLHL29	HGNC	29404	protein_coding	YES	CCDS54335.1	ENSP00000420659	KLH29_HUMAN	Q53T86_HUMAN	UPI000058F1B6	.	deleterious(0.03)	possibly_damaging(0.562)	7/14	.	Superfamily_domains:SSF54695,SMART_domains:SM00225,Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR24412:SF10,hmmpanther:PTHR24412,PROSITE_profiles:PS50097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGACTCGGCCA	.	5	ESCA
ASXL2	0	.	GRCh37	2	26101071	26101078	+	Frame_Shift_Del	DEL	CCTACGTC	CCTACGTC	-	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	CCTACGTC	CCTACGTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14_21delGACGTAGG	p.Gly5GlufsTer25	p.G5Efs*25	ENST00000435504	1/13	99	71	28	123	123	0	ASXL2,frameshift_variant,p.Gly5GlufsTer25,ENST00000435504,;ASXL2,5_prime_UTR_variant,,ENST00000272341,;ASXL2,5_prime_UTR_variant,,ENST00000336112,;	-	ENSG00000143970	ENST00000435504	Transcript	frameshift_variant	308-315	14-21	5-7	GRR/X	gGACGTAGG/g	.	.	.	-1	ASXL2	HGNC	23805	protein_coding	YES	.	ENSP00000391447	ASXL2_HUMAN	.	UPI00001DFBE8	.	.	.	1/13	.	hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTCTTCCTACGTCCCTTT	.	3	ESCA
ADI1	0	.	GRCh37	2	3502816	3502816	+	Missense_Mutation	SNP	G	G	A	rs771440115	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.458C>T	p.Pro153Leu	p.P153L	ENST00000327435	4/4	64	41	23	87	87	0	ADI1,missense_variant,p.Pro147Leu,ENST00000382093,;ADI1,missense_variant,p.Pro153Leu,ENST00000327435,;ADI1,missense_variant,p.Pro91Leu,ENST00000415131,;RP11-1293J14.1,downstream_gene_variant,,ENST00000607415,;	A	ENSG00000182551	ENST00000327435	Transcript	missense_variant	707	458	153	P/L	cCg/cTg	rs771440115	.	.	-1	ADI1	HGNC	30576	protein_coding	YES	CCDS1653.1	ENSP00000333666	MTND_HUMAN	.	UPI000006D8C6	.	deleterious(0.03)	benign(0.405)	4/4	.	HAMAP:MF_03154,hmmpanther:PTHR23418,Gene3D:2.60.120.10,Pfam_domain:PF03079,Superfamily_domains:SSF51182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCGGTTCT	.	5	ESCA
FBXO11	0	.	GRCh37	2	48034444	48034444	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*813T>C	.	.	ENST00000403359	23/23	103	69	33	100	100	0	FBXO11,3_prime_UTR_variant,,ENST00000316377,;FBXO11,3_prime_UTR_variant,,ENST00000403359,;MSH6,3_prime_UTR_variant,,ENST00000234420,;FBXO11,3_prime_UTR_variant,,ENST00000402508,;FBXO11,intron_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000538136,;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,downstream_gene_variant,,ENST00000540021,;FBXO11,non_coding_transcript_exon_variant,,ENST00000465204,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000470899,;MSH6,downstream_gene_variant,,ENST00000445503,;	G	ENSG00000138081	ENST00000403359	Transcript	3_prime_UTR_variant	3670	.	.	.	.	.	.	.	-1	FBXO11	HGNC	13590	protein_coding	YES	CCDS54357.1	ENSP00000384823	FBX11_HUMAN	E7EP88_HUMAN,C9IYF0_HUMAN,B5MCV6_HUMAN	UPI00005793B7	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTACCTTT	.	5	ESCA
STON1-GTF2A1L	0	.	GRCh37	2	48808503	48808503	+	Nonsense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731C>G	p.Ser244Ter	p.S244*	ENST00000394754	2/11	53	32	21	73	73	0	STON1-GTF2A1L,stop_gained,p.Ser244Ter,ENST00000309827,;STON1-GTF2A1L,stop_gained,p.Ser244Ter,ENST00000394754,;STON1,stop_gained,p.Ser244Ter,ENST00000406226,;STON1-GTF2A1L,stop_gained,p.Ser244Ter,ENST00000402114,;STON1-GTF2A1L,stop_gained,p.Ser244Ter,ENST00000405008,;STON1-GTF2A1L,stop_gained,p.Ser244Ter,ENST00000394751,;STON1,stop_gained,p.Ser244Ter,ENST00000404752,;STON1,stop_gained,p.Ser244Ter,ENST00000309835,;STON1,upstream_gene_variant,,ENST00000444932,;	G	ENSG00000068781	ENST00000394754	Transcript	stop_gained	845	731	244	S/*	tCa/tGa	COSM3799045,COSM3799044	.	.	1	STON1-GTF2A1L	HGNC	30651	protein_coding	YES	CCDS1840.1	ENSP00000378236	.	Q53S48_HUMAN	UPI000013C976	.	.	.	2/11	.	hmmpanther:PTHR11998,hmmpanther:PTHR11998:SF18	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACTCACTTA	.	5	ESCA
TET3	0	.	GRCh37	2	74329136	74329136	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4816G>A	p.Gly1606Arg	p.G1606R	ENST00000409262	9/9	19	11	8	9	9	0	TET3,missense_variant,p.Gly1606Arg,ENST00000409262,;	A	ENSG00000187605	ENST00000409262	Transcript	missense_variant	4816	4816	1606	G/R	Ggg/Agg	.	.	.	1	TET3	HGNC	28313	protein_coding	YES	CCDS46339.1	ENSP00000386869	TET3_HUMAN	K9JJH7_HUMAN	UPI0000DD79F5	.	deleterious(0)	probably_damaging(0.962)	9/9	.	hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTACGGGAAG	.	3	ESCA
MBOAT2	0	.	GRCh37	2	8998163	8998163	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*646G>T	.	.	ENST00000305997	13/13	57	41	16	60	60	0	MBOAT2,3_prime_UTR_variant,,ENST00000305997,;MBOAT2,downstream_gene_variant,,ENST00000486484,;MBOAT2,downstream_gene_variant,,ENST00000471753,;MBOAT2,downstream_gene_variant,,ENST00000486315,;MBOAT2,downstream_gene_variant,,ENST00000494760,;MBOAT2,downstream_gene_variant,,ENST00000473432,;	A	ENSG00000143797	ENST00000305997	Transcript	3_prime_UTR_variant	2408	.	.	.	.	.	.	.	-1	MBOAT2	HGNC	25193	protein_coding	YES	CCDS1660.1	ENSP00000302177	MBOA2_HUMAN	B0AZU0_HUMAN	UPI0000231CFB	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGCAAAAT	.	5	ESCA
IGKV1D-17	0	.	GRCh37	2	90122042	90122042	+	Missense_Mutation	SNP	G	G	A	rs759658002	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.260G>A	p.Ser87Asn	p.S87N	ENST00000483379	2/2	221	146	74	227	227	0	IGKV1D-17,missense_variant,p.Ser87Asn,ENST00000483379,;	A	ENSG00000242766	ENST00000483379	Transcript	missense_variant	441	260	87	S/N	aGt/aAt	rs759658002	.	.	1	IGKV1D-17	HGNC	5749	IG_V_gene	YES	.	ENSP00000418292	.	.	UPI0000176CBA	.	deleterious(0)	benign(0.331)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267,hmmpanther:PTHR23267:SF122,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCAGTGGAT	byFrequency	5	ESCA
SLC15A2	0	.	GRCh37	3	121616250	121616250	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.209A>G	p.Tyr70Cys	p.Y70C	ENST00000489711	3/22	42	24	17	40	40	0	SLC15A2,missense_variant,p.Tyr8Cys,ENST00000469013,;SLC15A2,missense_variant,p.Tyr70Cys,ENST00000295605,;SLC15A2,missense_variant,p.Tyr70Cys,ENST00000489711,;	G	ENSG00000163406	ENST00000489711	Transcript	missense_variant	597	209	70	Y/C	tAt/tGt	.	.	.	1	SLC15A2	HGNC	10921	protein_coding	YES	CCDS3007.1	ENSP00000417085	S15A2_HUMAN	C9IZ38_HUMAN	UPI000013E27D	.	deleterious(0)	possibly_damaging(0.627)	3/22	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11654:SF15,hmmpanther:PTHR11654,TIGRFAM_domain:TIGR00926,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGTATTTCC	.	5	ESCA
RP11-723O4.6	0	.	GRCh37	3	128629068	128629068	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*74C>T	.	.	ENST00000508239	8/8	49	35	13	53	53	0	KIAA1257,3_prime_UTR_variant,,ENST00000511438,;RP11-723O4.6,3_prime_UTR_variant,,ENST00000508239,;ACAD9,intron_variant,,ENST00000308982,;ACAD9,intron_variant,,ENST00000511526,;ACAD9,intron_variant,,ENST00000505867,;ACAD9,intron_variant,,ENST00000511325,;ACAD9,intron_variant,,ENST00000508971,;ACAD9,intron_variant,,ENST00000511227,;ACAD9,downstream_gene_variant,,ENST00000505192,;	A	ENSG00000187695	ENST00000508239	Transcript	3_prime_UTR_variant	1940	.	.	.	.	.	.	.	-1	RP11-723O4.6	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000424951	YC006_HUMAN	D6RBZ9_HUMAN	UPI00001C0B67	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTGAGGAG	.	5	ESCA
CNBP	0	.	GRCh37	3	128888569	128888569	+	3'Flank	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000441626	.	68	50	18	74	74	0	CNBP,3_prime_UTR_variant,,ENST00000502976,;CNBP,3_prime_UTR_variant,,ENST00000451728,;CNBP,3_prime_UTR_variant,,ENST00000446936,;CNBP,3_prime_UTR_variant,,ENST00000500450,;CNBP,3_prime_UTR_variant,,ENST00000422453,;CNBP,3_prime_UTR_variant,,ENST00000504813,;CNBP,downstream_gene_variant,,ENST00000512338,;CNBP,downstream_gene_variant,,ENST00000441626,;CNBP,downstream_gene_variant,,ENST00000507573,;CNBP,downstream_gene_variant,,ENST00000502372,;	T	ENSG00000169714	ENST00000441626	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	376	-1	CNBP	HGNC	13164	protein_coding	YES	CCDS46906.1	ENSP00000410769	CNBP_HUMAN	Q6T598_HUMAN	UPI0000496743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATCTTGAT	.	5	ESCA
NPHP3	0	.	GRCh37	3	132432010	132432010	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1078delA	p.Ser360ValfsTer3	p.S360Vfs*3	ENST00000337331	6/27	197	140	57	146	146	0	NPHP3,frameshift_variant,p.Ser360ValfsTer3,ENST00000326682,;NPHP3,frameshift_variant,p.Ser360ValfsTer3,ENST00000337331,;NPHP3,downstream_gene_variant,,ENST00000343113,;NPHP3,non_coding_transcript_exon_variant,,ENST00000476742,;NPHP3,downstream_gene_variant,,ENST00000471145,;NPHP3,frameshift_variant,p.Ser360ValfsTer3,ENST00000471702,;NPHP3,frameshift_variant,p.Ser262ValfsTer3,ENST00000465756,;NPHP3,3_prime_UTR_variant,,ENST00000469232,;NPHP3,non_coding_transcript_exon_variant,,ENST00000490993,;	-	ENSG00000113971	ENST00000337331	Transcript	frameshift_variant	1165	1078	360	S/X	Agt/gt	.	.	.	-1	NPHP3	HGNC	7907	protein_coding	YES	CCDS3078.1	ENSP00000338766	NPHP3_HUMAN	.	UPI00001B6B30	.	.	.	6/27	.	hmmpanther:PTHR19959:SF133,hmmpanther:PTHR19959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGAACTTTTCT	.	3	ESCA
PPP2R3A	0	.	GRCh37	3	135866318	135866318	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2310T>C	.	.	ENST00000264977	14/14	65	38	26	73	73	0	PPP2R3A,3_prime_UTR_variant,,ENST00000264977,;MSL2,downstream_gene_variant,,ENST00000434835,;MSL2,downstream_gene_variant,,ENST00000481989,;PPP2R3A,downstream_gene_variant,,ENST00000490467,;MSL2,downstream_gene_variant,,ENST00000491050,;MSL2,downstream_gene_variant,,ENST00000309993,;MSL2,downstream_gene_variant,,ENST00000473093,;PPP2R3A,downstream_gene_variant,,ENST00000334546,;	C	ENSG00000073711	ENST00000264977	Transcript	3_prime_UTR_variant	6380	.	.	.	.	.	.	.	1	PPP2R3A	HGNC	9307	protein_coding	YES	CCDS3087.1	ENSP00000264977	P2R3A_HUMAN	.	UPI0000124EAC	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTATTGTAC	.	5	ESCA
CEP70	0	.	GRCh37	3	138224144	138224144	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1214C>T	p.Ser405Phe	p.S405F	ENST00000264982	13/18	115	78	37	150	150	0	CEP70,missense_variant,p.Ser405Phe,ENST00000481834,;CEP70,missense_variant,p.Ser387Phe,ENST00000474781,;CEP70,missense_variant,p.Ser253Phe,ENST00000489254,;CEP70,missense_variant,p.Ser385Phe,ENST00000542237,;CEP70,missense_variant,p.Ser405Phe,ENST00000484888,;CEP70,missense_variant,p.Ser405Phe,ENST00000264982,;	A	ENSG00000114107	ENST00000264982	Transcript	missense_variant	1481	1214	405	S/F	tCc/tTc	.	.	.	-1	CEP70	HGNC	29972	protein_coding	YES	CCDS3102.1	ENSP00000264982	CEP70_HUMAN	C9JZ04_HUMAN,C9J0F4_HUMAN	UPI000013D5A3	.	tolerated(0.18)	benign(0.176)	13/18	.	hmmpanther:PTHR14594:SF1,hmmpanther:PTHR14594	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAGGATGTC	.	5	ESCA
TFDP2	0	.	GRCh37	3	141820587	141820587	+	Missense_Mutation	SNP	G	G	A	rs755075231	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5C>T	p.Thr2Met	p.T2M	ENST00000489671	2/13	82	60	22	87	87	0	TFDP2,missense_variant,p.Thr2Met,ENST00000489671,;TFDP2,missense_variant,p.Thr2Met,ENST00000467634,;TFDP2,5_prime_UTR_variant,,ENST00000467072,;TFDP2,5_prime_UTR_variant,,ENST00000499676,;TFDP2,5_prime_UTR_variant,,ENST00000317104,;TFDP2,5_prime_UTR_variant,,ENST00000494358,;TFDP2,intron_variant,,ENST00000475734,;TFDP2,non_coding_transcript_exon_variant,,ENST00000476617,;TFDP2,non_coding_transcript_exon_variant,,ENST00000495095,;TFDP2,intron_variant,,ENST00000464782,;TFDP2,missense_variant,p.Thr2Met,ENST00000487734,;TFDP2,non_coding_transcript_exon_variant,,ENST00000491667,;	A	ENSG00000114126	ENST00000489671	Transcript	missense_variant	436	5	2	T/M	aCg/aTg	rs755075231	.	.	-1	TFDP2	HGNC	11751	protein_coding	YES	CCDS54650.1	ENSP00000420616	TFDP2_HUMAN	C9JTZ9_HUMAN,C9JNB6_HUMAN,C9JCY5_HUMAN,C9J5D5_HUMAN,C9J461_HUMAN	UPI0000136B56	.	tolerated_low_confidence(0.63)	benign(0.004)	2/13	.	hmmpanther:PTHR12548,hmmpanther:PTHR12548:SF5,PIRSF_domain:PIRSF009404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCGTCATG	.	5	ESCA
IFT80	0	.	GRCh37	3	159976308	159976308	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5C>T	.	.	ENST00000326448	20/20	62	42	19	50	50	0	IFT80,3_prime_UTR_variant,,ENST00000483465,;IFT80,3_prime_UTR_variant,,ENST00000496589,;IFT80,3_prime_UTR_variant,,ENST00000326448,;IFT80,non_coding_transcript_exon_variant,,ENST00000463240,;RP11-432B6.3,3_prime_UTR_variant,,ENST00000483754,;IFT80,non_coding_transcript_exon_variant,,ENST00000487943,;IFT80,non_coding_transcript_exon_variant,,ENST00000478278,;	A	ENSG00000068885	ENST00000326448	Transcript	3_prime_UTR_variant	2772	.	.	.	.	.	.	.	-1	IFT80	HGNC	29262	protein_coding	YES	CCDS3188.1	ENSP00000312778	IFT80_HUMAN	C9JUJ1_HUMAN,C9JUI1_HUMAN,C9JSB1_HUMAN,C9J6I5_HUMAN,C9J6G8_HUMAN,C9J627_HUMAN,C9IZR2_HUMAN	UPI0000160F16	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCATGGCATT	.	5	ESCA
PIK3CA	0	.	GRCh37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	T	rs121913279	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	21/21	44	34	10	50	50	0	PIK3CA,missense_variant,p.His1047Leu,ENST00000263967,;RP11-245C23.3,downstream_gene_variant,,ENST00000609807,;	T	ENSG00000121879	ENST00000263967	Transcript	missense_variant	3297	3140	1047	H/L	cAt/cTt	rs121913279,COSM776,COSM775,COSM249874,COSM94987,COSM94986	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	tolerated(0.44)	benign(0.085)	21/21	.	PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	pathogenic	0,1,1,1,1,1	25710561	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H1047L|c.3140A>T|236,SITE|p.H1047L|c.3140A>T|45,CODON|p.H1047Y|c.3139C>T|8,CODON|p.H1047Y|c.3139C>T|54,CODON|p.H1047R|c.3140A>G|1687,CODON|p.H1047R|c.3140A>G|242,BUFFER|p.M1043I|c.3129G>T|4,BUFFER|p.M1043I|c.3129G>A|8,BUFFER|p.M1043I|c.3129G>T|45,BUFFER|p.M1043I|c.3129G>A|22,BUFFER|p.M1043I|c.3129G>C|4,BUFFER|p.M1043I|c.3129G>C|6,BUFFER|p.N1044D|c.3130A>G|4,BUFFER|p.N1044Y|c.3130A>T|3,BUFFER|p.N1044S|c.3131A>G|5,BUFFER|p.N1044S|c.3131A>G|3,BUFFER|p.N1044K|c.3132T>G|5,BUFFER|p.N1044K|c.3132T>A|15,BUFFER|p.N1044K|c.3132T>A|7,BUFFER|p.D1045N|c.3133G>A|6,BUFFER|p.A1046T|c.3136G>A|6,BUFFER|p.A1046E|c.3137C>A|3,BUFFER|p.H1047Q|c.3141T>G|4,BUFFER|p.H1048R|c.3143A>G|6,BUFFER|p.H1048R|c.3143A>G|3,BUFFER|p.G1049S|c.3145G>A|16,BUFFER|p.G1049R|c.3145G>C|29,BUFFER|p.G1049R|c.3145G>C|5,BUFFER|p.G1049A|c.3146G>C|3,BUFFER|p.G1049D|c.3146G>A|4,BUFFER|p.G1049G|c.3147T>C|10,BUFFER|p.G1050S|c.3148G>A|3,BUFFER|p.G1050D|c.3149G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACATCATG	byFrequency|byCluster	5	ESCA
ETV5	0	.	GRCh37	3	185765065	185765065	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1363A>T	.	.	ENST00000306376	13/13	60	38	22	70	70	0	ETV5,3_prime_UTR_variant,,ENST00000306376,;ETV5,downstream_gene_variant,,ENST00000537818,;ETV5,downstream_gene_variant,,ENST00000434744,;ETV5,downstream_gene_variant,,ENST00000480706,;ETV5,downstream_gene_variant,,ENST00000433149,;	A	ENSG00000244405	ENST00000306376	Transcript	3_prime_UTR_variant	3143	.	.	.	.	.	.	.	-1	ETV5	HGNC	3494	protein_coding	YES	CCDS33906.1	ENSP00000306894	ETV5_HUMAN	C9JMF0_HUMAN,C9J5A5_HUMAN,C9J0Z2_HUMAN	UPI000012A175	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTTAAAAA	.	5	ESCA
ADIPOQ	0	.	GRCh37	3	186572507	186572507	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*14A>T	.	.	ENST00000412955	3/3	32	23	9	63	63	0	ADIPOQ,3_prime_UTR_variant,,ENST00000412955,;ADIPOQ,3_prime_UTR_variant,,ENST00000444204,;ADIPOQ,3_prime_UTR_variant,,ENST00000320741,;ADIPOQ-AS1,non_coding_transcript_exon_variant,,ENST00000422718,;	T	ENSG00000181092	ENST00000412955	Transcript	3_prime_UTR_variant	890	.	.	.	.	.	.	.	1	ADIPOQ	HGNC	13633	protein_coding	YES	CCDS3284.1	ENSP00000405611	ADIPO_HUMAN	A8K660_HUMAN	UPI0000034252	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTCAGAGCC	.	5	ESCA
MUC4	0	.	GRCh37	3	195511581	195511581	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6870T>C	p.%3D	p.P2290P	ENST00000463781	2/25	209	166	43	242	242	0	MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000477086,;MUC4,synonymous_variant,p.%3D,ENST00000466475,;MUC4,synonymous_variant,p.%3D,ENST00000478156,;MUC4,synonymous_variant,p.%3D,ENST00000470451,;MUC4,synonymous_variant,p.%3D,ENST00000479406,;MUC4,synonymous_variant,p.%3D,ENST00000477756,;MUC4,synonymous_variant,p.%3D,ENST00000462323,;MUC4,synonymous_variant,p.%3D,ENST00000480843,;	G	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	7330	6870	2290	P	ccT/ccC	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGACAGGAAG	.	4	ESCA
CEP19	0	.	GRCh37	3	196434354	196434354	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*68A>G	.	.	ENST00000409690	3/3	33	23	9	38	38	0	CEP19,3_prime_UTR_variant,,ENST00000399942,;CEP19,3_prime_UTR_variant,,ENST00000409690,;PIGX,intron_variant,,ENST00000426755,;PIGX,upstream_gene_variant,,ENST00000392391,;PIGX,upstream_gene_variant,,ENST00000314118,;PIGX,upstream_gene_variant,,ENST00000296333,;RNU6-646P,downstream_gene_variant,,ENST00000364571,;	C	ENSG00000174007	ENST00000409690	Transcript	3_prime_UTR_variant	995	.	.	.	.	.	.	.	-1	CEP19	HGNC	28209	protein_coding	YES	CCDS43193.2	ENSP00000387209	CEP19_HUMAN	.	UPI0000071B37	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTCTTCCAG	.	5	ESCA
CMC1	0	.	GRCh37	3	28365409	28365409	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4289A>G	.	.	ENST00000466830	4/4	11	6	5	10	10	0	CMC1,3_prime_UTR_variant,,ENST00000466830,;AZI2,3_prime_UTR_variant,,ENST00000479665,;AZI2,intron_variant,,ENST00000429369,;CMC1,downstream_gene_variant,,ENST00000423894,;CMC1,downstream_gene_variant,,ENST00000418849,;AZI2,non_coding_transcript_exon_variant,,ENST00000295748,;CMC1,downstream_gene_variant,,ENST00000495428,;CMC1,downstream_gene_variant,,ENST00000469102,;CMC1,downstream_gene_variant,,ENST00000467644,;CMC1,downstream_gene_variant,,ENST00000482499,;AZI2,downstream_gene_variant,,ENST00000476174,;CMC1,downstream_gene_variant,,ENST00000396610,;CMC1,downstream_gene_variant,,ENST00000477739,;AZI2,downstream_gene_variant,,ENST00000492044,;CMC1,downstream_gene_variant,,ENST00000334841,;AZI2,downstream_gene_variant,,ENST00000463512,;	G	ENSG00000187118	ENST00000466830	Transcript	3_prime_UTR_variant	4809	.	.	.	.	.	.	.	1	CMC1	HGNC	28783	protein_coding	YES	CCDS33722.1	ENSP00000418348	COXM1_HUMAN	.	UPI0000161ABD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAAATATAGAT	.	3	ESCA
TGFBR2	0	.	GRCh37	3	30715618	30715618	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351G>A	p.Ala451Thr	p.A451T	ENST00000359013	6/8	89	58	30	83	83	0	TGFBR2,missense_variant,p.Ala426Thr,ENST00000295754,;TGFBR2,missense_variant,p.Ala451Thr,ENST00000359013,;	A	ENSG00000163513	ENST00000359013	Transcript	missense_variant	1634	1351	451	A/T	Gct/Act	CM086983	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	deleterious(0)	probably_damaging(0.999)	6/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037393,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATGGCTCCA	.	5	ESCA
ZNF660	0	.	GRCh37	3	44637008	44637009	+	3'UTR	INS	-	-	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*334dupA	.	.	ENST00000322734	3/3	99	65	33	119	119	0	ZNF660,3_prime_UTR_variant,,ENST00000322734,;ZNF197,intron_variant,,ENST00000412641,;ZNF660,downstream_gene_variant,,ENST00000441021,;ZNF660,downstream_gene_variant,,ENST00000416644,;RP11-944L7.5,downstream_gene_variant,,ENST00000419137,;RP11-944L7.4,intron_variant,,ENST00000457331,;	A	ENSG00000144792	ENST00000322734	Transcript	3_prime_UTR_variant	1656-1657	.	.	.	.	.	.	.	1	ZNF660	HGNC	26720	protein_coding	YES	CCDS2716.1	ENSP00000324605	ZN660_HUMAN	C9J3N9_HUMAN,C9J3D4_HUMAN	UPI0000140EF2	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAATTTAAAAA	.	2	ESCA
KIF15	0	.	GRCh37	3	44819651	44819651	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291C>T	p.%3D	p.C97C	ENST00000326047	4/35	88	63	25	71	71	0	KIF15,synonymous_variant,p.%3D,ENST00000326047,;KIF15,intron_variant,,ENST00000481166,;KIF15,missense_variant,p.Ala83Val,ENST00000438321,;	T	ENSG00000163808	ENST00000326047	Transcript	synonymous_variant	440	291	97	C	tgC/tgT	.	.	.	1	KIF15	HGNC	17273	protein_coding	YES	CCDS33744.1	ENSP00000324020	KIF15_HUMAN	D6RCT7_HUMAN	UPI000006DB0E	.	.	.	4/35	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF87,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTGCATGAG	.	5	ESCA
AMT	0	.	GRCh37	3	49457771	49457771	+	Missense_Mutation	SNP	G	G	A	rs758774866	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.344C>T	p.Thr115Ile	p.T115I	ENST00000273588	4/9	72	43	28	60	60	0	AMT,missense_variant,p.Thr59Ile,ENST00000538581,;AMT,missense_variant,p.Thr18Ile,ENST00000546031,;AMT,missense_variant,p.Thr115Ile,ENST00000273588,;AMT,missense_variant,p.Thr113Ile,ENST00000427987,;AMT,missense_variant,p.Thr59Ile,ENST00000430521,;AMT,missense_variant,p.Thr115Ile,ENST00000395338,;AMT,intron_variant,,ENST00000458307,;NICN1,downstream_gene_variant,,ENST00000436744,;NICN1,downstream_gene_variant,,ENST00000273598,;TCTA,downstream_gene_variant,,ENST00000273590,;NICN1-AS1,upstream_gene_variant,,ENST00000424915,;AMT,non_coding_transcript_exon_variant,,ENST00000487589,;AMT,non_coding_transcript_exon_variant,,ENST00000476226,;AMT,non_coding_transcript_exon_variant,,ENST00000480957,;AMT,non_coding_transcript_exon_variant,,ENST00000493046,;AMT,non_coding_transcript_exon_variant,,ENST00000485108,;AMT,non_coding_transcript_exon_variant,,ENST00000462048,;TCTA,downstream_gene_variant,,ENST00000493381,;NICN1,downstream_gene_variant,,ENST00000422593,;AMT,3_prime_UTR_variant,,ENST00000399379,;AMT,non_coding_transcript_exon_variant,,ENST00000461210,;AMT,non_coding_transcript_exon_variant,,ENST00000476828,;AMT,non_coding_transcript_exon_variant,,ENST00000465925,;AMT,non_coding_transcript_exon_variant,,ENST00000478594,;AMT,intron_variant,,ENST00000495436,;AMT,upstream_gene_variant,,ENST00000476127,;AMT,downstream_gene_variant,,ENST00000498571,;NICN1,downstream_gene_variant,,ENST00000497742,;NICN1,downstream_gene_variant,,ENST00000423832,;AMT,upstream_gene_variant,,ENST00000473163,;AMT,upstream_gene_variant,,ENST00000491800,;NICN1,downstream_gene_variant,,ENST00000461015,;NICN1,downstream_gene_variant,,ENST00000494057,;	A	ENSG00000145020	ENST00000273588	Transcript	missense_variant	647	344	115	T/I	aCa/aTa	rs758774866	.	.	-1	AMT	HGNC	473	protein_coding	YES	CCDS2797.1	ENSP00000273588	GCST_HUMAN	B4DGG9_HUMAN,B3KTU4_HUMAN	UPI000012B35E	.	deleterious(0.02)	benign(0.162)	4/9	.	hmmpanther:PTHR13847,hmmpanther:PTHR13847:SF5,TIGRFAM_domain:TIGR00528,Gene3D:3.30.70.1400,Pfam_domain:PF01571,PIRSF_domain:PIRSF006487,Superfamily_domains:SSF103025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGTGTCCCC	byFrequency	5	ESCA
TTC29	0	.	GRCh37	4	147824756	147824756	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526G>A	p.Asp176Asn	p.D176N	ENST00000325106	6/13	75	56	18	98	98	0	TTC29,missense_variant,p.Asp176Asn,ENST00000504425,;TTC29,missense_variant,p.Asp202Asn,ENST00000398886,;TTC29,missense_variant,p.Asp202Asn,ENST00000513335,;TTC29,missense_variant,p.Asp176Asn,ENST00000325106,;TTC29,missense_variant,p.Asp176Asn,ENST00000508306,;	T	ENSG00000137473	ENST00000325106	Transcript	missense_variant	753	526	176	D/N	Gac/Aac	.	.	.	-1	TTC29	HGNC	29936	protein_coding	YES	CCDS47141.1	ENSP00000316740	TTC29_HUMAN	D6RJF6_HUMAN	UPI00001AE7CF	.	deleterious(0.01)	probably_damaging(0.996)	6/13	.	hmmpanther:PTHR10098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGTCAATTT	.	5	ESCA
LRBA	0	.	GRCh37	4	151604720	151604720	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5904G>A	p.Trp1968Ter	p.W1968*	ENST00000357115	37/58	69	46	22	84	84	0	LRBA,stop_gained,p.Trp1968Ter,ENST00000535741,;LRBA,stop_gained,p.Trp1968Ter,ENST00000507224,;LRBA,stop_gained,p.Trp1968Ter,ENST00000357115,;LRBA,stop_gained,p.Trp1968Ter,ENST00000510413,;LRBA,stop_gained,p.Trp621Ter,ENST00000509835,;LRBA,upstream_gene_variant,,ENST00000513021,;LRBA,downstream_gene_variant,,ENST00000508396,;	T	ENSG00000198589	ENST00000357115	Transcript	stop_gained	6148	5904	1968	W/*	tgG/tgA	.	.	.	-1	LRBA	HGNC	1742	protein_coding	YES	CCDS3773.1	ENSP00000349629	LRBA_HUMAN	Q7KZN3_HUMAN	UPI000013E35C	.	.	.	37/58	.	hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64,Pfam_domain:PF06469	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTCCCCAGGC	.	4	ESCA
PET112	0	.	GRCh37	4	152601009	152601009	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1366G>T	p.Asp456Tyr	p.D456Y	ENST00000263985	11/13	72	44	27	92	92	0	PET112,missense_variant,p.Asp456Tyr,ENST00000263985,;PET112,missense_variant,p.Asp415Tyr,ENST00000515812,;RP11-164P12.3,downstream_gene_variant,,ENST00000514269,;PET112,non_coding_transcript_exon_variant,,ENST00000507592,;PET112,non_coding_transcript_exon_variant,,ENST00000513504,;PET112,3_prime_UTR_variant,,ENST00000503160,;PET112,non_coding_transcript_exon_variant,,ENST00000515564,;PET112,intron_variant,,ENST00000510720,;PET112,upstream_gene_variant,,ENST00000510396,;	A	ENSG00000059691	ENST00000263985	Transcript	missense_variant	1407	1366	456	D/Y	Gac/Tac	.	.	.	-1	PET112	HGNC	8849	protein_coding	YES	CCDS3776.1	ENSP00000263985	GATB_HUMAN	.	UPI000012B14C	.	deleterious(0)	possibly_damaging(0.797)	11/13	.	Low_complexity_(Seg):seg,HAMAP:MF_00121,hmmpanther:PTHR11659,hmmpanther:PTHR11659:SF0,Pfam_domain:PF02637,TIGRFAM_domain:TIGR00133,SMART_domains:SM00845,Superfamily_domains:SSF89095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGTCAAGAA	.	5	ESCA
GUCY1B3	0	.	GRCh37	4	156727730	156727730	+	3'UTR	SNP	T	T	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*169T>G	.	.	ENST00000264424	14/14	26	19	7	34	34	0	GUCY1B3,3_prime_UTR_variant,,ENST00000513437,;GUCY1B3,3_prime_UTR_variant,,ENST00000264424,;GUCY1B3,3_prime_UTR_variant,,ENST00000502959,;GUCY1B3,3_prime_UTR_variant,,ENST00000507146,;GUCY1B3,3_prime_UTR_variant,,ENST00000505764,;GUCY1B3,3_prime_UTR_variant,,ENST00000505154,;GUCY1B3,downstream_gene_variant,,ENST00000503520,;	G	ENSG00000061918	ENST00000264424	Transcript	3_prime_UTR_variant	2111	.	.	.	.	.	.	.	1	GUCY1B3	HGNC	4687	protein_coding	YES	CCDS47154.1	ENSP00000264424	GCYB1_HUMAN	B7Z685_HUMAN	UPI0000033344	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTTAGCTC	.	5	ESCA
DDX60	0	.	GRCh37	4	169197311	169197311	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2000G>T	p.Ser667Ile	p.S667I	ENST00000393743	15/38	49	34	15	55	55	0	DDX60,missense_variant,p.Ser667Ile,ENST00000393743,;	A	ENSG00000137628	ENST00000393743	Transcript	missense_variant	2292	2000	667	S/I	aGt/aTt	.	.	.	-1	DDX60	HGNC	25942	protein_coding	YES	CCDS34097.1	ENSP00000377344	DDX60_HUMAN	Q9NXV7_HUMAN,Q9H616_HUMAN,Q6B0F7_HUMAN,D6R944_HUMAN	UPI000020B6AB	.	deleterious(0)	possibly_damaging(0.866)	15/38	.	hmmpanther:PTHR11752:SF61,hmmpanther:PTHR11752	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T663T|c.1989G>A|4,BUFFER|p.T663T|c.1989G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATACTTAAA	.	5	ESCA
FAM92A1P2	0	.	GRCh37	4	183960276	183960276	+	RNA	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1459C>T	.	.	ENST00000502308	1/1	64	45	19	50	50	0	FAM92A1P2,non_coding_transcript_exon_variant,,ENST00000502308,;FAM92A1P2,non_coding_transcript_exon_variant,,ENST00000504766,;	T	ENSG00000230219	ENST00000502308	Transcript	non_coding_transcript_exon_variant	1459	.	.	.	.	.	.	.	1	FAM92A1P2	HGNC	32287	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGACAATTT	.	5	ESCA
WHSC1	0	.	GRCh37	4	1980408	1980409	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3872dupC	p.Ser1292PhefsTer14	p.S1292Ffs*14	ENST00000382895	24/24	105	82	23	82	82	0	WHSC1,frameshift_variant,p.Ser1292PhefsTer14,ENST00000508803,;WHSC1,frameshift_variant,p.Ser640PhefsTer14,ENST00000382888,;WHSC1,frameshift_variant,p.Ser1292PhefsTer14,ENST00000382892,;WHSC1,frameshift_variant,p.Ser1292PhefsTer14,ENST00000382895,;WHSC1,frameshift_variant,p.Ser1292PhefsTer14,ENST00000382891,;NELFA,downstream_gene_variant,,ENST00000411638,;NELFA,downstream_gene_variant,,ENST00000416258,;NELFA,downstream_gene_variant,,ENST00000542778,;NELFA,downstream_gene_variant,,ENST00000382882,;SCARNA22,downstream_gene_variant,,ENST00000503991,;WHSC1,non_coding_transcript_exon_variant,,ENST00000482415,;WHSC1,3_prime_UTR_variant,,ENST00000312087,;WHSC1,3_prime_UTR_variant,,ENST00000353275,;WHSC1,non_coding_transcript_exon_variant,,ENST00000508299,;NELFA,downstream_gene_variant,,ENST00000333877,;NELFA,downstream_gene_variant,,ENST00000463820,;NELFA,downstream_gene_variant,,ENST00000467661,;WHSC1,downstream_gene_variant,,ENST00000515695,;	C	ENSG00000109685	ENST00000382895	Transcript	frameshift_variant	4301-4302	3870-3871	1290-1291	-/X	-/C	.	.	.	1	WHSC1	HGNC	12766	protein_coding	YES	CCDS33940.1	ENSP00000372351	NSD2_HUMAN	D6RIS1_HUMAN,D6RFE7_HUMAN,D6R9V2_HUMAN	UPI0000073F57	.	.	.	24/24	.	Gene3D:3.30.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCAAACCTTC	.	3	ESCA
HTT	0	.	GRCh37	4	3208383	3208383	+	Missense_Mutation	SNP	G	G	A	rs762436871	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5879G>A	p.Arg1960His	p.R1960H	ENST00000355072	43/67	25	15	10	36	36	0	HTT,missense_variant,p.Arg1960His,ENST00000355072,;HTT,downstream_gene_variant,,ENST00000502820,;HTT,non_coding_transcript_exon_variant,,ENST00000510626,;	A	ENSG00000197386	ENST00000355072	Transcript	missense_variant	6024	5879	1960	R/H	cGt/cAt	rs762436871	.	.	1	HTT	HGNC	4851	protein_coding	YES	CCDS43206.1	ENSP00000347184	HD_HUMAN	D3DVR8_HUMAN,D2CTD8_HUMAN,D2CTD7_HUMAN,D2CTD4_HUMAN,D2CTD2_HUMAN	UPI000013D567	.	.	probably_damaging(0.999)	43/67	.	hmmpanther:PTHR10170:SF10,hmmpanther:PTHR10170	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTCGTTGTG	.	5	ESCA
ADRA2C	0	.	GRCh37	4	3769693	3769693	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360C>T	p.Arg454Ter	p.R454*	ENST00000330055	1/1	75	57	18	60	60	0	ADRA2C,stop_gained,p.Arg454Ter,ENST00000330055,;ADRA2C,intron_variant,,ENST00000509482,;AC141928.1,upstream_gene_variant,,ENST00000511928,;	T	ENSG00000184160	ENST00000330055	Transcript	stop_gained	1569	1360	454	R/*	Cga/Tga	.	.	.	1	ADRA2C	HGNC	283	protein_coding	YES	CCDS47004.1	ENSP00000386069	ADA2C_HUMAN	Q4W594_HUMAN	UPI000012500C	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF25,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTCCGACGG	.	5	ESCA
RUFY3	0	.	GRCh37	4	71655520	71655520	+	Intron	SNP	T	T	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1337+211T>A	.	.	ENST00000381006	.	10	7	3	11	11	0	RUFY3,3_prime_UTR_variant,,ENST00000417478,;RUFY3,intron_variant,,ENST00000226328,;RUFY3,intron_variant,,ENST00000502653,;RUFY3,intron_variant,,ENST00000381006,;RUFY3,intron_variant,,ENST00000536664,;RUFY3,upstream_gene_variant,,ENST00000507333,;RUFY3,intron_variant,,ENST00000512103,;RUFY3,intron_variant,,ENST00000504805,;RUFY3,upstream_gene_variant,,ENST00000503025,;	A	ENSG00000018189	ENST00000381006	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RUFY3	HGNC	30285	protein_coding	YES	CCDS34001.1	ENSP00000370394	RUFY3_HUMAN	D6REM9_HUMAN,D6RCQ1_HUMAN	UPI00005FB126	.	.	.	.	12/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTTAAAAA	.	2	ESCA
TRMT44	0	.	GRCh37	4	8448312	8448312	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729A>G	p.%3D	p.E243E	ENST00000389737	2/11	110	69	41	138	138	0	TRMT44,missense_variant,p.Lys12Arg,ENST00000513449,;TRMT44,synonymous_variant,p.%3D,ENST00000389737,;TRMT44,intron_variant,,ENST00000504134,;TRMT44,non_coding_transcript_exon_variant,,ENST00000528167,;	G	ENSG00000155275	ENST00000389737	Transcript	synonymous_variant	729	729	243	E	gaA/gaG	.	.	.	1	TRMT44	HGNC	26653	protein_coding	YES	CCDS3402.2	ENSP00000374387	TRM44_HUMAN	.	UPI0000DE1FA2	.	.	.	2/11	.	hmmpanther:PTHR21210:SF0,hmmpanther:PTHR21210	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAAGAATG	.	5	ESCA
UBE2D2	0	.	GRCh37	5	139003036	139003036	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388G>C	p.Asp130His	p.D130H	ENST00000398733	6/7	83	46	36	77	77	0	UBE2D2,missense_variant,p.Asp101His,ENST00000505548,;UBE2D2,missense_variant,p.Asp130His,ENST00000398733,;UBE2D2,missense_variant,p.Asp101His,ENST00000511725,;UBE2D2,missense_variant,p.Asp101His,ENST00000253815,;UBE2D2,downstream_gene_variant,,ENST00000505007,;UBE2D2,missense_variant,p.Asp130His,ENST00000398734,;UBE2D2,non_coding_transcript_exon_variant,,ENST00000511691,;	C	ENSG00000131508	ENST00000398733	Transcript	missense_variant	1014	388	130	D/H	Gat/Cat	.	.	.	1	UBE2D2	HGNC	12475	protein_coding	YES	CCDS43369.1	ENSP00000381717	UB2D2_HUMAN	D6RFM0_HUMAN,D6RAW0_HUMAN	UPI0000006BD0	.	deleterious_low_confidence(0)	probably_damaging(0.969)	6/7	.	PROSITE_profiles:PS50127,hmmpanther:PTHR24068:SF48,hmmpanther:PTHR24068,Pfam_domain:PF00179,Gene3D:3.10.110.10,SMART_domains:SM00212,Superfamily_domains:SSF54495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACAGATAGA	.	5	ESCA
PCDHA4	0	.	GRCh37	5	140187662	140187662	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.890C>T	p.Pro297Leu	p.P297L	ENST00000530339	1/4	51	39	11	81	81	0	PCDHA4,missense_variant,p.Pro297Leu,ENST00000530339,;PCDHA4,missense_variant,p.Pro297Leu,ENST00000356878,;PCDHA4,missense_variant,p.Pro297Leu,ENST00000512229,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA3,downstream_gene_variant,,ENST00000532566,;PCDHA2,downstream_gene_variant,,ENST00000520672,;	T	ENSG00000204967	ENST00000530339	Transcript	missense_variant	890	890	297	P/L	cCa/cTa	.	.	.	1	PCDHA4	HGNC	8670	protein_coding	YES	CCDS54916.1	ENSP00000435300	PCDA4_HUMAN	.	UPI00001273CC	.	tolerated_low_confidence(0.09)	benign(0.033)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF82,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATCCAATTA	.	5	ESCA
PCDHAC1	0	.	GRCh37	5	140306328	140306328	+	5'Flank	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000253807	.	9	5	4	10	10	0	PCDHAC1,5_prime_UTR_variant,,ENST00000409700,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA13,intron_variant,,ENST00000289272,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA13,intron_variant,,ENST00000409494,;PCDHAC1,upstream_gene_variant,,ENST00000253807,;	A	ENSG00000248383	ENST00000253807	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	150	1	PCDHAC1	HGNC	8676	protein_coding	YES	CCDS4241.1	ENSP00000253807	PCDC1_HUMAN	.	UPI000013CDF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCAACGTCGGC	.	3	ESCA
TAF7	0	.	GRCh37	5	140699108	140699108	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.504A>G	p.%3D	p.R168R	ENST00000313368	1/1	26	18	8	34	34	0	TAF7,synonymous_variant,p.%3D,ENST00000313368,;AC005618.1,downstream_gene_variant,,ENST00000535969,;	C	ENSG00000178913	ENST00000313368	Transcript	synonymous_variant	1223	504	168	R	cgA/cgG	.	.	.	-1	TAF7	HGNC	11541	protein_coding	YES	CCDS4259.1	ENSP00000312709	TAF7_HUMAN	.	UPI00001367E8	.	.	.	1/1	.	Pfam_domain:PF04658,hmmpanther:PTHR12228,hmmpanther:PTHR12228:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAATCGTTT	.	5	ESCA
SLC36A2	0	.	GRCh37	5	150694888	150694888	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1490C>A	.	.	ENST00000335244	10/10	12	8	4	15	15	0	SLC36A2,3_prime_UTR_variant,,ENST00000450886,;SLC36A2,3_prime_UTR_variant,,ENST00000335244,;SLC36A2,downstream_gene_variant,,ENST00000518280,;SLC36A2,downstream_gene_variant,,ENST00000518617,;CTC-224D3.1,upstream_gene_variant,,ENST00000604421,;	T	ENSG00000186335	ENST00000335244	Transcript	3_prime_UTR_variant	3072	.	.	.	.	.	.	.	-1	SLC36A2	HGNC	18762	protein_coding	YES	CCDS4315.1	ENSP00000334223	S36A2_HUMAN	E5RGH8_HUMAN	UPI000020D008	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCCAAGATCAA	.	2	ESCA
ITK	0	.	GRCh37	5	156649947	156649947	+	Silent	SNP	C	C	T	rs764897415	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570C>T	p.%3D	p.L190L	ENST00000422843	6/17	59	40	19	73	73	0	ITK,synonymous_variant,p.%3D,ENST00000521769,;ITK,synonymous_variant,p.%3D,ENST00000422843,;CTB-4E7.1,intron_variant,,ENST00000519375,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,non_coding_transcript_exon_variant,,ENST00000519759,;	T	ENSG00000113263	ENST00000422843	Transcript	synonymous_variant	722	570	190	L	ctC/ctT	rs764897415	.	.	1	ITK	HGNC	6171	protein_coding	YES	CCDS4336.1	ENSP00000398655	ITK_HUMAN	Q7Z318_HUMAN,E5RFR5_HUMAN	UPI000004CADA	.	.	.	6/17	.	PROSITE_profiles:PS50002,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,Pfam_domain:PF00018,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACTCGCACT	.	5	ESCA
WWC1	0	.	GRCh37	5	167826550	167826550	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.568C>A	p.Arg190Ser	p.R190S	ENST00000521089	5/23	37	34	3	36	36	0	WWC1,missense_variant,p.Arg152Ser,ENST00000393895,;WWC1,missense_variant,p.Arg190Ser,ENST00000265293,;WWC1,missense_variant,p.Arg190Ser,ENST00000521089,;WWC1,non_coding_transcript_exon_variant,,ENST00000523043,;WWC1,downstream_gene_variant,,ENST00000519859,;	A	ENSG00000113645	ENST00000521089	Transcript	missense_variant	571	568	190	R/S	Cgt/Agt	.	.	.	1	WWC1	HGNC	29435	protein_coding	YES	CCDS54945.1	ENSP00000427772	KIBRA_HUMAN	.	UPI00017A7149	.	deleterious(0.01)	benign(0.106)	5/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14791:SF22,hmmpanther:PTHR14791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGAGCGTGGC	.	2	ESCA
NKX2-5	0	.	GRCh37	5	172661786	172661786	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301G>A	p.Asp101Asn	p.D101N	ENST00000329198	1/2	81	58	22	86	86	0	NKX2-5,missense_variant,p.Asp101Asn,ENST00000521848,;NKX2-5,missense_variant,p.Asp101Asn,ENST00000329198,;NKX2-5,missense_variant,p.Asp101Asn,ENST00000424406,;NKX2-5,missense_variant,p.Asp101Asn,ENST00000517440,;	T	ENSG00000183072	ENST00000329198	Transcript	missense_variant	575	301	101	D/N	Gac/Aac	.	.	.	-1	NKX2-5	HGNC	2488	protein_coding	YES	CCDS4387.1	ENSP00000327758	NKX25_HUMAN	A1ECB8_HUMAN	UPI0000062197	.	tolerated(0.08)	probably_damaging(0.959)	1/2	.	hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTCGGGGT	.	5	ESCA
LMAN2	0	.	GRCh37	5	176761300	176761300	+	Missense_Mutation	SNP	G	G	A	rs769775648	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895C>T	p.Leu299Phe	p.L299F	ENST00000303127	7/8	64	38	26	62	62	0	LMAN2,missense_variant,p.Pro184Leu,ENST00000514458,;LMAN2,missense_variant,p.Leu299Phe,ENST00000303127,;LMAN2,missense_variant,p.Leu299Phe,ENST00000515209,;LMAN2,downstream_gene_variant,,ENST00000502560,;LMAN2,downstream_gene_variant,,ENST00000513877,;LMAN2,downstream_gene_variant,,ENST00000506310,;LMAN2,non_coding_transcript_exon_variant,,ENST00000504071,;LMAN2,downstream_gene_variant,,ENST00000502721,;	A	ENSG00000169223	ENST00000303127	Transcript	missense_variant	1100	895	299	L/F	Ctc/Ttc	rs769775648	.	.	-1	LMAN2	HGNC	16986	protein_coding	YES	CCDS4417.1	ENSP00000303366	LMAN2_HUMAN	D6RIU4_HUMAN,B4DWN1_HUMAN	UPI0000037B35	.	tolerated(1)	benign(0.004)	7/8	.	hmmpanther:PTHR12223:SF22,hmmpanther:PTHR12223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGAGGAAGT	.	5	ESCA
ZNF354C	0	.	GRCh37	5	178506868	178506868	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000315475	5/5	80	64	15	90	90	0	ZNF354C,stop_gained,p.Gln479Ter,ENST00000315475,;RP11-281O15.7,downstream_gene_variant,,ENST00000523735,;	T	ENSG00000177932	ENST00000315475	Transcript	stop_gained	1741	1435	479	Q/*	Cag/Tag	.	.	.	1	ZNF354C	HGNC	16736	protein_coding	YES	CCDS4443.1	ENSP00000324064	Z354C_HUMAN	Q9NT78_HUMAN	UPI0000161A6A	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF140,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGCCAGTAT	.	5	ESCA
CNOT6	0	.	GRCh37	5	180002753	180002753	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1553G>A	.	.	ENST00000393356	14/14	106	72	34	92	92	0	CNOT6,3_prime_UTR_variant,,ENST00000393356,;CNOT6,3_prime_UTR_variant,,ENST00000261951,;	A	ENSG00000113300	ENST00000393356	Transcript	3_prime_UTR_variant	3651	.	.	.	.	.	.	.	1	CNOT6	HGNC	14099	protein_coding	YES	CCDS4455.1	ENSP00000377024	CNOT6_HUMAN	.	UPI000013D22B	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGAGGGAGC	.	5	ESCA
KIAA0947	0	.	GRCh37	5	5463973	5463973	+	Missense_Mutation	SNP	G	G	A	rs749575254	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4526G>A	p.Arg1509His	p.R1509H	ENST00000296564	13/19	66	46	19	67	67	0	KIAA0947,missense_variant,p.Arg1509His,ENST00000296564,;	A	ENSG00000164151	ENST00000296564	Transcript	missense_variant	4748	4526	1509	R/H	cGt/cAt	rs749575254	.	.	1	KIAA0947	HGNC	29154	protein_coding	YES	CCDS47187.1	ENSP00000296564	K0947_HUMAN	.	UPI00015542F9	.	deleterious(0.03)	benign(0.287)	13/19	.	hmmpanther:PTHR11852,hmmpanther:PTHR11852:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCGTTTGC	.	5	ESCA
SMIM15	0	.	GRCh37	5	60455314	60455314	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*460T>C	.	.	ENST00000339020	3/3	77	48	29	80	80	0	SMIM15,3_prime_UTR_variant,,ENST00000339020,;SMIM15,downstream_gene_variant,,ENST00000507416,;CTC-436P18.1,upstream_gene_variant,,ENST00000506902,;	G	ENSG00000188725	ENST00000339020	Transcript	3_prime_UTR_variant	1111	.	.	.	.	.	.	.	-1	SMIM15	HGNC	33861	protein_coding	YES	CCDS34165.1	ENSP00000339324	SIM15_HUMAN	.	UPI000015EFE6	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGTAATTAA	.	5	ESCA
ZSWIM6	0	.	GRCh37	5	60768825	60768825	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.994G>A	p.Glu332Lys	p.E332K	ENST00000252744	2/14	43	27	16	32	32	0	ZSWIM6,missense_variant,p.Glu332Lys,ENST00000252744,;	A	ENSG00000130449	ENST00000252744	Transcript	missense_variant	994	994	332	E/K	Gaa/Aaa	.	.	.	1	ZSWIM6	HGNC	29316	protein_coding	YES	CCDS47215.1	ENSP00000252744	ZSWM6_HUMAN	.	UPI0001837EA2	.	deleterious(0.01)	probably_damaging(0.939)	2/14	.	hmmpanther:PTHR22619:SF3,hmmpanther:PTHR22619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATGAAATT	.	5	ESCA
TULP4	0	.	GRCh37	6	158924056	158924056	+	Missense_Mutation	SNP	C	C	G	rs758491143	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3361C>G	p.Pro1121Ala	p.P1121A	ENST00000367097	13/14	69	41	28	113	113	0	TULP4,missense_variant,p.Pro1121Ala,ENST00000367097,;TULP4,intron_variant,,ENST00000367094,;	G	ENSG00000130338	ENST00000367097	Transcript	missense_variant	4718	3361	1121	P/A	Cct/Gct	rs758491143	.	.	1	TULP4	HGNC	15530	protein_coding	YES	CCDS34561.1	ENSP00000356064	TULP4_HUMAN	.	UPI000013CD76	.	deleterious_low_confidence(0)	probably_damaging(0.997)	13/14	.	hmmpanther:PTHR16517,hmmpanther:PTHR16517:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCCCTTAC	byFrequency	5	ESCA
MAS1	0	.	GRCh37	6	160328513	160328513	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526G>A	p.Glu176Lys	p.E176K	ENST00000252660	1/1	21	15	6	18	18	0	MAS1,missense_variant,p.Glu176Lys,ENST00000252660,;RP1-249F5.3,downstream_gene_variant,,ENST00000434562,;	A	ENSG00000130368	ENST00000252660	Transcript	missense_variant	540	526	176	E/K	Gaa/Aaa	.	.	.	1	MAS1	HGNC	6899	protein_coding	YES	CCDS5272.1	ENSP00000252660	MAS_HUMAN	.	UPI0000050458	.	tolerated(0.39)	benign(0.003)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF4,hmmpanther:PTHR11334,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00533	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGAAGAG	.	5	ESCA
SLC22A2	0	.	GRCh37	6	160679860	160679860	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-71G>T	.	.	ENST00000366953	1/11	13	8	5	15	15	0	SLC22A2,5_prime_UTR_variant,,ENST00000366953,;SLC22A2,intron_variant,,ENST00000366952,;SLC22A2,upstream_gene_variant,,ENST00000489644,;SLC22A2,upstream_gene_variant,,ENST00000491092,;	A	ENSG00000112499	ENST00000366953	Transcript	5_prime_UTR_variant	189	.	.	.	.	.	.	.	-1	SLC22A2	HGNC	10966	protein_coding	YES	CCDS5276.1	ENSP00000355920	S22A2_HUMAN	Q5T7Q5_HUMAN	UPI000013D5BB	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GCCAGCTCAGC	.	4	ESCA
RP1-265C24.8	0	.	GRCh37	6	28104687	28104687	+	RNA	SNP	T	T	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.61T>C	.	.	ENST00000565046	1/1	216	154	61	219	219	0	RP1-265C24.8,non_coding_transcript_exon_variant,,ENST00000565046,;ZSCAN16-AS1,non_coding_transcript_exon_variant,,ENST00000600652,;ZSCAN16-AS1,upstream_gene_variant,,ENST00000602810,;	C	ENSG00000261839	ENST00000565046	Transcript	non_coding_transcript_exon_variant	61	.	.	.	.	.	.	.	1	RP1-265C24.8	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGGTTCCGG	.	5	ESCA
HLA-A	0	.	GRCh37	6	29910684	29910685	+	Frame_Shift_Ins	INS	-	-	GATA	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227_230dupTAGA	p.Glu77AspfsTer23	p.E77Dfs*23	ENST00000396634	4/10	75	67	8	66	66	0	HLA-A,frameshift_variant,p.Glu77AspfsTer23,ENST00000396634,;HLA-A,frameshift_variant,p.Glu77AspfsTer23,ENST00000376806,;HLA-A,frameshift_variant,p.Glu77AspfsTer23,ENST00000376809,;HLA-A,frameshift_variant,p.Glu77AspfsTer23,ENST00000376802,;HLA-A,non_coding_transcript_exon_variant,,ENST00000479320,;HLA-A,non_coding_transcript_exon_variant,,ENST00000495183,;HLA-A,non_coding_transcript_exon_variant,,ENST00000461903,;HLA-A,intron_variant,,ENST00000496081,;HCG4P5,non_coding_transcript_exon_variant,,ENST00000429656,;	GATA	ENSG00000206503	ENST00000396634	Transcript	frameshift_variant	565-566	224-225	75	W/WIX	tgg/tgGATAg	.	.	.	1	HLA-A	HGNC	4931	protein_coding	YES	CCDS34373.1	ENSP00000379873	1A03_HUMAN,1A30_HUMAN,1A11_HUMAN	S5CRT1_HUMAN,S4TZI2_HUMAN,S4TZE1_HUMAN,R9WYX8_HUMAN,R4I501_HUMAN,R4I3H2_HUMAN,M9PNR0_HUMAN,M9PAA7_HUMAN,M9PAA4_HUMAN,M9P8Z4_HUMAN,M4N6L9_HUMAN,M1SQT4_HUMAN,M1KE04_HUMAN,M1FYE6_HUMAN,M1FYE3_HUMAN,M1FWW6_HUMAN,M1F5P2_HUMAN,Q9UEX6_HUMAN,Q9TQ84_HUMAN,Q9MYA8_HUMAN,Q8HWS5_HUMAN,Q861Q7_HUMAN,Q5XLD1_HUMAN,Q2L4E7_HUMAN,Q29840_HUMAN,Q1M2R8_HUMAN,Q0MSI1_HUMAN,O78086_HUMAN,O78085_HUMAN,O78081_HUMAN,O19689_HUMAN,L7PHV2_HUMAN,L7PHU7_HUMAN,L7PH13_HUMAN,L0BVP5_HUMAN,K9LDJ0_HUMAN,K9LCM8_HUMAN,K9L7Y8_HUMAN,K7WPD7_HUMAN,K7P600_HUMAN,K7P5W6_HUMAN,K7P5U2_HUMAN,K7P5E0_HUMAN,K7P5B6_HUMAN,K7P562_HUMAN,K7P558_HUMAN,J9UP83_HUMAN,J9TNR8_HUMAN,J9PWV5_HUMAN,J9PWL3_HUMAN,J7GM07_HUMAN,J7FNZ2_HUMAN,J7F8L2_HUMAN,I6SJ64_HUMAN,I6QU16_HUMAN,I6NS25_HUMAN,I6NS19_HUMAN,I3UI58_HUMAN,I3UI47_HUMAN,I3QHQ4_HUMAN,I2B2Z9_HUMAN,I1W1L8_HUMAN,H9BQ78_HUMAN,H6UV72_HUMAN,H6UV69_HUMAN,H6UV68_HUMAN,H2BE80_HUMAN,H2BDP5_HUMAN,G9I2J6_HUMAN,G9HW24_HUMAN,G3DR81_HUMAN,G1EPB1_HUMAN,G1EP98_HUMAN,G1EP96_HUMAN,G1EP95_HUMAN,G1EP88_HUMAN,G1EP78_HUMAN,G1EP71_HUMAN,G1EP55_HUMAN,G1EP50_HUMAN,G1EP19_HUMAN,G1EP18_HUMAN,G1EP05_HUMAN,G1ENY5_HUMAN,G1DUW4_HUMAN,G0ZMG9_HUMAN,G0ZMG4_HUMAN,G0ZMG3_HUMAN,G0ZMF4_HUMAN,G0ZDS9_HUMAN,G0WVA6_HUMAN,G0WVA0_HUMAN,F8RHD1_HUMAN,F8RHC2_HUMAN,F8RHB9_HUMAN,F8R8I1_HUMAN,F8R119_HUMAN,F8R110_HUMAN,F6KRP1_HUMAN,F6KRM4_HUMAN,F6IQV7_HUMAN,F4YU26_HUMAN,F4YU20_HUMAN,F2X604_HUMAN,F2X5Y0_HUMAN,F2X5X9_HUMAN,F2VNH3_HUMAN,F2VNH0_HUMAN,F2VNG0_HUMAN,F2VNF7_HUMAN,F2VNF2_HUMAN,F2VNE0_HUMAN,F2VND0_HUMAN,F2VNC4_HUMAN,E9LY14_HUMAN,E9LY02_HUMAN,E9LY00_HUMAN,E8ZF52_HUMAN,E7BY93_HUMAN,E7BY85_HUMAN,E7BBA1_HUMAN,E5DCM4_HUMAN,E5DCM2_HUMAN,E5DCM0_HUMAN,E3SG86_HUMAN,E2DH82_HUMAN,E2D5M3_HUMAN,E2D5L9_HUMAN,E2D5K9_HUMAN,E0YTI8_HUMAN,E0YTI1_HUMAN,E0X9K2_HUMAN,E0WBX4_HUMAN,E0WBX1_HUMAN,D7NSP0_HUMAN,D7NPA3_HUMAN,D7NP98_HUMAN,D7NP92_HUMAN,D7NNU1_HUMAN,D7NNT9_HUMAN,D7NNT6_HUMAN,D7NNT3_HUMAN,D7NNS2_HUMAN,D7NNR5_HUMAN,D7NNM6_HUMAN,D6MLN9_HUMAN,D6MLN3_HUMAN,D6MLM4_HUMAN,D6MLL1_HUMAN,D6MLK2_HUMAN,D6MLJ4_HUMAN,D6MLJ1_HUMAN,D6ML56_HUMAN,D6ML55_HUMAN,D6ML54_HUMAN,D6ML44_HUMAN,D6ML42_HUMAN,D6ML40_HUMAN,D6ML35_HUMAN,D6ML33_HUMAN,D6ML18_HUMAN,D6ML16_HUMAN,D6ML10_HUMAN,D6ML09_HUMAN,D6ML06_HUMAN,D6ML01_HUMAN,D6MKY9_HUMAN,D6MJF7_HUMAN,D5M8G4_HUMAN,D5M8G1_HUMAN,D5M8E4_HUMAN,D5G2J2_HUMAN,D5FIG9_HUMAN,D5FHQ9_HUMAN,D5FHN7_HUMAN,D5FHM5_HUMAN,D5FHM3_HUMAN,D5FHM1_HUMAN,D5FHK5_HUMAN,D5FHG0_HUMAN,D3U484_HUMAN,D3U454_HUMAN,D3U442_HUMAN,D1MYY8_HUMAN,D0RAY3_HUMAN,D0EZK0_HUMAN,D0EZJ9_HUMAN,D0AB29_HUMAN,C9WEL3_HUMAN,C9WEL2_HUMAN,C9WEL1_HUMAN,C9E1E8_HUMAN,C9E1E7_HUMAN,C8XTP8_HUMAN,C8XTP7_HUMAN,C8XTN9_HUMAN,C8XTN7_HUMAN,C8CH66_HUMAN,C6K4J6_HUMAN,C6K4I6_HUMAN,C6K4I1_HUMAN,C6K4H8_HUMAN,C6K4H3_HUMAN,C6K4H0_HUMAN,C6K4G0_HUMAN,C6K4E3_HUMAN,C5J029_HUMAN,C5J027_HUMAN,C5IZR4_HUMAN,C5IZQ3_HUMAN,C4PFZ1_HUMAN,B8YCR7_HUMAN,B8XRE8_HUMAN,B6VA02_HUMAN,B6ECH2_HUMAN,B4DVC4_HUMAN,B1PKY1_HUMAN,A7MAP4_HUMAN,A5PHP7_HUMAN,A0ZXY8_HUMAN	UPI000008AB1D	.	.	.	4/10	.	hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF149,Pfam_domain:PF00129,Gene3D:3.30.500.10,Superfamily_domains:SSF54452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Q78R|c.233A>G|14	INDELOCATOR|VARSCANI	GCCGTGGATAG	.	2	ESCA
VARS	0	.	GRCh37	6	31747232	31747232	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3370G>A	p.Asp1124Asn	p.D1124N	ENST00000375663	28/30	44	29	15	48	48	0	VARS,missense_variant,p.Asp1124Asn,ENST00000375663,;VWA7,upstream_gene_variant,,ENST00000375686,;VWA7,upstream_gene_variant,,ENST00000447450,;VWA7,upstream_gene_variant,,ENST00000375688,;VARS,downstream_gene_variant,,ENST00000428445,;VARS,downstream_gene_variant,,ENST00000444930,;Y_RNA,upstream_gene_variant,,ENST00000364685,;VWA7,upstream_gene_variant,,ENST00000467576,;VARS,upstream_gene_variant,,ENST00000470953,;VARS,downstream_gene_variant,,ENST00000482996,;VARS,downstream_gene_variant,,ENST00000483275,;VWA7,upstream_gene_variant,,ENST00000497645,;VARS,non_coding_transcript_exon_variant,,ENST00000463184,;VARS,downstream_gene_variant,,ENST00000474643,;VARS,downstream_gene_variant,,ENST00000461328,;VARS,downstream_gene_variant,,ENST00000479051,;VARS,downstream_gene_variant,,ENST00000461874,;VARS,downstream_gene_variant,,ENST00000459667,;	T	ENSG00000204394	ENST00000375663	Transcript	missense_variant	3811	3370	1124	D/N	Gac/Aac	.	.	.	-1	VARS	HGNC	12651	protein_coding	YES	CCDS34412.1	ENSP00000364815	SYVC_HUMAN	A2ABF4_HUMAN	UPI00001366EA	.	tolerated(0.07)	probably_damaging(0.977)	28/30	.	Superfamily_domains:SSF47323,Gene3D:1.10.730.10,TIGRFAM_domain:TIGR00422,Pfam_domain:PF08264,hmmpanther:PTHR11946,hmmpanther:PTHR11946:SF54,HAMAP:MF_02004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGTCGGCCC	.	5	ESCA
DAAM2	0	.	GRCh37	6	39853770	39853770	+	Intron	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1954-1492G>T	.	.	ENST00000398904	.	16	13	3	8	8	0	DAAM2,intron_variant,,ENST00000538976,;DAAM2,intron_variant,,ENST00000274867,;DAAM2,intron_variant,,ENST00000398904,;RP11-61I13.3,non_coding_transcript_exon_variant,,ENST00000607675,;RP11-61I13.3,non_coding_transcript_exon_variant,,ENST00000607215,;RP11-61I13.3,downstream_gene_variant,,ENST00000606829,;RP11-61I13.3,downstream_gene_variant,,ENST00000430595,;RP11-61I13.3,downstream_gene_variant,,ENST00000420293,;DAAM2,upstream_gene_variant,,ENST00000496787,;	T	ENSG00000146122	ENST00000398904	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	DAAM2	HGNC	18143	protein_coding	YES	CCDS56426.1	ENSP00000381876	DAAM2_HUMAN	.	UPI000020DC88	.	.	.	.	15/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCAGATCGA	.	2	ESCA
CNR1	0	.	GRCh37	6	88853531	88853531	+	3'UTR	DEL	A	A	-	rs758887693,rs762494727	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*44delT	.	.	ENST00000537554	2/2	32	16	16	34	33	0	CNR1,3_prime_UTR_variant,,ENST00000369499,;CNR1,3_prime_UTR_variant,,ENST00000535130,;CNR1,3_prime_UTR_variant,,ENST00000369501,;CNR1,3_prime_UTR_variant,,ENST00000537554,;CNR1,3_prime_UTR_variant,,ENST00000549890,;CNR1,downstream_gene_variant,,ENST00000551417,;CNR1,downstream_gene_variant,,ENST00000428600,;CNR1,downstream_gene_variant,,ENST00000549716,;CNR1,downstream_gene_variant,,ENST00000468898,;CNR1,downstream_gene_variant,,ENST00000362094,;	-	ENSG00000118432	ENST00000537554	Transcript	3_prime_UTR_variant	5026	.	.	.	.	rs758887693,rs762494727	.	.	-1	CNR1	HGNC	2159	protein_coding	YES	CCDS5015.1	ENSP00000441046	CNR1_HUMAN	S5TLS4_HUMAN,Q9BYY6_HUMAN,F8W187_HUMAN	UPI00000008AA	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGCTTAAAAAA	.	2	ESCA
TRIM56	0	.	GRCh37	7	100730776	100730776	+	Silent	SNP	G	G	A	rs778188310	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.183G>A	p.%3D	p.E61E	ENST00000306085	3/3	41	32	9	22	22	0	TRIM56,synonymous_variant,p.%3D,ENST00000306085,;TRIM56,synonymous_variant,p.%3D,ENST00000412507,;TRIM56,upstream_gene_variant,,ENST00000487252,;TRIM56,non_coding_transcript_exon_variant,,ENST00000467847,;	A	ENSG00000169871	ENST00000306085	Transcript	synonymous_variant	480	183	61	E	gaG/gaA	rs778188310	.	.	1	TRIM56	HGNC	19028	protein_coding	YES	CCDS43625.1	ENSP00000305161	TRI56_HUMAN	.	UPI0000171C4A	.	.	.	3/3	.	Superfamily_domains:SSF57850,Gene3D:3.30.40.10,hmmpanther:PTHR24103:SF287,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGCGAGACAGT	.	3	ESCA
TRIM56	0	.	GRCh37	7	100730795	100730795	+	Missense_Mutation	SNP	G	G	C	rs745831716	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202G>C	p.Glu68Gln	p.E68Q	ENST00000306085	3/3	36	27	9	21	21	0	TRIM56,missense_variant,p.Glu68Gln,ENST00000306085,;TRIM56,missense_variant,p.Glu68Gln,ENST00000412507,;TRIM56,upstream_gene_variant,,ENST00000487252,;TRIM56,downstream_gene_variant,,ENST00000467847,;	C	ENSG00000169871	ENST00000306085	Transcript	missense_variant	499	202	68	E/Q	Gag/Cag	rs745831716	.	.	1	TRIM56	HGNC	19028	protein_coding	YES	CCDS43625.1	ENSP00000305161	TRI56_HUMAN	.	UPI0000171C4A	.	tolerated_low_confidence(0.33)	benign(0.01)	3/3	.	Gene3D:3.30.40.10,hmmpanther:PTHR24103:SF287,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCCCGAGGGT	byFrequency	2	ESCA
TRIM56	0	.	GRCh37	7	100731162	100731162	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569G>C	p.Arg190Thr	p.R190T	ENST00000306085	3/3	34	28	6	54	54	0	TRIM56,missense_variant,p.Arg190Thr,ENST00000306085,;TRIM56,missense_variant,p.Arg190Thr,ENST00000412507,;TRIM56,upstream_gene_variant,,ENST00000487252,;TRIM56,downstream_gene_variant,,ENST00000467847,;	C	ENSG00000169871	ENST00000306085	Transcript	missense_variant	866	569	190	R/T	aGa/aCa	.	.	.	1	TRIM56	HGNC	19028	protein_coding	YES	CCDS43625.1	ENSP00000305161	TRI56_HUMAN	.	UPI0000171C4A	.	deleterious(0)	possibly_damaging(0.688)	3/3	.	Superfamily_domains:SSF57845,SMART_domains:SM00336,Pfam_domain:PF00643,hmmpanther:PTHR24103:SF287,hmmpanther:PTHR24103,PROSITE_profiles:PS50119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCAGAGAGT	.	5	ESCA
RABL5	0	.	GRCh37	7	100958483	100958483	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490T>C	p.Tyr164His	p.Y164H	ENST00000315322	5/5	92	68	23	82	82	0	RABL5,missense_variant,p.Tyr87His,ENST00000498704,;RABL5,missense_variant,p.Tyr164His,ENST00000315322,;RABL5,missense_variant,p.Tyr134His,ENST00000437644,;RABL5,missense_variant,p.Tyr87His,ENST00000517481,;RP11-132A1.4,downstream_gene_variant,,ENST00000419422,;RABL5,non_coding_transcript_exon_variant,,ENST00000495166,;RABL5,missense_variant,p.Tyr164His,ENST00000422177,;RABL5,3_prime_UTR_variant,,ENST00000430911,;RABL5,non_coding_transcript_exon_variant,,ENST00000440362,;RABL5,downstream_gene_variant,,ENST00000468833,;RABL5,downstream_gene_variant,,ENST00000485695,;	G	ENSG00000128581	ENST00000315322	Transcript	missense_variant	584	490	164	Y/H	Tat/Cat	.	.	.	-1	RABL5	HGNC	21895	protein_coding	YES	CCDS5719.1	ENSP00000320359	RABL5_HUMAN	.	UPI000006DC5A	.	deleterious(0)	probably_damaging(0.993)	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATACTTTA	.	5	ESCA
CAV2	0	.	GRCh37	7	116139910	116139910	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75C>G	p.%3D	p.L25L	ENST00000222693	1/3	125	83	42	112	112	0	CAV2,synonymous_variant,p.%3D,ENST00000393480,;CAV2,synonymous_variant,p.%3D,ENST00000222693,;CAV2,synonymous_variant,p.%3D,ENST00000343213,;AC002066.1,upstream_gene_variant,,ENST00000446355,;CAV2,non_coding_transcript_exon_variant,,ENST00000498493,;CAV2,non_coding_transcript_exon_variant,,ENST00000484871,;CAV2,non_coding_transcript_exon_variant,,ENST00000462876,;CAV2,intron_variant,,ENST00000467035,;CAV2,intron_variant,,ENST00000477018,;CAV2,intron_variant,,ENST00000478226,;CAV2,intron_variant,,ENST00000472470,;CAV2,intron_variant,,ENST00000485561,;CAV2,upstream_gene_variant,,ENST00000495841,;	G	ENSG00000105971	ENST00000222693	Transcript	synonymous_variant	467	75	25	L	ctC/ctG	.	.	.	1	CAV2	HGNC	1528	protein_coding	YES	CCDS5766.1	ENSP00000222693	CAV2_HUMAN	Q712N7_HUMAN,Q53X57_HUMAN,E9PCT3_HUMAN	UPI00001270F1	.	.	.	1/3	.	Pfam_domain:PF01146,hmmpanther:PTHR10844:SF3,hmmpanther:PTHR10844	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCGAGTA	.	5	ESCA
CCDC136	0	.	GRCh37	7	128454861	128454861	+	Missense_Mutation	SNP	C	C	G	rs749000859	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2933C>G	p.Ala978Gly	p.A978G	ENST00000297788	15/18	69	54	15	73	73	0	CCDC136,missense_variant,p.Ala978Gly,ENST00000297788,;CCDC136,missense_variant,p.Ala855Gly,ENST00000494552,;CCDC136,intron_variant,,ENST00000464832,;CCDC136,intron_variant,,ENST00000487361,;CCDC136,intron_variant,,ENST00000378685,;CCDC136,intron_variant,,ENST00000464672,;CCDC136,non_coding_transcript_exon_variant,,ENST00000471729,;CCDC136,non_coding_transcript_exon_variant,,ENST00000480137,;CCDC136,intron_variant,,ENST00000528772,;CCDC136,downstream_gene_variant,,ENST00000460941,;	G	ENSG00000128596	ENST00000297788	Transcript	missense_variant	3300	2933	978	A/G	gCc/gGc	rs749000859	.	.	1	CCDC136	HGNC	22225	protein_coding	YES	CCDS47704.1	ENSP00000297788	CC136_HUMAN	C9JAD8_HUMAN,C9J884_HUMAN,C9IYI5_HUMAN	UPI0000E445DE	.	tolerated(0.06)	benign(0.138)	15/18	.	hmmpanther:PTHR18889:SF9,hmmpanther:PTHR18889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGCCCGGG	.	5	ESCA
FLNC	0	.	GRCh37	7	128486431	128486431	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4041C>T	p.%3D	p.G1347G	ENST00000325888	23/48	53	40	13	34	34	0	FLNC,synonymous_variant,p.%3D,ENST00000325888,;FLNC,synonymous_variant,p.%3D,ENST00000346177,;RP11-309L24.2,downstream_gene_variant,,ENST00000469965,;FLNC,downstream_gene_variant,,ENST00000388853,;	T	ENSG00000128591	ENST00000325888	Transcript	synonymous_variant	4302	4041	1347	G	ggC/ggT	.	.	.	1	FLNC	HGNC	3756	protein_coding	YES	CCDS43644.1	ENSP00000327145	FLNC_HUMAN	Q59H94_HUMAN,B3KM41_HUMAN	UPI000006DE6D	.	.	.	23/48	.	Superfamily_domains:SSF81296,Superfamily_domains:SSF81296,SMART_domains:SM00557,Gene3D:2.60.40.10,hmmpanther:PTHR11915:SF173,hmmpanther:PTHR11915,PROSITE_profiles:PS50194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGGCTGTGA	.	5	ESCA
HIPK2	0	.	GRCh37	7	139416253	139416253	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.581C>G	p.Ser194Cys	p.S194C	ENST00000406875	2/15	42	24	17	43	43	0	HIPK2,missense_variant,p.Ser194Cys,ENST00000342645,;HIPK2,missense_variant,p.Ser194Cys,ENST00000428878,;HIPK2,missense_variant,p.Ser194Cys,ENST00000406875,;	C	ENSG00000064393	ENST00000406875	Transcript	missense_variant	676	581	194	S/C	tCc/tGc	.	.	.	-1	HIPK2	HGNC	14402	protein_coding	YES	.	ENSP00000385571	HIPK2_HUMAN	A4D1R9_HUMAN	UPI000012C71E	.	deleterious(0)	probably_damaging(1)	2/15	.	hmmpanther:PTHR24058:SF45,hmmpanther:PTHR24058,Gene3D:3.30.200.20,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATGGAGCAC	.	5	ESCA
GIMAP2	0	.	GRCh37	7	150389763	150389763	+	Missense_Mutation	SNP	A	A	C	rs754733684	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389A>C	p.Lys130Thr	p.K130T	ENST00000223293	3/3	60	43	17	57	57	0	GIMAP2,missense_variant,p.Lys130Thr,ENST00000223293,;GIMAP2,downstream_gene_variant,,ENST00000474605,;	C	ENSG00000106560	ENST00000223293	Transcript	missense_variant	483	389	130	K/T	aAg/aCg	rs754733684	.	.	1	GIMAP2	HGNC	21789	protein_coding	YES	CCDS5905.1	ENSP00000223293	GIMA2_HUMAN	.	UPI000006D114	.	deleterious(0.03)	possibly_damaging(0.793)	3/3	.	PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF28,hmmpanther:PTHR10903,Gene3D:3.40.50.300,Pfam_domain:PF04548,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGAAGGAGA	byFrequency	5	ESCA
CHN2	0	.	GRCh37	7	29440273	29440273	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405C>T	p.%3D	p.Y135Y	ENST00000222792	6/13	48	37	10	34	34	0	CHN2,synonymous_variant,p.%3D,ENST00000409350,;CHN2,synonymous_variant,p.%3D,ENST00000546235,;CHN2,synonymous_variant,p.%3D,ENST00000539406,;CHN2,synonymous_variant,p.%3D,ENST00000495789,;CHN2,synonymous_variant,p.%3D,ENST00000222792,;CHN2,intron_variant,,ENST00000435288,;CHN2,intron_variant,,ENST00000539389,;CHN2,upstream_gene_variant,,ENST00000446446,;CHN2,downstream_gene_variant,,ENST00000439384,;CHN2,non_coding_transcript_exon_variant,,ENST00000409922,;CHN2,non_coding_transcript_exon_variant,,ENST00000412536,;CHN2,downstream_gene_variant,,ENST00000409964,;CHN2,downstream_gene_variant,,ENST00000482820,;CHN2,downstream_gene_variant,,ENST00000478128,;CHN2,3_prime_UTR_variant,,ENST00000474070,;CHN2,non_coding_transcript_exon_variant,,ENST00000491856,;	T	ENSG00000106069	ENST00000222792	Transcript	synonymous_variant	935	405	135	Y	taC/taT	.	.	.	1	CHN2	HGNC	1944	protein_coding	YES	CCDS5420.1	ENSP00000222792	CHIO_HUMAN	A4D1A2_HUMAN	UPI000012781F	.	.	.	6/13	.	Superfamily_domains:SSF55550,PIRSF_domain:PIRSF038015,SMART_domains:SM00252,hmmpanther:PTHR23178,hmmpanther:PTHR23178:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTACATAGA	.	5	ESCA
RAC1	0	.	GRCh37	7	6426904	6426904	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97A>T	p.Ile33Phe	p.I33F	ENST00000356142	2/7	86	66	19	131	131	0	RAC1,missense_variant,p.Ile33Phe,ENST00000356142,;RAC1,missense_variant,p.Ile33Phe,ENST00000348035,;RAC1,non_coding_transcript_exon_variant,,ENST00000488373,;RAC1,upstream_gene_variant,,ENST00000497741,;	T	ENSG00000136238	ENST00000356142	Transcript	missense_variant	294	97	33	I/F	Atc/Ttc	.	.	.	1	RAC1	HGNC	9801	protein_coding	YES	CCDS5349.1	ENSP00000348461	RAC1_HUMAN	A4D2P0_HUMAN	UPI000002B20E	.	deleterious(0)	probably_damaging(0.941)	2/7	.	PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF107,hmmpanther:PTHR24072,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P29L|c.86C>T|4,BUFFER|p.P29L|c.86C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATATCCCT	.	5	ESCA
TBL2	0	.	GRCh37	7	72987738	72987738	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510G>A	p.%3D	p.E170E	ENST00000305632	4/7	39	31	8	39	39	0	TBL2,synonymous_variant,p.%3D,ENST00000452475,;TBL2,synonymous_variant,p.%3D,ENST00000432538,;TBL2,synonymous_variant,p.%3D,ENST00000305632,;TBL2,non_coding_transcript_exon_variant,,ENST00000465279,;TBL2,non_coding_transcript_exon_variant,,ENST00000459913,;TBL2,non_coding_transcript_exon_variant,,ENST00000476136,;TBL2,non_coding_transcript_exon_variant,,ENST00000479892,;TBL2,downstream_gene_variant,,ENST00000468669,;TBL2,missense_variant,p.Gly163Arg,ENST00000450285,;TBL2,3_prime_UTR_variant,,ENST00000437521,;TBL2,3_prime_UTR_variant,,ENST00000435792,;TBL2,3_prime_UTR_variant,,ENST00000426966,;TBL2,3_prime_UTR_variant,,ENST00000424598,;TBL2,3_prime_UTR_variant,,ENST00000417008,;TBL2,3_prime_UTR_variant,,ENST00000433464,;TBL2,3_prime_UTR_variant,,ENST00000452125,;TBL2,downstream_gene_variant,,ENST00000496056,;TBL2,downstream_gene_variant,,ENST00000458466,;TBL2,upstream_gene_variant,,ENST00000495885,;TBL2,upstream_gene_variant,,ENST00000488915,;TBL2,downstream_gene_variant,,ENST00000469518,;	T	ENSG00000106638	ENST00000305632	Transcript	synonymous_variant	752	510	170	E	gaG/gaA	.	.	.	-1	TBL2	HGNC	11586	protein_coding	YES	CCDS5551.1	ENSP00000307260	TBL2_HUMAN	F2Z3G3_HUMAN,B4DY59_HUMAN	UPI0000048EF4	.	.	.	4/7	.	PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF380,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCTCCCG	.	5	ESCA
CSMD3	0	.	GRCh37	8	114389036	114389036	+	Intron	SNP	G	G	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.178+59870C>G	.	.	ENST00000297405	.	115	85	30	141	141	0	CSMD3,5_prime_UTR_variant,,ENST00000343508,;CSMD3,intron_variant,,ENST00000352409,;CSMD3,intron_variant,,ENST00000455883,;CSMD3,intron_variant,,ENST00000297405,;CSMD3,intron_variant,,ENST00000497026,;CSMD3,intron_variant,,ENST00000493303,;RP11-709P2.1,non_coding_transcript_exon_variant,,ENST00000422478,;	C	ENSG00000164796	ENST00000297405	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	.	.	.	1/70	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTTGTGCTG	.	5	ESCA
ATAD2	0	.	GRCh37	8	124335278	124335279	+	Frame_Shift_Ins	INS	-	-	T	rs775812316	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4030dupA	p.Ser1344LysfsTer28	p.S1344Kfs*28	ENST00000287394	27/28	79	54	25	75	75	0	ATAD2,frameshift_variant,p.Ser1344LysfsTer28,ENST00000287394,;ATAD2,frameshift_variant,p.Ser662LysfsTer28,ENST00000521903,;ATAD2,3_prime_UTR_variant,,ENST00000517666,;ATAD2,3_prime_UTR_variant,,ENST00000519124,;	T	ENSG00000156802	ENST00000287394	Transcript	frameshift_variant	4138-4139	4030-4031	1344	S/KX	agt/aAgt	rs775812316	.	.	-1	ATAD2	HGNC	30123	protein_coding	YES	CCDS6343.1	ENSP00000287394	ATAD2_HUMAN	.	UPI0000052A8C	.	.	.	27/28	.	hmmpanther:PTHR23069,hmmpanther:PTHR23069:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTGACTTTTT	.	2	ESCA
EFR3A	0	.	GRCh37	8	132991105	132991105	+	Silent	SNP	A	A	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1338A>T	p.%3D	p.G446G	ENST00000254624	13/23	68	46	21	63	63	0	EFR3A,synonymous_variant,p.%3D,ENST00000254624,;EFR3A,synonymous_variant,p.%3D,ENST00000519656,;EFR3A,synonymous_variant,p.%3D,ENST00000334503,;	T	ENSG00000132294	ENST00000254624	Transcript	synonymous_variant	1563	1338	446	G	ggA/ggT	.	.	.	1	EFR3A	HGNC	28970	protein_coding	YES	CCDS34942.2	ENSP00000254624	EFR3A_HUMAN	E5RJS1_HUMAN,B4DZ89_HUMAN	UPI00001C1E8F	.	.	.	13/23	.	hmmpanther:PTHR12444,hmmpanther:PTHR12444:SF1,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGGATATAA	.	5	ESCA
RPL8	0	.	GRCh37	8	146015317	146015317	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.646C>T	p.His216Tyr	p.H216Y	ENST00000262584	6/6	42	29	13	51	51	0	RPL8,missense_variant,p.His107Tyr,ENST00000527914,;RPL8,missense_variant,p.His216Tyr,ENST00000394920,;RPL8,missense_variant,p.His216Tyr,ENST00000262584,;RPL8,missense_variant,p.His195Tyr,ENST00000533397,;RPL8,missense_variant,p.His216Tyr,ENST00000528957,;ZNF34,upstream_gene_variant,,ENST00000534445,;ZNF34,upstream_gene_variant,,ENST00000429371,;ZNF34,upstream_gene_variant,,ENST00000343459,;RPL8,downstream_gene_variant,,ENST00000532702,;RN7SL395P,downstream_gene_variant,,ENST00000462960,;RPL8,non_coding_transcript_exon_variant,,ENST00000528296,;RPL8,non_coding_transcript_exon_variant,,ENST00000529163,;RPL8,3_prime_UTR_variant,,ENST00000531975,;RPL8,3_prime_UTR_variant,,ENST00000529920,;RPL8,non_coding_transcript_exon_variant,,ENST00000526668,;RPL8,non_coding_transcript_exon_variant,,ENST00000534781,;RPL8,downstream_gene_variant,,ENST00000531767,;RPL8,downstream_gene_variant,,ENST00000525232,;ZNF34,upstream_gene_variant,,ENST00000527740,;	A	ENSG00000161016	ENST00000262584	Transcript	missense_variant	879	646	216	H/Y	Cac/Tac	.	.	.	-1	RPL8	HGNC	10368	protein_coding	YES	CCDS6433.1	ENSP00000262584	RL8_HUMAN	G3V1A1_HUMAN,E9PKZ0_HUMAN	UPI000000419E	.	deleterious(0)	probably_damaging(0.965)	6/6	.	HAMAP:MF_01320_A,hmmpanther:PTHR13691,hmmpanther:PTHR13691:SF16,Gene3D:4.10.950.10,Pfam_domain:PF03947,PIRSF_domain:PIRSF002158,Superfamily_domains:SSF50104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTGGTTGC	.	5	ESCA
BMP1	0	.	GRCh37	8	22035217	22035217	+	Intron	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731-148C>A	.	.	ENST00000306385	.	52	38	13	59	59	0	BMP1,missense_variant,p.Leu290Ile,ENST00000354870,;BMP1,intron_variant,,ENST00000306385,;BMP1,intron_variant,,ENST00000306349,;BMP1,intron_variant,,ENST00000397816,;BMP1,intron_variant,,ENST00000397814,;BMP1,downstream_gene_variant,,ENST00000521521,;BMP1,downstream_gene_variant,,ENST00000523849,;BMP1,missense_variant,p.Leu290Ile,ENST00000483364,;BMP1,3_prime_UTR_variant,,ENST00000518656,;BMP1,intron_variant,,ENST00000521385,;BMP1,intron_variant,,ENST00000520626,;BMP1,intron_variant,,ENST00000471755,;BMP1,intron_variant,,ENST00000518913,;BMP1,intron_variant,,ENST00000520970,;BMP1,intron_variant,,ENST00000520982,;BMP1,upstream_gene_variant,,ENST00000523457,;	A	ENSG00000168487	ENST00000306385	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	BMP1	HGNC	1067	protein_coding	YES	CCDS6026.1	ENSP00000305714	BMP1_HUMAN	.	UPI0000049818	.	.	.	.	5/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGCTCCCC	.	5	ESCA
ADAM7	0	.	GRCh37	8	24298629	24298629	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8C>A	p.Pro3His	p.P3H	ENST00000175238	1/22	59	41	18	93	93	0	ADAM7,missense_variant,p.Pro3His,ENST00000175238,;ADAM7,missense_variant,p.Pro3His,ENST00000441335,;ADAM7,missense_variant,p.Pro3His,ENST00000380789,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,;	A	ENSG00000069206	ENST00000175238	Transcript	missense_variant	91	8	3	P/H	cCc/cAc	.	.	.	1	ADAM7	HGNC	214	protein_coding	YES	CCDS6045.1	ENSP00000175238	ADAM7_HUMAN	.	UPI000013C5CC	.	deleterious(0.01)	possibly_damaging(0.832)	1/22	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11905:SF21,hmmpanther:PTHR11905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTCCCGGGT	.	5	ESCA
ADAM7	0	.	GRCh37	8	24365023	24365023	+	Missense_Mutation	SNP	G	G	A	rs367681847	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2239G>A	p.Ala747Thr	p.A747T	ENST00000175238	21/22	83	58	24	108	108	0	ADAM7,missense_variant,p.Ala747Thr,ENST00000175238,;ADAM7,missense_variant,p.Ala769Thr,ENST00000380789,;ADAM7,intron_variant,,ENST00000520720,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,;RP11-561E1.1,intron_variant,,ENST00000519364,;RP11-561E1.1,downstream_gene_variant,,ENST00000517428,;RP11-561E1.1,downstream_gene_variant,,ENST00000519893,;RP11-561E1.1,downstream_gene_variant,,ENST00000520256,;	A	ENSG00000069206	ENST00000175238	Transcript	missense_variant	2322	2239	747	A/T	Gca/Aca	rs367681847	.	.	1	ADAM7	HGNC	214	protein_coding	YES	CCDS6045.1	ENSP00000175238	ADAM7_HUMAN	.	UPI000013C5CC	.	tolerated_low_confidence(0.17)	benign(0.016)	21/22	.	hmmpanther:PTHR11905:SF21,hmmpanther:PTHR11905	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCGCAGAT	byFrequency|byCluster	5	ESCA
TRIM35	0	.	GRCh37	8	27156030	27156030	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482C>T	p.Ala161Val	p.A161V	ENST00000305364	2/6	29	20	8	37	37	0	TRIM35,missense_variant,p.Ala161Val,ENST00000305364,;TRIM35,intron_variant,,ENST00000521253,;TRIM35,upstream_gene_variant,,ENST00000521283,;TRIM35,non_coding_transcript_exon_variant,,ENST00000519219,;	A	ENSG00000104228	ENST00000305364	Transcript	missense_variant	566	482	161	A/V	gCc/gTc	.	.	.	-1	TRIM35	HGNC	16285	protein_coding	YES	CCDS6056.2	ENSP00000301924	TRI35_HUMAN	.	UPI00001649FB	.	tolerated(0.24)	benign(0.021)	2/6	.	hmmpanther:PTHR24103:SF213,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGGCCTTG	.	5	ESCA
KIF13B	0	.	GRCh37	8	28980968	28980968	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3394G>C	p.Glu1132Gln	p.E1132Q	ENST00000524189	28/40	41	28	12	60	60	0	KIF13B,missense_variant,p.Glu1132Gln,ENST00000524189,;CTD-2647L4.1,intron_variant,,ENST00000523661,;	G	ENSG00000197892	ENST00000524189	Transcript	missense_variant	3433	3394	1132	E/Q	Gag/Cag	.	.	.	-1	KIF13B	HGNC	14405	protein_coding	YES	CCDS55217.1	ENSP00000427900	KI13B_HUMAN	.	UPI000035B257	.	tolerated(0.05)	probably_damaging(0.94)	28/40	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCCAGAA	.	5	ESCA
FGFR1	0	.	GRCh37	8	38270040	38270040	+	3'UTR	SNP	A	A	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1106T>G	.	.	ENST00000425967	19/19	8	5	3	15	15	0	FGFR1,3_prime_UTR_variant,,ENST00000532791,;FGFR1,3_prime_UTR_variant,,ENST00000447712,;FGFR1,3_prime_UTR_variant,,ENST00000341462,;FGFR1,3_prime_UTR_variant,,ENST00000425967,;FGFR1,3_prime_UTR_variant,,ENST00000397091,;FGFR1,downstream_gene_variant,,ENST00000326324,;LETM2,downstream_gene_variant,,ENST00000297720,;FGFR1,downstream_gene_variant,,ENST00000397103,;LETM2,downstream_gene_variant,,ENST00000527710,;LETM2,downstream_gene_variant,,ENST00000524874,;LETM2,downstream_gene_variant,,ENST00000523983,;FGFR1,downstream_gene_variant,,ENST00000356207,;FGFR1,downstream_gene_variant,,ENST00000397113,;FGFR1,downstream_gene_variant,,ENST00000335922,;LETM2,downstream_gene_variant,,ENST00000379957,;LETM2,downstream_gene_variant,,ENST00000527175,;FGFR1,downstream_gene_variant,,ENST00000397108,;RP11-350N15.6,upstream_gene_variant,,ENST00000606593,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526688,;FGFR1,downstream_gene_variant,,ENST00000466021,;LETM2,downstream_gene_variant,,ENST00000530448,;LETM2,downstream_gene_variant,,ENST00000523268,;FGFR1,downstream_gene_variant,,ENST00000531196,;FGFR1,downstream_gene_variant,,ENST00000533619,;FGFR1,downstream_gene_variant,,ENST00000527114,;FGFR1,downstream_gene_variant,,ENST00000527745,;LETM2,downstream_gene_variant,,ENST00000518883,;FGFR1,downstream_gene_variant,,ENST00000487647,;FGFR1,downstream_gene_variant,,ENST00000526570,;LETM2,downstream_gene_variant,,ENST00000526075,;	C	ENSG00000077782	ENST00000425967	Transcript	3_prime_UTR_variant	3991	.	.	.	.	.	.	.	-1	FGFR1	HGNC	3688	protein_coding	YES	CCDS55223.1	ENSP00000393312	FGFR1_HUMAN	E9PN14_HUMAN,D3DSX2_HUMAN,C9J205_HUMAN	UPI0001CE06A3	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GAAGCAGACAT	.	2	ESCA
PXDNL	0	.	GRCh37	8	52384761	52384761	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.798T>G	p.Ile266Met	p.I266M	ENST00000356297	8/23	64	41	22	81	81	0	PXDNL,missense_variant,p.Ile266Met,ENST00000543296,;PXDNL,missense_variant,p.Ile266Met,ENST00000356297,;	C	ENSG00000147485	ENST00000356297	Transcript	missense_variant	899	798	266	I/M	atT/atG	.	.	.	-1	PXDNL	HGNC	26359	protein_coding	YES	CCDS47855.1	ENSP00000348645	PXDNL_HUMAN	.	UPI0001AE6ED6	.	deleterious(0.01)	probably_damaging(0.976)	8/23	.	PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCAAATAAT	.	5	ESCA
CHD7	0	.	GRCh37	8	61750713	61750713	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4432G>A	p.Glu1478Lys	p.E1478K	ENST00000423902	19/38	98	69	29	103	103	0	CHD7,missense_variant,p.Glu1478Lys,ENST00000423902,;CHD7,intron_variant,,ENST00000524602,;	A	ENSG00000171316	ENST00000423902	Transcript	missense_variant	4911	4432	1478	E/K	Gaa/Aaa	.	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	probably_damaging(0.986)	19/38	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF551,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGAAGGG	.	5	ESCA
TRPA1	0	.	GRCh37	8	72935276	72935276	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3225C>T	p.%3D	p.I1075I	ENST00000262209	27/27	73	49	24	66	66	0	TRPA1,synonymous_variant,p.%3D,ENST00000262209,;RP11-383H13.1,intron_variant,,ENST00000537896,;TRPA1,intron_variant,,ENST00000523582,;RP11-383H13.1,intron_variant,,ENST00000524152,;RP11-383H13.1,intron_variant,,ENST00000519751,;RP11-383H13.1,intron_variant,,ENST00000457356,;RP11-383H13.1,intron_variant,,ENST00000518916,;TRPA1,downstream_gene_variant,,ENST00000520596,;RP11-383H13.1,intron_variant,,ENST00000522519,;RP11-383H13.1,intron_variant,,ENST00000519068,;	A	ENSG00000104321	ENST00000262209	Transcript	synonymous_variant	3433	3225	1075	I	atC/atT	.	.	.	-1	TRPA1	HGNC	497	protein_coding	YES	CCDS34908.1	ENSP00000262209	TRPA1_HUMAN	.	UPI000021081A	.	.	.	27/27	.	hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGAGATGAT	.	5	ESCA
TMEM38B	0	.	GRCh37	9	108536579	108536579	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*218A>T	.	.	ENST00000374692	6/6	81	41	40	149	149	0	TMEM38B,3_prime_UTR_variant,,ENST00000374692,;TMEM38B,3_prime_UTR_variant,,ENST00000374688,;TMEM38B,downstream_gene_variant,,ENST00000435034,;	T	ENSG00000095209	ENST00000374692	Transcript	3_prime_UTR_variant	1211	.	.	.	.	.	.	.	1	TMEM38B	HGNC	25535	protein_coding	YES	CCDS6768.1	ENSP00000363824	TM38B_HUMAN	.	UPI0000034FF4	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTATAAGAGA	.	5	ESCA
BRD3	0	.	GRCh37	9	136913402	136913402	+	Missense_Mutation	SNP	C	C	T	rs531283531	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.889G>A	p.Glu297Lys	p.E297K	ENST00000303407	6/12	20	12	8	29	29	0	BRD3,missense_variant,p.Glu297Lys,ENST00000371834,;BRD3,missense_variant,p.Glu297Lys,ENST00000303407,;BRD3,missense_variant,p.Glu297Lys,ENST00000357885,;BRD3,downstream_gene_variant,,ENST00000371842,;BRD3,non_coding_transcript_exon_variant,,ENST00000494743,;	T	ENSG00000169925	ENST00000303407	Transcript	missense_variant	1075	889	297	E/K	Gag/Aag	rs531283531	.	.	-1	BRD3	HGNC	1104	protein_coding	YES	CCDS6980.1	ENSP00000305918	BRD3_HUMAN	B4DS09_HUMAN,A9J575_HUMAN,A9J571_HUMAN	UPI0000126ACD	.	deleterious(0.02)	possibly_damaging(0.905)	6/12	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF126,Gene3D:1.20.920.10	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCTCGCCGT	by1000G	2	ESCA
CCIN	0	.	GRCh37	9	36170954	36170954	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1455G>A	p.%3D	p.R485R	ENST00000335119	1/1	33	30	3	34	34	0	CCIN,synonymous_variant,p.%3D,ENST00000335119,;	A	ENSG00000185972	ENST00000335119	Transcript	synonymous_variant	1566	1455	485	R	cgG/cgA	.	.	.	1	CCIN	HGNC	1568	protein_coding	YES	CCDS6599.1	ENSP00000334996	CALI_HUMAN	Q8WX35_HUMAN	UPI000006EB8E	.	.	.	1/1	.	Gene3D:1k3iA02,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF163	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCGGCAGAG	.	2	ESCA
NRK	0	.	GRCh37	X	105183880	105183880	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3817C>G	p.Leu1273Val	p.L1273V	ENST00000428173	23/29	27	13	14	31	31	0	NRK,missense_variant,p.Leu1273Val,ENST00000428173,;NRK,missense_variant,p.Leu1272Val,ENST00000243300,;	G	ENSG00000123572	ENST00000428173	Transcript	missense_variant	4120	3817	1273	L/V	Ctt/Gtt	.	.	.	1	NRK	HGNC	25391	protein_coding	YES	.	ENSP00000438378	.	F5H049_HUMAN,B7Z6I7_HUMAN	UPI00015E03BB	.	tolerated(0.07)	probably_damaging(0.99)	23/29	.	PROSITE_profiles:PS50219,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF216,Pfam_domain:PF00780,SMART_domains:SM00036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGACTTCGG	.	5	ESCA
RP11-364B14.1	0	.	GRCh37	X	139100021	139100021	+	RNA	SNP	G	G	T	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.407G>T	.	.	ENST00000417426	2/2	45	26	18	62	62	0	RP11-364B14.1,non_coding_transcript_exon_variant,,ENST00000417426,;	T	ENSG00000233145	ENST00000417426	Transcript	non_coding_transcript_exon_variant	407	.	.	.	.	.	.	.	1	RP11-364B14.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCCGCTGGC	.	5	ESCA
MBTPS2	0	.	GRCh37	X	21896680	21896681	+	Frame_Shift_Ins	INS	-	-	A	.	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1138dupA	p.Ser380LysfsTer28	p.S380Kfs*28	ENST00000379484	9/11	46	19	27	52	52	0	MBTPS2,frameshift_variant,p.Ser380LysfsTer28,ENST00000379484,;	A	ENSG00000012174	ENST00000379484	Transcript	frameshift_variant	1230-1231	1131-1132	377-378	-/X	-/A	COSM308679	.	.	1	MBTPS2	HGNC	15455	protein_coding	YES	CCDS14201.1	ENSP00000368798	MBTP2_HUMAN	.	UPI000012F5A0	.	.	.	9/11	.	hmmpanther:PTHR13325:SF2,hmmpanther:PTHR13325,Pfam_domain:PF02163	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	insertion	.	7	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GACTGTAAAAA	.	2	ESCA
PHF8	0	.	GRCh37	X	53964450	53964450	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88W-01A-11D-A351-09	TCGA-L5-A88W-11A-11D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1141C>T	.	.	ENST00000357988	22/22	26	6	20	23	23	0	PHF8,synonymous_variant,p.%3D,ENST00000396282,;PHF8,synonymous_variant,p.%3D,ENST00000338946,;PHF8,3_prime_UTR_variant,,ENST00000357988,;PHF8,3_prime_UTR_variant,,ENST00000338154,;PHF8,downstream_gene_variant,,ENST00000443302,;PHF8,downstream_gene_variant,,ENST00000470103,;	A	ENSG00000172943	ENST00000357988	Transcript	3_prime_UTR_variant	4683	.	.	.	.	.	.	.	-1	PHF8	HGNC	20672	protein_coding	YES	CCDS55420.1	ENSP00000350676	PHF8_HUMAN	Q5JPR8_HUMAN,B3KMV4_HUMAN,B0QZZ4_HUMAN,B0QZZ3_HUMAN,B0QZZ2_HUMAN,B0QZE1_HUMAN	UPI00001C2071	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCGTGAAT	.	5	ESCA
CNNM2	0	.	GRCh37	10	104809565	104809565	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1723G>T	p.Glu575Ter	p.E575*	ENST00000369878	2/8	83	55	28	97	97	0	CNNM2,stop_gained,p.Glu575Ter,ENST00000369878,;CNNM2,stop_gained,p.Glu575Ter,ENST00000433628,;	T	ENSG00000148842	ENST00000369878	Transcript	stop_gained	1911	1723	575	E/*	Gaa/Taa	.	.	.	1	CNNM2	HGNC	103	protein_coding	YES	CCDS44474.1	ENSP00000358894	CNNM2_HUMAN	.	UPI0000231CA6	.	.	.	2/8	.	PROSITE_profiles:PS51371,hmmpanther:PTHR12064,hmmpanther:PTHR12064:SF22,Gene3D:3.10.580.10,Pfam_domain:PF00571,Superfamily_domains:SSF54631	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAAGAAATC	.	5	ESCA
SVIL	0	.	GRCh37	10	29769362	29769362	+	Intron	SNP	C	C	T	rs768128912	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5377+104G>A	.	.	ENST00000375398	.	22	14	8	23	23	0	SVIL,3_prime_UTR_variant,,ENST00000538146,;SVIL,intron_variant,,ENST00000375398,;SVIL,intron_variant,,ENST00000375400,;SVIL,intron_variant,,ENST00000355867,;SVIL,intron_variant,,ENST00000535393,;PTCHD3P1,intron_variant,,ENST00000446807,;PTCHD3P1,intron_variant,,ENST00000413405,;PTCHD3P1,intron_variant,,ENST00000423223,;PTCHD3P1,intron_variant,,ENST00000414457,;SVIL,intron_variant,,ENST00000460007,;SVIL,downstream_gene_variant,,ENST00000482607,;	T	ENSG00000197321	ENST00000375398	Transcript	intron_variant	.	.	.	.	.	rs768128912	.	.	-1	SVIL	HGNC	11480	protein_coding	YES	CCDS7164.1	ENSP00000364547	SVIL_HUMAN	Q569J5_HUMAN	UPI0000366678	.	.	.	.	31/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCACGGACG	.	2	ESCA
MAP3K8	0	.	GRCh37	10	30736816	30736816	+	Missense_Mutation	SNP	G	G	A	rs3751449	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442G>A	p.Ala148Thr	p.A148T	ENST00000263056	4/9	59	36	22	78	78	0	MAP3K8,missense_variant,p.Ala148Thr,ENST00000263056,;MAP3K8,missense_variant,p.Ala148Thr,ENST00000542547,;MAP3K8,missense_variant,p.Ala148Thr,ENST00000415139,;MAP3K8,missense_variant,p.Ala148Thr,ENST00000375321,;MAP3K8,missense_variant,p.Ala148Thr,ENST00000413724,;MAP3K8,non_coding_transcript_exon_variant,,ENST00000430603,;	A	ENSG00000107968	ENST00000263056	Transcript	missense_variant	1138	442	148	A/T	Gcc/Acc	rs3751449	.	.	1	MAP3K8	HGNC	6860	protein_coding	YES	CCDS7166.1	ENSP00000263056	M3K8_HUMAN	Q5T857_HUMAN,Q5T853_HUMAN	UPI000013D395	.	tolerated(0.09)	possibly_damaging(0.852)	4/9	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF94,hmmpanther:PTHR24361,Gene3D:3.30.200.20,Pfam_domain:PF00069,PIRSF_domain:PIRSF038171,SMART_domains:SM00220,Superfamily_domains:SSF56112	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCGCCTTT	byFrequency|byCluster|byHapMap|by1000G	5	ESCA
ERCC6	0	.	GRCh37	10	50691461	50691461	+	Missense_Mutation	SNP	G	G	T	rs757815168	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1923C>A	p.His641Gln	p.H641Q	ENST00000355832	9/21	92	54	38	92	92	0	ERCC6,missense_variant,p.His11Gln,ENST00000542458,;ERCC6,missense_variant,p.His641Gln,ENST00000355832,;ERCC6,non_coding_transcript_exon_variant,,ENST00000475116,;	T	ENSG00000225830	ENST00000355832	Transcript	missense_variant	2002	1923	641	H/Q	caC/caA	rs757815168	.	.	-1	ERCC6	HGNC	3438	protein_coding	YES	CCDS7229.1	ENSP00000348089	ERCC6_HUMAN	F5H493_HUMAN,D6R9X7_HUMAN	UPI000000D8DA	.	deleterious(0.03)	benign(0.374)	9/21	.	PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF49,hmmpanther:PTHR10799,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATAGTGCCA	.	5	ESCA
COMTD1	0	.	GRCh37	10	76994397	76994397	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607C>T	p.Arg203Ter	p.R203*	ENST00000372538	6/7	62	37	24	94	93	1	COMTD1,stop_gained,p.Arg201Ter,ENST00000469299,;COMTD1,stop_gained,p.Arg203Ter,ENST00000372538,;VDAC2,downstream_gene_variant,,ENST00000298468,;VDAC2,downstream_gene_variant,,ENST00000332211,;VDAC2,downstream_gene_variant,,ENST00000543351,;VDAC2,downstream_gene_variant,,ENST00000535553,;VDAC2,downstream_gene_variant,,ENST00000313132,;COMTD1,non_coding_transcript_exon_variant,,ENST00000490521,;COMTD1,non_coding_transcript_exon_variant,,ENST00000460899,;COMTD1,non_coding_transcript_exon_variant,,ENST00000494596,;COMTD1,non_coding_transcript_exon_variant,,ENST00000470947,;COMTD1,downstream_gene_variant,,ENST00000491270,;VDAC2,downstream_gene_variant,,ENST00000460044,;	A	ENSG00000165644	ENST00000372538	Transcript	stop_gained	690	607	203	R/*	Cga/Tga	.	.	.	-1	COMTD1	HGNC	26309	protein_coding	YES	CCDS7349.1	ENSP00000361616	CMTD1_HUMAN	.	UPI000000DC5A	.	.	.	6/7	.	PROSITE_profiles:PS51682,hmmpanther:PTHR10509:SF14,hmmpanther:PTHR10509,Gene3D:3.40.50.150,Pfam_domain:PF01596,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCGCAGCA	.	5	ESCA
MMP3	0	.	GRCh37	11	102712941	102712941	+	Missense_Mutation	SNP	C	C	A	rs782385032	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569G>T	p.Gly190Val	p.G190V	ENST00000299855	4/10	104	66	38	85	85	0	MMP3,missense_variant,p.Gly190Val,ENST00000299855,;MMP3,upstream_gene_variant,,ENST00000434103,;MMP3,downstream_gene_variant,,ENST00000524478,;	A	ENSG00000149968	ENST00000299855	Transcript	missense_variant	826	569	190	G/V	gGg/gTg	rs782385032,COSM1492416	.	.	-1	MMP3	HGNC	7173	protein_coding	YES	CCDS8323.1	ENSP00000299855	MMP3_HUMAN	.	UPI00000422BF	.	deleterious(0)	probably_damaging(0.996)	4/10	.	hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF38,Pfam_domain:PF00413,Gene3D:3.40.390.10,SMART_domains:SM00235,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATCCCTGGC	.	5	ESCA
DSCAML1	0	.	GRCh37	11	117352705	117352705	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2712C>T	p.%3D	p.N904N	ENST00000321322	12/33	47	23	24	44	44	0	DSCAML1,synonymous_variant,p.%3D,ENST00000527706,;DSCAML1,synonymous_variant,p.%3D,ENST00000321322,;	A	ENSG00000177103	ENST00000321322	Transcript	synonymous_variant	2714	2712	904	N	aaC/aaT	.	.	.	-1	DSCAML1	HGNC	14656	protein_coding	YES	CCDS8384.1	ENSP00000315465	DSCL1_HUMAN	.	UPI00000726E2	.	.	.	12/33	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCCGTTGTC	.	5	ESCA
CRTAM	0	.	GRCh37	11	122722490	122722490	+	Missense_Mutation	SNP	G	G	A	rs757374307	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283G>A	p.Val95Met	p.V95M	ENST00000227348	3/10	103	58	45	88	88	0	CRTAM,missense_variant,p.Val95Met,ENST00000227348,;	A	ENSG00000109943	ENST00000227348	Transcript	missense_variant	330	283	95	V/M	Gtg/Atg	rs757374307	.	.	1	CRTAM	HGNC	24313	protein_coding	YES	CCDS8437.1	ENSP00000227348	CRTAM_HUMAN	.	UPI000013C8B4	.	deleterious(0.04)	benign(0.128)	3/10	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF48,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGCGTGTAC	.	5	ESCA
MUC5B	0	.	GRCh37	11	1260766	1260766	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3553C>A	p.His1185Asn	p.H1185N	ENST00000529681	27/49	120	81	39	125	125	0	MUC5B,missense_variant,p.His1185Asn,ENST00000529681,;MUC5B,missense_variant,p.His1188Asn,ENST00000447027,;RP11-532E4.2,downstream_gene_variant,,ENST00000532061,;MUC5B,non_coding_transcript_exon_variant,,ENST00000525715,;	A	ENSG00000117983	ENST00000529681	Transcript	missense_variant	3611	3553	1185	H/N	Cac/Aac	.	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	unknown(0)	27/49	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237,Gene3D:2.10.25.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGGCACTGC	.	5	ESCA
RAG1	0	.	GRCh37	11	36599943	36599943	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1957T>C	.	.	ENST00000299440	2/2	35	32	3	46	46	0	RAG1,3_prime_UTR_variant,,ENST00000299440,;RAG2,intron_variant,,ENST00000524423,;RAG1,intron_variant,,ENST00000534663,;	C	ENSG00000166349	ENST00000299440	Transcript	3_prime_UTR_variant	5201	.	.	.	.	.	.	.	1	RAG1	HGNC	9831	protein_coding	YES	CCDS7902.1	ENSP00000299440	RAG1_HUMAN	.	UPI000013E5A0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GGAAATGAGTG	.	2	ESCA
PTPRJ	0	.	GRCh37	11	48131629	48131630	+	Splice_Site	DEL	GT	GT	-	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	GT	GT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115+2_115+3delTG	.	p.X39_splice	ENST00000418331	.	26	16	10	18	18	0	PTPRJ,splice_donor_variant,,ENST00000440289,;PTPRJ,splice_donor_variant,,ENST00000527952,;PTPRJ,splice_donor_variant,,ENST00000418331,;PTPRJ,splice_donor_variant,,ENST00000534219,;PTPRJ,splice_donor_variant,,ENST00000526550,;	-	ENSG00000149177	ENST00000418331	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	PTPRJ	HGNC	9673	protein_coding	YES	CCDS7945.1	ENSP00000400010	PTPRJ_HUMAN	Q9NPR5_HUMAN	UPI00004564C8	.	.	.	.	2/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTGGCAGTGAGTA	.	2	ESCA
OR4A5	0	.	GRCh37	11	51412174	51412174	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.222C>T	p.%3D	p.T74T	ENST00000319760	1/1	52	30	22	51	51	0	OR4A5,synonymous_variant,p.%3D,ENST00000319760,;	A	ENSG00000221840	ENST00000319760	Transcript	synonymous_variant	275	222	74	T	acC/acT	.	.	.	-1	OR4A5	HGNC	15162	protein_coding	YES	CCDS31497.1	ENSP00000367664	OR4A5_HUMAN	.	UPI0000041D58	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF299,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATGGTAGT	.	5	ESCA
OR5B2	0	.	GRCh37	11	58190660	58190660	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75C>T	p.%3D	p.L25L	ENST00000302581	1/1	78	50	27	82	82	0	OR5B2,synonymous_variant,p.%3D,ENST00000302581,;	A	ENSG00000172365	ENST00000302581	Transcript	synonymous_variant	127	75	25	L	ctC/ctT	.	.	.	-1	OR5B2	HGNC	8323	protein_coding	YES	CCDS31550.1	ENSP00000303076	OR5B2_HUMAN	.	UPI000004B227	.	.	.	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26452:SF3,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAAGAGGGG	.	5	ESCA
C11orf84	0	.	GRCh37	11	63585506	63585506	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.357C>T	p.%3D	p.D119D	ENST00000294244	2/6	34	31	3	44	44	0	C11orf84,synonymous_variant,p.%3D,ENST00000294244,;C11orf84,upstream_gene_variant,,ENST00000535820,;C11orf84,upstream_gene_variant,,ENST00000540893,;	T	ENSG00000168005	ENST00000294244	Transcript	synonymous_variant	656	357	119	D	gaC/gaT	.	.	.	1	C11orf84	HGNC	25115	protein_coding	YES	CCDS31594.1	ENSP00000294244	CK084_HUMAN	.	UPI00001BDB3C	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TTGGACCTGAG	.	2	ESCA
PHOX2A	0	.	GRCh37	11	71952305	71952305	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246C>T	p.%3D	p.S82S	ENST00000298231	2/3	17	12	5	27	27	0	PHOX2A,synonymous_variant,p.%3D,ENST00000298231,;INPPL1,downstream_gene_variant,,ENST00000541752,;INPPL1,downstream_gene_variant,,ENST00000538751,;INPPL1,downstream_gene_variant,,ENST00000298229,;INPPL1,downstream_gene_variant,,ENST00000541756,;INPPL1,downstream_gene_variant,,ENST00000320683,;PHOX2A,upstream_gene_variant,,ENST00000546310,;PHOX2A,non_coding_transcript_exon_variant,,ENST00000544057,;INPPL1,downstream_gene_variant,,ENST00000535985,;	A	ENSG00000165462	ENST00000298231	Transcript	synonymous_variant	418	246	82	S	tcC/tcT	.	.	.	-1	PHOX2A	HGNC	691	protein_coding	YES	CCDS8214.1	ENSP00000298231	PHX2A_HUMAN	.	UPI0000074593	.	.	.	2/3	.	hmmpanther:PTHR24329:SF303,hmmpanther:PTHR24329	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCCGGATGG	.	5	ESCA
CREBZF	0	.	GRCh37	11	85373022	85373022	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1833T>C	.	.	ENST00000527447	1/1	70	65	5	60	60	0	CREBZF,3_prime_UTR_variant,,ENST00000398294,;CREBZF,3_prime_UTR_variant,,ENST00000527447,;CREBZF,intron_variant,,ENST00000534224,;CREBZF,intron_variant,,ENST00000531515,;CREBZF,3_prime_UTR_variant,,ENST00000490820,;CREBZF,non_coding_transcript_exon_variant,,ENST00000528889,;CREBZF,intron_variant,,ENST00000260058,;CREBZF,intron_variant,,ENST00000525639,;CREBZF,intron_variant,,ENST00000527529,;CREBZF,intron_variant,,ENST00000528561,;	G	ENSG00000137504	ENST00000527447	Transcript	3_prime_UTR_variant	3125	.	.	.	.	.	.	.	-1	CREBZF	HGNC	24905	protein_coding	YES	CCDS41697.1	ENSP00000433459	ZHANG_HUMAN	.	UPI0000405F55	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATATATGTAT	.	2	ESCA
EIF2B1	0	.	GRCh37	12	124114969	124114969	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227T>C	p.Ile76Thr	p.I76T	ENST00000424014	3/9	55	52	3	52	52	0	EIF2B1,missense_variant,p.Ile76Thr,ENST00000537073,;EIF2B1,missense_variant,p.Ile63Thr,ENST00000539951,;EIF2B1,missense_variant,p.Ile76Thr,ENST00000424014,;EIF2B1,missense_variant,p.Ile92Thr,ENST00000534960,;GTF2H3,upstream_gene_variant,,ENST00000538845,;GTF2H3,upstream_gene_variant,,ENST00000543341,;GTF2H3,upstream_gene_variant,,ENST00000228955,;GTF2H3,upstream_gene_variant,,ENST00000536375,;GTF2H3,upstream_gene_variant,,ENST00000539994,;EIF2B1,non_coding_transcript_exon_variant,,ENST00000543940,;EIF2B1,non_coding_transcript_exon_variant,,ENST00000452159,;GTF2H3,upstream_gene_variant,,ENST00000542279,;GTF2H3,upstream_gene_variant,,ENST00000537368,;GTF2H3,upstream_gene_variant,,ENST00000537695,;GTF2H3,upstream_gene_variant,,ENST00000543005,;	G	ENSG00000111361	ENST00000424014	Transcript	missense_variant	436	227	76	I/T	aTc/aCc	.	.	.	-1	EIF2B1	HGNC	3257	protein_coding	YES	CCDS31924.1	ENSP00000416250	EI2BA_HUMAN	.	UPI0000129AAE	.	deleterious(0)	probably_damaging(0.945)	3/9	.	hmmpanther:PTHR10233,hmmpanther:PTHR10233:SF18,Pfam_domain:PF01008,Superfamily_domains:SSF100950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACTGATGAAG	.	2	ESCA
KLHL42	0	.	GRCh37	12	27951413	27951413	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*314A>T	.	.	ENST00000381271	3/3	15	12	3	12	12	0	KLHL42,3_prime_UTR_variant,,ENST00000381271,;RP11-860B13.3,downstream_gene_variant,,ENST00000543527,;KLHL42,downstream_gene_variant,,ENST00000539176,;	T	ENSG00000087448	ENST00000381271	Transcript	3_prime_UTR_variant	2143	.	.	.	.	.	.	.	1	KLHL42	HGNC	29252	protein_coding	YES	CCDS31763.1	ENSP00000370671	KLH42_HUMAN	B2RNT7_HUMAN	UPI0000185FB1	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAAAGTCAA	.	2	ESCA
C12orf4	0	.	GRCh37	12	4598858	4598858	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*115C>G	.	.	ENST00000261250	14/14	33	22	10	23	23	0	C12orf4,3_prime_UTR_variant,,ENST00000545746,;C12orf4,3_prime_UTR_variant,,ENST00000261250,;C12orf4,downstream_gene_variant,,ENST00000544258,;	C	ENSG00000047621	ENST00000261250	Transcript	3_prime_UTR_variant	1862	.	.	.	.	.	.	.	-1	C12orf4	HGNC	1184	protein_coding	YES	CCDS8528.1	ENSP00000261250	CL004_HUMAN	F5H744_HUMAN,F5GXX6_HUMAN	UPI0000038C60	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTGGATTGA	.	5	ESCA
DUSP6	0	.	GRCh37	12	89746259	89746259	+	5'UTR	SNP	G	G	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-443C>G	.	.	ENST00000279488	1/3	89	53	35	114	114	0	DUSP6,5_prime_UTR_variant,,ENST00000279488,;DUSP6,5_prime_UTR_variant,,ENST00000548755,;DUSP6,upstream_gene_variant,,ENST00000547291,;DUSP6,upstream_gene_variant,,ENST00000308385,;DUSP6,upstream_gene_variant,,ENST00000547140,;	C	ENSG00000139318	ENST00000279488	Transcript	5_prime_UTR_variant	790	.	.	.	.	.	.	.	-1	DUSP6	HGNC	3072	protein_coding	YES	CCDS9033.1	ENSP00000279488	DUS6_HUMAN	F8VZA4_HUMAN	UPI000013ED2F	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGCGAGGCA	.	5	ESCA
PCDH8	0	.	GRCh37	13	53418445	53418445	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*250A>G	.	.	ENST00000377942	3/3	85	54	30	83	83	0	PCDH8,3_prime_UTR_variant,,ENST00000338862,;PCDH8,3_prime_UTR_variant,,ENST00000377942,;	C	ENSG00000136099	ENST00000377942	Transcript	3_prime_UTR_variant	3667	.	.	.	.	.	.	.	-1	PCDH8	HGNC	8660	protein_coding	YES	CCDS9438.1	ENSP00000367177	PCDH8_HUMAN	.	UPI0000072D47	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAATGGCAA	.	5	ESCA
OR4L1	0	.	GRCh37	14	20528746	20528747	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547dupC	p.Leu183ProfsTer9	p.L183Pfs*9	ENST00000315683	1/1	66	47	19	41	41	0	OR4L1,frameshift_variant,p.Leu183ProfsTer9,ENST00000315683,;	C	ENSG00000176246	ENST00000315683	Transcript	frameshift_variant	543-544	543-544	181-182	-/X	-/C	.	.	.	1	OR4L1	HGNC	15356	protein_coding	YES	CCDS32029.1	ENSP00000319217	OR4L1_HUMAN	.	UPI0000041CE3	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF221,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATCTTCCCCT	.	3	ESCA
MIA2	0	.	GRCh37	14	39716400	39716400	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.622C>G	p.Arg208Gly	p.R208G	ENST00000280082	4/6	83	57	26	77	77	0	RP11-407N17.3,missense_variant,p.Arg208Gly,ENST00000553728,;MIA2,missense_variant,p.Arg207Gly,ENST00000556784,;MIA2,missense_variant,p.Arg208Gly,ENST00000280082,;	G	ENSG00000150526	ENST00000280082	Transcript	missense_variant	821	622	208	R/G	Cgt/Ggt	COSM230285	.	.	1	MIA2	HGNC	18432	protein_coding	YES	CCDS9672.1	ENSP00000280082	MIA2_HUMAN	G3V4M1_HUMAN,B2RA73_HUMAN	UPI0000351D6B	.	tolerated(0.34)	benign(0.001)	4/6	.	hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF42	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R208C|c.622C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATCGTATT	.	5	ESCA
SIX4	0	.	GRCh37	14	61176524	61176524	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3601C>T	.	.	ENST00000216513	3/3	71	43	28	68	68	0	SIX4,3_prime_UTR_variant,,ENST00000216513,;SIX4,downstream_gene_variant,,ENST00000554079,;	A	ENSG00000100625	ENST00000216513	Transcript	3_prime_UTR_variant	6007	.	.	.	.	.	.	.	-1	SIX4	HGNC	10890	protein_coding	YES	CCDS9749.2	ENSP00000216513	SIX4_HUMAN	.	UPI000066D924	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACAGTAAAA	.	5	ESCA
FLRT2	0	.	GRCh37	14	86092845	86092845	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3004A>G	.	.	ENST00000330753	2/2	59	56	3	71	71	0	FLRT2,3_prime_UTR_variant,,ENST00000330753,;FLRT2,downstream_gene_variant,,ENST00000554746,;FLRT2,downstream_gene_variant,,ENST00000553650,;	G	ENSG00000185070	ENST00000330753	Transcript	3_prime_UTR_variant	5754	.	.	.	.	.	.	.	1	FLRT2	HGNC	3761	protein_coding	YES	CCDS9877.1	ENSP00000332879	FLRT2_HUMAN	B4DM15_HUMAN	UPI0000049E10	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTGAAAAGG	.	2	ESCA
FOXN3	0	.	GRCh37	14	89623547	89623547	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5211C>G	.	.	ENST00000345097	7/7	28	18	10	26	26	0	FOXN3,3_prime_UTR_variant,,ENST00000345097,;FOXN3,3_prime_UTR_variant,,ENST00000261302,;FOXN3,intron_variant,,ENST00000557572,;FOXN3,downstream_gene_variant,,ENST00000557258,;	C	ENSG00000053254	ENST00000345097	Transcript	3_prime_UTR_variant	6801	.	.	.	.	.	.	.	-1	FOXN3	HGNC	1928	protein_coding	YES	CCDS41977.1	ENSP00000343288	FOXN3_HUMAN	G3V5C7_HUMAN,G3V4N5_HUMAN,G3V3A7_HUMAN	UPI000003B451	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCAGAAGTA	.	2	ESCA
BCL11B	0	.	GRCh37	14	99638792	99638792	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1696G>T	.	.	ENST00000357195	4/4	77	51	25	60	60	0	BCL11B,3_prime_UTR_variant,,ENST00000345514,;BCL11B,3_prime_UTR_variant,,ENST00000357195,;BCL11B,downstream_gene_variant,,ENST00000443726,;	A	ENSG00000127152	ENST00000357195	Transcript	3_prime_UTR_variant	4391	.	.	.	.	.	.	.	-1	BCL11B	HGNC	13222	protein_coding	YES	CCDS9950.1	ENSP00000349723	BC11B_HUMAN	L8B7P7_HUMAN	UPI000006E083	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTACTTTTC	.	5	ESCA
NIPA1	0	.	GRCh37	15	23049305	23049306	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.513dupG	p.Leu172AlafsTer48	p.L172Afs*48	ENST00000337435	5/5	48	32	16	44	44	0	NIPA1,frameshift_variant,p.Leu2AlafsTer48,ENST00000538684,;NIPA1,frameshift_variant,p.Leu97AlafsTer48,ENST00000561183,;NIPA1,frameshift_variant,p.Leu172AlafsTer48,ENST00000337435,;NIPA1,frameshift_variant,p.Leu97AlafsTer48,ENST00000437912,;NIPA1,3_prime_UTR_variant,,ENST00000559448,;NIPA1,3_prime_UTR_variant,,ENST00000560069,;NIPA1,3_prime_UTR_variant,,ENST00000557930,;	C	ENSG00000170113	ENST00000337435	Transcript	frameshift_variant	538-539	513-514	171-172	-/X	-/G	.	.	.	-1	NIPA1	HGNC	17043	protein_coding	YES	CCDS10011.1	ENSP00000337452	NIPA1_HUMAN	Q3SYP4_HUMAN	UPI00001D9756	.	.	.	5/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12570,hmmpanther:PTHR12570:SF17,Pfam_domain:PF05653	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGCAGCATGA	.	3	ESCA
AQR	0	.	GRCh37	15	35222464	35222464	+	Silent	SNP	G	G	A	rs750164753	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009C>T	p.%3D	p.L337L	ENST00000156471	12/35	53	33	20	43	43	0	AQR,synonymous_variant,p.%3D,ENST00000156471,;AQR,synonymous_variant,p.%3D,ENST00000543879,;	A	ENSG00000021776	ENST00000156471	Transcript	synonymous_variant	1235	1009	337	L	Cta/Tta	rs750164753	.	.	-1	AQR	HGNC	29513	protein_coding	YES	CCDS42013.1	ENSP00000156471	AQR_HUMAN	.	UPI00001C1F85	.	.	.	12/35	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF5,PIRSF_domain:PIRSF038901	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTAGAGAAG	.	5	ESCA
STARD9	0	.	GRCh37	15	42984297	42984297	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10521T>G	p.Asn3507Lys	p.N3507K	ENST00000290607	23/33	55	31	23	62	62	0	STARD9,missense_variant,p.Asn3507Lys,ENST00000290607,;STARD9,missense_variant,p.Asn835Lys,ENST00000562619,;	G	ENSG00000159433	ENST00000290607	Transcript	missense_variant	10578	10521	3507	N/K	aaT/aaG	.	.	.	1	STARD9	HGNC	19162	protein_coding	YES	CCDS53935.1	ENSP00000290607	STAR9_HUMAN	B4DMS6_HUMAN	UPI0001BE8155	.	.	benign(0.133)	23/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAATGTGGC	.	5	ESCA
SLC24A5	0	.	GRCh37	15	48426713	48426713	+	Missense_Mutation	SNP	C	C	T	rs538198029	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.467C>T	p.Ala156Val	p.A156V	ENST00000341459	4/9	43	20	23	44	44	0	SLC24A5,missense_variant,p.Ala156Val,ENST00000341459,;SLC24A5,missense_variant,p.Ala96Val,ENST00000449382,;MYEF2,downstream_gene_variant,,ENST00000324324,;SLC24A5,non_coding_transcript_exon_variant,,ENST00000463289,;MYEF2,downstream_gene_variant,,ENST00000558289,;	T	ENSG00000188467	ENST00000341459	Transcript	missense_variant	540	467	156	A/V	gCc/gTc	rs538198029	.	.	1	SLC24A5	HGNC	20611	protein_coding	YES	CCDS10128.1	ENSP00000341550	NCKX5_HUMAN	.	UPI0000242BC9	.	tolerated(0.99)	benign(0.044)	4/9	.	Pfam_domain:PF01699,TIGRFAM_domain:TIGR00367,hmmpanther:PTHR10846:SF27,hmmpanther:PTHR10846,Transmembrane_helices:TMhelix	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGCCTGTG	by1000G	5	ESCA
TMEM202	0	.	GRCh37	15	72700132	72700132	+	Silent	SNP	G	G	A	rs140026568	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.720G>A	p.%3D	p.P240P	ENST00000341689	5/5	121	67	53	108	108	0	TMEM202,synonymous_variant,p.%3D,ENST00000341689,;TMEM202,3_prime_UTR_variant,,ENST00000567679,;RP11-1007O24.3,non_coding_transcript_exon_variant,,ENST00000562573,;TMEM202,3_prime_UTR_variant,,ENST00000568167,;	A	ENSG00000187806	ENST00000341689	Transcript	synonymous_variant	774	720	240	P	ccG/ccA	rs140026568	.	.	1	TMEM202	HGNC	33733	protein_coding	YES	CCDS32287.1	ENSP00000340212	TM202_HUMAN	.	UPI000049DDE8	.	.	.	5/5	.	hmmpanther:PTHR10671:SF31,hmmpanther:PTHR10671	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0011	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCCGGTGAC	byCluster|by1000G	5	ESCA
PSTPIP1	0	.	GRCh37	15	77310844	77310844	+	Missense_Mutation	SNP	C	C	T	rs375063664	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.184C>T	p.Arg62Trp	p.R62W	ENST00000558012	3/15	39	27	11	54	54	0	PSTPIP1,missense_variant,p.Arg53Trp,ENST00000559859,;PSTPIP1,missense_variant,p.Arg127Trp,ENST00000558407,;PSTPIP1,missense_variant,p.Arg61Trp,ENST00000267939,;PSTPIP1,missense_variant,p.Arg62Trp,ENST00000559295,;PSTPIP1,missense_variant,p.Arg16Trp,ENST00000559856,;PSTPIP1,missense_variant,p.Arg62Trp,ENST00000558012,;PSTPIP1,missense_variant,p.Arg62Trp,ENST00000559161,;PSTPIP1,missense_variant,p.Arg62Trp,ENST00000379595,;PSTPIP1,non_coding_transcript_exon_variant,,ENST00000560621,;PSTPIP1,missense_variant,p.Arg127Trp,ENST00000559785,;PSTPIP1,missense_variant,p.Arg28Trp,ENST00000560796,;PSTPIP1,missense_variant,p.Arg62Trp,ENST00000559750,;PSTPIP1,3_prime_UTR_variant,,ENST00000560223,;PSTPIP1,non_coding_transcript_exon_variant,,ENST00000559795,;PSTPIP1,non_coding_transcript_exon_variant,,ENST00000560377,;	T	ENSG00000140368	ENST00000558012	Transcript	missense_variant	673	184	62	R/W	Cgg/Tgg	rs375063664,COSM965153,COSM965154	.	.	1	PSTPIP1	HGNC	9580	protein_coding	YES	CCDS45312.1	ENSP00000452746	PPIP1_HUMAN	.	UPI00000703D7	.	deleterious(0)	probably_damaging(0.997)	3/15	.	PROSITE_profiles:PS50133,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF3,Pfam_domain:PF00611,SMART_domains:SM00055,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCACGGAAG	byFrequency|byCluster	5	ESCA
SHCBP1	0	.	GRCh37	16	46617507	46617507	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1614T>C	p.%3D	p.N538N	ENST00000303383	12/13	101	93	8	106	106	0	SHCBP1,synonymous_variant,p.%3D,ENST00000303383,;SHCBP1,non_coding_transcript_exon_variant,,ENST00000567698,;	G	ENSG00000171241	ENST00000303383	Transcript	synonymous_variant	1881	1614	538	N	aaT/aaC	.	.	.	-1	SHCBP1	HGNC	29547	protein_coding	YES	CCDS10720.1	ENSP00000306473	SHCBP_HUMAN	.	UPI000013E898	.	.	.	12/13	.	hmmpanther:PTHR14695,hmmpanther:PTHR14695:SF6,Pfam_domain:PF13229,Gene3D:2.160.20.10,SMART_domains:SM00710,Superfamily_domains:SSF51126	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCATTATTATG	.	2	ESCA
NLRC5	0	.	GRCh37	16	57101728	57101729	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4488dupG	p.Lys1497GlufsTer35	p.K1497Efs*35	ENST00000262510	36/49	60	43	17	59	59	0	NLRC5,frameshift_variant,p.Lys1468GlufsTer35,ENST00000308149,;NLRC5,frameshift_variant,p.Lys1468GlufsTer35,ENST00000539144,;NLRC5,frameshift_variant,p.Lys1497GlufsTer17,ENST00000436936,;NLRC5,frameshift_variant,p.Lys1497GlufsTer35,ENST00000262510,;NLRC5,frameshift_variant,p.Lys648GlufsTer17,ENST00000538453,;NLRC5,3_prime_UTR_variant,,ENST00000537056,;NLRC5,3_prime_UTR_variant,,ENST00000540182,;NLRC5,3_prime_UTR_variant,,ENST00000545081,;NLRC5,upstream_gene_variant,,ENST00000545349,;	G	ENSG00000140853	ENST00000262510	Transcript	frameshift_variant	4712-4713	4487-4488	1496	L/LX	ctg/ctGg	.	.	.	1	NLRC5	HGNC	29933	protein_coding	YES	CCDS10773.1	ENSP00000262510	NLRC5_HUMAN	F5H274_HUMAN,F5GYP0_HUMAN	UPI00001AEE94	.	.	.	36/49	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24106:SF69,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,SMART_domains:SM00367,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGAGCTGAAGA	.	3	ESCA
NLRC5	0	.	GRCh37	16	57113144	57113144	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5177A>G	p.Asn1726Ser	p.N1726S	ENST00000262510	45/49	95	62	32	106	106	0	NLRC5,missense_variant,p.Asn1697Ser,ENST00000308149,;NLRC5,missense_variant,p.Asn1697Ser,ENST00000539144,;NLRC5,missense_variant,p.Asn1726Ser,ENST00000262510,;NLRC5,3_prime_UTR_variant,,ENST00000436936,;NLRC5,3_prime_UTR_variant,,ENST00000537056,;NLRC5,3_prime_UTR_variant,,ENST00000540182,;NLRC5,3_prime_UTR_variant,,ENST00000545081,;NLRC5,3_prime_UTR_variant,,ENST00000538453,;NLRC5,non_coding_transcript_exon_variant,,ENST00000534927,;NLRC5,downstream_gene_variant,,ENST00000545349,;NLRC5,downstream_gene_variant,,ENST00000544189,;NLRC5,upstream_gene_variant,,ENST00000543103,;NLRC5,upstream_gene_variant,,ENST00000543049,;	G	ENSG00000140853	ENST00000262510	Transcript	missense_variant	5402	5177	1726	N/S	aAc/aGc	.	.	.	1	NLRC5	HGNC	29933	protein_coding	YES	CCDS10773.1	ENSP00000262510	NLRC5_HUMAN	F5H274_HUMAN,F5GYP0_HUMAN	UPI00001AEE94	.	deleterious(0.01)	probably_damaging(0.999)	45/49	.	hmmpanther:PTHR24106:SF69,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAAACAACC	.	5	ESCA
C16orf86	0	.	GRCh37	16	67702161	67702161	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612G>A	p.%3D	p.L204L	ENST00000403458	4/4	82	40	41	79	79	0	C16orf86,synonymous_variant,p.%3D,ENST00000403458,;ENKD1,upstream_gene_variant,,ENST00000243878,;ENKD1,upstream_gene_variant,,ENST00000602644,;C16orf86,downstream_gene_variant,,ENST00000602365,;ENKD1,upstream_gene_variant,,ENST00000602409,;C16orf86,downstream_gene_variant,,ENST00000602974,;C16orf86,3_prime_UTR_variant,,ENST00000445068,;C16orf86,non_coding_transcript_exon_variant,,ENST00000459925,;ENKD1,upstream_gene_variant,,ENST00000602415,;ENKD1,upstream_gene_variant,,ENST00000602942,;C16orf86,downstream_gene_variant,,ENST00000602987,;ENKD1,upstream_gene_variant,,ENST00000602642,;ENKD1,upstream_gene_variant,,ENST00000602531,;	A	ENSG00000159761	ENST00000403458	Transcript	synonymous_variant	767	612	204	L	ctG/ctA	.	.	.	1	C16orf86	HGNC	33755	protein_coding	YES	CCDS32468.2	ENSP00000384117	CP086_HUMAN	.	UPI00001982F7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTGAACCA	.	5	ESCA
ALDOC	0	.	GRCh37	17	26902474	26902474	+	Missense_Mutation	SNP	G	G	A	rs752045255	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77C>T	p.Pro26Leu	p.P26L	ENST00000226253	2/9	47	35	12	60	60	0	ALDOC,missense_variant,p.Pro26Leu,ENST00000578590,;ALDOC,missense_variant,p.Pro26Leu,ENST00000395319,;ALDOC,missense_variant,p.Pro26Leu,ENST00000460201,;ALDOC,missense_variant,p.Pro26Leu,ENST00000395321,;ALDOC,missense_variant,p.Pro26Leu,ENST00000226253,;ALDOC,missense_variant,p.Pro26Leu,ENST00000584086,;ALDOC,missense_variant,p.Pro26Leu,ENST00000435638,;ALDOC,5_prime_UTR_variant,,ENST00000581807,;PIGS,upstream_gene_variant,,ENST00000395346,;RP11-192H23.4,downstream_gene_variant,,ENST00000531839,;PIGS,upstream_gene_variant,,ENST00000308360,;SPAG5,downstream_gene_variant,,ENST00000321765,;PIGS,upstream_gene_variant,,ENST00000543734,;SPAG5,downstream_gene_variant,,ENST00000582076,;RP11-192H23.5,downstream_gene_variant,,ENST00000585189,;PIGS,upstream_gene_variant,,ENST00000584413,;ALDOC,non_coding_transcript_exon_variant,,ENST00000582381,;RP11-192H23.4,intron_variant,,ENST00000481916,;SPAG5,downstream_gene_variant,,ENST00000581133,;PIGS,upstream_gene_variant,,ENST00000584080,;SPAG5,downstream_gene_variant,,ENST00000580676,;PIGS,upstream_gene_variant,,ENST00000582721,;SPAG5,downstream_gene_variant,,ENST00000580682,;SPAG5,downstream_gene_variant,,ENST00000582175,;SPAG5,downstream_gene_variant,,ENST00000578230,;PIGS,upstream_gene_variant,,ENST00000268758,;SPAG5,downstream_gene_variant,,ENST00000577259,;SPAG5,downstream_gene_variant,,ENST00000580406,;PIGS,upstream_gene_variant,,ENST00000577594,;SPAG5,downstream_gene_variant,,ENST00000580377,;SPAG5,downstream_gene_variant,,ENST00000378976,;PIGS,upstream_gene_variant,,ENST00000583631,;SPAG5,downstream_gene_variant,,ENST00000580083,;	A	ENSG00000109107	ENST00000226253	Transcript	missense_variant	553	77	26	P/L	cCg/cTg	rs752045255,COSM1520897	.	.	-1	ALDOC	HGNC	418	protein_coding	YES	CCDS11236.1	ENSP00000226253	ALDOC_HUMAN	K7EKH5_HUMAN,J3QKP5_HUMAN,J3QKK1_HUMAN,J3KSV6_HUMAN,C9J8F3_HUMAN,B7Z1N6_HUMAN	UPI0000000C53	.	tolerated(0.1)	benign(0.068)	2/9	.	hmmpanther:PTHR11627,hmmpanther:PTHR11627:SF3,Pfam_domain:PF00274,Gene3D:3.20.20.70,Superfamily_domains:SSF51569	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCCGGGGCT	byFrequency	5	ESCA
MKS1	0	.	GRCh37	17	56282841	56282841	+	3'UTR	DEL	C	C	-	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*599delG	.	.	ENST00000393119	18/18	39	35	4	20	20	0	MKS1,3_prime_UTR_variant,,ENST00000393119,;MKS1,3_prime_UTR_variant,,ENST00000313863,;MKS1,downstream_gene_variant,,ENST00000537529,;MKS1,downstream_gene_variant,,ENST00000337050,;MKS1,downstream_gene_variant,,ENST00000577315,;EPX,downstream_gene_variant,,ENST00000225371,;MKS1,downstream_gene_variant,,ENST00000546108,;MKS1,downstream_gene_variant,,ENST00000585134,;MKS1,downstream_gene_variant,,ENST00000577824,;MKS1,downstream_gene_variant,,ENST00000579358,;MKS1,downstream_gene_variant,,ENST00000393120,;MKS1,downstream_gene_variant,,ENST00000583577,;	-	ENSG00000011143	ENST00000393119	Transcript	3_prime_UTR_variant	2354	.	.	.	.	.	.	.	-1	MKS1	HGNC	7121	protein_coding	YES	CCDS11603.2	ENSP00000376827	MKS1_HUMAN	F5H5Y8_HUMAN	UPI00002010BB	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAAAACAAACA	.	3	ESCA
C17orf47	0	.	GRCh37	17	56620413	56620413	+	Missense_Mutation	SNP	G	G	T	rs747493386	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135C>A	p.Pro379Thr	p.P379T	ENST00000321691	1/2	97	63	34	82	82	0	C17orf47,missense_variant,p.Pro379Thr,ENST00000321691,;SEPT4,upstream_gene_variant,,ENST00000457347,;SEPT4,upstream_gene_variant,,ENST00000412945,;RP11-112H10.4,intron_variant,,ENST00000580589,;RP11-112H10.4,intron_variant,,ENST00000578022,;RP11-112H10.4,intron_variant,,ENST00000580769,;SEPT4,upstream_gene_variant,,ENST00000581921,;	T	ENSG00000181013	ENST00000321691	Transcript	missense_variant	1317	1135	379	P/T	Ccc/Acc	rs747493386,COSM309624	.	.	-1	C17orf47	HGNC	26844	protein_coding	YES	CCDS32691.1	ENSP00000354874	CQ047_HUMAN	.	UPI0000140BFA	.	tolerated(0.08)	probably_damaging(0.958)	1/2	.	Pfam_domain:PF15548	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGGTTTTT	.	5	ESCA
TEX14	0	.	GRCh37	17	56676583	56676583	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2141C>G	p.Ser714Ter	p.S714*	ENST00000240361	14/33	53	46	7	36	36	0	TEX14,stop_gained,p.Ser708Ter,ENST00000349033,;TEX14,stop_gained,p.Ser708Ter,ENST00000389934,;TEX14,stop_gained,p.Ser714Ter,ENST00000240361,;TEX14,3_prime_UTR_variant,,ENST00000582740,;	C	ENSG00000121101	ENST00000240361	Transcript	stop_gained	2227	2141	714	S/*	tCa/tGa	.	.	.	-1	TEX14	HGNC	11737	protein_coding	YES	CCDS56042.1	ENSP00000240361	TEX14_HUMAN	.	UPI0000DAC9CA	.	.	.	14/33	.	hmmpanther:PTHR23060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTGACTCA	.	4	ESCA
TP53	0	.	GRCh37	17	7578407	7578407	+	Missense_Mutation	SNP	G	G	C	rs138729528	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	5/11	38	25	13	43	43	0	TP53,missense_variant,p.Arg175Gly,ENST00000413465,;TP53,missense_variant,p.Arg175Gly,ENST00000420246,;TP53,missense_variant,p.Arg175Gly,ENST00000269305,;TP53,missense_variant,p.Arg43Gly,ENST00000509690,;TP53,missense_variant,p.Arg175Gly,ENST00000359597,;TP53,missense_variant,p.Arg82Gly,ENST00000514944,;TP53,missense_variant,p.Arg175Gly,ENST00000445888,;TP53,missense_variant,p.Arg175Gly,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	713	523	175	R/G	Cgc/Ggc	CM118880,rs138729528,CM011013,TP53_g.12511del,TP53_g.12511C>A,TP53_g.12511C>T,TP53_g.12511C>G,COSM10870,COSM43680,COSM43931,COSM45936,COSM707880,COSM179827,COSM707881,COSM179826,COSM707883,COSM179828,COSM4070040,COSM3691867,COSM1640852,COSM3691866,COSM179829,COSM707882	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.985)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	A:0.0002	A:0,A:0	A:0,A:0	.	A:0,A:0	A:0,A:0	A:0.001,A:0.001	.	.	.	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R82G|c.244C>G|5,SITE|p.R43G|c.127C>G|8,SITE|p.R175G|c.523C>G|5,SITE|p.R175G|c.523C>G|5,SITE|p.R175G|c.523C>G|16,CODON|p.0?|c.1_1182del1182|6,CODON|p.R175L|c.524G>T|20,CODON|p.R175H|c.524G>A|181,CODON|p.R175P|c.524G>C|6,CODON|p.R43H|c.128G>A|183,CODON|p.R82H|c.245G>A|183,CODON|p.R175H|c.524G>A|124,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R175H|c.524G>A|180,CODON|p.R175H|c.524G>A|926,CODON|p.R175L|c.524G>T|3,CODON|p.R175H|c.524G>A|88,CODON|p.R43L|c.128G>T|3,CODON|p.R82L|c.245G>T|3,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.P177_C182delPHHERC|c.526_543del18|3,BUFFER|p.H179Y|c.534_535CC>TT|8,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R174K|c.521G>A|5,BUFFER|p.R174W|c.520A>T|11,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V172D|c.515T>A|11,BUFFER|p.V172A|c.515T>C|4,BUFFER|p.V172G|c.515T>G|4,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.E171G|c.512A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCGCCTCA	by1000G	5	ESCA
TP53	0	.	GRCh37	17	7579359	7579359	+	Missense_Mutation	SNP	G	G	A	rs587780066,rs587781371	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	4/11	158	73	84	142	142	0	TP53,missense_variant,p.Arg110Cys,ENST00000508793,;TP53,missense_variant,p.Arg110Cys,ENST00000413465,;TP53,missense_variant,p.Arg110Cys,ENST00000604348,;TP53,missense_variant,p.Arg110Cys,ENST00000420246,;TP53,missense_variant,p.Arg110Cys,ENST00000269305,;TP53,missense_variant,p.Arg110Cys,ENST00000359597,;TP53,missense_variant,p.Arg110Cys,ENST00000445888,;TP53,missense_variant,p.Arg110Cys,ENST00000503591,;TP53,missense_variant,p.Arg110Cys,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	518	328	110	R/C	Cgt/Tgt	rs587780066,rs587781371,TP53_g.11559del,TP53_g.11559C>A,TP53_g.11559C>T,TP53_g.11559C>G,COSM44669,COSM43682,COSM45604,COSM166234,COSM247949,COSM247948,COSM166233	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.14)	probably_damaging(0.985)	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	pathogenic,uncertain_significance	0,0,0,0,0,0,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R110C|c.328C>T|6,CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,CODON|p.R110fs*13|c.329delG|3,CODON|p.R110fs*13|c.328delC|4,CODON|p.R110L|c.329G>T|27,CODON|p.R110P|c.329G>C|11,CODON|p.R110L|c.329G>T|5,CODON|p.R110L|c.329G>T|8,CODON|p.R110L|c.329G>T|8,BUFFER|p.F113L|c.339C>G|4,BUFFER|p.F113C|c.338T>G|4,BUFFER|p.F113C|c.338T>G|8,BUFFER|p.F113S|c.338T>C|3,BUFFER|p.F113C|c.338T>G|4,BUFFER|p.F113V|c.337T>G|3,BUFFER|p.F113V|c.337T>G|3,BUFFER|p.F113V|c.337T>G|6,BUFFER|p.L111R|c.332T>G|5,BUFFER|p.L111Q|c.332T>A|7,BUFFER|p.L111P|c.332T>C|9,BUFFER|p.L111Q|c.332T>A|3,BUFFER|p.L111R|c.332T>G|10,BUFFER|p.L111Q|c.332T>A|3,BUFFER|p.L111P|c.332T>C|3,BUFFER|p.L111R|c.332T>G|5,BUFFER|p.L111P|c.332T>C|3,BUFFER|p.F109C|c.326T>G|3,BUFFER|p.F109C|c.326T>G|4,BUFFER|p.F109C|c.326T>G|3,BUFFER|p.G108delG|c.322_324delGGT|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.Y107*|c.321C>A|6,BUFFER|p.Y107Y|c.321C>T|3,BUFFER|p.Y107*|c.321C>G|3,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|8,BUFFER|p.S106R|c.318C>G|3,BUFFER|p.S106R|c.318C>G|3,BUFFER|p.S106R|c.318C>G|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGACGGAAAC	byCluster	5	ESCA
SALL3	0	.	GRCh37	18	76753906	76753906	+	Missense_Mutation	SNP	G	G	A	rs557725030	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1915G>A	p.Val639Ile	p.V639I	ENST00000537592	2/3	21	14	7	12	12	0	SALL3,missense_variant,p.Val506Ile,ENST00000536229,;SALL3,missense_variant,p.Val639Ile,ENST00000537592,;SALL3,missense_variant,p.Val639Ile,ENST00000575389,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,;	A	ENSG00000256463	ENST00000537592	Transcript	missense_variant	1915	1915	639	V/I	Gtc/Atc	rs557725030	.	.	1	SALL3	HGNC	10527	protein_coding	YES	CCDS12013.1	ENSP00000441823	SALL3_HUMAN	.	UPI000013E5A7	.	tolerated(0.57)	benign(0.008)	2/3	.	hmmpanther:PTHR23233:SF46,hmmpanther:PTHR23233	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCCGTCTCC	byFrequency|by1000G	5	ESCA
KEAP1	0	.	GRCh37	19	10602340	10602340	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1238G>A	p.Arg413His	p.R413H	ENST00000171111	3/6	35	22	13	24	24	0	KEAP1,missense_variant,p.Arg413His,ENST00000393623,;KEAP1,missense_variant,p.Arg20His,ENST00000592478,;KEAP1,missense_variant,p.Arg413His,ENST00000171111,;KEAP1,downstream_gene_variant,,ENST00000592055,;KEAP1,downstream_gene_variant,,ENST00000591419,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,missense_variant,p.Arg73His,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,;	T	ENSG00000079999	ENST00000171111	Transcript	missense_variant	1786	1238	413	R/H	cGt/cAt	.	.	.	-1	KEAP1	HGNC	23177	protein_coding	YES	CCDS12239.1	ENSP00000171111	KEAP1_HUMAN	K7ESE0_HUMAN,K7EJD8_HUMAN,K7EJ49_HUMAN	UPI000007139C	.	deleterious(0)	probably_damaging(0.962)	3/6	.	hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF01344,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTACGGGGC	.	5	ESCA
S1PR5	0	.	GRCh37	19	10624599	10624599	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089G>A	p.%3D	p.S363S	ENST00000439028	2/2	17	5	11	11	11	0	S1PR5,synonymous_variant,p.%3D,ENST00000333430,;S1PR5,synonymous_variant,p.%3D,ENST00000439028,;S1PR5,downstream_gene_variant,,ENST00000590601,;	T	ENSG00000180739	ENST00000439028	Transcript	synonymous_variant	1215	1089	363	S	tcG/tcA	.	.	.	-1	S1PR5	HGNC	14299	protein_coding	YES	CCDS12240.1	ENSP00000416915	S1PR5_HUMAN	.	UPI000003BC79	.	.	.	2/2	.	hmmpanther:PTHR22750:SF20,hmmpanther:PTHR22750,Prints_domain:PR01561	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTCCGAGCC	.	5	ESCA
ATP8B3	0	.	GRCh37	19	1785540	1785540	+	Silent	SNP	G	G	A	rs772876130	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3321C>T	p.%3D	p.P1107P	ENST00000310127	26/29	63	39	24	77	77	0	ATP8B3,synonymous_variant,p.%3D,ENST00000310127,;ATP8B3,synonymous_variant,p.%3D,ENST00000539485,;ATP8B3,synonymous_variant,p.%3D,ENST00000525591,;ONECUT3,downstream_gene_variant,,ENST00000382349,;ATP8B3,3_prime_UTR_variant,,ENST00000531925,;ATP8B3,downstream_gene_variant,,ENST00000526847,;	A	ENSG00000130270	ENST00000310127	Transcript	synonymous_variant	3560	3321	1107	P	ccC/ccT	rs772876130	.	.	-1	ATP8B3	HGNC	13535	protein_coding	YES	CCDS45901.1	ENSP00000311336	AT8B3_HUMAN	.	UPI0000074660	.	.	.	26/29	.	hmmpanther:PTHR24092:SF44,hmmpanther:PTHR24092,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGGGTCC	byCluster	5	ESCA
EML2	0	.	GRCh37	19	46124822	46124822	+	Silent	SNP	G	G	A	rs148351202	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1518C>T	p.%3D	p.D506D	ENST00000587152	13/22	90	57	33	103	103	0	EML2,synonymous_variant,p.%3D,ENST00000590575,;EML2,synonymous_variant,p.%3D,ENST00000587152,;EML2,synonymous_variant,p.%3D,ENST00000536630,;EML2,synonymous_variant,p.%3D,ENST00000245925,;EML2,synonymous_variant,p.%3D,ENST00000589876,;EML2,synonymous_variant,p.%3D,ENST00000588496,;EML2,intron_variant,,ENST00000588272,;EML2,upstream_gene_variant,,ENST00000587484,;EML2,non_coding_transcript_exon_variant,,ENST00000586902,;EML2,downstream_gene_variant,,ENST00000590580,;EML2,synonymous_variant,p.%3D,ENST00000399594,;EML2,synonymous_variant,p.%3D,ENST00000588308,;EML2,3_prime_UTR_variant,,ENST00000586195,;EML2,non_coding_transcript_exon_variant,,ENST00000588000,;EML2,non_coding_transcript_exon_variant,,ENST00000588610,;EML2,intron_variant,,ENST00000590819,;EML2,upstream_gene_variant,,ENST00000592482,;EML2,downstream_gene_variant,,ENST00000592853,;	A	ENSG00000125746	ENST00000587152	Transcript	synonymous_variant	1703	1518	506	D	gaC/gaT	rs148351202,COSM190936	.	.	-1	EML2	HGNC	18035	protein_coding	YES	CCDS59399.1	ENSP00000468312	EMAL2_HUMAN	K7ESL7_HUMAN,K7ERY9_HUMAN,K7ERR2_HUMAN,K7EQR0_HUMAN,K7EKU5_HUMAN,K7EIM1_HUMAN	UPI0001DD21BF	.	.	.	13/22	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13720:SF22,hmmpanther:PTHR13720,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	A:0.0002	A:0.0002	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCCGTCCCG	byCluster	5	ESCA
TMEM190	0	.	GRCh37	19	55889435	55889435	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398G>A	p.Arg133Gln	p.R133Q	ENST00000291934	5/5	102	57	44	118	118	0	TMEM190,missense_variant,p.Arg133Gln,ENST00000291934,;TMEM238,downstream_gene_variant,,ENST00000444469,;CTD-2105E13.15,non_coding_transcript_exon_variant,,ENST00000595064,;	A	ENSG00000160472	ENST00000291934	Transcript	missense_variant	416	398	133	R/Q	cGa/cAa	COSM714633	.	.	1	TMEM190	HGNC	29632	protein_coding	YES	CCDS33113.1	ENSP00000291934	TM190_HUMAN	.	UPI000006F8C2	.	tolerated_low_confidence(0.14)	possibly_damaging(0.776)	5/5	.	Pfam_domain:PF15431	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACCGAGGGA	.	5	ESCA
ZNF784	0	.	GRCh37	19	56133668	56133668	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.421T>A	p.Leu141Met	p.L141M	ENST00000325351	2/2	10	6	3	16	16	0	ZNF784,missense_variant,p.Leu141Met,ENST00000325351,;ZNF784,3_prime_UTR_variant,,ENST00000591479,;	T	ENSG00000179922	ENST00000325351	Transcript	missense_variant	461	421	141	L/M	Ttg/Atg	.	.	.	-1	ZNF784	HGNC	33111	protein_coding	YES	CCDS12930.1	ENSP00000320096	ZN784_HUMAN	.	UPI000006D6D0	.	tolerated(0.16)	possibly_damaging(0.855)	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF36,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGCCAAGGCCT	.	3	ESCA
C19orf70	0	.	GRCh37	19	5680249	5680249	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29+220G>A	.	.	ENST00000309324	.	67	42	24	88	88	0	C19orf70,5_prime_UTR_variant,,ENST00000587950,;RPL36,intron_variant,,ENST00000579649,;C19orf70,intron_variant,,ENST00000587589,;C19orf70,intron_variant,,ENST00000309324,;HSD11B1L,upstream_gene_variant,,ENST00000342970,;HSD11B1L,upstream_gene_variant,,ENST00000577917,;C19orf70,upstream_gene_variant,,ENST00000590389,;HSD11B1L,upstream_gene_variant,,ENST00000339423,;HSD11B1L,upstream_gene_variant,,ENST00000423665,;HSD11B1L,upstream_gene_variant,,ENST00000578046,;HSD11B1L,upstream_gene_variant,,ENST00000581521,;HSD11B1L,upstream_gene_variant,,ENST00000579559,;HSD11B1L,upstream_gene_variant,,ENST00000581893,;HSD11B1L,upstream_gene_variant,,ENST00000583928,;RPL36,upstream_gene_variant,,ENST00000577222,;HSD11B1L,upstream_gene_variant,,ENST00000422535,;HSD11B1L,upstream_gene_variant,,ENST00000411793,;HSD11B1L,upstream_gene_variant,,ENST00000301382,;HSD11B1L,upstream_gene_variant,,ENST00000577257,;HSD11B1L,upstream_gene_variant,,ENST00000581773,;RPL36,upstream_gene_variant,,ENST00000582380,;HSD11B1L,upstream_gene_variant,,ENST00000577701,;C19orf70,upstream_gene_variant,,ENST00000585605,;C19orf70,intron_variant,,ENST00000590075,;HSD11B1L,upstream_gene_variant,,ENST00000578832,;HSD11B1L,upstream_gene_variant,,ENST00000579562,;HSD11B1L,upstream_gene_variant,,ENST00000584904,;HSD11B1L,upstream_gene_variant,,ENST00000582346,;HSD11B1L,upstream_gene_variant,,ENST00000577920,;HSD11B1L,upstream_gene_variant,,ENST00000578167,;	T	ENSG00000174917	ENST00000309324	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	C19orf70	HGNC	33702	protein_coding	YES	CCDS12143.1	ENSP00000309561	QIL1_HUMAN	K7EIR2_HUMAN	UPI0000034FEA	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAACGCCAA	.	5	ESCA
RAB11B	0	.	GRCh37	19	8455255	8455255	+	5'UTR	SNP	G	G	T	rs372737756	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-46G>T	.	.	ENST00000328024	1/5	88	61	26	98	98	0	RAB11B,5_prime_UTR_variant,,ENST00000328024,;RAB11B,intron_variant,,ENST00000600719,;RAB11B,upstream_gene_variant,,ENST00000594216,;RAB11B,upstream_gene_variant,,ENST00000601897,;MIR4999,upstream_gene_variant,,ENST00000585029,;RAB11B-AS1,non_coding_transcript_exon_variant,,ENST00000593581,;RAB11B-AS1,upstream_gene_variant,,ENST00000597785,;RAB11B,non_coding_transcript_exon_variant,,ENST00000598706,;	T	ENSG00000185236	ENST00000328024	Transcript	5_prime_UTR_variant	173	.	.	.	.	rs372737756	.	.	1	RAB11B	HGNC	9761	protein_coding	YES	CCDS12201.1	ENSP00000333547	RB11B_HUMAN	M0R377_HUMAN	UPI000006CF2D	.	.	.	1/5	.	.	.	.	.	.	.	.	.	C:0.0009	C:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTGTGGTG	byFrequency|byCluster	5	ESCA
MIIP	0	.	GRCh37	1	12082207	12082207	+	Missense_Mutation	SNP	C	C	T	rs200638129	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.170C>T	p.Thr57Met	p.T57M	ENST00000235332	3/10	48	13	34	109	109	0	MIIP,missense_variant,p.Thr57Met,ENST00000235332,;MIIP,missense_variant,p.Thr57Met,ENST00000436478,;Y_RNA,downstream_gene_variant,,ENST00000365591,;MIIP,non_coding_transcript_exon_variant,,ENST00000478749,;MIIP,upstream_gene_variant,,ENST00000498685,;MIIP,upstream_gene_variant,,ENST00000466860,;RP5-1077B9.5,upstream_gene_variant,,ENST00000603287,;	T	ENSG00000116691	ENST00000235332	Transcript	missense_variant	339	170	57	T/M	aCg/aTg	rs200638129	.	.	1	MIIP	HGNC	25715	protein_coding	YES	CCDS143.1	ENSP00000235332	MIIP_HUMAN	.	UPI000013C9CB	.	tolerated(0.23)	benign(0.424)	3/10	.	Low_complexity_(Seg):seg	T:0.0004	T:0.0008	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGACGTCCT	byFrequency|byCluster|by1000G	5	ESCA
VANGL2	0	.	GRCh37	1	160390311	160390311	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.911G>A	p.Gly304Asp	p.G304D	ENST00000368061	5/8	135	52	82	91	91	0	VANGL2,missense_variant,p.Gly304Asp,ENST00000368061,;VANGL2,intron_variant,,ENST00000483408,;	A	ENSG00000162738	ENST00000368061	Transcript	missense_variant	1385	911	304	G/D	gGc/gAc	.	.	.	1	VANGL2	HGNC	15511	protein_coding	YES	CCDS30915.1	ENSP00000357040	VANG2_HUMAN	.	UPI00001C1D79	.	deleterious(0.02)	possibly_damaging(0.824)	5/8	.	hmmpanther:PTHR20886,hmmpanther:PTHR20886:SF10,Pfam_domain:PF06638,PIRSF_domain:PIRSF007991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGGCTTCA	.	5	ESCA
METTL11B	0	.	GRCh37	1	170129813	170129813	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.309A>G	p.%3D	p.K103K	ENST00000439373	2/4	101	73	28	72	72	0	METTL11B,synonymous_variant,p.%3D,ENST00000439373,;METTL11B,non_coding_transcript_exon_variant,,ENST00000367764,;	G	ENSG00000203740	ENST00000439373	Transcript	synonymous_variant	416	309	103	K	aaA/aaG	.	.	.	1	METTL11B	HGNC	31932	protein_coding	YES	CCDS44275.1	ENSP00000408058	NTM1B_HUMAN	.	UPI0000418EF1	.	.	.	2/4	.	hmmpanther:PTHR12753:SF2,hmmpanther:PTHR12753,Pfam_domain:PF05891,Gene3D:3.40.50.150,PIRSF_domain:PIRSF016958,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAAATTTCT	.	5	ESCA
PAPPA2	0	.	GRCh37	1	176564652	176564652	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1912G>A	p.Asp638Asn	p.D638N	ENST00000367662	3/23	86	60	26	56	56	0	PAPPA2,missense_variant,p.Asp638Asn,ENST00000367661,;PAPPA2,missense_variant,p.Asp638Asn,ENST00000367662,;	A	ENSG00000116183	ENST00000367662	Transcript	missense_variant	3076	1912	638	D/N	Gac/Aac	COSM1560435,COSM1560436	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	tolerated(0.34)	benign(0.435)	3/23	.	hmmpanther:PTHR19325:SF349,hmmpanther:PTHR19325	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACGACTTT	.	5	ESCA
NVL	0	.	GRCh37	1	224495770	224495770	+	Missense_Mutation	SNP	T	T	A	rs750744570	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538A>T	p.Ser180Cys	p.S180C	ENST00000281701	6/23	157	118	39	141	141	0	NVL,missense_variant,p.Ser74Cys,ENST00000361463,;NVL,missense_variant,p.Ser76Cys,ENST00000436927,;NVL,missense_variant,p.Ser85Cys,ENST00000492281,;NVL,missense_variant,p.Ser74Cys,ENST00000391875,;NVL,missense_variant,p.Ser180Cys,ENST00000281701,;NVL,intron_variant,,ENST00000340871,;NVL,intron_variant,,ENST00000469075,;NVL,intron_variant,,ENST00000482491,;NVL,intron_variant,,ENST00000488718,;NVL,intron_variant,,ENST00000469968,;NVL,downstream_gene_variant,,ENST00000461546,;RNU6-1008P,downstream_gene_variant,,ENST00000384160,;NVL,non_coding_transcript_exon_variant,,ENST00000470903,;NVL,non_coding_transcript_exon_variant,,ENST00000461466,;NVL,downstream_gene_variant,,ENST00000487758,;NVL,downstream_gene_variant,,ENST00000468673,;NVL,missense_variant,p.Ser180Cys,ENST00000467882,;NVL,non_coding_transcript_exon_variant,,ENST00000498767,;NVL,intron_variant,,ENST00000470989,;	A	ENSG00000143748	ENST00000281701	Transcript	missense_variant	798	538	180	S/C	Agt/Tgt	rs750744570	.	.	-1	NVL	HGNC	8070	protein_coding	YES	CCDS1541.1	ENSP00000281701	NVL_HUMAN	Q96PA2_HUMAN	UPI0000073F3E	.	tolerated(0.24)	benign(0.002)	6/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACACTTGGGG	.	5	ESCA
OBSCN	0	.	GRCh37	1	228495134	228495134	+	Missense_Mutation	SNP	C	C	T	rs765062164	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15239C>T	p.Thr5080Met	p.T5080M	ENST00000570156	57/116	71	31	40	48	48	0	OBSCN,missense_variant,p.Thr1757Met,ENST00000366707,;OBSCN,missense_variant,p.Thr1242Met,ENST00000366709,;OBSCN,missense_variant,p.Thr4123Met,ENST00000284548,;OBSCN,missense_variant,p.Thr5080Met,ENST00000570156,;OBSCN,missense_variant,p.Thr4123Met,ENST00000422127,;OBSCN,downstream_gene_variant,,ENST00000483539,;OBSCN,downstream_gene_variant,,ENST00000359599,;RP5-1139B12.4,upstream_gene_variant,,ENST00000602778,;OBSCN,downstream_gene_variant,,ENST00000602832,;	T	ENSG00000154358	ENST00000570156	Transcript	missense_variant	15313	15239	5080	T/M	aCg/aTg	rs765062164	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	benign(0.038)	57/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCACGCGGG	.	5	ESCA
FMN2	0	.	GRCh37	1	240370709	240370709	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2597C>T	p.Ser866Phe	p.S866F	ENST00000319653	5/18	58	39	18	51	51	0	FMN2,missense_variant,p.Ser866Phe,ENST00000319653,;FMN2,downstream_gene_variant,,ENST00000447095,;	T	ENSG00000155816	ENST00000319653	Transcript	missense_variant	2827	2597	866	S/F	tCc/tTc	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	unknown(0)	5/18	.	hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,SMART_domains:SM00498	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGTCCTCCA	.	5	ESCA
ARID1A	0	.	GRCh37	1	27106916	27106916	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6527delA	p.Gln2176ArgfsTer24	p.Q2176Rfs*24	ENST00000324856	20/20	45	29	16	53	53	0	ARID1A,frameshift_variant,p.Gln1959ArgfsTer24,ENST00000457599,;ARID1A,frameshift_variant,p.Gln1793ArgfsTer24,ENST00000374152,;ARID1A,frameshift_variant,p.Gln1073ArgfsTer24,ENST00000430799,;ARID1A,frameshift_variant,p.Gln504ArgfsTer24,ENST00000540690,;ARID1A,frameshift_variant,p.Gln2176ArgfsTer24,ENST00000324856,;ARID1A,3_prime_UTR_variant,,ENST00000466382,;ARID1A,3_prime_UTR_variant,,ENST00000532781,;	-	ENSG00000117713	ENST00000324856	Transcript	frameshift_variant	6898	6527	2176	Q/X	cAg/cg	.	.	.	1	ARID1A	HGNC	11110	protein_coding	YES	CCDS285.1	ENSP00000320485	ARI1A_HUMAN	Q96T01_HUMAN,Q96SY8_HUMAN,Q96SM7_HUMAN,E9PQW6_HUMAN,C1KEN7_HUMAN,A4FU79_HUMAN	UPI0000167B91	.	.	.	20/20	.	hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12,Pfam_domain:PF12031,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGCTCAGGGGG	.	3	ESCA
GBP7	0	.	GRCh37	1	89599004	89599004	+	Missense_Mutation	SNP	C	C	G	rs571294599	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1599G>C	p.Lys533Asn	p.K533N	ENST00000294671	10/11	50	30	19	72	72	0	GBP7,missense_variant,p.Lys533Asn,ENST00000294671,;GBP2,intron_variant,,ENST00000464839,;	G	ENSG00000213512	ENST00000294671	Transcript	missense_variant	1738	1599	533	K/N	aaG/aaC	rs571294599	.	.	-1	GBP7	HGNC	29606	protein_coding	YES	CCDS720.1	ENSP00000294671	GBP7_HUMAN	.	UPI000013E1A3	.	deleterious(0.01)	probably_damaging(0.975)	10/11	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:0037397,Gene3D:1f5nA01,Pfam_domain:PF02841,hmmpanther:PTHR10751:SF18,hmmpanther:PTHR10751	T:0.0010	T:0	T:0	.	T:0	T:0	T:0.0051	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCTTCTT	byFrequency|by1000G	5	ESCA
C20orf26	0	.	GRCh37	20	20177348	20177348	+	Silent	SNP	G	G	T	.	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1725G>T	p.%3D	p.L575L	ENST00000245957	16/27	75	47	28	70	70	0	C20orf26,synonymous_variant,p.%3D,ENST00000431753,;C20orf26,synonymous_variant,p.%3D,ENST00000245957,;C20orf26,5_prime_UTR_variant,,ENST00000389656,;C20orf26,5_prime_UTR_variant,,ENST00000377309,;C20orf26,non_coding_transcript_exon_variant,,ENST00000476414,;C20orf26,non_coding_transcript_exon_variant,,ENST00000468719,;C20orf26,non_coding_transcript_exon_variant,,ENST00000471716,;	T	ENSG00000089101	ENST00000245957	Transcript	synonymous_variant	1801	1725	575	L	ctG/ctT	COSM3799372	.	.	1	C20orf26	HGNC	15872	protein_coding	YES	CCDS33447.1	ENSP00000245957	CT026_HUMAN	C9JMV0_HUMAN,C9JHE8_HUMAN,C9J610_HUMAN	UPI0000206AE4	.	.	.	16/27	.	hmmpanther:PTHR21178:SF8,hmmpanther:PTHR21178	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTGAAGGA	.	5	ESCA
PYGB	0	.	GRCh37	20	25257924	25257924	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817G>A	p.Ala273Thr	p.A273T	ENST00000216962	7/20	51	30	21	83	82	0	PYGB,missense_variant,p.Ala273Thr,ENST00000216962,;	A	ENSG00000100994	ENST00000216962	Transcript	missense_variant	927	817	273	A/T	Gct/Act	.	.	.	1	PYGB	HGNC	9723	protein_coding	YES	CCDS13171.1	ENSP00000216962	PYGB_HUMAN	Q8TDG6_HUMAN	UPI0000131A0A	.	tolerated(0.08)	possibly_damaging(0.702)	7/20	.	hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF1,Gene3D:3.40.50.2000,TIGRFAM_domain:TIGR02093,Pfam_domain:PF00343,PIRSF_domain:PIRSF000460,Superfamily_domains:SSF53756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTGGCTGAG	.	5	ESCA
KCNQ2	0	.	GRCh37	20	62103553	62103553	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264G>A	p.%3D	p.P88P	ENST00000359125	1/17	61	41	19	69	69	0	KCNQ2,synonymous_variant,p.%3D,ENST00000359689,;KCNQ2,synonymous_variant,p.%3D,ENST00000354587,;KCNQ2,synonymous_variant,p.%3D,ENST00000360480,;KCNQ2,synonymous_variant,p.%3D,ENST00000359125,;KCNQ2,synonymous_variant,p.%3D,ENST00000344425,;KCNQ2,synonymous_variant,p.%3D,ENST00000370224,;KCNQ2,synonymous_variant,p.%3D,ENST00000357249,;KCNQ2,synonymous_variant,p.%3D,ENST00000344462,;KCNQ2,non_coding_transcript_exon_variant,,ENST00000370221,;	T	ENSG00000075043	ENST00000359125	Transcript	synonymous_variant	439	264	88	P	ccG/ccA	.	.	.	-1	KCNQ2	HGNC	6296	protein_coding	YES	CCDS13520.1	ENSP00000352035	KCNQ2_HUMAN	.	UPI00001279ED	.	.	.	1/17	.	hmmpanther:PTHR11537:SF6,hmmpanther:PTHR11537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCGCGGCCG	.	5	ESCA
NCAM2	0	.	GRCh37	21	22664561	22664561	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619G>A	p.Val207Met	p.V207M	ENST00000400546	5/18	31	28	3	51	51	0	NCAM2,missense_variant,p.Val207Met,ENST00000400546,;NCAM2,missense_variant,p.Val65Met,ENST00000284894,;NCAM2,missense_variant,p.Val232Met,ENST00000535285,;NCAM2,splice_region_variant,,ENST00000461281,;NCAM2,downstream_gene_variant,,ENST00000486367,;	A	ENSG00000154654	ENST00000400546	Transcript	missense_variant	868	619	207	V/M	Gtg/Atg	.	.	.	1	NCAM2	HGNC	7657	protein_coding	YES	CCDS42910.1	ENSP00000383392	NCAM2_HUMAN	D3DSC5_HUMAN	UPI00001A3703	.	deleterious(0)	probably_damaging(0.96)	5/18	.	hmmpanther:PTHR10489:SF35,hmmpanther:PTHR10489,Superfamily_domains:SSF48726,Superfamily_domains:SSF48726,Prints_domain:PR01838	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTAATGGTAAG	.	2	ESCA
GSTT1	0	.	GRCh37	22	24379392	24379392	+	Missense_Mutation	SNP	C	C	T	rs201658659	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320G>A	p.Arg107Gln	p.R107Q	ENST00000248935	3/5	71	18	52	64	64	0	GSTT1,missense_variant,p.Arg107Gln,ENST00000248935,;GSTT1,missense_variant,p.Arg34Gln,ENST00000436103,;GSTT1,5_prime_UTR_variant,,ENST00000439996,;GSTT1,intron_variant,,ENST00000417870,;GSTT1,downstream_gene_variant,,ENST00000447865,;KB-226F1.1,downstream_gene_variant,,ENST00000608619,;GSTT1,missense_variant,p.Gly87Arg,ENST00000458231,;GSTT1,3_prime_UTR_variant,,ENST00000426209,;GSTT1,3_prime_UTR_variant,,ENST00000417489,;GSTT1,3_prime_UTR_variant,,ENST00000418883,;GSTT1,intron_variant,,ENST00000417831,;GSTT1,downstream_gene_variant,,ENST00000486544,;GSTT1,downstream_gene_variant,,ENST00000428175,;GSTT1,downstream_gene_variant,,ENST00000480898,;	T	ENSG00000184674	ENST00000248935	Transcript	missense_variant	373	320	107	R/Q	cGg/cAg	rs201658659	.	.	-1	GSTT1	HGNC	4641	protein_coding	YES	CCDS13822.1	ENSP00000248935	GSTT1_HUMAN	Q6IC69_HUMAN,Q4GZS9_HUMAN,C9JA47_HUMAN	UPI000004A942	.	tolerated(0.18)	possibly_damaging(0.487)	3/5	.	Superfamily_domains:SSF47616,Gene3D:1.20.1050.10,hmmpanther:PTHR11260,hmmpanther:PTHR11260:SF168,PROSITE_profiles:PS50405	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0.0003	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCCGCAGA	byCluster|by1000G	5	ESCA
PITPNB	0	.	GRCh37	22	28293845	28293845	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.233A>T	p.Glu78Val	p.E78V	ENST00000335272	4/12	56	52	4	60	60	0	PITPNB,missense_variant,p.Glu78Val,ENST00000335272,;PITPNB,missense_variant,p.Glu80Val,ENST00000436663,;PITPNB,missense_variant,p.Glu78Val,ENST00000320996,;PITPNB,missense_variant,p.Glu5Val,ENST00000415296,;PITPNB,missense_variant,p.Glu80Val,ENST00000455418,;PITPNB,non_coding_transcript_exon_variant,,ENST00000477861,;PITPNB,non_coding_transcript_exon_variant,,ENST00000460566,;PITPNB,upstream_gene_variant,,ENST00000465179,;	A	ENSG00000180957	ENST00000335272	Transcript	missense_variant	310	233	78	E/V	gAg/gTg	.	.	.	-1	PITPNB	HGNC	9002	protein_coding	YES	CCDS13842.1	ENSP00000334738	PIPNB_HUMAN	B3KYB6_HUMAN	UPI0000043C3A	.	deleterious(0.02)	benign(0.072)	4/12	.	hmmpanther:PTHR10658,Pfam_domain:PF02121,Gene3D:3.30.530.20,Superfamily_domains:SSF55961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCCCTCGGGA	.	3	ESCA
RFPL3	0	.	GRCh37	22	32756307	32756307	+	Nonsense_Mutation	SNP	C	C	T	rs374358387	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442C>T	p.Arg148Ter	p.R148*	ENST00000249007	2/2	106	58	48	128	128	0	RFPL3,stop_gained,p.Arg148Ter,ENST00000249007,;RFPL3,stop_gained,p.Arg119Ter,ENST00000397468,;RFPL3,stop_gained,p.Arg119Ter,ENST00000382088,;RFPL3S,3_prime_UTR_variant,,ENST00000400234,;RFPL3S,3_prime_UTR_variant,,ENST00000382084,;RFPL3S,downstream_gene_variant,,ENST00000382086,;RFPL3S,downstream_gene_variant,,ENST00000577714,;RFPL3S,downstream_gene_variant,,ENST00000461833,;IGLCOR22-2,upstream_gene_variant,,ENST00000605398,;	T	ENSG00000128276	ENST00000249007	Transcript	stop_gained	647	442	148	R/*	Cga/Tga	rs374358387	.	.	1	RFPL3	HGNC	9980	protein_coding	YES	CCDS43011.1	ENSP00000249007	RFPL3_HUMAN	.	UPI000013CC68	.	.	.	2/2	.	Prints_domain:PR01407,Superfamily_domains:SSF49899,SMART_domains:SM00589,Pfam_domain:PF13765,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF211,PROSITE_profiles:PS50188	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGTCCGAAGT	byCluster	5	ESCA
RGPD3	0	.	GRCh37	2	107074073	107074073	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202C>T	p.Leu68Phe	p.L68F	ENST00000409886	3/23	132	102	30	164	164	0	RGPD3,missense_variant,p.Leu68Phe,ENST00000409886,;RGPD3,missense_variant,p.Leu68Phe,ENST00000304514,;	A	ENSG00000153165	ENST00000409886	Transcript	missense_variant	290	202	68	L/F	Ctt/Ttt	.	.	.	-1	RGPD3	HGNC	32416	protein_coding	YES	CCDS46379.1	ENSP00000386588	RGPD3_HUMAN	I1Z9D1_HUMAN	UPI00006C049F	.	tolerated(0.14)	benign(0.425)	3/23	.	Superfamily_domains:SSF48452,SMART_domains:SM00028,Gene3D:1.25.40.10,Pfam_domain:PF00515,hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF86,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AAGAAGACCCA	.	2	ESCA
CCDC115	0	.	GRCh37	2	131097266	131097266	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431-461C>T	.	.	ENST00000259229	.	15	7	8	29	29	0	CCDC115,missense_variant,p.Ala162Val,ENST00000437688,;CCDC115,intron_variant,,ENST00000409127,;CCDC115,intron_variant,,ENST00000259229,;IMP4,upstream_gene_variant,,ENST00000259239,;IMP4,upstream_gene_variant,,ENST00000428740,;IMP4,upstream_gene_variant,,ENST00000409649,;IMP4,upstream_gene_variant,,ENST00000452955,;IMP4,upstream_gene_variant,,ENST00000409935,;CCDC115,missense_variant,p.Ala167Val,ENST00000442217,;CCDC115,non_coding_transcript_exon_variant,,ENST00000465315,;IMP4,upstream_gene_variant,,ENST00000477375,;IMP4,upstream_gene_variant,,ENST00000460766,;IMP4,upstream_gene_variant,,ENST00000462392,;IMP4,upstream_gene_variant,,ENST00000470672,;IMP4,upstream_gene_variant,,ENST00000490895,;IMP4,upstream_gene_variant,,ENST00000464432,;IMP4,upstream_gene_variant,,ENST00000473689,;IMP4,upstream_gene_variant,,ENST00000456713,;IMP4,upstream_gene_variant,,ENST00000495606,;	A	ENSG00000136710	ENST00000259229	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CCDC115	HGNC	28178	protein_coding	YES	CCDS2159.1	ENSP00000259229	CC115_HUMAN	.	UPI000006E81C	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCAGCAGCA	.	5	ESCA
GCG	0	.	GRCh37	2	163000642	163000642	+	Missense_Mutation	SNP	C	C	T	rs757350391	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431G>A	p.Arg144His	p.R144H	ENST00000418842	5/6	22	17	5	41	41	0	GCG,missense_variant,p.Arg144His,ENST00000418842,;GCG,missense_variant,p.Arg144His,ENST00000375497,;GCG,non_coding_transcript_exon_variant,,ENST00000483769,;GCG,downstream_gene_variant,,ENST00000497568,;GCG,downstream_gene_variant,,ENST00000492913,;	T	ENSG00000115263	ENST00000418842	Transcript	missense_variant	686	431	144	R/H	cGc/cAc	rs757350391	.	.	-1	GCG	HGNC	4191	protein_coding	YES	CCDS46439.1	ENSP00000387662	GLUC_HUMAN	.	UPI000012B832	.	deleterious(0)	probably_damaging(0.993)	5/6	.	hmmpanther:PTHR11418:SF0,hmmpanther:PTHR11418	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGCGGCCA	byFrequency	5	ESCA
NFE2L2	0	.	GRCh37	2	178098975	178098975	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70T>A	p.Trp24Arg	p.W24R	ENST00000397062	2/5	23	11	12	29	29	0	NFE2L2,missense_variant,p.Trp8Arg,ENST00000449627,;NFE2L2,missense_variant,p.Trp8Arg,ENST00000423513,;NFE2L2,missense_variant,p.Trp24Arg,ENST00000397062,;NFE2L2,missense_variant,p.Trp8Arg,ENST00000446151,;NFE2L2,missense_variant,p.Trp8Arg,ENST00000588123,;NFE2L2,missense_variant,p.Trp23Arg,ENST00000586532,;NFE2L2,missense_variant,p.Trp8Arg,ENST00000421929,;NFE2L2,missense_variant,p.Trp8Arg,ENST00000464747,;NFE2L2,missense_variant,p.Trp8Arg,ENST00000448782,;NFE2L2,missense_variant,p.Trp8Arg,ENST00000397063,;NFE2L2,splice_region_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	T	ENSG00000116044	ENST00000397062	Transcript	missense_variant	625	70	24	W/R	Tgg/Agg	COSM132985	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.W24C|c.72G>C|5,BUFFER|p.D27G|c.80A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCAAAGTA	.	5	ESCA
SSFA2	0	.	GRCh37	2	182794855	182794855	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*581A>G	.	.	ENST00000431877	18/18	33	21	12	31	31	0	SSFA2,3_prime_UTR_variant,,ENST00000409001,;SSFA2,3_prime_UTR_variant,,ENST00000409136,;SSFA2,3_prime_UTR_variant,,ENST00000431877,;SSFA2,3_prime_UTR_variant,,ENST00000320370,;SSFA2,downstream_gene_variant,,ENST00000428267,;SSFA2,downstream_gene_variant,,ENST00000451836,;SSFA2,downstream_gene_variant,,ENST00000467172,;SSFA2,3_prime_UTR_variant,,ENST00000416081,;SSFA2,3_prime_UTR_variant,,ENST00000440623,;SSFA2,non_coding_transcript_exon_variant,,ENST00000491720,;SSFA2,downstream_gene_variant,,ENST00000454579,;	G	ENSG00000138434	ENST00000431877	Transcript	3_prime_UTR_variant	4540	.	.	.	.	.	.	.	1	SSFA2	HGNC	11319	protein_coding	YES	CCDS46467.1	ENSP00000388731	SSFA2_HUMAN	B3KXT1_HUMAN	UPI000019B17A	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AATGTACTTAC	.	4	ESCA
DNAH7	0	.	GRCh37	2	196709863	196709863	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8808G>T	p.Leu2936Phe	p.L2936F	ENST00000312428	47/65	75	67	7	90	90	0	DNAH7,missense_variant,p.Leu2936Phe,ENST00000312428,;	A	ENSG00000118997	ENST00000312428	Transcript	missense_variant	8909	8808	2936	L/F	ttG/ttT	.	.	.	-1	DNAH7	HGNC	18661	protein_coding	YES	CCDS42794.1	ENSP00000311273	DYH7_HUMAN	C9JUY3_HUMAN	UPI0000141B95	.	tolerated(0.06)	benign(0.02)	47/65	.	hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTGCACAAAGT	.	3	ESCA
NYAP2	0	.	GRCh37	2	226378162	226378162	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297G>A	p.Met99Ile	p.M99I	ENST00000272907	3/6	34	31	3	33	33	0	NYAP2,missense_variant,p.Met99Ile,ENST00000272907,;NYAP2,intron_variant,,ENST00000409269,;	A	ENSG00000144460	ENST00000272907	Transcript	missense_variant	710	297	99	M/I	atG/atA	.	.	.	1	NYAP2	HGNC	29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	NYAP2_HUMAN	.	UPI00001C1DB6	.	tolerated(0.07)	benign(0.007)	3/6	.	Pfam_domain:PF15439,hmmpanther:PTHR22633	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACAATGCCTGC	.	2	ESCA
ERLEC1	0	.	GRCh37	2	54040157	54040157	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1173G>A	p.%3D	p.K391K	ENST00000185150	11/14	57	33	24	43	43	0	ERLEC1,synonymous_variant,p.%3D,ENST00000185150,;ERLEC1,synonymous_variant,p.%3D,ENST00000405123,;ERLEC1,synonymous_variant,p.%3D,ENST00000378239,;ASB3,intron_variant,,ENST00000406625,;GPR75-ASB3,intron_variant,,ENST00000352846,;ASB3,intron_variant,,ENST00000498475,;ASB3,intron_variant,,ENST00000459916,;	A	ENSG00000068912	ENST00000185150	Transcript	synonymous_variant	1304	1173	391	K	aaG/aaA	.	.	.	1	ERLEC1	HGNC	25222	protein_coding	YES	CCDS1848.1	ENSP00000185150	ERLEC_HUMAN	.	UPI00000373C1	.	.	.	11/14	.	hmmpanther:PTHR15414,hmmpanther:PTHR15414:SF0,Pfam_domain:PF07915,Superfamily_domains:SSF50911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTAAGAAGAA	.	5	ESCA
DCTN1	0	.	GRCh37	2	74597805	74597805	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.991C>T	p.Arg331Trp	p.R331W	ENST00000361874	10/32	49	37	11	38	38	0	DCTN1,missense_variant,p.Arg324Trp,ENST00000394003,;DCTN1,missense_variant,p.Arg314Trp,ENST00000409868,;DCTN1,missense_variant,p.Arg197Trp,ENST00000407639,;DCTN1,missense_variant,p.Arg294Trp,ENST00000409240,;DCTN1,missense_variant,p.Arg331Trp,ENST00000361874,;DCTN1,missense_variant,p.Arg311Trp,ENST00000409567,;DCTN1,missense_variant,p.Arg197Trp,ENST00000409438,;DCTN1,downstream_gene_variant,,ENST00000458655,;DCTN1,upstream_gene_variant,,ENST00000495643,;DCTN1,upstream_gene_variant,,ENST00000497666,;DCTN1,downstream_gene_variant,,ENST00000463583,;DCTN1,missense_variant,p.Arg294Trp,ENST00000434055,;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110,;DCTN1,downstream_gene_variant,,ENST00000462813,;DCTN1,downstream_gene_variant,,ENST00000470351,;DCTN1,upstream_gene_variant,,ENST00000495895,;DCTN1,downstream_gene_variant,,ENST00000477966,;	A	ENSG00000204843	ENST00000361874	Transcript	missense_variant	1309	991	331	R/W	Cgg/Tgg	.	.	.	-1	DCTN1	HGNC	2711	protein_coding	YES	CCDS1939.1	ENSP00000354791	DCTN1_HUMAN	Q6LCB2_HUMAN,E7EWF7_HUMAN,C9JZA4_HUMAN,C9JTE5_HUMAN,C9JJN7_HUMAN,C9JJD0_HUMAN,C9J1B7_HUMAN	UPI0000129A25	.	deleterious(0)	possibly_damaging(0.834)	10/32	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18916:SF29,hmmpanther:PTHR18916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCGCTCCT	.	5	ESCA
SNRNP200	0	.	GRCh37	2	96944361	96944361	+	Silent	SNP	G	G	A	rs142524062	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5412C>T	p.%3D	p.I1804I	ENST00000323853	38/45	28	20	8	36	36	0	SNRNP200,synonymous_variant,p.%3D,ENST00000323853,;SNRNP200,intron_variant,,ENST00000349783,;SNRNP200,synonymous_variant,p.%3D,ENST00000429650,;SNRNP200,non_coding_transcript_exon_variant,,ENST00000497539,;SNRNP200,downstream_gene_variant,,ENST00000484372,;SNRNP200,downstream_gene_variant,,ENST00000493271,;SNRNP200,upstream_gene_variant,,ENST00000480835,;SNRNP200,downstream_gene_variant,,ENST00000480242,;	A	ENSG00000144028	ENST00000323853	Transcript	synonymous_variant	5490	5412	1804	I	atC/atT	rs142524062,COSM287978	.	.	-1	SNRNP200	HGNC	30859	protein_coding	YES	CCDS2020.1	ENSP00000317123	U520_HUMAN	Q9P172_HUMAN,Q7L5W4_HUMAN,Q5ZF01_HUMAN,A4FU77_HUMAN,A2RRQ7_HUMAN	UPI0000207C53	.	.	.	38/45	.	hmmpanther:PTHR11752:SF55,hmmpanther:PTHR11752,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCGATGCT	byCluster	5	ESCA
PCNP	0	.	GRCh37	3	101313192	101313192	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1595A>G	.	.	ENST00000265260	5/5	73	41	32	53	53	0	PCNP,3_prime_UTR_variant,,ENST00000265260,;PCNP,3_prime_UTR_variant,,ENST00000469941,;PCNP,3_prime_UTR_variant,,ENST00000296024,;PCNP,downstream_gene_variant,,ENST00000486406,;PCNP,downstream_gene_variant,,ENST00000470490,;PCNP,3_prime_UTR_variant,,ENST00000460231,;PCNP,downstream_gene_variant,,ENST00000498274,;PCNP,downstream_gene_variant,,ENST00000465366,;RP11-454H13.1,downstream_gene_variant,,ENST00000477747,;	G	ENSG00000081154	ENST00000265260	Transcript	3_prime_UTR_variant	2253	.	.	.	.	.	.	.	1	PCNP	HGNC	30023	protein_coding	YES	CCDS2942.1	ENSP00000265260	PCNP_HUMAN	.	UPI0000070241	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCAAATGAA	.	5	ESCA
STAG1	0	.	GRCh37	3	136141419	136141419	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870G>T	p.Val624Leu	p.V624L	ENST00000383202	19/34	71	31	40	41	41	0	STAG1,missense_variant,p.Val208Leu,ENST00000536929,;STAG1,missense_variant,p.Val398Leu,ENST00000434713,;STAG1,missense_variant,p.Val624Leu,ENST00000383202,;STAG1,missense_variant,p.Val624Leu,ENST00000236698,;STAG1,downstream_gene_variant,,ENST00000492318,;STAG1,3_prime_UTR_variant,,ENST00000483235,;STAG1,3_prime_UTR_variant,,ENST00000487065,;	A	ENSG00000118007	ENST00000383202	Transcript	missense_variant	2127	1870	624	V/L	Gtg/Ttg	.	.	.	-1	STAG1	HGNC	11354	protein_coding	YES	CCDS3090.1	ENSP00000372689	STAG1_HUMAN	Q4LE48_HUMAN	UPI000020A2DE	.	deleterious(0)	benign(0.061)	19/34	.	hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF6,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCACAACAA	.	5	ESCA
TTC14	0	.	GRCh37	3	180326257	180326257	+	Intron	SNP	G	G	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1291-232G>C	.	.	ENST00000296015	.	18	12	6	13	13	0	TTC14,3_prime_UTR_variant,,ENST00000412756,;TTC14,intron_variant,,ENST00000382584,;TTC14,intron_variant,,ENST00000296015,;CCDC39,intron_variant,,ENST00000473854,;TTC14,downstream_gene_variant,,ENST00000491380,;TTC14,downstream_gene_variant,,ENST00000492617,;CCDC39,downstream_gene_variant,,ENST00000489868,;TTC14,downstream_gene_variant,,ENST00000495660,;TTC14,intron_variant,,ENST00000465625,;TTC14,upstream_gene_variant,,ENST00000487397,;TTC14,3_prime_UTR_variant,,ENST00000465065,;TTC14,intron_variant,,ENST00000470669,;TTC14,downstream_gene_variant,,ENST00000462895,;	C	ENSG00000163728	ENST00000296015	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TTC14	HGNC	24697	protein_coding	YES	CCDS3237.1	ENSP00000296015	TTC14_HUMAN	C9JBA2_HUMAN,C9J974_HUMAN	UPI00000720AE	.	.	.	.	10/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGGATACC	.	5	ESCA
ITPR1	0	.	GRCh37	3	4703790	4703790	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1231G>C	p.Asp411His	p.D411H	ENST00000302640	14/61	55	27	28	88	88	0	ITPR1,missense_variant,p.Asp426His,ENST00000423119,;ITPR1,missense_variant,p.Asp411His,ENST00000456211,;ITPR1,missense_variant,p.Asp426His,ENST00000357086,;ITPR1,missense_variant,p.Asp411His,ENST00000302640,;ITPR1,missense_variant,p.Asp411His,ENST00000443694,;ITPR1,missense_variant,p.Asp426His,ENST00000354582,;ITPR1,intron_variant,,ENST00000544951,;ITPR1,non_coding_transcript_exon_variant,,ENST00000477577,;	C	ENSG00000150995	ENST00000302640	Transcript	missense_variant	1581	1231	411	D/H	Gat/Cat	.	.	.	1	ITPR1	HGNC	6180	protein_coding	YES	CCDS54551.1	ENSP00000306253	ITPR1_HUMAN	.	UPI0000E5A461	.	deleterious(0)	probably_damaging(1)	14/61	.	PROSITE_profiles:PS50919,hmmpanther:PTHR13715:SF52,hmmpanther:PTHR13715,Pfam_domain:PF02815,Gene3D:2.80.10.50,Superfamily_domains:SSF82109,Prints_domain:PR00779	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAGGATAAG	.	5	ESCA
IFRD2	0	.	GRCh37	3	50327194	50327195	+	Splice_Site	DEL	CT	CT	-	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	CT	CT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.739-2_739-1delAG	.	p.X247_splice	ENST00000429673	.	37	23	14	37	37	0	IFRD2,splice_acceptor_variant,,ENST00000429673,;IFRD2,splice_acceptor_variant,,ENST00000336089,;IFRD2,splice_acceptor_variant,,ENST00000417626,;IFRD2,splice_acceptor_variant,,ENST00000436390,;HYAL3,downstream_gene_variant,,ENST00000450982,;IFRD2,upstream_gene_variant,,ENST00000426499,;HYAL3,downstream_gene_variant,,ENST00000336307,;LSMEM2,downstream_gene_variant,,ENST00000316436,;HYAL3,downstream_gene_variant,,ENST00000359051,;HYAL3,downstream_gene_variant,,ENST00000415204,;HYAL3,downstream_gene_variant,,ENST00000513170,;IFRD2,downstream_gene_variant,,ENST00000484043,;IFRD2,downstream_gene_variant,,ENST00000468737,;IFRD2,splice_acceptor_variant,,ENST00000414734,;IFRD2,splice_acceptor_variant,,ENST00000474556,;IFRD2,splice_acceptor_variant,,ENST00000438296,;IFRD2,splice_acceptor_variant,,ENST00000489569,;IFRD2,non_coding_transcript_exon_variant,,ENST00000483071,;IFRD2,upstream_gene_variant,,ENST00000469855,;IFRD2,downstream_gene_variant,,ENST00000462001,;IFRD2,upstream_gene_variant,,ENST00000486322,;IFRD2,upstream_gene_variant,,ENST00000464258,;IFRD2,upstream_gene_variant,,ENST00000492387,;	-	ENSG00000214706	ENST00000429673	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	IFRD2	HGNC	5457	protein_coding	YES	CCDS46831.1	ENSP00000398971	IFRD2_HUMAN	.	UPI0000E5A694	.	.	.	.	5/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGCACACTGTTGG	.	3	ESCA
TET2	0	.	GRCh37	4	106197248	106197248	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5581G>A	p.Gly1861Arg	p.G1861R	ENST00000540549	11/11	11	7	4	28	28	0	TET2,missense_variant,p.Gly1861Arg,ENST00000540549,;TET2,missense_variant,p.Gly1882Arg,ENST00000513237,;TET2,missense_variant,p.Gly1861Arg,ENST00000380013,;TET2,3_prime_UTR_variant,,ENST00000545826,;TET2,3_prime_UTR_variant,,ENST00000265149,;	A	ENSG00000168769	ENST00000540549	Transcript	missense_variant	6441	5581	1861	G/R	Gga/Aga	COSM42051	.	.	1	TET2	HGNC	25941	protein_coding	YES	CCDS47120.1	ENSP00000442788	TET2_HUMAN	E7EPB1_HUMAN,D6RE87_HUMAN	UPI00001D75E4	.	deleterious(0)	probably_damaging(1)	11/11	.	hmmpanther:PTHR23358:SF3,hmmpanther:PTHR23358,Pfam_domain:PF12851	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTGGGGGAGTG	.	2	ESCA
COL25A1	0	.	GRCh37	4	109862572	109862572	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514C>A	p.His172Asn	p.H172N	ENST00000399132	9/38	51	31	20	77	77	0	COL25A1,missense_variant,p.His172Asn,ENST00000399132,;COL25A1,missense_variant,p.His172Asn,ENST00000399126,;COL25A1,intron_variant,,ENST00000399127,;COL25A1,intron_variant,,ENST00000494183,;	T	ENSG00000188517	ENST00000399132	Transcript	missense_variant	1045	514	172	H/N	Cat/Aat	.	.	.	-1	COL25A1	HGNC	18603	protein_coding	YES	CCDS43258.1	ENSP00000382083	COPA1_HUMAN	D6R8Y2_HUMAN	UPI0000225CD2	.	tolerated(0.32)	unknown(0)	9/38	.	hmmpanther:PTHR24023:SF412,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATGATTGA	.	5	ESCA
KIAA1109	0	.	GRCh37	4	123118429	123118429	+	Missense_Mutation	SNP	G	G	A	rs775448550	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1288G>A	p.Gly430Ser	p.G430S	ENST00000264501	13/86	245	151	93	256	256	0	KIAA1109,missense_variant,p.Gly263Ser,ENST00000424425,;KIAA1109,missense_variant,p.Gly430Ser,ENST00000455637,;KIAA1109,missense_variant,p.Gly430Ser,ENST00000264501,;KIAA1109,missense_variant,p.Gly430Ser,ENST00000388738,;KIAA1109,splice_region_variant,,ENST00000495260,;	A	ENSG00000138688	ENST00000264501	Transcript	missense_variant	1661	1288	430	G/S	Ggt/Agt	rs775448550	.	.	1	KIAA1109	HGNC	26953	protein_coding	YES	CCDS43267.1	ENSP00000264501	K1109_HUMAN	B3KN93_HUMAN	UPI0000DD87B4	.	.	probably_damaging(0.999)	13/86	.	hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATGGTAAG	.	5	ESCA
GYPE	0	.	GRCh37	4	144793349	144793349	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66T>A	.	.	ENST00000358615	4/4	49	38	11	58	58	0	GYPE,3_prime_UTR_variant,,ENST00000358615,;GYPE,downstream_gene_variant,,ENST00000437468,;GYPE,3_prime_UTR_variant,,ENST00000506264,;	T	ENSG00000197465	ENST00000358615	Transcript	3_prime_UTR_variant	355	.	.	.	.	.	.	.	-1	GYPE	HGNC	4705	protein_coding	YES	CCDS47138.1	ENSP00000351430	GLPE_HUMAN	Q9NRB2_HUMAN	UPI000012B76B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTAAAAAAA	.	5	ESCA
FBXW7	0	.	GRCh37	4	153247174	153247175	+	Nonsense_Mutation	INS	-	-	TATT	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1624_1627dupAATA	p.Arg543LysfsTer2	p.R543Kfs*2	ENST00000281708	10/12	90	66	24	92	92	0	FBXW7,stop_gained,p.Arg543LysfsTer2,ENST00000603548,;FBXW7,stop_gained,p.Arg463LysfsTer2,ENST00000263981,;FBXW7,stop_gained,p.Arg425LysfsTer2,ENST00000296555,;FBXW7,stop_gained,p.Arg367LysfsTer2,ENST00000393956,;FBXW7,stop_gained,p.Arg543LysfsTer2,ENST00000281708,;FBXW7,stop_gained,p.Arg543LysfsTer2,ENST00000603841,;RP11-461L13.3,upstream_gene_variant,,ENST00000603766,;FBXW7,non_coding_transcript_exon_variant,,ENST00000603821,;FBXW7,upstream_gene_variant,,ENST00000604316,;FBXW7,downstream_gene_variant,,ENST00000604069,;	TATT	ENSG00000109670	ENST00000281708	Transcript	stop_gained	2857-2858	1627-1628	543	R/K*X	aga/aAATAga	.	.	.	-1	FBXW7	HGNC	16712	protein_coding	YES	CCDS3777.1	ENSP00000281708	FBXW7_HUMAN	S4R3N3_HUMAN,H9CWI3_HUMAN,H9CWI2_HUMAN,G0Z2K0_HUMAN,A7BJS8_HUMAN	UPI000007007E	.	.	.	10/12	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Pfam_domain:PF00400,Gene3D:2.130.10.10,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF116,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Y545C|c.1634A>G|4,BUFFER|p.Y545C|c.1634A>G|3,BUFFER|p.Y465C|c.1394A>G|3,BUFFER|p.Y306C|c.917A>G|3	INDELOCATOR*|VARSCANI*|PINDEL	AGACTCTATTA	.	3	ESCA
FBXW7	0	.	GRCh37	4	153247289	153247289	+	Missense_Mutation	SNP	G	G	C	rs149680468	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	10/12	59	29	29	57	57	0	FBXW7,missense_variant,p.Arg505Gly,ENST00000603548,;FBXW7,missense_variant,p.Arg425Gly,ENST00000263981,;FBXW7,missense_variant,p.Arg387Gly,ENST00000296555,;FBXW7,missense_variant,p.Arg329Gly,ENST00000393956,;FBXW7,missense_variant,p.Arg505Gly,ENST00000281708,;FBXW7,missense_variant,p.Arg505Gly,ENST00000603841,;FBXW7,non_coding_transcript_exon_variant,,ENST00000603821,;FBXW7,upstream_gene_variant,,ENST00000604316,;FBXW7,downstream_gene_variant,,ENST00000604069,;	C	ENSG00000109670	ENST00000281708	Transcript	missense_variant	2743	1513	505	R/G	Cgc/Ggc	rs149680468,COSM33763,COSM22975,COSM99604,COSM99606,COSM732380,COSM108572,COSM1154290,COSM1133711,COSM1149853,COSM108571,COSM732382,COSM99605,COSM74637,COSM99603,COSM732381	.	.	-1	FBXW7	HGNC	16712	protein_coding	YES	CCDS3777.1	ENSP00000281708	FBXW7_HUMAN	S4R3N3_HUMAN,H9CWI3_HUMAN,H9CWI2_HUMAN,G0Z2K0_HUMAN,A7BJS8_HUMAN	UPI000007007E	.	deleterious(0)	probably_damaging(1)	10/12	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Pfam_domain:PF00400,Gene3D:2.130.10.10,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF116,PROSITE_profiles:PS50294,PROSITE_profiles:PS50082	.	.	.	.	.	.	.	.	.	not_provided	1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	21499247	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R387G|c.1159C>G|7,SITE|p.R505G|c.1513C>G|11,SITE|p.R505G|c.1513C>G|11,SITE|p.R425G|c.1273C>G|11,CODON|p.R505L|c.1514G>T|8,CODON|p.R505?|c.1514G>H|14,CODON|p.R505H|c.1514G>A|3,BUFFER|p.R266G|c.796C>G|11,BUFFER|p.R266C|c.796C>T|32,BUFFER|p.R425C|c.1273C>T|33,BUFFER|p.R505C|c.1513C>T|32,BUFFER|p.R505S|c.1513C>A|3,BUFFER|p.R505C|c.1513C>T|66,BUFFER|p.R387C|c.1159C>T|19	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCGGACTG	.	5	ESCA
ADAM29	0	.	GRCh37	4	175899049	175899049	+	Silent	SNP	G	G	A	rs372859702	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2373G>A	p.%3D	p.T791T	ENST00000359240	5/5	109	63	46	108	108	0	ADAM29,synonymous_variant,p.%3D,ENST00000514159,;ADAM29,synonymous_variant,p.%3D,ENST00000445694,;ADAM29,synonymous_variant,p.%3D,ENST00000404450,;ADAM29,synonymous_variant,p.%3D,ENST00000359240,;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000502940,;ADAM29,downstream_gene_variant,,ENST00000505141,;RP13-577H12.2,intron_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,;	A	ENSG00000168594	ENST00000359240	Transcript	synonymous_variant	3043	2373	791	T	acG/acA	rs372859702,COSM420111	.	.	1	ADAM29	HGNC	207	protein_coding	YES	CCDS3823.1	ENSP00000352177	ADA29_HUMAN	D6RHU0_HUMAN,D6RBU0_HUMAN	UPI000013E9DE	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF34	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACGCCTTC	byCluster|by1000G	5	ESCA
FBN2	0	.	GRCh37	5	127614384	127614384	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7288A>G	p.Thr2430Ala	p.T2430A	ENST00000508053	63/71	57	40	16	54	54	0	FBN2,missense_variant,p.Thr2430Ala,ENST00000262464,;FBN2,missense_variant,p.Thr2430Ala,ENST00000508053,;	C	ENSG00000138829	ENST00000508053	Transcript	missense_variant	8263	7288	2430	T/A	Act/Gct	.	.	.	-1	FBN2	HGNC	3604	protein_coding	YES	CCDS34222.1	ENSP00000424571	FBN2_HUMAN	.	UPI0000519468	.	deleterious(0)	probably_damaging(0.968)	63/71	.	Superfamily_domains:SSF57581,PIRSF_domain:PIRSF036312,Pfam_domain:PF00683,Gene3D:3.90.290.10,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF19,PROSITE_profiles:PS51364	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAGTTCCAG	.	5	ESCA
SEPT8	0	.	GRCh37	5	132096579	132096579	+	Missense_Mutation	SNP	G	G	A	rs374687255	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1201C>T	p.Arg401Trp	p.R401W	ENST00000378719	9/10	45	29	16	49	49	0	SEPT8,missense_variant,p.Arg401Trp,ENST00000378706,;SEPT8,missense_variant,p.Arg341Trp,ENST00000448933,;SEPT8,missense_variant,p.Arg399Trp,ENST00000378701,;SEPT8,missense_variant,p.Arg399Trp,ENST00000378721,;SEPT8,missense_variant,p.Arg401Trp,ENST00000458488,;SEPT8,missense_variant,p.Arg401Trp,ENST00000296873,;SEPT8,missense_variant,p.Arg401Trp,ENST00000378719,;SEPT8,missense_variant,p.Arg341Trp,ENST00000378699,;SEPT8,downstream_gene_variant,,ENST00000414594,;SEPT8,downstream_gene_variant,,ENST00000453480,;SEPT8,downstream_gene_variant,,ENST00000371493,;SEPT8,upstream_gene_variant,,ENST00000481030,;SEPT8,downstream_gene_variant,,ENST00000492490,;SEPT8,downstream_gene_variant,,ENST00000371478,;SEPT8,downstream_gene_variant,,ENST00000481794,;	A	ENSG00000164402	ENST00000378719	Transcript	missense_variant	1439	1201	401	R/W	Cgg/Tgg	rs374687255	.	.	-1	SEPT8	HGNC	16511	protein_coding	YES	CCDS43358.1	ENSP00000367991	SEPT8_HUMAN	H7C604_HUMAN,C9J4G8_HUMAN	UPI00001C1E27	.	deleterious(0)	probably_damaging(0.941)	9/10	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18884:SF54,hmmpanther:PTHR18884,PIRSF_domain:PIRSF006698	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCGGCGAT	byCluster	5	ESCA
CYFIP2	0	.	GRCh37	5	156727797	156727797	+	Silent	SNP	T	T	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.384T>C	p.%3D	p.S128S	ENST00000521420	5/30	35	27	7	48	48	0	CYFIP2,synonymous_variant,p.%3D,ENST00000521420,;CYFIP2,synonymous_variant,p.%3D,ENST00000377576,;CYFIP2,synonymous_variant,p.%3D,ENST00000541131,;CYFIP2,synonymous_variant,p.%3D,ENST00000318218,;CYFIP2,synonymous_variant,p.%3D,ENST00000347377,;CYFIP2,5_prime_UTR_variant,,ENST00000442283,;CYFIP2,intron_variant,,ENST00000522463,;CYFIP2,3_prime_UTR_variant,,ENST00000517850,;CYFIP2,3_prime_UTR_variant,,ENST00000523969,;CYFIP2,3_prime_UTR_variant,,ENST00000519002,;CYFIP2,3_prime_UTR_variant,,ENST00000522423,;CYFIP2,3_prime_UTR_variant,,ENST00000519153,;CYFIP2,3_prime_UTR_variant,,ENST00000517753,;CYFIP2,3_prime_UTR_variant,,ENST00000522637,;CYFIP2,3_prime_UTR_variant,,ENST00000519252,;CYFIP2,3_prime_UTR_variant,,ENST00000520759,;CYFIP2,3_prime_UTR_variant,,ENST00000520419,;CYFIP2,intron_variant,,ENST00000523119,;CYFIP2,upstream_gene_variant,,ENST00000518511,;	C	ENSG00000055163	ENST00000521420	Transcript	synonymous_variant	475	384	128	S	tcT/tcC	.	.	.	1	CYFIP2	HGNC	13760	protein_coding	YES	.	ENSP00000430904	.	E7EVJ5_HUMAN	UPI0001D55E6B	.	.	.	5/30	.	hmmpanther:PTHR12195,hmmpanther:PTHR12195:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTCTGAGGC	.	5	ESCA
TRIM41	0	.	GRCh37	5	180661650	180661657	+	Frame_Shift_Del	DEL	CTGGGCTT	CTGGGCTT	-	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	CTGGGCTT	CTGGGCTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1770_1777delGGGCTTCT	p.Gly591GlnfsTer61	p.G591Qfs*61	ENST00000315073	6/6	51	43	8	64	64	0	TRIM41,frameshift_variant,p.Gly591GlnfsTer61,ENST00000315073,;TRIM41,intron_variant,,ENST00000351937,;GNB2L1,downstream_gene_variant,,ENST00000511900,;GNB2L1,downstream_gene_variant,,ENST00000509148,;GNB2L1,downstream_gene_variant,,ENST00000504128,;GNB2L1,downstream_gene_variant,,ENST00000503081,;GNB2L1,downstream_gene_variant,,ENST00000513027,;GNB2L1,downstream_gene_variant,,ENST00000504726,;GNB2L1,downstream_gene_variant,,ENST00000514455,;GNB2L1,downstream_gene_variant,,ENST00000512968,;GNB2L1,downstream_gene_variant,,ENST00000502844,;GNB2L1,downstream_gene_variant,,ENST00000502905,;TRIM41,downstream_gene_variant,,ENST00000515499,;GNB2L1,downstream_gene_variant,,ENST00000507756,;GNB2L1,downstream_gene_variant,,ENST00000376817,;GNB2L1,downstream_gene_variant,,ENST00000509535,;GNB2L1,downstream_gene_variant,,ENST00000511566,;GNB2L1,downstream_gene_variant,,ENST00000507000,;GNB2L1,downstream_gene_variant,,ENST00000510199,;GNB2L1,downstream_gene_variant,,ENST00000512805,;CTC-338M12.7,upstream_gene_variant,,ENST00000499096,;TRIM41,non_coding_transcript_exon_variant,,ENST00000510072,;TRIM41,non_coding_transcript_exon_variant,,ENST00000515223,;TRIM41,non_coding_transcript_exon_variant,,ENST00000508930,;TRIM41,intron_variant,,ENST00000503114,;TRIM41,intron_variant,,ENST00000514219,;GNB2L1,downstream_gene_variant,,ENST00000514183,;GNB2L1,downstream_gene_variant,,ENST00000507273,;GNB2L1,downstream_gene_variant,,ENST00000508682,;GNB2L1,downstream_gene_variant,,ENST00000503494,;GNB2L1,downstream_gene_variant,,ENST00000504325,;GNB2L1,downstream_gene_variant,,ENST00000502548,;TRIM41,downstream_gene_variant,,ENST00000515834,;GNB2L1,downstream_gene_variant,,ENST00000508044,;GNB2L1,downstream_gene_variant,,ENST00000506312,;GNB2L1,downstream_gene_variant,,ENST00000513060,;GNB2L1,downstream_gene_variant,,ENST00000515417,;GNB2L1,downstream_gene_variant,,ENST00000502890,;GNB2L1,downstream_gene_variant,,ENST00000511473,;	-	ENSG00000146063	ENST00000315073	Transcript	frameshift_variant	2478-2485	1768-1775	590-592	LGF/X	CTGGGCTTc/c	.	.	.	1	TRIM41	HGNC	19013	protein_coding	YES	CCDS4466.1	ENSP00000320869	TRI41_HUMAN	D6REK2_HUMAN	UPI00001B248B	.	.	.	6/6	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF286,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGGCGCCTGGGCTTCTACA	.	3	ESCA
CDH12	0	.	GRCh37	5	21802277	21802277	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1255A>G	p.Arg419Gly	p.R419G	ENST00000382254	10/15	46	29	16	41	41	0	CDH12,missense_variant,p.Arg379Gly,ENST00000522262,;CDH12,missense_variant,p.Arg419Gly,ENST00000504376,;CDH12,missense_variant,p.Arg419Gly,ENST00000382254,;CDH12,splice_region_variant,,ENST00000521384,;CDH12,splice_region_variant,,ENST00000517378,;	C	ENSG00000154162	ENST00000382254	Transcript	missense_variant	2342	1255	419	R/G	Agg/Ggg	.	.	.	-1	CDH12	HGNC	1751	protein_coding	YES	CCDS3890.1	ENSP00000371689	CAD12_HUMAN	B3KRT0_HUMAN	UPI00000622EB	.	deleterious(0.01)	possibly_damaging(0.873)	10/15	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCTAACAG	.	5	ESCA
AGXT2	0	.	GRCh37	5	35013131	35013131	+	Silent	SNP	C	C	T	.	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1116G>A	p.%3D	p.A372A	ENST00000231420	11/14	61	36	24	72	72	0	AGXT2,synonymous_variant,p.%3D,ENST00000231420,;AGXT2,non_coding_transcript_exon_variant,,ENST00000512135,;AGXT2,non_coding_transcript_exon_variant,,ENST00000505349,;AGXT2,intron_variant,,ENST00000510428,;	T	ENSG00000113492	ENST00000231420	Transcript	synonymous_variant	1317	1116	372	A	gcG/gcA	COSM449575	.	.	-1	AGXT2	HGNC	14412	protein_coding	YES	CCDS3908.1	ENSP00000231420	AGT2_HUMAN	.	UPI0000125709	.	.	.	11/14	.	Superfamily_domains:SSF53383,PIRSF_domain:PIRSF000521,Pfam_domain:PF00202,Gene3D:3.40.640.10,hmmpanther:PTHR11986,hmmpanther:PTHR11986:SF58	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A372A|c.1116G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTCGCCAA	.	5	ESCA
DEPDC1B	0	.	GRCh37	5	59892880	59892880	+	3'UTR	SNP	A	A	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*700T>G	.	.	ENST00000265036	11/11	90	53	37	87	87	0	DEPDC1B,3_prime_UTR_variant,,ENST00000265036,;DEPDC1B,downstream_gene_variant,,ENST00000453022,;DEPDC1B,downstream_gene_variant,,ENST00000545085,;DEPDC1B,downstream_gene_variant,,ENST00000512078,;	C	ENSG00000035499	ENST00000265036	Transcript	3_prime_UTR_variant	2358	.	.	.	.	.	.	.	-1	DEPDC1B	HGNC	24902	protein_coding	YES	CCDS3977.1	ENSP00000265036	DEP1B_HUMAN	.	UPI000020C7D4	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGAATTTAT	.	5	ESCA
ERAP1	0	.	GRCh37	5	96097652	96097652	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1252T>A	.	.	ENST00000296754	20/20	87	47	39	81	81	0	ERAP1,3_prime_UTR_variant,,ENST00000296754,;CAST,intron_variant,,ENST00000508608,;CAST,intron_variant,,ENST00000395813,;CAST,intron_variant,,ENST00000511049,;CAST,intron_variant,,ENST00000508579,;CAST,intron_variant,,ENST00000508830,;CAST,intron_variant,,ENST00000325674,;CAST,intron_variant,,ENST00000510756,;CAST,intron_variant,,ENST00000511782,;CAST,intron_variant,,ENST00000510156,;CAST,intron_variant,,ENST00000359176,;CAST,intron_variant,,ENST00000395812,;CAST,intron_variant,,ENST00000309190,;CAST,intron_variant,,ENST00000509903,;CAST,intron_variant,,ENST00000341926,;CAST,intron_variant,,ENST00000510500,;CAST,intron_variant,,ENST00000338252,;CAST,intron_variant,,ENST00000437034,;CAST,intron_variant,,ENST00000515663,;CAST,intron_variant,,ENST00000504465,;CAST,intron_variant,,ENST00000348386,;CAST,intron_variant,,ENST00000484552,;CAST,intron_variant,,ENST00000510098,;	T	ENSG00000164307	ENST00000296754	Transcript	3_prime_UTR_variant	4357	.	.	.	.	.	.	.	-1	ERAP1	HGNC	18173	protein_coding	YES	CCDS4085.1	ENSP00000296754	ERAP1_HUMAN	D6RAL9_HUMAN	UPI000045731D	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGAGCAAT	.	5	ESCA
ROS1	0	.	GRCh37	6	117704507	117704507	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2469G>T	p.Gln823His	p.Q823H	ENST00000368508	16/43	39	20	19	51	51	0	ROS1,missense_variant,p.Gln818His,ENST00000368507,;ROS1,missense_variant,p.Gln823His,ENST00000368508,;GOPC,intron_variant,,ENST00000467125,;	A	ENSG00000047936	ENST00000368508	Transcript	missense_variant	2668	2469	823	Q/H	caG/caT	.	.	.	-1	ROS1	HGNC	10261	protein_coding	YES	CCDS5116.1	ENSP00000357494	ROS1_HUMAN	.	UPI000013D467	.	tolerated(0.25)	probably_damaging(0.999)	16/43	.	hmmpanther:PTHR24416:SF304,hmmpanther:PTHR24416,Gene3D:2.120.10.30,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGTCTGTAG	.	5	ESCA
HIST1H2AC	0	.	GRCh37	6	26124452	26124452	+	5'UTR	SNP	C	C	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-9C>G	.	.	ENST00000602637	1/2	63	43	19	92	92	0	HIST1H2AC,5_prime_UTR_variant,,ENST00000377791,;HIST1H2AC,5_prime_UTR_variant,,ENST00000602637,;HIST1H2BC,upstream_gene_variant,,ENST00000314332,;HIST1H2BC,upstream_gene_variant,,ENST00000396984,;HIST1H2AC,5_prime_UTR_variant,,ENST00000314088,;	G	ENSG00000180573	ENST00000602637	Transcript	5_prime_UTR_variant	22	.	.	.	.	.	.	.	1	HIST1H2AC	HGNC	4733	protein_coding	YES	CCDS4585.1	ENSP00000473534	H2A1C_HUMAN	.	UPI0000000DB8	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCTGATT	.	5	ESCA
COL9A1	0	.	GRCh37	6	70965094	70965094	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1504-1G>C	.	p.X502_splice	ENST00000357250	.	41	27	14	39	39	0	COL9A1,splice_acceptor_variant,,ENST00000370499,;COL9A1,splice_acceptor_variant,,ENST00000320755,;COL9A1,splice_acceptor_variant,,ENST00000357250,;COL9A1,splice_acceptor_variant,,ENST00000360859,;COL9A1,splice_acceptor_variant,,ENST00000489611,;COL9A1,upstream_gene_variant,,ENST00000447041,;COL9A1,splice_acceptor_variant,,ENST00000493682,;COL9A1,upstream_gene_variant,,ENST00000489861,;	G	ENSG00000112280	ENST00000357250	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	COL9A1	HGNC	2217	protein_coding	YES	CCDS4971.1	ENSP00000349790	CO9A1_HUMAN	.	UPI000020D14B	.	.	.	.	21/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCCTGTAT	.	5	ESCA
EPHB4	0	.	GRCh37	7	100414847	100414847	+	Missense_Mutation	SNP	C	C	T	rs761047725	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555G>A	p.Gly519Ser	p.G519S	ENST00000358173	8/17	178	163	15	149	148	0	EPHB4,missense_variant,p.Gly519Ser,ENST00000360620,;EPHB4,missense_variant,p.Gly519Ser,ENST00000358173,;RN7SL750P,downstream_gene_variant,,ENST00000582814,;EPHB4,intron_variant,,ENST00000477446,;EPHB4,downstream_gene_variant,,ENST00000489808,;EPHB4,non_coding_transcript_exon_variant,,ENST00000487222,;EPHB4,upstream_gene_variant,,ENST00000467515,;EPHB4,downstream_gene_variant,,ENST00000492878,;EPHB4,upstream_gene_variant,,ENST00000478459,;	T	ENSG00000196411	ENST00000358173	Transcript	missense_variant	2024	1555	519	G/S	Ggc/Agc	rs761047725	.	.	-1	EPHB4	HGNC	3395	protein_coding	YES	CCDS5706.1	ENSP00000350896	EPHB4_HUMAN	Q541P7_HUMAN	UPI0000000DBB	.	tolerated(1)	benign(0.01)	8/17	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF296,hmmpanther:PTHR24416,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGGCCGAAGG	byFrequency	3	ESCA
MYL10	0	.	GRCh37	7	101256805	101256805	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>C	p.Asp211His	p.D211H	ENST00000223167	8/8	51	37	14	71	71	0	MYL10,missense_variant,p.Asp211His,ENST00000223167,;	G	ENSG00000106436	ENST00000223167	Transcript	missense_variant	809	631	211	D/H	Gac/Cac	.	.	.	-1	MYL10	HGNC	29825	protein_coding	YES	CCDS34713.1	ENSP00000223167	MYL10_HUMAN	.	UPI00001BBFAD	.	deleterious(0.01)	probably_damaging(0.986)	8/8	.	PROSITE_profiles:PS50222,hmmpanther:PTHR23049,hmmpanther:PTHR23049:SF36,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTAGTCCAGGT	.	3	ESCA
LRRN3	0	.	GRCh37	7	110765259	110765260	+	3'UTR	INS	-	-	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*312dupT	.	.	ENST00000451085	4/4	71	49	22	77	77	0	LRRN3,3_prime_UTR_variant,,ENST00000422987,;LRRN3,3_prime_UTR_variant,,ENST00000451085,;IMMP2L,intron_variant,,ENST00000450877,;IMMP2L,intron_variant,,ENST00000437687,;IMMP2L,intron_variant,,ENST00000415362,;IMMP2L,intron_variant,,ENST00000452895,;IMMP2L,intron_variant,,ENST00000405709,;IMMP2L,intron_variant,,ENST00000447215,;IMMP2L,intron_variant,,ENST00000331762,;LRRN3,downstream_gene_variant,,ENST00000421101,;LRRN3,downstream_gene_variant,,ENST00000308478,;IMMP2L,intron_variant,,ENST00000489381,;	T	ENSG00000173114	ENST00000451085	Transcript	3_prime_UTR_variant	3477-3478	.	.	.	.	.	.	.	1	LRRN3	HGNC	17200	protein_coding	YES	CCDS5754.1	ENSP00000397312	LRRN3_HUMAN	A4D0T1_HUMAN,E7EW58_HUMAN	UPI0000037517	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCTGTATTTTT	.	2	ESCA
WASL	0	.	GRCh37	7	123388731	123388731	+	Missense_Mutation	SNP	G	G	C	rs766540174	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58C>G	p.Leu20Val	p.L20V	ENST00000223023	1/11	192	172	20	222	222	0	WASL,missense_variant,p.Leu20Val,ENST00000223023,;RP11-390E23.6,upstream_gene_variant,,ENST00000607957,;	C	ENSG00000106299	ENST00000223023	Transcript	missense_variant	391	58	20	L/V	Ctg/Gtg	rs766540174	.	.	-1	WASL	HGNC	12735	protein_coding	YES	CCDS34743.1	ENSP00000223023	WASL_HUMAN	.	UPI000013C821	.	tolerated(0.45)	unknown(0)	1/11	.	Gene3D:2.30.29.30,hmmpanther:PTHR12779:SF3,hmmpanther:PTHR12779	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACAGGGACC	.	4	ESCA
PLXNA4	0	.	GRCh37	7	131913111	131913111	+	Silent	SNP	G	G	A	rs759386370	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1722C>T	p.%3D	p.N574N	ENST00000359827	6/32	94	53	41	97	97	0	PLXNA4,synonymous_variant,p.%3D,ENST00000321063,;PLXNA4,synonymous_variant,p.%3D,ENST00000359827,;	A	ENSG00000221866	ENST00000359827	Transcript	synonymous_variant	2685	1722	574	N	aaC/aaT	rs759386370,COSM599242,COSM1085659,COSM1085660,COSM599243	.	.	-1	PLXNA4	HGNC	9102	protein_coding	YES	CCDS43646.1	ENSP00000352882	PLXA4_HUMAN	.	UPI000004E55B	.	.	.	6/32	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.N574N|c.1722C>T|3,SITE|p.N574N|c.1722C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCACGTTGTA	byFrequency	5	ESCA
TMEM178B	0	.	GRCh37	7	141176691	141176691	+	3'UTR	SNP	A	A	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6105A>C	.	.	ENST00000565468	4/4	54	49	5	58	58	0	TMEM178B,3_prime_UTR_variant,,ENST00000565468,;	C	ENSG00000261115	ENST00000565468	Transcript	3_prime_UTR_variant	7069	.	.	.	.	.	.	.	1	TMEM178B	HGNC	44112	protein_coding	YES	CCDS59086.1	ENSP00000456594	T178B_HUMAN	.	UPI0000E217DE	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTCAGGTGT	.	2	ESCA
ESYT2	0	.	GRCh37	7	158526647	158526647	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*251C>T	.	.	ENST00000251527	22/22	57	45	12	48	48	0	ESYT2,3_prime_UTR_variant,,ENST00000435514,;ESYT2,3_prime_UTR_variant,,ENST00000251527,;ESYT2,3_prime_UTR_variant,,ENST00000275418,;	A	ENSG00000117868	ENST00000251527	Transcript	3_prime_UTR_variant	2999	.	.	.	.	.	.	.	-1	ESYT2	HGNC	22211	protein_coding	YES	CCDS34791.1	ENSP00000251527	ESYT2_HUMAN	.	UPI00002339BD	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACAGACACA	.	4	ESCA
TSPAN13	0	.	GRCh37	7	16823720	16823720	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*604G>A	.	.	ENST00000262067	6/6	97	59	37	97	97	0	TSPAN13,3_prime_UTR_variant,,ENST00000262067,;	A	ENSG00000106537	ENST00000262067	Transcript	3_prime_UTR_variant	1652	.	.	.	.	.	.	.	1	TSPAN13	HGNC	21643	protein_coding	YES	CCDS5363.1	ENSP00000262067	TSN13_HUMAN	Q6FGK0_HUMAN	UPI0000048EB9	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTGACTTT	.	5	ESCA
TOMM7	0	.	GRCh37	7	22852721	22852721	+	3'UTR	SNP	C	C	G	rs760881080	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*68G>C	.	.	ENST00000358435	3/3	39	23	16	56	56	0	TOMM7,missense_variant,p.Gly125Arg,ENST00000372879,;TOMM7,3_prime_UTR_variant,,ENST00000358435,;TOMM7,3_prime_UTR_variant,,ENST00000405021,;TOMM7,non_coding_transcript_exon_variant,,ENST00000463284,;TOMM7,non_coding_transcript_exon_variant,,ENST00000483581,;TOMM7,downstream_gene_variant,,ENST00000496129,;	G	ENSG00000196683	ENST00000358435	Transcript	3_prime_UTR_variant	308	.	.	.	.	rs760881080	.	.	-1	TOMM7	HGNC	21648	protein_coding	YES	CCDS5376.1	ENSP00000351214	TOM7_HUMAN	Q75MR5_HUMAN	UPI0000000C34	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATCCGAGCC	.	5	ESCA
IQCE	0	.	GRCh37	7	2645596	2645596	+	Silent	SNP	C	C	T	rs764063887	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1830C>T	p.%3D	p.S610S	ENST00000402050	20/22	146	84	61	108	108	0	IQCE,synonymous_variant,p.%3D,ENST00000404984,;IQCE,synonymous_variant,p.%3D,ENST00000402050,;IQCE,synonymous_variant,p.%3D,ENST00000438376,;IQCE,synonymous_variant,p.%3D,ENST00000325979,;IQCE,synonymous_variant,p.%3D,ENST00000423196,;IQCE,non_coding_transcript_exon_variant,,ENST00000486730,;IQCE,3_prime_UTR_variant,,ENST00000325997,;IQCE,non_coding_transcript_exon_variant,,ENST00000476665,;IQCE,downstream_gene_variant,,ENST00000470731,;	T	ENSG00000106012	ENST00000402050	Transcript	synonymous_variant	2014	1830	610	S	tcC/tcT	rs764063887	.	.	1	IQCE	HGNC	29171	protein_coding	YES	CCDS43542.1	ENSP00000385597	IQCE_HUMAN	C9JX25_HUMAN,C9JP75_HUMAN	UPI000020E9EF	.	.	.	20/22	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50096,hmmpanther:PTHR22590,Pfam_domain:PF00612,SMART_domains:SM00015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCCGCTCT	byFrequency	5	ESCA
SRRM3	0	.	GRCh37	7	75915205	75915205	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*212C>T	.	.	ENST00000326382	15/15	42	38	4	78	78	0	SRRM3,3_prime_UTR_variant,,ENST00000326382,;SRRM3,3_prime_UTR_variant,,ENST00000413003,;SRRM3,3_prime_UTR_variant,,ENST00000388802,;RN7SL212P,upstream_gene_variant,,ENST00000583729,;SRRM3,downstream_gene_variant,,ENST00000479284,;	T	ENSG00000177679	ENST00000326382	Transcript	3_prime_UTR_variant	2213	.	.	.	.	.	.	.	1	SRRM3	HGNC	26729	protein_coding	YES	.	ENSP00000325298	SRRM3_HUMAN	.	UPI0000E5ADAA	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGGCGAGGG	.	4	ESCA
LMTK2	0	.	GRCh37	7	97821009	97821009	+	Missense_Mutation	SNP	G	G	A	rs531778656	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1232G>A	p.Arg411Gln	p.R411Q	ENST00000297293	11/14	51	47	4	41	41	0	LMTK2,missense_variant,p.Arg411Gln,ENST00000297293,;	A	ENSG00000164715	ENST00000297293	Transcript	missense_variant	1525	1232	411	R/Q	cGg/cAg	rs531778656	.	.	1	LMTK2	HGNC	17880	protein_coding	YES	CCDS5654.1	ENSP00000297293	LMTK2_HUMAN	.	UPI000014F277	.	deleterious(0.01)	probably_damaging(0.999)	11/14	.	hmmpanther:PTHR24416:SF265,hmmpanther:PTHR24416,Superfamily_domains:SSF56112	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTGCGGCTGC	by1000G	3	ESCA
XKR6	0	.	GRCh37	8	10756035	10756035	+	Silent	SNP	G	G	A	rs142242465	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1353C>T	p.%3D	p.T451T	ENST00000416569	3/3	35	22	12	47	47	0	XKR6,synonymous_variant,p.%3D,ENST00000304437,;XKR6,synonymous_variant,p.%3D,ENST00000416569,;XKR6,synonymous_variant,p.%3D,ENST00000382461,;	A	ENSG00000171044	ENST00000416569	Transcript	synonymous_variant	1380	1353	451	T	acC/acT	rs142242465	.	.	-1	XKR6	HGNC	27806	protein_coding	YES	CCDS5978.2	ENSP00000416707	XKR6_HUMAN	.	UPI00004C7A9D	.	.	.	3/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR32129:SF7,hmmpanther:PTHR32129,Pfam_domain:PF09815	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCGGTCAA	byCluster|by1000G	5	ESCA
EXT1	0	.	GRCh37	8	118811971	118811971	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2221C>T	p.Arg741Ter	p.R741*	ENST00000378204	11/11	54	35	19	69	69	0	EXT1,stop_gained,p.Arg741Ter,ENST00000378204,;EXT1,downstream_gene_variant,,ENST00000437196,;	A	ENSG00000182197	ENST00000378204	Transcript	stop_gained	3028	2221	741	R/*	Cga/Tga	.	.	.	-1	EXT1	HGNC	3512	protein_coding	YES	CCDS6324.1	ENSP00000367446	EXT1_HUMAN	T2FFJ4_HUMAN,S5Y321_HUMAN,D7RTA7_HUMAN	UPI000012A3A1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTCGGTATT	.	5	ESCA
DLGAP2	0	.	GRCh37	8	1496874	1496874	+	Silent	SNP	C	C	T	rs759970752	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15C>T	p.%3D	p.S5S	ENST00000421627	2/12	20	14	6	35	35	0	DLGAP2,synonymous_variant,p.%3D,ENST00000520901,;DLGAP2,synonymous_variant,p.%3D,ENST00000421627,;	T	ENSG00000198010	ENST00000421627	Transcript	synonymous_variant	149	15	5	S	tcC/tcT	rs759970752	.	.	1	DLGAP2	HGNC	2906	protein_coding	YES	CCDS47760.1	ENSP00000400258	DLGP2_HUMAN	.	UPI000021BFBC	.	.	.	2/12	.	hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCCGGAAG	.	5	ESCA
KCTD9	0	.	GRCh37	8	25287265	25287265	+	3'UTR	SNP	A	A	T	rs183817821	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*108T>A	.	.	ENST00000221200	12/12	51	47	4	53	53	0	KCTD9,3_prime_UTR_variant,,ENST00000221200,;RP11-395I14.2,upstream_gene_variant,,ENST00000523840,;KCTD9,3_prime_UTR_variant,,ENST00000519665,;	T	ENSG00000104756	ENST00000221200	Transcript	3_prime_UTR_variant	1499	.	.	.	.	rs183817821	.	.	-1	KCTD9	HGNC	22401	protein_coding	YES	CCDS6048.1	ENSP00000221200	KCTD9_HUMAN	K7ENB5_HUMAN	UPI00001540AF	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTAAATTT	by1000G	2	ESCA
PTK2B	0	.	GRCh37	8	27296648	27296648	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1744G>T	p.Ala582Ser	p.A582S	ENST00000397501	24/36	53	38	14	76	76	0	PTK2B,missense_variant,p.Ala582Ser,ENST00000338238,;PTK2B,missense_variant,p.Ala582Ser,ENST00000517339,;PTK2B,missense_variant,p.Ala582Ser,ENST00000420218,;PTK2B,missense_variant,p.Ala328Ser,ENST00000397497,;PTK2B,missense_variant,p.Ala582Ser,ENST00000544172,;PTK2B,missense_variant,p.Ala582Ser,ENST00000397501,;PTK2B,missense_variant,p.Ala582Ser,ENST00000346049,;PTK2B,downstream_gene_variant,,ENST00000519512,;PTK2B,downstream_gene_variant,,ENST00000495097,;PTK2B,downstream_gene_variant,,ENST00000461615,;	T	ENSG00000120899	ENST00000397501	Transcript	missense_variant	2552	1744	582	A/S	Gcc/Tcc	.	.	.	1	PTK2B	HGNC	9612	protein_coding	YES	CCDS6057.1	ENSP00000380638	FAK2_HUMAN	E5RK84_HUMAN,E5RJ77_HUMAN,E5RHL2_HUMAN,C9JHV9_HUMAN	UPI000000D9EC	.	deleterious(0)	benign(0.305)	24/36	.	Superfamily_domains:SSF56112,SMART_domains:SM00219,Gene3D:1.10.510.10,Pfam_domain:PF07714,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF94,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAAAGGTGAG	.	5	ESCA
PROSC	0	.	GRCh37	8	37633454	37633454	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616G>T	p.Glu206Ter	p.E206*	ENST00000328195	7/8	48	31	16	60	60	0	PROSC,stop_gained,p.Glu206Ter,ENST00000328195,;PROSC,downstream_gene_variant,,ENST00000523187,;PROSC,downstream_gene_variant,,ENST00000523358,;PROSC,downstream_gene_variant,,ENST00000523521,;PROSC,non_coding_transcript_exon_variant,,ENST00000522808,;PROSC,downstream_gene_variant,,ENST00000518036,;PROSC,downstream_gene_variant,,ENST00000521631,;	T	ENSG00000147471	ENST00000328195	Transcript	stop_gained	683	616	206	E/*	Gag/Tag	.	.	.	1	PROSC	HGNC	9457	protein_coding	YES	CCDS6096.1	ENSP00000333551	PROSC_HUMAN	E5RG77_HUMAN,E5RFX7_HUMAN,D3DSW3_HUMAN	UPI0000131F89	.	.	.	7/8	.	hmmpanther:PTHR10146,Gene3D:3.20.20.10,TIGRFAM_domain:TIGR00044,Pfam_domain:PF01168,PIRSF_domain:PIRSF004848,Superfamily_domains:SSF51419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGGAGGAG	.	5	ESCA
SMC2	0	.	GRCh37	9	106864708	106864708	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874A>C	p.Thr292Pro	p.T292P	ENST00000286398	9/25	102	58	44	74	74	0	SMC2,missense_variant,p.Thr292Pro,ENST00000303219,;SMC2,missense_variant,p.Thr292Pro,ENST00000374793,;SMC2,missense_variant,p.Thr292Pro,ENST00000286398,;SMC2,missense_variant,p.Thr292Pro,ENST00000374787,;SMC2,downstream_gene_variant,,ENST00000440179,;	C	ENSG00000136824	ENST00000286398	Transcript	missense_variant	1162	874	292	T/P	Act/Cct	.	.	.	1	SMC2	HGNC	14011	protein_coding	YES	CCDS35086.1	ENSP00000286398	SMC2_HUMAN	Q5T821_HUMAN	UPI000013DE44	.	tolerated(0.35)	benign(0.217)	9/25	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937:SF9,hmmpanther:PTHR18937,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAACTGGA	.	5	ESCA
PHF2	0	.	GRCh37	9	96441108	96441108	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1150A>T	.	.	ENST00000359246	22/22	45	26	19	69	69	0	PHF2,3_prime_UTR_variant,,ENST00000375376,;PHF2,3_prime_UTR_variant,,ENST00000359246,;	T	ENSG00000197724	ENST00000359246	Transcript	3_prime_UTR_variant	4808	.	.	.	.	.	.	.	1	PHF2	HGNC	8920	protein_coding	YES	CCDS35069.1	ENSP00000352185	PHF2_HUMAN	.	UPI0000211A97	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAGATGGAC	.	5	ESCA
GYG2	0	.	GRCh37	X	2799152	2799152	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1404C>T	p.%3D	p.S468S	ENST00000381163	12/12	34	30	3	45	45	0	GYG2,synonymous_variant,p.%3D,ENST00000381163,;GYG2,synonymous_variant,p.%3D,ENST00000338623,;GYG2,synonymous_variant,p.%3D,ENST00000542787,;GYG2,synonymous_variant,p.%3D,ENST00000398806,;GYG2,downstream_gene_variant,,ENST00000381157,;GYG2,non_coding_transcript_exon_variant,,ENST00000353656,;GYG2,non_coding_transcript_exon_variant,,ENST00000381161,;GYG2,downstream_gene_variant,,ENST00000453106,;	T	ENSG00000056998	ENST00000381163	Transcript	synonymous_variant	1686	1404	468	S	agC/agT	.	.	.	1	GYG2	HGNC	4700	protein_coding	YES	CCDS14121.1	ENSP00000370555	GLYG2_HUMAN	.	UPI000049E10B	.	.	.	12/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11183:SF41,hmmpanther:PTHR11183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTGAGCCCCGA	.	3	ESCA
AWAT1	0	.	GRCh37	X	69455666	69455666	+	Silent	SNP	A	A	G	novel	.	TCGA-L5-A88Z-01A-11D-A36J-09	TCGA-L5-A88Z-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177A>G	p.%3D	p.P59P	ENST00000374521	2/7	58	18	40	85	85	0	AWAT1,synonymous_variant,p.%3D,ENST00000374521,;AWAT1,non_coding_transcript_exon_variant,,ENST00000480702,;	G	ENSG00000204195	ENST00000374521	Transcript	synonymous_variant	218	177	59	P	ccA/ccG	.	.	.	1	AWAT1	HGNC	23252	protein_coding	YES	CCDS35321.1	ENSP00000363645	AWAT1_HUMAN	.	UPI00002122D8	.	.	.	2/7	.	Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCCAGAGCG	.	5	ESCA
PLEKHS1	0	.	GRCh37	10	115515071	115515071	+	Intron	SNP	G	G	A	rs781093639	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.28+7G>A	.	.	ENST00000361048	.	40	34	6	29	29	0	PLEKHS1,splice_region_variant,,ENST00000361048,;PLEKHS1,5_prime_UTR_variant,,ENST00000369312,;	A	ENSG00000148735	ENST00000361048	Transcript	splice_region_variant	.	.	.	.	.	rs781093639	.	.	1	PLEKHS1	HGNC	26285	protein_coding	.	CCDS7583.1	ENSP00000354332	PKHS1_HUMAN	.	UPI00001C1099	.	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCCGAGGGG	byFrequency	5	ESCA
IKZF5	0	.	GRCh37	10	124752339	124752339	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*957G>A	.	.	ENST00000368886	5/5	20	16	4	24	24	0	IKZF5,3_prime_UTR_variant,,ENST00000368886,;PSTK,downstream_gene_variant,,ENST00000368887,;PSTK,downstream_gene_variant,,ENST00000406217,;PSTK,downstream_gene_variant,,ENST00000405485,;PSTK,intron_variant,,ENST00000496079,;PSTK,intron_variant,,ENST00000497219,;IKZF5,downstream_gene_variant,,ENST00000469821,;PSTK,downstream_gene_variant,,ENST00000483455,;IKZF5,downstream_gene_variant,,ENST00000496605,;PSTK,downstream_gene_variant,,ENST00000483755,;PSTK,downstream_gene_variant,,ENST00000465232,;	T	ENSG00000095574	ENST00000368886	Transcript	3_prime_UTR_variant	2538	.	.	.	.	.	.	.	-1	IKZF5	HGNC	14283	protein_coding	YES	CCDS41574.1	ENSP00000357881	IKZF5_HUMAN	.	UPI000006DBBE	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCTCATGTG	.	2	ESCA
MKI67	0	.	GRCh37	10	129903622	129903622	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6482G>A	p.Arg2161Lys	p.R2161K	ENST00000368654	13/15	44	37	7	43	43	0	MKI67,missense_variant,p.Arg2161Lys,ENST00000368654,;MKI67,missense_variant,p.Arg1801Lys,ENST00000368653,;MKI67,upstream_gene_variant,,ENST00000464771,;	T	ENSG00000148773	ENST00000368654	Transcript	missense_variant	6858	6482	2161	R/K	aGg/aAg	.	.	.	-1	MKI67	HGNC	7107	protein_coding	YES	CCDS7659.1	ENSP00000357643	KI67_HUMAN	.	UPI000013DB54	.	tolerated(1)	benign(0.002)	13/15	.	hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF3,Pfam_domain:PF08065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCCTGAAC	.	5	ESCA
KNDC1	0	.	GRCh37	10	135025251	135025251	+	Silent	SNP	C	C	T	rs138202794	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4125C>T	p.%3D	p.A1375A	ENST00000304613	23/30	40	30	9	35	34	1	KNDC1,synonymous_variant,p.%3D,ENST00000304613,;KNDC1,synonymous_variant,p.%3D,ENST00000368572,;KNDC1,downstream_gene_variant,,ENST00000368571,;	T	ENSG00000171798	ENST00000304613	Transcript	synonymous_variant	4146	4125	1375	A	gcC/gcT	rs138202794	.	.	1	KNDC1	HGNC	29374	protein_coding	YES	CCDS7674.1	ENSP00000304437	VKIND_HUMAN	B4DFN0_HUMAN	UPI00003529F7	.	.	.	23/30	.	Superfamily_domains:0041591,Gene3D:2ii0A01,hmmpanther:PTHR21560:SF0,hmmpanther:PTHR21560	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGGGCCGAGGG	byCluster	4	ESCA
TUBGCP2	0	.	GRCh37	10	135098607	135098607	+	Missense_Mutation	SNP	G	G	A	rs561848773	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2090C>T	p.Ser697Leu	p.S697L	ENST00000543663	13/18	75	58	16	83	83	0	TUBGCP2,missense_variant,p.Ser669Leu,ENST00000252936,;TUBGCP2,missense_variant,p.Ser262Leu,ENST00000368562,;TUBGCP2,missense_variant,p.Ser539Leu,ENST00000417178,;TUBGCP2,missense_variant,p.Ser669Leu,ENST00000368563,;TUBGCP2,missense_variant,p.Ser697Leu,ENST00000543663,;TUBGCP2,upstream_gene_variant,,ENST00000477923,;TUBGCP2,missense_variant,p.Ser669Leu,ENST00000482278,;	A	ENSG00000130640	ENST00000543663	Transcript	missense_variant	2130	2090	697	S/L	tCg/tTg	rs561848773	.	.	-1	TUBGCP2	HGNC	18599	protein_coding	YES	CCDS58105.1	ENSP00000446093	GCP2_HUMAN	B3KTU7_HUMAN	UPI00020651C0	.	tolerated(0.09)	benign(0.102)	13/18	.	hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF13,Pfam_domain:PF04130	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCAGCGAGTGC	by1000G	4	ESCA
STAM	0	.	GRCh37	10	17737170	17737170	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658G>T	p.Asp220Tyr	p.D220Y	ENST00000377524	7/14	63	53	10	69	69	0	STAM,missense_variant,p.Asp220Tyr,ENST00000377524,;STAM,missense_variant,p.Asp109Tyr,ENST00000540523,;STAM,missense_variant,p.Asp109Tyr,ENST00000377500,;RP11-390B4.3,downstream_gene_variant,,ENST00000445235,;STAM,non_coding_transcript_exon_variant,,ENST00000494250,;STAM,downstream_gene_variant,,ENST00000445846,;	T	ENSG00000136738	ENST00000377524	Transcript	missense_variant	873	658	220	D/Y	Gac/Tac	.	.	.	1	STAM	HGNC	11357	protein_coding	YES	CCDS7122.1	ENSP00000366746	STAM1_HUMAN	C9J1E5_HUMAN,B4DZT2_HUMAN,A6NMU3_HUMAN	UPI000006E278	.	deleterious(0)	probably_damaging(1)	7/14	.	PROSITE_profiles:PS50002,hmmpanther:PTHR13856:SF26,hmmpanther:PTHR13856,Pfam_domain:PF00018,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00499,Prints_domain:PR00452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATATGACTTT	.	4	ESCA
PARD3	0	.	GRCh37	10	34400148	34400148	+	Silent	SNP	C	C	T	rs533880946	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4020G>A	p.%3D	p.A1340A	ENST00000374789	25/25	64	55	8	43	43	0	PARD3,synonymous_variant,p.%3D,ENST00000545260,;PARD3,synonymous_variant,p.%3D,ENST00000545693,;PARD3,synonymous_variant,p.%3D,ENST00000374788,;PARD3,synonymous_variant,p.%3D,ENST00000374790,;PARD3,synonymous_variant,p.%3D,ENST00000374794,;PARD3,synonymous_variant,p.%3D,ENST00000350537,;PARD3,synonymous_variant,p.%3D,ENST00000374789,;PARD3,synonymous_variant,p.%3D,ENST00000346874,;	T	ENSG00000148498	ENST00000374789	Transcript	synonymous_variant	4346	4020	1340	A	gcG/gcA	rs533880946	.	.	-1	PARD3	HGNC	16051	protein_coding	YES	CCDS7178.1	ENSP00000363921	PARD3_HUMAN	.	UPI0000073A9F	.	.	.	25/25	.	hmmpanther:PTHR16484:SF10,hmmpanther:PTHR16484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCTCGCAAC	byCluster	4	ESCA
PARD3	0	.	GRCh37	10	34649188	34649188	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1708-1G>C	.	p.X570_splice	ENST00000374789	.	32	27	5	20	20	0	PARD3,splice_acceptor_variant,,ENST00000545260,;PARD3,splice_acceptor_variant,,ENST00000545693,;PARD3,splice_acceptor_variant,,ENST00000374788,;PARD3,splice_acceptor_variant,,ENST00000544292,;PARD3,splice_acceptor_variant,,ENST00000340077,;PARD3,splice_acceptor_variant,,ENST00000374790,;PARD3,splice_acceptor_variant,,ENST00000374776,;PARD3,splice_acceptor_variant,,ENST00000374773,;PARD3,splice_acceptor_variant,,ENST00000374794,;PARD3,splice_acceptor_variant,,ENST00000350537,;PARD3,splice_acceptor_variant,,ENST00000374768,;PARD3,splice_acceptor_variant,,ENST00000374789,;PARD3,splice_acceptor_variant,,ENST00000346874,;	G	ENSG00000148498	ENST00000374789	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	PARD3	HGNC	16051	protein_coding	YES	CCDS7178.1	ENSP00000363921	PARD3_HUMAN	.	UPI0000073A9F	.	.	.	.	12/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTTCTAATA	.	4	ESCA
PALD1	0	.	GRCh37	10	72327301	72327301	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*812G>A	.	.	ENST00000263563	20/20	16	12	4	19	19	0	PALD1,3_prime_UTR_variant,,ENST00000263563,;	A	ENSG00000107719	ENST00000263563	Transcript	3_prime_UTR_variant	3651	.	.	.	.	.	.	.	1	PALD1	HGNC	23530	protein_coding	YES	CCDS31215.1	ENSP00000263563	PALD_HUMAN	.	UPI00001C1EDC	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	CCCCCGGCATC	.	3	ESCA
KIF20B	0	.	GRCh37	10	91478507	91478507	+	Missense_Mutation	SNP	C	C	T	rs765780636	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1312C>T	p.His438Tyr	p.H438Y	ENST00000260753	12/33	63	47	16	59	59	0	KIF20B,missense_variant,p.His438Tyr,ENST00000371728,;KIF20B,missense_variant,p.His438Tyr,ENST00000416354,;KIF20B,missense_variant,p.His438Tyr,ENST00000260753,;KIF20B,missense_variant,p.His438Tyr,ENST00000394289,;KIF20B,upstream_gene_variant,,ENST00000478929,;	T	ENSG00000138182	ENST00000260753	Transcript	missense_variant	1384	1312	438	H/Y	Cac/Tac	rs765780636	.	.	1	KIF20B	HGNC	7212	protein_coding	YES	CCDS7407.1	ENSP00000260753	KI20B_HUMAN	.	UPI00001F9377	.	deleterious(0)	probably_damaging(0.986)	12/33	.	PROSITE_profiles:PS50067,hmmpanther:PTHR23165,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACTCACTAT	.	5	ESCA
ABCG4	0	.	GRCh37	11	119025273	119025273	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528G>A	p.%3D	p.V176V	ENST00000307417	5/15	25	22	3	38	38	0	ABCG4,synonymous_variant,p.%3D,ENST00000307417,;ABCG4,synonymous_variant,p.%3D,ENST00000449422,;ABCG4,synonymous_variant,p.%3D,ENST00000531739,;AP002956.1,downstream_gene_variant,,ENST00000599663,;ABCG4,downstream_gene_variant,,ENST00000524604,;ABCG4,upstream_gene_variant,,ENST00000534402,;ABCG4,non_coding_transcript_exon_variant,,ENST00000533694,;	A	ENSG00000172350	ENST00000307417	Transcript	synonymous_variant	892	528	176	V	gtG/gtA	.	.	.	1	ABCG4	HGNC	13884	protein_coding	YES	CCDS8415.1	ENSP00000304111	ABCG4_HUMAN	Q9NT30_HUMAN,E9PJ00_HUMAN	UPI000000D999	.	.	.	5/15	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Gene3D:3.40.50.300,Pfam_domain:PF00005,hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF211,PROSITE_profiles:PS50893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGGTGAAGAA	.	2	ESCA
HSPA8	0	.	GRCh37	11	122928600	122928600	+	Missense_Mutation	SNP	G	G	C	rs776255814	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1783C>G	p.Gln595Glu	p.Q595E	ENST00000534624	9/9	45	29	16	54	53	1	HSPA8,missense_variant,p.Gln359Glu,ENST00000534319,;HSPA8,missense_variant,p.Gln576Glu,ENST00000526110,;HSPA8,missense_variant,p.Gln186Glu,ENST00000524552,;HSPA8,missense_variant,p.Gln595Glu,ENST00000227378,;HSPA8,missense_variant,p.Gln595Glu,ENST00000532636,;HSPA8,missense_variant,p.Gln449Glu,ENST00000533540,;HSPA8,missense_variant,p.Gln147Glu,ENST00000526686,;HSPA8,missense_variant,p.Gln595Glu,ENST00000534624,;HSPA8,intron_variant,,ENST00000453788,;HSPA8,downstream_gene_variant,,ENST00000525463,;HSPA8,downstream_gene_variant,,ENST00000525624,;HSPA8,downstream_gene_variant,,ENST00000528292,;HSPA8,downstream_gene_variant,,ENST00000532182,;HSPA8,downstream_gene_variant,,ENST00000534567,;HSPA8,downstream_gene_variant,,ENST00000530391,;HSPA8,downstream_gene_variant,,ENST00000527387,;HSPA8,downstream_gene_variant,,ENST00000524590,;SNORD14D,downstream_gene_variant,,ENST00000384390,;SNORD14E,downstream_gene_variant,,ENST00000364009,;SNORD14C,downstream_gene_variant,,ENST00000365382,;HSPA8,downstream_gene_variant,,ENST00000526862,;HSPA8,downstream_gene_variant,,ENST00000533238,;HSPA8,non_coding_transcript_exon_variant,,ENST00000532091,;HSPA8,downstream_gene_variant,,ENST00000527983,;HSPA8,downstream_gene_variant,,ENST00000532780,;HSPA8,downstream_gene_variant,,ENST00000531063,;HSPA8,downstream_gene_variant,,ENST00000532167,;	C	ENSG00000109971	ENST00000534624	Transcript	missense_variant	2060	1783	595	Q/E	Caa/Gaa	rs776255814	.	.	-1	HSPA8	HGNC	5241	protein_coding	YES	CCDS8440.1	ENSP00000432083	HSP7C_HUMAN	Q9NZ87_HUMAN,Q96IS6_HUMAN,Q96H53_HUMAN,Q96BE0_HUMAN,E9PS65_HUMAN,E9PQQ4_HUMAN,E9PQK7_HUMAN,E9PPY6_HUMAN,E9PN89_HUMAN,E9PN25_HUMAN,E9PM13_HUMAN,E9PLF4_HUMAN,E9PK54_HUMAN,A8K7Q2_HUMAN	UPI0000000801	.	tolerated_low_confidence(0.07)	benign(0.357)	9/9	.	hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF156,Pfam_domain:PF00012,Gene3D:1.20.1270.10,Superfamily_domains:SSF100934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTGATGTT	byFrequency	5	ESCA
ABCC8	0	.	GRCh37	11	17434248	17434248	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2521C>T	p.Arg841Ter	p.R841*	ENST00000389817	21/39	26	17	9	19	19	0	ABCC8,stop_gained,p.Arg841Ter,ENST00000389817,;ABCC8,stop_gained,p.Arg842Ter,ENST00000302539,;ABCC8,stop_gained,p.Arg831Ter,ENST00000527905,;ABCC8,non_coding_transcript_exon_variant,,ENST00000531911,;ABCC8,non_coding_transcript_exon_variant,,ENST00000530147,;ABCC8,non_coding_transcript_exon_variant,,ENST00000529967,;ABCC8,non_coding_transcript_exon_variant,,ENST00000526921,;	A	ENSG00000006071	ENST00000389817	Transcript	stop_gained	2590	2521	841	R/*	Cga/Tga	CM011258,CM086758,COSM3666885	.	.	-1	ABCC8	HGNC	59	protein_coding	YES	CCDS31437.1	ENSP00000374467	ABCC8_HUMAN	.	UPI0000DBEF32	.	.	.	21/39	.	PROSITE_profiles:PS50893,hmmpanther:PTHR24223:SF187,hmmpanther:PTHR24223,PROSITE_patterns:PS00211,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCTCGGGCCA	.	3	ESCA
ART5	0	.	GRCh37	11	3656575	3656575	+	3'Flank	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000397068	.	75	55	20	69	69	0	ART5,downstream_gene_variant,,ENST00000425767,;ART5,downstream_gene_variant,,ENST00000397068,;ART5,downstream_gene_variant,,ENST00000453353,;ART5,downstream_gene_variant,,ENST00000397067,;ART5,downstream_gene_variant,,ENST00000359918,;TRPC2,non_coding_transcript_exon_variant,,ENST00000526541,;TRPC2,intron_variant,,ENST00000451043,;	A	ENSG00000167311	ENST00000397068	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3158	-1	ART5	HGNC	24049	protein_coding	YES	CCDS7743.1	ENSP00000380258	NAR5_HUMAN	.	UPI000013E694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGATCCCTACT	.	5	ESCA
ALKBH3	0	.	GRCh37	11	43904227	43904227	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25C>T	p.Arg9Ter	p.R9*	ENST00000302708	2/10	41	35	6	22	22	0	ALKBH3,stop_gained,p.Arg9Ter,ENST00000302708,;ALKBH3,stop_gained,p.Arg9Ter,ENST00000529366,;ALKBH3,stop_gained,p.Arg9Ter,ENST00000524742,;ALKBH3,stop_gained,p.Arg9Ter,ENST00000378840,;RP11-613D13.5,upstream_gene_variant,,ENST00000528765,;RP11-613D13.5,upstream_gene_variant,,ENST00000530450,;ALKBH3,non_coding_transcript_exon_variant,,ENST00000533200,;ALKBH3,upstream_gene_variant,,ENST00000532410,;ALKBH3,stop_gained,p.Arg9Ter,ENST00000534171,;ALKBH3,stop_gained,p.Arg9Ter,ENST00000532962,;ALKBH3,stop_gained,p.Arg9Ter,ENST00000530803,;ALKBH3,non_coding_transcript_exon_variant,,ENST00000527029,;ALKBH3,upstream_gene_variant,,ENST00000530754,;	T	ENSG00000166199	ENST00000302708	Transcript	stop_gained	436	25	9	R/*	Cga/Tga	.	.	.	1	ALKBH3	HGNC	30141	protein_coding	YES	CCDS7906.1	ENSP00000302232	ALKB3_HUMAN	E9PRD0_HUMAN	UPI0000039EA0	.	.	.	2/10	.	hmmpanther:PTHR31212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCCCGAGTT	.	4	ESCA
OR51A7	0	.	GRCh37	11	4928760	4928760	+	Missense_Mutation	SNP	C	C	T	rs753338342	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161C>T	p.Ser54Leu	p.S54L	ENST00000359350	1/1	43	28	14	56	56	0	OR51A7,missense_variant,p.Ser54Leu,ENST00000359350,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	T	ENSG00000176895	ENST00000359350	Transcript	missense_variant	161	161	54	S/L	tCg/tTg	rs753338342,COSM1746291	.	.	1	OR51A7	HGNC	15188	protein_coding	YES	CCDS31364.1	ENSP00000352305	O51A7_HUMAN	.	UPI0000041C23	.	deleterious(0.01)	benign(0.365)	1/1	.	Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,hmmpanther:PTHR26450:SF114,hmmpanther:PTHR26450,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCGCTTC	byFrequency	5	ESCA
CTNND1	0	.	GRCh37	11	57584990	57584990	+	3'UTR	SNP	G	G	A	rs1803000	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1210G>A	.	.	ENST00000399050	21/21	28	19	9	20	20	0	CTNND1,3_prime_UTR_variant,,ENST00000361796,;CTNND1,3_prime_UTR_variant,,ENST00000532787,;CTNND1,3_prime_UTR_variant,,ENST00000526357,;CTNND1,3_prime_UTR_variant,,ENST00000428599,;CTNND1,3_prime_UTR_variant,,ENST00000533667,;CTNND1,3_prime_UTR_variant,,ENST00000532649,;CTNND1,3_prime_UTR_variant,,ENST00000528232,;CTNND1,3_prime_UTR_variant,,ENST00000529919,;CTNND1,3_prime_UTR_variant,,ENST00000529873,;CTNND1,3_prime_UTR_variant,,ENST00000532844,;CTNND1,3_prime_UTR_variant,,ENST00000531014,;CTNND1,3_prime_UTR_variant,,ENST00000532463,;CTNND1,3_prime_UTR_variant,,ENST00000415361,;CTNND1,3_prime_UTR_variant,,ENST00000530094,;CTNND1,3_prime_UTR_variant,,ENST00000529986,;CTNND1,3_prime_UTR_variant,,ENST00000527467,;CTNND1,3_prime_UTR_variant,,ENST00000532245,;CTNND1,3_prime_UTR_variant,,ENST00000530748,;CTNND1,3_prime_UTR_variant,,ENST00000528621,;CTNND1,3_prime_UTR_variant,,ENST00000361391,;CTNND1,3_prime_UTR_variant,,ENST00000399050,;CTNND1,3_prime_UTR_variant,,ENST00000534579,;CTNND1,3_prime_UTR_variant,,ENST00000529526,;CTNND1,3_prime_UTR_variant,,ENST00000399039,;CTNND1,3_prime_UTR_variant,,ENST00000360682,;CTNND1,3_prime_UTR_variant,,ENST00000524630,;CTNND1,3_prime_UTR_variant,,ENST00000358694,;CTNND1,3_prime_UTR_variant,,ENST00000426142,;CTNND1,3_prime_UTR_variant,,ENST00000526772,;CTNND1,3_prime_UTR_variant,,ENST00000361332,;CTNND1,3_prime_UTR_variant,,ENST00000525902,;CTNND1,downstream_gene_variant,,ENST00000531007,;CTNND1,downstream_gene_variant,,ENST00000526938,;CTNND1,downstream_gene_variant,,ENST00000525821,;	A	ENSG00000198561	ENST00000399050	Transcript	3_prime_UTR_variant	4653	.	.	.	.	rs1803000	.	.	1	CTNND1	HGNC	2515	protein_coding	YES	CCDS44604.1	ENSP00000382004	CTND1_HUMAN	E9PKY0_HUMAN,E9PKL1_HUMAN	UPI000012860B	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAAGAGAAG	.	5	ESCA
OR4D9	0	.	GRCh37	11	59282609	59282609	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224C>T	p.Ser75Phe	p.S75F	ENST00000329328	1/1	80	56	23	57	57	0	OR4D9,missense_variant,p.Ser75Phe,ENST00000329328,;	T	ENSG00000172742	ENST00000329328	Transcript	missense_variant	224	224	75	S/F	tCc/tTc	COSM3869632	.	.	1	OR4D9	HGNC	15178	protein_coding	YES	CCDS31564.1	ENSP00000328563	OR4D9_HUMAN	.	UPI0000061EE8	.	deleterious(0.04)	benign(0.078)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF272,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCCATCA	.	5	ESCA
ILK	0	.	GRCh37	11	6631827	6631827	+	Missense_Mutation	SNP	G	G	C	rs759952356	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1344G>C	p.Lys448Asn	p.K448N	ENST00000396751	12/12	37	24	13	40	40	0	ILK,missense_variant,p.Lys387Asn,ENST00000528995,;ILK,missense_variant,p.Lys448Asn,ENST00000420936,;ILK,missense_variant,p.Lys448Asn,ENST00000396751,;ILK,missense_variant,p.Lys314Asn,ENST00000537806,;ILK,missense_variant,p.Lys448Asn,ENST00000299421,;TAF10,downstream_gene_variant,,ENST00000299424,;TPP1,downstream_gene_variant,,ENST00000533371,;TPP1,downstream_gene_variant,,ENST00000299427,;RP11-732A19.2,upstream_gene_variant,,ENST00000527398,;ILK,splice_region_variant,,ENST00000526318,;ILK,downstream_gene_variant,,ENST00000534706,;ILK,downstream_gene_variant,,ENST00000526711,;ILK,downstream_gene_variant,,ENST00000528784,;TPP1,downstream_gene_variant,,ENST00000524924,;TAF10,downstream_gene_variant,,ENST00000531760,;TPP1,downstream_gene_variant,,ENST00000524611,;ILK,downstream_gene_variant,,ENST00000524735,;TPP1,downstream_gene_variant,,ENST00000532191,;ILK,downstream_gene_variant,,ENST00000530016,;TAF10,downstream_gene_variant,,ENST00000527248,;ILK,3_prime_UTR_variant,,ENST00000527394,;ILK,3_prime_UTR_variant,,ENST00000527327,;ILK,3_prime_UTR_variant,,ENST00000532063,;TAF10,non_coding_transcript_exon_variant,,ENST00000526743,;ILK,downstream_gene_variant,,ENST00000526114,;TAF10,downstream_gene_variant,,ENST00000532344,;ILK,downstream_gene_variant,,ENST00000527121,;	C	ENSG00000166333	ENST00000396751	Transcript	missense_variant	1800	1344	448	K/N	aaG/aaC	rs759952356	.	.	1	ILK	HGNC	6040	protein_coding	YES	CCDS7768.1	ENSP00000379975	ILK_HUMAN	B7Z1I0_HUMAN	UPI0000000DC2	.	deleterious(0)	possibly_damaging(0.886)	12/12	.	PIRSF_domain:PIRSF000654,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGATGCA	.	5	ESCA
RELT	0	.	GRCh37	11	73107274	73107274	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*738G>T	.	.	ENST00000064780	11/11	16	4	12	31	31	0	RELT,3_prime_UTR_variant,,ENST00000064780,;RELT,3_prime_UTR_variant,,ENST00000393580,;FAM168A,downstream_gene_variant,,ENST00000064778,;RP11-809N8.2,non_coding_transcript_exon_variant,,ENST00000544674,;RELT,non_coding_transcript_exon_variant,,ENST00000545886,;RELT,non_coding_transcript_exon_variant,,ENST00000539134,;RELT,downstream_gene_variant,,ENST00000537771,;RELT,downstream_gene_variant,,ENST00000544075,;	T	ENSG00000054967	ENST00000064780	Transcript	3_prime_UTR_variant	2292	.	.	.	.	.	.	.	1	RELT	HGNC	13764	protein_coding	YES	CCDS8222.1	ENSP00000064780	TR19L_HUMAN	F5H2T5_HUMAN	UPI000003C9E6	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTGCCTAC	.	5	ESCA
XRRA1	0	.	GRCh37	11	74638464	74638464	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470T>G	p.Val157Gly	p.V157G	ENST00000340360	7/19	40	35	4	44	44	0	XRRA1,missense_variant,p.Val165Gly,ENST00000525407,;XRRA1,missense_variant,p.Val157Gly,ENST00000527087,;XRRA1,missense_variant,p.Val157Gly,ENST00000340360,;XRRA1,5_prime_UTR_variant,,ENST00000528219,;XRRA1,5_prime_UTR_variant,,ENST00000321448,;XRRA1,intron_variant,,ENST00000531852,;XRRA1,non_coding_transcript_exon_variant,,ENST00000533598,;XRRA1,non_coding_transcript_exon_variant,,ENST00000534798,;XRRA1,intron_variant,,ENST00000534041,;XRRA1,downstream_gene_variant,,ENST00000524430,;XRRA1,downstream_gene_variant,,ENST00000529400,;XRRA1,5_prime_UTR_variant,,ENST00000531849,;XRRA1,intron_variant,,ENST00000530562,;	C	ENSG00000166435	ENST00000340360	Transcript	missense_variant	802	470	157	V/G	gTg/gGg	.	.	.	-1	XRRA1	HGNC	18868	protein_coding	YES	CCDS44680.1	ENSP00000339918	XRRA1_HUMAN	E9PJ58_HUMAN	UPI0001572CC6	.	deleterious(0)	probably_damaging(0.987)	7/19	.	hmmpanther:PTHR22710,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTTCACGTAG	.	3	ESCA
C11orf30	0	.	GRCh37	11	76237670	76237670	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1986G>A	p.%3D	p.G662G	ENST00000529032	12/20	29	26	3	21	21	0	C11orf30,synonymous_variant,p.%3D,ENST00000524451,;C11orf30,synonymous_variant,p.%3D,ENST00000533248,;C11orf30,synonymous_variant,p.%3D,ENST00000524767,;C11orf30,synonymous_variant,p.%3D,ENST00000524490,;C11orf30,synonymous_variant,p.%3D,ENST00000334736,;C11orf30,synonymous_variant,p.%3D,ENST00000525919,;C11orf30,synonymous_variant,p.%3D,ENST00000525038,;C11orf30,synonymous_variant,p.%3D,ENST00000343878,;C11orf30,synonymous_variant,p.%3D,ENST00000529032,;C11orf30,non_coding_transcript_exon_variant,,ENST00000531641,;	A	ENSG00000158636	ENST00000529032	Transcript	synonymous_variant	1986	1986	662	G	ggG/ggA	.	.	.	1	C11orf30	HGNC	18071	protein_coding	YES	CCDS8244.1	ENSP00000432327	EMSY_HUMAN	.	UPI0000071307	.	.	.	12/20	.	hmmpanther:PTHR16500:SF2,hmmpanther:PTHR16500	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAGGGAAAAC	.	2	ESCA
TRIM49	0	.	GRCh37	11	89531759	89531759	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.898A>G	p.Ile300Val	p.I300V	ENST00000329758	8/8	99	79	19	96	96	0	TRIM49,missense_variant,p.Ile223Val,ENST00000532501,;TRIM49,missense_variant,p.Ile300Val,ENST00000329758,;	C	ENSG00000168930	ENST00000329758	Transcript	missense_variant	1227	898	300	I/V	Atc/Gtc	.	.	.	-1	TRIM49	HGNC	13431	protein_coding	YES	CCDS8287.1	ENSP00000327604	TRI49_HUMAN	I1YAQ5_HUMAN	UPI000013431B	.	tolerated(0.16)	benign(0.04)	8/8	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF268,hmmpanther:PTHR24103,Superfamily_domains:SSF49899,Prints_domain:PR01407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGATATCAT	.	5	ESCA
PAH	0	.	GRCh37	12	103238176	103238176	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003A>G	p.Lys335Glu	p.K335E	ENST00000553106	10/13	67	51	16	74	74	0	PAH,missense_variant,p.Lys335Glu,ENST00000553106,;PAH,missense_variant,p.Lys330Glu,ENST00000307000,;PAH,non_coding_transcript_exon_variant,,ENST00000549247,;PAH,non_coding_transcript_exon_variant,,ENST00000551114,;	C	ENSG00000171759	ENST00000553106	Transcript	missense_variant	1476	1003	335	K/E	Aaa/Gaa	.	.	.	-1	PAH	HGNC	8582	protein_coding	YES	CCDS9092.1	ENSP00000448059	PH4H_HUMAN	F8W1D4_HUMAN,F8W0A0_HUMAN	UPI00001318A0	.	deleterious(0.01)	benign(0.043)	10/13	.	Superfamily_domains:SSF56534,PIRSF_domain:PIRSF000336,Pfam_domain:PF00351,TIGRFAM_domain:TIGR01268,Gene3D:1.10.800.10,hmmpanther:PTHR11473,PROSITE_profiles:PS51410	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTTGCAGA	.	5	ESCA
KLRC2	0	.	GRCh37	12	10588462	10588462	+	Missense_Mutation	SNP	C	C	G	rs780702318	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>C	p.Glu42Gln	p.E42Q	ENST00000381902	1/6	148	133	14	111	111	0	KLRC2,missense_variant,p.Glu42Gln,ENST00000381902,;NKG2-E,missense_variant,p.Glu42Gln,ENST00000539033,;KLRC2,missense_variant,p.Glu42Gln,ENST00000381901,;KLRC2,intron_variant,,ENST00000536833,;KLRC2,upstream_gene_variant,,ENST00000537017,;KLRC2,missense_variant,p.Glu15Gln,ENST00000535069,;	G	ENSG00000205809	ENST00000381902	Transcript	missense_variant	131	124	42	E/Q	Gaa/Caa	rs780702318,COSM117980	.	.	-1	KLRC2	HGNC	6375	protein_coding	YES	CCDS31745.1	ENSP00000371327	NKG2C_HUMAN	.	UPI0000140823	.	deleterious(0)	possibly_damaging(0.836)	1/6	.	hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF162	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAATTCTACTT	.	4	ESCA
ATXN2	0	.	GRCh37	12	111958776	111958776	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1178C>G	p.Ser393Cys	p.S393C	ENST00000377617	7/25	48	35	12	37	37	0	ATXN2,missense_variant,p.Ser136Cys,ENST00000548492,;ATXN2,missense_variant,p.Ser128Cys,ENST00000542287,;ATXN2,missense_variant,p.Ser104Cys,ENST00000535949,;ATXN2,missense_variant,p.Ser128Cys,ENST00000389153,;ATXN2,missense_variant,p.Ser233Cys,ENST00000608853,;ATXN2,missense_variant,p.Ser393Cys,ENST00000550104,;ATXN2,missense_variant,p.Ser393Cys,ENST00000377617,;ATXN2,upstream_gene_variant,,ENST00000550236,;ATXN2,upstream_gene_variant,,ENST00000492467,;ATXN2,splice_region_variant,,ENST00000549455,;ATXN2,upstream_gene_variant,,ENST00000481331,;ATXN2,missense_variant,p.Ser314Cys,ENST00000483311,;ATXN2,splice_region_variant,,ENST00000392645,;ATXN2,splice_region_variant,,ENST00000471866,;	C	ENSG00000204842	ENST00000377617	Transcript	missense_variant	1340	1178	393	S/C	tCt/tGt	.	.	.	-1	ATXN2	HGNC	10555	protein_coding	YES	CCDS31902.1	ENSP00000366843	ATX2_HUMAN	D2CTA6_HUMAN,D2CTA5_HUMAN,D2CTA3_HUMAN	UPI0000DBEEFC	.	.	probably_damaging(0.95)	7/25	.	hmmpanther:PTHR12854,hmmpanther:PTHR12854:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTAGACTAG	.	5	ESCA
NAA25	0	.	GRCh37	12	112509837	112509837	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.898delG	p.Glu300LysfsTer4	p.E300Kfs*4	ENST00000261745	10/24	39	35	4	34	34	0	NAA25,frameshift_variant,p.Glu300LysfsTer4,ENST00000261745,;Y_RNA,downstream_gene_variant,,ENST00000363818,;NAA25,3_prime_UTR_variant,,ENST00000549711,;NAA25,3_prime_UTR_variant,,ENST00000551858,;NAA25,non_coding_transcript_exon_variant,,ENST00000552527,;	-	ENSG00000111300	ENST00000261745	Transcript	frameshift_variant	1147	898	300	E/X	Gaa/aa	.	.	.	-1	NAA25	HGNC	25783	protein_coding	YES	CCDS9159.1	ENSP00000261745	NAA25_HUMAN	.	UPI00001FBB50	.	.	.	10/24	.	hmmpanther:PTHR22767,hmmpanther:PTHR22767:SF3,Pfam_domain:PF09797	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTTTTCTGCAG	.	3	ESCA
RBM19	0	.	GRCh37	12	114397134	114397134	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454G>A	p.Asp152Asn	p.D152N	ENST00000545145	5/25	48	43	5	44	44	0	RBM19,missense_variant,p.Asp152Asn,ENST00000545145,;RBM19,missense_variant,p.Asp152Asn,ENST00000392561,;RBM19,missense_variant,p.Asp152Asn,ENST00000261741,;RBM19,intron_variant,,ENST00000546876,;	T	ENSG00000122965	ENST00000545145	Transcript	missense_variant	533	454	152	D/N	Gat/Aat	.	.	.	-1	RBM19	HGNC	29098	protein_coding	YES	CCDS9172.1	ENSP00000442053	RBM19_HUMAN	.	UPI000013D1EC	.	deleterious(0.02)	probably_damaging(0.994)	5/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCATCATTCG	.	3	ESCA
PRB2	0	.	GRCh37	12	11546807	11546807	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205C>G	p.Gln69Glu	p.Q69E	ENST00000389362	3/4	130	111	19	107	107	0	PRB2,missense_variant,p.Gln69Glu,ENST00000389362,;PRB1,intron_variant,,ENST00000546254,;PRB2,downstream_gene_variant,,ENST00000565533,;PRB2,downstream_gene_variant,,ENST00000545829,;	C	ENSG00000121335	ENST00000389362	Transcript	missense_variant	241	205	69	Q/E	Caa/Gaa	.	.	.	-1	PRB2	HGNC	9338	protein_coding	YES	CCDS41757.2	ENSP00000374013	PRB2_HUMAN	.	UPI0000EE5993	.	tolerated(0.06)	unknown(0)	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23203,hmmpanther:PTHR23203:SF2,Pfam_domain:PF15240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P50P|c.150C>T|3,BUFFER|p.P71P|c.213C>T|3	RADIA|MUTECT|MUSE|VARSCANS	ACCTTGAGGCT	.	4	ESCA
NOC4L	0	.	GRCh37	12	132629510	132629510	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.229G>A	p.Val77Ile	p.V77I	ENST00000330579	2/15	57	40	17	50	50	0	NOC4L,missense_variant,p.Val77Ile,ENST00000330579,;NOC4L,missense_variant,p.Val2Ile,ENST00000541954,;DDX51,upstream_gene_variant,,ENST00000397333,;NOC4L,upstream_gene_variant,,ENST00000535343,;DDX51,upstream_gene_variant,,ENST00000329073,;DDX51,upstream_gene_variant,,ENST00000462829,;DDX51,upstream_gene_variant,,ENST00000541489,;DDX51,upstream_gene_variant,,ENST00000545991,;DDX51,upstream_gene_variant,,ENST00000546058,;	A	ENSG00000184967	ENST00000330579	Transcript	missense_variant	270	229	77	V/I	Gtc/Atc	.	.	.	1	NOC4L	HGNC	28461	protein_coding	YES	CCDS9277.1	ENSP00000328854	NOC4L_HUMAN	F5H5K6_HUMAN	UPI00000723C4	.	tolerated(0.32)	benign(0.071)	2/15	.	hmmpanther:PTHR12455:SF0,hmmpanther:PTHR12455	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGGTCATG	.	5	ESCA
POLE	0	.	GRCh37	12	133219481	133219481	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4653C>T	p.%3D	p.H1551H	ENST00000320574	36/49	25	14	11	24	24	0	POLE,synonymous_variant,p.%3D,ENST00000320574,;POLE,synonymous_variant,p.%3D,ENST00000535270,;POLE,upstream_gene_variant,,ENST00000434528,;POLE,3_prime_UTR_variant,,ENST00000537064,;POLE,upstream_gene_variant,,ENST00000542362,;POLE,upstream_gene_variant,,ENST00000541213,;	A	ENSG00000177084	ENST00000320574	Transcript	synonymous_variant	4697	4653	1551	H	caC/caT	COSM1605832,COSM1605833	.	.	-1	POLE	HGNC	9177	protein_coding	YES	CCDS9278.1	ENSP00000322570	DPOE1_HUMAN	Q9UNE8_HUMAN,Q96IE1_HUMAN,Q8WU23_HUMAN,F5H7H6_HUMAN,F5H5Q5_HUMAN,F5H3W5_HUMAN,F5H0H8_HUMAN,D3DXI9_HUMAN	UPI00001FBF97	.	.	.	36/49	.	hmmpanther:PTHR10670,hmmpanther:PTHR10670:SF0,Pfam_domain:PF08490	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGTGTGTTT	.	5	ESCA
GOLGA3	0	.	GRCh37	12	133365747	133365747	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2677G>C	p.Glu893Gln	p.E893Q	ENST00000204726	13/24	32	26	6	29	29	0	GOLGA3,missense_variant,p.Glu893Gln,ENST00000204726,;GOLGA3,missense_variant,p.Glu893Gln,ENST00000537452,;GOLGA3,missense_variant,p.Glu893Gln,ENST00000450791,;GOLGA3,missense_variant,p.Glu893Gln,ENST00000456883,;GOLGA3,missense_variant,p.Glu893Gln,ENST00000545875,;	G	ENSG00000090615	ENST00000204726	Transcript	missense_variant	3236	2677	893	E/Q	Gag/Cag	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	tolerated(0.08)	possibly_damaging(0.877)	13/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902:SF20,hmmpanther:PTHR18902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTCCCCGT	.	5	ESCA
GOLGA3	0	.	GRCh37	12	133365805	133365805	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2619G>T	p.Arg873Ser	p.R873S	ENST00000204726	13/24	32	25	6	41	41	0	GOLGA3,missense_variant,p.Arg873Ser,ENST00000204726,;GOLGA3,missense_variant,p.Arg873Ser,ENST00000537452,;GOLGA3,missense_variant,p.Arg873Ser,ENST00000450791,;GOLGA3,missense_variant,p.Arg873Ser,ENST00000456883,;GOLGA3,missense_variant,p.Arg873Ser,ENST00000545875,;	A	ENSG00000090615	ENST00000204726	Transcript	missense_variant	3178	2619	873	R/S	agG/agT	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	deleterious(0)	benign(0.209)	13/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902:SF20,hmmpanther:PTHR18902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCCTGGT	.	5	ESCA
SLCO1C1	0	.	GRCh37	12	20903690	20903690	+	Missense_Mutation	SNP	G	G	C	rs757439490	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1880G>C	p.Arg627Thr	p.R627T	ENST00000381552	14/15	58	43	15	55	55	0	SLCO1C1,missense_variant,p.Arg627Thr,ENST00000381552,;SLCO1C1,missense_variant,p.Arg627Thr,ENST00000545604,;SLCO1C1,missense_variant,p.Arg509Thr,ENST00000545102,;SLCO1C1,missense_variant,p.Arg627Thr,ENST00000266509,;SLCO1C1,missense_variant,p.Arg578Thr,ENST00000540354,;SLCO1C1,3_prime_UTR_variant,,ENST00000539415,;	C	ENSG00000139155	ENST00000381552	Transcript	missense_variant	2248	1880	627	R/T	aGa/aCa	rs757439490	.	.	1	SLCO1C1	HGNC	13819	protein_coding	YES	CCDS53757.1	ENSP00000370964	SO1C1_HUMAN	.	UPI00004C3E1B	.	deleterious(0.03)	benign(0.297)	14/15	.	hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF18,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTAGAGGAT	.	5	ESCA
ITPR2	0	.	GRCh37	12	26592183	26592183	+	Missense_Mutation	SNP	G	G	C	rs144805961	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6520C>G	p.Arg2174Gly	p.R2174G	ENST00000381340	47/57	97	80	16	73	73	0	ITPR2,missense_variant,p.Arg2174Gly,ENST00000381340,;ITPR2,3_prime_UTR_variant,,ENST00000451599,;	C	ENSG00000123104	ENST00000381340	Transcript	missense_variant	6937	6520	2174	R/G	Cga/Gga	rs144805961	.	.	-1	ITPR2	HGNC	6181	protein_coding	YES	CCDS41764.1	ENSP00000370744	ITPR2_HUMAN	I1VE21_HUMAN	UPI00001FB7D2	.	tolerated(0.12)	benign(0.008)	47/57	.	hmmpanther:PTHR13715	C:0.0004	C:0	C:0	.	C:0.002	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCGAGTGA	byFrequency|byCluster|by1000G	5	ESCA
CACNA1C	0	.	GRCh37	12	2787022	2787022	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5224G>A	p.Asp1742Asn	p.D1742N	ENST00000347598	43/49	59	52	7	39	39	0	CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399644,;CACNA1C,missense_variant,p.Asp1702Asn,ENST00000399595,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000406454,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399617,;CACNA1C,missense_variant,p.Asp1742Asn,ENST00000347598,;CACNA1C,missense_variant,p.Asp1713Asn,ENST00000402845,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000327702,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399634,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399641,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399603,;CACNA1C,missense_variant,p.Asp1711Asn,ENST00000399629,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399601,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399597,;CACNA1C,missense_variant,p.Asp1694Asn,ENST00000399655,;CACNA1C,missense_variant,p.Asp1714Asn,ENST00000399606,;CACNA1C,missense_variant,p.Asp1713Asn,ENST00000399637,;CACNA1C,missense_variant,p.Asp1719Asn,ENST00000335762,;CACNA1C,missense_variant,p.Asp1702Asn,ENST00000399591,;CACNA1C,missense_variant,p.Asp1713Asn,ENST00000399621,;CACNA1C,missense_variant,p.Asp1722Asn,ENST00000399638,;CACNA1C,missense_variant,p.Asp1735Asn,ENST00000344100,;CACNA1C,missense_variant,p.Asp1700Asn,ENST00000399649,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000501371,;CACNA1C,downstream_gene_variant,,ENST00000465934,;	A	ENSG00000151067	ENST00000347598	Transcript	missense_variant	5224	5224	1742	D/N	Gac/Aac	COSM3459933,COSM3459931,COSM3459930,COSM3459932,COSM3459934,COSM3459935	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	tolerated(0.11)	benign(0.12)	43/49	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGATGACATC	.	4	ESCA
CCDC91	0	.	GRCh37	12	28515424	28515424	+	Silent	SNP	C	C	T	rs758479417	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630C>T	p.%3D	p.L210L	ENST00000545336	10/16	46	34	12	21	21	0	CCDC91,synonymous_variant,p.%3D,ENST00000381256,;CCDC91,synonymous_variant,p.%3D,ENST00000545336,;CCDC91,synonymous_variant,p.%3D,ENST00000306172,;CCDC91,synonymous_variant,p.%3D,ENST00000539107,;CCDC91,synonymous_variant,p.%3D,ENST00000381259,;CCDC91,intron_variant,,ENST00000540794,;CCDC91,intron_variant,,ENST00000536154,;CCDC91,non_coding_transcript_exon_variant,,ENST00000540401,;CCDC91,non_coding_transcript_exon_variant,,ENST00000539904,;CCDC91,synonymous_variant,p.%3D,ENST00000536442,;CCDC91,synonymous_variant,p.%3D,ENST00000543809,;CCDC91,synonymous_variant,p.%3D,ENST00000545737,;CCDC91,3_prime_UTR_variant,,ENST00000535520,;	T	ENSG00000123106	ENST00000545336	Transcript	synonymous_variant	1049	630	210	L	ctC/ctT	rs758479417	.	.	1	CCDC91	HGNC	24855	protein_coding	YES	CCDS8716.1	ENSP00000438040	CCD91_HUMAN	F5H4N8_HUMAN,F5GZH9_HUMAN,F5GXK6_HUMAN	UPI00001AEE23	.	.	.	10/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCAGCAT	byFrequency	5	ESCA
CPNE8	0	.	GRCh37	12	39170060	39170060	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451G>C	p.Glu151Gln	p.E151Q	ENST00000331366	7/20	184	153	31	176	176	0	CPNE8,missense_variant,p.Glu139Gln,ENST00000360449,;CPNE8,missense_variant,p.Glu151Gln,ENST00000331366,;CPNE8,5_prime_UTR_variant,,ENST00000550863,;	G	ENSG00000139117	ENST00000331366	Transcript	missense_variant	548	451	151	E/Q	Gag/Cag	.	.	.	-1	CPNE8	HGNC	23498	protein_coding	YES	CCDS8733.1	ENSP00000329748	CPNE8_HUMAN	Q86VY2_HUMAN	UPI000015FF59	.	tolerated(0.09)	probably_damaging(0.997)	7/20	.	hmmpanther:PTHR10857:SF9,hmmpanther:PTHR10857,Gene3D:2.60.40.150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTGCTG	.	4	ESCA
MUC19	0	.	GRCh37	12	40921250	40921250	+	Intron	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5783-15114C>A	.	.	ENST00000454784	.	36	28	8	13	13	0	MUC19,intron_variant,,ENST00000454784,;MUC19,upstream_gene_variant,,ENST00000424466,;MUC19,non_coding_transcript_exon_variant,,ENST00000474954,;MUC19,downstream_gene_variant,,ENST00000398702,;	A	ENSG00000205592	ENST00000454784	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MUC19	HGNC	14362	protein_coding	YES	.	ENSP00000476404	.	C9JCE7_HUMAN	UPI0003B927DE	.	.	.	.	49/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATTCAAAAT	.	5	ESCA
TMEM117	0	.	GRCh37	12	44781966	44781966	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1056G>C	p.Leu352Phe	p.L352F	ENST00000266534	8/8	55	44	11	45	45	0	TMEM117,missense_variant,p.Leu352Phe,ENST00000266534,;TMEM117,missense_variant,p.Leu248Phe,ENST00000536799,;TMEM117,3_prime_UTR_variant,,ENST00000551577,;TMEM117,downstream_gene_variant,,ENST00000550495,;TMEM117,non_coding_transcript_exon_variant,,ENST00000546978,;TMEM117,3_prime_UTR_variant,,ENST00000546868,;	C	ENSG00000139173	ENST00000266534	Transcript	missense_variant	1183	1056	352	L/F	ttG/ttC	.	.	.	1	TMEM117	HGNC	25308	protein_coding	YES	CCDS8745.1	ENSP00000266534	TM117_HUMAN	H0YI63_HUMAN	UPI0000037D18	.	tolerated(0.73)	benign(0.136)	8/8	.	hmmpanther:PTHR31226,Pfam_domain:PF15113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTTGAACAG	.	5	ESCA
PLEKHA8P1	0	.	GRCh37	12	45567215	45567215	+	RNA	SNP	C	C	A	rs147039982	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1471G>T	.	.	ENST00000256692	3/3	65	59	6	57	57	0	PLEKHA8P1,non_coding_transcript_exon_variant,,ENST00000256692,;PLEKHA8P1,downstream_gene_variant,,ENST00000545609,;PLEKHA8P1,downstream_gene_variant,,ENST00000550498,;PLEKHA8P1,non_coding_transcript_exon_variant,,ENST00000336399,;	A	ENSG00000134297	ENST00000256692	Transcript	non_coding_transcript_exon_variant	1471	.	.	.	.	rs147039982	.	.	-1	PLEKHA8P1	HGNC	30222	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GATATCCTTTT	byCluster	3	ESCA
NEUROD4	0	.	GRCh37	12	55420518	55420518	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295C>T	p.Arg99Trp	p.R99W	ENST00000242994	2/2	32	28	4	35	35	0	NEUROD4,missense_variant,p.Arg99Trp,ENST00000242994,;	T	ENSG00000123307	ENST00000242994	Transcript	missense_variant	673	295	99	R/W	Cgg/Tgg	COSM4150220	.	.	1	NEUROD4	HGNC	13802	protein_coding	YES	CCDS8886.1	ENSP00000242994	NDF4_HUMAN	Q8IW56_HUMAN	UPI000013CB1E	.	deleterious(0)	probably_damaging(1)	2/2	.	PROSITE_profiles:PS50888,hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF86,Gene3D:4.10.280.10,Pfam_domain:PF00010,PIRSF_domain:PIRSF015618,SMART_domains:SM00353,Superfamily_domains:SSF47459	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGACCCGGATG	.	4	ESCA
NAB2	0	.	GRCh37	12	57485167	57485167	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343C>T	p.Gln115Ter	p.Q115*	ENST00000300131	2/7	50	41	9	27	27	0	NAB2,stop_gained,p.Gln115Ter,ENST00000300131,;NAB2,stop_gained,p.Gln115Ter,ENST00000342556,;NAB2,stop_gained,p.Gln115Ter,ENST00000357680,;STAT6,downstream_gene_variant,,ENST00000537215,;STAT6,downstream_gene_variant,,ENST00000454075,;STAT6,downstream_gene_variant,,ENST00000300134,;STAT6,downstream_gene_variant,,ENST00000543873,;STAT6,downstream_gene_variant,,ENST00000538913,;STAT6,downstream_gene_variant,,ENST00000556155,;NAB2,non_coding_transcript_exon_variant,,ENST00000554718,;NAB2,non_coding_transcript_exon_variant,,ENST00000555857,;TMEM194A,upstream_gene_variant,,ENST00000553654,;NAB2,upstream_gene_variant,,ENST00000554839,;STAT6,downstream_gene_variant,,ENST00000557563,;STAT6,downstream_gene_variant,,ENST00000555222,;	T	ENSG00000166886	ENST00000300131	Transcript	stop_gained	721	343	115	Q/*	Caa/Taa	.	.	.	1	NAB2	HGNC	7627	protein_coding	YES	CCDS8930.1	ENSP00000300131	NAB2_HUMAN	.	UPI000012FC41	.	.	.	2/7	.	hmmpanther:PTHR12623,hmmpanther:PTHR12623:SF6,Pfam_domain:PF04904	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAGTCAACCA	.	4	ESCA
ATP2B1	0	.	GRCh37	12	89984419	89984419	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*342A>G	.	.	ENST00000428670	21/21	36	32	4	41	41	0	ATP2B1,3_prime_UTR_variant,,ENST00000428670,;ATP2B1,3_prime_UTR_variant,,ENST00000359142,;ATP2B1,3_prime_UTR_variant,,ENST00000261173,;ATP2B1,3_prime_UTR_variant,,ENST00000348959,;ATP2B1,downstream_gene_variant,,ENST00000550716,;ATP2B1,downstream_gene_variant,,ENST00000393164,;AC068641.1,upstream_gene_variant,,ENST00000585304,;RP11-981P6.1,intron_variant,,ENST00000552778,;	C	ENSG00000070961	ENST00000428670	Transcript	3_prime_UTR_variant	4462	.	.	.	.	.	.	.	-1	ATP2B1	HGNC	814	protein_coding	YES	CCDS9035.1	ENSP00000392043	AT2B1_HUMAN	Q3L582_HUMAN	UPI000002A436	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CAGTTTTACTC	.	3	ESCA
HAL	0	.	GRCh37	12	96380981	96380981	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915C>G	p.%3D	p.L305L	ENST00000261208	12/21	35	28	7	30	30	0	HAL,synonymous_variant,p.%3D,ENST00000541929,;HAL,synonymous_variant,p.%3D,ENST00000261208,;HAL,synonymous_variant,p.%3D,ENST00000552509,;HAL,synonymous_variant,p.%3D,ENST00000538703,;HAL,downstream_gene_variant,,ENST00000546579,;HAL,downstream_gene_variant,,ENST00000551562,;HAL,3_prime_UTR_variant,,ENST00000544080,;HAL,3_prime_UTR_variant,,ENST00000546999,;HAL,upstream_gene_variant,,ENST00000548636,;HAL,downstream_gene_variant,,ENST00000549376,;	C	ENSG00000084110	ENST00000261208	Transcript	synonymous_variant	1284	915	305	L	ctC/ctG	.	.	.	-1	HAL	HGNC	4806	protein_coding	YES	CCDS9058.1	ENSP00000261208	HUTH_HUMAN	Q2PH61_HUMAN,Q2PH60_HUMAN,Q2PH56_HUMAN	UPI000012CE8E	.	.	.	12/21	.	Superfamily_domains:SSF48557,Pfam_domain:PF00221,Gene3D:1.10.275.10,TIGRFAM_domain:TIGR01225,hmmpanther:PTHR10362,hmmpanther:PTHR10362:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTGATGAGTGC	.	3	ESCA
ZIC2	0	.	GRCh37	13	100638392	100638392	+	3'UTR	SNP	G	G	A	rs13542	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*456G>A	.	.	ENST00000376335	3/3	17	2	15	8	8	0	ZIC2,3_prime_UTR_variant,,ENST00000376335,;ZIC2,downstream_gene_variant,,ENST00000468291,;ZIC2,downstream_gene_variant,,ENST00000477213,;ZIC2,downstream_gene_variant,,ENST00000490085,;ZIC2,downstream_gene_variant,,ENST00000481565,;	A	ENSG00000043355	ENST00000376335	Transcript	3_prime_UTR_variant	2348	.	.	.	.	rs13542	.	.	1	ZIC2	HGNC	12873	protein_coding	YES	CCDS9495.1	ENSP00000365514	ZIC2_HUMAN	.	UPI000013C3DC	.	.	.	3/3	.	.	A:0.3105	A:0.4871	A:0.2608	.	A:0.2669	A:0.2376	A:0.227	.	.	.	.	22863734,22859937	.	.	.	.	MODIFIER	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CTTCCGCCCCT	byFrequency|byCluster|by2Hit2Allele|byHapMap|by1000G	2	ESCA
NALCN	0	.	GRCh37	13	101710386	101710386	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4928T>C	p.Leu1643Pro	p.L1643P	ENST00000251127	43/44	20	17	3	25	25	0	NALCN,missense_variant,p.Leu1643Pro,ENST00000251127,;NALCN-AS1,non_coding_transcript_exon_variant,,ENST00000457843,;	G	ENSG00000102452	ENST00000251127	Transcript	missense_variant	5010	4928	1643	L/P	cTg/cCg	.	.	.	-1	NALCN	HGNC	19082	protein_coding	YES	CCDS9498.1	ENSP00000251127	NALCN_HUMAN	B3KX53_HUMAN,B3KMK1_HUMAN	UPI000004EBBD	.	deleterious(0.02)	benign(0.036)	43/44	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10037:SF176,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTCAGGAGC	.	2	ESCA
FAM155A	0	.	GRCh37	13	108518473	108518473	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472C>G	p.Leu158Val	p.L158V	ENST00000375915	1/3	50	34	15	36	36	0	FAM155A,missense_variant,p.Leu158Val,ENST00000375915,;	C	ENSG00000204442	ENST00000375915	Transcript	missense_variant	611	472	158	L/V	Cta/Gta	.	.	.	-1	FAM155A	HGNC	33877	protein_coding	YES	CCDS32006.1	ENSP00000365080	F155A_HUMAN	.	UPI000045882C	.	tolerated(0.71)	benign(0.218)	1/3	.	hmmpanther:PTHR15819,hmmpanther:PTHR15819:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTAGAAAAA	.	5	ESCA
GJB6	0	.	GRCh37	13	20796168	20796168	+	3'UTR	SNP	G	G	A	rs777860026	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*666C>T	.	.	ENST00000356192	5/5	21	8	13	12	12	0	GJB6,3_prime_UTR_variant,,ENST00000241124,;GJB6,3_prime_UTR_variant,,ENST00000356192,;GJB6,3_prime_UTR_variant,,ENST00000400065,;GJB6,3_prime_UTR_variant,,ENST00000400066,;	A	ENSG00000121742	ENST00000356192	Transcript	3_prime_UTR_variant	2073	.	.	.	.	rs777860026	.	.	-1	GJB6	HGNC	4288	protein_coding	YES	CCDS9291.1	ENSP00000348521	CXB6_HUMAN	.	UPI0000074737	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAATGATTGG	byCluster	5	ESCA
GJB6	0	.	GRCh37	13	20796587	20796587	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247C>T	.	.	ENST00000356192	5/5	64	41	22	44	44	0	GJB6,3_prime_UTR_variant,,ENST00000241124,;GJB6,3_prime_UTR_variant,,ENST00000356192,;GJB6,3_prime_UTR_variant,,ENST00000400065,;GJB6,3_prime_UTR_variant,,ENST00000400066,;	A	ENSG00000121742	ENST00000356192	Transcript	3_prime_UTR_variant	1654	.	.	.	.	.	.	.	-1	GJB6	HGNC	4288	protein_coding	YES	CCDS9291.1	ENSP00000348521	CXB6_HUMAN	.	UPI0000074737	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGGAACCT	.	5	ESCA
SPATA13	0	.	GRCh37	13	24798292	24798292	+	Missense_Mutation	SNP	G	G	A	rs565957473	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1225G>A	p.Val409Ile	p.V409I	ENST00000424834	4/15	57	30	26	63	63	0	SPATA13,missense_variant,p.Val409Ile,ENST00000382108,;SPATA13,missense_variant,p.Val409Ile,ENST00000424834,;SPATA13,intron_variant,,ENST00000382095,;SPATA13,upstream_gene_variant,,ENST00000474317,;RP11-307N16.6,missense_variant,p.Val409Ile,ENST00000382141,;SPATA13,non_coding_transcript_exon_variant,,ENST00000466831,;	A	ENSG00000182957	ENST00000424834	Transcript	missense_variant	1698	1225	409	V/I	Gta/Ata	rs565957473	.	.	1	SPATA13	HGNC	23222	protein_coding	YES	CCDS53857.1	ENSP00000398560	.	J3KQH2_HUMAN	UPI000165C148	.	tolerated_low_confidence(0.05)	benign(0.446)	4/15	.	hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGTATTT	byFrequency|byCluster	5	ESCA
FLT3	0	.	GRCh37	13	28626732	28626732	+	Silent	SNP	G	G	A	rs774682624	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564C>T	p.%3D	p.S188S	ENST00000241453	5/24	53	29	23	47	47	0	FLT3,synonymous_variant,p.%3D,ENST00000241453,;FLT3,synonymous_variant,p.%3D,ENST00000537084,;FLT3,synonymous_variant,p.%3D,ENST00000380982,;FLT3,synonymous_variant,p.%3D,ENST00000380987,;	A	ENSG00000122025	ENST00000241453	Transcript	synonymous_variant	646	564	188	S	agC/agT	rs774682624	.	.	-1	FLT3	HGNC	3765	protein_coding	YES	CCDS31953.1	ENSP00000241453	FLT3_HUMAN	.	UPI00001FC90B	.	.	.	5/24	.	PIRSF_domain:PIRSF000615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAACGCTCTC	byFrequency	5	ESCA
NBEA	0	.	GRCh37	13	35733522	35733522	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3214G>A	p.Asp1072Asn	p.D1072N	ENST00000400445	22/58	56	36	20	49	49	0	NBEA,missense_variant,p.Asp1072Asn,ENST00000400445,;NBEA,missense_variant,p.Asp1072Asn,ENST00000540320,;NBEA,missense_variant,p.Asp1072Asn,ENST00000310336,;NBEA,missense_variant,p.Asp1072Asn,ENST00000379939,;	A	ENSG00000172915	ENST00000400445	Transcript	missense_variant	3748	3214	1072	D/N	Gat/Aat	.	.	.	1	NBEA	HGNC	7648	protein_coding	YES	CCDS45026.1	ENSP00000383295	NBEA_HUMAN	.	UPI00004FF92F	.	tolerated_low_confidence(0.1)	benign(0.004)	22/58	.	hmmpanther:PTHR13743:SF62,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCGATGAT	.	5	ESCA
PPP1R13B	0	.	GRCh37	14	104206306	104206306	+	Missense_Mutation	SNP	G	G	A	rs200606453	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2447C>T	p.Pro816Leu	p.P816L	ENST00000202556	12/17	34	31	3	30	30	0	PPP1R13B,missense_variant,p.Pro235Leu,ENST00000423488,;PPP1R13B,missense_variant,p.Pro816Leu,ENST00000202556,;PPP1R13B,non_coding_transcript_exon_variant,,ENST00000555391,;PPP1R13B,non_coding_transcript_exon_variant,,ENST00000556325,;PPP1R13B,downstream_gene_variant,,ENST00000555991,;PPP1R13B,missense_variant,p.Pro472Leu,ENST00000556597,;PPP1R13B,3_prime_UTR_variant,,ENST00000557082,;PPP1R13B,downstream_gene_variant,,ENST00000557744,;PPP1R13B,upstream_gene_variant,,ENST00000556334,;PPP1R13B,upstream_gene_variant,,ENST00000557587,;PPP1R13B,upstream_gene_variant,,ENST00000554432,;PPP1R13B,upstream_gene_variant,,ENST00000555825,;	A	ENSG00000088808	ENST00000202556	Transcript	missense_variant	2730	2447	816	P/L	cCg/cTg	rs200606453	.	.	-1	PPP1R13B	HGNC	14950	protein_coding	YES	CCDS41997.1	ENSP00000202556	ASPP1_HUMAN	G3V5J1_HUMAN	UPI000049DDC7	.	tolerated(0.2)	benign(0.075)	12/17	.	hmmpanther:PTHR24131,hmmpanther:PTHR24131:SF5	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCCGGCTCG	byCluster	4	ESCA
OR4K14	0	.	GRCh37	14	20483328	20483328	+	Missense_Mutation	SNP	C	C	T	rs745737183	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25G>A	p.Val9Met	p.V9M	ENST00000305045	1/1	40	24	15	26	26	0	OR4K14,missense_variant,p.Val9Met,ENST00000305045,;	T	ENSG00000169484	ENST00000305045	Transcript	missense_variant	25	25	9	V/M	Gtg/Atg	rs745737183	.	.	-1	OR4K14	HGNC	15352	protein_coding	YES	CCDS32027.1	ENSP00000305011	OR4KE_HUMAN	.	UPI0000041CED	.	deleterious(0.01)	benign(0.411)	1/1	.	hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF31,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACACCAAGG	byFrequency	5	ESCA
OR5AU1	0	.	GRCh37	14	21623201	21623201	+	Silent	SNP	G	G	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.984C>A	p.%3D	p.I328I	ENST00000304418	1/1	51	37	14	46	46	0	OR5AU1,synonymous_variant,p.%3D,ENST00000304418,;	T	ENSG00000169327	ENST00000304418	Transcript	synonymous_variant	1022	984	328	I	atC/atA	COSM355379	.	.	-1	OR5AU1	HGNC	15362	protein_coding	YES	CCDS32042.1	ENSP00000302057	O5AU1_HUMAN	.	UPI000015F240	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF186,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTAGATGAC	.	5	ESCA
MMP14	0	.	GRCh37	14	23306043	23306043	+	Missense_Mutation	SNP	G	G	A	rs17884647	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17G>A	p.Arg6Lys	p.R6K	ENST00000311852	1/10	193	150	43	141	141	0	MMP14,missense_variant,p.Arg6Lys,ENST00000547279,;MMP14,missense_variant,p.Arg6Lys,ENST00000311852,;MRPL52,downstream_gene_variant,,ENST00000553711,;MRPL52,downstream_gene_variant,,ENST00000432849,;MRPL52,downstream_gene_variant,,ENST00000557221,;MRPL52,downstream_gene_variant,,ENST00000397505,;MRPL52,downstream_gene_variant,,ENST00000355151,;MRPL52,downstream_gene_variant,,ENST00000556465,;MRPL52,downstream_gene_variant,,ENST00000397496,;MRPL52,downstream_gene_variant,,ENST00000556840,;MRPL52,downstream_gene_variant,,ENST00000555536,;MRPL52,downstream_gene_variant,,ENST00000555345,;MMP14,upstream_gene_variant,,ENST00000548761,;MRPL52,downstream_gene_variant,,ENST00000311892,;MMP14,non_coding_transcript_exon_variant,,ENST00000548162,;MRPL52,downstream_gene_variant,,ENST00000461594,;MRPL52,downstream_gene_variant,,ENST00000556654,;MMP14,non_coding_transcript_exon_variant,,ENST00000547074,;MRPL52,downstream_gene_variant,,ENST00000553965,;MMP14,upstream_gene_variant,,ENST00000547596,;MRPL52,downstream_gene_variant,,ENST00000557543,;	A	ENSG00000157227	ENST00000311852	Transcript	missense_variant	278	17	6	R/K	aGa/aAa	rs17884647	.	.	1	MMP14	HGNC	7160	protein_coding	YES	CCDS9577.1	ENSP00000308208	MMP14_HUMAN	.	UPI0000048136	.	tolerated(0.66)	unknown(0)	1/10	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF24,PIRSF_domain:PIRSF001191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P8S|c.22C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAAGACCCC	.	5	ESCA
AJUBA	0	.	GRCh37	14	23450684	23450685	+	Frame_Shift_Del	DEL	CA	CA	-	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.791_792delTG	p.Val264AspfsTer41	p.V264Dfs*41	ENST00000262713	1/8	21	12	9	20	20	0	AJUBA,frameshift_variant,p.Val264AspfsTer41,ENST00000361265,;AJUBA,frameshift_variant,p.Val38AspfsTer41,ENST00000553736,;AJUBA,frameshift_variant,p.Val264AspfsTer41,ENST00000262713,;RP11-298I3.5,intron_variant,,ENST00000555074,;AJUBA,upstream_gene_variant,,ENST00000553911,;AJUBA,upstream_gene_variant,,ENST00000556731,;AJUBA,upstream_gene_variant,,ENST00000397388,;AJUBA,upstream_gene_variant,,ENST00000553592,;RP11-298I3.4,upstream_gene_variant,,ENST00000555294,;RP11-298I3.4,upstream_gene_variant,,ENST00000556503,;RP11-298I3.4,upstream_gene_variant,,ENST00000557615,;	-	ENSG00000129474	ENST00000262713	Transcript	frameshift_variant	1167-1168	791-792	264	V/X	gTG/g	.	.	.	-1	AJUBA	HGNC	20250	protein_coding	YES	CCDS9581.1	ENSP00000262713	AJUBA_HUMAN	G3V5F5_HUMAN,G3V481_HUMAN	UPI0000040AEC	.	.	.	1/8	.	hmmpanther:PTHR24219,hmmpanther:PTHR24219:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCCGGTCACAGAG	.	2	ESCA
KIAA0391	0	.	GRCh37	14	35596726	35596726	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076A>G	p.Gln359Arg	p.Q359R	ENST00000534898	4/8	89	84	5	64	64	0	KIAA0391,missense_variant,p.Gln264Arg,ENST00000604948,;KIAA0391,missense_variant,p.Gln264Arg,ENST00000250377,;KIAA0391,missense_variant,p.Gln343Arg,ENST00000603544,;KIAA0391,missense_variant,p.Gln359Arg,ENST00000534898,;KIAA0391,missense_variant,p.Gln343Arg,ENST00000321130,;KIAA0391,5_prime_UTR_variant,,ENST00000557404,;KIAA0391,5_prime_UTR_variant,,ENST00000605870,;KIAA0391,downstream_gene_variant,,ENST00000604073,;KIAA0391,downstream_gene_variant,,ENST00000603611,;KIAA0391,downstream_gene_variant,,ENST00000605201,;KIAA0391,non_coding_transcript_exon_variant,,ENST00000603588,;KIAA0391,missense_variant,p.Gln359Arg,ENST00000557565,;	G	ENSG00000100890	ENST00000534898	Transcript	missense_variant	1436	1076	359	Q/R	cAg/cGg	.	.	.	1	KIAA0391	HGNC	19958	protein_coding	YES	CCDS32063.1	ENSP00000440915	MRRP3_HUMAN	S4R416_HUMAN,S4R3T4_HUMAN,S4R3S1_HUMAN	UPI000000CC23	.	deleterious(0.05)	possibly_damaging(0.888)	4/8	.	hmmpanther:PTHR13547,hmmpanther:PTHR13547:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATTCAGCTGA	.	2	ESCA
LRFN5	0	.	GRCh37	14	42077703	42077703	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-259G>A	.	.	ENST00000298119	1/6	93	71	21	70	70	0	LRFN5,5_prime_UTR_variant,,ENST00000298119,;LRFN5,5_prime_UTR_variant,,ENST00000554120,;CTD-2298J14.2,upstream_gene_variant,,ENST00000557067,;LRFN5,non_coding_transcript_exon_variant,,ENST00000555279,;LRFN5,non_coding_transcript_exon_variant,,ENST00000553926,;	A	ENSG00000165379	ENST00000298119	Transcript	5_prime_UTR_variant	931	.	.	.	.	.	.	.	1	LRFN5	HGNC	20360	protein_coding	YES	CCDS9678.1	ENSP00000298119	LRFN5_HUMAN	.	UPI000000DA1E	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGCCGGG	.	5	ESCA
LRFN5	0	.	GRCh37	14	42077704	42077704	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-258C>A	.	.	ENST00000298119	1/6	91	71	20	67	67	0	LRFN5,5_prime_UTR_variant,,ENST00000298119,;LRFN5,5_prime_UTR_variant,,ENST00000554120,;CTD-2298J14.2,upstream_gene_variant,,ENST00000557067,;LRFN5,non_coding_transcript_exon_variant,,ENST00000555279,;LRFN5,non_coding_transcript_exon_variant,,ENST00000553926,;	A	ENSG00000165379	ENST00000298119	Transcript	5_prime_UTR_variant	932	.	.	.	.	.	.	.	1	LRFN5	HGNC	20360	protein_coding	YES	CCDS9678.1	ENSP00000298119	LRFN5_HUMAN	.	UPI000000DA1E	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGCCGGGA	.	5	ESCA
MDGA2	0	.	GRCh37	14	47613337	47613337	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736G>A	p.Val246Ile	p.V246I	ENST00000439988	4/17	74	53	20	58	58	0	MDGA2,missense_variant,p.Val246Ile,ENST00000439988,;MDGA2,missense_variant,p.Val177Ile,ENST00000399232,;MDGA2,5_prime_UTR_variant,,ENST00000357362,;MDGA2,5_prime_UTR_variant,,ENST00000426342,;MDGA2,5_prime_UTR_variant,,ENST00000482848,;MDGA2,5_prime_UTR_variant,,ENST00000557238,;	T	ENSG00000272781	ENST00000439988	Transcript	missense_variant	736	736	246	V/I	Gtc/Atc	.	.	.	-1	MDGA2	Uniprot_gn	19835	protein_coding	YES	.	ENSP00000400011	MDGA2_HUMAN	F8WE89_HUMAN	UPI0001DD21C1	.	tolerated(0.37)	benign(0.004)	4/17	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGACCTCCT	.	5	ESCA
AKAP5	0	.	GRCh37	14	64939527	64939527	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3131G>C	.	.	ENST00000394718	2/2	87	69	18	69	69	0	AKAP5,3_prime_UTR_variant,,ENST00000394718,;ZBTB25,intron_variant,,ENST00000555424,;ZBTB25,intron_variant,,ENST00000555220,;AKAP5,downstream_gene_variant,,ENST00000320636,;	C	ENSG00000179841	ENST00000394718	Transcript	3_prime_UTR_variant	4793	.	.	.	.	.	.	.	1	AKAP5	HGNC	375	protein_coding	YES	CCDS9764.1	ENSP00000378207	AKAP5_HUMAN	.	UPI0000140927	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTGACCTT	.	5	ESCA
GPHN	0	.	GRCh37	14	67291233	67291233	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.243G>C	p.Leu81Phe	p.L81F	ENST00000478722	4/23	51	41	10	31	31	0	GPHN,missense_variant,p.Leu81Phe,ENST00000543237,;GPHN,missense_variant,p.Leu14Phe,ENST00000555456,;GPHN,missense_variant,p.Leu81Phe,ENST00000315266,;GPHN,missense_variant,p.Leu81Phe,ENST00000478722,;GPHN,intron_variant,,ENST00000459628,;GPHN,intron_variant,,ENST00000305960,;GPHN,non_coding_transcript_exon_variant,,ENST00000544752,;GPHN,non_coding_transcript_exon_variant,,ENST00000556020,;GPHN,3_prime_UTR_variant,,ENST00000555668,;GPHN,3_prime_UTR_variant,,ENST00000556633,;GPHN,3_prime_UTR_variant,,ENST00000557654,;GPHN,3_prime_UTR_variant,,ENST00000553936,;	C	ENSG00000171723	ENST00000478722	Transcript	missense_variant	1364	243	81	L/F	ttG/ttC	.	.	.	1	GPHN	HGNC	15465	protein_coding	YES	CCDS9777.1	ENSP00000417901	GEPH_HUMAN	.	UPI0000072592	.	deleterious(0)	probably_damaging(0.997)	4/23	.	hmmpanther:PTHR10192:SF5,hmmpanther:PTHR10192,PROSITE_patterns:PS01078,Pfam_domain:PF00994,Gene3D:3.40.980.10,TIGRFAM_domain:TIGR00177,SMART_domains:SM00852,Superfamily_domains:SSF53218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTGATATT	.	5	ESCA
MAP3K9	0	.	GRCh37	14	71204982	71204982	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1824G>A	p.%3D	p.E608E	ENST00000555993	8/13	38	35	3	40	40	0	MAP3K9,synonymous_variant,p.%3D,ENST00000553414,;MAP3K9,synonymous_variant,p.%3D,ENST00000554146,;MAP3K9,synonymous_variant,p.%3D,ENST00000381250,;MAP3K9,synonymous_variant,p.%3D,ENST00000555993,;MAP3K9,synonymous_variant,p.%3D,ENST00000554752,;	T	ENSG00000006432	ENST00000555993	Transcript	synonymous_variant	2187	1824	608	E	gaG/gaA	.	.	.	-1	MAP3K9	HGNC	6861	protein_coding	YES	CCDS32112.1	ENSP00000451263	M3K9_HUMAN	Q8NEB1_HUMAN,B4DSG3_HUMAN,B4DGF4_HUMAN,B3KRI5_HUMAN	UPI00001D7B5C	.	.	.	8/13	.	PIRSF_domain:PIRSF000556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GCAAGCTCCTT	.	2	ESCA
NUMB	0	.	GRCh37	14	73742091	73742091	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1195G>C	.	.	ENST00000355058	13/13	34	24	10	29	29	0	NUMB,3_prime_UTR_variant,,ENST00000356296,;NUMB,3_prime_UTR_variant,,ENST00000556772,;NUMB,3_prime_UTR_variant,,ENST00000557597,;NUMB,3_prime_UTR_variant,,ENST00000355058,;NUMB,3_prime_UTR_variant,,ENST00000554546,;NUMB,3_prime_UTR_variant,,ENST00000359560,;NUMB,3_prime_UTR_variant,,ENST00000555238,;PAPLN,downstream_gene_variant,,ENST00000559759,;NUMB,downstream_gene_variant,,ENST00000555394,;NUMB,downstream_gene_variant,,ENST00000544991,;PAPLN,downstream_gene_variant,,ENST00000381166,;NUMB,downstream_gene_variant,,ENST00000454166,;NUMB,downstream_gene_variant,,ENST00000554521,;NUMB,downstream_gene_variant,,ENST00000535282,;NUMB,downstream_gene_variant,,ENST00000560335,;PAPLN,downstream_gene_variant,,ENST00000555445,;NUMB,downstream_gene_variant,,ENST00000555738,;PAPLN,downstream_gene_variant,,ENST00000427855,;NUMB,downstream_gene_variant,,ENST00000559312,;PAPLN,downstream_gene_variant,,ENST00000554301,;PAPLN,downstream_gene_variant,,ENST00000340738,;RP4-647C14.3,upstream_gene_variant,,ENST00000556578,;PAPLN,downstream_gene_variant,,ENST00000216658,;PAPLN,downstream_gene_variant,,ENST00000555700,;PAPLN,downstream_gene_variant,,ENST00000554527,;PAPLN,downstream_gene_variant,,ENST00000557061,;NUMB,downstream_gene_variant,,ENST00000554014,;PAPLN,downstream_gene_variant,,ENST00000555123,;	G	ENSG00000133961	ENST00000355058	Transcript	3_prime_UTR_variant	3430	.	.	.	.	.	.	.	-1	NUMB	HGNC	8060	protein_coding	YES	CCDS32116.1	ENSP00000347169	NUMB_HUMAN	Q5D0E5_HUMAN,G3V4S6_HUMAN,G3V3Z8_HUMAN,G3V3R1_HUMAN	UPI00001309BF	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GTTCTCACCAA	.	3	ESCA
TMED10	0	.	GRCh37	14	75601670	75601670	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578C>T	p.Ser193Leu	p.S193L	ENST00000303575	5/5	42	33	9	31	31	0	TMED10,missense_variant,p.Ser193Leu,ENST00000303575,;RP11-950C14.7,intron_variant,,ENST00000556236,;TMED10,non_coding_transcript_exon_variant,,ENST00000557670,;TMED10,3_prime_UTR_variant,,ENST00000555873,;TMED10,non_coding_transcript_exon_variant,,ENST00000556969,;TMED10,non_coding_transcript_exon_variant,,ENST00000555036,;	A	ENSG00000170348	ENST00000303575	Transcript	missense_variant	630	578	193	S/L	tCa/tTa	.	.	.	-1	TMED10	HGNC	16998	protein_coding	YES	CCDS9840.1	ENSP00000303145	TMEDA_HUMAN	B4DZH3_HUMAN	UPI0000137068	.	deleterious(0.02)	benign(0.443)	5/5	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50866,hmmpanther:PTHR22811:SF58,hmmpanther:PTHR22811,Pfam_domain:PF01105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTGAAAAG	.	5	ESCA
FLVCR2	0	.	GRCh37	14	76113997	76113997	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1182C>A	.	.	ENST00000238667	10/10	31	27	4	39	39	0	FLVCR2,3_prime_UTR_variant,,ENST00000238667,;FLVCR2,intron_variant,,ENST00000553587,;FLVCR2,downstream_gene_variant,,ENST00000539311,;FLVCR2,downstream_gene_variant,,ENST00000555027,;C14orf1,downstream_gene_variant,,ENST00000256319,;FLVCR2,downstream_gene_variant,,ENST00000556856,;FLVCR2,intron_variant,,ENST00000555385,;FLVCR2,intron_variant,,ENST00000556241,;TTLL5,intron_variant,,ENST00000554132,;TTLL5,intron_variant,,ENST00000556265,;FLVCR2,downstream_gene_variant,,ENST00000554496,;	A	ENSG00000119686	ENST00000238667	Transcript	3_prime_UTR_variant	3119	.	.	.	.	.	.	.	1	FLVCR2	HGNC	20105	protein_coding	YES	CCDS9844.1	ENSP00000238667	FLVC2_HUMAN	G3V391_HUMAN	UPI0000073CD6	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGATCTTTCC	.	4	ESCA
SNORD116-18	0	.	GRCh37	15	25328575	25328575	+	5'Flank	SNP	G	G	C	rs545397267	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000383961	.	89	80	9	74	74	0	SNORD116-18,upstream_gene_variant,,ENST00000383961,;SNORD116-15,downstream_gene_variant,,ENST00000384445,;SNORD116-19,upstream_gene_variant,,ENST00000384729,;SNORD116-16,downstream_gene_variant,,ENST00000384533,;SNORD116-17,upstream_gene_variant,,ENST00000383929,;SNORD116-20,upstream_gene_variant,,ENST00000567527,;SNORD116-13,downstream_gene_variant,,ENST00000384408,;SNORD116-20,upstream_gene_variant,,ENST00000384529,;SNORD116-14,downstream_gene_variant,,ENST00000383894,;SNHG14,non_coding_transcript_exon_variant,,ENST00000546682,;SNHG14,non_coding_transcript_exon_variant,,ENST00000549804,;SNHG14,upstream_gene_variant,,ENST00000553108,;SNHG14,non_coding_transcript_exon_variant,,ENST00000383025,;	C	ENSG00000206688	ENST00000383961	Transcript	upstream_gene_variant	.	.	.	.	.	rs545397267	.	1957	1	SNORD116-18	HGNC	33084	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	A:0.0024	A:0	A:0	.	A:0	A:0	A:0.0123	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTCGAGGGA	byFrequency|by1000G	4	ESCA
GABRB3	0	.	GRCh37	15	27018791	27018791	+	5'Flank	SNP	C	C	T	rs764425381	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000311550	.	18	14	4	9	9	0	GABRB3,splice_donor_variant,,ENST00000299267,;GABRB3,intron_variant,,ENST00000541819,;GABRB3,upstream_gene_variant,,ENST00000311550,;GABRB3,splice_donor_variant,,ENST00000554722,;GABRB3,intron_variant,,ENST00000557641,;GABRB3,upstream_gene_variant,,ENST00000554556,;GABRB3,upstream_gene_variant,,ENST00000555632,;	T	ENSG00000166206	ENST00000311550	Transcript	upstream_gene_variant	.	.	.	.	.	rs764425381	.	570	-1	GABRB3	HGNC	4083	protein_coding	YES	CCDS10019.1	ENSP00000308725	GBRB3_HUMAN	G3V5B4_HUMAN	UPI000012AFB0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCACCTGCG	byFrequency	4	ESCA
HERC2	0	.	GRCh37	15	28501404	28501404	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2577C>T	p.%3D	p.S859S	ENST00000261609	18/93	123	110	13	77	77	0	HERC2,synonymous_variant,p.%3D,ENST00000261609,;HERC2,3_prime_UTR_variant,,ENST00000564734,;	A	ENSG00000128731	ENST00000261609	Transcript	synonymous_variant	2686	2577	859	S	agC/agT	.	.	.	-1	HERC2	HGNC	4868	protein_coding	YES	CCDS10021.1	ENSP00000261609	HERC2_HUMAN	.	UPI00004578F7	.	.	.	18/93	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATGCTGCC	.	4	ESCA
MGA	0	.	GRCh37	15	42040914	42040914	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5292G>C	p.Leu1764Phe	p.L1764F	ENST00000219905	16/24	49	29	20	61	61	0	MGA,missense_variant,p.Leu412Phe,ENST00000564190,;MGA,missense_variant,p.Leu1764Phe,ENST00000219905,;MGA,missense_variant,p.Leu1764Phe,ENST00000570161,;MGA,missense_variant,p.Leu1555Phe,ENST00000545763,;MGA,missense_variant,p.Leu1555Phe,ENST00000566586,;MGA,splice_region_variant,,ENST00000389936,;MGA,upstream_gene_variant,,ENST00000566288,;	C	ENSG00000174197	ENST00000219905	Transcript	missense_variant	5473	5292	1764	L/F	ttG/ttC	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	deleterious(0)	probably_damaging(0.999)	16/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTGATTCC	.	5	ESCA
MGA	0	.	GRCh37	15	42041585	42041585	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5780G>C	p.Gly1927Ala	p.G1927A	ENST00000219905	17/24	37	24	12	36	36	0	MGA,missense_variant,p.Gly575Ala,ENST00000564190,;MGA,missense_variant,p.Gly1927Ala,ENST00000219905,;MGA,missense_variant,p.Gly1927Ala,ENST00000570161,;MGA,missense_variant,p.Gly1718Ala,ENST00000545763,;MGA,missense_variant,p.Gly1888Ala,ENST00000389936,;MGA,missense_variant,p.Gly1718Ala,ENST00000566586,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,;	C	ENSG00000174197	ENST00000219905	Transcript	missense_variant	5961	5780	1927	G/A	gGa/gCa	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	deleterious(0.01)	benign(0.073)	17/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGGAGGAC	.	5	ESCA
MGA	0	.	GRCh37	15	42041731	42041736	+	Frame_Shift_Del	DEL	GACCAG	GACCAG	CACCA	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	GACCAG	GACCAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5926_5931delGACCAGinsCACCA	p.Asp1976HisfsTer9	p.D1976Hfs*9	ENST00000219905	17/24	27	21	6	26	26	0	MGA,frameshift_variant,p.Asp624HisfsTer9,ENST00000564190,;MGA,frameshift_variant,p.Asp1976HisfsTer9,ENST00000219905,;MGA,frameshift_variant,p.Asp1976HisfsTer9,ENST00000570161,;MGA,frameshift_variant,p.Asp1767HisfsTer9,ENST00000545763,;MGA,frameshift_variant,p.Asp1937HisfsTer9,ENST00000389936,;MGA,frameshift_variant,p.Asp1767HisfsTer9,ENST00000566586,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,;	CACCA	ENSG00000174197	ENST00000219905	Transcript	frameshift_variant	6107-6112	5926-5931	1976-1977	DQ/HX	GACCAG/CACCA	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	.	.	17/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	AATCCAGACCAGAAAGA	.	5	ESCA
MGA	0	.	GRCh37	15	42041908	42041908	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6103G>C	p.Glu2035Gln	p.E2035Q	ENST00000219905	17/24	38	26	11	21	21	0	MGA,missense_variant,p.Glu683Gln,ENST00000564190,;MGA,missense_variant,p.Glu2035Gln,ENST00000219905,;MGA,missense_variant,p.Glu2035Gln,ENST00000570161,;MGA,missense_variant,p.Glu1826Gln,ENST00000545763,;MGA,missense_variant,p.Glu1996Gln,ENST00000389936,;MGA,missense_variant,p.Glu1826Gln,ENST00000566586,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,;	C	ENSG00000174197	ENST00000219905	Transcript	missense_variant	6284	6103	2035	E/Q	Gaa/Caa	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	deleterious_low_confidence(0.04)	benign(0.306)	17/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAAGAATGC	.	5	ESCA
MGA	0	.	GRCh37	15	42042323	42042323	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6518G>T	p.Arg2173Ile	p.R2173I	ENST00000219905	17/24	35	23	11	21	21	0	MGA,missense_variant,p.Arg821Ile,ENST00000564190,;MGA,missense_variant,p.Arg2173Ile,ENST00000219905,;MGA,missense_variant,p.Arg2173Ile,ENST00000570161,;MGA,missense_variant,p.Arg1964Ile,ENST00000545763,;MGA,missense_variant,p.Arg2134Ile,ENST00000389936,;MGA,missense_variant,p.Arg1964Ile,ENST00000566586,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,;	T	ENSG00000174197	ENST00000219905	Transcript	missense_variant	6699	6518	2173	R/I	aGa/aTa	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	deleterious_low_confidence(0.01)	possibly_damaging(0.522)	17/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAAGATGGA	.	5	ESCA
MGA	0	.	GRCh37	15	42042387	42042387	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6582G>A	p.%3D	p.K2194K	ENST00000219905	17/24	33	23	9	15	15	0	MGA,synonymous_variant,p.%3D,ENST00000564190,;MGA,synonymous_variant,p.%3D,ENST00000219905,;MGA,synonymous_variant,p.%3D,ENST00000570161,;MGA,synonymous_variant,p.%3D,ENST00000545763,;MGA,synonymous_variant,p.%3D,ENST00000389936,;MGA,synonymous_variant,p.%3D,ENST00000566586,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,;	A	ENSG00000174197	ENST00000219905	Transcript	synonymous_variant	6763	6582	2194	K	aaG/aaA	.	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	.	.	17/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAAGAAAGA	.	5	ESCA
NARG2	0	.	GRCh37	15	60748894	60748894	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628G>C	p.Glu210Gln	p.E210Q	ENST00000261520	6/16	91	55	36	81	81	0	NARG2,missense_variant,p.Glu210Gln,ENST00000561114,;NARG2,missense_variant,p.Glu210Gln,ENST00000261520,;NARG2,missense_variant,p.Glu210Gln,ENST00000558512,;NARG2,missense_variant,p.Glu73Gln,ENST00000439632,;NARG2,downstream_gene_variant,,ENST00000561087,;NARG2,3_prime_UTR_variant,,ENST00000558181,;NARG2,3_prime_UTR_variant,,ENST00000561446,;NARG2,3_prime_UTR_variant,,ENST00000560895,;NARG2,upstream_gene_variant,,ENST00000561328,;NARG2,downstream_gene_variant,,ENST00000560668,;NARG2,upstream_gene_variant,,ENST00000558451,;	G	ENSG00000128915	ENST00000261520	Transcript	missense_variant	863	628	210	E/Q	Gag/Cag	.	.	.	-1	NARG2	HGNC	29885	protein_coding	YES	CCDS10176.1	ENSP00000261520	NARG2_HUMAN	H0YMX6_HUMAN,H0YL35_HUMAN,H0YK97_HUMAN,H0YK14_HUMAN,G3V0H6_HUMAN,B3KXT2_HUMAN	UPI00001A828C	.	tolerated(0.63)	probably_damaging(0.92)	6/16	.	hmmpanther:PTHR14633:SF3,hmmpanther:PTHR14633	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCTACTC	.	5	ESCA
MAN2C1	0	.	GRCh37	15	75651724	75651724	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2004C>T	p.%3D	p.S668S	ENST00000565683	17/26	69	56	12	47	47	0	MAN2C1,missense_variant,p.Pro565Leu,ENST00000563622,;MAN2C1,missense_variant,p.Pro664Leu,ENST00000267978,;MAN2C1,missense_variant,p.Pro664Leu,ENST00000569482,;MAN2C1,synonymous_variant,p.%3D,ENST00000565683,;NEIL1,downstream_gene_variant,,ENST00000564784,;MAN2C1,downstream_gene_variant,,ENST00000568374,;NEIL1,downstream_gene_variant,,ENST00000355059,;NEIL1,downstream_gene_variant,,ENST00000569035,;RP11-817O13.6,upstream_gene_variant,,ENST00000563660,;MAN2C1,downstream_gene_variant,,ENST00000563539,;MAN2C1,downstream_gene_variant,,ENST00000566253,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563794,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563441,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000566013,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000567163,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000564785,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563368,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000565953,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000569176,;MAN2C1,downstream_gene_variant,,ENST00000421803,;MAN2C1,downstream_gene_variant,,ENST00000565699,;MAN2C1,upstream_gene_variant,,ENST00000566099,;MAN2C1,upstream_gene_variant,,ENST00000561693,;MAN2C1,upstream_gene_variant,,ENST00000566569,;MAN2C1,upstream_gene_variant,,ENST00000567360,;NEIL1,downstream_gene_variant,,ENST00000569758,;MAN2C1,downstream_gene_variant,,ENST00000565784,;MAN2C1,downstream_gene_variant,,ENST00000563058,;MAN2C1,upstream_gene_variant,,ENST00000562067,;MAN2C1,downstream_gene_variant,,ENST00000569355,;MAN2C1,downstream_gene_variant,,ENST00000566634,;MAN2C1,downstream_gene_variant,,ENST00000562461,;MAN2C1,downstream_gene_variant,,ENST00000568944,;MAN2C1,downstream_gene_variant,,ENST00000565801,;MAN2C1,upstream_gene_variant,,ENST00000564570,;MAN2C1,downstream_gene_variant,,ENST00000563596,;NEIL1,downstream_gene_variant,,ENST00000561643,;MAN2C1,downstream_gene_variant,,ENST00000565534,;NEIL1,downstream_gene_variant,,ENST00000565121,;MAN2C1,downstream_gene_variant,,ENST00000563013,;MAN2C1,upstream_gene_variant,,ENST00000564929,;MAN2C1,downstream_gene_variant,,ENST00000570257,;NEIL1,downstream_gene_variant,,ENST00000567393,;MAN2C1,downstream_gene_variant,,ENST00000562228,;MAN2C1,upstream_gene_variant,,ENST00000563528,;	A	ENSG00000140400	ENST00000565683	Transcript	synonymous_variant	2016	2004	668	S	tcC/tcT	.	.	.	-1	MAN2C1	HGNC	6827	protein_coding	YES	CCDS58391.1	ENSP00000457788	MA2C1_HUMAN	H3BRV3_HUMAN	UPI0000229CBC	.	.	.	17/26	.	hmmpanther:PTHR11607:SF15,hmmpanther:PTHR11607,Pfam_domain:PF07748,Superfamily_domains:SSF74650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGGGAGGA	.	5	ESCA
CSPG4	0	.	GRCh37	15	75981846	75981846	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1560G>A	p.%3D	p.L520L	ENST00000308508	3/10	207	124	83	186	186	0	CSPG4,synonymous_variant,p.%3D,ENST00000308508,;	T	ENSG00000173546	ENST00000308508	Transcript	synonymous_variant	1653	1560	520	L	ctG/ctA	.	.	.	-1	CSPG4	HGNC	2466	protein_coding	YES	CCDS10284.1	ENSP00000312506	CSPG4_HUMAN	.	UPI00001AEEB6	.	.	.	3/10	.	hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTCCAGCAC	.	5	ESCA
MRPS11	0	.	GRCh37	15	89018446	89018446	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387G>A	p.%3D	p.Q129Q	ENST00000325844	4/6	78	51	27	60	60	0	MRPS11,synonymous_variant,p.%3D,ENST00000325844,;MRPS11,synonymous_variant,p.%3D,ENST00000353598,;MRPS11,non_coding_transcript_exon_variant,,ENST00000557974,;RP11-97O12.7,intron_variant,,ENST00000561140,;MRPS11,missense_variant,p.Asp109Asn,ENST00000560708,;MRPS11,non_coding_transcript_exon_variant,,ENST00000558548,;MRPS11,non_coding_transcript_exon_variant,,ENST00000559323,;MRPS11,non_coding_transcript_exon_variant,,ENST00000558406,;MRPS11,downstream_gene_variant,,ENST00000559557,;MRPS11,upstream_gene_variant,,ENST00000561262,;MRPS11,downstream_gene_variant,,ENST00000560850,;	A	ENSG00000181991	ENST00000325844	Transcript	synonymous_variant	652	387	129	Q	caG/caA	.	.	.	1	MRPS11	HGNC	14050	protein_coding	YES	CCDS10342.1	ENSP00000317376	RT11_HUMAN	.	UPI0000035FC4	.	.	.	4/6	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF53137,Pfam_domain:PF00411,Gene3D:3.30.420.80,hmmpanther:PTHR11759:SF3,hmmpanther:PTHR11759,HAMAP:MF_01310	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACAGACAGC	.	5	ESCA
POLG	0	.	GRCh37	15	89862174	89862174	+	Silent	SNP	A	A	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3261T>A	p.%3D	p.A1087A	ENST00000268124	20/23	16	9	7	22	22	0	POLG,synonymous_variant,p.%3D,ENST00000268124,;POLG,synonymous_variant,p.%3D,ENST00000442287,;FANCI,downstream_gene_variant,,ENST00000310775,;POLG,downstream_gene_variant,,ENST00000526314,;FANCI,downstream_gene_variant,,ENST00000561894,;FANCI,downstream_gene_variant,,ENST00000300027,;FANCI,downstream_gene_variant,,ENST00000566615,;FANCI,downstream_gene_variant,,ENST00000565522,;POLG,synonymous_variant,p.%3D,ENST00000530292,;POLG,downstream_gene_variant,,ENST00000533857,;POLG,downstream_gene_variant,,ENST00000532584,;POLG,downstream_gene_variant,,ENST00000530715,;POLG,upstream_gene_variant,,ENST00000526671,;POLG,downstream_gene_variant,,ENST00000528881,;POLG,downstream_gene_variant,,ENST00000526398,;POLG,downstream_gene_variant,,ENST00000526573,;FANCI,downstream_gene_variant,,ENST00000447611,;FANCI,downstream_gene_variant,,ENST00000566895,;	T	ENSG00000140521	ENST00000268124	Transcript	synonymous_variant	3595	3261	1087	A	gcT/gcA	.	.	.	-1	POLG	HGNC	9179	protein_coding	YES	CCDS10350.1	ENSP00000268124	DPOG1_HUMAN	E5KNU5_HUMAN,Q6LCA9_HUMAN,Q2V8X9_HUMAN	UPI000000D9E8	.	.	.	20/23	.	Superfamily_domains:SSF56672,SMART_domains:SM00482,PIRSF_domain:PIRSF000797,Pfam_domain:PF00476,hmmpanther:PTHR10267:SF0,hmmpanther:PTHR10267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACAGCCGA	.	5	ESCA
METTL9	0	.	GRCh37	16	21666772	21666772	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*19C>G	.	.	ENST00000358154	5/5	26	20	6	28	28	0	METTL9,3_prime_UTR_variant,,ENST00000396014,;METTL9,3_prime_UTR_variant,,ENST00000358154,;IGSF6,upstream_gene_variant,,ENST00000569602,;METTL9,downstream_gene_variant,,ENST00000568826,;METTL9,downstream_gene_variant,,ENST00000567404,;IGSF6,upstream_gene_variant,,ENST00000268389,;METTL9,non_coding_transcript_exon_variant,,ENST00000564733,;IGSF6,upstream_gene_variant,,ENST00000565499,;	G	ENSG00000197006	ENST00000358154	Transcript	3_prime_UTR_variant	1234	.	.	.	.	.	.	.	1	METTL9	HGNC	24586	protein_coding	YES	CCDS10598.2	ENSP00000350874	METL9_HUMAN	Q8TD49_HUMAN,H3BM54_HUMAN,B2R7Q6_HUMAN	UPI0000071713	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGTCTTCAG	.	5	ESCA
SRRM2	0	.	GRCh37	16	2812373	2812373	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1844C>T	p.Ser615Phe	p.S615F	ENST00000301740	11/15	44	37	7	53	53	0	SRRM2,missense_variant,p.Ser615Phe,ENST00000576924,;SRRM2,missense_variant,p.Ser519Phe,ENST00000571378,;SRRM2,missense_variant,p.Ser615Phe,ENST00000301740,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000574340,;SRRM2,downstream_gene_variant,,ENST00000576415,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,downstream_gene_variant,,ENST00000575701,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,downstream_gene_variant,,ENST00000573451,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000572952,;	T	ENSG00000167978	ENST00000301740	Transcript	missense_variant	2393	1844	615	S/F	tCt/tTt	.	.	.	1	SRRM2	HGNC	16639	protein_coding	YES	CCDS32373.1	ENSP00000301740	SRRM2_HUMAN	I3L4D8_HUMAN,I3L1I8_HUMAN,I3L1C0_HUMAN,I3L182_HUMAN,I3L0N7_HUMAN	UPI000049DDFC	.	.	unknown(0)	11/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093,SMART_domains:SM01104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGGTCTCGGT	.	3	ESCA
SRRM2	0	.	GRCh37	16	2812379	2812379	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1850C>G	p.Ser617Cys	p.S617C	ENST00000301740	11/15	43	35	7	52	52	0	SRRM2,missense_variant,p.Ser617Cys,ENST00000576924,;SRRM2,missense_variant,p.Ser521Cys,ENST00000571378,;SRRM2,missense_variant,p.Ser617Cys,ENST00000301740,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000574340,;SRRM2,downstream_gene_variant,,ENST00000576415,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,downstream_gene_variant,,ENST00000575701,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,downstream_gene_variant,,ENST00000573451,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000572952,;	G	ENSG00000167978	ENST00000301740	Transcript	missense_variant	2399	1850	617	S/C	tCt/tGt	.	.	.	1	SRRM2	HGNC	16639	protein_coding	YES	CCDS32373.1	ENSP00000301740	SRRM2_HUMAN	I3L4D8_HUMAN,I3L1I8_HUMAN,I3L1C0_HUMAN,I3L182_HUMAN,I3L0N7_HUMAN	UPI000049DDFC	.	.	unknown(0)	11/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093,SMART_domains:SM01104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCGGTCTAGAA	.	3	ESCA
SRRM2	0	.	GRCh37	16	2812817	2812817	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2288C>G	p.Ser763Cys	p.S763C	ENST00000301740	11/15	32	29	3	30	30	0	SRRM2,missense_variant,p.Ser763Cys,ENST00000576924,;SRRM2,missense_variant,p.Ser667Cys,ENST00000571378,;SRRM2,missense_variant,p.Ser763Cys,ENST00000301740,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000576415,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000574593,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,downstream_gene_variant,,ENST00000575701,;SRRM2,upstream_gene_variant,,ENST00000572883,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,downstream_gene_variant,,ENST00000573451,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000572952,;	G	ENSG00000167978	ENST00000301740	Transcript	missense_variant	2837	2288	763	S/C	tCt/tGt	.	.	.	1	SRRM2	HGNC	16639	protein_coding	YES	CCDS32373.1	ENSP00000301740	SRRM2_HUMAN	I3L4D8_HUMAN,I3L1I8_HUMAN,I3L1C0_HUMAN,I3L182_HUMAN,I3L0N7_HUMAN	UPI000049DDFC	.	.	benign(0.184)	11/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCTCTTCAC	.	2	ESCA
SRRM2	0	.	GRCh37	16	2812877	2812877	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2348C>T	p.Ser783Phe	p.S783F	ENST00000301740	11/15	46	41	4	31	31	0	SRRM2,missense_variant,p.Ser783Phe,ENST00000576924,;SRRM2,missense_variant,p.Ser687Phe,ENST00000571378,;SRRM2,missense_variant,p.Ser783Phe,ENST00000301740,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000576415,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,upstream_gene_variant,,ENST00000572721,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000574593,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,upstream_gene_variant,,ENST00000572883,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,downstream_gene_variant,,ENST00000573451,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000572952,;	T	ENSG00000167978	ENST00000301740	Transcript	missense_variant	2897	2348	783	S/F	tCc/tTc	.	.	.	1	SRRM2	HGNC	16639	protein_coding	YES	CCDS32373.1	ENSP00000301740	SRRM2_HUMAN	I3L4D8_HUMAN,I3L1I8_HUMAN,I3L1C0_HUMAN,I3L182_HUMAN,I3L0N7_HUMAN	UPI000049DDFC	.	.	benign(0.184)	11/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GTCTTCCCCAT	.	3	ESCA
LAT	0	.	GRCh37	16	28996145	28996145	+	5'Flank	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000395461	.	36	28	7	29	29	0	LAT,upstream_gene_variant,,ENST00000395461,;SPNS1,downstream_gene_variant,,ENST00000311008,;SPNS1,downstream_gene_variant,,ENST00000352260,;LAT,upstream_gene_variant,,ENST00000354453,;LAT,upstream_gene_variant,,ENST00000564277,;SPNS1,downstream_gene_variant,,ENST00000565975,;SPNS1,downstream_gene_variant,,ENST00000334536,;SPNS1,downstream_gene_variant,,ENST00000566059,;LAT,upstream_gene_variant,,ENST00000570232,;LAT,upstream_gene_variant,,ENST00000395456,;SPNS1,downstream_gene_variant,,ENST00000323081,;SPNS1,downstream_gene_variant,,ENST00000568829,;LAT,upstream_gene_variant,,ENST00000360872,;SPNS1,downstream_gene_variant,,ENST00000564476,;LAT,upstream_gene_variant,,ENST00000566177,;LAT,upstream_gene_variant,,ENST00000454369,;RP11-264B17.5,downstream_gene_variant,,ENST00000561471,;SPNS1,downstream_gene_variant,,ENST00000561868,;LAT,upstream_gene_variant,,ENST00000563964,;RP11-264B17.3,non_coding_transcript_exon_variant,,ENST00000569969,;LAT,upstream_gene_variant,,ENST00000562472,;LAT,upstream_gene_variant,,ENST00000566270,;LAT,upstream_gene_variant,,ENST00000564447,;LAT,upstream_gene_variant,,ENST00000566415,;SPNS1,downstream_gene_variant,,ENST00000568900,;LAT,upstream_gene_variant,,ENST00000568440,;LAT,upstream_gene_variant,,ENST00000568899,;LAT,upstream_gene_variant,,ENST00000562701,;	T	ENSG00000213658	ENST00000395461	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2	1	LAT	HGNC	18874	protein_coding	YES	CCDS53999.1	ENSP00000378845	.	B7WPI0_HUMAN	UPI00005A7621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTCAGGGC	.	5	ESCA
CCDC64B	0	.	GRCh37	16	3081445	3081445	+	Intron	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283-294G>C	.	.	ENST00000572449	.	52	37	15	56	56	0	CCDC64B,5_prime_UTR_variant,,ENST00000573514,;CCDC64B,intron_variant,,ENST00000572449,;CCDC64B,intron_variant,,ENST00000389347,;THOC6,downstream_gene_variant,,ENST00000575576,;THOC6,downstream_gene_variant,,ENST00000574549,;THOC6,downstream_gene_variant,,ENST00000326266,;THOC6,downstream_gene_variant,,ENST00000253952,;RP11-473M20.5,upstream_gene_variant,,ENST00000382225,;CCDC64B,non_coding_transcript_exon_variant,,ENST00000572240,;CCDC64B,intron_variant,,ENST00000576826,;THOC6,downstream_gene_variant,,ENST00000571057,;THOC6,downstream_gene_variant,,ENST00000574498,;THOC6,downstream_gene_variant,,ENST00000576143,;THOC6,downstream_gene_variant,,ENST00000574957,;THOC6,downstream_gene_variant,,ENST00000573704,;	G	ENSG00000162069	ENST00000572449	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CCDC64B	HGNC	33584	protein_coding	YES	CCDS45393.1	ENSP00000459043	BICR2_HUMAN	.	UPI00001D78D6	.	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTCGCAAG	.	5	ESCA
VKORC1	0	.	GRCh37	16	31104658	31104658	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258C>T	p.%3D	p.I86I	ENST00000394975	2/3	87	78	9	66	66	0	VKORC1,missense_variant,p.Leu118Phe,ENST00000394971,;VKORC1,missense_variant,p.Leu119Phe,ENST00000498155,;VKORC1,missense_variant,p.Leu107Phe,ENST00000300851,;VKORC1,synonymous_variant,p.%3D,ENST00000394975,;VKORC1,synonymous_variant,p.%3D,ENST00000319788,;RP11-196G11.1,synonymous_variant,p.%3D,ENST00000529564,;VKORC1,5_prime_UTR_variant,,ENST00000472468,;RP11-196G11.1,intron_variant,,ENST00000532364,;VKORC1,intron_variant,,ENST00000420057,;VKORC1,intron_variant,,ENST00000354895,;PRSS53,upstream_gene_variant,,ENST00000280606,;RP11-196G11.1,synonymous_variant,p.%3D,ENST00000533518,;PRSS53,upstream_gene_variant,,ENST00000486499,;PRSS53,upstream_gene_variant,,ENST00000492427,;	A	ENSG00000167397	ENST00000394975	Transcript	synonymous_variant	486	258	86	I	atC/atT	.	.	.	-1	VKORC1	HGNC	23663	protein_coding	YES	CCDS10703.1	ENSP00000378426	VKOR1_HUMAN	I3L1P9_HUMAN	UPI000006DDEE	.	.	.	2/3	.	SMART_domains:SM00756,Pfam_domain:PF07884,hmmpanther:PTHR14519	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGAAGATGCA	.	4	ESCA
CORO7	0	.	GRCh37	16	4408369	4408369	+	Missense_Mutation	SNP	C	C	T	rs569079730	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2456G>A	p.Arg819Gln	p.R819Q	ENST00000251166	24/28	58	39	18	49	49	0	CORO7,missense_variant,p.Arg599Gln,ENST00000539968,;CORO7,missense_variant,p.Arg734Gln,ENST00000574025,;CORO7-PAM16,missense_variant,p.Arg819Gln,ENST00000572467,;CORO7,missense_variant,p.Arg28Gln,ENST00000570779,;CORO7,missense_variant,p.Arg801Gln,ENST00000537233,;CORO7,missense_variant,p.Arg819Gln,ENST00000251166,;PAM16,upstream_gene_variant,,ENST00000576217,;CORO7,downstream_gene_variant,,ENST00000423908,;CORO7-PAM16,splice_region_variant,,ENST00000572274,;CORO7,missense_variant,p.Arg119Gln,ENST00000576637,;CORO7-PAM16,splice_region_variant,,ENST00000575334,;CORO7,splice_region_variant,,ENST00000571227,;CORO7,splice_region_variant,,ENST00000574849,;CORO7,splice_region_variant,,ENST00000575531,;CORO7,non_coding_transcript_exon_variant,,ENST00000575714,;CORO7,downstream_gene_variant,,ENST00000571756,;CORO7,downstream_gene_variant,,ENST00000576437,;CORO7,downstream_gene_variant,,ENST00000572666,;CORO7,downstream_gene_variant,,ENST00000574311,;CORO7,downstream_gene_variant,,ENST00000573773,;CORO7,downstream_gene_variant,,ENST00000572125,;	T	ENSG00000262246	ENST00000251166	Transcript	missense_variant	2602	2456	819	R/Q	cGg/cAg	rs569079730	.	.	-1	CORO7	HGNC	26161	protein_coding	YES	CCDS10513.1	ENSP00000251166	CORO7_HUMAN	I3L258_HUMAN,B3KSY4_HUMAN	UPI00001FF898	.	deleterious(0.01)	benign(0.403)	24/28	.	hmmpanther:PTHR10856:SF20,hmmpanther:PTHR10856,Pfam_domain:PF08954	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCCGGACT	by1000G	5	ESCA
GPT2	0	.	GRCh37	16	46943697	46943697	+	Silent	SNP	C	C	T	rs761253609	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.678C>T	p.%3D	p.L226L	ENST00000340124	6/12	44	29	15	42	41	1	GPT2,synonymous_variant,p.%3D,ENST00000562132,;GPT2,synonymous_variant,p.%3D,ENST00000340124,;GPT2,synonymous_variant,p.%3D,ENST00000440783,;	T	ENSG00000166123	ENST00000340124	Transcript	synonymous_variant	790	678	226	L	ctC/ctT	rs761253609	.	.	1	GPT2	HGNC	18062	protein_coding	YES	CCDS10725.1	ENSP00000345282	ALAT2_HUMAN	B3KR40_HUMAN	UPI000004DBE2	.	.	.	6/12	.	hmmpanther:PTHR11751:SF311,hmmpanther:PTHR11751,Gene3D:3.40.640.10,Pfam_domain:PF00155,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GAGCTCGACGC	.	4	ESCA
GPT2	0	.	GRCh37	16	46964835	46964835	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1926G>A	.	.	ENST00000340124	12/12	63	52	10	50	50	0	GPT2,3_prime_UTR_variant,,ENST00000340124,;GPT2,3_prime_UTR_variant,,ENST00000440783,;GPT2,non_coding_transcript_exon_variant,,ENST00000569193,;GPT2,downstream_gene_variant,,ENST00000562801,;	A	ENSG00000166123	ENST00000340124	Transcript	3_prime_UTR_variant	3610	.	.	.	.	.	.	.	1	GPT2	HGNC	18062	protein_coding	YES	CCDS10725.1	ENSP00000345282	ALAT2_HUMAN	B3KR40_HUMAN	UPI000004DBE2	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATGATAGG	.	5	ESCA
MVD	0	.	GRCh37	16	88722868	88722868	+	Intron	SNP	G	G	T	rs142373947	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404-156C>A	.	.	ENST00000301012	.	11	5	6	10	10	0	MVD,intron_variant,,ENST00000301012,;MVD,intron_variant,,ENST00000569177,;MVD,non_coding_transcript_exon_variant,,ENST00000565720,;MVD,non_coding_transcript_exon_variant,,ENST00000568709,;MVD,downstream_gene_variant,,ENST00000563463,;MVD,non_coding_transcript_exon_variant,,ENST00000565149,;MVD,intron_variant,,ENST00000563170,;MVD,intron_variant,,ENST00000568133,;MVD,intron_variant,,ENST00000566636,;MVD,intron_variant,,ENST00000567064,;MVD,intron_variant,,ENST00000563785,;MVD,downstream_gene_variant,,ENST00000565610,;MVD,upstream_gene_variant,,ENST00000561895,;MVD,downstream_gene_variant,,ENST00000562651,;MVD,upstream_gene_variant,,ENST00000562981,;	T	ENSG00000167508	ENST00000301012	Transcript	intron_variant	.	.	.	.	.	rs142373947	.	.	-1	MVD	HGNC	7529	protein_coding	YES	CCDS10968.1	ENSP00000301012	MVD1_HUMAN	.	UPI000012A0C6	.	.	.	.	4/9	.	A:0.0000	A:0	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TCACCGGCCCA	by1000G	2	ESCA
LLGL1	0	.	GRCh37	17	18147900	18147900	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*680C>T	.	.	ENST00000316843	23/23	14	5	9	12	12	0	LLGL1,3_prime_UTR_variant,,ENST00000316843,;FLII,downstream_gene_variant,,ENST00000327031,;FLII,downstream_gene_variant,,ENST00000577398,;FLII,downstream_gene_variant,,ENST00000577485,;FLII,downstream_gene_variant,,ENST00000379450,;FLII,downstream_gene_variant,,ENST00000579294,;FLII,downstream_gene_variant,,ENST00000578558,;FLII,downstream_gene_variant,,ENST00000545457,;LLGL1,non_coding_transcript_exon_variant,,ENST00000479155,;FLII,downstream_gene_variant,,ENST00000493600,;FLII,downstream_gene_variant,,ENST00000459958,;FLII,downstream_gene_variant,,ENST00000487693,;FLII,downstream_gene_variant,,ENST00000578101,;FLII,downstream_gene_variant,,ENST00000580966,;FLII,downstream_gene_variant,,ENST00000577402,;FLII,downstream_gene_variant,,ENST00000581858,;FLII,downstream_gene_variant,,ENST00000493401,;FLII,downstream_gene_variant,,ENST00000465046,;FLII,downstream_gene_variant,,ENST00000496727,;FLII,downstream_gene_variant,,ENST00000487369,;FLII,downstream_gene_variant,,ENST00000474265,;FLII,downstream_gene_variant,,ENST00000580453,;	T	ENSG00000131899	ENST00000316843	Transcript	3_prime_UTR_variant	3971	.	.	.	.	.	.	.	1	LLGL1	HGNC	6628	protein_coding	YES	CCDS32586.1	ENSP00000321537	L2GL1_HUMAN	A0PJG1_HUMAN	UPI000049DE38	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTCTAAAA	.	5	ESCA
FLII	0	.	GRCh37	17	18150102	18150102	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2857G>C	p.Glu953Gln	p.E953Q	ENST00000327031	23/30	31	27	4	22	22	0	FLII,missense_variant,p.Glu953Gln,ENST00000327031,;FLII,missense_variant,p.Glu867Gln,ENST00000379450,;FLII,missense_variant,p.Glu942Gln,ENST00000579294,;FLII,missense_variant,p.Glu898Gln,ENST00000545457,;FLII,intron_variant,,ENST00000577485,;FLII,intron_variant,,ENST00000578558,;FLII,upstream_gene_variant,,ENST00000577398,;LLGL1,downstream_gene_variant,,ENST00000316843,;FLII,3_prime_UTR_variant,,ENST00000578101,;FLII,non_coding_transcript_exon_variant,,ENST00000459958,;FLII,non_coding_transcript_exon_variant,,ENST00000580453,;FLII,upstream_gene_variant,,ENST00000493600,;FLII,downstream_gene_variant,,ENST00000488221,;FLII,upstream_gene_variant,,ENST00000487693,;FLII,upstream_gene_variant,,ENST00000580966,;FLII,downstream_gene_variant,,ENST00000577402,;FLII,upstream_gene_variant,,ENST00000581858,;FLII,upstream_gene_variant,,ENST00000493401,;FLII,upstream_gene_variant,,ENST00000465046,;FLII,downstream_gene_variant,,ENST00000496727,;FLII,upstream_gene_variant,,ENST00000487369,;FLII,upstream_gene_variant,,ENST00000474265,;LLGL1,downstream_gene_variant,,ENST00000479155,;	G	ENSG00000177731	ENST00000327031	Transcript	missense_variant	3083	2857	953	E/Q	Gaa/Caa	.	.	.	-1	FLII	HGNC	3750	protein_coding	YES	CCDS11192.1	ENSP00000324573	FLII_HUMAN	K7EP37_HUMAN,K7EP27_HUMAN	UPI0000001284	.	tolerated(0.21)	benign(0.009)	23/30	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF16,SMART_domains:SM00262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCCTTCT	.	5	ESCA
FAM83G	0	.	GRCh37	17	18907093	18907093	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.262C>T	p.Gln88Ter	p.Q88*	ENST00000388995	2/6	70	54	15	50	50	0	FAM83G,stop_gained,p.Gln88Ter,ENST00000585154,;FAM83G,stop_gained,p.Gln88Ter,ENST00000388995,;FAM83G,stop_gained,p.Gln88Ter,ENST00000345041,;SLC5A10,intron_variant,,ENST00000417251,;SLC5A10,intron_variant,,ENST00000395647,;SLC5A10,intron_variant,,ENST00000395643,;SLC5A10,intron_variant,,ENST00000395642,;SLC5A10,intron_variant,,ENST00000395645,;SLC5A10,intron_variant,,ENST00000317977,;FAM83G,non_coding_transcript_exon_variant,,ENST00000399096,;	A	ENSG00000188522	ENST00000388995	Transcript	stop_gained	486	262	88	Q/*	Cag/Tag	COSM1302480	.	.	-1	FAM83G	HGNC	32554	protein_coding	YES	CCDS42276.1	ENSP00000373647	FA83G_HUMAN	.	UPI0000E03260	.	.	.	2/6	.	hmmpanther:PTHR16181:SF5,hmmpanther:PTHR16181,Pfam_domain:PF07894	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTGAGAGG	.	5	ESCA
SMG6	0	.	GRCh37	17	2203562	2203562	+	Missense_Mutation	SNP	C	C	T	rs748739928	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.485G>A	p.Arg162Gln	p.R162Q	ENST00000263073	2/19	58	44	14	56	56	0	SMG6,missense_variant,p.Arg131Gln,ENST00000544865,;SMG6,missense_variant,p.Arg162Gln,ENST00000263073,;SRR,upstream_gene_variant,,ENST00000576620,;SRR,upstream_gene_variant,,ENST00000575840,;SRR,upstream_gene_variant,,ENST00000576848,;SRR,upstream_gene_variant,,ENST00000344595,;SRR,upstream_gene_variant,,ENST00000574987,;SRR,upstream_gene_variant,,ENST00000572709,;	T	ENSG00000070366	ENST00000263073	Transcript	missense_variant	536	485	162	R/Q	cGg/cAg	rs748739928,COSM705907	.	.	-1	SMG6	HGNC	17809	protein_coding	YES	CCDS11016.1	ENSP00000263073	EST1A_HUMAN	K7ENH7_HUMAN,K7ELM2_HUMAN,K7EKV2_HUMAN,I3L421_HUMAN,I3L3A9_HUMAN,I3L355_HUMAN,I3L1W8_HUMAN,I3L176_HUMAN	UPI00002005C8	.	tolerated_low_confidence(0.28)	benign(0.003)	2/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13548:SF1,hmmpanther:PTHR13548	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCCGACTG	byFrequency	5	ESCA
PAFAH1B1	0	.	GRCh37	17	2587958	2587958	+	3'UTR	SNP	G	G	A	rs145845266	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2862G>A	.	.	ENST00000397195	11/11	56	37	18	65	65	0	PAFAH1B1,3_prime_UTR_variant,,ENST00000397195,;PAFAH1B1,downstream_gene_variant,,ENST00000451360,;CLUH,downstream_gene_variant,,ENST00000570628,;PAFAH1B1,downstream_gene_variant,,ENST00000574468,;CLUH,downstream_gene_variant,,ENST00000435359,;CLUH,downstream_gene_variant,,ENST00000575014,;CLUH,downstream_gene_variant,,ENST00000538975,;RP11-74E22.6,upstream_gene_variant,,ENST00000608984,;RP11-74E22.5,intron_variant,,ENST00000610120,;RN7SL608P,downstream_gene_variant,,ENST00000492377,;PAFAH1B1,downstream_gene_variant,,ENST00000572915,;PAFAH1B1,downstream_gene_variant,,ENST00000397193,;PAFAH1B1,downstream_gene_variant,,ENST00000574213,;PAFAH1B1,downstream_gene_variant,,ENST00000574816,;PAFAH1B1,downstream_gene_variant,,ENST00000610190,;PAFAH1B1,downstream_gene_variant,,ENST00000571495,;	A	ENSG00000007168	ENST00000397195	Transcript	3_prime_UTR_variant	4546	.	.	.	.	rs145845266	.	.	1	PAFAH1B1	HGNC	8574	protein_coding	YES	CCDS32528.1	ENSP00000380378	LIS1_HUMAN	I3L495_HUMAN,B4DZN3_HUMAN	UPI0000163BF4	.	.	.	11/11	.	.	A:0.0012	A:0	A:0.0029	.	A:0.001	A:0.003	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCACGGCATC	byFrequency|byCluster|by1000G	5	ESCA
CLUH	0	.	GRCh37	17	2597225	2597225	+	Missense_Mutation	SNP	C	C	T	rs777344374	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3083G>A	p.Arg1028His	p.R1028H	ENST00000570628	19/26	98	89	9	98	98	0	CLUH,missense_variant,p.Arg1028His,ENST00000435359,;CLUH,missense_variant,p.Arg970His,ENST00000575014,;CLUH,missense_variant,p.Arg1016His,ENST00000574426,;CLUH,missense_variant,p.Arg1028His,ENST00000538975,;CLUH,missense_variant,p.Arg1028His,ENST00000570628,;CLUH,downstream_gene_variant,,ENST00000572129,;RP11-74E22.6,downstream_gene_variant,,ENST00000608984,;CLUH,non_coding_transcript_exon_variant,,ENST00000574210,;CLUH,non_coding_transcript_exon_variant,,ENST00000572014,;CLUH,downstream_gene_variant,,ENST00000574166,;CLUH,downstream_gene_variant,,ENST00000573641,;CLUH,downstream_gene_variant,,ENST00000575624,;	T	ENSG00000132361	ENST00000570628	Transcript	missense_variant	3189	3083	1028	R/H	cGc/cAc	rs777344374	.	.	-1	CLUH	HGNC	29094	protein_coding	YES	CCDS45572.1	ENSP00000458986	CLU_HUMAN	I3L3A3_HUMAN,I3L350_HUMAN,I3L318_HUMAN	UPI00004C8042	.	deleterious(0)	probably_damaging(1)	19/26	.	HAMAP:MF_03013,hmmpanther:PTHR12601,hmmpanther:PTHR12601:SF10,Gene3D:1.25.40.10,Pfam_domain:PF13374,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGAGGCGGGCG	.	3	ESCA
CDK12	0	.	GRCh37	17	37680952	37680952	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3121G>A	p.Glu1041Lys	p.E1041K	ENST00000447079	12/14	52	45	7	65	65	0	CDK12,missense_variant,p.Glu1041Lys,ENST00000447079,;CDK12,missense_variant,p.Glu1040Lys,ENST00000584632,;CDK12,missense_variant,p.Glu1041Lys,ENST00000430627,;CDK12,upstream_gene_variant,,ENST00000559663,;	A	ENSG00000167258	ENST00000447079	Transcript	missense_variant	3154	3121	1041	E/K	Gag/Aag	.	.	.	1	CDK12	HGNC	24224	protein_coding	YES	CCDS11337.1	ENSP00000398880	CDK12_HUMAN	.	UPI000013E688	.	.	probably_damaging(0.91)	12/14	.	Gene3D:1.10.510.10,hmmpanther:PTHR24056:SF126,hmmpanther:PTHR24056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCATGAGTTG	.	4	ESCA
KRTAP4-1	0	.	GRCh37	17	39341434	39341434	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-328G>T	.	.	ENST00000398472	1/1	36	23	13	25	25	0	KRTAP4-1,5_prime_UTR_variant,,ENST00000398472,;KRTAP9-1,upstream_gene_variant,,ENST00000398470,;KRTAP9-1,upstream_gene_variant,,ENST00000318329,;KRTAP9-1,upstream_gene_variant,,ENST00000377723,;AC006070.12,downstream_gene_variant,,ENST00000508151,;	A	ENSG00000198443	ENST00000398472	Transcript	5_prime_UTR_variant	161	.	.	.	.	.	.	.	-1	KRTAP4-1	HGNC	18907	protein_coding	YES	.	ENSP00000381489	KRA41_HUMAN	.	UPI0000246F4A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTCGATTG	.	5	ESCA
EFCAB13	0	.	GRCh37	17	45447865	45447865	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.868G>C	p.Glu290Gln	p.E290Q	ENST00000331493	11/25	50	42	8	54	54	0	EFCAB13,missense_variant,p.Glu46Gln,ENST00000517310,;EFCAB13,missense_variant,p.Glu194Gln,ENST00000517484,;EFCAB13,missense_variant,p.Glu290Gln,ENST00000331493,;EFCAB13,non_coding_transcript_exon_variant,,ENST00000523978,;EFCAB13,non_coding_transcript_exon_variant,,ENST00000520776,;	C	ENSG00000178852	ENST00000331493	Transcript	missense_variant	1279	868	290	E/Q	Gag/Cag	.	.	.	1	EFCAB13	HGNC	26864	protein_coding	YES	CCDS11512.1	ENSP00000332111	EFC13_HUMAN	E5RI18_HUMAN,E5RFW6_HUMAN	UPI00001AFEA2	.	deleterious(0)	probably_damaging(0.999)	11/25	.	hmmpanther:PTHR22656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTATGAGGAT	.	5	ESCA
ABI3	0	.	GRCh37	17	47297620	47297628	+	In_Frame_Del	DEL	CTCCACCAG	CTCCACCAG	-	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	CTCCACCAG	CTCCACCAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.735_743delTCCACCAGC	p.Pro246_Ala248del	p.P246_A248del	ENST00000225941	6/8	77	63	14	80	80	0	ABI3,inframe_deletion,p.Pro240_Ala242del,ENST00000419580,;ABI3,inframe_deletion,p.Pro246_Ala248del,ENST00000225941,;ABI3,inframe_deletion,p.Pro64_Ala66del,ENST00000571035,;ABI3,inframe_deletion,p.Pro85_Ala87del,ENST00000573347,;PHOSPHO1,downstream_gene_variant,,ENST00000574638,;PHOSPHO1,downstream_gene_variant,,ENST00000503902,;PHOSPHO1,downstream_gene_variant,,ENST00000413580,;PHOSPHO1,downstream_gene_variant,,ENST00000514112,;PHOSPHO1,downstream_gene_variant,,ENST00000512250,;PHOSPHO1,downstream_gene_variant,,ENST00000511066,;PHOSPHO1,downstream_gene_variant,,ENST00000310544,;	-	ENSG00000108798	ENST00000225941	Transcript	inframe_deletion	1232-1240	734-742	245-248	PPPA/P	cCTCCACCAGca/cca	.	.	.	1	ABI3	HGNC	29859	protein_coding	YES	CCDS11546.1	ENSP00000225941	ABI3_HUMAN	.	UPI000013C888	.	.	.	6/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10460:SF6,hmmpanther:PTHR10460	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CACCTCCTCCACCAGCAGCC	.	3	ESCA
VMP1	0	.	GRCh37	17	57917764	57917764	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*492C>G	.	.	ENST00000262291	12/12	40	33	6	46	46	0	VMP1,3_prime_UTR_variant,,ENST00000262291,;VMP1,downstream_gene_variant,,ENST00000536180,;VMP1,downstream_gene_variant,,ENST00000545362,;VMP1,downstream_gene_variant,,ENST00000591877,;VMP1,downstream_gene_variant,,ENST00000537567,;VMP1,downstream_gene_variant,,ENST00000539763,;MIR21,upstream_gene_variant,,ENST00000362134,;VMP1,downstream_gene_variant,,ENST00000591782,;VMP1,downstream_gene_variant,,ENST00000588617,;VMP1,non_coding_transcript_exon_variant,,ENST00000592790,;VMP1,downstream_gene_variant,,ENST00000592619,;VMP1,downstream_gene_variant,,ENST00000587470,;	G	ENSG00000062716	ENST00000262291	Transcript	3_prime_UTR_variant	2023	.	.	.	.	.	.	.	1	VMP1	HGNC	29559	protein_coding	YES	CCDS11619.1	ENSP00000262291	VMP1_HUMAN	K7ENU2_HUMAN,K7EMI0_HUMAN,K7EM96_HUMAN,K7EK01_HUMAN,D3DU01_HUMAN,B4DVV9_HUMAN	UPI0000037791	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCCCATC	.	5	ESCA
VMP1	0	.	GRCh37	17	57918642	57918642	+	3'Flank	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000262291	.	52	40	12	42	42	0	VMP1,downstream_gene_variant,,ENST00000536180,;VMP1,downstream_gene_variant,,ENST00000545362,;VMP1,downstream_gene_variant,,ENST00000262291,;VMP1,downstream_gene_variant,,ENST00000591877,;VMP1,downstream_gene_variant,,ENST00000537567,;VMP1,downstream_gene_variant,,ENST00000539763,;MIR21,non_coding_transcript_exon_variant,,ENST00000362134,;VMP1,downstream_gene_variant,,ENST00000591782,;VMP1,downstream_gene_variant,,ENST00000588617,;VMP1,non_coding_transcript_exon_variant,,ENST00000592790,;VMP1,downstream_gene_variant,,ENST00000592619,;VMP1,downstream_gene_variant,,ENST00000587470,;	T	ENSG00000062716	ENST00000262291	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	189	1	VMP1	HGNC	29559	protein_coding	YES	CCDS11619.1	ENSP00000262291	VMP1_HUMAN	K7ENU2_HUMAN,K7EMI0_HUMAN,K7EM96_HUMAN,K7EK01_HUMAN,D3DU01_HUMAN,B4DVV9_HUMAN	UPI0000037791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTATCAGACT	.	5	ESCA
BCAS3	0	.	GRCh37	17	59067470	59067470	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360C>T	p.Arg454Cys	p.R454C	ENST00000390652	15/25	52	47	5	37	37	0	BCAS3,missense_variant,p.Arg454Cys,ENST00000589222,;BCAS3,missense_variant,p.Arg454Cys,ENST00000408905,;BCAS3,missense_variant,p.Arg454Cys,ENST00000588462,;BCAS3,missense_variant,p.Arg454Cys,ENST00000390652,;BCAS3,missense_variant,p.Arg225Cys,ENST00000585744,;BCAS3,missense_variant,p.Arg454Cys,ENST00000407086,;BCAS3,missense_variant,p.Arg225Cys,ENST00000588874,;BCAS3,downstream_gene_variant,,ENST00000586484,;BCAS3,non_coding_transcript_exon_variant,,ENST00000590352,;	T	ENSG00000141376	ENST00000390652	Transcript	missense_variant	1391	1360	454	R/C	Cgc/Tgc	.	.	.	1	BCAS3	HGNC	14347	protein_coding	YES	CCDS45749.1	ENSP00000375067	BCAS3_HUMAN	K7ESE9_HUMAN,K7EML5_HUMAN,K7EKB0_HUMAN,K7EJU7_HUMAN,K7EJH7_HUMAN	UPI00001AE949	.	deleterious(0)	probably_damaging(0.944)	15/25	.	hmmpanther:PTHR13268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAATCGCATG	.	2	ESCA
SCN4A	0	.	GRCh37	17	62034633	62034633	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2265C>T	p.%3D	p.F755F	ENST00000435607	13/24	55	45	10	57	57	0	SCN4A,synonymous_variant,p.%3D,ENST00000435607,;SCN4A,synonymous_variant,p.%3D,ENST00000578147,;SCN4A,downstream_gene_variant,,ENST00000581514,;	A	ENSG00000007314	ENST00000435607	Transcript	synonymous_variant	2342	2265	755	F	ttC/ttT	.	.	.	-1	SCN4A	HGNC	10591	protein_coding	YES	CCDS45761.1	ENSP00000396320	SCN4A_HUMAN	Q9H3L9_HUMAN	UPI0000201254	.	.	.	13/24	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF193,Pfam_domain:PF00520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCGGAAGAC	.	5	ESCA
CEP95	0	.	GRCh37	17	62525459	62525459	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360C>G	p.Pro454Ala	p.P454A	ENST00000556440	12/20	60	47	13	42	42	0	CEP95,missense_variant,p.Pro454Ala,ENST00000556440,;CEP95,missense_variant,p.Pro82Ala,ENST00000583457,;CEP95,missense_variant,p.Pro290Ala,ENST00000553412,;AC009994.2,downstream_gene_variant,,ENST00000579926,;CEP95,non_coding_transcript_exon_variant,,ENST00000577476,;CEP95,3_prime_UTR_variant,,ENST00000553956,;CEP95,non_coding_transcript_exon_variant,,ENST00000584857,;CEP95,non_coding_transcript_exon_variant,,ENST00000579117,;CEP95,non_coding_transcript_exon_variant,,ENST00000579478,;CEP95,upstream_gene_variant,,ENST00000580285,;CEP95,upstream_gene_variant,,ENST00000579637,;CEP95,upstream_gene_variant,,ENST00000582698,;CEP95,upstream_gene_variant,,ENST00000581885,;CEP95,downstream_gene_variant,,ENST00000577960,;	G	ENSG00000258890	ENST00000556440	Transcript	missense_variant	1870	1360	454	P/A	Cca/Gca	.	.	.	1	CEP95	HGNC	25141	protein_coding	YES	CCDS45763.1	ENSP00000450461	CEP95_HUMAN	K7ENV0_HUMAN,B4DMD2_HUMAN	UPI000006F4B3	.	tolerated(0.21)	benign(0.439)	12/20	.	hmmpanther:PTHR22545:SF0,hmmpanther:PTHR22545	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCCAGTT	.	5	ESCA
ACOX1	0	.	GRCh37	17	73974917	73974917	+	Intron	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.109+129G>C	.	.	ENST00000293217	.	26	19	7	21	21	0	ACOX1,5_prime_UTR_variant,,ENST00000537812,;ACOX1,intron_variant,,ENST00000293217,;ACOX1,intron_variant,,ENST00000588176,;ACOX1,intron_variant,,ENST00000301608,;TEN1,upstream_gene_variant,,ENST00000586891,;TEN1,upstream_gene_variant,,ENST00000416485,;ACOX1,upstream_gene_variant,,ENST00000576743,;TEN1,upstream_gene_variant,,ENST00000590676,;TEN1,upstream_gene_variant,,ENST00000588202,;TEN1,upstream_gene_variant,,ENST00000397640,;ACOX1,intron_variant,,ENST00000591857,;ACOX1,3_prime_UTR_variant,,ENST00000589301,;ACOX1,3_prime_UTR_variant,,ENST00000572047,;ACOX1,intron_variant,,ENST00000573078,;ACOX1,intron_variant,,ENST00000592329,;TEN1-CDK3,upstream_gene_variant,,ENST00000567351,;TEN1-CDK3,upstream_gene_variant,,ENST00000569284,;	G	ENSG00000161533	ENST00000293217	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ACOX1	HGNC	119	protein_coding	YES	CCDS11734.1	ENSP00000293217	ACOX1_HUMAN	.	UPI000013E0F5	.	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCGAAGT	.	5	ESCA
TP53	0	.	GRCh37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	8/11	25	20	5	27	27	0	TP53,missense_variant,p.Arg273Cys,ENST00000420246,;TP53,missense_variant,p.Arg273Cys,ENST00000269305,;TP53,missense_variant,p.Arg141Cys,ENST00000509690,;TP53,missense_variant,p.Arg273Cys,ENST00000359597,;TP53,missense_variant,p.Arg273Cys,ENST00000445888,;TP53,missense_variant,p.Arg273Cys,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1007	817	273	R/C	Cgt/Tgt	CM951233,CM010473,rs121913343,CM010471,TP53_g.13797C>G,TP53_g.13797del,TP53_g.13797C>T,TP53_g.13797C>A,COSM43909,COSM44701,COSM10659,COSM43843,COSM417971,COSM99933,COSM3719990,COSM3355991,COSM3958802,COSM3719992,COSM1645518,COSM3719991,COSM3958801	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.998)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	uncertain_significance,pathogenic	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R273C|c.817C>T|131,SITE|p.R273C|c.817C>T|571,SITE|p.R273C|c.817C>T|75,SITE|p.R273C|c.817C>T|59,CODON|p.0?|c.1_1182del1182|6,CODON|p.R273L|c.818G>T|98,CODON|p.R273P|c.818G>C|4,CODON|p.R273H|c.818G>A|116,CODON|p.R273H|c.818G>A|64,CODON|p.R273H|c.818G>A|588,CODON|p.R273L|c.818G>T|5,CODON|p.R273H|c.818G>A|83,CODON|p.R273P|c.818G>C|29,CODON|p.R273L|c.818G>T|18,CODON|p.R273L|c.818G>T|12,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3,BUFFER|p.E271Q|c.811G>C|4,BUFFER|p.E271K|c.811G>A|35,BUFFER|p.E271*|c.811G>T|16,BUFFER|p.E271*|c.811G>T|3,BUFFER|p.E271K|c.811G>A|13,BUFFER|p.E271K|c.811G>A|4,BUFFER|p.E271K|c.811G>A|8,BUFFER|p.F270L|c.810T>G|4,BUFFER|p.F270L|c.810T>A|5,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270Y|c.809T>A|5,BUFFER|p.F270C|c.809T>G|16,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270S|c.809T>C|14,BUFFER|p.F270S|c.809T>C|6,BUFFER|p.F270L|c.808T>C|16,BUFFER|p.F270I|c.808T>A|3,BUFFER|p.F270V|c.808T>G|8,BUFFER|p.F270L|c.808T>C|3,BUFFER|p.F270I|c.808T>A|6,BUFFER|p.S269S|c.807C>T|3,BUFFER|p.S269N|c.806G>A|4	RADIA|MUTECT|MUSE|VARSCANS	AACACGCACCT	byFrequency|byCluster	4	ESCA
TP53	0	.	GRCh37	17	7578260	7578260	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.589G>T	p.Val197Leu	p.V197L	ENST00000269305	6/11	53	36	17	56	56	0	TP53,missense_variant,p.Val197Leu,ENST00000413465,;TP53,missense_variant,p.Val197Leu,ENST00000420246,;TP53,missense_variant,p.Val197Leu,ENST00000269305,;TP53,missense_variant,p.Val65Leu,ENST00000509690,;TP53,missense_variant,p.Val197Leu,ENST00000359597,;TP53,missense_variant,p.Val104Leu,ENST00000514944,;TP53,missense_variant,p.Val197Leu,ENST00000445888,;TP53,missense_variant,p.Val197Leu,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	779	589	197	V/L	Gtg/Ttg	CM070297,TP53_g.12658G>A,TP53_g.12658G>C,TP53_g.12658G>T,COSM43779,COSM46212,COSM45265,COSM307272,COSM3712578,COSM307271,COSM3712581,COSM307273,COSM3712583,COSM3712580,COSM3712579,COSM1645189,COSM307274,COSM3712582	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.03)	probably_damaging(0.999)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.V197L|c.589G>T|3,SITE|p.V65L|c.193G>T|3,SITE|p.V197L|c.589G>T|5,SITE|p.V104L|c.310G>T|3,SITE|p.V197L|c.589G>T|3,CODON|p.0?|c.1_1182del1182|6,CODON|p.A189_V197delAPPQHLIRV|c.565_591del27|4,CODON|p.V197G|c.590T>G|15,CODON|p.V197E|c.590T>A|8,BUFFER|p.N200fs*47|c.598delA|5,BUFFER|p.G199V|c.596G>T|10,BUFFER|p.G106V|c.317G>T|6,BUFFER|p.G67V|c.200G>T|6,BUFFER|p.G199V|c.596G>T|6,BUFFER|p.G199V|c.596G>T|6,BUFFER|p.G199E|c.596G>A|11,BUFFER|p.G199*|c.595G>T|5,BUFFER|p.G199R|c.595G>A|9,BUFFER|p.E198*|c.592G>T|5,BUFFER|p.E198K|c.592G>A|5,BUFFER|p.E198*|c.592G>T|4,BUFFER|p.E105*|c.313G>T|9,BUFFER|p.E198*|c.592G>T|27,BUFFER|p.E198*|c.592G>T|9,BUFFER|p.E66*|c.196G>T|9,BUFFER|p.E198*|c.592G>T|9,BUFFER|p.V197M|c.589G>A|12,BUFFER|p.R196R|c.588A>G|4,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R196P|c.587G>C|18,BUFFER|p.R64P|c.191G>C|7,BUFFER|p.R196Q|c.587G>A|4,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R103P|c.308G>C|7,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196*|c.585_586CC>TT|7,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R64fs*>27|c.190delC|3,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R103fs*51|c.307delC|3,BUFFER|p.R196fs*51|c.586delC|7,BUFFER|p.R64*|c.190C>T|65,BUFFER|p.R196*|c.586C>T|45,BUFFER|p.R196*|c.586C>T|33,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R103*|c.307C>T|64,BUFFER|p.R196*|c.586C>T|180,BUFFER|p.I102N|c.305T>A|10,BUFFER|p.I102T|c.305T>C|21,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I63S|c.188T>G|3,BUFFER|p.I195T|c.584T>C|88,BUFFER|p.I195N|c.584T>A|4,BUFFER|p.I195T|c.584T>C|21,BUFFER|p.I63N|c.188T>A|10,BUFFER|p.I195T|c.584T>C|12,BUFFER|p.I63T|c.188T>C|21,BUFFER|p.I195T|c.584T>C|21,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I195N|c.584T>A|23,BUFFER|p.I195T|c.584T>C|10,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I195S|c.584T>G|7,BUFFER|p.I195F|c.583A>T|6,BUFFER|p.I195F|c.583A>T|28,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.I63F|c.187A>T|9,BUFFER|p.I102F|c.304A>T|9,BUFFER|p.I195F|c.583A>T|5,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.L194L|c.582T>C|3,BUFFER|p.L62R|c.185T>G|17,BUFFER|p.L194R|c.581T>G|50,BUFFER|p.L194R|c.581T>G|11,BUFFER|p.L194H|c.581T>A|6,BUFFER|p.L194P|c.581T>C|9,BUFFER|p.L101R|c.302T>G|17,BUFFER|p.L194R|c.581T>G|9,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|19,BUFFER|p.L101F|c.301C>T|3,BUFFER|p.L62F|c.184C>T|3,BUFFER|p.H193fs*16|c.577_578insN|3,BUFFER|p.H193R|c.578A>G|8,BUFFER|p.H193L|c.578A>T|8,BUFFER|p.H193R|c.578A>G|89,BUFFER|p.H61P|c.182A>C|4,BUFFER|p.H100L|c.299A>T|8,BUFFER|p.H61R|c.182A>G|23,BUFFER|p.H193R|c.578A>G|21,BUFFER|p.H193L|c.578A>T|8,BUFFER|p.H193R|c.578A>G|22,BUFFER|p.H100R|c.299A>G|22,BUFFER|p.H100P|c.299A>C|4,BUFFER|p.H193P|c.578A>C|4,BUFFER|p.H193L|c.578A>T|3,BUFFER|p.H193L|c.578A>T|3,BUFFER|p.H193P|c.578A>C|16,BUFFER|p.H193R|c.578A>G|5,BUFFER|p.H193P|c.578A>C|3,BUFFER|p.H193L|c.578A>T|37,BUFFER|p.H61L|c.182A>T|10	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCACTCGGA	.	5	ESCA
PGS1	0	.	GRCh37	17	76415780	76415780	+	Intron	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10+24C>A	.	.	ENST00000262764	.	35	29	6	36	36	0	PGS1,3_prime_UTR_variant,,ENST00000329897,;PGS1,3_prime_UTR_variant,,ENST00000586355,;PGS1,3_prime_UTR_variant,,ENST00000586019,;PGS1,intron_variant,,ENST00000262764,;DNAH17,downstream_gene_variant,,ENST00000585328,;DNAH17,downstream_gene_variant,,ENST00000389840,;PGS1,non_coding_transcript_exon_variant,,ENST00000588281,;PGS1,downstream_gene_variant,,ENST00000585521,;DNAH17,downstream_gene_variant,,ENST00000586052,;PGS1,upstream_gene_variant,,ENST00000586880,;PGS1,3_prime_UTR_variant,,ENST00000588169,;PGS1,non_coding_transcript_exon_variant,,ENST00000591996,;PGS1,intron_variant,,ENST00000589425,;PGS1,intron_variant,,ENST00000589426,;DNAH17,downstream_gene_variant,,ENST00000591369,;DNAH17,downstream_gene_variant,,ENST00000590227,;	A	ENSG00000087157	ENST00000262764	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PGS1	HGNC	30029	protein_coding	YES	CCDS42391.1	ENSP00000262764	PGPS1_HUMAN	.	UPI00000435E5	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCAGCAC	.	5	ESCA
CBX8	0	.	GRCh37	17	77770322	77770322	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.87C>G	p.%3D	p.L29L	ENST00000269385	2/5	36	32	4	36	36	0	CBX8,synonymous_variant,p.%3D,ENST00000427800,;CBX8,synonymous_variant,p.%3D,ENST00000269385,;CBX8,synonymous_variant,p.%3D,ENST00000413392,;RP11-353N14.1,upstream_gene_variant,,ENST00000570512,;CBX8,intron_variant,,ENST00000485449,;	C	ENSG00000141570	ENST00000269385	Transcript	synonymous_variant	205	87	29	L	ctC/ctG	.	.	.	-1	CBX8	HGNC	15962	protein_coding	YES	CCDS11765.1	ENSP00000269385	CBX8_HUMAN	C9JM54_HUMAN	UPI000013D82A	.	.	.	2/5	.	PROSITE_profiles:PS50013,hmmpanther:PTHR22812:SF81,hmmpanther:PTHR22812,PROSITE_patterns:PS00598,Pfam_domain:PF00385,Gene3D:2.40.50.40,SMART_domains:SM00298,Superfamily_domains:SSF54160	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCACGAGGTA	.	4	ESCA
ANKRD62	0	.	GRCh37	18	12125725	12125725	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1905C>G	p.%3D	p.L635L	ENST00000587848	13/14	61	42	19	53	53	0	ANKRD62,synonymous_variant,p.%3D,ENST00000314074,;ANKRD62,synonymous_variant,p.%3D,ENST00000587848,;ANKRD62,non_coding_transcript_exon_variant,,ENST00000418274,;	G	ENSG00000181626	ENST00000587848	Transcript	synonymous_variant	2070	1905	635	L	ctC/ctG	.	.	.	1	ANKRD62	HGNC	35241	protein_coding	YES	CCDS67439.1	ENSP00000467740	ANR62_HUMAN	K7EQA3_HUMAN,J3QTZ2_HUMAN	UPI0000DD848C	.	.	.	13/14	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24147,Pfam_domain:PF14915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTCAATTC	.	5	ESCA
POTEC	0	.	GRCh37	18	14542835	14542835	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311A>C	p.His104Pro	p.H104P	ENST00000358970	1/11	178	147	31	182	181	0	POTEC,missense_variant,p.His104Pro,ENST00000358970,;POTEC,non_coding_transcript_exon_variant,,ENST00000389891,;POTEC,missense_variant,p.His104Pro,ENST00000511306,;	G	ENSG00000183206	ENST00000358970	Transcript	missense_variant	311	311	104	H/P	cAc/cCc	.	.	.	-1	POTEC	HGNC	33894	protein_coding	YES	CCDS45835.1	ENSP00000351856	POTEC_HUMAN	.	UPI0000197B83	.	deleterious_low_confidence(0.02)	probably_damaging(0.924)	1/11	.	hmmpanther:PTHR24118:SF38,hmmpanther:PTHR24118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGTGACAG	.	5	ESCA
EMILIN2	0	.	GRCh37	18	2891917	2891917	+	Missense_Mutation	SNP	G	G	A	rs115304890	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1792G>A	p.Glu598Lys	p.E598K	ENST00000254528	4/8	25	20	5	19	19	0	EMILIN2,missense_variant,p.Glu598Lys,ENST00000254528,;	A	ENSG00000132205	ENST00000254528	Transcript	missense_variant	1951	1792	598	E/K	Gaa/Aaa	rs115304890,COSM292396	.	.	1	EMILIN2	HGNC	19881	protein_coding	YES	CCDS11828.1	ENSP00000254528	EMIL2_HUMAN	.	UPI000013CE3E	.	tolerated(0.29)	benign(0.006)	4/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF5	A:0.0008	A:0.003	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACCGAACAA	byFrequency|byCluster|by1000G	4	ESCA
DTNA	0	.	GRCh37	18	32335947	32335947	+	Missense_Mutation	SNP	G	G	A	rs200021359	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7G>A	p.Glu3Lys	p.E3K	ENST00000598334	3/20	46	34	12	35	35	0	DTNA,missense_variant,p.Glu3Lys,ENST00000399113,;DTNA,missense_variant,p.Glu3Lys,ENST00000588684,;DTNA,missense_variant,p.Glu3Lys,ENST00000588125,;DTNA,missense_variant,p.Glu3Lys,ENST00000348997,;DTNA,missense_variant,p.Glu3Lys,ENST00000598334,;DTNA,missense_variant,p.Glu3Lys,ENST00000315456,;DTNA,missense_variant,p.Glu3Lys,ENST00000598774,;DTNA,missense_variant,p.Glu3Lys,ENST00000597599,;DTNA,missense_variant,p.Glu3Lys,ENST00000590598,;DTNA,missense_variant,p.Glu3Lys,ENST00000444659,;DTNA,missense_variant,p.Glu3Lys,ENST00000399121,;DTNA,missense_variant,p.Glu3Lys,ENST00000269190,;DTNA,missense_variant,p.Glu3Lys,ENST00000269191,;DTNA,missense_variant,p.Glu3Lys,ENST00000590412,;DTNA,missense_variant,p.Glu3Lys,ENST00000596745,;DTNA,missense_variant,p.Glu3Lys,ENST00000598142,;DTNA,missense_variant,p.Glu3Lys,ENST00000554864,;DTNA,missense_variant,p.Glu3Lys,ENST00000595022,;DTNA,missense_variant,p.Glu3Lys,ENST00000283365,;DTNA,5_prime_UTR_variant,,ENST00000588949,;DTNA,5_prime_UTR_variant,,ENST00000591816,;DTNA,5_prime_UTR_variant,,ENST00000399097,;RP11-138H11.1,intron_variant,,ENST00000596954,;DTNA,intron_variant,,ENST00000585446,;	A	ENSG00000134769	ENST00000598334	Transcript	missense_variant	333	7	3	E/K	Gaa/Aaa	rs200021359,COSM3937735,COSM3937734,COSM3937736,COSM3937732,COSM3937733,COSM3937731,COSM3937730	.	.	1	DTNA	HGNC	3057	protein_coding	YES	CCDS59312.1	ENSP00000470152	.	M0QYX6_HUMAN,K7ERZ2_HUMAN,K7ERH7_HUMAN,K7ER73_HUMAN,K7ENJ7_HUMAN,K7EMN1_HUMAN,K7EJ84_HUMAN	UPI0001E92A2F	.	deleterious_low_confidence(0)	possibly_damaging(0.702)	3/20	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF268,PIRSF_domain:PIRSF038204	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTGAAGAT	byCluster|by1000G	5	ESCA
TCEB3B	0	.	GRCh37	18	44561247	44561247	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389G>A	p.Arg130Gln	p.R130Q	ENST00000332567	1/1	87	56	30	94	94	0	TCEB3B,missense_variant,p.Arg130Gln,ENST00000332567,;KATNAL2,intron_variant,,ENST00000245121,;KATNAL2,intron_variant,,ENST00000356157,;KATNAL2,intron_variant,,ENST00000592005,;KATNAL2,intron_variant,,ENST00000585469,;TCEB3C,upstream_gene_variant,,ENST00000330682,;	T	ENSG00000206181	ENST00000332567	Transcript	missense_variant	742	389	130	R/Q	cGg/cAg	COSM3526064	.	.	-1	TCEB3B	HGNC	30771	protein_coding	YES	CCDS11932.1	ENSP00000331302	ELOA2_HUMAN	.	UPI0000140A82	.	tolerated(1)	benign(0.118)	1/1	.	hmmpanther:PTHR15141:SF7,hmmpanther:PTHR15141	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCCGTCTG	.	5	ESCA
BCL2	0	.	GRCh37	18	60986083	60986083	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-184C>T	.	.	ENST00000398117	1/2	44	39	5	39	39	0	BCL2,5_prime_UTR_variant,,ENST00000333681,;BCL2,5_prime_UTR_variant,,ENST00000444484,;BCL2,5_prime_UTR_variant,,ENST00000398117,;BCL2,upstream_gene_variant,,ENST00000589955,;RP11-28F1.2,upstream_gene_variant,,ENST00000588307,;	A	ENSG00000171791	ENST00000398117	Transcript	5_prime_UTR_variant	1279	.	.	.	.	.	.	.	-1	BCL2	HGNC	990	protein_coding	YES	CCDS11981.1	ENSP00000381185	BCL2_HUMAN	Q96PA0_HUMAN	UPI000000D90E	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCATGAGATG	.	4	ESCA
KRI1	0	.	GRCh37	19	10671094	10671094	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712G>C	p.Glu238Gln	p.E238Q	ENST00000312962	9/19	28	24	4	31	31	0	KRI1,missense_variant,p.Glu238Gln,ENST00000312962,;KRI1,missense_variant,p.Glu234Gln,ENST00000361821,;KRI1,missense_variant,p.Glu176Gln,ENST00000543682,;KRI1,intron_variant,,ENST00000539027,;KRI1,downstream_gene_variant,,ENST00000537964,;KRI1,3_prime_UTR_variant,,ENST00000546063,;KRI1,3_prime_UTR_variant,,ENST00000432197,;KRI1,non_coding_transcript_exon_variant,,ENST00000536689,;KRI1,non_coding_transcript_exon_variant,,ENST00000478863,;KRI1,downstream_gene_variant,,ENST00000544397,;KRI1,upstream_gene_variant,,ENST00000543842,;KRI1,upstream_gene_variant,,ENST00000537433,;KRI1,upstream_gene_variant,,ENST00000537363,;KRI1,upstream_gene_variant,,ENST00000536714,;	G	ENSG00000129347	ENST00000312962	Transcript	missense_variant	732	712	238	E/Q	Gag/Cag	COSM710176	.	.	-1	KRI1	HGNC	25769	protein_coding	YES	CCDS12242.1	ENSP00000320917	KRI1_HUMAN	.	UPI0000246DCC	.	tolerated(0.24)	benign(0.04)	9/19	.	hmmpanther:PTHR14490	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACTCAGGGT	.	4	ESCA
ILF3	0	.	GRCh37	19	10789847	10789847	+	Silent	SNP	C	C	T	rs767239358	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726C>T	p.%3D	p.T242T	ENST00000449870	7/20	28	24	4	42	42	0	ILF3,synonymous_variant,p.%3D,ENST00000590261,;ILF3,synonymous_variant,p.%3D,ENST00000318511,;ILF3,synonymous_variant,p.%3D,ENST00000589998,;ILF3,synonymous_variant,p.%3D,ENST00000407004,;ILF3,synonymous_variant,p.%3D,ENST00000592763,;ILF3,synonymous_variant,p.%3D,ENST00000590009,;ILF3,synonymous_variant,p.%3D,ENST00000250241,;ILF3,synonymous_variant,p.%3D,ENST00000588657,;ILF3,synonymous_variant,p.%3D,ENST00000420083,;ILF3,synonymous_variant,p.%3D,ENST00000449870,;ILF3,downstream_gene_variant,,ENST00000589600,;ILF3,upstream_gene_variant,,ENST00000593061,;ILF3,upstream_gene_variant,,ENST00000590869,;ILF3,synonymous_variant,p.%3D,ENST00000585835,;ILF3,synonymous_variant,p.%3D,ENST00000589416,;ILF3,synonymous_variant,p.%3D,ENST00000589485,;ILF3,3_prime_UTR_variant,,ENST00000587840,;ILF3,3_prime_UTR_variant,,ENST00000587505,;ILF3,non_coding_transcript_exon_variant,,ENST00000587928,;ILF3,upstream_gene_variant,,ENST00000589173,;ILF3,downstream_gene_variant,,ENST00000589052,;	T	ENSG00000129351	ENST00000449870	Transcript	synonymous_variant	1043	726	242	T	acC/acT	rs767239358	.	.	1	ILF3	HGNC	6038	protein_coding	YES	CCDS45965.1	ENSP00000404121	ILF3_HUMAN	K7ERM6_HUMAN,K7ER69_HUMAN,K7EM82_HUMAN,K7EKJ9_HUMAN,K7EJ09_HUMAN	UPI000059D66A	.	.	.	7/20	.	SMART_domains:SM00572,Pfam_domain:PF07528,hmmpanther:PTHR10910:SF34,hmmpanther:PTHR10910,PROSITE_profiles:PS51703	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCACCTGGGG	byFrequency	4	ESCA
CCDC151	0	.	GRCh37	19	11537020	11537020	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.907G>C	p.Glu303Gln	p.E303Q	ENST00000356392	7/13	53	46	7	66	66	0	CCDC151,missense_variant,p.Glu243Gln,ENST00000591179,;CCDC151,missense_variant,p.Glu303Gln,ENST00000356392,;CCDC151,missense_variant,p.Glu112Gln,ENST00000586836,;CCDC151,missense_variant,p.Glu249Gln,ENST00000545100,;CCDC151,3_prime_UTR_variant,,ENST00000591345,;CCDC151,downstream_gene_variant,,ENST00000593281,;	G	ENSG00000198003	ENST00000356392	Transcript	missense_variant	995	907	303	E/Q	Gag/Cag	.	.	.	-1	CCDC151	HGNC	28303	protein_coding	YES	CCDS42501.1	ENSP00000348757	CC151_HUMAN	K7EPK8_HUMAN,B7ZMB9_HUMAN	UPI000040CC83	.	tolerated(0.06)	possibly_damaging(0.743)	7/13	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21694:SF1,hmmpanther:PTHR21694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACTCACTTA	.	4	ESCA
CD97	0	.	GRCh37	19	14513415	14513415	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1190C>T	p.Ala397Val	p.A397V	ENST00000242786	12/20	23	20	3	30	30	0	CD97,missense_variant,p.Ala397Val,ENST00000242786,;CD97,missense_variant,p.Ala348Val,ENST00000357355,;CD97,missense_variant,p.Ala304Val,ENST00000358600,;CD97,downstream_gene_variant,,ENST00000586517,;CTC-548K16.5,downstream_gene_variant,,ENST00000590626,;CD97,downstream_gene_variant,,ENST00000587728,;CD97,downstream_gene_variant,,ENST00000587319,;CD97,downstream_gene_variant,,ENST00000593028,;CD97,downstream_gene_variant,,ENST00000591737,;CD97,upstream_gene_variant,,ENST00000591565,;CD97,downstream_gene_variant,,ENST00000590567,;CD97,downstream_gene_variant,,ENST00000586849,;CD97,downstream_gene_variant,,ENST00000592341,;	T	ENSG00000123146	ENST00000242786	Transcript	missense_variant	1270	1190	397	A/V	gCc/gTc	.	.	.	1	CD97	HGNC	1711	protein_coding	YES	CCDS32929.1	ENSP00000242786	CD97_HUMAN	.	UPI0000161C9A	.	tolerated(0.1)	benign(0.032)	12/20	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF253	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CCCCGCCGTGG	.	2	ESCA
F2RL3	0	.	GRCh37	19	17000097	17000097	+	Missense_Mutation	SNP	G	G	A	rs200284465	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>A	p.Gly33Arg	p.G33R	ENST00000248076	1/2	90	76	14	103	103	0	F2RL3,missense_variant,p.Gly33Arg,ENST00000599210,;F2RL3,missense_variant,p.Gly33Arg,ENST00000248076,;CPAMD8,downstream_gene_variant,,ENST00000598792,;CPAMD8,downstream_gene_variant,,ENST00000443236,;CPAMD8,downstream_gene_variant,,ENST00000594249,;CPAMD8,downstream_gene_variant,,ENST00000598547,;CPAMD8,downstream_gene_variant,,ENST00000602132,;CPAMD8,downstream_gene_variant,,ENST00000597335,;CPAMD8,downstream_gene_variant,,ENST00000600235,;CPAMD8,downstream_gene_variant,,ENST00000596224,;CPAMD8,downstream_gene_variant,,ENST00000601782,;	A	ENSG00000127533	ENST00000248076	Transcript	missense_variant	427	97	33	G/R	Gga/Aga	rs200284465	.	.	1	F2RL3	HGNC	3540	protein_coding	YES	CCDS12350.1	ENSP00000248076	PAR4_HUMAN	.	UPI000013CC36	.	tolerated(0.19)	benign(0.007)	1/2	.	Low_complexity_(Seg):seg,Prints_domain:PR01430	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACCGGAGGT	byCluster|by1000G	4	ESCA
UNC13A	0	.	GRCh37	19	17715907	17715907	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*956C>T	.	.	ENST00000519716	44/44	71	64	6	60	60	0	UNC13A,3_prime_UTR_variant,,ENST00000252773,;UNC13A,3_prime_UTR_variant,,ENST00000519716,;UNC13A,3_prime_UTR_variant,,ENST00000428389,;UNC13A,downstream_gene_variant,,ENST00000552293,;UNC13A,downstream_gene_variant,,ENST00000550896,;UNC13A,downstream_gene_variant,,ENST00000551649,;UNC13A,downstream_gene_variant,,ENST00000523229,;UNC13A,downstream_gene_variant,,ENST00000517497,;	A	ENSG00000130477	ENST00000519716	Transcript	3_prime_UTR_variant	6068	.	.	.	.	.	.	.	-1	UNC13A	HGNC	23150	protein_coding	YES	CCDS46013.2	ENSP00000429562	UN13A_HUMAN	.	UPI00006C19A7	.	.	.	44/44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGGCGAAGTA	.	3	ESCA
C19orf12	0	.	GRCh37	19	30193476	30193476	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*143G>C	.	.	ENST00000392278	3/3	27	16	11	14	14	0	C19orf12,3_prime_UTR_variant,,ENST00000392276,;C19orf12,3_prime_UTR_variant,,ENST00000392278,;C19orf12,3_prime_UTR_variant,,ENST00000323670,;C19orf12,3_prime_UTR_variant,,ENST00000592153,;C19orf12,downstream_gene_variant,,ENST00000591243,;C19orf12,non_coding_transcript_exon_variant,,ENST00000392275,;C19orf12,downstream_gene_variant,,ENST00000342680,;	G	ENSG00000131943	ENST00000392278	Transcript	3_prime_UTR_variant	729	.	.	.	.	.	.	.	-1	C19orf12	HGNC	25443	protein_coding	YES	CCDS42542.1	ENSP00000376103	CS012_HUMAN	K7EPS8_HUMAN	UPI0000DB2738	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCTCCAG	.	5	ESCA
SLC7A9	0	.	GRCh37	19	33333110	33333110	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1188G>A	p.Met396Ile	p.M396I	ENST00000023064	11/13	41	37	4	26	26	0	SLC7A9,missense_variant,p.Met396Ile,ENST00000023064,;SLC7A9,missense_variant,p.Met396Ile,ENST00000590341,;SLC7A9,missense_variant,p.Met396Ile,ENST00000587772,;SLC7A9,3_prime_UTR_variant,,ENST00000592232,;SLC7A9,3_prime_UTR_variant,,ENST00000590465,;	T	ENSG00000021488	ENST00000023064	Transcript	missense_variant	1380	1188	396	M/I	atG/atA	.	.	.	-1	SLC7A9	HGNC	11067	protein_coding	YES	CCDS12425.1	ENSP00000023064	BAT1_HUMAN	K7EIF5_HUMAN	UPI0000037773	.	deleterious(0.01)	possibly_damaging(0.542)	11/13	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF305,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATCTCATCAC	.	4	ESCA
ZNF540	0	.	GRCh37	19	38102736	38102736	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555G>A	p.%3D	p.V185V	ENST00000592533	5/5	57	44	12	32	32	0	ZNF540,synonymous_variant,p.%3D,ENST00000316433,;ZNF540,synonymous_variant,p.%3D,ENST00000343599,;ZNF540,synonymous_variant,p.%3D,ENST00000589117,;ZNF540,synonymous_variant,p.%3D,ENST00000586134,;ZNF540,synonymous_variant,p.%3D,ENST00000592533,;ZNF540,3_prime_UTR_variant,,ENST00000586792,;ZNF540,downstream_gene_variant,,ENST00000590588,;ZFP30,downstream_gene_variant,,ENST00000589018,;ZNF540,downstream_gene_variant,,ENST00000589857,;ZNF540,non_coding_transcript_exon_variant,,ENST00000589285,;	A	ENSG00000171817	ENST00000592533	Transcript	synonymous_variant	887	555	185	V	gtG/gtA	.	.	.	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	.	.	5/5	.	hmmpanther:PTHR24377:SF138,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGTGAAACA	.	5	ESCA
GPR32	0	.	GRCh37	19	51273966	51273966	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.109G>C	p.Glu37Gln	p.E37Q	ENST00000270590	1/1	94	87	7	62	62	0	GPR32,missense_variant,p.Glu37Gln,ENST00000270590,;	C	ENSG00000142511	ENST00000270590	Transcript	missense_variant	246	109	37	E/Q	Gag/Cag	COSM1718987	.	.	1	GPR32	HGNC	4487	protein_coding	YES	CCDS12801.1	ENSP00000270590	GPR32_HUMAN	H9NIL6_HUMAN	UPI000005045C	.	tolerated(0.18)	benign(0.06)	1/1	.	hmmpanther:PTHR24225:SF27,hmmpanther:PTHR24225,Gene3D:1.20.1070.10	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTCTGAGGAG	.	2	ESCA
SPACA6P	0	.	GRCh37	19	52196977	52196977	+	RNA	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.381C>G	.	.	ENST00000573266	1/8	15	11	4	10	10	0	SPACA6P,non_coding_transcript_exon_variant,,ENST00000576093,;SPACA6P,non_coding_transcript_exon_variant,,ENST00000573266,;MIRLET7E,downstream_gene_variant,,ENST00000362102,;SPACA6P-AS,upstream_gene_variant,,ENST00000602324,;MIR99B,downstream_gene_variant,,ENST00000384819,;MIR125A,downstream_gene_variant,,ENST00000385273,;SPACA6P,upstream_gene_variant,,ENST00000574072,;SPACA6P,upstream_gene_variant,,ENST00000576494,;SPACA6P,upstream_gene_variant,,ENST00000571328,;AC018755.2,non_coding_transcript_exon_variant,,ENST00000331594,;	G	ENSG00000182310	ENST00000573266	Transcript	non_coding_transcript_exon_variant	381	.	.	.	.	.	.	.	1	SPACA6P	HGNC	27113	lincRNA	YES	.	.	.	.	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCTCTGA	.	5	ESCA
FPR2	0	.	GRCh37	19	52272700	52272700	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.789G>T	p.%3D	p.L263L	ENST00000598776	2/2	80	65	15	39	39	0	FPR2,synonymous_variant,p.%3D,ENST00000340023,;FPR2,synonymous_variant,p.%3D,ENST00000598953,;FPR2,synonymous_variant,p.%3D,ENST00000598776,;FPR1,intron_variant,,ENST00000594900,;FPR2,downstream_gene_variant,,ENST00000599326,;FPR2,downstream_gene_variant,,ENST00000600258,;FPR2,downstream_gene_variant,,ENST00000600722,;	T	ENSG00000171049	ENST00000598776	Transcript	synonymous_variant	1561	789	263	L	ctG/ctT	.	.	.	1	FPR2	HGNC	3827	protein_coding	YES	CCDS12840.1	ENSP00000468897	FPR2_HUMAN	M0R222_HUMAN,M0QZ89_HUMAN,M0QXD3_HUMAN	UPI00000012D0	.	.	.	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF16,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTGGGCAC	.	5	ESCA
MIR520B	0	.	GRCh37	19	54204512	54204512	+	RNA	SNP	A	A	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.32A>C	.	.	ENST00000384989	1/1	57	51	5	37	37	0	MIR520B,non_coding_transcript_exon_variant,,ENST00000384989,;MIR525,downstream_gene_variant,,ENST00000384978,;MIR518B,upstream_gene_variant,,ENST00000385127,;MIR518F,downstream_gene_variant,,ENST00000384973,;MIR523,downstream_gene_variant,,ENST00000385281,;MIR526A1,upstream_gene_variant,,ENST00000384897,;	C	ENSG00000207722	ENST00000384989	Transcript	non_coding_transcript_exon_variant	32	.	.	.	.	.	.	.	1	MIR520B	HGNC	32105	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTGAAAGAA	.	4	ESCA
CACNG8	0	.	GRCh37	19	54485522	54485522	+	Missense_Mutation	SNP	G	G	C	rs750396252	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.697G>C	p.Glu233Gln	p.E233Q	ENST00000270458	4/4	67	52	14	55	55	0	CACNG8,missense_variant,p.Glu233Gln,ENST00000270458,;MIR935,upstream_gene_variant,,ENST00000401179,;	C	ENSG00000142408	ENST00000270458	Transcript	missense_variant	800	697	233	E/Q	Gag/Cag	rs750396252,COSM1305069	.	.	1	CACNG8	HGNC	13628	protein_coding	YES	CCDS33104.1	ENSP00000270458	CCG8_HUMAN	.	UPI000013D88B	.	tolerated(0.32)	probably_damaging(0.982)	4/4	.	hmmpanther:PTHR12107,hmmpanther:PTHR12107:SF2,Prints_domain:PR01796	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCGAGGCG	byFrequency	5	ESCA
LENG1	0	.	GRCh37	19	54659418	54659418	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*41C>G	.	.	ENST00000222224	4/4	100	72	28	70	70	0	LENG1,3_prime_UTR_variant,,ENST00000222224,;CNOT3,3_prime_UTR_variant,,ENST00000406403,;CNOT3,3_prime_UTR_variant,,ENST00000471126,;CNOT3,3_prime_UTR_variant,,ENST00000221232,;TMC4,downstream_gene_variant,,ENST00000376591,;TMC4,downstream_gene_variant,,ENST00000301187,;CNOT3,downstream_gene_variant,,ENST00000457463,;TMC4,downstream_gene_variant,,ENST00000416963,;CNOT3,downstream_gene_variant,,ENST00000358389,;CNOT3,downstream_gene_variant,,ENST00000496327,;CNOT3,3_prime_UTR_variant,,ENST00000447684,;CNOT3,non_coding_transcript_exon_variant,,ENST00000482247,;CNOT3,non_coding_transcript_exon_variant,,ENST00000489953,;TMC4,downstream_gene_variant,,ENST00000449860,;TMC4,downstream_gene_variant,,ENST00000494594,;TMC4,downstream_gene_variant,,ENST00000465790,;	C	ENSG00000105617	ENST00000222224	Transcript	3_prime_UTR_variant	1023	.	.	.	.	.	.	.	-1	LENG1	HGNC	15502	protein_coding	YES	CCDS12881.1	ENSP00000222224	LENG1_HUMAN	.	UPI0000073A30	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATGACGGC	.	5	ESCA
AC003006.7	0	.	GRCh37	19	58264886	58264886	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388C>T	p.His130Tyr	p.H130Y	ENST00000594684	3/3	49	41	8	44	44	0	AC003006.7,missense_variant,p.His130Tyr,ENST00000594684,;ZNF776,missense_variant,p.His130Tyr,ENST00000317178,;ZNF776,intron_variant,,ENST00000451849,;ZNF776,downstream_gene_variant,,ENST00000431353,;ZNF776,upstream_gene_variant,,ENST00000489376,;ZNF776,downstream_gene_variant,,ENST00000473585,;	T	ENSG00000269026	ENST00000594684	Transcript	missense_variant	555	388	130	H/Y	Cat/Tat	.	.	.	1	AC003006.7	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000472160	.	M0R1X1_HUMAN	UPI0002A47213	.	tolerated(0.21)	benign(0.012)	3/3	.	hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCATCATCAA	.	4	ESCA
ZNF587B	0	.	GRCh37	19	58341865	58341865	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-32C>T	.	.	ENST00000442832	1/4	60	49	11	32	32	0	ZNF587B,5_prime_UTR_variant,,ENST00000594901,;ZNF587B,5_prime_UTR_variant,,ENST00000442832,;CTD-2583A14.10,intron_variant,,ENST00000598031,;ZNF587B,intron_variant,,ENST00000594328,;ZNF587B,intron_variant,,ENST00000316462,;CTD-2583A14.10,intron_variant,,ENST00000597134,;CTD-2583A14.10,intron_variant,,ENST00000593873,;CTD-2583A14.10,intron_variant,,ENST00000596498,;CTD-2583A14.10,intron_variant,,ENST00000603271,;CTD-2583A14.10,5_prime_UTR_variant,,ENST00000604231,;AC010522.1,upstream_gene_variant,,ENST00000594588,;	T	ENSG00000269343	ENST00000442832	Transcript	5_prime_UTR_variant	203	.	.	.	.	.	.	.	1	ZNF587B	HGNC	37142	protein_coding	YES	CCDS56109.1	ENSP00000392410	Z587B_HUMAN	.	UPI0001AE657B	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CCTCTCCTCCC	.	3	ESCA
RANBP3	0	.	GRCh37	19	5921258	5921258	+	Silent	SNP	G	G	C	rs774907276	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1284C>G	p.%3D	p.L428L	ENST00000340578	14/17	47	41	6	44	44	0	RANBP3,synonymous_variant,p.%3D,ENST00000591092,;RANBP3,synonymous_variant,p.%3D,ENST00000439268,;RANBP3,synonymous_variant,p.%3D,ENST00000340578,;RANBP3,synonymous_variant,p.%3D,ENST00000541471,;RANBP3,synonymous_variant,p.%3D,ENST00000034275,;RANBP3,synonymous_variant,p.%3D,ENST00000587479,;RANBP3,downstream_gene_variant,,ENST00000590623,;RANBP3,downstream_gene_variant,,ENST00000591736,;RANBP3,downstream_gene_variant,,ENST00000592621,;RANBP3,3_prime_UTR_variant,,ENST00000592771,;RANBP3,non_coding_transcript_exon_variant,,ENST00000592197,;RANBP3,non_coding_transcript_exon_variant,,ENST00000587411,;RANBP3,non_coding_transcript_exon_variant,,ENST00000586344,;RANBP3,downstream_gene_variant,,ENST00000587799,;RANBP3,downstream_gene_variant,,ENST00000593025,;	C	ENSG00000031823	ENST00000340578	Transcript	synonymous_variant	1342	1284	428	L	ctC/ctG	rs774907276	.	.	-1	RANBP3	HGNC	9850	protein_coding	YES	CCDS42478.1	ENSP00000341483	RANB3_HUMAN	K7ESQ0_HUMAN,K7EMH9_HUMAN,K7EIJ4_HUMAN	UPI000006F919	.	.	.	14/17	.	PROSITE_profiles:PS50196,hmmpanther:PTHR23138:SF91,hmmpanther:PTHR23138,Pfam_domain:PF00638,Gene3D:2.30.29.30,SMART_domains:SM00160,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATTGAGTCT	.	4	ESCA
ZNF358	0	.	GRCh37	19	7585086	7585086	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958C>T	p.Arg320Cys	p.R320C	ENST00000597229	2/2	25	18	7	24	24	0	ZNF358,missense_variant,p.Arg320Cys,ENST00000394341,;ZNF358,missense_variant,p.Arg320Cys,ENST00000597229,;CTD-2207O23.12,downstream_gene_variant,,ENST00000599312,;MCOLN1,upstream_gene_variant,,ENST00000264079,;MCOLN1,upstream_gene_variant,,ENST00000601003,;ZNF358,downstream_gene_variant,,ENST00000596712,;CTD-2207O23.11,intron_variant,,ENST00000602083,;CTD-2207O23.12,downstream_gene_variant,,ENST00000597384,;MCOLN1,upstream_gene_variant,,ENST00000394321,;MCOLN1,upstream_gene_variant,,ENST00000596390,;	T	ENSG00000198816	ENST00000597229	Transcript	missense_variant	1128	958	320	R/C	Cgc/Tgc	.	.	.	1	ZNF358	HGNC	16838	protein_coding	YES	CCDS32890.2	ENSP00000472305	ZN358_HUMAN	M0R2S5_HUMAN	UPI0000201F0C	.	deleterious(0)	probably_damaging(0.999)	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF1,hmmpanther:PTHR24409,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTACCGCTGC	.	5	ESCA
CD209	0	.	GRCh37	19	7805640	7805640	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2285G>A	.	.	ENST00000315599	7/7	21	15	5	27	27	0	CD209,3_prime_UTR_variant,,ENST00000301357,;CD209,3_prime_UTR_variant,,ENST00000315599,;CD209,downstream_gene_variant,,ENST00000315591,;CD209,downstream_gene_variant,,ENST00000593660,;CD209,downstream_gene_variant,,ENST00000601256,;CD209,downstream_gene_variant,,ENST00000204801,;CD209,downstream_gene_variant,,ENST00000394161,;CD209,downstream_gene_variant,,ENST00000394173,;CD209,downstream_gene_variant,,ENST00000354397,;CD209,downstream_gene_variant,,ENST00000602261,;CD209,downstream_gene_variant,,ENST00000601951,;CD209,downstream_gene_variant,,ENST00000593821,;	T	ENSG00000090659	ENST00000315599	Transcript	3_prime_UTR_variant	3523	.	.	.	.	.	.	.	-1	CD209	HGNC	1641	protein_coding	YES	CCDS12186.1	ENSP00000315477	CD209_HUMAN	B4E2A8_HUMAN	UPI000003422C	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAGCGAAAG	.	5	ESCA
LAMTOR5	0	.	GRCh37	1	110950516	110950516	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-28G>A	.	.	ENST00000256644	1/4	25	21	4	26	26	0	LAMTOR5,5_prime_UTR_variant,,ENST00000256644,;LAMTOR5,upstream_gene_variant,,ENST00000483260,;LAMTOR5,upstream_gene_variant,,ENST00000602318,;LAMTOR5,upstream_gene_variant,,ENST00000474861,;LAMTOR5,upstream_gene_variant,,ENST00000602858,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000598454,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000610148,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000608499,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000608067,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000609709,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000587691,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000609244,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000457535,;LAMTOR5-AS1,non_coding_transcript_exon_variant,,ENST00000608486,;LAMTOR5-AS1,intron_variant,,ENST00000590413,;LAMTOR5-AS1,upstream_gene_variant,,ENST00000590826,;LAMTOR5-AS1,upstream_gene_variant,,ENST00000608253,;LAMTOR5-AS1,upstream_gene_variant,,ENST00000609512,;LAMTOR5-AS1,upstream_gene_variant,,ENST00000585330,;LAMTOR5-AS1,upstream_gene_variant,,ENST00000609653,;LAMTOR5-AS1,upstream_gene_variant,,ENST00000608602,;LAMTOR5,upstream_gene_variant,,ENST00000531779,;LAMTOR5,upstream_gene_variant,,ENST00000464240,;	T	ENSG00000134248	ENST00000256644	Transcript	5_prime_UTR_variant	49	.	.	.	.	.	.	.	-1	LAMTOR5	HGNC	17955	protein_coding	YES	CCDS824.1	ENSP00000256644	LTOR5_HUMAN	R4GMU8_HUMAN	UPI0000205288	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TATTCCCCTCT	.	2	ESCA
CHIA	0	.	GRCh37	1	111833492	111833494	+	5'Flank	INS	CTC	CTC	TCCTG	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000369740	.	27	18	9	20	20	0	CHIA,frameshift_variant,p.Ser4ProfsTer26,ENST00000422815,;CHIA,5_prime_UTR_variant,,ENST00000483391,;CHIA,upstream_gene_variant,,ENST00000369740,;CHIAP2,downstream_gene_variant,,ENST00000449687,;CHIAP2,downstream_gene_variant,,ENST00000369743,;CHIAP2,downstream_gene_variant,,ENST00000532686,;	TCCTG	ENSG00000134216	ENST00000369740	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	44	1	CHIA	HGNC	17432	protein_coding	YES	CCDS41368.1	ENSP00000358755	CHIA_HUMAN	E9PLJ2_HUMAN	UPI00000727DC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT*|PINDEL	AACCTCCTCGTCTG	.	2	ESCA
OLFML3	0	.	GRCh37	1	114524823	114524823	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*432C>G	.	.	ENST00000320334	3/3	68	55	12	51	51	0	OLFML3,3_prime_UTR_variant,,ENST00000369551,;OLFML3,3_prime_UTR_variant,,ENST00000393300,;OLFML3,3_prime_UTR_variant,,ENST00000320334,;HIPK1,downstream_gene_variant,,ENST00000361587,;HIPK1,downstream_gene_variant,,ENST00000369554,;HIPK1,downstream_gene_variant,,ENST00000406344,;HIPK1,downstream_gene_variant,,ENST00000369558,;HIPK1,downstream_gene_variant,,ENST00000340480,;OLFML3,non_coding_transcript_exon_variant,,ENST00000491700,;	G	ENSG00000116774	ENST00000320334	Transcript	3_prime_UTR_variant	1727	.	.	.	.	.	.	.	1	OLFML3	HGNC	24956	protein_coding	YES	CCDS870.1	ENSP00000322273	OLFL3_HUMAN	M1LAK4_HUMAN,B4DNG0_HUMAN	UPI000003B091	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTCTCCAC	.	5	ESCA
TNFRSF8	0	.	GRCh37	1	12164492	12164492	+	Nonsense_Mutation	SNP	C	C	T	rs148756853	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.325C>T	p.Arg109Ter	p.R109*	ENST00000263932	4/15	53	41	11	58	58	0	TNFRSF8,stop_gained,p.Arg109Ter,ENST00000263932,;TNFRSF8,5_prime_UTR_variant,,ENST00000417814,;TNFRSF8,3_prime_UTR_variant,,ENST00000514649,;	T	ENSG00000120949	ENST00000263932	Transcript	stop_gained	547	325	109	R/*	Cga/Tga	rs148756853,COSM3399616	.	.	1	TNFRSF8	HGNC	11923	protein_coding	YES	CCDS144.1	ENSP00000263932	.	A5D8T4_HUMAN	UPI000013D48C	.	.	.	4/15	.	PROSITE_profiles:PS50050,hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF85,Gene3D:2.10.50.10,SMART_domains:SM00208,Superfamily_domains:SSF57586	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGTCGACCC	byCluster	5	ESCA
PRKAB2	0	.	GRCh37	1	146627394	146627394	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3750C>G	.	.	ENST00000254101	8/8	36	27	9	29	29	0	PRKAB2,3_prime_UTR_variant,,ENST00000254101,;PRKAB2,downstream_gene_variant,,ENST00000425272,;PRKAB2,downstream_gene_variant,,ENST00000496858,;	C	ENSG00000131791	ENST00000254101	Transcript	3_prime_UTR_variant	4708	.	.	.	.	.	.	.	-1	PRKAB2	HGNC	9379	protein_coding	YES	CCDS925.1	ENSP00000254101	AAKB2_HUMAN	.	UPI00001250AF	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACTAGAATCC	.	2	ESCA
MTMR11	0	.	GRCh37	1	149902816	149902816	+	Silent	SNP	G	G	A	rs782240807	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1332C>T	p.%3D	p.L444L	ENST00000439741	14/17	37	30	7	29	29	0	MTMR11,missense_variant,p.Ser242Phe,ENST00000361405,;MTMR11,synonymous_variant,p.%3D,ENST00000369140,;MTMR11,synonymous_variant,p.%3D,ENST00000439741,;MTMR11,3_prime_UTR_variant,,ENST00000406732,;SF3B4,upstream_gene_variant,,ENST00000457312,;SF3B4,upstream_gene_variant,,ENST00000271628,;MTMR11,non_coding_transcript_exon_variant,,ENST00000495054,;MTMR11,non_coding_transcript_exon_variant,,ENST00000492824,;MTMR11,non_coding_transcript_exon_variant,,ENST00000482025,;MTMR11,non_coding_transcript_exon_variant,,ENST00000466496,;MTMR11,non_coding_transcript_exon_variant,,ENST00000490310,;MTMR11,downstream_gene_variant,,ENST00000493562,;MTMR11,downstream_gene_variant,,ENST00000479272,;MTMR11,non_coding_transcript_exon_variant,,ENST00000482343,;	A	ENSG00000014914	ENST00000439741	Transcript	synonymous_variant	1583	1332	444	L	ctC/ctT	rs782240807	.	.	-1	MTMR11	HGNC	24307	protein_coding	YES	CCDS53360.1	ENSP00000391668	MTMRB_HUMAN	.	UPI000173AA17	.	.	.	14/17	.	Superfamily_domains:SSF52799,Pfam_domain:PF06602,hmmpanther:PTHR10807:SF51,hmmpanther:PTHR10807,PROSITE_profiles:PS51339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGGAGCTG	.	5	ESCA
RPTN	0	.	GRCh37	1	152128077	152128077	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498G>A	p.Gly500Ser	p.G500S	ENST00000316073	3/3	225	178	47	205	205	0	RPTN,missense_variant,p.Gly500Ser,ENST00000316073,;	T	ENSG00000215853	ENST00000316073	Transcript	missense_variant	1563	1498	500	G/S	Ggt/Agt	.	.	.	-1	RPTN	HGNC	26809	protein_coding	YES	CCDS41397.1	ENSP00000317895	RPTN_HUMAN	Q8N1M7_HUMAN,Q2M1U7_HUMAN	UPI00002371E2	.	tolerated(0.06)	possibly_damaging(0.45)	3/3	.	hmmpanther:PTHR22571:SF22,hmmpanther:PTHR22571	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACCATAAT	.	5	ESCA
KPRP	0	.	GRCh37	1	152732307	152732307	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.243G>A	p.%3D	p.V81V	ENST00000368773	2/2	45	38	6	28	28	0	KPRP,synonymous_variant,p.%3D,ENST00000368773,;KPRP,synonymous_variant,p.%3D,ENST00000606109,;	A	ENSG00000203786	ENST00000368773	Transcript	synonymous_variant	301	243	81	V	gtG/gtA	.	.	.	1	KPRP	HGNC	31823	protein_coding	YES	CCDS30862.1	ENSP00000357762	KPRP_HUMAN	.	UPI0000199942	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CAGGTGAAGGG	.	3	ESCA
NUP210L	0	.	GRCh37	1	154091197	154091197	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1414C>G	p.Leu472Val	p.L472V	ENST00000368559	11/40	49	36	13	36	36	0	NUP210L,missense_variant,p.Leu472Val,ENST00000368559,;NUP210L,missense_variant,p.Leu472Val,ENST00000271854,;	C	ENSG00000143552	ENST00000368559	Transcript	missense_variant	1486	1414	472	L/V	Ctg/Gtg	.	.	.	-1	NUP210L	HGNC	29915	protein_coding	YES	CCDS41399.1	ENSP00000357547	P210L_HUMAN	.	UPI000023724F	.	deleterious(0)	possibly_damaging(0.696)	11/40	.	hmmpanther:PTHR23019:SF1,hmmpanther:PTHR23019,Gene3D:2.60.40.1080,Superfamily_domains:SSF49373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCAGAAATT	.	5	ESCA
DAP3	0	.	GRCh37	1	155698908	155698908	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679G>C	p.Glu227Gln	p.E227Q	ENST00000368336	8/13	57	45	11	42	42	0	DAP3,missense_variant,p.Glu186Gln,ENST00000535183,;DAP3,missense_variant,p.Glu227Gln,ENST00000343043,;DAP3,missense_variant,p.Glu169Gln,ENST00000497826,;DAP3,missense_variant,p.Glu10Gln,ENST00000477394,;DAP3,missense_variant,p.Glu227Gln,ENST00000471214,;DAP3,missense_variant,p.Glu227Gln,ENST00000368336,;DAP3,missense_variant,p.Glu186Gln,ENST00000471642,;DAP3,missense_variant,p.Glu193Gln,ENST00000421487,;DAP3,intron_variant,,ENST00000463575,;MSTO1,intron_variant,,ENST00000538143,;DAP3,intron_variant,,ENST00000479151,;MSTO1,intron_variant,,ENST00000452804,;DAP3,upstream_gene_variant,,ENST00000490249,;DAP3,downstream_gene_variant,,ENST00000470830,;DAP3,upstream_gene_variant,,ENST00000463295,;DAP3,upstream_gene_variant,,ENST00000475056,;DAP3,downstream_gene_variant,,ENST00000496863,;DAP3,downstream_gene_variant,,ENST00000462002,;DAP3,non_coding_transcript_exon_variant,,ENST00000462978,;DAP3,non_coding_transcript_exon_variant,,ENST00000466384,;DAP3,downstream_gene_variant,,ENST00000471523,;DAP3,upstream_gene_variant,,ENST00000497433,;MSTO2P,intron_variant,,ENST00000538914,;	C	ENSG00000132676	ENST00000368336	Transcript	missense_variant	803	679	227	E/Q	Gaa/Caa	.	.	.	1	DAP3	HGNC	2673	protein_coding	YES	CCDS1120.1	ENSP00000357320	RT29_HUMAN	E2JL21_HUMAN	UPI000004ABE5	.	deleterious(0)	probably_damaging(0.944)	8/13	.	hmmpanther:PTHR12810,hmmpanther:PTHR12810:SF0,Pfam_domain:PF10236,Prints_domain:PR01716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTTGAACAG	.	5	ESCA
IQGAP3	0	.	GRCh37	1	156509318	156509318	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2904C>G	p.Ile968Met	p.I968M	ENST00000361170	25/38	46	43	3	25	25	0	IQGAP3,missense_variant,p.Ile968Met,ENST00000361170,;IQGAP3,upstream_gene_variant,,ENST00000476565,;IQGAP3,upstream_gene_variant,,ENST00000498755,;IQGAP3,missense_variant,p.Ile925Met,ENST00000491900,;	C	ENSG00000183856	ENST00000361170	Transcript	missense_variant	2915	2904	968	I/M	atC/atG	.	.	.	-1	IQGAP3	HGNC	20669	protein_coding	YES	CCDS1144.1	ENSP00000354451	IQGA3_HUMAN	F2Z2E2_HUMAN	UPI000046FFDD	.	tolerated(0.27)	benign(0.004)	25/38	.	hmmpanther:PTHR14149,hmmpanther:PTHR14149:SF10,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTAGATGGG	.	2	ESCA
ZBTB17	0	.	GRCh37	1	16269652	16269652	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735C>T	p.His579Tyr	p.H579Y	ENST00000375743	13/16	68	58	10	53	53	0	ZBTB17,missense_variant,p.His579Tyr,ENST00000375743,;ZBTB17,missense_variant,p.His136Tyr,ENST00000444358,;ZBTB17,missense_variant,p.His579Tyr,ENST00000375733,;ZBTB17,missense_variant,p.His497Tyr,ENST00000537142,;SPEN,downstream_gene_variant,,ENST00000375759,;ZBTB17,downstream_gene_variant,,ENST00000448462,;ZBTB17,upstream_gene_variant,,ENST00000440560,;ZBTB17,non_coding_transcript_exon_variant,,ENST00000488008,;ZBTB17,upstream_gene_variant,,ENST00000462525,;ZBTB17,downstream_gene_variant,,ENST00000474511,;ZBTB17,downstream_gene_variant,,ENST00000472658,;ZBTB17,downstream_gene_variant,,ENST00000471805,;ZBTB17,downstream_gene_variant,,ENST00000479282,;ZBTB17,downstream_gene_variant,,ENST00000464719,;SPEN,downstream_gene_variant,,ENST00000487496,;ZBTB17,downstream_gene_variant,,ENST00000490899,;ZBTB17,downstream_gene_variant,,ENST00000487785,;ZBTB17,downstream_gene_variant,,ENST00000494020,;ZBTB17,downstream_gene_variant,,ENST00000492834,;	A	ENSG00000116809	ENST00000375743	Transcript	missense_variant	1968	1735	579	H/Y	Cac/Tac	.	.	.	-1	ZBTB17	HGNC	12936	protein_coding	YES	CCDS165.1	ENSP00000364895	ZBT17_HUMAN	.	UPI000013C9D2	.	tolerated(0.35)	probably_damaging(0.968)	13/16	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24402:SF165,hmmpanther:PTHR24402,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGTGGCGAA	.	4	ESCA
RGS4	0	.	GRCh37	1	163042230	163042230	+	Silent	SNP	T	T	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381T>A	p.%3D	p.S127S	ENST00000421743	3/6	49	44	5	45	45	0	RGS4,synonymous_variant,p.%3D,ENST00000367908,;RGS4,synonymous_variant,p.%3D,ENST00000367909,;RGS4,synonymous_variant,p.%3D,ENST00000528938,;RGS4,synonymous_variant,p.%3D,ENST00000531057,;RGS4,synonymous_variant,p.%3D,ENST00000367906,;RGS4,synonymous_variant,p.%3D,ENST00000421743,;RGS4,synonymous_variant,p.%3D,ENST00000527809,;RGS4,non_coding_transcript_exon_variant,,ENST00000491263,;RGS4,non_coding_transcript_exon_variant,,ENST00000533019,;RGS4,non_coding_transcript_exon_variant,,ENST00000527393,;	A	ENSG00000117152	ENST00000421743	Transcript	synonymous_variant	541	381	127	S	tcT/tcA	.	.	.	1	RGS4	HGNC	10000	protein_coding	YES	CCDS44270.1	ENSP00000397181	RGS4_HUMAN	E9PS05_HUMAN	UPI0000E1EDBA	.	.	.	3/6	.	hmmpanther:PTHR10845:SF40,hmmpanther:PTHR10845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAATCTGATTC	.	3	ESCA
PBX1	0	.	GRCh37	1	164789343	164789343	+	Silent	SNP	A	A	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032A>T	p.%3D	p.G344G	ENST00000420696	7/9	51	43	7	68	68	0	PBX1,synonymous_variant,p.%3D,ENST00000540236,;PBX1,synonymous_variant,p.%3D,ENST00000560641,;PBX1,synonymous_variant,p.%3D,ENST00000420696,;PBX1,synonymous_variant,p.%3D,ENST00000540246,;PBX1,intron_variant,,ENST00000559240,;PBX1,intron_variant,,ENST00000367897,;PBX1,intron_variant,,ENST00000401534,;PBX1,non_coding_transcript_exon_variant,,ENST00000468104,;PBX1,non_coding_transcript_exon_variant,,ENST00000560469,;PBX1,non_coding_transcript_exon_variant,,ENST00000496120,;PBX1,intron_variant,,ENST00000558796,;PBX1,non_coding_transcript_exon_variant,,ENST00000465089,;	T	ENSG00000185630	ENST00000420696	Transcript	synonymous_variant	1220	1032	344	G	ggA/ggT	.	.	.	1	PBX1	HGNC	8632	protein_coding	YES	CCDS1246.1	ENSP00000405890	PBX1_HUMAN	Q68DD6_HUMAN,H0YLT4_HUMAN,H0YLM3_HUMAN,H0YLD4_HUMAN,H0YLB0_HUMAN,H0YKH1_HUMAN,F8WA05_HUMAN	UPI00000213E1	.	.	.	7/9	.	hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF58,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGGAGATTT	.	4	ESCA
ATP13A2	0	.	GRCh37	1	17314657	17314657	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2835C>G	p.Phe945Leu	p.F945L	ENST00000326735	25/29	39	36	3	25	25	0	ATP13A2,missense_variant,p.Phe141Leu,ENST00000502418,;ATP13A2,missense_variant,p.Phe940Leu,ENST00000452699,;ATP13A2,missense_variant,p.Phe901Leu,ENST00000341676,;ATP13A2,missense_variant,p.Phe945Leu,ENST00000326735,;ATP13A2,downstream_gene_variant,,ENST00000503552,;RP1-37C10.3,intron_variant,,ENST00000446261,;ATP13A2,non_coding_transcript_exon_variant,,ENST00000466561,;	C	ENSG00000159363	ENST00000326735	Transcript	missense_variant	2869	2835	945	F/L	ttC/ttG	.	.	.	-1	ATP13A2	HGNC	30213	protein_coding	YES	CCDS175.1	ENSP00000327214	AT132_HUMAN	Q8N4D4_HUMAN	UPI0000049724	.	deleterious(0)	probably_damaging(0.972)	25/29	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24093:SF86,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01657,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGATGAACTG	.	2	ESCA
CACYBP	0	.	GRCh37	1	174979138	174979138	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>A	p.Asp204Asn	p.D204N	ENST00000367679	6/6	43	36	7	44	44	0	CACYBP,missense_variant,p.Asp161Asn,ENST00000405362,;CACYBP,missense_variant,p.Asp161Asn,ENST00000367681,;CACYBP,missense_variant,p.Asp204Asn,ENST00000367679,;MRPS14,downstream_gene_variant,,ENST00000476371,;CACYBP,downstream_gene_variant,,ENST00000406752,;MRPS14,downstream_gene_variant,,ENST00000498253,;CACYBP,downstream_gene_variant,,ENST00000469173,;MRPS14,downstream_gene_variant,,ENST00000367677,;CACYBP,downstream_gene_variant,,ENST00000483307,;CACYBP,downstream_gene_variant,,ENST00000473925,;	A	ENSG00000116161	ENST00000367679	Transcript	missense_variant	1058	610	204	D/N	Gat/Aat	.	.	.	1	CACYBP	HGNC	30423	protein_coding	YES	CCDS1315.1	ENSP00000356652	CYBP_HUMAN	B2ZWH1_HUMAN	UPI0000032D9C	.	deleterious(0)	probably_damaging(1)	6/6	.	PROSITE_profiles:PS51048,hmmpanther:PTHR13164,Pfam_domain:PF05002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACGATGAT	.	5	ESCA
STX6	0	.	GRCh37	1	180943948	180943948	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1758C>G	.	.	ENST00000258301	8/8	24	20	4	28	28	0	STX6,3_prime_UTR_variant,,ENST00000258301,;AL162431.1,intron_variant,,ENST00000457152,;STX6,downstream_gene_variant,,ENST00000542060,;RP11-46A10.5,intron_variant,,ENST00000358073,;STX6,non_coding_transcript_exon_variant,,ENST00000469135,;RP11-46A10.8,downstream_gene_variant,,ENST00000604674,;	C	ENSG00000135823	ENST00000258301	Transcript	3_prime_UTR_variant	2764	.	.	.	.	.	.	.	-1	STX6	HGNC	11441	protein_coding	YES	CCDS1341.1	ENSP00000258301	STX6_HUMAN	B4DR17_HUMAN	UPI00000490D6	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATTTGAAAAT	.	2	ESCA
FAM129A	0	.	GRCh37	1	184792837	184792837	+	Missense_Mutation	SNP	G	G	C	rs769888720	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757C>G	p.Leu253Val	p.L253V	ENST00000367511	7/14	45	37	8	29	29	0	FAM129A,missense_variant,p.Leu253Val,ENST00000367511,;RNU7-13P,upstream_gene_variant,,ENST00000516413,;FAM129A,non_coding_transcript_exon_variant,,ENST00000461167,;FAM129A,intron_variant,,ENST00000487074,;	C	ENSG00000135842	ENST00000367511	Transcript	missense_variant	951	757	253	L/V	Ctt/Gtt	rs769888720	.	.	-1	FAM129A	HGNC	16784	protein_coding	YES	CCDS1364.1	ENSP00000356481	NIBAN_HUMAN	.	UPI00000375B3	.	deleterious(0)	probably_damaging(1)	7/14	.	hmmpanther:PTHR14392:SF3,hmmpanther:PTHR14392	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAGAGTGG	.	5	ESCA
CFH	0	.	GRCh37	1	196706631	196706631	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2623C>T	p.Gln875Ter	p.Q875*	ENST00000367429	17/22	57	47	10	46	46	0	CFH,stop_gained,p.Gln875Ter,ENST00000367429,;CFH,non_coding_transcript_exon_variant,,ENST00000470918,;CFH,non_coding_transcript_exon_variant,,ENST00000466229,;	T	ENSG00000000971	ENST00000367429	Transcript	stop_gained	2863	2623	875	Q/*	Cag/Tag	.	.	.	1	CFH	HGNC	4883	protein_coding	YES	CCDS1385.1	ENSP00000356399	CFAH_HUMAN	.	UPI000013C4D1	.	.	.	17/22	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF310,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCAGATA	.	5	ESCA
CFHR2	0	.	GRCh37	1	196927174	196927174	+	Missense_Mutation	SNP	G	G	A	rs776884192	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.584G>A	p.Gly195Glu	p.G195E	ENST00000367415	4/5	63	53	10	53	53	0	CFHR2,missense_variant,p.Gly195Glu,ENST00000367421,;CFHR2,missense_variant,p.Gly195Glu,ENST00000367415,;CFHR2,missense_variant,p.Gly179Glu,ENST00000476712,;CFHR2,non_coding_transcript_exon_variant,,ENST00000473386,;CFHR2,non_coding_transcript_exon_variant,,ENST00000496448,;	A	ENSG00000080910	ENST00000367415	Transcript	missense_variant	684	584	195	G/E	gGa/gAa	rs776884192	.	.	1	CFHR2	HGNC	4890	protein_coding	YES	CCDS30959.1	ENSP00000356385	FHR2_HUMAN	.	UPI000012A73B	.	deleterious(0)	possibly_damaging(0.5)	4/5	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF325,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACGGACAAT	.	4	ESCA
DENND1B	0	.	GRCh37	1	197552366	197552366	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1065C>T	p.%3D	p.F355F	ENST00000367396	15/16	22	19	3	30	30	0	DENND1B,synonymous_variant,p.%3D,ENST00000235453,;DENND1B,synonymous_variant,p.%3D,ENST00000367396,;DENND1B,synonymous_variant,p.%3D,ENST00000400967,;DENND1B,upstream_gene_variant,,ENST00000391979,;DENND1B,intron_variant,,ENST00000294737,;	A	ENSG00000213047	ENST00000367396	Transcript	synonymous_variant	1235	1065	355	F	ttC/ttT	.	.	.	-1	DENND1B	HGNC	28404	protein_coding	YES	CCDS41452.2	ENSP00000356366	DEN1B_HUMAN	.	UPI0000227E74	.	.	.	15/16	.	PROSITE_profiles:PS50947,hmmpanther:PTHR13196,hmmpanther:PTHR13196:SF24,Pfam_domain:PF03455,SMART_domains:SM00801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCACAGAAAGT	.	2	ESCA
TMCO4	0	.	GRCh37	1	20097816	20097816	+	Silent	SNP	C	C	T	rs767233859	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339G>A	p.%3D	p.P113P	ENST00000294543	5/16	41	32	9	33	33	0	TMCO4,synonymous_variant,p.%3D,ENST00000375127,;TMCO4,synonymous_variant,p.%3D,ENST00000294543,;TMCO4,synonymous_variant,p.%3D,ENST00000375122,;TMCO4,non_coding_transcript_exon_variant,,ENST00000489135,;TMCO4,non_coding_transcript_exon_variant,,ENST00000496528,;TMCO4,non_coding_transcript_exon_variant,,ENST00000462171,;TMCO4,downstream_gene_variant,,ENST00000488449,;	T	ENSG00000162542	ENST00000294543	Transcript	synonymous_variant	581	339	113	P	ccG/ccA	rs767233859	.	.	-1	TMCO4	HGNC	27393	protein_coding	YES	CCDS198.1	ENSP00000294543	TMCO4_HUMAN	Q6ZSC6_HUMAN	UPI0000197EC6	.	.	.	5/16	.	hmmpanther:PTHR17920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGTCGGGTC	byFrequency	5	ESCA
LINC00303	0	.	GRCh37	1	204010308	204010308	+	RNA	SNP	G	G	A	rs555100193	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.85C>T	.	.	ENST00000418245	1/5	28	21	7	26	26	0	LINC00303,non_coding_transcript_exon_variant,,ENST00000418245,;LINC00303,non_coding_transcript_exon_variant,,ENST00000367207,;LINC00303,non_coding_transcript_exon_variant,,ENST00000427799,;	A	ENSG00000176754	ENST00000418245	Transcript	non_coding_transcript_exon_variant	85	.	.	.	.	rs555100193	.	.	-1	LINC00303	HGNC	26865	lincRNA	YES	.	.	.	.	.	.	.	.	1/5	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATGAAAGT	by1000G	5	ESCA
LYPD8	0	.	GRCh37	1	248903064	248903064	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.87C>G	p.Leu30Val	p.L30V	ENST00000590317	1/1	56	45	11	43	43	0	LYPD8,missense_variant,p.Leu30Val,ENST00000590317,;	C	ENSG00000266949	ENST00000590317	Transcript	missense_variant	87	88	30	L/V	Ctt/Gtt	.	.	.	-1	LYPD8	HGNC	44208	protein_coding	YES	.	ENSP00000466070	.	.	UPI0002841284	.	tolerated(1)	benign(0)	1/1	.	hmmpanther:PTHR20914,hmmpanther:PTHR20914:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGAGTCT	.	5	ESCA
SLC30A2	0	.	GRCh37	1	26365766	26365766	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1004A>T	p.Lys335Met	p.K335M	ENST00000374276	8/8	42	37	5	26	26	0	SLC30A2,missense_variant,p.Lys286Met,ENST00000374278,;SLC30A2,missense_variant,p.Lys335Met,ENST00000374276,;EXTL1,downstream_gene_variant,,ENST00000374280,;EXTL1,downstream_gene_variant,,ENST00000470037,;SLC30A2,downstream_gene_variant,,ENST00000498060,;	A	ENSG00000158014	ENST00000374276	Transcript	missense_variant	1241	1004	335	K/M	aAg/aTg	.	.	.	-1	SLC30A2	HGNC	11013	protein_coding	YES	CCDS30644.1	ENSP00000363394	ZNT2_HUMAN	.	UPI0000049F98	.	tolerated(0.06)	benign(0.248)	8/8	.	hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF30,Pfam_domain:PF01545,TIGRFAM_domain:TIGR01297,Superfamily_domains:SSF160240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTCTTCAGC	.	4	ESCA
KIAA0319L	0	.	GRCh37	1	35919200	35919200	+	Nonsense_Mutation	SNP	G	G	C	rs775336331	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1871C>G	p.Ser624Ter	p.S624*	ENST00000325722	12/21	55	44	11	45	45	0	KIAA0319L,stop_gained,p.Ser61Ter,ENST00000373266,;KIAA0319L,stop_gained,p.Ser624Ter,ENST00000440579,;KIAA0319L,stop_gained,p.Ser624Ter,ENST00000325722,;KIAA0319L,stop_gained,p.Ser624Ter,ENST00000426982,;KIAA0319L,non_coding_transcript_exon_variant,,ENST00000492544,;KIAA0319L,non_coding_transcript_exon_variant,,ENST00000485551,;KIAA0319L,upstream_gene_variant,,ENST00000473844,;KIAA0319L,non_coding_transcript_exon_variant,,ENST00000467109,;	C	ENSG00000142687	ENST00000325722	Transcript	stop_gained	2106	1871	624	S/*	tCa/tGa	rs775336331	.	.	-1	KIAA0319L	HGNC	30071	protein_coding	YES	CCDS390.1	ENSP00000318406	K319L_HUMAN	E7EN73_HUMAN,C9JVB2_HUMAN,C9JQ56_HUMAN,C9J519_HUMAN,B1AN15_HUMAN	UPI000003F081	.	.	.	12/21	.	Superfamily_domains:SSF49299,SMART_domains:SM00089,hmmpanther:PTHR10083:SF166,hmmpanther:PTHR10083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTGAGCTC	byFrequency	5	ESCA
MAST2	0	.	GRCh37	1	46499772	46499772	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3702G>C	p.Lys1234Asn	p.K1234N	ENST00000361297	28/29	41	34	6	39	39	0	MAST2,missense_variant,p.Lys1234Asn,ENST00000361297,;MAST2,missense_variant,p.Lys1141Asn,ENST00000372009,;MAST2,downstream_gene_variant,,ENST00000372008,;MAST2,non_coding_transcript_exon_variant,,ENST00000492813,;MAST2,downstream_gene_variant,,ENST00000477968,;	C	ENSG00000086015	ENST00000361297	Transcript	missense_variant	3985	3702	1234	K/N	aaG/aaC	.	.	.	1	MAST2	HGNC	19035	protein_coding	YES	CCDS41326.1	ENSP00000354671	MAST2_HUMAN	Q9NT11_HUMAN	UPI0000458AEB	.	deleterious_low_confidence(0)	probably_damaging(0.997)	28/29	.	hmmpanther:PTHR24356:SF136,hmmpanther:PTHR24356	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCAAGATCAC	.	5	ESCA
PAX1	0	.	GRCh37	20	21686544	21686544	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194G>A	p.Gly65Asp	p.G65D	ENST00000398485	1/5	17	13	4	24	24	0	PAX1,missense_variant,p.Gly65Asp,ENST00000398485,;PAX1,upstream_gene_variant,,ENST00000444366,;PAX1,intron_variant,,ENST00000460221,;PAX1,upstream_gene_variant,,ENST00000485038,;	A	ENSG00000125813	ENST00000398485	Transcript	missense_variant	248	194	65	G/D	gGc/gAc	.	.	.	1	PAX1	HGNC	8615	protein_coding	YES	CCDS13146.2	ENSP00000381499	PAX1_HUMAN	.	UPI000179A786	.	tolerated_low_confidence(0.25)	benign(0)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCGGCGGCG	.	5	ESCA
PTPRT	0	.	GRCh37	20	41514563	41514563	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98C>T	p.Ser33Phe	p.S33F	ENST00000373187	2/31	73	58	15	43	43	0	PTPRT,missense_variant,p.Ser33Phe,ENST00000373201,;PTPRT,missense_variant,p.Ser33Phe,ENST00000373198,;PTPRT,missense_variant,p.Ser33Phe,ENST00000373193,;PTPRT,missense_variant,p.Ser33Phe,ENST00000373187,;PTPRT,missense_variant,p.Ser33Phe,ENST00000356100,;PTPRT,missense_variant,p.Ser33Phe,ENST00000373184,;PTPRT,missense_variant,p.Ser33Phe,ENST00000373190,;PTPRT,non_coding_transcript_exon_variant,,ENST00000485499,;	A	ENSG00000196090	ENST00000373187	Transcript	missense_variant	98	98	33	S/F	tCc/tTc	COSM3546649,COSM3546650	.	.	-1	PTPRT	HGNC	9682	protein_coding	YES	CCDS42874.1	ENSP00000362283	PTPRT_HUMAN	.	UPI0000246C03	.	deleterious(0)	possibly_damaging(0.701)	2/31	.	PROSITE_profiles:PS50060,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGGAACAG	.	5	ESCA
SERINC3	0	.	GRCh37	20	43150680	43150680	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-88C>T	.	.	ENST00000342374	1/10	64	49	15	51	51	0	SERINC3,5_prime_UTR_variant,,ENST00000255175,;SERINC3,5_prime_UTR_variant,,ENST00000342374,;SERINC3,upstream_gene_variant,,ENST00000541235,;SERINC3,non_coding_transcript_exon_variant,,ENST00000468234,;	A	ENSG00000132824	ENST00000342374	Transcript	5_prime_UTR_variant	71	.	.	.	.	.	.	.	-1	SERINC3	HGNC	11699	protein_coding	YES	CCDS13333.1	ENSP00000340243	SERC3_HUMAN	Q5H936_HUMAN,B4DUE9_HUMAN	UPI0000136B4D	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATGACGGT	.	5	ESCA
LINC00654	0	.	GRCh37	20	5479726	5479726	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3100C>T	.	.	ENST00000379053	2/2	57	43	13	50	50	0	LINC00654,non_coding_transcript_exon_variant,,ENST00000379053,;LINC00654,downstream_gene_variant,,ENST00000589201,;RP5-1022P6.7,upstream_gene_variant,,ENST00000587737,;	A	ENSG00000205181	ENST00000379053	Transcript	non_coding_transcript_exon_variant	3100	.	.	.	.	.	.	.	-1	LINC00654	HGNC	27154	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTGAGCTC	.	5	ESCA
DIDO1	0	.	GRCh37	20	61513083	61513083	+	Missense_Mutation	SNP	C	C	T	rs770549757	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4225G>A	p.Glu1409Lys	p.E1409K	ENST00000266070	16/16	44	37	7	30	30	0	DIDO1,missense_variant,p.Glu1409Lys,ENST00000266070,;DIDO1,missense_variant,p.Glu1409Lys,ENST00000395343,;	T	ENSG00000101191	ENST00000266070	Transcript	missense_variant	4551	4225	1409	E/K	Gag/Aag	rs770549757,COSM578563,COSM1649942	.	.	-1	DIDO1	HGNC	2680	protein_coding	YES	CCDS33506.1	ENSP00000266070	DIDO1_HUMAN	.	UPI0000206380	.	.	benign(0.114)	16/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14914:SF7,hmmpanther:PTHR14914	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCTCGTGGC	.	2	ESCA
MORC3	0	.	GRCh37	21	37741333	37741333	+	Missense_Mutation	SNP	A	A	G	rs771013022	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1667A>G	p.Asn556Ser	p.N556S	ENST00000400485	15/17	30	24	6	34	33	1	MORC3,missense_variant,p.Asn556Ser,ENST00000400485,;MORC3,non_coding_transcript_exon_variant,,ENST00000487909,;MORC3,upstream_gene_variant,,ENST00000547657,;MORC3,upstream_gene_variant,,ENST00000551367,;MORC3,non_coding_transcript_exon_variant,,ENST00000484028,;MORC3,upstream_gene_variant,,ENST00000552581,;MORC3,upstream_gene_variant,,ENST00000551788,;MORC3,upstream_gene_variant,,ENST00000549948,;MORC3,upstream_gene_variant,,ENST00000546482,;	G	ENSG00000159256	ENST00000400485	Transcript	missense_variant	1743	1667	556	N/S	aAt/aGt	rs771013022	.	.	1	MORC3	HGNC	23572	protein_coding	YES	CCDS42924.1	ENSP00000383333	MORC3_HUMAN	Q86YD6_HUMAN,H0YHQ4_HUMAN,B4DHJ4_HUMAN,A2RU29_HUMAN	UPI0000167F94	.	tolerated(0.69)	benign(0.002)	15/17	.	hmmpanther:PTHR23336:SF12,hmmpanther:PTHR23336	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAAGAATCGGA	.	4	ESCA
CLDN14	0	.	GRCh37	21	37834039	37834039	+	5'UTR	SNP	C	C	A	rs779699092	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-46G>T	.	.	ENST00000399137	3/3	23	19	4	14	14	0	CLDN14,5_prime_UTR_variant,,ENST00000342108,;CLDN14,5_prime_UTR_variant,,ENST00000399136,;CLDN14,5_prime_UTR_variant,,ENST00000399135,;CLDN14,5_prime_UTR_variant,,ENST00000399139,;CLDN14,5_prime_UTR_variant,,ENST00000399137,;AP000695.4,intron_variant,,ENST00000428667,;AP000695.6,intron_variant,,ENST00000429588,;AP000695.4,downstream_gene_variant,,ENST00000454980,;	A	ENSG00000159261	ENST00000399137	Transcript	5_prime_UTR_variant	822	.	.	.	.	rs779699092	.	.	-1	CLDN14	HGNC	2035	protein_coding	YES	CCDS13645.1	ENSP00000382090	CLD14_HUMAN	.	UPI0000048F0B	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGGGGT	byFrequency	4	ESCA
HLCS	0	.	GRCh37	21	38123572	38123572	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2975G>A	.	.	ENST00000399120	12/12	41	35	6	73	73	0	HLCS,3_prime_UTR_variant,,ENST00000399120,;HLCS,3_prime_UTR_variant,,ENST00000336648,;SIM2,downstream_gene_variant,,ENST00000290399,;SIM2,downstream_gene_variant,,ENST00000481185,;	T	ENSG00000159267	ENST00000399120	Transcript	3_prime_UTR_variant	6387	.	.	.	.	.	.	.	-1	HLCS	HGNC	4976	protein_coding	YES	CCDS13647.1	ENSP00000382071	BPL1_HUMAN	C9JD75_HUMAN,C9JCQ9_HUMAN	UPI0000126A8C	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATCCTTTGA	.	4	ESCA
C2CD2	0	.	GRCh37	21	43339044	43339044	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.518G>C	p.Arg173Thr	p.R173T	ENST00000380486	4/14	59	50	9	38	38	0	C2CD2,missense_variant,p.Arg18Thr,ENST00000329623,;C2CD2,missense_variant,p.Arg173Thr,ENST00000380486,;C2CD2,non_coding_transcript_exon_variant,,ENST00000467074,;C2CD2,non_coding_transcript_exon_variant,,ENST00000490479,;C2CD2,non_coding_transcript_exon_variant,,ENST00000482084,;	G	ENSG00000157617	ENST00000380486	Transcript	missense_variant	760	518	173	R/T	aGa/aCa	.	.	.	-1	C2CD2	HGNC	1266	protein_coding	YES	CCDS42933.1	ENSP00000369853	CU025_HUMAN	.	UPI0000206BBE	.	tolerated(0.21)	benign(0.091)	4/14	.	hmmpanther:PTHR21119:SF6,hmmpanther:PTHR21119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCTCTTC	.	5	ESCA
KRTAP10-11	0	.	GRCh37	21	46066408	46066408	+	Missense_Mutation	SNP	C	C	A	rs587690905,rs763945679	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33C>A	p.Ser11Arg	p.S11R	ENST00000334670	1/1	117	111	6	152	152	0	KRTAP10-11,missense_variant,p.Ser11Arg,ENST00000334670,;TSPEAR,intron_variant,,ENST00000323084,;	A	ENSG00000243489	ENST00000334670	Transcript	missense_variant	78	33	11	S/R	agC/agA	rs587690905,rs763945679,COSM118213	.	.	1	KRTAP10-11	HGNC	20528	protein_coding	YES	CCDS42962.1	ENSP00000334197	KR10B_HUMAN	.	UPI000040FC94	.	deleterious(0)	unknown(0)	1/1	.	hmmpanther:PTHR23262:SF19,hmmpanther:PTHR23262	T:0.0002	T:0.0008,T:0.0008	T:0,T:0	.	T:0,T:0	T:0,T:0	T:0,T:0	.	.	.	0,0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAGCGCTTA	byCluster|by1000G	2	ESCA
LARGE	0	.	GRCh37	22	33733678	33733678	+	Missense_Mutation	SNP	C	C	T	rs200603479	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000354992	11/16	58	41	17	52	52	0	LARGE,missense_variant,p.Arg213Gln,ENST00000452586,;LARGE,missense_variant,p.Arg414Gln,ENST00000354992,;LARGE,missense_variant,p.Arg414Gln,ENST00000437602,;LARGE,missense_variant,p.Arg91Gln,ENST00000609799,;LARGE,missense_variant,p.Arg91Gln,ENST00000608642,;LARGE,missense_variant,p.Arg91Gln,ENST00000610186,;LARGE,missense_variant,p.Arg414Gln,ENST00000397394,;LARGE,intron_variant,,ENST00000337431,;LARGE,intron_variant,,ENST00000402320,;LARGE,downstream_gene_variant,,ENST00000421768,;	T	ENSG00000133424	ENST00000354992	Transcript	missense_variant	1813	1241	414	R/Q	cGg/cAg	rs200603479	.	.	-1	LARGE	HGNC	6511	protein_coding	YES	CCDS13912.1	ENSP00000347088	LARGE_HUMAN	B0QZ02_HUMAN,B0QZ01_HUMAN,B0QZ00_HUMAN,B0QYZ9_HUMAN,B0QYZ8_HUMAN	UPI000012E200	.	deleterious(0.01)	possibly_damaging(0.787)	11/16	.	hmmpanther:PTHR12270,hmmpanther:PTHR12270:SF18	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCCCGCCTC	byCluster|by1000G	5	ESCA
TBC1D22A	0	.	GRCh37	22	47507497	47507497	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1423C>G	p.Gln475Glu	p.Q475E	ENST00000337137	12/13	49	34	15	52	52	0	TBC1D22A,missense_variant,p.Gln428Glu,ENST00000406733,;TBC1D22A,missense_variant,p.Gln475Glu,ENST00000337137,;TBC1D22A,missense_variant,p.Gln397Glu,ENST00000355704,;TBC1D22A,missense_variant,p.Gln416Glu,ENST00000407381,;TBC1D22A,splice_region_variant,,ENST00000441162,;TBC1D22A,splice_region_variant,,ENST00000394449,;	G	ENSG00000054611	ENST00000337137	Transcript	missense_variant	1589	1423	475	Q/E	Caa/Gaa	.	.	.	1	TBC1D22A	HGNC	1309	protein_coding	YES	CCDS14078.1	ENSP00000336724	TB22A_HUMAN	B9A6M3_HUMAN,B0QYI3_HUMAN	UPI0000128722	.	deleterious(0)	benign(0.307)	12/13	.	Superfamily_domains:SSF47923,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCAAGTA	.	5	ESCA
FAM19A5	0	.	GRCh37	22	49147147	49147147	+	3'Flank	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000402357	.	36	32	4	24	24	0	FAM19A5,3_prime_UTR_variant,,ENST00000358295,;FAM19A5,intron_variant,,ENST00000336769,;FAM19A5,downstream_gene_variant,,ENST00000406880,;FAM19A5,downstream_gene_variant,,ENST00000402357,;FAM19A5,downstream_gene_variant,,ENST00000473898,;	T	ENSG00000219438	ENST00000402357	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	512	1	FAM19A5	HGNC	21592	protein_coding	YES	CCDS46728.1	ENSP00000383933	F19A5_HUMAN	.	UPI0000074351	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCAGGCGGGGC	.	3	ESCA
BUB1	0	.	GRCh37	2	111427127	111427127	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470G>C	p.Arg157Thr	p.R157T	ENST00000302759	6/25	42	38	3	32	32	0	BUB1,missense_variant,p.Arg137Thr,ENST00000535254,;BUB1,missense_variant,p.Arg157Thr,ENST00000409311,;BUB1,missense_variant,p.Arg157Thr,ENST00000302759,;BUB1,downstream_gene_variant,,ENST00000420328,;BUB1,downstream_gene_variant,,ENST00000447014,;BUB1,downstream_gene_variant,,ENST00000436916,;BUB1,non_coding_transcript_exon_variant,,ENST00000465029,;BUB1,non_coding_transcript_exon_variant,,ENST00000466333,;BUB1,upstream_gene_variant,,ENST00000477481,;BUB1,upstream_gene_variant,,ENST00000468927,;	G	ENSG00000169679	ENST00000302759	Transcript	missense_variant	589	470	157	R/T	aGa/aCa	.	.	.	-1	BUB1	HGNC	1148	protein_coding	YES	CCDS33273.1	ENSP00000302530	BUB1_HUMAN	Q9BXX5_HUMAN,C9JRC7_HUMAN,C9JQA4_HUMAN,C9IYH4_HUMAN	UPI00000012C4	.	tolerated(0.33)	benign(0.025)	6/25	.	PROSITE_profiles:PS51489,hmmpanther:PTHR14030:SF3,hmmpanther:PTHR14030	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTTCTAGCT	.	2	ESCA
ROCK2	0	.	GRCh37	2	11355639	11355639	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594G>T	p.Asp532Tyr	p.D532Y	ENST00000315872	14/33	76	57	18	56	56	0	ROCK2,missense_variant,p.Asp532Tyr,ENST00000315872,;ROCK2,missense_variant,p.Asp289Tyr,ENST00000401753,;ROCK2,3_prime_UTR_variant,,ENST00000261535,;ROCK2,downstream_gene_variant,,ENST00000484951,;	A	ENSG00000134318	ENST00000315872	Transcript	missense_variant	2043	1594	532	D/Y	Gat/Tat	.	.	.	-1	ROCK2	HGNC	10252	protein_coding	YES	CCDS42654.1	ENSP00000317985	ROCK2_HUMAN	Q14DU5_HUMAN,E9PF63_HUMAN	UPI000034ECB0	.	tolerated(0.1)	possibly_damaging(0.718)	14/33	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22988:SF24,hmmpanther:PTHR22988,Pfam_domain:PF02185,PIRSF_domain:PIRSF037568	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATCATTTT	.	5	ESCA
GLI2	0	.	GRCh37	2	121746894	121746894	+	Missense_Mutation	SNP	C	C	G	rs140601980	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3404C>G	p.Ser1135Cys	p.S1135C	ENST00000452319	14/14	49	43	6	38	38	0	GLI2,missense_variant,p.Ser1135Cys,ENST00000452319,;GLI2,missense_variant,p.Ser1135Cys,ENST00000361492,;GLI2,missense_variant,p.Ser807Cys,ENST00000314490,;GLI2,downstream_gene_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000438299,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,3_prime_UTR_variant,,ENST00000452692,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,downstream_gene_variant,,ENST00000437950,;	G	ENSG00000074047	ENST00000452319	Transcript	missense_variant	3464	3404	1135	S/C	tCc/tGc	rs140601980	.	.	1	GLI2	HGNC	4318	protein_coding	YES	CCDS33283.1	ENSP00000390436	GLI2_HUMAN	Q6RSW2_HUMAN,Q59FV5_HUMAN,Q1PSW9_HUMAN	UPI000053FCB4	.	deleterious(0.01)	possibly_damaging(0.498)	14/14	.	hmmpanther:PTHR19818:SF73,hmmpanther:PTHR19818	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCCAGCC	byCluster	5	ESCA
HS6ST1	0	.	GRCh37	2	129026040	129026040	+	Missense_Mutation	SNP	T	T	C	rs752189949	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932A>G	p.Lys311Arg	p.K311R	ENST00000259241	2/2	49	37	11	71	71	0	HS6ST1,missense_variant,p.Lys311Arg,ENST00000259241,;HS6ST1,intron_variant,,ENST00000469019,;HS6ST1,downstream_gene_variant,,ENST00000463963,;	C	ENSG00000136720	ENST00000259241	Transcript	missense_variant	946	932	311	K/R	aAg/aGg	rs752189949	.	.	-1	HS6ST1	HGNC	5201	protein_coding	YES	CCDS42748.1	ENSP00000259241	H6ST1_HUMAN	B4E2L3_HUMAN	UPI0000D61231	.	tolerated(0.9)	benign(0.04)	2/2	.	hmmpanther:PTHR12812,hmmpanther:PTHR12812:SF1,Pfam_domain:PF03567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACTTGAGG	.	5	ESCA
IFIH1	0	.	GRCh37	2	163133265	163133265	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2236G>A	p.Glu746Lys	p.E746K	ENST00000263642	11/16	66	47	19	61	61	0	IFIH1,missense_variant,p.Glu746Lys,ENST00000263642,;	T	ENSG00000115267	ENST00000263642	Transcript	missense_variant	2632	2236	746	E/K	Gaa/Aaa	COSM1528590	.	.	-1	IFIH1	HGNC	18873	protein_coding	YES	CCDS2217.1	ENSP00000263642	IFIH1_HUMAN	Q53TP4_HUMAN,Q53TB6_HUMAN	UPI000013D436	.	deleterious(0.01)	benign(0.426)	11/16	.	Superfamily_domains:SSF52540,SMART_domains:SM00490,Gene3D:3.40.50.300,hmmpanther:PTHR14074:SF14,hmmpanther:PTHR14074,PROSITE_profiles:PS51194	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTCAGCAA	.	5	ESCA
FAM49A	0	.	GRCh37	2	16769367	16769367	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21C>G	p.%3D	p.V7V	ENST00000381323	3/12	61	54	7	61	61	0	FAM49A,synonymous_variant,p.%3D,ENST00000451689,;FAM49A,synonymous_variant,p.%3D,ENST00000381323,;FAM49A,synonymous_variant,p.%3D,ENST00000355549,;FAM49A,synonymous_variant,p.%3D,ENST00000445605,;FAM49A,synonymous_variant,p.%3D,ENST00000406434,;	C	ENSG00000197872	ENST00000381323	Transcript	synonymous_variant	242	21	7	V	gtC/gtG	.	.	.	-1	FAM49A	HGNC	25373	protein_coding	YES	CCDS1688.1	ENSP00000370724	FA49A_HUMAN	Q53QW2_HUMAN,C9JPE5_HUMAN,C9IYV6_HUMAN,B3KRB1_HUMAN	UPI0000037BBB	.	.	.	3/12	.	hmmpanther:PTHR12422:SF4,hmmpanther:PTHR12422	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAAGGACTTT	.	4	ESCA
LRP2	0	.	GRCh37	2	170032935	170032935	+	Silent	SNP	G	G	A	rs113268518	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10557C>T	p.%3D	p.C3519C	ENST00000263816	54/79	34	26	8	39	39	0	LRP2,synonymous_variant,p.%3D,ENST00000263816,;LRP2,downstream_gene_variant,,ENST00000461418,;	A	ENSG00000081479	ENST00000263816	Transcript	synonymous_variant	10843	10557	3519	C	tgC/tgT	rs113268518	.	.	-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	LRP2_HUMAN	Q9NP34_HUMAN,Q53TL0_HUMAN,Q4ZG84_HUMAN	UPI0000141BA5	.	.	.	54/79	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF220,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGCGCACAG	byCluster|by1000G	5	ESCA
UBR3	0	.	GRCh37	2	170865359	170865359	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4276A>G	p.Ile1426Val	p.I1426V	ENST00000418381	29/39	78	65	13	57	57	0	UBR3,missense_variant,p.Ile247Val,ENST00000392631,;UBR3,missense_variant,p.Ile1426Val,ENST00000418381,;UBR3,missense_variant,p.Ile1426Val,ENST00000272793,;UBR3,missense_variant,p.Ile97Val,ENST00000439681,;UBR3,missense_variant,p.Ile488Val,ENST00000392632,;UBR3,missense_variant,p.Ile4Val,ENST00000444475,;UBR3,3_prime_UTR_variant,,ENST00000430321,;	G	ENSG00000144357	ENST00000418381	Transcript	missense_variant	4276	4276	1426	I/V	Ata/Gta	.	.	.	1	UBR3	HGNC	30467	protein_coding	YES	CCDS2238.2	ENSP00000396068	UBR3_HUMAN	Q68DC1_HUMAN	UPI00015FA088	.	deleterious(0.04)	benign(0.222)	29/39	.	hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATATAAAA	.	5	ESCA
TTN	0	.	GRCh37	2	179424251	179424251	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86608G>C	p.Glu28870Gln	p.E28870Q	ENST00000589042	326/363	42	35	7	44	44	0	TTN,missense_variant,p.Glu19930Gln,ENST00000359218,;TTN,missense_variant,p.Glu27229Gln,ENST00000591111,;TTN,missense_variant,p.Glu28870Gln,ENST00000589042,;TTN,missense_variant,p.Glu19997Gln,ENST00000342175,;TTN,missense_variant,p.Glu26302Gln,ENST00000342992,;TTN,missense_variant,p.Glu19805Gln,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	86833	86608	28870	E/Q	Gaa/Caa	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	326/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTCAGGAA	.	5	ESCA
TTN	0	.	GRCh37	2	179610671	179610671	+	Intron	SNP	T	T	C	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11312-4023A>G	.	.	ENST00000589042	.	24	19	5	32	32	0	TTN,missense_variant,p.Thr5486Ala,ENST00000360870,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000342992,;TTN,intron_variant,,ENST00000589042,;TTN,intron_variant,,ENST00000591111,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000578746,;TTN-AS1,downstream_gene_variant,,ENST00000582847,;	C	ENSG00000155657	ENST00000589042	Transcript	intron_variant	.	.	.	.	.	COSM4088967	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	.	47/362	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODIFIER	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TAAAGTCACTT	.	4	ESCA
TTN	0	.	GRCh37	2	179647638	179647638	+	Missense_Mutation	SNP	G	G	A	rs142000511	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2995C>T	p.Arg999Cys	p.R999C	ENST00000589042	18/363	30	26	3	18	18	0	TTN,missense_variant,p.Arg999Cys,ENST00000360870,;TTN,missense_variant,p.Arg999Cys,ENST00000342992,;TTN,missense_variant,p.Arg953Cys,ENST00000342175,;TTN,missense_variant,p.Arg953Cys,ENST00000359218,;TTN,missense_variant,p.Arg999Cys,ENST00000589042,;TTN,missense_variant,p.Arg999Cys,ENST00000591111,;TTN,missense_variant,p.Arg953Cys,ENST00000460472,;TTN,downstream_gene_variant,,ENST00000436599,;RP11-88L24.4,downstream_gene_variant,,ENST00000582038,;	A	ENSG00000155657	ENST00000589042	Transcript	missense_variant	3220	2995	999	R/C	Cgt/Tgt	rs142000511	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	18/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0.0002	A:0	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AAGACGAGCAA	byFrequency|byCluster	3	ESCA
SESTD1	0	.	GRCh37	2	180016092	180016092	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396G>A	p.%3D	p.L132L	ENST00000428443	6/18	54	45	9	63	63	0	SESTD1,synonymous_variant,p.%3D,ENST00000428443,;SESTD1,synonymous_variant,p.%3D,ENST00000435047,;SESTD1,synonymous_variant,p.%3D,ENST00000440010,;SESTD1,upstream_gene_variant,,ENST00000335289,;SESTD1,upstream_gene_variant,,ENST00000489901,;SESTD1,upstream_gene_variant,,ENST00000426988,;	T	ENSG00000187231	ENST00000428443	Transcript	synonymous_variant	713	396	132	L	ttG/ttA	.	.	.	-1	SESTD1	HGNC	18379	protein_coding	YES	CCDS33338.1	ENSP00000415332	SESD1_HUMAN	Q7Z6D3_HUMAN,C9JHW6_HUMAN,C9J4X8_HUMAN	UPI0000043424	.	.	.	6/18	.	Pfam_domain:PF13716,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF19,PROSITE_profiles:PS50191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGTCAATTT	.	5	ESCA
NT5C1B	0	.	GRCh37	2	18765458	18765458	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967G>A	p.Gly323Ser	p.G323S	ENST00000359846	6/10	28	21	7	33	33	0	NT5C1B,missense_variant,p.Gly323Ser,ENST00000359846,;NT5C1B,missense_variant,p.Gly263Ser,ENST00000304081,;NT5C1B,missense_variant,p.Gly323Ser,ENST00000600945,;NT5C1B-RDH14,missense_variant,p.Gly323Ser,ENST00000532967,;NT5C1B-RDH14,missense_variant,p.Gly265Ser,ENST00000444297,;NT5C1B,upstream_gene_variant,,ENST00000418427,;NT5C1B,downstream_gene_variant,,ENST00000416783,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,downstream_gene_variant,,ENST00000460052,;NT5C1B,3_prime_UTR_variant,,ENST00000406971,;NT5C1B,non_coding_transcript_exon_variant,,ENST00000490687,;	T	ENSG00000185013	ENST00000359846	Transcript	missense_variant	1045	967	323	G/S	Ggc/Agc	COSM269742	.	.	-1	NT5C1B	HGNC	17818	protein_coding	YES	CCDS33150.1	ENSP00000352904	5NT1B_HUMAN	B4DZ86_HUMAN	UPI000035B1B0	.	tolerated(0.67)	benign(0.023)	6/10	.	hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R324R|c.972G>A|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCCGTCCA	.	5	ESCA
PIKFYVE	0	.	GRCh37	2	209200537	209200537	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4278delC	p.Ile1427LeufsTer8	p.I1427Lfs*8	ENST00000264380	26/42	57	44	13	47	47	0	PIKFYVE,frameshift_variant,p.Ile1371LeufsTer8,ENST00000452564,;PIKFYVE,frameshift_variant,p.Ile1427LeufsTer8,ENST00000264380,;PIKFYVE,non_coding_transcript_exon_variant,,ENST00000474721,;	-	ENSG00000115020	ENST00000264380	Transcript	frameshift_variant	4435	4277	1426	A/X	gCc/gc	.	.	.	1	PIKFYVE	HGNC	23785	protein_coding	YES	CCDS2382.1	ENSP00000264380	FYV1_HUMAN	.	UPI0000366FD6	.	.	.	26/42	.	hmmpanther:PTHR11353:SF57,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGTTGCCATTG	.	3	ESCA
ERBB4	0	.	GRCh37	2	212248141	212248141	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*199G>A	.	.	ENST00000342788	28/28	25	20	5	24	24	0	ERBB4,3_prime_UTR_variant,,ENST00000436443,;ERBB4,3_prime_UTR_variant,,ENST00000342788,;ERBB4,downstream_gene_variant,,ENST00000402597,;	T	ENSG00000178568	ENST00000342788	Transcript	3_prime_UTR_variant	4437	.	.	.	.	.	.	.	-1	ERBB4	HGNC	3432	protein_coding	YES	CCDS2394.1	ENSP00000342235	ERBB4_HUMAN	Q580Q7_HUMAN,Q53T57_HUMAN,Q53R48_HUMAN,Q53R25_HUMAN,Q53QS8_HUMAN,Q4ZG14_HUMAN,E9PDR1_HUMAN	UPI00000499DF	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTTCCTCCT	.	5	ESCA
PTPRN	0	.	GRCh37	2	220164085	220164085	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1545C>G	p.%3D	p.T515T	ENST00000295718	11/23	38	33	4	30	30	0	PTPRN,synonymous_variant,p.%3D,ENST00000423636,;PTPRN,synonymous_variant,p.%3D,ENST00000295718,;PTPRN,synonymous_variant,p.%3D,ENST00000409251,;PTPRN,downstream_gene_variant,,ENST00000412847,;PTPRN,upstream_gene_variant,,ENST00000443981,;PTPRN,downstream_gene_variant,,ENST00000440552,;PTPRN,downstream_gene_variant,,ENST00000442029,;PTPRN,downstream_gene_variant,,ENST00000446182,;PTPRN,downstream_gene_variant,,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,upstream_gene_variant,,ENST00000497977,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,non_coding_transcript_exon_variant,,ENST00000486480,;PTPRN,non_coding_transcript_exon_variant,,ENST00000489650,;PTPRN,downstream_gene_variant,,ENST00000476930,;PTPRN,downstream_gene_variant,,ENST00000606213,;	C	ENSG00000054356	ENST00000295718	Transcript	synonymous_variant	1786	1545	515	T	acC/acG	.	.	.	-1	PTPRN	HGNC	9676	protein_coding	YES	CCDS2440.1	ENSP00000295718	PTPRN_HUMAN	Q96IA0_HUMAN,Q7KZS4_HUMAN,C9JJL7_HUMAN,C9JCQ0_HUMAN,C9J392_HUMAN	UPI0000132999	.	.	.	11/23	.	hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2,Pfam_domain:PF11548	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGAAGGTGAG	.	4	ESCA
OBSL1	0	.	GRCh37	2	220430012	220430012	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2359G>C	p.Glu787Gln	p.E787Q	ENST00000404537	6/21	44	38	6	39	39	0	OBSL1,missense_variant,p.Glu787Gln,ENST00000603926,;OBSL1,missense_variant,p.Glu374Gln,ENST00000289656,;OBSL1,missense_variant,p.Glu787Gln,ENST00000373876,;OBSL1,missense_variant,p.Glu787Gln,ENST00000265318,;OBSL1,missense_variant,p.Glu787Gln,ENST00000404537,;OBSL1,missense_variant,p.Glu787Gln,ENST00000373873,;OBSL1,upstream_gene_variant,,ENST00000604031,;INHA,upstream_gene_variant,,ENST00000489456,;OBSL1,downstream_gene_variant,,ENST00000465589,;OBSL1,non_coding_transcript_exon_variant,,ENST00000465149,;OBSL1,non_coding_transcript_exon_variant,,ENST00000462385,;	G	ENSG00000124006	ENST00000404537	Transcript	missense_variant	2416	2359	787	E/Q	Gag/Cag	.	.	.	-1	OBSL1	HGNC	29092	protein_coding	YES	CCDS46520.1	ENSP00000385636	OBSL1_HUMAN	.	UPI0000E07EA0	.	tolerated(0.25)	benign(0.068)	6/21	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19900,hmmpanther:PTHR19900:SF1,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACTCAAACT	.	4	ESCA
TRIP12	0	.	GRCh37	2	230744732	230744732	+	Missense_Mutation	SNP	C	C	T	rs200837058	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64G>A	p.Gly22Arg	p.G22R	ENST00000283943	2/41	61	50	11	34	34	0	TRIP12,missense_variant,p.Gly22Arg,ENST00000389045,;TRIP12,missense_variant,p.Gly22Arg,ENST00000543084,;TRIP12,missense_variant,p.Gly22Arg,ENST00000343290,;TRIP12,missense_variant,p.Gly22Arg,ENST00000409677,;TRIP12,missense_variant,p.Gly22Arg,ENST00000389044,;TRIP12,missense_variant,p.Gly22Arg,ENST00000283943,;TRIP12,missense_variant,p.Gly22Arg,ENST00000428959,;TRIP12,missense_variant,p.Gly22Arg,ENST00000430954,;TRIP12,missense_variant,p.Gly22Arg,ENST00000435716,;TRIP12,non_coding_transcript_exon_variant,,ENST00000479037,;	T	ENSG00000153827	ENST00000283943	Transcript	missense_variant	243	64	22	G/R	Ggg/Agg	rs200837058,COSM1530998	.	.	-1	TRIP12	HGNC	12306	protein_coding	YES	CCDS33391.1	ENSP00000283943	TRIPC_HUMAN	Q57Z94_HUMAN,F8W9P3_HUMAN,C9JSX9_HUMAN,C9JLJ5_HUMAN	UPI000013739D	.	deleterious_low_confidence(0)	possibly_damaging(0.559)	2/41	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCCCGGCAG	byCluster|by1000G	5	ESCA
B3GNT7	0	.	GRCh37	2	232262814	232262814	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.384G>C	p.Glu128Asp	p.E128D	ENST00000287590	2/2	37	32	4	39	39	0	B3GNT7,missense_variant,p.Glu128Asp,ENST00000287590,;AC017104.6,downstream_gene_variant,,ENST00000415129,;AC017104.6,downstream_gene_variant,,ENST00000454416,;B3GNT7,non_coding_transcript_exon_variant,,ENST00000479618,;AC017104.6,downstream_gene_variant,,ENST00000418050,;	C	ENSG00000156966	ENST00000287590	Transcript	missense_variant	645	384	128	E/D	gaG/gaC	.	.	.	1	B3GNT7	HGNC	18811	protein_coding	YES	CCDS46540.1	ENSP00000287590	B3GN7_HUMAN	.	UPI000006D18A	.	tolerated(0.06)	possibly_damaging(0.752)	2/2	.	hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGGAGAAGTG	.	4	ESCA
RAB10	0	.	GRCh37	2	26358681	26358681	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*791C>T	.	.	ENST00000264710	6/6	31	27	4	25	25	0	RAB10,3_prime_UTR_variant,,ENST00000264710,;RAB10,downstream_gene_variant,,ENST00000473035,;RAB10,downstream_gene_variant,,ENST00000462003,;RAB10,downstream_gene_variant,,ENST00000495146,;AC011742.3,downstream_gene_variant,,ENST00000443818,;	T	ENSG00000084733	ENST00000264710	Transcript	3_prime_UTR_variant	1893	.	.	.	.	.	.	.	1	RAB10	HGNC	9759	protein_coding	YES	CCDS1720.1	ENSP00000264710	RAB10_HUMAN	Q9UL28_HUMAN,Q53T70_HUMAN,Q53SX4_HUMAN	UPI0000001263	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTTCTCCCT	.	4	ESCA
RBKS	0	.	GRCh37	2	28065945	28065945	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.503G>C	p.Arg168Pro	p.R168P	ENST00000302188	5/8	75	60	15	71	71	0	RBKS,missense_variant,p.Arg168Pro,ENST00000302188,;RBKS,missense_variant,p.Arg168Pro,ENST00000444339,;RBKS,missense_variant,p.Arg29Pro,ENST00000458185,;RBKS,3_prime_UTR_variant,,ENST00000449378,;MRPL33,intron_variant,,ENST00000448427,;	G	ENSG00000171174	ENST00000302188	Transcript	missense_variant	1256	503	168	R/P	cGc/cCc	.	.	.	-1	RBKS	HGNC	30325	protein_coding	YES	CCDS1762.1	ENSP00000306817	RBSK_HUMAN	Q53SD1_HUMAN	UPI000003B021	.	deleterious(0.01)	possibly_damaging(0.785)	5/8	.	hmmpanther:PTHR10584,hmmpanther:PTHR10584:SF166,Gene3D:3.40.1190.20,Pfam_domain:PF00294,TIGRFAM_domain:TIGR02152,Superfamily_domains:SSF53613	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGCGGGCC	.	5	ESCA
ALLC	0	.	GRCh37	2	3743330	3743330	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535G>T	p.Val179Leu	p.V179L	ENST00000252505	8/12	38	31	6	50	50	0	ALLC,missense_variant,p.Val179Leu,ENST00000252505,;ALLC,non_coding_transcript_exon_variant,,ENST00000471711,;ALLC,non_coding_transcript_exon_variant,,ENST00000476389,;	T	ENSG00000151360	ENST00000252505	Transcript	missense_variant	697	535	179	V/L	Gta/Tta	.	.	.	1	ALLC	HGNC	17377	protein_coding	YES	CCDS46223.1	ENSP00000252505	ALLC_HUMAN	B4DY77_HUMAN	UPI000050BBEF	.	deleterious(0)	possibly_damaging(0.702)	8/12	.	hmmpanther:PTHR12045,Pfam_domain:PF03561,TIGRFAM_domain:TIGR02961,Gene3D:2.60.120.260,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTAGAGTATTC	.	4	ESCA
CDC42EP3	0	.	GRCh37	2	37872846	37872846	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120C>T	.	.	ENST00000295324	2/2	71	64	7	61	61	0	CDC42EP3,3_prime_UTR_variant,,ENST00000295324,;CDC42EP3,downstream_gene_variant,,ENST00000457889,;CDC42EP3,downstream_gene_variant,,ENST00000422687,;CDC42EP3,downstream_gene_variant,,ENST00000453555,;AC006369.2,intron_variant,,ENST00000419425,;	A	ENSG00000163171	ENST00000295324	Transcript	3_prime_UTR_variant	1886	.	.	.	.	.	.	.	-1	CDC42EP3	HGNC	16943	protein_coding	YES	CCDS1791.1	ENSP00000295324	BORG2_HUMAN	C9JEZ4_HUMAN,C9J7F7_HUMAN	UPI0000073D2A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTAAGAATAT	.	3	ESCA
PUS10	0	.	GRCh37	2	61237711	61237711	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126+1189G>A	.	.	ENST00000316752	.	26	21	5	25	25	0	PUS10,3_prime_UTR_variant,,ENST00000398658,;PUS10,intron_variant,,ENST00000407787,;PUS10,intron_variant,,ENST00000316752,;PUS10,intron_variant,,ENST00000421319,;PUS10,intron_variant,,ENST00000430495,;PUS10,intron_variant,,ENST00000602599,;	T	ENSG00000162927	ENST00000316752	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PUS10	HGNC	26505	protein_coding	YES	CCDS1865.1	ENSP00000326003	PUS10_HUMAN	C9JNL8_HUMAN	UPI000013E1F4	.	.	.	.	2/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCCTCGGCCT	.	4	ESCA
CTNNA2	0	.	GRCh37	2	80874927	80874927	+	Missense_Mutation	SNP	G	G	A	rs529691509	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2648G>A	p.Arg883Gln	p.R883Q	ENST00000466387	22/22	32	27	5	27	27	0	CTNNA2,missense_variant,p.Arg883Gln,ENST00000496558,;CTNNA2,missense_variant,p.Arg838Gln,ENST00000540488,;CTNNA2,missense_variant,p.Arg917Gln,ENST00000361291,;CTNNA2,missense_variant,p.Arg883Gln,ENST00000466387,;CTNNA2,missense_variant,p.Arg883Gln,ENST00000541047,;CTNNA2,missense_variant,p.Arg562Gln,ENST00000343114,;CTNNA2,missense_variant,p.Arg931Gln,ENST00000402739,;	A	ENSG00000066032	ENST00000466387	Transcript	missense_variant	3372	2648	883	R/Q	cGa/cAa	rs529691509,COSM226919,COSM1483305,COSM3840114,COSM1483304,COSM226918	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	deleterious(0.03)	possibly_damaging(0.852)	22/22	.	hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R931*|c.2791C>T|6,BUFFER|p.R882*|c.2644C>T|6	MUTECT|MUSE	TCGACGAGGTT	.	2	ESCA
SNRNP200	0	.	GRCh37	2	96956138	96956138	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2668G>A	p.Glu890Lys	p.E890K	ENST00000323853	20/45	29	21	8	46	46	0	SNRNP200,missense_variant,p.Glu890Lys,ENST00000323853,;SNRNP200,intron_variant,,ENST00000349783,;SNRNP200,upstream_gene_variant,,ENST00000480615,;	T	ENSG00000144028	ENST00000323853	Transcript	missense_variant	2746	2668	890	E/K	Gaa/Aaa	.	.	.	-1	SNRNP200	HGNC	30859	protein_coding	YES	CCDS2020.1	ENSP00000317123	U520_HUMAN	Q9P172_HUMAN,Q7L5W4_HUMAN,Q5ZF01_HUMAN,A4FU77_HUMAN,A2RRQ7_HUMAN	UPI0000207C53	.	deleterious(0)	probably_damaging(0.999)	20/45	.	PROSITE_profiles:PS51194,hmmpanther:PTHR11752:SF55,hmmpanther:PTHR11752,Gene3D:3.40.50.300,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTCAATAG	.	5	ESCA
MGAT4A	0	.	GRCh37	2	99271934	99271934	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.748C>G	p.Gln250Glu	p.Q250E	ENST00000264968	7/15	24	21	3	19	19	0	MGAT4A,missense_variant,p.Gln122Glu,ENST00000414521,;MGAT4A,missense_variant,p.Gln250Glu,ENST00000393487,;MGAT4A,missense_variant,p.Gln250Glu,ENST00000409391,;MGAT4A,missense_variant,p.Gln250Glu,ENST00000264968,;MGAT4A,non_coding_transcript_exon_variant,,ENST00000492163,;MGAT4A,downstream_gene_variant,,ENST00000461884,;	C	ENSG00000071073	ENST00000264968	Transcript	missense_variant	1112	748	250	Q/E	Caa/Gaa	.	.	.	-1	MGAT4A	HGNC	7047	protein_coding	YES	CCDS2036.1	ENSP00000264968	MGT4A_HUMAN	.	UPI000003F051	.	deleterious(0)	benign(0.11)	7/15	.	hmmpanther:PTHR12062:SF4,hmmpanther:PTHR12062,Pfam_domain:PF04666	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTTGAGCAT	.	2	ESCA
TSGA10	0	.	GRCh37	2	99697803	99697803	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.669G>C	p.Lys223Asn	p.K223N	ENST00000393483	11/21	109	85	24	96	96	0	TSGA10,missense_variant,p.Lys223Asn,ENST00000410001,;TSGA10,missense_variant,p.Lys223Asn,ENST00000542655,;TSGA10,missense_variant,p.Lys223Asn,ENST00000409564,;TSGA10,missense_variant,p.Lys223Asn,ENST00000539964,;TSGA10,missense_variant,p.Lys223Asn,ENST00000355053,;TSGA10,missense_variant,p.Lys223Asn,ENST00000393483,;TSGA10,missense_variant,p.Lys223Asn,ENST00000393482,;TSGA10,non_coding_transcript_exon_variant,,ENST00000478090,;TSGA10,non_coding_transcript_exon_variant,,ENST00000488960,;TSGA10,upstream_gene_variant,,ENST00000489546,;	G	ENSG00000135951	ENST00000393483	Transcript	missense_variant	1514	669	223	K/N	aaG/aaC	.	.	.	-1	TSGA10	HGNC	14927	protein_coding	YES	CCDS2037.1	ENSP00000377123	TSG10_HUMAN	F8WA32_HUMAN	UPI0000072CE3	.	tolerated(0.11)	benign(0.142)	11/21	.	hmmpanther:PTHR23159:SF9,hmmpanther:PTHR23159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTCTTAGC	.	5	ESCA
C3orf30	0	.	GRCh37	3	118865478	118865478	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442C>T	p.Arg148Ter	p.R148*	ENST00000295622	1/3	30	24	5	23	23	0	C3orf30,stop_gained,p.Arg148Ter,ENST00000295622,;C3orf30,stop_gained,p.Arg112Ter,ENST00000460150,;IGSF11,upstream_gene_variant,,ENST00000425327,;C3orf30,upstream_gene_variant,,ENST00000492792,;RP11-484M3.5,upstream_gene_variant,,ENST00000490594,;IGSF11,upstream_gene_variant,,ENST00000354673,;C3orf30,upstream_gene_variant,,ENST00000473121,;IGSF11,upstream_gene_variant,,ENST00000441144,;IGSF11,upstream_gene_variant,,ENST00000494802,;C3orf30,stop_gained,p.Arg148Ter,ENST00000494105,;	T	ENSG00000163424	ENST00000295622	Transcript	stop_gained	482	442	148	R/*	Cga/Tga	.	.	.	1	C3orf30	HGNC	26553	protein_coding	YES	CCDS2984.1	ENSP00000295622	CC030_HUMAN	.	UPI000013E280	.	.	.	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21847:SF1,hmmpanther:PTHR21847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAACGAAGA	.	5	ESCA
CCDC37	0	.	GRCh37	3	126139001	126139001	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1011G>C	p.%3D	p.R337R	ENST00000352312	11/17	73	55	18	55	55	0	CCDC37,synonymous_variant,p.%3D,ENST00000505024,;CCDC37,synonymous_variant,p.%3D,ENST00000393425,;CCDC37,synonymous_variant,p.%3D,ENST00000352312,;CCDC37,non_coding_transcript_exon_variant,,ENST00000507830,;CCDC37,downstream_gene_variant,,ENST00000533201,;CCDC37,downstream_gene_variant,,ENST00000503905,;	C	ENSG00000163885	ENST00000352312	Transcript	synonymous_variant	1110	1011	337	R	cgG/cgC	.	.	.	1	CCDC37	HGNC	26842	protein_coding	YES	CCDS3037.1	ENSP00000344749	CCD37_HUMAN	.	UPI000013E315	.	.	.	11/17	.	hmmpanther:PTHR21683:SF5,hmmpanther:PTHR21683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCGGAGCCC	.	5	ESCA
PPP2R3A	0	.	GRCh37	3	135864524	135864524	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*516G>A	.	.	ENST00000264977	14/14	60	47	13	42	42	0	PPP2R3A,3_prime_UTR_variant,,ENST00000264977,;PPP2R3A,downstream_gene_variant,,ENST00000490467,;MSL2,downstream_gene_variant,,ENST00000309993,;MSL2,downstream_gene_variant,,ENST00000434835,;PPP2R3A,downstream_gene_variant,,ENST00000334546,;	A	ENSG00000073711	ENST00000264977	Transcript	3_prime_UTR_variant	4586	.	.	.	.	.	.	.	1	PPP2R3A	HGNC	9307	protein_coding	YES	CCDS3087.1	ENSP00000264977	P2R3A_HUMAN	.	UPI0000124EAC	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTGGAGTTC	.	5	ESCA
SLC35G2	0	.	GRCh37	3	136574698	136574698	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*157C>G	.	.	ENST00000446465	2/2	23	18	5	19	19	0	SLC35G2,3_prime_UTR_variant,,ENST00000393079,;SLC35G2,3_prime_UTR_variant,,ENST00000446465,;RP11-85F14.5,intron_variant,,ENST00000474250,;RP11-85F14.5,intron_variant,,ENST00000470236,;RP11-85F14.5,intron_variant,,ENST00000461864,;	G	ENSG00000168917	ENST00000446465	Transcript	3_prime_UTR_variant	2024	.	.	.	.	.	.	.	1	SLC35G2	HGNC	28480	protein_coding	YES	CCDS3091.1	ENSP00000400839	S35G2_HUMAN	.	UPI000013EB08	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCAAATA	.	5	ESCA
DZIP1L	0	.	GRCh37	3	137822572	137822572	+	Missense_Mutation	SNP	G	G	A	rs747572718	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242C>T	p.Pro81Leu	p.P81L	ENST00000327532	2/16	56	42	14	47	47	0	DZIP1L,missense_variant,p.Pro81Leu,ENST00000469243,;DZIP1L,missense_variant,p.Pro81Leu,ENST00000327532,;DZIP1L,downstream_gene_variant,,ENST00000467030,;DZIP1L,downstream_gene_variant,,ENST00000492010,;DZIP1L,non_coding_transcript_exon_variant,,ENST00000490472,;KRT8P36,upstream_gene_variant,,ENST00000489121,;	A	ENSG00000158163	ENST00000327532	Transcript	missense_variant	605	242	81	P/L	cCg/cTg	rs747572718	.	.	-1	DZIP1L	HGNC	26551	protein_coding	YES	CCDS3096.1	ENSP00000332148	DZI1L_HUMAN	C9JRW2_HUMAN,C9JD19_HUMAN	UPI0000161A66	.	deleterious(0)	possibly_damaging(0.87)	2/16	.	hmmpanther:PTHR21502:SF8,hmmpanther:PTHR21502,Pfam_domain:PF13815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCGGGTCC	.	5	ESCA
LEKR1	0	.	GRCh37	3	156763598	156763598	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*59G>A	.	.	ENST00000356539	13/13	17	14	3	15	15	0	LEKR1,3_prime_UTR_variant,,ENST00000356539,;LEKR1,3_prime_UTR_variant,,ENST00000470811,;	A	ENSG00000197980	ENST00000356539	Transcript	3_prime_UTR_variant	2252	.	.	.	.	.	.	.	1	LEKR1	HGNC	33765	protein_coding	.	.	ENSP00000348936	.	J3KP02_HUMAN	UPI0001BB2D45	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAGGAATTC	.	2	ESCA
KCNMB3	0	.	GRCh37	3	178960754	178960754	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778G>C	p.Glu260Gln	p.E260Q	ENST00000314235	4/4	81	62	19	70	70	0	KCNMB3,missense_variant,p.Glu258Gln,ENST00000349697,;KCNMB3,missense_variant,p.Glu260Gln,ENST00000314235,;KCNMB3,missense_variant,p.Glu256Gln,ENST00000392685,;KCNMB3,missense_variant,p.Glu238Gln,ENST00000485523,;KCNMB3,intron_variant,,ENST00000497599,;PIK3CA,downstream_gene_variant,,ENST00000263967,;KCNMB3,intron_variant,,ENST00000486944,;KCNMB3,missense_variant,p.Glu238Gln,ENST00000392686,;	G	ENSG00000171121	ENST00000314235	Transcript	missense_variant	1290	778	260	E/Q	Gaa/Caa	.	.	.	-1	KCNMB3	HGNC	6287	protein_coding	YES	CCDS3226.1	ENSP00000319370	KCMB3_HUMAN	.	UPI000013EA98	.	tolerated_low_confidence(0.3)	benign(0.151)	4/4	.	hmmpanther:PTHR10258,hmmpanther:PTHR10258:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTCTATAT	.	5	ESCA
VPS8	0	.	GRCh37	3	184711826	184711826	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3641T>A	p.Met1214Lys	p.M1214K	ENST00000437079	43/48	99	82	16	98	98	0	VPS8,missense_variant,p.Met1122Lys,ENST00000446204,;VPS8,missense_variant,p.Met1212Lys,ENST00000436792,;VPS8,missense_variant,p.Met1214Lys,ENST00000437079,;VPS8,missense_variant,p.Met1214Lys,ENST00000287546,;VPS8,non_coding_transcript_exon_variant,,ENST00000492449,;VPS8,non_coding_transcript_exon_variant,,ENST00000488255,;	A	ENSG00000156931	ENST00000437079	Transcript	missense_variant	3812	3641	1214	M/K	aTg/aAg	.	.	.	1	VPS8	HGNC	29122	protein_coding	YES	CCDS46971.1	ENSP00000397879	VPS8_HUMAN	C9JPI1_HUMAN,C9JKL0_HUMAN,C9JIA0_HUMAN	UPI0000160BDC	.	deleterious(0)	probably_damaging(0.993)	43/48	.	hmmpanther:PTHR12816,hmmpanther:PTHR12816:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGAATGTTAG	.	4	ESCA
RNF168	0	.	GRCh37	3	196199528	196199528	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.878C>T	p.Ser293Leu	p.S293L	ENST00000318037	6/6	29	14	15	15	15	0	RNF168,missense_variant,p.Ser293Leu,ENST00000318037,;CTD-2002J20.1,upstream_gene_variant,,ENST00000610042,;RNF168,3_prime_UTR_variant,,ENST00000437070,;	A	ENSG00000163961	ENST00000318037	Transcript	missense_variant	1473	878	293	S/L	tCa/tTa	.	.	.	-1	RNF168	HGNC	26661	protein_coding	YES	CCDS3317.1	ENSP00000320898	RN168_HUMAN	.	UPI00000741D1	.	tolerated(0.65)	benign(0.025)	6/6	.	hmmpanther:PTHR23328:SF1,hmmpanther:PTHR23328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATTGAAGAA	.	5	ESCA
CNTN4	0	.	GRCh37	3	3067916	3067916	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1617G>C	p.%3D	p.L539L	ENST00000397461	14/24	46	32	13	55	55	0	CNTN4,synonymous_variant,p.%3D,ENST00000397459,;CNTN4,synonymous_variant,p.%3D,ENST00000397461,;CNTN4,synonymous_variant,p.%3D,ENST00000448906,;CNTN4,synonymous_variant,p.%3D,ENST00000418658,;CNTN4,synonymous_variant,p.%3D,ENST00000358480,;CNTN4,synonymous_variant,p.%3D,ENST00000427331,;CNTN4,3_prime_UTR_variant,,ENST00000427741,;CNTN4,non_coding_transcript_exon_variant,,ENST00000430505,;	C	ENSG00000144619	ENST00000397461	Transcript	synonymous_variant	2001	1617	539	L	ctG/ctC	.	.	.	1	CNTN4	HGNC	2174	protein_coding	YES	CCDS43041.1	ENSP00000380602	CNTN4_HUMAN	G3XAD4_HUMAN,C9JMQ2_HUMAN,C9JGK9_HUMAN	UPI000007446C	.	.	.	14/24	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00408,Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR10489:SF568,hmmpanther:PTHR10489,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CACCTGATAGA	.	3	ESCA
ITIH4	0	.	GRCh37	3	52864530	52864530	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90+39G>A	.	.	ENST00000266041	.	34	20	14	61	61	0	ITIH4,intron_variant,,ENST00000346281,;ITIH4,intron_variant,,ENST00000266041,;ITIH4,intron_variant,,ENST00000434759,;ITIH4,intron_variant,,ENST00000485816,;ITIH4,intron_variant,,ENST00000406595,;TMEM110-MUSTN1,downstream_gene_variant,,ENST00000514466,;MUSTN1,downstream_gene_variant,,ENST00000486659,;TMEM110-MUSTN1,downstream_gene_variant,,ENST00000504329,;ITIH4,upstream_gene_variant,,ENST00000441637,;MUSTN1,downstream_gene_variant,,ENST00000446157,;RP5-966M1.6,non_coding_transcript_exon_variant,,ENST00000513520,;ITIH4,non_coding_transcript_exon_variant,,ENST00000473904,;RP5-966M1.6,intron_variant,,ENST00000468472,;ITIH4,intron_variant,,ENST00000537897,;ITIH4,intron_variant,,ENST00000491663,;TMEM110-MUSTN1,downstream_gene_variant,,ENST00000495552,;	T	ENSG00000055955	ENST00000266041	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ITIH4	HGNC	6169	protein_coding	YES	CCDS2865.1	ENSP00000266041	ITIH4_HUMAN	.	UPI000013D6C3	.	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCATCCC	.	5	ESCA
CLNK	0	.	GRCh37	4	10492148	10492148	+	Silent	SNP	C	C	T	rs762843460	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1230G>A	p.%3D	p.R410R	ENST00000226951	19/19	55	40	15	64	64	0	CLNK,synonymous_variant,p.%3D,ENST00000226951,;CLNK,synonymous_variant,p.%3D,ENST00000515667,;	T	ENSG00000109684	ENST00000226951	Transcript	synonymous_variant	1470	1230	410	R	agG/agA	rs762843460	.	.	-1	CLNK	HGNC	17438	protein_coding	YES	CCDS47024.1	ENSP00000226951	CLNK_HUMAN	D6RJB9_HUMAN	UPI000004A23A	.	.	.	19/19	.	PROSITE_profiles:PS50001,hmmpanther:PTHR14098,hmmpanther:PTHR14098:SF2,Gene3D:3.30.505.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTCCTGTG	.	5	ESCA
PDE5A	0	.	GRCh37	4	120528239	120528239	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366G>A	p.%3D	p.V122V	ENST00000354960	2/21	62	44	18	52	52	0	PDE5A,synonymous_variant,p.%3D,ENST00000354960,;PDE5A,synonymous_variant,p.%3D,ENST00000420633,;PDE5A,synonymous_variant,p.%3D,ENST00000264805,;PDE5A,synonymous_variant,p.%3D,ENST00000394439,;	T	ENSG00000138735	ENST00000354960	Transcript	synonymous_variant	686	366	122	V	gtG/gtA	.	.	.	-1	PDE5A	HGNC	8784	protein_coding	YES	CCDS3713.1	ENSP00000347046	PDE5A_HUMAN	Q9P0K6_HUMAN,Q9P0K4_HUMAN,Q4W5L4_HUMAN,G5E9C5_HUMAN,C9JGT3_HUMAN	UPI000013D571	.	.	.	2/21	.	hmmpanther:PTHR11347:SF21,hmmpanther:PTHR11347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTCACAGT	.	5	ESCA
ANXA5	0	.	GRCh37	4	122599640	122599640	+	Nonsense_Mutation	SNP	G	G	C	rs765003645	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404C>G	p.Ser135Ter	p.S135*	ENST00000296511	7/13	24	18	6	29	29	0	ANXA5,stop_gained,p.Ser35Ter,ENST00000515017,;ANXA5,stop_gained,p.Ser135Ter,ENST00000296511,;ANXA5,stop_gained,p.Ser75Ter,ENST00000501272,;ANXA5,non_coding_transcript_exon_variant,,ENST00000509016,;ANXA5,stop_gained,p.Ser135Ter,ENST00000506395,;ANXA5,non_coding_transcript_exon_variant,,ENST00000511552,;ANXA5,downstream_gene_variant,,ENST00000513523,;ANXA5,upstream_gene_variant,,ENST00000509648,;ANXA5,downstream_gene_variant,,ENST00000513728,;ANXA5,downstream_gene_variant,,ENST00000513428,;	C	ENSG00000164111	ENST00000296511	Transcript	stop_gained	690	404	135	S/*	tCa/tGa	rs765003645	.	.	-1	ANXA5	HGNC	543	protein_coding	YES	CCDS3720.1	ENSP00000296511	ANXA5_HUMAN	.	UPI000002BA00	.	.	.	7/13	.	hmmpanther:PTHR10502,hmmpanther:PTHR10502:SF26,PROSITE_patterns:PS00223,Gene3D:1.10.220.10,Pfam_domain:PF00191,SMART_domains:SM00335,Superfamily_domains:SSF47874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTGAGCCA	byFrequency	5	ESCA
FAT4	0	.	GRCh37	4	126242132	126242132	+	Silent	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4566C>A	p.%3D	p.L1522L	ENST00000394329	1/17	20	16	4	17	17	0	FAT4,synonymous_variant,p.%3D,ENST00000394329,;	A	ENSG00000196159	ENST00000394329	Transcript	synonymous_variant	4579	4566	1522	L	ctC/ctA	.	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	.	1/17	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCTCAATGA	.	4	ESCA
PCDH10	0	.	GRCh37	4	134072089	134072089	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.794C>A	p.Pro265Gln	p.P265Q	ENST00000264360	1/5	28	20	8	34	34	0	PCDH10,missense_variant,p.Pro265Gln,ENST00000264360,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;PCDH10,upstream_gene_variant,,ENST00000511112,;	A	ENSG00000138650	ENST00000264360	Transcript	missense_variant	1620	794	265	P/Q	cCa/cAa	.	.	.	1	PCDH10	HGNC	13404	protein_coding	YES	CCDS34063.1	ENSP00000264360	PCD10_HUMAN	Q9NSR3_HUMAN	UPI0000161C61	.	tolerated(0.36)	possibly_damaging(0.828)	1/5	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028:SF0,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P264S|c.790C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCCAGGCA	.	5	ESCA
DCHS2	0	.	GRCh37	4	155156083	155156083	+	Missense_Mutation	SNP	C	C	T	rs375321525	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8356G>A	p.Glu2786Lys	p.E2786K	ENST00000357232	25/25	20	9	10	23	23	0	DCHS2,missense_variant,p.Glu2786Lys,ENST00000357232,;	T	ENSG00000197410	ENST00000357232	Transcript	missense_variant	8356	8356	2786	E/K	Gag/Aag	rs375321525	.	.	-1	DCHS2	HGNC	23111	protein_coding	YES	CCDS3785.1	ENSP00000349768	PCD23_HUMAN	B3KT73_HUMAN	UPI000035B018	.	deleterious(0.01)	possibly_damaging(0.685)	25/25	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF257	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTCCCAAC	byCluster	5	ESCA
DCHS2	0	.	GRCh37	4	155219049	155219049	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5052C>T	p.%3D	p.F1684F	ENST00000357232	18/25	41	32	8	40	40	0	DCHS2,synonymous_variant,p.%3D,ENST00000357232,;	A	ENSG00000197410	ENST00000357232	Transcript	synonymous_variant	5052	5052	1684	F	ttC/ttT	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	YES	CCDS3785.1	ENSP00000349768	PCD23_HUMAN	B3KT73_HUMAN	UPI000035B018	.	.	.	18/25	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF257,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTGAAGGA	.	5	ESCA
DCHS2	0	.	GRCh37	4	155254137	155254137	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1726A>T	p.Lys576Ter	p.K576*	ENST00000357232	9/25	30	23	6	20	20	0	DCHS2,stop_gained,p.Lys1075Ter,ENST00000339452,;DCHS2,stop_gained,p.Lys576Ter,ENST00000357232,;DCHS2,downstream_gene_variant,,ENST00000507542,;DCHS2,downstream_gene_variant,,ENST00000504580,;	A	ENSG00000197410	ENST00000357232	Transcript	stop_gained	1726	1726	576	K/*	Aaa/Taa	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	YES	CCDS3785.1	ENSP00000349768	PCD23_HUMAN	B3KT73_HUMAN	UPI000035B018	.	.	.	9/25	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF257,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGTTTCTCGA	.	5	ESCA
DCHS2	0	.	GRCh37	4	155410844	155410844	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1664G>T	p.Gly555Val	p.G555V	ENST00000443500	1/2	51	44	6	28	28	0	DCHS2,missense_variant,p.Gly555Val,ENST00000443500,;DCHS2,missense_variant,p.Gly555Val,ENST00000339452,;DCHS2,missense_variant,p.Gly548Val,ENST00000456341,;	A	ENSG00000197410	ENST00000443500	Transcript	missense_variant	2087	1664	555	G/V	gGc/gTc	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	.	CCDS47151.1	ENSP00000395539	.	Q6V1P8_HUMAN,E9PG03_HUMAN	UPI0001881B4E	.	deleterious(0)	probably_damaging(0.998)	1/2	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF262,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTGCCAGGG	.	4	ESCA
DCHS2	0	.	GRCh37	4	155411596	155411596	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912G>A	p.%3D	p.A304A	ENST00000443500	1/2	11	8	3	15	15	0	DCHS2,synonymous_variant,p.%3D,ENST00000443500,;DCHS2,synonymous_variant,p.%3D,ENST00000339452,;DCHS2,synonymous_variant,p.%3D,ENST00000456341,;	T	ENSG00000197410	ENST00000443500	Transcript	synonymous_variant	1335	912	304	A	gcG/gcA	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	.	CCDS47151.1	ENSP00000395539	.	Q6V1P8_HUMAN,E9PG03_HUMAN	UPI0001881B4E	.	.	.	1/2	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF262,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCACCGCGGC	.	2	ESCA
DCAF16	0	.	GRCh37	4	17805730	17805730	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35C>T	p.Ser12Leu	p.S12L	ENST00000382247	3/3	15	10	5	24	24	0	DCAF16,missense_variant,p.Ser12Leu,ENST00000382247,;DCAF16,missense_variant,p.Ser12Leu,ENST00000536863,;DCAF16,downstream_gene_variant,,ENST00000507768,;	A	ENSG00000163257	ENST00000382247	Transcript	missense_variant	1096	35	12	S/L	tCa/tTa	.	.	.	-1	DCAF16	HGNC	25987	protein_coding	YES	CCDS3423.1	ENSP00000371682	DCA16_HUMAN	.	UPI000006D3DE	.	deleterious_low_confidence(0.03)	benign(0.012)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16194,hmmpanther:PTHR16194:SF0,Pfam_domain:PF15349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S14S|c.42A>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTGACAAG	.	5	ESCA
SH3BP2	0	.	GRCh37	4	2835719	2835719	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*158T>C	.	.	ENST00000503393	13/13	15	11	4	14	14	0	SH3BP2,3_prime_UTR_variant,,ENST00000503393,;SH3BP2,3_prime_UTR_variant,,ENST00000442312,;SH3BP2,3_prime_UTR_variant,,ENST00000435136,;SH3BP2,3_prime_UTR_variant,,ENST00000356331,;SH3BP2,3_prime_UTR_variant,,ENST00000452765,;SH3BP2,3_prime_UTR_variant,,ENST00000511747,;SH3BP2,downstream_gene_variant,,ENST00000515183,;SH3BP2,3_prime_UTR_variant,,ENST00000515737,;SH3BP2,non_coding_transcript_exon_variant,,ENST00000510204,;SH3BP2,non_coding_transcript_exon_variant,,ENST00000515802,;SH3BP2,downstream_gene_variant,,ENST00000504450,;SH3BP2,downstream_gene_variant,,ENST00000505941,;SH3BP2,downstream_gene_variant,,ENST00000513069,;	C	ENSG00000087266	ENST00000503393	Transcript	3_prime_UTR_variant	2054	.	.	.	.	.	.	.	1	SH3BP2	HGNC	10825	protein_coding	YES	CCDS54716.1	ENSP00000422168	.	D6RER9_HUMAN,D6RC64_HUMAN,D6RBL6_HUMAN,D6RAB4_HUMAN,D6R995_HUMAN,D6R919_HUMAN	UPI00019638E3	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCATCCAGC	.	5	ESCA
WFS1	0	.	GRCh37	4	6293094	6293094	+	Missense_Mutation	SNP	G	G	A	rs138682654	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Asp211Asn	p.D211N	ENST00000226760	5/8	14	8	6	10	10	0	WFS1,missense_variant,p.Asp211Asn,ENST00000503569,;WFS1,missense_variant,p.Asp77Asn,ENST00000506362,;WFS1,missense_variant,p.Asp211Asn,ENST00000226760,;WFS1,splice_region_variant,,ENST00000507765,;WFS1,downstream_gene_variant,,ENST00000506588,;WFS1,upstream_gene_variant,,ENST00000513395,;	A	ENSG00000109501	ENST00000226760	Transcript	missense_variant	801	631	211	D/N	Gat/Aat	CM033824,rs138682654	.	.	1	WFS1	HGNC	12762	protein_coding	YES	CCDS3386.1	ENSP00000226760	WFS1_HUMAN	B4DJ99_HUMAN	UPI00000715C3	.	tolerated(0.17)	possibly_damaging(0.495)	5/8	.	hmmpanther:PTHR13098,Prints_domain:PR02061	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCACGGTGCG	byCluster	4	ESCA
EPHA5	0	.	GRCh37	4	66189745	66189745	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*87A>G	.	.	ENST00000273854	18/18	70	66	4	58	58	0	EPHA5,3_prime_UTR_variant,,ENST00000273854,;EPHA5,3_prime_UTR_variant,,ENST00000432638,;EPHA5,3_prime_UTR_variant,,ENST00000354839,;	C	ENSG00000145242	ENST00000273854	Transcript	3_prime_UTR_variant	3802	.	.	.	.	.	.	.	-1	EPHA5	HGNC	3389	protein_coding	YES	CCDS3513.1	ENSP00000273854	EPHA5_HUMAN	.	UPI000013D9D9	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCCTTTTCC	.	2	ESCA
AMBN	0	.	GRCh37	4	71467351	71467351	+	Missense_Mutation	SNP	G	G	A	rs745938371	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.511G>A	p.Asp171Asn	p.D171N	ENST00000322937	6/13	62	54	8	33	33	0	AMBN,missense_variant,p.Asp156Asn,ENST00000449493,;AMBN,missense_variant,p.Asp171Asn,ENST00000322937,;	A	ENSG00000178522	ENST00000322937	Transcript	missense_variant	614	511	171	D/N	Gat/Aat	rs745938371	.	.	1	AMBN	HGNC	452	protein_coding	YES	CCDS3543.1	ENSP00000313809	AMBN_HUMAN	Q546D7_HUMAN	UPI000000DCCB	.	deleterious(0.02)	possibly_damaging(0.597)	6/13	.	SMART_domains:SM00817,Pfam_domain:PF05111,hmmpanther:PTHR14115:SF0,hmmpanther:PTHR14115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCAGATAAG	byFrequency	4	ESCA
GC	0	.	GRCh37	4	72607471	72607471	+	3'UTR	SNP	T	T	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*142A>C	.	.	ENST00000504199	14/14	39	28	10	31	31	0	GC,3_prime_UTR_variant,,ENST00000273951,;GC,3_prime_UTR_variant,,ENST00000504199,;GC,3_prime_UTR_variant,,ENST00000513476,;GC,non_coding_transcript_exon_variant,,ENST00000503364,;GC,non_coding_transcript_exon_variant,,ENST00000503472,;GC,3_prime_UTR_variant,,ENST00000509740,;	G	ENSG00000145321	ENST00000504199	Transcript	3_prime_UTR_variant	1719	.	.	.	.	.	.	.	-1	GC	HGNC	4187	protein_coding	YES	CCDS56332.1	ENSP00000421725	VTDB_HUMAN	D6RF20_HUMAN	UPI0001D3B4EE	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTATGAAGA	.	5	ESCA
SH3TC1	0	.	GRCh37	4	8207065	8207065	+	Silent	SNP	C	C	T	rs765366188	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144C>T	p.%3D	p.P48P	ENST00000245105	2/18	56	46	10	53	53	0	SH3TC1,synonymous_variant,p.%3D,ENST00000382521,;SH3TC1,synonymous_variant,p.%3D,ENST00000245105,;SH3TC1,synonymous_variant,p.%3D,ENST00000457650,;SH3TC1,5_prime_UTR_variant,,ENST00000539824,;SH3TC1,intron_variant,,ENST00000509119,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000503284,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000510763,;SH3TC1,downstream_gene_variant,,ENST00000504822,;SH3TC1,synonymous_variant,p.%3D,ENST00000502669,;SH3TC1,synonymous_variant,p.%3D,ENST00000515682,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000507123,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000506360,;SH3TC1,upstream_gene_variant,,ENST00000512100,;SH3TC1,upstream_gene_variant,,ENST00000504223,;	T	ENSG00000125089	ENST00000245105	Transcript	synonymous_variant	211	144	48	P	ccC/ccT	rs765366188	.	.	1	SH3TC1	HGNC	26009	protein_coding	YES	CCDS3399.1	ENSP00000245105	S3TC1_HUMAN	F5GXD3_HUMAN,E7EQR1_HUMAN,D6RC98_HUMAN	UPI000013CB93	.	.	.	2/18	.	hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCCCGAGGA	byFrequency	2	ESCA
C4orf36	0	.	GRCh37	4	87809349	87809349	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.145G>T	p.Glu49Ter	p.E49*	ENST00000473559	6/7	52	39	13	37	37	0	C4orf36,stop_gained,p.Glu49Ter,ENST00000473559,;C4orf36,stop_gained,p.Glu49Ter,ENST00000295898,;C4orf36,stop_gained,p.Glu49Ter,ENST00000504008,;C4orf36,stop_gained,p.Glu49Ter,ENST00000506308,;C4orf36,non_coding_transcript_exon_variant,,ENST00000504371,;C4orf36,non_coding_transcript_exon_variant,,ENST00000503001,;C4orf36,3_prime_UTR_variant,,ENST00000462714,;C4orf36,3_prime_UTR_variant,,ENST00000512468,;	A	ENSG00000163633	ENST00000473559	Transcript	stop_gained	809	145	49	E/*	Gaa/Taa	COSM389507	.	.	-1	C4orf36	HGNC	28386	protein_coding	YES	CCDS3615.1	ENSP00000420949	CD036_HUMAN	D6RGW9_HUMAN,D6RAE1_HUMAN	UPI000013E2CB	.	.	.	6/7	.	Pfam_domain:PF15022	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTCTTCCA	.	5	ESCA
SMARCAD1	0	.	GRCh37	4	95199585	95199585	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2095G>C	p.Glu699Gln	p.E699Q	ENST00000359052	17/24	51	41	10	44	44	0	SMARCAD1,missense_variant,p.Glu269Gln,ENST00000509418,;SMARCAD1,missense_variant,p.Glu699Gln,ENST00000457823,;SMARCAD1,missense_variant,p.Glu699Gln,ENST00000354268,;SMARCAD1,missense_variant,p.Glu699Gln,ENST00000359052,;SMARCAD1,3_prime_UTR_variant,,ENST00000394961,;SMARCAD1,downstream_gene_variant,,ENST00000506089,;SMARCAD1,downstream_gene_variant,,ENST00000514232,;SMARCAD1,downstream_gene_variant,,ENST00000510105,;	C	ENSG00000163104	ENST00000359052	Transcript	missense_variant	2269	2095	699	E/Q	Gag/Cag	.	.	.	1	SMARCAD1	HGNC	18398	protein_coding	YES	CCDS47101.1	ENSP00000351947	SMRCD_HUMAN	.	UPI000020B1CF	.	deleterious(0.04)	benign(0.113)	17/24	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF271,Pfam_domain:PF00176,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATGAGCAA	.	5	ESCA
ADAMTS19	0	.	GRCh37	5	129019948	129019948	+	Missense_Mutation	SNP	G	G	A	rs755466580	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2782G>A	p.Asp928Asn	p.D928N	ENST00000274487	18/23	31	27	4	24	24	0	ADAMTS19,missense_variant,p.Asp928Asn,ENST00000274487,;CTC-575N7.1,intron_variant,,ENST00000503616,;ADAMTS19,upstream_gene_variant,,ENST00000509467,;	A	ENSG00000145808	ENST00000274487	Transcript	missense_variant	2927	2782	928	D/N	Gat/Aat	rs755466580,COSM170818	.	.	1	ADAMTS19	HGNC	17111	protein_coding	YES	CCDS4146.1	ENSP00000274487	ATS19_HUMAN	.	UPI000013DA0D	.	tolerated(0.3)	benign(0.005)	18/23	.	PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF151,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTGCGATGCC	.	3	ESCA
PURA	0	.	GRCh37	5	139494603	139494603	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837G>A	p.%3D	p.K279K	ENST00000331327	1/1	27	23	4	28	28	0	PURA,synonymous_variant,p.%3D,ENST00000331327,;PURA,downstream_gene_variant,,ENST00000505703,;PURA,downstream_gene_variant,,ENST00000502351,;	A	ENSG00000185129	ENST00000331327	Transcript	synonymous_variant	896	837	279	K	aaG/aaA	.	.	.	1	PURA	HGNC	9701	protein_coding	YES	CCDS4220.1	ENSP00000332706	PURA_HUMAN	.	UPI0000132B76	.	.	.	1/1	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12611,hmmpanther:PTHR12611:SF2,SMART_domains:SM00712	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGAAGAAGAT	.	4	ESCA
PCDHA7	0	.	GRCh37	5	140214165	140214165	+	Missense_Mutation	SNP	C	C	T	rs782011323	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.197C>T	p.Ala66Val	p.A66V	ENST00000525929	1/4	122	101	20	122	122	0	PCDHA7,missense_variant,p.Ala66Val,ENST00000378125,;PCDHA7,missense_variant,p.Ala66Val,ENST00000525929,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	T	ENSG00000204963	ENST00000525929	Transcript	missense_variant	197	197	66	A/V	gCg/gTg	rs782011323,COSM1219609,COSM1219608	.	.	1	PCDHA7	HGNC	8673	protein_coding	YES	CCDS54918.1	ENSP00000436426	PCDA7_HUMAN	.	UPI00001273CF	.	tolerated_low_confidence(1)	benign(0.002)	1/4	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGGGCGGTGT	byFrequency	4	ESCA
PCDHAC2	0	.	GRCh37	5	140347393	140347393	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1042C>G	p.His348Asp	p.H348D	ENST00000289269	1/4	35	31	3	35	35	0	PCDHAC2,missense_variant,p.His348Asp,ENST00000289269,;PCDHAC1,intron_variant,,ENST00000253807,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA13,intron_variant,,ENST00000289272,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA13,intron_variant,,ENST00000409494,;	G	ENSG00000243232	ENST00000289269	Transcript	missense_variant	1574	1042	348	H/D	Cac/Gac	.	.	.	1	PCDHAC2	HGNC	8677	protein_coding	YES	CCDS4242.1	ENSP00000289269	PCDC2_HUMAN	.	UPI0000127786	.	deleterious(0)	probably_damaging(0.99)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF10,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGTCACTGC	.	4	ESCA
TCOF1	0	.	GRCh37	5	149755735	149755735	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1984G>T	p.Gly662Cys	p.G662C	ENST00000504761	13/26	30	23	7	18	18	0	TCOF1,missense_variant,p.Gly662Cys,ENST00000427724,;TCOF1,missense_variant,p.Gly662Cys,ENST00000513346,;TCOF1,missense_variant,p.Gly662Cys,ENST00000394269,;TCOF1,missense_variant,p.Gly662Cys,ENST00000439160,;TCOF1,missense_variant,p.Gly662Cys,ENST00000377797,;TCOF1,missense_variant,p.Gly662Cys,ENST00000451292,;TCOF1,missense_variant,p.Gly585Cys,ENST00000445265,;TCOF1,missense_variant,p.Gly585Cys,ENST00000323668,;TCOF1,missense_variant,p.Gly662Cys,ENST00000504761,;TCOF1,intron_variant,,ENST00000515516,;TCOF1,upstream_gene_variant,,ENST00000513538,;TCOF1,upstream_gene_variant,,ENST00000506063,;TCOF1,non_coding_transcript_exon_variant,,ENST00000515035,;TCOF1,non_coding_transcript_exon_variant,,ENST00000514442,;TCOF1,upstream_gene_variant,,ENST00000506767,;	T	ENSG00000070814	ENST00000504761	Transcript	missense_variant	1984	1984	662	G/C	Ggc/Tgc	.	.	.	1	TCOF1	HGNC	11654	protein_coding	YES	CCDS54936.1	ENSP00000421655	TCOF_HUMAN	Q9UFD4_HUMAN	UPI0000EE3736	.	deleterious(0)	probably_damaging(0.997)	13/26	.	hmmpanther:PTHR20787,Pfam_domain:PF03546	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTGGGCACC	.	5	ESCA
GM2A	0	.	GRCh37	5	150647048	150647048	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*36G>A	.	.	ENST00000357164	4/4	52	40	12	46	46	0	GM2A,3_prime_UTR_variant,,ENST00000357164,;GM2A,downstream_gene_variant,,ENST00000523466,;GM2A,downstream_gene_variant,,ENST00000523004,;	A	ENSG00000196743	ENST00000357164	Transcript	3_prime_UTR_variant	943	.	.	.	.	.	.	.	1	GM2A	HGNC	4367	protein_coding	YES	CCDS4313.1	ENSP00000349687	SAP3_HUMAN	.	UPI00001AEC37	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGAGGAAGG	.	5	ESCA
FAM196B	0	.	GRCh37	5	169310792	169310792	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111G>A	p.%3D	p.V37V	ENST00000377365	2/4	46	38	8	27	27	0	FAM196B,synonymous_variant,p.%3D,ENST00000377365,;DOCK2,intron_variant,,ENST00000540750,;DOCK2,intron_variant,,ENST00000256935,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,;	T	ENSG00000204767	ENST00000377365	Transcript	synonymous_variant	1493	111	37	V	gtG/gtA	.	.	.	-1	FAM196B	HGNC	37271	protein_coding	YES	CCDS47336.1	ENSP00000366582	F196B_HUMAN	.	UPI0000480500	.	.	.	2/4	.	Pfam_domain:PF15265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTCACCTG	.	5	ESCA
COL23A1	0	.	GRCh37	5	177733909	177733909	+	Missense_Mutation	SNP	G	G	A	rs779240932	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.373C>T	p.Arg125Trp	p.R125W	ENST00000390654	3/29	53	45	7	57	57	0	COL23A1,missense_variant,p.Arg98Trp,ENST00000407622,;COL23A1,missense_variant,p.Arg125Trp,ENST00000390654,;	A	ENSG00000050767	ENST00000390654	Transcript	missense_variant	731	373	125	R/W	Cgg/Tgg	rs779240932	.	.	-1	COL23A1	HGNC	22990	protein_coding	YES	CCDS4436.1	ENSP00000375069	CONA1_HUMAN	.	UPI0000062274	.	deleterious(0.02)	unknown(0)	3/29	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GCGCCGTCCAG	byFrequency	3	ESCA
ADAMTS12	0	.	GRCh37	5	33637836	33637836	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1734G>A	p.%3D	p.G578G	ENST00000504830	12/24	102	92	10	72	72	0	ADAMTS12,synonymous_variant,p.%3D,ENST00000504830,;ADAMTS12,synonymous_variant,p.%3D,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,;	T	ENSG00000151388	ENST00000504830	Transcript	synonymous_variant	2070	1734	578	G	ggG/ggA	.	.	.	-1	ADAMTS12	HGNC	14605	protein_coding	YES	CCDS34140.1	ENSP00000422554	ATS12_HUMAN	.	UPI000013DC51	.	.	.	12/24	.	PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF150,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTTCCCTCC	.	4	ESCA
ANKRD55	0	.	GRCh37	5	55422898	55422898	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.648C>T	p.%3D	p.S216S	ENST00000341048	8/12	41	37	3	38	38	0	ANKRD55,synonymous_variant,p.%3D,ENST00000341048,;ANKRD55,synonymous_variant,p.%3D,ENST00000504958,;RNU6-299P,downstream_gene_variant,,ENST00000517223,;ANKRD55,intron_variant,,ENST00000505970,;	A	ENSG00000164512	ENST00000341048	Transcript	synonymous_variant	800	648	216	S	agC/agT	COSM1068994	.	.	-1	ANKRD55	HGNC	25681	protein_coding	YES	CCDS34161.1	ENSP00000342295	ANR55_HUMAN	.	UPI00004572EF	.	.	.	8/12	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24158:SF21,hmmpanther:PTHR24158,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUSE|VARSCANS	TGATGGCTCAG	.	2	ESCA
MAST4	0	.	GRCh37	5	66461496	66461496	+	Silent	SNP	G	G	A	rs750408242	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6489G>A	p.%3D	p.P2163P	ENST00000403625	29/29	23	18	5	33	33	0	MAST4,synonymous_variant,p.%3D,ENST00000403666,;MAST4,synonymous_variant,p.%3D,ENST00000404260,;MAST4,synonymous_variant,p.%3D,ENST00000443808,;MAST4,synonymous_variant,p.%3D,ENST00000261569,;MAST4,synonymous_variant,p.%3D,ENST00000405643,;MAST4,synonymous_variant,p.%3D,ENST00000403625,;	A	ENSG00000069020	ENST00000403625	Transcript	synonymous_variant	6784	6489	2163	P	ccG/ccA	rs750408242	.	.	1	MAST4	HGNC	19037	protein_coding	YES	CCDS54861.1	ENSP00000385727	.	J3QT34_HUMAN	UPI000173A2B0	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGGGGGC	.	5	ESCA
CMYA5	0	.	GRCh37	5	79030935	79030935	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6347C>T	p.Ala2116Val	p.A2116V	ENST00000446378	2/13	35	32	3	36	36	0	CMYA5,missense_variant,p.Ala2116Val,ENST00000446378,;CMYA5,upstream_gene_variant,,ENST00000506603,;	T	ENSG00000164309	ENST00000446378	Transcript	missense_variant	6378	6347	2116	A/V	gCt/gTt	.	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	benign(0.004)	2/13	.	hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TGATGCTGATG	.	3	ESCA
CDC40	0	.	GRCh37	6	110501659	110501659	+	Silent	SNP	G	G	T	rs764478943	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12G>T	p.%3D	p.A4A	ENST00000368932	2/16	29	16	12	19	19	0	CDC40,synonymous_variant,p.%3D,ENST00000307731,;CDC40,synonymous_variant,p.%3D,ENST00000368932,;CDC40,synonymous_variant,p.%3D,ENST00000368930,;WASF1,upstream_gene_variant,,ENST00000392588,;WASF1,upstream_gene_variant,,ENST00000368938,;WASF1,upstream_gene_variant,,ENST00000392586,;WASF1,upstream_gene_variant,,ENST00000419252,;WASF1,upstream_gene_variant,,ENST00000447287,;WASF1,upstream_gene_variant,,ENST00000359451,;WASF1,upstream_gene_variant,,ENST00000265601,;WASF1,upstream_gene_variant,,ENST00000444391,;WASF1,upstream_gene_variant,,ENST00000392587,;WASF1,upstream_gene_variant,,ENST00000392589,;CDC40,non_coding_transcript_exon_variant,,ENST00000606893,;	T	ENSG00000168438	ENST00000368932	Transcript	synonymous_variant	113	12	4	A	gcG/gcT	rs764478943	.	.	1	CDC40	HGNC	17350	protein_coding	YES	CCDS5081.1	ENSP00000357928	PRP17_HUMAN	Q5SRM9_HUMAN	UPI0000132145	.	.	.	2/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR19852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCGATTGC	.	5	ESCA
CDC40	0	.	GRCh37	6	110501702	110501702	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55G>C	p.Glu19Gln	p.E19Q	ENST00000368932	2/16	32	19	13	25	25	0	CDC40,missense_variant,p.Glu19Gln,ENST00000307731,;CDC40,missense_variant,p.Glu19Gln,ENST00000368932,;CDC40,missense_variant,p.Glu19Gln,ENST00000368930,;WASF1,upstream_gene_variant,,ENST00000392588,;WASF1,upstream_gene_variant,,ENST00000368938,;WASF1,upstream_gene_variant,,ENST00000392586,;WASF1,upstream_gene_variant,,ENST00000419252,;WASF1,upstream_gene_variant,,ENST00000447287,;WASF1,upstream_gene_variant,,ENST00000359451,;WASF1,upstream_gene_variant,,ENST00000265601,;WASF1,upstream_gene_variant,,ENST00000444391,;WASF1,upstream_gene_variant,,ENST00000392587,;WASF1,upstream_gene_variant,,ENST00000392589,;CDC40,non_coding_transcript_exon_variant,,ENST00000606893,;	C	ENSG00000168438	ENST00000368932	Transcript	missense_variant	156	55	19	E/Q	Gaa/Caa	.	.	.	1	CDC40	HGNC	17350	protein_coding	YES	CCDS5081.1	ENSP00000357928	PRP17_HUMAN	Q5SRM9_HUMAN	UPI0000132145	.	tolerated(0.1)	unknown(0)	2/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR19852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGTCCGAATCG	.	3	ESCA
HIST1H2BB	0	.	GRCh37	6	26043872	26043872	+	Missense_Mutation	SNP	G	G	T	rs372198960	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14C>A	p.Ser5Tyr	p.S5Y	ENST00000357905	1/1	54	42	11	41	41	0	HIST1H2BB,missense_variant,p.Ser5Tyr,ENST00000357905,;HIST1H3C,upstream_gene_variant,,ENST00000540144,;U91328.2,upstream_gene_variant,,ENST00000454320,;	T	ENSG00000196226	ENST00000357905	Transcript	missense_variant	14	14	5	S/Y	tCt/tAt	rs372198960	.	.	-1	HIST1H2BB	HGNC	4751	protein_coding	YES	CCDS4575.1	ENSP00000350580	H2B1B_HUMAN	.	UPI0000001BD2	.	deleterious_low_confidence(0)	benign(0.039)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23428,Gene3D:1.10.20.10	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTAGAGGGT	byFrequency|byCluster	5	ESCA
HFE	0	.	GRCh37	6	26092860	26092860	+	Intron	SNP	C	C	T	rs776104762	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617-53C>T	.	.	ENST00000357618	.	45	32	13	36	36	0	HFE,missense_variant,p.Pro214Ser,ENST00000470149,;HFE,intron_variant,,ENST00000317896,;HFE,intron_variant,,ENST00000353147,;HFE,intron_variant,,ENST00000357618,;HFE,intron_variant,,ENST00000309234,;HFE,intron_variant,,ENST00000488199,;HFE,intron_variant,,ENST00000397022,;HFE,intron_variant,,ENST00000349999,;HFE,intron_variant,,ENST00000352392,;HFE,intron_variant,,ENST00000336625,;HFE,intron_variant,,ENST00000461397,;HFE,upstream_gene_variant,,ENST00000485729,;HFE,non_coding_transcript_exon_variant,,ENST00000486147,;HFE,intron_variant,,ENST00000483782,;	T	ENSG00000010704	ENST00000357618	Transcript	intron_variant	.	.	.	.	.	rs776104762	.	.	1	HFE	HGNC	4886	protein_coding	YES	CCDS4578.1	ENSP00000417404	HFE_HUMAN	Q9UK37_HUMAN,Q9BXI5_HUMAN,Q8MH46_HUMAN,Q86WL1_HUMAN,I1VA72_HUMAN,I1VA66_HUMAN,I1VA63_HUMAN,I1VA60_HUMAN,I1VA56_HUMAN,I1VA55_HUMAN,H2E8T5_HUMAN,G3LGR1_HUMAN,G3LGR0_HUMAN,G3LGQ9_HUMAN,G3LGQ6_HUMAN,F5B2M9_HUMAN	UPI0000001700	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCCTGGC	.	5	ESCA
HIST1H3E	0	.	GRCh37	6	26225496	26225496	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114delG	p.Lys38AsnfsTer25	p.K38Nfs*25	ENST00000360408	1/1	81	71	10	88	88	0	HIST1H3E,frameshift_variant,p.Lys38AsnfsTer25,ENST00000360408,;	-	ENSG00000196966	ENST00000360408	Transcript	frameshift_variant	114	114	38	K/X	aaG/aa	.	.	.	1	HIST1H3E	HGNC	4769	protein_coding	YES	CCDS4596.1	ENSP00000353581	H31_HUMAN	.	UPI00000003C7	.	.	.	1/1	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAGAAGCCCCA	.	3	ESCA
BTN2A3P	0	.	GRCh37	6	26423187	26423187	+	RNA	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.106G>A	.	.	ENST00000466808	2/7	96	82	14	94	94	0	BTN2A3P,non_coding_transcript_exon_variant,,ENST00000466808,;BTN2A3P,non_coding_transcript_exon_variant,,ENST00000465856,;BTN2A3P,upstream_gene_variant,,ENST00000463944,;BTN2A3P,upstream_gene_variant,,ENST00000475151,;BTN2A3P,non_coding_transcript_exon_variant,,ENST00000377662,;BTN2A3P,non_coding_transcript_exon_variant,,ENST00000297020,;	A	ENSG00000124549	ENST00000466808	Transcript	non_coding_transcript_exon_variant	106	.	.	.	.	.	.	.	1	BTN2A3P	HGNC	13229	processed_transcript	YES	.	.	.	.	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACTGATCCC	.	4	ESCA
HMGN4	0	.	GRCh37	6	26545537	26545537	+	Missense_Mutation	SNP	C	C	T	rs146576097	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103C>T	p.Pro35Ser	p.P35S	ENST00000377575	2/2	31	26	4	31	31	0	HMGN4,missense_variant,p.Pro35Ser,ENST00000377575,;	T	ENSG00000182952	ENST00000377575	Transcript	missense_variant	280	103	35	P/S	Cca/Tca	rs146576097	.	.	1	HMGN4	HGNC	4989	protein_coding	YES	CCDS4615.1	ENSP00000366798	HMGN4_HUMAN	.	UPI000013E3BB	.	deleterious(0.04)	possibly_damaging(0.465)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23087:SF11,hmmpanther:PTHR23087,Pfam_domain:PF01101,SMART_domains:SM00527,Prints_domain:PR00925	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCAAAA	.	4	ESCA
HIST1H1B	0	.	GRCh37	6	27834849	27834849	+	Missense_Mutation	SNP	C	C	A	rs776470457	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459G>T	p.Lys153Asn	p.K153N	ENST00000331442	1/1	43	25	17	40	40	0	HIST1H1B,missense_variant,p.Lys153Asn,ENST00000331442,;HIST1H2AL,downstream_gene_variant,,ENST00000357320,;HIST1H3I,downstream_gene_variant,,ENST00000328488,;HIST1H2BPS2,upstream_gene_variant,,ENST00000402707,;	A	ENSG00000184357	ENST00000331442	Transcript	missense_variant	511	459	153	K/N	aaG/aaT	rs776470457	.	.	-1	HIST1H1B	HGNC	4719	protein_coding	YES	CCDS4635.1	ENSP00000330074	H15_HUMAN	.	UPI0000001BDA	.	tolerated(0.13)	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11467:SF24,hmmpanther:PTHR11467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCTTCAC	.	5	ESCA
TAPBP	0	.	GRCh37	6	33272235	33272235	+	Missense_Mutation	SNP	G	G	A	rs374308480	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1049C>T	p.Ser350Leu	p.S350L	ENST00000426633	5/7	82	67	15	46	46	0	TAPBP,missense_variant,p.Ser263Leu,ENST00000489157,;TAPBP,missense_variant,p.Ser350Leu,ENST00000456592,;TAPBP,missense_variant,p.Ser350Leu,ENST00000426633,;TAPBP,missense_variant,p.Ser368Leu,ENST00000475304,;TAPBP,missense_variant,p.Ser350Leu,ENST00000434618,;TAPBP,downstream_gene_variant,,ENST00000467025,;TAPBP,non_coding_transcript_exon_variant,,ENST00000480730,;TAPBP,non_coding_transcript_exon_variant,,ENST00000437116,;	A	ENSG00000231925	ENST00000426633	Transcript	missense_variant	1220	1049	350	S/L	tCg/tTg	rs374308480	.	.	-1	TAPBP	HGNC	11566	protein_coding	YES	CCDS34428.2	ENSP00000404833	.	.	UPI0000E5AD4C	.	deleterious(0)	probably_damaging(1)	5/7	.	Prints_domain:PR01669,Superfamily_domains:SSF48726,Pfam_domain:PF07654,Gene3D:2.60.40.10,hmmpanther:PTHR23411:SF5,hmmpanther:PTHR23411,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCGAGAGC	byCluster	5	ESCA
C6orf222	0	.	GRCh37	6	36291264	36291264	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1277C>T	p.Pro426Leu	p.P426L	ENST00000437635	8/12	54	47	7	60	60	0	C6orf222,missense_variant,p.Pro426Leu,ENST00000437635,;	A	ENSG00000189325	ENST00000437635	Transcript	missense_variant	1455	1277	426	P/L	cCa/cTa	.	.	.	-1	C6orf222	HGNC	33769	protein_coding	YES	CCDS34439.1	ENSP00000418983	CF222_HUMAN	.	UPI000022CB9B	.	tolerated(0.2)	probably_damaging(0.958)	8/12	.	hmmpanther:PTHR22435,hmmpanther:PTHR22435:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTGTGGGGCC	.	4	ESCA
PTK7	0	.	GRCh37	6	43098368	43098368	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805G>A	p.Glu269Lys	p.E269K	ENST00000481273	5/20	26	22	4	30	30	0	PTK7,missense_variant,p.Glu261Lys,ENST00000349241,;PTK7,missense_variant,p.Glu261Lys,ENST00000352931,;PTK7,missense_variant,p.Glu269Lys,ENST00000481273,;PTK7,missense_variant,p.Glu261Lys,ENST00000230419,;PTK7,missense_variant,p.Glu261Lys,ENST00000345201,;PTK7,missense_variant,p.Glu261Lys,ENST00000471863,;PTK7,missense_variant,p.Glu14Lys,ENST00000481946,;PTK7,upstream_gene_variant,,ENST00000489707,;PTK7,downstream_gene_variant,,ENST00000476760,;PTK7,missense_variant,p.Glu261Lys,ENST00000230418,;PTK7,3_prime_UTR_variant,,ENST00000470019,;PTK7,non_coding_transcript_exon_variant,,ENST00000487673,;PTK7,upstream_gene_variant,,ENST00000490710,;	A	ENSG00000112655	ENST00000481273	Transcript	missense_variant	875	805	269	E/K	Gag/Aag	COSM163826	.	.	1	PTK7	HGNC	9618	protein_coding	YES	CCDS59021.1	ENSP00000418754	PTK7_HUMAN	.	UPI0001B79423	.	tolerated(0.28)	probably_damaging(0.969)	5/20	.	PROSITE_profiles:PS50835,hmmpanther:PTHR26391,hmmpanther:PTHR26391:SF14,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTTGAGGAT	.	4	ESCA
PTP4A1	0	.	GRCh37	6	64282504	64282504	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-566G>A	.	.	ENST00000370651	1/6	16	11	5	20	20	0	PTP4A1,5_prime_UTR_variant,,ENST00000370650,;PTP4A1,5_prime_UTR_variant,,ENST00000370651,;PTP4A1,upstream_gene_variant,,ENST00000578299,;RP5-1148A21.3,upstream_gene_variant,,ENST00000584934,;PTP4A1,intron_variant,,ENST00000470661,;PTP4A1,upstream_gene_variant,,ENST00000473334,;	A	ENSG00000112245	ENST00000370651	Transcript	5_prime_UTR_variant	588	.	.	.	.	.	.	.	1	PTP4A1	HGNC	9634	protein_coding	YES	CCDS4965.1	ENSP00000359685	TP4A1_HUMAN	.	UPI00000227B8	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCGCCGCT	.	5	ESCA
IMPG1	0	.	GRCh37	6	76751789	76751789	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.122G>A	p.Arg41Lys	p.R41K	ENST00000369950	2/17	60	49	10	44	44	0	IMPG1,missense_variant,p.Arg41Lys,ENST00000369950,;IMPG1,intron_variant,,ENST00000369963,;	T	ENSG00000112706	ENST00000369950	Transcript	missense_variant	312	122	41	R/K	aGa/aAa	COSM3630061	.	.	-1	IMPG1	HGNC	6055	protein_coding	YES	CCDS4985.1	ENSP00000358966	IMPG1_HUMAN	H0UI08_HUMAN	UPI0000073F12	.	tolerated(0.5)	benign(0.037)	2/17	.	hmmpanther:PTHR12199	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTCTTGGG	.	5	ESCA
BMP6	0	.	GRCh37	6	7880445	7880445	+	Missense_Mutation	SNP	G	G	C	rs368529770	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1411G>C	p.Glu471Gln	p.E471Q	ENST00000283147	7/7	52	37	14	63	63	0	BMP6,missense_variant,p.Glu471Gln,ENST00000283147,;TXNDC5,downstream_gene_variant,,ENST00000539054,;TXNDC5,downstream_gene_variant,,ENST00000379757,;TXNDC5,downstream_gene_variant,,ENST00000473453,;TXNDC5,downstream_gene_variant,,ENST00000475802,;BLOC1S5-TXNDC5,downstream_gene_variant,,ENST00000439343,;TXNDC5,downstream_gene_variant,,ENST00000460138,;	C	ENSG00000153162	ENST00000283147	Transcript	missense_variant	1570	1411	471	E/Q	Gag/Cag	rs368529770	.	.	1	BMP6	HGNC	1073	protein_coding	YES	CCDS4503.1	ENSP00000283147	BMP6_HUMAN	B4DUF7_HUMAN	UPI0000126A2D	.	deleterious(0.03)	benign(0.248)	7/7	.	PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF137,hmmpanther:PTHR11848,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCCGAGTAT	byFrequency|byCluster	5	ESCA
FUT9	0	.	GRCh37	6	96662651	96662651	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10540G>T	.	.	ENST00000302103	3/3	21	17	4	15	15	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	T	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	11946	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGGTAATT	.	5	ESCA
GNB2	0	.	GRCh37	7	100276334	100276334	+	Silent	SNP	C	C	T	rs755263504	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933C>T	p.%3D	p.H311H	ENST00000303210	10/10	68	38	29	35	35	0	GNB2,synonymous_variant,p.%3D,ENST00000393926,;GNB2,synonymous_variant,p.%3D,ENST00000419828,;GNB2,synonymous_variant,p.%3D,ENST00000427895,;GNB2,synonymous_variant,p.%3D,ENST00000303210,;GNB2,synonymous_variant,p.%3D,ENST00000393924,;GNB2,synonymous_variant,p.%3D,ENST00000424361,;GNB2,synonymous_variant,p.%3D,ENST00000436220,;GNB2,downstream_gene_variant,,ENST00000431068,;GNB2,downstream_gene_variant,,ENST00000451587,;GIGYF1,downstream_gene_variant,,ENST00000275732,;GNB2,downstream_gene_variant,,ENST00000412215,;GNB2,non_coding_transcript_exon_variant,,ENST00000470354,;GNB2,non_coding_transcript_exon_variant,,ENST00000469287,;GNB2,downstream_gene_variant,,ENST00000480159,;	T	ENSG00000172354	ENST00000303210	Transcript	synonymous_variant	1415	933	311	H	caC/caT	rs755263504	.	.	1	GNB2	HGNC	4398	protein_coding	YES	CCDS5703.1	ENSP00000305260	GBB2_HUMAN	Q6FHM2_HUMAN,E7EP32_HUMAN,C9JZN1_HUMAN,C9JXA5_HUMAN,C9JIS1_HUMAN,B3KPU1_HUMAN	UPI0000000934	.	.	.	10/10	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,PIRSF_domain:PIRSF002394,Pfam_domain:PF00400,Gene3D:2.130.10.10,hmmpanther:PTHR19850:SF27,hmmpanther:PTHR19850,PROSITE_profiles:PS50294,PROSITE_profiles:PS50082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCACGACAA	byFrequency	5	ESCA
MUC17	0	.	GRCh37	7	100680134	100680134	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5437A>C	p.Thr1813Pro	p.T1813P	ENST00000306151	3/13	124	106	17	78	78	0	MUC17,missense_variant,p.Thr1813Pro,ENST00000306151,;MUC17,missense_variant,p.Thr1813Pro,ENST00000379439,;	C	ENSG00000169876	ENST00000306151	Transcript	missense_variant	5501	5437	1813	T/P	Aca/Cca	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	benign(0.004)	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAGCACACCT	.	4	ESCA
PRKRIP1	0	.	GRCh37	7	102065491	102065491	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.488G>C	p.Ser163Thr	p.S163T	ENST00000496391	10/10	39	24	15	24	24	0	PRKRIP1,missense_variant,p.Gln103His,ENST00000354783,;PRKRIP1,missense_variant,p.Ser163Thr,ENST00000397912,;PRKRIP1,missense_variant,p.Ser106Thr,ENST00000462601,;PRKRIP1,missense_variant,p.Ser163Thr,ENST00000496391,;RP11-514P8.2,downstream_gene_variant,,ENST00000468165,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000469763,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000482465,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000482549,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000468316,;	C	ENSG00000128563	ENST00000496391	Transcript	missense_variant	1798	488	163	S/T	aGc/aCc	.	.	.	1	PRKRIP1	HGNC	21894	protein_coding	YES	CCDS34714.1	ENSP00000419270	PKRI1_HUMAN	.	UPI000003587A	.	tolerated(0.13)	benign(0.418)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13507,Pfam_domain:PF06658	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCCAGCAGCT	.	3	ESCA
PRKRIP1	0	.	GRCh37	7	102065493	102065493	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490A>C	p.Ser164Arg	p.S164R	ENST00000496391	10/10	40	24	16	24	24	0	PRKRIP1,missense_variant,p.Gln104Pro,ENST00000354783,;PRKRIP1,missense_variant,p.Ser164Arg,ENST00000397912,;PRKRIP1,missense_variant,p.Ser107Arg,ENST00000462601,;PRKRIP1,missense_variant,p.Ser164Arg,ENST00000496391,;RP11-514P8.2,downstream_gene_variant,,ENST00000468165,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000469763,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000482465,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000482549,;PRKRIP1,non_coding_transcript_exon_variant,,ENST00000468316,;	C	ENSG00000128563	ENST00000496391	Transcript	missense_variant	1800	490	164	S/R	Agc/Cgc	.	.	.	1	PRKRIP1	HGNC	21894	protein_coding	YES	CCDS34714.1	ENSP00000419270	PKRI1_HUMAN	.	UPI000003587A	.	tolerated(0.05)	possibly_damaging(0.637)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13507,Pfam_domain:PF06658	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCAGCAGCTCT	.	3	ESCA
MGAM	0	.	GRCh37	7	141754576	141754576	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3182G>T	p.Arg1061Leu	p.R1061L	ENST00000549489	27/48	56	42	13	79	79	0	MGAM,missense_variant,p.Arg1061Leu,ENST00000475668,;MGAM,missense_variant,p.Arg1061Leu,ENST00000549489,;	T	ENSG00000257335	ENST00000549489	Transcript	missense_variant	3277	3182	1061	R/L	cGg/cTg	COSM1292450,COSM1292449,COSM1292448	.	.	1	MGAM	HGNC	7043	protein_coding	YES	CCDS47727.1	ENSP00000447378	MGA_HUMAN	Q8TE25_HUMAN,E9PEQ5_HUMAN,E7EW87_HUMAN	UPI000183CB7B	.	deleterious(0)	probably_damaging(0.999)	27/48	.	Superfamily_domains:SSF74650	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCGGTATG	.	5	ESCA
KMT2C	0	.	GRCh37	7	151873959	151873959	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8579C>G	p.Ser2860Ter	p.S2860*	ENST00000262189	38/59	42	25	16	18	18	0	KMT2C,stop_gained,p.Ser2860Ter,ENST00000355193,;KMT2C,stop_gained,p.Ser366Ter,ENST00000360104,;KMT2C,stop_gained,p.Ser2860Ter,ENST00000262189,;KMT2C,downstream_gene_variant,,ENST00000558665,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;	C	ENSG00000055609	ENST00000262189	Transcript	stop_gained	8798	8579	2860	S/*	tCa/tGa	COSM3636485,COSM3636484	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	.	38/59	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTGAGTGA	.	5	ESCA
SP4	0	.	GRCh37	7	21553774	21553774	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2887G>T	.	.	ENST00000222584	6/6	58	45	13	36	36	0	SP4,3_prime_UTR_variant,,ENST00000222584,;SP4,3_prime_UTR_variant,,ENST00000448246,;	T	ENSG00000105866	ENST00000222584	Transcript	3_prime_UTR_variant	5460	.	.	.	.	.	.	.	1	SP4	HGNC	11209	protein_coding	YES	CCDS5373.1	ENSP00000222584	SP4_HUMAN	Q32M51_HUMAN	UPI000013C807	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATGTGTTG	.	5	ESCA
HOXA7	0	.	GRCh37	7	27192510	27192510	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000242159	.	158	134	24	148	148	0	HOXA7,downstream_gene_variant,,ENST00000242159,;HOXA7,downstream_gene_variant,,ENST00000519842,;HOXA-AS3,non_coding_transcript_exon_variant,,ENST00000518947,;HOXA-AS3,downstream_gene_variant,,ENST00000521197,;HOXA-AS3,downstream_gene_variant,,ENST00000524304,;HOXA-AS3,downstream_gene_variant,,ENST00000521231,;HOXA-AS3,downstream_gene_variant,,ENST00000518848,;HOXA7,downstream_gene_variant,,ENST00000523796,;HOXA6,upstream_gene_variant,,ENST00000521478,;HOXA3,upstream_gene_variant,,ENST00000518451,;RP1-170O19.23,upstream_gene_variant,,ENST00000498652,;RP1-170O19.22,upstream_gene_variant,,ENST00000467897,;	A	ENSG00000122592	ENST00000242159	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	825	-1	HOXA7	HGNC	5108	protein_coding	YES	CCDS5408.1	ENSP00000242159	HXA7_HUMAN	E5RHM9_HUMAN	UPI000013CAF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGACGAGGTC	.	4	ESCA
FOXK1	0	.	GRCh37	7	4800867	4800867	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1869C>T	p.%3D	p.T623T	ENST00000328914	8/9	110	95	15	88	88	0	FOXK1,synonymous_variant,p.%3D,ENST00000446823,;FOXK1,synonymous_variant,p.%3D,ENST00000328914,;FOXK1,downstream_gene_variant,,ENST00000496023,;	T	ENSG00000164916	ENST00000328914	Transcript	synonymous_variant	1869	1869	623	T	acC/acT	.	.	.	1	FOXK1	HGNC	23480	protein_coding	YES	CCDS34591.1	ENSP00000328720	FOXK1_HUMAN	B3KV39_HUMAN	UPI00004158EB	.	.	.	8/9	.	hmmpanther:PTHR11829:SF107,hmmpanther:PTHR11829	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGACCCAGAA	.	4	ESCA
NUPR1L	0	.	GRCh37	7	56183800	56183800	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.208C>T	p.Arg70Cys	p.R70C	ENST00000329309	1/2	40	35	5	26	26	0	NUPR1L,missense_variant,p.Arg70Cys,ENST00000329309,;	A	ENSG00000185290	ENST00000329309	Transcript	missense_variant	294	208	70	R/C	Cgc/Tgc	.	.	.	-1	NUPR1L	HGNC	44164	protein_coding	YES	CCDS59058.1	ENSP00000455442	NUR1L_HUMAN	.	UPI00001D751D	.	deleterious(0)	possibly_damaging(0.898)	1/2	.	hmmpanther:PTHR17149:SF3,hmmpanther:PTHR17149,Pfam_domain:PF10195	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTGCGCTCGT	.	4	ESCA
AC006455.1	0	.	GRCh37	7	62809611	62809611	+	5'UTR	SNP	G	G	A	rs543493893	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-399G>A	.	.	ENST00000456890	1/1	180	172	7	107	107	0	AC006455.1,5_prime_UTR_variant,,ENST00000456890,;RP5-905H7.9,intron_variant,,ENST00000426550,;RP5-905H7.10,non_coding_transcript_exon_variant,,ENST00000429931,;RP5-905H7.7,upstream_gene_variant,,ENST00000454641,;RP5-905H7.6,downstream_gene_variant,,ENST00000426192,;	A	ENSG00000230000	ENST00000456890	Transcript	5_prime_UTR_variant	373	.	.	.	.	rs543493893	.	.	1	AC006455.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000407928	.	.	UPI000019793E	.	.	.	1/1	.	.	T:0.0006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGACGCGGTC	byFrequency|by1000G	2	ESCA
FZD9	0	.	GRCh37	7	72849459	72849459	+	Silent	SNP	G	G	C	rs781784393	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1122G>C	p.%3D	p.L374L	ENST00000344575	1/1	44	30	14	22	22	0	FZD9,synonymous_variant,p.%3D,ENST00000344575,;	C	ENSG00000188763	ENST00000344575	Transcript	synonymous_variant	1351	1122	374	L	ctG/ctC	rs781784393	.	.	1	FZD9	HGNC	4047	protein_coding	YES	CCDS5548.1	ENSP00000345785	FZD9_HUMAN	.	UPI000004EC98	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF79,Pfam_domain:PF01534,Prints_domain:PR00489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCTGACCCT	.	5	ESCA
VPS13B	0	.	GRCh37	8	100147953	100147953	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555C>T	p.His519Tyr	p.H519Y	ENST00000358544	11/62	65	41	24	40	40	0	VPS13B,missense_variant,p.His519Tyr,ENST00000355155,;VPS13B,missense_variant,p.His519Tyr,ENST00000395996,;VPS13B,missense_variant,p.His519Tyr,ENST00000358544,;VPS13B,missense_variant,p.His519Tyr,ENST00000357162,;VPS13B,missense_variant,p.His519Tyr,ENST00000496144,;	T	ENSG00000132549	ENST00000358544	Transcript	missense_variant	1666	1555	519	H/Y	Cat/Tat	.	.	.	1	VPS13B	HGNC	2183	protein_coding	YES	CCDS6280.1	ENSP00000351346	VP13B_HUMAN	.	UPI00001D2D35	.	deleterious(0.04)	benign(0.403)	11/62	.	hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCATCAT	.	5	ESCA
CSMD3	0	.	GRCh37	8	113678558	113678558	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2764G>A	p.Glu922Lys	p.E922K	ENST00000297405	17/71	97	82	14	70	70	0	CSMD3,missense_variant,p.Glu922Lys,ENST00000352409,;CSMD3,missense_variant,p.Glu818Lys,ENST00000455883,;CSMD3,missense_variant,p.Glu922Lys,ENST00000297405,;CSMD3,missense_variant,p.Glu262Lys,ENST00000339701,;CSMD3,missense_variant,p.Glu882Lys,ENST00000343508,;	T	ENSG00000164796	ENST00000297405	Transcript	missense_variant	3009	2764	922	E/K	Gag/Aag	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.18)	probably_damaging(0.999)	17/71	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACTCACAAT	.	4	ESCA
TG	0	.	GRCh37	8	134144053	134144053	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7863-3C>T	.	.	ENST00000220616	.	112	71	41	87	87	0	TG,splice_region_variant,,ENST00000220616,;TG,splice_region_variant,,ENST00000542445,;TG,splice_region_variant,,ENST00000377869,;TG,splice_region_variant,,ENST00000519543,;TG,splice_region_variant,,ENST00000519178,;TG,intron_variant,,ENST00000521107,;TG,splice_region_variant,,ENST00000523756,;TG,upstream_gene_variant,,ENST00000522691,;	T	ENSG00000042832	ENST00000220616	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	TG	HGNC	11764	protein_coding	YES	CCDS34944.1	ENSP00000220616	THYG_HUMAN	Q9NYM1_HUMAN,Q9NYD9_HUMAN,E5RG33_HUMAN	UPI000013C79F	.	.	.	.	45/47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCAGCCT	.	4	ESCA
ZFAT	0	.	GRCh37	8	135614789	135614789	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1173C>T	p.%3D	p.L391L	ENST00000377838	6/16	32	22	10	20	20	0	ZFAT,synonymous_variant,p.%3D,ENST00000429442,;ZFAT,synonymous_variant,p.%3D,ENST00000520214,;ZFAT,synonymous_variant,p.%3D,ENST00000377838,;ZFAT,synonymous_variant,p.%3D,ENST00000523399,;ZFAT,synonymous_variant,p.%3D,ENST00000520727,;ZFAT,synonymous_variant,p.%3D,ENST00000520356,;ZFAT-AS1,downstream_gene_variant,,ENST00000505776,;ZFAT,downstream_gene_variant,,ENST00000523040,;ZFAT,synonymous_variant,p.%3D,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000522974,;ZFAT,upstream_gene_variant,,ENST00000519827,;	A	ENSG00000066827	ENST00000377838	Transcript	synonymous_variant	1348	1173	391	L	ctC/ctT	.	.	.	-1	ZFAT	HGNC	19899	protein_coding	YES	CCDS47924.1	ENSP00000367069	ZFAT_HUMAN	.	UPI0000210061	.	.	.	6/16	.	hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGAGCTC	.	5	ESCA
CHD7	0	.	GRCh37	8	61778006	61778006	+	Silent	SNP	G	G	T	rs371399850	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8508G>T	p.%3D	p.P2836P	ENST00000423902	38/38	39	26	13	30	30	0	CHD7,synonymous_variant,p.%3D,ENST00000423902,;CHD7,synonymous_variant,p.%3D,ENST00000524602,;CHD7,non_coding_transcript_exon_variant,,ENST00000528280,;CHD7,downstream_gene_variant,,ENST00000532149,;CHD7,downstream_gene_variant,,ENST00000531695,;	T	ENSG00000171316	ENST00000423902	Transcript	synonymous_variant	8987	8508	2836	P	ccG/ccT	rs371399850	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	.	38/38	.	.	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACCGGAAGA	byCluster	5	ESCA
RIPK2	0	.	GRCh37	8	90801591	90801591	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1166C>G	p.Pro389Arg	p.P389R	ENST00000220751	10/11	42	31	11	42	42	0	RIPK2,missense_variant,p.Pro252Arg,ENST00000540020,;RIPK2,missense_variant,p.Pro389Arg,ENST00000220751,;RIPK2,3_prime_UTR_variant,,ENST00000522965,;	G	ENSG00000104312	ENST00000220751	Transcript	missense_variant	1480	1166	389	P/R	cCt/cGt	.	.	.	1	RIPK2	HGNC	10020	protein_coding	YES	CCDS6247.1	ENSP00000220751	RIPK2_HUMAN	.	UPI00001338F2	.	deleterious(0.04)	benign(0.003)	10/11	.	PIRSF_domain:PIRSF037921,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF323	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCCTGGAA	.	5	ESCA
EPB41L4B	0	.	GRCh37	9	111936619	111936619	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*215G>C	.	.	ENST00000374566	26/26	26	14	12	10	10	0	EPB41L4B,3_prime_UTR_variant,,ENST00000374566,;	G	ENSG00000095203	ENST00000374566	Transcript	3_prime_UTR_variant	3436	.	.	.	.	.	.	.	-1	EPB41L4B	HGNC	19818	protein_coding	YES	CCDS43859.1	ENSP00000363694	E41LB_HUMAN	.	UPI0000458994	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGTCTCAACTA	.	3	ESCA
PIGO	0	.	GRCh37	9	35094020	35094020	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657G>A	p.Met219Ile	p.M219I	ENST00000378617	4/11	56	33	23	39	39	0	PIGO,missense_variant,p.Met219Ile,ENST00000341666,;PIGO,missense_variant,p.Met219Ile,ENST00000361778,;PIGO,missense_variant,p.Met219Ile,ENST00000298004,;PIGO,missense_variant,p.Met219Ile,ENST00000378617,;RP11-182N22.8,upstream_gene_variant,,ENST00000431804,;PIGO,downstream_gene_variant,,ENST00000492770,;PIGO,upstream_gene_variant,,ENST00000491687,;PIGO,downstream_gene_variant,,ENST00000472208,;PIGO,splice_region_variant,,ENST00000474436,;PIGO,non_coding_transcript_exon_variant,,ENST00000465745,;	T	ENSG00000165282	ENST00000378617	Transcript	missense_variant	1052	657	219	M/I	atG/atA	.	.	.	-1	PIGO	HGNC	23215	protein_coding	YES	CCDS6575.1	ENSP00000367880	PIGO_HUMAN	.	UPI0000048EF6	.	tolerated(0.21)	benign(0.141)	4/11	.	hmmpanther:PTHR23071,Pfam_domain:PF01663,Gene3D:3.40.720.10,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCCACTGT	.	5	ESCA
TLN1	0	.	GRCh37	9	35700035	35700035	+	Missense_Mutation	SNP	C	C	T	rs752190315	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6704G>A	p.Arg2235Gln	p.R2235Q	ENST00000314888	50/57	33	15	17	27	27	0	TLN1,missense_variant,p.Arg2235Gln,ENST00000314888,;TLN1,missense_variant,p.Arg2123Gln,ENST00000540444,;TLN1,downstream_gene_variant,,ENST00000464379,;TLN1,upstream_gene_variant,,ENST00000489255,;TLN1,downstream_gene_variant,,ENST00000466916,;TLN1,downstream_gene_variant,,ENST00000465002,;TLN1,downstream_gene_variant,,ENST00000486788,;	T	ENSG00000137076	ENST00000314888	Transcript	missense_variant	7058	6704	2235	R/Q	cGa/cAa	rs752190315	.	.	-1	TLN1	HGNC	11845	protein_coding	YES	CCDS35009.1	ENSP00000316029	TLN1_HUMAN	.	UPI0000211375	.	deleterious(0.01)	probably_damaging(0.957)	50/57	.	hmmpanther:PTHR19981:SF7,hmmpanther:PTHR19981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTCGAAGC	byFrequency	5	ESCA
CSTF2	0	.	GRCh37	X	100079173	100079173	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.629G>A	p.Gly210Asp	p.G210D	ENST00000372972	6/14	50	31	19	64	64	0	CSTF2,missense_variant,p.Gly210Asp,ENST00000372972,;CSTF2,missense_variant,p.Gly201Asp,ENST00000413437,;CSTF2,missense_variant,p.Gly210Asp,ENST00000415585,;SNORA9,upstream_gene_variant,,ENST00000365361,;CSTF2,missense_variant,p.Gly210Asp,ENST00000475126,;	A	ENSG00000101811	ENST00000372972	Transcript	missense_variant	645	629	210	G/D	gGt/gAt	.	.	.	1	CSTF2	HGNC	2484	protein_coding	YES	CCDS14473.1	ENSP00000362063	CSTF2_HUMAN	.	UPI000003BCAF	.	tolerated(0.08)	benign(0.008)	6/14	.	hmmpanther:PTHR23139,hmmpanther:PTHR23139:SF57	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGGTGCTG	.	5	ESCA
ARHGAP6	0	.	GRCh37	X	11156578	11156578	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*405T>A	.	.	ENST00000337414	13/13	22	17	5	30	30	0	ARHGAP6,3_prime_UTR_variant,,ENST00000337414,;ARHGAP6,3_prime_UTR_variant,,ENST00000303025,;ARHGAP6,3_prime_UTR_variant,,ENST00000380736,;ARHGAP6,intron_variant,,ENST00000534860,;ARHGAP6,downstream_gene_variant,,ENST00000380718,;ARHGAP6,downstream_gene_variant,,ENST00000380717,;ARHGAP6,3_prime_UTR_variant,,ENST00000495242,;ARHGAP6,non_coding_transcript_exon_variant,,ENST00000489330,;	T	ENSG00000047648	ENST00000337414	Transcript	3_prime_UTR_variant	4203	.	.	.	.	.	.	.	-1	ARHGAP6	HGNC	676	protein_coding	YES	CCDS14140.1	ENSP00000338967	RHG06_HUMAN	B4DN35_HUMAN	UPI00001AED54	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTAAAAGT	.	2	ESCA
AMOT	0	.	GRCh37	X	112021158	112021158	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*637G>T	.	.	ENST00000371959	11/11	85	68	16	81	81	0	AMOT,3_prime_UTR_variant,,ENST00000371959,;AMOT,3_prime_UTR_variant,,ENST00000304758,;AMOT,downstream_gene_variant,,ENST00000371962,;AMOT,downstream_gene_variant,,ENST00000524145,;AMOT,downstream_gene_variant,,ENST00000371958,;MIR4329,downstream_gene_variant,,ENST00000582643,;	A	ENSG00000126016	ENST00000371959	Transcript	3_prime_UTR_variant	3892	.	.	.	.	.	.	.	-1	AMOT	HGNC	17810	protein_coding	YES	CCDS48154.1	ENSP00000361027	AMOT_HUMAN	E7ERM3_HUMAN	UPI000050ED33	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCCATTTC	.	5	ESCA
TMEM255A	0	.	GRCh37	X	119392534	119392534	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2191C>G	.	.	ENST00000309720	10/10	60	39	20	56	56	0	TMEM255A,3_prime_UTR_variant,,ENST00000371369,;TMEM255A,3_prime_UTR_variant,,ENST00000440464,;TMEM255A,3_prime_UTR_variant,,ENST00000371352,;TMEM255A,3_prime_UTR_variant,,ENST00000309720,;ZBTB33,downstream_gene_variant,,ENST00000326624,;ZBTB33,downstream_gene_variant,,ENST00000557385,;	C	ENSG00000125355	ENST00000309720	Transcript	3_prime_UTR_variant	3365	.	.	.	.	.	.	.	-1	TMEM255A	HGNC	26086	protein_coding	YES	CCDS14597.1	ENSP00000310110	T255A_HUMAN	.	UPI0000246DA1	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTGAAACA	.	5	ESCA
PRRG3	0	.	GRCh37	X	150869317	150869317	+	Missense_Mutation	SNP	C	C	T	rs143276868	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.508C>T	p.Arg170Trp	p.R170W	ENST00000370353	4/4	61	52	9	44	44	0	PRRG3,missense_variant,p.Arg170Trp,ENST00000538575,;PRRG3,missense_variant,p.Arg170Trp,ENST00000370353,;PRRG3,intron_variant,,ENST00000448324,;PRRG3,downstream_gene_variant,,ENST00000448726,;PRRG3,downstream_gene_variant,,ENST00000370354,;	T	ENSG00000130032	ENST00000370353	Transcript	missense_variant	898	508	170	R/W	Cgg/Tgg	rs143276868	.	.	1	PRRG3	HGNC	30798	protein_coding	YES	CCDS14699.1	ENSP00000359378	TMG3_HUMAN	C9J7E6_HUMAN	UPI00004578A5	.	tolerated(0.18)	possibly_damaging(0.732)	4/4	.	hmmpanther:PTHR24251:SF12,hmmpanther:PTHR24251	.	.	.	.	.	.	.	T:0.0003	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTCCGGCTA	byFrequency|byCluster	4	ESCA
SYAP1	0	.	GRCh37	X	16761850	16761850	+	Silent	SNP	T	T	A	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462T>A	p.%3D	p.P154P	ENST00000380155	5/9	44	39	5	50	50	0	SYAP1,synonymous_variant,p.%3D,ENST00000380155,;	A	ENSG00000169895	ENST00000380155	Transcript	synonymous_variant	555	462	154	P	ccT/ccA	.	.	.	1	SYAP1	HGNC	16273	protein_coding	YES	CCDS14177.1	ENSP00000369500	SYAP1_HUMAN	B4DHY7_HUMAN	UPI000006E658	.	.	.	5/9	.	hmmpanther:PTHR16019:SF6,hmmpanther:PTHR16019,Superfamily_domains:SSF140383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GACCCTCCGGC	.	3	ESCA
PHKA2	0	.	GRCh37	X	18936848	18936848	+	Silent	SNP	C	C	T	rs151240321	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2088G>A	p.%3D	p.T696T	ENST00000379942	19/33	38	33	5	38	38	0	PHKA2,synonymous_variant,p.%3D,ENST00000379942,;RN7SL48P,upstream_gene_variant,,ENST00000579283,;	T	ENSG00000044446	ENST00000379942	Transcript	synonymous_variant	2754	2088	696	T	acG/acA	rs151240321	.	.	-1	PHKA2	HGNC	8926	protein_coding	YES	CCDS14190.1	ENSP00000369274	KPB2_HUMAN	.	UPI000012DF4B	.	.	.	19/33	.	hmmpanther:PTHR10749,hmmpanther:PTHR10749:SF5,Pfam_domain:PF00723	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCGCGTGGA	byCluster	4	ESCA
SH3KBP1	0	.	GRCh37	X	19553831	19553831	+	3'UTR	SNP	A	A	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*704T>A	.	.	ENST00000397821	18/18	35	30	5	45	45	0	SH3KBP1,3_prime_UTR_variant,,ENST00000379698,;SH3KBP1,3_prime_UTR_variant,,ENST00000397821,;SH3KBP1,3_prime_UTR_variant,,ENST00000379716,;SH3KBP1,downstream_gene_variant,,ENST00000379726,;SH3KBP1,downstream_gene_variant,,ENST00000541422,;	T	ENSG00000147010	ENST00000397821	Transcript	3_prime_UTR_variant	2993	.	.	.	.	.	.	.	-1	SH3KBP1	HGNC	13867	protein_coding	YES	CCDS14193.1	ENSP00000380921	SH3K1_HUMAN	Q5JPT6_HUMAN,B7Z6E8_HUMAN	UPI000006CC82	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTAATTTTT	.	4	ESCA
CNKSR2	0	.	GRCh37	X	21670710	21670710	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*71C>G	.	.	ENST00000379510	22/22	39	30	9	39	39	0	CNKSR2,3_prime_UTR_variant,,ENST00000379510,;CNKSR2,3_prime_UTR_variant,,ENST00000425654,;KLHL34,downstream_gene_variant,,ENST00000379499,;	G	ENSG00000149970	ENST00000379510	Transcript	3_prime_UTR_variant	3212	.	.	.	.	.	.	.	1	CNKSR2	HGNC	19701	protein_coding	YES	CCDS14198.1	ENSP00000368824	CNKR2_HUMAN	.	UPI0000070D72	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATATCAATGT	.	5	ESCA
MBTPS2	0	.	GRCh37	X	21902186	21902186	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1413G>C	.	.	ENST00000379484	11/11	12	8	4	14	14	0	MBTPS2,3_prime_UTR_variant,,ENST00000379484,;	C	ENSG00000012174	ENST00000379484	Transcript	3_prime_UTR_variant	3072	.	.	.	.	.	.	.	1	MBTPS2	HGNC	15455	protein_coding	YES	CCDS14201.1	ENSP00000368798	MBTP2_HUMAN	.	UPI000012F5A0	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTATTGAGTTG	.	2	ESCA
USP9X	0	.	GRCh37	X	41091836	41091836	+	3'UTR	SNP	T	T	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*59T>G	.	.	ENST00000324545	45/45	48	43	5	71	71	0	USP9X,3_prime_UTR_variant,,ENST00000378308,;USP9X,3_prime_UTR_variant,,ENST00000324545,;RP5-1172N10.4,upstream_gene_variant,,ENST00000602481,;USP9X,downstream_gene_variant,,ENST00000485180,;	G	ENSG00000124486	ENST00000324545	Transcript	3_prime_UTR_variant	8405	.	.	.	.	.	.	.	1	USP9X	HGNC	12632	protein_coding	YES	CCDS43930.1	ENSP00000316357	USP9X_HUMAN	.	UPI00001AF419	.	.	.	45/45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACCTTTTTC	.	4	ESCA
RP2	0	.	GRCh37	X	46713020	46713020	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212A>G	p.Asn71Ser	p.N71S	ENST00000218340	2/5	36	31	4	59	59	0	RP2,missense_variant,p.Asn71Ser,ENST00000218340,;	G	ENSG00000102218	ENST00000218340	Transcript	missense_variant	373	212	71	N/S	aAc/aGc	.	.	.	1	RP2	HGNC	10274	protein_coding	YES	CCDS14270.1	ENSP00000218340	XRP2_HUMAN	.	UPI000000DA35	.	tolerated(0.34)	benign(0.001)	2/5	.	PROSITE_profiles:PS51329,hmmpanther:PTHR15440:SF0,hmmpanther:PTHR15440,Gene3D:2.160.20.70,Pfam_domain:PF07986,SMART_domains:SM00673,PIRSF_domain:PIRSF037947,Superfamily_domains:SSF69340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTAACATCT	.	4	ESCA
HDAC6	0	.	GRCh37	X	48678643	48678643	+	Missense_Mutation	SNP	G	G	A	rs186499554	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2318G>A	p.Arg773His	p.R773H	ENST00000334136	23/29	23	20	3	33	33	0	HDAC6,missense_variant,p.Arg773His,ENST00000376619,;HDAC6,missense_variant,p.Arg773His,ENST00000334136,;HDAC6,missense_variant,p.Arg787His,ENST00000444343,;HDAC6,upstream_gene_variant,,ENST00000430858,;HDAC6,non_coding_transcript_exon_variant,,ENST00000498808,;HDAC6,intron_variant,,ENST00000480525,;HDAC6,downstream_gene_variant,,ENST00000486665,;HDAC6,non_coding_transcript_exon_variant,,ENST00000477528,;HDAC6,non_coding_transcript_exon_variant,,ENST00000486227,;HDAC6,non_coding_transcript_exon_variant,,ENST00000488543,;HDAC6,downstream_gene_variant,,ENST00000495515,;HDAC6,downstream_gene_variant,,ENST00000485102,;HDAC6,downstream_gene_variant,,ENST00000478095,;HDAC6,downstream_gene_variant,,ENST00000488905,;HDAC6,downstream_gene_variant,,ENST00000470942,;HDAC6,downstream_gene_variant,,ENST00000483506,;HDAC6,downstream_gene_variant,,ENST00000465457,;HDAC6,downstream_gene_variant,,ENST00000489053,;	A	ENSG00000094631	ENST00000334136	Transcript	missense_variant	2496	2318	773	R/H	cGc/cAc	rs186499554	.	.	1	HDAC6	HGNC	14064	protein_coding	YES	CCDS14306.1	ENSP00000334061	HDAC6_HUMAN	E9PEH1_HUMAN,E7ER52_HUMAN,E7EP63_HUMAN,C9JEF4_HUMAN,C9J172_HUMAN,A6NDI8_HUMAN	UPI0000073E04	.	tolerated(0.16)	benign(0.243)	23/29	.	hmmpanther:PTHR10625:SF102,hmmpanther:PTHR10625,Pfam_domain:PF00850,Gene3D:3.40.800.20,Superfamily_domains:SSF52768	A:0.0003	A:0	A:0.0014	.	A:0	A:0	A:0	A:0	A:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCCGCATTA	byCluster|by1000G	4	ESCA
HDX	0	.	GRCh37	X	83599383	83599383	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1535C>A	p.Ser512Tyr	p.S512Y	ENST00000297977	6/10	49	40	9	71	71	0	HDX,missense_variant,p.Ser454Tyr,ENST00000506585,;HDX,missense_variant,p.Ser512Tyr,ENST00000373177,;HDX,missense_variant,p.Ser512Tyr,ENST00000297977,;	T	ENSG00000165259	ENST00000297977	Transcript	missense_variant	1647	1535	512	S/Y	tCt/tAt	.	.	.	-1	HDX	HGNC	26411	protein_coding	YES	CCDS35342.1	ENSP00000297977	HDX_HUMAN	E2QRN0_HUMAN	UPI00001A9DA4	.	deleterious(0)	probably_damaging(0.996)	6/10	.	hmmpanther:PTHR11636:SF80,hmmpanther:PTHR11636	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCAGAGAAA	.	5	ESCA
PCDH11X	0	.	GRCh37	X	91874250	91874250	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A8NK-01A-21D-A37C-09	TCGA-L5-A8NK-11A-11D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*311A>G	.	.	ENST00000373094	7/7	43	29	13	54	54	0	PCDH11X,3_prime_UTR_variant,,ENST00000373097,;PCDH11X,3_prime_UTR_variant,,ENST00000373094,;PCDH11X,downstream_gene_variant,,ENST00000406881,;PCDH11X,downstream_gene_variant,,ENST00000373088,;PCDH11X,downstream_gene_variant,,ENST00000361655,;PCDH11X,downstream_gene_variant,,ENST00000298274,;PCDH11X,downstream_gene_variant,,ENST00000504220,;	G	ENSG00000102290	ENST00000373094	Transcript	3_prime_UTR_variant	5200	.	.	.	.	.	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCAATATTA	.	5	ESCA
SORCS1	0	.	GRCh37	10	108439438	108439438	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1615G>C	p.Gly539Arg	p.G539R	ENST00000344440	11/27	62	56	6	42	42	0	SORCS1,missense_variant,p.Gly539Arg,ENST00000263054,;SORCS1,missense_variant,p.Gly74Arg,ENST00000369698,;SORCS1,missense_variant,p.Gly539Arg,ENST00000344440,;SORCS1,upstream_gene_variant,,ENST00000472196,;	G	ENSG00000108018	ENST00000344440	Transcript	missense_variant	1615	1615	539	G/R	Ggg/Cgg	.	.	.	-1	SORCS1	HGNC	16697	protein_coding	YES	CCDS31283.1	ENSP00000345964	SORC1_HUMAN	B3KVZ0_HUMAN	UPI000036671B	.	deleterious(0.03)	probably_damaging(0.998)	11/27	.	hmmpanther:PTHR12106:SF8,hmmpanther:PTHR12106,Gene3D:2.130.10.140,SMART_domains:SM00602,Superfamily_domains:SSF110296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GATCCCTGATG	.	3	ESCA
RAB11FIP2	0	.	GRCh37	10	119765535	119765535	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2974G>A	.	.	ENST00000355624	5/5	30	27	3	65	65	0	RAB11FIP2,3_prime_UTR_variant,,ENST00000355624,;RAB11FIP2,downstream_gene_variant,,ENST00000369199,;RAB11FIP2,intron_variant,,ENST00000476207,;	T	ENSG00000107560	ENST00000355624	Transcript	3_prime_UTR_variant	4953	.	.	.	.	.	.	.	-1	RAB11FIP2	HGNC	29152	protein_coding	YES	CCDS7602.1	ENSP00000347839	RFIP2_HUMAN	.	UPI0000073B4B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATTCAGGGG	.	2	ESCA
NANOS1	0	.	GRCh37	10	120792173	120792173	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1981G>A	.	.	ENST00000425699	1/1	130	119	11	121	121	0	NANOS1,3_prime_UTR_variant,,ENST00000425699,;EIF3A,downstream_gene_variant,,ENST00000541549,;NANOS1,downstream_gene_variant,,ENST00000340087,;EIF3A,downstream_gene_variant,,ENST00000369144,;	A	ENSG00000188613	ENST00000425699	Transcript	3_prime_UTR_variant	2946	.	.	.	.	.	.	.	1	NANOS1	HGNC	23044	protein_coding	YES	CCDS7607.1	ENSP00000393275	NANO1_HUMAN	Q5T9H5_HUMAN	UPI00001D68E9	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTTTGTATTT	.	3	ESCA
TACC2	0	.	GRCh37	10	123842878	123842878	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.863G>C	p.Arg288Thr	p.R288T	ENST00000369005	4/23	77	71	6	136	135	1	TACC2,missense_variant,p.Arg288Thr,ENST00000453444,;TACC2,missense_variant,p.Arg288Thr,ENST00000369005,;TACC2,missense_variant,p.Arg288Thr,ENST00000334433,;TACC2,missense_variant,p.Arg288Thr,ENST00000515603,;TACC2,missense_variant,p.Arg288Thr,ENST00000515273,;TACC2,intron_variant,,ENST00000358010,;TACC2,intron_variant,,ENST00000513429,;TACC2,downstream_gene_variant,,ENST00000491540,;TACC2,downstream_gene_variant,,ENST00000498721,;	C	ENSG00000138162	ENST00000369005	Transcript	missense_variant	1203	863	288	R/T	aGa/aCa	.	.	.	1	TACC2	HGNC	11523	protein_coding	YES	CCDS7626.1	ENSP00000358001	TACC2_HUMAN	.	UPI0000246F6B	.	.	benign(0.1)	4/23	.	hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGACAGAGAAA	.	2	ESCA
DHX32	0	.	GRCh37	10	127529527	127529527	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1582G>C	p.Glu528Gln	p.E528Q	ENST00000284690	8/11	73	66	7	106	106	0	DHX32,missense_variant,p.Glu447Gln,ENST00000284688,;DHX32,missense_variant,p.Glu152Gln,ENST00000368721,;DHX32,missense_variant,p.Glu528Gln,ENST00000284690,;BCCIP,intron_variant,,ENST00000299130,;BCCIP,intron_variant,,ENST00000429863,;BCCIP,intron_variant,,ENST00000368759,;BCCIP,downstream_gene_variant,,ENST00000278100,;AL360176.1,upstream_gene_variant,,ENST00000401153,;	G	ENSG00000089876	ENST00000284690	Transcript	missense_variant	2073	1582	528	E/Q	Gag/Cag	.	.	.	-1	DHX32	HGNC	16717	protein_coding	YES	CCDS7652.1	ENSP00000284690	DHX32_HUMAN	.	UPI00000467F4	.	tolerated(0.12)	benign(0.039)	8/11	.	hmmpanther:PTHR18934:SF88,hmmpanther:PTHR18934,Pfam_domain:PF04408,SMART_domains:SM00847,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCCTCTTCAG	.	3	ESCA
ADAM12	0	.	GRCh37	10	127726813	127726813	+	Silent	SNP	C	C	T	rs375026997	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2355G>A	p.%3D	p.P785P	ENST00000368679	20/23	52	42	10	36	36	0	ADAM12,synonymous_variant,p.%3D,ENST00000368679,;ADAM12,downstream_gene_variant,,ENST00000368676,;	T	ENSG00000148848	ENST00000368679	Transcript	synonymous_variant	2665	2355	785	P	ccG/ccA	rs375026997	.	.	-1	ADAM12	HGNC	190	protein_coding	YES	CCDS7653.1	ENSP00000357668	ADA12_HUMAN	.	UPI000036672C	.	.	.	20/23	.	hmmpanther:PTHR11905:SF112,hmmpanther:PTHR11905	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTCGGTGG	byFrequency|byCluster	5	ESCA
SEPHS1	0	.	GRCh37	10	13380806	13380806	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196A>G	p.Ile66Val	p.I66V	ENST00000327347	3/9	44	38	6	77	77	0	SEPHS1,missense_variant,p.Ile66Val,ENST00000545675,;SEPHS1,missense_variant,p.Ile66Val,ENST00000378614,;SEPHS1,missense_variant,p.Ile66Val,ENST00000413411,;SEPHS1,missense_variant,p.Ile66Val,ENST00000327347,;SEPHS1,splice_region_variant,,ENST00000425947,;SEPHS1,splice_region_variant,,ENST00000537130,;SEPHS1,splice_region_variant,,ENST00000494329,;	C	ENSG00000086475	ENST00000327347	Transcript	missense_variant	572	196	66	I/V	Att/Gtt	.	.	.	-1	SEPHS1	HGNC	19685	protein_coding	YES	CCDS7098.1	ENSP00000367893	SPS1_HUMAN	Q5T5U7_HUMAN,Q5T5U6_HUMAN	UPI0000135E82	.	tolerated(0.19)	benign(0.025)	3/9	.	Superfamily_domains:SSF55326,PIRSF_domain:PIRSF036407,TIGRFAM_domain:TIGR00476,Gene3D:3.30.1330.10,hmmpanther:PTHR10256,hmmpanther:PTHR10256:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAATGCCTG	.	2	ESCA
SYCE1	0	.	GRCh37	10	135371408	135371408	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334C>G	p.Leu112Val	p.L112V	ENST00000343131	6/13	58	53	5	48	48	0	SYCE1,missense_variant,p.Leu112Val,ENST00000303903,;SYCE1,missense_variant,p.Leu76Val,ENST00000432597,;SYCE1,missense_variant,p.Leu112Val,ENST00000343131,;SYCE1,missense_variant,p.Leu76Val,ENST00000368517,;SPRN,intron_variant,,ENST00000541506,;CYP2E1,non_coding_transcript_exon_variant,,ENST00000368520,;SYCE1,non_coding_transcript_exon_variant,,ENST00000479535,;	C	ENSG00000171772	ENST00000343131	Transcript	missense_variant	439	334	112	L/V	Ctc/Gtc	.	.	.	-1	SYCE1	HGNC	28852	protein_coding	YES	CCDS44501.1	ENSP00000341282	SYCE1_HUMAN	.	UPI000013F901	.	deleterious(0.02)	possibly_damaging(0.548)	6/13	.	Pfam_domain:PF15233,hmmpanther:PTHR21731,hmmpanther:PTHR21731:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCGGAGGATCC	.	3	ESCA
FAM107B	0	.	GRCh37	10	14563922	14563922	+	Missense_Mutation	SNP	C	C	G	rs756406965	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.750G>C	p.Lys250Asn	p.K250N	ENST00000181796	4/5	111	101	10	121	121	0	FAM107B,missense_variant,p.Lys75Asn,ENST00000482277,;FAM107B,missense_variant,p.Lys75Asn,ENST00000488576,;FAM107B,missense_variant,p.Lys75Asn,ENST00000378465,;FAM107B,missense_variant,p.Lys75Asn,ENST00000468747,;FAM107B,missense_variant,p.Lys75Asn,ENST00000489100,;FAM107B,missense_variant,p.Lys75Asn,ENST00000378470,;FAM107B,missense_variant,p.Lys75Asn,ENST00000478076,;FAM107B,missense_variant,p.Lys75Asn,ENST00000442012,;FAM107B,missense_variant,p.Lys75Asn,ENST00000479731,;FAM107B,missense_variant,p.Lys75Asn,ENST00000468492,;FAM107B,missense_variant,p.Lys75Asn,ENST00000496330,;FAM107B,missense_variant,p.Lys250Asn,ENST00000181796,;FAM107B,missense_variant,p.Lys75Asn,ENST00000378458,;FAM107B,missense_variant,p.Lys75Asn,ENST00000494865,;FAM107B,missense_variant,p.Lys75Asn,ENST00000378462,;FAM107B,missense_variant,p.Lys75Asn,ENST00000378467,;FAM107B,missense_variant,p.Lys75Asn,ENST00000452706,;FAM107B,missense_variant,p.Lys75Asn,ENST00000475786,;FAM107B,downstream_gene_variant,,ENST00000472095,;FAM107B,3_prime_UTR_variant,,ENST00000481209,;FAM107B,3_prime_UTR_variant,,ENST00000487335,;FAM107B,non_coding_transcript_exon_variant,,ENST00000474143,;FAM107B,non_coding_transcript_exon_variant,,ENST00000475858,;FAM107B,non_coding_transcript_exon_variant,,ENST00000492700,;	G	ENSG00000065809	ENST00000181796	Transcript	missense_variant	984	750	250	K/N	aaG/aaC	rs756406965	.	.	-1	FAM107B	HGNC	23726	protein_coding	YES	CCDS7102.1	ENSP00000181796	F107B_HUMAN	C9JYP1_HUMAN,C9JW51_HUMAN,C9JQ40_HUMAN,C9JP05_HUMAN,C9J6Y8_HUMAN,C9J6N5_HUMAN,C9J3Q3_HUMAN	UPI00001C0E1E	.	deleterious(0.03)	probably_damaging(0.973)	4/5	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16768:SF1,hmmpanther:PTHR16768,Pfam_domain:PF06625	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCTTCTTCTG	.	3	ESCA
STAM	0	.	GRCh37	10	17757553	17757553	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*774C>T	.	.	ENST00000377524	14/14	18	15	3	40	40	0	STAM,3_prime_UTR_variant,,ENST00000377524,;STAM,downstream_gene_variant,,ENST00000540523,;	T	ENSG00000136738	ENST00000377524	Transcript	3_prime_UTR_variant	2612	.	.	.	.	.	.	.	1	STAM	HGNC	11357	protein_coding	YES	CCDS7122.1	ENSP00000366746	STAM1_HUMAN	C9J1E5_HUMAN,B4DZT2_HUMAN,A6NMU3_HUMAN	UPI000006E278	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTCAGAGT	.	2	ESCA
KIF5B	0	.	GRCh37	10	32327107	32327107	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482G>A	p.Arg161Gln	p.R161Q	ENST00000302418	6/26	55	45	9	68	68	0	KIF5B,missense_variant,p.Arg161Gln,ENST00000302418,;	T	ENSG00000170759	ENST00000302418	Transcript	missense_variant	940	482	161	R/Q	cGa/cAa	.	.	.	-1	KIF5B	HGNC	6324	protein_coding	YES	CCDS7171.1	ENSP00000307078	KINH_HUMAN	A8K048_HUMAN	UPI000012DE68	.	deleterious(0)	benign(0.236)	6/26	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTCGGTTT	.	5	ESCA
CDH23	0	.	GRCh37	10	73492057	73492057	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4044C>T	p.%3D	p.L1348L	ENST00000224721	31/69	39	34	4	91	91	0	CDH23,synonymous_variant,p.%3D,ENST00000224721,;C10orf105,intron_variant,,ENST00000398786,;CDH23,non_coding_transcript_exon_variant,,ENST00000398792,;	T	ENSG00000107736	ENST00000224721	Transcript	synonymous_variant	4049	4044	1348	L	ctC/ctT	.	.	.	1	CDH23	HGNC	13733	protein_coding	.	.	ENSP00000224721	.	.	UPI0002B831D5	.	.	.	31/69	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF277,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACCTCAACCA	.	4	ESCA
FAM149B1	0	.	GRCh37	10	74953335	74953335	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526G>A	p.Glu176Lys	p.E176K	ENST00000242505	5/14	60	55	5	81	81	0	FAM149B1,missense_variant,p.Glu117Lys,ENST00000372955,;FAM149B1,missense_variant,p.Glu176Lys,ENST00000242505,;Y_RNA,upstream_gene_variant,,ENST00000362331,;DNAJC9,intron_variant,,ENST00000469143,;	A	ENSG00000138286	ENST00000242505	Transcript	missense_variant	700	526	176	E/K	Gaa/Aaa	.	.	.	1	FAM149B1	HGNC	29162	protein_coding	YES	CCDS44435.1	ENSP00000242505	F149B_HUMAN	.	UPI00001617A8	.	tolerated(0.05)	benign(0.286)	5/14	.	hmmpanther:PTHR31997:SF0,hmmpanther:PTHR31997,Pfam_domain:PF12516	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCAAGAAAGA	.	3	ESCA
PLAU	0	.	GRCh37	10	75672811	75672811	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.323G>A	p.Arg108Lys	p.R108K	ENST00000372764	5/11	59	52	7	81	81	0	PLAU,missense_variant,p.Arg91Lys,ENST00000446342,;PLAU,missense_variant,p.Arg72Lys,ENST00000372762,;PLAU,missense_variant,p.Arg108Lys,ENST00000372764,;C10orf55,5_prime_UTR_variant,,ENST00000412307,;C10orf55,5_prime_UTR_variant,,ENST00000409178,;PLAU,downstream_gene_variant,,ENST00000481390,;PLAU,non_coding_transcript_exon_variant,,ENST00000494287,;PLAU,downstream_gene_variant,,ENST00000496926,;	A	ENSG00000122861	ENST00000372764	Transcript	missense_variant	416	323	108	R/K	aGa/aAa	.	.	.	1	PLAU	HGNC	9052	protein_coding	YES	CCDS7339.1	ENSP00000361850	UROK_HUMAN	S4R3G7_HUMAN,Q9UEJ5_HUMAN,Q96SE8_HUMAN	UPI000013CB02	.	tolerated(0.28)	possibly_damaging(0.827)	5/11	.	PROSITE_profiles:PS50070,hmmpanther:PTHR24264,hmmpanther:PTHR24264:SF9,Gene3D:2.40.20.10,Pfam_domain:PF00051,SMART_domains:SM00130,Superfamily_domains:SSF57440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACAGATCTG	.	4	ESCA
ZNF503	0	.	GRCh37	10	77158212	77158212	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*295G>C	.	.	ENST00000372524	2/2	57	48	9	94	94	0	ZNF503,3_prime_UTR_variant,,ENST00000372524,;ZNF503,downstream_gene_variant,,ENST00000535216,;RP11-399K21.11,intron_variant,,ENST00000418818,;ZNF503-AS2,upstream_gene_variant,,ENST00000425916,;ZNF503-AS2,upstream_gene_variant,,ENST00000486015,;ZNF503-AS2,upstream_gene_variant,,ENST00000466942,;ZNF503-AS2,upstream_gene_variant,,ENST00000438638,;	G	ENSG00000165655	ENST00000372524	Transcript	3_prime_UTR_variant	2723	.	.	.	.	.	.	.	-1	ZNF503	HGNC	23589	protein_coding	YES	CCDS7350.1	ENSP00000361602	ZN503_HUMAN	B3KXM8_HUMAN	UPI000004A951	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTCAGATG	.	5	ESCA
MYOF	0	.	GRCh37	10	95085666	95085666	+	Missense_Mutation	SNP	G	G	A	rs777800718	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5188C>T	p.His1730Tyr	p.H1730Y	ENST00000359263	46/54	51	44	6	66	66	0	MYOF,missense_variant,p.His1749Tyr,ENST00000371502,;MYOF,missense_variant,p.His1717Tyr,ENST00000358334,;MYOF,missense_variant,p.His1730Tyr,ENST00000371501,;MYOF,missense_variant,p.His1730Tyr,ENST00000359263,;MYOF,non_coding_transcript_exon_variant,,ENST00000485212,;MYOF,missense_variant,p.His1124Tyr,ENST00000463743,;MYOF,upstream_gene_variant,,ENST00000474161,;	A	ENSG00000138119	ENST00000359263	Transcript	missense_variant	5188	5188	1730	H/Y	Cac/Tac	rs777800718	.	.	-1	MYOF	HGNC	3656	protein_coding	YES	CCDS41551.1	ENSP00000352208	MYOF_HUMAN	.	UPI000012FBA1	.	tolerated(0.22)	benign(0.004)	46/54	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GATGTGAAGAG	.	3	ESCA
RBP4	0	.	GRCh37	10	95353631	95353631	+	Missense_Mutation	SNP	G	G	A	rs139534453	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.517C>T	p.Arg173Trp	p.R173W	ENST00000371467	5/6	43	33	10	61	61	0	RBP4,missense_variant,p.Arg173Trp,ENST00000371464,;RBP4,missense_variant,p.Arg171Trp,ENST00000371469,;RBP4,missense_variant,p.Arg173Trp,ENST00000371467,;FFAR4,intron_variant,,ENST00000604414,;FFAR4,downstream_gene_variant,,ENST00000371481,;FFAR4,downstream_gene_variant,,ENST00000371483,;	A	ENSG00000138207	ENST00000371467	Transcript	missense_variant	837	517	173	R/W	Cgg/Tgg	rs139534453	.	.	-1	RBP4	HGNC	9922	protein_coding	YES	CCDS31249.1	ENSP00000360522	RET4_HUMAN	.	UPI0000044958	.	deleterious(0)	probably_damaging(0.981)	5/6	.	hmmpanther:PTHR11873,hmmpanther:PTHR11873:SF2,Gene3D:2.40.128.20,Pfam_domain:PF00061,PIRSF_domain:PIRSF036893,PIRSF_domain:PIRSF500204,Superfamily_domains:SSF50814	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGCTGCC	byFrequency|byCluster	5	ESCA
CWF19L2	0	.	GRCh37	11	107207409	107207409	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2233G>C	p.Glu745Gln	p.E745Q	ENST00000282251	15/18	63	57	6	55	55	0	CWF19L2,missense_variant,p.Glu745Gln,ENST00000282251,;CWF19L2,3_prime_UTR_variant,,ENST00000431778,;CWF19L2,3_prime_UTR_variant,,ENST00000532251,;	G	ENSG00000152404	ENST00000282251	Transcript	missense_variant	2261	2233	745	E/Q	Gaa/Caa	.	.	.	-1	CWF19L2	HGNC	26508	protein_coding	YES	CCDS8336.2	ENSP00000282251	C19L2_HUMAN	Q6PIV4_HUMAN	UPI00005A81B4	.	deleterious(0.03)	benign(0.314)	15/18	.	hmmpanther:PTHR12072:SF5,hmmpanther:PTHR12072,Gene3D:3.30.428.10,Pfam_domain:PF04677,Superfamily_domains:SSF54197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATCTTCAAACA	.	3	ESCA
MUC2	0	.	GRCh37	11	1079734	1079734	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951G>C	p.%3D	p.V317V	ENST00000441003	7/49	111	103	8	107	107	0	MUC2,synonymous_variant,p.%3D,ENST00000441003,;MUC2,synonymous_variant,p.%3D,ENST00000359061,;	C	ENSG00000198788	ENST00000441003	Transcript	synonymous_variant	978	951	317	V	gtG/gtC	.	.	.	1	MUC2	HGNC	7512	protein_coding	YES	.	ENSP00000415183	.	Q9UMI9_HUMAN,Q9HBC6_HUMAN,H0Y2U6_HUMAN,E7EUV1_HUMAN	UPI00006C10F2	.	.	.	7/49	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF261,Pfam_domain:PF01826,Gene3D:2.10.25.10,Superfamily_domains:SSF57567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGGTGAGCAG	.	2	ESCA
ATM	0	.	GRCh37	11	108216597	108216597	+	Missense_Mutation	SNP	G	G	A	rs587782202	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8546G>A	p.Arg2849Gln	p.R2849Q	ENST00000278616	58/63	83	76	7	86	86	0	ATM,missense_variant,p.Arg2849Gln,ENST00000278616,;ATM,missense_variant,p.Arg2849Gln,ENST00000452508,;C11orf65,intron_variant,,ENST00000524755,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000526725,;ATM,upstream_gene_variant,,ENST00000525178,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,;	A	ENSG00000149311	ENST00000278616	Transcript	missense_variant	8931	8546	2849	R/Q	cGa/cAa	rs587782202,CM990219	.	.	1	ATM	HGNC	795	protein_coding	YES	CCDS31669.1	ENSP00000278616	ATM_HUMAN	M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN	UPI0000DBEF44	.	deleterious(0)	probably_damaging(0.998)	58/63	.	Superfamily_domains:SSF56112,SMART_domains:SM00146,Gene3D:1.10.1070.11,Pfam_domain:PF00454,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66,PROSITE_profiles:PS50290	.	.	.	.	.	.	.	.	.	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAAGCGATTGG	byFrequency|byCluster	3	ESCA
COPB1	0	.	GRCh37	11	14487906	14487906	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2212G>C	p.Asp738His	p.D738H	ENST00000249923	17/22	68	59	9	53	53	0	COPB1,missense_variant,p.Asp738His,ENST00000439561,;COPB1,missense_variant,p.Asp738His,ENST00000249923,;	G	ENSG00000129083	ENST00000249923	Transcript	missense_variant	2513	2212	738	D/H	Gat/Cat	.	.	.	-1	COPB1	HGNC	2231	protein_coding	YES	CCDS7815.1	ENSP00000249923	COPB_HUMAN	E9PP63_HUMAN,E9PKQ1_HUMAN	UPI000000103D	.	deleterious(0)	probably_damaging(1)	17/22	.	hmmpanther:PTHR10635,Pfam_domain:PF07718,PIRSF_domain:PIRSF005727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATATCATATT	.	4	ESCA
SERGEF	0	.	GRCh37	11	18014501	18014501	+	Nonsense_Mutation	SNP	G	G	C	rs552461036	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662C>G	p.Ser221Ter	p.S221*	ENST00000265965	7/11	68	63	5	89	89	0	SERGEF,stop_gained,p.Ser85Ter,ENST00000529151,;SERGEF,stop_gained,p.Ser107Ter,ENST00000530613,;SERGEF,stop_gained,p.Ser221Ter,ENST00000528200,;SERGEF,stop_gained,p.Ser107Ter,ENST00000532389,;SERGEF,stop_gained,p.Ser107Ter,ENST00000532265,;SERGEF,stop_gained,p.Ser107Ter,ENST00000529728,;SERGEF,stop_gained,p.Ser221Ter,ENST00000265965,;SERGEF,stop_gained,p.Ser91Ter,ENST00000525920,;SERGEF,upstream_gene_variant,,ENST00000533241,;SERGEF,intron_variant,,ENST00000529440,;SERGEF,stop_gained,p.Ser221Ter,ENST00000525422,;SERGEF,stop_gained,p.Ser37Ter,ENST00000532546,;SERGEF,3_prime_UTR_variant,,ENST00000527494,;SERGEF,3_prime_UTR_variant,,ENST00000530925,;SERGEF,downstream_gene_variant,,ENST00000533328,;	C	ENSG00000129158	ENST00000265965	Transcript	stop_gained	814	662	221	S/*	tCa/tGa	rs552461036	.	.	-1	SERGEF	HGNC	17499	protein_coding	YES	CCDS7828.1	ENSP00000265965	SRGEF_HUMAN	E9PS70_HUMAN,E9PR50_HUMAN	UPI000007326C	.	.	.	7/11	.	Superfamily_domains:SSF50985,Gene3D:2.130.10.30,Pfam_domain:PF13540,hmmpanther:PTHR22870,hmmpanther:PTHR22870:SF7,PROSITE_profiles:PS50012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTCTGAGCCA	.	3	ESCA
KCNA4	0	.	GRCh37	11	30034880	30034880	+	5'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-655C>G	.	.	ENST00000328224	2/2	57	50	6	65	65	0	KCNA4,5_prime_UTR_variant,,ENST00000328224,;KCNA4,non_coding_transcript_exon_variant,,ENST00000526518,;	C	ENSG00000182255	ENST00000328224	Transcript	5_prime_UTR_variant	580	.	.	.	.	.	.	.	-1	KCNA4	HGNC	6222	protein_coding	YES	CCDS41629.1	ENSP00000328511	KCNA4_HUMAN	.	UPI00001649FF	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAAAGACCCT	.	4	ESCA
B4GALNT4	0	.	GRCh37	11	373228	373228	+	Silent	SNP	G	G	A	rs781751398	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.573G>A	p.%3D	p.S191S	ENST00000329962	6/20	49	45	4	50	50	0	B4GALNT4,synonymous_variant,p.%3D,ENST00000329962,;B4GALNT4,downstream_gene_variant,,ENST00000530717,;B4GALNT4,upstream_gene_variant,,ENST00000524443,;	A	ENSG00000182272	ENST00000329962	Transcript	synonymous_variant	573	573	191	S	tcG/tcA	rs781751398	.	.	1	B4GALNT4	HGNC	26315	protein_coding	YES	CCDS7694.1	ENSP00000328277	B4GN4_HUMAN	.	UPI00002326B6	.	.	.	6/20	.	hmmpanther:PTHR12369:SF9,hmmpanther:PTHR12369,Pfam_domain:PF07691,Gene3D:1accA01,SMART_domains:SM00758	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AACTCGGAGTT	byFrequency	2	ESCA
LRRC4C	0	.	GRCh37	11	40137176	40137176	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.667G>C	p.Glu223Gln	p.E223Q	ENST00000278198	2/2	24	18	5	31	31	0	LRRC4C,missense_variant,p.Glu223Gln,ENST00000528697,;LRRC4C,missense_variant,p.Glu223Gln,ENST00000278198,;LRRC4C,missense_variant,p.Glu223Gln,ENST00000530763,;LRRC4C,missense_variant,p.Glu223Gln,ENST00000527150,;LRRC4C,downstream_gene_variant,,ENST00000533474,;	G	ENSG00000148948	ENST00000278198	Transcript	missense_variant	2631	667	223	E/Q	Gag/Cag	COSM368514	.	.	-1	LRRC4C	HGNC	29317	protein_coding	YES	CCDS31464.1	ENSP00000278198	LRC4C_HUMAN	E9PLP4_HUMAN	UPI000000D9A7	.	deleterious(0.04)	possibly_damaging(0.859)	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24369:SF8,hmmpanther:PTHR24369,Gene3D:3.80.10.10,Pfam_domain:PF00560,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCATCTA	.	5	ESCA
MMP26	0	.	GRCh37	11	5009524	5009524	+	Missense_Mutation	SNP	G	G	C	rs773132017	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.83G>C	p.Gly28Ala	p.G28A	ENST00000380390	2/7	50	45	5	60	60	0	MMP26,missense_variant,p.Gly28Ala,ENST00000300762,;MMP26,missense_variant,p.Gly28Ala,ENST00000380390,;MMP26,non_coding_transcript_exon_variant,,ENST00000477339,;	C	ENSG00000167346	ENST00000380390	Transcript	missense_variant	299	83	28	G/A	gGa/gCa	rs773132017	.	.	1	MMP26	HGNC	14249	protein_coding	YES	CCDS7752.1	ENSP00000369753	MMP26_HUMAN	.	UPI0000047AFC	.	tolerated(0.29)	benign(0.336)	2/7	.	hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF76,Gene3D:3.40.390.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAAAGGATGGG	byFrequency	3	ESCA
OR5T1	0	.	GRCh37	11	56044027	56044027	+	Missense_Mutation	SNP	C	C	T	rs374592813	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.913C>T	p.Arg305Trp	p.R305W	ENST00000313033	1/1	58	48	10	52	52	0	OR5T1,missense_variant,p.Arg305Trp,ENST00000313033,;	T	ENSG00000181698	ENST00000313033	Transcript	missense_variant	999	913	305	R/W	Cgg/Tgg	rs374592813	.	.	1	OR5T1	HGNC	14821	protein_coding	YES	CCDS31525.1	ENSP00000323612	OR5T1_HUMAN	.	UPI000004B22E	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24248:SF33,hmmpanther:PTHR24248,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237	T:0.0008	T:0.0015	T:0	.	T:0	T:0	T:0.002	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTGCGGAAC	byFrequency|byCluster|by1000G	2	ESCA
OR56A3	0	.	GRCh37	11	5969263	5969263	+	Silent	SNP	G	G	C	rs756511868	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.687G>C	p.%3D	p.V229V	ENST00000329564	1/1	42	35	7	38	38	0	OR56A3,synonymous_variant,p.%3D,ENST00000329564,;AC025016.1,downstream_gene_variant,,ENST00000528915,;	C	ENSG00000184478	ENST00000329564	Transcript	synonymous_variant	694	687	229	V	gtG/gtC	rs756511868,COSM543611	.	.	1	OR56A3	HGNC	14786	protein_coding	YES	CCDS41614.1	ENSP00000331572	O56A3_HUMAN	.	UPI0000041BF7	.	.	.	1/1	.	Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26450:SF40,hmmpanther:PTHR26450,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGTGCTGAG	byFrequency	5	ESCA
PTGDR2	0	.	GRCh37	11	60621068	60621068	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128C>T	p.Ser43Leu	p.S43L	ENST00000332539	2/2	88	82	6	63	63	0	PTGDR2,missense_variant,p.Ser43Leu,ENST00000332539,;CCDC86,downstream_gene_variant,,ENST00000227520,;CCDC86,downstream_gene_variant,,ENST00000545580,;RP11-804A23.4,upstream_gene_variant,,ENST00000538705,;CCDC86,downstream_gene_variant,,ENST00000535217,;	A	ENSG00000183134	ENST00000332539	Transcript	missense_variant	240	128	43	S/L	tCg/tTg	.	.	.	-1	PTGDR2	HGNC	4502	protein_coding	YES	CCDS7994.1	ENSP00000332812	PD2R2_HUMAN	.	UPI00001B011A	.	tolerated(0.05)	possibly_damaging(0.478)	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF8,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCGAGGCC	.	2	ESCA
SPDYC	0	.	GRCh37	11	64940167	64940167	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.529G>C	p.Glu177Gln	p.E177Q	ENST00000377185	6/7	81	69	11	120	120	0	SPDYC,missense_variant,p.Glu177Gln,ENST00000377185,;AP003068.18,downstream_gene_variant,,ENST00000534819,;AP003068.23,downstream_gene_variant,,ENST00000528551,;AP003068.18,downstream_gene_variant,,ENST00000526979,;PGAM1P8,downstream_gene_variant,,ENST00000505544,;	C	ENSG00000204710	ENST00000377185	Transcript	missense_variant	611	529	177	E/Q	Gag/Cag	.	.	.	1	SPDYC	HGNC	32681	protein_coding	YES	CCDS31606.1	ENSP00000366390	SPDYC_HUMAN	.	UPI00004A072F	.	tolerated(0.13)	possibly_damaging(0.824)	6/7	.	hmmpanther:PTHR31545:SF2,hmmpanther:PTHR31545,Pfam_domain:PF11357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGGAGCCA	.	5	ESCA
BRMS1	0	.	GRCh37	11	66108786	66108786	+	Silent	SNP	C	C	G	rs769414940	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.249G>C	p.%3D	p.L83L	ENST00000425825	4/10	39	33	5	59	59	0	BRMS1,synonymous_variant,p.%3D,ENST00000359957,;BRMS1,synonymous_variant,p.%3D,ENST00000524699,;BRMS1,synonymous_variant,p.%3D,ENST00000530756,;BRMS1,synonymous_variant,p.%3D,ENST00000425825,;RIN1,upstream_gene_variant,,ENST00000311320,;RIN1,upstream_gene_variant,,ENST00000424433,;RIN1,upstream_gene_variant,,ENST00000530056,;B3GNT1,downstream_gene_variant,,ENST00000311181,;RP11-867G23.12,downstream_gene_variant,,ENST00000526655,;BRMS1,synonymous_variant,p.%3D,ENST00000527375,;BRMS1,non_coding_transcript_exon_variant,,ENST00000534617,;BRMS1,non_coding_transcript_exon_variant,,ENST00000530238,;BRMS1,non_coding_transcript_exon_variant,,ENST00000525127,;BRMS1,downstream_gene_variant,,ENST00000529544,;RIN1,upstream_gene_variant,,ENST00000530745,;	G	ENSG00000174744	ENST00000425825	Transcript	synonymous_variant	404	249	83	L	ctG/ctC	rs769414940	.	.	-1	BRMS1	HGNC	17262	protein_coding	YES	CCDS44654.1	ENSP00000396052	.	G5E9I4_HUMAN,E9PJF5_HUMAN	UPI0000545267	.	.	.	4/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21964,hmmpanther:PTHR21964:SF9,Pfam_domain:PF08598	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TGACTCAGTCG	byFrequency	4	ESCA
RBM14-RBM4	0	.	GRCh37	11	66384308	66384308	+	Silent	SNP	C	C	T	rs754533623	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117C>T	p.%3D	p.F39F	ENST00000412278	1/3	70	59	11	94	93	1	RBM14-RBM4,synonymous_variant,p.%3D,ENST00000412278,;RBM14,synonymous_variant,p.%3D,ENST00000310137,;RBM4,synonymous_variant,p.%3D,ENST00000514361,;RBM14-RBM4,synonymous_variant,p.%3D,ENST00000500635,;RBM14,synonymous_variant,p.%3D,ENST00000443702,;RBM14,synonymous_variant,p.%3D,ENST00000393979,;RBM14,synonymous_variant,p.%3D,ENST00000409738,;RBM14,synonymous_variant,p.%3D,ENST00000409372,;RBM4,5_prime_UTR_variant,,ENST00000503028,;RNU4-39P,upstream_gene_variant,,ENST00000362455,;RBM14-RBM4,non_coding_transcript_exon_variant,,ENST00000511114,;RBM14,non_coding_transcript_exon_variant,,ENST00000512283,;RBM14,upstream_gene_variant,,ENST00000496694,;RBM14,upstream_gene_variant,,ENST00000461478,;RBM14,upstream_gene_variant,,ENST00000460762,;RBM14-RBM4,synonymous_variant,p.%3D,ENST00000421355,;	T	ENSG00000248643	ENST00000412278	Transcript	synonymous_variant	212	117	39	F	ttC/ttT	rs754533623	.	.	1	RBM14-RBM4	HGNC	38840	protein_coding	YES	CCDS55774.1	ENSP00000388552	.	.	UPI0001641710	.	.	.	1/3	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF242,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCGTGCA	.	5	ESCA
MYEOV	0	.	GRCh37	11	69063413	69063413	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496G>A	p.Gly166Arg	p.G166R	ENST00000308946	3/3	201	41	159	64	64	0	MYEOV,missense_variant,p.Gly166Arg,ENST00000308946,;MYEOV,missense_variant,p.Gly108Arg,ENST00000535407,;MYEOV,missense_variant,p.Gly166Arg,ENST00000441339,;MYEOV,non_coding_transcript_exon_variant,,ENST00000535597,;MYEOV,intron_variant,,ENST00000544008,;MYEOV,downstream_gene_variant,,ENST00000539691,;MYEOV,downstream_gene_variant,,ENST00000540760,;MYEOV,non_coding_transcript_exon_variant,,ENST00000535653,;MYEOV,upstream_gene_variant,,ENST00000544781,;	A	ENSG00000172927	ENST00000308946	Transcript	missense_variant	946	496	166	G/R	Gga/Aga	.	.	.	1	MYEOV	HGNC	7563	protein_coding	YES	CCDS8190.1	ENSP00000308330	MYEOV_HUMAN	F5H0B3_HUMAN	UPI0000039DE8	.	deleterious_low_confidence(0)	probably_damaging(0.991)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGGGAGAA	.	5	ESCA
FCHSD2	0	.	GRCh37	11	72700022	72700022	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.508G>A	p.Asp170Asn	p.D170N	ENST00000409418	6/20	73	65	7	57	57	0	FCHSD2,missense_variant,p.Asp170Asn,ENST00000409314,;FCHSD2,missense_variant,p.Asp10Asn,ENST00000458644,;FCHSD2,missense_variant,p.Asp114Asn,ENST00000409853,;FCHSD2,missense_variant,p.Asp13Asn,ENST00000543644,;FCHSD2,missense_variant,p.Asp170Asn,ENST00000409418,;FCHSD2,missense_variant,p.Asp114Asn,ENST00000311172,;FCHSD2,downstream_gene_variant,,ENST00000422375,;	T	ENSG00000137478	ENST00000409418	Transcript	missense_variant	892	508	170	D/N	Gac/Aac	.	.	.	-1	FCHSD2	HGNC	29114	protein_coding	YES	CCDS8218.2	ENSP00000386722	FCSD2_HUMAN	C9JM66_HUMAN	UPI0000251F08	.	deleterious(0)	possibly_damaging(0.907)	6/20	.	Superfamily_domains:SSF103657,hmmpanther:PTHR15735,hmmpanther:PTHR15735:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATGTCAGCTT	.	4	ESCA
ARHGEF17	0	.	GRCh37	11	73020556	73020556	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.873G>A	p.%3D	p.G291G	ENST00000263674	1/21	21	16	5	29	29	0	ARHGEF17,synonymous_variant,p.%3D,ENST00000263674,;ARHGEF17,upstream_gene_variant,,ENST00000544519,;RP11-800A3.7,upstream_gene_variant,,ENST00000546324,;	A	ENSG00000110237	ENST00000263674	Transcript	synonymous_variant	1223	873	291	G	ggG/ggA	.	.	.	1	ARHGEF17	HGNC	21726	protein_coding	YES	CCDS8221.1	ENSP00000263674	ARHGH_HUMAN	.	UPI000004980B	.	.	.	1/21	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGAGGGAGGCC	.	4	ESCA
DAO	0	.	GRCh37	12	109273444	109273444	+	5'Flank	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000228476	.	73	64	9	90	90	0	DAO,intron_variant,,ENST00000551281,;DAO,upstream_gene_variant,,ENST00000547166,;DAO,upstream_gene_variant,,ENST00000547768,;DAO,upstream_gene_variant,,ENST00000228476,;DAO,non_coding_transcript_exon_variant,,ENST00000548052,;DAO,upstream_gene_variant,,ENST00000549215,;DAO,upstream_gene_variant,,ENST00000547122,;	T	ENSG00000110887	ENST00000228476	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	362	1	DAO	HGNC	2671	protein_coding	YES	CCDS9122.1	ENSP00000228476	OXDA_HUMAN	Q7Z312_HUMAN,F8W152_HUMAN,F8VV35_HUMAN	UPI0000130F5F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCATCTC	.	4	ESCA
PPP1CC	0	.	GRCh37	12	111157791	111157791	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*148G>C	.	.	ENST00000340766	8/8	82	73	9	117	117	0	PPP1CC,3_prime_UTR_variant,,ENST00000340766,;PPP1CC,3_prime_UTR_variant,,ENST00000335007,;PPP1CC,downstream_gene_variant,,ENST00000551676,;PPP1CC,downstream_gene_variant,,ENST00000550991,;PPP1CC,downstream_gene_variant,,ENST00000551582,;PPP1CC,downstream_gene_variant,,ENST00000546933,;PPP1CC,3_prime_UTR_variant,,ENST00000550261,;PPP1CC,downstream_gene_variant,,ENST00000546904,;PPP1CC,downstream_gene_variant,,ENST00000553024,;	G	ENSG00000186298	ENST00000340766	Transcript	3_prime_UTR_variant	1394	.	.	.	.	.	.	.	-1	PPP1CC	HGNC	9283	protein_coding	YES	CCDS58279.1	ENSP00000341779	PP1G_HUMAN	Q9UPN1_HUMAN,C4TNW6_HUMAN,C4TNW5_HUMAN	UPI000002B16F	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GATTTCTTTTT	.	3	ESCA
SMCO2	0	.	GRCh37	12	27628521	27628521	+	Silent	SNP	G	G	A	rs77197438	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369G>A	p.%3D	p.L123L	ENST00000416383	5/9	84	76	8	128	128	0	SMCO2,synonymous_variant,p.%3D,ENST00000535986,;SMCO2,synonymous_variant,p.%3D,ENST00000416383,;SMCO2,intron_variant,,ENST00000298876,;SMCO2,non_coding_transcript_exon_variant,,ENST00000538647,;SMCO2,downstream_gene_variant,,ENST00000543991,;	A	ENSG00000165935	ENST00000416383	Transcript	synonymous_variant	545	369	123	L	ctG/ctA	rs77197438	.	.	1	SMCO2	HGNC	34448	protein_coding	YES	CCDS44852.1	ENSP00000387617	SMCO2_HUMAN	.	UPI000166275D	.	.	.	5/9	.	Pfam_domain:PF14992,hmmpanther:PTHR22422,hmmpanther:PTHR22422:SF5	C:0.0062	C:0.0219	C:0.0029	.	C:0	C:0	C:0	C:0.0332	C:0.0003	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGTCTGAAGGG	byFrequency|byCluster|by1000G	3	ESCA
PPFIBP1	0	.	GRCh37	12	27829365	27829365	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1466G>C	p.Arg489Thr	p.R489T	ENST00000318304	18/29	52	47	5	40	40	0	PPFIBP1,missense_variant,p.Arg472Thr,ENST00000228425,;PPFIBP1,missense_variant,p.Arg489Thr,ENST00000318304,;PPFIBP1,missense_variant,p.Arg336Thr,ENST00000537927,;PPFIBP1,missense_variant,p.Arg164Thr,ENST00000537261,;PPFIBP1,missense_variant,p.Arg458Thr,ENST00000542629,;PPFIBP1,missense_variant,p.Arg320Thr,ENST00000540114,;PPFIBP1,upstream_gene_variant,,ENST00000540503,;	C	ENSG00000110841	ENST00000318304	Transcript	missense_variant	1749	1466	489	R/T	aGa/aCa	.	.	.	1	PPFIBP1	HGNC	9249	protein_coding	YES	CCDS55812.1	ENSP00000314724	LIPB1_HUMAN	F5H6Q7_HUMAN	UPI00004565E6	.	tolerated(0.25)	benign(0.056)	18/29	.	hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGACAGAGCTC	.	3	ESCA
CAPRIN2	0	.	GRCh37	12	30881712	30881712	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1652A>T	p.Asn551Ile	p.N551I	ENST00000298892	8/17	180	158	21	125	125	0	CAPRIN2,missense_variant,p.Asn297Ile,ENST00000433722,;CAPRIN2,missense_variant,p.Asn218Ile,ENST00000308433,;CAPRIN2,missense_variant,p.Asn551Ile,ENST00000251071,;CAPRIN2,missense_variant,p.Asn470Ile,ENST00000537108,;CAPRIN2,missense_variant,p.Asn551Ile,ENST00000395805,;CAPRIN2,missense_variant,p.Asn551Ile,ENST00000298892,;CAPRIN2,missense_variant,p.Asn551Ile,ENST00000417045,;CAPRIN2,downstream_gene_variant,,ENST00000541765,;CAPRIN2,downstream_gene_variant,,ENST00000543380,;CAPRIN2,non_coding_transcript_exon_variant,,ENST00000538387,;CAPRIN2,downstream_gene_variant,,ENST00000534897,;CAPRIN2,3_prime_UTR_variant,,ENST00000548676,;CAPRIN2,3_prime_UTR_variant,,ENST00000537553,;CAPRIN2,3_prime_UTR_variant,,ENST00000454014,;CAPRIN2,non_coding_transcript_exon_variant,,ENST00000553026,;	A	ENSG00000110888	ENST00000298892	Transcript	missense_variant	2403	1652	551	N/I	aAt/aTt	.	.	.	-1	CAPRIN2	HGNC	21259	protein_coding	YES	CCDS8720.1	ENSP00000298892	CAPR2_HUMAN	F5H7T6_HUMAN,F5H5J8_HUMAN,F5GZX3_HUMAN,F5GYA1_HUMAN,F5GXI7_HUMAN	UPI000007080A	.	tolerated(0.16)	benign(0.22)	8/17	.	hmmpanther:PTHR22922,hmmpanther:PTHR22922:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACATTGTTT	.	4	ESCA
KIF21A	0	.	GRCh37	12	39696800	39696800	+	Missense_Mutation	SNP	C	C	A	rs781366144	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4698G>T	p.Lys1566Asn	p.K1566N	ENST00000361418	36/38	79	73	6	112	112	0	KIF21A,missense_variant,p.Lys1513Asn,ENST00000541463,;KIF21A,missense_variant,p.Lys1553Asn,ENST00000361961,;KIF21A,missense_variant,p.Lys867Asn,ENST00000552961,;KIF21A,missense_variant,p.Lys1566Asn,ENST00000361418,;KIF21A,missense_variant,p.Lys547Asn,ENST00000551264,;KIF21A,missense_variant,p.Lys1529Asn,ENST00000544797,;KIF21A,missense_variant,p.Lys1567Asn,ENST00000395670,;KIF21A,non_coding_transcript_exon_variant,,ENST00000547733,;	A	ENSG00000139116	ENST00000361418	Transcript	missense_variant	4714	4698	1566	K/N	aaG/aaT	rs781366144	.	.	-1	KIF21A	HGNC	19349	protein_coding	YES	CCDS53776.1	ENSP00000354878	KI21A_HUMAN	.	UPI0000212ED9	.	deleterious(0)	probably_damaging(0.99)	36/38	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF398,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTCTTGAT	.	2	ESCA
CNTN1	0	.	GRCh37	12	41423007	41423007	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2966A>G	p.Gln989Arg	p.Q989R	ENST00000551295	23/24	38	32	5	66	66	0	CNTN1,missense_variant,p.Gln989Arg,ENST00000551295,;CNTN1,missense_variant,p.Gln989Arg,ENST00000347616,;CNTN1,missense_variant,p.Gln978Arg,ENST00000348761,;CNTN1,downstream_gene_variant,,ENST00000550305,;CNTN1,missense_variant,p.Gln31Arg,ENST00000548481,;	G	ENSG00000018236	ENST00000551295	Transcript	missense_variant	3083	2966	989	Q/R	cAa/cGa	.	.	.	1	CNTN1	HGNC	2171	protein_coding	YES	CCDS8737.1	ENSP00000447006	CNTN1_HUMAN	F8VX96_HUMAN,F8VUI9_HUMAN,F8VUI8_HUMAN,F8VQW3_HUMAN	UPI0000127EBA	.	tolerated(0.1)	benign(0.017)	23/24	.	Superfamily_domains:SSF49265,Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF531,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTCAAGTCA	.	4	ESCA
SLC38A1	0	.	GRCh37	12	46594904	46594904	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.980T>C	p.Ile327Thr	p.I327T	ENST00000398637	13/17	181	167	14	234	234	0	SLC38A1,missense_variant,p.Ile327Thr,ENST00000549049,;SLC38A1,missense_variant,p.Ile327Thr,ENST00000398637,;SLC38A1,missense_variant,p.Ile327Thr,ENST00000546893,;SLC38A1,missense_variant,p.Ile327Thr,ENST00000552197,;SLC38A1,missense_variant,p.Ile327Thr,ENST00000439706,;SLC38A1,non_coding_transcript_exon_variant,,ENST00000549633,;SLC38A1,upstream_gene_variant,,ENST00000548979,;	G	ENSG00000111371	ENST00000398637	Transcript	missense_variant	1675	980	327	I/T	aTt/aCt	.	.	.	-1	SLC38A1	HGNC	13447	protein_coding	YES	CCDS41774.1	ENSP00000381634	S38A1_HUMAN	Q8NCD8_HUMAN,F8VX12_HUMAN	UPI000004D33C	.	tolerated(0.26)	benign(0.197)	13/17	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22950:SF184,hmmpanther:PTHR22950,Pfam_domain:PF01490	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAAAATGGCA	.	2	ESCA
SENP1	0	.	GRCh37	12	48491881	48491881	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31G>C	p.Asp11His	p.D11H	ENST00000004980	3/18	147	131	16	116	116	0	SENP1,missense_variant,p.Asp11His,ENST00000549595,;SENP1,missense_variant,p.Asp4His,ENST00000551798,;SENP1,missense_variant,p.Asp11His,ENST00000004980,;SENP1,missense_variant,p.Asp43His,ENST00000339976,;SENP1,missense_variant,p.Asp11His,ENST00000551330,;SENP1,missense_variant,p.Asp11His,ENST00000549518,;SENP1,missense_variant,p.Asp11His,ENST00000448372,;SENP1,upstream_gene_variant,,ENST00000547886,;SENP1,upstream_gene_variant,,ENST00000551592,;SENP1,missense_variant,p.Asp11His,ENST00000552189,;SENP1,non_coding_transcript_exon_variant,,ENST00000547181,;SENP1,non_coding_transcript_exon_variant,,ENST00000549882,;	G	ENSG00000079387	ENST00000004980	Transcript	missense_variant	510	31	11	D/H	Gat/Cat	.	.	.	-1	SENP1	HGNC	17927	protein_coding	YES	CCDS44868.2	ENSP00000004980	SENP1_HUMAN	F8VRZ8_HUMAN	UPI0000E595D2	.	deleterious_low_confidence(0)	unknown(0)	3/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12606,hmmpanther:PTHR12606:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCATCCATCC	.	4	ESCA
METTL7A	0	.	GRCh37	12	51319145	51319145	+	Silent	SNP	C	C	T	rs773109369	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.324C>T	p.%3D	p.I108I	ENST00000548553	2/3	89	80	9	76	76	0	METTL7A,synonymous_variant,p.%3D,ENST00000332160,;METTL7A,synonymous_variant,p.%3D,ENST00000548553,;METTL7A,synonymous_variant,p.%3D,ENST00000550502,;METTL7A,synonymous_variant,p.%3D,ENST00000546513,;METTL7A,synonymous_variant,p.%3D,ENST00000547104,;METTL7A,synonymous_variant,p.%3D,ENST00000550097,;	T	ENSG00000185432	ENST00000548553	Transcript	synonymous_variant	1305	324	108	I	atC/atT	rs773109369	.	.	1	METTL7A	HGNC	24550	protein_coding	YES	CCDS8804.1	ENSP00000448785	MET7A_HUMAN	F8VQX6_HUMAN	UPI000003B00C	.	.	.	2/3	.	hmmpanther:PTHR10108:SF734,hmmpanther:PTHR10108,Pfam_domain:PF08241,Gene3D:3.40.50.150,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGATCAAGAG	.	4	ESCA
RARG	0	.	GRCh37	12	53613943	53613943	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.185-4365G>A	.	.	ENST00000425354	.	91	83	8	132	132	0	RARG,missense_variant,p.Glu20Lys,ENST00000543726,;RARG,5_prime_UTR_variant,,ENST00000338561,;RARG,intron_variant,,ENST00000425354,;RARG,intron_variant,,ENST00000327550,;RARG,intron_variant,,ENST00000394426,;RARG,intron_variant,,ENST00000543762,;RARG,non_coding_transcript_exon_variant,,ENST00000550265,;RARG,upstream_gene_variant,,ENST00000548284,;RARG,upstream_gene_variant,,ENST00000548317,;	T	ENSG00000172819	ENST00000425354	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RARG	HGNC	9866	protein_coding	YES	CCDS8850.1	ENSP00000388510	RARG_HUMAN	H3BMY6_HUMAN,H3BMK1_HUMAN,A8K3H3_HUMAN	UPI000000105D	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGATTCCCCCT	.	4	ESCA
ATF7	0	.	GRCh37	12	54020157	54020157	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-116G>T	.	.	ENST00000420353	1/12	117	106	11	154	154	0	ATF7,5_prime_UTR_variant,,ENST00000591397,;ATF7,5_prime_UTR_variant,,ENST00000420353,;ATF7,5_prime_UTR_variant,,ENST00000415113,;ATF7,upstream_gene_variant,,ENST00000548118,;ATF7,upstream_gene_variant,,ENST00000456903,;ATF7,upstream_gene_variant,,ENST00000588078,;ATF7,upstream_gene_variant,,ENST00000548446,;ATF7,upstream_gene_variant,,ENST00000588232,;ATF7,upstream_gene_variant,,ENST00000551480,;RP11-793H13.10,upstream_gene_variant,,ENST00000591834,;ATF7,non_coding_transcript_exon_variant,,ENST00000589726,;	A	ENSG00000170653	ENST00000420353	Transcript	5_prime_UTR_variant	35	.	.	.	.	.	.	.	-1	ATF7	HGNC	792	protein_coding	YES	CCDS44906.1	ENSP00000399465	ATF7_HUMAN	K7EKZ7_HUMAN,F8VWG7_HUMAN	UPI0000161877	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTTTCCTCCC	.	3	ESCA
ANO2	0	.	GRCh37	12	5841762	5841762	+	Missense_Mutation	SNP	C	C	G	rs375457985	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1469G>C	p.Arg490Pro	p.R490P	ENST00000327087	15/26	114	97	16	100	100	0	ANO2,missense_variant,p.Arg490Pro,ENST00000327087,;ANO2,missense_variant,p.Arg491Pro,ENST00000546188,;ANO2,missense_variant,p.Arg50Pro,ENST00000545860,;ANO2,missense_variant,p.Arg491Pro,ENST00000356134,;ANO2,non_coding_transcript_exon_variant,,ENST00000540543,;ANO2,non_coding_transcript_exon_variant,,ENST00000542326,;ANO2,non_coding_transcript_exon_variant,,ENST00000538154,;	G	ENSG00000047617	ENST00000327087	Transcript	missense_variant	1541	1469	490	R/P	cGa/cCa	rs375457985	.	.	-1	ANO2	HGNC	1183	protein_coding	YES	.	ENSP00000314048	ANO2_HUMAN	Q69YW4_HUMAN	UPI0001823FDD	.	tolerated(0.28)	possibly_damaging(0.884)	15/26	.	hmmpanther:PTHR12308:SF20,hmmpanther:PTHR12308,Pfam_domain:PF04547	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCGAACT	byCluster|by1000G	5	ESCA
MRPL51	0	.	GRCh37	12	6602314	6602314	+	5'UTR	SNP	C	C	T	rs749020356	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12G>A	.	.	ENST00000229238	1/3	106	99	7	117	117	0	MRPL51,5_prime_UTR_variant,,ENST00000229238,;MRPL51,intron_variant,,ENST00000543703,;NCAPD2,upstream_gene_variant,,ENST00000545962,;NCAPD2,upstream_gene_variant,,ENST00000315579,;NCAPD2,upstream_gene_variant,,ENST00000539714,;NCAPD2,upstream_gene_variant,,ENST00000382457,;MRPL51,intron_variant,,ENST00000543164,;MRPL51,intron_variant,,ENST00000540949,;MRPL51,intron_variant,,ENST00000537701,;MRPL51,intron_variant,,ENST00000543959,;NCAPD2,upstream_gene_variant,,ENST00000536538,;NCAPD2,upstream_gene_variant,,ENST00000541399,;MRPL51,upstream_gene_variant,,ENST00000538814,;NCAPD2,upstream_gene_variant,,ENST00000539084,;	T	ENSG00000111639	ENST00000229238	Transcript	5_prime_UTR_variant	451	.	.	.	.	rs749020356	.	.	-1	MRPL51	HGNC	14044	protein_coding	YES	CCDS8547.1	ENSP00000229238	RM51_HUMAN	M0R176_HUMAN	UPI00000527A8	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTCTCCCCCC	.	2	ESCA
CPSF6	0	.	GRCh37	12	69633375	69633375	+	5'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-52G>C	.	.	ENST00000435070	1/10	91	76	14	138	137	0	CPSF6,5_prime_UTR_variant,,ENST00000435070,;CPSF6,upstream_gene_variant,,ENST00000266679,;CPSF6,upstream_gene_variant,,ENST00000551516,;CPSF6,upstream_gene_variant,,ENST00000456847,;CPSF6,upstream_gene_variant,,ENST00000550987,;CPSF6,5_prime_UTR_variant,,ENST00000550075,;	C	ENSG00000111605	ENST00000435070	Transcript	5_prime_UTR_variant	59	.	.	.	.	.	.	.	1	CPSF6	HGNC	13871	protein_coding	YES	CCDS8988.1	ENSP00000391774	CPSF6_HUMAN	.	UPI00001FC746	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGGCGGGCAG	.	4	ESCA
ZNF705A	0	.	GRCh37	12	8329832	8329832	+	Missense_Mutation	SNP	C	C	T	rs768253035	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556C>T	p.Arg186Cys	p.R186C	ENST00000359286	5/5	247	234	13	300	300	0	ZNF705A,missense_variant,p.Arg186Cys,ENST00000396570,;ZNF705A,missense_variant,p.Arg186Cys,ENST00000359286,;ZNF705A,intron_variant,,ENST00000398526,;ZNF705A,downstream_gene_variant,,ENST00000402465,;FAM66C,upstream_gene_variant,,ENST00000454799,;FAM66C,upstream_gene_variant,,ENST00000541558,;FAM66C,upstream_gene_variant,,ENST00000456135,;FAM66C,upstream_gene_variant,,ENST00000544214,;	T	ENSG00000196946	ENST00000359286	Transcript	missense_variant	645	556	186	R/C	Cgc/Tgc	rs768253035	.	.	1	ZNF705A	HGNC	32281	protein_coding	YES	CCDS31737.1	ENSP00000352233	Z705A_HUMAN	J3KPU9_HUMAN,B5MCH6_HUMAN	UPI000035E780	.	tolerated(0.2)	benign(0.002)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF18,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R186H|c.557G>A|5	MUTECT|MUSE	GCTTTCGCCTT	byFrequency	2	ESCA
A2M	0	.	GRCh37	12	9243977	9243977	+	Silent	SNP	G	G	A	rs753034102	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2289C>T	p.%3D	p.T763T	ENST00000318602	19/36	80	73	7	82	82	0	A2M,synonymous_variant,p.%3D,ENST00000543436,;A2M,synonymous_variant,p.%3D,ENST00000318602,;A2M,intron_variant,,ENST00000545828,;A2M,upstream_gene_variant,,ENST00000462568,;A2M,downstream_gene_variant,,ENST00000546069,;	A	ENSG00000175899	ENST00000318602	Transcript	synonymous_variant	2597	2289	763	T	acC/acT	rs753034102,COSM3968491	.	.	-1	A2M	HGNC	7	protein_coding	YES	CCDS44827.1	ENSP00000323929	A2MG_HUMAN	Q9BQ22_HUMAN,F8W7L3_HUMAN,F5H1E8_HUMAN	UPI000014038F	.	.	.	19/36	.	hmmpanther:PTHR11412:SF75,hmmpanther:PTHR11412,Pfam_domain:PF00207	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CACTCGGTGAT	.	3	ESCA
C12orf55	0	.	GRCh37	12	97045517	97045517	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5024C>G	p.Ser1675Cys	p.S1675C	ENST00000524981	36/68	99	88	10	120	120	0	C12orf55,missense_variant,p.Ser1675Cys,ENST00000524981,;C12orf55,downstream_gene_variant,,ENST00000550977,;C12orf55,non_coding_transcript_exon_variant,,ENST00000342887,;	G	ENSG00000188596	ENST00000524981	Transcript	missense_variant	5047	5024	1675	S/C	tCt/tGt	.	.	.	1	C12orf55	HGNC	26456	protein_coding	YES	.	ENSP00000431759	.	R4GNI2_HUMAN,E9PJL5_HUMAN	UPI0001F77A4D	.	tolerated(0.2)	benign(0.006)	36/68	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V101V|c.303T>C|3	RADIA|MUTECT|MUSE|VARSCANS	CACCTCTGTTT	.	4	ESCA
PCCA	0	.	GRCh37	13	100909873	100909873	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662C>T	p.Ser221Leu	p.S221L	ENST00000376285	9/24	77	59	17	65	65	0	PCCA,missense_variant,p.Ser195Leu,ENST00000376286,;PCCA,missense_variant,p.Ser221Leu,ENST00000376279,;PCCA,missense_variant,p.Ser221Leu,ENST00000376285,;	T	ENSG00000175198	ENST00000376285	Transcript	missense_variant	700	662	221	S/L	tCa/tTa	.	.	.	1	PCCA	HGNC	8653	protein_coding	YES	CCDS9496.2	ENSP00000365462	PCCA_HUMAN	.	UPI0000070089	.	deleterious(0.01)	probably_damaging(0.942)	9/24	.	PROSITE_profiles:PS50975,PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF33,hmmpanther:PTHR18866,PROSITE_patterns:PS00866,Gene3D:3.30.1490.20,Pfam_domain:PF02786,Superfamily_domains:SSF56059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCAGCAG	.	5	ESCA
MYO16	0	.	GRCh37	13	109318403	109318403	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132C>A	p.Phe44Leu	p.F44L	ENST00000356711	2/35	55	37	18	87	87	0	MYO16,missense_variant,p.Phe44Leu,ENST00000251041,;MYO16,missense_variant,p.Phe44Leu,ENST00000356711,;MYO16,missense_variant,p.Phe44Leu,ENST00000357550,;	A	ENSG00000041515	ENST00000356711	Transcript	missense_variant	258	132	44	F/L	ttC/ttA	COSM3467029,COSM3467030	.	.	1	MYO16	HGNC	29822	protein_coding	YES	CCDS32008.1	ENSP00000349145	MYO16_HUMAN	.	UPI0000160FF2	.	tolerated(0.93)	benign(0.001)	2/35	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTTCCTGAA	.	5	ESCA
TUBGCP3	0	.	GRCh37	13	113140013	113140013	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*294C>G	.	.	ENST00000261965	22/22	53	46	7	110	110	0	TUBGCP3,3_prime_UTR_variant,,ENST00000261965,;TUBGCP3,downstream_gene_variant,,ENST00000469302,;	C	ENSG00000126216	ENST00000261965	Transcript	3_prime_UTR_variant	3205	.	.	.	.	.	.	.	-1	TUBGCP3	HGNC	18598	protein_coding	YES	CCDS9525.1	ENSP00000261965	GCP3_HUMAN	.	UPI000000DB88	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATAGAAAGC	.	5	ESCA
MPHOSPH8	0	.	GRCh37	13	20216300	20216300	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259G>A	p.Asp87Asn	p.D87N	ENST00000361479	2/14	110	87	23	210	210	0	MPHOSPH8,missense_variant,p.Asp87Asn,ENST00000361479,;MPHOSPH8,missense_variant,p.Asp87Asn,ENST00000414242,;	A	ENSG00000196199	ENST00000361479	Transcript	missense_variant	327	259	87	D/N	Gat/Aat	.	.	.	1	MPHOSPH8	HGNC	29810	protein_coding	YES	CCDS9287.1	ENSP00000355388	MPP8_HUMAN	.	UPI0000051C18	.	deleterious_low_confidence(0)	probably_damaging(0.938)	2/14	.	Superfamily_domains:SSF54160,SMART_domains:SM00298,Gene3D:2.40.50.40,Pfam_domain:PF00385,PROSITE_patterns:PS00598,hmmpanther:PTHR24188:SF6,hmmpanther:PTHR24188,PROSITE_profiles:PS50013	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGATGATGAT	.	5	ESCA
IFT88	0	.	GRCh37	13	21265264	21265264	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2452G>A	p.Glu818Lys	p.E818K	ENST00000319980	28/28	121	97	23	192	192	0	IFT88,missense_variant,p.Glu818Lys,ENST00000319980,;IFT88,missense_variant,p.Glu809Lys,ENST00000351808,;IFT88,missense_variant,p.Glu790Lys,ENST00000537103,;IFT88,3_prime_UTR_variant,,ENST00000382778,;IFT88,non_coding_transcript_exon_variant,,ENST00000482172,;	A	ENSG00000032742	ENST00000319980	Transcript	missense_variant	2779	2452	818	E/K	Gag/Aag	.	.	.	1	IFT88	HGNC	20606	protein_coding	YES	CCDS31944.1	ENSP00000323580	IFT88_HUMAN	F6SRW8_HUMAN	UPI0000160108	.	deleterious(0.05)	benign(0.074)	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGATGAGGAT	.	5	ESCA
DCLK1	0	.	GRCh37	13	36382446	36382446	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1778A>C	p.Asp593Ala	p.D593A	ENST00000255448	14/18	38	35	3	63	63	0	DCLK1,missense_variant,p.Asp593Ala,ENST00000360631,;DCLK1,missense_variant,p.Asp286Ala,ENST00000379893,;DCLK1,missense_variant,p.Asp593Ala,ENST00000255448,;DCLK1,non_coding_transcript_exon_variant,,ENST00000486239,;	G	ENSG00000133083	ENST00000255448	Transcript	missense_variant	1990	1778	593	D/A	gAc/gCc	.	.	.	-1	DCLK1	HGNC	2700	protein_coding	YES	CCDS9354.1	ENSP00000255448	DCLK1_HUMAN	.	UPI000002A7C2	.	tolerated(0.63)	possibly_damaging(0.728)	14/18	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR24347:SF123,hmmpanther:PTHR24347,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGGTCATCA	.	2	ESCA
TRPC4	0	.	GRCh37	13	38211354	38211354	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000379681	11/11	78	55	23	68	68	0	TRPC4,stop_gained,p.Gln725Ter,ENST00000379673,;TRPC4,stop_gained,p.Gln701Ter,ENST00000338947,;TRPC4,stop_gained,p.Gln879Ter,ENST00000379681,;TRPC4,stop_gained,p.Gln733Ter,ENST00000447043,;TRPC4,stop_gained,p.Gln701Ter,ENST00000379679,;TRPC4,stop_gained,p.Gln733Ter,ENST00000355779,;TRPC4,stop_gained,p.Gln790Ter,ENST00000358477,;TRPC4,stop_gained,p.Gln874Ter,ENST00000379705,;TRPC4,3_prime_UTR_variant,,ENST00000426868,;TRPC4,3_prime_UTR_variant,,ENST00000488717,;	A	ENSG00000133107	ENST00000379681	Transcript	stop_gained	2870	2635	879	Q/*	Caa/Taa	.	.	.	-1	TRPC4	HGNC	12336	protein_coding	YES	CCDS45037.1	ENSP00000369003	TRPC4_HUMAN	.	UPI000006E5BE	.	.	.	11/11	.	hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTGACGAG	.	5	ESCA
TEP1	0	.	GRCh37	14	20863723	20863723	+	Missense_Mutation	SNP	C	C	T	rs201323276	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1814G>A	p.Arg605His	p.R605H	ENST00000262715	12/55	49	43	6	44	44	0	TEP1,missense_variant,p.Arg497His,ENST00000556935,;TEP1,missense_variant,p.Arg605His,ENST00000262715,;TEP1,missense_variant,p.Arg605His,ENST00000555727,;TEP1,upstream_gene_variant,,ENST00000555008,;	T	ENSG00000129566	ENST00000262715	Transcript	missense_variant	1855	1814	605	R/H	cGt/cAt	rs201323276	.	.	-1	TEP1	HGNC	11726	protein_coding	YES	CCDS9548.1	ENSP00000262715	TEP1_HUMAN	G3V591_HUMAN	UPI000013D30B	.	tolerated(0.54)	benign(0.214)	12/55	.	Pfam_domain:PF05731,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF402,PROSITE_profiles:PS50988	T:0.0000	T:0	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGACGGTTC	byCluster|by1000G	4	ESCA
KLHL33	0	.	GRCh37	14	20898456	20898456	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.379G>A	p.Glu127Lys	p.E127K	ENST00000344581	2/4	44	37	6	52	52	0	KLHL33,missense_variant,p.Glu127Lys,ENST00000344581,;	T	ENSG00000185271	ENST00000344581	Transcript	missense_variant	602	379	127	E/K	Gag/Aag	.	.	.	-1	KLHL33	HGNC	31952	protein_coding	YES	CCDS53882.1	ENSP00000341549	KLH33_HUMAN	B2RUZ8_HUMAN	UPI00016630E8	.	tolerated(0.24)	benign(0.243)	2/4	.	hmmpanther:PTHR24412:SF158,hmmpanther:PTHR24412,Pfam_domain:PF07707,SMART_domains:SM00875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GAGCTCATCAC	.	3	ESCA
REM2	0	.	GRCh37	14	23354124	23354124	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.345C>G	p.Phe115Leu	p.F115L	ENST00000267396	2/5	43	39	4	59	59	0	REM2,missense_variant,p.Phe115Leu,ENST00000267396,;REM2,missense_variant,p.Phe115Leu,ENST00000536884,;LRP10,downstream_gene_variant,,ENST00000551466,;LRP10,downstream_gene_variant,,ENST00000359591,;	G	ENSG00000139890	ENST00000267396	Transcript	missense_variant	468	345	115	F/L	ttC/ttG	.	.	.	1	REM2	HGNC	20248	protein_coding	YES	CCDS45082.1	ENSP00000267396	REM2_HUMAN	.	UPI00000716C5	.	tolerated(0.35)	possibly_damaging(0.447)	2/5	.	PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF197,Gene3D:3.40.50.300,SMART_domains:SM00175,PIRSF_domain:PIRSF038017,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATCTTCAAGGT	.	3	ESCA
SEC23A	0	.	GRCh37	14	39502532	39502532	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2209G>T	p.Glu737Ter	p.E737*	ENST00000307712	20/20	154	139	15	154	154	0	SEC23A,stop_gained,p.Glu737Ter,ENST00000307712,;SEC23A,stop_gained,p.Glu635Ter,ENST00000536508,;SEC23A,stop_gained,p.Glu708Ter,ENST00000545328,;SEC23A,stop_gained,p.Glu535Ter,ENST00000537403,;SEC23A,splice_region_variant,,ENST00000554615,;SEC23A,splice_region_variant,,ENST00000555363,;	A	ENSG00000100934	ENST00000307712	Transcript	stop_gained	2727	2209	737	E/*	Gag/Tag	.	.	.	-1	SEC23A	HGNC	10701	protein_coding	YES	CCDS9668.1	ENSP00000306881	SC23A_HUMAN	G3V5K1_HUMAN,G3V3G5_HUMAN,G3V2R6_HUMAN,B3KXI2_HUMAN	UPI000013EC46	.	.	.	20/20	.	hmmpanther:PTHR11141,hmmpanther:PTHR11141:SF5,Gene3D:3.40.20.10,Superfamily_domains:SSF82754	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGACTCCTAGA	.	4	ESCA
NEMF	0	.	GRCh37	14	50319482	50319482	+	5'UTR	SNP	G	G	A	rs771537306	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11C>T	.	.	ENST00000298310	1/33	29	21	7	24	24	0	NEMF,5_prime_UTR_variant,,ENST00000546046,;NEMF,5_prime_UTR_variant,,ENST00000554626,;NEMF,5_prime_UTR_variant,,ENST00000555970,;NEMF,5_prime_UTR_variant,,ENST00000298310,;NEMF,5_prime_UTR_variant,,ENST00000545773,;NEMF,5_prime_UTR_variant,,ENST00000556672,;RN7SL3,downstream_gene_variant,,ENST00000578231,;NEMF,non_coding_transcript_exon_variant,,ENST00000557380,;NEMF,non_coding_transcript_exon_variant,,ENST00000554162,;	A	ENSG00000165525	ENST00000298310	Transcript	5_prime_UTR_variant	440	.	.	.	.	rs771537306	.	.	-1	NEMF	HGNC	10663	protein_coding	YES	CCDS9694.1	ENSP00000298310	NEMF_HUMAN	.	UPI0000246D16	.	.	.	1/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCCGAGGGT	.	5	ESCA
AP5M1	0	.	GRCh37	14	57753022	57753022	+	Missense_Mutation	SNP	C	C	G	rs774102971	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1375C>G	p.Pro459Ala	p.P459A	ENST00000261558	7/8	59	53	5	45	45	0	AP5M1,missense_variant,p.Pro80Ala,ENST00000554863,;AP5M1,missense_variant,p.Pro459Ala,ENST00000261558,;AP5M1,missense_variant,p.Pro473Ala,ENST00000431972,;AP5M1,downstream_gene_variant,,ENST00000556723,;AP5M1,missense_variant,p.Pro28Ala,ENST00000556377,;AP5M1,downstream_gene_variant,,ENST00000555448,;	G	ENSG00000053770	ENST00000261558	Transcript	missense_variant	1781	1375	459	P/A	Cca/Gca	rs774102971	.	.	1	AP5M1	HGNC	20192	protein_coding	YES	CCDS9729.1	ENSP00000261558	AP5M1_HUMAN	H0YIY0_HUMAN,G3V573_HUMAN	UPI00000719DE	.	tolerated(0.19)	benign(0.032)	7/8	.	PROSITE_profiles:PS51072,hmmpanther:PTHR16082:SF2,hmmpanther:PTHR16082,Superfamily_domains:0038852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAACCAAAA	.	2	ESCA
RGS6	0	.	GRCh37	14	72945037	72945037	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.854G>C	p.Ser285Thr	p.S285T	ENST00000553525	12/18	72	62	10	95	95	0	RGS6,missense_variant,p.Ser285Thr,ENST00000406236,;RGS6,missense_variant,p.Ser285Thr,ENST00000553530,;RGS6,missense_variant,p.Ser285Thr,ENST00000553525,;RGS6,missense_variant,p.Ser285Thr,ENST00000556437,;RGS6,missense_variant,p.Ser146Thr,ENST00000554782,;RGS6,missense_variant,p.Ser285Thr,ENST00000407322,;RGS6,missense_variant,p.Ser285Thr,ENST00000555571,;RGS6,missense_variant,p.Ser285Thr,ENST00000355512,;RGS6,missense_variant,p.Ser285Thr,ENST00000404301,;RGS6,missense_variant,p.Ser216Thr,ENST00000434263,;RGS6,missense_variant,p.Ser285Thr,ENST00000343854,;RGS6,missense_variant,p.Ser285Thr,ENST00000402788,;RGS6,non_coding_transcript_exon_variant,,ENST00000555368,;RGS6,downstream_gene_variant,,ENST00000553690,;RGS6,missense_variant,p.Ser285Thr,ENST00000554474,;RGS6,downstream_gene_variant,,ENST00000554734,;	C	ENSG00000182732	ENST00000553525	Transcript	missense_variant	1377	854	285	S/T	aGt/aCt	.	.	.	1	RGS6	HGNC	10002	protein_coding	YES	CCDS55924.1	ENSP00000451030	RGS6_HUMAN	Q59FJ8_HUMAN	UPI00001698D0	.	tolerated(0.14)	benign(0.02)	12/18	.	Superfamily_domains:SSF48670,SMART_domains:SM00224,Gene3D:4.10.260.10,Pfam_domain:PF00631,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAAAGGTATG	.	4	ESCA
PNMA1	0	.	GRCh37	14	74179248	74179248	+	3'UTR	SNP	C	C	G	rs554501949	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*33G>C	.	.	ENST00000316836	1/1	68	61	7	63	63	0	PNMA1,3_prime_UTR_variant,,ENST00000316836,;ELMSAN1,downstream_gene_variant,,ENST00000286523,;ELMSAN1,downstream_gene_variant,,ENST00000394071,;ELMSAN1,downstream_gene_variant,,ENST00000476562,;	G	ENSG00000176903	ENST00000316836	Transcript	3_prime_UTR_variant	1881	.	.	.	.	rs554501949	.	.	-1	PNMA1	HGNC	9158	protein_coding	YES	CCDS9818.1	ENSP00000318914	PNMA1_HUMAN	.	UPI000003779C	.	.	.	1/1	.	.	G:0.0004	G:0	G:0	.	G:0	G:0	G:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGATCTAGGT	byFrequency|by1000G	4	ESCA
ALDH6A1	0	.	GRCh37	14	74551166	74551166	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-69G>A	.	.	ENST00000553458	1/12	110	101	9	36	36	0	ALDH6A1,5_prime_UTR_variant,,ENST00000553458,;LIN52,upstream_gene_variant,,ENST00000554938,;LIN52,upstream_gene_variant,,ENST00000555028,;CCDC176,downstream_gene_variant,,ENST00000553773,;ALDH6A1,upstream_gene_variant,,ENST00000350259,;LIN52,upstream_gene_variant,,ENST00000554076,;ALDH6A1,upstream_gene_variant,,ENST00000553814,;ALDH6A1,upstream_gene_variant,,ENST00000556852,;AC005484.5,downstream_gene_variant,,ENST00000492026,;ALDH6A1,non_coding_transcript_exon_variant,,ENST00000554231,;LIN52,upstream_gene_variant,,ENST00000554289,;LIN52,upstream_gene_variant,,ENST00000553404,;ALDH6A1,upstream_gene_variant,,ENST00000554501,;	T	ENSG00000119711	ENST00000553458	Transcript	5_prime_UTR_variant	31	.	.	.	.	.	.	.	-1	ALDH6A1	HGNC	7179	protein_coding	YES	CCDS9826.1	ENSP00000450436	MMSA_HUMAN	G3V4Z4_HUMAN	UPI0000001610	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGCCTCGCCCT	.	3	ESCA
RPS6KL1	0	.	GRCh37	14	75388118	75388118	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.127G>A	p.Asp43Asn	p.D43N	ENST00000555647	3/12	56	41	14	24	24	0	RPS6KL1,missense_variant,p.Asp43Asn,ENST00000557413,;RPS6KL1,missense_variant,p.Asp43Asn,ENST00000354625,;RPS6KL1,missense_variant,p.Asp43Asn,ENST00000358328,;RPS6KL1,missense_variant,p.Asp43Asn,ENST00000555647,;RPS6KL1,downstream_gene_variant,,ENST00000556776,;RPS6KL1,intron_variant,,ENST00000554900,;RPS6KL1,missense_variant,p.Asp43Asn,ENST00000555009,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000555834,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000557383,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000553894,;RPS6KL1,upstream_gene_variant,,ENST00000554834,;	T	ENSG00000198208	ENST00000555647	Transcript	missense_variant	415	127	43	D/N	Gac/Aac	.	.	.	-1	RPS6KL1	HGNC	20222	protein_coding	YES	CCDS9834.2	ENSP00000452027	RPKL1_HUMAN	.	UPI0000035B53	.	deleterious(0.01)	possibly_damaging(0.867)	3/12	.	hmmpanther:PTHR15508,Gene3D:1.20.58.280	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGTCAGGCA	.	5	ESCA
ASB2	0	.	GRCh37	14	94400972	94400972	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*30C>A	.	.	ENST00000555019	10/10	55	44	10	48	48	0	ASB2,3_prime_UTR_variant,,ENST00000315988,;ASB2,3_prime_UTR_variant,,ENST00000555019,;ASB2,downstream_gene_variant,,ENST00000555507,;RP11-131H24.4,upstream_gene_variant,,ENST00000557646,;ASB2,downstream_gene_variant,,ENST00000556337,;ASB2,non_coding_transcript_exon_variant,,ENST00000553883,;	T	ENSG00000100628	ENST00000555019	Transcript	3_prime_UTR_variant	2369	.	.	.	.	.	.	.	-1	ASB2	HGNC	16012	protein_coding	YES	CCDS55940.1	ENSP00000451575	ASB2_HUMAN	G3V484_HUMAN,B3KPZ6_HUMAN	UPI000013D23C	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGAGGGGCT	.	5	ESCA
ASB2	0	.	GRCh37	14	94404059	94404059	+	Missense_Mutation	SNP	T	T	C	rs769737457	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1756A>G	p.Ile586Val	p.I586V	ENST00000555019	9/10	45	41	3	56	56	0	ASB2,missense_variant,p.Ile538Val,ENST00000315988,;ASB2,missense_variant,p.Ile586Val,ENST00000555019,;ASB2,downstream_gene_variant,,ENST00000555507,;RP11-131H24.4,upstream_gene_variant,,ENST00000557646,;ASB2,downstream_gene_variant,,ENST00000556337,;ASB2,non_coding_transcript_exon_variant,,ENST00000553883,;	C	ENSG00000100628	ENST00000555019	Transcript	missense_variant	2187	1756	586	I/V	Atc/Gtc	rs769737457	.	.	-1	ASB2	HGNC	16012	protein_coding	YES	CCDS55940.1	ENSP00000451575	ASB2_HUMAN	G3V484_HUMAN,B3KPZ6_HUMAN	UPI000013D23C	.	tolerated(0.23)	benign(0.05)	9/10	.	PROSITE_profiles:PS50225,hmmpanther:PTHR24196:SF0,hmmpanther:PTHR24196,Superfamily_domains:SSF158235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGATGACGG	.	2	ESCA
PCSK6	0	.	GRCh37	15	101853633	101853633	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2644G>T	p.Glu882Ter	p.E882*	ENST00000348070	21/23	71	64	6	61	61	0	PCSK6,stop_gained,p.Glu869Ter,ENST00000358417,;PCSK6,stop_gained,p.Glu711Ter,ENST00000398185,;PCSK6,stop_gained,p.Glu882Ter,ENST00000348070,;PCSK6,intron_variant,,ENST00000558951,;PCSK6,upstream_gene_variant,,ENST00000558864,;PCSK6,non_coding_transcript_exon_variant,,ENST00000558433,;PCSK6,non_coding_transcript_exon_variant,,ENST00000560921,;PCSK6,non_coding_transcript_exon_variant,,ENST00000557794,;PCSK6,non_coding_transcript_exon_variant,,ENST00000561109,;PCSK6,non_coding_transcript_exon_variant,,ENST00000559678,;PCSK6,non_coding_transcript_exon_variant,,ENST00000561177,;PCSK6,upstream_gene_variant,,ENST00000559430,;PCSK6,non_coding_transcript_exon_variant,,ENST00000560785,;PCSK6,upstream_gene_variant,,ENST00000559499,;	A	ENSG00000140479	ENST00000348070	Transcript	stop_gained	2644	2644	882	E/*	Gag/Tag	.	.	.	-1	PCSK6	HGNC	8569	protein_coding	YES	.	ENSP00000305056	PCSK6_HUMAN	A2RQD9_HUMAN	UPI00001AE92B	.	.	.	21/23	.	hmmpanther:PTHR10795:SF345,hmmpanther:PTHR10795,Gene3D:2.10.220.10,SMART_domains:SM00261,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTCACCAC	.	4	ESCA
GABRB3	0	.	GRCh37	15	26790056	26790056	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2884C>T	.	.	ENST00000311550	9/9	87	80	7	94	93	1	GABRB3,3_prime_UTR_variant,,ENST00000541819,;GABRB3,3_prime_UTR_variant,,ENST00000311550,;GABRB3,downstream_gene_variant,,ENST00000545868,;GABRB3,downstream_gene_variant,,ENST00000299267,;GABRB3,downstream_gene_variant,,ENST00000400188,;GABRB3,downstream_gene_variant,,ENST00000555632,;	A	ENSG00000166206	ENST00000311550	Transcript	3_prime_UTR_variant	4418	.	.	.	.	.	.	.	-1	GABRB3	HGNC	4083	protein_coding	YES	CCDS10019.1	ENSP00000308725	GBRB3_HUMAN	G3V5B4_HUMAN	UPI000012AFB0	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CGTCAGAGGTC	.	2	ESCA
HERC2	0	.	GRCh37	15	28419589	28419589	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10009C>T	p.Pro3337Ser	p.P3337S	ENST00000261609	65/93	133	95	37	105	105	0	HERC2,missense_variant,p.Pro3337Ser,ENST00000261609,;HERC2,upstream_gene_variant,,ENST00000569772,;	A	ENSG00000128731	ENST00000261609	Transcript	missense_variant	10118	10009	3337	P/S	Ccc/Tcc	.	.	.	-1	HERC2	HGNC	4868	protein_coding	YES	CCDS10021.1	ENSP00000261609	HERC2_HUMAN	.	UPI00004578F7	.	.	benign(0.213)	65/93	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGGGCTCGT	.	5	ESCA
MTMR10	0	.	GRCh37	15	31253256	31253256	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586C>T	p.Pro196Ser	p.P196S	ENST00000435680	7/16	50	45	5	39	39	0	MTMR10,missense_variant,p.Pro114Ser,ENST00000563714,;MTMR10,missense_variant,p.Pro196Ser,ENST00000435680,;MTMR10,synonymous_variant,p.%3D,ENST00000425768,;MTMR10,5_prime_UTR_variant,,ENST00000314404,;MTMR10,upstream_gene_variant,,ENST00000566981,;RNU6-466P,upstream_gene_variant,,ENST00000391224,;MTMR10,synonymous_variant,p.%3D,ENST00000568547,;MTMR10,synonymous_variant,p.%3D,ENST00000568604,;MTMR10,3_prime_UTR_variant,,ENST00000564787,;MTMR10,3_prime_UTR_variant,,ENST00000567567,;MTMR10,non_coding_transcript_exon_variant,,ENST00000565728,;MTMR10,non_coding_transcript_exon_variant,,ENST00000568611,;	A	ENSG00000166912	ENST00000435680	Transcript	missense_variant	684	586	196	P/S	Ccc/Tcc	.	.	.	-1	MTMR10	HGNC	25999	protein_coding	YES	CCDS45204.1	ENSP00000402537	MTMRA_HUMAN	B4E157_HUMAN	UPI00001FE130	.	tolerated(0.18)	benign(0)	7/16	.	hmmpanther:PTHR10807:SF39,hmmpanther:PTHR10807,Pfam_domain:PF06602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAGGGAATTC	.	2	ESCA
FBN1	0	.	GRCh37	15	48719785	48719785	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7183G>A	p.Gly2395Arg	p.G2395R	ENST00000316623	58/66	35	31	4	63	63	0	FBN1,missense_variant,p.Gly2395Arg,ENST00000316623,;FBN1,synonymous_variant,p.%3D,ENST00000559133,;FBN1,downstream_gene_variant,,ENST00000537463,;FBN1,downstream_gene_variant,,ENST00000560720,;	T	ENSG00000166147	ENST00000316623	Transcript	missense_variant	7639	7183	2395	G/R	Gga/Aga	.	.	.	-1	FBN1	HGNC	3603	protein_coding	YES	CCDS32232.1	ENSP00000325527	FBN1_HUMAN	Q75N89_HUMAN,Q75N88_HUMAN,H0YN80_HUMAN	UPI0000163B0B	.	.	probably_damaging(1)	58/66	.	hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,Gene3D:3.90.290.10,PIRSF_domain:PIRSF036312,Superfamily_domains:SSF57581	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAATCCTCGGC	.	4	ESCA
NEDD4	0	.	GRCh37	15	56207921	56207921	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109C>G	p.Ser370Cys	p.S370C	ENST00000338963	1/22	44	40	3	42	42	0	NEDD4,missense_variant,p.Ser370Cys,ENST00000506154,;NEDD4,missense_variant,p.Ser370Cys,ENST00000338963,;NEDD4,missense_variant,p.Ser370Cys,ENST00000508342,;NEDD4,intron_variant,,ENST00000435532,;NEDD4,upstream_gene_variant,,ENST00000508871,;NEDD4,intron_variant,,ENST00000514893,;NEDD4,missense_variant,p.Ser250Cys,ENST00000503468,;NEDD4,intron_variant,,ENST00000507063,;NEDD4,intron_variant,,ENST00000502612,;	C	ENSG00000069869	ENST00000338963	Transcript	missense_variant	1409	1109	370	S/C	tCt/tGt	.	.	.	-1	NEDD4	HGNC	7727	protein_coding	YES	CCDS10156.1	ENSP00000345530	NEDD4_HUMAN	.	UPI00001418FE	.	tolerated_low_confidence(0.1)	possibly_damaging(0.513)	1/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCAGATGAC	.	2	ESCA
FAM81A	0	.	GRCh37	15	59814456	59814456	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*879A>G	.	.	ENST00000288228	9/9	98	92	6	81	81	0	FAM81A,3_prime_UTR_variant,,ENST00000288228,;RP11-112N19.1,downstream_gene_variant,,ENST00000463506,;	G	ENSG00000157470	ENST00000288228	Transcript	3_prime_UTR_variant	2173	.	.	.	.	.	.	.	1	FAM81A	HGNC	28379	protein_coding	YES	CCDS45269.1	ENSP00000288228	FA81A_HUMAN	H0YN94_HUMAN,H0YN47_HUMAN,H0YMX7_HUMAN,H0YMW3_HUMAN,H0YMF2_HUMAN,H0YKW2_HUMAN,H0YKQ6_HUMAN	UPI000015DCFD	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTATATACAC	.	2	ESCA
LACTB	0	.	GRCh37	15	63419078	63419078	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.445G>C	p.Glu149Gln	p.E149Q	ENST00000261893	3/6	62	59	3	81	81	0	LACTB,missense_variant,p.Glu149Gln,ENST00000261893,;LACTB,missense_variant,p.Glu149Gln,ENST00000413507,;LACTB,5_prime_UTR_variant,,ENST00000557972,;RPS27L,intron_variant,,ENST00000559763,;LACTB,upstream_gene_variant,,ENST00000559782,;	C	ENSG00000103642	ENST00000261893	Transcript	missense_variant	517	445	149	E/Q	Gag/Cag	.	.	.	1	LACTB	HGNC	16468	protein_coding	YES	CCDS10182.1	ENSP00000261893	LACTB_HUMAN	H0YNN5_HUMAN	UPI000013D220	.	deleterious(0)	probably_damaging(0.984)	3/6	.	hmmpanther:PTHR22935,hmmpanther:PTHR22935:SF64,Pfam_domain:PF00144,Gene3D:3.40.710.10,Superfamily_domains:SSF56601	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTTGAGAAC	.	2	ESCA
PPIB	0	.	GRCh37	15	64452363	64452363	+	Missense_Mutation	SNP	G	G	A	rs757275030	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283C>T	p.Arg95Cys	p.R95C	ENST00000300026	3/5	72	62	10	93	93	0	PPIB,missense_variant,p.Arg95Cys,ENST00000300026,;SNX22,downstream_gene_variant,,ENST00000325881,;PPIB,non_coding_transcript_exon_variant,,ENST00000558492,;PPIB,non_coding_transcript_exon_variant,,ENST00000561048,;SNX22,downstream_gene_variant,,ENST00000560997,;SNX22,downstream_gene_variant,,ENST00000557789,;SNX22,downstream_gene_variant,,ENST00000558466,;	A	ENSG00000166794	ENST00000300026	Transcript	missense_variant	502	283	95	R/C	Cgt/Tgt	rs757275030,COSM1374024	.	.	-1	PPIB	HGNC	9255	protein_coding	YES	CCDS10191.1	ENSP00000300026	PPIB_HUMAN	.	UPI0000072333	.	deleterious(0)	probably_damaging(0.999)	3/5	.	PROSITE_profiles:PS50072,hmmpanther:PTHR11071:SF63,hmmpanther:PTHR11071,PROSITE_patterns:PS00170,Gene3D:2.40.100.10,Pfam_domain:PF00160,Superfamily_domains:SSF50891,Prints_domain:PR00153	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACACGATGGA	byFrequency	4	ESCA
MAP2K5	0	.	GRCh37	15	67835662	67835662	+	5'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12C>G	.	.	ENST00000178640	1/22	49	42	6	98	98	0	MAP2K5,5_prime_UTR_variant,,ENST00000178640,;MAP2K5,upstream_gene_variant,,ENST00000395476,;RP11-502I4.3,upstream_gene_variant,,ENST00000604760,;MAP2K5,non_coding_transcript_exon_variant,,ENST00000560591,;MAP2K5,upstream_gene_variant,,ENST00000560086,;	G	ENSG00000137764	ENST00000178640	Transcript	5_prime_UTR_variant	616	.	.	.	.	.	.	.	1	MAP2K5	HGNC	6845	protein_coding	YES	CCDS10224.1	ENSP00000178640	MP2K5_HUMAN	H7BZL1_HUMAN	UPI0000072D4A	.	.	.	1/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCTCTTTAA	.	4	ESCA
SIN3A	0	.	GRCh37	15	75664135	75664135	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*185G>A	.	.	ENST00000394947	21/21	39	35	4	34	34	0	SIN3A,3_prime_UTR_variant,,ENST00000394949,;SIN3A,3_prime_UTR_variant,,ENST00000394947,;SIN3A,3_prime_UTR_variant,,ENST00000360439,;MAN2C1,upstream_gene_variant,,ENST00000566256,;MAN2C1,upstream_gene_variant,,ENST00000568374,;MAN2C1,upstream_gene_variant,,ENST00000565683,;MAN2C1,upstream_gene_variant,,ENST00000561615,;MAN2C1,upstream_gene_variant,,ENST00000563622,;MAN2C1,upstream_gene_variant,,ENST00000267978,;MAN2C1,upstream_gene_variant,,ENST00000569482,;RP11-817O13.8,downstream_gene_variant,,ENST00000563278,;MAN2C1,upstream_gene_variant,,ENST00000563539,;SIN3A,downstream_gene_variant,,ENST00000570124,;MAN2C1,upstream_gene_variant,,ENST00000421803,;MAN2C1,upstream_gene_variant,,ENST00000569069,;MAN2C1,upstream_gene_variant,,ENST00000565784,;SIN3A,downstream_gene_variant,,ENST00000566640,;MAN2C1,upstream_gene_variant,,ENST00000565534,;MAN2C1,upstream_gene_variant,,ENST00000565652,;MAN2C1,upstream_gene_variant,,ENST00000563441,;MAN2C1,upstream_gene_variant,,ENST00000569355,;MAN2C1,upstream_gene_variant,,ENST00000562071,;MAN2C1,upstream_gene_variant,,ENST00000566634,;	T	ENSG00000169375	ENST00000394947	Transcript	3_prime_UTR_variant	4322	.	.	.	.	.	.	.	-1	SIN3A	HGNC	19353	protein_coding	YES	CCDS10279.1	ENSP00000378402	SIN3A_HUMAN	H3BT34_HUMAN,H3BQ88_HUMAN,H3BQ76_HUMAN,H3BP90_HUMAN,H3BNZ3_HUMAN,H3BNA0_HUMAN	UPI000013EAD4	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTATTCATGTT	.	3	ESCA
PEAK1	0	.	GRCh37	15	77425505	77425505	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3919G>A	p.Asp1307Asn	p.D1307N	ENST00000560626	6/7	74	70	4	122	122	0	PEAK1,missense_variant,p.Asp1307Asn,ENST00000560626,;PEAK1,missense_variant,p.Asp1307Asn,ENST00000312493,;	T	ENSG00000173517	ENST00000560626	Transcript	missense_variant	4395	3919	1307	D/N	Gac/Aac	.	.	.	-1	PEAK1	HGNC	29431	protein_coding	YES	CCDS42062.1	ENSP00000452796	PEAK1_HUMAN	H3BUZ5_HUMAN,H3BUE6_HUMAN	UPI00002378D0	.	deleterious(0.01)	probably_damaging(0.998)	6/7	.	hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGTCTTCGC	.	2	ESCA
LINGO1	0	.	GRCh37	15	77907918	77907918	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331G>C	p.Glu111Gln	p.E111Q	ENST00000355300	2/2	39	34	4	43	43	0	LINGO1,missense_variant,p.Glu111Gln,ENST00000355300,;LINGO1,missense_variant,p.Glu105Gln,ENST00000567726,;LINGO1,missense_variant,p.Glu105Gln,ENST00000561030,;LINGO1,missense_variant,p.Glu105Gln,ENST00000561686,;LINGO1,missense_variant,p.Glu116Gln,ENST00000557798,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000566711,;LINGO1,downstream_gene_variant,,ENST00000564472,;	G	ENSG00000169783	ENST00000355300	Transcript	missense_variant	506	331	111	E/Q	Gag/Cag	COSM3816814	.	.	-1	LINGO1	HGNC	21205	protein_coding	YES	CCDS45313.1	ENSP00000347451	LIGO1_HUMAN	H3BQ49_HUMAN,H3BN48_HUMAN,H3BMW2_HUMAN,H3BMN3_HUMAN,H3BM59_HUMAN,H0YNK7_HUMAN	UPI00000377A0	.	deleterious(0)	probably_damaging(1)	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGCTCCACGG	.	3	ESCA
IL16	0	.	GRCh37	15	81558085	81558085	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.L169L	ENST00000302987	3/18	78	72	5	80	80	0	IL16,synonymous_variant,p.%3D,ENST00000302987,;IL16,synonymous_variant,p.%3D,ENST00000394660,;IL16,synonymous_variant,p.%3D,ENST00000559383,;IL16,synonymous_variant,p.%3D,ENST00000559388,;IL16,synonymous_variant,p.%3D,ENST00000560241,;IL16,synonymous_variant,p.%3D,ENST00000360547,;	T	ENSG00000172349	ENST00000302987	Transcript	synonymous_variant	507	507	169	L	ctC/ctT	.	.	.	1	IL16	HGNC	5980	protein_coding	YES	CCDS42069.1	ENSP00000302935	IL16_HUMAN	H0YLL1_HUMAN	UPI0000229CE7	.	.	.	3/18	.	hmmpanther:PTHR11324,hmmpanther:PTHR11324:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCTCTGCAG	.	2	ESCA
IL16	0	.	GRCh37	15	81561931	81561931	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617C>G	p.Ser206Cys	p.S206C	ENST00000302987	4/18	65	58	7	57	57	0	IL16,missense_variant,p.Ser206Cys,ENST00000302987,;IL16,missense_variant,p.Ser206Cys,ENST00000394660,;IL16,missense_variant,p.Ser206Cys,ENST00000559383,;IL16,missense_variant,p.Ser206Cys,ENST00000559388,;IL16,missense_variant,p.Ser206Cys,ENST00000560241,;IL16,missense_variant,p.Ser206Cys,ENST00000360547,;	G	ENSG00000172349	ENST00000302987	Transcript	missense_variant	617	617	206	S/C	tCt/tGt	.	.	.	1	IL16	HGNC	5980	protein_coding	YES	CCDS42069.1	ENSP00000302935	IL16_HUMAN	H0YLL1_HUMAN	UPI0000229CE7	.	tolerated(0.2)	possibly_damaging(0.867)	4/18	.	hmmpanther:PTHR11324,hmmpanther:PTHR11324:SF2,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCATCTGGGG	.	4	ESCA
IL16	0	.	GRCh37	15	81595959	81595959	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3388G>A	p.Gly1130Arg	p.G1130R	ENST00000302987	15/18	72	61	10	59	59	0	IL16,missense_variant,p.Gly434Arg,ENST00000558332,;IL16,missense_variant,p.Gly1130Arg,ENST00000394660,;IL16,missense_variant,p.Gly1084Arg,ENST00000559388,;IL16,missense_variant,p.Gly1130Arg,ENST00000302987,;IL16,missense_variant,p.Gly429Arg,ENST00000394652,;RP11-761I4.4,non_coding_transcript_exon_variant,,ENST00000607019,;IL16,non_coding_transcript_exon_variant,,ENST00000559342,;IL16,downstream_gene_variant,,ENST00000560230,;IL16,3_prime_UTR_variant,,ENST00000558857,;IL16,3_prime_UTR_variant,,ENST00000560115,;IL16,3_prime_UTR_variant,,ENST00000360547,;IL16,upstream_gene_variant,,ENST00000559953,;	A	ENSG00000172349	ENST00000302987	Transcript	missense_variant	3388	3388	1130	G/R	Gga/Aga	.	.	.	1	IL16	HGNC	5980	protein_coding	YES	CCDS42069.1	ENSP00000302935	IL16_HUMAN	H0YLL1_HUMAN	UPI0000229CE7	.	deleterious(0)	probably_damaging(1)	15/18	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50106,hmmpanther:PTHR11324,hmmpanther:PTHR11324:SF2,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156,Prints_domain:PR01931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCAGGAGGA	.	5	ESCA
KIF7	0	.	GRCh37	15	90193070	90193070	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431C>T	p.Ser144Phe	p.S144F	ENST00000394412	3/19	65	61	4	86	86	0	KIF7,missense_variant,p.Ser144Phe,ENST00000394412,;KIF7,3_prime_UTR_variant,,ENST00000445906,;	A	ENSG00000166813	ENST00000394412	Transcript	missense_variant	508	431	144	S/F	tCc/tTc	.	.	.	-1	KIF7	HGNC	30497	protein_coding	YES	CCDS32325.2	ENSP00000377934	KIF7_HUMAN	B7ZKY4_HUMAN	UPI00015F81C7	.	deleterious(0)	probably_damaging(1)	3/19	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF342,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGTAGGACACA	.	2	ESCA
IQGAP1	0	.	GRCh37	15	90992790	90992790	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1078-1G>C	.	p.X360_splice	ENST00000268182	.	51	48	3	53	53	0	IQGAP1,splice_acceptor_variant,,ENST00000268182,;IQGAP1,intron_variant,,ENST00000560738,;	C	ENSG00000140575	ENST00000268182	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	IQGAP1	HGNC	6110	protein_coding	YES	CCDS10362.1	ENSP00000268182	IQGA1_HUMAN	H0YKA5_HUMAN	UPI000012D863	.	.	.	.	10/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCAGAGTGG	.	2	ESCA
BLM	0	.	GRCh37	15	91292721	91292721	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.223G>A	p.Glu75Lys	p.E75K	ENST00000355112	3/22	85	80	5	94	94	0	BLM,missense_variant,p.Glu75Lys,ENST00000560509,;BLM,missense_variant,p.Glu75Lys,ENST00000355112,;BLM,non_coding_transcript_exon_variant,,ENST00000559282,;BLM,upstream_gene_variant,,ENST00000558599,;BLM,missense_variant,p.Glu75Lys,ENST00000559724,;	A	ENSG00000197299	ENST00000355112	Transcript	missense_variant	341	223	75	E/K	Gaa/Aaa	.	.	.	1	BLM	HGNC	1058	protein_coding	YES	CCDS10363.1	ENSP00000347232	BLM_HUMAN	.	UPI00001269FA	.	tolerated(0.47)	benign(0.026)	3/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TCAGTGAACCT	.	2	ESCA
LITAF	0	.	GRCh37	16	11643480	11643480	+	3'UTR	SNP	G	G	A	rs199839533	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13C>T	.	.	ENST00000571688	4/4	47	40	6	77	77	0	LITAF,missense_variant,p.Thr167Met,ENST00000381810,;LITAF,3_prime_UTR_variant,,ENST00000413364,;LITAF,3_prime_UTR_variant,,ENST00000339430,;LITAF,3_prime_UTR_variant,,ENST00000571459,;LITAF,3_prime_UTR_variant,,ENST00000571688,;LITAF,3_prime_UTR_variant,,ENST00000570904,;LITAF,3_prime_UTR_variant,,ENST00000576036,;LITAF,3_prime_UTR_variant,,ENST00000572255,;LITAF,downstream_gene_variant,,ENST00000574763,;LITAF,downstream_gene_variant,,ENST00000570798,;LITAF,downstream_gene_variant,,ENST00000574701,;LITAF,downstream_gene_variant,,ENST00000571976,;LITAF,downstream_gene_variant,,ENST00000571627,;LITAF,3_prime_UTR_variant,,ENST00000575426,;LITAF,3_prime_UTR_variant,,ENST00000573332,;	A	ENSG00000189067	ENST00000571688	Transcript	3_prime_UTR_variant	730	.	.	.	.	rs199839533	.	.	-1	LITAF	HGNC	16841	protein_coding	YES	CCDS32386.1	ENSP00000459533	LITAF_HUMAN	I3L3U8_HUMAN,I3L329_HUMAN,I3L1R0_HUMAN,I3L1I9_HUMAN,I3L1H3_HUMAN	UPI000007094D	.	.	.	4/4	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCACGTCTGG	byCluster|by1000G	4	ESCA
CRYM	0	.	GRCh37	16	21289590	21289590	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-18G>A	.	.	ENST00000219599	3/10	124	114	10	164	164	0	CRYM,5_prime_UTR_variant,,ENST00000396023,;CRYM,5_prime_UTR_variant,,ENST00000571358,;CRYM,5_prime_UTR_variant,,ENST00000219599,;CRYM,5_prime_UTR_variant,,ENST00000572914,;CRYM,5_prime_UTR_variant,,ENST00000543948,;CRYM,5_prime_UTR_variant,,ENST00000415987,;CRYM,intron_variant,,ENST00000576703,;CRYM,downstream_gene_variant,,ENST00000574787,;CRYM,5_prime_UTR_variant,,ENST00000574448,;CRYM,upstream_gene_variant,,ENST00000571666,;	T	ENSG00000103316	ENST00000219599	Transcript	5_prime_UTR_variant	249	.	.	.	.	.	.	.	-1	CRYM	HGNC	2418	protein_coding	YES	CCDS10597.1	ENSP00000219599	CRYM_HUMAN	I3NI53_HUMAN,I3L3J9_HUMAN,I3L325_HUMAN,H9KVC2_HUMAN	UPI00001284E5	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCTAACC	.	2	ESCA
CRYM	0	.	GRCh37	16	21289597	21289597	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25G>A	.	.	ENST00000219599	3/10	118	109	8	160	160	0	CRYM,5_prime_UTR_variant,,ENST00000396023,;CRYM,5_prime_UTR_variant,,ENST00000571358,;CRYM,5_prime_UTR_variant,,ENST00000219599,;CRYM,5_prime_UTR_variant,,ENST00000572914,;CRYM,5_prime_UTR_variant,,ENST00000543948,;CRYM,5_prime_UTR_variant,,ENST00000415987,;CRYM,intron_variant,,ENST00000576703,;CRYM,downstream_gene_variant,,ENST00000574787,;CRYM,upstream_gene_variant,,ENST00000571666,;CRYM,upstream_gene_variant,,ENST00000574448,;	T	ENSG00000103316	ENST00000219599	Transcript	5_prime_UTR_variant	242	.	.	.	.	.	.	.	-1	CRYM	HGNC	2418	protein_coding	YES	CCDS10597.1	ENSP00000219599	CRYM_HUMAN	I3NI53_HUMAN,I3L3J9_HUMAN,I3L325_HUMAN,H9KVC2_HUMAN	UPI00001284E5	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACCTCAGTCT	.	2	ESCA
NPIPB4	0	.	GRCh37	16	21858850	21858850	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.133C>G	p.Leu45Val	p.L45V	ENST00000415645	2/9	262	235	27	373	373	0	NPIPB4,missense_variant,p.Leu45Val,ENST00000357370,;NPIPB4,missense_variant,p.Leu45Val,ENST00000415645,;NPIPB4,missense_variant,p.Leu45Val,ENST00000518761,;NPIPB4,missense_variant,p.Leu45Val,ENST00000341400,;NPIPB4,missense_variant,p.Leu26Val,ENST00000543654,;NPIPB4,5_prime_UTR_variant,,ENST00000451409,;NPIPB4,non_coding_transcript_exon_variant,,ENST00000539318,;NPIPB4,non_coding_transcript_exon_variant,,ENST00000539191,;NPIPB4,non_coding_transcript_exon_variant,,ENST00000542338,;NPIPB4,upstream_gene_variant,,ENST00000165086,;NPIPB4,upstream_gene_variant,,ENST00000541329,;NPIPB4,downstream_gene_variant,,ENST00000540103,;NPIPB4,3_prime_UTR_variant,,ENST00000542133,;NPIPB4,3_prime_UTR_variant,,ENST00000529969,;NPIPB4,3_prime_UTR_variant,,ENST00000536041,;NPIPB4,3_prime_UTR_variant,,ENST00000520808,;NPIPB4,upstream_gene_variant,,ENST00000543660,;	C	ENSG00000185864	ENST00000415645	Transcript	missense_variant	173	133	45	L/V	Ctg/Gtg	.	.	.	-1	NPIPB4	HGNC	41985	protein_coding	YES	.	ENSP00000404439	NPIB4_HUMAN	U3KRG3_HUMAN,H3BQU5_HUMAN,F5H8A1_HUMAN,F5H6Y6_HUMAN,F5H5F2_HUMAN,F5H3W2_HUMAN,F5GYP3_HUMAN,F5GWQ4_HUMAN,E7EQW1_HUMAN,C9JB18_HUMAN	UPI00020651A0	.	.	possibly_damaging(0.672)	2/9	.	hmmpanther:PTHR15438,hmmpanther:PTHR15438:SF1,Pfam_domain:PF06409	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCAGAGTAT	.	4	ESCA
ITGAM	0	.	GRCh37	16	31341910	31341910	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3263C>T	p.Ala1088Val	p.A1088V	ENST00000544665	28/30	55	49	6	47	47	0	ITGAM,missense_variant,p.Ala1087Val,ENST00000287497,;ITGAM,missense_variant,p.Ala1088Val,ENST00000544665,;ITGAM,missense_variant,p.Ala43Val,ENST00000565142,;ITGAM,downstream_gene_variant,,ENST00000569746,;ITGAM,downstream_gene_variant,,ENST00000567178,;ITGAM,downstream_gene_variant,,ENST00000561838,;	T	ENSG00000169896	ENST00000544665	Transcript	missense_variant	3334	3263	1088	A/V	gCg/gTg	.	.	.	1	ITGAM	HGNC	6149	protein_coding	YES	CCDS54004.1	ENSP00000441691	ITAM_HUMAN	B3KXM6_HUMAN	UPI000004B26A	.	deleterious(0.05)	benign(0.009)	28/30	.	hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Superfamily_domains:SSF69179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGGCGTTTG	.	4	ESCA
RP11-80F22.9	0	.	GRCh37	16	34713056	34713056	+	RNA	SNP	G	G	C	rs756469389	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.299C>G	.	.	ENST00000569028	2/2	17	14	3	15	15	0	RP11-80F22.9,non_coding_transcript_exon_variant,,ENST00000564452,;RP11-80F22.9,non_coding_transcript_exon_variant,,ENST00000569028,;RP11-80F22.9,non_coding_transcript_exon_variant,,ENST00000566967,;	C	ENSG00000261711	ENST00000569028	Transcript	non_coding_transcript_exon_variant	299	.	.	.	.	rs756469389	.	.	-1	RP11-80F22.9	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGCTCGACTCT	.	4	ESCA
CPNE2	0	.	GRCh37	16	57171066	57171066	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1174G>C	p.Asp392His	p.D392H	ENST00000535318	15/17	115	103	12	101	101	0	CPNE2,missense_variant,p.Asp392His,ENST00000565874,;CPNE2,missense_variant,p.Asp392His,ENST00000535318,;CPNE2,missense_variant,p.Asp392His,ENST00000290776,;CPNE2,missense_variant,p.Asp251His,ENST00000565766,;CPNE2,missense_variant,p.Asp290His,ENST00000537605,;CPNE2,non_coding_transcript_exon_variant,,ENST00000566910,;CPNE2,intron_variant,,ENST00000565951,;CPNE2,intron_variant,,ENST00000566042,;	C	ENSG00000140848	ENST00000535318	Transcript	missense_variant	1535	1174	392	D/H	Gat/Cat	.	.	.	1	CPNE2	HGNC	2315	protein_coding	YES	CCDS10774.1	ENSP00000439018	CPNE2_HUMAN	Q719H8_HUMAN,H3BQQ3_HUMAN,H3BPR8_HUMAN	UPI000017DA4F	.	deleterious(0)	possibly_damaging(0.722)	15/17	.	hmmpanther:PTHR10857:SF3,hmmpanther:PTHR10857,Pfam_domain:PF07002,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTGGATGGT	.	4	ESCA
SLC38A7	0	.	GRCh37	16	58713919	58713919	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.112G>A	p.Glu38Lys	p.E38K	ENST00000570101	2/11	41	32	9	64	64	0	SLC38A7,missense_variant,p.Glu38Lys,ENST00000563196,;SLC38A7,missense_variant,p.Glu38Lys,ENST00000564391,;SLC38A7,missense_variant,p.Glu38Lys,ENST00000219320,;SLC38A7,missense_variant,p.Glu38Lys,ENST00000562397,;SLC38A7,missense_variant,p.Glu38Lys,ENST00000564100,;SLC38A7,missense_variant,p.Glu38Lys,ENST00000570101,;SLC38A7,intron_variant,,ENST00000564010,;SLC38A7,intron_variant,,ENST00000570214,;SLC38A7,intron_variant,,ENST00000566953,;SLC38A7,downstream_gene_variant,,ENST00000567930,;SLC38A7,missense_variant,p.Glu38Lys,ENST00000566598,;SLC38A7,non_coding_transcript_exon_variant,,ENST00000562149,;SLC38A7,downstream_gene_variant,,ENST00000564964,;SLC38A7,downstream_gene_variant,,ENST00000564720,;SLC38A7,upstream_gene_variant,,ENST00000565785,;SLC38A7,upstream_gene_variant,,ENST00000569209,;	T	ENSG00000103042	ENST00000570101	Transcript	missense_variant	996	112	38	E/K	Gag/Aag	.	.	.	-1	SLC38A7	HGNC	25582	protein_coding	YES	CCDS10800.1	ENSP00000454646	S38A7_HUMAN	H3BRZ0_HUMAN,H3BPV9_HUMAN,H3BPK8_HUMAN,H3BN87_HUMAN	UPI000004EC72	.	tolerated(0.26)	benign(0.031)	2/11	.	hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTCACTCT	.	5	ESCA
CKLF	0	.	GRCh37	16	66600077	66600077	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000264001	.	37	32	4	36	36	0	CKLF,3_prime_UTR_variant,,ENST00000417030,;CKLF-CMTM1,3_prime_UTR_variant,,ENST00000532838,;CKLF-CMTM1,intron_variant,,ENST00000527729,;CKLF-CMTM1,intron_variant,,ENST00000529718,;CMTM1,upstream_gene_variant,,ENST00000379500,;CKLF,downstream_gene_variant,,ENST00000351137,;CKLF,downstream_gene_variant,,ENST00000264001,;CMTM1,upstream_gene_variant,,ENST00000533953,;CMTM1,upstream_gene_variant,,ENST00000332695,;CKLF,downstream_gene_variant,,ENST00000345436,;CMTM1,upstream_gene_variant,,ENST00000533666,;CMTM1,upstream_gene_variant,,ENST00000336328,;CMTM1,upstream_gene_variant,,ENST00000457188,;CKLF,downstream_gene_variant,,ENST00000362093,;CMTM1,upstream_gene_variant,,ENST00000528324,;CMTM1,upstream_gene_variant,,ENST00000531885,;CMTM1,upstream_gene_variant,,ENST00000529506,;CMTM1,upstream_gene_variant,,ENST00000328020,;CMTM1,upstream_gene_variant,,ENST00000535705,;CKLF,downstream_gene_variant,,ENST00000563092,;CKLF,3_prime_UTR_variant,,ENST00000534692,;CKLF-CMTM1,intron_variant,,ENST00000527845,;CMTM1,upstream_gene_variant,,ENST00000533078,;CMTM1,upstream_gene_variant,,ENST00000528441,;CMTM1,upstream_gene_variant,,ENST00000533915,;CMTM1,upstream_gene_variant,,ENST00000333001,;CMTM1,upstream_gene_variant,,ENST00000530141,;CMTM1,upstream_gene_variant,,ENST00000528484,;CMTM1,upstream_gene_variant,,ENST00000465057,;CMTM1,upstream_gene_variant,,ENST00000529386,;CMTM1,upstream_gene_variant,,ENST00000479381,;CMTM1,upstream_gene_variant,,ENST00000534143,;	A	ENSG00000217555	ENST00000264001	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	102	1	CKLF	HGNC	13253	protein_coding	YES	CCDS10807.1	ENSP00000264001	CKLF_HUMAN	.	UPI0000036209	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGGGAGCAG	.	4	ESCA
NFAT5	0	.	GRCh37	16	69600040	69600040	+	5'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-165C>G	.	.	ENST00000432919	1/15	10	7	3	11	11	0	NFAT5,5_prime_UTR_variant,,ENST00000567239,;NFAT5,5_prime_UTR_variant,,ENST00000432919,;NFAT5,5_prime_UTR_variant,,ENST00000354436,;NFAT5,5_prime_UTR_variant,,ENST00000349945,;NFAT5,upstream_gene_variant,,ENST00000393742,;NFAT5,upstream_gene_variant,,ENST00000566899,;MIR1538,upstream_gene_variant,,ENST00000411177,;NFAT5,5_prime_UTR_variant,,ENST00000426654,;NFAT5,5_prime_UTR_variant,,ENST00000567990,;	G	ENSG00000102908	ENST00000432919	Transcript	5_prime_UTR_variant	1044	.	.	.	.	.	.	.	1	NFAT5	HGNC	7774	protein_coding	YES	CCDS45518.1	ENSP00000396538	NFAT5_HUMAN	.	UPI000049DE1B	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCGGTCC	.	2	ESCA
PDPR	0	.	GRCh37	16	70154466	70154466	+	Missense_Mutation	SNP	C	C	T	rs368906299	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71C>T	p.Ser24Phe	p.S24F	ENST00000288050	3/19	93	84	8	62	62	0	PDPR,missense_variant,p.Ser24Phe,ENST00000288050,;PDPR,missense_variant,p.Ser24Phe,ENST00000568530,;PDPR,intron_variant,,ENST00000398122,;PDPR,missense_variant,p.Ser24Phe,ENST00000565186,;PDPR,non_coding_transcript_exon_variant,,ENST00000561920,;	T	ENSG00000090857	ENST00000288050	Transcript	missense_variant	1028	71	24	S/F	tCt/tTt	rs368906299	.	.	1	PDPR	HGNC	30264	protein_coding	YES	CCDS45520.1	ENSP00000288050	PDPR_HUMAN	H3BV59_HUMAN,H3BU60_HUMAN,B7ZAR9_HUMAN,B3KSE1_HUMAN,A8MT40_HUMAN	UPI00001FF513	.	tolerated(0.22)	benign(0.068)	3/19	.	hmmpanther:PTHR13847:SF146,hmmpanther:PTHR13847	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCCTCTGCAA	byFrequency|byCluster	3	ESCA
COG4	0	.	GRCh37	16	70551570	70551570	+	Nonsense_Mutation	SNP	C	C	A	rs778505582	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.328G>T	p.Glu110Ter	p.E110*	ENST00000323786	3/19	51	46	5	56	56	0	COG4,stop_gained,p.Glu106Ter,ENST00000393612,;COG4,stop_gained,p.Glu110Ter,ENST00000564653,;COG4,stop_gained,p.Glu110Ter,ENST00000323786,;COG4,stop_gained,p.Glu33Ter,ENST00000534772,;COG4,stop_gained,p.Glu106Ter,ENST00000482252,;COG4,stop_gained,p.Glu110Ter,ENST00000564415,;COG4,3_prime_UTR_variant,,ENST00000524584,;COG4,non_coding_transcript_exon_variant,,ENST00000562200,;COG4,non_coding_transcript_exon_variant,,ENST00000530314,;COG4,intron_variant,,ENST00000530160,;	A	ENSG00000103051	ENST00000323786	Transcript	stop_gained	350	328	110	E/*	Gag/Tag	rs778505582,COSM1293621	.	.	-1	COG4	HGNC	18620	protein_coding	YES	CCDS10892.2	ENSP00000315775	.	J3KRB5_HUMAN,J3KNI1_HUMAN,B4DDL2_HUMAN	UPI000059D3B0	.	.	.	3/19	.	hmmpanther:PTHR24016:SF0,hmmpanther:PTHR24016	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTCTCAGCCA	byFrequency	4	ESCA
MLKL	0	.	GRCh37	16	74725292	74725292	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.605C>T	p.Ser202Leu	p.S202L	ENST00000308807	4/11	101	86	14	79	79	0	MLKL,missense_variant,p.Ser202Leu,ENST00000573267,;MLKL,missense_variant,p.Ser202Leu,ENST00000308807,;MLKL,intron_variant,,ENST00000306247,;MLKL,downstream_gene_variant,,ENST00000575686,;MLKL,missense_variant,p.Ser26Leu,ENST00000571303,;	A	ENSG00000168404	ENST00000308807	Transcript	missense_variant	1069	605	202	S/L	tCa/tTa	.	.	.	-1	MLKL	HGNC	26617	protein_coding	YES	CCDS32487.1	ENSP00000308351	MLKL_HUMAN	I3L4Z5_HUMAN,I3L2T9_HUMAN	UPI000004073C	.	tolerated(0.25)	benign(0.003)	4/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF347,Gene3D:3.30.200.20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCCTGAAAGC	.	4	ESCA
MYH1	0	.	GRCh37	17	10416983	10416983	+	Silent	SNP	G	G	A	rs565550881	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.765C>T	p.%3D	p.F255F	ENST00000226207	9/40	65	56	8	69	69	0	MYH1,synonymous_variant,p.%3D,ENST00000226207,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	A	ENSG00000109061	ENST00000226207	Transcript	synonymous_variant	860	765	255	F	ttC/ttT	rs565550881,COSM1479217	.	.	-1	MYH1	HGNC	7567	protein_coding	YES	CCDS11155.1	ENSP00000226207	MYH1_HUMAN	.	UPI000013C891	.	.	.	9/40	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF264,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540,Prints_domain:PR00193	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTACCGAAGTG	by1000G	4	ESCA
NCOR1	0	.	GRCh37	17	15995266	15995266	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2927A>C	p.Gln976Pro	p.Q976P	ENST00000268712	22/46	62	54	8	56	56	0	NCOR1,missense_variant,p.Gln883Pro,ENST00000395848,;NCOR1,missense_variant,p.Gln992Pro,ENST00000395851,;NCOR1,missense_variant,p.Gln976Pro,ENST00000268712,;NCOR1,upstream_gene_variant,,ENST00000436068,;	G	ENSG00000141027	ENST00000268712	Transcript	missense_variant	3185	2927	976	Q/P	cAg/cCg	.	.	.	-1	NCOR1	HGNC	7672	protein_coding	YES	CCDS11175.1	ENSP00000268712	NCOR1_HUMAN	Q9NSZ0_HUMAN,C9JAP0_HUMAN,B4DJ25_HUMAN	UPI000013D7D5	.	.	probably_damaging(0.99)	22/46	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCGCTGCTCC	.	4	ESCA
MED1	0	.	GRCh37	17	37565965	37565965	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2509G>C	p.Asp837His	p.D837H	ENST00000300651	17/17	34	30	4	51	51	0	MED1,missense_variant,p.Asp837His,ENST00000300651,;MED1,intron_variant,,ENST00000394287,;CTB-131K11.1,downstream_gene_variant,,ENST00000582842,;MED1,3_prime_UTR_variant,,ENST00000577831,;	G	ENSG00000125686	ENST00000300651	Transcript	missense_variant	2733	2509	837	D/H	Gat/Cat	.	.	.	-1	MED1	HGNC	9234	protein_coding	YES	CCDS11336.1	ENSP00000300651	MED1_HUMAN	.	UPI0000167F57	.	deleterious_low_confidence(0)	probably_damaging(0.999)	17/17	.	hmmpanther:PTHR12881	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGATCAGTGT	.	4	ESCA
KANSL1	0	.	GRCh37	17	44109060	44109060	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3100C>T	p.Pro1034Ser	p.P1034S	ENST00000262419	15/15	55	48	6	65	65	0	KANSL1,missense_variant,p.Pro328Ser,ENST00000393476,;KANSL1,missense_variant,p.Pro1034Ser,ENST00000574590,;KANSL1,missense_variant,p.Pro970Ser,ENST00000575318,;KANSL1,missense_variant,p.Pro1034Ser,ENST00000432791,;KANSL1,missense_variant,p.Pro1034Ser,ENST00000262419,;KANSL1,missense_variant,p.Pro1034Ser,ENST00000572904,;MAPT,downstream_gene_variant,,ENST00000340799,;MAPT,downstream_gene_variant,,ENST00000262410,;MAPT,downstream_gene_variant,,ENST00000446361,;MAPT,downstream_gene_variant,,ENST00000535772,;MAPT,downstream_gene_variant,,ENST00000351559,;MAPT,downstream_gene_variant,,ENST00000344290,;MAPT,downstream_gene_variant,,ENST00000347967,;RP11-669E14.6,upstream_gene_variant,,ENST00000570454,;KANSL1,non_coding_transcript_exon_variant,,ENST00000574963,;KANSL1,non_coding_transcript_exon_variant,,ENST00000572218,;KANSL1,non_coding_transcript_exon_variant,,ENST00000576870,;KANSL1,downstream_gene_variant,,ENST00000576137,;KANSL1,downstream_gene_variant,,ENST00000573682,;	A	ENSG00000120071	ENST00000262419	Transcript	missense_variant	3571	3100	1034	P/S	Ccc/Tcc	.	.	.	-1	KANSL1	HGNC	24565	protein_coding	YES	CCDS11503.1	ENSP00000262419	KANL1_HUMAN	I3L243_HUMAN,I3L233_HUMAN	UPI0001AE66EA	.	deleterious(0)	probably_damaging(1)	15/15	.	hmmpanther:PTHR22443:SF14,hmmpanther:PTHR22443,Pfam_domain:PF15275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGGGCTGGA	.	4	ESCA
ABI3	0	.	GRCh37	17	47299509	47299509	+	Missense_Mutation	SNP	G	G	A	rs199538050	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.859G>A	p.Glu287Lys	p.E287K	ENST00000225941	7/8	70	64	6	76	76	0	ABI3,missense_variant,p.Glu281Lys,ENST00000419580,;ABI3,missense_variant,p.Glu287Lys,ENST00000225941,;ABI3,missense_variant,p.Glu112Lys,ENST00000571035,;ABI3,missense_variant,p.Glu133Lys,ENST00000573347,;PHOSPHO1,downstream_gene_variant,,ENST00000574638,;PHOSPHO1,downstream_gene_variant,,ENST00000503902,;PHOSPHO1,downstream_gene_variant,,ENST00000413580,;PHOSPHO1,downstream_gene_variant,,ENST00000514112,;PHOSPHO1,downstream_gene_variant,,ENST00000512250,;PHOSPHO1,downstream_gene_variant,,ENST00000511066,;PHOSPHO1,downstream_gene_variant,,ENST00000310544,;	A	ENSG00000108798	ENST00000225941	Transcript	missense_variant	1357	859	287	E/K	Gaa/Aaa	rs199538050	.	.	1	ABI3	HGNC	29859	protein_coding	YES	CCDS11546.1	ENSP00000225941	ABI3_HUMAN	.	UPI000013C888	.	tolerated(0.71)	benign(0.292)	7/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10460:SF6,hmmpanther:PTHR10460	A:0.0004	A:0	A:0.0029	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGATGAATTG	byFrequency|byCluster|by1000G	2	ESCA
COL1A1	0	.	GRCh37	17	48261771	48261771	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1092C>G	.	.	ENST00000225964	51/51	119	97	22	167	167	0	COL1A1,3_prime_UTR_variant,,ENST00000225964,;HILS1,upstream_gene_variant,,ENST00000504307,;COL1A1,downstream_gene_variant,,ENST00000511732,;COL1A1,downstream_gene_variant,,ENST00000510710,;COL1A1,downstream_gene_variant,,ENST00000486572,;	C	ENSG00000108821	ENST00000225964	Transcript	3_prime_UTR_variant	5606	.	.	.	.	.	.	.	-1	COL1A1	HGNC	2197	protein_coding	YES	CCDS11561.1	ENSP00000225964	CO1A1_HUMAN	Q9UMA6_HUMAN,Q6LAN8_HUMAN	UPI000013C88B	.	.	.	51/51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTGGAGCCG	.	5	ESCA
MPO	0	.	GRCh37	17	56349125	56349125	+	Missense_Mutation	SNP	C	C	G	rs763078734	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1921G>C	p.Asp641His	p.D641H	ENST00000225275	11/12	64	45	19	68	68	0	MPO,missense_variant,p.Asp673His,ENST00000340482,;MPO,missense_variant,p.Asp641His,ENST00000225275,;MPO,intron_variant,,ENST00000577220,;LPO,downstream_gene_variant,,ENST00000421678,;LPO,downstream_gene_variant,,ENST00000262290,;LPO,downstream_gene_variant,,ENST00000543544,;LPO,downstream_gene_variant,,ENST00000582328,;MPO,downstream_gene_variant,,ENST00000578493,;LPO,downstream_gene_variant,,ENST00000580890,;LPO,downstream_gene_variant,,ENST00000389576,;	G	ENSG00000005381	ENST00000225275	Transcript	missense_variant	2098	1921	641	D/H	Gac/Cac	rs763078734,COSM981779	.	.	-1	MPO	HGNC	7218	protein_coding	YES	CCDS11604.1	ENSP00000225275	PERM_HUMAN	.	UPI0000131634	.	deleterious(0)	probably_damaging(0.999)	11/12	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF46,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGTCGATGT	.	5	ESCA
MTMR4	0	.	GRCh37	17	56585555	56585555	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.632G>A	p.Arg211His	p.R211H	ENST00000323456	8/19	65	56	8	64	64	0	MTMR4,missense_variant,p.Arg211His,ENST00000323456,;MTMR4,missense_variant,p.Arg211His,ENST00000579925,;MTMR4,downstream_gene_variant,,ENST00000583243,;MTMR4,downstream_gene_variant,,ENST00000583656,;MTMR4,downstream_gene_variant,,ENST00000579921,;MTMR4,3_prime_UTR_variant,,ENST00000582663,;MTMR4,non_coding_transcript_exon_variant,,ENST00000580983,;MTMR4,downstream_gene_variant,,ENST00000582390,;MTMR4,downstream_gene_variant,,ENST00000583966,;	T	ENSG00000108389	ENST00000323456	Transcript	missense_variant	757	632	211	R/H	cGc/cAc	.	.	.	-1	MTMR4	HGNC	7452	protein_coding	YES	CCDS11608.1	ENSP00000325285	MTMR4_HUMAN	J3QRJ2_HUMAN	UPI00002010DE	.	deleterious(0)	probably_damaging(1)	8/19	.	PROSITE_profiles:PS51339,hmmpanther:PTHR10807:SF64,hmmpanther:PTHR10807,Pfam_domain:PF06602,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGAGCGGAAG	.	4	ESCA
PRPSAP1	0	.	GRCh37	17	74326692	74326692	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.519C>T	p.%3D	p.F173F	ENST00000446526	5/10	80	63	17	112	111	0	PRPSAP1,synonymous_variant,p.%3D,ENST00000324684,;PRPSAP1,synonymous_variant,p.%3D,ENST00000435555,;PRPSAP1,synonymous_variant,p.%3D,ENST00000423915,;PRPSAP1,synonymous_variant,p.%3D,ENST00000446526,;PRPSAP1,synonymous_variant,p.%3D,ENST00000436498,;PRPSAP1,downstream_gene_variant,,ENST00000442767,;PRPSAP1,non_coding_transcript_exon_variant,,ENST00000494662,;PRPSAP1,upstream_gene_variant,,ENST00000472686,;PRPSAP1,upstream_gene_variant,,ENST00000488339,;PRPSAP1,upstream_gene_variant,,ENST00000586137,;	A	ENSG00000161542	ENST00000446526	Transcript	synonymous_variant	965	519	173	F	ttC/ttT	.	.	.	-1	PRPSAP1	HGNC	9466	protein_coding	YES	CCDS11743.2	ENSP00000414624	KPRA_HUMAN	C9JUN4_HUMAN,C9JKT9_HUMAN,C9J168_HUMAN,B4DP31_HUMAN	UPI0000D4D88C	.	.	.	5/10	.	Superfamily_domains:SSF53271,TIGRFAM_domain:TIGR01251,Gene3D:3.40.50.2020,hmmpanther:PTHR10210,hmmpanther:PTHR10210:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTGAAAAA	.	5	ESCA
TP53	0	.	GRCh37	17	7578235	7578235	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	6/11	69	56	13	116	116	0	TP53,missense_variant,p.Tyr205Cys,ENST00000413465,;TP53,missense_variant,p.Tyr205Cys,ENST00000420246,;TP53,missense_variant,p.Tyr205Cys,ENST00000269305,;TP53,missense_variant,p.Tyr73Cys,ENST00000509690,;TP53,missense_variant,p.Tyr205Cys,ENST00000359597,;TP53,missense_variant,p.Tyr112Cys,ENST00000514944,;TP53,missense_variant,p.Tyr205Cys,ENST00000445888,;TP53,missense_variant,p.Tyr205Cys,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	804	614	205	Y/C	tAt/tGt	TP53_g.12683A>T,TP53_g.12683A>C,TP53_g.12683A>G,COSM43947,COSM44169,COSM11351,COSM99633,COSM215720,COSM99630,COSM215719,COSM99631,COSM215721,COSM3378351,COSM3421935,COSM3421934,COSM1649393,COSM99632,COSM215722	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.99)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Y73C|c.218A>G|19,SITE|p.Y112C|c.335A>G|18,SITE|p.Y205C|c.614A>G|17,SITE|p.Y205C|c.614A>G|5,SITE|p.Y205C|c.614A>G|72,SITE|p.Y205C|c.614A>G|18,SITE|p.Y205C|c.614A>G|8,CODON|p.0?|c.1_1182del1182|6,CODON|p.Y112S|c.335A>C|3,CODON|p.Y205S|c.614A>C|3,CODON|p.Y205F|c.614A>T|7,CODON|p.Y205S|c.614A>C|14,CODON|p.Y205S|c.614A>C|3,CODON|p.Y73S|c.218A>C|3,CODON|p.Y205fs*4|c.613_614insC|4,CODON|p.Y112fs*4|c.334_335insC|4,CODON|p.Y73fs*4|c.217_218insC|4,CODON|p.Y205fs*4|c.613_614insC|4,CODON|p.Y205fs*4|c.613_614insC|4,CODON|p.Y205fs*4|c.613_614insC|4,BUFFER|p.R209fs*6|c.625_626delAG|23,BUFFER|p.R209*|c.625A>T|4,BUFFER|p.R116*|c.346A>T|4,BUFFER|p.R209*|c.625A>T|4,BUFFER|p.R209*|c.625A>T|14,BUFFER|p.R77*|c.229A>T|4,BUFFER|p.D208E|c.624C>G|3,BUFFER|p.D208V|c.623A>T|14,BUFFER|p.D208G|c.623A>G|5,BUFFER|p.D207G|c.620A>G|4,BUFFER|p.L206fs*41|c.617delT|4,BUFFER|p.L206*|c.617T>A|9,BUFFER|p.Y205N|c.613T>A|5,BUFFER|p.Y205N|c.613T>A|3,BUFFER|p.Y112N|c.334T>A|3,BUFFER|p.Y205H|c.613T>C|6,BUFFER|p.Y205D|c.613T>G|14,BUFFER|p.Y73N|c.217T>A|3,BUFFER|p.E204fs*43|c.610delG|3,BUFFER|p.E204*|c.610G>T|3,BUFFER|p.E72*|c.214G>T|10,BUFFER|p.E204*|c.610G>T|32,BUFFER|p.E111*|c.331G>T|9,BUFFER|p.E204*|c.610G>T|9,BUFFER|p.E204*|c.610G>T|9,BUFFER|p.E204*|c.610G>T|4,BUFFER|p.V203V|c.609G>T|3,BUFFER|p.V203E|c.608T>A|6,BUFFER|p.V203L|c.607G>T|4,BUFFER|p.R202L|c.605G>T|3,BUFFER|p.R202H|c.605G>A|4,BUFFER|p.R202C|c.604C>T|4,BUFFER|p.R202S|c.604C>A|6,BUFFER|p.L201F|c.603G>T|3,BUFFER|p.L201F|c.603G>C|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAATACTCC	.	5	ESCA
NPTX1	0	.	GRCh37	17	78445639	78445639	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.970G>A	p.Gly324Arg	p.G324R	ENST00000306773	4/5	99	89	9	117	116	0	NPTX1,missense_variant,p.Gly324Arg,ENST00000306773,;NPTX1,downstream_gene_variant,,ENST00000575212,;NPTX1,non_coding_transcript_exon_variant,,ENST00000535681,;NPTX1,downstream_gene_variant,,ENST00000571100,;	T	ENSG00000171246	ENST00000306773	Transcript	missense_variant	1128	970	324	G/R	Ggg/Agg	.	.	.	-1	NPTX1	HGNC	7952	protein_coding	YES	CCDS32762.1	ENSP00000307549	NPTX1_HUMAN	.	UPI000013EB88	.	deleterious(0)	probably_damaging(0.997)	4/5	.	hmmpanther:PTHR19277,hmmpanther:PTHR19277:SF24,Pfam_domain:PF00354,Gene3D:2.60.120.200,SMART_domains:SM00159,Superfamily_domains:SSF49899,Prints_domain:PR00895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACCCCGTCCC	.	3	ESCA
PSMG2	0	.	GRCh37	18	12725469	12725469	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734G>C	p.Trp245Ser	p.W245S	ENST00000317615	7/7	126	110	15	146	146	0	PSMG2,missense_variant,p.Trp214Ser,ENST00000585331,;PSMG2,missense_variant,p.Trp245Ser,ENST00000317615,;PSMG2,downstream_gene_variant,,ENST00000590217,;PSMG2,downstream_gene_variant,,ENST00000586445,;PSMG2,3_prime_UTR_variant,,ENST00000586587,;PSMG2,non_coding_transcript_exon_variant,,ENST00000588824,;	C	ENSG00000128789	ENST00000317615	Transcript	missense_variant	1416	734	245	W/S	tGg/tCg	.	.	.	1	PSMG2	HGNC	24929	protein_coding	YES	CCDS11862.1	ENSP00000325919	PSMG2_HUMAN	.	UPI0000039F04	.	deleterious(0)	probably_damaging(0.98)	7/7	.	PIRSF_domain:PIRSF010044,hmmpanther:PTHR12970	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACGGTGGAAAA	.	4	ESCA
DSG3	0	.	GRCh37	18	29036436	29036436	+	Missense_Mutation	SNP	G	G	C	rs771167915	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.82G>C	p.Glu28Gln	p.E28Q	ENST00000257189	2/16	112	100	12	180	180	0	DSG3,missense_variant,p.Glu28Gln,ENST00000257189,;	C	ENSG00000134757	ENST00000257189	Transcript	missense_variant	165	82	28	E/Q	Gag/Cag	rs771167915,COSM3525191	.	.	1	DSG3	HGNC	3050	protein_coding	YES	CCDS11898.1	ENSP00000257189	DSG3_HUMAN	.	UPI000013CF4B	.	tolerated(0.13)	benign(0.017)	2/16	.	hmmpanther:PTHR24025:SF3,hmmpanther:PTHR24025	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAATAGAGGTA	.	4	ESCA
DSG3	0	.	GRCh37	18	29039116	29039116	+	Missense_Mutation	SNP	G	G	C	rs542631283	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493G>C	p.Glu165Gln	p.E165Q	ENST00000257189	5/16	75	70	4	118	118	0	DSG3,missense_variant,p.Glu165Gln,ENST00000257189,;	C	ENSG00000134757	ENST00000257189	Transcript	missense_variant	576	493	165	E/Q	Gaa/Caa	rs542631283	.	.	1	DSG3	HGNC	3050	protein_coding	YES	CCDS11898.1	ENSP00000257189	DSG3_HUMAN	.	UPI000013CF4B	.	tolerated(0.05)	probably_damaging(0.936)	5/16	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24025:SF3,hmmpanther:PTHR24025,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGGTGAAATT	.	2	ESCA
MOCOS	0	.	GRCh37	18	33779937	33779937	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.591C>T	p.%3D	p.L197L	ENST00000261326	4/15	31	27	3	56	55	0	MOCOS,synonymous_variant,p.%3D,ENST00000261326,;	T	ENSG00000075643	ENST00000261326	Transcript	synonymous_variant	612	591	197	L	ctC/ctT	.	.	.	1	MOCOS	HGNC	18234	protein_coding	YES	CCDS11919.1	ENSP00000261326	MOCOS_HUMAN	.	UPI000013D165	.	.	.	4/15	.	Superfamily_domains:SSF53383,Gene3D:3.40.640.10,Pfam_domain:PF00266,hmmpanther:PTHR14237,hmmpanther:PTHR14237:SF19,HAMAP:MF_03050	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CATCTCTTCTG	.	3	ESCA
CELF4	0	.	GRCh37	18	34824441	34824441	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*764C>T	.	.	ENST00000420428	13/13	75	70	5	93	93	0	CELF4,3_prime_UTR_variant,,ENST00000420428,;CELF4,3_prime_UTR_variant,,ENST00000586009,;CELF4,3_prime_UTR_variant,,ENST00000412753,;CELF4,3_prime_UTR_variant,,ENST00000334919,;CELF4,3_prime_UTR_variant,,ENST00000591287,;CELF4,3_prime_UTR_variant,,ENST00000588591,;CELF4,downstream_gene_variant,,ENST00000361795,;CELF4,downstream_gene_variant,,ENST00000603232,;CELF4,downstream_gene_variant,,ENST00000587911,;CELF4,downstream_gene_variant,,ENST00000601019,;RP11-95O2.5,intron_variant,,ENST00000589281,;CELF4,downstream_gene_variant,,ENST00000590011,;CELF4,downstream_gene_variant,,ENST00000590112,;	A	ENSG00000101489	ENST00000420428	Transcript	3_prime_UTR_variant	2621	.	.	.	.	.	.	.	-1	CELF4	HGNC	14015	protein_coding	YES	CCDS32818.1	ENSP00000410584	CELF4_HUMAN	K7EJK3_HUMAN	UPI00000726FC	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGATGAGGGT	.	2	ESCA
ST8SIA3	0	.	GRCh37	18	55020185	55020185	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108G>A	p.%3D	p.E36E	ENST00000324000	1/4	41	37	4	72	72	0	ST8SIA3,synonymous_variant,p.%3D,ENST00000324000,;ST8SIA3,upstream_gene_variant,,ENST00000586360,;	A	ENSG00000177511	ENST00000324000	Transcript	synonymous_variant	2142	108	36	E	gaG/gaA	.	.	.	1	ST8SIA3	HGNC	14269	protein_coding	YES	CCDS32834.1	ENSP00000320431	SIA8C_HUMAN	Q59GW3_HUMAN	UPI000014126D	.	.	.	1/4	.	hmmpanther:PTHR11987:SF33,hmmpanther:PTHR11987,PIRSF_domain:PIRSF005557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGGAGAACAT	.	3	ESCA
VAPA	0	.	GRCh37	18	9945046	9945046	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543G>A	p.%3D	p.E181E	ENST00000340541	5/7	79	70	8	81	81	0	VAPA,synonymous_variant,p.%3D,ENST00000340541,;VAPA,intron_variant,,ENST00000400000,;VAPA,intron_variant,,ENST00000584796,;VAPA,intron_variant,,ENST00000583879,;VAPA,intron_variant,,ENST00000583475,;VAPA,upstream_gene_variant,,ENST00000577539,;	A	ENSG00000101558	ENST00000340541	Transcript	synonymous_variant	738	543	181	E	gaG/gaA	.	.	.	1	VAPA	HGNC	12648	protein_coding	YES	CCDS11847.2	ENSP00000345656	VAPA_HUMAN	.	UPI000059D45E	.	.	.	5/7	.	hmmpanther:PTHR10809,hmmpanther:PTHR10809:SF40,PIRSF_domain:PIRSF019693	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGGAGAAACA	.	3	ESCA
C19orf52	0	.	GRCh37	19	11040151	11040151	+	Missense_Mutation	SNP	G	G	A	rs771293577	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556G>A	p.Asp186Asn	p.D186N	ENST00000270502	2/2	98	92	6	66	66	0	C19orf52,missense_variant,p.Asp186Asn,ENST00000270502,;YIPF2,upstream_gene_variant,,ENST00000588347,;YIPF2,upstream_gene_variant,,ENST00000587943,;YIPF2,upstream_gene_variant,,ENST00000585858,;YIPF2,upstream_gene_variant,,ENST00000253031,;YIPF2,upstream_gene_variant,,ENST00000586575,;YIPF2,upstream_gene_variant,,ENST00000590329,;YIPF2,upstream_gene_variant,,ENST00000586748,;C19orf52,upstream_gene_variant,,ENST00000593162,;YIPF2,upstream_gene_variant,,ENST00000592505,;YIPF2,upstream_gene_variant,,ENST00000588962,;C19orf52,upstream_gene_variant,,ENST00000588807,;	A	ENSG00000142444	ENST00000270502	Transcript	missense_variant	646	556	186	D/N	Gac/Aac	rs771293577,COSM3796585	.	.	1	C19orf52	HGNC	25152	protein_coding	YES	CCDS12252.1	ENSP00000270502	CS052_HUMAN	.	UPI0000071552	.	tolerated(0.16)	benign(0.159)	2/2	.	hmmpanther:PTHR21435,hmmpanther:PTHR21435:SF1,Pfam_domain:PF10171	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAACGACGAC	.	2	ESCA
ZNF44	0	.	GRCh37	19	12383473	12383473	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1741G>A	p.Glu581Lys	p.E581K	ENST00000356109	5/5	49	45	4	62	62	0	ZNF44,missense_variant,p.Glu581Lys,ENST00000356109,;ZNF44,missense_variant,p.Glu533Lys,ENST00000355684,;ZNF44,missense_variant,p.Glu581Lys,ENST00000393337,;ZNF44,missense_variant,p.Glu533Lys,ENST00000397742,;ZNF44,intron_variant,,ENST00000600003,;ZNF44,downstream_gene_variant,,ENST00000354656,;	T	ENSG00000197857	ENST00000356109	Transcript	missense_variant	1860	1741	581	E/K	Gaa/Aaa	.	.	.	-1	ZNF44	HGNC	13110	protein_coding	YES	CCDS54223.1	ENSP00000348419	ZNF44_HUMAN	Q6LDH8_HUMAN,O14858_HUMAN	UPI00017A7462	.	tolerated(0.16)	benign(0.173)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF17,hmmpanther:PTHR24379,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACATTCATATG	.	3	ESCA
EMR2	0	.	GRCh37	19	14862359	14862359	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1913G>C	p.Ser638Thr	p.S638T	ENST00000315576	16/21	47	41	6	70	70	0	EMR2,missense_variant,p.Ser545Thr,ENST00000594076,;EMR2,missense_variant,p.Ser589Thr,ENST00000594294,;EMR2,missense_variant,p.Ser627Thr,ENST00000601345,;EMR2,missense_variant,p.Ser589Thr,ENST00000346057,;EMR2,missense_variant,p.Ser496Thr,ENST00000595839,;EMR2,missense_variant,p.Ser496Thr,ENST00000353005,;EMR2,missense_variant,p.Ser545Thr,ENST00000353876,;EMR2,missense_variant,p.Ser638Thr,ENST00000315576,;EMR2,missense_variant,p.Ser580Thr,ENST00000392965,;EMR2,missense_variant,p.Ser627Thr,ENST00000392967,;EMR2,missense_variant,p.Ser627Thr,ENST00000596991,;EMR2,3_prime_UTR_variant,,ENST00000392964,;EMR2,3_prime_UTR_variant,,ENST00000392962,;EMR2,3_prime_UTR_variant,,ENST00000595208,;EMR2,non_coding_transcript_exon_variant,,ENST00000360222,;	G	ENSG00000127507	ENST00000315576	Transcript	missense_variant	2365	1913	638	S/T	aGc/aCc	.	.	.	-1	EMR2	HGNC	3337	protein_coding	YES	CCDS32935.1	ENSP00000319883	EMR2_HUMAN	.	UPI000016393A	.	tolerated(0.33)	probably_damaging(0.93)	16/21	.	PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF179,hmmpanther:PTHR12011,Pfam_domain:PF00002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	TGATGCTTGAG	.	3	ESCA
BRD4	0	.	GRCh37	19	15366318	15366318	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1837G>A	p.Glu613Lys	p.E613K	ENST00000263377	10/20	43	38	5	48	48	0	BRD4,missense_variant,p.Glu613Lys,ENST00000371835,;BRD4,missense_variant,p.Glu613Lys,ENST00000263377,;BRD4,missense_variant,p.Glu613Lys,ENST00000360016,;BRD4,downstream_gene_variant,,ENST00000594841,;BRD4,downstream_gene_variant,,ENST00000602230,;BRD4,upstream_gene_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,;	T	ENSG00000141867	ENST00000263377	Transcript	missense_variant	2059	1837	613	E/K	Gag/Aag	.	.	.	-1	BRD4	HGNC	13575	protein_coding	YES	CCDS12328.1	ENSP00000263377	BRD4_HUMAN	Q96HN0_HUMAN,M0R0H4_HUMAN,M0QZD9_HUMAN	UPI0000126ACE	.	.	benign(0.292)	10/20	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF143,PROSITE_profiles:PS51525	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCCTCATAGG	.	3	ESCA
HSH2D	0	.	GRCh37	19	16268428	16268428	+	3'Flank	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000535834	.	54	50	4	96	96	0	HSH2D,missense_variant,p.Glu295Lys,ENST00000593154,;HSH2D,missense_variant,p.Glu295Lys,ENST00000588246,;HSH2D,synonymous_variant,p.%3D,ENST00000397372,;HSH2D,synonymous_variant,p.%3D,ENST00000253680,;HSH2D,downstream_gene_variant,,ENST00000593031,;CIB3,downstream_gene_variant,,ENST00000379859,;CIB3,downstream_gene_variant,,ENST00000269878,;CIB3,downstream_gene_variant,,ENST00000541493,;HSH2D,3_prime_UTR_variant,,ENST00000587963,;HSH2D,3_prime_UTR_variant,,ENST00000589463,;HSH2D,downstream_gene_variant,,ENST00000535834,;HSH2D,downstream_gene_variant,,ENST00000591154,;CIB3,downstream_gene_variant,,ENST00000597251,;HSH2D,downstream_gene_variant,,ENST00000586872,;	A	ENSG00000196684	ENST00000535834	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1957	1	HSH2D	HGNC	24920	nonsense_mediated_decay	YES	.	ENSP00000442140	.	B4DT26_HUMAN	UPI00017A7AD4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCGAGAGGTC	.	2	ESCA
ATP13A1	0	.	GRCh37	19	19760549	19760549	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2535+1G>A	.	p.X845_splice	ENST00000357324	.	32	28	3	27	27	0	ATP13A1,splice_donor_variant,,ENST00000291503,;ATP13A1,splice_donor_variant,,ENST00000357324,;ATP13A1,downstream_gene_variant,,ENST00000496082,;ATP13A1,splice_donor_variant,,ENST00000469641,;ATP13A1,splice_donor_variant,,ENST00000497556,;ATP13A1,splice_donor_variant,,ENST00000473243,;ATP13A1,downstream_gene_variant,,ENST00000497762,;ATP13A1,upstream_gene_variant,,ENST00000467160,;ATP13A1,downstream_gene_variant,,ENST00000491221,;ATP13A1,downstream_gene_variant,,ENST00000497156,;ATP13A1,downstream_gene_variant,,ENST00000471063,;	T	ENSG00000105726	ENST00000357324	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	ATP13A1	HGNC	24215	protein_coding	YES	CCDS32970.2	ENSP00000349877	AT131_HUMAN	Q8N3E5_HUMAN	UPI0000126647	.	.	.	.	18/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ACATACCTTCT	.	3	ESCA
LINGO3	0	.	GRCh37	19	2290967	2290967	+	Missense_Mutation	SNP	G	G	T	rs763605142	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.809C>A	p.Ala270Glu	p.A270E	ENST00000585527	1/1	17	11	5	9	9	0	LINGO3,missense_variant,p.Ala270Glu,ENST00000404279,;LINGO3,missense_variant,p.Ala270Glu,ENST00000585527,;	T	ENSG00000220008	ENST00000585527	Transcript	missense_variant	1057	809	270	A/E	gCg/gAg	rs763605142	.	.	-1	LINGO3	HGNC	21206	protein_coding	YES	CCDS45905.1	ENSP00000467753	LIGO3_HUMAN	.	UPI00000497E2	.	tolerated(0.11)	possibly_damaging(0.585)	1/1	.	hmmpanther:PTHR24371:SF61,hmmpanther:PTHR24371,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGCGCCTGG	byFrequency	5	ESCA
ZNF792	0	.	GRCh37	19	35451802	35451802	+	Silent	SNP	G	G	A	rs776486492	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.130C>T	p.%3D	p.L44L	ENST00000404801	2/4	98	87	10	136	136	0	ZNF792,synonymous_variant,p.%3D,ENST00000404801,;ZNF792,upstream_gene_variant,,ENST00000605484,;	A	ENSG00000180884	ENST00000404801	Transcript	synonymous_variant	517	130	44	L	Ctg/Ttg	rs776486492	.	.	-1	ZNF792	HGNC	24751	protein_coding	YES	CCDS12440.2	ENSP00000385099	ZN792_HUMAN	S4R3B8_HUMAN	UPI0000202090	.	.	.	2/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF187,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCAGCATCA	.	4	ESCA
HAUS5	0	.	GRCh37	19	36106012	36106012	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288G>A	p.%3D	p.Q96Q	ENST00000203166	5/19	51	46	5	48	48	0	HAUS5,synonymous_variant,p.%3D,ENST00000203166,;HAUS5,synonymous_variant,p.%3D,ENST00000379045,;HAUS5,upstream_gene_variant,,ENST00000590994,;AC002115.9,upstream_gene_variant,,ENST00000589603,;HAUS5,synonymous_variant,p.%3D,ENST00000587439,;HAUS5,3_prime_UTR_variant,,ENST00000592291,;HAUS5,3_prime_UTR_variant,,ENST00000424522,;HAUS5,non_coding_transcript_exon_variant,,ENST00000428854,;HAUS5,non_coding_transcript_exon_variant,,ENST00000585968,;HAUS5,upstream_gene_variant,,ENST00000430749,;HAUS5,downstream_gene_variant,,ENST00000588570,;	A	ENSG00000249115	ENST00000203166	Transcript	synonymous_variant	313	288	96	Q	caG/caA	.	.	.	1	HAUS5	HGNC	29130	protein_coding	YES	CCDS42550.1	ENSP00000439056	HAUS5_HUMAN	.	UPI0000169F45	.	.	.	5/19	.	Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GACCAGAGCCT	.	3	ESCA
ZNF850	0	.	GRCh37	19	37238823	37238823	+	Missense_Mutation	SNP	G	G	A	rs750764589	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3119C>T	p.Pro1040Leu	p.P1040L	ENST00000591344	5/5	72	62	10	89	89	0	ZNF850,missense_variant,p.Pro1040Leu,ENST00000591344,;ZNF850,intron_variant,,ENST00000589390,;	A	ENSG00000267041	ENST00000591344	Transcript	missense_variant	3278	3119	1040	P/L	cCg/cTg	rs750764589	.	.	-1	ZNF850	HGNC	27994	protein_coding	YES	CCDS59379.1	ENSP00000464976	ZN850_HUMAN	.	UPI00001D815D	.	tolerated(0.36)	possibly_damaging(0.889)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF10,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTCCGGACAT	byFrequency	4	ESCA
ZFP36	0	.	GRCh37	19	39899813	39899813	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*474C>T	.	.	ENST00000597629	2/2	62	46	16	84	83	1	ZFP36,3_prime_UTR_variant,,ENST00000597629,;ZFP36,3_prime_UTR_variant,,ENST00000594442,;ZFP36,3_prime_UTR_variant,,ENST00000248673,;PLEKHG2,upstream_gene_variant,,ENST00000378550,;ZFP36,downstream_gene_variant,,ENST00000600033,;PLEKHG2,upstream_gene_variant,,ENST00000409797,;PLEKHG2,upstream_gene_variant,,ENST00000451354,;PLEKHG2,upstream_gene_variant,,ENST00000409794,;PLEKHG2,upstream_gene_variant,,ENST00000458508,;ZFP36,downstream_gene_variant,,ENST00000594045,;PLEKHG2,upstream_gene_variant,,ENST00000425673,;PLEKHG2,upstream_gene_variant,,ENST00000595920,;PLEKHG2,upstream_gene_variant,,ENST00000438123,;MIR4530,downstream_gene_variant,,ENST00000581459,;	T	ENSG00000128016	ENST00000597629	Transcript	3_prime_UTR_variant	1547	.	.	.	.	.	.	.	1	ZFP36	HGNC	12862	protein_coding	YES	CCDS12534.2	ENSP00000469647	.	M0QY76_HUMAN	UPI000059D71E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCACCCATAAA	.	4	ESCA
TIMM50	0	.	GRCh37	19	39979191	39979191	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1175A>G	p.Asn392Ser	p.N392S	ENST00000314349	10/11	29	25	3	53	53	0	TIMM50,missense_variant,p.Asn176Ser,ENST00000544017,;TIMM50,missense_variant,p.Asn392Ser,ENST00000314349,;TIMM50,missense_variant,p.Asn93Ser,ENST00000599794,;TIMM50,missense_variant,p.Asn289Ser,ENST00000607714,;TIMM50,downstream_gene_variant,,ENST00000597666,;TIMM50,downstream_gene_variant,,ENST00000601403,;TIMM50,downstream_gene_variant,,ENST00000594583,;TIMM50,downstream_gene_variant,,ENST00000602028,;TIMM50,upstream_gene_variant,,ENST00000600878,;TIMM50,missense_variant,p.Asn40Ser,ENST00000601252,;TIMM50,3_prime_UTR_variant,,ENST00000601358,;TIMM50,3_prime_UTR_variant,,ENST00000602265,;TIMM50,non_coding_transcript_exon_variant,,ENST00000597552,;TIMM50,non_coding_transcript_exon_variant,,ENST00000595961,;TIMM50,downstream_gene_variant,,ENST00000596239,;TIMM50,downstream_gene_variant,,ENST00000597782,;TIMM50,upstream_gene_variant,,ENST00000595527,;TIMM50,downstream_gene_variant,,ENST00000599733,;	G	ENSG00000105197	ENST00000314349	Transcript	missense_variant	1308	1175	392	N/S	aAt/aGt	.	.	.	1	TIMM50	HGNC	23656	protein_coding	YES	CCDS33023.1	ENSP00000318115	TIM50_HUMAN	.	UPI0000161278	.	tolerated(0.66)	benign(0.024)	10/11	.	hmmpanther:PTHR12210:SF3,hmmpanther:PTHR12210,Pfam_domain:PF03031,Gene3D:3.40.50.1000,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACTGAATGGTG	.	2	ESCA
AKT2	0	.	GRCh37	19	40740796	40740796	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1366+156C>T	.	.	ENST00000392038	.	89	82	7	161	161	0	AKT2,missense_variant,p.Pro446Ser,ENST00000579047,;AKT2,intron_variant,,ENST00000476247,;AKT2,intron_variant,,ENST00000392038,;AKT2,intron_variant,,ENST00000497948,;AKT2,intron_variant,,ENST00000424901,;AKT2,intron_variant,,ENST00000311278,;AKT2,downstream_gene_variant,,ENST00000578615,;AKT2,downstream_gene_variant,,ENST00000578310,;AKT2,downstream_gene_variant,,ENST00000486647,;AKT2,downstream_gene_variant,,ENST00000480878,;AKT2,downstream_gene_variant,,ENST00000391845,;AKT2,intron_variant,,ENST00000391844,;AKT2,intron_variant,,ENST00000483166,;AKT2,intron_variant,,ENST00000476266,;AKT2,intron_variant,,ENST00000584288,;AKT2,intron_variant,,ENST00000489375,;AKT2,intron_variant,,ENST00000496089,;AKT2,downstream_gene_variant,,ENST00000579345,;AKT2,downstream_gene_variant,,ENST00000537834,;AKT2,downstream_gene_variant,,ENST00000601166,;AKT2,downstream_gene_variant,,ENST00000580878,;AKT2,downstream_gene_variant,,ENST00000578282,;AKT2,downstream_gene_variant,,ENST00000492463,;	A	ENSG00000105221	ENST00000392038	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AKT2	HGNC	392	protein_coding	YES	CCDS12552.1	ENSP00000375892	AKT2_HUMAN	Q05BV0_HUMAN,M0QZK3_HUMAN,J3QQM6_HUMAN,J3QLS6_HUMAN,J3QL45_HUMAN,J3KSY8_HUMAN,J3KRI8_HUMAN,E7EVP8_HUMAN,C9JIJ1_HUMAN,C9JIF6_HUMAN,C9JHS6_HUMAN,C9JC83_HUMAN,C9J258_HUMAN,B4DG79_HUMAN,B3KP61_HUMAN,A8MX96_HUMAN	UPI0000049EDB	.	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUSE|VARSCANS	AAGAGGACCAA	.	2	ESCA
ARHGEF1	0	.	GRCh37	19	42408469	42408469	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2140G>C	p.Asp714His	p.D714H	ENST00000337665	22/29	25	20	4	17	17	0	ARHGEF1,missense_variant,p.Asp755His,ENST00000599846,;ARHGEF1,missense_variant,p.Asp714His,ENST00000337665,;ARHGEF1,missense_variant,p.Asp457His,ENST00000599589,;ARHGEF1,missense_variant,p.Asp666His,ENST00000347545,;ARHGEF1,missense_variant,p.Asp699His,ENST00000354532,;ARHGEF1,missense_variant,p.Asp154His,ENST00000595723,;ARHGEF1,missense_variant,p.Asp681His,ENST00000378152,;ARHGEF1,downstream_gene_variant,,ENST00000594258,;ARHGEF1,downstream_gene_variant,,ENST00000594521,;CTD-2575K13.6,downstream_gene_variant,,ENST00000597630,;ARHGEF1,missense_variant,p.Asp35His,ENST00000600517,;ARHGEF1,non_coding_transcript_exon_variant,,ENST00000595897,;ARHGEF1,non_coding_transcript_exon_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000598444,;ARHGEF1,upstream_gene_variant,,ENST00000593609,;ARHGEF1,downstream_gene_variant,,ENST00000594044,;ARHGEF1,upstream_gene_variant,,ENST00000598587,;	C	ENSG00000076928	ENST00000337665	Transcript	missense_variant	2160	2140	714	D/H	Gat/Cat	.	.	.	1	ARHGEF1	HGNC	681	protein_coding	YES	CCDS12590.1	ENSP00000337261	ARHG1_HUMAN	.	UPI0000231C94	.	deleterious(0)	probably_damaging(0.999)	22/29	.	PROSITE_profiles:PS50003,hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF6,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCCGATGGC	.	5	ESCA
MEGF8	0	.	GRCh37	19	42840240	42840240	+	Missense_Mutation	SNP	C	C	T	rs750660042	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.986C>T	p.Ser329Leu	p.S329L	ENST00000334370	6/41	57	51	6	55	55	0	MEGF8,missense_variant,p.Ser329Leu,ENST00000334370,;MEGF8,missense_variant,p.Ser329Leu,ENST00000251268,;	T	ENSG00000105429	ENST00000334370	Transcript	missense_variant	1621	986	329	S/L	tCg/tTg	rs750660042	.	.	1	MEGF8	HGNC	3233	protein_coding	YES	CCDS12604.2	ENSP00000334219	MEGF8_HUMAN	.	UPI00003CF1A7	.	tolerated(0.92)	benign(0.002)	6/41	.	Low_complexity_(Seg):seg,Gene3D:1zgkA00,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTCCTCGGGGC	byFrequency	2	ESCA
TULP2	0	.	GRCh37	19	49385305	49385305	+	Silent	SNP	G	G	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1431C>A	p.%3D	p.I477I	ENST00000221399	12/13	84	66	18	142	142	0	TULP2,synonymous_variant,p.%3D,ENST00000522341,;TULP2,synonymous_variant,p.%3D,ENST00000221399,;	T	ENSG00000104804	ENST00000221399	Transcript	synonymous_variant	1576	1431	477	I	atC/atA	.	.	.	-1	TULP2	HGNC	12424	protein_coding	YES	CCDS12739.1	ENSP00000221399	TULP2_HUMAN	E5RHR0_HUMAN	UPI0000071877	.	.	.	12/13	.	hmmpanther:PTHR16517:SF24,hmmpanther:PTHR16517,Pfam_domain:PF01167,Gene3D:3c5nA00,Superfamily_domains:SSF54518,Prints_domain:PR01573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCACGATTTG	.	5	ESCA
RUVBL2	0	.	GRCh37	19	49513866	49513866	+	Nonsense_Mutation	SNP	C	C	G	rs375101517	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785C>G	p.Ser262Ter	p.S262*	ENST00000595090	9/15	18	14	4	40	40	0	RUVBL2,stop_gained,p.Ser262Ter,ENST00000595090,;RUVBL2,stop_gained,p.Ser217Ter,ENST00000413176,;RUVBL2,stop_gained,p.Ser217Ter,ENST00000601968,;RUVBL2,downstream_gene_variant,,ENST00000596837,;RUVBL2,synonymous_variant,p.%3D,ENST00000221413,;RUVBL2,splice_region_variant,,ENST00000596247,;RUVBL2,splice_region_variant,,ENST00000594338,;RUVBL2,upstream_gene_variant,,ENST00000595002,;RUVBL2,downstream_gene_variant,,ENST00000594017,;RUVBL2,downstream_gene_variant,,ENST00000593570,;	G	ENSG00000183207	ENST00000595090	Transcript	stop_gained	1249	785	262	S/*	tCa/tGa	rs375101517	.	.	1	RUVBL2	HGNC	10475	protein_coding	YES	CCDS42588.1	ENSP00000473172	RUVB2_HUMAN	M0QXI6_HUMAN,B3KQ59_HUMAN	UPI0000044738	.	.	.	9/15	.	hmmpanther:PTHR11093,Pfam_domain:PF06068,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	CTTCTCAGGTG	.	2	ESCA
TSKS	0	.	GRCh37	19	50251727	50251727	+	Splice_Site	SNP	C	C	G	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400-1G>C	.	p.X134_splice	ENST00000246801	.	71	58	13	68	68	0	TSKS,splice_acceptor_variant,,ENST00000246801,;TSKS,upstream_gene_variant,,ENST00000358830,;	G	ENSG00000126467	ENST00000246801	Transcript	splice_acceptor_variant	.	.	.	.	.	COSM378268	.	.	-1	TSKS	HGNC	30719	protein_coding	YES	CCDS12780.1	ENSP00000246801	TSKS_HUMAN	.	UPI000007272E	.	.	.	.	2/10	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTCTGGGG	.	5	ESCA
LILRA2	0	.	GRCh37	19	55087566	55087566	+	Silent	SNP	C	C	A	rs199807216	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245C>A	p.%3D	p.L415L	ENST00000251377	7/9	76	68	8	114	114	0	LILRA2,synonymous_variant,p.%3D,ENST00000251376,;LILRA2,synonymous_variant,p.%3D,ENST00000391738,;LILRA2,synonymous_variant,p.%3D,ENST00000391737,;LILRA2,synonymous_variant,p.%3D,ENST00000251377,;LILRB1,intron_variant,,ENST00000418536,;LILRB1,intron_variant,,ENST00000448689,;LILRB1,intron_variant,,ENST00000396321,;LILRA2,downstream_gene_variant,,ENST00000439534,;LILRA2,non_coding_transcript_exon_variant,,ENST00000472992,;LILRA2,downstream_gene_variant,,ENST00000495786,;	A	ENSG00000239998	ENST00000251377	Transcript	synonymous_variant	1378	1245	415	L	ctC/ctA	rs199807216	.	.	1	LILRA2	HGNC	6603	protein_coding	YES	CCDS46179.1	ENSP00000251377	LIRA2_HUMAN	E9PDF4_HUMAN	UPI0000034C01	.	.	.	7/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11738:SF90,hmmpanther:PTHR11738,Gene3D:2.60.40.10,PIRSF_domain:PIRSF001979,SMART_domains:SM00409,Superfamily_domains:SSF48726	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	GAGCTCGTGGT	byCluster|by1000G	2	ESCA
ZIM3	0	.	GRCh37	19	57647388	57647388	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.317C>T	p.Ser106Leu	p.S106L	ENST00000269834	5/5	125	113	12	83	83	0	ZIM3,missense_variant,p.Ser106Leu,ENST00000269834,;USP29,downstream_gene_variant,,ENST00000598197,;USP29,downstream_gene_variant,,ENST00000254181,;U3,upstream_gene_variant,,ENST00000516874,;	A	ENSG00000141946	ENST00000269834	Transcript	missense_variant	703	317	106	S/L	tCa/tTa	.	.	.	-1	ZIM3	HGNC	16366	protein_coding	YES	CCDS33125.1	ENSP00000269834	ZIM3_HUMAN	.	UPI000013C3E0	.	tolerated(0.81)	benign(0.002)	5/5	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGATTGATGGG	.	4	ESCA
MUC16	0	.	GRCh37	19	9062471	9062471	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.24975G>C	p.Leu8325Phe	p.L8325F	ENST00000397910	3/84	53	42	10	82	82	0	MUC16,missense_variant,p.Leu8325Phe,ENST00000397910,;	G	ENSG00000181143	ENST00000397910	Transcript	missense_variant	25179	24975	8325	L/F	ttG/ttC	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	3/84	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTCAAATT	.	5	ESCA
ZNF559	0	.	GRCh37	19	9449954	9449954	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.119G>C	p.Arg40Thr	p.R40T	ENST00000393883	4/6	126	112	14	126	126	0	ZNF559,missense_variant,p.Arg68Thr,ENST00000592896,;ZNF559,missense_variant,p.Arg40Thr,ENST00000393883,;ZNF559,missense_variant,p.Arg40Thr,ENST00000603380,;ZNF559,missense_variant,p.Arg68Thr,ENST00000586255,;ZNF559,missense_variant,p.Arg104Thr,ENST00000587557,;ZNF559,missense_variant,p.Arg8Thr,ENST00000591652,;ZNF559,missense_variant,p.Arg40Thr,ENST00000592504,;ZNF559,missense_variant,p.Arg40Thr,ENST00000317221,;ZNF559,missense_variant,p.Arg40Thr,ENST00000592298,;ZNF559,missense_variant,p.Arg68Thr,ENST00000588124,;ZNF559,missense_variant,p.Arg40Thr,ENST00000585352,;ZNF559,intron_variant,,ENST00000589208,;ZNF559,intron_variant,,ENST00000538743,;ZNF177,intron_variant,,ENST00000602856,;ZNF559-ZNF177,intron_variant,,ENST00000603656,;ZNF177,intron_variant,,ENST00000602738,;ZNF559,intron_variant,,ENST00000605750,;ZNF559-ZNF177,intron_variant,,ENST00000446085,;ZNF559-ZNF177,intron_variant,,ENST00000541595,;ZNF559,downstream_gene_variant,,ENST00000585377,;ZNF559-ZNF177,non_coding_transcript_exon_variant,,ENST00000605522,;ZNF559-ZNF177,non_coding_transcript_exon_variant,,ENST00000603099,;ZNF559-ZNF177,intron_variant,,ENST00000605301,;ZNF559-ZNF177,intron_variant,,ENST00000605471,;ZNF559-ZNF177,missense_variant,p.Arg40Thr,ENST00000603974,;ZNF559-ZNF177,missense_variant,p.Arg40Thr,ENST00000605071,;ZNF559-ZNF177,intron_variant,,ENST00000605775,;ZNF559-ZNF177,intron_variant,,ENST00000604886,;ZNF559-ZNF177,intron_variant,,ENST00000605093,;ZNF559-ZNF177,intron_variant,,ENST00000593242,;ZNF559-ZNF177,intron_variant,,ENST00000604543,;ZNF559-ZNF177,intron_variant,,ENST00000603024,;ZNF559-ZNF177,intron_variant,,ENST00000605006,;	C	ENSG00000188321	ENST00000393883	Transcript	missense_variant	767	119	40	R/T	aGa/aCa	.	.	.	1	ZNF559	HGNC	28197	protein_coding	YES	CCDS12211.1	ENSP00000377461	ZN559_HUMAN	S4R3F2_HUMAN,K7ERK9_HUMAN,B4DP29_HUMAN	UPI00000733B2	.	deleterious(0.01)	possibly_damaging(0.849)	4/6	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24381:SF77,hmmpanther:PTHR24381,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATACAGAGATG	.	4	ESCA
GNAI3	0	.	GRCh37	1	110091283	110091283	+	5'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-60G>C	.	.	ENST00000369851	1/9	65	62	3	65	65	0	GNAI3,5_prime_UTR_variant,,ENST00000369851,;GPR61,downstream_gene_variant,,ENST00000527748,;RP5-1160K1.8,upstream_gene_variant,,ENST00000526411,;GPR61,downstream_gene_variant,,ENST00000526744,;GPR61,downstream_gene_variant,,ENST00000404129,;GPR61,downstream_gene_variant,,ENST00000469383,;	C	ENSG00000065135	ENST00000369851	Transcript	5_prime_UTR_variant	51	.	.	.	.	.	.	.	1	GNAI3	HGNC	4387	protein_coding	YES	CCDS802.1	ENSP00000358867	GNAI3_HUMAN	Q5TZX1_HUMAN,C9J2Z2_HUMAN	UPI000004D205	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCCGAGCCG	.	2	ESCA
GNAI3	0	.	GRCh37	1	110135565	110135565	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*621C>T	.	.	ENST00000369851	9/9	54	44	10	42	42	0	GNAI3,3_prime_UTR_variant,,ENST00000369851,;RNU6V,upstream_gene_variant,,ENST00000384105,;RP5-1160K1.3,upstream_gene_variant,,ENST00000436416,;	T	ENSG00000065135	ENST00000369851	Transcript	3_prime_UTR_variant	1796	.	.	.	.	.	.	.	1	GNAI3	HGNC	4387	protein_coding	YES	CCDS802.1	ENSP00000358867	GNAI3_HUMAN	Q5TZX1_HUMAN,C9J2Z2_HUMAN	UPI000004D205	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGCTCAAA	.	5	ESCA
KCNC4	0	.	GRCh37	1	110765753	110765753	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.846C>G	p.%3D	p.T282T	ENST00000369787	2/4	36	32	3	30	30	0	KCNC4,synonymous_variant,p.%3D,ENST00000413138,;KCNC4,synonymous_variant,p.%3D,ENST00000369787,;KCNC4,synonymous_variant,p.%3D,ENST00000438661,;KCNC4,intron_variant,,ENST00000412512,;KCNC4,synonymous_variant,p.%3D,ENST00000469655,;KCNC4,non_coding_transcript_exon_variant,,ENST00000459877,;KCNC4,non_coding_transcript_exon_variant,,ENST00000489935,;	G	ENSG00000116396	ENST00000369787	Transcript	synonymous_variant	873	846	282	T	acC/acG	.	.	.	1	KCNC4	HGNC	6236	protein_coding	YES	CCDS821.1	ENSP00000358802	KCNC4_HUMAN	.	UPI000013CAC8	.	.	.	2/4	.	hmmpanther:PTHR11537:SF126,hmmpanther:PTHR11537,Gene3D:1.20.120.350,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTGACCTACAT	.	3	ESCA
HIPK1	0	.	GRCh37	1	114517135	114517135	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1001C>G	.	.	ENST00000369558	16/16	123	98	25	143	143	0	HIPK1,3_prime_UTR_variant,,ENST00000361587,;HIPK1,3_prime_UTR_variant,,ENST00000369554,;HIPK1,3_prime_UTR_variant,,ENST00000406344,;HIPK1,3_prime_UTR_variant,,ENST00000369558,;HIPK1,3_prime_UTR_variant,,ENST00000340480,;OLFML3,upstream_gene_variant,,ENST00000369551,;HIPK1,downstream_gene_variant,,ENST00000369561,;HIPK1,downstream_gene_variant,,ENST00000426820,;HIPK1,downstream_gene_variant,,ENST00000369553,;HIPK1,downstream_gene_variant,,ENST00000369559,;OLFML3,upstream_gene_variant,,ENST00000320334,;HIPK1,downstream_gene_variant,,ENST00000369555,;OLFML3,upstream_gene_variant,,ENST00000491700,;	G	ENSG00000163349	ENST00000369558	Transcript	3_prime_UTR_variant	4866	.	.	.	.	.	.	.	1	HIPK1	HGNC	19006	protein_coding	YES	CCDS867.1	ENSP00000358571	HIPK1_HUMAN	D6RF28_HUMAN,D6RC95_HUMAN	UPI000000D74E	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCTCCCT	.	5	ESCA
PRAMEF19	0	.	GRCh37	1	13695695	13695695	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1270C>T	p.Arg424Cys	p.R424C	ENST00000540591	3/3	40	35	5	48	48	0	PRAMEF19,missense_variant,p.Arg355Cys,ENST00000376101,;PRAMEF19,missense_variant,p.Arg424Cys,ENST00000540591,;	A	ENSG00000204480	ENST00000540591	Transcript	missense_variant	1317	1270	424	R/C	Cgt/Tgt	.	.	.	-1	PRAMEF19	HGNC	24908	protein_coding	YES	.	ENSP00000446004	.	F5H544_HUMAN	UPI0000237231	.	.	possibly_damaging(0.491)	3/3	.	hmmpanther:PTHR14224:SF5,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GACACGACCCC	.	2	ESCA
LCE1F	0	.	GRCh37	1	152749016	152749016	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.169G>A	p.Gly57Arg	p.G57R	ENST00000334371	1/1	151	128	22	121	121	0	LCE1F,missense_variant,p.Gly57Arg,ENST00000334371,;	A	ENSG00000240386	ENST00000334371	Transcript	missense_variant	169	169	57	G/R	Ggg/Agg	.	.	.	1	LCE1F	HGNC	29467	protein_coding	YES	CCDS1023.1	ENSP00000334187	LCE1F_HUMAN	.	UPI0000192764	.	deleterious_low_confidence(0.02)	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23263:SF46,hmmpanther:PTHR23263,Pfam_domain:PF14672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S54C|c.161C>G|3	RADIA|MUTECT|MUSE|VARSCANS	GCTCTGGGGGC	.	4	ESCA
FDPS	0	.	GRCh37	1	155289433	155289433	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.878A>G	p.Asn293Ser	p.N293S	ENST00000356657	9/11	84	75	8	112	111	1	FDPS,missense_variant,p.Asn293Ser,ENST00000356657,;FDPS,missense_variant,p.Asn227Ser,ENST00000447866,;FDPS,missense_variant,p.Asn293Ser,ENST00000368356,;RUSC1,upstream_gene_variant,,ENST00000368352,;RUSC1,upstream_gene_variant,,ENST00000368354,;RUSC1,upstream_gene_variant,,ENST00000292254,;RUSC1,upstream_gene_variant,,ENST00000368347,;RUSC1,upstream_gene_variant,,ENST00000368349,;RUSC1-AS1,intron_variant,,ENST00000443642,;RUSC1-AS1,intron_variant,,ENST00000543656,;RUSC1-AS1,intron_variant,,ENST00000446880,;RUSC1-AS1,downstream_gene_variant,,ENST00000450199,;FDPS,non_coding_transcript_exon_variant,,ENST00000490140,;FDPS,non_coding_transcript_exon_variant,,ENST00000492244,;FDPS,non_coding_transcript_exon_variant,,ENST00000467076,;FDPS,non_coding_transcript_exon_variant,,ENST00000468479,;FDPS,non_coding_transcript_exon_variant,,ENST00000492887,;FDPS,downstream_gene_variant,,ENST00000470171,;RUSC1,upstream_gene_variant,,ENST00000497930,;RUSC1,upstream_gene_variant,,ENST00000471876,;RUSC1,upstream_gene_variant,,ENST00000479924,;RUSC1,upstream_gene_variant,,ENST00000467820,;RUSC1,upstream_gene_variant,,ENST00000489860,;FDPS,downstream_gene_variant,,ENST00000474345,;FDPS,downstream_gene_variant,,ENST00000461507,;FDPS,downstream_gene_variant,,ENST00000471117,;RUSC1,upstream_gene_variant,,ENST00000468764,;RUSC1,upstream_gene_variant,,ENST00000484664,;RUSC1,upstream_gene_variant,,ENST00000462780,;FDPS,upstream_gene_variant,,ENST00000489324,;RUSC1,upstream_gene_variant,,ENST00000490373,;FDPS,downstream_gene_variant,,ENST00000489003,;FDPS,downstream_gene_variant,,ENST00000495308,;FDPS,downstream_gene_variant,,ENST00000465559,;RUSC1,upstream_gene_variant,,ENST00000492536,;FDPS,downstream_gene_variant,,ENST00000477057,;FDPS,downstream_gene_variant,,ENST00000491013,;	G	ENSG00000160752	ENST00000356657	Transcript	missense_variant	1040	878	293	N/S	aAt/aGt	.	.	.	1	FDPS	HGNC	3631	protein_coding	YES	CCDS1110.1	ENSP00000349078	FPPS_HUMAN	.	UPI000006E4F7	.	tolerated(0.22)	benign(0.017)	9/11	.	hmmpanther:PTHR11525:SF0,hmmpanther:PTHR11525,Pfam_domain:PF00348,Gene3D:1.10.600.10,Superfamily_domains:SSF48576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CGCCAATGCCA	.	3	ESCA
BCAN	0	.	GRCh37	1	156621307	156621307	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1123G>C	p.Asp375His	p.D375H	ENST00000329117	7/14	55	48	6	78	78	0	BCAN,missense_variant,p.Asp375His,ENST00000361588,;BCAN,missense_variant,p.Asp375His,ENST00000329117,;BCAN,downstream_gene_variant,,ENST00000441358,;BCAN,downstream_gene_variant,,ENST00000457777,;BCAN,downstream_gene_variant,,ENST00000424639,;RP11-284F21.7,intron_variant,,ENST00000448869,;BCAN,3_prime_UTR_variant,,ENST00000479949,;BCAN,3_prime_UTR_variant,,ENST00000491823,;	C	ENSG00000132692	ENST00000329117	Transcript	missense_variant	1459	1123	375	D/H	Gat/Cat	.	.	.	1	BCAN	HGNC	23059	protein_coding	YES	CCDS1149.1	ENSP00000331210	PGCB_HUMAN	Q9NT67_HUMAN,Q5T3I8_HUMAN,Q5T3I7_HUMAN,Q59F90_HUMAN	UPI000006F0E9	.	deleterious(0.03)	probably_damaging(0.999)	7/14	.	hmmpanther:PTHR22804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCTGATGGA	.	3	ESCA
BCAN	0	.	GRCh37	1	156621337	156621337	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1153G>A	p.Glu385Lys	p.E385K	ENST00000329117	7/14	59	54	5	81	81	0	BCAN,missense_variant,p.Glu385Lys,ENST00000361588,;BCAN,missense_variant,p.Glu385Lys,ENST00000329117,;BCAN,downstream_gene_variant,,ENST00000441358,;BCAN,downstream_gene_variant,,ENST00000457777,;BCAN,downstream_gene_variant,,ENST00000424639,;RP11-284F21.7,intron_variant,,ENST00000448869,;BCAN,3_prime_UTR_variant,,ENST00000479949,;BCAN,3_prime_UTR_variant,,ENST00000491823,;	A	ENSG00000132692	ENST00000329117	Transcript	missense_variant	1489	1153	385	E/K	Gag/Aag	.	.	.	1	BCAN	HGNC	23059	protein_coding	YES	CCDS1149.1	ENSP00000331210	PGCB_HUMAN	Q9NT67_HUMAN,Q5T3I8_HUMAN,Q5T3I7_HUMAN,Q59F90_HUMAN	UPI000006F0E9	.	tolerated(0.05)	probably_damaging(0.993)	7/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGACAGAGACC	.	2	ESCA
CADM3	0	.	GRCh37	1	159163319	159163319	+	Silent	SNP	C	C	T	rs554827373	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.591C>T	p.%3D	p.L197L	ENST00000368124	5/10	31	26	5	56	56	0	CADM3,synonymous_variant,p.%3D,ENST00000368124,;CADM3,synonymous_variant,p.%3D,ENST00000368125,;CADM3,synonymous_variant,p.%3D,ENST00000416746,;CTA-134P22.2,downstream_gene_variant,,ENST00000415675,;CADM3,upstream_gene_variant,,ENST00000497636,;	T	ENSG00000162706	ENST00000368124	Transcript	synonymous_variant	748	591	197	L	ctC/ctT	rs554827373	.	.	1	CADM3	HGNC	17601	protein_coding	YES	CCDS1182.1	ENSP00000357106	CADM3_HUMAN	.	UPI000006E8A2	.	.	.	5/10	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23277:SF57,hmmpanther:PTHR23277,Gene3D:2.60.40.10,Pfam_domain:PF08205,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGCTCACCTG	by1000G	4	ESCA
ATP1A2	0	.	GRCh37	1	160098826	160098826	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1273C>T	p.Leu425Phe	p.L425F	ENST00000361216	10/23	48	45	3	91	91	0	ATP1A2,missense_variant,p.Leu425Phe,ENST00000361216,;ATP1A2,missense_variant,p.Leu425Phe,ENST00000392233,;ATP1A2,missense_variant,p.Leu136Phe,ENST00000447527,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488,;ATP1A2,downstream_gene_variant,,ENST00000468587,;	T	ENSG00000018625	ENST00000361216	Transcript	missense_variant	1362	1273	425	L/F	Ctc/Ttc	.	.	.	1	ATP1A2	HGNC	800	protein_coding	YES	CCDS1196.1	ENSP00000354490	AT1A2_HUMAN	Q58I22_HUMAN	UPI0000124FC1	.	deleterious(0.01)	probably_damaging(0.996)	10/23	.	hmmpanther:PTHR24093:SF229,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01106,Gene3D:3.40.1110.10,Pfam_domain:PF00702,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGTCTCTGC	.	2	ESCA
RC3H1	0	.	GRCh37	1	173933996	173933996	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597C>T	p.Pro533Ser	p.P533S	ENST00000367696	10/20	57	51	6	68	68	0	RC3H1,missense_variant,p.Pro533Ser,ENST00000367694,;RC3H1,missense_variant,p.Pro533Ser,ENST00000258349,;RC3H1,missense_variant,p.Pro533Ser,ENST00000367696,;RNA5SP68,downstream_gene_variant,,ENST00000363885,;RC3H1,upstream_gene_variant,,ENST00000531594,;	A	ENSG00000135870	ENST00000367696	Transcript	missense_variant	1949	1597	533	P/S	Cct/Tct	.	.	.	-1	RC3H1	HGNC	29434	protein_coding	YES	CCDS30940.1	ENSP00000356669	RC3H1_HUMAN	B9EGU6_HUMAN	UPI00001D7DA8	.	tolerated(0.1)	probably_damaging(0.998)	10/20	.	hmmpanther:PTHR13139,hmmpanther:PTHR13139:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAGGAGCAC	.	4	ESCA
BRINP3	0	.	GRCh37	1	190066856	190066856	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*292T>C	.	.	ENST00000367462	8/8	50	44	6	80	80	0	BRINP3,3_prime_UTR_variant,,ENST00000534846,;BRINP3,3_prime_UTR_variant,,ENST00000367462,;	G	ENSG00000162670	ENST00000367462	Transcript	3_prime_UTR_variant	2825	.	.	.	.	.	.	.	-1	BRINP3	HGNC	22393	protein_coding	YES	CCDS1373.1	ENSP00000356432	BRNP3_HUMAN	.	UPI00001C1D9A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGTAATGCA	.	2	ESCA
BRINP3	0	.	GRCh37	1	190449679	190449679	+	5'Flank	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000367462	.	25	22	3	17	17	0	BRINP3,upstream_gene_variant,,ENST00000534846,;BRINP3,upstream_gene_variant,,ENST00000367462,;RP11-547I7.2,non_coding_transcript_exon_variant,,ENST00000424735,;RP11-547I7.2,non_coding_transcript_exon_variant,,ENST00000436905,;RP11-161I10.1,intron_variant,,ENST00000417409,;	A	ENSG00000162670	ENST00000367462	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2920	-1	BRINP3	HGNC	22393	protein_coding	YES	CCDS1373.1	ENSP00000356432	BRNP3_HUMAN	.	UPI00001C1D9A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTAGAGAGCAT	.	2	ESCA
KIF17	0	.	GRCh37	1	21014222	21014222	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597G>C	p.Glu533Gln	p.E533Q	ENST00000247986	8/15	43	34	8	49	49	0	KIF17,missense_variant,p.Glu533Gln,ENST00000247986,;KIF17,missense_variant,p.Glu533Gln,ENST00000400463,;KIF17,missense_variant,p.Glu433Gln,ENST00000375044,;KIF17,intron_variant,,ENST00000490034,;KIF17,upstream_gene_variant,,ENST00000477167,;KIF17,upstream_gene_variant,,ENST00000498225,;KIF17,upstream_gene_variant,,ENST00000462858,;	G	ENSG00000117245	ENST00000247986	Transcript	missense_variant	1908	1597	533	E/Q	Gag/Cag	.	.	.	-1	KIF17	HGNC	19167	protein_coding	YES	CCDS213.1	ENSP00000247986	KIF17_HUMAN	.	UPI0000185F1A	.	tolerated_low_confidence(0.05)	possibly_damaging(0.611)	8/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF415	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTCAGATT	.	5	ESCA
WDR26	0	.	GRCh37	1	224573319	224573319	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4218C>G	.	.	ENST00000414423	14/14	66	57	9	59	59	0	WDR26,3_prime_UTR_variant,,ENST00000414423,;WDR26,3_prime_UTR_variant,,ENST00000295024,;WDR26,downstream_gene_variant,,ENST00000366852,;WDR26,downstream_gene_variant,,ENST00000480676,;WDR26,downstream_gene_variant,,ENST00000486652,;	C	ENSG00000162923	ENST00000414423	Transcript	3_prime_UTR_variant	6398	.	.	.	.	.	.	.	-1	WDR26	HGNC	21208	protein_coding	YES	CCDS31037.2	ENSP00000408108	WDR26_HUMAN	C9JCS7_HUMAN	UPI0000203FB7	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGAGATCAA	.	5	ESCA
OBSCN	0	.	GRCh37	1	228529252	228529252	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20842A>T	p.Ile6948Phe	p.I6948F	ENST00000570156	85/116	125	111	14	116	116	0	OBSCN,missense_variant,p.Ile3625Phe,ENST00000366707,;OBSCN,missense_variant,p.Ile3110Phe,ENST00000366709,;OBSCN,missense_variant,p.Ile5991Phe,ENST00000284548,;OBSCN,missense_variant,p.Ile608Phe,ENST00000441106,;OBSCN,missense_variant,p.Ile5991Phe,ENST00000422127,;OBSCN,missense_variant,p.Ile6948Phe,ENST00000570156,;	T	ENSG00000154358	ENST00000570156	Transcript	missense_variant	20916	20842	6948	I/F	Atc/Ttc	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	possibly_damaging(0.804)	85/116	.	PROSITE_profiles:PS50003,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATTATCAAG	.	4	ESCA
ZNF436	0	.	GRCh37	1	23688650	23688650	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000314011	4/4	78	69	8	67	67	0	ZNF436,stop_gained,p.Gln409Ter,ENST00000314011,;ZNF436,stop_gained,p.Gln409Ter,ENST00000374608,;	A	ENSG00000125945	ENST00000314011	Transcript	stop_gained	1362	1225	409	Q/*	Cag/Tag	.	.	.	-1	ZNF436	HGNC	20814	protein_coding	YES	CCDS233.1	ENSP00000313582	ZN436_HUMAN	Q15921_HUMAN	UPI0000001669	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTCTGATGTT	.	4	ESCA
FMN2	0	.	GRCh37	1	240458161	240458161	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4193C>A	p.Thr1398Asn	p.T1398N	ENST00000319653	8/18	88	81	7	85	85	0	FMN2,missense_variant,p.Thr44Asn,ENST00000441342,;FMN2,missense_variant,p.Thr1398Asn,ENST00000319653,;FMN2,intron_variant,,ENST00000545751,;FMN2,non_coding_transcript_exon_variant,,ENST00000463398,;	A	ENSG00000155816	ENST00000319653	Transcript	missense_variant	4423	4193	1398	T/N	aCc/aAc	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	possibly_damaging(0.812)	8/18	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A1544T|c.4630G>A|3	MUTECT|MUSE	GGAGACCCTTC	.	2	ESCA
PLD5	0	.	GRCh37	1	242263986	242263986	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1338T>A	p.Asp446Glu	p.D446E	ENST00000536534	9/10	99	91	8	103	103	0	PLD5,missense_variant,p.Asp446Glu,ENST00000536534,;PLD5,missense_variant,p.Asp384Glu,ENST00000427495,;PLD5,missense_variant,p.Asp354Glu,ENST00000442594,;PLD5,3_prime_UTR_variant,,ENST00000366545,;PLD5,3_prime_UTR_variant,,ENST00000314833,;	T	ENSG00000180287	ENST00000536534	Transcript	missense_variant	1580	1338	446	D/E	gaT/gaA	.	.	.	-1	PLD5	HGNC	26879	protein_coding	YES	CCDS1621.2	ENSP00000440896	PLD5_HUMAN	J3KP61_HUMAN	UPI000040E1A4	.	tolerated(0.15)	possibly_damaging(0.695)	9/10	.	hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185,Gene3D:3.30.870.10,SMART_domains:SM00155,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTCCATCTGT	.	3	ESCA
KIAA1522	0	.	GRCh37	1	33237497	33237497	+	Missense_Mutation	SNP	C	C	T	rs776125780	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2717C>T	p.Ser906Leu	p.S906L	ENST00000401073	6/7	13	9	4	22	22	0	KIAA1522,missense_variant,p.Ser858Leu,ENST00000373481,;KIAA1522,missense_variant,p.Ser847Leu,ENST00000373480,;KIAA1522,missense_variant,p.Ser906Leu,ENST00000401073,;KIAA1522,intron_variant,,ENST00000294521,;YARS,downstream_gene_variant,,ENST00000373477,;YARS,downstream_gene_variant,,ENST00000487404,;YARS,downstream_gene_variant,,ENST00000469100,;YARS,downstream_gene_variant,,ENST00000490826,;YARS,downstream_gene_variant,,ENST00000478828,;KIAA1522,downstream_gene_variant,,ENST00000468130,;	T	ENSG00000162522	ENST00000401073	Transcript	missense_variant	2787	2717	906	S/L	tCg/tTg	rs776125780,COSM534909,COSM1648518	.	.	1	KIAA1522	HGNC	29301	protein_coding	YES	CCDS41298.1	ENSP00000383851	K1522_HUMAN	.	UPI000022ACD0	.	tolerated(0.11)	benign(0.362)	6/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF6	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GCCATCGGCCC	byFrequency	4	ESCA
ZMYM6	0	.	GRCh37	1	35480750	35480750	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442C>G	p.Pro148Ala	p.P148A	ENST00000357182	5/16	41	38	3	46	46	0	ZMYM6,missense_variant,p.Pro148Ala,ENST00000357182,;ZMYM6,missense_variant,p.Pro148Ala,ENST00000415531,;ZMYM6,missense_variant,p.Pro148Ala,ENST00000373340,;ZMYM6,downstream_gene_variant,,ENST00000373333,;ZMYM6,downstream_gene_variant,,ENST00000317538,;ZMYM6,non_coding_transcript_exon_variant,,ENST00000493328,;ZMYM6,downstream_gene_variant,,ENST00000460607,;ZMYM6,upstream_gene_variant,,ENST00000472971,;RP11-244H3.4,missense_variant,p.Pro148Ala,ENST00000487874,;	C	ENSG00000163867	ENST00000357182	Transcript	missense_variant	670	442	148	P/A	Cct/Gct	.	.	.	-1	ZMYM6	HGNC	13050	protein_coding	YES	CCDS387.2	ENSP00000349708	ZMYM6_HUMAN	Q7L9K1_HUMAN,A4Z946_HUMAN	UPI000040EBC6	.	tolerated(0.1)	possibly_damaging(0.865)	5/16	.	hmmpanther:PTHR11697:SF92,hmmpanther:PTHR11697,Pfam_domain:PF06467,SMART_domains:SM00746	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTAGGATTTA	.	2	ESCA
ZMYM6	0	.	GRCh37	1	35480759	35480759	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433A>G	p.Ile145Val	p.I145V	ENST00000357182	5/16	37	33	3	44	44	0	ZMYM6,missense_variant,p.Ile145Val,ENST00000357182,;ZMYM6,missense_variant,p.Ile145Val,ENST00000415531,;ZMYM6,missense_variant,p.Ile145Val,ENST00000373340,;ZMYM6,downstream_gene_variant,,ENST00000373333,;ZMYM6,downstream_gene_variant,,ENST00000317538,;ZMYM6,non_coding_transcript_exon_variant,,ENST00000493328,;ZMYM6,downstream_gene_variant,,ENST00000460607,;ZMYM6,upstream_gene_variant,,ENST00000472971,;RP11-244H3.4,missense_variant,p.Ile145Val,ENST00000487874,;	C	ENSG00000163867	ENST00000357182	Transcript	missense_variant	661	433	145	I/V	Att/Gtt	.	.	.	-1	ZMYM6	HGNC	13050	protein_coding	YES	CCDS387.2	ENSP00000349708	ZMYM6_HUMAN	Q7L9K1_HUMAN,A4Z946_HUMAN	UPI000040EBC6	.	deleterious(0.01)	probably_damaging(0.997)	5/16	.	hmmpanther:PTHR11697:SF92,hmmpanther:PTHR11697,Pfam_domain:PF06467,SMART_domains:SM00746	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAAAATGTCTC	.	3	ESCA
CSF3R	0	.	GRCh37	1	36931763	36931763	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*195G>C	.	.	ENST00000373103	17/17	65	57	8	70	70	0	CSF3R,missense_variant,p.Gln762His,ENST00000373104,;CSF3R,missense_variant,p.Gln762His,ENST00000331941,;CSF3R,3_prime_UTR_variant,,ENST00000464465,;CSF3R,3_prime_UTR_variant,,ENST00000418048,;CSF3R,3_prime_UTR_variant,,ENST00000338937,;CSF3R,3_prime_UTR_variant,,ENST00000373106,;CSF3R,3_prime_UTR_variant,,ENST00000373103,;CSF3R,3_prime_UTR_variant,,ENST00000361632,;CSF3R,downstream_gene_variant,,ENST00000440588,;MRPS15,upstream_gene_variant,,ENST00000373116,;CSF3R,non_coding_transcript_exon_variant,,ENST00000487540,;MRPS15,upstream_gene_variant,,ENST00000462067,;CSF3R,non_coding_transcript_exon_variant,,ENST00000480825,;CSF3R,downstream_gene_variant,,ENST00000466138,;CSF3R,downstream_gene_variant,,ENST00000484762,;CSF3R,downstream_gene_variant,,ENST00000464365,;	G	ENSG00000119535	ENST00000373103	Transcript	3_prime_UTR_variant	3335	.	.	.	.	.	.	.	-1	CSF3R	HGNC	2439	protein_coding	YES	CCDS414.1	ENSP00000362195	CSF3R_HUMAN	E9PK56_HUMAN	UPI000002AA5A	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGATCTGGTC	.	4	ESCA
ZMYND12	0	.	GRCh37	1	42902173	42902173	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.636G>C	p.Arg212Ser	p.R212S	ENST00000372565	5/8	90	83	6	85	85	0	ZMYND12,missense_variant,p.Arg102Ser,ENST00000433602,;ZMYND12,missense_variant,p.Arg212Ser,ENST00000372565,;ZMYND12,non_coding_transcript_exon_variant,,ENST00000461083,;ZMYND12,upstream_gene_variant,,ENST00000475426,;	G	ENSG00000066185	ENST00000372565	Transcript	missense_variant	906	636	212	R/S	agG/agC	.	.	.	-1	ZMYND12	HGNC	21192	protein_coding	YES	CCDS467.1	ENSP00000361646	ZMY12_HUMAN	.	UPI000020587B	.	tolerated(0.34)	benign(0.014)	5/8	.	hmmpanther:PTHR12298,Gene3D:1.25.40.10,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAGTCCTAAT	.	2	ESCA
KDM4A	0	.	GRCh37	1	44137335	44137335	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1523C>T	p.Ser508Leu	p.S508L	ENST00000372396	11/22	57	50	7	76	76	0	KDM4A,missense_variant,p.Ser508Leu,ENST00000372396,;KDM4A,downstream_gene_variant,,ENST00000463151,;KDM4A,downstream_gene_variant,,ENST00000472265,;KDM4A,downstream_gene_variant,,ENST00000485249,;	T	ENSG00000066135	ENST00000372396	Transcript	missense_variant	1657	1523	508	S/L	tCa/tTa	.	.	.	1	KDM4A	HGNC	22978	protein_coding	YES	CCDS491.1	ENSP00000361473	KDM4A_HUMAN	B4DGH3_HUMAN	UPI000013D35A	.	tolerated(0.29)	benign(0.004)	11/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10694:SF36,hmmpanther:PTHR10694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAATCATCTT	.	4	ESCA
RNF220	0	.	GRCh37	1	45110739	45110739	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1296G>A	p.%3D	p.R432R	ENST00000355387	10/15	64	60	4	48	48	0	RNF220,synonymous_variant,p.%3D,ENST00000440132,;RNF220,synonymous_variant,p.%3D,ENST00000361799,;RNF220,synonymous_variant,p.%3D,ENST00000335497,;RNF220,synonymous_variant,p.%3D,ENST00000443020,;RNF220,synonymous_variant,p.%3D,ENST00000355387,;RNF220,synonymous_variant,p.%3D,ENST00000372247,;TMEM53,intron_variant,,ENST00000372244,;TMEM53,intron_variant,,ENST00000372242,;TMEM53,intron_variant,,ENST00000372243,;RNF220,non_coding_transcript_exon_variant,,ENST00000474394,;RNF220,non_coding_transcript_exon_variant,,ENST00000497469,;RNF220,non_coding_transcript_exon_variant,,ENST00000484745,;RNF220,non_coding_transcript_exon_variant,,ENST00000480686,;RNF220,non_coding_transcript_exon_variant,,ENST00000471494,;RNF220,non_coding_transcript_exon_variant,,ENST00000474064,;RNF220,non_coding_transcript_exon_variant,,ENST00000475378,;TMEM53,intron_variant,,ENST00000495630,;RNF220,upstream_gene_variant,,ENST00000474956,;	A	ENSG00000187147	ENST00000355387	Transcript	synonymous_variant	1746	1296	432	R	cgG/cgA	.	.	.	1	RNF220	HGNC	25552	protein_coding	YES	CCDS510.1	ENSP00000347548	RN220_HUMAN	D3DPZ1_HUMAN	UPI000035895E	.	.	.	10/15	.	hmmpanther:PTHR13459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCGGGGCGC	.	2	ESCA
SLC5A9	0	.	GRCh37	1	48705040	48705040	+	Missense_Mutation	SNP	G	G	A	rs201842032	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1583G>A	p.Arg528His	p.R528H	ENST00000236495	13/15	93	80	12	116	116	0	SLC5A9,missense_variant,p.Arg524His,ENST00000533824,;SLC5A9,missense_variant,p.Arg503His,ENST00000438567,;SLC5A9,missense_variant,p.Arg528His,ENST00000236495,;SLC5A9,downstream_gene_variant,,ENST00000420136,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000525901,;SLC5A9,upstream_gene_variant,,ENST00000471020,;SLC5A9,3_prime_UTR_variant,,ENST00000425816,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000493837,;SLC5A9,downstream_gene_variant,,ENST00000441260,;SLC5A9,upstream_gene_variant,,ENST00000532322,;	A	ENSG00000117834	ENST00000236495	Transcript	missense_variant	1633	1583	528	R/H	cGt/cAt	rs201842032,COSM681853	.	.	1	SLC5A9	HGNC	22146	protein_coding	YES	CCDS44136.1	ENSP00000236495	SC5A9_HUMAN	.	UPI0000251D94	.	deleterious(0.01)	benign(0.082)	13/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF96,PROSITE_profiles:PS50283	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGCGTATGA	byCluster|by1000G	4	ESCA
DOCK7	0	.	GRCh37	1	62920905	62920905	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*180C>G	.	.	ENST00000340370	49/49	26	17	8	37	37	0	DOCK7,3_prime_UTR_variant,,ENST00000251157,;DOCK7,3_prime_UTR_variant,,ENST00000340370,;DOCK7,3_prime_UTR_variant,,ENST00000454575,;USP1,downstream_gene_variant,,ENST00000371146,;USP1,downstream_gene_variant,,ENST00000339950,;	C	ENSG00000116641	ENST00000340370	Transcript	3_prime_UTR_variant	6528	.	.	.	.	.	.	.	-1	DOCK7	HGNC	19190	protein_coding	YES	CCDS30734.1	ENSP00000340742	DOCK7_HUMAN	.	UPI000044FEA9	.	.	.	49/49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTAGAAACC	.	5	ESCA
MCOLN3	0	.	GRCh37	1	85506834	85506834	+	Silent	SNP	C	C	T	rs374738596	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255G>A	p.%3D	p.Q85Q	ENST00000370589	3/13	45	37	7	36	36	0	MCOLN3,synonymous_variant,p.%3D,ENST00000370589,;MCOLN3,synonymous_variant,p.%3D,ENST00000370587,;MCOLN3,intron_variant,,ENST00000341115,;WDR63,intron_variant,,ENST00000370596,;MCOLN3,synonymous_variant,p.%3D,ENST00000490600,;	T	ENSG00000055732	ENST00000370589	Transcript	synonymous_variant	308	255	85	Q	caG/caA	rs374738596	.	.	-1	MCOLN3	HGNC	13358	protein_coding	YES	CCDS701.1	ENSP00000359621	MCLN3_HUMAN	.	UPI0000073A4B	.	.	.	3/13	.	hmmpanther:PTHR12127,hmmpanther:PTHR12127:SF5	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATCTGGTT	byFrequency|byCluster	5	ESCA
ODF2L	0	.	GRCh37	1	86820363	86820363	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1617G>A	p.%3D	p.Q539Q	ENST00000359242	16/18	74	61	12	43	43	0	ODF2L,synonymous_variant,p.%3D,ENST00000370566,;ODF2L,synonymous_variant,p.%3D,ENST00000294678,;ODF2L,synonymous_variant,p.%3D,ENST00000359242,;ODF2L,synonymous_variant,p.%3D,ENST00000317336,;ODF2L,synonymous_variant,p.%3D,ENST00000370567,;ODF2L,synonymous_variant,p.%3D,ENST00000394731,;ODF2L,synonymous_variant,p.%3D,ENST00000460698,;ODF2L,synonymous_variant,p.%3D,ENST00000462648,;ODF2L,downstream_gene_variant,,ENST00000479890,;ODF2L,downstream_gene_variant,,ENST00000524695,;ODF2L,downstream_gene_variant,,ENST00000463933,;ODF2L,3_prime_UTR_variant,,ENST00000531412,;ODF2L,non_coding_transcript_exon_variant,,ENST00000473792,;ODF2L,non_coding_transcript_exon_variant,,ENST00000476054,;ODF2L,downstream_gene_variant,,ENST00000496592,;ODF2L,downstream_gene_variant,,ENST00000472144,;ODF2L,downstream_gene_variant,,ENST00000534092,;ODF2L,downstream_gene_variant,,ENST00000488879,;	T	ENSG00000122417	ENST00000359242	Transcript	synonymous_variant	1899	1617	539	Q	caG/caA	.	.	.	-1	ODF2L	HGNC	29225	protein_coding	YES	CCDS41354.2	ENSP00000359600	ODF2L_HUMAN	B5ME44_HUMAN	UPI00001C1D6A	.	.	.	16/18	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23162:SF7,hmmpanther:PTHR23162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCTGTTC	.	5	ESCA
KIF3B	0	.	GRCh37	20	30919335	30919335	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*213C>T	.	.	ENST00000375712	9/9	45	41	3	33	33	0	KIF3B,3_prime_UTR_variant,,ENST00000375712,;KIF3B,3_prime_UTR_variant,,ENST00000418717,;	T	ENSG00000101350	ENST00000375712	Transcript	3_prime_UTR_variant	2624	.	.	.	.	.	.	.	1	KIF3B	HGNC	6320	protein_coding	YES	CCDS13200.1	ENSP00000364864	KIF3B_HUMAN	.	UPI000012DDB1	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCATCTCAGA	.	2	ESCA
ASXL1	0	.	GRCh37	20	31024392	31024392	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000375687	13/13	81	70	11	74	74	0	ASXL1,missense_variant,p.Asp1293Asn,ENST00000375687,;ASXL1,missense_variant,p.Asp1288Asn,ENST00000306058,;ASXL1,downstream_gene_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000555564,;	A	ENSG00000171456	ENST00000375687	Transcript	missense_variant	4301	3877	1293	D/N	Gat/Aat	.	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	tolerated(0.82)	benign(0.004)	13/13	.	hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGTGATCAG	.	4	ESCA
EDEM2	0	.	GRCh37	20	33735139	33735139	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-78G>A	.	.	ENST00000374492	1/11	58	52	6	35	35	0	EDEM2,5_prime_UTR_variant,,ENST00000374492,;EDEM2,5_prime_UTR_variant,,ENST00000542871,;EDEM2,intron_variant,,ENST00000540582,;EDEM2,upstream_gene_variant,,ENST00000374491,;EDEM2,upstream_gene_variant,,ENST00000541621,;	T	ENSG00000088298	ENST00000374492	Transcript	5_prime_UTR_variant	29	.	.	.	.	.	.	.	-1	EDEM2	HGNC	15877	protein_coding	YES	CCDS13247.1	ENSP00000363616	EDEM2_HUMAN	B4E1F4_HUMAN	UPI00001285D9	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGTTCTTCCG	.	3	ESCA
CPNE1	0	.	GRCh37	20	34219461	34219461	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682C>G	p.Leu228Val	p.L228V	ENST00000317677	8/16	61	56	4	64	64	0	CPNE1,missense_variant,p.Leu223Val,ENST00000352393,;CPNE1,missense_variant,p.Leu223Val,ENST00000397443,;CPNE1,missense_variant,p.Leu228Val,ENST00000317677,;CPNE1,missense_variant,p.Leu223Val,ENST00000397442,;CPNE1,missense_variant,p.Leu199Val,ENST00000412056,;CPNE1,missense_variant,p.Leu223Val,ENST00000317619,;CPNE1,missense_variant,p.Leu199Val,ENST00000430570,;CPNE1,missense_variant,p.Leu199Val,ENST00000416778,;CPNE1,missense_variant,p.Leu223Val,ENST00000439806,;CPNE1,missense_variant,p.Leu223Val,ENST00000437340,;CPNE1,missense_variant,p.Leu223Val,ENST00000397445,;CPNE1,missense_variant,p.Leu223Val,ENST00000414664,;CPNE1,missense_variant,p.Leu223Val,ENST00000397446,;CPNE1,upstream_gene_variant,,ENST00000415920,;CPNE1,downstream_gene_variant,,ENST00000414711,;CPNE1,downstream_gene_variant,,ENST00000458038,;CPNE1,downstream_gene_variant,,ENST00000434795,;CPNE1,downstream_gene_variant,,ENST00000440240,;CPNE1,downstream_gene_variant,,ENST00000435747,;CPNE1,downstream_gene_variant,,ENST00000420363,;CPNE1,downstream_gene_variant,,ENST00000437100,;CPNE1,upstream_gene_variant,,ENST00000498056,;CPNE1,upstream_gene_variant,,ENST00000462352,;CPNE1,upstream_gene_variant,,ENST00000498814,;CPNE1,missense_variant,p.Leu223Val,ENST00000401607,;CPNE1,non_coding_transcript_exon_variant,,ENST00000486021,;CPNE1,non_coding_transcript_exon_variant,,ENST00000483495,;CPNE1,non_coding_transcript_exon_variant,,ENST00000483359,;RP1-309K20.6,downstream_gene_variant,,ENST00000541176,;RP1-309K20.6,downstream_gene_variant,,ENST00000454607,;CPNE1,upstream_gene_variant,,ENST00000473373,;CPNE1,downstream_gene_variant,,ENST00000439669,;RP1-309K20.6,downstream_gene_variant,,ENST00000441563,;	C	ENSG00000214078	ENST00000317677	Transcript	missense_variant	817	682	228	L/V	Ctc/Gtc	.	.	.	-1	CPNE1	HGNC	2314	protein_coding	YES	CCDS46595.1	ENSP00000317257	.	Q5JX60_HUMAN,Q5JX59_HUMAN,Q5JX58_HUMAN,Q5JX56_HUMAN,Q5JX55_HUMAN,Q5JX54_HUMAN,Q5JX53_HUMAN,Q5JX44_HUMAN,B0QZ18_HUMAN	UPI0000D4B36B	.	deleterious(0.01)	probably_damaging(0.94)	8/16	.	Superfamily_domains:SSF49562,SMART_domains:SM00239,Pfam_domain:PF00168,Gene3D:2.60.40.150,hmmpanther:PTHR10857:SF2,hmmpanther:PTHR10857,PROSITE_profiles:PS50004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGAGATCAT	.	2	ESCA
CNBD2	0	.	GRCh37	20	34556687	34556687	+	Translation_Start_Site	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3G>A	p.Met1?	p.M1?	ENST00000349339	1/12	41	35	5	26	26	0	CNBD2,start_lost,p.Met1?,ENST00000373973,;CNBD2,start_lost,p.Met1?,ENST00000538900,;CNBD2,start_lost,p.Met1?,ENST00000349339,;CNBD2,start_lost,p.Met1?,ENST00000463258,;CNBD2,non_coding_transcript_exon_variant,,ENST00000489667,;	A	ENSG00000149646	ENST00000349339	Transcript	start_lost	159	3	1	M/I	atG/atA	.	.	.	1	CNBD2	HGNC	16145	protein_coding	YES	CCDS13270.1	ENSP00000340954	CNBD2_HUMAN	.	UPI0000367038	.	deleterious_low_confidence(0)	possibly_damaging(0.882)	1/12	.	hmmpanther:PTHR23011:SF1,hmmpanther:PTHR23011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCATGAGGAG	.	4	ESCA
KIAA1755	0	.	GRCh37	20	36855583	36855583	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2025C>T	p.%3D	p.L675L	ENST00000279024	7/14	88	72	16	77	77	0	KIAA1755,synonymous_variant,p.%3D,ENST00000435901,;KIAA1755,synonymous_variant,p.%3D,ENST00000279024,;KIAA1755,non_coding_transcript_exon_variant,,ENST00000496900,;KIAA1755,upstream_gene_variant,,ENST00000484362,;	A	ENSG00000149633	ENST00000279024	Transcript	synonymous_variant	2297	2025	675	L	ctC/ctT	.	.	.	-1	KIAA1755	HGNC	29372	protein_coding	YES	CCDS33467.1	ENSP00000279024	K1755_HUMAN	.	UPI000041AADF	.	.	.	7/14	.	hmmpanther:PTHR22826:SF114,hmmpanther:PTHR22826,Pfam_domain:PF13716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGGAGAGC	.	5	ESCA
ACTR5	0	.	GRCh37	20	37378784	37378784	+	Silent	SNP	C	C	T	rs778434062	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.F169F	ENST00000243903	2/9	126	119	7	109	108	1	ACTR5,synonymous_variant,p.%3D,ENST00000243903,;	T	ENSG00000101442	ENST00000243903	Transcript	synonymous_variant	544	507	169	F	ttC/ttT	rs778434062	.	.	1	ACTR5	HGNC	14671	protein_coding	YES	CCDS13308.1	ENSP00000243903	ARP5_HUMAN	.	UPI000006F9EF	.	.	.	2/9	.	hmmpanther:PTHR11937:SF16,hmmpanther:PTHR11937,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCTTCAGCTT	.	2	ESCA
PPP1R16B	0	.	GRCh37	20	37536771	37536771	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129C>T	p.Gln377Ter	p.Q377*	ENST00000299824	10/11	74	64	10	113	113	0	PPP1R16B,stop_gained,p.Gln377Ter,ENST00000299824,;PPP1R16B,stop_gained,p.Gln335Ter,ENST00000373331,;	T	ENSG00000101445	ENST00000299824	Transcript	stop_gained	1318	1129	377	Q/*	Cag/Tag	COSM1751450	.	.	1	PPP1R16B	HGNC	15850	protein_coding	YES	CCDS13309.1	ENSP00000299824	PP16B_HUMAN	.	UPI0000132059	.	.	.	10/11	.	hmmpanther:PTHR24186,PIRSF_domain:PIRSF038159	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATCAGCGG	.	4	ESCA
PKIG	0	.	GRCh37	20	43243230	43243230	+	Silent	SNP	C	C	T	rs762724888	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33C>T	p.%3D	p.F11F	ENST00000372889	5/6	64	57	7	55	55	0	PKIG,synonymous_variant,p.%3D,ENST00000372891,;PKIG,synonymous_variant,p.%3D,ENST00000372882,;PKIG,synonymous_variant,p.%3D,ENST00000372894,;PKIG,synonymous_variant,p.%3D,ENST00000372892,;PKIG,synonymous_variant,p.%3D,ENST00000372887,;PKIG,synonymous_variant,p.%3D,ENST00000349959,;PKIG,synonymous_variant,p.%3D,ENST00000372886,;PKIG,synonymous_variant,p.%3D,ENST00000372889,;Z97053.1,intron_variant,,ENST00000597250,;ADA,downstream_gene_variant,,ENST00000372874,;PKIG,non_coding_transcript_exon_variant,,ENST00000477390,;ADA,downstream_gene_variant,,ENST00000464097,;ADA,downstream_gene_variant,,ENST00000536532,;	T	ENSG00000168734	ENST00000372889	Transcript	synonymous_variant	618	33	11	F	ttC/ttT	rs762724888	.	.	1	PKIG	HGNC	9019	protein_coding	YES	CCDS13334.1	ENSP00000361980	IPKG_HUMAN	Q549H9_HUMAN	UPI000012D7F5	.	.	.	5/6	.	hmmpanther:PTHR15416,hmmpanther:PTHR15416:SF5,Pfam_domain:PF02827,PIRSF_domain:PIRSF001667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GACTTCATCTC	.	3	ESCA
ARFGEF2	0	.	GRCh37	20	47587679	47587679	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213G>A	p.Val405Met	p.V405M	ENST00000371917	10/39	118	95	22	74	74	0	ARFGEF2,missense_variant,p.Val405Met,ENST00000371917,;	A	ENSG00000124198	ENST00000371917	Transcript	missense_variant	1213	1213	405	V/M	Gtg/Atg	.	.	.	1	ARFGEF2	HGNC	15853	protein_coding	YES	CCDS13411.1	ENSP00000360985	BIG2_HUMAN	Q59FR3_HUMAN	UPI000013D378	.	tolerated(0.05)	benign(0.207)	10/39	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF124,Pfam_domain:PF12783,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.R402C|c.1204C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGGTGGTT	.	5	ESCA
CSE1L	0	.	GRCh37	20	47710696	47710697	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2473dupA	p.Ile825AsnfsTer5	p.I825Nfs*5	ENST00000262982	23/25	99	78	21	117	117	0	CSE1L,frameshift_variant,p.Ile608AsnfsTer5,ENST00000542325,;CSE1L,frameshift_variant,p.Ile769AsnfsTer5,ENST00000396192,;CSE1L,frameshift_variant,p.Ile825AsnfsTer5,ENST00000262982,;CSE1L,non_coding_transcript_exon_variant,,ENST00000469700,;	A	ENSG00000124207	ENST00000262982	Transcript	frameshift_variant	2590-2591	2467-2468	823	E/EX	gaa/gAaa	.	.	.	1	CSE1L	HGNC	2431	protein_coding	YES	CCDS13412.1	ENSP00000262982	XPO2_HUMAN	.	UPI000013D377	.	.	.	23/25	.	hmmpanther:PTHR10997,hmmpanther:PTHR10997:SF8,Pfam_domain:PF03378,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTGGAAAAA	.	3	ESCA
SNAI1	0	.	GRCh37	20	48604987	48604987	+	3'UTR	SNP	C	C	A	rs188628261	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*394C>A	.	.	ENST00000244050	3/3	155	125	30	140	140	0	SNAI1,3_prime_UTR_variant,,ENST00000244050,;	A	ENSG00000124216	ENST00000244050	Transcript	3_prime_UTR_variant	1250	.	.	.	.	rs188628261	.	.	1	SNAI1	HGNC	11128	protein_coding	YES	CCDS13423.1	ENSP00000244050	SNAI1_HUMAN	.	UPI0000135B17	.	.	.	3/3	.	.	A:0.0008	A:0	A:0	.	A:0	A:0.004	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACACCCCCCC	byFrequency|byCluster|by1000G	4	ESCA
YTHDF1	0	.	GRCh37	20	61834342	61834342	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.950A>T	p.Tyr317Phe	p.Y317F	ENST00000370339	4/5	63	52	11	40	40	0	YTHDF1,missense_variant,p.Tyr317Phe,ENST00000370339,;YTHDF1,missense_variant,p.Tyr267Phe,ENST00000370333,;YTHDF1,intron_variant,,ENST00000370334,;	A	ENSG00000149658	ENST00000370339	Transcript	missense_variant	1292	950	317	Y/F	tAt/tTt	.	.	.	-1	YTHDF1	HGNC	15867	protein_coding	YES	CCDS13511.1	ENSP00000359364	YTHD1_HUMAN	F8W840_HUMAN	UPI0000128DD9	.	tolerated(0.61)	benign(0.001)	4/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12357,hmmpanther:PTHR12357:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGATACTGC	.	5	ESCA
HELZ2	0	.	GRCh37	20	62194139	62194139	+	Silent	SNP	G	G	A	rs140899217	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6036C>T	p.%3D	p.L2012L	ENST00000467148	8/19	77	72	5	51	51	0	HELZ2,synonymous_variant,p.%3D,ENST00000467148,;HELZ2,synonymous_variant,p.%3D,ENST00000427522,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,upstream_gene_variant,,ENST00000478861,;	A	ENSG00000130589	ENST00000467148	Transcript	synonymous_variant	6106	6036	2012	L	ctC/ctT	rs140899217	.	.	-1	HELZ2	HGNC	30021	protein_coding	YES	CCDS33508.1	ENSP00000417401	HELZ2_HUMAN	Q3C1U4_HUMAN	UPI0000246BF7	.	.	.	8/19	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF332	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P2016L|c.6047C>T|6	MUTECT|MUSE	CCCTCGAGCCG	byCluster|by1000G	2	ESCA
HUNK	0	.	GRCh37	21	33346945	33346945	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089C>G	p.Ile363Met	p.I363M	ENST00000270112	7/11	21	18	3	27	27	0	HUNK,missense_variant,p.Ile363Met,ENST00000270112,;HUNK,upstream_gene_variant,,ENST00000439107,;HUNK,non_coding_transcript_exon_variant,,ENST00000465574,;	G	ENSG00000142149	ENST00000270112	Transcript	missense_variant	1449	1089	363	I/M	atC/atG	.	.	.	1	HUNK	HGNC	13326	protein_coding	YES	CCDS13610.1	ENSP00000270112	HUNK_HUMAN	.	UPI0000035B66	.	deleterious(0.03)	possibly_damaging(0.757)	7/11	.	hmmpanther:PTHR24343:SF152,hmmpanther:PTHR24343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GTGATCAACAC	.	3	ESCA
OLIG1	0	.	GRCh37	21	34444062	34444062	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*694C>A	.	.	ENST00000382348	1/1	139	105	34	94	94	0	OLIG1,3_prime_UTR_variant,,ENST00000333063,;OLIG1,3_prime_UTR_variant,,ENST00000382348,;OLIG1,intron_variant,,ENST00000426947,;AP000282.2,upstream_gene_variant,,ENST00000454622,;AP000282.2,upstream_gene_variant,,ENST00000420356,;OLIG1,intron_variant,,ENST00000498799,;	A	ENSG00000184221	ENST00000382348	Transcript	3_prime_UTR_variant	1613	.	.	.	.	.	.	.	1	OLIG1	HGNC	16983	protein_coding	YES	CCDS42920.2	ENSP00000371785	OLIG1_HUMAN	Q59EM0_HUMAN	UPI0000130C80	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTCCACTTT	.	5	ESCA
IL10RB	0	.	GRCh37	21	34655516	34655516	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616G>C	p.Glu206Gln	p.E206Q	ENST00000290200	5/7	76	70	6	51	51	0	IL10RB,missense_variant,p.Glu206Gln,ENST00000290200,;AP000295.9,incomplete_terminal_codon_variant,p.%3D,ENST00000433395,;IL10RB,missense_variant,p.Glu143Gln,ENST00000451065,;AP000295.9,3_prime_UTR_variant,,ENST00000432231,;IL10RB,3_prime_UTR_variant,,ENST00000422891,;IL10RB,non_coding_transcript_exon_variant,,ENST00000493295,;IL10RB,non_coding_transcript_exon_variant,,ENST00000498371,;	C	ENSG00000243646	ENST00000290200	Transcript	missense_variant	724	616	206	E/Q	Gag/Cag	.	.	.	1	IL10RB	HGNC	5965	protein_coding	YES	CCDS13623.1	ENSP00000290200	I10R2_HUMAN	.	UPI0000072ECA	.	tolerated(0.4)	benign(0.014)	5/7	.	PROSITE_profiles:PS50853,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF50,Pfam_domain:PF09294,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGAGTGAGCCT	.	3	ESCA
BRWD1	0	.	GRCh37	21	40601246	40601246	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3117C>T	p.%3D	p.F1039F	ENST00000333229	26/42	51	44	7	83	83	0	BRWD1,synonymous_variant,p.%3D,ENST00000424441,;BRWD1,synonymous_variant,p.%3D,ENST00000342449,;BRWD1,synonymous_variant,p.%3D,ENST00000380800,;BRWD1,synonymous_variant,p.%3D,ENST00000333229,;BRWD1,synonymous_variant,p.%3D,ENST00000446924,;	A	ENSG00000185658	ENST00000333229	Transcript	synonymous_variant	3445	3117	1039	F	ttC/ttT	.	.	.	-1	BRWD1	HGNC	12760	protein_coding	YES	CCDS13662.1	ENSP00000330753	BRWD1_HUMAN	.	UPI0000163C12	.	.	.	26/42	.	hmmpanther:PTHR16266:SF26,hmmpanther:PTHR16266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGAGAAAGA	.	4	ESCA
AGPAT3	0	.	GRCh37	21	45404588	45404588	+	3'UTR	SNP	T	T	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2315T>G	.	.	ENST00000398063	9/9	28	23	5	30	29	1	AGPAT3,3_prime_UTR_variant,,ENST00000398063,;AGPAT3,3_prime_UTR_variant,,ENST00000291572,;AGPAT3,downstream_gene_variant,,ENST00000398061,;AGPAT3,downstream_gene_variant,,ENST00000546158,;AGPAT3,downstream_gene_variant,,ENST00000327505,;AGPAT3,downstream_gene_variant,,ENST00000398058,;AGPAT3,downstream_gene_variant,,ENST00000479117,;AGPAT3,downstream_gene_variant,,ENST00000484865,;AGPAT3,downstream_gene_variant,,ENST00000467358,;	G	ENSG00000160216	ENST00000398063	Transcript	3_prime_UTR_variant	3938	.	.	.	.	.	.	.	1	AGPAT3	HGNC	326	protein_coding	YES	CCDS13703.1	ENSP00000381140	PLCC_HUMAN	C9JQX8_HUMAN,C9JL26_HUMAN,C9JK35_HUMAN,C9J184_HUMAN	UPI000004616E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	GAGGGTGGATT	.	2	ESCA
COL6A2	0	.	GRCh37	21	47542073	47542073	+	Splice_Site	SNP	G	G	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1572+1G>A	.	p.X524_splice	ENST00000300527	.	59	52	6	79	79	0	COL6A2,splice_donor_variant,,ENST00000413758,;COL6A2,splice_donor_variant,,ENST00000397763,;COL6A2,splice_donor_variant,,ENST00000310645,;COL6A2,splice_donor_variant,,ENST00000300527,;COL6A2,splice_donor_variant,,ENST00000357838,;COL6A2,splice_donor_variant,,ENST00000409416,;COL6A2,downstream_gene_variant,,ENST00000485591,;	A	ENSG00000142173	ENST00000300527	Transcript	splice_donor_variant	.	.	.	.	.	CS075105	.	.	1	COL6A2	HGNC	2212	protein_coding	YES	CCDS13728.1	ENSP00000300527	CO6A2_HUMAN	C9JH44_HUMAN	UPI00001AECE0	.	.	.	.	19/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCCGTGAGT	.	4	ESCA
PI4KA	0	.	GRCh37	22	21062288	21062288	+	3'UTR	SNP	G	G	C	rs780944210	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*47C>G	.	.	ENST00000255882	55/55	77	54	22	93	93	0	PI4KA,3_prime_UTR_variant,,ENST00000255882,;PI4KA,3_prime_UTR_variant,,ENST00000399213,;PI4KA,3_prime_UTR_variant,,ENST00000414196,;PI4KA,3_prime_UTR_variant,,ENST00000572273,;TMEM191A,downstream_gene_variant,,ENST00000419950,;TMEM191A,downstream_gene_variant,,ENST00000445836,;TMEM191A,downstream_gene_variant,,ENST00000450925,;TMEM191A,downstream_gene_variant,,ENST00000442222,;PI4KA,non_coding_transcript_exon_variant,,ENST00000492581,;PI4KA,non_coding_transcript_exon_variant,,ENST00000466772,;PI4KA,non_coding_transcript_exon_variant,,ENST00000477245,;TMEM191A,downstream_gene_variant,,ENST00000454833,;TMEM191A,downstream_gene_variant,,ENST00000414022,;TMEM191A,downstream_gene_variant,,ENST00000436618,;TMEM191A,downstream_gene_variant,,ENST00000428752,;PI4KA,downstream_gene_variant,,ENST00000482030,;TMEM191A,downstream_gene_variant,,ENST00000422715,;PI4KA,downstream_gene_variant,,ENST00000466394,;TMEM191A,downstream_gene_variant,,ENST00000452055,;	C	ENSG00000241973	ENST00000255882	Transcript	3_prime_UTR_variant	6443	.	.	.	.	rs780944210	.	.	-1	PI4KA	HGNC	8983	protein_coding	YES	CCDS33603.2	ENSP00000255882	.	Q4LE69_HUMAN,J3KN10_HUMAN,C9JLI1_HUMAN	UPI0000E06BD6	.	.	.	55/55	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGGGACAGC	.	5	ESCA
MMP11	0	.	GRCh37	22	24121532	24121532	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267G>A	p.%3D	p.L89L	ENST00000215743	2/8	92	73	18	75	75	0	MMP11,synonymous_variant,p.%3D,ENST00000215743,;AP000349.1,downstream_gene_variant,,ENST00000598975,;MMP11,non_coding_transcript_exon_variant,,ENST00000489582,;MMP11,non_coding_transcript_exon_variant,,ENST00000477567,;MMP11,non_coding_transcript_exon_variant,,ENST00000460352,;MMP11,upstream_gene_variant,,ENST00000488363,;MMP11,upstream_gene_variant,,ENST00000480185,;MMP11,synonymous_variant,p.%3D,ENST00000428253,;MMP11,synonymous_variant,p.%3D,ENST00000437086,;MMP11,non_coding_transcript_exon_variant,,ENST00000465385,;MMP11,non_coding_transcript_exon_variant,,ENST00000465730,;MMP11,upstream_gene_variant,,ENST00000493132,;MMP11,upstream_gene_variant,,ENST00000434318,;MMP11,upstream_gene_variant,,ENST00000492464,;	A	ENSG00000099953	ENST00000215743	Transcript	synonymous_variant	319	267	89	L	ctG/ctA	COSM726169	.	.	1	MMP11	HGNC	7157	protein_coding	YES	CCDS13816.1	ENSP00000215743	MMP11_HUMAN	F8WDI7_HUMAN	UPI00001AE5D9	.	.	.	2/8	.	hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF20,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTGAGTGC	.	5	ESCA
ASPHD2	0	.	GRCh37	22	26830127	26830127	+	Silent	SNP	C	C	T	rs747823171	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.546C>T	p.%3D	p.D182D	ENST00000215906	2/4	58	43	14	69	69	0	ASPHD2,synonymous_variant,p.%3D,ENST00000215906,;	T	ENSG00000128203	ENST00000215906	Transcript	synonymous_variant	984	546	182	D	gaC/gaT	rs747823171	.	.	1	ASPHD2	HGNC	30437	protein_coding	YES	CCDS13834.2	ENSP00000215906	ASPH2_HUMAN	B3KUG5_HUMAN	UPI000037659F	.	.	.	2/4	.	hmmpanther:PTHR12366,hmmpanther:PTHR12366:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGACGCACA	.	5	ESCA
SMTN	0	.	GRCh37	22	31494798	31494798	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2305G>A	p.Glu769Lys	p.E769K	ENST00000358743	17/21	55	38	17	91	91	0	SMTN,missense_variant,p.Glu170Lys,ENST00000455608,;SMTN,missense_variant,p.Glu769Lys,ENST00000333137,;SMTN,missense_variant,p.Glu769Lys,ENST00000358743,;SMTN,missense_variant,p.Glu292Lys,ENST00000404574,;SMTN,missense_variant,p.Glu769Lys,ENST00000347557,;SMTN,non_coding_transcript_exon_variant,,ENST00000493335,;SMTN,non_coding_transcript_exon_variant,,ENST00000489337,;SMTN,non_coding_transcript_exon_variant,,ENST00000460658,;SMTN,upstream_gene_variant,,ENST00000472911,;SMTN,upstream_gene_variant,,ENST00000504335,;	A	ENSG00000183963	ENST00000358743	Transcript	missense_variant	2523	2305	769	E/K	Gag/Aag	.	.	.	1	SMTN	HGNC	11126	protein_coding	YES	CCDS13887.1	ENSP00000351593	SMTN_HUMAN	C9JP19_HUMAN,C9JGQ0_HUMAN	UPI00001B0272	.	deleterious(0.01)	benign(0.42)	17/21	.	hmmpanther:PTHR11915:SF208,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATTGAGAAG	.	5	ESCA
CHADL	0	.	GRCh37	22	41633274	41633274	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1802C>T	p.Ser601Leu	p.S601L	ENST00000216241	3/6	76	55	21	82	82	0	CHADL,missense_variant,p.Ser98Leu,ENST00000455425,;CHADL,missense_variant,p.Ser599Leu,ENST00000417999,;CHADL,missense_variant,p.Ser601Leu,ENST00000216241,;	A	ENSG00000100399	ENST00000216241	Transcript	missense_variant	1855	1802	601	S/L	tCg/tTg	.	.	.	-1	CHADL	HGNC	25165	protein_coding	YES	CCDS46715.1	ENSP00000216241	CHADL_HUMAN	.	UPI00001C2057	.	deleterious(0)	probably_damaging(0.971)	3/6	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF24,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00364,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCCGAGAGC	.	5	ESCA
GRAMD4	0	.	GRCh37	22	47069633	47069633	+	Missense_Mutation	SNP	G	G	A	rs751034556	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1306G>A	p.Ala436Thr	p.A436T	ENST00000406902	15/19	89	75	14	106	106	0	GRAMD4,missense_variant,p.Ala436Thr,ENST00000406902,;GRAMD4,missense_variant,p.Ala436Thr,ENST00000361034,;GRAMD4,downstream_gene_variant,,ENST00000456069,;GRAMD4,upstream_gene_variant,,ENST00000408031,;	A	ENSG00000075240	ENST00000406902	Transcript	missense_variant	1519	1306	436	A/T	Gcc/Acc	rs751034556	.	.	1	GRAMD4	HGNC	29113	protein_coding	YES	CCDS33672.1	ENSP00000385689	GRAM4_HUMAN	.	UPI0000161A59	.	tolerated(0.42)	benign(0.001)	15/19	.	hmmpanther:PTHR16122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGACGCCGGT	byFrequency	4	ESCA
ZBED4	0	.	GRCh37	22	50282293	50282293	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1467C>T	.	.	ENST00000216268	2/2	50	41	9	34	34	0	ZBED4,3_prime_UTR_variant,,ENST00000216268,;	T	ENSG00000100426	ENST00000216268	Transcript	3_prime_UTR_variant	5460	.	.	.	.	.	.	.	1	ZBED4	HGNC	20721	protein_coding	YES	CCDS33677.1	ENSP00000216268	ZBED4_HUMAN	.	UPI000013C6DB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GTGTTCAAGTG	.	4	ESCA
IL36B	0	.	GRCh37	2	113788674	113788674	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72G>C	p.%3D	p.L24L	ENST00000259213	3/6	77	70	7	100	100	0	IL36B,synonymous_variant,p.%3D,ENST00000327407,;IL36B,synonymous_variant,p.%3D,ENST00000259213,;	G	ENSG00000136696	ENST00000259213	Transcript	synonymous_variant	180	72	24	L	ctG/ctC	.	.	.	-1	IL36B	HGNC	15564	protein_coding	YES	CCDS2109.1	ENSP00000259213	IL36B_HUMAN	.	UPI000003C9C0	.	.	.	3/6	.	hmmpanther:PTHR10078,hmmpanther:PTHR10078:SF11,Gene3D:2.80.10.50,Superfamily_domains:SSF50353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G26R|c.76G>A|3,BUFFER|p.G26R|c.76G>A|3,BUFFER|p.G26R|c.76G>A|3	MUTECT|MUSE|VARSCANS	CCACTCAGGAC	.	3	ESCA
CCDC93	0	.	GRCh37	2	118732778	118732778	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736C>T	p.Arg246Ter	p.R246*	ENST00000376300	9/24	41	36	5	43	43	0	CCDC93,stop_gained,p.Arg246Ter,ENST00000376300,;CCDC93,stop_gained,p.Arg245Ter,ENST00000319432,;CCDC93,non_coding_transcript_exon_variant,,ENST00000460781,;	A	ENSG00000125633	ENST00000376300	Transcript	stop_gained	874	736	246	R/*	Cga/Tga	COSM3565667	.	.	-1	CCDC93	HGNC	25611	protein_coding	YES	CCDS2121.2	ENSP00000365477	CCD93_HUMAN	.	UPI0000207DEC	.	.	.	9/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16441	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTCGAAGCT	.	4	ESCA
SAP130	0	.	GRCh37	2	128757988	128757988	+	Missense_Mutation	SNP	T	T	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.988A>T	p.Ile330Phe	p.I330F	ENST00000357702	8/21	85	77	8	70	70	0	SAP130,missense_variant,p.Ile330Phe,ENST00000259235,;SAP130,missense_variant,p.Ile304Phe,ENST00000259234,;SAP130,missense_variant,p.Ile330Phe,ENST00000357702,;	A	ENSG00000136715	ENST00000357702	Transcript	missense_variant	1120	988	330	I/F	Atc/Ttc	COSM1613382,COSM1613381	.	.	-1	SAP130	HGNC	29813	protein_coding	YES	CCDS54397.1	ENSP00000350333	SP130_HUMAN	Q96DP1_HUMAN,C9J683_HUMAN	UPI00005989D6	.	deleterious_low_confidence(0)	probably_damaging(0.974)	8/21	.	hmmpanther:PTHR13497	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTGATTGCTG	.	3	ESCA
IMP4	0	.	GRCh37	2	131100504	131100504	+	5'UTR	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2A>G	.	.	ENST00000259239	1/9	65	57	8	79	79	0	IMP4,5_prime_UTR_variant,,ENST00000259239,;IMP4,5_prime_UTR_variant,,ENST00000428740,;IMP4,5_prime_UTR_variant,,ENST00000409649,;IMP4,5_prime_UTR_variant,,ENST00000409935,;CCDC115,upstream_gene_variant,,ENST00000409127,;CCDC115,upstream_gene_variant,,ENST00000437688,;IMP4,upstream_gene_variant,,ENST00000452955,;CCDC115,upstream_gene_variant,,ENST00000259229,;IMP4,5_prime_UTR_variant,,ENST00000456713,;IMP4,non_coding_transcript_exon_variant,,ENST00000477375,;IMP4,non_coding_transcript_exon_variant,,ENST00000460766,;IMP4,non_coding_transcript_exon_variant,,ENST00000462392,;IMP4,non_coding_transcript_exon_variant,,ENST00000470672,;IMP4,non_coding_transcript_exon_variant,,ENST00000490895,;IMP4,non_coding_transcript_exon_variant,,ENST00000464432,;IMP4,non_coding_transcript_exon_variant,,ENST00000473689,;IMP4,non_coding_transcript_exon_variant,,ENST00000495606,;IMP4,upstream_gene_variant,,ENST00000462357,;IMP4,upstream_gene_variant,,ENST00000475074,;CCDC115,upstream_gene_variant,,ENST00000442217,;CCDC115,upstream_gene_variant,,ENST00000465315,;IMP4,upstream_gene_variant,,ENST00000460100,;	G	ENSG00000136718	ENST00000259239	Transcript	5_prime_UTR_variant	707	.	.	.	.	.	.	.	1	IMP4	HGNC	30856	protein_coding	YES	CCDS2160.1	ENSP00000259239	IMP4_HUMAN	Q3ZTT3_HUMAN,B9A008_HUMAN	UPI0000071F26	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCAAGATGG	.	4	ESCA
ZEB2	0	.	GRCh37	2	145182392	145182392	+	Missense_Mutation	SNP	G	G	A	rs727504227	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.374C>T	p.Thr125Met	p.T125M	ENST00000558170	4/10	90	81	9	96	96	0	ZEB2,missense_variant,p.Thr125Met,ENST00000392861,;ZEB2,missense_variant,p.Thr125Met,ENST00000431672,;ZEB2,missense_variant,p.Thr125Met,ENST00000303660,;ZEB2,missense_variant,p.Thr112Met,ENST00000440875,;ZEB2,missense_variant,p.Thr125Met,ENST00000427902,;ZEB2,missense_variant,p.Thr125Met,ENST00000409487,;ZEB2,missense_variant,p.Thr125Met,ENST00000558170,;ZEB2,missense_variant,p.Thr125Met,ENST00000409211,;ZEB2,intron_variant,,ENST00000539609,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000434448,;ZEB2,downstream_gene_variant,,ENST00000479735,;ZEB2,downstream_gene_variant,,ENST00000461784,;ZEB2,downstream_gene_variant,,ENST00000560384,;ZEB2,downstream_gene_variant,,ENST00000472146,;ZEB2,downstream_gene_variant,,ENST00000465308,;ZEB2,downstream_gene_variant,,ENST00000476394,;	A	ENSG00000169554	ENST00000558170	Transcript	missense_variant	1559	374	125	T/M	aCg/aTg	rs727504227	.	.	-1	ZEB2	HGNC	14881	protein_coding	YES	CCDS2186.1	ENSP00000454157	ZEB2_HUMAN	U3KPV5_HUMAN,Q53TG0_HUMAN,Q53TD9_HUMAN,E7EUW9_HUMAN,E7ESP8_HUMAN,C9JUQ1_HUMAN,C9JU62_HUMAN,A0JP08_HUMAN	UPI00001359A2	.	tolerated(0.06)	benign(0.143)	4/10	.	hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF2	.	.	.	.	.	.	.	.	.	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATCGTGGCT	byFrequency|byCluster	4	ESCA
PKP4	0	.	GRCh37	2	159533373	159533373	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3250T>G	p.Tyr1084Asp	p.Y1084D	ENST00000389759	20/22	104	92	12	139	138	0	PKP4,missense_variant,p.Tyr1084Asp,ENST00000389759,;PKP4,intron_variant,,ENST00000389757,;AC005042.4,intron_variant,,ENST00000342892,;AC005042.4,downstream_gene_variant,,ENST00000442666,;PKP4,3_prime_UTR_variant,,ENST00000426248,;PKP4,non_coding_transcript_exon_variant,,ENST00000486254,;PKP4,non_coding_transcript_exon_variant,,ENST00000480171,;	G	ENSG00000144283	ENST00000389759	Transcript	missense_variant	3362	3250	1084	Y/D	Tac/Gac	.	.	.	1	PKP4	HGNC	9026	protein_coding	YES	CCDS33305.1	ENSP00000374409	PKP4_HUMAN	Q53TM5_HUMAN	UPI000044D379	.	tolerated(0.06)	possibly_damaging(0.634)	20/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTGTACCCT	.	4	ESCA
HNRNPA3	0	.	GRCh37	2	178084948	178084948	+	3'Flank	SNP	C	C	A	rs188233157	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000392524	.	107	96	11	58	58	0	HNRNPA3,3_prime_UTR_variant,,ENST00000411529,;HNRNPA3,downstream_gene_variant,,ENST00000435711,;HNRNPA3,downstream_gene_variant,,ENST00000432457,;HNRNPA3,downstream_gene_variant,,ENST00000392524,;HNRNPA3,downstream_gene_variant,,ENST00000483137,;	A	ENSG00000170144	ENST00000392524	Transcript	downstream_gene_variant	.	.	.	.	.	rs188233157	.	135	1	HNRNPA3	HGNC	24941	protein_coding	YES	CCDS2273.1	ENSP00000376309	ROA3_HUMAN	Q8NFG3_HUMAN	UPI00001BE8DE	.	.	.	.	.	.	A:0.0010	A:0	A:0	.	A:0	A:0.005	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACATCTCTAT	byFrequency|byCluster|by1000G	4	ESCA
TTN	0	.	GRCh37	2	179415774	179415774	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.91484G>C	p.Arg30495Thr	p.R30495T	ENST00000589042	336/363	61	55	6	66	66	0	TTN,missense_variant,p.Arg21555Thr,ENST00000359218,;TTN,missense_variant,p.Arg28854Thr,ENST00000591111,;TTN,missense_variant,p.Arg30495Thr,ENST00000589042,;TTN,missense_variant,p.Arg21622Thr,ENST00000342175,;TTN,missense_variant,p.Arg27927Thr,ENST00000342992,;TTN,missense_variant,p.Arg21430Thr,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;RP11-65L3.2,downstream_gene_variant,,ENST00000603415,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	91709	91484	30495	R/T	aGa/aCa	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	336/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTATTCTGAAC	.	3	ESCA
TTN	0	.	GRCh37	2	179547519	179547519	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.32999T>A	p.Phe11000Tyr	p.F11000Y	ENST00000589042	135/363	86	74	12	61	61	0	TTN,missense_variant,p.Phe614Tyr,ENST00000414766,;TTN,missense_variant,p.Phe9756Tyr,ENST00000342992,;TTN,missense_variant,p.Phe11000Tyr,ENST00000589042,;TTN,missense_variant,p.Phe10683Tyr,ENST00000591111,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000589830,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	33224	32999	11000	F/Y	tTt/tAt	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	135/363	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCAAATTCT	.	5	ESCA
STAT4	0	.	GRCh37	2	191896228	191896228	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2059G>C	p.Glu687Gln	p.E687Q	ENST00000392320	22/24	104	90	13	138	138	0	STAT4,missense_variant,p.Glu687Gln,ENST00000358470,;STAT4,missense_variant,p.Glu687Gln,ENST00000392320,;AC067945.4,intron_variant,,ENST00000456176,;STAT4,downstream_gene_variant,,ENST00000470708,;STAT4,non_coding_transcript_exon_variant,,ENST00000463951,;AC067945.4,intron_variant,,ENST00000429796,;STAT4,downstream_gene_variant,,ENST00000495849,;	G	ENSG00000138378	ENST00000392320	Transcript	missense_variant	2374	2059	687	E/Q	Gaa/Caa	.	.	.	-1	STAT4	HGNC	11365	protein_coding	YES	CCDS2310.1	ENSP00000376134	STAT4_HUMAN	Q53S87_HUMAN,Q53RU2_HUMAN,E9PBE2_HUMAN,C9JM11_HUMAN,C9JFG0_HUMAN,B7SIX5_HUMAN	UPI00000015F2	.	deleterious(0.03)	possibly_damaging(0.544)	22/24	.	hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF19,Gene3D:3.30.505.10,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTCTGTTG	.	5	ESCA
KCTD18	0	.	GRCh37	2	201363707	201363707	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473G>C	p.Arg158Thr	p.R158T	ENST00000359878	4/7	98	88	10	76	76	0	KCTD18,missense_variant,p.Arg158Thr,ENST00000359878,;KCTD18,missense_variant,p.Arg158Thr,ENST00000409157,;KCTD18,non_coding_transcript_exon_variant,,ENST00000468413,;KCTD18,downstream_gene_variant,,ENST00000447556,;KCTD18,non_coding_transcript_exon_variant,,ENST00000478816,;	G	ENSG00000155729	ENST00000359878	Transcript	missense_variant	984	473	158	R/T	aGa/aCa	.	.	.	-1	KCTD18	HGNC	26446	protein_coding	YES	CCDS2330.1	ENSP00000352941	KCD18_HUMAN	.	UPI0000209355	.	deleterious(0.02)	possibly_damaging(0.556)	4/7	.	hmmpanther:PTHR14499:SF4,hmmpanther:PTHR14499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAATTCTACTC	.	4	ESCA
CDK15	0	.	GRCh37	2	202725648	202725648	+	Intron	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009+5988G>A	.	.	ENST00000450471	.	28	24	4	21	21	0	CDK15,intron_variant,,ENST00000434439,;CDK15,intron_variant,,ENST00000450471,;CDK15,intron_variant,,ENST00000260967,;CDK15,intron_variant,,ENST00000410091,;CDK15,intron_variant,,ENST00000374598,;CDK15,non_coding_transcript_exon_variant,,ENST00000488419,;CDK15,intron_variant,,ENST00000466337,;CDK15,intron_variant,,ENST00000460149,;CDK15,intron_variant,,ENST00000451080,;	A	ENSG00000138395	ENST00000450471	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CDK15	HGNC	14434	protein_coding	YES	CCDS58747.1	ENSP00000406472	CDK15_HUMAN	.	UPI0001D3BDAF	.	.	.	.	10/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAAAGAGCTA	.	4	ESCA
PTH2R	0	.	GRCh37	2	209307162	209307162	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.485C>A	p.Ala162Asp	p.A162D	ENST00000272847	5/13	91	84	7	57	57	0	PTH2R,missense_variant,p.Ala162Asp,ENST00000272847,;PTH2R,non_coding_transcript_exon_variant,,ENST00000413482,;	A	ENSG00000144407	ENST00000272847	Transcript	missense_variant	698	485	162	A/D	gCt/gAt	.	.	.	1	PTH2R	HGNC	9609	protein_coding	YES	CCDS2383.1	ENSP00000272847	PTH2R_HUMAN	Q53T35_HUMAN,Q53SF6_HUMAN,B4DFN8_HUMAN	UPI000005041E	.	deleterious(0)	probably_damaging(0.989)	5/13	.	Prints_domain:PR00249,Superfamily_domains:SSF81321,Pfam_domain:PF00002,hmmpanther:PTHR12011:SF69,hmmpanther:PTHR12011,PROSITE_profiles:PS50261,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTGGCTATTC	.	2	ESCA
MAP2	0	.	GRCh37	2	210543349	210543349	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.316C>A	p.Leu106Met	p.L106M	ENST00000360351	5/15	50	44	6	39	39	0	MAP2,missense_variant,p.Leu106Met,ENST00000447185,;MAP2,missense_variant,p.Leu106Met,ENST00000392193,;MAP2,missense_variant,p.Leu106Met,ENST00000361559,;MAP2,missense_variant,p.Leu106Met,ENST00000360351,;MAP2,missense_variant,p.Leu106Met,ENST00000199940,;MAP2,missense_variant,p.Leu106Met,ENST00000392194,;MAP2,missense_variant,p.Leu106Met,ENST00000445941,;MAP2,missense_variant,p.Leu32Met,ENST00000452717,;MAP2,non_coding_transcript_exon_variant,,ENST00000482864,;MAP2,non_coding_transcript_exon_variant,,ENST00000471619,;	A	ENSG00000078018	ENST00000360351	Transcript	missense_variant	822	316	106	L/M	Ctg/Atg	.	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	deleterious_low_confidence(0)	probably_damaging(0.999)	5/15	.	hmmpanther:PTHR11501:SF15,hmmpanther:PTHR11501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTCCTGAAA	.	4	ESCA
LANCL1	0	.	GRCh37	2	211300158	211300158	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076G>C	p.Gly359Ala	p.G359A	ENST00000443314	8/9	94	86	7	119	119	0	LANCL1,missense_variant,p.Gly359Ala,ENST00000443314,;LANCL1,missense_variant,p.Gly359Ala,ENST00000441020,;LANCL1,missense_variant,p.Gly359Ala,ENST00000450366,;LANCL1,missense_variant,p.Gly359Ala,ENST00000233714,;LANCL1,missense_variant,p.Gly359Ala,ENST00000431941,;LANCL1,missense_variant,p.Gly118Ala,ENST00000412863,;AC007970.1,intron_variant,,ENST00000420418,;AC007970.1,intron_variant,,ENST00000433296,;	G	ENSG00000115365	ENST00000443314	Transcript	missense_variant	1419	1076	359	G/A	gGa/gCa	.	.	.	-1	LANCL1	HGNC	6508	protein_coding	YES	CCDS2392.1	ENSP00000388713	LANC1_HUMAN	Q53TN2_HUMAN,E9PHS0_HUMAN	UPI0000073D7C	.	deleterious(0)	probably_damaging(1)	8/9	.	hmmpanther:PTHR12736,hmmpanther:PTHR12736:SF5,Pfam_domain:PF05147,Gene3D:1.50.10.10,Superfamily_domains:0053930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTCTCCATAC	.	2	ESCA
AAMP	0	.	GRCh37	2	219129195	219129195	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*61C>T	.	.	ENST00000248450	11/11	84	73	11	63	63	0	AAMP,3_prime_UTR_variant,,ENST00000422731,;AAMP,3_prime_UTR_variant,,ENST00000248450,;AAMP,3_prime_UTR_variant,,ENST00000420660,;AAMP,3_prime_UTR_variant,,ENST00000444053,;GPBAR1,downstream_gene_variant,,ENST00000521462,;GPBAR1,downstream_gene_variant,,ENST00000522678,;GPBAR1,downstream_gene_variant,,ENST00000479077,;GPBAR1,downstream_gene_variant,,ENST00000519574,;AAMP,downstream_gene_variant,,ENST00000447885,;AAMP,non_coding_transcript_exon_variant,,ENST00000475678,;AAMP,non_coding_transcript_exon_variant,,ENST00000489767,;AAMP,non_coding_transcript_exon_variant,,ENST00000494720,;AAMP,downstream_gene_variant,,ENST00000465442,;AAMP,downstream_gene_variant,,ENST00000461911,;	A	ENSG00000127837	ENST00000248450	Transcript	3_prime_UTR_variant	1537	.	.	.	.	.	.	.	-1	AAMP	HGNC	18	protein_coding	YES	CCDS33378.1	ENSP00000248450	AAMP_HUMAN	C9JTS3_HUMAN	UPI0000209584	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCAGACAGG	.	4	ESCA
COL4A4	0	.	GRCh37	2	227872752	227872752	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4791C>T	p.%3D	p.I1597I	ENST00000396625	47/48	74	69	5	120	120	0	COL4A4,synonymous_variant,p.%3D,ENST00000329662,;COL4A4,synonymous_variant,p.%3D,ENST00000396625,;	A	ENSG00000081052	ENST00000396625	Transcript	synonymous_variant	4999	4791	1597	I	atC/atT	COSM3578363	.	.	-1	COL4A4	HGNC	2206	protein_coding	YES	CCDS42828.1	ENSP00000379866	CO4A4_HUMAN	.	UPI000013D987	.	.	.	47/48	.	PROSITE_profiles:PS51403,hmmpanther:PTHR24021:SF5,hmmpanther:PTHR24021,Pfam_domain:PF01413,Gene3D:1t60D00,SMART_domains:SM00111,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCCGATCCA	.	2	ESCA
SPHKAP	0	.	GRCh37	2	228883348	228883348	+	Missense_Mutation	SNP	G	G	A	rs755469563	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2222C>T	p.Thr741Ile	p.T741I	ENST00000392056	7/12	26	22	4	37	37	0	SPHKAP,missense_variant,p.Thr741Ile,ENST00000344657,;SPHKAP,missense_variant,p.Thr741Ile,ENST00000392056,;	A	ENSG00000153820	ENST00000392056	Transcript	missense_variant	2269	2222	741	T/I	aCc/aTc	rs755469563,COSM318062,COSM318063	.	.	-1	SPHKAP	HGNC	30619	protein_coding	YES	CCDS46537.1	ENSP00000375909	SPKAP_HUMAN	.	UPI0000411D7E	.	tolerated(0.08)	benign(0.013)	7/12	.	hmmpanther:PTHR10226,hmmpanther:PTHR10226:SF7	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGATGGTCTCC	.	2	ESCA
PID1	0	.	GRCh37	2	229890767	229890767	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.328G>A	p.Glu110Lys	p.E110K	ENST00000392054	4/4	41	33	8	51	51	0	PID1,missense_variant,p.Glu30Lys,ENST00000409462,;PID1,missense_variant,p.Glu112Lys,ENST00000354069,;PID1,missense_variant,p.Glu79Lys,ENST00000392055,;PID1,missense_variant,p.Glu110Lys,ENST00000392054,;PID1,intron_variant,,ENST00000482518,;PID1,3_prime_UTR_variant,,ENST00000534952,;	T	ENSG00000153823	ENST00000392054	Transcript	missense_variant	668	328	110	E/K	Gaa/Aaa	.	.	.	-1	PID1	HGNC	26084	protein_coding	YES	CCDS2471.1	ENSP00000375907	PCLI1_HUMAN	Q4ZG81_HUMAN	UPI00001C0AF7	.	deleterious(0.01)	probably_damaging(0.99)	4/4	.	hmmpanther:PTHR16265,hmmpanther:PTHR16265:SF0,Pfam_domain:PF14719,SMART_domains:SM00462,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTCTGTGC	.	5	ESCA
NGEF	0	.	GRCh37	2	233785105	233785105	+	Silent	SNP	G	G	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.717C>T	p.%3D	p.I239I	ENST00000264051	5/15	61	54	7	40	40	0	NGEF,synonymous_variant,p.%3D,ENST00000409079,;NGEF,synonymous_variant,p.%3D,ENST00000264051,;NGEF,synonymous_variant,p.%3D,ENST00000373552,;	A	ENSG00000066248	ENST00000264051	Transcript	synonymous_variant	996	717	239	I	atC/atT	COSM4128216,COSM4128217,COSM4128218	.	.	-1	NGEF	HGNC	7807	protein_coding	YES	CCDS2500.1	ENSP00000264051	NGEF_HUMAN	C9JTV7_HUMAN,B4DDI2_HUMAN	UPI000013D4AE	.	.	.	5/15	.	hmmpanther:PTHR12845:SF8,hmmpanther:PTHR12845	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCAGATCTG	.	4	ESCA
DGKD	0	.	GRCh37	2	234355361	234355361	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1338G>A	p.Trp446Ter	p.W446*	ENST00000264057	12/30	36	28	8	25	25	0	DGKD,stop_gained,p.Trp446Ter,ENST00000264057,;DGKD,stop_gained,p.Trp402Ter,ENST00000409813,;DGKD,upstream_gene_variant,,ENST00000480535,;DGKD,stop_gained,p.Trp107Ter,ENST00000430834,;DGKD,non_coding_transcript_exon_variant,,ENST00000490764,;DGKD,downstream_gene_variant,,ENST00000474488,;DGKD,upstream_gene_variant,,ENST00000465569,;	A	ENSG00000077044	ENST00000264057	Transcript	stop_gained	1350	1338	446	W/*	tgG/tgA	.	.	.	1	DGKD	HGNC	2851	protein_coding	YES	CCDS2504.1	ENSP00000264057	DGKD_HUMAN	Q53SV4_HUMAN,Q53SE4_HUMAN	UPI000013D4AF	.	.	.	12/30	.	PROSITE_profiles:PS50146,hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF30,Pfam_domain:PF00781,SMART_domains:SM00046,Superfamily_domains:SSF111331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTGGAGCGT	.	5	ESCA
ARL4C	0	.	GRCh37	2	235405081	235405081	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150G>A	p.%3D	p.E50E	ENST00000390645	1/1	48	41	7	69	69	0	ARL4C,synonymous_variant,p.%3D,ENST00000390645,;ARL4C,synonymous_variant,p.%3D,ENST00000339728,;	T	ENSG00000188042	ENST00000390645	Transcript	synonymous_variant	617	150	50	E	gaG/gaA	.	.	.	-1	ARL4C	HGNC	698	protein_coding	YES	CCDS2512.1	ENSP00000375057	ARL4C_HUMAN	.	UPI0000004144	.	.	.	1/1	.	PROSITE_profiles:PS51417,hmmpanther:PTHR11711:SF119,hmmpanther:PTHR11711,Pfam_domain:PF00025,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,SMART_domains:SM00178,SMART_domains:SM00177,SMART_domains:SM00175,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTTCTCGGT	.	4	ESCA
SPAST	0	.	GRCh37	2	32382422	32382422	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2857G>A	.	.	ENST00000315285	17/17	67	58	8	97	97	0	SPAST,3_prime_UTR_variant,,ENST00000315285,;SPAST,3_prime_UTR_variant,,ENST00000345662,;	A	ENSG00000021574	ENST00000315285	Transcript	3_prime_UTR_variant	4833	.	.	.	.	.	.	.	1	SPAST	HGNC	11233	protein_coding	YES	CCDS1778.1	ENSP00000320885	SPAST_HUMAN	E5KRP5_HUMAN	UPI0000038A6B	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAAGAATTA	.	4	ESCA
NLRC4	0	.	GRCh37	2	32475208	32475208	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1725T>A	p.Phe575Leu	p.F575L	ENST00000404025	5/10	38	33	5	65	65	0	NLRC4,missense_variant,p.Phe575Leu,ENST00000402280,;NLRC4,missense_variant,p.Phe575Leu,ENST00000360906,;NLRC4,missense_variant,p.Phe575Leu,ENST00000404025,;NLRC4,intron_variant,,ENST00000342905,;	T	ENSG00000091106	ENST00000404025	Transcript	missense_variant	2214	1725	575	F/L	ttT/ttA	.	.	.	-1	NLRC4	HGNC	16412	protein_coding	YES	CCDS33174.1	ENSP00000385090	NLRC4_HUMAN	.	UPI0000126FAD	.	deleterious(0.01)	possibly_damaging(0.888)	5/10	.	hmmpanther:PTHR10044:SF97,hmmpanther:PTHR10044,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTCAAATTC	.	2	ESCA
SLC3A1	0	.	GRCh37	2	44547672	44547672	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1952A>T	p.Asn651Ile	p.N651I	ENST00000260649	10/10	42	36	6	56	56	0	SLC3A1,missense_variant,p.Asn651Ile,ENST00000260649,;SLC3A1,missense_variant,p.Asn373Ile,ENST00000409380,;SLC3A1,missense_variant,p.Asn282Ile,ENST00000409740,;PREPL,3_prime_UTR_variant,,ENST00000409957,;PREPL,3_prime_UTR_variant,,ENST00000541738,;PREPL,3_prime_UTR_variant,,ENST00000409936,;PREPL,3_prime_UTR_variant,,ENST00000409411,;PREPL,3_prime_UTR_variant,,ENST00000444696,;PREPL,downstream_gene_variant,,ENST00000260648,;PREPL,downstream_gene_variant,,ENST00000410081,;PREPL,downstream_gene_variant,,ENST00000378511,;PREPL,downstream_gene_variant,,ENST00000378520,;SLC3A1,downstream_gene_variant,,ENST00000409387,;PREPL,downstream_gene_variant,,ENST00000420756,;PREPL,downstream_gene_variant,,ENST00000409272,;PREPL,3_prime_UTR_variant,,ENST00000426481,;PREPL,3_prime_UTR_variant,,ENST00000425263,;	T	ENSG00000138079	ENST00000260649	Transcript	missense_variant	2028	1952	651	N/I	aAc/aTc	.	.	.	1	SLC3A1	HGNC	11025	protein_coding	YES	CCDS1819.1	ENSP00000260649	SLC31_HUMAN	E7ENC4_HUMAN	UPI000013D0F2	.	deleterious(0.03)	benign(0.342)	10/10	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF73	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACAACACGA	.	4	ESCA
C2orf73	0	.	GRCh37	2	54558106	54558106	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-7G>A	.	.	ENST00000398634	1/5	83	75	8	114	114	0	C2orf73,5_prime_UTR_variant,,ENST00000447328,;C2orf73,5_prime_UTR_variant,,ENST00000398634,;C2orf73,5_prime_UTR_variant,,ENST00000405749,;C2orf73,intron_variant,,ENST00000486488,;C2orf73,upstream_gene_variant,,ENST00000491538,;C2orf73,5_prime_UTR_variant,,ENST00000317627,;C2orf73,upstream_gene_variant,,ENST00000414747,;	A	ENSG00000177994	ENST00000398634	Transcript	5_prime_UTR_variant	36	.	.	.	.	.	.	.	1	C2orf73	HGNC	26861	protein_coding	YES	CCDS46285.1	ENSP00000381631	CB073_HUMAN	B7ZM11_HUMAN	UPI00001C1DC4	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCGTAGAGGCC	.	3	ESCA
VPS54	0	.	GRCh37	2	64211108	64211108	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26C>T	p.Pro9Leu	p.P9L	ENST00000272322	2/23	35	28	7	34	34	0	VPS54,missense_variant,p.Pro9Leu,ENST00000272322,;VPS54,missense_variant,p.Pro9Leu,ENST00000409558,;	A	ENSG00000143952	ENST00000272322	Transcript	missense_variant	181	26	9	P/L	cCa/cTa	.	.	.	-1	VPS54	HGNC	18652	protein_coding	YES	CCDS33208.1	ENSP00000272322	VPS54_HUMAN	.	UPI0000053408	.	tolerated_low_confidence(0.14)	unknown(0)	2/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12965:SF0,hmmpanther:PTHR12965	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACTGGTGAA	.	5	ESCA
ADD2	0	.	GRCh37	2	70900406	70900406	+	Intron	SNP	G	G	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1742-268C>A	.	.	ENST00000264436	.	48	40	7	55	55	0	ADD2,missense_variant,p.Phe598Leu,ENST00000355733,;ADD2,intron_variant,,ENST00000264436,;ADD2,intron_variant,,ENST00000407644,;ADD2,downstream_gene_variant,,ENST00000413157,;ADD2,downstream_gene_variant,,ENST00000456320,;ADD2,downstream_gene_variant,,ENST00000430656,;ADD2,downstream_gene_variant,,ENST00000522886,;ADD2,non_coding_transcript_exon_variant,,ENST00000481675,;ADD2,intron_variant,,ENST00000403045,;	T	ENSG00000075340	ENST00000264436	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ADD2	HGNC	244	protein_coding	YES	CCDS1906.1	ENSP00000264436	ADDB_HUMAN	Q96HD4_HUMAN,C9J299_HUMAN,C9J080_HUMAN	UPI0000125503	.	.	.	.	14/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACGCTGAAGAA	.	4	ESCA
ATP6V1B1	0	.	GRCh37	2	71188135	71188135	+	Missense_Mutation	SNP	G	G	A	rs202215158	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670G>A	p.Val224Ile	p.V224I	ENST00000234396	7/14	51	46	4	60	60	0	ATP6V1B1,missense_variant,p.Val224Ile,ENST00000234396,;ATP6V1B1,missense_variant,p.Val241Ile,ENST00000454446,;ATP6V1B1,missense_variant,p.Val224Ile,ENST00000412314,;AC007040.11,intron_variant,,ENST00000606025,;ATP6V1B1,upstream_gene_variant,,ENST00000433895,;ATP6V1B1,downstream_gene_variant,,ENST00000432098,;RN7SL160P,upstream_gene_variant,,ENST00000468558,;ATP6V1B1,missense_variant,p.Val224Ile,ENST00000432367,;ATP6V1B1,non_coding_transcript_exon_variant,,ENST00000495118,;AC007040.11,intron_variant,,ENST00000453130,;ATP6V1B1,downstream_gene_variant,,ENST00000463380,;TCEB1P21,upstream_gene_variant,,ENST00000412558,;	A	ENSG00000116039	ENST00000234396	Transcript	missense_variant	743	670	224	V/I	Gtc/Atc	rs202215158	.	.	1	ATP6V1B1	HGNC	853	protein_coding	YES	CCDS1912.1	ENSP00000234396	VATB1_HUMAN	Q71UA2_HUMAN,C9JZ02_HUMAN,C9JTN0_HUMAN,B4DWH7_HUMAN	UPI000013C9A0	.	tolerated(0.08)	benign(0.325)	7/14	.	HAMAP:MF_00310,hmmpanther:PTHR15184:SF29,hmmpanther:PTHR15184,Pfam_domain:PF00006,TIGRFAM_domain:TIGR01040,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	A:0.0006	A:0	A:0	.	A:0	A:0.001	A:0.002	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCATCGTCTTT	byFrequency|byCluster|by1000G	3	ESCA
EMX1	0	.	GRCh37	2	73143662	73143662	+	5'Flank	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000258106	.	24	21	3	17	17	0	EMX1,upstream_gene_variant,,ENST00000258106,;EMX1,upstream_gene_variant,,ENST00000473732,;EMX1,non_coding_transcript_exon_variant,,ENST00000394111,;	T	ENSG00000135638	ENST00000258106	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	942	1	EMX1	HGNC	3340	protein_coding	YES	CCDS1921.2	ENSP00000258106	EMX1_HUMAN	.	UPI0000D47CF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGTCGTGAG	.	2	ESCA
LOXL3	0	.	GRCh37	2	74779641	74779641	+	Missense_Mutation	SNP	C	C	T	rs751944822	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.121G>A	p.Gly41Arg	p.G41R	ENST00000264094	2/14	65	53	12	62	62	0	LOXL3,missense_variant,p.Gly41Arg,ENST00000413469,;LOXL3,missense_variant,p.Gly41Arg,ENST00000264094,;LOXL3,missense_variant,p.Gly41Arg,ENST00000409986,;LOXL3,missense_variant,p.Gly41Arg,ENST00000409249,;LOXL3,missense_variant,p.Gly41Arg,ENST00000409549,;LOXL3,missense_variant,p.Gly41Arg,ENST00000393937,;DOK1,intron_variant,,ENST00000409429,;LOXL3,upstream_gene_variant,,ENST00000420535,;DOK1,upstream_gene_variant,,ENST00000233668,;DOK1,upstream_gene_variant,,ENST00000340004,;LOXL3,non_coding_transcript_exon_variant,,ENST00000484369,;DOK1,intron_variant,,ENST00000485132,;DOK1,upstream_gene_variant,,ENST00000488613,;DOK1,upstream_gene_variant,,ENST00000480318,;DOK1,upstream_gene_variant,,ENST00000489958,;LOXL3,upstream_gene_variant,,ENST00000481835,;DOK1,upstream_gene_variant,,ENST00000496966,;DOK1,upstream_gene_variant,,ENST00000429631,;DOK1,upstream_gene_variant,,ENST00000475191,;LOXL3,upstream_gene_variant,,ENST00000470907,;DOK1,upstream_gene_variant,,ENST00000464613,;DOK1,upstream_gene_variant,,ENST00000474924,;DOK1,upstream_gene_variant,,ENST00000482206,;	T	ENSG00000115318	ENST00000264094	Transcript	missense_variant	193	121	41	G/R	Ggg/Agg	rs751944822	.	.	-1	LOXL3	HGNC	13869	protein_coding	YES	CCDS1953.1	ENSP00000264094	LOXL3_HUMAN	Q8N505_HUMAN,Q53TY1_HUMAN,Q2EHP2_HUMAN,C9J5M1_HUMAN	UPI0000044959	.	tolerated(0.59)	benign(0.006)	2/14	.	hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCCCCTGGC	.	5	ESCA
USP39	0	.	GRCh37	2	85843346	85843346	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.28C>G	p.Arg10Gly	p.R10G	ENST00000323701	1/13	53	47	5	31	31	0	USP39,missense_variant,p.Arg10Gly,ENST00000323701,;USP39,missense_variant,p.Arg10Gly,ENST00000409766,;USP39,missense_variant,p.Arg10Gly,ENST00000409470,;USP39,missense_variant,p.Arg10Gly,ENST00000409025,;USP39,intron_variant,,ENST00000448971,;USP39,intron_variant,,ENST00000442708,;USP39,intron_variant,,ENST00000450066,;C2orf68,upstream_gene_variant,,ENST00000306336,;C2orf68,upstream_gene_variant,,ENST00000409734,;USP39,non_coding_transcript_exon_variant,,ENST00000455732,;USP39,intron_variant,,ENST00000465282,;USP39,intron_variant,,ENST00000459775,;USP39,intron_variant,,ENST00000474572,;USP39,intron_variant,,ENST00000491659,;C2orf68,upstream_gene_variant,,ENST00000478626,;USP39,missense_variant,p.Arg10Gly,ENST00000458268,;C2orf68,upstream_gene_variant,,ENST00000420686,;C2orf68,upstream_gene_variant,,ENST00000423181,;USP39,upstream_gene_variant,,ENST00000493829,;	G	ENSG00000168883	ENST00000323701	Transcript	missense_variant	38	28	10	R/G	Cgc/Ggc	.	.	.	1	USP39	HGNC	20071	protein_coding	YES	CCDS33234.1	ENSP00000312981	SNUT2_HUMAN	B3KPG7_HUMAN	UPI000003771A	.	deleterious_low_confidence(0.02)	benign(0.111)	1/13	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R10R|c.30C>T|3	RADIA|MUTECT|MUSE|VARSCANS	AGTCTCGCGGT	.	4	ESCA
YWHAQ	0	.	GRCh37	2	9770479	9770479	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103G>A	p.Glu35Lys	p.E35K	ENST00000381844	1/5	39	30	8	36	36	0	YWHAQ,missense_variant,p.Glu35Lys,ENST00000446619,;YWHAQ,missense_variant,p.Glu35Lys,ENST00000238081,;YWHAQ,missense_variant,p.Glu35Lys,ENST00000381844,;YWHAQ,upstream_gene_variant,,ENST00000460093,;	T	ENSG00000134308	ENST00000381844	Transcript	missense_variant	267	103	35	E/K	Gag/Aag	.	.	.	-1	YWHAQ	HGNC	12854	protein_coding	YES	CCDS1666.1	ENSP00000371267	1433T_HUMAN	Q53S41_HUMAN,Q53RR5_HUMAN,E9PG15_HUMAN,B4DY04_HUMAN	UPI0000124E01	.	tolerated_low_confidence(0.08)	benign(0.006)	1/5	.	hmmpanther:PTHR18860,Gene3D:3iquA00,Pfam_domain:PF00244,PIRSF_domain:PIRSF000868,SMART_domains:SM00101,Superfamily_domains:SSF48445,Prints_domain:PR00305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCGGCGC	.	5	ESCA
SLC41A3	0	.	GRCh37	3	125745256	125745256	+	Missense_Mutation	SNP	C	C	G	rs373931665	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520G>C	p.Glu174Gln	p.E174Q	ENST00000315891	5/12	76	71	5	79	79	0	SLC41A3,missense_variant,p.Glu165Gln,ENST00000510651,;SLC41A3,missense_variant,p.Glu174Gln,ENST00000360370,;SLC41A3,missense_variant,p.Glu148Gln,ENST00000383598,;SLC41A3,missense_variant,p.Glu138Gln,ENST00000346785,;SLC41A3,missense_variant,p.Glu226Gln,ENST00000513723,;SLC41A3,missense_variant,p.Glu174Gln,ENST00000315891,;SLC41A3,missense_variant,p.Glu174Gln,ENST00000512470,;SLC41A3,missense_variant,p.Glu189Gln,ENST00000514677,;SLC41A3,missense_variant,p.Glu57Gln,ENST00000508835,;SLC41A3,incomplete_terminal_codon_variant,p.%3D,ENST00000514333,;SLC41A3,non_coding_transcript_exon_variant,,ENST00000514023,;SLC41A3,missense_variant,p.Glu57Gln,ENST00000507008,;SLC41A3,non_coding_transcript_exon_variant,,ENST00000513464,;SLC41A3,upstream_gene_variant,,ENST00000512557,;SLC41A3,upstream_gene_variant,,ENST00000506102,;	G	ENSG00000114544	ENST00000315891	Transcript	missense_variant	759	520	174	E/Q	Gag/Cag	rs373931665	.	.	-1	SLC41A3	HGNC	31046	protein_coding	YES	CCDS33843.1	ENSP00000326070	S41A3_HUMAN	D6RF72_HUMAN,D6R9S7_HUMAN,D6R925_HUMAN	UPI000013D523	.	tolerated(0.24)	benign(0.129)	5/12	.	hmmpanther:PTHR16228:SF22,hmmpanther:PTHR16228,Gene3D:2zy9B03,Pfam_domain:PF01769,Superfamily_domains:0054748	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCTCGAG	.	2	ESCA
AMOTL2	0	.	GRCh37	3	134089688	134089688	+	Silent	SNP	C	C	T	rs200498719	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588G>A	p.%3D	p.L196L	ENST00000249883	2/10	26	20	5	33	33	0	AMOTL2,synonymous_variant,p.%3D,ENST00000514516,;AMOTL2,synonymous_variant,p.%3D,ENST00000422605,;AMOTL2,synonymous_variant,p.%3D,ENST00000249883,;AMOTL2,synonymous_variant,p.%3D,ENST00000513145,;AMOTL2,synonymous_variant,p.%3D,ENST00000510560,;AMOTL2,downstream_gene_variant,,ENST00000515172,;AMOTL2,downstream_gene_variant,,ENST00000504234,;AMOTL2,downstream_gene_variant,,ENST00000502491,;AMOTL2,downstream_gene_variant,,ENST00000506107,;AMOTL2,downstream_gene_variant,,ENST00000505596,;AMOTL2,intron_variant,,ENST00000512955,;AMOTL2,intron_variant,,ENST00000511759,;AMOTL2,upstream_gene_variant,,ENST00000506326,;	T	ENSG00000114019	ENST00000249883	Transcript	synonymous_variant	902	588	196	L	ctG/ctA	rs200498719	.	.	-1	AMOTL2	HGNC	17812	protein_coding	YES	CCDS33860.1	ENSP00000249883	AMOL2_HUMAN	D6RJA4_HUMAN,D6RIC7_HUMAN,D6RFG0_HUMAN,D6RF61_HUMAN,D6RCL7_HUMAN,D6RBK2_HUMAN,B3KQD2_HUMAN	UPI00001B216C	.	.	.	2/10	.	hmmpanther:PTHR14826,hmmpanther:PTHR14826:SF3	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	CCCCTCAGTGG	byCluster|by1000G	3	ESCA
PIK3CB	0	.	GRCh37	3	138478028	138478028	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.158C>T	p.Ser53Phe	p.S53F	ENST00000477593	2/23	55	51	4	82	82	0	PIK3CB,missense_variant,p.Ser53Phe,ENST00000465581,;PIK3CB,missense_variant,p.Ser53Phe,ENST00000477593,;PIK3CB,missense_variant,p.Ser53Phe,ENST00000483968,;PIK3CB,missense_variant,p.Ser53Phe,ENST00000461451,;PIK3CB,missense_variant,p.Ser53Phe,ENST00000289153,;PIK3CB,missense_variant,p.Ser53Phe,ENST00000462898,;	A	ENSG00000051382	ENST00000477593	Transcript	missense_variant	232	158	53	S/F	tCt/tTt	.	.	.	-1	PIK3CB	HGNC	8976	protein_coding	YES	CCDS3104.1	ENSP00000418143	PK3CB_HUMAN	Q9BTS4_HUMAN,Q6PJ60_HUMAN,C9JYX0_HUMAN,C9JNF6_HUMAN,C9J345_HUMAN	UPI0000046842	.	tolerated(0.09)	possibly_damaging(0.722)	2/23	.	PROSITE_profiles:PS51544,hmmpanther:PTHR10048:SF33,hmmpanther:PTHR10048,Gene3D:3.10.20.90,Pfam_domain:PF02192,SMART_domains:SM00143	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATAAGAAATG	.	2	ESCA
MRPS22	0	.	GRCh37	3	139062880	139062880	+	Silent	SNP	C	C	T	rs776015225	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12C>T	p.%3D	p.L4L	ENST00000495075	3/10	119	104	15	161	161	0	MRPS22,synonymous_variant,p.%3D,ENST00000495075,;MRPS22,synonymous_variant,p.%3D,ENST00000465056,;MRPS22,synonymous_variant,p.%3D,ENST00000310776,;MRPS22,intron_variant,,ENST00000495225,;MRPS22,upstream_gene_variant,,ENST00000465373,;MRPS22,upstream_gene_variant,,ENST00000478464,;MRPS22,upstream_gene_variant,,ENST00000480644,;RP11-219D15.3,downstream_gene_variant,,ENST00000608472,;MRPS22,downstream_gene_variant,,ENST00000489521,;MRPS22,synonymous_variant,p.%3D,ENST00000498505,;MRPS22,non_coding_transcript_exon_variant,,ENST00000480938,;MRPS22,upstream_gene_variant,,ENST00000486705,;MRPS22,upstream_gene_variant,,ENST00000483545,;MRPS22,upstream_gene_variant,,ENST00000466690,;	T	ENSG00000175110	ENST00000495075	Transcript	synonymous_variant	444	12	4	L	ctC/ctT	rs776015225	.	.	1	MRPS22	HGNC	14508	protein_coding	YES	CCDS3107.1	ENSP00000418008	RT22_HUMAN	Q96Q16_HUMAN	UPI0000042222	.	.	.	3/10	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR13071:SF4,hmmpanther:PTHR13071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCCTCGGAAC	.	4	ESCA
CHCHD4	0	.	GRCh37	3	14154317	14154317	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*70T>C	.	.	ENST00000295767	4/4	67	61	6	54	54	0	CHCHD4,3_prime_UTR_variant,,ENST00000295767,;CHCHD4,3_prime_UTR_variant,,ENST00000396914,;CHCHD4,downstream_gene_variant,,ENST00000420103,;	G	ENSG00000163528	ENST00000295767	Transcript	3_prime_UTR_variant	863	.	.	.	.	.	.	.	-1	CHCHD4	HGNC	26467	protein_coding	YES	CCDS2617.1	ENSP00000295767	MIA40_HUMAN	.	UPI000007370C	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGAAGGTGA	.	4	ESCA
ATR	0	.	GRCh37	3	142218487	142218487	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5362G>T	p.Glu1788Ter	p.E1788*	ENST00000350721	31/47	71	66	5	91	91	0	ATR,stop_gained,p.Glu1724Ter,ENST00000383101,;ATR,stop_gained,p.Glu1788Ter,ENST00000350721,;ATR,non_coding_transcript_exon_variant,,ENST00000507620,;ATR,upstream_gene_variant,,ENST00000514393,;	A	ENSG00000175054	ENST00000350721	Transcript	stop_gained	5484	5362	1788	E/*	Gaa/Taa	.	.	.	-1	ATR	HGNC	882	protein_coding	YES	CCDS3124.1	ENSP00000343741	ATR_HUMAN	.	UPI0000031A31	.	.	.	31/47	.	PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64,Pfam_domain:PF02259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTTCCACCA	.	2	ESCA
HLTF	0	.	GRCh37	3	148759441	148759441	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2212G>C	p.Glu738Gln	p.E738Q	ENST00000310053	20/25	65	53	11	65	65	0	HLTF,missense_variant,p.Glu738Gln,ENST00000310053,;HLTF,missense_variant,p.Glu738Gln,ENST00000494055,;HLTF,missense_variant,p.Glu737Gln,ENST00000465259,;HLTF,missense_variant,p.Glu738Gln,ENST00000392912,;HLTF,missense_variant,p.Glu206Gln,ENST00000467858,;HLTF,non_coding_transcript_exon_variant,,ENST00000497427,;HLTF,upstream_gene_variant,,ENST00000472830,;	G	ENSG00000071794	ENST00000310053	Transcript	missense_variant	2406	2212	738	E/Q	Gaa/Caa	.	.	.	-1	HLTF	HGNC	11099	protein_coding	YES	CCDS33875.1	ENSP00000308944	HLTF_HUMAN	.	UPI0000161FA7	.	tolerated(0.09)	probably_damaging(0.964)	20/25	.	hmmpanther:PTHR10799:SF596,hmmpanther:PTHR10799,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTCAGGTG	.	5	ESCA
DNAJB11	0	.	GRCh37	3	186299223	186299223	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520G>C	p.Glu174Gln	p.E174Q	ENST00000439351	6/11	36	31	5	54	54	0	DNAJB11,missense_variant,p.Glu174Gln,ENST00000265028,;DNAJB11,missense_variant,p.Glu174Gln,ENST00000439351,;DNAJB11,upstream_gene_variant,,ENST00000418776,;DNAJB11,non_coding_transcript_exon_variant,,ENST00000495390,;DNAJB11,downstream_gene_variant,,ENST00000464877,;	C	ENSG00000090520	ENST00000439351	Transcript	missense_variant	1449	520	174	E/Q	Gag/Cag	COSM420093	.	.	1	DNAJB11	HGNC	14889	protein_coding	YES	CCDS3277.1	ENSP00000414398	DJB11_HUMAN	B3KW63_HUMAN	UPI0000001BF7	.	deleterious(0.03)	benign(0.125)	6/11	.	hmmpanther:PTHR24077:SF210,hmmpanther:PTHR24077	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCAAGAGATG	.	2	ESCA
TP63	0	.	GRCh37	3	189614675	189614675	+	3'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2384C>A	.	.	ENST00000264731	14/14	53	48	5	70	70	0	TP63,3_prime_UTR_variant,,ENST00000354600,;TP63,3_prime_UTR_variant,,ENST00000264731,;TP63,3_prime_UTR_variant,,ENST00000382063,;TP63,downstream_gene_variant,,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000456148,;TP63,downstream_gene_variant,,ENST00000392460,;TP63,downstream_gene_variant,,ENST00000320472,;TP63,downstream_gene_variant,,ENST00000440651,;TP63,downstream_gene_variant,,ENST00000449992,;TP63,downstream_gene_variant,,ENST00000392463,;	A	ENSG00000073282	ENST00000264731	Transcript	3_prime_UTR_variant	4516	.	.	.	.	.	.	.	1	TP63	HGNC	15979	protein_coding	YES	CCDS3293.1	ENSP00000264731	P63_HUMAN	.	UPI0000073CF2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGCTCAATGC	.	3	ESCA
RARB	0	.	GRCh37	3	25639004	25639004	+	3'UTR	SNP	C	C	T	rs544555643	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*897C>T	.	.	ENST00000330688	8/8	74	65	9	51	51	0	RARB,3_prime_UTR_variant,,ENST00000330688,;RARB,3_prime_UTR_variant,,ENST00000458646,;RARB,3_prime_UTR_variant,,ENST00000437042,;TOP2B,downstream_gene_variant,,ENST00000540199,;RARB,downstream_gene_variant,,ENST00000404969,;TOP2B,downstream_gene_variant,,ENST00000264331,;TOP2B,downstream_gene_variant,,ENST00000435706,;RARB,downstream_gene_variant,,ENST00000383772,;TOP2B,downstream_gene_variant,,ENST00000542520,;RARB,downstream_gene_variant,,ENST00000462272,;RARB,downstream_gene_variant,,ENST00000479097,;RARB,downstream_gene_variant,,ENST00000480001,;TOP2B,downstream_gene_variant,,ENST00000413971,;	T	ENSG00000077092	ENST00000330688	Transcript	3_prime_UTR_variant	2665	.	.	.	.	rs544555643	.	.	1	RARB	HGNC	9865	protein_coding	YES	CCDS2642.1	ENSP00000332296	RARB_HUMAN	Q5QHG3_HUMAN,F1D8S6_HUMAN	UPI000002B2CB	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATTTCATGGG	.	4	ESCA
LRRC3B	0	.	GRCh37	3	26752197	26752197	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*254C>G	.	.	ENST00000396641	2/2	72	66	5	143	143	0	LRRC3B,3_prime_UTR_variant,,ENST00000396641,;LRRC3B,3_prime_UTR_variant,,ENST00000456208,;LRRC3B,3_prime_UTR_variant,,ENST00000417744,;LRRC3B,downstream_gene_variant,,ENST00000414619,;LRRC3B,downstream_gene_variant,,ENST00000432040,;AC114877.3,upstream_gene_variant,,ENST00000446601,;LRRC3B,downstream_gene_variant,,ENST00000469437,;	G	ENSG00000179796	ENST00000396641	Transcript	3_prime_UTR_variant	1626	.	.	.	.	.	.	.	1	LRRC3B	HGNC	28105	protein_coding	YES	CCDS2644.1	ENSP00000379880	LRC3B_HUMAN	C9JMC7_HUMAN,C9J6A1_HUMAN	UPI000000D990	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCTCACTAT	.	2	ESCA
PDCD6IP	0	.	GRCh37	3	33840163	33840163	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-58C>T	.	.	ENST00000457054	1/18	80	72	7	103	103	0	PDCD6IP,5_prime_UTR_variant,,ENST00000413073,;PDCD6IP,5_prime_UTR_variant,,ENST00000307296,;PDCD6IP,5_prime_UTR_variant,,ENST00000457054,;RP11-10C24.3,upstream_gene_variant,,ENST00000604982,;RP11-10C24.2,upstream_gene_variant,,ENST00000605502,;RP11-10C24.1,upstream_gene_variant,,ENST00000605513,;PDCD6IP,non_coding_transcript_exon_variant,,ENST00000477798,;PDCD6IP,upstream_gene_variant,,ENST00000498147,;PDCD6IP,5_prime_UTR_variant,,ENST00000435909,;PDCD6IP,5_prime_UTR_variant,,ENST00000430877,;	T	ENSG00000170248	ENST00000457054	Transcript	5_prime_UTR_variant	98	.	.	.	.	.	.	.	1	PDCD6IP	HGNC	8766	protein_coding	YES	CCDS54561.1	ENSP00000411825	PDC6I_HUMAN	.	UPI00004121D3	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCCTCGGCCC	.	3	ESCA
ARPP21	0	.	GRCh37	3	35770799	35770799	+	Silent	SNP	C	C	T	rs781699865	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1128C>T	p.%3D	p.S376S	ENST00000458225	14/20	52	45	7	45	45	0	ARPP21,synonymous_variant,p.%3D,ENST00000337271,;ARPP21,synonymous_variant,p.%3D,ENST00000417925,;ARPP21,synonymous_variant,p.%3D,ENST00000458225,;ARPP21,synonymous_variant,p.%3D,ENST00000425289,;ARPP21,synonymous_variant,p.%3D,ENST00000187397,;ARPP21,synonymous_variant,p.%3D,ENST00000444190,;ARPP21,non_coding_transcript_exon_variant,,ENST00000476327,;ARPP21,synonymous_variant,p.%3D,ENST00000457165,;ARPP21,3_prime_UTR_variant,,ENST00000427590,;ARPP21,non_coding_transcript_exon_variant,,ENST00000481854,;	T	ENSG00000172995	ENST00000458225	Transcript	synonymous_variant	1353	1128	376	S	tcC/tcT	rs781699865	.	.	1	ARPP21	HGNC	16968	protein_coding	YES	CCDS58823.1	ENSP00000414351	ARP21_HUMAN	C9JTX6_HUMAN,C9JTF2_HUMAN,C9JQQ6_HUMAN,C9JI74_HUMAN,C9J5R1_HUMAN,C9J2U3_HUMAN	UPI0000209B3D	.	.	.	14/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15672:SF14,hmmpanther:PTHR15672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTTCCGAGTC	byFrequency	4	ESCA
CAMKV	0	.	GRCh37	3	49897669	49897669	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.877G>C	p.Asp293His	p.D293H	ENST00000477224	10/11	62	50	12	72	72	0	CAMKV,missense_variant,p.Asp250His,ENST00000466940,;CAMKV,missense_variant,p.Asp293His,ENST00000463537,;CAMKV,missense_variant,p.Asp218His,ENST00000467248,;CAMKV,missense_variant,p.Asp293His,ENST00000488336,;CAMKV,missense_variant,p.Asp293His,ENST00000477224,;CAMKV,missense_variant,p.Asp265His,ENST00000296471,;CAMKV,downstream_gene_variant,,ENST00000480398,;TRAIP,upstream_gene_variant,,ENST00000482582,;TRAIP,upstream_gene_variant,,ENST00000469027,;TRAIP,upstream_gene_variant,,ENST00000331456,;TRAIP,upstream_gene_variant,,ENST00000482243,;RN7SL217P,downstream_gene_variant,,ENST00000584520,;CAMKV,downstream_gene_variant,,ENST00000498324,;TRAIP,upstream_gene_variant,,ENST00000473863,;CAMKV,3_prime_UTR_variant,,ENST00000466535,;CAMKV,3_prime_UTR_variant,,ENST00000487726,;CAMKV,non_coding_transcript_exon_variant,,ENST00000475665,;CAMKV,non_coding_transcript_exon_variant,,ENST00000478149,;TRAIP,upstream_gene_variant,,ENST00000473195,;CAMKV,downstream_gene_variant,,ENST00000472895,;CAMKV,downstream_gene_variant,,ENST00000476105,;CAMKV,downstream_gene_variant,,ENST00000483811,;TRAIP,upstream_gene_variant,,ENST00000477546,;TRAIP,upstream_gene_variant,,ENST00000489948,;CAMKV,downstream_gene_variant,,ENST00000479704,;	G	ENSG00000164076	ENST00000477224	Transcript	missense_variant	1356	877	293	D/H	Gat/Cat	.	.	.	-1	CAMKV	HGNC	28788	protein_coding	YES	CCDS33762.1	ENSP00000419195	CAMKV_HUMAN	B4DM24_HUMAN	UPI000004184F	.	tolerated(0.47)	probably_damaging(0.999)	10/11	.	hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF18,Gene3D:1.10.510.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTATCAGAAG	.	5	ESCA
PRKCD	0	.	GRCh37	3	53212438	53212438	+	5'UTR	SNP	C	C	T	rs782324280	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1C>T	.	.	ENST00000394729	2/18	78	67	11	52	52	0	PRKCD,5_prime_UTR_variant,,ENST00000464818,;PRKCD,5_prime_UTR_variant,,ENST00000487897,;PRKCD,5_prime_UTR_variant,,ENST00000330452,;PRKCD,5_prime_UTR_variant,,ENST00000394729,;PRKCD,5_prime_UTR_variant,,ENST00000478843,;PRKCD,non_coding_transcript_exon_variant,,ENST00000477794,;	T	ENSG00000163932	ENST00000394729	Transcript	5_prime_UTR_variant	328	.	.	.	.	rs782324280	.	.	1	PRKCD	HGNC	9399	protein_coding	YES	CCDS2870.1	ENSP00000378217	KPCD_HUMAN	C9JZU8_HUMAN,C9J9P1_HUMAN,B4DFV1_HUMAN	UPI000000DA36	.	.	.	2/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCACCATGGC	.	4	ESCA
KIAA1109	0	.	GRCh37	4	123128701	123128701	+	Missense_Mutation	SNP	C	C	G	rs775031653	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1660C>G	p.Leu554Val	p.L554V	ENST00000264501	17/86	77	72	5	69	69	0	KIAA1109,missense_variant,p.Leu387Val,ENST00000424425,;KIAA1109,missense_variant,p.Leu554Val,ENST00000455637,;KIAA1109,missense_variant,p.Leu554Val,ENST00000264501,;KIAA1109,missense_variant,p.Leu554Val,ENST00000388738,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000495260,;KIAA1109,upstream_gene_variant,,ENST00000482114,;	G	ENSG00000138688	ENST00000264501	Transcript	missense_variant	2033	1660	554	L/V	Ctg/Gtg	rs775031653	.	.	1	KIAA1109	HGNC	26953	protein_coding	YES	CCDS43267.1	ENSP00000264501	K1109_HUMAN	B3KN93_HUMAN	UPI0000DD87B4	.	.	benign(0.012)	17/86	.	hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTATCTGGCA	.	2	ESCA
KLB	0	.	GRCh37	4	39450011	39450011	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2840C>G	p.Ser947Cys	p.S947C	ENST00000257408	5/5	69	61	8	94	94	0	KLB,missense_variant,p.Ser947Cys,ENST00000257408,;	G	ENSG00000134962	ENST00000257408	Transcript	missense_variant	2937	2840	947	S/C	tCt/tGt	.	.	.	1	KLB	HGNC	15527	protein_coding	YES	CCDS3451.1	ENSP00000257408	KLOTB_HUMAN	.	UPI000000D726	.	deleterious(0)	probably_damaging(0.967)	5/5	.	hmmpanther:PTHR10353:SF7,hmmpanther:PTHR10353,Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACATCTGATT	.	4	ESCA
TMEM128	0	.	GRCh37	4	4248035	4248035	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61C>G	p.Leu21Val	p.L21V	ENST00000254742	2/5	51	46	5	55	55	0	TMEM128,missense_variant,p.Leu45Val,ENST00000540397,;TMEM128,missense_variant,p.Leu45Val,ENST00000382753,;TMEM128,missense_variant,p.Leu21Val,ENST00000254742,;TMEM128,missense_variant,p.Leu45Val,ENST00000538516,;	C	ENSG00000132406	ENST00000254742	Transcript	missense_variant	648	61	21	L/V	Ctt/Gtt	.	.	.	-1	TMEM128	HGNC	28201	protein_coding	YES	CCDS3373.1	ENSP00000254742	TM128_HUMAN	.	UPI0000073696	.	deleterious(0.03)	possibly_damaging(0.496)	2/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR31134:SF1,hmmpanther:PTHR31134	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAAGAGGTT	.	2	ESCA
THAP6	0	.	GRCh37	4	76465090	76465090	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436G>C	p.Glu146Gln	p.E146Q	ENST00000507556	5/6	60	53	7	71	71	0	THAP6,missense_variant,p.Glu146Gln,ENST00000507556,;THAP6,missense_variant,p.Glu105Gln,ENST00000507885,;THAP6,missense_variant,p.Glu63Gln,ENST00000504190,;THAP6,intron_variant,,ENST00000507557,;THAP6,intron_variant,,ENST00000502620,;	C	ENSG00000174796	ENST00000507556	Transcript	missense_variant	504	436	146	E/Q	Gaa/Caa	.	.	.	1	THAP6	HGNC	23189	protein_coding	.	.	ENSP00000427651	.	D6RJG2_HUMAN,D6RC19_HUMAN,D6RBC3_HUMAN,B4E146_HUMAN	UPI0000E08F90	.	tolerated_low_confidence(0.05)	unknown(0)	5/6	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACAAGAACAG	.	4	ESCA
PAM	0	.	GRCh37	5	102353101	102353101	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2395C>G	p.His799Asp	p.H799D	ENST00000304400	21/25	51	46	4	53	53	0	PAM,missense_variant,p.His572Asp,ENST00000379799,;PAM,missense_variant,p.His94Asp,ENST00000504691,;PAM,missense_variant,p.His692Asp,ENST00000348126,;PAM,missense_variant,p.His799Asp,ENST00000304400,;PAM,missense_variant,p.His799Asp,ENST00000346918,;PAM,missense_variant,p.His702Asp,ENST00000274392,;PAM,missense_variant,p.His799Asp,ENST00000438793,;PAM,missense_variant,p.His799Asp,ENST00000455264,;PAM,missense_variant,p.His179Asp,ENST00000379787,;PAM,non_coding_transcript_exon_variant,,ENST00000504456,;PAM,non_coding_transcript_exon_variant,,ENST00000515456,;PAM,intron_variant,,ENST00000510006,;PAM,3_prime_UTR_variant,,ENST00000345721,;	G	ENSG00000145730	ENST00000304400	Transcript	missense_variant	2581	2395	799	H/D	Cat/Gat	.	.	.	1	PAM	HGNC	8596	protein_coding	YES	CCDS43348.1	ENSP00000306100	AMD_HUMAN	D6RG20_HUMAN,D6RF09_HUMAN,D6RDU2_HUMAN,D6RCD5_HUMAN,D6RAQ2_HUMAN,D6R961_HUMAN	UPI000015618B	.	tolerated(0.72)	probably_damaging(0.955)	21/25	.	PROSITE_profiles:PS51125,hmmpanther:PTHR10680,hmmpanther:PTHR10680:SF13,Pfam_domain:PF01436,Gene3D:2.120.10.30,Superfamily_domains:SSF101898,Prints_domain:PR00790	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGCTCATACC	.	4	ESCA
PCDHGA3	0	.	GRCh37	5	140725576	140725576	+	Missense_Mutation	SNP	C	C	T	rs747365510	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1976C>T	p.Thr659Met	p.T659M	ENST00000253812	1/4	111	99	12	78	77	1	PCDHGA3,missense_variant,p.Thr659Met,ENST00000253812,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB1,upstream_gene_variant,,ENST00000523390,;PCDHGA2,downstream_gene_variant,,ENST00000528330,;	T	ENSG00000254245	ENST00000253812	Transcript	missense_variant	1976	1976	659	T/M	aCg/aTg	rs747365510	.	.	1	PCDHGA3	HGNC	8701	protein_coding	YES	CCDS47290.1	ENSP00000253812	PCDG3_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI0000161C1A	.	deleterious_low_confidence(0.01)	probably_damaging(0.978)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF75,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCACGCTCA	.	4	ESCA
KCTD16	0	.	GRCh37	5	143586748	143586748	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471C>G	p.%3D	p.L157L	ENST00000507359	2/3	79	72	7	106	106	0	KCTD16,synonymous_variant,p.%3D,ENST00000507359,;KCTD16,synonymous_variant,p.%3D,ENST00000512467,;	G	ENSG00000183775	ENST00000507359	Transcript	synonymous_variant	1562	471	157	L	ctC/ctG	.	.	.	1	KCTD16	HGNC	29244	protein_coding	YES	CCDS34260.1	ENSP00000426548	KCD16_HUMAN	.	UPI000004A046	.	.	.	2/3	.	hmmpanther:PTHR14499:SF28,hmmpanther:PTHR14499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGCTCCCTGC	.	3	ESCA
TRIO	0	.	GRCh37	5	14391097	14391097	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4216G>A	p.Asp1406Asn	p.D1406N	ENST00000344204	27/57	52	47	5	51	51	0	TRIO,missense_variant,p.Asp1406Asn,ENST00000537187,;TRIO,missense_variant,p.Asp1357Asn,ENST00000509967,;TRIO,missense_variant,p.Asp1406Asn,ENST00000344204,;TRIO,missense_variant,p.Asp1139Asn,ENST00000513206,;TRIO,missense_variant,p.Asp1347Asn,ENST00000512070,;TRIO,splice_region_variant,,ENST00000515144,;TRIO,splice_region_variant,,ENST00000502490,;TRIO,downstream_gene_variant,,ENST00000510757,;	A	ENSG00000038382	ENST00000344204	Transcript	missense_variant	4240	4216	1406	D/N	Gac/Aac	.	.	.	1	TRIO	HGNC	12303	protein_coding	YES	CCDS3883.1	ENSP00000339299	TRIO_HUMAN	.	UPI000034ECE6	.	.	probably_damaging(0.995)	27/57	.	Superfamily_domains:SSF48065,SMART_domains:SM00325,Gene3D:1.20.900.10,Pfam_domain:PF00621,hmmpanther:PTHR22826:SF104,hmmpanther:PTHR22826,PROSITE_profiles:PS50010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|VARSCANS	ATTTTGACGTA	.	2	ESCA
SPINK1	0	.	GRCh37	5	147204189	147204189	+	3'UTR	SNP	C	C	T	rs752062590	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*35G>A	.	.	ENST00000296695	4/4	42	37	5	66	66	0	SPINK1,3_prime_UTR_variant,,ENST00000296695,;SPINK1,downstream_gene_variant,,ENST00000510027,;SPINK1,non_coding_transcript_exon_variant,,ENST00000505722,;	T	ENSG00000164266	ENST00000296695	Transcript	3_prime_UTR_variant	484	.	.	.	.	rs752062590	.	.	-1	SPINK1	HGNC	11244	protein_coding	YES	CCDS4286.1	ENSP00000296695	ISK1_HUMAN	D6RIU5_HUMAN	UPI000012D7EC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCGCGGT	.	4	ESCA
GRPEL2	0	.	GRCh37	5	148732528	148732528	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1683A>G	.	.	ENST00000329271	4/4	37	30	7	39	39	0	GRPEL2,3_prime_UTR_variant,,ENST00000329271,;GRPEL2,downstream_gene_variant,,ENST00000513661,;GRPEL2,downstream_gene_variant,,ENST00000416916,;GRPEL2-AS1,intron_variant,,ENST00000521295,;GRPEL2,non_coding_transcript_exon_variant,,ENST00000507562,;	G	ENSG00000164284	ENST00000329271	Transcript	3_prime_UTR_variant	2471	.	.	.	.	.	.	.	1	GRPEL2	HGNC	21060	protein_coding	YES	CCDS4295.1	ENSP00000329558	GRPE2_HUMAN	Q8N3S0_HUMAN	UPI000004A0F1	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTATATAG	.	5	ESCA
PPARGC1B	0	.	GRCh37	5	149206271	149206271	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288C>T	p.%3D	p.L96L	ENST00000309241	3/12	67	62	5	105	105	0	PPARGC1B,synonymous_variant,p.%3D,ENST00000360453,;PPARGC1B,synonymous_variant,p.%3D,ENST00000403750,;PPARGC1B,synonymous_variant,p.%3D,ENST00000309241,;PPARGC1B,synonymous_variant,p.%3D,ENST00000394320,;	T	ENSG00000155846	ENST00000309241	Transcript	synonymous_variant	320	288	96	L	ctC/ctT	.	.	.	1	PPARGC1B	HGNC	30022	protein_coding	YES	CCDS4298.1	ENSP00000312649	PRGC2_HUMAN	.	UPI000006F49D	.	.	.	3/12	.	hmmpanther:PTHR15528:SF12,hmmpanther:PTHR15528	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGCTCACCAA	.	3	ESCA
GALNT10	0	.	GRCh37	5	153677529	153677529	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291C>T	p.%3D	p.P97P	ENST00000297107	3/12	69	58	10	60	60	0	GALNT10,synonymous_variant,p.%3D,ENST00000377661,;GALNT10,synonymous_variant,p.%3D,ENST00000425427,;GALNT10,synonymous_variant,p.%3D,ENST00000297107,;GALNT10,non_coding_transcript_exon_variant,,ENST00000521781,;GALNT10,non_coding_transcript_exon_variant,,ENST00000519571,;GALNT10,synonymous_variant,p.%3D,ENST00000520647,;	T	ENSG00000164574	ENST00000297107	Transcript	synonymous_variant	428	291	97	P	ccC/ccT	.	.	.	1	GALNT10	HGNC	19873	protein_coding	YES	CCDS4325.1	ENSP00000297107	GLT10_HUMAN	Q4G0E1_HUMAN,D3DQI7_HUMAN	UPI0000041292	.	.	.	3/12	.	hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCCCATGAC	.	5	ESCA
RNF145	0	.	GRCh37	5	158603819	158603819	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.532C>A	p.Leu178Met	p.L178M	ENST00000518802	5/11	77	63	14	145	145	0	RNF145,missense_variant,p.Leu162Met,ENST00000520638,;RNF145,missense_variant,p.Leu165Met,ENST00000521606,;RNF145,missense_variant,p.Leu148Met,ENST00000519865,;RNF145,missense_variant,p.Leu176Met,ENST00000274542,;RNF145,missense_variant,p.Leu178Met,ENST00000518802,;RNF145,missense_variant,p.Leu148Met,ENST00000424310,;RNF145,upstream_gene_variant,,ENST00000521266,;	T	ENSG00000145860	ENST00000518802	Transcript	missense_variant	682	532	178	L/M	Ctg/Atg	.	.	.	-1	RNF145	HGNC	20853	protein_coding	YES	CCDS56393.1	ENSP00000430955	RN145_HUMAN	Q8NDT8_HUMAN,Q8NC08_HUMAN,Q8N783_HUMAN,Q6MZY8_HUMAN,B7Z249_HUMAN,B3KWZ2_HUMAN	UPI0001E8F5CB	.	deleterious(0.01)	probably_damaging(0.992)	5/11	.	Pfam_domain:PF13705,hmmpanther:PTHR12477:SF68,hmmpanther:PTHR12477,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACAGCCAAA	.	5	ESCA
C1QTNF2	0	.	GRCh37	5	159776454	159776454	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.714G>A	p.%3D	p.G238G	ENST00000393975	3/3	39	35	4	38	38	0	C1QTNF2,synonymous_variant,p.%3D,ENST00000393975,;CCNJL,upstream_gene_variant,,ENST00000521643,;	T	ENSG00000145861	ENST00000393975	Transcript	synonymous_variant	718	714	238	G	ggG/ggA	.	.	.	-1	C1QTNF2	HGNC	14325	protein_coding	YES	CCDS4351.2	ENSP00000377545	C1QT2_HUMAN	.	UPI0000D4B9D3	.	.	.	3/3	.	Prints_domain:PR00007,Superfamily_domains:SSF49842,SMART_domains:SM00110,Pfam_domain:PF00386,Gene3D:2.60.120.40,hmmpanther:PTHR24022,hmmpanther:PTHR24022:SF8,PROSITE_profiles:PS50871	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAGATCCCAGG	.	3	ESCA
CREBRF	0	.	GRCh37	5	172513533	172513533	+	Silent	SNP	C	C	T	rs748475579	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39C>T	p.%3D	p.F13F	ENST00000296953	3/9	99	78	21	115	115	0	CREBRF,synonymous_variant,p.%3D,ENST00000523161,;CREBRF,synonymous_variant,p.%3D,ENST00000520420,;CREBRF,synonymous_variant,p.%3D,ENST00000540014,;CREBRF,synonymous_variant,p.%3D,ENST00000522692,;CREBRF,synonymous_variant,p.%3D,ENST00000296953,;CREBRF,non_coding_transcript_exon_variant,,ENST00000520464,;CDC42P5,upstream_gene_variant,,ENST00000518654,;	T	ENSG00000164463	ENST00000296953	Transcript	synonymous_variant	358	39	13	F	ttC/ttT	rs748475579	.	.	1	CREBRF	HGNC	24050	protein_coding	YES	CCDS34293.1	ENSP00000296953	CRERF_HUMAN	E5RI19_HUMAN,B3KV47_HUMAN	UPI000049E01D	.	.	.	3/9	.	hmmpanther:PTHR21552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTCGGGGA	byFrequency	5	ESCA
MGAT4B	0	.	GRCh37	5	179226605	179226605	+	Silent	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.987G>C	p.%3D	p.L329L	ENST00000337755	8/14	54	47	7	73	73	0	MGAT4B,synonymous_variant,p.%3D,ENST00000520875,;MGAT4B,synonymous_variant,p.%3D,ENST00000518778,;MGAT4B,synonymous_variant,p.%3D,ENST00000518867,;MGAT4B,synonymous_variant,p.%3D,ENST00000292591,;MGAT4B,synonymous_variant,p.%3D,ENST00000523108,;MGAT4B,synonymous_variant,p.%3D,ENST00000520969,;MGAT4B,synonymous_variant,p.%3D,ENST00000337755,;MGAT4B,intron_variant,,ENST00000519836,;MGAT4B,intron_variant,,ENST00000518980,;LTC4S,downstream_gene_variant,,ENST00000401985,;LTC4S,downstream_gene_variant,,ENST00000292596,;MIR1229,upstream_gene_variant,,ENST00000408467,;MGAT4B,intron_variant,,ENST00000523382,;MGAT4B,downstream_gene_variant,,ENST00000519965,;MGAT4B,downstream_gene_variant,,ENST00000521305,;MGAT4B,downstream_gene_variant,,ENST00000519616,;MAML1,downstream_gene_variant,,ENST00000503050,;MGAT4B,downstream_gene_variant,,ENST00000520019,;MGAT4B,upstream_gene_variant,,ENST00000522293,;MGAT4B,downstream_gene_variant,,ENST00000520134,;MGAT4B,non_coding_transcript_exon_variant,,ENST00000520822,;MGAT4B,non_coding_transcript_exon_variant,,ENST00000518702,;MGAT4B,downstream_gene_variant,,ENST00000518168,;LTC4S,downstream_gene_variant,,ENST00000505170,;MGAT4B,downstream_gene_variant,,ENST00000523329,;MGAT4B,downstream_gene_variant,,ENST00000521855,;LTC4S,downstream_gene_variant,,ENST00000465572,;MGAT4B,downstream_gene_variant,,ENST00000520918,;LTC4S,downstream_gene_variant,,ENST00000466071,;LTC4S,downstream_gene_variant,,ENST00000510544,;LTC4S,downstream_gene_variant,,ENST00000486713,;LTC4S,downstream_gene_variant,,ENST00000509898,;MGAT4B,upstream_gene_variant,,ENST00000522451,;	G	ENSG00000161013	ENST00000337755	Transcript	synonymous_variant	1874	987	329	L	ctG/ctC	.	.	.	-1	MGAT4B	HGNC	7048	protein_coding	YES	CCDS4449.1	ENSP00000338487	MGT4B_HUMAN	E5RFS3_HUMAN	UPI000015F50B	.	.	.	8/14	.	hmmpanther:PTHR12062:SF1,hmmpanther:PTHR12062,Pfam_domain:PF04666	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATCAGGCT	.	5	ESCA
FYB	0	.	GRCh37	5	39202037	39202037	+	Silent	SNP	C	C	T	rs776689421	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1056G>A	p.%3D	p.P352P	ENST00000540520	2/19	251	238	13	189	189	0	FYB,synonymous_variant,p.%3D,ENST00000515010,;FYB,synonymous_variant,p.%3D,ENST00000351578,;FYB,synonymous_variant,p.%3D,ENST00000505428,;FYB,synonymous_variant,p.%3D,ENST00000540520,;FYB,synonymous_variant,p.%3D,ENST00000512982,;FYB,downstream_gene_variant,,ENST00000512138,;FYB,downstream_gene_variant,,ENST00000506557,;FYB,downstream_gene_variant,,ENST00000510188,;FYB,downstream_gene_variant,,ENST00000509072,;FYB,downstream_gene_variant,,ENST00000504542,;	T	ENSG00000082074	ENST00000540520	Transcript	synonymous_variant	1142	1056	352	P	ccG/ccA	rs776689421,COSM3749931,COSM3749930,COSM3749929,COSM3749932	.	.	-1	FYB	HGNC	4036	protein_coding	YES	CCDS58945.1	ENSP00000442840	FYB_HUMAN	D6RFJ5_HUMAN,D6RER7_HUMAN,D6RC38_HUMAN,D6RAE8_HUMAN	UPI00017A75FB	.	.	.	2/19	.	hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF10	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P342P|c.1026G>A|3,SITE|p.P342P|c.1026G>A|3,SITE|p.P342P|c.1026G>A|3,SITE|p.P342P|c.1026G>A|3	MUTECT|MUSE	TGTTTCGGGGT	byFrequency	2	ESCA
PRKAA1	0	.	GRCh37	5	40771927	40771927	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.447C>T	p.%3D	p.I149I	ENST00000354209	5/10	88	82	6	81	81	0	PRKAA1,synonymous_variant,p.%3D,ENST00000296800,;PRKAA1,synonymous_variant,p.%3D,ENST00000397128,;PRKAA1,synonymous_variant,p.%3D,ENST00000354209,;PRKAA1,non_coding_transcript_exon_variant,,ENST00000506652,;PRKAA1,non_coding_transcript_exon_variant,,ENST00000509874,;PRKAA1,non_coding_transcript_exon_variant,,ENST00000505783,;	A	ENSG00000132356	ENST00000354209	Transcript	synonymous_variant	632	447	149	I	atC/atT	.	.	.	-1	PRKAA1	HGNC	9376	protein_coding	YES	CCDS3933.2	ENSP00000346148	AAPK1_HUMAN	.	UPI00003529FB	.	.	.	5/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF81,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAGGATCTG	.	2	ESCA
PLCXD3	0	.	GRCh37	5	41310851	41310851	+	3'UTR	SNP	C	C	T	rs149511699	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2868G>A	.	.	ENST00000377801	3/3	67	55	11	88	88	0	PLCXD3,3_prime_UTR_variant,,ENST00000328457,;PLCXD3,3_prime_UTR_variant,,ENST00000377801,;	T	ENSG00000182836	ENST00000377801	Transcript	3_prime_UTR_variant	3909	.	.	.	.	rs149511699	.	.	-1	PLCXD3	HGNC	31822	protein_coding	YES	CCDS34150.1	ENSP00000367032	PLCX3_HUMAN	B3KXD1_HUMAN	UPI0000049DBB	.	.	.	3/3	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCCCTTCTA	by1000G	5	ESCA
SPATA9	0	.	GRCh37	5	95018270	95018270	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.112G>C	p.Glu38Gln	p.E38Q	ENST00000274432	2/5	78	72	6	85	85	0	SPATA9,missense_variant,p.Glu38Gln,ENST00000395899,;SPATA9,missense_variant,p.Glu38Gln,ENST00000274432,;SPATA9,non_coding_transcript_exon_variant,,ENST00000477047,;RFESD,intron_variant,,ENST00000508206,;SPATA9,intron_variant,,ENST00000379990,;SPATA9,missense_variant,p.Glu38Gln,ENST00000489917,;SPATA9,missense_variant,p.Glu38Gln,ENST00000316087,;SPATA9,missense_variant,p.Glu38Gln,ENST00000477715,;	G	ENSG00000145757	ENST00000274432	Transcript	missense_variant	254	112	38	E/Q	Gaa/Caa	COSM3920513	.	.	-1	SPATA9	HGNC	22988	protein_coding	YES	CCDS4076.1	ENSP00000274432	SPAT9_HUMAN	.	UPI000000DBD8	.	deleterious(0.01)	possibly_damaging(0.714)	2/5	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATTCATCTT	.	2	ESCA
SIM1	0	.	GRCh37	6	100841766	100841766	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1168-1G>C	.	p.X390_splice	ENST00000369208	.	22	12	9	27	27	0	SIM1,splice_acceptor_variant,,ENST00000369208,;SIM1,splice_acceptor_variant,,ENST00000262901,;SIM1,non_coding_transcript_exon_variant,,ENST00000505753,;	G	ENSG00000112246	ENST00000369208	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	SIM1	HGNC	10882	protein_coding	YES	CCDS5045.1	ENSP00000358210	SIM1_HUMAN	.	UPI000013D355	.	.	.	.	10/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GAATACTGAAA	.	4	ESCA
GCM2	0	.	GRCh37	6	10877413	10877413	+	Silent	SNP	C	C	T	rs387907432	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303G>A	p.%3D	p.L101L	ENST00000379491	2/5	46	41	5	35	35	0	GCM2,synonymous_variant,p.%3D,ENST00000379491,;SYCP2L,intron_variant,,ENST00000543878,;RP11-637O19.2,upstream_gene_variant,,ENST00000436249,;RP11-637O19.3,intron_variant,,ENST00000480294,;	T	ENSG00000124827	ENST00000379491	Transcript	synonymous_variant	451	303	101	L	ctG/ctA	rs387907432	.	.	-1	GCM2	HGNC	4198	protein_coding	YES	CCDS4517.1	ENSP00000368805	GCM2_HUMAN	D3GDV6_HUMAN	UPI0000073DE7	.	.	.	2/5	.	PROSITE_profiles:PS50807,hmmpanther:PTHR12414,hmmpanther:PTHR12414:SF4,Pfam_domain:PF03615,Superfamily_domains:0041800	.	.	.	.	.	.	.	.	.	uncertain_significance	.	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCAGCTG	byCluster	4	ESCA
REV3L	0	.	GRCh37	6	111695431	111695431	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4127C>T	p.Ser1376Phe	p.S1376F	ENST00000358835	14/33	41	37	3	41	41	0	REV3L,missense_variant,p.Ser1298Phe,ENST00000435970,;REV3L,missense_variant,p.Ser1376Phe,ENST00000358835,;REV3L,missense_variant,p.Ser1376Phe,ENST00000368802,;REV3L,missense_variant,p.Ser1376Phe,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000434009,;REV3L,3_prime_UTR_variant,,ENST00000422377,;	A	ENSG00000009413	ENST00000358835	Transcript	missense_variant	4582	4127	1376	S/F	tCt/tTt	.	.	.	-1	REV3L	HGNC	9968	protein_coding	YES	CCDS5091.2	ENSP00000351697	DPOLZ_HUMAN	Q9UID5_HUMAN,C4TNX2_HUMAN,C4TNX1_HUMAN,C4TNX0_HUMAN,C4B7Q4_HUMAN	UPI0000140023	.	tolerated_low_confidence(0.06)	benign(0.235)	14/33	.	hmmpanther:PTHR10322:SF16,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACCAGAAGAT	.	3	ESCA
REV3L	0	.	GRCh37	6	111696179	111696179	+	Missense_Mutation	SNP	G	G	A	rs757261538	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3379C>T	p.Arg1127Cys	p.R1127C	ENST00000358835	14/33	58	52	5	59	59	0	REV3L,missense_variant,p.Arg1049Cys,ENST00000435970,;REV3L,missense_variant,p.Arg1127Cys,ENST00000358835,;REV3L,missense_variant,p.Arg1127Cys,ENST00000368802,;REV3L,missense_variant,p.Arg1127Cys,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000434009,;REV3L,3_prime_UTR_variant,,ENST00000422377,;	A	ENSG00000009413	ENST00000358835	Transcript	missense_variant	3834	3379	1127	R/C	Cgc/Tgc	rs757261538	.	.	-1	REV3L	HGNC	9968	protein_coding	YES	CCDS5091.2	ENSP00000351697	DPOLZ_HUMAN	Q9UID5_HUMAN,C4TNX2_HUMAN,C4TNX1_HUMAN,C4TNX0_HUMAN,C4B7Q4_HUMAN	UPI0000140023	.	deleterious(0)	probably_damaging(0.999)	14/33	.	hmmpanther:PTHR10322:SF16,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGCGAGGTG	byFrequency	4	ESCA
RFX6	0	.	GRCh37	6	117249991	117249991	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2468C>T	p.Ser823Phe	p.S823F	ENST00000332958	18/19	76	68	8	110	110	0	RFX6,missense_variant,p.Ser823Phe,ENST00000332958,;	T	ENSG00000185002	ENST00000332958	Transcript	missense_variant	2484	2468	823	S/F	tCt/tTt	COSM224690	.	.	1	RFX6	HGNC	21478	protein_coding	YES	CCDS5113.1	ENSP00000332208	RFX6_HUMAN	.	UPI00001609BE	.	deleterious_low_confidence(0)	probably_damaging(0.99)	18/19	.	hmmpanther:PTHR12619:SF16,hmmpanther:PTHR12619	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTTTCTGTCA	.	4	ESCA
PLN	0	.	GRCh37	6	118881046	118881046	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*803G>A	.	.	ENST00000357525	2/2	50	39	11	60	60	0	PLN,3_prime_UTR_variant,,ENST00000357525,;CEP85L,intron_variant,,ENST00000434604,;CEP85L,intron_variant,,ENST00000360290,;CEP85L,intron_variant,,ENST00000419517,;CEP85L,intron_variant,,ENST00000392500,;CEP85L,intron_variant,,ENST00000368488,;CEP85L,intron_variant,,ENST00000368491,;	A	ENSG00000198523	ENST00000357525	Transcript	3_prime_UTR_variant	1154	.	.	.	.	.	.	.	1	PLN	HGNC	9080	protein_coding	YES	CCDS5120.1	ENSP00000350132	PPLA_HUMAN	Q5R352_HUMAN	UPI0000113623	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACAGAATCT	.	5	ESCA
PERP	0	.	GRCh37	6	138413309	138413309	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452G>A	p.Trp151Ter	p.W151*	ENST00000421351	3/3	73	65	8	123	122	1	PERP,stop_gained,p.Trp151Ter,ENST00000421351,;	T	ENSG00000112378	ENST00000421351	Transcript	stop_gained	623	452	151	W/*	tGg/tAg	.	.	.	-1	PERP	HGNC	17637	protein_coding	YES	CCDS5188.1	ENSP00000397157	PERP_HUMAN	.	UPI00000734A2	.	.	.	3/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14399:SF1,hmmpanther:PTHR14399,Pfam_domain:PF00822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCCAGTTA	.	4	ESCA
FOXF2	0	.	GRCh37	6	1390656	1390656	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474C>T	p.%3D	p.F158F	ENST00000259806	1/2	74	63	11	66	66	0	FOXF2,synonymous_variant,p.%3D,ENST00000259806,;	T	ENSG00000137273	ENST00000259806	Transcript	synonymous_variant	588	474	158	F	ttC/ttT	.	.	.	1	FOXF2	HGNC	3810	protein_coding	YES	CCDS4472.1	ENSP00000259806	FOXF2_HUMAN	.	UPI000012ADD6	.	.	.	1/2	.	Prints_domain:PR00053,Superfamily_domains:SSF46785,SMART_domains:SM00339,Pfam_domain:PF00250,Gene3D:1.10.10.10,hmmpanther:PTHR25042,hmmpanther:PTHR25042:SF10,PROSITE_profiles:PS50039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTTCATCAA	.	4	ESCA
SYNE1	0	.	GRCh37	6	152831447	152831447	+	Silent	SNP	G	G	A	rs761939786	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462C>T	p.%3D	p.S154S	ENST00000367255	8/146	72	57	14	54	54	0	SYNE1,synonymous_variant,p.%3D,ENST00000466159,;SYNE1,synonymous_variant,p.%3D,ENST00000367248,;SYNE1,synonymous_variant,p.%3D,ENST00000423061,;SYNE1,synonymous_variant,p.%3D,ENST00000448038,;SYNE1,synonymous_variant,p.%3D,ENST00000367255,;SYNE1,synonymous_variant,p.%3D,ENST00000413186,;SYNE1,synonymous_variant,p.%3D,ENST00000537750,;SYNE1,synonymous_variant,p.%3D,ENST00000341594,;SYNE1,synonymous_variant,p.%3D,ENST00000367253,;SYNE1,synonymous_variant,p.%3D,ENST00000265368,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,;	A	ENSG00000131018	ENST00000367255	Transcript	synonymous_variant	1064	462	154	S	tcC/tcT	rs761939786	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	.	8/146	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCACGGAGGA	byFrequency	5	ESCA
C6orf118	0	.	GRCh37	6	165703509	165703509	+	Missense_Mutation	SNP	C	C	T	rs750287336	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1168G>A	p.Glu390Lys	p.E390K	ENST00000230301	7/9	50	43	7	42	42	0	C6orf118,missense_variant,p.Glu390Lys,ENST00000230301,;C6orf118,3_prime_UTR_variant,,ENST00000543069,;C6orf118,non_coding_transcript_exon_variant,,ENST00000494696,;	T	ENSG00000112539	ENST00000230301	Transcript	missense_variant	1189	1168	390	E/K	Gag/Aag	rs750287336	.	.	-1	C6orf118	HGNC	21233	protein_coding	YES	CCDS5288.1	ENSP00000230301	CF118_HUMAN	.	UPI0000367401	.	deleterious(0)	probably_damaging(0.967)	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCTCAGTAA	.	4	ESCA
PDE10A	0	.	GRCh37	6	165752833	165752833	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2112G>T	p.Lys704Asn	p.K704N	ENST00000539869	20/22	90	78	12	105	105	0	PDE10A,missense_variant,p.Lys694Asn,ENST00000354448,;PDE10A,missense_variant,p.Lys704Asn,ENST00000539869,;PDE10A,missense_variant,p.Lys694Asn,ENST00000366882,;	A	ENSG00000112541	ENST00000539869	Transcript	missense_variant	2168	2112	704	K/N	aaG/aaT	.	.	.	-1	PDE10A	HGNC	8772	protein_coding	YES	CCDS47513.1	ENSP00000438284	PDE10_HUMAN	.	UPI000006F80E	.	deleterious(0)	possibly_damaging(0.904)	20/22	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF79,Pfam_domain:PF00233,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATTTCTTCAT	.	4	ESCA
T	0	.	GRCh37	6	166578287	166578287	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668+1G>A	.	p.X223_splice	ENST00000296946	.	96	89	7	76	76	0	T,splice_donor_variant,,ENST00000461348,;T,splice_donor_variant,,ENST00000366876,;T,splice_donor_variant,,ENST00000366871,;T,splice_donor_variant,,ENST00000296946,;	T	ENSG00000164458	ENST00000296946	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	T	HGNC	11515	protein_coding	YES	CCDS5290.1	ENSP00000296946	BRAC_HUMAN	H0YM91_HUMAN	UPI0000126AB5	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCACCTTTC	.	2	ESCA
SLC17A2	0	.	GRCh37	6	25916027	25916027	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1000G>A	p.Asp334Asn	p.D334N	ENST00000360488	9/11	50	43	7	84	84	0	SLC17A2,missense_variant,p.Asp334Asn,ENST00000377850,;SLC17A2,missense_variant,p.Asp334Asn,ENST00000265425,;SLC17A2,missense_variant,p.Asp334Asn,ENST00000360488,;	T	ENSG00000112337	ENST00000360488	Transcript	missense_variant	1418	1000	334	D/N	Gat/Aat	.	.	.	-1	SLC17A2	HGNC	10930	protein_coding	YES	CCDS4567.1	ENSP00000353677	NPT3_HUMAN	.	UPI0000000DB7	.	deleterious(0)	probably_damaging(0.997)	9/11	.	Superfamily_domains:SSF103473,Pfam_domain:PF07690,Gene3D:1.20.1250.20,hmmpanther:PTHR11662:SF193,hmmpanther:PTHR11662,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAATCTGCCA	.	4	ESCA
HIST1H2BC	0	.	GRCh37	6	26123991	26123991	+	Missense_Mutation	SNP	G	G	C	rs752097717	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142C>G	p.Gln48Glu	p.Q48E	ENST00000314332	1/2	150	143	6	157	157	0	HIST1H2BC,missense_variant,p.Gln48Glu,ENST00000314332,;HIST1H2BC,missense_variant,p.Gln48Glu,ENST00000396984,;HIST1H2AC,upstream_gene_variant,,ENST00000377791,;HIST1H2AC,upstream_gene_variant,,ENST00000602637,;HIST1H2AC,upstream_gene_variant,,ENST00000314088,;	C	ENSG00000180596	ENST00000314332	Transcript	missense_variant	148	142	48	Q/E	Cag/Gag	rs752097717	.	.	-1	HIST1H2BC	HGNC	4757	protein_coding	YES	CCDS4584.1	ENSP00000321744	H2B1C_HUMAN	B2R4S9_HUMAN	UPI0000000C24	.	deleterious_low_confidence(0)	benign(0.314)	1/2	.	hmmpanther:PTHR23428,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTGTTTCA	.	2	ESCA
ZNF184	0	.	GRCh37	6	27420279	27420279	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059G>C	p.Gln353His	p.Q353H	ENST00000211936	6/6	111	94	16	81	81	0	ZNF184,missense_variant,p.Gln353His,ENST00000211936,;ZNF184,missense_variant,p.Gln353His,ENST00000377419,;	G	ENSG00000096654	ENST00000211936	Transcript	missense_variant	1344	1059	353	Q/H	caG/caC	.	.	.	-1	ZNF184	HGNC	12975	protein_coding	YES	CCDS4624.1	ENSP00000211936	ZN184_HUMAN	.	UPI000013C311	.	tolerated(0.05)	probably_damaging(1)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF108,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCTGATG	.	5	ESCA
ZFP57	0	.	GRCh37	6	29645002	29645002	+	5'Flank	SNP	T	T	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000488757	.	23	17	6	28	28	0	ZFP57,5_prime_UTR_variant,,ENST00000376883,;MOG,downstream_gene_variant,,ENST00000533330,;MOG,downstream_gene_variant,,ENST00000376917,;MOG,downstream_gene_variant,,ENST00000376902,;MOG,downstream_gene_variant,,ENST00000431798,;MOG,downstream_gene_variant,,ENST00000376894,;ZFP57,upstream_gene_variant,,ENST00000488757,;ZFP57,upstream_gene_variant,,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000376889,;	C	ENSG00000204644	ENST00000488757	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	71	-1	ZFP57	HGNC	18791	protein_coding	YES	CCDS43436.2	ENSP00000418259	ZFP57_HUMAN	.	UPI0001951170	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAATTGAGA	.	5	ESCA
RNF39	0	.	GRCh37	6	30038716	30038716	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*172C>T	.	.	ENST00000244360	4/4	81	76	5	104	104	0	RNF39,3_prime_UTR_variant,,ENST00000376751,;RNF39,3_prime_UTR_variant,,ENST00000244360,;PPP1R11,downstream_gene_variant,,ENST00000376769,;PPP1R11,downstream_gene_variant,,ENST00000376763,;PPP1R11,downstream_gene_variant,,ENST00000376772,;PPP1R11,downstream_gene_variant,,ENST00000376765,;PPP1R11,downstream_gene_variant,,ENST00000376773,;PPP1R11,downstream_gene_variant,,ENST00000376758,;	A	ENSG00000204618	ENST00000244360	Transcript	3_prime_UTR_variant	1533	.	.	.	.	.	.	.	-1	RNF39	HGNC	18064	protein_coding	YES	CCDS4673.1	ENSP00000244360	RNF39_HUMAN	Q96QB5_HUMAN	UPI000000D735	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGTGGAAACG	.	2	ESCA
NEU1	0	.	GRCh37	6	31828301	31828301	+	Missense_Mutation	SNP	G	G	A	rs769449286	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.713C>T	p.Ala238Val	p.A238V	ENST00000375631	4/6	37	33	3	46	46	0	NEU1,missense_variant,p.Ala238Val,ENST00000375631,;SLC44A4,downstream_gene_variant,,ENST00000544672,;SLC44A4,downstream_gene_variant,,ENST00000229729,;SLC44A4,downstream_gene_variant,,ENST00000375562,;SLC44A4,downstream_gene_variant,,ENST00000487680,;NEU1,missense_variant,p.Ala238Val,ENST00000491768,;NEU1,non_coding_transcript_exon_variant,,ENST00000495807,;NEU1,non_coding_transcript_exon_variant,,ENST00000480384,;	A	ENSG00000204386	ENST00000375631	Transcript	missense_variant	843	713	238	A/V	gCc/gTc	rs769449286	.	.	-1	NEU1	HGNC	7758	protein_coding	YES	CCDS4723.1	ENSP00000364782	NEUR1_HUMAN	Q6Q4G8_HUMAN,Q6Q4G7_HUMAN,Q5JQI0_HUMAN	UPI000012FF46	.	tolerated(0.29)	benign(0.008)	4/6	.	hmmpanther:PTHR10628,Pfam_domain:PF13088,Gene3D:2.120.10.10,Superfamily_domains:SSF50939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGGAGGCACCA	.	3	ESCA
NELFE	0	.	GRCh37	6	31922195	31922195	+	Missense_Mutation	SNP	C	C	T	rs775691868	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767G>A	p.Arg256Gln	p.R256Q	ENST00000375429	8/11	48	39	9	51	51	0	NELFE,missense_variant,p.Arg251Gln,ENST00000436289,;NELFE,missense_variant,p.Arg263Gln,ENST00000375425,;NELFE,missense_variant,p.Arg251Gln,ENST00000441998,;NELFE,missense_variant,p.Arg226Gln,ENST00000444811,;NELFE,missense_variant,p.Arg256Gln,ENST00000375429,;NELFE,missense_variant,p.Arg256Gln,ENST00000454913,;CFB,downstream_gene_variant,,ENST00000456570,;SKIV2L,upstream_gene_variant,,ENST00000544581,;SKIV2L,upstream_gene_variant,,ENST00000375394,;NELFE,downstream_gene_variant,,ENST00000426722,;CFB,downstream_gene_variant,,ENST00000483004,;CFB,downstream_gene_variant,,ENST00000477310,;CFB,downstream_gene_variant,,ENST00000498317,;CFB,downstream_gene_variant,,ENST00000556679,;CFB,downstream_gene_variant,,ENST00000425368,;MIR1236,downstream_gene_variant,,ENST00000408340,;SKIV2L,upstream_gene_variant,,ENST00000488648,;CFB,downstream_gene_variant,,ENST00000497841,;NELFE,non_coding_transcript_exon_variant,,ENST00000488426,;NELFE,non_coding_transcript_exon_variant,,ENST00000481121,;NELFE,non_coding_transcript_exon_variant,,ENST00000492185,;SKIV2L,upstream_gene_variant,,ENST00000492900,;CFB,downstream_gene_variant,,ENST00000452035,;NELFE,downstream_gene_variant,,ENST00000492539,;CFB,downstream_gene_variant,,ENST00000467360,;NELFE,downstream_gene_variant,,ENST00000491139,;SKIV2L,upstream_gene_variant,,ENST00000461073,;CFB,downstream_gene_variant,,ENST00000461483,;CFB,downstream_gene_variant,,ENST00000465750,;CFB,downstream_gene_variant,,ENST00000482312,;SKIV2L,upstream_gene_variant,,ENST00000474839,;SKIV2L,upstream_gene_variant,,ENST00000465703,;NELFE,downstream_gene_variant,,ENST00000494956,;CFB,downstream_gene_variant,,ENST00000467150,;	T	ENSG00000204356	ENST00000375429	Transcript	missense_variant	994	767	256	R/Q	cGa/cAa	rs775691868	.	.	-1	NELFE	HGNC	13974	protein_coding	YES	CCDS4730.1	ENSP00000364578	NELFE_HUMAN	Q9BQJ6_HUMAN,A2ABK4_HUMAN,A2ABK2_HUMAN	UPI000000127D	.	tolerated(0.06)	unknown(0)	8/11	.	hmmpanther:PTHR17250:SF0,hmmpanther:PTHR17250,Gene3D:3.30.70.330,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTCGCCGT	byFrequency	5	ESCA
BRPF3	0	.	GRCh37	6	36168850	36168850	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.751G>A	p.Glu251Lys	p.E251K	ENST00000357641	2/13	34	30	4	38	38	0	BRPF3,missense_variant,p.Glu251Lys,ENST00000443324,;BRPF3,missense_variant,p.Glu251Lys,ENST00000357641,;BRPF3,missense_variant,p.Glu251Lys,ENST00000534694,;BRPF3,missense_variant,p.Glu251Lys,ENST00000543502,;BRPF3,missense_variant,p.Glu251Lys,ENST00000339717,;BRPF3,missense_variant,p.Glu251Lys,ENST00000534400,;BRPF3,downstream_gene_variant,,ENST00000446974,;BRPF3,downstream_gene_variant,,ENST00000454960,;BRPF3,upstream_gene_variant,,ENST00000527657,;RP1-179N16.6,upstream_gene_variant,,ENST00000526611,;RP1-179N16.6,upstream_gene_variant,,ENST00000499560,;BRPF3,missense_variant,p.Glu224Lys,ENST00000441123,;BRPF3,missense_variant,p.Glu251Lys,ENST00000449261,;BRPF3,missense_variant,p.Glu251Lys,ENST00000532330,;	A	ENSG00000096070	ENST00000357641	Transcript	missense_variant	1004	751	251	E/K	Gag/Aag	.	.	.	1	BRPF3	HGNC	14256	protein_coding	YES	CCDS34437.1	ENSP00000350267	BRPF3_HUMAN	A8WI62_HUMAN,A8WI61_HUMAN	UPI00001C1E4C	.	deleterious(0)	probably_damaging(0.999)	2/13	.	PROSITE_profiles:PS50016,hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF19,PROSITE_patterns:PS01359,Pfam_domain:PF13831,Gene3D:3.30.40.10,SMART_domains:SM00249,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCCTGAGGGC	.	3	ESCA
FGD2	0	.	GRCh37	6	36988338	36988338	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1144G>A	p.Glu382Lys	p.E382K	ENST00000274963	10/16	95	88	7	105	105	0	FGD2,missense_variant,p.Glu382Lys,ENST00000274963,;FGD2,3_prime_UTR_variant,,ENST00000373535,;FGD2,non_coding_transcript_exon_variant,,ENST00000494343,;FGD2,non_coding_transcript_exon_variant,,ENST00000470273,;FGD2,non_coding_transcript_exon_variant,,ENST00000464083,;FGD2,non_coding_transcript_exon_variant,,ENST00000493635,;FGD2,upstream_gene_variant,,ENST00000487920,;	A	ENSG00000146192	ENST00000274963	Transcript	missense_variant	1315	1144	382	E/K	Gag/Aag	.	.	.	1	FGD2	HGNC	3664	protein_coding	YES	CCDS4829.1	ENSP00000274963	FGD2_HUMAN	.	UPI00001A9477	.	deleterious(0.05)	probably_damaging(0.923)	10/16	.	PROSITE_profiles:PS50003,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF82,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCTGAGTTT	.	2	ESCA
PXDC1	0	.	GRCh37	6	3722977	3722977	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*876C>T	.	.	ENST00000380283	5/5	109	96	13	108	108	0	PXDC1,3_prime_UTR_variant,,ENST00000380283,;PXDC1,3_prime_UTR_variant,,ENST00000380277,;PXDC1,non_coding_transcript_exon_variant,,ENST00000477592,;	A	ENSG00000168994	ENST00000380283	Transcript	3_prime_UTR_variant	2067	.	.	.	.	.	.	.	-1	PXDC1	HGNC	21361	protein_coding	YES	CCDS4486.1	ENSP00000369636	PXDC1_HUMAN	.	UPI000013EB28	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGAGAAGCT	.	4	ESCA
TRERF1	0	.	GRCh37	6	42224820	42224820	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2357G>C	p.Arg786Thr	p.R786T	ENST00000372922	11/18	49	41	7	53	53	0	TRERF1,missense_variant,p.Arg806Thr,ENST00000541110,;TRERF1,missense_variant,p.Arg703Thr,ENST00000340840,;TRERF1,missense_variant,p.Arg786Thr,ENST00000372922,;TRERF1,missense_variant,p.Arg703Thr,ENST00000372917,;TRERF1,missense_variant,p.Arg703Thr,ENST00000354325,;	G	ENSG00000124496	ENST00000372922	Transcript	missense_variant	2920	2357	786	R/T	aGa/aCa	.	.	.	-1	TRERF1	HGNC	18273	protein_coding	YES	CCDS4867.1	ENSP00000362013	TREF1_HUMAN	.	UPI0000052952	.	deleterious(0.01)	possibly_damaging(0.537)	11/18	.	PROSITE_profiles:PS51156,hmmpanther:PTHR16089:SF19,hmmpanther:PTHR16089,Pfam_domain:PF01448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATCTCAAG	.	5	ESCA
XPO5	0	.	GRCh37	6	43528002	43528002	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1134C>T	p.%3D	p.L378L	ENST00000265351	11/32	71	56	15	101	101	0	XPO5,synonymous_variant,p.%3D,ENST00000265351,;RP3-337H4.10,upstream_gene_variant,,ENST00000607635,;XPO5,upstream_gene_variant,,ENST00000424378,;XPO5,synonymous_variant,p.%3D,ENST00000496341,;	A	ENSG00000124571	ENST00000265351	Transcript	synonymous_variant	1345	1134	378	L	ctC/ctT	.	.	.	-1	XPO5	HGNC	17675	protein_coding	YES	CCDS47430.1	ENSP00000265351	XPO5_HUMAN	E2QRM3_HUMAN	UPI000006CC97	.	.	.	11/32	.	hmmpanther:PTHR11223,hmmpanther:PTHR11223:SF3,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAAGAGGGC	.	5	ESCA
TDRD6	0	.	GRCh37	6	46656919	46656919	+	Missense_Mutation	SNP	G	G	A	rs759445214	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1054G>A	p.Glu352Lys	p.E352K	ENST00000316081	1/4	38	33	5	63	63	0	TDRD6,missense_variant,p.Glu352Lys,ENST00000316081,;TDRD6,missense_variant,p.Glu352Lys,ENST00000544460,;TDRD6,upstream_gene_variant,,ENST00000450697,;RP11-446F17.3,upstream_gene_variant,,ENST00000422284,;RP11-446F17.3,upstream_gene_variant,,ENST00000571590,;RP11-446F17.3,upstream_gene_variant,,ENST00000434329,;	A	ENSG00000180113	ENST00000316081	Transcript	missense_variant	1054	1054	352	E/K	Gag/Aag	rs759445214	.	.	1	TDRD6	HGNC	21339	protein_coding	YES	CCDS34470.1	ENSP00000346065	TDRD6_HUMAN	.	UPI0000251E8A	.	deleterious(0)	probably_damaging(0.987)	1/4	.	Superfamily_domains:SSF63748,SMART_domains:SM00333,Gene3D:2.30.30.140,Pfam_domain:PF00567,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7,PROSITE_profiles:PS50304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAAGGAGTTA	.	4	ESCA
GSTA2	0	.	GRCh37	6	52615231	52615231	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*144C>G	.	.	ENST00000493422	7/7	59	50	8	57	57	0	GSTA2,3_prime_UTR_variant,,ENST00000493422,;	C	ENSG00000244067	ENST00000493422	Transcript	3_prime_UTR_variant	969	.	.	.	.	.	.	.	-1	GSTA2	HGNC	4627	protein_coding	YES	CCDS4944.1	ENSP00000420168	GSTA2_HUMAN	.	UPI0000072E13	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAGGAGTTG	.	5	ESCA
DST	0	.	GRCh37	6	56471743	56471743	+	Intron	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3672+3482G>C	.	.	ENST00000244364	.	38	35	3	37	37	0	DST,synonymous_variant,p.%3D,ENST00000439203,;DST,synonymous_variant,p.%3D,ENST00000446842,;DST,synonymous_variant,p.%3D,ENST00000370754,;DST,synonymous_variant,p.%3D,ENST00000361203,;DST,synonymous_variant,p.%3D,ENST00000370769,;DST,synonymous_variant,p.%3D,ENST00000312431,;DST,intron_variant,,ENST00000370788,;DST,intron_variant,,ENST00000244364,;DST,intron_variant,,ENST00000421834,;	G	ENSG00000151914	ENST00000244364	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	.	25/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGTCACAGC	.	2	ESCA
ZNF292	0	.	GRCh37	6	87969973	87969973	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6626C>T	p.Ala2209Val	p.A2209V	ENST00000369577	8/8	34	25	9	55	55	0	ZNF292,missense_variant,p.Ala2209Val,ENST00000369577,;ZNF292,missense_variant,p.Ala127Val,ENST00000496806,;ZNF292,missense_variant,p.Ala2204Val,ENST00000339907,;	T	ENSG00000188994	ENST00000369577	Transcript	missense_variant	6669	6626	2209	A/V	gCt/gTt	COSM1233833,COSM1233832	.	.	1	ZNF292	HGNC	18410	protein_coding	YES	CCDS47457.1	ENSP00000358590	ZN292_HUMAN	Q6ZS01_HUMAN,Q6P495_HUMAN,Q3MN16_HUMAN	UPI000020D2CC	.	tolerated(0.06)	benign(0.14)	8/8	.	hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGCTTCAG	.	5	ESCA
GIGYF1	0	.	GRCh37	7	100277315	100277315	+	3'UTR	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2027C>G	.	.	ENST00000275732	24/24	30	27	3	40	40	0	GIGYF1,3_prime_UTR_variant,,ENST00000275732,;GNB2,downstream_gene_variant,,ENST00000393926,;GNB2,downstream_gene_variant,,ENST00000419828,;GNB2,downstream_gene_variant,,ENST00000427895,;GNB2,downstream_gene_variant,,ENST00000431068,;GNB2,downstream_gene_variant,,ENST00000451587,;GNB2,downstream_gene_variant,,ENST00000303210,;GNB2,downstream_gene_variant,,ENST00000393924,;GNB2,downstream_gene_variant,,ENST00000424361,;GNB2,downstream_gene_variant,,ENST00000412215,;GNB2,downstream_gene_variant,,ENST00000436220,;GIGYF1,downstream_gene_variant,,ENST00000472105,;GNB2,downstream_gene_variant,,ENST00000480159,;GNB2,downstream_gene_variant,,ENST00000470354,;GNB2,downstream_gene_variant,,ENST00000469287,;	C	ENSG00000146830	ENST00000275732	Transcript	3_prime_UTR_variant	6345	.	.	.	.	.	.	.	-1	GIGYF1	HGNC	9126	protein_coding	YES	CCDS34708.1	ENSP00000275732	PERQ1_HUMAN	.	UPI00001BD8AD	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAAGACCGG	.	2	ESCA
MUC17	0	.	GRCh37	7	100678697	100678697	+	Missense_Mutation	SNP	G	G	A	rs750440406	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4000G>A	p.Glu1334Lys	p.E1334K	ENST00000306151	3/13	85	79	6	110	110	0	MUC17,missense_variant,p.Glu1334Lys,ENST00000306151,;MUC17,missense_variant,p.Glu1334Lys,ENST00000379439,;	A	ENSG00000169876	ENST00000306151	Transcript	missense_variant	4064	4000	1334	E/K	Gaa/Aaa	rs750440406	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	unknown(0)	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Y1332Y|c.3996T>C|3	MUTECT|MUSE	ATAGTGAAGGA	byFrequency	2	ESCA
PLOD3	0	.	GRCh37	7	100859262	100859262	+	Missense_Mutation	SNP	C	C	T	rs764596991	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542G>A	p.Arg181His	p.R181H	ENST00000223127	5/19	37	32	5	41	41	0	PLOD3,missense_variant,p.Arg14His,ENST00000421736,;PLOD3,missense_variant,p.Arg181His,ENST00000223127,;PLOD3,downstream_gene_variant,,ENST00000414785,;PLOD3,downstream_gene_variant,,ENST00000456079,;ZNHIT1,upstream_gene_variant,,ENST00000305105,;PLOD3,upstream_gene_variant,,ENST00000454310,;ZNHIT1,upstream_gene_variant,,ENST00000461205,;ZNHIT1,upstream_gene_variant,,ENST00000492315,;PLOD3,missense_variant,p.Ala103Thr,ENST00000424135,;PLOD3,non_coding_transcript_exon_variant,,ENST00000489927,;PLOD3,non_coding_transcript_exon_variant,,ENST00000478082,;PLOD3,upstream_gene_variant,,ENST00000478264,;PLOD3,upstream_gene_variant,,ENST00000463479,;PLOD3,upstream_gene_variant,,ENST00000466881,;ZNHIT1,upstream_gene_variant,,ENST00000485387,;PLOD3,downstream_gene_variant,,ENST00000481461,;PLOD3,upstream_gene_variant,,ENST00000440925,;PLOD3,upstream_gene_variant,,ENST00000460475,;	T	ENSG00000106397	ENST00000223127	Transcript	missense_variant	941	542	181	R/H	cGc/cAc	rs764596991	.	.	-1	PLOD3	HGNC	9083	protein_coding	YES	CCDS5715.1	ENSP00000223127	PLOD3_HUMAN	C9JIX5_HUMAN	UPI0000046664	.	tolerated(0.09)	benign(0.002)	5/19	.	hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGGCGCACG	byFrequency	4	ESCA
ALKBH4	0	.	GRCh37	7	102100206	102100206	+	Missense_Mutation	SNP	C	C	T	rs751425937	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166G>A	p.Val56Met	p.V56M	ENST00000292566	2/3	83	76	7	130	130	0	ALKBH4,missense_variant,p.Val56Met,ENST00000292566,;ORAI2,downstream_gene_variant,,ENST00000356387,;ALKBH4,non_coding_transcript_exon_variant,,ENST00000498283,;ALKBH4,intron_variant,,ENST00000490528,;	T	ENSG00000160993	ENST00000292566	Transcript	missense_variant	206	166	56	V/M	Gtg/Atg	rs751425937	.	.	-1	ALKBH4	HGNC	21900	protein_coding	YES	CCDS5723.1	ENSP00000292566	ALKB4_HUMAN	.	UPI0000073F0C	.	tolerated(0.12)	benign(0.018)	2/3	.	hmmpanther:PTHR12463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCCACGGCCC	.	3	ESCA
LAMB1	0	.	GRCh37	7	107615724	107615724	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1324G>A	p.Glu442Lys	p.E442K	ENST00000222399	11/34	45	39	6	63	63	0	LAMB1,missense_variant,p.Glu466Lys,ENST00000393561,;LAMB1,missense_variant,p.Glu442Lys,ENST00000393560,;LAMB1,missense_variant,p.Glu442Lys,ENST00000222399,;	T	ENSG00000091136	ENST00000222399	Transcript	missense_variant	1555	1324	442	E/K	Gaa/Aaa	.	.	.	-1	LAMB1	HGNC	6486	protein_coding	YES	CCDS5750.1	ENSP00000222399	LAMB1_HUMAN	Q75MC8_HUMAN,E9PCS6_HUMAN	UPI00001AE63F	.	tolerated(0.22)	benign(0.05)	11/34	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF233,hmmpanther:PTHR10574,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTTCTTTGC	.	4	ESCA
LAMB1	0	.	GRCh37	7	107616231	107616231	+	Silent	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1092C>T	p.%3D	p.D364D	ENST00000222399	10/34	73	66	7	57	57	0	LAMB1,synonymous_variant,p.%3D,ENST00000393561,;LAMB1,synonymous_variant,p.%3D,ENST00000393560,;LAMB1,synonymous_variant,p.%3D,ENST00000222399,;	A	ENSG00000091136	ENST00000222399	Transcript	synonymous_variant	1323	1092	364	D	gaC/gaT	.	.	.	-1	LAMB1	HGNC	6486	protein_coding	YES	CCDS5750.1	ENSP00000222399	LAMB1_HUMAN	Q75MC8_HUMAN,E9PCS6_HUMAN	UPI00001AE63F	.	.	.	10/34	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF233,hmmpanther:PTHR10574,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACAGTCATC	.	4	ESCA
RNF148	0	.	GRCh37	7	122342265	122342265	+	Silent	SNP	C	C	G	rs770706381	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.540G>C	p.%3D	p.G180G	ENST00000434824	1/1	45	40	5	51	51	0	RNF148,synonymous_variant,p.%3D,ENST00000447240,;RNF148,synonymous_variant,p.%3D,ENST00000434824,;CADPS2,intron_variant,,ENST00000334010,;CADPS2,intron_variant,,ENST00000449022,;CADPS2,intron_variant,,ENST00000313070,;CADPS2,intron_variant,,ENST00000412584,;RNF133,upstream_gene_variant,,ENST00000340112,;	G	ENSG00000235631	ENST00000434824	Transcript	synonymous_variant	757	540	180	G	ggG/ggC	rs770706381	.	.	-1	RNF148	HGNC	22411	protein_coding	YES	CCDS47692.1	ENSP00000388207	RN148_HUMAN	A4D0X4_HUMAN	UPI000006FF1E	.	.	.	1/1	.	hmmpanther:PTHR22765:SF31,hmmpanther:PTHR22765	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTCTCCCCAC	.	3	ESCA
MIR182	0	.	GRCh37	7	129410292	129410292	+	RNA	SNP	G	G	A	rs760187044	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.41C>T	.	.	ENST00000385255	1/1	78	70	8	140	140	0	MIR182,mature_miRNA_variant,,ENST00000385255,;MIR96,downstream_gene_variant,,ENST00000362288,;MIR183,downstream_gene_variant,,ENST00000384958,;	A	ENSG00000207990	ENST00000385255	Transcript	mature_miRNA_variant	41	.	.	.	.	rs760187044	.	.	-1	MIR182	HGNC	31553	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTGTGAGTTC	byFrequency	4	ESCA
HIPK2	0	.	GRCh37	7	139416675	139416675	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159G>C	p.Gln53His	p.Q53H	ENST00000406875	2/15	85	80	5	115	115	0	HIPK2,missense_variant,p.Gln53His,ENST00000342645,;HIPK2,missense_variant,p.Gln53His,ENST00000428878,;HIPK2,missense_variant,p.Gln53His,ENST00000406875,;	G	ENSG00000064393	ENST00000406875	Transcript	missense_variant	254	159	53	Q/H	caG/caC	.	.	.	-1	HIPK2	HGNC	14402	protein_coding	YES	.	ENSP00000385571	HIPK2_HUMAN	A4D1R9_HUMAN	UPI000012C71E	.	tolerated(0.91)	benign(0)	2/15	.	hmmpanther:PTHR24058:SF45,hmmpanther:PTHR24058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGCTCTGGCT	.	2	ESCA
SSPO	0	.	GRCh37	7	149522965	149522965	+	RNA	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.14187C>T	.	.	ENST00000378016	99/109	29	24	5	35	35	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000492965,;SSPO,non_coding_transcript_exon_variant,,ENST00000493567,;SSPO,intron_variant,,ENST00000488835,;SSPO,intron_variant,,ENST00000461331,;SSPO,downstream_gene_variant,,ENST00000464974,;SSPO,non_coding_transcript_exon_variant,,ENST00000472850,;SSPO,non_coding_transcript_exon_variant,,ENST00000465639,;	T	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	14187	.	.	.	.	.	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	99/109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTCCCCAGTGC	.	4	ESCA
SNX13	0	.	GRCh37	7	17980060	17980060	+	5'UTR	SNP	C	C	T	rs559554797	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-142G>A	.	.	ENST00000428135	1/26	35	31	4	22	22	0	SNX13,5_prime_UTR_variant,,ENST00000428135,;SNX13,5_prime_UTR_variant,,ENST00000409389,;SNX13,5_prime_UTR_variant,,ENST00000409604,;SNX13,non_coding_transcript_exon_variant,,ENST00000475800,;SNX13,non_coding_transcript_exon_variant,,ENST00000474067,;SNX13,non_coding_transcript_exon_variant,,ENST00000471744,;SNX13,5_prime_UTR_variant,,ENST00000409076,;SNX13,5_prime_UTR_variant,,ENST00000444712,;SNX13,upstream_gene_variant,,ENST00000482558,;	T	ENSG00000071189	ENST00000428135	Transcript	5_prime_UTR_variant	58	.	.	.	.	rs559554797	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	.	.	1/26	.	.	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTTCGCTGG	by1000G	2	ESCA
DNAH11	0	.	GRCh37	7	21603811	21603811	+	Silent	SNP	C	C	G	rs376448045	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990C>G	p.%3D	p.L330L	ENST00000328843	6/83	41	37	4	43	43	0	DNAH11,synonymous_variant,p.%3D,ENST00000328843,;DNAH11,synonymous_variant,p.%3D,ENST00000409508,;DNAH11,intron_variant,,ENST00000496218,;DNAH11,downstream_gene_variant,,ENST00000483691,;	G	ENSG00000105877	ENST00000328843	Transcript	synonymous_variant	1021	990	330	L	ctC/ctG	rs376448045,COSM1088375	.	.	1	DNAH11	HGNC	2942	protein_coding	YES	.	ENSP00000330671	DYH11_HUMAN	Q75MY1_HUMAN,Q75KM7_HUMAN,O95705_HUMAN,O43352_HUMAN,O15433_HUMAN	UPI000041AC4D	.	.	.	6/83	.	hmmpanther:PTHR10676:SF227,hmmpanther:PTHR10676,Pfam_domain:PF08385	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTTCTCGAAGC	byFrequency|byCluster	3	ESCA
GLI3	0	.	GRCh37	7	42085103	42085103	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.706G>A	p.Glu236Lys	p.E236K	ENST00000395925	6/15	92	77	14	70	70	0	GLI3,missense_variant,p.Glu236Lys,ENST00000395925,;GLI3,downstream_gene_variant,,ENST00000448703,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,;	T	ENSG00000106571	ENST00000395925	Transcript	missense_variant	791	706	236	E/K	Gaa/Aaa	CM990700,COSM1673129	.	.	-1	GLI3	HGNC	4319	protein_coding	YES	CCDS5465.1	ENSP00000379258	GLI3_HUMAN	C9J9N4_HUMAN	UPI000020EE4C	.	deleterious(0.01)	possibly_damaging(0.701)	6/15	.	hmmpanther:PTHR19818:SF5,hmmpanther:PTHR19818	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GTATTCTGCTG	.	3	ESCA
IGFBP3	0	.	GRCh37	7	45953307	45953307	+	3'Flank	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000381083	.	29	25	3	28	28	0	IGFBP3,3_prime_UTR_variant,,ENST00000275521,;IGFBP3,3_prime_UTR_variant,,ENST00000381086,;IGFBP3,downstream_gene_variant,,ENST00000448817,;IGFBP3,downstream_gene_variant,,ENST00000381083,;IGFBP3,downstream_gene_variant,,ENST00000428530,;IGFBP3,downstream_gene_variant,,ENST00000417621,;IGFBP3,downstream_gene_variant,,ENST00000465642,;IGFBP3,downstream_gene_variant,,ENST00000460477,;IGFBP3,downstream_gene_variant,,ENST00000460209,;	G	ENSG00000146674	ENST00000381083	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	97	-1	IGFBP3	HGNC	5472	protein_coding	YES	CCDS34632.1	ENSP00000370473	IBP3_HUMAN	B3KPF0_HUMAN	UPI00004F8E1F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TCTTTCTAAAC	.	3	ESCA
TNS3	0	.	GRCh37	7	47408374	47408374	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1869C>G	p.%3D	p.V623V	ENST00000398879	17/31	55	51	4	41	41	0	TNS3,synonymous_variant,p.%3D,ENST00000398879,;TNS3,synonymous_variant,p.%3D,ENST00000311160,;TNS3,synonymous_variant,p.%3D,ENST00000457718,;TNS3,synonymous_variant,p.%3D,ENST00000355730,;TNS3,downstream_gene_variant,,ENST00000450444,;TNS3,downstream_gene_variant,,ENST00000469470,;	C	ENSG00000136205	ENST00000398879	Transcript	synonymous_variant	2236	1869	623	V	gtC/gtG	.	.	.	-1	TNS3	HGNC	21616	protein_coding	YES	CCDS5506.2	ENSP00000381854	TENS3_HUMAN	C9JWN9_HUMAN,C9JTD0_HUMAN	UPI00001AE9DA	.	.	.	17/31	.	hmmpanther:PTHR12305:SF41,hmmpanther:PTHR12305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTGGACGAG	.	2	ESCA
MRPS17	0	.	GRCh37	7	56022736	56022736	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258C>T	p.%3D	p.F86F	ENST00000285298	3/3	71	62	8	106	106	0	MRPS17,synonymous_variant,p.%3D,ENST00000285298,;MRPS17,synonymous_variant,p.%3D,ENST00000426595,;MRPS17,synonymous_variant,p.%3D,ENST00000443449,;GBAS,intron_variant,,ENST00000446692,;	T	ENSG00000239789	ENST00000285298	Transcript	synonymous_variant	387	258	86	F	ttC/ttT	.	.	.	1	MRPS17	HGNC	14047	protein_coding	YES	CCDS5520.1	ENSP00000285298	RT17_HUMAN	Q96Q59_HUMAN,E9PE17_HUMAN	UPI00000473E2	.	.	.	3/3	.	HAMAP:MF_01345_B,hmmpanther:PTHR24088,Gene3D:2.40.50.140,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTCAAAGT	.	4	ESCA
ZNF117	0	.	GRCh37	7	64438943	64438943	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1006G>C	p.Glu336Gln	p.E336Q	ENST00000282869	4/4	47	44	3	90	90	0	ZNF117,missense_variant,p.Glu336Gln,ENST00000282869,;ZNF117,downstream_gene_variant,,ENST00000487644,;	G	ENSG00000152926	ENST00000282869	Transcript	missense_variant	2291	1006	336	E/Q	Gag/Cag	.	.	.	-1	ZNF117	HGNC	12897	protein_coding	YES	CCDS43593.1	ENSP00000282869	ZN117_HUMAN	.	UPI000049E07A	.	deleterious(0.02)	probably_damaging(0.995)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF120,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCACATT	.	2	ESCA
KCTD7	0	.	GRCh37	7	66103973	66103973	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624C>T	p.%3D	p.N208N	ENST00000443322	4/5	36	32	4	45	45	0	KCTD7,synonymous_variant,p.%3D,ENST00000443322,;KCTD7,synonymous_variant,p.%3D,ENST00000275532,;KCTD7,downstream_gene_variant,,ENST00000449064,;KCTD7,intron_variant,,ENST00000503687,;	T	ENSG00000243335	ENST00000443322	Transcript	synonymous_variant	746	624	208	N	aaC/aaT	.	.	.	1	KCTD7	HGNC	21957	protein_coding	.	CCDS55117.1	ENSP00000411624	KCTD7_HUMAN	.	UPI00000745E2	.	.	.	4/5	.	hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCAACTCCCT	.	3	ESCA
LIMK1	0	.	GRCh37	7	73521432	73521432	+	Missense_Mutation	SNP	G	G	A	rs782450849	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.974G>A	p.Arg325His	p.R325H	ENST00000336180	8/16	151	140	11	108	108	0	LIMK1,missense_variant,p.Arg355His,ENST00000418310,;LIMK1,missense_variant,p.Arg291His,ENST00000538333,;LIMK1,missense_variant,p.Arg325His,ENST00000336180,;LIMK1,downstream_gene_variant,,ENST00000491052,;LIMK1,missense_variant,p.Ala305Thr,ENST00000435201,;LIMK1,non_coding_transcript_exon_variant,,ENST00000483414,;	A	ENSG00000106683	ENST00000336180	Transcript	missense_variant	1025	974	325	R/H	cGc/cAc	rs782450849	.	.	1	LIMK1	HGNC	6613	protein_coding	YES	CCDS5563.1	ENSP00000336740	LIMK1_HUMAN	Q75MU4_HUMAN	UPI000013D678	.	deleterious(0.01)	benign(0.201)	8/16	.	Gene3D:3.30.200.20,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF379	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCCGCGTAG	byFrequency	2	ESCA
PHTF2	0	.	GRCh37	7	77584257	77584257	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62G>A	.	.	ENST00000416283	18/18	88	79	9	121	121	0	PHTF2,3_prime_UTR_variant,,ENST00000307305,;PHTF2,3_prime_UTR_variant,,ENST00000416283,;PHTF2,3_prime_UTR_variant,,ENST00000422959,;PHTF2,3_prime_UTR_variant,,ENST00000248550,;PHTF2,3_prime_UTR_variant,,ENST00000275575,;PHTF2,downstream_gene_variant,,ENST00000470215,;	A	ENSG00000006576	ENST00000416283	Transcript	3_prime_UTR_variant	2444	.	.	.	.	.	.	.	1	PHTF2	HGNC	13411	protein_coding	YES	CCDS47621.1	ENSP00000400958	PHTF2_HUMAN	.	UPI0000E674D3	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCCTGAAAGC	.	3	ESCA
GNG11	0	.	GRCh37	7	93551468	93551468	+	Missense_Mutation	SNP	G	G	C	rs758905574	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19G>C	p.Glu7Gln	p.E7Q	ENST00000248564	1/2	91	83	8	120	120	0	GNG11,missense_variant,p.Glu7Gln,ENST00000248564,;	C	ENSG00000127920	ENST00000248564	Transcript	missense_variant	458	19	7	E/Q	Gaa/Caa	rs758905574,COSM3431885	.	.	1	GNG11	HGNC	4403	protein_coding	YES	CCDS5634.1	ENSP00000248564	GBG11_HUMAN	Q53Y01_HUMAN	UPI0000001AD4	.	tolerated(0.93)	benign(0.205)	1/2	.	Superfamily_domains:SSF48670,hmmpanther:PTHR13809:SF20,hmmpanther:PTHR13809,PROSITE_profiles:PS50058	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACATCGAAGAT	byFrequency	3	ESCA
ZNF655	0	.	GRCh37	7	99171528	99171528	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*321A>G	.	.	ENST00000424881	4/4	46	42	4	55	55	0	ZNF655,3_prime_UTR_variant,,ENST00000424881,;ZNF655,3_prime_UTR_variant,,ENST00000252713,;ZNF655,3_prime_UTR_variant,,ENST00000394163,;ZNF655,3_prime_UTR_variant,,ENST00000425063,;ZNF655,downstream_gene_variant,,ENST00000422647,;ZNF655,downstream_gene_variant,,ENST00000493277,;ZNF655,downstream_gene_variant,,ENST00000449244,;ZNF655,downstream_gene_variant,,ENST00000422164,;ZNF655,downstream_gene_variant,,ENST00000427931,;ZNF655,downstream_gene_variant,,ENST00000454654,;ZNF655,non_coding_transcript_exon_variant,,ENST00000419215,;GS1-259H13.10,intron_variant,,ENST00000486324,;ZNF655,non_coding_transcript_exon_variant,,ENST00000494357,;GS1-259H13.10,intron_variant,,ENST00000455905,;ZNF655,downstream_gene_variant,,ENST00000412636,;ZNF655,downstream_gene_variant,,ENST00000493947,;	G	ENSG00000197343	ENST00000424881	Transcript	3_prime_UTR_variant	2122	.	.	.	.	.	.	.	1	ZNF655	HGNC	30899	protein_coding	YES	CCDS47655.1	ENSP00000393876	ZN655_HUMAN	Q68DU4_HUMAN,F8WEB1_HUMAN,C9JUB9_HUMAN,C9JS03_HUMAN,C9IYG2_HUMAN	UPI000020F66D	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGGAATAAAA	.	2	ESCA
MCM7	0	.	GRCh37	7	99699026	99699026	+	5'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-109C>T	.	.	ENST00000303887	1/15	52	46	6	22	22	0	MCM7,5_prime_UTR_variant,,ENST00000303887,;MCM7,5_prime_UTR_variant,,ENST00000343023,;AP4M1,upstream_gene_variant,,ENST00000422582,;MCM7,upstream_gene_variant,,ENST00000425308,;AP4M1,upstream_gene_variant,,ENST00000359593,;MCM7,upstream_gene_variant,,ENST00000354230,;AP4M1,upstream_gene_variant,,ENST00000450807,;AP4M1,upstream_gene_variant,,ENST00000438383,;AP4M1,upstream_gene_variant,,ENST00000421755,;AP4M1,upstream_gene_variant,,ENST00000429084,;AP4M1,upstream_gene_variant,,ENST00000439416,;AP4M1,upstream_gene_variant,,ENST00000445295,;AP4M1,upstream_gene_variant,,ENST00000495154,;AP4M1,upstream_gene_variant,,ENST00000478501,;MCM7,non_coding_transcript_exon_variant,,ENST00000463722,;AP4M1,upstream_gene_variant,,ENST00000446007,;MCM7,upstream_gene_variant,,ENST00000467516,;AP4M1,upstream_gene_variant,,ENST00000445208,;MCM7,upstream_gene_variant,,ENST00000465738,;AP4M1,upstream_gene_variant,,ENST00000416938,;AP4M1,upstream_gene_variant,,ENST00000463195,;MCM7,upstream_gene_variant,,ENST00000491245,;MCM7,upstream_gene_variant,,ENST00000477372,;MCM7,upstream_gene_variant,,ENST00000485286,;AP4M1,upstream_gene_variant,,ENST00000394061,;MCM7,upstream_gene_variant,,ENST00000465688,;MCM7,upstream_gene_variant,,ENST00000489841,;AP4M1,upstream_gene_variant,,ENST00000489387,;AP4M1,upstream_gene_variant,,ENST00000479916,;	A	ENSG00000166508	ENST00000303887	Transcript	5_prime_UTR_variant	538	.	.	.	.	.	.	.	-1	MCM7	HGNC	6950	protein_coding	YES	CCDS5683.1	ENSP00000307288	MCM7_HUMAN	Q9H4N9_HUMAN,C9J8M6_HUMAN	UPI000012ED9E	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCGCGAAACG	.	2	ESCA
RIMS2	0	.	GRCh37	8	104898096	104898096	+	Silent	SNP	T	T	C	rs778061023	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269T>C	p.%3D	p.S423S	ENST00000406091	4/24	25	16	8	30	30	0	RIMS2,synonymous_variant,p.%3D,ENST00000406091,;RIMS2,synonymous_variant,p.%3D,ENST00000408894,;RIMS2,synonymous_variant,p.%3D,ENST00000504942,;RIMS2,synonymous_variant,p.%3D,ENST00000507740,;RIMS2,synonymous_variant,p.%3D,ENST00000262231,;RIMS2,synonymous_variant,p.%3D,ENST00000515551,;RIMS2,synonymous_variant,p.%3D,ENST00000436393,;RIMS2,downstream_gene_variant,,ENST00000522174,;	C	ENSG00000176406	ENST00000406091	Transcript	synonymous_variant	1269	1269	423	S	tcT/tcC	rs778061023,COSM1264275,COSM51069,COSM3884368,COSM3884367,COSM290336,COSM1264274,COSM3884364,COSM1264192,COSM1264271,COSM290337,COSM3884366,COSM1264273,COSM1264193,COSM1264272,COSM3884365	.	.	1	RIMS2	HGNC	17283	protein_coding	YES	CCDS55269.1	ENSP00000384892	RIMS2_HUMAN	E9PFB6_HUMAN	UPI0001597063	.	.	.	4/24	.	hmmpanther:PTHR12157:SF15,hmmpanther:PTHR12157	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S231S|c.693T>C|4,SITE|p.S423S|c.1269T>C|4,SITE|p.S201S|c.603T>C|4,SITE|p.S231S|c.693T>C|4,CODON|p.S201S|c.603T>G|10,CODON|p.S459S|c.1377T>G|10,CODON|p.S231S|c.693T>G|8,CODON|p.S459S|c.1377T>C|4,CODON|p.S231S|c.693T>G|11,CODON|p.S423S|c.1269T>G|8	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTCTTATGC	.	5	ESCA
KIFC2	0	.	GRCh37	8	145694651	145694651	+	Intron	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114-3C>T	.	.	ENST00000301332	.	87	68	19	61	61	0	KIFC2,splice_region_variant,,ENST00000301331,;KIFC2,splice_region_variant,,ENST00000301332,;CYHR1,upstream_gene_variant,,ENST00000530637,;CYHR1,upstream_gene_variant,,ENST00000533764,;CYHR1,upstream_gene_variant,,ENST00000438911,;CYHR1,upstream_gene_variant,,ENST00000526887,;CYHR1,upstream_gene_variant,,ENST00000424149,;FOXH1,downstream_gene_variant,,ENST00000377317,;CYHR1,upstream_gene_variant,,ENST00000403000,;CYHR1,upstream_gene_variant,,ENST00000306145,;CTD-2517M22.16,downstream_gene_variant,,ENST00000525461,;KIFC2,upstream_gene_variant,,ENST00000531423,;KIFC2,splice_region_variant,,ENST00000529864,;KIFC2,downstream_gene_variant,,ENST00000529644,;KIFC2,downstream_gene_variant,,ENST00000533114,;CYHR1,upstream_gene_variant,,ENST00000524623,;KIFC2,upstream_gene_variant,,ENST00000531425,;	T	ENSG00000167702	ENST00000301332	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	KIFC2	HGNC	29530	protein_coding	YES	CCDS6427.1	ENSP00000301332	KIFC2_HUMAN	.	UPI000006D3B2	.	.	.	.	10/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTCAGGTG	.	4	ESCA
MSR1	0	.	GRCh37	8	15998556	15998556	+	Intron	SNP	T	T	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1033+2511A>C	.	.	ENST00000262101	.	37	32	5	67	67	0	MSR1,splice_acceptor_variant,,ENST00000536385,;MSR1,splice_acceptor_variant,,ENST00000381998,;MSR1,intron_variant,,ENST00000350896,;MSR1,intron_variant,,ENST00000355282,;MSR1,intron_variant,,ENST00000445506,;MSR1,intron_variant,,ENST00000262101,;MSR1,intron_variant,,ENST00000522672,;MSR1,3_prime_UTR_variant,,ENST00000519060,;	G	ENSG00000038945	ENST00000262101	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MSR1	HGNC	7376	protein_coding	YES	CCDS5995.1	ENSP00000262101	MSRE_HUMAN	E5RFW8_HUMAN	UPI000012F686	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGTCCTGACAC	.	2	ESCA
MAK16	0	.	GRCh37	8	33356961	33356961	+	3'UTR	SNP	T	T	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*814T>G	.	.	ENST00000360128	10/10	14	9	5	21	21	0	MAK16,3_prime_UTR_variant,,ENST00000360128,;TTI2,intron_variant,,ENST00000431156,;TTI2,intron_variant,,ENST00000520636,;TTI2,intron_variant,,ENST00000360742,;TTI2,intron_variant,,ENST00000519356,;MAK16,downstream_gene_variant,,ENST00000518389,;	G	ENSG00000198042	ENST00000360128	Transcript	3_prime_UTR_variant	2174	.	.	.	.	.	.	.	1	MAK16	HGNC	13703	protein_coding	YES	CCDS6089.1	ENSP00000353246	MAK16_HUMAN	.	UPI000019080B	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATTTTTAAAT	.	2	ESCA
IKBKB	0	.	GRCh37	8	42188469	42188469	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2243A>T	p.Glu748Val	p.E748V	ENST00000520810	22/22	54	41	12	79	79	0	IKBKB,missense_variant,p.Glu748Val,ENST00000520810,;IKBKB,missense_variant,p.Glu746Val,ENST00000520835,;IKBKB,missense_variant,p.Glu689Val,ENST00000416505,;IKBKB,missense_variant,p.Glu525Val,ENST00000379708,;IKBKB,intron_variant,,ENST00000522147,;IKBKB,downstream_gene_variant,,ENST00000521225,;IKBKB,3_prime_UTR_variant,,ENST00000520655,;IKBKB,3_prime_UTR_variant,,ENST00000517890,;IKBKB,3_prime_UTR_variant,,ENST00000518679,;IKBKB,3_prime_UTR_variant,,ENST00000523517,;IKBKB,3_prime_UTR_variant,,ENST00000342222,;IKBKB,non_coding_transcript_exon_variant,,ENST00000520201,;IKBKB,non_coding_transcript_exon_variant,,ENST00000519938,;IKBKB,non_coding_transcript_exon_variant,,ENST00000522103,;IKBKB,downstream_gene_variant,,ENST00000521661,;IKBKB,downstream_gene_variant,,ENST00000523018,;IKBKB,downstream_gene_variant,,ENST00000523599,;IKBKB,downstream_gene_variant,,ENST00000522133,;	T	ENSG00000104365	ENST00000520810	Transcript	missense_variant	2429	2243	748	E/V	gAg/gTg	.	.	.	1	IKBKB	HGNC	5960	protein_coding	YES	CCDS6128.1	ENSP00000430684	IKKB_HUMAN	E5RGW5_HUMAN	UPI0000033729	.	deleterious_low_confidence(0)	benign(0.134)	22/22	.	hmmpanther:PTHR22969:SF7,hmmpanther:PTHR22969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGAGCACA	.	5	ESCA
RB1CC1	0	.	GRCh37	8	53535579	53535579	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*763G>A	.	.	ENST00000025008	24/24	30	21	9	30	30	0	RB1CC1,3_prime_UTR_variant,,ENST00000025008,;RB1CC1,3_prime_UTR_variant,,ENST00000435644,;RB1CC1,downstream_gene_variant,,ENST00000539297,;RB1CC1,downstream_gene_variant,,ENST00000519912,;RB1CC1,downstream_gene_variant,,ENST00000521611,;RB1CC1,downstream_gene_variant,,ENST00000522957,;	T	ENSG00000023287	ENST00000025008	Transcript	3_prime_UTR_variant	6072	.	.	.	.	.	.	.	-1	RB1CC1	HGNC	15574	protein_coding	YES	CCDS34892.1	ENSP00000025008	RBCC1_HUMAN	E5RH63_HUMAN,B4DGF9_HUMAN	UPI0000DBEF23	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTACGATTT	.	5	ESCA
TTPA	0	.	GRCh37	8	63985593	63985593	+	Missense_Mutation	SNP	G	G	T	rs759510197	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259C>A	p.Leu87Ile	p.L87I	ENST00000260116	2/5	35	24	10	36	36	0	TTPA,missense_variant,p.Leu87Ile,ENST00000260116,;TTPA,intron_variant,,ENST00000521138,;	T	ENSG00000137561	ENST00000260116	Transcript	missense_variant	291	259	87	L/I	Cta/Ata	rs759510197	.	.	-1	TTPA	HGNC	12404	protein_coding	YES	CCDS6178.1	ENSP00000260116	TTPA_HUMAN	.	UPI00001377AC	.	deleterious(0.03)	possibly_damaging(0.833)	2/5	.	hmmpanther:PTHR23324:SF52,hmmpanther:PTHR23324,Superfamily_domains:SSF46938	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTAGATCTG	.	5	ESCA
YTHDF3	0	.	GRCh37	8	64124829	64124829	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2565C>G	.	.	ENST00000539294	5/5	81	60	20	77	77	0	YTHDF3,3_prime_UTR_variant,,ENST00000539294,;YTHDF3,3_prime_UTR_variant,,ENST00000517371,;YTHDF3,3_prime_UTR_variant,,ENST00000542911,;RP11-16E18.3,upstream_gene_variant,,ENST00000569835,;YTHDF3,non_coding_transcript_exon_variant,,ENST00000521674,;YTHDF3,downstream_gene_variant,,ENST00000520640,;YTHDF3,downstream_gene_variant,,ENST00000517303,;YTHDF3,3_prime_UTR_variant,,ENST00000524135,;	G	ENSG00000185728	ENST00000539294	Transcript	3_prime_UTR_variant	4636	.	.	.	.	.	.	.	1	YTHDF3	HGNC	26465	protein_coding	YES	.	ENSP00000473496	.	R4GN55_HUMAN,R4GMX0_HUMAN	UPI0002C8850B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCTATAC	.	5	ESCA
C8orf46	0	.	GRCh37	8	67425869	67425869	+	Missense_Mutation	SNP	G	G	C	rs747247257	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437G>C	p.Arg146Thr	p.R146T	ENST00000305454	5/6	67	46	21	52	52	0	C8orf46,missense_variant,p.Arg146Thr,ENST00000305454,;C8orf46,missense_variant,p.Glu125Asp,ENST00000522977,;C8orf46,missense_variant,p.Arg146Thr,ENST00000480005,;C8orf46,intron_variant,,ENST00000521495,;C8orf46,non_coding_transcript_exon_variant,,ENST00000519702,;C8orf46,non_coding_transcript_exon_variant,,ENST00000485639,;C8orf46,downstream_gene_variant,,ENST00000482608,;C8orf46,3_prime_UTR_variant,,ENST00000460144,;C8orf46,3_prime_UTR_variant,,ENST00000450307,;C8orf46,downstream_gene_variant,,ENST00000484919,;	C	ENSG00000169085	ENST00000305454	Transcript	missense_variant	878	437	146	R/T	aGa/aCa	rs747247257	.	.	1	C8orf46	HGNC	28498	protein_coding	YES	CCDS6191.2	ENSP00000302260	CH046_HUMAN	E5RH60_HUMAN	UPI00003750A4	.	tolerated(0.19)	probably_damaging(0.985)	5/6	.	hmmpanther:PTHR31520,Pfam_domain:PF15505	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGAGAGGGT	.	5	ESCA
SGK223	0	.	GRCh37	8	8239172	8239172	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86C>T	p.Ser29Phe	p.S29F	ENST00000520004	2/6	124	83	41	75	75	0	SGK223,missense_variant,p.Ser29Phe,ENST00000520004,;SGK223,missense_variant,p.Ser29Phe,ENST00000330777,;	A	ENSG00000182319	ENST00000520004	Transcript	missense_variant	351	86	29	S/F	tCc/tTc	.	.	.	-1	SGK223	Uniprot_gn	.	protein_coding	YES	CCDS43706.1	ENSP00000428054	SG223_HUMAN	.	UPI00001D82A6	.	.	probably_damaging(0.991)	2/6	.	hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGGACCCG	.	5	ESCA
CNGB3	0	.	GRCh37	8	87588200	87588200	+	Silent	SNP	A	A	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2262T>G	p.%3D	p.P754P	ENST00000320005	18/18	129	118	10	103	103	0	CNGB3,synonymous_variant,p.%3D,ENST00000320005,;CNGB3,intron_variant,,ENST00000517327,;	C	ENSG00000170289	ENST00000320005	Transcript	synonymous_variant	2310	2262	754	P	ccT/ccG	.	.	.	-1	CNGB3	HGNC	2153	protein_coding	YES	CCDS6244.1	ENSP00000316605	CNGB3_HUMAN	.	UPI000014076F	.	.	.	18/18	.	hmmpanther:PTHR10217:SF385,hmmpanther:PTHR10217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CATTCAGGTCT	.	3	ESCA
C9orf84	0	.	GRCh37	9	114510480	114510480	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.671-1G>A	.	p.X224_splice	ENST00000374287	.	53	47	6	48	48	0	C9orf84,splice_acceptor_variant,,ENST00000318737,;C9orf84,splice_acceptor_variant,,ENST00000374287,;C9orf84,splice_acceptor_variant,,ENST00000394779,;C9orf84,splice_acceptor_variant,,ENST00000374283,;C9orf84,splice_acceptor_variant,,ENST00000394777,;	T	ENSG00000165181	ENST00000374287	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	C9orf84	HGNC	26535	protein_coding	YES	CCDS6781.3	ENSP00000363405	CI084_HUMAN	.	UPI0000458916	.	.	.	.	8/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGATCTGAAA	.	4	ESCA
ZFP37	0	.	GRCh37	9	115812183	115812183	+	Intron	SNP	G	G	C	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.133-31C>G	.	.	ENST00000374227	.	53	43	10	56	56	0	ZFP37,missense_variant,p.Phe49Leu,ENST00000553380,;ZFP37,intron_variant,,ENST00000555206,;ZFP37,intron_variant,,ENST00000374227,;	C	ENSG00000136866	ENST00000374227	Transcript	intron_variant	.	.	.	.	.	COSM3925960	.	.	-1	ZFP37	HGNC	12863	protein_coding	YES	CCDS6787.1	ENSP00000363344	ZFP37_HUMAN	.	UPI000013D04B	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODIFIER	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTGAATGT	.	5	ESCA
WDR31	0	.	GRCh37	9	116085328	116085328	+	Silent	SNP	G	G	A	rs749155216	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432C>T	p.%3D	p.G144G	ENST00000374193	6/11	50	39	10	77	77	0	WDR31,synonymous_variant,p.%3D,ENST00000374195,;WDR31,synonymous_variant,p.%3D,ENST00000465979,;WDR31,synonymous_variant,p.%3D,ENST00000341761,;WDR31,synonymous_variant,p.%3D,ENST00000374193,;WDR31,non_coding_transcript_exon_variant,,ENST00000461942,;WDR31,3_prime_UTR_variant,,ENST00000465205,;	A	ENSG00000148225	ENST00000374193	Transcript	synonymous_variant	679	432	144	G	ggC/ggT	rs749155216	.	.	-1	WDR31	HGNC	21421	protein_coding	YES	CCDS35110.1	ENSP00000363308	WDR31_HUMAN	G5E996_HUMAN	UPI000006D080	.	.	.	6/11	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19869,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATGGCCACA	.	5	ESCA
AL354898.1	0	.	GRCh37	9	133274986	133274986	+	5'UTR	SNP	G	G	A	rs554164495	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-78G>A	.	.	ENST00000277491	2/8	70	61	8	92	92	0	AL354898.1,5_prime_UTR_variant,,ENST00000277491,;RN7SL665P,upstream_gene_variant,,ENST00000578793,;HMCN2,non_coding_transcript_exon_variant,,ENST00000480829,;HMCN2,non_coding_transcript_exon_variant,,ENST00000487727,;	A	ENSG00000215428	ENST00000277491	Transcript	5_prime_UTR_variant	155	.	.	.	.	rs554164495	.	.	1	AL354898.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000277491	.	.	UPI0000073E91	.	.	.	2/8	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGCGAGGCC	by1000G	4	ESCA
SH3GL2	0	.	GRCh37	9	17796339	17796339	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*598G>A	.	.	ENST00000380607	9/9	26	20	6	18	18	0	SH3GL2,3_prime_UTR_variant,,ENST00000380607,;SH3GL2,downstream_gene_variant,,ENST00000537391,;	A	ENSG00000107295	ENST00000380607	Transcript	3_prime_UTR_variant	1777	.	.	.	.	.	.	.	1	SH3GL2	HGNC	10831	protein_coding	YES	CCDS6483.1	ENSP00000369981	SH3G2_HUMAN	Q7Z376_HUMAN,Q3V639_HUMAN,F5H5J3_HUMAN,D3DRJ2_HUMAN	UPI0000135933	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGACGTATAG	.	2	ESCA
FOCAD	0	.	GRCh37	9	20986392	20986392	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4834G>A	p.Glu1612Lys	p.E1612K	ENST00000380249	42/46	65	54	11	88	87	0	FOCAD,missense_variant,p.Glu1612Lys,ENST00000380249,;FOCAD,missense_variant,p.Glu1048Lys,ENST00000605086,;FOCAD,missense_variant,p.Glu1612Lys,ENST00000338382,;FOCAD,downstream_gene_variant,,ENST00000603631,;	A	ENSG00000188352	ENST00000380249	Transcript	missense_variant	5198	4834	1612	E/K	Gag/Aag	.	.	.	1	FOCAD	HGNC	23377	protein_coding	YES	CCDS34993.1	ENSP00000369599	FOCAD_HUMAN	S4R450_HUMAN,S4R400_HUMAN,S4R3S9_HUMAN	UPI00002111D4	.	tolerated(0.26)	benign(0.044)	42/46	.	Pfam_domain:PF11229,hmmpanther:PTHR16212,hmmpanther:PTHR16212:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGTGAGAAA	.	5	ESCA
IFNA1	0	.	GRCh37	9	21441080	21441080	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4C>G	.	.	ENST00000276927	1/1	156	137	18	145	145	0	IFNA1,3_prime_UTR_variant,,ENST00000276927,;	G	ENSG00000197919	ENST00000276927	Transcript	3_prime_UTR_variant	641	.	.	.	.	.	.	.	1	IFNA1	HGNC	5417	protein_coding	YES	CCDS6508.1	ENSP00000276927	IFNA1_HUMAN	L0N195_HUMAN	UPI000002C6D3	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACATCTGGTC	.	4	ESCA
MTAP	0	.	GRCh37	9	21837923	21837923	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364C>G	p.Gln122Glu	p.Q122E	ENST00000380172	5/8	48	42	6	48	48	0	MTAP,missense_variant,p.Gln122Glu,ENST00000580900,;MTAP,missense_variant,p.Gln122Glu,ENST00000380172,;MTAP,missense_variant,p.Gln139Glu,ENST00000460874,;MTAP,non_coding_transcript_exon_variant,,ENST00000427788,;MTAP,missense_variant,p.Gln122Glu,ENST00000580718,;MTAP,3_prime_UTR_variant,,ENST00000419385,;RP11-145E5.5,intron_variant,,ENST00000404796,;	G	ENSG00000099810	ENST00000380172	Transcript	missense_variant	570	364	122	Q/E	Cag/Gag	.	.	.	1	MTAP	HGNC	7413	protein_coding	YES	CCDS6509.1	ENSP00000369519	MTAP_HUMAN	.	UPI0000110BBE	.	tolerated(0.56)	benign(0.193)	5/8	.	HAMAP:MF_01963,hmmpanther:PTHR11904:SF1,hmmpanther:PTHR11904,Gene3D:3.40.50.1580,Pfam_domain:PF01048,TIGRFAM_domain:TIGR01694,Superfamily_domains:SSF53167	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTCAGTCC	.	2	ESCA
SPATA31D1	0	.	GRCh37	9	84605340	84605340	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241G>A	p.Asp81Asn	p.D81N	ENST00000344803	3/4	71	65	6	53	53	0	SPATA31D1,missense_variant,p.Asp81Asn,ENST00000344803,;SPATA31D1,downstream_gene_variant,,ENST00000603921,;	A	ENSG00000214929	ENST00000344803	Transcript	missense_variant	288	241	81	D/N	Gac/Aac	.	.	.	1	SPATA31D1	HGNC	37283	protein_coding	YES	CCDS47986.1	ENSP00000341988	S31D1_HUMAN	.	UPI00001C10A6	.	tolerated(0.21)	possibly_damaging(0.798)	3/4	.	hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859,Pfam_domain:PF15371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCCAGACTGG	.	3	ESCA
THOC2	0	.	GRCh37	X	122799634	122799634	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245G>C	p.Lys415Asn	p.K415N	ENST00000245838	12/39	46	34	12	30	30	0	THOC2,missense_variant,p.Lys415Asn,ENST00000245838,;THOC2,missense_variant,p.Lys300Asn,ENST00000491737,;THOC2,missense_variant,p.Lys415Asn,ENST00000355725,;THOC2,downstream_gene_variant,,ENST00000433883,;	G	ENSG00000125676	ENST00000245838	Transcript	missense_variant	1277	1245	415	K/N	aaG/aaC	.	.	.	-1	THOC2	HGNC	19073	protein_coding	YES	CCDS43988.1	ENSP00000245838	THOC2_HUMAN	.	UPI00001D7C42	.	tolerated(0.34)	benign(0.003)	12/39	.	hmmpanther:PTHR21597,hmmpanther:PTHR21597:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCTTGTT	.	5	ESCA
MOSPD2	0	.	GRCh37	X	14921098	14921098	+	Silent	SNP	G	G	C	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549G>C	p.%3D	p.V183V	ENST00000380492	7/15	43	37	6	66	66	0	MOSPD2,synonymous_variant,p.%3D,ENST00000482354,;MOSPD2,synonymous_variant,p.%3D,ENST00000380492,;MOSPD2,non_coding_transcript_exon_variant,,ENST00000495110,;	C	ENSG00000130150	ENST00000380492	Transcript	synonymous_variant	637	549	183	V	gtG/gtC	.	.	.	1	MOSPD2	HGNC	28381	protein_coding	YES	CCDS14162.1	ENSP00000369860	MSPD2_HUMAN	.	UPI00000735BA	.	.	.	7/15	.	PROSITE_profiles:PS50191,hmmpanther:PTHR19993,hmmpanther:PTHR19993:SF1,Pfam_domain:PF00650,Gene3D:3.40.525.10,SMART_domains:SM00516,Superfamily_domains:SSF52087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGTGATCTT	.	4	ESCA
MAMLD1	0	.	GRCh37	X	149638836	149638836	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916C>G	p.Leu306Val	p.L306V	ENST00000432680	3/5	26	21	5	29	29	0	MAMLD1,missense_variant,p.Leu306Val,ENST00000426613,;MAMLD1,missense_variant,p.Leu331Val,ENST00000262858,;MAMLD1,missense_variant,p.Leu306Val,ENST00000432680,;MAMLD1,missense_variant,p.Leu331Val,ENST00000370401,;MAMLD1,upstream_gene_variant,,ENST00000455522,;MAMLD1,downstream_gene_variant,,ENST00000358892,;MAMLD1,downstream_gene_variant,,ENST00000468306,;	G	ENSG00000013619	ENST00000432680	Transcript	missense_variant	1091	916	306	L/V	Ctg/Gtg	.	.	.	1	MAMLD1	HGNC	2568	protein_coding	YES	CCDS55526.1	ENSP00000414517	MAMD1_HUMAN	Q6ZUZ1_HUMAN	UPI00017A6EBC	.	deleterious(0.01)	possibly_damaging(0.858)	3/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15275:SF0,hmmpanther:PTHR15275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGTCTGCCT	.	5	ESCA
MAGEA6	0	.	GRCh37	X	151869922	151869922	+	Silent	SNP	C	C	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612C>T	p.%3D	p.I204I	ENST00000329342	3/3	132	111	21	143	143	0	MAGEA6,synonymous_variant,p.%3D,ENST00000457643,;MAGEA6,synonymous_variant,p.%3D,ENST00000329342,;MAGEA6,downstream_gene_variant,,ENST00000412733,;	T	ENSG00000197172	ENST00000329342	Transcript	synonymous_variant	837	612	204	I	atC/atT	.	.	.	1	MAGEA6	HGNC	6804	protein_coding	YES	CCDS14708.1	ENSP00000329199	MAGA6_HUMAN	E7EUF2_HUMAN,E7ETG4_HUMAN,B9A060_HUMAN	UPI000000D9B0	.	.	.	3/3	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736,Pfam_domain:PF01454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAATCATCCT	.	4	ESCA
HCFC1	0	.	GRCh37	X	153221703	153221703	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2795C>T	p.Ser932Leu	p.S932L	ENST00000310441	16/26	79	60	18	70	70	0	HCFC1,missense_variant,p.Ser932Leu,ENST00000369984,;HCFC1,missense_variant,p.Ser932Leu,ENST00000310441,;HCFC1,missense_variant,p.Ser863Leu,ENST00000354233,;HCFC1,upstream_gene_variant,,ENST00000444191,;HCFC1,downstream_gene_variant,,ENST00000461098,;	A	ENSG00000172534	ENST00000310441	Transcript	missense_variant	3762	2795	932	S/L	tCg/tTg	COSM1719032,COSM1719031	.	.	-1	HCFC1	HGNC	4839	protein_coding	YES	CCDS44020.1	ENSP00000309555	HCFC1_HUMAN	Q05C05_HUMAN	UPI0000142F1F	.	tolerated_low_confidence(0.09)	probably_damaging(0.974)	16/26	.	hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF266	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCCGACACA	.	5	ESCA
ACE2	0	.	GRCh37	X	15584415	15584415	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2075C>T	p.Ser692Phe	p.S692F	ENST00000427411	17/19	44	38	6	44	44	0	ACE2,missense_variant,p.Ser692Phe,ENST00000427411,;ACE2,missense_variant,p.Ser692Phe,ENST00000252519,;ACE2,non_coding_transcript_exon_variant,,ENST00000473851,;ACE2,upstream_gene_variant,,ENST00000471548,;	A	ENSG00000130234	ENST00000427411	Transcript	missense_variant	2292	2075	692	S/F	tCt/tTt	.	.	.	-1	ACE2	HGNC	13557	protein_coding	YES	CCDS14169.1	ENSP00000389326	ACE2_HUMAN	.	UPI000000D907	.	deleterious_low_confidence(0)	possibly_damaging(0.823)	17/19	.	hmmpanther:PTHR10514:SF24,hmmpanther:PTHR10514	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TATCAGACACA	.	3	ESCA
EIF1AX	0	.	GRCh37	X	20143927	20143927	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2497C>T	.	.	ENST00000379607	7/7	48	43	5	91	91	0	EIF1AX,3_prime_UTR_variant,,ENST00000379607,;EIF1AX,downstream_gene_variant,,ENST00000379593,;	A	ENSG00000173674	ENST00000379607	Transcript	3_prime_UTR_variant	3136	.	.	.	.	.	.	.	-1	EIF1AX	HGNC	3250	protein_coding	YES	CCDS14196.1	ENSP00000368927	IF1AX_HUMAN	.	UPI00000041DF	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCATGATTCC	.	4	ESCA
PCYT1B	0	.	GRCh37	X	24579337	24579337	+	3'Flank	DEL	T	T	-	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000379144	.	40	34	6	51	51	0	PCYT1B,3_prime_UTR_variant,,ENST00000379145,;PCYT1B,downstream_gene_variant,,ENST00000379144,;PCYT1B,downstream_gene_variant,,ENST00000356768,;PCYT1B,downstream_gene_variant,,ENST00000496020,;	-	ENSG00000102230	ENST00000379144	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	622	-1	PCYT1B	HGNC	8755	protein_coding	YES	CCDS14213.1	ENSP00000368439	PCY1B_HUMAN	.	UPI000012864E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GTATTATGGTGG	.	2	ESCA
BCOR	0	.	GRCh37	X	39914677	39914677	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4685C>G	p.Ser1562Ter	p.S1562*	ENST00000378444	12/15	75	64	11	43	43	0	BCOR,stop_gained,p.Ser1528Ter,ENST00000397354,;BCOR,stop_gained,p.Ser235Ter,ENST00000442018,;BCOR,stop_gained,p.Ser1562Ter,ENST00000378444,;BCOR,stop_gained,p.Ser257Ter,ENST00000427012,;BCOR,stop_gained,p.Ser1510Ter,ENST00000378455,;BCOR,stop_gained,p.Ser405Ter,ENST00000378463,;BCOR,stop_gained,p.Ser432Ter,ENST00000413905,;BCOR,stop_gained,p.Ser1528Ter,ENST00000342274,;	C	ENSG00000183337	ENST00000378444	Transcript	stop_gained	4914	4685	1562	S/*	tCa/tGa	COSM3670285,COSM3670284,COSM3670286	.	.	-1	BCOR	HGNC	20893	protein_coding	YES	CCDS48093.1	ENSP00000367705	BCOR_HUMAN	H9A532_HUMAN,H7BZ37_HUMAN,C9JHP3_HUMAN,B3KTC2_HUMAN	UPI00002318CF	.	.	.	12/15	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24117,hmmpanther:PTHR24117:SF8,Gene3D:1.25.40.20,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTGAGTAC	.	5	ESCA
EFHC2	0	.	GRCh37	X	44107641	44107641	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.988C>A	p.Gln330Lys	p.Q330K	ENST00000420999	7/15	117	67	50	132	131	1	EFHC2,missense_variant,p.Gln330Lys,ENST00000420999,;	T	ENSG00000183690	ENST00000420999	Transcript	missense_variant	1072	988	330	Q/K	Caa/Aaa	.	.	.	-1	EFHC2	HGNC	26233	protein_coding	YES	CCDS55405.1	ENSP00000404232	EFHC2_HUMAN	.	UPI00000717F2	.	tolerated(0.06)	benign(0.206)	7/15	.	PROSITE_profiles:PS51336,hmmpanther:PTHR12086,hmmpanther:PTHR12086:SF11,SMART_domains:SM00676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTGGTCTA	.	5	ESCA
USP11	0	.	GRCh37	X	47101642	47101642	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1470C>G	p.Ile490Met	p.I490M	ENST00000218348	10/21	33	29	3	41	41	0	USP11,missense_variant,p.Ile490Met,ENST00000218348,;USP11,missense_variant,p.Ile447Met,ENST00000377107,;USP11,downstream_gene_variant,,ENST00000377078,;USP11,downstream_gene_variant,,ENST00000377080,;USP11,non_coding_transcript_exon_variant,,ENST00000469080,;USP11,non_coding_transcript_exon_variant,,ENST00000480104,;USP11,downstream_gene_variant,,ENST00000489111,;USP11,downstream_gene_variant,,ENST00000478596,;USP11,upstream_gene_variant,,ENST00000467378,;USP11,upstream_gene_variant,,ENST00000497179,;USP11,upstream_gene_variant,,ENST00000488848,;USP11,downstream_gene_variant,,ENST00000489030,;	G	ENSG00000102226	ENST00000218348	Transcript	missense_variant	1470	1470	490	I/M	atC/atG	.	.	.	1	USP11	HGNC	12609	protein_coding	YES	CCDS14277.1	ENSP00000218348	UBP11_HUMAN	Q6P453_HUMAN,Q5JXD3_HUMAN,G5E9A6_HUMAN,B4DGK3_HUMAN,B3KP28_HUMAN	UPI0000161434	.	tolerated(0.58)	benign(0.042)	10/21	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF403,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCTATCAGCCA	.	3	ESCA
FOXR2	0	.	GRCh37	X	55650499	55650499	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355G>A	p.Gly119Arg	p.G119R	ENST00000339140	1/1	43	33	10	36	36	0	FOXR2,missense_variant,p.Gly119Arg,ENST00000339140,;	A	ENSG00000189299	ENST00000339140	Transcript	missense_variant	667	355	119	G/R	Ggg/Agg	.	.	.	1	FOXR2	HGNC	30469	protein_coding	YES	CCDS35308.1	ENSP00000427329	FOXR2_HUMAN	.	UPI00001603CE	.	tolerated(0.4)	benign(0.001)	1/1	.	hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF73	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGAAGGGTCT	.	5	ESCA
RPA4	0	.	GRCh37	X	96139347	96139347	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38C>G	p.Ser13Cys	p.S13C	ENST00000373040	1/1	20	17	3	38	38	0	RPA4,missense_variant,p.Ser13Cys,ENST00000373040,;DIAPH2,intron_variant,,ENST00000373054,;DIAPH2,intron_variant,,ENST00000355827,;DIAPH2,intron_variant,,ENST00000324765,;DIAPH2,intron_variant,,ENST00000373049,;DIAPH2,intron_variant,,ENST00000373061,;	G	ENSG00000204086	ENST00000373040	Transcript	missense_variant	441	38	13	S/C	tCt/tGt	.	.	.	1	RPA4	HGNC	30305	protein_coding	YES	CCDS35345.1	ENSP00000362131	RFA4_HUMAN	.	UPI00001337A4	.	tolerated(0.13)	possibly_damaging(0.506)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13989:SF12,hmmpanther:PTHR13989,PIRSF_domain:PIRSF036949	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTCTGCTG	.	2	ESCA
PCDH19	0	.	GRCh37	X	99664132	99664132	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L5-A8NQ-01A-11D-A36J-09	TCGA-L5-A8NQ-11A-11D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-537G>T	.	.	ENST00000373034	1/6	70	55	14	94	94	0	PCDH19,5_prime_UTR_variant,,ENST00000255531,;PCDH19,5_prime_UTR_variant,,ENST00000373034,;PCDH19,upstream_gene_variant,,ENST00000420881,;	A	ENSG00000165194	ENST00000373034	Transcript	5_prime_UTR_variant	1140	.	.	.	.	.	.	.	-1	PCDH19	HGNC	14270	protein_coding	YES	CCDS55462.1	ENSP00000362125	PCD19_HUMAN	.	UPI00001D7BCD	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCGCTCCCA	.	5	ESCA
LDB1	0	.	GRCh37	10	103870344	103870344	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.467C>T	p.Ser156Phe	p.S156F	ENST00000425280	6/11	41	17	24	40	40	0	LDB1,missense_variant,p.Ser156Phe,ENST00000425280,;LDB1,missense_variant,p.Ser120Phe,ENST00000361198,;LDB1,non_coding_transcript_exon_variant,,ENST00000461873,;LDB1,downstream_gene_variant,,ENST00000490751,;	A	ENSG00000198728	ENST00000425280	Transcript	missense_variant	810	467	156	S/F	tCc/tTc	.	.	.	-1	LDB1	HGNC	6532	protein_coding	YES	CCDS44472.1	ENSP00000392466	LDB1_HUMAN	.	UPI00001F95EA	.	tolerated(0.26)	possibly_damaging(0.821)	6/11	.	hmmpanther:PTHR10378:SF7,hmmpanther:PTHR10378,Pfam_domain:PF01803	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGGGACACA	.	5	ESCA
TACC2	0	.	GRCh37	10	123970420	123970420	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6480G>C	p.Glu2160Asp	p.E2160D	ENST00000369005	9/23	71	46	25	53	53	0	TACC2,start_lost,p.Glu1?,ENST00000505639,;TACC2,missense_variant,p.Glu238Asp,ENST00000368999,;TACC2,missense_variant,p.Glu306Asp,ENST00000358010,;TACC2,missense_variant,p.Glu2164Asp,ENST00000453444,;TACC2,missense_variant,p.Glu238Asp,ENST00000260733,;TACC2,missense_variant,p.Glu2160Asp,ENST00000369005,;TACC2,missense_variant,p.Glu2160Asp,ENST00000334433,;TACC2,missense_variant,p.Glu2115Asp,ENST00000515603,;TACC2,missense_variant,p.Glu238Asp,ENST00000369004,;TACC2,missense_variant,p.Glu255Asp,ENST00000514539,;TACC2,missense_variant,p.Glu306Asp,ENST00000513429,;TACC2,missense_variant,p.Glu238Asp,ENST00000360561,;TACC2,missense_variant,p.Glu2164Asp,ENST00000515273,;TACC2,5_prime_UTR_variant,,ENST00000369000,;TACC2,5_prime_UTR_variant,,ENST00000369001,;TACC2,upstream_gene_variant,,ENST00000496913,;TACC2,upstream_gene_variant,,ENST00000508411,;TACC2,downstream_gene_variant,,ENST00000492237,;TACC2,downstream_gene_variant,,ENST00000493951,;TACC2,missense_variant,p.Glu7Asp,ENST00000440764,;TACC2,non_coding_transcript_exon_variant,,ENST00000368997,;	C	ENSG00000138162	ENST00000369005	Transcript	missense_variant	6820	6480	2160	E/D	gaG/gaC	.	.	.	1	TACC2	HGNC	11523	protein_coding	YES	CCDS7626.1	ENSP00000358001	TACC2_HUMAN	.	UPI0000246F6B	.	.	benign(0.442)	9/23	.	hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGAGAGCCT	.	5	ESCA
SVIL	0	.	GRCh37	10	29839859	29839859	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.494C>T	p.Ser165Phe	p.S165F	ENST00000375398	8/40	50	43	7	45	45	0	SVIL,missense_variant,p.Ser165Phe,ENST00000355867,;SVIL,missense_variant,p.Ser165Phe,ENST00000375400,;SVIL,missense_variant,p.Ser165Phe,ENST00000375398,;SVIL,downstream_gene_variant,,ENST00000483758,;	A	ENSG00000197321	ENST00000375398	Transcript	missense_variant	944	494	165	S/F	tCt/tTt	.	.	.	-1	SVIL	HGNC	11480	protein_coding	YES	CCDS7164.1	ENSP00000364547	SVIL_HUMAN	Q569J5_HUMAN	UPI0000366678	.	deleterious(0.03)	benign(0.432)	8/40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAGAGAACTA	.	4	ESCA
RBP3	0	.	GRCh37	10	48389039	48389039	+	Silent	SNP	G	G	A	rs782278294	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1839C>T	p.%3D	p.P613P	ENST00000224600	1/4	43	35	7	29	29	0	RBP3,synonymous_variant,p.%3D,ENST00000224600,;AL731561.2,downstream_gene_variant,,ENST00000581861,;	A	ENSG00000107618	ENST00000224600	Transcript	synonymous_variant	1953	1839	613	P	ccC/ccT	rs782278294	.	.	-1	RBP3	HGNC	9921	protein_coding	YES	CCDS7218.1	ENSP00000224600	RET3_HUMAN	.	UPI000012D87A	.	.	.	1/4	.	hmmpanther:PTHR11261,hmmpanther:PTHR11261:SF1,Pfam_domain:PF03572,Gene3D:3.90.226.10,SMART_domains:SM00245,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCGGGCAC	.	5	ESCA
DNA2	0	.	GRCh37	10	70190195	70190195	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2464C>A	p.Gln822Lys	p.Q822K	ENST00000399180	14/21	48	40	7	25	25	0	DNA2,missense_variant,p.Gln736Lys,ENST00000358410,;DNA2,missense_variant,p.Gln822Lys,ENST00000399180,;DNA2,missense_variant,p.Gln58Lys,ENST00000440722,;DNA2,intron_variant,,ENST00000399179,;DNA2,intron_variant,,ENST00000551118,;	T	ENSG00000138346	ENST00000399180	Transcript	missense_variant	2464	2464	822	Q/K	Caa/Aaa	.	.	.	-1	DNA2	HGNC	2939	protein_coding	YES	.	ENSP00000382133	.	J3KPX5_HUMAN	UPI00001D80EF	.	tolerated(0.35)	benign(0.041)	14/21	.	hmmpanther:PTHR10887:SF339,hmmpanther:PTHR10887,Gene3D:3.40.50.300,Pfam_domain:PF13086,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTGACTAT	.	5	ESCA
CHST3	0	.	GRCh37	10	73768109	73768109	+	Silent	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1320G>A	p.%3D	p.V440V	ENST00000373115	3/3	37	34	3	31	31	0	CHST3,synonymous_variant,p.%3D,ENST00000373115,;	A	ENSG00000122863	ENST00000373115	Transcript	synonymous_variant	1757	1320	440	V	gtG/gtA	.	.	.	1	CHST3	HGNC	1971	protein_coding	YES	CCDS7312.1	ENSP00000362207	CHST3_HUMAN	.	UPI000013CB04	.	.	.	3/3	.	Superfamily_domains:SSF52540,PIRSF_domain:PIRSF005883,Pfam_domain:PF00685,Gene3D:3.40.50.300,hmmpanther:PTHR10704:SF38,hmmpanther:PTHR10704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGTGCAGGC	.	4	ESCA
TMEM254	0	.	GRCh37	10	81841942	81841943	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234dupT	p.Ala79CysfsTer8	p.A79Cfs*8	ENST00000372281	3/4	88	72	16	63	63	0	TMEM254,frameshift_variant,p.Ala57CysfsTer8,ENST00000450179,;TMEM254,frameshift_variant,p.Ala79CysfsTer9,ENST00000372277,;TMEM254,frameshift_variant,p.Ala79CysfsTer9,ENST00000372274,;TMEM254,frameshift_variant,p.Ala79CysfsTer17,ENST00000372275,;TMEM254,frameshift_variant,p.Ala100CysfsTer8,ENST00000372273,;TMEM254,frameshift_variant,p.Ala79CysfsTer8,ENST00000372281,;TMEM254-AS1,upstream_gene_variant,,ENST00000432070,;TMEM254-AS1,upstream_gene_variant,,ENST00000448729,;TMEM254-AS1,upstream_gene_variant,,ENST00000412298,;TMEM254,non_coding_transcript_exon_variant,,ENST00000472622,;TMEM254,non_coding_transcript_exon_variant,,ENST00000476173,;TMEM254,non_coding_transcript_exon_variant,,ENST00000463209,;TMEM254,non_coding_transcript_exon_variant,,ENST00000467529,;TMEM254,non_coding_transcript_exon_variant,,ENST00000483732,;TMEM254,non_coding_transcript_exon_variant,,ENST00000463029,;	T	ENSG00000133678	ENST00000372281	Transcript	frameshift_variant	263-264	233-234	78	Y/YX	tat/taTt	.	.	.	1	TMEM254	HGNC	25804	protein_coding	YES	CCDS7363.1	ENSP00000361355	TM254_HUMAN	.	UPI0000072C96	.	.	.	3/4	.	Pfam_domain:PF14934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTGTATGCCA	.	3	ESCA
PGR	0	.	GRCh37	11	100999704	100999704	+	Missense_Mutation	SNP	G	G	A	rs779538755	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98C>T	p.Ala33Val	p.A33V	ENST00000325455	1/8	28	12	15	30	30	0	PGR,missense_variant,p.Ala33Val,ENST00000263463,;PGR,missense_variant,p.Ala33Val,ENST00000325455,;PGR,intron_variant,,ENST00000534013,;PGR,missense_variant,p.Ala33Val,ENST00000534780,;PGR,missense_variant,p.Ala33Val,ENST00000528960,;PGR,missense_variant,p.Ala33Val,ENST00000526300,;	A	ENSG00000082175	ENST00000325455	Transcript	missense_variant	1552	98	33	A/V	gCa/gTa	rs779538755	.	.	-1	PGR	HGNC	8910	protein_coding	YES	CCDS8310.1	ENSP00000325120	PRGR_HUMAN	Q6TZ07_HUMAN	UPI0000046E22	.	tolerated_low_confidence(0.05)	benign(0.028)	1/8	.	hmmpanther:PTHR24084:SF7,hmmpanther:PTHR24084,Pfam_domain:PF02161	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCTGCGGCT	.	5	ESCA
C2CD2L	0	.	GRCh37	11	118981761	118981761	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682-1G>A	.	p.X228_splice	ENST00000336702	.	16	8	8	24	24	0	C2CD2L,splice_acceptor_variant,,ENST00000336702,;C2CD2L,upstream_gene_variant,,ENST00000528586,;DPAGT1,upstream_gene_variant,,ENST00000409993,;C2CD2L,downstream_gene_variant,,ENST00000529885,;C2CD2L,downstream_gene_variant,,ENST00000529600,;C2CD2L,downstream_gene_variant,,ENST00000534024,;C2CD2L,downstream_gene_variant,,ENST00000528271,;C2CD2L,downstream_gene_variant,,ENST00000527854,;C2CD2L,splice_acceptor_variant,,ENST00000525598,;C2CD2L,splice_acceptor_variant,,ENST00000529874,;C2CD2L,upstream_gene_variant,,ENST00000533458,;	A	ENSG00000172375	ENST00000336702	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	C2CD2L	HGNC	29000	protein_coding	YES	CCDS8413.1	ENSP00000338885	C2C2L_HUMAN	.	UPI0000192105	.	.	.	.	4/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGAGAGG	.	5	ESCA
NAP1L4	0	.	GRCh37	11	2979674	2979674	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.847C>G	p.Gln283Glu	p.Q283E	ENST00000380542	10/16	77	60	17	74	74	0	NAP1L4,missense_variant,p.Gln283Glu,ENST00000380542,;NAP1L4,missense_variant,p.Gln283Glu,ENST00000526115,;NAP1L4,downstream_gene_variant,,ENST00000448187,;NAP1L4,downstream_gene_variant,,ENST00000532325,;NAP1L4,missense_variant,p.Gln139Glu,ENST00000492685,;NAP1L4,non_coding_transcript_exon_variant,,ENST00000528363,;NAP1L4,non_coding_transcript_exon_variant,,ENST00000528261,;NAP1L4,non_coding_transcript_exon_variant,,ENST00000483643,;NAP1L4,upstream_gene_variant,,ENST00000492594,;	C	ENSG00000205531	ENST00000380542	Transcript	missense_variant	988	847	283	Q/E	Caa/Gaa	.	.	.	-1	NAP1L4	HGNC	7640	protein_coding	YES	CCDS41599.1	ENSP00000369915	NP1L4_HUMAN	E9PS34_HUMAN,E9PNW0_HUMAN,E9PNJ7_HUMAN,E9PKI2_HUMAN,E9PJJ2_HUMAN,C9J6D1_HUMAN,A8MXH2_HUMAN	UPI00001303EA	.	tolerated(0.38)	benign(0.038)	10/16	.	hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF34,Pfam_domain:PF00956,Superfamily_domains:SSF143113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTGTTTCG	.	5	ESCA
ALKBH3	0	.	GRCh37	11	43918889	43918889	+	Intron	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460-4177G>A	.	.	ENST00000302708	.	36	21	15	35	35	0	ALKBH3,stop_retained_variant,p.%3D,ENST00000378840,;ALKBH3,intron_variant,,ENST00000302708,;ALKBH3,intron_variant,,ENST00000532129,;ALKBH3,intron_variant,,ENST00000529366,;ALKBH3,intron_variant,,ENST00000533200,;ALKBH3,intron_variant,,ENST00000532410,;ALKBH3,stop_retained_variant,p.%3D,ENST00000532962,;ALKBH3,stop_retained_variant,p.%3D,ENST00000530803,;ALKBH3,intron_variant,,ENST00000534171,;ALKBH3,intron_variant,,ENST00000530754,;SEC14L1P1,upstream_gene_variant,,ENST00000534767,;	A	ENSG00000166199	ENST00000302708	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ALKBH3	HGNC	30141	protein_coding	YES	CCDS7906.1	ENSP00000302232	ALKB3_HUMAN	E9PRD0_HUMAN	UPI0000039EA0	.	.	.	.	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTGAGAAT	.	5	ESCA
C11orf49	0	.	GRCh37	11	47182927	47182927	+	Intron	SNP	T	T	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822-70T>G	.	.	ENST00000378615	.	30	27	3	33	33	0	C11orf49,3_prime_UTR_variant,,ENST00000395460,;C11orf49,intron_variant,,ENST00000536126,;C11orf49,intron_variant,,ENST00000278460,;C11orf49,intron_variant,,ENST00000543718,;C11orf49,intron_variant,,ENST00000378615,;C11orf49,intron_variant,,ENST00000378618,;C11orf49,downstream_gene_variant,,ENST00000526827,;ARFGAP2,downstream_gene_variant,,ENST00000319543,;ARFGAP2,downstream_gene_variant,,ENST00000426335,;ARFGAP2,downstream_gene_variant,,ENST00000524782,;ARFGAP2,downstream_gene_variant,,ENST00000527776,;ARFGAP2,downstream_gene_variant,,ENST00000419701,;C11orf49,intron_variant,,ENST00000534581,;ARFGAP2,downstream_gene_variant,,ENST00000395449,;C11orf49,downstream_gene_variant,,ENST00000525953,;C11orf49,downstream_gene_variant,,ENST00000527234,;C11orf49,downstream_gene_variant,,ENST00000527268,;C11orf49,intron_variant,,ENST00000525895,;C11orf49,intron_variant,,ENST00000527784,;C11orf49,intron_variant,,ENST00000528488,;ARFGAP2,downstream_gene_variant,,ENST00000533243,;C11orf49,downstream_gene_variant,,ENST00000534249,;	G	ENSG00000149179	ENST00000378615	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C11orf49	HGNC	28720	protein_coding	YES	CCDS31480.1	ENSP00000367878	CK049_HUMAN	E9PI28_HUMAN	UPI0000070A8D	.	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGGTTTACC	.	2	ESCA
TRMT112	0	.	GRCh37	11	64084959	64084959	+	Missense_Mutation	SNP	G	G	A	rs200904021	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40C>T	p.Arg14Trp	p.R14W	ENST00000544844	1/4	57	37	19	67	67	0	TRMT112,missense_variant,p.Arg14Trp,ENST00000544844,;TRMT112,missense_variant,p.Arg14Trp,ENST00000308774,;TRMT112,missense_variant,p.Arg14Trp,ENST00000539854,;TRMT112,synonymous_variant,p.%3D,ENST00000535126,;TRMT112,5_prime_UTR_variant,,ENST00000535750,;PRDX5,upstream_gene_variant,,ENST00000265462,;ESRRA,downstream_gene_variant,,ENST00000545035,;ESRRA,downstream_gene_variant,,ENST00000405666,;ESRRA,downstream_gene_variant,,ENST00000000442,;PRDX5,upstream_gene_variant,,ENST00000352435,;ESRRA,downstream_gene_variant,,ENST00000406310,;PRDX5,upstream_gene_variant,,ENST00000347941,;ESRRA,downstream_gene_variant,,ENST00000539594,;TRMT112,upstream_gene_variant,,ENST00000537918,;ESRRA,downstream_gene_variant,,ENST00000467987,;	A	ENSG00000173113	ENST00000544844	Transcript	missense_variant	598	40	14	R/W	Cgg/Tgg	rs200904021	.	.	-1	TRMT112	HGNC	26940	protein_coding	YES	CCDS8068.1	ENSP00000438349	TR112_HUMAN	F5GYQ2_HUMAN	UPI00000473D9	.	deleterious(0)	benign(0.035)	1/4	.	hmmpanther:PTHR12773:SF2,hmmpanther:PTHR12773,Pfam_domain:PF03966	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCCGCACAT	byCluster|by1000G	5	ESCA
JRKL	0	.	GRCh37	11	96126297	96126297	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*909T>C	.	.	ENST00000458427	1/1	33	28	5	24	24	0	JRKL,3_prime_UTR_variant,,ENST00000458427,;JRKL,3_prime_UTR_variant,,ENST00000332349,;CCDC82,upstream_gene_variant,,ENST00000542662,;CCDC82,upstream_gene_variant,,ENST00000538597,;JRKL,intron_variant,,ENST00000546177,;CCDC82,upstream_gene_variant,,ENST00000524836,;CCDC82,upstream_gene_variant,,ENST00000525786,;	C	ENSG00000183340	ENST00000458427	Transcript	3_prime_UTR_variant	3140	.	.	.	.	.	.	.	1	JRKL	HGNC	6200	protein_coding	YES	CCDS8308.1	ENSP00000389989	JERKL_HUMAN	.	UPI0000167818	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTTTTTTT	.	5	ESCA
TAS2R13	0	.	GRCh37	12	11061567	11061567	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331A>G	p.Ile111Val	p.I111V	ENST00000390677	1/1	103	44	59	25	25	0	TAS2R13,missense_variant,p.Ile111Val,ENST00000390677,;PRR4,intron_variant,,ENST00000539853,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000536086,;PRR4,intron_variant,,ENST00000546317,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;	C	ENSG00000212128	ENST00000390677	Transcript	missense_variant	595	331	111	I/V	Ata/Gta	.	.	.	-1	TAS2R13	HGNC	14919	protein_coding	YES	CCDS8635.1	ENSP00000375095	T2R13_HUMAN	Q50KQ5_HUMAN	UPI0000038B15	.	deleterious(0)	probably_damaging(0.979)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11394:SF28,hmmpanther:PTHR11394,Pfam_domain:PF05296,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTATTTTGA	.	5	ESCA
DBX2	0	.	GRCh37	12	45410052	45410052	+	3'UTR	SNP	C	C	T	rs768260068	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*17G>A	.	.	ENST00000332700	4/4	42	33	9	18	18	0	DBX2,3_prime_UTR_variant,,ENST00000332700,;	T	ENSG00000185610	ENST00000332700	Transcript	3_prime_UTR_variant	1209	.	.	.	.	rs768260068	.	.	-1	DBX2	HGNC	33186	protein_coding	YES	CCDS31781.1	ENSP00000331470	DBX2_HUMAN	.	UPI000041A784	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACACGGAGG	byFrequency	5	ESCA
KCNA1	0	.	GRCh37	12	5024943	5024943	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2911C>T	.	.	ENST00000382545	2/2	192	89	102	52	52	0	KCNA1,3_prime_UTR_variant,,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	T	ENSG00000111262	ENST00000382545	Transcript	3_prime_UTR_variant	5506	.	.	.	.	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTCAGTAC	.	5	ESCA
DIP2B	0	.	GRCh37	12	51142213	51142213	+	3'UTR	SNP	T	T	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3591T>A	.	.	ENST00000301180	38/38	40	37	3	23	23	0	DIP2B,3_prime_UTR_variant,,ENST00000301180,;Y_RNA,downstream_gene_variant,,ENST00000363558,;DIP2B,downstream_gene_variant,,ENST00000546732,;	A	ENSG00000066084	ENST00000301180	Transcript	3_prime_UTR_variant	8356	.	.	.	.	.	.	.	1	DIP2B	HGNC	29284	protein_coding	YES	CCDS31799.1	ENSP00000301180	DIP2B_HUMAN	Q96IB4_HUMAN	UPI0000406CA1	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAGATATAAG	.	2	ESCA
PFDN5	0	.	GRCh37	12	53690038	53690038	+	Silent	SNP	A	A	G	rs769147478	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186A>G	p.%3D	p.L62L	ENST00000551018	3/6	49	26	23	34	34	0	PFDN5,synonymous_variant,p.%3D,ENST00000334478,;PFDN5,synonymous_variant,p.%3D,ENST00000551018,;PFDN5,intron_variant,,ENST00000550846,;PFDN5,intron_variant,,ENST00000351500,;PFDN5,intron_variant,,ENST00000549759,;C12orf10,upstream_gene_variant,,ENST00000549488,;ESPL1,downstream_gene_variant,,ENST00000552462,;ESPL1,downstream_gene_variant,,ENST00000257934,;C12orf10,upstream_gene_variant,,ENST00000548632,;C12orf10,upstream_gene_variant,,ENST00000267103,;RP11-680A11.5,downstream_gene_variant,,ENST00000550263,;PFDN5,non_coding_transcript_exon_variant,,ENST00000549995,;PFDN5,non_coding_transcript_exon_variant,,ENST00000547228,;PFDN5,non_coding_transcript_exon_variant,,ENST00000550069,;PFDN5,non_coding_transcript_exon_variant,,ENST00000552548,;PFDN5,non_coding_transcript_exon_variant,,ENST00000550513,;PFDN5,intron_variant,,ENST00000547130,;PFDN5,intron_variant,,ENST00000552341,;PFDN5,intron_variant,,ENST00000243040,;PFDN5,intron_variant,,ENST00000551223,;PFDN5,intron_variant,,ENST00000552742,;PFDN5,intron_variant,,ENST00000550880,;C12orf10,upstream_gene_variant,,ENST00000551670,;PFDN5,upstream_gene_variant,,ENST00000553171,;ESPL1,downstream_gene_variant,,ENST00000549154,;C12orf10,upstream_gene_variant,,ENST00000548845,;PFDN5,upstream_gene_variant,,ENST00000550964,;C12orf10,upstream_gene_variant,,ENST00000551131,;ESPL1,downstream_gene_variant,,ENST00000552671,;PFDN5,upstream_gene_variant,,ENST00000548984,;	G	ENSG00000123349	ENST00000551018	Transcript	synonymous_variant	463	186	62	L	ttA/ttG	rs769147478	.	.	1	PFDN5	HGNC	8869	protein_coding	YES	CCDS8853.1	ENSP00000447942	PFD5_HUMAN	.	UPI00000009FD	.	.	.	3/6	.	HAMAP:MF_00308,hmmpanther:PTHR12674,Pfam_domain:PF02996,Gene3D:1.10.287.370,TIGRFAM_domain:TIGR00293,Superfamily_domains:SSF46579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTACTCGT	.	5	ESCA
SHMT2	0	.	GRCh37	12	57627050	57627050	+	Silent	SNP	C	C	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.945C>A	p.%3D	p.I315I	ENST00000328923	8/12	83	67	16	64	64	0	SHMT2,synonymous_variant,p.%3D,ENST00000414700,;SHMT2,synonymous_variant,p.%3D,ENST00000557487,;SHMT2,synonymous_variant,p.%3D,ENST00000393827,;SHMT2,synonymous_variant,p.%3D,ENST00000328923,;SHMT2,synonymous_variant,p.%3D,ENST00000557529,;SHMT2,synonymous_variant,p.%3D,ENST00000449049,;SHMT2,synonymous_variant,p.%3D,ENST00000553474,;SHMT2,synonymous_variant,p.%3D,ENST00000555634,;NDUFA4L2,downstream_gene_variant,,ENST00000554503,;SHMT2,downstream_gene_variant,,ENST00000554975,;SHMT2,downstream_gene_variant,,ENST00000557427,;SHMT2,downstream_gene_variant,,ENST00000553529,;SHMT2,downstream_gene_variant,,ENST00000554310,;NDUFA4L2,downstream_gene_variant,,ENST00000556732,;SHMT2,downstream_gene_variant,,ENST00000555773,;SHMT2,downstream_gene_variant,,ENST00000556737,;SHMT2,downstream_gene_variant,,ENST00000556689,;SHMT2,downstream_gene_variant,,ENST00000557703,;NDUFA4L2,downstream_gene_variant,,ENST00000393825,;SHMT2,downstream_gene_variant,,ENST00000553949,;NDUFA4L2,downstream_gene_variant,,ENST00000556234,;SHMT2,downstream_gene_variant,,ENST00000554600,;SHMT2,downstream_gene_variant,,ENST00000554656,;SHMT2,downstream_gene_variant,,ENST00000557740,;SHMT2,3_prime_UTR_variant,,ENST00000556825,;SHMT2,3_prime_UTR_variant,,ENST00000553837,;SHMT2,3_prime_UTR_variant,,ENST00000557433,;SHMT2,3_prime_UTR_variant,,ENST00000557348,;SHMT2,3_prime_UTR_variant,,ENST00000555774,;SHMT2,3_prime_UTR_variant,,ENST00000555116,;SHMT2,non_coding_transcript_exon_variant,,ENST00000554467,;SHMT2,downstream_gene_variant,,ENST00000557302,;SHMT2,downstream_gene_variant,,ENST00000553868,;SHMT2,downstream_gene_variant,,ENST00000553950,;SHMT2,downstream_gene_variant,,ENST00000557269,;NDUFA4L2,downstream_gene_variant,,ENST00000555173,;SHMT2,upstream_gene_variant,,ENST00000556798,;SHMT2,downstream_gene_variant,,ENST00000555563,;NDUFA4L2,downstream_gene_variant,,ENST00000554688,;SHMT2,downstream_gene_variant,,ENST00000554604,;SHMT2,downstream_gene_variant,,ENST00000555213,;SHMT2,downstream_gene_variant,,ENST00000553324,;	A	ENSG00000182199	ENST00000328923	Transcript	synonymous_variant	1397	945	315	I	atC/atA	.	.	.	1	SHMT2	HGNC	10852	protein_coding	YES	CCDS8934.1	ENSP00000333667	GLYM_HUMAN	G3V5L0_HUMAN,G3V4X0_HUMAN,G3V4T0_HUMAN,G3V3Y8_HUMAN,G3V2Y4_HUMAN,G3V2W0_HUMAN,G3V241_HUMAN	UPI000000DA76	.	.	.	8/12	.	HAMAP:MF_00051,hmmpanther:PTHR11680:SF1,hmmpanther:PTHR11680,Gene3D:3.40.640.10,Pfam_domain:PF00464,PIRSF_domain:PIRSF000412,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAATCAACTT	.	5	ESCA
TAPBPL	0	.	GRCh37	12	6566732	6566732	+	Silent	SNP	C	C	T	rs758207098	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726C>T	p.%3D	p.T242T	ENST00000266556	4/7	106	84	22	49	49	0	TAPBPL,synonymous_variant,p.%3D,ENST00000266556,;TAPBPL,intron_variant,,ENST00000544021,;VAMP1,downstream_gene_variant,,ENST00000361716,;VAMP1,downstream_gene_variant,,ENST00000400911,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000539384,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000543567,;TAPBPL,intron_variant,,ENST00000545700,;TAPBPL,upstream_gene_variant,,ENST00000542160,;TAPBPL,downstream_gene_variant,,ENST00000544826,;TAPBPL,upstream_gene_variant,,ENST00000544289,;VAMP1,downstream_gene_variant,,ENST00000544432,;	T	ENSG00000139192	ENST00000266556	Transcript	synonymous_variant	891	726	242	T	acC/acT	rs758207098	.	.	1	TAPBPL	HGNC	30683	protein_coding	YES	CCDS8546.1	ENSP00000266556	TPSNR_HUMAN	.	UPI000013D6F6	.	.	.	4/7	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23411:SF3,hmmpanther:PTHR23411,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACCGCAGG	byFrequency|byCluster	5	ESCA
NANOG	0	.	GRCh37	12	7947704	7947704	+	3'UTR	SNP	C	C	T	rs769443721	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13C>T	.	.	ENST00000229307	4/4	101	85	15	49	48	0	NANOG,3_prime_UTR_variant,,ENST00000229307,;NANOG,downstream_gene_variant,,ENST00000526286,;NANOG,downstream_gene_variant,,ENST00000541267,;NANOG,downstream_gene_variant,,ENST00000526434,;	T	ENSG00000111704	ENST00000229307	Transcript	3_prime_UTR_variant	1150	.	.	.	.	rs769443721	.	.	1	NANOG	HGNC	20857	protein_coding	YES	CCDS31736.1	ENSP00000229307	NANOG_HUMAN	J7H4F6_HUMAN,F5GZI2_HUMAN	UPI000013C8F5	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TGAAACTGATA	byFrequency	2	ESCA
NANOG	0	.	GRCh37	12	7947717	7947717	+	3'UTR	SNP	A	A	G	rs750397932	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*26A>G	.	.	ENST00000229307	4/4	104	86	18	54	53	1	NANOG,3_prime_UTR_variant,,ENST00000229307,;NANOG,downstream_gene_variant,,ENST00000526286,;NANOG,downstream_gene_variant,,ENST00000541267,;NANOG,downstream_gene_variant,,ENST00000526434,;	G	ENSG00000111704	ENST00000229307	Transcript	3_prime_UTR_variant	1163	.	.	.	.	rs750397932	.	.	1	NANOG	HGNC	20857	protein_coding	YES	CCDS31736.1	ENSP00000229307	NANOG_HUMAN	J7H4F6_HUMAN,F5GZI2_HUMAN	UPI000013C8F5	.	.	.	4/4	.	.	.	G:0.0068	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACTCAATTTCA	by1000G	2	ESCA
LINC00987	0	.	GRCh37	12	9395192	9395192	+	RNA	SNP	C	C	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2016C>G	.	.	ENST00000427111	2/2	123	99	24	37	37	0	LINC00987,non_coding_transcript_exon_variant,,ENST00000427111,;RP11-118B22.4,upstream_gene_variant,,ENST00000538219,;A2MP1,intron_variant,,ENST00000566278,;PTMAP4,upstream_gene_variant,,ENST00000426188,;PTMAP4,upstream_gene_variant,,ENST00000595695,;	G	ENSG00000237248	ENST00000427111	Transcript	non_coding_transcript_exon_variant	2016	.	.	.	.	.	.	.	1	LINC00987	HGNC	48911	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAACTAAAT	.	5	ESCA
TRAV17	0	.	GRCh37	14	22466186	22466186	+	Missense_Mutation	SNP	C	C	A	rs770642421	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116C>A	p.Ala39Asp	p.A39D	ENST00000390445	2/2	30	22	8	21	21	0	TRAV17,missense_variant,p.Ala39Asp,ENST00000390445,;	A	ENSG00000211797	ENST00000390445	Transcript	missense_variant	263	116	39	A/D	gCc/gAc	rs770642421	.	.	1	TRAV17	HGNC	12113	TR_V_gene	YES	.	ENSP00000452087	.	.	UPI000011D121	.	tolerated(0.09)	possibly_damaging(0.885)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19433:SF66,hmmpanther:PTHR19433,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATGCCACCA	byFrequency	5	ESCA
NYNRIN	0	.	GRCh37	14	24880309	24880309	+	Silent	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2442C>T	p.%3D	p.C814C	ENST00000382554	5/9	35	30	5	50	50	0	NYNRIN,synonymous_variant,p.%3D,ENST00000382554,;NYNRIN,upstream_gene_variant,,ENST00000554505,;	T	ENSG00000205978	ENST00000382554	Transcript	synonymous_variant	2760	2442	814	C	tgC/tgT	.	.	.	1	NYNRIN	HGNC	20165	protein_coding	YES	CCDS45090.1	ENSP00000371994	NYNRI_HUMAN	.	UPI0000251E63	.	.	.	5/9	.	Pfam_domain:PF11977,hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTGCCGAGG	.	4	ESCA
MAX	0	.	GRCh37	14	65543336	65543336	+	Missense_Mutation	SNP	T	T	C	rs772912674	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.341A>G	p.Asn114Ser	p.N114S	ENST00000358664	5/5	51	27	24	52	52	0	MAX,missense_variant,p.Asn51Ser,ENST00000557277,;MAX,missense_variant,p.Asn41Ser,ENST00000556892,;MAX,missense_variant,p.Thr28Ala,ENST00000555932,;MAX,missense_variant,p.Asn78Ser,ENST00000555419,;MAX,missense_variant,p.Asn105Ser,ENST00000358402,;MAX,missense_variant,p.Asn114Ser,ENST00000358664,;MAX,3_prime_UTR_variant,,ENST00000284165,;MAX,intron_variant,,ENST00000341653,;MAX,downstream_gene_variant,,ENST00000556979,;MAX,downstream_gene_variant,,ENST00000556443,;MAX,downstream_gene_variant,,ENST00000557746,;MAX,downstream_gene_variant,,ENST00000555667,;MAX,3_prime_UTR_variant,,ENST00000394606,;MAX,3_prime_UTR_variant,,ENST00000553928,;MAX,downstream_gene_variant,,ENST00000553951,;	C	ENSG00000125952	ENST00000358664	Transcript	missense_variant	472	341	114	N/S	aAc/aGc	rs772912674	.	.	-1	MAX	HGNC	6913	protein_coding	YES	CCDS9771.1	ENSP00000351490	MAX_HUMAN	G3V570_HUMAN	UPI0000000C63	.	tolerated(0.34)	benign(0.001)	5/5	.	hmmpanther:PTHR10328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTAGTTGGTC	byFrequency	5	ESCA
ZFP36L1	0	.	GRCh37	14	69255290	69255296	+	3'UTR	DEL	ATTAACT	ATTAACT	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	ATTAACT	ATTAACT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*954_*960delAGTTAATinsG	.	.	ENST00000439696	2/2	28	22	6	41	41	0	ZFP36L1,3_prime_UTR_variant,,ENST00000439696,;ZFP36L1,3_prime_UTR_variant,,ENST00000555997,;ZFP36L1,downstream_gene_variant,,ENST00000557022,;ZFP36L1,downstream_gene_variant,,ENST00000336440,;ZFP36L1,downstream_gene_variant,,ENST00000553375,;ZFP36L1,downstream_gene_variant,,ENST00000557086,;	C	ENSG00000185650	ENST00000439696	Transcript	3_prime_UTR_variant	2273-2279	.	.	.	.	.	.	.	-1	ZFP36L1	HGNC	1107	protein_coding	YES	CCDS9791.1	ENSP00000388402	TISB_HUMAN	G3V2D5_HUMAN,B4E1N3_HUMAN,B4DG15_HUMAN	UPI0000136FBC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	AATACCATTAACTGCTCA	.	2	ESCA
RYR3	0	.	GRCh37	15	34014941	34014941	+	Silent	SNP	C	C	T	rs772207338	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6645C>T	p.%3D	p.S2215S	ENST00000389232	44/104	48	37	11	25	24	0	RYR3,synonymous_variant,p.%3D,ENST00000389232,;RYR3,synonymous_variant,p.%3D,ENST00000415757,;Y_RNA,downstream_gene_variant,,ENST00000363138,;	T	ENSG00000198838	ENST00000389232	Transcript	synonymous_variant	6715	6645	2215	S	agC/agT	rs772207338	.	.	1	RYR3	HGNC	10485	protein_coding	YES	CCDS45210.1	ENSP00000373884	RYR3_HUMAN	.	UPI0000E5B01A	.	.	.	44/104	.	Low_complexity_(Seg):seg,Pfam_domain:PF01365,hmmpanther:PTHR13715:SF16,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCCAGCGTTGT	.	4	ESCA
HERC1	0	.	GRCh37	15	64005610	64005610	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4405G>A	p.Glu1469Lys	p.E1469K	ENST00000443617	23/78	43	30	13	22	22	0	HERC1,missense_variant,p.Glu1469Lys,ENST00000443617,;HERC1,missense_variant,p.Glu453Lys,ENST00000561400,;RP11-317G6.1,intron_variant,,ENST00000559303,;	T	ENSG00000103657	ENST00000443617	Transcript	missense_variant	4493	4405	1469	E/K	Gaa/Aaa	.	.	.	-1	HERC1	HGNC	4867	protein_coding	YES	CCDS45277.1	ENSP00000390158	HERC1_HUMAN	H0YL74_HUMAN,H0YL07_HUMAN,H0YKW7_HUMAN	UPI0000212760	.	.	benign(0.008)	23/78	.	hmmpanther:PTHR22870:SF156,hmmpanther:PTHR22870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCTTCTC	.	5	ESCA
RASGRF1	0	.	GRCh37	15	79310155	79310155	+	Nonsense_Mutation	SNP	G	G	T	rs141668129	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1700C>A	p.Ser567Ter	p.S567*	ENST00000419573	12/28	71	41	30	50	50	0	RASGRF1,stop_gained,p.Ser567Ter,ENST00000558480,;RASGRF1,stop_gained,p.Ser567Ter,ENST00000419573,;RASGRF1,non_coding_transcript_exon_variant,,ENST00000560334,;	T	ENSG00000058335	ENST00000419573	Transcript	stop_gained	1975	1700	567	S/*	tCg/tAg	rs141668129	.	.	-1	RASGRF1	HGNC	9875	protein_coding	YES	CCDS10309.1	ENSP00000405963	.	J3KQP9_HUMAN	UPI000013D1F1	.	.	.	12/28	.	PROSITE_profiles:PS50003,hmmpanther:PTHR23113:SF193,hmmpanther:PTHR23113,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACGAGGCC	byCluster	5	ESCA
ANKRD34C	0	.	GRCh37	15	79590060	79590060	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2826C>T	.	.	ENST00000421388	2/2	53	32	20	29	29	0	ANKRD34C,3_prime_UTR_variant,,ENST00000421388,;ANKRD34C,downstream_gene_variant,,ENST00000558647,;	T	ENSG00000235711	ENST00000421388	Transcript	3_prime_UTR_variant	4903	.	.	.	.	.	.	.	1	ANKRD34C	HGNC	33888	protein_coding	YES	CCDS53965.1	ENSP00000401089	AN34C_HUMAN	.	UPI0000160A7F	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATACGCAAT	.	5	ESCA
NR2F2	0	.	GRCh37	15	96877712	96877712	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.850C>T	p.Arg284Trp	p.R284W	ENST00000394166	2/3	46	41	5	43	43	0	NR2F2,missense_variant,p.Arg131Trp,ENST00000453270,;NR2F2,missense_variant,p.Arg284Trp,ENST00000394166,;NR2F2,missense_variant,p.Arg151Trp,ENST00000421109,;NR2F2,missense_variant,p.Arg131Trp,ENST00000394171,;NR2F2,downstream_gene_variant,,ENST00000559679,;MIR1469,downstream_gene_variant,,ENST00000410719,;	T	ENSG00000185551	ENST00000394166	Transcript	missense_variant	2239	850	284	R/W	Cgg/Tgg	.	.	.	1	NR2F2	HGNC	7976	protein_coding	YES	CCDS10375.1	ENSP00000377721	COT2_HUMAN	H3BTC2_HUMAN,F1D8R0_HUMAN	UPI000000052E	.	deleterious(0)	probably_damaging(0.967)	2/3	.	hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF45,Pfam_domain:PF00104,Gene3D:1.10.565.10,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR01282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CCGACCGGGTG	.	3	ESCA
NUBP1	0	.	GRCh37	16	10855708	10855708	+	Missense_Mutation	SNP	C	C	T	rs372446215	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.812C>T	p.Pro271Leu	p.P271L	ENST00000283027	9/11	50	29	20	42	42	0	NUBP1,missense_variant,p.Pro271Leu,ENST00000283027,;NUBP1,missense_variant,p.Pro260Leu,ENST00000433392,;NUBP1,missense_variant,p.Pro121Leu,ENST00000571175,;NUBP1,intron_variant,,ENST00000574691,;TVP23A,downstream_gene_variant,,ENST00000299866,;NUBP1,downstream_gene_variant,,ENST00000574334,;TVP23A,downstream_gene_variant,,ENST00000572102,;TVP23A,downstream_gene_variant,,ENST00000572428,;NUBP1,non_coding_transcript_exon_variant,,ENST00000571790,;TVP23A,intron_variant,,ENST00000573857,;TVP23A,intron_variant,,ENST00000572980,;NUBP1,upstream_gene_variant,,ENST00000573663,;NUBP1,non_coding_transcript_exon_variant,,ENST00000574137,;TVP23A,intron_variant,,ENST00000575135,;TVP23A,intron_variant,,ENST00000456096,;TVP23A,downstream_gene_variant,,ENST00000573360,;	T	ENSG00000103274	ENST00000283027	Transcript	missense_variant	831	812	271	P/L	cCg/cTg	rs372446215	.	.	1	NUBP1	HGNC	8041	protein_coding	YES	CCDS10543.1	ENSP00000283027	NUBP1_HUMAN	.	UPI000013DD15	.	deleterious(0.01)	probably_damaging(1)	9/11	.	HAMAP:MF_03038,hmmpanther:PTHR23264:SF19,hmmpanther:PTHR23264,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	T:0.0006	T:0	T:0	.	T:0	T:0	T:0.0031	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATCCGCTCA	byFrequency|byCluster|by1000G	5	ESCA
TMC5	0	.	GRCh37	16	19485599	19485599	+	Splice_Site	SNP	G	G	A	rs760953105	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2090+1G>A	.	p.X697_splice	ENST00000396229	.	80	74	6	54	54	0	TMC5,splice_donor_variant,,ENST00000219821,;TMC5,splice_donor_variant,,ENST00000381414,;TMC5,splice_donor_variant,,ENST00000561503,;TMC5,splice_donor_variant,,ENST00000541464,;TMC5,splice_donor_variant,,ENST00000396229,;TMC5,splice_donor_variant,,ENST00000564959,;TMC5,splice_donor_variant,,ENST00000542583,;CTA-363E6.6,downstream_gene_variant,,ENST00000561762,;TMC5,splice_donor_variant,,ENST00000567478,;TMC5,splice_donor_variant,,ENST00000572147,;	A	ENSG00000103534	ENST00000396229	Transcript	splice_donor_variant	.	.	.	.	.	rs760953105	.	.	1	TMC5	HGNC	22999	protein_coding	YES	CCDS45431.1	ENSP00000379531	TMC5_HUMAN	.	UPI00001FEF87	.	.	.	.	12/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCGGTAGGT	.	2	ESCA
ZNF720	0	.	GRCh37	16	31724621	31724621	+	5'UTR	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-133G>T	.	.	ENST00000316491	1/5	28	24	4	14	14	0	ZNF720,5_prime_UTR_variant,,ENST00000539915,;ZNF720,5_prime_UTR_variant,,ENST00000398696,;ZNF720,5_prime_UTR_variant,,ENST00000534369,;ZNF720,5_prime_UTR_variant,,ENST00000316491,;ZNF720,5_prime_UTR_variant,,ENST00000399681,;ZNF720,upstream_gene_variant,,ENST00000529515,;ZNF720,upstream_gene_variant,,ENST00000530881,;CTD-2358C21.4,upstream_gene_variant,,ENST00000569175,;ZNF720,non_coding_transcript_exon_variant,,ENST00000542684,;ZNF720,non_coding_transcript_exon_variant,,ENST00000544044,;ZNF720,non_coding_transcript_exon_variant,,ENST00000533488,;ZNF720,non_coding_transcript_exon_variant,,ENST00000531864,;CLUHP3,downstream_gene_variant,,ENST00000562354,;ZNF720,5_prime_UTR_variant,,ENST00000534277,;ZNF720,5_prime_UTR_variant,,ENST00000529943,;ZNF720,5_prime_UTR_variant,,ENST00000398707,;CLUHP3,downstream_gene_variant,,ENST00000563678,;	T	ENSG00000197302	ENST00000316491	Transcript	5_prime_UTR_variant	67	.	.	.	.	.	.	.	1	ZNF720	HGNC	26987	protein_coding	YES	CCDS45473.1	ENSP00000319222	ZN720_HUMAN	.	UPI000003603E	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGGGCTCCC	.	2	ESCA
LRRC29	0	.	GRCh37	16	67244286	67244286	+	5'UTR	SNP	C	C	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-195G>T	.	.	ENST00000409037	1/5	13	8	5	13	13	0	LRRC29,5_prime_UTR_variant,,ENST00000409037,;AC040160.1,3_prime_UTR_variant,,ENST00000454102,;LRRC29,intron_variant,,ENST00000393992,;LRRC29,intron_variant,,ENST00000409509,;LRRC29,intron_variant,,ENST00000447579,;LRRC29,intron_variant,,ENST00000424285,;LRRC29,intron_variant,,ENST00000433915,;LRRC29,intron_variant,,ENST00000341546,;LRRC29,non_coding_transcript_exon_variant,,ENST00000462169,;LRRC29,downstream_gene_variant,,ENST00000485549,;	A	ENSG00000125122	ENST00000409037	Transcript	5_prime_UTR_variant	703	.	.	.	.	.	.	.	-1	LRRC29	HGNC	13605	protein_coding	YES	CCDS32465.1	ENSP00000387318	LRC29_HUMAN	C9JSY0_HUMAN	UPI0000049C46	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCAGCTCCTG	.	3	ESCA
ADAMTS18	0	.	GRCh37	16	77323161	77323161	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3550G>T	p.Glu1184Ter	p.E1184*	ENST00000282849	22/23	38	28	10	50	50	0	ADAMTS18,stop_gained,p.Glu1184Ter,ENST00000282849,;ADAMTS18,missense_variant,p.Asp33Tyr,ENST00000562332,;RP11-538I12.3,intron_variant,,ENST00000561672,;	A	ENSG00000140873	ENST00000282849	Transcript	stop_gained	3969	3550	1184	E/*	Gag/Tag	.	.	.	-1	ADAMTS18	HGNC	17110	protein_coding	YES	CCDS10926.1	ENSP00000282849	ATS18_HUMAN	.	UPI0000233610	.	.	.	22/23	.	PROSITE_profiles:PS50900,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF167	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTACCTCTCT	.	3	ESCA
FOXF1	0	.	GRCh37	16	86546701	86546701	+	3'UTR	SNP	C	C	T	rs779788319	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10C>T	.	.	ENST00000262426	2/2	61	44	17	51	51	0	FOXF1,3_prime_UTR_variant,,ENST00000262426,;FENDRR,upstream_gene_variant,,ENST00000599749,;FENDRR,upstream_gene_variant,,ENST00000593604,;FENDRR,upstream_gene_variant,,ENST00000597578,;FENDRR,upstream_gene_variant,,ENST00000595886,;	T	ENSG00000103241	ENST00000262426	Transcript	3_prime_UTR_variant	1193	.	.	.	.	rs779788319	.	.	1	FOXF1	HGNC	3809	protein_coding	YES	CCDS10957.2	ENSP00000262426	FOXF1_HUMAN	.	UPI000059D3CC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCCGCAGG	.	5	ESCA
TBC1D27	0	.	GRCh37	17	16827248	16827248	+	RNA	SNP	G	G	A	rs773972419	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3819C>T	.	.	ENST00000261651	14/14	42	37	5	30	30	0	TBC1D27,non_coding_transcript_exon_variant,,ENST00000261651,;TBC1D27,downstream_gene_variant,,ENST00000424239,;	A	ENSG00000128438	ENST00000261651	Transcript	non_coding_transcript_exon_variant	3819	.	.	.	.	rs773972419	.	.	-1	TBC1D27	HGNC	28104	processed_transcript	YES	.	.	.	.	.	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCCGTCGTG	.	4	ESCA
SLC47A1	0	.	GRCh37	17	19480714	19480714	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1561A>T	p.Met521Leu	p.M521L	ENST00000270570	17/17	38	18	19	36	36	0	SLC47A1,missense_variant,p.Met267Leu,ENST00000571335,;SLC47A1,missense_variant,p.Met48Leu,ENST00000581558,;SLC47A1,missense_variant,p.Met521Leu,ENST00000270570,;SLC47A1,missense_variant,p.Met521Leu,ENST00000457293,;SLC47A1,missense_variant,p.Met219Leu,ENST00000575023,;SLC47A1,missense_variant,p.Met521Leu,ENST00000395585,;SLC47A1,3_prime_UTR_variant,,ENST00000436810,;RP11-1113L8.1,intron_variant,,ENST00000574267,;AC025627.7,upstream_gene_variant,,ENST00000454535,;AC025627.7,upstream_gene_variant,,ENST00000420951,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000575377,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000495425,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000573009,;SLC47A1,non_coding_transcript_exon_variant,,ENST00000497548,;RP11-1113L8.2,downstream_gene_variant,,ENST00000576220,;	T	ENSG00000142494	ENST00000270570	Transcript	missense_variant	1647	1561	521	M/L	Atg/Ttg	.	.	.	1	SLC47A1	HGNC	25588	protein_coding	YES	CCDS11209.1	ENSP00000270570	S47A1_HUMAN	B4E3B2_HUMAN,B4DPA7_HUMAN	UPI0000071042	.	tolerated(0.76)	benign(0.001)	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGATGCGC	.	5	ESCA
KRT15	0	.	GRCh37	17	39671605	39671605	+	Intron	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1247+119C>T	.	.	ENST00000254043	.	13	10	3	11	11	0	KRT15,3_prime_UTR_variant,,ENST00000393981,;KRT15,intron_variant,,ENST00000393976,;KRT15,intron_variant,,ENST00000254043,;KRT15,intron_variant,,ENST00000393974,;KRT15,downstream_gene_variant,,ENST00000458290,;KRT15,non_coding_transcript_exon_variant,,ENST00000474031,;KRT15,downstream_gene_variant,,ENST00000470004,;KRT15,downstream_gene_variant,,ENST00000497016,;KRT15,upstream_gene_variant,,ENST00000586794,;KRT15,downstream_gene_variant,,ENST00000463447,;	A	ENSG00000171346	ENST00000254043	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KRT15	HGNC	6421	protein_coding	YES	CCDS11398.1	ENSP00000254043	K1C15_HUMAN	.	UPI000013CE0E	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCAGTTCTC	.	2	ESCA
GH1	0	.	GRCh37	17	61995831	61995831	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.46C>T	p.Leu16Phe	p.L16F	ENST00000323322	2/5	59	53	5	37	37	0	GH1,missense_variant,p.Leu16Phe,ENST00000342364,;GH1,missense_variant,p.Leu16Phe,ENST00000323322,;GH1,missense_variant,p.Leu16Phe,ENST00000458650,;GH1,missense_variant,p.Leu16Phe,ENST00000351388,;CSHL1,intron_variant,,ENST00000392824,;GH1,non_coding_transcript_exon_variant,,ENST00000579711,;	A	ENSG00000259384	ENST00000323322	Transcript	missense_variant	89	46	16	L/F	Ctc/Ttc	.	.	.	-1	GH1	HGNC	4261	protein_coding	YES	CCDS11653.1	ENSP00000312673	SOMA_HUMAN	B1A4G6_HUMAN	UPI000002B7EE	.	deleterious(0)	probably_damaging(1)	2/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11417:SF38,hmmpanther:PTHR11417,Pfam_domain:PF00103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGAGCAGGC	.	4	ESCA
KCNJ2	0	.	GRCh37	17	68171465	68171465	+	Silent	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285A>G	p.%3D	p.S95S	ENST00000243457	2/2	226	142	84	168	167	1	KCNJ2,synonymous_variant,p.%3D,ENST00000535240,;KCNJ2,synonymous_variant,p.%3D,ENST00000243457,;	G	ENSG00000123700	ENST00000243457	Transcript	synonymous_variant	668	285	95	S	tcA/tcG	.	.	.	1	KCNJ2	HGNC	6263	protein_coding	YES	CCDS11688.1	ENSP00000243457	IRK2_HUMAN	.	UPI000004F21A	.	.	.	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11767:SF43,hmmpanther:PTHR11767,Pfam_domain:PF01007,Gene3D:1.10.287.70,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81324,Prints_domain:PR01320	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCATGGCT	.	5	ESCA
GPR142	0	.	GRCh37	17	72367895	72367895	+	Missense_Mutation	SNP	C	C	T	rs552309071	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.545C>T	p.Ala182Val	p.A182V	ENST00000335666	4/4	38	30	7	27	27	0	GPR142,missense_variant,p.Ala182Val,ENST00000335666,;GPR142,3_prime_UTR_variant,,ENST00000585308,;GPR142,3_prime_UTR_variant,,ENST00000582579,;	T	ENSG00000257008	ENST00000335666	Transcript	missense_variant	593	545	182	A/V	gCg/gTg	rs552309071,COSM984030	.	.	1	GPR142	HGNC	20088	protein_coding	YES	CCDS11698.1	ENSP00000335158	GP142_HUMAN	.	UPI00001AA7F1	.	tolerated(0.06)	benign(0.342)	4/4	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22751,hmmpanther:PTHR22751:SF48,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGCGCGCC	byCluster|by1000G	5	ESCA
TP53	0	.	GRCh37	17	7577530	7577536	+	Frame_Shift_Del	DEL	TGGGCCT	TGGGCCT	AGGGAA	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	TGGGCCT	TGGGCCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.745_751delAGGCCCAinsTTCCCT	p.Arg249PhefsTer96	p.R249Ffs*96	ENST00000269305	7/11	181	98	83	247	247	0	TP53,frameshift_variant,p.Arg249PhefsTer20,ENST00000413465,;TP53,frameshift_variant,p.Arg249PhefsTer102,ENST00000420246,;TP53,frameshift_variant,p.Arg249PhefsTer96,ENST00000269305,;TP53,frameshift_variant,p.Arg117PhefsTer?,ENST00000509690,;TP53,frameshift_variant,p.Arg249PhefsTer103,ENST00000359597,;TP53,frameshift_variant,p.Arg249PhefsTer96,ENST00000445888,;TP53,frameshift_variant,p.Arg249PhefsTer94,ENST00000455263,;TP53,incomplete_terminal_codon_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	AGGGAA	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	935-941	745-751	249-251	RPI/FPX	AGGCCCAtc/TTCCCTtc	TP53_g.13382_13388del	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.L252_I254delLTI|c.754_762delCTCACCATC|4,CODON|p.L252_I254delLTI|c.751_759delATCCTCACC|4,CODON|p.L252delL|c.754_756delCTC|4,CODON|p.L252delL|c.754_756delCTC|9,CODON|p.L252delL|c.754_756delCTC|4,CODON|p.L252fs*93|c.754delC|5,CODON|p.L252F|c.754C>T|10,CODON|p.I251I|c.753C>A|3,CODON|p.I251N|c.752T>A|9,CODON|p.I251T|c.752T>C|6,CODON|p.I251T|c.752T>C|3,CODON|p.I251S|c.752T>G|12,CODON|p.I251T|c.752T>C|3,CODON|p.I251fs*94|c.751delA|6,CODON|p.I251L|c.751A>C|3,CODON|p.I251F|c.751A>T|8,CODON|p.P250P|c.750C>T|4,CODON|p.P250F|c.748_749CC>TT|3,CODON|p.I251fs*94|c.748delC|4,CODON|p.P250L|c.749C>T|49,CODON|p.P250L|c.749C>T|11,CODON|p.P250L|c.749C>T|8,CODON|p.P250L|c.749C>T|6,CODON|p.P250L|c.749C>T|11,CODON|p.P250S|c.748C>T|12,CODON|p.R249fs*96|c.746delG|4,CODON|p.R249S|c.747G>T|31,CODON|p.R249S|c.747G>C|22,CODON|p.R249S|c.747G>C|3,CODON|p.R249S|c.747G>T|15,CODON|p.R249R|c.747G>A|6,CODON|p.R249S|c.747G>C|3,CODON|p.R249S|c.747G>T|314,CODON|p.R249S|c.747G>T|30,BUFFER|p.I255delI|c.763_765delATC|8,BUFFER|p.I255delI|c.760_762delATC|3,BUFFER|p.I255fs*90|c.762delC|3,BUFFER|p.I255fs*9|c.762_763insN|3,BUFFER|p.I255V|c.763A>G|3,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|25,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254S|c.761T>G|9,BUFFER|p.I254N|c.761T>A|4,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254T|c.761T>C|3,BUFFER|p.I254F|c.760A>T|7,BUFFER|p.I254V|c.760A>G|6,BUFFER|p.I254fs*10|c.759_760insN|4,BUFFER|p.T253I|c.758C>T|4,BUFFER|p.T253N|c.758C>A|3,BUFFER|p.T253P|c.757A>C|3,BUFFER|p.T253S|c.757A>T|5,BUFFER|p.T253A|c.757A>G|3,BUFFER|p.L252P|c.755T>C|10,BUFFER|p.L252P|c.755T>C|3,BUFFER|p.L252P|c.755T>C|3,BUFFER|p.R249T|c.746G>C|3,BUFFER|p.R249M|c.746G>T|8,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249K|c.746G>A|17,BUFFER|p.R249M|c.746G>T|4,BUFFER|p.R249T|c.746G>C|20,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249M|c.746G>T|35,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R248Q|c.743_744GG>AA|5,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248R|c.744G>A|5,BUFFER|p.R248W|c.741_742CC>TT|15,BUFFER|p.R248Q|c.743G>A|113,BUFFER|p.R248Q|c.743G>A|633,BUFFER|p.R248L|c.743G>T|7,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|64,BUFFER|p.R155L|c.464G>T|12,BUFFER|p.R155P|c.464G>C|5,BUFFER|p.R248P|c.743G>C|17,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|42,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248L|c.743G>T|74,BUFFER|p.R155Q|c.464G>A|114,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248Q|c.743G>A|110,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87,BUFFER|p.N247N|c.741C>T|10,BUFFER|p.N247I|c.740A>T|7,BUFFER|p.N154I|c.461A>T|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247T|c.740A>C|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247S|c.740A>G|7,BUFFER|p.N247D|c.739A>G|5,BUFFER|p.N247Y|c.739A>T|3,BUFFER|p.M153I|c.459G>C|3,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>A|21,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>C|4,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246R|c.737T>G|12,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246T|c.737T>C|8,BUFFER|p.M153R|c.458T>G|3,BUFFER|p.M246K|c.737T>A|7,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246L|c.736A>T|3,BUFFER|p.M153V|c.457A>G|7,BUFFER|p.M246V|c.736A>G|3,BUFFER|p.M246V|c.736A>G|35,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246V|c.736A>G|4,BUFFER|p.G245G|c.735C>T|5,BUFFER|p.G245D|c.734G>A|10,BUFFER|p.G245V|c.734G>T|3,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245A|c.734G>C|8,BUFFER|p.G152D|c.455G>A|23,BUFFER|p.G152V|c.455G>T|15,BUFFER|p.G245V|c.734G>T|10,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245D|c.734G>A|119,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245D|c.734G>A|7,BUFFER|p.G245V|c.734G>T|69,BUFFER|p.G245V|c.734G>T|15	INDELOCATOR*|RADIA*|PINDEL	TGAGGATGGGCCTCCGGT	.	3	ESCA
ANKRD20A5P	0	.	GRCh37	18	14184125	14184125	+	Intron	SNP	C	C	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.492+24C>A	.	.	ENST00000431648	.	109	92	17	107	106	0	ANKRD20A5P,non_coding_transcript_exon_variant,,ENST00000581935,;ANKRD20A5P,intron_variant,,ENST00000581363,;ANKRD20A5P,intron_variant,,ENST00000581181,;ANKRD20A5P,non_coding_transcript_exon_variant,,ENST00000399814,;ANKRD20A5P,intron_variant,,ENST00000431648,;	A	ENSG00000186481	ENST00000431648	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ANKRD20A5P	HGNC	33833	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	3/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTTCCAAAA	.	4	ESCA
NOTCH3	0	.	GRCh37	19	15300089	15300089	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1187C>A	p.Ser396Tyr	p.S396Y	ENST00000263388	7/33	93	46	47	52	52	0	NOTCH3,missense_variant,p.Ser396Tyr,ENST00000263388,;NOTCH3,missense_variant,p.Ser395Tyr,ENST00000601011,;	T	ENSG00000074181	ENST00000263388	Transcript	missense_variant	1263	1187	396	S/Y	tCt/tAt	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	deleterious(0)	probably_damaging(1)	7/33	.	Superfamily_domains:SSF57184,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Pfam_domain:PF07645,Gene3D:2.10.25.10,PROSITE_patterns:PS01187,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGATAGAGCAC	.	5	ESCA
NOTCH3	0	.	GRCh37	19	15300181	15300181	+	Silent	SNP	G	G	A	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1095C>T	p.%3D	p.I365I	ENST00000263388	7/33	63	30	33	35	35	0	NOTCH3,synonymous_variant,p.%3D,ENST00000263388,;NOTCH3,synonymous_variant,p.%3D,ENST00000601011,;	A	ENSG00000074181	ENST00000263388	Transcript	synonymous_variant	1171	1095	365	I	atC/atT	COSM3712733,COSM3712734	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	.	.	7/33	.	Superfamily_domains:SSF57196,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,Gene3D:2.10.25.10,Pfam_domain:PF00008,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TCACAGATAGC	.	3	ESCA
NOTCH3	0	.	GRCh37	19	15300208	15300208	+	Silent	SNP	G	G	A	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1068C>T	p.%3D	p.V356V	ENST00000263388	7/33	52	26	26	21	21	0	NOTCH3,synonymous_variant,p.%3D,ENST00000263388,;NOTCH3,synonymous_variant,p.%3D,ENST00000601011,;	A	ENSG00000074181	ENST00000263388	Transcript	synonymous_variant	1144	1068	356	V	gtC/gtT	COSM4074952,COSM4074953	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	.	.	7/33	.	Superfamily_domains:SSF57196,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,Gene3D:2.10.25.10,Pfam_domain:PF00008,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TTGCTGACACA	.	3	ESCA
NOTCH3	0	.	GRCh37	19	15303192	15303192	+	Silent	SNP	G	G	A	rs745929332	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.336C>T	p.%3D	p.F112F	ENST00000263388	3/33	143	61	81	77	77	0	NOTCH3,synonymous_variant,p.%3D,ENST00000263388,;NOTCH3,synonymous_variant,p.%3D,ENST00000601011,;	A	ENSG00000074181	ENST00000263388	Transcript	synonymous_variant	412	336	112	F	ttC/ttT	rs745929332	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	.	.	3/33	.	Superfamily_domains:SSF57196,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,Gene3D:2.10.25.10,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCGGAAGCC	.	5	ESCA
NWD1	0	.	GRCh37	19	16918782	16918782	+	Silent	SNP	C	C	T	rs781251160	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4122C>T	p.%3D	p.Y1374Y	ENST00000524140	18/19	44	37	7	42	42	0	NWD1,synonymous_variant,p.%3D,ENST00000339803,;NWD1,synonymous_variant,p.%3D,ENST00000524140,;NWD1,synonymous_variant,p.%3D,ENST00000552788,;NWD1,synonymous_variant,p.%3D,ENST00000379808,;NWD1,synonymous_variant,p.%3D,ENST00000549814,;NWD1,synonymous_variant,p.%3D,ENST00000523826,;NWD1,3_prime_UTR_variant,,ENST00000438489,;NWD1,3_prime_UTR_variant,,ENST00000518676,;	T	ENSG00000188039	ENST00000524140	Transcript	synonymous_variant	4540	4122	1374	Y	taC/taT	rs781251160	.	.	1	NWD1	HGNC	27619	protein_coding	YES	CCDS32945.2	ENSP00000428579	NWD1_HUMAN	.	UPI0000D6173E	.	.	.	18/19	.	Superfamily_domains:SSF50978,Gene3D:2.130.10.10,hmmpanther:PTHR22847:SF273,hmmpanther:PTHR22847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTACGAGTG	byFrequency	5	ESCA
SELV	0	.	GRCh37	19	40006041	40006041	+	Silent	SNP	T	T	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189T>C	p.%3D	p.T63T	ENST00000335426	1/6	39	33	6	35	35	0	SELV,synonymous_variant,p.%3D,ENST00000423711,;SELV,synonymous_variant,p.%3D,ENST00000335426,;SELV,upstream_gene_variant,,ENST00000600586,;SELV,upstream_gene_variant,,ENST00000597876,;	C	ENSG00000186838	ENST00000335426	Transcript	synonymous_variant	289	189	63	T	acT/acC	.	.	.	1	SELV	Uniprot_gn	.	protein_coding	YES	CCDS54266.1	ENSP00000333956	SELV_HUMAN	.	UPI00001B2974	.	.	.	1/6	.	hmmpanther:PTHR15124:SF17,hmmpanther:PTHR15124,Prints_domain:PR01217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGACTCCTGC	.	4	ESCA
CEACAM6	0	.	GRCh37	19	42259490	42259490	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-57C>T	.	.	ENST00000199764	1/6	62	54	8	27	27	0	CEACAM6,5_prime_UTR_variant,,ENST00000595740,;CEACAM6,5_prime_UTR_variant,,ENST00000199764,;CEA,intron_variant,,ENST00000598976,;CEA,intron_variant,,ENST00000435837,;AC011513.4,downstream_gene_variant,,ENST00000601409,;	T	ENSG00000086548	ENST00000199764	Transcript	5_prime_UTR_variant	162	.	.	.	.	.	.	.	1	CEACAM6	HGNC	1818	protein_coding	YES	CCDS12585.1	ENSP00000199764	CEAM6_HUMAN	Q13985_HUMAN,M0QYD3_HUMAN	UPI000006DF42	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAGCATTCC	.	4	ESCA
CEACAM20	0	.	GRCh37	19	45015728	45015728	+	Intron	SNP	C	C	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1858G>T	.	.	ENST00000454753	10/12	45	39	6	35	35	0	CEACAM20,splice_region_variant,,ENST00000445209,;CEACAM20,splice_region_variant,,ENST00000431738,;CEACAM20,splice_region_variant,,ENST00000448350,;CEACAM20,splice_region_variant,,ENST00000316962,;CEACAM20,splice_region_variant,,ENST00000424903,;CEACAM20,splice_region_variant,,ENST00000454753,;CEACAM20,intron_variant,,ENST00000414638,;CEACAM20,intron_variant,,ENST00000412211,;CEACAM20,intron_variant,,ENST00000421432,;	A	ENSG00000176395	ENST00000454753	Transcript	splice_region_variant	1858	.	.	.	.	.	.	.	-1	CEACAM20	HGNC	24879	processed_transcript	YES	.	.	.	.	.	.	.	.	10/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTTGCATCTG	.	4	ESCA
AKT1S1	0	.	GRCh37	19	50376254	50376263	+	Frame_Shift_Del	DEL	CTGGCCAGGG	CTGGCCAGGG	-	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	CTGGCCAGGG	CTGGCCAGGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.350_359delCCCTGGCCAG	p.Thr117LysfsTer31	p.T117Kfs*31	ENST00000391835	2/5	64	34	30	56	56	0	AKT1S1,frameshift_variant,p.Thr117LysfsTer31,ENST00000391835,;AKT1S1,frameshift_variant,p.Thr97LysfsTer31,ENST00000391832,;AKT1S1,frameshift_variant,p.Thr97LysfsTer31,ENST00000344175,;AKT1S1,frameshift_variant,p.Thr97LysfsTer31,ENST00000391833,;AKT1S1,frameshift_variant,p.Thr97LysfsTer31,ENST00000391831,;AKT1S1,frameshift_variant,p.Thr97LysfsTer?,ENST00000391830,;AKT1S1,frameshift_variant,p.Thr97LysfsTer31,ENST00000391834,;TBC1D17,upstream_gene_variant,,ENST00000535102,;AKT1S1,downstream_gene_variant,,ENST00000599525,;TBC1D17,upstream_gene_variant,,ENST00000221543,;AKT1S1,downstream_gene_variant,,ENST00000482622,;TBC1D17,upstream_gene_variant,,ENST00000594996,;	-	ENSG00000204673	ENST00000391835	Transcript	frameshift_variant	1723-1732	350-359	117-120	TLAR/X	aCCCTGGCCAGa/aa	.	.	.	-1	AKT1S1	HGNC	28426	protein_coding	YES	CCDS59410.1	ENSP00000375711	AKTS1_HUMAN	M0R2V8_HUMAN,H9KV91_HUMAN	UPI00004A2415	.	.	.	2/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21844:SF1,hmmpanther:PTHR21844	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCTCTCTGGCCAGGGTAGGC	.	3	ESCA
MIR523	0	.	GRCh37	19	54201690	54201690	+	RNA	SNP	A	A	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.52A>C	.	.	ENST00000385281	1/1	91	77	13	62	62	0	MIR523,non_coding_transcript_exon_variant,,ENST00000385281,;MIR525,downstream_gene_variant,,ENST00000384978,;MIR526B,downstream_gene_variant,,ENST00000384848,;MIR518B,upstream_gene_variant,,ENST00000385127,;MIR518F,upstream_gene_variant,,ENST00000384973,;MIR520B,upstream_gene_variant,,ENST00000384989,;MIR519B,downstream_gene_variant,,ENST00000385090,;	C	ENSG00000208016	ENST00000385281	Transcript	non_coding_transcript_exon_variant	52	.	.	.	.	.	.	.	1	MIR523	HGNC	32103	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAAAGAACG	.	4	ESCA
MIR523	0	.	GRCh37	19	54201716	54201716	+	RNA	SNP	C	C	A	rs753891332	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.78C>A	.	.	ENST00000385281	1/1	71	65	6	46	46	0	MIR523,non_coding_transcript_exon_variant,,ENST00000385281,;MIR525,downstream_gene_variant,,ENST00000384978,;MIR526B,downstream_gene_variant,,ENST00000384848,;MIR518B,upstream_gene_variant,,ENST00000385127,;MIR518F,upstream_gene_variant,,ENST00000384973,;MIR520B,upstream_gene_variant,,ENST00000384989,;MIR519B,downstream_gene_variant,,ENST00000385090,;	A	ENSG00000208016	ENST00000385281	Transcript	non_coding_transcript_exon_variant	78	.	.	.	.	rs753891332	.	.	1	MIR523	HGNC	32103	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTTACCCTTT	.	3	ESCA
ZNF524	0	.	GRCh37	19	56114128	56114128	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650C>T	p.Ala217Val	p.A217V	ENST00000591046	1/1	76	51	24	46	46	0	ZNF524,missense_variant,p.Ala217Val,ENST00000591046,;ZNF524,missense_variant,p.Ala217Val,ENST00000301073,;ZNF865,upstream_gene_variant,,ENST00000568956,;FIZ1,upstream_gene_variant,,ENST00000592585,;FIZ1,upstream_gene_variant,,ENST00000221665,;ZNF524,downstream_gene_variant,,ENST00000589521,;FIZ1,upstream_gene_variant,,ENST00000587678,;FIZ1,upstream_gene_variant,,ENST00000590714,;FIZ1,upstream_gene_variant,,ENST00000587414,;	T	ENSG00000171443	ENST00000591046	Transcript	missense_variant	884	650	217	A/V	gCg/gTg	COSM1645156	.	.	1	ZNF524	HGNC	28322	protein_coding	YES	CCDS12929.1	ENSP00000466907	ZN524_HUMAN	K7EP10_HUMAN	UPI00000735DD	.	tolerated(0.45)	benign(0.11)	1/1	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23228:SF111,hmmpanther:PTHR23228,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGCGAAGC	.	5	ESCA
CD53	0	.	GRCh37	1	111441937	111441937	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120G>T	.	.	ENST00000271324	8/8	33	25	7	17	17	0	CD53,3_prime_UTR_variant,,ENST00000429072,;CD53,3_prime_UTR_variant,,ENST00000271324,;CD53,non_coding_transcript_exon_variant,,ENST00000464329,;CD53,non_coding_transcript_exon_variant,,ENST00000497404,;CD53,non_coding_transcript_exon_variant,,ENST00000476408,;	T	ENSG00000143119	ENST00000271324	Transcript	3_prime_UTR_variant	892	.	.	.	.	.	.	.	1	CD53	HGNC	1686	protein_coding	YES	CCDS829.1	ENSP00000271324	CD53_HUMAN	.	UPI000000D991	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TTTTAGGTCCC	.	2	ESCA
PFDN2	0	.	GRCh37	1	161070556	161070556	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382G>A	p.Gly128Arg	p.G128R	ENST00000368010	4/4	144	136	8	68	68	0	PFDN2,missense_variant,p.Gly128Arg,ENST00000368010,;KLHDC9,downstream_gene_variant,,ENST00000392192,;KLHDC9,downstream_gene_variant,,ENST00000368011,;PFDN2,non_coding_transcript_exon_variant,,ENST00000468311,;KLHDC9,downstream_gene_variant,,ENST00000494418,;KLHDC9,downstream_gene_variant,,ENST00000469647,;KLHDC9,downstream_gene_variant,,ENST00000490724,;KLHDC9,downstream_gene_variant,,ENST00000392191,;KLHDC9,downstream_gene_variant,,ENST00000475934,;KLHDC9,downstream_gene_variant,,ENST00000471613,;	T	ENSG00000143256	ENST00000368010	Transcript	missense_variant	467	382	128	G/R	Gga/Aga	.	.	.	-1	PFDN2	HGNC	8867	protein_coding	YES	CCDS1217.1	ENSP00000356989	PFD2_HUMAN	B1AQP2_HUMAN	UPI000000DBA5	.	deleterious(0)	probably_damaging(0.927)	4/4	.	hmmpanther:PTHR13303,Pfam_domain:PF01920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTCCCATGA	.	2	ESCA
EPHA8	0	.	GRCh37	1	22930078	22930078	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1844C>T	.	.	ENST00000166244	17/17	22	18	4	10	10	0	EPHA8,3_prime_UTR_variant,,ENST00000166244,;	T	ENSG00000070886	ENST00000166244	Transcript	3_prime_UTR_variant	4934	.	.	.	.	.	.	.	1	EPHA8	HGNC	3391	protein_coding	YES	CCDS225.1	ENSP00000166244	EPHA8_HUMAN	.	UPI000012A07B	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTGCCTCAT	.	2	ESCA
OR2T12	0	.	GRCh37	1	248457987	248457987	+	Silent	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.894C>A	p.%3D	p.A298A	ENST00000317996	1/1	108	89	18	91	91	0	OR2T12,synonymous_variant,p.%3D,ENST00000317996,;	T	ENSG00000177201	ENST00000317996	Transcript	synonymous_variant	894	894	298	A	gcC/gcA	.	.	.	-1	OR2T12	HGNC	19592	protein_coding	YES	CCDS31110.1	ENSP00000324583	O2T12_HUMAN	.	UPI000004B235	.	.	.	1/1	.	hmmpanther:PTHR26453:SF83,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTCAGGGCTTC	.	3	ESCA
RHCE	0	.	GRCh37	1	25718576	25718576	+	Silent	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543G>A	p.%3D	p.L181L	ENST00000294413	4/10	181	117	64	127	127	0	RHCE,synonymous_variant,p.%3D,ENST00000374352,;RHCE,synonymous_variant,p.%3D,ENST00000349320,;RHCE,synonymous_variant,p.%3D,ENST00000425135,;RHCE,synonymous_variant,p.%3D,ENST00000349438,;RHCE,synonymous_variant,p.%3D,ENST00000243186,;RHCE,synonymous_variant,p.%3D,ENST00000413854,;RHCE,synonymous_variant,p.%3D,ENST00000294413,;RHCE,intron_variant,,ENST00000455194,;RHCE,intron_variant,,ENST00000340849,;RHCE,intron_variant,,ENST00000527747,;RHCE,intron_variant,,ENST00000346452,;RHCE,non_coding_transcript_exon_variant,,ENST00000527187,;RHCE,intron_variant,,ENST00000533771,;	T	ENSG00000188672	ENST00000294413	Transcript	synonymous_variant	602	543	181	L	ctG/ctA	.	.	.	-1	RHCE	HGNC	10008	protein_coding	YES	CCDS30635.1	ENSP00000294413	RHCE_HUMAN	Q9UP89_HUMAN,Q9UEC6_HUMAN,Q8NDV4_HUMAN,Q5UD29_HUMAN,D0AB04_HUMAN,D0AB03_HUMAN,B6ZCF8_HUMAN,B6ZCF7_HUMAN,A8YPS4_HUMAN	UPI00001D9627	.	.	.	4/10	.	Prints_domain:PR00342,Superfamily_domains:0044218,Gene3D:1.10.3430.10,Pfam_domain:PF00909,hmmpanther:PTHR11883:SF24,hmmpanther:PTHR11883,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGTCAGCCC	.	5	ESCA
ELAVL4	0	.	GRCh37	1	50610816	50610816	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.248T>G	p.Phe83Cys	p.F83C	ENST00000357083	2/7	75	69	6	26	26	0	ELAVL4,missense_variant,p.Phe71Cys,ENST00000371819,;ELAVL4,missense_variant,p.Phe83Cys,ENST00000357083,;ELAVL4,missense_variant,p.Phe66Cys,ENST00000371824,;ELAVL4,missense_variant,p.Phe69Cys,ENST00000448907,;ELAVL4,missense_variant,p.Phe71Cys,ENST00000371821,;ELAVL4,missense_variant,p.Phe66Cys,ENST00000371827,;ELAVL4,missense_variant,p.Phe66Cys,ENST00000371823,;ELAVL4,non_coding_transcript_exon_variant,,ENST00000463650,;ELAVL4,non_coding_transcript_exon_variant,,ENST00000494555,;ELAVL4,non_coding_transcript_exon_variant,,ENST00000492299,;	G	ENSG00000162374	ENST00000357083	Transcript	missense_variant	290	248	83	F/C	tTc/tGc	.	.	.	1	ELAVL4	HGNC	3315	protein_coding	YES	CCDS44139.1	ENSP00000349594	ELAV4_HUMAN	B7Z5E0_HUMAN	UPI000006F633	.	deleterious(0.02)	probably_damaging(0.988)	2/7	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011,hmmpanther:PTHR24011:SF243,Gene3D:3.30.70.330,TIGRFAM_domain:TIGR01661,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTCTTCGGGA	.	3	ESCA
EPS15	0	.	GRCh37	1	51864773	51864773	+	Missense_Mutation	SNP	T	T	G	rs757320371	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1983A>C	p.Gln661His	p.Q661H	ENST00000371733	20/25	44	21	22	21	21	0	EPS15,missense_variant,p.Gln527His,ENST00000371730,;EPS15,missense_variant,p.Gln661His,ENST00000371733,;EPS15,missense_variant,p.Gln338His,ENST00000396122,;EPS15,downstream_gene_variant,,ENST00000493793,;EPS15,non_coding_transcript_exon_variant,,ENST00000478657,;EPS15,non_coding_transcript_exon_variant,,ENST00000486505,;	G	ENSG00000085832	ENST00000371733	Transcript	missense_variant	2080	1983	661	Q/H	caA/caC	rs757320371	.	.	-1	EPS15	HGNC	3419	protein_coding	YES	CCDS557.1	ENSP00000360798	EPS15_HUMAN	.	UPI0000161B29	.	deleterious(0.01)	probably_damaging(0.944)	20/25	.	hmmpanther:PTHR11216:SF54,hmmpanther:PTHR11216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGATTGCCT	byFrequency	5	ESCA
AK5	0	.	GRCh37	1	77748056	77748056	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>T	p.Glu20Ter	p.E20*	ENST00000354567	1/14	92	74	17	71	71	0	AK5,stop_gained,p.Glu20Ter,ENST00000354567,;AK5,upstream_gene_variant,,ENST00000344720,;AK5,upstream_gene_variant,,ENST00000478407,;AK5,splice_region_variant,,ENST00000317704,;	T	ENSG00000154027	ENST00000354567	Transcript	stop_gained	321	58	20	E/*	Gag/Tag	COSM426699	.	.	1	AK5	HGNC	365	protein_coding	YES	CCDS675.1	ENSP00000346577	KAD5_HUMAN	E9PQQ8_HUMAN,E9PIS7_HUMAN	UPI0000167E20	.	.	.	1/14	.	Superfamily_domains:SSF47391,hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF79	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTGAGGTA	.	5	ESCA
CDK5RAP1	0	.	GRCh37	20	31984794	31984794	+	Missense_Mutation	SNP	G	G	A	rs141733225	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77C>T	p.Ser26Leu	p.S26L	ENST00000346416	2/14	26	21	5	26	26	0	CDK5RAP1,missense_variant,p.Ser26Leu,ENST00000357886,;CDK5RAP1,missense_variant,p.Ser26Leu,ENST00000544843,;CDK5RAP1,missense_variant,p.Ser26Leu,ENST00000339269,;CDK5RAP1,missense_variant,p.Ser26Leu,ENST00000346416,;CDK5RAP1,intron_variant,,ENST00000473997,;CDK5RAP1,intron_variant,,ENST00000460043,;CDK5RAP1,intron_variant,,ENST00000488723,;CDK5RAP1,intron_variant,,ENST00000477105,;CDK5RAP1,intron_variant,,ENST00000461356,;CDK5RAP1,intron_variant,,ENST00000481964,;CDK5RAP1,intron_variant,,ENST00000496381,;CDK5RAP1,intron_variant,,ENST00000471264,;CDK5RAP1,intron_variant,,ENST00000482967,;	A	ENSG00000101391	ENST00000346416	Transcript	missense_variant	231	77	26	S/L	tCg/tTg	rs141733225,COSM388512	.	.	-1	CDK5RAP1	HGNC	15880	protein_coding	YES	CCDS13219.1	ENSP00000217372	CK5P1_HUMAN	Q53H36_HUMAN	UPI000004495E	.	tolerated_low_confidence(1)	benign(0)	2/14	.	.	A:0.0004	A:0	A:0.0029	.	A:0	A:0	A:0	A:0.0023	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCGACAGC	byFrequency|byCluster|by1000G	5	ESCA
SYCP2	0	.	GRCh37	20	58496487	58496487	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.46G>A	p.Asp16Asn	p.D16N	ENST00000357552	4/45	55	33	22	27	27	0	SYCP2,missense_variant,p.Asp16Asn,ENST00000446834,;SYCP2,missense_variant,p.Asp16Asn,ENST00000357552,;SYCP2,missense_variant,p.Asp16Asn,ENST00000371001,;SYCP2,missense_variant,p.Asp15Asn,ENST00000425931,;SYCP2,non_coding_transcript_exon_variant,,ENST00000476314,;	T	ENSG00000196074	ENST00000357552	Transcript	missense_variant	272	46	16	D/N	Gat/Aat	.	.	.	-1	SYCP2	HGNC	11490	protein_coding	YES	CCDS13482.1	ENSP00000350162	SYCP2_HUMAN	A2A341_HUMAN	UPI0000135683	.	tolerated(0.07)	benign(0.171)	4/45	.	hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATCATCAA	.	5	ESCA
CRKL	0	.	GRCh37	22	21306663	21306663	+	3'UTR	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2530C>T	.	.	ENST00000354336	3/3	20	11	9	15	15	0	CRKL,3_prime_UTR_variant,,ENST00000354336,;XXbac-B135H6.15,upstream_gene_variant,,ENST00000444039,;RN7SL389P,upstream_gene_variant,,ENST00000582413,;CRKL,intron_variant,,ENST00000411769,;	T	ENSG00000099942	ENST00000354336	Transcript	3_prime_UTR_variant	3951	.	.	.	.	.	.	.	1	CRKL	HGNC	2363	protein_coding	YES	CCDS13785.1	ENSP00000346300	CRKL_HUMAN	.	UPI000000DA57	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACTTCAGCCC	.	3	ESCA
FAM230B	0	.	GRCh37	22	21538119	21538119	+	RNA	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1105C>T	.	.	ENST00000451257	8/12	156	132	24	44	43	1	FAM230B,non_coding_transcript_exon_variant,,ENST00000451257,;FAM230B,intron_variant,,ENST00000415376,;FAM230B,downstream_gene_variant,,ENST00000421576,;KB-1592A4.14,upstream_gene_variant,,ENST00000417463,;FAM230B,downstream_gene_variant,,ENST00000424410,;FAM230B,downstream_gene_variant,,ENST00000446717,;	T	ENSG00000215498	ENST00000451257	Transcript	non_coding_transcript_exon_variant	1105	.	.	.	.	.	.	.	1	FAM230B	HGNC	32943	lincRNA	YES	.	.	.	.	.	.	.	.	8/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCCGCCCACGG	.	3	ESCA
BCR	0	.	GRCh37	22	23596130	23596130	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1424A>T	p.Asp475Val	p.D475V	ENST00000305877	2/23	36	19	16	29	29	0	BCR,missense_variant,p.Asp475Val,ENST00000359540,;BCR,missense_variant,p.Asp475Val,ENST00000305877,;BCR,upstream_gene_variant,,ENST00000427791,;BCR,non_coding_transcript_exon_variant,,ENST00000480973,;BCR,non_coding_transcript_exon_variant,,ENST00000479188,;BCR,downstream_gene_variant,,ENST00000487679,;BCR,downstream_gene_variant,,ENST00000463770,;	T	ENSG00000186716	ENST00000305877	Transcript	missense_variant	2175	1424	475	D/V	gAt/gTt	.	.	.	1	BCR	HGNC	1014	protein_coding	YES	CCDS13806.1	ENSP00000303507	BCR_HUMAN	.	UPI000016A088	.	deleterious(0)	probably_damaging(0.937)	2/23	.	hmmpanther:PTHR23182:SF3,hmmpanther:PTHR23182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGGATGCGC	.	5	ESCA
KIAA0930	0	.	GRCh37	22	45593679	45593679	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1181T>G	p.Ile394Ser	p.I394S	ENST00000251993	9/10	46	36	9	48	48	0	KIAA0930,missense_variant,p.Ile371Ser,ENST00000443310,;KIAA0930,missense_variant,p.Ile389Ser,ENST00000336156,;KIAA0930,missense_variant,p.Ile394Ser,ENST00000251993,;KIAA0930,missense_variant,p.Ile355Ser,ENST00000391627,;KIAA0930,missense_variant,p.Ile274Ser,ENST00000423262,;MIR1249,downstream_gene_variant,,ENST00000408671,;KIAA0930,non_coding_transcript_exon_variant,,ENST00000474515,;KIAA0930,non_coding_transcript_exon_variant,,ENST00000493003,;KIAA0930,non_coding_transcript_exon_variant,,ENST00000498418,;KIAA0930,non_coding_transcript_exon_variant,,ENST00000488038,;KIAA0930,non_coding_transcript_exon_variant,,ENST00000483374,;	C	ENSG00000100364	ENST00000251993	Transcript	missense_variant	1326	1181	394	I/S	aTt/aGt	.	.	.	-1	KIAA0930	HGNC	1314	protein_coding	YES	CCDS33666.1	ENSP00000251993	K0930_HUMAN	B0QY18_HUMAN	UPI00001C0A16	.	deleterious(0)	possibly_damaging(0.736)	9/10	.	hmmpanther:PTHR21477,hmmpanther:PTHR21477:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAAATCCGA	.	5	ESCA
CRELD2	0	.	GRCh37	22	50316310	50316310	+	Missense_Mutation	SNP	G	G	A	rs755543544	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.790G>A	p.Gly264Ser	p.G264S	ENST00000404488	7/11	56	46	10	56	56	0	CRELD2,missense_variant,p.Gly215Ser,ENST00000407217,;CRELD2,missense_variant,p.Gly215Ser,ENST00000328268,;CRELD2,missense_variant,p.Gly215Ser,ENST00000403427,;CRELD2,missense_variant,p.Gly264Ser,ENST00000404488,;CRELD2,missense_variant,p.Gly215Ser,ENST00000450207,;ALG12,upstream_gene_variant,,ENST00000330817,;CRELD2,non_coding_transcript_exon_variant,,ENST00000444954,;CRELD2,non_coding_transcript_exon_variant,,ENST00000462253,;CRELD2,downstream_gene_variant,,ENST00000498354,;CRELD2,non_coding_transcript_exon_variant,,ENST00000483652,;CRELD2,non_coding_transcript_exon_variant,,ENST00000482956,;CRELD2,upstream_gene_variant,,ENST00000487969,;	A	ENSG00000184164	ENST00000404488	Transcript	missense_variant	925	790	264	G/S	Ggc/Agc	rs755543544	.	.	1	CRELD2	HGNC	28150	protein_coding	YES	CCDS46730.1	ENSP00000383938	CREL2_HUMAN	.	UPI0000E56EE9	.	tolerated(0.73)	benign(0.011)	7/11	.	hmmpanther:PTHR24838:SF252,hmmpanther:PTHR24838,SMART_domains:SM00261,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGCGGCGAG	.	5	ESCA
ZC3H8	0	.	GRCh37	2	113007845	113007845	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000409573	2/9	88	78	10	52	52	0	ZC3H8,missense_variant,p.Asp27Tyr,ENST00000272570,;ZC3H8,missense_variant,p.Asp27Tyr,ENST00000409573,;ZC3H8,non_coding_transcript_exon_variant,,ENST00000474234,;ZC3H8,non_coding_transcript_exon_variant,,ENST00000464305,;ZC3H8,non_coding_transcript_exon_variant,,ENST00000495264,;	A	ENSG00000144161	ENST00000409573	Transcript	missense_variant	209	79	27	D/Y	Gat/Tat	.	.	.	-1	ZC3H8	HGNC	30941	protein_coding	YES	CCDS46392.1	ENSP00000386488	ZC3H8_HUMAN	Q53RD8_HUMAN,Q53QC9_HUMAN	UPI00000467EA	.	deleterious_low_confidence(0)	benign(0.06)	2/9	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13119,hmmpanther:PTHR13119:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCATCGATTC	.	4	ESCA
MIR1302-3	0	.	GRCh37	2	114340606	114340606	+	RNA	SNP	A	A	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.68T>A	.	.	ENST00000408128	1/1	475	418	56	255	255	0	MIR1302-3,non_coding_transcript_exon_variant,,ENST00000408128,;FAM138B,downstream_gene_variant,,ENST00000432583,;FAM138B,downstream_gene_variant,,ENST00000446648,;WASH2P,upstream_gene_variant,,ENST00000326632,;	T	ENSG00000221055	ENST00000408128	Transcript	non_coding_transcript_exon_variant	68	.	.	.	.	.	.	.	-1	MIR1302-3	HGNC	35295	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTAAGCTTG	.	4	ESCA
TMEFF2	0	.	GRCh37	2	192820998	192820998	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852G>A	p.Met284Ile	p.M284I	ENST00000272771	8/10	88	61	27	59	58	0	TMEFF2,missense_variant,p.Met284Ile,ENST00000272771,;TMEFF2,missense_variant,p.Met284Ile,ENST00000392314,;AC098617.1,intron_variant,,ENST00000424116,;AC098617.1,intron_variant,,ENST00000428980,;	T	ENSG00000144339	ENST00000272771	Transcript	missense_variant	2037	852	284	M/I	atG/atA	.	.	.	-1	TMEFF2	HGNC	11867	protein_coding	YES	CCDS2314.1	ENSP00000272771	TEFF2_HUMAN	.	UPI0000048F19	.	tolerated(0.4)	benign(0.006)	8/10	.	Superfamily_domains:SSF57196,Gene3D:2.10.25.10,hmmpanther:PTHR10574,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGCATATT	.	5	ESCA
COLEC11	0	.	GRCh37	2	3653823	3653823	+	Intron	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172+1763C>T	.	.	ENST00000418971	.	142	115	27	104	104	0	COLEC11,synonymous_variant,p.%3D,ENST00000402922,;COLEC11,synonymous_variant,p.%3D,ENST00000403096,;COLEC11,synonymous_variant,p.%3D,ENST00000402794,;COLEC11,synonymous_variant,p.%3D,ENST00000404205,;COLEC11,intron_variant,,ENST00000382062,;COLEC11,intron_variant,,ENST00000438814,;COLEC11,intron_variant,,ENST00000349077,;COLEC11,intron_variant,,ENST00000236693,;COLEC11,intron_variant,,ENST00000418971,;AC010907.2,upstream_gene_variant,,ENST00000456450,;COLEC11,intron_variant,,ENST00000487365,;COLEC11,intron_variant,,ENST00000460971,;COLEC11,downstream_gene_variant,,ENST00000419002,;COLEC11,intron_variant,,ENST00000416132,;	T	ENSG00000118004	ENST00000418971	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	COLEC11	HGNC	17213	protein_coding	YES	CCDS58689.1	ENSP00000411770	COL11_HUMAN	C9JWT5_HUMAN	UPI0001AE7699	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGCGCCCT	.	5	ESCA
PLEKHH2	0	.	GRCh37	2	43993451	43993451	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*714G>A	.	.	ENST00000282406	30/30	39	34	5	34	34	0	PLEKHH2,3_prime_UTR_variant,,ENST00000282406,;PLEKHH2,downstream_gene_variant,,ENST00000405000,;PLEKHH2,downstream_gene_variant,,ENST00000490038,;	A	ENSG00000152527	ENST00000282406	Transcript	3_prime_UTR_variant	5306	.	.	.	.	.	.	.	1	PLEKHH2	HGNC	30506	protein_coding	YES	CCDS1812.1	ENSP00000282406	PKHH2_HUMAN	.	UPI000016021B	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAAGAATAT	.	4	ESCA
SOCS5	0	.	GRCh37	2	46986968	46986968	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1299G>T	p.Trp433Cys	p.W433C	ENST00000306503	2/2	56	40	15	40	40	0	SOCS5,missense_variant,p.Trp433Cys,ENST00000394861,;SOCS5,missense_variant,p.Trp433Cys,ENST00000306503,;	T	ENSG00000171150	ENST00000306503	Transcript	missense_variant	1471	1299	433	W/C	tgG/tgT	.	.	.	1	SOCS5	HGNC	16852	protein_coding	YES	CCDS1830.1	ENSP00000305133	SOCS5_HUMAN	B4DL10_HUMAN	UPI0000135B69	.	deleterious(0)	probably_damaging(0.995)	2/2	.	PROSITE_profiles:PS50001,hmmpanther:PTHR10385,hmmpanther:PTHR10385:SF28,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTGGAATCA	.	5	ESCA
CCDC85A	0	.	GRCh37	2	56420246	56420246	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.911C>T	p.Thr304Met	p.T304M	ENST00000407595	2/6	46	41	5	17	17	0	CCDC85A,missense_variant,p.Thr304Met,ENST00000407595,;RP11-482H16.1,intron_variant,,ENST00000607540,;	T	ENSG00000055813	ENST00000407595	Transcript	missense_variant	1413	911	304	T/M	aCg/aTg	.	.	.	1	CCDC85A	HGNC	29400	protein_coding	YES	CCDS46290.1	ENSP00000384040	CC85A_HUMAN	.	UPI00001C1DC1	.	tolerated_low_confidence(0.13)	benign(0.03)	2/6	.	hmmpanther:PTHR13546,hmmpanther:PTHR13546:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAAACGCTGC	.	4	ESCA
DOK1	0	.	GRCh37	2	74784044	74784044	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1249A>T	p.Thr417Ser	p.T417S	ENST00000233668	5/5	17	11	6	17	17	0	DOK1,missense_variant,p.Thr278Ser,ENST00000409429,;DOK1,missense_variant,p.Thr417Ser,ENST00000233668,;DOK1,3_prime_UTR_variant,,ENST00000340004,;LOXL3,upstream_gene_variant,,ENST00000413469,;M1AP,downstream_gene_variant,,ENST00000290536,;M1AP,downstream_gene_variant,,ENST00000536235,;LOXL3,upstream_gene_variant,,ENST00000264094,;LOXL3,upstream_gene_variant,,ENST00000409986,;M1AP,downstream_gene_variant,,ENST00000409585,;LOXL3,upstream_gene_variant,,ENST00000409249,;M1AP,downstream_gene_variant,,ENST00000358434,;LOXL3,upstream_gene_variant,,ENST00000409549,;LOXL3,upstream_gene_variant,,ENST00000393937,;DOK1,non_coding_transcript_exon_variant,,ENST00000480318,;DOK1,non_coding_transcript_exon_variant,,ENST00000489958,;DOK1,downstream_gene_variant,,ENST00000488613,;M1AP,downstream_gene_variant,,ENST00000485997,;LOXL3,upstream_gene_variant,,ENST00000484369,;M1AP,downstream_gene_variant,,ENST00000464686,;DOK1,downstream_gene_variant,,ENST00000485132,;DOK1,downstream_gene_variant,,ENST00000496966,;DOK1,non_coding_transcript_exon_variant,,ENST00000464613,;DOK1,downstream_gene_variant,,ENST00000429631,;DOK1,downstream_gene_variant,,ENST00000475191,;DOK1,downstream_gene_variant,,ENST00000474924,;DOK1,downstream_gene_variant,,ENST00000482206,;	T	ENSG00000115325	ENST00000233668	Transcript	missense_variant	1918	1249	417	T/S	Aca/Tca	.	.	.	1	DOK1	HGNC	2990	protein_coding	YES	CCDS1954.1	ENSP00000233668	DOK1_HUMAN	Q2TA81_HUMAN	UPI00001296A9	.	tolerated(0.58)	benign(0.004)	5/5	.	hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCACAAAG	.	5	ESCA
HK2	0	.	GRCh37	2	75118933	75118933	+	3'UTR	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*865G>A	.	.	ENST00000290573	18/18	18	12	6	16	16	0	HK2,3_prime_UTR_variant,,ENST00000409174,;HK2,3_prime_UTR_variant,,ENST00000290573,;	A	ENSG00000159399	ENST00000290573	Transcript	3_prime_UTR_variant	4219	.	.	.	.	.	.	.	1	HK2	HGNC	4923	protein_coding	YES	CCDS1956.1	ENSP00000290573	HXK2_HUMAN	Q7Z7Q6_HUMAN,Q53SG7_HUMAN,Q53QX9_HUMAN,Q09LL6_HUMAN,E9PB90_HUMAN	UPI00000706E4	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	TGTACGTAATG	.	3	ESCA
CTNNA2	0	.	GRCh37	2	80875281	80875281	+	3'UTR	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*284G>T	.	.	ENST00000466387	22/22	28	21	6	16	16	0	CTNNA2,3_prime_UTR_variant,,ENST00000496558,;CTNNA2,3_prime_UTR_variant,,ENST00000466387,;CTNNA2,3_prime_UTR_variant,,ENST00000541047,;CTNNA2,3_prime_UTR_variant,,ENST00000343114,;CTNNA2,3_prime_UTR_variant,,ENST00000402739,;CTNNA2,downstream_gene_variant,,ENST00000540488,;CTNNA2,downstream_gene_variant,,ENST00000361291,;	T	ENSG00000066032	ENST00000466387	Transcript	3_prime_UTR_variant	3726	.	.	.	.	.	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGGGAGTGG	.	5	ESCA
CIAO1	0	.	GRCh37	2	96934194	96934194	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490-1G>T	.	p.X164_splice	ENST00000488633	.	60	42	18	49	49	0	CIAO1,splice_acceptor_variant,,ENST00000488633,;TMEM127,upstream_gene_variant,,ENST00000258439,;TMEM127,upstream_gene_variant,,ENST00000432959,;CIAO1,downstream_gene_variant,,ENST00000469320,;CIAO1,splice_acceptor_variant,,ENST00000272402,;CIAO1,downstream_gene_variant,,ENST00000491394,;	T	ENSG00000144021	ENST00000488633	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	CIAO1	HGNC	14280	protein_coding	YES	CCDS2019.1	ENSP00000418287	CIAO1_HUMAN	.	UPI0000127987	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCAGCTCTT	.	5	ESCA
SLC6A1	0	.	GRCh37	3	11064120	11064120	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.680T>C	p.Phe227Ser	p.F227S	ENST00000287766	7/16	45	35	9	70	70	0	SLC6A1,missense_variant,p.Phe49Ser,ENST00000536032,;SLC6A1,missense_variant,p.Phe227Ser,ENST00000287766,;SLC6A1-AS1,upstream_gene_variant,,ENST00000414969,;SLC6A1,non_coding_transcript_exon_variant,,ENST00000460480,;SLC6A1,downstream_gene_variant,,ENST00000462473,;	C	ENSG00000157103	ENST00000287766	Transcript	missense_variant	1101	680	227	F/S	tTc/tCc	.	.	.	1	SLC6A1	HGNC	11042	protein_coding	YES	CCDS2603.1	ENSP00000287766	SC6A1_HUMAN	C9J5P8_HUMAN,B7Z3C5_HUMAN	UPI000013DECF	.	deleterious(0)	probably_damaging(0.976)	7/16	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF138,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTATTTCTGTA	.	5	ESCA
NPHP3	0	.	GRCh37	3	132423181	132423181	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1385C>G	p.Thr462Ser	p.T462S	ENST00000337331	9/27	68	39	28	17	17	0	NPHP3,missense_variant,p.Thr462Ser,ENST00000326682,;NPHP3,missense_variant,p.Thr462Ser,ENST00000337331,;NPHP3,downstream_gene_variant,,ENST00000476742,;NPHP3,missense_variant,p.Thr462Ser,ENST00000471702,;NPHP3,missense_variant,p.Thr364Ser,ENST00000465756,;NPHP3,3_prime_UTR_variant,,ENST00000469232,;NPHP3,non_coding_transcript_exon_variant,,ENST00000490993,;	C	ENSG00000113971	ENST00000337331	Transcript	missense_variant	1472	1385	462	T/S	aCt/aGt	.	.	.	-1	NPHP3	HGNC	7907	protein_coding	YES	CCDS3078.1	ENSP00000338766	NPHP3_HUMAN	.	UPI00001B6B30	.	tolerated(0.84)	benign(0)	9/27	.	hmmpanther:PTHR19959:SF133,hmmpanther:PTHR19959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTAGTCTCC	.	5	ESCA
SLC25A36	0	.	GRCh37	3	140692768	140692768	+	Silent	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.663A>G	p.%3D	p.K221K	ENST00000324194	6/7	49	35	14	36	36	0	SLC25A36,synonymous_variant,p.%3D,ENST00000453248,;SLC25A36,synonymous_variant,p.%3D,ENST00000446041,;SLC25A36,synonymous_variant,p.%3D,ENST00000324194,;SLC25A36,downstream_gene_variant,,ENST00000513887,;RP11-231L11.3,downstream_gene_variant,,ENST00000513802,;SLC25A36,3_prime_UTR_variant,,ENST00000512506,;SLC25A36,3_prime_UTR_variant,,ENST00000502594,;SLC25A36,3_prime_UTR_variant,,ENST00000512023,;SLC25A36,non_coding_transcript_exon_variant,,ENST00000502866,;SLC25A36,non_coding_transcript_exon_variant,,ENST00000514629,;SLC25A36,non_coding_transcript_exon_variant,,ENST00000511757,;	G	ENSG00000114120	ENST00000324194	Transcript	synonymous_variant	831	663	221	K	aaA/aaG	.	.	.	1	SLC25A36	HGNC	25554	protein_coding	YES	CCDS46927.1	ENSP00000320688	S2536_HUMAN	.	UPI000006D558	.	.	.	6/7	.	hmmpanther:PTHR24089:SF180,hmmpanther:PTHR24089,Gene3D:1okcA00,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAAGAAGC	.	5	ESCA
RAP2B	0	.	GRCh37	3	152884905	152884905	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3871A>G	.	.	ENST00000323534	1/1	73	60	13	34	34	0	RAP2B,3_prime_UTR_variant,,ENST00000323534,;	G	ENSG00000181467	ENST00000323534	Transcript	3_prime_UTR_variant	4877	.	.	.	.	.	.	.	1	RAP2B	HGNC	9862	protein_coding	YES	CCDS3170.1	ENSP00000319096	RAP2B_HUMAN	Q5JQ44_HUMAN	UPI0000004042	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAAAGTTTG	.	5	ESCA
SLITRK3	0	.	GRCh37	3	164905509	164905509	+	3'UTR	SNP	G	G	A	rs754900428	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*176C>T	.	.	ENST00000475390	2/2	42	37	5	24	24	0	SLITRK3,3_prime_UTR_variant,,ENST00000475390,;SLITRK3,3_prime_UTR_variant,,ENST00000241274,;SLITRK3,downstream_gene_variant,,ENST00000497724,;	A	ENSG00000121871	ENST00000475390	Transcript	3_prime_UTR_variant	3554	.	.	.	.	rs754900428	.	.	-1	SLITRK3	HGNC	23501	protein_coding	YES	CCDS3197.1	ENSP00000420091	SLIK3_HUMAN	C9K0R4_HUMAN	UPI000004F259	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGAGGGGAG	.	4	ESCA
MECOM	0	.	GRCh37	3	168825727	168825727	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2222A>T	p.Asp741Val	p.D741V	ENST00000264674	10/17	58	47	11	33	33	0	MECOM,missense_variant,p.Asp677Val,ENST00000472280,;MECOM,missense_variant,p.Asp676Val,ENST00000468789,;MECOM,missense_variant,p.Asp677Val,ENST00000433243,;MECOM,missense_variant,p.Asp676Val,ENST00000392736,;MECOM,missense_variant,p.Asp741Val,ENST00000264674,;MECOM,intron_variant,,ENST00000460814,;MECOM,intron_variant,,ENST00000464456,;MECOM,intron_variant,,ENST00000494292,;MECOM,downstream_gene_variant,,ENST00000492586,;	A	ENSG00000085276	ENST00000264674	Transcript	missense_variant	2361	2222	741	D/V	gAt/gTt	.	.	.	-1	MECOM	HGNC	3498	protein_coding	YES	CCDS54670.1	ENSP00000264674	EVI1_HUMAN	Q9UBK3_HUMAN,Q8IU84_HUMAN,E9PGE9_HUMAN,E7EU48_HUMAN,E7ERX0_HUMAN,E7EPY2_HUMAN,D3DNP4_HUMAN	UPI00015D43FA	.	tolerated(0.13)	probably_damaging(0.931)	10/17	.	hmmpanther:PTHR24393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGATCAGGC	.	5	ESCA
YEATS2	0	.	GRCh37	3	183439772	183439772	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385A>G	p.Arg129Gly	p.R129G	ENST00000305135	5/31	86	45	41	36	36	0	YEATS2,missense_variant,p.Arg129Gly,ENST00000305135,;	G	ENSG00000163872	ENST00000305135	Transcript	missense_variant	580	385	129	R/G	Aga/Gga	.	.	.	1	YEATS2	HGNC	25489	protein_coding	YES	CCDS43175.1	ENSP00000306983	YETS2_HUMAN	.	UPI00001BB2B9	.	tolerated(0.65)	benign(0.001)	5/31	.	hmmpanther:PTHR23195,hmmpanther:PTHR23195:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAGAGAGCA	.	5	ESCA
CLCN2	0	.	GRCh37	3	184075627	184075627	+	Silent	SNP	G	G	A	rs370199115	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633C>T	p.%3D	p.I211I	ENST00000265593	6/24	70	52	17	51	51	0	CLCN2,synonymous_variant,p.%3D,ENST00000434054,;CLCN2,synonymous_variant,p.%3D,ENST00000265593,;CLCN2,synonymous_variant,p.%3D,ENST00000344937,;CLCN2,synonymous_variant,p.%3D,ENST00000457512,;CLCN2,5_prime_UTR_variant,,ENST00000423355,;EIF2B5,intron_variant,,ENST00000444495,;POLR2H,upstream_gene_variant,,ENST00000456318,;POLR2H,upstream_gene_variant,,ENST00000438240,;POLR2H,upstream_gene_variant,,ENST00000455712,;POLR2H,upstream_gene_variant,,ENST00000412877,;POLR2H,upstream_gene_variant,,ENST00000460083,;CLCN2,upstream_gene_variant,,ENST00000475279,;CLCN2,non_coding_transcript_exon_variant,,ENST00000485667,;CLCN2,upstream_gene_variant,,ENST00000430397,;CLCN2,downstream_gene_variant,,ENST00000465231,;CLCN2,upstream_gene_variant,,ENST00000491162,;	A	ENSG00000114859	ENST00000265593	Transcript	synonymous_variant	805	633	211	I	atC/atT	rs370199115	.	.	-1	CLCN2	HGNC	2020	protein_coding	YES	CCDS3263.1	ENSP00000265593	CLCN2_HUMAN	.	UPI000013D645	.	.	.	6/24	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF64,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCGATATG	byFrequency|byCluster	5	ESCA
DGKG	0	.	GRCh37	3	185866700	185866700	+	3'UTR	SNP	C	C	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1179G>C	.	.	ENST00000265022	25/25	45	33	12	13	13	0	DGKG,3_prime_UTR_variant,,ENST00000265022,;DGKG,downstream_gene_variant,,ENST00000544847,;DGKG,downstream_gene_variant,,ENST00000382164,;DGKG,downstream_gene_variant,,ENST00000344484,;DGKG,intron_variant,,ENST00000447054,;DGKG,downstream_gene_variant,,ENST00000490452,;	G	ENSG00000058866	ENST00000265022	Transcript	3_prime_UTR_variant	4095	.	.	.	.	.	.	.	-1	DGKG	HGNC	2853	protein_coding	YES	CCDS3274.1	ENSP00000265022	DGKG_HUMAN	.	UPI000013D5AB	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	ACTACCTATGT	.	2	ESCA
RBM6	0	.	GRCh37	3	50012786	50012786	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1444A>T	p.Met482Leu	p.M482L	ENST00000266022	5/21	47	27	19	53	53	0	RBM6,missense_variant,p.Met482Leu,ENST00000266022,;RBM6,missense_variant,p.Met350Leu,ENST00000443081,;RBM6,5_prime_UTR_variant,,ENST00000422955,;RBM6,intron_variant,,ENST00000539992,;RBM6,intron_variant,,ENST00000442092,;RBM6,non_coding_transcript_exon_variant,,ENST00000441115,;RBM6,missense_variant,p.Met482Leu,ENST00000425608,;RBM6,missense_variant,p.Met350Leu,ENST00000454079,;RBM6,5_prime_UTR_variant,,ENST00000434592,;RBM6,intron_variant,,ENST00000419610,;	T	ENSG00000004534	ENST00000266022	Transcript	missense_variant	1703	1444	482	M/L	Atg/Ttg	.	.	.	1	RBM6	HGNC	9903	protein_coding	YES	CCDS2809.1	ENSP00000266022	RBM6_HUMAN	E9PGM9_HUMAN,C9JSL1_HUMAN,C9JMC8_HUMAN,C9JII0_HUMAN,B4DNY1_HUMAN	UPI000013D6C0	.	tolerated(0.52)	benign(0.001)	5/21	.	Superfamily_domains:SSF54928,SMART_domains:SM00360,Gene3D:3.30.70.330,Pfam_domain:PF14259,hmmpanther:PTHR13948:SF22,hmmpanther:PTHR13948,PROSITE_profiles:PS50102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGCATGCCT	.	5	ESCA
TKTL2	0	.	GRCh37	4	164394964	164394964	+	5'UTR	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-78G>A	.	.	ENST00000280605	1/1	28	24	4	26	26	0	TKTL2,5_prime_UTR_variant,,ENST00000280605,;	T	ENSG00000151005	ENST00000280605	Transcript	5_prime_UTR_variant	84	.	.	.	.	.	.	.	-1	TKTL2	HGNC	25313	protein_coding	YES	CCDS3805.1	ENSP00000280605	TKTL2_HUMAN	Q96LZ0_HUMAN,Q8ND81_HUMAN	UPI0000037C67	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGACCGCCCC	.	4	ESCA
OCIAD1	0	.	GRCh37	4	48850413	48850413	+	Intron	SNP	T	T	C	rs773116024	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194-3T>C	.	.	ENST00000381473	.	65	47	17	44	44	0	OCIAD1,splice_region_variant,,ENST00000513391,;OCIAD1,splice_region_variant,,ENST00000508293,;OCIAD1,splice_region_variant,,ENST00000425583,;OCIAD1,splice_region_variant,,ENST00000264312,;OCIAD1,splice_region_variant,,ENST00000508996,;OCIAD1,splice_region_variant,,ENST00000510824,;OCIAD1,splice_region_variant,,ENST00000505922,;OCIAD1,splice_region_variant,,ENST00000509164,;OCIAD1,splice_region_variant,,ENST00000503016,;OCIAD1,splice_region_variant,,ENST00000509963,;OCIAD1,splice_region_variant,,ENST00000511102,;OCIAD1,splice_region_variant,,ENST00000509246,;OCIAD1,splice_region_variant,,ENST00000396448,;OCIAD1,splice_region_variant,,ENST00000506801,;OCIAD1,splice_region_variant,,ENST00000504654,;OCIAD1,splice_region_variant,,ENST00000507210,;OCIAD1,splice_region_variant,,ENST00000512236,;OCIAD1,splice_region_variant,,ENST00000514981,;OCIAD1,splice_region_variant,,ENST00000381473,;OCIAD1,splice_region_variant,,ENST00000509122,;OCIAD1,splice_region_variant,,ENST00000509664,;OCIAD1,splice_region_variant,,ENST00000444354,;OCIAD1-AS1,downstream_gene_variant,,ENST00000513576,;OCIAD1,splice_region_variant,,ENST00000512981,;OCIAD1,upstream_gene_variant,,ENST00000508329,;OCIAD1,splice_region_variant,,ENST00000507546,;OCIAD1,splice_region_variant,,ENST00000513641,;	C	ENSG00000109180	ENST00000381473	Transcript	splice_region_variant	.	.	.	.	.	rs773116024	.	.	1	OCIAD1	HGNC	16074	protein_coding	YES	CCDS3484.1	ENSP00000370882	OCAD1_HUMAN	D6RIT9_HUMAN,D6RI08_HUMAN,D6RG39_HUMAN,D6RF07_HUMAN,D6RF01_HUMAN,D6RDK6_HUMAN,D6RDK1_HUMAN,D6RDI5_HUMAN,D6RC55_HUMAN,D6RBC5_HUMAN,D6RA54_HUMAN,D6R918_HUMAN	UPI0000073D7F	.	.	.	.	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTTAGGAA	.	4	ESCA
FIP1L1	0	.	GRCh37	4	54249970	54249970	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259A>T	p.Ser87Cys	p.S87C	ENST00000337488	5/18	75	56	18	36	36	0	FIP1L1,missense_variant,p.Ser72Cys,ENST00000358575,;FIP1L1,missense_variant,p.Ser87Cys,ENST00000337488,;FIP1L1,missense_variant,p.Ser72Cys,ENST00000507922,;FIP1L1,missense_variant,p.Ser87Cys,ENST00000507166,;FIP1L1,missense_variant,p.Ser72Cys,ENST00000306932,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000510668,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000511376,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000505125,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000513975,;FIP1L1,intron_variant,,ENST00000514543,;	T	ENSG00000145216	ENST00000337488	Transcript	missense_variant	453	259	87	S/C	Agt/Tgt	.	.	.	1	FIP1L1	HGNC	19124	protein_coding	YES	CCDS3491.1	ENSP00000336752	FIP1_HUMAN	.	UPI0000035FBF	.	deleterious(0)	probably_damaging(0.998)	5/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATAGTGAC	.	5	ESCA
DNAH5	0	.	GRCh37	5	13766149	13766149	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10037C>G	p.Thr3346Ser	p.T3346S	ENST00000265104	59/79	38	35	3	22	22	0	DNAH5,missense_variant,p.Thr3346Ser,ENST00000265104,;DNAH5,intron_variant,,ENST00000504001,;	C	ENSG00000039139	ENST00000265104	Transcript	missense_variant	10142	10037	3346	T/S	aCc/aGc	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0)	59/79	.	Pfam_domain:PF12777,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCATGGTACAG	.	2	ESCA
APBB3	0	.	GRCh37	5	139941700	139941700	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.611G>A	p.Gly204Glu	p.G204E	ENST00000354402	6/13	30	26	4	23	23	0	APBB3,missense_variant,p.Gly204Glu,ENST00000356738,;APBB3,missense_variant,p.Gly204Glu,ENST00000357560,;APBB3,missense_variant,p.Gly204Glu,ENST00000511201,;APBB3,missense_variant,p.Gly204Glu,ENST00000412920,;APBB3,missense_variant,p.Gly204Glu,ENST00000354402,;APBB3,missense_variant,p.Gly204Glu,ENST00000358580,;APBB3,5_prime_UTR_variant,,ENST00000508496,;SRA1,upstream_gene_variant,,ENST00000336283,;SLC35A4,upstream_gene_variant,,ENST00000323146,;SLC35A4,upstream_gene_variant,,ENST00000514199,;APBB3,downstream_gene_variant,,ENST00000505617,;APBB3,downstream_gene_variant,,ENST00000507279,;SRA1,upstream_gene_variant,,ENST00000520427,;APBB3,downstream_gene_variant,,ENST00000513766,;SLC35A4,upstream_gene_variant,,ENST00000508770,;APBB3,missense_variant,p.Gly204Glu,ENST00000467078,;APBB3,missense_variant,p.Gly158Glu,ENST00000511896,;APBB3,non_coding_transcript_exon_variant,,ENST00000511463,;APBB3,non_coding_transcript_exon_variant,,ENST00000504872,;APBB3,non_coding_transcript_exon_variant,,ENST00000515056,;APBB3,non_coding_transcript_exon_variant,,ENST00000503979,;APBB3,non_coding_transcript_exon_variant,,ENST00000510241,;APBB3,non_coding_transcript_exon_variant,,ENST00000506289,;APBB3,non_coding_transcript_exon_variant,,ENST00000513507,;APBB3,intron_variant,,ENST00000509914,;SRA1,upstream_gene_variant,,ENST00000602775,;SRA1,upstream_gene_variant,,ENST00000523259,;APBB3,downstream_gene_variant,,ENST00000511459,;SLC35A4,upstream_gene_variant,,ENST00000514137,;APBB3,downstream_gene_variant,,ENST00000506165,;APBB3,downstream_gene_variant,,ENST00000503850,;SRA1,upstream_gene_variant,,ENST00000602875,;APBB3,downstream_gene_variant,,ENST00000506958,;	T	ENSG00000113108	ENST00000354402	Transcript	missense_variant	626	611	204	G/E	gGg/gAg	.	.	.	-1	APBB3	HGNC	20708	protein_coding	YES	CCDS4227.1	ENSP00000346378	APBB3_HUMAN	F5H1N5_HUMAN	UPI0000414594	.	deleterious(0)	probably_damaging(1)	6/13	.	PROSITE_profiles:PS01179,hmmpanther:PTHR14058,hmmpanther:PTHR14058:SF10,Pfam_domain:PF00640,Gene3D:2.30.29.30,SMART_domains:SM00462,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCTCCCCACG	.	4	ESCA
PCDHB11	0	.	GRCh37	5	140580326	140580326	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.979C>T	p.Leu327Phe	p.L327F	ENST00000354757	1/1	41	34	7	28	28	0	PCDHB11,missense_variant,p.Leu327Phe,ENST00000354757,;PCDHB11,5_prime_UTR_variant,,ENST00000536699,;	T	ENSG00000197479	ENST00000354757	Transcript	missense_variant	979	979	327	L/F	Ctt/Ttt	COSM391262	.	.	1	PCDHB11	HGNC	8682	protein_coding	YES	CCDS4253.1	ENSP00000346802	PCDBB_HUMAN	B4DSF7_HUMAN	UPI00001273E6	.	tolerated_low_confidence(0.07)	probably_damaging(0.967)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF91,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGGACTTTTT	.	2	ESCA
ZNF300P1	0	.	GRCh37	5	150310917	150310917	+	RNA	DEL	T	T	-	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2405delA	.	.	ENST00000520773	4/4	81	67	14	45	45	0	ZNF300P1,non_coding_transcript_exon_variant,,ENST00000520773,;ZNF300P1,non_coding_transcript_exon_variant,,ENST00000356555,;	-	ENSG00000197083	ENST00000520773	Transcript	non_coding_transcript_exon_variant	2405	.	.	.	.	.	.	.	-1	ZNF300P1	HGNC	27032	processed_transcript	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAGTATGAGCT	.	3	ESCA
FAT2	0	.	GRCh37	5	150923097	150923097	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7591A>G	p.Ile2531Val	p.I2531V	ENST00000261800	9/23	46	17	28	39	39	0	FAT2,missense_variant,p.Ile2531Val,ENST00000261800,;	C	ENSG00000086570	ENST00000261800	Transcript	missense_variant	7604	7591	2531	I/V	Ata/Gta	COSM3661284	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	possibly_damaging(0.576)	9/23	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTATGGAGA	.	5	ESCA
EBF1	0	.	GRCh37	5	158158087	158158087	+	Missense_Mutation	SNP	C	C	T	rs200547458	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1115G>A	p.Arg372His	p.R372H	ENST00000313708	11/16	35	22	12	30	30	0	EBF1,missense_variant,p.Arg341His,ENST00000380654,;EBF1,missense_variant,p.Arg372His,ENST00000313708,;EBF1,missense_variant,p.Arg364His,ENST00000517373,;EBF1,non_coding_transcript_exon_variant,,ENST00000518836,;EBF1,non_coding_transcript_exon_variant,,ENST00000523464,;EBF1,non_coding_transcript_exon_variant,,ENST00000519890,;EBF1,non_coding_transcript_exon_variant,,ENST00000522192,;EBF1,non_coding_transcript_exon_variant,,ENST00000519739,;	T	ENSG00000164330	ENST00000313708	Transcript	missense_variant	1398	1115	372	R/H	cGt/cAt	rs200547458,COSM3765183	.	.	-1	EBF1	HGNC	3126	protein_coding	YES	CCDS4343.1	ENSP00000322898	COE1_HUMAN	.	UPI000000D95E	.	deleterious(0)	probably_damaging(0.926)	11/16	.	hmmpanther:PTHR10747	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAACGCTCA	byCluster	5	ESCA
C6	0	.	GRCh37	5	41160290	41160290	+	Silent	SNP	G	G	C	rs202107773	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1638C>G	p.%3D	p.G546G	ENST00000263413	11/18	86	74	11	64	64	0	C6,synonymous_variant,p.%3D,ENST00000263413,;C6,synonymous_variant,p.%3D,ENST00000337836,;C6,downstream_gene_variant,,ENST00000475349,;C6,downstream_gene_variant,,ENST00000473450,;C6,non_coding_transcript_exon_variant,,ENST00000511470,;	C	ENSG00000039537	ENST00000263413	Transcript	synonymous_variant	1903	1638	546	G	ggC/ggG	rs202107773	.	.	-1	C6	HGNC	1339	protein_coding	YES	CCDS3936.1	ENSP00000263413	CO6_HUMAN	C9JX36_HUMAN,C9JC72_HUMAN	UPI000013D401	.	.	.	11/18	.	hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGTGCCACT	byCluster|by1000G	5	ESCA
ITGA2	0	.	GRCh37	5	52370296	52370296	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2653A>G	p.Arg885Gly	p.R885G	ENST00000296585	21/30	45	23	21	41	41	0	ITGA2,missense_variant,p.Arg885Gly,ENST00000296585,;ITGA2,missense_variant,p.Arg885Gly,ENST00000510722,;ITGA2,3_prime_UTR_variant,,ENST00000509960,;ITGA2,3_prime_UTR_variant,,ENST00000513685,;ITGA2,3_prime_UTR_variant,,ENST00000503810,;ITGA2,3_prime_UTR_variant,,ENST00000509814,;	G	ENSG00000164171	ENST00000296585	Transcript	missense_variant	2796	2653	885	R/G	Aga/Gga	.	.	.	1	ITGA2	HGNC	6137	protein_coding	YES	CCDS3957.1	ENSP00000296585	ITA2_HUMAN	Q71V33_HUMAN,G3LGR5_HUMAN,F1C629_HUMAN,F1C627_HUMAN,E7ESP4_HUMAN	UPI0000169C36	.	tolerated(0.37)	benign(0.047)	21/30	.	Superfamily_domains:SSF69179,Pfam_domain:PF08441,Gene3D:2.60.40.1510,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAGAGAGAA	.	5	ESCA
SLC30A5	0	.	GRCh37	5	68396658	68396658	+	Silent	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108A>G	p.%3D	p.L36L	ENST00000396591	2/16	25	9	16	22	22	0	SLC30A5,synonymous_variant,p.%3D,ENST00000396591,;SLC30A5,synonymous_variant,p.%3D,ENST00000380860,;SLC30A5,intron_variant,,ENST00000504103,;SLC30A5,intron_variant,,ENST00000502979,;SLC30A5,upstream_gene_variant,,ENST00000507354,;	G	ENSG00000145740	ENST00000396591	Transcript	synonymous_variant	718	108	36	L	ctA/ctG	.	.	.	1	SLC30A5	HGNC	19089	protein_coding	YES	CCDS3996.1	ENSP00000379836	ZNT5_HUMAN	Q9H9X0_HUMAN,Q9BY48_HUMAN,Q9BTR6_HUMAN	UPI0000073958	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACTATGTTT	.	5	ESCA
MAP3K5	0	.	GRCh37	6	137041712	137041712	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464A>T	p.Glu155Val	p.E155V	ENST00000359015	2/30	82	63	19	46	46	0	MAP3K5,missense_variant,p.Glu155Val,ENST00000359015,;	A	ENSG00000197442	ENST00000359015	Transcript	missense_variant	825	464	155	E/V	gAg/gTg	.	.	.	-1	MAP3K5	HGNC	6857	protein_coding	YES	CCDS5179.1	ENSP00000351908	M3K5_HUMAN	A6NIA0_HUMAN	UPI000012EAD5	.	deleterious(0)	possibly_damaging(0.601)	2/30	.	hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF332	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATCTCCACC	.	5	ESCA
STXBP5	0	.	GRCh37	6	147583481	147583481	+	Missense_Mutation	SNP	G	G	A	rs367614502	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.622G>A	p.Glu208Lys	p.E208K	ENST00000321680	6/28	79	62	16	55	55	0	STXBP5,missense_variant,p.Glu208Lys,ENST00000321680,;STXBP5,missense_variant,p.Glu208Lys,ENST00000367480,;STXBP5,missense_variant,p.Glu208Lys,ENST00000546097,;STXBP5,missense_variant,p.Glu208Lys,ENST00000367481,;STXBP5,5_prime_UTR_variant,,ENST00000179882,;	A	ENSG00000164506	ENST00000321680	Transcript	missense_variant	622	622	208	E/K	Gag/Aag	rs367614502,COSM263901	.	.	1	STXBP5	HGNC	19665	protein_coding	YES	CCDS47499.1	ENSP00000321826	STXB5_HUMAN	.	UPI0000199FE0	.	tolerated(0.1)	benign(0.124)	6/28	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF22	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACGAGGGA	byCluster|by1000G	5	ESCA
THBS2	0	.	GRCh37	6	169622459	169622459	+	Missense_Mutation	SNP	G	G	A	rs138017175	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3106C>T	p.Arg1036Cys	p.R1036C	ENST00000366787	20/23	61	47	13	48	48	0	THBS2,missense_variant,p.Arg1036Cys,ENST00000366787,;XXyac-YX65C7_A.2,intron_variant,,ENST00000444188,;THBS2,non_coding_transcript_exon_variant,,ENST00000488355,;	A	ENSG00000186340	ENST00000366787	Transcript	missense_variant	3356	3106	1036	R/C	Cgc/Tgc	rs138017175	.	.	-1	THBS2	HGNC	11786	protein_coding	YES	CCDS34574.1	ENSP00000355751	TSP2_HUMAN	Q6MZL6_HUMAN,Q5RI53_HUMAN	UPI0000231C7F	.	deleterious(0)	probably_damaging(0.997)	20/23	.	PROSITE_profiles:PS51236,hmmpanther:PTHR10199:SF10,hmmpanther:PTHR10199,Pfam_domain:PF05735,Gene3D:2.60.120.200,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCGGCTGC	.	5	ESCA
KDM1B	0	.	GRCh37	6	18223402	18223402	+	3'UTR	SNP	T	T	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1179T>C	.	.	ENST00000297792	18/18	84	56	28	39	39	0	KDM1B,3_prime_UTR_variant,,ENST00000297792,;KDM1B,3_prime_UTR_variant,,ENST00000388870,;KDM1B,3_prime_UTR_variant,,ENST00000397244,;KDM1B,downstream_gene_variant,,ENST00000546309,;KDM1B,downstream_gene_variant,,ENST00000449850,;DEK,downstream_gene_variant,,ENST00000507591,;DEK,downstream_gene_variant,,ENST00000244776,;DEK,downstream_gene_variant,,ENST00000397239,;DEK,downstream_gene_variant,,ENST00000505224,;	C	ENSG00000165097	ENST00000297792	Transcript	3_prime_UTR_variant	3129	.	.	.	.	.	.	.	1	KDM1B	HGNC	21577	protein_coding	YES	CCDS34343.1	ENSP00000297792	KDM1B_HUMAN	Q08EI0_HUMAN	UPI000023739E	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAATAATAT	.	5	ESCA
DDR1	0	.	GRCh37	6	30862388	30862388	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000376575	13/20	72	48	24	41	41	0	DDR1,stop_gained,p.Gln485Ter,ENST00000376567,;DDR1,stop_gained,p.Gln503Ter,ENST00000508312,;DDR1,stop_gained,p.Gln485Ter,ENST00000376575,;DDR1,stop_gained,p.Gln485Ter,ENST00000376569,;DDR1,stop_gained,p.Gln485Ter,ENST00000418800,;DDR1,stop_gained,p.Gln14Ter,ENST00000514434,;DDR1,stop_gained,p.Gln485Ter,ENST00000376568,;DDR1,stop_gained,p.Gln485Ter,ENST00000324771,;DDR1,stop_gained,p.Gln485Ter,ENST00000513240,;DDR1,stop_gained,p.Gln485Ter,ENST00000376570,;DDR1,stop_gained,p.Gln485Ter,ENST00000452441,;DDR1,stop_gained,p.Gln485Ter,ENST00000454612,;DDR1,synonymous_variant,p.%3D,ENST00000417521,;DDR1,synonymous_variant,p.%3D,ENST00000361741,;DDR1,3_prime_UTR_variant,,ENST00000446312,;DDR1,downstream_gene_variant,,ENST00000503495,;DDR1,downstream_gene_variant,,ENST00000421124,;DDR1,downstream_gene_variant,,ENST00000504927,;DDR1,downstream_gene_variant,,ENST00000460944,;DDR1,upstream_gene_variant,,ENST00000484556,;DDR1,downstream_gene_variant,,ENST00000424544,;DDR1,downstream_gene_variant,,ENST00000515219,;DDR1,downstream_gene_variant,,ENST00000511510,;DDR1,downstream_gene_variant,,ENST00000512694,;DDR1,downstream_gene_variant,,ENST00000396342,;DDR1,downstream_gene_variant,,ENST00000428153,;DDR1,downstream_gene_variant,,ENST00000437124,;MIR4640,downstream_gene_variant,,ENST00000581824,;DDR1,non_coding_transcript_exon_variant,,ENST00000513514,;DDR1,non_coding_transcript_exon_variant,,ENST00000465966,;DDR1,downstream_gene_variant,,ENST00000508472,;DDR1,3_prime_UTR_variant,,ENST00000482873,;DDR1,downstream_gene_variant,,ENST00000513749,;DDR1,downstream_gene_variant,,ENST00000507533,;DDR1,downstream_gene_variant,,ENST00000514534,;DDR1,downstream_gene_variant,,ENST00000431373,;DDR1,downstream_gene_variant,,ENST00000485023,;DDR1,downstream_gene_variant,,ENST00000503628,;	T	ENSG00000204580	ENST00000376575	Transcript	stop_gained	1786	1453	485	Q/*	Cag/Tag	.	.	.	1	DDR1	HGNC	2730	protein_coding	YES	CCDS47396.1	ENSP00000365759	DDR1_HUMAN	E7EXB0_HUMAN,E7EX99_HUMAN,E7EVW6_HUMAN,E7EVT1_HUMAN,E7EUD5_HUMAN,E7ETX3_HUMAN,E7ETI3_HUMAN,E7ESR9_HUMAN,E7ES06_HUMAN,E7ERN0_HUMAN,E7ERI6_HUMAN,E7EQ30_HUMAN,E7EQ23_HUMAN,E7EPN2_HUMAN,E7EPH4_HUMAN,E7ENJ2_HUMAN,E7EN94_HUMAN,D6RGW5_HUMAN,D6RBU7_HUMAN,D6RB82_HUMAN,D6RB35_HUMAN,D6R9C4_HUMAN,A2ABL2_HUMAN,A2ABL0_HUMAN	UPI0000146C6D	.	.	.	13/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGTACCAGGAG	.	3	ESCA
DNAH8	0	.	GRCh37	6	38743675	38743675	+	Missense_Mutation	SNP	C	C	G	rs779850498	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1259C>G	p.Thr420Arg	p.T420R	ENST00000359357	11/91	47	43	4	28	28	0	DNAH8,missense_variant,p.Thr420Arg,ENST00000359357,;DNAH8,missense_variant,p.Thr625Arg,ENST00000327475,;DNAH8,missense_variant,p.Thr420Arg,ENST00000441566,;DNAH8,missense_variant,p.Thr637Arg,ENST00000449981,;	G	ENSG00000124721	ENST00000359357	Transcript	missense_variant	1513	1259	420	T/R	aCa/aGa	rs779850498	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	benign(0.012)	11/91	.	Pfam_domain:PF08385,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGGACAGAAT	byFrequency	3	ESCA
CD109	0	.	GRCh37	6	74446224	74446224	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626A>G	p.Gln209Arg	p.Q209R	ENST00000287097	5/33	32	28	4	22	22	0	CD109,missense_variant,p.Gln209Arg,ENST00000287097,;CD109,missense_variant,p.Gln209Arg,ENST00000437994,;CD109,missense_variant,p.Gln132Arg,ENST00000422508,;	G	ENSG00000156535	ENST00000287097	Transcript	missense_variant	738	626	209	Q/R	cAa/cGa	.	.	.	1	CD109	HGNC	21685	protein_coding	YES	CCDS4982.1	ENSP00000287097	CD109_HUMAN	Q5XUN1_HUMAN,Q5XUM8_HUMAN,Q5XUM6_HUMAN,F1C639_HUMAN	UPI000013DE92	.	tolerated(0.16)	benign(0.012)	5/33	.	Pfam_domain:PF01835,hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGTTCAAGTGA	.	3	ESCA
HOXA10	0	.	GRCh37	7	27213291	27213291	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.635G>A	p.Gly212Asp	p.G212D	ENST00000283921	1/2	38	32	6	34	34	0	HOXA10,missense_variant,p.Gly212Asp,ENST00000283921,;HOXA10,intron_variant,,ENST00000396344,;RP1-170O19.20,intron_variant,,ENST00000470747,;MIR196B,upstream_gene_variant,,ENST00000384852,;HOXA10-AS,downstream_gene_variant,,ENST00000519694,;HOXA10-AS,downstream_gene_variant,,ENST00000523790,;HOXA10-AS,downstream_gene_variant,,ENST00000519935,;RP1-170O19.20,intron_variant,,ENST00000465941,;HOXA10,upstream_gene_variant,,ENST00000519593,;HOXA10,upstream_gene_variant,,ENST00000521421,;HOXA9,upstream_gene_variant,,ENST00000489695,;HOXA10,upstream_gene_variant,,ENST00000524368,;HOXA9,upstream_gene_variant,,ENST00000497089,;HOXA9,upstream_gene_variant,,ENST00000487384,;	T	ENSG00000253293	ENST00000283921	Transcript	missense_variant	635	635	212	G/D	gGc/gAc	.	.	.	-1	HOXA10	HGNC	5100	protein_coding	YES	CCDS5410.2	ENSP00000283921	HXA10_HUMAN	.	UPI0000EE42DA	.	deleterious(0)	probably_damaging(0.995)	1/2	.	hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTAGCCAGGC	.	4	ESCA
ZNF107	0	.	GRCh37	7	64168085	64168085	+	Missense_Mutation	SNP	A	A	T	rs778005102	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1403A>T	p.Tyr468Phe	p.Y468F	ENST00000395391	4/4	37	18	18	20	20	0	ZNF107,missense_variant,p.Tyr468Phe,ENST00000344930,;ZNF107,missense_variant,p.Tyr468Phe,ENST00000395391,;ZNF107,missense_variant,p.Tyr468Phe,ENST00000423627,;ZNF107,downstream_gene_variant,,ENST00000360117,;	T	ENSG00000196247	ENST00000395391	Transcript	missense_variant	2778	1403	468	Y/F	tAt/tTt	rs778005102	.	.	1	ZNF107	HGNC	12887	protein_coding	YES	CCDS5527.1	ENSP00000378789	ZN107_HUMAN	Q9H3U2_HUMAN,C9JSF9_HUMAN	UPI000000DBC2	.	tolerated(0.1)	benign(0.258)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF121,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTATAAAT	.	5	ESCA
HEATR2	0	.	GRCh37	7	825232	825232	+	Missense_Mutation	SNP	C	C	T	rs115620965	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2510C>T	p.Ser837Leu	p.S837L	ENST00000297440	13/13	72	62	10	42	42	0	HEATR2,missense_variant,p.Ser262Leu,ENST00000403952,;HEATR2,missense_variant,p.Ser639Leu,ENST00000440747,;HEATR2,missense_variant,p.Ser837Leu,ENST00000297440,;HEATR2,intron_variant,,ENST00000313147,;HEATR2,downstream_gene_variant,,ENST00000461576,;	T	ENSG00000164818	ENST00000297440	Transcript	missense_variant	2530	2510	837	S/L	tCg/tTg	rs115620965	.	.	1	HEATR2	HGNC	26013	protein_coding	YES	CCDS34580.1	ENSP00000297440	HEAT2_HUMAN	.	UPI0000D61BE2	.	deleterious(0)	possibly_damaging(0.892)	13/13	.	hmmpanther:PTHR16216:SF2,hmmpanther:PTHR16216	T:0.0006	T:0.0023	T:0	.	T:0	T:0	T:0	T:0.0014	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCTCGGCCA	byFrequency|byCluster|by1000G	4	ESCA
COL14A1	0	.	GRCh37	8	121262859	121262859	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2606C>T	p.Pro869Leu	p.P869L	ENST00000297848	22/48	56	48	8	33	33	0	COL14A1,missense_variant,p.Pro682Leu,ENST00000434620,;COL14A1,missense_variant,p.Pro869Leu,ENST00000309791,;COL14A1,missense_variant,p.Pro774Leu,ENST00000247781,;COL14A1,missense_variant,p.Pro869Leu,ENST00000297848,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,;	T	ENSG00000187955	ENST00000297848	Transcript	missense_variant	2876	2606	869	P/L	cCt/cTt	COSM603968	.	.	1	COL14A1	HGNC	2191	protein_coding	YES	CCDS34938.1	ENSP00000297848	COEA1_HUMAN	.	UPI000046D377	.	tolerated(0.06)	benign(0.115)	22/48	.	PROSITE_profiles:PS50853,hmmpanther:PTHR22992:SF89,hmmpanther:PTHR22992,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTCCTGGTC	.	5	ESCA
ASAP1	0	.	GRCh37	8	131124422	131124422	+	Silent	SNP	C	C	T	rs149904556	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2319G>A	p.%3D	p.Q773Q	ENST00000357668	23/29	241	205	35	122	122	0	ASAP1,synonymous_variant,p.%3D,ENST00000518721,;ASAP1,synonymous_variant,p.%3D,ENST00000524124,;ASAP1,synonymous_variant,p.%3D,ENST00000357668,;ASAP1,synonymous_variant,p.%3D,ENST00000519483,;ASAP1,3_prime_UTR_variant,,ENST00000521075,;ASAP1,non_coding_transcript_exon_variant,,ENST00000520189,;ASAP1,downstream_gene_variant,,ENST00000521057,;	T	ENSG00000153317	ENST00000357668	Transcript	synonymous_variant	2347	2319	773	Q	caG/caA	rs149904556	.	.	-1	ASAP1	HGNC	2720	protein_coding	YES	CCDS6362.1	ENSP00000350297	ASAP1_HUMAN	E5RFD9_HUMAN	UPI0000351D6E	.	.	.	23/29	.	hmmpanther:PTHR23180:SF192,hmmpanther:PTHR23180	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGATCTGGTT	byCluster	4	ESCA
PHF20L1	0	.	GRCh37	8	133859007	133859007	+	3'UTR	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*839A>G	.	.	ENST00000395386	21/21	41	27	14	25	25	0	PHF20L1,3_prime_UTR_variant,,ENST00000395390,;PHF20L1,3_prime_UTR_variant,,ENST00000395386,;PHF20L1,downstream_gene_variant,,ENST00000220847,;AF230666.2,upstream_gene_variant,,ENST00000429151,;AF230666.2,upstream_gene_variant,,ENST00000608375,;PHF20L1,3_prime_UTR_variant,,ENST00000460236,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000477051,;	G	ENSG00000129292	ENST00000395386	Transcript	3_prime_UTR_variant	4192	.	.	.	.	.	.	.	1	PHF20L1	HGNC	24280	protein_coding	YES	CCDS6367.2	ENSP00000378784	P20L1_HUMAN	E5RK91_HUMAN,B3KWX5_HUMAN	UPI0000DBD7AF	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATATAGTT	.	5	ESCA
PUF60	0	.	GRCh37	8	144900169	144900169	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.680G>A	p.Arg227His	p.R227H	ENST00000526683	8/12	93	71	21	65	65	0	PUF60,missense_variant,p.Arg247His,ENST00000529999,;PUF60,missense_variant,p.Arg210His,ENST00000349157,;PUF60,missense_variant,p.Arg167His,ENST00000313352,;PUF60,missense_variant,p.Arg181His,ENST00000527197,;PUF60,missense_variant,p.Arg227His,ENST00000526683,;PUF60,missense_variant,p.Arg184His,ENST00000453551,;PUF60,missense_variant,p.Arg198His,ENST00000456095,;PUF60,missense_variant,p.Arg247His,ENST00000531897,;PUF60,missense_variant,p.Arg225His,ENST00000527744,;PUF60,missense_variant,p.Arg209His,ENST00000526459,;PUF60,intron_variant,,ENST00000532884,;SCRIB,upstream_gene_variant,,ENST00000377533,;SCRIB,upstream_gene_variant,,ENST00000356994,;PUF60,downstream_gene_variant,,ENST00000533162,;SCRIB,upstream_gene_variant,,ENST00000320476,;MIR937,upstream_gene_variant,,ENST00000401271,;PUF60,non_coding_transcript_exon_variant,,ENST00000531951,;PUF60,non_coding_transcript_exon_variant,,ENST00000524570,;PUF60,non_coding_transcript_exon_variant,,ENST00000528999,;PUF60,downstream_gene_variant,,ENST00000533362,;PUF60,non_coding_transcript_exon_variant,,ENST00000528320,;PUF60,downstream_gene_variant,,ENST00000529693,;PUF60,downstream_gene_variant,,ENST00000531995,;PUF60,downstream_gene_variant,,ENST00000526151,;PUF60,downstream_gene_variant,,ENST00000532127,;PUF60,downstream_gene_variant,,ENST00000527584,;	T	ENSG00000179950	ENST00000526683	Transcript	missense_variant	1236	680	227	R/H	cGc/cAc	.	.	.	-1	PUF60	HGNC	17042	protein_coding	YES	CCDS47934.1	ENSP00000434359	PUF60_HUMAN	.	UPI00000713CF	.	deleterious(0)	benign(0.438)	8/12	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011:SF246,hmmpanther:PTHR24011,TIGRFAM_domain:TIGR01645,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGCGGTTG	.	5	ESCA
TOX	0	.	GRCh37	8	59718253	59718253	+	3'UTR	DEL	A	A	-	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2053delT	.	.	ENST00000361421	9/9	126	86	40	47	47	0	TOX,3_prime_UTR_variant,,ENST00000361421,;	-	ENSG00000198846	ENST00000361421	Transcript	3_prime_UTR_variant	3855	.	.	.	.	.	.	.	-1	TOX	HGNC	18988	protein_coding	YES	CCDS34897.1	ENSP00000354842	TOX_HUMAN	B4DYA1_HUMAN	UPI0000070A73	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATTAGTAGTGCT	.	3	ESCA
NECAB1	0	.	GRCh37	8	91962058	91962058	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.884A>T	p.Asn295Ile	p.N295I	ENST00000417640	11/13	107	99	8	57	57	0	NECAB1,missense_variant,p.Asn44Ile,ENST00000521366,;NECAB1,missense_variant,p.Asn44Ile,ENST00000522820,;NECAB1,missense_variant,p.Asn295Ile,ENST00000417640,;	T	ENSG00000123119	ENST00000417640	Transcript	missense_variant	1221	884	295	N/I	aAt/aTt	.	.	.	1	NECAB1	HGNC	20983	protein_coding	YES	CCDS47889.1	ENSP00000387380	NECA1_HUMAN	.	UPI0000070EEA	.	deleterious(0)	possibly_damaging(0.603)	11/13	.	hmmpanther:PTHR12178:SF11,hmmpanther:PTHR12178,Pfam_domain:PF03992,Gene3D:3.30.70.900,Superfamily_domains:SSF54909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCAAATGAAT	.	3	ESCA
RUNX1T1	0	.	GRCh37	8	92972690	92972690	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1628C>T	p.Ala543Val	p.A543V	ENST00000436581	11/11	60	54	5	34	34	0	RUNX1T1,missense_variant,p.Ala543Val,ENST00000436581,;RUNX1T1,missense_variant,p.Ala532Val,ENST00000265814,;RUNX1T1,missense_variant,p.Ala505Val,ENST00000518844,;RUNX1T1,missense_variant,p.Ala532Val,ENST00000523629,;RUNX1T1,missense_variant,p.Ala495Val,ENST00000360348,;RUNX1T1,missense_variant,p.Ala495Val,ENST00000520724,;RUNX1T1,missense_variant,p.Ala505Val,ENST00000396218,;RUNX1T1,missense_variant,p.Ala495Val,ENST00000422361,;RUNX1T1,3_prime_UTR_variant,,ENST00000521751,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000521078,;	A	ENSG00000079102	ENST00000436581	Transcript	missense_variant	1639	1628	543	A/V	gCc/gTc	.	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	deleterious(0)	probably_damaging(0.961)	11/11	.	PROSITE_profiles:PS50865,hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF5,PROSITE_patterns:PS01360,Pfam_domain:PF01753,Superfamily_domains:SSF144232,Prints_domain:PR01875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	ATCGGGCTGTG	.	3	ESCA
INTS8	0	.	GRCh37	8	95844270	95844270	+	Silent	SNP	A	A	G	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.621A>G	p.%3D	p.K207K	ENST00000523731	6/27	102	66	36	42	42	0	INTS8,synonymous_variant,p.%3D,ENST00000520526,;INTS8,synonymous_variant,p.%3D,ENST00000447247,;INTS8,synonymous_variant,p.%3D,ENST00000523731,;INTS8,synonymous_variant,p.%3D,ENST00000522171,;INTS8,downstream_gene_variant,,ENST00000519457,;INTS8,downstream_gene_variant,,ENST00000519053,;INTS8,downstream_gene_variant,,ENST00000523808,;INTS8,downstream_gene_variant,,ENST00000521860,;INTS8,synonymous_variant,p.%3D,ENST00000343161,;INTS8,synonymous_variant,p.%3D,ENST00000523206,;INTS8,synonymous_variant,p.%3D,ENST00000524333,;INTS8,non_coding_transcript_exon_variant,,ENST00000523321,;	G	ENSG00000164941	ENST00000523731	Transcript	synonymous_variant	754	621	207	K	aaA/aaG	.	.	.	1	INTS8	HGNC	26048	protein_coding	YES	CCDS34925.1	ENSP00000430338	INT8_HUMAN	E5RJL5_HUMAN,B3KRB0_HUMAN	UPI000023B7D0	.	.	.	6/27	.	hmmpanther:PTHR13350,Gene3D:1.25.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAAATTAAA	.	5	ESCA
FBXO10	0	.	GRCh37	9	37518154	37518154	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2482G>A	p.Gly828Arg	p.G828R	ENST00000432825	9/11	41	29	12	41	41	0	FBXO10,missense_variant,p.Gly828Arg,ENST00000432825,;FBXO10,missense_variant,p.Gly353Arg,ENST00000541829,;RP11-613M10.8,non_coding_transcript_exon_variant,,ENST00000544475,;RP11-613M10.8,non_coding_transcript_exon_variant,,ENST00000541804,;FBXO10,downstream_gene_variant,,ENST00000543968,;FBXO10,downstream_gene_variant,,ENST00000544208,;FBXO10,3_prime_UTR_variant,,ENST00000276960,;	T	ENSG00000147912	ENST00000432825	Transcript	missense_variant	2531	2482	828	G/R	Ggg/Agg	.	.	.	-1	FBXO10	HGNC	13589	protein_coding	YES	CCDS47966.1	ENSP00000403802	FBX10_HUMAN	Q08AL4_HUMAN,F5GXN9_HUMAN	UPI00001C1EC6	.	deleterious(0)	probably_damaging(0.998)	9/11	.	hmmpanther:PTHR22990,Pfam_domain:PF05048,Gene3D:2.160.20.10,Superfamily_domains:SSF51126	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	CAGCCCGCTGC	.	3	ESCA
TRPM3	0	.	GRCh37	9	73151532	73151532	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4461C>G	p.Asp1487Glu	p.D1487E	ENST00000377110	25/25	18	8	10	9	9	0	TRPM3,missense_variant,p.Asp1359Glu,ENST00000377106,;TRPM3,missense_variant,p.Asp1349Glu,ENST00000360823,;TRPM3,missense_variant,p.Asp1349Glu,ENST00000358082,;TRPM3,missense_variant,p.Asp1359Glu,ENST00000396292,;TRPM3,missense_variant,p.Asp1336Glu,ENST00000396280,;TRPM3,missense_variant,p.Asp1514Glu,ENST00000423814,;TRPM3,missense_variant,p.Asp1346Glu,ENST00000408909,;TRPM3,missense_variant,p.Asp1491Glu,ENST00000357533,;TRPM3,missense_variant,p.Asp1487Glu,ENST00000377110,;TRPM3,missense_variant,p.Asp1346Glu,ENST00000377105,;TRPM3,missense_variant,p.Asp1346Glu,ENST00000396285,;TRPM3,intron_variant,,ENST00000377111,;	C	ENSG00000083067	ENST00000377110	Transcript	missense_variant	4705	4461	1487	D/E	gaC/gaG	.	.	.	-1	TRPM3	HGNC	17992	protein_coding	YES	CCDS43835.1	ENSP00000366314	TRPM3_HUMAN	.	UPI0001596895	.	tolerated_low_confidence(0.07)	benign(0.034)	25/25	.	hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTGAGTCCCA	.	3	ESCA
FAM47C	0	.	GRCh37	X	37029350	37029350	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2867C>T	p.Pro956Leu	p.P956L	ENST00000358047	1/1	62	19	43	33	32	1	FAM47C,missense_variant,p.Pro956Leu,ENST00000358047,;	T	ENSG00000198173	ENST00000358047	Transcript	missense_variant	2919	2867	956	P/L	cCt/cTt	.	.	.	1	FAM47C	HGNC	25301	protein_coding	YES	CCDS35227.1	ENSP00000367913	FA47C_HUMAN	.	UPI000041ABF8	.	deleterious(0)	probably_damaging(0.977)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TGAACCTTTGA	.	2	ESCA
OGT	0	.	GRCh37	X	70787359	70787359	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2599C>T	p.Arg867Cys	p.R867C	ENST00000373719	20/22	38	12	26	18	18	0	OGT,missense_variant,p.Arg857Cys,ENST00000373701,;OGT,missense_variant,p.Arg867Cys,ENST00000373719,;OGT,non_coding_transcript_exon_variant,,ENST00000474633,;OGT,non_coding_transcript_exon_variant,,ENST00000488174,;	T	ENSG00000147162	ENST00000373719	Transcript	missense_variant	2816	2599	867	R/C	Cgt/Tgt	.	.	.	1	OGT	HGNC	8127	protein_coding	YES	CCDS14414.1	ENSP00000362824	OGT1_HUMAN	C9JZL3_HUMAN	UPI0000073C9F	.	deleterious(0)	probably_damaging(0.969)	20/22	.	hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF369,Pfam_domain:PF13844,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAGCGTGTT	.	5	ESCA
PHKA1	0	.	GRCh37	X	71802435	71802435	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-L7-A56G-01A-21D-A27G-09	TCGA-L7-A56G-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3311delA	p.Glu1104GlyfsTer12	p.E1104Gfs*12	ENST00000373542	31/32	18	6	12	14	14	0	PHKA1,frameshift_variant,p.Glu1062GlyfsTer12,ENST00000373545,;PHKA1,frameshift_variant,p.Glu1091GlyfsTer12,ENST00000339490,;PHKA1,frameshift_variant,p.Glu1104GlyfsTer12,ENST00000373542,;PHKA1,frameshift_variant,p.Glu1032GlyfsTer12,ENST00000541944,;PHKA1,frameshift_variant,p.Glu1121GlyfsTer12,ENST00000373539,;	-	ENSG00000067177	ENST00000373542	Transcript	frameshift_variant	3471	3311	1104	E/X	gAg/gg	.	.	.	-1	PHKA1	HGNC	8925	protein_coding	YES	CCDS14421.1	ENSP00000362643	KPB1_HUMAN	.	UPI000013D340	.	.	.	31/32	.	hmmpanther:PTHR10749:SF4,hmmpanther:PTHR10749	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTAATCTCACCT	.	2	ESCA
PTER	0	.	GRCh37	10	16553219	16553219	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015delA	p.Ile339Ter	p.I339*	ENST00000378000	6/6	42	38	4	33	33	0	PTER,frameshift_variant,p.Ile339Ter,ENST00000298942,;PTER,frameshift_variant,p.Ile339Ter,ENST00000378000,;PTER,frameshift_variant,p.Ile339Ter,ENST00000535784,;PTER,frameshift_variant,p.Ile292Ter,ENST00000423462,;C1QL3,downstream_gene_variant,,ENST00000298943,;	-	ENSG00000165983	ENST00000378000	Transcript	frameshift_variant	1260	1014	338	L/X	ctA/ct	.	.	.	1	PTER	HGNC	9590	protein_coding	YES	CCDS7111.1	ENSP00000367239	PTER_HUMAN	.	UPI00000492E9	.	.	.	6/6	.	PROSITE_profiles:PS51347,hmmpanther:PTHR10819,Gene3D:3.20.20.140,Pfam_domain:PF02126,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GATTCTAATAGA	.	2	ESCA
RP11-85G18.6	0	.	GRCh37	10	27538827	27538827	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.256-160T>C	.	.	ENST00000574842	.	124	112	12	88	87	1	RP11-85G18.6,intron_variant,,ENST00000574842,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000284414,;LRRC37A6P,downstream_gene_variant,,ENST00000575554,;LRRC37A6P,downstream_gene_variant,,ENST00000574795,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000448648,;	C	ENSG00000262412	ENST00000574842	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RP11-85G18.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGCTCTGGA	.	4	ESCA
ARMC4	0	.	GRCh37	10	28196695	28196695	+	Missense_Mutation	SNP	C	C	T	rs376281682	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2507G>A	p.Arg836His	p.R836H	ENST00000305242	17/20	38	21	17	14	14	0	ARMC4,missense_variant,p.Arg361His,ENST00000545014,;ARMC4,missense_variant,p.Arg836His,ENST00000305242,;ARMC4,missense_variant,p.Arg528His,ENST00000537576,;RPL36AP55,downstream_gene_variant,,ENST00000454114,;	T	ENSG00000169126	ENST00000305242	Transcript	missense_variant	2600	2507	836	R/H	cGc/cAc	rs376281682	.	.	-1	ARMC4	HGNC	25583	protein_coding	YES	CCDS7157.1	ENSP00000306410	ARMC4_HUMAN	R4GN11_HUMAN,A8K906_HUMAN	UPI00001A95E1	.	tolerated(0.13)	benign(0.052)	17/20	.	hmmpanther:PTHR23315:SF67,hmmpanther:PTHR23315,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAAGCGATCA	byFrequency|byCluster	5	ESCA
AASDHPPT	0	.	GRCh37	11	105948408	105948408	+	5'UTR	SNP	C	C	T	rs752179410	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-30C>T	.	.	ENST00000278618	1/6	125	103	21	61	61	0	AASDHPPT,5_prime_UTR_variant,,ENST00000278618,;KBTBD3,5_prime_UTR_variant,,ENST00000531837,;AASDHPPT,intron_variant,,ENST00000524411,;AASDHPPT,intron_variant,,ENST00000533423,;KBTBD3,upstream_gene_variant,,ENST00000526793,;KBTBD3,upstream_gene_variant,,ENST00000534815,;KBTBD3,upstream_gene_variant,,ENST00000532662,;AASDHPPT,5_prime_UTR_variant,,ENST00000525660,;KBTBD3,upstream_gene_variant,,ENST00000526805,;KBTBD3,upstream_gene_variant,,ENST00000528483,;	T	ENSG00000149313	ENST00000278618	Transcript	5_prime_UTR_variant	193	.	.	.	.	rs752179410	.	.	1	AASDHPPT	HGNC	14235	protein_coding	YES	CCDS31664.1	ENSP00000278618	ADPPT_HUMAN	E9PNF3_HUMAN,E9PLW6_HUMAN	UPI0000034CAD	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCCGAGAT	byFrequency	4	ESCA
GRIK4	0	.	GRCh37	11	120831733	120831733	+	Missense_Mutation	SNP	G	G	A	rs139636929	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1990G>A	p.Ala664Thr	p.A664T	ENST00000527524	17/21	35	25	9	50	50	0	GRIK4,missense_variant,p.Ala664Thr,ENST00000438375,;GRIK4,missense_variant,p.Ala664Thr,ENST00000527524,;GRIK4,non_coding_transcript_exon_variant,,ENST00000533291,;	A	ENSG00000149403	ENST00000527524	Transcript	missense_variant	2277	1990	664	A/T	Gcc/Acc	rs139636929	.	.	1	GRIK4	HGNC	4582	protein_coding	YES	CCDS8433.1	ENSP00000435648	GRIK4_HUMAN	.	UPI000013DB8D	.	tolerated(0.14)	benign(0.007)	17/21	.	hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Pfam_domain:PF00060,Gene3D:1.10.287.70,SMART_domains:SM00079,Superfamily_domains:SSF53850	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0014	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCGCCATT	byCluster|by1000G	5	ESCA
ARL14EP	0	.	GRCh37	11	30358340	30358340	+	Nonstop_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.781T>A	p.Ter261LysextTer15	p.*261Kext*15	ENST00000282032	4/4	30	17	13	27	27	0	ARL14EP,stop_lost,p.Ter261LysextTer15,ENST00000282032,;ARL14EP,downstream_gene_variant,,ENST00000530909,;ARL14EP,downstream_gene_variant,,ENST00000533457,;	A	ENSG00000152219	ENST00000282032	Transcript	stop_lost	996	781	261	*/K	Taa/Aaa	.	.	.	1	ARL14EP	HGNC	26798	protein_coding	YES	CCDS7869.1	ENSP00000282032	AL14E_HUMAN	E9PRK7_HUMAN	UPI000000DC5B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGATAATCT	.	2	ESCA
AMBRA1	0	.	GRCh37	11	46563800	46563800	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1497T>C	p.%3D	p.P499P	ENST00000314845	8/19	42	32	10	23	23	0	AMBRA1,synonymous_variant,p.%3D,ENST00000534300,;AMBRA1,synonymous_variant,p.%3D,ENST00000533727,;AMBRA1,synonymous_variant,p.%3D,ENST00000426438,;AMBRA1,synonymous_variant,p.%3D,ENST00000298834,;AMBRA1,synonymous_variant,p.%3D,ENST00000314845,;AMBRA1,synonymous_variant,p.%3D,ENST00000528950,;AMBRA1,synonymous_variant,p.%3D,ENST00000458649,;AMBRA1,downstream_gene_variant,,ENST00000524783,;AMBRA1,downstream_gene_variant,,ENST00000531542,;	G	ENSG00000110497	ENST00000314845	Transcript	synonymous_variant	1857	1497	499	P	ccT/ccC	.	.	.	-1	AMBRA1	HGNC	25990	protein_coding	YES	CCDS31475.1	ENSP00000318313	AMRA1_HUMAN	E9PL55_HUMAN	UPI0000237851	.	.	.	8/19	.	hmmpanther:PTHR22874:SF1,hmmpanther:PTHR22874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTTAGGTGT	.	5	ESCA
MS4A4E	0	.	GRCh37	11	59997541	59997541	+	5'Flank	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000425663	.	40	22	18	26	26	0	MS4A4E,5_prime_UTR_variant,,ENST00000427611,;MS4A4E,upstream_gene_variant,,ENST00000398984,;MS4A4E,upstream_gene_variant,,ENST00000528394,;MS4A4E,upstream_gene_variant,,ENST00000526086,;MS4A4E,upstream_gene_variant,,ENST00000398986,;MS4A4E,upstream_gene_variant,,ENST00000425663,;MS4A4E,5_prime_UTR_variant,,ENST00000532442,;MS4A4E,upstream_gene_variant,,ENST00000526153,;	T	ENSG00000214787	ENST00000425663	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	13	-1	MS4A4E	HGNC	14284	protein_coding	YES	.	ENSP00000389556	M4A4E_HUMAN	.	UPI000173AA13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGGTGCT	.	5	ESCA
DAGLA	0	.	GRCh37	11	61502404	61502404	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058C>T	p.Ala353Val	p.A353V	ENST00000257215	10/20	70	54	15	58	58	0	DAGLA,missense_variant,p.Ala353Val,ENST00000257215,;DAGLA,3_prime_UTR_variant,,ENST00000540717,;	T	ENSG00000134780	ENST00000257215	Transcript	missense_variant	1174	1058	353	A/V	gCc/gTc	.	.	.	1	DAGLA	HGNC	1165	protein_coding	YES	CCDS31578.1	ENSP00000257215	DGLA_HUMAN	.	UPI00001678B3	.	deleterious(0.01)	probably_damaging(0.989)	10/20	.	hmmpanther:PTHR21493,hmmpanther:PTHR21493:SF87,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGCCATCC	.	5	ESCA
GANAB	0	.	GRCh37	11	62397743	62397743	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1585G>T	p.Ala529Ser	p.A529S	ENST00000346178	14/25	70	57	13	38	38	0	GANAB,missense_variant,p.Ala507Ser,ENST00000356638,;GANAB,missense_variant,p.Ala529Ser,ENST00000346178,;GANAB,missense_variant,p.Ala415Ser,ENST00000534779,;GANAB,missense_variant,p.Ala410Ser,ENST00000540933,;GANAB,downstream_gene_variant,,ENST00000525994,;GANAB,downstream_gene_variant,,ENST00000534422,;GANAB,downstream_gene_variant,,ENST00000534419,;GANAB,3_prime_UTR_variant,,ENST00000532402,;GANAB,downstream_gene_variant,,ENST00000529737,;GANAB,downstream_gene_variant,,ENST00000526210,;GANAB,downstream_gene_variant,,ENST00000526392,;GANAB,upstream_gene_variant,,ENST00000528503,;GANAB,downstream_gene_variant,,ENST00000534613,;GANAB,downstream_gene_variant,,ENST00000526732,;GANAB,downstream_gene_variant,,ENST00000524437,;GANAB,upstream_gene_variant,,ENST00000531563,;	A	ENSG00000089597	ENST00000346178	Transcript	missense_variant	1601	1585	529	A/S	Gct/Tct	.	.	.	-1	GANAB	HGNC	4138	protein_coding	YES	CCDS41656.1	ENSP00000340466	GANAB_HUMAN	.	UPI0000052BE8	.	tolerated(1)	benign(0.009)	14/25	.	hmmpanther:PTHR22762:SF51,hmmpanther:PTHR22762,Pfam_domain:PF01055,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAGCTGAGC	.	5	ESCA
CCDC88B	0	.	GRCh37	11	64109782	64109782	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838C>A	p.Leu280Met	p.L280M	ENST00000356786	9/27	38	34	4	34	34	0	CCDC88B,missense_variant,p.Leu280Met,ENST00000356786,;CCDC88B,upstream_gene_variant,,ENST00000301897,;CCDC88B,non_coding_transcript_exon_variant,,ENST00000463837,;CCDC88B,non_coding_transcript_exon_variant,,ENST00000494080,;CCDC88B,upstream_gene_variant,,ENST00000494566,;CCDC88B,upstream_gene_variant,,ENST00000492980,;	A	ENSG00000168071	ENST00000356786	Transcript	missense_variant	882	838	280	L/M	Ctg/Atg	.	.	.	1	CCDC88B	HGNC	26757	protein_coding	YES	CCDS8072.2	ENSP00000349238	CC88B_HUMAN	.	UPI00001FAAA6	.	tolerated(0.21)	benign(0.238)	9/27	.	Coiled-coils_(Ncoils):Coil,Pfam_domain:PF05622,hmmpanther:PTHR18947:SF29,hmmpanther:PTHR18947	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGAGCTGCTG	.	4	ESCA
KCTD21	0	.	GRCh37	11	77885236	77885236	+	Missense_Mutation	SNP	G	G	A	rs370613583	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365C>T	p.Thr122Met	p.T122M	ENST00000340067	2/2	43	35	8	27	27	0	KCTD21,missense_variant,p.Thr122Met,ENST00000525447,;KCTD21,missense_variant,p.Thr122Met,ENST00000340067,;KCTD21,missense_variant,p.Thr122Met,ENST00000526208,;KCTD21,downstream_gene_variant,,ENST00000530018,;KCTD21,downstream_gene_variant,,ENST00000528776,;KCTD21,downstream_gene_variant,,ENST00000529350,;KCTD21-AS1,non_coding_transcript_exon_variant,,ENST00000600795,;KCTD21-AS1,downstream_gene_variant,,ENST00000530261,;KCTD21-AS1,downstream_gene_variant,,ENST00000528468,;KCTD21-AS1,downstream_gene_variant,,ENST00000523626,;	A	ENSG00000188997	ENST00000340067	Transcript	missense_variant	644	365	122	T/M	aCg/aTg	rs370613583,COSM932252	.	.	-1	KCTD21	HGNC	27452	protein_coding	YES	CCDS31645.1	ENSP00000339340	KCD21_HUMAN	E9PRT1_HUMAN,E9PMS5_HUMAN,E9PM10_HUMAN,E9PK99_HUMAN,E9PJJ5_HUMAN	UPI000016193F	.	tolerated(0.19)	benign(0.001)	2/2	.	hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF57	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACCGTCTGC	byFrequency|byCluster	5	ESCA
OR10A6	0	.	GRCh37	11	7949463	7949463	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.747C>G	p.%3D	p.T249T	ENST00000309838	1/1	51	40	11	51	51	0	OR10A6,synonymous_variant,p.%3D,ENST00000309838,;	C	ENSG00000175393	ENST00000309838	Transcript	synonymous_variant	747	747	249	T	acC/acG	.	.	.	-1	OR10A6	HGNC	15132	protein_coding	YES	CCDS31420.1	ENSP00000312470	O10A6_HUMAN	.	UPI0000041DF4	.	.	.	1/1	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26453:SF30,hmmpanther:PTHR26453,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAGGGTCAC	.	5	ESCA
PRCP	0	.	GRCh37	11	82611294	82611294	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.151C>T	p.Leu51Phe	p.L51F	ENST00000393399	1/10	143	122	21	62	62	0	PRCP,missense_variant,p.Leu51Phe,ENST00000393399,;PRCP,missense_variant,p.Leu51Phe,ENST00000313010,;PRCP,intron_variant,,ENST00000529671,;PRCP,intron_variant,,ENST00000531128,;PRCP,intron_variant,,ENST00000532809,;PRCP,intron_variant,,ENST00000528082,;PRCP,intron_variant,,ENST00000533126,;PRCP,intron_variant,,ENST00000534631,;C11orf82,intron_variant,,ENST00000532277,;PRCP,intron_variant,,ENST00000535099,;PRCP,intron_variant,,ENST00000531801,;PRCP,intron_variant,,ENST00000534396,;PRCP,intron_variant,,ENST00000527444,;C11orf82,upstream_gene_variant,,ENST00000525361,;C11orf82,upstream_gene_variant,,ENST00000532764,;C11orf82,upstream_gene_variant,,ENST00000525388,;C11orf82,upstream_gene_variant,,ENST00000532589,;C11orf82,upstream_gene_variant,,ENST00000430323,;C11orf82,upstream_gene_variant,,ENST00000524921,;C11orf82,upstream_gene_variant,,ENST00000528759,;C11orf82,upstream_gene_variant,,ENST00000533655,;C11orf82,upstream_gene_variant,,ENST00000528189,;	A	ENSG00000137509	ENST00000393399	Transcript	missense_variant	179	151	51	L/F	Ctc/Ttc	.	.	.	-1	PRCP	HGNC	9344	protein_coding	YES	CCDS41695.1	ENSP00000377055	PCP_HUMAN	E9PR42_HUMAN,E9PQN3_HUMAN,E9PQB5_HUMAN,E9PLY4_HUMAN,E9PL85_HUMAN,E9PL49_HUMAN,E9PKN6_HUMAN,E9PIG4_HUMAN,B7Z7Q6_HUMAN,B3KR26_HUMAN	UPI00001FB052	.	tolerated_low_confidence(0.47)	benign(0.003)	1/10	.	hmmpanther:PTHR11010:SF11,hmmpanther:PTHR11010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAGAGAACCG	.	4	ESCA
PTPRO	0	.	GRCh37	12	15710404	15710404	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2574T>C	p.%3D	p.G858G	ENST00000281171	16/27	66	45	20	37	37	0	PTPRO,synonymous_variant,p.%3D,ENST00000348962,;PTPRO,synonymous_variant,p.%3D,ENST00000281171,;PTPRO,synonymous_variant,p.%3D,ENST00000544244,;PTPRO,synonymous_variant,p.%3D,ENST00000445537,;PTPRO,synonymous_variant,p.%3D,ENST00000542557,;PTPRO,synonymous_variant,p.%3D,ENST00000442921,;PTPRO,missense_variant,p.Val81Ala,ENST00000535311,;	C	ENSG00000151490	ENST00000281171	Transcript	synonymous_variant	2904	2574	858	G	ggT/ggC	.	.	.	1	PTPRO	HGNC	9678	protein_coding	YES	CCDS8675.1	ENSP00000281171	PTPRO_HUMAN	B4DS16_HUMAN	UPI000013DC62	.	.	.	16/27	.	hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF251	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGTACATT	.	5	ESCA
SLCO1B1	0	.	GRCh37	12	21349897	21349897	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.745C>T	p.Pro249Ser	p.P249S	ENST00000256958	8/15	99	59	40	72	72	0	SLCO1B1,missense_variant,p.Pro249Ser,ENST00000256958,;	T	ENSG00000134538	ENST00000256958	Transcript	missense_variant	841	745	249	P/S	Cct/Tct	.	.	.	1	SLCO1B1	HGNC	10959	protein_coding	YES	CCDS8685.1	ENSP00000256958	SO1B1_HUMAN	K4P403_HUMAN	UPI0000043BED	.	deleterious(0.02)	probably_damaging(0.941)	8/15	.	PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF82,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAACTCCTACT	.	5	ESCA
ADAMTS20	0	.	GRCh37	12	43771250	43771250	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4913C>T	p.Pro1638Leu	p.P1638L	ENST00000389420	32/39	49	43	6	42	42	0	ADAMTS20,missense_variant,p.Pro1638Leu,ENST00000389420,;	A	ENSG00000173157	ENST00000389420	Transcript	missense_variant	4913	4913	1638	P/L	cCt/cTt	COSM188317	.	.	-1	ADAMTS20	HGNC	17178	protein_coding	YES	CCDS31778.2	ENSP00000374071	ATS20_HUMAN	.	UPI00004565F4	.	deleterious(0.04)	possibly_damaging(0.86)	32/39	.	hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACAGGGCAT	.	4	ESCA
KCNA1	0	.	GRCh37	12	5024612	5024612	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2580G>T	.	.	ENST00000382545	2/2	34	27	6	28	28	0	KCNA1,3_prime_UTR_variant,,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	T	ENSG00000111262	ENST00000382545	Transcript	3_prime_UTR_variant	5175	.	.	.	.	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTCGATTAA	.	5	ESCA
MICU2	0	.	GRCh37	13	22113447	22113447	+	Missense_Mutation	SNP	C	C	T	rs140786216	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460G>A	p.Asp154Asn	p.D154N	ENST00000382374	4/12	23	17	5	24	24	0	MICU2,missense_variant,p.Asp154Asn,ENST00000468222,;MICU2,missense_variant,p.Asp154Asn,ENST00000382374,;MICU2,non_coding_transcript_exon_variant,,ENST00000476895,;MICU2,non_coding_transcript_exon_variant,,ENST00000469058,;	T	ENSG00000165487	ENST00000382374	Transcript	missense_variant	526	460	154	D/N	Gat/Aat	rs140786216	.	.	-1	MICU2	HGNC	31830	protein_coding	YES	CCDS9297.1	ENSP00000371811	MICU2_HUMAN	.	UPI0000035DB8	.	deleterious(0)	probably_damaging(1)	4/12	.	hmmpanther:PTHR12294,hmmpanther:PTHR12294:SF3,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATCGCCAA	byCluster	5	ESCA
PPP1R2P4	0	.	GRCh37	13	47011854	47011854	+	RNA	SNP	T	T	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.472A>T	.	.	ENST00000535073	1/15	74	56	17	45	45	0	KIAA0226L,5_prime_UTR_variant,,ENST00000409879,;PPP1R2P4,non_coding_transcript_exon_variant,,ENST00000535073,;PPP1R2P4,non_coding_transcript_exon_variant,,ENST00000424051,;	A	ENSG00000241353	ENST00000535073	Transcript	non_coding_transcript_exon_variant	472	.	.	.	.	.	.	.	-1	PPP1R2P4	HGNC	16319	processed_pseudogene	YES	.	.	.	.	.	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTTTCTAT	.	5	ESCA
DYNC1H1	0	.	GRCh37	14	102460527	102460527	+	Missense_Mutation	SNP	G	G	T	rs765669418	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3022G>T	p.Val1008Leu	p.V1008L	ENST00000360184	12/78	64	37	27	59	59	0	DYNC1H1,missense_variant,p.Val1008Leu,ENST00000360184,;	T	ENSG00000197102	ENST00000360184	Transcript	missense_variant	3186	3022	1008	V/L	Gta/Tta	rs765669418	.	.	1	DYNC1H1	HGNC	2961	protein_coding	YES	CCDS9966.1	ENSP00000348965	DYHC1_HUMAN	Q92862_HUMAN,B4DSR6_HUMAN	UPI00001B515A	.	.	benign(0.002)	12/78	.	hmmpanther:PTHR10676:SF28,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGTGTACAT	.	5	ESCA
OR5AU1	0	.	GRCh37	14	21623754	21623754	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431C>T	p.Ser144Phe	p.S144F	ENST00000304418	1/1	39	36	3	30	30	0	OR5AU1,missense_variant,p.Ser144Phe,ENST00000304418,;	A	ENSG00000169327	ENST00000304418	Transcript	missense_variant	469	431	144	S/F	tCt/tTt	.	.	.	-1	OR5AU1	HGNC	15362	protein_coding	YES	CCDS32042.1	ENSP00000302057	O5AU1_HUMAN	.	UPI000015F240	.	deleterious(0)	possibly_damaging(0.754)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF186,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATAAGAGATC	.	2	ESCA
MDGA2	0	.	GRCh37	14	47351393	47351393	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2270T>A	p.Ile757Asn	p.I757N	ENST00000439988	11/17	50	35	15	40	40	0	MDGA2,missense_variant,p.Ile757Asn,ENST00000439988,;MDGA2,missense_variant,p.Ile688Asn,ENST00000399232,;MDGA2,missense_variant,p.Ile459Asn,ENST00000357362,;MDGA2,missense_variant,p.Ile459Asn,ENST00000426342,;MDGA2,upstream_gene_variant,,ENST00000399222,;MDGA2,3_prime_UTR_variant,,ENST00000557238,;MDGA2,non_coding_transcript_exon_variant,,ENST00000557516,;MDGA2,non_coding_transcript_exon_variant,,ENST00000555521,;	T	ENSG00000272781	ENST00000439988	Transcript	missense_variant	2270	2270	757	I/N	aTt/aAt	.	.	.	-1	MDGA2	Uniprot_gn	19835	protein_coding	YES	.	ENSP00000400011	MDGA2_HUMAN	F8WE89_HUMAN	UPI0001DD21C1	.	deleterious(0)	probably_damaging(0.999)	11/17	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTAATCTCC	.	5	ESCA
RTN1	0	.	GRCh37	14	60193708	60193708	+	Missense_Mutation	SNP	G	G	A	rs765134472	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1694C>T	p.Ala565Val	p.A565V	ENST00000267484	3/9	66	37	28	53	53	0	RTN1,missense_variant,p.Ala565Val,ENST00000267484,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,;	A	ENSG00000139970	ENST00000267484	Transcript	missense_variant	2030	1694	565	A/V	gCg/gTg	rs765134472,COSM698227	.	.	-1	RTN1	HGNC	10467	protein_coding	YES	CCDS9740.1	ENSP00000267484	RTN1_HUMAN	Q2NKQ5_HUMAN,Q2L7A7_HUMAN	UPI00001352DA	.	tolerated(0.54)	benign(0)	3/9	.	hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGCAGGA	byFrequency	5	ESCA
PRKCH	0	.	GRCh37	14	61788845	61788845	+	Missense_Mutation	SNP	A	A	G	rs371540089	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26A>G	p.Asn9Ser	p.N9S	ENST00000332981	1/14	34	18	15	24	24	0	PRKCH,missense_variant,p.Asn9Ser,ENST00000557294,;PRKCH,missense_variant,p.Asn9Ser,ENST00000332981,;PRKCH,intron_variant,,ENST00000556778,;PRKCH,intron_variant,,ENST00000555906,;PRKCH,intron_variant,,ENST00000555542,;PRKCH,intron_variant,,ENST00000555185,;PRKCH,upstream_gene_variant,,ENST00000553830,;PRKCH,upstream_gene_variant,,ENST00000555082,;RP11-902B17.1,intron_variant,,ENST00000500036,;RP11-902B17.1,intron_variant,,ENST00000554086,;PRKCH,upstream_gene_variant,,ENST00000552875,;	G	ENSG00000027075	ENST00000332981	Transcript	missense_variant	411	26	9	N/S	aAt/aGt	rs371540089	.	.	1	PRKCH	HGNC	9403	protein_coding	YES	CCDS9752.1	ENSP00000329127	KPCL_HUMAN	G3V5U5_HUMAN,G3V5F8_HUMAN,G3V520_HUMAN,G3V4X4_HUMAN,G3V4Q9_HUMAN,G3V4Q6_HUMAN,G3V4L3_HUMAN,G3V4H0_HUMAN,G3V3E7_HUMAN,G3V304_HUMAN,B4DV01_HUMAN,B4DJN5_HUMAN	UPI0000073BBF	.	tolerated(0.52)	benign(0.013)	1/14	.	hmmpanther:PTHR24357:SF51,hmmpanther:PTHR24357,Gene3D:2.60.40.150,PIRSF_domain:PIRSF000551,PIRSF_domain:PIRSF501107,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	G:0.0005	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCAATGGCT	byCluster	5	ESCA
GPHN	0	.	GRCh37	14	66974716	66974716	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-530T>C	.	.	ENST00000478722	1/23	139	132	7	81	81	0	GPHN,5_prime_UTR_variant,,ENST00000315266,;GPHN,5_prime_UTR_variant,,ENST00000478722,;GPHN,upstream_gene_variant,,ENST00000459628,;GPHN,upstream_gene_variant,,ENST00000543237,;GPHN,upstream_gene_variant,,ENST00000305960,;RP11-72M17.1,intron_variant,,ENST00000556874,;GPHN,upstream_gene_variant,,ENST00000556020,;GPHN,upstream_gene_variant,,ENST00000555668,;GPHN,upstream_gene_variant,,ENST00000556633,;GPHN,upstream_gene_variant,,ENST00000557654,;GPHN,upstream_gene_variant,,ENST00000553936,;	C	ENSG00000171723	ENST00000478722	Transcript	5_prime_UTR_variant	592	.	.	.	.	.	.	.	1	GPHN	HGNC	15465	protein_coding	YES	CCDS9777.1	ENSP00000417901	GEPH_HUMAN	.	UPI0000072592	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTCCTACTCA	.	2	ESCA
DIO2	0	.	GRCh37	14	80677773	80677773	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43C>A	p.Leu15Met	p.L15M	ENST00000555750	1/3	45	32	12	23	23	0	DIO2,missense_variant,p.Leu15Met,ENST00000557125,;DIO2,missense_variant,p.Leu15Met,ENST00000557010,;DIO2,missense_variant,p.Leu15Met,ENST00000554188,;DIO2,missense_variant,p.Leu15Met,ENST00000438257,;DIO2,missense_variant,p.Leu15Met,ENST00000555750,;DIO2,missense_variant,p.Leu15Met,ENST00000422005,;DIO2,downstream_gene_variant,,ENST00000553594,;DIO2,downstream_gene_variant,,ENST00000553968,;DIO2,upstream_gene_variant,,ENST00000556811,;DIO2-AS1,non_coding_transcript_exon_variant,,ENST00000553979,;DIO2,upstream_gene_variant,,ENST00000555844,;	T	ENSG00000211448	ENST00000555750	Transcript	missense_variant	71	43	15	L/M	Ctg/Atg	COSM3815425,COSM3815424	.	.	-1	DIO2	HGNC	2884	protein_coding	YES	CCDS55934.1	ENSP00000450980	.	Q9C0K2_HUMAN,G3V3A8_HUMAN	UPI000046D384	.	deleterious(0.02)	probably_damaging(0.999)	1/3	.	hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF3,Pfam_domain:PF00837	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCAGAATTT	.	5	ESCA
RPAP1	0	.	GRCh37	15	41829177	41829177	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147G>A	p.%3D	p.P49P	ENST00000304330	2/25	28	24	4	18	18	0	RPAP1,synonymous_variant,p.%3D,ENST00000566863,;RPAP1,synonymous_variant,p.%3D,ENST00000561603,;RPAP1,synonymous_variant,p.%3D,ENST00000567866,;RPAP1,synonymous_variant,p.%3D,ENST00000304330,;RPAP1,upstream_gene_variant,,ENST00000568413,;RPAP1,synonymous_variant,p.%3D,ENST00000562303,;RPAP1,non_coding_transcript_exon_variant,,ENST00000569829,;RPAP1,upstream_gene_variant,,ENST00000563293,;	T	ENSG00000103932	ENST00000304330	Transcript	synonymous_variant	264	147	49	P	ccG/ccA	COSM1516973	.	.	-1	RPAP1	HGNC	24567	protein_coding	YES	CCDS10079.1	ENSP00000306123	RPAP1_HUMAN	H3BPY8_HUMAN,H3BPM3_HUMAN	UPI000013D465	.	.	.	2/25	.	hmmpanther:PTHR21483:SF18,hmmpanther:PTHR21483	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGAGCGGAGG	.	4	ESCA
DPP8	0	.	GRCh37	15	65738879	65738879	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*343G>A	.	.	ENST00000341861	20/20	22	15	6	20	20	0	DPP8,3_prime_UTR_variant,,ENST00000341861,;DPP8,downstream_gene_variant,,ENST00000358939,;DPP8,downstream_gene_variant,,ENST00000321147,;DPP8,downstream_gene_variant,,ENST00000559233,;DPP8,downstream_gene_variant,,ENST00000558786,;DPP8,downstream_gene_variant,,ENST00000321118,;DPP8,downstream_gene_variant,,ENST00000300141,;DPP8,downstream_gene_variant,,ENST00000339244,;DPP8,downstream_gene_variant,,ENST00000560048,;DPP8,downstream_gene_variant,,ENST00000395652,;	T	ENSG00000074603	ENST00000341861	Transcript	3_prime_UTR_variant	4621	.	.	.	.	.	.	.	-1	DPP8	HGNC	16490	protein_coding	YES	CCDS10207.1	ENSP00000339208	DPP8_HUMAN	H0YN53_HUMAN,H0YMV1_HUMAN	UPI00001BFAFE	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATACACTAA	.	5	ESCA
SIN3A	0	.	GRCh37	15	75668064	75668064	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3533A>G	p.Tyr1178Cys	p.Y1178C	ENST00000394947	20/21	48	41	7	32	32	0	SIN3A,missense_variant,p.Tyr1178Cys,ENST00000394949,;SIN3A,missense_variant,p.Tyr1178Cys,ENST00000394947,;SIN3A,missense_variant,p.Tyr1178Cys,ENST00000360439,;SIN3A,non_coding_transcript_exon_variant,,ENST00000566640,;SIN3A,downstream_gene_variant,,ENST00000570124,;	C	ENSG00000169375	ENST00000394947	Transcript	missense_variant	3848	3533	1178	Y/C	tAt/tGt	.	.	.	-1	SIN3A	HGNC	19353	protein_coding	YES	CCDS10279.1	ENSP00000378402	SIN3A_HUMAN	H3BT34_HUMAN,H3BQ88_HUMAN,H3BQ76_HUMAN,H3BP90_HUMAN,H3BNZ3_HUMAN,H3BNA0_HUMAN	UPI000013EAD4	.	deleterious(0)	probably_damaging(0.968)	20/21	.	hmmpanther:PTHR12346,hmmpanther:PTHR12346:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACATACACC	.	5	ESCA
SMG1	0	.	GRCh37	16	18840639	18840639	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9572A>T	p.Gln3191Leu	p.Q3191L	ENST00000446231	54/63	37	34	3	14	14	0	SMG1,missense_variant,p.Gln3191Leu,ENST00000389467,;SMG1,missense_variant,p.Gln3081Leu,ENST00000565324,;SMG1,missense_variant,p.Gln3191Leu,ENST00000446231,;	A	ENSG00000157106	ENST00000446231	Transcript	missense_variant	9985	9572	3191	Q/L	cAg/cTg	.	.	.	-1	SMG1	HGNC	30045	protein_coding	YES	CCDS45430.1	ENSP00000402515	SMG1_HUMAN	H3BPS6_HUMAN	UPI00004F8E22	.	deleterious(0.04)	possibly_damaging(0.728)	54/63	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF59	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCGCTGCAGG	.	2	ESCA
COQ7	0	.	GRCh37	16	19080091	19080091	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73+1032T>C	.	.	ENST00000321998	.	40	29	11	26	26	0	COQ7,5_prime_UTR_variant,,ENST00000569127,;COQ7,intron_variant,,ENST00000544894,;COQ7,intron_variant,,ENST00000566110,;COQ7,intron_variant,,ENST00000321998,;COQ7,intron_variant,,ENST00000568985,;COQ7,intron_variant,,ENST00000561858,;TMC7,downstream_gene_variant,,ENST00000421369,;RP11-626G11.1,downstream_gene_variant,,ENST00000565802,;RP11-626G11.5,upstream_gene_variant,,ENST00000568971,;RP11-626G11.5,upstream_gene_variant,,ENST00000576433,;RP11-626G11.5,upstream_gene_variant,,ENST00000567047,;RP11-626G11.5,upstream_gene_variant,,ENST00000571934,;COQ7,intron_variant,,ENST00000564746,;COQ7,intron_variant,,ENST00000566049,;COQ7,intron_variant,,ENST00000569312,;	C	ENSG00000167186	ENST00000321998	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	COQ7	HGNC	2244	protein_coding	YES	CCDS10574.1	ENSP00000322316	COQ7_HUMAN	H3BTN8_HUMAN,H3BSZ3_HUMAN	UPI000006D56A	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATTACTAG	.	5	ESCA
UBFD1	0	.	GRCh37	16	23584907	23584907	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2996C>T	.	.	ENST00000395878	7/7	35	18	17	27	27	0	UBFD1,3_prime_UTR_variant,,ENST00000567212,;UBFD1,3_prime_UTR_variant,,ENST00000395878,;UBFD1,downstream_gene_variant,,ENST00000219638,;CTD-2196E14.6,downstream_gene_variant,,ENST00000568262,;UBFD1,downstream_gene_variant,,ENST00000564106,;UBFD1,downstream_gene_variant,,ENST00000563366,;UBFD1,downstream_gene_variant,,ENST00000565634,;UBFD1,downstream_gene_variant,,ENST00000566136,;	T	ENSG00000103353	ENST00000395878	Transcript	3_prime_UTR_variant	4307	.	.	.	.	.	.	.	1	UBFD1	HGNC	30565	protein_coding	YES	CCDS10613.2	ENSP00000379217	UBFD1_HUMAN	H3BRL3_HUMAN,B3KW52_HUMAN	UPI00001FF0A3	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGCTAAGG	.	5	ESCA
C16orf54	0	.	GRCh37	16	29756101	29756101	+	Missense_Mutation	SNP	G	G	A	rs200439714	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172C>T	p.Arg58Cys	p.R58C	ENST00000329410	2/2	35	26	8	35	35	0	C16orf54,missense_variant,p.Arg58Cys,ENST00000329410,;AC009133.17,upstream_gene_variant,,ENST00000565600,;	A	ENSG00000185905	ENST00000329410	Transcript	missense_variant	268	172	58	R/C	Cgc/Tgc	rs200439714	.	.	-1	C16orf54	HGNC	26649	protein_coding	YES	CCDS10652.1	ENSP00000327506	CP054_HUMAN	.	UPI0000141B48	.	deleterious_low_confidence(0)	probably_damaging(0.942)	2/2	.	.	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGCGGAACA	byFrequency|byCluster|by1000G	5	ESCA
SRCAP	0	.	GRCh37	16	30745119	30745119	+	Missense_Mutation	SNP	G	G	C	rs762723574	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6494G>C	p.Arg2165Thr	p.R2165T	ENST00000262518	29/34	49	28	20	30	30	0	SRCAP,missense_variant,p.Arg2165Thr,ENST00000262518,;SRCAP,missense_variant,p.Arg2007Thr,ENST00000344771,;SRCAP,missense_variant,p.Arg2103Thr,ENST00000395059,;SRCAP,missense_variant,p.Arg1988Thr,ENST00000380361,;SRCAP,upstream_gene_variant,,ENST00000474008,;	C	ENSG00000080603	ENST00000262518	Transcript	missense_variant	6879	6494	2165	R/T	aGg/aCg	rs762723574	.	.	1	SRCAP	HGNC	16974	protein_coding	YES	CCDS10689.2	ENSP00000262518	SRCAP_HUMAN	G1UI29_HUMAN,C9J4U4_HUMAN	UPI000059D368	.	.	possibly_damaging(0.766)	29/34	.	PROSITE_profiles:PS51194,hmmpanther:PTHR10799:SF581,hmmpanther:PTHR10799,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATAGGTATT	byFrequency	5	ESCA
SLC6A10P	0	.	GRCh37	16	32890602	32890602	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3197G>T	.	.	ENST00000330048	7/9	115	94	20	97	97	0	SLC6A10P,non_coding_transcript_exon_variant,,ENST00000330048,;SLC6A10P,downstream_gene_variant,,ENST00000561837,;SLC6A10P,non_coding_transcript_exon_variant,,ENST00000431994,;	A	ENSG00000214617	ENST00000330048	Transcript	non_coding_transcript_exon_variant	3197	.	.	.	.	.	.	.	-1	SLC6A10P	HGNC	11043	processed_transcript	YES	.	.	.	.	.	.	.	.	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACCACGGG	.	5	ESCA
CREBBP	0	.	GRCh37	16	3807902	3807902	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3517C>T	p.Arg1173Ter	p.R1173*	ENST00000262367	18/31	23	17	6	10	10	0	CREBBP,stop_gained,p.Arg1173Ter,ENST00000262367,;CREBBP,stop_gained,p.Arg1135Ter,ENST00000382070,;CREBBP,stop_gained,p.Arg128Ter,ENST00000570939,;	A	ENSG00000005339	ENST00000262367	Transcript	stop_gained	4327	3517	1173	R/*	Cga/Tga	CM065105,COSM88760,COSM1377843	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	.	18/31	.	PROSITE_profiles:PS50014,hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5,Gene3D:1.20.920.10,Pfam_domain:PF00439,SMART_domains:SM00297,Superfamily_domains:SSF47370,Prints_domain:PR00503	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R1173*|c.3517C>T|5	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GACTCGGGATG	.	4	ESCA
ZCCHC14	0	.	GRCh37	16	87451324	87451324	+	Silent	SNP	G	G	A	rs751888412	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.714C>T	p.%3D	p.I238I	ENST00000268616	8/13	39	36	3	26	26	0	ZCCHC14,synonymous_variant,p.%3D,ENST00000268616,;ZCCHC14,synonymous_variant,p.%3D,ENST00000561928,;ZCCHC14,synonymous_variant,p.%3D,ENST00000568020,;ZCCHC14,non_coding_transcript_exon_variant,,ENST00000565193,;	A	ENSG00000140948	ENST00000268616	Transcript	synonymous_variant	932	714	238	I	atC/atT	rs751888412	.	.	-1	ZCCHC14	HGNC	24134	protein_coding	YES	CCDS10961.1	ENSP00000268616	ZCH14_HUMAN	.	UPI00000705C4	.	.	.	8/13	.	hmmpanther:PTHR16195:SF12,hmmpanther:PTHR16195	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACGGGATACC	.	2	ESCA
ULK2	0	.	GRCh37	17	19687150	19687150	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2320G>A	p.Gly774Ser	p.G774S	ENST00000395544	22/27	19	13	6	12	12	0	ULK2,missense_variant,p.Gly774Ser,ENST00000395544,;ULK2,missense_variant,p.Gly774Ser,ENST00000361658,;ULK2,missense_variant,p.Gly93Ser,ENST00000575432,;ULK2,non_coding_transcript_exon_variant,,ENST00000571137,;ULK2,non_coding_transcript_exon_variant,,ENST00000571454,;	T	ENSG00000083290	ENST00000395544	Transcript	missense_variant	2820	2320	774	G/S	Ggc/Agc	COSM1520454,COSM1520453	.	.	-1	ULK2	HGNC	13480	protein_coding	YES	CCDS11213.1	ENSP00000378914	ULK2_HUMAN	.	UPI000013D19B	.	tolerated(0.11)	benign(0.082)	22/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24348,hmmpanther:PTHR24348:SF18,PIRSF_domain:PIRSF000580	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGGCCAGGCG	.	2	ESCA
TXNDC17	0	.	GRCh37	17	6546368	6546383	+	3'UTR	DEL	GTCCTGATTTGTTCTA	GTCCTGATTTGTTCTA	-	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	GTCCTGATTTGTTCTA	GTCCTGATTTGTTCTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*31_*46delCCTGATTTGTTCTAGT	.	.	ENST00000250101	4/4	29	21	8	36	36	0	TXNDC17,3_prime_UTR_variant,,ENST00000570330,;TXNDC17,3_prime_UTR_variant,,ENST00000574838,;TXNDC17,3_prime_UTR_variant,,ENST00000250101,;KIAA0753,upstream_gene_variant,,ENST00000571642,;KIAA0753,upstream_gene_variant,,ENST00000361413,;MED31,downstream_gene_variant,,ENST00000574128,;MED31,downstream_gene_variant,,ENST00000575197,;KIAA0753,upstream_gene_variant,,ENST00000572370,;MED31,downstream_gene_variant,,ENST00000225728,;TXNDC17,non_coding_transcript_exon_variant,,ENST00000571029,;TXNDC17,non_coding_transcript_exon_variant,,ENST00000577146,;TXNDC17,non_coding_transcript_exon_variant,,ENST00000573792,;TXNDC17,non_coding_transcript_exon_variant,,ENST00000576020,;TXNDC17,downstream_gene_variant,,ENST00000571957,;TXNDC17,3_prime_UTR_variant,,ENST00000574734,;TXNDC17,non_coding_transcript_exon_variant,,ENST00000574429,;KIAA0753,upstream_gene_variant,,ENST00000570455,;	-	ENSG00000129235	ENST00000250101	Transcript	3_prime_UTR_variant	726-741	.	.	.	.	.	.	.	1	TXNDC17	HGNC	28218	protein_coding	YES	CCDS11077.1	ENSP00000250101	TXD17_HUMAN	I3L0K2_HUMAN	UPI0000072BFD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTGATGTCCTGATTTGTTCTAGTATC	.	3	ESCA
HID1	0	.	GRCh37	17	72958339	72958339	+	Missense_Mutation	SNP	C	C	A	rs141799560	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.601G>T	p.Asp201Tyr	p.D201Y	ENST00000425042	5/19	29	11	18	30	30	0	HID1,missense_variant,p.Asp201Tyr,ENST00000425042,;HID1,missense_variant,p.Asp93Tyr,ENST00000530857,;HID1,downstream_gene_variant,,ENST00000581676,;HID1,upstream_gene_variant,,ENST00000318565,;HID1,downstream_gene_variant,,ENST00000530904,;HID1,downstream_gene_variant,,ENST00000532900,;HID1,downstream_gene_variant,,ENST00000579818,;HID1,synonymous_variant,p.%3D,ENST00000534480,;HID1,non_coding_transcript_exon_variant,,ENST00000528902,;HID1,downstream_gene_variant,,ENST00000525128,;HID1,upstream_gene_variant,,ENST00000532894,;HID1,upstream_gene_variant,,ENST00000583244,;	A	ENSG00000167861	ENST00000425042	Transcript	missense_variant	679	601	201	D/Y	Gat/Tat	rs141799560,COSM3522014	.	.	-1	HID1	HGNC	15736	protein_coding	YES	CCDS32726.1	ENSP00000413520	HID1_HUMAN	Q8NC03_HUMAN,B4E226_HUMAN	UPI00000746AC	.	deleterious(0.03)	benign(0.38)	5/19	.	Pfam_domain:PF12722,hmmpanther:PTHR21575,hmmpanther:PTHR21575:SF12	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0.0009	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATATCGTGGA	byCluster|by1000G	5	ESCA
TP53	0	.	GRCh37	17	7579321	7579322	+	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365_366delTG	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	4/11	81	47	34	55	55	0	TP53,frameshift_variant,p.Val122AspfsTer26,ENST00000508793,;TP53,frameshift_variant,p.Val122AspfsTer26,ENST00000413465,;TP53,frameshift_variant,p.Val122AspfsTer19,ENST00000604348,;TP53,frameshift_variant,p.Val122AspfsTer26,ENST00000420246,;TP53,frameshift_variant,p.Val122AspfsTer26,ENST00000269305,;TP53,frameshift_variant,p.Val122AspfsTer26,ENST00000359597,;TP53,frameshift_variant,p.Val122AspfsTer26,ENST00000445888,;TP53,frameshift_variant,p.Val122AspfsTer?,ENST00000503591,;TP53,frameshift_variant,p.Val122AspfsTer26,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	555-556	365-366	122	V/X	gTG/g	rs587780067,TP53_g.11596_11597del,COSM44882,COSM258972,COSM258971	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	1,0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.V122fs*26|c.365_366delTG|4,SITE|p.V122fs*26|c.365_366delTG|4,SITE|p.V122fs*26|c.365_366delTG|6,CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,BUFFER|p.?|c.375+2T>C|3,BUFFER|p.?|c.375+1G>A|7,BUFFER|p.?|c.375+1G>A|7,BUFFER|p.?|c.375+1G>T|5,BUFFER|p.?|c.375+1G>T|5,BUFFER|p.?|c.375+1G>T|3,BUFFER|p.?|c.375+1G>A|11,BUFFER|p.?|c.375+1G>A|6,BUFFER|p.?|c.375+1G>A|6,BUFFER|p.?|c.375+1G>T|8,BUFFER|p.T125T|c.375G>A|19,BUFFER|p.T125T|c.375G>C|3,BUFFER|p.T125T|c.375G>T|10,BUFFER|p.T125T|c.375G>T|3,BUFFER|p.T125T|c.375G>T|12,BUFFER|p.T125T|c.375G>A|3,BUFFER|p.T125T|c.375G>C|5,BUFFER|p.T125T|c.375G>C|3,BUFFER|p.T125T|c.375G>T|12,BUFFER|p.T125T|c.375G>T|17,BUFFER|p.T125T|c.375G>A|11,BUFFER|p.T125T|c.375G>A|11,BUFFER|p.T125T|c.375G>A|3,BUFFER|p.T125M|c.374C>T|10,BUFFER|p.T125M|c.374C>T|3,BUFFER|p.T125K|c.374C>A|4,BUFFER|p.T125M|c.374C>T|4,BUFFER|p.T125M|c.374C>T|17,BUFFER|p.T125M|c.374C>T|10,BUFFER|p.T125R|c.374C>G|3,BUFFER|p.T125P|c.373A>C|3,BUFFER|p.C124*|c.372C>A|4,BUFFER|p.C124*|c.372C>A|4,BUFFER|p.C124*|c.372C>A|4,BUFFER|p.C124G|c.370T>G|3,BUFFER|p.C124R|c.370T>C|3,BUFFER|p.K120M|c.359A>T|7,BUFFER|p.K120E|c.358A>G|4,BUFFER|p.K120E|c.358A>G|4,BUFFER|p.K120E|c.358A>G|7	INDELOCATOR*|VARSCANI*|PINDEL	GCAAGTCACAGAC	.	3	ESCA
VPS4B	0	.	GRCh37	18	61077552	61077552	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267A>G	p.%3D	p.E89E	ENST00000238497	3/11	59	32	27	35	35	0	VPS4B,synonymous_variant,p.%3D,ENST00000591519,;VPS4B,synonymous_variant,p.%3D,ENST00000238497,;VPS4B,synonymous_variant,p.%3D,ENST00000588059,;VPS4B,non_coding_transcript_exon_variant,,ENST00000589604,;VPS4B,non_coding_transcript_exon_variant,,ENST00000591475,;RP11-635N19.2,downstream_gene_variant,,ENST00000589763,;	C	ENSG00000119541	ENST00000238497	Transcript	synonymous_variant	471	267	89	E	gaA/gaG	.	.	.	-1	VPS4B	HGNC	10895	protein_coding	YES	CCDS11983.1	ENSP00000238497	VPS4B_HUMAN	.	UPI0000073CAF	.	.	.	3/11	.	hmmpanther:PTHR23074:SF72,hmmpanther:PTHR23074,Superfamily_domains:SSF116846	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCCTTCTTT	.	5	ESCA
ZNF236	0	.	GRCh37	18	74536169	74536169	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-145A>G	.	.	ENST00000253159	1/31	16	13	3	13	13	0	ZNF236,5_prime_UTR_variant,,ENST00000253159,;ZNF236,intron_variant,,ENST00000320610,;RP11-162A12.2,upstream_gene_variant,,ENST00000585258,;ZNF236,5_prime_UTR_variant,,ENST00000543926,;	G	ENSG00000130856	ENST00000253159	Transcript	5_prime_UTR_variant	54	.	.	.	.	.	.	.	1	ZNF236	HGNC	13028	protein_coding	YES	CCDS42447.1	ENSP00000253159	ZN236_HUMAN	.	UPI0000F6DCCB	.	.	.	1/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTAATGGGT	.	2	ESCA
CTD-3105H18.14	0	.	GRCh37	19	12490952	12490952	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1299C>T	.	.	ENST00000435033	4/4	36	32	4	29	29	0	CTD-3105H18.14,3_prime_UTR_variant,,ENST00000435033,;CTD-3105H18.4,non_coding_transcript_exon_variant,,ENST00000507003,;	A	ENSG00000268744	ENST00000435033	Transcript	3_prime_UTR_variant	1644	.	.	.	.	.	.	.	-1	CTD-3105H18.14	Clone_based_vega_gene	.	nonsense_mediated_decay	YES	.	ENSP00000394047	.	F2Z351_HUMAN	UPI00001CE054	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACATGTTTGA	.	2	ESCA
PLK5	0	.	GRCh37	19	1535315	1535315	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66C>T	.	.	ENST00000334770	13/13	26	22	4	17	17	0	PLK5,3_prime_UTR_variant,,ENST00000454744,;PLK5,3_prime_UTR_variant,,ENST00000334770,;PLK5,downstream_gene_variant,,ENST00000588430,;	T	ENSG00000185988	ENST00000334770	Transcript	3_prime_UTR_variant	1966	.	.	.	.	.	.	.	1	PLK5	HGNC	27001	protein_coding	YES	CCDS59328.1	ENSP00000466248	PLK5_HUMAN	.	UPI000015FEF2	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTCCTGTGG	.	2	ESCA
TLE2	0	.	GRCh37	19	2997811	2997811	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*35C>T	.	.	ENST00000262953	20/20	44	39	5	28	28	0	TLE2,3_prime_UTR_variant,,ENST00000447365,;TLE2,3_prime_UTR_variant,,ENST00000455444,;TLE2,3_prime_UTR_variant,,ENST00000443826,;TLE2,3_prime_UTR_variant,,ENST00000262953,;TLE2,3_prime_UTR_variant,,ENST00000591529,;TLE2,intron_variant,,ENST00000586422,;TLE2,downstream_gene_variant,,ENST00000426948,;TLE6,downstream_gene_variant,,ENST00000246112,;TLE6,downstream_gene_variant,,ENST00000452088,;TLE2,downstream_gene_variant,,ENST00000590536,;TLE6,downstream_gene_variant,,ENST00000497878,;	A	ENSG00000065717	ENST00000262953	Transcript	3_prime_UTR_variant	2530	.	.	.	.	.	.	.	-1	TLE2	HGNC	11838	protein_coding	YES	CCDS45911.1	ENSP00000262953	TLE2_HUMAN	.	UPI0000137038	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGGAGTCTGG	.	3	ESCA
ZNF565	0	.	GRCh37	19	36674504	36674504	+	Missense_Mutation	SNP	C	C	T	rs767613413	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364G>A	p.Glu122Lys	p.E122K	ENST00000392173	5/5	29	18	11	19	19	0	ZNF565,missense_variant,p.Glu57Lys,ENST00000591473,;ZNF565,missense_variant,p.Glu122Lys,ENST00000392173,;ZNF565,missense_variant,p.Glu122Lys,ENST00000304116,;ZNF565,missense_variant,p.Glu162Lys,ENST00000355114,;	T	ENSG00000196357	ENST00000392173	Transcript	missense_variant	623	364	122	E/K	Gaa/Aaa	rs767613413	.	.	-1	ZNF565	HGNC	26726	protein_coding	YES	CCDS12491.1	ENSP00000376013	ZN565_HUMAN	K7ESE2_HUMAN,K7EL42_HUMAN	UPI000006E728	.	tolerated(1)	benign(0)	5/5	.	hmmpanther:PTHR24377:SF70,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCGCATT	byFrequency	5	ESCA
MAP3K10	0	.	GRCh37	19	40704382	40704382	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783G>T	p.Met261Ile	p.M261I	ENST00000253055	2/10	35	22	13	29	29	0	MAP3K10,missense_variant,p.Met261Ile,ENST00000253055,;MAP3K10,non_coding_transcript_exon_variant,,ENST00000593906,;MAP3K10,stop_gained,p.Glu18Ter,ENST00000593502,;MAP3K10,missense_variant,p.Met11Ile,ENST00000597986,;MAP3K10,missense_variant,p.Met27Ile,ENST00000594951,;	T	ENSG00000130758	ENST00000253055	Transcript	missense_variant	1071	783	261	M/I	atG/atT	.	.	.	1	MAP3K10	HGNC	6849	protein_coding	YES	CCDS12549.1	ENSP00000253055	M3K10_HUMAN	.	UPI000013CDAC	.	deleterious(0.01)	probably_damaging(0.983)	2/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF370,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00220,PIRSF_domain:PIRSF000556,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATGAGCGC	.	5	ESCA
CYP2G1P	0	.	GRCh37	19	41404105	41404105	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1709C>T	.	.	ENST00000252909	3/5	62	54	8	35	35	0	CYP2G1P,non_coding_transcript_exon_variant,,ENST00000252909,;CTC-490E21.12,3_prime_UTR_variant,,ENST00000601627,;CYP2G1P,non_coding_transcript_exon_variant,,ENST00000597833,;	T	ENSG00000130612	ENST00000252909	Transcript	non_coding_transcript_exon_variant	1709	.	.	.	.	.	.	.	1	CYP2G1P	HGNC	2633	processed_transcript	YES	.	.	.	.	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGACCGGGTC	.	2	ESCA
MARK4	0	.	GRCh37	19	45801428	45801428	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1877+216G>C	.	.	ENST00000262891	.	57	42	15	62	62	0	MARK4,missense_variant,p.Gln635His,ENST00000300843,;MARK4,intron_variant,,ENST00000262891,;	C	ENSG00000007047	ENST00000262891	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MARK4	HGNC	13538	protein_coding	YES	CCDS56097.1	ENSP00000262891	MARK4_HUMAN	Q96GZ3_HUMAN,K7EKG8_HUMAN,K7EK17_HUMAN	UPI0000044D47	.	.	.	.	15/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCAGAACTC	.	5	ESCA
FBXO46	0	.	GRCh37	19	46214661	46214662	+	3'UTR	DEL	GG	GG	-	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	GG	GG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*280_*281delCC	.	.	ENST00000317683	2/2	35	31	4	27	27	0	FBXO46,3_prime_UTR_variant,,ENST00000317683,;FBXO46,downstream_gene_variant,,ENST00000591686,;FBXO46,downstream_gene_variant,,ENST00000586899,;	-	ENSG00000177051	ENST00000317683	Transcript	3_prime_UTR_variant	2226-2227	.	.	.	.	.	.	.	-1	FBXO46	HGNC	25069	protein_coding	YES	CCDS46116.1	ENSP00000410007	FBX46_HUMAN	K7ERN4_HUMAN	UPI00002026A5	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CAGGGAGGGGGTT	.	2	ESCA
MYBPC2	0	.	GRCh37	19	50951588	50951588	+	Nonsense_Mutation	SNP	G	G	A	rs34373957	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1413G>A	p.Trp471Ter	p.W471*	ENST00000357701	13/28	53	48	5	35	35	0	MYBPC2,stop_gained,p.Trp471Ter,ENST00000357701,;	A	ENSG00000086967	ENST00000357701	Transcript	stop_gained	1464	1413	471	W/*	tgG/tgA	rs34373957	.	.	1	MYBPC2	HGNC	7550	protein_coding	YES	CCDS46152.1	ENSP00000350332	MYPC2_HUMAN	.	UPI000013C628	.	.	.	13/28	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19900:SF56,hmmpanther:PTHR19900,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AAGTGGTATAA	byCluster	2	ESCA
FPR3	0	.	GRCh37	19	52329039	52329040	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*982dupT	.	.	ENST00000339223	2/2	86	68	18	65	65	0	FPR3,3_prime_UTR_variant,,ENST00000339223,;FPR3,3_prime_UTR_variant,,ENST00000595991,;	T	ENSG00000187474	ENST00000339223	Transcript	3_prime_UTR_variant	2217-2218	.	.	.	.	.	.	.	1	FPR3	HGNC	3828	protein_coding	YES	CCDS12841.1	ENSP00000341821	FPR3_HUMAN	Q6L5J4_HUMAN	UPI000011DFC1	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGTTATTTTT	.	3	ESCA
CELSR2	0	.	GRCh37	1	109811375	109811375	+	Missense_Mutation	SNP	C	C	T	rs775752921	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6491C>T	p.Thr2164Met	p.T2164M	ENST00000271332	18/34	59	30	29	63	63	0	CELSR2,missense_variant,p.Thr2164Met,ENST00000271332,;CELSR2,upstream_gene_variant,,ENST00000489018,;CELSR2,upstream_gene_variant,,ENST00000498157,;CELSR2,downstream_gene_variant,,ENST00000459940,;	T	ENSG00000143126	ENST00000271332	Transcript	missense_variant	6552	6491	2164	T/M	aCg/aTg	rs775752921,COSM1332433	.	.	1	CELSR2	HGNC	3231	protein_coding	YES	CCDS796.1	ENSP00000271332	CELR2_HUMAN	.	UPI00000015B6	.	deleterious(0)	probably_damaging(0.996)	18/34	.	hmmpanther:PTHR24026:SF32,hmmpanther:PTHR24026,Pfam_domain:PF12003	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCACGCCCA	byFrequency	5	ESCA
MOV10	0	.	GRCh37	1	113237086	113237086	+	Missense_Mutation	SNP	G	G	A	rs748592404	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1307G>A	p.Arg436His	p.R436H	ENST00000413052	9/21	49	21	28	61	61	0	MOV10,missense_variant,p.Arg380His,ENST00000369644,;MOV10,missense_variant,p.Arg436His,ENST00000357443,;MOV10,missense_variant,p.Arg436His,ENST00000369645,;MOV10,missense_variant,p.Arg436His,ENST00000413052,;RP11-426L16.3,intron_variant,,ENST00000421943,;MOV10,non_coding_transcript_exon_variant,,ENST00000479858,;MOV10,non_coding_transcript_exon_variant,,ENST00000468624,;MOV10,non_coding_transcript_exon_variant,,ENST00000496577,;MOV10,upstream_gene_variant,,ENST00000481711,;MOV10,upstream_gene_variant,,ENST00000490413,;MOV10,upstream_gene_variant,,ENST00000471160,;MOV10,upstream_gene_variant,,ENST00000482545,;MOV10,upstream_gene_variant,,ENST00000488160,;	A	ENSG00000155363	ENST00000413052	Transcript	missense_variant	1697	1307	436	R/H	cGc/cAc	rs748592404	.	.	1	MOV10	HGNC	7200	protein_coding	YES	CCDS853.1	ENSP00000399797	MOV10_HUMAN	Q5JR04_HUMAN,B3KQ43_HUMAN	UPI000012FA84	.	tolerated(0.06)	benign(0.074)	9/21	.	hmmpanther:PTHR10887:SF326,hmmpanther:PTHR10887	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGCTTTG	.	5	ESCA
ATAD3B	0	.	GRCh37	1	1412670	1412670	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.222C>T	p.%3D	p.A74A	ENST00000308647	2/16	49	24	25	70	70	0	ATAD3B,synonymous_variant,p.%3D,ENST00000308647,;ATAD3B,5_prime_UTR_variant,,ENST00000378741,;ATAD3B,upstream_gene_variant,,ENST00000378736,;ATAD3B,upstream_gene_variant,,ENST00000472194,;	T	ENSG00000160072	ENST00000308647	Transcript	synonymous_variant	338	222	74	A	gcC/gcT	.	.	.	1	ATAD3B	HGNC	24007	protein_coding	YES	CCDS30.1	ENSP00000311766	ATD3B_HUMAN	Q9H834_HUMAN	UPI000013E044	.	.	.	2/16	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23075:SF2,hmmpanther:PTHR23075,Pfam_domain:PF12037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCCCTGAA	.	5	ESCA
NBPF14	0	.	GRCh37	1	148004386	148004386	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*162C>G	.	.	ENST00000310701	22/22	33	24	9	14	14	0	NBPF14,3_prime_UTR_variant,,ENST00000310701,;NBPF14,3_prime_UTR_variant,,ENST00000369219,;NBPF14,downstream_gene_variant,,ENST00000392972,;NBPF14,downstream_gene_variant,,ENST00000458135,;NBPF14,downstream_gene_variant,,ENST00000444640,;NBPF14,downstream_gene_variant,,ENST00000436356,;NBPF14,downstream_gene_variant,,ENST00000431121,;NBPF14,downstream_gene_variant,,ENST00000448574,;RP3-328E19.4,downstream_gene_variant,,ENST00000416378,;	C	ENSG00000122497	ENST00000310701	Transcript	3_prime_UTR_variant	2945	.	.	.	.	.	.	.	-1	NBPF14	HGNC	25232	protein_coding	YES	.	ENSP00000309907	.	S4R3H5_HUMAN,H7BZX4_HUMAN,H7BYX2_HUMAN	UPI000059D042	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACTGAGCACAG	.	2	ESCA
OR10Z1	0	.	GRCh37	1	158576618	158576618	+	Silent	SNP	C	C	A	rs762893016	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390C>A	p.%3D	p.L130L	ENST00000361284	1/1	72	48	24	40	40	0	OR10Z1,synonymous_variant,p.%3D,ENST00000361284,;SPTA1,downstream_gene_variant,,ENST00000368147,;SPTA1,downstream_gene_variant,,ENST00000485680,;	A	ENSG00000198967	ENST00000361284	Transcript	synonymous_variant	390	390	130	L	ctC/ctA	rs762893016,COSM1499151	.	.	1	OR10Z1	HGNC	14996	protein_coding	YES	CCDS30901.1	ENSP00000354707	O10Z1_HUMAN	.	UPI000004CA23	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTCCACTA	byFrequency	5	ESCA
OLFML2B	0	.	GRCh37	1	161954722	161954722	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1523A>G	p.Asn508Ser	p.N508S	ENST00000294794	7/8	88	60	28	74	74	0	OLFML2B,missense_variant,p.Asn509Ser,ENST00000367940,;OLFML2B,missense_variant,p.Asn508Ser,ENST00000294794,;OLFML2B,5_prime_UTR_variant,,ENST00000367938,;OLFML2B,upstream_gene_variant,,ENST00000525589,;OLFML2B,upstream_gene_variant,,ENST00000533556,;	C	ENSG00000162745	ENST00000294794	Transcript	missense_variant	1947	1523	508	N/S	aAc/aGc	.	.	.	-1	OLFML2B	HGNC	24558	protein_coding	YES	CCDS1236.1	ENSP00000294794	OLM2B_HUMAN	H0YEW8_HUMAN,H0YE85_HUMAN	UPI00001D7DE0	.	deleterious(0.01)	possibly_damaging(0.808)	7/8	.	PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37,Pfam_domain:PF02191,SMART_domains:SM00284	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTGTTCTGG	.	5	ESCA
HMCN1	0	.	GRCh37	1	185946959	185946959	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2412G>A	p.Met804Ile	p.M804I	ENST00000271588	16/107	90	63	27	49	48	0	HMCN1,missense_variant,p.Met804Ile,ENST00000367492,;HMCN1,missense_variant,p.Met804Ile,ENST00000271588,;HMCN1,non_coding_transcript_exon_variant,,ENST00000493413,;HMCN1,non_coding_transcript_exon_variant,,ENST00000485744,;	A	ENSG00000143341	ENST00000271588	Transcript	missense_variant	2641	2412	804	M/I	atG/atA	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	benign(0.005)	16/107	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTATGGAAAT	.	5	ESCA
B3GALT2	0	.	GRCh37	1	193149736	193149736	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.957T>A	p.Phe319Leu	p.F319L	ENST00000367434	2/2	75	48	27	47	47	0	B3GALT2,missense_variant,p.Phe319Leu,ENST00000367434,;CDC73,intron_variant,,ENST00000367435,;	T	ENSG00000162630	ENST00000367434	Transcript	missense_variant	1713	957	319	F/L	ttT/ttA	.	.	.	-1	B3GALT2	HGNC	917	protein_coding	YES	CCDS1383.1	ENSP00000356404	B3GT2_HUMAN	.	UPI0000073BFF	.	tolerated(0.09)	benign(0.106)	2/2	.	hmmpanther:PTHR11214:SF19,hmmpanther:PTHR11214,Pfam_domain:PF01762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCAGAAAAAAC	.	4	ESCA
TP53BP2	0	.	GRCh37	1	223983606	223983606	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2635C>A	p.Pro879Thr	p.P879T	ENST00000343537	13/18	80	65	14	38	38	0	TP53BP2,missense_variant,p.Pro879Thr,ENST00000343537,;TP53BP2,missense_variant,p.Pro213Thr,ENST00000494100,;TP53BP2,missense_variant,p.Pro750Thr,ENST00000391878,;TP53BP2,missense_variant,p.Pro112Thr,ENST00000391879,;TP53BP2,non_coding_transcript_exon_variant,,ENST00000498843,;TP53BP2,downstream_gene_variant,,ENST00000489310,;TP53BP2,3_prime_UTR_variant,,ENST00000483398,;TP53BP2,downstream_gene_variant,,ENST00000464656,;TP53BP2,downstream_gene_variant,,ENST00000490896,;	T	ENSG00000143514	ENST00000343537	Transcript	missense_variant	2927	2635	879	P/T	Cca/Aca	.	.	.	-1	TP53BP2	HGNC	12000	protein_coding	YES	CCDS44319.1	ENSP00000341957	ASPP2_HUMAN	B7Z2E9_HUMAN,B4DI25_HUMAN,B4DH76_HUMAN	UPI0000D4B5F2	.	tolerated(0.11)	probably_damaging(0.999)	13/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24131:SF8,hmmpanther:PTHR24131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATGGTGGGG	.	5	ESCA
ZNF436	0	.	GRCh37	1	23687695	23687695	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*767A>G	.	.	ENST00000314011	4/4	26	12	14	31	31	0	ZNF436,3_prime_UTR_variant,,ENST00000314011,;ZNF436,3_prime_UTR_variant,,ENST00000374608,;	C	ENSG00000125945	ENST00000314011	Transcript	3_prime_UTR_variant	2317	.	.	.	.	.	.	.	-1	ZNF436	HGNC	20814	protein_coding	YES	CCDS233.1	ENSP00000313582	ZN436_HUMAN	Q15921_HUMAN	UPI0000001669	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTATAGTGA	.	5	ESCA
IL12RB2	0	.	GRCh37	1	67855810	67855810	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2045delA	p.Glu682GlyfsTer12	p.E682Gfs*12	ENST00000262345	15/16	49	42	7	35	35	0	IL12RB2,frameshift_variant,p.Glu596GlyfsTer12,ENST00000544434,;IL12RB2,frameshift_variant,p.Glu682GlyfsTer12,ENST00000262345,;IL12RB2,intron_variant,,ENST00000541374,;IL12RB2,intron_variant,,ENST00000371000,;IL12RB2,splice_region_variant,,ENST00000465396,;	-	ENSG00000081985	ENST00000262345	Transcript	frameshift_variant	2685	2045	682	E/X	gAg/gg	.	.	.	1	IL12RB2	HGNC	5972	protein_coding	YES	CCDS638.1	ENSP00000262345	I12R2_HUMAN	.	UPI0000046B13	.	.	.	15/16	.	hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF79	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TTGCAGAGGTAA	.	2	ESCA
LRRC7	0	.	GRCh37	1	70504428	70504428	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2807T>A	p.Met936Lys	p.M936K	ENST00000035383	19/25	24	20	4	18	18	0	LRRC7,missense_variant,p.Met220Lys,ENST00000415775,;LRRC7,missense_variant,p.Met936Lys,ENST00000035383,;LRRC7,missense_variant,p.Met941Lys,ENST00000310961,;	A	ENSG00000033122	ENST00000035383	Transcript	missense_variant	2837	2807	936	M/K	aTg/aAg	.	.	.	1	LRRC7	HGNC	18531	protein_coding	YES	CCDS645.1	ENSP00000035383	LRRC7_HUMAN	.	UPI000006F29B	.	tolerated(0.12)	probably_damaging(0.962)	19/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTAATGAAAG	.	4	ESCA
PLTP	0	.	GRCh37	20	44538215	44538215	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.425C>A	p.Ser142Tyr	p.S142Y	ENST00000477313	4/15	18	15	3	16	16	0	PLTP,missense_variant,p.Ser54Tyr,ENST00000372420,;PLTP,missense_variant,p.Ser142Tyr,ENST00000372431,;PLTP,missense_variant,p.Ser162Tyr,ENST00000542937,;PLTP,missense_variant,p.Ser142Tyr,ENST00000477313,;PLTP,intron_variant,,ENST00000420868,;PLTP,intron_variant,,ENST00000354050,;	T	ENSG00000100979	ENST00000477313	Transcript	missense_variant	1020	425	142	S/Y	tCc/tAc	.	.	.	-1	PLTP	HGNC	9093	protein_coding	YES	CCDS13386.1	ENSP00000417138	PLTP_HUMAN	.	UPI0000131C7C	.	deleterious(0.01)	possibly_damaging(0.786)	4/15	.	hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF16,Pfam_domain:PF01273,Gene3D:1ewfA01,SMART_domains:SM00328,Superfamily_domains:SSF55394	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTGGACACT	.	2	ESCA
RAB22A	0	.	GRCh37	20	56935675	56935675	+	3'UTR	SNP	G	G	C	rs563098622	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*916G>C	.	.	ENST00000244040	7/7	27	14	13	18	18	0	RAB22A,3_prime_UTR_variant,,ENST00000244040,;	C	ENSG00000124209	ENST00000244040	Transcript	3_prime_UTR_variant	1782	.	.	.	.	rs563098622	.	.	1	RAB22A	HGNC	9764	protein_coding	YES	CCDS33497.1	ENSP00000244040	RB22A_HUMAN	Q96IY7_HUMAN	UPI0000132F68	.	.	.	7/7	.	.	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAGATTAT	by1000G	5	ESCA
TPTE	0	.	GRCh37	21	10933879	10933879	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1000G>A	p.Val334Ile	p.V334I	ENST00000361285	17/24	171	136	34	185	185	0	TPTE,missense_variant,p.Val334Ile,ENST00000361285,;TPTE,missense_variant,p.Val296Ile,ENST00000342420,;TPTE,missense_variant,p.Val316Ile,ENST00000298232,;TPTE,non_coding_transcript_exon_variant,,ENST00000415664,;TPTE,non_coding_transcript_exon_variant,,ENST00000447568,;CYCSP41,downstream_gene_variant,,ENST00000451532,;	T	ENSG00000166157	ENST00000361285	Transcript	missense_variant	1330	1000	334	V/I	Gta/Ata	COSM3405309,COSM3405308	.	.	-1	TPTE	HGNC	12023	protein_coding	YES	CCDS13560.2	ENSP00000355208	TPTE_HUMAN	.	UPI000016A18A	.	tolerated(1)	benign(0.02)	17/24	.	PROSITE_profiles:PS51181,hmmpanther:PTHR12305,Gene3D:3.90.190.10,Pfam_domain:PF00782,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A335A|c.1005G>A|4,BUFFER|p.A317A|c.951G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTACGATGT	.	5	ESCA
SUMO3	0	.	GRCh37	21	46226696	46226696	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*170A>C	.	.	ENST00000332859	4/4	14	7	7	13	13	0	SUMO3,3_prime_UTR_variant,,ENST00000332859,;SUMO3,3_prime_UTR_variant,,ENST00000397898,;SUMO3,3_prime_UTR_variant,,ENST00000411651,;UBE2G2,upstream_gene_variant,,ENST00000345496,;SUMO3,downstream_gene_variant,,ENST00000397893,;AL773604.8,downstream_gene_variant,,ENST00000417820,;SUMO3,non_coding_transcript_exon_variant,,ENST00000479153,;UBE2G2,upstream_gene_variant,,ENST00000497664,;UBE2G2,upstream_gene_variant,,ENST00000497630,;UBE2G2,upstream_gene_variant,,ENST00000462569,;UBE2G2,upstream_gene_variant,,ENST00000491513,;UBE2G2,upstream_gene_variant,,ENST00000478200,;UBE2G2,upstream_gene_variant,,ENST00000490091,;	G	ENSG00000184900	ENST00000332859	Transcript	3_prime_UTR_variant	643	.	.	.	.	.	.	.	-1	SUMO3	HGNC	11124	protein_coding	YES	CCDS33587.1	ENSP00000330343	SUMO3_HUMAN	.	UPI0000135A5D	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATTCATCC	.	5	ESCA
LZTR1	0	.	GRCh37	22	21348483	21348483	+	Missense_Mutation	SNP	C	C	T	rs779673877	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1540C>T	p.Arg514Trp	p.R514W	ENST00000215739	14/21	40	29	11	55	55	0	LZTR1,missense_variant,p.Arg514Trp,ENST00000215739,;LZTR1,missense_variant,p.Arg495Trp,ENST00000389355,;LZTR1,upstream_gene_variant,,ENST00000415817,;LZTR1,non_coding_transcript_exon_variant,,ENST00000479606,;LZTR1,downstream_gene_variant,,ENST00000497716,;LZTR1,downstream_gene_variant,,ENST00000480895,;LZTR1,non_coding_transcript_exon_variant,,ENST00000492480,;LZTR1,upstream_gene_variant,,ENST00000464807,;LZTR1,upstream_gene_variant,,ENST00000452988,;LZTR1,upstream_gene_variant,,ENST00000498649,;LZTR1,upstream_gene_variant,,ENST00000491432,;LZTR1,upstream_gene_variant,,ENST00000463909,;LZTR1,upstream_gene_variant,,ENST00000439171,;THAP7,downstream_gene_variant,,ENST00000498406,;LZTR1,upstream_gene_variant,,ENST00000495142,;LZTR1,downstream_gene_variant,,ENST00000461510,;LZTR1,downstream_gene_variant,,ENST00000414985,;LZTR1,upstream_gene_variant,,ENST00000415354,;LZTR1,downstream_gene_variant,,ENST00000443265,;	T	ENSG00000099949	ENST00000215739	Transcript	missense_variant	1899	1540	514	R/W	Cgg/Tgg	rs779673877	.	.	1	LZTR1	HGNC	6742	protein_coding	YES	CCDS33606.1	ENSP00000215739	LZTR1_HUMAN	B2R8T5_HUMAN	UPI000013C695	.	deleterious(0.02)	possibly_damaging(0.882)	14/21	.	PROSITE_profiles:PS50097,hmmpanther:PTHR23244:SF15,hmmpanther:PTHR23244,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCCGGGAG	byFrequency	5	ESCA
MORC2	0	.	GRCh37	22	31324086	31324086	+	Missense_Mutation	SNP	C	C	T	rs773617883	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2764G>A	p.Glu922Lys	p.E922K	ENST00000215862	26/27	66	50	16	70	70	0	MORC2,missense_variant,p.Glu922Lys,ENST00000215862,;MORC2,missense_variant,p.Glu44Lys,ENST00000429468,;MORC2,missense_variant,p.Glu146Lys,ENST00000445980,;MORC2,missense_variant,p.Glu984Lys,ENST00000397641,;MORC2-AS1,intron_variant,,ENST00000441558,;MORC2-AS1,downstream_gene_variant,,ENST00000422995,;MORC2-AS1,downstream_gene_variant,,ENST00000609557,;MORC2-AS1,downstream_gene_variant,,ENST00000432624,;	T	ENSG00000133422	ENST00000215862	Transcript	missense_variant	4128	2764	922	E/K	Gag/Aag	rs773617883	.	.	-1	MORC2	HGNC	23573	protein_coding	YES	CCDS33636.1	ENSP00000215862	MORC2_HUMAN	.	UPI000012DB74	.	deleterious(0)	possibly_damaging(0.711)	26/27	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23337:SF7,hmmpanther:PTHR23337	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCGGAGG	.	5	ESCA
TBC1D22A	0	.	GRCh37	22	47308003	47308003	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934C>T	p.Arg312Cys	p.R312C	ENST00000337137	8/13	38	35	3	28	28	0	TBC1D22A,missense_variant,p.Arg265Cys,ENST00000406733,;TBC1D22A,missense_variant,p.Arg312Cys,ENST00000337137,;TBC1D22A,missense_variant,p.Arg234Cys,ENST00000355704,;TBC1D22A,missense_variant,p.Arg253Cys,ENST00000407381,;TBC1D22A,missense_variant,p.Arg265Cys,ENST00000380995,;TBC1D22A,missense_variant,p.Arg265Cys,ENST00000441162,;TBC1D22A,3_prime_UTR_variant,,ENST00000394449,;	T	ENSG00000054611	ENST00000337137	Transcript	missense_variant	1100	934	312	R/C	Cgc/Tgc	.	.	.	1	TBC1D22A	HGNC	1309	protein_coding	YES	CCDS14078.1	ENSP00000336724	TB22A_HUMAN	B9A6M3_HUMAN,B0QYI3_HUMAN	UPI0000128722	.	deleterious(0)	probably_damaging(1)	8/13	.	Superfamily_domains:SSF47923,SMART_domains:SM00164,hmmpanther:PTHR22957,Gene3D:2qq8A02,Pfam_domain:PF00566,hmmpanther:PTHR22957:SF255,PROSITE_profiles:PS50086	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGATCCGCCAC	.	2	ESCA
BRD1	0	.	GRCh37	22	50167067	50167067	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*814T>G	.	.	ENST00000216267	12/12	16	8	8	25	25	0	BRD1,3_prime_UTR_variant,,ENST00000457780,;BRD1,3_prime_UTR_variant,,ENST00000216267,;BRD1,3_prime_UTR_variant,,ENST00000404034,;BRD1,3_prime_UTR_variant,,ENST00000404760,;BRD1,downstream_gene_variant,,ENST00000542442,;BRD1,downstream_gene_variant,,ENST00000342989,;BRD1,3_prime_UTR_variant,,ENST00000438393,;BRD1,downstream_gene_variant,,ENST00000479985,;	C	ENSG00000100425	ENST00000216267	Transcript	3_prime_UTR_variant	4478	.	.	.	.	.	.	.	-1	BRD1	HGNC	1102	protein_coding	YES	CCDS14080.1	ENSP00000216267	BRD1_HUMAN	Q659H0_HUMAN	UPI0000126ACA	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAAATGTAT	.	5	ESCA
TMEM37	0	.	GRCh37	2	120194908	120194908	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.465C>T	p.%3D	p.L155L	ENST00000306406	2/2	81	57	23	44	44	0	TMEM37,synonymous_variant,p.%3D,ENST00000306406,;TMEM37,synonymous_variant,p.%3D,ENST00000409826,;TMEM37,downstream_gene_variant,,ENST00000417645,;SCTR,downstream_gene_variant,,ENST00000019103,;TMEM37,non_coding_transcript_exon_variant,,ENST00000465296,;SCTR,downstream_gene_variant,,ENST00000494326,;SCTR,downstream_gene_variant,,ENST00000485440,;	T	ENSG00000171227	ENST00000306406	Transcript	synonymous_variant	500	465	155	L	ctC/ctT	.	.	.	1	TMEM37	HGNC	18216	protein_coding	YES	CCDS33281.1	ENSP00000303148	CCGL_HUMAN	Q86SV2_HUMAN	UPI00001BE8EA	.	.	.	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR31767:SF0,hmmpanther:PTHR31767,Pfam_domain:PF15108	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTCATCGG	.	5	ESCA
LRP2	0	.	GRCh37	2	170030640	170030640	+	Silent	SNP	G	G	A	rs370876114	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10803C>T	p.%3D	p.C3601C	ENST00000263816	56/79	87	63	24	41	41	0	LRP2,synonymous_variant,p.%3D,ENST00000263816,;LRP2,downstream_gene_variant,,ENST00000461418,;	A	ENSG00000081479	ENST00000263816	Transcript	synonymous_variant	11089	10803	3601	C	tgC/tgT	rs370876114,COSM441451	.	.	-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	LRP2_HUMAN	Q9NP34_HUMAN,Q53TL0_HUMAN,Q4ZG84_HUMAN	UPI0000141BA5	.	.	.	56/79	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF220,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424	.	.	.	.	.	.	.	A:0	A:0.0002	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGCGCACTG	byFrequency|byCluster	5	ESCA
TTN	0	.	GRCh37	2	179606443	179606443	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11517G>A	p.%3D	p.L3839L	ENST00000589042	48/363	51	47	4	23	23	0	TTN,synonymous_variant,p.%3D,ENST00000359218,;TTN,synonymous_variant,p.%3D,ENST00000342175,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000460472,;TTN,intron_variant,,ENST00000342992,;TTN,downstream_gene_variant,,ENST00000360870,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000582847,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,upstream_gene_variant,,ENST00000578746,;	T	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	11742	11517	3839	L	ctG/ctA	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	48/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACAGACAGTGT	.	3	ESCA
UNC80	0	.	GRCh37	2	210806065	210806065	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6569T>C	p.Leu2190Pro	p.L2190P	ENST00000439458	43/64	80	71	9	64	64	0	UNC80,missense_variant,p.Leu2190Pro,ENST00000439458,;UNC80,missense_variant,p.Leu2185Pro,ENST00000272845,;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,;	C	ENSG00000144406	ENST00000439458	Transcript	missense_variant	6649	6569	2190	L/P	cTc/cCc	.	.	.	1	UNC80	HGNC	26582	protein_coding	YES	CCDS46504.1	ENSP00000391088	UNC80_HUMAN	.	UPI00017E10C9	.	.	probably_damaging(0.997)	43/64	.	hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCCTCAACG	.	4	ESCA
CUL3	0	.	GRCh37	2	225422486	225422486	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154C>T	p.Leu52Phe	p.L52F	ENST00000264414	2/16	38	19	19	46	46	0	CUL3,missense_variant,p.Leu52Phe,ENST00000264414,;CUL3,missense_variant,p.Leu28Phe,ENST00000409777,;CUL3,missense_variant,p.Leu28Phe,ENST00000409096,;CUL3,missense_variant,p.Leu73Phe,ENST00000436172,;CUL3,intron_variant,,ENST00000344951,;CUL3,non_coding_transcript_exon_variant,,ENST00000432260,;CUL3,non_coding_transcript_exon_variant,,ENST00000546102,;	A	ENSG00000036257	ENST00000264414	Transcript	missense_variant	493	154	52	L/F	Ctt/Ttt	COSM1669807	.	.	-1	CUL3	HGNC	2553	protein_coding	YES	CCDS2462.1	ENSP00000264414	CUL3_HUMAN	Q53S54_HUMAN,Q53RD1_HUMAN	UPI0000001C83	.	deleterious(0)	probably_damaging(0.98)	2/16	.	hmmpanther:PTHR11932,Pfam_domain:PF00888,Gene3D:1.20.1310.10,Superfamily_domains:SSF74788	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTAAGACCAC	.	5	ESCA
CCDC88A	0	.	GRCh37	2	55563852	55563852	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621A>T	p.Thr541Ser	p.T541S	ENST00000336838	14/33	40	25	14	26	26	0	CCDC88A,missense_variant,p.Thr541Ser,ENST00000413716,;CCDC88A,missense_variant,p.Thr541Ser,ENST00000436346,;CCDC88A,missense_variant,p.Thr541Ser,ENST00000263630,;CCDC88A,missense_variant,p.Thr541Ser,ENST00000336838,;CCDC88A,upstream_gene_variant,,ENST00000426576,;AC012358.8,intron_variant,,ENST00000608103,;AC012358.8,intron_variant,,ENST00000600219,;AC012358.8,intron_variant,,ENST00000594078,;AC012358.8,intron_variant,,ENST00000599475,;AC012358.8,intron_variant,,ENST00000599352,;CCDC88A,upstream_gene_variant,,ENST00000468534,;	A	ENSG00000115355	ENST00000336838	Transcript	missense_variant	2155	1621	541	T/S	Aca/Tca	.	.	.	-1	CCDC88A	HGNC	25523	protein_coding	YES	CCDS46288.1	ENSP00000338728	GRDN_HUMAN	C9J225_HUMAN,B4DSN0_HUMAN	UPI00005B7220	.	tolerated(0.33)	benign(0.052)	14/33	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF30,Pfam_domain:PF05622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTGTTTTTT	.	5	ESCA
CCT7	0	.	GRCh37	2	73471716	73471716	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.491G>T	p.Ser164Ile	p.S164I	ENST00000258091	6/12	63	42	21	36	36	0	CCT7,missense_variant,p.Ser77Ile,ENST00000540468,;CCT7,missense_variant,p.Ser164Ile,ENST00000258091,;CCT7,missense_variant,p.Ser36Ile,ENST00000538797,;CCT7,missense_variant,p.Ser120Ile,ENST00000539919,;CCT7,missense_variant,p.Ser64Ile,ENST00000537131,;CCT7,intron_variant,,ENST00000398422,;CCT7,downstream_gene_variant,,ENST00000399032,;CCT7,non_coding_transcript_exon_variant,,ENST00000473786,;CCT7,non_coding_transcript_exon_variant,,ENST00000469844,;CCT7,downstream_gene_variant,,ENST00000482064,;CCT7,downstream_gene_variant,,ENST00000471927,;CCT7,downstream_gene_variant,,ENST00000473197,;CCT7,downstream_gene_variant,,ENST00000492253,;CCT7,3_prime_UTR_variant,,ENST00000409924,;CCT7,non_coding_transcript_exon_variant,,ENST00000488856,;CCT7,downstream_gene_variant,,ENST00000464397,;CCT7,downstream_gene_variant,,ENST00000480489,;CCT7,downstream_gene_variant,,ENST00000461290,;	T	ENSG00000135624	ENST00000258091	Transcript	missense_variant	632	491	164	S/I	aGc/aTc	.	.	.	1	CCT7	HGNC	1622	protein_coding	YES	CCDS46336.1	ENSP00000258091	TCPH_HUMAN	F8WAM2_HUMAN	UPI0000136B06	.	deleterious(0)	benign(0.137)	6/12	.	Superfamily_domains:SSF54849,Pfam_domain:PF00118,Gene3D:3.30.260.10,TIGRFAM_domain:TIGR02345,hmmpanther:PTHR11353:SF22,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGAGCTCCA	.	5	ESCA
CTNNA2	0	.	GRCh37	2	80875207	80875207	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*210G>C	.	.	ENST00000466387	22/22	34	26	7	21	21	0	CTNNA2,3_prime_UTR_variant,,ENST00000496558,;CTNNA2,3_prime_UTR_variant,,ENST00000466387,;CTNNA2,3_prime_UTR_variant,,ENST00000541047,;CTNNA2,3_prime_UTR_variant,,ENST00000343114,;CTNNA2,3_prime_UTR_variant,,ENST00000402739,;CTNNA2,downstream_gene_variant,,ENST00000540488,;CTNNA2,downstream_gene_variant,,ENST00000361291,;	C	ENSG00000066032	ENST00000466387	Transcript	3_prime_UTR_variant	3652	.	.	.	.	.	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTAAGGTGGC	.	5	ESCA
RAB7A	0	.	GRCh37	3	128533176	128533176	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*911C>T	.	.	ENST00000265062	6/6	25	22	3	21	21	0	RAB7A,3_prime_UTR_variant,,ENST00000482525,;RAB7A,3_prime_UTR_variant,,ENST00000265062,;RAB7A,downstream_gene_variant,,ENST00000483906,;RAB7A,downstream_gene_variant,,ENST00000485280,;RAB7A,downstream_gene_variant,,ENST00000493186,;	T	ENSG00000075785	ENST00000265062	Transcript	3_prime_UTR_variant	1781	.	.	.	.	.	.	.	1	RAB7A	HGNC	9788	protein_coding	YES	CCDS3052.1	ENSP00000265062	RAB7A_HUMAN	C9J592_HUMAN	UPI0000001260	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAAACGTTGA	.	2	ESCA
VEPH1	0	.	GRCh37	3	156978891	156978891	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*32C>T	.	.	ENST00000362010	14/14	196	160	35	83	83	0	VEPH1,3_prime_UTR_variant,,ENST00000362010,;VEPH1,3_prime_UTR_variant,,ENST00000392833,;VEPH1,3_prime_UTR_variant,,ENST00000392832,;VEPH1,3_prime_UTR_variant,,ENST00000543418,;RP11-550I24.2,intron_variant,,ENST00000475102,;RP11-550I24.2,intron_variant,,ENST00000487238,;RP11-550I24.2,intron_variant,,ENST00000488040,;	A	ENSG00000197415	ENST00000362010	Transcript	3_prime_UTR_variant	2842	.	.	.	.	.	.	.	-1	VEPH1	HGNC	25735	protein_coding	YES	CCDS3179.1	ENSP00000354919	MELT_HUMAN	C9JRT0_HUMAN,C9J4U8_HUMAN,C9J379_HUMAN,C9IZY4_HUMAN	UPI000013F6EE	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTGGTGTAT	.	4	ESCA
MLF1	0	.	GRCh37	3	158314684	158314684	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.322C>A	p.Gln108Lys	p.Q108K	ENST00000392822	5/9	93	89	4	30	30	0	MLF1,missense_variant,p.Gln52Lys,ENST00000484955,;MLF1,missense_variant,p.Gln67Lys,ENST00000478894,;MLF1,missense_variant,p.Gln77Lys,ENST00000355893,;MLF1,missense_variant,p.Gln67Lys,ENST00000477042,;MLF1,missense_variant,p.Gln52Lys,ENST00000469452,;MLF1,missense_variant,p.Gln108Lys,ENST00000392822,;MLF1,missense_variant,p.Gln3Lys,ENST00000491767,;MLF1,missense_variant,p.Gln52Lys,ENST00000482628,;MLF1,missense_variant,p.Gln32Lys,ENST00000498592,;MLF1,missense_variant,p.Gln67Lys,ENST00000471745,;MLF1,missense_variant,p.Gln92Lys,ENST00000466246,;MLF1,missense_variant,p.Gln52Lys,ENST00000359117,;MLF1,non_coding_transcript_exon_variant,,ENST00000497004,;MLF1,3_prime_UTR_variant,,ENST00000487838,;MLF1,3_prime_UTR_variant,,ENST00000495452,;	A	ENSG00000178053	ENST00000392822	Transcript	missense_variant	589	322	108	Q/K	Caa/Aaa	.	.	.	1	MLF1	HGNC	7125	protein_coding	YES	CCDS56286.1	ENSP00000376568	MLF1_HUMAN	C9K0D3_HUMAN,C9JNE5_HUMAN	UPI000007134A	.	tolerated(0.06)	benign(0.102)	5/9	.	Pfam_domain:PF10248,hmmpanther:PTHR13105,hmmpanther:PTHR13105:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGACCAAATG	.	2	ESCA
SPATA16	0	.	GRCh37	3	172643275	172643275	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089A>G	p.%3D	p.Q363Q	ENST00000351008	7/11	99	76	23	51	51	0	SPATA16,synonymous_variant,p.%3D,ENST00000351008,;	C	ENSG00000144962	ENST00000351008	Transcript	synonymous_variant	1273	1089	363	Q	caA/caG	.	.	.	-1	SPATA16	HGNC	29935	protein_coding	YES	CCDS3221.1	ENSP00000341765	SPT16_HUMAN	.	UPI000013D9BF	.	.	.	7/11	.	hmmpanther:PTHR22904:SF283,hmmpanther:PTHR22904,Pfam_domain:PF15015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCTTGAAG	.	5	ESCA
CCDC39	0	.	GRCh37	3	180369978	180369978	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1007A>T	p.Lys336Met	p.K336M	ENST00000442201	8/20	62	56	5	35	35	0	CCDC39,missense_variant,p.Lys420Met,ENST00000273654,;CCDC39,missense_variant,p.Lys336Met,ENST00000442201,;CCDC39,missense_variant,p.Lys336Met,ENST00000476379,;	A	ENSG00000145075	ENST00000442201	Transcript	missense_variant	1127	1007	336	K/M	aAg/aTg	.	.	.	-1	CCDC39	HGNC	25244	protein_coding	YES	CCDS46964.1	ENSP00000405708	CCD39_HUMAN	.	UPI00015D7298	.	deleterious(0)	probably_damaging(0.993)	8/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18962:SF0,hmmpanther:PTHR18962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTTCTTTATC	.	3	ESCA
DGKG	0	.	GRCh37	3	185865165	185865165	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2714A>C	.	.	ENST00000265022	25/25	30	22	7	12	12	0	DGKG,3_prime_UTR_variant,,ENST00000265022,;DGKG,downstream_gene_variant,,ENST00000544847,;DGKG,downstream_gene_variant,,ENST00000382164,;DGKG,downstream_gene_variant,,ENST00000344484,;DGKG,intron_variant,,ENST00000447054,;DGKG,downstream_gene_variant,,ENST00000490452,;	G	ENSG00000058866	ENST00000265022	Transcript	3_prime_UTR_variant	5630	.	.	.	.	.	.	.	-1	DGKG	HGNC	2853	protein_coding	YES	CCDS3274.1	ENSP00000265022	DGKG_HUMAN	.	UPI000013D5AB	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTCATTGAGAT	.	4	ESCA
SCN11A	0	.	GRCh37	3	38962700	38962700	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.759G>T	p.%3D	p.L253L	ENST00000302328	6/26	18	14	4	17	17	0	SCN11A,synonymous_variant,p.%3D,ENST00000450244,;SCN11A,synonymous_variant,p.%3D,ENST00000302328,;SCN11A,synonymous_variant,p.%3D,ENST00000444237,;SCN11A,synonymous_variant,p.%3D,ENST00000456224,;	A	ENSG00000168356	ENST00000302328	Transcript	synonymous_variant	958	759	253	L	ctG/ctT	.	.	.	-1	SCN11A	HGNC	10583	protein_coding	YES	CCDS33737.1	ENSP00000307599	SCNBA_HUMAN	.	UPI000006CCD7	.	.	.	6/26	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF22,Pfam_domain:PF00520,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TTGACCAGCTT	.	4	ESCA
EPHA3	0	.	GRCh37	3	89530899	89530899	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2247A>G	.	.	ENST00000336596	17/17	77	66	11	28	28	0	EPHA3,3_prime_UTR_variant,,ENST00000336596,;EPHA3,downstream_gene_variant,,ENST00000494014,;	G	ENSG00000044524	ENST00000336596	Transcript	3_prime_UTR_variant	5424	.	.	.	.	.	.	.	1	EPHA3	HGNC	3387	protein_coding	YES	CCDS2922.1	ENSP00000337451	EPHA3_HUMAN	.	UPI0000163BE4	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTGTACGATT	.	3	ESCA
GLRB	0	.	GRCh37	4	158092612	158092612	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*732C>T	.	.	ENST00000264428	10/10	23	20	3	35	35	0	GLRB,3_prime_UTR_variant,,ENST00000264428,;GLRB,3_prime_UTR_variant,,ENST00000541722,;GLRB,downstream_gene_variant,,ENST00000509282,;GLRB,downstream_gene_variant,,ENST00000512619,;	T	ENSG00000109738	ENST00000264428	Transcript	3_prime_UTR_variant	2496	.	.	.	.	.	.	.	1	GLRB	HGNC	4329	protein_coding	YES	CCDS3796.1	ENSP00000264428	GLRB_HUMAN	.	UPI000000161E	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTAATCCACCT	.	2	ESCA
CTNND2	0	.	GRCh37	5	11082930	11082930	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2666G>T	p.Arg889Leu	p.R889L	ENST00000304623	16/22	36	26	9	22	22	0	CTNND2,missense_variant,p.Arg889Leu,ENST00000304623,;CTNND2,missense_variant,p.Arg831Leu,ENST00000359640,;CTNND2,missense_variant,p.Arg552Leu,ENST00000503622,;CTNND2,missense_variant,p.Arg798Leu,ENST00000511377,;CTNND2,missense_variant,p.Arg456Leu,ENST00000458100,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,missense_variant,p.Arg668Leu,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,;	A	ENSG00000169862	ENST00000304623	Transcript	missense_variant	2856	2666	889	R/L	cGa/cTa	COSM1202613	.	.	-1	CTNND2	HGNC	2516	protein_coding	YES	CCDS3881.1	ENSP00000307134	CTND2_HUMAN	E7EPC8_HUMAN,D6RF55_HUMAN,D6RBA8_HUMAN,D6R9A8_HUMAN	UPI000013E9AB	.	deleterious(0)	probably_damaging(1)	16/22	.	Superfamily_domains:SSF48371,SMART_domains:SM00185,Pfam_domain:PF00514,Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	CTTTTCGGACA	.	3	ESCA
KIF3A	0	.	GRCh37	5	132035914	132035914	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1920G>T	p.Glu640Asp	p.E640D	ENST00000378746	15/17	18	10	8	11	11	0	KIF3A,missense_variant,p.Glu126Asp,ENST00000450441,;KIF3A,missense_variant,p.Glu640Asp,ENST00000378746,;KIF3A,missense_variant,p.Glu643Asp,ENST00000378735,;KIF3A,missense_variant,p.Glu667Asp,ENST00000403231,;AC004237.1,intron_variant,,ENST00000431165,;KIF3A,downstream_gene_variant,,ENST00000487055,;KIF3A,upstream_gene_variant,,ENST00000488471,;	A	ENSG00000131437	ENST00000378746	Transcript	missense_variant	2139	1920	640	E/D	gaG/gaT	.	.	.	-1	KIF3A	HGNC	6319	protein_coding	YES	CCDS34235.1	ENSP00000368020	KIF3A_HUMAN	.	UPI000035B258	.	tolerated(0.57)	benign(0.024)	15/17	.	hmmpanther:PTHR24115:SF53,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCTCCTT	.	5	ESCA
DRD1	0	.	GRCh37	5	174870237	174870237	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-135C>A	.	.	ENST00000393752	2/2	31	17	14	40	40	0	DRD1,5_prime_UTR_variant,,ENST00000393752,;	T	ENSG00000184845	ENST00000393752	Transcript	5_prime_UTR_variant	859	.	.	.	.	.	.	.	-1	DRD1	HGNC	3020	protein_coding	YES	CCDS4393.1	ENSP00000377353	DRD1_HUMAN	.	UPI00000503F5	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGGGCCTC	.	5	ESCA
PDCD6	0	.	GRCh37	5	271762	271762	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-74G>T	.	.	ENST00000264933	1/6	16	10	6	14	14	0	PDCD6,5_prime_UTR_variant,,ENST00000505221,;PDCD6,5_prime_UTR_variant,,ENST00000264933,;PDCD6,upstream_gene_variant,,ENST00000507528,;PDCD6,upstream_gene_variant,,ENST00000507473,;PDCD6,upstream_gene_variant,,ENST00000509581,;CTD-2083E4.6,upstream_gene_variant,,ENST00000512642,;PDCD6,non_coding_transcript_exon_variant,,ENST00000515587,;PDCD6,non_coding_transcript_exon_variant,,ENST00000513582,;PDCD6,upstream_gene_variant,,ENST00000505526,;PDCD6,upstream_gene_variant,,ENST00000506909,;	T	ENSG00000249915	ENST00000264933	Transcript	5_prime_UTR_variant	27	.	.	.	.	.	.	.	1	PDCD6	HGNC	8765	protein_coding	YES	CCDS3854.1	ENSP00000264933	PDCD6_HUMAN	Q86W51_HUMAN	UPI00001313D9	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCAGAGGCG	.	5	ESCA
IL31RA	0	.	GRCh37	5	55149326	55149326	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.63+1865G>C	.	.	ENST00000447346	.	54	50	4	59	59	0	IL31RA,5_prime_UTR_variant,,ENST00000396834,;IL31RA,5_prime_UTR_variant,,ENST00000297015,;IL31RA,intron_variant,,ENST00000447346,;IL31RA,intron_variant,,ENST00000359040,;IL31RA,intron_variant,,ENST00000396836,;IL31RA,upstream_gene_variant,,ENST00000490985,;IL31RA,upstream_gene_variant,,ENST00000354961,;	C	ENSG00000164509	ENST00000447346	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	IL31RA	HGNC	18969	protein_coding	YES	CCDS3970.2	ENSP00000415900	IL31R_HUMAN	.	UPI00001A41DC	.	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGGAGGTGGAG	.	2	ESCA
TRIM23	0	.	GRCh37	5	64905171	64905171	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.943C>T	p.Arg315Cys	p.R315C	ENST00000231524	6/11	18	9	8	28	28	0	TRIM23,missense_variant,p.Arg315Cys,ENST00000381018,;TRIM23,missense_variant,p.Arg315Cys,ENST00000231524,;TRIM23,missense_variant,p.Arg315Cys,ENST00000274327,;RNU6-540P,upstream_gene_variant,,ENST00000384622,;TRIM23,non_coding_transcript_exon_variant,,ENST00000508808,;TRIM23,downstream_gene_variant,,ENST00000506400,;TRIM23,downstream_gene_variant,,ENST00000505205,;	A	ENSG00000113595	ENST00000231524	Transcript	missense_variant	1315	943	315	R/C	Cgt/Tgt	COSM3855888,COSM3855889	.	.	-1	TRIM23	HGNC	660	protein_coding	YES	CCDS3987.1	ENSP00000231524	TRI23_HUMAN	D6R9E9_HUMAN	UPI0000125DB3	.	deleterious(0)	possibly_damaging(0.745)	6/11	.	SMART_domains:SM00502	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCACGAACAT	.	5	ESCA
HAPLN1	0	.	GRCh37	5	82937133	82937133	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*182T>C	.	.	ENST00000274341	5/5	15	3	12	9	9	0	HAPLN1,3_prime_UTR_variant,,ENST00000274341,;HAPLN1,downstream_gene_variant,,ENST00000510978,;HAPLN1,downstream_gene_variant,,ENST00000508307,;HAPLN1,downstream_gene_variant,,ENST00000503117,;HAPLN1,downstream_gene_variant,,ENST00000504713,;	G	ENSG00000145681	ENST00000274341	Transcript	3_prime_UTR_variant	2098	.	.	.	.	.	.	.	-1	HAPLN1	HGNC	2380	protein_coding	YES	CCDS4061.1	ENSP00000274341	HPLN1_HUMAN	D6RG04_HUMAN,D6RC59_HUMAN,D6RBX9_HUMAN,D6RBS1_HUMAN	UPI0000131BFF	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATATATTG	.	5	ESCA
TMEM181	0	.	GRCh37	6	159005076	159005076	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670G>A	p.Glu224Lys	p.E224K	ENST00000367090	4/17	17	14	3	27	27	0	TMEM181,missense_variant,p.Glu224Lys,ENST00000367090,;	A	ENSG00000146433	ENST00000367090	Transcript	missense_variant	681	670	224	E/K	Gaa/Aaa	.	.	.	1	TMEM181	HGNC	20958	protein_coding	YES	CCDS43520.1	ENSP00000356057	TM181_HUMAN	.	UPI00001C1E40	.	tolerated(0.27)	benign(0.017)	4/17	.	hmmpanther:PTHR31918,hmmpanther:PTHR31918:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CAAAAGGTATG	.	4	ESCA
FNDC1	0	.	GRCh37	6	159621089	159621089	+	Silent	SNP	T	T	G	rs768691353	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366T>G	p.%3D	p.P122P	ENST00000297267	3/23	51	34	17	43	43	0	FNDC1,synonymous_variant,p.%3D,ENST00000340366,;FNDC1,synonymous_variant,p.%3D,ENST00000297267,;FNDC1,synonymous_variant,p.%3D,ENST00000329629,;	G	ENSG00000164694	ENST00000297267	Transcript	synonymous_variant	566	366	122	P	ccT/ccG	rs768691353	.	.	1	FNDC1	HGNC	21184	protein_coding	YES	CCDS47512.1	ENSP00000297267	FNDC1_HUMAN	.	UPI0000579B80	.	.	.	3/23	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23197:SF8,hmmpanther:PTHR23197,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCCTGTTTA	byFrequency	5	ESCA
BTN2A2	0	.	GRCh37	6	26390424	26390424	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916G>A	p.Glu306Lys	p.E306K	ENST00000356709	5/8	22	17	5	26	26	0	BTN2A2,missense_variant,p.Glu306Lys,ENST00000356709,;BTN2A2,missense_variant,p.Glu190Lys,ENST00000352867,;BTN2A2,missense_variant,p.Glu101Lys,ENST00000490025,;BTN2A2,missense_variant,p.Glu212Lys,ENST00000432533,;BTN2A2,missense_variant,p.Glu306Lys,ENST00000469230,;BTN2A2,missense_variant,p.Glu32Lys,ENST00000495632,;BTN2A2,missense_variant,p.Glu306Lys,ENST00000416795,;BTN2A2,missense_variant,p.Glu96Lys,ENST00000482536,;BTN2A2,downstream_gene_variant,,ENST00000482842,;BTN2A2,downstream_gene_variant,,ENST00000483410,;BTN2A2,downstream_gene_variant,,ENST00000472507,;BTN2A2,downstream_gene_variant,,ENST00000494184,;BTN2A2,downstream_gene_variant,,ENST00000493275,;BTN2A2,non_coding_transcript_exon_variant,,ENST00000467485,;BTN2A2,downstream_gene_variant,,ENST00000482636,;BTN2A2,downstream_gene_variant,,ENST00000471116,;	A	ENSG00000124508	ENST00000356709	Transcript	missense_variant	1027	916	306	E/K	Gaa/Aaa	COSM1076770,COSM1596197	.	.	1	BTN2A2	HGNC	1137	protein_coding	YES	CCDS4606.1	ENSP00000349143	BT2A2_HUMAN	C9JAJ6_HUMAN,C9J8R3_HUMAN,C9IZY2_HUMAN,C9IY66_HUMAN	UPI00000480EA	.	tolerated(0.18)	benign(0.033)	5/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24100:SF43,hmmpanther:PTHR24100	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGAGGAAAAA	.	2	ESCA
GUSBP2	0	.	GRCh37	6	26856948	26856948	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.123G>T	.	.	ENST00000463434	2/5	132	105	27	131	130	0	GUSBP2,non_coding_transcript_exon_variant,,ENST00000463434,;GUSBP2,non_coding_transcript_exon_variant,,ENST00000479900,;GUSBP2,non_coding_transcript_exon_variant,,ENST00000383335,;GUSBP2,non_coding_transcript_exon_variant,,ENST00000492832,;	A	ENSG00000241549	ENST00000463434	Transcript	non_coding_transcript_exon_variant	123	.	.	.	.	.	.	.	-1	GUSBP2	HGNC	18792	processed_transcript	YES	.	.	.	.	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCACTTGAC	.	4	ESCA
SBP1	0	.	GRCh37	6	33663453	33663453	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22C>T	p.Pro8Ser	p.P8S	ENST00000594414	1/1	25	22	3	21	21	0	SBP1,missense_variant,p.Pro8Ser,ENST00000594414,;ITPR3,intron_variant,,ENST00000374316,;ITPR3,intron_variant,,ENST00000605930,;UQCC2,intron_variant,,ENST00000374231,;UQCC2,downstream_gene_variant,,ENST00000374214,;UQCC2,downstream_gene_variant,,ENST00000607484,;MIR3934,upstream_gene_variant,,ENST00000579806,;UQCC2,non_coding_transcript_exon_variant,,ENST00000606961,;	A	ENSG00000269490	ENST00000594414	Transcript	missense_variant	22	22	8	P/S	Ccg/Tcg	.	.	.	-1	SBP1	Uniprot_gn	.	protein_coding	YES	.	ENSP00000469270	.	Q1M2P6_HUMAN	UPI0000D68C5E	.	.	unknown(0)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCGGCCTGA	.	2	ESCA
TRERF1	0	.	GRCh37	6	42236785	42236785	+	Missense_Mutation	SNP	G	G	A	rs201248674	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544C>T	p.Arg182Cys	p.R182C	ENST00000372922	5/18	22	9	13	8	8	0	TRERF1,missense_variant,p.Arg182Cys,ENST00000541110,;TRERF1,missense_variant,p.Arg182Cys,ENST00000340840,;TRERF1,missense_variant,p.Arg182Cys,ENST00000372922,;TRERF1,missense_variant,p.Arg182Cys,ENST00000372917,;TRERF1,missense_variant,p.Arg182Cys,ENST00000354325,;	A	ENSG00000124496	ENST00000372922	Transcript	missense_variant	1107	544	182	R/C	Cgc/Tgc	rs201248674,COSM1754811,COSM4006506,COSM4006505	.	.	-1	TRERF1	HGNC	18273	protein_coding	YES	CCDS4867.1	ENSP00000362013	TREF1_HUMAN	.	UPI0000052952	.	deleterious_low_confidence(0.03)	benign(0.177)	5/18	.	hmmpanther:PTHR16089:SF19,hmmpanther:PTHR16089	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGGCGGAGAG	byCluster	3	ESCA
ZNF318	0	.	GRCh37	6	43305393	43305393	+	Missense_Mutation	SNP	G	G	A	rs141160354	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6343C>T	p.Arg2115Cys	p.R2115C	ENST00000361428	10/10	28	19	9	18	18	0	ZNF318,missense_variant,p.Arg2115Cys,ENST00000361428,;ZNF318,intron_variant,,ENST00000606599,;ZNF318,intron_variant,,ENST00000318149,;ZNF318,intron_variant,,ENST00000605935,;	A	ENSG00000171467	ENST00000361428	Transcript	missense_variant	6421	6343	2115	R/C	Cgt/Tgt	rs141160354	.	.	-1	ZNF318	HGNC	13578	protein_coding	YES	CCDS4895.2	ENSP00000354964	ZN318_HUMAN	.	UPI000049E044	.	.	benign(0.004)	10/10	.	hmmpanther:PTHR15577:SF2,hmmpanther:PTHR15577	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACGGTCAA	byCluster|by1000G	4	ESCA
GTPBP2	0	.	GRCh37	6	43588707	43588707	+	3'UTR	SNP	G	G	A	rs530455578	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*644C>T	.	.	ENST00000307126	12/12	24	15	9	22	22	0	GTPBP2,3_prime_UTR_variant,,ENST00000307126,;GTPBP2,3_prime_UTR_variant,,ENST00000419497,;GTPBP2,3_prime_UTR_variant,,ENST00000432918,;GTPBP2,downstream_gene_variant,,ENST00000307114,;POLH,downstream_gene_variant,,ENST00000535400,;GTPBP2,downstream_gene_variant,,ENST00000452781,;GTPBP2,downstream_gene_variant,,ENST00000442748,;GTPBP2,non_coding_transcript_exon_variant,,ENST00000476510,;GTPBP2,downstream_gene_variant,,ENST00000480263,;GTPBP2,downstream_gene_variant,,ENST00000459959,;GTPBP2,intron_variant,,ENST00000496137,;	A	ENSG00000172432	ENST00000307126	Transcript	3_prime_UTR_variant	2453	.	.	.	.	rs530455578	.	.	-1	GTPBP2	HGNC	4670	protein_coding	YES	CCDS4903.1	ENSP00000303997	GTPB2_HUMAN	.	UPI0000070C45	.	.	.	12/12	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCCGGGAGG	by1000G	5	ESCA
SPAM1	0	.	GRCh37	7	123594116	123594116	+	Silent	SNP	C	C	T	rs777494909	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.492C>T	p.%3D	p.Y164Y	ENST00000340011	3/7	21	13	8	13	13	0	SPAM1,synonymous_variant,p.%3D,ENST00000223028,;SPAM1,synonymous_variant,p.%3D,ENST00000460182,;SPAM1,synonymous_variant,p.%3D,ENST00000439500,;SPAM1,synonymous_variant,p.%3D,ENST00000340011,;SPAM1,synonymous_variant,p.%3D,ENST00000402183,;SPAM1,downstream_gene_variant,,ENST00000413927,;	T	ENSG00000106304	ENST00000340011	Transcript	synonymous_variant	849	492	164	Y	taC/taT	rs777494909	.	.	1	SPAM1	HGNC	11217	protein_coding	YES	CCDS5790.1	ENSP00000345849	HYALP_HUMAN	C9J2X5_HUMAN	UPI0000072166	.	.	.	3/7	.	hmmpanther:PTHR11769:SF20,hmmpanther:PTHR11769,Pfam_domain:PF01630,Gene3D:3.20.20.70,PIRSF_domain:PIRSF500773,PIRSF_domain:PIRSF038193,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTACAAGAA	byFrequency	5	ESCA
LRGUK	0	.	GRCh37	7	133833054	133833054	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652A>C	p.Thr218Pro	p.T218P	ENST00000285928	5/20	16	11	5	15	15	0	LRGUK,missense_variant,p.Thr218Pro,ENST00000285928,;	C	ENSG00000155530	ENST00000285928	Transcript	missense_variant	721	652	218	T/P	Act/Cct	.	.	.	1	LRGUK	HGNC	21964	protein_coding	YES	CCDS5830.1	ENSP00000285928	LRGUK_HUMAN	.	UPI0000072C76	.	deleterious(0.01)	probably_damaging(0.98)	5/20	.	PROSITE_profiles:PS51450,hmmpanther:PTHR10588,hmmpanther:PTHR10588:SF35,Gene3D:3.80.10.10,SMART_domains:SM00365,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTCACTAAA	.	5	ESCA
RNY5	0	.	GRCh37	7	148638612	148638612	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.33T>C	.	.	ENST00000516501	1/1	35	22	12	27	27	0	RNY5,non_coding_transcript_exon_variant,,ENST00000516501,;	C	ENSG00000252310	ENST00000516501	Transcript	non_coding_transcript_exon_variant	33	.	.	.	.	.	.	.	1	RNY5	HGNC	10248	misc_RNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAGTTGATT	.	5	ESCA
NOS3	0	.	GRCh37	7	150695460	150695460	+	Missense_Mutation	SNP	G	G	A	rs746083381	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598G>A	p.Asp200Asn	p.D200N	ENST00000297494	6/27	36	22	13	31	31	0	NOS3,missense_variant,p.Asp200Asn,ENST00000467517,;NOS3,missense_variant,p.Asp200Asn,ENST00000484524,;NOS3,missense_variant,p.Asp200Asn,ENST00000297494,;NOS3,5_prime_UTR_variant,,ENST00000461406,;NOS3,upstream_gene_variant,,ENST00000460603,;	A	ENSG00000164867	ENST00000297494	Transcript	missense_variant	955	598	200	D/N	Gac/Aac	rs746083381	.	.	1	NOS3	HGNC	7876	protein_coding	YES	CCDS5912.1	ENSP00000297494	NOS3_HUMAN	Q96P37_HUMAN,Q96J98_HUMAN,O14937_HUMAN,E7ESA7_HUMAN	UPI000013E417	.	tolerated(0.21)	probably_damaging(0.974)	6/27	.	hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF66,Gene3D:3.90.340.10,Pfam_domain:PF02898,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGGGACTGC	.	5	ESCA
AMPH	0	.	GRCh37	7	38502672	38502672	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.791C>T	p.Pro264Leu	p.P264L	ENST00000356264	10/21	84	79	5	54	54	0	AMPH,missense_variant,p.Pro264Leu,ENST00000356264,;AMPH,missense_variant,p.Pro264Leu,ENST00000428293,;AMPH,missense_variant,p.Pro15Leu,ENST00000441628,;AMPH,missense_variant,p.Pro264Leu,ENST00000325590,;	A	ENSG00000078053	ENST00000356264	Transcript	missense_variant	1007	791	264	P/L	cCt/cTt	.	.	.	-1	AMPH	HGNC	471	protein_coding	YES	CCDS5456.1	ENSP00000348602	AMPH_HUMAN	Q9UQI5_HUMAN,Q9UQI4_HUMAN,Q9UQI3_HUMAN,Q9UQI2_HUMAN	UPI00001259EA	.	deleterious(0.02)	probably_damaging(0.999)	10/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10321,hmmpanther:PTHR10321:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCAGGCGGT	.	2	ESCA
OGDH	0	.	GRCh37	7	44736644	44736644	+	Missense_Mutation	SNP	G	G	A	rs139641350	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2032G>A	p.Val678Met	p.V678M	ENST00000222673	15/23	85	58	27	55	55	0	OGDH,missense_variant,p.Val678Met,ENST00000222673,;OGDH,missense_variant,p.Val629Met,ENST00000543843,;OGDH,missense_variant,p.Val693Met,ENST00000444676,;OGDH,missense_variant,p.Val674Met,ENST00000449767,;OGDH,missense_variant,p.Val689Met,ENST00000447398,;OGDH,missense_variant,p.Val528Met,ENST00000439616,;	A	ENSG00000105953	ENST00000222673	Transcript	missense_variant	2074	2032	678	V/M	Gtg/Atg	rs139641350	.	.	1	OGDH	HGNC	8124	protein_coding	YES	CCDS34627.1	ENSP00000222673	ODO1_HUMAN	C9J4G7_HUMAN	UPI000006D5FE	.	deleterious(0)	probably_damaging(1)	15/23	.	Superfamily_domains:SSF52518,SMART_domains:SM00861,PIRSF_domain:PIRSF000157,TIGRFAM_domain:TIGR00239,Pfam_domain:PF02779,hmmpanther:PTHR23152:SF7,hmmpanther:PTHR23152	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGACGTGGAG	byCluster	5	ESCA
POM121	0	.	GRCh37	7	72361516	72361516	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-349G>T	.	.	ENST00000395270	3/16	51	34	17	30	30	0	POM121,5_prime_UTR_variant,,ENST00000446813,;POM121,5_prime_UTR_variant,,ENST00000257622,;POM121,5_prime_UTR_variant,,ENST00000358357,;POM121,5_prime_UTR_variant,,ENST00000395270,;	T	ENSG00000196313	ENST00000395270	Transcript	5_prime_UTR_variant	693	.	.	.	.	.	.	.	1	POM121	HGNC	19702	protein_coding	YES	CCDS59059.1	ENSP00000378687	P121A_HUMAN	A8MY32_HUMAN	UPI000013DA6B	.	.	.	3/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGAGCAACT	.	5	ESCA
POM121	0	.	GRCh37	7	72361517	72361517	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-348C>T	.	.	ENST00000395270	3/16	51	33	18	30	30	0	POM121,5_prime_UTR_variant,,ENST00000446813,;POM121,5_prime_UTR_variant,,ENST00000257622,;POM121,5_prime_UTR_variant,,ENST00000358357,;POM121,5_prime_UTR_variant,,ENST00000395270,;	T	ENSG00000196313	ENST00000395270	Transcript	5_prime_UTR_variant	694	.	.	.	.	.	.	.	1	POM121	HGNC	19702	protein_coding	YES	CCDS59059.1	ENSP00000378687	P121A_HUMAN	A8MY32_HUMAN	UPI000013DA6B	.	.	.	3/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGAGCAACTT	.	5	ESCA
CASD1	0	.	GRCh37	7	94174972	94174972	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1592C>G	p.Thr531Ser	p.T531S	ENST00000297273	12/18	77	60	16	39	39	0	CASD1,missense_variant,p.Thr531Ser,ENST00000297273,;	G	ENSG00000127995	ENST00000297273	Transcript	missense_variant	1879	1592	531	T/S	aCt/aGt	.	.	.	1	CASD1	HGNC	16014	protein_coding	YES	CCDS5636.1	ENSP00000297273	CASD1_HUMAN	C9JDR3_HUMAN	UPI0000070404	.	deleterious(0.04)	benign(0.144)	12/18	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR13533:SF8,hmmpanther:PTHR13533,Pfam_domain:PF07779	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTACTTTAG	.	5	ESCA
CPSF4	0	.	GRCh37	7	99054131	99054131	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8T>A	.	.	ENST00000292476	8/8	80	55	24	46	46	0	CPSF4,missense_variant,p.Trp184Arg,ENST00000452047,;CPSF4,synonymous_variant,p.%3D,ENST00000440514,;CPSF4,3_prime_UTR_variant,,ENST00000436336,;CPSF4,3_prime_UTR_variant,,ENST00000451876,;CPSF4,3_prime_UTR_variant,,ENST00000292476,;CPSF4,3_prime_UTR_variant,,ENST00000441580,;PTCD1,intron_variant,,ENST00000555673,;ATP5J2-PTCD1,intron_variant,,ENST00000413834,;PTCD1,intron_variant,,ENST00000430982,;ATP5J2,downstream_gene_variant,,ENST00000523680,;ATP5J2,downstream_gene_variant,,ENST00000292475,;ATP5J2,downstream_gene_variant,,ENST00000449683,;ATP5J2,downstream_gene_variant,,ENST00000488775,;ATP5J2,downstream_gene_variant,,ENST00000544611,;ATP5J2,downstream_gene_variant,,ENST00000394186,;ATP5J2,downstream_gene_variant,,ENST00000359832,;ATP5J2,intron_variant,,ENST00000466753,;ATP5J2-PTCD1,intron_variant,,ENST00000437572,;CPSF4,downstream_gene_variant,,ENST00000471455,;CPSF4,non_coding_transcript_exon_variant,,ENST00000469897,;ATP5J2,intron_variant,,ENST00000414062,;ATP5J2-PTCD1,intron_variant,,ENST00000451138,;ATP5J2,downstream_gene_variant,,ENST00000485011,;ATP5J2,downstream_gene_variant,,ENST00000491560,;CPSF4,downstream_gene_variant,,ENST00000465132,;CPSF4,downstream_gene_variant,,ENST00000482251,;ATP5J2,downstream_gene_variant,,ENST00000481899,;ATP5J2,downstream_gene_variant,,ENST00000524321,;	A	ENSG00000160917	ENST00000292476	Transcript	3_prime_UTR_variant	828	.	.	.	.	.	.	.	1	CPSF4	HGNC	2327	protein_coding	YES	CCDS5664.1	ENSP00000292476	CPSF4_HUMAN	C9K0K2_HUMAN	UPI0000072392	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCTGGAGC	.	5	ESCA
LYPLA1	0	.	GRCh37	8	54965225	54965225	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452C>T	p.Ser151Phe	p.S151F	ENST00000316963	7/9	28	20	8	14	14	0	LYPLA1,missense_variant,p.Ser135Phe,ENST00000518546,;LYPLA1,missense_variant,p.Ser135Phe,ENST00000343231,;LYPLA1,missense_variant,p.Ser87Phe,ENST00000521352,;LYPLA1,missense_variant,p.Ser151Phe,ENST00000316963,;LYPLA1,intron_variant,,ENST00000522007,;LYPLA1,downstream_gene_variant,,ENST00000521898,;LYPLA1,non_coding_transcript_exon_variant,,ENST00000520718,;LYPLA1,non_coding_transcript_exon_variant,,ENST00000519272,;LYPLA1,non_coding_transcript_exon_variant,,ENST00000519891,;LYPLA1,downstream_gene_variant,,ENST00000520896,;LYPLA1,downstream_gene_variant,,ENST00000519926,;LYPLA1,downstream_gene_variant,,ENST00000517297,;	A	ENSG00000120992	ENST00000316963	Transcript	missense_variant	646	452	151	S/F	tCc/tTc	.	.	.	-1	LYPLA1	HGNC	6737	protein_coding	YES	CCDS6157.1	ENSP00000320043	LYPA1_HUMAN	Q6IAQ1_HUMAN,E5RJ48_HUMAN,B4DJV9_HUMAN	UPI0000072858	.	deleterious(0.01)	possibly_damaging(0.486)	7/9	.	hmmpanther:PTHR10655:SF22,hmmpanther:PTHR10655,Pfam_domain:PF02230,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGGAAGCC	.	5	ESCA
NSMAF	0	.	GRCh37	8	59510074	59510074	+	Missense_Mutation	SNP	G	G	A	rs781490588	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1757C>T	p.Thr586Met	p.T586M	ENST00000427130	21/31	55	30	25	38	38	0	NSMAF,missense_variant,p.Thr555Met,ENST00000038176,;NSMAF,missense_variant,p.Thr586Met,ENST00000427130,;NSMAF,non_coding_transcript_exon_variant,,ENST00000523982,;NSMAF,upstream_gene_variant,,ENST00000523177,;NSMAF,downstream_gene_variant,,ENST00000519858,;NSMAF,non_coding_transcript_exon_variant,,ENST00000523106,;NSMAF,non_coding_transcript_exon_variant,,ENST00000519227,;NSMAF,upstream_gene_variant,,ENST00000519166,;NSMAF,upstream_gene_variant,,ENST00000519174,;NSMAF,upstream_gene_variant,,ENST00000524148,;	A	ENSG00000035681	ENST00000427130	Transcript	missense_variant	1945	1757	586	T/M	aCg/aTg	rs781490588,COSM1457649,COSM1457648	.	.	-1	NSMAF	HGNC	8017	protein_coding	YES	CCDS47864.1	ENSP00000411012	FAN_HUMAN	.	UPI000192950C	.	deleterious(0.01)	probably_damaging(0.95)	21/31	.	PROSITE_profiles:PS50197,hmmpanther:PTHR13743,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCGTAAGC	byFrequency	5	ESCA
RUNX1T1	0	.	GRCh37	8	92972475	92972475	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1843C>T	p.Arg615Cys	p.R615C	ENST00000436581	11/11	93	79	14	85	85	0	RUNX1T1,missense_variant,p.Arg615Cys,ENST00000436581,;RUNX1T1,missense_variant,p.Arg604Cys,ENST00000265814,;RUNX1T1,missense_variant,p.Arg577Cys,ENST00000518844,;RUNX1T1,missense_variant,p.Arg604Cys,ENST00000523629,;RUNX1T1,missense_variant,p.Arg567Cys,ENST00000360348,;RUNX1T1,missense_variant,p.Arg567Cys,ENST00000520724,;RUNX1T1,missense_variant,p.Arg577Cys,ENST00000396218,;RUNX1T1,missense_variant,p.Arg567Cys,ENST00000422361,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000521078,;RUNX1T1,downstream_gene_variant,,ENST00000521751,;	A	ENSG00000079102	ENST00000436581	Transcript	missense_variant	1854	1843	615	R/C	Cgc/Tgc	COSM1224409,COSM1224408,COSM1224407	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	deleterious_low_confidence(0)	unknown(0)	11/11	.	hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF5	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAGCGAGGGG	.	5	ESCA
TEX10	0	.	GRCh37	9	103065971	103065971	+	Silent	SNP	G	G	A	rs191855673	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2619C>T	p.%3D	p.L873L	ENST00000374902	14/15	35	27	8	18	18	0	TEX10,synonymous_variant,p.%3D,ENST00000374902,;TEX10,synonymous_variant,p.%3D,ENST00000535814,;INVS,downstream_gene_variant,,ENST00000262457,;INVS,downstream_gene_variant,,ENST00000262456,;TEX10,non_coding_transcript_exon_variant,,ENST00000477648,;	A	ENSG00000136891	ENST00000374902	Transcript	synonymous_variant	2796	2619	873	L	ctC/ctT	rs191855673	.	.	-1	TEX10	HGNC	25988	protein_coding	YES	CCDS6748.1	ENSP00000364037	TEX10_HUMAN	.	UPI000013D052	.	.	.	14/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16056,hmmpanther:PTHR16056:SF2	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTGAGGGG	byCluster|by1000G	5	ESCA
OR1J1	0	.	GRCh37	9	125240137	125240137	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69G>T	p.Gln23His	p.Q23H	ENST00000259357	1/1	93	63	30	62	62	0	OR1J1,missense_variant,p.Gln23His,ENST00000259357,;RP11-542K23.9,downstream_gene_variant,,ENST00000412262,;	A	ENSG00000136834	ENST00000259357	Transcript	missense_variant	99	69	23	Q/H	caG/caT	.	.	.	-1	OR1J1	HGNC	8208	protein_coding	YES	CCDS35120.1	ENSP00000259357	OR1J1_HUMAN	.	UPI0000061E79	.	tolerated_low_confidence(0.09)	benign(0.006)	1/1	.	hmmpanther:PTHR26451:SF213,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTGCTGCTC	.	5	ESCA
SIGMAR1	0	.	GRCh37	9	34635103	34635104	+	3'UTR	INS	-	-	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*525dupT	.	.	ENST00000277010	4/4	53	28	25	36	36	0	SIGMAR1,3_prime_UTR_variant,,ENST00000277010,;SIGMAR1,3_prime_UTR_variant,,ENST00000378892,;SIGMAR1,downstream_gene_variant,,ENST00000477726,;SIGMAR1,downstream_gene_variant,,ENST00000497006,;SIGMAR1,downstream_gene_variant,,ENST00000461426,;SIGMAR1,downstream_gene_variant,,ENST00000478146,;SIGMAR1,3_prime_UTR_variant,,ENST00000353468,;GALT,upstream_gene_variant,,ENST00000605275,;	A	ENSG00000147955	ENST00000277010	Transcript	3_prime_UTR_variant	1271-1272	.	.	.	.	.	.	.	-1	SIGMAR1	HGNC	8157	protein_coding	YES	CCDS6562.1	ENSP00000277010	SGMR1_HUMAN	Q5T1J1_HUMAN	UPI00000340A6	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAAGGCATATG	.	3	ESCA
TLN1	0	.	GRCh37	9	35703897	35703897	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6232G>A	p.Val2078Met	p.V2078M	ENST00000314888	47/57	53	36	17	31	31	0	TLN1,missense_variant,p.Val1972Met,ENST00000540444,;TLN1,missense_variant,p.Val2078Met,ENST00000314888,;TLN1,splice_region_variant,,ENST00000464379,;TLN1,upstream_gene_variant,,ENST00000489255,;TLN1,downstream_gene_variant,,ENST00000495712,;TLN1,splice_region_variant,,ENST00000466916,;TLN1,splice_region_variant,,ENST00000465002,;TLN1,downstream_gene_variant,,ENST00000486788,;	T	ENSG00000137076	ENST00000314888	Transcript	missense_variant	6586	6232	2078	V/M	Gtg/Atg	.	.	.	-1	TLN1	HGNC	11845	protein_coding	YES	CCDS35009.1	ENSP00000316029	TLN1_HUMAN	.	UPI0000211375	.	deleterious(0)	probably_damaging(0.965)	47/57	.	Superfamily_domains:SSF47220,Gene3D:1.20.1440.10,hmmpanther:PTHR19981:SF7,hmmpanther:PTHR19981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCACCTGTG	.	5	ESCA
HNRNPH2	0	.	GRCh37	X	100668782	100668782	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*456C>A	.	.	ENST00000316594	2/2	30	25	5	18	18	0	HNRNPH2,3_prime_UTR_variant,,ENST00000316594,;RPL36A-HNRNPH2,downstream_gene_variant,,ENST00000409170,;RPL36A-HNRNPH2,downstream_gene_variant,,ENST00000409338,;ARMCX4,upstream_gene_variant,,ENST00000430461,;ARMCX4,upstream_gene_variant,,ENST00000431677,;ARMCX4,upstream_gene_variant,,ENST00000453574,;ARMCX4,upstream_gene_variant,,ENST00000433011,;	A	ENSG00000126945	ENST00000316594	Transcript	3_prime_UTR_variant	1884	.	.	.	.	.	.	.	1	HNRNPH2	HGNC	5042	protein_coding	YES	CCDS14485.1	ENSP00000361927	HNRH2_HUMAN	.	UPI0000134537	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATACATTGA	.	2	ESCA
F9	0	.	GRCh37	X	138643810	138643810	+	Silent	SNP	C	C	T	rs373107855	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.966C>T	p.%3D	p.D322D	ENST00000218099	8/8	54	9	45	29	29	0	F9,synonymous_variant,p.%3D,ENST00000394090,;F9,synonymous_variant,p.%3D,ENST00000218099,;	T	ENSG00000101981	ENST00000218099	Transcript	synonymous_variant	973	966	322	D	gaC/gaT	rs373107855	.	.	1	F9	HGNC	3551	protein_coding	YES	CCDS14666.1	ENSP00000218099	FA9_HUMAN	Q86XR9_HUMAN,Q19UL6_HUMAN,Q19UK7_HUMAN,Q19UK5_HUMAN,Q19UK4_HUMAN,Q19UK3_HUMAN,Q19UI2_HUMAN,Q19UH6_HUMAN,Q19UG6_HUMAN	UPI000002BA13	.	.	.	8/8	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24265,hmmpanther:PTHR24265:SF23,Pfam_domain:PF00089,Gene3D:2.40.10.10,PIRSF_domain:PIRSF001143,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGACGAACC	byFrequency|byCluster	5	ESCA
DMD	0	.	GRCh37	X	32659625	32659625	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1331+2624A>G	.	.	ENST00000357033	.	15	11	4	21	21	0	DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000357033,;DMD,intron_variant,,ENST00000378677,;DMD,intron_variant,,ENST00000288447,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000447523,;MIR548F5,mature_miRNA_variant,,ENST00000408421,;DMD,intron_variant,,ENST00000480751,;DMD,intron_variant,,ENST00000488902,;	C	ENSG00000198947	ENST00000357033	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	.	.	11/78	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTTTCCCAT	.	2	ESCA
HMGN5	0	.	GRCh37	X	80371790	80371790	+	Silent	SNP	G	G	T	.	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180C>A	p.%3D	p.A60A	ENST00000358130	6/7	27	22	5	20	20	0	HMGN5,synonymous_variant,p.%3D,ENST00000358130,;HMGN5,synonymous_variant,p.%3D,ENST00000451455,;HMGN5,synonymous_variant,p.%3D,ENST00000436386,;HMGN5,synonymous_variant,p.%3D,ENST00000430960,;HMGN5,synonymous_variant,p.%3D,ENST00000447319,;HMGN5,synonymous_variant,p.%3D,ENST00000373250,;HMGN5,non_coding_transcript_exon_variant,,ENST00000491275,;	T	ENSG00000198157	ENST00000358130	Transcript	synonymous_variant	509	180	60	A	gcC/gcA	COSM1125906	.	.	-1	HMGN5	HGNC	8013	protein_coding	YES	CCDS14448.1	ENSP00000350848	HMGN5_HUMAN	Q5JSL0_HUMAN,Q5JSK8_HUMAN,Q5JSK7_HUMAN	UPI0000130542	.	.	.	6/7	.	hmmpanther:PTHR23145,Pfam_domain:PF01101,SMART_domains:SM00527	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A60A|c.180C>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTGGGCACT	.	5	ESCA
SYTL4	0	.	GRCh37	X	99956215	99956215	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A49K-01A-11D-A247-09	TCGA-LN-A49K-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436+1G>A	.	p.X146_splice	ENST00000455616	.	30	27	3	13	13	0	SYTL4,splice_donor_variant,,ENST00000372989,;SYTL4,splice_donor_variant,,ENST00000372981,;SYTL4,splice_donor_variant,,ENST00000454200,;SYTL4,splice_donor_variant,,ENST00000263033,;SYTL4,splice_donor_variant,,ENST00000455616,;SYTL4,splice_donor_variant,,ENST00000276141,;	T	ENSG00000102362	ENST00000455616	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	SYTL4	HGNC	15588	protein_coding	YES	CCDS14472.1	ENSP00000390252	SYTL4_HUMAN	B3KUZ4_HUMAN	UPI00001AE9F2	.	.	.	.	5/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGTACCTGCA	.	3	ESCA
HTRA1	0	.	GRCh37	10	124273783	124273783	+	Missense_Mutation	SNP	G	G	A	rs149822364	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351G>A	p.Val451Ile	p.V451I	ENST00000368984	9/9	31	12	18	70	70	0	HTRA1,missense_variant,p.Val451Ile,ENST00000368984,;HTRA1,missense_variant,p.Val192Ile,ENST00000420892,;	A	ENSG00000166033	ENST00000368984	Transcript	missense_variant	1479	1351	451	V/I	Gtc/Atc	rs149822364,COSM3782519	.	.	1	HTRA1	HGNC	9476	protein_coding	YES	CCDS7630.1	ENSP00000357980	HTRA1_HUMAN	H0Y7G9_HUMAN,A8K224_HUMAN	UPI0000114888	.	tolerated(0.07)	benign(0.006)	9/9	.	PROSITE_profiles:PS50106,hmmpanther:PTHR22939:SF13,hmmpanther:PTHR22939,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	A:0	A:0.0005	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGACGTCATT	byFrequency|byCluster	5	ESCA
OPTN	0	.	GRCh37	10	13151284	13151284	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.162G>A	p.%3D	p.L54L	ENST00000378748	4/16	20	17	3	10	10	0	OPTN,synonymous_variant,p.%3D,ENST00000378748,;OPTN,synonymous_variant,p.%3D,ENST00000378764,;OPTN,synonymous_variant,p.%3D,ENST00000378757,;OPTN,synonymous_variant,p.%3D,ENST00000378752,;OPTN,synonymous_variant,p.%3D,ENST00000263036,;OPTN,synonymous_variant,p.%3D,ENST00000378747,;OPTN,5_prime_UTR_variant,,ENST00000430081,;OPTN,non_coding_transcript_exon_variant,,ENST00000482140,;OPTN,non_coding_transcript_exon_variant,,ENST00000487935,;OPTN,upstream_gene_variant,,ENST00000486862,;SNRPGP5,upstream_gene_variant,,ENST00000456003,;	A	ENSG00000123240	ENST00000378748	Transcript	synonymous_variant	524	162	54	L	ctG/ctA	.	.	.	1	OPTN	HGNC	17142	protein_coding	YES	CCDS7094.1	ENSP00000368022	OPTN_HUMAN	.	UPI000013D38D	.	.	.	4/16	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31553:SF2,hmmpanther:PTHR31553,Pfam_domain:PF11577	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAGCTGAAAGG	.	2	ESCA
DCLRE1C	0	.	GRCh37	10	14950954	14950954	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1532C>A	p.Thr511Lys	p.T511K	ENST00000378278	14/14	79	62	17	35	35	0	DCLRE1C,missense_variant,p.Thr391Lys,ENST00000396817,;DCLRE1C,missense_variant,p.Thr511Lys,ENST00000378278,;DCLRE1C,missense_variant,p.Thr391Lys,ENST00000378258,;DCLRE1C,missense_variant,p.Thr391Lys,ENST00000378254,;DCLRE1C,missense_variant,p.Thr164Lys,ENST00000378242,;DCLRE1C,missense_variant,p.Thr396Lys,ENST00000378246,;DCLRE1C,missense_variant,p.Thr391Lys,ENST00000378255,;DCLRE1C,missense_variant,p.Thr396Lys,ENST00000378249,;DCLRE1C,missense_variant,p.Thr396Lys,ENST00000357717,;DCLRE1C,missense_variant,p.Thr391Lys,ENST00000453695,;DCLRE1C,intron_variant,,ENST00000378289,;SUV39H2,downstream_gene_variant,,ENST00000313519,;DCLRE1C,non_coding_transcript_exon_variant,,ENST00000492201,;DCLRE1C,downstream_gene_variant,,ENST00000489845,;SUV39H2,downstream_gene_variant,,ENST00000378331,;	T	ENSG00000152457	ENST00000378278	Transcript	missense_variant	1570	1532	511	T/K	aCa/aAa	.	.	.	-1	DCLRE1C	HGNC	17642	protein_coding	YES	CCDS31149.1	ENSP00000367527	DCR1C_HUMAN	B3KSJ7_HUMAN	UPI000013EEDC	.	tolerated_low_confidence(0.05)	benign(0.009)	14/14	.	hmmpanther:PTHR23240,hmmpanther:PTHR23240:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTGTGGAG	.	5	ESCA
DCLRE1C	0	.	GRCh37	10	14950955	14950955	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1531A>C	p.Thr511Pro	p.T511P	ENST00000378278	14/14	80	62	17	34	34	0	DCLRE1C,missense_variant,p.Thr391Pro,ENST00000396817,;DCLRE1C,missense_variant,p.Thr511Pro,ENST00000378278,;DCLRE1C,missense_variant,p.Thr391Pro,ENST00000378258,;DCLRE1C,missense_variant,p.Thr391Pro,ENST00000378254,;DCLRE1C,missense_variant,p.Thr164Pro,ENST00000378242,;DCLRE1C,missense_variant,p.Thr396Pro,ENST00000378246,;DCLRE1C,missense_variant,p.Thr391Pro,ENST00000378255,;DCLRE1C,missense_variant,p.Thr396Pro,ENST00000378249,;DCLRE1C,missense_variant,p.Thr396Pro,ENST00000357717,;DCLRE1C,missense_variant,p.Thr391Pro,ENST00000453695,;DCLRE1C,intron_variant,,ENST00000378289,;SUV39H2,downstream_gene_variant,,ENST00000313519,;DCLRE1C,non_coding_transcript_exon_variant,,ENST00000492201,;DCLRE1C,downstream_gene_variant,,ENST00000489845,;SUV39H2,downstream_gene_variant,,ENST00000378331,;	G	ENSG00000152457	ENST00000378278	Transcript	missense_variant	1569	1531	511	T/P	Aca/Cca	.	.	.	-1	DCLRE1C	HGNC	17642	protein_coding	YES	CCDS31149.1	ENSP00000367527	DCR1C_HUMAN	B3KSJ7_HUMAN	UPI000013EEDC	.	deleterious_low_confidence(0.02)	benign(0.323)	14/14	.	hmmpanther:PTHR23240,hmmpanther:PTHR23240:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGTGGAGG	.	5	ESCA
CUBN	0	.	GRCh37	10	17171716	17171716	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.49A>G	p.Ile17Val	p.I17V	ENST00000377833	1/67	121	92	29	63	63	0	CUBN,missense_variant,p.Ile17Val,ENST00000377823,;CUBN,missense_variant,p.Ile17Val,ENST00000377833,;CUBN,upstream_gene_variant,,ENST00000433666,;	C	ENSG00000107611	ENST00000377833	Transcript	missense_variant	115	49	17	I/V	Ata/Gta	.	.	.	-1	CUBN	HGNC	2548	protein_coding	YES	CCDS7113.1	ENSP00000367064	CUBN_HUMAN	B3KQA6_HUMAN	UPI00001AE8F4	.	tolerated(0.7)	benign(0.006)	1/67	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATATTAATA	.	5	ESCA
CHAT	0	.	GRCh37	10	50854688	50854688	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1249G>A	p.Gly417Arg	p.G417R	ENST00000337653	8/15	50	27	23	22	22	0	CHAT,missense_variant,p.Gly299Arg,ENST00000351556,;CHAT,missense_variant,p.Gly335Arg,ENST00000395562,;CHAT,missense_variant,p.Gly299Arg,ENST00000395559,;CHAT,missense_variant,p.Gly299Arg,ENST00000339797,;CHAT,missense_variant,p.Gly299Arg,ENST00000455728,;CHAT,missense_variant,p.Gly417Arg,ENST00000337653,;CHAT,3_prime_UTR_variant,,ENST00000466590,;	A	ENSG00000070748	ENST00000337653	Transcript	missense_variant	1402	1249	417	G/R	Ggg/Agg	CM105868,COSM3709865,COSM3709866	.	.	1	CHAT	HGNC	1912	protein_coding	YES	CCDS7232.1	ENSP00000337103	CLAT_HUMAN	Q6LEN6_HUMAN,Q6LEN5_HUMAN,Q6LDF3_HUMAN	UPI000013F1B9	.	deleterious(0.01)	probably_damaging(0.999)	8/15	.	hmmpanther:PTHR22589:SF14,hmmpanther:PTHR22589,Pfam_domain:PF00755,Superfamily_domains:SSF52777	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACGGGGCC	.	5	ESCA
C10orf53	0	.	GRCh37	10	50916563	50916563	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.374C>T	p.Ser125Leu	p.S125L	ENST00000374112	3/3	180	151	28	84	84	0	C10orf53,missense_variant,p.Ser125Leu,ENST00000374112,;C10orf53,missense_variant,p.Ser125Leu,ENST00000535836,;	T	ENSG00000178645	ENST00000374112	Transcript	missense_variant	386	374	125	S/L	tCa/tTa	.	.	.	1	C10orf53	HGNC	27421	protein_coding	YES	CCDS31202.1	ENSP00000363226	CJ053_HUMAN	.	UPI00001406B3	.	deleterious_low_confidence(0)	unknown(0)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGATCATGTA	.	4	ESCA
ASB13	0	.	GRCh37	10	5682028	5682028	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*638G>A	.	.	ENST00000357700	6/6	51	45	6	29	29	0	ASB13,3_prime_UTR_variant,,ENST00000357700,;ASB13,non_coding_transcript_exon_variant,,ENST00000479033,;ASB13,intron_variant,,ENST00000493897,;ASB13,3_prime_UTR_variant,,ENST00000459912,;	T	ENSG00000196372	ENST00000357700	Transcript	3_prime_UTR_variant	1502	.	.	.	.	.	.	.	-1	ASB13	HGNC	19765	protein_coding	YES	CCDS7070.1	ENSP00000350331	ASB13_HUMAN	.	UPI00001260DE	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTTCCCCCA	.	4	ESCA
PSAP	0	.	GRCh37	10	73587809	73587809	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682G>C	p.Glu228Gln	p.E228Q	ENST00000394936	6/14	52	42	10	35	35	0	PSAP,missense_variant,p.Glu228Gln,ENST00000394934,;PSAP,missense_variant,p.Glu228Gln,ENST00000394936,;	G	ENSG00000197746	ENST00000394936	Transcript	missense_variant	830	682	228	E/Q	Gag/Cag	.	.	.	-1	PSAP	HGNC	9498	protein_coding	YES	CCDS7311.1	ENSP00000378394	SAP_HUMAN	.	UPI0000000DBF	.	tolerated(0.19)	benign(0.063)	6/14	.	PROSITE_profiles:PS50015,hmmpanther:PTHR11480,hmmpanther:PTHR11480:SF36,Gene3D:1.10.225.10,Pfam_domain:PF05184,PIRSF_domain:PIRSF002431,SMART_domains:SM00741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCTTGA	.	5	ESCA
DDIT4	0	.	GRCh37	10	74034859	74034859	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612C>T	p.%3D	p.F204F	ENST00000307365	3/3	34	18	16	26	26	0	DDIT4,synonymous_variant,p.%3D,ENST00000307365,;RP11-442H21.2,non_coding_transcript_exon_variant,,ENST00000491934,;DDIT4,downstream_gene_variant,,ENST00000471240,;DDIT4,downstream_gene_variant,,ENST00000473155,;	T	ENSG00000168209	ENST00000307365	Transcript	synonymous_variant	813	612	204	F	ttC/ttT	.	.	.	1	DDIT4	HGNC	24944	protein_coding	YES	CCDS7315.1	ENSP00000307305	DDIT4_HUMAN	.	UPI000004EC6A	.	.	.	3/3	.	Pfam_domain:PF07809,hmmpanther:PTHR12478:SF7,hmmpanther:PTHR12478	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCAGCCA	.	5	ESCA
NPAT	0	.	GRCh37	11	108031840	108031840	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3973G>C	p.Glu1325Gln	p.E1325Q	ENST00000278612	17/18	40	24	16	45	45	0	NPAT,missense_variant,p.Glu1325Gln,ENST00000278612,;NPAT,downstream_gene_variant,,ENST00000527296,;NPAT,non_coding_transcript_exon_variant,,ENST00000530859,;NPAT,intron_variant,,ENST00000530926,;	G	ENSG00000149308	ENST00000278612	Transcript	missense_variant	4079	3973	1325	E/Q	Gaa/Caa	.	.	.	-1	NPAT	HGNC	7896	protein_coding	YES	CCDS41710.1	ENSP00000278612	NPAT_HUMAN	.	UPI00001FA306	.	deleterious(0)	probably_damaging(0.999)	17/18	.	hmmpanther:PTHR15087:SF5,hmmpanther:PTHR15087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTCACTTC	.	5	ESCA
RDX	0	.	GRCh37	11	110100179	110100179	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1748+2419G>C	.	.	ENST00000405097	.	49	34	15	43	43	0	RDX,3_prime_UTR_variant,,ENST00000343115,;RDX,intron_variant,,ENST00000528900,;RDX,intron_variant,,ENST00000528498,;RDX,intron_variant,,ENST00000530301,;RDX,intron_variant,,ENST00000405097,;RDX,downstream_gene_variant,,ENST00000544551,;RDX,downstream_gene_variant,,ENST00000530085,;RDX,non_coding_transcript_exon_variant,,ENST00000527537,;RDX,non_coding_transcript_exon_variant,,ENST00000532461,;RDX,intron_variant,,ENST00000530749,;RDX,downstream_gene_variant,,ENST00000530131,;RDX,downstream_gene_variant,,ENST00000533961,;	G	ENSG00000137710	ENST00000405097	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RDX	HGNC	9944	protein_coding	YES	CCDS58174.1	ENSP00000384136	RADI_HUMAN	Q9NST9_HUMAN,E9PQ82_HUMAN,E9PNV3_HUMAN,E9PKN5_HUMAN,B0YJ88_HUMAN	UPI0000EE3914	.	.	.	.	14/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAGCTTTTG	.	5	ESCA
USP47	0	.	GRCh37	11	11958055	11958055	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1871G>A	p.Gly624Glu	p.G624E	ENST00000339865	16/27	32	27	5	15	15	0	USP47,missense_variant,p.Gly712Glu,ENST00000399455,;USP47,missense_variant,p.Gly692Glu,ENST00000527733,;USP47,missense_variant,p.Gly624Glu,ENST00000339865,;USP47,splice_region_variant,,ENST00000539466,;USP47,upstream_gene_variant,,ENST00000525078,;	A	ENSG00000170242	ENST00000339865	Transcript	missense_variant	2634	1871	624	G/E	gGa/gAa	.	.	.	1	USP47	HGNC	20076	protein_coding	YES	CCDS41619.1	ENSP00000339957	UBP47_HUMAN	.	UPI00001F9D69	.	deleterious(0)	probably_damaging(0.999)	16/27	.	Superfamily_domains:SSF54236,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTGGAGGTG	.	4	ESCA
GRIK4	0	.	GRCh37	11	120776146	120776146	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1420G>C	p.Gly474Arg	p.G474R	ENST00000527524	13/21	14	7	7	17	17	0	GRIK4,missense_variant,p.Gly474Arg,ENST00000438375,;GRIK4,missense_variant,p.Gly474Arg,ENST00000527524,;GRIK4,non_coding_transcript_exon_variant,,ENST00000533291,;	C	ENSG00000149403	ENST00000527524	Transcript	missense_variant	1707	1420	474	G/R	Ggc/Cgc	.	.	.	1	GRIK4	HGNC	4582	protein_coding	YES	CCDS8433.1	ENSP00000435648	GRIK4_HUMAN	.	UPI000013DB8D	.	deleterious(0)	probably_damaging(1)	13/21	.	hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Gene3D:3.40.190.10,Pfam_domain:PF10613,SMART_domains:SM00918,SMART_domains:SM00079,Superfamily_domains:SSF53850,Prints_domain:PR00177	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTACGGCGTT	.	5	ESCA
BLID	0	.	GRCh37	11	121986237	121986237	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67A>T	.	.	ENST00000560104	1/1	35	17	17	46	46	0	BLID,3_prime_UTR_variant,,ENST00000560104,;RP11-166D19.1,intron_variant,,ENST00000534297,;	A	ENSG00000259571	ENST00000560104	Transcript	3_prime_UTR_variant	687	.	.	.	.	.	.	.	-1	BLID	HGNC	33495	protein_coding	YES	CCDS31693.1	ENSP00000453153	BLID_HUMAN	.	UPI0000161930	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTTGTGCA	.	5	ESCA
ROBO3	0	.	GRCh37	11	124743663	124743663	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1689G>C	p.%3D	p.V563V	ENST00000397801	11/28	20	12	8	19	19	0	ROBO3,synonymous_variant,p.%3D,ENST00000538940,;ROBO3,synonymous_variant,p.%3D,ENST00000397801,;ROBO3,upstream_gene_variant,,ENST00000543966,;ROBO3,upstream_gene_variant,,ENST00000525482,;ROBO3,upstream_gene_variant,,ENST00000531075,;ROBO3,upstream_gene_variant,,ENST00000528144,;ROBO3,upstream_gene_variant,,ENST00000531545,;ROBO3,upstream_gene_variant,,ENST00000532472,;ROBO3,upstream_gene_variant,,ENST00000528820,;ROBO3,upstream_gene_variant,,ENST00000526551,;ROBO3,upstream_gene_variant,,ENST00000525304,;ROBO3,upstream_gene_variant,,ENST00000534598,;ROBO3,upstream_gene_variant,,ENST00000527196,;ROBO3,upstream_gene_variant,,ENST00000529658,;ROBO3,upstream_gene_variant,,ENST00000528068,;ROBO3,upstream_gene_variant,,ENST00000530647,;ROBO3,upstream_gene_variant,,ENST00000531119,;ROBO3,upstream_gene_variant,,ENST00000531888,;ROBO3,upstream_gene_variant,,ENST00000527245,;ROBO3,upstream_gene_variant,,ENST00000525448,;ROBO3,upstream_gene_variant,,ENST00000524971,;	C	ENSG00000154134	ENST00000397801	Transcript	synonymous_variant	1881	1689	563	V	gtG/gtC	.	.	.	1	ROBO3	HGNC	13433	protein_coding	YES	CCDS44755.1	ENSP00000380903	ROBO3_HUMAN	Q9H7C7_HUMAN,Q96HH0_HUMAN,F5H0K7_HUMAN	UPI000035AA82	.	.	.	11/28	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF92,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTGGTCAC	.	5	ESCA
JAM3	0	.	GRCh37	11	134014718	134014718	+	Silent	SNP	G	G	A	rs371009569	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441G>A	p.%3D	p.P147P	ENST00000299106	5/9	29	19	10	45	45	0	JAM3,synonymous_variant,p.%3D,ENST00000441717,;JAM3,synonymous_variant,p.%3D,ENST00000529443,;JAM3,synonymous_variant,p.%3D,ENST00000299106,;JAM3,synonymous_variant,p.%3D,ENST00000534549,;JAM3,non_coding_transcript_exon_variant,,ENST00000524969,;JAM3,non_coding_transcript_exon_variant,,ENST00000532165,;JAM3,3_prime_UTR_variant,,ENST00000532252,;JAM3,non_coding_transcript_exon_variant,,ENST00000531302,;JAM3,upstream_gene_variant,,ENST00000533711,;	A	ENSG00000166086	ENST00000299106	Transcript	synonymous_variant	600	441	147	P	ccG/ccA	rs371009569	.	.	1	JAM3	HGNC	15532	protein_coding	YES	CCDS8494.2	ENSP00000299106	JAM3_HUMAN	.	UPI0000034063	.	.	.	5/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12231:SF5,hmmpanther:PTHR12231,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCCGAAGGC	byFrequency|byCluster	5	ESCA
SLC6A5	0	.	GRCh37	11	20623033	20623033	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.362A>G	p.Lys121Arg	p.K121R	ENST00000525748	2/16	28	19	8	24	24	0	SLC6A5,missense_variant,p.Lys121Arg,ENST00000525748,;SLC6A5,missense_variant,p.Lys121Arg,ENST00000298923,;	G	ENSG00000165970	ENST00000525748	Transcript	missense_variant	635	362	121	K/R	aAg/aGg	.	.	.	1	SLC6A5	HGNC	11051	protein_coding	YES	CCDS7854.1	ENSP00000434364	SC6A5_HUMAN	.	UPI00004564A5	.	tolerated_low_confidence(0.11)	benign(0.002)	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L118L|c.352C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTAAGATCC	.	5	ESCA
FANCF	0	.	GRCh37	11	22647031	22647031	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326A>G	p.Tyr109Cys	p.Y109C	ENST00000327470	1/1	31	12	18	43	43	0	FANCF,missense_variant,p.Tyr109Cys,ENST00000327470,;AC103801.2,5_prime_UTR_variant,,ENST00000428556,;GAS2,upstream_gene_variant,,ENST00000528582,;	C	ENSG00000183161	ENST00000327470	Transcript	missense_variant	357	326	109	Y/C	tAc/tGc	.	.	.	-1	FANCF	HGNC	3587	protein_coding	YES	CCDS7857.1	ENSP00000330875	FANCF_HUMAN	A3KME0_HUMAN	UPI000012A4CA	.	tolerated(0.05)	possibly_damaging(0.455)	1/1	.	hmmpanther:PTHR14449,hmmpanther:PTHR14449:SF2,Pfam_domain:PF11107	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGGTAACGA	.	5	ESCA
OR4C16	0	.	GRCh37	11	55339985	55339985	+	Silent	SNP	C	C	T	rs756023612	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382C>T	p.%3D	p.L128L	ENST00000314634	1/1	55	19	36	51	51	0	OR4C16,synonymous_variant,p.%3D,ENST00000314634,;	T	ENSG00000181935	ENST00000314634	Transcript	synonymous_variant	382	382	128	L	Ctg/Ttg	rs756023612	.	.	1	OR4C16	HGNC	15172	protein_coding	YES	CCDS31502.1	ENSP00000324913	OR4CG_HUMAN	.	UPI000013F8A8	.	.	.	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF223,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCCTGCAC	.	5	ESCA
OR9G1	0	.	GRCh37	11	56468326	56468326	+	Missense_Mutation	SNP	T	T	C	rs746966678	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.463T>C	p.Ser155Pro	p.S155P	ENST00000312153	1/1	101	87	14	111	111	0	OR9G1,missense_variant,p.Ser155Pro,ENST00000312153,;	C	ENSG00000174914	ENST00000312153	Transcript	missense_variant	463	463	155	S/P	Tct/Cct	rs746966678	.	.	1	OR9G1	HGNC	15319	protein_coding	YES	CCDS31536.1	ENSP00000309012	OR9G1_HUMAN	.	UPI0000061E7E	.	deleterious(0)	benign(0.151)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR24242:SF158,hmmpanther:PTHR24242,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTAACTCTTCA	byFrequency	3	ESCA
FAM111A	0	.	GRCh37	11	58920609	58920609	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000528737	5/5	14	10	4	21	21	0	FAM111A,stop_gained,p.Gln490Ter,ENST00000361723,;FAM111A,stop_gained,p.Gln490Ter,ENST00000420244,;FAM111A,stop_gained,p.Gln490Ter,ENST00000528737,;FAM111A,stop_gained,p.Gln490Ter,ENST00000531147,;FAM111A,stop_gained,p.Gln490Ter,ENST00000533703,;FAM111A,downstream_gene_variant,,ENST00000531408,;FAM111A,downstream_gene_variant,,ENST00000527629,;FAM111A,downstream_gene_variant,,ENST00000529358,;FAM111A,downstream_gene_variant,,ENST00000532790,;	T	ENSG00000166801	ENST00000528737	Transcript	stop_gained	4286	1468	490	Q/*	Cag/Tag	.	.	.	1	FAM111A	HGNC	24725	protein_coding	YES	CCDS7973.1	ENSP00000434435	F111A_HUMAN	E9PR18_HUMAN,E9PNQ0_HUMAN	UPI00001FA7CB	.	.	.	5/5	.	hmmpanther:PTHR14389:SF14,hmmpanther:PTHR14389,Gene3D:2.40.10.10,Pfam_domain:PF13365,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTCAGGGT	.	5	ESCA
MS4A4E	0	.	GRCh37	11	59982060	59982060	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>A	p.Glu58Lys	p.E58K	ENST00000425663	2/4	23	17	5	26	26	0	MS4A4E,missense_variant,p.Glu101Lys,ENST00000398984,;MS4A4E,missense_variant,p.Glu101Lys,ENST00000528394,;MS4A4E,missense_variant,p.Glu88Lys,ENST00000427611,;MS4A4E,missense_variant,p.Arg69Lys,ENST00000526086,;MS4A4E,missense_variant,p.Arg69Lys,ENST00000398986,;MS4A4E,missense_variant,p.Glu58Lys,ENST00000425663,;MS4A4E,3_prime_UTR_variant,,ENST00000526153,;MS4A4E,3_prime_UTR_variant,,ENST00000532442,;	T	ENSG00000214787	ENST00000425663	Transcript	missense_variant	172	172	58	E/K	Gaa/Aaa	.	.	.	-1	MS4A4E	HGNC	14284	protein_coding	YES	.	ENSP00000389556	M4A4E_HUMAN	.	UPI000173AA13	.	tolerated_low_confidence(0.11)	possibly_damaging(0.486)	2/4	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTCTAATT	.	5	ESCA
SLC3A2	0	.	GRCh37	11	62623743	62623765	+	Frame_Shift_Del	DEL	TGGAGCTACAGCCTCCTGAAGCC	TGGAGCTACAGCCTCCTGAAGCC	-	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	TGGAGCTACAGCCTCCTGAAGCC	TGGAGCTACAGCCTCCTGAAGCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3_25delGGAGCTACAGCCTCCTGAAGCCT	p.Met1_?9	p.M1_?9	ENST00000377891	1/12	33	24	9	28	28	0	SLC3A2,frameshift_variant,p.Met1_?9,ENST00000377892,;SLC3A2,frameshift_variant,p.Met1_?9,ENST00000377891,;SLC3A2,frameshift_variant,p.Met1_?9,ENST00000377890,;SLC3A2,frameshift_variant,p.Met1_?9,ENST00000377889,;SLC3A2,frameshift_variant,p.Met1_?9,ENST00000535296,;SNHG1,upstream_gene_variant,,ENST00000365607,;SNHG1,upstream_gene_variant,,ENST00000384756,;SNHG1,upstream_gene_variant,,ENST00000384147,;SNHG1,upstream_gene_variant,,ENST00000539303,;SNHG1,upstream_gene_variant,,ENST00000383926,;SNHG1,upstream_gene_variant,,ENST00000537925,;SNHG1,upstream_gene_variant,,ENST00000545440,;SNHG1,upstream_gene_variant,,ENST00000540725,;SNHG1,upstream_gene_variant,,ENST00000537068,;SNHG1,upstream_gene_variant,,ENST00000539975,;SNHG1,upstream_gene_variant,,ENST00000364799,;SNHG1,upstream_gene_variant,,ENST00000541615,;SNHG1,upstream_gene_variant,,ENST00000538266,;SNHG1,upstream_gene_variant,,ENST00000537869,;SNHG1,upstream_gene_variant,,ENST00000384706,;SNHG1,upstream_gene_variant,,ENST00000516331,;SNHG1,upstream_gene_variant,,ENST00000384693,;SNHG1,upstream_gene_variant,,ENST00000541578,;SNHG1,upstream_gene_variant,,ENST00000539921,;SNHG1,upstream_gene_variant,,ENST00000542112,;SNHG1,upstream_gene_variant,,ENST00000363981,;SNHG1,upstream_gene_variant,,ENST00000540904,;SNHG1,upstream_gene_variant,,ENST00000544550,;SNHG1,upstream_gene_variant,,ENST00000537024,;SNHG1,upstream_gene_variant,,ENST00000545688,;SNHG1,upstream_gene_variant,,ENST00000541416,;SNHG1,upstream_gene_variant,,ENST00000545920,;SNHG1,upstream_gene_variant,,ENST00000545308,;SNHG1,upstream_gene_variant,,ENST00000535076,;SNHG1,upstream_gene_variant,,ENST00000537965,;SNHG1,upstream_gene_variant,,ENST00000538654,;SNHG1,upstream_gene_variant,,ENST00000544983,;SNHG1,upstream_gene_variant,,ENST00000540865,;SNHG1,upstream_gene_variant,,ENST00000535689,;	-	ENSG00000168003	ENST00000377891	Transcript	frameshift_variant	161-183	2-24	1-8	MELQPPEA/X	aTGGAGCTACAGCCTCCTGAAGCC/a	.	.	.	1	SLC3A2	HGNC	11026	protein_coding	YES	CCDS31588.1	ENSP00000367123	.	J3KPF3_HUMAN,F5H867_HUMAN,F5H056_HUMAN,F5GZI0_HUMAN,B4E2Z3_HUMAN	UPI00004EC298	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTCCATGGAGCTACAGCCTCCTGAAGCCTCGAT	.	3	ESCA
NRXN2	0	.	GRCh37	11	64428408	64428408	+	Nonsense_Mutation	SNP	G	G	A	rs770105914	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2002C>T	p.Arg668Ter	p.R668*	ENST00000265459	10/23	18	12	6	13	13	0	NRXN2,stop_gained,p.Arg668Ter,ENST00000377551,;NRXN2,stop_gained,p.Arg668Ter,ENST00000265459,;NRXN2,stop_gained,p.Arg661Ter,ENST00000409571,;NRXN2,stop_gained,p.Arg637Ter,ENST00000377559,;AP001092.4,downstream_gene_variant,,ENST00000433606,;NRXN2,non_coding_transcript_exon_variant,,ENST00000496291,;NRXN2,upstream_gene_variant,,ENST00000486057,;	A	ENSG00000110076	ENST00000265459	Transcript	stop_gained	2464	2002	668	R/*	Cga/Tga	rs770105914	.	.	-1	NRXN2	HGNC	8009	protein_coding	YES	CCDS8077.1	ENSP00000265459	NRX2A_HUMAN	.	UPI0000130AA2	.	.	.	10/23	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF593,hmmpanther:PTHR10127,Gene3D:2.60.120.200,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTCGGCTAC	.	5	ESCA
PYGM	0	.	GRCh37	11	64519395	64519395	+	Splice_Site	DEL	C	C	-	rs771427957	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1768+1delG	.	p.X590_splice	ENST00000164139	.	101	90	11	106	106	0	PYGM,splice_donor_variant,,ENST00000164139,;PYGM,splice_donor_variant,,ENST00000377432,;PYGM,splice_donor_variant,,ENST00000462303,;PYGM,downstream_gene_variant,,ENST00000460413,;PYGM,upstream_gene_variant,,ENST00000483742,;	-	ENSG00000068976	ENST00000164139	Transcript	splice_donor_variant	.	.	.	.	.	rs771427957,CS941537	.	.	-1	PYGM	HGNC	9726	protein_coding	YES	CCDS8079.1	ENSP00000164139	PYGM_HUMAN	.	UPI000013C5AC	.	.	.	.	14/19	.	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	HIGH	.	deletion	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CACTCACGGTTG	byFrequency	3	ESCA
CFL1	0	.	GRCh37	11	65623715	65623715	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4-2A>T	.	p.X2_splice	ENST00000525451	.	31	23	7	25	25	0	CFL1,splice_acceptor_variant,,ENST00000534769,;CFL1,splice_acceptor_variant,,ENST00000531407,;CFL1,splice_acceptor_variant,,ENST00000308162,;CFL1,splice_acceptor_variant,,ENST00000527344,;CFL1,splice_acceptor_variant,,ENST00000526975,;CFL1,splice_acceptor_variant,,ENST00000534784,;CFL1,splice_acceptor_variant,,ENST00000532134,;CFL1,splice_acceptor_variant,,ENST00000531413,;CFL1,splice_acceptor_variant,,ENST00000524553,;CFL1,splice_acceptor_variant,,ENST00000525451,;CFL1,5_prime_UTR_variant,,ENST00000530413,;MUS81,upstream_gene_variant,,ENST00000533035,;MUS81,upstream_gene_variant,,ENST00000529857,;SNX32,downstream_gene_variant,,ENST00000308342,;MUS81,upstream_gene_variant,,ENST00000525768,;MUS81,upstream_gene_variant,,ENST00000308110,;MUS81,upstream_gene_variant,,ENST00000529374,;CFL1,intron_variant,,ENST00000527752,;CFL1,splice_acceptor_variant,,ENST00000530945,;SNX32,non_coding_transcript_exon_variant,,ENST00000530101,;SNX32,downstream_gene_variant,,ENST00000526972,;SNX32,downstream_gene_variant,,ENST00000533236,;MUS81,upstream_gene_variant,,ENST00000524647,;	A	ENSG00000172757	ENST00000525451	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	CFL1	HGNC	1874	protein_coding	YES	CCDS8114.1	ENSP00000432660	COF1_HUMAN	G3V1A4_HUMAN,E9PS23_HUMAN,E9PQB7_HUMAN,E9PP50_HUMAN,E9PLJ3_HUMAN	UPI0000127E2C	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCTAGGAG	.	5	ESCA
FIBP	0	.	GRCh37	11	65653041	65653041	+	Silent	SNP	G	G	A	rs764460613	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606C>T	p.%3D	p.C202C	ENST00000338369	5/10	24	14	10	21	21	0	FIBP,synonymous_variant,p.%3D,ENST00000357519,;FIBP,synonymous_variant,p.%3D,ENST00000338369,;FIBP,synonymous_variant,p.%3D,ENST00000533045,;CTSW,downstream_gene_variant,,ENST00000526034,;CTSW,downstream_gene_variant,,ENST00000307886,;CTSW,downstream_gene_variant,,ENST00000528419,;CCDC85B,upstream_gene_variant,,ENST00000312579,;FIBP,downstream_gene_variant,,ENST00000426652,;FIBP,synonymous_variant,p.%3D,ENST00000531115,;FIBP,3_prime_UTR_variant,,ENST00000532229,;FIBP,3_prime_UTR_variant,,ENST00000533037,;FIBP,non_coding_transcript_exon_variant,,ENST00000532679,;FIBP,non_coding_transcript_exon_variant,,ENST00000525765,;FIBP,non_coding_transcript_exon_variant,,ENST00000534032,;FIBP,non_coding_transcript_exon_variant,,ENST00000532934,;FIBP,downstream_gene_variant,,ENST00000528937,;CTSW,downstream_gene_variant,,ENST00000524681,;FIBP,downstream_gene_variant,,ENST00000442885,;	A	ENSG00000172500	ENST00000338369	Transcript	synonymous_variant	719	606	202	C	tgC/tgT	rs764460613	.	.	-1	FIBP	HGNC	3705	protein_coding	YES	CCDS8119.1	ENSP00000344572	FIBP_HUMAN	B4DKH9_HUMAN	UPI000012A79E	.	.	.	5/10	.	Pfam_domain:PF05427,hmmpanther:PTHR13223,hmmpanther:PTHR13223:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCGCAGAA	byFrequency	5	ESCA
SCYL2	0	.	GRCh37	12	100676832	100676832	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84C>A	p.%3D	p.V28V	ENST00000360820	2/18	61	45	16	33	33	0	SCYL2,synonymous_variant,p.%3D,ENST00000360820,;SCYL2,synonymous_variant,p.%3D,ENST00000549687,;SCYL2,intron_variant,,ENST00000548392,;SCYL2,non_coding_transcript_exon_variant,,ENST00000550067,;SCYL2,upstream_gene_variant,,ENST00000549486,;	A	ENSG00000136021	ENST00000360820	Transcript	synonymous_variant	521	84	28	V	gtC/gtA	.	.	.	1	SCYL2	HGNC	19286	protein_coding	YES	CCDS9076.1	ENSP00000354061	SCYL2_HUMAN	F8VSC5_HUMAN,F8VPW3_HUMAN	UPI000004FD59	.	.	.	2/18	.	hmmpanther:PTHR12984,hmmpanther:PTHR12984:SF6,Gene3D:3.30.200.20,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGTCACTAG	.	5	ESCA
PARPBP	0	.	GRCh37	12	102558360	102558360	+	Nonsense_Mutation	SNP	C	C	T	rs753543416	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640C>T	p.Arg214Ter	p.R214*	ENST00000358383	5/11	38	26	11	34	34	0	PARPBP,stop_gained,p.Arg214Ter,ENST00000358383,;PARPBP,stop_gained,p.Arg100Ter,ENST00000543784,;PARPBP,stop_gained,p.Arg214Ter,ENST00000378128,;PARPBP,stop_gained,p.Arg291Ter,ENST00000541394,;PARPBP,stop_gained,p.Arg181Ter,ENST00000417507,;PARPBP,stop_gained,p.Arg133Ter,ENST00000327680,;PARPBP,stop_gained,p.Arg133Ter,ENST00000392911,;PARPBP,stop_gained,p.Arg181Ter,ENST00000412715,;PARPBP,intron_variant,,ENST00000535811,;PARPBP,intron_variant,,ENST00000457614,;	T	ENSG00000185480	ENST00000358383	Transcript	stop_gained	685	640	214	R/*	Cga/Tga	rs753543416	.	.	1	PARPBP	HGNC	26074	protein_coding	YES	CCDS9090.2	ENSP00000351153	PARI_HUMAN	.	UPI000004A06B	.	.	.	5/11	.	Superfamily_domains:SSF52540,Gene3D:1.10.486.10,hmmpanther:PTHR32121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCGAGAG	.	5	ESCA
ZNF268	0	.	GRCh37	12	133778860	133778860	+	Silent	SNP	A	A	T	rs773618062	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588A>T	p.%3D	p.S196S	ENST00000536435	6/6	24	16	8	36	36	0	ZNF268,missense_variant,p.Gln122Leu,ENST00000539248,;ZNF268,missense_variant,p.Gln154Leu,ENST00000541211,;ZNF268,missense_variant,p.Gln55Leu,ENST00000536899,;ZNF268,missense_variant,p.Gln87Leu,ENST00000542711,;ZNF268,synonymous_variant,p.%3D,ENST00000536435,;ZNF268,synonymous_variant,p.%3D,ENST00000537565,;ZNF268,synonymous_variant,p.%3D,ENST00000228289,;ZNF268,3_prime_UTR_variant,,ENST00000416488,;CTD-2140B24.4,3_prime_UTR_variant,,ENST00000540096,;ZNF268,3_prime_UTR_variant,,ENST00000591951,;ZNF268,3_prime_UTR_variant,,ENST00000542986,;ZNF268,3_prime_UTR_variant,,ENST00000541009,;ZNF268,3_prime_UTR_variant,,ENST00000592241,;ZNF268,downstream_gene_variant,,ENST00000500625,;ZNF268,3_prime_UTR_variant,,ENST00000588312,;ZNF268,non_coding_transcript_exon_variant,,ENST00000534953,;ZNF268,downstream_gene_variant,,ENST00000585488,;	T	ENSG00000090612	ENST00000536435	Transcript	synonymous_variant	918	588	196	S	tcA/tcT	rs773618062	.	.	1	ZNF268	HGNC	13061	protein_coding	YES	CCDS45012.1	ENSP00000444412	ZN268_HUMAN	Q9H337_HUMAN,K7EMS6_HUMAN,F5H467_HUMAN	UPI000013C33E	.	.	.	6/6	.	hmmpanther:PTHR24377:SF255,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTCAAGACA	.	5	ESCA
CAPRIN2	0	.	GRCh37	12	30873757	30873757	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2136A>T	p.%3D	p.S712S	ENST00000298892	12/17	36	28	8	25	25	0	CAPRIN2,synonymous_variant,p.%3D,ENST00000433722,;CAPRIN2,synonymous_variant,p.%3D,ENST00000308433,;CAPRIN2,synonymous_variant,p.%3D,ENST00000251071,;CAPRIN2,synonymous_variant,p.%3D,ENST00000537108,;CAPRIN2,synonymous_variant,p.%3D,ENST00000298892,;CAPRIN2,synonymous_variant,p.%3D,ENST00000417045,;CAPRIN2,intron_variant,,ENST00000395805,;CAPRIN2,3_prime_UTR_variant,,ENST00000548676,;CAPRIN2,3_prime_UTR_variant,,ENST00000537553,;CAPRIN2,3_prime_UTR_variant,,ENST00000454014,;	A	ENSG00000110888	ENST00000298892	Transcript	synonymous_variant	2887	2136	712	S	tcA/tcT	.	.	.	-1	CAPRIN2	HGNC	21259	protein_coding	YES	CCDS8720.1	ENSP00000298892	CAPR2_HUMAN	F5H7T6_HUMAN,F5H5J8_HUMAN,F5GZX3_HUMAN,F5GYA1_HUMAN,F5GXI7_HUMAN	UPI000007080A	.	.	.	12/17	.	hmmpanther:PTHR22922,hmmpanther:PTHR22922:SF5,Pfam_domain:PF12287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTCTGAGGT	.	5	ESCA
VDR	0	.	GRCh37	12	48238609	48238609	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1354C>G	p.Arg452Gly	p.R452G	ENST00000550325	10/10	89	74	14	70	70	0	VDR,missense_variant,p.Arg402Gly,ENST00000229022,;VDR,missense_variant,p.Arg370Gly,ENST00000535672,;VDR,missense_variant,p.Arg402Gly,ENST00000549336,;VDR,missense_variant,p.Arg452Gly,ENST00000550325,;VDR,missense_variant,p.Arg402Gly,ENST00000395324,;VDR,3_prime_UTR_variant,,ENST00000547065,;	C	ENSG00000111424	ENST00000550325	Transcript	missense_variant	1727	1354	452	R/G	Cgc/Ggc	.	.	.	-1	VDR	HGNC	12679	protein_coding	YES	CCDS55820.1	ENSP00000447173	VDR_HUMAN	T1WSQ6_HUMAN,Q6T928_HUMAN,F8VXQ9_HUMAN,F8VVY8_HUMAN,F8VRJ4_HUMAN,F8VPF8_HUMAN,F1D8P8_HUMAN	UPI000015B2DC	.	deleterious(0)	probably_damaging(0.992)	10/10	.	hmmpanther:PTHR24082:SF38,hmmpanther:PTHR24082,Gene3D:1.10.565.10,Pfam_domain:PF00104,Superfamily_domains:SSF48508	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGGTACT	.	5	ESCA
SENP1	0	.	GRCh37	12	48437107	48437107	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1998A>G	.	.	ENST00000004980	18/18	35	25	10	26	26	0	SENP1,3_prime_UTR_variant,,ENST00000339976,;SENP1,3_prime_UTR_variant,,ENST00000448372,;SENP1,3_prime_UTR_variant,,ENST00000004980,;SENP1,downstream_gene_variant,,ENST00000549595,;SENP1,downstream_gene_variant,,ENST00000549518,;SENP1,downstream_gene_variant,,ENST00000551330,;SENP1,3_prime_UTR_variant,,ENST00000552189,;	C	ENSG00000079387	ENST00000004980	Transcript	3_prime_UTR_variant	4412	.	.	.	.	.	.	.	-1	SENP1	HGNC	17927	protein_coding	YES	CCDS44868.2	ENSP00000004980	SENP1_HUMAN	F8VRZ8_HUMAN	UPI0000E595D2	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGTTACCT	.	5	ESCA
KCNA1	0	.	GRCh37	12	5022205	5022205	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*173A>G	.	.	ENST00000382545	2/2	43	30	13	36	36	0	KCNA1,3_prime_UTR_variant,,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	G	ENSG00000111262	ENST00000382545	Transcript	3_prime_UTR_variant	2768	.	.	.	.	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGAACCAG	.	5	ESCA
KRT73	0	.	GRCh37	12	53009995	53009995	+	Missense_Mutation	SNP	G	G	C	rs200530085	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617C>G	p.Ser206Trp	p.S206W	ENST00000305748	2/9	101	85	15	56	56	0	KRT73,missense_variant,p.Ser206Trp,ENST00000305748,;KRT73,upstream_gene_variant,,ENST00000552855,;RP11-641A6.2,downstream_gene_variant,,ENST00000549180,;RP11-641A6.2,downstream_gene_variant,,ENST00000551089,;RP11-641A6.2,downstream_gene_variant,,ENST00000552364,;KRT73,non_coding_transcript_exon_variant,,ENST00000546934,;	C	ENSG00000186049	ENST00000305748	Transcript	missense_variant	652	617	206	S/W	tCg/tGg	rs200530085,COSM3462392	.	.	-1	KRT73	HGNC	28928	protein_coding	YES	CCDS8834.1	ENSP00000307014	K2C73_HUMAN	.	UPI000000DCB8	.	deleterious(0)	probably_damaging(0.981)	2/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF122,Pfam_domain:PF00038,Superfamily_domains:SSF64593	A:0.0004	A:0	A:0	.	A:0.001	A:0.001	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCGAGTCC	byFrequency|byCluster|by1000G	5	ESCA
KRT2	0	.	GRCh37	12	53045389	53045389	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538G>A	p.Glu180Lys	p.E180K	ENST00000309680	1/9	82	67	15	39	39	0	KRT2,missense_variant,p.Glu180Lys,ENST00000309680,;KRT2,upstream_gene_variant,,ENST00000547106,;	T	ENSG00000172867	ENST00000309680	Transcript	missense_variant	560	538	180	E/K	Gag/Aag	.	.	.	-1	KRT2	HGNC	6439	protein_coding	YES	CCDS8835.1	ENSP00000310861	K22E_HUMAN	.	UPI0000367804	.	deleterious(0)	probably_damaging(0.998)	1/9	.	Prints_domain:PR01276,Superfamily_domains:SSF64593,Pfam_domain:PF00038,hmmpanther:PTHR23239:SF134,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCACGCT	.	5	ESCA
BAZ2A	0	.	GRCh37	12	56994255	56994255	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4628C>T	p.Pro1543Leu	p.P1543L	ENST00000551812	24/29	33	11	22	23	23	0	BAZ2A,missense_variant,p.Pro1513Leu,ENST00000379441,;BAZ2A,missense_variant,p.Pro475Leu,ENST00000549787,;BAZ2A,missense_variant,p.Pro1511Leu,ENST00000179765,;BAZ2A,missense_variant,p.Pro1543Leu,ENST00000551812,;BAZ2A,missense_variant,p.Pro1541Leu,ENST00000549884,;BAZ2A,downstream_gene_variant,,ENST00000547453,;BAZ2A,non_coding_transcript_exon_variant,,ENST00000553222,;BAZ2A,downstream_gene_variant,,ENST00000549763,;BAZ2A,downstream_gene_variant,,ENST00000551759,;BAZ2A,downstream_gene_variant,,ENST00000548578,;	A	ENSG00000076108	ENST00000551812	Transcript	missense_variant	4822	4628	1543	P/L	cCa/cTa	.	.	.	-1	BAZ2A	HGNC	962	protein_coding	YES	CCDS44924.1	ENSP00000446880	BAZ2A_HUMAN	F8W053_HUMAN,F8VWQ3_HUMAN,F8VU39_HUMAN	UPI0000D4FED1	.	tolerated(0.08)	benign(0.001)	24/29	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTGGGCTA	.	5	ESCA
R3HDM2	0	.	GRCh37	12	57704142	57704142	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70G>A	p.Glu24Lys	p.E24K	ENST00000347140	3/24	77	60	17	55	55	0	R3HDM2,missense_variant,p.Glu24Lys,ENST00000358907,;R3HDM2,missense_variant,p.Glu24Lys,ENST00000402412,;R3HDM2,missense_variant,p.Glu24Lys,ENST00000403821,;R3HDM2,missense_variant,p.Glu24Lys,ENST00000448732,;R3HDM2,missense_variant,p.Glu24Lys,ENST00000347140,;R3HDM2,non_coding_transcript_exon_variant,,ENST00000551465,;	T	ENSG00000179912	ENST00000347140	Transcript	missense_variant	461	70	24	E/K	Gaa/Aaa	.	.	.	-1	R3HDM2	HGNC	29167	protein_coding	YES	CCDS8937.2	ENSP00000317903	R3HD2_HUMAN	C9J7N6_HUMAN	UPI00005A60D3	.	deleterious(0.02)	probably_damaging(0.991)	3/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15672:SF13,hmmpanther:PTHR15672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTCTTCCA	.	5	ESCA
NALCN	0	.	GRCh37	13	101910850	101910850	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210A>G	p.Asn404Asp	p.N404D	ENST00000251127	11/44	32	23	9	27	27	0	NALCN,missense_variant,p.Asn404Asp,ENST00000251127,;NALCN,missense_variant,p.Asn404Asp,ENST00000376196,;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,;	C	ENSG00000102452	ENST00000251127	Transcript	missense_variant	1292	1210	404	N/D	Aac/Gac	.	.	.	-1	NALCN	HGNC	19082	protein_coding	YES	CCDS9498.1	ENSP00000251127	NALCN_HUMAN	B3KX53_HUMAN,B3KMK1_HUMAN	UPI000004EBBD	.	tolerated(0.2)	benign(0.379)	11/44	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10037:SF176,hmmpanther:PTHR10037,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGTTGCTAG	.	5	ESCA
ARGLU1	0	.	GRCh37	13	107211906	107211906	+	Missense_Mutation	SNP	C	C	A	rs750578052	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.447G>T	p.Arg149Ser	p.R149S	ENST00000400198	2/4	123	62	60	99	99	0	ARGLU1,missense_variant,p.Arg149Ser,ENST00000400198,;ARGLU1,5_prime_UTR_variant,,ENST00000375926,;ARGLU1,5_prime_UTR_variant,,ENST00000360629,;ARGLU1,upstream_gene_variant,,ENST00000472226,;	A	ENSG00000134884	ENST00000400198	Transcript	missense_variant	692	447	149	R/S	agG/agT	rs750578052	.	.	-1	ARGLU1	HGNC	25482	protein_coding	YES	CCDS41906.1	ENSP00000383059	ARGL1_HUMAN	.	UPI00000373ED	.	deleterious(0)	benign(0.402)	2/4	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31711,Pfam_domain:PF15346	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCCTTTT	byFrequency	5	ESCA
FNDC3A	0	.	GRCh37	13	49580412	49580412	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86A>G	p.Asp29Gly	p.D29G	ENST00000492622	2/26	27	17	10	34	34	0	FNDC3A,missense_variant,p.Asp29Gly,ENST00000541916,;FNDC3A,missense_variant,p.Asp29Gly,ENST00000492622,;FNDC3A,missense_variant,p.Asp29Gly,ENST00000484074,;FNDC3A,non_coding_transcript_exon_variant,,ENST00000378383,;	G	ENSG00000102531	ENST00000492622	Transcript	missense_variant	391	86	29	D/G	gAt/gGt	.	.	.	1	FNDC3A	HGNC	20296	protein_coding	YES	CCDS41886.1	ENSP00000417257	FND3A_HUMAN	.	UPI0000229601	.	deleterious(0)	benign(0.063)	2/26	.	hmmpanther:PTHR19900:SF38,hmmpanther:PTHR19900	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGATGGAA	.	5	ESCA
RTL1	0	.	GRCh37	14	101347804	101347804	+	Missense_Mutation	SNP	G	G	A	rs764909149	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3322C>T	p.Arg1108Trp	p.R1108W	ENST00000534062	1/1	22	15	7	32	32	0	RTL1,missense_variant,p.Arg1108Trp,ENST00000534062,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,upstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,;MIR127,upstream_gene_variant,,ENST00000384876,;MIR431,downstream_gene_variant,,ENST00000385266,;	A	ENSG00000254656	ENST00000534062	Transcript	missense_variant	3381	3322	1108	R/W	Cgg/Tgg	rs764909149	.	.	-1	RTL1	HGNC	14665	protein_coding	YES	CCDS53910.1	ENSP00000435342	RTL1_HUMAN	.	UPI00001D7B9E	.	deleterious_low_confidence(0.02)	benign(0.153)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCGCAGCG	.	5	ESCA
RTN1	0	.	GRCh37	14	60194345	60194345	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057G>A	p.Glu353Lys	p.E353K	ENST00000267484	3/9	13	8	5	13	13	0	RTN1,missense_variant,p.Glu353Lys,ENST00000267484,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,;	T	ENSG00000139970	ENST00000267484	Transcript	missense_variant	1393	1057	353	E/K	Gag/Aag	.	.	.	-1	RTN1	HGNC	10467	protein_coding	YES	CCDS9740.1	ENSP00000267484	RTN1_HUMAN	Q2NKQ5_HUMAN,Q2L7A7_HUMAN	UPI00001352DA	.	deleterious(0)	possibly_damaging(0.558)	3/9	.	hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	ATCCTCGGAGA	.	4	ESCA
NRDE2	0	.	GRCh37	14	90770449	90770449	+	Missense_Mutation	SNP	T	T	C	rs761651321	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835A>G	p.Thr279Ala	p.T279A	ENST00000354366	5/14	40	26	14	48	48	0	NRDE2,missense_variant,p.Thr48Ala,ENST00000357904,;NRDE2,missense_variant,p.Thr279Ala,ENST00000354366,;NRDE2,upstream_gene_variant,,ENST00000554464,;NRDE2,non_coding_transcript_exon_variant,,ENST00000557064,;NRDE2,missense_variant,p.Thr135Ala,ENST00000556189,;NRDE2,3_prime_UTR_variant,,ENST00000553409,;	C	ENSG00000119720	ENST00000354366	Transcript	missense_variant	1068	835	279	T/A	Acc/Gcc	rs761651321	.	.	-1	NRDE2	HGNC	20186	protein_coding	YES	CCDS9890.1	ENSP00000346335	NRDE2_HUMAN	Q658X2_HUMAN,E9PBK4_HUMAN	UPI00001FD9DB	.	deleterious(0)	probably_damaging(0.994)	5/14	.	hmmpanther:PTHR13471	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGGTTGACT	byFrequency	5	ESCA
UNC79	0	.	GRCh37	14	94079210	94079210	+	Silent	SNP	C	C	T	rs149617798	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3291C>T	p.%3D	p.H1097H	ENST00000256339	27/50	22	14	8	23	23	0	UNC79,synonymous_variant,p.%3D,ENST00000393151,;UNC79,synonymous_variant,p.%3D,ENST00000256339,;UNC79,synonymous_variant,p.%3D,ENST00000553484,;UNC79,synonymous_variant,p.%3D,ENST00000555664,;	T	ENSG00000133958	ENST00000256339	Transcript	synonymous_variant	3946	3291	1097	H	caC/caT	rs149617798,COSM699847,COSM699848	.	.	1	UNC79	HGNC	19966	protein_coding	YES	CCDS9911.2	ENSP00000256339	UNC79_HUMAN	.	UPI0000D62441	.	.	.	27/50	.	hmmpanther:PTHR21696:SF1,hmmpanther:PTHR21696	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0002	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCACCAGAC	byCluster|by1000G	5	ESCA
PPP4R4	0	.	GRCh37	14	94712823	94712823	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1558G>C	p.Asp520His	p.D520H	ENST00000304338	14/25	51	31	20	34	34	0	PPP4R4,missense_variant,p.Asp520His,ENST00000304338,;	C	ENSG00000119698	ENST00000304338	Transcript	missense_variant	1712	1558	520	D/H	Gat/Cat	COSM255573	.	.	1	PPP4R4	HGNC	23788	protein_coding	YES	CCDS9921.1	ENSP00000305924	PP4R4_HUMAN	G3V431_HUMAN,G3V422_HUMAN	UPI000016223B	.	deleterious(0)	probably_damaging(0.997)	14/25	.	hmmpanther:PTHR21467,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGCGATCAG	.	5	ESCA
LRRK1	0	.	GRCh37	15	101597188	101597188	+	Missense_Mutation	SNP	C	C	G	rs201964335	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4460C>G	p.Pro1487Arg	p.P1487R	ENST00000388948	28/34	15	11	4	11	11	0	LRRK1,missense_variant,p.Pro1487Arg,ENST00000388948,;LRRK1,missense_variant,p.Pro1484Arg,ENST00000284395,;RP11-505E24.2,intron_variant,,ENST00000559857,;LRRK1,upstream_gene_variant,,ENST00000525395,;LRRK1,missense_variant,p.Pro164Arg,ENST00000526457,;LRRK1,3_prime_UTR_variant,,ENST00000531270,;LRRK1,3_prime_UTR_variant,,ENST00000525284,;	G	ENSG00000154237	ENST00000388948	Transcript	missense_variant	4819	4460	1487	P/R	cCg/cGg	rs201964335	.	.	1	LRRK1	HGNC	18608	protein_coding	YES	CCDS42086.1	ENSP00000373600	LRRK1_HUMAN	E9PMK9_HUMAN,E9PLF8_HUMAN,E9PK39_HUMAN,B3KSX5_HUMAN	UPI0000D4FE63	.	tolerated(0.33)	probably_damaging(0.92)	28/34	.	PROSITE_profiles:PS50011,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCCGGAGG	byFrequency|byCluster	5	ESCA
TRPM7	0	.	GRCh37	15	50903479	50903479	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2091C>T	p.%3D	p.S697S	ENST00000313478	17/39	37	23	13	38	38	0	TRPM7,synonymous_variant,p.%3D,ENST00000560955,;TRPM7,synonymous_variant,p.%3D,ENST00000560638,;TRPM7,synonymous_variant,p.%3D,ENST00000313478,;	A	ENSG00000092439	ENST00000313478	Transcript	synonymous_variant	2373	2091	697	S	tcC/tcT	.	.	.	-1	TRPM7	HGNC	17994	protein_coding	YES	CCDS42035.1	ENSP00000320239	TRPM7_HUMAN	.	UPI0000071CBA	.	.	.	17/39	.	hmmpanther:PTHR13800:SF8,hmmpanther:PTHR13800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAGGACTG	.	5	ESCA
MAPK6	0	.	GRCh37	15	52353571	52353571	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941C>T	p.Pro314Leu	p.P314L	ENST00000261845	5/6	35	23	12	46	46	0	MAPK6,missense_variant,p.Pro314Leu,ENST00000261845,;CTD-2184D3.5,intron_variant,,ENST00000558607,;	T	ENSG00000069956	ENST00000261845	Transcript	missense_variant	1748	941	314	P/L	cCt/cTt	.	.	.	1	MAPK6	HGNC	6879	protein_coding	YES	CCDS10147.1	ENSP00000261845	MK06_HUMAN	.	UPI000012F177	.	deleterious(0.03)	probably_damaging(0.985)	5/6	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF171,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCTTACA	.	5	ESCA
CLN6	0	.	GRCh37	15	68504072	68504072	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427C>A	p.Gln143Lys	p.Q143K	ENST00000249806	4/7	42	27	15	28	28	0	CLN6,missense_variant,p.Gln175Lys,ENST00000538696,;CLN6,missense_variant,p.Gln143Lys,ENST00000564752,;CLN6,missense_variant,p.Gln143Lys,ENST00000249806,;CLN6,intron_variant,,ENST00000565471,;RP11-315D16.2,intron_variant,,ENST00000562767,;CLN6,intron_variant,,ENST00000566347,;CLN6,intron_variant,,ENST00000418702,;CLN6,non_coding_transcript_exon_variant,,ENST00000563917,;CLN6,intron_variant,,ENST00000567060,;CLN6,downstream_gene_variant,,ENST00000564846,;	T	ENSG00000128973	ENST00000249806	Transcript	missense_variant	585	427	143	Q/K	Cag/Aag	.	.	.	-1	CLN6	HGNC	2077	protein_coding	YES	CCDS10227.1	ENSP00000249806	CLN6_HUMAN	.	UPI000006D91F	.	tolerated(0.1)	probably_damaging(0.968)	4/7	.	hmmpanther:PTHR16244,Pfam_domain:PF15156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTGGTAGC	.	5	ESCA
EDC3	0	.	GRCh37	15	74925075	74925075	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1405G>A	p.Glu469Lys	p.E469K	ENST00000315127	7/7	54	50	4	38	38	0	EDC3,missense_variant,p.Glu469Lys,ENST00000315127,;EDC3,missense_variant,p.Glu469Lys,ENST00000568176,;EDC3,missense_variant,p.Glu469Lys,ENST00000426797,;EDC3,incomplete_terminal_codon_variant,p.%3D,ENST00000569606,;CLK3,intron_variant,,ENST00000563418,;CLK3,downstream_gene_variant,,ENST00000566926,;EDC3,downstream_gene_variant,,ENST00000562174,;CLK3,downstream_gene_variant,,ENST00000352989,;EDC3,downstream_gene_variant,,ENST00000566219,;CLK3,downstream_gene_variant,,ENST00000563842,;CLK3,downstream_gene_variant,,ENST00000395066,;CLK3,downstream_gene_variant,,ENST00000348245,;CLK3,downstream_gene_variant,,ENST00000345005,;CLK3,intron_variant,,ENST00000561673,;CLK3,downstream_gene_variant,,ENST00000567805,;EDC3,3_prime_UTR_variant,,ENST00000565602,;CLK3,downstream_gene_variant,,ENST00000562078,;CLK3,downstream_gene_variant,,ENST00000562626,;CLK3,downstream_gene_variant,,ENST00000454830,;CLK3,downstream_gene_variant,,ENST00000569406,;CLK3,downstream_gene_variant,,ENST00000568232,;CLK3,downstream_gene_variant,,ENST00000483723,;CLK3,downstream_gene_variant,,ENST00000564468,;	T	ENSG00000179151	ENST00000315127	Transcript	missense_variant	1587	1405	469	E/K	Gag/Aag	.	.	.	-1	EDC3	HGNC	26114	protein_coding	YES	CCDS10267.1	ENSP00000320503	EDC3_HUMAN	H3BU87_HUMAN,H3BTH0_HUMAN,H3BTF8_HUMAN,H3BSQ0_HUMAN,H3BQP5_HUMAN,H3BQA1_HUMAN,H3BQ37_HUMAN,H3BPW9_HUMAN,H3BN89_HUMAN,H3BMB8_HUMAN	UPI000007309A	.	tolerated(0.2)	benign(0.05)	7/7	.	PROSITE_profiles:PS51385,hmmpanther:PTHR13612:SF0,hmmpanther:PTHR13612,Gene3D:3.40.50.10260,Superfamily_domains:SSF64153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCTCCCCCA	.	2	ESCA
CSPG4	0	.	GRCh37	15	75980366	75980366	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3040G>A	p.Val1014Met	p.V1014M	ENST00000308508	3/10	82	67	14	42	42	0	CSPG4,missense_variant,p.Val1014Met,ENST00000308508,;	T	ENSG00000173546	ENST00000308508	Transcript	missense_variant	3133	3040	1014	V/M	Gtg/Atg	COSM4057017	.	.	-1	CSPG4	HGNC	2466	protein_coding	YES	CCDS10284.1	ENSP00000312506	CSPG4_HUMAN	.	UPI00001AEEB6	.	deleterious(0.02)	possibly_damaging(0.613)	3/10	.	hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF11	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCACGGGCT	.	5	ESCA
SEC11A	0	.	GRCh37	15	85259557	85259557	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-251G>C	.	.	ENST00000268220	1/6	75	55	19	45	45	0	SEC11A,5_prime_UTR_variant,,ENST00000268220,;SEC11A,upstream_gene_variant,,ENST00000558134,;SEC11A,upstream_gene_variant,,ENST00000560266,;SEC11A,upstream_gene_variant,,ENST00000558196,;SEC11A,upstream_gene_variant,,ENST00000455959,;SEC11A,upstream_gene_variant,,ENST00000559729,;SEC11A,upstream_gene_variant,,ENST00000558217,;SEC11A,upstream_gene_variant,,ENST00000560409,;	G	ENSG00000140612	ENST00000268220	Transcript	5_prime_UTR_variant	391	.	.	.	.	.	.	.	-1	SEC11A	HGNC	17718	protein_coding	YES	CCDS45340.1	ENSP00000268220	SC11A_HUMAN	H0YNX5_HUMAN,B4DUL4_HUMAN	UPI0000049B6F	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTCACGCT	.	5	ESCA
SV2B	0	.	GRCh37	15	91832773	91832773	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1731A>C	p.%3D	p.A577A	ENST00000394232	12/13	72	56	15	44	44	0	SV2B,synonymous_variant,p.%3D,ENST00000330276,;SV2B,synonymous_variant,p.%3D,ENST00000394232,;SV2B,synonymous_variant,p.%3D,ENST00000545111,;SV2B,synonymous_variant,p.%3D,ENST00000557410,;	C	ENSG00000185518	ENST00000394232	Transcript	synonymous_variant	2201	1731	577	A	gcA/gcC	.	.	.	1	SV2B	HGNC	16874	protein_coding	YES	CCDS10370.1	ENSP00000377779	SV2B_HUMAN	.	UPI000006FCF1	.	.	.	12/13	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24065,hmmpanther:PTHR24065:SF1,Gene3D:1.20.1250.20,Pfam_domain:PF07690,TIGRFAM_domain:TIGR01299,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCAGTCTG	.	5	ESCA
IGF1R	0	.	GRCh37	15	99506188	99506188	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5517T>C	.	.	ENST00000268035	21/21	111	88	22	78	78	0	IGF1R,3_prime_UTR_variant,,ENST00000558762,;IGF1R,3_prime_UTR_variant,,ENST00000268035,;RP11-654A16.3,intron_variant,,ENST00000559468,;	C	ENSG00000140443	ENST00000268035	Transcript	3_prime_UTR_variant	10232	.	.	.	.	.	.	.	1	IGF1R	HGNC	5465	protein_coding	YES	CCDS10378.1	ENSP00000268035	IGF1R_HUMAN	H0YNR0_HUMAN,H0YMJ5_HUMAN	UPI000012D3EA	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACGTGTGTG	.	5	ESCA
PRKCB	0	.	GRCh37	16	24105592	24105592	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.795A>T	p.Glu265Asp	p.E265D	ENST00000303531	7/17	69	42	26	38	38	0	PRKCB,missense_variant,p.Glu265Asp,ENST00000303531,;PRKCB,missense_variant,p.Glu80Asp,ENST00000498739,;PRKCB,missense_variant,p.Glu265Asp,ENST00000321728,;PRKCB,non_coding_transcript_exon_variant,,ENST00000482000,;PRKCB,downstream_gene_variant,,ENST00000486868,;	T	ENSG00000166501	ENST00000303531	Transcript	missense_variant	947	795	265	E/D	gaA/gaT	.	.	.	1	PRKCB	HGNC	9395	protein_coding	YES	CCDS10619.1	ENSP00000305355	KPCB_HUMAN	I3L1Z0_HUMAN	UPI000002ACF9	.	deleterious(0.04)	probably_damaging(0.925)	7/17	.	hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF63,Gene3D:2.60.40.150,PIRSF_domain:PIRSF000550,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGAACTTCA	.	5	ESCA
SEPT1	0	.	GRCh37	16	30393911	30393911	+	Missense_Mutation	SNP	T	T	C	rs767930540	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.79A>G	p.Ser27Gly	p.S27G	ENST00000321367	2/12	46	39	6	26	26	0	SEPT1,missense_variant,p.Ser27Gly,ENST00000321367,;SEPT1,5_prime_UTR_variant,,ENST00000571393,;ZNF48,intron_variant,,ENST00000495929,;ZNF48,intron_variant,,ENST00000528032,;MYLPF,downstream_gene_variant,,ENST00000566955,;SEPT1,upstream_gene_variant,,ENST00000566517,;SEPT1,upstream_gene_variant,,ENST00000605106,;MYLPF,downstream_gene_variant,,ENST00000322861,;MYLPF,downstream_gene_variant,,ENST00000568749,;SEPT1,downstream_gene_variant,,ENST00000570039,;SEPT1,downstream_gene_variant,,ENST00000567783,;SEPT1,non_coding_transcript_exon_variant,,ENST00000563957,;SEPT1,non_coding_transcript_exon_variant,,ENST00000562152,;SEPT1,intron_variant,,ENST00000568577,;SEPT1,upstream_gene_variant,,ENST00000573615,;MYLPF,downstream_gene_variant,,ENST00000563728,;SEPT1,upstream_gene_variant,,ENST00000563743,;SEPT1,upstream_gene_variant,,ENST00000572252,;	C	ENSG00000180096	ENST00000321367	Transcript	missense_variant	125	79	27	S/G	Agc/Ggc	rs767930540	.	.	-1	SEPT1	HGNC	2879	protein_coding	YES	CCDS10678.3	ENSP00000324511	.	S4R362_HUMAN,J3KNL2_HUMAN,H3BS29_HUMAN	UPI000066D948	.	tolerated_low_confidence(0.43)	benign(0)	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGCTGAGTG	.	4	ESCA
CCDC64B	0	.	GRCh37	16	3079364	3079364	+	Missense_Mutation	SNP	C	C	G	rs754344293	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>C	p.Glu342Gln	p.E342Q	ENST00000572449	7/10	14	7	6	29	29	0	CCDC64B,missense_variant,p.Glu135Gln,ENST00000573514,;CCDC64B,missense_variant,p.Glu342Gln,ENST00000572449,;CCDC64B,missense_variant,p.Glu342Gln,ENST00000389347,;THOC6,downstream_gene_variant,,ENST00000575576,;THOC6,downstream_gene_variant,,ENST00000574549,;THOC6,downstream_gene_variant,,ENST00000326266,;THOC6,downstream_gene_variant,,ENST00000253952,;RP11-473M20.5,upstream_gene_variant,,ENST00000382225,;CCDC64B,non_coding_transcript_exon_variant,,ENST00000572240,;THOC6,downstream_gene_variant,,ENST00000571046,;THOC6,downstream_gene_variant,,ENST00000571057,;THOC6,downstream_gene_variant,,ENST00000574498,;CCDC64B,downstream_gene_variant,,ENST00000576826,;THOC6,downstream_gene_variant,,ENST00000576143,;THOC6,downstream_gene_variant,,ENST00000574957,;THOC6,downstream_gene_variant,,ENST00000573704,;	G	ENSG00000162069	ENST00000572449	Transcript	missense_variant	1087	1024	342	E/Q	Gag/Cag	rs754344293	.	.	-1	CCDC64B	HGNC	33584	protein_coding	YES	CCDS45393.1	ENSP00000459043	BICR2_HUMAN	.	UPI00001D78D6	.	deleterious(0.01)	probably_damaging(0.999)	7/10	.	hmmpanther:PTHR32123,hmmpanther:PTHR32123:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	GGGCTCTAAGA	.	4	ESCA
HSD3B7	0	.	GRCh37	16	30999400	30999400	+	Missense_Mutation	SNP	G	G	T	rs372114914	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1006G>T	p.Asp336Tyr	p.D336Y	ENST00000297679	7/7	58	48	10	46	46	0	HSD3B7,missense_variant,p.Asp336Tyr,ENST00000297679,;HSD3B7,3_prime_UTR_variant,,ENST00000353250,;HSD3B7,3_prime_UTR_variant,,ENST00000262520,;STX1B,downstream_gene_variant,,ENST00000569638,;STX1B,downstream_gene_variant,,ENST00000565419,;SETD1A,downstream_gene_variant,,ENST00000262519,;AC135048.1,upstream_gene_variant,,ENST00000602217,;HSD3B7,downstream_gene_variant,,ENST00000574447,;HSD3B7,downstream_gene_variant,,ENST00000562932,;STX1B,downstream_gene_variant,,ENST00000215095,;	T	ENSG00000099377	ENST00000297679	Transcript	missense_variant	1099	1006	336	D/Y	Gac/Tac	rs372114914	.	.	1	HSD3B7	HGNC	18324	protein_coding	YES	CCDS10698.1	ENSP00000297679	3BHS7_HUMAN	I3L2H6_HUMAN	UPI000007399B	.	deleterious(0)	possibly_damaging(0.904)	7/7	.	hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF290,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCGACAAG	byFrequency|byCluster	5	ESCA
VKORC1	0	.	GRCh37	16	31106745	31106745	+	5'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000394975	.	31	21	10	37	37	0	VKORC1,missense_variant,p.Gly71Arg,ENST00000420057,;VKORC1,missense_variant,p.Gly79Arg,ENST00000498155,;VKORC1,upstream_gene_variant,,ENST00000394975,;RP11-196G11.1,upstream_gene_variant,,ENST00000532364,;VKORC1,upstream_gene_variant,,ENST00000319788,;VKORC1,upstream_gene_variant,,ENST00000394971,;RP11-196G11.1,upstream_gene_variant,,ENST00000529564,;VKORC1,upstream_gene_variant,,ENST00000354895,;VKORC1,upstream_gene_variant,,ENST00000300851,;VKORC1,upstream_gene_variant,,ENST00000472468,;RP11-196G11.1,upstream_gene_variant,,ENST00000533518,;	T	ENSG00000167397	ENST00000394975	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	467	-1	VKORC1	HGNC	23663	protein_coding	YES	CCDS10703.1	ENSP00000378426	VKOR1_HUMAN	I3L1P9_HUMAN	UPI000006DDEE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCCGGGAC	.	5	ESCA
ZNF720	0	.	GRCh37	16	31724640	31724640	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-114G>A	.	.	ENST00000316491	1/5	29	22	7	18	18	0	ZNF720,5_prime_UTR_variant,,ENST00000539915,;ZNF720,5_prime_UTR_variant,,ENST00000398696,;ZNF720,5_prime_UTR_variant,,ENST00000534369,;ZNF720,5_prime_UTR_variant,,ENST00000316491,;ZNF720,5_prime_UTR_variant,,ENST00000399681,;ZNF720,5_prime_UTR_variant,,ENST00000529515,;ZNF720,5_prime_UTR_variant,,ENST00000530881,;CTD-2358C21.4,upstream_gene_variant,,ENST00000569175,;ZNF720,non_coding_transcript_exon_variant,,ENST00000542684,;ZNF720,non_coding_transcript_exon_variant,,ENST00000544044,;ZNF720,non_coding_transcript_exon_variant,,ENST00000533488,;ZNF720,non_coding_transcript_exon_variant,,ENST00000531864,;CLUHP3,downstream_gene_variant,,ENST00000562354,;ZNF720,5_prime_UTR_variant,,ENST00000534277,;ZNF720,5_prime_UTR_variant,,ENST00000529943,;ZNF720,5_prime_UTR_variant,,ENST00000398707,;CLUHP3,downstream_gene_variant,,ENST00000563678,;	A	ENSG00000197302	ENST00000316491	Transcript	5_prime_UTR_variant	86	.	.	.	.	.	.	.	1	ZNF720	HGNC	26987	protein_coding	YES	CCDS45473.1	ENSP00000319222	ZN720_HUMAN	.	UPI000003603E	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTGGGAGG	.	5	ESCA
NAE1	0	.	GRCh37	16	66847533	66847533	+	Nonsense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.968T>G	p.Leu323Ter	p.L323*	ENST00000290810	13/20	52	23	29	32	32	0	NAE1,stop_gained,p.Leu234Ter,ENST00000394074,;NAE1,stop_gained,p.Leu326Ter,ENST00000359087,;NAE1,stop_gained,p.Leu317Ter,ENST00000379463,;NAE1,stop_gained,p.Leu323Ter,ENST00000290810,;NAE1,upstream_gene_variant,,ENST00000566663,;NAE1,downstream_gene_variant,,ENST00000563185,;NAE1,downstream_gene_variant,,ENST00000561579,;NAE1,non_coding_transcript_exon_variant,,ENST00000567521,;NAE1,downstream_gene_variant,,ENST00000567743,;NAE1,downstream_gene_variant,,ENST00000563253,;NAE1,upstream_gene_variant,,ENST00000562074,;	C	ENSG00000159593	ENST00000290810	Transcript	stop_gained	1066	968	323	L/*	tTa/tGa	.	.	.	-1	NAE1	HGNC	621	protein_coding	YES	CCDS10820.1	ENSP00000290810	ULA1_HUMAN	J3QRA5_HUMAN,A8MU28_HUMAN	UPI000006EBDC	.	.	.	13/20	.	hmmpanther:PTHR10953,Gene3D:3.40.50.720,Superfamily_domains:SSF69572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGTAAATTT	.	5	ESCA
TANGO6	0	.	GRCh37	16	69008066	69008066	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2837C>A	p.Ala946Glu	p.A946E	ENST00000261778	15/18	42	28	14	53	53	0	TANGO6,missense_variant,p.Ala946Glu,ENST00000261778,;TANGO6,non_coding_transcript_exon_variant,,ENST00000562000,;TANGO6,non_coding_transcript_exon_variant,,ENST00000568361,;	A	ENSG00000103047	ENST00000261778	Transcript	missense_variant	2849	2837	946	A/E	gCa/gAa	.	.	.	1	TANGO6	HGNC	25749	protein_coding	YES	CCDS45516.1	ENSP00000261778	TNG6_HUMAN	B3KTB6_HUMAN	UPI00001FF4A8	.	deleterious(0.02)	benign(0.04)	15/18	.	hmmpanther:PTHR20959:SF1,hmmpanther:PTHR20959,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCATTAG	.	5	ESCA
COG4	0	.	GRCh37	16	70546283	70546283	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.597C>G	p.%3D	p.L199L	ENST00000323786	5/19	19	12	7	16	16	0	COG4,synonymous_variant,p.%3D,ENST00000393612,;COG4,synonymous_variant,p.%3D,ENST00000323786,;COG4,synonymous_variant,p.%3D,ENST00000534772,;COG4,intron_variant,,ENST00000564653,;COG4,synonymous_variant,p.%3D,ENST00000482252,;COG4,3_prime_UTR_variant,,ENST00000524584,;COG4,3_prime_UTR_variant,,ENST00000564415,;COG4,3_prime_UTR_variant,,ENST00000530160,;COG4,non_coding_transcript_exon_variant,,ENST00000562200,;COG4,non_coding_transcript_exon_variant,,ENST00000530314,;COG4,upstream_gene_variant,,ENST00000526700,;	C	ENSG00000103051	ENST00000323786	Transcript	synonymous_variant	619	597	199	L	ctC/ctG	.	.	.	-1	COG4	HGNC	18620	protein_coding	YES	CCDS10892.2	ENSP00000315775	.	J3KRB5_HUMAN,J3KNI1_HUMAN,B4DDL2_HUMAN	UPI000059D3B0	.	.	.	5/19	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24016:SF0,hmmpanther:PTHR24016,Pfam_domain:PF08318,SMART_domains:SM00762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTGAGACG	.	5	ESCA
GSE1	0	.	GRCh37	16	85689343	85689343	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.809C>A	p.Ser270Tyr	p.S270Y	ENST00000253458	6/16	26	17	8	36	36	0	GSE1,missense_variant,p.Ser270Tyr,ENST00000253458,;GSE1,missense_variant,p.Ser166Tyr,ENST00000411612,;GSE1,missense_variant,p.Ser166Tyr,ENST00000405402,;GSE1,missense_variant,p.Ser77Tyr,ENST00000412692,;GSE1,missense_variant,p.Ser197Tyr,ENST00000393243,;RN7SL381P,upstream_gene_variant,,ENST00000577658,;	A	ENSG00000131149	ENST00000253458	Transcript	missense_variant	985	809	270	S/Y	tCc/tAc	.	.	.	1	GSE1	HGNC	28979	protein_coding	YES	CCDS10952.1	ENSP00000253458	GSE1_HUMAN	C9JLW9_HUMAN	UPI0000185F04	.	tolerated(0.05)	unknown(0)	6/16	.	hmmpanther:PTHR17608:SF3,hmmpanther:PTHR17608	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGACTCCTACT	.	5	ESCA
ZNF469	0	.	GRCh37	16	88499969	88499969	+	Missense_Mutation	SNP	G	G	A	rs273585622	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6007G>A	p.Glu2003Lys	p.E2003K	ENST00000437464	2/2	35	23	11	33	33	0	ZNF469,missense_variant,p.Glu2031Lys,ENST00000565624,;ZNF469,missense_variant,p.Glu2003Lys,ENST00000437464,;	A	ENSG00000225614	ENST00000437464	Transcript	missense_variant	6007	6007	2003	E/K	Gag/Aag	rs273585622	.	.	1	ZNF469	HGNC	23216	protein_coding	YES	CCDS45544.1	ENSP00000402343	ZN469_HUMAN	.	UPI0000DD837B	.	.	benign(0)	2/2	.	hmmpanther:PTHR21465,hmmpanther:PTHR21465:SF2	.	.	.	.	.	.	.	.	.	benign	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCGAGGGT	byFrequency|byCluster	5	ESCA
VPS9D1	0	.	GRCh37	16	89784476	89784476	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175+959G>A	.	.	ENST00000389386	.	147	118	28	108	108	0	VPS9D1,intron_variant,,ENST00000389386,;VPS9D1,intron_variant,,ENST00000561976,;ZNF276,upstream_gene_variant,,ENST00000446326,;ZNF276,upstream_gene_variant,,ENST00000568064,;ZNF276,upstream_gene_variant,,ENST00000443381,;ZNF276,upstream_gene_variant,,ENST00000289816,;VPS9D1-AS1,non_coding_transcript_exon_variant,,ENST00000562866,;VPS9D1-AS1,non_coding_transcript_exon_variant,,ENST00000562298,;VPS9D1,intron_variant,,ENST00000563798,;ZNF276,upstream_gene_variant,,ENST00000568295,;ZNF276,upstream_gene_variant,,ENST00000563983,;ZNF276,upstream_gene_variant,,ENST00000561536,;VPS9D1,upstream_gene_variant,,ENST00000568691,;ZNF276,upstream_gene_variant,,ENST00000562530,;	T	ENSG00000075399	ENST00000389386	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	VPS9D1	HGNC	13526	protein_coding	YES	CCDS42220.1	ENSP00000374037	VP9D1_HUMAN	H3BM58_HUMAN	UPI00001FF749	.	.	.	.	2/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACCTCTGT	.	5	ESCA
AP2B1	0	.	GRCh37	17	34044277	34044277	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2690G>T	p.Gly897Val	p.G897V	ENST00000312678	21/22	45	28	17	48	48	0	AP2B1,missense_variant,p.Gly897Val,ENST00000589344,;AP2B1,missense_variant,p.Gly883Val,ENST00000262325,;AP2B1,missense_variant,p.Gly897Val,ENST00000312678,;AP2B1,missense_variant,p.Gly859Val,ENST00000592545,;AP2B1,missense_variant,p.Gly826Val,ENST00000538556,;AP2B1,missense_variant,p.Gly897Val,ENST00000537622,;AP2B1,non_coding_transcript_exon_variant,,ENST00000545922,;AP2B1,3_prime_UTR_variant,,ENST00000592191,;AP2B1,non_coding_transcript_exon_variant,,ENST00000588493,;RPL17P42,upstream_gene_variant,,ENST00000474264,;	T	ENSG00000006125	ENST00000312678	Transcript	missense_variant	2820	2690	897	G/V	gGg/gTg	.	.	.	1	AP2B1	HGNC	563	protein_coding	YES	CCDS32621.1	ENSP00000314414	AP2B1_HUMAN	Q96EL6_HUMAN,K7ERB2_HUMAN,K7EN71_HUMAN,K7EJX1_HUMAN	UPI000006DD97	.	deleterious(0)	possibly_damaging(0.538)	21/22	.	hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF9,Pfam_domain:PF09066,Gene3D:3.30.310.10,SMART_domains:SM01020,Superfamily_domains:SSF55711	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGGGCAGG	.	5	ESCA
C17orf50	0	.	GRCh37	17	34091541	34091541	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429G>C	p.Lys143Asn	p.K143N	ENST00000285023	3/3	26	18	8	23	23	0	C17orf50,missense_variant,p.Glu114Gln,ENST00000586491,;C17orf50,missense_variant,p.Lys143Asn,ENST00000285023,;C17orf50,missense_variant,p.Glu151Gln,ENST00000588628,;MMP28,intron_variant,,ENST00000587687,;MMP28,intron_variant,,ENST00000587639,;MMP28,downstream_gene_variant,,ENST00000587923,;MMP28,downstream_gene_variant,,ENST00000590643,;MMP28,downstream_gene_variant,,ENST00000589061,;MMP28,downstream_gene_variant,,ENST00000589103,;	C	ENSG00000154768	ENST00000285023	Transcript	missense_variant	461	429	143	K/N	aaG/aaC	.	.	.	1	C17orf50	HGNC	29581	protein_coding	YES	CCDS42298.1	ENSP00000285023	CQ050_HUMAN	.	UPI00002016EC	.	deleterious(0.03)	possibly_damaging(0.895)	3/3	.	Pfam_domain:PF15470	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAAGAAATG	.	5	ESCA
SYNRG	0	.	GRCh37	17	35930849	35930849	+	Missense_Mutation	SNP	A	A	T	rs750660990	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234T>A	p.Ser412Thr	p.S412T	ENST00000339208	10/22	39	12	26	22	22	0	SYNRG,missense_variant,p.Ser334Thr,ENST00000394378,;SYNRG,missense_variant,p.Ser334Thr,ENST00000502449,;SYNRG,missense_variant,p.Ser412Thr,ENST00000339208,;SYNRG,missense_variant,p.Ser334Thr,ENST00000345615,;SYNRG,missense_variant,p.Ser333Thr,ENST00000585472,;SYNRG,missense_variant,p.Ser412Thr,ENST00000346661,;SYNRG,intron_variant,,ENST00000591288,;SYNRG,non_coding_transcript_exon_variant,,ENST00000588194,;SYNRG,downstream_gene_variant,,ENST00000394379,;SYNRG,upstream_gene_variant,,ENST00000587040,;SYNRG,non_coding_transcript_exon_variant,,ENST00000421408,;SYNRG,non_coding_transcript_exon_variant,,ENST00000378189,;	T	ENSG00000006114	ENST00000339208	Transcript	missense_variant	1375	1234	412	S/T	Tcc/Acc	rs750660990	.	.	-1	SYNRG	HGNC	557	protein_coding	YES	CCDS11321.1	ENSP00000343610	SYNRG_HUMAN	.	UPI000013C4EA	.	tolerated(0.05)	probably_damaging(0.981)	10/22	.	hmmpanther:PTHR15463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGAGCCCG	.	5	ESCA
MPP2	0	.	GRCh37	17	41977954	41977954	+	Intron	SNP	C	C	G	rs759805934	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.32-2206G>C	.	.	ENST00000269095	.	20	4	16	24	24	0	MPP2,5_prime_UTR_variant,,ENST00000377184,;MPP2,intron_variant,,ENST00000518766,;MPP2,intron_variant,,ENST00000269095,;MPP2,intron_variant,,ENST00000536246,;MPP2,intron_variant,,ENST00000520406,;MPP2,intron_variant,,ENST00000518478,;MPP2,intron_variant,,ENST00000521178,;MPP2,intron_variant,,ENST00000523762,;MPP2,intron_variant,,ENST00000520305,;MPP2,intron_variant,,ENST00000461854,;MPP2,intron_variant,,ENST00000522172,;MPP2,intron_variant,,ENST00000523934,;MPP2,intron_variant,,ENST00000520241,;MPP2,intron_variant,,ENST00000523220,;MPP2,intron_variant,,ENST00000523501,;MPP2,intron_variant,,ENST00000473246,;MPP2,intron_variant,,ENST00000524294,;MPP2,intron_variant,,ENST00000520319,;	G	ENSG00000108852	ENST00000269095	Transcript	intron_variant	.	.	.	.	.	rs759805934	.	.	-1	MPP2	HGNC	7220	protein_coding	YES	CCDS11471.1	ENSP00000269095	MPP2_HUMAN	E7EX01_HUMAN,E7EV91_HUMAN,E5RK50_HUMAN,E5RJK0_HUMAN,E5RIU3_HUMAN,E5RIM9_HUMAN,E5RI32_HUMAN,E5RFN8_HUMAN	UPI000013D7F7	.	.	.	.	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGTCCTACA	.	5	ESCA
WSCD1	0	.	GRCh37	17	6021393	6021393	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1260G>A	p.Met420Ile	p.M420I	ENST00000574946	8/9	24	12	12	21	21	0	WSCD1,missense_variant,p.Met304Ile,ENST00000573634,;WSCD1,missense_variant,p.Met420Ile,ENST00000574232,;WSCD1,missense_variant,p.Met420Ile,ENST00000317744,;WSCD1,missense_variant,p.Met420Ile,ENST00000539421,;WSCD1,missense_variant,p.Met420Ile,ENST00000574946,;WSCD1,3_prime_UTR_variant,,ENST00000571494,;	A	ENSG00000179314	ENST00000574946	Transcript	missense_variant	1650	1260	420	M/I	atG/atA	.	.	.	1	WSCD1	HGNC	29060	protein_coding	YES	CCDS32538.1	ENSP00000460825	WSCD1_HUMAN	I3NI40_HUMAN,I3L3G4_HUMAN,I3L2Y9_HUMAN,I3L127_HUMAN	UPI0000197208	.	tolerated(0.38)	benign(0.026)	8/9	.	hmmpanther:PTHR19297:SF90,hmmpanther:PTHR19297,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATGTTTGA	.	5	ESCA
MARCH10	0	.	GRCh37	17	60865859	60865859	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.192C>A	p.Ser64Arg	p.S64R	ENST00000311269	3/11	49	35	14	65	65	0	MARCH10,missense_variant,p.Ser64Arg,ENST00000583600,;MARCH10,missense_variant,p.Ser64Arg,ENST00000456609,;MARCH10,missense_variant,p.Ser64Arg,ENST00000311269,;MARCH10,missense_variant,p.Ser64Arg,ENST00000544856,;MARCH10,downstream_gene_variant,,ENST00000583803,;MARCH10,non_coding_transcript_exon_variant,,ENST00000578346,;	T	ENSG00000173838	ENST00000311269	Transcript	missense_variant	467	192	64	S/R	agC/agA	.	.	.	-1	MARCH10	HGNC	26655	protein_coding	YES	CCDS11635.1	ENSP00000311496	MARHA_HUMAN	J3KTK3_HUMAN	UPI000013F13A	.	tolerated(0.13)	possibly_damaging(0.839)	3/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14471,hmmpanther:PTHR14471:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTGCTAGA	.	5	ESCA
ICAM2	0	.	GRCh37	17	62082482	62082482	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313A>C	p.Asn105His	p.N105H	ENST00000412356	4/6	40	28	12	49	49	0	ICAM2,missense_variant,p.Asn105His,ENST00000418105,;ICAM2,missense_variant,p.Asn4His,ENST00000578379,;ICAM2,missense_variant,p.Asn105His,ENST00000579788,;ICAM2,missense_variant,p.Asn105His,ENST00000584084,;ICAM2,missense_variant,p.Asn105His,ENST00000579687,;ICAM2,missense_variant,p.Asn105His,ENST00000578313,;ICAM2,missense_variant,p.Asn81His,ENST00000578892,;ICAM2,missense_variant,p.Asn105His,ENST00000583366,;ICAM2,missense_variant,p.Asn105His,ENST00000449662,;ICAM2,missense_variant,p.Asn105His,ENST00000412356,;C17orf72,downstream_gene_variant,,ENST00000412177,;C17orf72,downstream_gene_variant,,ENST00000579184,;C17orf72,downstream_gene_variant,,ENST00000539996,;C17orf72,downstream_gene_variant,,ENST00000583891,;C17orf72,downstream_gene_variant,,ENST00000580752,;C17orf72,downstream_gene_variant,,ENST00000425164,;C17orf72,downstream_gene_variant,,ENST00000582540,;C17orf72,downstream_gene_variant,,ENST00000577953,;ICAM2,non_coding_transcript_exon_variant,,ENST00000584403,;ICAM2,non_coding_transcript_exon_variant,,ENST00000581417,;ICAM2,missense_variant,p.Gln26Pro,ENST00000583684,;ICAM2,non_coding_transcript_exon_variant,,ENST00000580389,;ICAM2,non_coding_transcript_exon_variant,,ENST00000580011,;C17orf72,downstream_gene_variant,,ENST00000582530,;C17orf72,downstream_gene_variant,,ENST00000225760,;ICAM2,downstream_gene_variant,,ENST00000583186,;C17orf72,downstream_gene_variant,,ENST00000579222,;	G	ENSG00000108622	ENST00000412356	Transcript	missense_variant	668	313	105	N/H	Aac/Cac	.	.	.	-1	ICAM2	HGNC	5345	protein_coding	YES	CCDS11657.1	ENSP00000415283	ICAM2_HUMAN	Q9NZC6_HUMAN,Q6FHE2_HUMAN,Q59ED3_HUMAN,J3QRQ1_HUMAN,J3QQX6_HUMAN,J3QQR8_HUMAN,J3QKR4_HUMAN	UPI000013C87E	.	tolerated(0.11)	benign(0.197)	4/6	.	hmmpanther:PTHR13771,hmmpanther:PTHR13771:SF3,Gene3D:2.60.40.10,Pfam_domain:PF03921,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGTTGGAAT	.	5	ESCA
SRP68	0	.	GRCh37	17	74035188	74035188	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*599G>A	.	.	ENST00000307877	16/16	39	27	11	43	43	0	SRP68,3_prime_UTR_variant,,ENST00000307877,;SRP68,3_prime_UTR_variant,,ENST00000602720,;SRP68,3_prime_UTR_variant,,ENST00000539137,;SRP68,downstream_gene_variant,,ENST00000355113,;SRP68,non_coding_transcript_exon_variant,,ENST00000542536,;SRP68,non_coding_transcript_exon_variant,,ENST00000588643,;SRP68,downstream_gene_variant,,ENST00000586859,;SRP68,downstream_gene_variant,,ENST00000592704,;	T	ENSG00000167881	ENST00000307877	Transcript	3_prime_UTR_variant	2645	.	.	.	.	.	.	.	-1	SRP68	HGNC	11302	protein_coding	YES	CCDS11738.1	ENSP00000312066	SRP68_HUMAN	Q96K97_HUMAN,F5H5Y3_HUMAN	UPI000006EAEC	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTCCGTCAT	.	4	ESCA
TP53	0	.	GRCh37	17	7578547	7578547	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383delC	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	5/11	22	14	8	31	31	0	TP53,frameshift_variant,p.Pro128LeufsTer?,ENST00000508793,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000413465,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000420246,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000269305,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000359597,;TP53,frameshift_variant,p.Pro35LeufsTer42,ENST00000514944,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000445888,;TP53,frameshift_variant,p.Pro128LeufsTer42,ENST00000455263,;TP53,incomplete_terminal_codon_variant,p.%3D,ENST00000503591,;TP53,5_prime_UTR_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	573	383	128	P/X	cCt/ct	TP53_g.12371C>T,TP53_g.12371C>G,COSM45131	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.Y126_K132delYSPALNK|c.376_396del21|6,CODON|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.N131delN|c.393_395delCAA|4,BUFFER|p.K132R|c.395A>G|5,BUFFER|p.K132T|c.395A>C|7,BUFFER|p.K39T|c.116A>C|3,BUFFER|p.K132R|c.395A>G|39,BUFFER|p.K132M|c.395A>T|10,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K39R|c.116A>G|7,BUFFER|p.K132Q|c.394A>C|13,BUFFER|p.K39E|c.115A>G|3,BUFFER|p.K132*|c.394A>T|5,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|19,BUFFER|p.N131delN|c.391_393delAAC|8,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131I|c.392A>T|7,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131S|c.392A>G|5,BUFFER|p.N38I|c.113A>T|3,BUFFER|p.N131Y|c.391A>T|8,BUFFER|p.L130L|c.390C>T|4,BUFFER|p.L130H|c.389T>A|5,BUFFER|p.L130P|c.389T>C|5,BUFFER|p.L130R|c.389T>G|8,BUFFER|p.L130F|c.388C>T|13,BUFFER|p.L130V|c.388C>G|5,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L130V|c.388C>G|3,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L37F|c.109C>T|7,BUFFER|p.L130F|c.388C>T|3,BUFFER|p.L130V|c.388C>G|5,BUFFER|p.L37V|c.109C>G|5,BUFFER|p.L130F|c.388C>T|4,BUFFER|p.L130V|c.388C>G|15,BUFFER|p.P128L|c.383C>T|3,BUFFER|p.P128fs*42|c.382delC|3,BUFFER|p.P128S|c.382C>T|7,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S127Y|c.380C>A|10,BUFFER|p.S34F|c.101C>T|11,BUFFER|p.S127F|c.380C>T|4,BUFFER|p.S127F|c.380C>T|33,BUFFER|p.S127F|c.380C>T|3,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S34P|c.100T>C|4,BUFFER|p.S34T|c.100T>A|4,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.S127P|c.379T>C|8,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127T|c.379T>A|10,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>G|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>A|4,BUFFER|p.Y33*|c.99C>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y33C|c.98A>G|6,BUFFER|p.Y126C|c.377A>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y126C|c.377A>G|9,BUFFER|p.Y126S|c.377A>C|3,BUFFER|p.Y126C|c.377A>G|5,BUFFER|p.Y126N|c.376T>A|7,BUFFER|p.Y33D|c.97T>G|7,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.Y126D|c.376T>G|10,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.?|c.97-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|10,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.97-1G>A|20,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>T|9,BUFFER|p.?|c.376-2A>G|4,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.97-2A>T|3,BUFFER|p.?|c.97-2A>G|10,BUFFER|p.?|c.376-2A>G|17,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-2A>G|6,BUFFER|p.?|c.376-2A>C|4,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-4A>G|3	INDELOCATOR*|VARSCANI*|PINDEL	AGGGCAGGGGAG	.	3	ESCA
DNAH2	0	.	GRCh37	17	7719967	7719967	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9808G>A	p.Glu3270Lys	p.E3270K	ENST00000572933	64/86	66	47	19	65	65	0	DNAH2,missense_variant,p.Glu3270Lys,ENST00000389173,;DNAH2,missense_variant,p.Glu3270Lys,ENST00000572933,;DNAH2,missense_variant,p.Glu219Lys,ENST00000575105,;	A	ENSG00000183914	ENST00000572933	Transcript	missense_variant	11268	9808	3270	E/K	Gaa/Aaa	.	.	.	1	DNAH2	HGNC	2948	protein_coding	YES	CCDS32551.1	ENSP00000458355	DYH2_HUMAN	.	UPI00005B2F0D	.	.	benign(0.11)	64/86	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183,Pfam_domain:PF12777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTGAAGAG	.	5	ESCA
NARF	0	.	GRCh37	17	80439050	80439050	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732G>T	p.Leu244Phe	p.L244F	ENST00000309794	7/11	41	12	29	24	24	0	NARF,missense_variant,p.Leu290Phe,ENST00000457415,;NARF,missense_variant,p.Leu185Phe,ENST00000390006,;NARF,missense_variant,p.Leu199Phe,ENST00000577432,;NARF,missense_variant,p.Leu116Phe,ENST00000412079,;NARF,missense_variant,p.Leu244Phe,ENST00000309794,;NARF,missense_variant,p.Leu196Phe,ENST00000345415,;NARF,missense_variant,p.Leu32Phe,ENST00000584513,;NARF,downstream_gene_variant,,ENST00000577410,;RP13-991F5.2,upstream_gene_variant,,ENST00000582249,;NARF-IT1,upstream_gene_variant,,ENST00000584012,;NARF,downstream_gene_variant,,ENST00000581743,;NARF,missense_variant,p.Leu199Phe,ENST00000581202,;NARF,missense_variant,p.Leu244Phe,ENST00000374611,;NARF,3_prime_UTR_variant,,ENST00000582907,;NARF,3_prime_UTR_variant,,ENST00000581795,;NARF,non_coding_transcript_exon_variant,,ENST00000577812,;NARF,non_coding_transcript_exon_variant,,ENST00000584965,;NARF,non_coding_transcript_exon_variant,,ENST00000584445,;NARF,upstream_gene_variant,,ENST00000583908,;NARF,downstream_gene_variant,,ENST00000578082,;NARF,downstream_gene_variant,,ENST00000579083,;NARF,upstream_gene_variant,,ENST00000578820,;	T	ENSG00000141562	ENST00000309794	Transcript	missense_variant	930	732	244	L/F	ttG/ttT	.	.	.	1	NARF	HGNC	29916	protein_coding	YES	CCDS32777.1	ENSP00000309899	NARF_HUMAN	J3QSD9_HUMAN,J3QRB0_HUMAN,J3QL28_HUMAN,J3KS03_HUMAN,B5KGZ1_HUMAN	UPI0000073D0C	.	deleterious(0.05)	possibly_damaging(0.756)	7/11	.	Superfamily_domains:SSF53920,Pfam_domain:PF02906,Gene3D:1hfeL01,hmmpanther:PTHR11615:SF124,hmmpanther:PTHR11615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTGCATGG	.	5	ESCA
C19orf52	0	.	GRCh37	19	11040536	11040536	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*158C>G	.	.	ENST00000270502	2/2	24	20	4	11	11	0	C19orf52,3_prime_UTR_variant,,ENST00000270502,;YIPF2,upstream_gene_variant,,ENST00000588347,;YIPF2,upstream_gene_variant,,ENST00000587943,;YIPF2,upstream_gene_variant,,ENST00000585858,;YIPF2,upstream_gene_variant,,ENST00000253031,;YIPF2,upstream_gene_variant,,ENST00000586575,;YIPF2,upstream_gene_variant,,ENST00000590329,;YIPF2,upstream_gene_variant,,ENST00000586748,;C19orf52,upstream_gene_variant,,ENST00000593162,;C19orf52,3_prime_UTR_variant,,ENST00000588807,;YIPF2,upstream_gene_variant,,ENST00000592505,;YIPF2,upstream_gene_variant,,ENST00000588962,;	G	ENSG00000142444	ENST00000270502	Transcript	3_prime_UTR_variant	1031	.	.	.	.	.	.	.	1	C19orf52	HGNC	25152	protein_coding	YES	CCDS12252.1	ENSP00000270502	CS052_HUMAN	.	UPI0000071552	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGTTCTTTAT	.	2	ESCA
ZNF653	0	.	GRCh37	19	11598149	11598149	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129A>G	p.Thr377Ala	p.T377A	ENST00000293771	4/9	92	83	9	39	39	0	ZNF653,missense_variant,p.Thr377Ala,ENST00000293771,;ZNF653,upstream_gene_variant,,ENST00000592756,;ZNF653,upstream_gene_variant,,ENST00000589051,;ZNF653,upstream_gene_variant,,ENST00000590296,;ZNF653,non_coding_transcript_exon_variant,,ENST00000590548,;CTC-398G3.6,intron_variant,,ENST00000585656,;	C	ENSG00000161914	ENST00000293771	Transcript	missense_variant	1266	1129	377	T/A	Acc/Gcc	.	.	.	-1	ZNF653	HGNC	25196	protein_coding	YES	CCDS12261.1	ENSP00000293771	ZN653_HUMAN	.	UPI000006FAFC	.	tolerated(0.51)	benign(0.002)	4/9	.	hmmpanther:PTHR11389:SF353,hmmpanther:PTHR11389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATGGTGCTAG	.	4	ESCA
ABHD8	0	.	GRCh37	19	17411829	17411829	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.597G>C	p.%3D	p.V199V	ENST00000247706	2/5	64	53	10	28	28	0	ABHD8,synonymous_variant,p.%3D,ENST00000247706,;MRPL34,intron_variant,,ENST00000600434,;MRPL34,intron_variant,,ENST00000595444,;ABHD8,downstream_gene_variant,,ENST00000594194,;MRPL34,upstream_gene_variant,,ENST00000252602,;ABHD8,downstream_gene_variant,,ENST00000593489,;MRPL34,upstream_gene_variant,,ENST00000602206,;MRPL34,upstream_gene_variant,,ENST00000594999,;CTD-2278I10.4,upstream_gene_variant,,ENST00000594077,;MRPL34,downstream_gene_variant,,ENST00000597996,;	G	ENSG00000127220	ENST00000247706	Transcript	synonymous_variant	837	597	199	V	gtG/gtC	.	.	.	-1	ABHD8	HGNC	23759	protein_coding	YES	CCDS12355.1	ENSP00000247706	ABHD8_HUMAN	B2C6G3_HUMAN	UPI0000043630	.	.	.	2/5	.	hmmpanther:PTHR10992,hmmpanther:PTHR10992:SF23,Pfam_domain:PF12697,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474,Prints_domain:PR00412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCGCACAAA	.	5	ESCA
ABHD8	0	.	GRCh37	19	17412239	17412239	+	Missense_Mutation	SNP	C	C	A	rs374386420	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.187G>T	p.Ala63Ser	p.A63S	ENST00000247706	2/5	22	13	9	21	21	0	ABHD8,missense_variant,p.Ala63Ser,ENST00000247706,;ABHD8,missense_variant,p.Ala84Ser,ENST00000594194,;ABHD8,missense_variant,p.Ala79Ser,ENST00000593489,;MRPL34,intron_variant,,ENST00000600434,;MRPL34,intron_variant,,ENST00000595444,;MRPL34,upstream_gene_variant,,ENST00000252602,;MRPL34,upstream_gene_variant,,ENST00000602206,;MRPL34,upstream_gene_variant,,ENST00000594999,;CTD-2278I10.4,upstream_gene_variant,,ENST00000594077,;MRPL34,downstream_gene_variant,,ENST00000597996,;	A	ENSG00000127220	ENST00000247706	Transcript	missense_variant	427	187	63	A/S	Gca/Tca	rs374386420,COSM1391437	.	.	-1	ABHD8	HGNC	23759	protein_coding	YES	CCDS12355.1	ENSP00000247706	ABHD8_HUMAN	B2C6G3_HUMAN	UPI0000043630	.	tolerated_low_confidence(0.72)	benign(0.003)	2/5	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	G:0	G:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGATGCGGATG	byFrequency|byCluster	2	ESCA
SUGP2	0	.	GRCh37	19	19120975	19120975	+	Missense_Mutation	SNP	G	G	A	rs372273190	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2027C>T	p.Pro676Leu	p.P676L	ENST00000601879	5/10	45	40	5	20	20	0	SUGP2,missense_variant,p.Pro676Leu,ENST00000452918,;SUGP2,missense_variant,p.Pro676Leu,ENST00000337018,;SUGP2,missense_variant,p.Pro676Leu,ENST00000601879,;SUGP2,missense_variant,p.Pro445Leu,ENST00000456085,;SUGP2,missense_variant,p.Pro690Leu,ENST00000600377,;SUGP2,missense_variant,p.Pro676Leu,ENST00000330854,;SUGP2,missense_variant,p.Pro676Leu,ENST00000594773,;SUGP2,missense_variant,p.Pro676Leu,ENST00000600239,;SUGP2,3_prime_UTR_variant,,ENST00000598240,;	A	ENSG00000064607	ENST00000601879	Transcript	missense_variant	2325	2027	676	P/L	cCg/cTg	rs372273190,COSM3742839,COSM3742838	.	.	-1	SUGP2	HGNC	18641	protein_coding	YES	CCDS12392.1	ENSP00000472286	SUGP2_HUMAN	M0R065_HUMAN	UPI000019825D	.	deleterious(0.01)	probably_damaging(0.943)	5/10	.	hmmpanther:PTHR23340:SF2,hmmpanther:PTHR23340	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCACGGAAGG	byFrequency|byCluster	4	ESCA
CD22	0	.	GRCh37	19	35837505	35837505	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2449G>C	p.Asp817His	p.D817H	ENST00000085219	14/14	83	79	4	38	38	0	CD22,missense_variant,p.Asp640His,ENST00000594250,;CD22,missense_variant,p.Asp729His,ENST00000536635,;CD22,missense_variant,p.Asp632His,ENST00000270311,;CD22,missense_variant,p.Asp645His,ENST00000419549,;CD22,missense_variant,p.Asp640His,ENST00000341773,;CD22,missense_variant,p.Asp817His,ENST00000085219,;CD22,3_prime_UTR_variant,,ENST00000544992,;FFAR1,upstream_gene_variant,,ENST00000246553,;MIR5196,downstream_gene_variant,,ENST00000578146,;CD22,downstream_gene_variant,,ENST00000598815,;CD22,3_prime_UTR_variant,,ENST00000601769,;CD22,downstream_gene_variant,,ENST00000600655,;CD22,downstream_gene_variant,,ENST00000594125,;CD22,downstream_gene_variant,,ENST00000602123,;CD22,downstream_gene_variant,,ENST00000593704,;	C	ENSG00000012124	ENST00000085219	Transcript	missense_variant	2515	2449	817	D/H	Gat/Cat	COSM3822737	.	.	1	CD22	HGNC	1643	protein_coding	YES	CCDS12457.1	ENSP00000085219	CD22_HUMAN	Q0EAF5_HUMAN,Q9UQB2_HUMAN,Q9UQB1_HUMAN,M0R3H1_HUMAN,M0R2M0_HUMAN,M0R1M2_HUMAN,M0QYP4_HUMAN	UPI000012733D	.	deleterious(0)	probably_damaging(0.992)	14/14	.	hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF39	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGAAGATGAG	.	2	ESCA
APLP1	0	.	GRCh37	19	36368698	36368698	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1523G>T	p.Gly508Val	p.G508V	ENST00000221891	12/17	45	38	7	12	12	0	APLP1,missense_variant,p.Gly155Val,ENST00000587274,;APLP1,missense_variant,p.Gly508Val,ENST00000221891,;APLP1,missense_variant,p.Gly502Val,ENST00000586861,;APLP1,missense_variant,p.Gly126Val,ENST00000588808,;APLP1,missense_variant,p.Gly469Val,ENST00000537454,;APLP1,downstream_gene_variant,,ENST00000592316,;RN7SL402P,upstream_gene_variant,,ENST00000465059,;APLP1,non_coding_transcript_exon_variant,,ENST00000589298,;APLP1,upstream_gene_variant,,ENST00000591165,;APLP1,3_prime_UTR_variant,,ENST00000590561,;APLP1,upstream_gene_variant,,ENST00000590926,;	T	ENSG00000105290	ENST00000221891	Transcript	missense_variant	1715	1523	508	G/V	gGt/gTt	.	.	.	1	APLP1	HGNC	597	protein_coding	YES	CCDS32997.1	ENSP00000221891	APLP1_HUMAN	K7EQJ4_HUMAN,K7ELK0_HUMAN,A4UCT6_HUMAN	UPI000020215E	.	tolerated(0.26)	benign(0.402)	12/17	.	hmmpanther:PTHR23103:SF13,hmmpanther:PTHR23103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGGGTGGGC	.	5	ESCA
ZNF570	0	.	GRCh37	19	37975938	37975938	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1414T>C	p.Cys472Arg	p.C472R	ENST00000330173	5/5	83	72	11	41	41	0	ZNF570,missense_variant,p.Cys269Arg,ENST00000388801,;ZNF570,missense_variant,p.Cys472Arg,ENST00000330173,;ZNF570,missense_variant,p.Cys528Arg,ENST00000586475,;ZNF570,downstream_gene_variant,,ENST00000589725,;CTD-2086O20.3,upstream_gene_variant,,ENST00000591976,;ZNF570,3_prime_UTR_variant,,ENST00000588644,;ZNF570,downstream_gene_variant,,ENST00000590664,;	C	ENSG00000171827	ENST00000330173	Transcript	missense_variant	1943	1414	472	C/R	Tgt/Cgt	.	.	.	1	ZNF570	HGNC	26416	protein_coding	YES	CCDS12504.1	ENSP00000331540	ZN570_HUMAN	K7EP64_HUMAN,K7ENX9_HUMAN,K7EMF5_HUMAN,B4DMP1_HUMAN	UPI000006DC96	.	deleterious(0)	probably_damaging(1)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF17,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAATGTACT	.	5	ESCA
WDR87	0	.	GRCh37	19	38386867	38386867	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129+28C>T	.	.	ENST00000303868	.	126	52	74	46	46	0	WDR87,stop_gained,p.Gln53Ter,ENST00000447313,;WDR87,intron_variant,,ENST00000303868,;WDR87,non_coding_transcript_exon_variant,,ENST00000473328,;	A	ENSG00000171804	ENST00000303868	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	WDR87	HGNC	29934	protein_coding	YES	CCDS46063.1	ENSP00000368025	WDR87_HUMAN	B4DXE9_HUMAN	UPI0001662BC1	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTGAGGAT	.	5	ESCA
PSMD8	0	.	GRCh37	19	38865577	38865577	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.336C>G	p.Cys112Trp	p.C112W	ENST00000215071	1/7	91	78	12	29	29	0	PSMD8,missense_variant,p.Cys49Trp,ENST00000602911,;PSMD8,missense_variant,p.Cys56Trp,ENST00000592561,;PSMD8,missense_variant,p.Cys112Trp,ENST00000215071,;PSMD8,missense_variant,p.Cys60Trp,ENST00000585598,;CATSPERG,downstream_gene_variant,,ENST00000215069,;PSMD8,upstream_gene_variant,,ENST00000592035,;CATSPERG,downstream_gene_variant,,ENST00000409235,;CATSPERG,downstream_gene_variant,,ENST00000410018,;PSMD8,upstream_gene_variant,,ENST00000591250,;PSMD8,non_coding_transcript_exon_variant,,ENST00000591216,;PSMD8,non_coding_transcript_exon_variant,,ENST00000592001,;CATSPERG,downstream_gene_variant,,ENST00000471517,;CATSPERG,downstream_gene_variant,,ENST00000312265,;CATSPERG,downstream_gene_variant,,ENST00000492088,;CATSPERG,downstream_gene_variant,,ENST00000412458,;	G	ENSG00000099341	ENST00000215071	Transcript	missense_variant	402	336	112	C/W	tgC/tgG	.	.	.	1	PSMD8	HGNC	9566	protein_coding	YES	CCDS12515.2	ENSP00000215071	PSMD8_HUMAN	R4GMR5_HUMAN,K7ERW6_HUMAN	UPI000059D712	.	deleterious(0)	probably_damaging(0.999)	1/7	.	hmmpanther:PTHR12387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTGCGGGGA	.	5	ESCA
GGN	0	.	GRCh37	19	38876738	38876738	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1164C>A	p.%3D	p.G388G	ENST00000334928	3/4	31	22	9	15	15	0	GGN,synonymous_variant,p.%3D,ENST00000334928,;GGN,downstream_gene_variant,,ENST00000587676,;SPRED3,upstream_gene_variant,,ENST00000338502,;PSMD8,downstream_gene_variant,,ENST00000602911,;PSMD8,downstream_gene_variant,,ENST00000592035,;SPRED3,upstream_gene_variant,,ENST00000587947,;PSMD8,downstream_gene_variant,,ENST00000592561,;PSMD8,downstream_gene_variant,,ENST00000215071,;GGN,downstream_gene_variant,,ENST00000586599,;PSMD8,downstream_gene_variant,,ENST00000585598,;SPRED3,upstream_gene_variant,,ENST00000586301,;SPRED3,upstream_gene_variant,,ENST00000587013,;AC005789.9,intron_variant,,ENST00000585411,;GGN,intron_variant,,ENST00000591809,;SPRED3,upstream_gene_variant,,ENST00000587564,;GGN,synonymous_variant,p.%3D,ENST00000585737,;SPRED3,upstream_gene_variant,,ENST00000586958,;PSMD8,downstream_gene_variant,,ENST00000592001,;PSMD8,downstream_gene_variant,,ENST00000590331,;	T	ENSG00000179168	ENST00000334928	Transcript	synonymous_variant	1297	1164	388	G	ggC/ggA	.	.	.	-1	GGN	HGNC	18869	protein_coding	YES	CCDS12516.1	ENSP00000334940	GGN_HUMAN	K7ENT5_HUMAN,K7EJI6_HUMAN	UPI0000073CAB	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22979:SF18,hmmpanther:PTHR22979	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGAGCCCCA	.	5	ESCA
RASGRP4	0	.	GRCh37	19	38904097	38904097	+	Silent	SNP	G	G	A	rs753112169	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1248C>T	p.%3D	p.F416F	ENST00000587738	10/17	61	51	9	24	24	0	RASGRP4,synonymous_variant,p.%3D,ENST00000426920,;RASGRP4,synonymous_variant,p.%3D,ENST00000293062,;RASGRP4,synonymous_variant,p.%3D,ENST00000587738,;RASGRP4,synonymous_variant,p.%3D,ENST00000587753,;RASGRP4,synonymous_variant,p.%3D,ENST00000454404,;RASGRP4,synonymous_variant,p.%3D,ENST00000586305,;RASGRP4,synonymous_variant,p.%3D,ENST00000433821,;FAM98C,downstream_gene_variant,,ENST00000588262,;FAM98C,downstream_gene_variant,,ENST00000252530,;FAM98C,downstream_gene_variant,,ENST00000343358,;RASGRP4,synonymous_variant,p.%3D,ENST00000589358,;RASGRP4,synonymous_variant,p.%3D,ENST00000589474,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000592322,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588708,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588404,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000589100,;RASGRP4,upstream_gene_variant,,ENST00000587287,;FAM98C,downstream_gene_variant,,ENST00000589027,;FAM98C,downstream_gene_variant,,ENST00000588348,;FAM98C,downstream_gene_variant,,ENST00000586372,;	A	ENSG00000171777	ENST00000587738	Transcript	synonymous_variant	1319	1248	416	F	ttC/ttT	rs753112169	.	.	-1	RASGRP4	HGNC	18958	protein_coding	YES	CCDS46068.1	ENSP00000465772	GRP4_HUMAN	.	UPI0000050F40	.	.	.	10/17	.	PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF157,hmmpanther:PTHR23113,SMART_domains:SM00147,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTAGAAGAG	.	5	ESCA
ARHGAP35	0	.	GRCh37	19	47503672	47503672	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4227C>A	p.Phe1409Leu	p.F1409L	ENST00000404338	6/6	34	20	13	25	25	0	ARHGAP35,missense_variant,p.Phe1409Leu,ENST00000404338,;ARHGAP35,downstream_gene_variant,,ENST00000598548,;ARHGAP35,downstream_gene_variant,,ENST00000596593,;ARHGAP35,non_coding_transcript_exon_variant,,ENST00000599284,;ARHGAP35,non_coding_transcript_exon_variant,,ENST00000595822,;	A	ENSG00000160007	ENST00000404338	Transcript	missense_variant	4227	4227	1409	F/L	ttC/ttA	.	.	.	1	ARHGAP35	HGNC	4591	protein_coding	YES	CCDS46127.1	ENSP00000385720	RHG35_HUMAN	.	UPI0000163F71	.	deleterious(0)	probably_damaging(0.913)	6/6	.	PROSITE_profiles:PS50238,hmmpanther:PTHR23178,hmmpanther:PTHR23178:SF26,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCAGCAC	.	5	ESCA
ZC3H4	0	.	GRCh37	19	47575222	47575222	+	Silent	SNP	C	C	T	rs746699853	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1959G>A	p.%3D	p.P653P	ENST00000253048	13/15	35	16	19	21	21	0	ZC3H4,synonymous_variant,p.%3D,ENST00000253048,;ZC3H4,synonymous_variant,p.%3D,ENST00000601973,;ZC3H4,intron_variant,,ENST00000594019,;	T	ENSG00000130749	ENST00000253048	Transcript	synonymous_variant	1997	1959	653	P	ccG/ccA	rs746699853	.	.	-1	ZC3H4	HGNC	17808	protein_coding	YES	CCDS42582.1	ENSP00000253048	ZC3H4_HUMAN	.	UPI00001C2000	.	.	.	13/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13119:SF23,hmmpanther:PTHR13119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCATCGGCAT	.	5	ESCA
ZNF880	0	.	GRCh37	19	52887707	52887707	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874G>T	p.Gly292Ter	p.G292*	ENST00000422689	4/4	43	28	15	42	42	0	ZNF880,stop_gained,p.Gly292Ter,ENST00000422689,;ZNF880,downstream_gene_variant,,ENST00000600321,;ZNF880,downstream_gene_variant,,ENST00000424032,;CTD-3018O17.3,downstream_gene_variant,,ENST00000601562,;CTD-3018O17.3,downstream_gene_variant,,ENST00000594119,;	T	ENSG00000221923	ENST00000422689	Transcript	stop_gained	889	874	292	G/*	Gga/Tga	.	.	.	1	ZNF880	HGNC	37249	protein_coding	YES	CCDS46164.1	ENSP00000406318	ZN880_HUMAN	.	UPI00001D818D	.	.	.	4/4	.	Superfamily_domains:SSF57667,Pfam_domain:PF13465,Gene3D:3.30.160.60,hmmpanther:PTHR24377:SF108,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACTGGAGAG	.	5	ESCA
BIRC8	0	.	GRCh37	19	53793633	53793633	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-6C>G	.	.	ENST00000426466	1/1	23	8	14	27	27	0	BIRC8,5_prime_UTR_variant,,ENST00000426466,;	C	ENSG00000163098	ENST00000426466	Transcript	5_prime_UTR_variant	1243	.	.	.	.	.	.	.	-1	BIRC8	HGNC	14878	protein_coding	YES	CCDS12863.1	ENSP00000412957	BIRC8_HUMAN	.	UPI000003966A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGGATTCC	.	5	ESCA
GP6	0	.	GRCh37	19	55526285	55526285	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1028C>T	p.Ala343Val	p.A343V	ENST00000310373	8/8	48	13	34	51	51	0	GP6,missense_variant,p.Ala343Val,ENST00000310373,;GP6,3_prime_UTR_variant,,ENST00000417454,;GP6,3_prime_UTR_variant,,ENST00000333884,;CTC-550B14.7,intron_variant,,ENST00000586845,;CTC-550B14.7,intron_variant,,ENST00000593060,;GP6,non_coding_transcript_exon_variant,,ENST00000465648,;	A	ENSG00000088053	ENST00000310373	Transcript	missense_variant	1056	1028	343	A/V	gCt/gTt	.	.	.	-1	GP6	HGNC	14388	protein_coding	YES	CCDS42626.1	ENSP00000308782	GPVI_HUMAN	K7EIW7_HUMAN	UPI000013C631	.	deleterious_low_confidence(0)	benign(0)	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCAGCGGTC	.	5	ESCA
GP6	0	.	GRCh37	19	55526286	55526286	+	Missense_Mutation	SNP	C	C	A	rs759751882	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027G>T	p.Ala343Ser	p.A343S	ENST00000310373	8/8	48	12	35	51	51	0	GP6,missense_variant,p.Ala343Ser,ENST00000310373,;GP6,3_prime_UTR_variant,,ENST00000417454,;GP6,3_prime_UTR_variant,,ENST00000333884,;CTC-550B14.7,intron_variant,,ENST00000586845,;CTC-550B14.7,intron_variant,,ENST00000593060,;GP6,non_coding_transcript_exon_variant,,ENST00000465648,;	A	ENSG00000088053	ENST00000310373	Transcript	missense_variant	1055	1027	343	A/S	Gct/Tct	rs759751882	.	.	-1	GP6	HGNC	14388	protein_coding	YES	CCDS42626.1	ENSP00000308782	GPVI_HUMAN	K7EIW7_HUMAN	UPI000013C631	.	deleterious_low_confidence(0)	benign(0)	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAGCGGTCA	byFrequency	5	ESCA
NLRP13	0	.	GRCh37	19	56416358	56416358	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2568G>A	p.%3D	p.K856K	ENST00000342929	8/11	49	2	47	40	40	0	NLRP13,synonymous_variant,p.%3D,ENST00000588751,;NLRP13,synonymous_variant,p.%3D,ENST00000342929,;	T	ENSG00000173572	ENST00000342929	Transcript	synonymous_variant	2568	2568	856	K	aaG/aaA	.	.	.	-1	NLRP13	HGNC	22937	protein_coding	YES	CCDS33119.1	ENSP00000343891	NAL13_HUMAN	.	UPI00001AEEC8	.	.	.	8/11	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF10,Pfam_domain:PF13516,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATAGCTTTAT	.	5	ESCA
NLRP13	0	.	GRCh37	19	56424072	56424072	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1111C>A	p.Leu371Ile	p.L371I	ENST00000342929	5/11	50	34	15	35	35	0	NLRP13,missense_variant,p.Leu371Ile,ENST00000588751,;NLRP13,missense_variant,p.Leu371Ile,ENST00000342929,;	T	ENSG00000173572	ENST00000342929	Transcript	missense_variant	1111	1111	371	L/I	Ctt/Att	COSM3835865	.	.	-1	NLRP13	HGNC	22937	protein_coding	YES	CCDS33119.1	ENSP00000343891	NAL13_HUMAN	.	UPI00001AEEC8	.	deleterious(0)	probably_damaging(0.998)	5/11	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF10,Pfam_domain:PF05729,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTAAGATCTC	.	5	ESCA
ZNF749	0	.	GRCh37	19	57955810	57955810	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1294C>A	p.His432Asn	p.H432N	ENST00000334181	3/3	46	17	29	38	38	0	ZNF749,missense_variant,p.His432Asn,ENST00000334181,;AC004076.9,intron_variant,,ENST00000596831,;ZNF749,downstream_gene_variant,,ENST00000415248,;	A	ENSG00000186230	ENST00000334181	Transcript	missense_variant	1544	1294	432	H/N	Cat/Aat	.	.	.	1	ZNF749	HGNC	32783	protein_coding	YES	CCDS33132.2	ENSP00000333980	ZN749_HUMAN	C9J756_HUMAN	UPI0000237933	.	deleterious(0)	possibly_damaging(0.758)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF5,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTCATACT	.	5	ESCA
ZNF551	0	.	GRCh37	19	58193488	58193488	+	5'UTR	SNP	C	C	T	rs531782402	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-44C>T	.	.	ENST00000282296	1/3	80	56	24	76	76	0	ZNF551,splice_region_variant,,ENST00000601064,;AC003006.7,5_prime_UTR_variant,,ENST00000594684,;ZNF551,5_prime_UTR_variant,,ENST00000282296,;ZNF551,5_prime_UTR_variant,,ENST00000596085,;ZNF551,5_prime_UTR_variant,,ENST00000356715,;ZSCAN4,downstream_gene_variant,,ENST00000318203,;AC003006.7,non_coding_transcript_exon_variant,,ENST00000599221,;ZNF551,non_coding_transcript_exon_variant,,ENST00000599402,;	T	ENSG00000204519	ENST00000282296	Transcript	5_prime_UTR_variant	142	.	.	.	.	rs531782402	.	.	1	ZNF551	HGNC	25108	protein_coding	YES	CCDS12959.2	ENSP00000282296	ZN551_HUMAN	M0R2M4_HUMAN	UPI000059D7C6	.	.	.	1/3	.	.	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTCGGGTG	byFrequency|by1000G	5	ESCA
ARHGEF18	0	.	GRCh37	19	7523441	7523442	+	Frame_Shift_Del	DEL	GG	GG	-	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	GG	GG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1662_1663delGG	p.Glu555SerfsTer22	p.E555Sfs*22	ENST00000359920	9/20	54	40	14	51	51	0	ARHGEF18,frameshift_variant,p.Glu555SerfsTer22,ENST00000359920,;ARHGEF18,frameshift_variant,p.Glu200SerfsTer22,ENST00000594665,;ARHGEF18,frameshift_variant,p.Glu397SerfsTer22,ENST00000319670,;CTD-2207O23.3,frameshift_variant,p.Glu513SerfsTer22,ENST00000593531,;	-	ENSG00000104880	ENST00000359920	Transcript	frameshift_variant	1914-1915	1661-1662	554	R/X	aGG/a	.	.	.	1	ARHGEF18	HGNC	17090	protein_coding	YES	CCDS45946.1	ENSP00000352995	ARHGI_HUMAN	M0R125_HUMAN	UPI0000D6170D	.	.	.	9/20	.	PROSITE_profiles:PS50003,hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF9,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCGTGAGGGAAGT	.	3	ESCA
AZU1	0	.	GRCh37	19	828365	828365	+	Missense_Mutation	SNP	C	C	T	rs746878090	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194C>T	p.Ala65Val	p.A65V	ENST00000233997	2/5	15	4	11	12	12	0	AZU1,missense_variant,p.Ala65Val,ENST00000233997,;AZU1,non_coding_transcript_exon_variant,,ENST00000592205,;	T	ENSG00000172232	ENST00000233997	Transcript	missense_variant	215	194	65	A/V	gCg/gTg	rs746878090	.	.	1	AZU1	HGNC	913	protein_coding	YES	CCDS12044.1	ENSP00000233997	CAP7_HUMAN	.	UPI0000126ECD	.	deleterious(0.01)	benign(0.058)	2/5	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF10,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCGCGGCCA	byFrequency	5	ESCA
PRTN3	0	.	GRCh37	19	846216	846216	+	Frame_Shift_Del	DEL	C	C	-	rs774177496	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442delC	p.His148ThrfsTer60	p.H148Tfs*60	ENST00000234347	4/5	36	24	12	23	23	0	PRTN3,frameshift_variant,p.His107ThrfsTer60,ENST00000544537,;PRTN3,frameshift_variant,p.His148ThrfsTer60,ENST00000234347,;ELANE,upstream_gene_variant,,ENST00000590230,;	-	ENSG00000196415	ENST00000234347	Transcript	frameshift_variant	485	439	147	P/X	Ccc/cc	rs774177496	.	.	1	PRTN3	HGNC	9495	protein_coding	YES	CCDS32860.1	ENSP00000234347	PRTN3_HUMAN	U3KPS2_HUMAN	UPI0000132263	.	.	.	4/5	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24257:SF15,hmmpanther:PTHR24257,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	CCAGTGCCCCAC	.	2	ESCA
RSBN1	0	.	GRCh37	1	114304727	114304727	+	3'UTR	DEL	T	T	-	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3875delA	.	.	ENST00000261441	7/7	35	27	8	34	34	0	RSBN1,3_prime_UTR_variant,,ENST00000261441,;PHTF1,upstream_gene_variant,,ENST00000357783,;PHTF1,upstream_gene_variant,,ENST00000369596,;PHTF1,upstream_gene_variant,,ENST00000369600,;PHTF1,upstream_gene_variant,,ENST00000369604,;PHTF1,upstream_gene_variant,,ENST00000447664,;PHTF1,upstream_gene_variant,,ENST00000393357,;PHTF1,upstream_gene_variant,,ENST00000446739,;PHTF1,upstream_gene_variant,,ENST00000369598,;PHTF1,upstream_gene_variant,,ENST00000493212,;RSBN1,downstream_gene_variant,,ENST00000369581,;RSBN1,downstream_gene_variant,,ENST00000476412,;	-	ENSG00000081019	ENST00000261441	Transcript	3_prime_UTR_variant	6348	.	.	.	.	.	.	.	-1	RSBN1	HGNC	25642	protein_coding	YES	CCDS862.1	ENSP00000261441	RSBN1_HUMAN	.	UPI00002263B4	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTATATGCAAA	.	3	ESCA
TAS1R3	0	.	GRCh37	1	1268382	1268382	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000339381	4/6	37	28	9	42	42	0	TAS1R3,missense_variant,p.Glu453Gln,ENST00000339381,;DVL1,downstream_gene_variant,,ENST00000378891,;GLTPD1,downstream_gene_variant,,ENST00000343938,;DVL1,downstream_gene_variant,,ENST00000378888,;	C	ENSG00000169962	ENST00000339381	Transcript	missense_variant	1389	1357	453	E/Q	Gag/Cag	.	.	.	1	TAS1R3	HGNC	15661	protein_coding	YES	CCDS30556.1	ENSP00000344411	TS1R3_HUMAN	.	UPI0000051F47	.	tolerated(0.11)	benign(0.076)	4/6	.	hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF2,Pfam_domain:PF01094,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATGGAGTAC	.	5	ESCA
POU2F1	0	.	GRCh37	1	167343527	167343527	+	Silent	SNP	C	C	T	rs562014026	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.585C>T	p.%3D	p.I195I	ENST00000367866	6/16	71	61	9	30	30	0	POU2F1,synonymous_variant,p.%3D,ENST00000420254,;POU2F1,synonymous_variant,p.%3D,ENST00000443275,;POU2F1,synonymous_variant,p.%3D,ENST00000367862,;POU2F1,synonymous_variant,p.%3D,ENST00000367866,;POU2F1,synonymous_variant,p.%3D,ENST00000452019,;POU2F1,synonymous_variant,p.%3D,ENST00000541643,;POU2F1,intron_variant,,ENST00000429375,;RP11-52A20.2,upstream_gene_variant,,ENST00000607611,;POU2F1,non_coding_transcript_exon_variant,,ENST00000492850,;POU2F1,non_coding_transcript_exon_variant,,ENST00000470928,;POU2F1,non_coding_transcript_exon_variant,,ENST00000367865,;POU2F1,downstream_gene_variant,,ENST00000557909,;POU2F1,3_prime_UTR_variant,,ENST00000560232,;POU2F1,3_prime_UTR_variant,,ENST00000271411,;POU2F1,non_coding_transcript_exon_variant,,ENST00000557874,;POU2F1,downstream_gene_variant,,ENST00000442313,;	T	ENSG00000143190	ENST00000367866	Transcript	synonymous_variant	654	585	195	I	atC/atT	rs562014026	.	.	1	POU2F1	HGNC	9212	protein_coding	YES	CCDS1259.2	ENSP00000356840	.	J3KP77_HUMAN	UPI0000EE3C74	.	.	.	6/16	.	hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGATCGCACA	.	4	ESCA
CROCCP2	0	.	GRCh37	1	16955139	16955139	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000362058	.	184	174	10	158	157	1	CROCCP2,non_coding_transcript_exon_variant,,ENST00000540383,;CROCCP2,non_coding_transcript_exon_variant,,ENST00000412962,;CROCCP2,downstream_gene_variant,,ENST00000362058,;	T	ENSG00000215908	ENST00000362058	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1026	-1	CROCCP2	HGNC	28170	retained_intron	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGCTCTTCTC	.	2	ESCA
EMC1	0	.	GRCh37	1	19559220	19559220	+	Nonsense_Mutation	SNP	A	A	T	rs777032041	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1680T>A	p.Tyr560Ter	p.Y560*	ENST00000477853	15/23	64	50	14	52	52	0	EMC1,stop_gained,p.Tyr538Ter,ENST00000375208,;EMC1,stop_gained,p.Tyr559Ter,ENST00000375199,;EMC1,stop_gained,p.Tyr560Ter,ENST00000477853,;RP1-43E13.2,intron_variant,,ENST00000437898,;EMC1,upstream_gene_variant,,ENST00000494770,;	T	ENSG00000127463	ENST00000477853	Transcript	stop_gained	1723	1680	560	Y/*	taT/taA	rs777032041	.	.	-1	EMC1	HGNC	28957	protein_coding	YES	CCDS190.1	ENSP00000420608	EMC1_HUMAN	.	UPI0000070A23	.	.	.	15/23	.	hmmpanther:PTHR21573,hmmpanther:PTHR21573:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTAGATACTG	.	5	ESCA
CD34	0	.	GRCh37	1	208070876	208070876	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559C>G	p.Gln187Glu	p.Q187E	ENST00000310833	4/8	35	29	5	15	15	0	CD34,missense_variant,p.Gln187Glu,ENST00000356522,;CD34,missense_variant,p.Gln52Glu,ENST00000537704,;CD34,missense_variant,p.Gln187Glu,ENST00000310833,;CD34,non_coding_transcript_exon_variant,,ENST00000485761,;	C	ENSG00000174059	ENST00000310833	Transcript	missense_variant	881	559	187	Q/E	Cag/Gag	.	.	.	-1	CD34	HGNC	1662	protein_coding	YES	CCDS31011.1	ENSP00000310036	CD34_HUMAN	Q9UH97_HUMAN,Q8IUM0_HUMAN,B4DUX4_HUMAN	UPI000012734B	.	tolerated(0.65)	benign(0.025)	4/8	.	hmmpanther:PTHR16677	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTGAGTCA	.	5	ESCA
ESRRG	0	.	GRCh37	1	216741436	216741436	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609G>C	p.%3D	p.V203V	ENST00000366937	5/8	90	81	9	37	37	0	ESRRG,synonymous_variant,p.%3D,ENST00000493748,;ESRRG,synonymous_variant,p.%3D,ENST00000487276,;ESRRG,synonymous_variant,p.%3D,ENST00000391890,;ESRRG,synonymous_variant,p.%3D,ENST00000366938,;ESRRG,synonymous_variant,p.%3D,ENST00000475275,;ESRRG,synonymous_variant,p.%3D,ENST00000463665,;ESRRG,synonymous_variant,p.%3D,ENST00000366937,;ESRRG,synonymous_variant,p.%3D,ENST00000360012,;ESRRG,synonymous_variant,p.%3D,ENST00000361395,;ESRRG,synonymous_variant,p.%3D,ENST00000408911,;ESRRG,synonymous_variant,p.%3D,ENST00000366940,;ESRRG,synonymous_variant,p.%3D,ENST00000361525,;ESRRG,synonymous_variant,p.%3D,ENST00000359162,;ESRRG,synonymous_variant,p.%3D,ENST00000493603,;ESRRG,3_prime_UTR_variant,,ENST00000586199,;	G	ENSG00000196482	ENST00000366937	Transcript	synonymous_variant	876	609	203	V	gtG/gtC	.	.	.	-1	ESRRG	HGNC	3474	protein_coding	YES	CCDS58061.1	ENSP00000355904	ERR3_HUMAN	C9JNX5_HUMAN,C9J5W9_HUMAN,C9J0E3_HUMAN	UPI0000D4BFAB	.	.	.	5/8	.	Prints_domain:PR00398,Superfamily_domains:SSF48508,Superfamily_domains:SSF57716,PIRSF_domain:PIRSF002527,PIRSF_domain:PIRSF500939,Gene3D:1.10.565.10,hmmpanther:PTHR24084,PROSITE_profiles:PS51030	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGACGCACCCC	.	4	ESCA
RAB3GAP2	0	.	GRCh37	1	220387305	220387305	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.197C>G	p.Thr66Ser	p.T66S	ENST00000358951	3/35	128	58	70	79	79	0	RAB3GAP2,missense_variant,p.Thr66Ser,ENST00000358951,;RAB3GAP2,upstream_gene_variant,,ENST00000484658,;RAB3GAP2,intron_variant,,ENST00000478976,;RAB3GAP2,intron_variant,,ENST00000474178,;RAB3GAP2,intron_variant,,ENST00000237724,;	C	ENSG00000118873	ENST00000358951	Transcript	missense_variant	314	197	66	T/S	aCt/aGt	.	.	.	-1	RAB3GAP2	HGNC	17168	protein_coding	YES	CCDS31028.1	ENSP00000351832	RBGPR_HUMAN	.	UPI0000072269	.	tolerated(0.57)	benign(0.002)	3/35	.	hmmpanther:PTHR12472	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAAGTATTT	.	5	ESCA
MARK1	0	.	GRCh37	1	220835947	220835947	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000366917	.	86	69	17	48	48	0	MARK1,3_prime_UTR_variant,,ENST00000366918,;MARK1,3_prime_UTR_variant,,ENST00000402574,;MARK1,downstream_gene_variant,,ENST00000366917,;RP11-322F10.2,non_coding_transcript_exon_variant,,ENST00000446040,;	G	ENSG00000116141	ENST00000366917	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	147	1	MARK1	HGNC	6896	protein_coding	YES	CCDS31029.2	ENSP00000355884	MARK1_HUMAN	B4DIB3_HUMAN	UPI0000048D8B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGCATAGAA	.	5	ESCA
EPHA8	0	.	GRCh37	1	22903214	22903214	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664G>A	p.Asp222Asn	p.D222N	ENST00000166244	3/17	67	44	22	49	48	0	EPHA8,missense_variant,p.Asp222Asn,ENST00000374644,;EPHA8,missense_variant,p.Asp222Asn,ENST00000538803,;EPHA8,missense_variant,p.Asp222Asn,ENST00000166244,;	A	ENSG00000070886	ENST00000166244	Transcript	missense_variant	736	664	222	D/N	Gac/Aac	COSM905215,COSM905216	.	.	1	EPHA8	HGNC	3391	protein_coding	YES	CCDS225.1	ENSP00000166244	EPHA8_HUMAN	.	UPI000012A07B	.	deleterious(0)	probably_damaging(0.998)	3/17	.	PIRSF_domain:PIRSF000666,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF274	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCGACTCG	.	5	ESCA
HEATR1	0	.	GRCh37	1	236751319	236751319	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555A>G	p.Lys519Glu	p.K519E	ENST00000366582	13/45	84	63	21	41	41	0	HEATR1,missense_variant,p.Lys519Glu,ENST00000366581,;HEATR1,missense_variant,p.Lys519Glu,ENST00000366582,;	C	ENSG00000119285	ENST00000366582	Transcript	missense_variant	1670	1555	519	K/E	Aaa/Gaa	.	.	.	-1	HEATR1	HGNC	25517	protein_coding	YES	CCDS31066.1	ENSP00000355541	HEAT1_HUMAN	Q6P664_HUMAN	UPI000013D4D4	.	tolerated(0.36)	benign(0.02)	13/45	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR13457:SF1,hmmpanther:PTHR13457	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTTTATGA	.	5	ESCA
MTR	0	.	GRCh37	1	236969525	236969525	+	Missense_Mutation	SNP	G	G	C	rs768491623	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331G>C	p.Glu111Gln	p.E111Q	ENST00000366577	3/33	70	63	7	16	16	0	MTR,missense_variant,p.Glu167Gln,ENST00000418145,;MTR,missense_variant,p.Glu111Gln,ENST00000366577,;MTR,missense_variant,p.Glu111Gln,ENST00000535889,;MTR,non_coding_transcript_exon_variant,,ENST00000463959,;	C	ENSG00000116984	ENST00000366577	Transcript	missense_variant	725	331	111	E/Q	Gaa/Caa	rs768491623	.	.	1	MTR	HGNC	7468	protein_coding	YES	CCDS1614.1	ENSP00000355536	METH_HUMAN	.	UPI0000036BC4	.	tolerated(0.16)	possibly_damaging(0.609)	3/33	.	Superfamily_domains:SSF82282,PIRSF_domain:PIRSF000381,Pfam_domain:PF02574,TIGRFAM_domain:TIGR02082,Gene3D:3.20.20.330,hmmpanther:PTHR21091:SF97,hmmpanther:PTHR21091,PROSITE_profiles:PS50970	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTTGAACAC	.	4	ESCA
RYR2	0	.	GRCh37	1	237753263	237753263	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3769C>T	p.Gln1257Ter	p.Q1257*	ENST00000366574	30/105	85	75	10	37	37	0	RYR2,stop_gained,p.Gln1241Ter,ENST00000542537,;RYR2,stop_gained,p.Gln1257Ter,ENST00000366574,;RYR2,stop_gained,p.Gln1255Ter,ENST00000360064,;	T	ENSG00000198626	ENST00000366574	Transcript	stop_gained	4086	3769	1257	Q/*	Cag/Tag	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	.	30/105	.	hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTCAGTTT	.	4	ESCA
GALE	0	.	GRCh37	1	24125155	24125155	+	Missense_Mutation	SNP	C	C	G	rs370693766	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.187G>C	p.Glu63Gln	p.E63Q	ENST00000374497	4/12	20	16	4	13	13	0	GALE,missense_variant,p.Glu63Gln,ENST00000425913,;GALE,missense_variant,p.Glu63Gln,ENST00000445705,;GALE,missense_variant,p.Glu63Gln,ENST00000374497,;GALE,5_prime_UTR_variant,,ENST00000418277,;GALE,5_prime_UTR_variant,,ENST00000429356,;LYPLA2,downstream_gene_variant,,ENST00000400061,;LYPLA2,downstream_gene_variant,,ENST00000420982,;HMGCL,downstream_gene_variant,,ENST00000374490,;HMGCL,downstream_gene_variant,,ENST00000235958,;LYPLA2,downstream_gene_variant,,ENST00000421070,;LYPLA2,downstream_gene_variant,,ENST00000374503,;HMGCL,downstream_gene_variant,,ENST00000374483,;LYPLA2,downstream_gene_variant,,ENST00000374501,;HMGCL,downstream_gene_variant,,ENST00000436439,;GALE,upstream_gene_variant,,ENST00000456977,;LYPLA2,downstream_gene_variant,,ENST00000374514,;LYPLA2,downstream_gene_variant,,ENST00000374502,;LYPLA2,downstream_gene_variant,,ENST00000374505,;GALE,non_coding_transcript_exon_variant,,ENST00000467493,;GALE,non_coding_transcript_exon_variant,,ENST00000486382,;GALE,non_coding_transcript_exon_variant,,ENST00000470949,;GALE,non_coding_transcript_exon_variant,,ENST00000459934,;GALE,non_coding_transcript_exon_variant,,ENST00000481736,;GALE,non_coding_transcript_exon_variant,,ENST00000470383,;GALE,non_coding_transcript_exon_variant,,ENST00000466250,;LYPLA2,downstream_gene_variant,,ENST00000472213,;LYPLA2,downstream_gene_variant,,ENST00000495365,;GALE,upstream_gene_variant,,ENST00000469556,;LYPLA2,downstream_gene_variant,,ENST00000492577,;GALE,downstream_gene_variant,,ENST00000467070,;HMGCL,downstream_gene_variant,,ENST00000509389,;HMGCL,downstream_gene_variant,,ENST00000374487,;	G	ENSG00000117308	ENST00000374497	Transcript	missense_variant	279	187	63	E/Q	Gag/Cag	rs370693766	.	.	-1	GALE	HGNC	4116	protein_coding	YES	CCDS242.1	ENSP00000363621	GALE_HUMAN	Q5QPP3_HUMAN,Q5QPP2_HUMAN,Q5QPP1_HUMAN,Q38G75_HUMAN	UPI000011133A	.	tolerated(0.13)	benign(0.003)	4/12	.	Superfamily_domains:SSF51735,Gene3D:3.40.50.720,TIGRFAM_domain:TIGR01179,Pfam_domain:PF01370,hmmpanther:PTHR10366:SF39,hmmpanther:PTHR10366	.	.	.	.	.	.	.	G:0	G:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAAACT	byFrequency|byCluster	5	ESCA
SCCPDH	0	.	GRCh37	1	246887741	246887741	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17G>A	p.Arg6Lys	p.R6K	ENST00000366510	1/12	34	29	4	14	14	0	SCCPDH,missense_variant,p.Arg6Lys,ENST00000366510,;	A	ENSG00000143653	ENST00000366510	Transcript	missense_variant	393	17	6	R/K	aGg/aAg	.	.	.	1	SCCPDH	HGNC	24275	protein_coding	YES	CCDS31084.1	ENSP00000355467	SCPDL_HUMAN	.	UPI00000350AB	.	tolerated(0.1)	benign(0.098)	1/12	.	hmmpanther:PTHR12286,hmmpanther:PTHR12286:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGAGGCCTT	.	4	ESCA
OR2M7	0	.	GRCh37	1	248487172	248487174	+	Frame_Shift_Del	DEL	TCC	TCC	GT	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	TCC	TCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.697_699delGGAinsAC	p.Gly233ThrfsTer53	p.G233Tfs*53	ENST00000317965	1/1	209	157	52	84	84	0	OR2M7,frameshift_variant,p.Gly233ThrfsTer53,ENST00000317965,;	GT	ENSG00000177186	ENST00000317965	Transcript	frameshift_variant	726-728	697-699	233	G/X	GGA/AC	.	.	.	-1	OR2M7	HGNC	19594	protein_coding	YES	CCDS31111.1	ENSP00000324557	OR2M7_HUMAN	.	UPI000004B236	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF233,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCGACGTCCCTCTC	.	3	ESCA
CSMD2	0	.	GRCh37	1	34090131	34090131	+	Silent	SNP	G	G	A	rs189437127	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5493C>T	p.%3D	p.G1831G	ENST00000241312	35/70	34	13	21	31	31	0	CSMD2,synonymous_variant,p.%3D,ENST00000373381,;CSMD2,synonymous_variant,p.%3D,ENST00000373380,;CSMD2,5_prime_UTR_variant,,ENST00000373377,;CSMD2,5_prime_UTR_variant,,ENST00000373388,;CSMD2,synonymous_variant,p.%3D,ENST00000241312,;	A	ENSG00000121904	ENST00000241312	Transcript	synonymous_variant	5522	5493	1831	G	ggC/ggT	rs189437127	.	.	-1	CSMD2	HGNC	19290	nonsense_mediated_decay	YES	CCDS380.1	ENSP00000241312	CSMD2_HUMAN	.	UPI00004561AB	.	.	.	35/70	.	Superfamily_domains:SSF49854,SMART_domains:SM00042,Pfam_domain:PF00431,Gene3D:2.60.120.290,hmmpanther:PTHR19325:SF334,hmmpanther:PTHR19325,PROSITE_profiles:PS01180	A:0.0004	A:0	A:0	.	A:0	A:0.002	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGCCTTC	byFrequency|byCluster|by1000G	5	ESCA
ZMYM1	0	.	GRCh37	1	35580160	35580160	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2729A>C	p.Lys910Thr	p.K910T	ENST00000373330	11/11	50	40	10	25	25	0	ZMYM1,missense_variant,p.Lys910Thr,ENST00000373330,;ZMYM1,missense_variant,p.Lys910Thr,ENST00000359858,;ZMYM1,downstream_gene_variant,,ENST00000417119,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000373329,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000488455,;ZMYM1,downstream_gene_variant,,ENST00000475654,;ZMYM1,downstream_gene_variant,,ENST00000463393,;	C	ENSG00000197056	ENST00000373330	Transcript	missense_variant	2903	2729	910	K/T	aAa/aCa	.	.	.	1	ZMYM1	HGNC	26253	protein_coding	YES	CCDS41302.1	ENSP00000362427	ZMYM1_HUMAN	Q9H5R2_HUMAN,Q5SW02_HUMAN,Q5SVZ7_HUMAN	UPI0000203ED6	.	deleterious(0.03)	probably_damaging(0.962)	11/11	.	hmmpanther:PTHR11697:SF88,hmmpanther:PTHR11697,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTAAAACAA	.	5	ESCA
JUN	0	.	GRCh37	1	59248922	59248922	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-180G>T	.	.	ENST00000371222	1/1	20	16	4	13	13	0	JUN,5_prime_UTR_variant,,ENST00000371222,;LINC01135,upstream_gene_variant,,ENST00000544621,;LINC01135,upstream_gene_variant,,ENST00000419531,;	A	ENSG00000177606	ENST00000371222	Transcript	5_prime_UTR_variant	864	.	.	.	.	.	.	.	-1	JUN	HGNC	6204	protein_coding	YES	CCDS610.1	ENSP00000360266	JUN_HUMAN	.	UPI000000D908	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCGCTCC	.	5	ESCA
DNAJC11	0	.	GRCh37	1	6694732	6694732	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1003G>A	.	.	ENST00000377577	16/16	38	25	12	28	28	0	DNAJC11,missense_variant,p.Glu271Lys,ENST00000349363,;DNAJC11,missense_variant,p.Glu285Lys,ENST00000451196,;DNAJC11,3_prime_UTR_variant,,ENST00000377577,;THAP3,3_prime_UTR_variant,,ENST00000377627,;DNAJC11,downstream_gene_variant,,ENST00000377573,;THAP3,downstream_gene_variant,,ENST00000307896,;THAP3,downstream_gene_variant,,ENST00000054650,;DNAJC11,downstream_gene_variant,,ENST00000294401,;THAP3,downstream_gene_variant,,ENST00000472925,;DNAJC11,downstream_gene_variant,,ENST00000542246,;DNAJC11,non_coding_transcript_exon_variant,,ENST00000465508,;DNAJC11,downstream_gene_variant,,ENST00000472414,;THAP3,downstream_gene_variant,,ENST00000484669,;THAP3,downstream_gene_variant,,ENST00000480647,;THAP3,downstream_gene_variant,,ENST00000487819,;	T	ENSG00000007923	ENST00000377577	Transcript	3_prime_UTR_variant	2807	.	.	.	.	.	.	.	-1	DNAJC11	HGNC	25570	protein_coding	YES	CCDS87.1	ENSP00000366800	DJC11_HUMAN	F5H1N1_HUMAN,B3KTC6_HUMAN	UPI000020544B	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTCTGCAT	.	5	ESCA
PIGK	0	.	GRCh37	1	77620211	77620211	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.909C>A	p.Phe303Leu	p.F303L	ENST00000370812	9/11	75	58	17	47	47	0	PIGK,missense_variant,p.Phe209Leu,ENST00000445065,;PIGK,missense_variant,p.Phe227Leu,ENST00000370813,;PIGK,missense_variant,p.Phe303Leu,ENST00000370812,;PIGK,missense_variant,p.Phe303Leu,ENST00000359130,;PIGK,non_coding_transcript_exon_variant,,ENST00000478391,;PIGK,3_prime_UTR_variant,,ENST00000487906,;	T	ENSG00000142892	ENST00000370812	Transcript	missense_variant	933	909	303	F/L	ttC/ttA	COSM3492452	.	.	-1	PIGK	HGNC	8965	protein_coding	YES	CCDS674.1	ENSP00000359848	GPI8_HUMAN	.	UPI000012B9D1	.	deleterious(0)	probably_damaging(0.973)	9/11	.	hmmpanther:PTHR12000:SF1,hmmpanther:PTHR12000,PIRSF_domain:PIRSF019663,PIRSF_domain:PIRSF500138	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAAGAAATC	.	5	ESCA
AK5	0	.	GRCh37	1	77949036	77949036	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1094C>G	p.Thr365Ser	p.T365S	ENST00000354567	9/14	94	66	27	55	55	0	AK5,missense_variant,p.Thr339Ser,ENST00000344720,;AK5,missense_variant,p.Thr365Ser,ENST00000354567,;AK5,non_coding_transcript_exon_variant,,ENST00000530826,;AK5,missense_variant,p.Thr20Ser,ENST00000527263,;	G	ENSG00000154027	ENST00000354567	Transcript	missense_variant	1357	1094	365	T/S	aCt/aGt	.	.	.	1	AK5	HGNC	365	protein_coding	YES	CCDS675.1	ENSP00000346577	KAD5_HUMAN	E9PQQ8_HUMAN,E9PIS7_HUMAN	UPI0000167E20	.	tolerated(0.68)	benign(0.002)	9/14	.	hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF79	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACACTATGG	.	5	ESCA
ZZZ3	0	.	GRCh37	1	78030640	78030640	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*685G>T	.	.	ENST00000370801	15/15	33	25	8	29	29	0	ZZZ3,3_prime_UTR_variant,,ENST00000370801,;ZZZ3,3_prime_UTR_variant,,ENST00000370798,;AK5,downstream_gene_variant,,ENST00000344720,;AK5,downstream_gene_variant,,ENST00000354567,;ZZZ3,non_coding_transcript_exon_variant,,ENST00000476275,;ZZZ3,non_coding_transcript_exon_variant,,ENST00000481346,;	A	ENSG00000036549	ENST00000370801	Transcript	3_prime_UTR_variant	3873	.	.	.	.	.	.	.	-1	ZZZ3	HGNC	24523	protein_coding	YES	CCDS677.1	ENSP00000359837	ZZZ3_HUMAN	C9JUA4_HUMAN,C9J283_HUMAN	UPI0000074256	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTACATTTA	.	5	ESCA
MAP1LC3A	0	.	GRCh37	20	33147159	33147159	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117C>T	p.%3D	p.I39I	ENST00000374837	4/5	21	9	11	8	8	0	MAP1LC3A,synonymous_variant,p.%3D,ENST00000397709,;MAP1LC3A,synonymous_variant,p.%3D,ENST00000374837,;MAP1LC3A,synonymous_variant,p.%3D,ENST00000360668,;PIGU,downstream_gene_variant,,ENST00000452740,;PIGU,downstream_gene_variant,,ENST00000217446,;PIGU,downstream_gene_variant,,ENST00000374820,;PIGU,downstream_gene_variant,,ENST00000438215,;MAP1LC3A,non_coding_transcript_exon_variant,,ENST00000476428,;	T	ENSG00000101460	ENST00000374837	Transcript	synonymous_variant	253	117	39	I	atC/atT	.	.	.	1	MAP1LC3A	HGNC	6838	protein_coding	YES	CCDS13237.1	ENSP00000363970	MLP3A_HUMAN	.	UPI000012F42A	.	.	.	4/5	.	Superfamily_domains:SSF54236,Pfam_domain:PF02991,Gene3D:3.10.20.90,hmmpanther:PTHR10969:SF14,hmmpanther:PTHR10969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATCATCGAGCG	.	3	ESCA
C20orf27	0	.	GRCh37	20	3734755	3734755	+	Missense_Mutation	SNP	C	C	A	rs747293739	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550G>T	p.Ala184Ser	p.A184S	ENST00000217195	6/6	9	3	6	15	15	0	C20orf27,missense_variant,p.Ala159Ser,ENST00000379772,;C20orf27,missense_variant,p.Ala159Ser,ENST00000399672,;C20orf27,missense_variant,p.Ala112Ser,ENST00000399683,;C20orf27,missense_variant,p.Ala184Ser,ENST00000217195,;HSPA12B,downstream_gene_variant,,ENST00000542646,;HSPA12B,downstream_gene_variant,,ENST00000254963,;HSPA12B,downstream_gene_variant,,ENST00000399701,;	A	ENSG00000101220	ENST00000217195	Transcript	missense_variant	702	550	184	A/S	Gcc/Tcc	rs747293739	.	.	-1	C20orf27	HGNC	15873	protein_coding	YES	CCDS33436.1	ENSP00000217195	CT027_HUMAN	.	UPI0000470A46	.	tolerated(0.08)	benign(0.355)	6/6	.	hmmpanther:PTHR13287,Pfam_domain:PF15006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGGCGCCCA	byFrequency	2	ESCA
PTPRT	0	.	GRCh37	20	40706749	40706749	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2770A>C	.	.	ENST00000373187	31/31	38	31	7	32	32	0	PTPRT,3_prime_UTR_variant,,ENST00000373201,;PTPRT,3_prime_UTR_variant,,ENST00000356100,;PTPRT,3_prime_UTR_variant,,ENST00000373198,;PTPRT,3_prime_UTR_variant,,ENST00000373193,;PTPRT,3_prime_UTR_variant,,ENST00000373184,;PTPRT,3_prime_UTR_variant,,ENST00000373190,;PTPRT,3_prime_UTR_variant,,ENST00000373187,;	G	ENSG00000196090	ENST00000373187	Transcript	3_prime_UTR_variant	7096	.	.	.	.	.	.	.	-1	PTPRT	HGNC	9682	protein_coding	YES	CCDS42874.1	ENSP00000362283	PTPRT_HUMAN	.	UPI0000246C03	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCCAGTGGGGG	.	4	ESCA
PTPRT	0	.	GRCh37	20	40706961	40706961	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2558C>T	.	.	ENST00000373187	31/31	50	21	28	56	56	0	PTPRT,3_prime_UTR_variant,,ENST00000373201,;PTPRT,3_prime_UTR_variant,,ENST00000356100,;PTPRT,3_prime_UTR_variant,,ENST00000373198,;PTPRT,3_prime_UTR_variant,,ENST00000373193,;PTPRT,3_prime_UTR_variant,,ENST00000373184,;PTPRT,3_prime_UTR_variant,,ENST00000373190,;PTPRT,3_prime_UTR_variant,,ENST00000373187,;	A	ENSG00000196090	ENST00000373187	Transcript	3_prime_UTR_variant	6884	.	.	.	.	.	.	.	-1	PTPRT	HGNC	9682	protein_coding	YES	CCDS42874.1	ENSP00000362283	PTPRT_HUMAN	.	UPI0000246C03	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCGGCTCCT	.	5	ESCA
ZSWIM1	0	.	GRCh37	20	44511684	44511684	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453C>A	p.Phe151Leu	p.F151L	ENST00000372523	2/2	40	28	11	27	27	0	ZSWIM1,missense_variant,p.Phe151Leu,ENST00000372520,;ZSWIM1,missense_variant,p.Phe151Leu,ENST00000372523,;ZSWIM3,downstream_gene_variant,,ENST00000454862,;SPATA25,downstream_gene_variant,,ENST00000372519,;ZSWIM3,downstream_gene_variant,,ENST00000255152,;	A	ENSG00000168612	ENST00000372523	Transcript	missense_variant	548	453	151	F/L	ttC/ttA	.	.	.	1	ZSWIM1	HGNC	16155	protein_coding	YES	CCDS13382.2	ENSP00000361601	ZSWM1_HUMAN	A8K5I9_HUMAN	UPI0000470896	.	tolerated(0.07)	benign(0.111)	2/2	.	hmmpanther:PTHR31569,hmmpanther:PTHR31569:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTCCTTCC	.	5	ESCA
PPP4R1L	0	.	GRCh37	20	56814841	56814841	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*526C>G	.	.	ENST00000493688	12/14	21	16	5	28	28	0	PPP4R1L,missense_variant,p.Gln33Glu,ENST00000457990,;PPP4R1L,3_prime_UTR_variant,,ENST00000334187,;PPP4R1L,non_coding_transcript_exon_variant,,ENST00000473210,;PPP4R1L,downstream_gene_variant,,ENST00000475130,;PPP4R1L,missense_variant,p.Gln125Glu,ENST00000497138,;PPP4R1L,3_prime_UTR_variant,,ENST00000493688,;PPP4R1L,non_coding_transcript_exon_variant,,ENST00000606437,;PPP4R1L,downstream_gene_variant,,ENST00000495058,;PPP4R1L,upstream_gene_variant,,ENST00000467784,;	C	ENSG00000124224	ENST00000493688	Transcript	3_prime_UTR_variant	1645	.	.	.	.	.	.	.	-1	PPP4R1L	HGNC	15755	nonsense_mediated_decay	YES	.	ENSP00000435897	.	Q96LY6_HUMAN	UPI0000072504	.	.	.	12/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTGGGCTC	.	5	ESCA
RAB22A	0	.	GRCh37	20	56936244	56936244	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1485G>A	.	.	ENST00000244040	7/7	65	51	14	37	37	0	RAB22A,3_prime_UTR_variant,,ENST00000244040,;	A	ENSG00000124209	ENST00000244040	Transcript	3_prime_UTR_variant	2351	.	.	.	.	.	.	.	1	RAB22A	HGNC	9764	protein_coding	YES	CCDS33497.1	ENSP00000244040	RB22A_HUMAN	Q96IY7_HUMAN	UPI0000132F68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGGGAAGGA	.	5	ESCA
AGPAT3	0	.	GRCh37	21	45406328	45406328	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4055C>T	.	.	ENST00000398063	9/9	67	60	6	33	33	0	AGPAT3,3_prime_UTR_variant,,ENST00000398063,;AGPAT3,3_prime_UTR_variant,,ENST00000291572,;AGPAT3,downstream_gene_variant,,ENST00000398061,;AGPAT3,downstream_gene_variant,,ENST00000546158,;AGPAT3,downstream_gene_variant,,ENST00000327505,;AGPAT3,downstream_gene_variant,,ENST00000398058,;AGPAT3,downstream_gene_variant,,ENST00000479117,;AGPAT3,downstream_gene_variant,,ENST00000467358,;	T	ENSG00000160216	ENST00000398063	Transcript	3_prime_UTR_variant	5678	.	.	.	.	.	.	.	1	AGPAT3	HGNC	326	protein_coding	YES	CCDS13703.1	ENSP00000381140	PLCC_HUMAN	C9JQX8_HUMAN,C9JL26_HUMAN,C9JK35_HUMAN,C9J184_HUMAN	UPI000004616E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGCACAAGTA	.	4	ESCA
PCBP3	0	.	GRCh37	21	47316257	47316257	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146G>A	p.Arg49His	p.R49H	ENST00000400314	4/16	108	52	55	58	58	0	PCBP3,missense_variant,p.Arg49His,ENST00000400310,;PCBP3,missense_variant,p.Arg49His,ENST00000400314,;PCBP3,missense_variant,p.Arg25His,ENST00000400305,;PCBP3,missense_variant,p.Arg49His,ENST00000449640,;PCBP3,missense_variant,p.Arg49His,ENST00000400309,;PCBP3,missense_variant,p.Arg17His,ENST00000400304,;PCBP3,missense_variant,p.Arg49His,ENST00000400308,;PCBP3,downstream_gene_variant,,ENST00000549265,;PCBP3,upstream_gene_variant,,ENST00000468429,;PCBP3,non_coding_transcript_exon_variant,,ENST00000498121,;	A	ENSG00000183570	ENST00000400314	Transcript	missense_variant	484	146	49	R/H	cGc/cAc	.	.	.	1	PCBP3	HGNC	8651	protein_coding	YES	CCDS42974.2	ENSP00000383168	PCBP3_HUMAN	.	UPI00005989D5	.	deleterious(0)	possibly_damaging(0.894)	4/16	.	Superfamily_domains:SSF54791,SMART_domains:SM00322,Gene3D:3.30.1370.10,Pfam_domain:PF00013,hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF98,PROSITE_profiles:PS50084	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCGCCTGC	.	5	ESCA
SPATC1L	0	.	GRCh37	21	47588410	47588410	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.356G>C	p.Ser119Thr	p.S119T	ENST00000291672	3/5	40	34	6	31	31	0	SPATC1L,missense_variant,p.Ser119Thr,ENST00000291672,;SPATC1L,5_prime_UTR_variant,,ENST00000330205,;	G	ENSG00000160284	ENST00000291672	Transcript	missense_variant	1418	356	119	S/T	aGt/aCt	.	.	.	-1	SPATC1L	HGNC	1298	protein_coding	YES	CCDS46653.1	ENSP00000291672	SPC1L_HUMAN	.	UPI000013E06B	.	tolerated(0.33)	benign(0.009)	3/5	.	hmmpanther:PTHR22192:SF1,hmmpanther:PTHR22192,Pfam_domain:PF15058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGACTGAGG	.	4	ESCA
PI4KA	0	.	GRCh37	22	21064264	21064264	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6105C>G	p.%3D	p.V2035V	ENST00000255882	53/55	47	33	14	46	46	0	PI4KA,synonymous_variant,p.%3D,ENST00000414196,;PI4KA,synonymous_variant,p.%3D,ENST00000572273,;PI4KA,synonymous_variant,p.%3D,ENST00000255882,;PI4KA,synonymous_variant,p.%3D,ENST00000399213,;PI4KA,non_coding_transcript_exon_variant,,ENST00000492581,;PI4KA,non_coding_transcript_exon_variant,,ENST00000477245,;PI4KA,non_coding_transcript_exon_variant,,ENST00000466772,;PI4KA,downstream_gene_variant,,ENST00000482030,;PI4KA,downstream_gene_variant,,ENST00000466394,;	C	ENSG00000241973	ENST00000255882	Transcript	synonymous_variant	6192	6105	2035	V	gtC/gtG	.	.	.	-1	PI4KA	HGNC	8983	protein_coding	YES	CCDS33603.2	ENSP00000255882	.	Q4LE69_HUMAN,J3KN10_HUMAN,C9JLI1_HUMAN	UPI0000E06BD6	.	.	.	53/55	.	Superfamily_domains:SSF56112,SMART_domains:SM00146,Pfam_domain:PF00454,Gene3D:1.10.1070.11,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF15,PROSITE_profiles:PS50290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGAGACGAC	.	5	ESCA
HIC2	0	.	GRCh37	22	21802971	21802971	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1939G>T	.	.	ENST00000443632	2/2	24	6	18	22	22	0	HIC2,3_prime_UTR_variant,,ENST00000443632,;HIC2,3_prime_UTR_variant,,ENST00000407598,;HIC2,3_prime_UTR_variant,,ENST00000407464,;	T	ENSG00000169635	ENST00000443632	Transcript	3_prime_UTR_variant	4159	.	.	.	.	.	.	.	1	HIC2	HGNC	18595	protein_coding	YES	CCDS13789.1	ENSP00000387757	HIC2_HUMAN	.	UPI000012C71C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGGGGGTGAGG	.	3	ESCA
TTC28	0	.	GRCh37	22	28503690	28503690	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2143C>T	p.Arg715Ter	p.R715*	ENST00000397906	7/23	28	18	10	48	48	0	TTC28,stop_gained,p.Arg715Ter,ENST00000397906,;	A	ENSG00000100154	ENST00000397906	Transcript	stop_gained	2285	2143	715	R/*	Cga/Tga	.	.	.	-1	TTC28	HGNC	29179	protein_coding	YES	CCDS46678.1	ENSP00000381003	TTC28_HUMAN	.	UPI00003E58F8	.	.	.	7/23	.	Superfamily_domains:SSF48452,SMART_domains:SM00028,Gene3D:1.25.40.10,hmmpanther:PTHR10098,hmmpanther:PTHR10098:SF106,PROSITE_profiles:PS50293,PROSITE_profiles:PS50005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCGAAATT	.	5	ESCA
SEC14L2	0	.	GRCh37	22	30812056	30812056	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.891C>T	p.%3D	p.L297L	ENST00000312932	10/12	41	11	30	33	33	0	SEC14L2,synonymous_variant,p.%3D,ENST00000405717,;SEC14L2,synonymous_variant,p.%3D,ENST00000312932,;SEC14L2,synonymous_variant,p.%3D,ENST00000402592,;RP4-539M6.19,synonymous_variant,p.%3D,ENST00000439838,;SEC14L2,synonymous_variant,p.%3D,ENST00000403484,;RP4-539M6.19,intron_variant,,ENST00000439023,;RNF215,intron_variant,,ENST00000431544,;KIAA1658,downstream_gene_variant,,ENST00000598426,;SEC14L2,downstream_gene_variant,,ENST00000428195,;RNU6-564P,upstream_gene_variant,,ENST00000410983,;RP4-539M6.20,upstream_gene_variant,,ENST00000608677,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000467218,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000478762,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000464335,;RP4-539M6.19,intron_variant,,ENST00000454552,;SEC14L2,downstream_gene_variant,,ENST00000483116,;	T	ENSG00000100003	ENST00000312932	Transcript	synonymous_variant	1151	891	297	L	ctC/ctT	.	.	.	1	SEC14L2	HGNC	10699	protein_coding	YES	CCDS13876.1	ENSP00000316203	S14L2_HUMAN	C9JZI9_HUMAN,B7Z3Z8_HUMAN	UPI0000135433	.	.	.	10/12	.	PROSITE_profiles:PS50866,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF64,Gene3D:3.40.525.10,Superfamily_domains:0041713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCTTCCC	.	5	ESCA
MICALL1	0	.	GRCh37	22	38333778	38333778	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2449G>T	p.Glu817Ter	p.E817*	ENST00000215957	15/16	24	19	5	25	25	0	MICALL1,stop_gained,p.Glu817Ter,ENST00000215957,;MICALL1,stop_gained,p.Glu131Ter,ENST00000424008,;MICALL1,downstream_gene_variant,,ENST00000454685,;MICALL1,non_coding_transcript_exon_variant,,ENST00000402631,;	T	ENSG00000100139	ENST00000215957	Transcript	stop_gained	2575	2449	817	E/*	Gaa/Taa	COSM32273	.	.	1	MICALL1	HGNC	29804	protein_coding	YES	CCDS13961.1	ENSP00000215957	MILK1_HUMAN	Q68D58_HUMAN,Q641Q8_HUMAN,B0QY86_HUMAN	UPI000000DCAE	.	.	.	15/16	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF33,Pfam_domain:PF12130	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGTTGGAAGCC	.	3	ESCA
C22orf34	0	.	GRCh37	22	50014114	50014114	+	3'UTR	SNP	C	C	A	rs779512376	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*12G>T	.	.	ENST00000400023	4/4	76	57	18	54	54	0	C22orf34,3_prime_UTR_variant,,ENST00000400023,;C22orf34,downstream_gene_variant,,ENST00000405854,;C22orf34,downstream_gene_variant,,ENST00000444628,;RP1-29C18.8,upstream_gene_variant,,ENST00000420902,;C22orf34,3_prime_UTR_variant,,ENST00000343999,;C22orf34,intron_variant,,ENST00000416411,;C22orf34,intron_variant,,ENST00000414287,;	A	ENSG00000188511	ENST00000400023	Transcript	3_prime_UTR_variant	647	.	.	.	.	rs779512376	.	.	-1	C22orf34	HGNC	28010	protein_coding	YES	.	ENSP00000382900	CV034_HUMAN	.	UPI00001984F9	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCTCCCATG	.	5	ESCA
DPP10	0	.	GRCh37	2	116525872	116525872	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1126-1G>T	.	p.X376_splice	ENST00000393147	.	34	25	9	27	27	0	DPP10,splice_acceptor_variant,,ENST00000393147,;DPP10,splice_acceptor_variant,,ENST00000409163,;DPP10,splice_acceptor_variant,,ENST00000310323,;DPP10,splice_acceptor_variant,,ENST00000410059,;	T	ENSG00000175497	ENST00000393147	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	DPP10	HGNC	20823	protein_coding	YES	CCDS54388.1	ENSP00000376855	DPP10_HUMAN	J3KQK8_HUMAN,C9J4M8_HUMAN	UPI00015E0A22	.	.	.	.	12/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTAGAATGA	.	5	ESCA
TUBA3D	0	.	GRCh37	2	132237994	132237994	+	Missense_Mutation	SNP	G	G	T	rs752428849	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.728G>T	p.Arg243Leu	p.R243L	ENST00000321253	4/5	40	33	7	58	58	0	TUBA3D,missense_variant,p.Arg243Leu,ENST00000321253,;MZT2A,downstream_gene_variant,,ENST00000309451,;MZT2A,downstream_gene_variant,,ENST00000410036,;TUBA3D,downstream_gene_variant,,ENST00000409047,;MZT2A,intron_variant,,ENST00000445782,;MZT2A,intron_variant,,ENST00000427024,;	T	ENSG00000075886	ENST00000321253	Transcript	missense_variant	835	728	243	R/L	cGa/cTa	rs752428849,COSM264494	.	.	1	TUBA3D	HGNC	24071	protein_coding	YES	CCDS33290.1	ENSP00000326042	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	deleterious_low_confidence(0)	possibly_damaging(0.705)	4/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T239T|c.717A>G|3	RADIA|MUTECT|VARSCANS	CCTGCGATTTG	byFrequency	3	ESCA
TNFAIP6	0	.	GRCh37	2	152226759	152226759	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.620G>T	p.Gly207Val	p.G207V	ENST00000243347	4/6	34	25	8	30	30	0	TNFAIP6,missense_variant,p.Gly207Val,ENST00000243347,;MIR4773-2,downstream_gene_variant,,ENST00000585225,;RN7SL124P,upstream_gene_variant,,ENST00000498656,;TNFAIP6,non_coding_transcript_exon_variant,,ENST00000460812,;	T	ENSG00000123610	ENST00000243347	Transcript	missense_variant	695	620	207	G/V	gGa/gTa	.	.	.	1	TNFAIP6	HGNC	11898	protein_coding	YES	CCDS2193.1	ENSP00000243347	TSG6_HUMAN	.	UPI0000071080	.	deleterious(0)	probably_damaging(0.991)	4/6	.	PROSITE_profiles:PS01180,hmmpanther:PTHR24038,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGGGAAGGT	.	5	ESCA
HSPE1-MOB4	0	.	GRCh37	2	198400257	198400257	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235A>G	p.Ile79Val	p.I79V	ENST00000604458	4/9	50	39	11	23	23	0	HSPE1-MOB4,missense_variant,p.Ile79Val,ENST00000604458,;MOB4,missense_variant,p.Ile11Val,ENST00000233892,;MOB4,missense_variant,p.Ile11Val,ENST00000409360,;MOB4,missense_variant,p.Ile22Val,ENST00000448447,;MOB4,missense_variant,p.Ile43Val,ENST00000323303,;MOB4,5_prime_UTR_variant,,ENST00000409916,;MOB4,intron_variant,,ENST00000497443,;MOB4,missense_variant,p.Ile22Val,ENST00000409355,;MOB4,intron_variant,,ENST00000417097,;AC020550.7,downstream_gene_variant,,ENST00000447385,;	G	ENSG00000270757	ENST00000604458	Transcript	missense_variant	259	235	79	I/V	Att/Gtt	.	.	.	1	HSPE1-MOB4	HGNC	49184	protein_coding	YES	CCDS63079.1	ENSP00000474534	.	S4R3N1_HUMAN,B4DM50_HUMAN	UPI0001F76FA6	.	deleterious(0)	probably_damaging(0.964)	4/9	.	hmmpanther:PTHR22599,hmmpanther:PTHR22599:SF1,Pfam_domain:PF03637,Superfamily_domains:0049093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTATATTCAA	.	5	ESCA
FZD7	0	.	GRCh37	2	202900687	202900688	+	In_Frame_Ins	INS	-	-	TTGCTG	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1318_1323dupTTGCTG	p.Leu440_Leu441dup	p.L440_L441dup	ENST00000286201	1/1	74	12	62	61	61	0	FZD7,inframe_insertion,p.Leu440_Leu441dup,ENST00000286201,;RP11-107N15.1,upstream_gene_variant,,ENST00000608741,;	TTGCTG	ENSG00000155760	ENST00000286201	Transcript	inframe_insertion	1378-1379	1317-1318	439-440	-/LL	-/TTGCTG	.	.	.	1	FZD7	HGNC	4045	protein_coding	YES	CCDS2351.1	ENSP00000286201	FZD7_HUMAN	.	UPI0000051051	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF31,Pfam_domain:PF01534,Prints_domain:PR00489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCTTCTTGCT	.	3	ESCA
ASIC4	0	.	GRCh37	2	220396750	220396750	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1136G>C	p.Arg379Pro	p.R379P	ENST00000347842	3/9	23	5	18	17	17	0	ASIC4,missense_variant,p.Arg379Pro,ENST00000358078,;ASIC4,missense_variant,p.Arg379Pro,ENST00000347842,;ASIC4,non_coding_transcript_exon_variant,,ENST00000473709,;ASIC4,non_coding_transcript_exon_variant,,ENST00000461395,;ASIC4,non_coding_transcript_exon_variant,,ENST00000474489,;	C	ENSG00000072182	ENST00000347842	Transcript	missense_variant	1150	1136	379	R/P	cGg/cCg	.	.	.	1	ASIC4	HGNC	21263	protein_coding	YES	CCDS2442.1	ENSP00000326627	ASIC4_HUMAN	.	UPI0000456EFC	.	deleterious(0)	probably_damaging(0.94)	3/9	.	hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF13,Gene3D:2qtsA02,Pfam_domain:PF00858	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTCGGGTGC	.	5	ESCA
IFT172	0	.	GRCh37	2	27668210	27668210	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5021T>C	p.Leu1674Pro	p.L1674P	ENST00000260570	46/48	32	28	4	32	32	0	IFT172,missense_variant,p.Leu1674Pro,ENST00000260570,;KRTCAP3,intron_variant,,ENST00000543753,;KRTCAP3,intron_variant,,ENST00000452499,;NRBP1,downstream_gene_variant,,ENST00000233557,;KRTCAP3,downstream_gene_variant,,ENST00000407293,;KRTCAP3,downstream_gene_variant,,ENST00000288873,;NRBP1,downstream_gene_variant,,ENST00000379863,;NRBP1,downstream_gene_variant,,ENST00000379852,;IFT172,3_prime_UTR_variant,,ENST00000509128,;IFT172,non_coding_transcript_exon_variant,,ENST00000494163,;IFT172,non_coding_transcript_exon_variant,,ENST00000507184,;IFT172,non_coding_transcript_exon_variant,,ENST00000479419,;IFT172,downstream_gene_variant,,ENST00000450564,;IFT172,downstream_gene_variant,,ENST00000420854,;NRBP1,downstream_gene_variant,,ENST00000460499,;NRBP1,downstream_gene_variant,,ENST00000486701,;KRTCAP3,downstream_gene_variant,,ENST00000453171,;KRTCAP3,downstream_gene_variant,,ENST00000464699,;IFT172,downstream_gene_variant,,ENST00000480892,;KRTCAP3,downstream_gene_variant,,ENST00000494572,;	G	ENSG00000138002	ENST00000260570	Transcript	missense_variant	5125	5021	1674	L/P	cTa/cCa	.	.	.	-1	IFT172	HGNC	30391	protein_coding	YES	CCDS1755.1	ENSP00000260570	IF172_HUMAN	H7C161_HUMAN	UPI0000353ABB	.	deleterious(0)	probably_damaging(0.999)	46/48	.	hmmpanther:PTHR15722,hmmpanther:PTHR15722:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCACTAGGGAG	.	3	ESCA
ALK	0	.	GRCh37	2	29917827	29917827	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841C>A	p.His281Asn	p.H281N	ENST00000389048	3/29	27	17	10	18	18	0	ALK,missense_variant,p.His281Asn,ENST00000389048,;ALK,intron_variant,,ENST00000431873,;	T	ENSG00000171094	ENST00000389048	Transcript	missense_variant	1748	841	281	H/N	Cat/Aat	.	.	.	-1	ALK	HGNC	427	protein_coding	YES	CCDS33172.1	ENSP00000373700	ALK_HUMAN	Q580I3_HUMAN	UPI00001684DA	.	deleterious(0.05)	benign(0.315)	3/29	.	PROSITE_profiles:PS50060,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATGCAGTG	.	5	ESCA
SLC8A1	0	.	GRCh37	2	40340927	40340927	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000403092	.	31	13	18	20	20	0	SLC8A1,3_prime_UTR_variant,,ENST00000542756,;SLC8A1,3_prime_UTR_variant,,ENST00000406785,;SLC8A1,downstream_gene_variant,,ENST00000408028,;SLC8A1,downstream_gene_variant,,ENST00000403092,;SLC8A1,downstream_gene_variant,,ENST00000405269,;SLC8A1,downstream_gene_variant,,ENST00000402441,;SLC8A1,downstream_gene_variant,,ENST00000542024,;SLC8A1,downstream_gene_variant,,ENST00000332839,;SLC8A1,downstream_gene_variant,,ENST00000406391,;SLC8A1,downstream_gene_variant,,ENST00000405901,;SLC8A1-AS1,intron_variant,,ENST00000599268,;SLC8A1-AS1,intron_variant,,ENST00000601679,;SLC8A1-AS1,intron_variant,,ENST00000599956,;SLC8A1-AS1,intron_variant,,ENST00000596532,;SLC8A1-AS1,intron_variant,,ENST00000597385,;SLC8A1-AS1,intron_variant,,ENST00000599740,;SLC8A1-AS1,intron_variant,,ENST00000597170,;SLC8A1-AS1,intron_variant,,ENST00000444629,;SLC8A1-AS1,intron_variant,,ENST00000593878,;SLC8A1-AS1,upstream_gene_variant,,ENST00000435515,;SLC8A1-AS1,upstream_gene_variant,,ENST00000598247,;SLC8A1-AS1,upstream_gene_variant,,ENST00000593848,;SLC8A1,downstream_gene_variant,,ENST00000407929,;	T	ENSG00000183023	ENST00000403092	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1244	-1	SLC8A1	HGNC	11068	protein_coding	YES	CCDS1806.1	ENSP00000384763	NAC1_HUMAN	Q6LAJ9_HUMAN,Q6LAJ8_HUMAN,Q4QQH3_HUMAN,E9PCL8_HUMAN,E9PB98_HUMAN	UPI000012FC46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACGTCTCTAT	.	5	ESCA
NRXN1	0	.	GRCh37	2	50573871	50573871	+	Intron	SNP	T	T	C	rs763472357	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3485-109763A>G	.	.	ENST00000404971	.	19	15	4	8	8	0	NRXN1,missense_variant,p.Ile73Val,ENST00000342183,;NRXN1,intron_variant,,ENST00000405472,;NRXN1,intron_variant,,ENST00000401710,;NRXN1,intron_variant,,ENST00000404971,;NRXN1,intron_variant,,ENST00000406316,;NRXN1,intron_variant,,ENST00000401669,;NRXN1,intron_variant,,ENST00000406859,;NRXN1,intron_variant,,ENST00000402717,;NRXN1,intron_variant,,ENST00000331040,;	C	ENSG00000179915	ENST00000404971	Transcript	intron_variant	.	.	.	.	.	rs763472357	.	.	-1	NRXN1	HGNC	8008	protein_coding	YES	CCDS46282.1	ENSP00000385142	NRX1A_HUMAN	Q08AH0_HUMAN	UPI00015A218A	.	.	.	.	18/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCAATAGGCA	.	3	ESCA
BCL11A	0	.	GRCh37	2	60684822	60684822	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2717G>A	.	.	ENST00000335712	4/4	17	12	5	8	8	0	BCL11A,3_prime_UTR_variant,,ENST00000335712,;BCL11A,intron_variant,,ENST00000538214,;BCL11A,intron_variant,,ENST00000359629,;BCL11A,intron_variant,,ENST00000356842,;BCL11A,intron_variant,,ENST00000537768,;BCL11A,downstream_gene_variant,,ENST00000358510,;BCL11A,intron_variant,,ENST00000479026,;BCL11A,intron_variant,,ENST00000489516,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,downstream_gene_variant,,ENST00000477659,;	T	ENSG00000119866	ENST00000335712	Transcript	3_prime_UTR_variant	5453	.	.	.	.	.	.	.	-1	BCL11A	HGNC	13221	protein_coding	YES	CCDS1862.1	ENSP00000338774	BC11A_HUMAN	D6W5D9_HUMAN,Q53TS1_HUMAN,Q53TE8_HUMAN	UPI000013DC00	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTCCTTTTT	.	2	ESCA
USP34	0	.	GRCh37	2	61468742	61468742	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6730G>T	p.Glu2244Ter	p.E2244*	ENST00000398571	53/80	57	49	7	32	32	0	USP34,stop_gained,p.Glu4Ter,ENST00000411912,;USP34,stop_gained,p.Glu522Ter,ENST00000453734,;USP34,stop_gained,p.Glu2244Ter,ENST00000398571,;USP34,intron_variant,,ENST00000472706,;USP34,non_coding_transcript_exon_variant,,ENST00000463046,;	A	ENSG00000115464	ENST00000398571	Transcript	stop_gained	6807	6730	2244	E/*	Gaa/Taa	.	.	.	-1	USP34	HGNC	20066	protein_coding	YES	CCDS42686.1	ENSP00000381577	UBP34_HUMAN	.	UPI0000410E09	.	.	.	53/80	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF97,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	ATTTTCTTCCT	.	3	ESCA
VAX2	0	.	GRCh37	2	71160355	71160355	+	3'UTR	SNP	G	G	A	rs782361299	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*21G>A	.	.	ENST00000234392	3/3	36	33	3	14	14	0	VAX2,3_prime_UTR_variant,,ENST00000234392,;ATP6V1B1,upstream_gene_variant,,ENST00000234396,;ATP6V1B1,upstream_gene_variant,,ENST00000412314,;snoU13,upstream_gene_variant,,ENST00000459218,;ATP6V1B1,upstream_gene_variant,,ENST00000432367,;	A	ENSG00000116035	ENST00000234392	Transcript	3_prime_UTR_variant	926	.	.	.	.	rs782361299	.	.	1	VAX2	HGNC	12661	protein_coding	YES	CCDS1911.1	ENSP00000234392	VAX2_HUMAN	F1T0K5_HUMAN	UPI0000138215	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACACTGAGTCC	byFrequency	2	ESCA
IGKV1D-43	0	.	GRCh37	2	90249103	90249103	+	Missense_Mutation	SNP	C	C	A	rs368187966	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>A	p.Ala20Asp	p.A20D	ENST00000468879	2/2	125	102	22	89	89	0	IGKV1D-43,missense_variant,p.Ala20Asp,ENST00000468879,;	A	ENSG00000242580	ENST00000468879	Transcript	missense_variant	240	59	20	A/D	gCc/gAc	rs368187966	.	.	1	IGKV1D-43	HGNC	5758	IG_V_gene	YES	.	ENSP00000417961	.	.	UPI0000116191	.	deleterious(0)	benign(0.03)	2/2	.	Cleavage_site_(Signalp):SignalP-noTM,PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF122,hmmpanther:PTHR23267,Gene3D:2.60.40.10	.	.	.	.	.	.	.	T:0.0003	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGCCAGAT	byFrequency|byCluster	5	ESCA
TMEM45A	0	.	GRCh37	3	100295770	100295770	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736T>G	p.Leu246Val	p.L246V	ENST00000323523	6/6	43	30	13	24	24	0	TMEM45A,missense_variant,p.Leu262Val,ENST00000403410,;TMEM45A,missense_variant,p.Leu246Val,ENST00000323523,;TMEM45A,splice_region_variant,,ENST00000488904,;TMEM45A,splice_region_variant,,ENST00000489060,;	G	ENSG00000181458	ENST00000323523	Transcript	missense_variant	1049	736	246	L/V	Ttg/Gtg	.	.	.	1	TMEM45A	HGNC	25480	protein_coding	YES	CCDS2937.1	ENSP00000319009	TM45A_HUMAN	.	UPI0000039E49	.	tolerated(0.18)	possibly_damaging(0.871)	6/6	.	hmmpanther:PTHR16007:SF10,hmmpanther:PTHR16007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGGTTGGTT	.	5	ESCA
NFKBIZ	0	.	GRCh37	3	101575996	101575996	+	Missense_Mutation	SNP	T	T	G	rs1043339	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1904T>G	p.Leu635Arg	p.L635R	ENST00000326172	10/12	39	30	8	25	25	0	NFKBIZ,missense_variant,p.Leu513Arg,ENST00000326151,;NFKBIZ,missense_variant,p.Leu535Arg,ENST00000394054,;NFKBIZ,missense_variant,p.Leu635Arg,ENST00000326172,;NFKBIZ,missense_variant,p.Leu535Arg,ENST00000483180,;NFKBIZ,intron_variant,,ENST00000477601,;NFKBIZ,downstream_gene_variant,,ENST00000491281,;NFKBIZ,non_coding_transcript_exon_variant,,ENST00000495089,;NFKBIZ,upstream_gene_variant,,ENST00000495719,;NFKBIZ,downstream_gene_variant,,ENST00000486444,;NFKBIZ,downstream_gene_variant,,ENST00000465476,;	G	ENSG00000144802	ENST00000326172	Transcript	missense_variant	2019	1904	635	L/R	cTg/cGg	rs1043339	.	.	1	NFKBIZ	HGNC	29805	protein_coding	YES	CCDS2946.1	ENSP00000325663	IKBZ_HUMAN	C9JZ23_HUMAN,C9J5I7_HUMAN,C9J5G8_HUMAN	UPI000006FBB1	.	deleterious(0.03)	possibly_damaging(0.643)	10/12	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24124,hmmpanther:PTHR24124:SF5,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|VARSCANS	GGAGCTGCCCA	byHapMap	3	ESCA
CCDC58	0	.	GRCh37	3	122087027	122087027	+	Missense_Mutation	SNP	G	G	T	rs752656989	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.320C>A	p.Thr107Lys	p.T107K	ENST00000291458	3/5	59	46	13	20	20	0	CCDC58,missense_variant,p.Thr107Lys,ENST00000291458,;CCDC58,missense_variant,p.Thr104Lys,ENST00000479414,;CCDC58,missense_variant,p.Thr93Lys,ENST00000479899,;CCDC58,intron_variant,,ENST00000497726,;CCDC58,upstream_gene_variant,,ENST00000460810,;CCDC58,upstream_gene_variant,,ENST00000466854,;CCDC58,non_coding_transcript_exon_variant,,ENST00000498466,;	T	ENSG00000160124	ENST00000291458	Transcript	missense_variant	327	320	107	T/K	aCa/aAa	rs752656989	.	.	-1	CCDC58	HGNC	31136	protein_coding	YES	CCDS33838.1	ENSP00000291458	CCD58_HUMAN	.	UPI000020A069	.	deleterious(0.05)	possibly_damaging(0.627)	3/5	.	hmmpanther:PTHR31905,Pfam_domain:PF09774	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTGTCTGC	.	5	ESCA
KALRN	0	.	GRCh37	3	124174024	124174024	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3547C>A	p.Gln1183Lys	p.Q1183K	ENST00000240874	22/34	54	33	20	33	33	0	KALRN,missense_variant,p.Gln1183Lys,ENST00000240874,;KALRN,missense_variant,p.Gln1174Lys,ENST00000460856,;KALRN,missense_variant,p.Gln1152Lys,ENST00000354186,;KALRN,missense_variant,p.Gln1183Lys,ENST00000360013,;KALRN,splice_region_variant,,ENST00000393501,;KALRN,non_coding_transcript_exon_variant,,ENST00000494648,;	A	ENSG00000160145	ENST00000240874	Transcript	missense_variant	3704	3547	1183	Q/K	Caa/Aaa	.	.	.	1	KALRN	HGNC	4814	protein_coding	YES	CCDS3027.1	ENSP00000240874	KALRN_HUMAN	.	UPI000012C095	.	deleterious(0.01)	possibly_damaging(0.712)	22/34	.	hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGCAAACA	.	5	ESCA
ALDH1L1	0	.	GRCh37	3	125824715	125824715	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2537C>T	p.Ser846Phe	p.S846F	ENST00000273450	22/23	40	37	3	32	32	0	ALDH1L1,missense_variant,p.Ser836Phe,ENST00000393434,;ALDH1L1,missense_variant,p.Ser846Phe,ENST00000273450,;ALDH1L1,missense_variant,p.Ser836Phe,ENST00000472186,;ALDH1L1,missense_variant,p.Ser735Phe,ENST00000452905,;ALDH1L1,3_prime_UTR_variant,,ENST00000393431,;SLC41A3,upstream_gene_variant,,ENST00000509064,;SLC41A3,upstream_gene_variant,,ENST00000508835,;ALDH1L1-AS1,intron_variant,,ENST00000512384,;ALDH1L1,non_coding_transcript_exon_variant,,ENST00000462808,;ALDH1L1,non_coding_transcript_exon_variant,,ENST00000467370,;SLC41A3,upstream_gene_variant,,ENST00000507008,;	A	ENSG00000144908	ENST00000273450	Transcript	missense_variant	2755	2537	846	S/F	tCt/tTt	.	.	.	-1	ALDH1L1	HGNC	3978	protein_coding	YES	CCDS58851.1	ENSP00000273450	AL1L1_HUMAN	D6RFJ7_HUMAN,C9JYZ6_HUMAN,C9JY00_HUMAN,C9IZ36_HUMAN	UPI0000425C57	.	deleterious(0)	probably_damaging(0.999)	22/23	.	hmmpanther:PTHR11699:SF120,hmmpanther:PTHR11699,Pfam_domain:PF00171,Gene3D:3.40.309.10,PIRSF_domain:PIRSF036489,Superfamily_domains:SSF53720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCAGAAGCC	.	2	ESCA
CNTN6	0	.	GRCh37	3	1339605	1339605	+	Missense_Mutation	SNP	G	G	C	rs373831062	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.691G>C	p.Val231Leu	p.V231L	ENST00000446702	7/23	55	48	7	48	48	0	CNTN6,missense_variant,p.Val159Leu,ENST00000539053,;CNTN6,missense_variant,p.Val231Leu,ENST00000446702,;CNTN6,missense_variant,p.Val231Leu,ENST00000350110,;CNTN6,3_prime_UTR_variant,,ENST00000394261,;CNTN6,3_prime_UTR_variant,,ENST00000397479,;	C	ENSG00000134115	ENST00000446702	Transcript	missense_variant	1318	691	231	V/L	Gtg/Ctg	rs373831062	.	.	1	CNTN6	HGNC	2176	protein_coding	YES	CCDS2557.1	ENSP00000407822	CNTN6_HUMAN	F5H752_HUMAN	UPI0000072430	.	deleterious(0.05)	possibly_damaging(0.582)	7/23	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF52,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAAGTGCGT	byFrequency|byCluster	4	ESCA
GRK7	0	.	GRCh37	3	141499459	141499459	+	Missense_Mutation	SNP	C	C	T	rs777683287	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.856C>T	p.Arg286Cys	p.R286C	ENST00000264952	2/4	70	56	14	25	25	0	GRK7,missense_variant,p.Arg286Cys,ENST00000264952,;	T	ENSG00000114124	ENST00000264952	Transcript	missense_variant	993	856	286	R/C	Cgt/Tgt	rs777683287	.	.	1	GRK7	HGNC	17031	protein_coding	YES	CCDS3120.1	ENSP00000264952	GRK7_HUMAN	.	UPI000004244D	.	deleterious(0)	probably_damaging(0.927)	2/4	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF12,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACGCGTGGC	.	5	ESCA
XRN1	0	.	GRCh37	3	142131431	142131431	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1668A>T	p.Lys556Asn	p.K556N	ENST00000264951	15/42	136	116	20	56	56	0	XRN1,missense_variant,p.Lys23Asn,ENST00000498077,;XRN1,missense_variant,p.Lys556Asn,ENST00000392981,;XRN1,missense_variant,p.Lys556Asn,ENST00000264951,;RNU6-1294P,upstream_gene_variant,,ENST00000515995,;XRN1,non_coding_transcript_exon_variant,,ENST00000465507,;XRN1,non_coding_transcript_exon_variant,,ENST00000472697,;	A	ENSG00000114127	ENST00000264951	Transcript	missense_variant	1786	1668	556	K/N	aaA/aaT	.	.	.	-1	XRN1	HGNC	30654	protein_coding	YES	CCDS3123.1	ENSP00000264951	XRN1_HUMAN	C9JCZ8_HUMAN	UPI0000074113	.	deleterious(0)	benign(0.184)	15/42	.	hmmpanther:PTHR12341:SF9,hmmpanther:PTHR12341,PIRSF_domain:PIRSF006743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTTGTTTCCC	.	4	ESCA
MLF1	0	.	GRCh37	3	158288956	158288956	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000392822	.	23	16	7	13	13	0	MLF1,5_prime_UTR_variant,,ENST00000355893,;MLF1,5_prime_UTR_variant,,ENST00000491767,;MLF1,upstream_gene_variant,,ENST00000484955,;MLF1,upstream_gene_variant,,ENST00000478894,;MLF1,upstream_gene_variant,,ENST00000477042,;MLF1,upstream_gene_variant,,ENST00000469452,;MLF1,upstream_gene_variant,,ENST00000392822,;MLF1,upstream_gene_variant,,ENST00000482628,;MLF1,upstream_gene_variant,,ENST00000471745,;MLF1,upstream_gene_variant,,ENST00000498592,;MLF1,upstream_gene_variant,,ENST00000466246,;MLF1,upstream_gene_variant,,ENST00000359117,;RP11-538P18.2,upstream_gene_variant,,ENST00000475981,;RP11-538P18.2,upstream_gene_variant,,ENST00000479233,;MLF1,upstream_gene_variant,,ENST00000497004,;MLF1,upstream_gene_variant,,ENST00000487838,;MLF1,upstream_gene_variant,,ENST00000495452,;	A	ENSG00000178053	ENST00000392822	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	93	1	MLF1	HGNC	7125	protein_coding	YES	CCDS56286.1	ENSP00000376568	MLF1_HUMAN	C9K0D3_HUMAN,C9JNE5_HUMAN	UPI000007134A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCTATCCCGGC	.	3	ESCA
RFTN1	0	.	GRCh37	3	16368365	16368365	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000334133	8/10	49	37	12	42	42	0	RFTN1,missense_variant,p.Asp353Tyr,ENST00000432519,;RFTN1,missense_variant,p.Asp389Tyr,ENST00000334133,;OXNAD1,intron_variant,,ENST00000606098,;OXNAD1,intron_variant,,ENST00000435829,;OXNAD1,intron_variant,,ENST00000544043,;OXNAD1,intron_variant,,ENST00000605932,;RFTN1,non_coding_transcript_exon_variant,,ENST00000483671,;RFTN1,missense_variant,p.Asp4Tyr,ENST00000607320,;	A	ENSG00000131378	ENST00000334133	Transcript	missense_variant	1438	1165	389	D/Y	Gac/Tac	.	.	.	-1	RFTN1	HGNC	30278	protein_coding	YES	CCDS33712.1	ENSP00000334153	RFTN1_HUMAN	C9JRN3_HUMAN,C9JWQ9_HUMAN,C9JHG2_HUMAN,B4E1H7_HUMAN	UPI00001C1DE7	.	deleterious(0)	probably_damaging(0.992)	8/10	.	hmmpanther:PTHR17601:SF3,hmmpanther:PTHR17601,Pfam_domain:PF15250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGTCTGTCT	.	5	ESCA
SI	0	.	GRCh37	3	164783167	164783167	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.689C>T	p.Ser230Leu	p.S230L	ENST00000264382	7/48	76	63	12	25	25	0	SI,missense_variant,p.Ser230Leu,ENST00000264382,;SI,downstream_gene_variant,,ENST00000476593,;	A	ENSG00000090402	ENST00000264382	Transcript	missense_variant	752	689	230	S/L	tCa/tTa	.	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	deleterious(0.01)	probably_damaging(0.978)	7/48	.	Superfamily_domains:SSF74650,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTTGAGATC	.	5	ESCA
KLHL6	0	.	GRCh37	3	183273193	183273193	+	Missense_Mutation	SNP	G	G	T	rs755341184	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.249C>A	p.Phe83Leu	p.F83L	ENST00000341319	1/7	27	19	7	22	22	0	KLHL6,missense_variant,p.Phe83Leu,ENST00000341319,;KLHL6-AS1,downstream_gene_variant,,ENST00000491676,;KLHL6,missense_variant,p.Phe72Leu,ENST00000468734,;KLHL6,non_coding_transcript_exon_variant,,ENST00000489245,;	T	ENSG00000172578	ENST00000341319	Transcript	missense_variant	285	249	83	F/L	ttC/ttA	rs755341184	.	.	-1	KLHL6	HGNC	18653	protein_coding	YES	CCDS3245.2	ENSP00000341342	KLHL6_HUMAN	.	UPI0000169CB9	.	deleterious(0)	probably_damaging(0.999)	1/7	.	PROSITE_profiles:PS50097,hmmpanther:PTHR24411:SF4,hmmpanther:PTHR24411,Pfam_domain:PF00651,Gene3D:3.30.710.10,PIRSF_domain:PIRSF037037,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGAGAATTC	.	5	ESCA
SGOL1	0	.	GRCh37	3	20216539	20216539	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484C>G	p.Pro162Ala	p.P162A	ENST00000263753	6/9	30	19	11	25	25	0	SGOL1,missense_variant,p.Pro162Ala,ENST00000412868,;SGOL1,missense_variant,p.Pro162Ala,ENST00000437051,;SGOL1,missense_variant,p.Pro162Ala,ENST00000425061,;SGOL1,missense_variant,p.Pro162Ala,ENST00000421451,;SGOL1,missense_variant,p.Pro162Ala,ENST00000383774,;SGOL1,missense_variant,p.Pro162Ala,ENST00000263753,;SGOL1,missense_variant,p.Pro162Ala,ENST00000417364,;SGOL1,missense_variant,p.Pro162Ala,ENST00000419233,;SGOL1,missense_variant,p.Pro162Ala,ENST00000443724,;SGOL1,missense_variant,p.Pro162Ala,ENST00000412997,;SGOL1,intron_variant,,ENST00000306698,;SGOL1,intron_variant,,ENST00000442720,;SGOL1,intron_variant,,ENST00000429446,;SGOL1,intron_variant,,ENST00000452020,;SGOL1-AS1,intron_variant,,ENST00000448208,;SGOL1-AS1,intron_variant,,ENST00000441442,;SGOL1,upstream_gene_variant,,ENST00000460637,;SGOL1,3_prime_UTR_variant,,ENST00000456624,;	C	ENSG00000129810	ENST00000263753	Transcript	missense_variant	624	484	162	P/A	Cct/Gct	.	.	.	-1	SGOL1	HGNC	25088	protein_coding	YES	CCDS33716.1	ENSP00000263753	SGOL1_HUMAN	.	UPI00004CE17A	.	deleterious(0.04)	benign(0.214)	6/9	.	hmmpanther:PTHR21577	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTAGGTATCT	.	2	ESCA
ZNF385D	0	.	GRCh37	3	22210428	22210428	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.140T>C	.	.	ENST00000466511	2/2	69	52	17	62	62	0	ZNF385D,non_coding_transcript_exon_variant,,ENST00000466511,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000497570,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494118,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000474607,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494108,;	G	ENSG00000151789	ENST00000466511	Transcript	non_coding_transcript_exon_variant	140	.	.	.	.	.	.	.	-1	ZNF385D	HGNC	26191	processed_transcript	.	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCACAAAGTA	.	5	ESCA
NBEAL2	0	.	GRCh37	3	47039969	47039969	+	Missense_Mutation	SNP	G	G	T	rs373596976	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3135G>T	p.Met1045Ile	p.M1045I	ENST00000450053	22/54	16	13	3	22	22	0	NBEAL2,missense_variant,p.Met1045Ile,ENST00000450053,;NBEAL2,missense_variant,p.Met517Ile,ENST00000416683,;NBEAL2,missense_variant,p.Met1045Ile,ENST00000292309,;NBEAL2,5_prime_UTR_variant,,ENST00000383740,;NBEAL2,upstream_gene_variant,,ENST00000443829,;NBEAL2,upstream_gene_variant,,ENST00000475689,;	T	ENSG00000160796	ENST00000450053	Transcript	missense_variant	3314	3135	1045	M/I	atG/atT	rs373596976	.	.	1	NBEAL2	HGNC	31928	protein_coding	YES	CCDS46817.1	ENSP00000415034	NBEL2_HUMAN	B4DVX0_HUMAN,B4DDY6_HUMAN	UPI000022C020	.	tolerated(0.05)	benign(0.005)	22/54	.	hmmpanther:PTHR13743:SF50,hmmpanther:PTHR13743	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACATGTCCAG	byFrequency|byCluster	2	ESCA
FAM19A4	0	.	GRCh37	3	68802149	68802149	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.151G>A	p.Gly51Arg	p.G51R	ENST00000295569	4/6	21	8	12	15	15	0	FAM19A4,missense_variant,p.Gly51Arg,ENST00000495737,;FAM19A4,missense_variant,p.Gly51Arg,ENST00000295569,;	T	ENSG00000163377	ENST00000295569	Transcript	missense_variant	644	151	51	G/R	Ggg/Agg	COSM1048242	.	.	-1	FAM19A4	HGNC	21591	protein_coding	YES	CCDS2907.1	ENSP00000295569	F19A4_HUMAN	C9JUW7_HUMAN	UPI0000071129	.	deleterious(0)	probably_damaging(1)	4/6	.	hmmpanther:PTHR31770:SF1,hmmpanther:PTHR31770,Pfam_domain:PF12020	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCCCTTGCT	.	5	ESCA
ADH6	0	.	GRCh37	4	100125300	100125300	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*76G>C	.	.	ENST00000394899	9/9	36	24	12	25	25	0	ADH6,3_prime_UTR_variant,,ENST00000407820,;ADH6,3_prime_UTR_variant,,ENST00000394899,;ADH6,3_prime_UTR_variant,,ENST00000394897,;ADH6,downstream_gene_variant,,ENST00000237653,;ADH6,downstream_gene_variant,,ENST00000508558,;RP11-696N14.1,intron_variant,,ENST00000500358,;RP11-696N14.1,intron_variant,,ENST00000506160,;RP11-696N14.1,intron_variant,,ENST00000506454,;ADH6,downstream_gene_variant,,ENST00000504257,;ADH6,3_prime_UTR_variant,,ENST00000507484,;ADH6,3_prime_UTR_variant,,ENST00000512708,;	G	ENSG00000172955	ENST00000394899	Transcript	3_prime_UTR_variant	1298	.	.	.	.	.	.	.	-1	ADH6	HGNC	255	protein_coding	YES	CCDS43255.1	ENSP00000378359	ADH6_HUMAN	Q9H1A0_HUMAN,B7ZAL1_HUMAN,B4DPD8_HUMAN	UPI000013CA1E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTAAAT	.	5	ESCA
ANK2	0	.	GRCh37	4	114279791	114279791	+	Silent	SNP	G	G	A	rs774143296	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10017G>A	p.%3D	p.A3339A	ENST00000357077	38/46	25	19	6	19	19	0	ANK2,synonymous_variant,p.%3D,ENST00000264366,;ANK2,synonymous_variant,p.%3D,ENST00000357077,;ANK2,synonymous_variant,p.%3D,ENST00000505342,;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000394537,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,intron_variant,,ENST00000506722,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,intron_variant,,ENST00000508007,;	A	ENSG00000145362	ENST00000357077	Transcript	synonymous_variant	10070	10017	3339	A	gcG/gcA	rs774143296,COSM301674	.	.	1	ANK2	HGNC	493	protein_coding	YES	CCDS3702.1	ENSP00000349588	ANK2_HUMAN	D6RHC5_HUMAN	UPI0000441EF3	.	.	.	38/46	.	hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AAGGCGGATGA	byFrequency	4	ESCA
TRAM1L1	0	.	GRCh37	4	118006437	118006454	+	In_Frame_Del	DEL	AGCCCCAGCAGGAAGAAC	AGCCCCAGCAGGAAGAAC	-	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	AGCCCCAGCAGGAAGAAC	AGCCCCAGCAGGAAGAAC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96_113delGTTCTTCCTGCTGGGGCT	p.Met32_Leu38delinsIle	p.M32_L38delinsI	ENST00000310754	1/1	36	25	11	38	38	0	TRAM1L1,inframe_deletion,p.Met32_Leu38delinsIle,ENST00000310754,;	-	ENSG00000174599	ENST00000310754	Transcript	inframe_deletion	283-300	96-113	32-38	MFFLLGL/I	atGTTCTTCCTGCTGGGGCTt/att	.	.	.	-1	TRAM1L1	HGNC	28371	protein_coding	YES	CCDS3707.1	ENSP00000309402	TR1L1_HUMAN	.	UPI000013F075	.	.	.	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12371:SF9,hmmpanther:PTHR12371,PIRSF_domain:PIRSF005449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AACACAAGCCCCAGCAGGAAGAACATCCC	.	3	ESCA
TMEM155	0	.	GRCh37	4	122681585	122681585	+	Missense_Mutation	SNP	C	C	A	rs750303927	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257G>T	p.Ser86Ile	p.S86I	ENST00000337677	6/6	46	33	12	28	28	0	TMEM155,missense_variant,p.Ser86Ile,ENST00000394396,;TMEM155,missense_variant,p.Ser86Ile,ENST00000394394,;TMEM155,missense_variant,p.Ser86Ile,ENST00000337677,;TMEM155,downstream_gene_variant,,ENST00000514885,;AC079341.1,upstream_gene_variant,,ENST00000424958,;TMEM155,non_coding_transcript_exon_variant,,ENST00000513254,;TMEM155,non_coding_transcript_exon_variant,,ENST00000461198,;TMEM155,downstream_gene_variant,,ENST00000506551,;TMEM155,downstream_gene_variant,,ENST00000505198,;	A	ENSG00000164112	ENST00000337677	Transcript	missense_variant	816	257	86	S/I	aGc/aTc	rs750303927	.	.	-1	TMEM155	HGNC	26418	protein_coding	YES	CCDS3721.1	ENSP00000336987	TM155_HUMAN	D6R9V5_HUMAN	UPI000013E350	.	deleterious_low_confidence(0.02)	benign(0.102)	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGGCTTCCT	.	5	ESCA
PCDH10	0	.	GRCh37	4	134073552	134073552	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2257G>A	p.Ala753Thr	p.A753T	ENST00000264360	1/5	34	25	9	27	27	0	PCDH10,missense_variant,p.Ala753Thr,ENST00000264360,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;PCDH10,upstream_gene_variant,,ENST00000511112,;	A	ENSG00000138650	ENST00000264360	Transcript	missense_variant	3083	2257	753	A/T	Gcc/Acc	.	.	.	1	PCDH10	HGNC	13404	protein_coding	YES	CCDS34063.1	ENSP00000264360	PCD10_HUMAN	Q9NSR3_HUMAN	UPI0000161C61	.	tolerated(0.5)	benign(0.026)	1/5	.	hmmpanther:PTHR24028:SF0,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGGCCAGC	.	5	ESCA
BOD1L1	0	.	GRCh37	4	13601756	13601756	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6768C>G	p.Ile2256Met	p.I2256M	ENST00000040738	10/26	49	33	15	39	39	0	BOD1L1,missense_variant,p.Ile2256Met,ENST00000040738,;	C	ENSG00000038219	ENST00000040738	Transcript	missense_variant	6904	6768	2256	I/M	atC/atG	.	.	.	-1	BOD1L1	HGNC	31792	protein_coding	YES	CCDS3411.2	ENSP00000040738	BD1L1_HUMAN	.	UPI000066D9E3	.	.	probably_damaging(0.99)	10/26	.	hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGAGATGAT	.	5	ESCA
PROM1	0	.	GRCh37	4	16010698	16010698	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1175A>G	p.Asp392Gly	p.D392G	ENST00000510224	12/28	36	21	14	29	29	0	PROM1,missense_variant,p.Asp383Gly,ENST00000505450,;PROM1,missense_variant,p.Asp392Gly,ENST00000510224,;PROM1,missense_variant,p.Asp383Gly,ENST00000508167,;PROM1,missense_variant,p.Asp383Gly,ENST00000543373,;PROM1,missense_variant,p.Asp392Gly,ENST00000447510,;PROM1,missense_variant,p.Asp392Gly,ENST00000539194,;PROM1,missense_variant,p.Asp392Gly,ENST00000540805,;RNU6-350P,upstream_gene_variant,,ENST00000515949,;PROM1,3_prime_UTR_variant,,ENST00000511153,;	C	ENSG00000007062	ENST00000510224	Transcript	missense_variant	1424	1175	392	D/G	gAt/gGt	.	.	.	-1	PROM1	HGNC	9454	protein_coding	YES	CCDS47029.1	ENSP00000426809	PROM1_HUMAN	D6RIF3_HUMAN,D6RBI0_HUMAN	UPI000004ECD6	.	deleterious(0.02)	benign(0.216)	12/28	.	Pfam_domain:PF05478,hmmpanther:PTHR22730,hmmpanther:PTHR22730:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGATATCTGAA	.	5	ESCA
NEK1	0	.	GRCh37	4	170520292	170520292	+	Nonsense_Mutation	SNP	G	G	A	rs781184197	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271C>T	p.Arg91Ter	p.R91*	ENST00000507142	5/36	33	24	8	18	18	0	NEK1,stop_gained,p.Arg91Ter,ENST00000510533,;NEK1,stop_gained,p.Arg91Ter,ENST00000511633,;NEK1,stop_gained,p.Arg91Ter,ENST00000439128,;NEK1,stop_gained,p.Arg91Ter,ENST00000512193,;NEK1,stop_gained,p.Arg91Ter,ENST00000507142,;NEK1,3_prime_UTR_variant,,ENST00000510108,;NEK1,non_coding_transcript_exon_variant,,ENST00000509912,;	A	ENSG00000137601	ENST00000507142	Transcript	stop_gained	851	271	91	R/*	Cga/Tga	rs781184197	.	.	-1	NEK1	HGNC	7744	protein_coding	YES	CCDS56351.1	ENSP00000424757	NEK1_HUMAN	Q5JXL9_HUMAN	UPI00001D76CA	.	.	.	5/36	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF51,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTCGCTTAA	.	5	ESCA
TMEM129	0	.	GRCh37	4	1720170	1720171	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388dupC	p.Leu130ProfsTer19	p.L130Pfs*19	ENST00000382936	2/4	31	25	6	22	22	0	TMEM129,frameshift_variant,p.Leu130ProfsTer19,ENST00000382936,;TMEM129,frameshift_variant,p.Leu130ProfsTer19,ENST00000303277,;TMEM129,frameshift_variant,p.Leu130ProfsTer19,ENST00000536901,;TACC3,upstream_gene_variant,,ENST00000313288,;TACC3,upstream_gene_variant,,ENST00000493975,;TACC3,upstream_gene_variant,,ENST00000458173,;TACC3,upstream_gene_variant,,ENST00000485989,;RP11-572O17.1,downstream_gene_variant,,ENST00000605571,;TMEM129,3_prime_UTR_variant,,ENST00000480360,;TMEM129,upstream_gene_variant,,ENST00000460722,;TMEM129,upstream_gene_variant,,ENST00000476253,;TACC3,upstream_gene_variant,,ENST00000467746,;TACC3,upstream_gene_variant,,ENST00000484651,;	G	ENSG00000168936	ENST00000382936	Transcript	frameshift_variant	882-883	388-389	130	L/PX	ctc/cCtc	.	.	.	-1	TMEM129	HGNC	25137	protein_coding	YES	CCDS46998.1	ENSP00000372394	TM129_HUMAN	.	UPI000011DC08	.	.	.	2/4	.	hmmpanther:PTHR31322,hmmpanther:PTHR31322:SF1,Pfam_domain:PF10272	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGTAGAGGGCC	.	3	ESCA
ADAM29	0	.	GRCh37	4	175898320	175898320	+	Missense_Mutation	SNP	T	T	A	rs763535563	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1644T>A	p.Asp548Glu	p.D548E	ENST00000359240	5/5	32	26	5	26	26	0	ADAM29,missense_variant,p.Asp548Glu,ENST00000514159,;ADAM29,missense_variant,p.Asp548Glu,ENST00000445694,;ADAM29,missense_variant,p.Asp548Glu,ENST00000404450,;ADAM29,missense_variant,p.Asp548Glu,ENST00000359240,;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000502940,;ADAM29,downstream_gene_variant,,ENST00000505141,;RP13-577H12.2,downstream_gene_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,;	A	ENSG00000168594	ENST00000359240	Transcript	missense_variant	2314	1644	548	D/E	gaT/gaA	rs763535563	.	.	1	ADAM29	HGNC	207	protein_coding	YES	CCDS3823.1	ENSP00000352177	ADA29_HUMAN	D6RHU0_HUMAN,D6RBU0_HUMAN	UPI000013E9DE	.	deleterious(0)	probably_damaging(0.99)	5/5	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF34,Pfam_domain:PF08516,SMART_domains:SM00608	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGATGTCCA	.	5	ESCA
TBC1D1	0	.	GRCh37	4	38139135	38139136	+	3'UTR	INS	-	-	T	rs140473695	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*187dupT	.	.	ENST00000261439	20/20	19	12	7	10	10	0	TBC1D1,3_prime_UTR_variant,,ENST00000261439,;TBC1D1,3_prime_UTR_variant,,ENST00000508802,;TBC1D1,non_coding_transcript_exon_variant,,ENST00000401554,;TBC1D1,non_coding_transcript_exon_variant,,ENST00000407365,;TBC1D1,non_coding_transcript_exon_variant,,ENST00000406664,;TBC1D1,downstream_gene_variant,,ENST00000405444,;TBC1D1,3_prime_UTR_variant,,ENST00000510573,;TBC1D1,downstream_gene_variant,,ENST00000492180,;	T	ENSG00000065882	ENST00000261439	Transcript	3_prime_UTR_variant	4041-4042	.	.	.	.	rs140473695	.	.	1	TBC1D1	HGNC	11578	protein_coding	YES	CCDS33972.1	ENSP00000261439	TBCD1_HUMAN	H0Y8P0_HUMAN,Q8NC59_HUMAN,Q7Z6H2_HUMAN,Q6PJJ8_HUMAN,B9A6J6_HUMAN,A0JNU9_HUMAN	UPI0000367235	.	.	.	20/20	.	.	T:0.0116	T:0.0416	T:0.0029	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCAGTGTTTTT	byFrequency|byCluster|by1000G	2	ESCA
ATP10D	0	.	GRCh37	4	47589054	47589054	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3772G>T	p.Val1258Phe	p.V1258F	ENST00000273859	22/23	125	79	46	62	62	0	ATP10D,missense_variant,p.Val1258Phe,ENST00000273859,;ATP10D,non_coding_transcript_exon_variant,,ENST00000505277,;ATP10D,non_coding_transcript_exon_variant,,ENST00000505476,;ATP10D,downstream_gene_variant,,ENST00000512393,;ATP10D,3_prime_UTR_variant,,ENST00000503288,;	T	ENSG00000145246	ENST00000273859	Transcript	missense_variant	4041	3772	1258	V/F	Gtc/Ttc	.	.	.	1	ATP10D	HGNC	13549	protein_coding	YES	CCDS3476.1	ENSP00000273859	AT10D_HUMAN	.	UPI00001AE9B7	.	deleterious(0.01)	probably_damaging(0.991)	22/23	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF61,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTGGTCATC	.	5	ESCA
KIT	0	.	GRCh37	4	55593704	55593704	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1770T>G	p.Ser590Arg	p.S590R	ENST00000288135	11/21	44	27	16	27	27	0	KIT,missense_variant,p.Ser586Arg,ENST00000412167,;KIT,missense_variant,p.Ser590Arg,ENST00000288135,;KIT,upstream_gene_variant,,ENST00000512959,;	G	ENSG00000157404	ENST00000288135	Transcript	missense_variant	1867	1770	590	S/R	agT/agG	.	.	.	1	KIT	HGNC	6342	protein_coding	YES	CCDS3496.1	ENSP00000288135	KIT_HUMAN	Q8TCG9_HUMAN	UPI000003F17D	.	tolerated(1)	benign(0.269)	11/21	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF46,Gene3D:3.30.200.20,Pfam_domain:PF07714,PIRSF_domain:PIRSF000615,SMART_domains:SM00219,PIRSF_domain:PIRSF500951,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.S590N|c.1769G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGTTTTGG	.	5	ESCA
PRKG2	0	.	GRCh37	4	82027067	82027067	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1963C>A	p.Gln655Lys	p.Q655K	ENST00000395578	16/19	33	24	9	36	36	0	PRKG2,missense_variant,p.Gln626Lys,ENST00000418486,;PRKG2,missense_variant,p.Gln655Lys,ENST00000395578,;PRKG2,missense_variant,p.Gln655Lys,ENST00000264399,;PRKG2,missense_variant,p.Gln235Lys,ENST00000545647,;PRKG2,non_coding_transcript_exon_variant,,ENST00000509474,;PRKG2,non_coding_transcript_exon_variant,,ENST00000509169,;	T	ENSG00000138669	ENST00000395578	Transcript	missense_variant	2080	1963	655	Q/K	Caa/Aaa	.	.	.	-1	PRKG2	HGNC	9416	protein_coding	YES	CCDS3589.1	ENSP00000378945	KGP2_HUMAN	B7ZA25_HUMAN	UPI000012DDC6	.	deleterious(0.02)	possibly_damaging(0.726)	16/19	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24353:SF24,hmmpanther:PTHR24353,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,PIRSF_domain:PIRSF000559,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTGGTCAA	.	5	ESCA
WDFY3	0	.	GRCh37	4	85711028	85711028	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3520G>T	p.Glu1174Ter	p.E1174*	ENST00000295888	22/68	19	15	4	21	21	0	WDFY3,stop_gained,p.Glu1174Ter,ENST00000295888,;WDFY3,stop_gained,p.Glu1174Ter,ENST00000322366,;	A	ENSG00000163625	ENST00000295888	Transcript	stop_gained	3928	3520	1174	E/*	Gaa/Taa	.	.	.	-1	WDFY3	HGNC	20751	protein_coding	YES	CCDS3609.1	ENSP00000295888	WDFY3_HUMAN	D6RJE4_HUMAN,A7E1Z6_HUMAN	UPI000013E2C7	.	.	.	22/68	.	Superfamily_domains:SSF49899,hmmpanther:PTHR13743:SF55,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTCATAAA	.	5	ESCA
MCC	0	.	GRCh37	5	112420928	112420928	+	Missense_Mutation	SNP	C	C	T	rs765539734	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1478G>A	p.Arg493His	p.R493H	ENST00000408903	9/19	64	56	8	46	46	0	MCC,missense_variant,p.Arg303His,ENST00000302475,;MCC,missense_variant,p.Arg240His,ENST00000515367,;MCC,missense_variant,p.Arg493His,ENST00000408903,;MCC,non_coding_transcript_exon_variant,,ENST00000514701,;	T	ENSG00000171444	ENST00000408903	Transcript	missense_variant	1894	1478	493	R/H	cGc/cAc	rs765539734	.	.	-1	MCC	HGNC	6935	protein_coding	YES	CCDS43351.1	ENSP00000386227	CRCM_HUMAN	D6REY2_HUMAN	UPI00015E06EA	.	tolerated(0.13)	probably_damaging(0.993)	9/19	.	hmmpanther:PTHR23347,hmmpanther:PTHR23347:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGGGCGGTTG	.	4	ESCA
PCDHA10	0	.	GRCh37	5	140237801	140237801	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2168C>T	p.Ala723Val	p.A723V	ENST00000307360	1/4	39	19	20	54	54	0	PCDHA10,missense_variant,p.Ala723Val,ENST00000307360,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA9,intron_variant,,ENST00000532602,;AC005609.1,downstream_gene_variant,,ENST00000502505,;PCDHA9,downstream_gene_variant,,ENST00000378122,;PCDHA14,upstream_gene_variant,,ENST00000562220,;PCDHA14,upstream_gene_variant,,ENST00000506751,;	T	ENSG00000250120	ENST00000307360	Transcript	missense_variant	2168	2168	723	A/V	gCg/gTg	.	.	.	1	PCDHA10	HGNC	8664	protein_coding	YES	CCDS54921.1	ENSP00000304234	PCDAA_HUMAN	.	UPI00001273D3	.	tolerated_low_confidence(0.09)	benign(0.024)	1/4	.	hmmpanther:PTHR24028:SF76,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCGGCGGCGC	.	5	ESCA
PCDHB17	0	.	GRCh37	5	140535760	140535760	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.184G>A	p.Ala62Thr	p.A62T	ENST00000539533	1/1	27	13	14	24	24	0	PCDHB17,missense_variant,p.Ala62Thr,ENST00000539533,;PCDHB6,downstream_gene_variant,,ENST00000543635,;PCDHB6,downstream_gene_variant,,ENST00000231136,;	A	ENSG00000255622	ENST00000539533	Transcript	missense_variant	184	184	62	A/T	Gcg/Acg	.	.	.	1	PCDHB17	Uniprot_gn	.	protein_coding	YES	.	ENSP00000438685	.	Q96T98_HUMAN	UPI000006CE19	.	tolerated_low_confidence(0.4)	benign(0.036)	1/1	.	Superfamily_domains:SSF49313,Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCGCGAGA	.	5	ESCA
PCDHB7	0	.	GRCh37	5	140554925	140554925	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*127C>A	.	.	ENST00000231137	1/1	36	31	5	76	76	0	PCDHB7,3_prime_UTR_variant,,ENST00000231137,;PCDHB8,upstream_gene_variant,,ENST00000239444,;	A	ENSG00000113212	ENST00000231137	Transcript	3_prime_UTR_variant	2683	.	.	.	.	.	.	.	1	PCDHB7	HGNC	8692	protein_coding	YES	CCDS4249.1	ENSP00000231137	PCDB7_HUMAN	.	UPI00001273E3	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATTTCTATAC	.	4	ESCA
GRIA1	0	.	GRCh37	5	153175034	153175034	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2415+739A>G	.	.	ENST00000518783	.	51	36	14	61	61	0	GRIA1,splice_acceptor_variant,,ENST00000448073,;GRIA1,splice_acceptor_variant,,ENST00000340592,;GRIA1,intron_variant,,ENST00000518142,;GRIA1,intron_variant,,ENST00000518783,;GRIA1,intron_variant,,ENST00000521843,;GRIA1,intron_variant,,ENST00000285900,;	G	ENSG00000155511	ENST00000518783	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GRIA1	HGNC	4571	protein_coding	YES	CCDS58987.1	ENSP00000428994	GRIA1_HUMAN	.	UPI0001E8F433	.	.	.	.	14/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGAAGAGGT	.	5	ESCA
AHRR	0	.	GRCh37	5	432961	432961	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1077A>G	p.%3D	p.E359E	ENST00000316418	11/12	19	12	7	33	33	0	AHRR,synonymous_variant,p.%3D,ENST00000505113,;AHRR,synonymous_variant,p.%3D,ENST00000506456,;AHRR,synonymous_variant,p.%3D,ENST00000512529,;AHRR,synonymous_variant,p.%3D,ENST00000316418,;AHRR,intron_variant,,ENST00000511487,;AHRR,non_coding_transcript_exon_variant,,ENST00000507048,;	G	ENSG00000063438	ENST00000316418	Transcript	synonymous_variant	1121	1077	359	E	gaA/gaG	.	.	.	1	AHRR	HGNC	346	protein_coding	YES	CCDS43297.1	ENSP00000323816	AHRR_HUMAN	E5RGQ2_HUMAN,E5RFG4_HUMAN	UPI00004572BE	.	.	.	11/12	.	hmmpanther:PTHR10649,hmmpanther:PTHR10649:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGAACAGAC	.	5	ESCA
PAPD7	0	.	GRCh37	5	6755684	6755684	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*626G>T	.	.	ENST00000230859	13/13	28	17	10	22	22	0	PAPD7,3_prime_UTR_variant,,ENST00000230859,;PAPD7,downstream_gene_variant,,ENST00000514410,;PAPD7,downstream_gene_variant,,ENST00000514697,;PAPD7,downstream_gene_variant,,ENST00000505457,;	T	ENSG00000112941	ENST00000230859	Transcript	3_prime_UTR_variant	2384	.	.	.	.	.	.	.	1	PAPD7	HGNC	16705	protein_coding	YES	CCDS3871.1	ENSP00000230859	PAPD7_HUMAN	M1JCE6_HUMAN,D6RJD0_HUMAN,B7ZLL4_HUMAN,B4E0T3_HUMAN	UPI0000071E30	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGTGTCGGC	.	5	ESCA
ADCY2	0	.	GRCh37	5	7827103	7827103	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*119C>A	.	.	ENST00000338316	25/25	16	6	9	26	26	0	ADCY2,3_prime_UTR_variant,,ENST00000338316,;ADCY2,3_prime_UTR_variant,,ENST00000537121,;C5orf49,downstream_gene_variant,,ENST00000509627,;C5orf49,downstream_gene_variant,,ENST00000399810,;ADCY2,non_coding_transcript_exon_variant,,ENST00000489501,;	A	ENSG00000078295	ENST00000338316	Transcript	3_prime_UTR_variant	3484	.	.	.	.	.	.	.	1	ADCY2	HGNC	233	protein_coding	YES	CCDS3872.2	ENSP00000342952	ADCY2_HUMAN	Q7RTV6_HUMAN,Q71UM8_HUMAN,D6REB8_HUMAN	UPI000066D9F2	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGCAGACT	.	5	ESCA
LPAL2	0	.	GRCh37	6	160888611	160888611	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1597G>C	.	.	ENST00000454031	11/17	55	46	9	25	25	0	LPAL2,non_coding_transcript_exon_variant,,ENST00000335388,;LPAL2,intron_variant,,ENST00000435757,;LPAL2,intron_variant,,ENST00000606083,;LPAL2,non_coding_transcript_exon_variant,,ENST00000454031,;	G	ENSG00000213071	ENST00000454031	Transcript	non_coding_transcript_exon_variant	1597	.	.	.	.	.	.	.	-1	LPAL2	HGNC	21210	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	11/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATAACAGTCG	.	5	ESCA
NUP153	0	.	GRCh37	6	17615565	17615565	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*763G>A	.	.	ENST00000262077	22/22	63	38	24	31	31	0	NUP153,3_prime_UTR_variant,,ENST00000262077,;NUP153,downstream_gene_variant,,ENST00000537253,;FAM8A1,downstream_gene_variant,,ENST00000259963,;RNU6-190P,upstream_gene_variant,,ENST00000384154,;	T	ENSG00000124789	ENST00000262077	Transcript	3_prime_UTR_variant	5191	.	.	.	.	.	.	.	-1	NUP153	HGNC	8062	protein_coding	YES	CCDS4541.1	ENSP00000262077	NU153_HUMAN	.	UPI000013D251	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGACAAGAC	.	5	ESCA
ZKSCAN3	0	.	GRCh37	6	28327648	28327648	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285G>T	p.%3D	p.L95L	ENST00000377255	3/7	58	33	25	33	33	0	ZKSCAN3,synonymous_variant,p.%3D,ENST00000252211,;ZKSCAN3,synonymous_variant,p.%3D,ENST00000377255,;ZKSCAN3,intron_variant,,ENST00000341464,;ZSCAN31,upstream_gene_variant,,ENST00000414429,;	T	ENSG00000189298	ENST00000377255	Transcript	synonymous_variant	582	285	95	L	ctG/ctT	.	.	.	1	ZKSCAN3	HGNC	13853	protein_coding	YES	CCDS4650.1	ENSP00000366465	ZKSC3_HUMAN	.	UPI000013CD4A	.	.	.	3/7	.	PROSITE_profiles:PS50804,hmmpanther:PTHR23226:SF55,hmmpanther:PTHR23226,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTGACCAT	.	5	ESCA
ZNRD1-AS1	0	.	GRCh37	6	29976907	29976907	+	RNA	SNP	G	G	A	rs746787154	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.773C>T	.	.	ENST00000376797	7/12	86	44	41	66	66	0	ZNRD1-AS1,non_coding_transcript_exon_variant,,ENST00000376797,;ZNRD1-AS1,intron_variant,,ENST00000420251,;ZNRD1-AS1,intron_variant,,ENST00000448093,;ZNRD1-AS1,intron_variant,,ENST00000425604,;ZNRD1-AS1,downstream_gene_variant,,ENST00000444051,;HLA-J,non_coding_transcript_exon_variant,,ENST00000495278,;HLA-J,non_coding_transcript_exon_variant,,ENST00000462773,;HLA-J,non_coding_transcript_exon_variant,,ENST00000469281,;HLA-J,intron_variant,,ENST00000494367,;HCG4P3,upstream_gene_variant,,ENST00000458060,;	A	ENSG00000204623	ENST00000376797	Transcript	non_coding_transcript_exon_variant	773	.	.	.	.	rs746787154	.	.	-1	ZNRD1-AS1	HGNC	13924	antisense	YES	.	.	.	.	.	.	.	.	7/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGACGTTTTC	byFrequency	5	ESCA
CRIP3	0	.	GRCh37	6	43274241	43274241	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343A>C	p.Lys115Gln	p.K115Q	ENST00000372569	5/8	26	21	4	18	18	0	CRIP3,missense_variant,p.Lys115Gln,ENST00000274990,;CRIP3,missense_variant,p.Lys115Gln,ENST00000372569,;CRIP3,intron_variant,,ENST00000416431,;CRIP3,upstream_gene_variant,,ENST00000451294,;SLC22A7,downstream_gene_variant,,ENST00000372589,;SLC22A7,downstream_gene_variant,,ENST00000372574,;SLC22A7,downstream_gene_variant,,ENST00000372585,;SLC22A7,downstream_gene_variant,,ENST00000436107,;SLC22A7,downstream_gene_variant,,ENST00000487175,;ZNF318,downstream_gene_variant,,ENST00000607252,;CRIP3,non_coding_transcript_exon_variant,,ENST00000487744,;CRIP3,non_coding_transcript_exon_variant,,ENST00000477866,;CRIP3,downstream_gene_variant,,ENST00000485819,;ZNF318,downstream_gene_variant,,ENST00000605935,;RP11-480N24.3,upstream_gene_variant,,ENST00000406185,;	G	ENSG00000146215	ENST00000372569	Transcript	missense_variant	348	343	115	K/Q	Aag/Cag	.	.	.	-1	CRIP3	HGNC	17751	protein_coding	YES	CCDS4894.2	ENSP00000361650	CRIP3_HUMAN	.	UPI00001AE9D2	.	tolerated(0.2)	benign(0.394)	5/8	.	hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF46,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTTCATAT	.	5	ESCA
DST	0	.	GRCh37	6	56470194	56470194	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3672+5031G>A	.	.	ENST00000244364	.	64	47	17	36	36	0	DST,missense_variant,p.Gly2541Ser,ENST00000439203,;DST,missense_variant,p.Gly2541Ser,ENST00000446842,;DST,missense_variant,p.Gly3045Ser,ENST00000370754,;DST,missense_variant,p.Gly2867Ser,ENST00000361203,;DST,missense_variant,p.Gly2867Ser,ENST00000370769,;DST,missense_variant,p.Gly2867Ser,ENST00000312431,;DST,intron_variant,,ENST00000370788,;DST,intron_variant,,ENST00000244364,;DST,intron_variant,,ENST00000421834,;	T	ENSG00000151914	ENST00000244364	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	.	25/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTACCAGGCA	.	5	ESCA
DST	0	.	GRCh37	6	56472332	56472332	+	Intron	SNP	A	A	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3672+2893T>G	.	.	ENST00000244364	.	61	46	15	45	45	0	DST,missense_variant,p.Ile1828Arg,ENST00000439203,;DST,missense_variant,p.Ile1828Arg,ENST00000446842,;DST,missense_variant,p.Ile2332Arg,ENST00000370754,;DST,missense_variant,p.Ile2154Arg,ENST00000361203,;DST,missense_variant,p.Ile2154Arg,ENST00000370769,;DST,missense_variant,p.Ile2154Arg,ENST00000312431,;DST,intron_variant,,ENST00000370788,;DST,intron_variant,,ENST00000244364,;DST,intron_variant,,ENST00000421834,;	C	ENSG00000151914	ENST00000244364	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	.	25/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGTATGTTT	.	5	ESCA
PHIP	0	.	GRCh37	6	79655198	79655198	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4647G>A	p.%3D	p.V1549V	ENST00000275034	39/40	44	33	10	42	42	0	PHIP,synonymous_variant,p.%3D,ENST00000275034,;PHIP,non_coding_transcript_exon_variant,,ENST00000479165,;IRAK1BP1,3_prime_UTR_variant,,ENST00000606868,;	T	ENSG00000146247	ENST00000275034	Transcript	synonymous_variant	4815	4647	1549	V	gtG/gtA	.	.	.	-1	PHIP	HGNC	15673	protein_coding	YES	CCDS4987.1	ENSP00000275034	PHIP_HUMAN	.	UPI000013DA40	.	.	.	39/40	.	hmmpanther:PTHR16266:SF4,hmmpanther:PTHR16266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S1548C|c.4643C>G|3	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGTTTCACAGA	.	4	ESCA
LAMB1	0	.	GRCh37	7	107572812	107572812	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4199C>A	p.Thr1400Lys	p.T1400K	ENST00000222399	28/34	69	51	18	28	27	1	LAMB1,missense_variant,p.Thr1424Lys,ENST00000393561,;LAMB1,missense_variant,p.Thr1400Lys,ENST00000222399,;LAMB1,non_coding_transcript_exon_variant,,ENST00000468518,;LAMB1,non_coding_transcript_exon_variant,,ENST00000474380,;LAMB1,downstream_gene_variant,,ENST00000491196,;LAMB1,downstream_gene_variant,,ENST00000468999,;LAMB1,downstream_gene_variant,,ENST00000470995,;LAMB1,upstream_gene_variant,,ENST00000472714,;DLD,downstream_gene_variant,,ENST00000417551,;	T	ENSG00000091136	ENST00000222399	Transcript	missense_variant	4430	4199	1400	T/K	aCa/aAa	.	.	.	-1	LAMB1	HGNC	6486	protein_coding	YES	CCDS5750.1	ENSP00000222399	LAMB1_HUMAN	Q75MC8_HUMAN,E9PCS6_HUMAN	UPI00001AE63F	.	deleterious(0.01)	benign(0.147)	28/34	.	hmmpanther:PTHR10574:SF233,hmmpanther:PTHR10574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGGGTGTTCCA	.	2	ESCA
AC009365.3	0	.	GRCh37	7	132412352	132412352	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204G>A	p.%3D	p.L68L	ENST00000332558	5/5	57	48	9	30	30	0	AC009365.3,synonymous_variant,p.%3D,ENST00000332558,;	A	ENSG00000183470	ENST00000332558	Transcript	synonymous_variant	822	204	68	L	ctG/ctA	.	.	.	1	AC009365.3	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000331939	YG018_HUMAN	.	UPI0000140A0D	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTGCCTGG	.	5	ESCA
DPP6	0	.	GRCh37	7	154667636	154667636	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1904A>T	p.Gln635Leu	p.Q635L	ENST00000377770	20/26	51	22	28	89	89	0	DPP6,missense_variant,p.Gln528Leu,ENST00000427557,;DPP6,missense_variant,p.Gln635Leu,ENST00000377770,;DPP6,missense_variant,p.Gln573Leu,ENST00000332007,;DPP6,missense_variant,p.Gln571Leu,ENST00000404039,;DPP6,non_coding_transcript_exon_variant,,ENST00000479637,;DPP6,non_coding_transcript_exon_variant,,ENST00000484789,;DPP6,non_coding_transcript_exon_variant,,ENST00000488512,;	T	ENSG00000130226	ENST00000377770	Transcript	missense_variant	2045	1904	635	Q/L	cAg/cTg	.	.	.	1	DPP6	HGNC	3010	protein_coding	YES	.	ENSP00000367001	DPP6_HUMAN	Q75MI8_HUMAN,Q75MI7_HUMAN,Q75MF0_HUMAN	UPI00001AE746	.	deleterious(0)	possibly_damaging(0.782)	20/26	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCCAGAGTG	.	5	ESCA
UBE3C	0	.	GRCh37	7	157000528	157000528	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1708G>C	p.Glu570Gln	p.E570Q	ENST00000348165	13/23	27	14	13	30	30	0	UBE3C,missense_variant,p.Glu570Gln,ENST00000348165,;UBE3C,non_coding_transcript_exon_variant,,ENST00000469336,;	C	ENSG00000009335	ENST00000348165	Transcript	missense_variant	2068	1708	570	E/Q	Gaa/Caa	.	.	.	1	UBE3C	HGNC	16803	protein_coding	YES	CCDS34789.1	ENSP00000309198	UBE3C_HUMAN	.	UPI000020E72A	.	tolerated(0.09)	benign(0.168)	13/23	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF85	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCGAGAAGAA	.	5	ESCA
SP4	0	.	GRCh37	7	21552442	21552442	+	3'UTR	SNP	G	G	T	rs556663510	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1555G>T	.	.	ENST00000222584	6/6	17	9	7	16	16	0	SP4,3_prime_UTR_variant,,ENST00000222584,;SP4,3_prime_UTR_variant,,ENST00000448246,;	T	ENSG00000105866	ENST00000222584	Transcript	3_prime_UTR_variant	4128	.	.	.	.	rs556663510	.	.	1	SP4	HGNC	11209	protein_coding	YES	CCDS5373.1	ENSP00000222584	SP4_HUMAN	Q32M51_HUMAN	UPI000013C807	.	.	.	6/6	.	.	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCAGAGTGC	byFrequency|by1000G	5	ESCA
SP4	0	.	GRCh37	7	21552443	21552443	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1556A>C	.	.	ENST00000222584	6/6	17	9	7	17	17	0	SP4,3_prime_UTR_variant,,ENST00000222584,;SP4,3_prime_UTR_variant,,ENST00000448246,;	C	ENSG00000105866	ENST00000222584	Transcript	3_prime_UTR_variant	4129	.	.	.	.	.	.	.	1	SP4	HGNC	11209	protein_coding	YES	CCDS5373.1	ENSP00000222584	SP4_HUMAN	Q32M51_HUMAN	UPI000013C807	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGAGTGCT	.	5	ESCA
ZNF727	0	.	GRCh37	7	63537932	63537932	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505A>C	p.%3D	p.R169R	ENST00000550760	4/4	43	35	8	20	20	0	ZNF727,synonymous_variant,p.%3D,ENST00000550760,;RP11-3N2.13,downstream_gene_variant,,ENST00000445978,;RP11-3N2.13,non_coding_transcript_exon_variant,,ENST00000456806,;RP11-3N2.13,upstream_gene_variant,,ENST00000430271,;	C	ENSG00000257482	ENST00000550760	Transcript	synonymous_variant	684	505	169	R	Aga/Cga	.	.	.	1	ZNF727	HGNC	22785	protein_coding	YES	CCDS55113.1	ENSP00000447987	ZN727_HUMAN	.	UPI0001A23134	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF79,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGCAGAGAG	.	5	ESCA
KIAA1324L	0	.	GRCh37	7	86568140	86568140	+	Silent	SNP	G	G	A	rs774408868	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.984C>T	p.%3D	p.D328D	ENST00000450689	7/22	37	24	13	29	29	0	KIAA1324L,synonymous_variant,p.%3D,ENST00000416314,;KIAA1324L,synonymous_variant,p.%3D,ENST00000297222,;KIAA1324L,synonymous_variant,p.%3D,ENST00000444627,;KIAA1324L,synonymous_variant,p.%3D,ENST00000423294,;KIAA1324L,synonymous_variant,p.%3D,ENST00000450689,;KIAA1324L,downstream_gene_variant,,ENST00000398276,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;	A	ENSG00000164659	ENST00000450689	Transcript	synonymous_variant	1170	984	328	D	gaC/gaT	rs774408868,COSM301120	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	.	.	7/22	.	hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727,Gene3D:3.90.10.10,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCGTCTTT	byFrequency	5	ESCA
PEG10	0	.	GRCh37	7	94295734	94295734	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1888C>T	.	.	ENST00000482108	2/2	37	28	9	33	33	0	PEG10,3_prime_UTR_variant,,ENST00000482108,;PEG10,downstream_gene_variant,,ENST00000488574,;PEG10,intron_variant,,ENST00000465184,;PEG10,intron_variant,,ENST00000493935,;	T	ENSG00000242265	ENST00000482108	Transcript	3_prime_UTR_variant	3345	.	.	.	.	.	.	.	1	PEG10	HGNC	14005	protein_coding	YES	CCDS55126.1	ENSP00000417587	PEG10_HUMAN	B4DSP0_HUMAN	UPI0000047FA3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCACATC	.	5	ESCA
DYNC1I1	0	.	GRCh37	7	95457368	95457368	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366-1G>A	.	p.X122_splice	ENST00000324972	.	124	70	53	79	79	0	DYNC1I1,splice_acceptor_variant,,ENST00000518089,;DYNC1I1,splice_acceptor_variant,,ENST00000457059,;DYNC1I1,splice_acceptor_variant,,ENST00000447467,;DYNC1I1,splice_acceptor_variant,,ENST00000324972,;DYNC1I1,intron_variant,,ENST00000359388,;DYNC1I1,intron_variant,,ENST00000437599,;DYNC1I1,intron_variant,,ENST00000537881,;	A	ENSG00000158560	ENST00000324972	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	DYNC1I1	HGNC	2963	protein_coding	YES	CCDS5644.1	ENSP00000320130	DC1I1_HUMAN	Q75MI9_HUMAN,Q75LS9_HUMAN,A4D1I7_HUMAN	UPI0000129A01	.	.	.	.	4/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTAGGACCC	.	5	ESCA
MCM7	0	.	GRCh37	7	99691652	99691652	+	Intron	SNP	C	C	T	rs72631827	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1848+144G>A	.	.	ENST00000303887	.	45	29	16	27	27	0	MCM7,intron_variant,,ENST00000354230,;MCM7,intron_variant,,ENST00000303887,;MCM7,intron_variant,,ENST00000343023,;MCM7,downstream_gene_variant,,ENST00000425308,;COPS6,downstream_gene_variant,,ENST00000419210,;COPS6,downstream_gene_variant,,ENST00000418625,;COPS6,downstream_gene_variant,,ENST00000303904,;MIR106B,non_coding_transcript_exon_variant,,ENST00000385301,;MIR93,upstream_gene_variant,,ENST00000385024,;MIR25,upstream_gene_variant,,ENST00000384816,;MCM7,intron_variant,,ENST00000493352,;MCM7,intron_variant,,ENST00000491245,;MCM7,intron_variant,,ENST00000485286,;MCM7,intron_variant,,ENST00000489841,;COPS6,downstream_gene_variant,,ENST00000474823,;COPS6,downstream_gene_variant,,ENST00000426712,;COPS6,downstream_gene_variant,,ENST00000496358,;MCM7,downstream_gene_variant,,ENST00000463722,;COPS6,downstream_gene_variant,,ENST00000472107,;MCM7,downstream_gene_variant,,ENST00000477372,;COPS6,downstream_gene_variant,,ENST00000468499,;COPS6,downstream_gene_variant,,ENST00000465027,;COPS6,downstream_gene_variant,,ENST00000483891,;	T	ENSG00000166508	ENST00000303887	Transcript	intron_variant	.	.	.	.	.	rs72631827	.	.	-1	MCM7	HGNC	6950	protein_coding	YES	CCDS5683.1	ENSP00000307288	MCM7_HUMAN	Q9H4N9_HUMAN,C9J8M6_HUMAN	UPI000012ED9E	.	.	.	.	13/14	.	A:0.0060	A:0.0227	A:0	.	A:0	A:0	A:0	A:0.0137	A:0.0001	.	.	19232555	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCACGGAGA	byFrequency|byCluster|by1000G	5	ESCA
SPAG1	0	.	GRCh37	8	101206670	101206670	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096+174C>G	.	.	ENST00000388798	.	42	27	15	24	24	0	SPAG1,3_prime_UTR_variant,,ENST00000520508,;SPAG1,3_prime_UTR_variant,,ENST00000520643,;SPAG1,intron_variant,,ENST00000388798,;SPAG1,intron_variant,,ENST00000251809,;	G	ENSG00000104450	ENST00000388798	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SPAG1	HGNC	11212	protein_coding	YES	CCDS34930.1	ENSP00000373450	SPAG1_HUMAN	.	UPI000016783D	.	.	.	.	10/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCTCTCAAA	.	5	ESCA
MAF1	0	.	GRCh37	8	145160882	145160882	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194C>A	p.Ser65Ter	p.S65*	ENST00000322428	3/8	14	8	6	19	19	0	MAF1,stop_gained,p.Ser65Ter,ENST00000534585,;MAF1,stop_gained,p.Ser65Ter,ENST00000532522,;MAF1,stop_gained,p.Ser65Ter,ENST00000527572,;MAF1,stop_gained,p.Ser65Ter,ENST00000322428,;MAF1,stop_gained,p.Ser65Ter,ENST00000527058,;SHARPIN,upstream_gene_variant,,ENST00000398712,;KIAA1875,upstream_gene_variant,,ENST00000323662,;MAF1,upstream_gene_variant,,ENST00000534811,;SHARPIN,intron_variant,,ENST00000533184,;SHARPIN,upstream_gene_variant,,ENST00000533948,;KIAA1875,upstream_gene_variant,,ENST00000533108,;SHARPIN,upstream_gene_variant,,ENST00000534242,;KIAA1875,upstream_gene_variant,,ENST00000534167,;SHARPIN,upstream_gene_variant,,ENST00000534435,;SHARPIN,upstream_gene_variant,,ENST00000359551,;SHARPIN,upstream_gene_variant,,ENST00000531375,;KIAA1875,upstream_gene_variant,,ENST00000525150,;KIAA1875,upstream_gene_variant,,ENST00000528691,;	A	ENSG00000179632	ENST00000322428	Transcript	stop_gained	598	194	65	S/*	tCa/tAa	.	.	.	1	MAF1	HGNC	24966	protein_coding	YES	CCDS6416.1	ENSP00000318604	MAF1_HUMAN	E9PJ05_HUMAN	UPI0000140E10	.	.	.	3/8	.	hmmpanther:PTHR22504,hmmpanther:PTHR22504:SF1,Pfam_domain:PF09174,PIRSF_domain:PIRSF037240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCAGGAC	.	5	ESCA
CPSF1	0	.	GRCh37	8	145624685	145624685	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1373T>C	p.Leu458Pro	p.L458P	ENST00000349769	14/38	28	17	10	40	40	0	CPSF1,missense_variant,p.Leu458Pro,ENST00000349769,;CPSF1,downstream_gene_variant,,ENST00000531042,;MIR1234,downstream_gene_variant,,ENST00000408875,;CPSF1,upstream_gene_variant,,ENST00000532935,;CPSF1,non_coding_transcript_exon_variant,,ENST00000533492,;CPSF1,non_coding_transcript_exon_variant,,ENST00000527916,;CPSF1,upstream_gene_variant,,ENST00000526271,;CPSF1,downstream_gene_variant,,ENST00000532560,;CPSF1,upstream_gene_variant,,ENST00000529288,;CPSF1,upstream_gene_variant,,ENST00000527827,;CPSF1,downstream_gene_variant,,ENST00000531683,;	G	ENSG00000071894	ENST00000349769	Transcript	missense_variant	1468	1373	458	L/P	cTg/cCg	.	.	.	-1	CPSF1	HGNC	2324	protein_coding	YES	CCDS34966.1	ENSP00000339353	CPSF1_HUMAN	Q9C0J6_HUMAN,E9PIM1_HUMAN,D3DWL9_HUMAN	UPI00001282EE	.	deleterious(0)	probably_damaging(0.972)	14/38	.	hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF2,Pfam_domain:PF10433	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCAGCTGT	.	5	ESCA
PPP3CC	0	.	GRCh37	8	22370817	22370817	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642T>C	p.%3D	p.F214F	ENST00000397775	6/15	91	60	30	73	73	0	PPP3CC,synonymous_variant,p.%3D,ENST00000523620,;PPP3CC,synonymous_variant,p.%3D,ENST00000240139,;PPP3CC,synonymous_variant,p.%3D,ENST00000522034,;PPP3CC,synonymous_variant,p.%3D,ENST00000521651,;PPP3CC,synonymous_variant,p.%3D,ENST00000518852,;PPP3CC,synonymous_variant,p.%3D,ENST00000397775,;PPP3CC,synonymous_variant,p.%3D,ENST00000289963,;	C	ENSG00000120910	ENST00000397775	Transcript	synonymous_variant	916	642	214	F	ttT/ttC	.	.	.	1	PPP3CC	HGNC	9316	protein_coding	YES	CCDS59093.1	ENSP00000380878	PP2BC_HUMAN	E5RJH4_HUMAN	UPI00017A7ABA	.	.	.	6/15	.	hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF186,Gene3D:3.60.21.10,Pfam_domain:PF00149,SMART_domains:SM00156,Superfamily_domains:SSF56300,Prints_domain:PR00114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTTACGGA	.	5	ESCA
WRN	0	.	GRCh37	8	31012243	31012243	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3791C>G	p.Ser1264Cys	p.S1264C	ENST00000298139	32/35	55	34	21	57	57	0	WRN,missense_variant,p.Ser1264Cys,ENST00000298139,;WRN,non_coding_transcript_exon_variant,,ENST00000521620,;	G	ENSG00000165392	ENST00000298139	Transcript	missense_variant	4040	3791	1264	S/C	tCt/tGt	.	.	.	1	WRN	HGNC	12791	protein_coding	YES	CCDS6082.1	ENSP00000298139	WRN_HUMAN	.	UPI000013E49D	.	tolerated(0.1)	possibly_damaging(0.827)	32/35	.	Pfam_domain:PF14493,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF80	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTCTTTAT	.	5	ESCA
DUSP26	0	.	GRCh37	8	33449263	33449263	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*268A>G	.	.	ENST00000256261	4/4	10	7	2	12	12	0	DUSP26,3_prime_UTR_variant,,ENST00000256261,;DUSP26,downstream_gene_variant,,ENST00000523956,;DUSP26,downstream_gene_variant,,ENST00000522982,;	C	ENSG00000133878	ENST00000256261	Transcript	3_prime_UTR_variant	1422	.	.	.	.	.	.	.	-1	DUSP26	HGNC	28161	protein_coding	YES	CCDS6092.1	ENSP00000256261	DUS26_HUMAN	E5RHD0_HUMAN	UPI000003E899	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCGGTGTTCG	.	2	ESCA
C8orf4	0	.	GRCh37	8	40012678	40012678	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1306C>A	.	.	ENST00000315792	1/1	68	51	16	33	32	1	C8orf4,3_prime_UTR_variant,,ENST00000315792,;	A	ENSG00000176907	ENST00000315792	Transcript	3_prime_UTR_variant	1690	.	.	.	.	.	.	.	1	C8orf4	HGNC	1357	protein_coding	YES	CCDS6115.1	ENSP00000319914	CH004_HUMAN	.	UPI000013FBD4	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TTTTTCCCAAG	.	2	ESCA
ANK1	0	.	GRCh37	8	41581100	41581100	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.862G>A	p.Val288Met	p.V288M	ENST00000265709	8/43	101	84	16	51	51	0	ANK1,missense_variant,p.Val288Met,ENST00000265709,;ANK1,missense_variant,p.Val255Met,ENST00000352337,;ANK1,missense_variant,p.Val255Met,ENST00000396942,;ANK1,missense_variant,p.Val255Met,ENST00000379758,;ANK1,missense_variant,p.Val255Met,ENST00000289734,;ANK1,missense_variant,p.Val255Met,ENST00000347528,;ANK1,missense_variant,p.Val255Met,ENST00000396945,;	T	ENSG00000029534	ENST00000265709	Transcript	missense_variant	1144	862	288	V/M	Gtg/Atg	.	.	.	-1	ANK1	HGNC	492	protein_coding	YES	CCDS47849.1	ENSP00000265709	ANK1_HUMAN	Q9UMG4_HUMAN	UPI0000E4453A	.	deleterious(0)	probably_damaging(1)	8/43	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF11,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCACCATGA	.	4	ESCA
COPS5	0	.	GRCh37	8	67968797	67968797	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616A>G	p.Ile206Val	p.I206V	ENST00000357849	5/8	32	23	9	33	33	0	COPS5,missense_variant,p.Ile142Val,ENST00000517736,;COPS5,missense_variant,p.Ile142Val,ENST00000518747,;COPS5,missense_variant,p.Ile206Val,ENST00000357849,;AC109335.1,upstream_gene_variant,,ENST00000578628,;PPP1R42,non_coding_transcript_exon_variant,,ENST00000517834,;COPS5,downstream_gene_variant,,ENST00000517793,;COPS5,downstream_gene_variant,,ENST00000519057,;COPS5,upstream_gene_variant,,ENST00000523086,;COPS5,downstream_gene_variant,,ENST00000519963,;COPS5,3_prime_UTR_variant,,ENST00000523890,;COPS5,3_prime_UTR_variant,,ENST00000518374,;COPS5,non_coding_transcript_exon_variant,,ENST00000521509,;COPS5,non_coding_transcript_exon_variant,,ENST00000521386,;COPS5,downstream_gene_variant,,ENST00000517406,;	C	ENSG00000121022	ENST00000357849	Transcript	missense_variant	937	616	206	I/V	Att/Gtt	.	.	.	-1	COPS5	HGNC	2240	protein_coding	YES	CCDS6198.1	ENSP00000350512	CSN5_HUMAN	E5RHF2_HUMAN	UPI000006D7AB	.	tolerated(0.27)	benign(0.088)	5/8	.	hmmpanther:PTHR10410,hmmpanther:PTHR10410:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAATAGTCT	.	5	ESCA
EYA1	0	.	GRCh37	8	72110756	72110756	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*819G>A	.	.	ENST00000340726	18/18	39	25	14	34	34	0	EYA1,3_prime_UTR_variant,,ENST00000388741,;EYA1,3_prime_UTR_variant,,ENST00000388742,;EYA1,3_prime_UTR_variant,,ENST00000340726,;EYA1,3_prime_UTR_variant,,ENST00000388740,;EYA1,3_prime_UTR_variant,,ENST00000303824,;EYA1,downstream_gene_variant,,ENST00000419131,;EYA1,downstream_gene_variant,,ENST00000388743,;RP11-326E22.1,intron_variant,,ENST00000521685,;EYA1,3_prime_UTR_variant,,ENST00000465115,;EYA1,downstream_gene_variant,,ENST00000496494,;	T	ENSG00000104313	ENST00000340726	Transcript	3_prime_UTR_variant	3238	.	.	.	.	.	.	.	-1	EYA1	HGNC	3519	protein_coding	YES	CCDS34906.1	ENSP00000342626	EYA1_HUMAN	Q4A4D0_HUMAN	UPI000012A3B3	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCATGCT	.	5	ESCA
STAU2	0	.	GRCh37	8	74332366	74332366	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000524300	.	21	14	6	27	27	0	STAU2,downstream_gene_variant,,ENST00000522695,;STAU2,downstream_gene_variant,,ENST00000524300,;STAU2,downstream_gene_variant,,ENST00000523558,;STAU2,downstream_gene_variant,,ENST00000521210,;STAU2-AS1,non_coding_transcript_exon_variant,,ENST00000522703,;STAU2-AS1,non_coding_transcript_exon_variant,,ENST00000517604,;STAU2,downstream_gene_variant,,ENST00000522818,;	T	ENSG00000040341	ENST00000524300	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	240	-1	STAU2	HGNC	11371	protein_coding	YES	CCDS55247.1	ENSP00000428756	.	E5RJN7_HUMAN	UPI000013D271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTCTCATT	.	5	ESCA
PTDSS1	0	.	GRCh37	8	97346553	97346553	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*759G>A	.	.	ENST00000517309	13/13	102	83	19	74	74	0	PTDSS1,3_prime_UTR_variant,,ENST00000517309,;PTDSS1,3_prime_UTR_variant,,ENST00000455950,;PTDSS1,downstream_gene_variant,,ENST00000522072,;PTDSS1,3_prime_UTR_variant,,ENST00000337004,;PTDSS1,downstream_gene_variant,,ENST00000517982,;	A	ENSG00000156471	ENST00000517309	Transcript	3_prime_UTR_variant	2507	.	.	.	.	.	.	.	1	PTDSS1	HGNC	9587	protein_coding	YES	CCDS6271.1	ENSP00000430548	PTSS1_HUMAN	Q9BUQ5_HUMAN	UPI0000132810	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACCTGCTAGA	.	4	ESCA
SDC2	0	.	GRCh37	8	97620584	97620584	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.328G>C	p.Glu110Gln	p.E110Q	ENST00000302190	4/5	44	41	3	34	34	0	SDC2,missense_variant,p.Glu81Gln,ENST00000522911,;SDC2,missense_variant,p.Glu81Gln,ENST00000521590,;SDC2,missense_variant,p.Glu81Gln,ENST00000523877,;SDC2,missense_variant,p.Glu110Gln,ENST00000302190,;SDC2,missense_variant,p.Glu74Gln,ENST00000518385,;SDC2,missense_variant,p.Glu81Gln,ENST00000519914,;	C	ENSG00000169439	ENST00000302190	Transcript	missense_variant	1249	328	110	E/Q	Gag/Cag	.	.	.	1	SDC2	HGNC	10659	protein_coding	YES	CCDS6272.1	ENSP00000307046	SDC2_HUMAN	E5RJB8_HUMAN,E9PBI9_HUMAN,E5RHU3_HUMAN,B4DT61_HUMAN	UPI000013E7A4	.	tolerated(0.33)	possibly_damaging(0.486)	4/5	.	hmmpanther:PTHR10915:SF6,hmmpanther:PTHR10915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATAAAGAGAAA	.	2	ESCA
SUSD1	0	.	GRCh37	9	114820919	114820919	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1898C>G	p.Ser633Cys	p.S633C	ENST00000374270	14/17	64	56	8	38	38	0	SUSD1,missense_variant,p.Ser633Cys,ENST00000374263,;SUSD1,missense_variant,p.Ser617Cys,ENST00000355396,;SUSD1,missense_variant,p.Ser633Cys,ENST00000374270,;SUSD1,missense_variant,p.Ser633Cys,ENST00000374264,;SUSD1,upstream_gene_variant,,ENST00000475283,;	C	ENSG00000106868	ENST00000374270	Transcript	missense_variant	2071	1898	633	S/C	tCt/tGt	.	.	.	-1	SUSD1	HGNC	25413	protein_coding	YES	CCDS6783.1	ENSP00000363388	SUSD1_HUMAN	.	UPI0000049E0D	.	tolerated(0.21)	possibly_damaging(0.625)	14/17	.	hmmpanther:PTHR24051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACAAGAAAAT	.	4	ESCA
OR1L6	0	.	GRCh37	9	125512324	125512324	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198C>A	p.Asn66Lys	p.N66K	ENST00000304720	1/1	67	23	43	58	58	0	OR1L6,missense_variant,p.Asn66Lys,ENST00000304720,;OR1L6,missense_variant,p.Asn102Lys,ENST00000373684,;	A	ENSG00000171459	ENST00000304720	Transcript	missense_variant	198	198	66	N/K	aaC/aaA	.	.	.	1	OR1L6	HGNC	8218	protein_coding	YES	CCDS35130.2	ENSP00000304235	OR1L6_HUMAN	.	UPI000003CAAE	.	deleterious(0.02)	benign(0.356)	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF194,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAACTTGTC	.	5	ESCA
PDCL	0	.	GRCh37	9	125582063	125582063	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*301C>G	.	.	ENST00000259467	4/4	25	15	9	19	19	0	PDCL,3_prime_UTR_variant,,ENST00000259467,;PDCL,intron_variant,,ENST00000436632,;PDCL,downstream_gene_variant,,ENST00000394285,;	C	ENSG00000136940	ENST00000259467	Transcript	3_prime_UTR_variant	1373	.	.	.	.	.	.	.	-1	PDCL	HGNC	8770	protein_coding	YES	CCDS6845.1	ENSP00000259467	PHLP_HUMAN	Q9UNX2_HUMAN,Q9UNX1_HUMAN	UPI0000131988	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAAGACCCT	.	5	ESCA
FNBP1	0	.	GRCh37	9	132681440	132681440	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1171-3181G>T	.	.	ENST00000446176	.	35	22	13	32	32	0	FNBP1,missense_variant,p.Val18Phe,ENST00000443566,;FNBP1,intron_variant,,ENST00000355681,;FNBP1,intron_variant,,ENST00000449089,;FNBP1,intron_variant,,ENST00000420781,;FNBP1,intron_variant,,ENST00000446176,;FNBP1,non_coding_transcript_exon_variant,,ENST00000482107,;FNBP1,intron_variant,,ENST00000478129,;FNBP1,upstream_gene_variant,,ENST00000462766,;	A	ENSG00000187239	ENST00000446176	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	FNBP1	HGNC	17069	protein_coding	YES	CCDS48040.1	ENSP00000413625	FNBP1_HUMAN	B7ZL12_HUMAN	UPI000022408C	.	.	.	.	10/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAACATAGT	.	5	ESCA
PRRC2B	0	.	GRCh37	9	134346214	134346214	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1951C>T	p.Pro651Ser	p.P651S	ENST00000357304	13/31	16	12	3	20	20	0	PRRC2B,missense_variant,p.Pro651Ser,ENST00000458550,;PRRC2B,missense_variant,p.Pro651Ser,ENST00000357304,;PRRC2B,missense_variant,p.Pro651Ser,ENST00000405995,;PRRC2B,5_prime_UTR_variant,,ENST00000372249,;PRRC2B,upstream_gene_variant,,ENST00000456307,;PRRC2B,downstream_gene_variant,,ENST00000422467,;	T	ENSG00000130723	ENST00000357304	Transcript	missense_variant	2006	1951	651	P/S	Ccc/Tcc	.	.	.	1	PRRC2B	HGNC	28121	protein_coding	YES	CCDS48044.1	ENSP00000349856	PRC2B_HUMAN	Q5JSZ9_HUMAN,B4E3S7_HUMAN	UPI00002374A3	.	tolerated(0.11)	probably_damaging(0.947)	13/31	.	hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TGTACCCCCCG	.	4	ESCA
PPP1R26	0	.	GRCh37	9	138377490	138377490	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1134G>A	p.%3D	p.Q378Q	ENST00000356818	4/4	54	37	17	59	59	0	PPP1R26,synonymous_variant,p.%3D,ENST00000604351,;PPP1R26,synonymous_variant,p.%3D,ENST00000605660,;PPP1R26,synonymous_variant,p.%3D,ENST00000356818,;PPP1R26,synonymous_variant,p.%3D,ENST00000401470,;PPP1R26,synonymous_variant,p.%3D,ENST00000605286,;PPP1R26-AS1,upstream_gene_variant,,ENST00000603893,;PPP1R26-AS1,upstream_gene_variant,,ENST00000605260,;PPP1R26-AS1,upstream_gene_variant,,ENST00000455039,;PPP1R26,intron_variant,,ENST00000602993,;	A	ENSG00000196422	ENST00000356818	Transcript	synonymous_variant	1683	1134	378	Q	caG/caA	.	.	.	1	PPP1R26	HGNC	29089	protein_coding	YES	CCDS6988.1	ENSP00000349274	PPR26_HUMAN	Q5T8A6_HUMAN	UPI000013DB17	.	.	.	4/4	.	hmmpanther:PTHR15724	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGAAAAC	.	5	ESCA
SNAPC4	0	.	GRCh37	9	139286514	139286514	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855G>T	p.Gln285His	p.Q285H	ENST00000298532	9/23	21	5	16	34	34	0	SNAPC4,missense_variant,p.Gln285His,ENST00000298532,;	A	ENSG00000165684	ENST00000298532	Transcript	missense_variant	1224	855	285	Q/H	caG/caT	.	.	.	-1	SNAPC4	HGNC	11137	protein_coding	YES	CCDS6998.1	ENSP00000298532	SNPC4_HUMAN	.	UPI000013E4EC	.	deleterious(0)	probably_damaging(0.991)	9/23	.	PROSITE_profiles:PS50090,hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF191,Gene3D:1.10.10.60,SMART_domains:SM00717	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTCTGCCA	.	5	ESCA
FOXD4L5	0	.	GRCh37	9	70177146	70177146	+	Missense_Mutation	SNP	C	C	T	rs781582393	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838G>A	p.Gly280Arg	p.G280R	ENST00000377420	1/1	89	78	11	59	59	0	FOXD4L5,missense_variant,p.Gly280Arg,ENST00000377420,;RP11-15J10.1,downstream_gene_variant,,ENST00000445695,;	T	ENSG00000204779	ENST00000377420	Transcript	missense_variant	1670	838	280	G/R	Ggg/Agg	rs781582393	.	.	-1	FOXD4L5	HGNC	18522	protein_coding	YES	CCDS47977.1	ENSP00000366637	FX4L5_HUMAN	Q8WTR0_HUMAN	UPI0000458A33	.	tolerated(0.08)	benign(0.126)	1/1	.	hmmpanther:PTHR11829:SF149,hmmpanther:PTHR11829	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGCCCCGGCAT	byFrequency	3	ESCA
SPATA31D1	0	.	GRCh37	9	84608402	84608402	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3017C>A	p.Ser1006Tyr	p.S1006Y	ENST00000344803	4/4	68	51	17	60	60	0	SPATA31D1,missense_variant,p.Ser1006Tyr,ENST00000344803,;SPATA31D1,downstream_gene_variant,,ENST00000603921,;	A	ENSG00000214929	ENST00000344803	Transcript	missense_variant	3064	3017	1006	S/Y	tCt/tAt	.	.	.	1	SPATA31D1	HGNC	37283	protein_coding	YES	CCDS47986.1	ENSP00000341988	S31D1_HUMAN	.	UPI00001C10A6	.	deleterious(0.02)	probably_damaging(0.919)	4/4	.	hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTCTGATA	.	5	ESCA
SPIN1	0	.	GRCh37	9	91041391	91041391	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-64A>T	.	.	ENST00000375859	2/6	22	5	17	13	13	0	SPIN1,5_prime_UTR_variant,,ENST00000375859,;SPIN1,5_prime_UTR_variant,,ENST00000541629,;SPIN1,non_coding_transcript_exon_variant,,ENST00000485565,;SPIN1,non_coding_transcript_exon_variant,,ENST00000469017,;SPIN1,non_coding_transcript_exon_variant,,ENST00000483785,;SPIN1,non_coding_transcript_exon_variant,,ENST00000462844,;SPIN1,intron_variant,,ENST00000485804,;	T	ENSG00000106723	ENST00000375859	Transcript	5_prime_UTR_variant	215	.	.	.	.	.	.	.	1	SPIN1	HGNC	11243	protein_coding	YES	CCDS43843.1	ENSP00000365019	SPIN1_HUMAN	.	UPI000006DD5B	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCAAATTGG	.	5	ESCA
MUM1L1	0	.	GRCh37	X	105450626	105450626	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1201C>G	p.Gln401Glu	p.Q401E	ENST00000337685	5/5	48	23	25	22	22	0	MUM1L1,missense_variant,p.Gln401Glu,ENST00000357175,;MUM1L1,missense_variant,p.Gln401Glu,ENST00000337685,;MUM1L1,missense_variant,p.Gln401Glu,ENST00000372552,;	G	ENSG00000157502	ENST00000337685	Transcript	missense_variant	1986	1201	401	Q/E	Cag/Gag	.	.	.	1	MUM1L1	HGNC	26583	protein_coding	YES	CCDS55469.1	ENSP00000338641	MUML1_HUMAN	.	UPI0000212206	.	deleterious(0.01)	benign(0.266)	5/5	.	hmmpanther:PTHR31333,hmmpanther:PTHR31333:SF3,Gene3D:2.30.30.160,Pfam_domain:PF00855,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCAGAAA	.	5	ESCA
SPANXN3	0	.	GRCh37	X	142596594	142596594	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50G>A	.	.	ENST00000370503	2/2	54	35	19	30	30	0	SPANXN3,3_prime_UTR_variant,,ENST00000370503,;GS1-256O22.5,intron_variant,,ENST00000431432,;	T	ENSG00000189252	ENST00000370503	Transcript	3_prime_UTR_variant	560	.	.	.	.	.	.	.	-1	SPANXN3	HGNC	33176	protein_coding	YES	CCDS35418.1	ENSP00000359534	SPXN3_HUMAN	.	UPI000016004A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAATCATCGC	.	5	ESCA
HEPH	0	.	GRCh37	X	65411972	65411972	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1226A>T	p.Asp409Val	p.D409V	ENST00000519389	7/21	51	33	18	19	19	0	HEPH,missense_variant,p.Asp355Val,ENST00000425114,;HEPH,missense_variant,p.Asp355Val,ENST00000343002,;HEPH,missense_variant,p.Asp409Val,ENST00000519389,;HEPH,missense_variant,p.Asp358Val,ENST00000441993,;HEPH,missense_variant,p.Asp358Val,ENST00000374727,;HEPH,missense_variant,p.Asp358Val,ENST00000419594,;HEPH,missense_variant,p.Asp88Val,ENST00000336279,;	T	ENSG00000089472	ENST00000519389	Transcript	missense_variant	1405	1226	409	D/V	gAt/gTt	.	.	.	1	HEPH	HGNC	4866	protein_coding	YES	CCDS14384.3	ENSP00000430620	HEPH_HUMAN	Q5JZ07_HUMAN,Q1HE23_HUMAN,B4DFV3_HUMAN	UPI0001C06560	.	deleterious(0.01)	benign(0.097)	7/21	.	Superfamily_domains:SSF49503,Gene3D:2.60.40.420,PROSITE_patterns:PS00079,hmmpanther:PTHR10127:SF317,hmmpanther:PTHR10127	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAGATGGCA	.	5	ESCA
DDX3Y	0	.	GRCh37	Y	15030207	15030207	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*173G>A	.	.	ENST00000336079	17/17	32	15	17	19	19	0	DDX3Y,3_prime_UTR_variant,,ENST00000360160,;DDX3Y,3_prime_UTR_variant,,ENST00000336079,;DDX3Y,downstream_gene_variant,,ENST00000440554,;DDX3Y,downstream_gene_variant,,ENST00000454054,;DDX3Y,downstream_gene_variant,,ENST00000472510,;DDX3Y,downstream_gene_variant,,ENST00000463199,;DDX3Y,downstream_gene_variant,,ENST00000469101,;DDX3Y,downstream_gene_variant,,ENST00000495478,;	A	ENSG00000067048	ENST00000336079	Transcript	3_prime_UTR_variant	2262	.	.	.	.	.	.	.	1	DDX3Y	HGNC	2699	protein_coding	YES	CCDS14782.1	ENSP00000336725	DDX3Y_HUMAN	C9J8G5_HUMAN	UPI00000741D9	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACAGCAGCC	.	5	ESCA
RBMY2FP	0	.	GRCh37	Y	24460678	24460678	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A49L-01A-11D-A247-09	TCGA-LN-A49L-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.368G>T	.	.	ENST00000303922	4/4	116	65	51	94	94	0	RBMY1J,intron_variant,,ENST00000414629,;RBMY1J,intron_variant,,ENST00000445779,;RBMY2FP,non_coding_transcript_exon_variant,,ENST00000303922,;RBMY2FP,non_coding_transcript_exon_variant,,ENST00000420346,;	T	ENSG00000243040	ENST00000303922	Transcript	non_coding_transcript_exon_variant	368	.	.	.	.	.	.	.	1	RBMY2FP	HGNC	23891	processed_transcript	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAAGAAACC	.	5	ESCA
CACUL1	0	.	GRCh37	10	120442047	120442047	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3593C>G	.	.	ENST00000369151	9/9	30	8	22	33	33	0	CACUL1,3_prime_UTR_variant,,ENST00000369151,;CACUL1,intron_variant,,ENST00000544392,;CACUL1,downstream_gene_variant,,ENST00000490610,;CACUL1,downstream_gene_variant,,ENST00000489169,;CACUL1,downstream_gene_variant,,ENST00000493518,;	C	ENSG00000151893	ENST00000369151	Transcript	3_prime_UTR_variant	5187	.	.	.	.	.	.	.	-1	CACUL1	HGNC	23727	protein_coding	YES	CCDS41570.1	ENSP00000358147	CACL1_HUMAN	.	UPI000000DCD0	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGAAACC	.	5	ESCA
TUBGCP2	0	.	GRCh37	10	135111525	135111525	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547G>C	p.Glu183Gln	p.E183Q	ENST00000543663	4/18	41	23	18	60	60	0	TUBGCP2,missense_variant,p.Glu183Gln,ENST00000252936,;TUBGCP2,missense_variant,p.Glu53Gln,ENST00000417178,;TUBGCP2,missense_variant,p.Glu183Gln,ENST00000368563,;TUBGCP2,missense_variant,p.Glu183Gln,ENST00000543663,;RP11-122K13.12,upstream_gene_variant,,ENST00000424450,;TUBGCP2,downstream_gene_variant,,ENST00000470829,;TUBGCP2,missense_variant,p.Glu183Gln,ENST00000482278,;TUBGCP2,3_prime_UTR_variant,,ENST00000487796,;TUBGCP2,downstream_gene_variant,,ENST00000480198,;	G	ENSG00000130640	ENST00000543663	Transcript	missense_variant	587	547	183	E/Q	Gag/Cag	.	.	.	-1	TUBGCP2	HGNC	18599	protein_coding	YES	CCDS58105.1	ENSP00000446093	GCP2_HUMAN	B3KTU7_HUMAN	UPI00020651C0	.	tolerated(0.12)	benign(0.109)	4/18	.	hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCATACA	.	5	ESCA
LRRTM3	0	.	GRCh37	10	68857428	68857428	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1620C>T	p.%3D	p.L540L	ENST00000361320	3/3	63	45	17	62	62	0	LRRTM3,synonymous_variant,p.%3D,ENST00000361320,;CTNNA3,intron_variant,,ENST00000433211,;CTNNA3,intron_variant,,ENST00000494580,;CTNNA3,intron_variant,,ENST00000373744,;LRRTM3,non_coding_transcript_exon_variant,,ENST00000485868,;	T	ENSG00000198739	ENST00000361320	Transcript	synonymous_variant	2198	1620	540	L	ctC/ctT	.	.	.	1	LRRTM3	HGNC	19410	protein_coding	YES	CCDS7270.1	ENSP00000355187	LRRT3_HUMAN	B4DFC3_HUMAN	UPI0000088C0F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCTCCCA	.	5	ESCA
LRRTM3	0	.	GRCh37	10	68857926	68857926	+	3'UTR	SNP	C	C	T	rs540200181	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*372C>T	.	.	ENST00000361320	3/3	31	23	8	40	40	0	LRRTM3,3_prime_UTR_variant,,ENST00000361320,;CTNNA3,intron_variant,,ENST00000433211,;CTNNA3,intron_variant,,ENST00000494580,;CTNNA3,intron_variant,,ENST00000373744,;LRRTM3,downstream_gene_variant,,ENST00000485868,;	T	ENSG00000198739	ENST00000361320	Transcript	3_prime_UTR_variant	2696	.	.	.	.	rs540200181	.	.	1	LRRTM3	HGNC	19410	protein_coding	YES	CCDS7270.1	ENSP00000355187	LRRT3_HUMAN	B4DFC3_HUMAN	UPI0000088C0F	.	.	.	3/3	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTACATTTT	by1000G	5	ESCA
MYPN	0	.	GRCh37	10	69961659	69961659	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3567G>A	p.%3D	p.V1189V	ENST00000358913	18/20	21	14	6	16	16	0	MYPN,synonymous_variant,p.%3D,ENST00000358913,;MYPN,synonymous_variant,p.%3D,ENST00000540630,;MYPN,synonymous_variant,p.%3D,ENST00000354393,;	A	ENSG00000138347	ENST00000358913	Transcript	synonymous_variant	4055	3567	1189	V	gtG/gtA	.	.	.	1	MYPN	HGNC	23246	protein_coding	YES	CCDS7275.1	ENSP00000351790	MYPN_HUMAN	A5PKT7_HUMAN	UPI00002288CF	.	.	.	18/20	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00408,Gene3D:2.60.40.10,Pfam_domain:PF07679,hmmpanther:PTHR19897,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGTGAGACT	.	5	ESCA
DDX21	0	.	GRCh37	10	70716052	70716052	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71G>C	p.Arg24Pro	p.R24P	ENST00000354185	1/15	14	9	4	17	17	0	DDX21,missense_variant,p.Arg24Pro,ENST00000354185,;	C	ENSG00000165732	ENST00000354185	Transcript	missense_variant	169	71	24	R/P	cGa/cCa	.	.	.	1	DDX21	HGNC	2744	protein_coding	YES	CCDS31211.1	ENSP00000346120	DDX21_HUMAN	Q8NI92_HUMAN	UPI00001A92E8	.	tolerated_low_confidence(0.15)	benign(0.004)	1/15	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	ACTGCGAAAGC	.	4	ESCA
VCL	0	.	GRCh37	10	75802874	75802874	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202C>T	p.Gln68Ter	p.Q68*	ENST00000211998	2/22	41	24	16	58	58	0	VCL,stop_gained,p.Gln68Ter,ENST00000211998,;VCL,stop_gained,p.Gln68Ter,ENST00000417648,;VCL,stop_gained,p.Gln68Ter,ENST00000372755,;VCL,non_coding_transcript_exon_variant,,ENST00000478896,;VCL,non_coding_transcript_exon_variant,,ENST00000461383,;	T	ENSG00000035403	ENST00000211998	Transcript	stop_gained	296	202	68	Q/*	Cag/Tag	.	.	.	1	VCL	HGNC	12665	protein_coding	YES	CCDS7341.1	ENSP00000211998	VINC_HUMAN	Q5JQ13_HUMAN	UPI0000167B54	.	.	.	2/22	.	hmmpanther:PTHR18914:SF22,hmmpanther:PTHR18914,Pfam_domain:PF01044,Gene3D:1.20.1490.10,Superfamily_domains:SSF47220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATCAGATT	.	5	ESCA
C10orf62	0	.	GRCh37	10	99350597	99350597	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*271G>A	.	.	ENST00000370640	1/1	20	12	7	19	19	0	C10orf62,3_prime_UTR_variant,,ENST00000370640,;HOGA1,intron_variant,,ENST00000370647,;PI4K2A,intron_variant,,ENST00000370649,;HOGA1,intron_variant,,ENST00000370646,;PI4K2A,intron_variant,,ENST00000555577,;HOGA1,intron_variant,,ENST00000465608,;	A	ENSG00000203942	ENST00000370640	Transcript	3_prime_UTR_variant	1148	.	.	.	.	.	.	.	1	C10orf62	HGNC	23294	protein_coding	YES	CCDS31261.1	ENSP00000359674	CJ062_HUMAN	.	UPI000046FEE3	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTGAAGAC	.	5	ESCA
GRIA4	0	.	GRCh37	11	105852150	105852150	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1684G>A	.	.	ENST00000282499	17/17	14	7	7	17	17	0	GRIA4,3_prime_UTR_variant,,ENST00000282499,;GRIA4,3_prime_UTR_variant,,ENST00000530497,;GRIA4,3_prime_UTR_variant,,ENST00000393127,;GRIA4,downstream_gene_variant,,ENST00000525187,;GRIA4,downstream_gene_variant,,ENST00000533094,;	A	ENSG00000152578	ENST00000282499	Transcript	3_prime_UTR_variant	4839	.	.	.	.	.	.	.	1	GRIA4	HGNC	4574	protein_coding	YES	CCDS8333.1	ENSP00000282499	GRIA4_HUMAN	E9PJZ5_HUMAN	UPI000013DCE6	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACTGAGAGT	.	5	ESCA
EIF4G2	0	.	GRCh37	11	10825579	10825579	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569A>T	p.Asn190Ile	p.N190I	ENST00000526148	8/22	31	14	16	49	49	0	EIF4G2,missense_variant,p.Asn190Ile,ENST00000531416,;EIF4G2,missense_variant,p.Asn190Ile,ENST00000525681,;EIF4G2,missense_variant,p.Asn190Ile,ENST00000396525,;EIF4G2,missense_variant,p.Asn190Ile,ENST00000532082,;EIF4G2,missense_variant,p.Asn190Ile,ENST00000339995,;EIF4G2,missense_variant,p.Asn190Ile,ENST00000526148,;EIF4G2,missense_variant,p.Asn190Ile,ENST00000524932,;EIF4G2,downstream_gene_variant,,ENST00000527526,;EIF4G2,upstream_gene_variant,,ENST00000531180,;EIF4G2,downstream_gene_variant,,ENST00000530702,;EIF4G2,upstream_gene_variant,,ENST00000528839,;EIF4G2,downstream_gene_variant,,ENST00000527419,;EIF4G2,downstream_gene_variant,,ENST00000532570,;EIF4G2,downstream_gene_variant,,ENST00000530211,;SNORD97,upstream_gene_variant,,ENST00000459187,;RP11-685M7.5,downstream_gene_variant,,ENST00000532365,;EIF4G2,downstream_gene_variant,,ENST00000531507,;EIF4G2,upstream_gene_variant,,ENST00000534272,;EIF4G2,downstream_gene_variant,,ENST00000525995,;EIF4G2,upstream_gene_variant,,ENST00000532120,;EIF4G2,downstream_gene_variant,,ENST00000525972,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000527015,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000532349,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000532383,;EIF4G2,intron_variant,,ENST00000531647,;EIF4G2,downstream_gene_variant,,ENST00000534246,;EIF4G2,downstream_gene_variant,,ENST00000533485,;EIF4G2,upstream_gene_variant,,ENST00000534470,;EIF4G2,upstream_gene_variant,,ENST00000525606,;EIF4G2,downstream_gene_variant,,ENST00000528562,;EIF4G2,downstream_gene_variant,,ENST00000534605,;EIF4G2,upstream_gene_variant,,ENST00000530564,;EIF4G2,downstream_gene_variant,,ENST00000532152,;	A	ENSG00000110321	ENST00000526148	Transcript	missense_variant	1080	569	190	N/I	aAt/aTt	.	.	.	-1	EIF4G2	HGNC	3297	protein_coding	YES	CCDS31428.1	ENSP00000433664	.	Q59G42_HUMAN,Q2TU89_HUMAN,H0YEN8_HUMAN,H0YEC5_HUMAN,H0YDC0_HUMAN,H0YD99_HUMAN,H0YD77_HUMAN,H0YCF8_HUMAN,D3DQV9_HUMAN,B4DZF2_HUMAN	UPI000013C8BE	.	deleterious(0)	benign(0.08)	8/22	.	hmmpanther:PTHR23253,Gene3D:1.25.40.180,Pfam_domain:PF02854,SMART_domains:SM00543,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGATTTTCA	.	5	ESCA
USP28	0	.	GRCh37	11	113672343	113672343	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2920G>A	p.Glu974Lys	p.E974K	ENST00000003302	24/25	30	12	17	31	31	0	USP28,missense_variant,p.Glu974Lys,ENST00000003302,;USP28,missense_variant,p.Glu817Lys,ENST00000545540,;USP28,missense_variant,p.Glu942Lys,ENST00000260188,;USP28,missense_variant,p.Glu650Lys,ENST00000544967,;USP28,downstream_gene_variant,,ENST00000538224,;USP28,3_prime_UTR_variant,,ENST00000540438,;USP28,non_coding_transcript_exon_variant,,ENST00000544272,;	T	ENSG00000048028	ENST00000003302	Transcript	missense_variant	2989	2920	974	E/K	Gag/Aag	.	.	.	-1	USP28	HGNC	12625	protein_coding	YES	CCDS31680.1	ENSP00000003302	UBP28_HUMAN	Q96SV4_HUMAN	UPI0000137A00	.	tolerated(0.1)	probably_damaging(0.989)	24/25	.	hmmpanther:PTHR24006:SF110,hmmpanther:PTHR24006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCAGTTA	.	5	ESCA
KCNC1	0	.	GRCh37	11	17794205	17794205	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1504+60G>C	.	.	ENST00000265969	.	43	23	19	57	57	0	KCNC1,3_prime_UTR_variant,,ENST00000379472,;KCNC1,intron_variant,,ENST00000265969,;KCNC1,upstream_gene_variant,,ENST00000525802,;	C	ENSG00000129159	ENST00000265969	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KCNC1	HGNC	6233	protein_coding	YES	CCDS44547.1	ENSP00000265969	.	K4DI87_HUMAN	UPI0000E2291F	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGATGATTCC	.	5	ESCA
WT1	0	.	GRCh37	11	32452269	32452269	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647-2104G>T	.	.	ENST00000332351	.	11	5	6	12	12	0	WT1,5_prime_UTR_variant,,ENST00000379079,;WT1,5_prime_UTR_variant,,ENST00000530998,;WT1,intron_variant,,ENST00000332351,;WT1,intron_variant,,ENST00000448076,;WT1,intron_variant,,ENST00000452863,;WT1,upstream_gene_variant,,ENST00000527775,;WT1-AS,upstream_gene_variant,,ENST00000395900,;WT1-AS,upstream_gene_variant,,ENST00000494911,;WT1,intron_variant,,ENST00000379077,;	A	ENSG00000184937	ENST00000332351	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	WT1	HGNC	12796	protein_coding	YES	CCDS7878.2	ENSP00000331327	.	Q6LBI3_HUMAN,J3KNN9_HUMAN,H0Y3F0_HUMAN,E9PPW3_HUMAN,E9PKS2_HUMAN,A8MN20_HUMAN,A0FJ58_HUMAN,A0FJ57_HUMAN	UPI0000D625D7	.	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCCTCCTCCC	.	3	ESCA
OR4C6	0	.	GRCh37	11	55432918	55432918	+	Silent	SNP	C	C	T	rs748058915	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.276C>T	p.%3D	p.L92L	ENST00000314259	1/1	22	18	4	21	21	0	OR4C6,synonymous_variant,p.%3D,ENST00000314259,;	T	ENSG00000181903	ENST00000314259	Transcript	synonymous_variant	305	276	92	L	ctC/ctT	rs748058915,COSM688898,COSM458558	.	.	1	OR4C6	HGNC	14743	protein_coding	YES	CCDS31506.1	ENSP00000324769	OR4C6_HUMAN	.	UPI0000041868	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF80,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTCTCAAAGG	.	4	ESCA
DAGLA	0	.	GRCh37	11	61491028	61491028	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.532C>T	p.Arg178Trp	p.R178W	ENST00000257215	5/20	37	27	10	24	24	0	DAGLA,missense_variant,p.Arg178Trp,ENST00000257215,;DAGLA,3_prime_UTR_variant,,ENST00000540717,;	T	ENSG00000134780	ENST00000257215	Transcript	missense_variant	648	532	178	R/W	Cgg/Tgg	COSM4034628	.	.	1	DAGLA	HGNC	1165	protein_coding	YES	CCDS31578.1	ENSP00000257215	DGLA_HUMAN	.	UPI00001678B3	.	deleterious(0)	possibly_damaging(0.846)	5/20	.	hmmpanther:PTHR21493,hmmpanther:PTHR21493:SF87	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTGCGGACC	.	5	ESCA
AHNAK	0	.	GRCh37	11	62289859	62289859	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12030G>C	p.%3D	p.L4010L	ENST00000378024	5/5	119	84	35	99	99	0	AHNAK,synonymous_variant,p.%3D,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;	G	ENSG00000124942	ENST00000378024	Transcript	synonymous_variant	12305	12030	4010	L	ctG/ctC	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	.	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTCAGATG	.	5	ESCA
AHNAK	0	.	GRCh37	11	62290087	62290087	+	Missense_Mutation	SNP	C	C	A	rs199930235	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11802G>T	p.Lys3934Asn	p.K3934N	ENST00000378024	5/5	147	91	56	107	107	0	AHNAK,missense_variant,p.Lys3934Asn,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;	A	ENSG00000124942	ENST00000378024	Transcript	missense_variant	12077	11802	3934	K/N	aaG/aaT	rs199930235	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	probably_damaging(0.999)	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATCTTAGG	byCluster|by1000G	5	ESCA
AHNAK	0	.	GRCh37	11	62299163	62299163	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2726C>A	p.Ser909Ter	p.S909*	ENST00000378024	5/5	146	106	40	136	136	0	AHNAK,stop_gained,p.Ser909Ter,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000531324,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000528508,;	T	ENSG00000124942	ENST00000378024	Transcript	stop_gained	3001	2726	909	S/*	tCa/tAa	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	.	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTGAGATG	.	5	ESCA
TAF6L	0	.	GRCh37	11	62554015	62554015	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1116G>A	p.Met372Ile	p.M372I	ENST00000294168	11/11	17	13	4	11	11	0	TAF6L,missense_variant,p.Met372Ile,ENST00000294168,;TMEM223,intron_variant,,ENST00000528367,;TMEM179B,upstream_gene_variant,,ENST00000526546,;TMEM179B,upstream_gene_variant,,ENST00000533861,;TMEM223,downstream_gene_variant,,ENST00000525631,;TMEM179B,upstream_gene_variant,,ENST00000333449,;TMEM223,downstream_gene_variant,,ENST00000307366,;RP11-727F15.12,non_coding_transcript_exon_variant,,ENST00000601484,;TMEM223,intron_variant,,ENST00000527073,;TMEM179B,upstream_gene_variant,,ENST00000532586,;TAF6L,downstream_gene_variant,,ENST00000533823,;TAF6L,downstream_gene_variant,,ENST00000531265,;TAF6L,downstream_gene_variant,,ENST00000524976,;TMEM179B,upstream_gene_variant,,ENST00000532345,;	A	ENSG00000162227	ENST00000294168	Transcript	missense_variant	1317	1116	372	M/I	atG/atA	.	.	.	1	TAF6L	HGNC	17305	protein_coding	YES	CCDS8035.1	ENSP00000294168	TAF6L_HUMAN	E9PP94_HUMAN,E9PLV8_HUMAN	UPI00000720C0	.	tolerated(0.27)	benign(0.002)	11/11	.	hmmpanther:PTHR10221:SF9,hmmpanther:PTHR10221	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AAGATGAAGGC	.	4	ESCA
FLRT1	0	.	GRCh37	11	63886343	63886343	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*579G>C	.	.	ENST00000246841	2/2	50	33	16	41	41	0	FLRT1,3_prime_UTR_variant,,ENST00000246841,;MACROD1,intron_variant,,ENST00000255681,;RP11-21A7A.3,intron_variant,,ENST00000543817,;MACROD1,intron_variant,,ENST00000543422,;MACROD1,intron_variant,,ENST00000542359,;MACROD1,intron_variant,,ENST00000545464,;	C	ENSG00000126500	ENST00000246841	Transcript	3_prime_UTR_variant	3647	.	.	.	.	.	.	.	1	FLRT1	HGNC	3760	protein_coding	YES	CCDS8057.1	ENSP00000246841	FLRT1_HUMAN	O43408_HUMAN	UPI0000039F94	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCAGATTTG	.	5	ESCA
PYGM	0	.	GRCh37	11	64527313	64527313	+	Missense_Mutation	SNP	C	C	G	rs775674324	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>C	p.Ala20Pro	p.A20P	ENST00000164139	1/20	74	51	23	47	47	0	PYGM,missense_variant,p.Ala20Pro,ENST00000164139,;PYGM,missense_variant,p.Ala20Pro,ENST00000377432,;SF1,downstream_gene_variant,,ENST00000377394,;SF1,downstream_gene_variant,,ENST00000227503,;SF1,downstream_gene_variant,,ENST00000377390,;SF1,downstream_gene_variant,,ENST00000377387,;SF1,downstream_gene_variant,,ENST00000334944,;SF1,downstream_gene_variant,,ENST00000448404,;	G	ENSG00000068976	ENST00000164139	Transcript	missense_variant	457	58	20	A/P	Gcc/Ccc	rs775674324	.	.	-1	PYGM	HGNC	9726	protein_coding	YES	CCDS8079.1	ENSP00000164139	PYGM_HUMAN	.	UPI000013C5AC	.	tolerated(0.09)	probably_damaging(0.996)	1/20	.	PIRSF_domain:PIRSF000460,hmmpanther:PTHR11468:SF1,hmmpanther:PTHR11468	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGGCCAGGC	.	5	ESCA
EHD1	0	.	GRCh37	11	64621765	64621765	+	3'UTR	SNP	C	C	T	rs554327697	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*40G>A	.	.	ENST00000320631	5/5	64	38	26	44	44	0	EHD1,3_prime_UTR_variant,,ENST00000359393,;EHD1,3_prime_UTR_variant,,ENST00000320631,;EHD1,downstream_gene_variant,,ENST00000421510,;EHD1,downstream_gene_variant,,ENST00000433803,;EHD1,non_coding_transcript_exon_variant,,ENST00000488711,;EHD1,non_coding_transcript_exon_variant,,ENST00000484846,;EHD1,downstream_gene_variant,,ENST00000498472,;	T	ENSG00000110047	ENST00000320631	Transcript	3_prime_UTR_variant	1900	.	.	.	.	rs554327697	.	.	-1	EHD1	HGNC	3242	protein_coding	YES	CCDS8084.1	ENSP00000320516	EHD1_HUMAN	C9JIJ3_HUMAN,C9JDQ8_HUMAN,C9J2Z4_HUMAN,C9IZH1_HUMAN,B2R5U3_HUMAN	UPI0000129E22	.	.	.	5/5	.	.	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCCGGCCG	by1000G	5	ESCA
NDUFS8	0	.	GRCh37	11	67800424	67800424	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144G>T	p.Met48Ile	p.M48I	ENST00000313468	4/7	77	49	27	48	48	0	NDUFS8,missense_variant,p.Met48Ile,ENST00000453471,;NDUFS8,missense_variant,p.Met48Ile,ENST00000526339,;NDUFS8,missense_variant,p.Met48Ile,ENST00000313468,;NDUFS8,missense_variant,p.Met48Ile,ENST00000525628,;NDUFS8,missense_variant,p.Met30Ile,ENST00000525419,;NDUFS8,intron_variant,,ENST00000528492,;ALDH3B1,downstream_gene_variant,,ENST00000342456,;ALDH3B1,downstream_gene_variant,,ENST00000539229,;ALDH3B1,downstream_gene_variant,,ENST00000007633,;ALDH3B1,downstream_gene_variant,,ENST00000316367,;MIR4691,upstream_gene_variant,,ENST00000583764,;RP5-901A4.1,upstream_gene_variant,,ENST00000532296,;ALDH3B1,downstream_gene_variant,,ENST00000433100,;ALDH3B1,downstream_gene_variant,,ENST00000527179,;ALDH3B1,downstream_gene_variant,,ENST00000530046,;NDUFS8,upstream_gene_variant,,ENST00000526542,;ALDH3B1,downstream_gene_variant,,ENST00000531459,;ALDH3B1,downstream_gene_variant,,ENST00000434449,;NDUFS8,stop_gained,p.Glu67Ter,ENST00000531228,;NDUFS8,3_prime_UTR_variant,,ENST00000529645,;NDUFS8,3_prime_UTR_variant,,ENST00000526446,;NDUFS8,non_coding_transcript_exon_variant,,ENST00000432321,;NDUFS8,non_coding_transcript_exon_variant,,ENST00000532399,;NDUFS8,upstream_gene_variant,,ENST00000524810,;NDUFS8,downstream_gene_variant,,ENST00000531796,;NDUFS8,upstream_gene_variant,,ENST00000531282,;ALDH3B1,downstream_gene_variant,,ENST00000529232,;	T	ENSG00000110717	ENST00000313468	Transcript	missense_variant	251	144	48	M/I	atG/atT	.	.	.	1	NDUFS8	HGNC	7715	protein_coding	YES	CCDS8176.1	ENSP00000315774	NDUS8_HUMAN	Q08E91_HUMAN,F8W9K7_HUMAN,E9PPW7_HUMAN,E9PN51_HUMAN	UPI000013094B	.	tolerated_low_confidence(0.45)	benign(0.004)	4/7	.	hmmpanther:PTHR10849	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACATGAAGTC	.	5	ESCA
IGHMBP2	0	.	GRCh37	11	68707045	68707045	+	Missense_Mutation	SNP	G	G	C	rs779871930	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2828G>C	p.Arg943Thr	p.R943T	ENST00000255078	15/15	94	63	31	59	59	0	IGHMBP2,missense_variant,p.Arg943Thr,ENST00000255078,;RP11-757G1.5,downstream_gene_variant,,ENST00000542410,;IGHMBP2,downstream_gene_variant,,ENST00000541229,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000544521,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000543739,;IGHMBP2,downstream_gene_variant,,ENST00000545475,;IGHMBP2,downstream_gene_variant,,ENST00000539064,;	C	ENSG00000132740	ENST00000255078	Transcript	missense_variant	2939	2828	943	R/T	aGa/aCa	rs779871930,COSM931332	.	.	1	IGHMBP2	HGNC	5542	protein_coding	YES	CCDS8187.1	ENSP00000255078	SMBP2_HUMAN	F5H5K3_HUMAN	UPI000013CE82	.	tolerated(0.08)	benign(0.142)	15/15	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF140,Gene3D:4.10.1110.10,Superfamily_domains:SSF118310	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGAGAATCA	.	5	ESCA
RSF1	0	.	GRCh37	11	77383154	77383154	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3684G>A	p.%3D	p.K1228K	ENST00000308488	15/16	35	16	18	51	51	0	RSF1,synonymous_variant,p.%3D,ENST00000480887,;RSF1,synonymous_variant,p.%3D,ENST00000308488,;RSF1,synonymous_variant,p.%3D,ENST00000360355,;RSF1,downstream_gene_variant,,ENST00000531026,;RSF1,downstream_gene_variant,,ENST00000529470,;	T	ENSG00000048649	ENST00000308488	Transcript	synonymous_variant	3987	3684	1228	K	aaG/aaA	.	.	.	-1	RSF1	HGNC	18118	protein_coding	YES	CCDS8253.1	ENSP00000311513	RSF1_HUMAN	H0YER1_HUMAN,H0YDG9_HUMAN,H0YCN2_HUMAN	UPI00001FB001	.	.	.	15/16	.	hmmpanther:PTHR10615,hmmpanther:PTHR10615:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTCTTCTG	.	5	ESCA
SYTL2	0	.	GRCh37	11	85437481	85437481	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19G>A	p.Glu7Lys	p.E7K	ENST00000354566	1/13	25	16	9	27	27	0	SYTL2,missense_variant,p.Glu531Lys,ENST00000359152,;SYTL2,missense_variant,p.Glu7Lys,ENST00000525423,;SYTL2,missense_variant,p.Glu7Lys,ENST00000354566,;SYTL2,intron_variant,,ENST00000528231,;SYTL2,intron_variant,,ENST00000389960,;SYTL2,intron_variant,,ENST00000527523,;SYTL2,intron_variant,,ENST00000524452,;SYTL2,intron_variant,,ENST00000316356,;SYTL2,upstream_gene_variant,,ENST00000530351,;SYTL2,missense_variant,p.Glu7Lys,ENST00000389959,;	T	ENSG00000137501	ENST00000354566	Transcript	missense_variant	31	19	7	E/K	Gaa/Aaa	.	.	.	-1	SYTL2	HGNC	15585	protein_coding	YES	CCDS31651.1	ENSP00000346576	SYTL2_HUMAN	Q9BQS1_HUMAN,E9PS39_HUMAN,E9PS29_HUMAN,E9PRW5_HUMAN,E9PK22_HUMAN	UPI0000352C78	.	tolerated_low_confidence(0.1)	benign(0.175)	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTCTGCAT	.	5	ESCA
TXNRD1	0	.	GRCh37	12	104742133	104742133	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1884A>G	p.%3D	p.V628V	ENST00000525566	17/17	56	42	14	55	55	0	TXNRD1,synonymous_variant,p.%3D,ENST00000354940,;TXNRD1,synonymous_variant,p.%3D,ENST00000388854,;TXNRD1,synonymous_variant,p.%3D,ENST00000529546,;TXNRD1,synonymous_variant,p.%3D,ENST00000526950,;TXNRD1,synonymous_variant,p.%3D,ENST00000526691,;TXNRD1,synonymous_variant,p.%3D,ENST00000524698,;TXNRD1,synonymous_variant,p.%3D,ENST00000429002,;TXNRD1,synonymous_variant,p.%3D,ENST00000526390,;TXNRD1,synonymous_variant,p.%3D,ENST00000427956,;TXNRD1,synonymous_variant,p.%3D,ENST00000397736,;TXNRD1,synonymous_variant,p.%3D,ENST00000503506,;TXNRD1,synonymous_variant,p.%3D,ENST00000525566,;TXNRD1,synonymous_variant,p.%3D,ENST00000542918,;TXNRD1,synonymous_variant,p.%3D,ENST00000540716,;TXNRD1,splice_region_variant,,ENST00000378070,;TXNRD1,splice_region_variant,,ENST00000525265,;TXNRD1,splice_region_variant,,ENST00000527688,;	G	ENSG00000198431	ENST00000525566	Transcript	synonymous_variant	1908	1884	628	V	gtA/gtG	.	.	.	1	TXNRD1	HGNC	12437	protein_coding	YES	CCDS53820.1	ENSP00000434516	TRXR1_HUMAN	F5H780_HUMAN,E9PRI8_HUMAN,E9PQI3_HUMAN,E9PLT3_HUMAN,E9PKI4_HUMAN,E9PKD3_HUMAN,B7Z904_HUMAN,B2R5P6_HUMAN	UPI00015294EE	.	.	.	17/17	.	Superfamily_domains:SSF55424,TIGRFAM_domain:TIGR01438,Pfam_domain:PF02852,Gene3D:3.30.390.30,hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF129	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGTATTCAC	.	5	ESCA
PTPN11	0	.	GRCh37	12	112924299	112924299	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245C>A	p.%3D	p.V415V	ENST00000351677	11/16	33	20	13	30	30	0	PTPN11,synonymous_variant,p.%3D,ENST00000351677,;PTPN11,synonymous_variant,p.%3D,ENST00000392597,;	A	ENSG00000179295	ENST00000351677	Transcript	synonymous_variant	1443	1245	415	V	gtC/gtA	.	.	.	1	PTPN11	HGNC	9644	protein_coding	YES	CCDS9163.1	ENSP00000340944	PTN11_HUMAN	B3GUD4_HUMAN,B3GUD3_HUMAN	UPI000013296E	.	.	.	11/16	.	PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF150,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,PIRSF_domain:PIRSF000929,SMART_domains:SM00404,Superfamily_domains:SSF52799,Prints_domain:PR00700	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGGTCTGGCA	.	5	ESCA
PXN	0	.	GRCh37	12	120651990	120651990	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351C>T	p.His451Tyr	p.H451Y	ENST00000267257	9/11	49	26	22	40	40	0	PXN,missense_variant,p.His437Tyr,ENST00000228307,;PXN,missense_variant,p.His270Tyr,ENST00000458477,;PXN,missense_variant,p.His451Tyr,ENST00000267257,;PXN,missense_variant,p.His403Tyr,ENST00000424649,;PXN,missense_variant,p.His249Tyr,ENST00000397506,;PXN,missense_variant,p.His435Tyr,ENST00000536957,;PXN,downstream_gene_variant,,ENST00000550795,;PXN-AS1,downstream_gene_variant,,ENST00000535200,;PXN-AS1,downstream_gene_variant,,ENST00000539446,;PXN-AS1,downstream_gene_variant,,ENST00000538804,;PXN-AS1,downstream_gene_variant,,ENST00000542314,;PXN-AS1,downstream_gene_variant,,ENST00000542265,;PXN,non_coding_transcript_exon_variant,,ENST00000538144,;PXN,non_coding_transcript_exon_variant,,ENST00000323871,;	A	ENSG00000089159	ENST00000267257	Transcript	missense_variant	1482	1351	451	H/Y	Cac/Tac	.	.	.	-1	PXN	HGNC	9718	protein_coding	YES	CCDS58281.1	ENSP00000267257	PAXI_HUMAN	F8W1E0_HUMAN,F8W0K8_HUMAN,F8W0G0_HUMAN	UPI000013C8CD	.	deleterious(0)	probably_damaging(1)	9/11	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24216,hmmpanther:PTHR24216:SF11,PROSITE_patterns:PS00478,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGTGCCACG	.	5	ESCA
CACNB3	0	.	GRCh37	12	49217550	49217550	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255C>G	p.%3D	p.V85V	ENST00000301050	3/13	43	28	14	57	57	0	CACNB3,synonymous_variant,p.%3D,ENST00000547392,;CACNB3,synonymous_variant,p.%3D,ENST00000548279,;CACNB3,synonymous_variant,p.%3D,ENST00000301050,;CACNB3,synonymous_variant,p.%3D,ENST00000536187,;CACNB3,synonymous_variant,p.%3D,ENST00000550190,;CACNB3,synonymous_variant,p.%3D,ENST00000540990,;CACNB3,5_prime_UTR_variant,,ENST00000550064,;CACNB3,5_prime_UTR_variant,,ENST00000547818,;CACNB3,intron_variant,,ENST00000547230,;CACNB3,non_coding_transcript_exon_variant,,ENST00000550168,;CACNB3,non_coding_transcript_exon_variant,,ENST00000552022,;CACNB3,non_coding_transcript_exon_variant,,ENST00000549971,;CACNB3,synonymous_variant,p.%3D,ENST00000550391,;CACNB3,synonymous_variant,p.%3D,ENST00000548874,;CACNB3,3_prime_UTR_variant,,ENST00000551544,;CACNB3,non_coding_transcript_exon_variant,,ENST00000549226,;CACNB3,non_coding_transcript_exon_variant,,ENST00000548860,;CACNB3,non_coding_transcript_exon_variant,,ENST00000551716,;CACNB3,non_coding_transcript_exon_variant,,ENST00000547693,;CACNB3,non_coding_transcript_exon_variant,,ENST00000550771,;CACNB3,upstream_gene_variant,,ENST00000552480,;CACNB3,upstream_gene_variant,,ENST00000550483,;CACNB3,downstream_gene_variant,,ENST00000552812,;	G	ENSG00000167535	ENST00000301050	Transcript	synonymous_variant	454	255	85	V	gtC/gtG	.	.	.	1	CACNB3	HGNC	1403	protein_coding	YES	CCDS8769.1	ENSP00000301050	CACB3_HUMAN	F8VUW8_HUMAN,F8VU10_HUMAN	UPI000000D9BA	.	.	.	3/13	.	hmmpanther:PTHR11824,Gene3D:2.30.30.40,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTCAACTT	.	5	ESCA
SP7	0	.	GRCh37	12	53729473	53729473	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-43C>T	.	.	ENST00000536324	2/3	24	17	7	10	10	0	SP7,5_prime_UTR_variant,,ENST00000536324,;SP7,5_prime_UTR_variant,,ENST00000303846,;SP7,intron_variant,,ENST00000537210,;SP7,intron_variant,,ENST00000547755,;	A	ENSG00000170374	ENST00000536324	Transcript	5_prime_UTR_variant	242	.	.	.	.	.	.	.	-1	SP7	HGNC	17321	protein_coding	YES	CCDS44897.1	ENSP00000443827	SP7_HUMAN	F8VV67_HUMAN	UPI000000D7AE	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGAGAGAGC	.	5	ESCA
HOXC4	0	.	GRCh37	12	54447759	54447759	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53C>A	p.Pro18His	p.P18H	ENST00000430889	1/2	51	32	18	59	59	0	HOXC4,missense_variant,p.Pro18His,ENST00000430889,;HOXC4,missense_variant,p.Pro18His,ENST00000609810,;HOXC4,missense_variant,p.Pro18His,ENST00000303406,;RP11-834C11.3,upstream_gene_variant,,ENST00000515617,;HOXC4,downstream_gene_variant,,ENST00000507650,;	A	ENSG00000273266	ENST00000430889	Transcript	missense_variant	99	53	18	P/H	cCt/cAt	.	.	.	1	HOXC4	Uniprot_gn	5126	protein_coding	YES	CCDS8873.1	ENSP00000399808	HXC4_HUMAN	.	UPI000013E89C	.	deleterious(0)	probably_damaging(0.996)	1/2	.	hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF146	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTCCTCCAT	.	5	ESCA
PRIM1	0	.	GRCh37	12	57140622	57140622	+	Missense_Mutation	SNP	G	G	C	rs776296667	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385C>G	p.Pro129Ala	p.P129A	ENST00000338193	4/13	80	44	35	76	76	0	PRIM1,missense_variant,p.Pro132Ala,ENST00000550770,;PRIM1,missense_variant,p.Pro129Ala,ENST00000338193,;PRIM1,upstream_gene_variant,,ENST00000549549,;PRIM1,intron_variant,,ENST00000546761,;PRIM1,downstream_gene_variant,,ENST00000552408,;PRIM1,missense_variant,p.Pro129Ala,ENST00000552590,;PRIM1,non_coding_transcript_exon_variant,,ENST00000550224,;PRIM1,non_coding_transcript_exon_variant,,ENST00000548173,;	C	ENSG00000198056	ENST00000338193	Transcript	missense_variant	422	385	129	P/A	Cct/Gct	rs776296667	.	.	-1	PRIM1	HGNC	9369	protein_coding	YES	CCDS44926.1	ENSP00000350491	PRI1_HUMAN	.	UPI00001321AF	.	tolerated(0.6)	benign(0.01)	4/13	.	Superfamily_domains:SSF56747,Pfam_domain:PF01896,TIGRFAM_domain:TIGR00335,Gene3D:1v33A01,hmmpanther:PTHR10536	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTAGGACATA	byFrequency	5	ESCA
SLC16A7	0	.	GRCh37	12	60173438	60173438	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1415C>T	p.Ser472Leu	p.S472L	ENST00000261187	5/5	32	28	3	37	37	0	SLC16A7,missense_variant,p.Ser373Leu,ENST00000543448,;SLC16A7,missense_variant,p.Ser472Leu,ENST00000552432,;SLC16A7,missense_variant,p.Ser472Leu,ENST00000261187,;SLC16A7,missense_variant,p.Ser472Leu,ENST00000547379,;SLC16A7,missense_variant,p.Ser472Leu,ENST00000552024,;SLC16A7,downstream_gene_variant,,ENST00000548610,;SLC16A7,downstream_gene_variant,,ENST00000548444,;SLC16A7,3_prime_UTR_variant,,ENST00000549033,;SLC16A7,3_prime_UTR_variant,,ENST00000549928,;	T	ENSG00000118596	ENST00000261187	Transcript	missense_variant	1579	1415	472	S/L	tCa/tTa	.	.	.	1	SLC16A7	HGNC	10928	protein_coding	YES	CCDS8961.1	ENSP00000261187	MOT2_HUMAN	F8W0N3_HUMAN,F8VS95_HUMAN,F5H843_HUMAN	UPI00000722FD	.	tolerated(0.19)	benign(0.15)	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AACCTCAGAAA	.	3	ESCA
CPSF6	0	.	GRCh37	12	69663377	69663377	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*89G>T	.	.	ENST00000435070	10/10	53	37	16	47	47	0	CPSF6,3_prime_UTR_variant,,ENST00000266679,;CPSF6,3_prime_UTR_variant,,ENST00000435070,;CPSF6,3_prime_UTR_variant,,ENST00000456847,;CPSF6,downstream_gene_variant,,ENST00000551516,;	T	ENSG00000111605	ENST00000435070	Transcript	3_prime_UTR_variant	1855	.	.	.	.	.	.	.	1	CPSF6	HGNC	13871	protein_coding	YES	CCDS8988.1	ENSP00000391774	CPSF6_HUMAN	.	UPI00001FC746	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTGAACTG	.	5	ESCA
CCT2	0	.	GRCh37	12	69980553	69980553	+	Silent	SNP	C	C	T	rs780733349	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99C>T	p.%3D	p.I33I	ENST00000299300	3/16	42	28	14	64	64	0	CCT2,synonymous_variant,p.%3D,ENST00000544368,;CCT2,synonymous_variant,p.%3D,ENST00000299300,;CCT2,5_prime_UTR_variant,,ENST00000543146,;MIR3913-1,upstream_gene_variant,,ENST00000577744,;CCT2,synonymous_variant,p.%3D,ENST00000550010,;CCT2,non_coding_transcript_exon_variant,,ENST00000550455,;CCT2,non_coding_transcript_exon_variant,,ENST00000546859,;CCT2,non_coding_transcript_exon_variant,,ENST00000551620,;CCT2,non_coding_transcript_exon_variant,,ENST00000549933,;CCT2,non_coding_transcript_exon_variant,,ENST00000550638,;CCT2,non_coding_transcript_exon_variant,,ENST00000551899,;CCT2,upstream_gene_variant,,ENST00000548787,;CCT2,upstream_gene_variant,,ENST00000546850,;	T	ENSG00000166226	ENST00000299300	Transcript	synonymous_variant	287	99	33	I	atC/atT	rs780733349,COSM943019	.	.	1	CCT2	HGNC	1615	protein_coding	YES	CCDS8991.1	ENSP00000299300	TCPB_HUMAN	Q9H369_HUMAN	UPI0000136AF3	.	.	.	3/16	.	hmmpanther:PTHR11353,TIGRFAM_domain:TIGR02341,Gene3D:1.10.560.10,Superfamily_domains:SSF48592	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCGCCAT	.	5	ESCA
TRHDE	0	.	GRCh37	12	72956810	72956810	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000261180	9/19	16	11	5	16	16	0	TRHDE,stop_gained,p.Gln633Ter,ENST00000261180,;TRHDE,downstream_gene_variant,,ENST00000547300,;TRHDE,non_coding_transcript_exon_variant,,ENST00000549138,;TRHDE,non_coding_transcript_exon_variant,,ENST00000549401,;	T	ENSG00000072657	ENST00000261180	Transcript	stop_gained	1993	1897	633	Q/*	Cag/Tag	COSM431828	.	.	1	TRHDE	HGNC	30748	protein_coding	YES	CCDS9004.1	ENSP00000261180	TRHDE_HUMAN	.	UPI0000136D52	.	.	.	9/19	.	hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Q633*|c.1897C>T|3	MUTECT|MUSE	AACTTCAGAAT	.	2	ESCA
METTL25	0	.	GRCh37	12	82780586	82780586	+	Missense_Mutation	SNP	G	G	C	rs558856672	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264G>C	p.Met88Ile	p.M88I	ENST00000248306	2/12	27	16	11	25	25	0	METTL25,missense_variant,p.Met47Ile,ENST00000550058,;METTL25,missense_variant,p.Met88Ile,ENST00000548200,;METTL25,missense_variant,p.Met88Ile,ENST00000248306,;METTL25,non_coding_transcript_exon_variant,,ENST00000547985,;METTL25,non_coding_transcript_exon_variant,,ENST00000548569,;METTL25,non_coding_transcript_exon_variant,,ENST00000551722,;METTL25,non_coding_transcript_exon_variant,,ENST00000547357,;	C	ENSG00000127720	ENST00000248306	Transcript	missense_variant	333	264	88	M/I	atG/atC	rs558856672	.	.	1	METTL25	HGNC	26228	protein_coding	YES	CCDS9024.1	ENSP00000248306	MET25_HUMAN	F8VZA8_HUMAN	UPI000013CC3E	.	tolerated(0.57)	benign(0)	2/12	.	hmmpanther:PTHR12496,hmmpanther:PTHR12496:SF0	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTATGACTGA	by1000G	5	ESCA
CCDC168	0	.	GRCh37	13	103388934	103388934	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226G>C	p.Glu76Gln	p.E76Q	ENST00000322527	1/1	58	43	15	54	54	0	CCDC168,missense_variant,p.Glu76Gln,ENST00000322527,;	G	ENSG00000175820	ENST00000322527	Transcript	missense_variant	226	226	76	E/Q	Gag/Cag	.	.	.	-1	CCDC168	HGNC	26851	protein_coding	YES	.	ENSP00000320232	CC168_HUMAN	.	UPI0000DD81F0	.	tolerated(0.12)	possibly_damaging(0.607)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTCAAGGA	.	5	ESCA
LINC00283	0	.	GRCh37	13	103396902	103396902	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1275C>G	.	.	ENST00000430111	2/2	45	23	22	43	43	0	LINC00283,non_coding_transcript_exon_variant,,ENST00000430111,;	G	ENSG00000231633	ENST00000430111	Transcript	non_coding_transcript_exon_variant	1275	.	.	.	.	.	.	.	1	LINC00283	HGNC	38809	antisense	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTTCTCTAA	.	5	ESCA
LINC00283	0	.	GRCh37	13	103397430	103397430	+	RNA	SNP	C	C	G	rs373154448	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1803C>G	.	.	ENST00000430111	2/2	33	26	7	31	31	0	LINC00283,non_coding_transcript_exon_variant,,ENST00000430111,;	G	ENSG00000231633	ENST00000430111	Transcript	non_coding_transcript_exon_variant	1803	.	.	.	.	rs373154448	.	.	1	LINC00283	HGNC	38809	antisense	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	G:0	G:0.0003	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCTGCAG	byCluster	5	ESCA
SACS	0	.	GRCh37	13	23913508	23913508	+	Missense_Mutation	SNP	T	T	C	rs755189624	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4507A>G	p.Met1503Val	p.M1503V	ENST00000382298	10/10	21	10	11	36	36	0	SACS,missense_variant,p.Met1503Val,ENST00000382292,;SACS,missense_variant,p.Met753Val,ENST00000402364,;SACS,missense_variant,p.Met1503Val,ENST00000382298,;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,;	C	ENSG00000151835	ENST00000382298	Transcript	missense_variant	5096	4507	1503	M/V	Atg/Gtg	rs755189624	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	benign(0.032)	10/10	.	hmmpanther:PTHR15600:SF26,hmmpanther:PTHR15600,Gene3D:3.30.565.10,Superfamily_domains:SSF55874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCATATTTC	byFrequency	5	ESCA
EEF1DP3	0	.	GRCh37	13	32527031	32527031	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2736G>A	.	.	ENST00000490410	1/1	28	14	14	28	28	0	EEF1DP3,non_coding_transcript_exon_variant,,ENST00000428783,;EEF1DP3,non_coding_transcript_exon_variant,,ENST00000490410,;EEF1DP3,non_coding_transcript_exon_variant,,ENST00000566025,;	A	ENSG00000229715	ENST00000490410	Transcript	non_coding_transcript_exon_variant	2736	.	.	.	.	.	.	.	1	EEF1DP3	HGNC	30486	retained_intron	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTGGGCCA	.	5	ESCA
SCEL	0	.	GRCh37	13	78191993	78191993	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000349847	26/33	28	16	11	21	21	0	SCEL,stop_gained,p.Gln503Ter,ENST00000377246,;SCEL,stop_gained,p.Gln523Ter,ENST00000349847,;SCEL,stop_gained,p.Gln481Ter,ENST00000535157,;SCEL,downstream_gene_variant,,ENST00000469982,;SCEL,downstream_gene_variant,,ENST00000471491,;	T	ENSG00000136155	ENST00000349847	Transcript	stop_gained	1651	1567	523	Q/*	Cag/Tag	.	.	.	1	SCEL	HGNC	10573	protein_coding	YES	CCDS9459.1	ENSP00000302579	SCEL_HUMAN	.	UPI000013CFF1	.	.	.	26/33	.	hmmpanther:PTHR15468:SF6,hmmpanther:PTHR15468	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATCAGAGG	.	5	ESCA
SNORD114-5	0	.	GRCh37	14	101421716	101421716	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.10G>A	.	.	ENST00000362928	1/1	42	25	17	44	44	0	SNORD114-5,non_coding_transcript_exon_variant,,ENST00000362928,;AL132709.5,intron_variant,,ENST00000414488,;AL132709.5,intron_variant,,ENST00000554369,;AL132709.5,intron_variant,,ENST00000434716,;AL132709.5,intron_variant,,ENST00000556637,;SNORD114-6,upstream_gene_variant,,ENST00000364393,;SNORD114-2,downstream_gene_variant,,ENST00000363953,;AL132709.5,upstream_gene_variant,,ENST00000443252,;SNORD113,upstream_gene_variant,,ENST00000363280,;SNORD114-4,downstream_gene_variant,,ENST00000363962,;AL132709.5,downstream_gene_variant,,ENST00000427085,;SNORD114-3,downstream_gene_variant,,ENST00000364969,;	A	ENSG00000199798	ENST00000362928	Transcript	non_coding_transcript_exon_variant	10	.	.	.	.	.	.	.	1	SNORD114-5	HGNC	32993	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGATGATGAC	.	5	ESCA
OR4N2	0	.	GRCh37	14	20295898	20295898	+	Silent	SNP	C	C	T	rs766308802	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291C>T	p.%3D	p.C97C	ENST00000315947	1/1	165	131	34	135	135	0	OR4N2,synonymous_variant,p.%3D,ENST00000557677,;OR4N2,synonymous_variant,p.%3D,ENST00000315947,;OR4N2,synonymous_variant,p.%3D,ENST00000568211,;OR4N2,downstream_gene_variant,,ENST00000557414,;	T	ENSG00000176294	ENST00000315947	Transcript	synonymous_variant	291	291	97	C	tgC/tgT	rs766308802,COSM1515054	.	.	1	OR4N2	HGNC	14742	protein_coding	YES	CCDS32022.1	ENSP00000319601	OR4N2_HUMAN	H3BTD8_HUMAN,G3V4W1_HUMAN,G3V3W5_HUMAN	UPI000004A5DF	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF155,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGCATCAC	.	5	ESCA
OR4K1	0	.	GRCh37	14	20404053	20404053	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228T>C	p.%3D	p.F76F	ENST00000285600	1/1	82	65	17	88	88	0	OR4K1,synonymous_variant,p.%3D,ENST00000285600,;	C	ENSG00000155249	ENST00000285600	Transcript	synonymous_variant	287	228	76	F	ttT/ttC	.	.	.	1	OR4K1	HGNC	14726	protein_coding	YES	CCDS32025.1	ENSP00000285600	OR4K1_HUMAN	.	UPI0000041B4A	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF182,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTTGCCAC	.	5	ESCA
CHD8	0	.	GRCh37	14	21861740	21861740	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6214G>C	p.Glu2072Gln	p.E2072Q	ENST00000399982	31/37	25	14	11	23	23	0	CHD8,missense_variant,p.Glu2072Gln,ENST00000557364,;CHD8,missense_variant,p.Glu1793Gln,ENST00000430710,;CHD8,missense_variant,p.Glu2072Gln,ENST00000399982,;CHD8,upstream_gene_variant,,ENST00000553870,;SNORD8,downstream_gene_variant,,ENST00000363915,;SNORD9,upstream_gene_variant,,ENST00000362566,;CHD8,downstream_gene_variant,,ENST00000555962,;CHD8,downstream_gene_variant,,ENST00000557329,;CHD8,downstream_gene_variant,,ENST00000555301,;	G	ENSG00000100888	ENST00000399982	Transcript	missense_variant	6279	6214	2072	E/Q	Gag/Cag	.	.	.	-1	CHD8	HGNC	20153	protein_coding	YES	CCDS53885.1	ENSP00000382863	CHD8_HUMAN	.	UPI00002375B9	.	tolerated_low_confidence(0.16)	benign(0.403)	31/37	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCAGAGT	.	5	ESCA
TRAJ9	0	.	GRCh37	14	23004519	23004519	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18C>T	p.%3D	p.F6F	ENST00000390528	1/1	45	30	15	37	37	0	TRAJ9,synonymous_variant,p.%3D,ENST00000390528,;TRAJ5,upstream_gene_variant,,ENST00000390532,;TRAJ7,upstream_gene_variant,,ENST00000390530,;TRAJ8,upstream_gene_variant,,ENST00000390529,;TRAJ10,downstream_gene_variant,,ENST00000390527,;TRAJ13,downstream_gene_variant,,ENST00000390524,;TRAJ6,upstream_gene_variant,,ENST00000390531,;TRAJ12,downstream_gene_variant,,ENST00000390525,;TRAJ11,downstream_gene_variant,,ENST00000390526,;	T	ENSG00000211880	ENST00000390528	Transcript	synonymous_variant	18	18	6	F	ttC/ttT	.	.	.	1	TRAJ9	HGNC	12097	TR_J_gene	YES	.	ENSP00000451766	.	A0N4Z8_HUMAN	UPI000011A710	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCAAAAC	.	5	ESCA
MYH7	0	.	GRCh37	14	23886443	23886443	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4438G>C	p.Glu1480Gln	p.E1480Q	ENST00000355349	32/40	37	29	8	32	32	0	MYH7,missense_variant,p.Glu1480Gln,ENST00000355349,;MIR208B,downstream_gene_variant,,ENST00000401172,;CTD-2201G16.1,downstream_gene_variant,,ENST00000557368,;	G	ENSG00000092054	ENST00000355349	Transcript	missense_variant	4601	4438	1480	E/Q	Gag/Cag	.	.	.	-1	MYH7	HGNC	7577	protein_coding	YES	CCDS9601.1	ENSP00000347507	MYH7_HUMAN	Q59EV3_HUMAN,L0L5E6_HUMAN,A8CLN2_HUMAN,A8CLL2_HUMAN,A6N931_HUMAN,A6N930_HUMAN	UPI000014019B	.	deleterious(0.02)	probably_damaging(0.998)	32/40	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF279,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTCTGTGC	.	5	ESCA
LTB4R	0	.	GRCh37	14	24785316	24785316	+	Silent	SNP	C	C	G	rs375670032	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459C>G	p.%3D	p.L153L	ENST00000396789	2/2	32	23	9	21	21	0	LTB4R,synonymous_variant,p.%3D,ENST00000396782,;LTB4R,synonymous_variant,p.%3D,ENST00000345363,;LTB4R,synonymous_variant,p.%3D,ENST00000396789,;LTB4R,synonymous_variant,p.%3D,ENST00000556141,;LTB4R2,downstream_gene_variant,,ENST00000527924,;LTB4R2,downstream_gene_variant,,ENST00000530080,;LTB4R2,downstream_gene_variant,,ENST00000543919,;LTB4R,downstream_gene_variant,,ENST00000553481,;CIDEB,upstream_gene_variant,,ENST00000336557,;CIDEB,upstream_gene_variant,,ENST00000258807,;LTB4R2,downstream_gene_variant,,ENST00000533293,;ADCY4,downstream_gene_variant,,ENST00000554068,;ADCY4,downstream_gene_variant,,ENST00000418030,;LTB4R2,downstream_gene_variant,,ENST00000528054,;ADCY4,downstream_gene_variant,,ENST00000310677,;CIDEB,upstream_gene_variant,,ENST00000555817,;ADCY4,downstream_gene_variant,,ENST00000555684,;ADCY4,downstream_gene_variant,,ENST00000554577,;ADCY4,downstream_gene_variant,,ENST00000561200,;ADCY4,downstream_gene_variant,,ENST00000545213,;ADCY4,downstream_gene_variant,,ENST00000557056,;ADCY4,downstream_gene_variant,,ENST00000560635,;ADCY4,downstream_gene_variant,,ENST00000554781,;	G	ENSG00000213903	ENST00000396789	Transcript	synonymous_variant	2184	459	153	L	ctC/ctG	rs375670032	.	.	1	LTB4R	HGNC	6713	protein_coding	YES	CCDS9626.1	ENSP00000380008	LT4R1_HUMAN	G3V4Q5_HUMAN,G3V244_HUMAN	UPI000003C106	.	.	.	2/2	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF00001,hmmpanther:PTHR24230:SF51,hmmpanther:PTHR24230,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTCGCGTA	.	5	ESCA
COCH	0	.	GRCh37	14	31355343	31355343	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1302C>G	p.Ile434Met	p.I434M	ENST00000396618	11/12	56	38	17	49	49	0	COCH,missense_variant,p.Ile285Met,ENST00000382493,;COCH,missense_variant,p.Ile318Met,ENST00000468826,;COCH,missense_variant,p.Ile434Met,ENST00000216361,;COCH,missense_variant,p.Ile322Met,ENST00000460581,;COCH,missense_variant,p.Ile434Met,ENST00000475087,;COCH,missense_variant,p.Ile434Met,ENST00000396618,;COCH,downstream_gene_variant,,ENST00000555881,;RP11-829H16.3,non_coding_transcript_exon_variant,,ENST00000555108,;RP11-829H16.3,upstream_gene_variant,,ENST00000555421,;RP11-829H16.3,downstream_gene_variant,,ENST00000556786,;RP11-829H16.3,downstream_gene_variant,,ENST00000468444,;COCH,downstream_gene_variant,,ENST00000557065,;COCH,downstream_gene_variant,,ENST00000553772,;	G	ENSG00000100473	ENST00000396618	Transcript	missense_variant	1358	1302	434	I/M	atC/atG	.	.	.	1	COCH	HGNC	2180	protein_coding	YES	CCDS9640.1	ENSP00000379862	COCH_HUMAN	G3V5G6_HUMAN,G3V4C4_HUMAN	UPI0000048EBB	.	deleterious(0)	possibly_damaging(0.462)	11/12	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF84,hmmpanther:PTHR22992,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATCAGAAA	.	5	ESCA
SRP54	0	.	GRCh37	14	35480717	35480717	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000556994	9/17	30	24	6	37	37	0	SRP54,missense_variant,p.Tyr163Cys,ENST00000556994,;SRP54,missense_variant,p.Tyr114Cys,ENST00000546080,;SRP54,missense_variant,p.Tyr99Cys,ENST00000555557,;SRP54,missense_variant,p.Tyr163Cys,ENST00000216774,;SRP54,splice_region_variant,,ENST00000556380,;SRP54,upstream_gene_variant,,ENST00000553923,;	G	ENSG00000100883	ENST00000556994	Transcript	missense_variant	885	488	163	Y/C	tAt/tGt	.	.	.	1	SRP54	HGNC	11301	protein_coding	YES	CCDS9652.1	ENSP00000451818	SRP54_HUMAN	G3V4F7_HUMAN,G3V480_HUMAN,G3V346_HUMAN	UPI0000135EE0	.	deleterious(0)	probably_damaging(0.97)	9/17	.	HAMAP:MF_00306,hmmpanther:PTHR11564:SF5,hmmpanther:PTHR11564,TIGRFAM_domain:TIGR01425,Gene3D:3.40.50.300,Pfam_domain:PF00448,SMART_domains:SM00962,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCTATACAG	.	5	ESCA
PNN	0	.	GRCh37	14	39651779	39651779	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*712C>T	.	.	ENST00000216832	9/9	13	8	5	8	8	0	PNN,3_prime_UTR_variant,,ENST00000216832,;PNN,downstream_gene_variant,,ENST00000553331,;PNN,downstream_gene_variant,,ENST00000556530,;PNN,non_coding_transcript_exon_variant,,ENST00000557680,;PNN,downstream_gene_variant,,ENST00000554902,;	T	ENSG00000100941	ENST00000216832	Transcript	3_prime_UTR_variant	2933	.	.	.	.	.	.	.	1	PNN	HGNC	9162	protein_coding	YES	CCDS9671.1	ENSP00000216832	PININ_HUMAN	.	UPI000013C70D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCGTCATTCT	.	2	ESCA
RPL10L	0	.	GRCh37	14	47120593	47120593	+	Missense_Mutation	SNP	C	C	G	rs779859790	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347G>C	p.Arg116Pro	p.R116P	ENST00000298283	1/1	54	40	14	66	66	0	RPL10L,missense_variant,p.Arg116Pro,ENST00000298283,;	G	ENSG00000165496	ENST00000298283	Transcript	missense_variant	436	347	116	R/P	cGa/cCa	rs779859790	.	.	-1	RPL10L	HGNC	17976	protein_coding	YES	CCDS32071.1	ENSP00000298283	RL10L_HUMAN	.	UPI0000073CA8	.	deleterious(0.05)	benign(0.123)	1/1	.	hmmpanther:PTHR11726:SF9,hmmpanther:PTHR11726,PROSITE_patterns:PS01257,TIGRFAM_domain:TIGR00279,Gene3D:3.90.1170.10,Pfam_domain:PF00252,PIRSF_domain:PIRSF005590,Superfamily_domains:SSF54686	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTCGCATA	.	5	ESCA
DLGAP5	0	.	GRCh37	14	55642728	55642728	+	Missense_Mutation	SNP	G	G	A	rs750563382	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058C>T	p.Ser353Phe	p.S353F	ENST00000247191	9/19	47	34	12	54	54	0	DLGAP5,missense_variant,p.Ser353Phe,ENST00000247191,;DLGAP5,missense_variant,p.Ser353Phe,ENST00000395425,;DLGAP5,downstream_gene_variant,,ENST00000557645,;	A	ENSG00000126787	ENST00000247191	Transcript	missense_variant	1275	1058	353	S/F	tCt/tTt	rs750563382	.	.	-1	DLGAP5	HGNC	16864	protein_coding	YES	CCDS9723.1	ENSP00000247191	DLGP5_HUMAN	G3V543_HUMAN,G3V4E5_HUMAN	UPI000013CC13	.	deleterious(0)	benign(0.435)	9/19	.	hmmpanther:PTHR12353,Pfam_domain:PF03359	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGAGACTCA	.	5	ESCA
IFI27	0	.	GRCh37	14	94582247	94582247	+	Missense_Mutation	SNP	C	C	T	rs755125237	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242C>T	p.Ser81Leu	p.S81L	ENST00000555744	4/5	107	79	28	73	73	0	IFI27,missense_variant,p.Ser71Leu,ENST00000557634,;IFI27,missense_variant,p.Ser81Leu,ENST00000555744,;IFI27,missense_variant,p.Ser84Leu,ENST00000448882,;IFI27,missense_variant,p.Ser84Leu,ENST00000444961,;IFI27,missense_variant,p.Ser81Leu,ENST00000556544,;IFI27,missense_variant,p.Ser36Leu,ENST00000557098,;IFI27,missense_variant,p.Ser81Leu,ENST00000298902,;IFI27,downstream_gene_variant,,ENST00000554448,;IFI27,downstream_gene_variant,,ENST00000555819,;IFI27,downstream_gene_variant,,ENST00000554800,;IFI27,missense_variant,p.Ser51Leu,ENST00000557035,;IFI27,non_coding_transcript_exon_variant,,ENST00000553285,;IFI27,non_coding_transcript_exon_variant,,ENST00000555121,;IFI27,downstream_gene_variant,,ENST00000557700,;IFI27,downstream_gene_variant,,ENST00000555081,;	T	ENSG00000165949	ENST00000555744	Transcript	missense_variant	430	242	81	S/L	tCg/tTg	rs755125237	.	.	1	IFI27	HGNC	5397	protein_coding	YES	CCDS32148.1	ENSP00000451956	IFI27_HUMAN	Q7Z5R2_HUMAN,G3V4U3_HUMAN,G3V4L7_HUMAN,G3V3Q7_HUMAN,G3V2M7_HUMAN	UPI000013E535	.	deleterious(0)	benign(0.001)	4/5	.	hmmpanther:PTHR16932,hmmpanther:PTHR16932:SF15,Pfam_domain:PF06140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCGGGCA	byFrequency	5	ESCA
ATG2B	0	.	GRCh37	14	96829287	96829287	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27C>G	p.Ile9Met	p.I9M	ENST00000359933	1/42	75	52	22	53	53	0	ATG2B,missense_variant,p.Ile9Met,ENST00000359933,;GSKIP,upstream_gene_variant,,ENST00000553699,;GSKIP,upstream_gene_variant,,ENST00000556095,;GSKIP,upstream_gene_variant,,ENST00000554182,;GSKIP,upstream_gene_variant,,ENST00000555181,;GSKIP,upstream_gene_variant,,ENST00000555088,;	C	ENSG00000066739	ENST00000359933	Transcript	missense_variant	921	27	9	I/M	atC/atG	.	.	.	-1	ATG2B	HGNC	20187	protein_coding	YES	CCDS9944.2	ENSP00000353010	ATG2B_HUMAN	.	UPI000155D51F	.	deleterious(0)	probably_damaging(0.924)	1/42	.	hmmpanther:PTHR13190:SF19,hmmpanther:PTHR13190	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTGATGGA	.	5	ESCA
SETD3	0	.	GRCh37	14	99864889	99864889	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*127A>G	.	.	ENST00000331768	13/13	21	14	6	27	27	0	SETD3,3_prime_UTR_variant,,ENST00000331768,;SETD3,3_prime_UTR_variant,,ENST00000446066,;SETD3,downstream_gene_variant,,ENST00000489770,;	C	ENSG00000183576	ENST00000331768	Transcript	3_prime_UTR_variant	2072	.	.	.	.	.	.	.	-1	SETD3	HGNC	20493	protein_coding	YES	CCDS9951.1	ENSP00000327436	SETD3_HUMAN	.	UPI000000CC6D	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTATATAAA	.	5	ESCA
NIPA2	0	.	GRCh37	15	23034295	23034295	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-500C>T	.	.	ENST00000337451	1/8	21	16	4	14	14	0	NIPA2,5_prime_UTR_variant,,ENST00000398013,;NIPA2,5_prime_UTR_variant,,ENST00000560039,;NIPA2,5_prime_UTR_variant,,ENST00000539711,;NIPA2,5_prime_UTR_variant,,ENST00000398014,;NIPA2,5_prime_UTR_variant,,ENST00000337451,;NIPA2,5_prime_UTR_variant,,ENST00000359727,;NIPA2,non_coding_transcript_exon_variant,,ENST00000561072,;NIPA2,non_coding_transcript_exon_variant,,ENST00000559571,;NIPA2,non_coding_transcript_exon_variant,,ENST00000560762,;NIPA2,non_coding_transcript_exon_variant,,ENST00000560205,;	A	ENSG00000140157	ENST00000337451	Transcript	5_prime_UTR_variant	114	.	.	.	.	.	.	.	-1	NIPA2	HGNC	17044	protein_coding	YES	CCDS10010.1	ENSP00000337618	NIPA2_HUMAN	H0YMQ7_HUMAN	UPI0000070013	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTGAAGCC	.	5	ESCA
APBA2	0	.	GRCh37	15	29400541	29400541	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1986C>T	p.%3D	p.I662I	ENST00000558402	14/16	58	40	18	38	38	0	APBA2,synonymous_variant,p.%3D,ENST00000558259,;APBA2,synonymous_variant,p.%3D,ENST00000561069,;APBA2,synonymous_variant,p.%3D,ENST00000558402,;APBA2,synonymous_variant,p.%3D,ENST00000411764,;APBA2,synonymous_variant,p.%3D,ENST00000558330,;APBA2,non_coding_transcript_exon_variant,,ENST00000559814,;	T	ENSG00000034053	ENST00000558402	Transcript	synonymous_variant	2585	1986	662	I	atC/atT	.	.	.	1	APBA2	HGNC	579	protein_coding	YES	CCDS10022.1	ENSP00000453293	APBA2_HUMAN	H0YNG7_HUMAN,H0YNE8_HUMAN,H0YMS0_HUMAN,H0YL28_HUMAN	UPI0000046798	.	.	.	14/16	.	PROSITE_profiles:PS50106,hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF12,Gene3D:2.30.42.10,Superfamily_domains:SSF50156,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTATCAAGCG	.	5	ESCA
NUTM1	0	.	GRCh37	15	34648143	34648143	+	Missense_Mutation	SNP	C	C	T	rs540031927	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1850C>T	p.Ser617Leu	p.S617L	ENST00000333756	7/7	36	23	13	35	35	0	NUTM1,missense_variant,p.Ser645Leu,ENST00000537011,;NUTM1,missense_variant,p.Ser617Leu,ENST00000333756,;NUTM1,missense_variant,p.Ser635Leu,ENST00000438749,;LPCAT4,downstream_gene_variant,,ENST00000314891,;LPCAT4,downstream_gene_variant,,ENST00000567507,;LPCAT4,downstream_gene_variant,,ENST00000563240,;LPCAT4,downstream_gene_variant,,ENST00000563748,;	T	ENSG00000184507	ENST00000333756	Transcript	missense_variant	2005	1850	617	S/L	tCa/tTa	rs540031927	.	.	1	NUTM1	HGNC	29919	protein_coding	YES	CCDS32190.1	ENSP00000329448	NUTM1_HUMAN	.	UPI000016159A	.	tolerated(0.19)	benign(0.014)	7/7	.	hmmpanther:PTHR22879:SF13,hmmpanther:PTHR22879	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCAGAGG	by1000G	5	ESCA
CEP152	0	.	GRCh37	15	49031177	49031177	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4402G>A	p.Glu1468Lys	p.E1468K	ENST00000380950	27/27	38	25	13	29	29	0	CEP152,missense_variant,p.Glu1468Lys,ENST00000380950,;CEP152,missense_variant,p.Glu1412Lys,ENST00000399334,;CEP152,downstream_gene_variant,,ENST00000325747,;CEP152,intron_variant,,ENST00000561245,;	T	ENSG00000103995	ENST00000380950	Transcript	missense_variant	4590	4402	1468	E/K	Gaa/Aaa	.	.	.	-1	CEP152	HGNC	29298	protein_coding	YES	CCDS58361.1	ENSP00000370337	CE152_HUMAN	H0YN91_HUMAN	UPI00002378C4	.	tolerated(0.08)	benign(0.034)	27/27	.	hmmpanther:PTHR10337,hmmpanther:PTHR10337:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.G1415R|c.4243G>A|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCACAAG	.	5	ESCA
UNC13C	0	.	GRCh37	15	54919645	54919645	+	3'UTR	SNP	G	G	A	rs750953485	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*334G>A	.	.	ENST00000260323	32/32	25	20	5	23	23	0	UNC13C,3_prime_UTR_variant,,ENST00000537900,;UNC13C,3_prime_UTR_variant,,ENST00000545554,;UNC13C,3_prime_UTR_variant,,ENST00000260323,;UNC13C,downstream_gene_variant,,ENST00000560537,;UNC13C,downstream_gene_variant,,ENST00000539562,;	A	ENSG00000137766	ENST00000260323	Transcript	3_prime_UTR_variant	6979	.	.	.	.	rs750953485	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAATGAGATT	.	5	ESCA
VPS13C	0	.	GRCh37	15	62207918	62207918	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8359G>C	p.Glu2787Gln	p.E2787Q	ENST00000261517	61/85	29	20	9	37	37	0	VPS13C,missense_variant,p.Glu2787Gln,ENST00000261517,;VPS13C,missense_variant,p.Glu2787Gln,ENST00000395896,;VPS13C,missense_variant,p.Glu2744Gln,ENST00000249837,;VPS13C,missense_variant,p.Glu2744Gln,ENST00000395898,;RN7SL613P,downstream_gene_variant,,ENST00000584412,;VPS13C,non_coding_transcript_exon_variant,,ENST00000558338,;	G	ENSG00000129003	ENST00000261517	Transcript	missense_variant	8433	8359	2787	E/Q	Gaa/Caa	COSM3502866,COSM3502867	.	.	-1	VPS13C	HGNC	23594	protein_coding	YES	CCDS32257.1	ENSP00000261517	VP13C_HUMAN	B4E2S9_HUMAN,B3KW10_HUMAN	UPI000023B7D3	.	deleterious(0)	probably_damaging(1)	61/85	.	hmmpanther:PTHR16166:SF69,hmmpanther:PTHR16166,Pfam_domain:PF06650	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTCTGAAC	.	5	ESCA
SLC24A1	0	.	GRCh37	15	65943238	65943238	+	Silent	SNP	C	C	T	rs368057501	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2751C>T	p.%3D	p.I917I	ENST00000261892	7/10	41	32	9	35	35	0	SLC24A1,synonymous_variant,p.%3D,ENST00000546330,;SLC24A1,synonymous_variant,p.%3D,ENST00000399033,;SLC24A1,synonymous_variant,p.%3D,ENST00000544319,;SLC24A1,synonymous_variant,p.%3D,ENST00000339868,;SLC24A1,synonymous_variant,p.%3D,ENST00000537259,;SLC24A1,synonymous_variant,p.%3D,ENST00000261892,;SLC24A1,upstream_gene_variant,,ENST00000505666,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000449142,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000434116,;SLC24A1,downstream_gene_variant,,ENST00000539516,;	T	ENSG00000074621	ENST00000261892	Transcript	synonymous_variant	3038	2751	917	I	atC/atT	rs368057501	.	.	1	SLC24A1	HGNC	10975	protein_coding	YES	CCDS45284.1	ENSP00000261892	NCKX1_HUMAN	.	UPI000013020C	.	.	.	7/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10846,hmmpanther:PTHR10846:SF6,TIGRFAM_domain:TIGR00367	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCATCGTGTT	byFrequency|byCluster	5	ESCA
GLCE	0	.	GRCh37	15	69548140	69548140	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-6C>G	.	.	ENST00000261858	3/5	21	15	6	26	26	0	GLCE,5_prime_UTR_variant,,ENST00000261858,;GLCE,5_prime_UTR_variant,,ENST00000559420,;GLCE,upstream_gene_variant,,ENST00000559500,;	G	ENSG00000138604	ENST00000261858	Transcript	5_prime_UTR_variant	223	.	.	.	.	.	.	.	1	GLCE	HGNC	17855	protein_coding	YES	CCDS32277.1	ENSP00000261858	GLCE_HUMAN	H0YNP1_HUMAN	UPI00001D7785	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGTCTGAAT	.	2	ESCA
PKM	0	.	GRCh37	15	72502159	72502159	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.420C>T	p.%3D	p.L140L	ENST00000319622	5/11	62	35	26	44	44	0	PKM,synonymous_variant,p.%3D,ENST00000567087,;PKM,synonymous_variant,p.%3D,ENST00000565184,;PKM,synonymous_variant,p.%3D,ENST00000335181,;PKM,synonymous_variant,p.%3D,ENST00000561609,;PKM,synonymous_variant,p.%3D,ENST00000568459,;PKM,synonymous_variant,p.%3D,ENST00000319622,;PKM,synonymous_variant,p.%3D,ENST00000449901,;PKM,synonymous_variant,p.%3D,ENST00000565154,;PKM,synonymous_variant,p.%3D,ENST00000562997,;PKM,synonymous_variant,p.%3D,ENST00000564178,;PKM,synonymous_variant,p.%3D,ENST00000389093,;PKM,intron_variant,,ENST00000568883,;PKM,synonymous_variant,p.%3D,ENST00000569857,;PKM,3_prime_UTR_variant,,ENST00000567118,;PKM,non_coding_transcript_exon_variant,,ENST00000562784,;PKM,non_coding_transcript_exon_variant,,ENST00000568743,;PKM,downstream_gene_variant,,ENST00000564276,;PKM,upstream_gene_variant,,ENST00000564993,;PKM,upstream_gene_variant,,ENST00000563986,;PKM,upstream_gene_variant,,ENST00000563275,;PKM,upstream_gene_variant,,ENST00000570166,;	A	ENSG00000067225	ENST00000319622	Transcript	synonymous_variant	877	420	140	L	ctC/ctT	.	.	.	-1	PKM	HGNC	9021	protein_coding	YES	CCDS32285.1	ENSP00000320171	KPYM_HUMAN	H3BUW1_HUMAN,H3BU13_HUMAN,H3BTN5_HUMAN,H3BTJ2_HUMAN,H3BT25_HUMAN,H3BN34_HUMAN	UPI000014064D	.	.	.	5/11	.	hmmpanther:PTHR11817:SF10,hmmpanther:PTHR11817,Pfam_domain:PF00224,Gene3D:2.40.33.10,TIGRFAM_domain:TIGR01064,Superfamily_domains:SSF50800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTGAGAGT	.	5	ESCA
CYP1A1	0	.	GRCh37	15	75014785	75014785	+	Silent	SNP	G	G	C	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.654C>G	p.%3D	p.V218V	ENST00000379727	2/7	73	54	18	67	67	0	CYP1A1,synonymous_variant,p.%3D,ENST00000567032,;CYP1A1,synonymous_variant,p.%3D,ENST00000379727,;CYP1A1,synonymous_variant,p.%3D,ENST00000395049,;CYP1A1,synonymous_variant,p.%3D,ENST00000395048,;CYP1A1,5_prime_UTR_variant,,ENST00000564596,;CYP1A1,5_prime_UTR_variant,,ENST00000566503,;CYP1A1,intron_variant,,ENST00000562201,;CYP1A1,intron_variant,,ENST00000569630,;	C	ENSG00000140465	ENST00000379727	Transcript	synonymous_variant	853	654	218	V	gtC/gtG	COSM3420607	.	.	-1	CYP1A1	HGNC	2595	protein_coding	YES	CCDS10268.1	ENSP00000369050	CP1A1_HUMAN	A4F4K4_HUMAN,A4F3V8_HUMAN,A0N0X8_HUMAN	UPI0000128195	.	.	.	2/7	.	Superfamily_domains:SSF48264,Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24299:SF8,hmmpanther:PTHR24299	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTGACTAG	.	5	ESCA
C15orf39	0	.	GRCh37	15	75500090	75500090	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1701A>G	p.%3D	p.S567S	ENST00000360639	2/3	46	32	14	31	31	0	C15orf39,synonymous_variant,p.%3D,ENST00000360639,;C15orf39,synonymous_variant,p.%3D,ENST00000394987,;C15orf39,synonymous_variant,p.%3D,ENST00000567617,;C15orf39,synonymous_variant,p.%3D,ENST00000565074,;C15orf39,downstream_gene_variant,,ENST00000562637,;C15orf39,downstream_gene_variant,,ENST00000564848,;C15orf39,downstream_gene_variant,,ENST00000563905,;RP11-69H7.3,downstream_gene_variant,,ENST00000563568,;	G	ENSG00000167173	ENST00000360639	Transcript	synonymous_variant	2021	1701	567	S	tcA/tcG	.	.	.	1	C15orf39	HGNC	24497	protein_coding	YES	CCDS10276.1	ENSP00000353854	CO039_HUMAN	H3BT66_HUMAN,H3BRS2_HUMAN,H3BN41_HUMAN	UPI000004F079	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCACTTAA	.	5	ESCA
SCAPER	0	.	GRCh37	15	77057706	77057706	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1585G>C	p.Glu529Gln	p.E529Q	ENST00000563290	13/32	33	19	13	26	26	0	SCAPER,missense_variant,p.Glu529Gln,ENST00000324767,;SCAPER,missense_variant,p.Glu283Gln,ENST00000538941,;SCAPER,missense_variant,p.Glu529Gln,ENST00000563290,;SCAPER,missense_variant,p.Glu535Gln,ENST00000564590,;SCAPER,missense_variant,p.Glu535Gln,ENST00000565970,;SCAPER,downstream_gene_variant,,ENST00000564022,;SCAPER,3_prime_UTR_variant,,ENST00000565507,;SCAPER,non_coding_transcript_exon_variant,,ENST00000303521,;	G	ENSG00000140386	ENST00000563290	Transcript	missense_variant	1681	1585	529	E/Q	Gaa/Caa	.	.	.	-1	SCAPER	HGNC	13081	protein_coding	YES	CCDS53962.1	ENSP00000454973	SCAPE_HUMAN	H3BTY2_HUMAN,H3BR40_HUMAN,H3BPB0_HUMAN	UPI0000E59CC3	.	deleterious(0)	probably_damaging(0.999)	13/32	.	hmmpanther:PTHR31434,hmmpanther:PTHR31434:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCATGCA	.	5	ESCA
SCAPER	0	.	GRCh37	15	77067388	77067388	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843G>A	p.%3D	p.V281V	ENST00000563290	9/32	48	30	18	39	39	0	SCAPER,synonymous_variant,p.%3D,ENST00000324767,;SCAPER,synonymous_variant,p.%3D,ENST00000538941,;SCAPER,synonymous_variant,p.%3D,ENST00000564022,;SCAPER,synonymous_variant,p.%3D,ENST00000563290,;SCAPER,synonymous_variant,p.%3D,ENST00000564590,;SCAPER,synonymous_variant,p.%3D,ENST00000565970,;SCAPER,non_coding_transcript_exon_variant,,ENST00000567618,;SCAPER,non_coding_transcript_exon_variant,,ENST00000562890,;SCAPER,3_prime_UTR_variant,,ENST00000568549,;SCAPER,3_prime_UTR_variant,,ENST00000565507,;SCAPER,non_coding_transcript_exon_variant,,ENST00000303521,;	T	ENSG00000140386	ENST00000563290	Transcript	synonymous_variant	939	843	281	V	gtG/gtA	.	.	.	-1	SCAPER	HGNC	13081	protein_coding	YES	CCDS53962.1	ENSP00000454973	SCAPE_HUMAN	H3BTY2_HUMAN,H3BR40_HUMAN,H3BPB0_HUMAN	UPI0000E59CC3	.	.	.	9/32	.	hmmpanther:PTHR31434,hmmpanther:PTHR31434:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATCACTGC	.	5	ESCA
KIF7	0	.	GRCh37	15	90171751	90171751	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3931G>A	p.Glu1311Lys	p.E1311K	ENST00000394412	19/19	23	18	5	24	24	0	KIF7,missense_variant,p.Glu1311Lys,ENST00000394412,;TICRR,downstream_gene_variant,,ENST00000560985,;TICRR,downstream_gene_variant,,ENST00000268138,;KIF7,intron_variant,,ENST00000558928,;TICRR,intron_variant,,ENST00000561095,;	T	ENSG00000166813	ENST00000394412	Transcript	missense_variant	4008	3931	1311	E/K	Gag/Aag	.	.	.	-1	KIF7	HGNC	30497	protein_coding	YES	CCDS32325.2	ENSP00000377934	KIF7_HUMAN	B7ZKY4_HUMAN	UPI00015F81C7	.	tolerated(0.13)	benign(0.11)	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCACCCA	.	5	ESCA
KIF7	0	.	GRCh37	15	90171829	90171829	+	Missense_Mutation	SNP	C	C	T	rs755333464	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3853G>A	p.Glu1285Lys	p.E1285K	ENST00000394412	19/19	15	11	4	15	15	0	KIF7,missense_variant,p.Glu1285Lys,ENST00000394412,;TICRR,downstream_gene_variant,,ENST00000560985,;TICRR,downstream_gene_variant,,ENST00000268138,;KIF7,splice_region_variant,,ENST00000558928,;TICRR,intron_variant,,ENST00000561095,;	T	ENSG00000166813	ENST00000394412	Transcript	missense_variant	3930	3853	1285	E/K	Gag/Aag	rs755333464	.	.	-1	KIF7	HGNC	30497	protein_coding	YES	CCDS32325.2	ENSP00000377934	KIF7_HUMAN	B7ZKY4_HUMAN	UPI00015F81C7	.	tolerated(0.09)	benign(0.05)	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTCCTCACCAC	byFrequency	2	ESCA
ZNF710	0	.	GRCh37	15	90610643	90610643	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274G>A	p.Glu92Lys	p.E92K	ENST00000268154	2/5	76	52	24	74	74	0	ZNF710,missense_variant,p.Glu92Lys,ENST00000268154,;ZNF710,upstream_gene_variant,,ENST00000559360,;ZNF710,downstream_gene_variant,,ENST00000559419,;ZNF710,upstream_gene_variant,,ENST00000558883,;	A	ENSG00000140548	ENST00000268154	Transcript	missense_variant	525	274	92	E/K	Gag/Aag	.	.	.	1	ZNF710	HGNC	25352	protein_coding	YES	CCDS10358.1	ENSP00000268154	ZN710_HUMAN	H0YKZ0_HUMAN	UPI000013D7A4	.	deleterious_low_confidence(0.02)	benign(0.239)	2/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGTGAGAAG	.	5	ESCA
PRM2	0	.	GRCh37	16	11370120	11370120	+	Silent	SNP	C	C	T	rs752229574	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108G>A	p.%3D	p.L36L	ENST00000241808	1/2	84	55	29	66	66	0	PRM2,synonymous_variant,p.%3D,ENST00000435245,;PRM2,synonymous_variant,p.%3D,ENST00000241808,;RMI2,intron_variant,,ENST00000572173,;PRM1,downstream_gene_variant,,ENST00000312511,;PRM3,upstream_gene_variant,,ENST00000327157,;SNORA48,upstream_gene_variant,,ENST00000390926,;RMI2,intron_variant,,ENST00000573910,;	T	ENSG00000122304	ENST00000241808	Transcript	synonymous_variant	218	108	36	L	ctG/ctA	rs752229574	.	.	-1	PRM2	HGNC	9448	protein_coding	YES	CCDS42118.1	ENSP00000241808	PRM2_HUMAN	Q1LZN1_HUMAN	UPI000012CD8E	.	.	.	1/2	.	Low_complexity_(Seg):seg,Pfam_domain:PF00841,hmmpanther:PTHR21341	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTCAGCCC	.	5	ESCA
KIAA0430	0	.	GRCh37	16	15692750	15692750	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4945G>T	p.Asp1649Tyr	p.D1649Y	ENST00000396368	26/27	67	49	18	74	74	0	KIAA0430,missense_variant,p.Asp1649Tyr,ENST00000551742,;KIAA0430,missense_variant,p.Asp1646Tyr,ENST00000602337,;KIAA0430,missense_variant,p.Asp1484Tyr,ENST00000540441,;KIAA0430,missense_variant,p.Asp1337Tyr,ENST00000344181,;KIAA0430,missense_variant,p.Asp1646Tyr,ENST00000548025,;KIAA0430,missense_variant,p.Asp1649Tyr,ENST00000396368,;C16orf45,intron_variant,,ENST00000565857,;KIAA0430,downstream_gene_variant,,ENST00000547936,;KIAA0430,3_prime_UTR_variant,,ENST00000551878,;KIAA0430,3_prime_UTR_variant,,ENST00000552553,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000552771,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000551579,;KIAA0430,downstream_gene_variant,,ENST00000549337,;	A	ENSG00000166783	ENST00000396368	Transcript	missense_variant	5152	4945	1649	D/Y	Gat/Tat	.	.	.	-1	KIAA0430	HGNC	29562	protein_coding	YES	CCDS10562.2	ENSP00000379654	MARF1_HUMAN	F8VRS5_HUMAN	UPI00006881BC	.	deleterious(0)	possibly_damaging(0.899)	26/27	.	hmmpanther:PTHR14379:SF3,hmmpanther:PTHR14379	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATCAGCAG	.	5	ESCA
VWA3A	0	.	GRCh37	16	22149768	22149768	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000389398	22/34	56	37	18	57	57	0	VWA3A,stop_gained,p.Gln125Ter,ENST00000563389,;VWA3A,stop_gained,p.Gln743Ter,ENST00000389398,;VWA3A,5_prime_UTR_variant,,ENST00000389397,;VWA3A,downstream_gene_variant,,ENST00000568328,;VWA3A,stop_gained,p.Gln353Ter,ENST00000299840,;VWA3A,downstream_gene_variant,,ENST00000566668,;	T	ENSG00000175267	ENST00000389398	Transcript	stop_gained	2323	2227	743	Q/*	Cag/Tag	.	.	.	1	VWA3A	HGNC	27088	protein_coding	YES	CCDS45441.1	ENSP00000374049	VWA3A_HUMAN	H3BTX3_HUMAN	UPI0001663067	.	.	.	22/34	.	hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCAGCTA	.	5	ESCA
ECI1	0	.	GRCh37	16	2296896	2296896	+	Silent	SNP	C	C	T	rs780047225	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258G>A	p.%3D	p.E86E	ENST00000301729	3/7	65	40	25	65	65	0	ECI1,synonymous_variant,p.%3D,ENST00000566379,;ECI1,synonymous_variant,p.%3D,ENST00000301729,;ECI1,synonymous_variant,p.%3D,ENST00000570258,;ECI1,synonymous_variant,p.%3D,ENST00000562238,;ECI1,non_coding_transcript_exon_variant,,ENST00000561688,;ECI1,non_coding_transcript_exon_variant,,ENST00000563029,;ECI1,upstream_gene_variant,,ENST00000563447,;	T	ENSG00000167969	ENST00000301729	Transcript	synonymous_variant	306	258	86	E	gaG/gaA	rs780047225	.	.	-1	ECI1	HGNC	2703	protein_coding	YES	CCDS10464.1	ENSP00000301729	ECI1_HUMAN	Q96DC0_HUMAN,H3BS70_HUMAN	UPI0000128DAE	.	.	.	3/7	.	hmmpanther:PTHR11941:SF55,hmmpanther:PTHR11941,Pfam_domain:PF00378,Gene3D:3.90.226.10,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTCTCCAG	.	5	ESCA
LCMT1	0	.	GRCh37	16	25186294	25186294	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.921G>T	p.%3D	p.L307L	ENST00000399069	10/11	29	19	10	21	21	0	LCMT1,synonymous_variant,p.%3D,ENST00000399069,;LCMT1,synonymous_variant,p.%3D,ENST00000380966,;LCMT1,intron_variant,,ENST00000575396,;LCMT1,non_coding_transcript_exon_variant,,ENST00000572869,;LCMT1,3_prime_UTR_variant,,ENST00000564011,;LCMT1,3_prime_UTR_variant,,ENST00000380962,;LCMT1,3_prime_UTR_variant,,ENST00000576625,;LCMT1,non_coding_transcript_exon_variant,,ENST00000574450,;	T	ENSG00000205629	ENST00000399069	Transcript	synonymous_variant	1076	921	307	L	ctG/ctT	.	.	.	1	LCMT1	HGNC	17557	protein_coding	YES	CCDS45445.1	ENSP00000382021	LCMT1_HUMAN	I3L2Q8_HUMAN	UPI0000000C29	.	.	.	10/11	.	hmmpanther:PTHR13600:SF6,hmmpanther:PTHR13600,Gene3D:3.40.50.150,PIRSF_domain:PIRSF016305,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTGCTGGA	.	5	ESCA
TBC1D10B	0	.	GRCh37	16	30380585	30380585	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.920A>G	p.Tyr307Cys	p.Y307C	ENST00000409939	1/9	61	31	29	39	39	0	TBC1D10B,missense_variant,p.Tyr307Cys,ENST00000409939,;MYLPF,upstream_gene_variant,,ENST00000568749,;TBC1D10B,upstream_gene_variant,,ENST00000490703,;MYLPF,upstream_gene_variant,,ENST00000563718,;TBC1D10B,upstream_gene_variant,,ENST00000478158,;TBC1D10B,upstream_gene_variant,,ENST00000464644,;	C	ENSG00000169221	ENST00000409939	Transcript	missense_variant	1001	920	307	Y/C	tAt/tGt	.	.	.	-1	TBC1D10B	HGNC	24510	protein_coding	YES	CCDS10676.2	ENSP00000386538	TB10B_HUMAN	.	UPI000164FA1A	.	deleterious(0)	probably_damaging(0.981)	1/9	.	hmmpanther:PTHR22957:SF207,hmmpanther:PTHR22957	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCATACTTG	.	5	ESCA
KAT8	0	.	GRCh37	16	31142622	31142622	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*309C>T	.	.	ENST00000448516	10/10	46	33	13	45	45	0	KAT8,3_prime_UTR_variant,,ENST00000543774,;KAT8,3_prime_UTR_variant,,ENST00000537402,;KAT8,3_prime_UTR_variant,,ENST00000448516,;KAT8,3_prime_UTR_variant,,ENST00000219797,;PRSS8,downstream_gene_variant,,ENST00000568261,;PRSS8,downstream_gene_variant,,ENST00000567797,;PRSS8,downstream_gene_variant,,ENST00000317508,;PRSS8,downstream_gene_variant,,ENST00000567531,;RP11-388M20.2,upstream_gene_variant,,ENST00000563605,;KAT8,non_coding_transcript_exon_variant,,ENST00000538768,;KAT8,non_coding_transcript_exon_variant,,ENST00000573144,;PRSS8,downstream_gene_variant,,ENST00000567833,;PRSS8,downstream_gene_variant,,ENST00000564025,;	T	ENSG00000103510	ENST00000448516	Transcript	3_prime_UTR_variant	1731	.	.	.	.	.	.	.	1	KAT8	HGNC	17933	protein_coding	YES	CCDS45468.1	ENSP00000406037	KAT8_HUMAN	.	UPI00001B02B6	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCAGCCT	.	5	ESCA
RGS11	0	.	GRCh37	16	320792	320792	+	Nonsense_Mutation	SNP	G	G	A	rs746717778	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1018C>T	p.Arg340Ter	p.R340*	ENST00000397770	14/17	328	209	118	285	285	0	RGS11,stop_gained,p.Arg340Ter,ENST00000397770,;RGS11,stop_gained,p.Arg319Ter,ENST00000316163,;RGS11,stop_gained,p.Arg329Ter,ENST00000359740,;ARHGDIG,intron_variant,,ENST00000435035,;ARHGDIG,intron_variant,,ENST00000412541,;ITFG3,downstream_gene_variant,,ENST00000442458,;ITFG3,downstream_gene_variant,,ENST00000301678,;ITFG3,downstream_gene_variant,,ENST00000399932,;ITFG3,downstream_gene_variant,,ENST00000600536,;RGS11,downstream_gene_variant,,ENST00000397768,;RGS11,downstream_gene_variant,,ENST00000431291,;ITFG3,downstream_gene_variant,,ENST00000301679,;ITFG3,downstream_gene_variant,,ENST00000450082,;ARHGDIG,intron_variant,,ENST00000464609,;RGS11,3_prime_UTR_variant,,ENST00000168869,;RGS11,non_coding_transcript_exon_variant,,ENST00000481672,;RGS11,non_coding_transcript_exon_variant,,ENST00000477143,;RGS11,downstream_gene_variant,,ENST00000472466,;RGS11,downstream_gene_variant,,ENST00000493449,;	A	ENSG00000076344	ENST00000397770	Transcript	stop_gained	1036	1018	340	R/*	Cga/Tga	rs746717778	.	.	-1	RGS11	HGNC	9993	protein_coding	YES	CCDS42088.1	ENSP00000380876	RGS11_HUMAN	Q4TT70_HUMAN	UPI000013382E	.	.	.	14/17	.	PROSITE_profiles:PS50132,hmmpanther:PTHR10845:SF21,hmmpanther:PTHR10845,Gene3D:1.10.167.10,Pfam_domain:PF00615,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATCGAAGCT	byFrequency	5	ESCA
ZNF597	0	.	GRCh37	16	3487023	3487023	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.676C>T	p.His226Tyr	p.H226Y	ENST00000301744	4/4	26	12	14	43	43	0	ZNF597,missense_variant,p.His226Tyr,ENST00000301744,;NAA60,intron_variant,,ENST00000575785,;	A	ENSG00000167981	ENST00000301744	Transcript	missense_variant	912	676	226	H/Y	Cat/Tat	.	.	.	-1	ZNF597	HGNC	26573	protein_coding	YES	CCDS10505.1	ENSP00000301744	ZN597_HUMAN	.	UPI0000070B73	.	tolerated(0.07)	benign(0.033)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24385,hmmpanther:PTHR24385:SF50,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGATGAGAGT	.	5	ESCA
PAPD5	0	.	GRCh37	16	50261884	50261884	+	Silent	SNP	T	T	C	rs373965165	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1890T>C	p.%3D	p.T630T	ENST00000436909	12/13	72	46	26	45	45	0	PAPD5,synonymous_variant,p.%3D,ENST00000561678,;PAPD5,synonymous_variant,p.%3D,ENST00000436909,;PAPD5,synonymous_variant,p.%3D,ENST00000357464,;PAPD5,non_coding_transcript_exon_variant,,ENST00000573002,;PAPD5,non_coding_transcript_exon_variant,,ENST00000562717,;	C	ENSG00000121274	ENST00000436909	Transcript	synonymous_variant	1925	1890	630	T	acT/acC	rs373965165	.	.	1	PAPD5	HGNC	30758	protein_coding	YES	CCDS54006.1	ENSP00000396995	PAPD5_HUMAN	Q5EBM7_HUMAN,G4U4J3_HUMAN,B7ZLC1_HUMAN,B4DRJ7_HUMAN	UPI00017A7DC6	.	.	.	12/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23092,hmmpanther:PTHR23092:SF26	.	.	.	.	.	.	.	G:0.0005	G:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACTAACAC	byFrequency|byCluster	5	ESCA
CKLF	0	.	GRCh37	16	66586512	66586512	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-107G>A	.	.	ENST00000264001	1/4	19	13	6	11	11	0	CKLF,5_prime_UTR_variant,,ENST00000417030,;CKLF,5_prime_UTR_variant,,ENST00000351137,;CKLF,5_prime_UTR_variant,,ENST00000264001,;CKLF,5_prime_UTR_variant,,ENST00000345436,;CKLF,5_prime_UTR_variant,,ENST00000362093,;CKLF-CMTM1,upstream_gene_variant,,ENST00000532838,;TK2,upstream_gene_variant,,ENST00000527800,;TK2,upstream_gene_variant,,ENST00000563369,;TK2,upstream_gene_variant,,ENST00000569718,;TK2,upstream_gene_variant,,ENST00000527284,;CKLF-CMTM1,upstream_gene_variant,,ENST00000527729,;TK2,upstream_gene_variant,,ENST00000299697,;TK2,upstream_gene_variant,,ENST00000525974,;TK2,upstream_gene_variant,,ENST00000544898,;TK2,upstream_gene_variant,,ENST00000563478,;TK2,upstream_gene_variant,,ENST00000417693,;TK2,upstream_gene_variant,,ENST00000451102,;TK2,upstream_gene_variant,,ENST00000562484,;TK2,upstream_gene_variant,,ENST00000564917,;TK2,upstream_gene_variant,,ENST00000545043,;Y_RNA,downstream_gene_variant,,ENST00000563151,;Y_RNA,downstream_gene_variant,,ENST00000411222,;TK2,upstream_gene_variant,,ENST00000565729,;CKLF,upstream_gene_variant,,ENST00000563092,;CKLF-CMTM1,5_prime_UTR_variant,,ENST00000527845,;CKLF,5_prime_UTR_variant,,ENST00000534692,;CKLF,non_coding_transcript_exon_variant,,ENST00000526149,;TK2,upstream_gene_variant,,ENST00000567357,;	A	ENSG00000217555	ENST00000264001	Transcript	5_prime_UTR_variant	43	.	.	.	.	.	.	.	1	CKLF	HGNC	13253	protein_coding	YES	CCDS10807.1	ENSP00000264001	CKLF_HUMAN	.	UPI0000036209	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGAGGGCGG	.	2	ESCA
DDX28	0	.	GRCh37	16	68055590	68055590	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516C>G	p.Pro506Ala	p.P506A	ENST00000332395	1/1	36	29	6	20	20	0	DDX28,missense_variant,p.Pro506Ala,ENST00000332395,;DUS2,intron_variant,,ENST00000571081,;DUS2,intron_variant,,ENST00000570709,;DUS2,intron_variant,,ENST00000566306,;DUS2,intron_variant,,ENST00000575677,;DUS2,intron_variant,,ENST00000576994,;DUS2,upstream_gene_variant,,ENST00000569289,;DUS2,upstream_gene_variant,,ENST00000567100,;DUS2,upstream_gene_variant,,ENST00000432752,;DUS2,upstream_gene_variant,,ENST00000568099,;DUS2,upstream_gene_variant,,ENST00000565263,;DUS2,upstream_gene_variant,,ENST00000564781,;DUS2,upstream_gene_variant,,ENST00000358896,;RNU6-359P,upstream_gene_variant,,ENST00000365466,;DUS2,upstream_gene_variant,,ENST00000564975,;	C	ENSG00000182810	ENST00000332395	Transcript	missense_variant	2181	1516	506	P/A	Ccc/Gcc	.	.	.	-1	DDX28	HGNC	17330	protein_coding	YES	CCDS10858.1	ENSP00000332340	DDX28_HUMAN	.	UPI000006D6C8	.	tolerated(0.08)	benign(0.115)	1/1	.	PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF35,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGGATGGG	.	5	ESCA
PRMT7	0	.	GRCh37	16	68371375	68371376	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.406dupT	p.Cys136LeufsTer12	p.C136Lfs*12	ENST00000339507	7/19	56	42	14	56	56	0	PRMT7,frameshift_variant,p.Cys86LeufsTer12,ENST00000441236,;PRMT7,frameshift_variant,p.Cys136LeufsTer12,ENST00000339507,;PRMT7,frameshift_variant,p.Cys136LeufsTer12,ENST00000569571,;PRMT7,frameshift_variant,p.Cys136LeufsTer12,ENST00000569047,;PRMT7,frameshift_variant,p.Cys86LeufsTer12,ENST00000449359,;PRMT7,intron_variant,,ENST00000348497,;PRMT7,non_coding_transcript_exon_variant,,ENST00000563520,;PRMT7,non_coding_transcript_exon_variant,,ENST00000564441,;PRMT7,non_coding_transcript_exon_variant,,ENST00000563562,;PRMT7,non_coding_transcript_exon_variant,,ENST00000564050,;PRMT7,frameshift_variant,p.Cys136LeufsTer12,ENST00000568975,;PRMT7,3_prime_UTR_variant,,ENST00000562381,;PRMT7,3_prime_UTR_variant,,ENST00000562050,;PRMT7,3_prime_UTR_variant,,ENST00000566341,;PRMT7,non_coding_transcript_exon_variant,,ENST00000565356,;PRMT7,intron_variant,,ENST00000567542,;	T	ENSG00000132600	ENST00000339507	Transcript	frameshift_variant	1235-1236	405-406	135-136	-/X	-/T	.	.	.	1	PRMT7	HGNC	25557	protein_coding	YES	CCDS10866.1	ENSP00000343103	ANM7_HUMAN	H3BSS9_HUMAN,H3BRQ9_HUMAN,H3BRD3_HUMAN,H3BPZ8_HUMAN,H3BNS2_HUMAN	UPI0000041857	.	.	.	7/19	.	PROSITE_profiles:PS51678,hmmpanther:PTHR11006:SF4,hmmpanther:PTHR11006,Gene3D:3.40.50.150,PIRSF_domain:PIRSF036946,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGCCATGCCG	.	3	ESCA
PDPR	0	.	GRCh37	16	70187389	70187389	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2148G>A	p.%3D	p.E716E	ENST00000288050	18/19	56	41	15	56	56	0	PDPR,synonymous_variant,p.%3D,ENST00000563930,;PDPR,synonymous_variant,p.%3D,ENST00000569042,;PDPR,synonymous_variant,p.%3D,ENST00000542659,;PDPR,synonymous_variant,p.%3D,ENST00000288050,;PDPR,synonymous_variant,p.%3D,ENST00000567896,;PDPR,synonymous_variant,p.%3D,ENST00000398122,;PDPR,synonymous_variant,p.%3D,ENST00000567046,;PDPR,synonymous_variant,p.%3D,ENST00000568530,;RP11-296I10.3,downstream_gene_variant,,ENST00000566989,;PDPR,intron_variant,,ENST00000562100,;PDPR,3_prime_UTR_variant,,ENST00000564563,;PDPR,intron_variant,,ENST00000565186,;PDPR,downstream_gene_variant,,ENST00000561920,;	A	ENSG00000090857	ENST00000288050	Transcript	synonymous_variant	3105	2148	716	E	gaG/gaA	.	.	.	1	PDPR	HGNC	30264	protein_coding	YES	CCDS45520.1	ENSP00000288050	PDPR_HUMAN	H3BV59_HUMAN,H3BU60_HUMAN,B7ZAR9_HUMAN,B3KSE1_HUMAN,A8MT40_HUMAN	UPI00001FF513	.	.	.	18/19	.	Gene3D:3.30.1360.120,Pfam_domain:PF01571,Superfamily_domains:SSF103025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGAGAAGTT	.	5	ESCA
MARVELD3	0	.	GRCh37	16	71668213	71668213	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595+4816A>G	.	.	ENST00000299952	.	28	14	14	23	23	0	MARVELD3,missense_variant,p.Tyr238Cys,ENST00000268485,;MARVELD3,synonymous_variant,p.%3D,ENST00000567501,;MARVELD3,intron_variant,,ENST00000299952,;MARVELD3,intron_variant,,ENST00000565261,;MARVELD3,downstream_gene_variant,,ENST00000567566,;PHLPP2,downstream_gene_variant,,ENST00000540628,;MARVELD3,upstream_gene_variant,,ENST00000561682,;PHLPP2,downstream_gene_variant,,ENST00000568004,;PHLPP2,downstream_gene_variant,,ENST00000564884,;	G	ENSG00000140832	ENST00000299952	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MARVELD3	HGNC	30525	protein_coding	YES	CCDS32478.1	ENSP00000299952	MALD3_HUMAN	.	UPI000013E601	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACTATCAGT	.	5	ESCA
PKD1L2	0	.	GRCh37	16	81173292	81173292	+	5'Flank	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000534142	.	50	31	18	33	33	0	PKD1L2,upstream_gene_variant,,ENST00000534142,;PKD1L2,non_coding_transcript_exon_variant,,ENST00000299598,;PKD1L2,intron_variant,,ENST00000530363,;PKD1L2,missense_variant,p.Gln1815Glu,ENST00000525539,;PKD1L2,missense_variant,p.Gln1130Glu,ENST00000533478,;	C	ENSG00000166473	ENST00000534142	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3315	-1	PKD1L2	HGNC	21715	processed_transcript	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTGAGGGG	.	5	ESCA
HSDL1	0	.	GRCh37	16	84163981	84163981	+	Silent	SNP	G	G	T	rs141648024	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.276C>A	p.%3D	p.L92L	ENST00000219439	4/6	40	28	12	39	39	0	HSDL1,synonymous_variant,p.%3D,ENST00000434463,;HSDL1,synonymous_variant,p.%3D,ENST00000568857,;HSDL1,synonymous_variant,p.%3D,ENST00000562224,;HSDL1,synonymous_variant,p.%3D,ENST00000219439,;HSDL1,downstream_gene_variant,,ENST00000564998,;HSDL1,downstream_gene_variant,,ENST00000567294,;	T	ENSG00000103160	ENST00000219439	Transcript	synonymous_variant	453	276	92	L	ctC/ctA	rs141648024	.	.	-1	HSDL1	HGNC	16475	protein_coding	YES	CCDS10942.1	ENSP00000219439	HSDL1_HUMAN	H3BT52_HUMAN,H3BQI7_HUMAN,H3BNH5_HUMAN	UPI0000049039	.	.	.	4/6	.	hmmpanther:PTHR24316,hmmpanther:PTHR24316:SF243,Pfam_domain:PF00106,Gene3D:3.40.50.720,PIRSF_domain:PIRSF000126,Superfamily_domains:SSF51735	C:0.0006	C:0.0015	C:0.0014	.	C:0	C:0	C:0	C:0.0009	C:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTGAGACC	byFrequency|byCluster|by1000G	5	ESCA
PRPF8	0	.	GRCh37	17	1561597	1561597	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5455C>G	p.Leu1819Val	p.L1819V	ENST00000572621	33/42	130	94	35	88	88	0	PRPF8,missense_variant,p.Leu1819Val,ENST00000572621,;PRPF8,missense_variant,p.Leu1819Val,ENST00000304992,;PRPF8,downstream_gene_variant,,ENST00000573725,;PRPF8,upstream_gene_variant,,ENST00000575116,;PRPF8,downstream_gene_variant,,ENST00000573681,;PRPF8,downstream_gene_variant,,ENST00000572445,;PRPF8,upstream_gene_variant,,ENST00000576585,;	C	ENSG00000174231	ENST00000572621	Transcript	missense_variant	5721	5455	1819	L/V	Ctc/Gtc	.	.	.	-1	PRPF8	HGNC	17340	protein_coding	YES	CCDS11010.1	ENSP00000460348	PRP8_HUMAN	.	UPI000006F2DD	.	tolerated(0.13)	possibly_damaging(0.892)	33/42	.	hmmpanther:PTHR11140:SF0,hmmpanther:PTHR11140,Pfam_domain:PF12134,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGAGGAACA	.	5	ESCA
COPS3	0	.	GRCh37	17	17150263	17150263	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*149A>T	.	.	ENST00000268717	12/12	16	8	8	36	36	0	COPS3,3_prime_UTR_variant,,ENST00000579716,;COPS3,3_prime_UTR_variant,,ENST00000439936,;COPS3,3_prime_UTR_variant,,ENST00000268717,;COPS3,3_prime_UTR_variant,,ENST00000539941,;AC055811.1,downstream_gene_variant,,ENST00000577389,;COPS3,3_prime_UTR_variant,,ENST00000578317,;COPS3,non_coding_transcript_exon_variant,,ENST00000486032,;COPS3,downstream_gene_variant,,ENST00000463097,;AC055811.5,downstream_gene_variant,,ENST00000423783,;	A	ENSG00000141030	ENST00000268717	Transcript	3_prime_UTR_variant	1528	.	.	.	.	.	.	.	-1	COPS3	HGNC	2239	protein_coding	YES	CCDS11183.1	ENSP00000268717	CSN3_HUMAN	J3QKR0_HUMAN	UPI0000073FD1	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCTGAAAG	.	5	ESCA
MYO15A	0	.	GRCh37	17	18023041	18023041	+	Silent	SNP	C	C	T	rs773152876	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.927C>T	p.%3D	p.Y309Y	ENST00000205890	2/66	61	31	30	87	87	0	MYO15A,synonymous_variant,p.%3D,ENST00000205890,;MYO15A,non_coding_transcript_exon_variant,,ENST00000583079,;	T	ENSG00000091536	ENST00000205890	Transcript	synonymous_variant	1265	927	309	Y	taC/taT	rs773152876,COSM295746	.	.	1	MYO15A	HGNC	7594	protein_coding	YES	CCDS42271.1	ENSP00000205890	MYO15_HUMAN	K7EQV1_HUMAN,G3V4G3_HUMAN	UPI0000E59E6E	.	.	.	2/66	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTACGACGA	byFrequency	5	ESCA
ULK2	0	.	GRCh37	17	19699506	19699506	+	Silent	SNP	C	C	T	rs201972720	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1899G>A	p.%3D	p.S633S	ENST00000395544	19/27	51	21	29	62	62	0	ULK2,synonymous_variant,p.%3D,ENST00000395544,;ULK2,synonymous_variant,p.%3D,ENST00000361658,;ULK2,upstream_gene_variant,,ENST00000575432,;ULK2,downstream_gene_variant,,ENST00000580130,;ULK2,non_coding_transcript_exon_variant,,ENST00000571137,;	T	ENSG00000083290	ENST00000395544	Transcript	synonymous_variant	2399	1899	633	S	tcG/tcA	rs201972720	.	.	-1	ULK2	HGNC	13480	protein_coding	YES	CCDS11213.1	ENSP00000378914	ULK2_HUMAN	.	UPI000013D19B	.	.	.	19/27	.	hmmpanther:PTHR24348,hmmpanther:PTHR24348:SF18,PIRSF_domain:PIRSF000580	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCGACTG	byCluster|by1000G	5	ESCA
C17orf66	0	.	GRCh37	17	34185297	34185297	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059C>G	p.%3D	p.L353L	ENST00000311880	11/15	69	45	24	35	35	0	C17orf66,synonymous_variant,p.%3D,ENST00000311880,;C17orf66,synonymous_variant,p.%3D,ENST00000592980,;TAF15,intron_variant,,ENST00000586593,;C17orf66,synonymous_variant,p.%3D,ENST00000589015,;C17orf66,synonymous_variant,p.%3D,ENST00000587573,;C17orf66,3_prime_UTR_variant,,ENST00000585840,;C17orf66,non_coding_transcript_exon_variant,,ENST00000462028,;AC015849.14,downstream_gene_variant,,ENST00000589274,;	C	ENSG00000172653	ENST00000311880	Transcript	synonymous_variant	1208	1059	353	L	ctC/ctG	.	.	.	-1	C17orf66	HGNC	26548	protein_coding	YES	CCDS11299.1	ENSP00000309560	CQ066_HUMAN	.	UPI000013F215	.	.	.	11/15	.	hmmpanther:PTHR12697,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTGAGCAT	.	5	ESCA
SYNRG	0	.	GRCh37	17	35900600	35900600	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3248G>A	p.Arg1083His	p.R1083H	ENST00000339208	16/22	55	33	21	70	70	0	SYNRG,missense_variant,p.Arg1005His,ENST00000345615,;SYNRG,missense_variant,p.Arg1005His,ENST00000394378,;SYNRG,missense_variant,p.Arg960His,ENST00000502449,;SYNRG,missense_variant,p.Arg877His,ENST00000591288,;SYNRG,missense_variant,p.Arg1004His,ENST00000585472,;SYNRG,missense_variant,p.Arg1083His,ENST00000339208,;SYNRG,missense_variant,p.Arg1083His,ENST00000346661,;SYNRG,intron_variant,,ENST00000591427,;SYNRG,upstream_gene_variant,,ENST00000508220,;SYNRG,downstream_gene_variant,,ENST00000421408,;	T	ENSG00000006114	ENST00000339208	Transcript	missense_variant	3389	3248	1083	R/H	cGt/cAt	COSM978331	.	.	-1	SYNRG	HGNC	557	protein_coding	YES	CCDS11321.1	ENSP00000343610	SYNRG_HUMAN	.	UPI000013C4EA	.	tolerated(0.12)	benign(0.109)	16/22	.	hmmpanther:PTHR15463	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAACGGCTT	.	5	ESCA
TNS4	0	.	GRCh37	17	38652532	38652532	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146G>A	p.Gly49Glu	p.G49E	ENST00000254051	2/13	22	13	9	9	9	0	TNS4,missense_variant,p.Gly49Glu,ENST00000254051,;	T	ENSG00000131746	ENST00000254051	Transcript	missense_variant	305	146	49	G/E	gGa/gAa	.	.	.	-1	TNS4	HGNC	24352	protein_coding	YES	CCDS11368.1	ENSP00000254051	TENS4_HUMAN	.	UPI000013CE0F	.	tolerated(0.08)	possibly_damaging(0.873)	2/13	.	hmmpanther:PTHR12583,hmmpanther:PTHR12583:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGCTCCCCAG	.	3	ESCA
KRT33A	0	.	GRCh37	17	39505616	39505616	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.413C>G	p.Ser138Ter	p.S138*	ENST00000007735	2/7	95	67	28	84	84	0	KRT33A,stop_gained,p.Ser138Ter,ENST00000007735,;	C	ENSG00000006059	ENST00000007735	Transcript	stop_gained	458	413	138	S/*	tCa/tGa	COSM254769	.	.	-1	KRT33A	HGNC	6450	protein_coding	YES	CCDS11388.1	ENSP00000007735	KT33A_HUMAN	.	UPI000013C503	.	.	.	2/7	.	Prints_domain:PR01248,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF98	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.S138L|c.413C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTGAGGCC	.	5	ESCA
KRT17	0	.	GRCh37	17	39777080	39777080	+	Nonsense_Mutation	SNP	G	G	A	rs749862409	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1012C>T	p.Gln338Ter	p.Q338*	ENST00000311208	6/8	78	48	30	58	58	0	JUP,stop_gained,p.Gln497Ter,ENST00000540235,;KRT17,stop_gained,p.Gln338Ter,ENST00000311208,;KRT17,downstream_gene_variant,,ENST00000577817,;KRT16,upstream_gene_variant,,ENST00000590990,;KRT17,downstream_gene_variant,,ENST00000590038,;KRT17,downstream_gene_variant,,ENST00000463128,;KRT17,non_coding_transcript_exon_variant,,ENST00000493253,;KRT17,downstream_gene_variant,,ENST00000491673,;	A	ENSG00000128422	ENST00000311208	Transcript	stop_gained	1080	1012	338	Q/*	Cag/Tag	rs749862409	.	.	-1	KRT17	HGNC	6427	protein_coding	YES	CCDS11402.1	ENSP00000308452	K1C17_HUMAN	K7ESE1_HUMAN,B4E2P9_HUMAN	UPI0000148FD6	.	.	.	6/8	.	hmmpanther:PTHR23239:SF91,hmmpanther:PTHR23239,Pfam_domain:PF00038,Gene3D:1.20.5.170,Superfamily_domains:SSF64593,Prints_domain:PR01248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGCACGC	byFrequency	5	ESCA
CDC27	0	.	GRCh37	17	45195869	45195869	+	3'Flank	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000531206	.	33	16	16	42	42	0	CDC27,3_prime_UTR_variant,,ENST00000066544,;CDC27,downstream_gene_variant,,ENST00000527547,;CDC27,downstream_gene_variant,,ENST00000571643,;CDC27,downstream_gene_variant,,ENST00000531206,;CDC27,downstream_gene_variant,,ENST00000446365,;AC002558.1,non_coding_transcript_exon_variant,,ENST00000408089,;CDC27,downstream_gene_variant,,ENST00000526866,;CDC27,downstream_gene_variant,,ENST00000533415,;CDC27,downstream_gene_variant,,ENST00000570740,;	C	ENSG00000004897	ENST00000531206	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1752	-1	CDC27	HGNC	1728	protein_coding	YES	CCDS45720.1	ENSP00000434614	CDC27_HUMAN	I0EZ72_HUMAN,I0EZ68_HUMAN	UPI0000E59FE6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATAGATGTA	.	5	ESCA
EFCAB13	0	.	GRCh37	17	45451874	45451874	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.914C>G	p.Ser305Ter	p.S305*	ENST00000331493	12/25	49	34	15	48	48	0	EFCAB13,stop_gained,p.Ser61Ter,ENST00000517310,;EFCAB13,stop_gained,p.Ser209Ter,ENST00000517484,;EFCAB13,stop_gained,p.Ser305Ter,ENST00000331493,;EFCAB13,upstream_gene_variant,,ENST00000523842,;EFCAB13,non_coding_transcript_exon_variant,,ENST00000523978,;EFCAB13,non_coding_transcript_exon_variant,,ENST00000520776,;EFCAB13,upstream_gene_variant,,ENST00000522326,;	G	ENSG00000178852	ENST00000331493	Transcript	stop_gained	1325	914	305	S/*	tCa/tGa	.	.	.	1	EFCAB13	HGNC	26864	protein_coding	YES	CCDS11512.1	ENSP00000332111	EFC13_HUMAN	E5RI18_HUMAN,E5RFW6_HUMAN	UPI00001AFEA2	.	.	.	12/25	.	hmmpanther:PTHR22656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTCAGACA	.	5	ESCA
NPEPPS	0	.	GRCh37	17	45699893	45699893	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*607C>T	.	.	ENST00000322157	23/23	30	16	13	34	34	0	NPEPPS,3_prime_UTR_variant,,ENST00000322157,;NPEPPS,downstream_gene_variant,,ENST00000528565,;NPEPPS,downstream_gene_variant,,ENST00000530173,;NPEPPS,downstream_gene_variant,,ENST00000544660,;RP11-580I16.2,intron_variant,,ENST00000582389,;RP11-580I16.2,intron_variant,,ENST00000584391,;RP11-580I16.2,intron_variant,,ENST00000582066,;RP11-580I16.2,downstream_gene_variant,,ENST00000580045,;NPEPPS,downstream_gene_variant,,ENST00000530514,;NPEPPS,downstream_gene_variant,,ENST00000531486,;NPEPPS,downstream_gene_variant,,ENST00000525048,;	T	ENSG00000141279	ENST00000322157	Transcript	3_prime_UTR_variant	3604	.	.	.	.	.	.	.	1	NPEPPS	HGNC	7900	protein_coding	YES	CCDS45721.1	ENSP00000320324	PSA_HUMAN	E9PJ74_HUMAN,B7Z1H4_HUMAN	UPI0000140D51	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTCTGTGT	.	5	ESCA
NFE2L1	0	.	GRCh37	17	46134843	46134843	+	Silent	SNP	C	C	T	rs374254839	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951C>T	p.%3D	p.L317L	ENST00000362042	5/6	42	26	16	41	41	0	NFE2L1,synonymous_variant,p.%3D,ENST00000536222,;NFE2L1,synonymous_variant,p.%3D,ENST00000362042,;NFE2L1,synonymous_variant,p.%3D,ENST00000357480,;NFE2L1,synonymous_variant,p.%3D,ENST00000585291,;NFE2L1,synonymous_variant,p.%3D,ENST00000582155,;NFE2L1,synonymous_variant,p.%3D,ENST00000583378,;NFE2L1,synonymous_variant,p.%3D,ENST00000577431,;NFE2L1,synonymous_variant,p.%3D,ENST00000361665,;NFE2L1,5_prime_UTR_variant,,ENST00000577411,;NFE2L1,5_prime_UTR_variant,,ENST00000584634,;NFE2L1,5_prime_UTR_variant,,ENST00000583210,;NFE2L1,5_prime_UTR_variant,,ENST00000580037,;NFE2L1,upstream_gene_variant,,ENST00000581319,;NFE2L1,downstream_gene_variant,,ENST00000580050,;NFE2L1,downstream_gene_variant,,ENST00000579537,;RP5-890E16.4,downstream_gene_variant,,ENST00000583349,;	T	ENSG00000082641	ENST00000362042	Transcript	synonymous_variant	1567	951	317	L	ctC/ctT	rs374254839	.	.	1	NFE2L1	HGNC	7781	protein_coding	YES	CCDS11524.1	ENSP00000354855	NF2L1_HUMAN	Q8NF22_HUMAN,J3QR31_HUMAN,J3QQY8_HUMAN,J3QQH8_HUMAN,J3QLQ1_HUMAN,J3KSR3_HUMAN	UPI000012FFCF	.	.	.	5/6	.	hmmpanther:PTHR24411:SF26,hmmpanther:PTHR24411	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTCATGTC	byFrequency|byCluster	5	ESCA
SNF8	0	.	GRCh37	17	47007863	47007863	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.751G>C	p.Glu251Gln	p.E251Q	ENST00000502492	8/8	52	34	18	40	40	0	SNF8,missense_variant,p.Glu250Gln,ENST00000290330,;SNF8,missense_variant,p.Glu251Gln,ENST00000502492,;UBE2Z,downstream_gene_variant,,ENST00000360943,;AC091133.1,upstream_gene_variant,,ENST00000435491,;SNF8,non_coding_transcript_exon_variant,,ENST00000514089,;SNF8,3_prime_UTR_variant,,ENST00000509989,;SNF8,3_prime_UTR_variant,,ENST00000509995,;SNF8,3_prime_UTR_variant,,ENST00000573795,;SNF8,3_prime_UTR_variant,,ENST00000510558,;SNF8,non_coding_transcript_exon_variant,,ENST00000504000,;SNF8,non_coding_transcript_exon_variant,,ENST00000515572,;UBE2Z,downstream_gene_variant,,ENST00000506271,;SNF8,downstream_gene_variant,,ENST00000514929,;SNF8,downstream_gene_variant,,ENST00000576353,;UBE2Z,downstream_gene_variant,,ENST00000506498,;UBE2Z,downstream_gene_variant,,ENST00000504684,;UBE2Z,downstream_gene_variant,,ENST00000513342,;SNF8,downstream_gene_variant,,ENST00000507302,;	G	ENSG00000159210	ENST00000502492	Transcript	missense_variant	1134	751	251	E/Q	Gag/Cag	.	.	.	-1	SNF8	HGNC	17028	protein_coding	YES	CCDS11541.1	ENSP00000421380	SNF8_HUMAN	D6RJ86_HUMAN	UPI0000071826	.	deleterious_low_confidence(0.03)	benign(0.295)	8/8	.	Gene3D:1.10.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAGCTG	.	5	ESCA
BZRAP1	0	.	GRCh37	17	56400114	56400114	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1218G>A	p.%3D	p.L406L	ENST00000343736	9/32	28	18	10	28	28	0	BZRAP1,synonymous_variant,p.%3D,ENST00000355701,;BZRAP1,synonymous_variant,p.%3D,ENST00000343736,;BZRAP1,synonymous_variant,p.%3D,ENST00000268893,;BZRAP1-AS1,upstream_gene_variant,,ENST00000579527,;BZRAP1,upstream_gene_variant,,ENST00000583624,;	T	ENSG00000005379	ENST00000343736	Transcript	synonymous_variant	1382	1218	406	L	ctG/ctA	.	.	.	-1	BZRAP1	HGNC	16831	protein_coding	YES	CCDS11605.1	ENSP00000345824	RIMB1_HUMAN	.	UPI000013D7E3	.	.	.	9/32	.	hmmpanther:PTHR14234:SF20,hmmpanther:PTHR14234	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCAGCTC	.	5	ESCA
MTMR4	0	.	GRCh37	17	56581711	56581711	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1438T>A	p.Leu480Met	p.L480M	ENST00000323456	13/19	36	29	7	34	34	0	MTMR4,missense_variant,p.Leu480Met,ENST00000323456,;MTMR4,missense_variant,p.Leu480Met,ENST00000579925,;MTMR4,downstream_gene_variant,,ENST00000583656,;MTMR4,downstream_gene_variant,,ENST00000583966,;MTMR4,downstream_gene_variant,,ENST00000580983,;MTMR4,downstream_gene_variant,,ENST00000582663,;	T	ENSG00000108389	ENST00000323456	Transcript	missense_variant	1563	1438	480	L/M	Ttg/Atg	.	.	.	-1	MTMR4	HGNC	7452	protein_coding	YES	CCDS11608.1	ENSP00000325285	MTMR4_HUMAN	J3QRJ2_HUMAN	UPI00002010DE	.	deleterious(0)	probably_damaging(0.977)	13/19	.	PROSITE_profiles:PS51339,hmmpanther:PTHR10807:SF64,hmmpanther:PTHR10807,Pfam_domain:PF06602,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCAACTGAT	.	2	ESCA
MED13	0	.	GRCh37	17	60032879	60032880	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5831dupT	p.Met1944IlefsTer36	p.M1944Ifs*36	ENST00000397786	26/30	83	58	25	42	42	0	MED13,frameshift_variant,p.Met1944IlefsTer36,ENST00000397786,;MED13,non_coding_transcript_exon_variant,,ENST00000582786,;	A	ENSG00000108510	ENST00000397786	Transcript	frameshift_variant	5908-5909	5831-5832	1944	M/IX	atg/atTg	.	.	.	-1	MED13	HGNC	22474	protein_coding	YES	CCDS42366.1	ENSP00000380888	MED13_HUMAN	.	UPI0000D7D6F6	.	.	.	26/30	.	hmmpanther:PTHR12950:SF22,hmmpanther:PTHR12950,Pfam_domain:PF06333	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCTGCATATT	.	3	ESCA
STRADA	0	.	GRCh37	17	61780982	61780982	+	Missense_Mutation	SNP	C	C	G	rs748003173	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1273G>C	p.Glu425Gln	p.E425Q	ENST00000336174	13/13	54	26	27	29	29	0	STRADA,missense_variant,p.Glu425Gln,ENST00000336174,;STRADA,missense_variant,p.Glu367Gln,ENST00000375840,;STRADA,3_prime_UTR_variant,,ENST00000245865,;STRADA,3_prime_UTR_variant,,ENST00000392950,;STRADA,3_prime_UTR_variant,,ENST00000582026,;STRADA,3_prime_UTR_variant,,ENST00000447001,;STRADA,downstream_gene_variant,,ENST00000582137,;LIMD2,upstream_gene_variant,,ENST00000578402,;LIMD2,upstream_gene_variant,,ENST00000584645,;STRADA,downstream_gene_variant,,ENST00000579340,;STRADA,downstream_gene_variant,,ENST00000578801,;LIMD2,upstream_gene_variant,,ENST00000578061,;LIMD2,upstream_gene_variant,,ENST00000578993,;LIMD2,upstream_gene_variant,,ENST00000583211,;STRADA,downstream_gene_variant,,ENST00000578008,;LIMD2,upstream_gene_variant,,ENST00000259006,;LIMD2,upstream_gene_variant,,ENST00000582055,;STRADA,downstream_gene_variant,,ENST00000581505,;STRADA,downstream_gene_variant,,ENST00000580039,;RP11-51F16.8,3_prime_UTR_variant,,ENST00000580553,;STRADA,non_coding_transcript_exon_variant,,ENST00000583085,;LIMD2,upstream_gene_variant,,ENST00000578297,;LIMD2,upstream_gene_variant,,ENST00000579814,;LIMD2,upstream_gene_variant,,ENST00000578067,;LIMD2,upstream_gene_variant,,ENST00000580222,;STRADA,downstream_gene_variant,,ENST00000581243,;LIMD2,upstream_gene_variant,,ENST00000579329,;	G	ENSG00000266173	ENST00000336174	Transcript	missense_variant	1386	1273	425	E/Q	Gag/Cag	rs748003173	.	.	-1	STRADA	HGNC	30172	protein_coding	YES	CCDS32703.1	ENSP00000336655	STRAA_HUMAN	J3QRC1_HUMAN,J3QKU4_HUMAN,J3QKR7_HUMAN	UPI000013CBBE	.	tolerated(0.08)	possibly_damaging(0.501)	13/13	.	hmmpanther:PTHR24361:SF248,hmmpanther:PTHR24361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTCCAGCT	byFrequency	5	ESCA
YBX2	0	.	GRCh37	17	7193791	7193791	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523C>T	p.Pro175Ser	p.P175S	ENST00000007699	5/9	65	39	26	56	56	0	YBX2,missense_variant,p.Pro175Ser,ENST00000007699,;YBX2,upstream_gene_variant,,ENST00000571464,;SLC2A4,downstream_gene_variant,,ENST00000317370,;SLC2A4,downstream_gene_variant,,ENST00000424875,;SLC2A4,downstream_gene_variant,,ENST00000571308,;YBX2,non_coding_transcript_exon_variant,,ENST00000570627,;YBX2,non_coding_transcript_exon_variant,,ENST00000571485,;YBX2,non_coding_transcript_exon_variant,,ENST00000570720,;YBX2,non_coding_transcript_exon_variant,,ENST00000571834,;YBX2,downstream_gene_variant,,ENST00000571127,;SLC2A4,downstream_gene_variant,,ENST00000570783,;SLC2A4,downstream_gene_variant,,ENST00000572485,;	A	ENSG00000006047	ENST00000007699	Transcript	missense_variant	587	523	175	P/S	Ccc/Tcc	.	.	.	-1	YBX2	HGNC	17948	protein_coding	YES	CCDS11098.1	ENSP00000007699	YBOX2_HUMAN	.	UPI000006E761	.	tolerated(0.08)	possibly_damaging(0.641)	5/9	.	hmmpanther:PTHR11544:SF41,hmmpanther:PTHR11544	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGGGGGCAT	.	5	ESCA
TP53	0	.	GRCh37	17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A	rs397516436	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	6/11	457	289	168	437	437	0	TP53,stop_gained,p.Arg213Ter,ENST00000413465,;TP53,stop_gained,p.Arg213Ter,ENST00000420246,;TP53,stop_gained,p.Arg213Ter,ENST00000269305,;TP53,stop_gained,p.Arg81Ter,ENST00000509690,;TP53,stop_gained,p.Arg213Ter,ENST00000359597,;TP53,stop_gained,p.Arg120Ter,ENST00000514944,;TP53,stop_gained,p.Arg213Ter,ENST00000445888,;TP53,stop_gained,p.Arg213Ter,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	827	637	213	R/*	Cga/Tga	CM951226,rs397516436,TP53_g.12706del,TP53_g.12706C>T,TP53_g.12706C>G,TP53_g.12706C>A,COSM10654,COSM43798,COSM43807,COSM44102,COSM99618,COSM99615,COSM99616,COSM707891,COSM3378350,COSM1638393,COSM99617	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R213*|c.637C>T|45,SITE|p.R120*|c.358C>T|84,SITE|p.R213*|c.637C>T|84,SITE|p.R213*|c.637C>T|84,SITE|p.R81*|c.241C>T|87,SITE|p.R213*|c.637C>T|267,SITE|p.R213*|c.637C>T|33,CODON|p.0?|c.1_1182del1182|6,CODON|p.R213R|c.639A>G|6,CODON|p.R81Q|c.242G>A|9,CODON|p.R213L|c.638G>T|12,CODON|p.R213L|c.638G>T|4,CODON|p.R213L|c.638G>T|39,CODON|p.R213Q|c.638G>A|9,CODON|p.R213Q|c.638G>A|31,CODON|p.R120L|c.359G>T|12,CODON|p.R213P|c.638G>C|6,CODON|p.R120Q|c.359G>A|9,CODON|p.R81L|c.242G>T|12,CODON|p.R213L|c.638G>T|6,CODON|p.R213L|c.638G>T|12,CODON|p.R213Q|c.638G>A|4,CODON|p.R213Q|c.638G>A|9,CODON|p.R213Q|c.638G>A|3,CODON|p.R213fs*34|c.637delC|3,BUFFER|p.V218delV|c.646_648delGTG|8,BUFFER|p.V216G|c.647T>G|5,BUFFER|p.V216A|c.647T>C|3,BUFFER|p.V216E|c.647T>A|4,BUFFER|p.V216M|c.646G>A|20,BUFFER|p.V216M|c.646G>A|12,BUFFER|p.V123M|c.367G>A|20,BUFFER|p.V216L|c.646G>T|8,BUFFER|p.V216M|c.646G>A|20,BUFFER|p.V216M|c.646G>A|7,BUFFER|p.V216M|c.646G>A|70,BUFFER|p.V84M|c.250G>A|20,BUFFER|p.S215R|c.645T>G|3,BUFFER|p.S215R|c.645T>A|4,BUFFER|p.S122R|c.366T>A|4,BUFFER|p.S215R|c.645T>G|13,BUFFER|p.S215R|c.645T>A|4,BUFFER|p.S83R|c.249T>A|4,BUFFER|p.S122R|c.366T>G|3,BUFFER|p.S215R|c.645T>G|3,BUFFER|p.S83R|c.249T>G|3,BUFFER|p.S215R|c.645T>A|8,BUFFER|p.S215I|c.644G>T|4,BUFFER|p.S215I|c.644G>T|4,BUFFER|p.S215I|c.644G>T|19,BUFFER|p.S215T|c.644G>C|3,BUFFER|p.S83I|c.248G>T|4,BUFFER|p.S122I|c.365G>T|4,BUFFER|p.S215N|c.644G>A|8,BUFFER|p.S215C|c.643A>T|4,BUFFER|p.S215G|c.643A>G|3,BUFFER|p.S83G|c.247A>G|3,BUFFER|p.S215G|c.643A>G|10,BUFFER|p.S215G|c.643A>G|3,BUFFER|p.S122G|c.364A>G|3,BUFFER|p.H214Q|c.642T>G|3,BUFFER|p.H214R|c.641A>G|66,BUFFER|p.H214R|c.641A>G|16,BUFFER|p.H214R|c.641A>G|5,BUFFER|p.H82R|c.245A>G|18,BUFFER|p.H121R|c.362A>G|16,BUFFER|p.H214R|c.641A>G|16,BUFFER|p.H214R|c.641A>G|6,BUFFER|p.H214Y|c.640C>T|5,BUFFER|p.H214D|c.640C>G|4,BUFFER|p.F212fs*3|c.635_636delTT|5,BUFFER|p.F212fs*3|c.634_635delTT|6,BUFFER|p.R213fs*34|c.634delT|5,BUFFER|p.T211T|c.633T>C|9,BUFFER|p.T211I|c.632C>T|3,BUFFER|p.T211I|c.632C>T|11,BUFFER|p.T211N|c.632C>A|4,BUFFER|p.T118I|c.353C>T|3,BUFFER|p.T79I|c.236C>T|3,BUFFER|p.T211I|c.632C>T|3,BUFFER|p.T211fs*36|c.631delA|4,BUFFER|p.T211A|c.631A>G|3,BUFFER|p.N210fs*37|c.628delA|3,BUFFER|p.R209fs*6|c.626_627delGA|3,BUFFER|p.R116fs*6|c.347_348delGA|3,BUFFER|p.R209fs*6|c.626_627delGA|3,BUFFER|p.R209fs*6|c.626_627delGA|11,BUFFER|p.R77fs*6|c.230_231delGA|3,BUFFER|p.R209fs*6|c.625_626delAG|23,BUFFER|p.R209K|c.626G>A|6,BUFFER|p.R209T|c.626G>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCGAAAAG	byCluster	5	ESCA
TP53	0	.	GRCh37	17	7578527	7578527	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	5/11	323	195	128	274	274	0	TP53,missense_variant,p.Cys135Arg,ENST00000508793,;TP53,missense_variant,p.Cys135Arg,ENST00000413465,;TP53,missense_variant,p.Cys128Arg,ENST00000604348,;TP53,missense_variant,p.Cys135Arg,ENST00000420246,;TP53,missense_variant,p.Cys135Arg,ENST00000269305,;TP53,missense_variant,p.Cys3Arg,ENST00000509690,;TP53,missense_variant,p.Cys135Arg,ENST00000359597,;TP53,missense_variant,p.Cys42Arg,ENST00000514944,;TP53,missense_variant,p.Cys135Arg,ENST00000445888,;TP53,missense_variant,p.Cys135Arg,ENST00000455263,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	G	ENSG00000141510	ENST00000269305	Transcript	missense_variant	593	403	135	C/R	Tgc/Cgc	TP53_g.12391T>C,TP53_g.12391del,TP53_g.12391T>A,TP53_g.12391T>G,COSM10684,COSM13156,COSM44829,COSM44910,COSM1645410,COSM392225,COSM308319,COSM1645412,COSM308318,COSM392226,COSM392228,COSM1645414,COSM308320,COSM3820724,COSM3937614,COSM1645208,COSM2744947,COSM1645411,COSM308321,COSM392227,COSM1645413	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.C135R|c.403T>C|11,CODON|p.0?|c.1_1182del1182|6,CODON|p.C3W|c.9C>G|4,CODON|p.C42W|c.126C>G|3,CODON|p.C135W|c.405C>G|3,CODON|p.C135W|c.405C>G|3,CODON|p.C135C|c.405C>T|5,CODON|p.C135*|c.405C>A|8,CODON|p.C135W|c.405C>G|24,CODON|p.C135F|c.404G>T|6,CODON|p.C3S|c.8G>C|3,CODON|p.C135S|c.404G>C|3,CODON|p.C3F|c.8G>T|13,CODON|p.C135S|c.404G>C|3,CODON|p.C42F|c.125G>T|13,CODON|p.C42S|c.125G>C|3,CODON|p.C135F|c.404G>T|6,CODON|p.C135Y|c.404G>A|8,CODON|p.C135Y|c.404G>A|54,CODON|p.C135S|c.404G>C|9,CODON|p.C135Y|c.404G>A|3,CODON|p.C42Y|c.125G>A|8,CODON|p.C135Y|c.404G>A|3,CODON|p.C135F|c.404G>T|13,CODON|p.C135F|c.404G>T|13,CODON|p.C135F|c.404G>T|49,CODON|p.C135Y|c.404G>A|8,CODON|p.C3Y|c.8G>A|8,CODON|p.C135fs*35|c.403delT|5,BUFFER|p.A138fs*32|c.412delG|5,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A6V|c.17C>T|4,BUFFER|p.A45V|c.134C>T|4,BUFFER|p.A138V|c.413C>T|21,BUFFER|p.A138P|c.412G>C|14,BUFFER|p.A138T|c.412G>A|5,BUFFER|p.A138fs*11|c.411_412insN|3,BUFFER|p.L137L|c.411G>A|3,BUFFER|p.L137P|c.410T>C|3,BUFFER|p.L137Q|c.410T>A|3,BUFFER|p.Q136H|c.408A>C|5,BUFFER|p.Q136Q|c.408A>G|4,BUFFER|p.Q136P|c.407A>C|3,BUFFER|p.Q136E|c.406C>G|9,BUFFER|p.Q136*|c.406C>T|35,BUFFER|p.Q4*|c.10C>T|5,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q43*|c.127C>T|5,BUFFER|p.Q4E|c.10C>G|6,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q136E|c.406C>G|4,BUFFER|p.Q136E|c.406C>G|5,BUFFER|p.Q43E|c.127C>G|6,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|3,BUFFER|p.C135G|c.403T>G|8,BUFFER|p.C135S|c.403T>A|4,BUFFER|p.C135fs*35|c.400delT|6,BUFFER|p.F134S|c.401T>C|4,BUFFER|p.F134C|c.401T>G|9,BUFFER|p.F134V|c.400T>G|11,BUFFER|p.F41L|c.121T>C|4,BUFFER|p.F134L|c.400T>C|3,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F2L|c.4T>C|4,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F134L|c.400T>C|18,BUFFER|p.M133T|c.398T>C|5,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M40T|c.119T>C|3,BUFFER|p.M1T|c.2T>C|3,BUFFER|p.M1R|c.2T>G|3,BUFFER|p.M133R|c.398T>G|7,BUFFER|p.M133K|c.398T>A|12,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M40R|c.119T>G|3,BUFFER|p.Y126_K132delYSPALNK|c.376_396del21|6,BUFFER|p.K132N|c.396G>C|29,BUFFER|p.K132N|c.396G>T|3,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>C|5,BUFFER|p.K132N|c.396G>T|24,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>T|6,BUFFER|p.N131delN|c.393_395delCAA|4,BUFFER|p.K132R|c.395A>G|5,BUFFER|p.K132T|c.395A>C|7,BUFFER|p.K39T|c.116A>C|3,BUFFER|p.K132R|c.395A>G|39,BUFFER|p.K132M|c.395A>T|10,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K39R|c.116A>G|7,BUFFER|p.K132Q|c.394A>C|13,BUFFER|p.K39E|c.115A>G|3,BUFFER|p.K132*|c.394A>T|5,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|19,BUFFER|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.N131delN|c.391_393delAAC|8,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131I|c.392A>T|7,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131S|c.392A>G|5,BUFFER|p.N38I|c.113A>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCAAAACA	.	5	ESCA
MYH10	0	.	GRCh37	17	8393817	8393817	+	Missense_Mutation	SNP	C	C	T	rs756783316	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4725G>A	p.Met1575Ile	p.M1575I	ENST00000360416	35/43	29	21	8	29	29	0	MYH10,missense_variant,p.Met1565Ile,ENST00000396239,;MYH10,missense_variant,p.Met1544Ile,ENST00000269243,;MYH10,missense_variant,p.Met1560Ile,ENST00000379980,;MYH10,missense_variant,p.Met1575Ile,ENST00000360416,;NDEL1,downstream_gene_variant,,ENST00000581679,;MYH10,downstream_gene_variant,,ENST00000488329,;	T	ENSG00000133026	ENST00000360416	Transcript	missense_variant	4864	4725	1575	M/I	atG/atA	rs756783316	.	.	-1	MYH10	HGNC	7568	protein_coding	YES	CCDS58515.1	ENSP00000353590	MYH10_HUMAN	Q9UMG3_HUMAN,Q9UE82_HUMAN,Q9BWG0_HUMAN,G1UI33_HUMAN,E7ERA5_HUMAN,D3DTS1_HUMAN	UPI0000E24926	.	.	probably_damaging(0.964)	35/43	.	Pfam_domain:PF01576,hmmpanther:PTHR13140:SF328,hmmpanther:PTHR13140,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTCATTTC	.	5	ESCA
PIK3R5	0	.	GRCh37	17	8791843	8791843	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1261T>A	p.Phe421Ile	p.F421I	ENST00000447110	10/19	50	33	17	45	45	0	PIK3R5,missense_variant,p.Phe421Ile,ENST00000584803,;PIK3R5,missense_variant,p.Phe421Ile,ENST00000581552,;PIK3R5,missense_variant,p.Phe421Ile,ENST00000447110,;PIK3R5,upstream_gene_variant,,ENST00000578743,;PIK3R5,downstream_gene_variant,,ENST00000583812,;PIK3R5,downstream_gene_variant,,ENST00000580959,;PIK3R5,downstream_gene_variant,,ENST00000577981,;PIK3R5,downstream_gene_variant,,ENST00000578457,;PIK3R5,downstream_gene_variant,,ENST00000584456,;PIK3R5,3_prime_UTR_variant,,ENST00000269300,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578515,;PIK3R5,upstream_gene_variant,,ENST00000583039,;PIK3R5,upstream_gene_variant,,ENST00000577214,;	T	ENSG00000141506	ENST00000447110	Transcript	missense_variant	1386	1261	421	F/I	Ttc/Atc	.	.	.	-1	PIK3R5	HGNC	30035	protein_coding	YES	CCDS11147.1	ENSP00000392812	PI3R5_HUMAN	L7RT34_HUMAN,J3KT66_HUMAN,J3KRE9_HUMAN	UPI0000071DB4	.	tolerated(0.28)	benign(0.038)	10/19	.	Pfam_domain:PF10486,hmmpanther:PTHR15593:SF2,hmmpanther:PTHR15593	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAACTTCT	.	5	ESCA
MIB1	0	.	GRCh37	18	19449390	19449390	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4763G>C	.	.	ENST00000261537	21/21	29	18	11	46	46	0	MIB1,3_prime_UTR_variant,,ENST00000261537,;RP11-268I9.3,downstream_gene_variant,,ENST00000583436,;MIB1,downstream_gene_variant,,ENST00000578646,;	C	ENSG00000101752	ENST00000261537	Transcript	3_prime_UTR_variant	8048	.	.	.	.	.	.	.	1	MIB1	HGNC	21086	protein_coding	YES	CCDS11871.1	ENSP00000261537	MIB1_HUMAN	B3KRA8_HUMAN	UPI000000D833	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTGAAAGA	.	5	ESCA
DCC	0	.	GRCh37	18	50731660	50731660	+	Missense_Mutation	SNP	C	C	T	rs769342452	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1648C>T	p.Pro550Ser	p.P550S	ENST00000442544	10/29	29	15	13	37	37	0	DCC,missense_variant,p.Pro205Ser,ENST00000581580,;DCC,missense_variant,p.Pro550Ser,ENST00000442544,;DCC,missense_variant,p.Pro398Ser,ENST00000412726,;DCC,missense_variant,p.Pro484Ser,ENST00000304775,;	T	ENSG00000187323	ENST00000442544	Transcript	missense_variant	2264	1648	550	P/S	Ccc/Tcc	rs769342452	.	.	1	DCC	HGNC	2701	protein_coding	YES	CCDS11952.1	ENSP00000389140	DCC_HUMAN	J3QQJ6_HUMAN	UPI00001AEDC6	.	tolerated(0.09)	possibly_damaging(0.476)	10/29	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF68,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265,Prints_domain:PR00014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAACCCCCT	.	5	ESCA
EPB41L3	0	.	GRCh37	18	5406961	5406961	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2164G>T	p.Glu722Ter	p.E722*	ENST00000341928	16/23	90	61	28	94	94	0	EPB41L3,stop_gained,p.Glu722Ter,ENST00000342933,;EPB41L3,stop_gained,p.Glu722Ter,ENST00000341928,;EPB41L3,stop_gained,p.Glu541Ter,ENST00000400111,;EPB41L3,stop_gained,p.Glu553Ter,ENST00000544123,;EPB41L3,stop_gained,p.Glu541Ter,ENST00000540638,;EPB41L3,5_prime_UTR_variant,,ENST00000427684,;EPB41L3,5_prime_UTR_variant,,ENST00000542146,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000578524,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000582729,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000578196,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000580316,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000542652,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000581292,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000545076,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000581387,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000578395,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000580647,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000579271,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000584055,;	A	ENSG00000082397	ENST00000341928	Transcript	stop_gained	2505	2164	722	E/*	Gaa/Taa	.	.	.	-1	EPB41L3	HGNC	3380	protein_coding	YES	CCDS11838.1	ENSP00000343158	E41L3_HUMAN	J3QS55_HUMAN,J3QRQ6_HUMAN,J3QR33_HUMAN,J3QKY2_HUMAN,J3QKK4_HUMAN,J3KS70_HUMAN,J3KRD1_HUMAN	UPI0000129AFA	.	.	.	16/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF20,Pfam_domain:PF04382,PIRSF_domain:PIRSF002304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCTAGCT	.	5	ESCA
SLC44A2	0	.	GRCh37	19	10747198	10747198	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1433C>T	p.Ala478Val	p.A478V	ENST00000335757	15/22	35	20	15	42	42	0	SLC44A2,missense_variant,p.Ala478Val,ENST00000586078,;SLC44A2,missense_variant,p.Ala476Val,ENST00000407327,;SLC44A2,missense_variant,p.Ala478Val,ENST00000335757,;SLC44A2,upstream_gene_variant,,ENST00000586549,;AC011475.1,upstream_gene_variant,,ENST00000430975,;SLC44A2,upstream_gene_variant,,ENST00000591194,;SLC44A2,downstream_gene_variant,,ENST00000588688,;SLC44A2,downstream_gene_variant,,ENST00000590382,;SLC44A2,downstream_gene_variant,,ENST00000590857,;SLC44A2,upstream_gene_variant,,ENST00000588214,;SLC44A2,non_coding_transcript_exon_variant,,ENST00000588393,;SLC44A2,non_coding_transcript_exon_variant,,ENST00000589561,;SLC44A2,downstream_gene_variant,,ENST00000592293,;SLC44A2,downstream_gene_variant,,ENST00000588465,;SLC44A2,downstream_gene_variant,,ENST00000588409,;	T	ENSG00000129353	ENST00000335757	Transcript	missense_variant	1809	1433	478	A/V	gCc/gTc	.	.	.	1	SLC44A2	HGNC	17292	protein_coding	YES	CCDS12245.1	ENSP00000336888	CTL2_HUMAN	B3KX31_HUMAN	UPI000013CCAB	.	deleterious(0)	benign(0.206)	15/22	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12385,hmmpanther:PTHR12385:SF34,Pfam_domain:PF04515	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGCCCTGC	.	5	ESCA
ELAVL3	0	.	GRCh37	19	11591461	11591462	+	5'UTR	DEL	GG	GG	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	GG	GG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39_-38delCCinsA	.	.	ENST00000359227	1/7	102	76	26	38	38	0	ELAVL3,5_prime_UTR_variant,,ENST00000588853,;ELAVL3,5_prime_UTR_variant,,ENST00000359227,;ZNF653,downstream_gene_variant,,ENST00000293771,;ELAVL3,upstream_gene_variant,,ENST00000438662,;ZNF653,downstream_gene_variant,,ENST00000592756,;ZNF653,downstream_gene_variant,,ENST00000589051,;ZNF653,downstream_gene_variant,,ENST00000590296,;ELAVL3,non_coding_transcript_exon_variant,,ENST00000592218,;CTC-398G3.6,intron_variant,,ENST00000585656,;ZNF653,downstream_gene_variant,,ENST00000590548,;	T	ENSG00000196361	ENST00000359227	Transcript	5_prime_UTR_variant	387-388	.	.	.	.	.	.	.	-1	ELAVL3	HGNC	3314	protein_coding	YES	CCDS32912.1	ENSP00000352162	ELAV3_HUMAN	Q96J71_HUMAN	UPI0000129E75	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	GAGGGGGGCTCCG	.	5	ESCA
ZNF791	0	.	GRCh37	19	12739636	12739636	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1293G>A	p.Met431Ile	p.M431I	ENST00000343325	4/4	99	63	36	74	74	0	ZNF791,missense_variant,p.Met431Ile,ENST00000343325,;ZNF791,missense_variant,p.Met322Ile,ENST00000540038,;ZNF791,missense_variant,p.Met399Ile,ENST00000458122,;ZNF791,3_prime_UTR_variant,,ENST00000446165,;ZNF791,downstream_gene_variant,,ENST00000600752,;AC010422.1,upstream_gene_variant,,ENST00000408416,;ZNF490,intron_variant,,ENST00000465656,;ZNF791,downstream_gene_variant,,ENST00000597691,;ZNF791,downstream_gene_variant,,ENST00000598225,;	A	ENSG00000173875	ENST00000343325	Transcript	missense_variant	1455	1293	431	M/I	atG/atA	.	.	.	1	ZNF791	HGNC	26895	protein_coding	YES	CCDS12273.1	ENSP00000342974	ZN791_HUMAN	M0R0E8_HUMAN,F5GXD7_HUMAN,B7Z586_HUMAN	UPI0000203455	.	tolerated(0.11)	benign(0.232)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24379,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATGATCAC	.	5	ESCA
RTBDN	0	.	GRCh37	19	12940696	12940696	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194C>G	p.Pro65Arg	p.P65R	ENST00000322912	3/7	81	55	25	56	56	0	RTBDN,missense_variant,p.Pro33Arg,ENST00000586969,;RTBDN,missense_variant,p.Pro33Arg,ENST00000589681,;RTBDN,missense_variant,p.Pro33Arg,ENST00000585384,;RTBDN,missense_variant,p.Pro65Arg,ENST00000587549,;RTBDN,missense_variant,p.Pro65Arg,ENST00000322912,;RTBDN,missense_variant,p.Pro33Arg,ENST00000589808,;RTBDN,missense_variant,p.Pro43Arg,ENST00000592204,;RTBDN,missense_variant,p.Pro65Arg,ENST00000589272,;RTBDN,missense_variant,p.Pro33Arg,ENST00000591512,;RTBDN,missense_variant,p.Pro33Arg,ENST00000458671,;RTBDN,missense_variant,p.Pro39Arg,ENST00000590404,;RTBDN,missense_variant,p.Pro33Arg,ENST00000589567,;RTBDN,5_prime_UTR_variant,,ENST00000393233,;MAST1,upstream_gene_variant,,ENST00000591495,;CTD-2265O21.3,intron_variant,,ENST00000588469,;HOOK2,intron_variant,,ENST00000589765,;	C	ENSG00000132026	ENST00000322912	Transcript	missense_variant	512	194	65	P/R	cCa/cGa	.	.	.	-1	RTBDN	HGNC	30310	protein_coding	YES	CCDS12283.1	ENSP00000326253	RTBDN_HUMAN	K7EN64_HUMAN,K7EKV3_HUMAN,K7EIS2_HUMAN	UPI000006D823	.	tolerated(0.19)	possibly_damaging(0.908)	3/7	.	Pfam_domain:PF03024,hmmpanther:PTHR10517	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTGGGCGG	.	5	ESCA
TECR	0	.	GRCh37	19	14676736	14676736	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53G>A	.	.	ENST00000215567	13/13	112	81	30	120	120	0	TECR,3_prime_UTR_variant,,ENST00000596073,;TECR,3_prime_UTR_variant,,ENST00000601187,;TECR,3_prime_UTR_variant,,ENST00000436007,;TECR,3_prime_UTR_variant,,ENST00000600083,;TECR,3_prime_UTR_variant,,ENST00000215567,;NDUFB7,downstream_gene_variant,,ENST00000215565,;TECR,downstream_gene_variant,,ENST00000594545,;TECR,downstream_gene_variant,,ENST00000598715,;TECR,downstream_gene_variant,,ENST00000598298,;TECR,downstream_gene_variant,,ENST00000596164,;TECR,3_prime_UTR_variant,,ENST00000598987,;TECR,non_coding_transcript_exon_variant,,ENST00000594958,;TECR,non_coding_transcript_exon_variant,,ENST00000598408,;TECR,non_coding_transcript_exon_variant,,ENST00000600395,;TECR,non_coding_transcript_exon_variant,,ENST00000599101,;TECR,non_coding_transcript_exon_variant,,ENST00000593775,;TECR,non_coding_transcript_exon_variant,,ENST00000597607,;TECR,downstream_gene_variant,,ENST00000601461,;TECR,downstream_gene_variant,,ENST00000598918,;TECR,downstream_gene_variant,,ENST00000600076,;TECR,downstream_gene_variant,,ENST00000593637,;TECR,downstream_gene_variant,,ENST00000601350,;TECR,downstream_gene_variant,,ENST00000598333,;TECR,downstream_gene_variant,,ENST00000596953,;TECR,downstream_gene_variant,,ENST00000601652,;NDUFB7,downstream_gene_variant,,ENST00000593353,;TECR,downstream_gene_variant,,ENST00000594807,;	A	ENSG00000099797	ENST00000215567	Transcript	3_prime_UTR_variant	1117	.	.	.	.	.	.	.	1	TECR	HGNC	4551	protein_coding	YES	CCDS12313.1	ENSP00000215567	TECR_HUMAN	M0R0N5_HUMAN,M0QXS1_HUMAN,B4DR74_HUMAN	UPI00000534C6	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGAGGAGTG	.	5	ESCA
SLC1A6	0	.	GRCh37	19	15083545	15083545	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.178C>T	p.%3D	p.L60L	ENST00000221742	1/9	28	23	5	30	30	0	SLC1A6,missense_variant,p.Ser64Phe,ENST00000599636,;SLC1A6,missense_variant,p.Ser64Phe,ENST00000430939,;SLC1A6,synonymous_variant,p.%3D,ENST00000544886,;SLC1A6,synonymous_variant,p.%3D,ENST00000601761,;SLC1A6,synonymous_variant,p.%3D,ENST00000600144,;SLC1A6,synonymous_variant,p.%3D,ENST00000597262,;SLC1A6,synonymous_variant,p.%3D,ENST00000595863,;SLC1A6,synonymous_variant,p.%3D,ENST00000221742,;SLC1A6,synonymous_variant,p.%3D,ENST00000598504,;SLC1A6,downstream_gene_variant,,ENST00000594383,;SLC1A6,non_coding_transcript_exon_variant,,ENST00000596697,;	A	ENSG00000105143	ENST00000221742	Transcript	synonymous_variant	186	178	60	L	Ctg/Ttg	.	.	.	-1	SLC1A6	HGNC	10944	protein_coding	YES	CCDS12321.1	ENSP00000221742	EAA4_HUMAN	Q8N753_HUMAN,M0R1V3_HUMAN,M0R106_HUMAN,M0QY32_HUMAN	UPI0000129B1A	.	.	.	1/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11958,hmmpanther:PTHR11958:SF29,Pfam_domain:PF00375,Gene3D:2nwlC00,Superfamily_domains:0053221,Prints_domain:PR00173	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCAGAATGA	.	5	ESCA
CPAMD8	0	.	GRCh37	19	17038839	17038839	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3491G>A	p.Arg1164Gln	p.R1164Q	ENST00000443236	25/42	46	33	12	37	37	0	CPAMD8,missense_variant,p.Arg1164Gln,ENST00000443236,;	T	ENSG00000160111	ENST00000443236	Transcript	missense_variant	3523	3491	1164	R/Q	cGa/cAa	COSM3530211	.	.	-1	CPAMD8	HGNC	23228	protein_coding	YES	CCDS42519.1	ENSP00000402505	CPMD8_HUMAN	.	UPI0000E8AC99	.	deleterious(0.03)	possibly_damaging(0.46)	25/42	.	hmmpanther:PTHR11412:SF76,hmmpanther:PTHR11412	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCGCTCA	.	5	ESCA
ZNF14	0	.	GRCh37	19	19823885	19823885	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205G>C	p.Glu69Gln	p.E69Q	ENST00000344099	4/4	61	45	16	47	47	0	ZNF14,missense_variant,p.Glu69Gln,ENST00000344099,;CTC-412M14.5,downstream_gene_variant,,ENST00000604034,;	G	ENSG00000105708	ENST00000344099	Transcript	missense_variant	344	205	69	E/Q	Gag/Cag	.	.	.	-1	ZNF14	HGNC	12924	protein_coding	YES	CCDS12409.1	ENSP00000340514	ZNF14_HUMAN	.	UPI00001E058E	.	tolerated(0.06)	benign(0.214)	4/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24379:SF21,hmmpanther:PTHR24379	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCAACCA	.	5	ESCA
ZNF98	0	.	GRCh37	19	22605125	22605125	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-99G>C	.	.	ENST00000357774	1/4	48	26	21	37	37	0	ZNF98,5_prime_UTR_variant,,ENST00000357774,;ZNF98,5_prime_UTR_variant,,ENST00000593657,;ZNF98,5_prime_UTR_variant,,ENST00000601553,;ZNF98,intron_variant,,ENST00000593802,;AC011516.1,upstream_gene_variant,,ENST00000599129,;	G	ENSG00000197360	ENST00000357774	Transcript	5_prime_UTR_variant	24	.	.	.	.	.	.	.	-1	ZNF98	HGNC	13174	protein_coding	YES	CCDS46031.1	ENSP00000350418	ZNF98_HUMAN	M0QZS3_HUMAN	UPI0000251DC5	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACTCCGGCT	.	5	ESCA
TSHZ3	0	.	GRCh37	19	31766581	31766581	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*872C>G	.	.	ENST00000240587	2/2	72	56	16	80	80	0	TSHZ3,3_prime_UTR_variant,,ENST00000240587,;TSHZ3,downstream_gene_variant,,ENST00000560707,;	C	ENSG00000121297	ENST00000240587	Transcript	3_prime_UTR_variant	4446	.	.	.	.	.	.	.	-1	TSHZ3	HGNC	30700	protein_coding	YES	CCDS12421.2	ENSP00000240587	TSH3_HUMAN	A1L0U7_HUMAN	UPI0000202000	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACTGTATAG	.	5	ESCA
ZNF569	0	.	GRCh37	19	37904952	37904952	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608G>C	p.Arg203Thr	p.R203T	ENST00000316950	6/6	34	28	6	53	53	0	ZNF569,missense_variant,p.Arg203Thr,ENST00000316950,;ZNF569,missense_variant,p.Arg203Thr,ENST00000392149,;ZNF569,missense_variant,p.Arg44Thr,ENST00000392150,;ZNF569,missense_variant,p.Arg227Thr,ENST00000448051,;ZNF569,downstream_gene_variant,,ENST00000592490,;	G	ENSG00000196437	ENST00000316950	Transcript	missense_variant	1166	608	203	R/T	aGa/aCa	.	.	.	-1	ZNF569	HGNC	24737	protein_coding	YES	CCDS12503.1	ENSP00000325018	ZN569_HUMAN	Q17RR6_HUMAN	UPI0000202203	.	tolerated(0.57)	possibly_damaging(0.9)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF68,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGTCTGATG	.	2	ESCA
ZNF573	0	.	GRCh37	19	38264380	38264380	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11C>G	.	.	ENST00000590414	1/4	28	20	8	19	19	0	ZNF573,5_prime_UTR_variant,,ENST00000357309,;ZNF573,5_prime_UTR_variant,,ENST00000588218,;ZNF573,5_prime_UTR_variant,,ENST00000585724,;ZNF573,5_prime_UTR_variant,,ENST00000339503,;ZNF573,5_prime_UTR_variant,,ENST00000378445,;ZNF573,5_prime_UTR_variant,,ENST00000590414,;ZNF573,5_prime_UTR_variant,,ENST00000536220,;ZNF573,intron_variant,,ENST00000392138,;ZNF573,intron_variant,,ENST00000494605,;ZNF573,5_prime_UTR_variant,,ENST00000591516,;ZNF573,5_prime_UTR_variant,,ENST00000489148,;ZNF573,5_prime_UTR_variant,,ENST00000589632,;ZNF573,5_prime_UTR_variant,,ENST00000586155,;	C	ENSG00000189144	ENST00000590414	Transcript	5_prime_UTR_variant	12	.	.	.	.	.	.	.	-1	ZNF573	HGNC	26420	protein_coding	YES	CCDS59381.1	ENSP00000465020	.	K7EJ45_HUMAN	UPI000059D70C	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCAGAGAAT	.	2	ESCA
RYR1	0	.	GRCh37	19	39062663	39062663	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13751C>G	p.Ser4584Ter	p.S4584*	ENST00000359596	95/106	52	34	18	38	38	0	RYR1,stop_gained,p.Ser4579Ter,ENST00000355481,;RYR1,stop_gained,p.Ser71Ter,ENST00000593677,;RYR1,stop_gained,p.Ser4579Ter,ENST00000360985,;RYR1,stop_gained,p.Ser4584Ter,ENST00000359596,;	G	ENSG00000196218	ENST00000359596	Transcript	stop_gained	13751	13751	4584	S/*	tCa/tGa	.	.	.	1	RYR1	HGNC	10483	protein_coding	YES	CCDS33011.1	ENSP00000352608	RYR1_HUMAN	O75591_HUMAN,B4DET7_HUMAN	UPI0000D7E62F	.	.	.	95/106	.	hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF06459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCAGACT	.	5	ESCA
PSMC4	0	.	GRCh37	19	40478056	40478056	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40G>A	p.Glu14Lys	p.E14K	ENST00000157812	2/11	36	27	8	18	18	0	PSMC4,missense_variant,p.Glu14Lys,ENST00000157812,;PSMC4,missense_variant,p.Glu14Lys,ENST00000455878,;PSMC4,non_coding_transcript_exon_variant,,ENST00000593455,;PSMC4,non_coding_transcript_exon_variant,,ENST00000596386,;PSMC4,non_coding_transcript_exon_variant,,ENST00000601697,;	A	ENSG00000013275	ENST00000157812	Transcript	missense_variant	238	40	14	E/K	Gag/Aag	COSM349588	.	.	1	PSMC4	HGNC	9551	protein_coding	YES	CCDS12547.1	ENSP00000157812	PRS6B_HUMAN	A8K2M0_HUMAN	UPI0000132373	.	tolerated_low_confidence(0.77)	benign(0.001)	2/11	.	hmmpanther:PTHR23073:SF8,hmmpanther:PTHR23073	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGAGATC	.	5	ESCA
ZNF546	0	.	GRCh37	19	40521329	40521329	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2152G>A	p.Glu718Lys	p.E718K	ENST00000347077	7/7	41	26	15	36	36	0	ZNF546,missense_variant,p.Glu692Lys,ENST00000600094,;ZNF546,missense_variant,p.Glu718Lys,ENST00000347077,;ZNF546,intron_variant,,ENST00000596894,;ZNF546,downstream_gene_variant,,ENST00000601138,;ZNF546,downstream_gene_variant,,ENST00000599504,;CTC-471F3.6,upstream_gene_variant,,ENST00000593658,;	A	ENSG00000187187	ENST00000347077	Transcript	missense_variant	2368	2152	718	E/K	Gag/Aag	.	.	.	1	ZNF546	HGNC	28671	protein_coding	YES	CCDS12548.1	ENSP00000339823	ZN546_HUMAN	M0R292_HUMAN,M0QXR6_HUMAN	UPI00001984E3	.	deleterious(0.01)	possibly_damaging(0.57)	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF142,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTGAGCTT	.	5	ESCA
CADM4	0	.	GRCh37	19	44126880	44126880	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*602C>T	.	.	ENST00000222374	9/9	40	28	12	23	23	0	CADM4,3_prime_UTR_variant,,ENST00000222374,;ZNF428,upstream_gene_variant,,ENST00000598676,;ZNF428,upstream_gene_variant,,ENST00000300811,;CADM4,downstream_gene_variant,,ENST00000593506,;ZNF428,upstream_gene_variant,,ENST00000595304,;	A	ENSG00000105767	ENST00000222374	Transcript	3_prime_UTR_variant	1818	.	.	.	.	.	.	.	-1	CADM4	HGNC	30825	protein_coding	YES	CCDS12627.1	ENSP00000222374	CADM4_HUMAN	.	UPI000004EE93	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGGGAGCCC	.	5	ESCA
PLAUR	0	.	GRCh37	19	44160758	44160758	+	Silent	SNP	G	G	A	rs752301270	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.345C>T	p.%3D	p.L115L	ENST00000340093	4/7	51	27	24	28	28	0	PLAUR,synonymous_variant,p.%3D,ENST00000601723,;PLAUR,synonymous_variant,p.%3D,ENST00000602141,;PLAUR,synonymous_variant,p.%3D,ENST00000599892,;PLAUR,synonymous_variant,p.%3D,ENST00000593714,;PLAUR,synonymous_variant,p.%3D,ENST00000593939,;PLAUR,synonymous_variant,p.%3D,ENST00000593447,;PLAUR,synonymous_variant,p.%3D,ENST00000221264,;PLAUR,synonymous_variant,p.%3D,ENST00000340093,;PLAUR,synonymous_variant,p.%3D,ENST00000339082,;PLAUR,upstream_gene_variant,,ENST00000595038,;RN7SL368P,downstream_gene_variant,,ENST00000473384,;PLAUR,3_prime_UTR_variant,,ENST00000597107,;PLAUR,non_coding_transcript_exon_variant,,ENST00000594364,;PLAUR,non_coding_transcript_exon_variant,,ENST00000593396,;	A	ENSG00000011422	ENST00000340093	Transcript	synonymous_variant	575	345	115	L	ctC/ctT	rs752301270	.	.	-1	PLAUR	HGNC	9053	protein_coding	YES	CCDS12628.1	ENSP00000339328	UPAR_HUMAN	Q9UPI5_HUMAN,Q6GY32_HUMAN,M0R0H5_HUMAN,M0QYR6_HUMAN	UPI000000D8C1	.	.	.	4/7	.	hmmpanther:PTHR10624:SF7,hmmpanther:PTHR10624,Gene3D:2.10.60.10,SMART_domains:SM00134,Superfamily_domains:SSF57302	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTCGAGGTA	.	5	ESCA
ZNF223	0	.	GRCh37	19	44559295	44559295	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-35C>G	.	.	ENST00000434772	2/5	57	35	22	49	49	0	ZNF223,5_prime_UTR_variant,,ENST00000585552,;ZNF223,5_prime_UTR_variant,,ENST00000434772,;ZNF223,non_coding_transcript_exon_variant,,ENST00000588518,;ZNF223,stop_gained,p.Ser99Ter,ENST00000591793,;ZNF223,5_prime_UTR_variant,,ENST00000593088,;	G	ENSG00000178386	ENST00000434772	Transcript	5_prime_UTR_variant	221	.	.	.	.	.	.	.	1	ZNF223	HGNC	13016	protein_coding	YES	CCDS12635.1	ENSP00000401947	ZN223_HUMAN	K7EQ32_HUMAN	UPI00002025B5	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATTCAGGAC	.	5	ESCA
PPP1R37	0	.	GRCh37	19	45649660	45649660	+	Missense_Mutation	SNP	C	C	T	rs747029064	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2006C>T	p.Ser669Phe	p.S669F	ENST00000221462	12/13	62	47	14	51	51	0	PPP1R37,missense_variant,p.Ser665Phe,ENST00000421905,;PPP1R37,missense_variant,p.Ser669Phe,ENST00000221462,;MARK4,intron_variant,,ENST00000587566,;PPP1R37,downstream_gene_variant,,ENST00000544069,;NKPD1,downstream_gene_variant,,ENST00000317951,;AC005757.7,downstream_gene_variant,,ENST00000589594,;PPP1R37,non_coding_transcript_exon_variant,,ENST00000422370,;PPP1R37,non_coding_transcript_exon_variant,,ENST00000540059,;	T	ENSG00000104866	ENST00000221462	Transcript	missense_variant	2370	2006	669	S/F	tCc/tTc	rs747029064	.	.	1	PPP1R37	HGNC	27607	protein_coding	YES	CCDS56096.1	ENSP00000221462	PPR37_HUMAN	.	UPI000041AA74	.	deleterious_low_confidence(0.01)	unknown(0)	12/13	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCCAAGA	.	5	ESCA
TRPM4	0	.	GRCh37	19	49705305	49705305	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3038C>T	p.Ser1013Phe	p.S1013F	ENST00000252826	20/25	49	34	14	31	31	0	TRPM4,missense_variant,p.Ser659Phe,ENST00000355712,;TRPM4,missense_variant,p.Ser868Phe,ENST00000427978,;TRPM4,missense_variant,p.Ser1013Phe,ENST00000252826,;TRPM4,3_prime_UTR_variant,,ENST00000595519,;TRPM4,3_prime_UTR_variant,,ENST00000598502,;TRPM4,3_prime_UTR_variant,,ENST00000598697,;TRPM4,non_coding_transcript_exon_variant,,ENST00000596338,;TRPM4,non_coding_transcript_exon_variant,,ENST00000595071,;	T	ENSG00000130529	ENST00000252826	Transcript	missense_variant	3164	3038	1013	S/F	tCc/tTc	COSM3536777	.	.	1	TRPM4	HGNC	17993	protein_coding	YES	CCDS33073.1	ENSP00000252826	TRPM4_HUMAN	.	UPI0000070598	.	deleterious(0.01)	possibly_damaging(0.845)	20/25	.	hmmpanther:PTHR13800:SF6,hmmpanther:PTHR13800	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCTCCCAGT	.	5	ESCA
MBOAT7	0	.	GRCh37	19	54677178	54677178	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*560C>T	.	.	ENST00000245615	8/8	33	19	14	37	37	0	MBOAT7,3_prime_UTR_variant,,ENST00000431666,;MBOAT7,3_prime_UTR_variant,,ENST00000338624,;MBOAT7,3_prime_UTR_variant,,ENST00000245615,;MBOAT7,downstream_gene_variant,,ENST00000449249,;TMC4,upstream_gene_variant,,ENST00000376591,;MBOAT7,downstream_gene_variant,,ENST00000391754,;TMC4,upstream_gene_variant,,ENST00000446291,;TMC4,upstream_gene_variant,,ENST00000301187,;TMC4,upstream_gene_variant,,ENST00000479750,;TMC4,upstream_gene_variant,,ENST00000476013,;MBOAT7,3_prime_UTR_variant,,ENST00000437868,;MBOAT7,non_coding_transcript_exon_variant,,ENST00000494142,;TMC4,upstream_gene_variant,,ENST00000497518,;	A	ENSG00000125505	ENST00000245615	Transcript	3_prime_UTR_variant	2460	.	.	.	.	.	.	.	-1	MBOAT7	HGNC	15505	protein_coding	YES	CCDS12883.1	ENSP00000245615	MBOA7_HUMAN	C9J4E9_HUMAN,A9C4B8_HUMAN	UPI000013CBAC	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAGGGCGCC	.	5	ESCA
LILRA6	0	.	GRCh37	19	54744236	54744236	+	Missense_Mutation	SNP	G	G	A	rs749816494	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1172C>T	p.Ala391Val	p.A391V	ENST00000396365	6/8	113	79	33	122	122	0	LILRA6,missense_variant,p.Ala391Val,ENST00000245621,;LILRA6,missense_variant,p.Ala391Val,ENST00000396365,;LILRA6,missense_variant,p.Ala391Val,ENST00000419410,;LILRA6,3_prime_UTR_variant,,ENST00000391735,;LILRB3,intron_variant,,ENST00000407860,;LILRA6,intron_variant,,ENST00000270464,;LILRA6,intron_variant,,ENST00000440558,;LILRA6,3_prime_UTR_variant,,ENST00000430421,;RPS9,intron_variant,,ENST00000448962,;LILRA6,downstream_gene_variant,,ENST00000474697,;	A	ENSG00000244482	ENST00000396365	Transcript	missense_variant	1212	1172	391	A/V	gCg/gTg	rs749816494,COSM1001046	.	.	-1	LILRA6	HGNC	15495	protein_coding	YES	CCDS42610.1	ENSP00000379651	LIRA6_HUMAN	.	UPI000022A9CA	.	deleterious(0.05)	benign(0.334)	6/8	.	Superfamily_domains:SSF48726,PIRSF_domain:PIRSF001979,SMART_domains:SM00409,SMART_domains:SM00408,Pfam_domain:PF13927,Gene3D:2.60.40.10,hmmpanther:PTHR11738:SF99,hmmpanther:PTHR11738	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCCCGCGTGG	byFrequency	3	ESCA
SUV420H2	0	.	GRCh37	19	55853307	55853307	+	Translation_Start_Site	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3G>A	p.Met1?	p.M1?	ENST00000255613	2/9	87	54	33	58	58	0	SUV420H2,start_lost,p.Met1?,ENST00000255613,;AC020922.1,5_prime_UTR_variant,,ENST00000539076,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000402499,;SUV420H2,upstream_gene_variant,,ENST00000460956,;SUV420H2,upstream_gene_variant,,ENST00000587442,;SUV420H2,start_lost,p.Met1?,ENST00000592631,;SUV420H2,start_lost,p.Met1?,ENST00000445196,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000464185,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000589338,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000498738,;SUV420H2,upstream_gene_variant,,ENST00000474492,;SUV420H2,upstream_gene_variant,,ENST00000468951,;	A	ENSG00000133247	ENST00000255613	Transcript	start_lost	251	3	1	M/I	atG/atA	.	.	.	1	SUV420H2	HGNC	28405	protein_coding	YES	CCDS12922.1	ENSP00000255613	SV422_HUMAN	.	UPI000000DABC	.	deleterious_low_confidence(0)	probably_damaging(0.942)	2/9	.	hmmpanther:PTHR12977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATGGGGCC	.	5	ESCA
NLRP5	0	.	GRCh37	19	56538599	56538599	+	Missense_Mutation	SNP	G	G	C	rs767653801	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1000G>C	p.Glu334Gln	p.E334Q	ENST00000390649	7/15	26	14	12	30	30	0	NLRP5,missense_variant,p.Glu334Gln,ENST00000390649,;	C	ENSG00000171487	ENST00000390649	Transcript	missense_variant	1000	1000	334	E/Q	Gag/Cag	rs767653801	.	.	1	NLRP5	HGNC	21269	protein_coding	YES	CCDS12938.1	ENSP00000375063	NALP5_HUMAN	.	UPI00001AEEBD	.	tolerated(0.16)	possibly_damaging(0.562)	7/15	.	PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106,Pfam_domain:PF05729,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAGAGTTC	byFrequency	5	ESCA
ELAVL1	0	.	GRCh37	19	8032642	8032642	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.463G>C	p.Asp155His	p.D155H	ENST00000407627	5/6	66	37	29	52	52	0	ELAVL1,missense_variant,p.Asp182His,ENST00000351593,;ELAVL1,missense_variant,p.Asp155His,ENST00000407627,;ELAVL1,missense_variant,p.Asp155His,ENST00000596459,;ELAVL1,intron_variant,,ENST00000593807,;ELAVL1,intron_variant,,ENST00000596154,;	G	ENSG00000066044	ENST00000407627	Transcript	missense_variant	593	463	155	D/H	Gac/Cac	.	.	.	-1	ELAVL1	HGNC	3312	protein_coding	YES	CCDS12193.1	ENSP00000385269	ELAV1_HUMAN	.	UPI0000129E74	.	deleterious(0)	probably_damaging(0.995)	5/6	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011,hmmpanther:PTHR24011:SF228,Gene3D:3.30.70.330,Pfam_domain:PF00076,TIGRFAM_domain:TIGR01661,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTGTCAAACC	.	3	ESCA
MUC16	0	.	GRCh37	19	9073176	9073176	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14270C>A	p.Pro4757His	p.P4757H	ENST00000397910	3/84	61	41	20	49	49	0	MUC16,missense_variant,p.Pro4757His,ENST00000397910,;	T	ENSG00000181143	ENST00000397910	Transcript	missense_variant	14474	14270	4757	P/H	cCt/cAt	COSM270952,COSM1003989,COSM270953,COSM1003990,COSM1003988,COSM270954	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	3/84	.	.	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAGGTAAG	.	5	ESCA
SLC16A4	0	.	GRCh37	1	110931944	110931944	+	Translation_Start_Site	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2T>C	p.Met1?	p.M1?	ENST00000369779	2/9	22	15	6	29	29	0	SLC16A4,start_lost,p.Met1?,ENST00000369781,;SLC16A4,start_lost,p.Met1?,ENST00000369779,;SLC16A4,start_lost,p.Met1?,ENST00000472422,;SLC16A4,5_prime_UTR_variant,,ENST00000541986,;SLC16A4,5_prime_UTR_variant,,ENST00000437429,;LAMTOR5-AS1,intron_variant,,ENST00000590413,;SLC16A4,non_coding_transcript_exon_variant,,ENST00000497687,;SLC16A4,start_lost,p.Met1?,ENST00000492412,;SLC16A4,start_lost,p.Met1?,ENST00000528649,;SLC16A4,start_lost,p.Met1?,ENST00000461647,;	G	ENSG00000168679	ENST00000369779	Transcript	start_lost	252	2	1	M/T	aTg/aCg	.	.	.	-1	SLC16A4	HGNC	10925	protein_coding	YES	CCDS823.1	ENSP00000358794	MOT5_HUMAN	.	UPI000004EE9B	.	deleterious_low_confidence(0)	benign(0.039)	2/9	.	hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCATGATG	.	5	ESCA
MTOR	0	.	GRCh37	1	11288958	11288958	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2797G>A	p.Glu933Lys	p.E933K	ENST00000361445	19/58	78	56	22	61	61	0	MTOR,missense_variant,p.Glu933Lys,ENST00000361445,;RNU6-291P,downstream_gene_variant,,ENST00000384720,;RPL39P6,upstream_gene_variant,,ENST00000448289,;	T	ENSG00000198793	ENST00000361445	Transcript	missense_variant	2874	2797	933	E/K	Gaa/Aaa	.	.	.	-1	MTOR	HGNC	3942	protein_coding	YES	CCDS127.1	ENSP00000354558	MTOR_HUMAN	Q96QW8_HUMAN,B1AKQ2_HUMAN,B1AKP8_HUMAN	UPI000012ABD3	.	tolerated(0.12)	probably_damaging(0.996)	19/58	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF63,Pfam_domain:PF11865,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTCACTAG	.	5	ESCA
ATP1A1	0	.	GRCh37	1	116916799	116916799	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-53G>A	.	.	ENST00000537345	1/23	81	58	23	81	81	0	ATP1A1,5_prime_UTR_variant,,ENST00000537345,;ATP1A1,intron_variant,,ENST00000418797,;AL136376.1,intron_variant,,ENST00000598661,;ATP1A1,intron_variant,,ENST00000295598,;ATP1A1,intron_variant,,ENST00000488733,;	A	ENSG00000163399	ENST00000537345	Transcript	5_prime_UTR_variant	311	.	.	.	.	.	.	.	1	ATP1A1	HGNC	799	protein_coding	YES	CCDS53351.1	ENSP00000445306	AT1A1_HUMAN	Q5TC02_HUMAN,Q5TC01_HUMAN	UPI0001A471A4	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGCGAAGCC	.	5	ESCA
NBPF20	0	.	GRCh37	1	148344692	148344692	+	Missense_Mutation	SNP	G	G	C	rs374322358	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226C>G	p.Gln76Glu	p.Q76E	ENST00000369202	3/111	198	165	33	157	157	0	NBPF20,missense_variant,p.Gln76Glu,ENST00000414710,;NBPF20,missense_variant,p.Gln76Glu,ENST00000369188,;NBPF20,missense_variant,p.Gln76Glu,ENST00000369202,;NBPF20,intron_variant,,ENST00000369189,;PFN1P3,upstream_gene_variant,,ENST00000443612,;	C	ENSG00000203832	ENST00000369202	Transcript	missense_variant	424	226	76	Q/E	Cag/Gag	rs374322358	.	.	-1	NBPF20	HGNC	32000	protein_coding	YES	.	ENSP00000358203	.	S4R3H5_HUMAN,I0CMK7_HUMAN,H7BY69_HUMAN,F5H1Q5_HUMAN,A2BH96_HUMAN	UPI000066DA61	.	.	benign(0.111)	3/111	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACTGTCGCT	byCluster	4	ESCA
HIST2H2BE	0	.	GRCh37	1	149858228	149858228	+	5'UTR	SNP	G	G	C	rs370873522	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-38C>G	.	.	ENST00000369155	1/1	27	19	8	19	19	0	HIST2H2BE,5_prime_UTR_variant,,ENST00000369155,;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,;HIST2H2AC,upstream_gene_variant,,ENST00000331380,;	C	ENSG00000184678	ENST00000369155	Transcript	5_prime_UTR_variant	5	.	.	.	.	rs370873522	.	.	-1	HIST2H2BE	HGNC	4760	protein_coding	YES	CCDS936.1	ENSP00000358151	H2B2E_HUMAN	.	UPI0000000C6F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAAGAAGTA	.	5	ESCA
ANP32E	0	.	GRCh37	1	150192438	150192438	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*555C>T	.	.	ENST00000314136	7/7	16	10	6	15	15	0	ANP32E,3_prime_UTR_variant,,ENST00000369119,;ANP32E,3_prime_UTR_variant,,ENST00000369116,;ANP32E,3_prime_UTR_variant,,ENST00000314136,;ANP32E,downstream_gene_variant,,ENST00000533654,;ANP32E,downstream_gene_variant,,ENST00000369114,;ANP32E,downstream_gene_variant,,ENST00000534437,;ANP32E,downstream_gene_variant,,ENST00000436748,;ANP32E,downstream_gene_variant,,ENST00000369115,;	A	ENSG00000143401	ENST00000314136	Transcript	3_prime_UTR_variant	1732	.	.	.	.	.	.	.	-1	ANP32E	HGNC	16673	protein_coding	YES	CCDS946.1	ENSP00000324074	AN32E_HUMAN	Q53F20_HUMAN	UPI0000071679	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAATAGAACCT	.	2	ESCA
LYSMD1	0	.	GRCh37	1	151134280	151134280	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.477G>A	p.%3D	p.K159K	ENST00000368908	2/3	95	57	37	79	79	0	LYSMD1,synonymous_variant,p.%3D,ENST00000440902,;LYSMD1,synonymous_variant,p.%3D,ENST00000368908,;SCNM1,intron_variant,,ENST00000602841,;SCNM1,upstream_gene_variant,,ENST00000368905,;TNFAIP8L2,downstream_gene_variant,,ENST00000368910,;SCNM1,upstream_gene_variant,,ENST00000368902,;SCNM1,upstream_gene_variant,,ENST00000471039,;SCNM1,upstream_gene_variant,,ENST00000461862,;SCNM1,upstream_gene_variant,,ENST00000497147,;	T	ENSG00000163155	ENST00000368908	Transcript	synonymous_variant	1138	477	159	K	aaG/aaA	.	.	.	-1	LYSMD1	HGNC	32070	protein_coding	YES	CCDS986.1	ENSP00000357904	LYSM1_HUMAN	.	UPI000007311C	.	.	.	2/3	.	hmmpanther:PTHR20932,hmmpanther:PTHR20932:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCTTAAG	.	5	ESCA
RFX5	0	.	GRCh37	1	151314765	151314765	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1748G>A	p.Gly583Glu	p.G583E	ENST00000290524	11/11	28	17	10	21	21	0	RFX5,missense_variant,p.Gly583Glu,ENST00000392746,;RFX5,missense_variant,p.Gly543Glu,ENST00000452513,;RFX5,missense_variant,p.Gly583Glu,ENST00000452671,;RFX5,missense_variant,p.Gly583Glu,ENST00000368870,;RFX5,missense_variant,p.Gly583Glu,ENST00000290524,;RFX5,intron_variant,,ENST00000436637,;RFX5,downstream_gene_variant,,ENST00000437327,;RFX5,downstream_gene_variant,,ENST00000412774,;RFX5,downstream_gene_variant,,ENST00000450506,;RFX5,downstream_gene_variant,,ENST00000458484,;RFX5,downstream_gene_variant,,ENST00000430227,;RFX5,downstream_gene_variant,,ENST00000436271,;RFX5,downstream_gene_variant,,ENST00000422595,;RP11-126K1.6,upstream_gene_variant,,ENST00000455503,;RP11-126K1.8,downstream_gene_variant,,ENST00000422153,;RFX5,downstream_gene_variant,,ENST00000478564,;RFX5,downstream_gene_variant,,ENST00000479681,;RFX5,downstream_gene_variant,,ENST00000452456,;RFX5,downstream_gene_variant,,ENST00000435314,;RFX5,downstream_gene_variant,,ENST00000469513,;RFX5,downstream_gene_variant,,ENST00000444392,;RFX5,downstream_gene_variant,,ENST00000421986,;RFX5,downstream_gene_variant,,ENST00000475144,;RFX5,downstream_gene_variant,,ENST00000494217,;	T	ENSG00000143390	ENST00000290524	Transcript	missense_variant	1927	1748	583	G/E	gGa/gAa	.	.	.	-1	RFX5	HGNC	9986	protein_coding	YES	CCDS994.1	ENSP00000290524	RFX5_HUMAN	Q9UG77_HUMAN,F8W689_HUMAN,F6X9D6_HUMAN,F6X8N2_HUMAN,F6UE82_HUMAN,F6U6P3_HUMAN,F6TYI9_HUMAN,F6S3S0_HUMAN,F6R6G4_HUMAN,F2Z2G0_HUMAN	UPI0000000E8B	.	tolerated_low_confidence(0.26)	benign(0.005)	11/11	.	Pfam_domain:PF14621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTCCCTTT	.	5	ESCA
TPM3	0	.	GRCh37	1	154155547	154155547	+	Intron	SNP	G	G	A	rs749857209	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244-6823C>T	.	.	ENST00000368530	.	49	33	16	34	34	0	TPM3,synonymous_variant,p.%3D,ENST00000328159,;TPM3,synonymous_variant,p.%3D,ENST00000323144,;TPM3,synonymous_variant,p.%3D,ENST00000341372,;TPM3,synonymous_variant,p.%3D,ENST00000368531,;TPM3,synonymous_variant,p.%3D,ENST00000341485,;TPM3,synonymous_variant,p.%3D,ENST00000330188,;TPM3,synonymous_variant,p.%3D,ENST00000368533,;TPM3,intron_variant,,ENST00000271850,;TPM3,intron_variant,,ENST00000368530,;TPM3,upstream_gene_variant,,ENST00000302206,;TPM3,non_coding_transcript_exon_variant,,ENST00000312970,;TPM3,non_coding_transcript_exon_variant,,ENST00000469717,;TPM3,intron_variant,,ENST00000368527,;TPM3,downstream_gene_variant,,ENST00000466010,;TPM3,synonymous_variant,p.%3D,ENST00000509601,;TPM3,synonymous_variant,p.%3D,ENST00000509409,;TPM3,non_coding_transcript_exon_variant,,ENST00000473036,;	A	ENSG00000143549	ENST00000368530	Transcript	intron_variant	.	.	.	.	.	rs749857209	.	.	-1	TPM3	HGNC	12012	protein_coding	YES	CCDS41403.1	ENSP00000357516	TPM3_HUMAN	Q5VU62_HUMAN,D6RGJ6_HUMAN	UPI000013D90D	.	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGAACCT	.	5	ESCA
ZBTB17	0	.	GRCh37	1	16271287	16271287	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.975C>T	p.%3D	p.I325I	ENST00000375743	8/16	15	12	3	8	8	0	ZBTB17,synonymous_variant,p.%3D,ENST00000375743,;ZBTB17,synonymous_variant,p.%3D,ENST00000448462,;ZBTB17,synonymous_variant,p.%3D,ENST00000375733,;ZBTB17,synonymous_variant,p.%3D,ENST00000537142,;SPEN,downstream_gene_variant,,ENST00000375759,;ZBTB17,upstream_gene_variant,,ENST00000444358,;ZBTB17,upstream_gene_variant,,ENST00000440560,;ZBTB17,non_coding_transcript_exon_variant,,ENST00000492834,;ZBTB17,upstream_gene_variant,,ENST00000462525,;ZBTB17,upstream_gene_variant,,ENST00000474511,;ZBTB17,upstream_gene_variant,,ENST00000488008,;ZBTB17,upstream_gene_variant,,ENST00000472658,;ZBTB17,upstream_gene_variant,,ENST00000471805,;ZBTB17,downstream_gene_variant,,ENST00000479282,;ZBTB17,downstream_gene_variant,,ENST00000464719,;ZBTB17,downstream_gene_variant,,ENST00000490899,;ZBTB17,upstream_gene_variant,,ENST00000487785,;ZBTB17,downstream_gene_variant,,ENST00000494020,;	A	ENSG00000116809	ENST00000375743	Transcript	synonymous_variant	1208	975	325	I	atC/atT	.	.	.	-1	ZBTB17	HGNC	12936	protein_coding	YES	CCDS165.1	ENSP00000364895	ZBT17_HUMAN	.	UPI000013C9D2	.	.	.	8/16	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24402:SF165,hmmpanther:PTHR24402,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCGGATGTG	.	2	ESCA
RCSD1	0	.	GRCh37	1	167674125	167674125	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*192G>A	.	.	ENST00000367854	7/7	18	9	9	12	12	0	RCSD1,3_prime_UTR_variant,,ENST00000367854,;RCSD1,downstream_gene_variant,,ENST00000537350,;	A	ENSG00000198771	ENST00000367854	Transcript	3_prime_UTR_variant	1774	.	.	.	.	.	.	.	1	RCSD1	HGNC	28310	protein_coding	YES	CCDS1263.1	ENSP00000356828	CPZIP_HUMAN	.	UPI0000204CFA	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTGAATCT	.	5	ESCA
ANKRD45	0	.	GRCh37	1	173638993	173638993	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-53G>A	.	.	ENST00000333279	1/6	42	34	8	22	22	0	ANKRD45,5_prime_UTR_variant,,ENST00000333279,;ANKRD45,upstream_gene_variant,,ENST00000367712,;	T	ENSG00000183831	ENST00000333279	Transcript	5_prime_UTR_variant	9	.	.	.	.	.	.	.	-1	ANKRD45	HGNC	24786	protein_coding	YES	CCDS1309.1	ENSP00000331268	ANR45_HUMAN	.	UPI000019851A	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAACGGCGC	.	2	ESCA
PAX7	0	.	GRCh37	1	19018262	19018262	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.601G>A	p.Glu201Lys	p.E201K	ENST00000375375	5/8	22	14	7	15	15	0	PAX7,missense_variant,p.Glu201Lys,ENST00000420770,;PAX7,missense_variant,p.Glu201Lys,ENST00000375375,;PAX7,missense_variant,p.Glu199Lys,ENST00000400661,;	A	ENSG00000009709	ENST00000375375	Transcript	missense_variant	1199	601	201	E/K	Gag/Aag	.	.	.	1	PAX7	HGNC	8621	protein_coding	YES	CCDS186.1	ENSP00000364524	PAX7_HUMAN	.	UPI000004A132	.	tolerated(0.06)	benign(0.109)	5/8	.	hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACGAGGGC	.	5	ESCA
NAV1	0	.	GRCh37	1	201791867	201791867	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2807G>A	.	.	ENST00000367296	30/30	63	42	20	59	59	0	NAV1,3_prime_UTR_variant,,ENST00000367297,;NAV1,3_prime_UTR_variant,,ENST00000367300,;NAV1,3_prime_UTR_variant,,ENST00000295624,;NAV1,3_prime_UTR_variant,,ENST00000367302,;NAV1,3_prime_UTR_variant,,ENST00000367296,;NAV1,3_prime_UTR_variant,,ENST00000367295,;IPO9-AS1,intron_variant,,ENST00000413035,;IPO9-AS1,intron_variant,,ENST00000421449,;IPO9-AS1,intron_variant,,ENST00000421159,;	A	ENSG00000134369	ENST00000367296	Transcript	3_prime_UTR_variant	8861	.	.	.	.	.	.	.	1	NAV1	HGNC	15989	protein_coding	YES	CCDS1414.2	ENSP00000356265	NAV1_HUMAN	.	UPI00004562D4	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTATTGAAGCC	.	5	ESCA
LRRN2	0	.	GRCh37	1	204587876	204587876	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245G>C	p.Glu415Asp	p.E415D	ENST00000367175	1/1	50	36	14	33	33	0	LRRN2,missense_variant,p.Glu415Asp,ENST00000367177,;LRRN2,missense_variant,p.Glu415Asp,ENST00000367176,;LRRN2,missense_variant,p.Glu415Asp,ENST00000367175,;RP11-430C7.4,downstream_gene_variant,,ENST00000453895,;LRRN2,downstream_gene_variant,,ENST00000496057,;	G	ENSG00000170382	ENST00000367175	Transcript	missense_variant	3458	1245	415	E/D	gaG/gaC	.	.	.	-1	LRRN2	HGNC	16914	protein_coding	YES	CCDS1448.1	ENSP00000356143	LRRN2_HUMAN	B3KM66_HUMAN	UPI000013E8AC	.	tolerated(0.24)	benign(0.276)	1/1	.	hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF9,SMART_domains:SM00082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATCTCCCG	.	5	ESCA
NUAK2	0	.	GRCh37	1	205290766	205290766	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-10C>T	.	.	ENST00000367157	1/7	20	11	9	10	10	0	NUAK2,5_prime_UTR_variant,,ENST00000367157,;	A	ENSG00000163545	ENST00000367157	Transcript	5_prime_UTR_variant	118	.	.	.	.	.	.	.	-1	NUAK2	HGNC	29558	protein_coding	YES	CCDS1453.1	ENSP00000356125	NUAK2_HUMAN	Q68E04_HUMAN,B4E0Y5_HUMAN	UPI0000037D77	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGGAGGTG	.	5	ESCA
RCOR3	0	.	GRCh37	1	211477433	211477433	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1026G>A	p.%3D	p.Q342Q	ENST00000419091	10/12	41	31	9	51	51	0	RCOR3,synonymous_variant,p.%3D,ENST00000529763,;RCOR3,synonymous_variant,p.%3D,ENST00000452621,;RCOR3,synonymous_variant,p.%3D,ENST00000367006,;RCOR3,synonymous_variant,p.%3D,ENST00000419091,;RCOR3,synonymous_variant,p.%3D,ENST00000367005,;RCOR3,intron_variant,,ENST00000534460,;RCOR3,synonymous_variant,p.%3D,ENST00000485186,;RCOR3,3_prime_UTR_variant,,ENST00000528926,;RCOR3,non_coding_transcript_exon_variant,,ENST00000486666,;RCOR3,non_coding_transcript_exon_variant,,ENST00000528066,;	A	ENSG00000117625	ENST00000419091	Transcript	synonymous_variant	1154	1026	342	Q	caG/caA	.	.	.	1	RCOR3	HGNC	25594	protein_coding	YES	CCDS44312.1	ENSP00000413929	RCOR3_HUMAN	E9PR63_HUMAN,E9PQE5_HUMAN	UPI00005AE45B	.	.	.	10/12	.	hmmpanther:PTHR16089,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCAGAAAAT	.	5	ESCA
INTS7	0	.	GRCh37	1	212125924	212125924	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2303C>T	p.Pro768Leu	p.P768L	ENST00000366994	17/20	34	23	10	42	42	0	INTS7,missense_variant,p.Pro768Leu,ENST00000366994,;INTS7,missense_variant,p.Pro719Leu,ENST00000440600,;INTS7,missense_variant,p.Pro768Leu,ENST00000366992,;INTS7,intron_variant,,ENST00000366993,;INTS7,non_coding_transcript_exon_variant,,ENST00000469606,;INTS7,non_coding_transcript_exon_variant,,ENST00000475798,;INTS7,non_coding_transcript_exon_variant,,ENST00000461212,;	A	ENSG00000143493	ENST00000366994	Transcript	missense_variant	2408	2303	768	P/L	cCt/cTt	.	.	.	-1	INTS7	HGNC	24484	protein_coding	YES	CCDS1501.1	ENSP00000355961	INT7_HUMAN	.	UPI000006FE2E	.	tolerated(0.19)	benign(0.204)	17/20	.	hmmpanther:PTHR13322,hmmpanther:PTHR13322:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACAGGGGTA	.	5	ESCA
ECE1	0	.	GRCh37	1	21582529	21582529	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.931G>C	p.Glu311Gln	p.E311Q	ENST00000374893	8/19	49	35	13	31	31	0	ECE1,missense_variant,p.Glu308Gln,ENST00000264205,;ECE1,missense_variant,p.Glu311Gln,ENST00000436918,;ECE1,missense_variant,p.Glu311Gln,ENST00000374893,;ECE1,missense_variant,p.Glu299Gln,ENST00000357071,;ECE1,missense_variant,p.Glu295Gln,ENST00000415912,;ECE1,downstream_gene_variant,,ENST00000473505,;ECE1,non_coding_transcript_exon_variant,,ENST00000528294,;ECE1,non_coding_transcript_exon_variant,,ENST00000526194,;	G	ENSG00000117298	ENST00000374893	Transcript	missense_variant	1006	931	311	E/Q	Gag/Cag	COSM1295866	.	.	-1	ECE1	HGNC	3146	protein_coding	YES	CCDS215.1	ENSP00000364028	ECE1_HUMAN	E9PN99_HUMAN,E9PJG1_HUMAN	UPI0000129B5E	.	deleterious(0)	possibly_damaging(0.899)	8/19	.	Superfamily_domains:SSF55486,Pfam_domain:PF05649,hmmpanther:PTHR11733:SF104,hmmpanther:PTHR11733	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCTCAAAGT	.	5	ESCA
MARK1	0	.	GRCh37	1	220791681	220791681	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.582G>A	p.Met194Ile	p.M194I	ENST00000366917	8/18	46	34	12	47	47	0	MARK1,missense_variant,p.Met172Ile,ENST00000366918,;MARK1,missense_variant,p.Met59Ile,ENST00000402574,;MARK1,missense_variant,p.Met194Ile,ENST00000366917,;	A	ENSG00000116141	ENST00000366917	Transcript	missense_variant	848	582	194	M/I	atG/atA	.	.	.	1	MARK1	HGNC	6896	protein_coding	YES	CCDS31029.2	ENSP00000355884	MARK1_HUMAN	B4DIB3_HUMAN	UPI0000048D8B	.	deleterious(0.02)	possibly_damaging(0.795)	8/18	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24346:SF21,hmmpanther:PTHR24346,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATATGAATAT	.	5	ESCA
CDC42	0	.	GRCh37	1	22416693	22416693	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.487-1228A>G	.	.	ENST00000344548	.	16	8	8	11	11	0	CDC42,3_prime_UTR_variant,,ENST00000315554,;CDC42,intron_variant,,ENST00000400259,;CDC42,intron_variant,,ENST00000344548,;CDC42,intron_variant,,ENST00000421089,;CDC42,downstream_gene_variant,,ENST00000411827,;CDC42,downstream_gene_variant,,ENST00000498236,;	G	ENSG00000070831	ENST00000344548	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CDC42	HGNC	1736	protein_coding	YES	CCDS221.1	ENSP00000341072	CDC42_HUMAN	Q9UJM1_HUMAN,Q9UJM0_HUMAN,Q5JYX0_HUMAN	UPI0000000356	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATATAAAT	.	5	ESCA
STPG1	0	.	GRCh37	1	24710447	24710447	+	Missense_Mutation	SNP	G	G	A	rs138455088	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236C>T	p.Pro79Leu	p.P79L	ENST00000374409	4/9	43	25	17	49	49	0	STPG1,missense_variant,p.Pro56Leu,ENST00000435187,;STPG1,missense_variant,p.Pro32Leu,ENST00000440416,;STPG1,missense_variant,p.Pro79Leu,ENST00000374409,;STPG1,missense_variant,p.Pro32Leu,ENST00000003583,;STPG1,missense_variant,p.Pro79Leu,ENST00000337248,;STPG1,upstream_gene_variant,,ENST00000438866,;STPG1,non_coding_transcript_exon_variant,,ENST00000468303,;STPG1,non_coding_transcript_exon_variant,,ENST00000497384,;	A	ENSG00000001460	ENST00000374409	Transcript	missense_variant	491	236	79	P/L	cCg/cTg	rs138455088	.	.	-1	STPG1	HGNC	28070	protein_coding	YES	CCDS55581.1	ENSP00000363530	STPG1_HUMAN	.	UPI0000049C6B	.	tolerated(0.12)	probably_damaging(0.975)	4/9	.	hmmpanther:PTHR21580,hmmpanther:PTHR21580:SF11	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACCGGTGAC	byCluster|by1000G	5	ESCA
ZNF695	0	.	GRCh37	1	247151124	247151124	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693G>A	p.%3D	p.K231K	ENST00000339986	4/4	42	25	17	37	37	0	ZNF695,synonymous_variant,p.%3D,ENST00000339986,;ZNF695,intron_variant,,ENST00000487338,;ZNF695,intron_variant,,ENST00000498046,;ZNF695,intron_variant,,ENST00000366504,;ZNF695,intron_variant,,ENST00000479214,;ZNF670,intron_variant,,ENST00000474541,;ZNF695,intron_variant,,ENST00000491337,;ZNF670,intron_variant,,ENST00000465049,;	T	ENSG00000197472	ENST00000339986	Transcript	synonymous_variant	841	693	231	K	aaG/aaA	.	.	.	-1	ZNF695	HGNC	30954	protein_coding	YES	CCDS44344.1	ENSP00000341236	ZN695_HUMAN	.	UPI0000F734A8	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF119,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTCTTACA	.	5	ESCA
OR2AK2	0	.	GRCh37	1	248129321	248129321	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.688C>G	p.Leu230Val	p.L230V	ENST00000366480	1/1	82	51	31	58	58	0	OR2AK2,missense_variant,p.Leu230Val,ENST00000366480,;OR2L13,intron_variant,,ENST00000366478,;	G	ENSG00000187080	ENST00000366480	Transcript	missense_variant	787	688	230	L/V	Ctg/Gtg	.	.	.	1	OR2AK2	HGNC	19569	protein_coding	YES	CCDS31102.1	ENSP00000355436	O2AK2_HUMAN	.	UPI00003B2873	.	tolerated(0.62)	benign(0.26)	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF1,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTCTGGCT	.	5	ESCA
ARID1A	0	.	GRCh37	1	27087879	27087879	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2166C>T	p.%3D	p.N722N	ENST00000324856	6/20	37	25	11	31	31	0	ARID1A,synonymous_variant,p.%3D,ENST00000457599,;ARID1A,synonymous_variant,p.%3D,ENST00000374152,;ARID1A,synonymous_variant,p.%3D,ENST00000324856,;RN7SL501P,upstream_gene_variant,,ENST00000578818,;ARID1A,upstream_gene_variant,,ENST00000430291,;	T	ENSG00000117713	ENST00000324856	Transcript	synonymous_variant	2537	2166	722	N	aaC/aaT	.	.	.	1	ARID1A	HGNC	11110	protein_coding	YES	CCDS285.1	ENSP00000320485	ARI1A_HUMAN	Q96T01_HUMAN,Q96SY8_HUMAN,Q96SM7_HUMAN,E9PQW6_HUMAN,C1KEN7_HUMAN,A4FU79_HUMAN	UPI0000167B91	.	.	.	6/20	.	hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAACCAGAT	.	5	ESCA
GPN2	0	.	GRCh37	1	27216261	27216261	+	Silent	SNP	G	G	A	rs753428953	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327C>T	p.%3D	p.F109F	ENST00000374135	1/5	127	82	45	99	99	0	GPN2,synonymous_variant,p.%3D,ENST00000374135,;GPN2,intron_variant,,ENST00000431781,;GPATCH3,downstream_gene_variant,,ENST00000361720,;GPATCH3,downstream_gene_variant,,ENST00000450844,;GPATCH3,downstream_gene_variant,,ENST00000445019,;GPN2,upstream_gene_variant,,ENST00000374133,;GPN2,upstream_gene_variant,,ENST00000461282,;GPN2,upstream_gene_variant,,ENST00000477418,;	A	ENSG00000142751	ENST00000374135	Transcript	synonymous_variant	528	327	109	F	ttC/ttT	rs753428953	.	.	-1	GPN2	HGNC	25513	protein_coding	YES	CCDS289.1	ENSP00000363250	GPN2_HUMAN	.	UPI0000071F43	.	.	.	1/5	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,Pfam_domain:PF03029,hmmpanther:PTHR21231:SF3,hmmpanther:PTHR21231	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCGAAGAG	.	5	ESCA
PTPRU	0	.	GRCh37	1	29631863	29631863	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2774-1G>A	.	p.X925_splice	ENST00000345512	.	26	15	11	24	24	0	PTPRU,splice_acceptor_variant,,ENST00000373779,;PTPRU,splice_acceptor_variant,,ENST00000428026,;PTPRU,splice_acceptor_variant,,ENST00000460170,;PTPRU,splice_acceptor_variant,,ENST00000323874,;PTPRU,splice_acceptor_variant,,ENST00000356870,;PTPRU,splice_acceptor_variant,,ENST00000345512,;PTPRU,splice_acceptor_variant,,ENST00000415600,;PTPRU,downstream_gene_variant,,ENST00000531385,;	A	ENSG00000060656	ENST00000345512	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	PTPRU	HGNC	9683	protein_coding	YES	CCDS334.1	ENSP00000334941	PTPRU_HUMAN	B3KT29_HUMAN	UPI000013C57E	.	.	.	.	18/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACAGATGAT	.	5	ESCA
DLGAP3	0	.	GRCh37	1	35370161	35370161	+	Missense_Mutation	SNP	G	G	A	rs146229611	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.824C>T	p.Ala275Val	p.A275V	ENST00000373347	3/12	35	24	10	33	33	0	DLGAP3,missense_variant,p.Ala275Val,ENST00000373347,;DLGAP3,missense_variant,p.Ala275Val,ENST00000235180,;DLGAP3,downstream_gene_variant,,ENST00000495979,;	A	ENSG00000116544	ENST00000373347	Transcript	missense_variant	1093	824	275	A/V	gCg/gTg	rs146229611	.	.	-1	DLGAP3	HGNC	30368	protein_coding	YES	CCDS30670.1	ENSP00000362444	DLGP3_HUMAN	B4DH33_HUMAN	UPI00003D4D81	.	tolerated(0.62)	benign(0.002)	3/12	.	hmmpanther:PTHR12353:SF4,hmmpanther:PTHR12353	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCGCCAGG	byCluster	5	ESCA
LSM10	0	.	GRCh37	1	36859249	36859249	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*110G>C	.	.	ENST00000315732	2/2	32	18	13	17	17	0	LSM10,3_prime_UTR_variant,,ENST00000315732,;LSM10,intron_variant,,ENST00000476041,;LSM10,downstream_gene_variant,,ENST00000489912,;	G	ENSG00000181817	ENST00000315732	Transcript	3_prime_UTR_variant	632	.	.	.	.	.	.	.	-1	LSM10	HGNC	17562	protein_coding	YES	CCDS408.1	ENSP00000319341	LSM10_HUMAN	.	UPI000012E96D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCTGGCC	.	5	ESCA
LSM10	0	.	GRCh37	1	36859680	36859680	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51G>C	p.%3D	p.L17L	ENST00000315732	2/2	51	36	15	56	56	0	LSM10,synonymous_variant,p.%3D,ENST00000315732,;LSM10,non_coding_transcript_exon_variant,,ENST00000476041,;LSM10,non_coding_transcript_exon_variant,,ENST00000489912,;	G	ENSG00000181817	ENST00000315732	Transcript	synonymous_variant	201	51	17	L	ctG/ctC	.	.	.	-1	LSM10	HGNC	17562	protein_coding	YES	CCDS408.1	ENSP00000319341	LSM10_HUMAN	.	UPI000012E96D	.	.	.	2/2	.	hmmpanther:PTHR21196,hmmpanther:PTHR21196:SF1,Gene3D:2.30.30.100	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATCAGGCT	.	5	ESCA
RSPO1	0	.	GRCh37	1	38095476	38095476	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-143G>A	.	.	ENST00000356545	4/9	35	24	11	36	36	0	RSPO1,5_prime_UTR_variant,,ENST00000401070,;RSPO1,5_prime_UTR_variant,,ENST00000401068,;RSPO1,5_prime_UTR_variant,,ENST00000401069,;RSPO1,5_prime_UTR_variant,,ENST00000401071,;RSPO1,5_prime_UTR_variant,,ENST00000356545,;RSPO1,intron_variant,,ENST00000373059,;	T	ENSG00000169218	ENST00000356545	Transcript	5_prime_UTR_variant	646	.	.	.	.	.	.	.	-1	RSPO1	HGNC	21679	protein_coding	YES	CCDS41304.1	ENSP00000348944	RSPO1_HUMAN	.	UPI0000674A16	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCTCAGCTG	.	5	ESCA
EPHA10	0	.	GRCh37	1	38201051	38201051	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1369G>A	p.Glu457Lys	p.E457K	ENST00000373048	6/17	44	29	14	38	38	0	EPHA10,missense_variant,p.Glu457Lys,ENST00000373048,;EPHA10,missense_variant,p.Glu457Lys,ENST00000427468,;EPHA10,5_prime_UTR_variant,,ENST00000540011,;EPHA10,5_prime_UTR_variant,,ENST00000330210,;Y_RNA,downstream_gene_variant,,ENST00000363551,;EPHA10,non_coding_transcript_exon_variant,,ENST00000446149,;EPHA10,missense_variant,p.Glu15Lys,ENST00000437645,;EPHA10,missense_variant,p.Glu45Lys,ENST00000525749,;EPHA10,upstream_gene_variant,,ENST00000534097,;EPHA10,upstream_gene_variant,,ENST00000432874,;	T	ENSG00000183317	ENST00000373048	Transcript	missense_variant	1369	1369	457	E/K	Gag/Aag	.	.	.	-1	EPHA10	HGNC	19987	protein_coding	YES	CCDS41305.1	ENSP00000362139	EPHAA_HUMAN	.	UPI00001A41BD	.	deleterious(0.01)	benign(0.36)	6/17	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF267,hmmpanther:PTHR24416,Gene3D:2.60.40.10,SMART_domains:SM00060,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCCTCCC	.	5	ESCA
MANEAL	0	.	GRCh37	1	38265236	38265236	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.738-3C>G	.	.	ENST00000373045	.	26	20	6	22	22	0	MANEAL,splice_region_variant,,ENST00000373045,;MANEAL,splice_region_variant,,ENST00000525897,;MANEAL,splice_region_variant,,ENST00000532512,;MANEAL,splice_region_variant,,ENST00000329006,;MANEAL,intron_variant,,ENST00000397631,;YRDC,downstream_gene_variant,,ENST00000373044,;RP11-109P14.9,downstream_gene_variant,,ENST00000433474,;	G	ENSG00000185090	ENST00000373045	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	MANEAL	HGNC	26452	protein_coding	YES	CCDS44110.1	ENSP00000362136	MANEL_HUMAN	E9PMU5_HUMAN	UPI0000203F8E	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTCAGGTA	.	4	ESCA
PABPC4	0	.	GRCh37	1	40034566	40034567	+	Frame_Shift_Del	DEL	AT	AT	-	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	AT	AT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783_784delAT	p.Phe262CysfsTer19	p.F262Cfs*19	ENST00000372858	6/16	58	42	16	40	40	0	PABPC4,frameshift_variant,p.Phe262CysfsTer19,ENST00000372858,;PABPC4,frameshift_variant,p.Phe262CysfsTer19,ENST00000372862,;PABPC4,frameshift_variant,p.Phe262CysfsTer19,ENST00000372857,;PABPC4,frameshift_variant,p.Phe175CysfsTer19,ENST00000474378,;PABPC4,frameshift_variant,p.Phe262CysfsTer19,ENST00000372856,;PABPC4,frameshift_variant,p.Phe164CysfsTer19,ENST00000421687,;PABPC4,downstream_gene_variant,,ENST00000451091,;PABPC4,upstream_gene_variant,,ENST00000437136,;PABPC4,upstream_gene_variant,,ENST00000527718,;SNORA55,upstream_gene_variant,,ENST00000364587,;RP11-69E11.8,intron_variant,,ENST00000415255,;PABPC4,non_coding_transcript_exon_variant,,ENST00000529216,;PABPC4,3_prime_UTR_variant,,ENST00000470443,;PABPC4,non_coding_transcript_exon_variant,,ENST00000525751,;PABPC4,upstream_gene_variant,,ENST00000468476,;PABPC4,downstream_gene_variant,,ENST00000492519,;PABPC4,upstream_gene_variant,,ENST00000492468,;PABPC4,upstream_gene_variant,,ENST00000525045,;PABPC4,upstream_gene_variant,,ENST00000461578,;PABPC4,upstream_gene_variant,,ENST00000513632,;PABPC4,upstream_gene_variant,,ENST00000484555,;PABPC4,upstream_gene_variant,,ENST00000483770,;PABPC4,upstream_gene_variant,,ENST00000525669,;PABPC4,upstream_gene_variant,,ENST00000477556,;	-	ENSG00000090621	ENST00000372858	Transcript	frameshift_variant	1233-1234	783-784	261-262	IF/IX	atATtt/attt	.	.	.	-1	PABPC4	HGNC	8557	protein_coding	YES	CCDS44115.1	ENSP00000361949	PABP4_HUMAN	B1ANR1_HUMAN	UPI00002057C5	.	.	.	6/16	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011,hmmpanther:PTHR24011:SF265,Pfam_domain:PF00076,TIGRFAM_domain:TIGR01628,Gene3D:3.30.70.330,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTACAAATATGAT	.	3	ESCA
YBX1	0	.	GRCh37	1	43162401	43162401	+	Missense_Mutation	SNP	A	A	G	rs772212080	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.443A>G	p.Tyr148Cys	p.Y148C	ENST00000321358	5/8	76	48	27	59	59	0	YBX1,missense_variant,p.Tyr118Cys,ENST00000332220,;YBX1,missense_variant,p.Tyr198Cys,ENST00000436427,;YBX1,missense_variant,p.Tyr148Cys,ENST00000321358,;YBX1,non_coding_transcript_exon_variant,,ENST00000467957,;	G	ENSG00000065978	ENST00000321358	Transcript	missense_variant	582	443	148	Y/C	tAt/tGt	rs772212080	.	.	1	YBX1	HGNC	8014	protein_coding	YES	CCDS470.1	ENSP00000361626	YBOX1_HUMAN	A0JLU4_HUMAN	UPI0000001C6B	.	tolerated(0.16)	probably_damaging(0.99)	5/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11544	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P149P|c.447A>G|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGCTATCCAC	.	5	ESCA
PLK3	0	.	GRCh37	1	45269890	45269890	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1314G>C	p.%3D	p.L438L	ENST00000372201	11/15	34	23	11	27	27	0	PLK3,synonymous_variant,p.%3D,ENST00000372201,;BTBD19,upstream_gene_variant,,ENST00000450269,;TCTEX1D4,downstream_gene_variant,,ENST00000372200,;BTBD19,upstream_gene_variant,,ENST00000409335,;BTBD19,upstream_gene_variant,,ENST00000453418,;TCTEX1D4,downstream_gene_variant,,ENST00000339355,;PLK3,non_coding_transcript_exon_variant,,ENST00000492398,;PLK3,non_coding_transcript_exon_variant,,ENST00000465443,;PLK3,non_coding_transcript_exon_variant,,ENST00000461769,;PLK3,non_coding_transcript_exon_variant,,ENST00000461358,;PLK3,downstream_gene_variant,,ENST00000476731,;PLK3,upstream_gene_variant,,ENST00000493100,;BTBD19,upstream_gene_variant,,ENST00000485668,;BTBD19,upstream_gene_variant,,ENST00000439563,;BTBD19,upstream_gene_variant,,ENST00000482715,;	C	ENSG00000173846	ENST00000372201	Transcript	synonymous_variant	1553	1314	438	L	ctG/ctC	.	.	.	1	PLK3	HGNC	2154	protein_coding	YES	CCDS515.1	ENSP00000361275	PLK3_HUMAN	.	UPI000013ED1D	.	.	.	11/15	.	Superfamily_domains:SSF82615,hmmpanther:PTHR24345:SF42,hmmpanther:PTHR24345	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTGAGAAA	.	5	ESCA
GLIS1	0	.	GRCh37	1	53980335	53980335	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1321C>G	p.Leu441Val	p.L441V	ENST00000312233	7/10	50	35	14	46	46	0	GLIS1,missense_variant,p.Leu441Val,ENST00000312233,;	C	ENSG00000174332	ENST00000312233	Transcript	missense_variant	1888	1321	441	L/V	Ctg/Gtg	.	.	.	-1	GLIS1	HGNC	29525	protein_coding	YES	CCDS582.1	ENSP00000309653	GLIS1_HUMAN	.	UPI000013F293	.	tolerated(0.12)	probably_damaging(0.978)	7/10	.	hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACAGATGGT	.	5	ESCA
CHD5	0	.	GRCh37	1	6172270	6172270	+	Silent	SNP	G	G	A	rs145305767	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5070C>T	p.%3D	p.D1690D	ENST00000262450	35/42	179	104	75	121	121	0	CHD5,synonymous_variant,p.%3D,ENST00000378021,;CHD5,synonymous_variant,p.%3D,ENST00000262450,;CHD5,3_prime_UTR_variant,,ENST00000377999,;CHD5,3_prime_UTR_variant,,ENST00000496404,;CHD5,3_prime_UTR_variant,,ENST00000462991,;	A	ENSG00000116254	ENST00000262450	Transcript	synonymous_variant	5170	5070	1690	D	gaC/gaT	rs145305767,COSM1243159	.	.	-1	CHD5	HGNC	16816	protein_coding	YES	CCDS57.1	ENSP00000262450	CHD5_HUMAN	.	UPI000006CD03	.	.	.	35/42	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF583	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0025	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTCGTCATC	byCluster|by1000G	5	ESCA
PLEKHG5	0	.	GRCh37	1	6526924	6526924	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000537245	.	40	32	8	16	16	0	PLEKHG5,3_prime_UTR_variant,,ENST00000400913,;PLEKHG5,3_prime_UTR_variant,,ENST00000340850,;PLEKHG5,3_prime_UTR_variant,,ENST00000377748,;PLEKHG5,downstream_gene_variant,,ENST00000377725,;TNFRSF25,upstream_gene_variant,,ENST00000356876,;TNFRSF25,upstream_gene_variant,,ENST00000348333,;PLEKHG5,downstream_gene_variant,,ENST00000535355,;TNFRSF25,upstream_gene_variant,,ENST00000481401,;TNFRSF25,upstream_gene_variant,,ENST00000351959,;PLEKHG5,downstream_gene_variant,,ENST00000400915,;PLEKHG5,downstream_gene_variant,,ENST00000377737,;PLEKHG5,downstream_gene_variant,,ENST00000537245,;PLEKHG5,downstream_gene_variant,,ENST00000544978,;PLEKHG5,downstream_gene_variant,,ENST00000377740,;PLEKHG5,downstream_gene_variant,,ENST00000377732,;PLEKHG5,downstream_gene_variant,,ENST00000377728,;TNFRSF25,upstream_gene_variant,,ENST00000377782,;TNFRSF25,upstream_gene_variant,,ENST00000351748,;TNFRSF25,upstream_gene_variant,,ENST00000461703,;TNFRSF25,upstream_gene_variant,,ENST00000475730,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000489097,;TNFRSF25,upstream_gene_variant,,ENST00000515145,;TNFRSF25,upstream_gene_variant,,ENST00000453260,;TNFRSF25,upstream_gene_variant,,ENST00000414040,;PLEKHG5,downstream_gene_variant,,ENST00000487949,;TNFRSF25,upstream_gene_variant,,ENST00000453341,;TNFRSF25,upstream_gene_variant,,ENST00000469691,;TNFRSF25,upstream_gene_variant,,ENST00000510563,;TNFRSF25,upstream_gene_variant,,ENST00000485036,;TNFRSF25,upstream_gene_variant,,ENST00000480393,;TNFRSF25,upstream_gene_variant,,ENST00000513135,;TNFRSF25,upstream_gene_variant,,ENST00000473343,;TNFRSF25,upstream_gene_variant,,ENST00000502588,;TNFRSF25,upstream_gene_variant,,ENST00000502730,;	A	ENSG00000171680	ENST00000537245	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	641	-1	PLEKHG5	HGNC	29105	protein_coding	YES	CCDS57969.1	ENSP00000439625	PKHG5_HUMAN	B3KR92_HUMAN	UPI000206539E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCTGAGTGT	.	2	ESCA
PLEKHG5	0	.	GRCh37	1	6530391	6530391	+	Missense_Mutation	SNP	C	C	G	rs200641225	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1942G>C	p.Asp648His	p.D648H	ENST00000537245	17/22	57	35	22	38	38	0	PLEKHG5,missense_variant,p.Asp569His,ENST00000377725,;PLEKHG5,missense_variant,p.Asp569His,ENST00000400913,;PLEKHG5,missense_variant,p.Asp638His,ENST00000535355,;PLEKHG5,missense_variant,p.Asp569His,ENST00000340850,;PLEKHG5,missense_variant,p.Asp625His,ENST00000400915,;PLEKHG5,missense_variant,p.Asp569His,ENST00000377737,;PLEKHG5,missense_variant,p.Asp648His,ENST00000537245,;PLEKHG5,missense_variant,p.Asp569His,ENST00000544978,;PLEKHG5,missense_variant,p.Asp646His,ENST00000377748,;PLEKHG5,missense_variant,p.Asp646His,ENST00000377740,;PLEKHG5,missense_variant,p.Asp606His,ENST00000377732,;PLEKHG5,missense_variant,p.Asp569His,ENST00000377728,;TNFRSF25,upstream_gene_variant,,ENST00000356876,;TNFRSF25,upstream_gene_variant,,ENST00000348333,;TNFRSF25,upstream_gene_variant,,ENST00000481401,;TNFRSF25,upstream_gene_variant,,ENST00000351959,;TNFRSF25,upstream_gene_variant,,ENST00000377782,;TNFRSF25,upstream_gene_variant,,ENST00000351748,;TNFRSF25,upstream_gene_variant,,ENST00000461703,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000487949,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000489097,;TNFRSF25,upstream_gene_variant,,ENST00000515145,;TNFRSF25,upstream_gene_variant,,ENST00000414040,;TNFRSF25,upstream_gene_variant,,ENST00000453341,;TNFRSF25,upstream_gene_variant,,ENST00000510563,;TNFRSF25,upstream_gene_variant,,ENST00000485036,;TNFRSF25,upstream_gene_variant,,ENST00000480393,;TNFRSF25,upstream_gene_variant,,ENST00000513135,;TNFRSF25,upstream_gene_variant,,ENST00000502588,;TNFRSF25,upstream_gene_variant,,ENST00000502730,;	G	ENSG00000171680	ENST00000537245	Transcript	missense_variant	2007	1942	648	D/H	Gac/Cac	rs200641225	.	.	-1	PLEKHG5	HGNC	29105	protein_coding	YES	CCDS57969.1	ENSP00000439625	PKHG5_HUMAN	B3KR92_HUMAN	UPI000206539E	.	deleterious(0)	probably_damaging(0.996)	17/22	.	hmmpanther:PTHR13217,hmmpanther:PTHR13217:SF6,Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	T:0	T:0.0006	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGTCCAGGT	byFrequency|byCluster	5	ESCA
THAP3	0	.	GRCh37	1	6693086	6693086	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.669C>G	p.Cys223Trp	p.C223W	ENST00000054650	6/6	41	28	13	22	22	0	THAP3,missense_variant,p.Cys223Trp,ENST00000054650,;THAP3,missense_variant,p.Cys222Trp,ENST00000307896,;THAP3,3_prime_UTR_variant,,ENST00000472925,;THAP3,intron_variant,,ENST00000377627,;DNAJC11,downstream_gene_variant,,ENST00000294401,;DNAJC11,downstream_gene_variant,,ENST00000349363,;DNAJC11,downstream_gene_variant,,ENST00000377577,;DNAJC11,downstream_gene_variant,,ENST00000542246,;DNAJC11,downstream_gene_variant,,ENST00000451196,;DNAJC11,downstream_gene_variant,,ENST00000377573,;THAP3,non_coding_transcript_exon_variant,,ENST00000484669,;THAP3,downstream_gene_variant,,ENST00000484676,;DNAJC11,downstream_gene_variant,,ENST00000465508,;DNAJC11,downstream_gene_variant,,ENST00000472414,;THAP3,3_prime_UTR_variant,,ENST00000487819,;THAP3,downstream_gene_variant,,ENST00000480647,;	G	ENSG00000041988	ENST00000054650	Transcript	missense_variant	827	669	223	C/W	tgC/tgG	.	.	.	1	THAP3	HGNC	20855	protein_coding	YES	CCDS55572.1	ENSP00000054650	THAP3_HUMAN	.	UPI000006CFCA	.	tolerated(0.18)	benign(0.24)	6/6	.	hmmpanther:PTHR23080,hmmpanther:PTHR23080:SF46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTTGCAAAGG	.	3	ESCA
WDR78	0	.	GRCh37	1	67279739	67279739	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*74T>C	.	.	ENST00000371026	17/17	62	46	16	69	69	0	WDR78,3_prime_UTR_variant,,ENST00000431318,;WDR78,3_prime_UTR_variant,,ENST00000371026,;WDR78,3_prime_UTR_variant,,ENST00000464352,;WDR78,3_prime_UTR_variant,,ENST00000491297,;	G	ENSG00000152763	ENST00000371026	Transcript	3_prime_UTR_variant	2677	.	.	.	.	.	.	.	-1	WDR78	HGNC	26252	protein_coding	YES	CCDS635.1	ENSP00000360065	WDR78_HUMAN	.	UPI00004561EF	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTACAGTATG	.	5	ESCA
RP11-413G15.1	0	.	GRCh37	1	83912348	83912348	+	RNA	SNP	C	C	T	rs370704857	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.613C>T	.	.	ENST00000446227	1/2	19	16	3	20	20	0	RP11-413G15.1,non_coding_transcript_exon_variant,,ENST00000446227,;	T	ENSG00000231364	ENST00000446227	Transcript	non_coding_transcript_exon_variant	613	.	.	.	.	rs370704857	.	.	1	RP11-413G15.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GGCAACATTCT	byCluster	2	ESCA
RPF1	0	.	GRCh37	1	84961569	84961569	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.704G>C	p.Arg235Thr	p.R235T	ENST00000370654	7/9	23	16	6	19	19	0	RPF1,missense_variant,p.Arg235Thr,ENST00000370654,;GNG5,downstream_gene_variant,,ENST00000370641,;GNG5,downstream_gene_variant,,ENST00000370645,;GNG5,downstream_gene_variant,,ENST00000487806,;	C	ENSG00000117133	ENST00000370654	Transcript	missense_variant	719	704	235	R/T	aGa/aCa	.	.	.	1	RPF1	HGNC	30350	protein_coding	YES	CCDS695.1	ENSP00000359688	RPF1_HUMAN	.	UPI0000034DF7	.	tolerated(0.12)	benign(0.044)	7/9	.	Superfamily_domains:SSF52954,SMART_domains:SM00879,Pfam_domain:PF04427,Gene3D:1w94A00,hmmpanther:PTHR22734:SF1,hmmpanther:PTHR22734,PROSITE_profiles:PS50833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGAGGCA	.	5	ESCA
DPYD	0	.	GRCh37	1	97771847	97771847	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2065G>A	p.Glu689Lys	p.E689K	ENST00000370192	17/23	23	18	5	16	16	0	DPYD,missense_variant,p.Glu689Lys,ENST00000370192,;DPYD-AS1,non_coding_transcript_exon_variant,,ENST00000422980,;	T	ENSG00000188641	ENST00000370192	Transcript	missense_variant	2166	2065	689	E/K	Gag/Aag	.	.	.	-1	DPYD	HGNC	3012	protein_coding	YES	CCDS30777.1	ENSP00000359211	DPYD_HUMAN	.	UPI0000458949	.	tolerated(0.19)	benign(0.008)	17/23	.	hmmpanther:PTHR11938,hmmpanther:PTHR11938:SF5,Pfam_domain:PF01180,Gene3D:3.20.20.70,TIGRFAM_domain:TIGR01037,Superfamily_domains:SSF51395	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CAGCTCTGGAT	.	4	ESCA
CEP250	0	.	GRCh37	20	34090592	34090592	+	Silent	SNP	G	G	A	rs377306728	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4395G>A	p.%3D	p.L1465L	ENST00000397527	30/35	26	18	8	24	24	0	CEP250,synonymous_variant,p.%3D,ENST00000342580,;CEP250,synonymous_variant,p.%3D,ENST00000397527,;CEP250,upstream_gene_variant,,ENST00000422671,;CEP250,3_prime_UTR_variant,,ENST00000425525,;	A	ENSG00000126001	ENST00000397527	Transcript	synonymous_variant	5115	4395	1465	L	ctG/ctA	rs377306728	.	.	1	CEP250	HGNC	1859	protein_coding	YES	CCDS13255.1	ENSP00000380661	CP250_HUMAN	Q5JWS6_HUMAN,Q5JWS5_HUMAN,G1UI40_HUMAN	UPI000006FE8F	.	.	.	30/35	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF1	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCTGAAGAA	.	5	ESCA
CEP250	0	.	GRCh37	20	34092542	34092542	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6345G>C	p.Glu2115Asp	p.E2115D	ENST00000397527	30/35	21	17	4	14	14	0	CEP250,missense_variant,p.Glu603Asp,ENST00000422671,;CEP250,missense_variant,p.Glu2059Asp,ENST00000342580,;CEP250,missense_variant,p.Glu2115Asp,ENST00000397527,;CEP250,downstream_gene_variant,,ENST00000425525,;	C	ENSG00000126001	ENST00000397527	Transcript	missense_variant	7065	6345	2115	E/D	gaG/gaC	.	.	.	1	CEP250	HGNC	1859	protein_coding	YES	CCDS13255.1	ENSP00000380661	CP250_HUMAN	Q5JWS6_HUMAN,Q5JWS5_HUMAN,G1UI40_HUMAN	UPI000006FE8F	.	.	possibly_damaging(0.46)	30/35	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGAGACCCA	.	5	ESCA
ARFGEF2	0	.	GRCh37	20	47589702	47589702	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1546A>G	p.Ile516Val	p.I516V	ENST00000371917	12/39	62	39	23	53	53	0	ARFGEF2,missense_variant,p.Ile516Val,ENST00000371917,;	G	ENSG00000124198	ENST00000371917	Transcript	missense_variant	1546	1546	516	I/V	Att/Gtt	.	.	.	1	ARFGEF2	HGNC	15853	protein_coding	YES	CCDS13411.1	ENSP00000360985	BIG2_HUMAN	Q59FR3_HUMAN	UPI000013D378	.	deleterious(0.02)	possibly_damaging(0.737)	12/39	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF124,Pfam_domain:PF12783,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGATATTTAT	.	5	ESCA
NFATC2	0	.	GRCh37	20	50048903	50048903	+	Missense_Mutation	SNP	G	G	A	rs779382116	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2423C>T	p.Ser808Leu	p.S808L	ENST00000396009	9/10	98	66	31	51	51	0	NFATC2,missense_variant,p.Ser808Leu,ENST00000396009,;NFATC2,missense_variant,p.Ser788Leu,ENST00000609943,;NFATC2,missense_variant,p.Ser808Leu,ENST00000371564,;NFATC2,missense_variant,p.Ser589Leu,ENST00000609507,;NFATC2,missense_variant,p.Ser589Leu,ENST00000610033,;NFATC2,missense_variant,p.Ser788Leu,ENST00000414705,;	A	ENSG00000101096	ENST00000396009	Transcript	missense_variant	2643	2423	808	S/L	tCg/tTg	rs779382116,COSM578238	.	.	-1	NFATC2	HGNC	7776	protein_coding	YES	CCDS13437.1	ENSP00000379330	NFAC2_HUMAN	B5B2P4_HUMAN,B5B2P3_HUMAN	UPI0000167D0F	.	deleterious(0.04)	possibly_damaging(0.449)	9/10	.	hmmpanther:PTHR12533:SF4,hmmpanther:PTHR12533	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGCGAGGCC	byFrequency	5	ESCA
AURKA	0	.	GRCh37	20	54945045	54945045	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*169C>G	.	.	ENST00000395909	11/11	8	4	4	11	11	0	AURKA,3_prime_UTR_variant,,ENST00000395909,;AURKA,3_prime_UTR_variant,,ENST00000395913,;AURKA,3_prime_UTR_variant,,ENST00000347343,;AURKA,3_prime_UTR_variant,,ENST00000371356,;AURKA,3_prime_UTR_variant,,ENST00000395915,;AURKA,3_prime_UTR_variant,,ENST00000395907,;AURKA,3_prime_UTR_variant,,ENST00000395911,;AURKA,3_prime_UTR_variant,,ENST00000395914,;AURKA,3_prime_UTR_variant,,ENST00000312783,;FAM210B,downstream_gene_variant,,ENST00000371384,;AURKA,downstream_gene_variant,,ENST00000441357,;	C	ENSG00000087586	ENST00000395909	Transcript	3_prime_UTR_variant	1947	.	.	.	.	.	.	.	-1	AURKA	HGNC	11393	protein_coding	YES	CCDS13451.1	ENSP00000379245	AURKA_HUMAN	Q5QPD4_HUMAN,Q5QPD2_HUMAN,Q5QPD1_HUMAN,A3KFJ2_HUMAN,A3KFJ1_HUMAN	UPI000013C70F	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTGGAGCTT	.	2	ESCA
PHACTR3	0	.	GRCh37	20	58342365	58342365	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.666G>A	p.%3D	p.E222E	ENST00000371015	5/13	29	20	8	28	28	0	PHACTR3,synonymous_variant,p.%3D,ENST00000355648,;PHACTR3,synonymous_variant,p.%3D,ENST00000541461,;PHACTR3,synonymous_variant,p.%3D,ENST00000395636,;PHACTR3,synonymous_variant,p.%3D,ENST00000371015,;PHACTR3,synonymous_variant,p.%3D,ENST00000359926,;PHACTR3,intron_variant,,ENST00000361300,;PHACTR3,intron_variant,,ENST00000395639,;	A	ENSG00000087495	ENST00000371015	Transcript	synonymous_variant	1133	666	222	E	gaG/gaA	.	.	.	1	PHACTR3	HGNC	15833	protein_coding	YES	CCDS13480.1	ENSP00000360054	PHAR3_HUMAN	F6RP66_HUMAN	UPI000006D452	.	.	.	5/13	.	hmmpanther:PTHR12751,hmmpanther:PTHR12751:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAGAGATC	.	5	ESCA
ZNF512B	0	.	GRCh37	20	62591015	62591015	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*226G>A	.	.	ENST00000450537	17/17	68	44	23	53	53	0	ZNF512B,3_prime_UTR_variant,,ENST00000450537,;ZNF512B,3_prime_UTR_variant,,ENST00000217130,;ZNF512B,3_prime_UTR_variant,,ENST00000369888,;UCKL1,upstream_gene_variant,,ENST00000354216,;UCKL1,upstream_gene_variant,,ENST00000358711,;UCKL1,upstream_gene_variant,,ENST00000369892,;UCKL1,upstream_gene_variant,,ENST00000483710,;	T	ENSG00000196700	ENST00000450537	Transcript	3_prime_UTR_variant	2966	.	.	.	.	.	.	.	-1	ZNF512B	HGNC	29212	protein_coding	YES	CCDS13548.1	ENSP00000393795	Z512B_HUMAN	.	UPI000013A290	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCTGCTG	.	5	ESCA
SYNJ1	0	.	GRCh37	21	34011322	34011322	+	Missense_Mutation	SNP	T	T	A	rs751069566	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3928A>T	p.Met1310Leu	p.M1310L	ENST00000433931	31/32	111	81	30	76	76	0	SYNJ1,missense_variant,p.Met1310Leu,ENST00000382499,;SYNJ1,missense_variant,p.Met1224Leu,ENST00000382491,;SYNJ1,missense_variant,p.Met92Leu,ENST00000418301,;SYNJ1,missense_variant,p.Met1310Leu,ENST00000433931,;SYNJ1,missense_variant,p.Met1255Leu,ENST00000357345,;SYNJ1,missense_variant,p.Met147Leu,ENST00000438952,;SYNJ1,missense_variant,p.Met1271Leu,ENST00000322229,;SYNJ1,downstream_gene_variant,,ENST00000416083,;	A	ENSG00000159082	ENST00000433931	Transcript	missense_variant	3936	3928	1310	M/L	Atg/Ttg	rs751069566	.	.	-1	SYNJ1	HGNC	11503	protein_coding	YES	CCDS33539.2	ENSP00000409667	.	J3KQV8_HUMAN,C9J1Z6_HUMAN	UPI0001A47572	.	tolerated_low_confidence(0.39)	benign(0.001)	31/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCATAGGTG	byFrequency	5	ESCA
DSCR3	0	.	GRCh37	21	38610793	38610793	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319G>C	p.Glu107Gln	p.E107Q	ENST00000309117	3/8	23	14	9	23	23	0	DSCR3,missense_variant,p.Glu65Gln,ENST00000288304,;DSCR3,missense_variant,p.Glu107Gln,ENST00000309117,;DSCR3,missense_variant,p.Glu107Gln,ENST00000476950,;DSCR3,missense_variant,p.Glu59Gln,ENST00000398998,;DSCR3,intron_variant,,ENST00000539844,;DSCR3,intron_variant,,ENST00000399001,;AP001432.14,downstream_gene_variant,,ENST00000440629,;DSCR3,non_coding_transcript_exon_variant,,ENST00000492514,;DSCR3,non_coding_transcript_exon_variant,,ENST00000488368,;DSCR3,non_coding_transcript_exon_variant,,ENST00000480452,;DSCR3,non_coding_transcript_exon_variant,,ENST00000399000,;DSCR3,non_coding_transcript_exon_variant,,ENST00000475009,;	G	ENSG00000157538	ENST00000309117	Transcript	missense_variant	557	319	107	E/Q	Gag/Cag	.	.	.	-1	DSCR3	HGNC	3044	protein_coding	YES	CCDS33553.1	ENSP00000311399	DSCR3_HUMAN	.	UPI000012990B	.	deleterious(0)	probably_damaging(0.996)	3/8	.	hmmpanther:PTHR12233:SF2,hmmpanther:PTHR12233,Pfam_domain:PF03643,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCTCATACA	.	5	ESCA
ERG	0	.	GRCh37	21	39754573	39754573	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*752G>C	.	.	ENST00000417133	12/12	18	13	5	18	18	0	ERG,3_prime_UTR_variant,,ENST00000398897,;ERG,3_prime_UTR_variant,,ENST00000398910,;ERG,3_prime_UTR_variant,,ENST00000288319,;ERG,3_prime_UTR_variant,,ENST00000442448,;ERG,3_prime_UTR_variant,,ENST00000398905,;ERG,3_prime_UTR_variant,,ENST00000417133,;ERG,3_prime_UTR_variant,,ENST00000398911,;ERG,3_prime_UTR_variant,,ENST00000398907,;ERG,downstream_gene_variant,,ENST00000453032,;ERG,downstream_gene_variant,,ENST00000398919,;	G	ENSG00000157554	ENST00000417133	Transcript	3_prime_UTR_variant	2399	.	.	.	.	.	.	.	-1	ERG	HGNC	3446	protein_coding	YES	CCDS46648.1	ENSP00000414150	ERG_HUMAN	Q16031_HUMAN,B4DVX5_HUMAN	UPI000018681C	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTCTTTCC	.	5	ESCA
C2CD2	0	.	GRCh37	21	43305718	43305718	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3515C>G	.	.	ENST00000380486	14/14	83	54	28	63	63	0	C2CD2,3_prime_UTR_variant,,ENST00000449165,;C2CD2,3_prime_UTR_variant,,ENST00000329623,;C2CD2,3_prime_UTR_variant,,ENST00000380486,;SNORA3,downstream_gene_variant,,ENST00000515969,;C2CD2,downstream_gene_variant,,ENST00000482186,;C2CD2,downstream_gene_variant,,ENST00000482084,;	C	ENSG00000157617	ENST00000380486	Transcript	3_prime_UTR_variant	5848	.	.	.	.	.	.	.	-1	C2CD2	HGNC	1266	protein_coding	YES	CCDS42933.1	ENSP00000369853	CU025_HUMAN	.	UPI0000206BBE	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGAGGTC	.	5	ESCA
LRRC3	0	.	GRCh37	21	45878125	45878125	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*824C>T	.	.	ENST00000291592	2/2	21	12	9	19	19	0	LRRC3,3_prime_UTR_variant,,ENST00000291592,;LRRC3DN,upstream_gene_variant,,ENST00000596691,;LRRC3-AS1,upstream_gene_variant,,ENST00000426578,;	T	ENSG00000160233	ENST00000291592	Transcript	3_prime_UTR_variant	1915	.	.	.	.	.	.	.	1	LRRC3	HGNC	14965	protein_coding	YES	CCDS13711.1	ENSP00000291592	LRRC3_HUMAN	.	UPI000012E946	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGCAACCT	.	5	ESCA
CCT8L2	0	.	GRCh37	22	17072518	17072518	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.923A>G	p.Asp308Gly	p.D308G	ENST00000359963	1/1	71	53	17	58	58	0	CCT8L2,missense_variant,p.Asp308Gly,ENST00000359963,;FABP5P11,downstream_gene_variant,,ENST00000430910,;	C	ENSG00000198445	ENST00000359963	Transcript	missense_variant	1183	923	308	D/G	gAc/gGc	.	.	.	-1	CCT8L2	HGNC	15553	protein_coding	YES	CCDS13738.1	ENSP00000353048	TCPQM_HUMAN	.	UPI000006CF87	.	deleterious(0.01)	possibly_damaging(0.842)	1/1	.	Superfamily_domains:SSF52029,Pfam_domain:PF00118,Gene3D:3.50.7.10,hmmpanther:PTHR11353:SF70,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTGTCCGCC	.	5	ESCA
IGLL1	0	.	GRCh37	22	23917210	23917210	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.266C>G	p.Ser89Cys	p.S89C	ENST00000330377	2/3	51	39	12	63	63	0	IGLL1,missense_variant,p.Ser89Cys,ENST00000330377,;IGLL1,missense_variant,p.Ser90Cys,ENST00000438703,;IGLL1,intron_variant,,ENST00000249053,;AP000345.2,downstream_gene_variant,,ENST00000454863,;AP000345.2,downstream_gene_variant,,ENST00000458318,;	C	ENSG00000128322	ENST00000330377	Transcript	missense_variant	384	266	89	S/C	tCc/tGc	.	.	.	-1	IGLL1	HGNC	5870	protein_coding	YES	CCDS13809.1	ENSP00000329312	IGLL1_HUMAN	.	UPI0000119C23	.	deleterious_low_confidence(0.05)	benign(0.022)	2/3	.	hmmpanther:PTHR23266:SF75,hmmpanther:PTHR23266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTTGGATTGA	.	3	ESCA
EWSR1	0	.	GRCh37	22	29678390	29678390	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.443G>C	p.Gly148Ala	p.G148A	ENST00000414183	7/18	49	36	13	53	53	0	EWSR1,missense_variant,p.Gly142Ala,ENST00000406548,;EWSR1,missense_variant,p.Gly148Ala,ENST00000414183,;EWSR1,missense_variant,p.Gly149Ala,ENST00000436425,;EWSR1,missense_variant,p.Gly142Ala,ENST00000332050,;EWSR1,missense_variant,p.Gly142Ala,ENST00000397938,;EWSR1,missense_variant,p.Gly142Ala,ENST00000333395,;EWSR1,missense_variant,p.Gly142Ala,ENST00000331029,;EWSR1,missense_variant,p.Gly143Ala,ENST00000437155,;EWSR1,missense_variant,p.Gly67Ala,ENST00000415761,;EWSR1,missense_variant,p.Gly148Ala,ENST00000447973,;EWSR1,intron_variant,,ENST00000332035,;EWSR1,intron_variant,,ENST00000455726,;EWSR1,downstream_gene_variant,,ENST00000444626,;EWSR1,non_coding_transcript_exon_variant,,ENST00000483415,;EWSR1,non_coding_transcript_exon_variant,,ENST00000479135,;	C	ENSG00000182944	ENST00000414183	Transcript	missense_variant	464	443	148	G/A	gGa/gCa	.	.	.	1	EWSR1	HGNC	3508	protein_coding	YES	CCDS13852.2	ENSP00000400142	EWS_HUMAN	.	UPI000006DE88	.	deleterious(0.01)	probably_damaging(0.973)	7/18	.	hmmpanther:PTHR23238:SF3,hmmpanther:PTHR23238	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGGAAACA	.	5	ESCA
RNF185	0	.	GRCh37	22	31592935	31592935	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.322C>G	p.Pro108Ala	p.P108A	ENST00000326132	5/7	55	37	18	46	46	0	RNF185,missense_variant,p.Pro108Ala,ENST00000326132,;RNF185,missense_variant,p.Pro46Ala,ENST00000426256,;RNF185,intron_variant,,ENST00000266252,;RNF185,missense_variant,p.Pro108Ala,ENST00000518626,;RNF185,non_coding_transcript_exon_variant,,ENST00000471384,;RNF185,non_coding_transcript_exon_variant,,ENST00000468921,;RNF185,non_coding_transcript_exon_variant,,ENST00000494514,;	G	ENSG00000138942	ENST00000326132	Transcript	missense_variant	481	322	108	P/A	Cct/Gct	.	.	.	1	RNF185	HGNC	26783	protein_coding	YES	CCDS13890.1	ENSP00000320508	RN185_HUMAN	.	UPI0000036022	.	deleterious(0)	probably_damaging(0.996)	5/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12313:SF3,hmmpanther:PTHR12313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCCTCGT	.	5	ESCA
EIF4ENIF1	0	.	GRCh37	22	31835930	31835930	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2894A>T	p.Gln965Leu	p.Q965L	ENST00000397525	19/19	51	32	19	34	34	0	EIF4ENIF1,missense_variant,p.Gln620Leu,ENST00000382180,;EIF4ENIF1,missense_variant,p.Gln791Leu,ENST00000344710,;EIF4ENIF1,missense_variant,p.Gln965Leu,ENST00000397525,;EIF4ENIF1,missense_variant,p.Gln941Leu,ENST00000397523,;EIF4ENIF1,missense_variant,p.Gln965Leu,ENST00000330125,;EIF4ENIF1,downstream_gene_variant,,ENST00000418321,;EIF4ENIF1,upstream_gene_variant,,ENST00000441289,;EIF4ENIF1,non_coding_transcript_exon_variant,,ENST00000495101,;DRG1,intron_variant,,ENST00000548143,;EIF4ENIF1,downstream_gene_variant,,ENST00000445424,;EIF4ENIF1,downstream_gene_variant,,ENST00000475437,;EIF4ENIF1,downstream_gene_variant,,ENST00000487671,;	A	ENSG00000184708	ENST00000397525	Transcript	missense_variant	3118	2894	965	Q/L	cAg/cTg	.	.	.	-1	EIF4ENIF1	HGNC	16687	protein_coding	YES	CCDS13898.1	ENSP00000380659	4ET_HUMAN	B1AKL6_HUMAN,B1AKL5_HUMAN	UPI0000124F14	.	deleterious(0)	probably_damaging(0.953)	19/19	.	hmmpanther:PTHR12269	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGCTGTAGC	.	5	ESCA
HMGXB4	0	.	GRCh37	22	35684359	35684359	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597G>A	p.Glu533Lys	p.E533K	ENST00000216106	9/11	18	13	4	12	12	0	HMGXB4,missense_variant,p.Glu424Lys,ENST00000444518,;HMGXB4,missense_variant,p.Glu533Lys,ENST00000216106,;HMGXB4,3_prime_UTR_variant,,ENST00000418170,;HMGXB4,non_coding_transcript_exon_variant,,ENST00000498212,;	A	ENSG00000100281	ENST00000216106	Transcript	missense_variant	1725	1597	533	E/K	Gag/Aag	.	.	.	1	HMGXB4	HGNC	5003	protein_coding	YES	CCDS33641.1	ENSP00000216106	HMGX4_HUMAN	Q7Z641_HUMAN,B0QXZ9_HUMAN,B0QXZ8_HUMAN	UPI00003765B4	.	deleterious(0)	probably_damaging(0.993)	9/11	.	hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGAGAGTCC	.	5	ESCA
TRIOBP	0	.	GRCh37	22	38109392	38109392	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.430G>C	p.Asp144His	p.D144H	ENST00000406386	5/24	24	21	3	21	21	0	TRIOBP,missense_variant,p.Asp144His,ENST00000406386,;NOL12,3_prime_UTR_variant,,ENST00000455236,;TRIOBP,intron_variant,,ENST00000344404,;TRIOBP,intron_variant,,ENST00000492485,;	C	ENSG00000100106	ENST00000406386	Transcript	missense_variant	685	430	144	D/H	Gat/Cat	.	.	.	1	TRIOBP	HGNC	17009	protein_coding	YES	CCDS43015.1	ENSP00000384312	TARA_HUMAN	F6WYE2_HUMAN,F6WMF4_HUMAN	UPI000067CB88	.	tolerated_low_confidence(0.06)	benign(0.124)	5/24	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCCTGATGAT	.	2	ESCA
ANKRD54	0	.	GRCh37	22	38228688	38228688	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.784G>A	p.Asp262Asn	p.D262N	ENST00000215941	7/8	43	30	13	25	25	0	ANKRD54,missense_variant,p.Asp142Asn,ENST00000406423,;ANKRD54,missense_variant,p.Asp246Asn,ENST00000411961,;ANKRD54,missense_variant,p.Asp262Asn,ENST00000215941,;ANKRD54,missense_variant,p.Asp69Asn,ENST00000609454,;ANKRD54,missense_variant,p.Asp178Asn,ENST00000458278,;ANKRD54,downstream_gene_variant,,ENST00000424350,;ANKRD54,downstream_gene_variant,,ENST00000434930,;ANKRD54,non_coding_transcript_exon_variant,,ENST00000498417,;ANKRD54,non_coding_transcript_exon_variant,,ENST00000464849,;ANKRD54,missense_variant,p.Asp129Asn,ENST00000407117,;ANKRD54,downstream_gene_variant,,ENST00000413497,;	T	ENSG00000100124	ENST00000215941	Transcript	missense_variant	977	784	262	D/N	Gat/Aat	.	.	.	-1	ANKRD54	HGNC	25185	protein_coding	YES	CCDS13959.1	ENSP00000215941	ANR54_HUMAN	.	UPI0000073164	.	tolerated(0.16)	benign(0.045)	7/8	.	hmmpanther:PTHR24197:SF33,hmmpanther:PTHR24197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATCCAGGC	.	5	ESCA
PNPLA3	0	.	GRCh37	22	44330533	44330533	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.744C>T	p.%3D	p.F248F	ENST00000216180	5/9	77	54	22	83	83	0	PNPLA3,synonymous_variant,p.%3D,ENST00000216180,;PNPLA3,synonymous_variant,p.%3D,ENST00000423180,;PNPLA3,non_coding_transcript_exon_variant,,ENST00000497129,;PNPLA3,downstream_gene_variant,,ENST00000478713,;PNPLA3,3_prime_UTR_variant,,ENST00000406117,;	T	ENSG00000100344	ENST00000216180	Transcript	synonymous_variant	917	744	248	F	ttC/ttT	.	.	.	1	PNPLA3	HGNC	18590	protein_coding	YES	CCDS14054.1	ENSP00000216180	PLPL3_HUMAN	U3N901_HUMAN	UPI000006CED5	.	.	.	5/9	.	hmmpanther:PTHR12406,hmmpanther:PTHR12406:SF22,Superfamily_domains:SSF52151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTCTTGGA	.	5	ESCA
GRAMD4	0	.	GRCh37	22	47054198	47054198	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398A>G	p.Lys133Arg	p.K133R	ENST00000406902	4/19	37	26	11	23	23	0	GRAMD4,missense_variant,p.Lys133Arg,ENST00000406902,;GRAMD4,missense_variant,p.Lys133Arg,ENST00000361034,;GRAMD4,upstream_gene_variant,,ENST00000456069,;	G	ENSG00000075240	ENST00000406902	Transcript	missense_variant	611	398	133	K/R	aAg/aGg	.	.	.	1	GRAMD4	HGNC	29113	protein_coding	YES	CCDS33672.1	ENSP00000385689	GRAM4_HUMAN	.	UPI0000161A59	.	tolerated(0.25)	benign(0.012)	4/19	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGAAGGCCA	.	2	ESCA
MOV10L1	0	.	GRCh37	22	50528851	50528851	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97+237C>T	.	.	ENST00000262794	.	45	31	14	32	32	0	MOV10L1,5_prime_UTR_variant,,ENST00000540615,;MOV10L1,intron_variant,,ENST00000262794,;MOV10L1,intron_variant,,ENST00000545383,;MOV10L1,intron_variant,,ENST00000395843,;MOV10L1,intron_variant,,ENST00000395858,;MLC1,upstream_gene_variant,,ENST00000311597,;MLC1,upstream_gene_variant,,ENST00000431262,;MOV10L1,intron_variant,,ENST00000475190,;MOV10L1,3_prime_UTR_variant,,ENST00000395854,;MOV10L1,3_prime_UTR_variant,,ENST00000419054,;	T	ENSG00000073146	ENST00000262794	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MOV10L1	HGNC	7201	protein_coding	YES	CCDS14084.1	ENSP00000262794	M10L1_HUMAN	.	UPI00000421FB	.	.	.	.	1/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCTTCCC	.	5	ESCA
BCL2L11	0	.	GRCh37	2	111907693	111907693	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.467G>A	p.Gly156Glu	p.G156E	ENST00000393256	3/4	44	29	14	49	49	0	BCL2L11,missense_variant,p.Gly156Glu,ENST00000393256,;BCL2L11,missense_variant,p.Gly96Glu,ENST00000308659,;BCL2L11,missense_variant,p.Gly66Glu,ENST00000393253,;BCL2L11,missense_variant,p.Gly156Glu,ENST00000357757,;BCL2L11,downstream_gene_variant,,ENST00000438054,;BCL2L11,missense_variant,p.Gly66Glu,ENST00000439718,;BCL2L11,missense_variant,p.Gly66Glu,ENST00000452231,;BCL2L11,missense_variant,p.Gly156Glu,ENST00000437029,;BCL2L11,missense_variant,p.Gly96Glu,ENST00000433098,;BCL2L11,3_prime_UTR_variant,,ENST00000361493,;BCL2L11,3_prime_UTR_variant,,ENST00000431217,;BCL2L11,intron_variant,,ENST00000436733,;BCL2L11,intron_variant,,ENST00000415458,;	A	ENSG00000153094	ENST00000393256	Transcript	missense_variant	740	467	156	G/E	gGa/gAa	.	.	.	1	BCL2L11	HGNC	994	protein_coding	YES	CCDS2089.1	ENSP00000376943	B2L11_HUMAN	E9PAM9_HUMAN,C9J417_HUMAN	UPI0000033ABA	.	deleterious(0)	probably_damaging(1)	3/4	.	hmmpanther:PTHR12044,Pfam_domain:PF08945,PIRSF_domain:PIRSF037827	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTGGAGACG	.	5	ESCA
TMEM177	0	.	GRCh37	2	120443383	120443383	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000424086	.	36	26	9	52	52	0	TMEM177,3_prime_UTR_variant,,ENST00000409951,;TMEM177,downstream_gene_variant,,ENST00000272521,;TMEM177,downstream_gene_variant,,ENST00000401466,;TMEM177,downstream_gene_variant,,ENST00000424086,;TMEM177,downstream_gene_variant,,ENST00000445518,;TMEM177,non_coding_transcript_exon_variant,,ENST00000496203,;	T	ENSG00000144120	ENST00000424086	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3689	1	TMEM177	HGNC	28143	protein_coding	YES	CCDS2128.1	ENSP00000402661	TM177_HUMAN	C9J6F8_HUMAN	UPI000013D95F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTCATGGT	.	5	ESCA
TUBA3D	0	.	GRCh37	2	132237645	132237645	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.379G>A	p.Asp127Asn	p.D127N	ENST00000321253	4/5	73	47	25	87	87	0	TUBA3D,missense_variant,p.Asp127Asn,ENST00000321253,;MZT2A,downstream_gene_variant,,ENST00000309451,;TUBA3D,non_coding_transcript_exon_variant,,ENST00000409047,;MZT2A,downstream_gene_variant,,ENST00000410036,;MZT2A,intron_variant,,ENST00000445782,;MZT2A,intron_variant,,ENST00000427024,;	A	ENSG00000075886	ENST00000321253	Transcript	missense_variant	486	379	127	D/N	Gat/Aat	.	.	.	1	TUBA3D	HGNC	24071	protein_coding	YES	CCDS33290.1	ENSP00000326042	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	deleterious_low_confidence(0.02)	possibly_damaging(0.684)	4/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01162,Prints_domain:PR01161	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCGGATCTG	.	5	ESCA
LRP1B	0	.	GRCh37	2	140992352	140992352	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13659+3G>A	.	.	ENST00000389484	.	48	36	12	58	58	0	LRP1B,splice_region_variant,,ENST00000389484,;LRP1B,intron_variant,,ENST00000437977,;LRP1B,downstream_gene_variant,,ENST00000442974,;	T	ENSG00000168702	ENST00000389484	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	.	90/90	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	TCTCTCACCCC	.	3	ESCA
RPRM	0	.	GRCh37	2	154334906	154334906	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174G>A	p.%3D	p.Q58Q	ENST00000325926	1/1	42	28	13	24	24	0	RPRM,synonymous_variant,p.%3D,ENST00000325926,;AC012501.2,intron_variant,,ENST00000424322,;	T	ENSG00000177519	ENST00000325926	Transcript	synonymous_variant	417	174	58	Q	caG/caA	.	.	.	-1	RPRM	HGNC	24201	protein_coding	YES	CCDS2198.1	ENSP00000314946	RPRM_HUMAN	.	UPI0000072BEC	.	.	.	1/1	.	Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGATCTGCAC	.	5	ESCA
NBAS	0	.	GRCh37	2	15651430	15651430	+	Missense_Mutation	SNP	G	G	A	rs149760582	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.791C>T	p.Ser264Leu	p.S264L	ENST00000281513	10/52	14	10	4	22	22	0	NBAS,missense_variant,p.Ser264Leu,ENST00000441750,;NBAS,missense_variant,p.Ser264Leu,ENST00000281513,;NBAS,upstream_gene_variant,,ENST00000427792,;	A	ENSG00000151779	ENST00000281513	Transcript	missense_variant	817	791	264	S/L	tCa/tTa	rs149760582	.	.	-1	NBAS	HGNC	15625	protein_coding	YES	CCDS1685.1	ENSP00000281513	NBAS_HUMAN	Q4ZG05_HUMAN,H7C007_HUMAN	UPI00001AEA68	.	deleterious(0)	benign(0.075)	10/52	.	Superfamily_domains:SSF50969,Pfam_domain:PF15492,hmmpanther:PTHR15922:SF2,hmmpanther:PTHR15922	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTGACATG	byCluster	5	ESCA
CDCA7	0	.	GRCh37	2	174231980	174231980	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1288C>T	p.His430Tyr	p.H430Y	ENST00000306721	9/10	48	25	22	63	63	0	CDCA7,missense_variant,p.His386Tyr,ENST00000410101,;CDCA7,missense_variant,p.His301Tyr,ENST00000392567,;CDCA7,missense_variant,p.His430Tyr,ENST00000306721,;CDCA7,missense_variant,p.His309Tyr,ENST00000410019,;CDCA7,missense_variant,p.His351Tyr,ENST00000347703,;CDCA7,non_coding_transcript_exon_variant,,ENST00000467411,;CDCA7,non_coding_transcript_exon_variant,,ENST00000496441,;CDCA7,downstream_gene_variant,,ENST00000468359,;CDCA7,downstream_gene_variant,,ENST00000435616,;	T	ENSG00000144354	ENST00000306721	Transcript	missense_variant	1391	1288	430	H/Y	Cat/Tat	.	.	.	1	CDCA7	HGNC	14628	protein_coding	YES	CCDS2252.1	ENSP00000306968	CDCA7_HUMAN	B4DM13_HUMAN	UPI0000456EA4	.	tolerated(0.86)	probably_damaging(0.964)	9/10	.	hmmpanther:PTHR31169:SF2,hmmpanther:PTHR31169,Pfam_domain:PF10497	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCATGGC	.	5	ESCA
WIPF1	0	.	GRCh37	2	175427262	175427262	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13C>G	.	.	ENST00000392547	8/8	74	49	25	44	44	0	WIPF1,3_prime_UTR_variant,,ENST00000359761,;WIPF1,3_prime_UTR_variant,,ENST00000392547,;WIPF1,3_prime_UTR_variant,,ENST00000392546,;WIPF1,intron_variant,,ENST00000272746,;WIPF1,downstream_gene_variant,,ENST00000409891,;RNU6-5P,upstream_gene_variant,,ENST00000384238,;AC018890.6,intron_variant,,ENST00000412835,;AC018890.6,intron_variant,,ENST00000442996,;WIPF1,downstream_gene_variant,,ENST00000467149,;	C	ENSG00000115935	ENST00000392547	Transcript	3_prime_UTR_variant	1625	.	.	.	.	.	.	.	-1	WIPF1	HGNC	12736	protein_coding	YES	CCDS2260.1	ENSP00000376330	WIPF1_HUMAN	C9JTB9_HUMAN	UPI000013D4BD	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGAGCAG	.	5	ESCA
TTN	0	.	GRCh37	2	179667001	179667001	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159C>T	p.%3D	p.G53G	ENST00000589042	3/363	59	41	18	38	38	0	TTN,synonymous_variant,p.%3D,ENST00000359218,;TTN,synonymous_variant,p.%3D,ENST00000342175,;TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000360870,;TTN,synonymous_variant,p.%3D,ENST00000460472,;TTN,downstream_gene_variant,,ENST00000412264,;TTN,non_coding_transcript_exon_variant,,ENST00000470257,;	A	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	384	159	53	G	ggC/ggT	COSM4089335,COSM4089334,COSM4089331,COSM4089333,COSM4089332,COSM4089336	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	3/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACGCCGGG	.	5	ESCA
BZW1	0	.	GRCh37	2	201688392	201688392	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000452790	.	29	22	6	29	29	0	BZW1,3_prime_UTR_variant,,ENST00000409600,;BZW1,downstream_gene_variant,,ENST00000359893,;BZW1,downstream_gene_variant,,ENST00000452790,;BZW1,downstream_gene_variant,,ENST00000409226,;BZW1,downstream_gene_variant,,ENST00000410110,;RP11-469M7.1,upstream_gene_variant,,ENST00000568571,;BZW1,downstream_gene_variant,,ENST00000463310,;BZW1,downstream_gene_variant,,ENST00000491576,;	A	ENSG00000082153	ENST00000452790	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1426	1	BZW1	HGNC	18380	protein_coding	YES	CCDS56155.1	ENSP00000394316	BZW1_HUMAN	Q3LIC9_HUMAN,D3DN77_HUMAN,C9JWF5_HUMAN,C9JFN4_HUMAN,C9J188_HUMAN,C9IZ80_HUMAN	UPI00006C0604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TAACTGATTGT	.	3	ESCA
ALS2	0	.	GRCh37	2	202584797	202584797	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3703-1864C>T	.	.	ENST00000264276	.	23	16	7	18	18	0	ALS2,synonymous_variant,p.%3D,ENST00000457679,;ALS2,intron_variant,,ENST00000264276,;ALS2,intron_variant,,ENST00000489440,;ALS2,synonymous_variant,p.%3D,ENST00000439495,;ALS2,downstream_gene_variant,,ENST00000482891,;	A	ENSG00000003393	ENST00000264276	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ALS2	HGNC	443	protein_coding	YES	CCDS42800.1	ENSP00000264276	ALS2_HUMAN	J3KQ43_HUMAN,J3KQ33_HUMAN,A8K4R4_HUMAN	UPI0000231C77	.	.	.	.	23/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TTTCAGAAAAT	.	4	ESCA
WNT10A	0	.	GRCh37	2	219757942	219757942	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1203C>T	p.%3D	p.F401F	ENST00000258411	4/4	33	15	18	35	35	0	WNT10A,synonymous_variant,p.%3D,ENST00000258411,;WNT10A,downstream_gene_variant,,ENST00000458582,;WNT10A,downstream_gene_variant,,ENST00000483911,;WNT10A,upstream_gene_variant,,ENST00000489887,;	T	ENSG00000135925	ENST00000258411	Transcript	synonymous_variant	1836	1203	401	F	ttC/ttT	.	.	.	1	WNT10A	HGNC	13829	protein_coding	YES	CCDS2426.1	ENSP00000258411	WN10A_HUMAN	Q9BTP0_HUMAN,Q05BQ6_HUMAN	UPI0000032F2A	.	.	.	4/4	.	hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF89,Pfam_domain:PF00110,SMART_domains:SM00097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTCGTGGT	.	5	ESCA
ALPI	0	.	GRCh37	2	233321734	233321734	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426G>A	p.%3D	p.T142T	ENST00000295463	4/11	29	13	15	42	41	0	ALPI,synonymous_variant,p.%3D,ENST00000295463,;ALPI,3_prime_UTR_variant,,ENST00000457560,;	A	ENSG00000163295	ENST00000295463	Transcript	synonymous_variant	503	426	142	T	acG/acA	.	.	.	1	ALPI	HGNC	437	protein_coding	YES	CCDS2492.1	ENSP00000295463	PPBI_HUMAN	.	UPI0000131FFE	.	.	.	4/11	.	hmmpanther:PTHR11596:SF30,hmmpanther:PTHR11596,Pfam_domain:PF00245,Gene3D:3.40.720.10,SMART_domains:SM00098,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACACGACACG	.	5	ESCA
PKDCC	0	.	GRCh37	2	42281407	42281407	+	Missense_Mutation	SNP	G	G	A	rs201349790	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.994G>A	p.Glu332Lys	p.E332K	ENST00000294964	3/7	21	9	12	25	25	0	PKDCC,missense_variant,p.Glu332Lys,ENST00000294964,;PKDCC,upstream_gene_variant,,ENST00000480099,;PKDCC,3_prime_UTR_variant,,ENST00000401498,;PKDCC,non_coding_transcript_exon_variant,,ENST00000492861,;PKDCC,upstream_gene_variant,,ENST00000470578,;PKDCC,upstream_gene_variant,,ENST00000475241,;PKDCC,downstream_gene_variant,,ENST00000485578,;PKDCC,upstream_gene_variant,,ENST00000475868,;PKDCC,upstream_gene_variant,,ENST00000490302,;	A	ENSG00000162878	ENST00000294964	Transcript	missense_variant	1174	994	332	E/K	Gag/Aag	rs201349790	.	.	1	PKDCC	HGNC	25123	protein_coding	YES	CCDS33186.2	ENSP00000294964	PKDCC_HUMAN	.	UPI0000EE25C6	.	tolerated(0.14)	benign(0.005)	3/7	.	PROSITE_profiles:PS50011,hmmpanther:PTHR26392,hmmpanther:PTHR26392:SF71,Pfam_domain:PF12260	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGCGAGGGC	byCluster	5	ESCA
MTA3	0	.	GRCh37	2	42931360	42931360	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1052C>G	p.Ser351Cys	p.S351C	ENST00000407270	12/14	41	27	14	38	38	0	MTA3,missense_variant,p.Ser294Cys,ENST00000406652,;MTA3,missense_variant,p.Ser351Cys,ENST00000407270,;MTA3,missense_variant,p.Ser350Cys,ENST00000406911,;MTA3,missense_variant,p.Ser294Cys,ENST00000405592,;MTA3,missense_variant,p.Ser351Cys,ENST00000405094,;MTA3,non_coding_transcript_exon_variant,,ENST00000472767,;MTA3,intron_variant,,ENST00000475383,;MTA3,missense_variant,p.Ser350Cys,ENST00000454356,;MTA3,missense_variant,p.Ser350Cys,ENST00000409019,;MTA3,non_coding_transcript_exon_variant,,ENST00000467925,;MTA3,non_coding_transcript_exon_variant,,ENST00000482875,;MTA3,upstream_gene_variant,,ENST00000478602,;	G	ENSG00000057935	ENST00000407270	Transcript	missense_variant	1281	1052	351	S/C	tCc/tGc	COSM1531916	.	.	1	MTA3	HGNC	23784	protein_coding	YES	CCDS46267.1	ENSP00000385045	MTA3_HUMAN	Q53SC0_HUMAN,Q53RX8_HUMAN,Q53QZ9_HUMAN	UPI000002AE6A	.	tolerated(0.05)	possibly_damaging(0.831)	12/14	.	hmmpanther:PTHR10865,hmmpanther:PTHR10865:SF6	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCCACTA	.	5	ESCA
MCFD2	0	.	GRCh37	2	47129464	47129464	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3138A>G	.	.	ENST00000409105	5/5	54	41	13	40	40	0	MCFD2,3_prime_UTR_variant,,ENST00000409800,;MCFD2,3_prime_UTR_variant,,ENST00000319466,;MCFD2,3_prime_UTR_variant,,ENST00000409913,;MCFD2,3_prime_UTR_variant,,ENST00000444761,;MCFD2,3_prime_UTR_variant,,ENST00000409105,;MCFD2,downstream_gene_variant,,ENST00000412438,;MCFD2,downstream_gene_variant,,ENST00000409207,;MCFD2,downstream_gene_variant,,ENST00000409218,;MCFD2,downstream_gene_variant,,ENST00000434262,;MCFD2,downstream_gene_variant,,ENST00000409147,;MCFD2,downstream_gene_variant,,ENST00000409973,;AC016722.4,intron_variant,,ENST00000429761,;MCFD2,downstream_gene_variant,,ENST00000470873,;MCFD2,downstream_gene_variant,,ENST00000493804,;	C	ENSG00000180398	ENST00000409105	Transcript	3_prime_UTR_variant	3759	.	.	.	.	.	.	.	-1	MCFD2	HGNC	18451	protein_coding	YES	CCDS33192.1	ENSP00000386651	MCFD2_HUMAN	C9JTR4_HUMAN	UPI000005275E	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTAATCATTG	.	5	ESCA
CLHC1	0	.	GRCh37	2	55439812	55439812	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.496C>G	p.Pro166Ala	p.P166A	ENST00000401408	5/13	32	20	11	36	36	0	CLHC1,missense_variant,p.Pro44Ala,ENST00000406076,;CLHC1,missense_variant,p.Pro166Ala,ENST00000407122,;CLHC1,missense_variant,p.Pro166Ala,ENST00000401408,;CLHC1,intron_variant,,ENST00000406437,;AC012358.7,downstream_gene_variant,,ENST00000366153,;CLHC1,intron_variant,,ENST00000494539,;CLHC1,intron_variant,,ENST00000487320,;CLHC1,intron_variant,,ENST00000466020,;CLHC1,intron_variant,,ENST00000428621,;CLHC1,upstream_gene_variant,,ENST00000411884,;	C	ENSG00000162994	ENST00000401408	Transcript	missense_variant	842	496	166	P/A	Cca/Gca	.	.	.	-1	CLHC1	HGNC	26453	protein_coding	YES	CCDS33201.1	ENSP00000384869	CLHC1_HUMAN	E7EVC5_HUMAN,D6W5C8_HUMAN,B5MC48_HUMAN	UPI00004DEC65	.	deleterious(0)	probably_damaging(1)	5/13	.	hmmpanther:PTHR10292,PIRSF_domain:PIRSF037469	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTGGAATAG	.	5	ESCA
CCDC104	0	.	GRCh37	2	55746805	55746805	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-133C>G	.	.	ENST00000349456	1/10	20	11	9	10	10	0	CCDC104,5_prime_UTR_variant,,ENST00000339012,;CCDC104,5_prime_UTR_variant,,ENST00000349456,;CCDC104,5_prime_UTR_variant,,ENST00000406691,;CCDC104,upstream_gene_variant,,ENST00000403007,;CCDC104,upstream_gene_variant,,ENST00000407816,;	G	ENSG00000163001	ENST00000349456	Transcript	5_prime_UTR_variant	16	.	.	.	.	.	.	.	1	CCDC104	HGNC	30540	protein_coding	YES	CCDS1854.2	ENSP00000295117	CC104_HUMAN	.	UPI000013E20A	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTAGCTTCTA	.	2	ESCA
EGR4	0	.	GRCh37	2	73518484	73518484	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*101G>C	.	.	ENST00000545030	2/2	14	6	8	9	9	0	EGR4,3_prime_UTR_variant,,ENST00000545030,;EGR4,3_prime_UTR_variant,,ENST00000436467,;	G	ENSG00000135625	ENST00000545030	Transcript	3_prime_UTR_variant	1946	.	.	.	.	.	.	.	-1	EGR4	HGNC	3241	protein_coding	YES	CCDS1925.2	ENSP00000445626	EGR4_HUMAN	B7ZKU3_HUMAN	UPI0000EE25D4	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GCCCTCGGGCG	.	2	ESCA
GCFC2	0	.	GRCh37	2	75929334	75929334	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>A	p.Glu204Lys	p.E204K	ENST00000321027	3/17	59	41	18	48	48	0	GCFC2,missense_variant,p.Glu204Lys,ENST00000321027,;GCFC2,missense_variant,p.Glu204Lys,ENST00000470503,;GCFC2,missense_variant,p.Glu204Lys,ENST00000541687,;GCFC2,intron_variant,,ENST00000409857,;GCFC2,intron_variant,,ENST00000442309,;RP11-342K6.3,downstream_gene_variant,,ENST00000604464,;GCFC2,3_prime_UTR_variant,,ENST00000472230,;GCFC2,upstream_gene_variant,,ENST00000470197,;	T	ENSG00000005436	ENST00000321027	Transcript	missense_variant	744	610	204	E/K	Gag/Aag	.	.	.	-1	GCFC2	HGNC	1317	protein_coding	YES	CCDS1961.1	ENSP00000318690	GCFC2_HUMAN	B3KUM5_HUMAN,A4UHR0_HUMAN	UPI000013C96B	.	deleterious(0.02)	benign(0.055)	3/17	.	hmmpanther:PTHR12214:SF1,hmmpanther:PTHR12214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCAGCCA	.	5	ESCA
KIDINS220	0	.	GRCh37	2	8930037	8930037	+	Missense_Mutation	SNP	A	A	C	rs369544460	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594T>G	p.Phe532Val	p.F532V	ENST00000256707	14/30	32	21	11	32	32	0	KIDINS220,missense_variant,p.Phe532Val,ENST00000427284,;KIDINS220,missense_variant,p.Phe533Val,ENST00000489024,;KIDINS220,missense_variant,p.Phe490Val,ENST00000418530,;KIDINS220,missense_variant,p.Phe532Val,ENST00000256707,;KIDINS220,missense_variant,p.Phe532Val,ENST00000473731,;KIDINS220,missense_variant,p.Phe279Val,ENST00000496383,;KIDINS220,missense_variant,p.Phe533Val,ENST00000319688,;KIDINS220,3_prime_UTR_variant,,ENST00000488729,;KIDINS220,downstream_gene_variant,,ENST00000474782,;	C	ENSG00000134313	ENST00000256707	Transcript	missense_variant	1776	1594	532	F/V	Ttc/Gtc	rs369544460	.	.	-1	KIDINS220	HGNC	29508	protein_coding	YES	CCDS42650.1	ENSP00000256707	KDIS_HUMAN	F8WAY8_HUMAN	UPI0000208E08	.	tolerated(0.1)	benign(0.001)	14/30	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24116,hmmpanther:PTHR24116:SF5,Pfam_domain:PF07693	.	.	.	.	.	.	.	G:0.0008	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGAAGCTCA	byFrequency|byCluster	5	ESCA
ABI3BP	0	.	GRCh37	3	100554487	100554487	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597+10729G>C	.	.	ENST00000284322	.	25	21	4	19	19	0	ABI3BP,missense_variant,p.Glu131Gln,ENST00000495591,;ABI3BP,missense_variant,p.Glu56Gln,ENST00000528490,;ABI3BP,missense_variant,p.Glu29Gln,ENST00000383691,;ABI3BP,missense_variant,p.Glu724Gln,ENST00000495063,;ABI3BP,missense_variant,p.Glu724Gln,ENST00000471714,;ABI3BP,missense_variant,p.Glu90Gln,ENST00000533795,;ABI3BP,missense_variant,p.Glu67Gln,ENST00000534413,;ABI3BP,intron_variant,,ENST00000466947,;ABI3BP,intron_variant,,ENST00000284322,;ABI3BP,intron_variant,,ENST00000528305,;ABI3BP,upstream_gene_variant,,ENST00000478235,;ABI3BP,upstream_gene_variant,,ENST00000471901,;ABI3BP,downstream_gene_variant,,ENST00000533855,;ABI3BP,downstream_gene_variant,,ENST00000534256,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487012,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487249,;ABI3BP,intron_variant,,ENST00000470336,;	G	ENSG00000154175	ENST00000284322	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ABI3BP	HGNC	17265	protein_coding	YES	CCDS46880.1	ENSP00000284322	TARSH_HUMAN	.	UPI000011C136	.	.	.	.	18/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTCAATGT	.	4	ESCA
KIAA2018	0	.	GRCh37	3	113376936	113376936	+	Missense_Mutation	SNP	G	G	T	rs755549731	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3593C>A	p.Ser1198Tyr	p.S1198Y	ENST00000316407	7/7	73	44	28	77	77	0	KIAA2018,missense_variant,p.Ser1198Tyr,ENST00000478658,;KIAA2018,missense_variant,p.Ser1198Tyr,ENST00000316407,;KIAA2018,intron_variant,,ENST00000491165,;KIAA2018,non_coding_transcript_exon_variant,,ENST00000496826,;	T	ENSG00000176542	ENST00000316407	Transcript	missense_variant	4004	3593	1198	S/Y	tCt/tAt	rs755549731,COSM282212	.	.	-1	KIAA2018	HGNC	30494	protein_coding	YES	CCDS43133.1	ENSP00000320794	K2018_HUMAN	.	UPI00004800D8	.	.	possibly_damaging(0.526)	7/7	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGAGAATTA	.	5	ESCA
CCDC14	0	.	GRCh37	3	123633065	123633065	+	3'Flank	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000433542	.	30	20	10	36	36	0	CCDC14,3_prime_UTR_variant,,ENST00000310351,;CCDC14,3_prime_UTR_variant,,ENST00000485727,;CCDC14,3_prime_UTR_variant,,ENST00000488653,;CCDC14,3_prime_UTR_variant,,ENST00000489746,;CCDC14,intron_variant,,ENST00000479903,;CCDC14,downstream_gene_variant,,ENST00000409697,;CCDC14,downstream_gene_variant,,ENST00000419247,;CCDC14,downstream_gene_variant,,ENST00000433542,;CCDC14,intron_variant,,ENST00000463996,;CCDC14,downstream_gene_variant,,ENST00000483247,;CCDC14,3_prime_UTR_variant,,ENST00000409657,;CCDC14,non_coding_transcript_exon_variant,,ENST00000495381,;	G	ENSG00000175455	ENST00000433542	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	101	-1	CCDC14	HGNC	25766	protein_coding	YES	CCDS3025.2	ENSP00000395706	CCD14_HUMAN	C9JWZ1_HUMAN	UPI00016632FB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTATCTATAT	.	5	ESCA
CCDC14	0	.	GRCh37	3	123650025	123650025	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1723G>A	p.Glu575Lys	p.E575K	ENST00000433542	11/12	37	24	12	51	51	0	CCDC14,missense_variant,p.Glu456Lys,ENST00000310351,;CCDC14,missense_variant,p.Glu416Lys,ENST00000485727,;CCDC14,missense_variant,p.Glu597Lys,ENST00000409697,;CCDC14,missense_variant,p.Glu257Lys,ENST00000419247,;CCDC14,missense_variant,p.Glu198Lys,ENST00000479903,;CCDC14,missense_variant,p.Glu616Lys,ENST00000488653,;CCDC14,missense_variant,p.Glu575Lys,ENST00000433542,;CCDC14,missense_variant,p.Glu416Lys,ENST00000489746,;CCDC14,intron_variant,,ENST00000463996,;CCDC14,intron_variant,,ENST00000483247,;CCDC14,3_prime_UTR_variant,,ENST00000409657,;CCDC14,non_coding_transcript_exon_variant,,ENST00000495381,;CCDC14,non_coding_transcript_exon_variant,,ENST00000487498,;CCDC14,downstream_gene_variant,,ENST00000485949,;CCDC14,downstream_gene_variant,,ENST00000471054,;	T	ENSG00000175455	ENST00000433542	Transcript	missense_variant	2123	1723	575	E/K	Gaa/Aaa	.	.	.	-1	CCDC14	HGNC	25766	protein_coding	YES	CCDS3025.2	ENSP00000395706	CCD14_HUMAN	C9JWZ1_HUMAN	UPI00016632FB	.	deleterious(0)	possibly_damaging(0.801)	11/12	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22367,hmmpanther:PTHR22367:SF1,Pfam_domain:PF15254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTCAGCAG	.	5	ESCA
KALRN	0	.	GRCh37	3	123813618	123813618	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-67C>G	.	.	ENST00000240874	1/34	69	46	23	42	42	0	KALRN,5_prime_UTR_variant,,ENST00000240874,;KALRN,5_prime_UTR_variant,,ENST00000460856,;KALRN,5_prime_UTR_variant,,ENST00000360013,;KALRN,intron_variant,,ENST00000448253,;KALRN,non_coding_transcript_exon_variant,,ENST00000483658,;KALRN,non_coding_transcript_exon_variant,,ENST00000488825,;KALRN,non_coding_transcript_exon_variant,,ENST00000477496,;	G	ENSG00000160145	ENST00000240874	Transcript	5_prime_UTR_variant	91	.	.	.	.	.	.	.	1	KALRN	HGNC	4814	protein_coding	YES	CCDS3027.1	ENSP00000240874	KALRN_HUMAN	.	UPI000012C095	.	.	.	1/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCGAGTC	.	5	ESCA
TRH	0	.	GRCh37	3	129695539	129695539	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212-3C>G	.	.	ENST00000302649	.	24	16	8	30	30	0	TRH,splice_region_variant,,ENST00000507066,;TRH,splice_region_variant,,ENST00000302649,;	G	ENSG00000170893	ENST00000302649	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	TRH	HGNC	12298	protein_coding	YES	CCDS3066.1	ENSP00000303452	TRH_HUMAN	.	UPI0000136F2B	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCCAGCGT	.	4	ESCA
MSL2	0	.	GRCh37	3	135867782	135867782	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2207A>G	.	.	ENST00000309993	2/2	35	17	18	22	22	0	MSL2,3_prime_UTR_variant,,ENST00000309993,;PPP2R3A,downstream_gene_variant,,ENST00000264977,;MSL2,downstream_gene_variant,,ENST00000434835,;MSL2,downstream_gene_variant,,ENST00000481989,;PPP2R3A,downstream_gene_variant,,ENST00000490467,;MSL2,downstream_gene_variant,,ENST00000491050,;MSL2,downstream_gene_variant,,ENST00000473093,;PPP2R3A,downstream_gene_variant,,ENST00000334546,;	C	ENSG00000174579	ENST00000309993	Transcript	3_prime_UTR_variant	4674	.	.	.	.	.	.	.	-1	MSL2	HGNC	25544	protein_coding	YES	CCDS33861.1	ENSP00000311827	MSL2_HUMAN	C9J5S2_HUMAN,C9IZG7_HUMAN,C9IZ03_HUMAN	UPI000020A2D7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTATTGATA	.	5	ESCA
TPRXL	0	.	GRCh37	3	14106434	14106434	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758G>A	p.%3D	p.%3D	ENST00000424053	3/3	55	41	14	34	34	0	TPRXL,stop_retained_variant,p.%3D,ENST00000326972,;TPRXL,stop_retained_variant,p.%3D,ENST00000424053,;TPRXL,stop_retained_variant,p.%3D,ENST00000429201,;TPRXL,downstream_gene_variant,,ENST00000530586,;TPRXL,downstream_gene_variant,,ENST00000528040,;TPRXL,downstream_gene_variant,,ENST00000532924,;TPRXL,downstream_gene_variant,,ENST00000529129,;TPRXL,downstream_gene_variant,,ENST00000528312,;TPRXL,downstream_gene_variant,,ENST00000532880,;TPRXL,downstream_gene_variant,,ENST00000528067,;TPRXL,downstream_gene_variant,,ENST00000524375,;TPRXL,intron_variant,,ENST00000532753,;	A	ENSG00000180438	ENST00000424053	Transcript	stop_retained_variant	1305	758	253	*	tGa/tAa	.	.	.	1	TPRXL	HGNC	32178	protein_coding	YES	.	ENSP00000400448	.	I3L0F9_HUMAN,E9PPR8_HUMAN,E9PPI8_HUMAN,E9PNC5_HUMAN,E9PLC2_HUMAN,E9PLB7_HUMAN,E9PK92_HUMAN,E9PJS2_HUMAN	UPI0000141A8E	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTGAAGCT	.	5	ESCA
KPNA4	0	.	GRCh37	3	160232848	160232848	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032+392G>A	.	.	ENST00000334256	.	33	26	6	24	24	0	KPNA4,intron_variant,,ENST00000483437,;KPNA4,intron_variant,,ENST00000334256,;SCARNA7,non_coding_transcript_exon_variant,,ENST00000458797,;	T	ENSG00000186432	ENST00000334256	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KPNA4	HGNC	6397	protein_coding	YES	CCDS3191.1	ENSP00000334373	IMA3_HUMAN	.	UPI0000001648	.	.	.	.	12/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCAGCAT	.	5	ESCA
PHC3	0	.	GRCh37	3	169820479	169820479	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2621C>G	p.Ser874Cys	p.S874C	ENST00000495893	14/15	35	17	17	26	26	0	PHC3,missense_variant,p.Ser874Cys,ENST00000495893,;PHC3,missense_variant,p.Ser862Cys,ENST00000494943,;PHC3,missense_variant,p.Ser40Cys,ENST00000484068,;PHC3,splice_region_variant,,ENST00000467570,;	C	ENSG00000173889	ENST00000495893	Transcript	missense_variant	2653	2621	874	S/C	tCt/tGt	.	.	.	-1	PHC3	HGNC	15682	protein_coding	YES	CCDS46952.1	ENSP00000420294	PHC3_HUMAN	C9JYH7_HUMAN	UPI00004DF1A6	.	deleterious(0.01)	probably_damaging(0.998)	14/15	.	hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGATGGA	.	5	ESCA
NCEH1	0	.	GRCh37	3	172350567	172350567	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*698A>G	.	.	ENST00000538775	5/5	37	19	18	20	20	0	NCEH1,3_prime_UTR_variant,,ENST00000543711,;NCEH1,3_prime_UTR_variant,,ENST00000538775,;NCEH1,3_prime_UTR_variant,,ENST00000475381,;NCEH1,3_prime_UTR_variant,,ENST00000273512,;NCEH1,downstream_gene_variant,,ENST00000424772,;NCEH1,downstream_gene_variant,,ENST00000470419,;NCEH1,downstream_gene_variant,,ENST00000421723,;	C	ENSG00000144959	ENST00000538775	Transcript	3_prime_UTR_variant	2183	.	.	.	.	.	.	.	-1	NCEH1	HGNC	29260	protein_coding	YES	CCDS54682.1	ENSP00000442464	.	F5H7K4_HUMAN	UPI000199A4B7	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTAATGATAT	.	5	ESCA
PIK3CA	0	.	GRCh37	3	178948136	178948136	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	20/21	32	18	14	27	27	0	PIK3CA,missense_variant,p.Glu970Lys,ENST00000263967,;PIK3CA,downstream_gene_variant,,ENST00000462255,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	3065	2908	970	E/K	Gaa/Aaa	COSM94980,COSM94981	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	tolerated(0.51)	benign(0.05)	20/21	.	PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Pfam_domain:PF00454,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E970K|c.2908G>A|6,SITE|p.E970K|c.2908G>A|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAAGAATGC	.	5	ESCA
PARL	0	.	GRCh37	3	183602518	183602518	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117C>T	p.%3D	p.L39L	ENST00000317096	1/10	160	79	81	91	91	0	PARL,synonymous_variant,p.%3D,ENST00000435888,;PARL,synonymous_variant,p.%3D,ENST00000311101,;PARL,synonymous_variant,p.%3D,ENST00000317096,;PARL,upstream_gene_variant,,ENST00000449306,;MIR4448,upstream_gene_variant,,ENST00000584360,;RP11-315J22.5,upstream_gene_variant,,ENST00000445165,;PARL,synonymous_variant,p.%3D,ENST00000421484,;PARL,intron_variant,,ENST00000469056,;RP11-315J22.5,upstream_gene_variant,,ENST00000448655,;RP11-315J22.5,upstream_gene_variant,,ENST00000416648,;	A	ENSG00000175193	ENST00000317096	Transcript	synonymous_variant	178	117	39	L	ctC/ctT	.	.	.	-1	PARL	HGNC	18253	protein_coding	YES	CCDS3248.1	ENSP00000325421	PARL_HUMAN	.	UPI00000711C6	.	.	.	1/10	.	hmmpanther:PTHR22936	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCCGAGGAG	.	5	ESCA
VWA5B2	0	.	GRCh37	3	183958839	183958839	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2906C>T	p.Pro969Leu	p.P969L	ENST00000426955	17/19	41	28	12	26	26	0	VWA5B2,missense_variant,p.Pro751Leu,ENST00000273794,;VWA5B2,missense_variant,p.Pro969Leu,ENST00000426955,;EIF2B5,intron_variant,,ENST00000444495,;ALG3,downstream_gene_variant,,ENST00000446569,;ALG3,downstream_gene_variant,,ENST00000418734,;ALG3,downstream_gene_variant,,ENST00000445626,;ALG3,downstream_gene_variant,,ENST00000455059,;ALG3,downstream_gene_variant,,ENST00000397676,;MIR1224,upstream_gene_variant,,ENST00000408193,;ALG3,downstream_gene_variant,,ENST00000463495,;VWA5B2,non_coding_transcript_exon_variant,,ENST00000493493,;VWA5B2,non_coding_transcript_exon_variant,,ENST00000461141,;ALG3,downstream_gene_variant,,ENST00000477959,;ALG3,downstream_gene_variant,,ENST00000423996,;VWA5B2,downstream_gene_variant,,ENST00000474580,;ALG3,downstream_gene_variant,,ENST00000411922,;ALG3,downstream_gene_variant,,ENST00000485912,;ALG3,downstream_gene_variant,,ENST00000482048,;ALG3,downstream_gene_variant,,ENST00000488976,;ALG3,downstream_gene_variant,,ENST00000461415,;ALG3,downstream_gene_variant,,ENST00000462735,;ALG3,downstream_gene_variant,,ENST00000414845,;	T	ENSG00000145198	ENST00000426955	Transcript	missense_variant	3006	2906	969	P/L	cCt/cTt	.	.	.	1	VWA5B2	HGNC	25144	protein_coding	YES	CCDS54686.1	ENSP00000398688	VW5B2_HUMAN	.	UPI0000412DE9	.	tolerated(0.73)	benign(0.001)	17/19	.	hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF107	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTCCTGCCT	.	5	ESCA
CHRD	0	.	GRCh37	3	184101106	184101107	+	Frame_Shift_Del	DEL	AA	AA	-	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	AA	AA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1221_1222delAA	p.Ser408CysfsTer6	p.S408Cfs*6	ENST00000204604	11/23	96	55	41	25	25	0	CHRD,frameshift_variant,p.Ser408CysfsTer6,ENST00000450923,;CHRD,frameshift_variant,p.Ser408CysfsTer6,ENST00000204604,;CHRD,frameshift_variant,p.Ser408CysfsTer6,ENST00000348986,;CHRD,frameshift_variant,p.Ser38CysfsTer6,ENST00000545352,;EIF2B5,intron_variant,,ENST00000444495,;CHRD,downstream_gene_variant,,ENST00000310236,;CHRD,downstream_gene_variant,,ENST00000482805,;CHRD,3_prime_UTR_variant,,ENST00000420973,;CHRD,3_prime_UTR_variant,,ENST00000448472,;CHRD,non_coding_transcript_exon_variant,,ENST00000470150,;CHRD,non_coding_transcript_exon_variant,,ENST00000460627,;CHRD,downstream_gene_variant,,ENST00000461120,;CHRD,downstream_gene_variant,,ENST00000459711,;CHRD,downstream_gene_variant,,ENST00000356534,;CHRD,downstream_gene_variant,,ENST00000482014,;CHRD,upstream_gene_variant,,ENST00000464833,;CHRD,downstream_gene_variant,,ENST00000496527,;CHRD,downstream_gene_variant,,ENST00000485883,;CHRD,downstream_gene_variant,,ENST00000486066,;CHRD,downstream_gene_variant,,ENST00000461684,;	-	ENSG00000090539	ENST00000204604	Transcript	frameshift_variant	1466-1467	1220-1221	407	Q/X	cAA/c	.	.	.	1	CHRD	HGNC	1949	protein_coding	YES	CCDS3266.1	ENSP00000204604	CHRD_HUMAN	Q8N2W7_HUMAN	UPI000013C64D	.	.	.	11/23	.	PROSITE_profiles:PS50933,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF263,Pfam_domain:PF07452,PIRSF_domain:PIRSF002496,SMART_domains:SM00754	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCTGCAAAGTGT	.	3	ESCA
OPA1	0	.	GRCh37	3	193409881	193409881	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2959G>C	p.Asp987His	p.D987H	ENST00000361908	29/30	74	33	40	60	60	0	OPA1,missense_variant,p.Asp951His,ENST00000361150,;OPA1,missense_variant,p.Asp969His,ENST00000361715,;OPA1,missense_variant,p.Asp987His,ENST00000361908,;OPA1,missense_variant,p.Asp968His,ENST00000361828,;OPA1,missense_variant,p.Asp950His,ENST00000392438,;OPA1,missense_variant,p.Asp1005His,ENST00000361510,;OPA1,non_coding_transcript_exon_variant,,ENST00000495261,;	C	ENSG00000198836	ENST00000361908	Transcript	missense_variant	3193	2959	987	D/H	Gat/Cat	CD070499	.	.	1	OPA1	HGNC	8140	protein_coding	YES	CCDS33917.1	ENSP00000354681	OPA1_HUMAN	Q6PEK6_HUMAN,E5KLJ7_HUMAN,C9JY58_HUMAN	UPI0000422960	.	deleterious(0)	benign(0.017)	29/30	.	hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTGATGCT	.	5	ESCA
ZNF197	0	.	GRCh37	3	44671001	44671001	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355G>A	p.Glu119Lys	p.E119K	ENST00000396058	1/5	52	37	15	18	18	0	ZNF197,missense_variant,p.Glu119Lys,ENST00000396058,;ZNF197,missense_variant,p.Glu119Lys,ENST00000383745,;ZNF197,missense_variant,p.Glu119Lys,ENST00000344387,;ZNF197,missense_variant,p.Glu119Lys,ENST00000383744,;ZNF197,downstream_gene_variant,,ENST00000412641,;RP11-944L7.4,intron_variant,,ENST00000457331,;ZNF197-AS1,upstream_gene_variant,,ENST00000447691,;ZNF197,missense_variant,p.Glu119Lys,ENST00000334075,;	A	ENSG00000186448	ENST00000396058	Transcript	missense_variant	522	355	119	E/K	Gag/Aag	.	.	.	1	ZNF197	HGNC	12988	protein_coding	YES	CCDS2717.1	ENSP00000379370	ZN197_HUMAN	C9JQH5_HUMAN	UPI000013C317	.	deleterious(0.03)	benign(0.26)	1/5	.	Superfamily_domains:SSF47353,SMART_domains:SM00431,Pfam_domain:PF02023,PROSITE_profiles:PS50804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGAGGAGCTG	.	5	ESCA
HHIP	0	.	GRCh37	4	145640083	145640083	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735C>T	p.Leu579Phe	p.L579F	ENST00000296575	11/13	32	22	9	47	47	0	HHIP,missense_variant,p.Leu579Phe,ENST00000296575,;HHIP,downstream_gene_variant,,ENST00000512791,;	T	ENSG00000164161	ENST00000296575	Transcript	missense_variant	2390	1735	579	L/F	Ctc/Ttc	.	.	.	1	HHIP	HGNC	14866	protein_coding	YES	CCDS3762.1	ENSP00000296575	HHIP_HUMAN	.	UPI0000071302	.	deleterious(0.01)	benign(0.165)	11/13	.	Gene3D:2.120.10.30,hmmpanther:PTHR19328,hmmpanther:PTHR19328:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAACTCTAC	.	5	ESCA
LRBA	0	.	GRCh37	4	151271258	151271258	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7281T>C	p.%3D	p.I2427I	ENST00000357115	49/58	29	14	15	41	41	0	LRBA,synonymous_variant,p.%3D,ENST00000535741,;LRBA,synonymous_variant,p.%3D,ENST00000507224,;LRBA,synonymous_variant,p.%3D,ENST00000357115,;LRBA,synonymous_variant,p.%3D,ENST00000510413,;LRBA,synonymous_variant,p.%3D,ENST00000509835,;LRBA,non_coding_transcript_exon_variant,,ENST00000503716,;	G	ENSG00000198589	ENST00000357115	Transcript	synonymous_variant	7525	7281	2427	I	atT/atC	.	.	.	-1	LRBA	HGNC	1742	protein_coding	YES	CCDS3773.1	ENSP00000349629	LRBA_HUMAN	Q7KZN3_HUMAN	UPI000013E35C	.	.	.	49/58	.	PROSITE_profiles:PS50197,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAAAATGAG	.	5	ESCA
LAP3	0	.	GRCh37	4	17579145	17579145	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57G>C	p.%3D	p.V19V	ENST00000226299	1/13	13	5	8	11	11	0	LAP3,synonymous_variant,p.%3D,ENST00000226299,;LAP3,5_prime_UTR_variant,,ENST00000606142,;LAP3,upstream_gene_variant,,ENST00000507960,;LAP3,synonymous_variant,p.%3D,ENST00000509583,;LAP3,non_coding_transcript_exon_variant,,ENST00000508497,;LAP3,non_coding_transcript_exon_variant,,ENST00000512397,;	C	ENSG00000002549	ENST00000226299	Transcript	synonymous_variant	331	57	19	V	gtG/gtC	.	.	.	1	LAP3	HGNC	18449	protein_coding	YES	CCDS3422.1	ENSP00000226299	AMPL_HUMAN	.	UPI000014F97D	.	.	.	1/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11963,hmmpanther:PTHR11963:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCCGTGAGACG	.	3	ESCA
TMEM33	0	.	GRCh37	4	41957645	41957645	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1429G>A	.	.	ENST00000504986	7/7	27	13	14	39	39	0	TMEM33,3_prime_UTR_variant,,ENST00000325094,;TMEM33,3_prime_UTR_variant,,ENST00000504986,;TMEM33,downstream_gene_variant,,ENST00000513558,;TMEM33,downstream_gene_variant,,ENST00000513702,;TMEM33,downstream_gene_variant,,ENST00000508448,;TMEM33,downstream_gene_variant,,ENST00000264452,;	A	ENSG00000109133	ENST00000504986	Transcript	3_prime_UTR_variant	2538	.	.	.	.	.	.	.	1	TMEM33	HGNC	25541	protein_coding	YES	CCDS3464.1	ENSP00000422473	TMM33_HUMAN	D6RAA6_HUMAN	UPI000004C095	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTGATAGC	.	5	ESCA
MOB1B	0	.	GRCh37	4	71849087	71849087	+	3'Flank	SNP	T	T	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000396051	.	14	7	7	13	13	0	MOB1B,3_prime_UTR_variant,,ENST00000309395,;MOB1B,downstream_gene_variant,,ENST00000396051,;MOB1B,intron_variant,,ENST00000511449,;	G	ENSG00000173542	ENST00000396051	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1128	1	MOB1B	HGNC	29801	protein_coding	YES	CCDS58903.1	ENSP00000379366	MOB1B_HUMAN	Q4W5E0_HUMAN,D6RCK3_HUMAN	UPI0000E203CF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGCTAATTC	.	5	ESCA
CNOT6L	0	.	GRCh37	4	78647324	78647324	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1452C>A	p.Phe484Leu	p.F484L	ENST00000264903	11/12	32	15	16	47	47	0	CNOT6L,missense_variant,p.Phe259Leu,ENST00000505983,;CNOT6L,missense_variant,p.Phe484Leu,ENST00000504123,;CNOT6L,missense_variant,p.Phe484Leu,ENST00000264903,;CNOT6L,missense_variant,p.Phe491Leu,ENST00000512485,;CNOT6L,intron_variant,,ENST00000515506,;CNOT6L,3_prime_UTR_variant,,ENST00000504804,;CNOT6L,downstream_gene_variant,,ENST00000508371,;	T	ENSG00000138767	ENST00000264903	Transcript	missense_variant	1534	1452	484	F/L	ttC/ttA	.	.	.	-1	CNOT6L	HGNC	18042	protein_coding	YES	CCDS47082.1	ENSP00000264903	CNO6L_HUMAN	D6RGK9_HUMAN	UPI0000E445DF	.	deleterious(0)	probably_damaging(0.999)	11/12	.	hmmpanther:PTHR12121,hmmpanther:PTHR12121:SF35,Pfam_domain:PF03372,Gene3D:3.60.10.10,Superfamily_domains:SSF56219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTGAAATC	.	5	ESCA
BMP2K	0	.	GRCh37	4	79832424	79832424	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2723A>G	p.Asn908Ser	p.N908S	ENST00000335016	16/16	44	22	22	55	55	0	BMP2K,missense_variant,p.Asn908Ser,ENST00000335016,;BMP2K,missense_variant,p.Asn601Ser,ENST00000502613,;PAQR3,intron_variant,,ENST00000295462,;PAQR3,downstream_gene_variant,,ENST00000512733,;PAQR3,downstream_gene_variant,,ENST00000515541,;PAQR3,downstream_gene_variant,,ENST00000503343,;PAQR3,3_prime_UTR_variant,,ENST00000511594,;PAQR3,intron_variant,,ENST00000512760,;PAQR3,intron_variant,,ENST00000342820,;	G	ENSG00000138756	ENST00000335016	Transcript	missense_variant	2889	2723	908	N/S	aAt/aGt	.	.	.	1	BMP2K	HGNC	18041	protein_coding	YES	CCDS47083.1	ENSP00000334836	BMP2K_HUMAN	.	UPI00001BDC7C	.	tolerated_low_confidence(0.97)	unknown(0)	16/16	.	hmmpanther:PTHR22967:SF10,hmmpanther:PTHR22967,Pfam_domain:PF15282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGAATGTAC	.	5	ESCA
PTPN13	0	.	GRCh37	4	87686556	87686556	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4173G>A	p.%3D	p.V1391V	ENST00000436978	26/48	39	14	25	50	50	0	PTPN13,synonymous_variant,p.%3D,ENST00000411767,;PTPN13,synonymous_variant,p.%3D,ENST00000436978,;PTPN13,synonymous_variant,p.%3D,ENST00000316707,;PTPN13,synonymous_variant,p.%3D,ENST00000511467,;PTPN13,synonymous_variant,p.%3D,ENST00000427191,;PTPN13,non_coding_transcript_exon_variant,,ENST00000511105,;PTPN13,downstream_gene_variant,,ENST00000508063,;	A	ENSG00000163629	ENST00000436978	Transcript	synonymous_variant	4653	4173	1391	V	gtG/gtA	.	.	.	1	PTPN13	HGNC	9646	protein_coding	YES	CCDS47093.1	ENSP00000394794	PTN13_HUMAN	Q4W5F5_HUMAN,D6R9X4_HUMAN	UPI000016075D	.	.	.	26/48	.	PROSITE_profiles:PS50106,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF197,Gene3D:2.30.42.10,Pfam_domain:PF00595,PIRSF_domain:PIRSF000933,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGTGAATAC	.	5	ESCA
MARCH6	0	.	GRCh37	5	10403651	10403651	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1330G>C	p.Glu444Gln	p.E444Q	ENST00000274140	15/26	62	41	20	47	47	0	MARCH6,missense_variant,p.Glu396Gln,ENST00000449913,;MARCH6,missense_variant,p.Glu142Gln,ENST00000510792,;MARCH6,missense_variant,p.Glu444Gln,ENST00000274140,;MARCH6,missense_variant,p.Glu339Gln,ENST00000503788,;MARCH6,splice_region_variant,,ENST00000511802,;MARCH6,downstream_gene_variant,,ENST00000514961,;	C	ENSG00000145495	ENST00000274140	Transcript	missense_variant	1462	1330	444	E/Q	Gag/Cag	.	.	.	1	MARCH6	HGNC	30550	protein_coding	YES	CCDS34135.1	ENSP00000274140	MARH6_HUMAN	.	UPI00001B94D6	.	deleterious(0)	probably_damaging(0.998)	15/26	.	hmmpanther:PTHR13145:SF0,hmmpanther:PTHR13145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGAGAGGTA	.	5	ESCA
TNFAIP8	0	.	GRCh37	5	118729075	118729075	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.596G>A	p.%3D	p.%3D	ENST00000504771	2/2	28	12	16	49	49	0	TNFAIP8,stop_retained_variant,p.%3D,ENST00000503646,;TNFAIP8,stop_retained_variant,p.%3D,ENST00000513374,;TNFAIP8,stop_retained_variant,p.%3D,ENST00000504642,;TNFAIP8,stop_retained_variant,p.%3D,ENST00000504771,;TNFAIP8,stop_retained_variant,p.%3D,ENST00000274456,;TNFAIP8,3_prime_UTR_variant,,ENST00000415806,;TNFAIP8,downstream_gene_variant,,ENST00000388882,;	A	ENSG00000145779	ENST00000504771	Transcript	stop_retained_variant	2373	596	199	*	tGa/tAa	.	.	.	1	TNFAIP8	HGNC	17260	protein_coding	YES	CCDS47258.1	ENSP00000422245	TFIP8_HUMAN	E5RIJ3_HUMAN	UPI000006EB3E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATATGAGCAC	.	2	ESCA
MYOT	0	.	GRCh37	5	137211532	137211532	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.371C>T	p.Ser124Leu	p.S124L	ENST00000239926	3/10	23	16	7	21	21	0	MYOT,missense_variant,p.Ser124Leu,ENST00000239926,;MYOT,missense_variant,p.Ser9Leu,ENST00000515645,;MYOT,5_prime_UTR_variant,,ENST00000421631,;RP11-381K20.2,intron_variant,,ENST00000514616,;MYOT,non_coding_transcript_exon_variant,,ENST00000509812,;MYOT,non_coding_transcript_exon_variant,,ENST00000511625,;MYOT,upstream_gene_variant,,ENST00000511254,;MYOT,upstream_gene_variant,,ENST00000503748,;	T	ENSG00000120729	ENST00000239926	Transcript	missense_variant	745	371	124	S/L	tCa/tTa	.	.	.	1	MYOT	HGNC	12399	protein_coding	YES	CCDS4194.1	ENSP00000239926	MYOTI_HUMAN	B4DT68_HUMAN	UPI000013CA96	.	tolerated(0.28)	benign(0.002)	3/10	.	hmmpanther:PTHR19897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTCAGCTG	.	5	ESCA
CTNNA1	0	.	GRCh37	5	138266577	138266577	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2251G>A	p.Glu751Lys	p.E751K	ENST00000302763	16/18	39	33	5	27	27	0	CTNNA1,missense_variant,p.Glu381Lys,ENST00000540387,;CTNNA1,missense_variant,p.Glu751Lys,ENST00000518825,;CTNNA1,missense_variant,p.Glu751Lys,ENST00000302763,;CTNNA1,missense_variant,p.Glu26Lys,ENST00000520520,;CTNNA1,missense_variant,p.Glu648Lys,ENST00000355078,;CTNNA1,3_prime_UTR_variant,,ENST00000521724,;CTNNA1,non_coding_transcript_exon_variant,,ENST00000521387,;CTNNA1,downstream_gene_variant,,ENST00000521368,;CTNNA1,upstream_gene_variant,,ENST00000522792,;	A	ENSG00000044115	ENST00000302763	Transcript	missense_variant	2341	2251	751	E/K	Gag/Aag	.	.	.	1	CTNNA1	HGNC	2509	protein_coding	YES	CCDS34243.1	ENSP00000304669	CTNA1_HUMAN	F8W845_HUMAN,E5RJP7_HUMAN,E5RJL0_HUMAN,E5RJC9_HUMAN,E5RJ43_HUMAN,E5RJ41_HUMAN,E5RIE0_HUMAN,E5RIB1_HUMAN,E5RHY5_HUMAN,E5RHV7_HUMAN,E5RHR7_HUMAN,E5RHJ5_HUMAN,E5RGY6_HUMAN,E5RGU3_HUMAN,E5RGS1_HUMAN,E5RGG4_HUMAN,E5RGD2_HUMAN,E5RG03_HUMAN,E5RFM5_HUMAN,E5RFM3_HUMAN,E5RFK9_HUMAN,E5RFG3_HUMAN,B4E2G8_HUMAN,B4DKT9_HUMAN	UPI000012862C	.	deleterious(0.04)	possibly_damaging(0.588)	16/18	.	hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF24,Gene3D:1.20.120.230,Pfam_domain:PF01044,Superfamily_domains:SSF47220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGCTGAGGCA	.	4	ESCA
PCDHB14	0	.	GRCh37	5	140603611	140603611	+	Missense_Mutation	SNP	C	C	G	rs201192118	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534C>G	p.Phe178Leu	p.F178L	ENST00000239449	1/1	43	32	11	24	24	0	PCDHB14,missense_variant,p.Phe178Leu,ENST00000239449,;PCDHB14,missense_variant,p.Phe25Leu,ENST00000515856,;	G	ENSG00000120327	ENST00000239449	Transcript	missense_variant	534	534	178	F/L	ttC/ttG	rs201192118,COSM3827092	.	.	1	PCDHB14	HGNC	8685	protein_coding	YES	CCDS4256.1	ENSP00000239449	PCDBE_HUMAN	B4DPE2_HUMAN	UPI00001273E7	.	deleterious_low_confidence(0.01)	possibly_damaging(0.717)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCTACAT	byCluster	5	ESCA
PCDHB14	0	.	GRCh37	5	140603882	140603882	+	Missense_Mutation	SNP	C	C	G	rs782376418	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805C>G	p.Leu269Val	p.L269V	ENST00000239449	1/1	37	33	4	26	26	0	PCDHB14,missense_variant,p.Leu269Val,ENST00000239449,;PCDHB14,missense_variant,p.Leu116Val,ENST00000515856,;	G	ENSG00000120327	ENST00000239449	Transcript	missense_variant	805	805	269	L/V	Ctg/Gtg	rs782376418	.	.	1	PCDHB14	HGNC	8685	protein_coding	YES	CCDS4256.1	ENSP00000239449	PCDBE_HUMAN	B4DPE2_HUMAN	UPI00001273E7	.	tolerated_low_confidence(0.13)	benign(0.17)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATCTGGAT	.	4	ESCA
GRIA1	0	.	GRCh37	5	153030051	153030051	+	Missense_Mutation	SNP	C	C	T	rs146865938	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652C>T	p.Arg218Cys	p.R218C	ENST00000518783	4/16	29	11	17	31	31	0	GRIA1,missense_variant,p.Arg128Cys,ENST00000518142,;GRIA1,missense_variant,p.Arg139Cys,ENST00000521843,;GRIA1,missense_variant,p.Arg208Cys,ENST00000285900,;GRIA1,missense_variant,p.Arg218Cys,ENST00000518783,;GRIA1,missense_variant,p.Arg218Cys,ENST00000448073,;GRIA1,missense_variant,p.Arg208Cys,ENST00000340592,;GRIA1,non_coding_transcript_exon_variant,,ENST00000518862,;GRIA1,non_coding_transcript_exon_variant,,ENST00000520966,;GRIA1,non_coding_transcript_exon_variant,,ENST00000481559,;	T	ENSG00000155511	ENST00000518783	Transcript	missense_variant	679	652	218	R/C	Cgc/Tgc	rs146865938,COSM206629,COSM3852967	.	.	1	GRIA1	HGNC	4571	protein_coding	YES	CCDS58987.1	ENSP00000428994	GRIA1_HUMAN	.	UPI0001E8F433	.	deleterious(0.01)	possibly_damaging(0.759)	4/16	.	Superfamily_domains:SSF53822,Pfam_domain:PF01094,Gene3D:3.40.50.2300,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF157	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R208C|c.622C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAACGCCTC	byCluster|by1000G	5	ESCA
C5orf58	0	.	GRCh37	5	169661118	169661119	+	5'UTR	INS	-	-	T	rs755756396	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-15dupT	.	.	ENST00000521850	1/3	22	12	10	35	35	0	C5orf58,splice_region_variant,,ENST00000593851,;C5orf58,5_prime_UTR_variant,,ENST00000521850,;C5orf58,intron_variant,,ENST00000517575,;C5orf58,upstream_gene_variant,,ENST00000518395,;C5orf58,splice_region_variant,,ENST00000524171,;C5orf58,upstream_gene_variant,,ENST00000421269,;	T	ENSG00000234511	ENST00000521850	Transcript	5_prime_UTR_variant	1668-1669	.	.	.	.	rs755756396	.	.	1	C5orf58	HGNC	37272	protein_coding	YES	CCDS47338.1	ENSP00000428956	CE058_HUMAN	.	UPI0000160413	.	.	.	1/3	.	.	.	.	.	.	.	.	.	T:0.0003	T:0	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AATTAGTTTTT	.	2	ESCA
CDH12	0	.	GRCh37	5	21842384	21842384	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.700C>T	p.Gln234Ter	p.Q234*	ENST00000382254	8/15	70	42	27	66	66	0	CDH12,stop_gained,p.Gln194Ter,ENST00000522262,;CDH12,stop_gained,p.Gln234Ter,ENST00000504376,;CDH12,stop_gained,p.Gln234Ter,ENST00000382254,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,;	A	ENSG00000154162	ENST00000382254	Transcript	stop_gained	1787	700	234	Q/*	Caa/Taa	.	.	.	-1	CDH12	HGNC	1751	protein_coding	YES	CCDS3890.1	ENSP00000371689	CAD12_HUMAN	B3KRT0_HUMAN	UPI00000622EB	.	.	.	8/15	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTGATATT	.	5	ESCA
AGXT2	0	.	GRCh37	5	35049202	35049202	+	5'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000231420	.	17	7	10	13	13	0	PRLR,3_prime_UTR_variant,,ENST00000348262,;PRLR,3_prime_UTR_variant,,ENST00000397391,;PRLR,3_prime_UTR_variant,,ENST00000542609,;PRLR,3_prime_UTR_variant,,ENST00000231423,;PRLR,3_prime_UTR_variant,,ENST00000513753,;AGXT2,upstream_gene_variant,,ENST00000231420,;AC010368.2,upstream_gene_variant,,ENST00000594869,;PRLR,3_prime_UTR_variant,,ENST00000509140,;PRLR,3_prime_UTR_variant,,ENST00000514088,;AGXT2,upstream_gene_variant,,ENST00000505542,;AGXT2,upstream_gene_variant,,ENST00000510428,;	T	ENSG00000113492	ENST00000231420	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1004	-1	AGXT2	HGNC	14412	protein_coding	YES	CCDS3908.1	ENSP00000231420	AGT2_HUMAN	.	UPI0000125709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTCCCAGT	.	2	ESCA
IL6ST	0	.	GRCh37	5	55247381	55247385	+	Frame_Shift_Del	DEL	CTAGT	CTAGT	-	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	CTAGT	CTAGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1747_1751delACTAG	p.Thr583Ter	p.T583*	ENST00000381298	14/17	46	32	14	47	47	0	IL6ST,frameshift_variant,p.Thr583Ter,ENST00000336909,;IL6ST,frameshift_variant,p.Thr583Ter,ENST00000381298,;IL6ST,frameshift_variant,p.Thr522Ter,ENST00000381294,;IL6ST,frameshift_variant,p.Thr583Ter,ENST00000502326,;IL6ST,3_prime_UTR_variant,,ENST00000522633,;IL6ST,3_prime_UTR_variant,,ENST00000381287,;IL6ST,3_prime_UTR_variant,,ENST00000536319,;IL6ST,intron_variant,,ENST00000381293,;IL6ST,intron_variant,,ENST00000381286,;IL6ST,upstream_gene_variant,,ENST00000423954,;IL6ST,3_prime_UTR_variant,,ENST00000503773,;IL6ST,non_coding_transcript_exon_variant,,ENST00000583149,;IL6ST,downstream_gene_variant,,ENST00000506241,;IL6ST,upstream_gene_variant,,ENST00000523039,;	-	ENSG00000134352	ENST00000381298	Transcript	frameshift_variant	2060-2064	1747-1751	583-584	TS/X	ACTAGt/t	.	.	.	-1	IL6ST	HGNC	6021	protein_coding	YES	CCDS3971.1	ENSP00000370698	IL6RB_HUMAN	.	UPI000013CF29	.	.	.	14/17	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF25,hmmpanther:PTHR23036,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGTCACTAGTCAAAG	.	3	ESCA
PLK2	0	.	GRCh37	5	57750116	57750116	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*294G>A	.	.	ENST00000274289	14/14	36	25	10	25	25	0	PLK2,3_prime_UTR_variant,,ENST00000274289,;PLK2,intron_variant,,ENST00000502671,;PLK2,downstream_gene_variant,,ENST00000509422,;PLK2,downstream_gene_variant,,ENST00000505244,;PLK2,downstream_gene_variant,,ENST00000514306,;PLK2,downstream_gene_variant,,ENST00000503115,;PLK2,downstream_gene_variant,,ENST00000515415,;PLK2,downstream_gene_variant,,ENST00000504196,;PLK2,downstream_gene_variant,,ENST00000509555,;PLK2,downstream_gene_variant,,ENST00000511326,;PLK2,downstream_gene_variant,,ENST00000503378,;PLK2,downstream_gene_variant,,ENST00000508300,;PLK2,downstream_gene_variant,,ENST00000510629,;PLK2,downstream_gene_variant,,ENST00000503713,;	T	ENSG00000145632	ENST00000274289	Transcript	3_prime_UTR_variant	2653	.	.	.	.	.	.	.	-1	PLK2	HGNC	19699	protein_coding	YES	CCDS3974.1	ENSP00000274289	PLK2_HUMAN	.	UPI0000135B35	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCTCTCAAC	.	5	ESCA
CWC27	0	.	GRCh37	5	64081312	64081312	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.401C>T	p.Thr134Ile	p.T134I	ENST00000381070	5/14	42	24	17	54	54	0	CWC27,missense_variant,p.Thr134Ile,ENST00000381070,;CWC27,missense_variant,p.Thr134Ile,ENST00000508024,;CWC27,non_coding_transcript_exon_variant,,ENST00000485990,;	T	ENSG00000153015	ENST00000381070	Transcript	missense_variant	618	401	134	T/I	aCa/aTa	.	.	.	1	CWC27	HGNC	10664	protein_coding	YES	CCDS3982.2	ENSP00000370460	CWC27_HUMAN	.	UPI0000048ECC	.	deleterious(0)	possibly_damaging(0.828)	5/14	.	PROSITE_profiles:PS50072,hmmpanther:PTHR11071,hmmpanther:PTHR11071:SF152,Pfam_domain:PF00160,Gene3D:2.40.100.10,Superfamily_domains:SSF50891,Prints_domain:PR00153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTACAGGGG	.	5	ESCA
CAST	0	.	GRCh37	5	96108510	96108510	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*190G>C	.	.	ENST00000395812	30/30	22	11	10	49	49	0	CAST,3_prime_UTR_variant,,ENST00000395813,;CAST,3_prime_UTR_variant,,ENST00000511049,;CAST,3_prime_UTR_variant,,ENST00000508579,;CAST,3_prime_UTR_variant,,ENST00000325674,;CAST,3_prime_UTR_variant,,ENST00000359176,;CAST,3_prime_UTR_variant,,ENST00000395812,;CAST,3_prime_UTR_variant,,ENST00000309190,;CAST,3_prime_UTR_variant,,ENST00000341926,;CAST,3_prime_UTR_variant,,ENST00000510500,;CAST,3_prime_UTR_variant,,ENST00000338252,;CAST,3_prime_UTR_variant,,ENST00000437034,;CAST,3_prime_UTR_variant,,ENST00000504465,;ERAP1,intron_variant,,ENST00000296754,;CAST,downstream_gene_variant,,ENST00000508608,;ERAP1,downstream_gene_variant,,ENST00000443439,;CAST,downstream_gene_variant,,ENST00000508830,;CAST,downstream_gene_variant,,ENST00000510756,;CAST,downstream_gene_variant,,ENST00000511782,;CAST,downstream_gene_variant,,ENST00000509903,;ERAP1,downstream_gene_variant,,ENST00000512852,;CAST,downstream_gene_variant,,ENST00000515663,;CAST,non_coding_transcript_exon_variant,,ENST00000348386,;CAST,3_prime_UTR_variant,,ENST00000484552,;CAST,3_prime_UTR_variant,,ENST00000510098,;CAST,non_coding_transcript_exon_variant,,ENST00000509529,;	C	ENSG00000153113	ENST00000395812	Transcript	3_prime_UTR_variant	2629	.	.	.	.	.	.	.	1	CAST	HGNC	1515	protein_coding	YES	CCDS54882.1	ENSP00000379157	ICAL_HUMAN	E7EQ12_HUMAN	UPI0000DA4C59	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTGACTGG	.	5	ESCA
CCNC	0	.	GRCh37	6	100016540	100016540	+	5'UTR	SNP	G	G	A	rs532788052	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-137C>T	.	.	ENST00000520429	1/12	45	32	13	37	37	0	CCNC,5_prime_UTR_variant,,ENST00000520371,;CCNC,5_prime_UTR_variant,,ENST00000520429,;CCNC,intron_variant,,ENST00000523799,;CCNC,upstream_gene_variant,,ENST00000369220,;CCNC,upstream_gene_variant,,ENST00000523985,;CCNC,upstream_gene_variant,,ENST00000518714,;CCNC,upstream_gene_variant,,ENST00000524049,;CCNC,upstream_gene_variant,,ENST00000482541,;CCNC,upstream_gene_variant,,ENST00000369217,;RP1-199J3.7,non_coding_transcript_exon_variant,,ENST00000607332,;CCNC,upstream_gene_variant,,ENST00000521017,;CCNC,non_coding_transcript_exon_variant,,ENST00000523541,;CCNC,non_coding_transcript_exon_variant,,ENST00000523639,;CCNC,upstream_gene_variant,,ENST00000523961,;CCNC,upstream_gene_variant,,ENST00000326298,;CCNC,upstream_gene_variant,,ENST00000484049,;	A	ENSG00000112237	ENST00000520429	Transcript	5_prime_UTR_variant	310	.	.	.	.	rs532788052	.	.	-1	CCNC	HGNC	1581	protein_coding	YES	CCDS34502.1	ENSP00000428982	CCNC_HUMAN	Q7Z4L3_HUMAN,E5RIH8_HUMAN,E5RFX8_HUMAN	UPI0000169CFB	.	.	.	1/12	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGGCGAAAGG	by1000G	5	ESCA
MCHR2	0	.	GRCh37	6	100395746	100395746	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284G>A	p.Arg95Gln	p.R95Q	ENST00000281806	3/6	35	21	14	33	33	0	MCHR2,missense_variant,p.Arg95Gln,ENST00000369212,;MCHR2,missense_variant,p.Arg95Gln,ENST00000281806,;	T	ENSG00000152034	ENST00000281806	Transcript	missense_variant	599	284	95	R/Q	cGa/cAa	.	.	.	-1	MCHR2	HGNC	20867	protein_coding	YES	CCDS5044.1	ENSP00000281806	MCHR2_HUMAN	.	UPI000003730F	.	tolerated(0.45)	benign(0.023)	3/6	.	Prints_domain:PR01784,Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,hmmpanther:PTHR24230:SF7,hmmpanther:PTHR24230,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCGGGCC	.	5	ESCA
SIM1	0	.	GRCh37	6	100911391	100911391	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-47G>A	.	.	ENST00000369208	2/12	43	31	11	39	39	0	SIM1,5_prime_UTR_variant,,ENST00000369208,;SIM1,5_prime_UTR_variant,,ENST00000262901,;SIM1,non_coding_transcript_exon_variant,,ENST00000511871,;	T	ENSG00000112246	ENST00000369208	Transcript	5_prime_UTR_variant	737	.	.	.	.	.	.	.	-1	SIM1	HGNC	10882	protein_coding	YES	CCDS5045.1	ENSP00000358210	SIM1_HUMAN	.	UPI000013D355	.	.	.	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCATCCA	.	5	ESCA
GRIK2	0	.	GRCh37	6	102337692	102337692	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1702C>T	p.%3D	p.L568L	ENST00000421544	11/16	27	18	8	11	11	0	GRIK2,synonymous_variant,p.%3D,ENST00000369138,;GRIK2,synonymous_variant,p.%3D,ENST00000413795,;GRIK2,synonymous_variant,p.%3D,ENST00000436862,;GRIK2,synonymous_variant,p.%3D,ENST00000318991,;GRIK2,synonymous_variant,p.%3D,ENST00000421544,;GRIK2,synonymous_variant,p.%3D,ENST00000369134,;GRIK2,intron_variant,,ENST00000369137,;	T	ENSG00000164418	ENST00000421544	Transcript	synonymous_variant	2192	1702	568	L	Ctg/Ttg	.	.	.	1	GRIK2	HGNC	4580	protein_coding	YES	CCDS5048.1	ENSP00000397026	GRIK2_HUMAN	Q9BZ15_HUMAN,Q6P3V6_HUMAN,H7C2P5_HUMAN,F8WEZ8_HUMAN,D7RWZ8_HUMAN	UPI000012B617	.	.	.	11/16	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,Pfam_domain:PF00060,Gene3D:1.10.287.70,SMART_domains:SM00079,Prints_domain:PR00177	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCTGCTG	.	5	ESCA
RFPL4B	0	.	GRCh37	6	112672181	112672181	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*479G>A	.	.	ENST00000441065	3/3	53	38	14	50	50	0	RFPL4B,3_prime_UTR_variant,,ENST00000441065,;RP11-506B6.6,downstream_gene_variant,,ENST00000585611,;RP11-506B6.6,downstream_gene_variant,,ENST00000590673,;RP11-506B6.6,downstream_gene_variant,,ENST00000587816,;RP11-506B6.3,downstream_gene_variant,,ENST00000401872,;	A	ENSG00000251258	ENST00000441065	Transcript	3_prime_UTR_variant	1583	.	.	.	.	.	.	.	1	RFPL4B	HGNC	33264	protein_coding	YES	CCDS34515.1	ENSP00000423391	RFPLB_HUMAN	.	UPI00001972F0	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTGTTGATACA	.	4	ESCA
NUS1	0	.	GRCh37	6	118029666	118029666	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1488A>G	.	.	ENST00000368494	5/5	41	27	13	32	32	0	NUS1,3_prime_UTR_variant,,ENST00000368494,;	G	ENSG00000153989	ENST00000368494	Transcript	3_prime_UTR_variant	2539	.	.	.	.	.	.	.	1	NUS1	HGNC	21042	protein_coding	YES	CCDS5118.1	ENSP00000357480	NGBR_HUMAN	.	UPI000006FECA	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AAGCTATGAAG	.	4	ESCA
CEP85L	0	.	GRCh37	6	118886706	118886706	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015G>C	p.Glu339Gln	p.E339Q	ENST00000368488	4/14	17	13	4	18	18	0	CEP85L,missense_variant,p.Glu234Gln,ENST00000360290,;CEP85L,missense_variant,p.Glu336Gln,ENST00000419517,;CEP85L,missense_variant,p.Glu339Gln,ENST00000368488,;CEP85L,missense_variant,p.Glu339Gln,ENST00000434604,;CEP85L,missense_variant,p.Glu339Gln,ENST00000392500,;CEP85L,missense_variant,p.Glu336Gln,ENST00000368491,;PLN,downstream_gene_variant,,ENST00000357525,;CEP85L,downstream_gene_variant,,ENST00000462101,;CEP85L,downstream_gene_variant,,ENST00000476150,;CEP85L,downstream_gene_variant,,ENST00000472713,;CEP85L,non_coding_transcript_exon_variant,,ENST00000483035,;	G	ENSG00000111860	ENST00000368488	Transcript	missense_variant	1082	1015	339	E/Q	Gaa/Caa	.	.	.	-1	CEP85L	HGNC	21638	protein_coding	YES	CCDS55052.1	ENSP00000357474	CE85L_HUMAN	A2A3P3_HUMAN	UPI0001D1E40A	.	tolerated(0.07)	possibly_damaging(0.686)	4/14	.	hmmpanther:PTHR31075,hmmpanther:PTHR31075:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTCACTTC	.	5	ESCA
HIVEP1	0	.	GRCh37	6	12121877	12121877	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1849G>A	p.Glu617Lys	p.E617K	ENST00000379388	4/9	45	33	12	28	28	0	HIVEP1,missense_variant,p.Glu617Lys,ENST00000379388,;HIVEP1,intron_variant,,ENST00000442081,;HIVEP1,downstream_gene_variant,,ENST00000487103,;HIVEP1,upstream_gene_variant,,ENST00000541134,;HIVEP1,downstream_gene_variant,,ENST00000491710,;HIVEP1,downstream_gene_variant,,ENST00000478545,;HIVEP1,upstream_gene_variant,,ENST00000399469,;	A	ENSG00000095951	ENST00000379388	Transcript	missense_variant	2181	1849	617	E/K	Gag/Aag	.	.	.	1	HIVEP1	HGNC	4920	protein_coding	YES	CCDS43426.1	ENSP00000368698	ZEP1_HUMAN	C9JZF8_HUMAN,C9JAW2_HUMAN,C9J2N3_HUMAN	UPI000020D52B	.	tolerated(0.08)	possibly_damaging(0.698)	4/9	.	hmmpanther:PTHR23233:SF48,hmmpanther:PTHR23233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTGGAGACT	.	5	ESCA
VTA1	0	.	GRCh37	6	142525187	142525187	+	Missense_Mutation	SNP	A	A	C	rs199631870	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763A>C	p.Asn255His	p.N255H	ENST00000367630	7/8	69	42	27	56	56	0	VTA1,missense_variant,p.Asn255His,ENST00000367630,;VTA1,missense_variant,p.Asn197His,ENST00000367621,;VTA1,intron_variant,,ENST00000452973,;	C	ENSG00000009844	ENST00000367630	Transcript	missense_variant	821	763	255	N/H	Aat/Cat	rs199631870	.	.	1	VTA1	HGNC	20954	protein_coding	YES	CCDS5197.1	ENSP00000356602	VTA1_HUMAN	.	UPI0000034E19	.	tolerated(0.19)	possibly_damaging(0.764)	7/8	.	hmmpanther:PTHR12741,Gene3D:1.20.5.420,Pfam_domain:PF04652	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCAATACA	byCluster|by1000G	5	ESCA
ADGB	0	.	GRCh37	6	146956593	146956593	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.157G>A	p.Glu53Lys	p.E53K	ENST00000397944	2/36	54	37	17	63	63	0	ADGB,missense_variant,p.Glu53Lys,ENST00000397944,;ADGB,missense_variant,p.Glu47Lys,ENST00000522242,;ADGB,5_prime_UTR_variant,,ENST00000367493,;RNU6-734P,upstream_gene_variant,,ENST00000384734,;ADGB,missense_variant,p.Glu53Lys,ENST00000493950,;ADGB,3_prime_UTR_variant,,ENST00000522396,;ADGB,non_coding_transcript_exon_variant,,ENST00000326929,;	A	ENSG00000118492	ENST00000397944	Transcript	missense_variant	233	157	53	E/K	Gaa/Aaa	.	.	.	1	ADGB	HGNC	21212	protein_coding	YES	.	ENSP00000381036	ADGB_HUMAN	.	UPI000020E382	.	deleterious(0)	probably_damaging(0.972)	2/36	.	hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF283,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTGAAGCT	.	5	ESCA
IGF2R	0	.	GRCh37	6	160501186	160501186	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5712C>G	p.%3D	p.V1904V	ENST00000356956	39/48	27	15	11	28	28	0	IGF2R,synonymous_variant,p.%3D,ENST00000356956,;IGF2R,upstream_gene_variant,,ENST00000475834,;	G	ENSG00000197081	ENST00000356956	Transcript	synonymous_variant	5860	5712	1904	V	gtC/gtG	.	.	.	1	IGF2R	HGNC	5467	protein_coding	YES	CCDS5273.1	ENSP00000349437	MPRI_HUMAN	A0N9R7_HUMAN,A0N9R6_HUMAN	UPI0000072478	.	.	.	39/48	.	PROSITE_profiles:PS51092,hmmpanther:PTHR10439:SF4,hmmpanther:PTHR10439,PROSITE_patterns:PS00023,Pfam_domain:PF00040,Gene3D:2.10.10.10,SMART_domains:SM00059,Superfamily_domains:SSF57440,Prints_domain:PR00013	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTCTTCCC	.	5	ESCA
MYLIP	0	.	GRCh37	6	16129565	16129565	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12T>C	p.%3D	p.Y4Y	ENST00000356840	1/7	55	34	20	52	52	0	MYLIP,synonymous_variant,p.%3D,ENST00000356840,;MYLIP,5_prime_UTR_variant,,ENST00000349606,;	C	ENSG00000007944	ENST00000356840	Transcript	synonymous_variant	210	12	4	Y	taT/taC	.	.	.	1	MYLIP	HGNC	21155	protein_coding	YES	CCDS4536.1	ENSP00000349298	MYLIP_HUMAN	Q5TIA5_HUMAN	UPI000006CDE0	.	.	.	1/7	.	Superfamily_domains:SSF54236,SMART_domains:SM00295,Gene3D:3.10.20.90,hmmpanther:PTHR23280,PROSITE_profiles:PS50057	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTATGTGAC	.	5	ESCA
HIST1H3I	0	.	GRCh37	6	27839638	27839638	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45T>C	.	.	ENST00000328488	1/1	15	6	9	43	43	0	HIST1H3I,3_prime_UTR_variant,,ENST00000328488,;HIST1H1B,upstream_gene_variant,,ENST00000331442,;HIST1H4L,downstream_gene_variant,,ENST00000355981,;	G	ENSG00000182572	ENST00000328488	Transcript	3_prime_UTR_variant	462	.	.	.	.	.	.	.	-1	HIST1H3I	HGNC	4771	protein_coding	YES	CCDS4636.1	ENSP00000329554	H31_HUMAN	.	UPI00000003C7	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAAAGAGCC	.	5	ESCA
NQO2	0	.	GRCh37	6	3006787	3006787	+	Translation_Start_Site	SNP	A	A	G	rs138748428	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1A>G	p.Met1?	p.M1?	ENST00000338130	5/10	62	37	25	46	46	0	NQO2,start_lost,p.Met1?,ENST00000380455,;NQO2,start_lost,p.Met1?,ENST00000426637,;NQO2,start_lost,p.Met1?,ENST00000606474,;NQO2,start_lost,p.Met1?,ENST00000380441,;NQO2,start_lost,p.Met1?,ENST00000380430,;NQO2,start_lost,p.Met1?,ENST00000397717,;NQO2,start_lost,p.Met1?,ENST00000380454,;NQO2,start_lost,p.Met1?,ENST00000380472,;NQO2,start_lost,p.Met1?,ENST00000338130,;	G	ENSG00000124588	ENST00000338130	Transcript	start_lost	713	1	1	M/V	Atg/Gtg	rs138748428	.	.	1	NQO2	HGNC	7856	protein_coding	YES	CCDS4481.1	ENSP00000337773	NQO2_HUMAN	Q5TD05_HUMAN,A2A2U4_HUMAN	UPI000020E40D	.	tolerated(0.09)	benign(0.002)	5/10	.	hmmpanther:PTHR10204,hmmpanther:PTHR10204:SF33	.	.	.	.	.	.	.	G:0.0005	G:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACGCTATGGCA	byCluster	4	ESCA
DDR1	0	.	GRCh37	6	30864803	30864803	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1882G>A	p.Glu628Lys	p.E628K	ENST00000376575	16/20	57	35	21	59	59	0	DDR1,missense_variant,p.Glu591Lys,ENST00000376567,;DDR1,missense_variant,p.Glu609Lys,ENST00000508312,;DDR1,missense_variant,p.Glu628Lys,ENST00000376575,;DDR1,missense_variant,p.Glu591Lys,ENST00000376569,;DDR1,missense_variant,p.Glu591Lys,ENST00000418800,;DDR1,missense_variant,p.Glu360Lys,ENST00000417521,;DDR1,missense_variant,p.Glu628Lys,ENST00000324771,;DDR1,missense_variant,p.Glu120Lys,ENST00000514434,;DDR1,missense_variant,p.Glu628Lys,ENST00000376568,;DDR1,missense_variant,p.Glu628Lys,ENST00000513240,;DDR1,missense_variant,p.Glu591Lys,ENST00000376570,;DDR1,missense_variant,p.Glu295Lys,ENST00000361741,;DDR1,missense_variant,p.Glu628Lys,ENST00000452441,;DDR1,missense_variant,p.Glu591Lys,ENST00000454612,;DDR1,3_prime_UTR_variant,,ENST00000446312,;DDR1,downstream_gene_variant,,ENST00000460944,;DDR1,upstream_gene_variant,,ENST00000484556,;DDR1,downstream_gene_variant,,ENST00000428153,;DDR1,non_coding_transcript_exon_variant,,ENST00000513514,;DDR1,non_coding_transcript_exon_variant,,ENST00000465966,;DDR1,downstream_gene_variant,,ENST00000508472,;DDR1,3_prime_UTR_variant,,ENST00000482873,;DDR1,downstream_gene_variant,,ENST00000514534,;DDR1,downstream_gene_variant,,ENST00000507533,;DDR1,downstream_gene_variant,,ENST00000485023,;	A	ENSG00000204580	ENST00000376575	Transcript	missense_variant	2215	1882	628	E/K	Gag/Aag	.	.	.	1	DDR1	HGNC	2730	protein_coding	YES	CCDS47396.1	ENSP00000365759	DDR1_HUMAN	E7EXB0_HUMAN,E7EX99_HUMAN,E7EVW6_HUMAN,E7EVT1_HUMAN,E7EUD5_HUMAN,E7ETX3_HUMAN,E7ETI3_HUMAN,E7ESR9_HUMAN,E7ES06_HUMAN,E7ERN0_HUMAN,E7ERI6_HUMAN,E7EQ30_HUMAN,E7EQ23_HUMAN,E7EPN2_HUMAN,E7EPH4_HUMAN,E7ENJ2_HUMAN,E7EN94_HUMAN,D6RGW5_HUMAN,D6RBU7_HUMAN,D6RB82_HUMAN,D6RB35_HUMAN,D6R9C4_HUMAN,A2ABL2_HUMAN,A2ABL0_HUMAN	UPI0000146C6D	.	deleterious(0)	possibly_damaging(0.622)	16/20	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF65,Gene3D:3.30.200.20,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTGAGGTC	.	5	ESCA
DPCR1	0	.	GRCh37	6	30917575	30917575	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1334G>C	p.Arg445Thr	p.R445T	ENST00000462446	2/3	70	44	25	62	62	0	DPCR1,missense_variant,p.Arg445Thr,ENST00000462446,;DPCR1,5_prime_UTR_variant,,ENST00000304311,;HCG21,intron_variant,,ENST00000419481,;	C	ENSG00000168631	ENST00000462446	Transcript	missense_variant	1362	1334	445	R/T	aGa/aCa	.	.	.	1	DPCR1	HGNC	21666	protein_coding	YES	CCDS4692.2	ENSP00000417182	.	E9PEI6_HUMAN	UPI0000596C17	.	tolerated(0.49)	unknown(0)	2/3	.	hmmpanther:PTHR22094,hmmpanther:PTHR22094:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATAGAGAAA	.	5	ESCA
PRRC2A	0	.	GRCh37	6	31600709	31600709	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4259G>C	p.Gly1420Ala	p.G1420A	ENST00000376033	16/31	32	15	16	30	30	0	PRRC2A,missense_variant,p.Gly1420Ala,ENST00000376033,;PRRC2A,missense_variant,p.Gly1420Ala,ENST00000376007,;PRRC2A,upstream_gene_variant,,ENST00000462617,;PRRC2A,upstream_gene_variant,,ENST00000482441,;PRRC2A,upstream_gene_variant,,ENST00000460302,;PRRC2A,upstream_gene_variant,,ENST00000487089,;PRRC2A,upstream_gene_variant,,ENST00000469501,;PRRC2A,upstream_gene_variant,,ENST00000487839,;PRRC2A,upstream_gene_variant,,ENST00000484787,;PRRC2A,upstream_gene_variant,,ENST00000492691,;PRRC2A,downstream_gene_variant,,ENST00000483470,;	C	ENSG00000204469	ENST00000376033	Transcript	missense_variant	4493	4259	1420	G/A	gGa/gCa	COSM1294244	.	.	1	PRRC2A	HGNC	13918	protein_coding	YES	CCDS4708.1	ENSP00000365201	PRC2A_HUMAN	.	UPI000020E56F	.	.	unknown(0)	16/31	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14038	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGGAGGAA	.	5	ESCA
KIFC1	0	.	GRCh37	6	33374170	33374170	+	Silent	SNP	C	C	T	rs774299603	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1734C>T	p.%3D	p.L578L	ENST00000428849	8/11	49	31	18	52	52	0	KIFC1,synonymous_variant,p.%3D,ENST00000428849,;PHF1,upstream_gene_variant,,ENST00000374512,;PHF1,upstream_gene_variant,,ENST00000374516,;KIFC1,downstream_gene_variant,,ENST00000450504,;PHF1,upstream_gene_variant,,ENST00000428274,;PHF1,upstream_gene_variant,,ENST00000427004,;PHF1,upstream_gene_variant,,ENST00000459809,;KIFC1,downstream_gene_variant,,ENST00000486695,;KIFC1,non_coding_transcript_exon_variant,,ENST00000494554,;PHF1,upstream_gene_variant,,ENST00000487667,;PHF1,upstream_gene_variant,,ENST00000495509,;	T	ENSG00000237649	ENST00000428849	Transcript	synonymous_variant	2184	1734	578	L	ctC/ctT	rs774299603,COSM3830261	.	.	1	KIFC1	HGNC	6389	protein_coding	YES	CCDS34430.1	ENSP00000393963	KIFC1_HUMAN	.	UPI000012DDB8	.	.	.	8/11	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGGCCC	byFrequency	5	ESCA
GRM4	0	.	GRCh37	6	34003781	34003781	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2106C>G	p.Ile702Met	p.I702M	ENST00000538487	9/11	44	32	12	28	28	0	GRM4,missense_variant,p.Ile533Met,ENST00000544773,;GRM4,missense_variant,p.Ile702Met,ENST00000374181,;GRM4,missense_variant,p.Ile569Met,ENST00000609222,;GRM4,missense_variant,p.Ile562Met,ENST00000455714,;GRM4,missense_variant,p.Ile569Met,ENST00000535756,;GRM4,missense_variant,p.Ile586Met,ENST00000374177,;GRM4,missense_variant,p.Ile702Met,ENST00000538487,;GRM4,downstream_gene_variant,,ENST00000609443,;GRM4,non_coding_transcript_exon_variant,,ENST00000545715,;GRM4,downstream_gene_variant,,ENST00000609915,;GRM4,3_prime_UTR_variant,,ENST00000609278,;GRM4,non_coding_transcript_exon_variant,,ENST00000609860,;	C	ENSG00000124493	ENST00000538487	Transcript	missense_variant	2550	2106	702	I/M	atC/atG	.	.	.	-1	GRM4	HGNC	4596	protein_coding	YES	CCDS4787.1	ENSP00000440556	GRM4_HUMAN	A8K0J8_HUMAN,A1L4F9_HUMAN	UPI000004A7DE	.	deleterious(0)	probably_damaging(0.975)	9/11	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24060:SF23,hmmpanther:PTHR24060,Pfam_domain:PF00003,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGTGATGGC	.	5	ESCA
TFEB	0	.	GRCh37	6	41651979	41651979	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*358G>C	.	.	ENST00000230323	10/10	18	9	9	12	12	0	TFEB,3_prime_UTR_variant,,ENST00000373033,;TFEB,3_prime_UTR_variant,,ENST00000403298,;TFEB,3_prime_UTR_variant,,ENST00000358871,;TFEB,3_prime_UTR_variant,,ENST00000420312,;TFEB,3_prime_UTR_variant,,ENST00000406563,;TFEB,3_prime_UTR_variant,,ENST00000343317,;TFEB,3_prime_UTR_variant,,ENST00000230323,;TFEB,downstream_gene_variant,,ENST00000416140,;TFEB,downstream_gene_variant,,ENST00000394283,;AL035588.1,upstream_gene_variant,,ENST00000597468,;TFEB,downstream_gene_variant,,ENST00000419396,;TFEB,downstream_gene_variant,,ENST00000419574,;TFEB,downstream_gene_variant,,ENST00000494822,;	G	ENSG00000112561	ENST00000230323	Transcript	3_prime_UTR_variant	2091	.	.	.	.	.	.	.	-1	TFEB	HGNC	11753	protein_coding	YES	CCDS4858.1	ENSP00000230323	TFEB_HUMAN	Q86WB1_HUMAN,Q709A9_HUMAN,Q709A8_HUMAN,B1AKB4_HUMAN,B1AKB2_HUMAN,B1AKB1_HUMAN,B1AKA9_HUMAN	UPI0000001615	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCAAGCA	.	5	ESCA
CDYL	0	.	GRCh37	6	4943930	4943930	+	Silent	SNP	C	C	T	rs372837191	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1272C>T	p.%3D	p.F424F	ENST00000397588	5/7	70	43	27	52	52	0	CDYL,synonymous_variant,p.%3D,ENST00000449732,;CDYL,synonymous_variant,p.%3D,ENST00000397588,;CDYL,synonymous_variant,p.%3D,ENST00000343762,;CDYL,synonymous_variant,p.%3D,ENST00000328908,;CDYL,downstream_gene_variant,,ENST00000440139,;CDYL,non_coding_transcript_exon_variant,,ENST00000472453,;CDYL,non_coding_transcript_exon_variant,,ENST00000469671,;	T	ENSG00000153046	ENST00000397588	Transcript	synonymous_variant	1621	1272	424	F	ttC/ttT	rs372837191,COSM3353939	.	.	1	CDYL	HGNC	1811	protein_coding	YES	CCDS4491.2	ENSP00000380718	CDYL1_HUMAN	.	UPI0000160F23	.	.	.	5/7	.	hmmpanther:PTHR11941:SF11,hmmpanther:PTHR11941,Pfam_domain:PF00378,Gene3D:3.90.226.10,Superfamily_domains:SSF52096	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCGGACA	byFrequency|byCluster	5	ESCA
DST	0	.	GRCh37	6	56535438	56535438	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.581+1G>C	.	p.X194_splice	ENST00000370788	.	38	27	11	23	23	0	DST,splice_donor_variant,,ENST00000370788,;DST,splice_donor_variant,,ENST00000520645,;DST,splice_donor_variant,,ENST00000449297,;DST,splice_donor_variant,,ENST00000370754,;DST,splice_donor_variant,,ENST00000361203,;DST,splice_donor_variant,,ENST00000370769,;DST,splice_donor_variant,,ENST00000312431,;DST,splice_donor_variant,,ENST00000421834,;DST,downstream_gene_variant,,ENST00000522538,;DST,downstream_gene_variant,,ENST00000523817,;DST,splice_donor_variant,,ENST00000521104,;DST,splice_donor_variant,,ENST00000523967,;DST,non_coding_transcript_exon_variant,,ENST00000521821,;	G	ENSG00000151914	ENST00000370788	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	DST	HGNC	1090	protein_coding	.	.	ENSP00000359824	.	Q8WXY3_HUMAN,E7ESK0_HUMAN,E7ERU0_HUMAN	UPI0001E8F796	.	.	.	.	6/92	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATACCTGTA	.	5	ESCA
DSP	0	.	GRCh37	6	7583820	7583820	+	Missense_Mutation	SNP	G	G	A	rs397516951	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6325G>A	p.Glu2109Lys	p.E2109K	ENST00000379802	24/24	32	18	14	29	29	0	DSP,missense_variant,p.Glu2109Lys,ENST00000379802,;DSP,missense_variant,p.Glu1510Lys,ENST00000418664,;	A	ENSG00000096696	ENST00000379802	Transcript	missense_variant	6666	6325	2109	E/K	Gaa/Aaa	rs397516951	.	.	1	DSP	HGNC	3052	protein_coding	YES	CCDS4501.1	ENSP00000369129	DESP_HUMAN	G1UI31_HUMAN,B4DKX6_HUMAN	UPI000013C67F	.	.	possibly_damaging(0.524)	24/24	.	Superfamily_domains:SSF75399,SMART_domains:SM00250,Gene3D:3.90.1290.10,hmmpanther:PTHR11915:SF234,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCAGAAGCC	.	5	ESCA
ZNF292	0	.	GRCh37	6	87970002	87970002	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6655G>A	p.Asp2219Asn	p.D2219N	ENST00000369577	8/8	42	25	17	41	41	0	ZNF292,missense_variant,p.Asp2219Asn,ENST00000369577,;ZNF292,missense_variant,p.Asp137Asn,ENST00000496806,;ZNF292,missense_variant,p.Asp2214Asn,ENST00000339907,;	A	ENSG00000188994	ENST00000369577	Transcript	missense_variant	6698	6655	2219	D/N	Gac/Aac	.	.	.	1	ZNF292	HGNC	18410	protein_coding	YES	CCDS47457.1	ENSP00000358590	ZN292_HUMAN	Q6ZS01_HUMAN,Q6P495_HUMAN,Q3MN16_HUMAN	UPI000020D2CC	.	deleterious(0.03)	probably_damaging(1)	8/8	.	SMART_domains:SM00355,PROSITE_patterns:PS00028,hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGTGACCAG	.	5	ESCA
CYP2W1	0	.	GRCh37	7	1024706	1024706	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.458G>T	p.Cys153Phe	p.C153F	ENST00000308919	3/9	101	73	27	78	78	0	CYP2W1,missense_variant,p.Cys97Phe,ENST00000340150,;CYP2W1,missense_variant,p.Cys153Phe,ENST00000308919,;CYP2W1,upstream_gene_variant,,ENST00000415893,;CYP2W1,upstream_gene_variant,,ENST00000468456,;CYP2W1,upstream_gene_variant,,ENST00000462453,;	T	ENSG00000073067	ENST00000308919	Transcript	missense_variant	471	458	153	C/F	tGc/tTc	.	.	.	1	CYP2W1	HGNC	20243	protein_coding	YES	CCDS5319.2	ENSP00000310149	CP2W1_HUMAN	.	UPI000013C59A	.	tolerated(0.74)	benign(0.006)	3/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF50,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAATGCCTCT	.	5	ESCA
WDR91	0	.	GRCh37	7	134878362	134878362	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1458C>T	p.%3D	p.L486L	ENST00000354475	10/15	85	66	19	75	75	0	WDR91,synonymous_variant,p.%3D,ENST00000354475,;WDR91,synonymous_variant,p.%3D,ENST00000344400,;WDR91,synonymous_variant,p.%3D,ENST00000423565,;AC009542.2,upstream_gene_variant,,ENST00000412549,;WDR91,downstream_gene_variant,,ENST00000476775,;WDR91,downstream_gene_variant,,ENST00000485942,;WDR91,non_coding_transcript_exon_variant,,ENST00000497853,;WDR91,non_coding_transcript_exon_variant,,ENST00000474411,;WDR91,non_coding_transcript_exon_variant,,ENST00000479698,;WDR91,non_coding_transcript_exon_variant,,ENST00000466182,;WDR91,upstream_gene_variant,,ENST00000462707,;	A	ENSG00000105875	ENST00000354475	Transcript	synonymous_variant	1490	1458	486	L	ctC/ctT	.	.	.	-1	WDR91	HGNC	24997	protein_coding	YES	CCDS34758.1	ENSP00000346466	WDR91_HUMAN	.	UPI000006F2DE	.	.	.	10/15	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13083,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAGAGATT	.	5	ESCA
CREB3L2	0	.	GRCh37	7	137686398	137686398	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54G>A	p.%3D	p.L18L	ENST00000330387	1/12	64	47	17	60	60	0	CREB3L2,synonymous_variant,p.%3D,ENST00000330387,;CREB3L2,synonymous_variant,p.%3D,ENST00000452463,;CREB3L2,synonymous_variant,p.%3D,ENST00000456390,;CREB3L2,non_coding_transcript_exon_variant,,ENST00000468127,;AKR1D1,upstream_gene_variant,,ENST00000468877,;	T	ENSG00000182158	ENST00000330387	Transcript	synonymous_variant	406	54	18	L	ctG/ctA	.	.	.	-1	CREB3L2	HGNC	23720	protein_coding	YES	CCDS34760.1	ENSP00000329140	CR3L2_HUMAN	.	UPI0000457614	.	.	.	1/12	.	hmmpanther:PTHR22952:SF96,hmmpanther:PTHR22952	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCTCAGCTT	.	5	ESCA
DENND2A	0	.	GRCh37	7	140269453	140269453	+	Nonsense_Mutation	SNP	G	G	C	rs752090246	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1532C>G	p.Ser511Ter	p.S511*	ENST00000275884	6/19	62	44	18	53	53	0	DENND2A,stop_gained,p.Ser511Ter,ENST00000496613,;DENND2A,stop_gained,p.Ser511Ter,ENST00000492720,;DENND2A,stop_gained,p.Ser511Ter,ENST00000537639,;DENND2A,stop_gained,p.Ser511Ter,ENST00000275884,;DENND2A,3_prime_UTR_variant,,ENST00000475837,;DENND2A,stop_gained,p.Ser511Ter,ENST00000461883,;	C	ENSG00000146966	ENST00000275884	Transcript	stop_gained	1950	1532	511	S/*	tCa/tGa	rs752090246	.	.	-1	DENND2A	HGNC	22212	protein_coding	YES	CCDS43659.1	ENSP00000275884	DEN2A_HUMAN	C9JD15_HUMAN,C9JAA0_HUMAN,C9IYZ8_HUMAN,C9IY76_HUMAN	UPI00001C1E63	.	.	.	6/19	.	hmmpanther:PTHR15288:SF3,hmmpanther:PTHR15288	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTGAGTTG	.	5	ESCA
ADCK2	0	.	GRCh37	7	140378976	140378976	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000072869	3/8	94	64	29	86	86	0	ADCK2,stop_gained,p.Gln206Ter,ENST00000483369,;ADCK2,stop_gained,p.Gln8Ter,ENST00000473512,;ADCK2,stop_gained,p.Gln368Ter,ENST00000476491,;ADCK2,stop_gained,p.Gln368Ter,ENST00000072869,;ADCK2,non_coding_transcript_exon_variant,,ENST00000498423,;	T	ENSG00000133597	ENST00000072869	Transcript	stop_gained	1280	1102	368	Q/*	Cag/Tag	.	.	.	1	ADCK2	HGNC	19039	protein_coding	YES	CCDS5861.1	ENSP00000072869	ADCK2_HUMAN	A4D1T6_HUMAN	UPI000003C962	.	.	.	3/8	.	hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF6,Pfam_domain:PF03109,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTCAGAAT	.	5	ESCA
TRBV7-4	0	.	GRCh37	7	142176408	142176408	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268G>C	p.Glu90Gln	p.E90Q	ENST00000390369	2/2	48	33	14	24	24	0	TRBV7-4,missense_variant,p.Glu90Gln,ENST00000390369,;TRBV6-5,downstream_gene_variant,,ENST00000390368,;	G	ENSG00000253409	ENST00000390369	Transcript	missense_variant	268	268	90	E/Q	Gag/Cag	.	.	.	-1	TRBV7-4	HGNC	12238	TR_V_gene	YES	.	ENSP00000374892	.	.	UPI0001AE7164	.	tolerated(0.18)	benign(0.194)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23268:SF20,hmmpanther:PTHR23268,Pfam_domain:PF07686,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCAGGCC	.	5	ESCA
TRPV5	0	.	GRCh37	7	142612479	142612479	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1284C>T	p.%3D	p.I428I	ENST00000265310	10/15	27	15	11	37	37	0	TRPV5,synonymous_variant,p.%3D,ENST00000439304,;TRPV5,synonymous_variant,p.%3D,ENST00000265310,;	A	ENSG00000127412	ENST00000265310	Transcript	synonymous_variant	1633	1284	428	I	atC/atT	.	.	.	-1	TRPV5	HGNC	3145	protein_coding	YES	CCDS5875.1	ENSP00000265310	TRPV5_HUMAN	Q9H480_HUMAN	UPI0000052B76	.	.	.	10/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10582:SF11,hmmpanther:PTHR10582,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520,Prints_domain:PR01765	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATGATGAC	.	5	ESCA
ISPD	0	.	GRCh37	7	16445718	16445718	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502C>G	p.Leu168Val	p.L168V	ENST00000407010	2/10	43	26	16	42	42	0	ISPD,missense_variant,p.Leu168Val,ENST00000407010,;ISPD,missense_variant,p.Leu168Val,ENST00000399310,;	C	ENSG00000214960	ENST00000407010	Transcript	missense_variant	502	502	168	L/V	Ctt/Gtt	.	.	.	-1	ISPD	HGNC	37276	protein_coding	YES	.	ENSP00000385478	ISPD_HUMAN	.	UPI00015CFC06	.	tolerated(0.11)	benign(0.232)	2/10	.	hmmpanther:PTHR19136,hmmpanther:PTHR19136:SF79,Gene3D:3.90.550.10,Pfam_domain:PF01128,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAAGAAGGA	.	5	ESCA
HOXA3	0	.	GRCh37	7	27147685	27147685	+	Missense_Mutation	SNP	C	C	T	rs772517713	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1181G>A	p.Gly394Asp	p.G394D	ENST00000396352	3/3	22	15	7	16	16	0	HOXA3,missense_variant,p.Gly394Asp,ENST00000317201,;HOXA3,missense_variant,p.Gly394Asp,ENST00000396352,;HOXA3,downstream_gene_variant,,ENST00000522456,;HOXA3,downstream_gene_variant,,ENST00000522788,;HOXA3,downstream_gene_variant,,ENST00000521779,;HOXA-AS2,intron_variant,,ENST00000518088,;HOXA3,downstream_gene_variant,,ENST00000521401,;	T	ENSG00000105997	ENST00000396352	Transcript	missense_variant	1381	1181	394	G/D	gGc/gAc	rs772517713	.	.	-1	HOXA3	HGNC	5104	protein_coding	YES	CCDS5404.1	ENSP00000379640	HXA3_HUMAN	F2Z3A4_HUMAN,E5RIJ8_HUMAN,A4D182_HUMAN	UPI000012CF22	.	deleterious(0.01)	benign(0.023)	3/3	.	Pfam_domain:PF13293,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCGCCCGAG	.	2	ESCA
HOXA10	0	.	GRCh37	7	27210226	27210226	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1292G>T	.	.	ENST00000283921	2/2	27	17	10	19	19	0	HOXA10,3_prime_UTR_variant,,ENST00000283921,;RP1-170O19.20,intron_variant,,ENST00000470747,;HOXA10,downstream_gene_variant,,ENST00000396344,;MIR196B,upstream_gene_variant,,ENST00000384852,;HOXA10-AS,intron_variant,,ENST00000519694,;HOXA10-AS,intron_variant,,ENST00000523790,;HOXA10-AS,intron_variant,,ENST00000519935,;RP1-170O19.20,intron_variant,,ENST00000465941,;HOXA10,downstream_gene_variant,,ENST00000519593,;HOXA10,downstream_gene_variant,,ENST00000521421,;HOXA9,upstream_gene_variant,,ENST00000489695,;HOXA10,downstream_gene_variant,,ENST00000524368,;HOXA9,upstream_gene_variant,,ENST00000497089,;HOXA9,upstream_gene_variant,,ENST00000487384,;	A	ENSG00000253293	ENST00000283921	Transcript	3_prime_UTR_variant	2525	.	.	.	.	.	.	.	-1	HOXA10	HGNC	5100	protein_coding	YES	CCDS5410.2	ENSP00000283921	HXA10_HUMAN	.	UPI0000EE42DA	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCATTCC	.	5	ESCA
FAM183B	0	.	GRCh37	7	38725305	38725305	+	Missense_Mutation	SNP	C	C	T	rs777801963	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301G>A	p.Asp101Asn	p.D101N	ENST00000409072	2/2	70	49	20	53	53	0	FAM183B,missense_variant,p.Asp101Asn,ENST00000409072,;	T	ENSG00000164556	ENST00000409072	Transcript	missense_variant	1236	301	101	D/N	Gac/Aac	rs777801963	.	.	-1	FAM183B	HGNC	34511	protein_coding	YES	.	ENSP00000386657	F183B_HUMAN	.	UPI000020EE1E	.	tolerated(1)	benign(0)	2/2	.	Pfam_domain:PF14886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTCGACCA	.	5	ESCA
CDK13	0	.	GRCh37	7	39991112	39991112	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.872C>T	p.Ser291Leu	p.S291L	ENST00000181839	1/14	8	4	4	8	8	0	CDK13,missense_variant,p.Ser291Leu,ENST00000340829,;CDK13,missense_variant,p.Ser291Leu,ENST00000181839,;RP11-467D6.1,upstream_gene_variant,,ENST00000569710,;	T	ENSG00000065883	ENST00000181839	Transcript	missense_variant	1477	872	291	S/L	tCg/tTg	.	.	.	1	CDK13	HGNC	1733	protein_coding	YES	CCDS5461.1	ENSP00000181839	CDK13_HUMAN	.	UPI000013C5E3	.	tolerated(0.12)	unknown(0)	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCGGCCT	.	2	ESCA
SLC29A4	0	.	GRCh37	7	5336607	5336607	+	Silent	SNP	G	G	A	rs138555653	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660G>A	p.%3D	p.T220T	ENST00000396872	7/11	71	66	5	53	53	0	SLC29A4,synonymous_variant,p.%3D,ENST00000297195,;SLC29A4,synonymous_variant,p.%3D,ENST00000396872,;SLC29A4,synonymous_variant,p.%3D,ENST00000406453,;SLC29A4,upstream_gene_variant,,ENST00000439491,;	A	ENSG00000164638	ENST00000396872	Transcript	synonymous_variant	821	660	220	T	acG/acA	rs138555653	.	.	1	SLC29A4	HGNC	23097	protein_coding	YES	CCDS5340.1	ENSP00000380081	S29A4_HUMAN	C9IYM7_HUMAN	UPI0000051F6F	.	.	.	7/11	.	hmmpanther:PTHR10332:SF4,hmmpanther:PTHR10332,Pfam_domain:PF01733,Superfamily_domains:SSF103473,Prints_domain:PR01130	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCACGAAGCT	byCluster	2	ESCA
TNRC18	0	.	GRCh37	7	5427355	5427355	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2100G>A	p.%3D	p.L700L	ENST00000430969	5/30	38	27	10	17	17	0	TNRC18,synonymous_variant,p.%3D,ENST00000430969,;TNRC18,synonymous_variant,p.%3D,ENST00000413081,;TNRC18,synonymous_variant,p.%3D,ENST00000399537,;TNRC18,downstream_gene_variant,,ENST00000399434,;TNRC18,downstream_gene_variant,,ENST00000434361,;	T	ENSG00000182095	ENST00000430969	Transcript	synonymous_variant	2449	2100	700	L	ctG/ctA	.	.	.	-1	TNRC18	HGNC	11962	protein_coding	YES	CCDS47534.1	ENSP00000395538	TNC18_HUMAN	H7C3U5_HUMAN,C9J9K1_HUMAN	UPI00016632FD	.	.	.	5/30	.	hmmpanther:PTHR12505:SF21,hmmpanther:PTHR12505	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCCAGCCG	.	5	ESCA
OCM	0	.	GRCh37	7	5920515	5920515	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-6T>C	.	.	ENST00000242104	1/4	64	41	23	58	58	0	OCM,splice_region_variant,,ENST00000416608,;OCM,5_prime_UTR_variant,,ENST00000242104,;	C	ENSG00000122543	ENST00000242104	Transcript	5_prime_UTR_variant	87	.	.	.	.	.	.	.	1	OCM	HGNC	8105	protein_coding	YES	CCDS43548.1	ENSP00000242104	ONCO_HUMAN	.	UPI00001D7522	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGGTAGAAA	.	5	ESCA
CRCP	0	.	GRCh37	7	65617254	65617254	+	Silent	SNP	C	C	T	rs758222904	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.357C>T	p.%3D	p.T119T	ENST00000395326	6/6	20	14	6	20	20	0	CRCP,synonymous_variant,p.%3D,ENST00000338592,;CRCP,synonymous_variant,p.%3D,ENST00000431089,;CRCP,synonymous_variant,p.%3D,ENST00000398684,;CRCP,synonymous_variant,p.%3D,ENST00000415001,;CRCP,synonymous_variant,p.%3D,ENST00000395326,;AC068533.7,downstream_gene_variant,,ENST00000450043,;RP5-1132H15.1,intron_variant,,ENST00000435524,;CRCP,non_coding_transcript_exon_variant,,ENST00000492264,;CRCP,3_prime_UTR_variant,,ENST00000360415,;	T	ENSG00000241258	ENST00000395326	Transcript	synonymous_variant	715	357	119	T	acC/acT	rs758222904	.	.	1	CRCP	HGNC	17888	protein_coding	YES	CCDS5532.1	ENSP00000378736	RPC9_HUMAN	.	UPI0000128406	.	.	.	6/6	.	Superfamily_domains:SSF47819,SMART_domains:SM00657,Pfam_domain:PF03874,hmmpanther:PTHR15561:SF0,hmmpanther:PTHR15561	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CACACCGTCAC	byFrequency	4	ESCA
RUNDC3B	0	.	GRCh37	7	87436700	87436700	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1020G>A	p.%3D	p.K340K	ENST00000338056	10/12	50	33	16	48	48	0	RUNDC3B,synonymous_variant,p.%3D,ENST00000338056,;RUNDC3B,synonymous_variant,p.%3D,ENST00000394654,;RUNDC3B,intron_variant,,ENST00000493037,;RUNDC3B,intron_variant,,ENST00000312373,;	A	ENSG00000105784	ENST00000338056	Transcript	synonymous_variant	1431	1020	340	K	aaG/aaA	.	.	.	1	RUNDC3B	HGNC	30286	protein_coding	YES	CCDS5609.1	ENSP00000337732	RUN3B_HUMAN	.	UPI0000071425	.	.	.	10/12	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22835:SF124,hmmpanther:PTHR22835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAAAGAATAA	.	5	ESCA
ZNF804B	0	.	GRCh37	7	88389161	88389161	+	5'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-130T>A	.	.	ENST00000333190	1/4	32	21	11	17	17	0	ZNF804B,5_prime_UTR_variant,,ENST00000333190,;AC002127.4,downstream_gene_variant,,ENST00000444032,;	A	ENSG00000182348	ENST00000333190	Transcript	5_prime_UTR_variant	480	.	.	.	.	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGCCTCCCCC	.	2	ESCA
GNG11	0	.	GRCh37	7	93551419	93551419	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-31G>T	.	.	ENST00000248564	1/2	19	12	7	24	24	0	GNG11,5_prime_UTR_variant,,ENST00000248564,;	T	ENSG00000127920	ENST00000248564	Transcript	5_prime_UTR_variant	409	.	.	.	.	.	.	.	1	GNG11	HGNC	4403	protein_coding	YES	CCDS5634.1	ENSP00000248564	GBG11_HUMAN	Q53Y01_HUMAN	UPI0000001AD4	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAGAGCTA	.	5	ESCA
CASD1	0	.	GRCh37	7	94184821	94184821	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2145T>A	p.Tyr715Ter	p.Y715*	ENST00000297273	18/18	66	42	24	36	36	0	CASD1,stop_gained,p.Tyr715Ter,ENST00000297273,;CASD1,non_coding_transcript_exon_variant,,ENST00000489196,;CASD1,non_coding_transcript_exon_variant,,ENST00000471944,;	A	ENSG00000127995	ENST00000297273	Transcript	stop_gained	2432	2145	715	Y/*	taT/taA	.	.	.	1	CASD1	HGNC	16014	protein_coding	YES	CCDS5636.1	ENSP00000297273	CASD1_HUMAN	C9JDR3_HUMAN	UPI0000070404	.	.	.	18/18	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR13533:SF8,hmmpanther:PTHR13533,Pfam_domain:PF07779	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTATCACAT	.	5	ESCA
TRRAP	0	.	GRCh37	7	98509816	98509816	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2179G>A	p.Glu727Lys	p.E727K	ENST00000359863	18/72	79	52	27	70	70	0	TRRAP,missense_variant,p.Glu727Lys,ENST00000355540,;TRRAP,missense_variant,p.Glu726Lys,ENST00000446306,;TRRAP,missense_variant,p.Glu442Lys,ENST00000456197,;TRRAP,missense_variant,p.Glu727Lys,ENST00000359863,;	A	ENSG00000196367	ENST00000359863	Transcript	missense_variant	2388	2179	727	E/K	Gaa/Aaa	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	possibly_damaging(0.81)	18/72	.	hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGAAAAT	.	5	ESCA
HAS2	0	.	GRCh37	8	122626754	122626754	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1254C>T	p.%3D	p.L418L	ENST00000303924	4/4	28	22	6	19	19	0	HAS2,synonymous_variant,p.%3D,ENST00000303924,;	A	ENSG00000170961	ENST00000303924	Transcript	synonymous_variant	1792	1254	418	L	ctC/ctT	.	.	.	-1	HAS2	HGNC	4819	protein_coding	YES	CCDS6335.1	ENSP00000306991	HYAS2_HUMAN	.	UPI000012C0A9	.	.	.	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTATGAGACC	.	3	ESCA
HAS2	0	.	GRCh37	8	122626768	122626768	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1240C>T	p.Gln414Ter	p.Q414*	ENST00000303924	4/4	29	21	8	23	23	0	HAS2,stop_gained,p.Gln414Ter,ENST00000303924,;	A	ENSG00000170961	ENST00000303924	Transcript	stop_gained	1778	1240	414	Q/*	Cag/Tag	.	.	.	-1	HAS2	HGNC	4819	protein_coding	YES	CCDS6335.1	ENSP00000306991	HYAS2_HUMAN	.	UPI000012C0A9	.	.	.	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAGCTGGACAG	.	3	ESCA
FER1L6	0	.	GRCh37	8	125033904	125033904	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2128G>A	p.Asp710Asn	p.D710N	ENST00000522917	17/41	45	33	11	29	29	0	FER1L6,missense_variant,p.Asp710Asn,ENST00000522917,;FER1L6,missense_variant,p.Asp710Asn,ENST00000399018,;FER1L6-AS1,intron_variant,,ENST00000518567,;	A	ENSG00000214814	ENST00000522917	Transcript	missense_variant	2334	2128	710	D/N	Gat/Aat	.	.	.	1	FER1L6	HGNC	28065	protein_coding	YES	CCDS43767.1	ENSP00000428280	FR1L6_HUMAN	.	UPI0000E9B4AA	.	deleterious(0.01)	possibly_damaging(0.48)	17/41	.	hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTGATGAG	.	5	ESCA
KCNQ3	0	.	GRCh37	8	133187730	133187730	+	Missense_Mutation	SNP	C	C	G	rs764285990	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903G>C	p.Glu301Asp	p.E301D	ENST00000388996	5/15	73	56	17	65	65	0	KCNQ3,missense_variant,p.Glu181Asp,ENST00000521134,;KCNQ3,missense_variant,p.Glu301Asp,ENST00000388996,;KCNQ3,missense_variant,p.Glu301Asp,ENST00000519445,;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,;	G	ENSG00000184156	ENST00000388996	Transcript	missense_variant	1324	903	301	E/D	gaG/gaC	rs764285990	.	.	-1	KCNQ3	HGNC	6297	protein_coding	YES	CCDS34943.1	ENSP00000373648	KCNQ3_HUMAN	.	UPI00001279F0	.	tolerated(0.69)	benign(0.137)	5/15	.	hmmpanther:PTHR11537:SF5,hmmpanther:PTHR11537,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR00169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGTCTCAAA	.	5	ESCA
COL22A1	0	.	GRCh37	8	139603732	139603732	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4628C>G	p.Ala1543Gly	p.A1543G	ENST00000303045	64/65	49	41	7	38	38	0	COL22A1,missense_variant,p.Ala1543Gly,ENST00000303045,;COL22A1,missense_variant,p.Ala1523Gly,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,;	C	ENSG00000169436	ENST00000303045	Transcript	missense_variant	5075	4628	1543	A/G	gCc/gGc	.	.	.	-1	COL22A1	HGNC	22989	protein_coding	YES	CCDS6376.1	ENSP00000303153	COMA1_HUMAN	.	UPI00001C1EA1	.	.	unknown(0)	64/65	.	hmmpanther:PTHR24023:SF379,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTGGCTCCT	.	5	ESCA
CPSF1	0	.	GRCh37	8	145622125	145622125	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2612T>C	p.Leu871Pro	p.L871P	ENST00000349769	24/38	139	105	33	79	79	0	CPSF1,missense_variant,p.Leu871Pro,ENST00000349769,;CPSF1,downstream_gene_variant,,ENST00000531042,;ADCK5,downstream_gene_variant,,ENST00000308860,;MIR1234,downstream_gene_variant,,ENST00000408875,;MIR939,upstream_gene_variant,,ENST00000401314,;CPSF1,upstream_gene_variant,,ENST00000531727,;CPSF1,upstream_gene_variant,,ENST00000532935,;CPSF1,downstream_gene_variant,,ENST00000533492,;ADCK5,downstream_gene_variant,,ENST00000529654,;CPSF1,upstream_gene_variant,,ENST00000531480,;CPSF1,upstream_gene_variant,,ENST00000527827,;CPSF1,upstream_gene_variant,,ENST00000532725,;CPSF1,upstream_gene_variant,,ENST00000526271,;CPSF1,upstream_gene_variant,,ENST00000529288,;CPSF1,downstream_gene_variant,,ENST00000532560,;CPSF1,downstream_gene_variant,,ENST00000527916,;CPSF1,downstream_gene_variant,,ENST00000531683,;	G	ENSG00000071894	ENST00000349769	Transcript	missense_variant	2707	2612	871	L/P	cTg/cCg	.	.	.	-1	CPSF1	HGNC	2324	protein_coding	YES	CCDS34966.1	ENSP00000339353	CPSF1_HUMAN	Q9C0J6_HUMAN,E9PIM1_HUMAN,D3DWL9_HUMAN	UPI00001282EE	.	deleterious(0)	probably_damaging(0.99)	24/38	.	hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGCAGCTCT	.	5	ESCA
ZNF517	0	.	GRCh37	8	146032926	146032926	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.625G>C	p.Glu209Gln	p.E209Q	ENST00000359971	5/5	57	43	14	47	47	0	ZNF517,missense_variant,p.Glu209Gln,ENST00000359971,;ZNF517,missense_variant,p.Glu209Gln,ENST00000531720,;ZNF517,missense_variant,p.Glu176Gln,ENST00000529429,;ZNF517,intron_variant,,ENST00000525105,;ZNF517,downstream_gene_variant,,ENST00000528012,;ZNF517,intron_variant,,ENST00000526178,;ZNF517,missense_variant,p.Glu209Gln,ENST00000533965,;ZNF517,non_coding_transcript_exon_variant,,ENST00000530879,;	C	ENSG00000197363	ENST00000359971	Transcript	missense_variant	732	625	209	E/Q	Gag/Cag	COSM1755643	.	.	1	ZNF517	HGNC	27984	protein_coding	YES	CCDS6434.1	ENSP00000353058	ZN517_HUMAN	.	UPI000045770F	.	tolerated(0.26)	benign(0.406)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24379:SF20,hmmpanther:PTHR24379,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACAGAGTGC	.	5	ESCA
CSMD1	0	.	GRCh37	8	2830754	2830754	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8808T>C	p.%3D	p.F2936F	ENST00000537824	57/70	18	5	13	33	33	0	CSMD1,synonymous_variant,p.%3D,ENST00000400186,;CSMD1,synonymous_variant,p.%3D,ENST00000542608,;CSMD1,synonymous_variant,p.%3D,ENST00000602723,;CSMD1,synonymous_variant,p.%3D,ENST00000335551,;CSMD1,synonymous_variant,p.%3D,ENST00000537824,;CSMD1,synonymous_variant,p.%3D,ENST00000602557,;CSMD1,synonymous_variant,p.%3D,ENST00000520002,;	G	ENSG00000183117	ENST00000537824	Transcript	synonymous_variant	8808	8808	2936	F	ttT/ttC	.	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	.	57/70	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF323,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTAAAGTC	.	5	ESCA
C8orf86	0	.	GRCh37	8	38369630	38369630	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*275A>T	.	.	ENST00000358138	3/3	20	14	6	21	21	0	C8orf86,3_prime_UTR_variant,,ENST00000437935,;C8orf86,3_prime_UTR_variant,,ENST00000358138,;	A	ENSG00000196166	ENST00000358138	Transcript	3_prime_UTR_variant	972	.	.	.	.	.	.	.	-1	C8orf86	HGNC	33774	protein_coding	YES	CCDS6108.1	ENSP00000350856	CH086_HUMAN	.	UPI00001C0B34	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATATGGCCA	.	5	ESCA
FNTA	0	.	GRCh37	8	42940448	42940448	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*23G>C	.	.	ENST00000302279	9/9	11	4	7	20	20	0	FNTA,3_prime_UTR_variant,,ENST00000302279,;FNTA,3_prime_UTR_variant,,ENST00000342116,;FNTA,3_prime_UTR_variant,,ENST00000529687,;FNTA,downstream_gene_variant,,ENST00000533336,;FNTA,3_prime_UTR_variant,,ENST00000526755,;FNTA,non_coding_transcript_exon_variant,,ENST00000525099,;FNTA,non_coding_transcript_exon_variant,,ENST00000528400,;FNTA,downstream_gene_variant,,ENST00000533383,;FNTA,downstream_gene_variant,,ENST00000533998,;	C	ENSG00000168522	ENST00000302279	Transcript	3_prime_UTR_variant	1357	.	.	.	.	.	.	.	1	FNTA	HGNC	3782	protein_coding	YES	CCDS6140.1	ENSP00000303423	FNTA_HUMAN	E9PPM9_HUMAN,D3DSY9_HUMAN,B3KVN2_HUMAN	UPI000013176D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGATGGAATGC	.	3	ESCA
NSMAF	0	.	GRCh37	8	59515783	59515783	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1124C>T	p.Ser375Phe	p.S375F	ENST00000427130	13/31	48	31	16	40	40	0	NSMAF,missense_variant,p.Ser344Phe,ENST00000038176,;NSMAF,missense_variant,p.Ser375Phe,ENST00000427130,;NSMAF,non_coding_transcript_exon_variant,,ENST00000519858,;NSMAF,upstream_gene_variant,,ENST00000523982,;NSMAF,upstream_gene_variant,,ENST00000523106,;NSMAF,upstream_gene_variant,,ENST00000519227,;	A	ENSG00000035681	ENST00000427130	Transcript	missense_variant	1312	1124	375	S/F	tCc/tTc	.	.	.	-1	NSMAF	HGNC	8017	protein_coding	YES	CCDS47864.1	ENSP00000411012	FAN_HUMAN	.	UPI000192950C	.	tolerated(0.15)	benign(0.005)	13/31	.	PROSITE_profiles:PS50197,hmmpanther:PTHR13743,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGGAATAA	.	5	ESCA
MCPH1	0	.	GRCh37	8	6289088	6289088	+	Nonsense_Mutation	SNP	C	C	G	rs755862917	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302C>G	p.Ser101Ter	p.S101*	ENST00000344683	4/14	11	5	6	12	12	0	MCPH1,stop_gained,p.Ser101Ter,ENST00000519480,;MCPH1,stop_gained,p.Ser101Ter,ENST00000522905,;MCPH1,stop_gained,p.Ser101Ter,ENST00000344683,;	G	ENSG00000147316	ENST00000344683	Transcript	stop_gained	378	302	101	S/*	tCa/tGa	CM100524,rs755862917	.	.	1	MCPH1	HGNC	6954	protein_coding	YES	CCDS43689.1	ENSP00000342924	.	Q6W7E5_HUMAN,Q6RBX4_HUMAN,Q6RBQ8_HUMAN,Q6RBJ2_HUMAN,Q6RBC6_HUMAN,Q6RB60_HUMAN,Q6RAZ4_HUMAN,Q6RAP8_HUMAN,Q6RAB6_HUMAN,Q6RA50_HUMAN	UPI000020FF7E	.	.	.	4/14	.	hmmpanther:PTHR14625:SF3,hmmpanther:PTHR14625	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.K107fs*39|c.313delA|5	MUTECT|MUSE	CTTATCAAGCC	.	2	ESCA
E2F5	0	.	GRCh37	8	86118428	86118428	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523C>T	p.His175Tyr	p.H175Y	ENST00000416274	4/8	36	30	6	52	52	0	E2F5,missense_variant,p.His14Tyr,ENST00000517476,;E2F5,missense_variant,p.His176Tyr,ENST00000256117,;E2F5,missense_variant,p.His175Tyr,ENST00000416274,;E2F5,missense_variant,p.His11Tyr,ENST00000518234,;E2F5,missense_variant,p.His175Tyr,ENST00000418930,;E2F5,5_prime_UTR_variant,,ENST00000521429,;E2F5,upstream_gene_variant,,ENST00000520225,;E2F5,non_coding_transcript_exon_variant,,ENST00000519128,;E2F5,downstream_gene_variant,,ENST00000521234,;	T	ENSG00000133740	ENST00000416274	Transcript	missense_variant	557	523	175	H/Y	Cat/Tat	.	.	.	1	E2F5	HGNC	3119	protein_coding	YES	CCDS47885.1	ENSP00000398124	E2F5_HUMAN	.	UPI000002E057	.	tolerated(0.13)	benign(0.013)	4/8	.	hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF35,Superfamily_domains:SSF144074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTCATGAA	.	5	ESCA
SLC7A13	0	.	GRCh37	8	87229753	87229753	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125G>A	p.Met375Ile	p.M375I	ENST00000297524	3/4	26	15	11	48	48	0	SLC7A13,missense_variant,p.Met366Ile,ENST00000419776,;SLC7A13,missense_variant,p.Met375Ile,ENST00000297524,;SLC7A13,downstream_gene_variant,,ENST00000520624,;	T	ENSG00000164893	ENST00000297524	Transcript	missense_variant	1229	1125	375	M/I	atG/atA	.	.	.	-1	SLC7A13	HGNC	23092	protein_coding	YES	CCDS34917.1	ENSP00000297524	S7A13_HUMAN	.	UPI000006DF39	.	tolerated(0.1)	benign(0.05)	3/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF238,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATCATTAA	.	5	ESCA
DCAF4L2	0	.	GRCh37	8	88886083	88886083	+	Silent	SNP	G	G	A	rs779092689	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117C>T	p.%3D	p.F39F	ENST00000319675	1/1	108	71	37	102	102	0	DCAF4L2,synonymous_variant,p.%3D,ENST00000319675,;	A	ENSG00000176566	ENST00000319675	Transcript	synonymous_variant	214	117	39	F	ttC/ttT	rs779092689,COSM176945	.	.	-1	DCAF4L2	HGNC	26657	protein_coding	YES	CCDS6245.1	ENSP00000316496	DC4L2_HUMAN	Q8N7W3_HUMAN	UPI0000072860	.	.	.	1/1	.	hmmpanther:PTHR22847:SF401,hmmpanther:PTHR22847	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L37L|c.111C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGCGAATCT	byFrequency	5	ESCA
RUNX1T1	0	.	GRCh37	8	93074912	93074912	+	Intron	SNP	G	G	A	rs560780392	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.121+32663C>T	.	.	ENST00000436581	.	32	21	10	28	28	0	RUNX1T1,synonymous_variant,p.%3D,ENST00000518449,;RUNX1T1,5_prime_UTR_variant,,ENST00000518317,;RUNX1T1,5_prime_UTR_variant,,ENST00000521319,;RUNX1T1,5_prime_UTR_variant,,ENST00000519061,;RUNX1T1,5_prime_UTR_variant,,ENST00000521733,;RUNX1T1,5_prime_UTR_variant,,ENST00000396218,;RUNX1T1,intron_variant,,ENST00000523168,;RUNX1T1,intron_variant,,ENST00000517792,;RUNX1T1,intron_variant,,ENST00000520583,;RUNX1T1,intron_variant,,ENST00000518832,;RUNX1T1,intron_variant,,ENST00000522467,;RUNX1T1,intron_variant,,ENST00000436581,;RUNX1T1,intron_variant,,ENST00000518954,;RUNX1T1,intron_variant,,ENST00000360348,;RUNX1T1,intron_variant,,ENST00000518823,;RUNX1T1,intron_variant,,ENST00000520974,;RUNX1T1,intron_variant,,ENST00000518844,;RUNX1T1,intron_variant,,ENST00000523629,;RUNX1T1,intron_variant,,ENST00000520724,;RUNX1T1,intron_variant,,ENST00000520428,;RUNX1T1,intron_variant,,ENST00000517919,;RUNX1T1,intron_variant,,ENST00000519847,;RUNX1T1,intron_variant,,ENST00000518992,;RUNX1T1,intron_variant,,ENST00000265814,;RUNX1T1,intron_variant,,ENST00000520556,;RUNX1T1,intron_variant,,ENST00000521375,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000522163,;RUNX1T1,intron_variant,,ENST00000520172,;RUNX1T1,intron_variant,,ENST00000522860,;RUNX1T1,intron_variant,,ENST00000522065,;RUNX1T1,intron_variant,,ENST00000518256,;RUNX1T1,intron_variant,,ENST00000522316,;RUNX1T1,synonymous_variant,p.%3D,ENST00000517493,;RUNX1T1,synonymous_variant,p.%3D,ENST00000524215,;RUNX1T1,intron_variant,,ENST00000521897,;RUNX1T1,intron_variant,,ENST00000519422,;RUNX1T1,intron_variant,,ENST00000519577,;RUNX1T1,intron_variant,,ENST00000523290,;RUNX1T1,intron_variant,,ENST00000521902,;	A	ENSG00000079102	ENST00000436581	Transcript	intron_variant	.	.	.	.	.	rs560780392	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	.	.	.	1/10	.	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCCGGAGGC	byFrequency|by1000G	5	ESCA
MATN2	0	.	GRCh37	8	99033468	99033468	+	Missense_Mutation	SNP	G	G	A	rs758729757	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1855G>A	p.Glu619Lys	p.E619K	ENST00000520016	12/18	40	29	11	44	44	0	MATN2,missense_variant,p.Glu402Lys,ENST00000518154,;MATN2,missense_variant,p.Glu619Lys,ENST00000521689,;MATN2,missense_variant,p.Glu619Lys,ENST00000254898,;MATN2,missense_variant,p.Glu619Lys,ENST00000520016,;MATN2,missense_variant,p.Glu578Lys,ENST00000524308,;MATN2,missense_variant,p.Glu335Lys,ENST00000522025,;MATN2,intron_variant,,ENST00000517321,;RPL30,downstream_gene_variant,,ENST00000518164,;MATN2,synonymous_variant,p.%3D,ENST00000521952,;MATN2,non_coding_transcript_exon_variant,,ENST00000518370,;	A	ENSG00000132561	ENST00000520016	Transcript	missense_variant	1979	1855	619	E/K	Gaa/Aaa	rs758729757,COSM276001,COSM276002	.	.	1	MATN2	HGNC	6908	protein_coding	YES	CCDS55264.1	ENSP00000430487	MATN2_HUMAN	E5RJM4_HUMAN	UPI000021037B	.	deleterious(0.01)	probably_damaging(0.989)	12/18	.	hmmpanther:PTHR22992:SF17,hmmpanther:PTHR22992,Gene3D:2.10.25.10,Pfam_domain:PF14670,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCGAACAC	byFrequency	5	ESCA
SMC2	0	.	GRCh37	9	106901433	106901433	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3431C>T	p.Ser1144Leu	p.S1144L	ENST00000286398	25/25	21	13	8	14	14	0	SMC2,missense_variant,p.Ser1144Leu,ENST00000374793,;SMC2,missense_variant,p.Ser1144Leu,ENST00000286398,;SMC2,missense_variant,p.Ser1144Leu,ENST00000374787,;SMC2,downstream_gene_variant,,ENST00000303219,;SMC2,3_prime_UTR_variant,,ENST00000493955,;	T	ENSG00000136824	ENST00000286398	Transcript	missense_variant	3719	3431	1144	S/L	tCa/tTa	.	.	.	1	SMC2	HGNC	14011	protein_coding	YES	CCDS35086.1	ENSP00000286398	SMC2_HUMAN	Q5T821_HUMAN	UPI000013DE44	.	deleterious(0)	probably_damaging(0.999)	25/25	.	hmmpanther:PTHR18937:SF9,hmmpanther:PTHR18937,Gene3D:3.40.50.300,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGTCACTAA	.	5	ESCA
GGTA1P	0	.	GRCh37	9	124241446	124241446	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.275C>T	.	.	ENST00000495328	2/8	20	14	6	19	19	0	GGTA1P,non_coding_transcript_exon_variant,,ENST00000495328,;GGTA1P,non_coding_transcript_exon_variant,,ENST00000373793,;GGTA1P,non_coding_transcript_exon_variant,,ENST00000481534,;GGTA1P,intron_variant,,ENST00000481799,;	A	ENSG00000204136	ENST00000495328	Transcript	non_coding_transcript_exon_variant	275	.	.	.	.	.	.	.	-1	GGTA1P	HGNC	4253	processed_transcript	YES	.	.	.	.	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGGGCGATC	.	5	ESCA
ENG	0	.	GRCh37	9	130578263	130578263	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1811C>A	p.Ala604Asp	p.A604D	ENST00000373203	14/15	51	34	17	43	43	0	ENG,missense_variant,p.Ala604Asp,ENST00000344849,;ENG,missense_variant,p.Ala604Asp,ENST00000373203,;FPGS,downstream_gene_variant,,ENST00000373228,;FPGS,downstream_gene_variant,,ENST00000373225,;FPGS,downstream_gene_variant,,ENST00000373245,;FPGS,downstream_gene_variant,,ENST00000373247,;FPGS,downstream_gene_variant,,ENST00000393706,;RP11-228B15.4,upstream_gene_variant,,ENST00000439298,;RP11-228B15.4,upstream_gene_variant,,ENST00000425991,;FPGS,downstream_gene_variant,,ENST00000475270,;ENG,downstream_gene_variant,,ENST00000486329,;FPGS,downstream_gene_variant,,ENST00000467826,;FPGS,downstream_gene_variant,,ENST00000488506,;FPGS,downstream_gene_variant,,ENST00000460181,;ENG,downstream_gene_variant,,ENST00000480266,;	T	ENSG00000106991	ENST00000373203	Transcript	missense_variant	2212	1811	604	A/D	gCc/gAc	CM062599	.	.	-1	ENG	HGNC	3349	protein_coding	YES	CCDS48029.1	ENSP00000362299	EGLN_HUMAN	Q71V36_HUMAN,F5GX88_HUMAN	UPI0000129E00	.	deleterious(0)	probably_damaging(0.986)	14/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14002:SF1,hmmpanther:PTHR14002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGGGCCCCG	.	5	ESCA
ENG	0	.	GRCh37	9	130578264	130578264	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1810G>A	p.Ala604Thr	p.A604T	ENST00000373203	14/15	50	33	17	43	42	0	ENG,missense_variant,p.Ala604Thr,ENST00000344849,;ENG,missense_variant,p.Ala604Thr,ENST00000373203,;FPGS,downstream_gene_variant,,ENST00000373228,;FPGS,downstream_gene_variant,,ENST00000373225,;FPGS,downstream_gene_variant,,ENST00000373245,;FPGS,downstream_gene_variant,,ENST00000373247,;FPGS,downstream_gene_variant,,ENST00000393706,;RP11-228B15.4,upstream_gene_variant,,ENST00000439298,;RP11-228B15.4,upstream_gene_variant,,ENST00000425991,;FPGS,downstream_gene_variant,,ENST00000475270,;ENG,downstream_gene_variant,,ENST00000486329,;FPGS,downstream_gene_variant,,ENST00000467826,;FPGS,downstream_gene_variant,,ENST00000488506,;FPGS,downstream_gene_variant,,ENST00000460181,;ENG,downstream_gene_variant,,ENST00000480266,;	T	ENSG00000106991	ENST00000373203	Transcript	missense_variant	2211	1810	604	A/T	Gcc/Acc	.	.	.	-1	ENG	HGNC	3349	protein_coding	YES	CCDS48029.1	ENSP00000362299	EGLN_HUMAN	Q71V36_HUMAN,F5GX88_HUMAN	UPI0000129E00	.	deleterious(0)	probably_damaging(0.927)	14/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14002:SF1,hmmpanther:PTHR14002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CAGGGCCCCGA	.	4	ESCA
DPM2	0	.	GRCh37	9	130698040	130698040	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216G>A	p.%3D	p.V72V	ENST00000314392	4/4	36	30	6	42	42	0	DPM2,synonymous_variant,p.%3D,ENST00000314392,;FAM102A,downstream_gene_variant,,ENST00000373095,;DPM2,downstream_gene_variant,,ENST00000373110,;PIP5KL1,upstream_gene_variant,,ENST00000388747,;RP11-203J24.8,intron_variant,,ENST00000592240,;RP11-203J24.8,upstream_gene_variant,,ENST00000590283,;RP11-203J24.8,upstream_gene_variant,,ENST00000587978,;RP11-203J24.8,upstream_gene_variant,,ENST00000588890,;RP11-203J24.8,upstream_gene_variant,,ENST00000591408,;RP11-203J24.8,upstream_gene_variant,,ENST00000587355,;RP11-203J24.8,upstream_gene_variant,,ENST00000415141,;RP11-203J24.8,upstream_gene_variant,,ENST00000608805,;RP11-203J24.8,upstream_gene_variant,,ENST00000586374,;PIP5KL1,upstream_gene_variant,,ENST00000492296,;DPM2,non_coding_transcript_exon_variant,,ENST00000495270,;DPM2,non_coding_transcript_exon_variant,,ENST00000473360,;DPM2,non_coding_transcript_exon_variant,,ENST00000470181,;	T	ENSG00000136908	ENST00000314392	Transcript	synonymous_variant	880	216	72	V	gtG/gtA	.	.	.	-1	DPM2	HGNC	3006	protein_coding	YES	CCDS6886.1	ENSP00000322181	DPM2_HUMAN	.	UPI00000009FE	.	.	.	4/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15039:SF11,hmmpanther:PTHR15039,Pfam_domain:PF07297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	AGCATCACATA	.	2	ESCA
FAM73B	0	.	GRCh37	9	131834225	131834226	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1496dupT	.	.	ENST00000358369	16/16	167	117	50	81	81	0	FAM73B,3_prime_UTR_variant,,ENST00000277475,;FAM73B,3_prime_UTR_variant,,ENST00000406926,;FAM73B,3_prime_UTR_variant,,ENST00000358369,;FAM73B,downstream_gene_variant,,ENST00000495975,;FAM73B,downstream_gene_variant,,ENST00000474639,;FAM73B,3_prime_UTR_variant,,ENST00000445183,;FAM73B,3_prime_UTR_variant,,ENST00000439290,;FAM73B,non_coding_transcript_exon_variant,,ENST00000483458,;FAM73B,downstream_gene_variant,,ENST00000492279,;FAM73B,downstream_gene_variant,,ENST00000471943,;FAM73B,downstream_gene_variant,,ENST00000414342,;	T	ENSG00000148343	ENST00000358369	Transcript	3_prime_UTR_variant	3501-3502	.	.	.	.	.	.	.	1	FAM73B	HGNC	23621	protein_coding	YES	CCDS6917.1	ENSP00000351138	FA73B_HUMAN	B0QZG3_HUMAN	UPI00001B4EFD	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCTGATTTGC	.	3	ESCA
OLFM1	0	.	GRCh37	9	138011671	138011671	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1051G>A	p.Ala351Thr	p.A351T	ENST00000252854	6/6	28	20	8	16	16	0	OLFM1,missense_variant,p.Ala342Thr,ENST00000371796,;OLFM1,missense_variant,p.Ala369Thr,ENST00000371793,;OLFM1,missense_variant,p.Ala351Thr,ENST00000252854,;OLFM1,3_prime_UTR_variant,,ENST00000545657,;OLFM1,downstream_gene_variant,,ENST00000539877,;OLFM1,non_coding_transcript_exon_variant,,ENST00000483042,;	A	ENSG00000130558	ENST00000252854	Transcript	missense_variant	1238	1051	351	A/T	Gcc/Acc	.	.	.	1	OLFM1	HGNC	17187	protein_coding	YES	CCDS6986.1	ENSP00000252854	NOE1_HUMAN	Q6IMJ8_HUMAN,Q96BL8_HUMAN,F5H810_HUMAN,F5GZQ2_HUMAN,B3KR22_HUMAN	UPI000013CD8C	.	tolerated(0.66)	probably_damaging(0.948)	6/6	.	PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF34,Pfam_domain:PF02191,SMART_domains:SM00284,Superfamily_domains:SSF50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTACGCCACC	.	5	ESCA
SNAPC4	0	.	GRCh37	9	139282959	139282959	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1060G>A	p.Asp354Asn	p.D354N	ENST00000298532	10/23	31	19	12	25	25	0	SNAPC4,missense_variant,p.Asp354Asn,ENST00000298532,;	T	ENSG00000165684	ENST00000298532	Transcript	missense_variant	1429	1060	354	D/N	Gac/Aac	.	.	.	-1	SNAPC4	HGNC	11137	protein_coding	YES	CCDS6998.1	ENSP00000298532	SNPC4_HUMAN	.	UPI000013E4EC	.	deleterious(0)	probably_damaging(1)	10/23	.	PROSITE_profiles:PS50090,hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF191,Gene3D:1.10.10.60,Pfam_domain:PF13921,SMART_domains:SM00717,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGTCCTCCT	.	5	ESCA
BNC2	0	.	GRCh37	9	16437354	16437354	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838T>C	p.Ser280Pro	p.S280P	ENST00000380672	6/7	35	17	18	62	62	0	BNC2,missense_variant,p.Ser185Pro,ENST00000545497,;BNC2,missense_variant,p.Ser213Pro,ENST00000380667,;BNC2,missense_variant,p.Ser202Pro,ENST00000603713,;BNC2,missense_variant,p.Ser280Pro,ENST00000380672,;BNC2,missense_variant,p.Ser280Pro,ENST00000380666,;BNC2,missense_variant,p.Ser237Pro,ENST00000418777,;BNC2,upstream_gene_variant,,ENST00000411752,;BNC2,missense_variant,p.Ser280Pro,ENST00000484726,;	G	ENSG00000173068	ENST00000380672	Transcript	missense_variant	896	838	280	S/P	Tca/Cca	COSM1246171	.	.	-1	BNC2	HGNC	30988	protein_coding	YES	CCDS6482.2	ENSP00000370047	BNC2_HUMAN	S4R351_HUMAN,Q06HC7_HUMAN,Q06HC2_HUMAN,Q06HB9_HUMAN,D3DRJ1_HUMAN	UPI000035E7B0	.	tolerated(0.1)	probably_damaging(0.987)	6/7	.	hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF2	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTGAGTCTG	.	5	ESCA
TEK	0	.	GRCh37	9	27158043	27158043	+	Missense_Mutation	SNP	G	G	C	rs764880845	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267G>C	p.Lys89Asn	p.K89N	ENST00000380036	2/23	55	21	33	75	75	0	TEK,missense_variant,p.Lys89Asn,ENST00000406359,;TEK,missense_variant,p.Lys89Asn,ENST00000380036,;TEK,intron_variant,,ENST00000519097,;TEK,intron_variant,,ENST00000519080,;	C	ENSG00000120156	ENST00000380036	Transcript	missense_variant	709	267	89	K/N	aaG/aaC	rs764880845	.	.	1	TEK	HGNC	11724	protein_coding	YES	CCDS6519.1	ENSP00000369375	TIE2_HUMAN	.	UPI000021121E	.	deleterious(0.01)	possibly_damaging(0.558)	2/23	.	hmmpanther:PTHR24416:SF125,hmmpanther:PTHR24416,Gene3D:2.60.40.10,Pfam_domain:PF10430	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAAGAGAGA	byFrequency	5	ESCA
PTENP1	0	.	GRCh37	9	33676330	33676330	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1168A>G	.	.	ENST00000532280	1/1	56	24	32	72	72	0	PTENP1,non_coding_transcript_exon_variant,,ENST00000532280,;PTENP1,non_coding_transcript_exon_variant,,ENST00000447117,;PTENP1,non_coding_transcript_exon_variant,,ENST00000451527,;	C	ENSG00000237984	ENST00000532280	Transcript	non_coding_transcript_exon_variant	1168	.	.	.	.	.	.	.	-1	PTENP1	HGNC	9589	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGATCTTCA	.	5	ESCA
KDM4C	0	.	GRCh37	9	7013942	7013942	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2123A>T	p.Glu708Val	p.E708V	ENST00000381309	14/22	28	18	10	36	36	0	KDM4C,missense_variant,p.Glu708Val,ENST00000381306,;KDM4C,missense_variant,p.Glu708Val,ENST00000381309,;KDM4C,missense_variant,p.Glu730Val,ENST00000535193,;KDM4C,missense_variant,p.Glu708Val,ENST00000543771,;KDM4C,missense_variant,p.Glu527Val,ENST00000536108,;KDM4C,missense_variant,p.Glu395Val,ENST00000428870,;KDM4C,missense_variant,p.Glu52Val,ENST00000420847,;KDM4C,missense_variant,p.Glu453Val,ENST00000442236,;KDM4C,3_prime_UTR_variant,,ENST00000438023,;	T	ENSG00000107077	ENST00000381309	Transcript	missense_variant	2688	2123	708	E/V	gAa/gTa	.	.	.	1	KDM4C	HGNC	17071	protein_coding	YES	CCDS6471.1	ENSP00000370710	KDM4C_HUMAN	C9J879_HUMAN	UPI0000367602	.	deleterious(0.04)	possibly_damaging(0.575)	14/22	.	hmmpanther:PTHR10694:SF32,hmmpanther:PTHR10694,SMART_domains:SM00249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTGAAGAGG	.	5	ESCA
FAM122A	0	.	GRCh37	9	71396510	71396510	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*566G>C	.	.	ENST00000394264	1/1	30	19	11	43	43	0	FAM122A,3_prime_UTR_variant,,ENST00000394264,;PIP5K1B,intron_variant,,ENST00000437200,;PIP5K1B,intron_variant,,ENST00000377284,;PIP5K1B,intron_variant,,ENST00000440050,;PIP5K1B,intron_variant,,ENST00000541509,;PIP5K1B,intron_variant,,ENST00000265382,;PIP5K1B,intron_variant,,ENST00000472907,;PIP5K1B,intron_variant,,ENST00000478500,;	C	ENSG00000187866	ENST00000394264	Transcript	3_prime_UTR_variant	1547	.	.	.	.	.	.	.	1	FAM122A	HGNC	23490	protein_coding	YES	CCDS6623.1	ENSP00000377807	F122A_HUMAN	B4E242_HUMAN	UPI0000071E32	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAATGATTAA	.	5	ESCA
FAM122A	0	.	GRCh37	9	71397219	71397219	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1275G>A	.	.	ENST00000394264	1/1	14	8	6	31	31	0	FAM122A,3_prime_UTR_variant,,ENST00000394264,;PIP5K1B,intron_variant,,ENST00000437200,;PIP5K1B,intron_variant,,ENST00000377284,;PIP5K1B,intron_variant,,ENST00000440050,;PIP5K1B,intron_variant,,ENST00000541509,;PIP5K1B,intron_variant,,ENST00000265382,;PIP5K1B,intron_variant,,ENST00000472907,;PIP5K1B,intron_variant,,ENST00000478500,;	A	ENSG00000187866	ENST00000394264	Transcript	3_prime_UTR_variant	2256	.	.	.	.	.	.	.	1	FAM122A	HGNC	23490	protein_coding	YES	CCDS6623.1	ENSP00000377807	F122A_HUMAN	B4E242_HUMAN	UPI0000071E32	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGAGAGTCA	.	5	ESCA
GDA	0	.	GRCh37	9	74863633	74863633	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1361+379T>C	.	.	ENST00000238018	.	11	4	7	10	10	0	GDA,3_prime_UTR_variant,,ENST00000358399,;GDA,intron_variant,,ENST00000238018,;GDA,intron_variant,,ENST00000376986,;GDA,intron_variant,,ENST00000436438,;GDA,intron_variant,,ENST00000376989,;GDA,downstream_gene_variant,,ENST00000545168,;GDA,intron_variant,,ENST00000475764,;GDA,intron_variant,,ENST00000489618,;	C	ENSG00000119125	ENST00000238018	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GDA	HGNC	4212	protein_coding	YES	CCDS56576.1	ENSP00000238018	GUAD_HUMAN	Q5SZC3_HUMAN,B4DIP8_HUMAN,B3KUM3_HUMAN	UPI000015828B	.	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AATAATTGCAA	.	3	ESCA
DAPK1	0	.	GRCh37	9	90252871	90252871	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298G>A	p.Glu100Lys	p.E100K	ENST00000408954	4/26	32	12	19	43	43	0	DAPK1,missense_variant,p.Glu100Lys,ENST00000358077,;DAPK1,missense_variant,p.Glu100Lys,ENST00000491893,;DAPK1,missense_variant,p.Glu100Lys,ENST00000408954,;DAPK1,missense_variant,p.Glu100Lys,ENST00000469640,;DAPK1,missense_variant,p.Glu100Lys,ENST00000472284,;DAPK1,non_coding_transcript_exon_variant,,ENST00000496522,;DAPK1,intron_variant,,ENST00000472344,;DAPK1,missense_variant,p.Glu100Lys,ENST00000489291,;DAPK1,non_coding_transcript_exon_variant,,ENST00000469067,;DAPK1,upstream_gene_variant,,ENST00000463069,;	A	ENSG00000196730	ENST00000408954	Transcript	missense_variant	633	298	100	E/K	Gag/Aag	.	.	.	1	DAPK1	HGNC	2674	protein_coding	YES	CCDS43842.1	ENSP00000386135	DAPK1_HUMAN	.	UPI0000210C2F	.	deleterious(0)	probably_damaging(0.998)	4/26	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:3.30.200.20,Pfam_domain:PF00069,hmmpanther:PTHR22964:SF54,hmmpanther:PTHR22964,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCGAGCTG	.	5	ESCA
AMOT	0	.	GRCh37	X	112024179	112024179	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2408C>T	p.Ser803Phe	p.S803F	ENST00000371959	9/11	33	21	12	20	20	0	AMOT,missense_variant,p.Ser803Phe,ENST00000371959,;AMOT,missense_variant,p.Ser571Phe,ENST00000371962,;AMOT,missense_variant,p.Ser394Phe,ENST00000304758,;AMOT,missense_variant,p.Ser803Phe,ENST00000524145,;AMOT,missense_variant,p.Ser571Phe,ENST00000371958,;MIR4329,upstream_gene_variant,,ENST00000582643,;	A	ENSG00000126016	ENST00000371959	Transcript	missense_variant	2408	2408	803	S/F	tCc/tTc	.	.	.	-1	AMOT	HGNC	17810	protein_coding	YES	CCDS48154.1	ENSP00000361027	AMOT_HUMAN	E7ERM3_HUMAN	UPI000050ED33	.	.	unknown(0)	9/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14826,hmmpanther:PTHR14826:SF6,Pfam_domain:PF12240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTGGATGAG	.	5	ESCA
XPNPEP2	0	.	GRCh37	X	128885744	128885744	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763G>C	p.Asp255His	p.D255H	ENST00000371106	9/21	62	30	31	47	47	0	XPNPEP2,missense_variant,p.Asp255His,ENST00000371106,;XPNPEP2,downstream_gene_variant,,ENST00000371105,;	C	ENSG00000122121	ENST00000371106	Transcript	missense_variant	955	763	255	D/H	Gac/Cac	.	.	.	1	XPNPEP2	HGNC	12823	protein_coding	YES	CCDS14613.1	ENSP00000360147	XPP2_HUMAN	.	UPI000013901A	.	deleterious(0)	probably_damaging(0.999)	9/21	.	hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTGACATC	.	5	ESCA
MAGEC2	0	.	GRCh37	X	141290896	141290896	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.878C>T	p.Ser293Phe	p.S293F	ENST00000247452	3/3	59	42	17	19	19	0	MAGEC2,missense_variant,p.Ser293Phe,ENST00000247452,;	A	ENSG00000046774	ENST00000247452	Transcript	missense_variant	1226	878	293	S/F	tCt/tTt	.	.	.	-1	MAGEC2	HGNC	13574	protein_coding	YES	CCDS14678.1	ENSP00000354660	MAGC2_HUMAN	.	UPI000012F059	.	deleterious(0)	probably_damaging(0.939)	3/3	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF29,Pfam_domain:PF01454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGAGAACTG	.	5	ESCA
GLRA2	0	.	GRCh37	X	14627271	14627271	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874A>T	p.Thr292Ser	p.T292S	ENST00000218075	7/9	27	9	18	13	13	0	GLRA2,missense_variant,p.Thr203Ser,ENST00000443437,;GLRA2,missense_variant,p.Thr292Ser,ENST00000355020,;GLRA2,missense_variant,p.Thr292Ser,ENST00000218075,;GLRA2,downstream_gene_variant,,ENST00000415367,;	T	ENSG00000101958	ENST00000218075	Transcript	missense_variant	1404	874	292	T/S	Acc/Tcc	.	.	.	1	GLRA2	HGNC	4327	protein_coding	YES	CCDS14160.1	ENSP00000218075	GLRA2_HUMAN	.	UPI000012BA64	.	deleterious(0)	probably_damaging(0.917)	7/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF28,Gene3D:1.20.58.390,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR00253	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCACCACA	.	5	ESCA
MIR509-2	0	.	GRCh37	X	146340315	146340315	+	RNA	SNP	T	T	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.54A>C	.	.	ENST00000390724	1/1	126	87	38	45	45	0	MIR509-2,non_coding_transcript_exon_variant,,ENST00000390724,;MIR509-1,downstream_gene_variant,,ENST00000385265,;MIR509-3,downstream_gene_variant,,ENST00000390725,;	G	ENSG00000212013	ENST00000390724	Transcript	non_coding_transcript_exon_variant	54	.	.	.	.	.	.	.	-1	MIR509-2	HGNC	33641	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCATTTTTA	.	5	ESCA
AVPR2	0	.	GRCh37	X	153171021	153171021	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61A>G	p.Ser21Gly	p.S21G	ENST00000358927	3/4	76	71	5	24	24	0	AVPR2,missense_variant,p.Ser21Gly,ENST00000358927,;AVPR2,missense_variant,p.Ser21Gly,ENST00000337474,;AVPR2,missense_variant,p.Ser21Gly,ENST00000430697,;AVPR2,missense_variant,p.Ser21Gly,ENST00000370049,;ARHGAP4,downstream_gene_variant,,ENST00000442172,;ARHGAP4,downstream_gene_variant,,ENST00000454164,;ARHGAP4,downstream_gene_variant,,ENST00000537206,;ARHGAP4,downstream_gene_variant,,ENST00000350060,;ARHGAP4,downstream_gene_variant,,ENST00000393721,;ARHGAP4,downstream_gene_variant,,ENST00000370028,;ARHGAP4,downstream_gene_variant,,ENST00000370016,;ARHGAP4,downstream_gene_variant,,ENST00000467421,;AVPR2,intron_variant,,ENST00000434679,;L1CAM,intron_variant,,ENST00000464967,;ARHGAP4,downstream_gene_variant,,ENST00000466928,;ARHGAP4,downstream_gene_variant,,ENST00000494397,;ARHGAP4,downstream_gene_variant,,ENST00000494302,;ARHGAP4,downstream_gene_variant,,ENST00000470209,;ARHGAP4,downstream_gene_variant,,ENST00000420383,;ARHGAP4,downstream_gene_variant,,ENST00000461739,;ARHGAP4,downstream_gene_variant,,ENST00000404127,;	G	ENSG00000126895	ENST00000358927	Transcript	missense_variant	270	61	21	S/G	Agc/Ggc	.	.	.	1	AVPR2	HGNC	897	protein_coding	YES	CCDS14735.1	ENSP00000351805	V2R_HUMAN	.	UPI000005043B	.	tolerated(0.74)	benign(0)	3/4	.	Low_complexity_(Seg):seg,Prints_domain:PR00898,hmmpanther:PTHR24241:SF20,hmmpanther:PTHR24241	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCCAGCAAC	.	2	ESCA
IRAK1	0	.	GRCh37	X	153287340	153287340	+	5'Flank	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000369980	.	97	70	27	45	45	0	MECP2,3_prime_UTR_variant,,ENST00000303391,;IRAK1,upstream_gene_variant,,ENST00000369980,;IRAK1,upstream_gene_variant,,ENST00000443220,;IRAK1,upstream_gene_variant,,ENST00000429936,;IRAK1,upstream_gene_variant,,ENST00000369974,;IRAK1,upstream_gene_variant,,ENST00000444230,;IRAK1,upstream_gene_variant,,ENST00000393687,;IRAK1,upstream_gene_variant,,ENST00000393682,;IRAK1,upstream_gene_variant,,ENST00000437278,;MIR718,upstream_gene_variant,,ENST00000390190,;IRAK1,upstream_gene_variant,,ENST00000477274,;IRAK1,upstream_gene_variant,,ENST00000369973,;IRAK1,upstream_gene_variant,,ENST00000463031,;	C	ENSG00000184216	ENST00000369980	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1909	-1	IRAK1	HGNC	6112	protein_coding	YES	CCDS14740.1	ENSP00000358997	IRAK1_HUMAN	.	UPI000012D873	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTATACAGG	.	5	ESCA
FLNA	0	.	GRCh37	X	153589759	153589759	+	Nonsense_Mutation	SNP	C	C	A	rs782052055	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3124G>T	p.Glu1042Ter	p.E1042*	ENST00000369850	21/48	67	54	12	35	35	0	FLNA,stop_gained,p.Glu1042Ter,ENST00000422373,;FLNA,stop_gained,p.Glu1042Ter,ENST00000360319,;FLNA,stop_gained,p.Glu1042Ter,ENST00000344736,;FLNA,stop_gained,p.Glu1042Ter,ENST00000369850,;FLNA,upstream_gene_variant,,ENST00000369856,;FLNA,upstream_gene_variant,,ENST00000466319,;FLNA,3_prime_UTR_variant,,ENST00000420627,;FLNA,upstream_gene_variant,,ENST00000490936,;FLNA,downstream_gene_variant,,ENST00000465144,;	A	ENSG00000196924	ENST00000369850	Transcript	stop_gained	3361	3124	1042	E/*	Gag/Tag	rs782052055	.	.	-1	FLNA	HGNC	3754	protein_coding	YES	CCDS48194.1	ENSP00000358866	FLNA_HUMAN	Q96C61_HUMAN,Q86TQ3_HUMAN,Q6NXF2_HUMAN,Q60FE5_HUMAN	UPI000013C596	.	.	.	21/48	.	PROSITE_profiles:PS50194,hmmpanther:PTHR11915:SF173,hmmpanther:PTHR11915,Pfam_domain:PF00630,Gene3D:2.60.40.10,SMART_domains:SM00557,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCATAGG	.	5	ESCA
PIR	0	.	GRCh37	X	15403203	15403203	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.796C>G	p.Gln266Glu	p.Q266E	ENST00000380421	10/10	21	4	16	14	14	0	PIR,missense_variant,p.Gln266Glu,ENST00000380421,;PIR,missense_variant,p.Gln266Glu,ENST00000380420,;FIGF,upstream_gene_variant,,ENST00000297904,;PIR,non_coding_transcript_exon_variant,,ENST00000492432,;PIR,downstream_gene_variant,,ENST00000484433,;	C	ENSG00000087842	ENST00000380421	Transcript	missense_variant	1257	796	266	Q/E	Caa/Gaa	.	.	.	-1	PIR	HGNC	30048	protein_coding	YES	CCDS14167.1	ENSP00000369786	PIR_HUMAN	.	UPI0000049C30	.	tolerated(0.11)	benign(0.002)	10/10	.	hmmpanther:PTHR13903:SF8,hmmpanther:PTHR13903,Pfam_domain:PF05726,PIRSF_domain:PIRSF006232,Superfamily_domains:SSF51182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTGAGAAA	.	5	ESCA
MAP7D2	0	.	GRCh37	X	20030483	20030483	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2056C>T	p.Gln686Ter	p.Q686*	ENST00000379643	15/17	21	6	14	27	27	0	MAP7D2,stop_gained,p.Gln686Ter,ENST00000379643,;MAP7D2,stop_gained,p.Gln600Ter,ENST00000443379,;MAP7D2,stop_gained,p.Gln530Ter,ENST00000543767,;MAP7D2,stop_gained,p.Gln593Ter,ENST00000452324,;MAP7D2,stop_gained,p.Gln645Ter,ENST00000379651,;MIR23C,downstream_gene_variant,,ENST00000579846,;MAP7D2,intron_variant,,ENST00000485173,;	A	ENSG00000184368	ENST00000379643	Transcript	stop_gained	2094	2056	686	Q/*	Cag/Tag	.	.	.	-1	MAP7D2	HGNC	25899	protein_coding	YES	CCDS55386.1	ENSP00000368964	MA7D2_HUMAN	.	UPI00015E039B	.	.	.	15/17	.	hmmpanther:PTHR15073:SF3,hmmpanther:PTHR15073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTGAACTT	.	5	ESCA
ZC3H12B	0	.	GRCh37	X	64722232	64722232	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1654T>C	p.Phe552Leu	p.F552L	ENST00000338957	5/5	25	5	20	17	17	0	ZC3H12B,missense_variant,p.Phe541Leu,ENST00000423889,;ZC3H12B,missense_variant,p.Phe552Leu,ENST00000338957,;	C	ENSG00000102053	ENST00000338957	Transcript	missense_variant	1721	1654	552	F/L	Ttc/Ctc	.	.	.	1	ZC3H12B	HGNC	17407	protein_coding	YES	CCDS48131.2	ENSP00000340839	.	E9PAJ6_HUMAN	UPI00001D7BEA	.	deleterious(0)	benign(0.033)	5/5	.	hmmpanther:PTHR12876:SF27,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGACTTCTCC	.	5	ESCA
AWAT2	0	.	GRCh37	X	69263824	69263824	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.219G>C	p.%3D	p.V73V	ENST00000276101	3/8	40	14	25	30	30	0	AWAT2,synonymous_variant,p.%3D,ENST00000276101,;EDA,downstream_gene_variant,,ENST00000374553,;EDA,downstream_gene_variant,,ENST00000374552,;AWAT2,non_coding_transcript_exon_variant,,ENST00000443056,;AWAT2,upstream_gene_variant,,ENST00000440401,;	G	ENSG00000147160	ENST00000276101	Transcript	synonymous_variant	225	219	73	V	gtG/gtC	.	.	.	-1	AWAT2	HGNC	23251	protein_coding	YES	CCDS35320.1	ENSP00000421172	AWAT2_HUMAN	.	UPI00001D7BE0	.	.	.	3/8	.	hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF12,Pfam_domain:PF03982	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R77H|c.230G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCACACA	.	5	ESCA
DLG3	0	.	GRCh37	X	69723646	69723646	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1527C>T	.	.	ENST00000374360	19/19	13	5	8	13	13	0	DLG3,3_prime_UTR_variant,,ENST00000542398,;DLG3,3_prime_UTR_variant,,ENST00000374355,;DLG3,3_prime_UTR_variant,,ENST00000194900,;DLG3,3_prime_UTR_variant,,ENST00000374360,;DLG3,downstream_gene_variant,,ENST00000466140,;DLG3,downstream_gene_variant,,ENST00000461646,;DLG3,non_coding_transcript_exon_variant,,ENST00000463252,;DLG3,downstream_gene_variant,,ENST00000496931,;	T	ENSG00000082458	ENST00000374360	Transcript	3_prime_UTR_variant	4214	.	.	.	.	.	.	.	1	DLG3	HGNC	2902	protein_coding	YES	CCDS14403.1	ENSP00000363480	DLG3_HUMAN	Q59FY1_HUMAN	UPI000013C60C	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GGAATCTTCAC	.	4	ESCA
TEX11	0	.	GRCh37	X	69871378	69871378	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1450G>A	p.Glu484Lys	p.E484K	ENST00000395889	18/31	38	13	25	22	22	0	TEX11,missense_variant,p.Glu159Lys,ENST00000374320,;TEX11,missense_variant,p.Glu469Lys,ENST00000374333,;TEX11,missense_variant,p.Glu484Lys,ENST00000395889,;TEX11,missense_variant,p.Glu484Lys,ENST00000344304,;	T	ENSG00000120498	ENST00000395889	Transcript	missense_variant	1606	1450	484	E/K	Gaa/Aaa	.	.	.	-1	TEX11	HGNC	11733	protein_coding	YES	CCDS35323.1	ENSP00000379226	TEX11_HUMAN	.	UPI000013CA89	.	deleterious(0.03)	possibly_damaging(0.874)	18/31	.	hmmpanther:PTHR22904:SF291,hmmpanther:PTHR22904,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTTCAGCTT	.	5	ESCA
RPS6KA6	0	.	GRCh37	X	83361419	83361419	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49M-01A-21D-A27G-09	TCGA-LN-A49M-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1319G>T	p.Cys440Phe	p.C440F	ENST00000262752	15/22	36	19	16	18	18	0	RPS6KA6,missense_variant,p.Cys440Phe,ENST00000262752,;RPS6KA6,missense_variant,p.Cys440Phe,ENST00000543399,;RPS6KA6,non_coding_transcript_exon_variant,,ENST00000495332,;	A	ENSG00000072133	ENST00000262752	Transcript	missense_variant	1327	1319	440	C/F	tGc/tTc	.	.	.	-1	RPS6KA6	HGNC	10435	protein_coding	YES	CCDS14451.1	ENSP00000262752	KS6A6_HUMAN	.	UPI0000035B52	.	deleterious(0)	probably_damaging(1)	15/22	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,PIRSF_domain:PIRSF000606,Pfam_domain:PF00069,PROSITE_patterns:PS00107,hmmpanther:PTHR24351:SF49,hmmpanther:PTHR24351,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTGCAAACA	.	5	ESCA
TTC40	0	.	GRCh37	10	134755135	134755135	+	Missense_Mutation	SNP	C	C	A	rs769027201	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.266G>T	p.Cys89Phe	p.C89F	ENST00000368586	3/58	30	23	7	35	35	0	TTC40,missense_variant,p.Cys89Phe,ENST00000368582,;TTC40,missense_variant,p.Cys89Phe,ENST00000368585,;TTC40,missense_variant,p.Cys89Phe,ENST00000368586,;LINC01166,downstream_gene_variant,,ENST00000443633,;TTC40,non_coding_transcript_exon_variant,,ENST00000475340,;	A	ENSG00000171811	ENST00000368586	Transcript	missense_variant	367	266	89	C/F	tGc/tTc	rs769027201	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	deleterious(0)	probably_damaging(1)	3/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTGCACAGG	.	5	ESCA
C10orf105	0	.	GRCh37	10	73497503	73497503	+	5'UTR	SNP	T	T	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-24A>C	.	.	ENST00000398786	1/2	115	83	32	103	102	0	C10orf105,5_prime_UTR_variant,,ENST00000398786,;CDH23,intron_variant,,ENST00000224721,;CDH23,intron_variant,,ENST00000398792,;	G	ENSG00000214688	ENST00000398786	Transcript	5_prime_UTR_variant	79	.	.	.	.	.	.	.	-1	C10orf105	HGNC	20304	protein_coding	.	CCDS44430.1	ENSP00000381766	CJ105_HUMAN	B1AVV1_HUMAN	UPI00001F8E63	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCAGTGGCCT	.	5	ESCA
KAT6B	0	.	GRCh37	10	76792088	76792088	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1284A>G	.	.	ENST00000287239	18/18	23	18	5	21	21	0	KAT6B,3_prime_UTR_variant,,ENST00000372711,;KAT6B,3_prime_UTR_variant,,ENST00000287239,;KAT6B,downstream_gene_variant,,ENST00000372714,;KAT6B,downstream_gene_variant,,ENST00000372725,;KAT6B,downstream_gene_variant,,ENST00000372724,;	G	ENSG00000156650	ENST00000287239	Transcript	3_prime_UTR_variant	7995	.	.	.	.	.	.	.	1	KAT6B	HGNC	17582	protein_coding	YES	CCDS7345.1	ENSP00000287239	KAT6B_HUMAN	.	UPI000013DEA0	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAATGACC	.	5	ESCA
BLNK	0	.	GRCh37	10	97967644	97967644	+	Missense_Mutation	SNP	G	G	A	rs782667010	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758C>T	p.Thr253Met	p.T253M	ENST00000224337	10/17	31	28	3	31	31	0	BLNK,missense_variant,p.Thr253Met,ENST00000427367,;BLNK,missense_variant,p.Thr253Met,ENST00000224337,;BLNK,missense_variant,p.Thr230Met,ENST00000371176,;BLNK,missense_variant,p.Thr253Met,ENST00000413476,;ZNF518A,downstream_gene_variant,,ENST00000442635,;ZNF518A,downstream_gene_variant,,ENST00000563195,;BLNK,3_prime_UTR_variant,,ENST00000467799,;BLNK,non_coding_transcript_exon_variant,,ENST00000468252,;BLNK,upstream_gene_variant,,ENST00000485193,;	A	ENSG00000095585	ENST00000224337	Transcript	missense_variant	900	758	253	T/M	aCg/aTg	rs782667010	.	.	-1	BLNK	HGNC	14211	protein_coding	YES	CCDS7446.1	ENSP00000224337	BLNK_HUMAN	Q2MD56_HUMAN	UPI000006FDD6	.	tolerated(0.08)	benign(0.004)	10/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14098:SF3,hmmpanther:PTHR14098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTCGTTGGT	byFrequency	4	ESCA
ATM	0	.	GRCh37	11	108203581	108203581	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7881T>C	p.%3D	p.Y2627Y	ENST00000278616	53/63	32	22	9	29	29	0	ATM,synonymous_variant,p.%3D,ENST00000452508,;ATM,synonymous_variant,p.%3D,ENST00000278616,;C11orf65,intron_variant,,ENST00000524755,;C11orf65,intron_variant,,ENST00000525729,;ATM,non_coding_transcript_exon_variant,,ENST00000533979,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000525056,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;C11orf65,intron_variant,,ENST00000527531,;ATM,downstream_gene_variant,,ENST00000527389,;ATM,downstream_gene_variant,,ENST00000525537,;	C	ENSG00000149311	ENST00000278616	Transcript	synonymous_variant	8266	7881	2627	Y	taT/taC	.	.	.	1	ATM	HGNC	795	protein_coding	YES	CCDS31669.1	ENSP00000278616	ATM_HUMAN	M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN	UPI0000DBEF44	.	.	.	53/63	.	Superfamily_domains:SSF56112,Gene3D:3.30.1010.10,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTATATTAT	.	5	ESCA
LRRC32	0	.	GRCh37	11	76370908	76370908	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1729G>A	p.Gly577Ser	p.G577S	ENST00000407242	3/3	58	40	17	34	34	0	LRRC32,missense_variant,p.Gly577Ser,ENST00000260061,;LRRC32,missense_variant,p.Gly577Ser,ENST00000407242,;LRRC32,missense_variant,p.Gly577Ser,ENST00000404995,;LRRC32,downstream_gene_variant,,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,;	T	ENSG00000137507	ENST00000407242	Transcript	missense_variant	1972	1729	577	G/S	Ggc/Agc	COSM932089	.	.	-1	LRRC32	HGNC	4161	protein_coding	YES	CCDS8245.1	ENSP00000384126	LRC32_HUMAN	C9JYU3_HUMAN	UPI000012B0DF	.	tolerated(0.19)	benign(0.115)	3/3	.	SMART_domains:SM00368,Gene3D:3.80.10.10,hmmpanther:PTHR24365:SF237,hmmpanther:PTHR24365,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGCCGCAGC	.	5	ESCA
LRP6	0	.	GRCh37	12	12311822	12311822	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2732delG	p.Gly911ValfsTer38	p.G911Vfs*38	ENST00000261349	12/23	51	38	13	27	27	0	LRP6,frameshift_variant,p.Gly911ValfsTer38,ENST00000543091,;LRP6,frameshift_variant,p.Gly911ValfsTer38,ENST00000261349,;LRP6,frameshift_variant,p.Gly776ValfsTer38,ENST00000538239,;BCL2L14,intron_variant,,ENST00000298566,;RP11-267J23.1,downstream_gene_variant,,ENST00000472093,;	-	ENSG00000070018	ENST00000261349	Transcript	frameshift_variant	2809	2732	911	G/X	gGt/gt	.	.	.	-1	LRP6	HGNC	6698	protein_coding	YES	CCDS8647.1	ENSP00000261349	LRP6_HUMAN	F5H0Z3_HUMAN,B3KQA9_HUMAN	UPI00001FB66C	.	.	.	12/23	.	Superfamily_domains:SSF57196,SMART_domains:SM00181,PIRSF_domain:PIRSF036314,Pfam_domain:PF14670,Gene3D:2.10.25.10,hmmpanther:PTHR10529:SF109,hmmpanther:PTHR10529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAAAACCCCCA	.	3	ESCA
ERP27	0	.	GRCh37	12	15070212	15070224	+	Frame_Shift_Del	DEL	ACGCTGTTGAATA	ACGCTGTTGAATA	-	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	ACGCTGTTGAATA	ACGCTGTTGAATA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464_476delTATTCAACAGCGT	p.Leu155Ter	p.L155*	ENST00000266397	5/7	65	55	10	73	73	0	ERP27,frameshift_variant,p.Leu155Ter,ENST00000266397,;ERP27,frameshift_variant,p.Leu54Ter,ENST00000540097,;ERP27,non_coding_transcript_exon_variant,,ENST00000544881,;	-	ENSG00000139055	ENST00000266397	Transcript	frameshift_variant	1038-1050	464-476	155-159	LFNSV/X	tTATTCAACAGCGTa/ta	.	.	.	-1	ERP27	HGNC	26495	protein_coding	YES	CCDS8670.1	ENSP00000266397	ERP27_HUMAN	.	UPI0000037A99	.	.	.	5/7	.	hmmpanther:PTHR18929:SF77,hmmpanther:PTHR18929,Pfam_domain:PF13848,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGAATTACGCTGTTGAATAACCCA	.	3	ESCA
STRAP	0	.	GRCh37	12	16043540	16043540	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340T>G	p.Tyr114Asp	p.Y114D	ENST00000419869	4/10	45	34	11	49	49	0	STRAP,missense_variant,p.Tyr127Asp,ENST00000025399,;STRAP,missense_variant,p.Tyr114Asp,ENST00000419869,;STRAP,missense_variant,p.Tyr20Asp,ENST00000538352,;STRAP,3_prime_UTR_variant,,ENST00000541731,;STRAP,upstream_gene_variant,,ENST00000536737,;	G	ENSG00000023734	ENST00000419869	Transcript	missense_variant	653	340	114	Y/D	Tat/Gat	.	.	.	1	STRAP	HGNC	30796	protein_coding	YES	CCDS8676.1	ENSP00000392270	STRAP_HUMAN	B0AZV0_HUMAN	UPI0000137C97	.	tolerated(0.19)	benign(0.173)	4/10	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR19877,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAATTATTTG	.	5	ESCA
ANO6	0	.	GRCh37	12	45695847	45695847	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.184A>T	p.Ser62Cys	p.S62C	ENST00000423947	3/21	65	51	14	60	60	0	ANO6,missense_variant,p.Ser23Cys,ENST00000441606,;ANO6,missense_variant,p.Ser41Cys,ENST00000320560,;ANO6,missense_variant,p.Ser62Cys,ENST00000423947,;ANO6,missense_variant,p.Ser41Cys,ENST00000435642,;ANO6,missense_variant,p.Ser41Cys,ENST00000425752,;ANO6,intron_variant,,ENST00000426898,;ANO6,3_prime_UTR_variant,,ENST00000550630,;	T	ENSG00000177119	ENST00000423947	Transcript	missense_variant	421	184	62	S/C	Agt/Tgt	.	.	.	1	ANO6	HGNC	25240	protein_coding	YES	CCDS55819.1	ENSP00000409126	ANO6_HUMAN	.	UPI000022935A	.	deleterious(0.02)	benign(0.302)	3/21	.	hmmpanther:PTHR12308:SF21,hmmpanther:PTHR12308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAAAGTCAG	.	5	ESCA
DDX23	0	.	GRCh37	12	49229911	49229911	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1375A>G	p.Ile459Val	p.I459V	ENST00000308025	11/17	19	12	7	33	33	0	DDX23,missense_variant,p.Ile459Val,ENST00000308025,;DDX23,intron_variant,,ENST00000550834,;DDX23,downstream_gene_variant,,ENST00000552512,;DDX23,downstream_gene_variant,,ENST00000551468,;DDX23,downstream_gene_variant,,ENST00000552369,;DDX23,downstream_gene_variant,,ENST00000553182,;DDX23,downstream_gene_variant,,ENST00000552555,;DDX23,missense_variant,p.Ile85Val,ENST00000552802,;DDX23,3_prime_UTR_variant,,ENST00000547135,;DDX23,upstream_gene_variant,,ENST00000551331,;DDX23,downstream_gene_variant,,ENST00000551098,;DDX23,downstream_gene_variant,,ENST00000551189,;DDX23,upstream_gene_variant,,ENST00000547842,;DDX23,downstream_gene_variant,,ENST00000552069,;DDX23,upstream_gene_variant,,ENST00000547290,;DDX23,downstream_gene_variant,,ENST00000547165,;DDX23,upstream_gene_variant,,ENST00000553065,;DDX23,upstream_gene_variant,,ENST00000549795,;	C	ENSG00000174243	ENST00000308025	Transcript	missense_variant	1455	1375	459	I/V	Att/Gtt	.	.	.	-1	DDX23	HGNC	17347	protein_coding	YES	CCDS8770.1	ENSP00000310723	DDX23_HUMAN	F8W1J5_HUMAN,F8VVA2_HUMAN,B3KY11_HUMAN	UPI0000073875	.	deleterious(0.02)	benign(0.309)	11/17	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF23,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAATTTTGG	.	5	ESCA
OR4Q3	0	.	GRCh37	14	20215877	20215877	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291A>G	p.%3D	p.G97G	ENST00000331723	1/1	132	120	12	142	142	0	OR4Q3,synonymous_variant,p.%3D,ENST00000331723,;OR4N2,intron_variant,,ENST00000557414,;OR11K2P,intron_variant,,ENST00000593630,;	G	ENSG00000182652	ENST00000331723	Transcript	synonymous_variant	291	291	97	G	ggA/ggG	.	.	.	1	OR4Q3	HGNC	15426	protein_coding	YES	CCDS32020.1	ENSP00000330049	OR4Q3_HUMAN	.	UPI0000061EF0	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF208,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAGGATGCCT	.	3	ESCA
RFX7	0	.	GRCh37	15	56435084	56435085	+	Frame_Shift_Ins	INS	-	-	TG	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291_292dupCA	p.Met98ThrfsTer20	p.M98Tfs*20	ENST00000423270	4/9	54	40	14	40	40	0	RFX7,frameshift_variant,p.Met1?,ENST00000560792,;RFX7,frameshift_variant,p.Met98ThrfsTer20,ENST00000423270,;RFX7,frameshift_variant,p.Met1?,ENST00000559447,;RFX7,frameshift_variant,p.Met98ThrfsTer20,ENST00000317318,;RFX7,frameshift_variant,p.Met1?,ENST00000422057,;RFX7,frameshift_variant,p.Met1?,ENST00000559847,;	TG	ENSG00000181827	ENST00000423270	Transcript	frameshift_variant	292-293	292-293	98	M/TX	atg/aCAtg	.	.	.	-1	RFX7	HGNC	25777	protein_coding	YES	.	ENSP00000397644	RFX7_HUMAN	H0YMH6_HUMAN,H0YLP2_HUMAN	UPI000057809D	.	.	.	4/9	.	hmmpanther:PTHR12619:SF2,hmmpanther:PTHR12619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGACATGGCA	.	3	ESCA
PML	0	.	GRCh37	15	74336717	74336717	+	Missense_Mutation	SNP	A	A	G	rs367820386	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2017A>G	p.Ile673Val	p.I673V	ENST00000268058	9/9	29	22	7	19	19	0	PML,missense_variant,p.Ile673Val,ENST00000268058,;PML,missense_variant,p.Ile625Val,ENST00000565898,;PML,downstream_gene_variant,,ENST00000569965,;PML,downstream_gene_variant,,ENST00000395135,;PML,downstream_gene_variant,,ENST00000359928,;PML,downstream_gene_variant,,ENST00000564428,;PML,downstream_gene_variant,,ENST00000565317,;	G	ENSG00000140464	ENST00000268058	Transcript	missense_variant	2113	2017	673	I/V	Atc/Gtc	rs367820386	.	.	1	PML	HGNC	9113	protein_coding	YES	CCDS10255.1	ENSP00000268058	PML_HUMAN	Q9UE85_HUMAN,Q05835_HUMAN	UPI000013D78F	.	tolerated(0.3)	benign(0.015)	9/9	.	.	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTATCTTG	byFrequency|byCluster	5	ESCA
KIAA1024	0	.	GRCh37	15	79750680	79750680	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2191A>T	p.Arg731Ter	p.R731*	ENST00000305428	2/4	36	27	9	24	24	0	KIAA1024,stop_gained,p.Arg731Ter,ENST00000305428,;KIAA1024,stop_gained,p.Arg731Ter,ENST00000559272,;	T	ENSG00000169330	ENST00000305428	Transcript	stop_gained	2266	2191	731	R/*	Aga/Tga	.	.	.	1	KIAA1024	HGNC	29172	protein_coding	YES	CCDS32306.1	ENSP00000307461	K1024_HUMAN	.	UPI00001B2F56	.	.	.	2/4	.	hmmpanther:PTHR31530,hmmpanther:PTHR31530:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCCAGAGAC	.	5	ESCA
FANCI	0	.	GRCh37	15	89804864	89804864	+	Missense_Mutation	SNP	A	A	G	rs766158703	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337A>G	p.Ile113Val	p.I113V	ENST00000310775	5/38	33	26	7	32	32	0	FANCI,missense_variant,p.Ile113Val,ENST00000563250,;FANCI,missense_variant,p.Ile113Val,ENST00000564920,;FANCI,missense_variant,p.Ile113Val,ENST00000310775,;FANCI,missense_variant,p.Ile113Val,ENST00000300027,;FANCI,missense_variant,p.Ile113Val,ENST00000567891,;FANCI,missense_variant,p.Ile113Val,ENST00000565255,;FANCI,missense_variant,p.Ile113Val,ENST00000567996,;FANCI,5_prime_UTR_variant,,ENST00000451393,;FANCI,upstream_gene_variant,,ENST00000561894,;FANCI,upstream_gene_variant,,ENST00000570225,;FANCI,intron_variant,,ENST00000565522,;FANCI,downstream_gene_variant,,ENST00000568670,;FANCI,missense_variant,p.Ile113Val,ENST00000447611,;FANCI,downstream_gene_variant,,ENST00000564636,;FANCI,downstream_gene_variant,,ENST00000570110,;	G	ENSG00000140525	ENST00000310775	Transcript	missense_variant	423	337	113	I/V	Att/Gtt	rs766158703	.	.	1	FANCI	HGNC	25568	protein_coding	YES	CCDS45346.1	ENSP00000310842	FANCI_HUMAN	H3BT54_HUMAN,H3BS60_HUMAN,H3BQE2_HUMAN	UPI00001FEB1D	.	tolerated(1)	benign(0.002)	5/38	.	hmmpanther:PTHR21818,hmmpanther:PTHR21818:SF0,Pfam_domain:PF14675	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTATTAGT	.	5	ESCA
FTO	0	.	GRCh37	16	53860093	53860093	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441G>T	p.Gln147His	p.Q147H	ENST00000471389	3/9	25	15	10	26	26	0	FTO,missense_variant,p.Gln147His,ENST00000471389,;FTO,intron_variant,,ENST00000394647,;FTO,downstream_gene_variant,,ENST00000570395,;FTO,intron_variant,,ENST00000464071,;	T	ENSG00000140718	ENST00000471389	Transcript	missense_variant	663	441	147	Q/H	caG/caT	.	.	.	1	FTO	HGNC	24678	protein_coding	YES	CCDS32448.1	ENSP00000418823	FTO_HUMAN	B4DHN4_HUMAN	UPI000013D7B3	.	tolerated(0.63)	possibly_damaging(0.766)	3/9	.	hmmpanther:PTHR31291,hmmpanther:PTHR31291:SF2,Pfam_domain:PF12933	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGATAGA	.	5	ESCA
IRX6	0	.	GRCh37	16	55361662	55361662	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578T>A	p.Val193Glu	p.V193E	ENST00000290552	4/6	55	44	11	57	57	0	IRX6,missense_variant,p.Val193Glu,ENST00000290552,;RP11-26L20.4,upstream_gene_variant,,ENST00000573934,;RP11-26L20.3,intron_variant,,ENST00000558730,;IRX6,non_coding_transcript_exon_variant,,ENST00000558315,;	A	ENSG00000159387	ENST00000290552	Transcript	missense_variant	1910	578	193	V/E	gTg/gAg	.	.	.	1	IRX6	HGNC	14675	protein_coding	YES	CCDS32449.1	ENSP00000290552	IRX6_HUMAN	Q9BZI2_HUMAN	UPI00001C0A88	.	deleterious(0)	probably_damaging(1)	4/6	.	PROSITE_profiles:PS50071,hmmpanther:PTHR11211:SF11,hmmpanther:PTHR11211,PROSITE_patterns:PS00027,Gene3D:1.10.10.60,Pfam_domain:PF05920,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGTGTCCA	.	5	ESCA
WDR24	0	.	GRCh37	16	740386	740386	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-746G>A	.	.	ENST00000293883	1/9	52	39	12	64	64	0	WDR24,missense_variant,p.Arg20Gln,ENST00000248142,;WDR24,5_prime_UTR_variant,,ENST00000293883,;FBXL16,downstream_gene_variant,,ENST00000324361,;FBXL16,downstream_gene_variant,,ENST00000397621,;FBXL16,downstream_gene_variant,,ENST00000562563,;LA16c-313D11.12,intron_variant,,ENST00000566927,;FBXL16,downstream_gene_variant,,ENST00000562585,;LA16c-313D11.12,non_coding_transcript_exon_variant,,ENST00000575305,;WDR24,upstream_gene_variant,,ENST00000567014,;FBXL16,downstream_gene_variant,,ENST00000562648,;	T	ENSG00000127580	ENST00000293883	Transcript	5_prime_UTR_variant	15	.	.	.	.	.	.	.	-1	WDR24	HGNC	20852	protein_coding	YES	CCDS10420.1	ENSP00000293883	WDR24_HUMAN	.	UPI0000037D32	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGCCGCGCC	.	5	ESCA
CDC27	0	.	GRCh37	17	45235625	45235625	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.422G>C	p.Ser141Thr	p.S141T	ENST00000531206	5/19	28	18	10	10	10	0	CDC27,missense_variant,p.Ser141Thr,ENST00000531206,;CDC27,missense_variant,p.Ser141Thr,ENST00000066544,;CDC27,missense_variant,p.Ser141Thr,ENST00000527547,;CDC27,missense_variant,p.Ser141Thr,ENST00000575483,;CDC27,missense_variant,p.Ser80Thr,ENST00000446365,;RP5-867C24.4,downstream_gene_variant,,ENST00000574021,;CDC27,non_coding_transcript_exon_variant,,ENST00000528748,;CDC27,non_coding_transcript_exon_variant,,ENST00000532575,;CDC27,upstream_gene_variant,,ENST00000575830,;CDC27,missense_variant,p.Ala92Pro,ENST00000533415,;CDC27,missense_variant,p.Ala73Pro,ENST00000573550,;CDC27,missense_variant,p.Ser141Thr,ENST00000526866,;CDC27,missense_variant,p.Ser36Thr,ENST00000574304,;CDC27,missense_variant,p.Ala50Pro,ENST00000532893,;CDC27,non_coding_transcript_exon_variant,,ENST00000525495,;CDC27,intron_variant,,ENST00000570818,;CDC27,upstream_gene_variant,,ENST00000576484,;RP5-867C24.1,downstream_gene_variant,,ENST00000488906,;	G	ENSG00000004897	ENST00000531206	Transcript	missense_variant	426	422	141	S/T	aGc/aCc	.	.	.	-1	CDC27	HGNC	1728	protein_coding	YES	CCDS45720.1	ENSP00000434614	CDC27_HUMAN	I0EZ72_HUMAN,I0EZ68_HUMAN	UPI0000E59FE6	.	deleterious(0.02)	possibly_damaging(0.574)	5/19	.	Superfamily_domains:SSF48452,SMART_domains:SM00028,Pfam_domain:PF00515,Gene3D:1.25.40.120,hmmpanther:PTHR12558,hmmpanther:PTHR12558:SF11,PROSITE_profiles:PS50293,PROSITE_profiles:PS50005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L144*|c.431T>G|3,BUFFER|p.L144*|c.431T>G|3,BUFFER|p.S143R|c.427A>C|3,BUFFER|p.S143R|c.427A>C|3,BUFFER|p.Y138D|c.412T>G|3,BUFFER|p.Y138D|c.412T>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGGCTCTTT	.	5	ESCA
NLRP1	0	.	GRCh37	17	5462637	5462637	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1379C>A	p.Thr460Asn	p.T460N	ENST00000572272	4/17	35	26	8	35	35	0	NLRP1,missense_variant,p.Thr460Asn,ENST00000572272,;NLRP1,missense_variant,p.Thr460Asn,ENST00000345221,;NLRP1,missense_variant,p.Thr460Asn,ENST00000269280,;NLRP1,missense_variant,p.Thr460Asn,ENST00000354411,;NLRP1,missense_variant,p.Thr460Asn,ENST00000577119,;NLRP1,missense_variant,p.Thr460Asn,ENST00000262467,;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,missense_variant,p.Thr460Asn,ENST00000544378,;NLRP1,missense_variant,p.Thr460Asn,ENST00000571451,;	T	ENSG00000091592	ENST00000572272	Transcript	missense_variant	1379	1379	460	T/N	aCc/aAc	.	.	.	-1	NLRP1	HGNC	14374	protein_coding	YES	CCDS42246.1	ENSP00000460475	NALP1_HUMAN	I3L2G5_HUMAN,I3L0S2_HUMAN	UPI0000038309	.	deleterious(0.02)	probably_damaging(0.997)	4/17	.	PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF13,Gene3D:3.40.50.300,Pfam_domain:PF05729,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGGTCCGA	.	5	ESCA
UNC13D	0	.	GRCh37	17	73827330	73827330	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2547C>T	p.%3D	p.A849A	ENST00000207549	26/32	42	24	17	33	33	0	UNC13D,synonymous_variant,p.%3D,ENST00000207549,;UNC13D,synonymous_variant,p.%3D,ENST00000412096,;UNC13D,downstream_gene_variant,,ENST00000586147,;UNC13D,upstream_gene_variant,,ENST00000589670,;UNC13D,downstream_gene_variant,,ENST00000586930,;UNC13D,downstream_gene_variant,,ENST00000591616,;UNC13D,upstream_gene_variant,,ENST00000590856,;UNC13D,upstream_gene_variant,,ENST00000586519,;UNC13D,downstream_gene_variant,,ENST00000587105,;UNC13D,downstream_gene_variant,,ENST00000591563,;	A	ENSG00000092929	ENST00000207549	Transcript	synonymous_variant	2927	2547	849	A	gcC/gcT	.	.	.	-1	UNC13D	HGNC	23147	protein_coding	YES	CCDS11730.1	ENSP00000207549	UN13D_HUMAN	K7EIH3_HUMAN	UPI000015FC91	.	.	.	26/32	.	Pfam_domain:PF10540,hmmpanther:PTHR15015:SF20,hmmpanther:PTHR15015,PROSITE_profiles:PS51259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGGGCAAT	.	5	ESCA
TP53	0	.	GRCh37	17	7577527	7577528	+	Frame_Shift_Del	DEL	GG	GG	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	GG	GG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753_754delCCinsA	p.Leu252SerfsTer93	p.L252Sfs*93	ENST00000269305	7/11	70	44	26	55	55	0	TP53,frameshift_variant,p.Leu252SerfsTer17,ENST00000413465,;TP53,frameshift_variant,p.Leu252SerfsTer99,ENST00000420246,;TP53,frameshift_variant,p.Leu252SerfsTer93,ENST00000269305,;TP53,frameshift_variant,p.Leu120SerfsTer?,ENST00000509690,;TP53,frameshift_variant,p.Leu252SerfsTer100,ENST00000359597,;TP53,frameshift_variant,p.Leu252SerfsTer93,ENST00000445888,;TP53,frameshift_variant,p.Leu252SerfsTer91,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	943-944	753-754	251-252	IL/IX	atCCtc/atAtc	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.L252_I254delLTI|c.754_762delCTCACCATC|4,CODON|p.L252_I254delLTI|c.751_759delATCCTCACC|4,CODON|p.L252delL|c.754_756delCTC|4,CODON|p.L252delL|c.754_756delCTC|9,CODON|p.L252delL|c.754_756delCTC|4,CODON|p.T253P|c.757A>C|3,CODON|p.T253S|c.757A>T|5,CODON|p.T253A|c.757A>G|3,CODON|p.L252fs*93|c.754delC|5,CODON|p.L252P|c.755T>C|10,CODON|p.L252P|c.755T>C|3,CODON|p.L252P|c.755T>C|3,CODON|p.L252F|c.754C>T|10,CODON|p.I251I|c.753C>A|3,BUFFER|p.T256fs*89|c.766delA|3,BUFFER|p.T256A|c.766A>G|3,BUFFER|p.I255delI|c.763_765delATC|8,BUFFER|p.I255S|c.764T>G|4,BUFFER|p.I255S|c.764T>G|5,BUFFER|p.I255T|c.764T>C|7,BUFFER|p.I255N|c.764T>A|9,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255S|c.764T>G|5,BUFFER|p.I255S|c.764T>G|10,BUFFER|p.I255delI|c.760_762delATC|3,BUFFER|p.I255fs*90|c.762delC|3,BUFFER|p.I255fs*9|c.762_763insN|3,BUFFER|p.I255V|c.763A>G|3,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|25,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254S|c.761T>G|9,BUFFER|p.I254N|c.761T>A|4,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254T|c.761T>C|3,BUFFER|p.I254F|c.760A>T|7,BUFFER|p.I254V|c.760A>G|6,BUFFER|p.I254fs*10|c.759_760insN|4,BUFFER|p.T253I|c.758C>T|4,BUFFER|p.T253N|c.758C>A|3,BUFFER|p.I251N|c.752T>A|9,BUFFER|p.I251T|c.752T>C|6,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251S|c.752T>G|12,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251fs*94|c.751delA|6,BUFFER|p.I251L|c.751A>C|3,BUFFER|p.I251F|c.751A>T|8,BUFFER|p.P250P|c.750C>T|4,BUFFER|p.P250F|c.748_749CC>TT|3,BUFFER|p.I251fs*94|c.748delC|4,BUFFER|p.P250L|c.749C>T|49,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250L|c.749C>T|8,BUFFER|p.P250L|c.749C>T|6,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250S|c.748C>T|12,BUFFER|p.R249fs*96|c.746delG|4,BUFFER|p.R249S|c.747G>T|31,BUFFER|p.R249S|c.747G>C|22,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|15,BUFFER|p.R249R|c.747G>A|6,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|314,BUFFER|p.R249S|c.747G>T|30,BUFFER|p.R249T|c.746G>C|3,BUFFER|p.R249M|c.746G>T|8,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249K|c.746G>A|17,BUFFER|p.R249M|c.746G>T|4,BUFFER|p.R249T|c.746G>C|20,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249M|c.746G>T|35,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R248Q|c.743_744GG>AA|5,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248R|c.744G>A|5,BUFFER|p.R248W|c.741_742CC>TT|15,BUFFER|p.R248Q|c.743G>A|113,BUFFER|p.R248Q|c.743G>A|633,BUFFER|p.R248L|c.743G>T|7,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|64,BUFFER|p.R155L|c.464G>T|12,BUFFER|p.R155P|c.464G>C|5,BUFFER|p.R248P|c.743G>C|17,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|42,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248L|c.743G>T|74,BUFFER|p.R155Q|c.464G>A|114,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248Q|c.743G>A|110,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	TGGTGAGGATGGG	.	5	ESCA
TAF4B	0	.	GRCh37	18	23873435	23873435	+	Missense_Mutation	SNP	C	C	T	rs776819395	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1772C>T	p.Ser591Leu	p.S591L	ENST00000269142	9/15	42	39	3	26	26	0	TAF4B,missense_variant,p.Ser596Leu,ENST00000578121,;TAF4B,missense_variant,p.Ser591Leu,ENST00000269142,;TAF4B,missense_variant,p.Ser591Leu,ENST00000400466,;TAF4B,missense_variant,p.Ser591Leu,ENST00000418698,;	T	ENSG00000141384	ENST00000269142	Transcript	missense_variant	2770	1772	591	S/L	tCa/tTa	rs776819395	.	.	1	TAF4B	HGNC	11538	protein_coding	YES	CCDS42421.1	ENSP00000269142	TAF4B_HUMAN	B4DYT3_HUMAN,A4PBF8_HUMAN	UPI00006C65F2	.	deleterious(0)	possibly_damaging(0.884)	9/15	.	hmmpanther:PTHR15138,hmmpanther:PTHR15138:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGTCACTTC	byFrequency	2	ESCA
BCL2	0	.	GRCh37	18	60795795	60795795	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63C>A	.	.	ENST00000398117	2/2	14	10	3	20	20	0	BCL2,3_prime_UTR_variant,,ENST00000333681,;BCL2,3_prime_UTR_variant,,ENST00000398117,;BCL2,non_coding_transcript_exon_variant,,ENST00000590515,;	T	ENSG00000171791	ENST00000398117	Transcript	3_prime_UTR_variant	2245	.	.	.	.	.	.	.	-1	BCL2	HGNC	990	protein_coding	YES	CCDS11981.1	ENSP00000381185	BCL2_HUMAN	Q96PA0_HUMAN	UPI000000D90E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT	ACAATGCATAT	.	2	ESCA
ANKRD27	0	.	GRCh37	19	33134495	33134495	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.568C>T	p.%3D	p.L190L	ENST00000306065	6/29	56	41	15	55	55	0	ANKRD27,synonymous_variant,p.%3D,ENST00000306065,;ANKRD27,synonymous_variant,p.%3D,ENST00000587352,;ANKRD27,5_prime_UTR_variant,,ENST00000586463,;ANKRD27,downstream_gene_variant,,ENST00000590519,;ANKRD27,downstream_gene_variant,,ENST00000586693,;ANKRD27,upstream_gene_variant,,ENST00000591100,;ANKRD27,3_prime_UTR_variant,,ENST00000588700,;ANKRD27,non_coding_transcript_exon_variant,,ENST00000593232,;	A	ENSG00000105186	ENST00000306065	Transcript	synonymous_variant	727	568	190	L	Ctg/Ttg	.	.	.	-1	ANKRD27	HGNC	25310	protein_coding	YES	CCDS32986.1	ENSP00000304292	ANR27_HUMAN	K7EPM2_HUMAN,K7EIN0_HUMAN,K7EIH4_HUMAN	UPI000004FDE9	.	.	.	6/29	.	Superfamily_domains:0044157,hmmpanther:PTHR24170,hmmpanther:PTHR24170:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCAGAAGCT	.	5	ESCA
ERCC2	0	.	GRCh37	19	45860787	45860787	+	Missense_Mutation	SNP	G	G	A	rs760834335	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1322C>T	p.Ser441Leu	p.S441L	ENST00000391945	14/23	31	22	8	41	41	0	ERCC2,missense_variant,p.Ser417Leu,ENST00000391941,;ERCC2,missense_variant,p.Ser363Leu,ENST00000391944,;ERCC2,missense_variant,p.Ser441Leu,ENST00000391945,;ERCC2,downstream_gene_variant,,ENST00000485403,;ERCC2,downstream_gene_variant,,ENST00000391940,;ERCC2,missense_variant,p.Ser149Leu,ENST00000587376,;ERCC2,non_coding_transcript_exon_variant,,ENST00000588652,;ERCC2,non_coding_transcript_exon_variant,,ENST00000391942,;	A	ENSG00000104884	ENST00000391945	Transcript	missense_variant	1400	1322	441	S/L	tCg/tTg	rs760834335	.	.	-1	ERCC2	HGNC	3434	protein_coding	YES	CCDS33049.1	ENSP00000375809	ERCC2_HUMAN	K7EIT8_HUMAN,A8MX75_HUMAN	UPI0000139012	.	deleterious(0.01)	possibly_damaging(0.852)	14/23	.	hmmpanther:PTHR11472:SF1,hmmpanther:PTHR11472,TIGRFAM_domain:TIGR00604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGAGGCG	byFrequency	5	ESCA
MIR519A1	0	.	GRCh37	19	54255702	54255702	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.52G>A	.	.	ENST00000385257	1/1	64	51	13	73	73	0	MIR519A1,non_coding_transcript_exon_variant,,ENST00000385257,;MIR527,upstream_gene_variant,,ENST00000385244,;RNU6-751P,upstream_gene_variant,,ENST00000516382,;MIR521-1,downstream_gene_variant,,ENST00000384902,;MIR516A1,upstream_gene_variant,,ENST00000385033,;MIR522,downstream_gene_variant,,ENST00000385071,;	A	ENSG00000207992	ENST00000385257	Transcript	non_coding_transcript_exon_variant	52	.	.	.	.	.	.	.	1	MIR519A1	HGNC	32128	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGGAAAGT	.	5	ESCA
LENG8	0	.	GRCh37	19	54968055	54968055	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1686G>C	p.%3D	p.L562L	ENST00000326764	11/16	34	24	10	47	47	0	LENG8,synonymous_variant,p.%3D,ENST00000326764,;LENG8,synonymous_variant,p.%3D,ENST00000431846,;LENG8,synonymous_variant,p.%3D,ENST00000376526,;LENG8,intron_variant,,ENST00000376514,;LENG8,downstream_gene_variant,,ENST00000436479,;LENG8,downstream_gene_variant,,ENST00000443957,;LENG8,upstream_gene_variant,,ENST00000421200,;LENG8,downstream_gene_variant,,ENST00000439657,;LENG9,downstream_gene_variant,,ENST00000333834,;LENG8,downstream_gene_variant,,ENST00000462541,;	C	ENSG00000167615	ENST00000326764	Transcript	synonymous_variant	2165	1686	562	L	ctG/ctC	.	.	.	1	LENG8	HGNC	15500	protein_coding	YES	CCDS12894.1	ENSP00000318374	LENG8_HUMAN	E7EWC7_HUMAN,C9J1N5_HUMAN,B0VJY8_HUMAN	UPI0000074196	.	.	.	11/16	.	hmmpanther:PTHR12436:SF4,hmmpanther:PTHR12436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCTGCGCCT	.	5	ESCA
UBE2T	0	.	GRCh37	1	202302447	202302447	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302C>A	p.Ser101Tyr	p.S101Y	ENST00000367274	5/7	39	31	8	55	55	0	UBE2T,missense_variant,p.Ser101Tyr,ENST00000367274,;UBE2T,non_coding_transcript_exon_variant,,ENST00000460852,;UBE2T,non_coding_transcript_exon_variant,,ENST00000487227,;	T	ENSG00000077152	ENST00000367274	Transcript	missense_variant	452	302	101	S/Y	tCc/tAc	.	.	.	-1	UBE2T	HGNC	25009	protein_coding	YES	CCDS1425.1	ENSP00000356243	UBE2T_HUMAN	.	UPI0000047FD7	.	deleterious(0)	probably_damaging(0.964)	5/7	.	Superfamily_domains:SSF54495,SMART_domains:SM00212,Pfam_domain:PF00179,Gene3D:3.10.110.10,hmmpanther:PTHR24067:SF59,hmmpanther:PTHR24067,PROSITE_profiles:PS50127	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGGGATGGT	.	5	ESCA
CEP170	0	.	GRCh37	1	243303566	243303566	+	Intron	SNP	A	A	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4060-157T>G	.	.	ENST00000366542	.	30	25	5	30	30	0	CEP170,intron_variant,,ENST00000336415,;CEP170,intron_variant,,ENST00000366544,;CEP170,intron_variant,,ENST00000366543,;CEP170,intron_variant,,ENST00000481987,;CEP170,intron_variant,,ENST00000366542,;CEP170,intron_variant,,ENST00000490813,;CEP170,intron_variant,,ENST00000464936,;CEP170,intron_variant,,ENST00000413359,;CEP170,intron_variant,,ENST00000492145,;RP11-261C10.5,non_coding_transcript_exon_variant,,ENST00000439562,;CEP170,non_coding_transcript_exon_variant,,ENST00000468254,;CEP170,upstream_gene_variant,,ENST00000468697,;CEP170,upstream_gene_variant,,ENST00000439296,;	C	ENSG00000143702	ENST00000366542	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CEP170	HGNC	28920	protein_coding	YES	CCDS44339.1	ENSP00000355500	CE170_HUMAN	Q9NSN9_HUMAN,E5RJT5_HUMAN,E5RIH6_HUMAN,E5RFU8_HUMAN	UPI0000470238	.	.	.	.	15/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATAAGCAC	.	5	ESCA
MACF1	0	.	GRCh37	1	39775986	39775986	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3001C>T	p.%3D	p.L1001L	ENST00000545844	25/94	35	25	10	26	26	0	MACF1,synonymous_variant,p.%3D,ENST00000372925,;MACF1,synonymous_variant,p.%3D,ENST00000361689,;MACF1,synonymous_variant,p.%3D,ENST00000564288,;MACF1,synonymous_variant,p.%3D,ENST00000530262,;MACF1,synonymous_variant,p.%3D,ENST00000539005,;MACF1,synonymous_variant,p.%3D,ENST00000372915,;MACF1,synonymous_variant,p.%3D,ENST00000317713,;MACF1,synonymous_variant,p.%3D,ENST00000567887,;MACF1,synonymous_variant,p.%3D,ENST00000545844,;MACF1,synonymous_variant,p.%3D,ENST00000524432,;MACF1,non_coding_transcript_exon_variant,,ENST00000476350,;MACF1,3_prime_UTR_variant,,ENST00000496804,;	T	ENSG00000127603	ENST00000545844	Transcript	synonymous_variant	3109	3001	1001	L	Ctg/Ttg	.	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	.	25/94	.	hmmpanther:PTHR11915:SF37,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTCTGCAG	.	5	ESCA
TEX38	0	.	GRCh37	1	47138746	47138746	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239C>G	p.Ala80Gly	p.A80G	ENST00000334122	2/2	25	20	5	36	36	0	TEX38,missense_variant,p.Ala26Gly,ENST00000564373,;TEX38,missense_variant,p.Ala4Gly,ENST00000415500,;TEX38,missense_variant,p.Ala81Gly,ENST00000564071,;TEX38,missense_variant,p.Ala134Gly,ENST00000569393,;TEX38,missense_variant,p.Ala80Gly,ENST00000334122,;EFCAB14,intron_variant,,ENST00000544071,;EFCAB14,downstream_gene_variant,,ENST00000371933,;ATPAF1,upstream_gene_variant,,ENST00000371937,;ATPAF1,upstream_gene_variant,,ENST00000574428,;ATPAF1,upstream_gene_variant,,ENST00000329231,;ATPAF1,upstream_gene_variant,,ENST00000576409,;EFCAB14-AS1,upstream_gene_variant,,ENST00000442839,;EFCAB14-AS1,upstream_gene_variant,,ENST00000418985,;ATPAF1,intron_variant,,ENST00000525633,;ATPAF1,upstream_gene_variant,,ENST00000474020,;ATPAF1,upstream_gene_variant,,ENST00000487193,;ATPAF1,upstream_gene_variant,,ENST00000460928,;	G	ENSG00000186118	ENST00000334122	Transcript	missense_variant	346	239	80	A/G	gCc/gGc	.	.	.	1	TEX38	HGNC	29589	protein_coding	YES	CCDS57999.1	ENSP00000455854	TEX38_HUMAN	C9W8M6_HUMAN,B7ZLT2_HUMAN,B7ZLT1_HUMAN	UPI00001D7D06	.	tolerated(0.1)	possibly_damaging(0.783)	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TGCAGCCATCA	.	4	ESCA
C1orf173	0	.	GRCh37	1	75039106	75039106	+	Missense_Mutation	SNP	A	A	G	rs762652290	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2288T>C	p.Val763Ala	p.V763A	ENST00000326665	14/15	65	58	7	71	71	0	C1orf173,missense_variant,p.Val763Ala,ENST00000326665,;C1orf173,non_coding_transcript_exon_variant,,ENST00000433746,;	G	ENSG00000178965	ENST00000326665	Transcript	missense_variant	2507	2288	763	V/A	gTg/gCg	rs762652290	.	.	-1	C1orf173	HGNC	25346	protein_coding	YES	CCDS30755.1	ENSP00000322609	CA173_HUMAN	.	UPI0000237200	.	tolerated(1)	benign(0)	14/15	.	hmmpanther:PTHR23034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGCACCAAT	.	4	ESCA
ANGPT4	0	.	GRCh37	20	861854	861854	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.911T>C	p.Val304Ala	p.V304A	ENST00000381922	5/9	27	21	6	42	42	0	ANGPT4,missense_variant,p.Val304Ala,ENST00000546022,;ANGPT4,missense_variant,p.Val304Ala,ENST00000381922,;	G	ENSG00000101280	ENST00000381922	Transcript	missense_variant	1014	911	304	V/A	gTc/gCc	.	.	.	-1	ANGPT4	HGNC	487	protein_coding	YES	CCDS13009.1	ENSP00000371347	ANGP4_HUMAN	.	UPI0000062232	.	deleterious(0)	possibly_damaging(0.903)	5/9	.	PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF31,hmmpanther:PTHR19143,Pfam_domain:PF00147,Gene3D:3.90.215.10,SMART_domains:SM00186,Superfamily_domains:SSF56496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAGACACCA	.	5	ESCA
POTEH	0	.	GRCh37	22	16287537	16287537	+	Missense_Mutation	SNP	C	C	T	rs758952557	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349G>A	p.Val117Met	p.V117M	ENST00000343518	1/11	209	179	30	207	207	0	POTEH,missense_variant,p.Val117Met,ENST00000343518,;POTEH,missense_variant,p.Val61Met,ENST00000452800,;	T	ENSG00000198062	ENST00000343518	Transcript	missense_variant	401	349	117	V/M	Gtg/Atg	rs758952557,COSM354197	.	.	-1	POTEH	HGNC	133	protein_coding	YES	CCDS46658.1	ENSP00000340610	POTEH_HUMAN	.	UPI0000E5A425	.	tolerated_low_confidence(0.07)	benign(0.086)	1/11	.	hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCACGTTGC	byFrequency	4	ESCA
SNTG2	0	.	GRCh37	2	1204912	1204912	+	Missense_Mutation	SNP	T	T	A	rs751893436	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715T>A	p.Leu239Ile	p.L239I	ENST00000308624	9/17	35	24	11	36	36	0	SNTG2,missense_variant,p.Leu239Ile,ENST00000308624,;SNTG2,missense_variant,p.Leu112Ile,ENST00000407292,;SNTG2,non_coding_transcript_exon_variant,,ENST00000467759,;SNTG2,non_coding_transcript_exon_variant,,ENST00000463442,;SNTG2,non_coding_transcript_exon_variant,,ENST00000494178,;SNTG2,non_coding_transcript_exon_variant,,ENST00000498321,;SNTG2,intron_variant,,ENST00000475201,;	A	ENSG00000172554	ENST00000308624	Transcript	missense_variant	844	715	239	L/I	Tta/Ata	rs751893436	.	.	1	SNTG2	HGNC	13741	protein_coding	YES	CCDS46220.1	ENSP00000311837	SNTG2_HUMAN	.	UPI0000456D73	.	deleterious(0.02)	benign(0.068)	9/17	.	Superfamily_domains:SSF50729,hmmpanther:PTHR10554:SF3,hmmpanther:PTHR10554	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T236T|c.708G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAATTAAGG	.	5	ESCA
TTN	0	.	GRCh37	2	179571596	179571596	+	Silent	SNP	G	G	A	rs769063245	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29127C>T	p.%3D	p.V9709V	ENST00000589042	101/363	31	25	5	30	30	0	TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN,upstream_gene_variant,,ENST00000414766,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000589830,;	A	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	29352	29127	9709	V	gtC/gtT	rs769063245,COSM1148711,COSM1647221	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	101/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTACGACTCT	byFrequency	5	ESCA
ITGAV	0	.	GRCh37	2	187543403	187543403	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1384A>G	.	.	ENST00000261023	30/30	58	45	13	46	46	0	ITGAV,3_prime_UTR_variant,,ENST00000374907,;ITGAV,3_prime_UTR_variant,,ENST00000261023,;ITGAV,downstream_gene_variant,,ENST00000430709,;ITGAV,downstream_gene_variant,,ENST00000433736,;AC017101.10,intron_variant,,ENST00000453665,;ITGAV,downstream_gene_variant,,ENST00000496477,;	G	ENSG00000138448	ENST00000261023	Transcript	3_prime_UTR_variant	4805	.	.	.	.	.	.	.	1	ITGAV	HGNC	6150	protein_coding	YES	CCDS2292.1	ENSP00000261023	ITAV_HUMAN	L7RXH0_HUMAN	UPI000013D12E	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAATATATGA	.	5	ESCA
MYO1B	0	.	GRCh37	2	192279278	192279278	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3042T>C	p.%3D	p.N1014N	ENST00000392318	29/31	17	14	3	11	11	0	MYO1B,synonymous_variant,p.%3D,ENST00000392316,;MYO1B,synonymous_variant,p.%3D,ENST00000392318,;MYO1B,synonymous_variant,p.%3D,ENST00000339514,;MYO1B,synonymous_variant,p.%3D,ENST00000439065,;MYO1B,synonymous_variant,p.%3D,ENST00000427152,;MYO1B,synonymous_variant,p.%3D,ENST00000304164,;MYO1B,non_coding_transcript_exon_variant,,ENST00000490069,;	C	ENSG00000128641	ENST00000392318	Transcript	synonymous_variant	3289	3042	1014	N	aaT/aaC	.	.	.	1	MYO1B	HGNC	7596	protein_coding	YES	CCDS46477.1	ENSP00000376132	MYO1B_HUMAN	Q14777_HUMAN,E7EQD9_HUMAN,C9K0I9_HUMAN,C9JYW1_HUMAN,C9JUP5_HUMAN,B0I1S9_HUMAN	UPI00001A9466	.	.	.	29/31	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF277,Pfam_domain:PF06017	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATAATCTCCT	.	2	ESCA
ABI2	0	.	GRCh37	2	204259537	204259537	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.675A>C	p.%3D	p.T225T	ENST00000261017	5/10	22	19	3	29	29	0	ABI2,synonymous_variant,p.%3D,ENST00000261017,;ABI2,synonymous_variant,p.%3D,ENST00000422511,;ABI2,synonymous_variant,p.%3D,ENST00000451591,;ABI2,synonymous_variant,p.%3D,ENST00000417864,;ABI2,synonymous_variant,p.%3D,ENST00000261016,;ABI2,synonymous_variant,p.%3D,ENST00000295851,;ABI2,synonymous_variant,p.%3D,ENST00000424558,;ABI2,synonymous_variant,p.%3D,ENST00000454023,;RAPH1,3_prime_UTR_variant,,ENST00000457812,;ABI2,intron_variant,,ENST00000430418,;ABI2,intron_variant,,ENST00000261018,;ABI2,non_coding_transcript_exon_variant,,ENST00000416396,;ABI2,non_coding_transcript_exon_variant,,ENST00000430574,;ABI2,intron_variant,,ENST00000422719,;ABI2,intron_variant,,ENST00000411547,;ABI2,3_prime_UTR_variant,,ENST00000441061,;ABI2,intron_variant,,ENST00000416001,;	C	ENSG00000138443	ENST00000261017	Transcript	synonymous_variant	910	675	225	T	acA/acC	.	.	.	1	ABI2	HGNC	24011	protein_coding	YES	CCDS2358.1	ENSP00000261017	ABI2_HUMAN	Q53SH3_HUMAN,Q53RS4_HUMAN,B7ZAM8_HUMAN	UPI0000070712	.	.	.	5/10	.	hmmpanther:PTHR10460:SF3,hmmpanther:PTHR10460	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGACAGCTTC	.	2	ESCA
FBXO11	0	.	GRCh37	2	48040404	48040405	+	Frame_Shift_Ins	INS	-	-	TC	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2194_2195dupGA	p.Asp732GlufsTer38	p.D732Efs*38	ENST00000403359	18/23	32	28	4	29	29	0	FBXO11,frameshift_variant,p.Asp648GlufsTer38,ENST00000316377,;FBXO11,frameshift_variant,p.Asp732GlufsTer38,ENST00000403359,;FBXO11,frameshift_variant,p.Asp648GlufsTer38,ENST00000402508,;FBXO11,frameshift_variant,p.Asp524GlufsTer20,ENST00000493962,;FBXO11,frameshift_variant,p.Asp156GlufsTer38,ENST00000434523,;FBXO11,upstream_gene_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000234420,;FBXO11,non_coding_transcript_exon_variant,,ENST00000470899,;FBXO11,upstream_gene_variant,,ENST00000465204,;FBXO11,upstream_gene_variant,,ENST00000434234,;	TC	ENSG00000138081	ENST00000403359	Transcript	frameshift_variant	2268-2269	2195-2196	732	D/EX	gat/gaGAt	.	.	.	-1	FBXO11	HGNC	13590	protein_coding	YES	CCDS54357.1	ENSP00000384823	FBX11_HUMAN	E7EP88_HUMAN,C9IYF0_HUMAN,B5MCV6_HUMAN	UPI00005793B7	.	.	.	18/23	.	hmmpanther:PTHR22990:SF12,hmmpanther:PTHR22990,Gene3D:2.160.20.10,Pfam_domain:PF13229,SMART_domains:SM00710,SMART_domains:SM00722,Superfamily_domains:SSF51126	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCACCATCTCT	.	2	ESCA
SOX11	0	.	GRCh37	2	5841194	5841194	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7015A>T	.	.	ENST00000322002	1/1	33	27	5	28	28	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	T	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	8396	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCAAAGTTT	.	5	ESCA
ATG7	0	.	GRCh37	3	11372893	11372893	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758C>A	p.Ala253Asp	p.A253D	ENST00000354449	8/19	48	35	12	71	71	0	ATG7,missense_variant,p.Ala214Asp,ENST00000446450,;ATG7,missense_variant,p.Ala253Asp,ENST00000354449,;ATG7,missense_variant,p.Ala253Asp,ENST00000354956,;ATG7,non_coding_transcript_exon_variant,,ENST00000478638,;ATG7,downstream_gene_variant,,ENST00000488924,;ATG7,missense_variant,p.Ala103Asp,ENST00000434066,;ATG7,intron_variant,,ENST00000424071,;ATG7,upstream_gene_variant,,ENST00000461278,;	A	ENSG00000197548	ENST00000354449	Transcript	missense_variant	783	758	253	A/D	gCc/gAc	.	.	.	1	ATG7	HGNC	16935	protein_coding	YES	CCDS2605.1	ENSP00000346437	ATG7_HUMAN	H7C059_HUMAN,C9JNU2_HUMAN,C9JKA3_HUMAN,C9JGL2_HUMAN,C9JFF4_HUMAN,C9JE55_HUMAN	UPI00000705C7	.	tolerated(0.07)	benign(0.379)	8/19	.	hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF3,TIGRFAM_domain:TIGR01381	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGCCCACA	.	5	ESCA
CCDC14	0	.	GRCh37	3	123632984	123632984	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000433542	.	61	44	16	43	43	0	CCDC14,3_prime_UTR_variant,,ENST00000310351,;CCDC14,3_prime_UTR_variant,,ENST00000485727,;CCDC14,3_prime_UTR_variant,,ENST00000488653,;CCDC14,3_prime_UTR_variant,,ENST00000489746,;CCDC14,intron_variant,,ENST00000479903,;CCDC14,downstream_gene_variant,,ENST00000409697,;CCDC14,downstream_gene_variant,,ENST00000419247,;CCDC14,downstream_gene_variant,,ENST00000433542,;CCDC14,intron_variant,,ENST00000463996,;CCDC14,downstream_gene_variant,,ENST00000483247,;CCDC14,3_prime_UTR_variant,,ENST00000409657,;CCDC14,non_coding_transcript_exon_variant,,ENST00000495381,;	A	ENSG00000175455	ENST00000433542	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	182	-1	CCDC14	HGNC	25766	protein_coding	YES	CCDS3025.2	ENSP00000395706	CCD14_HUMAN	C9JWZ1_HUMAN	UPI00016632FB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAAGGCCTT	.	5	ESCA
ACAD11	0	.	GRCh37	3	132297707	132297707	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1707G>A	p.Met569Ile	p.M569I	ENST00000264990	15/20	54	48	6	46	46	0	ACAD11,missense_variant,p.Met569Ile,ENST00000264990,;ACAD11,missense_variant,p.Met94Ile,ENST00000545291,;ACAD11,intron_variant,,ENST00000355458,;ACAD11,non_coding_transcript_exon_variant,,ENST00000507705,;NPHP3,3_prime_UTR_variant,,ENST00000471702,;ACAD11,3_prime_UTR_variant,,ENST00000485198,;ACAD11,3_prime_UTR_variant,,ENST00000510100,;ACAD11,non_coding_transcript_exon_variant,,ENST00000496418,;ACAD11,non_coding_transcript_exon_variant,,ENST00000477604,;ACAD11,non_coding_transcript_exon_variant,,ENST00000469042,;ACAD11,downstream_gene_variant,,ENST00000487024,;	T	ENSG00000240303	ENST00000264990	Transcript	missense_variant	2679	1707	569	M/I	atG/atA	.	.	.	-1	ACAD11	HGNC	30211	protein_coding	YES	CCDS3074.1	ENSP00000264990	ACD11_HUMAN	Q08AE9_HUMAN,B4DQ41_HUMAN	UPI00003671B7	.	deleterious(0.03)	possibly_damaging(0.52)	15/20	.	hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF195,Gene3D:2.40.110.10,Superfamily_domains:SSF56645	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAATCATGCT	.	4	ESCA
MRAS	0	.	GRCh37	3	138116171	138116171	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199G>A	p.Asp67Asn	p.D67N	ENST00000289104	3/6	50	38	12	32	32	0	MRAS,missense_variant,p.Asp67Asn,ENST00000474559,;MRAS,missense_variant,p.Asp67Asn,ENST00000423968,;MRAS,missense_variant,p.Asp67Asn,ENST00000289104,;MRAS,5_prime_UTR_variant,,ENST00000464896,;MRAS,5_prime_UTR_variant,,ENST00000494949,;MRAS,upstream_gene_variant,,ENST00000478647,;	A	ENSG00000158186	ENST00000289104	Transcript	missense_variant	846	199	67	D/N	Gac/Aac	.	.	.	1	MRAS	HGNC	7227	protein_coding	YES	CCDS3100.1	ENSP00000289104	RASM_HUMAN	Q6FGP0_HUMAN,C9J8Q6_HUMAN,C9J601_HUMAN	UPI0000001253	.	deleterious(0)	probably_damaging(1)	3/6	.	Prints_domain:PR00449,Superfamily_domains:SSF52540,SMART_domains:SM00176,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00174,Gene3D:3.40.50.300,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,hmmpanther:PTHR24070:SF179,hmmpanther:PTHR24070,PROSITE_profiles:PS51421	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGGACACA	.	5	ESCA
COPB2	0	.	GRCh37	3	139077077	139077077	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2590A>G	p.Ile864Val	p.I864V	ENST00000333188	21/22	28	22	6	31	31	0	COPB2,missense_variant,p.Ile864Val,ENST00000333188,;COPB2,missense_variant,p.Ile78Val,ENST00000503326,;COPB2,missense_variant,p.Ile835Val,ENST00000507777,;COPB2,intron_variant,,ENST00000512309,;MRPS22,downstream_gene_variant,,ENST00000495075,;MRPS22,downstream_gene_variant,,ENST00000465056,;MRPS22,downstream_gene_variant,,ENST00000310776,;MRPS22,downstream_gene_variant,,ENST00000478464,;COPB2,non_coding_transcript_exon_variant,,ENST00000502734,;MRPS22,downstream_gene_variant,,ENST00000492644,;MRPS22,downstream_gene_variant,,ENST00000480938,;MRPS22,downstream_gene_variant,,ENST00000498505,;	C	ENSG00000184432	ENST00000333188	Transcript	missense_variant	2772	2590	864	I/V	Att/Gtt	.	.	.	-1	COPB2	HGNC	2232	protein_coding	YES	CCDS3108.1	ENSP00000329419	COPB2_HUMAN	D6RCL6_HUMAN,D6RBZ7_HUMAN,D6RBT6_HUMAN,D6RBG7_HUMAN,B4DZI8_HUMAN	UPI0000161FB4	.	tolerated(1)	benign(0)	21/22	.	PIRSF_domain:PIRSF005567,hmmpanther:PTHR19876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAATAACCG	.	5	ESCA
CHRD	0	.	GRCh37	3	184102443	184102443	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1559C>A	p.Ala520Asp	p.A520D	ENST00000204604	13/23	21	16	5	19	19	0	CHRD,missense_variant,p.Ala520Asp,ENST00000450923,;CHRD,missense_variant,p.Ala520Asp,ENST00000204604,;CHRD,missense_variant,p.Ala480Asp,ENST00000348986,;CHRD,missense_variant,p.Ala150Asp,ENST00000545352,;EIF2B5,intron_variant,,ENST00000444495,;CHRD,downstream_gene_variant,,ENST00000310236,;CHRD,downstream_gene_variant,,ENST00000482805,;CHRD,3_prime_UTR_variant,,ENST00000420973,;CHRD,3_prime_UTR_variant,,ENST00000448472,;CHRD,non_coding_transcript_exon_variant,,ENST00000470150,;CHRD,non_coding_transcript_exon_variant,,ENST00000460627,;CHRD,downstream_gene_variant,,ENST00000461120,;CHRD,downstream_gene_variant,,ENST00000459711,;CHRD,downstream_gene_variant,,ENST00000356534,;CHRD,downstream_gene_variant,,ENST00000482014,;CHRD,upstream_gene_variant,,ENST00000464833,;CHRD,downstream_gene_variant,,ENST00000496527,;CHRD,downstream_gene_variant,,ENST00000485883,;CHRD,downstream_gene_variant,,ENST00000486066,;CHRD,downstream_gene_variant,,ENST00000461684,;	A	ENSG00000090539	ENST00000204604	Transcript	missense_variant	1805	1559	520	A/D	gCt/gAt	.	.	.	1	CHRD	HGNC	1949	protein_coding	YES	CCDS3266.1	ENSP00000204604	CHRD_HUMAN	Q8N2W7_HUMAN	UPI000013C64D	.	tolerated(0.41)	possibly_damaging(0.609)	13/23	.	PROSITE_profiles:PS50933,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF263,PIRSF_domain:PIRSF002496,SMART_domains:SM00754	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGGCTGCCC	.	5	ESCA
SATB1	0	.	GRCh37	3	18436270	18436270	+	Missense_Mutation	SNP	C	C	T	rs751519264	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.890G>A	p.Arg297Gln	p.R297Q	ENST00000417717	7/12	43	32	10	76	76	0	SATB1,missense_variant,p.Arg297Gln,ENST00000454909,;SATB1,missense_variant,p.Arg297Gln,ENST00000417717,;SATB1,missense_variant,p.Arg297Gln,ENST00000338745,;SATB1,downstream_gene_variant,,ENST00000440737,;TBC1D5,intron_variant,,ENST00000414318,;SATB1,downstream_gene_variant,,ENST00000475083,;	T	ENSG00000182568	ENST00000417717	Transcript	missense_variant	1861	890	297	R/Q	cGg/cAg	rs751519264	.	.	-1	SATB1	HGNC	10541	protein_coding	YES	CCDS56242.1	ENSP00000399518	SATB1_HUMAN	C9JP21_HUMAN,C9JLL5_HUMAN,C9JGL9_HUMAN,C9J7F3_HUMAN,C9J3I0_HUMAN	UPI0000E1FB67	.	tolerated(0.12)	possibly_damaging(0.787)	7/12	.	hmmpanther:PTHR15116,hmmpanther:PTHR15116:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S295C|c.884C>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTCCGGACA	.	5	ESCA
LIPH	0	.	GRCh37	3	185252682	185252682	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288C>G	p.%3D	p.L96L	ENST00000296252	2/10	54	51	3	39	39	0	LIPH,synonymous_variant,p.%3D,ENST00000424591,;LIPH,synonymous_variant,p.%3D,ENST00000296252,;LIPH,upstream_gene_variant,,ENST00000452897,;LIPH,3_prime_UTR_variant,,ENST00000429510,;	C	ENSG00000163898	ENST00000296252	Transcript	synonymous_variant	430	288	96	L	ctC/ctG	.	.	.	-1	LIPH	HGNC	18483	protein_coding	YES	CCDS3272.1	ENSP00000296252	LIPH_HUMAN	A2IBA8_HUMAN	UPI000003AEB8	.	.	.	2/10	.	hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF12,Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAGAGAGCAA	.	2	ESCA
TGFBR2	0	.	GRCh37	3	30691947	30691947	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524C>G	p.Ser175Ter	p.S175*	ENST00000359013	4/8	24	20	4	37	37	0	TGFBR2,stop_gained,p.Ser150Ter,ENST00000295754,;TGFBR2,stop_gained,p.Ser175Ter,ENST00000359013,;	G	ENSG00000163513	ENST00000359013	Transcript	stop_gained	807	524	175	S/*	tCa/tGa	.	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	.	.	4/8	.	hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:2.10.60.10,Pfam_domain:PF08917,PIRSF_domain:PIRSF037393,Superfamily_domains:SSF57302	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCAGAAG	.	5	ESCA
ATXN7	0	.	GRCh37	3	63986059	63986059	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*824A>G	.	.	ENST00000398590	14/14	25	13	12	39	39	0	ATXN7,3_prime_UTR_variant,,ENST00000398590,;ATXN7,3_prime_UTR_variant,,ENST00000295900,;ATXN7,3_prime_UTR_variant,,ENST00000538065,;ATXN7,downstream_gene_variant,,ENST00000522345,;ATXN7,downstream_gene_variant,,ENST00000484332,;ATXN7,downstream_gene_variant,,ENST00000487717,;PSMD6-AS2,upstream_gene_variant,,ENST00000472046,;ATXN7,downstream_gene_variant,,ENST00000477516,;ATXN7,downstream_gene_variant,,ENST00000474112,;	G	ENSG00000163635	ENST00000398590	Transcript	3_prime_UTR_variant	4215	.	.	.	.	.	.	.	1	ATXN7	HGNC	10560	protein_coding	YES	CCDS54603.1	ENSP00000381590	ATX7_HUMAN	Q9UPD8_HUMAN,Q8TEZ8_HUMAN,H0YAT6_HUMAN	UPI00001B07C4	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCATAGTA	.	5	ESCA
SEC24B	0	.	GRCh37	4	110427592	110427592	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597A>G	p.Ile533Val	p.I533V	ENST00000265175	7/24	25	18	6	21	21	0	SEC24B,missense_variant,p.Ile533Val,ENST00000265175,;SEC24B,missense_variant,p.Ile563Val,ENST00000504968,;SEC24B,missense_variant,p.Ile498Val,ENST00000399100,;	G	ENSG00000138802	ENST00000265175	Transcript	missense_variant	1652	1597	533	I/V	Att/Gtt	.	.	.	1	SEC24B	HGNC	10704	protein_coding	YES	CCDS47124.1	ENSP00000265175	SC24B_HUMAN	B4E2E1_HUMAN	UPI00004F6ED7	.	tolerated(0.38)	benign(0.001)	7/24	.	hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF7,Superfamily_domains:SSF81995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAATATTTTA	.	5	ESCA
ETFDH	0	.	GRCh37	4	159624578	159624579	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1121dupT	p.Pro375ThrfsTer14	p.P375Tfs*14	ENST00000511912	10/13	64	49	15	62	62	0	ETFDH,frameshift_variant,p.Pro328ThrfsTer14,ENST00000307738,;ETFDH,frameshift_variant,p.Pro375ThrfsTer14,ENST00000511912,;ETFDH,downstream_gene_variant,,ENST00000507475,;U3,downstream_gene_variant,,ENST00000607547,;ETFDH,non_coding_transcript_exon_variant,,ENST00000506422,;	T	ENSG00000171503	ENST00000511912	Transcript	frameshift_variant	1452-1453	1120-1121	374	I/IX	ata/aTta	.	.	.	1	ETFDH	HGNC	3483	protein_coding	YES	CCDS3800.1	ENSP00000426638	ETFD_HUMAN	D6RAD5_HUMAN,B4DEQ0_HUMAN	UPI000013EC48	.	.	.	10/13	.	Superfamily_domains:SSF51905,hmmpanther:PTHR10617,hmmpanther:PTHR10617:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTCTATACCA	.	3	ESCA
DDX60	0	.	GRCh37	4	169138093	169138093	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5130C>G	p.Asn1710Lys	p.N1710K	ENST00000393743	38/38	71	61	10	70	70	0	DDX60,missense_variant,p.Asn1710Lys,ENST00000393743,;DDX60,downstream_gene_variant,,ENST00000511317,;	C	ENSG00000137628	ENST00000393743	Transcript	missense_variant	5422	5130	1710	N/K	aaC/aaG	.	.	.	-1	DDX60	HGNC	25942	protein_coding	YES	CCDS34097.1	ENSP00000377344	DDX60_HUMAN	Q9NXV7_HUMAN,Q9H616_HUMAN,Q6B0F7_HUMAN,D6R944_HUMAN	UPI000020B6AB	.	tolerated(0.88)	benign(0.001)	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTGTTTAA	.	5	ESCA
FAM149A	0	.	GRCh37	4	187078796	187078796	+	Missense_Mutation	SNP	G	G	A	rs369514269	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652G>A	p.Asp218Asn	p.D218N	ENST00000227065	8/14	32	20	12	38	38	0	FAM149A,missense_variant,p.Asp218Asn,ENST00000514153,;FAM149A,missense_variant,p.Asp218Asn,ENST00000389354,;FAM149A,missense_variant,p.Asp218Asn,ENST00000502970,;FAM149A,missense_variant,p.Asp218Asn,ENST00000503432,;FAM149A,missense_variant,p.Asp218Asn,ENST00000227065,;FAM149A,missense_variant,p.Asp509Asn,ENST00000356371,;FAM149A,downstream_gene_variant,,ENST00000504330,;FAM149A,downstream_gene_variant,,ENST00000509574,;FAM149A,downstream_gene_variant,,ENST00000510790,;FAM149A,non_coding_transcript_exon_variant,,ENST00000513030,;FAM149A,non_coding_transcript_exon_variant,,ENST00000514829,;FAM149A,non_coding_transcript_exon_variant,,ENST00000515078,;RP11-173M11.2,upstream_gene_variant,,ENST00000504462,;	A	ENSG00000109794	ENST00000227065	Transcript	missense_variant	1231	652	218	D/N	Gat/Aat	rs369514269	.	.	1	FAM149A	HGNC	24527	protein_coding	YES	CCDS34117.1	ENSP00000227065	F149A_HUMAN	D6RGX1_HUMAN,D6RC92_HUMAN,D6RAL4_HUMAN	UPI00001C1E1F	.	tolerated(0.05)	benign(0.133)	8/14	.	hmmpanther:PTHR31997,hmmpanther:PTHR31997:SF2	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGCCGATGGA	byFrequency|byCluster	5	ESCA
FNDC9	0	.	GRCh37	5	156770149	156770149	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396C>T	p.%3D	p.C132C	ENST00000312349	2/2	30	25	5	41	41	0	FNDC9,synonymous_variant,p.%3D,ENST00000520782,;FNDC9,synonymous_variant,p.%3D,ENST00000312349,;CYFIP2,intron_variant,,ENST00000377576,;CYFIP2,intron_variant,,ENST00000541131,;CYFIP2,intron_variant,,ENST00000318218,;CYFIP2,intron_variant,,ENST00000435847,;CYFIP2,intron_variant,,ENST00000442283,;CYFIP2,intron_variant,,ENST00000347377,;CYFIP2,intron_variant,,ENST00000522463,;CYFIP2,intron_variant,,ENST00000521420,;CYFIP2,intron_variant,,ENST00000517753,;CYFIP2,intron_variant,,ENST00000523119,;CYFIP2,intron_variant,,ENST00000523969,;CYFIP2,intron_variant,,ENST00000520759,;CYFIP2,intron_variant,,ENST00000519153,;CYFIP2,downstream_gene_variant,,ENST00000520424,;	A	ENSG00000172568	ENST00000312349	Transcript	synonymous_variant	584	396	132	C	tgC/tgT	.	.	.	-1	FNDC9	HGNC	33547	protein_coding	YES	CCDS4337.1	ENSP00000310594	FNDC9_HUMAN	E5RIJ1_HUMAN	UPI000013F2AC	.	.	.	2/2	.	Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGGCAGAT	.	5	ESCA
Y_RNA	0	.	GRCh37	5	56469848	56469848	+	5'Flank	SNP	C	C	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000384563	.	17	11	6	22	22	0	GPBP1,5_prime_UTR_variant,,ENST00000424459,;GPBP1,upstream_gene_variant,,ENST00000506184,;GPBP1,upstream_gene_variant,,ENST00000454432,;GPBP1,upstream_gene_variant,,ENST00000511209,;GPBP1,upstream_gene_variant,,ENST00000514387,;Y_RNA,upstream_gene_variant,,ENST00000384563,;	G	ENSG00000207293	ENST00000384563	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4812	-1	Y_RNA	RFAM	.	misc_RNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTCGCCAC	.	5	ESCA
HACE1	0	.	GRCh37	6	105177312	105177312	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*225T>C	.	.	ENST00000262903	24/24	15	12	3	14	14	0	HACE1,3_prime_UTR_variant,,ENST00000518503,;HACE1,3_prime_UTR_variant,,ENST00000262903,;HACE1,3_prime_UTR_variant,,ENST00000369125,;HACE1,3_prime_UTR_variant,,ENST00000518402,;HACE1,non_coding_transcript_exon_variant,,ENST00000517995,;HACE1,3_prime_UTR_variant,,ENST00000517424,;HACE1,3_prime_UTR_variant,,ENST00000416605,;HACE1,non_coding_transcript_exon_variant,,ENST00000369127,;HACE1,non_coding_transcript_exon_variant,,ENST00000518228,;	G	ENSG00000085382	ENST00000262903	Transcript	3_prime_UTR_variant	3232	.	.	.	.	.	.	.	-1	HACE1	HGNC	21033	protein_coding	YES	CCDS5050.1	ENSP00000262903	HACE1_HUMAN	E5RFX0_HUMAN,E3W983_HUMAN	UPI00001602DC	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTTAAAAAA	.	2	ESCA
NEDD9	0	.	GRCh37	6	11201147	11201147	+	Intron	SNP	C	C	T	rs372890721	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460-7222G>A	.	.	ENST00000379446	.	23	14	9	34	34	0	NEDD9,3_prime_UTR_variant,,ENST00000379433,;NEDD9,intron_variant,,ENST00000504387,;NEDD9,intron_variant,,ENST00000379446,;RP3-510L9.1,intron_variant,,ENST00000500636,;NEDD9,intron_variant,,ENST00000448183,;	T	ENSG00000111859	ENST00000379446	Transcript	intron_variant	.	.	.	.	.	rs372890721	.	.	-1	NEDD9	HGNC	7733	protein_coding	YES	CCDS4520.1	ENSP00000368759	CASL_HUMAN	D6RGD7_HUMAN	UPI000000D981	.	.	.	.	2/6	.	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAGACGGCAA	.	2	ESCA
TAAR9	0	.	GRCh37	6	132859987	132859987	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559G>T	p.Val187Leu	p.V187L	ENST00000434551	1/1	25	17	8	33	33	0	TAAR9,missense_variant,p.Val187Leu,ENST00000434551,;	T	ENSG00000237110	ENST00000434551	Transcript	missense_variant	559	559	187	V/L	Gta/Tta	.	.	.	1	TAAR9	HGNC	20977	polymorphic_pseudogene	YES	.	ENSP00000424607	.	.	.	.	tolerated(0.06)	benign(0.095)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGTGTAGGA	.	5	ESCA
STXBP5	0	.	GRCh37	6	147632620	147632620	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1102C>A	p.Leu368Ile	p.L368I	ENST00000321680	11/28	36	31	4	35	35	0	STXBP5,missense_variant,p.Leu368Ile,ENST00000321680,;STXBP5,missense_variant,p.Leu368Ile,ENST00000367480,;STXBP5,missense_variant,p.Leu39Ile,ENST00000179882,;STXBP5,missense_variant,p.Leu368Ile,ENST00000367481,;	A	ENSG00000164506	ENST00000321680	Transcript	missense_variant	1102	1102	368	L/I	Ctt/Att	.	.	.	1	STXBP5	HGNC	19665	protein_coding	YES	CCDS47499.1	ENSP00000321826	STXB5_HUMAN	.	UPI0000199FE0	.	deleterious(0)	probably_damaging(0.983)	11/28	.	Prints_domain:PR00962,Superfamily_domains:SSF50978,Pfam_domain:PF08366,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTGTTCTTCTA	.	3	ESCA
DNAH8	0	.	GRCh37	6	38874095	38874095	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8609G>C	p.Gly2870Ala	p.G2870A	ENST00000359357	61/91	24	16	7	31	31	0	DNAH8,missense_variant,p.Gly2870Ala,ENST00000359357,;DNAH8,missense_variant,p.Gly3075Ala,ENST00000327475,;DNAH8,missense_variant,p.Gly2834Ala,ENST00000441566,;DNAH8,missense_variant,p.Gly3087Ala,ENST00000449981,;	C	ENSG00000124721	ENST00000359357	Transcript	missense_variant	8863	8609	2870	G/A	gGa/gCa	.	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	possibly_damaging(0.651)	61/91	.	Superfamily_domains:SSF52540,Pfam_domain:PF12780,Gene3D:3.40.50.300,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATGGAAAAG	.	5	ESCA
THSD7A	0	.	GRCh37	7	11486945	11486945	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2712G>A	p.%3D	p.Q904Q	ENST00000423059	12/28	48	34	14	37	37	0	THSD7A,synonymous_variant,p.%3D,ENST00000423059,;AC004538.3,intron_variant,,ENST00000445839,;THSD7A,non_coding_transcript_exon_variant,,ENST00000497575,;	T	ENSG00000005108	ENST00000423059	Transcript	synonymous_variant	2964	2712	904	Q	caG/caA	.	.	.	-1	THSD7A	HGNC	22207	protein_coding	YES	CCDS47543.1	ENSP00000406482	THS7A_HUMAN	.	UPI00006C0B74	.	.	.	12/28	.	hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,Gene3D:2.20.100.10,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCATCCTGGCA	.	3	ESCA
CAPZA2	0	.	GRCh37	7	116559239	116559239	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1318A>T	.	.	ENST00000361183	10/10	15	9	5	28	28	0	CAPZA2,3_prime_UTR_variant,,ENST00000361183,;CAPZA2,downstream_gene_variant,,ENST00000458284,;CAPZA2,downstream_gene_variant,,ENST00000426421,;CAPZA2,downstream_gene_variant,,ENST00000496161,;CAPZA2,downstream_gene_variant,,ENST00000465607,;CAPZA2,downstream_gene_variant,,ENST00000449080,;	T	ENSG00000198898	ENST00000361183	Transcript	3_prime_UTR_variant	2318	.	.	.	.	.	.	.	1	CAPZA2	HGNC	1490	protein_coding	YES	CCDS5768.1	ENSP00000354947	CAZA2_HUMAN	A4D0V4_HUMAN	UPI00001270FC	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGAAAGCAT	.	5	ESCA
ABCB8	0	.	GRCh37	7	150725613	150725613	+	Missense_Mutation	SNP	A	A	G	rs751158127	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11A>G	p.His4Arg	p.H4R	ENST00000358849	1/16	25	20	5	66	66	0	ABCB8,missense_variant,p.His4Arg,ENST00000356058,;ABCB8,missense_variant,p.His4Arg,ENST00000297504,;ABCB8,missense_variant,p.His4Arg,ENST00000498578,;ABCB8,missense_variant,p.His4Arg,ENST00000358849,;ABCB8,missense_variant,p.His4Arg,ENST00000477092,;ABCB8,missense_variant,p.His4Arg,ENST00000461373,;ABCB8,missense_variant,p.His4Arg,ENST00000477719,;ABCB8,synonymous_variant,p.%3D,ENST00000542328,;ATG9B,upstream_gene_variant,,ENST00000444312,;ATG9B,upstream_gene_variant,,ENST00000605938,;ATG9B,upstream_gene_variant,,ENST00000377974,;ATG9B,upstream_gene_variant,,ENST00000605952,;RP11-148K1.10,downstream_gene_variant,,ENST00000479085,;ABCB8,non_coding_transcript_exon_variant,,ENST00000472698,;ABCB8,non_coding_transcript_exon_variant,,ENST00000488370,;ABCB8,non_coding_transcript_exon_variant,,ENST00000471796,;ABCB8,non_coding_transcript_exon_variant,,ENST00000488826,;ABCB8,non_coding_transcript_exon_variant,,ENST00000466956,;ATG9B,upstream_gene_variant,,ENST00000494791,;ABCB8,upstream_gene_variant,,ENST00000469410,;ATG9B,upstream_gene_variant,,ENST00000466157,;ABCB8,upstream_gene_variant,,ENST00000493338,;ATG9B,upstream_gene_variant,,ENST00000486407,;ATG9B,upstream_gene_variant,,ENST00000473409,;ABCB8,missense_variant,p.His4Arg,ENST00000488551,;ABCB8,missense_variant,p.His4Arg,ENST00000470645,;ABCB8,missense_variant,p.His4Arg,ENST00000466514,;ABCB8,missense_variant,p.His4Arg,ENST00000482309,;ABCB8,missense_variant,p.His4Arg,ENST00000489192,;ABCB8,non_coding_transcript_exon_variant,,ENST00000462605,;	G	ENSG00000197150	ENST00000358849	Transcript	missense_variant	104	11	4	H/R	cAt/cGt	rs751158127	.	.	1	ABCB8	HGNC	49	protein_coding	YES	CCDS5913.1	ENSP00000351717	ABCB8_HUMAN	B3KSN3_HUMAN,B3KND2_HUMAN	UPI000013E41B	.	deleterious_low_confidence(0)	probably_damaging(0.998)	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGCATTTAT	byFrequency	5	ESCA
HOXA3	0	.	GRCh37	7	27148113	27148113	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753G>A	p.%3D	p.K251K	ENST00000396352	3/3	59	36	23	50	50	0	HOXA3,synonymous_variant,p.%3D,ENST00000317201,;HOXA3,synonymous_variant,p.%3D,ENST00000396352,;HOXA3,downstream_gene_variant,,ENST00000522456,;HOXA3,downstream_gene_variant,,ENST00000522788,;HOXA3,downstream_gene_variant,,ENST00000521779,;HOXA-AS2,intron_variant,,ENST00000518088,;HOXA3,downstream_gene_variant,,ENST00000521401,;	T	ENSG00000105997	ENST00000396352	Transcript	synonymous_variant	953	753	251	K	aaG/aaA	.	.	.	-1	HOXA3	HGNC	5104	protein_coding	YES	CCDS5404.1	ENSP00000379640	HXA3_HUMAN	F2Z3A4_HUMAN,E5RIJ8_HUMAN,A4D182_HUMAN	UPI000012CF22	.	.	.	3/3	.	Superfamily_domains:SSF46689,SMART_domains:SM00389,Gene3D:1.10.10.60,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCCTTCTG	.	5	ESCA
FAM133B	0	.	GRCh37	7	92190856	92190856	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*740A>T	.	.	ENST00000445716	11/11	32	22	9	33	33	0	FAM133B,3_prime_UTR_variant,,ENST00000445716,;FAM133B,3_prime_UTR_variant,,ENST00000438306,;FAM133B,downstream_gene_variant,,ENST00000494079,;FAM133B,downstream_gene_variant,,ENST00000427372,;FAM133B,3_prime_UTR_variant,,ENST00000415397,;FAM133B,non_coding_transcript_exon_variant,,ENST00000481407,;FAM133B,downstream_gene_variant,,ENST00000468931,;	A	ENSG00000234545	ENST00000445716	Transcript	3_prime_UTR_variant	1587	.	.	.	.	.	.	.	-1	FAM133B	HGNC	28629	protein_coding	YES	CCDS47640.1	ENSP00000398401	F133B_HUMAN	C9JUX2_HUMAN	UPI000004471D	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATTATTAC	.	5	ESCA
CSMD1	0	.	GRCh37	8	3200963	3200963	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3484G>T	p.Gly1162Ter	p.G1162*	ENST00000537824	23/70	35	26	9	63	63	0	CSMD1,stop_gained,p.Gly1163Ter,ENST00000400186,;CSMD1,stop_gained,p.Gly1162Ter,ENST00000542608,;CSMD1,stop_gained,p.Gly1163Ter,ENST00000602723,;CSMD1,stop_gained,p.Gly643Ter,ENST00000335551,;CSMD1,stop_gained,p.Gly1162Ter,ENST00000537824,;CSMD1,stop_gained,p.Gly1163Ter,ENST00000520002,;CSMD1,stop_gained,p.Gly1162Ter,ENST00000539096,;CSMD1,stop_gained,p.Gly1163Ter,ENST00000602557,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,;	A	ENSG00000183117	ENST00000537824	Transcript	stop_gained	3484	3484	1162	G/*	Gga/Tga	.	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	.	23/70	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTTCCATCAT	.	3	ESCA
MATN2	0	.	GRCh37	8	99039880	99039880	+	Missense_Mutation	SNP	T	T	C	rs554199301	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2179T>C	p.Tyr727His	p.Y727H	ENST00000520016	13/18	47	33	13	19	19	0	MATN2,missense_variant,p.Tyr510His,ENST00000518154,;MATN2,missense_variant,p.Tyr161His,ENST00000517321,;MATN2,missense_variant,p.Tyr727His,ENST00000521689,;MATN2,missense_variant,p.Tyr727His,ENST00000254898,;MATN2,missense_variant,p.Tyr727His,ENST00000520016,;MATN2,missense_variant,p.Tyr686His,ENST00000524308,;MATN2,missense_variant,p.Tyr443His,ENST00000522025,;MATN2,upstream_gene_variant,,ENST00000522135,;MATN2,upstream_gene_variant,,ENST00000519582,;RPL30,intron_variant,,ENST00000518164,;MATN2,non_coding_transcript_exon_variant,,ENST00000518370,;MATN2,intron_variant,,ENST00000521952,;MATN2,upstream_gene_variant,,ENST00000523561,;	C	ENSG00000132561	ENST00000520016	Transcript	missense_variant	2303	2179	727	Y/H	Tac/Cac	rs554199301	.	.	1	MATN2	HGNC	6908	protein_coding	YES	CCDS55264.1	ENSP00000430487	MATN2_HUMAN	E5RJM4_HUMAN	UPI000021037B	.	tolerated(0.18)	probably_damaging(1)	13/18	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF17,hmmpanther:PTHR22992,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAATACATG	.	5	ESCA
NAIF1	0	.	GRCh37	9	130826154	130826154	+	Silent	SNP	C	C	T	rs757109726	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.537G>A	p.%3D	p.T179T	ENST00000373078	2/2	25	13	11	24	24	0	NAIF1,synonymous_variant,p.%3D,ENST00000373078,;SLC25A25,upstream_gene_variant,,ENST00000373068,;SLC25A25,upstream_gene_variant,,ENST00000373069,;NAIF1,non_coding_transcript_exon_variant,,ENST00000488519,;NAIF1,non_coding_transcript_exon_variant,,ENST00000466139,;NAIF1,upstream_gene_variant,,ENST00000470245,;	T	ENSG00000171169	ENST00000373078	Transcript	synonymous_variant	757	537	179	T	acG/acA	rs757109726	.	.	-1	NAIF1	HGNC	25446	protein_coding	YES	CCDS6889.1	ENSP00000362170	NAIF1_HUMAN	.	UPI0000160C94	.	.	.	2/2	.	hmmpanther:PTHR23098,hmmpanther:PTHR23098:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGCGTGTG	byFrequency	5	ESCA
NOTCH1	0	.	GRCh37	9	139402553	139402553	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3364T>A	p.Cys1122Ser	p.C1122S	ENST00000277541	21/34	48	15	33	51	51	0	NOTCH1,missense_variant,p.Cys1122Ser,ENST00000277541,;NOTCH1,upstream_gene_variant,,ENST00000494783,;	T	ENSG00000148400	ENST00000277541	Transcript	missense_variant	3440	3364	1122	C/S	Tgt/Agt	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	deleterious(0)	probably_damaging(1)	21/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,Gene3D:2.10.25.10,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACAGAGCC	.	5	ESCA
BNC2	0	.	GRCh37	9	16419544	16419544	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2743G>C	p.Glu915Gln	p.E915Q	ENST00000380672	7/7	30	23	7	35	35	0	BNC2,missense_variant,p.Glu820Gln,ENST00000545497,;BNC2,missense_variant,p.Glu848Gln,ENST00000380667,;BNC2,missense_variant,p.Glu915Gln,ENST00000380672,;BNC2,3_prime_UTR_variant,,ENST00000418777,;BNC2,3_prime_UTR_variant,,ENST00000411752,;BNC2,3_prime_UTR_variant,,ENST00000484726,;	G	ENSG00000173068	ENST00000380672	Transcript	missense_variant	2801	2743	915	E/Q	Gaa/Caa	.	.	.	-1	BNC2	HGNC	30988	protein_coding	YES	CCDS6482.2	ENSP00000370047	BNC2_HUMAN	S4R351_HUMAN,Q06HC7_HUMAN,Q06HC2_HUMAN,Q06HB9_HUMAN,D3DRJ1_HUMAN	UPI000035E7B0	.	tolerated(0.19)	probably_damaging(0.979)	7/7	.	hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTCATCGC	.	5	ESCA
ZBED1	0	.	GRCh37	X	2408163	2408169	+	In_Frame_Del	DEL	TGTCGGT	TGTCGGT	C	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	TGTCGGT	TGTCGGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592_598delACCGACAinsG	p.Thr198_Met200delinsVal	p.T198_M200delinsV	ENST00000381223	2/2	69	44	25	55	55	0	ZBED1,protein_altering_variant,p.Thr198_Met200delinsVal,ENST00000381223,;ZBED1,protein_altering_variant,p.Thr198_Met200delinsVal,ENST00000461691,;ZBED1,protein_altering_variant,p.Thr198_Met200delinsVal,ENST00000381222,;ZBED1,protein_altering_variant,p.Thr198_Met200delinsVal,ENST00000381218,;DHRSX,intron_variant,,ENST00000444280,;DHRSX,intron_variant,,ENST00000334651,;DHRSX,intron_variant,,ENST00000412516,;DHRSX,intron_variant,,ENST00000430536,;ZBED1,upstream_gene_variant,,ENST00000515319,;DHRSX,intron_variant,,ENST00000478825,;DHRSX,intron_variant,,ENST00000441131,;	C	ENSG00000214717	ENST00000381223	Transcript	protein_altering_variant	796-802	592-598	198-200	TDM/V	ACCGACAtg/Gtg	.	.	.	-1	ZBED1	HGNC	447	protein_coding	YES	CCDS14118.1	ENSP00000370621	ZBED1_HUMAN	C9JXP4_HUMAN	UPI0000073DE9	.	.	.	2/2	.	Superfamily_domains:SSF53098,hmmpanther:PTHR23272,hmmpanther:PTHR23272:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	TCCACATGTCGGTGGAGA	.	2	ESCA
USP27X	0	.	GRCh37	X	49645918	49645918	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49N-01A-11D-A247-09	TCGA-LN-A49N-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1008G>A	p.%3D	p.T336T	ENST00000508866	1/1	16	8	8	28	28	0	USP27X,synonymous_variant,p.%3D,ENST00000508866,;USP27X-AS1,upstream_gene_variant,,ENST00000437322,;	A	ENSG00000242013	ENST00000508866	Transcript	synonymous_variant	1449	1008	336	T	acG/acA	.	.	.	1	USP27X	HGNC	13486	protein_coding	YES	CCDS65260.1	ENSP00000475071	UBP27_HUMAN	.	UPI0000EE7A8D	.	.	.	1/1	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF368,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACGCCGTT	.	5	ESCA
ADRA2A	0	.	GRCh37	10	112837931	112837931	+	Missense_Mutation	SNP	G	G	T	rs376175216	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177G>T	p.Met59Ile	p.M59I	ENST00000280155	1/1	34	26	8	58	58	0	ADRA2A,missense_variant,p.Met59Ile,ENST00000280155,;	T	ENSG00000150594	ENST00000280155	Transcript	missense_variant	1142	177	59	M/I	atG/atT	rs376175216	.	.	1	ADRA2A	HGNC	281	protein_coding	YES	CCDS7569.2	ENSP00000280155	ADA2A_HUMAN	.	UPI000018CE86	.	tolerated(1)	benign(0.001)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF24,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATGCTGCT	byCluster	5	ESCA
NANOS1	0	.	GRCh37	10	120792374	120792374	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2182G>C	.	.	ENST00000425699	1/1	73	18	54	92	92	0	NANOS1,3_prime_UTR_variant,,ENST00000425699,;EIF3A,downstream_gene_variant,,ENST00000541549,;NANOS1,downstream_gene_variant,,ENST00000340087,;EIF3A,downstream_gene_variant,,ENST00000369144,;	C	ENSG00000188613	ENST00000425699	Transcript	3_prime_UTR_variant	3147	.	.	.	.	.	.	.	1	NANOS1	HGNC	23044	protein_coding	YES	CCDS7607.1	ENSP00000393275	NANO1_HUMAN	Q5T9H5_HUMAN	UPI00001D68E9	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGACCCT	.	5	ESCA
SKIDA1	0	.	GRCh37	10	21802640	21802640	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1385delT	.	.	ENST00000449193	4/4	15	9	6	19	19	0	SKIDA1,3_prime_UTR_variant,,ENST00000449193,;SKIDA1,downstream_gene_variant,,ENST00000444772,;	-	ENSG00000180592	ENST00000449193	Transcript	3_prime_UTR_variant	6365	.	.	.	.	.	.	.	-1	SKIDA1	HGNC	32697	protein_coding	YES	CCDS44363.1	ENSP00000410041	.	E9PAX1_HUMAN	UPI00015386B3	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CACAGGATGGTC	.	2	ESCA
SEPT7P9	0	.	GRCh37	10	38680984	38680984	+	RNA	SNP	G	G	A	rs771103277	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.410C>T	.	.	ENST00000489259	2/3	105	82	22	198	198	0	SEPT7P9,non_coding_transcript_exon_variant,,ENST00000489259,;SEPT7P9,non_coding_transcript_exon_variant,,ENST00000475691,;SEPT7P9,non_coding_transcript_exon_variant,,ENST00000328105,;SEPT7P9,non_coding_transcript_exon_variant,,ENST00000604116,;	A	ENSG00000120555	ENST00000489259	Transcript	non_coding_transcript_exon_variant	410	.	.	.	.	rs771103277	.	.	-1	SEPT7P9	HGNC	30810	processed_transcript	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCGCGATT	.	5	ESCA
PCDH15	0	.	GRCh37	10	55849756	55849756	+	Missense_Mutation	SNP	T	T	C	rs373731707	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1985A>G	p.Asn662Ser	p.N662S	ENST00000361849	16/34	32	15	16	35	35	0	PCDH15,missense_variant,p.Asn640Ser,ENST00000395433,;PCDH15,missense_variant,p.Asn669Ser,ENST00000395445,;PCDH15,missense_variant,p.Asn662Ser,ENST00000320301,;PCDH15,missense_variant,p.Asn273Ser,ENST00000409834,;PCDH15,missense_variant,p.Asn625Ser,ENST00000395432,;PCDH15,missense_variant,p.Asn662Ser,ENST00000373955,;PCDH15,missense_variant,p.Asn640Ser,ENST00000373957,;PCDH15,missense_variant,p.Asn662Ser,ENST00000361849,;PCDH15,missense_variant,p.Asn662Ser,ENST00000395438,;PCDH15,missense_variant,p.Asn662Ser,ENST00000395446,;PCDH15,missense_variant,p.Asn667Ser,ENST00000414778,;PCDH15,missense_variant,p.Asn669Ser,ENST00000373965,;PCDH15,missense_variant,p.Asn662Ser,ENST00000395430,;PCDH15,intron_variant,,ENST00000437009,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000448885,;PCDH15,intron_variant,,ENST00000414367,;	C	ENSG00000150275	ENST00000361849	Transcript	missense_variant	2380	1985	662	N/S	aAt/aGt	rs373731707	.	.	-1	PCDH15	HGNC	14674	protein_coding	YES	CCDS44404.1	ENSP00000354950	.	A2A3E7_HUMAN,A2A3D9_HUMAN	UPI0000EE048B	.	tolerated(0.42)	benign(0.217)	16/34	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,PROSITE_profiles:PS50268	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	C:0.0002	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGATTAAAA	byCluster|by1000G	5	ESCA
GDI2	0	.	GRCh37	10	5807199	5807199	+	3'UTR	SNP	T	T	C	rs576613566	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*770A>G	.	.	ENST00000380191	11/11	20	15	4	30	30	0	GDI2,3_prime_UTR_variant,,ENST00000380191,;GDI2,downstream_gene_variant,,ENST00000380132,;FAM208B,downstream_gene_variant,,ENST00000328090,;GDI2,downstream_gene_variant,,ENST00000380181,;GDI2,downstream_gene_variant,,ENST00000447751,;GDI2,non_coding_transcript_exon_variant,,ENST00000479928,;FAM208B,downstream_gene_variant,,ENST00000459693,;FAM208B,downstream_gene_variant,,ENST00000487196,;	C	ENSG00000057608	ENST00000380191	Transcript	3_prime_UTR_variant	2399	.	.	.	.	rs576613566	.	.	-1	GDI2	HGNC	4227	protein_coding	YES	CCDS7071.1	ENSP00000369538	GDIB_HUMAN	Q6IAT1_HUMAN,B3KVE3_HUMAN	UPI000012B39E	.	.	.	11/11	.	.	G:0.0004	G:0	G:0	.	G:0.002	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AGAATTTGGCT	byFrequency|by1000G	4	ESCA
RHOBTB1	0	.	GRCh37	10	62648194	62648194	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1232T>C	p.Phe411Ser	p.F411S	ENST00000337910	6/11	26	14	12	26	26	0	RHOBTB1,missense_variant,p.Phe411Ser,ENST00000337910,;RHOBTB1,missense_variant,p.Phe411Ser,ENST00000357917,;RHOBTB1,non_coding_transcript_exon_variant,,ENST00000483488,;	G	ENSG00000072422	ENST00000337910	Transcript	missense_variant	1570	1232	411	F/S	tTt/tCt	.	.	.	-1	RHOBTB1	HGNC	18738	protein_coding	YES	CCDS7261.1	ENSP00000338671	RHBT1_HUMAN	Q567T3_HUMAN	UPI000000D9B7	.	deleterious(0)	probably_damaging(0.999)	6/11	.	PROSITE_profiles:PS50097,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCGAAAAGGG	.	5	ESCA
ARID5B	0	.	GRCh37	10	63855176	63855176	+	3'UTR	SNP	A	A	G	rs541748596	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2387A>G	.	.	ENST00000279873	10/10	21	9	12	25	25	0	ARID5B,3_prime_UTR_variant,,ENST00000279873,;ARID5B,downstream_gene_variant,,ENST00000309334,;	G	ENSG00000150347	ENST00000279873	Transcript	3_prime_UTR_variant	6364	.	.	.	.	rs541748596	.	.	1	ARID5B	HGNC	17362	protein_coding	YES	CCDS31208.1	ENSP00000279873	ARI5B_HUMAN	.	UPI00001606F0	.	.	.	10/10	.	.	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTATTTGG	by1000G	5	ESCA
PLAU	0	.	GRCh37	10	75677220	75677220	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*897A>G	.	.	ENST00000372764	11/11	42	26	15	55	55	0	PLAU,3_prime_UTR_variant,,ENST00000446342,;PLAU,3_prime_UTR_variant,,ENST00000372762,;PLAU,3_prime_UTR_variant,,ENST00000372764,;C10orf55,intron_variant,,ENST00000409178,;PLAU,downstream_gene_variant,,ENST00000481390,;C10orf55,upstream_gene_variant,,ENST00000412307,;PLAU,downstream_gene_variant,,ENST00000494287,;	G	ENSG00000122861	ENST00000372764	Transcript	3_prime_UTR_variant	2286	.	.	.	.	.	.	.	1	PLAU	HGNC	9052	protein_coding	YES	CCDS7339.1	ENSP00000361850	UROK_HUMAN	S4R3G7_HUMAN,Q9UEJ5_HUMAN,Q96SE8_HUMAN	UPI000013CB02	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAAATAAAA	.	5	ESCA
CDON	0	.	GRCh37	11	125887056	125887056	+	Silent	SNP	G	G	T	rs141221434	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855C>A	p.%3D	p.S285S	ENST00000392693	6/20	44	33	11	45	45	0	CDON,synonymous_variant,p.%3D,ENST00000534661,;CDON,synonymous_variant,p.%3D,ENST00000263577,;CDON,synonymous_variant,p.%3D,ENST00000392693,;CDON,downstream_gene_variant,,ENST00000534818,;CDON,downstream_gene_variant,,ENST00000527967,;CDON,downstream_gene_variant,,ENST00000531586,;CDON,synonymous_variant,p.%3D,ENST00000531830,;CDON,non_coding_transcript_exon_variant,,ENST00000525625,;	T	ENSG00000064309	ENST00000392693	Transcript	synonymous_variant	983	855	285	S	tcC/tcA	rs141221434,COSM106853	.	.	-1	CDON	HGNC	17104	protein_coding	YES	CCDS58192.1	ENSP00000376458	CDON_HUMAN	E9PRD8_HUMAN,E9PPQ7_HUMAN,E9PNF2_HUMAN	UPI0000E0013A	.	.	.	6/20	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF12,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	C:0.0004	.	.	.	.	.	.	.	.	not_provided	1,1	21499247	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTCCGGAGTC	byFrequency|byCluster|by1000G	4	ESCA
AP003039.3	0	.	GRCh37	11	131530893	131530893	+	3'Flank	SNP	C	C	T	rs751773341	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000416725	.	16	10	6	32	32	0	NTM,synonymous_variant,p.%3D,ENST00000416661,;NTM,synonymous_variant,p.%3D,ENST00000436745,;NTM,synonymous_variant,p.%3D,ENST00000550167,;NTM,synonymous_variant,p.%3D,ENST00000427481,;NTM,intron_variant,,ENST00000374791,;NTM,intron_variant,,ENST00000539799,;AP003039.3,downstream_gene_variant,,ENST00000416725,;NTM,non_coding_transcript_exon_variant,,ENST00000477098,;	T	ENSG00000224795	ENST00000416725	Transcript	downstream_gene_variant	.	.	.	.	.	rs751773341	.	1132	-1	AP003039.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAACGGAAA	byFrequency	5	ESCA
NTM	0	.	GRCh37	11	132184551	132184551	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.888G>T	p.%3D	p.V296V	ENST00000425719	6/8	29	23	6	61	61	0	NTM,synonymous_variant,p.%3D,ENST00000457381,;NTM,synonymous_variant,p.%3D,ENST00000374784,;NTM,synonymous_variant,p.%3D,ENST00000374791,;NTM,synonymous_variant,p.%3D,ENST00000539799,;NTM,synonymous_variant,p.%3D,ENST00000425719,;NTM,synonymous_variant,p.%3D,ENST00000374786,;NTM,synonymous_variant,p.%3D,ENST00000427481,;NTM,non_coding_transcript_exon_variant,,ENST00000467255,;NTM,non_coding_transcript_exon_variant,,ENST00000496094,;NTM,non_coding_transcript_exon_variant,,ENST00000474900,;NTM,downstream_gene_variant,,ENST00000498764,;NTM,downstream_gene_variant,,ENST00000490356,;	T	ENSG00000182667	ENST00000425719	Transcript	synonymous_variant	908	888	296	V	gtG/gtT	.	.	.	1	NTM	HGNC	17941	protein_coding	YES	CCDS44777.1	ENSP00000396722	NTRI_HUMAN	.	UPI00001A58B9	.	.	.	6/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19831:SF46,hmmpanther:PTHR19831,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCGTGGCCTC	.	5	ESCA
NCR3LG1	0	.	GRCh37	11	17394103	17394103	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*44C>T	.	.	ENST00000338965	5/5	9	4	5	27	27	0	NCR3LG1,3_prime_UTR_variant,,ENST00000338965,;NCR3LG1,3_prime_UTR_variant,,ENST00000530403,;	T	ENSG00000188211	ENST00000338965	Transcript	3_prime_UTR_variant	1653	.	.	.	.	.	.	.	1	NCR3LG1	HGNC	42400	protein_coding	YES	CCDS55748.1	ENSP00000341637	NR3L1_HUMAN	.	UPI00001F9E11	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTTCATTAC	.	2	ESCA
OR8H3	0	.	GRCh37	11	55890163	55890163	+	Silent	SNP	C	C	G	rs768401704	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315C>G	p.%3D	p.V105V	ENST00000313472	1/1	84	57	26	152	152	0	OR8H3,synonymous_variant,p.%3D,ENST00000313472,;	G	ENSG00000181761	ENST00000313472	Transcript	synonymous_variant	315	315	105	V	gtC/gtG	rs768401704	.	.	1	OR8H3	HGNC	15309	protein_coding	YES	CCDS31519.1	ENSP00000323928	OR8H3_HUMAN	.	UPI0000041D25	.	.	.	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452:SF280,hmmpanther:PTHR26452,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCTTCTT	byFrequency	5	ESCA
RTN3	0	.	GRCh37	11	63531137	63531137	+	3'Flank	SNP	C	C	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000377819	.	47	20	27	44	44	0	RTN3,downstream_gene_variant,,ENST00000537981,;RTN3,downstream_gene_variant,,ENST00000356000,;RTN3,downstream_gene_variant,,ENST00000354497,;RTN3,downstream_gene_variant,,ENST00000339997,;RTN3,downstream_gene_variant,,ENST00000377819,;RTN3,downstream_gene_variant,,ENST00000341307,;C11orf95,non_coding_transcript_exon_variant,,ENST00000433688,;C11orf95,downstream_gene_variant,,ENST00000338498,;RP11-466C23.4,downstream_gene_variant,,ENST00000546282,;C11orf95,downstream_gene_variant,,ENST00000458348,;C11orf95,downstream_gene_variant,,ENST00000445014,;	A	ENSG00000133318	ENST00000377819	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3780	1	RTN3	HGNC	10469	protein_coding	YES	CCDS58141.1	ENSP00000367050	RTN3_HUMAN	.	UPI00004546A2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCGCCGGCTG	.	5	ESCA
STARD10	0	.	GRCh37	11	72466800	72466800	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578-2A>G	.	p.X193_splice	ENST00000334805	.	17	9	8	38	38	0	STARD10,splice_acceptor_variant,,ENST00000545082,;STARD10,splice_acceptor_variant,,ENST00000538536,;STARD10,splice_acceptor_variant,,ENST00000543304,;STARD10,splice_acceptor_variant,,ENST00000400925,;STARD10,splice_acceptor_variant,,ENST00000544767,;STARD10,splice_acceptor_variant,,ENST00000334805,;STARD10,splice_acceptor_variant,,ENST00000537351,;STARD10,splice_acceptor_variant,,ENST00000537947,;STARD10,intron_variant,,ENST00000536728,;ARAP1,intron_variant,,ENST00000359373,;STARD10,downstream_gene_variant,,ENST00000535054,;STARD10,downstream_gene_variant,,ENST00000539138,;ARAP1,upstream_gene_variant,,ENST00000393609,;STARD10,downstream_gene_variant,,ENST00000546314,;STARD10,downstream_gene_variant,,ENST00000536290,;STARD10,downstream_gene_variant,,ENST00000542989,;STARD10,splice_acceptor_variant,,ENST00000538437,;STARD10,splice_acceptor_variant,,ENST00000543089,;STARD10,non_coding_transcript_exon_variant,,ENST00000535075,;STARD10,downstream_gene_variant,,ENST00000535267,;	C	ENSG00000214530	ENST00000334805	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	STARD10	HGNC	10666	protein_coding	YES	CCDS41688.1	ENSP00000335247	PCTL_HUMAN	F5H8G1_HUMAN,F5H5A8_HUMAN,F5H1Z6_HUMAN,F5H0V7_HUMAN	UPI0000035BCF	.	.	.	.	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCCTGTGAG	.	5	ESCA
NCOR2	0	.	GRCh37	12	124826549	124826549	+	Missense_Mutation	SNP	T	T	C	rs772634427	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5008A>G	p.Ile1670Val	p.I1670V	ENST00000405201	34/47	79	36	43	168	168	0	NCOR2,missense_variant,p.Ile1677Val,ENST00000356219,;NCOR2,missense_variant,p.Ile19Val,ENST00000453428,;NCOR2,missense_variant,p.Ile1231Val,ENST00000404121,;NCOR2,missense_variant,p.Ile1660Val,ENST00000429285,;NCOR2,missense_variant,p.Ile1670Val,ENST00000405201,;NCOR2,missense_variant,p.Ile1660Val,ENST00000404621,;NCOR2,missense_variant,p.Ile1661Val,ENST00000397355,;NCOR2,downstream_gene_variant,,ENST00000458234,;NCOR2,upstream_gene_variant,,ENST00000440187,;	C	ENSG00000196498	ENST00000405201	Transcript	missense_variant	5009	5008	1670	I/V	Atc/Gtc	rs772634427	.	.	-1	NCOR2	HGNC	7673	protein_coding	YES	CCDS41858.2	ENSP00000384018	.	C9JFD3_HUMAN,C9J330_HUMAN	UPI000013D737	.	.	possibly_damaging(0.544)	34/47	.	hmmpanther:PTHR13992:SF21,hmmpanther:PTHR13992	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGATGAGGT	.	5	ESCA
WNT5B	0	.	GRCh37	12	1755098	1755098	+	Missense_Mutation	SNP	G	G	A	rs774388139	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.760G>A	p.Ala254Thr	p.A254T	ENST00000397196	5/5	71	51	20	49	49	0	WNT5B,missense_variant,p.Ala254Thr,ENST00000537031,;WNT5B,missense_variant,p.Ala254Thr,ENST00000310594,;WNT5B,missense_variant,p.Ala254Thr,ENST00000397196,;WNT5B,incomplete_terminal_codon_variant,p.%3D,ENST00000543071,;WNT5B,3_prime_UTR_variant,,ENST00000542408,;WNT5B,non_coding_transcript_exon_variant,,ENST00000545747,;	A	ENSG00000111186	ENST00000397196	Transcript	missense_variant	992	760	254	A/T	Gcc/Acc	rs774388139	.	.	1	WNT5B	HGNC	16265	protein_coding	YES	CCDS8510.1	ENSP00000380379	WNT5B_HUMAN	F5H7Q6_HUMAN,F5H364_HUMAN,F5H034_HUMAN	UPI0000138F3C	.	tolerated(0.36)	possibly_damaging(0.782)	5/5	.	hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF87,Pfam_domain:PF00110,SMART_domains:SM00097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCGCCATG	.	5	ESCA
MFSD5	0	.	GRCh37	12	53647345	53647345	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1047C>T	p.%3D	p.C349C	ENST00000534842	2/2	44	39	5	73	73	0	MFSD5,synonymous_variant,p.%3D,ENST00000329548,;MFSD5,synonymous_variant,p.%3D,ENST00000534842,;MFSD5,synonymous_variant,p.%3D,ENST00000551660,;MFSD5,downstream_gene_variant,,ENST00000546655,;MFSD5,downstream_gene_variant,,ENST00000552097,;	T	ENSG00000182544	ENST00000534842	Transcript	synonymous_variant	1194	1047	349	C	tgC/tgT	.	.	.	1	MFSD5	HGNC	28156	protein_coding	YES	CCDS53796.1	ENSP00000442688	MFSD5_HUMAN	F8VV69_HUMAN	UPI0000EE2648	.	.	.	2/2	.	hmmpanther:PTHR24003:SF500,hmmpanther:PTHR24003,Pfam_domain:PF05631,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCTGCCTCCT	.	2	ESCA
USP15	0	.	GRCh37	12	62799539	62799539	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1384A>T	.	.	ENST00000280377	22/22	60	47	13	76	76	0	USP15,3_prime_UTR_variant,,ENST00000353364,;USP15,3_prime_UTR_variant,,ENST00000393654,;USP15,3_prime_UTR_variant,,ENST00000280377,;USP15,intron_variant,,ENST00000549415,;USP15,downstream_gene_variant,,ENST00000552346,;USP15,downstream_gene_variant,,ENST00000549101,;USP15,downstream_gene_variant,,ENST00000548620,;	T	ENSG00000135655	ENST00000280377	Transcript	3_prime_UTR_variant	4388	.	.	.	.	.	.	.	1	USP15	HGNC	12613	protein_coding	YES	CCDS58251.1	ENSP00000280377	UBP15_HUMAN	F8VZG8_HUMAN,F8VVY7_HUMAN	UPI00001379F8	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTAATCAAA	.	5	ESCA
FOXJ2	0	.	GRCh37	12	8196342	8196342	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454A>G	p.Arg152Gly	p.R152G	ENST00000162391	4/11	93	51	42	64	64	0	FOXJ2,missense_variant,p.Arg152Gly,ENST00000428177,;FOXJ2,missense_variant,p.Arg152Gly,ENST00000162391,;	G	ENSG00000065970	ENST00000162391	Transcript	missense_variant	1599	454	152	R/G	Aga/Gga	.	.	.	1	FOXJ2	HGNC	24818	protein_coding	YES	CCDS8587.1	ENSP00000162391	FOXJ2_HUMAN	.	UPI000012ADE1	.	deleterious(0)	probably_damaging(0.989)	4/11	.	SMART_domains:SM00339,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGAGAAGA	.	5	ESCA
OR11H4	0	.	GRCh37	14	20711735	20711735	+	Missense_Mutation	SNP	A	A	G	rs758843352	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785A>G	p.Tyr262Cys	p.Y262C	ENST00000315409	1/1	73	20	53	102	102	0	OR11H4,missense_variant,p.Tyr262Cys,ENST00000315409,;	G	ENSG00000176198	ENST00000315409	Transcript	missense_variant	838	785	262	Y/C	tAt/tGt	rs758843352	.	.	1	OR11H4	HGNC	15347	protein_coding	YES	CCDS32034.1	ENSP00000318997	O11H4_HUMAN	.	UPI0000041C42	.	deleterious(0.02)	benign(0.182)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF99,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTATGGGA	.	5	ESCA
RNF31	0	.	GRCh37	14	24620076	24620076	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1467C>T	p.%3D	p.L489L	ENST00000324103	8/21	42	6	35	68	68	0	RNF31,synonymous_variant,p.%3D,ENST00000560787,;RNF31,synonymous_variant,p.%3D,ENST00000324103,;RNF31,synonymous_variant,p.%3D,ENST00000382687,;RNF31,synonymous_variant,p.%3D,ENST00000559275,;RNF31,downstream_gene_variant,,ENST00000557991,;RNF31,downstream_gene_variant,,ENST00000559533,;PSME2,upstream_gene_variant,,ENST00000216802,;PSME2,upstream_gene_variant,,ENST00000559056,;RNF31,downstream_gene_variant,,ENST00000560071,;RNF31,downstream_gene_variant,,ENST00000560875,;RNF31,upstream_gene_variant,,ENST00000560754,;RNF31,downstream_gene_variant,,ENST00000559308,;PSME2,upstream_gene_variant,,ENST00000560410,;RNF31,downstream_gene_variant,,ENST00000559260,;PSME2,upstream_gene_variant,,ENST00000471700,;PSME2,upstream_gene_variant,,ENST00000559613,;RNF31,downstream_gene_variant,,ENST00000558634,;RNF31,downstream_gene_variant,,ENST00000559438,;PSME2,upstream_gene_variant,,ENST00000561103,;RNF31,downstream_gene_variant,,ENST00000559882,;RNF31,downstream_gene_variant,,ENST00000559583,;RNF31,downstream_gene_variant,,ENST00000557878,;RNF31,intron_variant,,ENST00000491351,;PSME2,upstream_gene_variant,,ENST00000560370,;PSME2,upstream_gene_variant,,ENST00000560788,;RNF31,downstream_gene_variant,,ENST00000558907,;PSME2,upstream_gene_variant,,ENST00000558273,;RP11-468E2.4,upstream_gene_variant,,ENST00000558468,;RNF31,upstream_gene_variant,,ENST00000559071,;RNF31,upstream_gene_variant,,ENST00000559449,;RNF31,upstream_gene_variant,,ENST00000558452,;PSME2,upstream_gene_variant,,ENST00000559453,;PSME2,upstream_gene_variant,,ENST00000559493,;PSME2,upstream_gene_variant,,ENST00000558931,;RNF31,downstream_gene_variant,,ENST00000560342,;PSME2,upstream_gene_variant,,ENST00000560592,;	T	ENSG00000092098	ENST00000324103	Transcript	synonymous_variant	1787	1467	489	L	ctC/ctT	.	.	.	1	RNF31	HGNC	16031	protein_coding	YES	CCDS41931.1	ENSP00000315112	RNF31_HUMAN	H0YNK5_HUMAN,H0YNJ0_HUMAN,H0YNC1_HUMAN,H0YMK6_HUMAN,H0YM83_HUMAN,H0YM57_HUMAN,H0YM13_HUMAN	UPI0000072F93	.	.	.	8/21	.	hmmpanther:PTHR16004,hmmpanther:PTHR16004:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCCAGCT	.	5	ESCA
NID2	0	.	GRCh37	14	52471568	52471568	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*636T>A	.	.	ENST00000216286	22/22	53	37	16	46	46	0	NID2,3_prime_UTR_variant,,ENST00000541773,;NID2,3_prime_UTR_variant,,ENST00000216286,;C14orf166,downstream_gene_variant,,ENST00000553362,;NID2,downstream_gene_variant,,ENST00000556572,;C14orf166,downstream_gene_variant,,ENST00000261700,;C14orf166,downstream_gene_variant,,ENST00000556760,;C14orf166,downstream_gene_variant,,ENST00000555319,;NID2,downstream_gene_variant,,ENST00000553297,;NID2,downstream_gene_variant,,ENST00000555310,;C14orf166,downstream_gene_variant,,ENST00000553707,;C14orf166,downstream_gene_variant,,ENST00000557553,;NID2,downstream_gene_variant,,ENST00000556686,;C14orf166,downstream_gene_variant,,ENST00000553479,;	T	ENSG00000087303	ENST00000216286	Transcript	3_prime_UTR_variant	4764	.	.	.	.	.	.	.	-1	NID2	HGNC	13389	protein_coding	YES	CCDS9706.1	ENSP00000216286	NID2_HUMAN	.	UPI000013C6E1	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTAAAATTG	.	5	ESCA
MAX	0	.	GRCh37	14	65542003	65542003	+	3'Flank	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000358664	.	29	14	15	30	30	0	MAX,3_prime_UTR_variant,,ENST00000284165,;MAX,3_prime_UTR_variant,,ENST00000555932,;MAX,3_prime_UTR_variant,,ENST00000358402,;MAX,intron_variant,,ENST00000341653,;MAX,downstream_gene_variant,,ENST00000556979,;MAX,downstream_gene_variant,,ENST00000556443,;MAX,downstream_gene_variant,,ENST00000557277,;MAX,downstream_gene_variant,,ENST00000556892,;MAX,downstream_gene_variant,,ENST00000557746,;MAX,downstream_gene_variant,,ENST00000555419,;MAX,downstream_gene_variant,,ENST00000555667,;MAX,downstream_gene_variant,,ENST00000358664,;MAX,3_prime_UTR_variant,,ENST00000394606,;MAX,downstream_gene_variant,,ENST00000553928,;MAX,downstream_gene_variant,,ENST00000553951,;	C	ENSG00000125952	ENST00000358664	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	259	-1	MAX	HGNC	6913	protein_coding	YES	CCDS9771.1	ENSP00000351490	MAX_HUMAN	G3V570_HUMAN	UPI0000000C63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAATGCCAG	.	5	ESCA
SERPINA9	0	.	GRCh37	14	94942497	94942497	+	Missense_Mutation	SNP	C	C	A	rs767013285	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13G>T	p.Gly5Cys	p.G5C	ENST00000337425	1/5	118	87	31	132	132	0	SERPINA9,missense_variant,p.Gly32Val,ENST00000546329,;SERPINA9,missense_variant,p.Gly5Cys,ENST00000298845,;SERPINA9,missense_variant,p.Gly5Cys,ENST00000337425,;SERPINA9,5_prime_UTR_variant,,ENST00000448305,;SERPINA9,5_prime_UTR_variant,,ENST00000424550,;SERPINA9,upstream_gene_variant,,ENST00000380365,;SERPINA9,intron_variant,,ENST00000539349,;SERPINA9,missense_variant,p.Gly32Val,ENST00000538527,;	A	ENSG00000170054	ENST00000337425	Transcript	missense_variant	88	13	5	G/C	Ggc/Tgc	rs767013285	.	.	-1	SERPINA9	HGNC	15995	protein_coding	YES	CCDS41982.1	ENSP00000337133	SPA9_HUMAN	.	UPI000024706E	.	deleterious_low_confidence(0.02)	benign(0.418)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCCCTGTC	byFrequency	5	ESCA
KNSTRN	0	.	GRCh37	15	40685826	40685826	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*28T>C	.	.	ENST00000249776	9/9	26	17	9	43	43	0	KNSTRN,3_prime_UTR_variant,,ENST00000608100,;KNSTRN,3_prime_UTR_variant,,ENST00000448395,;KNSTRN,3_prime_UTR_variant,,ENST00000416151,;KNSTRN,3_prime_UTR_variant,,ENST00000249776,;KNSTRN,downstream_gene_variant,,ENST00000557920,;KNSTRN,3_prime_UTR_variant,,ENST00000560220,;KNSTRN,3_prime_UTR_variant,,ENST00000560321,;KNSTRN,3_prime_UTR_variant,,ENST00000560981,;KNSTRN,3_prime_UTR_variant,,ENST00000561169,;KNSTRN,downstream_gene_variant,,ENST00000559083,;KNSTRN,downstream_gene_variant,,ENST00000561367,;KNSTRN,downstream_gene_variant,,ENST00000559304,;	C	ENSG00000128944	ENST00000249776	Transcript	3_prime_UTR_variant	1094	.	.	.	.	.	.	.	1	KNSTRN	HGNC	30767	protein_coding	YES	CCDS42021.1	ENSP00000249776	SKAP_HUMAN	.	UPI000016074A	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCCTCTTGG	.	2	ESCA
RTF1	0	.	GRCh37	15	41775265	41775265	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2380A>T	.	.	ENST00000389629	18/18	14	9	5	19	19	0	RTF1,3_prime_UTR_variant,,ENST00000389629,;RTF1,downstream_gene_variant,,ENST00000561076,;RTF1,downstream_gene_variant,,ENST00000558117,;	T	ENSG00000137815	ENST00000389629	Transcript	3_prime_UTR_variant	4525	.	.	.	.	.	.	.	1	RTF1	HGNC	28996	protein_coding	YES	CCDS32200.2	ENSP00000374280	RTF1_HUMAN	I7GPQ7_HUMAN	UPI0000E23C14	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGAAAAGCCAA	.	4	ESCA
SCAPER	0	.	GRCh37	15	77096904	77096904	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464A>T	p.Glu155Val	p.E155V	ENST00000563290	6/32	22	17	4	49	49	0	SCAPER,missense_variant,p.Glu155Val,ENST00000324767,;SCAPER,missense_variant,p.Glu21Val,ENST00000564177,;SCAPER,missense_variant,p.Glu155Val,ENST00000563290,;SCAPER,missense_variant,p.Glu89Val,ENST00000565372,;SCAPER,missense_variant,p.Glu155Val,ENST00000564590,;SCAPER,missense_variant,p.Glu155Val,ENST00000565970,;SCAPER,missense_variant,p.Glu21Val,ENST00000568382,;SCAPER,5_prime_UTR_variant,,ENST00000538941,;SCAPER,3_prime_UTR_variant,,ENST00000565507,;SCAPER,non_coding_transcript_exon_variant,,ENST00000303521,;SCAPER,upstream_gene_variant,,ENST00000568549,;	A	ENSG00000140386	ENST00000563290	Transcript	missense_variant	560	464	155	E/V	gAa/gTa	.	.	.	-1	SCAPER	HGNC	13081	protein_coding	YES	CCDS53962.1	ENSP00000454973	SCAPE_HUMAN	H3BTY2_HUMAN,H3BR40_HUMAN,H3BPB0_HUMAN	UPI0000E59CC3	.	deleterious(0)	possibly_damaging(0.858)	6/32	.	hmmpanther:PTHR31434,hmmpanther:PTHR31434:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GCTTTTCCTGA	.	4	ESCA
DET1	0	.	GRCh37	15	89074355	89074355	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615T>C	p.%3D	p.H205H	ENST00000564406	3/6	59	35	24	77	77	0	DET1,synonymous_variant,p.%3D,ENST00000564406,;DET1,synonymous_variant,p.%3D,ENST00000444300,;DET1,synonymous_variant,p.%3D,ENST00000268148,;DET1,intron_variant,,ENST00000558413,;DET1,downstream_gene_variant,,ENST00000559656,;DET1,3_prime_UTR_variant,,ENST00000557842,;DET1,3_prime_UTR_variant,,ENST00000557837,;	G	ENSG00000140543	ENST00000564406	Transcript	synonymous_variant	776	615	205	H	caT/caC	.	.	.	-1	DET1	HGNC	25477	protein_coding	YES	CCDS45343.1	ENSP00000456340	DET1_HUMAN	.	UPI00001A8183	.	.	.	3/6	.	Pfam_domain:PF09737,hmmpanther:PTHR13374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATATGGAG	.	5	ESCA
ITFG3	0	.	GRCh37	16	318798	318798	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1471A>T	p.Arg491Trp	p.R491W	ENST00000600536	12/13	43	28	14	67	67	0	ITFG3,missense_variant,p.Arg491Trp,ENST00000442458,;ITFG3,missense_variant,p.Arg491Trp,ENST00000600536,;ITFG3,missense_variant,p.Arg523Ser,ENST00000301679,;ITFG3,missense_variant,p.Arg523Ser,ENST00000450082,;RGS11,3_prime_UTR_variant,,ENST00000397770,;ARHGDIG,5_prime_UTR_variant,,ENST00000435035,;ARHGDIG,5_prime_UTR_variant,,ENST00000412541,;RGS11,3_prime_UTR_variant,,ENST00000316163,;ITFG3,downstream_gene_variant,,ENST00000301678,;ITFG3,downstream_gene_variant,,ENST00000399932,;RGS11,downstream_gene_variant,,ENST00000397768,;ITFG3,downstream_gene_variant,,ENST00000424016,;RGS11,downstream_gene_variant,,ENST00000359740,;ARHGDIG,upstream_gene_variant,,ENST00000464609,;RGS11,3_prime_UTR_variant,,ENST00000168869,;RGS11,non_coding_transcript_exon_variant,,ENST00000477143,;RGS11,downstream_gene_variant,,ENST00000481672,;RGS11,downstream_gene_variant,,ENST00000493449,;	T	ENSG00000269881	ENST00000600536	Transcript	missense_variant	1612	1471	491	R/W	Agg/Tgg	.	.	.	1	ITFG3	Uniprot_gn	14163	protein_coding	YES	.	ENSP00000471331	.	C9JR71_HUMAN,C9JJN3_HUMAN,C9J8V3_HUMAN,C9J3Y6_HUMAN,C9J1M4_HUMAN,C9IYB9_HUMAN,B4DGG1_HUMAN	UPI00017A6FC8	.	tolerated(0.09)	benign(0.011)	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGAGAGGCTC	.	5	ESCA
KIFC3	0	.	GRCh37	16	57806195	57806195	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321A>G	p.%3D	p.E107E	ENST00000379655	4/19	21	17	4	42	41	1	KIFC3,synonymous_variant,p.%3D,ENST00000565684,;KIFC3,synonymous_variant,p.%3D,ENST00000539578,;KIFC3,synonymous_variant,p.%3D,ENST00000379655,;KIFC3,synonymous_variant,p.%3D,ENST00000566648,;KIFC3,synonymous_variant,p.%3D,ENST00000569222,;KIFC3,synonymous_variant,p.%3D,ENST00000540079,;KIFC3,synonymous_variant,p.%3D,ENST00000562503,;KIFC3,synonymous_variant,p.%3D,ENST00000561524,;KIFC3,synonymous_variant,p.%3D,ENST00000445690,;KIFC3,synonymous_variant,p.%3D,ENST00000541240,;KIFC3,5_prime_UTR_variant,,ENST00000562984,;KIFC3,5_prime_UTR_variant,,ENST00000543930,;KIFC3,5_prime_UTR_variant,,ENST00000562311,;KIFC3,5_prime_UTR_variant,,ENST00000421376,;KIFC3,5_prime_UTR_variant,,ENST00000465878,;KIFC3,5_prime_UTR_variant,,ENST00000565351,;KIFC3,5_prime_UTR_variant,,ENST00000565481,;KIFC3,5_prime_UTR_variant,,ENST00000562903,;KIFC3,5_prime_UTR_variant,,ENST00000569619,;KIFC3,5_prime_UTR_variant,,ENST00000569112,;KIFC3,non_coding_transcript_exon_variant,,ENST00000567204,;KIFC3,non_coding_transcript_exon_variant,,ENST00000566975,;KIFC3,downstream_gene_variant,,ENST00000567479,;KIFC3,5_prime_UTR_variant,,ENST00000564136,;KIFC3,downstream_gene_variant,,ENST00000564204,;	C	ENSG00000140859	ENST00000379655	Transcript	synonymous_variant	579	321	107	E	gaA/gaG	.	.	.	-1	KIFC3	HGNC	6326	protein_coding	YES	CCDS10789.2	ENSP00000368976	KIFC3_HUMAN	H3BTU1_HUMAN,H3BTN1_HUMAN,H3BTL6_HUMAN,H3BPE2_HUMAN,H3BNZ0_HUMAN,H3BMR0_HUMAN,H3BMJ1_HUMAN	UPI000059D399	.	.	.	4/19	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTGTTCTAC	.	2	ESCA
CNOT1	0	.	GRCh37	16	58615277	58615277	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1187A>G	p.Tyr396Cys	p.Y396C	ENST00000317147	11/49	45	34	10	84	84	0	CNOT1,missense_variant,p.Tyr396Cys,ENST00000317147,;CNOT1,missense_variant,p.Tyr396Cys,ENST00000569240,;CNOT1,missense_variant,p.Tyr396Cys,ENST00000441024,;CNOT1,missense_variant,p.Tyr396Cys,ENST00000567188,;CNOT1,intron_variant,,ENST00000565605,;	C	ENSG00000125107	ENST00000317147	Transcript	missense_variant	1520	1187	396	Y/C	tAt/tGt	.	.	.	-1	CNOT1	HGNC	7877	protein_coding	YES	CCDS10799.1	ENSP00000320949	CNOT1_HUMAN	H3BUY8_HUMAN,H3BT18_HUMAN,H3BPF1_HUMAN,B7Z6X2_HUMAN,B3KS60_HUMAN	UPI00001FF2F6	.	deleterious(0.05)	possibly_damaging(0.538)	11/49	.	hmmpanther:PTHR13162:SF8,hmmpanther:PTHR13162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTATATATG	.	5	ESCA
CIRH1A	0	.	GRCh37	16	69173784	69173785	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.494dupT	p.Asp166ArgfsTer4	p.D166Rfs*4	ENST00000314423	5/17	52	42	10	110	110	0	CIRH1A,frameshift_variant,p.Asp166ArgfsTer4,ENST00000314423,;CIRH1A,frameshift_variant,p.Asp118ArgfsTer4,ENST00000566227,;CIRH1A,frameshift_variant,p.Asp177ArgfsTer4,ENST00000563299,;CIRH1A,frameshift_variant,p.Asp166ArgfsTer4,ENST00000563094,;CIRH1A,frameshift_variant,p.Asp166ArgfsTer4,ENST00000352319,;CIRH1A,frameshift_variant,p.Asp83ArgfsTer4,ENST00000567460,;CIRH1A,frameshift_variant,p.Asp180ArgfsTer4,ENST00000562237,;CIRH1A,downstream_gene_variant,,ENST00000567235,;CIRH1A,downstream_gene_variant,,ENST00000568448,;CIRH1A,non_coding_transcript_exon_variant,,ENST00000569014,;CIRH1A,upstream_gene_variant,,ENST00000569615,;CIRH1A,non_coding_transcript_exon_variant,,ENST00000564408,;CIRH1A,non_coding_transcript_exon_variant,,ENST00000567015,;CIRH1A,downstream_gene_variant,,ENST00000569800,;	T	ENSG00000141076	ENST00000314423	Transcript	frameshift_variant	670-671	493-494	165	I/IX	ata/aTta	.	.	.	1	CIRH1A	HGNC	1983	protein_coding	YES	CCDS10872.1	ENSP00000327179	CIR1A_HUMAN	J3KTR0_HUMAN,J3KSE6_HUMAN,H3BPD7_HUMAN	UPI0000037300	.	.	.	5/17	.	PROSITE_profiles:PS50294,hmmpanther:PTHR22841,hmmpanther:PTHR22841:SF4,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTCCATAGAC	.	3	ESCA
CHST5	0	.	GRCh37	16	75563364	75563364	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.919C>T	p.Arg307Cys	p.R307C	ENST00000336257	3/3	21	14	6	43	43	0	CHST5,missense_variant,p.Arg313Cys,ENST00000541075,;CHST5,missense_variant,p.Arg307Cys,ENST00000336257,;CHST5,downstream_gene_variant,,ENST00000565039,;RP11-77K12.7,3_prime_UTR_variant,,ENST00000460606,;	A	ENSG00000135702	ENST00000336257	Transcript	missense_variant	2314	919	307	R/C	Cgc/Tgc	.	.	.	-1	CHST5	HGNC	1973	protein_coding	YES	CCDS10919.1	ENSP00000338783	CHST5_HUMAN	.	UPI000006EAEA	.	deleterious(0.03)	probably_damaging(0.959)	3/3	.	hmmpanther:PTHR10704:SF13,hmmpanther:PTHR10704,Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCGCGGATCT	.	5	ESCA
CDH13	0	.	GRCh37	16	83711879	83711879	+	Missense_Mutation	SNP	G	G	A	rs776340601	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1492G>A	p.Val498Ile	p.V498I	ENST00000268613	11/15	33	24	8	71	71	0	CDH13,missense_variant,p.Val412Ile,ENST00000428848,;CDH13,missense_variant,p.Val498Ile,ENST00000268613,;CDH13,missense_variant,p.Val451Ile,ENST00000566620,;CDH13,3_prime_UTR_variant,,ENST00000539548,;	A	ENSG00000140945	ENST00000268613	Transcript	missense_variant	1585	1492	498	V/I	Gta/Ata	rs776340601	.	.	1	CDH13	HGNC	1753	protein_coding	YES	CCDS58485.1	ENSP00000268613	CAD13_HUMAN	.	UPI00020E71A6	.	tolerated(0.21)	benign(0.089)	11/15	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF80,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCGTACCC	byFrequency	5	ESCA
RAI1	0	.	GRCh37	17	17701660	17701660	+	Missense_Mutation	SNP	G	G	A	rs777865239	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5398G>A	p.Asp1800Asn	p.D1800N	ENST00000353383	3/6	31	23	8	54	54	0	RAI1,missense_variant,p.Asp1800Asn,ENST00000353383,;RAI1,intron_variant,,ENST00000261641,;RAI1,upstream_gene_variant,,ENST00000583166,;RAI1,downstream_gene_variant,,ENST00000395774,;	A	ENSG00000108557	ENST00000353383	Transcript	missense_variant	5867	5398	1800	D/N	Gac/Aac	rs777865239,COSM976134	.	.	1	RAI1	HGNC	9834	protein_coding	YES	CCDS11188.1	ENSP00000323074	RAI1_HUMAN	J3QLL5_HUMAN,A8MXE8_HUMAN	UPI0000200AAF	.	deleterious(0.01)	possibly_damaging(0.484)	3/6	.	hmmpanther:PTHR14955:SF6,hmmpanther:PTHR14955	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCCGACAAG	byFrequency	5	ESCA
SPPL2C	0	.	GRCh37	17	43922586	43922586	+	Missense_Mutation	SNP	C	C	T	rs139470538	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.314C>T	p.Thr105Met	p.T105M	ENST00000329196	1/1	42	10	32	44	44	0	SPPL2C,missense_variant,p.Thr105Met,ENST00000329196,;MAPT-AS1,intron_variant,,ENST00000579599,;MAPT-AS1,intron_variant,,ENST00000579244,;MAPT-AS1,upstream_gene_variant,,ENST00000581125,;	T	ENSG00000185294	ENST00000329196	Transcript	missense_variant	331	314	105	T/M	aCg/aTg	rs139470538,COSM4067120	.	.	1	SPPL2C	HGNC	28902	protein_coding	YES	CCDS32673.1	ENSP00000332488	SPP2C_HUMAN	.	UPI0000EE80B4	.	deleterious(0.01)	possibly_damaging(0.883)	1/1	.	hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF38,Pfam_domain:PF02225,Gene3D:3.50.30.30	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0006	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T105T|c.315G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACACGAAAG	byCluster|by1000G	5	ESCA
SKA2	0	.	GRCh37	17	57189207	57189207	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*431T>C	.	.	ENST00000330137	4/4	22	8	14	19	19	0	SKA2,3_prime_UTR_variant,,ENST00000330137,;SKA2,downstream_gene_variant,,ENST00000580541,;SKA2,downstream_gene_variant,,ENST00000437036,;TRIM37,upstream_gene_variant,,ENST00000393066,;SKA2,downstream_gene_variant,,ENST00000583380,;SKA2,downstream_gene_variant,,ENST00000581068,;SKA2,downstream_gene_variant,,ENST00000578105,;TRIM37,upstream_gene_variant,,ENST00000376149,;AC099850.1,intron_variant,,ENST00000451775,;SKA2,downstream_gene_variant,,ENST00000583927,;SKA2,downstream_gene_variant,,ENST00000578519,;SKA2,downstream_gene_variant,,ENST00000583976,;	G	ENSG00000182628	ENST00000330137	Transcript	3_prime_UTR_variant	903	.	.	.	.	.	.	.	-1	SKA2	HGNC	28006	protein_coding	YES	CCDS45747.1	ENSP00000333433	SKA2_HUMAN	J3QL03_HUMAN	UPI0000070DA6	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGTATAACA	.	5	ESCA
PLEKHM1P	0	.	GRCh37	17	62800958	62800958	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1108G>A	.	.	ENST00000578036	6/18	47	31	16	64	64	0	PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000578036,;PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000582986,;PLEKHM1P,downstream_gene_variant,,ENST00000580919,;PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000440036,;PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000582201,;	T	ENSG00000214176	ENST00000578036	Transcript	non_coding_transcript_exon_variant	1108	.	.	.	.	.	.	.	-1	PLEKHM1P	HGNC	35411	processed_transcript	.	.	.	.	.	.	.	.	.	6/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCCGGTG	.	5	ESCA
H3F3B	0	.	GRCh37	17	73774627	73774628	+	3'UTR	INS	-	-	AAGTATTTTT	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*48_*49insAAAAATACTT	.	.	ENST00000254810	4/4	19	9	10	50	50	0	H3F3B,3_prime_UTR_variant,,ENST00000591890,;H3F3B,3_prime_UTR_variant,,ENST00000592643,;H3F3B,3_prime_UTR_variant,,ENST00000254810,;H3F3B,downstream_gene_variant,,ENST00000587560,;H3F3B,downstream_gene_variant,,ENST00000586270,;H3F3B,downstream_gene_variant,,ENST00000589599,;H3F3B,downstream_gene_variant,,ENST00000586607,;H3F3B,downstream_gene_variant,,ENST00000587171,;H3F3B,non_coding_transcript_exon_variant,,ENST00000593254,;H3F3B,non_coding_transcript_exon_variant,,ENST00000586518,;H3F3B,non_coding_transcript_exon_variant,,ENST00000589949,;H3F3B,downstream_gene_variant,,ENST00000589417,;H3F3B,downstream_gene_variant,,ENST00000591893,;	AAGTATTTTT	ENSG00000132475	ENST00000254810	Transcript	3_prime_UTR_variant	592-593	.	.	.	.	.	.	.	-1	H3F3B	HGNC	4765	protein_coding	YES	CCDS11729.1	ENSP00000254810	H33_HUMAN	K7EK07_HUMAN,B4E380_HUMAN,B2R4P9_HUMAN	UPI00000007B0	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAACCAAAGTA	.	2	ESCA
TP53	0	.	GRCh37	17	7578403	7578403	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	5/11	26	6	20	41	41	0	TP53,missense_variant,p.Cys176Tyr,ENST00000413465,;TP53,missense_variant,p.Cys176Tyr,ENST00000420246,;TP53,missense_variant,p.Cys176Tyr,ENST00000269305,;TP53,missense_variant,p.Cys44Tyr,ENST00000509690,;TP53,missense_variant,p.Cys176Tyr,ENST00000359597,;TP53,missense_variant,p.Cys83Tyr,ENST00000514944,;TP53,missense_variant,p.Cys176Tyr,ENST00000445888,;TP53,missense_variant,p.Cys176Tyr,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	717	527	176	C/Y	tGc/tAc	TP53_g.12515G>A,TP53_g.12515del,TP53_g.12515G>T,TP53_g.12515G>C,COSM10645,COSM44645,COSM10687,COSM117398,COSM99672,COSM3773309,COSM99669,COSM117395,COSM3773312,COSM117396,COSM99670,COSM3773314,COSM3388204,COSM3378352,COSM3773311,COSM1640850,COSM1649384,COSM3773310,COSM99671,COSM117397,COSM3773313	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.995)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.C44Y|c.131G>A|20,SITE|p.C176Y|c.527G>A|73,SITE|p.C176Y|c.527G>A|19,SITE|p.C83Y|c.248G>A|19,SITE|p.C176Y|c.527G>A|19,SITE|p.C176Y|c.527G>A|11,SITE|p.C176Y|c.527G>A|9,CODON|p.0?|c.1_1182del1182|6,CODON|p.P177_C182delPHHERC|c.526_543del18|3,CODON|p.H178fs*69|c.528delC|3,CODON|p.C176*|c.528C>A|3,CODON|p.C44*|c.132C>A|3,CODON|p.C176*|c.528C>A|11,CODON|p.C176W|c.528C>G|12,CODON|p.C83*|c.249C>A|3,CODON|p.C176*|c.528C>A|3,CODON|p.C176fs*71|c.526delT|7,CODON|p.C176F|c.527G>T|33,CODON|p.C176F|c.527G>T|133,CODON|p.C176F|c.527G>T|11,CODON|p.C176F|c.527G>T|33,CODON|p.C176S|c.527G>C|9,CODON|p.C83F|c.248G>T|33,CODON|p.C44F|c.131G>T|34,CODON|p.C176F|c.527G>T|17,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.E180K|c.538G>A|6,BUFFER|p.E180*|c.538G>T|14,BUFFER|p.H179Q|c.537T>A|7,BUFFER|p.H179Q|c.537T>A|16,BUFFER|p.H179Q|c.537T>A|7,BUFFER|p.H179Q|c.537T>A|5,BUFFER|p.H86Q|c.258T>A|7,BUFFER|p.H47Q|c.141T>A|7,BUFFER|p.H179Q|c.537T>G|9,BUFFER|p.H179R|c.536A>G|17,BUFFER|p.H179L|c.536A>T|40,BUFFER|p.H47R|c.140A>G|31,BUFFER|p.H86R|c.257A>G|30,BUFFER|p.H179L|c.536A>T|4,BUFFER|p.H179R|c.536A>G|136,BUFFER|p.H179L|c.536A>T|7,BUFFER|p.H179R|c.536A>G|30,BUFFER|p.H179L|c.536A>T|7,BUFFER|p.H47L|c.140A>T|9,BUFFER|p.H179P|c.536A>C|5,BUFFER|p.H179R|c.536A>G|21,BUFFER|p.H86L|c.257A>T|7,BUFFER|p.H179R|c.536A>G|30,BUFFER|p.H179Y|c.534_535CC>TT|8,BUFFER|p.H179D|c.535C>G|12,BUFFER|p.H179Y|c.535C>T|4,BUFFER|p.H47Y|c.139C>T|15,BUFFER|p.H179Y|c.535C>T|5,BUFFER|p.H179Y|c.535C>T|88,BUFFER|p.H179N|c.535C>A|15,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H86Y|c.256C>T|14,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175L|c.524G>T|20,BUFFER|p.R175H|c.524G>A|181,BUFFER|p.R175P|c.524G>C|6,BUFFER|p.R43H|c.128G>A|183,BUFFER|p.R82H|c.245G>A|183,BUFFER|p.R175H|c.524G>A|124,BUFFER|p.R175L|c.524G>T|3,BUFFER|p.R175L|c.524G>T|3,BUFFER|p.R175H|c.524G>A|180,BUFFER|p.R175H|c.524G>A|926,BUFFER|p.R175L|c.524G>T|3,BUFFER|p.R175H|c.524G>A|88,BUFFER|p.R43L|c.128G>T|3,BUFFER|p.R82L|c.245G>T|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R82G|c.244C>G|5,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43G|c.127C>G|8,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175G|c.523C>G|16,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R174K|c.521G>A|5,BUFFER|p.R174W|c.520A>T|11,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGCAGCGC	.	5	ESCA
RNF213	0	.	GRCh37	17	78328011	78328011	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10726+45C>G	.	.	ENST00000582970	.	11	2	8	12	12	0	RNF213,intron_variant,,ENST00000582970,;RNF213,intron_variant,,ENST00000336301,;RNF213,intron_variant,,ENST00000508628,;CTD-2047H16.4,non_coding_transcript_exon_variant,,ENST00000575034,;CTD-2047H16.4,downstream_gene_variant,,ENST00000572151,;RNF213,intron_variant,,ENST00000558116,;RNF213,upstream_gene_variant,,ENST00000560694,;	G	ENSG00000173821	ENST00000582970	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RNF213	HGNC	14539	protein_coding	YES	CCDS58606.1	ENSP00000464087	RN213_HUMAN	H3BLU6_HUMAN	UPI0001D3BDB1	.	.	.	.	35/67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGCTCTTCCT	.	3	ESCA
RNF213	0	.	GRCh37	17	78360667	78360667	+	Missense_Mutation	SNP	G	G	T	rs768274164	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14898G>T	p.Gln4966His	p.Q4966H	ENST00000582970	63/68	19	6	13	32	32	0	RNF213,missense_variant,p.Gln3039His,ENST00000336301,;RNF213,missense_variant,p.Gln4966His,ENST00000582970,;RNF213,missense_variant,p.Gln5015His,ENST00000508628,;CTD-2047H16.4,intron_variant,,ENST00000572151,;CTD-2047H16.4,intron_variant,,ENST00000575034,;CTD-2047H16.4,intron_variant,,ENST00000573394,;RNF213,non_coding_transcript_exon_variant,,ENST00000427003,;RNF213,non_coding_transcript_exon_variant,,ENST00000560083,;RNF213,non_coding_transcript_exon_variant,,ENST00000411702,;RNF213,upstream_gene_variant,,ENST00000573919,;RNF213,downstream_gene_variant,,ENST00000558116,;RNF213,downstream_gene_variant,,ENST00000570776,;	T	ENSG00000173821	ENST00000582970	Transcript	missense_variant	15041	14898	4966	Q/H	caG/caT	rs768274164	.	.	1	RNF213	HGNC	14539	protein_coding	YES	CCDS58606.1	ENSP00000464087	RN213_HUMAN	H3BLU6_HUMAN	UPI0001D3BDB1	.	.	probably_damaging(0.987)	63/68	.	hmmpanther:PTHR22605,hmmpanther:PTHR22605:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCAGGGCAA	.	5	ESCA
ZNF750	0	.	GRCh37	17	80790098	80790131	+	Frame_Shift_Del	DEL	TGGTTGGTTTGCTTGGGGTCTAGTGAGTTAGATT	TGGTTGGTTTGCTTGGGGTCTAGTGAGTTAGATT	-	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	TGGTTGGTTTGCTTGGGGTCTAGTGAGTTAGATT	TGGTTGGTTTGCTTGGGGTCTAGTGAGTTAGATT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200_233delAATCTAACTCACTAGACCCCAAGCAAACCAACCA	p.Lys67SerfsTer288	p.K67Sfs*288	ENST00000269394	2/3	53	24	29	58	58	0	ZNF750,frameshift_variant,p.Lys67SerfsTer288,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	-	ENSG00000141579	ENST00000269394	Transcript	frameshift_variant	1034-1067	200-233	67-78	KSNSLDPKQTNQ/X	aAATCTAACTCACTAGACCCCAAGCAAACCAACCAg/ag	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCGGGCTGGTTGGTTTGCTTGGGGTCTAGTGAGTTAGATTTAGGG	.	3	ESCA
CEP192	0	.	GRCh37	18	13015442	13015442	+	Missense_Mutation	SNP	C	C	G	rs768286853	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.635C>G	p.Ser212Cys	p.S212C	ENST00000506447	6/45	17	8	9	35	35	0	CEP192,missense_variant,p.Ser212Cys,ENST00000589596,;CEP192,missense_variant,p.Ser212Cys,ENST00000506447,;CEP192,5_prime_UTR_variant,,ENST00000325971,;CEP192,missense_variant,p.Ser101Cys,ENST00000513432,;	G	ENSG00000101639	ENST00000506447	Transcript	missense_variant	715	635	212	S/C	tCt/tGt	rs768286853	.	.	1	CEP192	HGNC	25515	protein_coding	YES	CCDS32792.2	ENSP00000427550	.	E9PF99_HUMAN	UPI0001B09235	.	deleterious(0)	probably_damaging(0.983)	6/45	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTCTTCTG	.	5	ESCA
ZNF709	0	.	GRCh37	19	12576489	12576489	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247A>G	p.Ile83Val	p.I83V	ENST00000428311	4/4	55	26	29	73	73	0	ZNF709,missense_variant,p.Ile112Val,ENST00000455490,;ZNF709,missense_variant,p.Ile83Val,ENST00000428311,;ZNF709,missense_variant,p.Ile83Val,ENST00000397732,;CTD-3105H18.7,downstream_gene_variant,,ENST00000420038,;CTD-3105H18.18,intron_variant,,ENST00000598753,;	C	ENSG00000196826	ENST00000428311	Transcript	missense_variant	389	247	83	I/V	Atc/Gtc	.	.	.	-1	ZNF709	Uniprot_gn	20629	protein_coding	YES	.	ENSP00000404127	.	.	UPI000006CF50	.	tolerated(0.11)	benign(0)	4/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24379	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGATGGTTT	.	5	ESCA
CC2D1A	0	.	GRCh37	19	14037327	14037327	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1941-3A>G	.	.	ENST00000318003	.	29	14	14	60	60	0	CC2D1A,splice_region_variant,,ENST00000589606,;CC2D1A,splice_region_variant,,ENST00000587508,;CC2D1A,splice_region_variant,,ENST00000318003,;PODNL1,downstream_gene_variant,,ENST00000538517,;PODNL1,downstream_gene_variant,,ENST00000587954,;PODNL1,downstream_gene_variant,,ENST00000588872,;CC2D1A,splice_region_variant,,ENST00000586955,;CC2D1A,splice_region_variant,,ENST00000589224,;CC2D1A,splice_region_variant,,ENST00000589138,;CC2D1A,downstream_gene_variant,,ENST00000589679,;CC2D1A,downstream_gene_variant,,ENST00000588932,;	G	ENSG00000132024	ENST00000318003	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	CC2D1A	HGNC	30237	protein_coding	YES	CCDS42512.1	ENSP00000313601	C2D1A_HUMAN	.	UPI0000203524	.	.	.	.	17/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGGAAGGAT	.	4	ESCA
COLGALT1	0	.	GRCh37	19	17692130	17692130	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1746C>T	p.%3D	p.V582V	ENST00000252599	12/12	32	24	7	40	40	0	COLGALT1,synonymous_variant,p.%3D,ENST00000252599,;COLGALT1,downstream_gene_variant,,ENST00000597147,;COLGALT1,non_coding_transcript_exon_variant,,ENST00000593832,;COLGALT1,downstream_gene_variant,,ENST00000597075,;	T	ENSG00000130309	ENST00000252599	Transcript	synonymous_variant	1866	1746	582	V	gtC/gtT	.	.	.	1	COLGALT1	HGNC	26182	protein_coding	YES	CCDS12363.1	ENSP00000252599	GT251_HUMAN	Q8WUI9_HUMAN,M0QYH0_HUMAN,B3KQ10_HUMAN	UPI000003B0F7	.	.	.	12/12	.	hmmpanther:PTHR10730:SF10,hmmpanther:PTHR10730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACGTCAAGAC	.	5	ESCA
ARRDC2	0	.	GRCh37	19	18119840	18119840	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402C>A	p.%3D	p.T134T	ENST00000222250	3/8	53	29	24	74	74	0	ARRDC2,synonymous_variant,p.%3D,ENST00000593560,;ARRDC2,synonymous_variant,p.%3D,ENST00000379656,;ARRDC2,synonymous_variant,p.%3D,ENST00000222250,;ARRDC2,5_prime_UTR_variant,,ENST00000595712,;ARRDC2,non_coding_transcript_exon_variant,,ENST00000608009,;ARRDC2,downstream_gene_variant,,ENST00000600788,;ARRDC2,non_coding_transcript_exon_variant,,ENST00000593460,;ARRDC2,upstream_gene_variant,,ENST00000594411,;ARRDC2,downstream_gene_variant,,ENST00000596105,;	A	ENSG00000105643	ENST00000222250	Transcript	synonymous_variant	545	402	134	T	acC/acA	.	.	.	1	ARRDC2	HGNC	25225	protein_coding	YES	CCDS12370.1	ENSP00000222250	ARRD2_HUMAN	.	UPI000003F083	.	.	.	3/8	.	hmmpanther:PTHR11188:SF48,hmmpanther:PTHR11188,Pfam_domain:PF00339,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCACCCTGCA	.	5	ESCA
ZNF221	0	.	GRCh37	19	44470083	44470083	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429C>T	p.%3D	p.S143S	ENST00000251269	6/6	23	13	9	70	70	0	ZNF221,synonymous_variant,p.%3D,ENST00000592350,;ZNF221,synonymous_variant,p.%3D,ENST00000587682,;ZNF221,synonymous_variant,p.%3D,ENST00000251269,;ZNF155,upstream_gene_variant,,ENST00000590411,;ZNF221,downstream_gene_variant,,ENST00000591168,;	T	ENSG00000159905	ENST00000251269	Transcript	synonymous_variant	757	429	143	S	agC/agT	.	.	.	1	ZNF221	HGNC	13014	protein_coding	YES	CCDS12633.1	ENSP00000251269	ZN221_HUMAN	Q16646_HUMAN,K7EIT6_HUMAN	UPI000013CCF3	.	.	.	6/6	.	hmmpanther:PTHR24388:SF3,hmmpanther:PTHR24388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAGCTCTCA	.	5	ESCA
KDM4B	0	.	GRCh37	19	5131966	5131966	+	Silent	SNP	G	G	A	rs755937200	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1854G>A	p.%3D	p.P618P	ENST00000159111	13/23	30	17	13	56	56	0	KDM4B,synonymous_variant,p.%3D,ENST00000588361,;KDM4B,synonymous_variant,p.%3D,ENST00000536461,;KDM4B,synonymous_variant,p.%3D,ENST00000159111,;KDM4B,upstream_gene_variant,,ENST00000588166,;KDM4B,non_coding_transcript_exon_variant,,ENST00000589104,;	A	ENSG00000127663	ENST00000159111	Transcript	synonymous_variant	2072	1854	618	P	ccG/ccA	rs755937200	.	.	1	KDM4B	HGNC	29136	protein_coding	YES	CCDS12138.1	ENSP00000159111	KDM4B_HUMAN	K7ES23_HUMAN	UPI00001C202B	.	.	.	13/23	.	hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCGCCCAC	byFrequency	5	ESCA
ZSCAN18	0	.	GRCh37	19	58595787	58595787	+	3'Flank	SNP	C	C	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000600404	.	32	20	11	56	56	0	ZSCAN18,3_prime_UTR_variant,,ENST00000240727,;ZSCAN18,3_prime_UTR_variant,,ENST00000433686,;ZSCAN18,3_prime_UTR_variant,,ENST00000601144,;ZSCAN18,downstream_gene_variant,,ENST00000600897,;ZSCAN18,downstream_gene_variant,,ENST00000421612,;ZSCAN18,downstream_gene_variant,,ENST00000600845,;ZSCAN18,downstream_gene_variant,,ENST00000600404,;ZSCAN18,downstream_gene_variant,,ENST00000600522,;ZNF135,3_prime_UTR_variant,,ENST00000515535,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000596372,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000598497,;ZSCAN18,downstream_gene_variant,,ENST00000595784,;ZSCAN18,downstream_gene_variant,,ENST00000594191,;ZSCAN18,downstream_gene_variant,,ENST00000600318,;	A	ENSG00000121413	ENST00000600404	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	62	-1	ZSCAN18	HGNC	21037	protein_coding	YES	CCDS46214.1	ENSP00000470123	ZSC18_HUMAN	Q69Z04_HUMAN,M0R1U9_HUMAN	UPI00017A6DAF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGCTGCAG	.	5	ESCA
UBIAD1	0	.	GRCh37	1	11333860	11333860	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272T>A	p.Val91Asp	p.V91D	ENST00000376810	1/2	49	24	25	71	71	0	UBIAD1,missense_variant,p.Val91Asp,ENST00000376804,;UBIAD1,missense_variant,p.Val91Asp,ENST00000376810,;UBIAD1,upstream_gene_variant,,ENST00000483738,;UBIAD1,upstream_gene_variant,,ENST00000486588,;UBE2V2P3,downstream_gene_variant,,ENST00000433562,;	A	ENSG00000120942	ENST00000376810	Transcript	missense_variant	598	272	91	V/D	gTc/gAc	.	.	.	1	UBIAD1	HGNC	30791	protein_coding	YES	CCDS129.1	ENSP00000366006	UBIA1_HUMAN	.	UPI0000073E35	.	deleterious(0)	probably_damaging(0.969)	1/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR13929,hmmpanther:PTHR13929:SF5,Pfam_domain:PF01040,PIRSF_domain:PIRSF005355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGTCCTGG	.	5	ESCA
ADAMTSL4	0	.	GRCh37	1	150529724	150529724	+	Missense_Mutation	SNP	C	C	T	rs745841113	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1960C>T	p.Pro654Ser	p.P654S	ENST00000271643	12/19	21	15	6	29	29	0	ADAMTSL4,missense_variant,p.Pro654Ser,ENST00000271643,;ADAMTSL4,missense_variant,p.Pro654Ser,ENST00000369038,;ADAMTSL4,missense_variant,p.Pro654Ser,ENST00000369041,;ADAMTSL4,missense_variant,p.Pro677Ser,ENST00000369039,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000369035,;RP11-54A4.2,intron_variant,,ENST00000442435,;ADAMTSL4,upstream_gene_variant,,ENST00000489159,;	T	ENSG00000143382	ENST00000271643	Transcript	missense_variant	2196	1960	654	P/S	Ccg/Tcg	rs745841113,CM104797	.	.	1	ADAMTSL4	HGNC	19706	protein_coding	YES	CCDS955.1	ENSP00000271643	ATL4_HUMAN	Q9UFG7_HUMAN,A8KAH2_HUMAN	UPI00001E0572	.	tolerated(0.07)	benign(0.341)	12/19	.	hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF144	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCGCCCCGCCC	byFrequency	4	ESCA
FLG	0	.	GRCh37	1	152279527	152279527	+	Missense_Mutation	SNP	T	T	C	rs200423945	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7835A>G	p.Asp2612Gly	p.D2612G	ENST00000368799	3/3	30	26	4	50	50	0	FLG,missense_variant,p.Asp2612Gly,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	C	ENSG00000143631	ENST00000368799	Transcript	missense_variant	7871	7835	2612	D/G	gAc/gGc	rs200423945	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	possibly_damaging(0.753)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTCTGTCTTCT	byFrequency|byCluster	2	ESCA
PLXNA2	0	.	GRCh37	1	208213028	208213028	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4438G>A	p.Glu1480Lys	p.E1480K	ENST00000367033	24/32	26	17	9	43	43	0	PLXNA2,missense_variant,p.Glu1480Lys,ENST00000367033,;PLXNA2,non_coding_transcript_exon_variant,,ENST00000463510,;	T	ENSG00000076356	ENST00000367033	Transcript	missense_variant	5196	4438	1480	E/K	Gag/Aag	COSM383762	.	.	-1	PLXNA2	HGNC	9100	protein_coding	YES	CCDS31013.1	ENSP00000356000	PLXA2_HUMAN	.	UPI000022B239	.	deleterious(0.02)	probably_damaging(0.983)	24/32	.	hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625,Pfam_domain:PF08337	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E1480K|c.4438G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCGCCCG	.	5	ESCA
MUL1	0	.	GRCh37	1	20827583	20827583	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000264198	4/4	23	19	4	47	47	0	MUL1,missense_variant,p.Tyr220Cys,ENST00000264198,;	C	ENSG00000090432	ENST00000264198	Transcript	missense_variant	796	659	220	Y/C	tAt/tGt	.	.	.	-1	MUL1	HGNC	25762	protein_coding	YES	CCDS208.1	ENSP00000264198	MUL1_HUMAN	B7Z8S4_HUMAN	UPI00000361FC	.	deleterious(0)	probably_damaging(0.959)	4/4	.	hmmpanther:PTHR12183:SF4,hmmpanther:PTHR12183,Pfam_domain:PF12483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTAGATAGTAC	.	3	ESCA
ITPKB	0	.	GRCh37	1	226822143	226822143	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*229A>G	.	.	ENST00000429204	8/8	19	11	7	30	30	0	ITPKB,3_prime_UTR_variant,,ENST00000272117,;ITPKB,3_prime_UTR_variant,,ENST00000429204,;	C	ENSG00000143772	ENST00000429204	Transcript	3_prime_UTR_variant	3398	.	.	.	.	.	.	.	-1	ITPKB	HGNC	6179	protein_coding	YES	CCDS1555.1	ENSP00000411152	IP3KB_HUMAN	.	UPI000013D92B	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCATTTCTC	.	5	ESCA
OR14A16	0	.	GRCh37	1	247978881	247978881	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.151C>T	p.His51Tyr	p.H51Y	ENST00000357627	1/1	16	12	4	22	22	0	OR14A16,missense_variant,p.His51Tyr,ENST00000357627,;	A	ENSG00000196772	ENST00000357627	Transcript	missense_variant	151	151	51	H/Y	Cat/Tat	.	.	.	-1	OR14A16	HGNC	15022	protein_coding	YES	CCDS31097.1	ENSP00000350248	O14AG_HUMAN	.	UPI0000041CE2	.	tolerated(0.48)	benign(0.37)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	ATGATGGTCCA	.	4	ESCA
GMEB1	0	.	GRCh37	1	29030774	29030774	+	Silent	SNP	G	G	A	rs761435111	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.831G>A	p.%3D	p.Q277Q	ENST00000294409	8/10	23	11	12	40	40	0	GMEB1,synonymous_variant,p.%3D,ENST00000294409,;GMEB1,synonymous_variant,p.%3D,ENST00000373816,;GMEB1,synonymous_variant,p.%3D,ENST00000361872,;GMEB1,non_coding_transcript_exon_variant,,ENST00000480454,;	A	ENSG00000162419	ENST00000294409	Transcript	synonymous_variant	921	831	277	Q	caG/caA	rs761435111	.	.	1	GMEB1	HGNC	4370	protein_coding	YES	CCDS327.1	ENSP00000294409	GMEB1_HUMAN	.	UPI000012B8AB	.	.	.	8/10	.	hmmpanther:PTHR10417,hmmpanther:PTHR10417:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACAGAAGGA	.	5	ESCA
RLF	0	.	GRCh37	1	40654740	40654740	+	Missense_Mutation	SNP	A	A	G	rs761298030	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.251A>G	p.Tyr84Cys	p.Y84C	ENST00000372771	2/8	35	24	11	42	42	0	RLF,missense_variant,p.Tyr84Cys,ENST00000372771,;	G	ENSG00000117000	ENST00000372771	Transcript	missense_variant	278	251	84	Y/C	tAt/tGt	rs761298030	.	.	1	RLF	HGNC	10025	protein_coding	YES	CCDS448.1	ENSP00000361857	RLF_HUMAN	.	UPI000013C9DA	.	deleterious(0)	probably_damaging(0.996)	2/8	.	hmmpanther:PTHR15507:SF18,hmmpanther:PTHR15507	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAATATGCAA	byFrequency	5	ESCA
RNF220	0	.	GRCh37	1	44871073	44871075	+	5'UTR	DEL	GCC	GCC	-	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	GCC	GCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-226_-224delCGC	.	.	ENST00000355387	1/15	55	49	6	67	67	0	RNF220,5_prime_UTR_variant,,ENST00000361799,;RNF220,5_prime_UTR_variant,,ENST00000355387,;RNF220,upstream_gene_variant,,ENST00000487332,;	-	ENSG00000187147	ENST00000355387	Transcript	5_prime_UTR_variant	208-210	.	.	.	.	.	.	.	1	RNF220	HGNC	25552	protein_coding	YES	CCDS510.1	ENSP00000347548	RN220_HUMAN	D3DPZ1_HUMAN	UPI000035895E	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	17	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCCGCTGCCGCCGC	.	2	ESCA
NSUN4	0	.	GRCh37	1	46826379	46826380	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758dupT	p.Val254GlyfsTer14	p.V254Gfs*14	ENST00000474844	5/6	39	31	8	53	53	0	NSUN4,frameshift_variant,p.Val205GlyfsTer14,ENST00000536062,;NSUN4,frameshift_variant,p.Val254GlyfsTer14,ENST00000474844,;NSUN4,frameshift_variant,p.Val205GlyfsTer14,ENST00000537428,;NSUN4,non_coding_transcript_exon_variant,,ENST00000495427,;NSUN4,non_coding_transcript_exon_variant,,ENST00000471871,;NSUN4,non_coding_transcript_exon_variant,,ENST00000498008,;NSUN4,non_coding_transcript_exon_variant,,ENST00000486270,;NSUN4,3_prime_UTR_variant,,ENST00000307089,;	T	ENSG00000117481	ENST00000474844	Transcript	frameshift_variant	1407-1408	757-758	253	L/LX	ctg/cTtg	.	.	.	1	NSUN4	HGNC	31802	protein_coding	YES	CCDS534.1	ENSP00000419740	NSUN4_HUMAN	.	UPI000013EBC5	.	.	.	5/6	.	PROSITE_profiles:PS51686,hmmpanther:PTHR22808,hmmpanther:PTHR22808:SF3,Gene3D:3.40.50.150,Pfam_domain:PF01189,Superfamily_domains:SSF53335,Prints_domain:PR02008	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGTGCTGGTG	.	3	ESCA
SNX7	0	.	GRCh37	1	99157106	99157106	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490T>G	p.Phe164Val	p.F164V	ENST00000306121	4/9	33	25	7	48	48	0	SNX7,missense_variant,p.Phe100Val,ENST00000370189,;SNX7,missense_variant,p.Phe164Val,ENST00000306121,;SNX7,missense_variant,p.Phe100Val,ENST00000454199,;SNX7,intron_variant,,ENST00000529992,;SNX7,3_prime_UTR_variant,,ENST00000528824,;	G	ENSG00000162627	ENST00000306121	Transcript	missense_variant	499	490	164	F/V	Ttt/Gtt	.	.	.	1	SNX7	HGNC	14971	protein_coding	YES	CCDS755.2	ENSP00000304429	SNX7_HUMAN	B7ZC83_HUMAN	UPI0000205396	.	deleterious(0.01)	probably_damaging(0.964)	4/9	.	Superfamily_domains:SSF64268,SMART_domains:SM00312,Gene3D:3.30.1520.10,Pfam_domain:PF00787,hmmpanther:PTHR10555:SF21,hmmpanther:PTHR10555,PROSITE_profiles:PS50195	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAGTTTATA	.	5	ESCA
HNF4A	0	.	GRCh37	20	43058230	43058230	+	Silent	SNP	G	G	A	rs377052026	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1350G>A	p.%3D	p.P450P	ENST00000316099	10/10	78	45	32	101	101	0	HNF4A,synonymous_variant,p.%3D,ENST00000415691,;HNF4A,synonymous_variant,p.%3D,ENST00000316099,;HNF4A,synonymous_variant,p.%3D,ENST00000316673,;HNF4A,synonymous_variant,p.%3D,ENST00000457232,;HNF4A,downstream_gene_variant,,ENST00000443598,;AL132772.1,upstream_gene_variant,,ENST00000581483,;RP5-1013A22.5,upstream_gene_variant,,ENST00000608247,;HNF4A,3_prime_UTR_variant,,ENST00000372920,;	A	ENSG00000101076	ENST00000316099	Transcript	synonymous_variant	1439	1350	450	P	ccG/ccA	rs377052026	.	.	1	HNF4A	HGNC	5024	protein_coding	YES	CCDS13330.1	ENSP00000312987	HNF4A_HUMAN	F1D8T1_HUMAN	UPI000016A0BA	.	.	.	10/10	.	.	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCGGGAGC	byCluster|by1000G	5	ESCA
PREX1	0	.	GRCh37	20	47251277	47251277	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4204A>G	p.Thr1402Ala	p.T1402A	ENST00000371941	33/40	22	18	3	39	39	0	PREX1,missense_variant,p.Thr1402Ala,ENST00000396220,;PREX1,missense_variant,p.Thr1402Ala,ENST00000371941,;PREX1,missense_variant,p.Thr724Ala,ENST00000482556,;	C	ENSG00000124126	ENST00000371941	Transcript	missense_variant	4227	4204	1402	T/A	Acg/Gcg	.	.	.	-1	PREX1	HGNC	32594	protein_coding	YES	CCDS13410.1	ENSP00000361009	PREX1_HUMAN	.	UPI000013D375	.	tolerated(1)	benign(0.003)	33/40	.	hmmpanther:PTHR22829,hmmpanther:PTHR22829:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCGTCACCC	.	2	ESCA
NFATC2	0	.	GRCh37	20	50140465	50140466	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.314_315insT	p.Ala106GlyfsTer66	p.A106Gfs*66	ENST00000396009	2/10	34	26	8	36	36	0	NFATC2,frameshift_variant,p.Ala106GlyfsTer66,ENST00000396009,;NFATC2,frameshift_variant,p.Ala86GlyfsTer66,ENST00000609943,;NFATC2,frameshift_variant,p.Ala106GlyfsTer66,ENST00000371564,;NFATC2,frameshift_variant,p.Ala86GlyfsTer66,ENST00000414705,;NFATC2,intron_variant,,ENST00000609507,;NFATC2,intron_variant,,ENST00000610033,;	A	ENSG00000101096	ENST00000396009	Transcript	frameshift_variant	534-535	314-315	105	G/GX	ggg/ggTg	.	.	.	-1	NFATC2	HGNC	7776	protein_coding	YES	CCDS13437.1	ENSP00000379330	NFAC2_HUMAN	B5B2P4_HUMAN,B5B2P3_HUMAN	UPI0000167D0F	.	.	.	2/10	.	hmmpanther:PTHR12533:SF4,hmmpanther:PTHR12533	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAGGCCCCTGC	.	3	ESCA
UCKL1	0	.	GRCh37	20	62572378	62572378	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041C>T	p.%3D	p.R347R	ENST00000354216	10/15	23	18	4	37	37	0	UCKL1,stop_gained,p.Arg364Ter,ENST00000358711,;UCKL1,synonymous_variant,p.%3D,ENST00000369908,;UCKL1,synonymous_variant,p.%3D,ENST00000354216,;UCKL1,synonymous_variant,p.%3D,ENST00000430743,;UCKL1,synonymous_variant,p.%3D,ENST00000369892,;DNAJC5,downstream_gene_variant,,ENST00000360864,;MIR1914,downstream_gene_variant,,ENST00000607800,;MIR647,downstream_gene_variant,,ENST00000384823,;UCKL1,downstream_gene_variant,,ENST00000492660,;DNAJC5,downstream_gene_variant,,ENST00000470551,;	A	ENSG00000198276	ENST00000354216	Transcript	synonymous_variant	1084	1041	347	R	cgC/cgT	.	.	.	-1	UCKL1	HGNC	15938	protein_coding	YES	CCDS13547.1	ENSP00000346155	UCKL1_HUMAN	Q5JWV1_HUMAN	UPI000004A08C	.	.	.	10/15	.	hmmpanther:PTHR10285:SF64,hmmpanther:PTHR10285,Gene3D:3.40.50.2020,Pfam_domain:PF14681,Superfamily_domains:SSF53271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTCGCGACT	.	5	ESCA
PAK7	0	.	GRCh37	20	9520070	9520070	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39A>G	.	.	ENST00000378429	11/11	96	66	30	186	186	0	PAK7,3_prime_UTR_variant,,ENST00000378423,;PAK7,3_prime_UTR_variant,,ENST00000378429,;PAK7,3_prime_UTR_variant,,ENST00000353224,;	C	ENSG00000101349	ENST00000378429	Transcript	3_prime_UTR_variant	2746	.	.	.	.	.	.	.	-1	PAK7	HGNC	15916	protein_coding	YES	CCDS13107.1	ENSP00000367686	PAK7_HUMAN	Q9UJQ0_HUMAN	UPI0000035BAD	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCATGTCCT	.	5	ESCA
CECR2	0	.	GRCh37	22	18003287	18003287	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.975G>T	p.Lys325Asn	p.K325N	ENST00000262608	8/18	26	8	17	54	54	0	CECR2,missense_variant,p.Lys344Asn,ENST00000400573,;CECR2,missense_variant,p.Lys203Asn,ENST00000400585,;CECR2,missense_variant,p.Lys296Asn,ENST00000342247,;CECR2,missense_variant,p.Lys325Asn,ENST00000262608,;	T	ENSG00000099954	ENST00000262608	Transcript	missense_variant	975	975	325	K/N	aaG/aaT	.	.	.	1	CECR2	HGNC	1840	protein_coding	YES	.	ENSP00000262608	CECR2_HUMAN	.	UPI0001AE62C8	.	deleterious(0.01)	possibly_damaging(0.853)	8/18	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF123,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAAGGCAGT	.	5	ESCA
MGAT3	0	.	GRCh37	22	39883900	39883900	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.548G>A	p.Gly183Asp	p.G183D	ENST00000341184	2/2	22	16	5	26	26	0	MGAT3,missense_variant,p.Gly183Asp,ENST00000341184,;MGAT3,downstream_gene_variant,,ENST00000418314,;MGAT3,downstream_gene_variant,,ENST00000429402,;	A	ENSG00000128268	ENST00000341184	Transcript	missense_variant	763	548	183	G/D	gGc/gAc	.	.	.	1	MGAT3	HGNC	7046	protein_coding	YES	CCDS13994.2	ENSP00000345270	MGAT3_HUMAN	B2R969_HUMAN,B0QY93_HUMAN	UPI00003765B6	.	tolerated(0.07)	probably_damaging(0.927)	2/2	.	hmmpanther:PTHR12224,hmmpanther:PTHR12224:SF0,Pfam_domain:PF04724	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCGGCGTGC	.	5	ESCA
PHOSPHO2	0	.	GRCh37	2	170557861	170557862	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.384dupT	p.Asn129Ter	p.N129*	ENST00000359744	4/4	28	21	7	38	38	0	PHOSPHO2,frameshift_variant,p.Asn129Ter,ENST00000438710,;PHOSPHO2,frameshift_variant,p.Asn129Ter,ENST00000359744,;KLHL23,intron_variant,,ENST00000602521,;KLHL23,intron_variant,,ENST00000272797,;KLHL23,intron_variant,,ENST00000498202,;PHOSPHO2,downstream_gene_variant,,ENST00000449906,;PHOSPHO2,downstream_gene_variant,,ENST00000438838,;PHOSPHO2,downstream_gene_variant,,ENST00000476919,;	T	ENSG00000144362	ENST00000359744	Transcript	frameshift_variant	768-769	380-381	127	A/AX	gct/gcTt	.	.	.	1	PHOSPHO2	HGNC	28316	protein_coding	YES	CCDS33319.1	ENSP00000352782	PHOP2_HUMAN	C9JZQ7_HUMAN,C9JD35_HUMAN,C9J4G2_HUMAN	UPI000006D7F5	.	.	.	4/4	.	hmmpanther:PTHR20889,hmmpanther:PTHR20889:SF1,Pfam_domain:PF06888,TIGRFAM_domain:TIGR01488,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01489,PIRSF_domain:PIRSF031051,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGCAGCTTTTA	.	3	ESCA
HDLBP	0	.	GRCh37	2	242179062	242179062	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2565T>C	p.%3D	p.C855C	ENST00000391975	19/28	19	9	10	45	45	0	HDLBP,synonymous_variant,p.%3D,ENST00000310931,;HDLBP,synonymous_variant,p.%3D,ENST00000427183,;HDLBP,synonymous_variant,p.%3D,ENST00000373292,;HDLBP,synonymous_variant,p.%3D,ENST00000391976,;HDLBP,synonymous_variant,p.%3D,ENST00000427487,;HDLBP,synonymous_variant,p.%3D,ENST00000391975,;HDLBP,downstream_gene_variant,,ENST00000452931,;HDLBP,non_coding_transcript_exon_variant,,ENST00000483086,;HDLBP,upstream_gene_variant,,ENST00000470482,;HDLBP,downstream_gene_variant,,ENST00000471294,;HDLBP,non_coding_transcript_exon_variant,,ENST00000487169,;HDLBP,non_coding_transcript_exon_variant,,ENST00000479169,;HDLBP,upstream_gene_variant,,ENST00000479894,;HDLBP,downstream_gene_variant,,ENST00000459788,;	G	ENSG00000115677	ENST00000391975	Transcript	synonymous_variant	2793	2565	855	C	tgT/tgC	.	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	.	.	19/28	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50084,hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACACAGTC	.	5	ESCA
SERTAD2	0	.	GRCh37	2	64859071	64859071	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3990T>A	.	.	ENST00000313349	2/2	54	17	36	66	66	0	SERTAD2,3_prime_UTR_variant,,ENST00000313349,;SERTAD2,downstream_gene_variant,,ENST00000476805,;	T	ENSG00000179833	ENST00000313349	Transcript	3_prime_UTR_variant	5233	.	.	.	.	.	.	.	-1	SERTAD2	HGNC	30784	protein_coding	YES	CCDS33210.1	ENSP00000326933	SRTD2_HUMAN	.	UPI000004EC6D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTGTTATCCCC	.	3	ESCA
SERTAD2	0	.	GRCh37	2	64859078	64859078	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3983T>C	.	.	ENST00000313349	2/2	53	17	35	66	66	0	SERTAD2,3_prime_UTR_variant,,ENST00000313349,;SERTAD2,downstream_gene_variant,,ENST00000476805,;	G	ENSG00000179833	ENST00000313349	Transcript	3_prime_UTR_variant	5226	.	.	.	.	.	.	.	-1	SERTAD2	HGNC	30784	protein_coding	YES	CCDS33210.1	ENSP00000326933	SRTD2_HUMAN	.	UPI000004EC6D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCCAAAAGAA	.	3	ESCA
MORC1	0	.	GRCh37	3	108723734	108723734	+	Missense_Mutation	SNP	C	C	G	rs749399375	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2015G>C	p.Arg672Thr	p.R672T	ENST00000232603	20/28	38	22	15	34	34	0	MORC1,missense_variant,p.Arg651Thr,ENST00000483760,;MORC1,missense_variant,p.Arg672Thr,ENST00000232603,;	G	ENSG00000114487	ENST00000232603	Transcript	missense_variant	2098	2015	672	R/T	aGa/aCa	rs749399375	.	.	-1	MORC1	HGNC	7198	protein_coding	YES	CCDS2955.1	ENSP00000232603	MORC1_HUMAN	.	UPI000013C964	.	tolerated(0.47)	benign(0)	20/28	.	hmmpanther:PTHR23337,hmmpanther:PTHR23337:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCTCTTT	byFrequency	5	ESCA
ARHGAP31	0	.	GRCh37	3	119101244	119101244	+	Silent	SNP	C	C	G	.	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.537C>G	p.%3D	p.L179L	ENST00000264245	5/12	43	26	17	36	36	0	ARHGAP31,synonymous_variant,p.%3D,ENST00000482743,;ARHGAP31,synonymous_variant,p.%3D,ENST00000264245,;	G	ENSG00000031081	ENST00000264245	Transcript	synonymous_variant	1069	537	179	L	ctC/ctG	COSM445352	.	.	1	ARHGAP31	HGNC	29216	protein_coding	YES	CCDS43135.1	ENSP00000264245	RHG31_HUMAN	.	UPI00001C1DFD	.	.	.	5/12	.	PROSITE_profiles:PS50238,hmmpanther:PTHR15729:SF3,hmmpanther:PTHR15729,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAGGTA	.	5	ESCA
SLC15A2	0	.	GRCh37	3	121634493	121634493	+	Missense_Mutation	SNP	A	A	G	rs757477203	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650A>G	p.Tyr217Cys	p.Y217C	ENST00000489711	7/22	58	37	20	56	56	0	SLC15A2,missense_variant,p.Tyr186Cys,ENST00000295605,;SLC15A2,missense_variant,p.Tyr217Cys,ENST00000489711,;SLC15A2,downstream_gene_variant,,ENST00000469013,;SLC15A2,non_coding_transcript_exon_variant,,ENST00000489886,;	G	ENSG00000163406	ENST00000489711	Transcript	missense_variant	1038	650	217	Y/C	tAt/tGt	rs757477203	.	.	1	SLC15A2	HGNC	10921	protein_coding	YES	CCDS3007.1	ENSP00000417085	S15A2_HUMAN	C9IZ38_HUMAN	UPI000013E27D	.	deleterious(0)	probably_damaging(0.999)	7/22	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11654:SF15,hmmpanther:PTHR11654,Pfam_domain:PF00854,TIGRFAM_domain:TIGR00926,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTATGCAT	.	5	ESCA
KPNA4	0	.	GRCh37	3	160227638	160227638	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1159G>A	p.Glu387Lys	p.E387K	ENST00000334256	14/17	57	47	10	53	53	0	KPNA4,missense_variant,p.Glu387Lys,ENST00000334256,;KPNA4,intron_variant,,ENST00000483437,;	T	ENSG00000186432	ENST00000334256	Transcript	missense_variant	1465	1159	387	E/K	Gaa/Aaa	.	.	.	-1	KPNA4	HGNC	6397	protein_coding	YES	CCDS3191.1	ENSP00000334373	IMA3_HUMAN	.	UPI0000001648	.	deleterious(0)	probably_damaging(1)	14/17	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF005673,SMART_domains:SM00185,Pfam_domain:PF00514,Gene3D:1.25.10.10,hmmpanther:PTHR23316:SF7,hmmpanther:PTHR23316	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCTTTTT	.	5	ESCA
SI	0	.	GRCh37	3	164783108	164783108	+	Missense_Mutation	SNP	G	G	A	rs200745562	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.748C>T	p.Arg250Cys	p.R250C	ENST00000264382	7/48	31	21	9	42	42	0	SI,missense_variant,p.Arg250Cys,ENST00000264382,;SI,downstream_gene_variant,,ENST00000476593,;	A	ENSG00000090402	ENST00000264382	Transcript	missense_variant	811	748	250	R/C	Cgt/Tgt	rs200745562,COSM116707	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	deleterious(0)	probably_damaging(0.929)	7/48	.	Superfamily_domains:SSF74650,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R250C|c.748C>T|3,BUFFER|p.R248I|c.743G>T|3	RADIA|MUTECT|MUSE	ATGACGAAATC	byFrequency|byCluster	3	ESCA
MFN1	0	.	GRCh37	3	179069778	179069778	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.203G>A	p.Gly68Asp	p.G68D	ENST00000471841	3/18	68	42	26	80	80	0	MFN1,missense_variant,p.Gly68Asp,ENST00000280653,;MFN1,missense_variant,p.Gly68Asp,ENST00000471841,;MFN1,missense_variant,p.Gly68Asp,ENST00000467174,;MFN1,missense_variant,p.Gly68Asp,ENST00000263969,;MFN1,missense_variant,p.Gly68Asp,ENST00000357390,;	A	ENSG00000171109	ENST00000471841	Transcript	missense_variant	329	203	68	G/D	gGt/gAt	.	.	.	1	MFN1	HGNC	18262	protein_coding	YES	CCDS3228.1	ENSP00000420617	MFN1_HUMAN	C9JXQ1_HUMAN,C9JQT7_HUMAN	UPI000013D495	.	tolerated(0.28)	benign(0.174)	3/18	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,hmmpanther:PTHR10465,hmmpanther:PTHR10465:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTGGTGAGG	.	5	ESCA
AZI2	0	.	GRCh37	3	28373231	28373231	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647+629G>A	.	.	ENST00000479665	.	18	14	4	34	34	0	AZI2,3_prime_UTR_variant,,ENST00000334100,;AZI2,3_prime_UTR_variant,,ENST00000420543,;AZI2,intron_variant,,ENST00000429369,;AZI2,intron_variant,,ENST00000479665,;AZI2,downstream_gene_variant,,ENST00000414162,;AZI2,downstream_gene_variant,,ENST00000457172,;AZI2,intron_variant,,ENST00000295748,;AZI2,non_coding_transcript_exon_variant,,ENST00000470234,;AZI2,non_coding_transcript_exon_variant,,ENST00000488978,;AZI2,intron_variant,,ENST00000492044,;AZI2,intron_variant,,ENST00000463512,;AZI2,upstream_gene_variant,,ENST00000476174,;	T	ENSG00000163512	ENST00000479665	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AZI2	HGNC	24002	protein_coding	YES	CCDS2647.1	ENSP00000419371	AZI2_HUMAN	C9JVK8_HUMAN,C9JGA2_HUMAN	UPI000006CE34	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTATCTTAAC	.	5	ESCA
SCN11A	0	.	GRCh37	3	38888583	38888583	+	Missense_Mutation	SNP	C	C	T	rs564668486	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4978G>A	p.Ala1660Thr	p.A1660T	ENST00000302328	26/26	20	4	16	56	56	0	SCN11A,missense_variant,p.Ala1660Thr,ENST00000450244,;SCN11A,missense_variant,p.Ala1660Thr,ENST00000302328,;SCN11A,missense_variant,p.Ala1622Thr,ENST00000456224,;SCN11A,downstream_gene_variant,,ENST00000444237,;	T	ENSG00000168356	ENST00000302328	Transcript	missense_variant	5177	4978	1660	A/T	Gca/Aca	rs564668486	.	.	-1	SCN11A	HGNC	10583	protein_coding	YES	CCDS33737.1	ENSP00000307599	SCNBA_HUMAN	.	UPI000006CCD7	.	deleterious(0)	possibly_damaging(0.489)	26/26	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF22	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTGCGACAC	by1000G	5	ESCA
SLC7A11	0	.	GRCh37	4	139103481	139103481	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1086G>T	p.Lys362Asn	p.K362N	ENST00000280612	9/12	25	9	15	54	54	0	SLC7A11,missense_variant,p.Lys362Asn,ENST00000280612,;SLC7A11-AS1,downstream_gene_variant,,ENST00000510767,;SLC7A11,intron_variant,,ENST00000509248,;	A	ENSG00000151012	ENST00000280612	Transcript	missense_variant	1366	1086	362	K/N	aaG/aaT	.	.	.	-1	SLC7A11	HGNC	11059	protein_coding	YES	CCDS3742.1	ENSP00000280612	XCT_HUMAN	Q9P1X0_HUMAN,Q4W5A5_HUMAN	UPI0000138FD5	.	deleterious(0.02)	probably_damaging(0.924)	9/12	.	hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF248,Pfam_domain:PF13520,TIGRFAM_domain:TIGR00911,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTGCTTGCG	.	5	ESCA
DCAF16	0	.	GRCh37	4	17805701	17805701	+	Missense_Mutation	SNP	T	T	C	rs184417488	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64A>G	p.Ile22Val	p.I22V	ENST00000382247	3/3	22	9	12	26	26	0	DCAF16,missense_variant,p.Ile22Val,ENST00000382247,;DCAF16,missense_variant,p.Ile22Val,ENST00000536863,;DCAF16,downstream_gene_variant,,ENST00000507768,;	C	ENSG00000163257	ENST00000382247	Transcript	missense_variant	1125	64	22	I/V	Att/Gtt	rs184417488	.	.	-1	DCAF16	HGNC	25987	protein_coding	YES	CCDS3423.1	ENSP00000371682	DCA16_HUMAN	.	UPI000006D3DE	.	tolerated_low_confidence(1)	benign(0)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16194,hmmpanther:PTHR16194:SF0,Pfam_domain:PF15349	G:0.0002	G:0	G:0.0014	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTAATATTTT	byCluster|by1000G	5	ESCA
GRAMD3	0	.	GRCh37	5	125821384	125821384	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1022C>A	p.Ser341Ter	p.S341*	ENST00000513040	11/14	57	26	31	62	62	0	GRAMD3,stop_gained,p.Ser304Ter,ENST00000515200,;GRAMD3,stop_gained,p.Ser217Ter,ENST00000502348,;GRAMD3,stop_gained,p.Ser334Ter,ENST00000542322,;GRAMD3,stop_gained,p.Ser304Ter,ENST00000543198,;GRAMD3,stop_gained,p.Ser326Ter,ENST00000285689,;GRAMD3,stop_gained,p.Ser341Ter,ENST00000513040,;GRAMD3,stop_gained,p.Ser310Ter,ENST00000511134,;GRAMD3,stop_gained,p.Ser222Ter,ENST00000544396,;GRAMD3,downstream_gene_variant,,ENST00000506445,;RP11-517I3.1,intron_variant,,ENST00000512500,;RP11-517I3.1,intron_variant,,ENST00000515808,;GRAMD3,non_coding_transcript_exon_variant,,ENST00000512579,;GRAMD3,3_prime_UTR_variant,,ENST00000514099,;GRAMD3,3_prime_UTR_variant,,ENST00000513978,;GRAMD3,downstream_gene_variant,,ENST00000504859,;GRAMD3,downstream_gene_variant,,ENST00000508523,;	A	ENSG00000155324	ENST00000513040	Transcript	stop_gained	1222	1022	341	S/*	tCa/tAa	.	.	.	1	GRAMD3	HGNC	24911	protein_coding	YES	CCDS54891.1	ENSP00000426120	GRAM3_HUMAN	Q9BYJ8_HUMAN,B7Z4W8_HUMAN	UPI0001914E8F	.	.	.	11/14	.	hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTCAGAAA	.	5	ESCA
PCDHB3	0	.	GRCh37	5	140482555	140482555	+	Silent	SNP	C	C	T	rs782811619	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2322C>T	p.%3D	p.F774F	ENST00000231130	1/1	60	22	37	88	88	0	PCDHB3,synonymous_variant,p.%3D,ENST00000231130,;AC005754.7,upstream_gene_variant,,ENST00000607216,;	T	ENSG00000113205	ENST00000231130	Transcript	synonymous_variant	2322	2322	774	F	ttC/ttT	rs782811619,COSM1486379,COSM1722461	.	.	1	PCDHB3	HGNC	8688	protein_coding	YES	CCDS4245.1	ENSP00000231130	PCDB3_HUMAN	.	UPI00001273DD	.	.	.	1/1	.	hmmpanther:PTHR24028:SF19,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.F774F|c.2322C>T|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTCGTTGC	.	5	ESCA
CSF1R	0	.	GRCh37	5	149449523	149449523	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1423G>A	p.Glu475Lys	p.E475K	ENST00000286301	10/22	32	24	7	55	55	0	CSF1R,missense_variant,p.Glu475Lys,ENST00000286301,;CSF1R,downstream_gene_variant,,ENST00000543093,;CSF1R,upstream_gene_variant,,ENST00000515239,;CSF1R,missense_variant,p.Glu475Lys,ENST00000504875,;CSF1R,upstream_gene_variant,,ENST00000513609,;	T	ENSG00000182578	ENST00000286301	Transcript	missense_variant	1715	1423	475	E/K	Gag/Aag	COSM3827395,COSM3827396	.	.	-1	CSF1R	HGNC	2433	protein_coding	YES	CCDS4302.1	ENSP00000286301	CSF1R_HUMAN	Q6LEI2_HUMAN,D6RGW1_HUMAN	UPI000004984A	.	tolerated(0.57)	benign(0.014)	10/22	.	PROSITE_profiles:PS50835,hmmpanther:PTHR24416:SF47,hmmpanther:PTHR24416,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,PIRSF_domain:PIRSF500947,PIRSF_domain:PIRSF000615,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCAACAG	.	5	ESCA
SLC38A9	0	.	GRCh37	5	55008260	55008260	+	5'UTR	SNP	C	C	A	rs190705960	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-298G>T	.	.	ENST00000396865	1/16	24	5	18	42	42	0	SLC38A9,5_prime_UTR_variant,,ENST00000396865,;SLC38A9,upstream_gene_variant,,ENST00000507109,;SLC38A9,upstream_gene_variant,,ENST00000506624,;SLC38A9,upstream_gene_variant,,ENST00000503891,;SLC38A9,upstream_gene_variant,,ENST00000512208,;SLC38A9,upstream_gene_variant,,ENST00000513993,;SLC38A9,upstream_gene_variant,,ENST00000513275,;SLC38A9,non_coding_transcript_exon_variant,,ENST00000504880,;SLC38A9,upstream_gene_variant,,ENST00000507216,;SLC38A9,upstream_gene_variant,,ENST00000502416,;SLC38A9,upstream_gene_variant,,ENST00000514806,;SLC38A9,upstream_gene_variant,,ENST00000508124,;SLC38A9,upstream_gene_variant,,ENST00000505563,;	A	ENSG00000177058	ENST00000396865	Transcript	5_prime_UTR_variant	295	.	.	.	.	rs190705960	.	.	-1	SLC38A9	HGNC	26907	protein_coding	YES	CCDS3968.1	ENSP00000380074	S38A9_HUMAN	E7ESU6_HUMAN,D6RIW7_HUMAN,D6RHW0_HUMAN,D6RG31_HUMAN,D6RER8_HUMAN,D6RDH2_HUMAN,D6R9X0_HUMAN,B3KVK8_HUMAN	UPI00001403C2	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGGCTCTGC	by1000G	5	ESCA
DSE	0	.	GRCh37	6	116747882	116747882	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562A>T	p.Met188Leu	p.M188L	ENST00000331677	4/7	62	51	11	69	69	0	DSE,missense_variant,p.Met188Leu,ENST00000452085,;DSE,missense_variant,p.Met188Leu,ENST00000331677,;DSE,missense_variant,p.Met207Leu,ENST00000537543,;DSE,missense_variant,p.Met188Leu,ENST00000359564,;DSE,downstream_gene_variant,,ENST00000540275,;DSE,downstream_gene_variant,,ENST00000430252,;DSE,non_coding_transcript_exon_variant,,ENST00000606265,;	T	ENSG00000111817	ENST00000331677	Transcript	missense_variant	1006	562	188	M/L	Atg/Ttg	.	.	.	1	DSE	HGNC	21144	protein_coding	YES	CCDS5107.1	ENSP00000332151	DSE_HUMAN	B3KY37_HUMAN	UPI0000073CB8	.	tolerated(0.35)	probably_damaging(0.909)	4/7	.	hmmpanther:PTHR15532:SF3,hmmpanther:PTHR15532,Superfamily_domains:SSF48230	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTATATGTAT	.	5	ESCA
OR2A4	0	.	GRCh37	6	132021790	132021790	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.752A>G	p.Tyr251Cys	p.Y251C	ENST00000315453	1/1	30	19	11	60	60	0	OR2A4,missense_variant,p.Tyr251Cys,ENST00000315453,;ENPP3,intron_variant,,ENST00000358229,;ENPP3,intron_variant,,ENST00000357639,;ENPP3,intron_variant,,ENST00000414305,;	C	ENSG00000180658	ENST00000315453	Transcript	missense_variant	846	752	251	Y/C	tAt/tGt	.	.	.	-1	OR2A4	HGNC	14729	protein_coding	YES	CCDS5149.1	ENSP00000319546	OR2A4_HUMAN	.	UPI000003F21F	.	deleterious(0)	probably_damaging(0.988)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF135,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCATAAACG	.	5	ESCA
FRMD1	0	.	GRCh37	6	168479699	168479699	+	Nonsense_Mutation	SNP	G	G	A	rs767627123	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76C>T	p.Arg26Ter	p.R26*	ENST00000283309	1/11	63	51	12	72	72	0	FRMD1,stop_gained,p.Arg68Ter,ENST00000511714,;FRMD1,stop_gained,p.Arg26Ter,ENST00000283309,;FRMD1,upstream_gene_variant,,ENST00000440994,;FRMD1,stop_gained,p.Arg65Ter,ENST00000509157,;FRMD1,stop_gained,p.Arg65Ter,ENST00000468647,;FRMD1,non_coding_transcript_exon_variant,,ENST00000358587,;	A	ENSG00000153303	ENST00000283309	Transcript	stop_gained	141	76	26	R/*	Cga/Tga	rs767627123	.	.	-1	FRMD1	HGNC	21240	protein_coding	YES	CCDS5306.1	ENSP00000283309	FRMD1_HUMAN	F5GXR0_HUMAN	UPI000013F36A	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCGCGCCC	.	5	ESCA
MOG	0	.	GRCh37	6	29637970	29637970	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.593-88A>G	.	.	ENST00000376898	.	33	20	13	38	38	0	MOG,synonymous_variant,p.%3D,ENST00000490427,;MOG,synonymous_variant,p.%3D,ENST00000396704,;MOG,synonymous_variant,p.%3D,ENST00000494692,;MOG,intron_variant,,ENST00000533330,;MOG,intron_variant,,ENST00000483013,;MOG,intron_variant,,ENST00000376891,;MOG,intron_variant,,ENST00000376898,;MOG,intron_variant,,ENST00000376917,;MOG,intron_variant,,ENST00000376888,;MOG,intron_variant,,ENST00000376902,;MOG,intron_variant,,ENST00000416766,;MOG,intron_variant,,ENST00000431798,;MOG,intron_variant,,ENST00000376894,;MOG,intron_variant,,ENST00000396701,;ZFP57,downstream_gene_variant,,ENST00000376883,;ZFP57,downstream_gene_variant,,ENST00000488757,;ZFP57,downstream_gene_variant,,ENST00000376881,;MOG,non_coding_transcript_exon_variant,,ENST00000485885,;MOG,intron_variant,,ENST00000376889,;MOG,intron_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000376903,;	G	ENSG00000204655	ENST00000376898	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MOG	HGNC	7197	protein_coding	YES	CCDS4667.1	ENSP00000366095	MOG_HUMAN	.	UPI00004573E8	.	.	.	.	5/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTAGGACCCCA	.	4	ESCA
DPCR1	0	.	GRCh37	6	30919708	30919708	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3467A>G	p.His1156Arg	p.H1156R	ENST00000462446	2/3	9	6	3	29	29	0	DPCR1,missense_variant,p.His1156Arg,ENST00000462446,;DPCR1,5_prime_UTR_variant,,ENST00000304311,;HCG21,intron_variant,,ENST00000419481,;	G	ENSG00000168631	ENST00000462446	Transcript	missense_variant	3495	3467	1156	H/R	cAt/cGt	.	.	.	1	DPCR1	HGNC	21666	protein_coding	YES	CCDS4692.2	ENSP00000417182	.	E9PEI6_HUMAN	UPI0000596C17	.	deleterious(0.03)	benign(0.159)	2/3	.	hmmpanther:PTHR22094,hmmpanther:PTHR22094:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCCATGAGA	.	2	ESCA
PI16	0	.	GRCh37	6	36927007	36927007	+	Silent	SNP	C	C	T	rs770111668,rs772745462	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258C>T	p.%3D	p.G86G	ENST00000373674	2/7	60	28	32	88	88	0	PI16,synonymous_variant,p.%3D,ENST00000373674,;PI16,upstream_gene_variant,,ENST00000491324,;	T	ENSG00000164530	ENST00000373674	Transcript	synonymous_variant	586	258	86	G	ggC/ggT	rs770111668,rs772745462	.	.	1	PI16	HGNC	21245	protein_coding	YES	CCDS34440.1	ENSP00000362778	PI16_HUMAN	B4DXZ3_HUMAN	UPI000004C657	.	.	.	2/7	.	hmmpanther:PTHR10334,Pfam_domain:PF00188,Gene3D:3.40.33.10,SMART_domains:SM00198,Superfamily_domains:SSF55797	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCGGCGAGAA	byFrequency	5	ESCA
FILIP1	0	.	GRCh37	6	76024322	76024322	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1226A>G	p.Lys409Arg	p.K409R	ENST00000237172	5/6	53	44	9	73	73	0	FILIP1,missense_variant,p.Lys310Arg,ENST00000370020,;FILIP1,missense_variant,p.Lys409Arg,ENST00000393004,;FILIP1,missense_variant,p.Lys409Arg,ENST00000237172,;FILIP1,non_coding_transcript_exon_variant,,ENST00000498523,;HMGB1P39,downstream_gene_variant,,ENST00000366304,;	C	ENSG00000118407	ENST00000237172	Transcript	missense_variant	1557	1226	409	K/R	aAg/aGg	.	.	.	-1	FILIP1	HGNC	21015	protein_coding	YES	CCDS4984.1	ENSP00000237172	FLIP1_HUMAN	.	UPI0000160071	.	tolerated(0.24)	benign(0.027)	5/6	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23166,hmmpanther:PTHR23166:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTCTTCCTC	.	5	ESCA
CASP2	0	.	GRCh37	7	142997478	142997478	+	Intron	SNP	A	A	G	rs763709140	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967+91A>G	.	.	ENST00000310447	.	29	9	20	45	45	0	CASP2,intron_variant,,ENST00000310447,;RN7SL481P,downstream_gene_variant,,ENST00000477764,;CASP2,non_coding_transcript_exon_variant,,ENST00000493642,;CASP2,non_coding_transcript_exon_variant,,ENST00000472067,;CASP2,intron_variant,,ENST00000350623,;	G	ENSG00000106144	ENST00000310447	Transcript	intron_variant	.	.	.	.	.	rs763709140	.	.	1	CASP2	HGNC	1503	protein_coding	YES	CCDS5879.1	ENSP00000312664	CASP2_HUMAN	B4E0I5_HUMAN	UPI000020F1E8	.	.	.	.	8/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTATTGGA	byCluster	5	ESCA
ABCB5	0	.	GRCh37	7	20768053	20768053	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2842C>T	p.Arg948Ter	p.R948*	ENST00000404938	23/28	29	18	10	43	43	0	ABCB5,stop_gained,p.Arg503Ter,ENST00000258738,;ABCB5,stop_gained,p.Arg948Ter,ENST00000404938,;ABCB5,stop_gained,p.Arg115Ter,ENST00000441315,;	T	ENSG00000004846	ENST00000404938	Transcript	stop_gained	3494	2842	948	R/*	Cga/Tga	.	.	.	1	ABCB5	HGNC	46	protein_coding	YES	CCDS55090.1	ENSP00000384881	ABCB5_HUMAN	.	UPI000173A253	.	.	.	23/28	.	PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF2,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGACGAATG	.	5	ESCA
CRCP	0	.	GRCh37	7	65617872	65617872	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*528C>T	.	.	ENST00000395326	6/6	16	11	5	24	24	0	CRCP,3_prime_UTR_variant,,ENST00000338592,;CRCP,3_prime_UTR_variant,,ENST00000415001,;CRCP,3_prime_UTR_variant,,ENST00000395326,;CRCP,downstream_gene_variant,,ENST00000431089,;CRCP,downstream_gene_variant,,ENST00000398684,;AC068533.7,downstream_gene_variant,,ENST00000450043,;RP5-1132H15.1,intron_variant,,ENST00000435524,;CRCP,downstream_gene_variant,,ENST00000492264,;CRCP,3_prime_UTR_variant,,ENST00000360415,;	T	ENSG00000241258	ENST00000395326	Transcript	3_prime_UTR_variant	1333	.	.	.	.	.	.	.	1	CRCP	HGNC	17888	protein_coding	YES	CCDS5532.1	ENSP00000378736	RPC9_HUMAN	.	UPI0000128406	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTTCAACAG	.	2	ESCA
CALN1	0	.	GRCh37	7	71248560	71248560	+	3'UTR	SNP	G	G	C	rs754999826	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4200C>G	.	.	ENST00000395275	7/7	21	8	13	17	17	0	CALN1,3_prime_UTR_variant,,ENST00000395276,;CALN1,3_prime_UTR_variant,,ENST00000395275,;CALN1,3_prime_UTR_variant,,ENST00000329008,;CALN1,downstream_gene_variant,,ENST00000431984,;CALN1,downstream_gene_variant,,ENST00000405452,;CALN1,downstream_gene_variant,,ENST00000412588,;	C	ENSG00000183166	ENST00000395275	Transcript	3_prime_UTR_variant	5375	.	.	.	.	rs754999826	.	.	-1	CALN1	HGNC	13248	protein_coding	YES	CCDS47603.1	ENSP00000378690	CABP8_HUMAN	Q86UM7_HUMAN,Q86UL5_HUMAN,Q75MW5_HUMAN,Q75MP5_HUMAN,Q75MI2_HUMAN,E9PFU3_HUMAN,A4D1Z1_HUMAN	UPI0000D4B903	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCAGGGAGC	byCluster	5	ESCA
ZNF804B	0	.	GRCh37	7	88963384	88963384	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1088C>A	p.Ala363Glu	p.A363E	ENST00000333190	4/4	25	19	5	20	20	0	ZNF804B,missense_variant,p.Ala363Glu,ENST00000333190,;	A	ENSG00000182348	ENST00000333190	Transcript	missense_variant	1697	1088	363	A/E	gCa/gAa	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	tolerated(0.23)	benign(0.015)	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAGCAAATG	.	5	ESCA
TRRAP	0	.	GRCh37	7	98548596	98548596	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5411C>A	p.Pro1804Gln	p.P1804Q	ENST00000359863	38/72	99	71	28	90	90	0	TRRAP,missense_variant,p.Pro1786Gln,ENST00000355540,;TRRAP,missense_variant,p.Pro1785Gln,ENST00000446306,;TRRAP,missense_variant,p.Pro1526Gln,ENST00000456197,;TRRAP,missense_variant,p.Pro1804Gln,ENST00000359863,;	A	ENSG00000196367	ENST00000359863	Transcript	missense_variant	5620	5411	1804	P/Q	cCa/cAa	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	possibly_damaging(0.897)	38/72	.	hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACCCAGAAA	.	5	ESCA
GRHL2	0	.	GRCh37	8	102570742	102570742	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380A>G	p.Asn127Ser	p.N127S	ENST00000251808	4/16	47	36	11	36	36	0	GRHL2,missense_variant,p.Asn127Ser,ENST00000251808,;GRHL2,missense_variant,p.Asn111Ser,ENST00000395927,;KB-1562D12.3,downstream_gene_variant,,ENST00000524051,;	G	ENSG00000083307	ENST00000251808	Transcript	missense_variant	718	380	127	N/S	aAt/aGt	.	.	.	1	GRHL2	HGNC	2799	protein_coding	YES	CCDS34931.1	ENSP00000251808	GRHL2_HUMAN	.	UPI000013CD16	.	tolerated(0.33)	benign(0.012)	4/16	.	hmmpanther:PTHR11037:SF17,hmmpanther:PTHR11037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTAAATCAAG	.	5	ESCA
PKHD1L1	0	.	GRCh37	8	110376813	110376813	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111A>G	p.Ile37Met	p.I37M	ENST00000378402	2/78	63	47	16	77	77	0	PKHD1L1,missense_variant,p.Ile37Met,ENST00000378402,;	G	ENSG00000205038	ENST00000378402	Transcript	missense_variant	215	111	37	I/M	atA/atG	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	tolerated(0.26)	benign(0.051)	2/78	.	Pfam_domain:PF01833,Gene3D:2.60.40.10,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAATACCTAA	.	5	ESCA
JRK	0	.	GRCh37	8	143746717	143746717	+	RNA	SNP	T	T	C	rs369670710	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1094A>G	.	.	ENST00000507178	2/2	56	38	17	35	35	0	JRK,non_coding_transcript_exon_variant,,ENST00000422119,;JRK,non_coding_transcript_exon_variant,,ENST00000507178,;JRK,non_coding_transcript_exon_variant,,ENST00000512113,;JRK,downstream_gene_variant,,ENST00000503272,;JRK,downstream_gene_variant,,ENST00000591357,;JRK,upstream_gene_variant,,ENST00000506774,;	C	ENSG00000234616	ENST00000507178	Transcript	non_coding_transcript_exon_variant	1094	.	.	.	.	rs369670710	.	.	-1	JRK	HGNC	6199	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	C:0.0004	C:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTATAGGCG	byCluster	5	ESCA
PSKH2	0	.	GRCh37	8	87060700	87060700	+	Silent	SNP	C	C	T	rs773303354	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1149G>A	p.%3D	p.A383A	ENST00000276616	3/3	70	49	21	92	92	0	PSKH2,synonymous_variant,p.%3D,ENST00000276616,;ATP6V0D2,intron_variant,,ENST00000521564,;RP11-216N21.2,downstream_gene_variant,,ENST00000465398,;	T	ENSG00000147613	ENST00000276616	Transcript	synonymous_variant	1224	1149	383	A	gcG/gcA	rs773303354	.	.	-1	PSKH2	HGNC	18997	protein_coding	YES	CCDS6240.1	ENSP00000276616	KPSH2_HUMAN	.	UPI000006F951	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAGCGCAGA	.	5	ESCA
LCN1	0	.	GRCh37	9	138413998	138413998	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196A>T	p.Asn66Tyr	p.N66Y	ENST00000263598	2/7	111	31	80	113	113	0	LCN1,missense_variant,p.Asn66Tyr,ENST00000263598,;LCN1,missense_variant,p.Asn66Tyr,ENST00000371781,;	T	ENSG00000160349	ENST00000263598	Transcript	missense_variant	256	196	66	N/Y	Aac/Tac	.	.	.	1	LCN1	HGNC	6525	protein_coding	YES	CCDS6991.1	ENSP00000263598	LCN1_HUMAN	.	UPI0000040631	.	deleterious(0)	probably_damaging(0.997)	2/7	.	Superfamily_domains:SSF50814,Gene3D:2.40.128.20,Pfam_domain:PF00061,hmmpanther:PTHR11430:SF3,hmmpanther:PTHR11430	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCAACCTG	.	5	ESCA
CACNA1B	0	.	GRCh37	9	140777395	140777395	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530+60C>T	.	.	ENST00000371372	.	35	31	4	51	51	0	CACNA1B,intron_variant,,ENST00000371355,;CACNA1B,intron_variant,,ENST00000371357,;CACNA1B,intron_variant,,ENST00000277549,;CACNA1B,intron_variant,,ENST00000277551,;CACNA1B,intron_variant,,ENST00000371363,;CACNA1B,intron_variant,,ENST00000371372,;RP11-188C12.3,non_coding_transcript_exon_variant,,ENST00000371390,;	T	ENSG00000148408	ENST00000371372	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CACNA1B	HGNC	1389	protein_coding	YES	CCDS59522.1	ENSP00000360423	CAC1B_HUMAN	Q9HBI3_HUMAN,Q9HBH4_HUMAN,Q9HBG3_HUMAN,Q9HBG2_HUMAN,Q9HAT5_HUMAN,Q9HAT4_HUMAN	UPI0000127267	.	.	.	.	3/46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGAAGCTCAGT	.	3	ESCA
UBE2A	0	.	GRCh37	X	118715461	118715461	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.152-9T>C	.	.	ENST00000371558	.	29	7	22	41	41	0	UBE2A,5_prime_UTR_variant,,ENST00000371569,;UBE2A,intron_variant,,ENST00000346330,;UBE2A,intron_variant,,ENST00000371558,;	C	ENSG00000077721	ENST00000371558	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	UBE2A	HGNC	12472	protein_coding	YES	CCDS14580.1	ENSP00000360613	UBE2A_HUMAN	Q8WXB3_HUMAN,B4DWT6_HUMAN	UPI00000043A0	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCTAACCA	.	5	ESCA
NHSL2	0	.	GRCh37	X	71359229	71359229	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49O-01A-11D-A247-09	TCGA-LN-A49O-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1831C>G	p.His611Asp	p.H611D	ENST00000540800	6/8	18	2	15	17	17	0	NHSL2,missense_variant,p.His611Asp,ENST00000540800,;NHSL2,missense_variant,p.His245Asp,ENST00000373677,;NHSL2,missense_variant,p.His380Asp,ENST00000510661,;NHSL2,missense_variant,p.His245Asp,ENST00000535692,;RP11-262D11.2,upstream_gene_variant,,ENST00000456343,;RP11-262D11.1,downstream_gene_variant,,ENST00000513469,;	G	ENSG00000204131	ENST00000540800	Transcript	missense_variant	1831	1831	611	H/D	Cac/Gac	COSM458008,COSM458007	.	.	1	NHSL2	HGNC	33737	protein_coding	YES	.	ENSP00000444617	.	F5H593_HUMAN	UPI0001B09231	.	tolerated(0.67)	benign(0.096)	6/8	.	hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF2	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACATCACTCG	.	5	ESCA
HIF1AN	0	.	GRCh37	10	102308299	102308299	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*405A>G	.	.	ENST00000299163	8/8	9	6	3	14	14	0	HIF1AN,3_prime_UTR_variant,,ENST00000299163,;HIF1AN,downstream_gene_variant,,ENST00000533589,;HIF1AN,downstream_gene_variant,,ENST00000478787,;HIF1AN,downstream_gene_variant,,ENST00000526476,;	G	ENSG00000166135	ENST00000299163	Transcript	3_prime_UTR_variant	1555	.	.	.	.	.	.	.	1	HIF1AN	HGNC	17113	protein_coding	YES	CCDS7498.1	ENSP00000299163	HIF1N_HUMAN	E9PL41_HUMAN	UPI000006D2A7	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCTCAGCCCT	.	2	ESCA
MXI1	0	.	GRCh37	10	112038963	112038963	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.463G>A	p.Glu155Lys	p.E155K	ENST00000332674	4/6	81	65	15	82	82	0	MXI1,missense_variant,p.Glu145Lys,ENST00000453116,;MXI1,missense_variant,p.Glu42Lys,ENST00000361248,;MXI1,missense_variant,p.Glu52Lys,ENST00000369612,;MXI1,missense_variant,p.Glu78Lys,ENST00000393134,;MXI1,missense_variant,p.Glu88Lys,ENST00000239007,;MXI1,missense_variant,p.Glu155Lys,ENST00000332674,;MXI1,missense_variant,p.Glu52Lys,ENST00000442296,;MXI1,non_coding_transcript_exon_variant,,ENST00000484030,;MXI1,non_coding_transcript_exon_variant,,ENST00000460667,;MXI1,non_coding_transcript_exon_variant,,ENST00000485566,;	A	ENSG00000119950	ENST00000332674	Transcript	missense_variant	667	463	155	E/K	Gaa/Aaa	.	.	.	1	MXI1	HGNC	7534	protein_coding	YES	CCDS7563.1	ENSP00000331152	MXI1_HUMAN	Q5V9L6_HUMAN,F6WCI9_HUMAN	UPI0000376B16	.	deleterious(0)	probably_damaging(0.986)	4/6	.	PROSITE_profiles:PS50888,hmmpanther:PTHR11969:SF13,hmmpanther:PTHR11969,Pfam_domain:PF00010,Gene3D:4.10.280.10,SMART_domains:SM00353,Superfamily_domains:SSF47459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTAGAACGC	.	5	ESCA
C10orf71	0	.	GRCh37	10	50535437	50535437	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*539G>C	.	.	ENST00000374144	3/3	45	34	10	52	52	0	C10orf71,3_prime_UTR_variant,,ENST00000374144,;C10orf71,3_prime_UTR_variant,,ENST00000323868,;	C	ENSG00000177354	ENST00000374144	Transcript	3_prime_UTR_variant	5135	.	.	.	.	.	.	.	1	C10orf71	HGNC	26973	protein_coding	YES	CCDS44387.1	ENSP00000363259	CJ071_HUMAN	.	UPI0000161572	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGGTTTCC	.	5	ESCA
NCOA4	0	.	GRCh37	10	51590570	51590570	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1369T>A	.	.	ENST00000452682	12/12	28	22	5	15	15	0	NCOA4,3_prime_UTR_variant,,ENST00000374082,;NCOA4,3_prime_UTR_variant,,ENST00000452682,;NCOA4,3_prime_UTR_variant,,ENST00000344348,;NCOA4,3_prime_UTR_variant,,ENST00000443446,;NCOA4,3_prime_UTR_variant,,ENST00000374087,;NCOA4,3_prime_UTR_variant,,ENST00000438493,;TIMM23,downstream_gene_variant,,ENST00000374064,;NCOA4,downstream_gene_variant,,ENST00000430396,;TIMM23,downstream_gene_variant,,ENST00000260867,;NCOA4,downstream_gene_variant,,ENST00000414907,;TIMM23,downstream_gene_variant,,ENST00000374065,;TIMM23,downstream_gene_variant,,ENST00000444743,;TIMM23,downstream_gene_variant,,ENST00000485812,;TIMM23,downstream_gene_variant,,ENST00000476778,;TIMM23,downstream_gene_variant,,ENST00000469116,;	A	ENSG00000138293	ENST00000452682	Transcript	3_prime_UTR_variant	3574	.	.	.	.	.	.	.	1	NCOA4	HGNC	7671	protein_coding	YES	CCDS44394.1	ENSP00000395465	NCOA4_HUMAN	.	UPI0001932817	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTTCCAGT	.	5	ESCA
CTNNA3	0	.	GRCh37	10	67680368	67680368	+	Missense_Mutation	SNP	C	C	T	rs772544958	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2408G>A	p.Ser803Asn	p.S803N	ENST00000433211	18/18	54	46	8	51	51	0	CTNNA3,missense_variant,p.Ser803Asn,ENST00000433211,;CTNNA3,missense_variant,p.Ser803Asn,ENST00000373744,;CTNNA3,non_coding_transcript_exon_variant,,ENST00000373735,;	T	ENSG00000183230	ENST00000433211	Transcript	missense_variant	2583	2408	803	S/N	aGt/aAt	rs772544958	.	.	-1	CTNNA3	HGNC	2511	protein_coding	YES	CCDS7269.1	ENSP00000389714	CTNA3_HUMAN	Q5SW23_HUMAN,A6NKP0_HUMAN	UPI000004A0E6	.	deleterious(0)	unknown(0)	18/18	.	hmmpanther:PTHR18914:SF21,hmmpanther:PTHR18914,Pfam_domain:PF01044,Gene3D:1.20.120.230,Superfamily_domains:SSF47220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACACTGTCC	.	5	ESCA
KIRREL3	0	.	GRCh37	11	126306730	126306730	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1528G>A	p.Glu510Lys	p.E510K	ENST00000525144	12/17	79	50	29	46	45	0	KIRREL3,missense_variant,p.Glu510Lys,ENST00000529097,;KIRREL3,missense_variant,p.Glu510Lys,ENST00000525144,;KIRREL3,missense_variant,p.Glu510Lys,ENST00000525704,;KIRREL3,5_prime_UTR_variant,,ENST00000416561,;KIRREL3,non_coding_transcript_exon_variant,,ENST00000526519,;KIRREL3,non_coding_transcript_exon_variant,,ENST00000532647,;ST3GAL4,intron_variant,,ENST00000524834,;KIRREL3,downstream_gene_variant,,ENST00000526764,;	T	ENSG00000149571	ENST00000525144	Transcript	missense_variant	1778	1528	510	E/K	Gag/Aag	.	.	.	-1	KIRREL3	HGNC	23204	protein_coding	YES	CCDS53723.1	ENSP00000435466	KIRR3_HUMAN	B4DT91_HUMAN	UPI00000740A0	.	tolerated(0.3)	benign(0.008)	12/17	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11640:SF49,hmmpanther:PTHR11640,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GATCTCAGTGT	.	4	ESCA
MUC5B	0	.	GRCh37	11	1271669	1271669	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13559C>A	p.Thr4520Asn	p.T4520N	ENST00000529681	31/49	143	101	42	137	137	0	MUC5B,missense_variant,p.Thr4520Asn,ENST00000529681,;MUC5B,missense_variant,p.Thr4523Asn,ENST00000447027,;RP11-532E4.2,upstream_gene_variant,,ENST00000532061,;	A	ENSG00000117983	ENST00000529681	Transcript	missense_variant	13617	13559	4520	T/N	aCc/aAc	.	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	unknown(0)	31/49	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTACCAGCT	.	5	ESCA
MYRF	0	.	GRCh37	11	61537890	61537912	+	Frame_Shift_Del	DEL	CCCGATCCCCCACTACGCTGCCA	CCCGATCCCCCACTACGCTGCCA	ATGCCT	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	CCCGATCCCCCACTACGCTGCCA	CCCGATCCCCCACTACGCTGCCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633_655delCCCGATCCCCCACTACGCTGCCAinsATGCCT	p.Pro212CysfsTer10	p.P212Cfs*10	ENST00000278836	5/27	63	33	30	50	50	0	MYRF,frameshift_variant,p.Pro212CysfsTer10,ENST00000278836,;MYRF,frameshift_variant,p.Pro203CysfsTer10,ENST00000265460,;MYRF,upstream_gene_variant,,ENST00000327797,;TMEM258,intron_variant,,ENST00000535042,;MYRF,downstream_gene_variant,,ENST00000537766,;	ATGCCT	ENSG00000124920	ENST00000278836	Transcript	frameshift_variant	729-751	633-655	211-219	PPIPHYAAM/PCLX	ccCCCGATCCCCCACTACGCTGCCAtg/ccATGCCTtg	.	.	.	1	MYRF	HGNC	1181	protein_coding	YES	CCDS44622.1	ENSP00000278836	MRF_HUMAN	.	UPI0000D45F7B	.	.	.	5/27	.	hmmpanther:PTHR13029,hmmpanther:PTHR13029:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	CGAGCCCCCGATCCCCCACTACGCTGCCATGGGG	.	2	ESCA
MYRF	0	.	GRCh37	11	61537912	61537912	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.655A>T	p.Met219Leu	p.M219L	ENST00000278836	5/27	53	34	19	53	53	0	MYRF,missense_variant,p.Met219Leu,ENST00000278836,;MYRF,missense_variant,p.Met210Leu,ENST00000265460,;MYRF,upstream_gene_variant,,ENST00000327797,;TMEM258,intron_variant,,ENST00000535042,;MYRF,downstream_gene_variant,,ENST00000537766,;	T	ENSG00000124920	ENST00000278836	Transcript	missense_variant	751	655	219	M/L	Atg/Ttg	.	.	.	1	MYRF	HGNC	1181	protein_coding	YES	CCDS44622.1	ENSP00000278836	MRF_HUMAN	.	UPI0000D45F7B	.	tolerated(0.87)	benign(0.001)	5/27	.	hmmpanther:PTHR13029,hmmpanther:PTHR13029:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CTGCCATGGGG	.	2	ESCA
AHNAK	0	.	GRCh37	11	62300523	62300523	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1366C>T	p.Pro456Ser	p.P456S	ENST00000378024	5/5	33	10	23	24	24	0	AHNAK,missense_variant,p.Pro456Ser,ENST00000378024,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,downstream_gene_variant,,ENST00000531324,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000528508,;RP11-864I4.3,upstream_gene_variant,,ENST00000544108,;	A	ENSG00000124942	ENST00000378024	Transcript	missense_variant	1641	1366	456	P/S	Cct/Tct	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	benign(0.279)	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAGGCAGTG	.	5	ESCA
SLC3A2	0	.	GRCh37	11	62622798	62622798	+	5'Flank	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000377891	.	40	31	9	30	30	0	SLC3A2,upstream_gene_variant,,ENST00000377892,;SLC3A2,upstream_gene_variant,,ENST00000377891,;SLC3A2,upstream_gene_variant,,ENST00000377890,;SLC3A2,upstream_gene_variant,,ENST00000377889,;SLC3A2,upstream_gene_variant,,ENST00000535296,;SNHG1,non_coding_transcript_exon_variant,,ENST00000384147,;SNHG1,intron_variant,,ENST00000537925,;SNHG1,intron_variant,,ENST00000545440,;SNHG1,intron_variant,,ENST00000540725,;SNHG1,intron_variant,,ENST00000537068,;SNHG1,intron_variant,,ENST00000541615,;SNHG1,intron_variant,,ENST00000538266,;SNHG1,intron_variant,,ENST00000537869,;SNHG1,intron_variant,,ENST00000541578,;SNHG1,intron_variant,,ENST00000542112,;SNHG1,downstream_gene_variant,,ENST00000365607,;SNHG1,upstream_gene_variant,,ENST00000384756,;SNHG1,upstream_gene_variant,,ENST00000539303,;SNHG1,upstream_gene_variant,,ENST00000383926,;SNHG1,upstream_gene_variant,,ENST00000539975,;SNHG1,upstream_gene_variant,,ENST00000364799,;SNHG1,upstream_gene_variant,,ENST00000384706,;SNHG1,upstream_gene_variant,,ENST00000516331,;SNHG1,upstream_gene_variant,,ENST00000384693,;SNHG1,upstream_gene_variant,,ENST00000539921,;SNHG1,upstream_gene_variant,,ENST00000363981,;SNHG1,non_coding_transcript_exon_variant,,ENST00000538654,;SNHG1,intron_variant,,ENST00000540904,;SNHG1,intron_variant,,ENST00000544550,;SNHG1,intron_variant,,ENST00000537024,;SNHG1,intron_variant,,ENST00000545688,;SNHG1,intron_variant,,ENST00000541416,;SNHG1,intron_variant,,ENST00000545308,;SNHG1,intron_variant,,ENST00000537965,;SNHG1,intron_variant,,ENST00000544983,;SNHG1,intron_variant,,ENST00000540865,;SNHG1,intron_variant,,ENST00000535689,;SNHG1,upstream_gene_variant,,ENST00000545920,;SNHG1,upstream_gene_variant,,ENST00000535076,;	G	ENSG00000168003	ENST00000377891	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	785	1	SLC3A2	HGNC	11026	protein_coding	YES	CCDS31588.1	ENSP00000367123	.	J3KPF3_HUMAN,F5H867_HUMAN,F5H056_HUMAN,F5GZI0_HUMAN,B4E2Z3_HUMAN	UPI00004EC298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCCATCAGA	.	5	ESCA
PPP6R3	0	.	GRCh37	11	68381752	68381752	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1167A>T	.	.	ENST00000393801	25/25	55	31	24	44	44	0	PPP6R3,3_prime_UTR_variant,,ENST00000527403,;PPP6R3,3_prime_UTR_variant,,ENST00000265637,;PPP6R3,3_prime_UTR_variant,,ENST00000393799,;PPP6R3,3_prime_UTR_variant,,ENST00000524904,;PPP6R3,3_prime_UTR_variant,,ENST00000393800,;PPP6R3,3_prime_UTR_variant,,ENST00000265636,;PPP6R3,3_prime_UTR_variant,,ENST00000393801,;PPP6R3,intron_variant,,ENST00000529710,;PPP6R3,downstream_gene_variant,,ENST00000534534,;PPP6R3,downstream_gene_variant,,ENST00000524845,;PPP6R3,downstream_gene_variant,,ENST00000530734,;PPP6R3,downstream_gene_variant,,ENST00000534190,;CTD-2007L18.5,intron_variant,,ENST00000565199,;CTD-2007L18.5,downstream_gene_variant,,ENST00000564469,;CTD-2007L18.5,downstream_gene_variant,,ENST00000565473,;PPP6R3,non_coding_transcript_exon_variant,,ENST00000526307,;PPP6R3,downstream_gene_variant,,ENST00000525152,;PPP6R3,downstream_gene_variant,,ENST00000526593,;	T	ENSG00000110075	ENST00000393801	Transcript	3_prime_UTR_variant	4022	.	.	.	.	.	.	.	1	PPP6R3	HGNC	1173	protein_coding	YES	CCDS53671.1	ENSP00000377390	PP6R3_HUMAN	E9PNN8_HUMAN,E9PKG4_HUMAN,E9PK08_HUMAN,E9PJD8_HUMAN	UPI0000688150	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTATAATT	.	5	ESCA
KIAA1731	0	.	GRCh37	11	93463755	93463755	+	3'Flank	SNP	G	G	C	rs748406822	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000325212	.	67	52	15	66	66	0	KIAA1731,downstream_gene_variant,,ENST00000531404,;KIAA1731,downstream_gene_variant,,ENST00000344196,;KIAA1731,downstream_gene_variant,,ENST00000325212,;KIAA1731,downstream_gene_variant,,ENST00000411936,;KIAA1731,downstream_gene_variant,,ENST00000531700,;KIAA1731,downstream_gene_variant,,ENST00000529185,;TAF1D,downstream_gene_variant,,ENST00000448108,;SNORA25,non_coding_transcript_exon_variant,,ENST00000384384,;SNORA1,downstream_gene_variant,,ENST00000384107,;MIR1304,downstream_gene_variant,,ENST00000408243,;SNORD5,downstream_gene_variant,,ENST00000459342,;SNORA8,downstream_gene_variant,,ENST00000384574,;SNORA32,downstream_gene_variant,,ENST00000384072,;SNORA40,downstream_gene_variant,,ENST00000388090,;SNORD6,downstream_gene_variant,,ENST00000365444,;SNORA18,downstream_gene_variant,,ENST00000384416,;TAF1D,intron_variant,,ENST00000546088,;TAF1D,downstream_gene_variant,,ENST00000530089,;TAF1D,3_prime_UTR_variant,,ENST00000323981,;TAF1D,intron_variant,,ENST00000393259,;TAF1D,intron_variant,,ENST00000526015,;TAF1D,intron_variant,,ENST00000530769,;TAF1D,intron_variant,,ENST00000529435,;TAF1D,intron_variant,,ENST00000534079,;TAF1D,intron_variant,,ENST00000525928,;TAF1D,downstream_gene_variant,,ENST00000533794,;TAF1D,downstream_gene_variant,,ENST00000527068,;TAF1D,downstream_gene_variant,,ENST00000540232,;TAF1D,downstream_gene_variant,,ENST00000529794,;TAF1D,downstream_gene_variant,,ENST00000529900,;TAF1D,downstream_gene_variant,,ENST00000527169,;	C	ENSG00000166004	ENST00000325212	Transcript	downstream_gene_variant	.	.	.	.	.	rs748406822	.	233	1	KIAA1731	HGNC	29366	protein_coding	YES	CCDS44708.1	ENSP00000316681	K1731_HUMAN	E9PM20_HUMAN	UPI0000251F0E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGGTCACA	byFrequency	5	ESCA
FAM71C	0	.	GRCh37	12	100041871	100041871	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-82C>A	.	.	ENST00000324341	1/2	45	34	11	39	38	0	FAM71C,5_prime_UTR_variant,,ENST00000324341,;ANKS1B,intron_variant,,ENST00000329257,;ANKS1B,intron_variant,,ENST00000549866,;ANKS1B,intron_variant,,ENST00000547010,;ANKS1B,intron_variant,,ENST00000547776,;ANKS1B,intron_variant,,ENST00000552232,;	A	ENSG00000180219	ENST00000324341	Transcript	5_prime_UTR_variant	341	.	.	.	.	.	.	.	1	FAM71C	HGNC	28594	protein_coding	YES	CCDS9072.1	ENSP00000315247	FA71C_HUMAN	.	UPI0000073857	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGTAGCCAAGG	.	4	ESCA
PRB2	0	.	GRCh37	12	11546795	11546795	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217C>T	p.Pro73Ser	p.P73S	ENST00000389362	3/4	44	40	4	83	83	0	PRB2,missense_variant,p.Pro73Ser,ENST00000389362,;PRB1,intron_variant,,ENST00000546254,;PRB2,downstream_gene_variant,,ENST00000565533,;PRB2,downstream_gene_variant,,ENST00000545829,;	A	ENSG00000121335	ENST00000389362	Transcript	missense_variant	253	217	73	P/S	Cct/Tct	.	.	.	-1	PRB2	HGNC	9338	protein_coding	YES	CCDS41757.2	ENSP00000374013	PRB2_HUMAN	.	UPI0000EE5993	.	tolerated(0.13)	unknown(0)	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23203,hmmpanther:PTHR23203:SF2,Pfam_domain:PF15240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P50P|c.150C>T|3,BUFFER|p.P71P|c.213C>T|3	MUTECT|VARSCANS	AGGAGGTGGGG	.	2	ESCA
MSI1	0	.	GRCh37	12	120785277	120785277	+	Silent	SNP	C	C	T	rs561139090	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.831G>A	p.%3D	p.A277A	ENST00000257552	12/15	38	33	5	45	45	0	MSI1,synonymous_variant,p.%3D,ENST00000257552,;MSI1,synonymous_variant,p.%3D,ENST00000546985,;	T	ENSG00000135097	ENST00000257552	Transcript	synonymous_variant	920	831	277	A	gcG/gcA	rs561139090	.	.	-1	MSI1	HGNC	7330	protein_coding	YES	CCDS9196.1	ENSP00000257552	MSI1H_HUMAN	B3KN16_HUMAN	UPI0000073DD8	.	.	.	12/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24012:SF262,hmmpanther:PTHR24012	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCGCCGCTGC	by1000G	4	ESCA
TMEM132C	0	.	GRCh37	12	129190651	129190651	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3138G>A	p.%3D	p.S1046S	ENST00000435159	9/9	41	30	11	43	43	0	TMEM132C,synonymous_variant,p.%3D,ENST00000537538,;TMEM132C,synonymous_variant,p.%3D,ENST00000315208,;TMEM132C,synonymous_variant,p.%3D,ENST00000435159,;	A	ENSG00000181234	ENST00000435159	Transcript	synonymous_variant	3138	3138	1046	S	tcG/tcA	.	.	.	1	TMEM132C	HGNC	25436	protein_coding	YES	.	ENSP00000410852	T132C_HUMAN	F5H439_HUMAN,E9PC33_HUMAN	UPI0001C0B37C	.	.	.	9/9	.	hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTCGCCCAC	.	5	ESCA
KCNA1	0	.	GRCh37	12	5020720	5020720	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.176C>G	p.Pro59Arg	p.P59R	ENST00000382545	2/2	119	89	29	110	109	1	KCNA1,missense_variant,p.Pro59Arg,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	G	ENSG00000111262	ENST00000382545	Transcript	missense_variant	1283	176	59	P/R	cCc/cGc	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	deleterious(0)	probably_damaging(1)	2/2	.	Superfamily_domains:SSF54695,SMART_domains:SM00225,Pfam_domain:PF02214,Gene3D:3.30.710.10,hmmpanther:PTHR11537:SF24,hmmpanther:PTHR11537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCCCCAACA	.	5	ESCA
R3HDM2	0	.	GRCh37	12	57647828	57647828	+	3'UTR	DEL	T	T	-	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*728delA	.	.	ENST00000347140	24/24	61	50	11	44	44	0	R3HDM2,3_prime_UTR_variant,,ENST00000402412,;R3HDM2,3_prime_UTR_variant,,ENST00000347140,;R3HDM2,3_prime_UTR_variant,,ENST00000358907,;R3HDM2,intron_variant,,ENST00000413953,;R3HDM2,downstream_gene_variant,,ENST00000429355,;STAC3,upstream_gene_variant,,ENST00000332782,;STAC3,upstream_gene_variant,,ENST00000546246,;STAC3,upstream_gene_variant,,ENST00000553489,;STAC3,upstream_gene_variant,,ENST00000554578,;R3HDM2,downstream_gene_variant,,ENST00000403821,;R3HDM2,downstream_gene_variant,,ENST00000548161,;R3HDM2,downstream_gene_variant,,ENST00000441731,;R3HDM2,downstream_gene_variant,,ENST00000546843,;R3HDM2,non_coding_transcript_exon_variant,,ENST00000393811,;RP11-123K3.4,intron_variant,,ENST00000548184,;STAC3,upstream_gene_variant,,ENST00000553294,;STAC3,upstream_gene_variant,,ENST00000557176,;	-	ENSG00000179912	ENST00000347140	Transcript	3_prime_UTR_variant	4050	.	.	.	.	.	.	.	-1	R3HDM2	HGNC	29167	protein_coding	YES	CCDS8937.2	ENSP00000317903	R3HD2_HUMAN	C9J7N6_HUMAN	UPI00005A60D3	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTTTATCTTAA	.	3	ESCA
VWF	0	.	GRCh37	12	6062682	6062682	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7966G>A	p.Gly2656Arg	p.G2656R	ENST00000261405	48/52	56	50	6	26	26	0	VWF,missense_variant,p.Gly2656Arg,ENST00000261405,;	T	ENSG00000110799	ENST00000261405	Transcript	missense_variant	8221	7966	2656	G/R	Gga/Aga	.	.	.	-1	VWF	HGNC	12726	protein_coding	YES	CCDS8539.1	ENSP00000261405	VWF_HUMAN	H2DLA2_HUMAN	UPI00001AE7EE	.	deleterious(0.03)	probably_damaging(0.979)	48/52	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF259,PIRSF_domain:PIRSF002495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTCCTCCTC	.	4	ESCA
LPCAT3	0	.	GRCh37	12	7086639	7086639	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1237A>G	p.Ile413Val	p.I413V	ENST00000261407	11/13	50	37	13	38	38	0	LPCAT3,missense_variant,p.Ile413Val,ENST00000261407,;EMG1,downstream_gene_variant,,ENST00000261406,;U47924.30,upstream_gene_variant,,ENST00000606112,;LPCAT3,non_coding_transcript_exon_variant,,ENST00000535021,;EMG1,intron_variant,,ENST00000564245,;EMG1,intron_variant,,ENST00000539535,;LPCAT3,downstream_gene_variant,,ENST00000540060,;EMG1,downstream_gene_variant,,ENST00000541016,;LPCAT3,downstream_gene_variant,,ENST00000536971,;EMG1,downstream_gene_variant,,ENST00000607161,;LPCAT3,downstream_gene_variant,,ENST00000539868,;EMG1,downstream_gene_variant,,ENST00000539196,;EMG1,downstream_gene_variant,,ENST00000546220,;LPCAT3,downstream_gene_variant,,ENST00000545459,;LPCAT3,3_prime_UTR_variant,,ENST00000535479,;LPCAT3,downstream_gene_variant,,ENST00000540090,;EMG1,downstream_gene_variant,,ENST00000451846,;EMG1,downstream_gene_variant,,ENST00000539440,;LPCAT3,downstream_gene_variant,,ENST00000537179,;LPCAT3,downstream_gene_variant,,ENST00000536797,;LPCAT3,downstream_gene_variant,,ENST00000538910,;LPCAT3,downstream_gene_variant,,ENST00000538987,;LPCAT3,downstream_gene_variant,,ENST00000543794,;	C	ENSG00000111684	ENST00000261407	Transcript	missense_variant	1323	1237	413	I/V	Att/Gtt	.	.	.	-1	LPCAT3	HGNC	30244	protein_coding	YES	CCDS8572.1	ENSP00000261407	MBOA5_HUMAN	F5H0M4_HUMAN	UPI0000034DFC	.	tolerated(0.38)	benign(0.006)	11/13	.	hmmpanther:PTHR13906:SF9,hmmpanther:PTHR13906,Pfam_domain:PF03062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAATGGCGG	.	5	ESCA
PPFIA2	0	.	GRCh37	12	81991809	81991809	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303+78761G>C	.	.	ENST00000549396	.	64	52	11	37	37	0	PPFIA2,start_lost,p.Met1?,ENST00000407050,;PPFIA2,start_lost,p.Met1?,ENST00000443686,;PPFIA2,intron_variant,,ENST00000333447,;PPFIA2,intron_variant,,ENST00000551442,;PPFIA2,intron_variant,,ENST00000549396,;PPFIA2,intron_variant,,ENST00000549325,;PPFIA2,intron_variant,,ENST00000548586,;PPFIA2,intron_variant,,ENST00000547623,;PPFIA2,intron_variant,,ENST00000550584,;PPFIA2,intron_variant,,ENST00000552948,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000545296,;PPFIA2,intron_variant,,ENST00000552020,;	G	ENSG00000139220	ENST00000549396	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PPFIA2	HGNC	9246	protein_coding	YES	CCDS55857.1	ENSP00000450337	LIPA2_HUMAN	H0YHK3_HUMAN,F8W1Y8_HUMAN,F8VU88_HUMAN	UPI0000168655	.	.	.	.	4/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATCATTTC	.	5	ESCA
NEDD1	0	.	GRCh37	12	97306394	97306394	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.158-107C>T	.	.	ENST00000557644	.	39	30	9	30	30	0	NEDD1,5_prime_UTR_variant,,ENST00000457368,;NEDD1,intron_variant,,ENST00000557644,;NEDD1,intron_variant,,ENST00000554226,;NEDD1,intron_variant,,ENST00000411739,;NEDD1,intron_variant,,ENST00000553609,;NEDD1,intron_variant,,ENST00000266742,;NEDD1,intron_variant,,ENST00000429527,;NEDD1,intron_variant,,ENST00000557478,;NEDD1,intron_variant,,ENST00000557092,;NEDD1,intron_variant,,ENST00000557454,;NEDD1,intron_variant,,ENST00000557400,;NEDD1,intron_variant,,ENST00000555114,;NEDD1,intron_variant,,ENST00000555806,;	T	ENSG00000139350	ENST00000557644	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NEDD1	HGNC	7723	protein_coding	YES	CCDS44955.1	ENSP00000451211	.	G3V4L2_HUMAN,G3V4I9_HUMAN,G3V3F1_HUMAN,G3V2V3_HUMAN,G3V2M9_HUMAN	UPI000004D249	.	.	.	.	2/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACTCATTGC	.	5	ESCA
TMPO	0	.	GRCh37	12	98931427	98931427	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000266732	.	24	18	6	15	15	0	TMPO,missense_variant,p.Asn247Ser,ENST00000261210,;TMPO,intron_variant,,ENST00000393053,;TMPO,intron_variant,,ENST00000343315,;TMPO,intron_variant,,ENST00000556029,;TMPO,intron_variant,,ENST00000556678,;TMPO,downstream_gene_variant,,ENST00000266732,;TMPO,downstream_gene_variant,,ENST00000549938,;TMPO,downstream_gene_variant,,ENST00000552831,;	G	ENSG00000120802	ENST00000266732	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2015	1	TMPO	HGNC	11875	protein_coding	YES	CCDS9064.1	ENSP00000266732	LAP2A_HUMAN	.	UPI000013D709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTTTAATGGTT	.	4	ESCA
AL445989.1	0	.	GRCh37	13	64320963	64320963	+	Missense_Mutation	SNP	T	T	G	rs531532468	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.30T>G	p.Cys10Trp	p.C10W	ENST00000453638	1/1	70	56	13	70	70	0	AL445989.1,missense_variant,p.Cys10Trp,ENST00000453638,;RP11-473M10.3,upstream_gene_variant,,ENST00000418943,;OR7E156P,downstream_gene_variant,,ENST00000400303,;	G	ENSG00000226974	ENST00000453638	Transcript	missense_variant	30	30	10	C/W	tgT/tgG	rs531532468	.	.	1	AL445989.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000443634	.	F5H8E9_HUMAN	UPI0001A5EA97	.	.	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31294:SF3,hmmpanther:PTHR31294	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TCCTGTGGCTA	by1000G	3	ESCA
LMO7	0	.	GRCh37	13	76397787	76397787	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2028G>A	p.%3D	p.P676P	ENST00000465261	12/27	94	76	18	63	63	0	LMO7,synonymous_variant,p.%3D,ENST00000357063,;LMO7,synonymous_variant,p.%3D,ENST00000321797,;LMO7,synonymous_variant,p.%3D,ENST00000526202,;LMO7,synonymous_variant,p.%3D,ENST00000465261,;LMO7,synonymous_variant,p.%3D,ENST00000341547,;LMO7,synonymous_variant,p.%3D,ENST00000377534,;LMO7,synonymous_variant,p.%3D,ENST00000377499,;LMO7,synonymous_variant,p.%3D,ENST00000447038,;LMO7,upstream_gene_variant,,ENST00000524651,;LMO7,downstream_gene_variant,,ENST00000489941,;LMO7,downstream_gene_variant,,ENST00000525373,;LMO7,non_coding_transcript_exon_variant,,ENST00000485987,;LMO7,downstream_gene_variant,,ENST00000532785,;LMO7,downstream_gene_variant,,ENST00000532377,;	A	ENSG00000136153	ENST00000465261	Transcript	synonymous_variant	2788	2028	676	P	ccG/ccA	COSM1161092,COSM948456,COSM948457,COSM1161093,COSM1587178,COSM1161091	.	.	1	LMO7	HGNC	6646	protein_coding	YES	CCDS53876.1	ENSP00000433352	.	E9PRJ0_HUMAN,E9PLH4_HUMAN	UPI0001929501	.	.	.	12/27	.	hmmpanther:PTHR15551,hmmpanther:PTHR15551:SF4,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCGGACGC	.	5	ESCA
MDGA2	0	.	GRCh37	14	47342646	47342646	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2742A>G	p.%3D	p.G914G	ENST00000439988	14/17	93	76	16	65	65	0	MDGA2,synonymous_variant,p.%3D,ENST00000439988,;MDGA2,synonymous_variant,p.%3D,ENST00000399232,;MDGA2,synonymous_variant,p.%3D,ENST00000357362,;MDGA2,synonymous_variant,p.%3D,ENST00000399222,;MDGA2,synonymous_variant,p.%3D,ENST00000426342,;MDGA2,3_prime_UTR_variant,,ENST00000557238,;MDGA2,non_coding_transcript_exon_variant,,ENST00000557516,;MDGA2,downstream_gene_variant,,ENST00000555521,;	C	ENSG00000272781	ENST00000439988	Transcript	synonymous_variant	2742	2742	914	G	ggA/ggG	.	.	.	-1	MDGA2	Uniprot_gn	19835	protein_coding	YES	.	ENSP00000400011	MDGA2_HUMAN	F8WE89_HUMAN	UPI0001DD21C1	.	.	.	14/17	.	PROSITE_profiles:PS50060,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTGTCCATA	.	5	ESCA
PELI2	0	.	GRCh37	14	56645145	56645145	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.170G>T	p.Ser57Ile	p.S57I	ENST00000267460	2/6	135	105	29	103	103	0	PELI2,missense_variant,p.Ser57Ile,ENST00000267460,;PELI2,5_prime_UTR_variant,,ENST00000561019,;PELI2,5_prime_UTR_variant,,ENST00000559044,;	T	ENSG00000139946	ENST00000267460	Transcript	missense_variant	456	170	57	S/I	aGc/aTc	.	.	.	1	PELI2	HGNC	8828	protein_coding	YES	CCDS9726.1	ENSP00000267460	PELI2_HUMAN	Q659D8_HUMAN,H0YNF4_HUMAN,H0YK56_HUMAN	UPI0000062262	.	tolerated(0.2)	probably_damaging(0.999)	2/6	.	hmmpanther:PTHR12098:SF5,hmmpanther:PTHR12098,Pfam_domain:PF04710,PIRSF_domain:PIRSF038886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCAGCACCG	.	5	ESCA
GALC	0	.	GRCh37	14	88399739	88399739	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1337T>C	.	.	ENST00000261304	17/17	36	26	9	32	32	0	GALC,3_prime_UTR_variant,,ENST00000261304,;GALC,downstream_gene_variant,,ENST00000393568,;GALC,downstream_gene_variant,,ENST00000544807,;GALC,downstream_gene_variant,,ENST00000393569,;GALC,intron_variant,,ENST00000555000,;GALC,downstream_gene_variant,,ENST00000555179,;	G	ENSG00000054983	ENST00000261304	Transcript	3_prime_UTR_variant	3502	.	.	.	.	.	.	.	-1	GALC	HGNC	4115	protein_coding	YES	CCDS9878.2	ENSP00000261304	GALC_HUMAN	.	UPI00001FD982	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTCACTGAA	.	5	ESCA
RP11-371E8.4	0	.	GRCh37	14	93676302	93676302	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340A>T	p.Arg114Ter	p.R114*	ENST00000557574	3/5	96	72	24	67	67	0	RP11-371E8.4,stop_gained,p.Arg114Ter,ENST00000557574,;UBR7,stop_gained,p.Arg21Ter,ENST00000553857,;UBR7,stop_gained,p.Arg95Ter,ENST00000554232,;UBR7,stop_gained,p.Arg95Ter,ENST00000013070,;UBR7,missense_variant,p.Ser95Cys,ENST00000555113,;UBR7,intron_variant,,ENST00000556871,;UBR7,intron_variant,,ENST00000416753,;C14orf142,upstream_gene_variant,,ENST00000306954,;C14orf142,upstream_gene_variant,,ENST00000556566,;RP11-371E8.4,splice_region_variant,,ENST00000557048,;RP11-371E8.4,3_prime_UTR_variant,,ENST00000554824,;UBR7,intron_variant,,ENST00000553674,;	T	ENSG00000259066	ENST00000557574	Transcript	stop_gained	396	340	114	R/*	Aga/Tga	.	.	.	1	RP11-371E8.4	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000451369	.	G3V3Q6_HUMAN	UPI00021CF3D0	.	.	.	3/5	.	PROSITE_profiles:PS51157,hmmpanther:PTHR13513,Pfam_domain:PF02207,SMART_domains:SM00396	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAAAGGTAA	.	5	ESCA
ASB7	0	.	GRCh37	15	101189293	101189294	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*636dupT	.	.	ENST00000332783	6/6	59	50	9	30	30	0	ASB7,3_prime_UTR_variant,,ENST00000332783,;ASB7,3_prime_UTR_variant,,ENST00000558747,;RP11-192M23.1,upstream_gene_variant,,ENST00000561269,;	T	ENSG00000183475	ENST00000332783	Transcript	3_prime_UTR_variant	2368-2369	.	.	.	.	.	.	.	1	ASB7	HGNC	17182	protein_coding	YES	CCDS10387.1	ENSP00000328327	ASB7_HUMAN	.	UPI00001B3F4D	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AACTTATTTTT	.	2	ESCA
CSPG4	0	.	GRCh37	15	75979614	75979614	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3789+3G>A	.	.	ENST00000308508	.	161	87	74	149	149	0	CSPG4,splice_region_variant,,ENST00000308508,;	T	ENSG00000173546	ENST00000308508	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	CSPG4	HGNC	2466	protein_coding	YES	CCDS10284.1	ENSP00000312506	CSPG4_HUMAN	.	UPI00001AEEB6	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCACCTC	.	4	ESCA
TTLL13	0	.	GRCh37	15	90801306	90801306	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972C>T	p.%3D	p.H324H	ENST00000339615	9/10	44	24	20	37	37	0	TTLL13,synonymous_variant,p.%3D,ENST00000339615,;TTLL13,synonymous_variant,p.%3D,ENST00000438251,;RP11-697E2.6,intron_variant,,ENST00000561573,;	T	ENSG00000213471	ENST00000339615	Transcript	synonymous_variant	1262	972	324	H	caC/caT	.	.	.	1	TTLL13	HGNC	32484	protein_coding	YES	.	ENSP00000345294	TTL13_HUMAN	.	UPI00005B2F05	.	.	.	9/10	.	PROSITE_profiles:PS51221,hmmpanther:PTHR12241:SF91,hmmpanther:PTHR12241,Pfam_domain:PF03133,Superfamily_domains:SSF56059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCACAGCTA	.	5	ESCA
NPRL3	0	.	GRCh37	16	136635	136635	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69C>T	.	.	ENST00000399953	14/14	33	27	5	17	17	0	NPRL3,3_prime_UTR_variant,,ENST00000399953,;NPRL3,3_prime_UTR_variant,,ENST00000399951,;MPG,downstream_gene_variant,,ENST00000436333,;MPG,downstream_gene_variant,,ENST00000356432,;MPG,downstream_gene_variant,,ENST00000397817,;MPG,downstream_gene_variant,,ENST00000219431,;Z69720.2,upstream_gene_variant,,ENST00000601483,;NPRL3,non_coding_transcript_exon_variant,,ENST00000405960,;NPRL3,non_coding_transcript_exon_variant,,ENST00000428323,;NPRL3,3_prime_UTR_variant,,ENST00000399957,;NPRL3,3_prime_UTR_variant,,ENST00000445810,;NPRL3,intron_variant,,ENST00000463178,;	A	ENSG00000103148	ENST00000399953	Transcript	3_prime_UTR_variant	2179	.	.	.	.	.	.	.	-1	NPRL3	HGNC	14124	protein_coding	YES	.	ENSP00000382834	NPRL3_HUMAN	.	UPI00004568D2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGGGAGCCC	.	4	ESCA
ACSM2B	0	.	GRCh37	16	20548562	20548562	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*18C>T	.	.	ENST00000329697	14/14	110	77	33	114	114	0	ACSM2B,3_prime_UTR_variant,,ENST00000568098,;ACSM2B,3_prime_UTR_variant,,ENST00000565232,;ACSM2B,3_prime_UTR_variant,,ENST00000329697,;ACSM2B,3_prime_UTR_variant,,ENST00000567001,;ACSM2B,3_prime_UTR_variant,,ENST00000565322,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000566998,;ACSM2B,downstream_gene_variant,,ENST00000569131,;ACSM2B,downstream_gene_variant,,ENST00000564849,;	A	ENSG00000066813	ENST00000329697	Transcript	3_prime_UTR_variant	1921	.	.	.	.	.	.	.	-1	ACSM2B	HGNC	30931	protein_coding	YES	CCDS10586.1	ENSP00000327453	ACS2B_HUMAN	H3BTX9_HUMAN,H3BQ84_HUMAN,H3BP79_HUMAN,H3BM61_HUMAN	UPI00001AFAA7	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAATGAATGT	.	5	ESCA
RP11-231C14.4	0	.	GRCh37	16	29496887	29496887	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388C>A	p.Pro130Thr	p.P130T	ENST00000354563	3/3	18	10	8	12	12	0	RP11-231C14.4,missense_variant,p.Pro304Thr,ENST00000550665,;RP11-231C14.4,missense_variant,p.Pro130Thr,ENST00000354563,;SNX29P2,intron_variant,,ENST00000398878,;RP11-231C14.4,downstream_gene_variant,,ENST00000552123,;RP11-231C14.4,downstream_gene_variant,,ENST00000549733,;RP11-231C14.4,downstream_gene_variant,,ENST00000551448,;RP11-231C14.5,downstream_gene_variant,,ENST00000546408,;	T	ENSG00000169203	ENST00000354563	Transcript	missense_variant	799	388	130	P/T	Cct/Act	.	.	.	-1	RP11-231C14.4	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000346572	.	A8MQ56_HUMAN	UPI0000D619CE	.	.	benign(0.213)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15438,hmmpanther:PTHR15438:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	AGGAGGTGTCT	.	2	ESCA
ATP2C2	0	.	GRCh37	16	84494107	84494108	+	Intron	INS	-	-	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2334-151dupG	.	.	ENST00000262429	.	143	106	37	100	100	0	ATP2C2,intron_variant,,ENST00000416219,;ATP2C2,intron_variant,,ENST00000262429,;RP11-517C16.2,non_coding_transcript_exon_variant,,ENST00000565700,;ATP2C2,intron_variant,,ENST00000420010,;ATP2C2,non_coding_transcript_exon_variant,,ENST00000567222,;ATP2C2,intron_variant,,ENST00000567892,;ATP2C2,intron_variant,,ENST00000565631,;ATP2C2,upstream_gene_variant,,ENST00000567629,;ATP2C2,upstream_gene_variant,,ENST00000566874,;	G	ENSG00000064270	ENST00000262429	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ATP2C2	HGNC	29103	protein_coding	YES	CCDS42207.1	ENSP00000262429	AT2C2_HUMAN	.	UPI0000252110	.	.	.	.	23/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCCGAGGAGG	.	3	ESCA
OR3A2	0	.	GRCh37	17	3182035	3182035	+	Silent	SNP	G	G	A	rs529347635	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.195C>T	p.%3D	p.H65H	ENST00000408891	1/1	13	6	7	17	17	0	OR3A2,synonymous_variant,p.%3D,ENST00000408891,;RP11-64J4.2,downstream_gene_variant,,ENST00000576166,;RP11-64J4.2,downstream_gene_variant,,ENST00000573491,;	A	ENSG00000221882	ENST00000408891	Transcript	synonymous_variant	234	195	65	H	caC/caT	rs529347635	.	.	-1	OR3A2	HGNC	8283	protein_coding	YES	CCDS42233.1	ENSP00000386180	OR3A2_HUMAN	.	UPI0000050B3C	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF7,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	A:0.0008	A:0	A:0	.	A:0	A:0	A:0.0041	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	GGGGCGTGGAG	byFrequency|by1000G	2	ESCA
CDC27	0	.	GRCh37	17	45235588	45235588	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459A>G	p.%3D	p.E153E	ENST00000531206	5/19	40	31	8	18	18	0	CDC27,synonymous_variant,p.%3D,ENST00000531206,;CDC27,synonymous_variant,p.%3D,ENST00000066544,;CDC27,synonymous_variant,p.%3D,ENST00000527547,;CDC27,synonymous_variant,p.%3D,ENST00000575483,;CDC27,synonymous_variant,p.%3D,ENST00000446365,;RP5-867C24.4,downstream_gene_variant,,ENST00000574021,;CDC27,non_coding_transcript_exon_variant,,ENST00000528748,;CDC27,non_coding_transcript_exon_variant,,ENST00000532575,;CDC27,upstream_gene_variant,,ENST00000575830,;CDC27,synonymous_variant,p.%3D,ENST00000526866,;CDC27,synonymous_variant,p.%3D,ENST00000574304,;CDC27,3_prime_UTR_variant,,ENST00000533415,;CDC27,3_prime_UTR_variant,,ENST00000573550,;CDC27,3_prime_UTR_variant,,ENST00000532893,;CDC27,non_coding_transcript_exon_variant,,ENST00000525495,;CDC27,intron_variant,,ENST00000570818,;CDC27,upstream_gene_variant,,ENST00000576484,;RP5-867C24.1,downstream_gene_variant,,ENST00000488906,;	C	ENSG00000004897	ENST00000531206	Transcript	synonymous_variant	463	459	153	E	gaA/gaG	.	.	.	-1	CDC27	HGNC	1728	protein_coding	YES	CCDS45720.1	ENSP00000434614	CDC27_HUMAN	I0EZ72_HUMAN,I0EZ68_HUMAN	UPI0000E59FE6	.	.	.	5/19	.	Superfamily_domains:SSF48452,hmmpanther:PTHR12558,hmmpanther:PTHR12558:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGATTCAAA	.	5	ESCA
VMP1	0	.	GRCh37	17	57889104	57889104	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.869G>A	p.Gly290Asp	p.G290D	ENST00000262291	9/12	75	62	12	57	57	0	VMP1,missense_variant,p.Gly96Asp,ENST00000591877,;VMP1,missense_variant,p.Gly193Asp,ENST00000536180,;VMP1,missense_variant,p.Gly234Asp,ENST00000545362,;VMP1,missense_variant,p.Gly156Asp,ENST00000537567,;VMP1,missense_variant,p.Gly290Asp,ENST00000262291,;VMP1,missense_variant,p.Gly98Asp,ENST00000539763,;VMP1,3_prime_UTR_variant,,ENST00000592619,;	A	ENSG00000062716	ENST00000262291	Transcript	missense_variant	1179	869	290	G/D	gGt/gAt	.	.	.	1	VMP1	HGNC	29559	protein_coding	YES	CCDS11619.1	ENSP00000262291	VMP1_HUMAN	K7ENU2_HUMAN,K7EMI0_HUMAN,K7EM96_HUMAN,K7EK01_HUMAN,D3DU01_HUMAN,B4DVV9_HUMAN	UPI0000037791	.	deleterious(0)	probably_damaging(0.997)	9/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10281:SF1,hmmpanther:PTHR10281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGGTGCAA	.	5	ESCA
SMARCD2	0	.	GRCh37	17	61909557	61909570	+	3'UTR	DEL	CCCCATTCACCTTA	CCCCATTCACCTTA	-	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	CCCCATTCACCTTA	CCCCATTCACCTTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*728_*741delTAAGGTGAATGGGG	.	.	ENST00000448276	13/13	42	32	10	40	40	0	SMARCD2,3_prime_UTR_variant,,ENST00000448276,;PSMC5,downstream_gene_variant,,ENST00000581882,;SMARCD2,downstream_gene_variant,,ENST00000323347,;PSMC5,downstream_gene_variant,,ENST00000579708,;PSMC5,downstream_gene_variant,,ENST00000375812,;SMARCD2,downstream_gene_variant,,ENST00000225742,;PSMC5,downstream_gene_variant,,ENST00000585123,;FTSJ3,upstream_gene_variant,,ENST00000581209,;FTSJ3,upstream_gene_variant,,ENST00000585145,;PSMC5,downstream_gene_variant,,ENST00000310144,;SMARCD2,downstream_gene_variant,,ENST00000450364,;FTSJ3,upstream_gene_variant,,ENST00000427159,;PSMC5,downstream_gene_variant,,ENST00000580864,;FTSJ3,upstream_gene_variant,,ENST00000584574,;PSMC5,downstream_gene_variant,,ENST00000581842,;PSMC5,downstream_gene_variant,,ENST00000584320,;PSMC5,downstream_gene_variant,,ENST00000582130,;FTSJ3,upstream_gene_variant,,ENST00000580295,;PSMC5,downstream_gene_variant,,ENST00000582420,;SMARCD2,downstream_gene_variant,,ENST00000584483,;PSMC5,downstream_gene_variant,,ENST00000580265,;PSMC5,downstream_gene_variant,,ENST00000578570,;PSMC5,downstream_gene_variant,,ENST00000579031,;PSMC5,downstream_gene_variant,,ENST00000581764,;PSMC5,downstream_gene_variant,,ENST00000584880,;SMARCD2,downstream_gene_variant,,ENST00000584400,;SMARCD2,downstream_gene_variant,,ENST00000577686,;PSMC5,downstream_gene_variant,,ENST00000583283,;PSMC5,downstream_gene_variant,,ENST00000584657,;PSMC5,downstream_gene_variant,,ENST00000584536,;SMARCD2,downstream_gene_variant,,ENST00000578234,;PSMC5,downstream_gene_variant,,ENST00000580063,;SMARCD2,downstream_gene_variant,,ENST00000580054,;SMARCD2,downstream_gene_variant,,ENST00000581832,;PSMC5,downstream_gene_variant,,ENST00000579147,;PSMC5,downstream_gene_variant,,ENST00000585242,;	-	ENSG00000108604	ENST00000448276	Transcript	3_prime_UTR_variant	2590-2603	.	.	.	.	.	.	.	-1	SMARCD2	HGNC	11107	protein_coding	YES	CCDS45756.1	ENSP00000392617	SMRD2_HUMAN	J3KT18_HUMAN,J3KMX2_HUMAN	UPI0000D695F8	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CAGCCTCCCCATTCACCTTACCCTG	.	2	ESCA
TP53	0	.	GRCh37	17	7577610	7577610	+	Splice_Site	SNP	T	T	C	.	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673-2A>G	.	p.X225_splice	ENST00000269305	.	99	52	47	63	63	0	TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000269305,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,splice_acceptor_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000504937,;TP53,splice_acceptor_variant,,ENST00000504290,;TP53,splice_acceptor_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	C	ENSG00000141510	ENST00000269305	Transcript	splice_acceptor_variant	.	.	.	.	.	CS109519,TP53_g.13308A>G,TP53_g.13308A>T,TP53_g.13308A>C,COSM6908,COSM12559,COSM25225,COSM33649,COSM41575,COSM98015,COSM119001,COSM323938,COSM323937,COSM118999,COSM98016,COSM3742466,COSM1649397,COSM119000,COSM323939	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.673-2A>G|12,SITE|p.?|c.673-2A>G|9,SITE|p.?|c.394-2A>G|13,SITE|p.?|c.673-2A>G|9,SITE|p.?|c.673-2A>G|13,SITE|p.?|c.673-2A>G|13,SITE|p.?|c.673-2A>G|5,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.D228Y|c.682G>T|3,BUFFER|p.D228N|c.682G>A|6,BUFFER|p.S227F|c.680C>T|8,BUFFER|p.S227P|c.679T>C|3,BUFFER|p.S134P|c.400T>C|3,BUFFER|p.S227P|c.679T>C|3,BUFFER|p.S227P|c.679T>C|3,BUFFER|p.G226D|c.677G>A|5,BUFFER|p.G226V|c.677G>T|4,BUFFER|p.V225A|c.674T>C|3,BUFFER|p.?|c.394-1G>A|7,BUFFER|p.?|c.673-1G>A|15,BUFFER|p.?|c.673-1G>T|3,BUFFER|p.?|c.673-1G>A|7,BUFFER|p.?|c.394-1G>T|3,BUFFER|p.?|c.673-1G>C|3,BUFFER|p.?|c.673-1G>T|6,BUFFER|p.?|c.673-1G>A|7,BUFFER|p.?|c.673-1G>T|3,BUFFER|p.?|c.673-2A>T|6,BUFFER|p.?|c.673-2A>T|3,BUFFER|p.?|c.673-2A>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACCTAGGAG	.	5	ESCA
TMED1	0	.	GRCh37	19	10943499	10943517	+	3'UTR	DEL	GAGGTGTTCCCTGCCCGCT	GAGGTGTTCCCTGCCCGCT	-	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	GAGGTGTTCCCTGCCCGCT	GAGGTGTTCCCTGCCCGCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*154_*172delAGCGGGCAGGGAACACCTC	.	.	ENST00000214869	4/4	41	30	11	34	34	0	TMED1,3_prime_UTR_variant,,ENST00000214869,;TMED1,3_prime_UTR_variant,,ENST00000591695,;TMED1,3_prime_UTR_variant,,ENST00000586835,;DNM2,intron_variant,,ENST00000591818,;DNM2,downstream_gene_variant,,ENST00000359692,;DNM2,downstream_gene_variant,,ENST00000585892,;TMED1,downstream_gene_variant,,ENST00000589638,;C19orf38,upstream_gene_variant,,ENST00000592854,;TMED1,downstream_gene_variant,,ENST00000588289,;DNM2,downstream_gene_variant,,ENST00000389253,;DNM2,downstream_gene_variant,,ENST00000355667,;DNM2,downstream_gene_variant,,ENST00000314646,;DNM2,downstream_gene_variant,,ENST00000589106,;DNM2,downstream_gene_variant,,ENST00000408974,;DNM2,non_coding_transcript_exon_variant,,ENST00000593203,;TMED1,downstream_gene_variant,,ENST00000591157,;TMED1,downstream_gene_variant,,ENST00000588259,;DNM2,downstream_gene_variant,,ENST00000590806,;	-	ENSG00000099203	ENST00000214869	Transcript	3_prime_UTR_variant	937-955	.	.	.	.	.	.	.	-1	TMED1	HGNC	17291	protein_coding	YES	CCDS12249.1	ENSP00000214869	TMED1_HUMAN	K7EIN4_HUMAN	UPI00000722CE	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	AAGCCAGAGGTGTTCCCTGCCCGCTGAGGA	.	2	ESCA
ELOF1	0	.	GRCh37	19	11663932	11663932	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*629T>G	.	.	ENST00000252445	4/4	31	26	5	30	30	0	ELOF1,3_prime_UTR_variant,,ENST00000587806,;ELOF1,3_prime_UTR_variant,,ENST00000252445,;ELOF1,intron_variant,,ENST00000586683,;ELOF1,downstream_gene_variant,,ENST00000591912,;CNN1,downstream_gene_variant,,ENST00000587087,;CNN1,downstream_gene_variant,,ENST00000544952,;ELOF1,downstream_gene_variant,,ENST00000586120,;CNN1,downstream_gene_variant,,ENST00000252456,;CNN1,downstream_gene_variant,,ENST00000592923,;CNN1,downstream_gene_variant,,ENST00000586577,;ELOF1,downstream_gene_variant,,ENST00000590700,;ELOF1,downstream_gene_variant,,ENST00000591674,;CNN1,downstream_gene_variant,,ENST00000592338,;CNN1,downstream_gene_variant,,ENST00000588935,;ELOF1,downstream_gene_variant,,ENST00000589171,;CNN1,downstream_gene_variant,,ENST00000535659,;ELOF1,downstream_gene_variant,,ENST00000593077,;	C	ENSG00000130165	ENST00000252445	Transcript	3_prime_UTR_variant	945	.	.	.	.	.	.	.	-1	ELOF1	HGNC	28691	protein_coding	YES	CCDS12264.1	ENSP00000252445	ELOF1_HUMAN	.	UPI0000003E48	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTACAAAAGC	.	2	ESCA
ZNF441	0	.	GRCh37	19	11891849	11891849	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210T>G	p.Tyr404Asp	p.Y404D	ENST00000357901	4/4	64	48	15	50	50	0	ZNF441,missense_variant,p.Tyr404Asp,ENST00000357901,;ZNF441,missense_variant,p.Tyr337Asp,ENST00000454339,;ZNF441,3_prime_UTR_variant,,ENST00000409902,;ZNF441,downstream_gene_variant,,ENST00000462251,;	G	ENSG00000197044	ENST00000357901	Transcript	missense_variant	1312	1210	404	Y/D	Tat/Gat	.	.	.	1	ZNF441	HGNC	20875	protein_coding	YES	CCDS12266.2	ENSP00000350576	ZN441_HUMAN	J3KQM6_HUMAN	UPI000059D677	.	tolerated(0.09)	benign(0.101)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF22,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCTATTAC	.	5	ESCA
ZNF563	0	.	GRCh37	19	12444333	12444333	+	5'UTR	SNP	G	G	A	rs764385861	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-37C>T	.	.	ENST00000293725	1/4	166	124	42	134	134	0	ZNF563,5_prime_UTR_variant,,ENST00000293725,;ZNF563,5_prime_UTR_variant,,ENST00000595977,;ZNF563,upstream_gene_variant,,ENST00000601858,;ZNF563,upstream_gene_variant,,ENST00000594577,;	A	ENSG00000188868	ENST00000293725	Transcript	5_prime_UTR_variant	170	.	.	.	.	rs764385861	.	.	-1	ZNF563	HGNC	30498	protein_coding	YES	CCDS12270.1	ENSP00000293725	ZN563_HUMAN	M0R1Q6_HUMAN	UPI0000072E62	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTGCCTCC	.	5	ESCA
CTD-2521M24.10	0	.	GRCh37	19	17556067	17556067	+	Missense_Mutation	SNP	C	C	T	rs558870960	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302G>A	p.Arg101His	p.R101H	ENST00000594663	3/4	59	48	10	54	54	0	CTD-2521M24.10,missense_variant,p.Arg101His,ENST00000594663,;TMEM221,missense_variant,p.Arg116His,ENST00000341130,;TMEM221,non_coding_transcript_exon_variant,,ENST00000593461,;	T	ENSG00000269035	ENST00000594663	Transcript	missense_variant	516	302	101	R/H	cGc/cAc	rs558870960	.	.	-1	CTD-2521M24.10	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000472415	.	M0R296_HUMAN	UPI0002A47210	.	deleterious_low_confidence(0.04)	probably_damaging(0.994)	3/4	.	Pfam_domain:PF15038	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGCGGCAG	byFrequency|by1000G	5	ESCA
KCTD15	0	.	GRCh37	19	34304841	34304841	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*988C>T	.	.	ENST00000430256	6/6	64	44	20	28	28	0	KCTD15,3_prime_UTR_variant,,ENST00000284006,;KCTD15,3_prime_UTR_variant,,ENST00000430256,;KCTD15,downstream_gene_variant,,ENST00000588881,;KCTD15,downstream_gene_variant,,ENST00000589786,;KCTD15,downstream_gene_variant,,ENST00000590385,;KCTD15,intron_variant,,ENST00000592363,;	T	ENSG00000153885	ENST00000430256	Transcript	3_prime_UTR_variant	2248	.	.	.	.	.	.	.	1	KCTD15	HGNC	23297	protein_coding	YES	CCDS46039.1	ENSP00000394390	KCD15_HUMAN	K7EQS3_HUMAN,K7EPF0_HUMAN,K7EN63_HUMAN,K7EM48_HUMAN,K7EIF1_HUMAN	UPI000004D340	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGCGCTCT	.	5	ESCA
LSM14A	0	.	GRCh37	19	34719180	34719180	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*887G>A	.	.	ENST00000544216	10/10	73	49	23	44	44	0	LSM14A,3_prime_UTR_variant,,ENST00000544216,;LSM14A,3_prime_UTR_variant,,ENST00000433627,;LSM14A,downstream_gene_variant,,ENST00000586157,;LSM14A,downstream_gene_variant,,ENST00000540746,;LSM14A,non_coding_transcript_exon_variant,,ENST00000588582,;LSM14A,downstream_gene_variant,,ENST00000590416,;	A	ENSG00000257103	ENST00000544216	Transcript	3_prime_UTR_variant	2356	.	.	.	.	.	.	.	1	LSM14A	HGNC	24489	protein_coding	YES	CCDS12435.1	ENSP00000446271	LS14A_HUMAN	.	UPI000006E20E	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAAGAACTT	.	5	ESCA
NKPD1	0	.	GRCh37	19	45656064	45656064	+	Missense_Mutation	SNP	G	G	A	rs373185063	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1631C>T	p.Ala544Val	p.A544V	ENST00000317951	4/4	128	52	76	64	64	0	NKPD1,missense_variant,p.Ala322Val,ENST00000589776,;NKPD1,missense_variant,p.Ala544Val,ENST00000317951,;NKPD1,missense_variant,p.Ala322Val,ENST00000438936,;NKPD1,missense_variant,p.Ala322Val,ENST00000429338,;MARK4,intron_variant,,ENST00000587566,;AC005757.7,upstream_gene_variant,,ENST00000589594,;PPP1R37,downstream_gene_variant,,ENST00000422370,;	A	ENSG00000179846	ENST00000317951	Transcript	missense_variant	1631	1631	544	A/V	gCg/gTg	rs373185063	.	.	-1	NKPD1	HGNC	24739	protein_coding	YES	.	ENSP00000321976	.	J3KNK3_HUMAN	UPI000059D74A	.	tolerated(0.58)	possibly_damaging(0.763)	4/4	.	hmmpanther:PTHR22674,hmmpanther:PTHR22674:SF4,Pfam_domain:PF07693	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACCGCATCG	.	5	ESCA
GPR32	0	.	GRCh37	19	51274591	51274591	+	Missense_Mutation	SNP	G	G	A	rs756541448	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734G>A	p.Arg245Gln	p.R245Q	ENST00000270590	1/1	107	81	26	102	102	0	GPR32,missense_variant,p.Arg245Gln,ENST00000270590,;CTD-2568A17.1,downstream_gene_variant,,ENST00000563228,;	A	ENSG00000142511	ENST00000270590	Transcript	missense_variant	871	734	245	R/Q	cGg/cAg	rs756541448,COSM338223	.	.	1	GPR32	HGNC	4487	protein_coding	YES	CCDS12801.1	ENSP00000270590	GPR32_HUMAN	H9NIL6_HUMAN	UPI000005045C	.	tolerated(0.47)	benign(0.105)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF27,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00526	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGCGGGAGG	.	5	ESCA
TIMM44	0	.	GRCh37	19	7999973	7999973	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370G>T	p.Glu124Ter	p.E124*	ENST00000270538	4/13	98	77	20	113	112	1	TIMM44,stop_gained,p.Glu124Ter,ENST00000270538,;TIMM44,stop_gained,p.Glu92Ter,ENST00000597926,;TIMM44,upstream_gene_variant,,ENST00000595565,;TIMM44,upstream_gene_variant,,ENST00000598968,;TIMM44,stop_gained,p.Glu119Ter,ENST00000595831,;TIMM44,3_prime_UTR_variant,,ENST00000595876,;TIMM44,non_coding_transcript_exon_variant,,ENST00000600748,;TIMM44,upstream_gene_variant,,ENST00000598481,;TIMM44,downstream_gene_variant,,ENST00000600000,;TIMM44,upstream_gene_variant,,ENST00000598675,;TIMM44,upstream_gene_variant,,ENST00000599650,;	A	ENSG00000104980	ENST00000270538	Transcript	stop_gained	639	370	124	E/*	Gag/Tag	.	.	.	-1	TIMM44	HGNC	17316	protein_coding	YES	CCDS12192.1	ENSP00000270538	TIM44_HUMAN	Q6AI07_HUMAN	UPI000012D5E2	.	.	.	4/13	.	hmmpanther:PTHR10721,TIGRFAM_domain:TIGR00984,PIRSF_domain:PIRSF037871	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCCCCAA	.	5	ESCA
SLC16A4	0	.	GRCh37	1	110921577	110921577	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.928C>G	p.Leu310Val	p.L310V	ENST00000369779	6/9	36	31	5	28	28	0	SLC16A4,missense_variant,p.Leu310Val,ENST00000369779,;SLC16A4,missense_variant,p.Leu248Val,ENST00000541986,;SLC16A4,missense_variant,p.Leu77Val,ENST00000467986,;SLC16A4,missense_variant,p.Leu262Val,ENST00000472422,;SLC16A4,missense_variant,p.Leu200Val,ENST00000437429,;SLC16A4,intron_variant,,ENST00000369781,;LAMTOR5-AS1,upstream_gene_variant,,ENST00000590413,;SLC16A4,non_coding_transcript_exon_variant,,ENST00000497687,;SLC16A4,3_prime_UTR_variant,,ENST00000492412,;SLC16A4,3_prime_UTR_variant,,ENST00000528649,;SLC16A4,intron_variant,,ENST00000461647,;	C	ENSG00000168679	ENST00000369779	Transcript	missense_variant	1178	928	310	L/V	Ctc/Gtc	.	.	.	-1	SLC16A4	HGNC	10925	protein_coding	YES	CCDS823.1	ENSP00000358794	MOT5_HUMAN	.	UPI000004EE9B	.	deleterious(0)	possibly_damaging(0.507)	6/9	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF14,Gene3D:1.20.1250.20,Pfam_domain:PF07690,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S307S|c.921T>C|4	RADIA|MUTECT|MUSE|VARSCANS	ACTGAGGAGAA	.	4	ESCA
TCHH	0	.	GRCh37	1	152081839	152081839	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3854G>A	p.Arg1285His	p.R1285H	ENST00000368804	2/2	49	37	11	36	36	0	TCHH,missense_variant,p.Arg1285His,ENST00000368804,;	T	ENSG00000159450	ENST00000368804	Transcript	missense_variant	3854	3854	1285	R/H	cGc/cAc	.	.	.	-1	TCHH	HGNC	11791	protein_coding	YES	CCDS41396.1	ENSP00000357794	TRHY_HUMAN	Q5D861_HUMAN,A2RRS3_HUMAN	UPI0000458A5E	.	.	unknown(0)	2/2	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGCGCCTC	.	5	ESCA
MSTO1	0	.	GRCh37	1	155583355	155583355	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1386G>C	p.Met462Ile	p.M462I	ENST00000245564	12/14	70	58	12	64	64	0	MSTO1,missense_variant,p.Met39Ile,ENST00000462250,;MSTO1,missense_variant,p.Met427Ile,ENST00000368341,;MSTO1,missense_variant,p.Met462Ile,ENST00000245564,;MSTO1,intron_variant,,ENST00000538143,;MSTO1,intron_variant,,ENST00000452804,;RP11-29H23.4,upstream_gene_variant,,ENST00000456382,;MSTO1,splice_region_variant,,ENST00000475253,;MSTO1,splice_region_variant,,ENST00000483734,;MSTO1,splice_region_variant,,ENST00000466815,;MSTO1,downstream_gene_variant,,ENST00000465137,;MSTO1,downstream_gene_variant,,ENST00000483832,;MSTO1,downstream_gene_variant,,ENST00000488901,;MSTO1,downstream_gene_variant,,ENST00000491308,;MSTO1,downstream_gene_variant,,ENST00000490642,;MSTO1,downstream_gene_variant,,ENST00000473327,;MSTO1,splice_region_variant,,ENST00000490743,;MSTO1,splice_region_variant,,ENST00000494995,;MSTO1,downstream_gene_variant,,ENST00000482284,;MSTO1,downstream_gene_variant,,ENST00000478756,;MSTO1,downstream_gene_variant,,ENST00000471209,;MSTO1,downstream_gene_variant,,ENST00000460199,;MSTO2P,intron_variant,,ENST00000538914,;RP11-29H23.5,downstream_gene_variant,,ENST00000500626,;	C	ENSG00000125459	ENST00000245564	Transcript	missense_variant	1410	1386	462	M/I	atG/atC	.	.	.	1	MSTO1	HGNC	29678	protein_coding	YES	CCDS1114.1	ENSP00000245564	MSTO1_HUMAN	D3DV95_HUMAN	UPI000006F52F	.	tolerated(0.45)	benign(0)	12/14	.	hmmpanther:PTHR13391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GTCATGAGGTC	.	2	ESCA
KIRREL	0	.	GRCh37	1	158064444	158064444	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1808A>G	p.Asn603Ser	p.N603S	ENST00000359209	15/15	71	56	14	69	69	0	KIRREL,missense_variant,p.Asn439Ser,ENST00000360089,;KIRREL,missense_variant,p.Asn619Ser,ENST00000368173,;KIRREL,missense_variant,p.Asn417Ser,ENST00000368172,;KIRREL,missense_variant,p.Asn503Ser,ENST00000416935,;KIRREL,missense_variant,p.Asn603Ser,ENST00000359209,;KIRREL,missense_variant,p.Asn500Ser,ENST00000392272,;	G	ENSG00000183853	ENST00000359209	Transcript	missense_variant	1875	1808	603	N/S	aAt/aGt	.	.	.	1	KIRREL	HGNC	15734	protein_coding	YES	CCDS1172.2	ENSP00000352138	KIRR1_HUMAN	.	UPI0000443FBD	.	deleterious(0)	benign(0.26)	15/15	.	hmmpanther:PTHR11640:SF14,hmmpanther:PTHR11640	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCAATGGCT	.	5	ESCA
RP5-1182A14.5	0	.	GRCh37	1	16946163	16946163	+	3'Flank	SNP	C	C	G	rs689371	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000607700	.	20	9	11	20	19	1	CROCCP2,non_coding_transcript_exon_variant,,ENST00000412962,;CROCCP2,intron_variant,,ENST00000540383,;RP5-1182A14.5,downstream_gene_variant,,ENST00000607700,;	G	ENSG00000271732	ENST00000607700	Transcript	downstream_gene_variant	.	.	.	.	.	rs689371	.	1939	1	RP5-1182A14.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GAGCACAGCAA	byCluster|by2Hit2Allele	2	ESCA
TOR1AIP2	0	.	GRCh37	1	179815756	179815756	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.863C>T	p.Ser288Phe	p.S288F	ENST00000367612	6/6	85	69	16	68	68	0	TOR1AIP2,missense_variant,p.Ser288Phe,ENST00000609928,;TOR1AIP2,missense_variant,p.Ser288Phe,ENST00000367612,;	A	ENSG00000169905	ENST00000367612	Transcript	missense_variant	1251	863	288	S/F	tCc/tTc	.	.	.	-1	TOR1AIP2	HGNC	24055	protein_coding	YES	CCDS1334.1	ENSP00000356584	TOIP2_HUMAN	.	UPI00000711A4	.	deleterious(0)	probably_damaging(0.998)	6/6	.	Pfam_domain:PF05609,hmmpanther:PTHR18843:SF2,hmmpanther:PTHR18843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTGGAAGCA	.	5	ESCA
CENPF	0	.	GRCh37	1	214794199	214794199	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775T>G	p.Leu259Val	p.L259V	ENST00000366955	6/20	36	26	9	24	24	0	CENPF,missense_variant,p.Leu259Val,ENST00000366955,;	G	ENSG00000117724	ENST00000366955	Transcript	missense_variant	943	775	259	L/V	Ttg/Gtg	.	.	.	1	CENPF	HGNC	1857	protein_coding	YES	CCDS31023.1	ENSP00000355922	CENPF_HUMAN	.	UPI00001AE985	.	.	benign(0.106)	6/20	.	Pfam_domain:PF10481,hmmpanther:PTHR18874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACTTTGCAA	.	5	ESCA
ESRRG	0	.	GRCh37	1	216678104	216678104	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2177G>C	.	.	ENST00000366937	8/8	58	49	9	52	52	0	ESRRG,3_prime_UTR_variant,,ENST00000391890,;ESRRG,3_prime_UTR_variant,,ENST00000366938,;ESRRG,3_prime_UTR_variant,,ENST00000366937,;ESRRG,3_prime_UTR_variant,,ENST00000360012,;ESRRG,3_prime_UTR_variant,,ENST00000361395,;ESRRG,3_prime_UTR_variant,,ENST00000408911,;ESRRG,3_prime_UTR_variant,,ENST00000366940,;ESRRG,3_prime_UTR_variant,,ENST00000361525,;ESRRG,3_prime_UTR_variant,,ENST00000359162,;ESRRG,3_prime_UTR_variant,,ENST00000493603,;ESRRG,downstream_gene_variant,,ENST00000493748,;ESRRG,downstream_gene_variant,,ENST00000487276,;ESRRG,downstream_gene_variant,,ENST00000463665,;	G	ENSG00000196482	ENST00000366937	Transcript	3_prime_UTR_variant	3857	.	.	.	.	.	.	.	-1	ESRRG	HGNC	3474	protein_coding	YES	CCDS58061.1	ENSP00000355904	ERR3_HUMAN	C9JNX5_HUMAN,C9J5W9_HUMAN,C9J0E3_HUMAN	UPI0000D4BFAB	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTATTCTATAA	.	3	ESCA
RAB3GAP2	0	.	GRCh37	1	220440106	220440106	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115+5459A>G	.	.	ENST00000358951	.	108	81	26	83	83	0	RAB3GAP2,intron_variant,,ENST00000358951,;RAB3GAP2,non_coding_transcript_exon_variant,,ENST00000462353,;RAB3GAP2,intron_variant,,ENST00000478976,;RAB3GAP2,intron_variant,,ENST00000475769,;RAB3GAP2,intron_variant,,ENST00000474178,;RAB3GAP2,intron_variant,,ENST00000237724,;AURKAPS1,non_coding_transcript_exon_variant,,ENST00000451805,;	C	ENSG00000118873	ENST00000358951	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RAB3GAP2	HGNC	17168	protein_coding	YES	CCDS31028.1	ENSP00000351832	RBGPR_HUMAN	.	UPI0000072269	.	.	.	.	1/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCTGTGAT	.	5	ESCA
MARK1	0	.	GRCh37	1	220835772	220835772	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*264A>G	.	.	ENST00000366917	18/18	108	89	19	75	75	0	MARK1,3_prime_UTR_variant,,ENST00000366918,;MARK1,3_prime_UTR_variant,,ENST00000402574,;MARK1,3_prime_UTR_variant,,ENST00000366917,;RP11-322F10.2,downstream_gene_variant,,ENST00000446040,;	G	ENSG00000116141	ENST00000366917	Transcript	3_prime_UTR_variant	2918	.	.	.	.	.	.	.	1	MARK1	HGNC	6896	protein_coding	YES	CCDS31029.2	ENSP00000355884	MARK1_HUMAN	B4DIB3_HUMAN	UPI0000048D8B	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTATAATA	.	5	ESCA
WNT9A	0	.	GRCh37	1	228111888	228111888	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.566A>G	p.Lys189Arg	p.K189R	ENST00000272164	3/4	99	75	24	73	73	0	WNT9A,missense_variant,p.Lys189Arg,ENST00000272164,;	C	ENSG00000143816	ENST00000272164	Transcript	missense_variant	577	566	189	K/R	aAg/aGg	.	.	.	-1	WNT9A	HGNC	12778	protein_coding	YES	CCDS31045.1	ENSP00000272164	WNT9A_HUMAN	D9ZGG3_HUMAN	UPI000005104B	.	tolerated(0.34)	benign(0.119)	3/4	.	hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF75,Pfam_domain:PF00110,SMART_domains:SM00097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCCTTGCTT	.	5	ESCA
ACTA1	0	.	GRCh37	1	229567224	229567224	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*22C>T	.	.	ENST00000366684	7/7	54	44	10	56	56	0	ACTA1,3_prime_UTR_variant,,ENST00000366683,;ACTA1,3_prime_UTR_variant,,ENST00000366684,;	A	ENSG00000143632	ENST00000366684	Transcript	3_prime_UTR_variant	1259	.	.	.	.	.	.	.	-1	ACTA1	HGNC	129	protein_coding	YES	CCDS1578.1	ENSP00000355645	ACTS_HUMAN	.	UPI0000000860	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTCGCGTGC	.	5	ESCA
PCSK9	0	.	GRCh37	1	55512211	55512211	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415C>T	p.His139Tyr	p.H139Y	ENST00000302118	3/12	61	27	34	53	53	0	PCSK9,missense_variant,p.His139Tyr,ENST00000452118,;PCSK9,missense_variant,p.His139Tyr,ENST00000302118,;PCSK9,intron_variant,,ENST00000543384,;PCSK9,upstream_gene_variant,,ENST00000490692,;	T	ENSG00000169174	ENST00000302118	Transcript	missense_variant	705	415	139	H/Y	Cat/Tat	.	.	.	1	PCSK9	HGNC	20001	protein_coding	YES	CCDS603.1	ENSP00000303208	PCSK9_HUMAN	.	UPI00001615E1	.	tolerated(0.05)	benign(0.114)	3/12	.	hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF333,Gene3D:3.30.70.80,Pfam_domain:PF05922,Superfamily_domains:SSF54897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCCCATGTC	.	5	ESCA
SNAP25	0	.	GRCh37	20	10287391	10287391	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*546A>G	.	.	ENST00000254976	8/8	72	47	25	49	49	0	SNAP25,3_prime_UTR_variant,,ENST00000304886,;SNAP25,3_prime_UTR_variant,,ENST00000254976,;SNAP25-AS1,intron_variant,,ENST00000453544,;SNAP25-AS1,intron_variant,,ENST00000421143,;SNAP25,non_coding_transcript_exon_variant,,ENST00000495883,;	G	ENSG00000132639	ENST00000254976	Transcript	3_prime_UTR_variant	1378	.	.	.	.	.	.	.	1	SNAP25	HGNC	11132	protein_coding	YES	CCDS13110.1	ENSP00000254976	SNP25_HUMAN	.	UPI0000001103	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATAGATTT	.	5	ESCA
ASXL1	0	.	GRCh37	20	31022250	31022250	+	Missense_Mutation	SNP	A	A	T	rs368930454	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735A>T	p.Ile579Phe	p.I579F	ENST00000375687	13/13	72	62	10	41	41	0	ASXL1,missense_variant,p.Ile579Phe,ENST00000375687,;ASXL1,missense_variant,p.Ile574Phe,ENST00000306058,;ASXL1,downstream_gene_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000470145,;ASXL1,downstream_gene_variant,,ENST00000555564,;	T	ENSG00000171456	ENST00000375687	Transcript	missense_variant	2159	1735	579	I/F	Atc/Ttc	rs368930454	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	deleterious(0)	probably_damaging(0.996)	13/13	.	hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACGTATCAAA	byFrequency|byCluster	4	ESCA
TRIB3	0	.	GRCh37	20	371973	371973	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334G>A	p.Ala112Thr	p.A112T	ENST00000217233	3/4	77	49	27	42	42	0	TRIB3,missense_variant,p.Ala139Thr,ENST00000422053,;TRIB3,missense_variant,p.Ala112Thr,ENST00000449710,;TRIB3,missense_variant,p.Ala112Thr,ENST00000217233,;TRIB3,downstream_gene_variant,,ENST00000485293,;	A	ENSG00000101255	ENST00000217233	Transcript	missense_variant	887	334	112	A/T	Gcg/Acg	.	.	.	1	TRIB3	HGNC	16228	protein_coding	YES	CCDS12997.1	ENSP00000217233	TRIB3_HUMAN	B0QYQ2_HUMAN	UPI000003C950	.	tolerated(0.43)	benign(0.026)	3/4	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22961,hmmpanther:PTHR22961:SF12,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTATGCGCGG	.	5	ESCA
EP300	0	.	GRCh37	22	41565533	41565533	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4199G>T	p.Ser1400Ile	p.S1400I	ENST00000263253	26/31	70	46	24	23	23	0	EP300,missense_variant,p.Ser1400Ile,ENST00000263253,;RNU6-375P,downstream_gene_variant,,ENST00000517050,;RP1-85F18.6,non_coding_transcript_exon_variant,,ENST00000415054,;	T	ENSG00000100393	ENST00000263253	Transcript	missense_variant	5418	4199	1400	S/I	aGt/aTt	.	.	.	1	EP300	HGNC	3373	protein_coding	YES	CCDS14010.1	ENSP00000263253	EP300_HUMAN	B5A250_HUMAN	UPI00001AE876	.	.	probably_damaging(0.999)	26/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF4,Pfam_domain:PF08214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D1399N|c.4195G>A|8,BUFFER|p.D1399Y|c.4195G>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGATAGTGTTC	.	5	ESCA
RANBP2	0	.	GRCh37	2	109381161	109381161	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4166C>T	p.Pro1389Leu	p.P1389L	ENST00000283195	20/29	34	31	3	27	27	0	RANBP2,missense_variant,p.Pro1389Leu,ENST00000283195,;	T	ENSG00000153201	ENST00000283195	Transcript	missense_variant	4292	4166	1389	P/L	cCa/cTa	.	.	.	1	RANBP2	HGNC	9848	protein_coding	YES	CCDS2079.1	ENSP00000283195	RBP2_HUMAN	I1Z9D1_HUMAN	UPI0000207FB9	.	deleterious(0.03)	benign(0.135)	20/29	.	hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCACCATTAG	.	2	ESCA
SLC35F5	0	.	GRCh37	2	114514063	114514063	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-77C>T	.	.	ENST00000245680	1/16	26	11	15	25	25	0	SLC35F5,5_prime_UTR_variant,,ENST00000409342,;SLC35F5,5_prime_UTR_variant,,ENST00000245680,;SLC35F5,5_prime_UTR_variant,,ENST00000409106,;SLC35F5,non_coding_transcript_exon_variant,,ENST00000498768,;	A	ENSG00000115084	ENST00000245680	Transcript	5_prime_UTR_variant	338	.	.	.	.	.	.	.	-1	SLC35F5	HGNC	23617	protein_coding	YES	CCDS2119.1	ENSP00000245680	S35F5_HUMAN	.	UPI000004C648	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCTGACATC	.	5	ESCA
FIGN	0	.	GRCh37	2	164466292	164466292	+	Missense_Mutation	SNP	G	G	A	rs747101469	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2050C>T	p.Arg684Cys	p.R684C	ENST00000333129	3/3	82	52	29	50	50	0	FIGN,missense_variant,p.Arg684Cys,ENST00000333129,;FIGN,intron_variant,,ENST00000409634,;FIGN,downstream_gene_variant,,ENST00000482917,;	A	ENSG00000182263	ENST00000333129	Transcript	missense_variant	2365	2050	684	R/C	Cgc/Tgc	rs747101469,COSM1207142	.	.	-1	FIGN	HGNC	13285	protein_coding	YES	CCDS2221.2	ENSP00000333836	FIGN_HUMAN	.	UPI000022BD13	.	deleterious(0)	probably_damaging(0.965)	3/3	.	Superfamily_domains:SSF52540,Gene3D:1.10.8.60,hmmpanther:PTHR23074:SF14,hmmpanther:PTHR23074	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCGCTGGA	.	5	ESCA
XIRP2	0	.	GRCh37	2	168115690	168115690	+	3'UTR	SNP	G	G	C	rs759841457	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1363G>C	.	.	ENST00000409195	11/11	100	83	17	78	78	0	XIRP2,missense_variant,p.Lys656Asn,ENST00000409605,;XIRP2,missense_variant,p.Lys911Asn,ENST00000420519,;XIRP2,missense_variant,p.Lys878Asn,ENST00000409756,;XIRP2,missense_variant,p.Lys878Asn,ENST00000409043,;XIRP2,missense_variant,p.Lys911Asn,ENST00000409728,;XIRP2,3_prime_UTR_variant,,ENST00000409273,;XIRP2,3_prime_UTR_variant,,ENST00000409195,;XIRP2,3_prime_UTR_variant,,ENST00000295237,;	C	ENSG00000163092	ENST00000409195	Transcript	3_prime_UTR_variant	12102	.	.	.	.	rs759841457	.	.	1	XIRP2	HGNC	14303	protein_coding	YES	CCDS42769.1	ENSP00000386840	.	J3KNB1_HUMAN	UPI0000E9BBED	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAAGGATGT	byFrequency	5	ESCA
DNAH7	0	.	GRCh37	2	196729159	196729159	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7220C>G	p.Ser2407Cys	p.S2407C	ENST00000312428	41/65	56	42	14	36	36	0	DNAH7,missense_variant,p.Ser2407Cys,ENST00000312428,;	C	ENSG00000118997	ENST00000312428	Transcript	missense_variant	7321	7220	2407	S/C	tCt/tGt	COSM3425895	.	.	-1	DNAH7	HGNC	18661	protein_coding	YES	CCDS42794.1	ENSP00000311273	DYH7_HUMAN	C9JUY3_HUMAN	UPI0000141B95	.	deleterious(0)	probably_damaging(0.918)	41/65	.	hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Pfam_domain:PF12780,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGACTCT	.	5	ESCA
AOX1	0	.	GRCh37	2	201535448	201535448	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*46G>A	.	.	ENST00000374700	35/35	44	37	7	25	25	0	AOX1,3_prime_UTR_variant,,ENST00000374700,;AOX1,intron_variant,,ENST00000439380,;AOX1,downstream_gene_variant,,ENST00000260930,;AOX1,non_coding_transcript_exon_variant,,ENST00000485106,;AOX1,non_coding_transcript_exon_variant,,ENST00000465297,;	A	ENSG00000138356	ENST00000374700	Transcript	3_prime_UTR_variant	4304	.	.	.	.	.	.	.	1	AOX1	HGNC	553	protein_coding	YES	CCDS33360.1	ENSP00000363832	ADO_HUMAN	C9J244_HUMAN,B4DNI5_HUMAN	UPI0000071863	.	.	.	35/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATGGCAAT	.	2	ESCA
PIKFYVE	0	.	GRCh37	2	209198070	209198070	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3995C>T	p.Ser1332Phe	p.S1332F	ENST00000264380	24/42	80	66	13	58	58	0	PIKFYVE,missense_variant,p.Ser1276Phe,ENST00000452564,;PIKFYVE,missense_variant,p.Ser1332Phe,ENST00000264380,;PIKFYVE,upstream_gene_variant,,ENST00000474721,;	T	ENSG00000115020	ENST00000264380	Transcript	missense_variant	4153	3995	1332	S/F	tCc/tTc	.	.	.	1	PIKFYVE	HGNC	23785	protein_coding	YES	CCDS2382.1	ENSP00000264380	FYV1_HUMAN	.	UPI0000366FD6	.	deleterious(0)	probably_damaging(0.989)	24/42	.	hmmpanther:PTHR11353:SF57,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGTCCTGGT	.	5	ESCA
PID1	0	.	GRCh37	2	229890645	229890645	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450G>A	p.%3D	p.G150G	ENST00000392054	4/4	141	121	19	100	100	0	PID1,synonymous_variant,p.%3D,ENST00000409462,;PID1,synonymous_variant,p.%3D,ENST00000354069,;PID1,synonymous_variant,p.%3D,ENST00000392055,;PID1,synonymous_variant,p.%3D,ENST00000392054,;PID1,intron_variant,,ENST00000482518,;PID1,downstream_gene_variant,,ENST00000534952,;	T	ENSG00000153823	ENST00000392054	Transcript	synonymous_variant	790	450	150	G	ggG/ggA	.	.	.	-1	PID1	HGNC	26084	protein_coding	YES	CCDS2471.1	ENSP00000375907	PCLI1_HUMAN	Q4ZG81_HUMAN	UPI00001C0AF7	.	.	.	4/4	.	hmmpanther:PTHR16265,hmmpanther:PTHR16265:SF0,Pfam_domain:PF14719,SMART_domains:SM00462,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTCCCCTTT	.	4	ESCA
GAL3ST2	0	.	GRCh37	2	242742979	242742979	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595T>A	p.Phe199Ile	p.F199I	ENST00000192314	4/4	58	51	7	43	43	0	GAL3ST2,missense_variant,p.Phe199Ile,ENST00000192314,;AC114730.5,upstream_gene_variant,,ENST00000437438,;	A	ENSG00000154252	ENST00000192314	Transcript	missense_variant	726	595	199	F/I	Ttc/Atc	.	.	.	1	GAL3ST2	HGNC	24869	protein_coding	YES	CCDS33427.1	ENSP00000192314	G3ST2_HUMAN	.	UPI000049DF44	.	deleterious(0.01)	probably_damaging(0.943)	4/4	.	hmmpanther:PTHR14647:SF58,hmmpanther:PTHR14647,Pfam_domain:PF06990	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGGCTTCGAC	.	4	ESCA
CAD	0	.	GRCh37	2	27445849	27445849	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753C>G	p.Ile251Met	p.I251M	ENST00000264705	6/44	92	71	21	83	83	0	CAD,missense_variant,p.Ile251Met,ENST00000264705,;CAD,missense_variant,p.Ile251Met,ENST00000403525,;CAD,upstream_gene_variant,,ENST00000464159,;CAD,upstream_gene_variant,,ENST00000491891,;	G	ENSG00000084774	ENST00000264705	Transcript	missense_variant	915	753	251	I/M	atC/atG	.	.	.	1	CAD	HGNC	1424	protein_coding	YES	CCDS1742.1	ENSP00000264705	PYR1_HUMAN	Q53SZ4_HUMAN,Q53SY7_HUMAN,G1UI39_HUMAN	UPI000013D558	.	deleterious(0)	probably_damaging(0.997)	6/44	.	PROSITE_profiles:PS51273,HAMAP:MF_01209,hmmpanther:PTHR11405:SF5,hmmpanther:PTHR11405,Pfam_domain:PF00117,Gene3D:3.40.50.880,TIGRFAM_domain:TIGR01368,Superfamily_domains:SSF52317,Prints_domain:PR00099	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGATCTGCCT	.	5	ESCA
THUMPD2	0	.	GRCh37	2	39996163	39996163	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673-522A>T	.	.	ENST00000505747	.	61	53	7	36	35	0	THUMPD2,missense_variant,p.Glu218Val,ENST00000454352,;THUMPD2,intron_variant,,ENST00000505747,;THUMPD2,intron_variant,,ENST00000260619,;THUMPD2,non_coding_transcript_exon_variant,,ENST00000403537,;THUMPD2,downstream_gene_variant,,ENST00000531687,;THUMPD2,missense_variant,p.Glu219Val,ENST00000510781,;THUMPD2,non_coding_transcript_exon_variant,,ENST00000460072,;THUMPD2,intron_variant,,ENST00000530522,;THUMPD2,intron_variant,,ENST00000378727,;THUMPD2,upstream_gene_variant,,ENST00000527689,;	A	ENSG00000138050	ENST00000505747	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	THUMPD2	HGNC	14890	protein_coding	YES	CCDS1805.2	ENSP00000423933	THUM2_HUMAN	D6W593_HUMAN	UPI0000D6DA73	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCGCTCTTCT	.	4	ESCA
LRPPRC	0	.	GRCh37	2	44128499	44128499	+	Missense_Mutation	SNP	T	T	C	rs564191181	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3529A>G	p.Met1177Val	p.M1177V	ENST00000260665	32/38	83	67	16	58	58	0	LRPPRC,missense_variant,p.Met1177Val,ENST00000260665,;LRPPRC,upstream_gene_variant,,ENST00000419884,;LRPPRC,non_coding_transcript_exon_variant,,ENST00000463456,;LRPPRC,upstream_gene_variant,,ENST00000472420,;LRPPRC,upstream_gene_variant,,ENST00000483489,;	C	ENSG00000138095	ENST00000260665	Transcript	missense_variant	3587	3529	1177	M/V	Atg/Gtg	rs564191181	.	.	-1	LRPPRC	HGNC	15714	protein_coding	YES	CCDS33189.1	ENSP00000260665	LPPRC_HUMAN	E5KNY5_HUMAN	UPI000019B4D2	.	tolerated(0.06)	possibly_damaging(0.77)	32/38	.	Gene3D:1.25.40.10	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCATTTTTG	by1000G	5	ESCA
EML6	0	.	GRCh37	2	55091009	55091009	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1915A>G	p.Ile639Val	p.I639V	ENST00000356458	12/41	67	58	8	36	36	0	EML6,missense_variant,p.Ile639Val,ENST00000356458,;EML6,non_coding_transcript_exon_variant,,ENST00000493997,;	G	ENSG00000214595	ENST00000356458	Transcript	missense_variant	2435	1915	639	I/V	Atc/Gtc	.	.	.	1	EML6	HGNC	35412	protein_coding	YES	CCDS46286.1	ENSP00000348842	EMAL6_HUMAN	.	UPI00006C0432	.	tolerated(0.55)	benign(0.006)	12/41	.	hmmpanther:PTHR13720:SF8,hmmpanther:PTHR13720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAAATCAAT	.	5	ESCA
CCDC14	0	.	GRCh37	3	123675052	123675052	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304-90A>G	.	.	ENST00000433542	.	49	36	13	49	49	0	CCDC14,5_prime_UTR_variant,,ENST00000485727,;CCDC14,5_prime_UTR_variant,,ENST00000489746,;CCDC14,intron_variant,,ENST00000409697,;CCDC14,intron_variant,,ENST00000488653,;CCDC14,intron_variant,,ENST00000433542,;CCDC14,upstream_gene_variant,,ENST00000310351,;CCDC14,intron_variant,,ENST00000463996,;CCDC14,intron_variant,,ENST00000477268,;CCDC14,intron_variant,,ENST00000483247,;CCDC14,non_coding_transcript_exon_variant,,ENST00000495381,;CCDC14,intron_variant,,ENST00000409657,;CCDC14,intron_variant,,ENST00000478956,;CCDC14,intron_variant,,ENST00000435910,;CCDC14,intron_variant,,ENST00000438440,;CCDC14,intron_variant,,ENST00000417438,;	C	ENSG00000175455	ENST00000433542	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CCDC14	HGNC	25766	protein_coding	YES	CCDS3025.2	ENSP00000395706	CCD14_HUMAN	C9JWZ1_HUMAN	UPI00016632FB	.	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTATTTACA	.	5	ESCA
TMCC1	0	.	GRCh37	3	129373823	129373823	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1635C>G	p.%3D	p.A545A	ENST00000393238	5/6	59	43	16	37	37	0	TMCC1,synonymous_variant,p.%3D,ENST00000329333,;TMCC1,synonymous_variant,p.%3D,ENST00000426664,;TMCC1,synonymous_variant,p.%3D,ENST00000432054,;TMCC1,synonymous_variant,p.%3D,ENST00000510323,;TMCC1,synonymous_variant,p.%3D,ENST00000393238,;	C	ENSG00000172765	ENST00000393238	Transcript	synonymous_variant	1976	1635	545	A	gcC/gcG	.	.	.	-1	TMCC1	HGNC	29116	protein_coding	YES	CCDS33855.1	ENSP00000376930	TMCC1_HUMAN	Q8N4H2_HUMAN,Q6N039_HUMAN,E9PC87_HUMAN,D6RBT7_HUMAN	UPI0000197B80	.	.	.	5/6	.	Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10267,hmmpanther:PTHR17613,hmmpanther:PTHR17613:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGGGCCCG	.	5	ESCA
TF	0	.	GRCh37	3	133478024	133478024	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1054G>A	p.Glu352Lys	p.E352K	ENST00000402696	9/17	42	36	6	23	23	0	TF,missense_variant,p.Glu352Lys,ENST00000402696,;TF,missense_variant,p.Glu225Lys,ENST00000264998,;TF,downstream_gene_variant,,ENST00000466911,;TF,downstream_gene_variant,,ENST00000482271,;TFP1,downstream_gene_variant,,ENST00000460564,;TF,downstream_gene_variant,,ENST00000475382,;TF,3_prime_UTR_variant,,ENST00000485977,;TF,downstream_gene_variant,,ENST00000493011,;TF,downstream_gene_variant,,ENST00000494430,;TF,downstream_gene_variant,,ENST00000414694,;TF,downstream_gene_variant,,ENST00000498622,;RP11-404G16.2,upstream_gene_variant,,ENST00000474389,;	A	ENSG00000091513	ENST00000402696	Transcript	missense_variant	1539	1054	352	E/K	Gaa/Aaa	.	.	.	1	TF	HGNC	11740	protein_coding	YES	CCDS3080.1	ENSP00000385834	TRFE_HUMAN	J3KN47_HUMAN,C9JVG0_HUMAN,C9JB55_HUMAN,B4DEX9_HUMAN	UPI000013D5A6	.	tolerated(0.42)	benign(0.054)	9/17	.	PIRSF_domain:PIRSF002549,SMART_domains:SM00094,PIRSF_domain:PIRSF500682,Gene3D:3.40.190.10,hmmpanther:PTHR11485,hmmpanther:PTHR11485:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCAGAAGCC	.	5	ESCA
SEC62	0	.	GRCh37	3	169711623	169711623	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*772A>C	.	.	ENST00000337002	8/8	48	40	7	19	19	0	SEC62,3_prime_UTR_variant,,ENST00000337002,;SEC62,downstream_gene_variant,,ENST00000480708,;SEC62,downstream_gene_variant,,ENST00000470355,;	C	ENSG00000008952	ENST00000337002	Transcript	3_prime_UTR_variant	2030	.	.	.	.	.	.	.	1	SEC62	HGNC	11846	protein_coding	YES	CCDS3210.1	ENSP00000337688	SEC62_HUMAN	D3DNQ1_HUMAN	UPI000007186C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTTATTATT	.	5	ESCA
PEX5L	0	.	GRCh37	3	179592166	179592166	+	Silent	SNP	G	G	A	rs139208096	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.675C>T	p.%3D	p.S225S	ENST00000467460	7/15	95	80	14	78	78	0	PEX5L,synonymous_variant,p.%3D,ENST00000491640,;PEX5L,synonymous_variant,p.%3D,ENST00000392649,;PEX5L,synonymous_variant,p.%3D,ENST00000472994,;PEX5L,synonymous_variant,p.%3D,ENST00000464614,;PEX5L,synonymous_variant,p.%3D,ENST00000263962,;PEX5L,synonymous_variant,p.%3D,ENST00000476138,;PEX5L,synonymous_variant,p.%3D,ENST00000485199,;PEX5L,synonymous_variant,p.%3D,ENST00000468741,;PEX5L,synonymous_variant,p.%3D,ENST00000467460,;PEX5L,synonymous_variant,p.%3D,ENST00000496721,;PEX5L,synonymous_variant,p.%3D,ENST00000465751,;PEX5L,downstream_gene_variant,,ENST00000463761,;PEX5L,downstream_gene_variant,,ENST00000469198,;PEX5L-AS1,upstream_gene_variant,,ENST00000466064,;PEX5L,non_coding_transcript_exon_variant,,ENST00000467440,;	A	ENSG00000114757	ENST00000467460	Transcript	synonymous_variant	1006	675	225	S	agC/agT	rs139208096	.	.	-1	PEX5L	HGNC	30024	protein_coding	YES	CCDS3236.1	ENSP00000419975	PEX5R_HUMAN	C9JZE2_HUMAN,C9IZ09_HUMAN	UPI0000049CE2	.	.	.	7/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10130:SF1,hmmpanther:PTHR10130	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCGCTTTT	byCluster	5	ESCA
ABCC5	0	.	GRCh37	3	183669325	183669325	+	Missense_Mutation	SNP	C	C	T	rs369345548	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2848G>A	p.Glu950Lys	p.E950K	ENST00000334444	20/30	47	38	8	38	38	0	ABCC5,missense_variant,p.Glu950Lys,ENST00000265586,;ABCC5,missense_variant,p.Glu950Lys,ENST00000334444,;ABCC5,3_prime_UTR_variant,,ENST00000437205,;	T	ENSG00000114770	ENST00000334444	Transcript	missense_variant	3089	2848	950	E/K	Gag/Aag	rs369345548,COSM3590591	.	.	-1	ABCC5	HGNC	56	protein_coding	YES	CCDS43176.1	ENSP00000333926	MRP5_HUMAN	C9JZL5_HUMAN	UPI000004A33C	.	tolerated(0.91)	benign(0.002)	20/30	.	PROSITE_profiles:PS50929,hmmpanther:PTHR24223:SF196,hmmpanther:PTHR24223,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTCGTCAT	byFrequency|byCluster	5	ESCA
TGFBR2	0	.	GRCh37	3	30715678	30715678	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1411G>A	p.Asp471Asn	p.D471N	ENST00000359013	6/8	116	94	21	121	121	0	TGFBR2,missense_variant,p.Asp446Asn,ENST00000295754,;TGFBR2,missense_variant,p.Asp471Asn,ENST00000359013,;	A	ENSG00000163513	ENST00000359013	Transcript	missense_variant	1694	1411	471	D/N	Gat/Aat	CM086981,CM060085,COSM95333,COSM1593641	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	deleterious(0)	probably_damaging(1)	6/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037393,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	0,0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.D471N|c.1411G>A|3,SITE|p.D446N|c.1336G>A|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCGATGTC	.	5	ESCA
ZBTB47	0	.	GRCh37	3	42707266	42707266	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1176G>A	.	.	ENST00000232974	6/6	32	24	8	28	28	0	ZBTB47,3_prime_UTR_variant,,ENST00000232974,;ZBTB47,3_prime_UTR_variant,,ENST00000505904,;ZBTB47,3_prime_UTR_variant,,ENST00000457842,;	A	ENSG00000114853	ENST00000232974	Transcript	3_prime_UTR_variant	3701	.	.	.	.	.	.	.	1	ZBTB47	HGNC	26955	protein_coding	YES	CCDS46805.2	ENSP00000232974	.	H7BXD3_HUMAN,D6RDG5_HUMAN	UPI0001BB2D41	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGGGGGGAC	.	5	ESCA
CGGBP1	0	.	GRCh37	3	88102780	88102780	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1843G>C	.	.	ENST00000398392	1/1	30	24	6	16	16	0	CGGBP1,3_prime_UTR_variant,,ENST00000309534,;CGGBP1,3_prime_UTR_variant,,ENST00000398392,;CGGBP1,downstream_gene_variant,,ENST00000482016,;CGGBP1,downstream_gene_variant,,ENST00000462901,;CGGBP1,downstream_gene_variant,,ENST00000467332,;CGGBP1,downstream_gene_variant,,ENST00000474441,;	G	ENSG00000163320	ENST00000398392	Transcript	3_prime_UTR_variant	3680	.	.	.	.	.	.	.	-1	CGGBP1	HGNC	1888	protein_coding	YES	CCDS43111.1	ENSP00000381429	CGBP1_HUMAN	C9JUJ0_HUMAN	UPI000006DF25	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATTTCAAAAA	.	2	ESCA
OTUD4	0	.	GRCh37	4	146056332	146056332	+	3'UTR	SNP	A	A	G	rs773865503	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2250T>C	.	.	ENST00000454497	21/21	18	14	4	13	13	0	OTUD4,3_prime_UTR_variant,,ENST00000454497,;OTUD4,downstream_gene_variant,,ENST00000447906,;OTUD4,intron_variant,,ENST00000455611,;	G	ENSG00000164164	ENST00000454497	Transcript	3_prime_UTR_variant	5538	.	.	.	.	rs773865503	.	.	-1	OTUD4	HGNC	24949	protein_coding	YES	CCDS47139.1	ENSP00000409279	OTUD4_HUMAN	D6RA27_HUMAN	UPI0000DA6D4D	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GTACCATCTGC	.	2	ESCA
TMA16	0	.	GRCh37	4	164415804	164415804	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-150C>T	.	.	ENST00000358572	1/7	19	14	5	31	31	0	TMA16,5_prime_UTR_variant,,ENST00000358572,;TMA16,intron_variant,,ENST00000509657,;TMA16,upstream_gene_variant,,ENST00000508268,;TMA16,upstream_gene_variant,,ENST00000513134,;TMA16,upstream_gene_variant,,ENST00000513272,;TMA16,upstream_gene_variant,,ENST00000511562,;TMA16,upstream_gene_variant,,ENST00000508652,;	T	ENSG00000198498	ENST00000358572	Transcript	5_prime_UTR_variant	192	.	.	.	.	.	.	.	1	TMA16	HGNC	25638	protein_coding	YES	CCDS43278.1	ENSP00000351380	TMA16_HUMAN	D6RA57_HUMAN	UPI0000457298	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACTCGCCTC	.	5	ESCA
PARM1	0	.	GRCh37	4	75937793	75937793	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202G>A	p.Val68Ile	p.V68I	ENST00000307428	2/4	68	34	33	45	45	0	PARM1,missense_variant,p.Val68Ile,ENST00000307428,;PARM1,intron_variant,,ENST00000513238,;RP11-44F21.2,intron_variant,,ENST00000513770,;	A	ENSG00000169116	ENST00000307428	Transcript	missense_variant	414	202	68	V/I	Gtt/Att	.	.	.	1	PARM1	HGNC	24536	protein_coding	YES	CCDS47077.1	ENSP00000370224	PARM1_HUMAN	.	UPI000004457B	.	tolerated(0.13)	benign(0.025)	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCAGTTACA	.	5	ESCA
FAM13A	0	.	GRCh37	4	89859293	89859293	+	Silent	SNP	A	A	G	.	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.705T>C	p.%3D	p.Y235Y	ENST00000264344	5/24	34	28	6	31	31	0	FAM13A,synonymous_variant,p.%3D,ENST00000511976,;FAM13A,synonymous_variant,p.%3D,ENST00000509094,;FAM13A,synonymous_variant,p.%3D,ENST00000264344,;FAM13A,non_coding_transcript_exon_variant,,ENST00000502459,;FAM13A,upstream_gene_variant,,ENST00000511145,;FAM13A,3_prime_UTR_variant,,ENST00000512339,;	G	ENSG00000138640	ENST00000264344	Transcript	synonymous_variant	913	705	235	Y	taT/taC	COSM275050	.	.	-1	FAM13A	HGNC	19367	protein_coding	YES	CCDS34029.1	ENSP00000264344	FA13A_HUMAN	B4DPB4_HUMAN	UPI0000481AF3	.	.	.	5/24	.	Gene3D:1.10.555.10,hmmpanther:PTHR15904:SF18,hmmpanther:PTHR15904	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGTATACTC	.	5	ESCA
MARCH3	0	.	GRCh37	5	126205957	126205958	+	3'UTR	DEL	AT	AT	-	rs113861488	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	AT	AT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*367_*368delAT	.	.	ENST00000308660	5/5	19	12	7	19	19	0	MARCH3,3_prime_UTR_variant,,ENST00000308660,;MARCH3,non_coding_transcript_exon_variant,,ENST00000506088,;	-	ENSG00000173926	ENST00000308660	Transcript	3_prime_UTR_variant	1644-1645	.	.	.	.	rs113861488	.	.	-1	MARCH3	HGNC	28728	protein_coding	YES	CCDS4141.1	ENSP00000309141	MARH3_HUMAN	.	UPI000000DC16	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGTTTAATATATA	byCluster	2	ESCA
JADE2	0	.	GRCh37	5	133895550	133895550	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342C>T	p.%3D	p.A114A	ENST00000395003	5/11	90	77	13	50	50	0	JADE2,synonymous_variant,p.%3D,ENST00000402835,;JADE2,synonymous_variant,p.%3D,ENST00000282605,;JADE2,synonymous_variant,p.%3D,ENST00000395003,;JADE2,synonymous_variant,p.%3D,ENST00000512386,;JADE2,synonymous_variant,p.%3D,ENST00000361895,;JADE2,synonymous_variant,p.%3D,ENST00000431355,;JADE2,non_coding_transcript_exon_variant,,ENST00000453515,;JADE2,upstream_gene_variant,,ENST00000470876,;	T	ENSG00000043143	ENST00000395003	Transcript	synonymous_variant	521	342	114	A	gcC/gcT	.	.	.	1	JADE2	HGNC	22984	protein_coding	YES	CCDS4176.1	ENSP00000378451	JADE2_HUMAN	D6R9B8_HUMAN,C9J929_HUMAN	UPI00002331C9	.	.	.	5/11	.	Pfam_domain:PF10513,hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCCCAGGC	.	5	ESCA
ADRB2	0	.	GRCh37	5	148207798	148207798	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*162A>T	.	.	ENST00000305988	1/1	66	53	12	61	61	0	ADRB2,3_prime_UTR_variant,,ENST00000305988,;	T	ENSG00000169252	ENST00000305988	Transcript	3_prime_UTR_variant	1643	.	.	.	.	.	.	.	1	ADRB2	HGNC	286	protein_coding	YES	CCDS4292.1	ENSP00000305372	ADRB2_HUMAN	Q9BYZ0_HUMAN	UPI000013EAD0	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGAGAGAA	.	5	ESCA
NDST1	0	.	GRCh37	5	149937504	149937504	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4610G>T	.	.	ENST00000261797	15/15	139	64	74	86	86	0	NDST1,3_prime_UTR_variant,,ENST00000261797,;NDST1,downstream_gene_variant,,ENST00000523767,;NDST1,downstream_gene_variant,,ENST00000521752,;	T	ENSG00000070614	ENST00000261797	Transcript	3_prime_UTR_variant	7761	.	.	.	.	.	.	.	1	NDST1	HGNC	7680	protein_coding	YES	CCDS34277.1	ENSP00000261797	NDST1_HUMAN	E5RGN9_HUMAN,E5RG58_HUMAN,E5RG24_HUMAN	UPI000012CDA5	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAAGAGGGC	.	5	ESCA
SYNPO	0	.	GRCh37	5	150029259	150029259	+	Silent	SNP	C	C	T	rs761150754	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2154C>T	p.%3D	p.S718S	ENST00000394243	3/3	29	12	17	30	30	0	SYNPO,synonymous_variant,p.%3D,ENST00000519664,;SYNPO,synonymous_variant,p.%3D,ENST00000394243,;SYNPO,synonymous_variant,p.%3D,ENST00000522122,;SYNPO,synonymous_variant,p.%3D,ENST00000307662,;SYNPO,downstream_gene_variant,,ENST00000518872,;	T	ENSG00000171992	ENST00000394243	Transcript	synonymous_variant	2528	2154	718	S	tcC/tcT	rs761150754	.	.	1	SYNPO	HGNC	30672	protein_coding	YES	CCDS54937.1	ENSP00000377789	SYNPO_HUMAN	Q71HJ6_HUMAN	UPI000013F943	.	.	.	3/3	.	hmmpanther:PTHR24217:SF11,hmmpanther:PTHR24217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTCCGAGGC	.	5	ESCA
DOCK2	0	.	GRCh37	5	169507274	169507274	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5274G>A	p.Met1758Ile	p.M1758I	ENST00000256935	50/52	77	69	8	54	54	0	DOCK2,missense_variant,p.Met819Ile,ENST00000540750,;DOCK2,missense_variant,p.Met1758Ile,ENST00000256935,;DOCK2,missense_variant,p.Met1250Ile,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,non_coding_transcript_exon_variant,,ENST00000519868,;DOCK2,non_coding_transcript_exon_variant,,ENST00000520450,;	A	ENSG00000134516	ENST00000256935	Transcript	missense_variant	5354	5274	1758	M/I	atG/atA	.	.	.	1	DOCK2	HGNC	2988	protein_coding	YES	CCDS4371.1	ENSP00000256935	DOCK2_HUMAN	Q5XG91_HUMAN,B3KXW9_HUMAN	UPI00001A38CC	.	tolerated_low_confidence(0.09)	benign(0.079)	50/52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCATGCCTAC	.	3	ESCA
SNX18	0	.	GRCh37	5	53816170	53816171	+	3'UTR	INS	-	-	CTT	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*502_*504dupCTT	.	.	ENST00000326277	1/1	64	55	9	45	45	0	SNX18,3_prime_UTR_variant,,ENST00000326277,;SNX18,intron_variant,,ENST00000343017,;SNX18,intron_variant,,ENST00000381410,;	CTT	ENSG00000178996	ENST00000326277	Transcript	3_prime_UTR_variant	2578-2579	.	.	.	.	.	.	.	1	SNX18	HGNC	19245	protein_coding	YES	CCDS3962.1	ENSP00000317332	SNX18_HUMAN	.	UPI00001418B0	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTGACCTTTG	.	3	ESCA
MAP3K1	0	.	GRCh37	5	56180554	56180554	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3883delA	p.Ile1295Ter	p.I1295*	ENST00000399503	16/20	54	44	10	29	29	0	MAP3K1,frameshift_variant,p.Ile1295Ter,ENST00000399503,;MAP3K1,upstream_gene_variant,,ENST00000469188,;	-	ENSG00000095015	ENST00000399503	Transcript	frameshift_variant	3883	3883	1295	I/X	Ata/ta	.	.	.	1	MAP3K1	HGNC	6848	protein_coding	YES	CCDS43318.1	ENSP00000382423	M3K1_HUMAN	.	UPI000015153B	.	.	.	16/20	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF255,hmmpanther:PTHR24361,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAGAGATAAGA	.	3	ESCA
CTC-534A2.2	0	.	GRCh37	5	64926000	64926000	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586G>A	p.Glu196Lys	p.E196K	ENST00000510585	2/2	40	32	8	31	31	0	CTC-534A2.2,missense_variant,p.Glu196Lys,ENST00000510585,;TRAPPC13,intron_variant,,ENST00000231526,;TRAPPC13,intron_variant,,ENST00000505553,;TRAPPC13,intron_variant,,ENST00000545191,;TRAPPC13,intron_variant,,ENST00000438419,;TRAPPC13,intron_variant,,ENST00000399438,;TRIM23,upstream_gene_variant,,ENST00000513794,;CTC-534A2.2,downstream_gene_variant,,ENST00000514404,;TRAPPC13,intron_variant,,ENST00000512009,;TRAPPC13,intron_variant,,ENST00000508304,;TRAPPC13,intron_variant,,ENST00000504751,;	A	ENSG00000253251	ENST00000510585	Transcript	missense_variant	1048	586	196	E/K	Gaa/Aaa	.	.	.	1	CTC-534A2.2	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000424007	.	Q6ZNX1_HUMAN	UPI00001C1180	.	deleterious(0.04)	probably_damaging(0.986)	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATGAACTT	.	5	ESCA
POPDC3	0	.	GRCh37	6	105606536	105606536	+	Missense_Mutation	SNP	G	G	A	rs745683947	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.685C>T	p.Arg229Cys	p.R229C	ENST00000254765	4/4	50	27	22	31	31	0	POPDC3,missense_variant,p.Arg75Cys,ENST00000429112,;POPDC3,missense_variant,p.Arg229Cys,ENST00000254765,;BVES-AS1,intron_variant,,ENST00000580511,;BVES-AS1,intron_variant,,ENST00000369120,;BVES-AS1,intron_variant,,ENST00000369122,;BVES-AS1,intron_variant,,ENST00000580854,;POPDC3,non_coding_transcript_exon_variant,,ENST00000474760,;POPDC3,non_coding_transcript_exon_variant,,ENST00000489134,;	A	ENSG00000132429	ENST00000254765	Transcript	missense_variant	964	685	229	R/C	Cgc/Tgc	rs745683947	.	.	-1	POPDC3	HGNC	17649	protein_coding	YES	CCDS5052.1	ENSP00000254765	POPD3_HUMAN	.	UPI000006FA58	.	deleterious(0.03)	probably_damaging(0.976)	4/4	.	hmmpanther:PTHR12101:SF18,hmmpanther:PTHR12101,Pfam_domain:PF04831,Gene3D:2.60.120.10,Superfamily_domains:SSF51206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGCGGGAGA	byFrequency	5	ESCA
ARID1B	0	.	GRCh37	6	157469897	157469897	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2691A>T	p.%3D	p.G897G	ENST00000346085	9/20	76	53	22	59	59	0	ARID1B,synonymous_variant,p.%3D,ENST00000319584,;ARID1B,synonymous_variant,p.%3D,ENST00000367148,;ARID1B,synonymous_variant,p.%3D,ENST00000346085,;ARID1B,synonymous_variant,p.%3D,ENST00000350026,;ARID1B,synonymous_variant,p.%3D,ENST00000414678,;ARID1B,synonymous_variant,p.%3D,ENST00000275248,;ARID1B,upstream_gene_variant,,ENST00000400790,;ARID1B,upstream_gene_variant,,ENST00000478761,;ARID1B,non_coding_transcript_exon_variant,,ENST00000452544,;	T	ENSG00000049618	ENST00000346085	Transcript	synonymous_variant	2692	2691	897	G	ggA/ggT	.	.	.	1	ARID1B	HGNC	18040	protein_coding	YES	CCDS55072.1	ENSP00000344546	ARI1B_HUMAN	.	UPI000058E4B2	.	.	.	9/20	.	hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGACGAAT	.	5	ESCA
FNDC1	0	.	GRCh37	6	159692412	159692412	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5623G>A	p.Gly1875Arg	p.G1875R	ENST00000297267	23/23	88	45	43	85	85	0	FNDC1,missense_variant,p.Gly1812Arg,ENST00000340366,;FNDC1,missense_variant,p.Gly1875Arg,ENST00000297267,;FNDC1,missense_variant,p.Gly1771Arg,ENST00000329629,;	A	ENSG00000164694	ENST00000297267	Transcript	missense_variant	5823	5623	1875	G/R	Gga/Aga	.	.	.	1	FNDC1	HGNC	21184	protein_coding	YES	CCDS47512.1	ENSP00000297267	FNDC1_HUMAN	.	UPI0000579B80	.	tolerated(0.36)	benign(0.299)	23/23	.	hmmpanther:PTHR23197:SF8,hmmpanther:PTHR23197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTCGGAACC	.	5	ESCA
FAM135A	0	.	GRCh37	6	71234985	71234985	+	Missense_Mutation	SNP	G	G	A	rs143752744	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2198G>A	p.Arg733Gln	p.R733Q	ENST00000418814	15/22	37	30	7	26	26	0	FAM135A,missense_variant,p.Arg520Gln,ENST00000457062,;FAM135A,missense_variant,p.Arg733Gln,ENST00000505868,;FAM135A,missense_variant,p.Arg537Gln,ENST00000361499,;FAM135A,missense_variant,p.Arg733Gln,ENST00000418814,;FAM135A,missense_variant,p.Arg520Gln,ENST00000370479,;FAM135A,intron_variant,,ENST00000505769,;FAM135A,downstream_gene_variant,,ENST00000515323,;FAM135A,3_prime_UTR_variant,,ENST00000194672,;FAM135A,downstream_gene_variant,,ENST00000393299,;	A	ENSG00000082269	ENST00000418814	Transcript	missense_variant	2812	2198	733	R/Q	cGa/cAa	rs143752744	.	.	1	FAM135A	HGNC	21084	protein_coding	YES	CCDS55028.1	ENSP00000410768	F135A_HUMAN	D6RFG9_HUMAN,D6REA8_HUMAN,D6RC17_HUMAN	UPI000004A0FF	.	tolerated(0.14)	benign(0.01)	15/22	.	hmmpanther:PTHR12482,hmmpanther:PTHR12482:SF12	A:0.0010	A:0.0038	A:0	.	A:0	A:0	A:0	A:0.0025	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTACGAAGTA	byFrequency|byCluster|by1000G	5	ESCA
GRM8	0	.	GRCh37	7	126173838	126173838	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1598delC	p.Pro533LeufsTer32	p.P533Lfs*32	ENST00000339582	9/11	167	143	24	92	92	0	GRM8,frameshift_variant,p.Pro533LeufsTer32,ENST00000358373,;GRM8,frameshift_variant,p.Pro533LeufsTer32,ENST00000444921,;GRM8,frameshift_variant,p.Pro533LeufsTer32,ENST00000339582,;GRM8,splice_region_variant,,ENST00000480995,;GRM8,frameshift_variant,p.Pro533LeufsTer32,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,;	-	ENSG00000179603	ENST00000339582	Transcript	frameshift_variant	2407	1598	533	P/X	cCt/ct	.	.	.	-1	GRM8	HGNC	4600	protein_coding	YES	CCDS5794.1	ENSP00000344173	GRM8_HUMAN	E7ETK3_HUMAN,C9J7I1_HUMAN	UPI000012F085	.	.	.	9/11	.	hmmpanther:PTHR24060:SF26,hmmpanther:PTHR24060,Pfam_domain:PF07562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGCAAGGGACC	.	3	ESCA
DGKI	0	.	GRCh37	7	137206686	137206686	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2174G>C	p.Arg725Thr	p.R725T	ENST00000288490	21/34	59	48	10	38	38	0	DGKI,missense_variant,p.Arg725Thr,ENST00000288490,;DGKI,missense_variant,p.Arg746Thr,ENST00000424189,;DGKI,missense_variant,p.Arg425Thr,ENST00000453654,;DGKI,missense_variant,p.Arg725Thr,ENST00000446122,;DGKI,non_coding_transcript_exon_variant,,ENST00000460662,;	G	ENSG00000157680	ENST00000288490	Transcript	missense_variant	2175	2174	725	R/T	aGg/aCg	.	.	.	-1	DGKI	HGNC	2855	protein_coding	YES	CCDS5845.1	ENSP00000288490	DGKI_HUMAN	B3KR69_HUMAN	UPI000012DD23	.	tolerated(0.06)	probably_damaging(0.996)	21/34	.	hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R744C|c.2230C>T|5,BUFFER|p.R723C|c.2167C>T|8,BUFFER|p.R723C|c.2167C>T|8	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATCCTCAGA	.	5	ESCA
SP4	0	.	GRCh37	7	21553939	21553939	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3052A>G	.	.	ENST00000222584	6/6	98	58	39	95	95	0	SP4,3_prime_UTR_variant,,ENST00000222584,;SP4,3_prime_UTR_variant,,ENST00000448246,;	G	ENSG00000105866	ENST00000222584	Transcript	3_prime_UTR_variant	5625	.	.	.	.	.	.	.	1	SP4	HGNC	11209	protein_coding	YES	CCDS5373.1	ENSP00000222584	SP4_HUMAN	Q32M51_HUMAN	UPI000013C807	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATATTTGT	.	5	ESCA
PKD1L1	0	.	GRCh37	7	47851429	47851429	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7567C>T	p.Leu2523Phe	p.L2523F	ENST00000289672	50/57	61	52	9	51	51	0	PKD1L1,missense_variant,p.Leu114Phe,ENST00000433506,;PKD1L1,missense_variant,p.Leu2523Phe,ENST00000289672,;C7orf69,intron_variant,,ENST00000418326,;C7orf69,intron_variant,,ENST00000258776,;PKD1L1,upstream_gene_variant,,ENST00000462350,;PKD1L1,non_coding_transcript_exon_variant,,ENST00000483616,;HUS1,intron_variant,,ENST00000436444,;	A	ENSG00000158683	ENST00000289672	Transcript	missense_variant	7618	7567	2523	L/F	Ctc/Ttc	.	.	.	-1	PKD1L1	HGNC	18053	protein_coding	YES	CCDS34633.1	ENSP00000289672	PK1L1_HUMAN	.	UPI0000130FA9	.	deleterious(0.04)	probably_damaging(0.963)	50/57	.	Transmembrane_helices:TMhelix,Pfam_domain:PF08016,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGAGGTGGT	.	5	ESCA
DMTF1	0	.	GRCh37	7	86815159	86815162	+	Frame_Shift_Del	DEL	ATGT	ATGT	-	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	ATGT	ATGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1065_1068delTGTA	p.Asp355GlufsTer12	p.D355Efs*12	ENST00000394703	14/20	158	106	52	109	109	0	DMTF1,frameshift_variant,p.Asp355GlufsTer12,ENST00000394703,;DMTF1,frameshift_variant,p.Asp89GlufsTer12,ENST00000414194,;DMTF1,frameshift_variant,p.Asp267GlufsTer12,ENST00000432937,;DMTF1,frameshift_variant,p.Asp355GlufsTer12,ENST00000413276,;DMTF1,frameshift_variant,p.Asp355GlufsTer12,ENST00000331242,;DMTF1,downstream_gene_variant,,ENST00000411766,;DMTF1,downstream_gene_variant,,ENST00000394702,;DMTF1,frameshift_variant,p.Asp314GlufsTer12,ENST00000579850,;DMTF1,coding_sequence_variant,,ENST00000547146,;DMTF1,3_prime_UTR_variant,,ENST00000447863,;DMTF1,3_prime_UTR_variant,,ENST00000412139,;DMTF1,3_prime_UTR_variant,,ENST00000579677,;DMTF1,3_prime_UTR_variant,,ENST00000425406,;DMTF1,3_prime_UTR_variant,,ENST00000584619,;DMTF1,non_coding_transcript_exon_variant,,ENST00000473521,;DMTF1,non_coding_transcript_exon_variant,,ENST00000578926,;DMTF1,non_coding_transcript_exon_variant,,ENST00000582887,;DMTF1,upstream_gene_variant,,ENST00000480982,;DMTF1,upstream_gene_variant,,ENST00000580803,;	-	ENSG00000135164	ENST00000394703	Transcript	frameshift_variant	1627-1630	1064-1067	355-356	DV/X	gATGTa/ga	.	.	.	1	DMTF1	HGNC	14603	protein_coding	YES	CCDS5601.1	ENSP00000378193	DMTF1_HUMAN	J3KRC1_HUMAN,D6W5P0_HUMAN,C9K0L9_HUMAN,C9K0K9_HUMAN,C9JZZ6_HUMAN,C9JVQ7_HUMAN,C9JLR5_HUMAN,C9JGT5_HUMAN,C9JFR2_HUMAN,C9JED5_HUMAN,C9J8Y5_HUMAN,C9J4F7_HUMAN,B3KVS2_HUMAN	UPI000006FB78	.	.	.	14/20	.	Superfamily_domains:SSF46689,SMART_domains:SM00717,hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF463,PROSITE_profiles:PS50090	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AACTTGATGTAGCTG	.	3	ESCA
CSMD3	0	.	GRCh37	8	113267492	113267492	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10027C>T	p.His3343Tyr	p.H3343Y	ENST00000297405	62/71	66	52	14	47	47	0	CSMD3,missense_variant,p.His3273Tyr,ENST00000352409,;CSMD3,missense_variant,p.His3174Tyr,ENST00000455883,;CSMD3,missense_variant,p.His3343Tyr,ENST00000297405,;CSMD3,missense_variant,p.His2613Tyr,ENST00000339701,;CSMD3,missense_variant,p.His3303Tyr,ENST00000343508,;CSMD3,non_coding_transcript_exon_variant,,ENST00000534172,;	A	ENSG00000164796	ENST00000297405	Transcript	missense_variant	10272	10027	3343	H/Y	Cac/Tac	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.08)	benign(0.088)	62/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTGAGGTG	.	5	ESCA
GINS4	0	.	GRCh37	8	41393951	41393951	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.169C>T	p.Gln57Ter	p.Q57*	ENST00000276533	3/8	81	66	15	62	62	0	GINS4,stop_gained,p.Gln57Ter,ENST00000276533,;GINS4,stop_gained,p.Gln57Ter,ENST00000520710,;GINS4,stop_gained,p.Gln57Ter,ENST00000523277,;GINS4,stop_gained,p.Gln57Ter,ENST00000518671,;RP11-360L9.4,intron_variant,,ENST00000523081,;RP11-360L9.7,downstream_gene_variant,,ENST00000524133,;GINS4,stop_gained,p.Gln57Ter,ENST00000520354,;GINS4,non_coding_transcript_exon_variant,,ENST00000522642,;GINS4,non_coding_transcript_exon_variant,,ENST00000520736,;GINS4,non_coding_transcript_exon_variant,,ENST00000520631,;	T	ENSG00000147536	ENST00000276533	Transcript	stop_gained	379	169	57	Q/*	Cag/Tag	.	.	.	1	GINS4	HGNC	28226	protein_coding	YES	CCDS6116.1	ENSP00000276533	SLD5_HUMAN	E5RFF9_HUMAN	UPI000007007B	.	.	.	3/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21206,hmmpanther:PTHR21206:SF0,PIRSF_domain:PIRSF007764,Superfamily_domains:SSF158573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAACAGCTG	.	5	ESCA
ANK1	0	.	GRCh37	8	41754056	41754056	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-58C>T	.	.	ENST00000265709	1/43	55	49	5	39	39	0	ANK1,5_prime_UTR_variant,,ENST00000265709,;	A	ENSG00000029534	ENST00000265709	Transcript	5_prime_UTR_variant	225	.	.	.	.	.	.	.	-1	ANK1	HGNC	492	protein_coding	YES	CCDS47849.1	ENSP00000265709	ANK1_HUMAN	Q9UMG4_HUMAN	UPI0000E4453A	.	.	.	1/43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCCGAGGCG	.	4	ESCA
EFCAB1	0	.	GRCh37	8	49643126	49643126	+	Nonsense_Mutation	SNP	G	G	A	rs751867551	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292C>T	p.Arg98Ter	p.R98*	ENST00000262103	3/6	38	34	4	20	20	0	EFCAB1,stop_gained,p.Arg98Ter,ENST00000262103,;EFCAB1,stop_gained,p.Arg46Ter,ENST00000523092,;EFCAB1,stop_gained,p.Arg46Ter,ENST00000433756,;EFCAB1,stop_gained,p.Arg16Ter,ENST00000522254,;EFCAB1,upstream_gene_variant,,ENST00000523008,;EFCAB1,non_coding_transcript_exon_variant,,ENST00000521721,;EFCAB1,intron_variant,,ENST00000521002,;EFCAB1,stop_gained,p.Arg46Ter,ENST00000521701,;EFCAB1,upstream_gene_variant,,ENST00000519425,;	A	ENSG00000034239	ENST00000262103	Transcript	stop_gained	373	292	98	R/*	Cga/Tga	rs751867551	.	.	-1	EFCAB1	HGNC	25678	protein_coding	YES	CCDS6145.1	ENSP00000262103	EFCB1_HUMAN	.	UPI000006E520	.	.	.	3/6	.	PROSITE_profiles:PS50222,hmmpanther:PTHR23055,hmmpanther:PTHR23055:SF75,Gene3D:1.10.238.10,Superfamily_domains:SSF47473,Prints_domain:PR00450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TCCTCGAAGAA	.	3	ESCA
PRDM14	0	.	GRCh37	8	70964528	70964528	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1500C>T	p.%3D	p.A500A	ENST00000276594	8/8	144	109	34	70	70	0	PRDM14,synonymous_variant,p.%3D,ENST00000276594,;	A	ENSG00000147596	ENST00000276594	Transcript	synonymous_variant	1702	1500	500	A	gcC/gcT	.	.	.	-1	PRDM14	HGNC	14001	protein_coding	YES	CCDS6206.1	ENSP00000276594	PRD14_HUMAN	C9JMM8_HUMAN	UPI0000132186	.	.	.	8/8	.	PROSITE_profiles:PS50157,hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF354,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGGCTGT	.	5	ESCA
NBN	0	.	GRCh37	8	90993677	90993677	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246A>T	p.Lys82Asn	p.K82N	ENST00000265433	3/16	102	72	29	55	55	0	NBN,missense_variant,p.Lys82Asn,ENST00000265433,;NBN,missense_variant,p.Lys82Asn,ENST00000519426,;NBN,5_prime_UTR_variant,,ENST00000517772,;NBN,5_prime_UTR_variant,,ENST00000517337,;NBN,5_prime_UTR_variant,,ENST00000409330,;NBN,3_prime_UTR_variant,,ENST00000523444,;NBN,3_prime_UTR_variant,,ENST00000396252,;NBN,downstream_gene_variant,,ENST00000494804,;	A	ENSG00000104320	ENST00000265433	Transcript	missense_variant	401	246	82	K/N	aaA/aaT	.	.	.	-1	NBN	HGNC	7652	protein_coding	YES	CCDS6249.1	ENSP00000265433	NBN_HUMAN	E5RGR7_HUMAN,E5RGN7_HUMAN	UPI0000073BF4	.	deleterious(0.03)	benign(0.364)	3/16	.	PROSITE_profiles:PS50006,hmmpanther:PTHR12162,Pfam_domain:PF00498,Gene3D:2.60.200.20,PIRSF_domain:PIRSF011869,SMART_domains:SM00240,Superfamily_domains:SSF49879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCATTTTTTC	.	5	ESCA
SLC26A7	0	.	GRCh37	8	92307786	92307786	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.332C>T	p.Ser111Leu	p.S111L	ENST00000309536	4/19	99	85	13	45	45	0	SLC26A7,missense_variant,p.Ser111Leu,ENST00000276609,;SLC26A7,missense_variant,p.Ser111Leu,ENST00000309536,;SLC26A7,missense_variant,p.Ser111Leu,ENST00000522862,;SLC26A7,missense_variant,p.Ser111Leu,ENST00000523719,;SLC26A7,upstream_gene_variant,,ENST00000520818,;SLC26A7,missense_variant,p.Ser111Leu,ENST00000522181,;	T	ENSG00000147606	ENST00000309536	Transcript	missense_variant	552	332	111	S/L	tCa/tTa	.	.	.	1	SLC26A7	HGNC	14467	protein_coding	YES	CCDS6255.1	ENSP00000309504	S26A7_HUMAN	E5RFH2_HUMAN	UPI0000046B1C	.	tolerated(0.2)	probably_damaging(0.999)	4/19	.	hmmpanther:PTHR11814:SF75,hmmpanther:PTHR11814,Pfam_domain:PF13792	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATATCAGCCA	.	4	ESCA
GAPVD1	0	.	GRCh37	9	128083774	128083774	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1665C>T	p.%3D	p.L555L	ENST00000394105	8/27	106	82	24	54	54	0	GAPVD1,synonymous_variant,p.%3D,ENST00000297933,;GAPVD1,synonymous_variant,p.%3D,ENST00000470056,;GAPVD1,synonymous_variant,p.%3D,ENST00000394104,;GAPVD1,synonymous_variant,p.%3D,ENST00000394105,;GAPVD1,synonymous_variant,p.%3D,ENST00000431329,;GAPVD1,synonymous_variant,p.%3D,ENST00000265956,;GAPVD1,synonymous_variant,p.%3D,ENST00000394083,;GAPVD1,synonymous_variant,p.%3D,ENST00000467750,;GAPVD1,synonymous_variant,p.%3D,ENST00000436712,;GAPVD1,synonymous_variant,p.%3D,ENST00000495955,;GAPVD1,synonymous_variant,p.%3D,ENST00000312123,;GAPVD1,synonymous_variant,p.%3D,ENST00000497580,;	T	ENSG00000165219	ENST00000394105	Transcript	synonymous_variant	1825	1665	555	L	ctC/ctT	.	.	.	1	GAPVD1	HGNC	23375	protein_coding	YES	CCDS35138.1	ENSP00000377665	GAPD1_HUMAN	C9IZX9_HUMAN	UPI00001D76F1	.	.	.	8/27	.	hmmpanther:PTHR23101:SF55,hmmpanther:PTHR23101	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTCCATGG	.	5	ESCA
PTGDS	0	.	GRCh37	9	139873468	139873468	+	Silent	SNP	G	G	A	rs749983173	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138G>A	p.%3D	p.A46A	ENST00000371625	2/7	33	27	6	20	20	0	PTGDS,synonymous_variant,p.%3D,ENST00000371623,;PTGDS,synonymous_variant,p.%3D,ENST00000224167,;PTGDS,synonymous_variant,p.%3D,ENST00000446677,;PTGDS,synonymous_variant,p.%3D,ENST00000457950,;PTGDS,synonymous_variant,p.%3D,ENST00000371625,;PTGDS,upstream_gene_variant,,ENST00000444903,;LCNL1,upstream_gene_variant,,ENST00000408973,;PTGDS,non_coding_transcript_exon_variant,,ENST00000460340,;PTGDS,upstream_gene_variant,,ENST00000462514,;LCNL1,upstream_gene_variant,,ENST00000432827,;RP11-229P13.19,downstream_gene_variant,,ENST00000413913,;PTGDS,upstream_gene_variant,,ENST00000492068,;PTGDS,upstream_gene_variant,,ENST00000467871,;PTGDS,synonymous_variant,p.%3D,ENST00000471521,;LCNL1,upstream_gene_variant,,ENST00000460177,;LCNL1,upstream_gene_variant,,ENST00000482657,;	A	ENSG00000107317	ENST00000371625	Transcript	synonymous_variant	212	138	46	A	gcG/gcA	rs749983173	.	.	1	PTGDS	HGNC	9592	protein_coding	YES	CCDS7019.1	ENSP00000360687	PTGDS_HUMAN	.	UPI00001317A4	.	.	.	2/7	.	hmmpanther:PTHR11430:SF64,hmmpanther:PTHR11430,PROSITE_patterns:PS00213,Pfam_domain:PF00061,Gene3D:2.40.128.20,Superfamily_domains:SSF50814,Prints_domain:PR00179,Prints_domain:PR01254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCGCGGGCCT	.	5	ESCA
UNC13B	0	.	GRCh37	9	35396854	35396854	+	Missense_Mutation	SNP	G	G	A	rs140663072	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3205G>A	p.Val1069Met	p.V1069M	ENST00000378495	27/39	110	89	21	52	52	0	UNC13B,missense_variant,p.Val1069Met,ENST00000378495,;UNC13B,missense_variant,p.Val1081Met,ENST00000396787,;UNC13B,missense_variant,p.Val1069Met,ENST00000378496,;UNC13B,non_coding_transcript_exon_variant,,ENST00000481299,;	A	ENSG00000198722	ENST00000378495	Transcript	missense_variant	3427	3205	1069	V/M	Gtg/Atg	rs140663072,COSM3907132,COSM3907133	.	.	1	UNC13B	HGNC	12566	protein_coding	YES	CCDS6579.1	ENSP00000367756	UN13B_HUMAN	.	UPI0000211336	.	deleterious(0)	probably_damaging(0.953)	27/39	.	PROSITE_profiles:PS51258,hmmpanther:PTHR10480	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0005	A:0	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTCGTGCTA	byCluster|by1000G	5	ESCA
ARMCX5	0	.	GRCh37	X	101858368	101858368	+	Nonsense_Mutation	SNP	T	T	G	.	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1299T>G	p.Tyr433Ter	p.Y433*	ENST00000604957	1/1	112	41	71	41	41	0	ARMCX5,stop_gained,p.Tyr433Ter,ENST00000246174,;ARMCX5,stop_gained,p.Tyr433Ter,ENST00000604957,;ARMCX5,stop_gained,p.Tyr433Ter,ENST00000541409,;ARMCX5,stop_gained,p.Tyr433Ter,ENST00000537008,;ARMCX5,stop_gained,p.Tyr433Ter,ENST00000372742,;ARMCX5,stop_gained,p.Tyr433Ter,ENST00000536530,;ARMCX5,downstream_gene_variant,,ENST00000479502,;ARMCX5,downstream_gene_variant,,ENST00000477663,;ARMCX5,downstream_gene_variant,,ENST00000473968,;RP4-769N13.7,intron_variant,,ENST00000602441,;RP4-769N13.6,intron_variant,,ENST00000475738,;RP4-769N13.6,intron_variant,,ENST00000602366,;RP4-769N13.6,intron_variant,,ENST00000466616,;RP4-769N13.6,intron_variant,,ENST00000486740,;RP4-769N13.6,intron_variant,,ENST00000602463,;RP4-769N13.6,intron_variant,,ENST00000476910,;RP4-769N13.6,intron_variant,,ENST00000460793,;RP4-769N13.6,intron_variant,,ENST00000460026,;RP4-769N13.6,intron_variant,,ENST00000465548,;	G	ENSG00000125962	ENST00000604957	Transcript	stop_gained	3921	1299	433	Y/*	taT/taG	COSM456366	.	.	1	ARMCX5	HGNC	25772	protein_coding	YES	CCDS14500.1	ENSP00000474720	ARMX5_HUMAN	S4R3L5_HUMAN,S4R3L0_HUMAN	UPI000013CBDB	.	.	.	1/1	.	hmmpanther:PTHR15712:SF12,hmmpanther:PTHR15712,Pfam_domain:PF04826,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTATATTCC	.	5	ESCA
NXF3	0	.	GRCh37	X	102347947	102347947	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5C>A	p.Ser2Ter	p.S2*	ENST00000395065	1/20	81	29	52	33	33	0	NXF3,stop_gained,p.Ser2Ter,ENST00000395065,;NXF3,5_prime_UTR_variant,,ENST00000425463,;NXF3,5_prime_UTR_variant,,ENST00000425644,;LL0XNC01-221F2.2,downstream_gene_variant,,ENST00000440243,;	T	ENSG00000147206	ENST00000395065	Transcript	stop_gained	107	5	2	S/*	tCa/tAa	.	.	.	-1	NXF3	HGNC	8073	protein_coding	YES	CCDS14503.1	ENSP00000378504	NXF3_HUMAN	.	UPI00000015F8	.	.	.	1/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTGACATT	.	5	ESCA
SLITRK2	0	.	GRCh37	X	144905225	144905225	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1282C>A	p.Leu428Ile	p.L428I	ENST00000370490	1/1	58	51	7	34	34	0	SLITRK2,missense_variant,p.Leu428Ile,ENST00000370490,;SLITRK2,missense_variant,p.Leu428Ile,ENST00000434188,;SLITRK2,missense_variant,p.Leu428Ile,ENST00000428560,;SLITRK2,missense_variant,p.Leu428Ile,ENST00000413937,;SLITRK2,missense_variant,p.Leu428Ile,ENST00000447897,;SLITRK2,missense_variant,p.Leu428Ile,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,;	A	ENSG00000185985	ENST00000370490	Transcript	missense_variant	5537	1282	428	L/I	Ctt/Att	.	.	.	1	SLITRK2	HGNC	13449	protein_coding	YES	CCDS14680.1	ENSP00000359521	SLIK2_HUMAN	B3KTY4_HUMAN	UPI000004E64B	.	deleterious(0)	probably_damaging(0.999)	1/1	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF36,hmmpanther:PTHR24373,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGACTTTAT	.	4	ESCA
MAGEA9B	0	.	GRCh37	X	148664813	148664813	+	Missense_Mutation	SNP	G	G	A	rs782470689	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.23C>T	p.Pro8Leu	p.P8L	ENST00000243314	4/4	133	114	19	91	91	0	MAGEA9B,missense_variant,p.Pro8Leu,ENST00000243314,;	A	ENSG00000123584	ENST00000243314	Transcript	missense_variant	310	23	8	P/L	cCg/cTg	rs782470689	.	.	-1	MAGEA9B	HGNC	31909	protein_coding	YES	CCDS35423.1	ENSP00000243314	MAGA9_HUMAN	E5RJI2_HUMAN,E5RJ34_HUMAN,E5RH97_HUMAN,E5RFS8_HUMAN	UPI000012EB2B	.	tolerated(0.19)	benign(0.001)	4/4	.	hmmpanther:PTHR11736:SF62,hmmpanther:PTHR11736,Pfam_domain:PF12440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGTGCGGACTC	byFrequency	3	ESCA
FAM9A	0	.	GRCh37	X	8763118	8763118	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-LN-A49P-01A-11D-A247-09	TCGA-LN-A49P-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.831+1G>T	.	p.X277_splice	ENST00000543214	.	53	30	22	37	37	0	FAM9A,splice_donor_variant,,ENST00000543214,;FAM9A,splice_donor_variant,,ENST00000381003,;	A	ENSG00000183304	ENST00000543214	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	FAM9A	HGNC	18403	protein_coding	YES	CCDS14131.1	ENSP00000440163	FAM9A_HUMAN	.	UPI000012A418	.	.	.	.	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAACAATTT	.	5	ESCA
TAF5	0	.	GRCh37	10	105147814	105147814	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2237A>G	p.Asp746Gly	p.D746G	ENST00000369839	11/11	27	6	21	30	30	0	TAF5,missense_variant,p.Asp691Gly,ENST00000351396,;TAF5,missense_variant,p.Asp746Gly,ENST00000369839,;USMG5,downstream_gene_variant,,ENST00000369811,;USMG5,downstream_gene_variant,,ENST00000337003,;USMG5,downstream_gene_variant,,ENST00000369825,;USMG5,downstream_gene_variant,,ENST00000309579,;USMG5,downstream_gene_variant,,ENST00000369815,;	G	ENSG00000148835	ENST00000369839	Transcript	missense_variant	2260	2237	746	D/G	gAt/gGt	.	.	.	1	TAF5	HGNC	11539	protein_coding	YES	CCDS7547.1	ENSP00000358854	TAF5_HUMAN	.	UPI000013DB5B	.	deleterious(0)	benign(0.032)	11/11	.	PROSITE_profiles:PS50294,hmmpanther:PTHR19879,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAGATTTAG	.	5	ESCA
COL17A1	0	.	GRCh37	10	105792467	105792468	+	Frame_Shift_Ins	INS	-	-	CA	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4401_4402dupTG	p.Gly1468ValfsTer45	p.G1468Vfs*45	ENST00000353479	55/56	58	30	28	43	43	0	COL17A1,frameshift_variant,p.Gly1468ValfsTer45,ENST00000353479,;COL17A1,frameshift_variant,p.Gly1386ValfsTer45,ENST00000369733,;COL17A1,frameshift_variant,p.Gly37ValfsTer82,ENST00000433822,;SLK,downstream_gene_variant,,ENST00000369755,;SLK,downstream_gene_variant,,ENST00000335753,;	CA	ENSG00000065618	ENST00000353479	Transcript	frameshift_variant	4693-4694	4402-4403	1468	G/VX	ggc/gTGgc	.	.	.	-1	COL17A1	HGNC	2194	protein_coding	YES	CCDS7554.1	ENSP00000340937	COHA1_HUMAN	.	UPI000006DB58	.	.	.	55/56	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF455,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAGGGCCAGGT	.	3	ESCA
RPP38	0	.	GRCh37	10	15145535	15145535	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.222A>T	p.Lys74Asn	p.K74N	ENST00000378197	3/3	17	14	3	10	10	0	RPP38,missense_variant,p.Lys74Asn,ENST00000378203,;RPP38,missense_variant,p.Lys74Asn,ENST00000378202,;RPP38,missense_variant,p.Lys74Asn,ENST00000378197,;RPP38,missense_variant,p.Lys74Asn,ENST00000378201,;RPP38,missense_variant,p.Lys74Asn,ENST00000441850,;NMT2,downstream_gene_variant,,ENST00000378165,;NMT2,downstream_gene_variant,,ENST00000378150,;NMT2,non_coding_transcript_exon_variant,,ENST00000466201,;RPP38,intron_variant,,ENST00000451677,;NMT2,downstream_gene_variant,,ENST00000486786,;	T	ENSG00000152464	ENST00000378197	Transcript	missense_variant	736	222	74	K/N	aaA/aaT	.	.	.	1	RPP38	HGNC	30329	protein_coding	YES	CCDS7108.1	ENSP00000367439	RPP38_HUMAN	Q5VUC3_HUMAN	UPI000006F1AE	.	tolerated(0.08)	benign(0.006)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21596,hmmpanther:PTHR21596:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAAAGAAAG	.	2	ESCA
ARHGAP21	0	.	GRCh37	10	24874807	24874807	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4411A>G	p.Ile1471Val	p.I1471V	ENST00000396432	26/26	224	165	59	140	140	0	ARHGAP21,missense_variant,p.Ile1471Val,ENST00000396432,;ARHGAP21,downstream_gene_variant,,ENST00000320481,;ARHGAP21,downstream_gene_variant,,ENST00000418033,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000486374,;ARHGAP21,downstream_gene_variant,,ENST00000477190,;	C	ENSG00000107863	ENST00000396432	Transcript	missense_variant	4898	4411	1471	I/V	Atc/Gtc	.	.	.	-1	ARHGAP21	HGNC	23725	protein_coding	YES	CCDS7144.2	ENSP00000379709	RHG21_HUMAN	E7ESW5_HUMAN	UPI0001639C78	.	tolerated(0.31)	benign(0.001)	26/26	.	hmmpanther:PTHR23175:SF16,hmmpanther:PTHR23175	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGATCTTCT	.	5	ESCA
ITGB1	0	.	GRCh37	10	33196044	33196044	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2331+1252A>G	.	.	ENST00000396033	.	31	8	22	32	32	0	ITGB1,missense_variant,p.Ile787Val,ENST00000423113,;ITGB1,missense_variant,p.Ile56Val,ENST00000488427,;ITGB1,intron_variant,,ENST00000374956,;ITGB1,intron_variant,,ENST00000396033,;ITGB1,intron_variant,,ENST00000302278,;ITGB1,intron_variant,,ENST00000494395,;	C	ENSG00000150093	ENST00000396033	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ITGB1	HGNC	6153	protein_coding	YES	CCDS7174.1	ENSP00000379350	ITB1_HUMAN	Q5T3E6_HUMAN,Q5T3E5_HUMAN,Q5T3E4_HUMAN,E9PQJ2_HUMAN,E9PLR6_HUMAN,E7ERX5_HUMAN,E7EQW5_HUMAN,C9JPK5_HUMAN,C9JJP8_HUMAN	UPI0000070EEB	.	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTAATAGGAC	.	5	ESCA
EGR2	0	.	GRCh37	10	64575631	64575631	+	Silent	SNP	T	T	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159A>C	p.%3D	p.G53G	ENST00000242480	1/2	14	1	13	16	16	0	EGR2,synonymous_variant,p.%3D,ENST00000439032,;EGR2,synonymous_variant,p.%3D,ENST00000242480,;EGR2,synonymous_variant,p.%3D,ENST00000411732,;EGR2,non_coding_transcript_exon_variant,,ENST00000493899,;	G	ENSG00000122877	ENST00000242480	Transcript	synonymous_variant	485	159	53	G	ggA/ggC	.	.	.	-1	EGR2	HGNC	3239	protein_coding	YES	CCDS7267.1	ENSP00000242480	EGR2_HUMAN	.	UPI000013CB07	.	.	.	1/2	.	hmmpanther:PTHR10042,hmmpanther:PTHR10042:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACTCCGTT	.	5	ESCA
CBL	0	.	GRCh37	11	119149355	119149355	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1363T>A	p.Tyr455Asn	p.Y455N	ENST00000264033	9/16	19	14	5	28	28	0	CBL,missense_variant,p.Tyr455Asn,ENST00000264033,;	A	ENSG00000110395	ENST00000264033	Transcript	missense_variant	1739	1363	455	Y/N	Tat/Aat	.	.	.	1	CBL	HGNC	1541	protein_coding	YES	CCDS8418.1	ENSP00000264033	CBL_HUMAN	.	UPI000013D4A7	.	tolerated(0.3)	benign(0.01)	9/16	.	hmmpanther:PTHR23007:SF5,hmmpanther:PTHR23007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAATTATGAT	.	5	ESCA
OR10G7	0	.	GRCh37	11	123909033	123909033	+	Missense_Mutation	SNP	G	G	A	rs150421981	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.676C>T	p.Arg226Trp	p.R226W	ENST00000330487	1/1	89	29	59	130	130	0	OR10G7,missense_variant,p.Arg226Trp,ENST00000330487,;	A	ENSG00000182634	ENST00000330487	Transcript	missense_variant	685	676	226	R/W	Cgg/Tgg	rs150421981,COSM363672	.	.	-1	OR10G7	HGNC	14842	protein_coding	YES	CCDS31705.1	ENSP00000329689	O10G7_HUMAN	.	UPI0000040A84	.	deleterious(0)	probably_damaging(0.927)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF7,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	A:0.0011	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R226Q|c.677G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCCGCAGGA	byFrequency|byCluster|by1000G	5	ESCA
IGSF9B	0	.	GRCh37	11	133794746	133794746	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2088G>T	p.Glu696Asp	p.E696D	ENST00000533871	15/20	21	6	15	40	40	0	IGSF9B,missense_variant,p.Glu696Asp,ENST00000533871,;IGSF9B,missense_variant,p.Glu696Asp,ENST00000321016,;IGSF9B,non_coding_transcript_exon_variant,,ENST00000527648,;	A	ENSG00000080854	ENST00000533871	Transcript	missense_variant	2319	2088	696	E/D	gaG/gaT	.	.	.	-1	IGSF9B	HGNC	32326	protein_coding	YES	CCDS61010.1	ENSP00000436552	.	G5EA26_HUMAN	UPI0002C439DB	.	tolerated(0.26)	probably_damaging(0.995)	15/20	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF575,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCTCGCT	.	5	ESCA
UBE2L6	0	.	GRCh37	11	57322082	57322082	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138C>A	p.Tyr46Ter	p.Y46*	ENST00000287156	3/4	92	61	30	102	102	0	UBE2L6,stop_gained,p.Tyr46Ter,ENST00000287156,;UBE2L6,stop_gained,p.Tyr53Ter,ENST00000526659,;UBE2L6,5_prime_UTR_variant,,ENST00000340573,;UBE2L6,5_prime_UTR_variant,,ENST00000527022,;SMTNL1,downstream_gene_variant,,ENST00000527972,;SMTNL1,downstream_gene_variant,,ENST00000399154,;SMTNL1,downstream_gene_variant,,ENST00000457912,;UBE2L6,non_coding_transcript_exon_variant,,ENST00000528275,;	T	ENSG00000156587	ENST00000287156	Transcript	stop_gained	334	138	46	Y/*	taC/taA	.	.	.	-1	UBE2L6	HGNC	12490	protein_coding	YES	CCDS7960.1	ENSP00000287156	UB2L6_HUMAN	E9PKW8_HUMAN	UPI00000712E4	.	.	.	3/4	.	Superfamily_domains:SSF54495,SMART_domains:SM00212,Gene3D:3.10.110.10,Pfam_domain:PF00179,hmmpanther:PTHR24068:SF43,hmmpanther:PTHR24068,PROSITE_profiles:PS50127	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTGGTAGGG	.	5	ESCA
OR52L1	0	.	GRCh37	11	6007374	6007374	+	Missense_Mutation	SNP	T	T	C	rs199647565	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787A>G	p.Ile263Val	p.I263V	ENST00000332249	1/1	37	12	25	34	34	0	OR52L1,missense_variant,p.Ile263Val,ENST00000332249,;	C	ENSG00000183313	ENST00000332249	Transcript	missense_variant	842	787	263	I/V	Att/Gtt	rs199647565	.	.	-1	OR52L1	HGNC	14785	protein_coding	YES	CCDS44529.1	ENSP00000330338	O52L1_HUMAN	.	UPI00001B006D	.	tolerated(1)	benign(0.003)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF96,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	C:0.001	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAATATGAG	byCluster|by1000G	5	ESCA
RNF169	0	.	GRCh37	11	74546844	74546844	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1196G>A	p.Gly399Asp	p.G399D	ENST00000299563	6/6	60	48	12	38	38	0	RNF169,missense_variant,p.Gly399Asp,ENST00000299563,;RNF169,upstream_gene_variant,,ENST00000527301,;XRRA1,downstream_gene_variant,,ENST00000340360,;XRRA1,intron_variant,,ENST00000530562,;	A	ENSG00000166439	ENST00000299563	Transcript	missense_variant	1209	1196	399	G/D	gGc/gAc	.	.	.	1	RNF169	HGNC	26961	protein_coding	YES	CCDS41691.1	ENSP00000299563	RN169_HUMAN	.	UPI00001C1F15	.	deleterious(0)	probably_damaging(1)	6/6	.	hmmpanther:PTHR23328:SF2,hmmpanther:PTHR23328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGATGGCCGTG	.	4	ESCA
EFCAB4A	0	.	GRCh37	11	829507	829508	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427dupG	p.Glu143GlyfsTer147	p.E143Gfs*147	ENST00000450448	4/9	54	45	9	45	45	0	EFCAB4A,frameshift_variant,p.Glu143GlyfsTer147,ENST00000528542,;EFCAB4A,frameshift_variant,p.Glu143GlyfsTer209,ENST00000525077,;EFCAB4A,frameshift_variant,p.Glu143GlyfsTer147,ENST00000450448,;CD151,upstream_gene_variant,,ENST00000525333,;EFCAB4A,downstream_gene_variant,,ENST00000533803,;CD151,upstream_gene_variant,,ENST00000527341,;CD151,upstream_gene_variant,,ENST00000524748,;PNPLA2,downstream_gene_variant,,ENST00000336615,;CD151,upstream_gene_variant,,ENST00000526693,;EFCAB4A,downstream_gene_variant,,ENST00000527089,;EFCAB4A,downstream_gene_variant,,ENST00000528315,;EFCAB4A,downstream_gene_variant,,ENST00000530183,;CD151,upstream_gene_variant,,ENST00000525718,;CD151,upstream_gene_variant,,ENST00000397420,;CD151,upstream_gene_variant,,ENST00000322008,;CD151,upstream_gene_variant,,ENST00000529810,;CD151,upstream_gene_variant,,ENST00000397421,;AP006621.8,intron_variant,,ENST00000532946,;AP006621.8,upstream_gene_variant,,ENST00000528982,;EFCAB4A,non_coding_transcript_exon_variant,,ENST00000530737,;EFCAB4A,non_coding_transcript_exon_variant,,ENST00000530688,;EFCAB4A,non_coding_transcript_exon_variant,,ENST00000527763,;EFCAB4A,non_coding_transcript_exon_variant,,ENST00000528694,;CD151,upstream_gene_variant,,ENST00000530155,;PNPLA2,downstream_gene_variant,,ENST00000529255,;CD151,upstream_gene_variant,,ENST00000530726,;PNPLA2,downstream_gene_variant,,ENST00000525250,;CD151,upstream_gene_variant,,ENST00000531999,;EFCAB4A,upstream_gene_variant,,ENST00000526531,;EFCAB4A,downstream_gene_variant,,ENST00000534606,;EFCAB4A,downstream_gene_variant,,ENST00000534191,;CD151,upstream_gene_variant,,ENST00000526661,;CD151,upstream_gene_variant,,ENST00000525868,;	G	ENSG00000177685	ENST00000450448	Transcript	frameshift_variant	930-931	425-426	142	L/LX	ctg/ctGg	.	.	.	1	EFCAB4A	HGNC	28703	protein_coding	YES	CCDS41588.1	ENSP00000409256	EFC4A_HUMAN	E9PRE5_HUMAN,E9PPF3_HUMAN,E9PK04_HUMAN,E9PHZ8_HUMAN	UPI000045644C	.	.	.	4/9	.	hmmpanther:PTHR22621,hmmpanther:PTHR22621:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTGCTGGAGC	.	3	ESCA
KIAA1731	0	.	GRCh37	11	93440055	93440055	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5741A>G	p.Asp1914Gly	p.D1914G	ENST00000325212	18/30	32	29	3	57	57	0	KIAA1731,missense_variant,p.Asp94Gly,ENST00000344196,;KIAA1731,missense_variant,p.Asp1914Gly,ENST00000325212,;KIAA1731,missense_variant,p.Asp94Gly,ENST00000531700,;KIAA1731,missense_variant,p.Asp1914Gly,ENST00000411936,;KIAA1731,missense_variant,p.Asp94Gly,ENST00000530425,;	G	ENSG00000166004	ENST00000325212	Transcript	missense_variant	5903	5741	1914	D/G	gAt/gGt	.	.	.	1	KIAA1731	HGNC	29366	protein_coding	YES	CCDS44708.1	ENSP00000316681	K1731_HUMAN	E9PM20_HUMAN	UPI0000251F0E	.	tolerated(0.07)	benign(0.228)	18/30	.	hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTATGATGAAG	.	4	ESCA
PARPBP	0	.	GRCh37	12	102514034	102514034	+	5'UTR	SNP	A	A	G	rs564563291	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-34A>G	.	.	ENST00000358383	1/11	12	8	4	12	12	0	PARPBP,5_prime_UTR_variant,,ENST00000537257,;PARPBP,5_prime_UTR_variant,,ENST00000543784,;PARPBP,5_prime_UTR_variant,,ENST00000541394,;PARPBP,5_prime_UTR_variant,,ENST00000392911,;PARPBP,5_prime_UTR_variant,,ENST00000358383,;PARPBP,5_prime_UTR_variant,,ENST00000378128,;PARPBP,5_prime_UTR_variant,,ENST00000327680,;NUP37,upstream_gene_variant,,ENST00000550459,;NUP37,upstream_gene_variant,,ENST00000251074,;NUP37,upstream_gene_variant,,ENST00000551744,;PARPBP,upstream_gene_variant,,ENST00000417507,;NUP37,upstream_gene_variant,,ENST00000552283,;PARPBP,upstream_gene_variant,,ENST00000412715,;NUP37,upstream_gene_variant,,ENST00000543021,;PARPBP,upstream_gene_variant,,ENST00000541668,;NUP37,upstream_gene_variant,,ENST00000548994,;PARPBP,upstream_gene_variant,,ENST00000535811,;PARPBP,5_prime_UTR_variant,,ENST00000392909,;PARPBP,upstream_gene_variant,,ENST00000457614,;PARPBP,upstream_gene_variant,,ENST00000392914,;NUP37,upstream_gene_variant,,ENST00000551200,;	G	ENSG00000185480	ENST00000358383	Transcript	5_prime_UTR_variant	12	.	.	.	.	rs564563291	.	.	1	PARPBP	HGNC	26074	protein_coding	YES	CCDS9090.2	ENSP00000351153	PARI_HUMAN	.	UPI000004A06B	.	.	.	1/11	.	.	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTGAAGAGTA	by1000G	2	ESCA
C12orf23	0	.	GRCh37	12	107365611	107365611	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*442A>G	.	.	ENST00000280756	4/4	24	8	16	20	20	0	C12orf23,3_prime_UTR_variant,,ENST00000551813,;C12orf23,3_prime_UTR_variant,,ENST00000548125,;C12orf23,3_prime_UTR_variant,,ENST00000280756,;C12orf23,downstream_gene_variant,,ENST00000550344,;C12orf23,downstream_gene_variant,,ENST00000547081,;C12orf23,downstream_gene_variant,,ENST00000547242,;C12orf23,downstream_gene_variant,,ENST00000551489,;C12orf23,intron_variant,,ENST00000551237,;C12orf23,intron_variant,,ENST00000548806,;	G	ENSG00000151135	ENST00000280756	Transcript	3_prime_UTR_variant	1211	.	.	.	.	.	.	.	1	C12orf23	HGNC	28281	protein_coding	YES	CCDS9110.1	ENSP00000280756	CL023_HUMAN	.	UPI0000070E98	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTATAACC	.	5	ESCA
MED13L	0	.	GRCh37	12	116408453	116408453	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6013A>G	p.Ile2005Val	p.I2005V	ENST00000281928	27/31	79	33	46	46	46	0	MED13L,missense_variant,p.Ile2005Val,ENST00000281928,;MED13L,downstream_gene_variant,,ENST00000552447,;MED13L,downstream_gene_variant,,ENST00000548694,;MED13L,downstream_gene_variant,,ENST00000548784,;	C	ENSG00000123066	ENST00000281928	Transcript	missense_variant	6220	6013	2005	I/V	Atc/Gtc	.	.	.	-1	MED13L	HGNC	22962	protein_coding	YES	CCDS9177.1	ENSP00000281928	MD13L_HUMAN	Q9H6Z7_HUMAN	UPI0000241C1E	.	tolerated(1)	possibly_damaging(0.651)	27/31	.	Pfam_domain:PF06333,hmmpanther:PTHR12950,hmmpanther:PTHR12950:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGATGGTTG	.	5	ESCA
FBXO21	0	.	GRCh37	12	117595684	117595684	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1532A>C	p.His511Pro	p.H511P	ENST00000330622	10/12	32	23	9	31	31	0	FBXO21,missense_variant,p.His163Pro,ENST00000548840,;FBXO21,missense_variant,p.His388Pro,ENST00000550180,;FBXO21,missense_variant,p.His504Pro,ENST00000427718,;FBXO21,missense_variant,p.His511Pro,ENST00000330622,;FBXO21,non_coding_transcript_exon_variant,,ENST00000547806,;	G	ENSG00000135108	ENST00000330622	Transcript	missense_variant	1532	1532	511	H/P	cAt/cCt	.	.	.	-1	FBXO21	HGNC	13592	protein_coding	YES	CCDS9184.1	ENSP00000328187	FBX21_HUMAN	.	UPI000013CF6D	.	deleterious(0)	probably_damaging(1)	10/12	.	Superfamily_domains:0050131,SMART_domains:SM00992,TIGRFAM_domain:TIGR02097,Pfam_domain:PF08755,hmmpanther:PTHR31350,hmmpanther:PTHR31350:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCTTATGCTTC	.	4	ESCA
PTPRO	0	.	GRCh37	12	15734634	15734634	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000281171	23/27	32	26	6	30	30	0	PTPRO,missense_variant,p.Pro1024Ser,ENST00000348962,;PTPRO,missense_variant,p.Pro241Ser,ENST00000445537,;PTPRO,missense_variant,p.Pro213Ser,ENST00000542557,;PTPRO,missense_variant,p.Pro1052Ser,ENST00000281171,;PTPRO,missense_variant,p.Pro213Ser,ENST00000544244,;PTPRO,missense_variant,p.Pro31Ser,ENST00000535322,;PTPRO,missense_variant,p.Pro241Ser,ENST00000442921,;PTPRO,downstream_gene_variant,,ENST00000538907,;PTPRO,downstream_gene_variant,,ENST00000535311,;	T	ENSG00000151490	ENST00000281171	Transcript	missense_variant	3484	3154	1052	P/S	Cca/Tca	.	.	.	1	PTPRO	HGNC	9678	protein_coding	YES	CCDS8675.1	ENSP00000281171	PTPRO_HUMAN	B4DS16_HUMAN	UPI000013DC62	.	tolerated(0.07)	possibly_damaging(0.613)	23/27	.	PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF251,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGGCCATTC	.	4	ESCA
LRRK2	0	.	GRCh37	12	40618892	40618892	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-42C>A	.	.	ENST00000298910	1/51	17	7	9	27	27	0	LRRK2,5_prime_UTR_variant,,ENST00000343742,;LRRK2,5_prime_UTR_variant,,ENST00000298910,;LRRK2,intron_variant,,ENST00000416796,;AC079630.4,upstream_gene_variant,,ENST00000412812,;LRRK2,upstream_gene_variant,,ENST00000474202,;	A	ENSG00000188906	ENST00000298910	Transcript	5_prime_UTR_variant	17	.	.	.	.	.	.	.	1	LRRK2	HGNC	18618	protein_coding	YES	CCDS31774.1	ENSP00000298910	LRRK2_HUMAN	.	UPI00006C128E	.	.	.	1/51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGACGTTCA	.	5	ESCA
C12orf68	0	.	GRCh37	12	48579525	48579525	+	3'UTR	SNP	C	C	T	rs546043897	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1035C>T	.	.	ENST00000316554	1/1	66	41	24	73	73	0	C12orf68,3_prime_UTR_variant,,ENST00000316554,;ASB8,upstream_gene_variant,,ENST00000539503,;	T	ENSG00000177875	ENST00000316554	Transcript	3_prime_UTR_variant	2160	.	.	.	.	rs546043897	.	.	1	C12orf68	HGNC	33749	protein_coding	YES	CCDS31785.1	ENSP00000320849	CL068_HUMAN	.	UPI000006F320	.	.	.	1/1	.	.	T:0.0016	T:0	T:0	.	T:0.0079	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGGCGCTTT	byFrequency|by1000G	5	ESCA
KMT2D	0	.	GRCh37	12	49431645	49431646	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9493dupG	p.Asp3165GlyfsTer11	p.D3165Gfs*11	ENST00000301067	34/54	23	15	8	23	23	0	KMT2D,frameshift_variant,p.Asp3165GlyfsTer11,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,upstream_gene_variant,,ENST00000549743,;	C	ENSG00000167548	ENST00000301067	Transcript	frameshift_variant	9493-9494	9493-9494	3165	D/GX	gat/gGat	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	34/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGGTATCCCGG	.	3	ESCA
RACGAP1	0	.	GRCh37	12	50398047	50398047	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.466A>G	p.Ile156Val	p.I156V	ENST00000434422	6/18	29	19	10	27	27	0	RACGAP1,missense_variant,p.Ile156Val,ENST00000312377,;RACGAP1,missense_variant,p.Ile82Val,ENST00000546786,;RACGAP1,missense_variant,p.Ile156Val,ENST00000454520,;RACGAP1,missense_variant,p.Ile98Val,ENST00000551145,;RACGAP1,missense_variant,p.Ile156Val,ENST00000434422,;RACGAP1,missense_variant,p.Ile156Val,ENST00000548824,;RACGAP1,missense_variant,p.Ile156Val,ENST00000551016,;RACGAP1,missense_variant,p.Ile82Val,ENST00000550149,;RACGAP1,missense_variant,p.Ile98Val,ENST00000546595,;RACGAP1,missense_variant,p.Ile156Val,ENST00000547905,;RACGAP1,missense_variant,p.Ile156Val,ENST00000427314,;RACGAP1,missense_variant,p.Ile168Val,ENST00000548644,;RACGAP1,missense_variant,p.Ile156Val,ENST00000552310,;RACGAP1,intron_variant,,ENST00000548320,;RACGAP1,downstream_gene_variant,,ENST00000552157,;RACGAP1,downstream_gene_variant,,ENST00000546723,;RACGAP1,upstream_gene_variant,,ENST00000549342,;RACGAP1,downstream_gene_variant,,ENST00000552921,;RACGAP1,downstream_gene_variant,,ENST00000548247,;RACGAP1,downstream_gene_variant,,ENST00000551876,;RACGAP1,downstream_gene_variant,,ENST00000550651,;RACGAP1,downstream_gene_variant,,ENST00000546764,;RACGAP1,downstream_gene_variant,,ENST00000549777,;RACGAP1,downstream_gene_variant,,ENST00000552004,;RACGAP1,upstream_gene_variant,,ENST00000547061,;RACGAP1,3_prime_UTR_variant,,ENST00000551260,;RACGAP1,non_coding_transcript_exon_variant,,ENST00000548158,;RACGAP1,intron_variant,,ENST00000548598,;	C	ENSG00000161800	ENST00000434422	Transcript	missense_variant	768	466	156	I/V	Atc/Gtc	.	.	.	-1	RACGAP1	HGNC	9804	protein_coding	YES	CCDS8795.1	ENSP00000413241	RGAP1_HUMAN	F8W0L1_HUMAN,F8VZ66_HUMAN,F8VYH6_HUMAN,F8VWY4_HUMAN,F8VWX0_HUMAN,F8VV47_HUMAN,F8VV39_HUMAN,F8VV37_HUMAN,F8VUW9_HUMAN,F8VS54_HUMAN,F8VRL2_HUMAN,F8VRD2_HUMAN,F8VQZ5_HUMAN	UPI0000037CA0	.	deleterious(0.04)	probably_damaging(0.994)	6/18	.	hmmpanther:PTHR23174:SF7,hmmpanther:PTHR23174	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGATATCTG	.	5	ESCA
DAZAP2	0	.	GRCh37	12	51634217	51634218	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.105dupT	p.Thr36TyrfsTer89	p.T36Yfs*89	ENST00000549555	2/4	73	50	23	56	56	0	DAZAP2,frameshift_variant,p.Thr36TyrfsTer76,ENST00000425012,;DAZAP2,frameshift_variant,p.Thr36TyrfsTer89,ENST00000549555,;DAZAP2,frameshift_variant,p.Thr36TyrfsTer54,ENST00000449723,;DAZAP2,frameshift_variant,p.Thr36TyrfsTer117,ENST00000439799,;DAZAP2,frameshift_variant,p.Thr36TyrfsTer76,ENST00000604900,;DAZAP2,frameshift_variant,p.Thr36TyrfsTer76,ENST00000412716,;DAZAP2,frameshift_variant,p.Thr36TyrfsTer44,ENST00000549732,;DAZAP2,5_prime_UTR_variant,,ENST00000551313,;SMAGP,downstream_gene_variant,,ENST00000603864,;SMAGP,downstream_gene_variant,,ENST00000398453,;SMAGP,downstream_gene_variant,,ENST00000603798,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000552173,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000549497,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000551534,;DAZAP2,intron_variant,,ENST00000551919,;DAZAP2,frameshift_variant,p.Thr36TyrfsTer125,ENST00000436900,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000552459,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000549041,;SMAGP,downstream_gene_variant,,ENST00000380103,;	T	ENSG00000183283	ENST00000549555	Transcript	frameshift_variant	188-189	104-105	35	Y/YX	tat/taTt	.	.	.	1	DAZAP2	HGNC	2684	protein_coding	YES	CCDS44885.1	ENSP00000448051	DAZP2_HUMAN	.	UPI000183CBDB	.	.	.	2/4	.	Pfam_domain:PF11029,hmmpanther:PTHR31638:SF1,hmmpanther:PTHR31638	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCCTATACCG	.	3	ESCA
PLEKHG6	0	.	GRCh37	12	6427985	6427985	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1350G>A	p.%3D	p.K450K	ENST00000396988	12/16	55	35	19	50	50	0	PLEKHG6,synonymous_variant,p.%3D,ENST00000011684,;PLEKHG6,synonymous_variant,p.%3D,ENST00000536531,;PLEKHG6,synonymous_variant,p.%3D,ENST00000396988,;PLEKHG6,synonymous_variant,p.%3D,ENST00000449001,;PLEKHG6,upstream_gene_variant,,ENST00000304581,;PLEKHG6,non_coding_transcript_exon_variant,,ENST00000544743,;PLEKHG6,non_coding_transcript_exon_variant,,ENST00000535616,;PLEKHG6,downstream_gene_variant,,ENST00000543000,;	A	ENSG00000008323	ENST00000396988	Transcript	synonymous_variant	1580	1350	450	K	aaG/aaA	.	.	.	1	PLEKHG6	HGNC	25562	protein_coding	YES	CCDS8541.1	ENSP00000380185	PKHG6_HUMAN	.	UPI000013EFF6	.	.	.	12/16	.	PROSITE_profiles:PS50003,hmmpanther:PTHR22825:SF13,hmmpanther:PTHR22825,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAAGGTCAT	.	5	ESCA
CAND1	0	.	GRCh37	12	67700046	67700046	+	Silent	SNP	A	A	T	rs745695627	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2598A>T	p.%3D	p.S866S	ENST00000545606	10/15	25	13	12	21	21	0	CAND1,synonymous_variant,p.%3D,ENST00000545606,;CAND1,synonymous_variant,p.%3D,ENST00000544619,;CAND1,intron_variant,,ENST00000540319,;	T	ENSG00000111530	ENST00000545606	Transcript	synonymous_variant	3035	2598	866	S	tcA/tcT	rs745695627	.	.	1	CAND1	HGNC	30688	protein_coding	YES	CCDS8977.1	ENSP00000442318	CAND1_HUMAN	F5H6I6_HUMAN,B3KMG3_HUMAN	UPI0000037CC5	.	.	.	10/15	.	hmmpanther:PTHR12696:SF1,hmmpanther:PTHR12696,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCATCTCC	.	5	ESCA
CEP290	0	.	GRCh37	12	88477689	88477689	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4747A>T	p.Ile1583Phe	p.I1583F	ENST00000552810	36/54	17	12	5	30	30	0	CEP290,missense_variant,p.Ile1583Phe,ENST00000552810,;CEP290,missense_variant,p.Ile643Phe,ENST00000397838,;CEP290,missense_variant,p.Ile1585Phe,ENST00000309041,;CEP290,missense_variant,p.Ile643Phe,ENST00000547691,;	A	ENSG00000198707	ENST00000552810	Transcript	missense_variant	5091	4747	1583	I/F	Att/Ttt	.	.	.	-1	CEP290	HGNC	29021	protein_coding	YES	CCDS55858.1	ENSP00000448012	CE290_HUMAN	.	UPI0000D60D15	.	.	benign(0.354)	36/54	.	hmmpanther:PTHR18879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAATATGAA	.	5	ESCA
DUSP6	0	.	GRCh37	12	89742670	89742670	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*361A>G	.	.	ENST00000279488	3/3	23	11	12	20	20	0	DUSP6,3_prime_UTR_variant,,ENST00000279488,;DUSP6,3_prime_UTR_variant,,ENST00000308385,;DUSP6,downstream_gene_variant,,ENST00000547291,;DUSP6,downstream_gene_variant,,ENST00000548755,;DUSP6,downstream_gene_variant,,ENST00000547140,;	C	ENSG00000139318	ENST00000279488	Transcript	3_prime_UTR_variant	2739	.	.	.	.	.	.	.	-1	DUSP6	HGNC	3072	protein_coding	YES	CCDS9033.1	ENSP00000279488	DUS6_HUMAN	F8VZA4_HUMAN	UPI000013ED2F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGATGCAAA	.	5	ESCA
SACS	0	.	GRCh37	13	23912397	23912397	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5618A>G	p.Tyr1873Cys	p.Y1873C	ENST00000382298	10/10	17	4	12	18	18	0	SACS,missense_variant,p.Tyr1873Cys,ENST00000382292,;SACS,missense_variant,p.Tyr1123Cys,ENST00000402364,;SACS,missense_variant,p.Tyr1873Cys,ENST00000382298,;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,;	C	ENSG00000151835	ENST00000382298	Transcript	missense_variant	6207	5618	1873	Y/C	tAt/tGt	.	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	probably_damaging(0.998)	10/10	.	hmmpanther:PTHR15600:SF26,hmmpanther:PTHR15600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAAATAGCAA	.	5	ESCA
TDRD3	0	.	GRCh37	13	61103130	61103130	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1771G>A	p.Val591Ile	p.V591I	ENST00000535286	11/14	28	8	20	24	24	0	TDRD3,missense_variant,p.Val498Ile,ENST00000377894,;TDRD3,missense_variant,p.Val498Ile,ENST00000196169,;TDRD3,missense_variant,p.Val498Ile,ENST00000377881,;TDRD3,missense_variant,p.Val591Ile,ENST00000535286,;TDRD3,non_coding_transcript_exon_variant,,ENST00000471710,;TDRD3,downstream_gene_variant,,ENST00000484389,;	A	ENSG00000083544	ENST00000535286	Transcript	missense_variant	1843	1771	591	V/I	Gta/Ata	.	.	.	1	TDRD3	HGNC	20612	protein_coding	YES	CCDS53872.1	ENSP00000440190	TDRD3_HUMAN	B1AMN9_HUMAN	UPI000174200C	.	tolerated(0.29)	benign(0.003)	11/14	.	hmmpanther:PTHR13681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGTAGAA	.	4	ESCA
RCOR1	0	.	GRCh37	14	103195443	103195443	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2600A>G	.	.	ENST00000262241	12/12	39	27	11	50	50	0	RCOR1,3_prime_UTR_variant,,ENST00000262241,;RCOR1,3_prime_UTR_variant,,ENST00000570597,;RCOR1,downstream_gene_variant,,ENST00000560472,;	G	ENSG00000089902	ENST00000262241	Transcript	3_prime_UTR_variant	4284	.	.	.	.	.	.	.	1	RCOR1	HGNC	17441	protein_coding	YES	CCDS9974.2	ENSP00000262241	.	J3KN32_HUMAN	UPI0000D6A053	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTATATATAT	.	5	ESCA
EGLN3	0	.	GRCh37	14	34394893	34394893	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*204G>A	.	.	ENST00000250457	5/5	22	15	7	29	29	0	EGLN3,3_prime_UTR_variant,,ENST00000553215,;EGLN3,3_prime_UTR_variant,,ENST00000250457,;EGLN3,downstream_gene_variant,,ENST00000487915,;EGLN3,non_coding_transcript_exon_variant,,ENST00000556785,;	T	ENSG00000129521	ENST00000250457	Transcript	3_prime_UTR_variant	1253	.	.	.	.	.	.	.	-1	EGLN3	HGNC	14661	protein_coding	YES	CCDS9646.1	ENSP00000250457	EGLN3_HUMAN	Q3T1B0_HUMAN,A6XP73_HUMAN	UPI000004F8A8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTTCATCTG	.	5	ESCA
DIO2	0	.	GRCh37	14	80669418	80669418	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544C>A	p.Leu182Met	p.L182M	ENST00000555750	3/3	21	10	11	33	33	0	DIO2,missense_variant,p.Leu182Met,ENST00000555750,;DIO2,missense_variant,p.Asn20Lys,ENST00000557125,;DIO2,missense_variant,p.Leu146Met,ENST00000557010,;DIO2,missense_variant,p.Leu146Met,ENST00000438257,;DIO2,3_prime_UTR_variant,,ENST00000422005,;DIO2,3_prime_UTR_variant,,ENST00000556811,;DIO2,3_prime_UTR_variant,,ENST00000555844,;	T	ENSG00000211448	ENST00000555750	Transcript	missense_variant	572	544	182	L/M	Ctg/Atg	.	.	.	-1	DIO2	HGNC	2884	protein_coding	YES	CCDS55934.1	ENSP00000450980	.	Q9C0K2_HUMAN,G3V3A8_HUMAN	UPI000046D384	.	tolerated(0.09)	benign(0.249)	3/3	.	hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF3,Pfam_domain:PF00837,Gene3D:3.40.30.10,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCAGTTTGC	.	5	ESCA
NPAP1	0	.	GRCh37	15	24924081	24924081	+	Missense_Mutation	SNP	A	A	C	rs762162226	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3067A>C	p.Ser1023Arg	p.S1023R	ENST00000329468	1/1	22	17	5	33	33	0	NPAP1,missense_variant,p.Ser1023Arg,ENST00000329468,;	C	ENSG00000185823	ENST00000329468	Transcript	missense_variant	3541	3067	1023	S/R	Agc/Cgc	rs762162226	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	tolerated_low_confidence(0.14)	benign(0.095)	1/1	.	hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCAGCATG	.	5	ESCA
SNRPN	0	.	GRCh37	15	25219552	25219552	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-49G>A	.	.	ENST00000400100	7/13	63	46	16	73	73	0	SNRPN,5_prime_UTR_variant,,ENST00000400100,;SNRPN,5_prime_UTR_variant,,ENST00000400098,;SNRPN,5_prime_UTR_variant,,ENST00000584968,;SNURF,3_prime_UTR_variant,,ENST00000338094,;SNRPN,5_prime_UTR_variant,,ENST00000400097,;SNRPN,5_prime_UTR_variant,,ENST00000554227,;SNRPN,5_prime_UTR_variant,,ENST00000390687,;SNRPN,5_prime_UTR_variant,,ENST00000579070,;SNRPN,5_prime_UTR_variant,,ENST00000444203,;SNRPN,5_prime_UTR_variant,,ENST00000577565,;SNRPN,5_prime_UTR_variant,,ENST00000346403,;SNRPN,non_coding_transcript_exon_variant,,ENST00000553597,;SNURF,intron_variant,,ENST00000551312,;SNURF,intron_variant,,ENST00000580062,;SNURF,intron_variant,,ENST00000557230,;SNHG14,upstream_gene_variant,,ENST00000557108,;	A	ENSG00000128739	ENST00000400100	Transcript	5_prime_UTR_variant	842	.	.	.	.	.	.	.	1	SNRPN	HGNC	11164	protein_coding	YES	CCDS10017.1	ENSP00000382972	RSMN_HUMAN	Q9UKR4_HUMAN,Q6LBS1_HUMAN,J3QLE5_HUMAN,J3KRY3_HUMAN	UPI000002948A	.	.	.	7/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCAGAAGCA	.	5	ESCA
AP4E1	0	.	GRCh37	15	51250986	51250986	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1846T>C	p.%3D	p.L616L	ENST00000261842	14/21	32	28	3	27	27	0	AP4E1,synonymous_variant,p.%3D,ENST00000261842,;AP4E1,synonymous_variant,p.%3D,ENST00000560508,;AP4E1,3_prime_UTR_variant,,ENST00000558439,;AP4E1,3_prime_UTR_variant,,ENST00000561393,;	C	ENSG00000081014	ENST00000261842	Transcript	synonymous_variant	1952	1846	616	L	Ttg/Ctg	.	.	.	1	AP4E1	HGNC	573	protein_coding	YES	CCDS32240.1	ENSP00000261842	AP4E1_HUMAN	.	UPI00001D89D8	.	.	.	14/21	.	hmmpanther:PTHR22780:SF13,hmmpanther:PTHR22780,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGACTTGGTG	.	4	ESCA
C2CD4A	0	.	GRCh37	15	62362130	62362130	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1208T>C	.	.	ENST00000355522	2/2	16	8	8	17	17	0	C2CD4A,3_prime_UTR_variant,,ENST00000355522,;	C	ENSG00000198535	ENST00000355522	Transcript	3_prime_UTR_variant	2459	.	.	.	.	.	.	.	1	C2CD4A	HGNC	33627	protein_coding	YES	CCDS32258.1	ENSP00000347712	C2C4A_HUMAN	.	UPI0000140CF2	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCATTGAGA	.	5	ESCA
MAP2K5	0	.	GRCh37	15	67923233	67923233	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553C>G	p.His185Asp	p.H185D	ENST00000178640	9/22	37	18	18	26	26	0	MAP2K5,missense_variant,p.His185Asp,ENST00000395476,;MAP2K5,missense_variant,p.His185Asp,ENST00000178640,;MAP2K5,missense_variant,p.His118Asp,ENST00000439036,;MAP2K5,missense_variant,p.His149Asp,ENST00000354498,;MAP2K5,non_coding_transcript_exon_variant,,ENST00000559262,;MAP2K5,non_coding_transcript_exon_variant,,ENST00000560591,;MAP2K5,non_coding_transcript_exon_variant,,ENST00000558392,;HNRNPA1P5,downstream_gene_variant,,ENST00000558213,;	G	ENSG00000137764	ENST00000178640	Transcript	missense_variant	1180	553	185	H/D	Cat/Gat	.	.	.	1	MAP2K5	HGNC	6845	protein_coding	YES	CCDS10224.1	ENSP00000178640	MP2K5_HUMAN	H7BZL1_HUMAN	UPI0000072D4A	.	deleterious(0)	probably_damaging(0.993)	9/22	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24360:SF42,hmmpanther:PTHR24360,PROSITE_patterns:PS00107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATATCATGTC	.	5	ESCA
NPRL3	0	.	GRCh37	16	136688	136688	+	3'UTR	SNP	C	C	T	rs376243144	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*16G>A	.	.	ENST00000399953	14/14	26	10	16	22	22	0	NPRL3,3_prime_UTR_variant,,ENST00000399953,;NPRL3,3_prime_UTR_variant,,ENST00000399951,;MPG,downstream_gene_variant,,ENST00000436333,;MPG,downstream_gene_variant,,ENST00000356432,;MPG,downstream_gene_variant,,ENST00000397817,;MPG,downstream_gene_variant,,ENST00000219431,;Z69720.2,upstream_gene_variant,,ENST00000601483,;NPRL3,non_coding_transcript_exon_variant,,ENST00000405960,;NPRL3,non_coding_transcript_exon_variant,,ENST00000428323,;NPRL3,3_prime_UTR_variant,,ENST00000399957,;NPRL3,3_prime_UTR_variant,,ENST00000445810,;NPRL3,non_coding_transcript_exon_variant,,ENST00000463178,;	T	ENSG00000103148	ENST00000399953	Transcript	3_prime_UTR_variant	2126	.	.	.	.	rs376243144	.	.	-1	NPRL3	HGNC	14124	protein_coding	YES	.	ENSP00000382834	NPRL3_HUMAN	.	UPI00004568D2	.	.	.	14/14	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCCGCCCT	byCluster|by1000G	5	ESCA
UBE2I	0	.	GRCh37	16	1374899	1374900	+	3'UTR	INS	-	-	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*112dupG	.	.	ENST00000355803	7/7	23	17	6	22	22	0	UBE2I,3_prime_UTR_variant,,ENST00000406620,;UBE2I,3_prime_UTR_variant,,ENST00000566587,;UBE2I,3_prime_UTR_variant,,ENST00000325437,;UBE2I,3_prime_UTR_variant,,ENST00000397515,;UBE2I,3_prime_UTR_variant,,ENST00000403747,;UBE2I,3_prime_UTR_variant,,ENST00000355803,;UBE2I,3_prime_UTR_variant,,ENST00000397514,;UBE2I,downstream_gene_variant,,ENST00000567074,;UBE2I,downstream_gene_variant,,ENST00000402301,;LA16c-358B7.3,upstream_gene_variant,,ENST00000567829,;LA16c-358B7.3,upstream_gene_variant,,ENST00000568106,;UBE2I,downstream_gene_variant,,ENST00000568209,;UBE2I,downstream_gene_variant,,ENST00000568288,;UBE2I,downstream_gene_variant,,ENST00000566775,;UBE2I,downstream_gene_variant,,ENST00000568989,;RPS20P2,upstream_gene_variant,,ENST00000402520,;	G	ENSG00000103275	ENST00000355803	Transcript	3_prime_UTR_variant	1133-1134	.	.	.	.	.	.	.	1	UBE2I	HGNC	12485	protein_coding	YES	CCDS10433.1	ENSP00000348056	UBC9_HUMAN	H3BRD1_HUMAN,H3BQQ9_HUMAN	UPI00000010F8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCACCTGGGGG	.	2	ESCA
GP2	0	.	GRCh37	16	20327307	20327307	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1481T>C	p.Val494Ala	p.V494A	ENST00000381362	10/12	31	27	4	45	45	0	GP2,missense_variant,p.Val344Ala,ENST00000341642,;GP2,missense_variant,p.Val494Ala,ENST00000381362,;GP2,missense_variant,p.Val491Ala,ENST00000302555,;GP2,missense_variant,p.Val347Ala,ENST00000381360,;GP2,downstream_gene_variant,,ENST00000575582,;GP2,downstream_gene_variant,,ENST00000572478,;GP2,downstream_gene_variant,,ENST00000572347,;GP2,downstream_gene_variant,,ENST00000573897,;GP2,downstream_gene_variant,,ENST00000574982,;	G	ENSG00000169347	ENST00000381362	Transcript	missense_variant	1558	1481	494	V/A	gTt/gCt	.	.	.	-1	GP2	HGNC	4441	protein_coding	YES	CCDS42128.1	ENSP00000370767	GP2_HUMAN	I3L2Z7_HUMAN	UPI000059D333	.	tolerated(0.05)	benign(0.212)	10/12	.	hmmpanther:PTHR22962:SF129,hmmpanther:PTHR22962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTAGAACCCGG	.	4	ESCA
TRAF7	0	.	GRCh37	16	2225837	2225837	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1629C>T	p.%3D	p.I543I	ENST00000326181	18/21	30	18	11	19	19	0	TRAF7,synonymous_variant,p.%3D,ENST00000326181,;CASKIN1,downstream_gene_variant,,ENST00000343516,;TRAF7,downstream_gene_variant,,ENST00000567645,;TRAF7,downstream_gene_variant,,ENST00000570169,;TRAF7,downstream_gene_variant,,ENST00000569686,;TRAF7,downstream_gene_variant,,ENST00000564067,;	T	ENSG00000131653	ENST00000326181	Transcript	synonymous_variant	1761	1629	543	I	atC/atT	.	.	.	1	TRAF7	HGNC	20456	protein_coding	YES	CCDS10461.1	ENSP00000318944	TRAF7_HUMAN	H3BR17_HUMAN,D3DU86_HUMAN	UPI000014186F	.	.	.	18/21	.	PROSITE_profiles:PS50294,hmmpanther:PTHR22844:SF164,hmmpanther:PTHR22844,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATCTGGGA	.	5	ESCA
GGA2	0	.	GRCh37	16	23497446	23497446	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.688A>G	p.Lys230Glu	p.K230E	ENST00000309859	8/17	40	26	14	38	38	0	GGA2,missense_variant,p.Lys230Glu,ENST00000309859,;GGA2,intron_variant,,ENST00000567468,;GGA2,non_coding_transcript_exon_variant,,ENST00000567201,;GGA2,downstream_gene_variant,,ENST00000570111,;	C	ENSG00000103365	ENST00000309859	Transcript	missense_variant	771	688	230	K/E	Aag/Gag	.	.	.	-1	GGA2	HGNC	16064	protein_coding	YES	CCDS10611.1	ENSP00000311962	GGA2_HUMAN	H3BMN6_HUMAN	UPI000013EF46	.	deleterious(0.02)	possibly_damaging(0.626)	8/17	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50909,hmmpanther:PTHR13856:SF74,hmmpanther:PTHR13856,Pfam_domain:PF03127,Gene3D:1.20.58.160,Superfamily_domains:SSF89009	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTTGGACA	.	5	ESCA
ITGAX	0	.	GRCh37	16	31373951	31373951	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1236C>G	p.%3D	p.A412A	ENST00000268296	12/30	18	13	4	30	30	0	ITGAX,synonymous_variant,p.%3D,ENST00000562522,;ITGAX,synonymous_variant,p.%3D,ENST00000268296,;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000567409,;RP11-120K18.3,upstream_gene_variant,,ENST00000561830,;	G	ENSG00000140678	ENST00000268296	Transcript	synonymous_variant	1357	1236	412	A	gcC/gcG	.	.	.	1	ITGAX	HGNC	6152	protein_coding	YES	CCDS10711.1	ENSP00000268296	ITAX_HUMAN	B4DDX0_HUMAN	UPI00001C0366	.	.	.	12/30	.	Prints_domain:PR01185,Superfamily_domains:SSF69318,SMART_domains:SM00191,Gene3D:3nigC00,hmmpanther:PTHR23220:SF17,hmmpanther:PTHR23220,PROSITE_profiles:PS51470	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTGGCCCTCTG	.	4	ESCA
CIAPIN1	0	.	GRCh37	16	57468081	57468081	+	Missense_Mutation	SNP	C	C	T	rs200237459	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431G>A	p.Arg144Gln	p.R144Q	ENST00000394391	5/9	53	35	17	33	33	0	CIAPIN1,missense_variant,p.Arg144Gln,ENST00000394391,;CIAPIN1,missense_variant,p.Arg131Gln,ENST00000567518,;CIAPIN1,missense_variant,p.Arg144Gln,ENST00000569370,;CIAPIN1,missense_variant,p.Arg144Gln,ENST00000568940,;CIAPIN1,missense_variant,p.Arg144Gln,ENST00000569979,;CIAPIN1,missense_variant,p.Arg117Gln,ENST00000565961,;CIAPIN1,5_prime_UTR_variant,,ENST00000565786,;CIAPIN1,intron_variant,,ENST00000567751,;CIAPIN1,downstream_gene_variant,,ENST00000563341,;CIAPIN1,non_coding_transcript_exon_variant,,ENST00000565368,;CIAPIN1,non_coding_transcript_exon_variant,,ENST00000569246,;CIAPIN1,missense_variant,p.Arg144Gln,ENST00000570000,;CIAPIN1,non_coding_transcript_exon_variant,,ENST00000566284,;CIAPIN1,non_coding_transcript_exon_variant,,ENST00000563561,;CIAPIN1,upstream_gene_variant,,ENST00000564885,;	T	ENSG00000005194	ENST00000394391	Transcript	missense_variant	673	431	144	R/Q	cGa/cAa	rs200237459,COSM416964	.	.	-1	CIAPIN1	HGNC	28050	protein_coding	YES	CCDS10781.2	ENSP00000377914	CPIN1_HUMAN	H3BTZ8_HUMAN,H3BTT4_HUMAN,H3BQ23_HUMAN	UPI0000073D9C	.	tolerated(1)	benign(0.001)	5/9	.	HAMAP:MF_03115,hmmpanther:PTHR13273	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTCGAACA	byCluster|by1000G	5	ESCA
SLC38A7	0	.	GRCh37	16	58701331	58701331	+	Silent	SNP	G	G	A	rs766024243	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1347C>T	p.%3D	p.G449G	ENST00000570101	11/11	27	21	5	24	24	0	SLC38A7,missense_variant,p.Ala315Val,ENST00000564100,;SLC38A7,synonymous_variant,p.%3D,ENST00000564010,;SLC38A7,synonymous_variant,p.%3D,ENST00000219320,;SLC38A7,synonymous_variant,p.%3D,ENST00000570101,;SLC38A7,non_coding_transcript_exon_variant,,ENST00000566953,;SLC38A7,3_prime_UTR_variant,,ENST00000566598,;SLC38A7,downstream_gene_variant,,ENST00000562149,;SLC38A7,downstream_gene_variant,,ENST00000565785,;SLC38A7,downstream_gene_variant,,ENST00000569209,;	A	ENSG00000103042	ENST00000570101	Transcript	synonymous_variant	2231	1347	449	G	ggC/ggT	rs766024243	.	.	-1	SLC38A7	HGNC	25582	protein_coding	YES	CCDS10800.1	ENSP00000454646	S38A7_HUMAN	H3BRZ0_HUMAN,H3BPV9_HUMAN,H3BPK8_HUMAN,H3BN87_HUMAN	UPI000004EC72	.	.	.	11/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGGCCGAA	.	5	ESCA
RANBP10	0	.	GRCh37	16	67760012	67760012	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*319C>T	.	.	ENST00000317506	14/14	49	30	19	19	19	0	RANBP10,3_prime_UTR_variant,,ENST00000317506,;RANBP10,3_prime_UTR_variant,,ENST00000536251,;RANBP10,3_prime_UTR_variant,,ENST00000602677,;RANBP10,3_prime_UTR_variant,,ENST00000411657,;RANBP10,3_prime_UTR_variant,,ENST00000448631,;RANBP10,downstream_gene_variant,,ENST00000425512,;RANBP10,3_prime_UTR_variant,,ENST00000602506,;RANBP10,downstream_gene_variant,,ENST00000602638,;RANBP10,downstream_gene_variant,,ENST00000602525,;	A	ENSG00000141084	ENST00000317506	Transcript	3_prime_UTR_variant	2298	.	.	.	.	.	.	.	-1	RANBP10	HGNC	29285	protein_coding	YES	CCDS32469.1	ENSP00000316589	RBP10_HUMAN	B3KP49_HUMAN	UPI00001C1FA6	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCAGTCAGG	.	5	ESCA
ESRP2	0	.	GRCh37	16	68266687	68266688	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686dupA	p.Gln230AlafsTer12	p.Q230Afs*12	ENST00000473183	6/15	24	9	14	18	18	0	ESRP2,frameshift_variant,p.Gln230AlafsTer12,ENST00000473183,;ESRP2,frameshift_variant,p.Gln230AlafsTer10,ENST00000565858,;NFATC3,downstream_gene_variant,,ENST00000346183,;ESRP2,downstream_gene_variant,,ENST00000562724,;NFATC3,downstream_gene_variant,,ENST00000329524,;NFATC3,downstream_gene_variant,,ENST00000349223,;ESRP2,downstream_gene_variant,,ENST00000564382,;RP11-96D1.11,upstream_gene_variant,,ENST00000571197,;RP11-96D1.6,downstream_gene_variant,,ENST00000564147,;ESRP2,frameshift_variant,p.Gln12AlafsTer12,ENST00000566774,;ESRP2,non_coding_transcript_exon_variant,,ENST00000562738,;ESRP2,non_coding_transcript_exon_variant,,ENST00000251366,;ESRP2,downstream_gene_variant,,ENST00000562567,;ESRP2,downstream_gene_variant,,ENST00000564465,;ESRP2,downstream_gene_variant,,ENST00000563159,;ESRP2,downstream_gene_variant,,ENST00000569964,;ESRP2,upstream_gene_variant,,ENST00000565213,;	T	ENSG00000103067	ENST00000473183	Transcript	frameshift_variant	1225-1226	686-687	229	K/KX	aag/aaAg	.	.	.	-1	ESRP2	HGNC	26152	protein_coding	YES	CCDS10863.1	ENSP00000418748	ESRP2_HUMAN	J3QQJ9_HUMAN,J3KRF2_HUMAN	UPI000006FB08	.	.	.	6/15	.	hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTCTGCTTTAT	.	2	ESCA
CLEC18B	0	.	GRCh37	16	74452168	74452168	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245C>T	p.Ala82Val	p.A82V	ENST00000339953	3/13	43	37	6	40	40	0	CLEC18B,missense_variant,p.Ala82Val,ENST00000339953,;RP11-252A24.5,upstream_gene_variant,,ENST00000566506,;RP11-252A24.5,upstream_gene_variant,,ENST00000567148,;CLEC18B,intron_variant,,ENST00000425714,;	A	ENSG00000140839	ENST00000339953	Transcript	missense_variant	367	245	82	A/V	gCt/gTt	.	.	.	-1	CLEC18B	HGNC	33849	protein_coding	YES	CCDS32484.1	ENSP00000341051	CL18B_HUMAN	.	UPI000025210E	.	deleterious(0)	probably_damaging(0.96)	3/13	.	Low_complexity_(Seg):seg,Prints_domain:PR00837,Superfamily_domains:SSF55797,SMART_domains:SM00198,Gene3D:3.40.33.10,Pfam_domain:PF00188,hmmpanther:PTHR10334:SF180,hmmpanther:PTHR10334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTTGAGCCAGT	.	2	ESCA
MYO18A	0	.	GRCh37	17	27448072	27448072	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1529A>G	p.His510Arg	p.H510R	ENST00000527372	6/42	50	30	19	70	70	0	MYO18A,missense_variant,p.His510Arg,ENST00000527372,;MYO18A,missense_variant,p.His510Arg,ENST00000533112,;MYO18A,missense_variant,p.His510Arg,ENST00000354329,;MYO18A,missense_variant,p.His510Arg,ENST00000531253,;MYO18A,downstream_gene_variant,,ENST00000528564,;MYO18A,non_coding_transcript_exon_variant,,ENST00000590242,;MYO18A,downstream_gene_variant,,ENST00000531267,;MYO18A,downstream_gene_variant,,ENST00000533420,;MYO18A,downstream_gene_variant,,ENST00000585573,;MYO18A,3_prime_UTR_variant,,ENST00000530254,;MYO18A,downstream_gene_variant,,ENST00000528322,;MYO18A,upstream_gene_variant,,ENST00000588791,;	C	ENSG00000196535	ENST00000527372	Transcript	missense_variant	1710	1529	510	H/R	cAt/cGt	.	.	.	-1	MYO18A	HGNC	31104	protein_coding	YES	CCDS45642.1	ENSP00000437073	MY18A_HUMAN	.	UPI0000167F32	.	tolerated(0.13)	benign(0.232)	6/42	.	Prints_domain:PR00193,Superfamily_domains:SSF52540,SMART_domains:SM00242,Gene3D:3.40.50.300,Pfam_domain:PF00063,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF293,PROSITE_profiles:PS51456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGATGCTGG	.	5	ESCA
TMIGD1	0	.	GRCh37	17	28656289	28656289	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.341C>T	p.Ser114Leu	p.S114L	ENST00000328886	3/7	35	26	9	42	42	0	TMIGD1,missense_variant,p.Ser114Leu,ENST00000328886,;TMIGD1,missense_variant,p.Ser114Leu,ENST00000538566,;	A	ENSG00000182271	ENST00000328886	Transcript	missense_variant	414	341	114	S/L	tCg/tTg	.	.	.	-1	TMIGD1	HGNC	32431	protein_coding	YES	CCDS32605.1	ENSP00000332404	TMIG1_HUMAN	.	UPI00001D6918	.	deleterious(0)	probably_damaging(0.922)	3/7	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCGAAACG	.	5	ESCA
NF1	0	.	GRCh37	17	29554303	29554303	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2319C>T	p.%3D	p.N773N	ENST00000358273	19/58	20	9	11	27	27	0	NF1,synonymous_variant,p.%3D,ENST00000456735,;NF1,synonymous_variant,p.%3D,ENST00000358273,;NF1,synonymous_variant,p.%3D,ENST00000356175,;NF1,downstream_gene_variant,,ENST00000431387,;NF1,synonymous_variant,p.%3D,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000493220,;	T	ENSG00000196712	ENST00000358273	Transcript	synonymous_variant	2702	2319	773	N	aaC/aaT	.	.	.	1	NF1	HGNC	7765	protein_coding	YES	CCDS42292.1	ENSP00000351015	NF1_HUMAN	Q9UMU3_HUMAN,Q4W6X4_HUMAN,K7EP94_HUMAN	UPI000012FFAE	.	.	.	19/58	.	hmmpanther:PTHR10194:SF60,hmmpanther:PTHR10194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAACACTGA	.	5	ESCA
LRRC37B	0	.	GRCh37	17	30374917	30374917	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2380G>T	p.Gly794Trp	p.G794W	ENST00000341671	9/12	93	56	37	92	92	0	LRRC37B,missense_variant,p.Gly47Trp,ENST00000582117,;LRRC37B,missense_variant,p.Gly821Trp,ENST00000327564,;LRRC37B,missense_variant,p.Gly755Trp,ENST00000584368,;LRRC37B,missense_variant,p.Gly743Trp,ENST00000394713,;LRRC37B,missense_variant,p.Gly712Trp,ENST00000543378,;LRRC37B,missense_variant,p.Gly794Trp,ENST00000341671,;LRRC37B,3_prime_UTR_variant,,ENST00000578674,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000579094,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000578118,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000581086,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000583758,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000582815,;LRRC37B,upstream_gene_variant,,ENST00000579766,;	T	ENSG00000185158	ENST00000341671	Transcript	missense_variant	2385	2380	794	G/W	Ggg/Tgg	COSM1242479	.	.	1	LRRC37B	HGNC	29070	protein_coding	YES	CCDS32609.1	ENSP00000340519	LR37B_HUMAN	J3QL10_HUMAN,F5H5K1_HUMAN	UPI000044D37B	.	tolerated(0.19)	probably_damaging(0.979)	9/12	.	hmmpanther:PTHR23045:SF5,hmmpanther:PTHR23045	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTTGGGGGT	.	5	ESCA
PLXDC1	0	.	GRCh37	17	37237471	37237471	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990-2054A>G	.	.	ENST00000315392	.	14	9	5	24	24	0	PLXDC1,intron_variant,,ENST00000579279,;PLXDC1,intron_variant,,ENST00000539608,;PLXDC1,intron_variant,,ENST00000444911,;PLXDC1,intron_variant,,ENST00000315392,;PLXDC1,downstream_gene_variant,,ENST00000394316,;AC091178.1,downstream_gene_variant,,ENST00000410562,;CTD-2206N4.4,non_coding_transcript_exon_variant,,ENST00000583447,;CTD-2206N4.4,intron_variant,,ENST00000578423,;PLXDC1,intron_variant,,ENST00000493200,;PLXDC1,intron_variant,,ENST00000578517,;PLXDC1,intron_variant,,ENST00000394318,;PLXDC1,intron_variant,,ENST00000578390,;PLXDC1,intron_variant,,ENST00000461225,;PLXDC1,upstream_gene_variant,,ENST00000579417,;PLXDC1,upstream_gene_variant,,ENST00000582025,;	C	ENSG00000161381	ENST00000315392	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PLXDC1	HGNC	20945	protein_coding	YES	CCDS11333.1	ENSP00000323927	PLDX1_HUMAN	J3QR40_HUMAN,C9JWQ3_HUMAN,C9JCL2_HUMAN	UPI0000049814	.	.	.	.	9/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GACTATTCTGC	.	4	ESCA
TP53	0	.	GRCh37	17	7578370	7578370	+	Splice_Site	SNP	C	C	A	.	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559+1G>T	.	p.X187_splice	ENST00000269305	.	40	2	37	26	26	0	TP53,splice_donor_variant,,ENST00000413465,;TP53,splice_donor_variant,,ENST00000420246,;TP53,splice_donor_variant,,ENST00000269305,;TP53,splice_donor_variant,,ENST00000509690,;TP53,splice_donor_variant,,ENST00000359597,;TP53,splice_donor_variant,,ENST00000514944,;TP53,splice_donor_variant,,ENST00000445888,;TP53,splice_donor_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,splice_donor_variant,,ENST00000574684,;TP53,splice_donor_variant,,ENST00000504937,;TP53,splice_donor_variant,,ENST00000505014,;TP53,splice_donor_variant,,ENST00000504290,;TP53,splice_donor_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	splice_donor_variant	.	.	.	.	.	TP53_g.12548G>C,TP53_g.12548G>T,TP53_g.12548G>A,COSM6901,COSM44268,COSM33648,COSM131534,COSM437533,COSM254992,COSM131535,COSM254991,COSM437534,COSM437536,COSM131537,COSM254993,COSM3388354,COSM3932745,COSM1756958,COSM2744800,COSM1649387,COSM131536,COSM254994,COSM437535	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	5/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.559+1G>T|7,SITE|p.?|c.163+1G>T|3,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.?|c.559+2T>G|5,BUFFER|p.?|c.559+1G>A|4,BUFFER|p.?|c.559+1G>A|11,BUFFER|p.?|c.559+1G>A|25,BUFFER|p.?|c.163+1G>C|3,BUFFER|p.?|c.559+1G>C|3,BUFFER|p.?|c.559+1G>A|4,BUFFER|p.?|c.163+1G>A|11,BUFFER|p.?|c.280+1G>C|3,BUFFER|p.?|c.559+1G>C|3,BUFFER|p.?|c.559+1G>A|11,BUFFER|p.?|c.559+1G>C|4,BUFFER|p.?|c.280+1G>A|11,BUFFER|p.G187S|c.559G>A|3,BUFFER|p.G187S|c.559G>A|17,BUFFER|p.G55S|c.163G>A|3,BUFFER|p.G94S|c.280G>A|3,BUFFER|p.G187S|c.559G>A|3,BUFFER|p.D186fs*61|c.556delG|3,BUFFER|p.D186G|c.557A>G|4,BUFFER|p.D54G|c.161A>G|4,BUFFER|p.D186G|c.557A>G|4,BUFFER|p.D186G|c.557A>G|5,BUFFER|p.D93G|c.278A>G|4,BUFFER|p.D186N|c.556G>A|5,BUFFER|p.D186H|c.556G>C|4,BUFFER|p.S185R|c.555C>A|4,BUFFER|p.S185S|c.555C>T|3,BUFFER|p.D184H|c.550G>C|6,BUFFER|p.D184N|c.550G>A|14,BUFFER|p.D184Y|c.550G>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCACCATCG	.	5	ESCA
POTEC	0	.	GRCh37	18	14542753	14542753	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393G>A	p.%3D	p.P131P	ENST00000358970	1/11	140	105	35	182	182	0	POTEC,synonymous_variant,p.%3D,ENST00000358970,;POTEC,non_coding_transcript_exon_variant,,ENST00000389891,;POTEC,synonymous_variant,p.%3D,ENST00000511306,;	T	ENSG00000183206	ENST00000358970	Transcript	synonymous_variant	393	393	131	P	ccG/ccA	.	.	.	-1	POTEC	HGNC	33894	protein_coding	YES	CCDS45835.1	ENSP00000351856	POTEC_HUMAN	.	UPI0000197B83	.	.	.	1/11	.	hmmpanther:PTHR24118:SF38,hmmpanther:PTHR24118,Gene3D:1.25.40.20,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E130K|c.388G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCGGCTC	.	5	ESCA
SMCHD1	0	.	GRCh37	18	2688439	2688439	+	Missense_Mutation	SNP	A	A	G	rs371805529	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686A>G	p.Asn229Ser	p.N229S	ENST00000320876	6/48	43	21	21	50	50	0	SMCHD1,missense_variant,p.Asn229Ser,ENST00000320876,;SMCHD1,missense_variant,p.Asn229Ser,ENST00000261598,;RP11-703M24.5,downstream_gene_variant,,ENST00000583546,;SMCHD1,upstream_gene_variant,,ENST00000581226,;	G	ENSG00000101596	ENST00000320876	Transcript	missense_variant	1024	686	229	N/S	aAt/aGt	rs371805529	.	.	1	SMCHD1	HGNC	29090	protein_coding	YES	CCDS45822.1	ENSP00000326603	SMHD1_HUMAN	.	UPI00001D7AAD	.	deleterious(0.01)	possibly_damaging(0.559)	6/48	.	hmmpanther:PTHR22640:SF2,hmmpanther:PTHR22640,Pfam_domain:PF13589,Gene3D:3.30.565.10,Superfamily_domains:SSF55874	.	.	.	.	.	.	.	G:0.0003	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAAATAGTG	.	5	ESCA
SLC14A1	0	.	GRCh37	18	43310429	43310429	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312G>A	p.%3D	p.Q104Q	ENST00000436407	2/9	16	11	4	19	19	0	SLC14A1,synonymous_variant,p.%3D,ENST00000589700,;SLC14A1,synonymous_variant,p.%3D,ENST00000436407,;SLC14A1,synonymous_variant,p.%3D,ENST00000586142,;SLC14A1,synonymous_variant,p.%3D,ENST00000586951,;SLC14A1,synonymous_variant,p.%3D,ENST00000589891,;SLC14A1,synonymous_variant,p.%3D,ENST00000321925,;SLC14A1,synonymous_variant,p.%3D,ENST00000586056,;SLC14A1,synonymous_variant,p.%3D,ENST00000415427,;SLC14A1,intron_variant,,ENST00000589322,;SLC14A1,intron_variant,,ENST00000535474,;SLC14A1,intron_variant,,ENST00000587601,;SLC14A1,intron_variant,,ENST00000590246,;SLC14A1,intron_variant,,ENST00000402943,;SLC14A1,intron_variant,,ENST00000502059,;SLC14A1,upstream_gene_variant,,ENST00000590377,;RP11-116O18.3,intron_variant,,ENST00000589510,;RP11-116O18.3,downstream_gene_variant,,ENST00000586213,;SLC14A1,non_coding_transcript_exon_variant,,ENST00000591943,;SLC14A1,synonymous_variant,p.%3D,ENST00000588179,;SLC14A1,upstream_gene_variant,,ENST00000591642,;	A	ENSG00000141469	ENST00000436407	Transcript	synonymous_variant	859	312	104	Q	caG/caA	.	.	.	1	SLC14A1	HGNC	10918	protein_coding	YES	CCDS45860.1	ENSP00000390637	UT1_HUMAN	G0W2N5_HUMAN,Q96KQ5_HUMAN,Q8WXW8_HUMAN,Q71UV7_HUMAN,M0QYS8_HUMAN,M0QX00_HUMAN,K7ESL3_HUMAN,K7ELI3_HUMAN,K7EL30_HUMAN,K7EKN6_HUMAN,K7EJ54_HUMAN,J7FHA1_HUMAN,G3K397_HUMAN,F5GWS2_HUMAN,B4DFJ8_HUMAN	UPI0000201C67	.	.	.	2/9	.	hmmpanther:PTHR10464,Gene3D:1.10.3430.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AACCAGCTTAA	.	3	ESCA
SLC25A42	0	.	GRCh37	19	19223641	19223641	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1956T>C	.	.	ENST00000318596	8/8	59	33	26	50	50	0	SLC25A42,3_prime_UTR_variant,,ENST00000318596,;SLC25A42,downstream_gene_variant,,ENST00000600275,;SLC25A42,downstream_gene_variant,,ENST00000596819,;	C	ENSG00000181035	ENST00000318596	Transcript	3_prime_UTR_variant	3064	.	.	.	.	.	.	.	1	SLC25A42	HGNC	28380	protein_coding	YES	CCDS32966.1	ENSP00000326693	S2542_HUMAN	.	UPI0000198748	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTATATATT	.	5	ESCA
ZNF726	0	.	GRCh37	19	24097771	24097771	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-26G>C	.	.	ENST00000594466	1/4	51	32	19	35	35	0	ZNF726,5_prime_UTR_variant,,ENST00000322487,;ZNF726,5_prime_UTR_variant,,ENST00000531821,;ZNF726,5_prime_UTR_variant,,ENST00000334589,;ZNF726,5_prime_UTR_variant,,ENST00000525354,;ZNF726,5_prime_UTR_variant,,ENST00000575986,;ZNF726,5_prime_UTR_variant,,ENST00000594466,;CTB-92J24.3,downstream_gene_variant,,ENST00000596326,;	C	ENSG00000213967	ENST00000594466	Transcript	5_prime_UTR_variant	80	.	.	.	.	.	.	.	1	ZNF726	HGNC	32462	protein_coding	YES	CCDS59372.1	ENSP00000471516	.	M0R0X8_HUMAN	UPI0002255F7F	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTGTGACC	.	5	ESCA
LMNB2	0	.	GRCh37	19	2434295	2434295	+	Missense_Mutation	SNP	C	C	G	rs764433406	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1200G>C	p.Glu400Asp	p.E400D	ENST00000325327	7/12	32	17	14	29	29	0	LMNB2,missense_variant,p.Glu380Asp,ENST00000582871,;LMNB2,missense_variant,p.Glu400Asp,ENST00000325327,;LMNB2,non_coding_transcript_exon_variant,,ENST00000527409,;LMNB2,upstream_gene_variant,,ENST00000532465,;LMNB2,downstream_gene_variant,,ENST00000534495,;LMNB2,upstream_gene_variant,,ENST00000475819,;LMNB2,splice_region_variant,,ENST00000490554,;	G	ENSG00000176619	ENST00000325327	Transcript	missense_variant	1263	1200	400	E/D	gaG/gaC	rs764433406	.	.	-1	LMNB2	HGNC	6638	protein_coding	YES	CCDS12090.2	ENSP00000327054	.	J9JID7_HUMAN	UPI000059D625	.	deleterious(0.05)	benign(0.05)	7/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF152,hmmpanther:PTHR23239,Pfam_domain:PF00038,Gene3D:1.20.5.170	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCTCCTC	.	5	ESCA
CEBPG	0	.	GRCh37	19	33870773	33870774	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*177dupT	.	.	ENST00000284000	2/2	27	14	13	14	14	0	CEBPG,3_prime_UTR_variant,,ENST00000585933,;CEBPG,3_prime_UTR_variant,,ENST00000284000,;	T	ENSG00000153879	ENST00000284000	Transcript	3_prime_UTR_variant	1290-1291	.	.	.	.	.	.	.	1	CEBPG	HGNC	1837	protein_coding	YES	CCDS12432.1	ENSP00000284000	CEBPG_HUMAN	K7ELC9_HUMAN	UPI00001274A6	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTGTAATTCGA	.	2	ESCA
PPFIA3	0	.	GRCh37	19	49652529	49652529	+	Missense_Mutation	SNP	G	G	A	rs759007680	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3301G>A	p.Glu1101Lys	p.E1101K	ENST00000334186	27/30	35	26	9	46	46	0	PPFIA3,missense_variant,p.Glu1101Lys,ENST00000334186,;PPFIA3,missense_variant,p.Glu1092Lys,ENST00000602351,;PPFIA3,missense_variant,p.Glu150Lys,ENST00000602897,;PPFIA3,missense_variant,p.Glu184Lys,ENST00000602848,;HRC,downstream_gene_variant,,ENST00000598858,;HRC,downstream_gene_variant,,ENST00000595625,;HRC,downstream_gene_variant,,ENST00000252825,;PPFIA3,3_prime_UTR_variant,,ENST00000602655,;PPFIA3,non_coding_transcript_exon_variant,,ENST00000602905,;PPFIA3,upstream_gene_variant,,ENST00000602783,;HRC,downstream_gene_variant,,ENST00000595167,;PPFIA3,downstream_gene_variant,,ENST00000602800,;	A	ENSG00000177380	ENST00000334186	Transcript	missense_variant	3650	3301	1101	E/K	Gag/Aag	rs759007680	.	.	1	PPFIA3	HGNC	9247	protein_coding	YES	CCDS12758.1	ENSP00000335614	LIPA3_HUMAN	R4GNF1_HUMAN	UPI00001AE464	.	deleterious(0)	possibly_damaging(0.633)	27/30	.	PROSITE_profiles:PS50105,hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF4,Pfam_domain:PF07647,SMART_domains:SM00454,Superfamily_domains:SSF47769	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGGAGAAG	byFrequency	5	ESCA
ZNF611	0	.	GRCh37	19	53207544	53207544	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*646A>G	.	.	ENST00000543227	6/6	16	7	8	33	33	0	ZNF611,3_prime_UTR_variant,,ENST00000453741,;ZNF611,3_prime_UTR_variant,,ENST00000543227,;ZNF611,3_prime_UTR_variant,,ENST00000319783,;ZNF611,3_prime_UTR_variant,,ENST00000602162,;ZNF611,3_prime_UTR_variant,,ENST00000540744,;ZNF611,downstream_gene_variant,,ENST00000596702,;ZNF611,downstream_gene_variant,,ENST00000600943,;ZNF611,downstream_gene_variant,,ENST00000595798,;ZNF611,downstream_gene_variant,,ENST00000601643,;ZNF611,downstream_gene_variant,,ENST00000602046,;ZNF611,3_prime_UTR_variant,,ENST00000595001,;ZNF611,downstream_gene_variant,,ENST00000601249,;ZNF611,downstream_gene_variant,,ENST00000597343,;ZNF611,downstream_gene_variant,,ENST00000598639,;ZNF611,downstream_gene_variant,,ENST00000598723,;	C	ENSG00000213020	ENST00000543227	Transcript	3_prime_UTR_variant	3039	.	.	.	.	.	.	.	-1	ZNF611	HGNC	28766	protein_coding	YES	CCDS12855.1	ENSP00000437616	ZN611_HUMAN	M0QYR0_HUMAN	UPI00001406C1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAATTTTCT	.	5	ESCA
ZNF543	0	.	GRCh37	19	57839161	57839161	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331G>A	p.Gly111Arg	p.G111R	ENST00000321545	4/4	26	19	6	35	35	0	ZNF543,missense_variant,p.Gly111Arg,ENST00000321545,;	A	ENSG00000178229	ENST00000321545	Transcript	missense_variant	676	331	111	G/R	Gga/Aga	.	.	.	1	ZNF543	HGNC	25281	protein_coding	YES	CCDS33130.1	ENSP00000322545	ZN543_HUMAN	.	UPI00001D8197	.	tolerated(0.49)	benign(0.011)	4/4	.	hmmpanther:PTHR24384:SF99,hmmpanther:PTHR24384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAAGGAGCC	.	5	ESCA
ZNF134	0	.	GRCh37	19	58131694	58131694	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207G>T	p.Gln69His	p.Q69H	ENST00000396161	3/3	34	20	13	46	46	0	ZNF134,missense_variant,p.Gln69His,ENST00000396161,;ZNF134,downstream_gene_variant,,ENST00000600883,;ZNF134,downstream_gene_variant,,ENST00000600344,;AC003682.16,upstream_gene_variant,,ENST00000599190,;ZNF134,non_coding_transcript_exon_variant,,ENST00000597975,;	T	ENSG00000213762	ENST00000396161	Transcript	missense_variant	517	207	69	Q/H	caG/caT	.	.	.	1	ZNF134	HGNC	12918	protein_coding	YES	CCDS42638.1	ENSP00000379464	ZN134_HUMAN	M0QXC7_HUMAN	UPI0000071FFE	.	deleterious(0.04)	benign(0.018)	3/3	.	hmmpanther:PTHR24399:SF4,hmmpanther:PTHR24399,PROSITE_patterns:PS00028,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCAGGGTAC	.	5	ESCA
ZNF274	0	.	GRCh37	19	58718140	58718140	+	Missense_Mutation	SNP	C	C	T	rs201074514	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310C>T	p.Pro104Ser	p.P104S	ENST00000326804	5/9	62	30	32	60	60	0	ZNF274,missense_variant,p.Pro104Ser,ENST00000594839,;ZNF274,missense_variant,p.Pro72Ser,ENST00000345813,;ZNF274,missense_variant,p.Pro104Ser,ENST00000326804,;ZNF274,5_prime_UTR_variant,,ENST00000424679,;ZNF274,non_coding_transcript_exon_variant,,ENST00000595772,;ZNF274,non_coding_transcript_exon_variant,,ENST00000599438,;ZNF274,non_coding_transcript_exon_variant,,ENST00000597818,;ZNF274,non_coding_transcript_exon_variant,,ENST00000601777,;ZNF274,downstream_gene_variant,,ENST00000601995,;ZNF274,non_coding_transcript_exon_variant,,ENST00000599081,;ZNF274,non_coding_transcript_exon_variant,,ENST00000598143,;ZNF274,non_coding_transcript_exon_variant,,ENST00000601156,;ZNF274,upstream_gene_variant,,ENST00000595146,;	T	ENSG00000171606	ENST00000326804	Transcript	missense_variant	769	310	104	P/S	Ccc/Tcc	rs201074514	.	.	1	ZNF274	HGNC	13068	protein_coding	YES	.	ENSP00000321209	ZN274_HUMAN	M0QY30_HUMAN,M0QXW4_HUMAN	UPI000013D855	.	deleterious(0.01)	probably_damaging(0.996)	5/9	.	hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF47	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0.0003	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGTCCCCTA	byCluster|by1000G	5	ESCA
HIAT1	0	.	GRCh37	1	100547882	100547882	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*117A>G	.	.	ENST00000370152	12/12	15	9	6	24	24	0	HIAT1,3_prime_UTR_variant,,ENST00000370152,;SASS6,downstream_gene_variant,,ENST00000535161,;SASS6,downstream_gene_variant,,ENST00000287482,;RP4-714D9.2,intron_variant,,ENST00000432294,;SASS6,downstream_gene_variant,,ENST00000462159,;	G	ENSG00000156875	ENST00000370152	Transcript	3_prime_UTR_variant	1726	.	.	.	.	.	.	.	1	HIAT1	HGNC	23363	protein_coding	YES	CCDS763.1	ENSP00000359171	HIAT1_HUMAN	.	UPI0000049F99	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AATGTATCTGC	.	4	ESCA
AMY2B	0	.	GRCh37	1	104116487	104116487	+	Missense_Mutation	SNP	C	C	A	rs749735334	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.671C>A	p.Ala224Glu	p.A224E	ENST00000361355	6/12	117	50	67	123	123	0	AMY2B,missense_variant,p.Ala224Glu,ENST00000361355,;AMY2B,downstream_gene_variant,,ENST00000435302,;AMY2B,downstream_gene_variant,,ENST00000453959,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,upstream_gene_variant,,ENST00000481821,;AMY2B,missense_variant,p.Ala224Glu,ENST00000477657,;ACTG1P4,downstream_gene_variant,,ENST00000425123,;	A	ENSG00000240038	ENST00000361355	Transcript	missense_variant	1287	671	224	A/E	gCa/gAa	rs749735334	.	.	1	AMY2B	HGNC	478	protein_coding	YES	CCDS782.1	ENSP00000354610	AMY2B_HUMAN	C9JWK7_HUMAN,C9J2Z5_HUMAN	UPI0000000CB1	.	tolerated(0.17)	possibly_damaging(0.785)	6/12	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Gene3D:3.20.20.80,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGGCAATTT	.	5	ESCA
AMY2B	0	.	GRCh37	1	104117883	104117883	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.917G>A	p.Arg306Lys	p.R306K	ENST00000361355	8/12	85	63	22	96	96	0	AMY2B,missense_variant,p.Arg306Lys,ENST00000361355,;AMY2B,downstream_gene_variant,,ENST00000435302,;AMY2B,downstream_gene_variant,,ENST00000453959,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,upstream_gene_variant,,ENST00000481821,;AMY2B,missense_variant,p.Arg306Lys,ENST00000477657,;ACTG1P4,downstream_gene_variant,,ENST00000425123,;	A	ENSG00000240038	ENST00000361355	Transcript	missense_variant	1533	917	306	R/K	aGa/aAa	.	.	.	1	AMY2B	HGNC	478	protein_coding	YES	CCDS782.1	ENSP00000354610	AMY2B_HUMAN	C9JWK7_HUMAN,C9J2Z5_HUMAN	UPI0000000CB1	.	tolerated(0.48)	benign(0.002)	8/12	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Gene3D:3.20.20.80,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445,Prints_domain:PR00110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACAGAGCAC	.	5	ESCA
NTNG1	0	.	GRCh37	1	107961248	107961248	+	Intron	SNP	G	G	T	rs750377313	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1087+10918G>T	.	.	ENST00000370068	.	25	13	11	21	21	0	NTNG1,missense_variant,p.Glu378Asp,ENST00000370070,;NTNG1,missense_variant,p.Glu378Asp,ENST00000370071,;NTNG1,missense_variant,p.Glu378Asp,ENST00000370067,;NTNG1,missense_variant,p.Glu378Asp,ENST00000370061,;NTNG1,missense_variant,p.Glu378Asp,ENST00000370066,;NTNG1,intron_variant,,ENST00000370074,;NTNG1,intron_variant,,ENST00000370072,;NTNG1,intron_variant,,ENST00000370073,;NTNG1,intron_variant,,ENST00000542803,;NTNG1,intron_variant,,ENST00000370068,;NTNG1,intron_variant,,ENST00000370065,;	T	ENSG00000162631	ENST00000370068	Transcript	intron_variant	.	.	.	.	.	rs750377313	.	.	1	NTNG1	HGNC	23319	protein_coding	YES	CCDS44180.1	ENSP00000359085	NTNG1_HUMAN	Q5IEC8_HUMAN	UPI0000458A3E	.	.	.	.	5/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGAGGTTTC	.	5	ESCA
HSD3B2	0	.	GRCh37	1	119964528	119964528	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.406delA	p.Ile136SerfsTer38	p.I136Sfs*38	ENST00000543831	4/4	52	39	13	24	24	0	HSD3B2,frameshift_variant,p.Ile136SerfsTer38,ENST00000543831,;HSD3B2,frameshift_variant,p.Ile136SerfsTer38,ENST00000433745,;HSD3B2,frameshift_variant,p.Ile136SerfsTer38,ENST00000369416,;HSD3B2,non_coding_transcript_exon_variant,,ENST00000448448,;HSD3B2,downstream_gene_variant,,ENST00000443865,;HSD3B2,downstream_gene_variant,,ENST00000471656,;	-	ENSG00000203859	ENST00000543831	Transcript	frameshift_variant	653	404	135	E/X	gAa/ga	.	.	.	1	HSD3B2	HGNC	5218	protein_coding	YES	CCDS902.1	ENSP00000445122	3BHS2_HUMAN	Q5QP01_HUMAN	UPI0000001C6C	.	.	.	4/4	.	hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF296,Pfam_domain:PF01073,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAAGGAAATCA	.	3	ESCA
TAS1R3	0	.	GRCh37	1	1266824	1266824	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99G>T	p.%3D	p.G33G	ENST00000339381	1/6	33	23	10	33	33	0	TAS1R3,synonymous_variant,p.%3D,ENST00000339381,;DVL1,downstream_gene_variant,,ENST00000378891,;GLTPD1,downstream_gene_variant,,ENST00000488011,;GLTPD1,downstream_gene_variant,,ENST00000343938,;DVL1,downstream_gene_variant,,ENST00000378888,;GLTPD1,downstream_gene_variant,,ENST00000464957,;	T	ENSG00000169962	ENST00000339381	Transcript	synonymous_variant	131	99	33	G	ggG/ggT	.	.	.	1	TAS1R3	HGNC	15661	protein_coding	YES	CCDS30556.1	ENSP00000344411	TS1R3_HUMAN	.	UPI0000051F47	.	.	.	1/6	.	hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF2,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGGGGACTA	.	5	ESCA
MLLT11	0	.	GRCh37	1	151040227	151040227	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*256delA	.	.	ENST00000368921	2/2	30	22	8	23	23	0	MLLT11,3_prime_UTR_variant,,ENST00000368921,;CDC42SE1,intron_variant,,ENST00000439374,;GABPB2,upstream_gene_variant,,ENST00000368917,;GABPB2,upstream_gene_variant,,ENST00000368918,;GABPB2,upstream_gene_variant,,ENST00000486076,;GABPB2,upstream_gene_variant,,ENST00000462520,;GABPB2,upstream_gene_variant,,ENST00000489549,;	-	ENSG00000213190	ENST00000368921	Transcript	3_prime_UTR_variant	3329	.	.	.	.	.	.	.	1	MLLT11	HGNC	16997	protein_coding	YES	CCDS982.1	ENSP00000357917	AF1Q_HUMAN	Q6FGF7_HUMAN	UPI0000125650	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCCCCAAATAT	.	3	ESCA
SEMA6C	0	.	GRCh37	1	151105028	151105028	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2821C>T	p.%3D	p.L941L	ENST00000368913	20/20	59	31	28	59	59	0	SEMA6C,synonymous_variant,p.%3D,ENST00000368914,;SEMA6C,synonymous_variant,p.%3D,ENST00000368913,;SEMA6C,synonymous_variant,p.%3D,ENST00000341697,;SEMA6C,synonymous_variant,p.%3D,ENST00000368912,;RP11-68I18.10,upstream_gene_variant,,ENST00000563624,;SEMA6C,intron_variant,,ENST00000479820,;SEMA6C,downstream_gene_variant,,ENST00000464018,;SEMA6C,downstream_gene_variant,,ENST00000489944,;	A	ENSG00000143434	ENST00000368913	Transcript	synonymous_variant	2950	2821	941	L	Ctg/Ttg	.	.	.	-1	SEMA6C	HGNC	10740	protein_coding	YES	CCDS53364.1	ENSP00000357909	SEM6C_HUMAN	Q9UFI1_HUMAN	UPI00001414D0	.	.	.	20/20	.	hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCAGGGACA	.	5	ESCA
TCHH	0	.	GRCh37	1	152080950	152080950	+	Missense_Mutation	SNP	G	G	T	rs774651770	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4743C>A	p.Phe1581Leu	p.F1581L	ENST00000368804	2/2	44	23	21	43	42	0	TCHH,missense_variant,p.Phe1581Leu,ENST00000368804,;	T	ENSG00000159450	ENST00000368804	Transcript	missense_variant	4743	4743	1581	F/L	ttC/ttA	rs774651770	.	.	-1	TCHH	HGNC	11791	protein_coding	YES	CCDS41396.1	ENSP00000357794	TRHY_HUMAN	Q5D861_HUMAN,A2RRS3_HUMAN	UPI0000458A5E	.	.	unknown(0)	2/2	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACGGAATTT	.	5	ESCA
DARS2	0	.	GRCh37	1	173807358	173807358	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801T>G	p.Asp267Glu	p.D267E	ENST00000361951	9/17	48	37	11	51	51	0	DARS2,missense_variant,p.Asp267Glu,ENST00000361951,;DARS2,5_prime_UTR_variant,,ENST00000239457,;DARS2,upstream_gene_variant,,ENST00000471476,;	G	ENSG00000117593	ENST00000361951	Transcript	missense_variant	1528	801	267	D/E	gaT/gaG	.	.	.	1	DARS2	HGNC	25538	protein_coding	YES	CCDS1311.1	ENSP00000355086	SYDM_HUMAN	Q9H9J7_HUMAN	UPI00001C1D5B	.	deleterious(0)	probably_damaging(0.999)	9/17	.	PROSITE_profiles:PS50862,hmmpanther:PTHR22594,hmmpanther:PTHR22594:SF5,Pfam_domain:PF00152,Gene3D:3.30.930.10,TIGRFAM_domain:TIGR00459,Superfamily_domains:SSF55681,Prints_domain:PR01042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGATGAAGG	.	5	ESCA
TNR	0	.	GRCh37	1	175372316	175372316	+	Silent	SNP	G	G	A	rs754692586	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936C>T	p.%3D	p.C312C	ENST00000367674	4/23	13	5	8	11	11	0	TNR,synonymous_variant,p.%3D,ENST00000367674,;TNR,synonymous_variant,p.%3D,ENST00000263525,;TNR,intron_variant,,ENST00000422274,;	A	ENSG00000116147	ENST00000367674	Transcript	synonymous_variant	1645	936	312	C	tgC/tgT	rs754692586	.	.	-1	TNR	HGNC	11953	protein_coding	YES	CCDS1318.1	ENSP00000356646	TENR_HUMAN	A1L306_HUMAN	UPI000013D41C	.	.	.	4/23	.	hmmpanther:PTHR19143:SF39,hmmpanther:PTHR19143,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Pfam_domain:PF07974,Gene3D:2.10.25.10,SMART_domains:SM00181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGACGCAGAG	.	5	ESCA
SMG7	0	.	GRCh37	1	183506344	183506344	+	Missense_Mutation	SNP	A	A	G	rs745521666	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1228A>G	p.Ile410Val	p.I410V	ENST00000507469	11/23	61	46	15	78	78	0	SMG7,missense_variant,p.Ile368Val,ENST00000419169,;SMG7,missense_variant,p.Ile439Val,ENST00000367537,;SMG7,missense_variant,p.Ile410Val,ENST00000347615,;SMG7,missense_variant,p.Ile410Val,ENST00000507469,;SMG7,missense_variant,p.Ile368Val,ENST00000456731,;SMG7,missense_variant,p.Ile410Val,ENST00000515829,;SMG7,missense_variant,p.Ile368Val,ENST00000508461,;	G	ENSG00000116698	ENST00000507469	Transcript	missense_variant	1346	1228	410	I/V	Att/Gtt	rs745521666	.	.	1	SMG7	HGNC	16792	protein_coding	YES	CCDS41445.2	ENSP00000425133	SMG7_HUMAN	Q96N31_HUMAN,B1ALB4_HUMAN	UPI0000D6205B	.	tolerated(0.5)	benign(0.009)	11/23	.	hmmpanther:PTHR15696:SF0,hmmpanther:PTHR15696,Pfam_domain:PF10373,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGTATTAGT	.	5	ESCA
HMCN1	0	.	GRCh37	1	186092111	186092111	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12258G>A	p.%3D	p.K4086K	ENST00000271588	81/107	24	11	13	28	28	0	HMCN1,synonymous_variant,p.%3D,ENST00000367492,;HMCN1,synonymous_variant,p.%3D,ENST00000271588,;	A	ENSG00000143341	ENST00000271588	Transcript	synonymous_variant	12487	12258	4086	K	aaG/aaA	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	.	81/107	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAAAGGAATA	.	5	ESCA
CDK18	0	.	GRCh37	1	205498558	205498558	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1268+1G>T	.	p.X423_splice	ENST00000506784	.	16	6	10	28	28	0	CDK18,splice_donor_variant,,ENST00000360066,;CDK18,splice_donor_variant,,ENST00000506784,;CDK18,splice_donor_variant,,ENST00000429964,;CDK18,downstream_gene_variant,,ENST00000478560,;CDK18,downstream_gene_variant,,ENST00000443813,;CDK18,downstream_gene_variant,,ENST00000419301,;CDK18,splice_donor_variant,,ENST00000484080,;CDK18,splice_donor_variant,,ENST00000515514,;CDK18,splice_donor_variant,,ENST00000505932,;CDK18,splice_donor_variant,,ENST00000512008,;CDK18,non_coding_transcript_exon_variant,,ENST00000509056,;CDK18,non_coding_transcript_exon_variant,,ENST00000468954,;CDK18,downstream_gene_variant,,ENST00000506489,;CDK18,upstream_gene_variant,,ENST00000459862,;CDK18,splice_donor_variant,,ENST00000489617,;CDK18,splice_donor_variant,,ENST00000504648,;CDK18,splice_donor_variant,,ENST00000515494,;CDK18,non_coding_transcript_exon_variant,,ENST00000504162,;CDK18,downstream_gene_variant,,ENST00000476153,;CDK18,downstream_gene_variant,,ENST00000512922,;	T	ENSG00000117266	ENST00000506784	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	CDK18	HGNC	8751	protein_coding	YES	CCDS1454.1	ENSP00000423665	CDK18_HUMAN	Q9BWF9_HUMAN,E9PMF2_HUMAN,D6RGH0_HUMAN,B4DHU6_HUMAN,B3KX76_HUMAN	UPI000035030C	.	.	.	.	12/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCAGGTAGCC	.	3	ESCA
DTL	0	.	GRCh37	1	212241588	212241588	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736C>T	p.Arg246Cys	p.R246C	ENST00000366991	9/15	55	39	15	67	67	0	DTL,missense_variant,p.Arg204Cys,ENST00000542077,;DTL,missense_variant,p.Arg246Cys,ENST00000366991,;DTL,intron_variant,,ENST00000475419,;DTL,upstream_gene_variant,,ENST00000489149,;	T	ENSG00000143476	ENST00000366991	Transcript	missense_variant	1050	736	246	R/C	Cgt/Tgt	.	.	.	1	DTL	HGNC	30288	protein_coding	YES	CCDS1502.1	ENSP00000355958	DTL_HUMAN	.	UPI000013E1C1	.	deleterious(0)	probably_damaging(1)	9/15	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22852,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTACGTAAG	.	5	ESCA
PTPN14	0	.	GRCh37	1	214705746	214705746	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-155+18780T>C	.	.	ENST00000366956	.	33	17	16	35	35	0	PTPN14,intron_variant,,ENST00000366956,;PTPN14,non_coding_transcript_exon_variant,,ENST00000491277,;PTPN14,intron_variant,,ENST00000486173,;KRT18P12,non_coding_transcript_exon_variant,,ENST00000425245,;	G	ENSG00000152104	ENST00000366956	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PTPN14	HGNC	9647	protein_coding	YES	CCDS1514.1	ENSP00000355923	PTN14_HUMAN	.	UPI000013DCA6	.	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATAGGAGG	.	5	ESCA
INADL	0	.	GRCh37	1	62418003	62418003	+	Intron	SNP	A	A	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3670+24502A>C	.	.	ENST00000371158	.	41	37	4	36	36	0	INADL,5_prime_UTR_variant,,ENST00000543708,;INADL,5_prime_UTR_variant,,ENST00000307297,;INADL,intron_variant,,ENST00000316485,;INADL,intron_variant,,ENST00000371158,;INADL,intron_variant,,ENST00000490547,;INADL,intron_variant,,ENST00000494842,;INADL,intron_variant,,ENST00000484937,;INADL,intron_variant,,ENST00000459752,;INADL,intron_variant,,ENST00000484562,;	C	ENSG00000132849	ENST00000371158	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	INADL	HGNC	28881	protein_coding	YES	CCDS617.2	ENSP00000360200	INADL_HUMAN	.	UPI0000204487	.	.	.	.	27/42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTGAGCTGC	.	2	ESCA
TOX2	0	.	GRCh37	20	42697596	42697596	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*270C>A	.	.	ENST00000341197	9/9	35	17	18	31	31	0	TOX2,3_prime_UTR_variant,,ENST00000413823,;TOX2,3_prime_UTR_variant,,ENST00000372999,;TOX2,3_prime_UTR_variant,,ENST00000358131,;TOX2,3_prime_UTR_variant,,ENST00000341197,;TOX2,downstream_gene_variant,,ENST00000423191,;TOX2,non_coding_transcript_exon_variant,,ENST00000435864,;	A	ENSG00000124191	ENST00000341197	Transcript	3_prime_UTR_variant	1819	.	.	.	.	.	.	.	1	TOX2	HGNC	16095	protein_coding	YES	CCDS46603.1	ENSP00000344724	TOX2_HUMAN	.	UPI000040F535	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCGCCCTGCG	.	5	ESCA
AL118506.1	0	.	GRCh37	20	62585290	62585290	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284G>A	p.Arg95His	p.R95H	ENST00000595604	1/1	22	8	14	18	18	0	AL118506.1,missense_variant,p.Arg95His,ENST00000595604,;UCKL1,intron_variant,,ENST00000358711,;UCKL1,intron_variant,,ENST00000354216,;UCKL1,intron_variant,,ENST00000369892,;UCKL1,upstream_gene_variant,,ENST00000369908,;ZNF512B,downstream_gene_variant,,ENST00000217130,;ZNF512B,downstream_gene_variant,,ENST00000450537,;ZNF512B,downstream_gene_variant,,ENST00000369888,;UCKL1,intron_variant,,ENST00000483710,;	A	ENSG00000267848	ENST00000595604	Transcript	missense_variant	284	284	95	R/H	cGc/cAc	.	.	.	1	AL118506.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000471917	.	M0R1J9_HUMAN	UPI00001C1007	.	.	unknown(0)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCGCCCAC	.	5	ESCA
CCT8L2	0	.	GRCh37	22	17072831	17072831	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>A	p.Gly204Arg	p.G204R	ENST00000359963	1/1	21	13	8	59	59	0	CCT8L2,missense_variant,p.Gly204Arg,ENST00000359963,;FABP5P11,downstream_gene_variant,,ENST00000430910,;	T	ENSG00000198445	ENST00000359963	Transcript	missense_variant	870	610	204	G/R	Ggg/Agg	.	.	.	-1	CCT8L2	HGNC	15553	protein_coding	YES	CCDS13738.1	ENSP00000353048	TCPQM_HUMAN	.	UPI000006CF87	.	tolerated(0.69)	benign(0.077)	1/1	.	Superfamily_domains:SSF54849,Pfam_domain:PF00118,Gene3D:3.30.260.10,hmmpanther:PTHR11353:SF70,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CACCCCAACAC	.	4	ESCA
DGCR2	0	.	GRCh37	22	19052582	19052582	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329-2A>G	.	p.X110_splice	ENST00000263196	.	16	8	8	14	14	0	DGCR2,splice_acceptor_variant,,ENST00000263196,;DGCR2,splice_acceptor_variant,,ENST00000537045,;DGCR2,intron_variant,,ENST00000545799,;DGCR2,intron_variant,,ENST00000473832,;DGCR2,upstream_gene_variant,,ENST00000608548,;DGCR2,intron_variant,,ENST00000389262,;	C	ENSG00000070413	ENST00000263196	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	DGCR2	HGNC	2845	protein_coding	YES	CCDS33598.1	ENSP00000263196	IDD_HUMAN	B7Z8B7_HUMAN,B7Z3C4_HUMAN	UPI0000001613	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACATAAAGG	.	5	ESCA
FAM83F	0	.	GRCh37	22	40417725	40417726	+	Frame_Shift_Ins	INS	-	-	CTCGG	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1214_1215insGGCTC	p.His406AlafsTer8	p.H406Afs*8	ENST00000333407	4/5	43	29	14	50	50	0	FAM83F,frameshift_variant,p.His238AlafsTer8,ENST00000473717,;FAM83F,frameshift_variant,p.His406AlafsTer8,ENST00000333407,;	CTCGG	ENSG00000133477	ENST00000333407	Transcript	frameshift_variant	1305-1306	1211-1212	404	V/VSX	gtc/gtCTCGGc	.	.	.	1	FAM83F	HGNC	25148	protein_coding	YES	CCDS14000.2	ENSP00000330432	FA83F_HUMAN	.	UPI0000071BF1	.	.	.	4/5	.	hmmpanther:PTHR16181:SF9,hmmpanther:PTHR16181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATGGTCTCTC	.	3	ESCA
LINC01123	0	.	GRCh37	2	110746139	110746139	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1130A>G	.	.	ENST00000419296	2/4	34	18	15	35	35	0	LINC01123,non_coding_transcript_exon_variant,,ENST00000336905,;LINC01123,non_coding_transcript_exon_variant,,ENST00000419296,;AC013271.3,downstream_gene_variant,,ENST00000454928,;ZBTB45P1,upstream_gene_variant,,ENST00000452761,;GPAA1P1,downstream_gene_variant,,ENST00000453019,;	G	ENSG00000204588	ENST00000419296	Transcript	non_coding_transcript_exon_variant	1130	.	.	.	.	.	.	.	1	LINC01123	HGNC	49269	lincRNA	YES	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATATATTC	.	4	ESCA
CLASP1	0	.	GRCh37	2	122363745	122363745	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-274G>T	.	.	ENST00000263710	2/40	16	8	8	23	23	0	CLASP1,5_prime_UTR_variant,,ENST00000397587,;CLASP1,5_prime_UTR_variant,,ENST00000263710,;CLASP1,5_prime_UTR_variant,,ENST00000455322,;CLASP1,5_prime_UTR_variant,,ENST00000541377,;CLASP1,5_prime_UTR_variant,,ENST00000409078,;Y_RNA,upstream_gene_variant,,ENST00000410535,;	A	ENSG00000074054	ENST00000263710	Transcript	5_prime_UTR_variant	117	.	.	.	.	.	.	.	-1	CLASP1	HGNC	17088	protein_coding	YES	.	ENSP00000263710	CLAP1_HUMAN	C9JP76_HUMAN,C9J151_HUMAN	UPI00001A8BFF	.	.	.	2/40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TAATTCAGCAG	.	2	ESCA
TRIB2	0	.	GRCh37	2	12882618	12882618	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1698A>G	.	.	ENST00000155926	3/3	71	36	35	81	81	0	TRIB2,3_prime_UTR_variant,,ENST00000381465,;TRIB2,3_prime_UTR_variant,,ENST00000155926,;	G	ENSG00000071575	ENST00000155926	Transcript	3_prime_UTR_variant	4149	.	.	.	.	.	.	.	1	TRIB2	HGNC	30809	protein_coding	YES	CCDS1683.1	ENSP00000155926	TRIB2_HUMAN	F8WA18_HUMAN	UPI0000051C55	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTATTTTG	.	5	ESCA
UGGT1	0	.	GRCh37	2	128872722	128872722	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.721C>T	p.Leu241Phe	p.L241F	ENST00000259253	7/41	66	30	35	56	56	0	UGGT1,missense_variant,p.Leu241Phe,ENST00000259253,;UGGT1,missense_variant,p.Leu217Phe,ENST00000375990,;UGGT1,3_prime_UTR_variant,,ENST00000376723,;UGGT1,3_prime_UTR_variant,,ENST00000438277,;	T	ENSG00000136731	ENST00000259253	Transcript	missense_variant	768	721	241	L/F	Ctc/Ttc	.	.	.	1	UGGT1	HGNC	15663	protein_coding	YES	CCDS2154.1	ENSP00000259253	UGGG1_HUMAN	.	UPI00000707D8	.	deleterious(0)	probably_damaging(0.999)	7/41	.	hmmpanther:PTHR11226:SF3,hmmpanther:PTHR11226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTACCTCTCT	.	5	ESCA
THSD7B	0	.	GRCh37	2	138320891	138320891	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3248G>T	p.Arg1083Leu	p.R1083L	ENST00000272643	16/28	23	14	8	33	33	0	THSD7B,missense_variant,p.Arg1080Leu,ENST00000409968,;THSD7B,missense_variant,p.Arg1052Leu,ENST00000413152,;THSD7B,missense_variant,p.Arg1083Leu,ENST00000272643,;THSD7B,intron_variant,,ENST00000543459,;	T	ENSG00000144229	ENST00000272643	Transcript	missense_variant	3248	3248	1083	R/L	cGc/cTc	.	.	.	1	THSD7B	HGNC	29348	protein_coding	YES	.	ENSP00000272643	THS7B_HUMAN	.	UPI00015E0A18	.	tolerated(0.21)	unknown(0)	16/28	.	PROSITE_profiles:PS50092,hmmpanther:PTHR11311:SF7,hmmpanther:PTHR11311,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCGCTGTG	.	5	ESCA
TANK	0	.	GRCh37	2	162036193	162036193	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20A>T	p.Glu7Val	p.E7V	ENST00000392749	2/8	38	19	18	33	33	0	TANK,missense_variant,p.Glu7Val,ENST00000429217,;TANK,missense_variant,p.Glu7Val,ENST00000432002,;TANK,missense_variant,p.Glu7Val,ENST00000457476,;TANK,missense_variant,p.Glu7Val,ENST00000403609,;TANK,missense_variant,p.Glu65Val,ENST00000406287,;TANK,missense_variant,p.Glu65Val,ENST00000402568,;TANK,missense_variant,p.Glu7Val,ENST00000259075,;TANK,missense_variant,p.Glu7Val,ENST00000405852,;TANK,missense_variant,p.Glu7Val,ENST00000440506,;TANK,missense_variant,p.Glu7Val,ENST00000392749,;TANK,missense_variant,p.Glu33Val,ENST00000456358,;TANK,non_coding_transcript_exon_variant,,ENST00000489393,;TANK,non_coding_transcript_exon_variant,,ENST00000463502,;TANK,missense_variant,p.Glu7Val,ENST00000457887,;TANK,missense_variant,p.Glu7Val,ENST00000432692,;TANK,missense_variant,p.Glu7Val,ENST00000441987,;TANK,non_coding_transcript_exon_variant,,ENST00000468831,;	T	ENSG00000136560	ENST00000392749	Transcript	missense_variant	259	20	7	E/V	gAg/gTg	.	.	.	1	TANK	HGNC	11562	protein_coding	YES	CCDS2215.1	ENSP00000376505	TANK_HUMAN	Q53TI5_HUMAN,Q4ZG76_HUMAN,E7EWR8_HUMAN	UPI000013D02B	.	deleterious(0)	probably_damaging(0.912)	2/8	.	hmmpanther:PTHR15249:SF0,hmmpanther:PTHR15249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCGAGCAAC	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098945	178098945	+	Missense_Mutation	SNP	G	G	C	rs748696421	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	2/5	37	18	19	47	47	0	NFE2L2,missense_variant,p.Arg18Gly,ENST00000449627,;NFE2L2,missense_variant,p.Arg18Gly,ENST00000423513,;NFE2L2,missense_variant,p.Arg34Gly,ENST00000397062,;NFE2L2,missense_variant,p.Arg18Gly,ENST00000446151,;NFE2L2,missense_variant,p.Arg18Gly,ENST00000588123,;NFE2L2,missense_variant,p.Arg33Gly,ENST00000586532,;NFE2L2,missense_variant,p.Arg18Gly,ENST00000421929,;NFE2L2,missense_variant,p.Arg18Gly,ENST00000464747,;NFE2L2,missense_variant,p.Arg18Gly,ENST00000448782,;NFE2L2,missense_variant,p.Arg18Gly,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	C	ENSG00000116044	ENST00000397062	Transcript	missense_variant	655	100	34	R/G	Cga/Gga	rs748696421,COSM132847,COSM3961575	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R34G|c.100C>G|11,CODON|p.R34P|c.101G>C|3,CODON|p.R34Q|c.101G>A|11,BUFFER|p.G31E|c.92G>A|5,BUFFER|p.G31A|c.92G>C|7,BUFFER|p.L30R|c.89T>G|7	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCGACTTA	byFrequency	5	ESCA
TTN	0	.	GRCh37	2	179407958	179407972	+	In_Frame_Del	DEL	TCTCTGTGCCAGCTT	TCTCTGTGCCAGCTT	-	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	TCTCTGTGCCAGCTT	TCTCTGTGCCAGCTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96728_96742delAAGCTGGCACAGAGA	p.Lys32243_Glu32247del	p.K32243_E32247del	ENST00000589042	347/363	55	40	15	32	32	0	TTN,inframe_deletion,p.Lys23303_Glu23307del,ENST00000359218,;TTN,inframe_deletion,p.Lys30602_Glu30606del,ENST00000591111,;TTN,inframe_deletion,p.Lys32243_Glu32247del,ENST00000589042,;TTN,inframe_deletion,p.Lys23370_Glu23374del,ENST00000342175,;TTN,inframe_deletion,p.Lys29675_Glu29679del,ENST00000342992,;TTN,inframe_deletion,p.Lys23178_Glu23182del,ENST00000460472,;TTN-AS1,splice_acceptor_variant,,ENST00000590040,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,downstream_gene_variant,,ENST00000589434,;TTN-AS1,downstream_gene_variant,,ENST00000585358,;TTN-AS1,downstream_gene_variant,,ENST00000588716,;TTN-AS1,downstream_gene_variant,,ENST00000589391,;RP11-65L3.4,downstream_gene_variant,,ENST00000604692,;TTN-AS1,downstream_gene_variant,,ENST00000592182,;TTN-AS1,downstream_gene_variant,,ENST00000450692,;TTN-AS1,downstream_gene_variant,,ENST00000592836,;TTN-AS1,downstream_gene_variant,,ENST00000415561,;TTN-AS1,downstream_gene_variant,,ENST00000588244,;TTN-AS1,downstream_gene_variant,,ENST00000588804,;TTN-AS1,downstream_gene_variant,,ENST00000585487,;	-	ENSG00000155657	ENST00000589042	Transcript	inframe_deletion	96953-96967	96728-96742	32243-32248	KAGTER/R	aAAGCTGGCACAGAGAga/aga	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	347/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCATCTCTCTGTGCCAGCTTTGCAG	.	3	ESCA
PUM2	0	.	GRCh37	2	20448581	20448581	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2765T>A	.	.	ENST00000338086	20/20	24	16	7	22	22	0	PUM2,3_prime_UTR_variant,,ENST00000319801,;PUM2,3_prime_UTR_variant,,ENST00000338086,;PUM2,3_prime_UTR_variant,,ENST00000361078,;PUM2,downstream_gene_variant,,ENST00000403432,;PUM2,downstream_gene_variant,,ENST00000440577,;PUM2,downstream_gene_variant,,ENST00000536417,;RNU7-113P,upstream_gene_variant,,ENST00000459273,;	T	ENSG00000055917	ENST00000338086	Transcript	3_prime_UTR_variant	5983	.	.	.	.	.	.	.	-1	PUM2	HGNC	14958	protein_coding	YES	CCDS1698.1	ENSP00000338173	PUM2_HUMAN	C9JW01_HUMAN,C9JE24_HUMAN,B4E2B6_HUMAN	UPI0000001665	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTCATATGA	.	5	ESCA
APOB	0	.	GRCh37	2	21227283	21227283	+	Missense_Mutation	SNP	G	G	A	rs747463777	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11945C>T	p.Ala3982Val	p.A3982V	ENST00000233242	28/29	112	64	48	109	109	0	APOB,missense_variant,p.Ala3982Val,ENST00000233242,;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,;	A	ENSG00000084674	ENST00000233242	Transcript	missense_variant	12073	11945	3982	A/V	gCg/gTg	rs747463777	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	benign(0.003)	28/29	.	hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACGCTGGG	.	5	ESCA
APOB	0	.	GRCh37	2	21234621	21234621	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5119G>A	p.Glu1707Lys	p.E1707K	ENST00000233242	26/29	38	23	15	26	26	0	APOB,missense_variant,p.Glu1707Lys,ENST00000233242,;	T	ENSG00000084674	ENST00000233242	Transcript	missense_variant	5247	5119	1707	E/K	Gag/Aag	.	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	probably_damaging(0.985)	26/29	.	hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCTCTGTGA	.	5	ESCA
GIGYF2	0	.	GRCh37	2	233723189	233723189	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1619C>T	.	.	ENST00000409451	31/31	34	26	8	23	23	0	GIGYF2,3_prime_UTR_variant,,ENST00000409196,;GIGYF2,3_prime_UTR_variant,,ENST00000409480,;GIGYF2,3_prime_UTR_variant,,ENST00000373566,;GIGYF2,3_prime_UTR_variant,,ENST00000373563,;GIGYF2,3_prime_UTR_variant,,ENST00000409547,;GIGYF2,3_prime_UTR_variant,,ENST00000409451,;C2orf82,intron_variant,,ENST00000448993,;GIGYF2,non_coding_transcript_exon_variant,,ENST00000474312,;	T	ENSG00000204120	ENST00000409451	Transcript	3_prime_UTR_variant	5808	.	.	.	.	.	.	.	1	GIGYF2	HGNC	11960	protein_coding	YES	CCDS46542.1	ENSP00000387170	PERQ2_HUMAN	C9JZC0_HUMAN,C9JXQ0_HUMAN,C9JRZ2_HUMAN,C9JPV7_HUMAN,C9JHT0_HUMAN,C9JH18_HUMAN,C9J1A6_HUMAN,C9J0V6_HUMAN	UPI00003FEC8F	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGCTCCTA	.	5	ESCA
AGAP1	0	.	GRCh37	2	236649666	236649666	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370G>T	p.Asp124Tyr	p.D124Y	ENST00000304032	4/18	56	32	24	40	40	0	AGAP1,missense_variant,p.Asp124Tyr,ENST00000304032,;AGAP1,missense_variant,p.Asp124Tyr,ENST00000409457,;AGAP1,missense_variant,p.Asp124Tyr,ENST00000336665,;AGAP1,missense_variant,p.Asp71Tyr,ENST00000402604,;AGAP1,missense_variant,p.Asp389Tyr,ENST00000409538,;AGAP1,upstream_gene_variant,,ENST00000428334,;	T	ENSG00000157985	ENST00000304032	Transcript	missense_variant	950	370	124	D/Y	Gat/Tat	.	.	.	1	AGAP1	HGNC	16922	protein_coding	YES	CCDS33408.1	ENSP00000307634	AGAP1_HUMAN	Q53S93_HUMAN,Q4ZG54_HUMAN,Q4ZG22_HUMAN,F5GXM9_HUMAN	UPI00005E1AE1	.	deleterious(0)	probably_damaging(1)	4/18	.	PROSITE_profiles:PS51419,hmmpanther:PTHR23180:SF226,hmmpanther:PTHR23180,Gene3D:3.40.50.300,Pfam_domain:PF08477,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAGATGAA	.	5	ESCA
CENPO	0	.	GRCh37	2	25037312	25037312	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284A>C	p.Glu95Ala	p.E95A	ENST00000380834	4/8	51	24	26	59	59	0	CENPO,missense_variant,p.Glu95Ala,ENST00000260662,;CENPO,missense_variant,p.Glu95Ala,ENST00000380834,;CENPO,missense_variant,p.Glu89Ala,ENST00000473706,;ADCY3,downstream_gene_variant,,ENST00000260600,;ADCY3,downstream_gene_variant,,ENST00000498288,;ADCY3,downstream_gene_variant,,ENST00000606682,;ADCY3,downstream_gene_variant,,ENST00000405392,;CENPO,non_coding_transcript_exon_variant,,ENST00000498362,;CENPO,upstream_gene_variant,,ENST00000395845,;CENPO,upstream_gene_variant,,ENST00000464156,;CENPO,non_coding_transcript_exon_variant,,ENST00000491031,;CENPO,non_coding_transcript_exon_variant,,ENST00000486527,;	C	ENSG00000138092	ENST00000380834	Transcript	missense_variant	709	284	95	E/A	gAa/gCa	.	.	.	1	CENPO	HGNC	28152	protein_coding	YES	CCDS1714.1	ENSP00000370214	CENPO_HUMAN	.	UPI000006F5F6	.	deleterious(0.02)	benign(0.059)	4/8	.	hmmpanther:PTHR14582	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGGAAGAGA	.	5	ESCA
FOXN2	0	.	GRCh37	2	48602929	48602929	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*347A>G	.	.	ENST00000340553	7/7	17	6	10	32	32	0	FOXN2,3_prime_UTR_variant,,ENST00000340553,;FOXN2,downstream_gene_variant,,ENST00000413569,;	G	ENSG00000170802	ENST00000340553	Transcript	3_prime_UTR_variant	1904	.	.	.	.	.	.	.	1	FOXN2	HGNC	5281	protein_coding	YES	CCDS1838.1	ENSP00000343633	FOXN2_HUMAN	Q6IS90_HUMAN,C9JTA7_HUMAN	UPI0000226321	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGATAAATTT	.	5	ESCA
BCL11A	0	.	GRCh37	2	60685126	60685126	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2413A>G	.	.	ENST00000335712	4/4	8	2	6	15	15	0	BCL11A,3_prime_UTR_variant,,ENST00000335712,;BCL11A,intron_variant,,ENST00000538214,;BCL11A,intron_variant,,ENST00000359629,;BCL11A,intron_variant,,ENST00000356842,;BCL11A,intron_variant,,ENST00000537768,;BCL11A,downstream_gene_variant,,ENST00000358510,;BCL11A,intron_variant,,ENST00000479026,;BCL11A,intron_variant,,ENST00000489516,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,downstream_gene_variant,,ENST00000477659,;	C	ENSG00000119866	ENST00000335712	Transcript	3_prime_UTR_variant	5149	.	.	.	.	.	.	.	-1	BCL11A	HGNC	13221	protein_coding	YES	CCDS1862.1	ENSP00000338774	BC11A_HUMAN	D6W5D9_HUMAN,Q53TS1_HUMAN,Q53TE8_HUMAN	UPI000013DC00	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACTATATTAT	.	2	ESCA
MXD1	0	.	GRCh37	2	70148870	70148870	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.176C>G	p.Ser59Ter	p.S59*	ENST00000264444	3/6	84	79	5	71	71	0	MXD1,stop_gained,p.Ser59Ter,ENST00000264444,;MXD1,stop_gained,p.Ser27Ter,ENST00000435990,;MXD1,intron_variant,,ENST00000540449,;MXD1,intron_variant,,ENST00000409442,;	G	ENSG00000059728	ENST00000264444	Transcript	stop_gained	436	176	59	S/*	tCa/tGa	.	.	.	1	MXD1	HGNC	6761	protein_coding	YES	CCDS1896.1	ENSP00000264444	MAD1_HUMAN	C9JBE8_HUMAN,B7ZLI7_HUMAN	UPI0000035C7D	.	.	.	3/6	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50888,hmmpanther:PTHR11969,hmmpanther:PTHR11969:SF18,Gene3D:4.10.280.10,Pfam_domain:PF00010,Superfamily_domains:SSF47459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATCAACTC	.	2	ESCA
DYSF	0	.	GRCh37	2	71896314	71896314	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5619G>T	p.Lys1873Asn	p.K1873N	ENST00000410020	50/56	35	26	8	42	42	0	DYSF,missense_variant,p.Lys1872Asn,ENST00000409582,;DYSF,missense_variant,p.Lys1873Asn,ENST00000410020,;DYSF,missense_variant,p.Lys1842Asn,ENST00000409744,;DYSF,missense_variant,p.Lys1855Asn,ENST00000429174,;DYSF,missense_variant,p.Lys1851Asn,ENST00000409762,;DYSF,missense_variant,p.Lys1852Asn,ENST00000410041,;DYSF,missense_variant,p.Lys1866Asn,ENST00000409651,;DYSF,missense_variant,p.Lys1835Asn,ENST00000394120,;DYSF,missense_variant,p.Lys1856Asn,ENST00000409366,;DYSF,missense_variant,p.Lys1865Asn,ENST00000413539,;DYSF,missense_variant,p.Lys1834Asn,ENST00000258104,;DYSF,non_coding_transcript_exon_variant,,ENST00000479049,;	T	ENSG00000135636	ENST00000410020	Transcript	missense_variant	5760	5619	1873	K/N	aaG/aaT	.	.	.	1	DYSF	HGNC	3097	protein_coding	YES	CCDS46328.1	ENSP00000386881	DYSF_HUMAN	A0FK00_HUMAN	UPI000171F710	.	tolerated(0.25)	benign(0.091)	50/56	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF35,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGATGAG	.	5	ESCA
ELMOD3	0	.	GRCh37	2	85618819	85618820	+	3'UTR	INS	-	-	AGGC	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1201_*1202insCAGG	.	.	ENST00000315658	11/11	33	18	15	23	23	0	ELMOD3,3_prime_UTR_variant,,ENST00000409344,;ELMOD3,3_prime_UTR_variant,,ENST00000409013,;ELMOD3,3_prime_UTR_variant,,ENST00000409890,;ELMOD3,3_prime_UTR_variant,,ENST00000315658,;ELMOD3,3_prime_UTR_variant,,ENST00000393852,;CAPG,downstream_gene_variant,,ENST00000263867,;CAPG,downstream_gene_variant,,ENST00000409670,;CAPG,downstream_gene_variant,,ENST00000409921,;CAPG,downstream_gene_variant,,ENST00000453973,;ELMOD3,downstream_gene_variant,,ENST00000428955,;CAPG,downstream_gene_variant,,ENST00000409724,;RP11-717A5.2,upstream_gene_variant,,ENST00000610137,;ELMOD3,non_coding_transcript_exon_variant,,ENST00000490508,;ELMOD3,downstream_gene_variant,,ENST00000496957,;CAPG,downstream_gene_variant,,ENST00000483659,;ELMOD3,3_prime_UTR_variant,,ENST00000446464,;ELMOD3,3_prime_UTR_variant,,ENST00000414593,;ELMOD3,3_prime_UTR_variant,,ENST00000423095,;ELMOD3,downstream_gene_variant,,ENST00000410106,;ELMOD3,downstream_gene_variant,,ENST00000486908,;ELMOD3,downstream_gene_variant,,ENST00000444108,;CAPG,downstream_gene_variant,,ENST00000471064,;ELMOD3,downstream_gene_variant,,ENST00000429764,;	AGGC	ENSG00000115459	ENST00000315658	Transcript	3_prime_UTR_variant	2633-2634	.	.	.	.	.	.	.	1	ELMOD3	HGNC	26158	protein_coding	YES	CCDS1973.1	ENSP00000318264	ELMD3_HUMAN	E9PI96_HUMAN,D3YTJ5_HUMAN,B8ZZT8_HUMAN	UPI0000072463	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAATTGAGGGA	.	3	ESCA
LMAN2L	0	.	GRCh37	2	97373133	97373133	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.940A>T	p.Thr314Ser	p.T314S	ENST00000377079	9/9	26	16	9	26	26	0	LMAN2L,missense_variant,p.Thr169Ser,ENST00000426463,;LMAN2L,missense_variant,p.Thr314Ser,ENST00000377079,;LMAN2L,missense_variant,p.Thr165Ser,ENST00000537039,;LMAN2L,missense_variant,p.Thr303Ser,ENST00000264963,;LMAN2L,missense_variant,p.Thr158Ser,ENST00000534882,;LMAN2L,splice_region_variant,,ENST00000440610,;LMAN2L,splice_region_variant,,ENST00000449221,;LMAN2L,splice_region_variant,,ENST00000434524,;LMAN2L,splice_region_variant,,ENST00000434865,;LMAN2L,splice_region_variant,,ENST00000446780,;LMAN2L,downstream_gene_variant,,ENST00000474494,;FER1L5,downstream_gene_variant,,ENST00000457909,;LMAN2L,downstream_gene_variant,,ENST00000480869,;FER1L5,downstream_gene_variant,,ENST00000424961,;FER1L5,downstream_gene_variant,,ENST00000436930,;FER1L5,downstream_gene_variant,,ENST00000414152,;FER1L5,downstream_gene_variant,,ENST00000397978,;	A	ENSG00000114988	ENST00000377079	Transcript	missense_variant	964	940	314	T/S	Aca/Tca	.	.	.	-1	LMAN2L	HGNC	19263	protein_coding	YES	CCDS46365.1	ENSP00000366280	LMA2L_HUMAN	B4DI83_HUMAN	UPI000044099B	.	tolerated(0.5)	benign(0.002)	9/9	.	hmmpanther:PTHR12223,hmmpanther:PTHR12223:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGTCACTG	.	5	ESCA
KPNA1	0	.	GRCh37	3	122144649	122144649	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1183T>C	.	.	ENST00000344337	14/14	32	12	19	32	32	0	KPNA1,3_prime_UTR_variant,,ENST00000344337,;RP11-299J3.8,intron_variant,,ENST00000608756,;RP11-299J3.8,intron_variant,,ENST00000608015,;RP11-299J3.8,intron_variant,,ENST00000609469,;RP11-299J3.8,intron_variant,,ENST00000608346,;RP11-299J3.8,downstream_gene_variant,,ENST00000608465,;KPNA1,non_coding_transcript_exon_variant,,ENST00000470904,;KPNA1,downstream_gene_variant,,ENST00000466923,;KPNA1,downstream_gene_variant,,ENST00000494339,;KPNA1,downstream_gene_variant,,ENST00000485027,;	G	ENSG00000114030	ENST00000344337	Transcript	3_prime_UTR_variant	2977	.	.	.	.	.	.	.	-1	KPNA1	HGNC	6394	protein_coding	YES	CCDS3013.1	ENSP00000343701	IMA5_HUMAN	C9JYI4_HUMAN,C9JWD9_HUMAN,C9J4U1_HUMAN,B3KXZ2_HUMAN	UPI000013D524	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTATTTGG	.	5	ESCA
ALDH1L1	0	.	GRCh37	3	125855621	125855621	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360C>A	p.Pro454Thr	p.P454T	ENST00000273450	11/23	33	23	9	36	36	0	ALDH1L1,missense_variant,p.Pro444Thr,ENST00000393434,;ALDH1L1,missense_variant,p.Pro444Thr,ENST00000393431,;ALDH1L1,missense_variant,p.Pro343Thr,ENST00000452905,;ALDH1L1,missense_variant,p.Pro454Thr,ENST00000273450,;ALDH1L1,missense_variant,p.Pro444Thr,ENST00000472186,;ALDH1L1,3_prime_UTR_variant,,ENST00000473607,;ALDH1L1,non_coding_transcript_exon_variant,,ENST00000476245,;	T	ENSG00000144908	ENST00000273450	Transcript	missense_variant	1578	1360	454	P/T	Ccc/Acc	.	.	.	-1	ALDH1L1	HGNC	3978	protein_coding	YES	CCDS58851.1	ENSP00000273450	AL1L1_HUMAN	D6RFJ7_HUMAN,C9JYZ6_HUMAN,C9JY00_HUMAN,C9IZ36_HUMAN	UPI0000425C57	.	deleterious(0.01)	probably_damaging(0.999)	11/23	.	hmmpanther:PTHR11699:SF120,hmmpanther:PTHR11699,Pfam_domain:PF00171,Gene3D:3.40.605.10,PIRSF_domain:PIRSF036489,Superfamily_domains:SSF53720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGGATTGA	.	5	ESCA
TMCC1	0	.	GRCh37	3	129547076	129547076	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146G>A	p.Gly49Asp	p.G49D	ENST00000393238	3/6	88	76	12	41	41	0	TMCC1,missense_variant,p.Gly49Asp,ENST00000393238,;TMCC1,intron_variant,,ENST00000505616,;TMCC1,intron_variant,,ENST00000426664,;TMCC1,intron_variant,,ENST00000513411,;TMCC1,downstream_gene_variant,,ENST00000512902,;TMCC1,intron_variant,,ENST00000505924,;TMCC1,downstream_gene_variant,,ENST00000508869,;	T	ENSG00000172765	ENST00000393238	Transcript	missense_variant	487	146	49	G/D	gGc/gAc	COSM203995,COSM203996	.	.	-1	TMCC1	HGNC	29116	protein_coding	YES	CCDS33855.1	ENSP00000376930	TMCC1_HUMAN	Q8N4H2_HUMAN,Q6N039_HUMAN,E9PC87_HUMAN,D6RBT7_HUMAN	UPI0000197B80	.	deleterious_low_confidence(0)	probably_damaging(0.999)	3/6	.	hmmpanther:PTHR17613,hmmpanther:PTHR17613:SF11	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTGGCCAATC	.	4	ESCA
DNAJC13	0	.	GRCh37	3	132169648	132169648	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.494A>G	p.Tyr165Cys	p.Y165C	ENST00000260818	6/56	50	9	40	18	18	0	DNAJC13,missense_variant,p.Tyr165Cys,ENST00000260818,;DNAJC13,non_coding_transcript_exon_variant,,ENST00000486798,;	G	ENSG00000138246	ENST00000260818	Transcript	missense_variant	742	494	165	Y/C	tAt/tGt	.	.	.	1	DNAJC13	HGNC	30343	protein_coding	YES	CCDS33857.1	ENSP00000260818	DJC13_HUMAN	.	UPI000022C1FD	.	tolerated(0.22)	benign(0)	6/56	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTATCAAG	.	5	ESCA
OXNAD1	0	.	GRCh37	3	16312569	16312569	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110C>T	p.Thr37Ile	p.T37I	ENST00000285083	3/9	22	5	17	46	46	0	OXNAD1,missense_variant,p.Thr37Ile,ENST00000606098,;OXNAD1,missense_variant,p.Thr37Ile,ENST00000285083,;OXNAD1,missense_variant,p.Thr55Ile,ENST00000435829,;OXNAD1,missense_variant,p.Thr55Ile,ENST00000544043,;OXNAD1,missense_variant,p.Thr37Ile,ENST00000605932,;OXNAD1,missense_variant,p.Thr37Ile,ENST00000452581,;OXNAD1,missense_variant,p.Thr37Ile,ENST00000442255,;OXNAD1,non_coding_transcript_exon_variant,,ENST00000486267,;RP11-608O8.2,downstream_gene_variant,,ENST00000604305,;	T	ENSG00000154814	ENST00000285083	Transcript	missense_variant	575	110	37	T/I	aCt/aTt	.	.	.	1	OXNAD1	HGNC	25128	protein_coding	YES	CCDS2630.1	ENSP00000285083	OXND1_HUMAN	.	UPI0000071465	.	deleterious(0.03)	possibly_damaging(0.721)	3/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR19370:SF68,hmmpanther:PTHR19370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.H35H|c.105C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTACTCTAA	.	5	ESCA
CCDC39	0	.	GRCh37	3	180337677	180337677	+	Missense_Mutation	SNP	C	C	T	rs769886847	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2080G>A	p.Ala694Thr	p.A694T	ENST00000442201	15/20	73	46	27	36	36	0	CCDC39,missense_variant,p.Ala694Thr,ENST00000442201,;CCDC39,intron_variant,,ENST00000273654,;TTC14,downstream_gene_variant,,ENST00000382584,;CCDC39,upstream_gene_variant,,ENST00000489868,;CCDC39,upstream_gene_variant,,ENST00000473854,;CCDC39,intron_variant,,ENST00000476379,;	T	ENSG00000145075	ENST00000442201	Transcript	missense_variant	2200	2080	694	A/T	Gct/Act	rs769886847	.	.	-1	CCDC39	HGNC	25244	protein_coding	YES	CCDS46964.1	ENSP00000405708	CCD39_HUMAN	.	UPI00015D7298	.	deleterious(0)	probably_damaging(0.929)	15/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18962:SF0,hmmpanther:PTHR18962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGAGCGTAGA	byFrequency|byCluster	5	ESCA
MUC4	0	.	GRCh37	3	195509501	195509501	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8950T>A	p.Ser2984Thr	p.S2984T	ENST00000463781	2/25	245	225	20	208	208	0	MUC4,missense_variant,p.Ser2984Thr,ENST00000463781,;MUC4,missense_variant,p.Ser2984Thr,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.Ser2984Thr,ENST00000470451,;MUC4,missense_variant,p.Ser2984Thr,ENST00000477086,;MUC4,missense_variant,p.Ser2984Thr,ENST00000466475,;MUC4,missense_variant,p.Ser2984Thr,ENST00000478156,;MUC4,missense_variant,p.Ser2984Thr,ENST00000479406,;MUC4,missense_variant,p.Ser2984Thr,ENST00000477756,;MUC4,missense_variant,p.Ser2984Thr,ENST00000462323,;MUC4,missense_variant,p.Ser2984Thr,ENST00000480843,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,;	T	ENSG00000145113	ENST00000463781	Transcript	missense_variant	9410	8950	2984	S/T	Tca/Aca	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	benign(0.044)	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A2985T|c.8953G>A|3	MUTECT|MUSE	TGCTGAGGAAG	.	2	ESCA
ZNF385D	0	.	GRCh37	3	21552422	21552422	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370A>G	p.Lys124Glu	p.K124E	ENST00000281523	4/8	83	56	26	143	143	0	ZNF385D,missense_variant,p.Lys124Glu,ENST00000281523,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000495739,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494118,;ZNF385D,3_prime_UTR_variant,,ENST00000446749,;	C	ENSG00000151789	ENST00000281523	Transcript	missense_variant	889	370	124	K/E	Aag/Gag	.	.	.	-1	ZNF385D	HGNC	26191	protein_coding	YES	CCDS2636.1	ENSP00000281523	Z385D_HUMAN	.	UPI00000724AC	.	tolerated(0.43)	possibly_damaging(0.899)	4/8	.	hmmpanther:PTHR23067,hmmpanther:PTHR23067:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTTGGCAG	.	5	ESCA
FBXW12	0	.	GRCh37	3	48420016	48420016	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615G>A	p.Met205Ile	p.M205I	ENST00000296438	6/11	18	3	14	15	15	0	FBXW12,missense_variant,p.Met186Ile,ENST00000445170,;FBXW12,missense_variant,p.Met48Ile,ENST00000436231,;FBXW12,missense_variant,p.Met205Ile,ENST00000296438,;FBXW12,intron_variant,,ENST00000415155,;RN7SL321P,upstream_gene_variant,,ENST00000581742,;FBXW12,upstream_gene_variant,,ENST00000468158,;FBXW12,splice_region_variant,,ENST00000477542,;	A	ENSG00000164049	ENST00000296438	Transcript	missense_variant	801	615	205	M/I	atG/atA	.	.	.	1	FBXW12	HGNC	20729	protein_coding	YES	CCDS2764.1	ENSP00000296438	FBW12_HUMAN	C9JK86_HUMAN	UPI00004123F1	.	deleterious(0.03)	benign(0.001)	6/11	.	hmmpanther:PTHR22844:SF113,hmmpanther:PTHR22844,Gene3D:2.130.10.10,Superfamily_domains:SSF50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGATGGTAAG	.	5	ESCA
COL7A1	0	.	GRCh37	3	48615783	48615783	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5503G>T	p.Asp1835Tyr	p.D1835Y	ENST00000328333	64/118	22	5	17	37	37	0	COL7A1,missense_variant,p.Asp1835Tyr,ENST00000328333,;COL7A1,missense_variant,p.Asp1835Tyr,ENST00000454817,;MIR711,downstream_gene_variant,,ENST00000390201,;COL7A1,non_coding_transcript_exon_variant,,ENST00000487017,;	A	ENSG00000114270	ENST00000328333	Transcript	missense_variant	5611	5503	1835	D/Y	Gat/Tat	.	.	.	-1	COL7A1	HGNC	2214	protein_coding	YES	CCDS2773.1	ENSP00000332371	CO7A1_HUMAN	.	UPI0000126D20	.	.	unknown(0)	64/118	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATCCTCGC	.	5	ESCA
SEMA3F	0	.	GRCh37	3	50222050	50222050	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1259C>A	p.Ser420Tyr	p.S420Y	ENST00000002829	13/19	22	2	20	52	52	0	SEMA3F,missense_variant,p.Ser321Tyr,ENST00000413852,;SEMA3F,missense_variant,p.Ser389Tyr,ENST00000434342,;SEMA3F,missense_variant,p.Ser420Tyr,ENST00000002829,;SEMA3F,downstream_gene_variant,,ENST00000414301,;SEMA3F,downstream_gene_variant,,ENST00000450338,;SEMA3F,non_coding_transcript_exon_variant,,ENST00000470737,;SEMA3F,downstream_gene_variant,,ENST00000493743,;	A	ENSG00000001617	ENST00000002829	Transcript	missense_variant	1743	1259	420	S/Y	tCt/tAt	COSM1424115	.	.	1	SEMA3F	HGNC	10728	protein_coding	YES	CCDS2811.1	ENSP00000002829	SEM3F_HUMAN	.	UPI0000135A69	.	tolerated(0.87)	possibly_damaging(0.61)	13/19	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF27,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCTATGA	.	5	ESCA
RBM15B	0	.	GRCh37	3	51434793	51434793	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3290G>A	.	.	ENST00000323686	1/1	20	3	17	14	14	0	RBM15B,3_prime_UTR_variant,,ENST00000323686,;VPRBP,intron_variant,,ENST00000423656,;VPRBP,downstream_gene_variant,,ENST00000335891,;	A	ENSG00000179837	ENST00000323686	Transcript	3_prime_UTR_variant	6063	.	.	.	.	.	.	.	1	RBM15B	HGNC	24303	protein_coding	YES	CCDS33764.1	ENSP00000313890	RB15B_HUMAN	.	UPI0000160BDE	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCAGACAAG	.	5	ESCA
INTU	0	.	GRCh37	4	128584699	128584699	+	Missense_Mutation	SNP	A	A	G	rs758759703	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932A>G	p.Tyr311Cys	p.Y311C	ENST00000335251	4/16	11	2	9	17	17	0	INTU,missense_variant,p.Tyr311Cys,ENST00000296461,;INTU,missense_variant,p.Tyr311Cys,ENST00000335251,;INTU,missense_variant,p.Tyr311Cys,ENST00000503952,;INTU,missense_variant,p.Tyr311Cys,ENST00000503626,;	G	ENSG00000164066	ENST00000335251	Transcript	missense_variant	1035	932	311	Y/C	tAt/tGt	rs758759703	.	.	1	INTU	HGNC	29239	protein_coding	YES	CCDS34061.1	ENSP00000334003	INTU_HUMAN	B3KVS6_HUMAN	UPI00001C1E05	.	deleterious(0.03)	benign(0.073)	4/16	.	hmmpanther:PTHR21082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TATGTATCTCA	byFrequency	3	ESCA
SCLT1	0	.	GRCh37	4	129858002	129858002	+	Missense_Mutation	SNP	C	C	A	rs751079883	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1637G>T	p.Ser546Ile	p.S546I	ENST00000281142	18/21	23	20	3	37	37	0	SCLT1,missense_variant,p.Ser546Ile,ENST00000281142,;SCLT1,intron_variant,,ENST00000503215,;SCLT1,intron_variant,,ENST00000434680,;SCLT1,intron_variant,,ENST00000439369,;SCLT1,non_coding_transcript_exon_variant,,ENST00000502495,;SCLT1,upstream_gene_variant,,ENST00000503565,;SCLT1,non_coding_transcript_exon_variant,,ENST00000506233,;	A	ENSG00000151466	ENST00000281142	Transcript	missense_variant	2141	1637	546	S/I	aGt/aTt	rs751079883	.	.	-1	SCLT1	HGNC	26406	protein_coding	YES	CCDS3740.1	ENSP00000281142	SCLT1_HUMAN	.	UPI000013DC5F	.	deleterious(0)	probably_damaging(0.994)	18/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGTACTGATC	.	2	ESCA
FAM200B	0	.	GRCh37	4	15691676	15691676	+	3'Flank	SNP	C	C	T	rs75806234	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000422728	.	14	4	10	22	22	0	FAM200B,downstream_gene_variant,,ENST00000503617,;FAM200B,downstream_gene_variant,,ENST00000422728,;FAM200B,non_coding_transcript_exon_variant,,ENST00000504137,;FAM200B,intron_variant,,ENST00000504598,;FAM200B,downstream_gene_variant,,ENST00000515697,;FAM200B,downstream_gene_variant,,ENST00000502502,;FAM200B,downstream_gene_variant,,ENST00000509022,;FAM200B,downstream_gene_variant,,ENST00000514803,;FAM200B,downstream_gene_variant,,ENST00000504823,;FAM200B,downstream_gene_variant,,ENST00000515430,;FAM200B,downstream_gene_variant,,ENST00000506610,;FAM200B,downstream_gene_variant,,ENST00000505260,;FAM200B,downstream_gene_variant,,ENST00000502856,;FAM200B,downstream_gene_variant,,ENST00000510186,;FAM200B,downstream_gene_variant,,ENST00000510032,;FAM200B,downstream_gene_variant,,ENST00000507305,;FAM200B,downstream_gene_variant,,ENST00000513053,;FAM200B,downstream_gene_variant,,ENST00000507992,;FAM200B,downstream_gene_variant,,ENST00000508567,;FAM200B,downstream_gene_variant,,ENST00000512855,;FAM200B,downstream_gene_variant,,ENST00000510920,;FAM200B,downstream_gene_variant,,ENST00000503600,;	T	ENSG00000237765	ENST00000422728	Transcript	downstream_gene_variant	.	.	.	.	.	rs75806234	.	952	1	FAM200B	HGNC	27740	protein_coding	YES	CCDS47028.1	ENSP00000393017	F200B_HUMAN	D6RAC6_HUMAN	UPI0000160C4C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATCTCTAA	by1000G	5	ESCA
TLR1	0	.	GRCh37	4	38798859	38798859	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594C>G	p.Leu532Val	p.L532V	ENST00000308979	4/4	81	18	62	81	81	0	TLR1,missense_variant,p.Leu532Val,ENST00000308979,;TLR1,missense_variant,p.Leu532Val,ENST00000502213,;TLR1,downstream_gene_variant,,ENST00000506146,;TLR1,downstream_gene_variant,,ENST00000508364,;TLR1,downstream_gene_variant,,ENST00000505940,;TLR1,downstream_gene_variant,,ENST00000515861,;TLR1,intron_variant,,ENST00000505744,;TLR1,downstream_gene_variant,,ENST00000508535,;TLR1,upstream_gene_variant,,ENST00000510552,;TLR1,downstream_gene_variant,,ENST00000509754,;	C	ENSG00000174125	ENST00000308979	Transcript	missense_variant	1868	1594	532	L/V	Cta/Gta	.	.	.	-1	TLR1	HGNC	11847	protein_coding	YES	CCDS33973.1	ENSP00000354932	TLR1_HUMAN	Q32MK4_HUMAN,D6RF68_HUMAN,D6RCE8_HUMAN,D6RAP2_HUMAN,D6RA99_HUMAN	UPI000013EDFA	.	deleterious(0)	benign(0.232)	4/4	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF261,Gene3D:3.80.10.10,SMART_domains:SM00082,PIRSF_domain:PIRSF037595,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTAGCTCAC	.	5	ESCA
FRYL	0	.	GRCh37	4	48555255	48555255	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4412A>T	p.Tyr1471Phe	p.Y1471F	ENST00000358350	36/64	24	7	17	31	31	0	FRYL,missense_variant,p.Tyr1471Phe,ENST00000358350,;FRYL,missense_variant,p.Tyr1471Phe,ENST00000507711,;FRYL,missense_variant,p.Tyr342Phe,ENST00000514617,;FRYL,missense_variant,p.Tyr1471Phe,ENST00000503238,;FRYL,missense_variant,p.Tyr1471Phe,ENST00000537810,;FRYL,5_prime_UTR_variant,,ENST00000507873,;FRYL,5_prime_UTR_variant,,ENST00000264319,;FRYL,upstream_gene_variant,,ENST00000502925,;	A	ENSG00000075539	ENST00000358350	Transcript	missense_variant	5017	4412	1471	Y/F	tAt/tTt	.	.	.	-1	FRYL	HGNC	29127	protein_coding	YES	CCDS43227.1	ENSP00000351113	FRYL_HUMAN	.	UPI0000EBC149	.	tolerated(0.48)	benign(0.006)	36/64	.	hmmpanther:PTHR12295:SF9,hmmpanther:PTHR12295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTATAGCTG	.	5	ESCA
TECRL	0	.	GRCh37	4	65145912	65145912	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.970A>G	p.Ile324Val	p.I324V	ENST00000381210	12/12	26	11	14	30	30	0	TECRL,missense_variant,p.Ile324Val,ENST00000381210,;TECRL,synonymous_variant,p.%3D,ENST00000511997,;TECRL,intron_variant,,ENST00000507440,;	C	ENSG00000205678	ENST00000381210	Transcript	missense_variant	1081	970	324	I/V	Att/Gtt	COSM285653	.	.	-1	TECRL	HGNC	27365	protein_coding	YES	CCDS33990.1	ENSP00000370607	TECRL_HUMAN	D6RBZ3_HUMAN	UPI0000141A54	.	tolerated(0.23)	benign(0.02)	12/12	.	Transmembrane_helices:TMhelix,Pfam_domain:PF02544,hmmpanther:PTHR10556,hmmpanther:PTHR10556:SF27,PROSITE_profiles:PS50244	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAATTCCAA	.	5	ESCA
AFM	0	.	GRCh37	4	74364929	74364929	+	Missense_Mutation	SNP	C	C	T	rs772707726	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1388C>T	p.Thr463Met	p.T463M	ENST00000226355	11/15	111	87	24	40	39	0	AFM,missense_variant,p.Thr463Met,ENST00000226355,;AFM,downstream_gene_variant,,ENST00000505794,;	T	ENSG00000079557	ENST00000226355	Transcript	missense_variant	1481	1388	463	T/M	aCg/aTg	rs772707726,COSM168798	.	.	1	AFM	HGNC	316	protein_coding	YES	CCDS3557.1	ENSP00000226355	AFAM_HUMAN	.	UPI000012565D	.	tolerated(0.13)	possibly_damaging(0.593)	11/15	.	PROSITE_profiles:PS51438,hmmpanther:PTHR11385:SF13,hmmpanther:PTHR11385,Gene3D:1.10.246.10,Pfam_domain:PF00273,SMART_domains:SM00103,PIRSF_domain:PIRSF002520,Superfamily_domains:SSF48552	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTGTACGCTAA	byFrequency	4	ESCA
MTHFD2L	0	.	GRCh37	4	75025854	75025855	+	Intron	INS	-	-	TA	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143+1865_143+1866dupTA	.	.	ENST00000395759	.	79	68	11	50	50	0	MTHFD2L,intron_variant,,ENST00000395759,;MTHFD2L,intron_variant,,ENST00000359107,;MTHFD2L,intron_variant,,ENST00000331145,;MTHFD2L,intron_variant,,ENST00000325278,;MTHFD2L,intron_variant,,ENST00000433372,;AC093677.1,upstream_gene_variant,,ENST00000600169,;MTHFD2L,non_coding_transcript_exon_variant,,ENST00000461101,;MTHFD2L,intron_variant,,ENST00000484725,;MTHFD2L,non_coding_transcript_exon_variant,,ENST00000490698,;MTHFD2L,non_coding_transcript_exon_variant,,ENST00000475291,;MTHFD2L,intron_variant,,ENST00000423607,;MTHFD2L,intron_variant,,ENST00000429335,;MTHFD2L,intron_variant,,ENST00000429519,;	TA	ENSG00000163738	ENST00000395759	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MTHFD2L	HGNC	31865	protein_coding	YES	CCDS47075.1	ENSP00000379108	MTD2L_HUMAN	F8W7P9_HUMAN	UPI000192952C	.	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	10	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTTTTTATAT	.	2	ESCA
BMP2K	0	.	GRCh37	4	79808450	79808450	+	Intron	SNP	A	A	G	rs759468953	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2062+12A>G	.	.	ENST00000335016	.	20	2	17	53	53	0	PAQR3,3_prime_UTR_variant,,ENST00000295462,;BMP2K,intron_variant,,ENST00000335016,;BMP2K,intron_variant,,ENST00000502613,;PAQR3,3_prime_UTR_variant,,ENST00000512760,;PAQR3,3_prime_UTR_variant,,ENST00000342820,;	G	ENSG00000138756	ENST00000335016	Transcript	intron_variant	.	.	.	.	.	rs759468953	.	.	1	BMP2K	HGNC	18041	protein_coding	YES	CCDS47083.1	ENSP00000334836	BMP2K_HUMAN	.	UPI00001BDC7C	.	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACACATGTAA	.	5	ESCA
SLC6A18	0	.	GRCh37	5	1238137	1238137	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.694G>C	p.Gly232Arg	p.G232R	ENST00000324642	5/12	48	17	31	31	31	0	SLC6A18,missense_variant,p.Gly232Arg,ENST00000324642,;SLC6A18,missense_variant,p.Gly232Arg,ENST00000296821,;	C	ENSG00000164363	ENST00000324642	Transcript	missense_variant	817	694	232	G/R	Ggg/Cgg	.	.	.	1	SLC6A18	HGNC	26441	protein_coding	YES	CCDS3860.1	ENSP00000323549	S6A18_HUMAN	.	UPI0000197EA2	.	deleterious(0)	probably_damaging(0.941)	5/12	.	PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF109,Pfam_domain:PF00209,Superfamily_domains:0053687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAGGGGCA	.	5	ESCA
CDKL3	0	.	GRCh37	5	133643980	133643980	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213C>A	p.Pro405Thr	p.P405T	ENST00000265334	9/13	64	30	34	94	94	0	CDKL3,missense_variant,p.Pro405Thr,ENST00000523832,;CDKL3,missense_variant,p.Pro110Thr,ENST00000609383,;CDKL3,missense_variant,p.Pro216Thr,ENST00000609654,;CDKL3,missense_variant,p.Pro405Thr,ENST00000435211,;CDKL3,missense_variant,p.Pro405Thr,ENST00000265334,;CDKL3,missense_variant,p.Pro216Thr,ENST00000523054,;CDKL3,missense_variant,p.Pro110Thr,ENST00000435240,;CDKL3,missense_variant,p.Pro405Thr,ENST00000521118,;CDKL3,missense_variant,p.Pro110Thr,ENST00000536186,;CDKL3,3_prime_UTR_variant,,ENST00000521755,;CDKL3,upstream_gene_variant,,ENST00000518990,;CTD-2410N18.4,non_coding_transcript_exon_variant,,ENST00000518409,;CDKL3,3_prime_UTR_variant,,ENST00000520693,;CDKL3,3_prime_UTR_variant,,ENST00000520592,;CDKL3,3_prime_UTR_variant,,ENST00000519312,;CTD-2410N18.4,non_coding_transcript_exon_variant,,ENST00000520515,;	T	ENSG00000006837	ENST00000265334	Transcript	missense_variant	1332	1213	405	P/T	Cca/Aca	.	.	.	-1	CDKL3	HGNC	15483	protein_coding	YES	CCDS47264.1	ENSP00000265334	CDKL3_HUMAN	.	UPI00000745AD	.	tolerated(0.11)	benign(0.15)	9/13	.	hmmpanther:PTHR24056:SF177,hmmpanther:PTHR24056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTGGTTCAA	.	5	ESCA
FAM13B	0	.	GRCh37	5	137275979	137275979	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2683A>G	p.Ile895Val	p.I895V	ENST00000033079	23/23	28	11	17	31	31	0	FAM13B,missense_variant,p.Ile867Val,ENST00000420893,;FAM13B,missense_variant,p.Ile895Val,ENST00000033079,;FAM13B,missense_variant,p.Ile771Val,ENST00000425075,;PKD2L2,3_prime_UTR_variant,,ENST00000290431,;PKD2L2,3_prime_UTR_variant,,ENST00000502810,;PKD2L2,3_prime_UTR_variant,,ENST00000508638,;PKD2L2,intron_variant,,ENST00000508883,;PKD2L2,downstream_gene_variant,,ENST00000350250,;FAM13B,downstream_gene_variant,,ENST00000513640,;	C	ENSG00000031003	ENST00000033079	Transcript	missense_variant	3135	2683	895	I/V	Att/Gtt	.	.	.	-1	FAM13B	HGNC	1335	protein_coding	YES	CCDS4195.1	ENSP00000033079	FA13B_HUMAN	D6RE97_HUMAN,D6RDL7_HUMAN,D6RCA0_HUMAN,D6RBJ3_HUMAN,D6RAT6_HUMAN	UPI000004A03C	.	tolerated(0.37)	benign(0.014)	23/23	.	hmmpanther:PTHR15904:SF16,hmmpanther:PTHR15904	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAATTTTCT	.	5	ESCA
ANKHD1	0	.	GRCh37	5	139917797	139917797	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7355C>G	p.Ser2452Cys	p.S2452C	ENST00000297183	32/36	35	26	9	50	50	0	ANKHD1,missense_variant,p.Ser844Cys,ENST00000432301,;ANKHD1,missense_variant,p.Ser110Cys,ENST00000421706,;ANKHD1,missense_variant,p.Ser943Cys,ENST00000435794,;ANKHD1,missense_variant,p.Ser2452Cys,ENST00000360839,;ANKHD1,missense_variant,p.Ser776Cys,ENST00000544120,;ANKHD1,missense_variant,p.Ser2452Cys,ENST00000297183,;ANKHD1,missense_variant,p.Ser991Cys,ENST00000433049,;ANKHD1-EIF4EBP3,missense_variant,p.Ser480Cys,ENST00000437495,;ANKHD1,missense_variant,p.Ser1125Cys,ENST00000431508,;ANKHD1-EIF4EBP3,missense_variant,p.Ser2452Cys,ENST00000532219,;SRA1,intron_variant,,ENST00000602657,;ANKHD1-EIF4EBP3,non_coding_transcript_exon_variant,,ENST00000474060,;ANKHD1,non_coding_transcript_exon_variant,,ENST00000495578,;ANKHD1,downstream_gene_variant,,ENST00000475148,;	G	ENSG00000131503	ENST00000297183	Transcript	missense_variant	7479	7355	2452	S/C	tCt/tGt	.	.	.	1	ANKHD1	HGNC	24714	protein_coding	YES	CCDS4224.1	ENSP00000297183	ANKH1_HUMAN	.	UPI0000074448	.	.	possibly_damaging(0.884)	32/36	.	hmmpanther:PTHR23206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCTAACA	.	5	ESCA
GABRA1	0	.	GRCh37	5	161325969	161325969	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1541C>T	.	.	ENST00000428797	11/11	45	39	5	44	44	0	GABRA1,3_prime_UTR_variant,,ENST00000444819,;GABRA1,3_prime_UTR_variant,,ENST00000420560,;GABRA1,3_prime_UTR_variant,,ENST00000437025,;GABRA1,3_prime_UTR_variant,,ENST00000428797,;GABRA1,downstream_gene_variant,,ENST00000393943,;GABRA1,downstream_gene_variant,,ENST00000023897,;	T	ENSG00000022355	ENST00000428797	Transcript	3_prime_UTR_variant	3267	.	.	.	.	.	.	.	1	GABRA1	HGNC	4075	protein_coding	YES	CCDS4357.1	ENSP00000393097	GBRA1_HUMAN	E5RK60_HUMAN,E5RJS3_HUMAN	UPI000012AF95	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAATACTTCCT	.	4	ESCA
RMND5B	0	.	GRCh37	5	177565148	177565148	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.28G>T	p.Glu10Ter	p.E10*	ENST00000515098	4/12	27	13	14	34	34	0	RMND5B,stop_gained,p.Glu10Ter,ENST00000508647,;RMND5B,stop_gained,p.Glu10Ter,ENST00000313386,;RMND5B,stop_gained,p.Glu10Ter,ENST00000502814,;RMND5B,stop_gained,p.Glu10Ter,ENST00000515098,;RMND5B,stop_gained,p.Glu10Ter,ENST00000507457,;RMND5B,intron_variant,,ENST00000542098,;RMND5B,stop_gained,p.Glu10Ter,ENST00000512811,;RMND5B,stop_gained,p.Glu10Ter,ENST00000512663,;RMND5B,non_coding_transcript_exon_variant,,ENST00000507575,;RMND5B,upstream_gene_variant,,ENST00000513162,;RMND5B,upstream_gene_variant,,ENST00000515360,;	T	ENSG00000145916	ENST00000515098	Transcript	stop_gained	379	28	10	E/*	Gag/Tag	.	.	.	1	RMND5B	HGNC	26181	protein_coding	YES	CCDS4431.1	ENSP00000420875	RMD5B_HUMAN	Q659D3_HUMAN,D6RIF9_HUMAN,D6RFK1_HUMAN,D6RER3_HUMAN	UPI0000037C23	.	.	.	4/12	.	hmmpanther:PTHR12170,hmmpanther:PTHR12170:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGAGAGCTG	.	5	ESCA
DEPDC1B	0	.	GRCh37	5	59941316	59941316	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578+3A>G	.	.	ENST00000265036	.	27	23	3	30	30	0	DEPDC1B,splice_region_variant,,ENST00000453022,;DEPDC1B,splice_region_variant,,ENST00000265036,;DEPDC1B,splice_region_variant,,ENST00000545085,;DEPDC1B,splice_region_variant,,ENST00000512078,;DEPDC1B,downstream_gene_variant,,ENST00000505017,;DEPDC1B,downstream_gene_variant,,ENST00000512452,;	C	ENSG00000035499	ENST00000265036	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	DEPDC1B	HGNC	24902	protein_coding	YES	CCDS3977.1	ENSP00000265036	DEP1B_HUMAN	.	UPI000020C7D4	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GTACATACTAT	.	2	ESCA
SV2C	0	.	GRCh37	5	75428155	75428155	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.580G>A	p.Gly194Ser	p.G194S	ENST00000502798	2/13	35	7	28	44	44	0	SV2C,missense_variant,p.Gly194Ser,ENST00000502798,;SV2C,missense_variant,p.Gly194Ser,ENST00000322285,;	A	ENSG00000122012	ENST00000502798	Transcript	missense_variant	1022	580	194	G/S	Ggc/Agc	.	.	.	1	SV2C	HGNC	30670	protein_coding	YES	CCDS43331.1	ENSP00000423541	SV2C_HUMAN	.	UPI000011DDBB	.	tolerated(0.15)	probably_damaging(0.92)	2/13	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24065,hmmpanther:PTHR24065:SF3,TIGRFAM_domain:TIGR01299,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTAGGTGAG	.	5	ESCA
CMYA5	0	.	GRCh37	5	79025179	79025179	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.591C>A	p.%3D	p.T197T	ENST00000446378	2/13	17	11	6	16	16	0	CMYA5,synonymous_variant,p.%3D,ENST00000446378,;	A	ENSG00000164309	ENST00000446378	Transcript	synonymous_variant	622	591	197	T	acC/acA	.	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	.	2/13	.	hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGACCACTTC	.	5	ESCA
REV3L	0	.	GRCh37	6	111694879	111694879	+	Missense_Mutation	SNP	T	T	C	rs775832892	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4679A>G	p.Asn1560Ser	p.N1560S	ENST00000358835	14/33	49	44	5	74	74	0	REV3L,missense_variant,p.Asn1482Ser,ENST00000435970,;REV3L,missense_variant,p.Asn1560Ser,ENST00000358835,;REV3L,missense_variant,p.Asn1560Ser,ENST00000368802,;REV3L,missense_variant,p.Asn1560Ser,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000434009,;REV3L,3_prime_UTR_variant,,ENST00000422377,;	C	ENSG00000009413	ENST00000358835	Transcript	missense_variant	5134	4679	1560	N/S	aAt/aGt	rs775832892	.	.	-1	REV3L	HGNC	9968	protein_coding	YES	CCDS5091.2	ENSP00000351697	DPOLZ_HUMAN	Q9UID5_HUMAN,C4TNX2_HUMAN,C4TNX1_HUMAN,C4TNX0_HUMAN,C4B7Q4_HUMAN	UPI0000140023	.	tolerated(1)	benign(0.001)	14/33	.	hmmpanther:PTHR10322:SF16,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAATATTTTTA	.	3	ESCA
HIVEP1	0	.	GRCh37	6	12125356	12125356	+	Silent	SNP	C	C	T	rs539525903	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5328C>T	p.%3D	p.D1776D	ENST00000379388	4/9	30	20	9	16	16	0	HIVEP1,synonymous_variant,p.%3D,ENST00000379388,;HIVEP1,intron_variant,,ENST00000442081,;HIVEP1,downstream_gene_variant,,ENST00000487103,;HIVEP1,upstream_gene_variant,,ENST00000541134,;HIVEP1,downstream_gene_variant,,ENST00000491710,;HIVEP1,downstream_gene_variant,,ENST00000478545,;HIVEP1,upstream_gene_variant,,ENST00000399469,;	T	ENSG00000095951	ENST00000379388	Transcript	synonymous_variant	5660	5328	1776	D	gaC/gaT	rs539525903	.	.	1	HIVEP1	HGNC	4920	protein_coding	YES	CCDS43426.1	ENSP00000368698	ZEP1_HUMAN	C9JZF8_HUMAN,C9JAW2_HUMAN,C9J2N3_HUMAN	UPI000020D52B	.	.	.	4/9	.	hmmpanther:PTHR23233:SF48,hmmpanther:PTHR23233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGACGTGAG	byCluster	5	ESCA
PTPRK	0	.	GRCh37	6	128718824	128718824	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110C>A	p.Thr37Asn	p.T37N	ENST00000368213	2/31	20	16	4	26	26	0	PTPRK,missense_variant,p.Thr37Asn,ENST00000532331,;PTPRK,missense_variant,p.Thr37Asn,ENST00000368226,;PTPRK,missense_variant,p.Thr37Asn,ENST00000368215,;PTPRK,missense_variant,p.Thr37Asn,ENST00000368207,;PTPRK,missense_variant,p.Thr37Asn,ENST00000368210,;PTPRK,missense_variant,p.Thr37Asn,ENST00000368227,;PTPRK,missense_variant,p.Thr37Asn,ENST00000525459,;PTPRK,missense_variant,p.Thr37Asn,ENST00000368213,;PTPRK,non_coding_transcript_exon_variant,,ENST00000495748,;PTPRK,non_coding_transcript_exon_variant,,ENST00000524534,;PTPRK,non_coding_transcript_exon_variant,,ENST00000524481,;PTPRK,stop_gained,p.Tyr76Ter,ENST00000392449,;PTPRK,3_prime_UTR_variant,,ENST00000532751,;PTPRK,upstream_gene_variant,,ENST00000531050,;	T	ENSG00000152894	ENST00000368213	Transcript	missense_variant	335	110	37	T/N	aCt/aAt	.	.	.	-1	PTPRK	HGNC	9674	protein_coding	YES	CCDS47473.1	ENSP00000357196	PTPRK_HUMAN	.	UPI0001747A04	.	tolerated(0.17)	benign(0.385)	2/31	.	Superfamily_domains:SSF49899,SMART_domains:SM00137,Pfam_domain:PF00629,hmmpanther:PTHR19134:SF209,hmmpanther:PTHR19134,PROSITE_profiles:PS50060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CAAAAGTACAG	.	3	ESCA
GINM1	0	.	GRCh37	6	149900994	149900994	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454A>G	p.Ile152Val	p.I152V	ENST00000367419	5/8	18	1	17	32	32	0	GINM1,missense_variant,p.Ile26Val,ENST00000433539,;GINM1,missense_variant,p.Ile152Val,ENST00000367419,;RP1-12G14.6,upstream_gene_variant,,ENST00000435273,;	G	ENSG00000055211	ENST00000367419	Transcript	missense_variant	575	454	152	I/V	Att/Gtt	.	.	.	1	GINM1	HGNC	21074	protein_coding	YES	CCDS5216.1	ENSP00000356389	GINM1_HUMAN	.	UPI0000049E0C	.	tolerated(0.41)	benign(0.021)	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAAATTGAT	.	5	ESCA
PDCD2	0	.	GRCh37	6	170892195	170892195	+	Missense_Mutation	SNP	A	A	G	rs769614520	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608T>C	p.Met203Thr	p.M203T	ENST00000541970	3/6	33	4	28	29	29	0	PDCD2,start_lost,p.Met1?,ENST00000538195,;PDCD2,missense_variant,p.Met203Thr,ENST00000541970,;PDCD2,missense_variant,p.Met170Thr,ENST00000443345,;PDCD2,missense_variant,p.Met170Thr,ENST00000537445,;PDCD2,missense_variant,p.Met203Thr,ENST00000453163,;PDCD2,missense_variant,p.Met170Thr,ENST00000392090,;PDCD2,missense_variant,p.Met203Thr,ENST00000542896,;PDCD2,missense_variant,p.Met203Thr,ENST00000167218,;PDCD2,3_prime_UTR_variant,,ENST00000544755,;PDCD2,3_prime_UTR_variant,,ENST00000544866,;PDCD2,3_prime_UTR_variant,,ENST00000545869,;PDCD2,3_prime_UTR_variant,,ENST00000539212,;PDCD2,3_prime_UTR_variant,,ENST00000544336,;PDCD2,upstream_gene_variant,,ENST00000543284,;	G	ENSG00000071994	ENST00000541970	Transcript	missense_variant	687	608	203	M/T	aTg/aCg	rs769614520	.	.	-1	PDCD2	HGNC	8762	protein_coding	YES	CCDS5316.1	ENSP00000439467	PDCD2_HUMAN	F5H739_HUMAN	UPI000013149C	.	tolerated(0.64)	benign(0)	3/6	.	hmmpanther:PTHR12298,Pfam_domain:PF04194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGCATAATC	.	5	ESCA
ALDH5A1	0	.	GRCh37	6	24534212	24534212	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*272C>A	.	.	ENST00000348925	11/11	16	10	5	19	19	0	ALDH5A1,3_prime_UTR_variant,,ENST00000348925,;ALDH5A1,3_prime_UTR_variant,,ENST00000546278,;ALDH5A1,3_prime_UTR_variant,,ENST00000357578,;ALDH5A1,downstream_gene_variant,,ENST00000491546,;ALDH5A1,non_coding_transcript_exon_variant,,ENST00000479394,;ALDH5A1,downstream_gene_variant,,ENST00000492697,;	A	ENSG00000112294	ENST00000348925	Transcript	3_prime_UTR_variant	1947	.	.	.	.	.	.	.	1	ALDH5A1	HGNC	408	protein_coding	YES	CCDS4556.1	ENSP00000314649	SSDH_HUMAN	.	UPI00001619D2	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAGCTGCCT	.	5	ESCA
OR11A1	0	.	GRCh37	6	29394522	29394522	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.897T>C	p.%3D	p.H299H	ENST00000377149	5/5	20	9	11	23	23	0	OR11A1,synonymous_variant,p.%3D,ENST00000377149,;OR11A1,synonymous_variant,p.%3D,ENST00000377148,;OR11A1,synonymous_variant,p.%3D,ENST00000377147,;OR5V1,intron_variant,,ENST00000377154,;	G	ENSG00000204694	ENST00000377149	Transcript	synonymous_variant	1370	897	299	H	caT/caC	.	.	.	-1	OR11A1	HGNC	8176	protein_coding	YES	CCDS34363.1	ENSP00000366354	O11A1_HUMAN	.	UPI000000DCA8	.	.	.	5/5	.	hmmpanther:PTHR24242:SF178,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTGATGCAC	.	5	ESCA
SRPK1	0	.	GRCh37	6	35810356	35810356	+	Missense_Mutation	SNP	T	T	C	rs368604697	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1646A>G	p.Tyr549Cys	p.Y549C	ENST00000373825	14/16	15	11	4	12	12	0	SRPK1,missense_variant,p.Tyr565Cys,ENST00000361690,;SRPK1,missense_variant,p.Tyr533Cys,ENST00000423325,;SRPK1,missense_variant,p.Tyr441Cys,ENST00000373822,;SRPK1,missense_variant,p.Tyr549Cys,ENST00000373825,;SRPK1,non_coding_transcript_exon_variant,,ENST00000346162,;SRPK1,upstream_gene_variant,,ENST00000505885,;	C	ENSG00000096063	ENST00000373825	Transcript	missense_variant	1932	1646	549	Y/C	tAt/tGt	rs368604697	.	.	-1	SRPK1	HGNC	11305	protein_coding	YES	CCDS47415.1	ENSP00000362931	SRPK1_HUMAN	D6RBF8_HUMAN	UPI000020DBDD	.	deleterious(0)	probably_damaging(1)	14/16	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF101,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAAATAGTCA	.	5	ESCA
FBXO9	0	.	GRCh37	6	52960336	52960336	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109A>G	p.Tyr370Cys	p.Y370C	ENST00000244426	11/12	49	21	27	44	44	0	FBXO9,missense_variant,p.Tyr326Cys,ENST00000370939,;FBXO9,missense_variant,p.Tyr370Cys,ENST00000244426,;FBXO9,missense_variant,p.Tyr119Cys,ENST00000473318,;FBXO9,missense_variant,p.Tyr360Cys,ENST00000323557,;FBXO9,missense_variant,p.Tyr77Cys,ENST00000484436,;RN7SL244P,downstream_gene_variant,,ENST00000493405,;FBXO9,non_coding_transcript_exon_variant,,ENST00000474457,;FBXO9,downstream_gene_variant,,ENST00000480463,;FBXO9,downstream_gene_variant,,ENST00000484812,;	G	ENSG00000112146	ENST00000244426	Transcript	missense_variant	1281	1109	370	Y/C	tAt/tGt	.	.	.	1	FBXO9	HGNC	13588	protein_coding	YES	CCDS55023.1	ENSP00000244426	FBX9_HUMAN	C9JDZ9_HUMAN,C9J4V1_HUMAN,C9IY65_HUMAN	UPI000012A589	.	tolerated(0.13)	possibly_damaging(0.664)	11/12	.	hmmpanther:PTHR12874:SF9,hmmpanther:PTHR12874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATATTTTC	.	5	ESCA
PHIP	0	.	GRCh37	6	79698018	79698018	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2368C>A	p.Gln790Lys	p.Q790K	ENST00000275034	21/40	25	12	12	58	58	0	PHIP,missense_variant,p.Gln790Lys,ENST00000275034,;	T	ENSG00000146247	ENST00000275034	Transcript	missense_variant	2536	2368	790	Q/K	Cag/Aag	.	.	.	-1	PHIP	HGNC	15673	protein_coding	YES	CCDS4987.1	ENSP00000275034	PHIP_HUMAN	.	UPI000013DA40	.	tolerated(0.23)	benign(0.011)	21/40	.	hmmpanther:PTHR16266:SF4,hmmpanther:PTHR16266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTGTTGCT	.	5	ESCA
NAPEPLD	0	.	GRCh37	7	102741976	102741976	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1900T>C	.	.	ENST00000417955	5/5	19	12	6	13	13	0	NAPEPLD,3_prime_UTR_variant,,ENST00000341533,;NAPEPLD,3_prime_UTR_variant,,ENST00000417955,;ARMC10,downstream_gene_variant,,ENST00000454559,;NAPEPLD,downstream_gene_variant,,ENST00000427257,;ARMC10,downstream_gene_variant,,ENST00000323716,;ARMC10,downstream_gene_variant,,ENST00000434153,;ARMC10,downstream_gene_variant,,ENST00000428183,;ARMC10,downstream_gene_variant,,ENST00000431642,;NAPEPLD,downstream_gene_variant,,ENST00000455523,;ARMC10,downstream_gene_variant,,ENST00000441711,;ARMC10,downstream_gene_variant,,ENST00000541300,;ARMC10,downstream_gene_variant,,ENST00000425331,;NAPEPLD,downstream_gene_variant,,ENST00000465647,;NAPEPLD,non_coding_transcript_exon_variant,,ENST00000414118,;NAPEPLD,intron_variant,,ENST00000422589,;ARMC10,downstream_gene_variant,,ENST00000306450,;NAPEPLD,downstream_gene_variant,,ENST00000420631,;ARMC10,downstream_gene_variant,,ENST00000323735,;ARMC10,downstream_gene_variant,,ENST00000479145,;	G	ENSG00000161048	ENST00000417955	Transcript	3_prime_UTR_variant	3237	.	.	.	.	.	.	.	-1	NAPEPLD	HGNC	21683	protein_coding	YES	CCDS5729.1	ENSP00000407112	NAPEP_HUMAN	C9JGB1_HUMAN	UPI00001D74C6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGTATTTAG	.	5	ESCA
GRM8	0	.	GRCh37	7	126409920	126409920	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1356T>A	p.Asn452Lys	p.N452K	ENST00000339582	7/11	25	19	6	50	50	0	GRM8,missense_variant,p.Asn452Lys,ENST00000339582,;GRM8,missense_variant,p.Asn452Lys,ENST00000444921,;GRM8,missense_variant,p.Asn452Lys,ENST00000358373,;GRM8,missense_variant,p.Asn452Lys,ENST00000405249,;GRM8,splice_region_variant,,ENST00000480995,;GRM8,downstream_gene_variant,,ENST00000448250,;GRM8,missense_variant,p.Asn452Lys,ENST00000341617,;GRM8,missense_variant,p.Asn452Lys,ENST00000472701,;	T	ENSG00000179603	ENST00000339582	Transcript	missense_variant	2165	1356	452	N/K	aaT/aaA	.	.	.	-1	GRM8	HGNC	4600	protein_coding	YES	CCDS5794.1	ENSP00000344173	GRM8_HUMAN	E7ETK3_HUMAN,C9J7I1_HUMAN	UPI000012F085	.	tolerated(0.37)	benign(0.028)	7/11	.	hmmpanther:PTHR24060:SF26,hmmpanther:PTHR24060,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACCATTAAA	.	5	ESCA
TAS2R4	0	.	GRCh37	7	141478419	141478419	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.131C>G	p.Ser44Cys	p.S44C	ENST00000247881	1/1	33	29	4	59	59	0	TAS2R4,missense_variant,p.Ser44Cys,ENST00000247881,;SSBP1,intron_variant,,ENST00000465582,;	G	ENSG00000127364	ENST00000247881	Transcript	missense_variant	178	131	44	S/C	tCt/tGt	.	.	.	1	TAS2R4	HGNC	14911	protein_coding	YES	CCDS5868.1	ENSP00000247881	TA2R4_HUMAN	Q50KX7_HUMAN,Q50KX5_HUMAN	UPI0000038B0C	.	tolerated(0.09)	benign(0.315)	1/1	.	hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF55,Pfam_domain:PF05296,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTCTTCTGATA	.	3	ESCA
RBM33	0	.	GRCh37	7	155559292	155559292	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3318C>G	p.%3D	p.S1106S	ENST00000401878	16/18	12	9	3	15	15	0	RBM33,synonymous_variant,p.%3D,ENST00000401878,;RBM33,synonymous_variant,p.%3D,ENST00000341148,;RBM33,synonymous_variant,p.%3D,ENST00000392761,;RBM33,synonymous_variant,p.%3D,ENST00000392755,;RBM33,downstream_gene_variant,,ENST00000438356,;	G	ENSG00000184863	ENST00000401878	Transcript	synonymous_variant	3516	3318	1106	S	tcC/tcG	.	.	.	1	RBM33	HGNC	27223	protein_coding	YES	CCDS5941.2	ENSP00000384160	RBM33_HUMAN	C9J7M3_HUMAN	UPI00015743D7	.	.	.	16/18	.	Superfamily_domains:SSF54928,SMART_domains:SM00360,Gene3D:3.30.70.330,Pfam_domain:PF14259,hmmpanther:PTHR22014,hmmpanther:PTHR22014:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTCCTCGTC	.	2	ESCA
C7orf31	0	.	GRCh37	7	25191224	25191224	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.675A>G	p.%3D	p.V225V	ENST00000409280	7/10	34	15	19	34	34	0	C7orf31,synonymous_variant,p.%3D,ENST00000409280,;C7orf31,synonymous_variant,p.%3D,ENST00000283905,;C7orf31,downstream_gene_variant,,ENST00000443822,;	C	ENSG00000153790	ENST00000409280	Transcript	synonymous_variant	984	675	225	V	gtA/gtG	.	.	.	-1	C7orf31	HGNC	21722	protein_coding	YES	CCDS5394.1	ENSP00000386604	CG031_HUMAN	C9JTB1_HUMAN,C9JF06_HUMAN,C9J431_HUMAN	UPI000013DD61	.	.	.	7/10	.	hmmpanther:PTHR31393,Pfam_domain:PF15093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATATACACC	.	5	ESCA
TRGJP2	0	.	GRCh37	7	38295976	38295976	+	Missense_Mutation	SNP	G	G	C	rs374481045	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22C>G	p.Thr8Arg	p.T8R	ENST00000390334	1/1	38	23	15	39	39	0	TRGJP2,missense_variant,p.Thr8Arg,ENST00000390334,;TRGJ2,upstream_gene_variant,,ENST00000390333,;TRGC1,downstream_gene_variant,,ENST00000443402,;	C	ENSG00000211688	ENST00000390334	Transcript	missense_variant	22	23	8	T/R	aCg/aGg	rs374481045	.	.	-1	TRGJP2	HGNC	12281	TR_J_gene	YES	.	ENSP00000418697	.	.	UPI000198CE09	.	.	unknown(0)	1/1	.	.	A:0.0010	A:0.0038	A:0	.	A:0	A:0	A:0	A:0.0011	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAACGTCTTG	byFrequency|byCluster|by1000G	5	ESCA
AMPH	0	.	GRCh37	7	38423492	38423492	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*927C>A	.	.	ENST00000356264	21/21	18	11	7	25	25	0	AMPH,3_prime_UTR_variant,,ENST00000356264,;AMPH,3_prime_UTR_variant,,ENST00000428293,;AMPH,3_prime_UTR_variant,,ENST00000325590,;AMPH,downstream_gene_variant,,ENST00000441628,;	T	ENSG00000078053	ENST00000356264	Transcript	3_prime_UTR_variant	3231	.	.	.	.	.	.	.	-1	AMPH	HGNC	471	protein_coding	YES	CCDS5456.1	ENSP00000348602	AMPH_HUMAN	Q9UQI5_HUMAN,Q9UQI4_HUMAN,Q9UQI3_HUMAN,Q9UQI2_HUMAN	UPI00001259EA	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTGGGGGT	.	5	ESCA
POLD2	0	.	GRCh37	7	44156828	44156828	+	Missense_Mutation	SNP	A	A	T	rs762666447	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.485T>A	p.Phe162Tyr	p.F162Y	ENST00000406581	6/12	37	34	3	33	33	0	POLD2,missense_variant,p.Phe162Tyr,ENST00000406581,;POLD2,missense_variant,p.Phe162Tyr,ENST00000223361,;POLD2,missense_variant,p.Phe162Tyr,ENST00000433715,;POLD2,missense_variant,p.Phe162Tyr,ENST00000452185,;POLD2,missense_variant,p.Phe80Tyr,ENST00000436844,;POLD2,upstream_gene_variant,,ENST00000436400,;POLD2,downstream_gene_variant,,ENST00000456038,;POLD2,downstream_gene_variant,,ENST00000418438,;AEBP1,downstream_gene_variant,,ENST00000223357,;AEBP1,downstream_gene_variant,,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000481763,;POLD2,non_coding_transcript_exon_variant,,ENST00000481104,;POLD2,non_coding_transcript_exon_variant,,ENST00000463464,;POLD2,non_coding_transcript_exon_variant,,ENST00000470867,;POLD2,downstream_gene_variant,,ENST00000496539,;AEBP1,downstream_gene_variant,,ENST00000431035,;POLD2,downstream_gene_variant,,ENST00000467469,;POLD2,downstream_gene_variant,,ENST00000461116,;AEBP1,downstream_gene_variant,,ENST00000413907,;POLD2,downstream_gene_variant,,ENST00000464871,;POLD2,upstream_gene_variant,,ENST00000489883,;	T	ENSG00000106628	ENST00000406581	Transcript	missense_variant	1135	485	162	F/Y	tTt/tAt	rs762666447	.	.	-1	POLD2	HGNC	9176	protein_coding	YES	CCDS5477.1	ENSP00000386105	DPOD2_HUMAN	C9JLE1_HUMAN,C9J8Z7_HUMAN,C9IZD2_HUMAN,A4D2J4_HUMAN	UPI000004D0E7	.	tolerated(1)	benign(0)	6/12	.	hmmpanther:PTHR10416:SF0,hmmpanther:PTHR10416	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCAAACACA	.	2	ESCA
RBAK	0	.	GRCh37	7	5104863	5104863	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1776G>C	p.Glu592Asp	p.E592D	ENST00000396912	5/5	24	16	8	20	20	0	RBAK,missense_variant,p.Glu592Asp,ENST00000353796,;RBAK,missense_variant,p.Glu592Asp,ENST00000396912,;RBAK-RBAKDN,intron_variant,,ENST00000407184,;RBAK-RBAKDN,intron_variant,,ENST00000396904,;RBAK,downstream_gene_variant,,ENST00000476992,;	C	ENSG00000146587	ENST00000396912	Transcript	missense_variant	2295	1776	592	E/D	gaG/gaC	.	.	.	1	RBAK	HGNC	17680	protein_coding	YES	CCDS5337.1	ENSP00000380120	RBAK_HUMAN	.	UPI000004A03E	.	deleterious(0)	probably_damaging(0.986)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24392,hmmpanther:PTHR24392:SF18,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGAGAAACC	.	5	ESCA
COBL	0	.	GRCh37	7	51096150	51096150	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2643C>G	p.%3D	p.V881V	ENST00000265136	10/13	49	23	25	49	49	0	COBL,synonymous_variant,p.%3D,ENST00000431948,;COBL,synonymous_variant,p.%3D,ENST00000265136,;COBL,synonymous_variant,p.%3D,ENST00000395542,;COBL,synonymous_variant,p.%3D,ENST00000445054,;COBL,downstream_gene_variant,,ENST00000452534,;COBL,non_coding_transcript_exon_variant,,ENST00000462395,;	C	ENSG00000106078	ENST00000265136	Transcript	synonymous_variant	2809	2643	881	V	gtC/gtG	.	.	.	-1	COBL	HGNC	22199	protein_coding	YES	CCDS34637.1	ENSP00000265136	COBL_HUMAN	C9J9X1_HUMAN	UPI00001A9480	.	.	.	10/13	.	hmmpanther:PTHR21557,hmmpanther:PTHR21557:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATGGACTTT	.	5	ESCA
POM121L12	0	.	GRCh37	7	53104434	53104434	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*179C>G	.	.	ENST00000408890	1/1	34	23	11	28	28	0	POM121L12,3_prime_UTR_variant,,ENST00000408890,;	G	ENSG00000221900	ENST00000408890	Transcript	3_prime_UTR_variant	1086	.	.	.	.	.	.	.	1	POM121L12	HGNC	25369	protein_coding	YES	CCDS43584.1	ENSP00000386133	P1L12_HUMAN	.	UPI00001B6540	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGCTGTTG	.	5	ESCA
ZNF394	0	.	GRCh37	7	99091249	99091249	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1589G>C	p.Cys530Ser	p.C530S	ENST00000337673	3/3	89	42	46	67	67	0	ZNF394,missense_variant,p.Cys530Ser,ENST00000337673,;ZNF394,3_prime_UTR_variant,,ENST00000426306,;ZNF789,intron_variant,,ENST00000493485,;ZNF394,intron_variant,,ENST00000462024,;ZNF789,intron_variant,,ENST00000494186,;ZNF394,downstream_gene_variant,,ENST00000394177,;ZNF394,downstream_gene_variant,,ENST00000485576,;ZNF394,downstream_gene_variant,,ENST00000464401,;ZNF394,downstream_gene_variant,,ENST00000481881,;	G	ENSG00000160908	ENST00000337673	Transcript	missense_variant	1793	1589	530	C/S	tGt/tCt	COSM1319780	.	.	-1	ZNF394	HGNC	18832	protein_coding	YES	CCDS5666.1	ENSP00000337363	ZN394_HUMAN	.	UPI000006F498	.	deleterious(0)	probably_damaging(0.986)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF3,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCACATTCA	.	5	ESCA
GPC2	0	.	GRCh37	7	99767517	99767517	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*336G>T	.	.	ENST00000292377	10/10	55	30	25	45	45	0	GPC2,3_prime_UTR_variant,,ENST00000292377,;GAL3ST4,upstream_gene_variant,,ENST00000413800,;GAL3ST4,upstream_gene_variant,,ENST00000411994,;GAL3ST4,upstream_gene_variant,,ENST00000423751,;GAL3ST4,upstream_gene_variant,,ENST00000360039,;GAL3ST4,upstream_gene_variant,,ENST00000426974,;GPC2,non_coding_transcript_exon_variant,,ENST00000471050,;GAL3ST4,upstream_gene_variant,,ENST00000460995,;GPC2,downstream_gene_variant,,ENST00000480087,;GAL3ST4,upstream_gene_variant,,ENST00000482469,;GAL3ST4,upstream_gene_variant,,ENST00000498000,;GPC2,downstream_gene_variant,,ENST00000486702,;GPC2,downstream_gene_variant,,ENST00000471717,;GAL3ST4,upstream_gene_variant,,ENST00000495882,;GPC2,downstream_gene_variant,,ENST00000490629,;	A	ENSG00000213420	ENST00000292377	Transcript	3_prime_UTR_variant	2244	.	.	.	.	.	.	.	-1	GPC2	HGNC	4450	protein_coding	YES	CCDS5689.1	ENSP00000292377	GPC2_HUMAN	.	UPI000005340D	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTCCCCAG	.	5	ESCA
NUDCD1	0	.	GRCh37	8	110305659	110305659	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554T>C	p.Leu185Pro	p.L185P	ENST00000239690	4/10	34	30	4	30	30	0	NUDCD1,missense_variant,p.Leu185Pro,ENST00000239690,;NUDCD1,missense_variant,p.Leu156Pro,ENST00000427660,;NUDCD1,3_prime_UTR_variant,,ENST00000521439,;NUDCD1,3_prime_UTR_variant,,ENST00000519607,;	G	ENSG00000120526	ENST00000239690	Transcript	missense_variant	929	554	185	L/P	cTt/cCt	.	.	.	-1	NUDCD1	HGNC	24306	protein_coding	YES	CCDS6312.1	ENSP00000239690	NUDC1_HUMAN	.	UPI000021048A	.	deleterious(0)	probably_damaging(0.993)	4/10	.	hmmpanther:PTHR21664	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCGAAGAAGT	.	4	ESCA
CSMD3	0	.	GRCh37	8	113678609	113678609	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2713G>T	p.Val905Leu	p.V905L	ENST00000297405	17/71	56	37	19	33	33	0	CSMD3,missense_variant,p.Val905Leu,ENST00000352409,;CSMD3,missense_variant,p.Val801Leu,ENST00000455883,;CSMD3,missense_variant,p.Val905Leu,ENST00000297405,;CSMD3,missense_variant,p.Val245Leu,ENST00000339701,;CSMD3,missense_variant,p.Val865Leu,ENST00000343508,;	A	ENSG00000164796	ENST00000297405	Transcript	missense_variant	2958	2713	905	V/L	Gtg/Ttg	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.06)	benign(0.075)	17/71	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCACTCCAC	.	5	ESCA
RNF139	0	.	GRCh37	8	125498283	125498283	+	Silent	SNP	C	C	T	rs148121312	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393C>T	p.%3D	p.I131I	ENST00000303545	2/2	101	89	12	69	69	0	RNF139,synonymous_variant,p.%3D,ENST00000303545,;RNF139,synonymous_variant,p.%3D,ENST00000517684,;TATDN1,downstream_gene_variant,,ENST00000522810,;TATDN1,downstream_gene_variant,,ENST00000519548,;TATDN1,downstream_gene_variant,,ENST00000276692,;RP11-158K1.3,upstream_gene_variant,,ENST00000518639,;TATDN1,downstream_gene_variant,,ENST00000523214,;TATDN1,downstream_gene_variant,,ENST00000522927,;TATDN1,downstream_gene_variant,,ENST00000523631,;	T	ENSG00000170881	ENST00000303545	Transcript	synonymous_variant	765	393	131	I	atC/atT	rs148121312	.	.	1	RNF139	HGNC	17023	protein_coding	YES	CCDS6350.1	ENSP00000304051	RN139_HUMAN	E5RH85_HUMAN	UPI0000071331	.	.	.	2/2	.	Transmembrane_helices:TMhelix,Pfam_domain:PF13705	T:0.0006	T:0	T:0	.	T:0	T:0.001	T:0.002	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTATCGTTCT	byFrequency|byCluster|by1000G	4	ESCA
PHF20L1	0	.	GRCh37	8	133806767	133806767	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.195delG	p.Leu65PhefsTer9	p.L65Ffs*9	ENST00000395386	3/21	152	94	58	47	47	0	PHF20L1,frameshift_variant,p.Leu65PhefsTer9,ENST00000395390,;PHF20L1,frameshift_variant,p.Leu65PhefsTer9,ENST00000395376,;PHF20L1,frameshift_variant,p.Leu65PhefsTer9,ENST00000395379,;PHF20L1,frameshift_variant,p.Leu23PhefsTer9,ENST00000522580,;PHF20L1,frameshift_variant,p.Leu65PhefsTer9,ENST00000337920,;PHF20L1,frameshift_variant,p.Leu65PhefsTer9,ENST00000395386,;PHF20L1,5_prime_UTR_variant,,ENST00000220847,;PHF20L1,frameshift_variant,p.Leu65PhefsTer9,ENST00000486199,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000395383,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000315808,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000361997,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000485595,;PHF20L1,upstream_gene_variant,,ENST00000521038,;	-	ENSG00000129292	ENST00000395386	Transcript	frameshift_variant	494	195	65	L/X	ttG/tt	.	.	.	1	PHF20L1	HGNC	24280	protein_coding	YES	CCDS6367.2	ENSP00000378784	P20L1_HUMAN	E5RK91_HUMAN,B3KWX5_HUMAN	UPI0000DBD7AF	.	.	.	3/21	.	Superfamily_domains:SSF63748,SMART_domains:SM00743,SMART_domains:SM00333,Gene3D:2.30.30.160,hmmpanther:PTHR15856,hmmpanther:PTHR15856:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAGATTGCGACC	.	3	ESCA
SCARA5	0	.	GRCh37	8	27727905	27727905	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1546A>G	.	.	ENST00000354914	9/9	16	8	8	28	28	0	SCARA5,3_prime_UTR_variant,,ENST00000354914,;SCARA5,3_prime_UTR_variant,,ENST00000380385,;	C	ENSG00000168079	ENST00000354914	Transcript	3_prime_UTR_variant	3520	.	.	.	.	.	.	.	-1	SCARA5	HGNC	28701	protein_coding	YES	CCDS6064.1	ENSP00000346990	SCAR5_HUMAN	.	UPI000015FA6D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCATTAGGAC	.	5	ESCA
CEL	0	.	GRCh37	9	135945858	135945858	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1306A>G	p.Thr436Ala	p.T436A	ENST00000372080	10/11	55	29	25	30	30	0	CEL,missense_variant,p.Thr436Ala,ENST00000372080,;CEL,intron_variant,,ENST00000351304,;	G	ENSG00000170835	ENST00000372080	Transcript	missense_variant	1322	1306	436	T/A	Acc/Gcc	.	.	.	1	CEL	HGNC	1848	protein_coding	YES	CCDS43896.1	ENSP00000361151	.	Q9UMB1_HUMAN	UPI000013E8C6	.	deleterious(0)	possibly_damaging(0.836)	10/11	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGACCTAC	.	5	ESCA
NSMF	0	.	GRCh37	9	140346852	140346852	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1201G>C	p.Gly401Arg	p.G401R	ENST00000371475	12/16	33	21	12	29	29	0	NSMF,missense_variant,p.Gly376Arg,ENST00000371474,;NSMF,missense_variant,p.Gly401Arg,ENST00000371475,;NSMF,missense_variant,p.Gly378Arg,ENST00000437259,;NSMF,missense_variant,p.Gly371Arg,ENST00000371473,;NSMF,missense_variant,p.Gly65Arg,ENST00000371482,;NSMF,missense_variant,p.Gly399Arg,ENST00000371472,;NSMF,missense_variant,p.Gly378Arg,ENST00000392812,;NSMF,missense_variant,p.Gly198Arg,ENST00000541195,;NSMF,missense_variant,p.Gly198Arg,ENST00000339554,;NSMF,missense_variant,p.Gly399Arg,ENST00000265663,;NSMF,downstream_gene_variant,,ENST00000371468,;NSMF,non_coding_transcript_exon_variant,,ENST00000484316,;NSMF,non_coding_transcript_exon_variant,,ENST00000482448,;	G	ENSG00000165802	ENST00000371475	Transcript	missense_variant	1433	1201	401	G/R	Gga/Cga	.	.	.	-1	NSMF	HGNC	29843	protein_coding	YES	CCDS48069.1	ENSP00000360530	NSMF_HUMAN	Q9BT66_HUMAN,Q96AQ0_HUMAN,A8K7L5_HUMAN	UPI000035198D	.	deleterious(0)	probably_damaging(1)	12/16	.	hmmpanther:PTHR32061	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGCTCCCTTGT	.	4	ESCA
SH3GL2	0	.	GRCh37	9	17796622	17796622	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*881G>C	.	.	ENST00000380607	9/9	13	3	10	20	20	0	SH3GL2,3_prime_UTR_variant,,ENST00000380607,;SH3GL2,downstream_gene_variant,,ENST00000537391,;	C	ENSG00000107295	ENST00000380607	Transcript	3_prime_UTR_variant	2060	.	.	.	.	.	.	.	1	SH3GL2	HGNC	10831	protein_coding	YES	CCDS6483.1	ENSP00000369981	SH3G2_HUMAN	Q7Z376_HUMAN,Q3V639_HUMAN,F5H5J3_HUMAN,D3DRJ2_HUMAN	UPI0000135933	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGAGACACA	.	5	ESCA
CDKN2A	0	.	GRCh37	9	21971111	21971111	+	Missense_Mutation	SNP	G	G	A	rs121913385	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247C>T	p.His83Tyr	p.H83Y	ENST00000498124	2/4	11	1	10	10	10	0	CDKN2A,missense_variant,p.His32Tyr,ENST00000578845,;CDKN2A,missense_variant,p.Ala97Val,ENST00000579755,;CDKN2A,missense_variant,p.His32Tyr,ENST00000494262,;CDKN2A,missense_variant,p.His32Tyr,ENST00000498628,;CDKN2A,missense_variant,p.Ala97Val,ENST00000530628,;CDKN2A,missense_variant,p.His83Tyr,ENST00000446177,;CDKN2A,missense_variant,p.His83Tyr,ENST00000304494,;CDKN2A,missense_variant,p.Ala138Val,ENST00000361570,;CDKN2A,missense_variant,p.His83Tyr,ENST00000498124,;CDKN2A,missense_variant,p.His32Tyr,ENST00000479692,;CDKN2A,missense_variant,p.His83Tyr,ENST00000579122,;CDKN2A,missense_variant,p.His32Tyr,ENST00000497750,;C9orf53,downstream_gene_variant,,ENST00000441769,;CDKN2A,non_coding_transcript_exon_variant,,ENST00000380150,;CDKN2A,upstream_gene_variant,,ENST00000577854,;CDKN2A,3_prime_UTR_variant,,ENST00000380151,;RP11-145E5.5,intron_variant,,ENST00000404796,;	A	ENSG00000147889	ENST00000498124	Transcript	missense_variant	286	247	83	H/Y	Cac/Tac	CM056557,rs121913385,CM053801,COSM12504,COSM13705,COSM99723,COSM99724,COSM1650884	.	.	-1	CDKN2A	HGNC	1787	protein_coding	YES	CCDS56565.1	ENSP00000418915	CD2A1_HUMAN	Q9UPB7_HUMAN	UPI0001565711	.	deleterious(0)	probably_damaging(0.999)	2/4	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24144:SF30,hmmpanther:PTHR24144,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H83Y|c.247C>T|5,SITE|p.H83Y|c.247C>T|6,SITE|p.A138V|c.413C>T|6,SITE|p.H83Y|c.247C>T|39,CODON|p.0?|c.1_471del471|15,CODON|p.H83R|c.248A>G|3,BUFFER|p.D84V|c.251A>T|4,BUFFER|p.R139L|c.416G>T|6,BUFFER|p.R139Q|c.416G>A|4,BUFFER|p.D84N|c.250G>A|4,BUFFER|p.D84Y|c.250G>T|4,BUFFER|p.D84Y|c.250G>T|13,BUFFER|p.D84Y|c.250G>T|6,BUFFER|p.D84N|c.250G>A|7,BUFFER|p.V82M|c.244G>A|3,BUFFER|p.P81L|c.242C>T|9,BUFFER|p.R80*|c.237_238CC>TT|10,BUFFER|p.R80Q|c.239G>A|3,BUFFER|p.R80*|c.238C>T|116,BUFFER|p.P135L|c.404C>T|29,BUFFER|p.R80*|c.238C>T|14,BUFFER|p.R80*|c.238C>T|31	RADIA|MUTECT|MUSE	GTCGTGCACGG	.	3	ESCA
GOLM1	0	.	GRCh37	9	88650485	88650485	+	Silent	SNP	C	C	T	rs778114709	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813G>A	p.%3D	p.P271P	ENST00000388712	8/10	24	2	21	43	43	0	GOLM1,synonymous_variant,p.%3D,ENST00000388712,;GOLM1,synonymous_variant,p.%3D,ENST00000388711,;GOLM1,downstream_gene_variant,,ENST00000257504,;GOLM1,non_coding_transcript_exon_variant,,ENST00000464314,;	T	ENSG00000135052	ENST00000388712	Transcript	synonymous_variant	982	813	271	P	ccG/ccA	rs778114709,COSM3908635	.	.	-1	GOLM1	HGNC	15451	protein_coding	YES	CCDS35054.1	ENSP00000373364	GOLM1_HUMAN	C9JYM4_HUMAN,C9J941_HUMAN,B3KNK9_HUMAN	UPI000003B10E	.	.	.	8/10	.	hmmpanther:PTHR15896,hmmpanther:PTHR15896:SF8	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGCGGCAG	byFrequency	5	ESCA
PTCH1	0	.	GRCh37	9	98242324	98242324	+	Nonsense_Mutation	SNP	T	T	A	.	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.994A>T	p.Arg332Ter	p.R332*	ENST00000331920	7/24	27	5	22	26	26	0	PTCH1,stop_gained,p.Arg332Ter,ENST00000331920,;PTCH1,stop_gained,p.Arg266Ter,ENST00000430669,;PTCH1,stop_gained,p.Arg181Ter,ENST00000418258,;PTCH1,stop_gained,p.Arg181Ter,ENST00000421141,;PTCH1,stop_gained,p.Arg49Ter,ENST00000375271,;PTCH1,stop_gained,p.Arg331Ter,ENST00000375274,;PTCH1,stop_gained,p.Arg52Ter,ENST00000548420,;PTCH1,stop_gained,p.Arg181Ter,ENST00000429896,;PTCH1,stop_gained,p.Arg266Ter,ENST00000437951,;PTCH1,downstream_gene_variant,,ENST00000547672,;PTCH1,downstream_gene_variant,,ENST00000551630,;PTCH1,downstream_gene_variant,,ENST00000553011,;PTCH1,downstream_gene_variant,,ENST00000468211,;PTCH1,downstream_gene_variant,,ENST00000551845,;PTCH1,downstream_gene_variant,,ENST00000546820,;PTCH1,downstream_gene_variant,,ENST00000548379,;PTCH1,downstream_gene_variant,,ENST00000553256,;PTCH1,downstream_gene_variant,,ENST00000548945,;PTCH1,stop_gained,p.Arg211Ter,ENST00000375290,;PTCH1,non_coding_transcript_exon_variant,,ENST00000488809,;PTCH1,downstream_gene_variant,,ENST00000550914,;PTCH1,downstream_gene_variant,,ENST00000550136,;PTCH1,downstream_gene_variant,,ENST00000551623,;	A	ENSG00000185920	ENST00000331920	Transcript	stop_gained	1294	994	332	R/*	Aga/Tga	COSM144244	.	.	-1	PTCH1	HGNC	9585	protein_coding	YES	CCDS6714.1	ENSP00000332353	PTC1_HUMAN	Q6TKQ0_HUMAN,F8VXL8_HUMAN,F8VQS6_HUMAN	UPI00001AFF9C	.	.	.	7/24	.	TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796:SF61,hmmpanther:PTHR10796	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCTGGATA	.	5	ESCA
UBE2A	0	.	GRCh37	X	118717661	118717661	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*443T>C	.	.	ENST00000371558	6/6	19	3	16	12	12	0	UBE2A,3_prime_UTR_variant,,ENST00000371569,;UBE2A,3_prime_UTR_variant,,ENST00000371558,;UBE2A,downstream_gene_variant,,ENST00000346330,;NKRF,downstream_gene_variant,,ENST00000304449,;NKRF,downstream_gene_variant,,ENST00000371527,;NKRF,downstream_gene_variant,,ENST00000542113,;NKRF,downstream_gene_variant,,ENST00000487600,;	C	ENSG00000077721	ENST00000371558	Transcript	3_prime_UTR_variant	1076	.	.	.	.	.	.	.	1	UBE2A	HGNC	12472	protein_coding	YES	CCDS14580.1	ENSP00000360613	UBE2A_HUMAN	Q8WXB3_HUMAN,B4DWT6_HUMAN	UPI00000043A0	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATATGGCCT	.	5	ESCA
MAGEC2	0	.	GRCh37	X	141291732	141291732	+	Silent	SNP	G	G	A	rs770018745	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42C>T	p.%3D	p.N14N	ENST00000247452	3/3	14	2	11	18	18	0	MAGEC2,synonymous_variant,p.%3D,ENST00000247452,;	A	ENSG00000046774	ENST00000247452	Transcript	synonymous_variant	390	42	14	N	aaC/aaT	rs770018745	.	.	-1	MAGEC2	HGNC	13574	protein_coding	YES	CCDS14678.1	ENSP00000354660	MAGC2_HUMAN	.	UPI000012F059	.	.	.	3/3	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.N11K|c.33C>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE	GAGTCGTTGTC	byFrequency	4	ESCA
SLITRK2	0	.	GRCh37	X	144906924	144906924	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*443C>G	.	.	ENST00000370490	1/1	27	4	23	21	21	0	SLITRK2,3_prime_UTR_variant,,ENST00000370490,;SLITRK2,3_prime_UTR_variant,,ENST00000434188,;SLITRK2,3_prime_UTR_variant,,ENST00000428560,;SLITRK2,3_prime_UTR_variant,,ENST00000413937,;SLITRK2,3_prime_UTR_variant,,ENST00000447897,;TMEM257,upstream_gene_variant,,ENST00000408967,;SLITRK2,downstream_gene_variant,,ENST00000335565,;	G	ENSG00000185985	ENST00000370490	Transcript	3_prime_UTR_variant	7236	.	.	.	.	.	.	.	1	SLITRK2	HGNC	13449	protein_coding	YES	CCDS14680.1	ENSP00000359521	SLIK2_HUMAN	B3KTY4_HUMAN	UPI000004E64B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATCTTTTG	.	5	ESCA
BEND2	0	.	GRCh37	X	18189223	18189223	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000380033	13/14	11	2	9	16	16	0	BEND2,stop_gained,p.Gln604Ter,ENST00000380030,;BEND2,stop_gained,p.Gln695Ter,ENST00000380033,;	A	ENSG00000177324	ENST00000380033	Transcript	stop_gained	2216	2083	695	Q/*	Cag/Tag	.	.	.	-1	BEND2	HGNC	28509	protein_coding	YES	CCDS14184.1	ENSP00000369372	BEND2_HUMAN	.	UPI000013FE0F	.	.	.	13/14	.	PROSITE_profiles:PS51457,hmmpanther:PTHR16213,hmmpanther:PTHR16213:SF44,Pfam_domain:PF10523,SMART_domains:SM01025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTCTGAATAA	.	3	ESCA
DMD	0	.	GRCh37	X	32472792	32472792	+	Missense_Mutation	SNP	A	A	T	rs777955789	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3590T>A	p.Val1197Asp	p.V1197D	ENST00000357033	26/79	14	11	3	24	24	0	DMD,missense_variant,p.Val1197Asp,ENST00000357033,;DMD,missense_variant,p.Val1193Asp,ENST00000378677,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000488902,;	T	ENSG00000198947	ENST00000357033	Transcript	missense_variant	3797	3590	1197	V/D	gTt/gAt	rs777955789	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	probably_damaging(0.986)	26/79	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF261,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	CTTCAACTGCT	byFrequency	3	ESCA
KCND1	0	.	GRCh37	X	48819093	48819093	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49R-01A-11D-A247-09	TCGA-LN-A49R-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*749C>T	.	.	ENST00000218176	6/6	17	7	10	30	30	0	KCND1,3_prime_UTR_variant,,ENST00000218176,;KCND1,3_prime_UTR_variant,,ENST00000376477,;KCND1,downstream_gene_variant,,ENST00000419374,;OTUD5,upstream_gene_variant,,ENST00000376488,;OTUD5,upstream_gene_variant,,ENST00000156084,;OTUD5,upstream_gene_variant,,ENST00000455452,;OTUD5,upstream_gene_variant,,ENST00000428668,;OTUD5,upstream_gene_variant,,ENST00000396743,;RNU6-722P,upstream_gene_variant,,ENST00000411377,;OTUD5,upstream_gene_variant,,ENST00000484499,;	A	ENSG00000102057	ENST00000218176	Transcript	3_prime_UTR_variant	3991	.	.	.	.	.	.	.	-1	KCND1	HGNC	6237	protein_coding	YES	CCDS14314.1	ENSP00000218176	KCND1_HUMAN	A6NEF1_HUMAN	UPI000000DB05	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGCAGCA	.	5	ESCA
ADAM12	0	.	GRCh37	10	127708387	127708387	+	Missense_Mutation	SNP	C	C	T	rs374420879	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2546G>A	p.Cys849Tyr	p.C849Y	ENST00000368679	22/23	35	32	3	42	42	0	ADAM12,missense_variant,p.Cys849Tyr,ENST00000368679,;	T	ENSG00000148848	ENST00000368679	Transcript	missense_variant	2856	2546	849	C/Y	tGt/tAt	rs374420879	.	.	-1	ADAM12	HGNC	190	protein_coding	YES	CCDS7653.1	ENSP00000357668	ADA12_HUMAN	.	UPI000036672C	.	tolerated(1)	benign(0)	22/23	.	hmmpanther:PTHR11905:SF112,hmmpanther:PTHR11905	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTACAGGTC	byFrequency|byCluster	2	ESCA
PPP2R2D	0	.	GRCh37	10	133769299	133769299	+	Silent	SNP	C	C	G	rs370756365	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1101C>G	p.%3D	p.L367L	ENST00000455566	7/7	36	33	3	55	55	0	PPP2R2D,synonymous_variant,p.%3D,ENST00000455566,;PPP2R2D,3_prime_UTR_variant,,ENST00000422256,;PPP2R2D,downstream_gene_variant,,ENST00000470416,;PPP2R2D,3_prime_UTR_variant,,ENST00000482010,;PPP2R2D,non_coding_transcript_exon_variant,,ENST00000490777,;	G	ENSG00000175470	ENST00000455566	Transcript	synonymous_variant	1101	1101	367	L	ctC/ctG	rs370756365	.	.	1	PPP2R2D	HGNC	23732	protein_coding	YES	.	ENSP00000399970	2ABD_HUMAN	Q6IN90_HUMAN,B3KMA9_HUMAN	UPI000013EC98	.	.	.	7/7	.	hmmpanther:PTHR11871,hmmpanther:PTHR11871:SF6,Gene3D:2.130.10.10,PIRSF_domain:PIRSF037309	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	AGCCTCAAACC	byFrequency|byCluster	2	ESCA
FRMD4A	0	.	GRCh37	10	13749049	13749049	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.824A>T	p.His275Leu	p.H275L	ENST00000357447	13/25	42	33	9	56	56	0	FRMD4A,missense_variant,p.His291Leu,ENST00000342409,;FRMD4A,missense_variant,p.His275Leu,ENST00000357447,;FRMD4A,missense_variant,p.His260Leu,ENST00000358621,;FRMD4A,missense_variant,p.His275Leu,ENST00000378503,;FRMD4A,missense_variant,p.His308Leu,ENST00000264546,;AL157392.1,downstream_gene_variant,,ENST00000410303,;RP11-295P9.6,upstream_gene_variant,,ENST00000412388,;FRMD4A,non_coding_transcript_exon_variant,,ENST00000477221,;FRMD4A,non_coding_transcript_exon_variant,,ENST00000492155,;	A	ENSG00000151474	ENST00000357447	Transcript	missense_variant	1193	824	275	H/L	cAt/cTt	.	.	.	-1	FRMD4A	HGNC	25491	protein_coding	YES	CCDS7101.1	ENSP00000350032	FRM4A_HUMAN	F8WAN4_HUMAN	UPI0000366665	.	deleterious(0.03)	benign(0.006)	13/25	.	PROSITE_profiles:PS50057,hmmpanther:PTHR23281:SF12,hmmpanther:PTHR23281,Gene3D:2.30.29.30,Pfam_domain:PF09380,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCATGAACT	.	5	ESCA
LINC00700	0	.	GRCh37	10	2056458	2056458	+	RNA	SNP	T	T	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.85A>T	.	.	ENST00000413603	1/3	65	59	6	73	73	0	LINC00700,non_coding_transcript_exon_variant,,ENST00000413603,;LINC00700,non_coding_transcript_exon_variant,,ENST00000438372,;LINC00700,upstream_gene_variant,,ENST00000454424,;	A	ENSG00000234962	ENST00000413603	Transcript	non_coding_transcript_exon_variant	85	.	.	.	.	.	.	.	-1	LINC00700	HGNC	27422	lincRNA	YES	.	.	.	.	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATATTTCATGC	.	3	ESCA
ABI1	0	.	GRCh37	10	27066072	27066072	+	Silent	SNP	C	C	T	rs558636392	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.384G>A	p.%3D	p.A128A	ENST00000376142	3/12	59	45	13	64	64	0	ABI1,synonymous_variant,p.%3D,ENST00000536334,;ABI1,synonymous_variant,p.%3D,ENST00000376138,;ABI1,synonymous_variant,p.%3D,ENST00000376166,;ABI1,synonymous_variant,p.%3D,ENST00000359188,;ABI1,synonymous_variant,p.%3D,ENST00000376170,;ABI1,synonymous_variant,p.%3D,ENST00000346832,;ABI1,synonymous_variant,p.%3D,ENST00000376142,;ABI1,synonymous_variant,p.%3D,ENST00000376137,;ABI1,synonymous_variant,p.%3D,ENST00000376134,;ABI1,synonymous_variant,p.%3D,ENST00000376140,;ABI1,synonymous_variant,p.%3D,ENST00000355394,;ABI1,synonymous_variant,p.%3D,ENST00000376139,;ABI1,synonymous_variant,p.%3D,ENST00000376160,;ABI1,intron_variant,,ENST00000490841,;ABI1,non_coding_transcript_exon_variant,,ENST00000473481,;	T	ENSG00000136754	ENST00000376142	Transcript	synonymous_variant	456	384	128	A	gcG/gcA	rs558636392	.	.	-1	ABI1	HGNC	11320	protein_coding	YES	CCDS7150.1	ENSP00000365312	ABI1_HUMAN	.	UPI000006EA57	.	.	.	3/12	.	hmmpanther:PTHR10460:SF2,hmmpanther:PTHR10460,Pfam_domain:PF07815	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCGCAGG	byFrequency|by1000G	5	ESCA
FAM21C	0	.	GRCh37	10	46272800	46272800	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2222C>G	p.Ser741Cys	p.S741C	ENST00000374362	22/30	114	94	19	116	116	0	FAM21C,missense_variant,p.Ser741Cys,ENST00000374362,;FAM21C,missense_variant,p.Ser739Cys,ENST00000336378,;FAM21C,missense_variant,p.Ser683Cys,ENST00000359860,;FAM21C,missense_variant,p.Ser741Cys,ENST00000540872,;FAM21C,intron_variant,,ENST00000537517,;FAM21C,upstream_gene_variant,,ENST00000374359,;	G	ENSG00000172661	ENST00000374362	Transcript	missense_variant	2321	2222	741	S/C	tCt/tGt	.	.	.	1	FAM21C	HGNC	23414	protein_coding	YES	CCDS44374.2	ENSP00000363482	FA21C_HUMAN	.	UPI0000551BE9	.	tolerated(0.05)	benign(0.226)	22/30	.	hmmpanther:PTHR21669:SF4,hmmpanther:PTHR21669	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGTCTGTGG	.	5	ESCA
UBE2D1	0	.	GRCh37	10	60129134	60129134	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*609T>C	.	.	ENST00000373910	7/7	64	58	5	58	58	0	UBE2D1,3_prime_UTR_variant,,ENST00000373910,;UBE2D1,non_coding_transcript_exon_variant,,ENST00000606483,;UBE2D1,downstream_gene_variant,,ENST00000473824,;	C	ENSG00000072401	ENST00000373910	Transcript	3_prime_UTR_variant	1280	.	.	.	.	.	.	.	1	UBE2D1	HGNC	12474	protein_coding	YES	CCDS7252.1	ENSP00000363019	UB2D1_HUMAN	.	UPI0000001661	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTAATTCTCA	.	3	ESCA
NDST2	0	.	GRCh37	10	75564538	75564538	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1836G>A	p.%3D	p.Q612Q	ENST00000309979	9/15	59	54	5	63	63	0	NDST2,synonymous_variant,p.%3D,ENST00000299641,;NDST2,synonymous_variant,p.%3D,ENST00000309979,;ZSWIM8,downstream_gene_variant,,ENST00000603187,;ZSWIM8,downstream_gene_variant,,ENST00000604754,;ZSWIM8,downstream_gene_variant,,ENST00000604729,;ZSWIM8,downstream_gene_variant,,ENST00000604524,;ZSWIM8,downstream_gene_variant,,ENST00000412198,;ZSWIM8,downstream_gene_variant,,ENST00000603114,;NDST2,upstream_gene_variant,,ENST00000429742,;ZSWIM8,downstream_gene_variant,,ENST00000466354,;ZSWIM8,downstream_gene_variant,,ENST00000605216,;ZSWIM8,downstream_gene_variant,,ENST00000398706,;ZSWIM8-AS1,upstream_gene_variant,,ENST00000456638,;NDST2,downstream_gene_variant,,ENST00000465929,;ZSWIM8,downstream_gene_variant,,ENST00000466568,;ZSWIM8,downstream_gene_variant,,ENST00000603840,;NDST2,downstream_gene_variant,,ENST00000463410,;ZSWIM8,downstream_gene_variant,,ENST00000604165,;ZSWIM8,downstream_gene_variant,,ENST00000603409,;ZSWIM8,downstream_gene_variant,,ENST00000603309,;ZSWIM8,downstream_gene_variant,,ENST00000603195,;RP11-574K11.31,synonymous_variant,p.%3D,ENST00000603027,;ZSWIM8,downstream_gene_variant,,ENST00000492395,;ZSWIM8,downstream_gene_variant,,ENST00000433366,;RP11-574K11.31,upstream_gene_variant,,ENST00000603706,;	T	ENSG00000166507	ENST00000309979	Transcript	synonymous_variant	2393	1836	612	Q	caG/caA	.	.	.	-1	NDST2	HGNC	7681	protein_coding	YES	CCDS7335.1	ENSP00000310657	NDST2_HUMAN	J3KNC8_HUMAN,B4DVV6_HUMAN,B4DU70_HUMAN,B4DE98_HUMAN	UPI0000001C41	.	.	.	9/15	.	hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF36,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTTTCTGGGG	.	3	ESCA
TAF3	0	.	GRCh37	10	8006229	8006229	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756T>A	p.%3D	p.V252V	ENST00000344293	3/7	26	22	4	26	26	0	TAF3,synonymous_variant,p.%3D,ENST00000344293,;	A	ENSG00000165632	ENST00000344293	Transcript	synonymous_variant	962	756	252	V	gtT/gtA	.	.	.	1	TAF3	HGNC	17303	protein_coding	YES	CCDS41487.1	ENSP00000340271	TAF3_HUMAN	.	UPI00004588FA	.	.	.	3/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12321:SF34,hmmpanther:PTHR12321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGTTGCAAA	.	4	ESCA
LIPM	0	.	GRCh37	10	90565733	90565733	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148-2322G>C	.	.	ENST00000404743	.	52	49	3	61	61	0	LIPM,5_prime_UTR_variant,,ENST00000539337,;LIPM,intron_variant,,ENST00000404743,;	C	ENSG00000173239	ENST00000404743	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LIPM	HGNC	23455	protein_coding	YES	CCDS44457.1	ENSP00000383901	LIPM_HUMAN	.	UPI00004B21B5	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCTGAGATG	.	2	ESCA
ACTA2	0	.	GRCh37	10	90701066	90701066	+	Missense_Mutation	SNP	C	C	T	rs387906592	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.536G>A	p.Arg179His	p.R179H	ENST00000458208	6/9	58	48	10	81	81	0	ACTA2,missense_variant,p.Arg179His,ENST00000224784,;ACTA2,missense_variant,p.Arg179His,ENST00000458208,;STAMBPL1,intron_variant,,ENST00000371927,;ACTA2,downstream_gene_variant,,ENST00000415557,;ACTA2,downstream_gene_variant,,ENST00000458159,;ACTA2-AS1,downstream_gene_variant,,ENST00000596007,;ACTA2-AS1,downstream_gene_variant,,ENST00000437930,;ACTA2,non_coding_transcript_exon_variant,,ENST00000480297,;	T	ENSG00000107796	ENST00000458208	Transcript	missense_variant	1011	536	179	R/H	cGt/cAt	rs387906592,CM106014	.	.	-1	ACTA2	HGNC	130	protein_coding	YES	CCDS7392.1	ENSP00000402373	ACTA_HUMAN	D2JYH4_HUMAN,Q562S2_HUMAN,F6UVQ4_HUMAN,F6QUT6_HUMAN,B4DUI8_HUMAN,B3KPP5_HUMAN	UPI0000000E0F	.	tolerated_low_confidence(0.06)	benign(0.063)	6/9	.	hmmpanther:PTHR11937:SF197,hmmpanther:PTHR11937,Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGACGCATG	.	5	ESCA
IFIT1	0	.	GRCh37	10	91162762	91162762	+	Missense_Mutation	SNP	C	C	G	rs772301237	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.730C>G	p.Leu244Val	p.L244V	ENST00000371804	2/2	45	38	6	57	57	0	IFIT1,missense_variant,p.Leu213Val,ENST00000546318,;IFIT1,missense_variant,p.Leu244Val,ENST00000371804,;LIPA,intron_variant,,ENST00000371837,;	G	ENSG00000185745	ENST00000371804	Transcript	missense_variant	897	730	244	L/V	Cta/Gta	rs772301237	.	.	1	IFIT1	HGNC	5407	protein_coding	YES	CCDS31243.1	ENSP00000360869	IFIT1_HUMAN	D3DR31_HUMAN	UPI0000169E8F	.	deleterious(0)	possibly_damaging(0.87)	2/2	.	Superfamily_domains:SSF48452,Gene3D:1.25.40.10,hmmpanther:PTHR10271:SF15,hmmpanther:PTHR10271,PROSITE_profiles:PS50293	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTCTAGCC	byFrequency	5	ESCA
HECTD2	0	.	GRCh37	10	93221933	93221933	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592C>G	p.Leu198Val	p.L198V	ENST00000298068	5/21	43	38	5	43	42	0	HECTD2,missense_variant,p.Leu198Val,ENST00000298068,;HECTD2,missense_variant,p.Leu198Val,ENST00000371681,;HECTD2,missense_variant,p.Leu198Val,ENST00000446394,;HECTD2,5_prime_UTR_variant,,ENST00000536715,;RP11-108M11.3,downstream_gene_variant,,ENST00000604630,;	G	ENSG00000165338	ENST00000298068	Transcript	missense_variant	686	592	198	L/V	Ctt/Gtt	.	.	.	1	HECTD2	HGNC	26736	protein_coding	YES	CCDS7414.1	ENSP00000298068	HECD2_HUMAN	B3KV18_HUMAN	UPI0000246D14	.	tolerated(0.3)	benign(0.119)	5/21	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF69	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTTACTTAAT	.	3	ESCA
HOGA1	0	.	GRCh37	10	99371273	99371273	+	Missense_Mutation	SNP	C	C	T	rs764224799	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841C>T	p.Arg281Trp	p.R281W	ENST00000370646	7/7	52	42	10	67	67	0	HOGA1,missense_variant,p.Arg118Trp,ENST00000370647,;HOGA1,missense_variant,p.Arg281Trp,ENST00000370646,;PI4K2A,intron_variant,,ENST00000370649,;PI4K2A,intron_variant,,ENST00000555577,;MORN4,downstream_gene_variant,,ENST00000335628,;MORN4,downstream_gene_variant,,ENST00000478953,;MORN4,downstream_gene_variant,,ENST00000307450,;	T	ENSG00000241935	ENST00000370646	Transcript	missense_variant	1202	841	281	R/W	Cgg/Tgg	rs764224799,COSM540281	.	.	1	HOGA1	HGNC	25155	protein_coding	YES	CCDS7467.1	ENSP00000359680	HOGA1_HUMAN	.	UPI000000DAE5	.	deleterious(0)	benign(0.005)	7/7	.	Superfamily_domains:SSF51569,PIRSF_domain:PIRSF001365,Pfam_domain:PF00701,Gene3D:3.20.20.70,hmmpanther:PTHR12128,hmmpanther:PTHR12128:SF15	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACCCGGCGC	byFrequency	5	ESCA
MMP20	0	.	GRCh37	11	102496048	102496048	+	Translation_Start_Site	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3G>A	p.Met1?	p.M1?	ENST00000260228	1/10	23	19	4	26	26	0	MMP20,start_lost,p.Met1?,ENST00000260228,;RP11-817J15.2,intron_variant,,ENST00000542119,;	T	ENSG00000137674	ENST00000260228	Transcript	start_lost	16	3	1	M/I	atG/atA	.	.	.	-1	MMP20	HGNC	7167	protein_coding	YES	CCDS8318.1	ENSP00000260228	MMP20_HUMAN	.	UPI000013D0B3	.	deleterious(0.01)	possibly_damaging(0.643)	1/10	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF125,PIRSF_domain:PIRSF001191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCTTCATCCC	.	2	ESCA
MMP20	0	.	GRCh37	11	102496056	102496056	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-6G>A	.	.	ENST00000260228	1/10	23	19	4	28	28	0	MMP20,5_prime_UTR_variant,,ENST00000260228,;RP11-817J15.2,intron_variant,,ENST00000542119,;	T	ENSG00000137674	ENST00000260228	Transcript	5_prime_UTR_variant	8	.	.	.	.	.	.	.	-1	MMP20	HGNC	7167	protein_coding	YES	CCDS8318.1	ENSP00000260228	MMP20_HUMAN	.	UPI000013D0B3	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCCTCACAGT	.	3	ESCA
ZBTB16	0	.	GRCh37	11	114027093	114027093	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1303G>A	p.Glu435Lys	p.E435K	ENST00000335953	3/7	66	62	4	85	85	0	ZBTB16,missense_variant,p.Glu435Lys,ENST00000392996,;ZBTB16,missense_variant,p.Glu435Lys,ENST00000335953,;ZBTB16,3_prime_UTR_variant,,ENST00000539918,;ZBTB16,non_coding_transcript_exon_variant,,ENST00000541602,;	A	ENSG00000109906	ENST00000335953	Transcript	missense_variant	1683	1303	435	E/K	Gag/Aag	.	.	.	1	ZBTB16	HGNC	12930	protein_coding	YES	CCDS8367.1	ENSP00000338157	ZBT16_HUMAN	Q71UL7_HUMAN,Q71UL6_HUMAN,Q71UL5_HUMAN,F5H6C3_HUMAN,F5H5Y7_HUMAN	UPI000000018E	.	deleterious(0)	probably_damaging(0.976)	3/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR11389:SF425,hmmpanther:PTHR11389,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGCGAGCTC	.	2	ESCA
VWA5A	0	.	GRCh37	11	124012384	124012384	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1959G>A	p.%3D	p.K653K	ENST00000456829	16/19	81	77	4	108	108	0	VWA5A,missense_variant,p.Arg415Lys,ENST00000360334,;VWA5A,synonymous_variant,p.%3D,ENST00000456829,;VWA5A,synonymous_variant,p.%3D,ENST00000392748,;	A	ENSG00000110002	ENST00000456829	Transcript	synonymous_variant	2210	1959	653	K	aaG/aaA	.	.	.	1	VWA5A	HGNC	6658	protein_coding	YES	CCDS8444.1	ENSP00000407726	VMA5A_HUMAN	.	UPI0000158B80	.	.	.	16/19	.	hmmpanther:PTHR10338:SF100,hmmpanther:PTHR10338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAAGACATT	.	2	ESCA
HPS5	0	.	GRCh37	11	18305401	18305401	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2999G>C	p.Arg1000Thr	p.R1000T	ENST00000349215	21/23	43	38	4	69	69	0	HPS5,missense_variant,p.Arg886Thr,ENST00000438420,;HPS5,missense_variant,p.Arg107Thr,ENST00000537258,;HPS5,missense_variant,p.Arg1000Thr,ENST00000349215,;HPS5,missense_variant,p.Arg886Thr,ENST00000396253,;HPS5,downstream_gene_variant,,ENST00000544218,;HPS5,non_coding_transcript_exon_variant,,ENST00000352460,;HPS5,downstream_gene_variant,,ENST00000543728,;HPS5,non_coding_transcript_exon_variant,,ENST00000545561,;	G	ENSG00000110756	ENST00000349215	Transcript	missense_variant	3277	2999	1000	R/T	aGa/aCa	.	.	.	-1	HPS5	HGNC	17022	protein_coding	YES	CCDS7836.1	ENSP00000265967	HPS5_HUMAN	F5GWM5_HUMAN	UPI000000D7E9	.	tolerated(0.65)	benign(0.008)	21/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23287:SF15,hmmpanther:PTHR23287,PIRSF_domain:PIRSF037475	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCTCTTCTT	.	4	ESCA
LDHAL6A	0	.	GRCh37	11	18499176	18499176	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.720G>C	p.Glu240Asp	p.E240D	ENST00000280706	6/7	62	56	5	85	85	0	LDHAL6A,missense_variant,p.Glu240Asp,ENST00000396213,;LDHAL6A,missense_variant,p.Glu240Asp,ENST00000280706,;TSG101,intron_variant,,ENST00000536719,;TSG101,downstream_gene_variant,,ENST00000357193,;TSG101,downstream_gene_variant,,ENST00000251968,;TSG101,intron_variant,,ENST00000584526,;TSG101,intron_variant,,ENST00000580814,;TSG101,downstream_gene_variant,,ENST00000540555,;	C	ENSG00000166800	ENST00000280706	Transcript	missense_variant	1517	720	240	E/D	gaG/gaC	.	.	.	1	LDHAL6A	HGNC	28335	protein_coding	YES	CCDS7841.1	ENSP00000280706	LDH6A_HUMAN	.	UPI00001B24AC	.	tolerated(0.05)	benign(0.006)	6/7	.	HAMAP:MF_00488,hmmpanther:PTHR11540,hmmpanther:PTHR11540:SF13,Pfam_domain:PF02866,Gene3D:3.90.110.10,TIGRFAM_domain:TIGR01771,PIRSF_domain:PIRSF000102,Superfamily_domains:SSF56327	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TATGAGATGGT	.	3	ESCA
DEPDC7	0	.	GRCh37	11	33047376	33047376	+	Missense_Mutation	SNP	A	A	G	rs778104021	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245A>G	p.Asn82Ser	p.N82S	ENST00000241051	2/9	54	45	9	78	78	0	DEPDC7,missense_variant,p.Asn73Ser,ENST00000311388,;DEPDC7,missense_variant,p.Asn82Ser,ENST00000241051,;DEPDC7,non_coding_transcript_exon_variant,,ENST00000427755,;DEPDC7,non_coding_transcript_exon_variant,,ENST00000532078,;	G	ENSG00000121690	ENST00000241051	Transcript	missense_variant	337	245	82	N/S	aAt/aGt	rs778104021	.	.	1	DEPDC7	HGNC	29899	protein_coding	YES	CCDS41632.1	ENSP00000241051	DEPD7_HUMAN	.	UPI000006E96C	.	tolerated(0.41)	benign(0.206)	2/9	.	Superfamily_domains:SSF46785,SMART_domains:SM00049,Gene3D:1.10.10.10,Pfam_domain:PF00610,hmmpanther:PTHR16206,hmmpanther:PTHR16206:SF9,PROSITE_profiles:PS50186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAATAAGT	.	5	ESCA
RP11-707M1.1	0	.	GRCh37	11	49597796	49597796	+	RNA	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.400A>T	.	.	ENST00000527477	2/7	40	33	7	52	52	0	RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000527477,;RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000534201,;RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000530858,;	T	ENSG00000205035	ENST00000527477	Transcript	non_coding_transcript_exon_variant	400	.	.	.	.	.	.	.	1	RP11-707M1.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTAAAACGG	.	4	ESCA
SERPING1	0	.	GRCh37	11	57373936	57373936	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.945C>T	p.%3D	p.F315F	ENST00000278407	6/8	53	43	9	62	62	0	SERPING1,synonymous_variant,p.%3D,ENST00000278407,;SERPING1,synonymous_variant,p.%3D,ENST00000403558,;SERPING1,synonymous_variant,p.%3D,ENST00000378324,;SERPING1,synonymous_variant,p.%3D,ENST00000340687,;SERPING1,synonymous_variant,p.%3D,ENST00000378323,;SERPING1,downstream_gene_variant,,ENST00000531605,;SERPING1,synonymous_variant,p.%3D,ENST00000528996,;SERPING1,3_prime_UTR_variant,,ENST00000531133,;SERPING1,intron_variant,,ENST00000531797,;SERPING1,upstream_gene_variant,,ENST00000530113,;	T	ENSG00000149131	ENST00000278407	Transcript	synonymous_variant	1172	945	315	F	ttC/ttT	COSM3791601	.	.	1	SERPING1	HGNC	1228	protein_coding	YES	CCDS7962.1	ENSP00000278407	IC1_HUMAN	E9KL26_HUMAN,B5MCB9_HUMAN,B4E1H2_HUMAN	UPI000000123F	.	.	.	6/8	.	hmmpanther:PTHR11461:SF156,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:2.30.39.10,SMART_domains:SM00093,Superfamily_domains:SSF56574	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTTCAAAAA	.	5	ESCA
MED19	0	.	GRCh37	11	57471455	57471455	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*639G>T	.	.	ENST00000337672	4/4	55	52	3	57	57	0	MED19,3_prime_UTR_variant,,ENST00000337672,;MED19,3_prime_UTR_variant,,ENST00000431606,;ZDHHC5,downstream_gene_variant,,ENST00000287169,;ZDHHC5,downstream_gene_variant,,ENST00000527985,;ZDHHC5,downstream_gene_variant,,ENST00000529480,;MED19,downstream_gene_variant,,ENST00000534677,;MED19,downstream_gene_variant,,ENST00000528205,;	A	ENSG00000156603	ENST00000337672	Transcript	3_prime_UTR_variant	1246	.	.	.	.	.	.	.	-1	MED19	HGNC	29600	protein_coding	YES	CCDS7966.1	ENSP00000337340	MED19_HUMAN	.	UPI00000746CC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTATCAGCAG	.	2	ESCA
CTNND1	0	.	GRCh37	11	57583408	57583408	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2830C>G	p.Leu944Val	p.L944V	ENST00000399050	20/21	75	69	5	97	97	0	CTNND1,missense_variant,p.Leu816Val,ENST00000532787,;CTNND1,missense_variant,p.Leu884Val,ENST00000526357,;CTNND1,missense_variant,p.Leu594Val,ENST00000533667,;CTNND1,missense_variant,p.Leu863Val,ENST00000529873,;CTNND1,missense_variant,p.Leu890Val,ENST00000532844,;CTNND1,missense_variant,p.Leu615Val,ENST00000531014,;CTNND1,missense_variant,p.Leu843Val,ENST00000415361,;CTNND1,missense_variant,p.Leu837Val,ENST00000530094,;CTNND1,missense_variant,p.Leu621Val,ENST00000527467,;CTNND1,missense_variant,p.Leu917Val,ENST00000361391,;CTNND1,missense_variant,p.Leu944Val,ENST00000399050,;CTNND1,missense_variant,p.Leu923Val,ENST00000360682,;CTNND1,missense_variant,p.Leu938Val,ENST00000361332,;CTNND1,3_prime_UTR_variant,,ENST00000531007,;CTNND1,intron_variant,,ENST00000361796,;CTNND1,intron_variant,,ENST00000428599,;CTNND1,intron_variant,,ENST00000532649,;CTNND1,intron_variant,,ENST00000528232,;CTNND1,intron_variant,,ENST00000529919,;CTNND1,intron_variant,,ENST00000532463,;CTNND1,intron_variant,,ENST00000529986,;CTNND1,intron_variant,,ENST00000532245,;CTNND1,intron_variant,,ENST00000530748,;CTNND1,intron_variant,,ENST00000528621,;CTNND1,intron_variant,,ENST00000534579,;CTNND1,intron_variant,,ENST00000526938,;CTNND1,intron_variant,,ENST00000529526,;CTNND1,intron_variant,,ENST00000399039,;CTNND1,intron_variant,,ENST00000524630,;CTNND1,intron_variant,,ENST00000358694,;CTNND1,intron_variant,,ENST00000426142,;CTNND1,intron_variant,,ENST00000526772,;CTNND1,intron_variant,,ENST00000525902,;CTNND1,downstream_gene_variant,,ENST00000525821,;	G	ENSG00000198561	ENST00000399050	Transcript	missense_variant	3366	2830	944	L/V	Ctg/Gtg	COSM3449795,COSM3449794	.	.	1	CTNND1	HGNC	2515	protein_coding	YES	CCDS44604.1	ENSP00000382004	CTND1_HUMAN	E9PKY0_HUMAN,E9PKL1_HUMAN	UPI000012860B	.	tolerated_low_confidence(0.36)	benign(0.026)	20/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10372:SF6,hmmpanther:PTHR10372	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCTCTGGAG	.	2	ESCA
TMEM258	0	.	GRCh37	11	61556621	61556621	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*97A>G	.	.	ENST00000537328	4/4	18	15	3	21	21	0	TMEM258,3_prime_UTR_variant,,ENST00000537328,;TMEM258,3_prime_UTR_variant,,ENST00000543510,;FEN1,upstream_gene_variant,,ENST00000535723,;MYRF,downstream_gene_variant,,ENST00000278836,;FEN1,upstream_gene_variant,,ENST00000305885,;MYRF,downstream_gene_variant,,ENST00000389602,;FADS2,upstream_gene_variant,,ENST00000574708,;MYRF,downstream_gene_variant,,ENST00000265460,;MIR611,downstream_gene_variant,,ENST00000384869,;TMEM258,intron_variant,,ENST00000535042,;TMEM258,3_prime_UTR_variant,,ENST00000545210,;TMEM258,3_prime_UTR_variant,,ENST00000535297,;TMEM258,3_prime_UTR_variant,,ENST00000541893,;TMEM258,3_prime_UTR_variant,,ENST00000257262,;TMEM258,downstream_gene_variant,,ENST00000540434,;MYRF,downstream_gene_variant,,ENST00000539361,;	C	ENSG00000134825	ENST00000537328	Transcript	3_prime_UTR_variant	389	.	.	.	.	.	.	.	-1	TMEM258	HGNC	1164	protein_coding	YES	CCDS8009.1	ENSP00000443216	TM258_HUMAN	F5H7Z5_HUMAN	UPI000000109F	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATTTATTATGA	.	3	ESCA
AHNAK	0	.	GRCh37	11	62290215	62290215	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11674G>A	p.Asp3892Asn	p.D3892N	ENST00000378024	5/5	105	99	6	133	133	0	AHNAK,missense_variant,p.Asp3892Asn,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;	T	ENSG00000124942	ENST00000378024	Transcript	missense_variant	11949	11674	3892	D/N	Gat/Aat	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	probably_damaging(0.998)	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACATCCATAT	.	2	ESCA
FAM89B	0	.	GRCh37	11	65341543	65341543	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*431G>C	.	.	ENST00000530349	2/2	35	29	5	46	46	0	FAM89B,3_prime_UTR_variant,,ENST00000316409,;FAM89B,3_prime_UTR_variant,,ENST00000530349,;FAM89B,3_prime_UTR_variant,,ENST00000449319,;EHBP1L1,upstream_gene_variant,,ENST00000309295,;SSSCA1,downstream_gene_variant,,ENST00000526433,;SSSCA1,downstream_gene_variant,,ENST00000531405,;SSSCA1,downstream_gene_variant,,ENST00000309328,;SSSCA1,downstream_gene_variant,,ENST00000526877,;EHBP1L1,upstream_gene_variant,,ENST00000533237,;SSSCA1,downstream_gene_variant,,ENST00000527920,;SSSCA1,downstream_gene_variant,,ENST00000533115,;SSSCA1-AS1,upstream_gene_variant,,ENST00000567594,;EHBP1L1,upstream_gene_variant,,ENST00000531106,;SSSCA1,downstream_gene_variant,,ENST00000527413,;	C	ENSG00000176973	ENST00000530349	Transcript	3_prime_UTR_variant	1143	.	.	.	.	.	.	.	1	FAM89B	HGNC	16708	protein_coding	YES	CCDS53662.1	ENSP00000431459	FA89B_HUMAN	.	UPI00001FABAE	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGAAGGGCTC	.	4	ESCA
KCTD14	0	.	GRCh37	11	77727683	77727683	+	Missense_Mutation	SNP	C	C	T	rs374366969	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724G>A	p.Glu242Lys	p.E242K	ENST00000353172	2/2	33	25	8	39	39	0	KCTD14,missense_variant,p.Glu212Lys,ENST00000533144,;KCTD14,missense_variant,p.Glu242Lys,ENST00000353172,;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000528251,;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000530054,;RP11-7I15.3,downstream_gene_variant,,ENST00000533697,;	T	ENSG00000151364	ENST00000353172	Transcript	missense_variant	769	724	242	E/K	Gaa/Aaa	rs374366969,COSM196622	.	.	-1	KCTD14	HGNC	23295	protein_coding	YES	CCDS8255.2	ENSP00000316482	KCD14_HUMAN	B2R9R8_HUMAN	UPI000003E7AB	.	tolerated(1)	benign(0)	2/2	.	hmmpanther:PTHR14499:SF3,hmmpanther:PTHR14499	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATTCGTTTC	byFrequency|byCluster	5	ESCA
FAT3	0	.	GRCh37	11	92532190	92532190	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6011T>C	p.Val2004Ala	p.V2004A	ENST00000298047	9/27	42	23	18	35	35	0	FAT3,missense_variant,p.Val2004Ala,ENST00000298047,;FAT3,missense_variant,p.Val2004Ala,ENST00000409404,;FAT3,missense_variant,p.Val1854Ala,ENST00000525166,;	C	ENSG00000165323	ENST00000298047	Transcript	missense_variant	6028	6011	2004	V/A	gTc/gCc	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	possibly_damaging(0.73)	9/27	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTGTCAATG	.	5	ESCA
FAM76B	0	.	GRCh37	11	95504208	95504208	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*517G>A	.	.	ENST00000358780	10/10	35	28	7	43	43	0	FAM76B,3_prime_UTR_variant,,ENST00000536839,;FAM76B,3_prime_UTR_variant,,ENST00000358780,;FAM76B,3_prime_UTR_variant,,ENST00000398187,;FAM76B,intron_variant,,ENST00000543641,;FAM76B,downstream_gene_variant,,ENST00000541418,;FAM76B,downstream_gene_variant,,ENST00000545813,;	T	ENSG00000077458	ENST00000358780	Transcript	3_prime_UTR_variant	1850	.	.	.	.	.	.	.	-1	FAM76B	HGNC	28492	protein_coding	YES	CCDS41700.1	ENSP00000351631	FA76B_HUMAN	.	UPI0000D62675	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTTCATTTA	.	2	ESCA
LRRC43	0	.	GRCh37	12	122677396	122677396	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1194C>T	p.%3D	p.V398V	ENST00000339777	7/12	47	43	4	59	59	0	LRRC43,synonymous_variant,p.%3D,ENST00000339777,;LRRC43,synonymous_variant,p.%3D,ENST00000425921,;LRRC43,downstream_gene_variant,,ENST00000537729,;LRRC43,intron_variant,,ENST00000541498,;LRRC43,downstream_gene_variant,,ENST00000537113,;	T	ENSG00000158113	ENST00000339777	Transcript	synonymous_variant	1222	1194	398	V	gtC/gtT	.	.	.	1	LRRC43	HGNC	28562	protein_coding	YES	CCDS45001.1	ENSP00000344233	LRC43_HUMAN	F5H0N3_HUMAN	UPI00015347BE	.	.	.	7/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10588,hmmpanther:PTHR10588:SF224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGGTCGAAGG	.	3	ESCA
H2AFJ	0	.	GRCh37	12	14927628	14927628	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224A>G	p.Lys75Arg	p.K75R	ENST00000544848	1/1	49	45	4	59	59	0	H2AFJ,missense_variant,p.Lys75Arg,ENST00000544848,;HIST4H4,upstream_gene_variant,,ENST00000539745,;HIST4H4,upstream_gene_variant,,ENST00000537853,;HIST4H4,upstream_gene_variant,,ENST00000541592,;HIST4H4,upstream_gene_variant,,ENST00000540565,;H2AFJ,missense_variant,p.Lys75Arg,ENST00000389078,;H2AFJ,missense_variant,p.Lys38Arg,ENST00000501744,;HIST4H4,upstream_gene_variant,,ENST00000358064,;	G	ENSG00000246705	ENST00000544848	Transcript	missense_variant	359	224	75	K/R	aAg/aGg	.	.	.	1	H2AFJ	HGNC	14456	protein_coding	YES	CCDS31752.1	ENSP00000438553	H2AJ_HUMAN	H0YFX9_HUMAN	UPI000006D12E	.	deleterious_low_confidence(0.03)	benign(0.049)	1/1	.	hmmpanther:PTHR23430:SF24,hmmpanther:PTHR23430,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAACAAGAAGA	.	3	ESCA
GOLT1B	0	.	GRCh37	12	21670807	21670807	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2166A>G	.	.	ENST00000229314	5/5	39	36	3	76	76	0	GOLT1B,3_prime_UTR_variant,,ENST00000229314,;GOLT1B,downstream_gene_variant,,ENST00000540141,;GOLT1B,downstream_gene_variant,,ENST00000542038,;GOLT1B,downstream_gene_variant,,ENST00000545093,;GOLT1B,downstream_gene_variant,,ENST00000535593,;GOLT1B,downstream_gene_variant,,ENST00000539025,;GOLT1B,downstream_gene_variant,,ENST00000539663,;GOLT1B,downstream_gene_variant,,ENST00000542194,;	G	ENSG00000111711	ENST00000229314	Transcript	3_prime_UTR_variant	2692	.	.	.	.	.	.	.	1	GOLT1B	HGNC	20175	protein_coding	YES	CCDS8689.1	ENSP00000229314	GOT1B_HUMAN	G3V1U5_HUMAN	UPI0000048ED8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCTATTGTT	.	2	ESCA
COL2A1	0	.	GRCh37	12	48380220	48380220	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1426G>A	p.Ala476Thr	p.A476T	ENST00000380518	23/54	54	46	8	45	45	0	COL2A1,missense_variant,p.Ala476Thr,ENST00000380518,;COL2A1,missense_variant,p.Ala407Thr,ENST00000337299,;COL2A1,non_coding_transcript_exon_variant,,ENST00000493991,;COL2A1,upstream_gene_variant,,ENST00000483376,;	T	ENSG00000139219	ENST00000380518	Transcript	missense_variant	1591	1426	476	A/T	Gct/Act	.	.	.	-1	COL2A1	HGNC	2200	protein_coding	YES	CCDS41778.1	ENSP00000369889	CO2A1_HUMAN	.	UPI0000D79713	.	.	possibly_damaging(0.828)	23/54	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF58,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGCAGGGC	.	5	ESCA
KMT2D	0	.	GRCh37	12	49444573	49444573	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2798delA	p.Asp933ValfsTer25	p.D933Vfs*25	ENST00000301067	11/54	41	33	8	43	43	0	KMT2D,frameshift_variant,p.Asp933ValfsTer25,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000547610,;	-	ENSG00000167548	ENST00000301067	Transcript	frameshift_variant	2798	2798	933	D/X	gAt/gt	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	11/54	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGGGATCTGGA	.	3	ESCA
DAZAP2	0	.	GRCh37	12	51636556	51636556	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120A>T	.	.	ENST00000549555	4/4	47	42	5	27	27	0	DAZAP2,3_prime_UTR_variant,,ENST00000549555,;DAZAP2,3_prime_UTR_variant,,ENST00000449723,;DAZAP2,3_prime_UTR_variant,,ENST00000439799,;DAZAP2,3_prime_UTR_variant,,ENST00000412716,;DAZAP2,intron_variant,,ENST00000425012,;DAZAP2,intron_variant,,ENST00000604900,;SMAGP,downstream_gene_variant,,ENST00000603864,;SMAGP,downstream_gene_variant,,ENST00000605426,;SMAGP,downstream_gene_variant,,ENST00000605627,;DAZAP2,downstream_gene_variant,,ENST00000551313,;SMAGP,downstream_gene_variant,,ENST00000603838,;SMAGP,downstream_gene_variant,,ENST00000398453,;SMAGP,downstream_gene_variant,,ENST00000604188,;DAZAP2,downstream_gene_variant,,ENST00000549732,;SMAGP,downstream_gene_variant,,ENST00000603798,;DAZAP2,downstream_gene_variant,,ENST00000552173,;DAZAP2,downstream_gene_variant,,ENST00000551919,;DAZAP2,downstream_gene_variant,,ENST00000549497,;DAZAP2,downstream_gene_variant,,ENST00000551534,;DAZAP2,3_prime_UTR_variant,,ENST00000436900,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000552459,;SMAGP,downstream_gene_variant,,ENST00000380103,;DAZAP2,downstream_gene_variant,,ENST00000549041,;	T	ENSG00000183283	ENST00000549555	Transcript	3_prime_UTR_variant	828	.	.	.	.	.	.	.	1	DAZAP2	HGNC	2684	protein_coding	YES	CCDS44885.1	ENSP00000448051	DAZP2_HUMAN	.	UPI000183CBDB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGTAATAAAA	.	4	ESCA
OR6C68	0	.	GRCh37	12	55886520	55886520	+	Missense_Mutation	SNP	G	G	A	rs145845899	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359G>A	p.Arg120His	p.R120H	ENST00000548615	1/1	52	42	10	69	69	0	OR6C68,missense_variant,p.Arg120His,ENST00000548615,;OR6C68,missense_variant,p.Arg125His,ENST00000379662,;RP11-110A12.2,intron_variant,,ENST00000556750,;RP11-110A12.2,intron_variant,,ENST00000554049,;RP11-110A12.2,intron_variant,,ENST00000555138,;	A	ENSG00000205327	ENST00000548615	Transcript	missense_variant	359	359	120	R/H	cGc/cAc	rs145845899	.	.	1	OR6C68	HGNC	31297	protein_coding	YES	CCDS31826.2	ENSP00000448811	O6C68_HUMAN	.	UPI00015E1642	.	deleterious_low_confidence(0.02)	benign(0.368)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,PROSITE_patterns:PS00237,hmmpanther:PTHR26454:SF19,hmmpanther:PTHR26454,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATCGCTATG	byCluster	5	ESCA
ESYT1	0	.	GRCh37	12	56536626	56536626	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2926G>A	p.Glu976Lys	p.E976K	ENST00000541590	27/32	16	13	3	41	41	0	ESYT1,missense_variant,p.Glu976Lys,ENST00000267113,;ESYT1,missense_variant,p.Glu976Lys,ENST00000541590,;ESYT1,missense_variant,p.Glu966Lys,ENST00000394048,;ESYT1,non_coding_transcript_exon_variant,,ENST00000550878,;ESYT1,non_coding_transcript_exon_variant,,ENST00000548142,;ESYT1,downstream_gene_variant,,ENST00000547667,;ESYT1,upstream_gene_variant,,ENST00000550515,;ESYT1,downstream_gene_variant,,ENST00000551112,;	A	ENSG00000139641	ENST00000541590	Transcript	missense_variant	2979	2926	976	E/K	Gag/Aag	.	.	.	1	ESYT1	HGNC	29534	protein_coding	YES	CCDS53801.1	ENSP00000445952	ESYT1_HUMAN	F8VZB1_HUMAN	UPI0000D720B2	.	tolerated(0.68)	benign(0.096)	27/32	.	hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTTGAGGCT	.	2	ESCA
USP5	0	.	GRCh37	12	6970267	6970267	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1495A>G	p.Lys499Glu	p.K499E	ENST00000229268	12/20	48	40	7	40	40	0	USP5,missense_variant,p.Lys499Glu,ENST00000229268,;USP5,missense_variant,p.Lys499Glu,ENST00000389231,;USP5,downstream_gene_variant,,ENST00000542087,;USP5,non_coding_transcript_exon_variant,,ENST00000541969,;USP5,non_coding_transcript_exon_variant,,ENST00000537267,;USP5,upstream_gene_variant,,ENST00000542371,;USP5,downstream_gene_variant,,ENST00000535080,;	G	ENSG00000111667	ENST00000229268	Transcript	missense_variant	1547	1495	499	K/E	Aaa/Gaa	.	.	.	1	USP5	HGNC	12628	protein_coding	YES	CCDS41743.1	ENSP00000229268	UBP5_HUMAN	.	UPI00001379E1	.	deleterious(0.04)	possibly_damaging(0.808)	12/20	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF381,Pfam_domain:PF00443,PIRSF_domain:PIRSF016308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAACAAAGGT	.	5	ESCA
E2F7	0	.	GRCh37	12	77440035	77440035	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612G>C	p.Lys204Asn	p.K204N	ENST00000322886	5/13	53	49	4	74	74	0	E2F7,missense_variant,p.Lys204Asn,ENST00000416496,;E2F7,missense_variant,p.Lys204Asn,ENST00000322886,;E2F7,missense_variant,p.Lys204Asn,ENST00000550669,;E2F7,missense_variant,p.Lys82Asn,ENST00000551058,;E2F7,missense_variant,p.Lys80Asn,ENST00000552907,;E2F7,non_coding_transcript_exon_variant,,ENST00000551558,;	G	ENSG00000165891	ENST00000322886	Transcript	missense_variant	848	612	204	K/N	aaG/aaC	.	.	.	-1	E2F7	HGNC	23820	protein_coding	YES	CCDS9016.1	ENSP00000323246	E2F7_HUMAN	F8VXV5_HUMAN,F8VSE7_HUMAN	UPI00001B64A1	.	deleterious(0)	probably_damaging(1)	5/13	.	Superfamily_domains:SSF46785,Gene3D:1.10.10.10,Pfam_domain:PF02319,hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGATTCTTAGC	.	3	ESCA
CEP290	0	.	GRCh37	12	88474063	88474063	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5122C>T	p.Leu1708Phe	p.L1708F	ENST00000552810	38/54	51	46	5	93	93	0	CEP290,missense_variant,p.Leu1708Phe,ENST00000552810,;CEP290,missense_variant,p.Leu768Phe,ENST00000397838,;CEP290,missense_variant,p.Leu1710Phe,ENST00000309041,;CEP290,missense_variant,p.Leu768Phe,ENST00000547691,;	A	ENSG00000198707	ENST00000552810	Transcript	missense_variant	5466	5122	1708	L/F	Ctt/Ttt	.	.	.	-1	CEP290	HGNC	29021	protein_coding	YES	CCDS55858.1	ENSP00000448012	CE290_HUMAN	.	UPI0000D60D15	.	.	possibly_damaging(0.603)	38/54	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGAAGTTCAG	.	4	ESCA
F7	0	.	GRCh37	13	113765088	113765088	+	Missense_Mutation	SNP	C	C	G	rs546856641	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.215C>G	p.Ser72Cys	p.S72C	ENST00000375581	3/9	28	21	6	51	51	0	F7,missense_variant,p.Ser50Cys,ENST00000346342,;F7,missense_variant,p.Ser72Cys,ENST00000375581,;F7,intron_variant,,ENST00000541084,;F7,non_coding_transcript_exon_variant,,ENST00000473085,;F7,synonymous_variant,p.%3D,ENST00000444337,;F7,non_coding_transcript_exon_variant,,ENST00000479674,;	G	ENSG00000057593	ENST00000375581	Transcript	missense_variant	250	215	72	S/C	tCc/tGc	rs546856641	.	.	1	F7	HGNC	3544	protein_coding	YES	CCDS9528.1	ENSP00000364731	FA7_HUMAN	Q9UMU6_HUMAN,A3RKG7_HUMAN	UPI000012A414	.	deleterious(0)	probably_damaging(0.989)	3/9	.	PROSITE_profiles:PS50998,hmmpanther:PTHR24265:SF34,hmmpanther:PTHR24265,Gene3D:4.10.740.10,Pfam_domain:PF00594,SMART_domains:SM00069,PIRSF_domain:PIRSF001143,Superfamily_domains:SSF57630,Prints_domain:PR00001	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTCCCTGG	by1000G	5	ESCA
MTUS2	0	.	GRCh37	13	29600389	29600389	+	Missense_Mutation	SNP	G	G	T	rs777937026	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1584G>T	p.Lys528Asn	p.K528N	ENST00000431530	1/14	31	26	5	41	41	0	MTUS2,missense_variant,p.Lys528Asn,ENST00000431530,;	T	ENSG00000132938	ENST00000431530	Transcript	missense_variant	1642	1584	528	K/N	aaG/aaT	rs777937026	.	.	1	MTUS2	HGNC	20595	protein_coding	YES	CCDS45022.1	ENSP00000392057	.	J3KQA9_HUMAN,B4DWQ4_HUMAN	UPI0000F734AC	.	deleterious(0.03)	benign(0.361)	1/14	.	hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAAGATTGA	.	2	ESCA
FNDC3A	0	.	GRCh37	13	49783626	49783626	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2095A>T	.	.	ENST00000492622	26/26	22	11	11	43	43	0	FNDC3A,3_prime_UTR_variant,,ENST00000492622,;FNDC3A,3_prime_UTR_variant,,ENST00000398316,;FNDC3A,downstream_gene_variant,,ENST00000541916,;FNDC3A,3_prime_UTR_variant,,ENST00000484074,;OGFOD1P1,downstream_gene_variant,,ENST00000447552,;	T	ENSG00000102531	ENST00000492622	Transcript	3_prime_UTR_variant	5997	.	.	.	.	.	.	.	1	FNDC3A	HGNC	20296	protein_coding	YES	CCDS41886.1	ENSP00000417257	FND3A_HUMAN	.	UPI0000229601	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGAATGAAC	.	5	ESCA
WDFY2	0	.	GRCh37	13	52333896	52333896	+	Silent	SNP	C	C	T	rs777475103	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1194C>T	p.%3D	p.V398V	ENST00000298125	12/12	23	20	3	50	50	0	WDFY2,synonymous_variant,p.%3D,ENST00000298125,;	T	ENSG00000139668	ENST00000298125	Transcript	synonymous_variant	1374	1194	398	V	gtC/gtT	rs777475103	.	.	1	WDFY2	HGNC	20482	protein_coding	YES	CCDS9429.1	ENSP00000298125	WDFY2_HUMAN	.	UPI00000466AC	.	.	.	12/12	.	hmmpanther:PTHR13856,hmmpanther:PTHR13856:SF84,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGTCGTGTC	.	2	ESCA
HNRNPA1L2	0	.	GRCh37	13	53216549	53216549	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-79C>G	.	.	ENST00000342657	7/7	54	46	8	65	65	0	HNRNPA1L2,5_prime_UTR_variant,,ENST00000398039,;HNRNPA1L2,5_prime_UTR_variant,,ENST00000342657,;HNRNPA1L2,upstream_gene_variant,,ENST00000357495,;MRPS31P4,downstream_gene_variant,,ENST00000509685,;	G	ENSG00000139675	ENST00000342657	Transcript	5_prime_UTR_variant	995	.	.	.	.	.	.	.	1	HNRNPA1L2	HGNC	27067	protein_coding	YES	CCDS31980.1	ENSP00000341285	RA1L2_HUMAN	.	UPI00001618EB	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATATCTAAGA	.	5	ESCA
MOK	0	.	GRCh37	14	102732205	102732205	+	Missense_Mutation	SNP	C	C	T	rs746962840	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.167G>A	p.Arg56His	p.R56H	ENST00000361847	3/12	79	62	16	57	57	0	MOK,missense_variant,p.Arg56His,ENST00000522874,;MOK,missense_variant,p.Arg56His,ENST00000361847,;MOK,5_prime_UTR_variant,,ENST00000193029,;MOK,intron_variant,,ENST00000524214,;MOK,non_coding_transcript_exon_variant,,ENST00000521966,;MOK,intron_variant,,ENST00000524019,;MOK,intron_variant,,ENST00000521493,;MOK,missense_variant,p.Arg56His,ENST00000562292,;MOK,missense_variant,p.Arg56His,ENST00000517537,;MOK,3_prime_UTR_variant,,ENST00000524207,;MOK,non_coding_transcript_exon_variant,,ENST00000519569,;MOK,non_coding_transcript_exon_variant,,ENST00000518686,;MOK,intron_variant,,ENST00000521766,;MOK,intron_variant,,ENST00000518399,;MOK,intron_variant,,ENST00000519877,;MOK,intron_variant,,ENST00000522093,;MOK,intron_variant,,ENST00000520238,;MOK,intron_variant,,ENST00000521388,;MOK,intron_variant,,ENST00000518482,;MOK,upstream_gene_variant,,ENST00000523485,;	T	ENSG00000080823	ENST00000361847	Transcript	missense_variant	399	167	56	R/H	cGc/cAc	rs746962840	.	.	-1	MOK	HGNC	9833	protein_coding	YES	CCDS9971.1	ENSP00000355304	MOK_HUMAN	Q49A77_HUMAN	UPI0000035B77	.	deleterious(0.01)	probably_damaging(0.988)	3/12	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:3.30.200.20,hmmpanther:PTHR24055:SF72,hmmpanther:PTHR24055,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGCGCCTC	byFrequency	5	ESCA
MARK3	0	.	GRCh37	14	103852338	103852338	+	5'UTR	SNP	C	C	T	rs762941104	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-29C>T	.	.	ENST00000429436	1/18	53	47	6	42	42	0	MARK3,5_prime_UTR_variant,,ENST00000560417,;MARK3,5_prime_UTR_variant,,ENST00000416682,;MARK3,5_prime_UTR_variant,,ENST00000440884,;MARK3,5_prime_UTR_variant,,ENST00000429436,;MARK3,5_prime_UTR_variant,,ENST00000216288,;MARK3,5_prime_UTR_variant,,ENST00000553942,;MARK3,5_prime_UTR_variant,,ENST00000303622,;MARK3,upstream_gene_variant,,ENST00000335102,;MARK3,upstream_gene_variant,,ENST00000561225,;MARK3,intron_variant,,ENST00000559328,;MARK3,intron_variant,,ENST00000560603,;MARK3,upstream_gene_variant,,ENST00000558223,;	T	ENSG00000075413	ENST00000429436	Transcript	5_prime_UTR_variant	482	.	.	.	.	rs762941104	.	.	1	MARK3	HGNC	6897	protein_coding	YES	CCDS45165.1	ENSP00000411397	MARK3_HUMAN	Q86U11_HUMAN	UPI00004567CC	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCCTCGCATT	byFrequency	4	ESCA
TRMT61A	0	.	GRCh37	14	104001404	104001404	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*246A>G	.	.	ENST00000389749	4/4	62	56	6	81	81	0	TRMT61A,3_prime_UTR_variant,,ENST00000389749,;TRMT61A,3_prime_UTR_variant,,ENST00000299202,;	G	ENSG00000166166	ENST00000389749	Transcript	3_prime_UTR_variant	1223	.	.	.	.	.	.	.	1	TRMT61A	HGNC	23790	protein_coding	YES	CCDS41994.1	ENSP00000374399	TRM61_HUMAN	.	UPI0000072BC7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAATATGAAG	.	2	ESCA
IGHD3-22	0	.	GRCh37	14	106351909	106351909	+	Silent	SNP	C	C	T	rs547532541	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11G>A	p.%3D	p.%3D	ENST00000390571	1/1	142	133	9	163	163	0	IGHD3-22,stop_retained_variant,p.%3D,ENST00000390571,;IGHD2-21,downstream_gene_variant,,ENST00000390572,;IGHD4-23,upstream_gene_variant,,ENST00000437320,;IGHD5-24,upstream_gene_variant,,ENST00000390569,;IGHD6-25,upstream_gene_variant,,ENST00000452198,;IGHD1-26,upstream_gene_variant,,ENST00000390567,;AL122127.25,upstream_gene_variant,,ENST00000414005,;	T	ENSG00000211911	ENST00000390571	Transcript	stop_retained_variant	11	11	4	*	tGa/tAa	rs547532541	.	.	-1	IGHD3-22	HGNC	5497	IG_D_gene	YES	.	ENSP00000429952	.	.	.	.	.	.	1/1	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTATCATAGT	by1000G	2	ESCA
SLC7A7	0	.	GRCh37	14	23245096	23245096	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.944C>G	p.Ser315Ter	p.S315*	ENST00000397532	6/10	17	14	3	34	34	0	SLC7A7,stop_gained,p.Ser315Ter,ENST00000397528,;SLC7A7,stop_gained,p.Ser315Ter,ENST00000555702,;SLC7A7,stop_gained,p.Ser49Ter,ENST00000554517,;SLC7A7,stop_gained,p.Ser30Ter,ENST00000556350,;SLC7A7,stop_gained,p.Ser315Ter,ENST00000397529,;SLC7A7,stop_gained,p.Ser315Ter,ENST00000285850,;SLC7A7,stop_gained,p.Ser315Ter,ENST00000397532,;OXA1L,downstream_gene_variant,,ENST00000412791,;OXA1L,downstream_gene_variant,,ENST00000604262,;OXA1L,downstream_gene_variant,,ENST00000285848,;OXA1L,downstream_gene_variant,,ENST00000358043,;SLC7A7,non_coding_transcript_exon_variant,,ENST00000554061,;SLC7A7,intron_variant,,ENST00000556287,;SLC7A7,upstream_gene_variant,,ENST00000555678,;OXA1L,downstream_gene_variant,,ENST00000495424,;OXA1L,downstream_gene_variant,,ENST00000481218,;	C	ENSG00000155465	ENST00000397532	Transcript	stop_gained	1470	944	315	S/*	tCa/tGa	.	.	.	-1	SLC7A7	HGNC	11065	protein_coding	YES	CCDS9574.1	ENSP00000380666	YLAT1_HUMAN	G3V5W2_HUMAN,G3V5A1_HUMAN,G3V4Z6_HUMAN,G3V4U1_HUMAN,G3V362_HUMAN,G3V2L0_HUMAN,G3V2H8_HUMAN,G3V273_HUMAN,D6RFE5_HUMAN	UPI000000CC04	.	.	.	6/10	.	Transmembrane_helices:TMhelix,PIRSF_domain:PIRSF006060,Pfam_domain:PF13520,hmmpanther:PTHR11785:SF303,hmmpanther:PTHR11785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACTGACAGT	.	5	ESCA
PLEKHG3	0	.	GRCh37	14	65210415	65210415	+	Silent	SNP	C	C	T	rs752022533	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3486C>T	p.%3D	p.V1162V	ENST00000247226	15/15	39	31	8	51	51	0	PLEKHG3,synonymous_variant,p.%3D,ENST00000394691,;PLEKHG3,synonymous_variant,p.%3D,ENST00000247226,;PLEKHG3,synonymous_variant,p.%3D,ENST00000471182,;PLEKHG3,synonymous_variant,p.%3D,ENST00000484731,;SPTB,downstream_gene_variant,,ENST00000389722,;PLEKHG3,intron_variant,,ENST00000492928,;SPTB,downstream_gene_variant,,ENST00000342835,;PLEKHG3,non_coding_transcript_exon_variant,,ENST00000490180,;	T	ENSG00000126822	ENST00000247226	Transcript	synonymous_variant	3794	3486	1162	V	gtC/gtT	rs752022533	.	.	1	PLEKHG3	HGNC	20364	protein_coding	YES	CCDS32098.1	ENSP00000247226	PKHG3_HUMAN	G3V311_HUMAN	UPI0000407D62	.	.	.	15/15	.	hmmpanther:PTHR22143:SF4,hmmpanther:PTHR22143	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGTCGGTTG	.	5	ESCA
NRXN3	0	.	GRCh37	14	79434617	79434617	+	Silent	SNP	T	T	C	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1951T>C	p.%3D	p.L651L	ENST00000554719	11/17	50	43	7	78	78	0	NRXN3,synonymous_variant,p.%3D,ENST00000554719,;NRXN3,synonymous_variant,p.%3D,ENST00000335750,;NRXN3,synonymous_variant,p.%3D,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,;	C	ENSG00000021645	ENST00000554719	Transcript	synonymous_variant	2442	1951	651	L	Ttg/Ctg	COSM3498318	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	11/17	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF405,hmmpanther:PTHR10127,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R654C|c.1960C>T|4	RADIA|MUTECT|MUSE|VARSCANS	TGGACTTGAAT	.	4	ESCA
STON2	0	.	GRCh37	14	81744226	81744226	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1429G>T	p.Glu477Ter	p.E477*	ENST00000555447	6/8	46	42	4	45	45	0	STON2,stop_gained,p.Glu477Ter,ENST00000267540,;STON2,stop_gained,p.Glu477Ter,ENST00000555447,;STON2,upstream_gene_variant,,ENST00000553821,;STON2,downstream_gene_variant,,ENST00000556280,;STON2,non_coding_transcript_exon_variant,,ENST00000555284,;	A	ENSG00000140022	ENST00000555447	Transcript	stop_gained	1842	1429	477	E/*	Gag/Tag	.	.	.	-1	STON2	HGNC	30652	protein_coding	YES	CCDS58332.1	ENSP00000450857	STON2_HUMAN	G3V322_HUMAN	UPI00001FD96B	.	.	.	6/8	.	PIRSF_domain:PIRSF037099,hmmpanther:PTHR11998,hmmpanther:PTHR11998:SF19,PROSITE_profiles:PS51070	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GATCTCCAGCT	.	2	ESCA
STON2	0	.	GRCh37	14	81744227	81744227	+	Silent	SNP	C	C	A	rs760472834	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1428G>T	p.%3D	p.L476L	ENST00000555447	6/8	45	42	3	45	45	0	STON2,synonymous_variant,p.%3D,ENST00000267540,;STON2,synonymous_variant,p.%3D,ENST00000555447,;STON2,upstream_gene_variant,,ENST00000553821,;STON2,downstream_gene_variant,,ENST00000556280,;STON2,non_coding_transcript_exon_variant,,ENST00000555284,;	A	ENSG00000140022	ENST00000555447	Transcript	synonymous_variant	1841	1428	476	L	ctG/ctT	rs760472834	.	.	-1	STON2	HGNC	30652	protein_coding	YES	CCDS58332.1	ENSP00000450857	STON2_HUMAN	G3V322_HUMAN	UPI00001FD96B	.	.	.	6/8	.	PIRSF_domain:PIRSF037099,hmmpanther:PTHR11998,hmmpanther:PTHR11998:SF19,PROSITE_profiles:PS51070	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ATCTCCAGCTT	byFrequency	2	ESCA
SNORD115-11	0	.	GRCh37	15	25434591	25434591	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.31G>A	.	.	ENST00000363616	1/1	52	49	3	78	78	0	SNORD115-11,non_coding_transcript_exon_variant,,ENST00000363616,;SNORD115-10,downstream_gene_variant,,ENST00000365073,;SNHG14,upstream_gene_variant,,ENST00000363358,;SNORD115-12,upstream_gene_variant,,ENST00000362583,;SNORD115-9,downstream_gene_variant,,ENST00000362912,;SNHG14,intron_variant,,ENST00000414175,;SNHG14,intron_variant,,ENST00000424208,;SNHG14,upstream_gene_variant,,ENST00000456576,;	A	ENSG00000200486	ENST00000363616	Transcript	non_coding_transcript_exon_variant	31	.	.	.	.	.	.	.	1	SNORD115-11	HGNC	33030	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCTGAAGAG	.	2	ESCA
TJP1	0	.	GRCh37	15	30012102	30012102	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2882delC	p.Pro961GlnfsTer14	p.P961Qfs*14	ENST00000346128	20/28	61	46	15	82	82	0	TJP1,frameshift_variant,p.Pro961GlnfsTer14,ENST00000356107,;TJP1,frameshift_variant,p.Pro961GlnfsTer14,ENST00000346128,;TJP1,intron_variant,,ENST00000400011,;TJP1,intron_variant,,ENST00000545208,;TJP1,non_coding_transcript_exon_variant,,ENST00000561307,;	-	ENSG00000104067	ENST00000346128	Transcript	frameshift_variant	3357	2882	961	P/X	cCa/ca	.	.	.	-1	TJP1	HGNC	11827	protein_coding	YES	CCDS42007.1	ENSP00000281537	ZO1_HUMAN	.	UPI000013DC83	.	.	.	20/28	.	hmmpanther:PTHR13865,hmmpanther:PTHR13865:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAGCTGGGGTG	.	3	ESCA
KLF13	0	.	GRCh37	15	31664511	31664511	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9C>A	.	.	ENST00000307145	2/2	32	26	6	48	48	0	KLF13,3_prime_UTR_variant,,ENST00000307145,;KLF13,3_prime_UTR_variant,,ENST00000560473,;KLF13,downstream_gene_variant,,ENST00000558844,;KLF13,intron_variant,,ENST00000558921,;KLF13,upstream_gene_variant,,ENST00000558673,;	A	ENSG00000169926	ENST00000307145	Transcript	3_prime_UTR_variant	1234	.	.	.	.	.	.	.	1	KLF13	HGNC	13672	protein_coding	YES	CCDS10025.1	ENSP00000302456	KLF13_HUMAN	.	UPI000012DEDC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCACAGCCA	.	5	ESCA
GREM1	0	.	GRCh37	15	33022942	33022942	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51C>G	p.%3D	p.T17T	ENST00000300177	2/2	16	13	3	27	27	0	GREM1,synonymous_variant,p.%3D,ENST00000300177,;GREM1,synonymous_variant,p.%3D,ENST00000322805,;GREM1,synonymous_variant,p.%3D,ENST00000560830,;GREM1,synonymous_variant,p.%3D,ENST00000560677,;	G	ENSG00000166923	ENST00000300177	Transcript	synonymous_variant	240	51	17	T	acC/acG	.	.	.	1	GREM1	HGNC	2001	protein_coding	YES	CCDS10029.1	ENSP00000300177	GREM1_HUMAN	A6XAA7_HUMAN	UPI0000073D48	.	.	.	2/2	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR15283,hmmpanther:PTHR15283:SF3,PIRSF_domain:PIRSF037254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GGGACCCTGCT	.	4	ESCA
MEIS2	0	.	GRCh37	15	37391777	37391777	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-110C>G	.	.	ENST00000561208	1/12	12	9	3	33	33	0	MEIS2,5_prime_UTR_variant,,ENST00000424352,;MEIS2,5_prime_UTR_variant,,ENST00000559561,;MEIS2,5_prime_UTR_variant,,ENST00000338564,;MEIS2,5_prime_UTR_variant,,ENST00000444725,;MEIS2,5_prime_UTR_variant,,ENST00000382766,;MEIS2,5_prime_UTR_variant,,ENST00000561208,;MEIS2,intron_variant,,ENST00000558313,;MEIS2,intron_variant,,ENST00000340545,;MEIS2,upstream_gene_variant,,ENST00000219869,;MEIS2,upstream_gene_variant,,ENST00000560697,;MEIS2,upstream_gene_variant,,ENST00000397620,;MEIS2,upstream_gene_variant,,ENST00000560617,;MEIS2,upstream_gene_variant,,ENST00000607277,;MEIS2,upstream_gene_variant,,ENST00000397624,;MEIS2,upstream_gene_variant,,ENST00000559085,;MEIS2,upstream_gene_variant,,ENST00000557796,;RP11-128A17.1,intron_variant,,ENST00000559509,;MEIS2,5_prime_UTR_variant,,ENST00000314177,;MEIS2,upstream_gene_variant,,ENST00000561163,;MEIS2,upstream_gene_variant,,ENST00000560570,;MEIS2,upstream_gene_variant,,ENST00000559129,;	C	ENSG00000134138	ENST00000561208	Transcript	5_prime_UTR_variant	310	.	.	.	.	.	.	.	-1	MEIS2	HGNC	7001	protein_coding	YES	CCDS10044.1	ENSP00000453793	MEIS2_HUMAN	H0YKN2_HUMAN,H0YKE5_HUMAN	UPI000012EEBC	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AAAGAGACTTC	.	2	ESCA
EIF2AK4	0	.	GRCh37	15	40295507	40295507	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3349G>A	p.Asp1117Asn	p.D1117N	ENST00000263791	23/39	96	91	4	92	92	0	EIF2AK4,missense_variant,p.Asp895Asn,ENST00000560855,;EIF2AK4,missense_variant,p.Asp1089Asn,ENST00000382727,;EIF2AK4,missense_variant,p.Asp1117Asn,ENST00000263791,;EIF2AK4,non_coding_transcript_exon_variant,,ENST00000559311,;EIF2AK4,non_coding_transcript_exon_variant,,ENST00000558557,;EIF2AK4,non_coding_transcript_exon_variant,,ENST00000558629,;	A	ENSG00000128829	ENST00000263791	Transcript	missense_variant	3392	3349	1117	D/N	Gac/Aac	.	.	.	1	EIF2AK4	HGNC	19687	protein_coding	YES	CCDS42016.1	ENSP00000263791	E2AK4_HUMAN	.	UPI0000160791	.	deleterious(0.03)	possibly_damaging(0.833)	23/39	.	hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF70,Gene3D:3.30.930.10,Pfam_domain:PF13393,PIRSF_domain:PIRSF000660,Superfamily_domains:SSF55681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTTTTGACCTG	.	2	ESCA
IVD	0	.	GRCh37	15	40703768	40703768	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.574C>T	p.%3D	p.L192L	ENST00000487418	6/12	56	48	8	72	72	0	IVD,synonymous_variant,p.%3D,ENST00000473112,;IVD,synonymous_variant,p.%3D,ENST00000249760,;IVD,synonymous_variant,p.%3D,ENST00000479013,;IVD,synonymous_variant,p.%3D,ENST00000487418,;IVD,synonymous_variant,p.%3D,ENST00000558610,;IVD,upstream_gene_variant,,ENST00000559575,;IVD,upstream_gene_variant,,ENST00000466756,;IVD,upstream_gene_variant,,ENST00000491554,;IVD,downstream_gene_variant,,ENST00000490194,;IVD,upstream_gene_variant,,ENST00000497252,;IVD,synonymous_variant,p.%3D,ENST00000481262,;IVD,non_coding_transcript_exon_variant,,ENST00000484250,;IVD,upstream_gene_variant,,ENST00000560660,;IVD,upstream_gene_variant,,ENST00000497816,;	T	ENSG00000128928	ENST00000487418	Transcript	synonymous_variant	598	574	192	L	Ctg/Ttg	.	.	.	1	IVD	HGNC	6186	protein_coding	YES	CCDS10057.2	ENSP00000418397	.	O43577_HUMAN,J3KR54_HUMAN	UPI0000D4AF3D	.	.	.	6/12	.	hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF211,Pfam_domain:PF02770,Gene3D:2.40.110.10,Superfamily_domains:SSF56645	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATCCTGAAT	.	4	ESCA
VPS39	0	.	GRCh37	15	42470518	42470518	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.858G>T	p.%3D	p.V286V	ENST00000318006	10/25	20	12	7	31	31	0	VPS39,synonymous_variant,p.%3D,ENST00000348544,;VPS39,synonymous_variant,p.%3D,ENST00000318006,;VPS39,non_coding_transcript_exon_variant,,ENST00000568029,;VPS39,non_coding_transcript_exon_variant,,ENST00000570023,;	A	ENSG00000166887	ENST00000318006	Transcript	synonymous_variant	1021	858	286	V	gtG/gtT	.	.	.	-1	VPS39	HGNC	20593	protein_coding	YES	CCDS10083.1	ENSP00000326534	VPS39_HUMAN	.	UPI0000169BB1	.	.	.	10/25	.	hmmpanther:PTHR12894:SF10,hmmpanther:PTHR12894,SMART_domains:SM00036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCCACATA	.	5	ESCA
PPIP5K1	0	.	GRCh37	15	43825732	43825732	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1140G>C	.	.	ENST00000420765	31/31	28	22	6	32	32	0	PPIP5K1,3_prime_UTR_variant,,ENST00000396923,;PPIP5K1,3_prime_UTR_variant,,ENST00000360301,;PPIP5K1,3_prime_UTR_variant,,ENST00000381885,;PPIP5K1,3_prime_UTR_variant,,ENST00000381879,;PPIP5K1,3_prime_UTR_variant,,ENST00000420765,;PPIP5K1,3_prime_UTR_variant,,ENST00000360135,;PPIP5K1,3_prime_UTR_variant,,ENST00000334933,;MAP1A,downstream_gene_variant,,ENST00000300231,;MAP1A,downstream_gene_variant,,ENST00000382031,;MAP1A,downstream_gene_variant,,ENST00000399453,;PPIP5K1,downstream_gene_variant,,ENST00000348806,;	G	ENSG00000168781	ENST00000420765	Transcript	3_prime_UTR_variant	5625	.	.	.	.	.	.	.	-1	PPIP5K1	HGNC	29023	protein_coding	YES	CCDS45252.1	ENSP00000400887	VIP1_HUMAN	C9JZX6_HUMAN,C9J5E6_HUMAN,C9J490_HUMAN	UPI00001CE036	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGACCGCATT	.	5	ESCA
CEP152	0	.	GRCh37	15	49085560	49085560	+	Missense_Mutation	SNP	G	G	A	rs146482586	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.790C>T	p.Arg264Cys	p.R264C	ENST00000380950	7/27	80	69	10	70	70	0	CEP152,missense_variant,p.Arg264Cys,ENST00000380950,;CEP152,missense_variant,p.Arg171Cys,ENST00000325747,;CEP152,missense_variant,p.Arg264Cys,ENST00000399334,;CEP152,downstream_gene_variant,,ENST00000558591,;CEP152,upstream_gene_variant,,ENST00000558337,;CEP152,missense_variant,p.Arg264Cys,ENST00000560322,;CEP152,downstream_gene_variant,,ENST00000559444,;	A	ENSG00000103995	ENST00000380950	Transcript	missense_variant	978	790	264	R/C	Cgt/Tgt	rs146482586	.	.	-1	CEP152	HGNC	29298	protein_coding	YES	CCDS58361.1	ENSP00000370337	CE152_HUMAN	H0YN91_HUMAN	UPI00002378C4	.	deleterious(0.03)	benign(0.053)	7/27	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10337,hmmpanther:PTHR10337:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUSE|VARSCANS	TTGACGTTCAC	byCluster|by1000G	2	ESCA
LEO1	0	.	GRCh37	15	52258503	52258503	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257A>G	p.Asn86Ser	p.N86S	ENST00000299601	2/12	59	45	14	58	58	0	LEO1,missense_variant,p.Asn86Ser,ENST00000315141,;LEO1,missense_variant,p.Asn86Ser,ENST00000299601,;MAPK6,intron_variant,,ENST00000560802,;	C	ENSG00000166477	ENST00000299601	Transcript	missense_variant	318	257	86	N/S	aAt/aGt	.	.	.	-1	LEO1	HGNC	30401	protein_coding	YES	CCDS10146.1	ENSP00000299601	LEO1_HUMAN	.	UPI0000071CA0	.	deleterious_low_confidence(0.01)	benign(0.26)	2/12	.	hmmpanther:PTHR23146:SF0,hmmpanther:PTHR23146	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTATTGTCT	.	5	ESCA
ZNF609	0	.	GRCh37	15	64966881	64966881	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1828G>C	p.Asp610His	p.D610H	ENST00000326648	4/9	17	14	3	14	14	0	ZNF609,missense_variant,p.Asp610His,ENST00000326648,;RNU6-549P,downstream_gene_variant,,ENST00000384433,;ZNF609,non_coding_transcript_exon_variant,,ENST00000559364,;ZNF609,downstream_gene_variant,,ENST00000558680,;	C	ENSG00000180357	ENST00000326648	Transcript	missense_variant	1956	1828	610	D/H	Gat/Cat	.	.	.	1	ZNF609	HGNC	29003	protein_coding	YES	CCDS32270.1	ENSP00000316527	ZN609_HUMAN	.	UPI00001D7783	.	deleterious(0.05)	possibly_damaging(0.531)	4/9	.	hmmpanther:PTHR21564,hmmpanther:PTHR21564:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCTGATGAT	.	2	ESCA
CHRNA5	0	.	GRCh37	15	78882187	78882187	+	Missense_Mutation	SNP	A	A	T	rs749486168	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454A>T	p.Ile152Phe	p.I152F	ENST00000299565	5/6	78	66	11	89	89	0	CHRNA5,missense_variant,p.Ile91Phe,ENST00000394802,;CHRNA5,missense_variant,p.Ile152Phe,ENST00000559554,;CHRNA5,missense_variant,p.Ile152Phe,ENST00000299565,;CHRNA3,downstream_gene_variant,,ENST00000348639,;CHRNA5,upstream_gene_variant,,ENST00000559576,;RP11-650L12.2,non_coding_transcript_exon_variant,,ENST00000567141,;CHRNA3,downstream_gene_variant,,ENST00000559002,;CHRNA3,downstream_gene_variant,,ENST00000559658,;	T	ENSG00000169684	ENST00000299565	Transcript	missense_variant	654	454	152	I/F	Atc/Ttc	rs749486168	.	.	1	CHRNA5	HGNC	1959	protein_coding	YES	CCDS10304.1	ENSP00000299565	ACHA5_HUMAN	Q6EWN4_HUMAN	UPI0000001638	.	deleterious(0)	possibly_damaging(0.533)	5/6	.	hmmpanther:PTHR18945:SF76,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932,Prints_domain:PR00254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.T148T|c.444G>A|9	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCATCAGG	.	5	ESCA
CTD-3088G3.8	0	.	GRCh37	16	11540490	11540490	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4647C>T	p.%3D	p.V1549V	ENST00000598234	32/50	55	52	3	52	52	0	CTD-3088G3.8,synonymous_variant,p.%3D,ENST00000344649,;CTD-3088G3.8,synonymous_variant,p.%3D,ENST00000598234,;CTD-3088G3.8,splice_region_variant,,ENST00000595170,;CTD-3088G3.8,downstream_gene_variant,,ENST00000600877,;	A	ENSG00000188897	ENST00000598234	Transcript	synonymous_variant	4800	4647	1549	V	gtC/gtT	.	.	.	-1	CTD-3088G3.8	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000470478	.	M0QZD8_HUMAN	UPI0002A474E2	.	.	.	32/50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCACAGACCTG	.	2	ESCA
XYLT1	0	.	GRCh37	16	17202585	17202585	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2847G>A	p.%3D	p.L949L	ENST00000261381	12/12	30	25	5	22	22	0	XYLT1,synonymous_variant,p.%3D,ENST00000261381,;	T	ENSG00000103489	ENST00000261381	Transcript	synonymous_variant	2932	2847	949	L	ctG/ctA	.	.	.	-1	XYLT1	HGNC	15516	protein_coding	YES	CCDS10569.1	ENSP00000261381	XYLT1_HUMAN	.	UPI000000DCCE	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCCCCAGCTC	.	3	ESCA
GP2	0	.	GRCh37	16	20335452	20335452	+	Missense_Mutation	SNP	C	C	T	rs374063505	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221G>A	p.Arg74Gln	p.R74Q	ENST00000381362	3/12	49	27	22	38	38	0	GP2,missense_variant,p.Arg74Gln,ENST00000381362,;GP2,missense_variant,p.Arg74Gln,ENST00000575449,;GP2,missense_variant,p.Arg74Gln,ENST00000302555,;GP2,5_prime_UTR_variant,,ENST00000572347,;GP2,intron_variant,,ENST00000341642,;GP2,intron_variant,,ENST00000575582,;GP2,intron_variant,,ENST00000381360,;GP2,intron_variant,,ENST00000572478,;GP2,non_coding_transcript_exon_variant,,ENST00000575730,;GP2,upstream_gene_variant,,ENST00000573897,;GP2,intron_variant,,ENST00000574982,;	T	ENSG00000169347	ENST00000381362	Transcript	missense_variant	298	221	74	R/Q	cGa/cAa	rs374063505,COSM1376361	.	.	-1	GP2	HGNC	4441	protein_coding	YES	CCDS42128.1	ENSP00000370767	GP2_HUMAN	I3L2Z7_HUMAN	UPI000059D333	.	deleterious(0)	probably_damaging(1)	3/12	.	hmmpanther:PTHR22962:SF129,hmmpanther:PTHR22962	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTCGGAAG	byFrequency|byCluster	5	ESCA
NLRC3	0	.	GRCh37	16	3607659	3607659	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2175C>T	p.%3D	p.I725I	ENST00000448023	5/19	46	39	7	56	56	0	NLRC3,synonymous_variant,p.%3D,ENST00000301749,;NLRC3,synonymous_variant,p.%3D,ENST00000359128,;NLRC3,synonymous_variant,p.%3D,ENST00000448023,;NLRC3,non_coding_transcript_exon_variant,,ENST00000603128,;NLRC3,non_coding_transcript_exon_variant,,ENST00000419350,;NLRC3,upstream_gene_variant,,ENST00000604347,;NLRC3,synonymous_variant,p.%3D,ENST00000603507,;	A	ENSG00000167984	ENST00000448023	Transcript	synonymous_variant	2362	2175	725	I	atC/atT	.	.	.	-1	NLRC3	HGNC	29889	protein_coding	YES	.	ENSP00000414415	.	C9JLH9_HUMAN	UPI0000246E58	.	.	.	5/19	.	Superfamily_domains:SSF52047,SMART_domains:SM00368,Pfam_domain:PF13516,Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTGATCTG	.	5	ESCA
DNAJA3	0	.	GRCh37	16	4493076	4493076	+	Missense_Mutation	SNP	G	G	A	rs747052248	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.842G>A	p.Arg281His	p.R281H	ENST00000262375	6/12	85	78	7	70	70	0	DNAJA3,missense_variant,p.Arg281His,ENST00000262375,;DNAJA3,missense_variant,p.Arg281His,ENST00000355296,;DNAJA3,missense_variant,p.Arg128His,ENST00000431375,;DNAJA3,downstream_gene_variant,,ENST00000574895,;DNAJA3,downstream_gene_variant,,ENST00000572139,;DNAJA3,3_prime_UTR_variant,,ENST00000576911,;DNAJA3,non_coding_transcript_exon_variant,,ENST00000577083,;DNAJA3,downstream_gene_variant,,ENST00000575106,;DNAJA3,downstream_gene_variant,,ENST00000570857,;DNAJA3,downstream_gene_variant,,ENST00000572009,;	A	ENSG00000103423	ENST00000262375	Transcript	missense_variant	919	842	281	R/H	cGc/cAc	rs747052248	.	.	1	DNAJA3	HGNC	11808	protein_coding	YES	CCDS10515.1	ENSP00000262375	DNJA3_HUMAN	Q59E88_HUMAN,Q53G26_HUMAN	UPI0000043C38	.	tolerated(0.13)	benign(0.187)	6/12	.	Low_complexity_(Seg):seg,HAMAP:MF_01152,PROSITE_profiles:PS51188,hmmpanther:PTHR24076:SF79,hmmpanther:PTHR24076,Gene3D:2.10.230.10,Pfam_domain:PF00684,Superfamily_domains:SSF57938	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGCCGCGGCT	.	3	ESCA
HERPUD1	0	.	GRCh37	16	56977366	56977366	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*164G>A	.	.	ENST00000439977	8/8	28	24	3	36	36	0	HERPUD1,3_prime_UTR_variant,,ENST00000344114,;HERPUD1,3_prime_UTR_variant,,ENST00000563911,;HERPUD1,3_prime_UTR_variant,,ENST00000568358,;HERPUD1,3_prime_UTR_variant,,ENST00000379792,;HERPUD1,3_prime_UTR_variant,,ENST00000300302,;HERPUD1,3_prime_UTR_variant,,ENST00000439977,;HERPUD1,downstream_gene_variant,,ENST00000569429,;HERPUD1,downstream_gene_variant,,ENST00000563343,;HERPUD1,downstream_gene_variant,,ENST00000568651,;RP11-325K4.3,downstream_gene_variant,,ENST00000565861,;RP11-325K4.2,downstream_gene_variant,,ENST00000570210,;HERPUD1,non_coding_transcript_exon_variant,,ENST00000570273,;HERPUD1,downstream_gene_variant,,ENST00000568814,;HERPUD1,downstream_gene_variant,,ENST00000563781,;HERPUD1,non_coding_transcript_exon_variant,,ENST00000564678,;HERPUD1,downstream_gene_variant,,ENST00000565966,;HERPUD1,downstream_gene_variant,,ENST00000567944,;	A	ENSG00000051108	ENST00000439977	Transcript	3_prime_UTR_variant	1537	.	.	.	.	.	.	.	1	HERPUD1	HGNC	13744	protein_coding	YES	CCDS10771.1	ENSP00000409555	HERP1_HUMAN	Q9HBR2_HUMAN,B4E3N8_HUMAN	UPI0000000B03	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCGTGATACA	.	4	ESCA
CCDC102A	0	.	GRCh37	16	57546752	57546752	+	Silent	SNP	G	G	A	rs765905266	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1554C>T	p.%3D	p.L518L	ENST00000258214	9/9	52	46	6	58	58	0	CCDC102A,synonymous_variant,p.%3D,ENST00000258214,;CCDC102A,non_coding_transcript_exon_variant,,ENST00000569068,;	A	ENSG00000135736	ENST00000258214	Transcript	synonymous_variant	1801	1554	518	L	ctC/ctT	rs765905266	.	.	-1	CCDC102A	HGNC	28097	protein_coding	YES	CCDS10784.1	ENSP00000258214	C102A_HUMAN	.	UPI000013CFBA	.	.	.	9/9	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF269	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGAAGAGGGG	.	4	ESCA
CCDC113	0	.	GRCh37	16	58287930	58287930	+	Missense_Mutation	SNP	G	G	A	rs372193450	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257G>A	p.Arg86Gln	p.R86Q	ENST00000219299	3/9	97	86	10	137	137	0	CCDC113,missense_variant,p.Arg86Gln,ENST00000219299,;CCDC113,missense_variant,p.Arg41Gln,ENST00000569374,;CCDC113,intron_variant,,ENST00000443128,;CCDC113,downstream_gene_variant,,ENST00000566498,;CCDC113,intron_variant,,ENST00000561517,;	A	ENSG00000103021	ENST00000219299	Transcript	missense_variant	336	257	86	R/Q	cGg/cAg	rs372193450,COSM1378639	.	.	1	CCDC113	HGNC	25002	protein_coding	YES	CCDS10795.1	ENSP00000219299	CC113_HUMAN	H3BQS9_HUMAN	UPI000007254E	.	deleterious(0.03)	benign(0.337)	3/9	.	hmmpanther:PTHR15654,hmmpanther:PTHR15654:SF2	A:0.0006	A:0.0008	A:0	.	A:0	A:0	A:0.002	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCCCGGACAG	byFrequency|byCluster|by1000G	4	ESCA
CA7	0	.	GRCh37	16	66887278	66887278	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673-1G>C	.	p.X225_splice	ENST00000338437	.	58	53	5	57	57	0	CA7,splice_acceptor_variant,,ENST00000394069,;CA7,splice_acceptor_variant,,ENST00000338437,;NAE1,intron_variant,,ENST00000561579,;RP11-61A14.1,intron_variant,,ENST00000551187,;CA7,splice_acceptor_variant,,ENST00000548332,;	C	ENSG00000168748	ENST00000338437	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	CA7	HGNC	1381	protein_coding	YES	CCDS10821.1	ENSP00000345659	CAH7_HUMAN	.	UPI000000D814	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCAAGATGGG	.	3	ESCA
FHOD1	0	.	GRCh37	16	67265981	67265981	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2163C>G	p.%3D	p.L721L	ENST00000258201	14/22	91	87	4	100	100	0	FHOD1,synonymous_variant,p.%3D,ENST00000258201,;TMEM208,downstream_gene_variant,,ENST00000304800,;TMEM208,downstream_gene_variant,,ENST00000563953,;TMEM208,downstream_gene_variant,,ENST00000565201,;TMEM208,downstream_gene_variant,,ENST00000563426,;FHOD1,synonymous_variant,p.%3D,ENST00000567509,;FHOD1,non_coding_transcript_exon_variant,,ENST00000567752,;FHOD1,non_coding_transcript_exon_variant,,ENST00000569888,;FHOD1,upstream_gene_variant,,ENST00000567561,;FHOD1,downstream_gene_variant,,ENST00000561922,;TMEM208,downstream_gene_variant,,ENST00000564649,;TMEM208,downstream_gene_variant,,ENST00000563168,;FHOD1,downstream_gene_variant,,ENST00000568595,;TMEM208,downstream_gene_variant,,ENST00000564087,;TMEM208,downstream_gene_variant,,ENST00000566486,;FHOD1,upstream_gene_variant,,ENST00000566006,;TMEM208,downstream_gene_variant,,ENST00000567193,;FHOD1,downstream_gene_variant,,ENST00000562266,;TMEM208,downstream_gene_variant,,ENST00000562235,;TMEM208,downstream_gene_variant,,ENST00000561586,;TMEM208,downstream_gene_variant,,ENST00000563271,;FHOD1,upstream_gene_variant,,ENST00000569085,;	C	ENSG00000135723	ENST00000258201	Transcript	synonymous_variant	2411	2163	721	L	ctC/ctG	.	.	.	-1	FHOD1	HGNC	17905	protein_coding	YES	CCDS10834.1	ENSP00000258201	FHOD1_HUMAN	.	UPI000013CFB9	.	.	.	14/22	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF189,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTTGAGCAG	.	2	ESCA
EDC4	0	.	GRCh37	16	67914539	67914539	+	Missense_Mutation	SNP	G	G	A	rs151306360	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2177G>A	p.Arg726His	p.R726H	ENST00000358933	18/29	77	57	19	73	73	0	EDC4,missense_variant,p.Arg726His,ENST00000358933,;EDC4,upstream_gene_variant,,ENST00000577105,;NRN1L,upstream_gene_variant,,ENST00000576147,;NRN1L,upstream_gene_variant,,ENST00000339176,;NRN1L,upstream_gene_variant,,ENST00000576758,;EDC4,upstream_gene_variant,,ENST00000575033,;EDC4,upstream_gene_variant,,ENST00000573985,;CTC-479C5.10,upstream_gene_variant,,ENST00000572067,;AC040162.1,downstream_gene_variant,,ENST00000408599,;EDC4,downstream_gene_variant,,ENST00000574770,;EDC4,non_coding_transcript_exon_variant,,ENST00000577028,;EDC4,non_coding_transcript_exon_variant,,ENST00000573992,;EDC4,non_coding_transcript_exon_variant,,ENST00000572221,;EDC4,upstream_gene_variant,,ENST00000576972,;EDC4,downstream_gene_variant,,ENST00000536072,;EDC4,downstream_gene_variant,,ENST00000572031,;EDC4,upstream_gene_variant,,ENST00000575507,;EDC4,upstream_gene_variant,,ENST00000572724,;EDC4,upstream_gene_variant,,ENST00000575514,;	A	ENSG00000038358	ENST00000358933	Transcript	missense_variant	2416	2177	726	R/H	cGc/cAc	rs151306360	.	.	1	EDC4	HGNC	17157	protein_coding	YES	CCDS10849.1	ENSP00000351811	EDC4_HUMAN	.	UPI0000141377	.	deleterious(0)	probably_damaging(0.98)	18/29	.	hmmpanther:PTHR15598	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCCGCACTC	byCluster	5	ESCA
CMTR2	0	.	GRCh37	16	71316845	71316845	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*666A>G	.	.	ENST00000338099	3/3	84	69	14	76	76	0	CMTR2,3_prime_UTR_variant,,ENST00000434935,;CMTR2,3_prime_UTR_variant,,ENST00000338099,;CMTR2,downstream_gene_variant,,ENST00000564183,;CMTR2,downstream_gene_variant,,ENST00000568910,;CMTR2,downstream_gene_variant,,ENST00000565850,;CMTR2,downstream_gene_variant,,ENST00000567610,;CMTR2,downstream_gene_variant,,ENST00000563876,;CMTR2,downstream_gene_variant,,ENST00000564690,;	C	ENSG00000180917	ENST00000338099	Transcript	3_prime_UTR_variant	3316	.	.	.	.	.	.	.	-1	CMTR2	HGNC	25635	protein_coding	YES	CCDS10898.1	ENSP00000337512	CMTR2_HUMAN	H3BUK2_HUMAN,H3BTZ7_HUMAN,H3BS00_HUMAN,H3BR19_HUMAN,H3BNZ8_HUMAN	UPI000006EA8B	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATATTTTTA	.	5	ESCA
BCAR1	0	.	GRCh37	16	75271130	75271130	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.884A>G	p.Tyr295Cys	p.Y295C	ENST00000418647	4/8	51	43	8	49	49	0	BCAR1,missense_variant,p.Tyr247Cys,ENST00000542031,;BCAR1,missense_variant,p.Tyr267Cys,ENST00000393422,;BCAR1,missense_variant,p.Tyr249Cys,ENST00000538440,;BCAR1,missense_variant,p.Tyr101Cys,ENST00000535626,;BCAR1,missense_variant,p.Tyr267Cys,ENST00000420641,;BCAR1,missense_variant,p.Tyr249Cys,ENST00000162330,;BCAR1,missense_variant,p.Tyr249Cys,ENST00000393420,;BCAR1,missense_variant,p.Tyr295Cys,ENST00000418647,;BCAR1,missense_variant,p.Tyr220Cys,ENST00000546196,;BCAR1,missense_variant,p.Tyr116Cys,ENST00000569340,;BCAR1,non_coding_transcript_exon_variant,,ENST00000566982,;BCAR1,3_prime_UTR_variant,,ENST00000562556,;BCAR1,non_coding_transcript_exon_variant,,ENST00000564170,;BCAR1,upstream_gene_variant,,ENST00000563038,;	C	ENSG00000050820	ENST00000418647	Transcript	missense_variant	1168	884	295	Y/C	tAt/tGt	.	.	.	-1	BCAR1	HGNC	971	protein_coding	YES	CCDS54040.1	ENSP00000391669	BCAR1_HUMAN	Q8NC57_HUMAN,H3BVF0_HUMAN,H3BU42_HUMAN,H3BTL5_HUMAN,H3BTB0_HUMAN,H3BSY4_HUMAN,H3BSB2_HUMAN,H3BQJ7_HUMAN,F5H855_HUMAN	UPI0001AE689B	.	deleterious(0)	probably_damaging(0.995)	4/8	.	hmmpanther:PTHR10654,hmmpanther:PTHR10654:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCATAGATG	.	5	ESCA
VPS9D1	0	.	GRCh37	16	89785705	89785705	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100-195G>C	.	.	ENST00000389386	.	56	50	5	38	38	0	VPS9D1,5_prime_UTR_variant,,ENST00000561976,;VPS9D1,intron_variant,,ENST00000389386,;ZNF276,upstream_gene_variant,,ENST00000446326,;ZNF276,upstream_gene_variant,,ENST00000568064,;ZNF276,upstream_gene_variant,,ENST00000443381,;ZNF276,upstream_gene_variant,,ENST00000289816,;VPS9D1-AS1,downstream_gene_variant,,ENST00000562866,;VPS9D1-AS1,downstream_gene_variant,,ENST00000562298,;VPS9D1,intron_variant,,ENST00000563798,;ZNF276,upstream_gene_variant,,ENST00000569426,;ZNF276,upstream_gene_variant,,ENST00000568295,;ZNF276,upstream_gene_variant,,ENST00000563983,;ZNF276,upstream_gene_variant,,ENST00000561536,;ZNF276,upstream_gene_variant,,ENST00000562530,;ZNF276,upstream_gene_variant,,ENST00000563541,;	G	ENSG00000075399	ENST00000389386	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	VPS9D1	HGNC	13526	protein_coding	YES	CCDS42220.1	ENSP00000374037	VP9D1_HUMAN	H3BM58_HUMAN	UPI00001FF749	.	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCATCGCTGC	.	4	ESCA
ALKBH5	0	.	GRCh37	17	18110203	18110203	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.926A>T	p.Asp309Val	p.D309V	ENST00000399138	3/4	29	24	5	49	49	0	ALKBH5,missense_variant,p.Asp309Val,ENST00000399138,;ALKBH5,5_prime_UTR_variant,,ENST00000541285,;ALKBH5,non_coding_transcript_exon_variant,,ENST00000490106,;	T	ENSG00000091542	ENST00000399138	Transcript	missense_variant	931	926	309	D/V	gAt/gTt	.	.	.	1	ALKBH5	HGNC	25996	protein_coding	YES	CCDS42272.1	ENSP00000382091	ALKB5_HUMAN	K7ER58_HUMAN	UPI0000200AE2	.	deleterious_low_confidence(0.04)	possibly_damaging(0.773)	3/4	.	hmmpanther:PTHR32074:SF2,hmmpanther:PTHR32074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TTCAGATCGCC	.	4	ESCA
RTN4RL1	0	.	GRCh37	17	1840731	1840731	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385G>A	p.Ala129Thr	p.A129T	ENST00000331238	2/2	27	24	3	39	39	0	RTN4RL1,missense_variant,p.Ala129Thr,ENST00000331238,;	T	ENSG00000185924	ENST00000331238	Transcript	missense_variant	865	385	129	A/T	Gcc/Acc	.	.	.	-1	RTN4RL1	HGNC	21329	protein_coding	YES	CCDS45569.1	ENSP00000330631	R4RL1_HUMAN	.	UPI000018CD23	.	tolerated(0.81)	probably_damaging(1)	2/2	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF11,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGGGCGTGAA	.	3	ESCA
CDC6	0	.	GRCh37	17	38445741	38445741	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69G>C	p.Leu23Phe	p.L23F	ENST00000209728	2/12	88	79	9	79	79	0	CDC6,missense_variant,p.Leu23Phe,ENST00000209728,;CDC6,missense_variant,p.Leu23Phe,ENST00000577249,;CDC6,missense_variant,p.Leu23Phe,ENST00000580824,;CDC6,missense_variant,p.Leu23Phe,ENST00000473555,;CDC6,upstream_gene_variant,,ENST00000582402,;	C	ENSG00000094804	ENST00000209728	Transcript	missense_variant	540	69	23	L/F	ttG/ttC	.	.	.	1	CDC6	HGNC	1744	protein_coding	YES	CCDS11365.1	ENSP00000209728	CDC6_HUMAN	J3QR52_HUMAN,J3QLN7_HUMAN,J3KTI7_HUMAN	UPI0000073C6C	.	tolerated(0.68)	benign(0.193)	2/12	.	PIRSF_domain:PIRSF001767,hmmpanther:PTHR10763,hmmpanther:PTHR10763:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATTGAACAA	.	4	ESCA
RND2	0	.	GRCh37	17	41180632	41180632	+	Missense_Mutation	SNP	C	C	T	rs368469044	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619C>T	p.Arg207Trp	p.R207W	ENST00000587250	5/5	52	49	3	64	64	0	RND2,missense_variant,p.Arg208Trp,ENST00000544533,;RND2,missense_variant,p.Arg207Trp,ENST00000587250,;VAT1,upstream_gene_variant,,ENST00000587062,;VAT1,upstream_gene_variant,,ENST00000590924,;CTD-3199J23.4,upstream_gene_variant,,ENST00000225973,;RND2,downstream_gene_variant,,ENST00000587117,;	T	ENSG00000108830	ENST00000587250	Transcript	missense_variant	726	619	207	R/W	Cgg/Tgg	rs368469044	.	.	1	RND2	HGNC	18315	protein_coding	YES	CCDS11452.1	ENSP00000466680	RND2_HUMAN	.	UPI0000133895	.	deleterious(0)	possibly_damaging(0.852)	5/5	.	hmmpanther:PTHR24072,hmmpanther:PTHR24072:SF21	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGACGGCCA	byCluster|by1000G	2	ESCA
RNF43	0	.	GRCh37	17	56438273	56438273	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.720C>T	p.%3D	p.I240I	ENST00000584437	6/9	49	40	8	38	38	0	RNF43,synonymous_variant,p.%3D,ENST00000407977,;RNF43,synonymous_variant,p.%3D,ENST00000583753,;RNF43,synonymous_variant,p.%3D,ENST00000584437,;RNF43,synonymous_variant,p.%3D,ENST00000500597,;RNF43,synonymous_variant,p.%3D,ENST00000577716,;RNF43,synonymous_variant,p.%3D,ENST00000577625,;RNF43,synonymous_variant,p.%3D,ENST00000581868,;BZRAP1-AS1,intron_variant,,ENST00000583841,;RNF43,downstream_gene_variant,,ENST00000582293,;	A	ENSG00000108375	ENST00000584437	Transcript	synonymous_variant	2676	720	240	I	atC/atT	COSM390115	.	.	-1	RNF43	HGNC	18505	protein_coding	YES	CCDS11607.1	ENSP00000463069	RNF43_HUMAN	.	UPI000022A469	.	.	.	6/9	.	hmmpanther:PTHR16200,hmmpanther:PTHR16200:SF2	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTGATGGC	.	5	ESCA
PTRH2	0	.	GRCh37	17	57776307	57776307	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-968C>T	.	.	ENST00000470557	1/1	26	22	3	32	32	0	PTRH2,5_prime_UTR_variant,,ENST00000470557,;PTRH2,5_prime_UTR_variant,,ENST00000537860,;PTRH2,5_prime_UTR_variant,,ENST00000409433,;PTRH2,intron_variant,,ENST00000393038,;CLTC,downstream_gene_variant,,ENST00000579456,;CLTC,downstream_gene_variant,,ENST00000269122,;PTRH2,intron_variant,,ENST00000587935,;PTRH2,downstream_gene_variant,,ENST00000579915,;CLTC,downstream_gene_variant,,ENST00000498711,;	A	ENSG00000141378	ENST00000470557	Transcript	5_prime_UTR_variant	2480	.	.	.	.	.	.	.	-1	PTRH2	HGNC	24265	protein_coding	YES	CCDS11618.1	ENSP00000464327	PTH2_HUMAN	.	UPI000013A5FA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGATGATGGG	.	4	ESCA
ICT1	0	.	GRCh37	17	73015819	73015819	+	Missense_Mutation	SNP	G	G	A	rs779805621	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.248G>A	p.Arg83Gln	p.R83Q	ENST00000301585	3/6	88	78	10	93	93	0	ICT1,missense_variant,p.Arg83Gln,ENST00000301585,;ICT1,missense_variant,p.Arg83Gln,ENST00000584208,;ICT1,3_prime_UTR_variant,,ENST00000580800,;ICT1,upstream_gene_variant,,ENST00000583772,;	A	ENSG00000167862	ENST00000301585	Transcript	missense_variant	261	248	83	R/Q	cGg/cAg	rs779805621	.	.	1	ICT1	HGNC	5359	protein_coding	YES	CCDS11711.1	ENSP00000301585	ICT1_HUMAN	.	UPI0000000DF2	.	deleterious(0.01)	probably_damaging(0.943)	3/6	.	hmmpanther:PTHR11075,Gene3D:2jvaA00,Pfam_domain:PF00472,Superfamily_domains:0039326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTCGGAGTA	.	4	ESCA
TP53	0	.	GRCh37	17	7574003	7574003	+	Nonsense_Mutation	SNP	G	G	A	rs730882029	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	10/11	13	7	6	15	15	0	TP53,stop_gained,p.Arg342Ter,ENST00000269305,;TP53,stop_gained,p.Arg342Ter,ENST00000445888,;TP53,3_prime_UTR_variant,,ENST00000420246,;TP53,3_prime_UTR_variant,,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000359597,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	1214	1024	342	R/*	Cga/Tga	rs730882029,CM004908,TP53_g.16915del,TP53_g.16915C>T,COSM11073,COSM45639,COSM18597,COSM99721,COSM128665	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	10/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF07710,Gene3D:1olgA00,Superfamily_domains:SSF47719,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,0,0,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R342*|c.1024C>T|49,SITE|p.R342*|c.1024C>T|97,CODON|p.0?|c.1_1182del1182|6,CODON|p.R342P|c.1025G>C|4,CODON|p.R342P|c.1025G>C|7,CODON|p.R342fs*3|c.1024delC|3,CODON|p.R342fs*3|c.1024delC|3,BUFFER|p.E343*|c.1027G>T|8,BUFFER|p.E343*|c.1027G>T|5,BUFFER|p.R342fs*3|c.1023delC|3,BUFFER|p.E339*|c.1015G>T|16,BUFFER|p.E339*|c.1015G>T|7	MUTECT|RADIA|SOMATICSNIPER|MUSE	CTCTCGGAACA	.	4	ESCA
TP53	0	.	GRCh37	17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	rs121912666	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	6/11	41	35	6	67	67	0	TP53,missense_variant,p.Tyr220Cys,ENST00000413465,;TP53,missense_variant,p.Tyr220Cys,ENST00000420246,;TP53,missense_variant,p.Tyr220Cys,ENST00000269305,;TP53,missense_variant,p.Tyr88Cys,ENST00000509690,;TP53,missense_variant,p.Tyr220Cys,ENST00000359597,;TP53,missense_variant,p.Tyr127Cys,ENST00000514944,;TP53,missense_variant,p.Tyr220Cys,ENST00000445888,;TP53,missense_variant,p.Tyr220Cys,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	849	659	220	Y/C	tAt/tGt	CM015378,CM951227,rs121912666,TP53_g.12728A>T,TP53_g.12728A>C,TP53_g.12728A>G,COSM10758,COSM43850,COSM1564197,COSM99720,COSM251427,COSM1564198,COSM251426,COSM99718,COSM1564199,COSM3355993,COSM3675523,COSM1644277,COSM3675522,COSM99719,COSM251428,COSM1564200	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Y220C|c.659A>G|264,SITE|p.Y220C|c.659A>G|63,SITE|p.Y127C|c.380A>G|63,SITE|p.Y220C|c.659A>G|25,SITE|p.Y220C|c.659A>G|61,SITE|p.Y220C|c.659A>G|33,CODON|p.0?|c.1_1182del1182|6,CODON|p.Y220*|c.660T>G|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y127S|c.380A>C|4,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y220S|c.659A>C|13,BUFFER|p.E224K|c.670G>A|4,BUFFER|p.E224*|c.670G>T|5,BUFFER|p.P223L|c.668C>T|3,BUFFER|p.P222P|c.666G>C|3,BUFFER|p.P222L|c.665C>T|4,BUFFER|p.P222T|c.664C>A|3,BUFFER|p.E221G|c.662A>G|3,BUFFER|p.E221fs*4|c.660_661insN|3,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E128*|c.382G>T|6,BUFFER|p.E221*|c.661G>T|10,BUFFER|p.?|c.252+10T>A|3,BUFFER|p.Y220N|c.658T>A|16,BUFFER|p.?|c.252+10T>C|4,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220H|c.658T>C|13,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.Y127H|c.379T>C|4,BUFFER|p.Y127N|c.379T>A|3,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.P219P|c.657C>T|3,BUFFER|p.Y220fs*27|c.655delC|4,BUFFER|p.V218delV|c.652_654delGTG|3,BUFFER|p.P219S|c.655C>T|4,BUFFER|p.V218G|c.653T>G|6,BUFFER|p.V218A|c.653T>C|3,BUFFER|p.V218E|c.653T>A|8,BUFFER|p.V218M|c.652G>A|7,BUFFER|p.V217A|c.650T>C|5,BUFFER|p.V217G|c.650T>G|4,BUFFER|p.V217E|c.650T>A|3,BUFFER|p.V218delV|c.646_648delGTG|8	MUTECT|MUSE	GCTCATAGGGC	byFrequency|byCluster	2	ESCA
ZNF750	0	.	GRCh37	17	80790319	80790320	+	Frame_Shift_Ins	INS	-	-	AA	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11_12insTT	p.Lys5SerfsTer41	p.K5Sfs*41	ENST00000269394	2/3	111	85	26	110	110	0	ZNF750,frameshift_variant,p.Lys5SerfsTer41,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	AA	ENSG00000141579	ENST00000269394	Transcript	frameshift_variant	845-846	11-12	4	L/LX	ctc/ctTTc	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTTTGAGGAG	.	3	ESCA
DCC	0	.	GRCh37	18	51025708	51025708	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3939G>C	p.%3D	p.L1313L	ENST00000442544	27/29	67	52	15	99	99	0	DCC,synonymous_variant,p.%3D,ENST00000581580,;DCC,synonymous_variant,p.%3D,ENST00000442544,;RP11-671P2.1,intron_variant,,ENST00000582064,;DCC,non_coding_transcript_exon_variant,,ENST00000579702,;	C	ENSG00000187323	ENST00000442544	Transcript	synonymous_variant	4555	3939	1313	L	ctG/ctC	.	.	.	1	DCC	HGNC	2701	protein_coding	YES	CCDS11952.1	ENSP00000389140	DCC_HUMAN	J3QQJ6_HUMAN	UPI00001AEDC6	.	.	.	27/29	.	hmmpanther:PTHR10489:SF68,hmmpanther:PTHR10489,Pfam_domain:PF06583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGCCCCC	.	5	ESCA
PTPRM	0	.	GRCh37	18	8378361	8378361	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3561G>A	p.Met1187Ile	p.M1187I	ENST00000580170	27/33	80	74	6	60	60	0	PTPRM,missense_variant,p.Met1174Ile,ENST00000332175,;PTPRM,missense_variant,p.Met961Ile,ENST00000444013,;PTPRM,missense_variant,p.Met172Ile,ENST00000583153,;PTPRM,missense_variant,p.Met1112Ile,ENST00000400053,;PTPRM,missense_variant,p.Met1188Ile,ENST00000400060,;PTPRM,missense_variant,p.Met1187Ile,ENST00000580170,;PTPRM,non_coding_transcript_exon_variant,,ENST00000577827,;	A	ENSG00000173482	ENST00000580170	Transcript	missense_variant	4598	3561	1187	M/I	atG/atA	.	.	.	1	PTPRM	HGNC	9675	protein_coding	YES	CCDS58613.1	ENSP00000463325	PTPRM_HUMAN	Q49AC9_HUMAN	UPI00015CFC03	.	tolerated(0.4)	benign(0.023)	27/33	.	Superfamily_domains:SSF52799,Superfamily_domains:SSF52799,Gene3D:3.90.190.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACATGAACAA	.	2	ESCA
TXNDC2	0	.	GRCh37	18	9887037	9887037	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.561C>T	p.%3D	p.I187I	ENST00000306084	2/2	85	78	6	70	70	0	TXNDC2,synonymous_variant,p.%3D,ENST00000357775,;TXNDC2,synonymous_variant,p.%3D,ENST00000306084,;TXNDC2,intron_variant,,ENST00000536353,;TXNDC2,downstream_gene_variant,,ENST00000584255,;TXNDC2,downstream_gene_variant,,ENST00000426718,;	T	ENSG00000168454	ENST00000306084	Transcript	synonymous_variant	760	561	187	I	atC/atT	.	.	.	1	TXNDC2	HGNC	16470	protein_coding	YES	CCDS42414.1	ENSP00000304908	TXND2_HUMAN	F5H6S7_HUMAN	UPI000013EAE7	.	.	.	2/2	.	Pfam_domain:PF03157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCATCCAATC	.	2	ESCA
MYO9B	0	.	GRCh37	19	17316815	17316815	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5111G>A	p.Ser1704Asn	p.S1704N	ENST00000595618	32/40	45	42	3	63	63	0	MYO9B,missense_variant,p.Ser1704Asn,ENST00000595641,;MYO9B,missense_variant,p.Ser1704Asn,ENST00000397274,;MYO9B,missense_variant,p.Ser1704Asn,ENST00000595618,;MYO9B,missense_variant,p.Ser1704Asn,ENST00000594824,;MYO9B,upstream_gene_variant,,ENST00000596942,;MYO9B,upstream_gene_variant,,ENST00000597073,;MYO9B,upstream_gene_variant,,ENST00000598419,;CTD-3032J10.3,downstream_gene_variant,,ENST00000601929,;MYO9B,3_prime_UTR_variant,,ENST00000602158,;MYO9B,non_coding_transcript_exon_variant,,ENST00000599420,;MYO9B,intron_variant,,ENST00000593533,;MYO9B,upstream_gene_variant,,ENST00000597881,;MYO9B,upstream_gene_variant,,ENST00000597572,;	A	ENSG00000099331	ENST00000595618	Transcript	missense_variant	5263	5111	1704	S/N	aGc/aAc	.	.	.	1	MYO9B	HGNC	7609	protein_coding	YES	CCDS46010.1	ENSP00000471457	MYO9B_HUMAN	Q4LE74_HUMAN	UPI000020367C	.	tolerated(0.32)	benign(0.071)	32/40	.	PROSITE_profiles:PS50238,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF306,Gene3D:1.10.555.10,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AGACAGCCTGA	.	2	ESCA
ARHGAP33	0	.	GRCh37	19	36270045	36270045	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501+19C>T	.	.	ENST00000314737	.	17	11	5	28	28	0	ARHGAP33,intron_variant,,ENST00000007510,;ARHGAP33,intron_variant,,ENST00000378944,;ARHGAP33,intron_variant,,ENST00000314737,;ARHGAP33,upstream_gene_variant,,ENST00000587447,;ARHGAP33,upstream_gene_variant,,ENST00000588248,;ARHGAP33,non_coding_transcript_exon_variant,,ENST00000221905,;ARHGAP33,downstream_gene_variant,,ENST00000589133,;ARHGAP33,upstream_gene_variant,,ENST00000591438,;ARHGAP33,intron_variant,,ENST00000590893,;ARHGAP33,upstream_gene_variant,,ENST00000601474,;ARHGAP33,upstream_gene_variant,,ENST00000586918,;	T	ENSG00000004777	ENST00000314737	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ARHGAP33	HGNC	23085	protein_coding	YES	CCDS12477.1	ENSP00000320038	RHG33_HUMAN	.	UPI000013F8F9	.	.	.	.	6/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGCTTGGA	.	5	ESCA
MIR498	0	.	GRCh37	19	54177477	54177477	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.27G>A	.	.	ENST00000385134	1/1	32	19	12	43	43	0	MIR498,non_coding_transcript_exon_variant,,ENST00000385134,;MIR520E,upstream_gene_variant,,ENST00000384867,;MIR515-1,upstream_gene_variant,,ENST00000384884,;MIR512-2,downstream_gene_variant,,ENST00000384912,;MIR1323,downstream_gene_variant,,ENST00000408090,;	A	ENSG00000207869	ENST00000385134	Transcript	non_coding_transcript_exon_variant	27	.	.	.	.	.	.	.	1	MIR498	HGNC	32092	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAGGCTGTG	.	5	ESCA
TMC4	0	.	GRCh37	19	54669176	54669176	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.940C>T	p.Arg314Cys	p.R314C	ENST00000376591	6/15	27	24	3	47	47	0	TMC4,missense_variant,p.Arg314Cys,ENST00000376591,;TMC4,missense_variant,p.Arg308Cys,ENST00000301187,;TMC4,downstream_gene_variant,,ENST00000446291,;TMC4,upstream_gene_variant,,ENST00000416963,;TMC4,intron_variant,,ENST00000479750,;TMC4,intron_variant,,ENST00000476013,;TMC4,non_coding_transcript_exon_variant,,ENST00000497518,;TMC4,upstream_gene_variant,,ENST00000449860,;TMC4,upstream_gene_variant,,ENST00000494594,;TMC4,upstream_gene_variant,,ENST00000465790,;TMC4,upstream_gene_variant,,ENST00000468343,;TMC4,upstream_gene_variant,,ENST00000495398,;	A	ENSG00000167608	ENST00000376591	Transcript	missense_variant	1072	940	314	R/C	Cgc/Tgc	.	.	.	-1	TMC4	HGNC	22998	protein_coding	YES	CCDS46174.1	ENSP00000365776	TMC4_HUMAN	C9JFU4_HUMAN	UPI000040C55F	.	deleterious(0.02)	possibly_damaging(0.874)	6/15	.	hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGCGCTGGC	.	2	ESCA
LILRB1	0	.	GRCh37	19	55142048	55142048	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-85C>G	.	.	ENST00000324602	1/15	53	49	3	60	59	1	LILRB1,5_prime_UTR_variant,,ENST00000396331,;LILRB1,5_prime_UTR_variant,,ENST00000396327,;LILRB1,5_prime_UTR_variant,,ENST00000434867,;LILRB1,5_prime_UTR_variant,,ENST00000324602,;LILRB1,5_prime_UTR_variant,,ENST00000396332,;LILRB1,intron_variant,,ENST00000448689,;LILRB1,intron_variant,,ENST00000418536,;LILRB1,intron_variant,,ENST00000396321,;LILRB1,upstream_gene_variant,,ENST00000396317,;LILRB1,upstream_gene_variant,,ENST00000396315,;LILRB1,upstream_gene_variant,,ENST00000427581,;AC009892.1,upstream_gene_variant,,ENST00000578908,;LILRB1,upstream_gene_variant,,ENST00000462628,;LILRB1,upstream_gene_variant,,ENST00000473412,;LILRB1,upstream_gene_variant,,ENST00000480257,;LILRB1,upstream_gene_variant,,ENST00000480375,;LILRB1,upstream_gene_variant,,ENST00000487425,;LILRB1,upstream_gene_variant,,ENST00000421584,;	G	ENSG00000104972	ENST00000324602	Transcript	5_prime_UTR_variant	141	.	.	.	.	.	.	.	1	LILRB1	HGNC	6605	protein_coding	YES	CCDS42614.1	ENSP00000315997	LIRB1_HUMAN	.	UPI0000034BFC	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCCCTGAAG	.	2	ESCA
SUV420H2	0	.	GRCh37	19	55855145	55855145	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484A>T	p.Ile162Phe	p.I162F	ENST00000255613	5/9	29	25	4	39	39	0	SUV420H2,missense_variant,p.Ile162Phe,ENST00000255613,;AC020922.1,intron_variant,,ENST00000539076,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000460956,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000587442,;SUV420H2,intron_variant,,ENST00000402499,;SUV420H2,3_prime_UTR_variant,,ENST00000592631,;SUV420H2,3_prime_UTR_variant,,ENST00000445196,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000464185,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000589338,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000468951,;SUV420H2,upstream_gene_variant,,ENST00000474492,;SUV420H2,downstream_gene_variant,,ENST00000498738,;	T	ENSG00000133247	ENST00000255613	Transcript	missense_variant	732	484	162	I/F	Atc/Ttc	.	.	.	1	SUV420H2	HGNC	28405	protein_coding	YES	CCDS12922.1	ENSP00000255613	SV422_HUMAN	.	UPI000000DABC	.	deleterious(0)	possibly_damaging(0.805)	5/9	.	Superfamily_domains:SSF82199,SMART_domains:SM00317,Pfam_domain:PF00856,Gene3D:2.170.270.10,PROSITE_profiles:PS50280,hmmpanther:PTHR12977,PROSITE_profiles:PS51570	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAGCATCATG	.	4	ESCA
LONP1	0	.	GRCh37	19	5694527	5694527	+	Missense_Mutation	SNP	C	C	T	rs768949488	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2191G>A	p.Glu731Lys	p.E731K	ENST00000360614	15/18	17	10	7	32	32	0	LONP1,missense_variant,p.Glu11Lys,ENST00000589473,;LONP1,missense_variant,p.Glu601Lys,ENST00000590729,;LONP1,missense_variant,p.Glu731Lys,ENST00000360614,;LONP1,missense_variant,p.Glu667Lys,ENST00000593119,;LONP1,missense_variant,p.Glu535Lys,ENST00000540670,;LONP1,missense_variant,p.Glu617Lys,ENST00000585374,;RPL36,downstream_gene_variant,,ENST00000579649,;LONP1,downstream_gene_variant,,ENST00000590206,;RPL36,downstream_gene_variant,,ENST00000347512,;RPL36,downstream_gene_variant,,ENST00000579446,;RPL36,downstream_gene_variant,,ENST00000394580,;RPL36,downstream_gene_variant,,ENST00000582463,;RPL36,downstream_gene_variant,,ENST00000577222,;RPL36,downstream_gene_variant,,ENST00000582380,;LONP1,3_prime_UTR_variant,,ENST00000590558,;LONP1,non_coding_transcript_exon_variant,,ENST00000587552,;RPL36,downstream_gene_variant,,ENST00000590786,;	T	ENSG00000196365	ENST00000360614	Transcript	missense_variant	2349	2191	731	E/K	Gag/Aag	rs768949488	.	.	-1	LONP1	HGNC	9479	protein_coding	YES	CCDS12148.1	ENSP00000353826	LONM_HUMAN	K7EKE6_HUMAN,F5GZ27_HUMAN	UPI000012E7EF	.	tolerated(0.12)	benign(0.014)	15/18	.	HAMAP:MF_03120,hmmpanther:PTHR10046:SF23,hmmpanther:PTHR10046,Gene3D:1.10.8.60,TIGRFAM_domain:TIGR00763,PIRSF_domain:PIRSF001174,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GGCCTCGCCGC	.	4	ESCA
ZSCAN1	0	.	GRCh37	19	58565137	58565137	+	Silent	SNP	C	C	T	rs370513764	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.945C>T	p.%3D	p.R315R	ENST00000282326	6/6	24	18	5	41	41	0	ZSCAN1,synonymous_variant,p.%3D,ENST00000282326,;HNRNPDLP4,upstream_gene_variant,,ENST00000605144,;	T	ENSG00000152467	ENST00000282326	Transcript	synonymous_variant	1192	945	315	R	cgC/cgT	rs370513764	.	.	1	ZSCAN1	HGNC	23712	protein_coding	YES	CCDS12969.1	ENSP00000282326	ZSCA1_HUMAN	.	UPI000013DCD2	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF187,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R315H|c.944G>A|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCGCGAGGA	byFrequency|byCluster	5	ESCA
ZNF324	0	.	GRCh37	19	58983245	58983245	+	Missense_Mutation	SNP	C	C	A	rs770072493	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1386C>A	p.Phe462Leu	p.F462L	ENST00000536459	4/4	35	30	4	48	48	0	ZNF324,missense_variant,p.Phe239Leu,ENST00000535298,;ZNF324,missense_variant,p.Phe462Leu,ENST00000196482,;ZNF324,missense_variant,p.Phe321Leu,ENST00000593925,;ZNF324,missense_variant,p.Phe462Leu,ENST00000536459,;ZNF446,upstream_gene_variant,,ENST00000596341,;ZNF446,upstream_gene_variant,,ENST00000335841,;ZNF446,upstream_gene_variant,,ENST00000600013,;ZNF446,upstream_gene_variant,,ENST00000594369,;CTD-2619J13.23,downstream_gene_variant,,ENST00000598051,;ZNF446,upstream_gene_variant,,ENST00000599913,;ZNF446,upstream_gene_variant,,ENST00000391694,;ZNF446,upstream_gene_variant,,ENST00000594468,;	A	ENSG00000083812	ENST00000536459	Transcript	missense_variant	2095	1386	462	F/L	ttC/ttA	rs770072493	.	.	1	ZNF324	HGNC	14096	protein_coding	YES	CCDS12981.1	ENSP00000444812	Z324A_HUMAN	F5H1K2_HUMAN	UPI000013C359	.	deleterious(0)	probably_damaging(0.999)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24382,hmmpanther:PTHR24382:SF32,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTTCGCCAA	byFrequency	4	ESCA
PSPN	0	.	GRCh37	19	6375764	6375764	+	Missense_Mutation	SNP	C	C	T	rs751627297	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>A	p.Asp33Asn	p.D33N	ENST00000245810	1/2	45	40	5	77	77	0	PSPN,missense_variant,p.Asp33Asn,ENST00000597721,;PSPN,missense_variant,p.Asp33Asn,ENST00000245810,;ALKBH7,downstream_gene_variant,,ENST00000245812,;GTF2F1,downstream_gene_variant,,ENST00000429701,;ALKBH7,downstream_gene_variant,,ENST00000599849,;ALKBH7,downstream_gene_variant,,ENST00000596657,;GTF2F1,downstream_gene_variant,,ENST00000593678,;GTF2F1,downstream_gene_variant,,ENST00000394456,;GTF2F1,downstream_gene_variant,,ENST00000594965,;GTF2F1,downstream_gene_variant,,ENST00000594213,;	T	ENSG00000125650	ENST00000245810	Transcript	missense_variant	97	97	33	D/N	Gat/Aat	rs751627297	.	.	-1	PSPN	HGNC	9579	protein_coding	YES	CCDS12164.1	ENSP00000245810	PSPN_HUMAN	.	UPI0000050F8D	.	tolerated(0.16)	benign(0.002)	1/2	.	hmmpanther:PTHR12173,hmmpanther:PTHR12173:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCATCGGCCA	.	4	ESCA
VAV1	0	.	GRCh37	19	6833625	6833625	+	Missense_Mutation	SNP	G	G	A	rs749873161	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1697G>A	p.Arg566Gln	p.R566Q	ENST00000602142	17/27	86	56	29	132	132	0	VAV1,missense_variant,p.Arg469Gln,ENST00000539284,;VAV1,missense_variant,p.Arg534Gln,ENST00000596764,;VAV1,missense_variant,p.Arg511Gln,ENST00000599806,;VAV1,missense_variant,p.Arg566Gln,ENST00000304076,;VAV1,missense_variant,p.Arg566Gln,ENST00000602142,;VAV1,non_coding_transcript_exon_variant,,ENST00000601452,;VAV1,non_coding_transcript_exon_variant,,ENST00000600396,;VAV1,upstream_gene_variant,,ENST00000598270,;VAV1,downstream_gene_variant,,ENST00000597967,;	A	ENSG00000141968	ENST00000602142	Transcript	missense_variant	1779	1697	566	R/Q	cGa/cAa	rs749873161,COSM440606	.	.	1	VAV1	HGNC	12657	protein_coding	YES	CCDS12174.1	ENSP00000472929	VAV_HUMAN	.	UPI0000138213	.	deleterious(0.04)	possibly_damaging(0.783)	17/27	.	hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF112,Gene3D:3.30.60.20	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGACATG	.	5	ESCA
AGL	0	.	GRCh37	1	100361905	100361905	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3323G>C	p.Arg1108Thr	p.R1108T	ENST00000294724	25/34	66	62	4	79	79	0	AGL,missense_variant,p.Arg1108Thr,ENST00000370163,;AGL,missense_variant,p.Arg1092Thr,ENST00000361302,;AGL,missense_variant,p.Arg1108Thr,ENST00000294724,;AGL,missense_variant,p.Arg1108Thr,ENST00000370165,;AGL,missense_variant,p.Arg1091Thr,ENST00000361522,;AGL,missense_variant,p.Arg1092Thr,ENST00000370161,;AGL,missense_variant,p.Arg1108Thr,ENST00000361915,;	C	ENSG00000162688	ENST00000294724	Transcript	missense_variant	3801	3323	1108	R/T	aGa/aCa	.	.	.	1	AGL	HGNC	321	protein_coding	YES	CCDS759.1	ENSP00000294724	GDE_HUMAN	G1UI17_HUMAN	UPI00001694CB	.	deleterious(0.01)	probably_damaging(0.98)	25/34	.	hmmpanther:PTHR10569,Pfam_domain:PF06202,TIGRFAM_domain:TIGR01531,Superfamily_domains:SSF48208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTAGAGGTA	.	2	ESCA
RNPC3	0	.	GRCh37	1	104093612	104093612	+	Missense_Mutation	SNP	A	A	C	rs368201291	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1411A>C	p.Ile471Leu	p.I471L	ENST00000533099	14/16	23	18	5	38	38	0	RNPC3,missense_variant,p.Ile470Leu,ENST00000524631,;RNPC3,missense_variant,p.Ile471Leu,ENST00000533099,;RNPC3,missense_variant,p.Ile471Leu,ENST00000423855,;AMY2B,upstream_gene_variant,,ENST00000361355,;RNPC3,downstream_gene_variant,,ENST00000524641,;RNPC3,non_coding_transcript_exon_variant,,ENST00000525323,;RNPC3,non_coding_transcript_exon_variant,,ENST00000533834,;AMY2B,upstream_gene_variant,,ENST00000477657,;RNPC3,upstream_gene_variant,,ENST00000532117,;	C	ENSG00000185946	ENST00000533099	Transcript	missense_variant	1647	1411	471	I/L	Att/Ctt	rs368201291	.	.	1	RNPC3	HGNC	18666	protein_coding	YES	CCDS781.1	ENSP00000432886	RBM40_HUMAN	E9PPV2_HUMAN	UPI000006E703	.	tolerated(0.11)	benign(0.407)	14/16	.	PROSITE_profiles:PS50102,hmmpanther:PTHR16105:SF0,hmmpanther:PTHR16105,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	G:0.0003	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCATTGGA	byCluster	5	ESCA
STRIP1	0	.	GRCh37	1	110590208	110590208	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1533A>T	p.Gln511His	p.Q511H	ENST00000369795	14/21	45	36	9	45	45	0	STRIP1,missense_variant,p.Gln511His,ENST00000369795,;STRIP1,missense_variant,p.Gln416His,ENST00000369796,;STRIP1,non_coding_transcript_exon_variant,,ENST00000461054,;STRIP1,3_prime_UTR_variant,,ENST00000485775,;STRIP1,non_coding_transcript_exon_variant,,ENST00000473429,;STRIP1,downstream_gene_variant,,ENST00000535003,;STRIP1,downstream_gene_variant,,ENST00000539541,;	T	ENSG00000143093	ENST00000369795	Transcript	missense_variant	1555	1533	511	Q/H	caA/caT	.	.	.	1	STRIP1	HGNC	25916	protein_coding	YES	CCDS30798.1	ENSP00000358810	STRP1_HUMAN	.	UPI0000160E65	.	tolerated(0.05)	benign(0.005)	14/21	.	hmmpanther:PTHR13239,hmmpanther:PTHR13239:SF5,Pfam_domain:PF11882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TACCAAGGCTT	.	4	ESCA
LAMTOR5	0	.	GRCh37	1	110943975	110943975	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*170A>C	.	.	ENST00000256644	4/4	14	11	3	25	25	0	LAMTOR5,3_prime_UTR_variant,,ENST00000602858,;LAMTOR5,3_prime_UTR_variant,,ENST00000483260,;LAMTOR5,3_prime_UTR_variant,,ENST00000602318,;LAMTOR5,3_prime_UTR_variant,,ENST00000256644,;LAMTOR5,3_prime_UTR_variant,,ENST00000474861,;LAMTOR5-AS1,intron_variant,,ENST00000590413,;LAMTOR5,non_coding_transcript_exon_variant,,ENST00000464240,;LAMTOR5,downstream_gene_variant,,ENST00000531779,;	G	ENSG00000134248	ENST00000256644	Transcript	3_prime_UTR_variant	768	.	.	.	.	.	.	.	-1	LAMTOR5	HGNC	17955	protein_coding	YES	CCDS824.1	ENSP00000256644	LTOR5_HUMAN	R4GMU8_HUMAN	UPI0000205288	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGATAGTCG	.	2	ESCA
BCL9	0	.	GRCh37	1	147091780	147091780	+	Missense_Mutation	SNP	C	C	G	rs781996874	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1819C>G	p.Pro607Ala	p.P607A	ENST00000234739	8/10	87	82	5	99	99	0	BCL9,missense_variant,p.Pro607Ala,ENST00000234739,;BCL9,downstream_gene_variant,,ENST00000473292,;	G	ENSG00000116128	ENST00000234739	Transcript	missense_variant	2559	1819	607	P/A	Cct/Gct	rs781996874	.	.	1	BCL9	HGNC	1008	protein_coding	YES	CCDS30833.1	ENSP00000234739	BCL9_HUMAN	.	UPI000013C9B9	.	tolerated(0.41)	probably_damaging(0.98)	8/10	.	hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCCTGGC	.	2	ESCA
POGZ	0	.	GRCh37	1	151396497	151396497	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1451T>C	p.Leu484Pro	p.L484P	ENST00000271715	9/19	71	54	17	72	72	0	POGZ,missense_variant,p.Leu475Pro,ENST00000409503,;POGZ,missense_variant,p.Leu431Pro,ENST00000361398,;POGZ,missense_variant,p.Leu484Pro,ENST00000271715,;POGZ,missense_variant,p.Leu422Pro,ENST00000531094,;POGZ,missense_variant,p.Leu389Pro,ENST00000368863,;POGZ,missense_variant,p.Leu431Pro,ENST00000491586,;POGZ,missense_variant,p.Leu431Pro,ENST00000392723,;POGZ,intron_variant,,ENST00000540984,;POGZ,downstream_gene_variant,,ENST00000594456,;POGZ,upstream_gene_variant,,ENST00000529669,;POGZ,3_prime_UTR_variant,,ENST00000441516,;POGZ,non_coding_transcript_exon_variant,,ENST00000482678,;POGZ,non_coding_transcript_exon_variant,,ENST00000358476,;POGZ,non_coding_transcript_exon_variant,,ENST00000495253,;POGZ,downstream_gene_variant,,ENST00000485040,;	G	ENSG00000143442	ENST00000271715	Transcript	missense_variant	1766	1451	484	L/P	cTc/cCc	.	.	.	-1	POGZ	HGNC	18801	protein_coding	YES	CCDS997.1	ENSP00000271715	POGZ_HUMAN	F5H8H4_HUMAN,E9PJY9_HUMAN,E9PIR8_HUMAN	UPI000035895F	.	tolerated(0.11)	benign(0.17)	9/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTGAGCTGG	.	5	ESCA
S100A16	0	.	GRCh37	1	153580638	153580638	+	5'UTR	SNP	C	C	T	rs113696568	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11G>A	.	.	ENST00000368704	2/3	46	41	5	49	49	0	S100A16,5_prime_UTR_variant,,ENST00000368704,;S100A16,5_prime_UTR_variant,,ENST00000368706,;S100A16,5_prime_UTR_variant,,ENST00000368703,;S100A16,5_prime_UTR_variant,,ENST00000368705,;S100A16,non_coding_transcript_exon_variant,,ENST00000474991,;	T	ENSG00000188643	ENST00000368704	Transcript	5_prime_UTR_variant	176	.	.	.	.	rs113696568	.	.	-1	S100A16	HGNC	20441	protein_coding	YES	CCDS1045.1	ENSP00000357693	S10AG_HUMAN	.	UPI0000135414	.	.	.	2/3	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCTTCGCCTG	by1000G	3	ESCA
ZBTB7B	0	.	GRCh37	1	154975307	154975307	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-257C>T	.	.	ENST00000417934	1/5	20	16	3	25	25	0	ZBTB7B,5_prime_UTR_variant,,ENST00000417934,;ZBTB7B,intron_variant,,ENST00000535420,;ZBTB7B,intron_variant,,ENST00000368426,;ZBTB7B,non_coding_transcript_exon_variant,,ENST00000487542,;ZBTB7B,upstream_gene_variant,,ENST00000461530,;ZBTB7B,upstream_gene_variant,,ENST00000483226,;	T	ENSG00000160685	ENST00000417934	Transcript	5_prime_UTR_variant	13	.	.	.	.	.	.	.	1	ZBTB7B	HGNC	18668	protein_coding	YES	CCDS58030.1	ENSP00000406286	ZBT7B_HUMAN	.	UPI0001A5EB6F	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCGGCCTTCT	.	4	ESCA
MTX1	0	.	GRCh37	1	155184051	155184051	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000368376	.	24	19	4	31	31	0	MTX1,downstream_gene_variant,,ENST00000368376,;MTX1,downstream_gene_variant,,ENST00000609421,;MTX1,downstream_gene_variant,,ENST00000316721,;RP11-263K19.6,upstream_gene_variant,,ENST00000455788,;GBAP1,non_coding_transcript_exon_variant,,ENST00000368374,;GBAP1,non_coding_transcript_exon_variant,,ENST00000486869,;MTX1,downstream_gene_variant,,ENST00000495589,;GBAP1,downstream_gene_variant,,ENST00000462587,;GBAP1,non_coding_transcript_exon_variant,,ENST00000486197,;GBAP1,non_coding_transcript_exon_variant,,ENST00000473223,;GBAP1,non_coding_transcript_exon_variant,,ENST00000459805,;MTX1,downstream_gene_variant,,ENST00000481771,;MTX1,downstream_gene_variant,,ENST00000424959,;GBAP1,downstream_gene_variant,,ENST00000463838,;MTX1,downstream_gene_variant,,ENST00000495492,;GBAP1,non_coding_transcript_exon_variant,,ENST00000313929,;GBAP1,downstream_gene_variant,,ENST00000566701,;	A	ENSG00000173171	ENST00000368376	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	437	1	MTX1	HGNC	7504	protein_coding	YES	CCDS1100.1	ENSP00000357360	MTX1_HUMAN	.	UPI0000225CC9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAAGCTCAC	.	5	ESCA
MSTO1	0	.	GRCh37	1	155582929	155582929	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1188A>G	p.%3D	p.P396P	ENST00000245564	11/14	54	44	10	69	69	0	MSTO1,synonymous_variant,p.%3D,ENST00000368341,;MSTO1,synonymous_variant,p.%3D,ENST00000245564,;MSTO1,intron_variant,,ENST00000538143,;MSTO1,intron_variant,,ENST00000452804,;MSTO1,upstream_gene_variant,,ENST00000462250,;RP11-29H23.4,upstream_gene_variant,,ENST00000456382,;MSTO1,non_coding_transcript_exon_variant,,ENST00000475253,;MSTO1,non_coding_transcript_exon_variant,,ENST00000483734,;MSTO1,non_coding_transcript_exon_variant,,ENST00000466815,;MSTO1,downstream_gene_variant,,ENST00000465137,;MSTO1,downstream_gene_variant,,ENST00000483832,;MSTO1,downstream_gene_variant,,ENST00000488901,;MSTO1,downstream_gene_variant,,ENST00000491308,;MSTO1,downstream_gene_variant,,ENST00000490642,;MSTO1,downstream_gene_variant,,ENST00000473327,;MSTO1,3_prime_UTR_variant,,ENST00000490743,;MSTO1,non_coding_transcript_exon_variant,,ENST00000494995,;MSTO1,downstream_gene_variant,,ENST00000482284,;MSTO1,downstream_gene_variant,,ENST00000478756,;MSTO1,downstream_gene_variant,,ENST00000471209,;MSTO1,downstream_gene_variant,,ENST00000460199,;MSTO2P,intron_variant,,ENST00000538914,;RP11-29H23.5,downstream_gene_variant,,ENST00000500626,;	G	ENSG00000125459	ENST00000245564	Transcript	synonymous_variant	1212	1188	396	P	ccA/ccG	.	.	.	1	MSTO1	HGNC	29678	protein_coding	YES	CCDS1114.1	ENSP00000245564	MSTO1_HUMAN	D3DV95_HUMAN	UPI000006F52F	.	.	.	11/14	.	hmmpanther:PTHR13391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCATGGAC	.	5	ESCA
FCGR2A	0	.	GRCh37	1	161487943	161487943	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5T>C	.	.	ENST00000271450	7/7	38	33	4	35	35	0	FCGR2A,3_prime_UTR_variant,,ENST00000367972,;FCGR2A,3_prime_UTR_variant,,ENST00000271450,;FCGR2A,intron_variant,,ENST00000459885,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000461298,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000471026,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000486608,;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR2A,intron_variant,,ENST00000491841,;FCGR2A,3_prime_UTR_variant,,ENST00000483665,;FCGR2A,intron_variant,,ENST00000467525,;	C	ENSG00000143226	ENST00000271450	Transcript	3_prime_UTR_variant	997	.	.	.	.	.	.	.	1	FCGR2A	HGNC	3616	protein_coding	YES	CCDS44264.1	ENSP00000271450	FCG2A_HUMAN	F5H137_HUMAN,F5GY95_HUMAN	UPI000013D8DE	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAGTAACGT	.	4	ESCA
KIFAP3	0	.	GRCh37	1	169947249	169947249	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1874G>C	p.Arg625Thr	p.R625T	ENST00000361580	16/20	59	52	7	52	52	0	KIFAP3,missense_variant,p.Arg625Thr,ENST00000361580,;KIFAP3,missense_variant,p.Arg547Thr,ENST00000538366,;KIFAP3,missense_variant,p.Arg585Thr,ENST00000367765,;KIFAP3,missense_variant,p.Arg327Thr,ENST00000540905,;KIFAP3,missense_variant,p.Arg581Thr,ENST00000367767,;	G	ENSG00000075945	ENST00000361580	Transcript	missense_variant	2102	1874	625	R/T	aGa/aCa	.	.	.	-1	KIFAP3	HGNC	17060	protein_coding	YES	CCDS1288.1	ENSP00000354560	KIFA3_HUMAN	B7Z7E7_HUMAN	UPI000006CD6C	.	deleterious(0)	probably_damaging(0.995)	16/20	.	PROSITE_profiles:PS50176,hmmpanther:PTHR15605,Pfam_domain:PF05804,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTCTCTTGTG	.	4	ESCA
PRRC2C	0	.	GRCh37	1	171557645	171557645	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8193+1G>C	.	p.X2731_splice	ENST00000338920	.	85	81	4	73	73	0	PRRC2C,splice_donor_variant,,ENST00000338920,;PRRC2C,splice_donor_variant,,ENST00000367742,;PRRC2C,splice_donor_variant,,ENST00000426496,;PRRC2C,splice_donor_variant,,ENST00000392078,;PRRC2C,splice_donor_variant,,ENST00000495585,;PRRC2C,splice_donor_variant,,ENST00000492811,;PRRC2C,splice_donor_variant,,ENST00000498596,;	C	ENSG00000117523	ENST00000338920	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	PRRC2C	HGNC	24903	protein_coding	YES	CCDS1296.2	ENSP00000343629	PRC2C_HUMAN	.	UPI0000E265EC	.	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCAGGTGGGC	.	2	ESCA
RCC2	0	.	GRCh37	1	17747270	17747270	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.799A>G	p.Met267Val	p.M267V	ENST00000375436	7/13	35	31	4	27	27	0	RCC2,missense_variant,p.Met267Val,ENST00000375436,;RCC2,missense_variant,p.Met267Val,ENST00000375433,;	C	ENSG00000179051	ENST00000375436	Transcript	missense_variant	987	799	267	M/V	Atg/Gtg	.	.	.	-1	RCC2	HGNC	30297	protein_coding	YES	CCDS181.1	ENSP00000364585	RCC2_HUMAN	.	UPI0000074608	.	tolerated(0.31)	benign(0.145)	7/13	.	PROSITE_profiles:PS50012,hmmpanther:PTHR22870,hmmpanther:PTHR22870:SF146,Pfam_domain:PF00415,Gene3D:2.130.10.30,Superfamily_domains:SSF50985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATCATACTGA	.	4	ESCA
GLUL	0	.	GRCh37	1	182357713	182357713	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.160G>A	p.Val54Met	p.V54M	ENST00000311223	3/8	65	56	9	62	62	0	GLUL,missense_variant,p.Val54Met,ENST00000311223,;GLUL,missense_variant,p.Val54Met,ENST00000417584,;GLUL,missense_variant,p.Val54Met,ENST00000331872,;GLUL,missense_variant,p.Val54Met,ENST00000339526,;GLUL,non_coding_transcript_exon_variant,,ENST00000475808,;GLUL,non_coding_transcript_exon_variant,,ENST00000462444,;GLUL,non_coding_transcript_exon_variant,,ENST00000489818,;GLUL,non_coding_transcript_exon_variant,,ENST00000484996,;GLUL,non_coding_transcript_exon_variant,,ENST00000480604,;GLUL,non_coding_transcript_exon_variant,,ENST00000491322,;GLUL,intron_variant,,ENST00000463851,;GLUL,upstream_gene_variant,,ENST00000461447,;	T	ENSG00000135821	ENST00000311223	Transcript	missense_variant	1057	160	54	V/M	Gtg/Atg	.	.	.	-1	GLUL	HGNC	4341	protein_coding	YES	CCDS1344.1	ENSP00000307900	GLNA_HUMAN	B4DWM6_HUMAN,A8YXX4_HUMAN	UPI000012B6E3	.	deleterious(0.04)	possibly_damaging(0.502)	3/8	.	hmmpanther:PTHR20852,hmmpanther:PTHR20852:SF45,Pfam_domain:PF03951,Superfamily_domains:SSF54368	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCACACACT	.	4	ESCA
CDC73	0	.	GRCh37	1	193220740	193220740	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*898C>G	.	.	ENST00000367435	17/17	62	58	4	78	78	0	CDC73,3_prime_UTR_variant,,ENST00000367435,;CDC73,downstream_gene_variant,,ENST00000477868,;	G	ENSG00000134371	ENST00000367435	Transcript	3_prime_UTR_variant	2678	.	.	.	.	.	.	.	1	CDC73	HGNC	16783	protein_coding	YES	CCDS1382.1	ENSP00000356405	CDC73_HUMAN	.	UPI0000021592	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTTCCATTA	.	2	ESCA
NEK7	0	.	GRCh37	1	198222262	198222262	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150A>T	p.Arg50Ser	p.R50S	ENST00000367385	3/10	49	35	14	51	51	0	NEK7,missense_variant,p.Arg50Ser,ENST00000544035,;NEK7,missense_variant,p.Arg50Ser,ENST00000367383,;NEK7,missense_variant,p.Arg50Ser,ENST00000367385,;NEK7,missense_variant,p.Arg50Ser,ENST00000391974,;NEK7,missense_variant,p.Arg50Ser,ENST00000538004,;NEK7,downstream_gene_variant,,ENST00000442588,;	T	ENSG00000151414	ENST00000367385	Transcript	missense_variant	492	150	50	R/S	agA/agT	.	.	.	1	NEK7	HGNC	13386	protein_coding	YES	CCDS1394.1	ENSP00000356355	NEK7_HUMAN	F8WAG2_HUMAN,F5H3U7_HUMAN,C9J1H8_HUMAN	UPI0000073180	.	deleterious(0.03)	benign(0.292)	3/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24362:SF228,hmmpanther:PTHR24362,PROSITE_patterns:PS00107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAGAGCAGC	.	5	ESCA
CACNA1S	0	.	GRCh37	1	201042678	201042678	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2156A>G	p.Lys719Arg	p.K719R	ENST00000362061	15/44	25	20	5	34	34	0	CACNA1S,missense_variant,p.Lys719Arg,ENST00000367338,;CACNA1S,missense_variant,p.Lys719Arg,ENST00000362061,;	C	ENSG00000081248	ENST00000362061	Transcript	missense_variant	2383	2156	719	K/R	aAg/aGg	.	.	.	-1	CACNA1S	HGNC	1397	protein_coding	YES	CCDS1407.1	ENSP00000355192	CAC1S_HUMAN	Q13062_HUMAN,Q12966_HUMAN	UPI000020471D	.	tolerated(0.1)	benign(0.109)	15/44	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Prints_domain:PR01634	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCTTGGCA	.	5	ESCA
RBBP5	0	.	GRCh37	1	205068124	205068124	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089G>T	p.Glu363Asp	p.E363D	ENST00000264515	10/14	39	31	8	51	51	0	RBBP5,missense_variant,p.Glu363Asp,ENST00000264515,;RBBP5,missense_variant,p.Glu363Asp,ENST00000367164,;	A	ENSG00000117222	ENST00000264515	Transcript	missense_variant	1231	1089	363	E/D	gaG/gaT	.	.	.	-1	RBBP5	HGNC	9888	protein_coding	YES	CCDS30983.1	ENSP00000264515	RBBP5_HUMAN	.	UPI00001A9CA5	.	tolerated(0.22)	benign(0.018)	10/14	.	hmmpanther:PTHR12816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGCTCAGG	.	5	ESCA
PLXNA2	0	.	GRCh37	1	208391109	208391109	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159G>A	p.%3D	p.L53L	ENST00000367033	2/32	45	40	5	55	55	0	PLXNA2,synonymous_variant,p.%3D,ENST00000367033,;PLXNA2,upstream_gene_variant,,ENST00000460870,;	T	ENSG00000076356	ENST00000367033	Transcript	synonymous_variant	917	159	53	L	ttG/ttA	.	.	.	-1	PLXNA2	HGNC	9100	protein_coding	YES	CCDS31013.1	ENSP00000356000	PLXA2_HUMAN	.	UPI000022B239	.	.	.	2/32	.	PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACGGTCAAGTG	.	4	ESCA
RRP15	0	.	GRCh37	1	218480940	218480940	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.671C>T	p.Thr224Ile	p.T224I	ENST00000366932	4/5	61	34	27	66	66	0	RRP15,missense_variant,p.Thr224Ile,ENST00000366932,;RRP15,downstream_gene_variant,,ENST00000491428,;	T	ENSG00000067533	ENST00000366932	Transcript	missense_variant	701	671	224	T/I	aCt/aTt	.	.	.	1	RRP15	HGNC	24255	protein_coding	YES	CCDS1520.2	ENSP00000355899	RRP15_HUMAN	.	UPI0000205BC1	.	deleterious(0.05)	benign(0.122)	4/5	.	hmmpanther:PTHR13245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGACTGCTT	.	5	ESCA
RRP15	0	.	GRCh37	1	218509816	218509816	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5383G>A	.	.	ENST00000366932	5/5	55	51	4	61	61	0	RRP15,3_prime_UTR_variant,,ENST00000366932,;RP11-224O19.5,upstream_gene_variant,,ENST00000444678,;	A	ENSG00000067533	ENST00000366932	Transcript	3_prime_UTR_variant	6262	.	.	.	.	.	.	.	1	RRP15	HGNC	24255	protein_coding	YES	CCDS1520.2	ENSP00000355899	RRP15_HUMAN	.	UPI0000205BC1	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTGAGAGC	.	2	ESCA
SRRM1	0	.	GRCh37	1	24999012	24999013	+	3'UTR	INS	-	-	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*244dupA	.	.	ENST00000323848	17/17	33	26	7	34	34	0	SRRM1,3_prime_UTR_variant,,ENST00000447431,;SRRM1,3_prime_UTR_variant,,ENST00000323848,;SRRM1,3_prime_UTR_variant,,ENST00000374389,;SRRM1,downstream_gene_variant,,ENST00000596378,;SRRM1,downstream_gene_variant,,ENST00000479034,;SRRM1,downstream_gene_variant,,ENST00000474843,;SRRM1,downstream_gene_variant,,ENST00000489130,;	A	ENSG00000133226	ENST00000323848	Transcript	3_prime_UTR_variant	3265-3266	.	.	.	.	.	.	.	1	SRRM1	HGNC	16638	protein_coding	YES	CCDS255.1	ENSP00000326261	SRRM1_HUMAN	M0QXG5_HUMAN	UPI000013EBEB	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAAGCCAAAAA	.	2	ESCA
RHCE	0	.	GRCh37	1	25689023	25689023	+	Missense_Mutation	SNP	A	A	G	rs761433940	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1249T>C	p.Phe417Leu	p.F417L	ENST00000294413	10/10	51	45	6	74	74	0	RHCE,missense_variant,p.Phe312Leu,ENST00000455194,;RHCE,missense_variant,p.Phe401Leu,ENST00000374352,;RHCE,missense_variant,p.Phe401Leu,ENST00000349320,;RHCE,missense_variant,p.Phe266Leu,ENST00000346452,;RHCE,missense_variant,p.Phe417Leu,ENST00000294413,;RHCE,synonymous_variant,p.%3D,ENST00000413854,;RHCE,3_prime_UTR_variant,,ENST00000340849,;RHCE,3_prime_UTR_variant,,ENST00000527747,;RHCE,3_prime_UTR_variant,,ENST00000425135,;RHCE,3_prime_UTR_variant,,ENST00000349438,;RHCE,3_prime_UTR_variant,,ENST00000243186,;TMEM50A,downstream_gene_variant,,ENST00000374358,;TMEM50A,downstream_gene_variant,,ENST00000498135,;TMEM50A,downstream_gene_variant,,ENST00000491936,;TMEM50A,downstream_gene_variant,,ENST00000480937,;	G	ENSG00000188672	ENST00000294413	Transcript	missense_variant	1308	1249	417	F/L	Ttt/Ctt	rs761433940	.	.	-1	RHCE	HGNC	10008	protein_coding	YES	CCDS30635.1	ENSP00000294413	RHCE_HUMAN	Q9UP89_HUMAN,Q9UEC6_HUMAN,Q8NDV4_HUMAN,Q5UD29_HUMAN,D0AB04_HUMAN,D0AB03_HUMAN,B6ZCF8_HUMAN,B6ZCF7_HUMAN,A8YPS4_HUMAN	UPI00001D9627	.	deleterious(0)	possibly_damaging(0.841)	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TTAAAATCCAA	.	3	ESCA
MAN1C1	0	.	GRCh37	1	26104684	26104684	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1346G>T	p.Gly449Val	p.G449V	ENST00000374332	9/12	29	16	12	41	41	0	MAN1C1,missense_variant,p.Gly220Val,ENST00000374329,;MAN1C1,missense_variant,p.Gly449Val,ENST00000374332,;MAN1C1,missense_variant,p.Gly269Val,ENST00000263979,;MAN1C1,non_coding_transcript_exon_variant,,ENST00000475314,;MAN1C1,non_coding_transcript_exon_variant,,ENST00000496532,;MAN1C1,upstream_gene_variant,,ENST00000487493,;	T	ENSG00000117643	ENST00000374332	Transcript	missense_variant	1676	1346	449	G/V	gGg/gTg	.	.	.	1	MAN1C1	HGNC	19080	protein_coding	YES	CCDS265.1	ENSP00000363452	MA1C1_HUMAN	B1AJZ5_HUMAN,A6NGN6_HUMAN	UPI000012EABD	.	deleterious(0)	probably_damaging(0.98)	9/12	.	hmmpanther:PTHR11742,hmmpanther:PTHR11742:SF28,Pfam_domain:PF01532,Gene3D:1.50.10.50,Superfamily_domains:SSF48225,Prints_domain:PR00747	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGGGGCACC	.	5	ESCA
PUM1	0	.	GRCh37	1	31467963	31467963	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.825G>C	p.%3D	p.V275V	ENST00000426105	6/22	135	126	9	138	138	0	PUM1,synonymous_variant,p.%3D,ENST00000426105,;PUM1,synonymous_variant,p.%3D,ENST00000423018,;PUM1,synonymous_variant,p.%3D,ENST00000257075,;PUM1,synonymous_variant,p.%3D,ENST00000525843,;PUM1,synonymous_variant,p.%3D,ENST00000373747,;PUM1,synonymous_variant,p.%3D,ENST00000373742,;PUM1,synonymous_variant,p.%3D,ENST00000440538,;PUM1,synonymous_variant,p.%3D,ENST00000373741,;PUM1,intron_variant,,ENST00000424085,;PUM1,upstream_gene_variant,,ENST00000532678,;PUM1,upstream_gene_variant,,ENST00000498419,;PUM1,3_prime_UTR_variant,,ENST00000525948,;PUM1,intron_variant,,ENST00000526215,;PUM1,downstream_gene_variant,,ENST00000480602,;	G	ENSG00000134644	ENST00000426105	Transcript	synonymous_variant	916	825	275	V	gtG/gtC	.	.	.	-1	PUM1	HGNC	14957	protein_coding	YES	CCDS44099.1	ENSP00000391723	PUM1_HUMAN	E9PL65_HUMAN	UPI0000203D8E	.	.	.	6/22	.	hmmpanther:PTHR12537,hmmpanther:PTHR12537:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCATCACATC	.	2	ESCA
CSMD2	0	.	GRCh37	1	34164367	34164367	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3791T>C	p.Leu1264Pro	p.L1264P	ENST00000241312	24/70	31	23	8	30	30	0	CSMD2,missense_variant,p.Leu1304Pro,ENST00000373381,;CSMD2,missense_variant,p.Leu177Pro,ENST00000373380,;CSMD2,5_prime_UTR_variant,,ENST00000373388,;CSMD2,missense_variant,p.Leu1264Pro,ENST00000241312,;	G	ENSG00000121904	ENST00000241312	Transcript	missense_variant	3820	3791	1264	L/P	cTg/cCg	.	.	.	-1	CSMD2	HGNC	19290	nonsense_mediated_decay	YES	CCDS380.1	ENSP00000241312	CSMD2_HUMAN	.	UPI00004561AB	.	deleterious(0.04)	probably_damaging(0.997)	24/70	.	Superfamily_domains:SSF49854,Superfamily_domains:SSF57535,SMART_domains:SM00032,Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCAGAGGC	.	5	ESCA
ZMYM4	0	.	GRCh37	1	35886028	35886028	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*750T>A	.	.	ENST00000314607	30/30	12	7	5	12	12	0	ZMYM4,3_prime_UTR_variant,,ENST00000457946,;ZMYM4,3_prime_UTR_variant,,ENST00000373297,;ZMYM4,3_prime_UTR_variant,,ENST00000314607,;	A	ENSG00000146463	ENST00000314607	Transcript	3_prime_UTR_variant	5477	.	.	.	.	.	.	.	1	ZMYM4	HGNC	13055	protein_coding	YES	CCDS389.1	ENSP00000322915	ZMYM4_HUMAN	.	UPI0000203EE6	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCCTATCAG	.	2	ESCA
RIMS3	0	.	GRCh37	1	41088461	41088461	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3728C>T	.	.	ENST00000372684	8/8	79	69	9	86	86	0	RIMS3,3_prime_UTR_variant,,ENST00000372684,;RIMS3,downstream_gene_variant,,ENST00000372683,;	A	ENSG00000117016	ENST00000372684	Transcript	3_prime_UTR_variant	5125	.	.	.	.	.	.	.	-1	RIMS3	HGNC	21292	protein_coding	YES	CCDS30687.1	ENSP00000361769	RIMS3_HUMAN	.	UPI000006E06A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGAAGATGGG	.	4	ESCA
CCDC30	0	.	GRCh37	1	43102995	43102995	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1584G>C	p.Lys528Asn	p.K528N	ENST00000428554	18/23	56	53	3	32	32	0	CCDC30,missense_variant,p.Lys317Asn,ENST00000390640,;CCDC30,missense_variant,p.Lys317Asn,ENST00000507855,;CCDC30,missense_variant,p.Lys528Asn,ENST00000428554,;CCDC30,missense_variant,p.Lys528Asn,ENST00000340612,;CCDC30,missense_variant,p.Lys528Asn,ENST00000342022,;CCDC30,missense_variant,p.Lys226Asn,ENST00000477155,;CCDC30,3_prime_UTR_variant,,ENST00000471390,;	C	ENSG00000186409	ENST00000428554	Transcript	missense_variant	2727	1584	528	K/N	aaG/aaC	.	.	.	1	CCDC30	HGNC	26103	protein_coding	YES	CCDS30690.1	ENSP00000397035	CCD30_HUMAN	D6RFH8_HUMAN	UPI0000458A0B	.	tolerated(0.18)	benign(0.275)	18/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R526Q|c.1577G>A|5	MUTECT|MUSE	GATAAGAGAAT	.	2	ESCA
OSBPL9	0	.	GRCh37	1	52246895	52246895	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1346C>T	p.Ser449Leu	p.S449L	ENST00000447887	16/24	54	51	3	61	61	0	OSBPL9,missense_variant,p.Ser439Leu,ENST00000428468,;OSBPL9,missense_variant,p.Ser457Leu,ENST00000371710,;OSBPL9,missense_variant,p.Ser449Leu,ENST00000447887,;OSBPL9,missense_variant,p.Ser261Leu,ENST00000486942,;OSBPL9,missense_variant,p.Ser444Leu,ENST00000337809,;OSBPL9,missense_variant,p.Ser274Leu,ENST00000435686,;OSBPL9,missense_variant,p.Ser426Leu,ENST00000371714,;OSBPL9,missense_variant,p.Ser329Leu,ENST00000361556,;OSBPL9,missense_variant,p.Ser358Leu,ENST00000530544,;OSBPL9,missense_variant,p.Ser274Leu,ENST00000531828,;OSBPL9,missense_variant,p.Ser422Leu,ENST00000453295,;OSBPL9,missense_variant,p.Ser261Leu,ENST00000462759,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000533825,;OSBPL9,3_prime_UTR_variant,,ENST00000495776,;OSBPL9,3_prime_UTR_variant,,ENST00000435274,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000531819,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000475697,;OSBPL9,downstream_gene_variant,,ENST00000528603,;OSBPL9,downstream_gene_variant,,ENST00000531061,;OSBPL9,downstream_gene_variant,,ENST00000489990,;	T	ENSG00000117859	ENST00000447887	Transcript	missense_variant	1365	1346	449	S/L	tCa/tTa	.	.	.	1	OSBPL9	HGNC	16386	protein_coding	YES	CCDS44145.1	ENSP00000412733	OSBL9_HUMAN	Q9BRN2_HUMAN,E9PNR1_HUMAN,B3KW33_HUMAN	UPI0000167BAD	.	deleterious(0)	possibly_damaging(0.823)	16/24	.	hmmpanther:PTHR10972:SF27,hmmpanther:PTHR10972,Pfam_domain:PF01237,Superfamily_domains:0051579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCTCAGCCT	.	2	ESCA
SIRPG	0	.	GRCh37	20	1630038	1630038	+	Silent	SNP	C	C	T	rs201954358	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90G>A	p.%3D	p.E30E	ENST00000303415	2/6	56	52	4	45	45	0	SIRPG,synonymous_variant,p.%3D,ENST00000381583,;SIRPG,synonymous_variant,p.%3D,ENST00000303415,;SIRPG,synonymous_variant,p.%3D,ENST00000216927,;SIRPG,synonymous_variant,p.%3D,ENST00000344103,;SIRPG,5_prime_UTR_variant,,ENST00000381580,;RP11-77C3.3,downstream_gene_variant,,ENST00000456177,;	T	ENSG00000089012	ENST00000303415	Transcript	synonymous_variant	155	90	30	E	gaG/gaA	rs201954358	.	.	-1	SIRPG	HGNC	15757	protein_coding	YES	CCDS13020.2	ENSP00000305529	SIRPG_HUMAN	.	UPI00001AE5FD	.	.	.	2/6	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF6	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTCCTCCTC	byCluster|by1000G	2	ESCA
VPS16	0	.	GRCh37	20	2846872	2846872	+	Silent	SNP	C	C	T	rs759963744	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2286C>T	p.%3D	p.I762I	ENST00000380445	23/24	76	67	8	109	109	0	VPS16,synonymous_variant,p.%3D,ENST00000380443,;VPS16,synonymous_variant,p.%3D,ENST00000380469,;VPS16,synonymous_variant,p.%3D,ENST00000380445,;PTPRA,intron_variant,,ENST00000380393,;VPS16,downstream_gene_variant,,ENST00000417508,;VPS16,downstream_gene_variant,,ENST00000453689,;VPS16,non_coding_transcript_exon_variant,,ENST00000466415,;VPS16,downstream_gene_variant,,ENST00000481812,;VPS16,downstream_gene_variant,,ENST00000487461,;	T	ENSG00000215305	ENST00000380445	Transcript	synonymous_variant	2358	2286	762	I	atC/atT	rs759963744	.	.	1	VPS16	HGNC	14584	protein_coding	YES	CCDS13036.1	ENSP00000369810	VPS16_HUMAN	A1A4H0_HUMAN	UPI0000138B87	.	.	.	23/24	.	hmmpanther:PTHR12811,hmmpanther:PTHR12811:SF0,Pfam_domain:PF04840,PIRSF_domain:PIRSF007949	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGATCTGCAT	byFrequency	4	ESCA
SAMHD1	0	.	GRCh37	20	35533879	35533879	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1298C>G	p.Ser433Cys	p.S433C	ENST00000262878	12/16	90	84	6	48	47	1	SAMHD1,missense_variant,p.Ser433Cys,ENST00000262878,;SAMHD1,upstream_gene_variant,,ENST00000465985,;	C	ENSG00000101347	ENST00000262878	Transcript	missense_variant	1498	1298	433	S/C	tCt/tGt	.	.	.	-1	SAMHD1	HGNC	15925	protein_coding	YES	CCDS13288.1	ENSP00000262878	SAMH1_HUMAN	A6NDZ3_HUMAN	UPI0000035DA0	.	deleterious(0)	probably_damaging(0.987)	12/16	.	hmmpanther:PTHR11373:SF4,hmmpanther:PTHR11373,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAGTAGAGTAT	.	2	ESCA
MOCS3	0	.	GRCh37	20	49576374	49576374	+	Missense_Mutation	SNP	C	C	T	rs779470514	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.995C>T	p.Pro332Leu	p.P332L	ENST00000244051	1/1	46	34	12	41	41	0	MOCS3,missense_variant,p.Pro332Leu,ENST00000244051,;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000371582,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000371588,;DPM1,upstream_gene_variant,,ENST00000371583,;DPM1,upstream_gene_variant,,ENST00000466152,;	T	ENSG00000124217	ENST00000244051	Transcript	missense_variant	1012	995	332	P/L	cCa/cTa	rs779470514	.	.	1	MOCS3	HGNC	15765	protein_coding	YES	CCDS13435.1	ENSP00000244051	MOCS3_HUMAN	.	UPI000012F369	.	tolerated(0.1)	benign(0.001)	1/1	.	HAMAP:MF_03049,hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF102,Gene3D:3.40.250.10,Superfamily_domains:SSF69572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCCAGAGG	.	5	ESCA
DNMT3L	0	.	GRCh37	21	45668946	45668946	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958G>A	p.Ala320Thr	p.A320T	ENST00000270172	11/12	50	46	4	69	69	0	DNMT3L,missense_variant,p.Ala320Thr,ENST00000418993,;DNMT3L,missense_variant,p.Ala320Thr,ENST00000270172,;DNMT3L,missense_variant,p.Ala115Thr,ENST00000436357,;DNMT3L,downstream_gene_variant,,ENST00000431166,;AP001059.5,upstream_gene_variant,,ENST00000442785,;	T	ENSG00000142182	ENST00000270172	Transcript	missense_variant	1442	958	320	A/T	Gct/Act	.	.	.	-1	DNMT3L	HGNC	2980	protein_coding	YES	CCDS13705.1	ENSP00000270172	DNM3L_HUMAN	.	UPI00001294C2	.	deleterious(0.01)	benign(0.38)	11/12	.	hmmpanther:PTHR23068:SF5,hmmpanther:PTHR23068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACAGCATTCT	.	3	ESCA
TANGO2	0	.	GRCh37	22	20049072	20049072	+	Silent	SNP	C	C	T	rs148730599	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471C>T	p.%3D	p.N157N	ENST00000327374	7/9	37	31	5	47	47	0	TANGO2,synonymous_variant,p.%3D,ENST00000456048,;TANGO2,synonymous_variant,p.%3D,ENST00000447208,;TANGO2,synonymous_variant,p.%3D,ENST00000401833,;TANGO2,synonymous_variant,p.%3D,ENST00000420290,;TANGO2,synonymous_variant,p.%3D,ENST00000434168,;TANGO2,synonymous_variant,p.%3D,ENST00000450664,;TANGO2,synonymous_variant,p.%3D,ENST00000432883,;TANGO2,synonymous_variant,p.%3D,ENST00000398042,;TANGO2,synonymous_variant,p.%3D,ENST00000327374,;TANGO2,synonymous_variant,p.%3D,ENST00000401886,;TANGO2,intron_variant,,ENST00000434570,;AC006547.15,downstream_gene_variant,,ENST00000600090,;AC006547.13,downstream_gene_variant,,ENST00000600937,;AC006547.13,downstream_gene_variant,,ENST00000598339,;AC006547.13,downstream_gene_variant,,ENST00000595864,;AC006547.13,downstream_gene_variant,,ENST00000601746,;AC006547.13,downstream_gene_variant,,ENST00000415503,;AC006547.13,downstream_gene_variant,,ENST00000596334,;AC006547.13,downstream_gene_variant,,ENST00000609644,;AC006547.13,downstream_gene_variant,,ENST00000600617,;AC006547.13,downstream_gene_variant,,ENST00000608610,;AC006547.13,downstream_gene_variant,,ENST00000609191,;TANGO2,non_coding_transcript_exon_variant,,ENST00000490583,;TANGO2,non_coding_transcript_exon_variant,,ENST00000485715,;TANGO2,non_coding_transcript_exon_variant,,ENST00000411907,;TANGO2,upstream_gene_variant,,ENST00000476940,;TANGO2,downstream_gene_variant,,ENST00000490121,;TANGO2,3_prime_UTR_variant,,ENST00000430807,;TANGO2,3_prime_UTR_variant,,ENST00000450019,;TANGO2,3_prime_UTR_variant,,ENST00000399807,;TANGO2,non_coding_transcript_exon_variant,,ENST00000462579,;TANGO2,intron_variant,,ENST00000444651,;	T	ENSG00000183597	ENST00000327374	Transcript	synonymous_variant	649	471	157	N	aaC/aaT	rs148730599	.	.	1	TANGO2	HGNC	25439	protein_coding	YES	CCDS13772.1	ENSP00000332721	TNG2_HUMAN	C9JKN2_HUMAN,C9JDT9_HUMAN,C9J695_HUMAN	UPI0000050339	.	.	.	7/9	.	Pfam_domain:PF05742,hmmpanther:PTHR17985	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAACGCGCT	byCluster	5	ESCA
PI4KA	0	.	GRCh37	22	21119944	21119944	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2366C>T	p.Pro789Leu	p.P789L	ENST00000255882	20/55	34	30	4	63	63	0	PI4KA,missense_variant,p.Pro731Leu,ENST00000572273,;PI4KA,missense_variant,p.Pro789Leu,ENST00000255882,;PI4KA,non_coding_transcript_exon_variant,,ENST00000466162,;PI4KA,non_coding_transcript_exon_variant,,ENST00000490873,;PI4KA,non_coding_transcript_exon_variant,,ENST00000484220,;	A	ENSG00000241973	ENST00000255882	Transcript	missense_variant	2453	2366	789	P/L	cCt/cTt	.	.	.	-1	PI4KA	HGNC	8983	protein_coding	YES	CCDS33603.2	ENSP00000255882	.	Q4LE69_HUMAN,J3KN10_HUMAN,C9JLI1_HUMAN	UPI0000E06BD6	.	deleterious(0.05)	benign(0.321)	20/55	.	Superfamily_domains:SSF48371,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCGAGGCTTA	.	4	ESCA
MMP11	0	.	GRCh37	22	24122846	24122846	+	Missense_Mutation	SNP	G	G	A	rs767691945	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560G>A	p.Arg187Gln	p.R187Q	ENST00000215743	4/8	29	24	4	47	47	0	MMP11,missense_variant,p.Arg187Gln,ENST00000215743,;AP000349.1,downstream_gene_variant,,ENST00000598975,;MMP11,non_coding_transcript_exon_variant,,ENST00000489582,;MMP11,non_coding_transcript_exon_variant,,ENST00000477567,;MMP11,non_coding_transcript_exon_variant,,ENST00000460352,;MMP11,upstream_gene_variant,,ENST00000488363,;MMP11,upstream_gene_variant,,ENST00000480185,;MMP11,missense_variant,p.Arg171Gln,ENST00000437086,;MMP11,non_coding_transcript_exon_variant,,ENST00000465385,;MMP11,upstream_gene_variant,,ENST00000493132,;MMP11,downstream_gene_variant,,ENST00000428253,;MMP11,upstream_gene_variant,,ENST00000434318,;MMP11,downstream_gene_variant,,ENST00000465730,;MMP11,upstream_gene_variant,,ENST00000492464,;	A	ENSG00000099953	ENST00000215743	Transcript	missense_variant	612	560	187	R/Q	cGa/cAa	rs767691945	.	.	1	MMP11	HGNC	7157	protein_coding	YES	CCDS13816.1	ENSP00000215743	MMP11_HUMAN	F8WDI7_HUMAN	UPI00001AE5D9	.	deleterious(0.05)	probably_damaging(0.977)	4/8	.	hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF20,Pfam_domain:PF00413,Gene3D:3.40.390.10,SMART_domains:SM00235,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACCGAGAAG	byFrequency	4	ESCA
LRP1B	0	.	GRCh37	2	141215110	141215110	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9736G>A	p.Ala3246Thr	p.A3246T	ENST00000389484	61/91	49	43	5	79	79	0	LRP1B,missense_variant,p.Ala3246Thr,ENST00000389484,;	T	ENSG00000168702	ENST00000389484	Transcript	missense_variant	10708	9736	3246	A/T	Gca/Aca	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	possibly_damaging(0.483)	61/91	.	PROSITE_profiles:PS51120,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTGCTCCCG	.	4	ESCA
SCN1A	0	.	GRCh37	2	166846278	166846278	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1477G>A	.	.	ENST00000303395	26/26	52	47	5	71	71	0	SCN1A,3_prime_UTR_variant,,ENST00000423058,;SCN1A,3_prime_UTR_variant,,ENST00000303395,;SCN1A,3_prime_UTR_variant,,ENST00000375405,;SCN1A,downstream_gene_variant,,ENST00000409050,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000597623,;	T	ENSG00000144285	ENST00000303395	Transcript	3_prime_UTR_variant	7507	.	.	.	.	.	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCTTCATATT	.	3	ESCA
HOXD13	0	.	GRCh37	2	176958115	176958115	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.497A>G	p.Lys166Arg	p.K166R	ENST00000392539	1/2	78	72	6	94	94	0	HOXD13,missense_variant,p.Lys166Arg,ENST00000392539,;	G	ENSG00000128714	ENST00000392539	Transcript	missense_variant	497	497	166	K/R	aAg/aGg	.	.	.	1	HOXD13	HGNC	5136	protein_coding	YES	CCDS2264.2	ENSP00000376322	HXD13_HUMAN	.	UPI000020912A	.	deleterious(0.01)	probably_damaging(0.994)	1/2	.	hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF182,Pfam_domain:PF12284	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGAGAAGTACA	.	3	ESCA
TTN	0	.	GRCh37	2	179474483	179474483	+	Nonsense_Mutation	SNP	G	G	A	rs748956593	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51667C>T	p.Arg17223Ter	p.R17223*	ENST00000589042	272/363	59	50	8	59	59	0	TTN,stop_gained,p.Arg8283Ter,ENST00000359218,;TTN,stop_gained,p.Arg15582Ter,ENST00000591111,;TTN,stop_gained,p.Arg17223Ter,ENST00000589042,;TTN,stop_gained,p.Arg14655Ter,ENST00000342992,;TTN,stop_gained,p.Arg8350Ter,ENST00000342175,;TTN,stop_gained,p.Arg8158Ter,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000419746,;TTN-AS1,downstream_gene_variant,,ENST00000586452,;	A	ENSG00000155657	ENST00000589042	Transcript	stop_gained	51892	51667	17223	R/*	Cga/Tga	rs748956593	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	272/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTCGCACAC	.	4	ESCA
COL5A2	0	.	GRCh37	2	189917478	189917478	+	Silent	SNP	C	C	T	rs372869641	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2712G>A	p.%3D	p.P904P	ENST00000374866	40/54	45	30	14	38	38	0	COL5A2,synonymous_variant,p.%3D,ENST00000374866,;COL5A2,downstream_gene_variant,,ENST00000470524,;	T	ENSG00000204262	ENST00000374866	Transcript	synonymous_variant	2987	2712	904	P	ccG/ccA	rs372869641	.	.	-1	COL5A2	HGNC	2210	protein_coding	YES	CCDS33350.1	ENSP00000364000	CO5A2_HUMAN	D3DPH5_HUMAN	UPI00006C511C	.	.	.	40/54	.	hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF481	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGGCGGACC	byCluster|by1000G	5	ESCA
UGT1A6	0	.	GRCh37	2	234602073	234602073	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.423G>C	p.Glu141Asp	p.E141D	ENST00000305139	1/5	44	33	11	61	61	0	UGT1A6,missense_variant,p.Glu141Asp,ENST00000441351,;UGT1A6,missense_variant,p.Glu141Asp,ENST00000305139,;UGT1A10,intron_variant,,ENST00000373445,;UGT1A6,intron_variant,,ENST00000373424,;UGT1A7,intron_variant,,ENST00000373426,;UGT1A8,intron_variant,,ENST00000609637,;UGT1A10,intron_variant,,ENST00000344644,;UGT1A8,intron_variant,,ENST00000373450,;UGT1A9,intron_variant,,ENST00000354728,;UGT1A7,downstream_gene_variant,,ENST00000485022,;UGT1A6,upstream_gene_variant,,ENST00000406651,;AC114812.8,downstream_gene_variant,,ENST00000439336,;UGT1A6,intron_variant,,ENST00000480628,;UGT1A6,upstream_gene_variant,,ENST00000478062,;UGT1A6,intron_variant,,ENST00000446481,;UGT1A6,upstream_gene_variant,,ENST00000484784,;	C	ENSG00000167165	ENST00000305139	Transcript	missense_variant	562	423	141	E/D	gaG/gaC	.	.	.	1	UGT1A6	HGNC	12538	protein_coding	YES	CCDS2507.1	ENSP00000303174	UD16_HUMAN	Q5DSZ8_HUMAN,H7C5F8_HUMAN,C9JMY5_HUMAN	UPI000007021F	.	tolerated(0.31)	benign(0.015)	1/5	.	hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF170,Pfam_domain:PF00201,Superfamily_domains:SSF53756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGAGAGCAA	.	5	ESCA
AQP12A	0	.	GRCh37	2	241631539	241631539	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>A	p.Asp58Asn	p.D58N	ENST00000337801	2/4	48	45	3	70	70	0	AQP12A,missense_variant,p.Asp58Asn,ENST00000337801,;AQP12A,missense_variant,p.Asp70Asn,ENST00000429564,;AC011298.2,downstream_gene_variant,,ENST00000407635,;AC011298.2,downstream_gene_variant,,ENST00000600041,;AQP12A,upstream_gene_variant,,ENST00000474778,;AQP12A,upstream_gene_variant,,ENST00000471878,;AQP12A,upstream_gene_variant,,ENST00000460527,;	A	ENSG00000184945	ENST00000337801	Transcript	missense_variant	241	172	58	D/N	Gac/Aac	COSM3839052	.	.	1	AQP12A	HGNC	19941	protein_coding	YES	.	ENSP00000337144	AQ12A_HUMAN	.	UPI00000743B9	.	deleterious(0.02)	probably_damaging(0.999)	2/4	.	hmmpanther:PTHR21191:SF8,hmmpanther:PTHR21191,Gene3D:1.20.1080.10,PIRSF_domain:PIRSF017529,Superfamily_domains:SSF81338	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCTGACCTG	.	2	ESCA
CAPN13	0	.	GRCh37	2	31010080	31010080	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.112G>A	p.Glu38Lys	p.E38K	ENST00000295055	2/23	43	35	8	37	37	0	CAPN13,missense_variant,p.Glu38Lys,ENST00000534090,;CAPN13,missense_variant,p.Glu38Lys,ENST00000295055,;CAPN13,non_coding_transcript_exon_variant,,ENST00000465960,;CAPN13,missense_variant,p.Glu38Lys,ENST00000485248,;CAPN13,missense_variant,p.Glu38Lys,ENST00000458085,;	T	ENSG00000162949	ENST00000295055	Transcript	missense_variant	289	112	38	E/K	Gag/Aag	.	.	.	-1	CAPN13	HGNC	16663	protein_coding	YES	CCDS46252.1	ENSP00000295055	CAN13_HUMAN	.	UPI00000463E5	.	tolerated(0.05)	benign(0.133)	2/23	.	PROSITE_profiles:PS50203,hmmpanther:PTHR10183:SF37,hmmpanther:PTHR10183,Pfam_domain:PF00648,SMART_domains:SM00230,Superfamily_domains:SSF54001,Prints_domain:PR00704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTCATCCT	.	5	ESCA
NDUFAF7	0	.	GRCh37	2	37468805	37468805	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493C>T	p.Gln165Ter	p.Q165*	ENST00000002125	5/10	43	38	5	40	40	0	NDUFAF7,stop_gained,p.Gln86Ter,ENST00000431821,;NDUFAF7,stop_gained,p.Gln123Ter,ENST00000439218,;NDUFAF7,stop_gained,p.Gln165Ter,ENST00000002125,;NDUFAF7,stop_gained,p.Gln123Ter,ENST00000432075,;NDUFAF7,intron_variant,,ENST00000336237,;NDUFAF7,downstream_gene_variant,,ENST00000416653,;NDUFAF7,non_coding_transcript_exon_variant,,ENST00000483999,;NDUFAF7,upstream_gene_variant,,ENST00000419278,;NDUFAF7,non_coding_transcript_exon_variant,,ENST00000474154,;NDUFAF7,non_coding_transcript_exon_variant,,ENST00000469831,;NDUFAF7,intron_variant,,ENST00000455230,;NDUFAF7,upstream_gene_variant,,ENST00000474257,;	T	ENSG00000003509	ENST00000002125	Transcript	stop_gained	533	493	165	Q/*	Caa/Taa	.	.	.	1	NDUFAF7	HGNC	28816	protein_coding	YES	CCDS1788.1	ENSP00000002125	NDUF7_HUMAN	C9JS27_HUMAN,C9JP36_HUMAN,C9JEL7_HUMAN,C9J236_HUMAN	UPI000004A041	.	.	.	5/10	.	hmmpanther:PTHR12049,hmmpanther:PTHR12049:SF5,Pfam_domain:PF02636,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGATTCAAGCA	.	3	ESCA
ARHGAP25	0	.	GRCh37	2	69053487	69053487	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*161G>A	.	.	ENST00000409202	11/11	14	11	3	16	16	0	ARHGAP25,3_prime_UTR_variant,,ENST00000497259,;ARHGAP25,3_prime_UTR_variant,,ENST00000409030,;ARHGAP25,3_prime_UTR_variant,,ENST00000409202,;ARHGAP25,3_prime_UTR_variant,,ENST00000409220,;ARHGAP25,3_prime_UTR_variant,,ENST00000295381,;ARHGAP25,3_prime_UTR_variant,,ENST00000479844,;ARHGAP25,downstream_gene_variant,,ENST00000467265,;	A	ENSG00000163219	ENST00000409202	Transcript	3_prime_UTR_variant	2467	.	.	.	.	.	.	.	1	ARHGAP25	HGNC	28951	protein_coding	YES	CCDS33214.2	ENSP00000386911	RHG25_HUMAN	C9JB56_HUMAN	UPI0000251EDD	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCAGGAAGGT	.	2	ESCA
INO80B	0	.	GRCh37	2	74683272	74683272	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.413C>G	p.Ser138Ter	p.S138*	ENST00000233331	4/5	67	63	4	77	77	0	INO80B,stop_gained,p.Ser143Ter,ENST00000409493,;INO80B,stop_gained,p.Ser138Ter,ENST00000233331,;INO80B,stop_gained,p.Ser138Ter,ENST00000409917,;INO80B,splice_region_variant,,ENST00000431187,;WBP1,upstream_gene_variant,,ENST00000393972,;MOGS,downstream_gene_variant,,ENST00000233616,;WBP1,upstream_gene_variant,,ENST00000428943,;MOGS,downstream_gene_variant,,ENST00000452063,;WBP1,upstream_gene_variant,,ENST00000409737,;MOGS,downstream_gene_variant,,ENST00000409065,;WBP1,upstream_gene_variant,,ENST00000233615,;INO80B,non_coding_transcript_exon_variant,,ENST00000494986,;INO80B,non_coding_transcript_exon_variant,,ENST00000469849,;WBP1,upstream_gene_variant,,ENST00000474185,;WBP1,upstream_gene_variant,,ENST00000494741,;WBP1,upstream_gene_variant,,ENST00000464774,;WBP1,upstream_gene_variant,,ENST00000466835,;WBP1,upstream_gene_variant,,ENST00000470536,;INO80B,stop_gained,p.Ser138Ter,ENST00000452361,;INO80B,stop_gained,p.Ser138Ter,ENST00000441673,;INO80B,missense_variant,p.Gln95Glu,ENST00000455562,;INO80B,non_coding_transcript_exon_variant,,ENST00000473618,;INO80B,non_coding_transcript_exon_variant,,ENST00000471577,;WBP1,upstream_gene_variant,,ENST00000490120,;WBP1,upstream_gene_variant,,ENST00000492047,;WBP1,upstream_gene_variant,,ENST00000484744,;WBP1,upstream_gene_variant,,ENST00000473467,;MOGS,downstream_gene_variant,,ENST00000462189,;WBP1,upstream_gene_variant,,ENST00000466303,;	G	ENSG00000115274	ENST00000233331	Transcript	stop_gained	507	413	138	S/*	tCa/tGa	.	.	.	1	INO80B	HGNC	13324	protein_coding	YES	CCDS1942.2	ENSP00000233331	IN80B_HUMAN	B4DJ22_HUMAN	UPI0000456DE1	.	.	.	4/5	.	hmmpanther:PTHR21561:SF12,hmmpanther:PTHR21561	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTATCAGGAG	.	2	ESCA
FUNDC2P2	0	.	GRCh37	2	84518145	84518145	+	RNA	SNP	A	A	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.340A>C	.	.	ENST00000538499	1/1	92	79	13	97	97	0	FUNDC2P2,non_coding_transcript_exon_variant,,ENST00000331369,;FUNDC2P2,non_coding_transcript_exon_variant,,ENST00000538499,;FUNDC2P2,non_coding_transcript_exon_variant,,ENST00000443452,;	C	ENSG00000182814	ENST00000538499	Transcript	non_coding_transcript_exon_variant	340	.	.	.	.	.	.	.	1	FUNDC2P2	HGNC	17247	transcribed_processed_pseudogene	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGAAAGTTGG	.	4	ESCA
IGKV1-5	0	.	GRCh37	2	89247092	89247092	+	Missense_Mutation	SNP	C	C	T	rs373011628	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78G>A	p.Met26Ile	p.M26I	ENST00000496168	2/2	143	137	6	132	132	0	IGKV1-5,missense_variant,p.Met26Ile,ENST00000496168,;	T	ENSG00000243466	ENST00000496168	Transcript	missense_variant	259	78	26	M/I	atG/atA	rs373011628	.	.	-1	IGKV1-5	HGNC	5741	IG_V_gene	YES	.	ENSP00000420436	.	.	UPI0000140AA1	.	deleterious(0.02)	benign(0.176)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF122,hmmpanther:PTHR23267,Pfam_domain:PF07686,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0003	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGGTCATCTG	byCluster|by1000G	2	ESCA
SEMA4C	0	.	GRCh37	2	97530540	97530540	+	Silent	SNP	C	C	T	rs141614070	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864G>A	p.%3D	p.P288P	ENST00000305476	9/15	60	50	9	64	64	0	SEMA4C,synonymous_variant,p.%3D,ENST00000305476,;SEMA4C,downstream_gene_variant,,ENST00000442264,;SEMA4C,downstream_gene_variant,,ENST00000449330,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000482925,;SEMA4C,upstream_gene_variant,,ENST00000467747,;SEMA4C,upstream_gene_variant,,ENST00000474420,;	T	ENSG00000168758	ENST00000305476	Transcript	synonymous_variant	997	864	288	P	ccG/ccA	rs141614070	.	.	-1	SEMA4C	HGNC	10731	protein_coding	YES	CCDS2029.1	ENSP00000306844	SEM4C_HUMAN	Q8NBN9_HUMAN,Q6P5A5_HUMAN,Q53RE7_HUMAN,C9JV89_HUMAN,C9J4M7_HUMAN	UPI00001A7981	.	.	.	9/15	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF16,hmmpanther:PTHR11036,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCGGGGC	byCluster	5	ESCA
MGAT4A	0	.	GRCh37	2	99342758	99342758	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38C>T	p.Ala13Val	p.A13V	ENST00000264968	1/15	79	62	16	84	84	0	MGAT4A,missense_variant,p.Ala13Val,ENST00000393487,;MGAT4A,missense_variant,p.Ala13Val,ENST00000409391,;MGAT4A,missense_variant,p.Ala13Val,ENST00000264968,;MGAT4A,missense_variant,p.Ala13Val,ENST00000495056,;MGAT4A,non_coding_transcript_exon_variant,,ENST00000460768,;MGAT4A,non_coding_transcript_exon_variant,,ENST00000484936,;	A	ENSG00000071073	ENST00000264968	Transcript	missense_variant	402	38	13	A/V	gCa/gTa	.	.	.	-1	MGAT4A	HGNC	7047	protein_coding	YES	CCDS2036.1	ENSP00000264968	MGT4A_HUMAN	.	UPI000003F051	.	tolerated(0.99)	benign(0.001)	1/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12062:SF4,hmmpanther:PTHR12062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATGCTAAA	.	5	ESCA
PARP9	0	.	GRCh37	3	122255181	122255181	+	Silent	SNP	C	C	T	rs759283033	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2019G>A	p.%3D	p.K673K	ENST00000360356	10/11	71	65	6	63	63	0	PARP9,synonymous_variant,p.%3D,ENST00000477522,;PARP9,synonymous_variant,p.%3D,ENST00000462315,;PARP9,synonymous_variant,p.%3D,ENST00000471785,;PARP9,synonymous_variant,p.%3D,ENST00000492382,;PARP9,synonymous_variant,p.%3D,ENST00000360356,;PARP9,non_coding_transcript_exon_variant,,ENST00000489652,;	T	ENSG00000138496	ENST00000360356	Transcript	synonymous_variant	2247	2019	673	K	aaG/aaA	rs759283033	.	.	-1	PARP9	HGNC	24118	protein_coding	YES	CCDS3014.1	ENSP00000353512	PARP9_HUMAN	Q658Y0_HUMAN	UPI000013D133	.	.	.	10/11	.	PROSITE_profiles:PS51059,hmmpanther:PTHR14453:SF11,hmmpanther:PTHR14453,Gene3D:3.90.228.10,Superfamily_domains:SSF56399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTATCTTCTC	byFrequency	3	ESCA
AC083906.2	0	.	GRCh37	3	129813257	129813257	+	5'Flank	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000578837	.	132	125	6	109	109	0	AC083906.2,upstream_gene_variant,,ENST00000578837,;RP11-93K22.13,upstream_gene_variant,,ENST00000514010,;ALG1L2,non_coding_transcript_exon_variant,,ENST00000511726,;ALG1L2,non_coding_transcript_exon_variant,,ENST00000503500,;ALG1L2,non_coding_transcript_exon_variant,,ENST00000507643,;FAM86HP,downstream_gene_variant,,ENST00000511564,;ALG1L2,non_coding_transcript_exon_variant,,ENST00000506370,;ALG1L2,non_coding_transcript_exon_variant,,ENST00000425059,;FAM86HP,downstream_gene_variant,,ENST00000513466,;	G	ENSG00000266849	ENST00000578837	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1959	1	AC083906.2	Clone_based_ensembl_gene	.	miRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCTCTGAGG	.	2	ESCA
ACAD11	0	.	GRCh37	3	132277827	132277827	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2331A>G	p.%3D	p.T777T	ENST00000264990	20/20	79	66	13	84	84	0	ACAD11,synonymous_variant,p.%3D,ENST00000264990,;ACAD11,synonymous_variant,p.%3D,ENST00000545291,;ACAD11,synonymous_variant,p.%3D,ENST00000355458,;NPHP3,3_prime_UTR_variant,,ENST00000471702,;ACAD11,3_prime_UTR_variant,,ENST00000485198,;ACAD11,non_coding_transcript_exon_variant,,ENST00000496418,;ACAD11,non_coding_transcript_exon_variant,,ENST00000469042,;	C	ENSG00000240303	ENST00000264990	Transcript	synonymous_variant	3303	2331	777	T	acA/acG	.	.	.	-1	ACAD11	HGNC	30211	protein_coding	YES	CCDS3074.1	ENSP00000264990	ACD11_HUMAN	Q08AE9_HUMAN,B4DQ41_HUMAN	UPI00003671B7	.	.	.	20/20	.	hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF195	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGCTGTCAG	.	5	ESCA
CLCN2	0	.	GRCh37	3	184075806	184075806	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559G>C	p.Ala187Pro	p.A187P	ENST00000265593	5/24	18	8	9	33	33	0	CLCN2,missense_variant,p.Ala143Pro,ENST00000434054,;CLCN2,missense_variant,p.Ala187Pro,ENST00000265593,;CLCN2,missense_variant,p.Ala187Pro,ENST00000344937,;CLCN2,missense_variant,p.Ala187Pro,ENST00000457512,;CLCN2,5_prime_UTR_variant,,ENST00000423355,;EIF2B5,intron_variant,,ENST00000444495,;POLR2H,upstream_gene_variant,,ENST00000430783,;POLR2H,upstream_gene_variant,,ENST00000456318,;POLR2H,upstream_gene_variant,,ENST00000438240,;POLR2H,upstream_gene_variant,,ENST00000455712,;POLR2H,upstream_gene_variant,,ENST00000412877,;POLR2H,upstream_gene_variant,,ENST00000460083,;CLCN2,upstream_gene_variant,,ENST00000475279,;CLCN2,non_coding_transcript_exon_variant,,ENST00000465231,;CLCN2,non_coding_transcript_exon_variant,,ENST00000485667,;CLCN2,upstream_gene_variant,,ENST00000430397,;CLCN2,upstream_gene_variant,,ENST00000491162,;	G	ENSG00000114859	ENST00000265593	Transcript	missense_variant	731	559	187	A/P	Gct/Cct	.	.	.	-1	CLCN2	HGNC	2020	protein_coding	YES	CCDS3263.1	ENSP00000265593	CLCN2_HUMAN	.	UPI000013D645	.	deleterious(0)	probably_damaging(1)	5/24	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF64,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAGCTATAA	.	5	ESCA
ETV5	0	.	GRCh37	3	185766209	185766209	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*219C>G	.	.	ENST00000306376	13/13	37	33	4	25	25	0	ETV5,3_prime_UTR_variant,,ENST00000306376,;ETV5,3_prime_UTR_variant,,ENST00000434744,;ETV5,downstream_gene_variant,,ENST00000537818,;ETV5,downstream_gene_variant,,ENST00000480706,;ETV5,downstream_gene_variant,,ENST00000433149,;	C	ENSG00000244405	ENST00000306376	Transcript	3_prime_UTR_variant	1999	.	.	.	.	.	.	.	-1	ETV5	HGNC	3494	protein_coding	YES	CCDS33906.1	ENSP00000306894	ETV5_HUMAN	C9JMF0_HUMAN,C9J5A5_HUMAN,C9J0Z2_HUMAN	UPI000012A175	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAGGCACTG	.	4	ESCA
MUC4	0	.	GRCh37	3	195510076	195510076	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8375C>T	p.Ser2792Leu	p.S2792L	ENST00000463781	2/25	425	413	12	371	371	0	MUC4,missense_variant,p.Ser2792Leu,ENST00000463781,;MUC4,missense_variant,p.Ser2792Leu,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.Ser2792Leu,ENST00000470451,;MUC4,missense_variant,p.Ser2792Leu,ENST00000477086,;MUC4,missense_variant,p.Ser2792Leu,ENST00000466475,;MUC4,missense_variant,p.Ser2792Leu,ENST00000478156,;MUC4,missense_variant,p.Ser2792Leu,ENST00000479406,;MUC4,missense_variant,p.Ser2792Leu,ENST00000477756,;MUC4,missense_variant,p.Ser2792Leu,ENST00000462323,;MUC4,missense_variant,p.Ser2792Leu,ENST00000480843,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,;	A	ENSG00000145113	ENST00000463781	Transcript	missense_variant	8835	8375	2792	S/L	tCa/tTa	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	benign(0.044)	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCTGAGGAA	.	2	ESCA
TCTEX1D2	0	.	GRCh37	3	196044938	196044938	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86A>G	p.Tyr29Cys	p.Y29C	ENST00000325318	1/5	55	47	8	57	57	0	TCTEX1D2,missense_variant,p.Tyr29Cys,ENST00000325318,;TM4SF19,downstream_gene_variant,,ENST00000446879,;TM4SF19-AS1,upstream_gene_variant,,ENST00000444939,;TM4SF19-AS1,upstream_gene_variant,,ENST00000452051,;TM4SF19-AS1,upstream_gene_variant,,ENST00000420226,;RP11-447L10.1,missense_variant,p.Tyr29Cys,ENST00000431391,;TCTEX1D2,missense_variant,p.Tyr29Cys,ENST00000426563,;TCTEX1D2,missense_variant,p.Tyr29Cys,ENST00000446494,;TM4SF19,intron_variant,,ENST00000442633,;	C	ENSG00000213123	ENST00000325318	Transcript	missense_variant	222	86	29	Y/C	tAt/tGt	.	.	.	-1	TCTEX1D2	HGNC	28482	protein_coding	YES	CCDS33929.1	ENSP00000324323	TC1D2_HUMAN	E7ESA3_HUMAN	UPI000020AF09	.	deleterious(0)	probably_damaging(0.95)	1/5	.	hmmpanther:PTHR21255:SF7,hmmpanther:PTHR21255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATATAGGTG	.	5	ESCA
NKIRAS1	0	.	GRCh37	3	23942371	23942371	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264G>A	p.%3D	p.V88V	ENST00000443659	3/4	57	51	6	53	53	0	NKIRAS1,synonymous_variant,p.%3D,ENST00000443659,;NKIRAS1,synonymous_variant,p.%3D,ENST00000416026,;NKIRAS1,synonymous_variant,p.%3D,ENST00000425478,;NKIRAS1,synonymous_variant,p.%3D,ENST00000437230,;NKIRAS1,synonymous_variant,p.%3D,ENST00000388759,;NKIRAS1,synonymous_variant,p.%3D,ENST00000415901,;NKIRAS1,synonymous_variant,p.%3D,ENST00000412028,;NKIRAS1,synonymous_variant,p.%3D,ENST00000421515,;	T	ENSG00000197885	ENST00000443659	Transcript	synonymous_variant	1042	264	88	V	gtG/gtA	.	.	.	-1	NKIRAS1	HGNC	17899	protein_coding	YES	CCDS33717.1	ENSP00000393785	KBRS1_HUMAN	.	UPI000004A03F	.	.	.	3/4	.	Superfamily_domains:SSF52540,SMART_domains:SM00173,SMART_domains:SM00175,Gene3D:3.40.50.300,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF214,PROSITE_profiles:PS51419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTATTCACACT	.	4	ESCA
TRANK1	0	.	GRCh37	3	36900302	36900302	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1447C>G	p.Leu483Val	p.L483V	ENST00000429976	11/23	21	18	3	43	43	0	TRANK1,missense_variant,p.Leu483Val,ENST00000429976,;TRANK1,5_prime_UTR_variant,,ENST00000428977,;TRANK1,5_prime_UTR_variant,,ENST00000301807,;TRANK1,downstream_gene_variant,,ENST00000513141,;	C	ENSG00000168016	ENST00000429976	Transcript	missense_variant	1695	1447	483	L/V	Ctc/Gtc	.	.	.	-1	TRANK1	HGNC	29011	protein_coding	YES	CCDS46789.2	ENSP00000416168	TRNK1_HUMAN	B7WP88_HUMAN	UPI00017BE82B	.	deleterious(0.01)	benign(0.201)	11/23	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,Gene3D:1.25.40.20,hmmpanther:PTHR21529:SF5,hmmpanther:PTHR21529,PROSITE_profiles:PS50297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAAGAGAAGGA	.	4	ESCA
KLHL18	0	.	GRCh37	3	47387032	47387032	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1601C>G	.	.	ENST00000232766	10/10	32	26	5	35	35	0	KLHL18,3_prime_UTR_variant,,ENST00000232766,;KLHL18,downstream_gene_variant,,ENST00000455924,;KLHL18,downstream_gene_variant,,ENST00000442272,;	G	ENSG00000114648	ENST00000232766	Transcript	3_prime_UTR_variant	3346	.	.	.	.	.	.	.	1	KLHL18	HGNC	29120	protein_coding	YES	CCDS33749.1	ENSP00000232766	KLH18_HUMAN	Q6PJF0_HUMAN,C9J4G4_HUMAN,B4DHW4_HUMAN	UPI00004703A5	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTCAAAGA	.	5	ESCA
ARSJ	0	.	GRCh37	4	114823722	114823722	+	Missense_Mutation	SNP	T	T	C	rs780279615	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1508A>G	p.Tyr503Cys	p.Y503C	ENST00000315366	2/2	60	55	5	51	51	0	ARSJ,missense_variant,p.Tyr503Cys,ENST00000541197,;ARSJ,missense_variant,p.Tyr503Cys,ENST00000315366,;ARSJ,3_prime_UTR_variant,,ENST00000509829,;	C	ENSG00000180801	ENST00000315366	Transcript	missense_variant	2375	1508	503	Y/C	tAt/tGt	rs780279615	.	.	-1	ARSJ	HGNC	26286	protein_coding	YES	CCDS43264.1	ENSP00000320219	ARSJ_HUMAN	D6RGC1_HUMAN	UPI000003FD84	.	tolerated(0.16)	benign(0.306)	2/2	.	hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF69,Gene3D:3.30.1120.10,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTCATATGGG	.	3	ESCA
DCHS2	0	.	GRCh37	4	155226327	155226327	+	Missense_Mutation	SNP	C	C	G	rs759769096	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3952G>C	p.Glu1318Gln	p.E1318Q	ENST00000357232	16/25	33	28	5	28	28	0	DCHS2,missense_variant,p.Glu1318Gln,ENST00000357232,;	G	ENSG00000197410	ENST00000357232	Transcript	missense_variant	3952	3952	1318	E/Q	Gag/Cag	rs759769096,COSM1753600	.	.	-1	DCHS2	HGNC	23111	protein_coding	YES	CCDS3785.1	ENSP00000349768	PCD23_HUMAN	B3KT73_HUMAN	UPI000035B018	.	tolerated(0.43)	benign(0.02)	16/25	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF257,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TATCTCGAATA	byFrequency	3	ESCA
DCHS2	0	.	GRCh37	4	155298454	155298454	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377G>A	p.Arg126Lys	p.R126K	ENST00000357232	3/25	45	40	5	48	48	0	DCHS2,missense_variant,p.Arg732Lys,ENST00000339452,;DCHS2,missense_variant,p.Arg126Lys,ENST00000357232,;RP11-290O12.1,downstream_gene_variant,,ENST00000513721,;	T	ENSG00000197410	ENST00000357232	Transcript	missense_variant	377	377	126	R/K	aGg/aAg	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	YES	CCDS3785.1	ENSP00000349768	PCD23_HUMAN	B3KT73_HUMAN	UPI000035B018	.	tolerated(0.08)	probably_damaging(0.992)	3/25	.	PROSITE_profiles:PS50268,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCCCTGTCG	.	4	ESCA
NPY1R	0	.	GRCh37	4	164247644	164247644	+	Silent	SNP	C	C	T	rs761308479	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.63G>A	p.%3D	p.K21K	ENST00000296533	2/3	23	19	4	36	36	0	NPY1R,synonymous_variant,p.%3D,ENST00000511901,;NPY1R,synonymous_variant,p.%3D,ENST00000515701,;NPY1R,synonymous_variant,p.%3D,ENST00000504790,;NPY1R,synonymous_variant,p.%3D,ENST00000296533,;NPY1R,intron_variant,,ENST00000512819,;NPY1R,intron_variant,,ENST00000504391,;NPY1R,intron_variant,,ENST00000509586,;	T	ENSG00000164128	ENST00000296533	Transcript	synonymous_variant	595	63	21	K	aaG/aaA	rs761308479,COSM1052842	.	.	-1	NPY1R	HGNC	7956	protein_coding	YES	CCDS34089.1	ENSP00000354652	NPY1R_HUMAN	D6RI97_HUMAN,D6RHH6_HUMAN,D6REY0_HUMAN,D6RC44_HUMAN,D6R9D0_HUMAN,B4DKL9_HUMAN	UPI000002D509	.	.	.	2/3	.	Superfamily_domains:SSF81321,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF214	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCATTCTTCTC	.	3	ESCA
ZFP42	0	.	GRCh37	4	188924012	188924012	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51G>T	p.%3D	p.L17L	ENST00000326866	4/4	50	38	12	50	50	0	ZFP42,synonymous_variant,p.%3D,ENST00000326866,;ZFP42,synonymous_variant,p.%3D,ENST00000509524,;	T	ENSG00000179059	ENST00000326866	Transcript	synonymous_variant	459	51	17	L	ctG/ctT	.	.	.	1	ZFP42	HGNC	30949	protein_coding	YES	CCDS3849.1	ENSP00000317686	ZFP42_HUMAN	.	UPI0000049CA7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTGGGTGG	.	5	ESCA
KCTD8	0	.	GRCh37	4	44176944	44176944	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1285A>G	p.Lys429Glu	p.K429E	ENST00000360029	2/2	83	78	5	96	96	0	KCTD8,missense_variant,p.Lys429Glu,ENST00000360029,;KCTD8,downstream_gene_variant,,ENST00000515268,;	C	ENSG00000183783	ENST00000360029	Transcript	missense_variant	1569	1285	429	K/E	Aaa/Gaa	.	.	.	-1	KCTD8	HGNC	22394	protein_coding	YES	CCDS3467.1	ENSP00000353129	KCTD8_HUMAN	B4DQJ9_HUMAN	UPI00001C08D6	.	tolerated(0.3)	probably_damaging(0.956)	2/2	.	hmmpanther:PTHR14499:SF68,hmmpanther:PTHR14499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACTTTCTTTT	.	2	ESCA
CEP135	0	.	GRCh37	4	56837473	56837473	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1148G>C	p.Ser383Thr	p.S383T	ENST00000257287	10/26	39	28	11	45	45	0	CEP135,missense_variant,p.Ser383Thr,ENST00000257287,;CEP135,non_coding_transcript_exon_variant,,ENST00000506202,;CEP135,downstream_gene_variant,,ENST00000515081,;	C	ENSG00000174799	ENST00000257287	Transcript	missense_variant	1272	1148	383	S/T	aGt/aCt	.	.	.	1	CEP135	HGNC	29086	protein_coding	YES	CCDS33986.1	ENSP00000257287	CP135_HUMAN	.	UPI00003CE420	.	tolerated(0.41)	benign(0.006)	10/26	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGAGTGATG	.	5	ESCA
TECRL	0	.	GRCh37	4	65180404	65180404	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.513A>G	p.%3D	p.G171G	ENST00000381210	5/12	30	19	11	29	29	0	TECRL,synonymous_variant,p.%3D,ENST00000381210,;TECRL,synonymous_variant,p.%3D,ENST00000507440,;TECRL,non_coding_transcript_exon_variant,,ENST00000513125,;TECRL,non_coding_transcript_exon_variant,,ENST00000511356,;	C	ENSG00000205678	ENST00000381210	Transcript	synonymous_variant	624	513	171	G	ggA/ggG	.	.	.	-1	TECRL	HGNC	27365	protein_coding	YES	CCDS33990.1	ENSP00000370607	TECRL_HUMAN	D6RBZ3_HUMAN	UPI0000141A54	.	.	.	5/12	.	hmmpanther:PTHR10556,hmmpanther:PTHR10556:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTTCCATC	.	5	ESCA
NAA11	0	.	GRCh37	4	80247136	80247136	+	5'UTR	SNP	A	A	C	rs376132373	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-105T>G	.	.	ENST00000286794	1/2	25	21	4	38	38	0	NAA11,5_prime_UTR_variant,,ENST00000286794,;NAA11,upstream_gene_variant,,ENST00000513733,;NAA11,upstream_gene_variant,,ENST00000511542,;	C	ENSG00000156269	ENST00000286794	Transcript	5_prime_UTR_variant	69	.	.	.	.	rs376132373	.	.	-1	NAA11	HGNC	28125	protein_coding	YES	CCDS47084.1	ENSP00000286794	NAA11_HUMAN	H0Y8T0_HUMAN	UPI00000467CA	.	.	.	1/2	.	.	C:0.0004	C:0	C:0	.	C:0.002	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTAACACCA	byFrequency|byCluster|by1000G	4	ESCA
CCT5	0	.	GRCh37	5	10254857	10254857	+	Missense_Mutation	SNP	A	A	G	rs779876496	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.238A>G	p.Met80Val	p.M80V	ENST00000280326	3/11	70	46	23	87	87	0	CCT5,missense_variant,p.Met80Val,ENST00000280326,;CCT5,missense_variant,p.Met59Val,ENST00000503026,;CCT5,missense_variant,p.Met42Val,ENST00000515676,;CCT5,intron_variant,,ENST00000506600,;CCT5,intron_variant,,ENST00000515390,;FAM173B,upstream_gene_variant,,ENST00000511437,;FAM173B,upstream_gene_variant,,ENST00000280330,;FAM173B,upstream_gene_variant,,ENST00000510047,;CTD-2256P15.1,downstream_gene_variant,,ENST00000509915,;FAM173B,upstream_gene_variant,,ENST00000510052,;CCT5,non_coding_transcript_exon_variant,,ENST00000508451,;CCT5,intron_variant,,ENST00000423695,;CCT5,intron_variant,,ENST00000512975,;CCT5,intron_variant,,ENST00000503454,;CCT5,intron_variant,,ENST00000511700,;FAM173B,upstream_gene_variant,,ENST00000506108,;CCT5,upstream_gene_variant,,ENST00000509846,;CCT5,upstream_gene_variant,,ENST00000514674,;FAM173B,upstream_gene_variant,,ENST00000504390,;CCT5,downstream_gene_variant,,ENST00000510326,;FAM173B,upstream_gene_variant,,ENST00000508553,;	G	ENSG00000150753	ENST00000280326	Transcript	missense_variant	658	238	80	M/V	Atg/Gtg	rs779876496	.	.	1	CCT5	HGNC	1618	protein_coding	YES	CCDS3877.1	ENSP00000280326	TCPE_HUMAN	Q9HB74_HUMAN,Q9BU08_HUMAN,Q96GI1_HUMAN,B7ZAR1_HUMAN	UPI0000001C34	.	deleterious(0.03)	benign(0.007)	3/11	.	hmmpanther:PTHR11353,PROSITE_patterns:PS00751,Pfam_domain:PF00118,TIGRFAM_domain:TIGR02343,Gene3D:1.10.560.10,Superfamily_domains:SSF48592,Prints_domain:PR00304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGCATGATG	byFrequency	5	ESCA
PRRC1	0	.	GRCh37	5	126860507	126860507	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388A>G	p.Ile130Val	p.I130V	ENST00000296666	3/9	90	80	9	93	93	0	PRRC1,missense_variant,p.Ile130Val,ENST00000442138,;PRRC1,missense_variant,p.Ile130Val,ENST00000296666,;PRRC1,missense_variant,p.Ile130Val,ENST00000512635,;PRRC1,downstream_gene_variant,,ENST00000507774,;PRRC1,downstream_gene_variant,,ENST00000512871,;	G	ENSG00000164244	ENST00000296666	Transcript	missense_variant	576	388	130	I/V	Ata/Gta	.	.	.	1	PRRC1	HGNC	28164	protein_coding	YES	CCDS4143.1	ENSP00000296666	PRRC1_HUMAN	.	UPI0000073C8E	.	tolerated_low_confidence(0.56)	benign(0.004)	3/9	.	hmmpanther:PTHR23276,hmmpanther:PTHR23276:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCTATATCA	.	4	ESCA
PCDHB10	0	.	GRCh37	5	140574310	140574310	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2185G>C	p.Val729Leu	p.V729L	ENST00000239446	1/1	84	76	8	121	121	0	PCDHB10,missense_variant,p.Val729Leu,ENST00000239446,;PCDHB11,upstream_gene_variant,,ENST00000536699,;PCDHB9,downstream_gene_variant,,ENST00000316105,;	C	ENSG00000120324	ENST00000239446	Transcript	missense_variant	2369	2185	729	V/L	Gtg/Ctg	COSM736015	.	.	1	PCDHB10	HGNC	8681	protein_coding	YES	CCDS4252.1	ENSP00000239446	PCDBA_HUMAN	O95883_HUMAN	UPI0000048F2E	.	tolerated_low_confidence(0.05)	benign(0.022)	1/1	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF54	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTCGGTGCCC	.	3	ESCA
ANKH	0	.	GRCh37	5	14709981	14709981	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1325T>G	.	.	ENST00000284268	12/12	21	16	5	21	21	0	ANKH,3_prime_UTR_variant,,ENST00000284268,;ANKH,intron_variant,,ENST00000535119,;ANKH,downstream_gene_variant,,ENST00000502585,;	C	ENSG00000154122	ENST00000284268	Transcript	3_prime_UTR_variant	3135	.	.	.	.	.	.	.	-1	ANKH	HGNC	15492	protein_coding	YES	CCDS3885.1	ENSP00000284268	ANKH_HUMAN	B3KMG4_HUMAN	UPI000003F535	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCCTAAAATAA	.	2	ESCA
SCGB3A2	0	.	GRCh37	5	147258323	147258323	+	5'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-44T>A	.	.	ENST00000296694	1/3	40	33	7	66	66	0	SCGB3A2,5_prime_UTR_variant,,ENST00000296694,;SCGB3A2,intron_variant,,ENST00000504320,;SCGB3A2,intron_variant,,ENST00000514688,;SCGB3A2,intron_variant,,ENST00000507160,;C5orf46,downstream_gene_variant,,ENST00000510432,;	A	ENSG00000164265	ENST00000296694	Transcript	5_prime_UTR_variant	50	.	.	.	.	.	.	.	1	SCGB3A2	HGNC	18391	protein_coding	YES	CCDS4287.1	ENSP00000296694	SG3A2_HUMAN	Q2L6B3_HUMAN,D6RBX5_HUMAN	UPI0000001278	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATTTTTCT	.	5	ESCA
ITK	0	.	GRCh37	5	156671337	156671337	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1298T>G	p.Leu433Arg	p.L433R	ENST00000422843	13/17	38	31	7	59	59	0	ITK,missense_variant,p.Leu433Arg,ENST00000422843,;ITK,non_coding_transcript_exon_variant,,ENST00000519749,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,downstream_gene_variant,,ENST00000520173,;ITK,upstream_gene_variant,,ENST00000523926,;ITK,downstream_gene_variant,,ENST00000519759,;	G	ENSG00000113263	ENST00000422843	Transcript	missense_variant	1450	1298	433	L/R	cTg/cGg	.	.	.	1	ITK	HGNC	6171	protein_coding	YES	CCDS4336.1	ENSP00000398655	ITK_HUMAN	Q7Z318_HUMAN,E5RFR5_HUMAN	UPI000004CADA	.	deleterious(0)	probably_damaging(0.996)	13/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCTGGTGT	.	5	ESCA
CDH10	0	.	GRCh37	5	24537678	24537678	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337G>A	p.Ala113Thr	p.A113T	ENST00000264463	3/12	66	56	9	78	78	0	CDH10,missense_variant,p.Ala113Thr,ENST00000264463,;CDH10,missense_variant,p.Ala113Thr,ENST00000510477,;	T	ENSG00000040731	ENST00000264463	Transcript	missense_variant	845	337	113	A/T	Gcc/Acc	.	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	deleterious(0.01)	probably_damaging(0.992)	3/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.H112Y|c.334C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TGTGGCATGAA	.	4	ESCA
BCLAF1	0	.	GRCh37	6	136597032	136597032	+	Missense_Mutation	SNP	C	C	T	rs368236501	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1631G>A	p.Arg544His	p.R544H	ENST00000531224	5/13	185	177	7	181	181	0	BCLAF1,missense_variant,p.Arg544His,ENST00000529826,;BCLAF1,missense_variant,p.Arg544His,ENST00000527536,;BCLAF1,missense_variant,p.Arg542His,ENST00000392348,;BCLAF1,missense_variant,p.Arg371His,ENST00000530767,;BCLAF1,missense_variant,p.Arg544His,ENST00000531224,;BCLAF1,missense_variant,p.Arg542His,ENST00000353331,;BCLAF1,missense_variant,p.Arg542His,ENST00000527759,;BCLAF1,missense_variant,p.Arg544His,ENST00000527613,;BCLAF1,missense_variant,p.Arg369His,ENST00000534269,;BCLAF1,missense_variant,p.Arg542His,ENST00000530429,;BCLAF1,missense_variant,p.Arg544His,ENST00000532384,;BCLAF1,3_prime_UTR_variant,,ENST00000533621,;BCLAF1,upstream_gene_variant,,ENST00000476194,;BCLAF1,upstream_gene_variant,,ENST00000532076,;BCLAF1,upstream_gene_variant,,ENST00000534792,;BCLAF1,downstream_gene_variant,,ENST00000528229,;	T	ENSG00000029363	ENST00000531224	Transcript	missense_variant	1884	1631	544	R/H	cGt/cAt	rs368236501,COSM739980	.	.	-1	BCLAF1	HGNC	16863	protein_coding	YES	CCDS5177.1	ENSP00000435210	BCLF1_HUMAN	B0AZU3_HUMAN	UPI000006FCE7	.	tolerated(0.09)	possibly_damaging(0.715)	5/13	.	Pfam_domain:PF15440,hmmpanther:PTHR15268,hmmpanther:PTHR15268:SF4	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGACGGTGA	byFrequency|byCluster	2	ESCA
ECT2L	0	.	GRCh37	6	139170415	139170415	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.913G>A	p.Glu305Lys	p.E305K	ENST00000423192	8/21	62	57	4	71	71	0	ECT2L,missense_variant,p.Glu305Lys,ENST00000367682,;ECT2L,missense_variant,p.Glu236Lys,ENST00000541398,;ECT2L,missense_variant,p.Glu305Lys,ENST00000423192,;ECT2L,upstream_gene_variant,,ENST00000495970,;	A	ENSG00000203734	ENST00000423192	Transcript	missense_variant	1074	913	305	E/K	Gag/Aag	.	.	.	1	ECT2L	HGNC	21118	protein_coding	YES	CCDS43508.1	ENSP00000387388	ECT2L_HUMAN	B7ZBI6_HUMAN	UPI0000E86804	.	tolerated(0.08)	benign(0.034)	8/21	.	hmmpanther:PTHR12673:SF70,hmmpanther:PTHR12673	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGATGGAGAGT	.	2	ESCA
RNF39	0	.	GRCh37	6	30038738	30038738	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*150A>T	.	.	ENST00000244360	4/4	91	62	28	91	91	0	RNF39,3_prime_UTR_variant,,ENST00000376751,;RNF39,3_prime_UTR_variant,,ENST00000244360,;PPP1R11,downstream_gene_variant,,ENST00000376769,;PPP1R11,downstream_gene_variant,,ENST00000376763,;PPP1R11,downstream_gene_variant,,ENST00000376772,;PPP1R11,downstream_gene_variant,,ENST00000376765,;PPP1R11,downstream_gene_variant,,ENST00000376773,;PPP1R11,downstream_gene_variant,,ENST00000376758,;	A	ENSG00000204618	ENST00000244360	Transcript	3_prime_UTR_variant	1511	.	.	.	.	.	.	.	-1	RNF39	HGNC	18064	protein_coding	YES	CCDS4673.1	ENSP00000244360	RNF39_HUMAN	Q96QB5_HUMAN	UPI000000D735	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGGTCTCAT	.	5	ESCA
MUC21	0	.	GRCh37	6	30955265	30955265	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1313C>G	p.Ser438Cys	p.S438C	ENST00000376296	2/3	76	69	7	97	97	0	MUC21,missense_variant,p.Ser438Cys,ENST00000376296,;MUC21,5_prime_UTR_variant,,ENST00000486149,;	G	ENSG00000204544	ENST00000376296	Transcript	missense_variant	1554	1313	438	S/C	tCt/tGt	COSM3624463	.	.	1	MUC21	HGNC	21661	protein_coding	YES	CCDS34388.1	ENSP00000365473	MUC21_HUMAN	.	UPI000047030C	.	deleterious(0.01)	unknown(0)	2/3	.	Low_complexity_(Seg):seg,Pfam_domain:PF05647	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CAACTCTGGGT	.	2	ESCA
SAPCD1	0	.	GRCh37	6	31731219	31731219	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142G>A	p.Glu48Lys	p.E48K	ENST00000415669	2/5	60	56	4	64	64	0	SAPCD1,missense_variant,p.Glu48Lys,ENST00000415669,;SAPCD1,missense_variant,p.Glu48Lys,ENST00000433778,;SAPCD1,missense_variant,p.Glu48Lys,ENST00000425424,;MSH5,3_prime_UTR_variant,,ENST00000534153,;MSH5,downstream_gene_variant,,ENST00000395853,;VWA7,downstream_gene_variant,,ENST00000375686,;MSH5,downstream_gene_variant,,ENST00000375740,;MSH5,downstream_gene_variant,,ENST00000375755,;MSH5,downstream_gene_variant,,ENST00000375750,;VWA7,downstream_gene_variant,,ENST00000447450,;MSH5,downstream_gene_variant,,ENST00000375742,;MSH5,downstream_gene_variant,,ENST00000375703,;MSH5,downstream_gene_variant,,ENST00000431848,;MSH5,downstream_gene_variant,,ENST00000429846,;VWA7,downstream_gene_variant,,ENST00000375688,;MSH5,downstream_gene_variant,,ENST00000450148,;SAPCD1-AS1,downstream_gene_variant,,ENST00000419679,;VWA7,downstream_gene_variant,,ENST00000467576,;MSH5,downstream_gene_variant,,ENST00000468602,;MSH5-SAPCD1,downstream_gene_variant,,ENST00000491552,;MSH5-SAPCD1,3_prime_UTR_variant,,ENST00000476085,;MSH5-SAPCD1,3_prime_UTR_variant,,ENST00000498473,;MSH5-SAPCD1,3_prime_UTR_variant,,ENST00000493662,;MSH5,downstream_gene_variant,,ENST00000494646,;VWA7,downstream_gene_variant,,ENST00000486423,;MSH5,downstream_gene_variant,,ENST00000467319,;MSH5,downstream_gene_variant,,ENST00000423982,;MSH5,downstream_gene_variant,,ENST00000463144,;MSH5,downstream_gene_variant,,ENST00000468136,;SAPCD1,upstream_gene_variant,,ENST00000494299,;MSH5,downstream_gene_variant,,ENST00000484309,;MSH5,downstream_gene_variant,,ENST00000494458,;	A	ENSG00000228727	ENST00000415669	Transcript	missense_variant	201	142	48	E/K	Gaa/Aaa	.	.	.	1	SAPCD1	HGNC	13938	protein_coding	YES	CCDS34411.1	ENSP00000411948	SAPC1_HUMAN	F6XBR9_HUMAN	UPI000020D95B	.	deleterious(0.02)	benign(0.187)	2/5	.	hmmpanther:PTHR14907:SF4,hmmpanther:PTHR14907,Pfam_domain:PF11414	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGAGAACAG	.	2	ESCA
CFB	0	.	GRCh37	6	31914956	31914956	+	Silent	SNP	C	C	A	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1977C>A	p.%3D	p.I659I	ENST00000456570	15/30	19	16	3	39	39	0	CFB,synonymous_variant,p.%3D,ENST00000456570,;CFB,synonymous_variant,p.%3D,ENST00000477310,;CFB,synonymous_variant,p.%3D,ENST00000556679,;CFB,synonymous_variant,p.%3D,ENST00000425368,;CFB,upstream_gene_variant,,ENST00000483004,;C2,downstream_gene_variant,,ENST00000469372,;CFB,upstream_gene_variant,,ENST00000498317,;C2,downstream_gene_variant,,ENST00000442278,;C2,downstream_gene_variant,,ENST00000299367,;NELFE,downstream_gene_variant,,ENST00000375429,;C2,downstream_gene_variant,,ENST00000497706,;C2,downstream_gene_variant,,ENST00000383177,;C2,downstream_gene_variant,,ENST00000452323,;CFB,downstream_gene_variant,,ENST00000475617,;CFB,upstream_gene_variant,,ENST00000497841,;C2,downstream_gene_variant,,ENST00000468407,;CFB,3_prime_UTR_variant,,ENST00000460718,;CFB,non_coding_transcript_exon_variant,,ENST00000452035,;C2,downstream_gene_variant,,ENST00000486124,;CFB,upstream_gene_variant,,ENST00000482312,;CFB,upstream_gene_variant,,ENST00000465750,;CFB,downstream_gene_variant,,ENST00000472581,;CFB,upstream_gene_variant,,ENST00000482886,;C2,downstream_gene_variant,,ENST00000482060,;CFB,upstream_gene_variant,,ENST00000467360,;CFB,upstream_gene_variant,,ENST00000467150,;CFB,upstream_gene_variant,,ENST00000461483,;C2,downstream_gene_variant,,ENST00000485690,;	A	ENSG00000244255	ENST00000456570	Transcript	synonymous_variant	2032	1977	659	I	atC/atA	COSM4006374	.	.	1	CFB	Uniprot_gn	1037	protein_coding	YES	.	ENSP00000410815	.	B4E1Z4_HUMAN	UPI00017A8869	.	.	.	15/30	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF346,hmmpanther:PTHR19325,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGATCTGTGA	.	2	ESCA
ITPR3	0	.	GRCh37	6	33653186	33653186	+	Silent	SNP	C	C	T	rs747022423	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5358C>T	p.%3D	p.F1786F	ENST00000374316	41/59	44	39	5	47	47	0	ITPR3,synonymous_variant,p.%3D,ENST00000374316,;ITPR3,synonymous_variant,p.%3D,ENST00000605930,;	T	ENSG00000096433	ENST00000374316	Transcript	synonymous_variant	6418	5358	1786	F	ttC/ttT	rs747022423	.	.	1	ITPR3	HGNC	6182	protein_coding	YES	CCDS4783.1	ENSP00000363435	ITPR3_HUMAN	A6H8K3_HUMAN	UPI000013CB74	.	.	.	41/59	.	hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCTTCAAGGT	.	3	ESCA
RPL10A	0	.	GRCh37	6	35437953	35437953	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311-3C>A	.	.	ENST00000322203	.	43	35	8	47	47	0	RPL10A,splice_region_variant,,ENST00000322203,;TEAD3,downstream_gene_variant,,ENST00000402886,;TEAD3,downstream_gene_variant,,ENST00000338863,;FANCE,downstream_gene_variant,,ENST00000229769,;RPL10A,splice_region_variant,,ENST00000464112,;RPL10A,splice_region_variant,,ENST00000490335,;RPL10A,splice_region_variant,,ENST00000478340,;RPL10A,splice_region_variant,,ENST00000467020,;	A	ENSG00000198755	ENST00000322203	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	RPL10A	HGNC	10299	protein_coding	YES	CCDS4806.1	ENSP00000363018	RL10A_HUMAN	.	UPI0000025FC8	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	TCTATCAGCCA	.	3	ESCA
BRPF3	0	.	GRCh37	6	36198407	36198407	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*21C>T	.	.	ENST00000357641	13/13	62	58	4	82	82	0	BRPF3,3_prime_UTR_variant,,ENST00000443324,;BRPF3,3_prime_UTR_variant,,ENST00000357641,;BRPF3,3_prime_UTR_variant,,ENST00000534694,;BRPF3,3_prime_UTR_variant,,ENST00000543502,;BRPF3,3_prime_UTR_variant,,ENST00000339717,;BRPF3,3_prime_UTR_variant,,ENST00000534400,;BRPF3,3_prime_UTR_variant,,ENST00000441123,;BRPF3,3_prime_UTR_variant,,ENST00000441730,;BRPF3,3_prime_UTR_variant,,ENST00000449261,;BRPF3,3_prime_UTR_variant,,ENST00000532330,;	T	ENSG00000096070	ENST00000357641	Transcript	3_prime_UTR_variant	3892	.	.	.	.	.	.	.	1	BRPF3	HGNC	14256	protein_coding	YES	CCDS34437.1	ENSP00000350267	BRPF3_HUMAN	A8WI62_HUMAN,A8WI61_HUMAN	UPI00001C1E4C	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCATCCGCTT	.	2	ESCA
C6orf201	0	.	GRCh37	6	4115751	4115751	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285-6432C>T	.	.	ENST00000380175	.	41	37	4	45	45	0	C6orf201,intron_variant,,ENST00000333388,;C6orf201,intron_variant,,ENST00000380175,;C6orf201,intron_variant,,ENST00000430835,;ECI2,downstream_gene_variant,,ENST00000380118,;ECI2,downstream_gene_variant,,ENST00000380125,;ECI2,downstream_gene_variant,,ENST00000465828,;ECI2,downstream_gene_variant,,ENST00000413766,;ECI2,downstream_gene_variant,,ENST00000361538,;C6orf201,non_coding_transcript_exon_variant,,ENST00000360378,;C6orf201,3_prime_UTR_variant,,ENST00000436110,;C6orf201,intron_variant,,ENST00000451679,;C6orf201,intron_variant,,ENST00000427996,;ECI2,downstream_gene_variant,,ENST00000380120,;ECI2,downstream_gene_variant,,ENST00000464583,;ECI2,downstream_gene_variant,,ENST00000478266,;ECI2,downstream_gene_variant,,ENST00000464057,;ECI2,downstream_gene_variant,,ENST00000496241,;	T	ENSG00000185689	ENST00000380175	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C6orf201	HGNC	21620	protein_coding	YES	CCDS43419.1	ENSP00000420610	CF201_HUMAN	.	UPI00004573AE	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAATTCAGTCA	.	2	ESCA
DST	0	.	GRCh37	6	56426280	56426280	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6267C>G	p.%3D	p.L2089L	ENST00000244364	38/84	103	98	5	75	75	0	DST,synonymous_variant,p.%3D,ENST00000446842,;DST,synonymous_variant,p.%3D,ENST00000370788,;DST,synonymous_variant,p.%3D,ENST00000244364,;DST,synonymous_variant,p.%3D,ENST00000370754,;DST,synonymous_variant,p.%3D,ENST00000361203,;DST,synonymous_variant,p.%3D,ENST00000370769,;DST,synonymous_variant,p.%3D,ENST00000421834,;DST,3_prime_UTR_variant,,ENST00000312431,;DST,upstream_gene_variant,,ENST00000520144,;	C	ENSG00000151914	ENST00000244364	Transcript	synonymous_variant	6475	6267	2089	L	ctC/ctG	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	38/84	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF38,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTTGAGTAA	.	2	ESCA
EPHA7	0	.	GRCh37	6	93951484	93951484	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1660T>G	.	.	ENST00000369303	17/17	36	31	5	37	37	0	EPHA7,3_prime_UTR_variant,,ENST00000369303,;	C	ENSG00000135333	ENST00000369303	Transcript	3_prime_UTR_variant	4842	.	.	.	.	.	.	.	-1	EPHA7	HGNC	3390	protein_coding	YES	CCDS5031.1	ENSP00000358309	EPHA7_HUMAN	.	UPI0000044771	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAGAAAAATA	.	5	ESCA
RELN	0	.	GRCh37	7	103151393	103151393	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8179G>A	p.Asp2727Asn	p.D2727N	ENST00000428762	51/65	62	57	5	54	54	0	RELN,missense_variant,p.Asp2727Asn,ENST00000424685,;RELN,missense_variant,p.Asp2727Asn,ENST00000428762,;RELN,missense_variant,p.Asp2727Asn,ENST00000343529,;CTB-107G13.1,intron_variant,,ENST00000422488,;	T	ENSG00000189056	ENST00000428762	Transcript	missense_variant	8339	8179	2727	D/N	Gat/Aat	.	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	tolerated(0.25)	probably_damaging(0.985)	51/65	.	hmmpanther:PTHR11841,Gene3D:2.130.10.140,Superfamily_domains:SSF50939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ACCATCAGGGG	.	2	ESCA
BCAP29	0	.	GRCh37	7	107258830	107258830	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827A>G	p.Asn276Ser	p.N276S	ENST00000379119	8/8	69	34	35	51	51	0	BCAP29,missense_variant,p.Asn276Ser,ENST00000445771,;BCAP29,missense_variant,p.Asn276Ser,ENST00000379119,;BCAP29,3_prime_UTR_variant,,ENST00000465919,;BCAP29,3_prime_UTR_variant,,ENST00000005259,;BCAP29,3_prime_UTR_variant,,ENST00000379117,;BCAP29,intron_variant,,ENST00000491150,;BCAP29,downstream_gene_variant,,ENST00000379121,;BCAP29,downstream_gene_variant,,ENST00000436699,;BCAP29,downstream_gene_variant,,ENST00000457837,;BCAP29,non_coding_transcript_exon_variant,,ENST00000494086,;BCAP29,intron_variant,,ENST00000482371,;BCAP29,downstream_gene_variant,,ENST00000442065,;	G	ENSG00000075790	ENST00000379119	Transcript	missense_variant	841	827	276	N/S	aAt/aGt	.	.	.	1	BCAP29	HGNC	24131	protein_coding	YES	CCDS34730.1	ENSP00000368414	BAP29_HUMAN	C9JTE9_HUMAN,C9JP06_HUMAN,C9JGJ9_HUMAN,C9IYK6_HUMAN	UPI000049A621	.	deleterious_low_confidence(0.04)	benign(0.005)	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAATATAC	.	5	ESCA
LRRN3	0	.	GRCh37	7	110764419	110764419	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1591G>C	p.Asp531His	p.D531H	ENST00000451085	4/4	40	35	4	32	32	0	LRRN3,missense_variant,p.Asp531His,ENST00000422987,;LRRN3,missense_variant,p.Asp531His,ENST00000308478,;LRRN3,missense_variant,p.Asp531His,ENST00000451085,;IMMP2L,intron_variant,,ENST00000450877,;IMMP2L,intron_variant,,ENST00000437687,;IMMP2L,intron_variant,,ENST00000415362,;IMMP2L,intron_variant,,ENST00000452895,;IMMP2L,intron_variant,,ENST00000405709,;IMMP2L,intron_variant,,ENST00000447215,;IMMP2L,intron_variant,,ENST00000331762,;LRRN3,downstream_gene_variant,,ENST00000421101,;IMMP2L,intron_variant,,ENST00000489381,;	C	ENSG00000173114	ENST00000451085	Transcript	missense_variant	2637	1591	531	D/H	Gat/Cat	COSM124218	.	.	1	LRRN3	HGNC	17200	protein_coding	YES	CCDS5754.1	ENSP00000397312	LRRN3_HUMAN	A4D0T1_HUMAN,E7EW58_HUMAN	UPI0000037517	.	tolerated(0.09)	possibly_damaging(0.83)	4/4	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF7,Pfam_domain:PF00041,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAGAGATATT	.	4	ESCA
CPED1	0	.	GRCh37	7	120906460	120906460	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2490G>A	p.%3D	p.L830L	ENST00000310396	19/23	52	48	4	75	75	0	CPED1,synonymous_variant,p.%3D,ENST00000310396,;CPED1,downstream_gene_variant,,ENST00000423795,;CPED1,downstream_gene_variant,,ENST00000450913,;CPED1,downstream_gene_variant,,ENST00000466055,;	A	ENSG00000106034	ENST00000310396	Transcript	synonymous_variant	2957	2490	830	L	ttG/ttA	.	.	.	1	CPED1	HGNC	26159	protein_coding	YES	CCDS34739.1	ENSP00000309772	CPED1_HUMAN	Q75MM9_HUMAN,E9PCC8_HUMAN,E7ENG7_HUMAN	UPI000013C813	.	.	.	19/23	.	hmmpanther:PTHR14776,Pfam_domain:PF13839	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCATTGAGACC	.	2	ESCA
OR6B1	0	.	GRCh37	7	143701769	143701769	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000408922	1/1	50	35	15	59	59	0	OR6B1,missense_variant,p.Cys227Tyr,ENST00000408922,;	A	ENSG00000221813	ENST00000408922	Transcript	missense_variant	748	680	227	C/Y	tGc/tAc	.	.	.	1	OR6B1	HGNC	8354	protein_coding	YES	CCDS43667.1	ENSP00000386151	OR6B1_HUMAN	.	UPI0000041B18	.	deleterious(0)	benign(0.005)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF174,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTATGCATGC	.	5	ESCA
C1GALT1	0	.	GRCh37	7	7278131	7278131	+	Missense_Mutation	SNP	G	G	C	rs773916621	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.466G>C	p.Glu156Gln	p.E156Q	ENST00000436587	3/4	39	35	4	49	49	0	C1GALT1,missense_variant,p.Glu156Gln,ENST00000436587,;C1GALT1,missense_variant,p.Glu156Gln,ENST00000402468,;C1GALT1,missense_variant,p.Glu156Gln,ENST00000223122,;C1GALT1,downstream_gene_variant,,ENST00000429911,;C1GALT1,downstream_gene_variant,,ENST00000419721,;C1GALT1,downstream_gene_variant,,ENST00000476068,;	C	ENSG00000106392	ENST00000436587	Transcript	missense_variant	689	466	156	E/Q	Gaa/Caa	rs773916621	.	.	1	C1GALT1	HGNC	24337	protein_coding	YES	CCDS5355.1	ENSP00000389176	C1GLT_HUMAN	C9K0C8_HUMAN,C9JDX1_HUMAN	UPI000003DC31	.	tolerated(0.64)	benign(0.039)	3/4	.	hmmpanther:PTHR23033:SF13,hmmpanther:PTHR23033,Pfam_domain:PF02434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCATGAACAT	.	3	ESCA
COL28A1	0	.	GRCh37	7	7572463	7572463	+	Missense_Mutation	SNP	G	G	A	rs756091636	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44C>T	p.Ala15Val	p.A15V	ENST00000399429	2/35	18	14	4	12	12	0	COL28A1,missense_variant,p.Ala15Val,ENST00000399429,;	A	ENSG00000215018	ENST00000399429	Transcript	missense_variant	185	44	15	A/V	gCg/gTg	rs756091636,COSM362523,COSM1091815	.	.	-1	COL28A1	HGNC	22442	protein_coding	YES	CCDS43553.1	ENSP00000382356	COSA1_HUMAN	H7C3P2_HUMAN,H7BZU0_HUMAN	UPI000155D64E	.	tolerated(0.6)	benign(0.002)	2/35	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAACGCTGAC	byFrequency	5	ESCA
RP1L1	0	.	GRCh37	8	10469643	10469643	+	Silent	SNP	G	G	T	rs769633776	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1965C>A	p.%3D	p.G655G	ENST00000382483	4/4	22	18	4	37	37	0	RP1L1,synonymous_variant,p.%3D,ENST00000382483,;	T	ENSG00000183638	ENST00000382483	Transcript	synonymous_variant	2189	1965	655	G	ggC/ggA	rs769633776	.	.	-1	RP1L1	HGNC	15946	protein_coding	YES	CCDS43708.1	ENSP00000371923	.	A6NKC6_HUMAN	UPI00001AF9CC	.	.	.	4/4	.	hmmpanther:PTHR23005:SF3,hmmpanther:PTHR23005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE	CCAAGGCCAGG	.	2	ESCA
ZFPM2	0	.	GRCh37	8	106816123	106816123	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*357G>A	.	.	ENST00000407775	8/8	75	65	10	72	72	0	ZFPM2,3_prime_UTR_variant,,ENST00000407775,;ZFPM2,downstream_gene_variant,,ENST00000517361,;ZFPM2,downstream_gene_variant,,ENST00000378472,;ZFPM2,downstream_gene_variant,,ENST00000520492,;RP11-152P17.2,intron_variant,,ENST00000524045,;RP11-152P17.2,intron_variant,,ENST00000509144,;RP11-152P17.2,intron_variant,,ENST00000521622,;RP11-152P17.2,intron_variant,,ENST00000520594,;RP11-152P17.2,intron_variant,,ENST00000520433,;RP11-152P17.2,intron_variant,,ENST00000518932,;ZFPM2,downstream_gene_variant,,ENST00000522296,;RP11-152P17.2,intron_variant,,ENST00000520078,;	A	ENSG00000169946	ENST00000407775	Transcript	3_prime_UTR_variant	4063	.	.	.	.	.	.	.	1	ZFPM2	HGNC	16700	protein_coding	YES	CCDS47908.1	ENSP00000384179	FOG2_HUMAN	Q9NPQ0_HUMAN,F5H542_HUMAN,E7ET52_HUMAN,E5RJX0_HUMAN	UPI000057A0B4	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGCATTT	.	5	ESCA
CSMD3	0	.	GRCh37	8	113326823	113326823	+	Missense_Mutation	SNP	G	G	A	rs199998952	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7384C>T	p.Arg2462Trp	p.R2462W	ENST00000297405	48/71	48	36	12	38	38	0	CSMD3,missense_variant,p.Arg2392Trp,ENST00000352409,;CSMD3,missense_variant,p.Arg2358Trp,ENST00000455883,;CSMD3,missense_variant,p.Arg2462Trp,ENST00000297405,;CSMD3,missense_variant,p.Arg1732Trp,ENST00000339701,;CSMD3,missense_variant,p.Arg2422Trp,ENST00000343508,;CSMD3,non_coding_transcript_exon_variant,,ENST00000492692,;	A	ENSG00000164796	ENST00000297405	Transcript	missense_variant	7629	7384	2462	R/W	Cgg/Tgg	rs199998952,COSM3942474,COSM3942475	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.15)	probably_damaging(0.997)	48/71	.	PROSITE_profiles:PS01180,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,SMART_domains:SM00042	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCCGTAATT	byFrequency|byCluster|by1000G	5	ESCA
EXT1	0	.	GRCh37	8	119123371	119123371	+	5'UTR	DEL	T	T	-	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-86delA	.	.	ENST00000378204	1/11	59	54	5	53	53	0	EXT1,5_prime_UTR_variant,,ENST00000378204,;EXT1,upstream_gene_variant,,ENST00000436216,;EXT1,5_prime_UTR_variant,,ENST00000437196,;	-	ENSG00000182197	ENST00000378204	Transcript	5_prime_UTR_variant	722	.	.	.	.	.	.	.	-1	EXT1	HGNC	3512	protein_coding	YES	CCDS6324.1	ENSP00000367446	EXT1_HUMAN	T2FFJ4_HUMAN,S5Y321_HUMAN,D7RTA7_HUMAN	UPI000012A3A1	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	VARSCANI*|PINDEL	CCGCCATCTTCC	.	2	ESCA
SLC39A4	0	.	GRCh37	8	145640648	145640648	+	Silent	SNP	G	G	A	rs782268389	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630C>T	p.%3D	p.F210F	ENST00000301305	3/12	34	24	10	21	21	0	SLC39A4,synonymous_variant,p.%3D,ENST00000526658,;SLC39A4,synonymous_variant,p.%3D,ENST00000276833,;SLC39A4,synonymous_variant,p.%3D,ENST00000301305,;SLC39A4,upstream_gene_variant,,ENST00000532718,;SLC39A4,upstream_gene_variant,,ENST00000527148,;SLC39A4,upstream_gene_variant,,ENST00000531013,;SLC39A4,upstream_gene_variant,,ENST00000530807,;SLC39A4,upstream_gene_variant,,ENST00000531789,;SLC39A4,upstream_gene_variant,,ENST00000529462,;	A	ENSG00000147804	ENST00000301305	Transcript	synonymous_variant	736	630	210	F	ttC/ttT	rs782268389	.	.	-1	SLC39A4	HGNC	17129	protein_coding	YES	CCDS6424.1	ENSP00000301305	S39A4_HUMAN	Q9NX22_HUMAN	UPI00001AED01	.	.	.	3/12	.	hmmpanther:PTHR12191:SF11,hmmpanther:PTHR12191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGGAACAC	.	5	ESCA
CA8	0	.	GRCh37	8	61178529	61178529	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372G>A	p.%3D	p.Q124Q	ENST00000317995	3/9	30	20	10	34	34	0	CA8,synonymous_variant,p.%3D,ENST00000317995,;CA8,non_coding_transcript_exon_variant,,ENST00000529918,;CA8,non_coding_transcript_exon_variant,,ENST00000524872,;	T	ENSG00000178538	ENST00000317995	Transcript	synonymous_variant	637	372	124	Q	caG/caA	.	.	.	-1	CA8	HGNC	1382	protein_coding	YES	CCDS6174.1	ENSP00000314407	CAH8_HUMAN	B4DFA0_HUMAN	UPI000000D816	.	.	.	3/9	.	PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF99,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACGCTGGTT	.	5	ESCA
FOXE1	0	.	GRCh37	9	100617344	100617344	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*26G>C	.	.	ENST00000375123	1/1	73	66	6	63	63	0	FOXE1,3_prime_UTR_variant,,ENST00000375123,;	C	ENSG00000178919	ENST00000375123	Transcript	3_prime_UTR_variant	1809	.	.	.	.	.	.	.	1	FOXE1	HGNC	3806	protein_coding	YES	CCDS35078.1	ENSP00000364265	FOXE1_HUMAN	.	UPI0000167B2F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCATAGACACA	.	2	ESCA
AKNA	0	.	GRCh37	9	117139229	117139229	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.858A>G	p.%3D	p.R286R	ENST00000307564	3/22	18	11	7	34	34	0	AKNA,synonymous_variant,p.%3D,ENST00000307564,;AKNA,synonymous_variant,p.%3D,ENST00000312033,;AKNA,synonymous_variant,p.%3D,ENST00000374088,;AKNA,synonymous_variant,p.%3D,ENST00000374075,;AKNA,5_prime_UTR_variant,,ENST00000223791,;	C	ENSG00000106948	ENST00000307564	Transcript	synonymous_variant	1020	858	286	R	agA/agG	.	.	.	-1	AKNA	HGNC	24108	protein_coding	YES	CCDS6805.1	ENSP00000303769	AKNA_HUMAN	.	UPI000021168C	.	.	.	3/22	.	hmmpanther:PTHR21510:SF12,hmmpanther:PTHR21510	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAATCTGGT	.	5	ESCA
RAB14	0	.	GRCh37	9	123942066	123942066	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1608C>G	.	.	ENST00000373840	8/8	39	35	4	44	44	0	RAB14,3_prime_UTR_variant,,ENST00000373840,;CNTRL,downstream_gene_variant,,ENST00000373855,;CNTRL,downstream_gene_variant,,ENST00000373850,;CNTRL,downstream_gene_variant,,ENST00000238341,;RAB14,downstream_gene_variant,,ENST00000451303,;CNTRL,downstream_gene_variant,,ENST00000373845,;	C	ENSG00000119396	ENST00000373840	Transcript	3_prime_UTR_variant	2494	.	.	.	.	.	.	.	-1	RAB14	HGNC	16524	protein_coding	YES	CCDS6827.1	ENSP00000362946	RAB14_HUMAN	.	UPI0000006BF0	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAAGATGTA	.	4	ESCA
RAB14	0	.	GRCh37	9	123942822	123942822	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*852C>G	.	.	ENST00000373840	8/8	16	11	4	28	28	0	RAB14,3_prime_UTR_variant,,ENST00000373840,;CNTRL,downstream_gene_variant,,ENST00000373855,;CNTRL,downstream_gene_variant,,ENST00000373850,;CNTRL,downstream_gene_variant,,ENST00000238341,;RAB14,downstream_gene_variant,,ENST00000451303,;CNTRL,downstream_gene_variant,,ENST00000373845,;	C	ENSG00000119396	ENST00000373840	Transcript	3_prime_UTR_variant	1738	.	.	.	.	.	.	.	-1	RAB14	HGNC	16524	protein_coding	YES	CCDS6827.1	ENSP00000362946	RAB14_HUMAN	.	UPI0000006BF0	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CCAAGGGGTGG	.	4	ESCA
NCS1	0	.	GRCh37	9	132995350	132995350	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99C>T	.	.	ENST00000372398	8/8	29	26	3	34	34	0	NCS1,3_prime_UTR_variant,,ENST00000372398,;NCS1,3_prime_UTR_variant,,ENST00000458469,;	T	ENSG00000107130	ENST00000372398	Transcript	3_prime_UTR_variant	758	.	.	.	.	.	.	.	1	NCS1	HGNC	3953	protein_coding	YES	CCDS6932.1	ENSP00000361475	NCS1_HUMAN	.	UPI00000000FB	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCTTCCG	.	2	ESCA
SH3GL2	0	.	GRCh37	9	17761480	17761480	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.160A>T	p.Thr54Ser	p.T54S	ENST00000380607	3/9	112	104	8	129	129	0	SH3GL2,missense_variant,p.Thr54Ser,ENST00000380607,;SH3GL2,missense_variant,p.Thr7Ser,ENST00000537391,;	T	ENSG00000107295	ENST00000380607	Transcript	missense_variant	280	160	54	T/S	Aca/Tca	COSM1265491	.	.	1	SH3GL2	HGNC	10831	protein_coding	YES	CCDS6483.1	ENSP00000369981	SH3G2_HUMAN	Q7Z376_HUMAN,Q3V639_HUMAN,F5H5J3_HUMAN,D3DRJ2_HUMAN	UPI0000135933	.	tolerated(0.06)	benign(0.142)	3/9	.	PROSITE_profiles:PS51021,hmmpanther:PTHR10661:SF113,hmmpanther:PTHR10661,Gene3D:1.20.1270.60,Pfam_domain:PF03114,SMART_domains:SM00721,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTAAAACAATT	.	2	ESCA
ANKRD18B	0	.	GRCh37	9	33548488	33548488	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516C>G	p.Leu506Val	p.L506V	ENST00000290943	9/16	69	41	27	67	67	0	ANKRD18B,missense_variant,p.Leu506Val,ENST00000290943,;ANKRD18B,upstream_gene_variant,,ENST00000357927,;ANKRD18B,downstream_gene_variant,,ENST00000605687,;	G	ENSG00000230453	ENST00000290943	Transcript	missense_variant	1612	1516	506	L/V	Ctc/Gtc	.	.	.	1	ANKRD18B	HGNC	23644	protein_coding	YES	.	ENSP00000290943	AN18B_HUMAN	.	UPI0000EE047B	.	deleterious(0)	probably_damaging(0.954)	9/16	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24147:SF22,hmmpanther:PTHR24147,Pfam_domain:PF14915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTCTCAGG	.	5	ESCA
CDC37L1	0	.	GRCh37	9	4697769	4697769	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.637A>G	p.Met213Val	p.M213V	ENST00000381854	5/7	50	47	3	51	51	0	CDC37L1,missense_variant,p.Met213Val,ENST00000381854,;CDC37L1,missense_variant,p.Met213Val,ENST00000381858,;	G	ENSG00000106993	ENST00000381854	Transcript	missense_variant	839	637	213	M/V	Atg/Gtg	.	.	.	1	CDC37L1	HGNC	17179	protein_coding	YES	CCDS6454.1	ENSP00000371278	CD37L_HUMAN	.	UPI000006E86C	.	deleterious(0)	possibly_damaging(0.788)	5/7	.	hmmpanther:PTHR12800:SF2,hmmpanther:PTHR12800,Pfam_domain:PF08565,SMART_domains:SM01070,Superfamily_domains:0044500	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTAATGGAA	.	2	ESCA
RP11-87H9.3	0	.	GRCh37	9	69113648	69113648	+	5'Flank	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000412376	.	47	43	4	92	91	0	RP11-87H9.3,upstream_gene_variant,,ENST00000412376,;PGM5P2,non_coding_transcript_exon_variant,,ENST00000591037,;PGM5P2,non_coding_transcript_exon_variant,,ENST00000591207,;PGM5P2,non_coding_transcript_exon_variant,,ENST00000272546,;PGM5P2,non_coding_transcript_exon_variant,,ENST00000426020,;	C	ENSG00000231242	ENST00000412376	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4855	-1	RP11-87H9.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CAGAAGAGTCA	.	2	ESCA
TRPM6	0	.	GRCh37	9	77377554	77377554	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4033C>T	p.Leu1345Phe	p.L1345F	ENST00000360774	26/39	19	16	3	19	19	0	TRPM6,missense_variant,p.Leu1345Phe,ENST00000451710,;TRPM6,missense_variant,p.Leu1340Phe,ENST00000449912,;TRPM6,missense_variant,p.Leu1340Phe,ENST00000361255,;TRPM6,missense_variant,p.Leu1345Phe,ENST00000376864,;TRPM6,missense_variant,p.Leu1345Phe,ENST00000360774,;TRPM6,intron_variant,,ENST00000376871,;TRPM6,intron_variant,,ENST00000376872,;	A	ENSG00000119121	ENST00000360774	Transcript	missense_variant	4271	4033	1345	L/F	Ctt/Ttt	.	.	.	-1	TRPM6	HGNC	17995	protein_coding	YES	CCDS6647.1	ENSP00000354006	TRPM6_HUMAN	.	UPI000006E041	.	deleterious_low_confidence(0.01)	benign(0.111)	26/39	.	hmmpanther:PTHR13800:SF15,hmmpanther:PTHR13800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGAAGAAACT	.	2	ESCA
PCSK5	0	.	GRCh37	9	78973602	78973602	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5347G>T	p.Ala1783Ser	p.A1783S	ENST00000545128	37/37	34	27	7	50	50	0	PCSK5,missense_variant,p.Ala1483Ser,ENST00000424854,;PCSK5,missense_variant,p.Ala1783Ser,ENST00000545128,;	T	ENSG00000099139	ENST00000545128	Transcript	missense_variant	5885	5347	1783	A/S	Gcc/Tcc	.	.	.	1	PCSK5	HGNC	8747	protein_coding	YES	CCDS55320.1	ENSP00000446280	PCSK5_HUMAN	I0EZ71_HUMAN	UPI0001DAD817	.	tolerated(0.51)	benign(0.007)	37/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTGGCCGAC	.	5	ESCA
SPATA31D5P	0	.	GRCh37	9	84531951	84531951	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1973C>A	.	.	ENST00000527857	4/4	77	73	4	125	125	0	SPATA31D5P,non_coding_transcript_exon_variant,,ENST00000527857,;SPATA31D5P,non_coding_transcript_exon_variant,,ENST00000376459,;	A	ENSG00000240632	ENST00000527857	Transcript	non_coding_transcript_exon_variant	1973	.	.	.	.	.	.	.	1	SPATA31D5P	HGNC	38602	processed_transcript	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGTTCAAAAA	.	2	ESCA
RAP2C	0	.	GRCh37	X	131348451	131348451	+	Missense_Mutation	SNP	T	T	A	rs747147776	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297A>T	p.Gln99His	p.Q99H	ENST00000342983	3/4	35	23	12	33	33	0	RAP2C,missense_variant,p.Gln99His,ENST00000370874,;RAP2C,missense_variant,p.Gln99His,ENST00000342983,;RAP2C-AS1,upstream_gene_variant,,ENST00000421483,;RAP2C-AS1,upstream_gene_variant,,ENST00000441399,;RAP2C,non_coding_transcript_exon_variant,,ENST00000460462,;RAP2C,downstream_gene_variant,,ENST00000490400,;	A	ENSG00000123728	ENST00000342983	Transcript	missense_variant	1044	297	99	Q/H	caA/caT	rs747147776,COSM1292933	.	.	-1	RAP2C	HGNC	21165	protein_coding	YES	CCDS14632.1	ENSP00000340274	RAP2C_HUMAN	.	UPI00000236AB	.	deleterious(0.02)	possibly_damaging(0.863)	3/4	.	PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF200,hmmpanther:PTHR24070,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00173,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATTTGATC	byFrequency	5	ESCA
SLITRK2	0	.	GRCh37	X	144904330	144904330	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387C>A	p.%3D	p.T129T	ENST00000370490	1/1	40	35	5	26	26	0	SLITRK2,synonymous_variant,p.%3D,ENST00000370490,;SLITRK2,synonymous_variant,p.%3D,ENST00000434188,;SLITRK2,synonymous_variant,p.%3D,ENST00000428560,;SLITRK2,synonymous_variant,p.%3D,ENST00000413937,;SLITRK2,synonymous_variant,p.%3D,ENST00000447897,;SLITRK2,synonymous_variant,p.%3D,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,;	A	ENSG00000185985	ENST00000370490	Transcript	synonymous_variant	4642	387	129	T	acC/acA	.	.	.	1	SLITRK2	HGNC	13449	protein_coding	YES	CCDS14680.1	ENSP00000359521	SLIK2_HUMAN	B3KTY4_HUMAN	UPI000004E64B	.	.	.	1/1	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF36,hmmpanther:PTHR24373,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACACCTTCCT	.	4	ESCA
ARX	0	.	GRCh37	X	25028418	25028418	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1078G>A	p.Glu360Lys	p.E360K	ENST00000379044	3/5	36	31	4	29	29	0	ARX,missense_variant,p.Glu360Lys,ENST00000379044,;	T	ENSG00000004848	ENST00000379044	Transcript	missense_variant	1289	1078	360	E/K	Gaa/Aaa	COSM3844399	.	.	-1	ARX	HGNC	18060	protein_coding	YES	CCDS14215.1	ENSP00000368332	ARX_HUMAN	.	UPI00001260CA	.	deleterious(0.02)	benign(0.3)	3/5	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF269,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTTCCTCCC	.	4	ESCA
BCOR	0	.	GRCh37	X	39921446	39921446	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4374C>G	p.%3D	p.V1458V	ENST00000378444	10/15	38	35	3	48	48	0	BCOR,synonymous_variant,p.%3D,ENST00000397354,;BCOR,synonymous_variant,p.%3D,ENST00000442018,;BCOR,synonymous_variant,p.%3D,ENST00000378444,;BCOR,synonymous_variant,p.%3D,ENST00000378463,;BCOR,synonymous_variant,p.%3D,ENST00000427012,;BCOR,synonymous_variant,p.%3D,ENST00000378455,;BCOR,synonymous_variant,p.%3D,ENST00000413905,;BCOR,synonymous_variant,p.%3D,ENST00000342274,;BCOR,downstream_gene_variant,,ENST00000406200,;	C	ENSG00000183337	ENST00000378444	Transcript	synonymous_variant	4603	4374	1458	V	gtC/gtG	.	.	.	-1	BCOR	HGNC	20893	protein_coding	YES	CCDS48093.1	ENSP00000367705	BCOR_HUMAN	H9A532_HUMAN,H7BZ37_HUMAN,C9JHP3_HUMAN,B3KTC2_HUMAN	UPI00002318CF	.	.	.	10/15	.	hmmpanther:PTHR24117,hmmpanther:PTHR24117:SF8,Gene3D:1.25.40.20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.N1459S|c.4376A>G|14,BUFFER|p.N1425S|c.4274A>G|16	MUTECT|MUSE	TTATTGACAAT	.	2	ESCA
RP2	0	.	GRCh37	X	46696586	46696586	+	Silent	SNP	C	C	A	rs370530958	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51C>A	p.%3D	p.P17P	ENST00000218340	1/5	52	46	6	41	41	0	RP2,synonymous_variant,p.%3D,ENST00000218340,;	A	ENSG00000102218	ENST00000218340	Transcript	synonymous_variant	212	51	17	P	ccC/ccA	rs370530958	.	.	1	RP2	HGNC	10274	protein_coding	YES	CCDS14270.1	ENSP00000218340	XRP2_HUMAN	.	UPI000000DA35	.	.	.	1/5	.	hmmpanther:PTHR15440:SF0,hmmpanther:PTHR15440,PIRSF_domain:PIRSF037947	.	.	.	.	.	.	.	G:0	G:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CGGCCCGAGAA	byCluster	2	ESCA
MAGED1	0	.	GRCh37	X	51636756	51636756	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-132G>T	.	.	ENST00000375695	1/14	44	34	10	34	34	0	MAGED1,5_prime_UTR_variant,,ENST00000326587,;MAGED1,5_prime_UTR_variant,,ENST00000375722,;MAGED1,5_prime_UTR_variant,,ENST00000375695,;MAGED1,intron_variant,,ENST00000375772,;MAGED1,non_coding_transcript_exon_variant,,ENST00000494718,;MAGED1,non_coding_transcript_exon_variant,,ENST00000485420,;MAGED1,non_coding_transcript_exon_variant,,ENST00000470461,;MAGED1,upstream_gene_variant,,ENST00000482188,;MAGED1,upstream_gene_variant,,ENST00000473931,;MAGED1,upstream_gene_variant,,ENST00000482599,;	T	ENSG00000179222	ENST00000375695	Transcript	5_prime_UTR_variant	22	.	.	.	.	.	.	.	1	MAGED1	HGNC	6813	protein_coding	YES	CCDS35279.1	ENSP00000364847	MAGD1_HUMAN	.	UPI0000074161	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGAGAGTGC	.	5	ESCA
RRAGB	0	.	GRCh37	X	55748670	55748670	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.178A>T	p.Ile60Phe	p.I60F	ENST00000262850	3/11	39	31	7	31	31	0	RRAGB,missense_variant,p.Ile22Phe,ENST00000414239,;RRAGB,missense_variant,p.Ile60Phe,ENST00000374941,;RRAGB,missense_variant,p.Ile60Phe,ENST00000262850,;RRAGB,non_coding_transcript_exon_variant,,ENST00000498762,;	T	ENSG00000083750	ENST00000262850	Transcript	missense_variant	621	178	60	I/F	Atc/Ttc	.	.	.	1	RRAGB	HGNC	19901	protein_coding	YES	CCDS14372.1	ENSP00000262850	RRAGB_HUMAN	.	UPI00001AE856	.	deleterious(0)	probably_damaging(0.997)	3/11	.	hmmpanther:PTHR11259:SF4,hmmpanther:PTHR11259,Pfam_domain:PF04670,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATTATCTTT	.	5	ESCA
SPIN4	0	.	GRCh37	X	62570980	62570980	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-282C>T	.	.	ENST00000335144	1/1	34	30	4	21	21	0	SPIN4,5_prime_UTR_variant,,ENST00000335144,;SPIN4,5_prime_UTR_variant,,ENST00000374884,;RP11-357C3.3,intron_variant,,ENST00000610234,;RP11-357C3.3,intron_variant,,ENST00000610088,;SPIN4-AS1,intron_variant,,ENST00000451979,;	A	ENSG00000186767	ENST00000335144	Transcript	5_prime_UTR_variant	239	.	.	.	.	.	.	.	-1	SPIN4	HGNC	27040	protein_coding	YES	CCDS43964.1	ENSP00000334163	SPIN4_HUMAN	.	UPI000013FD3C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCGCGAGTGC	.	4	ESCA
ARHGEF9	0	.	GRCh37	X	62875450	62875450	+	Missense_Mutation	SNP	C	C	G	rs781947373	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1224G>C	p.Lys408Asn	p.K408N	ENST00000253401	8/10	36	32	4	30	30	0	ARHGEF9,missense_variant,p.Lys387Asn,ENST00000374872,;ARHGEF9,missense_variant,p.Lys135Asn,ENST00000433323,;ARHGEF9,missense_variant,p.Lys306Asn,ENST00000374870,;ARHGEF9,missense_variant,p.Lys355Asn,ENST00000437457,;ARHGEF9,missense_variant,p.Lys408Asn,ENST00000253401,;ARHGEF9,missense_variant,p.Lys406Asn,ENST00000374878,;ARHGEF9,non_coding_transcript_exon_variant,,ENST00000495564,;ARHGEF9,intron_variant,,ENST00000466925,;	G	ENSG00000131089	ENST00000253401	Transcript	missense_variant	2025	1224	408	K/N	aaG/aaC	rs781947373	.	.	-1	ARHGEF9	HGNC	14561	protein_coding	YES	CCDS35315.1	ENSP00000253401	ARHG9_HUMAN	B1AMR3_HUMAN	UPI000006F940	.	deleterious(0)	probably_damaging(0.965)	8/10	.	Superfamily_domains:SSF50729,SMART_domains:SM00233,Gene3D:2.30.29.30,Pfam_domain:PF00169,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF103,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCTTCTTGGC	.	4	ESCA
CHM	0	.	GRCh37	X	85117335	85117335	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49S-01A-11D-A247-09	TCGA-LN-A49S-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2300G>C	.	.	ENST00000357749	15/15	35	31	4	39	39	0	CHM,3_prime_UTR_variant,,ENST00000357749,;CHM,downstream_gene_variant,,ENST00000537751,;CHM,non_coding_transcript_exon_variant,,ENST00000467744,;	G	ENSG00000188419	ENST00000357749	Transcript	3_prime_UTR_variant	4292	.	.	.	.	.	.	.	-1	CHM	HGNC	1940	protein_coding	YES	CCDS14454.1	ENSP00000350386	RAE1_HUMAN	B4DRL9_HUMAN	UPI0000049C8C	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACTCTAAGA	.	2	ESCA
CDC123	0	.	GRCh37	10	12277093	12277093	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.536G>A	p.Arg179Gln	p.R179Q	ENST00000281141	8/13	196	165	31	87	87	0	CDC123,missense_variant,p.Arg33Gln,ENST00000440613,;CDC123,missense_variant,p.Arg179Gln,ENST00000378900,;CDC123,missense_variant,p.Arg147Gln,ENST00000442050,;CDC123,missense_variant,p.Arg179Gln,ENST00000281141,;CDC123,downstream_gene_variant,,ENST00000429258,;CDC123,non_coding_transcript_exon_variant,,ENST00000455773,;CDC123,non_coding_transcript_exon_variant,,ENST00000498747,;	A	ENSG00000151465	ENST00000281141	Transcript	missense_variant	816	536	179	R/Q	cGa/cAa	COSM4012140,COSM4012141	.	.	1	CDC123	HGNC	16827	protein_coding	YES	CCDS7090.1	ENSP00000281141	CD123_HUMAN	.	UPI000006FE36	.	deleterious(0.01)	probably_damaging(0.989)	8/13	.	hmmpanther:PTHR15323,hmmpanther:PTHR15323:SF6,Pfam_domain:PF07065,PIRSF_domain:PIRSF007807	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTCGATGTT	.	4	ESCA
ADAM8	0	.	GRCh37	10	135086008	135086008	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787G>A	p.Asp263Asn	p.D263N	ENST00000445355	9/23	63	19	44	70	70	0	ADAM8,missense_variant,p.Asp224Asn,ENST00000485491,;ADAM8,missense_variant,p.Asp263Asn,ENST00000415217,;ADAM8,missense_variant,p.Asp263Asn,ENST00000445355,;ADAM8,downstream_gene_variant,,ENST00000486609,;ADAM8,downstream_gene_variant,,ENST00000559180,;ADAM8,3_prime_UTR_variant,,ENST00000560135,;ADAM8,non_coding_transcript_exon_variant,,ENST00000537099,;ADAM8,non_coding_transcript_exon_variant,,ENST00000561175,;ADAM8,upstream_gene_variant,,ENST00000468964,;ADAM8,downstream_gene_variant,,ENST00000463298,;	T	ENSG00000151651	ENST00000445355	Transcript	missense_variant	838	787	263	D/N	Gac/Aac	.	.	.	-1	ADAM8	HGNC	215	protein_coding	YES	CCDS31319.2	ENSP00000453302	ADAM8_HUMAN	.	UPI0001AE6E16	.	tolerated(1)	benign(0.001)	9/23	.	PROSITE_profiles:PS50215,hmmpanther:PTHR11905:SF20,hmmpanther:PTHR11905,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGTCGGGGC	.	5	ESCA
ACBD5	0	.	GRCh37	10	27497335	27497335	+	Missense_Mutation	SNP	C	C	T	rs543720340	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000396271	10/13	60	31	28	29	29	0	ACBD5,missense_variant,p.Arg380Gln,ENST00000375905,;ACBD5,missense_variant,p.Arg238Gln,ENST00000375897,;ACBD5,missense_variant,p.Arg306Gln,ENST00000375901,;ACBD5,missense_variant,p.Arg424Gln,ENST00000375888,;ACBD5,missense_variant,p.Arg415Gln,ENST00000396271,;ACBD5,non_coding_transcript_exon_variant,,ENST00000476758,;	T	ENSG00000107897	ENST00000396271	Transcript	missense_variant	1371	1244	415	R/Q	cGg/cAg	rs543720340	.	.	-1	ACBD5	HGNC	23338	protein_coding	YES	CCDS44368.1	ENSP00000379568	ACBD5_HUMAN	.	UPI000046FE2B	.	tolerated(0.35)	benign(0.004)	10/13	.	hmmpanther:PTHR23310,hmmpanther:PTHR23310:SF6,PIRSF_domain:PIRSF002412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCCGGCCC	byFrequency|byCluster	5	ESCA
CCNY	0	.	GRCh37	10	35805450	35805450	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.265-1G>A	.	p.X89_splice	ENST00000374704	.	83	63	20	55	55	0	CCNY,splice_acceptor_variant,,ENST00000374704,;CCNY,splice_acceptor_variant,,ENST00000490012,;CCNY,splice_acceptor_variant,,ENST00000265375,;CCNY,splice_acceptor_variant,,ENST00000493157,;CCNY,splice_acceptor_variant,,ENST00000339497,;CCNY,splice_acceptor_variant,,ENST00000374706,;CCNY,splice_acceptor_variant,,ENST00000492478,;	A	ENSG00000108100	ENST00000374704	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	CCNY	HGNC	23354	protein_coding	YES	CCDS7189.1	ENSP00000363836	CCNY_HUMAN	R4GN48_HUMAN	UPI000013EFE5	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTAGCATCC	.	5	ESCA
ANKRD30A	0	.	GRCh37	10	37486225	37486225	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2463A>C	p.%3D	p.P821P	ENST00000361713	28/36	174	102	71	133	133	0	ANKRD30A,synonymous_variant,p.%3D,ENST00000374660,;ANKRD30A,synonymous_variant,p.%3D,ENST00000361713,;ANKRD30A,synonymous_variant,p.%3D,ENST00000602533,;ANKRD30A,downstream_gene_variant,,ENST00000475522,;	C	ENSG00000148513	ENST00000361713	Transcript	synonymous_variant	2562	2463	821	P	ccA/ccC	.	.	.	1	ANKRD30A	HGNC	17234	protein_coding	YES	CCDS7193.1	ENSP00000354432	AN30A_HUMAN	R4GNA2_HUMAN	UPI0000458879	.	.	.	28/36	.	hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P818P|c.2454C>A|5,BUFFER|p.P818P|c.2454C>T|7,BUFFER|p.F824F|c.2472C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCCATCTGC	.	5	ESCA
PHYHIPL	0	.	GRCh37	10	60994160	60994161	+	Frame_Shift_Del	DEL	TT	TT	-	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204_205delTT	p.Ser69MetfsTer17	p.S69Mfs*17	ENST00000373880	2/5	49	42	7	33	33	0	PHYHIPL,frameshift_variant,p.Ser43MetfsTer17,ENST00000373878,;PHYHIPL,frameshift_variant,p.Ser69MetfsTer17,ENST00000373880,;PHYHIPL,upstream_gene_variant,,ENST00000472199,;PHYHIPL,3_prime_UTR_variant,,ENST00000486074,;	-	ENSG00000165443	ENST00000373880	Transcript	frameshift_variant	467-468	203-204	68	I/X	aTT/a	.	.	.	1	PHYHIPL	HGNC	29378	protein_coding	YES	CCDS7254.1	ENSP00000362987	PHIPL_HUMAN	.	UPI0000199879	.	.	.	2/5	.	PROSITE_profiles:PS50853,hmmpanther:PTHR15698:SF6,hmmpanther:PTHR15698,Pfam_domain:PF00041,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TCAAGATTTCATG	.	2	ESCA
NOC3L	0	.	GRCh37	10	96100090	96100090	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1723A>G	p.Ile575Val	p.I575V	ENST00000371361	16/21	105	61	43	87	87	0	NOC3L,missense_variant,p.Ile313Val,ENST00000543788,;NOC3L,missense_variant,p.Ile575Val,ENST00000371361,;NOC3L,missense_variant,p.Ile575Val,ENST00000371350,;	C	ENSG00000173145	ENST00000371361	Transcript	missense_variant	1824	1723	575	I/V	Att/Gtt	.	.	.	-1	NOC3L	HGNC	24034	protein_coding	YES	CCDS7433.1	ENSP00000360412	NOC3L_HUMAN	.	UPI000006DE09	.	tolerated(0.09)	possibly_damaging(0.699)	16/21	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF028977,Pfam_domain:PF03914,hmmpanther:PTHR14428:SF5,hmmpanther:PTHR14428	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATCAATATTCA	.	3	ESCA
EIF4G2	0	.	GRCh37	11	10821682	10821682	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2074G>A	p.Glu692Lys	p.E692K	ENST00000526148	18/22	33	20	12	31	31	0	EIF4G2,missense_variant,p.Glu654Lys,ENST00000396525,;EIF4G2,missense_variant,p.Glu89Lys,ENST00000528839,;EIF4G2,missense_variant,p.Glu172Lys,ENST00000531180,;EIF4G2,missense_variant,p.Glu692Lys,ENST00000339995,;EIF4G2,missense_variant,p.Glu692Lys,ENST00000525681,;EIF4G2,missense_variant,p.Glu692Lys,ENST00000526148,;EIF4G2,downstream_gene_variant,,ENST00000532082,;EIF4G2,downstream_gene_variant,,ENST00000527526,;EIF4G2,downstream_gene_variant,,ENST00000531416,;EIF4G2,downstream_gene_variant,,ENST00000527419,;EIF4G2,downstream_gene_variant,,ENST00000530702,;EIF4G2,downstream_gene_variant,,ENST00000524932,;EIF4G2,downstream_gene_variant,,ENST00000530211,;EIF4G2,downstream_gene_variant,,ENST00000532570,;SNORD97,downstream_gene_variant,,ENST00000459187,;RP11-685M7.5,intron_variant,,ENST00000532365,;EIF4G2,intron_variant,,ENST00000532120,;EIF4G2,intron_variant,,ENST00000534272,;EIF4G2,downstream_gene_variant,,ENST00000525995,;EIF4G2,downstream_gene_variant,,ENST00000531507,;EIF4G2,downstream_gene_variant,,ENST00000525972,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000532383,;EIF4G2,downstream_gene_variant,,ENST00000528562,;EIF4G2,downstream_gene_variant,,ENST00000527015,;EIF4G2,downstream_gene_variant,,ENST00000532349,;EIF4G2,downstream_gene_variant,,ENST00000534605,;EIF4G2,downstream_gene_variant,,ENST00000530564,;EIF4G2,downstream_gene_variant,,ENST00000532152,;EIF4G2,downstream_gene_variant,,ENST00000531647,;EIF4G2,upstream_gene_variant,,ENST00000534470,;EIF4G2,upstream_gene_variant,,ENST00000525606,;	T	ENSG00000110321	ENST00000526148	Transcript	missense_variant	2585	2074	692	E/K	Gaa/Aaa	.	.	.	-1	EIF4G2	HGNC	3297	protein_coding	YES	CCDS31428.1	ENSP00000433664	.	Q59G42_HUMAN,Q2TU89_HUMAN,H0YEN8_HUMAN,H0YEC5_HUMAN,H0YDC0_HUMAN,H0YD99_HUMAN,H0YD77_HUMAN,H0YCF8_HUMAN,D3DQV9_HUMAN,B4DZF2_HUMAN	UPI000013C8BE	.	tolerated(0.1)	benign(0.244)	18/22	.	hmmpanther:PTHR23253,Gene3D:1.25.40.180,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L693R|c.2078T>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTCTGTTA	.	5	ESCA
BUD13	0	.	GRCh37	11	116619061	116619061	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*137G>C	.	.	ENST00000260210	10/10	47	30	17	42	42	0	BUD13,3_prime_UTR_variant,,ENST00000260210,;BUD13,3_prime_UTR_variant,,ENST00000375445,;BUD13,3_prime_UTR_variant,,ENST00000419189,;	G	ENSG00000137656	ENST00000260210	Transcript	3_prime_UTR_variant	2021	.	.	.	.	.	.	.	-1	BUD13	HGNC	28199	protein_coding	YES	CCDS8374.1	ENSP00000260210	BUD13_HUMAN	.	UPI0000072AE6	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTGTGG	.	5	ESCA
MPZL2	0	.	GRCh37	11	118124581	118124581	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1380T>A	.	.	ENST00000278937	6/6	29	21	8	30	30	0	MPZL2,3_prime_UTR_variant,,ENST00000278937,;MPZL3,upstream_gene_variant,,ENST00000527472,;MPZL3,upstream_gene_variant,,ENST00000278949,;MPZL2,downstream_gene_variant,,ENST00000438295,;MPZL3,upstream_gene_variant,,ENST00000525386,;MPZL3,upstream_gene_variant,,ENST00000446386,;MPZL2,downstream_gene_variant,,ENST00000534175,;MPZL2,downstream_gene_variant,,ENST00000528554,;	T	ENSG00000149573	ENST00000278937	Transcript	3_prime_UTR_variant	2157	.	.	.	.	.	.	.	-1	MPZL2	HGNC	3496	protein_coding	YES	CCDS8393.1	ENSP00000278937	MPZL2_HUMAN	.	UPI000004781C	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTAAAAAA	.	5	ESCA
IGSF9B	0	.	GRCh37	11	133796853	133796853	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1765G>T	p.Gly589Ter	p.G589*	ENST00000533871	13/20	65	40	24	39	39	0	IGSF9B,stop_gained,p.Gly589Ter,ENST00000533871,;IGSF9B,stop_gained,p.Gly589Ter,ENST00000321016,;IGSF9B,non_coding_transcript_exon_variant,,ENST00000527648,;	A	ENSG00000080854	ENST00000533871	Transcript	stop_gained	1996	1765	589	G/*	Gga/Tga	.	.	.	-1	IGSF9B	HGNC	32326	protein_coding	YES	CCDS61010.1	ENSP00000436552	.	G5EA26_HUMAN	UPI0002C439DB	.	.	.	13/20	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF575,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTCCCAGCT	.	5	ESCA
COPB1	0	.	GRCh37	11	14498549	14498549	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1371A>G	p.%3D	p.G457G	ENST00000249923	12/22	35	24	10	39	39	0	COPB1,synonymous_variant,p.%3D,ENST00000439561,;COPB1,synonymous_variant,p.%3D,ENST00000249923,;COPB1,synonymous_variant,p.%3D,ENST00000534234,;RNU7-49P,upstream_gene_variant,,ENST00000516182,;COPB1,upstream_gene_variant,,ENST00000526191,;	C	ENSG00000129083	ENST00000249923	Transcript	synonymous_variant	1672	1371	457	G	ggA/ggG	.	.	.	-1	COPB1	HGNC	2231	protein_coding	YES	CCDS7815.1	ENSP00000249923	COPB_HUMAN	E9PP63_HUMAN,E9PKQ1_HUMAN	UPI000000103D	.	.	.	12/22	.	hmmpanther:PTHR10635,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF005727,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGCTCCTCG	.	5	ESCA
PDE3B	0	.	GRCh37	11	14793546	14793547	+	Intron	INS	-	-	AT	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1029+16_1029+17dupAT	.	.	ENST00000282096	.	122	95	27	78	78	0	PDE3B,intron_variant,,ENST00000455098,;PDE3B,intron_variant,,ENST00000282096,;PDE3B,non_coding_transcript_exon_variant,,ENST00000534317,;	AT	ENSG00000152270	ENST00000282096	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PDE3B	HGNC	8779	protein_coding	YES	CCDS7817.1	ENSP00000282096	PDE3B_HUMAN	.	UPI000013DCB7	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAATTAATATC	.	3	ESCA
CALCB	0	.	GRCh37	11	15096643	15096643	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>T	p.%3D	p.L41L	ENST00000533448	3/5	82	61	20	40	40	0	CALCB,synonymous_variant,p.%3D,ENST00000533448,;CALCB,synonymous_variant,p.%3D,ENST00000324229,;CALCB,synonymous_variant,p.%3D,ENST00000523376,;	T	ENSG00000175868	ENST00000533448	Transcript	synonymous_variant	234	123	41	L	ctC/ctT	.	.	.	1	CALCB	HGNC	1438	protein_coding	YES	CCDS7820.1	ENSP00000433490	CALCB_HUMAN	.	UPI0000126E36	.	.	.	3/5	.	hmmpanther:PTHR10505,Pfam_domain:PF00214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTCAGTAA	.	5	ESCA
METTL15	0	.	GRCh37	11	28232685	28232685	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347A>G	p.Tyr116Cys	p.Y116C	ENST00000407364	4/7	87	54	33	102	102	0	METTL15,missense_variant,p.Tyr116Cys,ENST00000406787,;METTL15,missense_variant,p.Tyr116Cys,ENST00000342303,;METTL15,missense_variant,p.Tyr116Cys,ENST00000303459,;METTL15,missense_variant,p.Tyr116Cys,ENST00000407364,;METTL15,synonymous_variant,p.%3D,ENST00000451385,;	G	ENSG00000169519	ENST00000407364	Transcript	missense_variant	699	347	116	Y/C	tAt/tGt	.	.	.	1	METTL15	HGNC	26606	protein_coding	YES	CCDS44559.1	ENSP00000384369	MET15_HUMAN	.	UPI0000DBEF34	.	deleterious(0)	probably_damaging(0.964)	4/7	.	Superfamily_domains:SSF53335,TIGRFAM_domain:TIGR00006,Pfam_domain:PF01795,Gene3D:3.40.50.150,hmmpanther:PTHR11265:SF0,hmmpanther:PTHR11265,HAMAP:MF_01007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTATGCCT	.	5	ESCA
CARS	0	.	GRCh37	11	3040371	3040371	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1393G>A	p.Glu465Lys	p.E465K	ENST00000380525	12/23	53	32	21	52	52	0	CARS,missense_variant,p.Glu382Lys,ENST00000278224,;CARS,missense_variant,p.Glu382Lys,ENST00000397111,;CARS,missense_variant,p.Glu465Lys,ENST00000380525,;CARS,missense_variant,p.Glu372Lys,ENST00000397114,;CARS,missense_variant,p.Glu395Lys,ENST00000401769,;CARS,downstream_gene_variant,,ENST00000465240,;CARS,splice_region_variant,,ENST00000526890,;CARS,splice_region_variant,,ENST00000529772,;CARS,splice_region_variant,,ENST00000531387,;	T	ENSG00000110619	ENST00000380525	Transcript	missense_variant	1463	1393	465	E/K	Gag/Aag	.	.	.	-1	CARS	HGNC	1493	protein_coding	YES	CCDS41600.1	ENSP00000369897	SYCC_HUMAN	.	UPI00004C4152	.	deleterious(0)	probably_damaging(0.997)	12/23	.	HAMAP:MF_00041,hmmpanther:PTHR10890,hmmpanther:PTHR10890:SF3,Pfam_domain:PF01406,Gene3D:3.40.50.620,TIGRFAM_domain:TIGR00435,Superfamily_domains:SSF52374,Prints_domain:PR00983	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCCGACT	.	5	ESCA
AMBRA1	0	.	GRCh37	11	46563784	46563784	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1513G>A	p.Glu505Lys	p.E505K	ENST00000314845	8/19	63	41	21	41	41	0	AMBRA1,missense_variant,p.Glu595Lys,ENST00000534300,;AMBRA1,missense_variant,p.Glu505Lys,ENST00000533727,;AMBRA1,missense_variant,p.Glu595Lys,ENST00000426438,;AMBRA1,missense_variant,p.Glu595Lys,ENST00000298834,;AMBRA1,missense_variant,p.Glu505Lys,ENST00000314845,;AMBRA1,missense_variant,p.Glu595Lys,ENST00000528950,;AMBRA1,missense_variant,p.Glu595Lys,ENST00000458649,;AMBRA1,downstream_gene_variant,,ENST00000524783,;AMBRA1,downstream_gene_variant,,ENST00000531542,;	T	ENSG00000110497	ENST00000314845	Transcript	missense_variant	1873	1513	505	E/K	Gag/Aag	COSM3447598,COSM1508225,COSM1508226,COSM3447599	.	.	-1	AMBRA1	HGNC	25990	protein_coding	YES	CCDS31475.1	ENSP00000318313	AMRA1_HUMAN	E9PL55_HUMAN	UPI0000237851	.	tolerated_low_confidence(0.06)	probably_damaging(0.956)	8/19	.	hmmpanther:PTHR22874:SF1,hmmpanther:PTHR22874	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCGCCAG	.	5	ESCA
SLC39A13	0	.	GRCh37	11	47437463	47437469	+	3'UTR	DEL	CACTCAG	CACTCAG	-	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	CACTCAG	CACTCAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*553_*559delCAGCACT	.	.	ENST00000362021	10/10	63	35	28	54	54	0	SLC39A13,3_prime_UTR_variant,,ENST00000524928,;SLC39A13,3_prime_UTR_variant,,ENST00000354884,;SLC39A13,3_prime_UTR_variant,,ENST00000362021,;SLC39A13,intron_variant,,ENST00000533076,;PSMC3,downstream_gene_variant,,ENST00000524447,;SLC39A13,downstream_gene_variant,,ENST00000526614,;SLC39A13,downstream_gene_variant,,ENST00000527091,;PSMC3,downstream_gene_variant,,ENST00000530912,;PSMC3,downstream_gene_variant,,ENST00000602866,;SLC39A13,downstream_gene_variant,,ENST00000531865,;SLC39A13,downstream_gene_variant,,ENST00000531974,;PSMC3,downstream_gene_variant,,ENST00000298852,;SLC39A13,downstream_gene_variant,,ENST00000531419,;SLC39A13,downstream_gene_variant,,ENST00000528979,;SLC39A13,downstream_gene_variant,,ENST00000527829,;SLC39A13,downstream_gene_variant,,ENST00000524886,;SLC39A13,downstream_gene_variant,,ENST00000529740,;	-	ENSG00000165915	ENST00000362021	Transcript	3_prime_UTR_variant	1707-1713	.	.	.	.	.	.	.	1	SLC39A13	HGNC	20859	protein_coding	YES	CCDS44592.1	ENSP00000354689	S39AD_HUMAN	K4DIB5_HUMAN	UPI00004564C5	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGCCCCACTCAGCACTG	.	3	ESCA
OR5T3	0	.	GRCh37	11	56020398	56020398	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723C>A	p.%3D	p.I241I	ENST00000303059	1/1	110	67	43	75	75	0	OR5T3,synonymous_variant,p.%3D,ENST00000303059,;	A	ENSG00000172489	ENST00000303059	Transcript	synonymous_variant	723	723	241	I	atC/atA	.	.	.	1	OR5T3	HGNC	15297	protein_coding	YES	CCDS31524.1	ENSP00000305403	OR5T3_HUMAN	.	UPI0000061E96	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTATCCTGAT	.	5	ESCA
SPDYC	0	.	GRCh37	11	64938815	64938815	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44C>T	p.Ser15Phe	p.S15F	ENST00000377185	2/7	40	17	23	28	28	0	SPDYC,missense_variant,p.Ser15Phe,ENST00000377185,;AP003068.18,downstream_gene_variant,,ENST00000534819,;AP003068.18,downstream_gene_variant,,ENST00000526979,;PGAM1P8,downstream_gene_variant,,ENST00000505544,;	T	ENSG00000204710	ENST00000377185	Transcript	missense_variant	126	44	15	S/F	tCc/tTc	.	.	.	1	SPDYC	HGNC	32681	protein_coding	YES	CCDS31606.1	ENSP00000366390	SPDYC_HUMAN	.	UPI00004A072F	.	deleterious_low_confidence(0.01)	benign(0.099)	2/7	.	hmmpanther:PTHR31545:SF2,hmmpanther:PTHR31545	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCCATCT	.	5	ESCA
NUDT8	0	.	GRCh37	11	67395589	67395589	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.539G>T	p.Gly180Val	p.G180V	ENST00000376693	4/4	105	67	37	48	48	0	NUDT8,missense_variant,p.Gly180Val,ENST00000376693,;NUDT8,3_prime_UTR_variant,,ENST00000301490,;TBX10,downstream_gene_variant,,ENST00000335385,;RP11-655M14.13,upstream_gene_variant,,ENST00000533311,;NUDT8,non_coding_transcript_exon_variant,,ENST00000534054,;	A	ENSG00000167799	ENST00000376693	Transcript	missense_variant	549	539	180	G/V	gGc/gTc	.	.	.	-1	NUDT8	HGNC	8055	protein_coding	YES	CCDS58151.1	ENSP00000365883	NUDT8_HUMAN	.	UPI00000382E2	.	deleterious(0)	probably_damaging(1)	4/4	.	hmmpanther:PTHR12992,Gene3D:3.90.79.10,Superfamily_domains:SSF55811	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGGCCCCAG	.	5	ESCA
ANO1	0	.	GRCh37	11	70034989	70034989	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*879A>G	.	.	ENST00000355303	26/26	60	36	23	55	55	0	ANO1,3_prime_UTR_variant,,ENST00000531349,;ANO1,3_prime_UTR_variant,,ENST00000538023,;ANO1,3_prime_UTR_variant,,ENST00000398543,;ANO1,3_prime_UTR_variant,,ENST00000355303,;ANO1,intron_variant,,ENST00000530676,;ANO1-AS1,upstream_gene_variant,,ENST00000524987,;ANO1,downstream_gene_variant,,ENST00000525494,;	G	ENSG00000131620	ENST00000355303	Transcript	3_prime_UTR_variant	4145	.	.	.	.	.	.	.	1	ANO1	HGNC	21625	protein_coding	YES	CCDS44663.1	ENSP00000347454	ANO1_HUMAN	.	UPI000013CE03	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TATTTATGGGT	.	3	ESCA
PPME1	0	.	GRCh37	11	73941869	73941869	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554-88C>G	.	.	ENST00000328257	.	18	9	8	15	15	0	PPME1,5_prime_UTR_variant,,ENST00000543525,;PPME1,intron_variant,,ENST00000398427,;PPME1,intron_variant,,ENST00000328257,;P4HA3,downstream_gene_variant,,ENST00000540363,;PPME1,upstream_gene_variant,,ENST00000535205,;	G	ENSG00000214517	ENST00000328257	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PPME1	HGNC	30178	protein_coding	YES	CCDS44678.1	ENSP00000329867	PPME1_HUMAN	.	UPI00000382E3	.	.	.	.	6/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCATCAAGAG	.	5	ESCA
TAOK3	0	.	GRCh37	12	118693355	118693355	+	Silent	SNP	C	C	T	rs779780610	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18G>A	p.%3D	p.L6L	ENST00000392533	3/21	43	19	24	36	36	0	TAOK3,synonymous_variant,p.%3D,ENST00000541878,;TAOK3,synonymous_variant,p.%3D,ENST00000541786,;TAOK3,synonymous_variant,p.%3D,ENST00000392533,;TAOK3,synonymous_variant,p.%3D,ENST00000542532,;TAOK3,synonymous_variant,p.%3D,ENST00000542902,;TAOK3,synonymous_variant,p.%3D,ENST00000539872,;TAOK3,synonymous_variant,p.%3D,ENST00000535570,;TAOK3,synonymous_variant,p.%3D,ENST00000541186,;TAOK3,synonymous_variant,p.%3D,ENST00000419821,;TAOK3,downstream_gene_variant,,ENST00000542692,;	T	ENSG00000135090	ENST00000392533	Transcript	synonymous_variant	509	18	6	L	ctG/ctA	rs779780610	.	.	-1	TAOK3	HGNC	18133	protein_coding	YES	CCDS9188.1	ENSP00000376317	TAOK3_HUMAN	G3V1Q8_HUMAN,F5H7G4_HUMAN,F5H5E0_HUMAN,F5H5C7_HUMAN,F5H3L7_HUMAN,F5H005_HUMAN,F5GY38_HUMAN,F5GX96_HUMAN,F5GWV8_HUMAN	UPI000007231B	.	.	.	3/21	.	hmmpanther:PTHR24361:SF187,hmmpanther:PTHR24361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTCAGCAC	.	5	ESCA
EIF2B1	0	.	GRCh37	12	124116905	124116905	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.102G>C	p.Leu34Phe	p.L34F	ENST00000424014	2/9	42	25	17	41	41	0	EIF2B1,missense_variant,p.Leu34Phe,ENST00000537073,;EIF2B1,missense_variant,p.Leu21Phe,ENST00000539951,;EIF2B1,missense_variant,p.Leu34Phe,ENST00000424014,;EIF2B1,missense_variant,p.Leu50Phe,ENST00000534960,;GTF2H3,upstream_gene_variant,,ENST00000538845,;GTF2H3,upstream_gene_variant,,ENST00000543341,;GTF2H3,upstream_gene_variant,,ENST00000228955,;GTF2H3,upstream_gene_variant,,ENST00000536375,;GTF2H3,upstream_gene_variant,,ENST00000539994,;EIF2B1,non_coding_transcript_exon_variant,,ENST00000543940,;EIF2B1,non_coding_transcript_exon_variant,,ENST00000452159,;GTF2H3,upstream_gene_variant,,ENST00000542279,;GTF2H3,upstream_gene_variant,,ENST00000537368,;GTF2H3,upstream_gene_variant,,ENST00000537695,;GTF2H3,upstream_gene_variant,,ENST00000543005,;	G	ENSG00000111361	ENST00000424014	Transcript	missense_variant	311	102	34	L/F	ttG/ttC	.	.	.	-1	EIF2B1	HGNC	3257	protein_coding	YES	CCDS31924.1	ENSP00000416250	EI2BA_HUMAN	.	UPI0000129AAE	.	deleterious(0.01)	benign(0.252)	2/9	.	hmmpanther:PTHR10233,hmmpanther:PTHR10233:SF18,Pfam_domain:PF01008,Superfamily_domains:SSF100950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTCAAGAA	.	5	ESCA
TMEM132D	0	.	GRCh37	12	130184990	130184990	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333G>T	p.Met111Ile	p.M111I	ENST00000422113	2/9	47	28	18	42	42	0	TMEM132D,missense_variant,p.Met111Ile,ENST00000422113,;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,;	A	ENSG00000151952	ENST00000422113	Transcript	missense_variant	660	333	111	M/I	atG/atT	.	.	.	-1	TMEM132D	HGNC	29411	protein_coding	YES	CCDS9266.1	ENSP00000408581	T132D_HUMAN	.	UPI000023759C	.	deleterious(0.02)	benign(0.025)	2/9	.	hmmpanther:PTHR13388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTAGCATTAA	.	5	ESCA
TMEM132D	0	.	GRCh37	12	130184991	130184991	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.332T>G	p.Met111Arg	p.M111R	ENST00000422113	2/9	47	28	19	42	42	0	TMEM132D,missense_variant,p.Met111Arg,ENST00000422113,;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,;	C	ENSG00000151952	ENST00000422113	Transcript	missense_variant	659	332	111	M/R	aTg/aGg	.	.	.	-1	TMEM132D	HGNC	29411	protein_coding	YES	CCDS9266.1	ENSP00000408581	T132D_HUMAN	.	UPI000023759C	.	deleterious(0)	possibly_damaging(0.622)	2/9	.	hmmpanther:PTHR13388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGCATTAAA	.	5	ESCA
RP11-474D1.3	0	.	GRCh37	12	130520932	130520932	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1770C>G	.	.	ENST00000567788	2/3	35	27	8	29	29	0	RP11-474D1.3,non_coding_transcript_exon_variant,,ENST00000567788,;RP11-474D1.3,non_coding_transcript_exon_variant,,ENST00000291374,;RP11-474D1.4,intron_variant,,ENST00000561864,;	C	ENSG00000214039	ENST00000567788	Transcript	non_coding_transcript_exon_variant	1770	.	.	.	.	.	.	.	-1	RP11-474D1.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTGCAGATATT	.	4	ESCA
KMT2D	0	.	GRCh37	12	49435976	49435976	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6005G>T	p.Ser2002Ile	p.S2002I	ENST00000301067	28/54	36	17	19	24	24	0	KMT2D,missense_variant,p.Ser2002Ile,ENST00000301067,;KMT2D,upstream_gene_variant,,ENST00000549799,;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000550356,;	A	ENSG00000167548	ENST00000301067	Transcript	missense_variant	6005	6005	2002	S/I	aGt/aTt	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	probably_damaging(0.959)	28/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGACTCCGC	.	5	ESCA
BCDIN3D	0	.	GRCh37	12	50236730	50236730	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141C>A	p.%3D	p.L47L	ENST00000333924	1/2	37	23	14	31	31	0	BCDIN3D,synonymous_variant,p.%3D,ENST00000333924,;BCDIN3D-AS1,downstream_gene_variant,,ENST00000549124,;BCDIN3D-AS1,downstream_gene_variant,,ENST00000548872,;BCDIN3D,non_coding_transcript_exon_variant,,ENST00000550861,;	T	ENSG00000186666	ENST00000333924	Transcript	synonymous_variant	183	141	47	L	ctC/ctA	.	.	.	-1	BCDIN3D	HGNC	27050	protein_coding	YES	CCDS8790.1	ENSP00000335201	BN3D2_HUMAN	.	UPI0000160802	.	.	.	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12315:SF1,hmmpanther:PTHR12315,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCGGAGCCG	.	5	ESCA
SLC11A2	0	.	GRCh37	12	51375412	51375412	+	3'Flank	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000394904	.	25	16	9	12	12	0	SLC11A2,3_prime_UTR_variant,,ENST00000547198,;SLC11A2,3_prime_UTR_variant,,ENST00000262051,;SLC11A2,downstream_gene_variant,,ENST00000394904,;SLC11A2,downstream_gene_variant,,ENST00000262052,;SLC11A2,intron_variant,,ENST00000546636,;SLC11A2,intron_variant,,ENST00000551215,;SLC11A2,downstream_gene_variant,,ENST00000550782,;	G	ENSG00000110911	ENST00000394904	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4363	-1	SLC11A2	HGNC	10908	protein_coding	YES	CCDS53793.1	ENSP00000378364	NRAM2_HUMAN	F8W1P7_HUMAN,F8W1F2_HUMAN,F8W154_HUMAN,F8VZL6_HUMAN,F8VWB0_HUMAN,B3KY44_HUMAN	UPI00001FC234	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAACAAAAC	.	5	ESCA
HOXC11	0	.	GRCh37	12	54369204	54369204	+	3'UTR	SNP	G	G	C	rs768169872	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7G>C	.	.	ENST00000546378	2/2	26	17	9	21	21	0	HOXC11,missense_variant,p.Arg309Thr,ENST00000243082,;HOXC11,3_prime_UTR_variant,,ENST00000546378,;HOTAIR,upstream_gene_variant,,ENST00000424518,;HOTAIR,upstream_gene_variant,,ENST00000455246,;	C	ENSG00000123388	ENST00000546378	Transcript	3_prime_UTR_variant	1038	.	.	.	.	rs768169872	.	.	1	HOXC11	HGNC	5123	protein_coding	YES	CCDS8867.1	ENSP00000446680	HXC11_HUMAN	.	UPI000012CF7D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGACCGG	.	5	ESCA
HOXC10	0	.	GRCh37	12	54383371	54383371	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*141T>A	.	.	ENST00000303460	2/2	29	12	16	23	23	0	HOXC10,3_prime_UTR_variant,,ENST00000303460,;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC6,upstream_gene_variant,,ENST00000504315,;HOXC10,downstream_gene_variant,,ENST00000515593,;MIR196A2,upstream_gene_variant,,ENST00000385189,;HOXC-AS3,upstream_gene_variant,,ENST00000514702,;HOXC-AS3,upstream_gene_variant,,ENST00000513165,;HOXC-AS3,upstream_gene_variant,,ENST00000509870,;HOXC-AS2,downstream_gene_variant,,ENST00000604081,;HOXC10,non_coding_transcript_exon_variant,,ENST00000513413,;HOXC10,non_coding_transcript_exon_variant,,ENST00000514415,;HOXC10,non_coding_transcript_exon_variant,,ENST00000511575,;	A	ENSG00000180818	ENST00000303460	Transcript	3_prime_UTR_variant	1244	.	.	.	.	.	.	.	1	HOXC10	HGNC	5122	protein_coding	YES	CCDS8868.1	ENSP00000307321	HXC10_HUMAN	Q53XI4_HUMAN,D6RAG4_HUMAN	UPI000012CF7C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTTCCAAG	.	5	ESCA
RP11-834C11.4	0	.	GRCh37	12	54520191	54520191	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.310G>A	.	.	ENST00000508564	1/2	17	12	5	25	25	0	RP11-834C11.4,non_coding_transcript_exon_variant,,ENST00000508564,;RP11-834C11.5,upstream_gene_variant,,ENST00000508763,;RP11-834C11.5,upstream_gene_variant,,ENST00000504278,;RP11-834C11.5,upstream_gene_variant,,ENST00000513381,;RP11-834C11.3,downstream_gene_variant,,ENST00000515617,;RP11-834C11.5,upstream_gene_variant,,ENST00000505661,;	A	ENSG00000250742	ENST00000508564	Transcript	non_coding_transcript_exon_variant	310	.	.	.	.	.	.	.	1	RP11-834C11.4	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCTCCGGATCG	.	3	ESCA
SPSB2	0	.	GRCh37	12	6980330	6980330	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*26G>T	.	.	ENST00000524270	3/3	63	42	21	41	41	0	SPSB2,3_prime_UTR_variant,,ENST00000523102,;SPSB2,3_prime_UTR_variant,,ENST00000524270,;SPSB2,downstream_gene_variant,,ENST00000432205,;TPI1,downstream_gene_variant,,ENST00000396705,;SPSB2,downstream_gene_variant,,ENST00000519357,;TPI1,downstream_gene_variant,,ENST00000488464,;TPI1,downstream_gene_variant,,ENST00000495834,;LRRC23,upstream_gene_variant,,ENST00000433346,;TPI1,downstream_gene_variant,,ENST00000493987,;USP5,downstream_gene_variant,,ENST00000229268,;USP5,downstream_gene_variant,,ENST00000389231,;TPI1,downstream_gene_variant,,ENST00000229270,;TPI1,downstream_gene_variant,,ENST00000535434,;TPI1,downstream_gene_variant,,ENST00000462761,;LRRC23,upstream_gene_variant,,ENST00000449039,;RPL13P5,upstream_gene_variant,,ENST00000421824,;SPSB2,downstream_gene_variant,,ENST00000437851,;RPL13P5,upstream_gene_variant,,ENST00000412023,;RPL13P5,upstream_gene_variant,,ENST00000274820,;RPL13P5,upstream_gene_variant,,ENST00000451612,;USP5,downstream_gene_variant,,ENST00000537267,;TPI1,downstream_gene_variant,,ENST00000482209,;TPI1,downstream_gene_variant,,ENST00000474253,;	A	ENSG00000111671	ENST00000524270	Transcript	3_prime_UTR_variant	1005	.	.	.	.	.	.	.	-1	SPSB2	HGNC	29522	protein_coding	YES	CCDS8567.1	ENSP00000428338	SPSB2_HUMAN	E5RIC2_HUMAN	UPI000003316E	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTCAGCAC	.	5	ESCA
PAWR	0	.	GRCh37	12	79986092	79986092	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*295G>C	.	.	ENST00000328827	7/7	23	13	10	20	20	0	PAWR,3_prime_UTR_variant,,ENST00000328827,;PAWR,intron_variant,,ENST00000550603,;PAWR,intron_variant,,ENST00000549050,;PAWR,intron_variant,,ENST00000548075,;PAWR,downstream_gene_variant,,ENST00000547699,;	G	ENSG00000177425	ENST00000328827	Transcript	3_prime_UTR_variant	1691	.	.	.	.	.	.	.	-1	PAWR	HGNC	8614	protein_coding	YES	CCDS31863.1	ENSP00000328088	PAWR_HUMAN	F8W1M8_HUMAN	UPI0000070738	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCAAACG	.	5	ESCA
CHAMP1	0	.	GRCh37	13	115090850	115090850	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1533C>T	p.%3D	p.A511A	ENST00000361283	3/3	47	17	29	39	38	0	CHAMP1,synonymous_variant,p.%3D,ENST00000361283,;CHAMP1,downstream_gene_variant,,ENST00000463003,;LINC01054,downstream_gene_variant,,ENST00000446989,;CHAMP1,downstream_gene_variant,,ENST00000478022,;	T	ENSG00000198824	ENST00000361283	Transcript	synonymous_variant	1842	1533	511	A	gcC/gcT	.	.	.	1	CHAMP1	HGNC	20311	protein_coding	YES	CCDS9545.1	ENSP00000354730	CHAP1_HUMAN	S4R3K0_HUMAN	UPI00001C1F5B	.	.	.	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCAGCCTCAGA	.	4	ESCA
TUBA3C	0	.	GRCh37	13	19748259	19748259	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1097G>T	p.Gly366Val	p.G366V	ENST00000400113	5/5	66	23	43	71	71	0	TUBA3C,missense_variant,p.Gly366Val,ENST00000400113,;SMPD4P2,upstream_gene_variant,,ENST00000440167,;	A	ENSG00000198033	ENST00000400113	Transcript	missense_variant	1202	1097	366	G/V	gGa/gTa	COSM3467497	.	.	-1	TUBA3C	HGNC	12408	protein_coding	YES	CCDS9284.1	ENSP00000382982	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	deleterious_low_confidence(0)	probably_damaging(0.977)	5/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Pfam_domain:PF03953,Gene3D:3.30.1330.20,SMART_domains:SM00865,Superfamily_domains:SSF55307,Prints_domain:PR01162	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCTCCCCCA	.	5	ESCA
XPO4	0	.	GRCh37	13	21357559	21357559	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*302A>G	.	.	ENST00000255305	23/23	30	12	17	39	39	0	XPO4,3_prime_UTR_variant,,ENST00000255305,;XPO4,3_prime_UTR_variant,,ENST00000400602,;	C	ENSG00000132953	ENST00000255305	Transcript	3_prime_UTR_variant	3830	.	.	.	.	.	.	.	-1	XPO4	HGNC	17796	protein_coding	YES	CCDS41872.1	ENSP00000255305	XPO4_HUMAN	Q8IVQ8_HUMAN,Q0VG75_HUMAN	UPI0000139018	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCATATGTA	.	5	ESCA
FLT1	0	.	GRCh37	13	28908259	28908259	+	Silent	SNP	T	T	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2496A>C	p.%3D	p.S832S	ENST00000282397	18/30	20	4	16	17	17	0	FLT1,synonymous_variant,p.%3D,ENST00000540678,;FLT1,synonymous_variant,p.%3D,ENST00000282397,;	G	ENSG00000102755	ENST00000282397	Transcript	synonymous_variant	2748	2496	832	S	tcA/tcC	.	.	.	-1	FLT1	HGNC	3763	protein_coding	YES	CCDS9330.1	ENSP00000282397	VGFR1_HUMAN	S5U0M6_HUMAN,S5TRK2_HUMAN,L7RSL3_HUMAN,H9N1E8_HUMAN,H9N1E7_HUMAN	UPI000013DCDD	.	.	.	18/30	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF126,Pfam_domain:PF07714,Gene3D:3.30.200.20,SMART_domains:SM00219,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGTGATTT	.	5	ESCA
N4BP2L1	0	.	GRCh37	13	32976725	32976725	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*354C>T	.	.	ENST00000380130	5/5	13	2	11	8	8	0	N4BP2L1,3_prime_UTR_variant,,ENST00000530622,;N4BP2L1,3_prime_UTR_variant,,ENST00000380139,;N4BP2L1,3_prime_UTR_variant,,ENST00000380130,;N4BP2L1,intron_variant,,ENST00000495479,;N4BP2L1,intron_variant,,ENST00000380133,;N4BP2L1,downstream_gene_variant,,ENST00000343281,;BRCA2,downstream_gene_variant,,ENST00000544455,;BRCA2,downstream_gene_variant,,ENST00000380152,;N4BP2L1,non_coding_transcript_exon_variant,,ENST00000459716,;BRCA2,downstream_gene_variant,,ENST00000533776,;N4BP2L1,downstream_gene_variant,,ENST00000472298,;BRCA2,downstream_gene_variant,,ENST00000470094,;	A	ENSG00000139597	ENST00000380130	Transcript	3_prime_UTR_variant	1182	.	.	.	.	.	.	.	-1	N4BP2L1	HGNC	25037	protein_coding	YES	CCDS9345.2	ENSP00000369473	N42L1_HUMAN	Q9Y273_HUMAN,Q9UQP6_HUMAN	UPI000003CA35	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATAGATCAC	.	2	ESCA
DIS3	0	.	GRCh37	13	73345944	73345944	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594C>T	p.Leu532Phe	p.L532F	ENST00000377767	11/21	33	25	7	29	29	0	DIS3,missense_variant,p.Leu370Phe,ENST00000545453,;DIS3,missense_variant,p.Leu532Phe,ENST00000377767,;DIS3,missense_variant,p.Leu502Phe,ENST00000377780,;DIS3,intron_variant,,ENST00000469339,;DIS3,missense_variant,p.Leu532Phe,ENST00000490646,;	A	ENSG00000083520	ENST00000377767	Transcript	missense_variant	1695	1594	532	L/F	Ctt/Ttt	.	.	.	-1	DIS3	HGNC	20604	protein_coding	YES	CCDS9447.1	ENSP00000366997	RRP44_HUMAN	G3V1J5_HUMAN,B3KM83_HUMAN	UPI0000141B79	.	deleterious(0)	probably_damaging(1)	11/21	.	Superfamily_domains:SSF50249,SMART_domains:SM00955,Pfam_domain:PF00773,hmmpanther:PTHR23355,hmmpanther:PTHR23355:SF35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAAGATACA	.	5	ESCA
KIF26A	0	.	GRCh37	14	104640529	104640529	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2075C>T	p.Ala692Val	p.A692V	ENST00000423312	11/15	130	30	100	78	78	0	KIF26A,missense_variant,p.Ala553Val,ENST00000315264,;KIF26A,missense_variant,p.Ala692Val,ENST00000423312,;	T	ENSG00000066735	ENST00000423312	Transcript	missense_variant	2075	2075	692	A/V	gCt/gTt	.	.	.	1	KIF26A	HGNC	20226	protein_coding	YES	CCDS45171.1	ENSP00000388241	KI26A_HUMAN	C9JFF0_HUMAN	UPI00006C145D	.	tolerated(0.37)	benign(0.038)	11/15	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF407,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCGCTGGCT	.	5	ESCA
OR4K1	0	.	GRCh37	14	20404131	20404131	+	Silent	SNP	C	C	T	rs772261875	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306C>T	p.%3D	p.F102F	ENST00000285600	1/1	105	68	36	46	46	0	OR4K1,synonymous_variant,p.%3D,ENST00000285600,;	T	ENSG00000155249	ENST00000285600	Transcript	synonymous_variant	365	306	102	F	ttC/ttT	rs772261875,COSM432774	.	.	1	OR4K1	HGNC	14726	protein_coding	YES	CCDS32025.1	ENSP00000285600	OR4K1_HUMAN	.	UPI0000041B4A	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF182,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCGTTCT	byFrequency|byCluster	5	ESCA
NEDD8-MDP1	0	.	GRCh37	14	24687342	24687342	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146A>G	p.Gln49Arg	p.Q49R	ENST00000534348	3/7	57	12	45	26	26	0	NEDD8-MDP1,missense_variant,p.Gln49Arg,ENST00000534348,;NEDD8,missense_variant,p.Gln49Arg,ENST00000524927,;NEDD8,missense_variant,p.Gln49Arg,ENST00000250495,;CHMP4A,upstream_gene_variant,,ENST00000530996,;CHMP4A,upstream_gene_variant,,ENST00000609024,;TM9SF1,upstream_gene_variant,,ENST00000530611,;MDP1,upstream_gene_variant,,ENST00000396833,;MDP1,upstream_gene_variant,,ENST00000288087,;TM9SF1,upstream_gene_variant,,ENST00000556387,;CHMP4A,upstream_gene_variant,,ENST00000347519,;NEDD8,non_coding_transcript_exon_variant,,ENST00000531430,;NEDD8-MDP1,non_coding_transcript_exon_variant,,ENST00000604306,;NEDD8,non_coding_transcript_exon_variant,,ENST00000527046,;NEDD8,intron_variant,,ENST00000526430,;MDP1,upstream_gene_variant,,ENST00000532557,;MDP1,upstream_gene_variant,,ENST00000525696,;NEDD8,missense_variant,p.Gln49Arg,ENST00000396828,;NEDD8-MDP1,missense_variant,p.Gln49Arg,ENST00000605847,;NEDD8-MDP1,missense_variant,p.Gln49Arg,ENST00000530579,;NEDD8,non_coding_transcript_exon_variant,,ENST00000560427,;CHMP4A,upstream_gene_variant,,ENST00000527154,;MDP1,upstream_gene_variant,,ENST00000533536,;MDP1,upstream_gene_variant,,ENST00000532742,;AL136419.6,upstream_gene_variant,,ENST00000528804,;MDP1,upstream_gene_variant,,ENST00000466422,;MDP1,upstream_gene_variant,,ENST00000528849,;MDP1,upstream_gene_variant,,ENST00000531553,;CHMP4A,upstream_gene_variant,,ENST00000534106,;CHMP4A,upstream_gene_variant,,ENST00000533523,;MDP1,upstream_gene_variant,,ENST00000530222,;AL136419.6,upstream_gene_variant,,ENST00000565988,;	C	ENSG00000255526	ENST00000534348	Transcript	missense_variant	231	146	49	Q/R	cAg/cGg	.	.	.	-1	NEDD8-MDP1	HGNC	39551	protein_coding	YES	.	ENSP00000431482	.	E9PL57_HUMAN	UPI0001F77C18	.	tolerated(0.25)	benign(0.006)	3/7	.	PROSITE_profiles:PS50053,hmmpanther:PTHR17901:SF13,hmmpanther:PTHR17901,Gene3D:3.10.20.90,TIGRFAM_domain:TIGR01685,Pfam_domain:PF00240,SMART_domains:SM00213,Superfamily_domains:SSF54236,Prints_domain:PR00348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATCTGCTTG	.	5	ESCA
FAM81A	0	.	GRCh37	15	59750766	59750766	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-60G>C	.	.	ENST00000288228	2/9	49	25	24	31	31	0	FAM81A,5_prime_UTR_variant,,ENST00000559628,;FAM81A,5_prime_UTR_variant,,ENST00000288228,;FAM81A,5_prime_UTR_variant,,ENST00000560394,;FAM81A,5_prime_UTR_variant,,ENST00000561361,;FAM81A,5_prime_UTR_variant,,ENST00000560474,;FAM81A,5_prime_UTR_variant,,ENST00000560123,;FAM81A,5_prime_UTR_variant,,ENST00000557914,;FAM81A,5_prime_UTR_variant,,ENST00000560074,;FAM81A,5_prime_UTR_variant,,ENST00000558348,;FAM81A,5_prime_UTR_variant,,ENST00000560087,;FAM81A,non_coding_transcript_exon_variant,,ENST00000558513,;	C	ENSG00000157470	ENST00000288228	Transcript	5_prime_UTR_variant	128	.	.	.	.	.	.	.	1	FAM81A	HGNC	28379	protein_coding	YES	CCDS45269.1	ENSP00000288228	FA81A_HUMAN	H0YN94_HUMAN,H0YN47_HUMAN,H0YMX7_HUMAN,H0YMW3_HUMAN,H0YMF2_HUMAN,H0YKW2_HUMAN,H0YKQ6_HUMAN	UPI000015DCFD	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAGAAAAT	.	5	ESCA
DIS3L	0	.	GRCh37	15	66615878	66615878	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1622C>G	p.Ser541Cys	p.S541C	ENST00000319212	11/17	79	48	31	52	52	0	DIS3L,missense_variant,p.Ser541Cys,ENST00000319212,;DIS3L,missense_variant,p.Ser458Cys,ENST00000319194,;DIS3L,3_prime_UTR_variant,,ENST00000441424,;RP11-352G18.2,intron_variant,,ENST00000565993,;DIS3L,3_prime_UTR_variant,,ENST00000530537,;DIS3L,3_prime_UTR_variant,,ENST00000524795,;DIS3L,non_coding_transcript_exon_variant,,ENST00000565281,;DIS3L,non_coding_transcript_exon_variant,,ENST00000564909,;	G	ENSG00000166938	ENST00000319212	Transcript	missense_variant	1672	1622	541	S/C	tCc/tGc	.	.	.	1	DIS3L	HGNC	28698	protein_coding	YES	CCDS45286.1	ENSP00000321711	DI3L1_HUMAN	E9PS35_HUMAN,E9PIL0_HUMAN,E9PI27_HUMAN,E9PI20_HUMAN	UPI000162779D	.	deleterious(0.01)	possibly_damaging(0.759)	11/17	.	hmmpanther:PTHR23355,hmmpanther:PTHR23355:SF30,Pfam_domain:PF00773,SMART_domains:SM00955,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCCGTCC	.	5	ESCA
MPI	0	.	GRCh37	15	75190157	75190157	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*86C>G	.	.	ENST00000352410	8/8	48	34	14	34	34	0	MPI,3_prime_UTR_variant,,ENST00000566377,;MPI,3_prime_UTR_variant,,ENST00000352410,;MPI,3_prime_UTR_variant,,ENST00000323744,;MPI,3_prime_UTR_variant,,ENST00000563786,;MPI,3_prime_UTR_variant,,ENST00000535694,;MPI,3_prime_UTR_variant,,ENST00000567177,;FAM219B,downstream_gene_variant,,ENST00000563119,;MPI,downstream_gene_variant,,ENST00000568828,;MPI,downstream_gene_variant,,ENST00000563422,;MPI,downstream_gene_variant,,ENST00000569931,;MPI,downstream_gene_variant,,ENST00000562606,;MPI,downstream_gene_variant,,ENST00000564633,;FAM219B,downstream_gene_variant,,ENST00000565772,;FAM219B,downstream_gene_variant,,ENST00000562698,;MPI,downstream_gene_variant,,ENST00000564003,;MPI,downstream_gene_variant,,ENST00000567132,;MPI,downstream_gene_variant,,ENST00000565576,;MPI,downstream_gene_variant,,ENST00000562800,;FAM219B,downstream_gene_variant,,ENST00000357635,;MPI,downstream_gene_variant,,ENST00000568907,;CTD-2235H24.2,upstream_gene_variant,,ENST00000564692,;FAM219B,downstream_gene_variant,,ENST00000563706,;FAM219B,downstream_gene_variant,,ENST00000564723,;MPI,non_coding_transcript_exon_variant,,ENST00000566556,;FAM219B,downstream_gene_variant,,ENST00000563877,;FAM219B,downstream_gene_variant,,ENST00000569524,;FAM219B,downstream_gene_variant,,ENST00000566894,;FAM219B,downstream_gene_variant,,ENST00000569761,;FAM219B,downstream_gene_variant,,ENST00000563069,;MPI,downstream_gene_variant,,ENST00000561470,;MPI,downstream_gene_variant,,ENST00000567116,;FAM219B,downstream_gene_variant,,ENST00000563671,;FAM219B,downstream_gene_variant,,ENST00000564019,;FAM219B,downstream_gene_variant,,ENST00000566132,;FAM219B,downstream_gene_variant,,ENST00000570143,;FAM219B,downstream_gene_variant,,ENST00000566194,;MPI,downstream_gene_variant,,ENST00000568840,;FAM219B,downstream_gene_variant,,ENST00000567388,;FAM219B,downstream_gene_variant,,ENST00000564857,;FAM219B,downstream_gene_variant,,ENST00000563413,;	G	ENSG00000178802	ENST00000352410	Transcript	3_prime_UTR_variant	1425	.	.	.	.	.	.	.	1	MPI	HGNC	7216	protein_coding	YES	CCDS10272.1	ENSP00000318318	MPI_HUMAN	H3BPU7_HUMAN,H3BPM5_HUMAN,H3BPB8_HUMAN,H3BP57_HUMAN,F5GX71_HUMAN	UPI000000DB74	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTCCTTGC	.	5	ESCA
AKAP13	0	.	GRCh37	15	86262365	86262365	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6072C>T	p.%3D	p.Y2024Y	ENST00000361243	23/37	63	36	27	52	52	0	AKAP13,synonymous_variant,p.%3D,ENST00000394518,;AKAP13,synonymous_variant,p.%3D,ENST00000361243,;AKAP13,synonymous_variant,p.%3D,ENST00000394510,;AKAP13,non_coding_transcript_exon_variant,,ENST00000560676,;AKAP13,non_coding_transcript_exon_variant,,ENST00000560579,;AKAP13,non_coding_transcript_exon_variant,,ENST00000559820,;AKAP13,downstream_gene_variant,,ENST00000557852,;AKAP13,non_coding_transcript_exon_variant,,ENST00000558644,;AKAP13,upstream_gene_variant,,ENST00000558009,;AKAP13,downstream_gene_variant,,ENST00000559278,;AKAP13,downstream_gene_variant,,ENST00000560482,;	T	ENSG00000170776	ENST00000361243	Transcript	synonymous_variant	6153	6072	2024	Y	taC/taT	.	.	.	1	AKAP13	HGNC	371	protein_coding	YES	CCDS32320.1	ENSP00000354718	AKP13_HUMAN	H0YMI5_HUMAN,A8MYJ1_HUMAN	UPI00001A8BEB	.	.	.	23/37	.	PROSITE_profiles:PS50010,hmmpanther:PTHR13944:SF4,hmmpanther:PTHR13944,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTACAGCCA	.	5	ESCA
MYH11	0	.	GRCh37	16	15854505	15854505	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1161A>G	p.%3D	p.K387K	ENST00000396324	12/42	125	79	46	98	98	0	MYH11,synonymous_variant,p.%3D,ENST00000452625,;MYH11,synonymous_variant,p.%3D,ENST00000576790,;MYH11,synonymous_variant,p.%3D,ENST00000300036,;MYH11,synonymous_variant,p.%3D,ENST00000396324,;MYH11,non_coding_transcript_exon_variant,,ENST00000570785,;	C	ENSG00000133392	ENST00000396324	Transcript	synonymous_variant	1249	1161	387	K	aaA/aaG	.	.	.	-1	MYH11	HGNC	7569	protein_coding	YES	CCDS45423.1	ENSP00000379616	MYH11_HUMAN	Q68D89_HUMAN,Q66K75_HUMAN	UPI00005B7237	.	.	.	12/42	.	Superfamily_domains:SSF52540,SMART_domains:SM00242,Pfam_domain:PF00063,hmmpanther:PTHR13140:SF335,hmmpanther:PTHR13140,PROSITE_profiles:PS51456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAACTTTCTG	.	5	ESCA
LUC7L	0	.	GRCh37	16	239289	239289	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024A>T	p.Ser342Cys	p.S342C	ENST00000293872	10/10	55	26	29	54	54	0	LUC7L,missense_variant,p.Ser342Cys,ENST00000293872,;LUC7L,missense_variant,p.Ser141Cys,ENST00000429378,;LUC7L,3_prime_UTR_variant,,ENST00000397783,;LUC7L,3_prime_UTR_variant,,ENST00000337351,;LUC7L,3_prime_UTR_variant,,ENST00000442701,;LUC7L,downstream_gene_variant,,ENST00000397780,;LUC7L,downstream_gene_variant,,ENST00000430864,;LA16c-OS12.2,upstream_gene_variant,,ENST00000595428,;LUC7L,3_prime_UTR_variant,,ENST00000426094,;LUC7L,non_coding_transcript_exon_variant,,ENST00000468732,;LUC7L,non_coding_transcript_exon_variant,,ENST00000490762,;LUC7L,non_coding_transcript_exon_variant,,ENST00000464711,;LUC7L,downstream_gene_variant,,ENST00000418978,;LUC7L,downstream_gene_variant,,ENST00000495349,;LUC7L,downstream_gene_variant,,ENST00000419516,;	A	ENSG00000007392	ENST00000293872	Transcript	missense_variant	1135	1024	342	S/C	Agc/Tgc	.	.	.	-1	LUC7L	HGNC	6723	protein_coding	YES	CCDS32348.1	ENSP00000293872	LUC7L_HUMAN	Q1W6G4_HUMAN,B8ZZ12_HUMAN,B8ZZ10_HUMAN,B8ZZ09_HUMAN,A8MYV2_HUMAN,D3DU41_HUMAN	UPI00000467F8	.	deleterious_low_confidence(0)	unknown(0)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12375:SF31,hmmpanther:PTHR12375	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGCTCCGCC	.	5	ESCA
SRCAP	0	.	GRCh37	16	30734343	30734343	+	Missense_Mutation	SNP	C	C	T	rs753316154	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3952C>T	p.Arg1318Trp	p.R1318W	ENST00000262518	24/34	70	54	15	45	45	0	SRCAP,missense_variant,p.Arg1318Trp,ENST00000262518,;SRCAP,missense_variant,p.Arg1160Trp,ENST00000344771,;SRCAP,missense_variant,p.Arg1256Trp,ENST00000395059,;SRCAP,missense_variant,p.Arg1141Trp,ENST00000380361,;SRCAP,non_coding_transcript_exon_variant,,ENST00000483083,;	T	ENSG00000080603	ENST00000262518	Transcript	missense_variant	4337	3952	1318	R/W	Cgg/Tgg	rs753316154	.	.	1	SRCAP	HGNC	16974	protein_coding	YES	CCDS10689.2	ENSP00000262518	SRCAP_HUMAN	G1UI29_HUMAN,C9J4U4_HUMAN	UPI000059D368	.	.	possibly_damaging(0.689)	24/34	.	hmmpanther:PTHR10799:SF581,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTCGGGAT	.	5	ESCA
ANKS3	0	.	GRCh37	16	4777008	4777008	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.341A>G	p.Asn114Ser	p.N114S	ENST00000304283	4/18	41	26	15	25	25	0	ANKS3,missense_variant,p.Asn114Ser,ENST00000304283,;ANKS3,missense_variant,p.Asn41Ser,ENST00000585773,;ANKS3,missense_variant,p.Asn114Ser,ENST00000592190,;ANKS3,missense_variant,p.Asn114Ser,ENST00000590147,;ANKS3,5_prime_UTR_variant,,ENST00000592698,;ANKS3,intron_variant,,ENST00000586605,;ANKS3,intron_variant,,ENST00000592421,;ANKS3,intron_variant,,ENST00000446014,;ANKS3,intron_variant,,ENST00000592711,;ANKS3,intron_variant,,ENST00000450067,;ANKS3,intron_variant,,ENST00000586166,;ANKS3,intron_variant,,ENST00000589065,;RP11-127I20.7,downstream_gene_variant,,ENST00000588099,;ANKS3,missense_variant,p.Asn114Ser,ENST00000587005,;ANKS3,missense_variant,p.Asn114Ser,ENST00000590193,;ANKS3,non_coding_transcript_exon_variant,,ENST00000591653,;ANKS3,non_coding_transcript_exon_variant,,ENST00000590803,;ANKS3,intron_variant,,ENST00000592068,;ANKS3,intron_variant,,ENST00000592077,;ANKS3,intron_variant,,ENST00000590730,;ANKS3,intron_variant,,ENST00000593120,;ANKS3,intron_variant,,ENST00000586159,;ANKS3,intron_variant,,ENST00000591281,;ANKS3,downstream_gene_variant,,ENST00000590689,;ANKS3,upstream_gene_variant,,ENST00000586632,;	C	ENSG00000168096	ENST00000304283	Transcript	missense_variant	636	341	114	N/S	aAc/aGc	.	.	.	-1	ANKS3	HGNC	29422	protein_coding	YES	CCDS10520.1	ENSP00000304586	ANKS3_HUMAN	K7ERR7_HUMAN,K7ERF3_HUMAN,K7EQE0_HUMAN,K7EKD2_HUMAN,K7EJY2_HUMAN,D3DUE4_HUMAN	UPI00001C08FE	.	deleterious(0.03)	probably_damaging(0.999)	4/18	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24184:SF6,hmmpanther:PTHR24184,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01415	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCGTTGCCA	.	5	ESCA
SALL1	0	.	GRCh37	16	51173802	51173802	+	Silent	SNP	G	G	A	rs144747142	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2331C>T	p.%3D	p.N777N	ENST00000251020	2/3	60	39	20	52	52	0	SALL1,synonymous_variant,p.%3D,ENST00000251020,;SALL1,synonymous_variant,p.%3D,ENST00000570206,;SALL1,synonymous_variant,p.%3D,ENST00000440970,;SALL1,intron_variant,,ENST00000541611,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,;	A	ENSG00000103449	ENST00000251020	Transcript	synonymous_variant	2365	2331	777	N	aaC/aaT	rs144747142	.	.	-1	SALL1	HGNC	10524	protein_coding	YES	CCDS10747.1	ENSP00000251020	SALL1_HUMAN	H3BSM9_HUMAN	UPI000013CCD8	.	.	.	2/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	A:0.0010	A:0	A:0	.	A:0.005	A:0	A:0	A:0.0002	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCGTTCGT	byFrequency|byCluster|by1000G	5	ESCA
TOX3	0	.	GRCh37	16	52473227	52473227	+	Missense_Mutation	SNP	G	G	C	rs756934373	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1641C>G	p.Ile547Met	p.I547M	ENST00000219746	7/7	66	34	32	60	60	0	TOX3,missense_variant,p.Ile542Met,ENST00000407228,;TOX3,missense_variant,p.Ile547Met,ENST00000219746,;TOX3,non_coding_transcript_exon_variant,,ENST00000566696,;	C	ENSG00000103460	ENST00000219746	Transcript	missense_variant	1926	1641	547	I/M	atC/atG	rs756934373	.	.	-1	TOX3	HGNC	11972	protein_coding	YES	CCDS54009.1	ENSP00000219746	TOX3_HUMAN	H3BTZ9_HUMAN	UPI00001972E7	.	deleterious_low_confidence(0)	unknown(0)	7/7	.	hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCGATGGC	.	5	ESCA
DYNC1LI2	0	.	GRCh37	16	66755061	66755061	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2564C>T	.	.	ENST00000258198	13/13	19	14	5	19	19	0	DYNC1LI2,3_prime_UTR_variant,,ENST00000258198,;DYNC1LI2,downstream_gene_variant,,ENST00000563628,;DYNC1LI2,downstream_gene_variant,,ENST00000379482,;DYNC1LI2,downstream_gene_variant,,ENST00000443351,;DYNC1LI2,downstream_gene_variant,,ENST00000569320,;RP11-63M22.2,non_coding_transcript_exon_variant,,ENST00000569274,;DYNC1LI2,downstream_gene_variant,,ENST00000564559,;DYNC1LI2,downstream_gene_variant,,ENST00000567499,;DYNC1LI2,downstream_gene_variant,,ENST00000568453,;DYNC1LI2,downstream_gene_variant,,ENST00000564833,;	A	ENSG00000135720	ENST00000258198	Transcript	3_prime_UTR_variant	4250	.	.	.	.	.	.	.	-1	DYNC1LI2	HGNC	2966	protein_coding	YES	CCDS10818.1	ENSP00000258198	DC1L2_HUMAN	.	UPI0000129A0D	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTGTTAAA	.	5	ESCA
PSMB10	0	.	GRCh37	16	67968725	67968729	+	Frame_Shift_Del	DEL	TCAGT	TCAGT	-	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	TCAGT	TCAGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681_685delACTGA	p.Ser229ThrfsTer46	p.S229Tfs*46	ENST00000358514	7/8	34	24	10	21	21	0	PSMB10,frameshift_variant,p.Ser229ThrfsTer46,ENST00000358514,;PSMB10,frameshift_variant,p.Ser109ThrfsTer52,ENST00000574576,;CTRL,upstream_gene_variant,,ENST00000571605,;LCAT,downstream_gene_variant,,ENST00000264005,;CTRL,upstream_gene_variant,,ENST00000574481,;CTRL,upstream_gene_variant,,ENST00000571044,;CTRL,upstream_gene_variant,,ENST00000576408,;CTC-479C5.12,3_prime_UTR_variant,,ENST00000573493,;PSMB10,non_coding_transcript_exon_variant,,ENST00000570985,;CTC-479C5.12,non_coding_transcript_exon_variant,,ENST00000575231,;PSMB10,downstream_gene_variant,,ENST00000570304,;CTRL,upstream_gene_variant,,ENST00000575302,;CTRL,upstream_gene_variant,,ENST00000572144,;CTRL,upstream_gene_variant,,ENST00000576915,;PSMB10,downstream_gene_variant,,ENST00000575556,;	-	ENSG00000205220	ENST00000358514	Transcript	frameshift_variant	1019-1023	681-685	227-229	TLS/TX	acACTGAgc/acgc	.	.	.	-1	PSMB10	HGNC	9538	protein_coding	YES	CCDS10853.1	ENSP00000351314	PSB10_HUMAN	.	UPI00001325EC	.	.	.	7/8	.	hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF41,Gene3D:3.60.20.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTGAGCTCAGTGTCCG	.	3	ESCA
DHX38	0	.	GRCh37	16	72130051	72130051	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-6C>A	.	.	ENST00000268482	2/27	60	31	29	45	45	0	DHX38,5_prime_UTR_variant,,ENST00000566794,;DHX38,5_prime_UTR_variant,,ENST00000536867,;DHX38,5_prime_UTR_variant,,ENST00000268482,;DHX38,5_prime_UTR_variant,,ENST00000566489,;TXNL4B,upstream_gene_variant,,ENST00000423037,;TXNL4B,upstream_gene_variant,,ENST00000268483,;TXNL4B,upstream_gene_variant,,ENST00000569767,;TXNL4B,upstream_gene_variant,,ENST00000562153,;TXNL4B,upstream_gene_variant,,ENST00000426362,;DHX38,5_prime_UTR_variant,,ENST00000579387,;TXNL4B,upstream_gene_variant,,ENST00000565171,;DHX38,upstream_gene_variant,,ENST00000566329,;DHX38,upstream_gene_variant,,ENST00000563650,;DHX38,upstream_gene_variant,,ENST00000564307,;	A	ENSG00000140829	ENST00000268482	Transcript	5_prime_UTR_variant	504	.	.	.	.	.	.	.	1	DHX38	HGNC	17211	protein_coding	YES	CCDS10907.1	ENSP00000268482	PRP16_HUMAN	H3BV01_HUMAN,H3BQT9_HUMAN,B4DN69_HUMAN,B4DM30_HUMAN	UPI000002FBFE	.	.	.	2/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATCCTGTG	.	5	ESCA
CPD	0	.	GRCh37	17	28793667	28793667	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1835G>C	.	.	ENST00000225719	21/21	96	75	21	64	64	0	CPD,3_prime_UTR_variant,,ENST00000225719,;CPD,downstream_gene_variant,,ENST00000584221,;CPD,downstream_gene_variant,,ENST00000543464,;CPD,downstream_gene_variant,,ENST00000579502,;	C	ENSG00000108582	ENST00000225719	Transcript	3_prime_UTR_variant	6054	.	.	.	.	.	.	.	1	CPD	HGNC	2301	protein_coding	YES	CCDS11257.1	ENSP00000225719	CBPD_HUMAN	.	UPI000000DAF7	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAAGAGTAC	.	5	ESCA
MED1	0	.	GRCh37	17	37564050	37564050	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4424C>T	p.Ser1475Phe	p.S1475F	ENST00000300651	17/17	47	22	25	26	26	0	MED1,missense_variant,p.Ser1475Phe,ENST00000300651,;MED1,intron_variant,,ENST00000394287,;CTB-131K11.1,downstream_gene_variant,,ENST00000582842,;MED1,3_prime_UTR_variant,,ENST00000577831,;	A	ENSG00000125686	ENST00000300651	Transcript	missense_variant	4648	4424	1475	S/F	tCt/tTt	.	.	.	-1	MED1	HGNC	9234	protein_coding	YES	CCDS11336.1	ENSP00000300651	MED1_HUMAN	.	UPI0000167F57	.	deleterious_low_confidence(0)	unknown(0)	17/17	.	hmmpanther:PTHR12881	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATAAGATTTC	.	5	ESCA
KRTAP9-9	0	.	GRCh37	17	39411984	39411984	+	Missense_Mutation	SNP	A	A	G	rs771073194	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347A>G	p.Tyr116Cys	p.Y116C	ENST00000394008	1/1	217	106	111	113	113	0	KRTAP9-9,missense_variant,p.Tyr116Cys,ENST00000394008,;	G	ENSG00000198083	ENST00000394008	Transcript	missense_variant	349	347	116	Y/C	tAc/tGc	rs771073194	.	.	1	KRTAP9-9	HGNC	16773	protein_coding	YES	CCDS54127.1	ENSP00000377576	.	B5MDD6_HUMAN	UPI00002264BA	.	tolerated(0.12)	probably_damaging(0.929)	1/1	.	hmmpanther:PTHR23262:SF36,hmmpanther:PTHR23262,Pfam_domain:PF13885	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTACTACC	.	5	ESCA
KRT32	0	.	GRCh37	17	39616156	39616156	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*206C>G	.	.	ENST00000225899	7/7	61	38	23	43	43	0	KRT32,3_prime_UTR_variant,,ENST00000225899,;	C	ENSG00000108759	ENST00000225899	Transcript	3_prime_UTR_variant	1657	.	.	.	.	.	.	.	-1	KRT32	HGNC	6449	protein_coding	YES	CCDS11393.1	ENSP00000225899	K1H2_HUMAN	.	UPI000013C883	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGAACAG	.	5	ESCA
PYY	0	.	GRCh37	17	42030684	42030684	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168C>G	p.%3D	p.L56L	ENST00000360085	5/7	52	38	14	18	18	0	PYY,synonymous_variant,p.%3D,ENST00000360085,;PYY,synonymous_variant,p.%3D,ENST00000592796,;	C	ENSG00000131096	ENST00000360085	Transcript	synonymous_variant	709	168	56	L	ctC/ctG	.	.	.	-1	PYY	HGNC	9748	protein_coding	YES	CCDS32662.1	ENSP00000353198	PYY_HUMAN	.	UPI000013CDD0	.	.	.	5/7	.	PROSITE_profiles:PS50276,hmmpanther:PTHR10533:SF5,hmmpanther:PTHR10533,PROSITE_patterns:PS00265,Pfam_domain:PF00159,SMART_domains:SM00309,Prints_domain:PR00278	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTGAGGTA	.	5	ESCA
WNT3	0	.	GRCh37	17	44841730	44841730	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*266G>A	.	.	ENST00000225512	5/5	39	17	22	15	15	0	WNT3,3_prime_UTR_variant,,ENST00000225512,;	T	ENSG00000108379	ENST00000225512	Transcript	3_prime_UTR_variant	1497	.	.	.	.	.	.	.	-1	WNT3	HGNC	12782	protein_coding	YES	CCDS11505.1	ENSP00000225512	WNT3_HUMAN	.	UPI000003143C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATCAGACC	.	5	ESCA
LPO	0	.	GRCh37	17	56343639	56343639	+	Missense_Mutation	SNP	G	G	A	rs763760771	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1645G>A	p.Asp549Asn	p.D549N	ENST00000262290	11/13	39	32	7	28	28	0	LPO,missense_variant,p.Asp466Asn,ENST00000421678,;LPO,missense_variant,p.Asp549Asn,ENST00000262290,;LPO,missense_variant,p.Asp490Asn,ENST00000543544,;LPO,missense_variant,p.Asp466Asn,ENST00000582328,;MPO,downstream_gene_variant,,ENST00000340482,;MPO,downstream_gene_variant,,ENST00000225275,;MPO,downstream_gene_variant,,ENST00000577220,;LPO,3_prime_UTR_variant,,ENST00000580890,;LPO,3_prime_UTR_variant,,ENST00000389576,;	A	ENSG00000167419	ENST00000262290	Transcript	missense_variant	1961	1645	549	D/N	Gac/Aac	rs763760771	.	.	1	LPO	HGNC	6678	protein_coding	YES	CCDS32689.1	ENSP00000262290	PERL_HUMAN	J3QSD8_HUMAN,F5H386_HUMAN	UPI0000131631	.	deleterious(0)	probably_damaging(1)	11/13	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF53,hmmpanther:PTHR11475,Pfam_domain:PF03098,Gene3D:1.10.640.10,Superfamily_domains:SSF48113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTTGACCTG	.	5	ESCA
H3F3B	0	.	GRCh37	17	73774026	73774026	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*650C>T	.	.	ENST00000254810	4/4	57	39	18	51	51	0	H3F3B,3_prime_UTR_variant,,ENST00000254810,;H3F3B,downstream_gene_variant,,ENST00000591890,;H3F3B,downstream_gene_variant,,ENST00000587560,;H3F3B,downstream_gene_variant,,ENST00000592643,;H3F3B,downstream_gene_variant,,ENST00000586270,;H3F3B,downstream_gene_variant,,ENST00000589599,;H3F3B,downstream_gene_variant,,ENST00000586607,;H3F3B,downstream_gene_variant,,ENST00000587171,;H3F3B,downstream_gene_variant,,ENST00000593254,;H3F3B,downstream_gene_variant,,ENST00000589417,;H3F3B,downstream_gene_variant,,ENST00000586518,;H3F3B,downstream_gene_variant,,ENST00000589949,;	A	ENSG00000132475	ENST00000254810	Transcript	3_prime_UTR_variant	1194	.	.	.	.	.	.	.	-1	H3F3B	HGNC	4765	protein_coding	YES	CCDS11729.1	ENSP00000254810	H33_HUMAN	K7EK07_HUMAN,B4E380_HUMAN,B2R4P9_HUMAN	UPI00000007B0	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTATGAGAAC	.	5	ESCA
TP53	0	.	GRCh37	17	7579315	7579315	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	4/11	282	62	219	245	245	0	TP53,stop_gained,p.Cys124Ter,ENST00000508793,;TP53,stop_gained,p.Cys124Ter,ENST00000413465,;TP53,stop_gained,p.Cys124Ter,ENST00000604348,;TP53,stop_gained,p.Cys124Ter,ENST00000420246,;TP53,stop_gained,p.Cys124Ter,ENST00000269305,;TP53,stop_gained,p.Cys124Ter,ENST00000359597,;TP53,stop_gained,p.Cys124Ter,ENST00000445888,;TP53,stop_gained,p.Cys124Ter,ENST00000503591,;TP53,stop_gained,p.Cys124Ter,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	stop_gained	562	372	124	C/*	tgC/tgA	TP53_g.11603C>A,TP53_g.11603C>G,COSM69020,COSM326716,COSM326718,COSM326717,COSM3388233,COSM3388232	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.C124*|c.372C>A|4,SITE|p.C124*|c.372C>A|4,SITE|p.C124*|c.372C>A|4,CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,BUFFER|p.?|c.375+2T>C|3,BUFFER|p.?|c.375+1G>A|7,BUFFER|p.?|c.375+1G>A|7,BUFFER|p.?|c.375+1G>T|5,BUFFER|p.?|c.375+1G>T|5,BUFFER|p.?|c.375+1G>T|3,BUFFER|p.?|c.375+1G>A|11,BUFFER|p.?|c.375+1G>A|6,BUFFER|p.?|c.375+1G>A|6,BUFFER|p.?|c.375+1G>T|8,BUFFER|p.T125T|c.375G>A|19,BUFFER|p.T125T|c.375G>C|3,BUFFER|p.T125T|c.375G>T|10,BUFFER|p.T125T|c.375G>T|3,BUFFER|p.T125T|c.375G>T|12,BUFFER|p.T125T|c.375G>A|3,BUFFER|p.T125T|c.375G>C|5,BUFFER|p.T125T|c.375G>C|3,BUFFER|p.T125T|c.375G>T|12,BUFFER|p.T125T|c.375G>T|17,BUFFER|p.T125T|c.375G>A|11,BUFFER|p.T125T|c.375G>A|11,BUFFER|p.T125T|c.375G>A|3,BUFFER|p.T125M|c.374C>T|10,BUFFER|p.T125M|c.374C>T|3,BUFFER|p.T125K|c.374C>A|4,BUFFER|p.T125M|c.374C>T|4,BUFFER|p.T125M|c.374C>T|17,BUFFER|p.T125M|c.374C>T|10,BUFFER|p.T125R|c.374C>G|3,BUFFER|p.T125P|c.373A>C|3,BUFFER|p.C124G|c.370T>G|3,BUFFER|p.C124R|c.370T>C|3,BUFFER|p.V122fs*26|c.365_366delTG|4,BUFFER|p.V122fs*26|c.365_366delTG|4,BUFFER|p.V122fs*26|c.365_366delTG|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGTGCAAGT	.	5	ESCA
WBP11P1	0	.	GRCh37	18	30092380	30092380	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.755C>G	.	.	ENST00000567636	1/1	23	13	10	32	32	0	WBP11P1,non_coding_transcript_exon_variant,,ENST00000567636,;WBP11P1,non_coding_transcript_exon_variant,,ENST00000562560,;	G	ENSG00000260389	ENST00000567636	Transcript	non_coding_transcript_exon_variant	755	.	.	.	.	.	.	.	1	WBP11P1	HGNC	26250	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTGTTCCACAT	.	3	ESCA
CTDP1	0	.	GRCh37	18	77473117	77473117	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009G>C	p.Glu337Gln	p.E337Q	ENST00000299543	7/13	40	27	13	20	20	0	CTDP1,missense_variant,p.Glu269Gln,ENST00000591598,;CTDP1,missense_variant,p.Glu337Gln,ENST00000075430,;CTDP1,missense_variant,p.Glu337Gln,ENST00000299543,;	C	ENSG00000060069	ENST00000299543	Transcript	missense_variant	1156	1009	337	E/Q	Gaa/Caa	.	.	.	1	CTDP1	HGNC	2498	protein_coding	YES	CCDS12017.1	ENSP00000299543	CTDP1_HUMAN	K7EPW4_HUMAN	UPI000013C57B	.	deleterious(0)	possibly_damaging(0.878)	7/13	.	PROSITE_profiles:PS50969,hmmpanther:PTHR23081:SF0,hmmpanther:PTHR23081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCGAGAATCT	.	3	ESCA
PTPRM	0	.	GRCh37	18	8244113	8244113	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2358G>A	p.%3D	p.V786V	ENST00000580170	15/33	100	71	28	76	76	0	PTPRM,synonymous_variant,p.%3D,ENST00000332175,;PTPRM,synonymous_variant,p.%3D,ENST00000400060,;PTPRM,synonymous_variant,p.%3D,ENST00000444013,;PTPRM,synonymous_variant,p.%3D,ENST00000400053,;PTPRM,synonymous_variant,p.%3D,ENST00000577468,;PTPRM,synonymous_variant,p.%3D,ENST00000580170,;PTPRM,non_coding_transcript_exon_variant,,ENST00000578093,;PTPRM,upstream_gene_variant,,ENST00000580838,;PTPRM,non_coding_transcript_exon_variant,,ENST00000577827,;	A	ENSG00000173482	ENST00000580170	Transcript	synonymous_variant	3395	2358	786	V	gtG/gtA	.	.	.	1	PTPRM	HGNC	9675	protein_coding	YES	CCDS58613.1	ENSP00000463325	PTPRM_HUMAN	Q49AC9_HUMAN	UPI00015CFC03	.	.	.	15/33	.	hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTGATGGT	.	5	ESCA
DKFZP761J1410	0	.	GRCh37	19	11476057	11476057	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*691G>C	.	.	ENST00000591608	10/10	65	36	28	39	39	0	DKFZP761J1410,3_prime_UTR_variant,,ENST00000251473,;DKFZP761J1410,3_prime_UTR_variant,,ENST00000591608,;CTD-2342J14.6,downstream_gene_variant,,ENST00000590399,;DKFZP761J1410,downstream_gene_variant,,ENST00000588360,;DKFZP761J1410,downstream_gene_variant,,ENST00000587801,;	C	ENSG00000105520	ENST00000591608	Transcript	3_prime_UTR_variant	2239	.	.	.	.	.	.	.	1	DKFZP761J1410	Uniprot_gn	.	protein_coding	YES	CCDS59352.1	ENSP00000466898	.	Q69YU8_HUMAN,K7EMX8_HUMAN	UPI00001AE726	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAGGTTTT	.	5	ESCA
ZNF99	0	.	GRCh37	19	22940566	22940566	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2145C>T	p.%3D	p.S715S	ENST00000596209	4/4	50	30	20	47	47	0	ZNF99,synonymous_variant,p.%3D,ENST00000397104,;ZNF99,synonymous_variant,p.%3D,ENST00000596209,;CTC-451A6.4,upstream_gene_variant,,ENST00000442497,;	A	ENSG00000213973	ENST00000596209	Transcript	synonymous_variant	2236	2145	715	S	agC/agT	.	.	.	-1	ZNF99	HGNC	13175	protein_coding	YES	CCDS59369.1	ENSP00000472969	.	M0R335_HUMAN	UPI0000426011	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24375:SF102,hmmpanther:PTHR24375,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGGCTAAA	.	5	ESCA
PAK4	0	.	GRCh37	19	39665640	39665640	+	Missense_Mutation	SNP	G	G	A	rs780200774	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1168G>A	p.Glu390Lys	p.E390K	ENST00000593690	7/11	64	50	14	43	43	0	PAK4,missense_variant,p.Glu300Lys,ENST00000321944,;PAK4,missense_variant,p.Glu390Lys,ENST00000360442,;PAK4,missense_variant,p.Glu390Lys,ENST00000358301,;PAK4,missense_variant,p.Glu237Lys,ENST00000599470,;PAK4,missense_variant,p.Glu390Lys,ENST00000593690,;PAK4,missense_variant,p.Glu237Lys,ENST00000599386,;PAK4,missense_variant,p.Glu390Lys,ENST00000435673,;PAK4,intron_variant,,ENST00000597715,;PAK4,downstream_gene_variant,,ENST00000602004,;PAK4,downstream_gene_variant,,ENST00000599657,;PAK4,downstream_gene_variant,,ENST00000593480,;PAK4,upstream_gene_variant,,ENST00000600350,;	A	ENSG00000130669	ENST00000593690	Transcript	missense_variant	1595	1168	390	E/K	Gag/Aag	rs780200774	.	.	1	PAK4	HGNC	16059	protein_coding	YES	CCDS12528.1	ENSP00000469413	PAK4_HUMAN	M0R2X4_HUMAN,B4DUG0_HUMAN	UPI0000001281	.	deleterious(0)	probably_damaging(0.971)	7/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF181,Pfam_domain:PF00069,Gene3D:1.10.510.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGACGAGCTC	byFrequency	5	ESCA
PSMC4	0	.	GRCh37	19	40477127	40477127	+	Missense_Mutation	SNP	C	C	G	rs547778812	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18C>G	p.Ile6Met	p.I6M	ENST00000157812	1/11	130	83	47	57	57	0	PSMC4,missense_variant,p.Ile6Met,ENST00000157812,;PSMC4,missense_variant,p.Ile6Met,ENST00000455878,;PSMC4,non_coding_transcript_exon_variant,,ENST00000593455,;PSMC4,non_coding_transcript_exon_variant,,ENST00000596386,;PSMC4,non_coding_transcript_exon_variant,,ENST00000601697,;	G	ENSG00000013275	ENST00000157812	Transcript	missense_variant	216	18	6	I/M	atC/atG	rs547778812,COSM711435	.	.	1	PSMC4	HGNC	9551	protein_coding	YES	CCDS12547.1	ENSP00000157812	PRS6B_HUMAN	A8K2M0_HUMAN	UPI0000132373	.	deleterious_low_confidence(0)	benign(0.372)	1/11	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCATCTTGGT	by1000G	5	ESCA
ANKRD24	0	.	GRCh37	19	4219681	4219681	+	Missense_Mutation	SNP	G	G	A	rs546339422	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3097G>A	p.Glu1033Lys	p.E1033K	ENST00000600132	19/22	71	47	23	34	34	0	ANKRD24,missense_variant,p.Glu1123Lys,ENST00000262970,;ANKRD24,missense_variant,p.Glu1033Lys,ENST00000600132,;ANKRD24,missense_variant,p.Glu1033Lys,ENST00000318934,;ANKRD24,downstream_gene_variant,,ENST00000597689,;ANKRD24,downstream_gene_variant,,ENST00000595096,;	A	ENSG00000089847	ENST00000600132	Transcript	missense_variant	3373	3097	1033	E/K	Gag/Aag	rs546339422,COSM178897,COSM178898	.	.	1	ANKRD24	HGNC	29424	protein_coding	YES	CCDS45925.1	ENSP00000471252	ANR24_HUMAN	.	UPI000041F5A9	.	tolerated(0.15)	probably_damaging(0.911)	19/22	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24137,hmmpanther:PTHR24137:SF8	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACCGAGGCG	by1000G	5	ESCA
GRIN2D	0	.	GRCh37	19	48945210	48945210	+	Missense_Mutation	SNP	G	G	A	rs768177826	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2437G>A	p.Asp813Asn	p.D813N	ENST00000263269	11/13	48	37	11	29	29	0	GRIN2D,missense_variant,p.Asp813Asn,ENST00000263269,;GRWD1,upstream_gene_variant,,ENST00000253237,;GRWD1,upstream_gene_variant,,ENST00000598711,;GRWD1,upstream_gene_variant,,ENST00000599949,;	A	ENSG00000105464	ENST00000263269	Transcript	missense_variant	2525	2437	813	D/N	Gat/Aat	rs768177826,COSM3536497	.	.	1	GRIN2D	HGNC	4588	protein_coding	YES	CCDS12719.1	ENSP00000263269	NMDE4_HUMAN	.	UPI000013D3DA	.	tolerated(0.2)	probably_damaging(0.916)	11/13	.	hmmpanther:PTHR18966:SF105,hmmpanther:PTHR18966,Pfam_domain:PF00497,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGGATGGT	.	5	ESCA
DBP	0	.	GRCh37	19	49140364	49140364	+	5'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-113A>T	.	.	ENST00000222122	1/4	26	16	10	8	8	0	DBP,5_prime_UTR_variant,,ENST00000601104,;DBP,5_prime_UTR_variant,,ENST00000222122,;CA11,downstream_gene_variant,,ENST00000596080,;DBP,upstream_gene_variant,,ENST00000593500,;CA11,downstream_gene_variant,,ENST00000084798,;DBP,upstream_gene_variant,,ENST00000599385,;SEC1P,upstream_gene_variant,,ENST00000430145,;SEC1P,upstream_gene_variant,,ENST00000474419,;SEC1P,upstream_gene_variant,,ENST00000483163,;DBP,non_coding_transcript_exon_variant,,ENST00000594723,;CA11,downstream_gene_variant,,ENST00000594088,;CA11,downstream_gene_variant,,ENST00000599267,;SEC1P,upstream_gene_variant,,ENST00000521217,;	A	ENSG00000105516	ENST00000222122	Transcript	5_prime_UTR_variant	332	.	.	.	.	.	.	.	-1	DBP	HGNC	2697	protein_coding	YES	CCDS12728.1	ENSP00000222122	DBP_HUMAN	M0QXW3_HUMAN	UPI0000000CC1	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGAGTGTAGC	.	2	ESCA
MYH14	0	.	GRCh37	19	50783319	50783319	+	Missense_Mutation	SNP	C	C	T	rs561525083	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4058C>T	p.Ala1353Val	p.A1353V	ENST00000601313	31/43	85	69	16	50	50	0	MYH14,missense_variant,p.Ala1353Val,ENST00000440075,;MYH14,missense_variant,p.Ala1353Val,ENST00000601313,;MYH14,missense_variant,p.Ala1345Val,ENST00000376970,;MYH14,missense_variant,p.Ala1312Val,ENST00000596571,;MYH14,missense_variant,p.Ala1320Val,ENST00000425460,;MYH14,missense_variant,p.Ala1320Val,ENST00000598205,;MYH14,missense_variant,p.Ala1353Val,ENST00000262269,;MYH14,upstream_gene_variant,,ENST00000595016,;	T	ENSG00000105357	ENST00000601313	Transcript	missense_variant	4088	4058	1353	A/V	gCg/gTg	rs561525083	.	.	1	MYH14	HGNC	23212	protein_coding	YES	CCDS54295.1	ENSP00000470298	MYH14_HUMAN	A1L2Z2_HUMAN	UPI0001641C2F	.	tolerated(0.3)	benign(0.01)	31/43	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF318,Pfam_domain:PF01576,Superfamily_domains:SSF90257	T:0.0004	T:0	T:0	.	T:0.002	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGGGCGCTGA	byFrequency|by1000G	3	ESCA
ZNF320	0	.	GRCh37	19	53385226	53385226	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153C>T	p.%3D	p.S51S	ENST00000595635	8/8	187	135	52	101	101	0	ZNF320,synonymous_variant,p.%3D,ENST00000595635,;ZNF320,synonymous_variant,p.%3D,ENST00000594741,;ZNF320,synonymous_variant,p.%3D,ENST00000597265,;ZNF320,synonymous_variant,p.%3D,ENST00000391781,;ZNF320,synonymous_variant,p.%3D,ENST00000593618,;ZNF320,intron_variant,,ENST00000597909,;ZNF320,intron_variant,,ENST00000597091,;ZNF320,intron_variant,,ENST00000600930,;ZNF320,upstream_gene_variant,,ENST00000598199,;	A	ENSG00000182986	ENST00000595635	Transcript	synonymous_variant	655	153	51	S	tcC/tcT	.	.	.	-1	ZNF320	HGNC	13842	protein_coding	YES	CCDS33095.1	ENSP00000473091	ZN320_HUMAN	Q6ZP55_HUMAN,M0R2L4_HUMAN,M0R1K6_HUMAN,M0R0Z8_HUMAN,M0QZA2_HUMAN	UPI00004EC06C	.	.	.	8/8	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF197,SMART_domains:SM00349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTGGAAGA	.	5	ESCA
NLRP4	0	.	GRCh37	19	56388480	56388480	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2644C>A	p.Gln882Lys	p.Q882K	ENST00000301295	8/10	155	108	47	86	86	0	NLRP4,missense_variant,p.Gln392Lys,ENST00000589437,;NLRP4,missense_variant,p.Gln882Lys,ENST00000301295,;NLRP4,missense_variant,p.Gln826Lys,ENST00000346986,;NLRP4,missense_variant,p.Gln807Lys,ENST00000587891,;	A	ENSG00000160505	ENST00000301295	Transcript	missense_variant	3066	2644	882	Q/K	Cag/Aag	.	.	.	1	NLRP4	HGNC	22943	protein_coding	YES	CCDS12936.1	ENSP00000301295	NALP4_HUMAN	K7ES09_HUMAN	UPI000013E6FD	.	tolerated(1)	benign(0.001)	8/10	.	hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106,Pfam_domain:PF13516,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGCAGCTG	.	5	ESCA
ZNF671	0	.	GRCh37	19	58232613	58232613	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841G>T	p.Gly281Ter	p.G281*	ENST00000317398	4/4	262	238	23	50	50	0	ZNF671,stop_gained,p.Gly281Ter,ENST00000317398,;ZNF671,stop_gained,p.Gly183Ter,ENST00000335820,;AC003006.7,intron_variant,,ENST00000594684,;ZNF551,downstream_gene_variant,,ENST00000596085,;ZNF671,downstream_gene_variant,,ENST00000596939,;AC003006.7,intron_variant,,ENST00000599221,;ZNF671,downstream_gene_variant,,ENST00000599961,;ZNF671,downstream_gene_variant,,ENST00000594803,;ZNF671,3_prime_UTR_variant,,ENST00000601584,;ZNF671,3_prime_UTR_variant,,ENST00000600125,;	A	ENSG00000083814	ENST00000317398	Transcript	stop_gained	937	841	281	G/*	Gga/Tga	.	.	.	-1	ZNF671	HGNC	26279	protein_coding	YES	CCDS12961.1	ENSP00000321848	ZN671_HUMAN	C9J3V7_HUMAN	UPI000013C612	.	.	.	4/4	.	hmmpanther:PTHR24390:SF44,hmmpanther:PTHR24390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGTCCCATGA	.	3	ESCA
UBE2M	0	.	GRCh37	19	59068438	59068438	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196C>T	p.Pro66Ser	p.P66S	ENST00000253023	2/6	36	12	24	53	53	0	UBE2M,missense_variant,p.Pro7Ser,ENST00000596985,;UBE2M,missense_variant,p.Pro66Ser,ENST00000253023,;UBE2M,5_prime_UTR_variant,,ENST00000595957,;CHMP2A,upstream_gene_variant,,ENST00000312547,;CHMP2A,upstream_gene_variant,,ENST00000600118,;MZF1,downstream_gene_variant,,ENST00000594234,;CHMP2A,upstream_gene_variant,,ENST00000601220,;MZF1,downstream_gene_variant,,ENST00000599369,;CHMP2A,upstream_gene_variant,,ENST00000596708,;CHMP2A,upstream_gene_variant,,ENST00000597848,;MZF1,downstream_gene_variant,,ENST00000215057,;CHMP2A,upstream_gene_variant,,ENST00000600006,;AC016629.8,upstream_gene_variant,,ENST00000600534,;AC016629.8,upstream_gene_variant,,ENST00000593642,;AC016629.8,upstream_gene_variant,,ENST00000600726,;UBE2M,non_coding_transcript_exon_variant,,ENST00000599829,;UBE2M,non_coding_transcript_exon_variant,,ENST00000593801,;CHMP2A,upstream_gene_variant,,ENST00000600804,;CHMP2A,upstream_gene_variant,,ENST00000597209,;MZF1,downstream_gene_variant,,ENST00000600004,;	A	ENSG00000130725	ENST00000253023	Transcript	missense_variant	775	196	66	P/S	Cct/Tct	.	.	.	-1	UBE2M	HGNC	12491	protein_coding	YES	CCDS12987.1	ENSP00000253023	UBC12_HUMAN	M0QX69_HUMAN	UPI0000020ECC	.	deleterious(0)	probably_damaging(1)	2/6	.	PROSITE_profiles:PS50127,hmmpanther:PTHR24067,Gene3D:3.10.110.10,Pfam_domain:PF00179,SMART_domains:SM00212,Superfamily_domains:SSF54495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCAGGACAGA	.	5	ESCA
PTBP1	0	.	GRCh37	19	811243	811243	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*417G>C	.	.	ENST00000356948	15/15	12	4	7	9	9	0	PTBP1,3_prime_UTR_variant,,ENST00000349038,;PTBP1,3_prime_UTR_variant,,ENST00000394601,;PTBP1,3_prime_UTR_variant,,ENST00000356948,;PTBP1,3_prime_UTR_variant,,ENST00000350092,;PTBP1,downstream_gene_variant,,ENST00000585956,;LPPR3,downstream_gene_variant,,ENST00000519502,;LPPR3,downstream_gene_variant,,ENST00000517665,;LPPR3,downstream_gene_variant,,ENST00000359894,;LPPR3,downstream_gene_variant,,ENST00000520876,;MIR3187,upstream_gene_variant,,ENST00000583431,;PTBP1,non_coding_transcript_exon_variant,,ENST00000586944,;PTBP1,downstream_gene_variant,,ENST00000585932,;PTBP1,downstream_gene_variant,,ENST00000589883,;PTBP1,downstream_gene_variant,,ENST00000587191,;PTBP1,downstream_gene_variant,,ENST00000589770,;PTBP1,downstream_gene_variant,,ENST00000585856,;PTBP1,downstream_gene_variant,,ENST00000587136,;	C	ENSG00000011304	ENST00000356948	Transcript	3_prime_UTR_variant	2514	.	.	.	.	.	.	.	1	PTBP1	HGNC	9583	protein_coding	YES	CCDS42456.1	ENSP00000349428	PTBP1_HUMAN	.	UPI00000720B7	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGAGGCAGG	.	2	ESCA
CELSR2	0	.	GRCh37	1	109817677	109817677	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1006C>G	.	.	ENST00000271332	34/34	45	26	19	28	28	0	CELSR2,3_prime_UTR_variant,,ENST00000271332,;PSRC1,downstream_gene_variant,,ENST00000369909,;PSRC1,downstream_gene_variant,,ENST00000369904,;PSRC1,downstream_gene_variant,,ENST00000409267,;PSRC1,downstream_gene_variant,,ENST00000438534,;PSRC1,downstream_gene_variant,,ENST00000369907,;PSRC1,downstream_gene_variant,,ENST00000409138,;PSRC1,downstream_gene_variant,,ENST00000369903,;CELSR2,non_coding_transcript_exon_variant,,ENST00000498157,;CELSR2,downstream_gene_variant,,ENST00000489018,;PSRC1,downstream_gene_variant,,ENST00000492431,;	G	ENSG00000143126	ENST00000271332	Transcript	3_prime_UTR_variant	9839	.	.	.	.	.	.	.	1	CELSR2	HGNC	3231	protein_coding	YES	CCDS796.1	ENSP00000271332	CELR2_HUMAN	.	UPI00000015B6	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGTCTAACC	.	5	ESCA
B3GALT6	0	.	GRCh37	1	1169484	1169484	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*836C>T	.	.	ENST00000379198	1/1	59	40	18	44	44	0	B3GALT6,3_prime_UTR_variant,,ENST00000379198,;SDF4,upstream_gene_variant,,ENST00000360001,;SDF4,upstream_gene_variant,,ENST00000545427,;SDF4,upstream_gene_variant,,ENST00000263741,;SDF4,upstream_gene_variant,,ENST00000459994,;SDF4,upstream_gene_variant,,ENST00000465727,;	T	ENSG00000176022	ENST00000379198	Transcript	3_prime_UTR_variant	1856	.	.	.	.	.	.	.	1	B3GALT6	HGNC	17978	protein_coding	YES	CCDS13.1	ENSP00000368496	B3GT6_HUMAN	.	UPI0000141885	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCGTTTA	.	5	ESCA
ARNT	0	.	GRCh37	1	150783957	150783957	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*540G>A	.	.	ENST00000358595	22/22	24	19	5	16	16	0	ARNT,3_prime_UTR_variant,,ENST00000358595,;ARNT,3_prime_UTR_variant,,ENST00000354396,;ARNT,downstream_gene_variant,,ENST00000505755,;ARNT,downstream_gene_variant,,ENST00000515192,;CTSK,upstream_gene_variant,,ENST00000271651,;CTSK,upstream_gene_variant,,ENST00000443913,;RNU6-1309P,downstream_gene_variant,,ENST00000363305,;CTSK,upstream_gene_variant,,ENST00000480670,;ARNT,3_prime_UTR_variant,,ENST00000471844,;	T	ENSG00000143437	ENST00000358595	Transcript	3_prime_UTR_variant	3111	.	.	.	.	.	.	.	-1	ARNT	HGNC	700	protein_coding	YES	CCDS970.1	ENSP00000351407	ARNT_HUMAN	.	UPI0000030984	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATACACACA	.	2	ESCA
IL6R	0	.	GRCh37	1	154438564	154438564	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*708G>T	.	.	ENST00000368485	10/10	30	26	4	17	17	0	IL6R,3_prime_UTR_variant,,ENST00000368485,;IL6R,3_prime_UTR_variant,,ENST00000344086,;SHE,downstream_gene_variant,,ENST00000486773,;IL6R,downstream_gene_variant,,ENST00000507256,;IL6R,downstream_gene_variant,,ENST00000502679,;	T	ENSG00000160712	ENST00000368485	Transcript	3_prime_UTR_variant	2552	.	.	.	.	.	.	.	1	IL6R	HGNC	6019	protein_coding	YES	CCDS1067.1	ENSP00000357470	IL6RA_HUMAN	A0N0L5_HUMAN	UPI00000358BA	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGCTGAATAC	.	4	ESCA
VHLL	0	.	GRCh37	1	156269121	156269121	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-141C>T	.	.	ENST00000339922	1/1	81	58	23	40	40	0	VHLL,5_prime_UTR_variant,,ENST00000339922,;C1orf85,upstream_gene_variant,,ENST00000362007,;C1orf85,upstream_gene_variant,,ENST00000476177,;C1orf85,upstream_gene_variant,,ENST00000472870,;C1orf85,upstream_gene_variant,,ENST00000368264,;C1orf85,upstream_gene_variant,,ENST00000479084,;C1orf85,upstream_gene_variant,,ENST00000497955,;C1orf85,upstream_gene_variant,,ENST00000484214,;	A	ENSG00000189030	ENST00000339922	Transcript	5_prime_UTR_variant	308	.	.	.	.	.	.	.	-1	VHLL	HGNC	30666	protein_coding	YES	.	ENSP00000464258	VHLL_HUMAN	.	UPI0000253B18	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAAGACATC	.	5	ESCA
VHLL	0	.	GRCh37	1	156269245	156269245	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-265C>G	.	.	ENST00000339922	1/1	103	82	20	52	52	0	VHLL,5_prime_UTR_variant,,ENST00000339922,;C1orf85,upstream_gene_variant,,ENST00000362007,;C1orf85,upstream_gene_variant,,ENST00000476177,;C1orf85,upstream_gene_variant,,ENST00000472870,;C1orf85,upstream_gene_variant,,ENST00000368264,;C1orf85,upstream_gene_variant,,ENST00000479084,;C1orf85,upstream_gene_variant,,ENST00000497955,;C1orf85,upstream_gene_variant,,ENST00000484214,;	C	ENSG00000189030	ENST00000339922	Transcript	5_prime_UTR_variant	184	.	.	.	.	.	.	.	-1	VHLL	HGNC	30666	protein_coding	YES	.	ENSP00000464258	VHLL_HUMAN	.	UPI0000253B18	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCAGAGAGG	.	5	ESCA
DCAF8	0	.	GRCh37	1	160186742	160186742	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*640C>G	.	.	ENST00000368073	14/14	27	20	7	23	23	0	DCAF8,3_prime_UTR_variant,,ENST00000326837,;DCAF8,3_prime_UTR_variant,,ENST00000368073,;DCAF8,3_prime_UTR_variant,,ENST00000368074,;DCAF8,intron_variant,,ENST00000477163,;PEA15,downstream_gene_variant,,ENST00000360472,;PEA15,downstream_gene_variant,,ENST00000368077,;DCAF8,downstream_gene_variant,,ENST00000473382,;DCAF8,downstream_gene_variant,,ENST00000556710,;DCAF8,downstream_gene_variant,,ENST00000608310,;PEA15,downstream_gene_variant,,ENST00000368076,;PEA15,downstream_gene_variant,,ENST00000488858,;DCAF8,downstream_gene_variant,,ENST00000497354,;DCAF8,downstream_gene_variant,,ENST00000476033,;DCAF8,downstream_gene_variant,,ENST00000490368,;DCAF8,downstream_gene_variant,,ENST00000466253,;DCAF8,downstream_gene_variant,,ENST00000461888,;DCAF8,downstream_gene_variant,,ENST00000481831,;	C	ENSG00000132716	ENST00000368073	Transcript	3_prime_UTR_variant	2869	.	.	.	.	.	.	.	-1	DCAF8	HGNC	24891	protein_coding	YES	CCDS1200.1	ENSP00000357052	DCAF8_HUMAN	Q5TAQ8_HUMAN,Q5TAQ7_HUMAN,Q5TAQ6_HUMAN,Q5TAQ5_HUMAN,B7Z8C9_HUMAN	UPI0000141A39	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGAAGAGAGT	.	2	ESCA
SLAMF6	0	.	GRCh37	1	160465850	160465850	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382+1G>C	.	p.X128_splice	ENST00000368057	.	120	95	25	76	76	0	SLAMF6,splice_donor_variant,,ENST00000368057,;SLAMF6,splice_donor_variant,,ENST00000368059,;SLAMF6,intron_variant,,ENST00000368055,;	G	ENSG00000162739	ENST00000368057	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	SLAMF6	HGNC	21392	protein_coding	YES	CCDS53394.1	ENSP00000357036	SLAF6_HUMAN	.	UPI0000051E34	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTACTTAAT	.	5	ESCA
FBLIM1	0	.	GRCh37	1	16091469	16091469	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-10A>T	.	.	ENST00000441801	2/6	136	90	46	117	117	0	FBLIM1,5_prime_UTR_variant,,ENST00000431771,;FBLIM1,5_prime_UTR_variant,,ENST00000441801,;FBLIM1,5_prime_UTR_variant,,ENST00000400773,;FBLIM1,5_prime_UTR_variant,,ENST00000375771,;FBLIM1,5_prime_UTR_variant,,ENST00000508310,;FBLIM1,5_prime_UTR_variant,,ENST00000510929,;FBLIM1,5_prime_UTR_variant,,ENST00000332305,;FBLIM1,5_prime_UTR_variant,,ENST00000502638,;FBLIM1,5_prime_UTR_variant,,ENST00000375766,;FBLIM1,5_prime_UTR_variant,,ENST00000502739,;FBLIM1,5_prime_UTR_variant,,ENST00000483633,;FBLIM1,5_prime_UTR_variant,,ENST00000496928,;FBLIM1,5_prime_UTR_variant,,ENST00000510393,;FBLIM1,5_prime_UTR_variant,,ENST00000430076,;	T	ENSG00000162458	ENST00000441801	Transcript	5_prime_UTR_variant	198	.	.	.	.	.	.	.	1	FBLIM1	HGNC	24686	protein_coding	YES	CCDS44064.1	ENSP00000416387	FBLI1_HUMAN	E7EPI5_HUMAN,E7EN81_HUMAN,D6RAI6_HUMAN,D6RA19_HUMAN,D6R9V9_HUMAN,D6R9I4_HUMAN	UPI0000520D52	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGAGCTGA	.	5	ESCA
CDK11A	0	.	GRCh37	1	1634944	1634944	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2031C>G	p.%3D	p.L677L	ENST00000404249	18/20	95	62	32	80	80	0	CDK11A,synonymous_variant,p.%3D,ENST00000356200,;CDK11A,synonymous_variant,p.%3D,ENST00000404249,;CDK11A,synonymous_variant,p.%3D,ENST00000358779,;CDK11A,synonymous_variant,p.%3D,ENST00000378633,;CDK11A,synonymous_variant,p.%3D,ENST00000357760,;CDK11A,synonymous_variant,p.%3D,ENST00000378638,;CDK11A,downstream_gene_variant,,ENST00000378635,;RP1-283E3.8,non_coding_transcript_exon_variant,,ENST00000598846,;CDK11A,downstream_gene_variant,,ENST00000495016,;CDK11A,3_prime_UTR_variant,,ENST00000509982,;CDK11A,3_prime_UTR_variant,,ENST00000460465,;CDK11A,non_coding_transcript_exon_variant,,ENST00000468397,;CDK11A,non_coding_transcript_exon_variant,,ENST00000463652,;CDK11A,non_coding_transcript_exon_variant,,ENST00000356937,;CDK11A,non_coding_transcript_exon_variant,,ENST00000478901,;CDK11A,downstream_gene_variant,,ENST00000492390,;CDK11A,downstream_gene_variant,,ENST00000468800,;CDK11A,downstream_gene_variant,,ENST00000464748,;CDK11A,downstream_gene_variant,,ENST00000491311,;CDK11A,downstream_gene_variant,,ENST00000474916,;CDK11A,downstream_gene_variant,,ENST00000489300,;MMP23A,downstream_gene_variant,,ENST00000412810,;MMP23A,downstream_gene_variant,,ENST00000234610,;	C	ENSG00000008128	ENST00000404249	Transcript	synonymous_variant	2111	2031	677	L	ctC/ctG	.	.	.	-1	CDK11A	HGNC	1730	protein_coding	YES	CCDS44042.1	ENSP00000384442	CD11A_HUMAN	Q5QPQ9_HUMAN,Q4VBY6_HUMAN	UPI000022B1E1	.	.	.	18/20	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24056:SF107,hmmpanther:PTHR24056,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGAGAGCAG	.	5	ESCA
GPR52	0	.	GRCh37	1	174418064	174418064	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.815G>A	p.Ser272Asn	p.S272N	ENST00000367685	1/1	44	29	14	24	24	0	GPR52,missense_variant,p.Ser272Asn,ENST00000367685,;RABGAP1L,intron_variant,,ENST00000357444,;RABGAP1L,intron_variant,,ENST00000367689,;RABGAP1L,intron_variant,,ENST00000251507,;RABGAP1L,intron_variant,,ENST00000526253,;RABGAP1L,intron_variant,,ENST00000367690,;	A	ENSG00000203737	ENST00000367685	Transcript	missense_variant	853	815	272	S/N	aGt/aAt	.	.	.	1	GPR52	HGNC	4508	protein_coding	YES	CCDS30941.1	ENSP00000356658	GPR52_HUMAN	F2YGU0_HUMAN	UPI0000153A3C	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF248,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCAGTGTAT	.	5	ESCA
RASAL2	0	.	GRCh37	1	178426981	178426981	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2554G>A	p.Asp852Asn	p.D852N	ENST00000367649	14/18	45	32	13	23	23	0	RASAL2,missense_variant,p.Asp711Asn,ENST00000462775,;RASAL2,missense_variant,p.Asp852Asn,ENST00000367649,;RASAL2,missense_variant,p.Asp841Asn,ENST00000448150,;RASAL2,missense_variant,p.Asp262Asn,ENST00000433130,;RASAL2,non_coding_transcript_exon_variant,,ENST00000463079,;	A	ENSG00000075391	ENST00000367649	Transcript	missense_variant	2906	2554	852	D/N	Gac/Aac	.	.	.	1	RASAL2	HGNC	9874	protein_coding	YES	CCDS1321.2	ENSP00000356621	NGAP_HUMAN	Q8IW42_HUMAN,Q6P4F9_HUMAN	UPI00019B254F	.	deleterious(0.01)	probably_damaging(0.998)	14/18	.	hmmpanther:PTHR10194:SF52,hmmpanther:PTHR10194,Pfam_domain:PF12004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCATGGACCTC	.	3	ESCA
RASAL2	0	.	GRCh37	1	178427011	178427011	+	Missense_Mutation	SNP	G	G	C	rs746092573	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2584G>C	p.Glu862Gln	p.E862Q	ENST00000367649	14/18	38	28	10	21	21	0	RASAL2,missense_variant,p.Glu721Gln,ENST00000462775,;RASAL2,missense_variant,p.Glu862Gln,ENST00000367649,;RASAL2,missense_variant,p.Glu851Gln,ENST00000448150,;RASAL2,missense_variant,p.Glu272Gln,ENST00000433130,;RASAL2,non_coding_transcript_exon_variant,,ENST00000463079,;	C	ENSG00000075391	ENST00000367649	Transcript	missense_variant	2936	2584	862	E/Q	Gag/Cag	rs746092573	.	.	1	RASAL2	HGNC	9874	protein_coding	YES	CCDS1321.2	ENSP00000356621	NGAP_HUMAN	Q8IW42_HUMAN,Q6P4F9_HUMAN	UPI00019B254F	.	tolerated(0.5)	benign(0.088)	14/18	.	hmmpanther:PTHR10194:SF52,hmmpanther:PTHR10194,Pfam_domain:PF12004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGTGGAGCAT	.	3	ESCA
SWT1	0	.	GRCh37	1	185144184	185144184	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.905G>A	p.Arg302Gln	p.R302Q	ENST00000367500	5/19	60	43	17	41	41	0	SWT1,missense_variant,p.Arg302Gln,ENST00000367501,;SWT1,missense_variant,p.Arg302Gln,ENST00000367500,;SWT1,downstream_gene_variant,,ENST00000450350,;CTA-253N17.1,upstream_gene_variant,,ENST00000413694,;	A	ENSG00000116668	ENST00000367500	Transcript	missense_variant	1070	905	302	R/Q	cGa/cAa	COSM270692	.	.	1	SWT1	HGNC	16785	protein_coding	YES	CCDS1367.1	ENSP00000356470	SWT1_HUMAN	Q5TC96_HUMAN,B3KSB6_HUMAN	UPI000013D4C5	.	tolerated(0.58)	benign(0.116)	5/19	.	hmmpanther:PTHR16161,hmmpanther:PTHR16161:SF0	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R302Q|c.905G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAACGAAAAC	.	5	ESCA
C1orf27	0	.	GRCh37	1	186352217	186352217	+	Missense_Mutation	SNP	G	G	A	rs143106529	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163G>A	p.Glu55Lys	p.E55K	ENST00000287859	3/14	84	42	42	58	58	0	C1orf27,missense_variant,p.Glu55Lys,ENST00000432021,;C1orf27,missense_variant,p.Glu55Lys,ENST00000419367,;C1orf27,missense_variant,p.Glu55Lys,ENST00000367470,;C1orf27,missense_variant,p.Glu55Lys,ENST00000287859,;	A	ENSG00000157181	ENST00000287859	Transcript	missense_variant	288	163	55	E/K	Gag/Aag	rs143106529	.	.	1	C1orf27	HGNC	24299	protein_coding	YES	CCDS53448.1	ENSP00000287859	ODR4_HUMAN	.	UPI00003744FF	.	tolerated(0.08)	probably_damaging(0.969)	3/14	.	hmmpanther:PTHR11695:SF474,hmmpanther:PTHR11695,Pfam_domain:PF14778	C:0.0010	C:0.0038	C:0	.	C:0	C:0	C:0	C:0.0008	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTGAGAAC	byFrequency|byCluster|by1000G	5	ESCA
BRINP3	0	.	GRCh37	1	190250712	190250712	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405C>G	p.Phe135Leu	p.F135L	ENST00000367462	3/8	68	54	13	44	44	0	BRINP3,missense_variant,p.Phe135Leu,ENST00000367462,;BRINP3,intron_variant,,ENST00000534846,;RP11-547I7.1,intron_variant,,ENST00000452178,;	C	ENSG00000162670	ENST00000367462	Transcript	missense_variant	637	405	135	F/L	ttC/ttG	COSM2123680	.	.	-1	BRINP3	HGNC	22393	protein_coding	YES	CCDS1373.1	ENSP00000356432	BRNP3_HUMAN	.	UPI00001C1D9A	.	tolerated(0.3)	benign(0.015)	3/8	.	hmmpanther:PTHR15564:SF2,hmmpanther:PTHR15564,Pfam_domain:PF01823,SMART_domains:SM00457	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAAGAAATG	.	5	ESCA
CAMSAP2	0	.	GRCh37	1	200826893	200826893	+	Silent	SNP	A	A	G	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4143A>G	p.%3D	p.K1381K	ENST00000358823	17/17	54	23	30	21	21	0	CAMSAP2,synonymous_variant,p.%3D,ENST00000413307,;CAMSAP2,synonymous_variant,p.%3D,ENST00000358823,;CAMSAP2,synonymous_variant,p.%3D,ENST00000236925,;CAMSAP2,downstream_gene_variant,,ENST00000475326,;CAMSAP2,downstream_gene_variant,,ENST00000447701,;	G	ENSG00000118200	ENST00000358823	Transcript	synonymous_variant	4413	4143	1381	K	aaA/aaG	COSM1172087	.	.	1	CAMSAP2	HGNC	29188	protein_coding	YES	CCDS1404.1	ENSP00000351684	CAMP2_HUMAN	.	UPI000020470D	.	.	.	17/17	.	Superfamily_domains:SSF50346,SMART_domains:SM01051,Pfam_domain:PF08683,hmmpanther:PTHR21595:SF1,hmmpanther:PTHR21595,PROSITE_profiles:PS51508	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAATCAGA	.	5	ESCA
IGFN1	0	.	GRCh37	1	201185638	201185638	+	Missense_Mutation	SNP	G	G	A	rs574892301	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9352G>A	p.Val3118Ile	p.V3118I	ENST00000335211	16/24	107	78	28	59	59	0	IGFN1,missense_variant,p.Val278Ile,ENST00000295591,;IGFN1,missense_variant,p.Val536Ile,ENST00000412892,;IGFN1,missense_variant,p.Val3118Ile,ENST00000335211,;IGFN1,downstream_gene_variant,,ENST00000451870,;IGFN1,3_prime_UTR_variant,,ENST00000437879,;IGFN1,non_coding_transcript_exon_variant,,ENST00000473483,;	A	ENSG00000163395	ENST00000335211	Transcript	missense_variant	9482	9352	3118	V/I	Gtc/Atc	rs574892301	.	.	1	IGFN1	HGNC	24607	protein_coding	YES	CCDS53455.1	ENSP00000334714	IGFN1_HUMAN	.	UPI0001B300F4	.	.	possibly_damaging(0.66)	16/24	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,Pfam_domain:PF00041,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF145,PROSITE_profiles:PS50853	A:0.0004	A:0	A:0.0029	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGTCTGC	byFrequency|by1000G	5	ESCA
CSRP1	0	.	GRCh37	1	201453557	201453557	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*284G>A	.	.	ENST00000367306	7/7	61	40	21	35	35	0	CSRP1,3_prime_UTR_variant,,ENST00000367306,;CSRP1,3_prime_UTR_variant,,ENST00000340006,;CSRP1,3_prime_UTR_variant,,ENST00000533432,;CSRP1,3_prime_UTR_variant,,ENST00000532460,;CSRP1,intron_variant,,ENST00000531916,;CSRP1,downstream_gene_variant,,ENST00000524951,;CSRP1,downstream_gene_variant,,ENST00000526723,;CSRP1,non_coding_transcript_exon_variant,,ENST00000526256,;CSRP1,downstream_gene_variant,,ENST00000530120,;CSRP1,downstream_gene_variant,,ENST00000529975,;CSRP1,downstream_gene_variant,,ENST00000526317,;CSRP1,downstream_gene_variant,,ENST00000458271,;CSRP1,downstream_gene_variant,,ENST00000527573,;CSRP1,non_coding_transcript_exon_variant,,ENST00000527662,;CSRP1,non_coding_transcript_exon_variant,,ENST00000532313,;CSRP1,non_coding_transcript_exon_variant,,ENST00000533402,;CSRP1,downstream_gene_variant,,ENST00000533188,;	T	ENSG00000159176	ENST00000367306	Transcript	3_prime_UTR_variant	1230	.	.	.	.	.	.	.	-1	CSRP1	HGNC	2469	protein_coding	YES	CCDS1413.1	ENSP00000356275	CSRP1_HUMAN	Q9BTA4_HUMAN,Q6AWD1_HUMAN,Q5U0J2_HUMAN,E9PND2_HUMAN,B4DY28_HUMAN,B3KVC9_HUMAN	UPI000013DFD4	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTCTGTGG	.	5	ESCA
DYRK3	0	.	GRCh37	1	206810256	206810256	+	Intron	SNP	C	C	T	rs201854176	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78-739C>T	.	.	ENST00000367109	.	86	62	23	57	57	0	DYRK3,5_prime_UTR_variant,,ENST00000441486,;DYRK3,5_prime_UTR_variant,,ENST00000367106,;DYRK3,5_prime_UTR_variant,,ENST00000367108,;DYRK3,intron_variant,,ENST00000367109,;RP11-343H5.6,upstream_gene_variant,,ENST00000425161,;DYRK3,non_coding_transcript_exon_variant,,ENST00000489878,;	T	ENSG00000143479	ENST00000367109	Transcript	intron_variant	.	.	.	.	.	rs201854176	.	.	1	DYRK3	HGNC	3094	protein_coding	YES	CCDS30999.1	ENSP00000356076	DYRK3_HUMAN	.	UPI0000071267	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATCCTTAA	byCluster	5	ESCA
KIF17	0	.	GRCh37	1	21042067	21042067	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297C>T	p.%3D	p.F99F	ENST00000247986	2/15	59	45	14	35	35	0	KIF17,synonymous_variant,p.%3D,ENST00000247986,;KIF17,synonymous_variant,p.%3D,ENST00000400463,;KIF17,5_prime_UTR_variant,,ENST00000375044,;SH2D5,downstream_gene_variant,,ENST00000375031,;SH2D5,downstream_gene_variant,,ENST00000460804,;	A	ENSG00000117245	ENST00000247986	Transcript	synonymous_variant	608	297	99	F	ttC/ttT	COSM678765	.	.	-1	KIF17	HGNC	19167	protein_coding	YES	CCDS213.1	ENSP00000247986	KIF17_HUMAN	.	UPI0000185F1A	.	.	.	2/15	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF415,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATGGTGAAGGA	.	3	ESCA
HP1BP3	0	.	GRCh37	1	21100185	21100185	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351-82C>G	.	.	ENST00000312239	.	16	10	5	15	15	0	HP1BP3,5_prime_UTR_variant,,ENST00000375003,;HP1BP3,intron_variant,,ENST00000424732,;HP1BP3,intron_variant,,ENST00000419948,;HP1BP3,intron_variant,,ENST00000312239,;HP1BP3,intron_variant,,ENST00000438032,;HP1BP3,intron_variant,,ENST00000417710,;HP1BP3,downstream_gene_variant,,ENST00000375000,;HP1BP3,downstream_gene_variant,,ENST00000414993,;HP1BP3,downstream_gene_variant,,ENST00000419490,;HP1BP3,downstream_gene_variant,,ENST00000437575,;HP1BP3,downstream_gene_variant,,ENST00000487117,;	C	ENSG00000127483	ENST00000312239	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	HP1BP3	HGNC	24973	protein_coding	YES	CCDS30621.1	ENSP00000312625	HP1B3_HUMAN	Q5SWC8_HUMAN,B4E0N8_HUMAN,B0QZK9_HUMAN,B0QZK8_HUMAN,B0QZK6_HUMAN,B0QZK5_HUMAN	UPI0000036038	.	.	.	.	4/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGAGGGATA	.	5	ESCA
RCOR3	0	.	GRCh37	1	211447585	211447585	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.335A>G	p.His112Arg	p.H112R	ENST00000419091	4/12	114	85	29	77	77	0	RCOR3,missense_variant,p.His54Arg,ENST00000534478,;RCOR3,missense_variant,p.His112Arg,ENST00000452621,;RCOR3,missense_variant,p.His54Arg,ENST00000533469,;RCOR3,missense_variant,p.His112Arg,ENST00000367006,;RCOR3,missense_variant,p.His112Arg,ENST00000419091,;RCOR3,missense_variant,p.His54Arg,ENST00000367005,;RCOR3,upstream_gene_variant,,ENST00000534460,;RCOR3,missense_variant,p.His144Arg,ENST00000528926,;RCOR3,3_prime_UTR_variant,,ENST00000529572,;RCOR3,downstream_gene_variant,,ENST00000528408,;	G	ENSG00000117625	ENST00000419091	Transcript	missense_variant	463	335	112	H/R	cAt/cGt	.	.	.	1	RCOR3	HGNC	25594	protein_coding	YES	CCDS44312.1	ENSP00000413929	RCOR3_HUMAN	E9PR63_HUMAN,E9PQE5_HUMAN	UPI00005AE45B	.	deleterious(0)	probably_damaging(0.993)	4/12	.	PROSITE_profiles:PS51156,hmmpanther:PTHR16089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGCATGGCT	.	5	ESCA
CENPF	0	.	GRCh37	1	214802455	214802455	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135G>A	p.Glu379Lys	p.E379K	ENST00000366955	8/20	76	55	21	46	46	0	CENPF,missense_variant,p.Glu379Lys,ENST00000366955,;	A	ENSG00000117724	ENST00000366955	Transcript	missense_variant	1303	1135	379	E/K	Gaa/Aaa	.	.	.	1	CENPF	HGNC	1857	protein_coding	YES	CCDS31023.1	ENSP00000355922	CENPF_HUMAN	.	UPI00001AE985	.	.	benign(0.443)	8/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCAGAAAGT	.	5	ESCA
RAB3GAP2	0	.	GRCh37	1	220440993	220440993	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115+4572C>A	.	.	ENST00000358951	.	59	47	12	33	33	0	RAB3GAP2,intron_variant,,ENST00000358951,;RAB3GAP2,non_coding_transcript_exon_variant,,ENST00000462353,;RAB3GAP2,intron_variant,,ENST00000478976,;RAB3GAP2,intron_variant,,ENST00000475769,;RAB3GAP2,intron_variant,,ENST00000474178,;RAB3GAP2,intron_variant,,ENST00000237724,;AURKAPS1,non_coding_transcript_exon_variant,,ENST00000451805,;	T	ENSG00000118873	ENST00000358951	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RAB3GAP2	HGNC	17168	protein_coding	YES	CCDS31028.1	ENSP00000351832	RBGPR_HUMAN	.	UPI0000072269	.	.	.	.	1/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTGGAGGCA	.	5	ESCA
GJC2	0	.	GRCh37	1	228346302	228346302	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843C>T	p.%3D	p.L281L	ENST00000366714	2/2	43	32	11	25	25	0	GJC2,synonymous_variant,p.%3D,ENST00000366714,;	T	ENSG00000198835	ENST00000366714	Transcript	synonymous_variant	1018	843	281	L	ctC/ctT	.	.	.	1	GJC2	HGNC	17494	protein_coding	YES	CCDS1569.1	ENSP00000355675	CXG2_HUMAN	.	UPI000034ECE8	.	.	.	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF52,Gene3D:2zw3A00,Pfam_domain:PF10582,SMART_domains:SM01089,Prints_domain:PR00206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCAACCT	.	5	ESCA
SIPA1L2	0	.	GRCh37	1	232579369	232579369	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3416G>A	p.Arg1139Lys	p.R1139K	ENST00000366630	11/22	52	43	9	20	20	0	SIPA1L2,missense_variant,p.Arg1139Lys,ENST00000366630,;SIPA1L2,missense_variant,p.Arg213Lys,ENST00000308942,;SIPA1L2,missense_variant,p.Arg1139Lys,ENST00000262861,;	T	ENSG00000116991	ENST00000366630	Transcript	missense_variant	3775	3416	1139	R/K	aGa/aAa	COSM905573	.	.	-1	SIPA1L2	HGNC	23800	protein_coding	YES	CCDS41474.1	ENSP00000355589	SI1L2_HUMAN	.	UPI00001D7D6A	.	tolerated(0.32)	benign(0.269)	11/22	.	hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTCTCCAG	.	5	ESCA
ACTN2	0	.	GRCh37	1	236914838	236914838	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1725C>A	p.%3D	p.I575I	ENST00000366578	15/21	122	94	28	75	75	0	ACTN2,synonymous_variant,p.%3D,ENST00000542672,;ACTN2,synonymous_variant,p.%3D,ENST00000366578,;ACTN2,synonymous_variant,p.%3D,ENST00000546208,;ACTN2,upstream_gene_variant,,ENST00000461367,;ACTN2,downstream_gene_variant,,ENST00000492101,;	A	ENSG00000077522	ENST00000366578	Transcript	synonymous_variant	1891	1725	575	I	atC/atA	.	.	.	1	ACTN2	HGNC	164	protein_coding	YES	CCDS1613.1	ENSP00000355537	ACTN2_HUMAN	B7Z4P8_HUMAN	UPI0000125088	.	.	.	15/21	.	Superfamily_domains:SSF46966,SMART_domains:SM00150,Pfam_domain:PF00435,Gene3D:1.20.58.60,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCATGGC	.	5	ESCA
OR2G6	0	.	GRCh37	1	248685431	248685431	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484C>T	p.Leu162Phe	p.L162F	ENST00000343414	1/1	74	53	21	32	32	0	OR2G6,missense_variant,p.Leu162Phe,ENST00000343414,;	T	ENSG00000188558	ENST00000343414	Transcript	missense_variant	516	484	162	L/F	Ctc/Ttc	.	.	.	1	OR2G6	HGNC	27019	protein_coding	YES	CCDS31119.1	ENSP00000341291	OR2G6_HUMAN	.	UPI0000237253	.	tolerated(0.14)	benign(0.097)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF226,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCTCACT	.	5	ESCA
ZNF672	0	.	GRCh37	1	249142293	249142293	+	Missense_Mutation	SNP	C	C	T	rs371348856	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820C>T	p.Arg274Trp	p.R274W	ENST00000306562	4/4	25	18	7	17	17	0	ZNF672,missense_variant,p.Arg274Trp,ENST00000306562,;ZNF692,downstream_gene_variant,,ENST00000427146,;ZNF692,downstream_gene_variant,,ENST00000451251,;ZNF672,downstream_gene_variant,,ENST00000423362,;ZNF672,downstream_gene_variant,,ENST00000428515,;ZNF672,downstream_gene_variant,,ENST00000505503,;ZNF692,downstream_gene_variant,,ENST00000306601,;ZNF692,downstream_gene_variant,,ENST00000366471,;ZNF692,downstream_gene_variant,,ENST00000366469,;ZNF692,downstream_gene_variant,,ENST00000476503,;ZNF672,downstream_gene_variant,,ENST00000510904,;ZNF672,downstream_gene_variant,,ENST00000502697,;ZNF672,downstream_gene_variant,,ENST00000515369,;ZNF692,downstream_gene_variant,,ENST00000477070,;ZNF692,downstream_gene_variant,,ENST00000482023,;ZNF692,downstream_gene_variant,,ENST00000463519,;ZNF692,downstream_gene_variant,,ENST00000474351,;ZNF692,downstream_gene_variant,,ENST00000462037,;ZNF692,downstream_gene_variant,,ENST00000412341,;ZNF692,downstream_gene_variant,,ENST00000470787,;ZNF692,downstream_gene_variant,,ENST00000533927,;	T	ENSG00000171161	ENST00000306562	Transcript	missense_variant	1566	820	274	R/W	Cgg/Tgg	rs371348856	.	.	1	ZNF672	HGNC	26179	protein_coding	YES	CCDS1638.1	ENSP00000421915	ZN672_HUMAN	D6RH11_HUMAN,D6RD56_HUMAN	UPI0000070D6C	.	deleterious(0)	probably_damaging(0.91)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCGGCGC	byFrequency|byCluster	5	ESCA
ZMYM1	0	.	GRCh37	1	35576032	35576032	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.945G>A	p.%3D	p.K315K	ENST00000373330	8/11	102	61	41	82	82	0	ZMYM1,synonymous_variant,p.%3D,ENST00000417119,;ZMYM1,synonymous_variant,p.%3D,ENST00000373330,;ZMYM1,synonymous_variant,p.%3D,ENST00000359858,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000373329,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000475654,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000488455,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000463393,;	A	ENSG00000197056	ENST00000373330	Transcript	synonymous_variant	1119	945	315	K	aaG/aaA	.	.	.	1	ZMYM1	HGNC	26253	protein_coding	YES	CCDS41302.1	ENSP00000362427	ZMYM1_HUMAN	Q9H5R2_HUMAN,Q5SW02_HUMAN,Q5SVZ7_HUMAN	UPI0000203ED6	.	.	.	8/11	.	hmmpanther:PTHR11697:SF88,hmmpanther:PTHR11697,SMART_domains:SM00746	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTAAGATGGA	.	5	ESCA
HECTD3	0	.	GRCh37	1	45474116	45474116	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1238+92A>G	.	.	ENST00000372172	.	45	29	15	29	29	0	HECTD3,5_prime_UTR_variant,,ENST00000372168,;HECTD3,intron_variant,,ENST00000372172,;UROD,upstream_gene_variant,,ENST00000428106,;UROD,upstream_gene_variant,,ENST00000434478,;UROD,upstream_gene_variant,,ENST00000246337,;UROD,upstream_gene_variant,,ENST00000462688,;UROD,upstream_gene_variant,,ENST00000491773,;HECTD3,upstream_gene_variant,,ENST00000486132,;UROD,upstream_gene_variant,,ENST00000469548,;UROD,upstream_gene_variant,,ENST00000494399,;UROD,upstream_gene_variant,,ENST00000478467,;UROD,upstream_gene_variant,,ENST00000486699,;UROD,upstream_gene_variant,,ENST00000463092,;UROD,upstream_gene_variant,,ENST00000490385,;HECTD3,upstream_gene_variant,,ENST00000484564,;HECTD3,upstream_gene_variant,,ENST00000466423,;UROD,upstream_gene_variant,,ENST00000460334,;UROD,upstream_gene_variant,,ENST00000496439,;HECTD3,upstream_gene_variant,,ENST00000486296,;UROD,upstream_gene_variant,,ENST00000491300,;UROD,upstream_gene_variant,,ENST00000473012,;HECTD3,upstream_gene_variant,,ENST00000487488,;UROD,upstream_gene_variant,,ENST00000460906,;UROD,upstream_gene_variant,,ENST00000461035,;	C	ENSG00000126107	ENST00000372172	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	HECTD3	HGNC	26117	protein_coding	YES	CCDS41318.1	ENSP00000361245	HECD3_HUMAN	A1A4G1_HUMAN	UPI0000204F79	.	.	.	.	8/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTATACTAT	.	5	ESCA
ACOT11	0	.	GRCh37	1	55064996	55064996	+	Silent	SNP	G	G	A	rs779474654	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792G>A	p.%3D	p.L264L	ENST00000371316	8/17	57	35	21	24	24	0	ACOT11,synonymous_variant,p.%3D,ENST00000371316,;ACOT11,synonymous_variant,p.%3D,ENST00000343744,;ACOT11,non_coding_transcript_exon_variant,,ENST00000481208,;ACOT11,non_coding_transcript_exon_variant,,ENST00000479837,;ACOT11,downstream_gene_variant,,ENST00000498228,;	A	ENSG00000162390	ENST00000371316	Transcript	synonymous_variant	874	792	264	L	ctG/ctA	rs779474654,COSM365959,COSM365958	.	.	1	ACOT11	HGNC	18156	protein_coding	YES	CCDS592.1	ENSP00000360366	ACO11_HUMAN	.	UPI0000136D55	.	.	.	8/17	.	hmmpanther:PTHR11049,hmmpanther:PTHR11049:SF1,Gene3D:3.10.129.10,Pfam_domain:PF03061,Superfamily_domains:SSF54637	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCTGAAGGC	.	5	ESCA
ESPN	0	.	GRCh37	1	6517321	6517321	+	Missense_Mutation	SNP	G	G	C	rs145302595	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2403G>C	p.Glu801Asp	p.E801D	ENST00000377828	11/13	108	66	42	74	74	0	ESPN,missense_variant,p.Glu235Asp,ENST00000416731,;ESPN,missense_variant,p.Glu801Asp,ENST00000377828,;ESPN,missense_variant,p.Glu235Asp,ENST00000461727,;ESPN,missense_variant,p.Glu145Asp,ENST00000434576,;TNFRSF25,downstream_gene_variant,,ENST00000356876,;TNFRSF25,downstream_gene_variant,,ENST00000348333,;TNFRSF25,downstream_gene_variant,,ENST00000351959,;TNFRSF25,downstream_gene_variant,,ENST00000377782,;TNFRSF25,downstream_gene_variant,,ENST00000351748,;ESPN,splice_region_variant,,ENST00000475228,;ESPN,upstream_gene_variant,,ENST00000468561,;TNFRSF25,downstream_gene_variant,,ENST00000475730,;ESPN,splice_region_variant,,ENST00000477679,;TNFRSF25,downstream_gene_variant,,ENST00000453260,;TNFRSF25,downstream_gene_variant,,ENST00000414040,;TNFRSF25,downstream_gene_variant,,ENST00000469691,;TNFRSF25,downstream_gene_variant,,ENST00000510563,;TNFRSF25,downstream_gene_variant,,ENST00000485036,;TNFRSF25,downstream_gene_variant,,ENST00000480393,;TNFRSF25,downstream_gene_variant,,ENST00000513135,;TNFRSF25,downstream_gene_variant,,ENST00000473343,;TNFRSF25,downstream_gene_variant,,ENST00000502588,;TNFRSF25,downstream_gene_variant,,ENST00000502730,;	C	ENSG00000187017	ENST00000377828	Transcript	missense_variant	2571	2403	801	E/D	gaG/gaC	rs145302595	.	.	1	ESPN	HGNC	13281	protein_coding	YES	CCDS70.1	ENSP00000367059	ESPN_HUMAN	.	UPI000013D2B6	.	deleterious(0)	probably_damaging(0.997)	11/13	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24153,hmmpanther:PTHR24153:SF14	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGAGAGGTG	byCluster	5	ESCA
ESPN	0	.	GRCh37	1	6520077	6520077	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2436G>A	p.%3D	p.Q812Q	ENST00000377828	13/13	63	43	19	35	35	0	ESPN,synonymous_variant,p.%3D,ENST00000416731,;ESPN,synonymous_variant,p.%3D,ENST00000377828,;ESPN,synonymous_variant,p.%3D,ENST00000461727,;ESPN,synonymous_variant,p.%3D,ENST00000434576,;TNFRSF25,downstream_gene_variant,,ENST00000356876,;TNFRSF25,downstream_gene_variant,,ENST00000348333,;TNFRSF25,downstream_gene_variant,,ENST00000481401,;TNFRSF25,downstream_gene_variant,,ENST00000351959,;TNFRSF25,downstream_gene_variant,,ENST00000377782,;TNFRSF25,downstream_gene_variant,,ENST00000351748,;ESPN,non_coding_transcript_exon_variant,,ENST00000475228,;TNFRSF25,downstream_gene_variant,,ENST00000461703,;ESPN,upstream_gene_variant,,ENST00000468561,;TNFRSF25,downstream_gene_variant,,ENST00000475730,;ESPN,non_coding_transcript_exon_variant,,ENST00000477679,;TNFRSF25,downstream_gene_variant,,ENST00000515145,;TNFRSF25,downstream_gene_variant,,ENST00000453260,;TNFRSF25,downstream_gene_variant,,ENST00000414040,;TNFRSF25,downstream_gene_variant,,ENST00000453341,;TNFRSF25,downstream_gene_variant,,ENST00000469691,;TNFRSF25,downstream_gene_variant,,ENST00000510563,;TNFRSF25,downstream_gene_variant,,ENST00000485036,;TNFRSF25,downstream_gene_variant,,ENST00000480393,;TNFRSF25,downstream_gene_variant,,ENST00000513135,;TNFRSF25,downstream_gene_variant,,ENST00000473343,;TNFRSF25,downstream_gene_variant,,ENST00000502588,;TNFRSF25,downstream_gene_variant,,ENST00000502730,;	A	ENSG00000187017	ENST00000377828	Transcript	synonymous_variant	2604	2436	812	Q	caG/caA	.	.	.	1	ESPN	HGNC	13281	protein_coding	YES	CCDS70.1	ENSP00000367059	ESPN_HUMAN	.	UPI000013D2B6	.	.	.	13/13	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24153,hmmpanther:PTHR24153:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGACAGAAGCA	.	5	ESCA
PHF13	0	.	GRCh37	1	6682503	6682503	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*806C>T	.	.	ENST00000377648	4/4	46	27	18	31	31	0	PHF13,3_prime_UTR_variant,,ENST00000377648,;THAP3,upstream_gene_variant,,ENST00000307896,;THAP3,upstream_gene_variant,,ENST00000054650,;THAP3,upstream_gene_variant,,ENST00000472925,;THAP3,upstream_gene_variant,,ENST00000377627,;PHF13,non_coding_transcript_exon_variant,,ENST00000495385,;THAP3,upstream_gene_variant,,ENST00000484676,;THAP3,upstream_gene_variant,,ENST00000484669,;THAP3,upstream_gene_variant,,ENST00000487819,;	T	ENSG00000116273	ENST00000377648	Transcript	3_prime_UTR_variant	2091	.	.	.	.	.	.	.	1	PHF13	HGNC	22983	protein_coding	YES	CCDS85.1	ENSP00000366876	PHF13_HUMAN	.	UPI000013C9BF	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGTCTTGGT	.	5	ESCA
XKR7	0	.	GRCh37	20	30584580	30584580	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1060A>C	p.Lys354Gln	p.K354Q	ENST00000562532	3/3	46	28	17	39	39	0	XKR7,missense_variant,p.Lys354Gln,ENST00000562532,;	C	ENSG00000260903	ENST00000562532	Transcript	missense_variant	1234	1060	354	K/Q	Aag/Cag	.	.	.	1	XKR7	HGNC	23062	protein_coding	YES	CCDS33459.1	ENSP00000477059	XKR7_HUMAN	.	UPI00004C7A9E	.	deleterious(0)	probably_damaging(0.998)	3/3	.	hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF9,Pfam_domain:PF09815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCCAAGTGG	.	5	ESCA
ACSS2	0	.	GRCh37	20	33508430	33508430	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1100G>C	p.Trp367Ser	p.W367S	ENST00000253382	10/19	29	20	8	20	20	0	ACSS2,missense_variant,p.Trp354Ser,ENST00000360596,;ACSS2,missense_variant,p.Trp304Ser,ENST00000336325,;ACSS2,missense_variant,p.Trp367Ser,ENST00000253382,;ACSS2,non_coding_transcript_exon_variant,,ENST00000493250,;ACSS2,intron_variant,,ENST00000476922,;ACSS2,downstream_gene_variant,,ENST00000468550,;ACSS2,3_prime_UTR_variant,,ENST00000481284,;ACSS2,3_prime_UTR_variant,,ENST00000477932,;ACSS2,non_coding_transcript_exon_variant,,ENST00000491533,;ACSS2,intron_variant,,ENST00000480978,;ACSS2,downstream_gene_variant,,ENST00000475459,;ACSS2,upstream_gene_variant,,ENST00000490464,;ACSS2,upstream_gene_variant,,ENST00000494727,;ACSS2,upstream_gene_variant,,ENST00000470315,;	C	ENSG00000131069	ENST00000253382	Transcript	missense_variant	1132	1100	367	W/S	tGg/tCg	.	.	.	1	ACSS2	HGNC	15814	protein_coding	YES	CCDS42868.2	ENSP00000253382	ACSA_HUMAN	F8WCJ4_HUMAN,B3KUV2_HUMAN	UPI00004709E0	.	deleterious(0)	probably_damaging(1)	10/19	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF126,Pfam_domain:PF00501,Gene3D:3.40.50.980,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTGGTGCA	.	5	ESCA
ACSS2	0	.	GRCh37	20	33508850	33508850	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1224G>A	p.Trp408Ter	p.W408*	ENST00000253382	11/19	46	31	15	41	41	0	ACSS2,stop_gained,p.Trp395Ter,ENST00000360596,;ACSS2,stop_gained,p.Trp345Ter,ENST00000336325,;ACSS2,stop_gained,p.Trp408Ter,ENST00000253382,;ACSS2,intron_variant,,ENST00000476922,;ACSS2,downstream_gene_variant,,ENST00000493250,;ACSS2,downstream_gene_variant,,ENST00000468550,;ACSS2,3_prime_UTR_variant,,ENST00000481284,;ACSS2,3_prime_UTR_variant,,ENST00000477932,;ACSS2,non_coding_transcript_exon_variant,,ENST00000491533,;ACSS2,non_coding_transcript_exon_variant,,ENST00000490464,;ACSS2,intron_variant,,ENST00000480978,;ACSS2,downstream_gene_variant,,ENST00000475459,;ACSS2,upstream_gene_variant,,ENST00000494727,;ACSS2,upstream_gene_variant,,ENST00000470315,;	A	ENSG00000131069	ENST00000253382	Transcript	stop_gained	1256	1224	408	W/*	tgG/tgA	.	.	.	1	ACSS2	HGNC	15814	protein_coding	YES	CCDS42868.2	ENSP00000253382	ACSA_HUMAN	F8WCJ4_HUMAN,B3KUV2_HUMAN	UPI00004709E0	.	.	.	11/19	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF126,Pfam_domain:PF00501,Gene3D:3.40.50.980,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGTGGAGCAT	.	3	ESCA
ACSS2	0	.	GRCh37	20	33509173	33509173	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357G>A	p.Glu453Lys	p.E453K	ENST00000253382	12/19	53	38	15	30	30	0	ACSS2,missense_variant,p.Glu440Lys,ENST00000360596,;ACSS2,missense_variant,p.Glu390Lys,ENST00000336325,;ACSS2,missense_variant,p.Glu453Lys,ENST00000253382,;ACSS2,intron_variant,,ENST00000476922,;ACSS2,downstream_gene_variant,,ENST00000493250,;ACSS2,downstream_gene_variant,,ENST00000468550,;ACSS2,3_prime_UTR_variant,,ENST00000481284,;ACSS2,3_prime_UTR_variant,,ENST00000477932,;ACSS2,non_coding_transcript_exon_variant,,ENST00000491533,;ACSS2,non_coding_transcript_exon_variant,,ENST00000490464,;ACSS2,intron_variant,,ENST00000480978,;ACSS2,downstream_gene_variant,,ENST00000475459,;ACSS2,upstream_gene_variant,,ENST00000494727,;ACSS2,upstream_gene_variant,,ENST00000470315,;	A	ENSG00000131069	ENST00000253382	Transcript	missense_variant	1389	1357	453	E/K	Gaa/Aaa	.	.	.	1	ACSS2	HGNC	15814	protein_coding	YES	CCDS42868.2	ENSP00000253382	ACSA_HUMAN	F8WCJ4_HUMAN,B3KUV2_HUMAN	UPI00004709E0	.	deleterious(0)	probably_damaging(0.999)	12/19	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF126,Pfam_domain:PF00501,Gene3D:3.40.50.980,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTGAACCC	.	5	ESCA
ACSS2	0	.	GRCh37	20	33509628	33509628	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1546G>A	p.Glu516Lys	p.E516K	ENST00000253382	14/19	101	60	41	78	78	0	ACSS2,missense_variant,p.Glu503Lys,ENST00000360596,;ACSS2,missense_variant,p.Glu453Lys,ENST00000336325,;ACSS2,missense_variant,p.Glu516Lys,ENST00000253382,;ACSS2,intron_variant,,ENST00000476922,;ACSS2,downstream_gene_variant,,ENST00000493250,;ACSS2,downstream_gene_variant,,ENST00000468550,;ACSS2,3_prime_UTR_variant,,ENST00000481284,;ACSS2,3_prime_UTR_variant,,ENST00000477932,;ACSS2,non_coding_transcript_exon_variant,,ENST00000491533,;ACSS2,non_coding_transcript_exon_variant,,ENST00000470315,;ACSS2,intron_variant,,ENST00000480978,;ACSS2,downstream_gene_variant,,ENST00000475459,;ACSS2,downstream_gene_variant,,ENST00000490464,;ACSS2,upstream_gene_variant,,ENST00000494727,;	A	ENSG00000131069	ENST00000253382	Transcript	missense_variant	1578	1546	516	E/K	Gag/Aag	COSM3840828,COSM3840827	.	.	1	ACSS2	HGNC	15814	protein_coding	YES	CCDS42868.2	ENSP00000253382	ACSA_HUMAN	F8WCJ4_HUMAN,B3KUV2_HUMAN	UPI00004709E0	.	tolerated(0.07)	probably_damaging(0.999)	14/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF126,Pfam_domain:PF00501,Gene3D:2.30.38.10,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGAATGAGTCC	.	3	ESCA
ACSS2	0	.	GRCh37	20	33509640	33509640	+	Missense_Mutation	SNP	G	G	A	rs372652815	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1558G>A	p.Glu520Lys	p.E520K	ENST00000253382	14/19	96	57	39	81	81	0	ACSS2,missense_variant,p.Glu507Lys,ENST00000360596,;ACSS2,missense_variant,p.Glu457Lys,ENST00000336325,;ACSS2,missense_variant,p.Glu520Lys,ENST00000253382,;ACSS2,intron_variant,,ENST00000476922,;ACSS2,downstream_gene_variant,,ENST00000493250,;ACSS2,downstream_gene_variant,,ENST00000468550,;ACSS2,3_prime_UTR_variant,,ENST00000481284,;ACSS2,3_prime_UTR_variant,,ENST00000477932,;ACSS2,non_coding_transcript_exon_variant,,ENST00000491533,;ACSS2,non_coding_transcript_exon_variant,,ENST00000470315,;ACSS2,intron_variant,,ENST00000480978,;ACSS2,downstream_gene_variant,,ENST00000475459,;ACSS2,downstream_gene_variant,,ENST00000490464,;ACSS2,upstream_gene_variant,,ENST00000494727,;	A	ENSG00000131069	ENST00000253382	Transcript	missense_variant	1590	1558	520	E/K	Gag/Aag	rs372652815	.	.	1	ACSS2	HGNC	15814	protein_coding	YES	CCDS42868.2	ENSP00000253382	ACSA_HUMAN	F8WCJ4_HUMAN,B3KUV2_HUMAN	UPI00004709E0	.	tolerated(0.06)	probably_damaging(0.999)	14/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF126,Pfam_domain:PF00501,Gene3D:2.30.38.10,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGAAGAGTTG	byCluster	3	ESCA
ACSS2	0	.	GRCh37	20	33509658	33509658	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1576G>A	p.Glu526Lys	p.E526K	ENST00000253382	14/19	90	56	33	82	82	0	ACSS2,missense_variant,p.Glu513Lys,ENST00000360596,;ACSS2,missense_variant,p.Glu463Lys,ENST00000336325,;ACSS2,missense_variant,p.Glu526Lys,ENST00000253382,;ACSS2,intron_variant,,ENST00000476922,;ACSS2,downstream_gene_variant,,ENST00000493250,;ACSS2,downstream_gene_variant,,ENST00000468550,;ACSS2,3_prime_UTR_variant,,ENST00000481284,;ACSS2,3_prime_UTR_variant,,ENST00000477932,;ACSS2,non_coding_transcript_exon_variant,,ENST00000491533,;ACSS2,non_coding_transcript_exon_variant,,ENST00000470315,;ACSS2,intron_variant,,ENST00000480978,;ACSS2,downstream_gene_variant,,ENST00000475459,;ACSS2,downstream_gene_variant,,ENST00000490464,;ACSS2,upstream_gene_variant,,ENST00000494727,;	A	ENSG00000131069	ENST00000253382	Transcript	missense_variant	1608	1576	526	E/K	Gaa/Aaa	.	.	.	1	ACSS2	HGNC	15814	protein_coding	YES	CCDS42868.2	ENSP00000253382	ACSA_HUMAN	F8WCJ4_HUMAN,B3KUV2_HUMAN	UPI00004709E0	.	deleterious(0.04)	probably_damaging(0.947)	14/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF126,Pfam_domain:PF00501,Gene3D:2.30.38.10,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGCTGAAGGT	.	3	ESCA
SLA2	0	.	GRCh37	20	35242200	35242200	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69C>T	.	.	ENST00000262866	8/8	28	13	15	26	26	0	SLA2,3_prime_UTR_variant,,ENST00000360672,;SLA2,3_prime_UTR_variant,,ENST00000262866,;C20orf24,downstream_gene_variant,,ENST00000344795,;TGIF2-C20orf24,downstream_gene_variant,,ENST00000558530,;C20orf24,downstream_gene_variant,,ENST00000373852,;C20orf24,downstream_gene_variant,,ENST00000342422,;C20orf24,downstream_gene_variant,,ENST00000494506,;C20orf24,downstream_gene_variant,,ENST00000492721,;C20orf24,downstream_gene_variant,,ENST00000483815,;	A	ENSG00000101082	ENST00000262866	Transcript	3_prime_UTR_variant	1278	.	.	.	.	.	.	.	-1	SLA2	HGNC	17329	protein_coding	YES	CCDS13282.1	ENSP00000262866	SLAP2_HUMAN	.	UPI000004B142	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGGGGTGCCC	.	3	ESCA
SLA2	0	.	GRCh37	20	35242214	35242214	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*55C>T	.	.	ENST00000262866	8/8	31	15	16	30	30	0	SLA2,3_prime_UTR_variant,,ENST00000360672,;SLA2,3_prime_UTR_variant,,ENST00000262866,;C20orf24,downstream_gene_variant,,ENST00000344795,;TGIF2-C20orf24,downstream_gene_variant,,ENST00000558530,;C20orf24,downstream_gene_variant,,ENST00000373852,;C20orf24,downstream_gene_variant,,ENST00000342422,;C20orf24,downstream_gene_variant,,ENST00000494506,;C20orf24,downstream_gene_variant,,ENST00000492721,;C20orf24,downstream_gene_variant,,ENST00000483815,;	A	ENSG00000101082	ENST00000262866	Transcript	3_prime_UTR_variant	1264	.	.	.	.	.	.	.	-1	SLA2	HGNC	17329	protein_coding	YES	CCDS13282.1	ENSP00000262866	SLAP2_HUMAN	.	UPI000004B142	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGCTGAATTG	.	3	ESCA
SLA2	0	.	GRCh37	20	35242308	35242308	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.747C>G	p.Ile249Met	p.I249M	ENST00000262866	8/8	55	34	21	38	38	0	SLA2,missense_variant,p.Ile249Met,ENST00000262866,;SLA2,3_prime_UTR_variant,,ENST00000360672,;C20orf24,downstream_gene_variant,,ENST00000344795,;TGIF2-C20orf24,downstream_gene_variant,,ENST00000558530,;C20orf24,downstream_gene_variant,,ENST00000373852,;C20orf24,downstream_gene_variant,,ENST00000342422,;C20orf24,downstream_gene_variant,,ENST00000494506,;C20orf24,downstream_gene_variant,,ENST00000492721,;C20orf24,downstream_gene_variant,,ENST00000483815,;	C	ENSG00000101082	ENST00000262866	Transcript	missense_variant	1170	747	249	I/M	atC/atG	.	.	.	-1	SLA2	HGNC	17329	protein_coding	YES	CCDS13282.1	ENSP00000262866	SLAP2_HUMAN	.	UPI000004B142	.	tolerated(0.07)	benign(0.03)	8/8	.	hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCTGATGTA	.	5	ESCA
SLA2	0	.	GRCh37	20	35242375	35242375	+	Missense_Mutation	SNP	G	G	C	rs773526359	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.680C>G	p.Ser227Cys	p.S227C	ENST00000262866	8/8	38	29	9	37	37	0	SLA2,missense_variant,p.Phe210Leu,ENST00000360672,;SLA2,missense_variant,p.Ser227Cys,ENST00000262866,;C20orf24,downstream_gene_variant,,ENST00000344795,;TGIF2-C20orf24,downstream_gene_variant,,ENST00000558530,;C20orf24,downstream_gene_variant,,ENST00000373852,;C20orf24,downstream_gene_variant,,ENST00000342422,;C20orf24,downstream_gene_variant,,ENST00000494506,;C20orf24,downstream_gene_variant,,ENST00000492721,;C20orf24,downstream_gene_variant,,ENST00000483815,;	C	ENSG00000101082	ENST00000262866	Transcript	missense_variant	1103	680	227	S/C	tCt/tGt	rs773526359	.	.	-1	SLA2	HGNC	17329	protein_coding	YES	CCDS13282.1	ENSP00000262866	SLAP2_HUMAN	.	UPI000004B142	.	deleterious(0.01)	possibly_damaging(0.694)	8/8	.	hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTTCAGAAAAC	.	3	ESCA
SLA2	0	.	GRCh37	20	35242776	35242776	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.597C>G	p.%3D	p.L199L	ENST00000262866	7/8	104	80	23	68	68	0	SLA2,missense_variant,p.Pro183Ala,ENST00000360672,;SLA2,synonymous_variant,p.%3D,ENST00000262866,;C20orf24,downstream_gene_variant,,ENST00000344795,;TGIF2-C20orf24,downstream_gene_variant,,ENST00000558530,;C20orf24,downstream_gene_variant,,ENST00000373852,;C20orf24,downstream_gene_variant,,ENST00000342422,;C20orf24,downstream_gene_variant,,ENST00000494506,;C20orf24,downstream_gene_variant,,ENST00000492721,;C20orf24,downstream_gene_variant,,ENST00000483815,;	C	ENSG00000101082	ENST00000262866	Transcript	synonymous_variant	1020	597	199	L	ctC/ctG	.	.	.	-1	SLA2	HGNC	17329	protein_coding	YES	CCDS13282.1	ENSP00000262866	SLAP2_HUMAN	.	UPI000004B142	.	.	.	7/8	.	hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCAGGGAGCGG	.	3	ESCA
SLA2	0	.	GRCh37	20	35242812	35242812	+	Silent	SNP	G	G	C	rs771308916	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.561C>G	p.%3D	p.L187L	ENST00000262866	7/8	76	59	17	58	58	0	SLA2,synonymous_variant,p.%3D,ENST00000262866,;SLA2,intron_variant,,ENST00000360672,;C20orf24,downstream_gene_variant,,ENST00000344795,;TGIF2-C20orf24,downstream_gene_variant,,ENST00000558530,;C20orf24,downstream_gene_variant,,ENST00000373852,;C20orf24,downstream_gene_variant,,ENST00000342422,;C20orf24,downstream_gene_variant,,ENST00000494506,;C20orf24,downstream_gene_variant,,ENST00000492721,;C20orf24,downstream_gene_variant,,ENST00000483815,;	C	ENSG00000101082	ENST00000262866	Transcript	synonymous_variant	984	561	187	L	ctC/ctG	rs771308916,COSM1026390	.	.	-1	SLA2	HGNC	17329	protein_coding	YES	CCDS13282.1	ENSP00000262866	SLAP2_HUMAN	.	UPI000004B142	.	.	.	7/8	.	PROSITE_profiles:PS50001,hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF14,Gene3D:3.30.505.10,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCTTGAGTAG	.	3	ESCA
SLA2	0	.	GRCh37	20	35242824	35242824	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549C>G	p.Ile183Met	p.I183M	ENST00000262866	7/8	69	54	14	57	57	0	SLA2,missense_variant,p.Ile183Met,ENST00000262866,;SLA2,intron_variant,,ENST00000360672,;C20orf24,downstream_gene_variant,,ENST00000344795,;TGIF2-C20orf24,downstream_gene_variant,,ENST00000558530,;C20orf24,downstream_gene_variant,,ENST00000373852,;C20orf24,downstream_gene_variant,,ENST00000342422,;C20orf24,downstream_gene_variant,,ENST00000494506,;C20orf24,downstream_gene_variant,,ENST00000492721,;C20orf24,downstream_gene_variant,,ENST00000483815,;	C	ENSG00000101082	ENST00000262866	Transcript	missense_variant	972	549	183	I/M	atC/atG	.	.	.	-1	SLA2	HGNC	17329	protein_coding	YES	CCDS13282.1	ENSP00000262866	SLAP2_HUMAN	.	UPI000004B142	.	deleterious(0.01)	possibly_damaging(0.698)	7/8	.	PROSITE_profiles:PS50001,hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF14,Gene3D:3.30.505.10,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGCAGATGTC	.	3	ESCA
SLC12A5	0	.	GRCh37	20	44674582	44674582	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1704C>T	p.%3D	p.C568C	ENST00000454036	13/26	74	48	26	35	35	0	SLC12A5,synonymous_variant,p.%3D,ENST00000454036,;SLC12A5,synonymous_variant,p.%3D,ENST00000243964,;SLC12A5,downstream_gene_variant,,ENST00000372315,;SLC12A5,downstream_gene_variant,,ENST00000608594,;SLC12A5,3_prime_UTR_variant,,ENST00000539566,;	T	ENSG00000124140	ENST00000454036	Transcript	synonymous_variant	1753	1704	568	C	tgC/tgT	.	.	.	1	SLC12A5	HGNC	13818	protein_coding	YES	CCDS46610.1	ENSP00000387694	S12A5_HUMAN	B7Z3I0_HUMAN	UPI00015F4605	.	.	.	13/26	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11827:SF54,hmmpanther:PTHR11827,Pfam_domain:PF00324,TIGRFAM_domain:TIGR00930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGCGAGAT	.	5	ESCA
APOL4	0	.	GRCh37	22	36587208	36587208	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.968C>A	p.Ala323Asp	p.A323D	ENST00000352371	6/6	31	27	3	43	43	0	APOL4,missense_variant,p.Ala320Asp,ENST00000332987,;APOL4,missense_variant,p.Ala323Asp,ENST00000352371,;APOL4,3_prime_UTR_variant,,ENST00000404685,;APOL4,3_prime_UTR_variant,,ENST00000405511,;APOL4,3_prime_UTR_variant,,ENST00000429038,;APOL4,downstream_gene_variant,,ENST00000449084,;APOL4,downstream_gene_variant,,ENST00000419360,;APOL4,downstream_gene_variant,,ENST00000457630,;APOL4,non_coding_transcript_exon_variant,,ENST00000479929,;APOL4,downstream_gene_variant,,ENST00000524531,;APOL4,downstream_gene_variant,,ENST00000493203,;	T	ENSG00000100336	ENST00000352371	Transcript	missense_variant	1193	968	323	A/D	gCt/gAt	.	.	.	-1	APOL4	HGNC	14867	protein_coding	YES	.	ENSP00000338260	.	J3KNR9_HUMAN	UPI000013C6CD	.	deleterious(0)	probably_damaging(0.996)	6/6	.	hmmpanther:PTHR14096:SF25,hmmpanther:PTHR14096,Pfam_domain:PF05461	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ACTCAGCAGAC	.	3	ESCA
PDGFB	0	.	GRCh37	22	39620375	39620375	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*972A>T	.	.	ENST00000331163	7/7	10	4	6	9	9	0	PDGFB,3_prime_UTR_variant,,ENST00000331163,;PDGFB,downstream_gene_variant,,ENST00000381551,;	A	ENSG00000100311	ENST00000331163	Transcript	3_prime_UTR_variant	2486	.	.	.	.	.	.	.	-1	PDGFB	HGNC	8800	protein_coding	YES	CCDS13987.1	ENSP00000330382	PDGFB_HUMAN	Q9UE57_HUMAN,Q9UE56_HUMAN,P78450_HUMAN,A9UJP0_HUMAN,A9UJN9_HUMAN	UPI000004110E	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTACATGGCAG	.	2	ESCA
ATXN10	0	.	GRCh37	22	46098580	46098580	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.500A>G	p.Asn167Ser	p.N167S	ENST00000252934	5/12	153	90	63	116	116	0	ATXN10,missense_variant,p.Asn103Ser,ENST00000381061,;ATXN10,missense_variant,p.Asn167Ser,ENST00000252934,;ATXN10,non_coding_transcript_exon_variant,,ENST00000498009,;ATXN10,upstream_gene_variant,,ENST00000476998,;ATXN10,downstream_gene_variant,,ENST00000470722,;	G	ENSG00000130638	ENST00000252934	Transcript	missense_variant	765	500	167	N/S	aAt/aGt	.	.	.	1	ATXN10	HGNC	10549	protein_coding	YES	CCDS14070.1	ENSP00000252934	ATX10_HUMAN	Q9NTC6_HUMAN	UPI0000052A56	.	tolerated(0.39)	benign(0.077)	5/12	.	hmmpanther:PTHR13255,hmmpanther:PTHR13255:SF0,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAAATCATC	.	5	ESCA
ZBED4	0	.	GRCh37	22	50279480	50279480	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2170G>A	p.Glu724Lys	p.E724K	ENST00000216268	2/2	36	21	15	30	30	0	ZBED4,missense_variant,p.Glu724Lys,ENST00000216268,;	A	ENSG00000100426	ENST00000216268	Transcript	missense_variant	2647	2170	724	E/K	Gag/Aag	COSM445146	.	.	1	ZBED4	HGNC	20721	protein_coding	YES	CCDS33677.1	ENSP00000216268	ZBED4_HUMAN	.	UPI000013C6DB	.	deleterious(0)	probably_damaging(0.967)	2/2	.	hmmpanther:PTHR23272,hmmpanther:PTHR23272:SF6,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTGAGAGT	.	5	ESCA
KLF11	0	.	GRCh37	2	10187774	10187775	+	Intron	INS	-	-	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313-2dupA	.	.	ENST00000305883	.	50	40	10	41	41	0	KLF11,splice_region_variant,,ENST00000540845,;KLF11,splice_region_variant,,ENST00000440320,;KLF11,splice_region_variant,,ENST00000401510,;KLF11,splice_region_variant,,ENST00000535335,;KLF11,splice_region_variant,,ENST00000448523,;KLF11,splice_region_variant,,ENST00000305883,;	A	ENSG00000172059	ENST00000305883	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	KLF11	HGNC	11811	protein_coding	YES	CCDS1668.1	ENSP00000307023	KLF11_HUMAN	Q53QU8_HUMAN,E7EX78_HUMAN,C9JM94_HUMAN,B5MCC4_HUMAN	UPI000012DEDA	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTTTAGTGC	.	3	ESCA
EPB41L5	0	.	GRCh37	2	120799600	120799600	+	Missense_Mutation	SNP	G	G	A	rs777225490,rs142458983	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199G>A	p.Glu67Lys	p.E67K	ENST00000263713	3/25	57	39	18	53	53	0	EPB41L5,missense_variant,p.Glu67Lys,ENST00000331393,;EPB41L5,missense_variant,p.Glu67Lys,ENST00000443902,;EPB41L5,missense_variant,p.Glu67Lys,ENST00000263713,;EPB41L5,missense_variant,p.Glu67Lys,ENST00000452780,;EPB41L5,missense_variant,p.Glu67Lys,ENST00000443124,;EPB41L5,non_coding_transcript_exon_variant,,ENST00000466241,;	A	ENSG00000115109	ENST00000263713	Transcript	missense_variant	413	199	67	E/K	Gag/Aag	rs777225490,rs142458983	.	.	1	EPB41L5	HGNC	19819	protein_coding	YES	CCDS2130.1	ENSP00000263713	E41L5_HUMAN	Q53RT1_HUMAN,Q4ZG32_HUMAN	UPI00001B078A	.	tolerated(0.05)	benign(0.405)	3/25	.	PROSITE_profiles:PS50057,hmmpanther:PTHR23280:SF15,hmmpanther:PTHR23280,Pfam_domain:PF09379,Gene3D:3.10.20.90,SMART_domains:SM00295,Superfamily_domains:SSF54236,Prints_domain:PR00661	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACAAGAGTTG	byCluster	5	ESCA
FAR2P2	0	.	GRCh37	2	131175859	131175859	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3134G>A	.	.	ENST00000430785	2/2	46	32	14	28	28	0	FAR2P2,non_coding_transcript_exon_variant,,ENST00000424873,;FAR2P2,non_coding_transcript_exon_variant,,ENST00000423905,;FAR2P2,non_coding_transcript_exon_variant,,ENST00000433703,;FAR2P2,intron_variant,,ENST00000449066,;FAR2P2,downstream_gene_variant,,ENST00000438056,;FAR2P2,non_coding_transcript_exon_variant,,ENST00000430785,;FAR2P2,downstream_gene_variant,,ENST00000413041,;	T	ENSG00000178162	ENST00000430785	Transcript	non_coding_transcript_exon_variant	3134	.	.	.	.	.	.	.	-1	FAR2P2	HGNC	49279	retained_intron	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GGTATCTTCCT	.	3	ESCA
NR4A2	0	.	GRCh37	2	157186483	157186483	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216C>T	p.%3D	p.D72D	ENST00000339562	3/8	48	26	21	28	28	0	NR4A2,synonymous_variant,p.%3D,ENST00000421709,;NR4A2,synonymous_variant,p.%3D,ENST00000409108,;NR4A2,synonymous_variant,p.%3D,ENST00000429376,;NR4A2,synonymous_variant,p.%3D,ENST00000539077,;NR4A2,synonymous_variant,p.%3D,ENST00000406048,;NR4A2,synonymous_variant,p.%3D,ENST00000426264,;NR4A2,synonymous_variant,p.%3D,ENST00000424077,;NR4A2,synonymous_variant,p.%3D,ENST00000409572,;NR4A2,synonymous_variant,p.%3D,ENST00000339562,;NR4A2,synonymous_variant,p.%3D,ENST00000417764,;NR4A2,synonymous_variant,p.%3D,ENST00000417972,;	A	ENSG00000153234	ENST00000339562	Transcript	synonymous_variant	579	216	72	D	gaC/gaT	.	.	.	-1	NR4A2	HGNC	7981	protein_coding	YES	CCDS2201.1	ENSP00000344479	NR4A2_HUMAN	Q6NXU0_HUMAN,F1D8N6_HUMAN,C9JWQ1_HUMAN,C9IYM5_HUMAN	UPI0000036A18	.	.	.	3/8	.	hmmpanther:PTHR24085,hmmpanther:PTHR24085:SF0,Prints_domain:PR01287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACGTCGTA	.	5	ESCA
SP3	0	.	GRCh37	2	174774748	174774748	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2267C>G	p.Thr756Ser	p.T756S	ENST00000310015	7/7	30	21	9	32	32	0	SP3,missense_variant,p.Thr713Ser,ENST00000416195,;SP3,missense_variant,p.Thr688Ser,ENST00000418194,;SP3,missense_variant,p.Thr703Ser,ENST00000455789,;SP3,missense_variant,p.Thr756Ser,ENST00000310015,;SP3,non_coding_transcript_exon_variant,,ENST00000465379,;	C	ENSG00000172845	ENST00000310015	Transcript	missense_variant	2798	2267	756	T/S	aCc/aGc	.	.	.	-1	SP3	HGNC	11208	protein_coding	YES	CCDS2254.1	ENSP00000310301	SP3_HUMAN	Q68DP2_HUMAN,H0Y6K5_HUMAN	UPI000019B3E0	.	tolerated(0.38)	probably_damaging(0.931)	7/7	.	hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTGGTGGCG	.	5	ESCA
DUSP19	0	.	GRCh37	2	183943626	183943626	+	5'UTR	DEL	A	A	-	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-36delA	.	.	ENST00000354221	1/4	36	25	11	23	23	0	DUSP19,5_prime_UTR_variant,,ENST00000342619,;DUSP19,5_prime_UTR_variant,,ENST00000354221,;AC064871.3,downstream_gene_variant,,ENST00000444562,;DUSP19,upstream_gene_variant,,ENST00000469344,;	-	ENSG00000162999	ENST00000354221	Transcript	5_prime_UTR_variant	140	.	.	.	.	.	.	.	1	DUSP19	HGNC	18894	protein_coding	YES	CCDS2289.1	ENSP00000346160	DUS19_HUMAN	.	UPI000000D7B9	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCTGGATTTGT	.	3	ESCA
CTDSP1	0	.	GRCh37	2	219269237	219269237	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*89C>A	.	.	ENST00000273062	7/7	105	70	35	62	62	0	CTDSP1,3_prime_UTR_variant,,ENST00000273062,;CTDSP1,3_prime_UTR_variant,,ENST00000443891,;CTDSP1,downstream_gene_variant,,ENST00000452977,;CTDSP1,downstream_gene_variant,,ENST00000431127,;CTDSP1,downstream_gene_variant,,ENST00000428361,;MIR26B,downstream_gene_variant,,ENST00000362251,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000464255,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000488627,;CTDSP1,downstream_gene_variant,,ENST00000491064,;CTDSP1,downstream_gene_variant,,ENST00000473420,;CTDSP1,downstream_gene_variant,,ENST00000496785,;CTDSP1,downstream_gene_variant,,ENST00000492545,;CTDSP1,downstream_gene_variant,,ENST00000498160,;CTDSP1,downstream_gene_variant,,ENST00000482272,;CTDSP1,downstream_gene_variant,,ENST00000494067,;CTDSP1,downstream_gene_variant,,ENST00000497677,;	A	ENSG00000144579	ENST00000273062	Transcript	3_prime_UTR_variant	1211	.	.	.	.	.	.	.	1	CTDSP1	HGNC	21614	protein_coding	YES	CCDS2416.1	ENSP00000273062	CTDS1_HUMAN	.	UPI000013007C	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACCCATGGG	.	5	ESCA
BCS1L	0	.	GRCh37	2	219527683	219527683	+	Missense_Mutation	SNP	G	G	A	rs372817977	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967G>A	p.Glu323Lys	p.E323K	ENST00000431802	7/8	59	36	22	53	53	0	BCS1L,missense_variant,p.Glu323Lys,ENST00000412366,;BCS1L,missense_variant,p.Glu105Lys,ENST00000426649,;BCS1L,missense_variant,p.Glu323Lys,ENST00000439945,;BCS1L,missense_variant,p.Glu323Lys,ENST00000392109,;BCS1L,missense_variant,p.Glu323Lys,ENST00000359273,;BCS1L,missense_variant,p.Glu323Lys,ENST00000392111,;BCS1L,missense_variant,p.Glu105Lys,ENST00000436603,;BCS1L,missense_variant,p.Glu323Lys,ENST00000392110,;BCS1L,missense_variant,p.Glu323Lys,ENST00000431802,;BCS1L,downstream_gene_variant,,ENST00000423377,;BCS1L,downstream_gene_variant,,ENST00000430322,;BCS1L,downstream_gene_variant,,ENST00000443791,;BCS1L,downstream_gene_variant,,ENST00000456050,;ZNF142,upstream_gene_variant,,ENST00000411696,;ZNF142,upstream_gene_variant,,ENST00000432460,;RNF25,downstream_gene_variant,,ENST00000295704,;BCS1L,downstream_gene_variant,,ENST00000428880,;ZNF142,upstream_gene_variant,,ENST00000450560,;ZNF142,upstream_gene_variant,,ENST00000449707,;BCS1L,non_coding_transcript_exon_variant,,ENST00000465706,;BCS1L,non_coding_transcript_exon_variant,,ENST00000477422,;BCS1L,non_coding_transcript_exon_variant,,ENST00000460579,;RNF25,downstream_gene_variant,,ENST00000474339,;ZNF142,upstream_gene_variant,,ENST00000450765,;BCS1L,downstream_gene_variant,,ENST00000493376,;BCS1L,downstream_gene_variant,,ENST00000471576,;RNF25,downstream_gene_variant,,ENST00000497832,;BCS1L,downstream_gene_variant,,ENST00000490188,;ZNF142,upstream_gene_variant,,ENST00000433921,;RNF25,downstream_gene_variant,,ENST00000423170,;RNF25,downstream_gene_variant,,ENST00000473034,;RNF25,downstream_gene_variant,,ENST00000463188,;	A	ENSG00000074582	ENST00000431802	Transcript	missense_variant	1666	967	323	E/K	Gag/Aag	rs372817977	.	.	1	BCS1L	HGNC	1020	protein_coding	YES	CCDS2419.1	ENSP00000413908	BCS1_HUMAN	Q53RT4_HUMAN,C9JAS4_HUMAN,C9J8G3_HUMAN,C9J4Q9_HUMAN,C9J1S9_HUMAN	UPI0000073C9C	.	deleterious(0)	probably_damaging(0.996)	7/8	.	hmmpanther:PTHR23070:SF17,hmmpanther:PTHR23070,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCGAGGCC	byFrequency|byCluster	5	ESCA
CNPPD1	0	.	GRCh37	2	220037669	220037669	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.872C>T	p.Ser291Phe	p.S291F	ENST00000409789	9/9	35	21	13	30	30	0	CNPPD1,missense_variant,p.Ser291Phe,ENST00000409789,;CNPPD1,missense_variant,p.Ser291Phe,ENST00000453038,;CNPPD1,missense_variant,p.Ser291Phe,ENST00000360507,;FAM134A,upstream_gene_variant,,ENST00000443757,;SLC23A3,upstream_gene_variant,,ENST00000430764,;SLC23A3,upstream_gene_variant,,ENST00000409878,;SLC23A3,upstream_gene_variant,,ENST00000455516,;SLC23A3,upstream_gene_variant,,ENST00000295738,;SLC23A3,upstream_gene_variant,,ENST00000396775,;CNPPD1,downstream_gene_variant,,ENST00000451647,;SLC23A3,upstream_gene_variant,,ENST00000409370,;FAM134A,upstream_gene_variant,,ENST00000458520,;SLC23A3,upstream_gene_variant,,ENST00000497918,;SLC23A3,upstream_gene_variant,,ENST00000498327,;SLC23A3,upstream_gene_variant,,ENST00000465580,;SLC23A3,upstream_gene_variant,,ENST00000421779,;SLC23A3,upstream_gene_variant,,ENST00000414999,;SLC23A3,upstream_gene_variant,,ENST00000318673,;SLC23A3,upstream_gene_variant,,ENST00000461812,;	A	ENSG00000115649	ENST00000409789	Transcript	missense_variant	1300	872	291	S/F	tCt/tTt	COSM1631849	.	.	-1	CNPPD1	HGNC	25220	protein_coding	YES	CCDS2433.1	ENSP00000386277	CNPD1_HUMAN	C9JF31_HUMAN	UPI000013D5FA	.	deleterious_low_confidence(0.04)	benign(0.001)	9/9	.	hmmpanther:PTHR15615,hmmpanther:PTHR15615:SF0	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L292P|c.875T>C|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGAGACGGC	.	5	ESCA
EPHA4	0	.	GRCh37	2	222433469	222433469	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128T>A	p.Leu43His	p.L43H	ENST00000281821	2/18	66	42	24	55	55	0	EPHA4,missense_variant,p.Leu43His,ENST00000409854,;EPHA4,missense_variant,p.Leu43His,ENST00000434266,;EPHA4,missense_variant,p.Leu43His,ENST00000541600,;EPHA4,missense_variant,p.Leu43His,ENST00000409938,;EPHA4,missense_variant,p.Leu43His,ENST00000281821,;EPHA4,5_prime_UTR_variant,,ENST00000419964,;EPHA4,intron_variant,,ENST00000392071,;EPHA4,intron_variant,,ENST00000443796,;CTD-2308L22.1,upstream_gene_variant,,ENST00000609776,;EPHA4,intron_variant,,ENST00000415749,;	T	ENSG00000116106	ENST00000281821	Transcript	missense_variant	170	128	43	L/H	cTt/cAt	.	.	.	-1	EPHA4	HGNC	3388	protein_coding	YES	CCDS2447.1	ENSP00000281821	EPHA4_HUMAN	Q584H6_HUMAN,Q53TA0_HUMAN,F5GZZ5_HUMAN,E9PG71_HUMAN,C9JIX8_HUMAN,C9JEM6_HUMAN	UPI000012A077	.	deleterious(0)	probably_damaging(0.98)	2/18	.	Superfamily_domains:SSF49785,PIRSF_domain:PIRSF000666,SMART_domains:SM00615,Gene3D:2.60.120.260,Pfam_domain:PF01404,hmmpanther:PTHR24416:SF25,hmmpanther:PTHR24416,PROSITE_profiles:PS51550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCAAGTTCT	.	5	ESCA
PTMA	0	.	GRCh37	2	232573421	232573421	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5C>G	p.Ser2Ter	p.S2*	ENST00000341369	1/5	21	16	5	24	24	0	PTMA,stop_gained,p.Ser2Ter,ENST00000341369,;PTMA,stop_gained,p.Ser2Ter,ENST00000409115,;PTMA,stop_gained,p.Ser2Ter,ENST00000409683,;PTMA,splice_region_variant,,ENST00000409321,;PTMA,upstream_gene_variant,,ENST00000410064,;PTMA,upstream_gene_variant,,ENST00000412128,;MGC4771,upstream_gene_variant,,ENST00000595658,;PTMA,upstream_gene_variant,,ENST00000440384,;PTMA,intron_variant,,ENST00000466801,;PTMA,non_coding_transcript_exon_variant,,ENST00000481928,;PTMA,non_coding_transcript_exon_variant,,ENST00000468027,;PTMA,intron_variant,,ENST00000448874,;PTMA,upstream_gene_variant,,ENST00000467816,;	G	ENSG00000187514	ENST00000341369	Transcript	stop_gained	196	5	2	S/*	tCa/tGa	.	.	.	1	PTMA	HGNC	9623	protein_coding	YES	CCDS42833.1	ENSP00000344547	PTMA_HUMAN	.	UPI0000047512	.	.	.	1/5	.	hmmpanther:PTHR22745,Pfam_domain:PF03247	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	CATGTCAGACG	.	3	ESCA
NEU4	0	.	GRCh37	2	242756095	242756095	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>T	p.Ala83Ser	p.A83S	ENST00000325935	3/4	82	47	35	70	70	0	NEU4,missense_variant,p.Ala70Ser,ENST00000407683,;NEU4,missense_variant,p.Ala83Ser,ENST00000325935,;NEU4,missense_variant,p.Ala70Ser,ENST00000391969,;NEU4,missense_variant,p.Ala70Ser,ENST00000405370,;NEU4,missense_variant,p.Ala111Ser,ENST00000428592,;NEU4,missense_variant,p.Ala70Ser,ENST00000435894,;NEU4,missense_variant,p.Ala70Ser,ENST00000420288,;NEU4,missense_variant,p.Ala82Ser,ENST00000404257,;NEU4,missense_variant,p.Ala70Ser,ENST00000423583,;NEU4,intron_variant,,ENST00000415936,;NEU4,intron_variant,,ENST00000426032,;NEU4,downstream_gene_variant,,ENST00000435934,;AC114730.3,upstream_gene_variant,,ENST00000420272,;AC114730.3,upstream_gene_variant,,ENST00000413820,;AC114730.3,upstream_gene_variant,,ENST00000439270,;NEU4,missense_variant,p.Ala70Ser,ENST00000435855,;NEU4,non_coding_transcript_exon_variant,,ENST00000488997,;NEU4,non_coding_transcript_exon_variant,,ENST00000406147,;NEU4,non_coding_transcript_exon_variant,,ENST00000476542,;NEU4,downstream_gene_variant,,ENST00000494678,;	T	ENSG00000204099	ENST00000325935	Transcript	missense_variant	676	247	83	A/S	Gcc/Tcc	.	.	.	1	NEU4	HGNC	21328	protein_coding	YES	CCDS54441.1	ENSP00000320318	NEUR4_HUMAN	C9JRN9_HUMAN,C9J5X2_HUMAN,C9J2V4_HUMAN,B3KR54_HUMAN	UPI0000EE378E	.	tolerated(0.8)	benign(0.045)	3/4	.	Superfamily_domains:SSF50939,Pfam_domain:PF13088,Gene3D:2.120.10.10,hmmpanther:PTHR10628:SF8,hmmpanther:PTHR10628	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTGCCCTG	.	5	ESCA
EPT1	0	.	GRCh37	2	26596361	26596361	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437G>A	p.Arg146Lys	p.R146K	ENST00000260585	5/10	229	138	91	203	203	0	EPT1,missense_variant,p.Arg114Lys,ENST00000442141,;EPT1,missense_variant,p.Arg146Lys,ENST00000260585,;EPT1,intron_variant,,ENST00000447170,;	A	ENSG00000138018	ENST00000260585	Transcript	missense_variant	556	437	146	R/K	aGa/aAa	.	.	.	1	EPT1	HGNC	29361	protein_coding	YES	CCDS46240.1	ENSP00000260585	EPT1_HUMAN	G1UI38_HUMAN,C9JEZ2_HUMAN,C9J9I1_HUMAN	UPI00003CE422	.	deleterious(0.01)	possibly_damaging(0.856)	5/10	.	hmmpanther:PTHR10414,hmmpanther:PTHR10414:SF33,Pfam_domain:PF01066,PIRSF_domain:PIRSF015665	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAAGAGGAT	.	5	ESCA
SNX17	0	.	GRCh37	2	27599874	27599874	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*288A>T	.	.	ENST00000233575	15/15	61	34	27	30	30	0	SNX17,3_prime_UTR_variant,,ENST00000542478,;SNX17,3_prime_UTR_variant,,ENST00000233575,;PPM1G,downstream_gene_variant,,ENST00000344034,;SNX17,downstream_gene_variant,,ENST00000537606,;ZNF513,downstream_gene_variant,,ENST00000407879,;ZNF513,downstream_gene_variant,,ENST00000323703,;ZNF513,downstream_gene_variant,,ENST00000436006,;SNX17,downstream_gene_variant,,ENST00000543024,;PPM1G,downstream_gene_variant,,ENST00000350803,;ZNF513,downstream_gene_variant,,ENST00000491924,;SNX17,3_prime_UTR_variant,,ENST00000453453,;SNX17,3_prime_UTR_variant,,ENST00000440760,;SNX17,3_prime_UTR_variant,,ENST00000427123,;SNX17,downstream_gene_variant,,ENST00000493711,;SNX17,downstream_gene_variant,,ENST00000464279,;PPM1G,downstream_gene_variant,,ENST00000472077,;SNX17,downstream_gene_variant,,ENST00000494893,;SNX17,downstream_gene_variant,,ENST00000489402,;	T	ENSG00000115234	ENST00000233575	Transcript	3_prime_UTR_variant	1923	.	.	.	.	.	.	.	1	SNX17	HGNC	14979	protein_coding	YES	CCDS1750.1	ENSP00000233575	SNX17_HUMAN	B4DTB8_HUMAN,B4DLL7_HUMAN,B4DDM3_HUMAN	UPI0000135B4E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATATCTCC	.	5	ESCA
MTIF2	0	.	GRCh37	2	55470218	55470218	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1565-2A>G	.	p.X522_splice	ENST00000394600	.	24	12	11	11	11	0	MTIF2,splice_acceptor_variant,,ENST00000418823,;MTIF2,splice_acceptor_variant,,ENST00000394600,;MTIF2,splice_acceptor_variant,,ENST00000403721,;MTIF2,splice_acceptor_variant,,ENST00000263629,;	C	ENSG00000085760	ENST00000394600	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	MTIF2	HGNC	7441	protein_coding	YES	CCDS1853.1	ENSP00000378099	IF2M_HUMAN	E7EW07_HUMAN,E7ESE3_HUMAN,C9JIY5_HUMAN,B5MCU1_HUMAN	UPI000013D42F	.	.	.	.	13/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCTAAATA	.	5	ESCA
ALMS1	0	.	GRCh37	2	73678197	73678197	+	Missense_Mutation	SNP	G	G	A	rs183839621	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4540G>A	p.Ala1514Thr	p.A1514T	ENST00000264448	8/23	71	43	27	62	62	0	ALMS1,missense_variant,p.Ala1514Thr,ENST00000377715,;ALMS1,missense_variant,p.Ala1472Thr,ENST00000409009,;ALMS1,missense_variant,p.Ala1514Thr,ENST00000264448,;ALMS1,upstream_gene_variant,,ENST00000484298,;ALMS1,upstream_gene_variant,,ENST00000423048,;	A	ENSG00000116127	ENST00000264448	Transcript	missense_variant	4651	4540	1514	A/T	Gca/Aca	rs183839621,COSM1022804	.	.	1	ALMS1	HGNC	428	protein_coding	YES	CCDS42697.1	ENSP00000264448	ALMS1_HUMAN	A6NMY3_HUMAN	UPI0000212786	.	.	benign(0)	8/23	.	.	A:0.0004	A:0.0008	A:0	.	A:0	A:0.001	A:0	A:0.0005	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGCACCA	byFrequency|byCluster|by1000G	5	ESCA
CNNM4	0	.	GRCh37	2	97475826	97475826	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*572C>A	.	.	ENST00000377075	7/7	15	12	3	19	19	0	CNNM4,3_prime_UTR_variant,,ENST00000377075,;CNNM4,downstream_gene_variant,,ENST00000540067,;RP11-353K11.1,downstream_gene_variant,,ENST00000608609,;CNNM4,downstream_gene_variant,,ENST00000496186,;	A	ENSG00000158158	ENST00000377075	Transcript	3_prime_UTR_variant	2998	.	.	.	.	.	.	.	1	CNNM4	HGNC	105	protein_coding	YES	CCDS2024.2	ENSP00000366275	CNNM4_HUMAN	.	UPI0000207C95	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGATCAGCTG	.	2	ESCA
IQCB1	0	.	GRCh37	3	121547357	121547357	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.223G>A	p.Gly75Ser	p.G75S	ENST00000310864	4/15	73	68	4	68	68	0	IQCB1,missense_variant,p.Gly75Ser,ENST00000349820,;IQCB1,missense_variant,p.Gly75Ser,ENST00000310864,;IQCB1,missense_variant,p.Gly75Ser,ENST00000462442,;IQCB1,intron_variant,,ENST00000498104,;IQCB1,intron_variant,,ENST00000460108,;IQCB1,missense_variant,p.Gly75Ser,ENST00000393650,;	T	ENSG00000173226	ENST00000310864	Transcript	missense_variant	438	223	75	G/S	Ggt/Agt	.	.	.	-1	IQCB1	HGNC	28949	protein_coding	YES	CCDS33837.1	ENSP00000311505	IQCB1_HUMAN	C9JXD7_HUMAN,C9JVC4_HUMAN,C9J6Z7_HUMAN	UPI0000139154	.	deleterious(0)	probably_damaging(0.999)	4/15	.	Superfamily_domains:SSF48371,hmmpanther:PTHR15673,hmmpanther:PTHR15673:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCACCCTGGA	.	2	ESCA
PARP14	0	.	GRCh37	3	122447375	122447375	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5337T>C	p.%3D	p.H1779H	ENST00000474629	17/17	66	36	29	69	69	0	PARP14,synonymous_variant,p.%3D,ENST00000474629,;PARP14,3_prime_UTR_variant,,ENST00000460683,;	C	ENSG00000173193	ENST00000474629	Transcript	synonymous_variant	5603	5337	1779	H	caT/caC	.	.	.	1	PARP14	HGNC	29232	protein_coding	YES	CCDS46894.1	ENSP00000418194	PAR14_HUMAN	.	UPI00015A20AB	.	.	.	17/17	.	PROSITE_profiles:PS51059,hmmpanther:PTHR14453:SF53,hmmpanther:PTHR14453,Gene3D:3.90.228.10,Pfam_domain:PF00644,Superfamily_domains:SSF56399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCATCCAAG	.	5	ESCA
ATP2C1	0	.	GRCh37	3	130613527	130613527	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.109-35733C>A	.	.	ENST00000393221	.	45	40	5	34	34	0	ATP2C1,5_prime_UTR_variant,,ENST00000328560,;ATP2C1,5_prime_UTR_variant,,ENST00000359644,;ATP2C1,5_prime_UTR_variant,,ENST00000422190,;ATP2C1,5_prime_UTR_variant,,ENST00000428331,;ATP2C1,5_prime_UTR_variant,,ENST00000509662,;ATP2C1,5_prime_UTR_variant,,ENST00000510168,;ATP2C1,intron_variant,,ENST00000533801,;ATP2C1,intron_variant,,ENST00000508532,;ATP2C1,intron_variant,,ENST00000505330,;ATP2C1,intron_variant,,ENST00000504948,;ATP2C1,intron_variant,,ENST00000507488,;ATP2C1,intron_variant,,ENST00000393221,;ATP2C1,intron_variant,,ENST00000513801,;ATP2C1,intron_variant,,ENST00000505072,;ATP2C1,intron_variant,,ENST00000504381,;RP11-39E3.3,downstream_gene_variant,,ENST00000504737,;	A	ENSG00000017260	ENST00000393221	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ATP2C1	HGNC	13211	protein_coding	YES	CCDS56278.1	ENSP00000376914	AT2C1_HUMAN	D6RGE9_HUMAN,D6R9U9_HUMAN	UPI0000EE224C	.	.	.	.	1/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTGTCCTCCTC	.	3	ESCA
GPR149	0	.	GRCh37	3	154146875	154146875	+	Missense_Mutation	SNP	C	C	G	rs763187151	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530G>C	p.Arg177Pro	p.R177P	ENST00000389740	1/4	89	52	37	71	71	0	GPR149,missense_variant,p.Arg177Pro,ENST00000389740,;	G	ENSG00000174948	ENST00000389740	Transcript	missense_variant	630	530	177	R/P	cGc/cCc	rs763187151	.	.	-1	GPR149	HGNC	23627	protein_coding	YES	CCDS43162.1	ENSP00000374390	GP149_HUMAN	Q2MKA6_HUMAN	UPI00001AEEA9	.	tolerated(1)	benign(0.023)	1/4	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24229:SF32,hmmpanther:PTHR24229,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGTGCGCACG	.	5	ESCA
PDCD10	0	.	GRCh37	3	167452469	167452469	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-273G>A	.	.	ENST00000392750	1/9	14	6	8	14	14	0	PDCD10,5_prime_UTR_variant,,ENST00000392750,;PDCD10,intron_variant,,ENST00000470131,;PDCD10,intron_variant,,ENST00000464360,;PDCD10,intron_variant,,ENST00000492139,;PDCD10,intron_variant,,ENST00000497056,;PDCD10,intron_variant,,ENST00000471885,;PDCD10,intron_variant,,ENST00000473645,;SERPINI1,upstream_gene_variant,,ENST00000446050,;SERPINI1,upstream_gene_variant,,ENST00000472747,;PDCD10,upstream_gene_variant,,ENST00000475915,;PDCD10,upstream_gene_variant,,ENST00000461494,;SERPINI1,upstream_gene_variant,,ENST00000472941,;PDCD10,upstream_gene_variant,,ENST00000487947,;PDCD10,upstream_gene_variant,,ENST00000462725,;SERPINI1,upstream_gene_variant,,ENST00000295777,;PDCD10,upstream_gene_variant,,ENST00000487678,;PDCD10,non_coding_transcript_exon_variant,,ENST00000483451,;PDCD10,intron_variant,,ENST00000481136,;PDCD10,intron_variant,,ENST00000494502,;	T	ENSG00000114209	ENST00000392750	Transcript	5_prime_UTR_variant	146	.	.	.	.	.	.	.	-1	PDCD10	HGNC	8761	protein_coding	YES	CCDS3202.1	ENSP00000376506	PDC10_HUMAN	C9JSA3_HUMAN,C9JND6_HUMAN,C9J932_HUMAN,C9J6F3_HUMAN,C9J5C3_HUMAN,C9J363_HUMAN	UPI0000071E33	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCAGCCC	.	5	ESCA
RP11-298O21.5	0	.	GRCh37	3	167632982	167632982	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.625G>C	.	.	ENST00000481578	5/7	44	33	11	43	43	0	RP11-298O21.5,non_coding_transcript_exon_variant,,ENST00000481578,;RP11-298O21.5,non_coding_transcript_exon_variant,,ENST00000459923,;RP11-298O21.5,non_coding_transcript_exon_variant,,ENST00000496891,;RP11-298O21.5,intron_variant,,ENST00000469060,;RP11-298O21.5,intron_variant,,ENST00000493529,;RP11-298O21.5,downstream_gene_variant,,ENST00000490897,;RP11-298O21.5,downstream_gene_variant,,ENST00000494887,;	C	ENSG00000244227	ENST00000481578	Transcript	non_coding_transcript_exon_variant	625	.	.	.	.	.	.	.	1	RP11-298O21.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	5/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAAGATTGC	.	5	ESCA
MAP3K13	0	.	GRCh37	3	185155326	185155326	+	Silent	SNP	G	G	A	rs199761257	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567G>A	p.%3D	p.A189A	ENST00000265026	3/14	75	53	22	52	52	0	MAP3K13,synonymous_variant,p.%3D,ENST00000424227,;MAP3K13,synonymous_variant,p.%3D,ENST00000535426,;MAP3K13,synonymous_variant,p.%3D,ENST00000443863,;MAP3K13,synonymous_variant,p.%3D,ENST00000265026,;MAP3K13,intron_variant,,ENST00000446828,;MAP3K13,upstream_gene_variant,,ENST00000420577,;snoU13,upstream_gene_variant,,ENST00000459417,;MAP3K13,3_prime_UTR_variant,,ENST00000433092,;MAP3K13,non_coding_transcript_exon_variant,,ENST00000477582,;MAP3K13,intron_variant,,ENST00000438053,;MAP3K13,intron_variant,,ENST00000439882,;	A	ENSG00000073803	ENST00000265026	Transcript	synonymous_variant	901	567	189	A	gcG/gcA	rs199761257	.	.	1	MAP3K13	HGNC	6852	protein_coding	YES	CCDS3270.1	ENSP00000265026	M3K13_HUMAN	C9JP65_HUMAN,C9J4W2_HUMAN	UPI000006CF91	.	.	.	3/14	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF336,Gene3D:3.30.200.20,Pfam_domain:PF07714,SMART_domains:SM00220,PIRSF_domain:PIRSF038165,PIRSF_domain:PIRSF500742,Superfamily_domains:SSF56112	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGCGGAAGA	byCluster|by1000G	5	ESCA
MUC4	0	.	GRCh37	3	195518038	195518038	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.413T>C	p.Ile138Thr	p.I138T	ENST00000463781	2/25	133	81	51	102	102	0	MUC4,missense_variant,p.Ile138Thr,ENST00000475231,;MUC4,missense_variant,p.Ile138Thr,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.Ile138Thr,ENST00000477086,;MUC4,missense_variant,p.Ile138Thr,ENST00000466475,;MUC4,missense_variant,p.Ile138Thr,ENST00000478156,;MUC4,missense_variant,p.Ile138Thr,ENST00000470451,;MUC4,missense_variant,p.Ile138Thr,ENST00000479406,;MUC4,missense_variant,p.Ile138Thr,ENST00000477756,;MUC4,missense_variant,p.Ile138Thr,ENST00000462323,;MUC4,missense_variant,p.Ile138Thr,ENST00000480843,;	G	ENSG00000145113	ENST00000463781	Transcript	missense_variant	873	413	138	I/T	aTa/aCa	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	unknown(0)	2/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTATAGTC	.	5	ESCA
TMEM158	0	.	GRCh37	3	45266057	45266057	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*560G>A	.	.	ENST00000503771	1/1	52	19	33	47	47	0	TMEM158,3_prime_UTR_variant,,ENST00000503771,;AC010170.1,downstream_gene_variant,,ENST00000325090,;	T	ENSG00000249992	ENST00000503771	Transcript	3_prime_UTR_variant	1714	.	.	.	.	.	.	.	-1	TMEM158	HGNC	30293	protein_coding	YES	CCDS54573.1	ENSP00000422431	TM158_HUMAN	.	UPI0000E5DD5E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGTTCATAAA	.	3	ESCA
TMEM158	0	.	GRCh37	3	45266072	45266072	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*545G>A	.	.	ENST00000503771	1/1	50	18	32	51	51	0	TMEM158,3_prime_UTR_variant,,ENST00000503771,;AC010170.1,downstream_gene_variant,,ENST00000325090,;	T	ENSG00000249992	ENST00000503771	Transcript	3_prime_UTR_variant	1699	.	.	.	.	.	.	.	-1	TMEM158	HGNC	30293	protein_coding	YES	CCDS54573.1	ENSP00000422431	TM158_HUMAN	.	UPI0000E5DD5E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATTTTCAGCGG	.	3	ESCA
TMEM158	0	.	GRCh37	3	45266243	45266243	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*374G>A	.	.	ENST00000503771	1/1	10	3	7	19	19	0	TMEM158,3_prime_UTR_variant,,ENST00000503771,;AC010170.1,downstream_gene_variant,,ENST00000325090,;	T	ENSG00000249992	ENST00000503771	Transcript	3_prime_UTR_variant	1528	.	.	.	.	.	.	.	-1	TMEM158	HGNC	30293	protein_coding	YES	CCDS54573.1	ENSP00000422431	TM158_HUMAN	.	UPI0000E5DD5E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACTTTCATTTA	.	3	ESCA
TMEM158	0	.	GRCh37	3	45266411	45266411	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*206G>A	.	.	ENST00000503771	1/1	8	2	6	11	11	0	TMEM158,3_prime_UTR_variant,,ENST00000503771,;AC010170.1,downstream_gene_variant,,ENST00000325090,;	T	ENSG00000249992	ENST00000503771	Transcript	3_prime_UTR_variant	1360	.	.	.	.	.	.	.	-1	TMEM158	HGNC	30293	protein_coding	YES	CCDS54573.1	ENSP00000422431	TM158_HUMAN	.	UPI0000E5DD5E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCCTCAGTCC	.	2	ESCA
DNAJB14	0	.	GRCh37	4	100820811	100820811	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1374G>T	.	.	ENST00000442697	8/8	11	4	7	28	28	0	DNAJB14,3_prime_UTR_variant,,ENST00000442697,;DNAJB14,3_prime_UTR_variant,,ENST00000420137,;DNAJB14,3_prime_UTR_variant,,ENST00000334223,;DNAJB14,non_coding_transcript_exon_variant,,ENST00000471101,;DNAJB14,downstream_gene_variant,,ENST00000398991,;DNAJB14,downstream_gene_variant,,ENST00000455208,;	A	ENSG00000164031	ENST00000442697	Transcript	3_prime_UTR_variant	2669	.	.	.	.	.	.	.	-1	DNAJB14	HGNC	25881	protein_coding	YES	CCDS34035.1	ENSP00000404381	DJB14_HUMAN	F2Z2L8_HUMAN	UPI0000072A32	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCACTCACAAA	.	3	ESCA
TADA2B	0	.	GRCh37	4	7056084	7056084	+	Missense_Mutation	SNP	C	C	G	rs750763128	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.566C>G	p.Ser189Cys	p.S189C	ENST00000310074	2/2	10	3	7	15	15	0	TADA2B,missense_variant,p.Ser97Cys,ENST00000506692,;TADA2B,missense_variant,p.Ser97Cys,ENST00000515646,;TADA2B,missense_variant,p.Ser97Cys,ENST00000510704,;TADA2B,missense_variant,p.Ser189Cys,ENST00000310074,;TADA2B,missense_variant,p.Ser114Cys,ENST00000512388,;GRPEL1,downstream_gene_variant,,ENST00000264954,;	G	ENSG00000173011	ENST00000310074	Transcript	missense_variant	755	566	189	S/C	tCt/tGt	rs750763128	.	.	1	TADA2B	HGNC	30781	protein_coding	YES	CCDS47007.1	ENSP00000308022	TAD2B_HUMAN	D6RJ05_HUMAN,D6RC20_HUMAN	UPI00001996F4	.	tolerated(0.06)	benign(0.009)	2/2	.	hmmpanther:PTHR12374,PIRSF_domain:PIRSF025024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTCTCTGTCA	.	3	ESCA
TADA2B	0	.	GRCh37	4	7058162	7058162	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1381C>G	.	.	ENST00000310074	2/2	26	7	18	19	19	0	TADA2B,3_prime_UTR_variant,,ENST00000515646,;TADA2B,3_prime_UTR_variant,,ENST00000310074,;TADA2B,downstream_gene_variant,,ENST00000506692,;GRPEL1,downstream_gene_variant,,ENST00000264954,;TADA2B,downstream_gene_variant,,ENST00000510704,;TADA2B,downstream_gene_variant,,ENST00000512388,;GRPEL1,downstream_gene_variant,,ENST00000514056,;GRPEL1,downstream_gene_variant,,ENST00000509696,;GRPEL1,downstream_gene_variant,,ENST00000504920,;	G	ENSG00000173011	ENST00000310074	Transcript	3_prime_UTR_variant	2833	.	.	.	.	.	.	.	1	TADA2B	HGNC	30781	protein_coding	YES	CCDS47007.1	ENSP00000308022	TAD2B_HUMAN	D6RJ05_HUMAN,D6RC20_HUMAN	UPI00001996F4	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCCTCTCGGG	.	3	ESCA
TADA2B	0	.	GRCh37	4	7058164	7058164	+	3'UTR	SNP	C	C	T	rs548737039	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1383C>T	.	.	ENST00000310074	2/2	26	7	19	19	19	0	TADA2B,3_prime_UTR_variant,,ENST00000515646,;TADA2B,3_prime_UTR_variant,,ENST00000310074,;TADA2B,downstream_gene_variant,,ENST00000506692,;GRPEL1,downstream_gene_variant,,ENST00000264954,;TADA2B,downstream_gene_variant,,ENST00000510704,;TADA2B,downstream_gene_variant,,ENST00000512388,;GRPEL1,downstream_gene_variant,,ENST00000514056,;GRPEL1,downstream_gene_variant,,ENST00000509696,;GRPEL1,downstream_gene_variant,,ENST00000504920,;	T	ENSG00000173011	ENST00000310074	Transcript	3_prime_UTR_variant	2835	.	.	.	.	rs548737039	.	.	1	TADA2B	HGNC	30781	protein_coding	YES	CCDS47007.1	ENSP00000308022	TAD2B_HUMAN	D6RJ05_HUMAN,D6RC20_HUMAN	UPI00001996F4	.	.	.	2/2	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCTCGGGCC	by1000G	3	ESCA
ENAM	0	.	GRCh37	4	71508640	71508640	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1497A>T	p.%3D	p.G499G	ENST00000396073	9/9	12	6	6	14	14	0	ENAM,synonymous_variant,p.%3D,ENST00000396073,;ENAM,intron_variant,,ENST00000472903,;ENAM,downstream_gene_variant,,ENST00000472597,;	T	ENSG00000132464	ENST00000396073	Transcript	synonymous_variant	1778	1497	499	G	ggA/ggT	.	.	.	1	ENAM	HGNC	3344	protein_coding	YES	CCDS3544.2	ENSP00000379383	ENAM_HUMAN	Q8NFB4_HUMAN	UPI000013CE60	.	.	.	9/9	.	Pfam_domain:PF15362,hmmpanther:PTHR16784:SF2,hmmpanther:PTHR16784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AGAGGAGATTC	.	3	ESCA
SEC31A	0	.	GRCh37	4	83776067	83776067	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1997C>T	p.Ser666Leu	p.S666L	ENST00000395310	17/27	43	13	30	56	56	0	SEC31A,missense_variant,p.Ser666Leu,ENST00000448323,;SEC31A,missense_variant,p.Ser627Leu,ENST00000505984,;SEC31A,missense_variant,p.Ser399Leu,ENST00000264405,;SEC31A,missense_variant,p.Ser181Leu,ENST00000512664,;SEC31A,missense_variant,p.Ser666Leu,ENST00000311785,;SEC31A,missense_variant,p.Ser627Leu,ENST00000500777,;SEC31A,missense_variant,p.Ser254Leu,ENST00000510167,;SEC31A,missense_variant,p.Ser666Leu,ENST00000395310,;SEC31A,missense_variant,p.Ser666Leu,ENST00000509142,;SEC31A,missense_variant,p.Ser666Leu,ENST00000508502,;SEC31A,missense_variant,p.Ser666Leu,ENST00000505472,;SEC31A,missense_variant,p.Ser666Leu,ENST00000432794,;SEC31A,missense_variant,p.Ser283Leu,ENST00000507828,;SEC31A,missense_variant,p.Ser627Leu,ENST00000513858,;SEC31A,missense_variant,p.Ser666Leu,ENST00000355196,;SEC31A,missense_variant,p.Ser661Leu,ENST00000443462,;SEC31A,missense_variant,p.Ser666Leu,ENST00000508479,;SEC31A,missense_variant,p.Ser627Leu,ENST00000326950,;SEC31A,missense_variant,p.Ser627Leu,ENST00000348405,;SEC31A,non_coding_transcript_exon_variant,,ENST00000503226,;SEC31A,downstream_gene_variant,,ENST00000512732,;	A	ENSG00000138674	ENST00000395310	Transcript	missense_variant	2180	1997	666	S/L	tCa/tTa	.	.	.	-1	SEC31A	HGNC	17052	protein_coding	YES	CCDS3596.1	ENSP00000378721	SC31A_HUMAN	U3KQC9_HUMAN,D6REC0_HUMAN,D6REA9_HUMAN,D6RE64_HUMAN,D6RCQ9_HUMAN,D6RBT0_HUMAN	UPI000003E7E1	.	tolerated(0.05)	benign(0.261)	17/27	.	Pfam_domain:PF12931,hmmpanther:PTHR13923:SF23,hmmpanther:PTHR13923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTGAAAAT	.	5	ESCA
PKD2	0	.	GRCh37	4	88977399	88977399	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1878C>T	p.%3D	p.F626F	ENST00000237596	8/15	21	12	8	22	22	0	PKD2,synonymous_variant,p.%3D,ENST00000237596,;PKD2,synonymous_variant,p.%3D,ENST00000502363,;PKD2,synonymous_variant,p.%3D,ENST00000508588,;PKD2,non_coding_transcript_exon_variant,,ENST00000511337,;PKD2,non_coding_transcript_exon_variant,,ENST00000512858,;	T	ENSG00000118762	ENST00000237596	Transcript	synonymous_variant	1944	1878	626	F	ttC/ttT	.	.	.	1	PKD2	HGNC	9009	protein_coding	YES	CCDS3627.1	ENSP00000237596	PKD2_HUMAN	Q9UEU6_HUMAN,B7Z2D4_HUMAN,B4DFN3_HUMAN,B4DE45_HUMAN	UPI000013CA1D	.	.	.	8/15	.	hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF114,Pfam_domain:PF08016,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTCAGTAC	.	5	ESCA
PCDHB2	0	.	GRCh37	5	140476527	140476527	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2153G>C	p.Arg718Thr	p.R718T	ENST00000194155	1/1	123	62	61	142	142	0	PCDHB2,missense_variant,p.Arg718Thr,ENST00000194155,;PCDHB3,upstream_gene_variant,,ENST00000231130,;AC005754.7,downstream_gene_variant,,ENST00000607216,;	C	ENSG00000112852	ENST00000194155	Transcript	missense_variant	2301	2153	718	R/T	aGg/aCg	.	.	.	1	PCDHB2	HGNC	8687	protein_coding	YES	CCDS4244.1	ENSP00000194155	PCDB2_HUMAN	.	UPI00001273DC	.	deleterious_low_confidence(0)	probably_damaging(0.917)	1/1	.	hmmpanther:PTHR24028:SF77,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGAGGAGCA	.	5	ESCA
TENM2	0	.	GRCh37	5	167517587	167517587	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1524C>T	p.%3D	p.F508F	ENST00000518659	8/29	93	42	51	106	106	0	TENM2,synonymous_variant,p.%3D,ENST00000545108,;TENM2,synonymous_variant,p.%3D,ENST00000520394,;TENM2,synonymous_variant,p.%3D,ENST00000519204,;TENM2,synonymous_variant,p.%3D,ENST00000518659,;TENM2,synonymous_variant,p.%3D,ENST00000403607,;CTB-178M22.1,intron_variant,,ENST00000517408,;	T	ENSG00000145934	ENST00000518659	Transcript	synonymous_variant	1563	1524	508	F	ttC/ttT	.	.	.	1	TENM2	HGNC	29943	protein_coding	YES	.	ENSP00000429430	TEN2_HUMAN	G8BLJ6_HUMAN,G3CAS7_HUMAN	UPI0001C48FC2	.	.	.	8/29	.	hmmpanther:PTHR11219:SF8,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTCATGGA	.	5	ESCA
GPBP1	0	.	GRCh37	5	56545287	56545287	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.877C>T	p.Arg293Cys	p.R293C	ENST00000264779	8/11	45	24	20	55	55	0	GPBP1,missense_variant,p.Arg306Cys,ENST00000454432,;GPBP1,missense_variant,p.Arg293Cys,ENST00000538707,;GPBP1,missense_variant,p.Arg278Cys,ENST00000511209,;GPBP1,missense_variant,p.Arg286Cys,ENST00000506184,;GPBP1,missense_variant,p.Arg293Cys,ENST00000264779,;GPBP1,missense_variant,p.Arg306Cys,ENST00000424459,;GPBP1,missense_variant,p.Arg115Cys,ENST00000514387,;GPBP1,non_coding_transcript_exon_variant,,ENST00000513524,;GPBP1,non_coding_transcript_exon_variant,,ENST00000309096,;GPBP1,non_coding_transcript_exon_variant,,ENST00000515484,;	T	ENSG00000062194	ENST00000264779	Transcript	missense_variant	887	877	293	R/C	Cgt/Tgt	.	.	.	1	GPBP1	HGNC	29520	protein_coding	YES	CCDS47211.1	ENSP00000264779	GPBP1_HUMAN	.	UPI000006F55F	.	deleterious(0)	probably_damaging(0.96)	8/11	.	hmmpanther:PTHR14339:SF11,hmmpanther:PTHR14339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCGTCTA	.	5	ESCA
RASA1	0	.	GRCh37	5	86645150	86645150	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000274376	8/25	26	13	13	39	39	0	RASA1,stop_gained,p.Gln241Ter,ENST00000512763,;RASA1,stop_gained,p.Gln231Ter,ENST00000456692,;RASA1,stop_gained,p.Gln408Ter,ENST00000274376,;RASA1,stop_gained,p.Gln242Ter,ENST00000506290,;RASA1,stop_gained,p.Gln408Ter,ENST00000515800,;RASA1,non_coding_transcript_exon_variant,,ENST00000509953,;	T	ENSG00000145715	ENST00000274376	Transcript	stop_gained	1786	1222	408	Q/*	Cag/Tag	.	.	.	1	RASA1	HGNC	9871	protein_coding	YES	CCDS34200.1	ENSP00000274376	RASA1_HUMAN	B4DTL8_HUMAN	UPI00001351F3	.	.	.	8/25	.	PROSITE_profiles:PS50001,hmmpanther:PTHR10194,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATCAGTTT	.	5	ESCA
SEMA5A	0	.	GRCh37	5	9043022	9043022	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3212A>T	p.Tyr1071Phe	p.Y1071F	ENST00000382496	23/23	159	93	66	68	68	0	SEMA5A,missense_variant,p.Tyr1071Phe,ENST00000382496,;CTD-2215L10.1,intron_variant,,ENST00000506519,;	A	ENSG00000112902	ENST00000382496	Transcript	missense_variant	3878	3212	1071	Y/F	tAt/tTt	.	.	.	-1	SEMA5A	HGNC	10736	protein_coding	YES	CCDS3875.1	ENSP00000371936	SEM5A_HUMAN	D6RAF4_HUMAN,B4DE33_HUMAN	UPI000004F25D	.	tolerated_low_confidence(0.07)	probably_damaging(0.993)	23/23	.	hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCATAATTA	.	5	ESCA
HACE1	0	.	GRCh37	6	105177163	105177163	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*374A>G	.	.	ENST00000262903	24/24	49	30	19	44	44	0	HACE1,3_prime_UTR_variant,,ENST00000518503,;HACE1,3_prime_UTR_variant,,ENST00000262903,;HACE1,3_prime_UTR_variant,,ENST00000369125,;HACE1,3_prime_UTR_variant,,ENST00000518402,;HACE1,non_coding_transcript_exon_variant,,ENST00000517995,;HACE1,3_prime_UTR_variant,,ENST00000416605,;HACE1,non_coding_transcript_exon_variant,,ENST00000369127,;HACE1,non_coding_transcript_exon_variant,,ENST00000518228,;HACE1,downstream_gene_variant,,ENST00000517424,;	C	ENSG00000085382	ENST00000262903	Transcript	3_prime_UTR_variant	3381	.	.	.	.	.	.	.	-1	HACE1	HGNC	21033	protein_coding	YES	CCDS5050.1	ENSP00000262903	HACE1_HUMAN	E5RFX0_HUMAN,E3W983_HUMAN	UPI00001602DC	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATATAATAT	.	5	ESCA
TBC1D7	0	.	GRCh37	6	13295560	13295560	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39+9734C>T	.	.	ENST00000606214	.	70	43	27	50	50	0	TBC1D7,intron_variant,,ENST00000606214,;RP1-257A7.5,upstream_gene_variant,,ENST00000606393,;RP1-257A7.4,non_coding_transcript_exon_variant,,ENST00000606150,;TBC1D7,intron_variant,,ENST00000421203,;	A	ENSG00000145979	ENST00000606214	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TBC1D7	HGNC	21066	protein_coding	YES	CCDS4523.1	ENSP00000475727	TBCD7_HUMAN	U3KQ23_HUMAN,Q5SZM2_HUMAN,Q5SZM1_HUMAN,Q5SZL8_HUMAN,Q5SZL4_HUMAN	UPI0000073B32	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCTGCGGCT	.	5	ESCA
HIST1H2AM	0	.	GRCh37	6	27860488	27860488	+	3'UTR	SNP	G	G	C	rs373479655	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*47C>G	.	.	ENST00000359611	1/1	99	61	37	71	71	0	HIST1H2AM,3_prime_UTR_variant,,ENST00000359611,;HIST1H2BO,upstream_gene_variant,,ENST00000303806,;HIST1H3J,upstream_gene_variant,,ENST00000359303,;RNU7-26P,downstream_gene_variant,,ENST00000458980,;HIST1H3J,intron_variant,,ENST00000479986,;	C	ENSG00000233224	ENST00000359611	Transcript	3_prime_UTR_variant	476	.	.	.	.	rs373479655	.	.	-1	HIST1H2AM	HGNC	4735	protein_coding	YES	CCDS4639.1	ENSP00000352627	H2A1_HUMAN	A4FTV9_HUMAN,A3KPC7_HUMAN	UPI0000000E01	.	.	.	1/1	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTGAAAAG	byCluster	5	ESCA
ZKSCAN3	0	.	GRCh37	6	28331513	28331513	+	Silent	SNP	A	A	G	rs745896649	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.678A>G	p.%3D	p.E226E	ENST00000377255	6/7	65	43	22	71	71	0	ZKSCAN3,synonymous_variant,p.%3D,ENST00000252211,;ZKSCAN3,synonymous_variant,p.%3D,ENST00000341464,;ZKSCAN3,synonymous_variant,p.%3D,ENST00000377255,;	G	ENSG00000189298	ENST00000377255	Transcript	synonymous_variant	975	678	226	E	gaA/gaG	rs745896649	.	.	1	ZKSCAN3	HGNC	13853	protein_coding	YES	CCDS4650.1	ENSP00000366465	ZKSC3_HUMAN	.	UPI000013CD4A	.	.	.	6/7	.	hmmpanther:PTHR23226:SF55,hmmpanther:PTHR23226,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGAATGGAC	.	5	ESCA
IER3	0	.	GRCh37	6	30711532	30711547	+	3'UTR	DEL	TGCGCCTCGGTCTCTG	TGCGCCTCGGTCTCTG	-	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	TGCGCCTCGGTCTCTG	TGCGCCTCGGTCTCTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*166_*181delCAGAGACCGAGGCGCA	.	.	ENST00000259874	2/2	91	72	19	70	70	0	IER3,3_prime_UTR_variant,,ENST00000376377,;IER3,3_prime_UTR_variant,,ENST00000259874,;FLOT1,upstream_gene_variant,,ENST00000416018,;FLOT1,upstream_gene_variant,,ENST00000438162,;FLOT1,upstream_gene_variant,,ENST00000376389,;FLOT1,upstream_gene_variant,,ENST00000418160,;FLOT1,upstream_gene_variant,,ENST00000413165,;FLOT1,upstream_gene_variant,,ENST00000456573,;FLOT1,upstream_gene_variant,,ENST00000454845,;FLOT1,upstream_gene_variant,,ENST00000445853,;XXbac-BPG252P9.10,downstream_gene_variant,,ENST00000607333,;FLOT1,upstream_gene_variant,,ENST00000470643,;FLOT1,upstream_gene_variant,,ENST00000484693,;FLOT1,upstream_gene_variant,,ENST00000484168,;FLOT1,upstream_gene_variant,,ENST00000487376,;FLOT1,upstream_gene_variant,,ENST00000476729,;	-	ENSG00000137331	ENST00000259874	Transcript	3_prime_UTR_variant	673-688	.	.	.	.	.	.	.	-1	IER3	HGNC	5392	protein_coding	YES	CCDS4689.1	ENSP00000259874	IEX1_HUMAN	.	UPI00001AFA8D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCTCTATGCGCCTCGGTCTCTGTGCGC	.	2	ESCA
TUBB2A	0	.	GRCh37	6	3154963	3154963	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472G>C	p.Glu158Gln	p.E158Q	ENST00000333628	4/4	72	44	27	70	70	0	TUBB2A,missense_variant,p.Glu158Gln,ENST00000333628,;BPHL,downstream_gene_variant,,ENST00000380368,;BPHL,downstream_gene_variant,,ENST00000380379,;BPHL,downstream_gene_variant,,ENST00000423798,;BPHL,downstream_gene_variant,,ENST00000380375,;BPHL,downstream_gene_variant,,ENST00000434640,;RP1-40E16.11,upstream_gene_variant,,ENST00000447644,;TUBB2A,non_coding_transcript_exon_variant,,ENST00000489942,;BPHL,downstream_gene_variant,,ENST00000464040,;BPHL,downstream_gene_variant,,ENST00000490918,;BPHL,downstream_gene_variant,,ENST00000488487,;BPHL,downstream_gene_variant,,ENST00000424847,;BPHL,downstream_gene_variant,,ENST00000430655,;BPHL,downstream_gene_variant,,ENST00000433912,;	G	ENSG00000137267	ENST00000333628	Transcript	missense_variant	535	472	158	E/Q	Gag/Cag	.	.	.	-1	TUBB2A	HGNC	12412	protein_coding	YES	CCDS4484.1	ENSP00000369703	TBB2A_HUMAN	.	UPI000000DC98	.	deleterious_low_confidence(0.01)	probably_damaging(0.998)	4/4	.	hmmpanther:PTHR11588:SF56,hmmpanther:PTHR11588,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161,Prints_domain:PR01163	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACTCTTCCC	.	4	ESCA
HSPA1B	0	.	GRCh37	6	31797494	31797494	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1767G>A	p.%3D	p.K589K	ENST00000375650	1/1	81	53	28	51	51	0	HSPA1B,synonymous_variant,p.%3D,ENST00000545241,;HSPA1B,synonymous_variant,p.%3D,ENST00000375650,;C6orf48,upstream_gene_variant,,ENST00000375640,;C6orf48,upstream_gene_variant,,ENST00000375641,;	A	ENSG00000204388	ENST00000375650	Transcript	synonymous_variant	1983	1767	589	K	aaG/aaA	.	.	.	1	HSPA1B	HGNC	5233	protein_coding	YES	CCDS34415.1	ENSP00000364801	HSP71_HUMAN	A8K5I0_HUMAN	UPI0000000C40	.	.	.	1/1	.	Superfamily_domains:SSF100934,Pfam_domain:PF00012,Gene3D:1.20.1270.10,hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGGACGA	.	5	ESCA
SCUBE3	0	.	GRCh37	6	35211826	35211826	+	Missense_Mutation	SNP	C	C	T	rs752868196	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2158C>T	p.Arg720Trp	p.R720W	ENST00000274938	17/22	50	37	12	37	37	0	SCUBE3,missense_variant,p.Arg736Trp,ENST00000394681,;SCUBE3,missense_variant,p.Arg720Trp,ENST00000274938,;	T	ENSG00000146197	ENST00000274938	Transcript	missense_variant	2158	2158	720	R/W	Cgg/Tgg	rs752868196	.	.	1	SCUBE3	HGNC	13655	protein_coding	YES	CCDS4800.1	ENSP00000274938	SCUB3_HUMAN	Q7Z3I8_HUMAN	UPI0000074423	.	deleterious(0)	probably_damaging(1)	17/22	.	hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF2,Pfam_domain:PF07699,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGACGGACC	byFrequency	5	ESCA
TREM1	0	.	GRCh37	6	41250446	41250446	+	Silent	SNP	C	C	T	rs759126895	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.93G>A	p.%3D	p.L31L	ENST00000244709	2/4	44	25	18	43	43	0	TREM1,synonymous_variant,p.%3D,ENST00000334475,;TREM1,synonymous_variant,p.%3D,ENST00000244709,;TREM1,synonymous_variant,p.%3D,ENST00000589614,;TREM1,synonymous_variant,p.%3D,ENST00000591620,;TREM1,non_coding_transcript_exon_variant,,ENST00000586287,;TREM1,upstream_gene_variant,,ENST00000589695,;TREM1,upstream_gene_variant,,ENST00000589882,;	T	ENSG00000124731	ENST00000244709	Transcript	synonymous_variant	157	93	31	L	ctG/ctA	rs759126895	.	.	-1	TREM1	HGNC	17760	protein_coding	YES	CCDS4854.1	ENSP00000244709	TREM1_HUMAN	Q38L15_HUMAN	UPI0000047FA9	.	.	.	2/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR19357:SF1,hmmpanther:PTHR19357,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCAGTTC	.	5	ESCA
CUL7	0	.	GRCh37	6	43005697	43005697	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5078G>A	p.Ser1693Asn	p.S1693N	ENST00000535468	26/26	22	14	8	28	28	0	CUL7,missense_variant,p.Ser1693Asn,ENST00000535468,;CUL7,missense_variant,p.Ser1609Asn,ENST00000265348,;RN7SL403P,upstream_gene_variant,,ENST00000481783,;RP1-20C7.6,upstream_gene_variant,,ENST00000607790,;RRP36,downstream_gene_variant,,ENST00000607555,;RRP36,downstream_gene_variant,,ENST00000607394,;KLC4,upstream_gene_variant,,ENST00000467906,;	T	ENSG00000044090	ENST00000535468	Transcript	missense_variant	5165	5078	1693	S/N	aGc/aAc	.	.	.	-1	CUL7	HGNC	21024	protein_coding	YES	CCDS55003.1	ENSP00000438788	CUL7_HUMAN	.	UPI0001BE8116	.	tolerated(0.1)	benign(0.03)	26/26	.	SMART_domains:SM00884,hmmpanther:PTHR22771:SF3,hmmpanther:PTHR22771	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGCTGCTG	.	5	ESCA
TFAP2B	0	.	GRCh37	6	50815165	50815165	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4060T>C	.	.	ENST00000393655	7/7	54	33	20	51	51	0	TFAP2B,3_prime_UTR_variant,,ENST00000393655,;TFAP2B,3_prime_UTR_variant,,ENST00000263046,;	C	ENSG00000008196	ENST00000393655	Transcript	3_prime_UTR_variant	5612	.	.	.	.	.	.	.	1	TFAP2B	HGNC	11743	protein_coding	YES	CCDS4934.2	ENSP00000377265	AP2B_HUMAN	A8K557_HUMAN	UPI000020DE90	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTATACCTC	.	5	ESCA
ZNF451	0	.	GRCh37	6	57018677	57018677	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2902C>T	p.Gln968Ter	p.Q968*	ENST00000370706	13/15	33	17	15	32	32	0	ZNF451,stop_gained,p.Gln920Ter,ENST00000357489,;ZNF451,stop_gained,p.Gln968Ter,ENST00000370706,;ZNF451,stop_gained,p.Gln968Ter,ENST00000491832,;RP11-203B9.4,intron_variant,,ENST00000416069,;RP11-203B9.4,intron_variant,,ENST00000587815,;RP11-203B9.4,intron_variant,,ENST00000586432,;RP11-203B9.4,intron_variant,,ENST00000586053,;RP11-203B9.4,intron_variant,,ENST00000588811,;RP11-203B9.4,intron_variant,,ENST00000591553,;RP11-203B9.4,intron_variant,,ENST00000585792,;RP11-203B9.4,intron_variant,,ENST00000589263,;RP11-203B9.4,intron_variant,,ENST00000592038,;RP11-203B9.4,intron_variant,,ENST00000592500,;RP11-203B9.4,intron_variant,,ENST00000586466,;RP11-203B9.4,intron_variant,,ENST00000586668,;RP11-203B9.4,intron_variant,,ENST00000589549,;ZNF451,non_coding_transcript_exon_variant,,ENST00000508548,;ZNF451,intron_variant,,ENST00000504603,;ZNF451,downstream_gene_variant,,ENST00000444273,;	T	ENSG00000112200	ENST00000370706	Transcript	stop_gained	3146	2902	968	Q/*	Caa/Taa	.	.	.	1	ZNF451	HGNC	21091	protein_coding	YES	CCDS43477.1	ENSP00000359740	ZN451_HUMAN	Q96JY2_HUMAN,D6RAV4_HUMAN	UPI000004A571	.	.	.	13/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAACAACTA	.	5	ESCA
RP1-234P15.4	0	.	GRCh37	6	76005486	76005487	+	3'Flank	INS	-	-	A	rs557228127	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000607221	.	18	12	6	20	20	0	FILIP1,3_prime_UTR_variant,,ENST00000393004,;RP1-234P15.4,intron_variant,,ENST00000607799,;RP1-234P15.4,intron_variant,,ENST00000438676,;RP1-234P15.4,downstream_gene_variant,,ENST00000607221,;	A	ENSG00000225793	ENST00000607221	Transcript	downstream_gene_variant	.	.	.	.	.	rs557228127	.	4269	1	RP1-234P15.4	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATCCTTAAAAA	.	2	ESCA
ZNF292	0	.	GRCh37	6	87967531	87967531	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4184C>G	p.Ser1395Cys	p.S1395C	ENST00000369577	8/8	52	37	15	43	43	0	ZNF292,missense_variant,p.Ser1395Cys,ENST00000369577,;ZNF292,missense_variant,p.Ser1390Cys,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,downstream_gene_variant,,ENST00000466062,;	G	ENSG00000188994	ENST00000369577	Transcript	missense_variant	4227	4184	1395	S/C	tCc/tGc	.	.	.	1	ZNF292	HGNC	18410	protein_coding	YES	CCDS47457.1	ENSP00000358590	ZN292_HUMAN	Q6ZS01_HUMAN,Q6P495_HUMAN,Q3MN16_HUMAN	UPI000020D2CC	.	deleterious(0)	probably_damaging(0.999)	8/8	.	SMART_domains:SM00355,hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTATCCAAGC	.	5	ESCA
MMS22L	0	.	GRCh37	6	97599743	97599743	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3386T>A	p.Val1129Asp	p.V1129D	ENST00000275053	23/25	39	22	16	39	39	0	MMS22L,missense_variant,p.Val1129Asp,ENST00000275053,;MMS22L,missense_variant,p.Val1089Asp,ENST00000369251,;MMS22L,splice_region_variant,,ENST00000514790,;	T	ENSG00000146263	ENST00000275053	Transcript	missense_variant	3652	3386	1129	V/D	gTt/gAt	.	.	.	-1	MMS22L	HGNC	21475	protein_coding	YES	CCDS5039.1	ENSP00000275053	MMS22_HUMAN	H9KVD8_HUMAN	UPI00003673C9	.	deleterious(0)	probably_damaging(0.997)	23/25	.	Pfam_domain:PF14911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTAACTAGA	.	5	ESCA
MMS22L	0	.	GRCh37	6	97613184	97613184	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3159G>C	p.Leu1053Phe	p.L1053F	ENST00000275053	21/25	78	48	29	57	57	0	MMS22L,missense_variant,p.Leu1053Phe,ENST00000275053,;MMS22L,missense_variant,p.Leu1013Phe,ENST00000369251,;MMS22L,upstream_gene_variant,,ENST00000514790,;	G	ENSG00000146263	ENST00000275053	Transcript	missense_variant	3425	3159	1053	L/F	ttG/ttC	COSM3777923	.	.	-1	MMS22L	HGNC	21475	protein_coding	YES	CCDS5039.1	ENSP00000275053	MMS22_HUMAN	H9KVD8_HUMAN	UPI00003673C9	.	deleterious(0.04)	possibly_damaging(0.696)	21/25	.	Pfam_domain:PF14911	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCAATGC	.	5	ESCA
DPY19L2P2	0	.	GRCh37	7	102836007	102836007	+	RNA	SNP	G	G	C	rs568174835	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3593C>G	.	.	ENST00000312132	20/23	134	96	37	88	88	0	DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000438364,;DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000312132,;DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000439473,;DPY19L2P2,intron_variant,,ENST00000411491,;DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000435536,;	C	ENSG00000170629	ENST00000312132	Transcript	non_coding_transcript_exon_variant	3593	.	.	.	.	rs568174835	.	.	-1	DPY19L2P2	HGNC	21764	processed_transcript	YES	.	.	.	.	.	.	.	.	20/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTAGAATGC	.	5	ESCA
RELN	0	.	GRCh37	7	103159843	103159843	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7789G>A	p.Glu2597Lys	p.E2597K	ENST00000428762	49/65	132	106	26	67	67	0	RELN,missense_variant,p.Glu2597Lys,ENST00000424685,;RELN,missense_variant,p.Glu2597Lys,ENST00000428762,;RELN,missense_variant,p.Glu2597Lys,ENST00000343529,;RELN,downstream_gene_variant,,ENST00000478148,;	T	ENSG00000189056	ENST00000428762	Transcript	missense_variant	7949	7789	2597	E/K	Gaa/Aaa	.	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	tolerated(0.07)	probably_damaging(0.999)	49/65	.	hmmpanther:PTHR11841,Superfamily_domains:SSF50939,Superfamily_domains:SSF50939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCCAAGA	.	5	ESCA
RINT1	0	.	GRCh37	7	105183050	105183050	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.469C>T	p.Arg157Cys	p.R157C	ENST00000257700	4/15	94	72	22	56	55	1	RINT1,missense_variant,p.Arg126Cys,ENST00000493041,;RINT1,missense_variant,p.Arg157Cys,ENST00000257700,;RINT1,downstream_gene_variant,,ENST00000477285,;RINT1,3_prime_UTR_variant,,ENST00000467392,;RINT1,3_prime_UTR_variant,,ENST00000497979,;RINT1,non_coding_transcript_exon_variant,,ENST00000493258,;RINT1,downstream_gene_variant,,ENST00000482041,;	T	ENSG00000135249	ENST00000257700	Transcript	missense_variant	700	469	157	R/C	Cgt/Tgt	.	.	.	1	RINT1	HGNC	21876	protein_coding	YES	CCDS34726.1	ENSP00000257700	RINT1_HUMAN	.	UPI000020F898	.	deleterious(0)	possibly_damaging(0.893)	4/15	.	hmmpanther:PTHR13520:SF0,hmmpanther:PTHR13520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGAACGTCAT	.	5	ESCA
PHF14	0	.	GRCh37	7	11143171	11143171	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1046C>G	.	.	ENST00000403050	17/17	82	56	26	57	57	0	PHF14,3_prime_UTR_variant,,ENST00000403050,;PHF14,intron_variant,,ENST00000445996,;PHF14,non_coding_transcript_exon_variant,,ENST00000481418,;PHF14,intron_variant,,ENST00000470665,;PHF14,intron_variant,,ENST00000423760,;PHF14,downstream_gene_variant,,ENST00000521747,;	G	ENSG00000106443	ENST00000403050	Transcript	3_prime_UTR_variant	4165	.	.	.	.	.	.	.	1	PHF14	HGNC	22203	protein_coding	YES	CCDS47542.1	ENSP00000385795	PHF14_HUMAN	.	UPI000020EB41	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATCTTGAA	.	5	ESCA
PLXNA4	0	.	GRCh37	7	131848918	131848918	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4483A>T	p.Ile1495Phe	p.I1495F	ENST00000359827	24/32	73	34	38	44	44	0	PLXNA4,missense_variant,p.Ile1495Phe,ENST00000321063,;PLXNA4,missense_variant,p.Ile1495Phe,ENST00000359827,;	A	ENSG00000221866	ENST00000359827	Transcript	missense_variant	5446	4483	1495	I/F	Att/Ttt	.	.	.	-1	PLXNA4	HGNC	9102	protein_coding	YES	CCDS43646.1	ENSP00000352882	PLXA4_HUMAN	.	UPI000004E55B	.	deleterious(0)	possibly_damaging(0.879)	24/32	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,Pfam_domain:PF08337,Gene3D:3.10.20.90	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAATCTGCT	.	5	ESCA
SSPO	0	.	GRCh37	7	149512296	149512296	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.10616G>C	.	.	ENST00000378016	75/109	70	52	18	28	28	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000478854,;SSPO,downstream_gene_variant,,ENST00000481772,;SSPO,upstream_gene_variant,,ENST00000464974,;	C	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	10616	.	.	.	.	.	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	75/109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGGGCAGC	.	5	ESCA
SSPO	0	.	GRCh37	7	149512798	149512798	+	RNA	SNP	G	G	A	rs368616587	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.10805G>A	.	.	ENST00000378016	76/109	106	37	68	56	55	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000478854,;SSPO,downstream_gene_variant,,ENST00000481772,;SSPO,upstream_gene_variant,,ENST00000464974,;	A	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	10805	.	.	.	.	rs368616587	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	76/109	.	.	A:0.0014	A:0	A:0	.	A:0	A:0	A:0.0072	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCCGCTCAG	byFrequency|byCluster|by1000G	5	ESCA
PAXIP1	0	.	GRCh37	7	154746044	154746044	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2742C>G	p.Phe914Leu	p.F914L	ENST00000404141	16/21	81	58	22	41	41	0	PAXIP1,missense_variant,p.Phe914Leu,ENST00000397192,;PAXIP1,missense_variant,p.Phe914Leu,ENST00000404141,;RP11-5C23.2,upstream_gene_variant,,ENST00000609134,;RP11-5C23.1,downstream_gene_variant,,ENST00000608064,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000473219,;PAXIP1,3_prime_UTR_variant,,ENST00000457196,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000464717,;PAXIP1-AS2,downstream_gene_variant,,ENST00000449486,;	C	ENSG00000157212	ENST00000404141	Transcript	missense_variant	2897	2742	914	F/L	ttC/ttG	.	.	.	-1	PAXIP1	HGNC	8624	protein_coding	YES	CCDS47753.1	ENSP00000384048	PAXI1_HUMAN	.	UPI00004166F9	.	tolerated(0.21)	unknown(0)	16/21	.	PROSITE_profiles:PS50172,hmmpanther:PTHR23196:SF1,hmmpanther:PTHR23196,Pfam_domain:PF00533,Gene3D:3.40.50.10190,SMART_domains:SM00292,Superfamily_domains:SSF52113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAGGAACTT	.	5	ESCA
SNX13	0	.	GRCh37	7	17929992	17929992	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.434C>G	p.Ala145Gly	p.A145G	ENST00000428135	5/26	53	24	28	39	39	0	SNX13,missense_variant,p.Ala145Gly,ENST00000428135,;SNX13,missense_variant,p.Ala145Gly,ENST00000409389,;SNX13,missense_variant,p.Ala145Gly,ENST00000409604,;SNX13,downstream_gene_variant,,ENST00000475800,;SNX13,downstream_gene_variant,,ENST00000498463,;SNX13,downstream_gene_variant,,ENST00000474067,;SNX13,downstream_gene_variant,,ENST00000494402,;SNX13,missense_variant,p.Ala145Gly,ENST00000409076,;SNX13,3_prime_UTR_variant,,ENST00000444712,;SNX13,non_coding_transcript_exon_variant,,ENST00000492626,;SNX13,non_coding_transcript_exon_variant,,ENST00000482558,;	C	ENSG00000071189	ENST00000428135	Transcript	missense_variant	633	434	145	A/G	gCt/gGt	COSM1733645	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	deleterious(0.02)	benign(0.127)	5/26	.	PROSITE_profiles:PS51207,hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF26,Pfam_domain:PF02194,SMART_domains:SM00313	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTAGCAAAC	.	5	ESCA
SNX13	0	.	GRCh37	7	17929993	17929993	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433G>A	p.Ala145Thr	p.A145T	ENST00000428135	5/26	53	25	27	38	38	0	SNX13,missense_variant,p.Ala145Thr,ENST00000428135,;SNX13,missense_variant,p.Ala145Thr,ENST00000409389,;SNX13,missense_variant,p.Ala145Thr,ENST00000409604,;SNX13,downstream_gene_variant,,ENST00000475800,;SNX13,downstream_gene_variant,,ENST00000498463,;SNX13,downstream_gene_variant,,ENST00000474067,;SNX13,downstream_gene_variant,,ENST00000494402,;SNX13,missense_variant,p.Ala145Thr,ENST00000409076,;SNX13,3_prime_UTR_variant,,ENST00000444712,;SNX13,non_coding_transcript_exon_variant,,ENST00000492626,;SNX13,non_coding_transcript_exon_variant,,ENST00000482558,;	T	ENSG00000071189	ENST00000428135	Transcript	missense_variant	632	433	145	A/T	Gct/Act	.	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	tolerated(0.1)	benign(0.038)	5/26	.	PROSITE_profiles:PS51207,hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF26,Pfam_domain:PF02194,SMART_domains:SM00313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTAGCAAACT	.	5	ESCA
OSBPL3	0	.	GRCh37	7	24903154	24903155	+	Frame_Shift_Ins	INS	-	-	AGGA	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734_737dupTCCT	p.His247ProfsTer19	p.H247Pfs*19	ENST00000313367	8/23	100	73	27	30	30	0	OSBPL3,frameshift_variant,p.His247ProfsTer31,ENST00000431825,;OSBPL3,frameshift_variant,p.His247ProfsTer19,ENST00000396429,;OSBPL3,frameshift_variant,p.His247ProfsTer31,ENST00000352860,;OSBPL3,frameshift_variant,p.His247ProfsTer31,ENST00000409069,;OSBPL3,frameshift_variant,p.His247ProfsTer19,ENST00000353930,;OSBPL3,frameshift_variant,p.His247ProfsTer19,ENST00000313367,;OSBPL3,frameshift_variant,p.His247ProfsTer31,ENST00000396431,;OSBPL3,frameshift_variant,p.His247ProfsTer31,ENST00000409555,;OSBPL3,frameshift_variant,p.His247ProfsTer19,ENST00000409452,;OSBPL3,frameshift_variant,p.His247ProfsTer31,ENST00000409863,;OSBPL3,frameshift_variant,p.His247ProfsTer19,ENST00000409759,;	AGGA	ENSG00000070882	ENST00000313367	Transcript	frameshift_variant	1189-1190	737-738	246	L/LPX	ctg/ctTCCTg	.	.	.	-1	OSBPL3	HGNC	16370	protein_coding	YES	CCDS5390.1	ENSP00000315410	OSBL3_HUMAN	C9JZ19_HUMAN,C9JEF2_HUMAN,C9J8P4_HUMAN	UPI0000001244	.	.	.	8/23	.	hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGATGCAGGAC	.	3	ESCA
C7orf65	0	.	GRCh37	7	47698758	47698758	+	Missense_Mutation	SNP	C	C	A	rs527897958	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388C>A	p.Gln130Lys	p.Q130K	ENST00000408988	3/3	86	62	23	42	42	0	C7orf65,missense_variant,p.Gln130Lys,ENST00000408988,;	A	ENSG00000221845	ENST00000408988	Transcript	missense_variant	423	388	130	Q/K	Cag/Aag	rs527897958	.	.	1	C7orf65	HGNC	34432	protein_coding	YES	CCDS43580.1	ENSP00000386198	CG065_HUMAN	.	UPI00001C0C15	.	deleterious_low_confidence(0)	benign(0.092)	3/3	.	.	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTCAGGCC	byFrequency|byCluster|by1000G	5	ESCA
PAPOLB	0	.	GRCh37	7	4901496	4901496	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-58G>T	.	.	ENST00000404991	1/1	17	6	10	11	11	0	PAPOLB,5_prime_UTR_variant,,ENST00000404991,;RADIL,intron_variant,,ENST00000399583,;RADIL,intron_variant,,ENST00000536091,;RADIL,intron_variant,,ENST00000445392,;AC092610.12,downstream_gene_variant,,ENST00000454916,;	A	ENSG00000218823	ENST00000404991	Transcript	5_prime_UTR_variant	130	.	.	.	.	.	.	.	-1	PAPOLB	HGNC	15970	protein_coding	YES	.	ENSP00000384700	PAPOB_HUMAN	A4D1Z6_HUMAN	UPI0000131304	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGCCGCCGC	.	5	ESCA
CCT6A	0	.	GRCh37	7	56125732	56125732	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.661A>T	p.Met221Leu	p.M221L	ENST00000275603	6/14	96	43	53	57	57	0	CCT6A,missense_variant,p.Met190Leu,ENST00000540286,;CCT6A,missense_variant,p.Met221Leu,ENST00000275603,;CCT6A,missense_variant,p.Met176Leu,ENST00000335503,;SNORA22,downstream_gene_variant,,ENST00000383876,;SNORA15,upstream_gene_variant,,ENST00000384439,;CCT6A,upstream_gene_variant,,ENST00000462133,;CCT6A,non_coding_transcript_exon_variant,,ENST00000482776,;CCT6A,downstream_gene_variant,,ENST00000493855,;CCT6A,upstream_gene_variant,,ENST00000466572,;CCT6A,upstream_gene_variant,,ENST00000494736,;CCT6A,upstream_gene_variant,,ENST00000466479,;CCT6A,upstream_gene_variant,,ENST00000492618,;	T	ENSG00000146731	ENST00000275603	Transcript	missense_variant	880	661	221	M/L	Atg/Ttg	.	.	.	1	CCT6A	HGNC	1620	protein_coding	YES	CCDS5523.1	ENSP00000275603	TCPZ_HUMAN	.	UPI0000136B11	.	deleterious(0.03)	possibly_damaging(0.545)	6/14	.	Superfamily_domains:SSF52029,Gene3D:3.50.7.10,TIGRFAM_domain:TIGR02347,Pfam_domain:PF00118,hmmpanther:PTHR11353:SF54,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATATGAAG	.	5	ESCA
CCZ1	0	.	GRCh37	7	5951496	5951496	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785C>T	p.Ala262Val	p.A262V	ENST00000325974	9/15	36	25	11	19	19	0	CCZ1,missense_variant,p.Ala119Val,ENST00000537980,;CCZ1,missense_variant,p.Ala262Val,ENST00000325974,;CCZ1,downstream_gene_variant,,ENST00000483394,;	T	ENSG00000122674	ENST00000325974	Transcript	missense_variant	851	785	262	A/V	gCa/gTa	.	.	.	1	CCZ1	HGNC	21691	protein_coding	YES	CCDS34597.1	ENSP00000325681	CCZ1_HUMAN	Q7L8P3_HUMAN,F5H553_HUMAN	UPI000006CEFF	.	tolerated(0.26)	possibly_damaging(0.69)	9/15	.	Pfam_domain:PF08217,hmmpanther:PTHR13056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GTTAGCAGGAA	.	3	ESCA
CYTH3	0	.	GRCh37	7	6210572	6210572	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600C>G	p.%3D	p.L200L	ENST00000350796	8/13	122	99	23	61	61	0	CYTH3,synonymous_variant,p.%3D,ENST00000396741,;CYTH3,synonymous_variant,p.%3D,ENST00000350796,;Y_RNA,downstream_gene_variant,,ENST00000458975,;CYTH3,non_coding_transcript_exon_variant,,ENST00000488964,;CYTH3,non_coding_transcript_exon_variant,,ENST00000461891,;CYTH3,non_coding_transcript_exon_variant,,ENST00000491641,;CYTH3,upstream_gene_variant,,ENST00000465320,;CYTH3,non_coding_transcript_exon_variant,,ENST00000466543,;CYTH3,non_coding_transcript_exon_variant,,ENST00000495176,;CYTH3,downstream_gene_variant,,ENST00000478541,;CYTH3,downstream_gene_variant,,ENST00000481329,;	C	ENSG00000008256	ENST00000350796	Transcript	synonymous_variant	737	600	200	L	ctC/ctG	.	.	.	-1	CYTH3	HGNC	9504	protein_coding	YES	CCDS5346.1	ENSP00000297044	CYH3_HUMAN	Q96HS5_HUMAN	UPI000002A7A1	.	.	.	8/13	.	PROSITE_profiles:PS50190,hmmpanther:PTHR10663:SF129,hmmpanther:PTHR10663,Pfam_domain:PF01369,Gene3D:1.10.1000.11,SMART_domains:SM00222,Superfamily_domains:SSF48425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTTGAGCAT	.	5	ESCA
CYTH3	0	.	GRCh37	7	6210939	6210939	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.456C>G	p.Phe152Leu	p.F152L	ENST00000350796	7/13	55	39	15	28	28	0	CYTH3,missense_variant,p.Phe67Leu,ENST00000396741,;CYTH3,missense_variant,p.Phe152Leu,ENST00000350796,;Y_RNA,downstream_gene_variant,,ENST00000458975,;CYTH3,non_coding_transcript_exon_variant,,ENST00000488964,;CYTH3,non_coding_transcript_exon_variant,,ENST00000461891,;CYTH3,non_coding_transcript_exon_variant,,ENST00000491641,;CYTH3,upstream_gene_variant,,ENST00000465320,;CYTH3,non_coding_transcript_exon_variant,,ENST00000466543,;CYTH3,non_coding_transcript_exon_variant,,ENST00000478541,;CYTH3,non_coding_transcript_exon_variant,,ENST00000481329,;CYTH3,upstream_gene_variant,,ENST00000495176,;	C	ENSG00000008256	ENST00000350796	Transcript	missense_variant	593	456	152	F/L	ttC/ttG	.	.	.	-1	CYTH3	HGNC	9504	protein_coding	YES	CCDS5346.1	ENSP00000297044	CYH3_HUMAN	Q96HS5_HUMAN	UPI000002A7A1	.	deleterious(0.02)	possibly_damaging(0.736)	7/13	.	PROSITE_profiles:PS50190,hmmpanther:PTHR10663:SF129,hmmpanther:PTHR10663,Pfam_domain:PF01369,Gene3D:1.10.1000.11,SMART_domains:SM00222,Superfamily_domains:SSF48425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATAAGAACTG	.	5	ESCA
COL1A2	0	.	GRCh37	7	94060483	94060483	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*778A>G	.	.	ENST00000297268	52/52	127	59	68	76	76	0	COL1A2,3_prime_UTR_variant,,ENST00000297268,;COL1A2,downstream_gene_variant,,ENST00000488121,;COL1A2,downstream_gene_variant,,ENST00000492110,;COL1A2,downstream_gene_variant,,ENST00000464916,;COL1A2,downstream_gene_variant,,ENST00000481570,;COL1A2,downstream_gene_variant,,ENST00000478215,;	G	ENSG00000164692	ENST00000297268	Transcript	3_prime_UTR_variant	5350	.	.	.	.	.	.	.	1	COL1A2	HGNC	2198	protein_coding	YES	CCDS34682.1	ENSP00000297268	CO1A2_HUMAN	Q75N18_HUMAN,A2TIK1_HUMAN	UPI00003B0CFC	.	.	.	52/52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAGATGTTT	.	5	ESCA
COPS6	0	.	GRCh37	7	99688533	99688533	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495C>T	p.%3D	p.V165V	ENST00000303904	6/10	36	25	11	22	22	0	COPS6,synonymous_variant,p.%3D,ENST00000418625,;COPS6,synonymous_variant,p.%3D,ENST00000303904,;COPS6,downstream_gene_variant,,ENST00000419210,;MCM7,downstream_gene_variant,,ENST00000354230,;MCM7,downstream_gene_variant,,ENST00000303887,;MCM7,downstream_gene_variant,,ENST00000343023,;MIR93,downstream_gene_variant,,ENST00000385024,;MIR25,downstream_gene_variant,,ENST00000384816,;MIR106B,downstream_gene_variant,,ENST00000385301,;COPS6,synonymous_variant,p.%3D,ENST00000426712,;COPS6,non_coding_transcript_exon_variant,,ENST00000474823,;COPS6,non_coding_transcript_exon_variant,,ENST00000468499,;COPS6,non_coding_transcript_exon_variant,,ENST00000483891,;MCM7,downstream_gene_variant,,ENST00000493352,;COPS6,downstream_gene_variant,,ENST00000496358,;MCM7,downstream_gene_variant,,ENST00000491245,;COPS6,downstream_gene_variant,,ENST00000472107,;MCM7,downstream_gene_variant,,ENST00000485286,;MCM7,downstream_gene_variant,,ENST00000489841,;COPS6,downstream_gene_variant,,ENST00000465027,;	T	ENSG00000168090	ENST00000303904	Transcript	synonymous_variant	532	495	165	V	gtC/gtT	.	.	.	1	COPS6	HGNC	21749	protein_coding	YES	CCDS5682.1	ENSP00000304102	CSN6_HUMAN	C9JQK5_HUMAN,B2R514_HUMAN	UPI000014F97E	.	.	.	6/10	.	hmmpanther:PTHR10540:SF8,hmmpanther:PTHR10540,SMART_domains:SM00232	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGTCAGCGT	.	5	ESCA
PABPC1	0	.	GRCh37	8	101725016	101725016	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740C>A	p.Ala247Asp	p.A247D	ENST00000318607	6/15	19	12	7	15	15	0	PABPC1,missense_variant,p.Ala116Asp,ENST00000519100,;PABPC1,missense_variant,p.Ala202Asp,ENST00000519004,;PABPC1,missense_variant,p.Ala215Asp,ENST00000522387,;PABPC1,missense_variant,p.Ala247Asp,ENST00000318607,;PABPC1,upstream_gene_variant,,ENST00000517403,;PABPC1,downstream_gene_variant,,ENST00000523555,;AP001205.1,upstream_gene_variant,,ENST00000579868,;PABPC1,splice_region_variant,,ENST00000519596,;PABPC1,missense_variant,p.Ala45Asp,ENST00000519622,;PABPC1,downstream_gene_variant,,ENST00000517921,;PABPC1,upstream_gene_variant,,ENST00000523636,;PABPC1,upstream_gene_variant,,ENST00000518716,;	T	ENSG00000070756	ENST00000318607	Transcript	missense_variant	1869	740	247	A/D	gCt/gAt	.	.	.	-1	PABPC1	HGNC	8554	protein_coding	YES	CCDS6289.1	ENSP00000313007	PABP1_HUMAN	H0YB75_HUMAN,E7EQV3_HUMAN,E5RJM8_HUMAN,E5RJB9_HUMAN,E5RHG7_HUMAN,E5RH24_HUMAN,E5RGH3_HUMAN,E5RGC4_HUMAN,E5RFD8_HUMAN	UPI0000000BC4	.	deleterious(0)	probably_damaging(0.982)	6/15	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011:SF239,hmmpanther:PTHR24011,Gene3D:3.30.70.330,TIGRFAM_domain:TIGR01628,Pfam_domain:PF00076,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAGCCTTC	.	5	ESCA
PRSS51	0	.	GRCh37	8	10355353	10355353	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.478G>C	.	.	ENST00000523024	3/5	196	132	63	77	77	0	PRSS51,non_coding_transcript_exon_variant,,ENST00000523024,;PRSS51,intron_variant,,ENST00000521149,;	G	ENSG00000253649	ENST00000523024	Transcript	non_coding_transcript_exon_variant	478	.	.	.	.	.	.	.	-1	PRSS51	HGNC	37321	antisense	YES	.	.	.	.	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCACTGTCG	.	5	ESCA
EBAG9	0	.	GRCh37	8	110575650	110575650	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.522-1018C>T	.	.	ENST00000337573	.	170	73	96	84	84	0	EBAG9,synonymous_variant,p.%3D,ENST00000531677,;EBAG9,intron_variant,,ENST00000530629,;EBAG9,intron_variant,,ENST00000395785,;EBAG9,intron_variant,,ENST00000337573,;EBAG9,downstream_gene_variant,,ENST00000527709,;	T	ENSG00000147654	ENST00000337573	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	EBAG9	HGNC	3123	protein_coding	YES	CCDS6313.1	ENSP00000337675	RCAS1_HUMAN	Q6R3F1_HUMAN,E9PN10_HUMAN,E9PJ40_HUMAN,E9PJ38_HUMAN	UPI000013343D	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACTCTGCTC	.	5	ESCA
CSMD3	0	.	GRCh37	8	113316958	113316958	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8258A>G	p.Tyr2753Cys	p.Y2753C	ENST00000297405	52/71	48	34	14	45	45	0	CSMD3,missense_variant,p.Tyr2683Cys,ENST00000352409,;CSMD3,missense_variant,p.Tyr2753Cys,ENST00000297405,;CSMD3,missense_variant,p.Tyr2023Cys,ENST00000339701,;CSMD3,missense_variant,p.Tyr2713Cys,ENST00000343508,;CSMD3,intron_variant,,ENST00000455883,;	C	ENSG00000164796	ENST00000297405	Transcript	missense_variant	8503	8258	2753	Y/C	tAt/tGt	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.17)	probably_damaging(0.932)	52/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAATATGGT	.	5	ESCA
TRPS1	0	.	GRCh37	8	116423557	116423557	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2694A>G	.	.	ENST00000395715	7/7	23	17	6	17	17	0	TRPS1,3_prime_UTR_variant,,ENST00000395715,;TRPS1,downstream_gene_variant,,ENST00000520276,;TRPS1,downstream_gene_variant,,ENST00000220888,;TRPS1,downstream_gene_variant,,ENST00000518018,;TRPS1,downstream_gene_variant,,ENST00000519076,;	C	ENSG00000104447	ENST00000395715	Transcript	3_prime_UTR_variant	7157	.	.	.	.	.	.	.	-1	TRPS1	HGNC	12340	protein_coding	YES	CCDS6318.2	ENSP00000379065	TRPS1_HUMAN	F8W8T0_HUMAN,E7EVN4_HUMAN,C9J6L7_HUMAN	UPI00002104B8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAATAAAGA	.	5	ESCA
RHPN1	0	.	GRCh37	8	144464122	144464122	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1781C>G	p.Ser594Cys	p.S594C	ENST00000289013	14/15	105	59	45	37	37	0	RHPN1,missense_variant,p.Ser594Cys,ENST00000289013,;RHPN1,non_coding_transcript_exon_variant,,ENST00000522335,;RHPN1,non_coding_transcript_exon_variant,,ENST00000522899,;	G	ENSG00000158106	ENST00000289013	Transcript	missense_variant	1882	1781	594	S/C	tCt/tGt	COSM1096945,COSM1096944	.	.	1	RHPN1	HGNC	19973	protein_coding	YES	CCDS47927.1	ENSP00000289013	RHPN1_HUMAN	.	UPI0000071870	.	deleterious(0.01)	possibly_damaging(0.631)	14/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23031:SF6,hmmpanther:PTHR23031	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCTAGAC	.	5	ESCA
RHPN1	0	.	GRCh37	8	144464685	144464685	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1877C>G	p.Ser626Cys	p.S626C	ENST00000289013	15/15	43	26	16	14	14	0	RHPN1,missense_variant,p.Ser626Cys,ENST00000289013,;RHPN1,non_coding_transcript_exon_variant,,ENST00000522335,;RHPN1,non_coding_transcript_exon_variant,,ENST00000522899,;	G	ENSG00000158106	ENST00000289013	Transcript	missense_variant	1978	1877	626	S/C	tCc/tGc	.	.	.	1	RHPN1	HGNC	19973	protein_coding	YES	CCDS47927.1	ENSP00000289013	RHPN1_HUMAN	.	UPI0000071870	.	deleterious(0)	benign(0.009)	15/15	.	hmmpanther:PTHR23031:SF6,hmmpanther:PTHR23031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATCCACGT	.	5	ESCA
FOXH1	0	.	GRCh37	8	145701071	145701071	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69G>A	p.%3D	p.R23R	ENST00000377317	1/3	122	96	25	47	47	0	FOXH1,synonymous_variant,p.%3D,ENST00000377317,;KIFC2,downstream_gene_variant,,ENST00000301331,;KIFC2,downstream_gene_variant,,ENST00000301332,;FOXH1,non_coding_transcript_exon_variant,,ENST00000525197,;PPP1R16A,upstream_gene_variant,,ENST00000529283,;KIFC2,downstream_gene_variant,,ENST00000531423,;PPP1R16A,upstream_gene_variant,,ENST00000533088,;KIFC2,downstream_gene_variant,,ENST00000531425,;PPP1R16A,upstream_gene_variant,,ENST00000526183,;PPP1R16A,upstream_gene_variant,,ENST00000526643,;	T	ENSG00000160973	ENST00000377317	Transcript	synonymous_variant	648	69	23	R	agG/agA	.	.	.	-1	FOXH1	HGNC	3814	protein_coding	YES	CCDS6428.1	ENSP00000366534	FOXH1_HUMAN	.	UPI0000053417	.	.	.	1/3	.	hmmpanther:PTHR11829:SF122,hmmpanther:PTHR11829	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCCTCTT	.	5	ESCA
LZTS1	0	.	GRCh37	8	20106566	20106566	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*667G>C	.	.	ENST00000381569	4/4	51	31	20	28	28	0	LZTS1,3_prime_UTR_variant,,ENST00000381569,;LZTS1,3_prime_UTR_variant,,ENST00000265801,;LZTS1,downstream_gene_variant,,ENST00000522290,;	G	ENSG00000061337	ENST00000381569	Transcript	3_prime_UTR_variant	2816	.	.	.	.	.	.	.	-1	LZTS1	HGNC	13861	protein_coding	YES	CCDS6015.1	ENSP00000370981	LZTS1_HUMAN	.	UPI000006DEE8	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGCCATCA	.	5	ESCA
BIN3	0	.	GRCh37	8	22481554	22481554	+	Missense_Mutation	SNP	C	C	G	rs199588752	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.489G>C	p.Glu163Asp	p.E163D	ENST00000276416	8/9	67	47	19	26	26	0	BIN3,missense_variant,p.Glu163Asp,ENST00000276416,;BIN3,missense_variant,p.Glu115Asp,ENST00000399977,;BIN3,missense_variant,p.Glu109Asp,ENST00000519513,;BIN3,downstream_gene_variant,,ENST00000520292,;CCAR2,downstream_gene_variant,,ENST00000389279,;CCAR2,downstream_gene_variant,,ENST00000520738,;CCAR2,downstream_gene_variant,,ENST00000308511,;CCAR2,downstream_gene_variant,,ENST00000520861,;BIN3,non_coding_transcript_exon_variant,,ENST00000519335,;BIN3,non_coding_transcript_exon_variant,,ENST00000519863,;BIN3,non_coding_transcript_exon_variant,,ENST00000520489,;CCAR2,downstream_gene_variant,,ENST00000520536,;CCAR2,downstream_gene_variant,,ENST00000521436,;BIN3,downstream_gene_variant,,ENST00000522687,;	G	ENSG00000147439	ENST00000276416	Transcript	missense_variant	558	489	163	E/D	gaG/gaC	rs199588752	.	.	-1	BIN3	HGNC	1054	protein_coding	YES	CCDS47825.1	ENSP00000276416	BIN3_HUMAN	.	UPI00000735F3	.	tolerated(0.11)	benign(0.006)	8/9	.	PROSITE_profiles:PS51021,hmmpanther:PTHR10321,Pfam_domain:PF03114,Gene3D:1.20.1270.60,SMART_domains:SM00721,Superfamily_domains:SSF103657	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0	T:0.0013	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCCTCTCG	byCluster|by1000G	5	ESCA
CHRNB3	0	.	GRCh37	8	42586882	42586882	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432C>T	p.%3D	p.T144T	ENST00000289957	5/6	71	50	21	30	30	0	CHRNB3,synonymous_variant,p.%3D,ENST00000289957,;	T	ENSG00000147432	ENST00000289957	Transcript	synonymous_variant	560	432	144	T	acC/acT	.	.	.	1	CHRNB3	HGNC	1963	protein_coding	YES	CCDS6134.1	ENSP00000289957	ACHB3_HUMAN	.	UPI0000125272	.	.	.	5/6	.	Prints_domain:PR00254,Superfamily_domains:0038932,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,hmmpanther:PTHR18945:SF75,hmmpanther:PTHR18945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACCCCTCC	.	5	ESCA
MMP16	0	.	GRCh37	8	89052919	89052919	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*770C>T	.	.	ENST00000286614	10/10	84	40	44	63	63	0	MMP16,3_prime_UTR_variant,,ENST00000286614,;	A	ENSG00000156103	ENST00000286614	Transcript	3_prime_UTR_variant	2876	.	.	.	.	.	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATAGCTATG	.	5	ESCA
CORO2A	0	.	GRCh37	9	100892121	100892121	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.922A>T	p.Ser308Cys	p.S308C	ENST00000343933	8/12	75	42	33	46	46	0	CORO2A,missense_variant,p.Ser308Cys,ENST00000375077,;CORO2A,missense_variant,p.Ser308Cys,ENST00000343933,;	A	ENSG00000106789	ENST00000343933	Transcript	missense_variant	1180	922	308	S/C	Agc/Tgc	.	.	.	-1	CORO2A	HGNC	2255	protein_coding	YES	CCDS6735.1	ENSP00000343746	COR2A_HUMAN	.	UPI0000127C45	.	deleterious(0)	possibly_damaging(0.676)	8/12	.	hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF2,Gene3D:2.130.10.10,Pfam_domain:PF08954,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGCTCAGGT	.	5	ESCA
DFNB31	0	.	GRCh37	9	117165569	117165569	+	Silent	SNP	C	C	T	rs144207463	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2469G>A	p.%3D	p.A823A	ENST00000362057	11/12	83	44	39	43	43	0	DFNB31,synonymous_variant,p.%3D,ENST00000362057,;DFNB31,synonymous_variant,p.%3D,ENST00000265134,;DFNB31,synonymous_variant,p.%3D,ENST00000374059,;RP11-9M16.2,upstream_gene_variant,,ENST00000448674,;	T	ENSG00000095397	ENST00000362057	Transcript	synonymous_variant	2638	2469	823	A	gcG/gcA	rs144207463	.	.	-1	DFNB31	HGNC	16361	protein_coding	YES	CCDS6806.1	ENSP00000354623	WHRN_HUMAN	.	UPI00001C1EA6	.	.	.	11/12	.	PROSITE_profiles:PS50106,hmmpanther:PTHR23116:SF31,hmmpanther:PTHR23116,Gene3D:2.30.42.10,Pfam_domain:PF00595,Superfamily_domains:SSF50156	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0007	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCCGCACT	byCluster|by1000G	5	ESCA
ZBTB26	0	.	GRCh37	9	125680812	125680812	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*76C>T	.	.	ENST00000373656	2/2	17	10	7	11	11	0	ZBTB26,3_prime_UTR_variant,,ENST00000373654,;ZBTB26,3_prime_UTR_variant,,ENST00000373656,;	A	ENSG00000171448	ENST00000373656	Transcript	3_prime_UTR_variant	1476	.	.	.	.	.	.	.	-1	ZBTB26	HGNC	23383	protein_coding	YES	CCDS6847.1	ENSP00000362760	ZBT26_HUMAN	.	UPI0000126991	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTAGCAAAA	.	5	ESCA
CRB2	0	.	GRCh37	9	126133015	126133015	+	Silent	SNP	G	G	A	rs763374681	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1683G>A	p.%3D	p.P561P	ENST00000373631	7/13	48	28	19	33	33	0	CRB2,synonymous_variant,p.%3D,ENST00000373629,;CRB2,synonymous_variant,p.%3D,ENST00000373631,;CRB2,synonymous_variant,p.%3D,ENST00000359999,;CRB2,synonymous_variant,p.%3D,ENST00000460253,;	A	ENSG00000148204	ENST00000373631	Transcript	synonymous_variant	1684	1683	561	P	ccG/ccA	rs763374681	.	.	1	CRB2	HGNC	18688	protein_coding	YES	CCDS6852.2	ENSP00000362734	CRUM2_HUMAN	.	UPI000022D9DE	.	.	.	7/13	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24043:SF1,hmmpanther:PTHR24043,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCGCTGCC	.	5	ESCA
UBAP2	0	.	GRCh37	9	33923379	33923379	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2894C>G	p.Thr965Arg	p.T965R	ENST00000379238	25/29	70	47	22	36	36	0	UBAP2,missense_variant,p.Thr965Arg,ENST00000379238,;UBAP2,missense_variant,p.Thr698Arg,ENST00000379239,;UBAP2,missense_variant,p.Thr204Arg,ENST00000379235,;UBAP2,missense_variant,p.Thr965Arg,ENST00000449054,;UBAP2,missense_variant,p.Thr720Arg,ENST00000539807,;UBAP2,missense_variant,p.Thr965Arg,ENST00000360802,;UBAP2,downstream_gene_variant,,ENST00000418786,;UBE2R2,downstream_gene_variant,,ENST00000263228,;UBAP2,downstream_gene_variant,,ENST00000474372,;UBAP2,downstream_gene_variant,,ENST00000488443,;	C	ENSG00000137073	ENST00000379238	Transcript	missense_variant	3012	2894	965	T/R	aCa/aGa	.	.	.	-1	UBAP2	HGNC	14185	protein_coding	YES	CCDS6547.1	ENSP00000368540	UBAP2_HUMAN	Q5JV03_HUMAN	UPI0000140784	.	deleterious(0)	unknown(0)	25/29	.	hmmpanther:PTHR16308,hmmpanther:PTHR16308:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTGTACTG	.	5	ESCA
AK3	0	.	GRCh37	9	4719272	4719272	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.307G>A	p.Asp103Asn	p.D103N	ENST00000381809	3/5	22	6	16	36	36	0	AK3,missense_variant,p.Asp63Asn,ENST00000447596,;AK3,missense_variant,p.Asp103Asn,ENST00000381809,;AK3,missense_variant,p.Asp33Asn,ENST00000359883,;	T	ENSG00000147853	ENST00000381809	Transcript	missense_variant	538	307	103	D/N	Gat/Aat	.	.	.	-1	AK3	HGNC	17376	protein_coding	YES	CCDS6455.1	ENSP00000371230	KAD3_HUMAN	.	UPI000013DAE5	.	tolerated(0.38)	benign(0.011)	3/5	.	HAMAP:MF_03169,HAMAP:MF_00235,hmmpanther:PTHR23359:SF68,hmmpanther:PTHR23359,Gene3D:3.40.50.300,Pfam_domain:PF00406,TIGRFAM_domain:TIGR01351,Superfamily_domains:SSF52540,Prints_domain:PR00094	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTATCTAGGG	.	5	ESCA
RMI1	0	.	GRCh37	9	86618906	86618908	+	3'UTR	DEL	TGT	TGT	-	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	TGT	TGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1131_*1133delGTT	.	.	ENST00000325875	3/3	84	71	13	90	90	0	RMI1,3_prime_UTR_variant,,ENST00000325875,;RMI1,downstream_gene_variant,,ENST00000445877,;	-	ENSG00000178966	ENST00000325875	Transcript	3_prime_UTR_variant	3337-3339	.	.	.	.	.	.	.	1	RMI1	HGNC	25764	protein_coding	YES	CCDS6669.1	ENSP00000317039	RMI1_HUMAN	.	UPI000014178F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGTAATGTTGTTT	.	3	ESCA
SPATA31E1	0	.	GRCh37	9	90502183	90502183	+	Silent	SNP	G	G	A	rs556337873	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2781G>A	p.%3D	p.Q927Q	ENST00000325643	4/4	33	20	13	13	13	0	SPATA31E1,synonymous_variant,p.%3D,ENST00000325643,;	A	ENSG00000177992	ENST00000325643	Transcript	synonymous_variant	2847	2781	927	Q	caG/caA	rs556337873	.	.	1	SPATA31E1	HGNC	26672	protein_coding	YES	CCDS6676.1	ENSP00000322640	S31E1_HUMAN	.	UPI000036764A	.	.	.	4/4	.	hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF11	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCAGGAGGG	by1000G	5	ESCA
ARHGAP36	0	.	GRCh37	X	130222715	130222715	+	Missense_Mutation	SNP	C	C	G	rs371342192	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1600C>G	p.Arg534Gly	p.R534G	ENST00000276211	12/12	31	7	24	19	19	0	ARHGAP36,missense_variant,p.Arg534Gly,ENST00000276211,;ARHGAP36,missense_variant,p.Arg522Gly,ENST00000370922,;ARHGAP36,missense_variant,p.Arg503Gly,ENST00000412432,;ARHGAP36,missense_variant,p.Arg398Gly,ENST00000370921,;ARHGAP36,downstream_gene_variant,,ENST00000423277,;	G	ENSG00000147256	ENST00000276211	Transcript	missense_variant	1945	1600	534	R/G	Cgg/Ggg	rs371342192	.	.	1	ARHGAP36	HGNC	26388	protein_coding	YES	CCDS14628.1	ENSP00000276211	RHG36_HUMAN	.	UPI0000041347	.	deleterious_low_confidence(0.02)	benign(0.123)	12/12	.	hmmpanther:PTHR12635:SF5,hmmpanther:PTHR12635	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCCCGGGAG	byFrequency|byCluster	5	ESCA
DNASE1L1	0	.	GRCh37	X	153631450	153631450	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607G>A	p.Glu203Lys	p.E203K	ENST00000369809	9/10	41	14	27	29	29	0	DNASE1L1,missense_variant,p.Glu203Lys,ENST00000369808,;DNASE1L1,missense_variant,p.Glu203Lys,ENST00000309585,;DNASE1L1,missense_variant,p.Glu203Lys,ENST00000369809,;DNASE1L1,missense_variant,p.Glu203Lys,ENST00000451865,;DNASE1L1,missense_variant,p.Glu203Lys,ENST00000014935,;DNASE1L1,missense_variant,p.Glu203Lys,ENST00000369807,;DNASE1L1,missense_variant,p.Glu203Lys,ENST00000393638,;RPL10,3_prime_UTR_variant,,ENST00000449494,;DNASE1L1,intron_variant,,ENST00000447892,;RPL10,intron_variant,,ENST00000428169,;RPL10,intron_variant,,ENST00000427682,;RPL10,intron_variant,,ENST00000451365,;DNASE1L1,downstream_gene_variant,,ENST00000432135,;RPL10,downstream_gene_variant,,ENST00000344746,;RPL10,downstream_gene_variant,,ENST00000406022,;DNASE1L1,downstream_gene_variant,,ENST00000412184,;RPL10,downstream_gene_variant,,ENST00000436473,;DNASE1L1,downstream_gene_variant,,ENST00000424626,;RPL10,downstream_gene_variant,,ENST00000369817,;RPL10,downstream_gene_variant,,ENST00000458500,;RPL10,downstream_gene_variant,,ENST00000424325,;SNORA70,downstream_gene_variant,,ENST00000384436,;RPL10,downstream_gene_variant,,ENST00000479366,;DNASE1L1,non_coding_transcript_exon_variant,,ENST00000497242,;RPL10,downstream_gene_variant,,ENST00000482732,;RPL10,downstream_gene_variant,,ENST00000467168,;RPL10,downstream_gene_variant,,ENST00000491035,;RPL10,downstream_gene_variant,,ENST00000485196,;RPL10,downstream_gene_variant,,ENST00000474786,;RPL10,downstream_gene_variant,,ENST00000489200,;RPL10,downstream_gene_variant,,ENST00000492572,;	T	ENSG00000013563	ENST00000369809	Transcript	missense_variant	1237	607	203	E/K	Gag/Aag	.	.	.	-1	DNASE1L1	HGNC	2957	protein_coding	YES	CCDS14747.1	ENSP00000358824	DNSL1_HUMAN	Q5HY40_HUMAN,A6QRJ0_HUMAN,A3KQT1_HUMAN	UPI0000129891	.	tolerated(0.41)	benign(0.01)	9/10	.	hmmpanther:PTHR11371:SF22,hmmpanther:PTHR11371,Pfam_domain:PF03372,Gene3D:3.60.10.10,PIRSF_domain:PIRSF000988,SMART_domains:SM00476,Superfamily_domains:SSF56219,Prints_domain:PR00130	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCAGTCC	.	5	ESCA
RPL10	0	.	GRCh37	X	153631637	153631637	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000424325	.	29	5	24	19	19	0	RPL10,stop_gained,p.Gln86Ter,ENST00000427682,;DNASE1L1,synonymous_variant,p.%3D,ENST00000369808,;DNASE1L1,synonymous_variant,p.%3D,ENST00000309585,;DNASE1L1,synonymous_variant,p.%3D,ENST00000369809,;DNASE1L1,synonymous_variant,p.%3D,ENST00000451865,;DNASE1L1,synonymous_variant,p.%3D,ENST00000014935,;DNASE1L1,synonymous_variant,p.%3D,ENST00000369807,;DNASE1L1,synonymous_variant,p.%3D,ENST00000393638,;RPL10,synonymous_variant,p.%3D,ENST00000451365,;RPL10,3_prime_UTR_variant,,ENST00000449494,;DNASE1L1,intron_variant,,ENST00000447892,;RPL10,intron_variant,,ENST00000428169,;DNASE1L1,intron_variant,,ENST00000412184,;DNASE1L1,downstream_gene_variant,,ENST00000432135,;RPL10,downstream_gene_variant,,ENST00000344746,;RPL10,downstream_gene_variant,,ENST00000406022,;RPL10,downstream_gene_variant,,ENST00000436473,;DNASE1L1,downstream_gene_variant,,ENST00000424626,;RPL10,downstream_gene_variant,,ENST00000369817,;RPL10,downstream_gene_variant,,ENST00000458500,;RPL10,downstream_gene_variant,,ENST00000424325,;SNORA70,downstream_gene_variant,,ENST00000384436,;RPL10,downstream_gene_variant,,ENST00000479366,;DNASE1L1,non_coding_transcript_exon_variant,,ENST00000497242,;RPL10,downstream_gene_variant,,ENST00000482732,;RPL10,downstream_gene_variant,,ENST00000467168,;RPL10,downstream_gene_variant,,ENST00000491035,;RPL10,downstream_gene_variant,,ENST00000485196,;RPL10,downstream_gene_variant,,ENST00000474786,;RPL10,downstream_gene_variant,,ENST00000489200,;RPL10,downstream_gene_variant,,ENST00000492572,;	T	ENSG00000147403	ENST00000424325	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	957	1	RPL10	HGNC	10298	protein_coding	YES	CCDS14746.1	ENSP00000413436	RL10_HUMAN	F8W7C6_HUMAN	UPI00000019F3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCTCCAGAAA	.	3	ESCA
RPL10	0	.	GRCh37	X	153631661	153631661	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000424325	.	32	9	23	21	21	0	RPL10,stop_gained,p.Gln94Ter,ENST00000427682,;DNASE1L1,synonymous_variant,p.%3D,ENST00000369808,;DNASE1L1,synonymous_variant,p.%3D,ENST00000309585,;DNASE1L1,synonymous_variant,p.%3D,ENST00000369809,;DNASE1L1,synonymous_variant,p.%3D,ENST00000451865,;DNASE1L1,synonymous_variant,p.%3D,ENST00000014935,;DNASE1L1,synonymous_variant,p.%3D,ENST00000369807,;DNASE1L1,synonymous_variant,p.%3D,ENST00000393638,;RPL10,3_prime_UTR_variant,,ENST00000449494,;RPL10,3_prime_UTR_variant,,ENST00000451365,;DNASE1L1,intron_variant,,ENST00000447892,;RPL10,intron_variant,,ENST00000428169,;DNASE1L1,intron_variant,,ENST00000412184,;DNASE1L1,downstream_gene_variant,,ENST00000432135,;RPL10,downstream_gene_variant,,ENST00000344746,;RPL10,downstream_gene_variant,,ENST00000406022,;RPL10,downstream_gene_variant,,ENST00000436473,;DNASE1L1,downstream_gene_variant,,ENST00000424626,;RPL10,downstream_gene_variant,,ENST00000369817,;RPL10,downstream_gene_variant,,ENST00000458500,;RPL10,downstream_gene_variant,,ENST00000424325,;SNORA70,downstream_gene_variant,,ENST00000384436,;RPL10,downstream_gene_variant,,ENST00000479366,;DNASE1L1,non_coding_transcript_exon_variant,,ENST00000497242,;RPL10,downstream_gene_variant,,ENST00000482732,;RPL10,downstream_gene_variant,,ENST00000467168,;RPL10,downstream_gene_variant,,ENST00000491035,;RPL10,downstream_gene_variant,,ENST00000485196,;RPL10,downstream_gene_variant,,ENST00000474786,;RPL10,downstream_gene_variant,,ENST00000489200,;RPL10,downstream_gene_variant,,ENST00000492572,;	T	ENSG00000147403	ENST00000424325	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	981	1	RPL10	HGNC	10298	protein_coding	YES	CCDS14746.1	ENSP00000413436	RL10_HUMAN	F8W7C6_HUMAN	UPI00000019F3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCGTTCAGCTC	.	3	ESCA
DNASE1L1	0	.	GRCh37	X	153633251	153633251	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.229G>C	p.Asp77His	p.D77H	ENST00000369809	6/10	60	17	42	35	35	0	DNASE1L1,missense_variant,p.Asp77His,ENST00000369808,;DNASE1L1,missense_variant,p.Asp77His,ENST00000309585,;DNASE1L1,missense_variant,p.Asp77His,ENST00000369809,;DNASE1L1,missense_variant,p.Asp77His,ENST00000451865,;DNASE1L1,missense_variant,p.Asp77His,ENST00000424626,;DNASE1L1,missense_variant,p.Asp77His,ENST00000014935,;DNASE1L1,missense_variant,p.Asp77His,ENST00000369807,;DNASE1L1,missense_variant,p.Asp77His,ENST00000393638,;DNASE1L1,intron_variant,,ENST00000447892,;RPL10,intron_variant,,ENST00000428169,;DNASE1L1,intron_variant,,ENST00000412184,;DNASE1L1,downstream_gene_variant,,ENST00000432135,;RPL10,downstream_gene_variant,,ENST00000344746,;RPL10,downstream_gene_variant,,ENST00000406022,;RPL10,downstream_gene_variant,,ENST00000449494,;RPL10,downstream_gene_variant,,ENST00000436473,;RPL10,downstream_gene_variant,,ENST00000427682,;RPL10,downstream_gene_variant,,ENST00000369817,;RPL10,downstream_gene_variant,,ENST00000458500,;RPL10,downstream_gene_variant,,ENST00000451365,;RPL10,downstream_gene_variant,,ENST00000424325,;SNORA70,downstream_gene_variant,,ENST00000384436,;DNASE1L1,upstream_gene_variant,,ENST00000497242,;RPL10,downstream_gene_variant,,ENST00000482732,;RPL10,downstream_gene_variant,,ENST00000467168,;RPL10,downstream_gene_variant,,ENST00000491035,;RPL10,downstream_gene_variant,,ENST00000485196,;RPL10,downstream_gene_variant,,ENST00000474786,;RPL10,downstream_gene_variant,,ENST00000489200,;RPL10,downstream_gene_variant,,ENST00000492572,;	G	ENSG00000013563	ENST00000369809	Transcript	missense_variant	859	229	77	D/H	Gat/Cat	COSM756820	.	.	-1	DNASE1L1	HGNC	2957	protein_coding	YES	CCDS14747.1	ENSP00000358824	DNSL1_HUMAN	Q5HY40_HUMAN,A6QRJ0_HUMAN,A3KQT1_HUMAN	UPI0000129891	.	deleterious(0.03)	possibly_damaging(0.513)	6/10	.	hmmpanther:PTHR11371:SF22,hmmpanther:PTHR11371,Pfam_domain:PF03372,Gene3D:3.60.10.10,PIRSF_domain:PIRSF000988,SMART_domains:SM00476,Superfamily_domains:SSF56219,Prints_domain:PR00130	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCAAATC	.	5	ESCA
DNASE1L1	0	.	GRCh37	X	153637474	153637474	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-114G>C	.	.	ENST00000369809	3/10	49	7	41	31	31	0	RPL10,missense_variant,p.Leu88Val,ENST00000428169,;DNASE1L1,5_prime_UTR_variant,,ENST00000432135,;DNASE1L1,5_prime_UTR_variant,,ENST00000309585,;DNASE1L1,5_prime_UTR_variant,,ENST00000369809,;DNASE1L1,5_prime_UTR_variant,,ENST00000424626,;DNASE1L1,5_prime_UTR_variant,,ENST00000369808,;DNASE1L1,5_prime_UTR_variant,,ENST00000014935,;DNASE1L1,5_prime_UTR_variant,,ENST00000369807,;DNASE1L1,intron_variant,,ENST00000393638,;DNASE1L1,intron_variant,,ENST00000451865,;TAZ,upstream_gene_variant,,ENST00000475699,;TAZ,upstream_gene_variant,,ENST00000439735,;DNASE1L1,upstream_gene_variant,,ENST00000447892,;TAZ,upstream_gene_variant,,ENST00000351413,;TAZ,upstream_gene_variant,,ENST00000350743,;TAZ,upstream_gene_variant,,ENST00000426834,;DNASE1L1,upstream_gene_variant,,ENST00000412184,;TAZ,upstream_gene_variant,,ENST00000369776,;TAZ,upstream_gene_variant,,ENST00000369790,;TAZ,upstream_gene_variant,,ENST00000299328,;TAZ,upstream_gene_variant,,ENST00000454722,;TAZ,upstream_gene_variant,,ENST00000470127,;TAZ,upstream_gene_variant,,ENST00000479875,;TAZ,upstream_gene_variant,,ENST00000465540,;TAZ,upstream_gene_variant,,ENST00000369793,;TAZ,upstream_gene_variant,,ENST00000445994,;TAZ,upstream_gene_variant,,ENST00000433313,;TAZ,upstream_gene_variant,,ENST00000476679,;TAZ,upstream_gene_variant,,ENST00000476307,;TAZ,upstream_gene_variant,,ENST00000480812,;TAZ,upstream_gene_variant,,ENST00000483780,;TAZ,upstream_gene_variant,,ENST00000426231,;TAZ,upstream_gene_variant,,ENST00000455296,;TAZ,upstream_gene_variant,,ENST00000483674,;TAZ,upstream_gene_variant,,ENST00000476800,;	G	ENSG00000013563	ENST00000369809	Transcript	5_prime_UTR_variant	517	.	.	.	.	.	.	.	-1	DNASE1L1	HGNC	2957	protein_coding	YES	CCDS14747.1	ENSP00000358824	DNSL1_HUMAN	Q5HY40_HUMAN,A6QRJ0_HUMAN,A3KQT1_HUMAN	UPI0000129891	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGTCTGCCT	.	5	ESCA
ZNF81	0	.	GRCh37	X	47775250	47775250	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49U-01A-31D-A27G-09	TCGA-LN-A49U-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1205A>G	p.Asn402Ser	p.N402S	ENST00000376954	6/6	23	3	20	18	18	0	ZNF81,missense_variant,p.Asn402Ser,ENST00000338637,;ZNF81,missense_variant,p.Asn402Ser,ENST00000376954,;ZNF81,intron_variant,,ENST00000376950,;	G	ENSG00000197779	ENST00000376954	Transcript	missense_variant	1573	1205	402	N/S	aAt/aGt	.	.	.	1	ZNF81	HGNC	13156	protein_coding	YES	CCDS43933.1	ENSP00000366153	ZNF81_HUMAN	.	UPI000023FCDA	.	tolerated(0.82)	benign(0.036)	6/6	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF5,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCAATATAC	.	5	ESCA
NFKB2	0	.	GRCh37	10	104161038	104161038	+	Nonsense_Mutation	SNP	C	C	T	rs747113965	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2173C>T	p.Arg725Ter	p.R725*	ENST00000369966	19/23	27	22	5	33	33	0	NFKB2,stop_gained,p.Arg725Ter,ENST00000369966,;NFKB2,stop_gained,p.Arg725Ter,ENST00000428099,;NFKB2,stop_gained,p.Arg725Ter,ENST00000189444,;PSD,downstream_gene_variant,,ENST00000020673,;NFKB2,downstream_gene_variant,,ENST00000601386,;NFKB2,downstream_gene_variant,,ENST00000471698,;PSD,downstream_gene_variant,,ENST00000406432,;PSD,downstream_gene_variant,,ENST00000488194,;PSD,downstream_gene_variant,,ENST00000473507,;PSD,downstream_gene_variant,,ENST00000479172,;NFKB2,downstream_gene_variant,,ENST00000336486,;PSD,downstream_gene_variant,,ENST00000461698,;NFKB2,downstream_gene_variant,,ENST00000467116,;NFKB2,downstream_gene_variant,,ENST00000473400,;	T	ENSG00000077150	ENST00000369966	Transcript	stop_gained	2423	2173	725	R/*	Cga/Tga	rs747113965	.	.	1	NFKB2	HGNC	7795	protein_coding	YES	CCDS41564.1	ENSP00000358983	NFKB2_HUMAN	M0R119_HUMAN,M0QZX1_HUMAN	UPI000016A5CD	.	.	.	19/23	.	Gene3D:1.25.40.20,hmmpanther:PTHR24169:SF19,hmmpanther:PTHR24169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACCCGAAGC	.	5	ESCA
WBP1L	0	.	GRCh37	10	104574691	104574691	+	3'UTR	SNP	C	C	T	rs370123869	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1603C>T	.	.	ENST00000448841	4/4	59	47	12	51	51	0	WBP1L,3_prime_UTR_variant,,ENST00000448841,;WBP1L,3_prime_UTR_variant,,ENST00000369889,;	T	ENSG00000166272	ENST00000448841	Transcript	3_prime_UTR_variant	2779	.	.	.	.	rs370123869	.	.	1	WBP1L	HGNC	23510	protein_coding	YES	CCDS44473.1	ENSP00000414721	WBP1L_HUMAN	Q1EG69_HUMAN	UPI0000EE3B72	.	.	.	4/4	.	.	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAACGAGTG	byCluster|by1000G	5	ESCA
TDRD1	0	.	GRCh37	10	115986888	115986888	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3233T>G	p.Phe1078Cys	p.F1078C	ENST00000251864	23/26	55	36	18	42	42	0	TDRD1,missense_variant,p.Phe964Cys,ENST00000369281,;TDRD1,missense_variant,p.Phe1078Cys,ENST00000251864,;TDRD1,intron_variant,,ENST00000369282,;TDRD1,intron_variant,,ENST00000369280,;TDRD1,intron_variant,,ENST00000422662,;	G	ENSG00000095627	ENST00000251864	Transcript	missense_variant	3386	3233	1078	F/C	tTc/tGc	.	.	.	1	TDRD1	HGNC	11712	protein_coding	YES	CCDS7588.1	ENSP00000251864	TDRD1_HUMAN	.	UPI00001F9753	.	deleterious(0.02)	probably_damaging(0.938)	23/26	.	hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATTTCATGT	.	5	ESCA
ATRNL1	0	.	GRCh37	10	117221465	117221465	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3337G>T	p.Asp1113Tyr	p.D1113Y	ENST00000355044	22/29	66	41	25	31	31	0	ATRNL1,missense_variant,p.Asp197Tyr,ENST00000526373,;ATRNL1,missense_variant,p.Asp164Tyr,ENST00000423111,;ATRNL1,missense_variant,p.Asp1113Tyr,ENST00000355044,;ATRNL1,intron_variant,,ENST00000303745,;ATRNL1,intron_variant,,ENST00000534530,;	T	ENSG00000107518	ENST00000355044	Transcript	missense_variant	3463	3337	1113	D/Y	Gat/Tat	.	.	.	1	ATRNL1	HGNC	29063	protein_coding	YES	CCDS7592.1	ENSP00000347152	ATRN1_HUMAN	.	UPI000021CCF8	.	deleterious(0)	probably_damaging(0.959)	22/29	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTGATTAT	.	5	ESCA
C10orf82	0	.	GRCh37	10	118425180	118425180	+	Silent	SNP	G	G	A	rs374577819	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.213C>T	p.%3D	p.S71S	ENST00000369210	3/5	42	36	6	38	38	0	C10orf82,synonymous_variant,p.%3D,ENST00000369210,;C10orf82,synonymous_variant,p.%3D,ENST00000588184,;RP11-498B4.5,upstream_gene_variant,,ENST00000433600,;C10orf82,non_coding_transcript_exon_variant,,ENST00000588224,;C10orf82,non_coding_transcript_exon_variant,,ENST00000467153,;	A	ENSG00000165863	ENST00000369210	Transcript	synonymous_variant	268	213	71	S	tcC/tcT	rs374577819	.	.	-1	C10orf82	HGNC	28500	protein_coding	YES	CCDS7596.1	ENSP00000358212	CJ082_HUMAN	.	UPI000006DC12	.	.	.	3/5	.	.	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCGGAGTT	byFrequency|byCluster	5	ESCA
JAKMIP3	0	.	GRCh37	10	133946999	133946999	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817G>A	p.Ala273Thr	p.A273T	ENST00000298622	3/24	23	15	7	23	23	0	JAKMIP3,missense_variant,p.Ala273Thr,ENST00000298622,;	A	ENSG00000188385	ENST00000298622	Transcript	missense_variant	955	817	273	A/T	Gca/Aca	.	.	.	1	JAKMIP3	HGNC	23523	protein_coding	YES	CCDS44494.1	ENSP00000298622	JKIP3_HUMAN	.	UPI000157482F	.	tolerated(0.21)	possibly_damaging(0.693)	3/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR18935:SF5,hmmpanther:PTHR18935	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGTGCAGGA	.	5	ESCA
KIAA1217	0	.	GRCh37	10	24834065	24834065	+	Intron	SNP	C	C	T	rs759509189	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5334+33C>T	.	.	ENST00000376454	.	12	4	7	16	16	0	KIAA1217,3_prime_UTR_variant,,ENST00000396445,;KIAA1217,3_prime_UTR_variant,,ENST00000307544,;KIAA1217,3_prime_UTR_variant,,ENST00000396446,;KIAA1217,3_prime_UTR_variant,,ENST00000376451,;KIAA1217,intron_variant,,ENST00000376454,;KIAA1217,intron_variant,,ENST00000376452,;KIAA1217,intron_variant,,ENST00000376462,;KIAA1217,intron_variant,,ENST00000458595,;KIAA1217,downstream_gene_variant,,ENST00000492009,;	T	ENSG00000120549	ENST00000376454	Transcript	intron_variant	.	.	.	.	.	rs759509189	.	.	1	KIAA1217	HGNC	25428	protein_coding	YES	CCDS31165.1	ENSP00000365637	SKT_HUMAN	.	UPI000013EC2A	.	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGACGCTAT	byFrequency	2	ESCA
ARMC4	0	.	GRCh37	10	28229562	28229562	+	Missense_Mutation	SNP	C	C	T	rs148908705	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1916G>A	p.Arg639Gln	p.R639Q	ENST00000305242	13/20	27	19	8	26	26	0	ARMC4,missense_variant,p.Arg164Gln,ENST00000545014,;ARMC4,missense_variant,p.Arg639Gln,ENST00000305242,;ARMC4,missense_variant,p.Arg331Gln,ENST00000537576,;ARMC4,downstream_gene_variant,,ENST00000480504,;	T	ENSG00000169126	ENST00000305242	Transcript	missense_variant	2009	1916	639	R/Q	cGg/cAg	rs148908705,COSM184587	.	.	-1	ARMC4	HGNC	25583	protein_coding	YES	CCDS7157.1	ENSP00000306410	ARMC4_HUMAN	R4GN11_HUMAN,A8K906_HUMAN	UPI00001A95E1	.	tolerated(0.17)	benign(0.013)	13/20	.	hmmpanther:PTHR23315:SF67,hmmpanther:PTHR23315,Pfam_domain:PF00514,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	T:0.0005	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCCGAGCC	byCluster	5	ESCA
ALOX5	0	.	GRCh37	10	45907711	45907711	+	Silent	SNP	C	C	A	rs766792732	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.504C>A	p.%3D	p.I168I	ENST00000374391	4/14	60	38	22	59	59	0	ALOX5,synonymous_variant,p.%3D,ENST00000374391,;ALOX5,synonymous_variant,p.%3D,ENST00000542434,;	A	ENSG00000012779	ENST00000374391	Transcript	synonymous_variant	557	504	168	I	atC/atA	rs766792732	.	.	1	ALOX5	HGNC	435	protein_coding	YES	CCDS7212.1	ENSP00000363512	LOX5_HUMAN	E5FPY7_HUMAN	UPI0000043F84	.	.	.	4/14	.	PROSITE_profiles:PS51393,hmmpanther:PTHR11771:SF5,hmmpanther:PTHR11771,Pfam_domain:PF00305,Superfamily_domains:SSF48484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATATCCAGTT	byFrequency	5	ESCA
ANKRD16	0	.	GRCh37	10	5920183	5920183	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.996G>A	p.%3D	p.K332K	ENST00000380094	7/8	16	11	4	27	27	0	ANKRD16,synonymous_variant,p.%3D,ENST00000380092,;ANKRD16,synonymous_variant,p.%3D,ENST00000380094,;ANKRD16,3_prime_UTR_variant,,ENST00000191063,;ANKRD16,downstream_gene_variant,,ENST00000492368,;	T	ENSG00000134461	ENST00000380094	Transcript	synonymous_variant	1540	996	332	K	aaG/aaA	.	.	.	-1	ANKRD16	HGNC	23471	protein_coding	YES	CCDS31136.1	ENSP00000369436	ANR16_HUMAN	.	UPI00001D809F	.	.	.	7/8	.	hmmpanther:PTHR24181,hmmpanther:PTHR24181:SF20,Gene3D:1.25.40.20,SMART_domains:SM00248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCCTTCAG	.	5	ESCA
KIAA1279	0	.	GRCh37	10	70775906	70775906	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1600C>T	p.His534Tyr	p.H534Y	ENST00000361983	7/7	47	36	11	39	39	0	KIAA1279,missense_variant,p.His534Tyr,ENST00000361983,;KIAA1279,downstream_gene_variant,,ENST00000481912,;	T	ENSG00000198954	ENST00000361983	Transcript	missense_variant	1702	1600	534	H/Y	Cat/Tat	.	.	.	1	KIAA1279	HGNC	23419	protein_coding	YES	CCDS7284.1	ENSP00000354848	KBP_HUMAN	.	UPI000006FCAF	.	deleterious(0.03)	possibly_damaging(0.453)	7/7	.	hmmpanther:PTHR20956,hmmpanther:PTHR20956:SF0,Pfam_domain:PF12309	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGCATATA	.	5	ESCA
SEC24C	0	.	GRCh37	10	75531371	75531371	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*518G>A	.	.	ENST00000339365	24/24	28	23	4	19	19	0	SEC24C,3_prime_UTR_variant,,ENST00000345254,;SEC24C,3_prime_UTR_variant,,ENST00000339365,;SEC24C,downstream_gene_variant,,ENST00000540668,;AC022400.2,downstream_gene_variant,,ENST00000595757,;SEC24C,downstream_gene_variant,,ENST00000546025,;SEC24C,downstream_gene_variant,,ENST00000411652,;FUT11,upstream_gene_variant,,ENST00000372841,;SEC24C,downstream_gene_variant,,ENST00000535742,;FUT11,upstream_gene_variant,,ENST00000394790,;RMRPP1,downstream_gene_variant,,ENST00000517236,;SEC24C,downstream_gene_variant,,ENST00000496827,;FUT11,upstream_gene_variant,,ENST00000465695,;FUT11,upstream_gene_variant,,ENST00000489264,;SEC24C,3_prime_UTR_variant,,ENST00000465076,;	A	ENSG00000176986	ENST00000339365	Transcript	3_prime_UTR_variant	3965	.	.	.	.	.	.	.	1	SEC24C	HGNC	10705	protein_coding	YES	CCDS7332.1	ENSP00000343405	SC24C_HUMAN	B4DZT4_HUMAN	UPI000013F621	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGCAGTCAAG	.	4	ESCA
OPN4	0	.	GRCh37	10	88422152	88422152	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000372071	9/11	63	52	10	83	83	0	OPN4,missense_variant,p.Arg406Gln,ENST00000241891,;OPN4,missense_variant,p.Arg417Gln,ENST00000372071,;OPN4,missense_variant,p.Arg417Gln,ENST00000443292,;	A	ENSG00000122375	ENST00000372071	Transcript	missense_variant	1477	1250	417	R/Q	cGg/cAg	COSM4169255,COSM4169256	.	.	1	OPN4	HGNC	14449	protein_coding	YES	CCDS31237.1	ENSP00000361141	OPN4_HUMAN	.	UPI00001544ED	.	tolerated(0.18)	benign(0.031)	9/11	.	hmmpanther:PTHR24240,hmmpanther:PTHR24240:SF72	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATACGGAGGC	.	5	ESCA
RNLS	0	.	GRCh37	10	90122339	90122339	+	Missense_Mutation	SNP	C	C	T	rs760004178	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670G>A	p.Val224Ile	p.V224I	ENST00000331772	5/7	43	24	19	45	45	0	RNLS,missense_variant,p.Val224Ile,ENST00000371947,;RNLS,missense_variant,p.Val141Ile,ENST00000437752,;RNLS,missense_variant,p.Val224Ile,ENST00000331772,;RNLS,non_coding_transcript_exon_variant,,ENST00000481793,;RNLS,non_coding_transcript_exon_variant,,ENST00000466945,;	T	ENSG00000184719	ENST00000331772	Transcript	missense_variant	693	670	224	V/I	Gtc/Atc	rs760004178	.	.	-1	RNLS	HGNC	25641	protein_coding	YES	CCDS31239.1	ENSP00000332530	RNLS_HUMAN	G9G138_HUMAN,G9G137_HUMAN	UPI00001AFF46	.	tolerated(1)	benign(0.002)	5/7	.	hmmpanther:PTHR23357,Pfam_domain:PF01593,Gene3D:3.90.660.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGACGAAGC	.	5	ESCA
GALNT18	0	.	GRCh37	11	11314686	11314686	+	Missense_Mutation	SNP	C	C	T	rs529247669	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1567G>A	p.Val523Met	p.V523M	ENST00000227756	10/11	47	29	17	37	37	0	GALNT18,missense_variant,p.Val523Met,ENST00000227756,;	T	ENSG00000110328	ENST00000227756	Transcript	missense_variant	1979	1567	523	V/M	Gtg/Atg	rs529247669	.	.	-1	GALNT18	HGNC	30488	protein_coding	YES	CCDS7807.1	ENSP00000227756	GLT18_HUMAN	Q58A54_HUMAN	UPI000004B63C	.	tolerated(0.22)	benign(0.343)	10/11	.	Superfamily_domains:SSF50370,SMART_domains:SM00458,Gene3D:2.80.10.50,Pfam_domain:PF00652,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF37,PROSITE_profiles:PS50231	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCACGGTGG	by1000G	5	ESCA
UBASH3B	0	.	GRCh37	11	122667713	122667713	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1329G>T	p.%3D	p.V443V	ENST00000284273	9/14	24	20	4	63	63	0	UBASH3B,synonymous_variant,p.%3D,ENST00000284273,;UBASH3B,non_coding_transcript_exon_variant,,ENST00000530578,;UBASH3B,downstream_gene_variant,,ENST00000526493,;	T	ENSG00000154127	ENST00000284273	Transcript	synonymous_variant	1704	1329	443	V	gtG/gtT	.	.	.	1	UBASH3B	HGNC	29884	protein_coding	YES	CCDS31694.1	ENSP00000284273	UBS3B_HUMAN	.	UPI0000047471	.	.	.	9/14	.	Superfamily_domains:SSF53254,Pfam_domain:PF00300,Gene3D:3.40.50.1240,hmmpanther:PTHR16469,hmmpanther:PTHR16469:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	ACTGTGTTTGG	.	2	ESCA
DUSP8	0	.	GRCh37	11	1585172	1585172	+	Silent	SNP	C	C	T	rs141702492	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279G>A	p.%3D	p.T93T	ENST00000397374	3/7	31	21	10	45	45	0	DUSP8,synonymous_variant,p.%3D,ENST00000397374,;DUSP8,synonymous_variant,p.%3D,ENST00000331588,;DUSP8,upstream_gene_variant,,ENST00000528778,;	T	ENSG00000184545	ENST00000397374	Transcript	synonymous_variant	407	279	93	T	acG/acA	rs141702492	.	.	-1	DUSP8	HGNC	3074	protein_coding	YES	CCDS7724.1	ENSP00000380530	DUS8_HUMAN	.	UPI000000DAD1	.	.	.	3/7	.	PROSITE_profiles:PS50206,hmmpanther:PTHR10159:SF108,hmmpanther:PTHR10159,Gene3D:3.40.250.10,Pfam_domain:PF00581,SMART_domains:SM00450,Superfamily_domains:SSF52821	T:0.0004	T:0	T:0	.	T:0.001	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGCGTGCT	byFrequency|by1000G	5	ESCA
OR51F2	0	.	GRCh37	11	4842865	4842865	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000322110	1/1	81	53	28	49	49	0	OR51F2,missense_variant,p.Asp84Tyr,ENST00000322110,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	T	ENSG00000176925	ENST00000322110	Transcript	missense_variant	315	250	84	D/Y	Gac/Tac	COSM1475486,COSM4033369	.	.	1	OR51F2	HGNC	15197	protein_coding	YES	CCDS31361.1	ENSP00000323952	O51F2_HUMAN	.	UPI000004B219	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF87,Pfam_domain:PF10320,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAGACCTG	.	5	ESCA
OR51G2	0	.	GRCh37	11	4936276	4936276	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.618T>C	p.%3D	p.F206F	ENST00000322013	1/1	54	39	14	37	37	0	OR51G2,synonymous_variant,p.%3D,ENST00000322013,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	G	ENSG00000176893	ENST00000322013	Transcript	synonymous_variant	647	618	206	F	ttT/ttC	.	.	.	-1	OR51G2	HGNC	15198	protein_coding	YES	CCDS31365.1	ENSP00000322593	O51G2_HUMAN	.	UPI0000041C2F	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF133,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACAAACAT	.	5	ESCA
OR4A16	0	.	GRCh37	11	55110876	55110876	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200T>C	p.Met67Thr	p.M67T	ENST00000314721	1/1	50	43	7	40	40	0	OR4A16,missense_variant,p.Met67Thr,ENST00000314721,;	C	ENSG00000181961	ENST00000314721	Transcript	missense_variant	250	200	67	M/T	aTg/aCg	.	.	.	1	OR4A16	HGNC	15153	protein_coding	YES	CCDS31499.1	ENSP00000325128	O4A16_HUMAN	.	UPI0000061EB2	.	deleterious_low_confidence(0.03)	benign(0.005)	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451:SF153,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L64L|c.190T>C|4	RADIA|MUTECT|MUSE|VARSCANS	ACTTATGGATG	.	4	ESCA
PLCB3	0	.	GRCh37	11	64033845	64033845	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3325G>T	p.Ala1109Ser	p.A1109S	ENST00000540288	28/32	18	10	7	16	16	0	PLCB3,missense_variant,p.Ala1042Ser,ENST00000325234,;PLCB3,missense_variant,p.Ala1109Ser,ENST00000279230,;PLCB3,missense_variant,p.Ala1109Ser,ENST00000540288,;BAD,downstream_gene_variant,,ENST00000493798,;BAD,downstream_gene_variant,,ENST00000309032,;GPR137,upstream_gene_variant,,ENST00000546139,;BAD,downstream_gene_variant,,ENST00000544785,;BAD,downstream_gene_variant,,ENST00000492141,;BAD,downstream_gene_variant,,ENST00000394531,;BAD,downstream_gene_variant,,ENST00000394532,;PLCB3,downstream_gene_variant,,ENST00000536243,;	T	ENSG00000149782	ENST00000540288	Transcript	missense_variant	3428	3325	1109	A/S	Gcc/Tcc	.	.	.	1	PLCB3	HGNC	9056	protein_coding	YES	CCDS8064.1	ENSP00000443631	PLCB3_HUMAN	.	UPI0000131AFF	.	deleterious(0)	probably_damaging(0.998)	28/32	.	Superfamily_domains:0053448,PIRSF_domain:PIRSF000956,Pfam_domain:PF08703,Gene3D:1jadA00,hmmpanther:PTHR10336:SF11,hmmpanther:PTHR10336	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGAGGCCAAG	.	5	ESCA
PNPLA2	0	.	GRCh37	11	821670	821670	+	Missense_Mutation	SNP	G	G	A	rs373487598	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.230G>A	p.Arg77Gln	p.R77Q	ENST00000336615	3/10	34	29	5	16	16	0	PNPLA2,missense_variant,p.Arg77Gln,ENST00000336615,;EFCAB4A,upstream_gene_variant,,ENST00000528315,;EFCAB4A,upstream_gene_variant,,ENST00000533803,;AP006621.8,downstream_gene_variant,,ENST00000532946,;AP006621.8,downstream_gene_variant,,ENST00000528982,;PNPLA2,non_coding_transcript_exon_variant,,ENST00000525250,;EFCAB4A,upstream_gene_variant,,ENST00000534191,;PNPLA2,upstream_gene_variant,,ENST00000526083,;PNPLA2,upstream_gene_variant,,ENST00000534561,;PNPLA2,upstream_gene_variant,,ENST00000529255,;PNPLA2,upstream_gene_variant,,ENST00000531923,;	A	ENSG00000177666	ENST00000336615	Transcript	missense_variant	432	230	77	R/Q	cGg/cAg	rs373487598	.	.	1	PNPLA2	HGNC	30802	protein_coding	YES	CCDS7718.1	ENSP00000337701	PLPL2_HUMAN	.	UPI000003731E	.	deleterious(0)	probably_damaging(0.998)	3/10	.	hmmpanther:PTHR12406:SF24,hmmpanther:PTHR12406,Pfam_domain:PF01734,Superfamily_domains:SSF52151	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCCGGAAGC	byFrequency|byCluster	4	ESCA
CRY1	0	.	GRCh37	12	107391742	107391742	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1240T>C	p.Cys414Arg	p.C414R	ENST00000008527	8/13	20	17	3	18	18	0	CRY1,missense_variant,p.Cys414Arg,ENST00000008527,;CRY1,upstream_gene_variant,,ENST00000549356,;CRY1,non_coding_transcript_exon_variant,,ENST00000552790,;CRY1,downstream_gene_variant,,ENST00000546722,;	G	ENSG00000008405	ENST00000008527	Transcript	missense_variant	2108	1240	414	C/R	Tgc/Cgc	.	.	.	-1	CRY1	HGNC	2384	protein_coding	YES	CCDS9112.1	ENSP00000008527	CRY1_HUMAN	H0YHT0_HUMAN,A2I2P0_HUMAN	UPI0000073E80	.	deleterious(0)	possibly_damaging(0.831)	8/13	.	Superfamily_domains:SSF48173,Gene3D:1owlA03,Pfam_domain:PF03441,hmmpanther:PTHR11455:SF16,hmmpanther:PTHR11455	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGCAATAGC	.	2	ESCA
PRDM4	0	.	GRCh37	12	108127791	108127791	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*196G>A	.	.	ENST00000228437	12/12	73	67	5	57	57	0	PRDM4,3_prime_UTR_variant,,ENST00000228437,;RP11-864J10.4,upstream_gene_variant,,ENST00000546829,;RP11-864J10.4,upstream_gene_variant,,ENST00000546714,;PRDM4,downstream_gene_variant,,ENST00000550376,;	T	ENSG00000110851	ENST00000228437	Transcript	3_prime_UTR_variant	3062	.	.	.	.	.	.	.	-1	PRDM4	HGNC	9348	protein_coding	YES	CCDS9115.1	ENSP00000228437	PRDM4_HUMAN	F8VRG2_HUMAN	UPI000013217D	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCTCAGTTT	.	2	ESCA
MMP17	0	.	GRCh37	12	132335615	132335615	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1608G>A	p.%3D	p.V536V	ENST00000360564	10/10	74	61	13	73	73	0	MMP17,synonymous_variant,p.%3D,ENST00000535291,;MMP17,synonymous_variant,p.%3D,ENST00000360564,;MMP17,synonymous_variant,p.%3D,ENST00000535004,;MMP17,downstream_gene_variant,,ENST00000542648,;MMP17,downstream_gene_variant,,ENST00000534865,;MMP17,non_coding_transcript_exon_variant,,ENST00000535271,;MMP17,downstream_gene_variant,,ENST00000537848,;	A	ENSG00000198598	ENST00000360564	Transcript	synonymous_variant	1710	1608	536	V	gtG/gtA	.	.	.	1	MMP17	HGNC	7163	protein_coding	YES	CCDS31927.1	ENSP00000353767	MMP17_HUMAN	F5H881_HUMAN,F5H249_HUMAN,F5H209_HUMAN,F5GZA7_HUMAN,F5GWR3_HUMAN	UPI00001AF305	.	.	.	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGTGGACGC	.	5	ESCA
BIN2	0	.	GRCh37	12	51717865	51717865	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22G>A	p.Gly8Ser	p.G8S	ENST00000267012	1/13	46	37	8	51	51	0	BIN2,missense_variant,p.Gly8Ser,ENST00000267012,;BIN2,missense_variant,p.Gly8Ser,ENST00000604560,;BIN2,missense_variant,p.Gly8Ser,ENST00000452142,;BIN2,intron_variant,,ENST00000544402,;CELA1,downstream_gene_variant,,ENST00000293636,;BIN2,non_coding_transcript_exon_variant,,ENST00000603260,;BIN2,non_coding_transcript_exon_variant,,ENST00000604702,;BIN2,missense_variant,p.Gly8Ser,ENST00000605423,;BIN2,non_coding_transcript_exon_variant,,ENST00000605039,;	T	ENSG00000110934	ENST00000267012	Transcript	missense_variant	84	22	8	G/S	Ggc/Agc	.	.	.	-1	BIN2	HGNC	1053	protein_coding	YES	CCDS8811.1	ENSP00000267012	BIN2_HUMAN	.	UPI000013D71F	.	tolerated(0.47)	unknown(0)	1/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10321:SF11,hmmpanther:PTHR10321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGCCGCCTG	.	5	ESCA
SPRYD3	0	.	GRCh37	12	53459646	53459646	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1299C>T	p.%3D	p.V433V	ENST00000301463	11/11	29	12	17	54	54	0	SPRYD3,synonymous_variant,p.%3D,ENST00000301463,;SPRYD3,synonymous_variant,p.%3D,ENST00000547837,;TENC1,downstream_gene_variant,,ENST00000379902,;TENC1,downstream_gene_variant,,ENST00000546602,;TENC1,downstream_gene_variant,,ENST00000549700,;TENC1,downstream_gene_variant,,ENST00000314276,;TENC1,downstream_gene_variant,,ENST00000451358,;TENC1,downstream_gene_variant,,ENST00000314250,;TENC1,downstream_gene_variant,,ENST00000552570,;SPRYD3,synonymous_variant,p.%3D,ENST00000547257,;SPRYD3,downstream_gene_variant,,ENST00000550564,;TENC1,downstream_gene_variant,,ENST00000551583,;TENC1,downstream_gene_variant,,ENST00000550660,;SPRYD3,downstream_gene_variant,,ENST00000537540,;TENC1,downstream_gene_variant,,ENST00000552168,;TENC1,downstream_gene_variant,,ENST00000550048,;TENC1,downstream_gene_variant,,ENST00000546772,;TENC1,downstream_gene_variant,,ENST00000549311,;	A	ENSG00000167778	ENST00000301463	Transcript	synonymous_variant	1386	1299	433	V	gtC/gtT	.	.	.	-1	SPRYD3	HGNC	25920	protein_coding	YES	CCDS8845.1	ENSP00000301463	SPRY3_HUMAN	.	UPI0000038D00	.	.	.	11/11	.	SMART_domains:SM00449,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTGACTTT	.	5	ESCA
PCDH8	0	.	GRCh37	13	53418936	53418936	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2972C>T	p.Thr991Met	p.T991M	ENST00000377942	3/3	30	1	29	42	42	0	PCDH8,missense_variant,p.Thr894Met,ENST00000338862,;PCDH8,missense_variant,p.Thr991Met,ENST00000377942,;	A	ENSG00000136099	ENST00000377942	Transcript	missense_variant	3176	2972	991	T/M	aCg/aTg	.	.	.	-1	PCDH8	HGNC	8660	protein_coding	YES	CCDS9438.1	ENSP00000367177	PCDH8_HUMAN	.	UPI0000072D47	.	deleterious(0.02)	probably_damaging(0.993)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGACGTGCTC	.	5	ESCA
SLITRK5	0	.	GRCh37	13	88331374	88331374	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*854C>A	.	.	ENST00000325089	2/2	31	19	11	31	31	0	SLITRK5,3_prime_UTR_variant,,ENST00000325089,;SLITRK5,downstream_gene_variant,,ENST00000400028,;	A	ENSG00000165300	ENST00000325089	Transcript	3_prime_UTR_variant	3950	.	.	.	.	.	.	.	1	SLITRK5	HGNC	20295	protein_coding	YES	CCDS9465.1	ENSP00000366283	SLIK5_HUMAN	.	UPI000015F6F7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCAATCA	.	5	ESCA
TDRD9	0	.	GRCh37	14	104488603	104488603	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2542C>T	p.His848Tyr	p.H848Y	ENST00000409874	24/36	74	68	6	50	50	0	TDRD9,missense_variant,p.His575Tyr,ENST00000557332,;TDRD9,missense_variant,p.His848Tyr,ENST00000339063,;TDRD9,missense_variant,p.His848Tyr,ENST00000409874,;	T	ENSG00000156414	ENST00000409874	Transcript	missense_variant	2590	2542	848	H/Y	Cat/Tat	.	.	.	1	TDRD9	HGNC	20122	protein_coding	YES	CCDS9987.2	ENSP00000387303	TDRD9_HUMAN	.	UPI0001642306	.	tolerated(0.35)	benign(0.008)	24/36	.	hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF80	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCGTTCATTCT	.	3	ESCA
CEP170B	0	.	GRCh37	14	105359964	105359964	+	Silent	SNP	C	C	T	rs768674837	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4143C>T	p.%3D	p.D1381D	ENST00000414716	15/19	50	43	7	50	50	0	CEP170B,synonymous_variant,p.%3D,ENST00000414716,;CEP170B,synonymous_variant,p.%3D,ENST00000556508,;CEP170B,synonymous_variant,p.%3D,ENST00000418279,;CEP170B,synonymous_variant,p.%3D,ENST00000453495,;CEP170B,upstream_gene_variant,,ENST00000251181,;	T	ENSG00000099814	ENST00000414716	Transcript	synonymous_variant	4371	4143	1381	D	gaC/gaT	rs768674837	.	.	1	CEP170B	HGNC	20362	protein_coding	YES	CCDS45175.1	ENSP00000404151	C170B_HUMAN	E9PFC1_HUMAN	UPI00001FDCF7	.	.	.	15/19	.	hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF18,Pfam_domain:PF15308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGACGCCCT	byFrequency	4	ESCA
POTEM	0	.	GRCh37	14	20010438	20010438	+	Intron	SNP	A	A	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.918-198T>G	.	.	ENST00000551509	.	53	47	6	57	56	0	POTEM,intron_variant,,ENST00000551509,;RP11-244H18.1,non_coding_transcript_exon_variant,,ENST00000547584,;RNU6-1268P,upstream_gene_variant,,ENST00000391214,;POTEM,intron_variant,,ENST00000547848,;POTEM,intron_variant,,ENST00000547722,;	C	ENSG00000187537	ENST00000551509	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	POTEM	HGNC	37096	protein_coding	YES	CCDS45076.1	ENSP00000452296	POTEM_HUMAN	.	UPI00006C1407	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAAACCCTC	.	2	ESCA
TRAC	0	.	GRCh37	14	23016702	23016702	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256C>T	p.Thr86Ile	p.T86I	ENST00000478163	1/4	41	30	10	46	46	0	TRAC,missense_variant,p.Thr86Ile,ENST00000478163,;TRAJ3,downstream_gene_variant,,ENST00000390534,;TRAJ2,downstream_gene_variant,,ENST00000390535,;TRAJ1,downstream_gene_variant,,ENST00000390536,;	T	ENSG00000229164	ENST00000478163	Transcript	missense_variant	256	257	86	T/I	aCc/aTc	.	.	.	1	TRAC	HGNC	12029	TR_C_gene	YES	.	ENSP00000451333	.	.	UPI0000F30351	.	tolerated(0.1)	benign(0.355)	1/4	.	hmmpanther:PTHR19433,hmmpanther:PTHR19433:SF65,Gene3D:2.60.40.10,Pfam_domain:PF09291,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACACCTTCT	.	5	ESCA
PLEKHG3	0	.	GRCh37	14	65197520	65197520	+	Silent	SNP	C	C	T	rs776854734	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402C>T	p.%3D	p.S134S	ENST00000247226	4/15	66	45	20	39	39	0	PLEKHG3,synonymous_variant,p.%3D,ENST00000247226,;PLEKHG3,synonymous_variant,p.%3D,ENST00000394691,;PLEKHG3,downstream_gene_variant,,ENST00000554499,;PLEKHG3,downstream_gene_variant,,ENST00000554088,;PLEKHG3,downstream_gene_variant,,ENST00000555982,;PLEKHG3,downstream_gene_variant,,ENST00000556801,;PLEKHG3,non_coding_transcript_exon_variant,,ENST00000490180,;	T	ENSG00000126822	ENST00000247226	Transcript	synonymous_variant	710	402	134	S	tcC/tcT	rs776854734	.	.	1	PLEKHG3	HGNC	20364	protein_coding	YES	CCDS32098.1	ENSP00000247226	PKHG3_HUMAN	G3V311_HUMAN	UPI0000407D62	.	.	.	4/15	.	PROSITE_profiles:PS50010,hmmpanther:PTHR22143:SF4,hmmpanther:PTHR22143,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCCGTGGC	.	5	ESCA
LTBP2	0	.	GRCh37	14	74974791	74974791	+	Silent	SNP	G	G	A	rs764055325	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3660C>T	p.%3D	p.D1220D	ENST00000261978	25/36	30	25	4	30	30	0	LTBP2,synonymous_variant,p.%3D,ENST00000261978,;LTBP2,synonymous_variant,p.%3D,ENST00000556690,;LTBP2,intron_variant,,ENST00000556206,;LTBP2,synonymous_variant,p.%3D,ENST00000553939,;	A	ENSG00000119681	ENST00000261978	Transcript	synonymous_variant	4047	3660	1220	D	gaC/gaT	rs764055325	.	.	-1	LTBP2	HGNC	6715	protein_coding	YES	CCDS9831.1	ENSP00000261978	LTBP2_HUMAN	G3V254_HUMAN	UPI000013D239	.	.	.	25/36	.	Superfamily_domains:SSF57184,SMART_domains:SM00179,Pfam_domain:PF07645,Gene3D:2.10.25.10,PROSITE_patterns:PS01187,hmmpanther:PTHR24034:SF40,hmmpanther:PTHR24034,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	CACTCGTCCAC	byFrequency	3	ESCA
PRIMA1	0	.	GRCh37	14	94192299	94192299	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.360-4407G>A	.	.	ENST00000393140	.	29	25	4	18	18	0	PRIMA1,3_prime_UTR_variant,,ENST00000316227,;PRIMA1,intron_variant,,ENST00000393143,;PRIMA1,intron_variant,,ENST00000393140,;PRIMA1,3_prime_UTR_variant,,ENST00000477603,;	T	ENSG00000175785	ENST00000393140	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PRIMA1	HGNC	18319	protein_coding	YES	CCDS9912.1	ENSP00000376848	PRIMA_HUMAN	.	UPI0000051D0A	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CATTTCCACCC	.	2	ESCA
AC100757.1	0	.	GRCh37	15	23445535	23445535	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000458911	.	62	20	41	102	102	0	AC100757.1,downstream_gene_variant,,ENST00000458911,;RN7SL106P,downstream_gene_variant,,ENST00000488468,;GOLGA8EP,non_coding_transcript_exon_variant,,ENST00000526079,;GOLGA8EP,downstream_gene_variant,,ENST00000530246,;	G	ENSG00000238347	ENST00000458911	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	685	1	AC100757.1	Clone_based_ensembl_gene	.	miRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTACACAATT	.	4	ESCA
VPS18	0	.	GRCh37	15	41192273	41192273	+	Silent	SNP	C	C	T	rs778725367	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1257C>T	p.%3D	p.P419P	ENST00000220509	4/5	44	33	10	65	65	0	VPS18,synonymous_variant,p.%3D,ENST00000220509,;VPS18,intron_variant,,ENST00000558474,;VPS18,downstream_gene_variant,,ENST00000558855,;	T	ENSG00000104142	ENST00000220509	Transcript	synonymous_variant	1596	1257	419	P	ccC/ccT	rs778725367	.	.	1	VPS18	HGNC	15972	protein_coding	YES	CCDS10069.1	ENSP00000220509	VPS18_HUMAN	.	UPI0000049FBC	.	.	.	4/5	.	Pfam_domain:PF05131,hmmpanther:PTHR23323:SF26,hmmpanther:PTHR23323	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCCCGACTG	byFrequency	5	ESCA
UNC13C	0	.	GRCh37	15	54305791	54305791	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.691A>C	p.Ser231Arg	p.S231R	ENST00000260323	1/32	24	20	4	35	35	0	UNC13C,missense_variant,p.Ser231Arg,ENST00000537900,;UNC13C,missense_variant,p.Ser231Arg,ENST00000545554,;UNC13C,missense_variant,p.Ser231Arg,ENST00000260323,;	C	ENSG00000137766	ENST00000260323	Transcript	missense_variant	691	691	231	S/R	Agt/Cgt	.	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	deleterious_low_confidence(0)	probably_damaging(0.997)	1/32	.	hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTCAGTTCC	.	2	ESCA
ODF3L1	0	.	GRCh37	15	76019672	76019672	+	Nonsense_Mutation	SNP	C	C	T	rs372700633	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616C>T	p.Arg206Ter	p.R206*	ENST00000332145	4/4	37	14	23	33	33	0	ODF3L1,stop_gained,p.Arg206Ter,ENST00000332145,;DNM1P35,downstream_gene_variant,,ENST00000501931,;	T	ENSG00000182950	ENST00000332145	Transcript	stop_gained	839	616	206	R/*	Cga/Tga	rs372700633	.	.	1	ODF3L1	HGNC	28735	protein_coding	YES	CCDS10285.1	ENSP00000329584	OD3L1_HUMAN	.	UPI0000074378	.	.	.	4/4	.	hmmpanther:PTHR21580:SF3,hmmpanther:PTHR21580,Pfam_domain:PF07004	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCCCGACCT	.	5	ESCA
ISL2	0	.	GRCh37	15	76632669	76632669	+	Silent	SNP	G	G	A	rs748397463	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564G>A	p.%3D	p.T188T	ENST00000290759	4/6	23	16	6	26	26	0	ISL2,synonymous_variant,p.%3D,ENST00000290759,;RP11-685G9.4,upstream_gene_variant,,ENST00000602530,;RP11-685G9.2,non_coding_transcript_exon_variant,,ENST00000559539,;ISL2,missense_variant,p.Gly101Arg,ENST00000558656,;ISL2,downstream_gene_variant,,ENST00000558437,;	A	ENSG00000159556	ENST00000290759	Transcript	synonymous_variant	724	564	188	T	acG/acA	rs748397463	.	.	1	ISL2	HGNC	18524	protein_coding	YES	CCDS10290.1	ENSP00000290759	ISL2_HUMAN	.	UPI000012D8FC	.	.	.	4/6	.	hmmpanther:PTHR24204,hmmpanther:PTHR24204:SF2,Gene3D:1.10.10.60,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGACGGAGAA	.	5	ESCA
NTRK3	0	.	GRCh37	15	88420209	88420209	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2477C>T	p.Ala826Val	p.A826V	ENST00000360948	19/19	54	47	7	62	62	0	NTRK3,missense_variant,p.Ala818Val,ENST00000357724,;NTRK3,missense_variant,p.Ala804Val,ENST00000557856,;NTRK3,missense_variant,p.Ala812Val,ENST00000394480,;NTRK3,missense_variant,p.Ala812Val,ENST00000355254,;NTRK3,missense_variant,p.Ala826Val,ENST00000360948,;	A	ENSG00000140538	ENST00000360948	Transcript	missense_variant	2639	2477	826	A/V	gCt/gTt	.	.	.	-1	NTRK3	HGNC	8033	protein_coding	YES	CCDS32322.1	ENSP00000354207	NTRK3_HUMAN	R4GNH5_HUMAN	UPI000006DC82	.	tolerated(0.08)	benign(0.147)	19/19	.	hmmpanther:PTHR24416:SF66,hmmpanther:PTHR24416,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.L813F|c.2439G>T|3	RADIA|MUTECT|MUSE|VARSCANS	CCAAAGCATGG	.	4	ESCA
MESP2	0	.	GRCh37	15	90321579	90321579	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*14C>G	.	.	ENST00000341735	2/2	13	2	11	20	20	0	MESP2,3_prime_UTR_variant,,ENST00000560219,;MESP2,3_prime_UTR_variant,,ENST00000341735,;MESP2,non_coding_transcript_exon_variant,,ENST00000558723,;	G	ENSG00000188095	ENST00000341735	Transcript	3_prime_UTR_variant	1208	.	.	.	.	.	.	.	1	MESP2	HGNC	29659	protein_coding	YES	CCDS42078.1	ENSP00000342392	MESP2_HUMAN	.	UPI00006E232B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GGCTTCCCTCT	.	4	ESCA
MGRN1	0	.	GRCh37	16	4714709	4714709	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562-1G>A	.	p.X188_splice	ENST00000262370	.	52	41	11	89	89	0	MGRN1,splice_acceptor_variant,,ENST00000588994,;MGRN1,splice_acceptor_variant,,ENST00000415496,;MGRN1,splice_acceptor_variant,,ENST00000590790,;MGRN1,splice_acceptor_variant,,ENST00000262370,;MGRN1,splice_acceptor_variant,,ENST00000587747,;MGRN1,splice_acceptor_variant,,ENST00000399577,;MGRN1,splice_acceptor_variant,,ENST00000586183,;MGRN1,intron_variant,,ENST00000593224,;MGRN1,splice_acceptor_variant,,ENST00000587145,;MGRN1,upstream_gene_variant,,ENST00000588015,;MGRN1,upstream_gene_variant,,ENST00000591673,;MGRN1,splice_acceptor_variant,,ENST00000536343,;MGRN1,non_coding_transcript_exon_variant,,ENST00000590457,;	A	ENSG00000102858	ENST00000262370	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	MGRN1	HGNC	20254	protein_coding	YES	CCDS42115.1	ENSP00000262370	MGRN1_HUMAN	K7ERA1_HUMAN	UPI000018CE7F	.	.	.	.	5/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCAGCTGAA	.	5	ESCA
CNGB1	0	.	GRCh37	16	57965772	57965772	+	Silent	SNP	C	C	T	rs773350723	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1383G>A	p.%3D	p.T461T	ENST00000251102	17/33	30	26	3	57	57	0	CNGB1,synonymous_variant,p.%3D,ENST00000564448,;CNGB1,synonymous_variant,p.%3D,ENST00000251102,;CNGB1,non_coding_transcript_exon_variant,,ENST00000564654,;CNGB1,intron_variant,,ENST00000564450,;	T	ENSG00000070729	ENST00000251102	Transcript	synonymous_variant	1444	1383	461	T	acG/acA	rs773350723,COSM3510580	.	.	-1	CNGB1	HGNC	2151	protein_coding	YES	CCDS42169.1	ENSP00000251102	CNGB1_HUMAN	H3BQC3_HUMAN	UPI000013CCDF	.	.	.	17/33	.	hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF386	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGTTTCGTGGC	.	3	ESCA
FHOD1	0	.	GRCh37	16	67264528	67264528	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2834T>C	p.Ile945Thr	p.I945T	ENST00000258201	18/22	17	4	13	58	58	0	FHOD1,missense_variant,p.Ile945Thr,ENST00000258201,;TMEM208,downstream_gene_variant,,ENST00000304800,;LRRC29,upstream_gene_variant,,ENST00000433915,;TMEM208,downstream_gene_variant,,ENST00000563953,;LRRC29,upstream_gene_variant,,ENST00000393992,;TMEM208,downstream_gene_variant,,ENST00000565201,;LRRC29,upstream_gene_variant,,ENST00000409509,;LRRC29,upstream_gene_variant,,ENST00000447579,;LRRC29,upstream_gene_variant,,ENST00000424285,;AC040160.1,upstream_gene_variant,,ENST00000454102,;LRRC29,upstream_gene_variant,,ENST00000341546,;TMEM208,downstream_gene_variant,,ENST00000563426,;LRRC29,upstream_gene_variant,,ENST00000485549,;LRRC29,upstream_gene_variant,,ENST00000462169,;FHOD1,3_prime_UTR_variant,,ENST00000567561,;FHOD1,non_coding_transcript_exon_variant,,ENST00000567752,;FHOD1,non_coding_transcript_exon_variant,,ENST00000566006,;FHOD1,downstream_gene_variant,,ENST00000561922,;TMEM208,downstream_gene_variant,,ENST00000564649,;TMEM208,downstream_gene_variant,,ENST00000563168,;FHOD1,downstream_gene_variant,,ENST00000568595,;FHOD1,downstream_gene_variant,,ENST00000567509,;TMEM208,downstream_gene_variant,,ENST00000564087,;TMEM208,downstream_gene_variant,,ENST00000566486,;TMEM208,downstream_gene_variant,,ENST00000567193,;FHOD1,downstream_gene_variant,,ENST00000562266,;FHOD1,downstream_gene_variant,,ENST00000569888,;TMEM208,downstream_gene_variant,,ENST00000562235,;TMEM208,downstream_gene_variant,,ENST00000561586,;TMEM208,downstream_gene_variant,,ENST00000563271,;FHOD1,upstream_gene_variant,,ENST00000569085,;	G	ENSG00000135723	ENST00000258201	Transcript	missense_variant	3082	2834	945	I/T	aTa/aCa	.	.	.	-1	FHOD1	HGNC	17905	protein_coding	YES	CCDS10834.1	ENSP00000258201	FHOD1_HUMAN	.	UPI000013CFB9	.	deleterious(0.03)	benign(0.217)	18/22	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF189,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACTATCCTT	.	5	ESCA
ELAC2	0	.	GRCh37	17	12899085	12899085	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1743delC	p.Asn582ThrfsTer23	p.N582Tfs*23	ENST00000338034	19/24	31	27	4	25	25	0	ELAC2,frameshift_variant,p.Asn382ThrfsTer23,ENST00000584650,;ELAC2,frameshift_variant,p.Asn542ThrfsTer23,ENST00000426905,;ELAC2,frameshift_variant,p.Asn582ThrfsTer23,ENST00000338034,;ELAC2,frameshift_variant,p.Asn563ThrfsTer23,ENST00000395962,;ARHGAP44,downstream_gene_variant,,ENST00000340825,;ARHGAP44,downstream_gene_variant,,ENST00000379672,;ELAC2,downstream_gene_variant,,ENST00000446899,;ELAC2,non_coding_transcript_exon_variant,,ENST00000491478,;ELAC2,non_coding_transcript_exon_variant,,ENST00000484122,;ELAC2,non_coding_transcript_exon_variant,,ENST00000480891,;ELAC2,non_coding_transcript_exon_variant,,ENST00000492559,;ELAC2,non_coding_transcript_exon_variant,,ENST00000487229,;ELAC2,non_coding_transcript_exon_variant,,ENST00000465825,;ARHGAP44,downstream_gene_variant,,ENST00000580768,;ELAC2,downstream_gene_variant,,ENST00000578104,;ELAC2,downstream_gene_variant,,ENST00000578991,;ELAC2,downstream_gene_variant,,ENST00000476042,;	-	ENSG00000006744	ENST00000338034	Transcript	frameshift_variant	1983	1743	581	P/X	ccC/cc	.	.	.	-1	ELAC2	HGNC	14198	protein_coding	YES	CCDS11164.1	ENSP00000337445	RNZ2_HUMAN	Q9HAS7_HUMAN,J3QRS2_HUMAN,J3QL08_HUMAN,B4DT15_HUMAN	UPI000004A07E	.	.	.	19/24	.	hmmpanther:PTHR12553,hmmpanther:PTHR12553:SF44,Gene3D:3.60.15.10,Pfam_domain:PF12706,Superfamily_domains:SSF56281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CTGGTTGGGGGC	.	2	ESCA
MYO1C	0	.	GRCh37	17	1368846	1368846	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*174G>A	.	.	ENST00000359786	32/32	72	54	17	64	64	0	MYO1C,3_prime_UTR_variant,,ENST00000545534,;MYO1C,3_prime_UTR_variant,,ENST00000438665,;MYO1C,3_prime_UTR_variant,,ENST00000361007,;MYO1C,3_prime_UTR_variant,,ENST00000575158,;MYO1C,3_prime_UTR_variant,,ENST00000359786,;CRK,upstream_gene_variant,,ENST00000572145,;MYO1C,downstream_gene_variant,,ENST00000575011,;MYO1C,downstream_gene_variant,,ENST00000572615,;MYO1C,downstream_gene_variant,,ENST00000574341,;MYO1C,downstream_gene_variant,,ENST00000574308,;	T	ENSG00000197879	ENST00000359786	Transcript	3_prime_UTR_variant	3691	.	.	.	.	.	.	.	-1	MYO1C	HGNC	7597	protein_coding	YES	CCDS42226.1	ENSP00000352834	MYO1C_HUMAN	I3L4D4_HUMAN,I3L3Y6_HUMAN,I3L3F5_HUMAN,I3L204_HUMAN,I3L168_HUMAN	UPI0000200579	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAGCTCCTG	.	5	ESCA
ATPAF2	0	.	GRCh37	17	17925098	17925098	+	Missense_Mutation	SNP	C	C	T	rs778802460	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.577G>A	p.Val193Ile	p.V193I	ENST00000474627	6/8	24	12	11	22	22	0	ATPAF2,missense_variant,p.Val193Ile,ENST00000444058,;ATPAF2,missense_variant,p.Val193Ile,ENST00000474627,;ATPAF2,intron_variant,,ENST00000581698,;ATPAF2,intron_variant,,ENST00000585101,;LRRC48,downstream_gene_variant,,ENST00000313838,;LRRC48,downstream_gene_variant,,ENST00000399187,;ATPAF2,non_coding_transcript_exon_variant,,ENST00000469327,;LRRC48,downstream_gene_variant,,ENST00000583995,;ATPAF2,non_coding_transcript_exon_variant,,ENST00000496852,;ATPAF2,non_coding_transcript_exon_variant,,ENST00000465337,;ATPAF2,non_coding_transcript_exon_variant,,ENST00000488753,;ATPAF2,intron_variant,,ENST00000584205,;ATPAF2,intron_variant,,ENST00000462733,;ATPAF2,upstream_gene_variant,,ENST00000467560,;LRRC48,downstream_gene_variant,,ENST00000577477,;LRRC48,downstream_gene_variant,,ENST00000490517,;	T	ENSG00000171953	ENST00000474627	Transcript	missense_variant	732	577	193	V/I	Gtc/Atc	rs778802460	.	.	-1	ATPAF2	HGNC	18802	protein_coding	YES	CCDS32585.1	ENSP00000417190	ATPF2_HUMAN	C9J2Q2_HUMAN	UPI00000720DC	.	tolerated(0.33)	benign(0.001)	6/8	.	hmmpanther:PTHR21013,Gene3D:2r31A02,Superfamily_domains:SSF160909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGACGAGCA	byFrequency	5	ESCA
ASIC2	0	.	GRCh37	17	31618690	31618690	+	Missense_Mutation	SNP	C	C	G	rs753539011	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444G>C	p.Lys148Asn	p.K148N	ENST00000225823	1/10	37	18	19	70	70	0	ASIC2,missense_variant,p.Lys148Asn,ENST00000225823,;ASIC2,intron_variant,,ENST00000359872,;ASIC2,upstream_gene_variant,,ENST00000448983,;ASIC2,upstream_gene_variant,,ENST00000579816,;	G	ENSG00000108684	ENST00000225823	Transcript	missense_variant	1317	444	148	K/N	aaG/aaC	rs753539011	.	.	-1	ASIC2	HGNC	99	protein_coding	YES	CCDS11276.1	ENSP00000225823	ASIC2_HUMAN	B3KXQ3_HUMAN	UPI000013C881	.	tolerated(0.16)	possibly_damaging(0.639)	1/10	.	hmmpanther:PTHR11690:SF128,hmmpanther:PTHR11690,Pfam_domain:PF00858,Gene3D:2qtsA03	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCCTTGGA	.	5	ESCA
CACNB1	0	.	GRCh37	17	37343091	37343091	+	Missense_Mutation	SNP	C	C	T	rs746197912	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.506G>A	p.Arg169His	p.R169H	ENST00000394303	5/14	32	27	5	49	49	0	CACNB1,missense_variant,p.Arg169His,ENST00000344140,;CACNB1,missense_variant,p.Arg169His,ENST00000394303,;CACNB1,missense_variant,p.Arg169His,ENST00000394310,;CACNB1,non_coding_transcript_exon_variant,,ENST00000582877,;CACNB1,non_coding_transcript_exon_variant,,ENST00000492737,;CACNB1,non_coding_transcript_exon_variant,,ENST00000577582,;CACNB1,non_coding_transcript_exon_variant,,ENST00000536613,;CACNB1,non_coding_transcript_exon_variant,,ENST00000539338,;CACNB1,downstream_gene_variant,,ENST00000582414,;	T	ENSG00000067191	ENST00000394303	Transcript	missense_variant	714	506	169	R/H	cGc/cAc	rs746197912	.	.	-1	CACNB1	HGNC	1401	protein_coding	YES	CCDS42311.1	ENSP00000377840	CACB1_HUMAN	.	UPI0000127290	.	deleterious(0.02)	probably_damaging(0.996)	5/14	.	Superfamily_domains:SSF50044,Gene3D:2.30.30.40,hmmpanther:PTHR11824:SF6,hmmpanther:PTHR11824	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGGCGAAGG	.	4	ESCA
KPNB1	0	.	GRCh37	17	45750492	45750492	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1656G>T	p.Leu552Phe	p.L552F	ENST00000290158	13/22	31	24	6	61	61	0	KPNB1,missense_variant,p.Leu366Phe,ENST00000582097,;KPNB1,missense_variant,p.Leu407Phe,ENST00000535458,;KPNB1,missense_variant,p.Leu336Phe,ENST00000537679,;KPNB1,missense_variant,p.Leu407Phe,ENST00000540627,;KPNB1,missense_variant,p.Leu211Phe,ENST00000583013,;KPNB1,missense_variant,p.Leu552Phe,ENST00000290158,;KPNB1,non_coding_transcript_exon_variant,,ENST00000579901,;KPNB1,non_coding_transcript_exon_variant,,ENST00000578718,;KPNB1,non_coding_transcript_exon_variant,,ENST00000580019,;KPNB1,upstream_gene_variant,,ENST00000580573,;	T	ENSG00000108424	ENST00000290158	Transcript	missense_variant	2063	1656	552	L/F	ttG/ttT	COSM980472	.	.	1	KPNB1	HGNC	6400	protein_coding	YES	CCDS11513.1	ENSP00000290158	IMB1_HUMAN	J3QRG4_HUMAN,J3QR48_HUMAN,B7ZAV6_HUMAN	UPI0000001C21	.	tolerated(0.08)	benign(0.118)	13/22	.	hmmpanther:PTHR10527:SF1,hmmpanther:PTHR10527,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTGGTCAT	.	5	ESCA
MYCBPAP	0	.	GRCh37	17	48597137	48597137	+	Missense_Mutation	SNP	G	G	A	rs771543139	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1034G>A	p.Arg345Gln	p.R345Q	ENST00000323776	7/19	21	18	3	31	31	0	MYCBPAP,missense_variant,p.Arg308Gln,ENST00000436259,;MYCBPAP,missense_variant,p.Arg345Gln,ENST00000323776,;MYCBPAP,downstream_gene_variant,,ENST00000452039,;MYCBPAP,downstream_gene_variant,,ENST00000576179,;MYCBPAP,upstream_gene_variant,,ENST00000488432,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000468821,;MYCBPAP,missense_variant,p.Arg320Gln,ENST00000437498,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000470609,;MYCBPAP,downstream_gene_variant,,ENST00000458692,;MYCBPAP,upstream_gene_variant,,ENST00000459754,;	A	ENSG00000136449	ENST00000323776	Transcript	missense_variant	1196	1034	345	R/Q	cGg/cAg	rs771543139	.	.	1	MYCBPAP	HGNC	19677	protein_coding	YES	CCDS32680.2	ENSP00000323184	MYBPP_HUMAN	.	UPI0000E5A00B	.	tolerated(1)	benign(0.003)	7/19	.	hmmpanther:PTHR12276:SF44,hmmpanther:PTHR12276,Pfam_domain:PF14646	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CATCCGGGTGG	byFrequency	3	ESCA
USP32	0	.	GRCh37	17	58289386	58289386	+	Missense_Mutation	SNP	C	C	G	rs200946847	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2178G>C	p.Lys726Asn	p.K726N	ENST00000300896	19/34	53	48	5	40	40	0	USP32,missense_variant,p.Lys723Asn,ENST00000590133,;USP32,missense_variant,p.Lys396Asn,ENST00000592339,;USP32,missense_variant,p.Lys726Asn,ENST00000300896,;USP32,downstream_gene_variant,,ENST00000591768,;USP32,upstream_gene_variant,,ENST00000585720,;	G	ENSG00000170832	ENST00000300896	Transcript	missense_variant	2373	2178	726	K/N	aaG/aaC	rs200946847	.	.	-1	USP32	HGNC	19143	protein_coding	YES	CCDS32697.1	ENSP00000300896	UBP32_HUMAN	Q86WP5_HUMAN,Q6IRT0_HUMAN,Q4VC15_HUMAN,K7EQL6_HUMAN	UPI0000047AF8	.	tolerated(0.09)	probably_damaging(0.977)	19/34	.	hmmpanther:PTHR24006:SF392,hmmpanther:PTHR24006	T:0.0008	T:0	T:0	.	T:0.003	T:0	T:0.001	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTACCCTTGTG	byFrequency|byCluster|by1000G	4	ESCA
SLC16A13	0	.	GRCh37	17	6942095	6942095	+	Missense_Mutation	SNP	C	C	T	rs766655813	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.968C>T	p.Pro323Leu	p.P323L	ENST00000308027	3/4	32	27	5	32	32	0	SLC16A13,missense_variant,p.Pro323Leu,ENST00000308027,;SLC16A11,downstream_gene_variant,,ENST00000574600,;SLC16A11,downstream_gene_variant,,ENST00000308009,;SLC16A11,downstream_gene_variant,,ENST00000447225,;SLC16A11,downstream_gene_variant,,ENST00000573338,;SLC16A13,downstream_gene_variant,,ENST00000575844,;	T	ENSG00000174327	ENST00000308027	Transcript	missense_variant	1276	968	323	P/L	cCa/cTa	rs766655813	.	.	1	SLC16A13	HGNC	31037	protein_coding	YES	CCDS11085.1	ENSP00000309751	MOT13_HUMAN	.	UPI000015FA66	.	deleterious(0)	probably_damaging(0.997)	3/4	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF19,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCCCACTGG	.	4	ESCA
TP53	0	.	GRCh37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	C	rs28934574	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	8/11	34	0	34	50	50	0	TP53,missense_variant,p.Arg282Gly,ENST00000420246,;TP53,missense_variant,p.Arg282Gly,ENST00000269305,;TP53,missense_variant,p.Arg150Gly,ENST00000509690,;TP53,missense_variant,p.Arg282Gly,ENST00000359597,;TP53,missense_variant,p.Arg282Gly,ENST00000445888,;TP53,missense_variant,p.Arg282Gly,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1034	844	282	R/G	Cgg/Ggg	CM920678,CM056413,rs28934574,TP53_g.13824C>A,TP53_g.13824C>G,TP53_g.13824C>T,TP53_g.13824del,COSM43813,COSM10704,COSM10992,COSM44918,COSM99925,COSM99934,COSM3378339,COSM3675520,COSM1725698,COSM1636702	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.03)	benign(0.278)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	likely_benign,pathogenic	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1	25105660,25404506,22536362	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R282G|c.844C>G|5,SITE|p.R282G|c.844C>G|3,SITE|p.R282G|c.844C>G|29,CODON|p.0?|c.1_1182del1182|6,CODON|p.R282R|c.846G>A|4,CODON|p.R282Q|c.845G>A|5,CODON|p.R282Q|c.845G>A|26,CODON|p.R282L|c.845G>T|3,CODON|p.R282Q|c.845G>A|3,CODON|p.R282P|c.845G>C|17,CODON|p.R282W|c.843_844CC>TT|10,BUFFER|p.E285E|c.855G>A|3,BUFFER|p.E285V|c.854A>T|3,BUFFER|p.E285G|c.854A>G|4,BUFFER|p.E285V|c.854A>T|17,BUFFER|p.E285V|c.854A>T|4,BUFFER|p.E285K|c.853G>A|19,BUFFER|p.E285*|c.853G>T|5,BUFFER|p.E285K|c.853G>A|114,BUFFER|p.E285*|c.853G>T|9,BUFFER|p.E285Q|c.853G>C|4,BUFFER|p.E285*|c.853G>T|25,BUFFER|p.E285K|c.853G>A|5,BUFFER|p.E285K|c.853G>A|9,BUFFER|p.T284T|c.852A>T|3,BUFFER|p.T284A|c.850A>G|3,BUFFER|p.T284P|c.850A>C|8,BUFFER|p.R283fs*62|c.847delC|3,BUFFER|p.R283P|c.848G>C|4,BUFFER|p.R283H|c.848G>A|12,BUFFER|p.R283L|c.848G>T|4,BUFFER|p.R283P|c.848G>C|24,BUFFER|p.R283C|c.847C>T|19,BUFFER|p.R282W|c.844C>T|49,BUFFER|p.R282R|c.844C>A|3,BUFFER|p.R282W|c.844C>T|86,BUFFER|p.R282W|c.844C>T|450,BUFFER|p.R282W|c.844C>T|58,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12,BUFFER|p.D281V|c.842A>T|5,BUFFER|p.D281G|c.842A>G|10,BUFFER|p.D281H|c.841G>C|6,BUFFER|p.D281H|c.841G>C|28,BUFFER|p.D281H|c.841G>C|3,BUFFER|p.D281H|c.841G>C|4,BUFFER|p.D281Y|c.841G>T|7,BUFFER|p.D281N|c.841G>A|7,BUFFER|p.D281N|c.841G>A|3,BUFFER|p.D281Y|c.841G>T|13,BUFFER|p.D281Y|c.841G>T|4,BUFFER|p.D281N|c.841G>A|27,BUFFER|p.R280R|c.840A>G|3,BUFFER|p.R280S|c.840A>T|11,BUFFER|p.R280S|c.840A>C|6,BUFFER|p.R280T|c.839G>C|63,BUFFER|p.R280T|c.839G>C|4,BUFFER|p.R280I|c.839G>T|17,BUFFER|p.R280K|c.839G>A|17,BUFFER|p.R280K|c.839G>A|6,BUFFER|p.R280I|c.839G>T|4,BUFFER|p.R280K|c.839G>A|57,BUFFER|p.R280I|c.839G>T|3,BUFFER|p.R280T|c.839G>C|10,BUFFER|p.R280K|c.839G>A|11,BUFFER|p.R280*|c.838A>T|12,BUFFER|p.R280G|c.838A>G|6,BUFFER|p.R280G|c.838A>G|3,BUFFER|p.R280G|c.838A>G|23,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279E|c.836G>A|4,BUFFER|p.G279E|c.836G>A|34,BUFFER|p.G279V|c.836G>T|3,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278fs*67|c.833delC|3,BUFFER|p.P278F|c.832_833CC>TT|3,BUFFER|p.P278H|c.833C>A|15,BUFFER|p.P278R|c.833C>G|5,BUFFER|p.P278R|c.833C>G|30,BUFFER|p.P278R|c.833C>G|3,BUFFER|p.P278H|c.833C>A|3,BUFFER|p.P278L|c.833C>T|3,BUFFER|p.P278L|c.833C>T|11,BUFFER|p.P278L|c.833C>T|65,BUFFER|p.P278L|c.833C>T|8,BUFFER|p.P278fs*67|c.832delC|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCCGGTCTC	byFrequency|byCluster	5	ESCA
TCF3	0	.	GRCh37	19	1632397	1632397	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153G>T	p.Glu51Asp	p.E51D	ENST00000262965	4/19	21	14	6	28	28	0	TCF3,missense_variant,p.Glu51Asp,ENST00000588136,;TCF3,missense_variant,p.Glu51Asp,ENST00000344749,;TCF3,missense_variant,p.Glu51Asp,ENST00000587235,;TCF3,missense_variant,p.Glu51Asp,ENST00000586318,;TCF3,missense_variant,p.Glu51Asp,ENST00000262965,;TCF3,intron_variant,,ENST00000395423,;TCF3,upstream_gene_variant,,ENST00000453954,;	A	ENSG00000071564	ENST00000262965	Transcript	missense_variant	498	153	51	E/D	gaG/gaT	.	.	.	-1	TCF3	HGNC	11633	protein_coding	YES	CCDS12074.1	ENSP00000262965	TFE2_HUMAN	Q6PJU3_HUMAN,K7EPS2_HUMAN,K7ENI0_HUMAN,K7EKB9_HUMAN,B1NYC3_HUMAN	UPI0000136C80	.	tolerated(1)	benign(0.032)	4/19	.	hmmpanther:PTHR11793,hmmpanther:PTHR11793:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTCCTCAAG	.	5	ESCA
REXO1	0	.	GRCh37	19	1823683	1823683	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2118G>A	p.%3D	p.A706A	ENST00000170168	4/16	8	3	5	16	16	0	REXO1,synonymous_variant,p.%3D,ENST00000170168,;CTB-31O20.4,non_coding_transcript_exon_variant,,ENST00000593201,;CTB-31O20.4,non_coding_transcript_exon_variant,,ENST00000587741,;CTB-31O20.4,downstream_gene_variant,,ENST00000590531,;REXO1,downstream_gene_variant,,ENST00000587524,;REXO1,upstream_gene_variant,,ENST00000586343,;CTB-31O20.4,non_coding_transcript_exon_variant,,ENST00000590823,;REXO1,upstream_gene_variant,,ENST00000590936,;REXO1,upstream_gene_variant,,ENST00000588743,;	T	ENSG00000079313	ENST00000170168	Transcript	synonymous_variant	2213	2118	706	A	gcG/gcA	.	.	.	-1	REXO1	HGNC	24616	protein_coding	YES	CCDS32866.1	ENSP00000170168	REXO1_HUMAN	.	UPI0000202F63	.	.	.	4/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12801:SF62,hmmpanther:PTHR12801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCTCGCCGA	.	2	ESCA
RCN3	0	.	GRCh37	19	50031852	50031852	+	Silent	SNP	C	C	T	rs745347733	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>T	p.%3D	p.S41S	ENST00000270645	2/7	21	1	20	30	30	0	RCN3,synonymous_variant,p.%3D,ENST00000597801,;RCN3,synonymous_variant,p.%3D,ENST00000270645,;FCGRT,downstream_gene_variant,,ENST00000221466,;FCGRT,downstream_gene_variant,,ENST00000598076,;FCGRT,downstream_gene_variant,,ENST00000596975,;FCGRT,downstream_gene_variant,,ENST00000593381,;RCN3,upstream_gene_variant,,ENST00000598833,;FCGRT,downstream_gene_variant,,ENST00000599988,;FCGRT,downstream_gene_variant,,ENST00000426395,;RCN3,non_coding_transcript_exon_variant,,ENST00000593644,;FCGRT,downstream_gene_variant,,ENST00000594823,;FCGRT,downstream_gene_variant,,ENST00000593431,;FCGRT,downstream_gene_variant,,ENST00000596147,;FCGRT,downstream_gene_variant,,ENST00000598949,;FCGRT,downstream_gene_variant,,ENST00000598319,;FCGRT,downstream_gene_variant,,ENST00000598927,;FCGRT,downstream_gene_variant,,ENST00000598936,;FCGRT,downstream_gene_variant,,ENST00000452439,;FCGRT,downstream_gene_variant,,ENST00000595881,;	T	ENSG00000142552	ENST00000270645	Transcript	synonymous_variant	570	123	41	S	agC/agT	rs745347733	.	.	1	RCN3	HGNC	21145	protein_coding	YES	CCDS12771.1	ENSP00000270645	RCN3_HUMAN	.	UPI000000D8C5	.	.	.	2/7	.	hmmpanther:PTHR10827:SF47,hmmpanther:PTHR10827	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGCGACGC	byFrequency	5	ESCA
ZNF606	0	.	GRCh37	19	58514494	58514494	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-398G>C	.	.	ENST00000341164	1/7	10	6	4	12	12	0	ZNF606,5_prime_UTR_variant,,ENST00000341164,;CTD-2368P22.1,intron_variant,,ENST00000553254,;CTD-2368P22.1,intron_variant,,ENST00000547364,;CTD-2368P22.1,intron_variant,,ENST00000550135,;CTD-2368P22.1,intron_variant,,ENST00000546949,;ZNF606,upstream_gene_variant,,ENST00000547828,;ZNF606,upstream_gene_variant,,ENST00000552184,;ZNF606,upstream_gene_variant,,ENST00000536132,;ZNF606,upstream_gene_variant,,ENST00000547121,;ZNF606,upstream_gene_variant,,ENST00000546715,;ZNF606,upstream_gene_variant,,ENST00000551380,;ZNF606,upstream_gene_variant,,ENST00000552579,;CTD-2368P22.1,intron_variant,,ENST00000546956,;CTD-2368P22.1,intron_variant,,ENST00000313957,;ZNF606,upstream_gene_variant,,ENST00000550599,;ZNF606,upstream_gene_variant,,ENST00000550560,;	G	ENSG00000166704	ENST00000341164	Transcript	5_prime_UTR_variant	224	.	.	.	.	.	.	.	-1	ZNF606	HGNC	25879	protein_coding	YES	CCDS12968.1	ENSP00000343617	ZN606_HUMAN	Q9H7U2_HUMAN,F8W1C8_HUMAN,F5H208_HUMAN	UPI000013C35B	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GAGCTCGGCGA	.	2	ESCA
C3	0	.	GRCh37	19	6697509	6697509	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2642G>A	p.Arg881His	p.R881H	ENST00000245907	21/41	82	61	21	56	56	0	C3,missense_variant,p.Arg881His,ENST00000245907,;C3,non_coding_transcript_exon_variant,,ENST00000594005,;C3,upstream_gene_variant,,ENST00000598805,;C3,downstream_gene_variant,,ENST00000602053,;	T	ENSG00000125730	ENST00000245907	Transcript	missense_variant	2735	2642	881	R/H	cGt/cAt	.	.	.	-1	C3	HGNC	1318	protein_coding	YES	CCDS32883.1	ENSP00000245907	CO3_HUMAN	Q6LDJ0_HUMAN,M0R1Q1_HUMAN	UPI000013EC9B	.	deleterious(0.01)	benign(0.053)	21/41	.	hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF81	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGACGCCTC	.	5	ESCA
ZNF812	0	.	GRCh37	19	9801095	9801095	+	Missense_Mutation	SNP	C	C	T	rs772387534	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1084G>A	p.Gly362Arg	p.G362R	ENST00000457674	5/5	59	56	3	49	49	0	ZNF812,missense_variant,p.Gly362Arg,ENST00000457674,;ZNF812,downstream_gene_variant,,ENST00000590544,;ZNF812,downstream_gene_variant,,ENST00000585964,;ZNF812,non_coding_transcript_exon_variant,,ENST00000536819,;	T	ENSG00000224689	ENST00000457674	Transcript	missense_variant	1603	1084	362	G/R	Gga/Aga	rs772387534	.	.	-1	ZNF812	HGNC	33242	protein_coding	YES	CCDS54215.1	ENSP00000395629	ZN812_HUMAN	K7EN74_HUMAN,K7EK89_HUMAN	UPI0000E5A1A5	.	deleterious(0.02)	benign(0.003)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF199,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATCCATAAG	.	2	ESCA
CELSR2	0	.	GRCh37	1	109816112	109816112	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8564G>A	p.Arg2855Gln	p.R2855Q	ENST00000271332	33/34	19	11	7	21	21	0	CELSR2,missense_variant,p.Arg2855Gln,ENST00000271332,;CELSR2,non_coding_transcript_exon_variant,,ENST00000489018,;CELSR2,non_coding_transcript_exon_variant,,ENST00000498157,;	A	ENSG00000143126	ENST00000271332	Transcript	missense_variant	8625	8564	2855	R/Q	cGg/cAg	COSM1248053	.	.	1	CELSR2	HGNC	3231	protein_coding	YES	CCDS796.1	ENSP00000271332	CELR2_HUMAN	.	UPI00000015B6	.	deleterious_low_confidence(0.01)	benign(0.291)	33/34	.	hmmpanther:PTHR24026:SF32,hmmpanther:PTHR24026	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCGGCTCC	.	5	ESCA
CHD1L	0	.	GRCh37	1	146736211	146736211	+	Missense_Mutation	SNP	G	G	A	rs201333837	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.707G>A	p.Arg236His	p.R236H	ENST00000369258	7/23	46	43	3	13	13	0	CHD1L,missense_variant,p.Arg236His,ENST00000369258,;CHD1L,missense_variant,p.Arg236His,ENST00000431239,;CHD1L,intron_variant,,ENST00000369259,;CHD1L,intron_variant,,ENST00000361293,;CHD1L,non_coding_transcript_exon_variant,,ENST00000467213,;CHD1L,intron_variant,,ENST00000488864,;CHD1L,downstream_gene_variant,,ENST00000492728,;	A	ENSG00000131778	ENST00000369258	Transcript	missense_variant	727	707	236	R/H	cGc/cAc	rs201333837	.	.	1	CHD1L	HGNC	1916	protein_coding	YES	CCDS927.1	ENSP00000358262	CHD1L_HUMAN	B5MDZ7_HUMAN	UPI000020566F	.	tolerated(0.47)	benign(0.013)	7/23	.	Superfamily_domains:SSF52540,Pfam_domain:PF00176,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF558	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAACGCTACC	byCluster|by1000G	2	ESCA
BCL9	0	.	GRCh37	1	147096223	147096223	+	Silent	SNP	G	G	A	rs782211226	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3744G>A	p.%3D	p.T1248T	ENST00000234739	10/10	46	41	5	36	36	0	BCL9,synonymous_variant,p.%3D,ENST00000234739,;	A	ENSG00000116128	ENST00000234739	Transcript	synonymous_variant	4484	3744	1248	T	acG/acA	rs782211226	.	.	1	BCL9	HGNC	1008	protein_coding	YES	CCDS30833.1	ENSP00000234739	BCL9_HUMAN	.	UPI000013C9B9	.	.	.	10/10	.	hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGACGCTGCA	byFrequency	4	ESCA
FLG2	0	.	GRCh37	1	152331355	152331355	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6C>T	p.%3D	p.T2T	ENST00000388718	2/3	59	52	6	25	25	0	FLG2,synonymous_variant,p.%3D,ENST00000388718,;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;	A	ENSG00000143520	ENST00000388718	Transcript	synonymous_variant	79	6	2	T	acC/acT	.	.	.	-1	FLG2	HGNC	33276	protein_coding	YES	CCDS30861.1	ENSP00000373370	FILA2_HUMAN	.	UPI00004E1DE5	.	.	.	2/3	.	hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF24,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGTCGGTCAT	.	4	ESCA
NPR1	0	.	GRCh37	1	153655047	153655047	+	Silent	SNP	C	C	T	rs201584708	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245C>T	p.%3D	p.P415P	ENST00000368680	5/22	87	77	10	55	55	0	NPR1,synonymous_variant,p.%3D,ENST00000368680,;NPR1,downstream_gene_variant,,ENST00000413826,;	T	ENSG00000169418	ENST00000368680	Transcript	synonymous_variant	1717	1245	415	P	ccC/ccT	rs201584708	.	.	1	NPR1	HGNC	7943	protein_coding	YES	CCDS1051.1	ENSP00000357669	ANPRA_HUMAN	.	UPI0000125B3D	.	.	.	5/22	.	hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF232,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GATCCCGAGAA	byCluster	3	ESCA
SHE	0	.	GRCh37	1	154473951	154473951	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552C>T	p.%3D	p.P184P	ENST00000304760	1/6	87	73	14	57	57	0	SHE,synonymous_variant,p.%3D,ENST00000304760,;TDRD10,upstream_gene_variant,,ENST00000368482,;TDRD10,upstream_gene_variant,,ENST00000368480,;	A	ENSG00000169291	ENST00000304760	Transcript	synonymous_variant	639	552	184	P	ccC/ccT	.	.	.	-1	SHE	HGNC	27004	protein_coding	YES	CCDS30877.1	ENSP00000307369	SHE_HUMAN	.	UPI00004588E0	.	.	.	1/6	.	hmmpanther:PTHR15127,hmmpanther:PTHR15127:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCGGGCCC	.	5	ESCA
PLEKHM2	0	.	GRCh37	1	16054111	16054111	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000375799	9/20	28	25	3	26	26	0	PLEKHM2,missense_variant,p.Arg495Gln,ENST00000375793,;PLEKHM2,missense_variant,p.Arg515Gln,ENST00000375799,;RP11-288I21.1,intron_variant,,ENST00000453804,;PLEKHM2,upstream_gene_variant,,ENST00000477849,;	A	ENSG00000116786	ENST00000375799	Transcript	missense_variant	1771	1544	515	R/Q	cGg/cAg	.	.	.	1	PLEKHM2	HGNC	29131	protein_coding	YES	CCDS44063.1	ENSP00000364956	PKHM2_HUMAN	.	UPI00001C1D9C	.	tolerated_low_confidence(0.64)	benign(0.001)	9/20	.	hmmpanther:PTHR22835:SF132,hmmpanther:PTHR22835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTCGGCCCC	.	2	ESCA
NBPF1	0	.	GRCh37	1	16902825	16902825	+	Missense_Mutation	SNP	G	G	A	rs772049056	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2056C>T	p.Leu686Phe	p.L686F	ENST00000430580	19/29	326	257	69	386	386	0	NBPF1,missense_variant,p.Leu686Phe,ENST00000430580,;NBPF1,missense_variant,p.Leu51Phe,ENST00000287968,;NBPF1,missense_variant,p.Leu144Phe,ENST00000432949,;NBPF1,upstream_gene_variant,,ENST00000420031,;NBPF1,3_prime_UTR_variant,,ENST00000392963,;	A	ENSG00000219481	ENST00000430580	Transcript	missense_variant	2944	2056	686	L/F	Ctc/Ttc	rs772049056	.	.	-1	NBPF1	HGNC	26088	protein_coding	YES	.	ENSP00000474456	.	S4R3W5_HUMAN,S4R3K2_HUMAN,S4R3H5_HUMAN,Q3BBU8_HUMAN	UPI0000E04FDF	.	tolerated(0.39)	probably_damaging(0.996)	19/29	.	hmmpanther:PTHR14199:SF16,hmmpanther:PTHR14199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGAGGTCCT	byFrequency	4	ESCA
NR5A2	0	.	GRCh37	1	200144294	200144294	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*956A>G	.	.	ENST00000367362	8/8	21	13	8	12	12	0	NR5A2,3_prime_UTR_variant,,ENST00000236914,;NR5A2,3_prime_UTR_variant,,ENST00000367362,;NR5A2,downstream_gene_variant,,ENST00000544748,;	G	ENSG00000116833	ENST00000367362	Transcript	3_prime_UTR_variant	2828	.	.	.	.	.	.	.	1	NR5A2	HGNC	7984	protein_coding	YES	CCDS1401.1	ENSP00000356331	NR5A2_HUMAN	Q8WY08_HUMAN,B4E2P3_HUMAN	UPI0000130482	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTAAACAC	.	5	ESCA
LMOD1	0	.	GRCh37	1	201915358	201915358	+	Silent	SNP	G	G	A	rs774692839	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111C>T	p.%3D	p.D37D	ENST00000367288	1/3	92	70	21	57	57	0	LMOD1,synonymous_variant,p.%3D,ENST00000367288,;	A	ENSG00000163431	ENST00000367288	Transcript	synonymous_variant	358	111	37	D	gaC/gaT	rs774692839	.	.	-1	LMOD1	HGNC	6647	protein_coding	YES	CCDS53457.1	ENSP00000356257	LMOD1_HUMAN	B4DIX9_HUMAN	UPI00003665F4	.	.	.	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10901,hmmpanther:PTHR10901:SF5,Pfam_domain:PF03250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCACGTCCAG	.	5	ESCA
GPR37L1	0	.	GRCh37	1	202092359	202092359	+	Missense_Mutation	SNP	G	G	A	rs144676177	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268G>A	p.Gly90Ser	p.G90S	ENST00000367282	1/2	40	29	11	35	35	0	GPR37L1,missense_variant,p.Gly90Ser,ENST00000367282,;	A	ENSG00000170075	ENST00000367282	Transcript	missense_variant	374	268	90	G/S	Ggc/Agc	rs144676177	.	.	1	GPR37L1	HGNC	14923	protein_coding	YES	CCDS1420.1	ENSP00000356251	ETBR2_HUMAN	.	UPI000013E92C	.	tolerated(0.9)	benign(0.001)	1/2	.	hmmpanther:PTHR24243:SF33,hmmpanther:PTHR24243	C:0.0036	C:0.0129	C:0	.	C:0	C:0.001	C:0	C:0.0061	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCGGCAAG	byFrequency|byCluster|by1000G	5	ESCA
PLEKHA6	0	.	GRCh37	1	204237354	204237354	+	Silent	SNP	C	C	T	rs746976238	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189G>A	p.%3D	p.A63A	ENST00000272203	4/23	70	58	11	40	40	0	PLEKHA6,synonymous_variant,p.%3D,ENST00000414478,;PLEKHA6,synonymous_variant,p.%3D,ENST00000272203,;	T	ENSG00000143850	ENST00000272203	Transcript	synonymous_variant	506	189	63	A	gcG/gcA	rs746976238	.	.	-1	PLEKHA6	HGNC	17053	protein_coding	YES	CCDS1444.1	ENSP00000272203	PKHA6_HUMAN	.	UPI000013D935	.	.	.	4/23	.	PROSITE_profiles:PS50003,hmmpanther:PTHR12752:SF5,hmmpanther:PTHR12752,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCCCGCCTT	byFrequency	4	ESCA
FAM71A	0	.	GRCh37	1	212798804	212798804	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.585G>A	p.Met195Ile	p.M195I	ENST00000294829	1/1	46	24	22	19	19	0	FAM71A,missense_variant,p.Met195Ile,ENST00000294829,;ATF3,downstream_gene_variant,,ENST00000341491,;ATF3,downstream_gene_variant,,ENST00000366987,;RP11-338C15.5,non_coding_transcript_exon_variant,,ENST00000427949,;ATF3,downstream_gene_variant,,ENST00000492118,;	A	ENSG00000162771	ENST00000294829	Transcript	missense_variant	1016	585	195	M/I	atG/atA	.	.	.	1	FAM71A	HGNC	26541	protein_coding	YES	CCDS1507.1	ENSP00000294829	FA71A_HUMAN	.	UPI000013E1C2	.	tolerated(0.19)	benign(0.028)	1/1	.	hmmpanther:PTHR22574:SF9,hmmpanther:PTHR22574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATGCCTGT	.	5	ESCA
TGFB2	0	.	GRCh37	1	218519959	218519959	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-85T>C	.	.	ENST00000366929	1/8	23	15	8	14	14	0	TGFB2,5_prime_UTR_variant,,ENST00000366929,;TGFB2,5_prime_UTR_variant,,ENST00000366930,;RP11-224O19.2,upstream_gene_variant,,ENST00000414452,;TGFB2,upstream_gene_variant,,ENST00000488793,;	C	ENSG00000092969	ENST00000366929	Transcript	5_prime_UTR_variant	383	.	.	.	.	.	.	.	1	TGFB2	HGNC	11768	protein_coding	YES	CCDS44318.1	ENSP00000355896	TGFB2_HUMAN	.	UPI000016B0C1	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTCTCCTTG	.	5	ESCA
RAB3GAP2	0	.	GRCh37	1	220368697	220368699	+	In_Frame_Del	DEL	GAT	GAT	-	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	GAT	GAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.981_983delATC	p.Leu327_Ser328delinsPhe	p.L327_S328delinsF	ENST00000358951	11/35	56	50	6	30	30	0	RAB3GAP2,inframe_deletion,p.Leu327_Ser328delinsPhe,ENST00000358951,;RAB3GAP2,intron_variant,,ENST00000478976,;RAB3GAP2,downstream_gene_variant,,ENST00000237724,;	-	ENSG00000118873	ENST00000358951	Transcript	inframe_deletion	1098-1100	981-983	327-328	LS/F	ttATCc/ttc	.	.	.	-1	RAB3GAP2	HGNC	17168	protein_coding	YES	CCDS31028.1	ENSP00000351832	RBGPR_HUMAN	.	UPI0000072269	.	.	.	11/35	.	Pfam_domain:PF14655,hmmpanther:PTHR12472	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACATGGGATAATAA	.	3	ESCA
IBA57	0	.	GRCh37	1	228362718	228362718	+	Nonsense_Mutation	SNP	C	C	T	rs780008989	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.667C>T	p.Arg223Ter	p.R223*	ENST00000366711	2/3	43	40	3	37	37	0	IBA57,stop_gained,p.Arg223Ter,ENST00000366711,;IBA57,stop_gained,p.Arg30Ter,ENST00000546123,;IBA57,non_coding_transcript_exon_variant,,ENST00000484749,;	T	ENSG00000181873	ENST00000366711	Transcript	stop_gained	669	667	223	R/*	Cga/Tga	rs780008989	.	.	1	IBA57	HGNC	27302	protein_coding	YES	CCDS31046.1	ENSP00000355672	CAF17_HUMAN	G5EA38_HUMAN	UPI0000160A21	.	.	.	2/3	.	hmmpanther:PTHR22602:SF0,hmmpanther:PTHR22602,TIGRFAM_domain:TIGR03317,Pfam_domain:PF01571,Superfamily_domains:SSF103025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCACCGATAC	.	2	ESCA
TRIM17	0	.	GRCh37	1	228596974	228596974	+	Missense_Mutation	SNP	T	T	G	rs201224780	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.782A>C	p.Lys261Thr	p.K261T	ENST00000366697	5/6	76	57	19	46	46	0	TRIM17,missense_variant,p.Lys261Thr,ENST00000366697,;TRIM17,missense_variant,p.Lys261Thr,ENST00000456946,;TRIM17,missense_variant,p.Lys261Thr,ENST00000295033,;TRIM17,missense_variant,p.Lys261Thr,ENST00000366698,;TRIM17,missense_variant,p.Lys234Thr,ENST00000479800,;TRIM11,upstream_gene_variant,,ENST00000602308,;TRIM11,upstream_gene_variant,,ENST00000602582,;TRIM11,upstream_gene_variant,,ENST00000284551,;TRIM11,upstream_gene_variant,,ENST00000493030,;TRIM17,downstream_gene_variant,,ENST00000355586,;TRIM11,upstream_gene_variant,,ENST00000366699,;RP11-245P10.4,intron_variant,,ENST00000436779,;	G	ENSG00000162931	ENST00000366697	Transcript	missense_variant	1739	782	261	K/T	aAg/aCg	rs201224780	.	.	-1	TRIM17	HGNC	13430	protein_coding	YES	CCDS1571.1	ENSP00000355658	TRI17_HUMAN	J3KQG0_HUMAN,J3KNZ3_HUMAN,E5RJW6_HUMAN,E5RI62_HUMAN	UPI000000163B	.	tolerated(0.4)	benign(0.143)	5/6	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF313	C:0.0002	C:0	C:0	.	C:0.001	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCTTCCTC	byCluster|by1000G	5	ESCA
DHDDS	0	.	GRCh37	1	26793747	26793747	+	Intron	SNP	C	C	T	rs753068939	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766-1636C>T	.	.	ENST00000360009	.	41	29	12	40	40	0	DHDDS,intron_variant,,ENST00000416052,;DHDDS,intron_variant,,ENST00000431933,;DHDDS,intron_variant,,ENST00000360009,;DHDDS,intron_variant,,ENST00000526219,;DHDDS,intron_variant,,ENST00000236342,;DHDDS,intron_variant,,ENST00000525682,;RP3-476K8.3,non_coding_transcript_exon_variant,,ENST00000423060,;DHDDS,intron_variant,,ENST00000434391,;	T	ENSG00000117682	ENST00000360009	Transcript	intron_variant	.	.	.	.	.	rs753068939	.	.	1	DHDDS	HGNC	20603	protein_coding	YES	CCDS281.1	ENSP00000353104	DHDDS_HUMAN	Q5T0A2_HUMAN,E9PSH7_HUMAN,E9PRS7_HUMAN,E9PR24_HUMAN,E9PL99_HUMAN,E9PKJ5_HUMAN,E9PI64_HUMAN	UPI000003587D	.	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGCGCATC	.	5	ESCA
MAST2	0	.	GRCh37	1	46497918	46497918	+	Missense_Mutation	SNP	C	C	T	rs376892493	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3256C>T	p.Arg1086Trp	p.R1086W	ENST00000361297	25/29	66	28	37	56	56	0	MAST2,missense_variant,p.Arg1086Trp,ENST00000361297,;MAST2,missense_variant,p.Arg1016Trp,ENST00000372009,;MAST2,downstream_gene_variant,,ENST00000372008,;MAST2,upstream_gene_variant,,ENST00000492813,;MAST2,downstream_gene_variant,,ENST00000477968,;	T	ENSG00000086015	ENST00000361297	Transcript	missense_variant	3539	3256	1086	R/W	Cgg/Tgg	rs376892493	.	.	1	MAST2	HGNC	19035	protein_coding	YES	CCDS41326.1	ENSP00000354671	MAST2_HUMAN	Q9NT11_HUMAN	UPI0000458AEB	.	deleterious_low_confidence(0)	possibly_damaging(0.893)	25/29	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24356:SF136,hmmpanther:PTHR24356	.	.	.	.	.	.	.	T:0.0005	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCCGGGAC	byFrequency|byCluster	5	ESCA
CC2D1B	0	.	GRCh37	1	52821306	52821306	+	Missense_Mutation	SNP	G	G	A	rs746033572	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2179C>T	p.Arg727Trp	p.R727W	ENST00000371586	20/24	27	23	3	27	27	0	CC2D1B,missense_variant,p.Arg102Trp,ENST00000438831,;CC2D1B,missense_variant,p.Arg727Trp,ENST00000371586,;CC2D1B,missense_variant,p.Arg508Trp,ENST00000438021,;CC2D1B,missense_variant,p.Arg541Trp,ENST00000450942,;CC2D1B,missense_variant,p.Arg721Trp,ENST00000284376,;RP11-155O18.6,downstream_gene_variant,,ENST00000606527,;CC2D1B,non_coding_transcript_exon_variant,,ENST00000460261,;CC2D1B,downstream_gene_variant,,ENST00000494789,;CC2D1B,upstream_gene_variant,,ENST00000470844,;CC2D1B,non_coding_transcript_exon_variant,,ENST00000460370,;CC2D1B,non_coding_transcript_exon_variant,,ENST00000485966,;CC2D1B,non_coding_transcript_exon_variant,,ENST00000491136,;CC2D1B,upstream_gene_variant,,ENST00000492426,;	A	ENSG00000154222	ENST00000371586	Transcript	missense_variant	2318	2179	727	R/W	Cgg/Tgg	rs746033572,COSM1343364	.	.	-1	CC2D1B	HGNC	29386	protein_coding	YES	CCDS30714.1	ENSP00000360642	C2D1B_HUMAN	.	UPI00001609B7	.	deleterious(0)	probably_damaging(0.997)	20/24	.	hmmpanther:PTHR13076:SF5,hmmpanther:PTHR13076,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAACCGCACAA	.	3	ESCA
IL23R	0	.	GRCh37	1	67724850	67724850	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39C>T	.	.	ENST00000347310	11/11	22	2	20	16	16	0	IL23R,3_prime_UTR_variant,,ENST00000425614,;IL23R,3_prime_UTR_variant,,ENST00000347310,;IL23R,3_prime_UTR_variant,,ENST00000395227,;IL23R,3_prime_UTR_variant,,ENST00000371002,;IL23R,non_coding_transcript_exon_variant,,ENST00000473881,;	T	ENSG00000162594	ENST00000347310	Transcript	3_prime_UTR_variant	2100	.	.	.	.	.	.	.	1	IL23R	HGNC	19100	protein_coding	YES	CCDS637.1	ENSP00000321345	IL23R_HUMAN	D9N2T9_HUMAN,B6HY80_HUMAN	UPI000004CACD	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGCAATCT	.	5	ESCA
CCDC18	0	.	GRCh37	1	93730253	93730253	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3843-5T>C	.	.	ENST00000370276	.	10	6	3	12	12	0	CCDC18,splice_region_variant,,ENST00000334652,;CCDC18,splice_region_variant,,ENST00000401026,;CCDC18,splice_region_variant,,ENST00000557479,;CCDC18,splice_region_variant,,ENST00000343253,;CCDC18,splice_region_variant,,ENST00000338949,;CCDC18,splice_region_variant,,ENST00000370276,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000446528,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000455474,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000429859,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000457025,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000602488,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000415150,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000447577,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000424517,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000427669,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000414430,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000451302,;RP4-717I23.3,non_coding_transcript_exon_variant,,ENST00000442860,;RP4-717I23.3,intron_variant,,ENST00000413606,;CCDC18,splice_region_variant,,ENST00000447456,;	C	ENSG00000122483	ENST00000370276	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	CCDC18	HGNC	30370	protein_coding	YES	.	ENSP00000359299	.	.	UPI0001F78148	.	.	.	.	26/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCTATATAGA	.	3	ESCA
PHF20	0	.	GRCh37	20	34505482	34505482	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1902G>A	p.%3D	p.V634V	ENST00000374012	13/18	85	25	59	68	68	0	PHF20,synonymous_variant,p.%3D,ENST00000420233,;PHF20,synonymous_variant,p.%3D,ENST00000374012,;PHF20,3_prime_UTR_variant,,ENST00000439301,;PHF20,downstream_gene_variant,,ENST00000339089,;PHF20,downstream_gene_variant,,ENST00000374000,;PHF20,downstream_gene_variant,,ENST00000481202,;	A	ENSG00000025293	ENST00000374012	Transcript	synonymous_variant	2031	1902	634	V	gtG/gtA	.	.	.	1	PHF20	HGNC	16098	protein_coding	YES	CCDS13268.1	ENSP00000363124	PHF20_HUMAN	Q5JXL1_HUMAN,Q5JWZ0_HUMAN,B3KUL4_HUMAN	UPI000006E61B	.	.	.	13/18	.	hmmpanther:PTHR15856:SF27,hmmpanther:PTHR15856	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGTGACCAC	.	5	ESCA
C20orf62	0	.	GRCh37	20	43093921	43093921	+	5'UTR	SNP	C	C	T	rs571280917	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2G>A	.	.	ENST00000372910	1/2	38	34	4	26	26	0	C20orf62,5_prime_UTR_variant,,ENST00000372910,;C20orf62,5_prime_UTR_variant,,ENST00000306731,;RPL37AP1,downstream_gene_variant,,ENST00000412502,;	T	ENSG00000168746	ENST00000372910	Transcript	5_prime_UTR_variant	64	.	.	.	.	rs571280917	.	.	-1	C20orf62	HGNC	16195	protein_coding	YES	.	ENSP00000362001	CT062_HUMAN	.	UPI0000198842	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATTCGAAGC	byCluster	4	ESCA
DNTTIP1	0	.	GRCh37	20	44424079	44424079	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369G>T	p.Glu123Asp	p.E123D	ENST00000372622	4/13	25	19	5	27	27	0	DNTTIP1,missense_variant,p.Glu118Asp,ENST00000449078,;DNTTIP1,missense_variant,p.Glu123Asp,ENST00000372622,;DNTTIP1,missense_variant,p.Glu50Asp,ENST00000435014,;DNTTIP1,missense_variant,p.Glu83Asp,ENST00000415790,;DNTTIP1,intron_variant,,ENST00000456939,;WFDC3,upstream_gene_variant,,ENST00000243938,;WFDC3,upstream_gene_variant,,ENST00000337205,;WFDC3,upstream_gene_variant,,ENST00000471401,;WFDC3,upstream_gene_variant,,ENST00000487343,;WFDC3,upstream_gene_variant,,ENST00000493693,;WFDC3,upstream_gene_variant,,ENST00000481847,;WFDC3,upstream_gene_variant,,ENST00000467679,;WFDC3,upstream_gene_variant,,ENST00000462017,;WFDC3,upstream_gene_variant,,ENST00000490877,;WFDC3,upstream_gene_variant,,ENST00000465935,;	T	ENSG00000101457	ENST00000372622	Transcript	missense_variant	437	369	123	E/D	gaG/gaT	.	.	.	1	DNTTIP1	HGNC	16160	protein_coding	YES	CCDS13369.1	ENSP00000361705	TDIF1_HUMAN	F2Z2A4_HUMAN	UPI0000136B4E	.	tolerated(0.07)	benign(0.214)	4/13	.	hmmpanther:PTHR23399,hmmpanther:PTHR23399:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGCAGGT	.	5	ESCA
COL9A3	0	.	GRCh37	20	61472147	61472147	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63C>T	.	.	ENST00000343916	32/32	34	22	12	23	23	0	COL9A3,3_prime_UTR_variant,,ENST00000343916,;TCFL5,downstream_gene_variant,,ENST00000217162,;TCFL5,downstream_gene_variant,,ENST00000335351,;COL9A3,non_coding_transcript_exon_variant,,ENST00000467819,;COL9A3,non_coding_transcript_exon_variant,,ENST00000462700,;COL9A3,downstream_gene_variant,,ENST00000466532,;COL9A3,non_coding_transcript_exon_variant,,ENST00000466192,;COL9A3,downstream_gene_variant,,ENST00000472880,;COL9A3,downstream_gene_variant,,ENST00000481800,;COL9A3,downstream_gene_variant,,ENST00000469802,;COL9A3,downstream_gene_variant,,ENST00000469852,;COL9A3,downstream_gene_variant,,ENST00000490398,;DPH3P1,upstream_gene_variant,,ENST00000486648,;DPH3P1,upstream_gene_variant,,ENST00000502378,;	T	ENSG00000092758	ENST00000343916	Transcript	3_prime_UTR_variant	2121	.	.	.	.	.	.	.	1	COL9A3	HGNC	2219	protein_coding	YES	CCDS13505.1	ENSP00000341640	CO9A3_HUMAN	Q96IF4_HUMAN	UPI0000126D51	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGCGGGGG	.	5	ESCA
ITGB2	0	.	GRCh37	21	46320286	46320286	+	Silent	SNP	G	G	A	rs767870813	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.846C>T	p.%3D	p.N282N	ENST00000397850	8/17	89	80	9	72	72	0	ITGB2,synonymous_variant,p.%3D,ENST00000397850,;ITGB2,synonymous_variant,p.%3D,ENST00000320216,;ITGB2,synonymous_variant,p.%3D,ENST00000355153,;ITGB2,synonymous_variant,p.%3D,ENST00000397852,;ITGB2,synonymous_variant,p.%3D,ENST00000397857,;ITGB2,synonymous_variant,p.%3D,ENST00000302347,;ITGB2,synonymous_variant,p.%3D,ENST00000397854,;ITGB2,downstream_gene_variant,,ENST00000517563,;ITGB2,downstream_gene_variant,,ENST00000523663,;ITGB2,downstream_gene_variant,,ENST00000522688,;ITGB2,downstream_gene_variant,,ENST00000522931,;ITGB2,downstream_gene_variant,,ENST00000521987,;ITGB2,3_prime_UTR_variant,,ENST00000523323,;ITGB2,non_coding_transcript_exon_variant,,ENST00000498666,;ITGB2,downstream_gene_variant,,ENST00000520389,;	A	ENSG00000160255	ENST00000397850	Transcript	synonymous_variant	1299	846	282	N	aaC/aaT	rs767870813,COSM4102020	.	.	-1	ITGB2	HGNC	6155	protein_coding	YES	CCDS13716.1	ENSP00000380948	ITB2_HUMAN	Q96PT7_HUMAN,E7EVZ9_HUMAN,E5RK54_HUMAN,E5RK25_HUMAN,E5RIG7_HUMAN,E5RHT0_HUMAN,E5RHE6_HUMAN,E5RFI0_HUMAN	UPI000016A19B	.	.	.	8/17	.	Superfamily_domains:SSF53300,SMART_domains:SM00187,PIRSF_domain:PIRSF002512,Pfam_domain:PF00362,Gene3D:3.40.50.410,hmmpanther:PTHR10082:SF15,hmmpanther:PTHR10082	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCGTCGTTGGG	byFrequency	3	ESCA
COL18A1	0	.	GRCh37	21	46896265	46896283	+	Frame_Shift_Del	DEL	GGCGCGGCCCTAAAACCCA	GGCGCGGCCCTAAAACCCA	-	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	GGCGCGGCCCTAAAACCCA	GGCGCGGCCCTAAAACCCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1342_1360delGCGGCCCTAAAACCCAGGC	p.Ala448SerfsTer35	p.A448Sfs*35	ENST00000355480	5/41	25	16	9	31	31	0	COL18A1,frameshift_variant,p.Ala683SerfsTer35,ENST00000359759,;COL18A1,frameshift_variant,p.Ala448SerfsTer35,ENST00000355480,;COL18A1,frameshift_variant,p.Ala268SerfsTer35,ENST00000400337,;	-	ENSG00000182871	ENST00000355480	Transcript	frameshift_variant	1381-1399	1339-1357	447-453	GAALKPR/X	GGCGCGGCCCTAAAACCCAgg/gg	.	.	.	1	COL18A1	HGNC	2195	protein_coding	YES	CCDS42972.1	ENSP00000347665	COIA1_HUMAN	D3DSM5_HUMAN	UPI000016A19D	.	.	.	5/41	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CTCCAGGGCGCGGCCCTAAAACCCAGGCTC	.	2	ESCA
SYN3	0	.	GRCh37	22	32992674	32992674	+	Missense_Mutation	SNP	C	C	T	rs139005191	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.760G>A	p.Ala254Thr	p.A254T	ENST00000358763	7/14	61	57	4	49	49	0	SYN3,missense_variant,p.Ala254Thr,ENST00000358763,;SYN3,missense_variant,p.Ala254Thr,ENST00000332840,;	T	ENSG00000185666	ENST00000358763	Transcript	missense_variant	1003	760	254	A/T	Gct/Act	rs139005191	.	.	-1	SYN3	HGNC	11496	protein_coding	YES	CCDS13908.1	ENSP00000351614	SYN3_HUMAN	Q4TT46_HUMAN,Q17R54_HUMAN,A6ZJ82_HUMAN	UPI00001365D3	.	deleterious(0.01)	unknown(0)	7/14	.	hmmpanther:PTHR10841,PROSITE_patterns:PS00416,Gene3D:3.30.1490.20,Pfam_domain:PF02750,Superfamily_domains:SSF56059	.	.	.	.	.	.	.	T:0	T:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAGCGTGGG	byCluster	2	ESCA
EP300	0	.	GRCh37	22	41568668	41568668	+	Splice_Site	SNP	G	G	A	.	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4617+1G>A	.	p.X1539_splice	ENST00000263253	.	29	3	26	26	26	0	EP300,splice_donor_variant,,ENST00000263253,;RNU6-375P,downstream_gene_variant,,ENST00000517050,;RP1-85F18.6,intron_variant,,ENST00000415054,;RP1-85F18.5,downstream_gene_variant,,ENST00000420537,;	A	ENSG00000100393	ENST00000263253	Transcript	splice_donor_variant	.	.	.	.	.	COSM88793	.	.	1	EP300	HGNC	3373	protein_coding	YES	CCDS14010.1	ENSP00000263253	EP300_HUMAN	B5A250_HUMAN	UPI00001AE876	.	.	.	.	28/30	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.4617+1G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATGTAAGG	.	5	ESCA
SCUBE1	0	.	GRCh37	22	43600129	43600129	+	Silent	SNP	G	G	A	rs375344449	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2841C>T	p.%3D	p.F947F	ENST00000360835	22/22	35	22	13	21	21	0	SCUBE1,synonymous_variant,p.%3D,ENST00000360835,;	A	ENSG00000159307	ENST00000360835	Transcript	synonymous_variant	2968	2841	947	F	ttC/ttT	rs375344449	.	.	-1	SCUBE1	HGNC	13441	protein_coding	YES	CCDS14048.1	ENSP00000354080	SCUB1_HUMAN	.	UPI000020790F	.	.	.	22/22	.	hmmpanther:PTHR24046:SF4,hmmpanther:PTHR24046	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGTCGAAGAG	byCluster	5	ESCA
NPAS2	0	.	GRCh37	2	101549417	101549417	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227A>G	p.Lys76Arg	p.K76R	ENST00000335681	4/21	16	5	10	18	18	0	NPAS2,missense_variant,p.Lys62Arg,ENST00000451740,;NPAS2,missense_variant,p.Lys141Arg,ENST00000427413,;NPAS2,missense_variant,p.Lys76Arg,ENST00000335681,;NPAS2,missense_variant,p.Lys141Arg,ENST00000542504,;NPAS2,missense_variant,p.Lys66Arg,ENST00000448812,;NPAS2,non_coding_transcript_exon_variant,,ENST00000486017,;NPAS2,upstream_gene_variant,,ENST00000492373,;	G	ENSG00000170485	ENST00000335681	Transcript	missense_variant	512	227	76	K/R	aAg/aGg	.	.	.	1	NPAS2	HGNC	7895	protein_coding	YES	CCDS2048.1	ENSP00000338283	NPAS2_HUMAN	A2I2P5_HUMAN	UPI0000163B27	.	deleterious(0)	possibly_damaging(0.587)	4/21	.	hmmpanther:PTHR23042:SF4,hmmpanther:PTHR23042,Superfamily_domains:SSF47459,Prints_domain:PR00785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAAGCCTT	.	5	ESCA
ATP6V1C2	0	.	GRCh37	2	10863041	10863041	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66G>A	p.Met22Ile	p.M22I	ENST00000272238	2/14	51	42	9	79	79	0	ATP6V1C2,missense_variant,p.Met22Ile,ENST00000381661,;ATP6V1C2,missense_variant,p.Met22Ile,ENST00000272238,;AC092687.3,downstream_gene_variant,,ENST00000452909,;	A	ENSG00000143882	ENST00000272238	Transcript	missense_variant	175	66	22	M/I	atG/atA	.	.	.	1	ATP6V1C2	HGNC	18264	protein_coding	YES	CCDS42653.1	ENSP00000272238	VATC2_HUMAN	.	UPI0000208E71	.	deleterious(0.01)	benign(0.004)	2/14	.	hmmpanther:PTHR10137,hmmpanther:PTHR10137:SF1,Pfam_domain:PF03223,Superfamily_domains:0049812	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGAATAC	.	5	ESCA
SLC35F5	0	.	GRCh37	2	114492234	114492234	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.849C>T	p.%3D	p.I283I	ENST00000245680	9/16	31	28	3	33	33	0	SLC35F5,synonymous_variant,p.%3D,ENST00000447673,;SLC35F5,synonymous_variant,p.%3D,ENST00000245680,;SLC35F5,synonymous_variant,p.%3D,ENST00000409106,;	A	ENSG00000115084	ENST00000245680	Transcript	synonymous_variant	1263	849	283	I	atC/atT	.	.	.	-1	SLC35F5	HGNC	23617	protein_coding	YES	CCDS2119.1	ENSP00000245680	S35F5_HUMAN	.	UPI000004C648	.	.	.	9/16	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23051:SF0,hmmpanther:PTHR23051,Pfam_domain:PF00892,Superfamily_domains:0043518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAAGGATTAA	.	2	ESCA
RFTN2	0	.	GRCh37	2	198436723	198436723	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9G>A	.	.	ENST00000295049	9/9	43	36	6	39	39	0	RFTN2,3_prime_UTR_variant,,ENST00000295049,;RFTN2,downstream_gene_variant,,ENST00000454447,;RFTN2,non_coding_transcript_exon_variant,,ENST00000494346,;	T	ENSG00000162944	ENST00000295049	Transcript	3_prime_UTR_variant	2052	.	.	.	.	.	.	.	-1	RFTN2	HGNC	26402	protein_coding	YES	CCDS2323.1	ENSP00000295049	RFTN2_HUMAN	C9J6C2_HUMAN	UPI000013E1F9	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCACCTCAT	.	5	ESCA
GMPPA	0	.	GRCh37	2	220364857	220364857	+	Missense_Mutation	SNP	C	C	G	rs373605931	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55C>G	p.Pro19Ala	p.P19A	ENST00000358215	3/13	28	21	7	76	76	0	GMPPA,missense_variant,p.Pro19Ala,ENST00000455657,;GMPPA,missense_variant,p.Pro19Ala,ENST00000373908,;GMPPA,missense_variant,p.Pro19Ala,ENST00000341142,;GMPPA,missense_variant,p.Pro19Ala,ENST00000358215,;GMPPA,missense_variant,p.Pro19Ala,ENST00000373917,;GMPPA,missense_variant,p.Pro19Ala,ENST00000313597,;GMPPA,intron_variant,,ENST00000435316,;SPEG,downstream_gene_variant,,ENST00000412982,;AC053503.11,intron_variant,,ENST00000429882,;RP11-316O14.1,upstream_gene_variant,,ENST00000601508,;GMPPA,missense_variant,p.Pro19Ala,ENST00000443704,;GMPPA,non_coding_transcript_exon_variant,,ENST00000480506,;GMPPA,non_coding_transcript_exon_variant,,ENST00000481170,;SPEG,downstream_gene_variant,,ENST00000475104,;	G	ENSG00000144591	ENST00000358215	Transcript	missense_variant	424	55	19	P/A	Cct/Gct	rs373605931	.	.	1	GMPPA	HGNC	22923	protein_coding	YES	CCDS2441.1	ENSP00000350949	GMPPA_HUMAN	C9JAH0_HUMAN,C9J255_HUMAN	UPI000006D41C	.	deleterious(0)	probably_damaging(1)	3/13	.	hmmpanther:PTHR22572,hmmpanther:PTHR22572:SF85,Gene3D:3.90.550.10,Pfam_domain:PF00483,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGACCTTTG	byCluster	5	ESCA
SLC4A1AP	0	.	GRCh37	2	27892149	27892149	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1240G>A	p.Val414Met	p.V414M	ENST00000326019	5/14	31	1	30	39	38	0	SLC4A1AP,missense_variant,p.Val414Met,ENST00000326019,;SLC4A1AP,3_prime_UTR_variant,,ENST00000427424,;	A	ENSG00000163798	ENST00000326019	Transcript	missense_variant	1522	1240	414	V/M	Gtg/Atg	.	.	.	1	SLC4A1AP	HGNC	13813	protein_coding	YES	CCDS33166.1	ENSP00000323837	NADAP_HUMAN	B4DV74_HUMAN	UPI000006F66B	.	tolerated(0.11)	benign(0.285)	5/14	.	Pfam_domain:PF00035,hmmpanther:PTHR23308:SF2,hmmpanther:PTHR23308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTGGTGGCT	.	5	ESCA
EHBP1	0	.	GRCh37	2	63091905	63091905	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.902A>T	p.Asp301Val	p.D301V	ENST00000263991	10/25	18	1	16	20	20	0	EHBP1,missense_variant,p.Asp266Val,ENST00000405482,;EHBP1,missense_variant,p.Asp301Val,ENST00000263991,;EHBP1,missense_variant,p.Asp266Val,ENST00000354487,;EHBP1,missense_variant,p.Asp266Val,ENST00000405289,;EHBP1,missense_variant,p.Asp266Val,ENST00000405015,;EHBP1,missense_variant,p.Asp266Val,ENST00000431489,;	T	ENSG00000115504	ENST00000263991	Transcript	missense_variant	1384	902	301	D/V	gAc/gTc	.	.	.	1	EHBP1	HGNC	29144	protein_coding	YES	CCDS1872.1	ENSP00000263991	EHBP1_HUMAN	C9K0H9_HUMAN,C9JEP1_HUMAN,C9J268_HUMAN,B3KM32_HUMAN	UPI000013D49A	.	deleterious(0.01)	benign(0.147)	10/25	.	hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF124	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGACTCTT	.	5	ESCA
DYSF	0	.	GRCh37	2	71827929	71827929	+	Nonsense_Mutation	SNP	C	C	A	rs759487846	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3854C>A	p.Ser1285Ter	p.S1285*	ENST00000410020	34/56	48	38	9	61	61	0	DYSF,stop_gained,p.Ser1285Ter,ENST00000410020,;DYSF,stop_gained,p.Ser1268Ter,ENST00000394120,;DYSF,stop_gained,p.Ser1268Ter,ENST00000409366,;DYSF,stop_gained,p.Ser1267Ter,ENST00000258104,;DYSF,stop_gained,p.Ser1284Ter,ENST00000409582,;DYSF,stop_gained,p.Ser1267Ter,ENST00000429174,;DYSF,stop_gained,p.Ser1254Ter,ENST00000409744,;DYSF,stop_gained,p.Ser1284Ter,ENST00000409762,;DYSF,stop_gained,p.Ser1285Ter,ENST00000410041,;DYSF,stop_gained,p.Ser1299Ter,ENST00000409651,;DYSF,stop_gained,p.Ser1298Ter,ENST00000413539,;DYSF,non_coding_transcript_exon_variant,,ENST00000493767,;DYSF,non_coding_transcript_exon_variant,,ENST00000475076,;DYSF,non_coding_transcript_exon_variant,,ENST00000479049,;DYSF,upstream_gene_variant,,ENST00000487180,;DYSF,upstream_gene_variant,,ENST00000472873,;DYSF,upstream_gene_variant,,ENST00000494501,;	A	ENSG00000135636	ENST00000410020	Transcript	stop_gained	3995	3854	1285	S/*	tCg/tAg	rs759487846	.	.	1	DYSF	HGNC	3097	protein_coding	YES	CCDS46328.1	ENSP00000386881	DYSF_HUMAN	A0FK00_HUMAN	UPI000171F710	.	.	.	34/56	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF35,Gene3D:2.60.40.150,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGTCGGGGG	.	5	ESCA
KRCC1	0	.	GRCh37	2	88333726	88333726	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96C>T	.	.	ENST00000347055	3/4	22	10	12	29	29	0	KRCC1,5_prime_UTR_variant,,ENST00000347055,;	A	ENSG00000172086	ENST00000347055	Transcript	5_prime_UTR_variant	299	.	.	.	.	.	.	.	-1	KRCC1	HGNC	28039	protein_coding	YES	CCDS2000.1	ENSP00000340083	KRCC1_HUMAN	.	UPI000004A006	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATAGTGAGA	.	5	ESCA
ZPLD1	0	.	GRCh37	3	102196570	102196570	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*108G>T	.	.	ENST00000306176	11/11	9	3	6	9	9	0	ZPLD1,3_prime_UTR_variant,,ENST00000306176,;ZPLD1,downstream_gene_variant,,ENST00000466937,;ZPLD1,downstream_gene_variant,,ENST00000491959,;	T	ENSG00000170044	ENST00000306176	Transcript	3_prime_UTR_variant	1504	.	.	.	.	.	.	.	1	ZPLD1	HGNC	27022	protein_coding	YES	CCDS2947.1	ENSP00000307801	ZPLD1_HUMAN	.	UPI000006EC89	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGTAGGTTTG	.	2	ESCA
ILDR1	0	.	GRCh37	3	121724090	121724090	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.379+1G>A	.	p.X127_splice	ENST00000344209	.	35	32	3	25	25	0	ILDR1,splice_donor_variant,,ENST00000393631,;ILDR1,splice_donor_variant,,ENST00000273691,;ILDR1,splice_donor_variant,,ENST00000344209,;ILDR1,splice_donor_variant,,ENST00000462014,;ILDR1,splice_donor_variant,,ENST00000460554,;	T	ENSG00000145103	ENST00000344209	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	ILDR1	HGNC	28741	protein_coding	YES	CCDS56271.1	ENSP00000345667	ILDR1_HUMAN	.	UPI00003FF1E2	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ACTCACGGTTC	.	3	ESCA
KALRN	0	.	GRCh37	3	124281861	124281861	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.220G>C	p.Val74Leu	p.V74L	ENST00000393496	2/16	49	31	18	36	36	0	KALRN,missense_variant,p.Val74Leu,ENST00000393496,;KALRN,missense_variant,p.Val1670Leu,ENST00000354186,;KALRN,missense_variant,p.Val1701Leu,ENST00000360013,;KALRN,non_coding_transcript_exon_variant,,ENST00000471431,;	C	ENSG00000160145	ENST00000393496	Transcript	missense_variant	384	220	74	V/L	Gtc/Ctc	.	.	.	1	KALRN	HGNC	4814	protein_coding	.	.	ENSP00000377134	KALRN_HUMAN	E7EUZ8_HUMAN	UPI00001C0BD5	.	tolerated(0.14)	benign(0.04)	2/16	.	Superfamily_domains:SSF50044,SMART_domains:SM00326,Pfam_domain:PF00018,Gene3D:2.30.30.40,PROSITE_profiles:PS50002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGGTCCCC	.	5	ESCA
DNAJB8	0	.	GRCh37	3	128182859	128182859	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-771G>A	.	.	ENST00000469083	2/2	28	14	13	27	27	0	DNAJB8,5_prime_UTR_variant,,ENST00000319153,;DNAJB8,5_prime_UTR_variant,,ENST00000469083,;DNAJB8-AS1,non_coding_transcript_exon_variant,,ENST00000471626,;	T	ENSG00000179407	ENST00000469083	Transcript	5_prime_UTR_variant	1788	.	.	.	.	.	.	.	-1	DNAJB8	HGNC	23699	protein_coding	YES	CCDS3048.1	ENSP00000417418	DNJB8_HUMAN	.	UPI0000129437	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTGCTCAAG	.	5	ESCA
POLR2H	0	.	GRCh37	3	184086034	184086034	+	Silent	SNP	C	C	T	rs776845280	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405C>T	p.%3D	p.F135F	ENST00000456318	6/6	86	62	24	48	48	0	POLR2H,stop_gained,p.Arg157Ter,ENST00000429568,;POLR2H,synonymous_variant,p.%3D,ENST00000430783,;POLR2H,synonymous_variant,p.%3D,ENST00000296223,;POLR2H,synonymous_variant,p.%3D,ENST00000456318,;POLR2H,synonymous_variant,p.%3D,ENST00000438240,;POLR2H,synonymous_variant,p.%3D,ENST00000452961,;POLR2H,synonymous_variant,p.%3D,ENST00000455712,;POLR2H,synonymous_variant,p.%3D,ENST00000443489,;EIF2B5,intron_variant,,ENST00000444495,;THPO,downstream_gene_variant,,ENST00000445696,;THPO,downstream_gene_variant,,ENST00000204615,;POLR2H,downstream_gene_variant,,ENST00000412877,;THPO,downstream_gene_variant,,ENST00000421442,;POLR2H,downstream_gene_variant,,ENST00000460083,;THPO,downstream_gene_variant,,ENST00000477594,;POLR2H,non_coding_transcript_exon_variant,,ENST00000488213,;POLR2H,non_coding_transcript_exon_variant,,ENST00000476003,;POLR2H,non_coding_transcript_exon_variant,,ENST00000489043,;POLR2H,downstream_gene_variant,,ENST00000490958,;	T	ENSG00000163882	ENST00000456318	Transcript	synonymous_variant	1454	405	135	F	ttC/ttT	rs776845280	.	.	1	POLR2H	HGNC	9195	protein_coding	YES	CCDS3264.1	ENSP00000392913	RPAB3_HUMAN	C9JLU1_HUMAN,C9JBJ6_HUMAN	UPI0000021AB9	.	.	.	6/6	.	hmmpanther:PTHR10917:SF0,hmmpanther:PTHR10917,Pfam_domain:PF03870,Gene3D:2.40.50.140,PIRSF_domain:PIRSF000779,SMART_domains:SM00658,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATTCGAGGT	byFrequency	5	ESCA
THPO	0	.	GRCh37	3	184094123	184094123	+	5'UTR	SNP	C	C	T	rs572059358	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-76G>A	.	.	ENST00000204615	2/6	72	58	13	46	46	0	THPO,5_prime_UTR_variant,,ENST00000445696,;THPO,5_prime_UTR_variant,,ENST00000204615,;EIF2B5,intron_variant,,ENST00000444495,;CHRD,upstream_gene_variant,,ENST00000450923,;CHRD,upstream_gene_variant,,ENST00000204604,;CHRD,upstream_gene_variant,,ENST00000310236,;CHRD,upstream_gene_variant,,ENST00000348986,;THPO,upstream_gene_variant,,ENST00000421442,;THPO,upstream_gene_variant,,ENST00000477594,;CHRD,upstream_gene_variant,,ENST00000482805,;CHRD,upstream_gene_variant,,ENST00000459711,;CHRD,upstream_gene_variant,,ENST00000470150,;CHRD,upstream_gene_variant,,ENST00000356534,;CHRD,upstream_gene_variant,,ENST00000460627,;CHRD,upstream_gene_variant,,ENST00000496527,;CHRD,upstream_gene_variant,,ENST00000448472,;CHRD,upstream_gene_variant,,ENST00000420973,;CHRD,upstream_gene_variant,,ENST00000485883,;CHRD,upstream_gene_variant,,ENST00000486066,;CHRD,upstream_gene_variant,,ENST00000461684,;	T	ENSG00000090534	ENST00000204615	Transcript	5_prime_UTR_variant	140	.	.	.	.	rs572059358	.	.	-1	THPO	HGNC	11795	protein_coding	YES	CCDS3265.1	ENSP00000204615	TPO_HUMAN	.	UPI000004A8D1	.	.	.	2/6	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGGCGGCTT	by1000G	5	ESCA
OXSR1	0	.	GRCh37	3	38296471	38296471	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2089G>A	.	.	ENST00000311806	18/18	49	42	7	68	68	0	OXSR1,3_prime_UTR_variant,,ENST00000311806,;OXSR1,downstream_gene_variant,,ENST00000446845,;OXSR1,downstream_gene_variant,,ENST00000467900,;	A	ENSG00000172939	ENST00000311806	Transcript	3_prime_UTR_variant	4045	.	.	.	.	.	.	.	1	OXSR1	HGNC	8508	protein_coding	YES	CCDS2675.1	ENSP00000311713	OXSR1_HUMAN	.	UPI000006E0D0	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATGTCCCA	.	5	ESCA
CCDC71	0	.	GRCh37	3	49201104	49201104	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538G>A	p.Glu180Lys	p.E180K	ENST00000321895	2/2	22	16	5	39	39	0	CCDC71,missense_variant,p.Glu180Lys,ENST00000321895,;RP11-694I15.7,upstream_gene_variant,,ENST00000603877,;	T	ENSG00000177352	ENST00000321895	Transcript	missense_variant	645	538	180	E/K	Gag/Aag	COSM1309254	.	.	-1	CCDC71	HGNC	25760	protein_coding	YES	CCDS2790.1	ENSP00000319006	CCD71_HUMAN	.	UPI0000072BC0	.	deleterious(0)	probably_damaging(0.997)	2/2	.	hmmpanther:PTHR14484:SF0,hmmpanther:PTHR14484,Pfam_domain:PF15374	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCAAGGA	.	5	ESCA
TET2	0	.	GRCh37	4	106162811	106162811	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3500+225C>T	.	.	ENST00000540549	.	23	16	7	22	22	0	TET2,3_prime_UTR_variant,,ENST00000305737,;TET2,3_prime_UTR_variant,,ENST00000413648,;TET2,3_prime_UTR_variant,,ENST00000394764,;TET2,intron_variant,,ENST00000540549,;TET2,intron_variant,,ENST00000513237,;TET2,intron_variant,,ENST00000380013,;TET2,intron_variant,,ENST00000545826,;TET2,intron_variant,,ENST00000265149,;	T	ENSG00000168769	ENST00000540549	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TET2	HGNC	25941	protein_coding	YES	CCDS47120.1	ENSP00000442788	TET2_HUMAN	E7EPB1_HUMAN,D6RE87_HUMAN	UPI00001D75E4	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGCGATGG	.	5	ESCA
ANK2	0	.	GRCh37	4	114276595	114276595	+	Missense_Mutation	SNP	G	G	A	rs780257265	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6821G>A	p.Arg2274His	p.R2274H	ENST00000357077	38/46	12	1	11	8	8	0	ANK2,missense_variant,p.Arg2241His,ENST00000264366,;ANK2,missense_variant,p.Arg2274His,ENST00000357077,;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000394537,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,intron_variant,,ENST00000506722,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,intron_variant,,ENST00000508007,;ANK2,downstream_gene_variant,,ENST00000512298,;	A	ENSG00000145362	ENST00000357077	Transcript	missense_variant	6874	6821	2274	R/H	cGt/cAt	rs780257265	.	.	1	ANK2	HGNC	493	protein_coding	YES	CCDS3702.1	ENSP00000349588	ANK2_HUMAN	D6RHC5_HUMAN	UPI0000441EF3	.	.	benign(0.001)	38/46	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AATTCGTTCAG	byFrequency|byCluster	2	ESCA
PCDH18	0	.	GRCh37	4	138441619	138441619	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*564G>A	.	.	ENST00000344876	4/4	9	6	3	11	11	0	PCDH18,3_prime_UTR_variant,,ENST00000344876,;PCDH18,3_prime_UTR_variant,,ENST00000507846,;PCDH18,3_prime_UTR_variant,,ENST00000412923,;PCDH18,downstream_gene_variant,,ENST00000510305,;PCDH18,downstream_gene_variant,,ENST00000511115,;	T	ENSG00000189184	ENST00000344876	Transcript	3_prime_UTR_variant	4359	.	.	.	.	.	.	.	-1	PCDH18	HGNC	14268	protein_coding	YES	CCDS34064.1	ENSP00000355082	PCD18_HUMAN	Q9NT87_HUMAN,B4DQ29_HUMAN	UPI0000047A88	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATAAACTTTCA	.	2	ESCA
TENM3	0	.	GRCh37	4	183652249	183652249	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2924T>A	p.Phe975Tyr	p.F975Y	ENST00000511685	16/28	47	27	19	48	47	0	TENM3,missense_variant,p.Phe975Tyr,ENST00000511685,;TENM3,missense_variant,p.Phe975Tyr,ENST00000406950,;TENM3,non_coding_transcript_exon_variant,,ENST00000502950,;	A	ENSG00000218336	ENST00000511685	Transcript	missense_variant	3047	2924	975	F/Y	tTc/tAc	.	.	.	1	TENM3	HGNC	29944	protein_coding	YES	CCDS47165.1	ENSP00000424226	TEN3_HUMAN	G3CAS9_HUMAN,D6RGC5_HUMAN	UPI00006C0820	.	tolerated(1)	possibly_damaging(0.483)	16/28	.	hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTTCAGAT	.	5	ESCA
SLIT2	0	.	GRCh37	4	20543179	20543179	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2080C>G	p.Pro694Ala	p.P694A	ENST00000504154	20/37	59	47	12	61	61	0	SLIT2,missense_variant,p.Pro698Ala,ENST00000273739,;SLIT2,missense_variant,p.Pro694Ala,ENST00000504154,;SLIT2,missense_variant,p.Pro686Ala,ENST00000503823,;SLIT2,missense_variant,p.Pro690Ala,ENST00000503837,;SLIT2,upstream_gene_variant,,ENST00000511508,;SLIT2,upstream_gene_variant,,ENST00000509394,;SLIT2,downstream_gene_variant,,ENST00000509099,;	G	ENSG00000145147	ENST00000504154	Transcript	missense_variant	2332	2080	694	P/A	Cca/Gca	.	.	.	1	SLIT2	HGNC	11086	protein_coding	YES	CCDS3426.1	ENSP00000422591	SLIT2_HUMAN	Q4W5N0_HUMAN,Q4W5K2_HUMAN,B3KNE2_HUMAN	UPI00000747E4	.	deleterious(0)	probably_damaging(0.998)	20/37	.	hmmpanther:PTHR24373:SF107,hmmpanther:PTHR24373,Gene3D:3.80.10.10,Pfam_domain:PF01463,SMART_domains:SM00082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAACCATAC	.	5	ESCA
C4orf50	0	.	GRCh37	4	5981916	5981916	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1575G>A	p.%3D	p.E525E	ENST00000531445	2/7	54	44	9	45	45	0	C4orf50,synonymous_variant,p.%3D,ENST00000324058,;C4orf50,synonymous_variant,p.%3D,ENST00000531445,;	T	ENSG00000181215	ENST00000531445	Transcript	synonymous_variant	1622	1575	525	E	gaG/gaA	.	.	.	-1	C4orf50	HGNC	33766	protein_coding	YES	.	ENSP00000437121	.	E9PNW5_HUMAN	UPI0001F7863C	.	.	.	2/7	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15030	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCCTCCTG	.	5	ESCA
MAN2B2	0	.	GRCh37	4	6578408	6578408	+	Missense_Mutation	SNP	G	G	A	rs750214368	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242G>A	p.Arg81Gln	p.R81Q	ENST00000285599	2/19	35	28	6	36	36	0	MAN2B2,missense_variant,p.Arg81Gln,ENST00000504248,;MAN2B2,missense_variant,p.Arg80Gln,ENST00000505907,;MAN2B2,missense_variant,p.Arg81Gln,ENST00000285599,;	A	ENSG00000013288	ENST00000285599	Transcript	missense_variant	278	242	81	R/Q	cGg/cAg	rs750214368	.	.	1	MAN2B2	HGNC	29623	protein_coding	YES	CCDS33951.1	ENSP00000285599	MA2B2_HUMAN	Q05BN7_HUMAN,B3KQN1_HUMAN	UPI000004BF05	.	deleterious(0.01)	probably_damaging(0.999)	2/19	.	hmmpanther:PTHR11607:SF5,hmmpanther:PTHR11607,Gene3D:3.20.110.10,Pfam_domain:PF01074,Superfamily_domains:SSF88713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCGGCTGT	byFrequency	5	ESCA
CENPC	0	.	GRCh37	4	68338319	68338319	+	3'UTR	SNP	T	T	C	rs746222121	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4A>G	.	.	ENST00000273853	19/19	30	6	24	50	50	0	CENPC,3_prime_UTR_variant,,ENST00000273853,;RP11-584P21.2,upstream_gene_variant,,ENST00000502400,;CENPC,3_prime_UTR_variant,,ENST00000506882,;CENPC,3_prime_UTR_variant,,ENST00000513216,;CENPC,downstream_gene_variant,,ENST00000515140,;	C	ENSG00000145241	ENST00000273853	Transcript	3_prime_UTR_variant	3087	.	.	.	.	rs746222121	.	.	-1	CENPC	HGNC	1854	protein_coding	YES	CCDS47063.1	ENSP00000273853	CENPC_HUMAN	.	UPI00004135A3	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGATCTTTC	byFrequency	5	ESCA
UTP3	0	.	GRCh37	4	71554228	71554228	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-167C>T	.	.	ENST00000254803	1/1	12	2	10	17	17	0	UTP3,5_prime_UTR_variant,,ENST00000254803,;ENAM,downstream_gene_variant,,ENST00000472903,;	T	ENSG00000132467	ENST00000254803	Transcript	5_prime_UTR_variant	33	.	.	.	.	.	.	.	1	UTP3	HGNC	24477	protein_coding	YES	CCDS3546.1	ENSP00000254803	SAS10_HUMAN	.	UPI0000073D63	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGGCCGGAA	.	2	ESCA
ALB	0	.	GRCh37	4	74283887	74283887	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1511C>T	p.Ser504Phe	p.S504F	ENST00000295897	12/15	33	27	5	30	30	0	ALB,missense_variant,p.Ser504Phe,ENST00000509063,;ALB,missense_variant,p.Ser349Phe,ENST00000511370,;ALB,missense_variant,p.Ser312Phe,ENST00000415165,;ALB,missense_variant,p.Ser504Phe,ENST00000295897,;ALB,missense_variant,p.Ser354Phe,ENST00000503124,;ALB,missense_variant,p.Ser389Phe,ENST00000401494,;ALB,non_coding_transcript_exon_variant,,ENST00000505649,;ALB,upstream_gene_variant,,ENST00000495173,;ALB,3_prime_UTR_variant,,ENST00000476441,;ALB,non_coding_transcript_exon_variant,,ENST00000486939,;ALB,upstream_gene_variant,,ENST00000508932,;ALB,downstream_gene_variant,,ENST00000484992,;ALB,downstream_gene_variant,,ENST00000504043,;	T	ENSG00000163631	ENST00000295897	Transcript	missense_variant	1600	1511	504	S/F	tCc/tTc	.	.	.	1	ALB	HGNC	399	protein_coding	YES	CCDS3555.1	ENSP00000295897	ALBU_HUMAN	.	UPI000002C1AC	.	deleterious(0.01)	probably_damaging(0.994)	12/15	.	PROSITE_profiles:PS51438,hmmpanther:PTHR11385,hmmpanther:PTHR11385:SF6,Gene3D:1.10.246.10,Pfam_domain:PF00273,SMART_domains:SM00103,PIRSF_domain:PIRSF002520,Superfamily_domains:SSF48552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAATCCTTGG	.	5	ESCA
DMXL1	0	.	GRCh37	5	118556217	118556217	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8001G>C	p.%3D	p.L2667L	ENST00000311085	35/43	24	19	5	22	22	0	DMXL1,synonymous_variant,p.%3D,ENST00000539542,;DMXL1,synonymous_variant,p.%3D,ENST00000311085,;DMXL1,non_coding_transcript_exon_variant,,ENST00000505312,;DMXL1,non_coding_transcript_exon_variant,,ENST00000511622,;	C	ENSG00000172869	ENST00000311085	Transcript	synonymous_variant	8081	8001	2667	L	ctG/ctC	.	.	.	1	DMXL1	HGNC	2937	protein_coding	YES	CCDS4125.1	ENSP00000309690	DMXL1_HUMAN	F1T0K4_HUMAN,E7EMZ0_HUMAN	UPI000013F0EC	.	.	.	35/43	.	hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTGGATGT	.	5	ESCA
PCDHB7	0	.	GRCh37	5	140554656	140554656	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2240A>G	p.Tyr747Cys	p.Y747C	ENST00000231137	1/1	71	4	66	96	96	0	PCDHB7,missense_variant,p.Tyr747Cys,ENST00000231137,;PCDHB8,upstream_gene_variant,,ENST00000239444,;	G	ENSG00000113212	ENST00000231137	Transcript	missense_variant	2414	2240	747	Y/C	tAc/tGc	.	.	.	1	PCDHB7	HGNC	8692	protein_coding	YES	CCDS4249.1	ENSP00000231137	PCDB7_HUMAN	.	UPI00001273E3	.	deleterious_low_confidence(0.01)	possibly_damaging(0.666)	1/1	.	hmmpanther:PTHR24028:SF69,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTACCAGT	.	5	ESCA
DIAPH1	0	.	GRCh37	5	140957145	140957145	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1177G>A	p.Val393Ile	p.V393I	ENST00000398557	12/28	35	1	34	34	34	0	DIAPH1,missense_variant,p.Val393Ile,ENST00000253811,;DIAPH1,missense_variant,p.Val339Ile,ENST00000520569,;DIAPH1,missense_variant,p.Val384Ile,ENST00000389057,;DIAPH1,missense_variant,p.Val393Ile,ENST00000398557,;DIAPH1,missense_variant,p.Val384Ile,ENST00000518047,;DIAPH1,missense_variant,p.Val384Ile,ENST00000398562,;DIAPH1,missense_variant,p.Val393Ile,ENST00000389054,;DIAPH1,missense_variant,p.Val384Ile,ENST00000398566,;DIAPH1,missense_variant,p.Val384Ile,ENST00000521457,;DIAPH1,3_prime_UTR_variant,,ENST00000523100,;DIAPH1,downstream_gene_variant,,ENST00000472516,;	T	ENSG00000131504	ENST00000398557	Transcript	missense_variant	1318	1177	393	V/I	Gtc/Atc	.	.	.	-1	DIAPH1	HGNC	2876	protein_coding	YES	CCDS43374.1	ENSP00000381565	DIAP1_HUMAN	Q96IL1_HUMAN,Q7KZJ7_HUMAN,Q6UUU0_HUMAN,E5RJ79_HUMAN,B4DVR3_HUMAN,A0RZB7_HUMAN	UPI0000EA87E6	.	.	unknown(0)	12/28	.	PROSITE_profiles:PS51232,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF17,Pfam_domain:PF06367,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGACTTCAT	.	5	ESCA
SPINK5	0	.	GRCh37	5	147499615	147499615	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2357T>A	p.Leu786His	p.L786H	ENST00000359874	25/34	17	11	5	31	31	0	SPINK5,missense_variant,p.Leu786His,ENST00000256084,;SPINK5,missense_variant,p.Leu767His,ENST00000508733,;SPINK5,missense_variant,p.Leu786His,ENST00000398454,;SPINK5,missense_variant,p.Leu786His,ENST00000359874,;SPINK5,downstream_gene_variant,,ENST00000507988,;	A	ENSG00000133710	ENST00000359874	Transcript	missense_variant	2430	2357	786	L/H	cTc/cAc	.	.	.	1	SPINK5	HGNC	15464	protein_coding	YES	CCDS47300.1	ENSP00000352936	ISK5_HUMAN	.	UPI000020CF25	.	deleterious(0)	probably_damaging(1)	25/34	.	PROSITE_profiles:PS51465,hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF10,Gene3D:1.10.1890.10,SMART_domains:SM00280,Superfamily_domains:SSF100895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAACTCATCT	.	5	ESCA
CSNK1A1	0	.	GRCh37	5	148876034	148876034	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000515768	.	14	9	5	17	17	0	CSNK1A1,3_prime_UTR_variant,,ENST00000515435,;CSNK1A1,3_prime_UTR_variant,,ENST00000377843,;CSNK1A1,3_prime_UTR_variant,,ENST00000261798,;CSNK1A1,3_prime_UTR_variant,,ENST00000504676,;CSNK1A1,downstream_gene_variant,,ENST00000606719,;CSNK1A1,downstream_gene_variant,,ENST00000515768,;CTB-89H12.4,non_coding_transcript_exon_variant,,ENST00000412431,;CTB-89H12.4,non_coding_transcript_exon_variant,,ENST00000499521,;CSNK1A1,downstream_gene_variant,,ENST00000606826,;	A	ENSG00000113712	ENST00000515768	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	382	-1	CSNK1A1	HGNC	2451	protein_coding	YES	CCDS47304.1	ENSP00000421689	KC1A_HUMAN	U3KQ83_HUMAN,U3KPX3_HUMAN,B4DER9_HUMAN	UPI000053FD0F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	ATGCCGTTCTT	.	4	ESCA
SYNPO	0	.	GRCh37	5	150031078	150031078	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1183G>A	.	.	ENST00000394243	3/3	43	39	3	52	52	0	SYNPO,3_prime_UTR_variant,,ENST00000519664,;SYNPO,3_prime_UTR_variant,,ENST00000394243,;SYNPO,3_prime_UTR_variant,,ENST00000522122,;SYNPO,intron_variant,,ENST00000307662,;SYNPO,downstream_gene_variant,,ENST00000518872,;	A	ENSG00000171992	ENST00000394243	Transcript	3_prime_UTR_variant	4347	.	.	.	.	.	.	.	1	SYNPO	HGNC	30672	protein_coding	YES	CCDS54937.1	ENSP00000377789	SYNPO_HUMAN	Q71HJ6_HUMAN	UPI000013F943	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGCGTTAGA	.	2	ESCA
HMMR	0	.	GRCh37	5	162887691	162887691	+	5'UTR	SNP	C	C	T	rs774098944	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-8C>T	.	.	ENST00000393915	1/18	37	32	5	49	49	0	HMMR,5_prime_UTR_variant,,ENST00000358715,;HMMR,5_prime_UTR_variant,,ENST00000353866,;HMMR,5_prime_UTR_variant,,ENST00000393915,;HMMR,5_prime_UTR_variant,,ENST00000432118,;HMMR,intron_variant,,ENST00000522094,;HMMR,intron_variant,,ENST00000520345,;NUDCD2,upstream_gene_variant,,ENST00000302764,;NUDCD2,upstream_gene_variant,,ENST00000517501,;NUDCD2,upstream_gene_variant,,ENST00000519395,;NUDCD2,upstream_gene_variant,,ENST00000521797,;HMMR,non_coding_transcript_exon_variant,,ENST00000521108,;HMMR,non_coding_transcript_exon_variant,,ENST00000517936,;	T	ENSG00000072571	ENST00000393915	Transcript	5_prime_UTR_variant	136	.	.	.	.	rs774098944	.	.	1	HMMR	HGNC	5012	protein_coding	YES	CCDS47334.1	ENSP00000377492	HMMR_HUMAN	E5RIH2_HUMAN,E5RI30_HUMAN,E3W978_HUMAN,B9UCQ3_HUMAN	UPI00001AE676	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGGCCGTCA	byFrequency	4	ESCA
PAPD7	0	.	GRCh37	5	6755014	6755014	+	Missense_Mutation	SNP	C	C	A	rs748296365	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1585C>A	p.His529Asn	p.H529N	ENST00000230859	13/13	10	4	6	28	28	0	PAPD7,missense_variant,p.His529Asn,ENST00000230859,;PAPD7,non_coding_transcript_exon_variant,,ENST00000514697,;PAPD7,downstream_gene_variant,,ENST00000514410,;PAPD7,downstream_gene_variant,,ENST00000505457,;	A	ENSG00000112941	ENST00000230859	Transcript	missense_variant	1714	1585	529	H/N	Cac/Aac	rs748296365,COSM3856084	.	.	1	PAPD7	HGNC	16705	protein_coding	YES	CCDS3871.1	ENSP00000230859	PAPD7_HUMAN	M1JCE6_HUMAN,D6RJD0_HUMAN,B7ZLL4_HUMAN,B4E0T3_HUMAN	UPI0000071E30	.	deleterious_low_confidence(0.01)	possibly_damaging(0.526)	13/13	.	hmmpanther:PTHR23092:SF24,hmmpanther:PTHR23092	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R533fs*>10|c.1584_1585delAC|4	RADIA|MUTECT|MUSE	AAAAACACACA	byFrequency	3	ESCA
SEMA5A	0	.	GRCh37	5	9036883	9036883	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6126A>G	.	.	ENST00000382496	23/23	13	9	4	36	36	0	SEMA5A,3_prime_UTR_variant,,ENST00000382496,;CTD-2215L10.1,intron_variant,,ENST00000506519,;	C	ENSG00000112902	ENST00000382496	Transcript	3_prime_UTR_variant	10017	.	.	.	.	.	.	.	-1	SEMA5A	HGNC	10736	protein_coding	YES	CCDS3875.1	ENSP00000371936	SEM5A_HUMAN	D6RAF4_HUMAN,B4DE33_HUMAN	UPI000004F25D	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAATCTTCTCC	.	2	ESCA
QRSL1	0	.	GRCh37	6	107096922	107096922	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403T>G	p.Phe135Val	p.F135V	ENST00000369046	5/11	27	4	23	23	23	0	QRSL1,missense_variant,p.Phe135Val,ENST00000369046,;QRSL1,missense_variant,p.Phe135Val,ENST00000369044,;	G	ENSG00000130348	ENST00000369046	Transcript	missense_variant	507	403	135	F/V	Ttt/Gtt	.	.	.	1	QRSL1	HGNC	21020	protein_coding	YES	CCDS5057.1	ENSP00000358042	GATA_HUMAN	.	UPI0000047463	.	deleterious(0.01)	possibly_damaging(0.904)	5/11	.	HAMAP:MF_00120,hmmpanther:PTHR11895,hmmpanther:PTHR11895:SF7,TIGRFAM_domain:TIGR00132,Gene3D:3.90.1300.10,Pfam_domain:PF01425,Superfamily_domains:SSF75304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GTGTATTTGGA	.	4	ESCA
CDC40	0	.	GRCh37	6	110541037	110541037	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1305C>T	p.%3D	p.S435S	ENST00000368932	13/16	32	28	4	30	30	0	CDC40,synonymous_variant,p.%3D,ENST00000307731,;CDC40,synonymous_variant,p.%3D,ENST00000368932,;CDC40,synonymous_variant,p.%3D,ENST00000368930,;CDC40,upstream_gene_variant,,ENST00000445340,;CDC40,non_coding_transcript_exon_variant,,ENST00000606893,;	T	ENSG00000168438	ENST00000368932	Transcript	synonymous_variant	1406	1305	435	S	agC/agT	.	.	.	1	CDC40	HGNC	17350	protein_coding	YES	CCDS5081.1	ENSP00000357928	PRP17_HUMAN	Q5SRM9_HUMAN	UPI0000132145	.	.	.	13/16	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Pfam_domain:PF00400,Gene3D:2.130.10.10,hmmpanther:PTHR19852,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GTGAGCACATC	.	2	ESCA
LAMA2	0	.	GRCh37	6	129618820	129618836	+	Splice_Site	DEL	CCATTGCCAGGCTGGGA	CCATTGCCAGGCTGGGA	-	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	CCATTGCCAGGCTGGGA	CCATTGCCAGGCTGGGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2857-8_2865delATTGCCAGGCTGGGACC	.	p.X953_splice	ENST00000421865	21/65	59	52	7	53	53	0	LAMA2,splice_acceptor_variant,,ENST00000421865,;	-	ENSG00000196569	ENST00000421865	Transcript	splice_acceptor_variant	?-2912	?-2863	?-955	.	.	.	.	.	1	LAMA2	HGNC	6482	protein_coding	YES	CCDS5138.1	ENSP00000400365	LAMA2_HUMAN	Q59H37_HUMAN	UPI00003673E0	.	.	.	21/65	20/64	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCTCTTCCATTGCCAGGCTGGGACCTTT	.	2	ESCA
AKAP12	0	.	GRCh37	6	151673538	151673538	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4012G>A	p.Val1338Ile	p.V1338I	ENST00000402676	4/5	38	29	9	37	37	0	AKAP12,missense_variant,p.Val1233Ile,ENST00000359755,;AKAP12,missense_variant,p.Val1240Ile,ENST00000354675,;AKAP12,missense_variant,p.Val1338Ile,ENST00000253332,;AKAP12,missense_variant,p.Val1338Ile,ENST00000402676,;AKAP12,downstream_gene_variant,,ENST00000490177,;	A	ENSG00000131016	ENST00000402676	Transcript	missense_variant	4252	4012	1338	V/I	Gta/Ata	.	.	.	1	AKAP12	HGNC	370	protein_coding	YES	CCDS5229.1	ENSP00000384537	AKA12_HUMAN	.	UPI000013CDC7	.	tolerated(0.26)	benign(0.197)	4/5	.	hmmpanther:PTHR23209,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGGTAGTT	.	5	ESCA
ZBTB2	0	.	GRCh37	6	151687546	151687546	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.655G>C	p.Glu219Gln	p.E219Q	ENST00000325144	3/3	48	36	12	22	22	0	ZBTB2,missense_variant,p.Glu219Gln,ENST00000325144,;	G	ENSG00000181472	ENST00000325144	Transcript	missense_variant	796	655	219	E/Q	Gag/Cag	.	.	.	-1	ZBTB2	HGNC	20868	protein_coding	YES	CCDS5231.1	ENSP00000323183	ZBTB2_HUMAN	Q658W5_HUMAN	UPI00000728EE	.	tolerated(0.29)	probably_damaging(0.968)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24399,hmmpanther:PTHR24399:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCCTCCC	.	5	ESCA
RMND1	0	.	GRCh37	6	151742424	151742424	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1035T>A	p.%3D	p.S345S	ENST00000367303	9/12	42	29	13	43	43	0	RMND1,synonymous_variant,p.%3D,ENST00000444024,;RMND1,synonymous_variant,p.%3D,ENST00000336451,;RMND1,synonymous_variant,p.%3D,ENST00000367303,;	T	ENSG00000155906	ENST00000367303	Transcript	synonymous_variant	1158	1035	345	S	tcT/tcA	.	.	.	-1	RMND1	HGNC	21176	protein_coding	YES	CCDS5232.1	ENSP00000356272	RMND1_HUMAN	Q5SZ82_HUMAN	UPI00001AEAE1	.	.	.	9/12	.	hmmpanther:PTHR16255:SF1,hmmpanther:PTHR16255,Pfam_domain:PF02582	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCATGAGATAG	.	3	ESCA
MDC1	0	.	GRCh37	6	30671587	30671587	+	Silent	SNP	C	C	T	rs557483176	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5373G>A	p.%3D	p.V1791V	ENST00000376406	10/15	22	14	7	23	23	0	MDC1,synonymous_variant,p.%3D,ENST00000376406,;MDC1,synonymous_variant,p.%3D,ENST00000376405,;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,non_coding_transcript_exon_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,;	T	ENSG00000137337	ENST00000376406	Transcript	synonymous_variant	6021	5373	1791	V	gtG/gtA	rs557483176	.	.	-1	MDC1	HGNC	21163	protein_coding	YES	CCDS34384.1	ENSP00000365588	MDC1_HUMAN	A2AB07_HUMAN,A2AB06_HUMAN,A2AB05_HUMAN,A1Z5I9_HUMAN,A1Z5I7_HUMAN	UPI00001AF453	.	.	.	10/15	.	hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTCCACCTT	.	5	ESCA
IMPG1	0	.	GRCh37	6	76728472	76728472	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.770C>A	p.Pro257Gln	p.P257Q	ENST00000369950	7/17	32	14	17	32	32	0	IMPG1,missense_variant,p.Pro257Gln,ENST00000369950,;IMPG1,3_prime_UTR_variant,,ENST00000369963,;	T	ENSG00000112706	ENST00000369950	Transcript	missense_variant	960	770	257	P/Q	cCa/cAa	.	.	.	-1	IMPG1	HGNC	6055	protein_coding	YES	CCDS4985.1	ENSP00000358966	IMPG1_HUMAN	H0UI08_HUMAN	UPI0000073F12	.	deleterious(0.05)	probably_damaging(0.954)	7/17	.	PROSITE_profiles:PS50024,hmmpanther:PTHR12199,Gene3D:1ivzA00,Pfam_domain:PF01390,SMART_domains:SM00200,Superfamily_domains:0047452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATGGGGAC	.	5	ESCA
ABCF2	0	.	GRCh37	7	150918758	150918758	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827G>A	p.Arg276His	p.R276H	ENST00000222388	7/16	38	32	6	31	31	0	ABCF2,missense_variant,p.Arg276His,ENST00000287844,;ABCF2,missense_variant,p.Arg276His,ENST00000468073,;ABCF2,missense_variant,p.Arg276His,ENST00000222388,;ABCF2,downstream_gene_variant,,ENST00000441774,;ABCF2,non_coding_transcript_exon_variant,,ENST00000473874,;ABCF2,downstream_gene_variant,,ENST00000477252,;	T	ENSG00000033050	ENST00000222388	Transcript	missense_variant	873	827	276	R/H	cGc/cAc	.	.	.	-1	ABCF2	HGNC	71	protein_coding	YES	CCDS5922.1	ENSP00000222388	.	Q75MJ1_HUMAN,C9JZV3_HUMAN,C9JHK9_HUMAN	UPI000004C4C9	.	tolerated(0.22)	benign(0.03)	7/16	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19211:SF15,hmmpanther:PTHR19211,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AGATGCGCTTA	.	4	ESCA
WDR60	0	.	GRCh37	7	158695219	158695219	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1290T>C	p.%3D	p.I430I	ENST00000407559	10/25	29	25	4	26	26	0	WDR60,synonymous_variant,p.%3D,ENST00000407559,;WDR60,synonymous_variant,p.%3D,ENST00000444851,;WDR60,non_coding_transcript_exon_variant,,ENST00000467220,;	C	ENSG00000126870	ENST00000407559	Transcript	synonymous_variant	1448	1290	430	I	atT/atC	.	.	.	1	WDR60	HGNC	21862	protein_coding	YES	CCDS47757.1	ENSP00000384290	WDR60_HUMAN	H7C1E8_HUMAN,A4D230_HUMAN	UPI000020E761	.	.	.	10/25	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATTGGCGA	.	4	ESCA
FAM126A	0	.	GRCh37	7	23053671	23053671	+	5'UTR	SNP	G	G	C	rs760725721	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-156C>G	.	.	ENST00000432176	1/11	46	30	16	54	54	0	FAM126A,missense_variant,p.Thr27Ser,ENST00000440481,;FAM126A,5_prime_UTR_variant,,ENST00000409763,;FAM126A,5_prime_UTR_variant,,ENST00000432176,;FAM126A,5_prime_UTR_variant,,ENST00000409923,;FAM126A,non_coding_transcript_exon_variant,,ENST00000465661,;FAM126A,non_coding_transcript_exon_variant,,ENST00000477349,;FAM126A,non_coding_transcript_exon_variant,,ENST00000467005,;	C	ENSG00000122591	ENST00000432176	Transcript	5_prime_UTR_variant	78	.	.	.	.	rs760725721	.	.	-1	FAM126A	HGNC	24587	protein_coding	YES	CCDS5377.1	ENSP00000403396	HYCCI_HUMAN	.	UPI000006FF45	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACGGGTCCCG	.	5	ESCA
WBSCR27	0	.	GRCh37	7	73256371	73256371	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100C>T	p.Arg34Cys	p.R34C	ENST00000297873	2/6	62	34	27	62	62	0	WBSCR27,missense_variant,p.Arg34Cys,ENST00000297873,;WBSCR27,missense_variant,p.Arg34Cys,ENST00000458679,;WBSCR27,non_coding_transcript_exon_variant,,ENST00000493174,;	A	ENSG00000165171	ENST00000297873	Transcript	missense_variant	150	100	34	R/C	Cgc/Tgc	.	.	.	-1	WBSCR27	HGNC	19068	protein_coding	YES	CCDS5561.1	ENSP00000297873	WBS27_HUMAN	.	UPI000013E466	.	tolerated(0.07)	benign(0.009)	2/6	.	Superfamily_domains:SSF53335,Gene3D:3.40.50.150,hmmpanther:PTHR10108,hmmpanther:PTHR10108:SF693	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCGGTCAT	.	5	ESCA
CLIP2	0	.	GRCh37	7	73790244	73790244	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1513G>A	p.Val505Met	p.V505M	ENST00000223398	10/17	30	19	10	33	33	0	CLIP2,missense_variant,p.Val505Met,ENST00000395060,;CLIP2,missense_variant,p.Val470Met,ENST00000361545,;CLIP2,missense_variant,p.Val505Met,ENST00000223398,;CLIP2,upstream_gene_variant,,ENST00000493166,;CLIP2,upstream_gene_variant,,ENST00000487091,;CLIP2,upstream_gene_variant,,ENST00000482424,;	A	ENSG00000106665	ENST00000223398	Transcript	missense_variant	1840	1513	505	V/M	Gtg/Atg	COSM3882346,COSM3882345	.	.	1	CLIP2	HGNC	2586	protein_coding	YES	CCDS5569.1	ENSP00000223398	CLIP2_HUMAN	Q7Z5B7_HUMAN	UPI000007061E	.	deleterious(0)	possibly_damaging(0.726)	10/17	.	hmmpanther:PTHR18916:SF10,hmmpanther:PTHR18916	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCGCGTGCTG	.	5	ESCA
CALCR	0	.	GRCh37	7	93125259	93125259	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16C>T	.	.	ENST00000359558	3/16	32	13	19	33	33	0	CALCR,5_prime_UTR_variant,,ENST00000421592,;CALCR,5_prime_UTR_variant,,ENST00000359558,;CALCR,intron_variant,,ENST00000426151,;CALCR,intron_variant,,ENST00000394441,;CALCR,intron_variant,,ENST00000360249,;	A	ENSG00000004948	ENST00000359558	Transcript	5_prime_UTR_variant	285	.	.	.	.	.	.	.	-1	CALCR	HGNC	1440	protein_coding	YES	CCDS55125.1	ENSP00000352561	.	.	UPI0001B8380B	.	.	.	3/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAAAGTGGGT	.	5	ESCA
MBLAC1	0	.	GRCh37	7	99725388	99725388	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370G>T	p.Gly124Trp	p.G124W	ENST00000398075	2/2	45	35	10	29	29	0	MBLAC1,missense_variant,p.Gly124Trp,ENST00000398075,;MBLAC1,downstream_gene_variant,,ENST00000421390,;CNPY4,downstream_gene_variant,,ENST00000262932,;RP11-506M12.1,upstream_gene_variant,,ENST00000494221,;AC073842.19,upstream_gene_variant,,ENST00000376482,;CNPY4,downstream_gene_variant,,ENST00000480692,;CNPY4,downstream_gene_variant,,ENST00000483756,;CNPY4,downstream_gene_variant,,ENST00000462193,;	T	ENSG00000214309	ENST00000398075	Transcript	missense_variant	769	370	124	G/W	Ggg/Tgg	.	.	.	1	MBLAC1	HGNC	22180	protein_coding	YES	CCDS43620.1	ENSP00000381150	MBLC1_HUMAN	C9JAV3_HUMAN	UPI000013FF40	.	deleterious(0)	probably_damaging(0.994)	2/2	.	hmmpanther:PTHR23200,hmmpanther:PTHR23200:SF37,Gene3D:3.60.15.10,Pfam_domain:PF00753,SMART_domains:SM00849,Superfamily_domains:SSF56281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTGGGGCTG	.	5	ESCA
LRP12	0	.	GRCh37	8	105521276	105521276	+	Nonsense_Mutation	SNP	G	G	A	rs777398485	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163C>T	p.Arg55Ter	p.R55*	ENST00000276654	3/7	61	57	3	28	28	0	LRP12,stop_gained,p.Arg55Ter,ENST00000276654,;LRP12,stop_gained,p.Arg36Ter,ENST00000424843,;LRP12,non_coding_transcript_exon_variant,,ENST00000520770,;LRP12,non_coding_transcript_exon_variant,,ENST00000519675,;	A	ENSG00000147650	ENST00000276654	Transcript	stop_gained	272	163	55	R/*	Cga/Tga	rs777398485,COSM119913	.	.	-1	LRP12	HGNC	31708	protein_coding	YES	CCDS6303.1	ENSP00000276654	LRP12_HUMAN	E5RIW8_HUMAN,B3KWZ8_HUMAN	UPI0000047A9F	.	.	.	3/7	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF216,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTCGTATTT	byFrequency	2	ESCA
EIF3E	0	.	GRCh37	8	109252218	109252218	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292C>T	p.Pro98Ser	p.P98S	ENST00000220849	3/13	175	140	34	69	69	0	EIF3E,missense_variant,p.Pro5Ser,ENST00000519030,;EIF3E,missense_variant,p.Pro97Ser,ENST00000521440,;EIF3E,missense_variant,p.Pro49Ser,ENST00000518345,;EIF3E,missense_variant,p.Pro98Ser,ENST00000220849,;EIF3E,intron_variant,,ENST00000521297,;EIF3E,intron_variant,,ENST00000519627,;EIF3E,downstream_gene_variant,,ENST00000518634,;EIF3E,3_prime_UTR_variant,,ENST00000518100,;EIF3E,3_prime_UTR_variant,,ENST00000522445,;EIF3E,3_prime_UTR_variant,,ENST00000522887,;EIF3E,non_coding_transcript_exon_variant,,ENST00000518442,;EIF3E,non_coding_transcript_exon_variant,,ENST00000521614,;	A	ENSG00000104408	ENST00000220849	Transcript	missense_variant	355	292	98	P/S	Cca/Tca	.	.	.	-1	EIF3E	HGNC	3277	protein_coding	YES	CCDS6308.1	ENSP00000220849	EIF3E_HUMAN	E5RIT4_HUMAN,E5RGA2_HUMAN,B3KW56_HUMAN	UPI0000000C92	.	tolerated(0.11)	benign(0.111)	3/13	.	HAMAP:MF_03004,hmmpanther:PTHR10317,Pfam_domain:PF09440,PIRSF_domain:PIRSF016255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGGATCTT	.	5	ESCA
ZFAT	0	.	GRCh37	8	135614876	135614878	+	In_Frame_Del	DEL	CTT	CTT	-	rs767616893	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1084_1086delAAG	p.Lys362del	p.K362del	ENST00000377838	6/16	81	71	10	37	37	0	ZFAT,inframe_deletion,p.Lys350del,ENST00000429442,;ZFAT,inframe_deletion,p.Lys350del,ENST00000520214,;ZFAT,inframe_deletion,p.Lys362del,ENST00000377838,;ZFAT,inframe_deletion,p.Lys300del,ENST00000523399,;ZFAT,inframe_deletion,p.Lys350del,ENST00000520727,;ZFAT,inframe_deletion,p.Lys350del,ENST00000520356,;ZFAT-AS1,downstream_gene_variant,,ENST00000505776,;ZFAT,downstream_gene_variant,,ENST00000523040,;ZFAT,inframe_deletion,p.Lys362del,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000522974,;ZFAT,upstream_gene_variant,,ENST00000519827,;	-	ENSG00000066827	ENST00000377838	Transcript	inframe_deletion	1259-1261	1084-1086	362	K/-	AAG/-	rs767616893	.	.	-1	ZFAT	HGNC	19899	protein_coding	YES	CCDS47924.1	ENSP00000367069	ZFAT_HUMAN	.	UPI0000210061	.	.	.	6/16	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF0,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAGTACTTCTTCT	.	3	ESCA
TOP1MT	0	.	GRCh37	8	144399896	144399897	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1326dupG	p.Arg443AlafsTer9	p.R443Afs*9	ENST00000329245	10/14	47	29	18	21	21	0	TOP1MT,frameshift_variant,p.Arg345AlafsTer9,ENST00000523676,;TOP1MT,frameshift_variant,p.Arg345AlafsTer9,ENST00000519148,;TOP1MT,frameshift_variant,p.Arg345AlafsTer9,ENST00000521193,;TOP1MT,frameshift_variant,p.Arg443AlafsTer9,ENST00000329245,;TOP1MT,frameshift_variant,p.Arg364AlafsTer9,ENST00000519139,;TOP1MT,upstream_gene_variant,,ENST00000519977,;AC087793.1,downstream_gene_variant,,ENST00000585120,;TOP1MT,3_prime_UTR_variant,,ENST00000518951,;	C	ENSG00000184428	ENST00000329245	Transcript	frameshift_variant	1361-1362	1326-1327	442-443	-/X	-/G	.	.	.	-1	TOP1MT	HGNC	29787	protein_coding	YES	CCDS6400.1	ENSP00000328835	TOP1M_HUMAN	E5KMK7_HUMAN,Q8TBP3_HUMAN,E5RJ95_HUMAN,E5RJ33_HUMAN,E5RFS0_HUMAN	UPI000013716D	.	.	.	10/14	.	hmmpanther:PTHR10290,Pfam_domain:PF01028,Gene3D:1.10.132.10,SMART_domains:SM00435,Superfamily_domains:SSF56349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCGCGCGTCA	.	3	ESCA
CCDC166	0	.	GRCh37	8	144789923	144789923	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.357C>T	p.%3D	p.R119R	ENST00000542437	1/2	21	15	6	11	11	0	CCDC166,synonymous_variant,p.%3D,ENST00000533508,;CCDC166,synonymous_variant,p.%3D,ENST00000542437,;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,;	A	ENSG00000255181	ENST00000542437	Transcript	synonymous_variant	357	357	119	R	cgC/cgT	.	.	.	-1	CCDC166	HGNC	41910	protein_coding	YES	CCDS55280.1	ENSP00000437468	CC166_HUMAN	.	UPI00016623E2	.	.	.	1/2	.	Pfam_domain:PF14988,hmmpanther:PTHR14845:SF1,hmmpanther:PTHR14845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCGCGCCC	.	5	ESCA
TONSL	0	.	GRCh37	8	145659610	145659610	+	Silent	SNP	C	C	T	rs140867880	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3138G>A	p.%3D	p.S1046S	ENST00000409379	21/26	95	89	5	54	54	0	TONSL,synonymous_variant,p.%3D,ENST00000409379,;AC084125.4,upstream_gene_variant,,ENST00000544423,;AC084125.4,upstream_gene_variant,,ENST00000442850,;TONSL,non_coding_transcript_exon_variant,,ENST00000497613,;	T	ENSG00000160949	ENST00000409379	Transcript	synonymous_variant	3168	3138	1046	S	tcG/tcA	rs140867880	.	.	-1	TONSL	HGNC	7801	protein_coding	YES	CCDS34968.2	ENSP00000386239	TONSL_HUMAN	.	UPI0000424A3B	.	.	.	21/26	.	hmmpanther:PTHR24139:SF31,hmmpanther:PTHR24139,Superfamily_domains:SSF52047	T:0.0010	T:0.0038	T:0	.	T:0	T:0	T:0	T:0.0002	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGAACGAGAG	byFrequency|byCluster|by1000G	2	ESCA
RPL23AP53	0	.	GRCh37	8	169312	169312	+	RNA	SNP	C	C	A	rs199991867	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.189G>T	.	.	ENST00000606975	2/3	40	27	13	24	24	0	RPL23AP53,non_coding_transcript_exon_variant,,ENST00000606975,;	A	ENSG00000223508	ENST00000606975	Transcript	non_coding_transcript_exon_variant	189	.	.	.	.	rs199991867	.	.	-1	RPL23AP53	HGNC	35921	processed_transcript	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCACGTCTC	byCluster	2	ESCA
ADAM18	0	.	GRCh37	8	39581282	39581282	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2033A>C	p.Glu678Ala	p.E678A	ENST00000265707	19/20	55	52	3	69	69	0	ADAM18,missense_variant,p.Glu92Ala,ENST00000541111,;ADAM18,missense_variant,p.Glu678Ala,ENST00000265707,;ADAM18,missense_variant,p.Glu654Ala,ENST00000379866,;ADAM18,non_coding_transcript_exon_variant,,ENST00000523755,;ADAM18,3_prime_UTR_variant,,ENST00000520087,;ADAM18,non_coding_transcript_exon_variant,,ENST00000524117,;	C	ENSG00000168619	ENST00000265707	Transcript	missense_variant	2078	2033	678	E/A	gAa/gCa	.	.	.	1	ADAM18	HGNC	196	protein_coding	YES	CCDS6113.1	ENSP00000265707	ADA18_HUMAN	Q0VAI3_HUMAN,E5RK96_HUMAN	UPI00001254D7	.	tolerated(0.35)	benign(0.003)	19/20	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.E678K|c.2032G>A|3	MUTECT|MUSE	TACTGAAAAAG	.	2	ESCA
ANK1	0	.	GRCh37	8	41573341	41573341	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1530A>G	p.%3D	p.A510A	ENST00000265709	14/43	37	32	5	23	23	0	ANK1,synonymous_variant,p.%3D,ENST00000265709,;ANK1,synonymous_variant,p.%3D,ENST00000352337,;ANK1,synonymous_variant,p.%3D,ENST00000396942,;ANK1,synonymous_variant,p.%3D,ENST00000379758,;ANK1,synonymous_variant,p.%3D,ENST00000289734,;ANK1,synonymous_variant,p.%3D,ENST00000347528,;ANK1,synonymous_variant,p.%3D,ENST00000396945,;	C	ENSG00000029534	ENST00000265709	Transcript	synonymous_variant	1812	1530	510	A	gcA/gcG	.	.	.	-1	ANK1	HGNC	492	protein_coding	YES	CCDS47849.1	ENSP00000265709	ANK1_HUMAN	Q9UMG4_HUMAN	UPI0000E4453A	.	.	.	14/43	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF11,Gene3D:1.25.40.20,Pfam_domain:PF00023,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CGAGCTGCACA	.	2	ESCA
POTEA	0	.	GRCh37	8	43152432	43152432	+	RNA	SNP	G	G	A	rs370204067	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.420G>A	.	.	ENST00000519951	3/14	133	116	16	119	119	0	POTEA,non_coding_transcript_exon_variant,,ENST00000522175,;POTEA,non_coding_transcript_exon_variant,,ENST00000519951,;	A	ENSG00000188877	ENST00000519951	Transcript	non_coding_transcript_exon_variant	420	.	.	.	.	rs370204067	.	.	1	POTEA	HGNC	33893	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	3/14	.	.	A:0.0006	A:0	A:0	.	A:0.001	A:0.001	A:0.001	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCGTACAA	byFrequency|byCluster|by1000G	4	ESCA
CA8	0	.	GRCh37	8	61121437	61121437	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.780A>G	p.%3D	p.A260A	ENST00000317995	8/9	79	72	7	71	71	0	CA8,synonymous_variant,p.%3D,ENST00000317995,;CA8,non_coding_transcript_exon_variant,,ENST00000524872,;	C	ENSG00000178538	ENST00000317995	Transcript	synonymous_variant	1045	780	260	A	gcA/gcG	.	.	.	-1	CA8	HGNC	1382	protein_coding	YES	CCDS6174.1	ENSP00000314407	CAH8_HUMAN	B4DFA0_HUMAN	UPI000000D816	.	.	.	8/9	.	PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF99,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	AGTTCTGCCCC	.	3	ESCA
SULF1	0	.	GRCh37	8	70541903	70541903	+	Missense_Mutation	SNP	C	C	T	rs745984464	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2273C>T	p.Pro758Leu	p.P758L	ENST00000260128	19/23	52	39	13	27	27	0	SULF1,missense_variant,p.Pro758Leu,ENST00000260128,;SULF1,missense_variant,p.Pro758Leu,ENST00000402687,;SULF1,missense_variant,p.Pro758Leu,ENST00000419716,;SULF1,missense_variant,p.Pro758Leu,ENST00000458141,;SULF1,non_coding_transcript_exon_variant,,ENST00000521946,;SULF1,downstream_gene_variant,,ENST00000524731,;SULF1,missense_variant,p.Pro99Leu,ENST00000531512,;	T	ENSG00000137573	ENST00000260128	Transcript	missense_variant	2990	2273	758	P/L	cCg/cTg	rs745984464,COSM3675152	.	.	1	SULF1	HGNC	20391	protein_coding	YES	CCDS6204.1	ENSP00000260128	SULF1_HUMAN	Q96E28_HUMAN,E9PS14_HUMAN,E9PPQ3_HUMAN,E9PLS5_HUMAN,E9PJL8_HUMAN,E9PI06_HUMAN	UPI000003FD82	.	deleterious(0.01)	probably_damaging(0.951)	19/23	.	hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF210,PIRSF_domain:PIRSF036665,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCCGTTCT	.	5	ESCA
SGK223	0	.	GRCh37	8	8233763	8233763	+	Missense_Mutation	SNP	C	C	T	rs375344955	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2156G>A	p.Arg719Gln	p.R719Q	ENST00000520004	3/6	81	54	27	59	59	0	SGK223,missense_variant,p.Arg719Gln,ENST00000520004,;SGK223,missense_variant,p.Arg719Gln,ENST00000330777,;	T	ENSG00000182319	ENST00000520004	Transcript	missense_variant	2421	2156	719	R/Q	cGg/cAg	rs375344955,COSM751648	.	.	-1	SGK223	Uniprot_gn	.	protein_coding	YES	CCDS43706.1	ENSP00000428054	SG223_HUMAN	.	UPI00001D82A6	.	.	probably_damaging(0.978)	3/6	.	hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCACCGCGAC	byFrequency|byCluster	5	ESCA
RUNX1T1	0	.	GRCh37	8	93017367	93017367	+	Silent	SNP	G	G	A	rs187368715	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.750C>T	p.%3D	p.N250N	ENST00000436581	5/11	76	28	47	49	49	0	RUNX1T1,synonymous_variant,p.%3D,ENST00000436581,;RUNX1T1,synonymous_variant,p.%3D,ENST00000265814,;RUNX1T1,synonymous_variant,p.%3D,ENST00000518844,;RUNX1T1,synonymous_variant,p.%3D,ENST00000523629,;RUNX1T1,synonymous_variant,p.%3D,ENST00000360348,;RUNX1T1,synonymous_variant,p.%3D,ENST00000521553,;RUNX1T1,synonymous_variant,p.%3D,ENST00000520724,;RUNX1T1,synonymous_variant,p.%3D,ENST00000396218,;RUNX1T1,synonymous_variant,p.%3D,ENST00000422361,;RUNX1T1,downstream_gene_variant,,ENST00000518992,;RUNX1T1,downstream_gene_variant,,ENST00000521054,;RUNX1T1,downstream_gene_variant,,ENST00000522316,;RUNX1T1,missense_variant,p.Arg8Trp,ENST00000518361,;RUNX1T1,missense_variant,p.Arg13Trp,ENST00000520978,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000520047,;RUNX1T1,downstream_gene_variant,,ENST00000523290,;	A	ENSG00000079102	ENST00000436581	Transcript	synonymous_variant	761	750	250	N	aaC/aaT	rs187368715	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	.	.	5/11	.	hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF5	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.R254Q|c.761G>A|3,BUFFER|p.R206Q|c.617G>A|3,BUFFER|p.R243Q|c.728G>A|3,BUFFER|p.E249K|c.745G>A|7,BUFFER|p.E238K|c.712G>A|8,BUFFER|p.E201K|c.601G>A|7	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCGTTTTC	byCluster|by1000G	5	ESCA
PIP5KL1	0	.	GRCh37	9	130684122	130684122	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4G>A	.	.	ENST00000388747	10/10	50	44	5	37	37	0	PIP5KL1,3_prime_UTR_variant,,ENST00000388747,;PIP5KL1,3_prime_UTR_variant,,ENST00000300432,;ST6GALNAC4,upstream_gene_variant,,ENST00000335791,;ST6GALNAC4,upstream_gene_variant,,ENST00000361444,;ST6GALNAC4,upstream_gene_variant,,ENST00000343609,;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000495448,;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000464759,;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000485562,;PIP5KL1,downstream_gene_variant,,ENST00000498783,;PIP5KL1,downstream_gene_variant,,ENST00000464108,;ST6GALNAC4,upstream_gene_variant,,ENST00000479747,;ST6GALNAC4,upstream_gene_variant,,ENST00000467674,;PIP5KL1,downstream_gene_variant,,ENST00000490773,;PIP5KL1,downstream_gene_variant,,ENST00000476624,;PIP5KL1,upstream_gene_variant,,ENST00000477191,;PIP5KL1,downstream_gene_variant,,ENST00000497234,;	T	ENSG00000167103	ENST00000388747	Transcript	3_prime_UTR_variant	1234	.	.	.	.	.	.	.	-1	PIP5KL1	HGNC	28711	protein_coding	YES	CCDS48030.1	ENSP00000373399	PI5L1_HUMAN	.	UPI0000EDA26F	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCGCCCGTC	.	2	ESCA
PRRC2B	0	.	GRCh37	9	134321903	134321903	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729C>G	p.%3D	p.S243S	ENST00000357304	6/31	80	70	10	56	56	0	PRRC2B,synonymous_variant,p.%3D,ENST00000458550,;PRRC2B,synonymous_variant,p.%3D,ENST00000357304,;PRRC2B,synonymous_variant,p.%3D,ENST00000405995,;PRRC2B,upstream_gene_variant,,ENST00000372249,;PRRC2B,non_coding_transcript_exon_variant,,ENST00000489593,;	G	ENSG00000130723	ENST00000357304	Transcript	synonymous_variant	784	729	243	S	tcC/tcG	.	.	.	1	PRRC2B	HGNC	28121	protein_coding	YES	CCDS48044.1	ENSP00000349856	PRC2B_HUMAN	Q5JSZ9_HUMAN,B4E3S7_HUMAN	UPI00002374A3	.	.	.	6/31	.	hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCTCCTCGGC	.	4	ESCA
KCNT1	0	.	GRCh37	9	138662861	138662861	+	Missense_Mutation	SNP	G	G	A	rs141281093	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000371757	18/31	59	54	5	47	47	0	KCNT1,missense_variant,p.Arg604Gln,ENST00000486577,;KCNT1,missense_variant,p.Arg624Gln,ENST00000490355,;KCNT1,missense_variant,p.Arg624Gln,ENST00000263604,;KCNT1,missense_variant,p.Arg610Gln,ENST00000491806,;KCNT1,missense_variant,p.Arg643Gln,ENST00000298480,;KCNT1,missense_variant,p.Arg598Gln,ENST00000487664,;KCNT1,missense_variant,p.Arg643Gln,ENST00000371757,;KCNT1,missense_variant,p.Arg624Gln,ENST00000488444,;KCNT1,3_prime_UTR_variant,,ENST00000460750,;KCNT1,non_coding_transcript_exon_variant,,ENST00000490363,;	A	ENSG00000107147	ENST00000371757	Transcript	missense_variant	1995	1928	643	R/Q	cGg/cAg	rs141281093	.	.	1	KCNT1	HGNC	18865	protein_coding	YES	CCDS35175.2	ENSP00000360822	KCNT1_HUMAN	C9JBV2_HUMAN	UPI000192C42B	.	tolerated(1)	benign(0)	18/31	.	hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF14	.	.	.	.	.	.	.	A:0.0002	A:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAAGCGGAAGA	byFrequency|byCluster	3	ESCA
NOTCH1	0	.	GRCh37	9	139399766	139399766	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4582T>C	p.Cys1528Arg	p.C1528R	ENST00000277541	25/34	23	6	17	17	17	0	NOTCH1,missense_variant,p.Cys1528Arg,ENST00000277541,;NOTCH1,upstream_gene_variant,,ENST00000494783,;	G	ENSG00000148400	ENST00000277541	Transcript	missense_variant	4658	4582	1528	C/R	Tgc/Cgc	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	deleterious(0.02)	probably_damaging(0.999)	25/34	.	PROSITE_profiles:PS50258,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,Pfam_domain:PF00066,PIRSF_domain:PIRSF002279,SMART_domains:SM00004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGCACTGGC	.	5	ESCA
C8G	0	.	GRCh37	9	139839909	139839909	+	Missense_Mutation	SNP	A	A	G	rs754194146	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.137A>G	p.Gln46Arg	p.Q46R	ENST00000224181	1/7	98	79	19	59	59	0	C8G,missense_variant,p.Gln46Arg,ENST00000224181,;C8G,missense_variant,p.Gln46Arg,ENST00000371634,;FBXW5,upstream_gene_variant,,ENST00000443788,;FBXW5,upstream_gene_variant,,ENST00000325285,;FBXW5,upstream_gene_variant,,ENST00000433269,;FBXW5,upstream_gene_variant,,ENST00000428398,;LCN12,upstream_gene_variant,,ENST00000484304,;FBXW5,upstream_gene_variant,,ENST00000483559,;FBXW5,upstream_gene_variant,,ENST00000491246,;FBXW5,upstream_gene_variant,,ENST00000480818,;C8G,upstream_gene_variant,,ENST00000465773,;C8G,upstream_gene_variant,,ENST00000484376,;FBXW5,upstream_gene_variant,,ENST00000487794,;FBXW5,upstream_gene_variant,,ENST00000459905,;	G	ENSG00000176919	ENST00000224181	Transcript	missense_variant	197	137	46	Q/R	cAg/cGg	rs754194146	.	.	1	C8G	HGNC	1354	protein_coding	YES	CCDS7017.1	ENSP00000224181	CO8G_HUMAN	.	UPI0000210FCA	.	tolerated(0.11)	benign(0.01)	1/7	.	hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF193,PROSITE_patterns:PS00213,Gene3D:2.40.128.20,Superfamily_domains:SSF50814,Prints_domain:PR00179,Prints_domain:PR01215	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGCAGGTAG	byFrequency	5	ESCA
PIP5K1B	0	.	GRCh37	9	71439055	71439055	+	Intron	SNP	C	C	T	rs541206174	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69+1456C>T	.	.	ENST00000265382	.	48	22	26	48	48	0	PIP5K1B,intron_variant,,ENST00000437200,;PIP5K1B,intron_variant,,ENST00000265382,;PIP5K1B,intron_variant,,ENST00000377284,;PIP5K1B,intron_variant,,ENST00000440050,;PIP5K1B,intron_variant,,ENST00000541509,;RP11-203L2.4,non_coding_transcript_exon_variant,,ENST00000442103,;PIP5K1B,missense_variant,p.Pro38Leu,ENST00000478500,;	T	ENSG00000107242	ENST00000265382	Transcript	intron_variant	.	.	.	.	.	rs541206174	.	.	1	PIP5K1B	HGNC	8995	protein_coding	YES	CCDS6624.1	ENSP00000265382	PI51B_HUMAN	Q7KYT6_HUMAN,Q7KYT4_HUMAN,B4DIG7_HUMAN	UPI000002E327	.	.	.	.	4/15	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTCCGTGTA	by1000G	5	ESCA
UBQLN1	0	.	GRCh37	9	86294848	86294848	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553A>G	p.Met185Val	p.M185V	ENST00000376395	4/11	69	19	49	63	63	0	UBQLN1,missense_variant,p.Met185Val,ENST00000376395,;UBQLN1,missense_variant,p.Met185Val,ENST00000257468,;UBQLN1,intron_variant,,ENST00000529923,;UBQLN1,non_coding_transcript_exon_variant,,ENST00000533705,;	C	ENSG00000135018	ENST00000376395	Transcript	missense_variant	1077	553	185	M/V	Atg/Gtg	.	.	.	-1	UBQLN1	HGNC	12508	protein_coding	YES	CCDS6663.1	ENSP00000365576	UBQL1_HUMAN	.	UPI0000038DA1	.	deleterious(0.04)	possibly_damaging(0.448)	4/11	.	SMART_domains:SM00727,hmmpanther:PTHR10677:SF16,hmmpanther:PTHR10677	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCATTTCAG	.	5	ESCA
AGTPBP1	0	.	GRCh37	9	88292466	88292466	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321C>A	p.%3D	p.T107T	ENST00000376083	6/26	23	19	4	14	14	0	AGTPBP1,synonymous_variant,p.%3D,ENST00000357081,;AGTPBP1,synonymous_variant,p.%3D,ENST00000376083,;AGTPBP1,synonymous_variant,p.%3D,ENST00000376081,;AGTPBP1,synonymous_variant,p.%3D,ENST00000376109,;AGTPBP1,synonymous_variant,p.%3D,ENST00000337006,;AGTPBP1,synonymous_variant,p.%3D,ENST00000376080,;AGTPBP1,5_prime_UTR_variant,,ENST00000432218,;AGTPBP1,non_coding_transcript_exon_variant,,ENST00000491784,;	T	ENSG00000135049	ENST00000376083	Transcript	synonymous_variant	398	321	107	T	acC/acA	.	.	.	-1	AGTPBP1	HGNC	17258	protein_coding	YES	CCDS6672.1	ENSP00000365251	CBPC1_HUMAN	.	UPI000013CF66	.	.	.	6/26	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR12756:SF2,hmmpanther:PTHR12756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTGGTGAC	.	5	ESCA
GRIA3	0	.	GRCh37	X	122623557	122623557	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*996G>A	.	.	ENST00000264357	16/16	20	6	14	12	12	0	GRIA3,3_prime_UTR_variant,,ENST00000371256,;GRIA3,3_prime_UTR_variant,,ENST00000264357,;GRIA3,downstream_gene_variant,,ENST00000542149,;GRIA3,downstream_gene_variant,,ENST00000460123,;	A	ENSG00000125675	ENST00000264357	Transcript	3_prime_UTR_variant	3973	.	.	.	.	.	.	.	1	GRIA3	HGNC	4573	protein_coding	YES	CCDS14604.1	ENSP00000264357	GRIA3_HUMAN	Q9UHA9_HUMAN	UPI000013D503	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCGGCTTT	.	5	ESCA
GABRE	0	.	GRCh37	X	151138169	151138169	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.314G>T	p.Ser105Ile	p.S105I	ENST00000370328	3/9	24	3	20	31	31	0	GABRE,missense_variant,p.Ser105Ile,ENST00000370328,;GABRE,missense_variant,p.Ser105Ile,ENST00000370325,;GABRE,5_prime_UTR_variant,,ENST00000393914,;GABRE,3_prime_UTR_variant,,ENST00000441219,;GABRE,non_coding_transcript_exon_variant,,ENST00000465405,;GABRE,non_coding_transcript_exon_variant,,ENST00000474932,;GABRE,downstream_gene_variant,,ENST00000491339,;GABRE,downstream_gene_variant,,ENST00000417300,;	A	ENSG00000102287	ENST00000370328	Transcript	missense_variant	368	314	105	S/I	aGc/aTc	.	.	.	-1	GABRE	HGNC	4085	protein_coding	YES	CCDS14703.1	ENSP00000359353	GBRE_HUMAN	.	UPI00000307E6	.	deleterious(0)	probably_damaging(0.995)	3/9	.	Superfamily_domains:0038932,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF397	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGCTGTTG	.	5	ESCA
GPR64	0	.	GRCh37	X	19031890	19031890	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1013delC	p.Pro338HisfsTer4	p.P338Hfs*4	ENST00000379869	16/29	43	39	4	33	33	0	GPR64,frameshift_variant,p.Pro308HisfsTer4,ENST00000340581,;GPR64,frameshift_variant,p.Pro308HisfsTer4,ENST00000357544,;GPR64,frameshift_variant,p.Pro338HisfsTer4,ENST00000379869,;GPR64,frameshift_variant,p.Pro316HisfsTer4,ENST00000360279,;GPR64,frameshift_variant,p.Pro322HisfsTer4,ENST00000379878,;GPR64,frameshift_variant,p.Pro314HisfsTer4,ENST00000379876,;GPR64,frameshift_variant,p.Pro338HisfsTer4,ENST00000379873,;GPR64,frameshift_variant,p.Pro335HisfsTer4,ENST00000357991,;GPR64,frameshift_variant,p.Pro324HisfsTer4,ENST00000356606,;GPR64,frameshift_variant,p.Pro322HisfsTer4,ENST00000354791,;	-	ENSG00000173698	ENST00000379869	Transcript	frameshift_variant	1177	1013	338	P/X	cCa/ca	.	.	.	-1	GPR64	HGNC	4516	protein_coding	YES	CCDS43923.1	ENSP00000369198	GPR64_HUMAN	.	UPI000021246C	.	.	.	16/29	.	hmmpanther:PTHR12011:SF264,hmmpanther:PTHR12011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GGAGGTGGGGTG	.	2	ESCA
MAGEB6	0	.	GRCh37	X	26213137	26213137	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1174G>T	p.Glu392Ter	p.E392*	ENST00000379034	2/2	29	25	4	55	55	0	MAGEB6,stop_gained,p.Glu392Ter,ENST00000379034,;	T	ENSG00000176746	ENST00000379034	Transcript	stop_gained	1323	1174	392	E/*	Gaa/Taa	.	.	.	1	MAGEB6	HGNC	23796	protein_coding	YES	CCDS14217.1	ENSP00000368320	MAGB6_HUMAN	.	UPI00001413F4	.	.	.	2/2	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF67,hmmpanther:PTHR11736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TGTATGAAGAC	.	2	ESCA
DDX3X	0	.	GRCh37	X	41198321	41198321	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49V-01A-11D-A247-09	TCGA-LN-A49V-10A-01D-A247-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136C>T	p.Arg46Ter	p.R46*	ENST00000399959	3/17	24	14	10	21	21	0	DDX3X,stop_gained,p.Arg90Ter,ENST00000542215,;DDX3X,stop_gained,p.Arg46Ter,ENST00000399959,;DDX3X,stop_gained,p.Arg46Ter,ENST00000441189,;DDX3X,intron_variant,,ENST00000457138,;DDX3X,non_coding_transcript_exon_variant,,ENST00000478993,;DDX3X,downstream_gene_variant,,ENST00000480592,;	T	ENSG00000215301	ENST00000399959	Transcript	stop_gained	991	136	46	R/*	Cga/Tga	.	.	.	1	DDX3X	HGNC	2745	protein_coding	YES	CCDS43931.1	ENSP00000382840	DDX3X_HUMAN	Q59GX6_HUMAN	UPI000013CB6D	.	.	.	3/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAACCGAGAA	.	5	ESCA
CCDC6	0	.	GRCh37	10	61552831	61552831	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269C>G	p.Phe423Leu	p.F423L	ENST00000263102	9/9	100	93	7	99	99	0	CCDC6,missense_variant,p.Phe423Leu,ENST00000263102,;CCDC6,non_coding_transcript_exon_variant,,ENST00000491922,;	C	ENSG00000108091	ENST00000263102	Transcript	missense_variant	1501	1269	423	F/L	ttC/ttG	.	.	.	-1	CCDC6	HGNC	18782	protein_coding	YES	CCDS7257.1	ENSP00000263102	CCDC6_HUMAN	.	UPI000035B25A	.	deleterious(0.01)	possibly_damaging(0.899)	9/9	.	hmmpanther:PTHR15276:SF0,hmmpanther:PTHR15276	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CGTTTGAATTT	.	2	ESCA
HERC4	0	.	GRCh37	10	69832845	69832845	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21A>T	p.%3D	p.A7A	ENST00000395198	3/26	23	20	3	40	40	0	HERC4,synonymous_variant,p.%3D,ENST00000373700,;HERC4,synonymous_variant,p.%3D,ENST00000492996,;HERC4,synonymous_variant,p.%3D,ENST00000506515,;HERC4,synonymous_variant,p.%3D,ENST00000513996,;HERC4,synonymous_variant,p.%3D,ENST00000412272,;HERC4,synonymous_variant,p.%3D,ENST00000395187,;HERC4,synonymous_variant,p.%3D,ENST00000395198,;HERC4,non_coding_transcript_exon_variant,,ENST00000505760,;HERC4,non_coding_transcript_exon_variant,,ENST00000395185,;HERC4,downstream_gene_variant,,ENST00000515753,;HERC4,synonymous_variant,p.%3D,ENST00000473533,;HERC4,synonymous_variant,p.%3D,ENST00000427635,;	A	ENSG00000148634	ENST00000395198	Transcript	synonymous_variant	269	21	7	A	gcA/gcT	.	.	.	-1	HERC4	HGNC	24521	protein_coding	YES	CCDS41533.1	ENSP00000378624	HERC4_HUMAN	D6RFK9_HUMAN	UPI00004C6F56	.	.	.	3/26	.	PROSITE_profiles:PS50012,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF290,Pfam_domain:PF00415,Gene3D:2.130.10.30,Superfamily_domains:SSF50985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGATGCATT	.	2	ESCA
NRXN2	0	.	GRCh37	11	64435121	64435121	+	Missense_Mutation	SNP	G	G	A	rs142409712	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1399C>T	p.Arg467Cys	p.R467C	ENST00000265459	9/23	44	36	7	47	47	0	NRXN2,missense_variant,p.Arg467Cys,ENST00000377551,;NRXN2,missense_variant,p.Arg467Cys,ENST00000265459,;NRXN2,missense_variant,p.Arg223Cys,ENST00000442300,;NRXN2,missense_variant,p.Arg460Cys,ENST00000409571,;NRXN2,missense_variant,p.Arg436Cys,ENST00000377559,;NRXN2,downstream_gene_variant,,ENST00000417749,;NRXN2,downstream_gene_variant,,ENST00000437746,;	A	ENSG00000110076	ENST00000265459	Transcript	missense_variant	1861	1399	467	R/C	Cgc/Tgc	rs142409712	.	.	-1	NRXN2	HGNC	8009	protein_coding	YES	CCDS8077.1	ENSP00000265459	NRX2A_HUMAN	.	UPI0000130AA2	.	deleterious(0)	benign(0.025)	9/23	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF593,hmmpanther:PTHR10127	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGCGGGATA	byCluster	5	ESCA
C11orf24	0	.	GRCh37	11	68030003	68030003	+	Missense_Mutation	SNP	T	T	C	rs754691280	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460A>G	p.Met154Val	p.M154V	ENST00000304271	4/4	87	66	21	137	137	0	C11orf24,missense_variant,p.Met154Val,ENST00000304271,;C11orf24,intron_variant,,ENST00000533310,;C11orf24,downstream_gene_variant,,ENST00000527280,;C11orf24,non_coding_transcript_exon_variant,,ENST00000530166,;C11orf24,intron_variant,,ENST00000531745,;C11orf24,downstream_gene_variant,,ENST00000529590,;C11orf24,downstream_gene_variant,,ENST00000532534,;C11orf24,downstream_gene_variant,,ENST00000532969,;	C	ENSG00000171067	ENST00000304271	Transcript	missense_variant	863	460	154	M/V	Atg/Gtg	rs754691280	.	.	-1	C11orf24	HGNC	1174	protein_coding	YES	CCDS8180.1	ENSP00000307264	CK024_HUMAN	E9PI63_HUMAN	UPI000006E42A	.	tolerated(0.45)	unknown(0)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16021:SF9,hmmpanther:PTHR16021	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCATACTGG	.	5	ESCA
INPPL1	0	.	GRCh37	11	71949794	71949794	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*397A>G	.	.	ENST00000298229	28/28	48	35	12	57	57	0	INPPL1,3_prime_UTR_variant,,ENST00000538751,;INPPL1,3_prime_UTR_variant,,ENST00000298229,;INPPL1,3_prime_UTR_variant,,ENST00000541756,;INPPL1,downstream_gene_variant,,ENST00000541752,;PHOX2A,downstream_gene_variant,,ENST00000298231,;INPPL1,downstream_gene_variant,,ENST00000320683,;PHOX2A,downstream_gene_variant,,ENST00000546310,;PHOX2A,downstream_gene_variant,,ENST00000544057,;INPPL1,intron_variant,,ENST00000535985,;INPPL1,downstream_gene_variant,,ENST00000541303,;INPPL1,downstream_gene_variant,,ENST00000545355,;	G	ENSG00000165458	ENST00000298229	Transcript	3_prime_UTR_variant	4378	.	.	.	.	.	.	.	1	INPPL1	HGNC	6080	protein_coding	YES	CCDS8213.1	ENSP00000298229	SHIP2_HUMAN	H0YFZ4_HUMAN,F5H588_HUMAN,F5GYK9_HUMAN	UPI000013E4AF	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCTAAGACC	.	5	ESCA
NUAK1	0	.	GRCh37	12	106461007	106461007	+	Missense_Mutation	SNP	C	C	T	rs117517173	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1559G>A	p.Arg520Gln	p.R520Q	ENST00000261402	7/7	43	35	8	26	26	0	NUAK1,missense_variant,p.Arg520Gln,ENST00000261402,;NUAK1,downstream_gene_variant,,ENST00000548902,;NUAK1,downstream_gene_variant,,ENST00000553094,;NUAK1,downstream_gene_variant,,ENST00000549704,;	T	ENSG00000074590	ENST00000261402	Transcript	missense_variant	2939	1559	520	R/Q	cGg/cAg	rs117517173	.	.	-1	NUAK1	HGNC	14311	protein_coding	YES	CCDS31892.1	ENSP00000261402	NUAK1_HUMAN	F8VZ96_HUMAN,F8VXF0_HUMAN,F8VSH4_HUMAN	UPI00000403BC	.	tolerated(0.06)	benign(0.32)	7/7	.	hmmpanther:PTHR24343:SF79,hmmpanther:PTHR24343	T:0.0004	T:0	T:0	.	T:0	T:0.002	T:0	T:0	T:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCCGGCAG	byFrequency|byCluster|by1000G	5	ESCA
RPH3A	0	.	GRCh37	12	113334573	113334573	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2073G>A	p.%3D	p.V691V	ENST00000389385	22/22	16	10	6	30	30	0	RPH3A,synonymous_variant,p.%3D,ENST00000548866,;RPH3A,synonymous_variant,p.%3D,ENST00000420983,;RPH3A,synonymous_variant,p.%3D,ENST00000415485,;RPH3A,synonymous_variant,p.%3D,ENST00000551052,;RPH3A,synonymous_variant,p.%3D,ENST00000543106,;RPH3A,synonymous_variant,p.%3D,ENST00000389385,;RPH3A,synonymous_variant,p.%3D,ENST00000447659,;RPH3A,non_coding_transcript_exon_variant,,ENST00000549913,;RPH3A,non_coding_transcript_exon_variant,,ENST00000552352,;RPH3A,non_coding_transcript_exon_variant,,ENST00000549324,;	A	ENSG00000089169	ENST00000389385	Transcript	synonymous_variant	2570	2073	691	V	gtG/gtA	.	.	.	1	RPH3A	HGNC	17056	protein_coding	YES	CCDS44979.1	ENSP00000374036	RP3A_HUMAN	F8W1K7_HUMAN,F8W1A3_HUMAN,F8W131_HUMAN,F8W116_HUMAN,F8VZS2_HUMAN,F8VVK8_HUMAN,F8VV58_HUMAN,F8VTR7_HUMAN,F8VR41_HUMAN,F8VNW3_HUMAN,F8VNU2_HUMAN,F8VNP7_HUMAN	UPI000013456D	.	.	.	22/22	.	hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGTGTCAAG	.	5	ESCA
HIST4H4	0	.	GRCh37	12	14923843	14923844	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175dupC	p.Leu59ProfsTer11	p.L59Pfs*11	ENST00000539745	1/1	48	43	5	55	55	0	HIST4H4,frameshift_variant,p.Leu59ProfsTer11,ENST00000539745,;H2AFJ,upstream_gene_variant,,ENST00000544848,;RP11-174G6.5,upstream_gene_variant,,ENST00000562691,;HIST4H4,upstream_gene_variant,,ENST00000537853,;HIST4H4,upstream_gene_variant,,ENST00000537096,;HIST4H4,upstream_gene_variant,,ENST00000541592,;HIST4H4,upstream_gene_variant,,ENST00000540565,;HIST4H4,frameshift_variant,p.Leu59ProfsTer11,ENST00000358064,;H2AFJ,upstream_gene_variant,,ENST00000389078,;H2AFJ,upstream_gene_variant,,ENST00000501744,;	G	ENSG00000197837	ENST00000539745	Transcript	frameshift_variant	222-223	175-176	59	L/PX	ctc/cCtc	.	.	.	-1	HIST4H4	HGNC	20510	protein_coding	YES	CCDS8665.1	ENSP00000443017	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	.	.	1/1	.	hmmpanther:PTHR10484,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00803,SMART_domains:SM00417,Superfamily_domains:SSF47113,Prints_domain:PR00623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CTTTGAGGACT	.	2	ESCA
CACNA1C	0	.	GRCh37	12	2676738	2676738	+	Missense_Mutation	SNP	C	C	T	rs572234918	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1673C>T	p.Thr558Met	p.T558M	ENST00000347598	13/49	15	9	5	21	21	0	CACNA1C,missense_variant,p.Thr558Met,ENST00000399644,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399595,;CACNA1C,missense_variant,p.Thr558Met,ENST00000406454,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399617,;CACNA1C,missense_variant,p.Thr558Met,ENST00000347598,;CACNA1C,missense_variant,p.Thr558Met,ENST00000402845,;CACNA1C,missense_variant,p.Thr558Met,ENST00000327702,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399634,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399641,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399603,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399629,;CACNA1C,missense_variant,p.Thr558Met,ENST00000480911,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399601,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399597,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399655,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399606,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399637,;CACNA1C,missense_variant,p.Thr583Met,ENST00000335762,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399621,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399638,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399591,;CACNA1C,missense_variant,p.Thr558Met,ENST00000344100,;CACNA1C,missense_variant,p.Thr558Met,ENST00000399649,;CACNA1C,downstream_gene_variant,,ENST00000491104,;	T	ENSG00000151067	ENST00000347598	Transcript	missense_variant	1673	1673	558	T/M	aCg/aTg	rs572234918,COSM938240,COSM1360924,COSM938238,COSM1360922,COSM1360921,COSM938237,COSM1360923,COSM938239,COSM3721105,COSM938241,COSM1360925	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	tolerated(0.07)	benign(0.267)	13/49	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Gene3D:1.20.120.350,Superfamily_domains:SSF81324	T:0.0006	T:0	T:0	.	T:0.001	T:0	T:0.002	.	.	.	0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	AGACACGGCAA	byFrequency|by1000G	4	ESCA
PLEKHA8P1	0	.	GRCh37	12	45568029	45568029	+	RNA	SNP	T	T	C	rs754069040	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.657A>G	.	.	ENST00000256692	3/3	54	49	5	79	79	0	PLEKHA8P1,non_coding_transcript_exon_variant,,ENST00000256692,;PLEKHA8P1,downstream_gene_variant,,ENST00000545609,;PLEKHA8P1,downstream_gene_variant,,ENST00000550498,;PLEKHA8P1,non_coding_transcript_exon_variant,,ENST00000336399,;	C	ENSG00000134297	ENST00000256692	Transcript	non_coding_transcript_exon_variant	657	.	.	.	.	rs754069040	.	.	-1	PLEKHA8P1	HGNC	30222	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTGATTTCAG	.	2	ESCA
SLC38A2	0	.	GRCh37	12	46752700	46752700	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2194A>T	.	.	ENST00000256689	16/16	22	17	5	33	33	0	SLC38A2,3_prime_UTR_variant,,ENST00000256689,;SLC38A2,downstream_gene_variant,,ENST00000551374,;SLC38A2,downstream_gene_variant,,ENST00000548111,;SLC38A2,3_prime_UTR_variant,,ENST00000549258,;SLC38A2,downstream_gene_variant,,ENST00000548785,;SLC38A2,downstream_gene_variant,,ENST00000552414,;SLC38A2,downstream_gene_variant,,ENST00000552703,;SLC38A2,downstream_gene_variant,,ENST00000546520,;SLC38A2,downstream_gene_variant,,ENST00000548236,;	A	ENSG00000134294	ENST00000256689	Transcript	3_prime_UTR_variant	4160	.	.	.	.	.	.	.	-1	SLC38A2	HGNC	13448	protein_coding	YES	CCDS8749.1	ENSP00000256689	S38A2_HUMAN	.	UPI000000121A	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACCTCAAGG	.	5	ESCA
KRT6A	0	.	GRCh37	12	52882150	52882150	+	Silent	SNP	G	G	T	rs370853930	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1386C>A	p.%3D	p.I462I	ENST00000330722	7/9	81	68	13	75	75	0	KRT6A,synonymous_variant,p.%3D,ENST00000330722,;KRT6A,downstream_gene_variant,,ENST00000549600,;KRT6A,downstream_gene_variant,,ENST00000548735,;KRT6A,downstream_gene_variant,,ENST00000549898,;KRT6A,downstream_gene_variant,,ENST00000549754,;	T	ENSG00000205420	ENST00000330722	Transcript	synonymous_variant	1455	1386	462	I	atC/atA	rs370853930	.	.	-1	KRT6A	HGNC	6443	protein_coding	YES	CCDS41786.1	ENSP00000369317	K2C6A_HUMAN	.	UPI000013CD4C	.	.	.	7/9	.	Superfamily_domains:SSF64593,Pfam_domain:PF00038,Gene3D:1.20.5.170,PROSITE_patterns:PS00226,hmmpanther:PTHR23239:SF141,hmmpanther:PTHR23239	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGCGATCTC	byCluster|by1000G	4	ESCA
PDE1B	0	.	GRCh37	12	54963024	54963024	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284C>T	p.Ser95Leu	p.S95L	ENST00000243052	4/16	71	61	10	102	102	0	PDE1B,missense_variant,p.Ser54Leu,ENST00000538346,;PDE1B,missense_variant,p.Ser95Leu,ENST00000243052,;PDE1B,missense_variant,p.Ser75Leu,ENST00000550620,;PDE1B,intron_variant,,ENST00000394277,;PDE1B,intron_variant,,ENST00000542335,;PDE1B,missense_variant,p.Arg116Trp,ENST00000550285,;PDE1B,non_coding_transcript_exon_variant,,ENST00000548855,;	T	ENSG00000123360	ENST00000243052	Transcript	missense_variant	720	284	95	S/L	tCg/tTg	.	.	.	1	PDE1B	HGNC	8775	protein_coding	YES	CCDS8882.1	ENSP00000243052	PDE1B_HUMAN	Q7Z364_HUMAN,B4DK72_HUMAN,B3KX78_HUMAN	UPI0000001607	.	tolerated(0.25)	possibly_damaging(0.532)	4/16	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF83,Pfam_domain:PF08499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCGGAGG	.	5	ESCA
FRS2	0	.	GRCh37	12	69973085	69973085	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4350G>A	.	.	ENST00000299293	10/10	90	77	13	99	99	0	FRS2,3_prime_UTR_variant,,ENST00000550389,;FRS2,3_prime_UTR_variant,,ENST00000397997,;FRS2,3_prime_UTR_variant,,ENST00000299293,;FRS2,downstream_gene_variant,,ENST00000549921,;	A	ENSG00000166225	ENST00000299293	Transcript	3_prime_UTR_variant	6387	.	.	.	.	.	.	.	1	FRS2	HGNC	16971	protein_coding	YES	CCDS41809.1	ENSP00000299293	FRS2_HUMAN	L7RTG7_HUMAN,F8VZI4_HUMAN,F8VZ12_HUMAN,F8VYZ7_HUMAN,F8VX65_HUMAN,F8VW66_HUMAN,F8VS98_HUMAN	UPI000003F143	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATATGATGTA	.	5	ESCA
NAV3	0	.	GRCh37	12	78605103	78605103	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000536525	.	47	36	11	48	48	0	NAV3,3_prime_UTR_variant,,ENST00000397909,;NAV3,3_prime_UTR_variant,,ENST00000266692,;NAV3,3_prime_UTR_variant,,ENST00000228327,;NAV3,3_prime_UTR_variant,,ENST00000552895,;NAV3,downstream_gene_variant,,ENST00000541270,;NAV3,downstream_gene_variant,,ENST00000551162,;NAV3,downstream_gene_variant,,ENST00000536525,;	G	ENSG00000067798	ENST00000536525	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	685	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTATGGTG	.	5	ESCA
AICDA	0	.	GRCh37	12	8765388	8765388	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25G>A	.	.	ENST00000229335	1/5	43	34	9	69	69	0	AICDA,5_prime_UTR_variant,,ENST00000537228,;AICDA,5_prime_UTR_variant,,ENST00000229335,;AICDA,non_coding_transcript_exon_variant,,ENST00000545576,;	T	ENSG00000111732	ENST00000229335	Transcript	5_prime_UTR_variant	80	.	.	.	.	.	.	.	-1	AICDA	HGNC	13203	protein_coding	YES	CCDS41747.1	ENSP00000229335	AICDA_HUMAN	Q7Z599_HUMAN,Q5XM85_HUMAN,Q546Y9_HUMAN,A3QRX5_HUMAN	UPI000000171E	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTGCCTCCC	.	5	ESCA
C12orf50	0	.	GRCh37	12	88380170	88380170	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841A>C	p.Lys281Gln	p.K281Q	ENST00000298699	10/13	46	42	4	59	59	0	C12orf50,missense_variant,p.Lys242Gln,ENST00000550553,;C12orf50,missense_variant,p.Lys281Gln,ENST00000298699,;C12orf50,non_coding_transcript_exon_variant,,ENST00000551944,;	G	ENSG00000165805	ENST00000298699	Transcript	missense_variant	1022	841	281	K/Q	Aag/Cag	.	.	.	-1	C12orf50	HGNC	26665	protein_coding	YES	CCDS9031.1	ENSP00000298699	CL050_HUMAN	F8VXH4_HUMAN	UPI0000071382	.	deleterious(0.01)	probably_damaging(0.999)	10/13	.	hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AGGCTTCTTCA	.	2	ESCA
C12orf55	0	.	GRCh37	12	97051988	97051988	+	Splice_Site	SNP	G	G	C	rs747339252	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5325-1G>C	.	p.X1775_splice	ENST00000524981	.	32	22	10	30	30	0	C12orf55,splice_acceptor_variant,,ENST00000524981,;C12orf55,splice_acceptor_variant,,ENST00000342887,;	C	ENSG00000188596	ENST00000524981	Transcript	splice_acceptor_variant	.	.	.	.	.	rs747339252	.	.	1	C12orf55	HGNC	26456	protein_coding	YES	.	ENSP00000431759	.	R4GNI2_HUMAN,E9PJL5_HUMAN	UPI0001F77A4D	.	.	.	.	37/67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTAGTGAGA	.	5	ESCA
PARP4	0	.	GRCh37	13	25021304	25021304	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3135G>A	p.%3D	p.R1045R	ENST00000381989	26/34	31	27	4	49	49	0	PARP4,synonymous_variant,p.%3D,ENST00000381989,;PARP4,downstream_gene_variant,,ENST00000484989,;TPTE2P6,intron_variant,,ENST00000445572,;	T	ENSG00000102699	ENST00000381989	Transcript	synonymous_variant	3241	3135	1045	R	agG/agA	.	.	.	-1	PARP4	HGNC	271	protein_coding	YES	CCDS9307.1	ENSP00000371419	PARP4_HUMAN	.	UPI000013C76E	.	.	.	26/34	.	PROSITE_profiles:PS50234,hmmpanther:PTHR10338:SF7,hmmpanther:PTHR10338,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATAGCCTGGT	.	2	ESCA
KIAA0125	0	.	GRCh37	14	106391060	106391060	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000429431	.	84	55	28	109	108	0	KIAA0125,downstream_gene_variant,,ENST00000429431,;KIAA0125,downstream_gene_variant,,ENST00000449410,;KIAA0125,non_coding_transcript_exon_variant,,ENST00000482999,;KIAA0125,downstream_gene_variant,,ENST00000489911,;KIAA0125,downstream_gene_variant,,ENST00000484511,;	A	ENSG00000226777	ENST00000429431	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2529	1	KIAA0125	HGNC	19955	protein_coding	YES	.	ENSP00000410360	.	Q05DB7_HUMAN	UPI0000D49656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGGGTGT	.	5	ESCA
OR4K13	0	.	GRCh37	14	20502224	20502224	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.694C>T	p.Arg232Ter	p.R232*	ENST00000315693	1/1	26	17	9	21	21	0	OR4K13,stop_gained,p.Arg232Ter,ENST00000315693,;AL359218.1,downstream_gene_variant,,ENST00000580563,;	A	ENSG00000176253	ENST00000315693	Transcript	stop_gained	696	694	232	R/*	Cga/Tga	.	.	.	-1	OR4K13	HGNC	15351	protein_coding	YES	CCDS32028.1	ENSP00000319322	OR4KD_HUMAN	.	UPI0000041CEB	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF123,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATCGACTAG	.	5	ESCA
SNX6	0	.	GRCh37	14	35073350	35073350	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429-673T>A	.	.	ENST00000362031	.	18	12	5	25	25	0	SNX6,missense_variant,p.Leu16Gln,ENST00000355110,;SNX6,intron_variant,,ENST00000362031,;SNX6,intron_variant,,ENST00000396534,;SNX6,intron_variant,,ENST00000557265,;SNX6,intron_variant,,ENST00000396526,;SNX6,downstream_gene_variant,,ENST00000555648,;SNX6,synonymous_variant,p.%3D,ENST00000556712,;SNX6,3_prime_UTR_variant,,ENST00000556162,;SNX6,3_prime_UTR_variant,,ENST00000557341,;SNX6,3_prime_UTR_variant,,ENST00000555416,;SNX6,downstream_gene_variant,,ENST00000556303,;	T	ENSG00000129515	ENST00000362031	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SNX6	HGNC	14970	protein_coding	YES	CCDS41942.1	ENSP00000355217	.	Q5QTQ6_HUMAN	UPI00006AB832	.	.	.	.	5/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACCAGCAGG	.	5	ESCA
CTAGE5	0	.	GRCh37	14	39777653	39777653	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1070A>T	p.Glu357Val	p.E357V	ENST00000396158	13/24	34	22	12	56	56	0	CTAGE5,missense_variant,p.Glu323Val,ENST00000396165,;CTAGE5,missense_variant,p.Glu357Val,ENST00000396158,;RP11-407N17.3,missense_variant,p.Glu887Val,ENST00000553728,;CTAGE5,missense_variant,p.Glu352Val,ENST00000341502,;CTAGE5,missense_variant,p.Glu323Val,ENST00000553352,;CTAGE5,missense_variant,p.Glu352Val,ENST00000280083,;CTAGE5,missense_variant,p.Glu340Val,ENST00000341749,;CTAGE5,missense_variant,p.Glu277Val,ENST00000556148,;CTAGE5,missense_variant,p.Glu352Val,ENST00000348007,;RP11-407N17.3,missense_variant,p.Glu323Val,ENST00000603904,;CTAGE5,missense_variant,p.Glu272Val,ENST00000557038,;CTAGE5,upstream_gene_variant,,ENST00000556593,;	T	ENSG00000150527	ENST00000396158	Transcript	missense_variant	1406	1070	357	E/V	gAg/gTg	.	.	.	1	CTAGE5	HGNC	7057	protein_coding	YES	CCDS58316.1	ENSP00000379462	CTGE5_HUMAN	.	UPI0001AE69C9	.	deleterious(0.05)	possibly_damaging(0.511)	13/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAGAGCATA	.	5	ESCA
HERC2P3	0	.	GRCh37	15	20644266	20644266	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3298A>G	.	.	ENST00000428453	22/27	181	167	14	225	225	0	HERC2P3,non_coding_transcript_exon_variant,,ENST00000437318,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000428453,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000430598,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000426501,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000424611,;HERC2P3,downstream_gene_variant,,ENST00000436934,;HERC2P3,downstream_gene_variant,,ENST00000454045,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000429257,;HERC2P3,downstream_gene_variant,,ENST00000545640,;	C	ENSG00000180229	ENST00000428453	Transcript	non_coding_transcript_exon_variant	3298	.	.	.	.	.	.	.	-1	HERC2P3	HGNC	4871	processed_transcript	YES	.	.	.	.	.	.	.	.	22/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGAGTCAGGG	.	3	ESCA
CAPN3	0	.	GRCh37	15	42703106	42703106	+	Missense_Mutation	SNP	A	A	G	rs764459544	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2288A>G	p.Tyr763Cys	p.Y763C	ENST00000397163	22/24	53	41	12	51	51	0	CAPN3,missense_variant,p.Tyr98Cys,ENST00000397204,;CAPN3,missense_variant,p.Tyr671Cys,ENST00000349748,;CAPN3,missense_variant,p.Tyr207Cys,ENST00000569827,;CAPN3,missense_variant,p.Tyr157Cys,ENST00000565559,;CAPN3,missense_variant,p.Tyr111Cys,ENST00000564503,;CAPN3,missense_variant,p.Tyr763Cys,ENST00000397163,;CAPN3,missense_variant,p.Tyr98Cys,ENST00000569136,;CAPN3,missense_variant,p.Tyr670Cys,ENST00000356316,;CAPN3,missense_variant,p.Tyr251Cys,ENST00000397200,;CAPN3,missense_variant,p.Tyr757Cys,ENST00000318023,;CAPN3,missense_variant,p.Tyr98Cys,ENST00000561817,;CAPN3,missense_variant,p.Tyr757Cys,ENST00000357568,;CAPN3,missense_variant,p.Tyr98Cys,ENST00000337571,;ZNF106,downstream_gene_variant,,ENST00000569648,;CAPN3,downstream_gene_variant,,ENST00000567071,;ZNF106,downstream_gene_variant,,ENST00000565611,;ZNF106,downstream_gene_variant,,ENST00000565500,;ZNF106,downstream_gene_variant,,ENST00000263805,;ZNF106,downstream_gene_variant,,ENST00000565380,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000466369,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000495723,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000549793,;CAPN3,non_coding_transcript_exon_variant,,ENST00000562199,;CAPN3,missense_variant,p.Tyr9Cys,ENST00000568153,;CAPN3,missense_variant,p.Tyr35Cys,ENST00000567817,;CAPN3,3_prime_UTR_variant,,ENST00000565274,;CAPN3,non_coding_transcript_exon_variant,,ENST00000466222,;CAPN3,downstream_gene_variant,,ENST00000565173,;	G	ENSG00000092529	ENST00000397163	Transcript	missense_variant	2507	2288	763	Y/C	tAt/tGt	rs764459544,CM994482,CAPN3:c.2288A>G	.	.	1	CAPN3	HGNC	1480	protein_coding	YES	CCDS45245.1	ENSP00000380349	CAN3_HUMAN	H3BS30_HUMAN	UPI000000103F	.	deleterious(0.01)	probably_damaging(0.992)	22/24	.	Superfamily_domains:SSF47473,Gene3D:1.10.238.10,hmmpanther:PTHR10183:SF49,hmmpanther:PTHR10183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,0	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTATGACA	.	5	ESCA
NEIL1	0	.	GRCh37	15	75641271	75641271	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25C>T	p.%3D	p.L9L	ENST00000564784	3/11	58	55	3	59	59	0	NEIL1,synonymous_variant,p.%3D,ENST00000569506,;NEIL1,synonymous_variant,p.%3D,ENST00000564257,;NEIL1,synonymous_variant,p.%3D,ENST00000566313,;NEIL1,synonymous_variant,p.%3D,ENST00000355059,;NEIL1,synonymous_variant,p.%3D,ENST00000566752,;NEIL1,synonymous_variant,p.%3D,ENST00000564784,;NEIL1,synonymous_variant,p.%3D,ENST00000564500,;NEIL1,synonymous_variant,p.%3D,ENST00000565051,;NEIL1,synonymous_variant,p.%3D,ENST00000568881,;NEIL1,synonymous_variant,p.%3D,ENST00000567657,;NEIL1,synonymous_variant,p.%3D,ENST00000567005,;NEIL1,synonymous_variant,p.%3D,ENST00000568059,;NEIL1,synonymous_variant,p.%3D,ENST00000569035,;MIR631,downstream_gene_variant,,ENST00000384904,;NEIL1,intron_variant,,ENST00000567959,;NEIL1,downstream_gene_variant,,ENST00000567681,;NEIL1,downstream_gene_variant,,ENST00000569390,;NEIL1,synonymous_variant,p.%3D,ENST00000568519,;NEIL1,non_coding_transcript_exon_variant,,ENST00000561643,;NEIL1,non_coding_transcript_exon_variant,,ENST00000564951,;NEIL1,upstream_gene_variant,,ENST00000564738,;NEIL1,upstream_gene_variant,,ENST00000565121,;NEIL1,upstream_gene_variant,,ENST00000567393,;NEIL1,upstream_gene_variant,,ENST00000567547,;	T	ENSG00000140398	ENST00000564784	Transcript	synonymous_variant	654	25	9	L	Ctg/Ttg	.	.	.	1	NEIL1	HGNC	18448	protein_coding	YES	CCDS10278.1	ENSP00000457352	NEIL1_HUMAN	H3BU98_HUMAN,H3BTX5_HUMAN,H3BT94_HUMAN,H3BST2_HUMAN,H3BRZ2_HUMAN,H3BQU8_HUMAN,H3BQE8_HUMAN,H3BN83_HUMAN	UPI000013D787	.	.	.	3/11	.	PROSITE_profiles:PS51068,hmmpanther:PTHR22993,Pfam_domain:PF01149,Gene3D:1ee8A01,SMART_domains:SM00898,Superfamily_domains:SSF81624	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCACCTGGCC	.	2	ESCA
DET1	0	.	GRCh37	15	89074239	89074239	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731C>T	p.Ser244Phe	p.S244F	ENST00000564406	3/6	75	50	25	86	86	0	DET1,missense_variant,p.Ser244Phe,ENST00000564406,;DET1,missense_variant,p.Ser244Phe,ENST00000444300,;DET1,missense_variant,p.Ser233Phe,ENST00000268148,;DET1,intron_variant,,ENST00000558413,;DET1,downstream_gene_variant,,ENST00000559656,;DET1,3_prime_UTR_variant,,ENST00000557842,;DET1,3_prime_UTR_variant,,ENST00000557837,;	A	ENSG00000140543	ENST00000564406	Transcript	missense_variant	892	731	244	S/F	tCt/tTt	.	.	.	-1	DET1	HGNC	25477	protein_coding	YES	CCDS45343.1	ENSP00000456340	DET1_HUMAN	.	UPI00001A8183	.	deleterious(0)	probably_damaging(1)	3/6	.	Pfam_domain:PF09737,hmmpanther:PTHR13374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACAGACAAG	.	5	ESCA
ANKRD26P1	0	.	GRCh37	16	46534659	46534659	+	RNA	SNP	T	T	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.256A>T	.	.	ENST00000571006	3/10	34	27	7	72	72	0	ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000571006,;ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000574898,;ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000566201,;ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000569528,;	A	ENSG00000261239	ENST00000571006	Transcript	non_coding_transcript_exon_variant	256	.	.	.	.	.	.	.	-1	ANKRD26P1	HGNC	32955	processed_transcript	YES	.	.	.	.	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATTTTAATG	.	5	ESCA
C16orf71	0	.	GRCh37	16	4793092	4793093	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.834dupA	p.Glu279ArgfsTer17	p.E279Rfs*17	ENST00000299320	5/10	54	37	17	28	28	0	C16orf71,frameshift_variant,p.Glu293ArgfsTer17,ENST00000590191,;C16orf71,frameshift_variant,p.Glu279ArgfsTer17,ENST00000299320,;C16orf71,downstream_gene_variant,,ENST00000586724,;RP11-127I20.7,intron_variant,,ENST00000588099,;C16orf71,non_coding_transcript_exon_variant,,ENST00000586256,;	A	ENSG00000166246	ENST00000299320	Transcript	frameshift_variant	1310-1311	832-833	278	Q/QX	caa/cAaa	.	.	.	1	C16orf71	HGNC	25081	protein_coding	YES	CCDS10521.1	ENSP00000299320	CP071_HUMAN	K7ENX3_HUMAN	UPI000013E57E	.	.	.	5/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGGGACAAGAA	.	3	ESCA
POLR2C	0	.	GRCh37	16	57504037	57504038	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606dupA	p.Trp203MetfsTer5	p.W203Mfs*5	ENST00000219252	7/9	104	79	25	87	87	0	POLR2C,frameshift_variant,p.Trp203MetfsTer5,ENST00000219252,;DOK4,downstream_gene_variant,,ENST00000569010,;DOK4,downstream_gene_variant,,ENST00000566936,;DOK4,downstream_gene_variant,,ENST00000569548,;DOK4,downstream_gene_variant,,ENST00000340099,;POLR2C,non_coding_transcript_exon_variant,,ENST00000564651,;DOK4,downstream_gene_variant,,ENST00000561918,;POLR2C,non_coding_transcript_exon_variant,,ENST00000567982,;POLR2C,non_coding_transcript_exon_variant,,ENST00000562953,;POLR2C,downstream_gene_variant,,ENST00000563589,;DOK4,downstream_gene_variant,,ENST00000561659,;POLR2C,downstream_gene_variant,,ENST00000563115,;POLR2C,downstream_gene_variant,,ENST00000562599,;	A	ENSG00000102978	ENST00000219252	Transcript	frameshift_variant	942-943	604-605	202	E/EX	gaa/gAaa	.	.	.	1	POLR2C	HGNC	9189	protein_coding	YES	CCDS10782.1	ENSP00000219252	RPB3_HUMAN	Q6FGR6_HUMAN	UPI00000012C1	.	.	.	7/9	.	hmmpanther:PTHR11800,Gene3D:3.30.1360.10,Pfam_domain:PF01193,SMART_domains:SM00662,Superfamily_domains:SSF55257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCGAGGAATGG	.	3	ESCA
CDH11	0	.	GRCh37	16	64981513	64981513	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2384A>G	p.Asp795Gly	p.D795G	ENST00000268603	13/13	38	28	10	56	56	0	CDH11,missense_variant,p.Asp795Gly,ENST00000268603,;CDH11,missense_variant,p.Asp669Gly,ENST00000566827,;CDH11,3_prime_UTR_variant,,ENST00000394156,;	C	ENSG00000140937	ENST00000268603	Transcript	missense_variant	3000	2384	795	D/G	gAt/gGt	.	.	.	-1	CDH11	HGNC	1750	protein_coding	YES	CCDS10803.1	ENSP00000268603	CAD11_HUMAN	H3BUU9_HUMAN,H3BSM4_HUMAN,H3BR78_HUMAN,H3BQH2_HUMAN,H3BQB5_HUMAN,H3BPQ2_HUMAN,H3BP26_HUMAN	UPI000013D7C5	.	deleterious_low_confidence(0.01)	benign(0.194)	13/13	.	hmmpanther:PTHR24027:SF85,hmmpanther:PTHR24027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAATCGTCA	.	5	ESCA
ADAMTS18	0	.	GRCh37	16	77401444	77401444	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672T>C	p.%3D	p.Y224Y	ENST00000282849	4/23	33	28	5	46	46	0	ADAMTS18,synonymous_variant,p.%3D,ENST00000282849,;ADAMTS18,synonymous_variant,p.%3D,ENST00000562345,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567121,;ADAMTS18,downstream_gene_variant,,ENST00000564369,;ADAMTS18,synonymous_variant,p.%3D,ENST00000449265,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567914,;ADAMTS18,downstream_gene_variant,,ENST00000569309,;	G	ENSG00000140873	ENST00000282849	Transcript	synonymous_variant	1091	672	224	Y	taT/taC	.	.	.	-1	ADAMTS18	HGNC	17110	protein_coding	YES	CCDS10926.1	ENSP00000282849	ATS18_HUMAN	.	UPI0000233610	.	.	.	4/23	.	hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF167	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGGATAATT	.	4	ESCA
LASP1	0	.	GRCh37	17	37076595	37076595	+	3'UTR	DEL	G	G	-	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1566delG	.	.	ENST00000318008	7/7	23	18	5	21	21	0	LASP1,3_prime_UTR_variant,,ENST00000435347,;LASP1,3_prime_UTR_variant,,ENST00000318008,;LASP1,downstream_gene_variant,,ENST00000433206,;LASP1,downstream_gene_variant,,ENST00000579123,;LINC00672,upstream_gene_variant,,ENST00000583195,;RP1-56K13.3,intron_variant,,ENST00000580121,;LASP1,downstream_gene_variant,,ENST00000443937,;LASP1,downstream_gene_variant,,ENST00000585841,;	-	ENSG00000002834	ENST00000318008	Transcript	3_prime_UTR_variant	2681	.	.	.	.	.	.	.	1	LASP1	HGNC	6513	protein_coding	YES	CCDS11331.1	ENSP00000325240	LASP1_HUMAN	C9J9W2_HUMAN	UPI0000046841	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GAAAGAGGGTCC	.	2	ESCA
THRA	0	.	GRCh37	17	38245543	38245543	+	Missense_Mutation	SNP	G	G	A	rs762985147	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1067G>A	p.Arg356His	p.R356H	ENST00000264637	9/10	35	32	3	32	32	0	THRA,missense_variant,p.Arg356His,ENST00000264637,;THRA,missense_variant,p.Arg356His,ENST00000546243,;THRA,missense_variant,p.Arg356His,ENST00000584985,;THRA,missense_variant,p.Arg356His,ENST00000394121,;THRA,missense_variant,p.Arg356His,ENST00000450525,;NR1D1,downstream_gene_variant,,ENST00000246672,;THRA,downstream_gene_variant,,ENST00000577637,;	A	ENSG00000126351	ENST00000264637	Transcript	missense_variant	1647	1067	356	R/H	cGc/cAc	rs762985147	.	.	1	THRA	HGNC	11796	protein_coding	YES	CCDS11360.1	ENSP00000264637	THA_HUMAN	J3QRW5_HUMAN,J3QRA9_HUMAN,J3QR26_HUMAN,J3KTF3_HUMAN	UPI0000136D1E	.	tolerated(0.1)	possibly_damaging(0.858)	9/10	.	hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF42,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACCGCAAAC	.	2	ESCA
ANKFN1	0	.	GRCh37	17	54450102	54450102	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.706G>C	p.Gly236Arg	p.G236R	ENST00000318698	6/17	36	23	13	56	56	0	ANKFN1,missense_variant,p.Gly236Arg,ENST00000318698,;ANKFN1,missense_variant,p.Gly236Arg,ENST00000566473,;RP11-502F1.2,downstream_gene_variant,,ENST00000572529,;	C	ENSG00000153930	ENST00000318698	Transcript	missense_variant	741	706	236	G/R	Gga/Cga	.	.	.	1	ANKFN1	HGNC	26766	protein_coding	YES	CCDS32686.1	ENSP00000321627	ANKF1_HUMAN	.	UPI000049DE57	.	tolerated(0.07)	benign(0.001)	6/17	.	hmmpanther:PTHR21437:SF3,hmmpanther:PTHR21437	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAAGGATTC	.	5	ESCA
RNF43	0	.	GRCh37	17	56434566	56434566	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2308+263A>G	.	.	ENST00000584437	.	19	14	5	28	28	0	RNF43,synonymous_variant,p.%3D,ENST00000581868,;RNF43,intron_variant,,ENST00000407977,;RNF43,intron_variant,,ENST00000584437,;RNF43,intron_variant,,ENST00000583753,;RNF43,intron_variant,,ENST00000577716,;RNF43,intron_variant,,ENST00000500597,;RNF43,intron_variant,,ENST00000577625,;SUPT4H1,upstream_gene_variant,,ENST00000580947,;SUPT4H1,upstream_gene_variant,,ENST00000577396,;BZRAP1-AS1,intron_variant,,ENST00000583841,;BZRAP1-AS1,downstream_gene_variant,,ENST00000578334,;BZRAP1-AS1,downstream_gene_variant,,ENST00000583826,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580515,;BZRAP1-AS1,downstream_gene_variant,,ENST00000579527,;BZRAP1-AS1,downstream_gene_variant,,ENST00000578025,;BZRAP1-AS1,downstream_gene_variant,,ENST00000585236,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580633,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580022,;BZRAP1-AS1,downstream_gene_variant,,ENST00000579859,;	C	ENSG00000108375	ENST00000584437	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RNF43	HGNC	18505	protein_coding	YES	CCDS11607.1	ENSP00000463069	RNF43_HUMAN	.	UPI000022A469	.	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCTTTCTG	.	5	ESCA
TP53	0	.	GRCh37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	8/11	276	180	96	311	311	0	TP53,missense_variant,p.Arg273Cys,ENST00000420246,;TP53,missense_variant,p.Arg273Cys,ENST00000269305,;TP53,missense_variant,p.Arg141Cys,ENST00000509690,;TP53,missense_variant,p.Arg273Cys,ENST00000359597,;TP53,missense_variant,p.Arg273Cys,ENST00000445888,;TP53,missense_variant,p.Arg273Cys,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1007	817	273	R/C	Cgt/Tgt	CM951233,CM010473,rs121913343,CM010471,TP53_g.13797C>G,TP53_g.13797del,TP53_g.13797C>T,TP53_g.13797C>A,COSM43909,COSM44701,COSM10659,COSM43843,COSM417971,COSM99933,COSM3719990,COSM3355991,COSM3958802,COSM3719992,COSM1645518,COSM3719991,COSM3958801	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.998)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	uncertain_significance,pathogenic	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R273C|c.817C>T|131,SITE|p.R273C|c.817C>T|571,SITE|p.R273C|c.817C>T|75,SITE|p.R273C|c.817C>T|59,CODON|p.0?|c.1_1182del1182|6,CODON|p.R273L|c.818G>T|98,CODON|p.R273P|c.818G>C|4,CODON|p.R273H|c.818G>A|116,CODON|p.R273H|c.818G>A|64,CODON|p.R273H|c.818G>A|588,CODON|p.R273L|c.818G>T|5,CODON|p.R273H|c.818G>A|83,CODON|p.R273P|c.818G>C|29,CODON|p.R273L|c.818G>T|18,CODON|p.R273L|c.818G>T|12,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3,BUFFER|p.E271Q|c.811G>C|4,BUFFER|p.E271K|c.811G>A|35,BUFFER|p.E271*|c.811G>T|16,BUFFER|p.E271*|c.811G>T|3,BUFFER|p.E271K|c.811G>A|13,BUFFER|p.E271K|c.811G>A|4,BUFFER|p.E271K|c.811G>A|8,BUFFER|p.F270L|c.810T>G|4,BUFFER|p.F270L|c.810T>A|5,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270Y|c.809T>A|5,BUFFER|p.F270C|c.809T>G|16,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270S|c.809T>C|14,BUFFER|p.F270S|c.809T>C|6,BUFFER|p.F270L|c.808T>C|16,BUFFER|p.F270I|c.808T>A|3,BUFFER|p.F270V|c.808T>G|8,BUFFER|p.F270L|c.808T>C|3,BUFFER|p.F270I|c.808T>A|6,BUFFER|p.S269S|c.807C>T|3,BUFFER|p.S269N|c.806G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACACGCACCT	byFrequency|byCluster	5	ESCA
MPPE1	0	.	GRCh37	18	11888683	11888683	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554C>G	p.Ser185Cys	p.S185C	ENST00000588072	6/11	36	28	8	34	34	0	MPPE1,missense_variant,p.Ser111Cys,ENST00000592331,;MPPE1,missense_variant,p.Ser185Cys,ENST00000317235,;MPPE1,missense_variant,p.Ser185Cys,ENST00000399978,;MPPE1,missense_variant,p.Ser185Cys,ENST00000588072,;MPPE1,missense_variant,p.Ser185Cys,ENST00000309976,;MPPE1,missense_variant,p.Ser185Cys,ENST00000344987,;MPPE1,missense_variant,p.Ser185Cys,ENST00000592977,;MPPE1,intron_variant,,ENST00000587724,;MPPE1,downstream_gene_variant,,ENST00000588191,;MPPE1,downstream_gene_variant,,ENST00000589267,;MPPE1,downstream_gene_variant,,ENST00000588186,;GNAL,downstream_gene_variant,,ENST00000334049,;MPPE1,upstream_gene_variant,,ENST00000592755,;MPPE1,downstream_gene_variant,,ENST00000586364,;MPPE1,missense_variant,p.Ser185Cys,ENST00000496196,;MPPE1,missense_variant,p.Ser88Cys,ENST00000317251,;MPPE1,non_coding_transcript_exon_variant,,ENST00000592894,;MPPE1,non_coding_transcript_exon_variant,,ENST00000592447,;MPPE1,non_coding_transcript_exon_variant,,ENST00000589731,;MPPE1,upstream_gene_variant,,ENST00000592306,;MPPE1,downstream_gene_variant,,ENST00000592180,;	C	ENSG00000154889	ENST00000588072	Transcript	missense_variant	1776	554	185	S/C	tCt/tGt	.	.	.	-1	MPPE1	HGNC	15988	protein_coding	YES	CCDS11853.1	ENSP00000465894	MPPE1_HUMAN	K7ESB8_HUMAN,K7ES91_HUMAN,K7ERI3_HUMAN,K7ER13_HUMAN,K7EQV4_HUMAN,K7EQ74_HUMAN,K7EQ70_HUMAN,K7EJU0_HUMAN	UPI000013DDD8	.	deleterious(0)	probably_damaging(0.971)	6/11	.	hmmpanther:PTHR13315,hmmpanther:PTHR13315:SF0,Pfam_domain:PF12850,Gene3D:3.60.21.10,Superfamily_domains:SSF56300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGAAAAC	.	5	ESCA
CEP192	0	.	GRCh37	18	13030462	13030462	+	Splice_Site	SNP	A	A	G	rs568015143	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1391-2A>G	.	p.X464_splice	ENST00000506447	.	37	31	5	40	40	0	CEP192,splice_acceptor_variant,,ENST00000325971,;CEP192,splice_acceptor_variant,,ENST00000430049,;CEP192,splice_acceptor_variant,,ENST00000506447,;CEP192,splice_acceptor_variant,,ENST00000511820,;CEP192,intron_variant,,ENST00000589596,;CEP192,splice_acceptor_variant,,ENST00000510237,;CEP192,splice_acceptor_variant,,ENST00000513432,;	G	ENSG00000101639	ENST00000506447	Transcript	splice_acceptor_variant	.	.	.	.	.	rs568015143	.	.	1	CEP192	HGNC	25515	protein_coding	YES	CCDS32792.2	ENSP00000427550	.	E9PF99_HUMAN	UPI0001B09235	.	.	.	.	10/44	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTAGAAAC	by1000G	5	ESCA
METTL4	0	.	GRCh37	18	2554941	2554941	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556A>G	p.Ser186Gly	p.S186G	ENST00000574538	4/9	38	34	4	38	38	0	METTL4,missense_variant,p.Ser186Gly,ENST00000319888,;METTL4,missense_variant,p.Ser39Gly,ENST00000577166,;METTL4,missense_variant,p.Ser186Gly,ENST00000574538,;METTL4,upstream_gene_variant,,ENST00000576251,;snoU109,upstream_gene_variant,,ENST00000459316,;METTL4,non_coding_transcript_exon_variant,,ENST00000573134,;	C	ENSG00000101574	ENST00000574538	Transcript	missense_variant	1332	556	186	S/G	Agt/Ggt	.	.	.	-1	METTL4	HGNC	24726	protein_coding	YES	CCDS11826.1	ENSP00000458290	METL4_HUMAN	I3L4A0_HUMAN,I3L0Y1_HUMAN	UPI000020191B	.	tolerated(0.25)	benign(0.003)	4/9	.	hmmpanther:PTHR14475:SF2,hmmpanther:PTHR14475	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTACTACCCT	.	4	ESCA
LOXHD1	0	.	GRCh37	18	44063558	44063558	+	Silent	SNP	G	G	A	rs374858340	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3000C>T	p.%3D	p.Y1000Y	ENST00000300591	22/24	87	70	17	107	107	0	LOXHD1,synonymous_variant,p.%3D,ENST00000582408,;LOXHD1,synonymous_variant,p.%3D,ENST00000300591,;LOXHD1,synonymous_variant,p.%3D,ENST00000441551,;LOXHD1,synonymous_variant,p.%3D,ENST00000398705,;LOXHD1,synonymous_variant,p.%3D,ENST00000441893,;LOXHD1,synonymous_variant,p.%3D,ENST00000579038,;LOXHD1,synonymous_variant,p.%3D,ENST00000536736,;LOXHD1,synonymous_variant,p.%3D,ENST00000398722,;LOXHD1,synonymous_variant,p.%3D,ENST00000398686,;	A	ENSG00000167210	ENST00000300591	Transcript	synonymous_variant	3414	3000	1000	Y	taC/taT	rs374858340	.	.	-1	LOXHD1	HGNC	26521	protein_coding	YES	CCDS45861.1	ENSP00000300591	LOXH1_HUMAN	C9J269_HUMAN,C9IYQ1_HUMAN	UPI0000456B8D	.	.	.	22/24	.	PROSITE_profiles:PS50095,Gene3D:2.60.60.20,Pfam_domain:PF01477,Superfamily_domains:SSF49723	.	.	.	.	.	.	.	A:0	A:0.0003	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCCGTACTC	byCluster	5	ESCA
ICAM5	0	.	GRCh37	19	10403909	10403909	+	Silent	SNP	G	G	A	rs773640360	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1452G>A	p.%3D	p.T484T	ENST00000221980	6/11	32	27	5	41	41	0	ICAM5,synonymous_variant,p.%3D,ENST00000221980,;ICAM5,downstream_gene_variant,,ENST00000587398,;ICAM4,downstream_gene_variant,,ENST00000393717,;ICAM4,downstream_gene_variant,,ENST00000380770,;ICAM4,downstream_gene_variant,,ENST00000340992,;CTD-2369P2.8,upstream_gene_variant,,ENST00000589379,;ICAM5,downstream_gene_variant,,ENST00000586004,;ICAM5,non_coding_transcript_exon_variant,,ENST00000586480,;ICAM5,downstream_gene_variant,,ENST00000588912,;	A	ENSG00000105376	ENST00000221980	Transcript	synonymous_variant	1515	1452	484	T	acG/acA	rs773640360	.	.	1	ICAM5	HGNC	5348	protein_coding	YES	CCDS12233.1	ENSP00000221980	ICAM5_HUMAN	K7EIL3_HUMAN	UPI000013C7E4	.	.	.	6/11	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13771:SF6,hmmpanther:PTHR13771,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAACGCTAAC	.	4	ESCA
UNC13A	0	.	GRCh37	19	17716035	17716035	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*828C>G	.	.	ENST00000519716	44/44	38	33	5	39	39	0	UNC13A,3_prime_UTR_variant,,ENST00000252773,;UNC13A,3_prime_UTR_variant,,ENST00000519716,;UNC13A,3_prime_UTR_variant,,ENST00000428389,;UNC13A,downstream_gene_variant,,ENST00000552293,;UNC13A,downstream_gene_variant,,ENST00000550896,;UNC13A,downstream_gene_variant,,ENST00000551649,;UNC13A,downstream_gene_variant,,ENST00000523229,;UNC13A,downstream_gene_variant,,ENST00000517497,;	C	ENSG00000130477	ENST00000519716	Transcript	3_prime_UTR_variant	5940	.	.	.	.	.	.	.	-1	UNC13A	HGNC	23150	protein_coding	YES	CCDS46013.2	ENSP00000429562	UN13A_HUMAN	.	UPI00006C19A7	.	.	.	44/44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TAAGGGAGGGG	.	2	ESCA
AC004410.3	0	.	GRCh37	19	2334616	2334616	+	3'Flank	SNP	G	G	T	rs377325090	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000586111	.	63	45	17	112	112	0	AC004410.3,downstream_gene_variant,,ENST00000586111,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000592845,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000590982,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000586377,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000452401,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000590295,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000592738,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000382189,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000586332,;SPPL2B,intron_variant,,ENST00000585725,;SPPL2B,upstream_gene_variant,,ENST00000593243,;SPPL2B,non_coding_transcript_exon_variant,,ENST00000593198,;SPPL2B,upstream_gene_variant,,ENST00000587851,;SPPL2B,upstream_gene_variant,,ENST00000591959,;	T	ENSG00000273309	ENST00000586111	Transcript	downstream_gene_variant	.	.	.	.	.	rs377325090	.	3860	1	AC004410.3	Clone_based_vega_gene	.	sense_intronic	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTACGGCATG	byFrequency|byCluster	5	ESCA
LSM14A	0	.	GRCh37	19	34710734	34710735	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089dupT	p.Asp364Ter	p.D364*	ENST00000544216	8/10	50	45	5	56	56	0	LSM14A,frameshift_variant,p.Asp300Ter,ENST00000586157,;LSM14A,frameshift_variant,p.Asp364Ter,ENST00000544216,;LSM14A,frameshift_variant,p.Asp364Ter,ENST00000433627,;LSM14A,frameshift_variant,p.Asp323Ter,ENST00000540746,;LSM14A,non_coding_transcript_exon_variant,,ENST00000588582,;LSM14A,non_coding_transcript_exon_variant,,ENST00000585887,;LSM14A,upstream_gene_variant,,ENST00000590416,;	T	ENSG00000257103	ENST00000544216	Transcript	frameshift_variant	1165-1166	1088-1089	363	Y/YX	tat/taTt	.	.	.	1	LSM14A	HGNC	24489	protein_coding	YES	CCDS12435.1	ENSP00000446271	LS14A_HUMAN	.	UPI000006E20E	.	.	.	8/10	.	PROSITE_profiles:PS51513,hmmpanther:PTHR13586,hmmpanther:PTHR13586:SF2,Pfam_domain:PF09532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CTATTATGACA	.	2	ESCA
ZNF570	0	.	GRCh37	19	37975902	37975902	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1378C>T	p.His460Tyr	p.H460Y	ENST00000330173	5/5	39	33	5	42	42	0	ZNF570,missense_variant,p.His257Tyr,ENST00000388801,;ZNF570,missense_variant,p.His460Tyr,ENST00000330173,;ZNF570,missense_variant,p.His516Tyr,ENST00000586475,;ZNF570,downstream_gene_variant,,ENST00000589725,;CTD-2086O20.3,upstream_gene_variant,,ENST00000591976,;ZNF570,3_prime_UTR_variant,,ENST00000588644,;ZNF570,downstream_gene_variant,,ENST00000590664,;	T	ENSG00000171827	ENST00000330173	Transcript	missense_variant	1907	1378	460	H/Y	Cat/Tat	.	.	.	1	ZNF570	HGNC	26416	protein_coding	YES	CCDS12504.1	ENSP00000331540	ZN570_HUMAN	K7EP64_HUMAN,K7ENX9_HUMAN,K7EMF5_HUMAN,B4DMP1_HUMAN	UPI000006DC96	.	deleterious(0)	probably_damaging(0.996)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF17,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAACATCAG	.	4	ESCA
SAFB	0	.	GRCh37	19	5661536	5661536	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870C>T	p.Arg624Cys	p.R624C	ENST00000588852	15/21	29	25	4	34	34	0	SAFB,missense_variant,p.Arg624Cys,ENST00000588852,;SAFB,missense_variant,p.Arg555Cys,ENST00000454510,;SAFB,missense_variant,p.Arg624Cys,ENST00000292123,;SAFB,missense_variant,p.Arg466Cys,ENST00000538656,;SAFB,missense_variant,p.Arg454Cys,ENST00000433404,;SAFB,missense_variant,p.Arg623Cys,ENST00000592224,;SAFB,missense_variant,p.Arg21Cys,ENST00000589006,;SAFB,3_prime_UTR_variant,,ENST00000589863,;SAFB,upstream_gene_variant,,ENST00000586281,;SAFB,upstream_gene_variant,,ENST00000591991,;	T	ENSG00000160633	ENST00000588852	Transcript	missense_variant	1923	1870	624	R/C	Cgt/Tgt	.	.	.	1	SAFB	HGNC	10520	protein_coding	YES	CCDS59339.1	ENSP00000467423	SAFB1_HUMAN	Q68DW3_HUMAN,F5GZU3_HUMAN	UPI0000E5BE82	.	tolerated(0.06)	unknown(0)	15/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15683:SF6,hmmpanther:PTHR15683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTGCGTGAA	.	4	ESCA
NOTCH2	0	.	GRCh37	1	120512369	120512369	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.875-2A>T	.	p.X292_splice	ENST00000256646	.	100	91	8	30	30	0	NOTCH2,splice_acceptor_variant,,ENST00000256646,;NOTCH2,splice_acceptor_variant,,ENST00000479412,;	A	ENSG00000134250	ENST00000256646	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	NOTCH2	HGNC	7882	protein_coding	YES	CCDS908.1	ENSP00000256646	NOTC2_HUMAN	Q9UFD5_HUMAN,Q13560_HUMAN	UPI000013CF1D	.	.	.	.	5/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTCCTTTTAG	.	3	ESCA
PRAMEF10	0	.	GRCh37	1	12954510	12954510	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.773A>T	p.Asp258Val	p.D258V	ENST00000235347	3/4	160	141	19	121	121	0	PRAMEF10,missense_variant,p.Asp258Val,ENST00000235347,;	A	ENSG00000187545	ENST00000235347	Transcript	missense_variant	853	773	258	D/V	gAc/gTc	.	.	.	-1	PRAMEF10	HGNC	27997	protein_coding	YES	CCDS41255.1	ENSP00000235347	PRA10_HUMAN	.	UPI0000199949	.	deleterious(0)	benign(0.219)	3/4	.	Superfamily_domains:SSF52047,PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224:SF16,hmmpanther:PTHR14224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAAGTCAGGA	.	4	ESCA
HRNR	0	.	GRCh37	1	152187118	152187118	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6987C>T	p.%3D	p.G2329G	ENST00000368801	3/3	113	94	18	80	80	0	HRNR,synonymous_variant,p.%3D,ENST00000368801,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	A	ENSG00000197915	ENST00000368801	Transcript	synonymous_variant	7063	6987	2329	G	ggC/ggT	.	.	.	-1	HRNR	HGNC	20846	protein_coding	YES	CCDS30859.1	ENSP00000357791	HORN_HUMAN	Q5W8V9_HUMAN	UPI00001D7CAD	.	.	.	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TGTCGGCCACT	.	3	ESCA
F5	0	.	GRCh37	1	169497273	169497273	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5479A>G	p.Arg1827Gly	p.R1827G	ENST00000367797	17/25	34	31	3	37	37	0	F5,missense_variant,p.Arg1832Gly,ENST00000367796,;F5,missense_variant,p.Arg1827Gly,ENST00000367797,;	C	ENSG00000198734	ENST00000367797	Transcript	missense_variant	5681	5479	1827	R/G	Agg/Ggg	.	.	.	-1	F5	HGNC	3542	protein_coding	YES	CCDS1281.1	ENSP00000356771	FA5_HUMAN	Q8TD21_HUMAN,Q2HZZ1_HUMAN,Q1L610_HUMAN	UPI0000070F01	.	deleterious(0)	probably_damaging(0.922)	17/25	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.40.420,Superfamily_domains:SSF49503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACCTCACCC	.	2	ESCA
PRELP	0	.	GRCh37	1	203453189	203453189	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.877C>A	p.Leu293Met	p.L293M	ENST00000343110	2/3	25	13	11	23	23	0	PRELP,missense_variant,p.Leu293Met,ENST00000343110,;	A	ENSG00000188783	ENST00000343110	Transcript	missense_variant	1004	877	293	L/M	Ctg/Atg	.	.	.	1	PRELP	HGNC	9357	protein_coding	YES	CCDS1438.1	ENSP00000343924	PRELP_HUMAN	Q7Z4B2_HUMAN	UPI000013222E	.	deleterious(0.04)	possibly_damaging(0.897)	2/3	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24371,hmmpanther:PTHR24371:SF15,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAACCTGCTT	.	5	ESCA
CNTN2	0	.	GRCh37	1	205042860	205042860	+	Silent	SNP	G	G	T	rs772810010	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3090G>T	p.%3D	p.A1030A	ENST00000331830	23/23	28	19	8	27	27	0	CNTN2,synonymous_variant,p.%3D,ENST00000331830,;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,;CNTN2,downstream_gene_variant,,ENST00000525433,;	T	ENSG00000184144	ENST00000331830	Transcript	synonymous_variant	3374	3090	1030	A	gcG/gcT	rs772810010,COSM1500793	.	.	1	CNTN2	HGNC	2172	protein_coding	YES	CCDS1449.1	ENSP00000330633	CNTN2_HUMAN	.	UPI00001266A5	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCGATGCT	.	5	ESCA
KCNH1	0	.	GRCh37	1	211093142	211093142	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1302G>C	p.%3D	p.G434G	ENST00000271751	7/11	69	61	8	93	93	0	KCNH1,synonymous_variant,p.%3D,ENST00000367007,;KCNH1,synonymous_variant,p.%3D,ENST00000271751,;	G	ENSG00000143473	ENST00000271751	Transcript	synonymous_variant	1330	1302	434	G	ggG/ggC	.	.	.	-1	KCNH1	HGNC	6250	protein_coding	YES	CCDS1496.1	ENSP00000271751	KCNH1_HUMAN	.	UPI000003230D	.	.	.	7/11	.	hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF377,Pfam_domain:PF00520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGACCCATT	.	4	ESCA
FMN2	0	.	GRCh37	1	240255581	240255581	+	Missense_Mutation	SNP	G	G	T	rs753347899	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>T	p.Gly58Cys	p.G58C	ENST00000319653	1/18	24	15	8	20	20	0	FMN2,missense_variant,p.Gly58Cys,ENST00000319653,;FMN2,intron_variant,,ENST00000447095,;	T	ENSG00000155816	ENST00000319653	Transcript	missense_variant	402	172	58	G/C	Ggc/Tgc	rs753347899	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	unknown(0)	1/18	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G197delG|c.589_591delGGC|8,BUFFER|p.G201G|c.603C>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGCGGCGGG	.	5	ESCA
RBBP4	0	.	GRCh37	1	33138069	33138069	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.985A>T	p.Asn329Tyr	p.N329Y	ENST00000373493	9/12	26	22	4	57	57	0	RBBP4,missense_variant,p.Asn67Tyr,ENST00000482190,;RBBP4,missense_variant,p.Asn329Tyr,ENST00000373485,;RBBP4,missense_variant,p.Asn77Tyr,ENST00000544435,;RBBP4,missense_variant,p.Asn328Tyr,ENST00000414241,;RBBP4,missense_variant,p.Asn329Tyr,ENST00000373493,;RBBP4,missense_variant,p.Asn294Tyr,ENST00000458695,;RBBP4,missense_variant,p.Asn89Tyr,ENST00000463378,;RBBP4,missense_variant,p.Asn132Tyr,ENST00000475321,;RBBP4,downstream_gene_variant,,ENST00000445722,;RBBP4,downstream_gene_variant,,ENST00000524393,;RBBP4,missense_variant,p.Asn84Tyr,ENST00000460669,;RBBP4,3_prime_UTR_variant,,ENST00000492348,;RBBP4,downstream_gene_variant,,ENST00000531983,;RBBP4,downstream_gene_variant,,ENST00000526193,;RBBP4,downstream_gene_variant,,ENST00000527118,;RBBP4,downstream_gene_variant,,ENST00000401893,;RBBP4,downstream_gene_variant,,ENST00000477563,;	T	ENSG00000162521	ENST00000373493	Transcript	missense_variant	1144	985	329	N/Y	Aat/Tat	.	.	.	1	RBBP4	HGNC	9887	protein_coding	YES	CCDS366.1	ENSP00000362592	RBBP4_HUMAN	H0YCT5_HUMAN,E9PND5_HUMAN,C9JPP3_HUMAN,B4DRT0_HUMAN	UPI000013318C	.	deleterious(0.03)	benign(0.064)	9/12	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF90,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E330K|c.988G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCACAATGAG	.	5	ESCA
PTPRF	0	.	GRCh37	1	44063676	44063676	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2071G>C	p.Gly691Arg	p.G691R	ENST00000359947	12/34	63	39	24	47	47	0	PTPRF,missense_variant,p.Gly691Arg,ENST00000438120,;PTPRF,missense_variant,p.Gly691Arg,ENST00000359947,;PTPRF,missense_variant,p.Gly348Arg,ENST00000429895,;PTPRF,missense_variant,p.Gly691Arg,ENST00000372413,;PTPRF,missense_variant,p.Gly691Arg,ENST00000372414,;PTPRF,intron_variant,,ENST00000412568,;PTPRF,intron_variant,,ENST00000414879,;PTPRF,intron_variant,,ENST00000422171,;PTPRF,upstream_gene_variant,,ENST00000372407,;PTPRF,upstream_gene_variant,,ENST00000496447,;	C	ENSG00000142949	ENST00000359947	Transcript	missense_variant	2411	2071	691	G/R	Ggc/Cgc	.	.	.	1	PTPRF	HGNC	9670	protein_coding	YES	CCDS489.2	ENSP00000353030	PTPRF_HUMAN	G1UI20_HUMAN	UPI0000470154	.	deleterious(0)	benign(0.11)	12/34	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,Pfam_domain:PF00041,hmmpanther:PTHR19134:SF203,hmmpanther:PTHR19134,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGTGGGCCCC	.	5	ESCA
OSBPL9	0	.	GRCh37	1	52253066	52253066	+	Missense_Mutation	SNP	T	T	C	rs778762175	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2072T>C	p.Ile691Thr	p.I691T	ENST00000447887	23/24	20	13	7	30	30	0	OSBPL9,missense_variant,p.Ile681Thr,ENST00000428468,;OSBPL9,missense_variant,p.Ile699Thr,ENST00000371710,;OSBPL9,missense_variant,p.Ile691Thr,ENST00000447887,;OSBPL9,missense_variant,p.Ile503Thr,ENST00000486942,;OSBPL9,missense_variant,p.Ile686Thr,ENST00000337809,;OSBPL9,missense_variant,p.Ile516Thr,ENST00000435686,;OSBPL9,missense_variant,p.Ile668Thr,ENST00000371714,;OSBPL9,missense_variant,p.Ile571Thr,ENST00000361556,;OSBPL9,missense_variant,p.Ile600Thr,ENST00000530544,;OSBPL9,missense_variant,p.Ile516Thr,ENST00000531828,;OSBPL9,missense_variant,p.Ile664Thr,ENST00000453295,;OSBPL9,missense_variant,p.Ile503Thr,ENST00000462759,;NRD1,downstream_gene_variant,,ENST00000440943,;NRD1,downstream_gene_variant,,ENST00000354831,;NRD1,downstream_gene_variant,,ENST00000352171,;NRD1,downstream_gene_variant,,ENST00000539524,;NRD1,downstream_gene_variant,,ENST00000485608,;NRD1,downstream_gene_variant,,ENST00000464385,;OSBPL9,3_prime_UTR_variant,,ENST00000495776,;OSBPL9,3_prime_UTR_variant,,ENST00000435274,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000531819,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000475697,;	C	ENSG00000117859	ENST00000447887	Transcript	missense_variant	2091	2072	691	I/T	aTt/aCt	rs778762175	.	.	1	OSBPL9	HGNC	16386	protein_coding	YES	CCDS44145.1	ENSP00000412733	OSBL9_HUMAN	Q9BRN2_HUMAN,E9PNR1_HUMAN,B3KW33_HUMAN	UPI0000167BAD	.	deleterious(0)	probably_damaging(0.998)	23/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10972:SF27,hmmpanther:PTHR10972,Pfam_domain:PF01237,Superfamily_domains:0051579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACATTGATG	byFrequency	5	ESCA
ICMT	0	.	GRCh37	1	6285033	6285033	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*107A>G	.	.	ENST00000343813	5/5	19	14	5	12	12	0	ICMT,3_prime_UTR_variant,,ENST00000343813,;RNF207,downstream_gene_variant,,ENST00000377948,;RNF207,downstream_gene_variant,,ENST00000377939,;ICMT,upstream_gene_variant,,ENST00000495791,;ICMT,3_prime_UTR_variant,,ENST00000489498,;ICMT,3_prime_UTR_variant,,ENST00000474756,;RNF207,downstream_gene_variant,,ENST00000496676,;	C	ENSG00000116237	ENST00000343813	Transcript	3_prime_UTR_variant	991	.	.	.	.	.	.	.	-1	ICMT	HGNC	5350	protein_coding	YES	CCDS61.1	ENSP00000343552	ICMT_HUMAN	K7EQW0_HUMAN,B3KS61_HUMAN	UPI00000012C2	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTAATGACAT	.	5	ESCA
CAMTA1	0	.	GRCh37	1	7827834	7827834	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1283T>C	.	.	ENST00000303635	23/23	30	21	8	36	36	0	CAMTA1,3_prime_UTR_variant,,ENST00000490905,;CAMTA1,3_prime_UTR_variant,,ENST00000303635,;CAMTA1,3_prime_UTR_variant,,ENST00000495233,;VAMP3,upstream_gene_variant,,ENST00000470357,;VAMP3,upstream_gene_variant,,ENST00000054666,;CAMTA1,downstream_gene_variant,,ENST00000439411,;CAMTA1,downstream_gene_variant,,ENST00000476864,;	C	ENSG00000171735	ENST00000303635	Transcript	3_prime_UTR_variant	6512	.	.	.	.	.	.	.	1	CAMTA1	HGNC	18806	protein_coding	YES	CCDS30576.1	ENSP00000306522	CMTA1_HUMAN	.	UPI00001C1D72	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTATTTCAC	.	5	ESCA
DPYD	0	.	GRCh37	1	97658623	97658623	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2622+2T>G	.	p.X874_splice	ENST00000370192	.	71	62	8	62	62	0	DPYD,splice_donor_variant,,ENST00000370192,;DPYD-AS1,intron_variant,,ENST00000422980,;	C	ENSG00000188641	ENST00000370192	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	DPYD	HGNC	3012	protein_coding	YES	CCDS30777.1	ENSP00000359211	DPYD_HUMAN	.	UPI0000458949	.	.	.	.	20/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACATACCTTG	.	4	ESCA
PLAGL2	0	.	GRCh37	20	30784583	30784583	+	Missense_Mutation	SNP	G	G	A	rs768542815	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1163C>T	p.Ala388Val	p.A388V	ENST00000246229	3/3	32	26	6	50	50	0	PLAGL2,missense_variant,p.Ala388Val,ENST00000246229,;	A	ENSG00000126003	ENST00000246229	Transcript	missense_variant	1428	1163	388	A/V	gCg/gTg	rs768542815	.	.	-1	PLAGL2	HGNC	9047	protein_coding	YES	CCDS13197.1	ENSP00000246229	PLAL2_HUMAN	.	UPI0000001C1D	.	tolerated(0.27)	benign(0.016)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10032:SF190,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCGCAGCT	byFrequency	5	ESCA
NCOA6	0	.	GRCh37	20	33330205	33330205	+	Silent	SNP	T	T	C	rs769062649	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3855A>G	p.%3D	p.Q1285Q	ENST00000374796	12/16	50	43	7	83	83	0	NCOA6,synonymous_variant,p.%3D,ENST00000374796,;NCOA6,synonymous_variant,p.%3D,ENST00000359003,;	C	ENSG00000198646	ENST00000374796	Transcript	synonymous_variant	6426	3855	1285	Q	caA/caG	rs769062649	.	.	-1	NCOA6	HGNC	15936	protein_coding	YES	CCDS13241.1	ENSP00000363929	NCOA6_HUMAN	.	UPI000013C634	.	.	.	12/16	.	hmmpanther:PTHR15690:SF0,hmmpanther:PTHR15690	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGCTTGCCC	byFrequency	5	ESCA
PHF20	0	.	GRCh37	20	34536334	34536334	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*785G>A	.	.	ENST00000374012	18/18	29	25	4	58	58	0	PHF20,3_prime_UTR_variant,,ENST00000439301,;PHF20,3_prime_UTR_variant,,ENST00000374012,;	A	ENSG00000025293	ENST00000374012	Transcript	3_prime_UTR_variant	3953	.	.	.	.	.	.	.	1	PHF20	HGNC	16098	protein_coding	YES	CCDS13268.1	ENSP00000363124	PHF20_HUMAN	Q5JXL1_HUMAN,Q5JWZ0_HUMAN,B3KUL4_HUMAN	UPI000006E61B	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TCCCCGTTCTA	.	2	ESCA
PHF20	0	.	GRCh37	20	34538089	34538089	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2540T>C	.	.	ENST00000374012	18/18	48	37	10	46	46	0	PHF20,3_prime_UTR_variant,,ENST00000439301,;PHF20,3_prime_UTR_variant,,ENST00000374012,;SCAND1,downstream_gene_variant,,ENST00000305978,;SCAND1,downstream_gene_variant,,ENST00000373991,;	C	ENSG00000025293	ENST00000374012	Transcript	3_prime_UTR_variant	5708	.	.	.	.	.	.	.	1	PHF20	HGNC	16098	protein_coding	YES	CCDS13268.1	ENSP00000363124	PHF20_HUMAN	Q5JXL1_HUMAN,Q5JWZ0_HUMAN,B3KUL4_HUMAN	UPI000006E61B	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACTAATCA	.	5	ESCA
TGIF2	0	.	GRCh37	20	35221020	35221020	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1186G>A	.	.	ENST00000373874	3/3	10	7	3	12	12	0	TGIF2,3_prime_UTR_variant,,ENST00000373872,;TGIF2,3_prime_UTR_variant,,ENST00000373874,;TGIF2-C20orf24,intron_variant,,ENST00000558530,;TGIF2,downstream_gene_variant,,ENST00000561398,;TGIF2,downstream_gene_variant,,ENST00000558465,;TGIF2,downstream_gene_variant,,ENST00000557885,;TGIF2,downstream_gene_variant,,ENST00000560025,;TGIF2,downstream_gene_variant,,ENST00000558028,;RP5-977B1.11,intron_variant,,ENST00000561134,;	A	ENSG00000118707	ENST00000373874	Transcript	3_prime_UTR_variant	2099	.	.	.	.	.	.	.	1	TGIF2	HGNC	15764	protein_coding	YES	CCDS13278.1	ENSP00000362981	TGIF2_HUMAN	H0YKN5_HUMAN	UPI0000136CC1	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAATGGTGTCC	.	2	ESCA
PCIF1	0	.	GRCh37	20	44573647	44573647	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1146C>T	p.%3D	p.I382I	ENST00000372409	11/17	45	38	7	36	36	0	PCIF1,synonymous_variant,p.%3D,ENST00000372409,;ZNF335,downstream_gene_variant,,ENST00000322927,;ZNF335,downstream_gene_variant,,ENST00000426788,;PCIF1,non_coding_transcript_exon_variant,,ENST00000479348,;	T	ENSG00000100982	ENST00000372409	Transcript	synonymous_variant	1510	1146	382	I	atC/atT	.	.	.	1	PCIF1	HGNC	16200	protein_coding	YES	CCDS13388.1	ENSP00000361486	PCIF1_HUMAN	.	UPI000000D717	.	.	.	11/17	.	hmmpanther:PTHR21727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCCTCAA	.	5	ESCA
GCNT7	0	.	GRCh37	20	55072460	55072460	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-162T>C	.	.	ENST00000243913	5/7	54	41	13	57	57	0	GCNT7,5_prime_UTR_variant,,ENST00000243913,;RTFDC1,intron_variant,,ENST00000357348,;RTFDC1,intron_variant,,ENST00000395881,;RTFDC1,intron_variant,,ENST00000449062,;RTFDC1,intron_variant,,ENST00000023939,;	G	ENSG00000124091	ENST00000243913	Transcript	5_prime_UTR_variant	911	.	.	.	.	.	.	.	-1	GCNT7	HGNC	16099	protein_coding	YES	.	ENSP00000243913	GCNT7_HUMAN	F2Z6J8_HUMAN	UPI0000E5A355	.	.	.	5/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAAATTTTG	.	5	ESCA
BRWD1	0	.	GRCh37	21	40567638	40567638	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6571+786A>G	.	.	ENST00000333229	.	23	19	3	39	39	0	BRWD1,3_prime_UTR_variant,,ENST00000342449,;BRWD1,intron_variant,,ENST00000380800,;BRWD1,intron_variant,,ENST00000333229,;BRWD1,intron_variant,,ENST00000446924,;BRWD1,downstream_gene_variant,,ENST00000491564,;	C	ENSG00000185658	ENST00000333229	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	BRWD1	HGNC	12760	protein_coding	YES	CCDS13662.1	ENSP00000330753	BRWD1_HUMAN	.	UPI0000163C12	.	.	.	.	41/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTATAATGC	.	4	ESCA
ZNF280B	0	.	GRCh37	22	22842160	22842160	+	Missense_Mutation	SNP	C	C	G	rs144549774	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1564G>C	p.Val522Leu	p.V522L	ENST00000360412	4/4	28	25	3	61	61	0	ZNF280B,missense_variant,p.Val522Leu,ENST00000406426,;ZNF280B,missense_variant,p.Val522Leu,ENST00000360412,;	G	ENSG00000198477	ENST00000360412	Transcript	missense_variant	2340	1564	522	V/L	Gtg/Ctg	rs144549774	.	.	-1	ZNF280B	HGNC	23022	protein_coding	YES	CCDS13799.1	ENSP00000353586	Z280B_HUMAN	.	UPI000013FF86	.	tolerated(0.06)	benign(0.216)	4/4	.	hmmpanther:PTHR23228:SF108,hmmpanther:PTHR23228	G:0.0004	G:0.0015	G:0	.	G:0	G:0	G:0	G:0.0007	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GCTCACAGTTA	byFrequency|byCluster|by1000G	2	ESCA
CABIN1	0	.	GRCh37	22	24483514	24483514	+	Missense_Mutation	SNP	G	G	A	rs148592192	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3373G>A	p.Val1125Ile	p.V1125I	ENST00000398319	23/37	19	14	4	48	48	0	CABIN1,missense_variant,p.Val1125Ile,ENST00000398319,;CABIN1,missense_variant,p.Val1075Ile,ENST00000405822,;CABIN1,missense_variant,p.Val1125Ile,ENST00000263119,;CABIN1,upstream_gene_variant,,ENST00000496016,;	A	ENSG00000099991	ENST00000398319	Transcript	missense_variant	3758	3373	1125	V/I	Gtc/Atc	rs148592192,COSM3405550	.	.	1	CABIN1	HGNC	24187	protein_coding	YES	CCDS13823.1	ENSP00000381364	CABIN_HUMAN	.	UPI0000126D6C	.	deleterious(0.03)	probably_damaging(0.987)	23/37	.	Superfamily_domains:SSF48452,Gene3D:1.25.40.10,hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCCGTCTTG	byCluster	5	ESCA
LMF2	0	.	GRCh37	22	50944766	50944766	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543C>A	p.%3D	p.A181A	ENST00000474879	4/14	14	11	3	28	28	0	LMF2,synonymous_variant,p.%3D,ENST00000216080,;LMF2,synonymous_variant,p.%3D,ENST00000380796,;LMF2,synonymous_variant,p.%3D,ENST00000474879,;NCAPH2,upstream_gene_variant,,ENST00000523045,;NCAPH2,upstream_gene_variant,,ENST00000395701,;NCAPH2,upstream_gene_variant,,ENST00000420993,;NCAPH2,upstream_gene_variant,,ENST00000299821,;NCAPH2,upstream_gene_variant,,ENST00000395698,;LMF2,non_coding_transcript_exon_variant,,ENST00000505981,;LMF2,downstream_gene_variant,,ENST00000507607,;NCAPH2,upstream_gene_variant,,ENST00000418794,;LMF2,upstream_gene_variant,,ENST00000514938,;NCAPH2,upstream_gene_variant,,ENST00000518394,;LMF2,upstream_gene_variant,,ENST00000504717,;	T	ENSG00000100258	ENST00000474879	Transcript	synonymous_variant	559	543	181	A	gcC/gcA	.	.	.	-1	LMF2	HGNC	25096	protein_coding	YES	CCDS14093.2	ENSP00000424381	LMF2_HUMAN	.	UPI0000071DF9	.	.	.	4/14	.	hmmpanther:PTHR14463,hmmpanther:PTHR14463:SF5,Pfam_domain:PF06762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGAGGCGAA	.	2	ESCA
NPAS2	0	.	GRCh37	2	101565927	101565927	+	Missense_Mutation	SNP	C	C	T	rs763172499	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583C>T	p.Arg195Cys	p.R195C	ENST00000335681	7/21	23	19	4	30	30	0	NPAS2,missense_variant,p.Arg195Cys,ENST00000335681,;NPAS2,missense_variant,p.Arg260Cys,ENST00000542504,;NPAS2,missense_variant,p.Arg185Cys,ENST00000448812,;NPAS2,downstream_gene_variant,,ENST00000427413,;NPAS2,non_coding_transcript_exon_variant,,ENST00000486017,;NPAS2,non_coding_transcript_exon_variant,,ENST00000492373,;	T	ENSG00000170485	ENST00000335681	Transcript	missense_variant	868	583	195	R/C	Cgc/Tgc	rs763172499	.	.	1	NPAS2	HGNC	7895	protein_coding	YES	CCDS2048.1	ENSP00000338283	NPAS2_HUMAN	A2I2P5_HUMAN	UPI0000163B27	.	deleterious(0)	probably_damaging(0.964)	7/21	.	hmmpanther:PTHR23042:SF4,hmmpanther:PTHR23042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATTTTCGCTCT	byFrequency	3	ESCA
CNTNAP5	0	.	GRCh37	2	125192188	125192188	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657C>A	p.Phe219Leu	p.F219L	ENST00000431078	5/24	30	24	6	37	37	0	CNTNAP5,missense_variant,p.Phe219Leu,ENST00000431078,;	A	ENSG00000155052	ENST00000431078	Transcript	missense_variant	1021	657	219	F/L	ttC/ttA	COSM3566011	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	tolerated(1)	benign(0.075)	5/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTCCATGG	.	5	ESCA
AMER3	0	.	GRCh37	2	131520725	131520725	+	Silent	SNP	C	C	T	rs778862261	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1080C>T	p.%3D	p.S360S	ENST00000423981	2/2	22	19	3	29	29	0	AMER3,synonymous_variant,p.%3D,ENST00000321420,;AMER3,synonymous_variant,p.%3D,ENST00000423981,;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,;	T	ENSG00000178171	ENST00000423981	Transcript	synonymous_variant	1190	1080	360	S	agC/agT	rs778862261	.	.	1	AMER3	HGNC	26771	protein_coding	YES	CCDS2164.1	ENSP00000392700	AMER3_HUMAN	C9JS07_HUMAN,C9J4B8_HUMAN	UPI0000D61239	.	.	.	2/2	.	hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2,Pfam_domain:PF09422	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCAGCGGCTC	byFrequency	2	ESCA
LCT	0	.	GRCh37	2	136566569	136566569	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3348G>A	p.%3D	p.Q1116Q	ENST00000264162	8/17	26	21	5	51	51	0	LCT,synonymous_variant,p.%3D,ENST00000264162,;Y_RNA,downstream_gene_variant,,ENST00000363794,;LCT,synonymous_variant,p.%3D,ENST00000452974,;	T	ENSG00000115850	ENST00000264162	Transcript	synonymous_variant	3359	3348	1116	Q	caG/caA	.	.	.	-1	LCT	HGNC	6530	protein_coding	YES	CCDS2178.1	ENSP00000264162	LPH_HUMAN	.	UPI000013D4D2	.	.	.	8/17	.	hmmpanther:PTHR10353,hmmpanther:PTHR10353:SF38,Gene3D:3.20.20.80,Pfam_domain:PF00232,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTCTGCTC	.	5	ESCA
ZEB2	0	.	GRCh37	2	145182382	145182382	+	Silent	SNP	G	G	A	rs573552493	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.384C>T	p.%3D	p.T128T	ENST00000558170	4/10	121	89	32	157	157	0	ZEB2,synonymous_variant,p.%3D,ENST00000392861,;ZEB2,synonymous_variant,p.%3D,ENST00000303660,;ZEB2,synonymous_variant,p.%3D,ENST00000440875,;ZEB2,synonymous_variant,p.%3D,ENST00000427902,;ZEB2,synonymous_variant,p.%3D,ENST00000409487,;ZEB2,synonymous_variant,p.%3D,ENST00000558170,;ZEB2,synonymous_variant,p.%3D,ENST00000409211,;ZEB2,intron_variant,,ENST00000539609,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000431672,;ZEB2,downstream_gene_variant,,ENST00000434448,;ZEB2,downstream_gene_variant,,ENST00000479735,;ZEB2,downstream_gene_variant,,ENST00000461784,;ZEB2,downstream_gene_variant,,ENST00000560384,;ZEB2,downstream_gene_variant,,ENST00000472146,;ZEB2,downstream_gene_variant,,ENST00000465308,;ZEB2,downstream_gene_variant,,ENST00000476394,;	A	ENSG00000169554	ENST00000558170	Transcript	synonymous_variant	1569	384	128	T	acC/acT	rs573552493,COSM165691	.	.	-1	ZEB2	HGNC	14881	protein_coding	YES	CCDS2186.1	ENSP00000454157	ZEB2_HUMAN	U3KPV5_HUMAN,Q53TG0_HUMAN,Q53TD9_HUMAN,E7EUW9_HUMAN,E7ESP8_HUMAN,C9JUQ1_HUMAN,C9JU62_HUMAN,A0JP08_HUMAN	UPI00001359A2	.	.	.	4/10	.	hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF2	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGCGGTCTG	by1000G	5	ESCA
MYCN	0	.	GRCh37	2	16085729	16085729	+	Missense_Mutation	SNP	G	G	A	rs140581169	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.905G>A	p.Arg302His	p.R302H	ENST00000281043	3/3	29	22	7	56	56	0	MYCN,missense_variant,p.Arg302His,ENST00000281043,;MYCNOS,upstream_gene_variant,,ENST00000448719,;MYCNOS,upstream_gene_variant,,ENST00000439180,;MYCNOS,upstream_gene_variant,,ENST00000453400,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000420452,;	A	ENSG00000134323	ENST00000281043	Transcript	missense_variant	1202	905	302	R/H	cGt/cAt	rs140581169	.	.	1	MYCN	HGNC	7559	protein_coding	YES	CCDS1687.1	ENSP00000281043	MYCN_HUMAN	Q9UMQ5_HUMAN,Q7Z7Q9_HUMAN,Q53XS5_HUMAN	UPI000012FAF8	.	tolerated(0.27)	possibly_damaging(0.703)	3/3	.	hmmpanther:PTHR11514:SF3,hmmpanther:PTHR11514,Pfam_domain:PF01056,PIRSF_domain:PIRSF001705	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGCGTCCCA	byCluster	5	ESCA
ITGB6	0	.	GRCh37	2	161030646	161030646	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598A>G	p.Ile200Val	p.I200V	ENST00000283249	5/15	36	28	8	26	26	0	ITGB6,missense_variant,p.Ile158Val,ENST00000428609,;ITGB6,missense_variant,p.Ile200Val,ENST00000409872,;ITGB6,missense_variant,p.Ile200Val,ENST00000409967,;ITGB6,missense_variant,p.Ile200Val,ENST00000283249,;ITGB6,non_coding_transcript_exon_variant,,ENST00000485635,;ITGB6,3_prime_UTR_variant,,ENST00000409583,;	C	ENSG00000115221	ENST00000283249	Transcript	missense_variant	836	598	200	I/V	Att/Gtt	.	.	.	-1	ITGB6	HGNC	6161	protein_coding	YES	CCDS2212.1	ENSP00000283249	ITB6_HUMAN	.	UPI000012DA13	.	tolerated(0.55)	benign(0.009)	5/15	.	hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF11,Gene3D:3.40.50.410,Pfam_domain:PF00362,PIRSF_domain:PIRSF002512,SMART_domains:SM00187,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAATACTAC	.	5	ESCA
TTN	0	.	GRCh37	2	179554284	179554284	+	Missense_Mutation	SNP	T	T	C	rs753824961	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31885A>G	p.Ile10629Val	p.I10629V	ENST00000589042	123/363	27	23	4	33	33	0	TTN,missense_variant,p.Ile507Val,ENST00000414766,;TTN,missense_variant,p.Ile9385Val,ENST00000342992,;TTN,missense_variant,p.Ile10629Val,ENST00000589042,;TTN,missense_variant,p.Ile10312Val,ENST00000591111,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000589830,;	C	ENSG00000155657	ENST00000589042	Transcript	missense_variant	32110	31885	10629	I/V	Ata/Gta	rs753824961	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	123/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF02818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTATTTTTT	byFrequency	5	ESCA
NOP58	0	.	GRCh37	2	203152394	203152394	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.446A>G	p.Tyr149Cys	p.Y149C	ENST00000264279	6/15	71	46	25	87	87	0	NOP58,missense_variant,p.Tyr149Cys,ENST00000264279,;SNORD11B,upstream_gene_variant,,ENST00000607707,;NOP58,non_coding_transcript_exon_variant,,ENST00000492688,;NOP58,downstream_gene_variant,,ENST00000472050,;NOP58,downstream_gene_variant,,ENST00000467734,;NOP58,missense_variant,p.Tyr19Cys,ENST00000433543,;NOP58,intron_variant,,ENST00000478941,;NOP58,downstream_gene_variant,,ENST00000488403,;NOP58,downstream_gene_variant,,ENST00000426814,;	G	ENSG00000055044	ENST00000264279	Transcript	missense_variant	672	446	149	Y/C	tAt/tGt	COSM1015002	.	.	1	NOP58	HGNC	29926	protein_coding	YES	CCDS2353.1	ENSP00000264279	NOP58_HUMAN	.	UPI0000130366	.	deleterious(0)	probably_damaging(0.954)	6/15	.	hmmpanther:PTHR10894	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCGATATAGAT	.	3	ESCA
HDAC4	0	.	GRCh37	2	240036937	240036937	+	Missense_Mutation	SNP	G	G	A	rs202206567	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1588C>T	p.Arg530Cys	p.R530C	ENST00000345617	13/27	30	26	4	39	39	0	HDAC4,missense_variant,p.Arg504Cys,ENST00000541256,;HDAC4,missense_variant,p.Arg114Cys,ENST00000543185,;HDAC4,missense_variant,p.Arg530Cys,ENST00000345617,;HDAC4,non_coding_transcript_exon_variant,,ENST00000535493,;HDAC4,non_coding_transcript_exon_variant,,ENST00000463007,;HDAC4,non_coding_transcript_exon_variant,,ENST00000493582,;	A	ENSG00000068024	ENST00000345617	Transcript	missense_variant	2380	1588	530	R/C	Cgt/Tgt	rs202206567	.	.	-1	HDAC4	HGNC	14063	protein_coding	YES	CCDS2529.1	ENSP00000264606	HDAC4_HUMAN	Q53SM2_HUMAN,Q53SB4_HUMAN,F5H0B1_HUMAN,F5GX36_HUMAN,C9J0X4_HUMAN	UPI000013D541	.	tolerated(0.08)	probably_damaging(0.999)	13/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10625:SF100,hmmpanther:PTHR10625,PIRSF_domain:PIRSF037911	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCACGGAGCT	byCluster	2	ESCA
AGBL5	0	.	GRCh37	2	27280243	27280243	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1608G>A	p.%3D	p.G536G	ENST00000360131	9/15	35	28	7	45	45	0	AGBL5,synonymous_variant,p.%3D,ENST00000360131,;AGBL5,synonymous_variant,p.%3D,ENST00000323064,;AGBL5,downstream_gene_variant,,ENST00000421915,;AGBL5,downstream_gene_variant,,ENST00000453161,;AGBL5,downstream_gene_variant,,ENST00000451003,;AGBL5,upstream_gene_variant,,ENST00000441931,;AGBL5,downstream_gene_variant,,ENST00000437006,;AGBL5-IT1,upstream_gene_variant,,ENST00000411862,;RP11-503P10.1,upstream_gene_variant,,ENST00000607407,;AGBL5,synonymous_variant,p.%3D,ENST00000487078,;AGBL5,downstream_gene_variant,,ENST00000477136,;AGBL5,downstream_gene_variant,,ENST00000489683,;	A	ENSG00000084693	ENST00000360131	Transcript	synonymous_variant	1767	1608	536	G	ggG/ggA	.	.	.	1	AGBL5	HGNC	26147	protein_coding	YES	CCDS1732.3	ENSP00000353249	CBPC5_HUMAN	C9JTY1_HUMAN,C9JQG9_HUMAN,C9JHM6_HUMAN,C9JCE1_HUMAN	UPI000006FE54	.	.	.	9/15	.	hmmpanther:PTHR12756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGGGCGTGC	.	5	ESCA
PRKD3	0	.	GRCh37	2	37516571	37516571	+	Silent	SNP	T	T	C	rs760047457	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.645A>G	p.%3D	p.V215V	ENST00000379066	5/19	46	38	8	65	65	0	PRKD3,synonymous_variant,p.%3D,ENST00000443187,;PRKD3,synonymous_variant,p.%3D,ENST00000234179,;PRKD3,synonymous_variant,p.%3D,ENST00000379066,;PRKD3,non_coding_transcript_exon_variant,,ENST00000494667,;PRKD3,non_coding_transcript_exon_variant,,ENST00000475912,;PRKD3,downstream_gene_variant,,ENST00000464552,;	C	ENSG00000115825	ENST00000379066	Transcript	synonymous_variant	1408	645	215	V	gtA/gtG	rs760047457	.	.	-1	PRKD3	HGNC	9408	protein_coding	YES	CCDS1789.1	ENSP00000368356	KPCD3_HUMAN	C9JKP8_HUMAN	UPI0000035B4D	.	.	.	5/19	.	hmmpanther:PTHR22968,hmmpanther:PTHR22968:SF11,PIRSF_domain:PIRSF000552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGATACATT	.	5	ESCA
AAK1	0	.	GRCh37	2	69702234	69702234	+	3'UTR	SNP	T	T	C	rs183297839	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*767A>G	.	.	ENST00000409085	22/22	31	19	11	55	55	0	AAK1,3_prime_UTR_variant,,ENST00000409085,;AAK1,intron_variant,,ENST00000409068,;AAK1,downstream_gene_variant,,ENST00000489327,;	C	ENSG00000115977	ENST00000409085	Transcript	3_prime_UTR_variant	4030	.	.	.	.	rs183297839	.	.	-1	AAK1	HGNC	19679	protein_coding	YES	CCDS1893.2	ENSP00000386456	AAK1_HUMAN	.	UPI0001881663	.	.	.	22/22	.	.	G:0.0044	G:0	G:0.0231	.	G:0.004	G:0.002	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTATATAAC	byFrequency|byCluster|by1000G	5	ESCA
PHLDB2	0	.	GRCh37	3	111603832	111603832	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.908A>G	p.Asn303Ser	p.N303S	ENST00000431670	2/18	26	21	4	37	37	0	PHLDB2,missense_variant,p.Asn303Ser,ENST00000477695,;PHLDB2,missense_variant,p.Asn303Ser,ENST00000478922,;PHLDB2,missense_variant,p.Asn330Ser,ENST00000393923,;PHLDB2,missense_variant,p.Asn303Ser,ENST00000412622,;PHLDB2,missense_variant,p.Asn303Ser,ENST00000481953,;PHLDB2,missense_variant,p.Asn303Ser,ENST00000498699,;PHLDB2,missense_variant,p.Asn303Ser,ENST00000431670,;PHLDB2,missense_variant,p.Asn303Ser,ENST00000393925,;	G	ENSG00000144824	ENST00000431670	Transcript	missense_variant	1319	908	303	N/S	aAt/aGt	.	.	.	1	PHLDB2	HGNC	29573	protein_coding	YES	CCDS46886.1	ENSP00000405405	PHLB2_HUMAN	Q8NEI7_HUMAN,Q659D2_HUMAN	UPI0000457152	.	tolerated(0.17)	benign(0.003)	2/18	.	hmmpanther:PTHR12156:SF17,hmmpanther:PTHR12156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTAATTTTT	.	5	ESCA
ZNF148	0	.	GRCh37	3	124947627	124947627	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3558C>A	.	.	ENST00000360647	9/9	15	11	4	30	30	0	ZNF148,3_prime_UTR_variant,,ENST00000360647,;SLC12A8,intron_variant,,ENST00000423114,;ZNF148,downstream_gene_variant,,ENST00000485866,;ZNF148,downstream_gene_variant,,ENST00000492394,;ZNF148,downstream_gene_variant,,ENST00000544464,;ZNF148,downstream_gene_variant,,ENST00000468369,;ZNF148,downstream_gene_variant,,ENST00000484491,;ZNF148,downstream_gene_variant,,ENST00000496732,;ZNF148,downstream_gene_variant,,ENST00000497929,;	T	ENSG00000163848	ENST00000360647	Transcript	3_prime_UTR_variant	6429	.	.	.	.	.	.	.	-1	ZNF148	HGNC	12933	protein_coding	YES	CCDS3031.1	ENSP00000353863	ZN148_HUMAN	C9K0U4_HUMAN,C9JRX0_HUMAN,C9J6Y6_HUMAN	UPI000013C2FF	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCAGAATTA	.	2	ESCA
ASTE1	0	.	GRCh37	3	130732925	130732925	+	Silent	SNP	A	A	G	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2016T>C	p.%3D	p.H672H	ENST00000264992	6/6	16	11	5	17	17	0	ASTE1,synonymous_variant,p.%3D,ENST00000514044,;ASTE1,synonymous_variant,p.%3D,ENST00000264992,;ATP2C1,intron_variant,,ENST00000533801,;ATP2C1,intron_variant,,ENST00000328560,;ATP2C1,intron_variant,,ENST00000504612,;ATP2C1,intron_variant,,ENST00000359644,;ATP2C1,intron_variant,,ENST00000507488,;ATP2C1,intron_variant,,ENST00000393221,;ATP2C1,intron_variant,,ENST00000422190,;ATP2C1,intron_variant,,ENST00000513801,;ATP2C1,intron_variant,,ENST00000504381,;ASTE1,downstream_gene_variant,,ENST00000505290,;ASTE1,3_prime_UTR_variant,,ENST00000507978,;ASTE1,downstream_gene_variant,,ENST00000504964,;	G	ENSG00000034533	ENST00000264992	Transcript	synonymous_variant	2458	2016	672	H	caT/caC	COSM3944856	.	.	-1	ASTE1	HGNC	25021	protein_coding	YES	CCDS3068.1	ENSP00000264992	ASTE1_HUMAN	D6RJF1_HUMAN,D6R9W5_HUMAN	UPI00001B6B0B	.	.	.	6/6	.	hmmpanther:PTHR15665	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCACTATGTTC	.	2	ESCA
ARMC8	0	.	GRCh37	3	137991875	137991875	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1504C>T	p.%3D	p.L502L	ENST00000481646	18/23	30	23	7	41	41	0	ARMC8,synonymous_variant,p.%3D,ENST00000538260,;ARMC8,synonymous_variant,p.%3D,ENST00000461822,;ARMC8,synonymous_variant,p.%3D,ENST00000491704,;ARMC8,synonymous_variant,p.%3D,ENST00000469044,;ARMC8,synonymous_variant,p.%3D,ENST00000485396,;ARMC8,synonymous_variant,p.%3D,ENST00000393058,;ARMC8,synonymous_variant,p.%3D,ENST00000481646,;NME9,intron_variant,,ENST00000536478,;NME9,intron_variant,,ENST00000383180,;NME9,intron_variant,,ENST00000341790,;NME9,intron_variant,,ENST00000317876,;NME9,intron_variant,,ENST00000484930,;ARMC8,upstream_gene_variant,,ENST00000464181,;ARMC8,non_coding_transcript_exon_variant,,ENST00000460495,;ARMC8,non_coding_transcript_exon_variant,,ENST00000466762,;NME9,intron_variant,,ENST00000492993,;	T	ENSG00000114098	ENST00000481646	Transcript	synonymous_variant	1910	1504	502	L	Cta/Tta	.	.	.	1	ARMC8	HGNC	24999	protein_coding	YES	CCDS54646.1	ENSP00000420333	ARMC8_HUMAN	C9J8P8_HUMAN,C9J625_HUMAN,B7Z979_HUMAN	UPI000007471D	.	.	.	18/23	.	Superfamily_domains:SSF48371,SMART_domains:SM00185,Gene3D:1.25.10.10,hmmpanther:PTHR15651,hmmpanther:PTHR15651:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAGCTATTC	.	5	ESCA
NLGN1	0	.	GRCh37	3	173997346	173997346	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555G>A	p.Gly519Ser	p.G519S	ENST00000457714	6/7	47	34	13	67	67	0	NLGN1,missense_variant,p.Gly559Ser,ENST00000401917,;NLGN1,missense_variant,p.Gly519Ser,ENST00000457714,;NLGN1,missense_variant,p.Gly519Ser,ENST00000361589,;NLGN1,missense_variant,p.Gly519Ser,ENST00000545397,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000469564,;NLGN1,downstream_gene_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000490929,;NLGN1,downstream_gene_variant,,ENST00000469727,;	A	ENSG00000169760	ENST00000457714	Transcript	missense_variant	1984	1555	519	G/S	Ggc/Agc	COSM313243	.	.	1	NLGN1	HGNC	14291	protein_coding	YES	CCDS3222.1	ENSP00000392500	NLGN1_HUMAN	.	UPI0000072F54	.	tolerated(0.11)	probably_damaging(0.997)	6/7	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF52	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATTGGCCCT	.	5	ESCA
ACAP2	0	.	GRCh37	3	195013077	195013077	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870G>A	p.Glu624Lys	p.E624K	ENST00000326793	19/23	44	38	6	36	36	0	ACAP2,missense_variant,p.Glu218Lys,ENST00000450200,;ACAP2,missense_variant,p.Glu624Lys,ENST00000326793,;ACAP2,downstream_gene_variant,,ENST00000484296,;ACAP2,upstream_gene_variant,,ENST00000466876,;ACAP2,downstream_gene_variant,,ENST00000475905,;	T	ENSG00000114331	ENST00000326793	Transcript	missense_variant	2101	1870	624	E/K	Gag/Aag	.	.	.	-1	ACAP2	HGNC	16469	protein_coding	YES	CCDS33924.1	ENSP00000324287	ACAP2_HUMAN	C9J8L1_HUMAN	UPI0000141A1A	.	tolerated(0.08)	benign(0.039)	19/23	.	PROSITE_profiles:PS50297,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF241,Pfam_domain:PF12796,Gene3D:1.25.40.20,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCTCAGCCA	.	4	ESCA
CXCR6	0	.	GRCh37	3	45989477	45989477	+	3'Flank	SNP	G	G	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000458629	.	49	37	12	67	67	0	CXCR6,3_prime_UTR_variant,,ENST00000304552,;CXCR6,3_prime_UTR_variant,,ENST00000438735,;FYCO1,intron_variant,,ENST00000296137,;FYCO1,intron_variant,,ENST00000433878,;FYCO1,intron_variant,,ENST00000438446,;FYCO1,intron_variant,,ENST00000535325,;CXCR6,downstream_gene_variant,,ENST00000457814,;CXCR6,downstream_gene_variant,,ENST00000458629,;	T	ENSG00000172215	ENST00000458629	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	162	1	CXCR6	HGNC	16647	protein_coding	YES	CCDS2735.1	ENSP00000395704	CXCR6_HUMAN	A0N0N3_HUMAN	UPI0000001635	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGAGATCAG	.	5	ESCA
FAM208A	0	.	GRCh37	3	56703801	56703801	+	Missense_Mutation	SNP	T	T	A	rs762493863	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662A>T	p.Tyr221Phe	p.Y221F	ENST00000493960	5/24	35	21	14	51	51	0	FAM208A,missense_variant,p.Tyr221Phe,ENST00000355628,;FAM208A,missense_variant,p.Tyr221Phe,ENST00000493960,;FAM208A,upstream_gene_variant,,ENST00000478052,;FAM208A,downstream_gene_variant,,ENST00000477406,;	A	ENSG00000163946	ENST00000493960	Transcript	missense_variant	673	662	221	Y/F	tAt/tTt	rs762493863	.	.	-1	FAM208A	HGNC	30314	protein_coding	YES	CCDS46853.1	ENSP00000417509	F208A_HUMAN	.	UPI0000422561	.	deleterious(0.04)	probably_damaging(0.944)	5/24	.	Pfam_domain:PF12509,hmmpanther:PTHR16207:SF1,hmmpanther:PTHR16207	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCATACCTA	.	5	ESCA
EPHA3	0	.	GRCh37	3	89529574	89529574	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*922T>C	.	.	ENST00000336596	17/17	41	29	12	32	32	0	EPHA3,3_prime_UTR_variant,,ENST00000336596,;EPHA3,downstream_gene_variant,,ENST00000494014,;	C	ENSG00000044524	ENST00000336596	Transcript	3_prime_UTR_variant	4099	.	.	.	.	.	.	.	1	EPHA3	HGNC	3387	protein_coding	YES	CCDS2922.1	ENSP00000337451	EPHA3_HUMAN	.	UPI0000163BE4	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAATATACC	.	5	ESCA
CXXC4	0	.	GRCh37	4	105412091	105412091	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.869C>G	p.Ser290Cys	p.S290C	ENST00000394767	2/3	49	45	4	62	62	0	CXXC4,missense_variant,p.Ser121Cys,ENST00000426831,;CXXC4,missense_variant,p.Ser290Cys,ENST00000394767,;AC093628.1,mature_miRNA_variant,,ENST00000606234,;AC004053.1,upstream_gene_variant,,ENST00000500179,;CXXC4,intron_variant,,ENST00000466963,;	C	ENSG00000168772	ENST00000394767	Transcript	missense_variant	1320	869	290	S/C	tCc/tGc	.	.	.	-1	CXXC4	HGNC	24593	protein_coding	YES	CCDS3665.2	ENSP00000378248	.	J9JIF5_HUMAN	UPI0000E5AC2D	.	deleterious(0.01)	possibly_damaging(0.629)	2/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13419:SF1,hmmpanther:PTHR13419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGAGGACGAG	.	3	ESCA
PCDH10	0	.	GRCh37	4	134073819	134073819	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2524C>A	p.Pro842Thr	p.P842T	ENST00000264360	1/5	27	21	6	41	41	0	PCDH10,missense_variant,p.Pro842Thr,ENST00000264360,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;PCDH10,upstream_gene_variant,,ENST00000511112,;	A	ENSG00000138650	ENST00000264360	Transcript	missense_variant	3350	2524	842	P/T	Cct/Act	.	.	.	1	PCDH10	HGNC	13404	protein_coding	YES	CCDS34063.1	ENSP00000264360	PCD10_HUMAN	Q9NSR3_HUMAN	UPI0000161C61	.	deleterious(0)	possibly_damaging(0.701)	1/5	.	hmmpanther:PTHR24028:SF0,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCCCTTCG	.	5	ESCA
TLL1	0	.	GRCh37	4	166924650	166924650	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740G>T	p.Gly247Val	p.G247V	ENST00000061240	6/21	56	46	10	79	79	0	TLL1,missense_variant,p.Gly247Val,ENST00000061240,;TLL1,missense_variant,p.Gly247Val,ENST00000513213,;TLL1,missense_variant,p.Gly247Val,ENST00000507499,;TLL1,3_prime_UTR_variant,,ENST00000509505,;	T	ENSG00000038295	ENST00000061240	Transcript	missense_variant	1387	740	247	G/V	gGc/gTc	.	.	.	1	TLL1	HGNC	11843	protein_coding	YES	CCDS3811.1	ENSP00000061240	TLL1_HUMAN	D6RCE0_HUMAN	UPI0000072EED	.	deleterious(0)	probably_damaging(0.999)	6/21	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,Pfam_domain:PF01400,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001199,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00480	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATAGGCTTTT	.	5	ESCA
LGI2	0	.	GRCh37	4	25019636	25019636	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630C>A	p.Ser210Arg	p.S210R	ENST00000382114	6/8	53	42	11	71	71	0	LGI2,missense_variant,p.Ser210Arg,ENST00000382114,;LGI2,missense_variant,p.Ser201Arg,ENST00000512108,;	T	ENSG00000153012	ENST00000382114	Transcript	missense_variant	816	630	210	S/R	agC/agA	.	.	.	-1	LGI2	HGNC	18710	protein_coding	YES	CCDS3431.1	ENSP00000371548	LGI2_HUMAN	.	UPI0000047256	.	tolerated(0.22)	possibly_damaging(0.701)	6/8	.	SMART_domains:SM00082,hmmpanther:PTHR24367:SF21,hmmpanther:PTHR24367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAAGCTGGT	.	5	ESCA
RGS12	0	.	GRCh37	4	3418649	3418649	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2437C>A	p.Leu813Ile	p.L813I	ENST00000344733	8/18	33	28	5	36	36	0	RGS12,missense_variant,p.Leu155Ile,ENST00000538395,;RGS12,missense_variant,p.Leu813Ile,ENST00000336727,;RGS12,missense_variant,p.Leu813Ile,ENST00000382788,;RGS12,missense_variant,p.Leu211Ile,ENST00000306648,;RGS12,missense_variant,p.Leu813Ile,ENST00000344733,;RGS12,missense_variant,p.Leu165Ile,ENST00000338806,;RGS12,3_prime_UTR_variant,,ENST00000543385,;RGS12,non_coding_transcript_exon_variant,,ENST00000508158,;RGS12,downstream_gene_variant,,ENST00000505570,;RGS12,downstream_gene_variant,,ENST00000512990,;RGS12,downstream_gene_variant,,ENST00000503041,;RGS12,downstream_gene_variant,,ENST00000513784,;RGS12,upstream_gene_variant,,ENST00000515521,;RGS12,3_prime_UTR_variant,,ENST00000514268,;RGS12,non_coding_transcript_exon_variant,,ENST00000506998,;RGS12,non_coding_transcript_exon_variant,,ENST00000512266,;RGS12,non_coding_transcript_exon_variant,,ENST00000506631,;RGS12,non_coding_transcript_exon_variant,,ENST00000504194,;RGS12,non_coding_transcript_exon_variant,,ENST00000513991,;RGS12,upstream_gene_variant,,ENST00000510803,;	A	ENSG00000159788	ENST00000344733	Transcript	missense_variant	3341	2437	813	L/I	Ctc/Atc	.	.	.	1	RGS12	HGNC	9994	protein_coding	YES	CCDS3366.1	ENSP00000339381	RGS12_HUMAN	Q69YN1_HUMAN,Q56A82_HUMAN,E9PBG5_HUMAN	UPI0000133830	.	deleterious(0)	possibly_damaging(0.822)	8/18	.	PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF149,Pfam_domain:PF00615,Gene3D:1.10.167.10,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAATCTCATG	.	4	ESCA
DCK	0	.	GRCh37	4	71895846	71895846	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*751A>G	.	.	ENST00000286648	7/7	40	32	7	70	70	0	DCK,3_prime_UTR_variant,,ENST00000286648,;DCK,3_prime_UTR_variant,,ENST00000504952,;DCK,3_prime_UTR_variant,,ENST00000504730,;DCK,3_prime_UTR_variant,,ENST00000503359,;DCK,downstream_gene_variant,,ENST00000509764,;	G	ENSG00000156136	ENST00000286648	Transcript	3_prime_UTR_variant	1931	.	.	.	.	.	.	.	1	DCK	HGNC	2704	protein_coding	YES	CCDS3548.1	ENSP00000286648	DCK_HUMAN	F5CTF3_HUMAN,B4E0A5_HUMAN	UPI0000128FC6	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATATCCTG	.	5	ESCA
BMPR1B	0	.	GRCh37	4	96070005	96070005	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1273T>G	p.Tyr425Asp	p.Y425D	ENST00000440890	9/11	69	61	8	92	92	0	BMPR1B,missense_variant,p.Tyr425Asp,ENST00000440890,;BMPR1B,missense_variant,p.Tyr395Asp,ENST00000264568,;BMPR1B,missense_variant,p.Tyr395Asp,ENST00000509540,;BMPR1B,missense_variant,p.Tyr395Asp,ENST00000512312,;BMPR1B,missense_variant,p.Tyr395Asp,ENST00000394931,;BMPR1B,missense_variant,p.Tyr395Asp,ENST00000515059,;	G	ENSG00000138696	ENST00000440890	Transcript	missense_variant	1294	1273	425	Y/D	Tac/Gac	.	.	.	1	BMPR1B	HGNC	1077	protein_coding	YES	CCDS58919.1	ENSP00000401907	BMR1B_HUMAN	D6RGW8_HUMAN	UPI00017A7CB9	.	deleterious(0)	probably_damaging(0.992)	9/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255:SF62,hmmpanther:PTHR23255,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTCTTACATC	.	4	ESCA
ST8SIA4	0	.	GRCh37	5	100222259	100222259	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291G>A	p.%3D	p.V97V	ENST00000231461	3/5	19	15	4	19	19	0	ST8SIA4,synonymous_variant,p.%3D,ENST00000451528,;ST8SIA4,synonymous_variant,p.%3D,ENST00000231461,;ST8SIA4,non_coding_transcript_exon_variant,,ENST00000507360,;	T	ENSG00000113532	ENST00000231461	Transcript	synonymous_variant	602	291	97	V	gtG/gtA	.	.	.	-1	ST8SIA4	HGNC	10871	protein_coding	YES	CCDS4091.1	ENSP00000231461	SIA8D_HUMAN	.	UPI0000135973	.	.	.	3/5	.	PIRSF_domain:PIRSF005557,Pfam_domain:PF00777,hmmpanther:PTHR11987,hmmpanther:PTHR11987:SF31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACCACTGA	.	5	ESCA
FNIP1	0	.	GRCh37	5	131008447	131008447	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1690A>G	p.Met564Val	p.M564V	ENST00000510461	14/18	95	69	25	97	97	0	FNIP1,missense_variant,p.Met536Val,ENST00000307968,;FNIP1,missense_variant,p.Met564Val,ENST00000510461,;FNIP1,missense_variant,p.Met519Val,ENST00000307954,;CTC-432M15.3,intron_variant,,ENST00000514667,;FNIP1,downstream_gene_variant,,ENST00000511848,;	C	ENSG00000217128	ENST00000510461	Transcript	missense_variant	1786	1690	564	M/V	Atg/Gtg	.	.	.	-1	FNIP1	HGNC	29418	protein_coding	YES	CCDS34227.1	ENSP00000421985	FNIP1_HUMAN	B3KX44_HUMAN	UPI00001AEE81	.	tolerated(0.13)	probably_damaging(0.968)	14/18	.	hmmpanther:PTHR21634,hmmpanther:PTHR21634:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCATAACGA	.	5	ESCA
C5orf24	0	.	GRCh37	5	134190864	134190864	+	Missense_Mutation	SNP	C	C	T	rs755244010	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274C>T	p.Arg92Trp	p.R92W	ENST00000394976	2/2	19	15	3	33	33	0	C5orf24,missense_variant,p.Arg92Trp,ENST00000504727,;C5orf24,missense_variant,p.Arg92Trp,ENST00000394976,;C5orf24,missense_variant,p.Arg92Trp,ENST00000435259,;C5orf24,missense_variant,p.Arg92Trp,ENST00000338051,;C5orf24,intron_variant,,ENST00000507390,;C5orf24,downstream_gene_variant,,ENST00000508791,;DDX46,downstream_gene_variant,,ENST00000507053,;	T	ENSG00000181904	ENST00000394976	Transcript	missense_variant	502	274	92	R/W	Cgg/Tgg	rs755244010,COSM1060950	.	.	1	C5orf24	HGNC	26746	protein_coding	YES	CCDS4179.1	ENSP00000378427	CE024_HUMAN	.	UPI000013FCBD	.	deleterious(0)	probably_damaging(0.997)	2/2	.	hmmpanther:PTHR31894	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R90C|c.268C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCCGGCCT	.	5	ESCA
PCDHB7	0	.	GRCh37	5	140555274	140555274	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*476A>T	.	.	ENST00000231137	1/1	35	24	10	56	56	0	PCDHB7,3_prime_UTR_variant,,ENST00000231137,;PCDHB8,upstream_gene_variant,,ENST00000239444,;	T	ENSG00000113212	ENST00000231137	Transcript	3_prime_UTR_variant	3032	.	.	.	.	.	.	.	1	PCDHB7	HGNC	8692	protein_coding	YES	CCDS4249.1	ENSP00000231137	PCDB7_HUMAN	.	UPI00001273E3	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAGATGGTC	.	5	ESCA
PCDHB11	0	.	GRCh37	5	140580848	140580848	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501G>T	p.Ala501Ser	p.A501S	ENST00000354757	1/1	145	108	36	144	144	0	PCDHB11,missense_variant,p.Ala136Ser,ENST00000536699,;PCDHB11,missense_variant,p.Ala501Ser,ENST00000354757,;	T	ENSG00000197479	ENST00000354757	Transcript	missense_variant	1501	1501	501	A/S	Gcc/Tcc	COSM3851538	.	.	1	PCDHB11	HGNC	8682	protein_coding	YES	CCDS4253.1	ENSP00000346802	PCDBB_HUMAN	B4DSF7_HUMAN	UPI00001273E6	.	tolerated_low_confidence(0.23)	benign(0.092)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF91,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCGCCTCC	.	5	ESCA
RASGEF1C	0	.	GRCh37	5	179545653	179545653	+	Missense_Mutation	SNP	C	C	T	rs146808625	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1039G>A	p.Gly347Arg	p.G347R	ENST00000393371	9/13	51	46	5	61	61	0	RASGEF1C,missense_variant,p.Gly196Arg,ENST00000522500,;RASGEF1C,missense_variant,p.Gly347Arg,ENST00000361132,;RASGEF1C,missense_variant,p.Gly347Arg,ENST00000393371,;RASGEF1C,downstream_gene_variant,,ENST00000519883,;RASGEF1C,upstream_gene_variant,,ENST00000519456,;RASGEF1C,missense_variant,p.Gly196Arg,ENST00000520209,;	T	ENSG00000146090	ENST00000393371	Transcript	missense_variant	1336	1039	347	G/R	Ggg/Agg	rs146808625,COSM1543528,COSM1543527	.	.	-1	RASGEF1C	HGNC	27400	protein_coding	YES	CCDS4452.1	ENSP00000377037	RGF1C_HUMAN	.	UPI0000037308	.	deleterious(0.05)	benign(0.393)	9/13	.	PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF186,hmmpanther:PTHR23113,Pfam_domain:PF00617,Gene3D:2ii0A02,SMART_domains:SM00147,Superfamily_domains:0041591	.	.	.	.	.	.	.	T:0.0005	T:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGCCCCGCGCA	byCluster	3	ESCA
IPO11	0	.	GRCh37	5	61826585	61826585	+	Missense_Mutation	SNP	A	A	G	rs776372328	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2182A>G	p.Ile728Val	p.I728V	ENST00000409296	22/30	44	28	15	74	74	0	IPO11,missense_variant,p.Ile728Val,ENST00000409296,;IPO11,missense_variant,p.Ile688Val,ENST00000325324,;IPO11,intron_variant,,ENST00000511713,;KIF2A,non_coding_transcript_exon_variant,,ENST00000509663,;IPO11,missense_variant,p.Ile688Val,ENST00000424533,;IPO11,downstream_gene_variant,,ENST00000502862,;	G	ENSG00000086200	ENST00000409296	Transcript	missense_variant	2312	2182	728	I/V	Ata/Gta	rs776372328	.	.	1	IPO11	HGNC	20628	protein_coding	YES	CCDS47217.1	ENSP00000386992	IPO11_HUMAN	E7EMB7_HUMAN,D6RJB1_HUMAN,D6RCQ2_HUMAN,D6RCN7_HUMAN	UPI00017EE9F4	.	tolerated(0.15)	benign(0.002)	22/30	.	hmmpanther:PTHR10997:SF7,hmmpanther:PTHR10997,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGTATATTT	byFrequency	5	ESCA
ANKRD32	0	.	GRCh37	5	94022349	94022349	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2047G>C	p.Glu683Gln	p.E683Q	ENST00000265140	16/21	30	26	4	37	37	0	ANKRD32,missense_variant,p.Glu683Gln,ENST00000265140,;ANKRD32,non_coding_transcript_exon_variant,,ENST00000450932,;ANKRD32,upstream_gene_variant,,ENST00000475916,;	C	ENSG00000133302	ENST00000265140	Transcript	missense_variant	2466	2047	683	E/Q	Gag/Cag	COSM738899,COSM738898	.	.	1	ANKRD32	HGNC	25408	protein_coding	YES	CCDS4071.2	ENSP00000265140	ANR32_HUMAN	I6L9F1_HUMAN,D6RED9_HUMAN	UPI000066D9F9	.	deleterious(0)	probably_damaging(0.998)	16/21	.	hmmpanther:PTHR13561,hmmpanther:PTHR13561:SF22	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGCAGAGGCA	.	4	ESCA
TRDN	0	.	GRCh37	6	123576225	123576225	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1951+1G>T	.	p.X651_splice	ENST00000398178	.	31	27	4	58	58	0	TRDN,splice_donor_variant,,ENST00000398178,;TRDN,splice_donor_variant,,ENST00000334268,;	A	ENSG00000186439	ENST00000398178	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	TRDN	HGNC	12261	protein_coding	YES	CCDS55053.1	ENSP00000381240	TRDN_HUMAN	.	UPI0000D820CC	.	.	.	.	37/40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATTACCTTTT	.	4	ESCA
SCAND3	0	.	GRCh37	6	28547054	28547054	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.563A>T	p.Asp188Val	p.D188V	ENST00000452236	2/4	52	35	17	77	77	0	SCAND3,missense_variant,p.Asp188Val,ENST00000452236,;SCAND3,non_coding_transcript_exon_variant,,ENST00000530247,;	A	ENSG00000232040	ENST00000452236	Transcript	missense_variant	1181	563	188	D/V	gAt/gTt	.	.	.	-1	SCAND3	HGNC	13851	protein_coding	YES	CCDS34355.1	ENSP00000395259	SCND3_HUMAN	.	UPI00001618B7	.	deleterious_low_confidence(0)	benign(0.03)	2/4	.	hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF90	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTATCTTGA	.	5	ESCA
C6orf106	0	.	GRCh37	6	34574629	34574629	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564G>A	p.%3D	p.T188T	ENST00000374023	4/5	43	40	3	73	73	0	C6orf106,synonymous_variant,p.%3D,ENST00000374021,;C6orf106,synonymous_variant,p.%3D,ENST00000374026,;C6orf106,synonymous_variant,p.%3D,ENST00000374023,;	T	ENSG00000196821	ENST00000374023	Transcript	synonymous_variant	808	564	188	T	acG/acA	.	.	.	-1	C6orf106	HGNC	21215	protein_coding	YES	CCDS4796.1	ENSP00000363135	CF106_HUMAN	Q5TH58_HUMAN	UPI000006F934	.	.	.	4/5	.	hmmpanther:PTHR20930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTGCGTTAC	.	2	ESCA
STK38	0	.	GRCh37	6	36462284	36462284	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1277C>T	.	.	ENST00000229812	14/14	15	12	3	30	30	0	STK38,3_prime_UTR_variant,,ENST00000229812,;KCTD20,downstream_gene_variant,,ENST00000449081,;KCTD20,downstream_gene_variant,,ENST00000373731,;	A	ENSG00000112079	ENST00000229812	Transcript	3_prime_UTR_variant	2961	.	.	.	.	.	.	.	-1	STK38	HGNC	17847	protein_coding	YES	CCDS4822.1	ENSP00000229812	STK38_HUMAN	.	UPI0000047AC1	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTGTGAAA	.	2	ESCA
FBXL4	0	.	GRCh37	6	99374651	99374651	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214T>C	p.Ser72Pro	p.S72P	ENST00000369244	4/10	34	29	5	47	47	0	FBXL4,missense_variant,p.Ser72Pro,ENST00000229971,;FBXL4,missense_variant,p.Ser72Pro,ENST00000369244,;	G	ENSG00000112234	ENST00000369244	Transcript	missense_variant	643	214	72	S/P	Tcc/Ccc	.	.	.	-1	FBXL4	HGNC	13601	protein_coding	YES	CCDS5041.1	ENSP00000358247	FBXL4_HUMAN	.	UPI000012ADE3	.	deleterious(0)	probably_damaging(0.997)	4/10	.	hmmpanther:PTHR23125:SF244,hmmpanther:PTHR23125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGGACATAC	.	4	ESCA
SLC35B4	0	.	GRCh37	7	133994143	133994143	+	Missense_Mutation	SNP	T	T	C	rs183333675	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166A>G	p.Arg56Gly	p.R56G	ENST00000378509	2/10	20	14	5	39	39	0	SLC35B4,missense_variant,p.Arg56Gly,ENST00000378509,;SLC35B4,missense_variant,p.Arg56Gly,ENST00000416907,;SLC35B4,non_coding_transcript_exon_variant,,ENST00000470969,;	C	ENSG00000205060	ENST00000378509	Transcript	missense_variant	466	166	56	R/G	Agg/Ggg	rs183333675	.	.	-1	SLC35B4	HGNC	20584	protein_coding	YES	CCDS34756.1	ENSP00000367770	S35B4_HUMAN	.	UPI00000377B5	.	tolerated(0.25)	benign(0.219)	2/10	.	hmmpanther:PTHR10778:SF4,hmmpanther:PTHR10778,Pfam_domain:PF08449	C:0.0004	C:0	C:0.0029	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCTTCCCA	byFrequency|byCluster|by1000G	5	ESCA
VPS41	0	.	GRCh37	7	38766586	38766586	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2407G>C	p.Ala803Pro	p.A803P	ENST00000310301	28/29	32	25	7	23	23	0	VPS41,missense_variant,p.Ala803Pro,ENST00000310301,;VPS41,missense_variant,p.Ala778Pro,ENST00000395969,;VPS41,splice_region_variant,,ENST00000448833,;VPS41,splice_region_variant,,ENST00000482217,;VPS41,non_coding_transcript_exon_variant,,ENST00000490924,;	G	ENSG00000006715	ENST00000310301	Transcript	missense_variant	2462	2407	803	A/P	Gca/Cca	.	.	.	-1	VPS41	HGNC	12713	protein_coding	YES	CCDS5457.1	ENSP00000309457	VPS41_HUMAN	Q75MS2_HUMAN,C9J2U9_HUMAN	UPI000000DAB7	.	tolerated(0.3)	benign(0.002)	28/29	.	PROSITE_profiles:PS50089,hmmpanther:PTHR12616,Gene3D:3.30.40.10,PIRSF_domain:PIRSF028921,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTGCATCTG	.	2	ESCA
ABCA13	0	.	GRCh37	7	48308594	48308594	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2023C>A	p.Pro675Thr	p.P675T	ENST00000435803	16/62	41	29	11	53	53	0	ABCA13,missense_variant,p.Pro675Thr,ENST00000435803,;ABCA13,3_prime_UTR_variant,,ENST00000417403,;	A	ENSG00000179869	ENST00000435803	Transcript	missense_variant	2047	2023	675	P/T	Cct/Act	COSM3639279,COSM3639278	.	.	1	ABCA13	HGNC	14638	protein_coding	YES	CCDS47584.1	ENSP00000411096	ABCAD_HUMAN	.	UPI00001A95EA	.	.	probably_damaging(0.989)	16/62	.	hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTCCTTGT	.	5	ESCA
EGFR	0	.	GRCh37	7	55273092	55273092	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3415C>T	p.Leu1139Phe	p.L1139F	ENST00000275493	28/28	27	20	7	24	24	0	EGFR,missense_variant,p.Leu1086Phe,ENST00000454757,;EGFR,missense_variant,p.Leu1139Phe,ENST00000275493,;EGFR,intron_variant,,ENST00000442591,;EGFR,downstream_gene_variant,,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000485503,;	T	ENSG00000146648	ENST00000275493	Transcript	missense_variant	3592	3415	1139	L/F	Ctc/Ttc	.	.	.	1	EGFR	HGNC	3236	protein_coding	YES	CCDS5514.1	ENSP00000275493	EGFR_HUMAN	Q75MF2_HUMAN,I3WA73_HUMAN,I3WA72_HUMAN,G9MC81_HUMAN,F1JTL6_HUMAN,E9PFD7_HUMAN,C9JYS6_HUMAN,A7VN06_HUMAN	UPI000003E750	.	deleterious(0)	probably_damaging(0.999)	28/28	.	PIRSF_domain:PIRSF000619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTATCTCAAC	.	5	ESCA
SYBU	0	.	GRCh37	8	110657603	110657603	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-57-658C>T	.	.	ENST00000422135	.	20	15	5	27	27	0	SYBU,5_prime_UTR_variant,,ENST00000534501,;SYBU,5_prime_UTR_variant,,ENST00000528647,;SYBU,5_prime_UTR_variant,,ENST00000440310,;RP11-422N16.3,3_prime_UTR_variant,,ENST00000499579,;SYBU,5_prime_UTR_variant,,ENST00000530841,;SYBU,intron_variant,,ENST00000422135,;SYBU,intron_variant,,ENST00000532779,;SYBU,intron_variant,,ENST00000534578,;SYBU,intron_variant,,ENST00000424158,;SYBU,intron_variant,,ENST00000527600,;SYBU,intron_variant,,ENST00000533821,;SYBU,intron_variant,,ENST00000408908,;SYBU,intron_variant,,ENST00000528045,;SYBU,intron_variant,,ENST00000528331,;SYBU,intron_variant,,ENST00000408889,;SYBU,intron_variant,,ENST00000526302,;SYBU,intron_variant,,ENST00000524720,;SYBU,intron_variant,,ENST00000419099,;SYBU,intron_variant,,ENST00000533171,;SYBU,intron_variant,,ENST00000532189,;SYBU,intron_variant,,ENST00000433638,;SYBU,intron_variant,,ENST00000529190,;SYBU,intron_variant,,ENST00000446070,;SYBU,intron_variant,,ENST00000534184,;SYBU,intron_variant,,ENST00000531230,;SYBU,intron_variant,,ENST00000533895,;SYBU,intron_variant,,ENST00000528716,;SYBU,upstream_gene_variant,,ENST00000528569,;SYBU,upstream_gene_variant,,ENST00000533065,;SYBU,upstream_gene_variant,,ENST00000399066,;SYBU,upstream_gene_variant,,ENST00000276646,;SYBU,intron_variant,,ENST00000527664,;SYBU,upstream_gene_variant,,ENST00000531284,;	A	ENSG00000147642	ENST00000422135	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SYBU	HGNC	26011	protein_coding	YES	CCDS47912.1	ENSP00000407118	SYBU_HUMAN	E9PRT7_HUMAN,E9PQG2_HUMAN,E9PPS4_HUMAN,E9PPC2_HUMAN,E9PN31_HUMAN,E9PLB9_HUMAN,E9PL50_HUMAN,E9PK96_HUMAN,E9PJ11_HUMAN,E9PI48_HUMAN,B3KRD1_HUMAN	UPI00000407AB	.	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAAGGGGTT	.	2	ESCA
RAD21	0	.	GRCh37	8	117887052	117887052	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-235T>C	.	.	ENST00000297338	1/14	33	18	15	52	52	0	RAD21,5_prime_UTR_variant,,ENST00000297338,;RAD21,upstream_gene_variant,,ENST00000519837,;RAD21,upstream_gene_variant,,ENST00000517485,;RAD21,upstream_gene_variant,,ENST00000522699,;RAD21,upstream_gene_variant,,ENST00000520992,;MIR3610,upstream_gene_variant,,ENST00000582903,;RAD21-AS1,non_coding_transcript_exon_variant,,ENST00000521487,;RAD21,upstream_gene_variant,,ENST00000523547,;	G	ENSG00000164754	ENST00000297338	Transcript	5_prime_UTR_variant	54	.	.	.	.	.	.	.	-1	RAD21	HGNC	9811	protein_coding	YES	CCDS6321.1	ENSP00000297338	RAD21_HUMAN	E5RJW1_HUMAN,E5RJK5_HUMAN,E5RIN7_HUMAN,E5RI01_HUMAN,E5RG18_HUMAN,E5RFZ5_HUMAN,E5RFV8_HUMAN	UPI0000133018	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAAATCCTC	.	5	ESCA
NOV	0	.	GRCh37	8	120430329	120430329	+	Silent	SNP	G	G	C	rs773828328	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342G>C	p.%3D	p.G114G	ENST00000259526	3/5	97	90	6	143	143	0	NOV,synonymous_variant,p.%3D,ENST00000259526,;RP11-775B15.2,downstream_gene_variant,,ENST00000519786,;NOV,downstream_gene_variant,,ENST00000520082,;	C	ENSG00000136999	ENST00000259526	Transcript	synonymous_variant	569	342	114	G	ggG/ggC	rs773828328	.	.	1	NOV	HGNC	7885	protein_coding	YES	CCDS6328.1	ENSP00000259526	NOV_HUMAN	B3FHX2_HUMAN	UPI00001303BE	.	.	.	3/5	.	Superfamily_domains:SSF57603,Superfamily_domains:SSF57184,PIRSF_domain:PIRSF036495,SMART_domains:SM00214,Pfam_domain:PF00093,hmmpanther:PTHR11348:SF8,hmmpanther:PTHR11348,PROSITE_profiles:PS50184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R118H|c.353G>A|3	MUTECT|MUSE	GATGGGGTCAT	.	2	ESCA
LRRC6	0	.	GRCh37	8	133595957	133595957	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210G>T	p.Glu404Ter	p.E404*	ENST00000250173	11/12	65	56	9	51	51	0	LRRC6,stop_gained,p.Glu404Ter,ENST00000519595,;LRRC6,stop_gained,p.Glu401Ter,ENST00000518642,;LRRC6,stop_gained,p.Glu404Ter,ENST00000250173,;LRRC6,stop_gained,p.Glu144Ter,ENST00000522789,;LRRC6,non_coding_transcript_exon_variant,,ENST00000522597,;	A	ENSG00000129295	ENST00000250173	Transcript	stop_gained	1284	1210	404	E/*	Gaa/Taa	COSM3645213	.	.	-1	LRRC6	HGNC	16725	protein_coding	YES	CCDS6365.1	ENSP00000250173	TILB_HUMAN	.	UPI000000DBC5	.	.	.	11/12	.	hmmpanther:PTHR10588:SF114,hmmpanther:PTHR10588	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTTCTCTGC	.	4	ESCA
SLC39A4	0	.	GRCh37	8	145641663	145641663	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193-188G>A	.	.	ENST00000301305	.	34	17	16	41	41	0	SLC39A4,5_prime_UTR_variant,,ENST00000276833,;SLC39A4,intron_variant,,ENST00000526658,;SLC39A4,intron_variant,,ENST00000301305,;SLC39A4,upstream_gene_variant,,ENST00000532718,;SLC39A4,upstream_gene_variant,,ENST00000527148,;SLC39A4,upstream_gene_variant,,ENST00000531013,;SLC39A4,upstream_gene_variant,,ENST00000530807,;SLC39A4,upstream_gene_variant,,ENST00000531789,;SLC39A4,upstream_gene_variant,,ENST00000529462,;	T	ENSG00000147804	ENST00000301305	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SLC39A4	HGNC	17129	protein_coding	YES	CCDS6424.1	ENSP00000301305	S39A4_HUMAN	Q9NX22_HUMAN	UPI00001AED01	.	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCACGCAGA	.	5	ESCA
MTUS1	0	.	GRCh37	8	17532707	17532707	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2893C>T	p.Arg965Trp	p.R965W	ENST00000262102	8/15	48	43	4	52	52	0	MTUS1,missense_variant,p.Arg911Trp,ENST00000381869,;MTUS1,missense_variant,p.Arg212Trp,ENST00000381861,;MTUS1,missense_variant,p.Arg37Trp,ENST00000400046,;MTUS1,missense_variant,p.Arg131Trp,ENST00000297488,;MTUS1,missense_variant,p.Arg110Trp,ENST00000544260,;MTUS1,missense_variant,p.Arg911Trp,ENST00000519263,;MTUS1,missense_variant,p.Arg965Trp,ENST00000262102,;MTUS1,non_coding_transcript_exon_variant,,ENST00000517818,;MTUS1,non_coding_transcript_exon_variant,,ENST00000524044,;MTUS1,non_coding_transcript_exon_variant,,ENST00000521772,;MTUS1,non_coding_transcript_exon_variant,,ENST00000521635,;MTUS1,non_coding_transcript_exon_variant,,ENST00000522757,;MTUS1,non_coding_transcript_exon_variant,,ENST00000523183,;MTUS1,non_coding_transcript_exon_variant,,ENST00000518713,;MTUS1,non_coding_transcript_exon_variant,,ENST00000524371,;MTUS1,non_coding_transcript_exon_variant,,ENST00000519066,;MTUS1,downstream_gene_variant,,ENST00000522149,;MTUS1,3_prime_UTR_variant,,ENST00000520196,;MTUS1,non_coding_transcript_exon_variant,,ENST00000517413,;	A	ENSG00000129422	ENST00000262102	Transcript	missense_variant	3118	2893	965	R/W	Cgg/Tgg	.	.	.	-1	MTUS1	HGNC	29789	protein_coding	YES	CCDS43717.1	ENSP00000262102	MTUS1_HUMAN	.	UPI000003FF3C	.	deleterious(0)	probably_damaging(0.951)	8/15	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24200:SF7,hmmpanther:PTHR24200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCCCGGAGGT	.	3	ESCA
E2F5	0	.	GRCh37	8	86126557	86126557	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*460T>C	.	.	ENST00000416274	8/8	41	25	16	45	45	0	E2F5,3_prime_UTR_variant,,ENST00000256117,;C8orf59,3_prime_UTR_variant,,ENST00000417663,;E2F5,3_prime_UTR_variant,,ENST00000416274,;E2F5,3_prime_UTR_variant,,ENST00000418930,;E2F5,3_prime_UTR_variant,,ENST00000521429,;E2F5,3_prime_UTR_variant,,ENST00000520225,;C8orf59,3_prime_UTR_variant,,ENST00000431163,;E2F5,intron_variant,,ENST00000518234,;E2F5,downstream_gene_variant,,ENST00000517476,;C8orf59,downstream_gene_variant,,ENST00000524353,;C8orf59,downstream_gene_variant,,ENST00000321777,;C8orf59,downstream_gene_variant,,ENST00000421308,;C8orf59,downstream_gene_variant,,ENST00000518091,;C8orf59,downstream_gene_variant,,ENST00000523281,;C8orf59,downstream_gene_variant,,ENST00000545322,;C8orf59,downstream_gene_variant,,ENST00000518562,;C8orf59,downstream_gene_variant,,ENST00000458398,;E2F5,non_coding_transcript_exon_variant,,ENST00000519128,;C8orf59,downstream_gene_variant,,ENST00000520236,;C8orf59,downstream_gene_variant,,ENST00000521286,;C8orf59,downstream_gene_variant,,ENST00000523245,;C8orf59,downstream_gene_variant,,ENST00000518786,;	C	ENSG00000133740	ENST00000416274	Transcript	3_prime_UTR_variant	1535	.	.	.	.	.	.	.	1	E2F5	HGNC	3119	protein_coding	YES	CCDS47885.1	ENSP00000398124	E2F5_HUMAN	.	UPI000002E057	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGATATATA	.	5	ESCA
DPY19L4	0	.	GRCh37	8	95751917	95751917	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510A>G	p.%3D	p.G170G	ENST00000414645	6/19	64	44	19	70	70	0	DPY19L4,synonymous_variant,p.%3D,ENST00000519176,;DPY19L4,synonymous_variant,p.%3D,ENST00000414645,;DPY19L4,synonymous_variant,p.%3D,ENST00000521525,;DPY19L4,synonymous_variant,p.%3D,ENST00000519353,;DPY19L4,synonymous_variant,p.%3D,ENST00000523020,;DPY19L4,synonymous_variant,p.%3D,ENST00000522422,;DPY19L4,3_prime_UTR_variant,,ENST00000520774,;	G	ENSG00000156162	ENST00000414645	Transcript	synonymous_variant	609	510	170	G	ggA/ggG	.	.	.	1	DPY19L4	HGNC	27829	protein_coding	YES	CCDS34924.1	ENSP00000389630	D19L4_HUMAN	.	UPI00001A9D7A	.	.	.	6/19	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR31488:SF2,hmmpanther:PTHR31488,Pfam_domain:PF10034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGGATTGCA	.	5	ESCA
TNKS	0	.	GRCh37	8	9592385	9592385	+	Missense_Mutation	SNP	A	A	G	rs772098188	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2324A>G	p.Asp775Gly	p.D775G	ENST00000310430	16/27	31	27	4	53	53	0	TNKS,missense_variant,p.Asp538Gly,ENST00000518281,;TNKS,missense_variant,p.Asp775Gly,ENST00000310430,;TNKS,downstream_gene_variant,,ENST00000519930,;TNKS,upstream_gene_variant,,ENST00000518635,;	G	ENSG00000173273	ENST00000310430	Transcript	missense_variant	2350	2324	775	D/G	gAt/gGt	rs772098188	.	.	1	TNKS	HGNC	11941	protein_coding	YES	CCDS5974.1	ENSP00000311579	TNKS1_HUMAN	Q59FX0_HUMAN,E7EQ52_HUMAN	UPI000013F00D	.	deleterious(0)	probably_damaging(0.998)	16/27	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24180:SF3,hmmpanther:PTHR24180,Pfam_domain:PF13637,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAGATCCAA	.	2	ESCA
SMC5	0	.	GRCh37	9	72962880	72962880	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2815A>G	p.Ile939Val	p.I939V	ENST00000361138	22/25	38	27	11	53	53	0	SMC5,missense_variant,p.Ile939Val,ENST00000361138,;SMC5,non_coding_transcript_exon_variant,,ENST00000471372,;SMC5,downstream_gene_variant,,ENST00000475540,;	G	ENSG00000198887	ENST00000361138	Transcript	missense_variant	2873	2815	939	I/V	Att/Gtt	.	.	.	1	SMC5	HGNC	20465	protein_coding	YES	CCDS6632.1	ENSP00000354957	SMC5_HUMAN	.	UPI000036763A	.	deleterious(0.05)	probably_damaging(0.923)	22/25	.	hmmpanther:PTHR19306:SF1,hmmpanther:PTHR19306,Pfam_domain:PF02463,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAATTAAT	.	5	ESCA
KIAA1210	0	.	GRCh37	X	118257580	118257580	+	Missense_Mutation	SNP	G	G	A	rs776668198	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.446C>T	p.Ser149Phe	p.S149F	ENST00000402510	3/14	20	15	5	20	20	0	KIAA1210,missense_variant,p.Ser149Phe,ENST00000402510,;	A	ENSG00000250423	ENST00000402510	Transcript	missense_variant	446	446	149	S/F	tCt/tTt	rs776668198,COSM212624,COSM212623	.	.	-1	KIAA1210	HGNC	29218	protein_coding	YES	CCDS48156.1	ENSP00000384670	K1210_HUMAN	.	UPI0001596C4C	.	deleterious(0)	benign(0.311)	3/14	.	hmmpanther:PTHR12036:SF19,hmmpanther:PTHR12036	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCAGAAATT	byFrequency	5	ESCA
ARAF	0	.	GRCh37	X	47424691	47424691	+	Missense_Mutation	SNP	C	C	A	rs761480447	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499C>A	p.Gln167Lys	p.Q167K	ENST00000377045	6/16	27	22	4	43	43	0	ARAF,missense_variant,p.Gln167Lys,ENST00000377039,;ARAF,missense_variant,p.Gln167Lys,ENST00000290277,;ARAF,missense_variant,p.Gln167Lys,ENST00000377045,;ARAF,downstream_gene_variant,,ENST00000489496,;ARAF,upstream_gene_variant,,ENST00000469505,;ARAF,upstream_gene_variant,,ENST00000470206,;	A	ENSG00000078061	ENST00000377045	Transcript	missense_variant	693	499	167	Q/K	Cag/Aag	rs761480447	.	.	1	ARAF	HGNC	646	protein_coding	YES	CCDS35232.1	ENSP00000366244	ARAF_HUMAN	Q96II5_HUMAN	UPI0000000C41	.	tolerated(0.32)	benign(0.014)	6/16	.	hmmpanther:PTHR23257:SF43,hmmpanther:PTHR23257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGACAGCAT	byFrequency	5	ESCA
PCDH19	0	.	GRCh37	X	99662990	99662990	+	Silent	SNP	C	C	T	rs761463596	.	TCGA-LN-A49W-01A-11D-A27G-09	TCGA-LN-A49W-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606G>A	p.%3D	p.S202S	ENST00000373034	1/6	33	25	7	25	25	0	PCDH19,synonymous_variant,p.%3D,ENST00000420881,;PCDH19,synonymous_variant,p.%3D,ENST00000255531,;PCDH19,synonymous_variant,p.%3D,ENST00000373034,;	T	ENSG00000165194	ENST00000373034	Transcript	synonymous_variant	2282	606	202	S	tcG/tcA	rs761463596,COSM269838	.	.	-1	PCDH19	HGNC	14270	protein_coding	YES	CCDS55462.1	ENSP00000362125	PCD19_HUMAN	.	UPI00001D7BCD	.	.	.	1/6	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF40,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTGCGACTG	byFrequency	5	ESCA
DPCD	0	.	GRCh37	10	103354421	103354421	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71G>C	p.Arg24Thr	p.R24T	ENST00000370151	2/6	71	60	11	101	101	0	DPCD,missense_variant,p.Arg24Thr,ENST00000370148,;DPCD,missense_variant,p.Arg24Thr,ENST00000370147,;DPCD,missense_variant,p.Arg24Thr,ENST00000370151,;DPCD,upstream_gene_variant,,ENST00000434727,;DPCD,non_coding_transcript_exon_variant,,ENST00000470165,;	C	ENSG00000166171	ENST00000370151	Transcript	missense_variant	120	71	24	R/T	aGg/aCg	.	.	.	1	DPCD	HGNC	24542	protein_coding	YES	CCDS7514.1	ENSP00000359170	DPCD_HUMAN	.	UPI0000073BC7	.	deleterious(0.04)	probably_damaging(0.928)	2/6	.	hmmpanther:PTHR31921:SF1,hmmpanther:PTHR31921,Pfam_domain:PF14913	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGGAAGG	.	5	ESCA
SFXN4	0	.	GRCh37	10	120897154	120897154	+	3'Flank	SNP	T	T	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000355697	.	40	34	5	27	27	0	SFXN4,downstream_gene_variant,,ENST00000355697,;SFXN4,downstream_gene_variant,,ENST00000330036,;FAM45A,downstream_gene_variant,,ENST00000544016,;FAM45A,downstream_gene_variant,,ENST00000535029,;FAM45A,downstream_gene_variant,,ENST00000361432,;FAM45A,non_coding_transcript_exon_variant,,ENST00000489988,;FAM45A,downstream_gene_variant,,ENST00000498549,;SFXN4,downstream_gene_variant,,ENST00000461438,;FAM45A,downstream_gene_variant,,ENST00000489936,;FAM45A,downstream_gene_variant,,ENST00000462327,;SFXN4,downstream_gene_variant,,ENST00000484960,;SFXN4,downstream_gene_variant,,ENST00000490417,;	A	ENSG00000183605	ENST00000355697	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3271	-1	SFXN4	HGNC	16088	protein_coding	YES	CCDS7610.1	ENSP00000347924	SFXN4_HUMAN	B1AMV8_HUMAN,B1AMV7_HUMAN	UPI000004D333	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGTAAAGG	.	5	ESCA
ANKRD26	0	.	GRCh37	10	27317825	27317825	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3928G>T	p.Asp1310Tyr	p.D1310Y	ENST00000376087	27/34	25	21	4	24	24	0	ANKRD26,missense_variant,p.Asp1310Tyr,ENST00000376087,;ANKRD26,missense_variant,p.Asp867Tyr,ENST00000376070,;ANKRD26,missense_variant,p.Asp1326Tyr,ENST00000436985,;	A	ENSG00000107890	ENST00000376087	Transcript	missense_variant	4094	3928	1310	D/Y	Gac/Tac	.	.	.	-1	ANKRD26	HGNC	29186	protein_coding	YES	CCDS41499.1	ENSP00000365255	ANR26_HUMAN	.	UPI000006FC41	.	tolerated(0.3)	benign(0.143)	27/34	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF57997,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGTCCATTT	.	4	ESCA
SGMS1	0	.	GRCh37	10	52066168	52066168	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*734T>A	.	.	ENST00000361781	11/11	27	20	7	27	27	0	SGMS1,3_prime_UTR_variant,,ENST00000361781,;SGMS1,downstream_gene_variant,,ENST00000429490,;SGMS1,downstream_gene_variant,,ENST00000602619,;	T	ENSG00000198964	ENST00000361781	Transcript	3_prime_UTR_variant	2936	.	.	.	.	.	.	.	-1	SGMS1	HGNC	29799	protein_coding	YES	CCDS7240.1	ENSP00000354829	.	R4GNI5_HUMAN,D3DWC4_HUMAN,E6ZCI7_HUMAN	UPI000000D9FC	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATAGACAA	.	5	ESCA
TLL2	0	.	GRCh37	10	98144480	98144480	+	Silent	SNP	G	G	A	rs751509792,rs762651565	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2058C>T	p.%3D	p.P686P	ENST00000357947	16/21	31	27	4	46	46	0	TLL2,synonymous_variant,p.%3D,ENST00000357947,;	A	ENSG00000095587	ENST00000357947	Transcript	synonymous_variant	2284	2058	686	P	ccC/ccT	rs751509792,rs762651565	.	.	-1	TLL2	HGNC	11844	protein_coding	YES	CCDS7449.1	ENSP00000350630	TLL2_HUMAN	.	UPI0000073AEE	.	.	.	16/21	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF613,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,PIRSF_domain:PIRSF001199,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGTCGGGGGA	byFrequency	4	ESCA
ZFYVE27	0	.	GRCh37	10	99509265	99509265	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586C>T	p.%3D	p.L196L	ENST00000356257	5/12	51	43	7	63	63	0	ZFYVE27,synonymous_variant,p.%3D,ENST00000370613,;ZFYVE27,synonymous_variant,p.%3D,ENST00000423811,;ZFYVE27,synonymous_variant,p.%3D,ENST00000337540,;ZFYVE27,synonymous_variant,p.%3D,ENST00000393677,;ZFYVE27,synonymous_variant,p.%3D,ENST00000359980,;ZFYVE27,synonymous_variant,p.%3D,ENST00000357540,;ZFYVE27,synonymous_variant,p.%3D,ENST00000453958,;ZFYVE27,synonymous_variant,p.%3D,ENST00000370610,;ZFYVE27,synonymous_variant,p.%3D,ENST00000356257,;ZFYVE27,upstream_gene_variant,,ENST00000481956,;	T	ENSG00000155256	ENST00000356257	Transcript	synonymous_variant	587	586	196	L	Ctg/Ttg	.	.	.	1	ZFYVE27	HGNC	26559	protein_coding	YES	CCDS31262.1	ENSP00000348593	ZFY27_HUMAN	.	UPI00003FE526	.	.	.	5/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14543	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATGCTGTAT	.	4	ESCA
B3GAT1	0	.	GRCh37	11	134253770	134253770	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.425C>T	p.Thr142Met	p.T142M	ENST00000524765	3/6	81	62	19	21	21	0	B3GAT1,missense_variant,p.Thr142Met,ENST00000524765,;B3GAT1,missense_variant,p.Thr155Met,ENST00000537389,;B3GAT1,missense_variant,p.Thr142Met,ENST00000312527,;B3GAT1,missense_variant,p.Thr142Met,ENST00000392580,;B3GAT1,downstream_gene_variant,,ENST00000531510,;B3GAT1,non_coding_transcript_exon_variant,,ENST00000531778,;	A	ENSG00000109956	ENST00000524765	Transcript	missense_variant	4970	425	142	T/M	aCg/aTg	COSM3769250,COSM3769251	.	.	-1	B3GAT1	HGNC	921	protein_coding	YES	CCDS8500.1	ENSP00000433847	B3GA1_HUMAN	Q8ND18_HUMAN	UPI0000073281	.	deleterious(0)	probably_damaging(1)	3/6	.	hmmpanther:PTHR10896,hmmpanther:PTHR10896:SF21,Gene3D:3.90.550.10,Pfam_domain:PF03360,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGCGTGTAG	.	5	ESCA
TRIM34	0	.	GRCh37	11	5664786	5664786	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1314C>T	p.%3D	p.D438D	ENST00000514226	8/8	77	73	4	103	103	0	TRIM34,synonymous_variant,p.%3D,ENST00000514226,;TRIM34,synonymous_variant,p.%3D,ENST00000429814,;TRIM6-TRIM34,synonymous_variant,p.%3D,ENST00000457787,;TRIM6-TRIM34,synonymous_variant,p.%3D,ENST00000354852,;HBG2,intron_variant,,ENST00000380259,;TRIM34,non_coding_transcript_exon_variant,,ENST00000495668,;TRIM34,downstream_gene_variant,,ENST00000491385,;	T	ENSG00000258659	ENST00000514226	Transcript	synonymous_variant	1651	1314	438	D	gaC/gaT	.	.	.	1	TRIM34	HGNC	10063	protein_coding	YES	CCDS31391.1	ENSP00000422947	TRI34_HUMAN	.	UPI000006F93F	.	.	.	8/8	.	Prints_domain:PR01407,Superfamily_domains:SSF49899,SMART_domains:SM00449,Pfam_domain:PF00622,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF51,PROSITE_profiles:PS50188	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGACTATGA	.	2	ESCA
OR9Q1	0	.	GRCh37	11	57948287	57948287	+	3'UTR	SNP	C	C	T	rs767402837	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*438C>T	.	.	ENST00000335397	3/3	38	32	6	56	56	0	OR9Q1,3_prime_UTR_variant,,ENST00000335397,;	T	ENSG00000186509	ENST00000335397	Transcript	3_prime_UTR_variant	1687	.	.	.	.	rs767402837	.	.	1	OR9Q1	HGNC	14724	protein_coding	YES	CCDS31543.1	ENSP00000334934	OR9Q1_HUMAN	.	UPI0000041B48	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATCCGTGAG	byCluster	5	ESCA
TMEM151A	0	.	GRCh37	11	66063542	66063542	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*418C>T	.	.	ENST00000327259	2/2	142	134	8	122	122	0	TMEM151A,3_prime_UTR_variant,,ENST00000327259,;	T	ENSG00000179292	ENST00000327259	Transcript	3_prime_UTR_variant	1969	.	.	.	.	.	.	.	1	TMEM151A	HGNC	28497	protein_coding	YES	CCDS8133.1	ENSP00000326244	T151A_HUMAN	.	UPI0000070F9B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGGCTTGGG	.	2	ESCA
CABP4	0	.	GRCh37	11	67225884	67225884	+	Missense_Mutation	SNP	C	C	T	rs762298430	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.694C>T	p.Arg232Trp	p.R232W	ENST00000325656	5/6	32	24	8	29	29	0	CABP4,missense_variant,p.Arg232Trp,ENST00000325656,;CABP4,missense_variant,p.Arg127Trp,ENST00000438189,;CTC-1337H24.1,upstream_gene_variant,,ENST00000602912,;CTC-1337H24.2,downstream_gene_variant,,ENST00000602944,;CABP4,downstream_gene_variant,,ENST00000542233,;CABP4,downstream_gene_variant,,ENST00000542025,;CABP4,downstream_gene_variant,,ENST00000538060,;CABP4,downstream_gene_variant,,ENST00000545040,;CABP4,downstream_gene_variant,,ENST00000545777,;	T	ENSG00000175544	ENST00000325656	Transcript	missense_variant	771	694	232	R/W	Cgg/Tgg	rs762298430	.	.	1	CABP4	HGNC	1386	protein_coding	YES	CCDS8166.1	ENSP00000324960	CABP4_HUMAN	.	UPI0000126D68	.	deleterious(0.02)	probably_damaging(0.998)	5/6	.	Superfamily_domains:SSF47473,SMART_domains:SM00054,Pfam_domain:PF13499,Gene3D:1.10.238.10,hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF129,PROSITE_profiles:PS50222	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGCGGGAG	byFrequency	5	ESCA
VPS29	0	.	GRCh37	12	110930988	110930988	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256A>G	p.Ile86Val	p.I86V	ENST00000360579	4/5	16	11	5	20	20	0	VPS29,missense_variant,p.Ile114Val,ENST00000546588,;VPS29,missense_variant,p.Ile82Val,ENST00000549578,;VPS29,missense_variant,p.Ile86Val,ENST00000360579,;VPS29,5_prime_UTR_variant,,ENST00000552130,;VPS29,5_prime_UTR_variant,,ENST00000447578,;VPS29,5_prime_UTR_variant,,ENST00000549970,;FAM216A,downstream_gene_variant,,ENST00000377673,;SNORD50,downstream_gene_variant,,ENST00000365465,;VPS29,non_coding_transcript_exon_variant,,ENST00000548259,;VPS29,downstream_gene_variant,,ENST00000553128,;VPS29,downstream_gene_variant,,ENST00000551655,;VPS29,intron_variant,,ENST00000548539,;FAM216A,downstream_gene_variant,,ENST00000546396,;FAM216A,downstream_gene_variant,,ENST00000547539,;	C	ENSG00000111237	ENST00000360579	Transcript	missense_variant	304	256	86	I/V	Att/Gtt	.	.	.	-1	VPS29	HGNC	14340	protein_coding	YES	CCDS53832.1	ENSP00000353786	VPS29_HUMAN	Q05DG7_HUMAN	UPI000002B6C8	.	tolerated(0.09)	benign(0.014)	4/5	.	hmmpanther:PTHR11124,Pfam_domain:PF12850,Gene3D:3.60.21.10,TIGRFAM_domain:TIGR00040,Superfamily_domains:SSF56300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAATTTTGA	.	5	ESCA
EP400	0	.	GRCh37	12	132512560	132512560	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5110-2A>G	.	p.X1704_splice	ENST00000389561	.	39	36	3	54	54	0	EP400,splice_acceptor_variant,,ENST00000389562,;EP400,splice_acceptor_variant,,ENST00000332482,;EP400,splice_acceptor_variant,,ENST00000389561,;EP400,splice_acceptor_variant,,ENST00000333577,;EP400,splice_acceptor_variant,,ENST00000330386,;SNORA49,upstream_gene_variant,,ENST00000386157,;	G	ENSG00000183495	ENST00000389561	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	EP400	HGNC	11958	protein_coding	YES	CCDS31929.2	ENSP00000374212	EP400_HUMAN	.	UPI00004566BC	.	.	.	.	26/52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAAAGGAGG	.	2	ESCA
BCDIN3D	0	.	GRCh37	12	50232768	50232768	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.265C>A	p.Leu89Ile	p.L89I	ENST00000333924	2/2	20	15	5	28	28	0	BCDIN3D,missense_variant,p.Leu89Ile,ENST00000333924,;BCDIN3D-AS1,non_coding_transcript_exon_variant,,ENST00000548872,;BCDIN3D-AS1,intron_variant,,ENST00000549124,;BCDIN3D,non_coding_transcript_exon_variant,,ENST00000550861,;	T	ENSG00000186666	ENST00000333924	Transcript	missense_variant	307	265	89	L/I	Ctc/Atc	COSM940257	.	.	-1	BCDIN3D	HGNC	27050	protein_coding	YES	CCDS8790.1	ENSP00000335201	BN3D2_HUMAN	.	UPI0000160802	.	deleterious(0.02)	benign(0.242)	2/2	.	PROSITE_profiles:PS51515,hmmpanther:PTHR12315:SF1,hmmpanther:PTHR12315,Gene3D:3.40.50.150,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGAGGAAGT	.	2	ESCA
GDF11	0	.	GRCh37	12	56143474	56143474	+	Missense_Mutation	SNP	G	G	C	rs750335692	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032G>C	p.Gln344His	p.Q344H	ENST00000257868	3/3	38	32	5	46	46	0	GDF11,missense_variant,p.Gln317His,ENST00000546799,;GDF11,missense_variant,p.Gln344His,ENST00000257868,;SARNP,downstream_gene_variant,,ENST00000444631,;SARNP,downstream_gene_variant,,ENST00000552884,;SARNP,downstream_gene_variant,,ENST00000546604,;	C	ENSG00000135414	ENST00000257868	Transcript	missense_variant	1069	1032	344	Q/H	caG/caC	rs750335692	.	.	1	GDF11	HGNC	4216	protein_coding	YES	CCDS8891.1	ENSP00000257868	GDF11_HUMAN	.	UPI000004C158	.	deleterious(0)	possibly_damaging(0.871)	3/3	.	Superfamily_domains:SSF57501,SMART_domains:SM00204,Gene3D:2.10.90.10,Pfam_domain:PF00019,PROSITE_patterns:PS00250,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF140,PROSITE_profiles:PS51362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCAGTGCGA	.	4	ESCA
OTOGL	0	.	GRCh37	12	80647261	80647261	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1274A>G	p.Asn425Ser	p.N425S	ENST00000458043	13/58	40	29	10	74	74	0	OTOGL,missense_variant,p.Asn425Ser,ENST00000458043,;OTOGL,missense_variant,p.Asn425Ser,ENST00000547103,;	G	ENSG00000165899	ENST00000458043	Transcript	missense_variant	1280	1274	425	N/S	aAt/aGt	.	.	.	1	OTOGL	HGNC	26901	protein_coding	YES	.	ENSP00000400895	.	E2QRK2_HUMAN	UPI0001D089C5	.	deleterious(0)	probably_damaging(0.998)	13/58	.	Superfamily_domains:SSF57567,Gene3D:2.10.25.10,Pfam_domain:PF01826,hmmpanther:PTHR11339:SF225,hmmpanther:PTHR11339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACAATGGGA	.	5	ESCA
ZIC5	0	.	GRCh37	13	100615424	100615424	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2207A>T	.	.	ENST00000267294	2/2	28	25	3	37	37	0	ZIC5,3_prime_UTR_variant,,ENST00000267294,;	A	ENSG00000139800	ENST00000267294	Transcript	3_prime_UTR_variant	4433	.	.	.	.	.	.	.	-1	ZIC5	HGNC	20322	protein_coding	YES	CCDS9494.2	ENSP00000267294	ZIC5_HUMAN	.	UPI0000458928	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ATACATAAAAT	.	2	ESCA
FGF14	0	.	GRCh37	13	102568817	102568817	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.209-41171G>C	.	.	ENST00000376131	.	52	46	6	56	56	0	FGF14,missense_variant,p.Arg60Thr,ENST00000376143,;FGF14,intron_variant,,ENST00000376131,;	G	ENSG00000102466	ENST00000376131	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	FGF14	HGNC	3671	protein_coding	YES	CCDS9500.1	ENSP00000365301	FGF14_HUMAN	.	UPI000000D898	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAACCTGCGC	.	3	ESCA
RXFP2	0	.	GRCh37	13	32365960	32365960	+	Missense_Mutation	SNP	G	G	A	rs778183013	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1163G>A	p.Arg388Gln	p.R388Q	ENST00000298386	15/18	69	58	10	73	73	0	RXFP2,missense_variant,p.Arg364Gln,ENST00000380314,;RXFP2,missense_variant,p.Arg388Gln,ENST00000298386,;	A	ENSG00000133105	ENST00000298386	Transcript	missense_variant	1234	1163	388	R/Q	cGa/cAa	rs778183013	.	.	1	RXFP2	HGNC	17318	protein_coding	YES	CCDS9342.1	ENSP00000298386	RXFP2_HUMAN	.	UPI0000049589	.	tolerated(1)	benign(0.005)	15/18	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF226,Gene3D:3.80.10.10,Superfamily_domains:SSF52058,Prints_domain:PR01739	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R388*|c.1162C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCGATACT	.	5	ESCA
KLF5	0	.	GRCh37	13	73651613	73651613	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1589G>A	.	.	ENST00000377687	4/4	19	15	4	27	27	0	KLF5,3_prime_UTR_variant,,ENST00000377687,;KLF5,downstream_gene_variant,,ENST00000539231,;KLF5,downstream_gene_variant,,ENST00000464404,;	A	ENSG00000102554	ENST00000377687	Transcript	3_prime_UTR_variant	3499	.	.	.	.	.	.	.	1	KLF5	HGNC	6349	protein_coding	YES	CCDS9448.1	ENSP00000366915	KLF5_HUMAN	Q5T6X2_HUMAN,B4DL96_HUMAN,A2TJX0_HUMAN	UPI0000000C89	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTGAGAGAAT	.	2	ESCA
TRAV14DV4	0	.	GRCh37	14	22392776	22392776	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.299C>G	p.Ser100Cys	p.S100C	ENST00000390440	2/2	55	49	6	65	65	0	TRAV14DV4,missense_variant,p.Ser100Cys,ENST00000390440,;	G	ENSG00000211792	ENST00000390440	Transcript	missense_variant	374	299	100	S/C	tCc/tGc	.	.	.	1	TRAV14DV4	HGNC	12110	TR_V_gene	YES	.	ENSP00000446015	.	A0JD09_HUMAN	UPI000011C70F	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF6,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCCGCTT	.	4	ESCA
TRAV16	0	.	GRCh37	14	22459103	22459103	+	Silent	SNP	C	C	T	rs748578059	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255C>T	p.%3D	p.G85G	ENST00000390444	2/2	36	29	6	39	39	0	TRAV16,synonymous_variant,p.%3D,ENST00000390444,;	T	ENSG00000211796	ENST00000390444	Transcript	synonymous_variant	255	255	85	G	ggC/ggT	rs748578059	.	.	1	TRAV16	HGNC	12112	TR_V_gene	YES	.	ENSP00000451359	.	.	UPI000011C713	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19367,hmmpanther:PTHR19367:SF4,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGGCGAGAC	.	5	ESCA
CLEC14A	0	.	GRCh37	14	38724771	38724771	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457G>T	p.Glu153Ter	p.E153*	ENST00000342213	1/1	52	46	5	64	64	0	CLEC14A,stop_gained,p.Glu153Ter,ENST00000342213,;	A	ENSG00000176435	ENST00000342213	Transcript	stop_gained	804	457	153	E/*	Gag/Tag	.	.	.	-1	CLEC14A	HGNC	19832	protein_coding	YES	CCDS9667.1	ENSP00000353013	CLC14_HUMAN	.	UPI000000CBD4	.	.	.	1/1	.	PROSITE_profiles:PS50041,hmmpanther:PTHR24838:SF258,hmmpanther:PTHR24838,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGCTCGACCC	.	4	ESCA
GALNT16	0	.	GRCh37	14	69805402	69805402	+	Silent	SNP	T	T	C	rs755771930	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1002T>C	p.%3D	p.S334S	ENST00000337827	10/16	87	76	11	101	101	0	GALNT16,synonymous_variant,p.%3D,ENST00000448469,;GALNT16,synonymous_variant,p.%3D,ENST00000553669,;GALNT16,synonymous_variant,p.%3D,ENST00000337827,;GALNT16,non_coding_transcript_exon_variant,,ENST00000556677,;GALNT16,synonymous_variant,p.%3D,ENST00000553471,;	C	ENSG00000100626	ENST00000337827	Transcript	synonymous_variant	1329	1002	334	S	agT/agC	rs755771930	.	.	1	GALNT16	HGNC	23233	protein_coding	YES	CCDS32107.1	ENSP00000336729	GLT16_HUMAN	Q68VJ8_HUMAN	UPI000004D296	.	.	.	10/16	.	hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF3,Gene3D:3.90.550.10,Pfam_domain:PF02709,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCAGTCTGGA	.	4	ESCA
FBXL22	0	.	GRCh37	15	63893968	63893968	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*83C>G	.	.	ENST00000360587	2/2	24	21	3	23	23	0	FBXL22,3_prime_UTR_variant,,ENST00000360587,;FBXL22,3_prime_UTR_variant,,ENST00000539570,;FBXL22,downstream_gene_variant,,ENST00000560325,;FBXL22,downstream_gene_variant,,ENST00000534939,;USP3-AS1,upstream_gene_variant,,ENST00000560962,;USP3-AS1,upstream_gene_variant,,ENST00000560622,;USP3-AS1,upstream_gene_variant,,ENST00000559737,;USP3-AS1,upstream_gene_variant,,ENST00000558831,;USP3-AS1,upstream_gene_variant,,ENST00000561256,;USP3-AS1,upstream_gene_variant,,ENST00000561191,;	G	ENSG00000197361	ENST00000360587	Transcript	3_prime_UTR_variant	867	.	.	.	.	.	.	.	1	FBXL22	HGNC	27537	protein_coding	YES	CCDS10187.2	ENSP00000353794	FXL22_HUMAN	.	UPI0000408A7A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTTCTCATA	.	2	ESCA
PHKG2	0	.	GRCh37	16	30764831	30764831	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.509C>T	p.Ser170Leu	p.S170L	ENST00000563588	6/10	37	31	6	37	37	0	PHKG2,missense_variant,p.Ser62Leu,ENST00000561712,;PHKG2,missense_variant,p.Ser170Leu,ENST00000565897,;PHKG2,missense_variant,p.Ser170Leu,ENST00000565924,;PHKG2,missense_variant,p.Ser170Leu,ENST00000328273,;PHKG2,missense_variant,p.Ser170Leu,ENST00000424889,;PHKG2,missense_variant,p.Ser170Leu,ENST00000563588,;C16orf93,downstream_gene_variant,,ENST00000541260,;C16orf93,downstream_gene_variant,,ENST00000535476,;C16orf93,downstream_gene_variant,,ENST00000544613,;C16orf93,downstream_gene_variant,,ENST00000543610,;RP11-2C24.4,downstream_gene_variant,,ENST00000483578,;PHKG2,3_prime_UTR_variant,,ENST00000563607,;PHKG2,non_coding_transcript_exon_variant,,ENST00000563913,;PHKG2,non_coding_transcript_exon_variant,,ENST00000569684,;PHKG2,non_coding_transcript_exon_variant,,ENST00000564838,;C16orf93,downstream_gene_variant,,ENST00000544487,;C16orf93,downstream_gene_variant,,ENST00000544643,;PHKG2,downstream_gene_variant,,ENST00000569762,;C16orf93,downstream_gene_variant,,ENST00000543128,;C16orf93,downstream_gene_variant,,ENST00000546006,;C16orf93,downstream_gene_variant,,ENST00000433909,;C16orf93,downstream_gene_variant,,ENST00000537986,;	T	ENSG00000156873	ENST00000563588	Transcript	missense_variant	748	509	170	S/L	tCa/tTa	.	.	.	1	PHKG2	HGNC	8931	protein_coding	YES	CCDS10690.1	ENSP00000455607	PHKG2_HUMAN	Q59GQ4_HUMAN,H3BTW6_HUMAN,H3BP07_HUMAN	UPI000012DF54	.	deleterious(0)	possibly_damaging(0.874)	6/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF121,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTTTCAGATT	.	4	ESCA
ITGAD	0	.	GRCh37	16	31414942	31414942	+	Missense_Mutation	SNP	C	C	T	rs199750609	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.680C>T	p.Thr227Met	p.T227M	ENST00000389202	7/30	35	32	3	38	38	0	ITGAD,missense_variant,p.Thr227Met,ENST00000389202,;RP11-120K18.2,non_coding_transcript_exon_variant,,ENST00000567545,;ITGAD,non_coding_transcript_exon_variant,,ENST00000444228,;	T	ENSG00000156886	ENST00000389202	Transcript	missense_variant	729	680	227	T/M	aCg/aTg	rs199750609	.	.	1	ITGAD	HGNC	6146	protein_coding	YES	CCDS32438.1	ENSP00000373854	ITAD_HUMAN	Q59H14_HUMAN	UPI000004B27A	.	deleterious(0)	probably_damaging(1)	7/30	.	Superfamily_domains:SSF53300,SMART_domains:SM00327,Pfam_domain:PF00092,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19,PROSITE_profiles:PS50234	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTCACGGCCA	byFrequency|byCluster	2	ESCA
DPEP2	0	.	GRCh37	16	68023258	68023258	+	Silent	SNP	G	G	A	rs777330949	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1038C>T	p.%3D	p.I346I	ENST00000412757	10/12	63	53	10	66	66	0	DPEP2,synonymous_variant,p.%3D,ENST00000572888,;DPEP2,synonymous_variant,p.%3D,ENST00000393847,;DPEP2,synonymous_variant,p.%3D,ENST00000412757,;DUS2,intron_variant,,ENST00000571081,;DUS2,intron_variant,,ENST00000570709,;DPEP2,downstream_gene_variant,,ENST00000574865,;DPEP2,downstream_gene_variant,,ENST00000573808,;DPEP2,downstream_gene_variant,,ENST00000572624,;DPEP2,downstream_gene_variant,,ENST00000575510,;DPEP2,3_prime_UTR_variant,,ENST00000575203,;DPEP2,downstream_gene_variant,,ENST00000574316,;DPEP2,downstream_gene_variant,,ENST00000268795,;	A	ENSG00000167261	ENST00000412757	Transcript	synonymous_variant	1704	1038	346	I	atC/atT	rs777330949	.	.	-1	DPEP2	HGNC	23028	protein_coding	YES	CCDS10857.1	ENSP00000412549	DPEP2_HUMAN	I3L4H3_HUMAN,I3L348_HUMAN	UPI000013D7DC	.	.	.	10/12	.	PROSITE_profiles:PS51365,hmmpanther:PTHR10443:SF9,hmmpanther:PTHR10443,Pfam_domain:PF01244,Gene3D:3.20.20.140,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCCGATGAA	.	5	ESCA
BANP	0	.	GRCh37	16	87985117	87985117	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-311A>G	.	.	ENST00000454563	1/4	68	63	5	95	94	1	BANP,5_prime_UTR_variant,,ENST00000454563,;BANP,5_prime_UTR_variant,,ENST00000393208,;BANP,5_prime_UTR_variant,,ENST00000479780,;BANP,5_prime_UTR_variant,,ENST00000286122,;BANP,5_prime_UTR_variant,,ENST00000439677,;BANP,5_prime_UTR_variant,,ENST00000412691,;BANP,5_prime_UTR_variant,,ENST00000355163,;BANP,5_prime_UTR_variant,,ENST00000355022,;BANP,intron_variant,,ENST00000423252,;BANP,non_coding_transcript_exon_variant,,ENST00000526460,;BANP,intron_variant,,ENST00000488074,;BANP,intron_variant,,ENST00000569400,;BANP,5_prime_UTR_variant,,ENST00000466197,;BANP,5_prime_UTR_variant,,ENST00000459966,;BANP,5_prime_UTR_variant,,ENST00000485772,;	G	ENSG00000172530	ENST00000454563	Transcript	5_prime_UTR_variant	78	.	.	.	.	.	.	.	1	BANP	HGNC	13450	protein_coding	.	.	ENSP00000413717	.	C9JLS0_HUMAN	UPI000155D548	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCCACACGG	.	2	ESCA
PAFAH1B1	0	.	GRCh37	17	2585957	2585957	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*861A>G	.	.	ENST00000397195	11/11	69	52	16	91	91	0	PAFAH1B1,3_prime_UTR_variant,,ENST00000397195,;PAFAH1B1,downstream_gene_variant,,ENST00000574468,;PAFAH1B1,downstream_gene_variant,,ENST00000451360,;RP11-74E22.5,downstream_gene_variant,,ENST00000610120,;RN7SL608P,downstream_gene_variant,,ENST00000492377,;PAFAH1B1,intron_variant,,ENST00000572915,;PAFAH1B1,downstream_gene_variant,,ENST00000397193,;PAFAH1B1,downstream_gene_variant,,ENST00000574213,;PAFAH1B1,downstream_gene_variant,,ENST00000574816,;PAFAH1B1,downstream_gene_variant,,ENST00000610190,;PAFAH1B1,downstream_gene_variant,,ENST00000571495,;	G	ENSG00000007168	ENST00000397195	Transcript	3_prime_UTR_variant	2545	.	.	.	.	.	.	.	1	PAFAH1B1	HGNC	8574	protein_coding	YES	CCDS32528.1	ENSP00000380378	LIS1_HUMAN	I3L495_HUMAN,B4DZN3_HUMAN	UPI0000163BF4	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAAATCACT	.	5	ESCA
GGNBP2	0	.	GRCh37	17	34923570	34923570	+	Missense_Mutation	SNP	C	C	T	rs752364975	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.596C>T	p.Ser199Leu	p.S199L	ENST00000304718	6/14	82	71	11	85	85	0	GGNBP2,missense_variant,p.Ser199Leu,ENST00000304718,;GGNBP2,non_coding_transcript_exon_variant,,ENST00000486208,;GGNBP2,non_coding_transcript_exon_variant,,ENST00000495023,;	T	ENSG00000005955	ENST00000304718	Transcript	missense_variant	912	596	199	S/L	tCg/tTg	rs752364975	.	.	1	GGNBP2	HGNC	19357	protein_coding	YES	CCDS11314.1	ENSP00000307617	GGNB2_HUMAN	K7ELA8_HUMAN,B4DWN7_HUMAN	UPI00000728CB	.	tolerated(0.08)	benign(0.24)	6/14	.	hmmpanther:PTHR13601	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACTCGAGTT	byFrequency	4	ESCA
KRT14	0	.	GRCh37	17	39740052	39740058	+	Frame_Shift_Del	DEL	TCTGCCA	TCTGCCA	-	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	TCTGCCA	TCTGCCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.881_887delTGGCAGA	p.Met294ArgfsTer18	p.M294Rfs*18	ENST00000167586	4/8	101	86	15	113	113	0	KRT14,frameshift_variant,p.Met294ArgfsTer18,ENST00000167586,;KRT14,non_coding_transcript_exon_variant,,ENST00000476662,;KRT14,upstream_gene_variant,,ENST00000441550,;	-	ENSG00000186847	ENST00000167586	Transcript	frameshift_variant	968-974	881-887	294-296	MAE/X	aTGGCAGAg/ag	.	.	.	-1	KRT14	HGNC	6416	protein_coding	YES	CCDS11400.1	ENSP00000167586	K1C14_HUMAN	K7ENV3_HUMAN	UPI00001AE5AA	.	.	.	4/8	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF46579,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTTCTCTGCCATCTTC	.	3	ESCA
RECQL5	0	.	GRCh37	17	73662528	73662528	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110C>T	p.Ala37Val	p.A37V	ENST00000317905	2/20	42	31	11	47	47	0	RECQL5,missense_variant,p.Ala37Val,ENST00000578201,;RECQL5,missense_variant,p.Ala37Val,ENST00000584999,;RECQL5,missense_variant,p.Ala37Val,ENST00000420326,;RECQL5,missense_variant,p.Ala37Val,ENST00000423245,;RECQL5,missense_variant,p.Ala37Val,ENST00000317905,;RECQL5,missense_variant,p.Ala37Val,ENST00000340830,;SAP30BP,upstream_gene_variant,,ENST00000355423,;SAP30BP,upstream_gene_variant,,ENST00000584667,;RECQL5,upstream_gene_variant,,ENST00000580078,;SAP30BP,upstream_gene_variant,,ENST00000583536,;SAP30BP,upstream_gene_variant,,ENST00000578909,;SAP30BP,upstream_gene_variant,,ENST00000578354,;SAP30BP,upstream_gene_variant,,ENST00000579864,;SAP30BP,upstream_gene_variant,,ENST00000583737,;SAP30BP,upstream_gene_variant,,ENST00000579877,;SAP30BP,upstream_gene_variant,,ENST00000542343,;SAP30BP,upstream_gene_variant,,ENST00000580322,;SAP30BP,upstream_gene_variant,,ENST00000580484,;SAP30BP,upstream_gene_variant,,ENST00000582022,;SAP30BP,upstream_gene_variant,,ENST00000293208,;SAP30BP,upstream_gene_variant,,ENST00000584861,;SAP30BP,upstream_gene_variant,,ENST00000577292,;SAP30BP,upstream_gene_variant,,ENST00000583170,;SAP30BP,upstream_gene_variant,,ENST00000578288,;	A	ENSG00000108469	ENST00000317905	Transcript	missense_variant	270	110	37	A/V	gCg/gTg	.	.	.	-1	RECQL5	HGNC	9950	protein_coding	YES	CCDS42380.1	ENSP00000317636	RECQ5_HUMAN	Q9BW80_HUMAN,Q9BSD6_HUMAN,J3QLU0_HUMAN,J3KTQ2_HUMAN	UPI0000133477	.	tolerated(0.25)	probably_damaging(0.954)	2/20	.	hmmpanther:PTHR13710:SF81,hmmpanther:PTHR13710,TIGRFAM_domain:TIGR00614,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTCGCACTC	.	5	ESCA
TP53	0	.	GRCh37	17	7578461	7578461	+	Missense_Mutation	SNP	C	C	A	rs121912654	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	5/11	400	280	119	422	422	0	TP53,missense_variant,p.Val157Phe,ENST00000508793,;TP53,missense_variant,p.Val157Phe,ENST00000413465,;TP53,missense_variant,p.Val157Phe,ENST00000420246,;TP53,missense_variant,p.Val157Phe,ENST00000269305,;TP53,missense_variant,p.Val25Phe,ENST00000509690,;TP53,missense_variant,p.Val157Phe,ENST00000359597,;TP53,missense_variant,p.Val64Phe,ENST00000514944,;TP53,missense_variant,p.Val157Phe,ENST00000445888,;TP53,missense_variant,p.Val157Phe,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	659	469	157	V/F	Gtc/Ttc	rs121912654,TP53_g.12457del,TP53_g.12457G>A,TP53_g.12457G>C,TP53_g.12457G>T,COSM10670,COSM43625,COSM45120,COSM131480,COSM131481,COSM131483,COSM3388217,COSM1679513,COSM131482	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.997)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	uncertain_significance,pathogenic	0,0,0,0,0,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.V157F|c.469G>T|7,SITE|p.V157F|c.469G>T|8,SITE|p.V157F|c.469G>T|22,SITE|p.V157F|c.469G>T|162,SITE|p.V157F|c.469G>T|22,SITE|p.V25F|c.73G>T|25,SITE|p.V64F|c.190G>T|22,CODON|p.0?|c.1_1182del1182|6,CODON|p.R158C|c.471_472CC>TT|6,CODON|p.V157V|c.471C>A|3,CODON|p.V157G|c.470T>G|9,CODON|p.V157D|c.470T>A|8,BUFFER|p.M160I|c.480G>T|4,BUFFER|p.M160I|c.480G>A|3,BUFFER|p.M160K|c.479T>A|4,BUFFER|p.M160L|c.478A>C|3,BUFFER|p.M160V|c.478A>G|5,BUFFER|p.A159A|c.477C>T|8,BUFFER|p.A159fs*11|c.475delG|4,BUFFER|p.R158fs*11|c.472_475delCGCG|3,BUFFER|p.A159V|c.476C>T|9,BUFFER|p.A66V|c.197C>T|9,BUFFER|p.A27V|c.80C>T|9,BUFFER|p.A159V|c.476C>T|39,BUFFER|p.A159V|c.476C>T|9,BUFFER|p.A159D|c.476C>A|6,BUFFER|p.A159S|c.475G>T|5,BUFFER|p.A159P|c.475G>C|3,BUFFER|p.A159P|c.475G>C|5,BUFFER|p.A159T|c.475G>A|7,BUFFER|p.A66P|c.196G>C|5,BUFFER|p.A159P|c.475G>C|20,BUFFER|p.A159P|c.475G>C|5,BUFFER|p.A27P|c.79G>C|5,BUFFER|p.R158_A159insX|c.473_474insNNN|4,BUFFER|p.R158R|c.474C>T|6,BUFFER|p.R158L|c.473G>T|14,BUFFER|p.R158H|c.473G>A|24,BUFFER|p.R158H|c.473G>A|24,BUFFER|p.R158H|c.473G>A|78,BUFFER|p.R158H|c.473G>A|7,BUFFER|p.R158L|c.473G>T|63,BUFFER|p.R158H|c.473G>A|11,BUFFER|p.R158P|c.473G>C|10,BUFFER|p.R158L|c.473G>T|5,BUFFER|p.R158L|c.473G>T|14,BUFFER|p.R65H|c.194G>A|24,BUFFER|p.R26L|c.77G>T|19,BUFFER|p.R26H|c.77G>A|25,BUFFER|p.R65L|c.194G>T|14,BUFFER|p.R158fs*12|c.472delC|6,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R158C|c.472C>T|17,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R26C|c.76C>T|7,BUFFER|p.R65C|c.193C>T|7,BUFFER|p.R158G|c.472C>G|12,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R65G|c.193C>G|3,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R26G|c.76C>G|4,BUFFER|p.V157L|c.469G>C|6,BUFFER|p.V157I|c.469G>A|10,BUFFER|p.V157fs*13|c.468delC|3,BUFFER|p.R156P|c.467G>C|26,BUFFER|p.R63P|c.188G>C|4,BUFFER|p.R156H|c.467G>A|11,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R24P|c.71G>C|4,BUFFER|p.R156L|c.467G>T|3,BUFFER|p.P152fs*14|c.454_466del13|5,BUFFER|p.R156fs*14|c.466delC|9,BUFFER|p.R156S|c.466C>A|3,BUFFER|p.R156G|c.466C>G|3,BUFFER|p.R156C|c.466C>T|4,BUFFER|p.T155T|c.465C>T|4,BUFFER|p.T155N|c.464C>A|4,BUFFER|p.T155N|c.464C>A|5,BUFFER|p.T62N|c.185C>A|6,BUFFER|p.T155N|c.464C>A|25,BUFFER|p.T155I|c.464C>T|15,BUFFER|p.T23N|c.68C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.T62P|c.184A>C|3,BUFFER|p.T155P|c.463A>C|16,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T23P|c.67A>C|4,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T155A|c.463A>G|8,BUFFER|p.G154I|c.460_461GG>AT|3,BUFFER|p.G154G|c.462C>T|9,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G61V|c.182G>T|3,BUFFER|p.G22V|c.65G>T|4,BUFFER|p.G154D|c.461G>A|6,BUFFER|p.G154V|c.461G>T|38,BUFFER|p.T150fs*16|c.448_460del13|4,BUFFER|p.G154S|c.460G>A|9,BUFFER|p.P153P|c.459C>T|6,BUFFER|p.P153L|c.458C>T|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGACGCGGG	byFrequency|byCluster	5	ESCA
CHD3	0	.	GRCh37	17	7809966	7809966	+	Missense_Mutation	SNP	G	G	A	rs775142325	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4631G>A	p.Arg1544His	p.R1544H	ENST00000380358	29/40	37	31	5	44	44	0	CHD3,missense_variant,p.Arg1544His,ENST00000380358,;CHD3,missense_variant,p.Arg1485His,ENST00000358181,;CHD3,missense_variant,p.Arg1485His,ENST00000330494,;CHD3,upstream_gene_variant,,ENST00000439235,;CHD3,upstream_gene_variant,,ENST00000449744,;CHD3,upstream_gene_variant,,ENST00000573936,;SCARNA21,downstream_gene_variant,,ENST00000517026,;CHD3,3_prime_UTR_variant,,ENST00000470531,;CHD3,downstream_gene_variant,,ENST00000466233,;CHD3,downstream_gene_variant,,ENST00000473376,;CHD3,upstream_gene_variant,,ENST00000572750,;CHD3,upstream_gene_variant,,ENST00000481999,;	A	ENSG00000170004	ENST00000380358	Transcript	missense_variant	4632	4631	1544	R/H	cGc/cAc	rs775142325	.	.	1	CHD3	HGNC	1918	protein_coding	YES	CCDS32553.2	ENSP00000369716	CHD3_HUMAN	Q2TAZ1_HUMAN	UPI00004DDA7C	.	.	possibly_damaging(0.812)	29/40	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF544,Pfam_domain:PF06461	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGTCGCCAGC	.	4	ESCA
ACTG1	0	.	GRCh37	17	79477568	79477568	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*148C>A	.	.	ENST00000575842	5/5	24	19	5	32	32	0	ACTG1,3_prime_UTR_variant,,ENST00000575842,;ACTG1,3_prime_UTR_variant,,ENST00000573283,;ACTG1,3_prime_UTR_variant,,ENST00000331925,;ACTG1,3_prime_UTR_variant,,ENST00000575087,;ACTG1,downstream_gene_variant,,ENST00000575994,;ACTG1,downstream_gene_variant,,ENST00000571691,;ACTG1,downstream_gene_variant,,ENST00000571721,;ACTG1,downstream_gene_variant,,ENST00000575659,;ACTG1,downstream_gene_variant,,ENST00000570382,;AC139149.1,downstream_gene_variant,,ENST00000584254,;RP13-766D20.2,upstream_gene_variant,,ENST00000430912,;ACTG1,3_prime_UTR_variant,,ENST00000576544,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576209,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576917,;ACTG1,non_coding_transcript_exon_variant,,ENST00000574671,;ACTG1,downstream_gene_variant,,ENST00000576214,;ACTG1,downstream_gene_variant,,ENST00000572105,;RP13-766D20.1,upstream_gene_variant,,ENST00000448147,;	T	ENSG00000184009	ENST00000575842	Transcript	3_prime_UTR_variant	1703	.	.	.	.	.	.	.	-1	ACTG1	HGNC	144	protein_coding	YES	CCDS11782.1	ENSP00000458162	ACTG_HUMAN	Q9UE89_HUMAN,Q96FU6_HUMAN,Q96DE1_HUMAN,Q6PJ43_HUMAN,Q562Z7_HUMAN,I3L3R2_HUMAN,I3L3I0_HUMAN,I3L1U9_HUMAN,B4E3A4_HUMAN,B3KWQ3_HUMAN,A5GZ75_HUMAN,A4UCT3_HUMAN,A1E282_HUMAN	UPI0000000C38	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCTGATATC	.	5	ESCA
PIK3R6	0	.	GRCh37	17	8733047	8733047	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.865T>A	p.Leu289Met	p.L289M	ENST00000311434	10/21	46	40	6	44	44	0	PIK3R6,missense_variant,p.Leu289Met,ENST00000311434,;PIK3R6,non_coding_transcript_exon_variant,,ENST00000434064,;PIK3R6,3_prime_UTR_variant,,ENST00000452122,;PIK3R6,3_prime_UTR_variant,,ENST00000583984,;	T	ENSG00000174083	ENST00000311434	Transcript	missense_variant	1105	865	289	L/M	Ttg/Atg	.	.	.	-1	PIK3R6	HGNC	27101	protein_coding	YES	.	ENSP00000475670	PI3R6_HUMAN	U3KQ99_HUMAN	UPI00015DFB1F	.	deleterious(0.03)	probably_damaging(1)	10/21	.	hmmpanther:PTHR15593,hmmpanther:PTHR15593:SF1,Pfam_domain:PF10486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAAGTGGA	.	5	ESCA
NPC1	0	.	GRCh37	18	21125043	21125043	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1828G>A	p.Glu610Lys	p.E610K	ENST00000269228	12/25	55	52	3	46	46	0	NPC1,missense_variant,p.Glu610Lys,ENST00000269228,;NPC1,missense_variant,p.Glu292Lys,ENST00000412552,;NPC1,missense_variant,p.Glu303Lys,ENST00000591051,;NPC1,non_coding_transcript_exon_variant,,ENST00000540608,;NPC1,upstream_gene_variant,,ENST00000586718,;	T	ENSG00000141458	ENST00000269228	Transcript	missense_variant	2383	1828	610	E/K	Gaa/Aaa	.	.	.	-1	NPC1	HGNC	7897	protein_coding	YES	CCDS11878.1	ENSP00000269228	NPC1_HUMAN	.	UPI000013D80F	.	deleterious(0)	possibly_damaging(0.858)	12/25	.	hmmpanther:PTHR10796:SF35,hmmpanther:PTHR10796,Gene3D:2j8sB01,TIGRFAM_domain:TIGR00917,Superfamily_domains:SSF82866	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTTCAATAC	.	2	ESCA
SERPINB11	0	.	GRCh37	18	61390626	61390626	+	Missense_Mutation	SNP	C	C	T	rs771887411	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1172C>T	p.Ser391Phe	p.S391F	ENST00000544088	8/8	22	19	3	20	20	0	SERPINB11,missense_variant,p.Ser216Phe,ENST00000536691,;SERPINB11,missense_variant,p.Ser189Phe,ENST00000538847,;SERPINB11,missense_variant,p.Ser391Phe,ENST00000544088,;SERPINB11,downstream_gene_variant,,ENST00000489748,;SERPINB11,missense_variant,p.Ser391Phe,ENST00000382749,;	T	ENSG00000206072	ENST00000544088	Transcript	missense_variant	1234	1172	391	S/F	tCt/tTt	rs771887411	.	.	1	SERPINB11	HGNC	14221	protein_coding	YES	.	ENSP00000441497	.	F5GYW9_HUMAN,F5GWT8_HUMAN	UPI00015AAB67	.	deleterious(0)	probably_damaging(0.998)	8/8	.	hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF137,Pfam_domain:PF00079,Gene3D:2.30.39.10,SMART_domains:SM00093,Superfamily_domains:SSF56574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCTCTCCCT	byFrequency	5	ESCA
NOTCH3	0	.	GRCh37	19	15296491	15296491	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1952-1G>A	.	p.X651_splice	ENST00000263388	.	42	32	10	41	41	0	NOTCH3,splice_acceptor_variant,,ENST00000263388,;NOTCH3,splice_acceptor_variant,,ENST00000601011,;	T	ENSG00000074181	ENST00000263388	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	.	.	.	12/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCCTGGGG	.	5	ESCA
ZNF780A	0	.	GRCh37	19	40580618	40580618	+	Silent	SNP	T	T	C	rs779961382	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1734A>G	p.%3D	p.K578K	ENST00000455521	6/6	78	72	5	84	84	0	ZNF780A,synonymous_variant,p.%3D,ENST00000594395,;ZNF780A,synonymous_variant,p.%3D,ENST00000340963,;ZNF780A,synonymous_variant,p.%3D,ENST00000450241,;ZNF780A,synonymous_variant,p.%3D,ENST00000595687,;ZNF780A,synonymous_variant,p.%3D,ENST00000455521,;ZNF780A,intron_variant,,ENST00000414720,;ZNF780A,downstream_gene_variant,,ENST00000595773,;ZNF780A,downstream_gene_variant,,ENST00000599972,;AC005614.5,intron_variant,,ENST00000595508,;ZNF780A,downstream_gene_variant,,ENST00000601688,;ZNF780A,downstream_gene_variant,,ENST00000601715,;ZNF780A,downstream_gene_variant,,ENST00000599368,;	C	ENSG00000197782	ENST00000455521	Transcript	synonymous_variant	1882	1734	578	K	aaA/aaG	rs779961382,COSM2152397,COSM996573,COSM1590091,COSM2152396	.	.	-1	ZNF780A	HGNC	27603	protein_coding	YES	CCDS46079.1	ENSP00000400997	Z780A_HUMAN	.	UPI0001881B53	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF124,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCAATTTCTG	.	2	ESCA
TRMT13	0	.	GRCh37	1	100613525	100613525	+	Missense_Mutation	SNP	G	G	T	rs779650558	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.893G>T	p.Arg298Leu	p.R298L	ENST00000370141	10/11	29	25	4	31	31	0	TRMT13,missense_variant,p.Arg298Leu,ENST00000370141,;LRRC39,downstream_gene_variant,,ENST00000342895,;LRRC39,downstream_gene_variant,,ENST00000370137,;LRRC39,downstream_gene_variant,,ENST00000370138,;TRMT13,downstream_gene_variant,,ENST00000493651,;TRMT13,downstream_gene_variant,,ENST00000482437,;	T	ENSG00000122435	ENST00000370141	Transcript	missense_variant	899	893	298	R/L	cGc/cTc	rs779650558	.	.	1	TRMT13	HGNC	25502	protein_coding	YES	CCDS765.1	ENSP00000359160	TRM13_HUMAN	.	UPI000013CAE6	.	deleterious(0.01)	possibly_damaging(0.803)	10/11	.	hmmpanther:PTHR12998,hmmpanther:PTHR12998:SF0,Pfam_domain:PF05206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAACGCATAA	.	2	ESCA
SORT1	0	.	GRCh37	1	109867695	109867695	+	Missense_Mutation	SNP	C	C	T	rs759848600	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1660G>A	p.Gly554Ser	p.G554S	ENST00000256637	14/20	31	28	3	35	35	0	SORT1,missense_variant,p.Gly417Ser,ENST00000538502,;SORT1,missense_variant,p.Gly554Ser,ENST00000256637,;SORT1,downstream_gene_variant,,ENST00000466471,;	T	ENSG00000134243	ENST00000256637	Transcript	missense_variant	1719	1660	554	G/S	Ggt/Agt	rs759848600	.	.	-1	SORT1	HGNC	11186	protein_coding	YES	CCDS798.1	ENSP00000256637	SORT_HUMAN	.	UPI0000074182	.	deleterious(0)	probably_damaging(1)	14/20	.	hmmpanther:PTHR12106:SF23,hmmpanther:PTHR12106,Gene3D:2.130.10.140,SMART_domains:SM00602,Superfamily_domains:SSF110296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGACCTTCGT	.	2	ESCA
TTF2	0	.	GRCh37	1	117602959	117602959	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-10A>G	.	.	ENST00000369466	1/23	74	63	10	80	80	0	TTF2,5_prime_UTR_variant,,ENST00000369466,;RP11-27K13.3,upstream_gene_variant,,ENST00000445523,;TTF2,upstream_gene_variant,,ENST00000470935,;	G	ENSG00000116830	ENST00000369466	Transcript	5_prime_UTR_variant	35	.	.	.	.	.	.	.	1	TTF2	HGNC	12398	protein_coding	YES	CCDS892.1	ENSP00000358478	TTF2_HUMAN	.	UPI000013CCE7	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGACCCAG	.	5	ESCA
NOTCH2	0	.	GRCh37	1	120483302	120483302	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3059C>T	p.Ser1020Phe	p.S1020F	ENST00000256646	19/34	46	39	7	57	56	0	NOTCH2,missense_variant,p.Ser1020Phe,ENST00000256646,;NOTCH2,upstream_gene_variant,,ENST00000478864,;	A	ENSG00000134250	ENST00000256646	Transcript	missense_variant	3279	3059	1020	S/F	tCc/tTc	.	.	.	-1	NOTCH2	HGNC	7882	protein_coding	YES	CCDS908.1	ENSP00000256646	NOTC2_HUMAN	Q9UFD5_HUMAN,Q13560_HUMAN	UPI000013CF1D	.	deleterious(0.01)	benign(0.098)	19/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF4,hmmpanther:PTHR24033,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00179,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAGGATCCA	.	4	ESCA
HIST2H3PS2	0	.	GRCh37	1	149398805	149398805	+	3'Flank	SNP	C	C	G	rs782084069	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000392948	.	74	64	10	75	75	0	HIST2H3PS2,downstream_gene_variant,,ENST00000392948,;RP5-998N21.7,upstream_gene_variant,,ENST00000444624,;HIST2H2BB,splice_region_variant,,ENST00000609585,;RP5-998N21.10,downstream_gene_variant,,ENST00000609879,;HIST2H2BB,non_coding_transcript_exon_variant,,ENST00000449108,;	G	ENSG00000203818	ENST00000392948	Transcript	downstream_gene_variant	.	.	.	.	.	rs782084069	.	1326	-1	HIST2H3PS2	HGNC	32060	protein_coding	YES	.	ENSP00000476960	.	Q5TEC6_HUMAN	UPI0000470A88	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TACTTCGAGCT	.	3	ESCA
FLG	0	.	GRCh37	1	152277667	152277667	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9695C>T	p.Ser3232Phe	p.S3232F	ENST00000368799	3/3	125	108	17	144	144	0	FLG,missense_variant,p.Ser3232Phe,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	A	ENSG00000143631	ENST00000368799	Transcript	missense_variant	9731	9695	3232	S/F	tCt/tTt	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	unknown(0)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCCAGACCAC	.	4	ESCA
ADAR	0	.	GRCh37	1	154574789	154574789	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329A>G	p.His110Arg	p.H110R	ENST00000368474	2/15	49	40	9	59	59	0	ADAR,missense_variant,p.His153Arg,ENST00000292205,;ADAR,missense_variant,p.His105Arg,ENST00000529168,;ADAR,missense_variant,p.His110Arg,ENST00000368474,;ADAR,5_prime_UTR_variant,,ENST00000368471,;ADAR,non_coding_transcript_exon_variant,,ENST00000471068,;ADAR,non_coding_transcript_exon_variant,,ENST00000526905,;ADAR,intron_variant,,ENST00000494866,;ADAR,intron_variant,,ENST00000463920,;	C	ENSG00000160710	ENST00000368474	Transcript	missense_variant	529	329	110	H/R	cAt/cGt	.	.	.	-1	ADAR	HGNC	225	protein_coding	YES	CCDS1071.1	ENSP00000357459	DSRAD_HUMAN	.	UPI000045626B	.	tolerated(0.45)	benign(0.002)	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGATGCTGG	.	5	ESCA
QSOX1	0	.	GRCh37	1	180166101	180166101	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2173C>T	p.%3D	p.L725L	ENST00000367602	12/12	65	54	11	105	105	0	QSOX1,synonymous_variant,p.%3D,ENST00000367602,;QSOX1,intron_variant,,ENST00000443059,;QSOX1,intron_variant,,ENST00000367600,;	T	ENSG00000116260	ENST00000367602	Transcript	synonymous_variant	2247	2173	725	L	Ctg/Ttg	.	.	.	1	QSOX1	HGNC	9756	protein_coding	YES	CCDS1337.1	ENSP00000356574	QSOX1_HUMAN	.	UPI000004C63C	.	.	.	12/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22897,hmmpanther:PTHR22897:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTGCTGGCC	.	5	ESCA
CAMSAP2	0	.	GRCh37	1	200828539	200828539	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1352T>C	.	.	ENST00000358823	17/17	23	19	4	37	37	0	CAMSAP2,3_prime_UTR_variant,,ENST00000358823,;CAMSAP2,3_prime_UTR_variant,,ENST00000236925,;CAMSAP2,downstream_gene_variant,,ENST00000413307,;CAMSAP2,downstream_gene_variant,,ENST00000475326,;RPL34P6,upstream_gene_variant,,ENST00000432390,;	C	ENSG00000118200	ENST00000358823	Transcript	3_prime_UTR_variant	6059	.	.	.	.	.	.	.	1	CAMSAP2	HGNC	29188	protein_coding	YES	CCDS1404.1	ENSP00000351684	CAMP2_HUMAN	.	UPI000020470D	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTCTCATAT	.	2	ESCA
SLC26A9	0	.	GRCh37	1	205899089	205899089	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.648G>C	p.%3D	p.L216L	ENST00000367134	6/22	37	33	4	52	52	0	SLC26A9,synonymous_variant,p.%3D,ENST00000367135,;SLC26A9,synonymous_variant,p.%3D,ENST00000340781,;SLC26A9,synonymous_variant,p.%3D,ENST00000367134,;SLC26A9,non_coding_transcript_exon_variant,,ENST00000469392,;SLC26A9,upstream_gene_variant,,ENST00000491127,;	G	ENSG00000174502	ENST00000367134	Transcript	synonymous_variant	762	648	216	L	ctG/ctC	.	.	.	-1	SLC26A9	HGNC	14469	protein_coding	YES	CCDS30989.1	ENSP00000356102	.	B1AVM8_HUMAN	UPI000013DF98	.	.	.	6/22	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11814:SF17,hmmpanther:PTHR11814,TIGRFAM_domain:TIGR00815,Pfam_domain:PF00916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S218L|c.653C>T|3,BUFFER|p.S218L|c.653C>T|3	MUTECT|MUSE	GAAATCAGGAT	.	2	ESCA
COG2	0	.	GRCh37	1	230822767	230822767	+	Silent	SNP	A	A	G	rs747018671	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1467A>G	p.%3D	p.Q489Q	ENST00000366669	13/18	36	32	4	37	37	0	COG2,synonymous_variant,p.%3D,ENST00000366669,;COG2,synonymous_variant,p.%3D,ENST00000535166,;COG2,synonymous_variant,p.%3D,ENST00000366668,;COG2,synonymous_variant,p.%3D,ENST00000546013,;COG2,synonymous_variant,p.%3D,ENST00000534989,;COG2,non_coding_transcript_exon_variant,,ENST00000482012,;COG2,upstream_gene_variant,,ENST00000478710,;COG2,upstream_gene_variant,,ENST00000490900,;COG2,3_prime_UTR_variant,,ENST00000468893,;COG2,downstream_gene_variant,,ENST00000494371,;	G	ENSG00000135775	ENST00000366669	Transcript	synonymous_variant	1582	1467	489	Q	caA/caG	rs747018671	.	.	1	COG2	HGNC	6546	protein_coding	YES	CCDS1584.1	ENSP00000355629	COG2_HUMAN	F5H1E5_HUMAN,B7Z2Y2_HUMAN,B1ALW7_HUMAN	UPI0000127E38	.	.	.	13/18	.	hmmpanther:PTHR12961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCCAAGGAAA	.	4	ESCA
AGBL4	0	.	GRCh37	1	49511430	49511430	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.420G>A	p.%3D	p.P140P	ENST00000371839	5/14	45	42	3	40	40	0	AGBL4,synonymous_variant,p.%3D,ENST00000371839,;AGBL4,synonymous_variant,p.%3D,ENST00000371838,;AGBL4,synonymous_variant,p.%3D,ENST00000371836,;AGBL4,upstream_gene_variant,,ENST00000416121,;RP11-141A19.1,upstream_gene_variant,,ENST00000456002,;	T	ENSG00000186094	ENST00000371839	Transcript	synonymous_variant	537	420	140	P	ccG/ccA	.	.	.	-1	AGBL4	HGNC	25892	protein_coding	YES	CCDS44137.1	ENSP00000360905	CBPC6_HUMAN	.	UPI00002042F9	.	.	.	5/14	.	hmmpanther:PTHR12756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGTCCGGGCA	.	2	ESCA
SLC24A3	0	.	GRCh37	20	19702169	19702169	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*385G>C	.	.	ENST00000328041	17/17	36	32	4	40	40	0	SLC24A3,3_prime_UTR_variant,,ENST00000328041,;	C	ENSG00000185052	ENST00000328041	Transcript	3_prime_UTR_variant	2517	.	.	.	.	.	.	.	1	SLC24A3	HGNC	10977	protein_coding	YES	CCDS13140.1	ENSP00000333519	NCKX3_HUMAN	.	UPI00001A8BFD	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTGAGACT	.	2	ESCA
RALGAPB	0	.	GRCh37	20	37153456	37153456	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1655A>G	p.Asn552Ser	p.N552S	ENST00000262879	11/30	103	95	7	129	129	0	RALGAPB,missense_variant,p.Asn330Ser,ENST00000397038,;RALGAPB,missense_variant,p.Asn552Ser,ENST00000397040,;RALGAPB,missense_variant,p.Asn552Ser,ENST00000397042,;RALGAPB,missense_variant,p.Asn552Ser,ENST00000262879,;RALGAPB,missense_variant,p.Asn380Ser,ENST00000438490,;RALGAPB,3_prime_UTR_variant,,ENST00000537204,;RALGAPB,non_coding_transcript_exon_variant,,ENST00000461423,;	G	ENSG00000170471	ENST00000262879	Transcript	missense_variant	1939	1655	552	N/S	aAt/aGt	.	.	.	1	RALGAPB	HGNC	29221	protein_coding	YES	CCDS13305.1	ENSP00000262879	RLGPB_HUMAN	Q6MZJ2_HUMAN	UPI000000DBFD	.	tolerated(0.89)	benign(0)	11/30	.	hmmpanther:PTHR21344	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAAATGATT	.	2	ESCA
TTPAL	0	.	GRCh37	20	43115335	43115335	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.739A>G	p.Ile247Val	p.I247V	ENST00000372904	5/6	43	39	4	25	25	0	TTPAL,missense_variant,p.Ile247Val,ENST00000262605,;TTPAL,missense_variant,p.Ile247Val,ENST00000372904,;TTPAL,missense_variant,p.Ile213Val,ENST00000456317,;TTPAL,intron_variant,,ENST00000372906,;TTPAL,non_coding_transcript_exon_variant,,ENST00000461134,;	G	ENSG00000124120	ENST00000372904	Transcript	missense_variant	882	739	247	I/V	Ata/Gta	.	.	.	1	TTPAL	HGNC	16114	protein_coding	YES	CCDS13332.2	ENSP00000361995	TTPAL_HUMAN	B2RA57_HUMAN	UPI000020657C	.	tolerated(0.05)	benign(0.032)	5/6	.	PROSITE_profiles:PS50191,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF110,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087,Prints_domain:PR00180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGAAAATAGCA	.	3	ESCA
ZFP64	0	.	GRCh37	20	50769335	50769335	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1396G>A	p.Asp466Asn	p.D466N	ENST00000216923	6/6	27	18	9	20	20	0	ZFP64,missense_variant,p.Asp464Asn,ENST00000371515,;ZFP64,missense_variant,p.Asp412Asn,ENST00000346617,;ZFP64,missense_variant,p.Asp466Asn,ENST00000216923,;ZFP64,intron_variant,,ENST00000371518,;ZFP64,intron_variant,,ENST00000361387,;ZFP64,intron_variant,,ENST00000477786,;	T	ENSG00000020256	ENST00000216923	Transcript	missense_variant	1746	1396	466	D/N	Gac/Aac	.	.	.	-1	ZFP64	HGNC	15940	protein_coding	YES	CCDS13440.1	ENSP00000216923	ZF64A_HUMAN	B3KQX0_HUMAN	UPI000006D699	.	tolerated(0.16)	benign(0.02)	6/6	.	hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGTCGATCT	.	5	ESCA
ZNF217	0	.	GRCh37	20	52184518	52184518	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1309A>G	.	.	ENST00000371471	6/6	23	18	5	27	27	0	ZNF217,3_prime_UTR_variant,,ENST00000302342,;ZNF217,3_prime_UTR_variant,,ENST00000371471,;ZNF217,downstream_gene_variant,,ENST00000437222,;RP4-724E16.2,intron_variant,,ENST00000424252,;	C	ENSG00000171940	ENST00000371471	Transcript	3_prime_UTR_variant	4882	.	.	.	.	.	.	.	-1	ZNF217	HGNC	13009	protein_coding	YES	CCDS13443.1	ENSP00000360526	ZN217_HUMAN	A2A326_HUMAN	UPI000013C323	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCATGGACA	.	5	ESCA
PITPNB	0	.	GRCh37	22	28292539	28292539	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372+1G>A	.	p.X124_splice	ENST00000335272	.	22	16	6	18	18	0	PITPNB,splice_donor_variant,,ENST00000335272,;PITPNB,splice_donor_variant,,ENST00000436663,;PITPNB,splice_donor_variant,,ENST00000320996,;PITPNB,splice_donor_variant,,ENST00000415296,;PITPNB,splice_donor_variant,,ENST00000455418,;PITPNB,splice_donor_variant,,ENST00000465179,;PITPNB,splice_donor_variant,,ENST00000477861,;PITPNB,downstream_gene_variant,,ENST00000460566,;	T	ENSG00000180957	ENST00000335272	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	PITPNB	HGNC	9002	protein_coding	YES	CCDS13842.1	ENSP00000334738	PIPNB_HUMAN	B3KYB6_HUMAN	UPI0000043C3A	.	.	.	.	6/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTACATTTT	.	5	ESCA
ZBED4	0	.	GRCh37	22	50280738	50280739	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3430dupC	p.Leu1144ProfsTer12	p.L1144Pfs*12	ENST00000216268	2/2	62	50	12	54	54	0	ZBED4,frameshift_variant,p.Leu1144ProfsTer12,ENST00000216268,;	C	ENSG00000100426	ENST00000216268	Transcript	frameshift_variant	3905-3906	3428-3429	1143	S/SX	agc/agCc	.	.	.	1	ZBED4	HGNC	20721	protein_coding	YES	CCDS33677.1	ENSP00000216268	ZBED4_HUMAN	.	UPI000013C6DB	.	.	.	2/2	.	hmmpanther:PTHR23272,hmmpanther:PTHR23272:SF6,Pfam_domain:PF05699,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGGTAGCCTTG	.	3	ESCA
SCN9A	0	.	GRCh37	2	167056175	167056175	+	Silent	SNP	G	G	A	rs757858235	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4941C>T	p.%3D	p.Y1647Y	ENST00000409672	27/27	115	103	12	133	133	0	SCN9A,synonymous_variant,p.%3D,ENST00000409672,;SCN9A,synonymous_variant,p.%3D,ENST00000375387,;SCN9A,synonymous_variant,p.%3D,ENST00000409435,;SCN9A,synonymous_variant,p.%3D,ENST00000303354,;AC010127.3,non_coding_transcript_exon_variant,,ENST00000447809,;	A	ENSG00000169432	ENST00000409672	Transcript	synonymous_variant	5288	4941	1647	Y	taC/taT	rs757858235,COSM267387	.	.	-1	SCN9A	HGNC	10597	protein_coding	YES	CCDS46441.1	ENSP00000386306	SCN9A_HUMAN	Q53QP0_HUMAN	UPI0000140AC7	.	.	.	27/27	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF28,Pfam_domain:PF00520,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGGCGTAGAT	byFrequency	4	ESCA
TTN	0	.	GRCh37	2	179611634	179611634	+	Intron	SNP	C	C	T	rs762675930	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11312-4986G>A	.	.	ENST00000589042	.	70	60	10	81	81	0	TTN,missense_variant,p.Asp5165Asn,ENST00000360870,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000342992,;TTN,intron_variant,,ENST00000589042,;TTN,intron_variant,,ENST00000591111,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000578746,;TTN-AS1,downstream_gene_variant,,ENST00000582847,;	T	ENSG00000155657	ENST00000589042	Transcript	intron_variant	.	.	.	.	.	rs762675930	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	.	47/362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R5163H|c.15488G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCGGAAC	byFrequency	5	ESCA
ALPP	0	.	GRCh37	2	233245015	233245015	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.777G>A	p.Trp259Ter	p.W259*	ENST00000392027	6/11	93	83	10	136	136	0	ALPP,stop_gained,p.Trp259Ter,ENST00000392027,;AC068134.8,intron_variant,,ENST00000439072,;AC068134.8,intron_variant,,ENST00000441266,;ALPP,downstream_gene_variant,,ENST00000474529,;ALPP,upstream_gene_variant,,ENST00000485563,;	A	ENSG00000163283	ENST00000392027	Transcript	stop_gained	1046	777	259	W/*	tgG/tgA	.	.	.	1	ALPP	HGNC	439	protein_coding	YES	CCDS2490.1	ENSP00000375881	PPB1_HUMAN	.	UPI0000131FF9	.	.	.	6/11	.	hmmpanther:PTHR11596,hmmpanther:PTHR11596:SF31,Gene3D:3.40.720.10,Pfam_domain:PF00245,SMART_domains:SM00098,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAATGGCTGGC	.	4	ESCA
SNED1	0	.	GRCh37	2	241969711	241969711	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224A>T	p.Asn75Ile	p.N75I	ENST00000310397	2/32	79	70	9	88	88	0	SNED1,missense_variant,p.Asn75Ile,ENST00000405547,;SNED1,missense_variant,p.Asn75Ile,ENST00000342631,;SNED1,missense_variant,p.Asn75Ile,ENST00000310397,;SNED1,missense_variant,p.Asn75Ile,ENST00000401884,;AC005237.4,intron_variant,,ENST00000458377,;	T	ENSG00000162804	ENST00000310397	Transcript	missense_variant	224	224	75	N/I	aAc/aTc	.	.	.	1	SNED1	HGNC	24696	protein_coding	YES	CCDS46562.1	ENSP00000308893	SNED1_HUMAN	.	UPI0000DD7AB0	.	deleterious(0)	probably_damaging(0.999)	2/32	.	hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACAACGGGA	.	4	ESCA
THAP4	0	.	GRCh37	2	242573291	242573292	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280dupG	p.Ala94GlyfsTer59	p.A94Gfs*59	ENST00000407315	2/6	71	57	14	63	63	0	THAP4,frameshift_variant,p.Ala94GlyfsTer59,ENST00000407315,;ATG4B,upstream_gene_variant,,ENST00000419606,;ATG4B,upstream_gene_variant,,ENST00000474739,;ATG4B,upstream_gene_variant,,ENST00000404914,;ATG4B,upstream_gene_variant,,ENST00000396411,;ATG4B,upstream_gene_variant,,ENST00000402096,;ATG4B,upstream_gene_variant,,ENST00000425239,;ATG4B,upstream_gene_variant,,ENST00000400771,;ATG4B,upstream_gene_variant,,ENST00000430617,;ATG4B,upstream_gene_variant,,ENST00000405546,;ATG4B,upstream_gene_variant,,ENST00000491867,;ATG4B,upstream_gene_variant,,ENST00000415107,;ATG4B,upstream_gene_variant,,ENST00000475195,;ATG4B,upstream_gene_variant,,ENST00000479554,;ATG4B,upstream_gene_variant,,ENST00000494465,;ATG4B,upstream_gene_variant,,ENST00000468018,;ATG4B,upstream_gene_variant,,ENST00000493618,;ATG4B,upstream_gene_variant,,ENST00000483778,;ATG4B,upstream_gene_variant,,ENST00000400772,;ATG4B,upstream_gene_variant,,ENST00000465399,;ATG4B,upstream_gene_variant,,ENST00000482507,;	C	ENSG00000176946	ENST00000407315	Transcript	frameshift_variant	712-713	280-281	94	A/GX	gct/gGct	.	.	.	-1	THAP4	HGNC	23187	protein_coding	YES	CCDS2551.1	ENSP00000385006	THAP4_HUMAN	.	UPI000018DBC4	.	.	.	2/6	.	hmmpanther:PTHR15854,hmmpanther:PTHR15854:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCCAGCCCCC	.	3	ESCA
MSH6	0	.	GRCh37	2	48030583	48030583	+	Missense_Mutation	SNP	A	A	G	rs372103816	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3197A>G	p.Tyr1066Cys	p.Y1066C	ENST00000234420	5/10	35	28	6	42	42	0	MSH6,missense_variant,p.Tyr764Cys,ENST00000538136,;MSH6,missense_variant,p.Tyr1066Cys,ENST00000234420,;MSH6,missense_variant,p.Tyr936Cys,ENST00000540021,;FBXO11,intron_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000411819,;FBXO11,downstream_gene_variant,,ENST00000316377,;FBXO11,downstream_gene_variant,,ENST00000403359,;FBXO11,downstream_gene_variant,,ENST00000402508,;MSH6,downstream_gene_variant,,ENST00000455383,;FBXO11,downstream_gene_variant,,ENST00000434523,;MSH6,3_prime_UTR_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;FBXO11,downstream_gene_variant,,ENST00000465204,;MSH6,downstream_gene_variant,,ENST00000456246,;	G	ENSG00000116062	ENST00000234420	Transcript	missense_variant	3349	3197	1066	Y/C	tAt/tGt	rs372103816	.	.	1	MSH6	HGNC	7329	protein_coding	YES	CCDS1836.1	ENSP00000234420	MSH6_HUMAN	U3KQ72_HUMAN,F5H2F9_HUMAN,C9JH55_HUMAN,C9J8Y8_HUMAN,C9J7Y7_HUMAN	UPI00000405F8	.	deleterious(0)	possibly_damaging(0.907)	5/10	.	hmmpanther:PTHR11361:SF31,hmmpanther:PTHR11361,SMART_domains:SM00533,PIRSF_domain:PIRSF037677,Superfamily_domains:SSF48334	.	.	.	.	.	.	.	G:0	G:0.0001	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTATAGTC	byFrequency|byCluster	5	ESCA
ASAP2	0	.	GRCh37	2	9517087	9517087	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1797C>T	p.%3D	p.T599T	ENST00000281419	18/28	43	29	14	45	45	0	ASAP2,synonymous_variant,p.%3D,ENST00000281419,;ASAP2,synonymous_variant,p.%3D,ENST00000315273,;	T	ENSG00000151693	ENST00000281419	Transcript	synonymous_variant	2137	1797	599	T	acC/acT	.	.	.	1	ASAP2	HGNC	2721	protein_coding	YES	CCDS1661.1	ENSP00000281419	ASAP2_HUMAN	Q53RT9_HUMAN,Q53RS3_HUMAN,Q53R39_HUMAN	UPI0000073459	.	.	.	18/28	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,Gene3D:1.25.40.20,Pfam_domain:PF12796,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF238,PROSITE_profiles:PS50297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAACCTCTCT	.	5	ESCA
TMEM131	0	.	GRCh37	2	98409874	98409874	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3529A>G	p.Ile1177Val	p.I1177V	ENST00000186436	30/41	96	87	9	78	78	0	TMEM131,missense_variant,p.Ile94Val,ENST00000409721,;TMEM131,missense_variant,p.Ile1177Val,ENST00000186436,;TMEM131,non_coding_transcript_exon_variant,,ENST00000480724,;	C	ENSG00000075568	ENST00000186436	Transcript	missense_variant	3758	3529	1177	I/V	Att/Gtt	.	.	.	-1	TMEM131	HGNC	30366	protein_coding	YES	CCDS46368.1	ENSP00000186436	TM131_HUMAN	C9J6W0_HUMAN	UPI00006C0498	.	tolerated(0.12)	benign(0.004)	30/41	.	hmmpanther:PTHR22050,hmmpanther:PTHR22050:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGAAATACCAA	.	3	ESCA
MIR548I1	0	.	GRCh37	3	125509324	125509324	+	RNA	SNP	A	A	G	rs770769535	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.72T>C	.	.	ENST00000408810	1/1	199	186	13	225	225	0	MIR548I1,non_coding_transcript_exon_variant,,ENST00000408810,;RP11-379B18.6,intron_variant,,ENST00000610060,;RP11-379B18.1,upstream_gene_variant,,ENST00000486999,;RPS3AP14,upstream_gene_variant,,ENST00000483907,;	G	ENSG00000221737	ENST00000408810	Transcript	non_coding_transcript_exon_variant	72	.	.	.	.	rs770769535	.	.	-1	MIR548I1	HGNC	35352	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGCCATTACT	.	2	ESCA
STAG1	0	.	GRCh37	3	136141859	136141859	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1678C>G	p.Gln560Glu	p.Q560E	ENST00000383202	17/34	70	66	4	70	70	0	STAG1,missense_variant,p.Gln144Glu,ENST00000536929,;STAG1,missense_variant,p.Gln334Glu,ENST00000434713,;STAG1,missense_variant,p.Gln560Glu,ENST00000383202,;STAG1,missense_variant,p.Gln171Glu,ENST00000492318,;STAG1,missense_variant,p.Gln560Glu,ENST00000236698,;STAG1,3_prime_UTR_variant,,ENST00000483235,;STAG1,3_prime_UTR_variant,,ENST00000487065,;	C	ENSG00000118007	ENST00000383202	Transcript	missense_variant	1935	1678	560	Q/E	Caa/Gaa	.	.	.	-1	STAG1	HGNC	11354	protein_coding	YES	CCDS3090.1	ENSP00000372689	STAG1_HUMAN	Q4LE48_HUMAN	UPI000020A2DE	.	tolerated(0.06)	benign(0.076)	17/34	.	hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATTTGAGTTT	.	2	ESCA
ATP13A3	0	.	GRCh37	3	194147972	194147972	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2957A>G	p.Asn986Ser	p.N986S	ENST00000439040	29/33	31	26	4	39	39	0	ATP13A3,missense_variant,p.Asn986Ser,ENST00000256031,;ATP13A3,missense_variant,p.Asn986Ser,ENST00000439040,;ATP13A3,upstream_gene_variant,,ENST00000429136,;ATP13A3,downstream_gene_variant,,ENST00000484023,;	C	ENSG00000133657	ENST00000439040	Transcript	missense_variant	3749	2957	986	N/S	aAt/aGt	.	.	.	-1	ATP13A3	HGNC	24113	protein_coding	YES	CCDS43187.1	ENSP00000416508	AT133_HUMAN	C9JAP7_HUMAN,C9J7Z7_HUMAN	UPI000049DFC3	.	deleterious(0.05)	benign(0.418)	29/33	.	hmmpanther:PTHR24093:SF249,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01657,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGATTTAAA	.	5	ESCA
TNK2	0	.	GRCh37	3	195615459	195615459	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.190A>G	p.Met64Val	p.M64V	ENST00000381916	2/15	42	37	5	46	46	0	TNK2,start_lost,p.Met1?,ENST00000333602,;TNK2,start_lost,p.Met1?,ENST00000316664,;TNK2,start_lost,p.Met1?,ENST00000392400,;TNK2,start_lost,p.Met1?,ENST00000433111,;TNK2,missense_variant,p.Met33Val,ENST00000428187,;TNK2,missense_variant,p.Met64Val,ENST00000381916,;TNK2,missense_variant,p.Met65Val,ENST00000427576,;TNK2,upstream_gene_variant,,ENST00000438207,;TNK2,non_coding_transcript_exon_variant,,ENST00000468819,;TNK2,intron_variant,,ENST00000486523,;TNK2,start_lost,p.Met1?,ENST00000439230,;TNK2,start_lost,p.Met1?,ENST00000447060,;TNK2,non_coding_transcript_exon_variant,,ENST00000464041,;TNK2,upstream_gene_variant,,ENST00000430929,;TNK2,upstream_gene_variant,,ENST00000481865,;	C	ENSG00000061938	ENST00000381916	Transcript	missense_variant	335	190	64	M/V	Atg/Gtg	.	.	.	-1	TNK2	HGNC	19297	protein_coding	YES	CCDS33927.1	ENSP00000371341	ACK1_HUMAN	C9JDG3_HUMAN	UPI00004C9B08	.	deleterious(0)	possibly_damaging(0.882)	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCATTCTGC	.	4	ESCA
USP19	0	.	GRCh37	3	49148789	49148789	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3221C>G	p.Pro1074Arg	p.P1074R	ENST00000434032	22/27	25	20	4	27	27	0	USP19,missense_variant,p.Pro1076Arg,ENST00000417901,;USP19,missense_variant,p.Pro1013Arg,ENST00000398892,;USP19,missense_variant,p.Pro1013Arg,ENST00000398898,;USP19,missense_variant,p.Pro1064Arg,ENST00000453664,;USP19,missense_variant,p.Pro1074Arg,ENST00000434032,;USP19,missense_variant,p.Pro781Arg,ENST00000398896,;USP19,missense_variant,p.Pro973Arg,ENST00000398888,;USP19,downstream_gene_variant,,ENST00000306026,;USP19,downstream_gene_variant,,ENST00000464931,;USP19,upstream_gene_variant,,ENST00000483667,;	C	ENSG00000172046	ENST00000434032	Transcript	missense_variant	3433	3221	1074	P/R	cCt/cGt	.	.	.	-1	USP19	HGNC	12617	protein_coding	YES	CCDS56254.1	ENSP00000401197	UBP19_HUMAN	.	UPI000198CAB3	.	deleterious(0.01)	possibly_damaging(0.493)	22/27	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF404,Pfam_domain:PF00443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ACCCAGGCACA	.	3	ESCA
SETD7	0	.	GRCh37	4	140432140	140432140	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*677A>T	.	.	ENST00000274031	8/8	14	11	3	18	18	0	SETD7,3_prime_UTR_variant,,ENST00000274031,;SETD7,intron_variant,,ENST00000506866,;SETD7,intron_variant,,ENST00000515101,;	A	ENSG00000145391	ENST00000274031	Transcript	3_prime_UTR_variant	2415	.	.	.	.	.	.	.	-1	SETD7	HGNC	30412	protein_coding	YES	CCDS3748.1	ENSP00000274031	SETD7_HUMAN	.	UPI0000135893	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGACATAATAA	.	2	ESCA
OTUD4	0	.	GRCh37	4	146056332	146056332	+	3'UTR	SNP	A	A	G	rs773865503	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2250T>C	.	.	ENST00000454497	21/21	24	19	4	17	17	0	OTUD4,3_prime_UTR_variant,,ENST00000454497,;OTUD4,downstream_gene_variant,,ENST00000447906,;OTUD4,intron_variant,,ENST00000455611,;	G	ENSG00000164164	ENST00000454497	Transcript	3_prime_UTR_variant	5538	.	.	.	.	rs773865503	.	.	-1	OTUD4	HGNC	24949	protein_coding	YES	CCDS47139.1	ENSP00000409279	OTUD4_HUMAN	D6RA27_HUMAN	UPI0000DA6D4D	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACCATCTGC	.	5	ESCA
MRFAP1	0	.	GRCh37	4	6643775	6643775	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*331C>G	.	.	ENST00000320912	3/3	89	76	12	111	111	0	MRFAP1,3_prime_UTR_variant,,ENST00000382581,;MRFAP1,3_prime_UTR_variant,,ENST00000320912,;MRFAP1,downstream_gene_variant,,ENST00000507420,;MRFAP1,non_coding_transcript_exon_variant,,ENST00000512914,;	G	ENSG00000179010	ENST00000320912	Transcript	3_prime_UTR_variant	1368	.	.	.	.	.	.	.	1	MRFAP1	HGNC	24549	protein_coding	YES	CCDS3389.1	ENSP00000318352	MOFA1_HUMAN	.	UPI000006F0BC	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTCTTGTG	.	5	ESCA
RCHY1	0	.	GRCh37	4	76439454	76439454	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43C>T	p.Arg15Ter	p.R15*	ENST00000324439	1/9	45	39	5	42	42	0	RCHY1,stop_gained,p.Arg15Ter,ENST00000513257,;RCHY1,stop_gained,p.Arg15Ter,ENST00000324439,;RCHY1,stop_gained,p.Arg15Ter,ENST00000451788,;RCHY1,stop_gained,p.Arg15Ter,ENST00000380840,;RCHY1,stop_gained,p.Arg15Ter,ENST00000507014,;RCHY1,synonymous_variant,p.%3D,ENST00000512706,;THAP6,5_prime_UTR_variant,,ENST00000504218,;THAP6,intron_variant,,ENST00000506261,;THAP6,upstream_gene_variant,,ENST00000507556,;THAP6,upstream_gene_variant,,ENST00000507885,;THAP6,upstream_gene_variant,,ENST00000504190,;THAP6,upstream_gene_variant,,ENST00000311638,;THAP6,upstream_gene_variant,,ENST00000508105,;THAP6,upstream_gene_variant,,ENST00000507557,;THAP6,upstream_gene_variant,,ENST00000502620,;THAP6,upstream_gene_variant,,ENST00000380837,;THAP6,upstream_gene_variant,,ENST00000514480,;RCHY1,intron_variant,,ENST00000514021,;RCHY1,stop_gained,p.Arg5Ter,ENST00000513909,;RCHY1,stop_gained,p.Arg15Ter,ENST00000505105,;RCHY1,stop_gained,p.Arg15Ter,ENST00000504085,;RCHY1,non_coding_transcript_exon_variant,,ENST00000514589,;RCHY1,non_coding_transcript_exon_variant,,ENST00000513083,;THAP6,upstream_gene_variant,,ENST00000504384,;THAP6,upstream_gene_variant,,ENST00000503831,;RCHY1,upstream_gene_variant,,ENST00000505514,;	A	ENSG00000163743	ENST00000324439	Transcript	stop_gained	442	43	15	R/*	Cga/Tga	.	.	.	-1	RCHY1	HGNC	17479	protein_coding	YES	CCDS3567.1	ENSP00000321239	ZN363_HUMAN	G3FDP5_HUMAN,G3FDP4_HUMAN,D6RAF6_HUMAN	UPI000013C366	.	.	.	1/9	.	hmmpanther:PTHR21319,PROSITE_profiles:PS51266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCTCGCTCTT	.	3	ESCA
PJA2	0	.	GRCh37	5	108672903	108672903	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29A>G	.	.	ENST00000361189	10/10	25	22	3	26	26	0	PJA2,3_prime_UTR_variant,,ENST00000361189,;PJA2,3_prime_UTR_variant,,ENST00000361557,;	C	ENSG00000198961	ENST00000361189	Transcript	3_prime_UTR_variant	2396	.	.	.	.	.	.	.	-1	PJA2	HGNC	17481	protein_coding	YES	CCDS4099.1	ENSP00000354775	PJA2_HUMAN	.	UPI000013D192	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTGATACACT	.	2	ESCA
KDM3B	0	.	GRCh37	5	137753253	137753253	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3389A>T	p.Gln1130Leu	p.Q1130L	ENST00000314358	13/24	81	67	13	91	91	0	KDM3B,missense_variant,p.Gln162Leu,ENST00000542866,;KDM3B,missense_variant,p.Gln786Leu,ENST00000394866,;KDM3B,missense_variant,p.Gln1130Leu,ENST00000314358,;KDM3B,upstream_gene_variant,,ENST00000508386,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,3_prime_UTR_variant,,ENST00000507996,;	T	ENSG00000120733	ENST00000314358	Transcript	missense_variant	3589	3389	1130	Q/L	cAg/cTg	.	.	.	1	KDM3B	HGNC	1337	protein_coding	YES	CCDS34242.1	ENSP00000326563	KDM3B_HUMAN	F5H275_HUMAN	UPI000020C6A8	.	deleterious(0.01)	benign(0.306)	13/24	.	hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGACAGAACA	.	5	ESCA
CTNNA1	0	.	GRCh37	5	138221923	138221923	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1085A>T	p.Asp362Val	p.D362V	ENST00000302763	8/18	52	47	5	59	59	0	CTNNA1,missense_variant,p.Asp362Val,ENST00000302763,;CTNNA1,missense_variant,p.Asp259Val,ENST00000355078,;CTNNA1,missense_variant,p.Asp362Val,ENST00000518825,;CTNNA1,5_prime_UTR_variant,,ENST00000521640,;CTNNA1,5_prime_UTR_variant,,ENST00000517656,;CTNNA1,5_prime_UTR_variant,,ENST00000522013,;CTNNA1,5_prime_UTR_variant,,ENST00000520522,;CTNNA1,5_prime_UTR_variant,,ENST00000520865,;CTNNA1,5_prime_UTR_variant,,ENST00000520260,;CTNNA1,5_prime_UTR_variant,,ENST00000518381,;CTNNA1,5_prime_UTR_variant,,ENST00000523298,;CTNNA1,5_prime_UTR_variant,,ENST00000523685,;CTNNA1,5_prime_UTR_variant,,ENST00000519634,;CTNNA1,5_prime_UTR_variant,,ENST00000540387,;CTNNA1,5_prime_UTR_variant,,ENST00000519768,;CTNNA1,5_prime_UTR_variant,,ENST00000519116,;CTNNA1,5_prime_UTR_variant,,ENST00000521683,;CTNNA1,5_prime_UTR_variant,,ENST00000517533,;CTNNA1,non_coding_transcript_exon_variant,,ENST00000520400,;CTNNA1,non_coding_transcript_exon_variant,,ENST00000522052,;CTNNA1,3_prime_UTR_variant,,ENST00000521724,;CTNNA1,3_prime_UTR_variant,,ENST00000523275,;CTNNA1,non_coding_transcript_exon_variant,,ENST00000517904,;CTNNA1,non_coding_transcript_exon_variant,,ENST00000517534,;	T	ENSG00000044115	ENST00000302763	Transcript	missense_variant	1175	1085	362	D/V	gAt/gTt	.	.	.	1	CTNNA1	HGNC	2509	protein_coding	YES	CCDS34243.1	ENSP00000304669	CTNA1_HUMAN	F8W845_HUMAN,E5RJP7_HUMAN,E5RJL0_HUMAN,E5RJC9_HUMAN,E5RJ43_HUMAN,E5RJ41_HUMAN,E5RIE0_HUMAN,E5RIB1_HUMAN,E5RHY5_HUMAN,E5RHV7_HUMAN,E5RHR7_HUMAN,E5RHJ5_HUMAN,E5RGY6_HUMAN,E5RGU3_HUMAN,E5RGS1_HUMAN,E5RGG4_HUMAN,E5RGD2_HUMAN,E5RG03_HUMAN,E5RFM5_HUMAN,E5RFM3_HUMAN,E5RFK9_HUMAN,E5RFG3_HUMAN,B4E2G8_HUMAN,B4DKT9_HUMAN	UPI000012862C	.	tolerated(0.17)	benign(0.065)	8/18	.	hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF24,Pfam_domain:PF01044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGTGATGCAC	.	4	ESCA
PCDHA3	0	.	GRCh37	5	140182336	140182336	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1554C>T	p.%3D	p.Y518Y	ENST00000522353	1/4	191	180	10	201	201	0	PCDHA3,synonymous_variant,p.%3D,ENST00000532566,;PCDHA3,synonymous_variant,p.%3D,ENST00000522353,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA2,intron_variant,,ENST00000520672,;PCDHA4,upstream_gene_variant,,ENST00000530339,;PCDHA4,upstream_gene_variant,,ENST00000356878,;PCDHA4,upstream_gene_variant,,ENST00000512229,;	T	ENSG00000255408	ENST00000522353	Transcript	synonymous_variant	1554	1554	518	Y	taC/taT	.	.	.	1	PCDHA3	HGNC	8669	protein_coding	YES	CCDS54915.1	ENSP00000429808	PCDA3_HUMAN	.	UPI00001273CB	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF93,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGTACGCGCT	.	2	ESCA
AC005609.1	0	.	GRCh37	5	140242612	140242612	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364G>C	p.Val122Leu	p.V122L	ENST00000502505	1/1	66	60	6	79	79	0	AC005609.1,missense_variant,p.Val122Leu,ENST00000502505,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA14,upstream_gene_variant,,ENST00000562220,;PCDHA14,non_coding_transcript_exon_variant,,ENST00000506751,;	G	ENSG00000249034	ENST00000502505	Transcript	missense_variant	613	364	122	V/L	Gtt/Ctt	.	.	.	-1	AC005609.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000424817	.	Q8NB83_HUMAN	UPI0000073A41	.	tolerated_low_confidence(0.22)	benign(0.198)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGCAACAGCTG	.	3	ESCA
PCDHB15	0	.	GRCh37	5	140626138	140626138	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.992G>T	p.Cys331Phe	p.C331F	ENST00000231173	1/1	43	35	8	46	45	0	PCDHB15,missense_variant,p.Cys331Phe,ENST00000231173,;PCDHB19P,downstream_gene_variant,,ENST00000570871,;	T	ENSG00000113248	ENST00000231173	Transcript	missense_variant	992	992	331	C/F	tGc/tTc	.	.	.	1	PCDHB15	HGNC	8686	protein_coding	YES	CCDS4257.1	ENSP00000231173	PCDBF_HUMAN	.	UPI00001273E8	.	deleterious_low_confidence(0)	probably_damaging(0.918)	1/1	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028:SF97,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATGCTCTG	.	5	ESCA
PCDHGC5	0	.	GRCh37	5	140870083	140870083	+	Missense_Mutation	SNP	G	G	A	rs768123119	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1276G>A	p.Ala426Thr	p.A426T	ENST00000252087	1/4	44	38	6	52	52	0	PCDHGC5,missense_variant,p.Ala426Thr,ENST00000252087,;PCDHGB6,intron_variant,,ENST00000520790,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGA10,intron_variant,,ENST00000398610,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA12,intron_variant,,ENST00000252085,;PCDHGA11,intron_variant,,ENST00000398587,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGC3,intron_variant,,ENST00000308177,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA11,intron_variant,,ENST00000518882,;PCDHGC4,intron_variant,,ENST00000306593,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGB7,intron_variant,,ENST00000398594,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;	A	ENSG00000240764	ENST00000252087	Transcript	missense_variant	1276	1276	426	A/T	Gcc/Acc	rs768123119	.	.	1	PCDHGC5	HGNC	8718	protein_coding	YES	CCDS4263.1	ENSP00000252087	PCDGM_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006D689	.	deleterious(0)	probably_damaging(0.999)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF80,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTGGCCAGC	byFrequency	4	ESCA
FAM105B	0	.	GRCh37	5	14693028	14693028	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.930C>A	p.Tyr310Ter	p.Y310*	ENST00000284274	7/7	98	67	30	66	66	0	FAM105B,stop_gained,p.Tyr310Ter,ENST00000284274,;FAM105B,stop_gained,p.Tyr42Ter,ENST00000506417,;FAM105B,downstream_gene_variant,,ENST00000503023,;FAM105B,downstream_gene_variant,,ENST00000508678,;FAM105B,downstream_gene_variant,,ENST00000514913,;	A	ENSG00000154124	ENST00000284274	Transcript	stop_gained	1008	930	310	Y/*	taC/taA	.	.	.	1	FAM105B	HGNC	25118	protein_coding	YES	CCDS43302.1	ENSP00000284274	OTUL_HUMAN	.	UPI0000374C00	.	.	.	7/7	.	Prints_domain:PR02055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTACAACAC	.	5	ESCA
BRD9	0	.	GRCh37	5	884124	884124	+	Missense_Mutation	SNP	C	C	T	rs753813330	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895G>A	p.Val299Met	p.V299M	ENST00000467963	8/16	40	24	15	40	40	0	BRD9,missense_variant,p.Val299Met,ENST00000467963,;BRD9,missense_variant,p.Val203Met,ENST00000323510,;BRD9,missense_variant,p.Val183Met,ENST00000388890,;BRD9,missense_variant,p.Val203Met,ENST00000489093,;BRD9,missense_variant,p.Val246Met,ENST00000483173,;BRD9,missense_variant,p.Val183Met,ENST00000435709,;BRD9,intron_variant,,ENST00000494422,;BRD9,upstream_gene_variant,,ENST00000519838,;BRD9,3_prime_UTR_variant,,ENST00000489816,;BRD9,3_prime_UTR_variant,,ENST00000495265,;BRD9,3_prime_UTR_variant,,ENST00000466684,;BRD9,3_prime_UTR_variant,,ENST00000490814,;BRD9,non_coding_transcript_exon_variant,,ENST00000495794,;BRD9,upstream_gene_variant,,ENST00000493082,;BRD9,upstream_gene_variant,,ENST00000483234,;BRD9,upstream_gene_variant,,ENST00000475706,;	T	ENSG00000028310	ENST00000467963	Transcript	missense_variant	1062	895	299	V/M	Gtg/Atg	rs753813330	.	.	-1	BRD9	HGNC	25818	protein_coding	YES	CCDS34127.2	ENSP00000419765	BRD9_HUMAN	.	UPI000020BEBE	.	tolerated(0.06)	probably_damaging(0.975)	8/16	.	Pfam_domain:PF12024,hmmpanther:PTHR22881,hmmpanther:PTHR22881:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCACGTGCT	.	5	ESCA
TBC1D32	0	.	GRCh37	6	121638672	121638672	+	Missense_Mutation	SNP	T	T	C	rs774938386	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464A>G	p.Asn155Ser	p.N155S	ENST00000398212	3/32	93	89	4	121	121	0	TBC1D32,missense_variant,p.Asn155Ser,ENST00000422369,;TBC1D32,missense_variant,p.Asn155Ser,ENST00000398212,;TBC1D32,missense_variant,p.Asn155Ser,ENST00000275159,;TBC1D32,3_prime_UTR_variant,,ENST00000464622,;	C	ENSG00000146350	ENST00000398212	Transcript	missense_variant	514	464	155	N/S	aAt/aGt	rs774938386	.	.	-1	TBC1D32	HGNC	21485	protein_coding	YES	CCDS43501.1	ENSP00000381270	BROMI_HUMAN	A2A304_HUMAN	UPI0000E67203	.	tolerated(0.1)	benign(0.108)	3/32	.	hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3,Pfam_domain:PF14961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S157P|c.469T>C|4,BUFFER|p.R152H|c.455G>A|3	MUTECT|MUSE	AGCAATTGTCT	byFrequency	2	ESCA
TULP4	0	.	GRCh37	6	158932256	158932256	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4530T>A	.	.	ENST00000367097	14/14	36	32	4	36	36	0	TULP4,3_prime_UTR_variant,,ENST00000367097,;TULP4,downstream_gene_variant,,ENST00000367094,;CACYBPP3,downstream_gene_variant,,ENST00000406011,;	A	ENSG00000130338	ENST00000367097	Transcript	3_prime_UTR_variant	10519	.	.	.	.	.	.	.	1	TULP4	HGNC	15530	protein_coding	YES	CCDS34561.1	ENSP00000356064	TULP4_HUMAN	.	UPI000013CD76	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAAATTTTTT	.	3	ESCA
NUP153	0	.	GRCh37	6	17661926	17661926	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1353A>G	p.%3D	p.R451R	ENST00000262077	11/22	27	22	5	44	44	0	NUP153,synonymous_variant,p.%3D,ENST00000537253,;NUP153,synonymous_variant,p.%3D,ENST00000262077,;	C	ENSG00000124789	ENST00000262077	Transcript	synonymous_variant	1353	1353	451	R	cgA/cgG	.	.	.	-1	NUP153	HGNC	8062	protein_coding	YES	CCDS4541.1	ENSP00000262077	NU153_HUMAN	.	UPI000013D251	.	.	.	11/22	.	Pfam_domain:PF08604,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCTCGTCT	.	5	ESCA
C6orf62	0	.	GRCh37	6	24705881	24705881	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*484C>G	.	.	ENST00000378119	5/5	47	40	7	33	33	0	C6orf62,3_prime_UTR_variant,,ENST00000378119,;ACOT13,downstream_gene_variant,,ENST00000230048,;ACOT13,downstream_gene_variant,,ENST00000537591,;C6orf62,downstream_gene_variant,,ENST00000378102,;C6orf62,downstream_gene_variant,,ENST00000540769,;RP1-30M3.6,upstream_gene_variant,,ENST00000606921,;RP1-30M3.5,upstream_gene_variant,,ENST00000607014,;ACOT13,downstream_gene_variant,,ENST00000476436,;	C	ENSG00000112308	ENST00000378119	Transcript	3_prime_UTR_variant	3342	.	.	.	.	.	.	.	-1	C6orf62	HGNC	20998	protein_coding	YES	CCDS4559.1	ENSP00000367359	CF062_HUMAN	B4DWX7_HUMAN	UPI000000DC64	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTAGAATGT	.	5	ESCA
HIST1H3B	0	.	GRCh37	6	26032006	26032006	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283G>T	p.Glu95Ter	p.E95*	ENST00000244661	1/1	95	82	13	91	91	0	HIST1H3B,stop_gained,p.Glu95Ter,ENST00000244661,;HIST1H2AB,downstream_gene_variant,,ENST00000259791,;HIST1H4B,upstream_gene_variant,,ENST00000377364,;	A	ENSG00000124693	ENST00000244661	Transcript	stop_gained	283	283	95	E/*	Gag/Tag	COSM1487519	.	.	-1	HIST1H3B	HGNC	4776	protein_coding	YES	CCDS4573.1	ENSP00000244661	H31_HUMAN	.	UPI00000003C7	.	.	.	1/1	.	hmmpanther:PTHR11426,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCTCCTGCA	.	4	ESCA
HIST1H2BH	0	.	GRCh37	6	26251922	26251922	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44C>G	p.Ser15Cys	p.S15C	ENST00000356350	1/1	111	99	12	136	136	0	HIST1H2BH,missense_variant,p.Ser15Cys,ENST00000356350,;HIST1H4G,upstream_gene_variant,,ENST00000244537,;HIST1H3F,upstream_gene_variant,,ENST00000446824,;	G	ENSG00000197459	ENST00000356350	Transcript	missense_variant	44	44	15	S/C	tCc/tGc	.	.	.	1	HIST1H2BH	HGNC	4755	protein_coding	YES	CCDS4601.1	ENSP00000348706	H2B1H_HUMAN	.	UPI0000001BD4	.	deleterious_low_confidence(0.02)	benign(0.031)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23428,Gene3D:1.10.20.10,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGCTCCAAGA	.	4	ESCA
TFEC	0	.	GRCh37	7	115580576	115580576	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29G>A	.	.	ENST00000265440	8/8	38	28	10	37	37	0	TFEC,3_prime_UTR_variant,,ENST00000457268,;TFEC,3_prime_UTR_variant,,ENST00000320239,;TFEC,3_prime_UTR_variant,,ENST00000393485,;TFEC,3_prime_UTR_variant,,ENST00000265440,;TFEC,downstream_gene_variant,,ENST00000484212,;TFEC,intron_variant,,ENST00000462828,;	T	ENSG00000105967	ENST00000265440	Transcript	3_prime_UTR_variant	1254	.	.	.	.	.	.	.	-1	TFEC	HGNC	11754	protein_coding	YES	CCDS5762.1	ENSP00000265440	TFEC_HUMAN	Q75MG2_HUMAN,Q75KY0_HUMAN	UPI000006CC81	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTTCCAGTT	.	5	ESCA
VWDE	0	.	GRCh37	7	12414695	12414695	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1183G>A	p.Val395Met	p.V395M	ENST00000275358	8/29	70	60	9	65	65	0	VWDE,missense_variant,p.Val395Met,ENST00000275358,;VWDE,missense_variant,p.Val395Met,ENST00000452576,;VWDE,intron_variant,,ENST00000521169,;VWDE,downstream_gene_variant,,ENST00000326715,;	T	ENSG00000146530	ENST00000275358	Transcript	missense_variant	1372	1183	395	V/M	Gtg/Atg	.	.	.	-1	VWDE	HGNC	21897	protein_coding	YES	CCDS47544.1	ENSP00000275358	VWDE_HUMAN	.	UPI00006C0B98	.	deleterious(0)	probably_damaging(0.958)	8/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCACTACAA	.	5	ESCA
SCIN	0	.	GRCh37	7	12680126	12680126	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1565T>C	p.Ile522Thr	p.I522T	ENST00000297029	11/16	42	36	6	44	44	0	SCIN,missense_variant,p.Ile275Thr,ENST00000445618,;SCIN,missense_variant,p.Ile275Thr,ENST00000519209,;SCIN,missense_variant,p.Ile522Thr,ENST00000297029,;SCIN,missense_variant,p.Ile522Thr,ENST00000341757,;	C	ENSG00000006747	ENST00000297029	Transcript	missense_variant	1666	1565	522	I/T	aTc/aCc	.	.	.	1	SCIN	HGNC	21695	protein_coding	YES	CCDS47545.1	ENSP00000297029	ADSV_HUMAN	Q8NBV9_HUMAN,Q75MG0_HUMAN	UPI000013C4DF	.	tolerated(0.16)	possibly_damaging(0.738)	11/16	.	hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF14,Gene3D:3.40.20.10,SMART_domains:SM00262,Superfamily_domains:SSF55753	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTATCACCA	.	4	ESCA
GPR141	0	.	GRCh37	7	37780568	37780568	+	Silent	SNP	C	C	A	rs189762711	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.573C>A	p.%3D	p.A191A	ENST00000447769	4/4	94	84	10	89	89	0	GPR141,synonymous_variant,p.%3D,ENST00000334425,;GPR141,synonymous_variant,p.%3D,ENST00000447769,;EPDR1,intron_variant,,ENST00000476620,;GPR141,downstream_gene_variant,,ENST00000450180,;GPR141,intron_variant,,ENST00000461610,;	A	ENSG00000187037	ENST00000447769	Transcript	synonymous_variant	862	573	191	A	gcC/gcA	rs189762711	.	.	1	GPR141	HGNC	19997	protein_coding	YES	CCDS5451.1	ENSP00000390410	GP141_HUMAN	C9JDP7_HUMAN	UPI000004B92B	.	.	.	4/4	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF0,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGCCGTTGC	byCluster|by1000G	4	ESCA
NAPRT1	0	.	GRCh37	8	144657109	144657109	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555-39C>A	.	.	ENST00000449291	.	57	44	13	61	61	0	NAPRT1,missense_variant,p.Leu534Ile,ENST00000276844,;NAPRT1,missense_variant,p.Pro534His,ENST00000340490,;NAPRT1,3_prime_UTR_variant,,ENST00000435154,;NAPRT1,intron_variant,,ENST00000449291,;NAPRT1,intron_variant,,ENST00000426292,;EEF1D,downstream_gene_variant,,ENST00000423316,;EEF1D,downstream_gene_variant,,ENST00000528610,;EEF1D,downstream_gene_variant,,ENST00000530109,;EEF1D,downstream_gene_variant,,ENST00000529272,;EEF1D,downstream_gene_variant,,ENST00000419152,;EEF1D,downstream_gene_variant,,ENST00000526838,;MROH6,upstream_gene_variant,,ENST00000398882,;EEF1D,downstream_gene_variant,,ENST00000532400,;EEF1D,downstream_gene_variant,,ENST00000524624,;EEF1D,downstream_gene_variant,,ENST00000529576,;EEF1D,downstream_gene_variant,,ENST00000532741,;EEF1D,downstream_gene_variant,,ENST00000395119,;EEF1D,downstream_gene_variant,,ENST00000317198,;MROH6,upstream_gene_variant,,ENST00000529971,;EEF1D,downstream_gene_variant,,ENST00000531621,;EEF1D,downstream_gene_variant,,ENST00000442189,;RP11-661A12.9,intron_variant,,ENST00000531730,;RP11-661A12.7,upstream_gene_variant,,ENST00000529247,;NAPRT1,non_coding_transcript_exon_variant,,ENST00000460623,;NAPRT1,intron_variant,,ENST00000464332,;NAPRT1,intron_variant,,ENST00000498076,;NAPRT1,intron_variant,,ENST00000529179,;NAPRT1,downstream_gene_variant,,ENST00000462059,;NAPRT1,downstream_gene_variant,,ENST00000491904,;NAPRT1,downstream_gene_variant,,ENST00000480946,;NAPRT1,downstream_gene_variant,,ENST00000532645,;EEF1D,downstream_gene_variant,,ENST00000529007,;EEF1D,downstream_gene_variant,,ENST00000527741,;EEF1D,downstream_gene_variant,,ENST00000533833,;NAPRT1,downstream_gene_variant,,ENST00000488096,;NAPRT1,downstream_gene_variant,,ENST00000525583,;	T	ENSG00000147813	ENST00000449291	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NAPRT1	HGNC	30450	protein_coding	YES	CCDS6403.2	ENSP00000401508	PNCB_HUMAN	.	UPI000058EC33	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGAGGGCGG	.	5	ESCA
FZD3	0	.	GRCh37	8	28421393	28421393	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*866delA	.	.	ENST00000240093	8/8	94	80	14	70	70	0	FZD3,3_prime_UTR_variant,,ENST00000240093,;FZD3,downstream_gene_variant,,ENST00000537916,;FZD3,intron_variant,,ENST00000517911,;	-	ENSG00000104290	ENST00000240093	Transcript	3_prime_UTR_variant	3344	.	.	.	.	.	.	.	1	FZD3	HGNC	4041	protein_coding	YES	CCDS6069.1	ENSP00000240093	FZD3_HUMAN	E5RGI9_HUMAN	UPI000003156A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATTATAAGGTA	.	3	ESCA
KAT6A	0	.	GRCh37	8	41906575	41906575	+	5'UTR	SNP	T	T	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-80A>T	.	.	ENST00000396930	3/18	23	20	3	10	10	0	KAT6A,5_prime_UTR_variant,,ENST00000396930,;KAT6A,5_prime_UTR_variant,,ENST00000406337,;KAT6A,5_prime_UTR_variant,,ENST00000485568,;KAT6A,5_prime_UTR_variant,,ENST00000265713,;KAT6A,5_prime_UTR_variant,,ENST00000426524,;	A	ENSG00000083168	ENST00000396930	Transcript	5_prime_UTR_variant	465	.	.	.	.	.	.	.	-1	KAT6A	HGNC	13013	protein_coding	YES	CCDS6124.1	ENSP00000380136	KAT6A_HUMAN	A5PKX7_HUMAN	UPI000013D666	.	.	.	3/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAAGATTCTCG	.	2	ESCA
PLAT	0	.	GRCh37	8	42037508	42037508	+	Silent	SNP	C	C	T	rs188811714	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1299G>A	p.%3D	p.P433P	ENST00000220809	12/14	46	41	5	31	31	0	PLAT,synonymous_variant,p.%3D,ENST00000220809,;PLAT,synonymous_variant,p.%3D,ENST00000429089,;PLAT,synonymous_variant,p.%3D,ENST00000429710,;PLAT,synonymous_variant,p.%3D,ENST00000352041,;PLAT,synonymous_variant,p.%3D,ENST00000524009,;PLAT,synonymous_variant,p.%3D,ENST00000519510,;PLAT,intron_variant,,ENST00000270189,;PLAT,downstream_gene_variant,,ENST00000521042,;PLAT,downstream_gene_variant,,ENST00000521647,;PLAT,downstream_gene_variant,,ENST00000522812,;PLAT,downstream_gene_variant,,ENST00000524261,;	T	ENSG00000104368	ENST00000220809	Transcript	synonymous_variant	1556	1299	433	P	ccG/ccA	rs188811714	.	.	-1	PLAT	HGNC	9051	protein_coding	YES	CCDS6126.1	ENSP00000220809	TPA_HUMAN	Q6LBF5_HUMAN,E5RHG4_HUMAN,E5RGA1_HUMAN	UPI0000000DD4	.	.	.	12/14	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24259:SF0,hmmpanther:PTHR24259,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,PIRSF_domain:PIRSF001145,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCGCCGGGGG	byFrequency|by1000G	4	ESCA
ST18	0	.	GRCh37	8	53050009	53050009	+	Missense_Mutation	SNP	C	C	T	rs369893285	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2203G>A	p.Val735Met	p.V735M	ENST00000276480	18/26	78	62	16	67	67	0	ST18,missense_variant,p.Val735Met,ENST00000276480,;ST18,non_coding_transcript_exon_variant,,ENST00000518501,;ST18,3_prime_UTR_variant,,ENST00000521824,;ST18,3_prime_UTR_variant,,ENST00000522251,;ST18,3_prime_UTR_variant,,ENST00000521582,;ST18,upstream_gene_variant,,ENST00000522861,;ST18,upstream_gene_variant,,ENST00000518053,;	T	ENSG00000147488	ENST00000276480	Transcript	missense_variant	2887	2203	735	V/M	Gtg/Atg	rs369893285	.	.	-1	ST18	HGNC	18695	protein_coding	YES	CCDS6149.1	ENSP00000276480	ST18_HUMAN	E5RHS3_HUMAN	UPI0000046C30	.	deleterious(0.02)	probably_damaging(1)	18/26	.	hmmpanther:PTHR10816:SF9,hmmpanther:PTHR10816,Pfam_domain:PF01530,Superfamily_domains:0042508	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCACGTGGC	.	5	ESCA
LYPLA1	0	.	GRCh37	8	54960502	54960502	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*123G>A	.	.	ENST00000316963	9/9	52	47	5	48	48	0	LYPLA1,3_prime_UTR_variant,,ENST00000343231,;LYPLA1,3_prime_UTR_variant,,ENST00000316963,;LYPLA1,downstream_gene_variant,,ENST00000518546,;LYPLA1,downstream_gene_variant,,ENST00000521352,;LYPLA1,downstream_gene_variant,,ENST00000522007,;RP11-30L15.6,upstream_gene_variant,,ENST00000565668,;LYPLA1,non_coding_transcript_exon_variant,,ENST00000519272,;LYPLA1,downstream_gene_variant,,ENST00000520718,;LYPLA1,downstream_gene_variant,,ENST00000519891,;	T	ENSG00000120992	ENST00000316963	Transcript	3_prime_UTR_variant	1010	.	.	.	.	.	.	.	-1	LYPLA1	HGNC	6737	protein_coding	YES	CCDS6157.1	ENSP00000320043	LYPA1_HUMAN	Q6IAQ1_HUMAN,E5RJ48_HUMAN,B4DJV9_HUMAN	UPI0000072858	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTGGCATGTA	.	4	ESCA
PENK	0	.	GRCh37	8	57358292	57358292	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138+83C>T	.	.	ENST00000314922	.	65	59	6	73	73	0	PENK,missense_variant,p.Ala74Val,ENST00000518770,;PENK,intron_variant,,ENST00000314922,;PENK,intron_variant,,ENST00000451791,;PENK,intron_variant,,ENST00000518974,;PENK,intron_variant,,ENST00000523051,;PENK,intron_variant,,ENST00000517415,;RP11-17A4.2,upstream_gene_variant,,ENST00000518662,;PENK,upstream_gene_variant,,ENST00000523274,;PENK,downstream_gene_variant,,ENST00000521153,;	A	ENSG00000181195	ENST00000314922	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PENK	HGNC	8831	protein_coding	YES	CCDS6168.1	ENSP00000324248	PENK_HUMAN	E5RFR1_HUMAN	UPI00001315A9	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCGCGCGGTG	.	4	ESCA
NSMAF	0	.	GRCh37	8	59496579	59496579	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*86A>G	.	.	ENST00000427130	31/31	57	53	4	35	35	0	NSMAF,3_prime_UTR_variant,,ENST00000038176,;NSMAF,3_prime_UTR_variant,,ENST00000427130,;SDCBP,downstream_gene_variant,,ENST00000413219,;SDCBP,downstream_gene_variant,,ENST00000260130,;SDCBP,downstream_gene_variant,,ENST00000447267,;SDCBP,downstream_gene_variant,,ENST00000422546,;SDCBP,downstream_gene_variant,,ENST00000447182,;SDCBP,downstream_gene_variant,,ENST00000520168,;SDCBP,downstream_gene_variant,,ENST00000523483,;SDCBP,downstream_gene_variant,,ENST00000424270,;NSMAF,downstream_gene_variant,,ENST00000523177,;NSMAF,non_coding_transcript_exon_variant,,ENST00000521972,;SDCBP,downstream_gene_variant,,ENST00000523441,;NSMAF,downstream_gene_variant,,ENST00000517612,;NSMAF,downstream_gene_variant,,ENST00000521712,;AC068522.4,downstream_gene_variant,,ENST00000482895,;	C	ENSG00000035681	ENST00000427130	Transcript	3_prime_UTR_variant	3121	.	.	.	.	.	.	.	-1	NSMAF	HGNC	8017	protein_coding	YES	CCDS47864.1	ENSP00000411012	FAN_HUMAN	.	UPI000192950C	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACATTGCAC	.	2	ESCA
SLC25A25	0	.	GRCh37	9	130868491	130868491	+	Silent	SNP	G	G	T	rs765217256	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.963G>T	p.%3D	p.G321G	ENST00000373068	7/10	64	43	21	72	72	0	SLC25A25,synonymous_variant,p.%3D,ENST00000433501,;SLC25A25,synonymous_variant,p.%3D,ENST00000373066,;SLC25A25,synonymous_variant,p.%3D,ENST00000373068,;SLC25A25,synonymous_variant,p.%3D,ENST00000373064,;SLC25A25,synonymous_variant,p.%3D,ENST00000373069,;SLC25A25,synonymous_variant,p.%3D,ENST00000432073,;SLC25A25,intron_variant,,ENST00000466983,;RP11-395P17.3,downstream_gene_variant,,ENST00000418747,;RP11-395P17.11,downstream_gene_variant,,ENST00000602939,;SLC25A25,downstream_gene_variant,,ENST00000445012,;SLC25A25,downstream_gene_variant,,ENST00000472769,;	T	ENSG00000148339	ENST00000373068	Transcript	synonymous_variant	1082	963	321	G	ggG/ggT	rs765217256	.	.	1	SLC25A25	HGNC	20663	protein_coding	YES	CCDS35151.1	ENSP00000362159	SCMC2_HUMAN	.	UPI00002118BE	.	.	.	7/10	.	Prints_domain:PR00928,Superfamily_domains:0048588,Pfam_domain:PF00153,Gene3D:1okcA00,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF222,PROSITE_profiles:PS50920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGGTCCTT	.	5	ESCA
MORC4	0	.	GRCh37	X	106224650	106224650	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732A>G	p.%3D	p.V244V	ENST00000355610	6/17	39	34	5	25	24	0	MORC4,synonymous_variant,p.%3D,ENST00000255495,;MORC4,synonymous_variant,p.%3D,ENST00000355610,;MORC4,5_prime_UTR_variant,,ENST00000535534,;MORC4,intron_variant,,ENST00000604604,;	C	ENSG00000133131	ENST00000355610	Transcript	synonymous_variant	1007	732	244	V	gtA/gtG	.	.	.	-1	MORC4	HGNC	23485	protein_coding	YES	CCDS14525.2	ENSP00000347821	MORC4_HUMAN	.	UPI00003E75D3	.	.	.	6/17	.	hmmpanther:PTHR23336,hmmpanther:PTHR23336:SF1,Superfamily_domains:SSF55874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTGATACCAG	.	3	ESCA
IL9R	0	.	GRCh37	X	155233447	155233447	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.360C>T	p.%3D	p.I120I	ENST00000244174	4/9	79	58	20	84	84	0	IL9R,missense_variant,p.Ser165Leu,ENST00000369423,;IL9R,missense_variant,p.Ser155Leu,ENST00000540897,;IL9R,synonymous_variant,p.%3D,ENST00000244174,;IL9R,synonymous_variant,p.%3D,ENST00000424344,;IL9R,downstream_gene_variant,,ENST00000489233,;IL9R,upstream_gene_variant,,ENST00000494962,;AJ271736.10,upstream_gene_variant,,ENST00000483543,;	T	ENSG00000124334	ENST00000244174	Transcript	synonymous_variant	539	360	120	I	atC/atT	.	.	.	1	IL9R	HGNC	6030	protein_coding	YES	CCDS14771.4	ENSP00000244174	IL9R_HUMAN	.	UPI000016864A	.	.	.	4/9	.	hmmpanther:PTHR23037:SF26,hmmpanther:PTHR23037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATCACTTT	.	5	ESCA
RPA4	0	.	GRCh37	X	96140055	96140055	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49X-01A-31D-A27G-09	TCGA-LN-A49X-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.746A>G	p.Tyr249Cys	p.Y249C	ENST00000373040	1/1	10	3	7	21	21	0	RPA4,missense_variant,p.Tyr249Cys,ENST00000373040,;DIAPH2,intron_variant,,ENST00000373054,;DIAPH2,intron_variant,,ENST00000355827,;DIAPH2,intron_variant,,ENST00000324765,;DIAPH2,intron_variant,,ENST00000373049,;DIAPH2,intron_variant,,ENST00000373061,;	G	ENSG00000204086	ENST00000373040	Transcript	missense_variant	1149	746	249	Y/C	tAt/tGt	.	.	.	1	RPA4	HGNC	30305	protein_coding	YES	CCDS35345.1	ENSP00000362131	RFA4_HUMAN	.	UPI00001337A4	.	deleterious(0)	probably_damaging(0.984)	1/1	.	hmmpanther:PTHR13989:SF12,hmmpanther:PTHR13989,Gene3D:1.10.10.10,Pfam_domain:PF08784,PIRSF_domain:PIRSF036949,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CATCTATCCCA	.	3	ESCA
DNMBP	0	.	GRCh37	10	101716195	101716195	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1036G>T	p.Ala346Ser	p.A346S	ENST00000324109	4/17	10	0	10	21	21	0	DNMBP,missense_variant,p.Ala346Ser,ENST00000324109,;DNMBP,missense_variant,p.Ala346Ser,ENST00000342239,;DNMBP-AS1,intron_variant,,ENST00000434409,;	A	ENSG00000107554	ENST00000324109	Transcript	missense_variant	1128	1036	346	A/S	Gcc/Tcc	.	.	.	-1	DNMBP	HGNC	30373	protein_coding	YES	CCDS7485.1	ENSP00000315659	DNMBP_HUMAN	B4E0Q3_HUMAN	UPI000013D6C9	.	tolerated_low_confidence(0.3)	benign(0.014)	4/17	.	hmmpanther:PTHR22834:SF19,hmmpanther:PTHR22834	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCGGCCTCAT	.	3	ESCA
INPP5F	0	.	GRCh37	10	121565957	121565957	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1405C>T	p.Gln469Ter	p.Q469*	ENST00000361976	12/20	22	2	19	42	42	0	INPP5F,stop_gained,p.Gln469Ter,ENST00000361976,;	T	ENSG00000198825	ENST00000361976	Transcript	stop_gained	1571	1405	469	Q/*	Caa/Taa	.	.	.	1	INPP5F	HGNC	17054	protein_coding	YES	CCDS7616.1	ENSP00000354519	SAC2_HUMAN	.	UPI000006FBCA	.	.	.	12/20	.	PROSITE_profiles:PS50275,hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF129	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTCCAAGCT	.	5	ESCA
FANK1	0	.	GRCh37	10	127686054	127686054	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.539G>T	p.Ser180Ile	p.S180I	ENST00000368693	6/11	39	5	34	53	53	0	FANK1,missense_variant,p.Ser174Ile,ENST00000368695,;FANK1,missense_variant,p.Ser75Ile,ENST00000456942,;FANK1,missense_variant,p.Ser180Ile,ENST00000368693,;FANK1,intron_variant,,ENST00000368691,;FANK1,downstream_gene_variant,,ENST00000417114,;FANK1,downstream_gene_variant,,ENST00000445510,;FANK1,downstream_gene_variant,,ENST00000368689,;FANK1,splice_region_variant,,ENST00000492670,;FANK1,splice_region_variant,,ENST00000464130,;	T	ENSG00000203780	ENST00000368693	Transcript	missense_variant	643	539	180	S/I	aGt/aTt	.	.	.	1	FANK1	HGNC	23527	protein_coding	YES	CCDS31309.1	ENSP00000357682	FANK1_HUMAN	C9JD80_HUMAN,A6NH44_HUMAN	UPI000046FFD6	.	deleterious(0.01)	probably_damaging(0.951)	6/11	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24183,hmmpanther:PTHR24183:SF1,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACAGGTAGG	.	5	ESCA
KNDC1	0	.	GRCh37	10	135015190	135015190	+	Missense_Mutation	SNP	G	G	T	rs138733656	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3175G>T	p.Gly1059Trp	p.G1059W	ENST00000304613	17/30	17	6	10	19	19	0	KNDC1,missense_variant,p.Gly994Trp,ENST00000368571,;KNDC1,missense_variant,p.Gly1059Trp,ENST00000304613,;KNDC1,missense_variant,p.Gly1061Trp,ENST00000368572,;	T	ENSG00000171798	ENST00000304613	Transcript	missense_variant	3196	3175	1059	G/W	Ggg/Tgg	rs138733656	.	.	1	KNDC1	HGNC	29374	protein_coding	YES	CCDS7674.1	ENSP00000304437	VKIND_HUMAN	B4DFN0_HUMAN	UPI00003529F7	.	deleterious(0.01)	possibly_damaging(0.734)	17/30	.	hmmpanther:PTHR21560:SF0,hmmpanther:PTHR21560	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0.0007	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGGGGCC	byCluster|by1000G	5	ESCA
MKX	0	.	GRCh37	10	28023695	28023695	+	Missense_Mutation	SNP	G	G	C	rs754164534	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528C>G	p.His176Gln	p.H176Q	ENST00000375790	5/7	47	27	20	52	52	0	MKX,missense_variant,p.His176Gln,ENST00000375790,;MKX,missense_variant,p.His176Gln,ENST00000419761,;MKX,missense_variant,p.His176Gln,ENST00000460919,;	C	ENSG00000150051	ENST00000375790	Transcript	missense_variant	961	528	176	H/Q	caC/caG	rs754164534	.	.	-1	MKX	HGNC	23729	protein_coding	YES	CCDS7156.1	ENSP00000364946	MKX_HUMAN	H0YMU2_HUMAN	UPI0000161911	.	tolerated(0.44)	benign(0.257)	5/7	.	hmmpanther:PTHR11211:SF3,hmmpanther:PTHR11211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATGTGGGT	.	5	ESCA
ANTXRL	0	.	GRCh37	10	47678036	47678036	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.896-3T>C	.	.	ENST00000447511	.	15	5	10	26	26	0	ANTXRL,splice_region_variant,,ENST00000447511,;ANTXRL,splice_region_variant,,ENST00000537271,;ANTXRL,splice_region_variant,,ENST00000424375,;ANTXRL,intron_variant,,ENST00000434908,;	C	ENSG00000198250	ENST00000447511	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	ANTXRL	HGNC	27277	protein_coding	YES	CCDS60524.1	ENSP00000455449	.	H3BVE1_HUMAN,H3BPS2_HUMAN	UPI00015B6A6A	.	.	.	.	10/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	TCTTTTAGATG	.	3	ESCA
PCDH15	0	.	GRCh37	10	56106232	56106232	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.487G>T	p.Gly163Cys	p.G163C	ENST00000361849	6/34	30	3	26	45	45	0	PCDH15,missense_variant,p.Gly163Cys,ENST00000437009,;PCDH15,missense_variant,p.Gly141Cys,ENST00000395433,;PCDH15,missense_variant,p.Gly163Cys,ENST00000395445,;PCDH15,missense_variant,p.Gly163Cys,ENST00000320301,;PCDH15,missense_variant,p.Gly163Cys,ENST00000395432,;PCDH15,missense_variant,p.Gly163Cys,ENST00000373955,;PCDH15,missense_variant,p.Gly141Cys,ENST00000373957,;PCDH15,missense_variant,p.Gly163Cys,ENST00000395440,;PCDH15,missense_variant,p.Gly163Cys,ENST00000361849,;PCDH15,missense_variant,p.Gly163Cys,ENST00000395438,;PCDH15,missense_variant,p.Gly163Cys,ENST00000395446,;PCDH15,missense_variant,p.Gly163Cys,ENST00000395442,;PCDH15,missense_variant,p.Gly168Cys,ENST00000414778,;PCDH15,missense_variant,p.Gly163Cys,ENST00000373965,;PCDH15,missense_variant,p.Gly163Cys,ENST00000395430,;PCDH15,intron_variant,,ENST00000409834,;AC013737.1,downstream_gene_variant,,ENST00000583830,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Gly163Cys,ENST00000448885,;PCDH15,missense_variant,p.Gly163Cys,ENST00000414367,;PCDH15,intron_variant,,ENST00000373956,;	A	ENSG00000150275	ENST00000361849	Transcript	missense_variant	882	487	163	G/C	Ggt/Tgt	COSM336334,COSM336336,COSM336335	.	.	-1	PCDH15	HGNC	14674	protein_coding	YES	CCDS44404.1	ENSP00000354950	.	A2A3E7_HUMAN,A2A3D9_HUMAN	UPI0000EE048B	.	deleterious(0)	probably_damaging(1)	6/34	.	Superfamily_domains:SSF49313,Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTACCAACTG	.	5	ESCA
AGAP5	0	.	GRCh37	10	75434061	75434061	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*296G>T	.	.	ENST00000374094	8/8	37	34	3	43	43	0	AGAP5,3_prime_UTR_variant,,ENST00000443782,;AGAP5,3_prime_UTR_variant,,ENST00000374094,;RP11-464F9.21,intron_variant,,ENST00000607450,;RP11-464F9.1,non_coding_transcript_exon_variant,,ENST00000399449,;AGAP5,downstream_gene_variant,,ENST00000607663,;	A	ENSG00000172650	ENST00000374094	Transcript	3_prime_UTR_variant	2398	.	.	.	.	.	.	.	-1	AGAP5	HGNC	23467	protein_coding	YES	CCDS44439.1	ENSP00000363207	AGAP5_HUMAN	.	UPI000049DCFD	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGAACTTTTT	.	3	ESCA
ATP5C1	0	.	GRCh37	10	7848961	7848961	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*18C>A	.	.	ENST00000356708	9/10	87	50	36	63	63	0	ATP5C1,3_prime_UTR_variant,,ENST00000356708,;ATP5C1,intron_variant,,ENST00000335698,;ATP5C1,downstream_gene_variant,,ENST00000541227,;ATP5C1,non_coding_transcript_exon_variant,,ENST00000473809,;ATP5C1,non_coding_transcript_exon_variant,,ENST00000480528,;ATP5C1,non_coding_transcript_exon_variant,,ENST00000493053,;ATP5C1,non_coding_transcript_exon_variant,,ENST00000465936,;ATP5C1,downstream_gene_variant,,ENST00000460820,;	A	ENSG00000165629	ENST00000356708	Transcript	3_prime_UTR_variant	994	.	.	.	.	.	.	.	1	ATP5C1	HGNC	833	protein_coding	YES	CCDS31142.1	ENSP00000349142	ATPG_HUMAN	Q8TAS0_HUMAN,B4DL14_HUMAN,B4DFE6_HUMAN	UPI0000126574	.	.	.	9/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCCTCAG	.	5	ESCA
TUBB8	0	.	GRCh37	10	93704	93704	+	Missense_Mutation	SNP	T	T	C	rs781853492	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628A>G	p.Ile210Val	p.I210V	ENST00000309812	4/4	104	53	51	106	106	0	TUBB8,missense_variant,p.Ile138Val,ENST00000447903,;TUBB8,missense_variant,p.Ile210Val,ENST00000309812,;TUBB8,3_prime_UTR_variant,,ENST00000332708,;TUBB8,non_coding_transcript_exon_variant,,ENST00000413237,;TUBB8,non_coding_transcript_exon_variant,,ENST00000482075,;RP11-631M21.6,downstream_gene_variant,,ENST00000416477,;	C	ENSG00000173876	ENST00000309812	Transcript	missense_variant	691	628	210	I/V	Ata/Gta	rs781853492	.	.	-1	TUBB8	HGNC	20773	protein_coding	YES	CCDS7051.1	ENSP00000311042	TBB8_HUMAN	F5H0I4_HUMAN	UPI000007238E	.	deleterious_low_confidence(0.01)	benign(0.245)	4/4	.	Prints_domain:PR01161,Superfamily_domains:SSF52490,SMART_domains:SM00864,Pfam_domain:PF00091,Gene3D:3.40.50.1440,hmmpanther:PTHR11588:SF55,hmmpanther:PTHR11588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATATGTCAT	byFrequency	5	ESCA
ELMOD1	0	.	GRCh37	11	107518316	107518316	+	Silent	SNP	G	G	T	rs758259493	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543G>T	p.%3D	p.L181L	ENST00000265840	7/12	67	35	32	45	45	0	ELMOD1,synonymous_variant,p.%3D,ENST00000443271,;ELMOD1,synonymous_variant,p.%3D,ENST00000531234,;ELMOD1,synonymous_variant,p.%3D,ENST00000265840,;AP000889.1,upstream_gene_variant,,ENST00000530968,;	T	ENSG00000110675	ENST00000265840	Transcript	synonymous_variant	808	543	181	L	ctG/ctT	rs758259493	.	.	1	ELMOD1	HGNC	25334	protein_coding	YES	CCDS44723.1	ENSP00000265840	ELMD1_HUMAN	E9PLM8_HUMAN	UPI000006DF30	.	.	.	7/12	.	Pfam_domain:PF04727,hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF18,PROSITE_profiles:PS51335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGACTGTACAA	.	4	ESCA
ATM	0	.	GRCh37	11	108117828	108117828	+	Missense_Mutation	SNP	G	G	A	rs529202615	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1039G>A	p.Glu347Lys	p.E347K	ENST00000278616	8/63	36	20	15	25	25	0	ATM,missense_variant,p.Glu347Lys,ENST00000278616,;ATM,missense_variant,p.Glu347Lys,ENST00000527805,;ATM,missense_variant,p.Glu347Lys,ENST00000452508,;ATM,downstream_gene_variant,,ENST00000527891,;	A	ENSG00000149311	ENST00000278616	Transcript	missense_variant	1424	1039	347	E/K	Gaa/Aaa	rs529202615	.	.	1	ATM	HGNC	795	protein_coding	YES	CCDS31669.1	ENSP00000278616	ATM_HUMAN	M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN	UPI0000DBEF44	.	deleterious(0.01)	benign(0.283)	8/63	.	Superfamily_domains:SSF48371,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66	T:0.0004	T:0	T:0.0029	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGATTGAATTG	byFrequency|by1000G	3	ESCA
ATM	0	.	GRCh37	11	108117836	108117836	+	Missense_Mutation	SNP	G	G	A	rs768480943	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1047G>A	p.Met349Ile	p.M349I	ENST00000278616	8/63	33	20	12	26	26	0	ATM,missense_variant,p.Met349Ile,ENST00000278616,;ATM,missense_variant,p.Met349Ile,ENST00000527805,;ATM,missense_variant,p.Met349Ile,ENST00000452508,;ATM,downstream_gene_variant,,ENST00000527891,;	A	ENSG00000149311	ENST00000278616	Transcript	missense_variant	1432	1047	349	M/I	atG/atA	rs768480943	.	.	1	ATM	HGNC	795	protein_coding	YES	CCDS31669.1	ENSP00000278616	ATM_HUMAN	M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN	UPI0000DBEF44	.	tolerated(0.19)	benign(0.027)	8/63	.	Superfamily_domains:SSF48371,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTGATGGCAGA	byFrequency	3	ESCA
TMPRSS5	0	.	GRCh37	11	113569745	113569745	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210G>T	p.%3D	p.L70L	ENST00000299882	4/13	40	12	27	36	36	0	TMPRSS5,synonymous_variant,p.%3D,ENST00000544476,;TMPRSS5,synonymous_variant,p.%3D,ENST00000538955,;TMPRSS5,synonymous_variant,p.%3D,ENST00000544634,;TMPRSS5,synonymous_variant,p.%3D,ENST00000545579,;TMPRSS5,synonymous_variant,p.%3D,ENST00000299882,;TMPRSS5,5_prime_UTR_variant,,ENST00000540540,;TMPRSS5,5_prime_UTR_variant,,ENST00000536856,;TMPRSS5,intron_variant,,ENST00000539732,;TMPRSS5,intron_variant,,ENST00000538770,;TMPRSS5,upstream_gene_variant,,ENST00000545412,;TMPRSS5,3_prime_UTR_variant,,ENST00000538091,;	A	ENSG00000166682	ENST00000299882	Transcript	synonymous_variant	359	210	70	L	ctG/ctT	.	.	.	-1	TMPRSS5	HGNC	14908	protein_coding	YES	CCDS44735.1	ENSP00000299882	TMPS5_HUMAN	G5EA43_HUMAN,F5H2M3_HUMAN,B0YJB1_HUMAN	UPI00001FA3AA	.	.	.	4/13	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24256:SF18,hmmpanther:PTHR24256	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATACAGCAC	.	5	ESCA
OR6T1	0	.	GRCh37	11	123814164	123814164	+	Nonsense_Mutation	SNP	G	G	A	rs755409697	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382C>T	p.Arg128Ter	p.R128*	ENST00000321252	1/1	79	31	48	39	39	0	OR6T1,stop_gained,p.Arg128Ter,ENST00000321252,;OR4D5,downstream_gene_variant,,ENST00000307033,;	A	ENSG00000181499	ENST00000321252	Transcript	stop_gained	417	382	128	R/*	Cga/Tga	rs755409697,COSM4018859	.	.	-1	OR6T1	HGNC	14848	protein_coding	YES	CCDS31700.1	ENSP00000325203	OR6T1_HUMAN	.	UPI0000040A85	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF91,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTCGGCAGA	byFrequency	5	ESCA
NUCB2	0	.	GRCh37	11	17333611	17333611	+	Missense_Mutation	SNP	G	G	T	rs757033019	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.856G>T	p.Asp286Tyr	p.D286Y	ENST00000529010	10/14	105	11	94	73	73	0	NUCB2,missense_variant,p.Asp286Tyr,ENST00000458064,;NUCB2,missense_variant,p.Asp286Tyr,ENST00000529010,;NUCB2,missense_variant,p.Asp286Tyr,ENST00000323688,;NUCB2,missense_variant,p.Asp94Tyr,ENST00000527580,;NUCB2,downstream_gene_variant,,ENST00000529313,;NUCB2,downstream_gene_variant,,ENST00000530527,;NUCB2,upstream_gene_variant,,ENST00000527735,;NUCB2,missense_variant,p.Asp286Tyr,ENST00000533773,;NUCB2,non_coding_transcript_exon_variant,,ENST00000531242,;	T	ENSG00000070081	ENST00000529010	Transcript	missense_variant	1075	856	286	D/Y	Gat/Tat	rs757033019	.	.	1	NUCB2	HGNC	8044	protein_coding	YES	CCDS41623.1	ENSP00000436455	NUCB2_HUMAN	E9PRQ3_HUMAN,E9PM22_HUMAN,E9PLR5_HUMAN,E9PLR0_HUMAN,E9PLE9_HUMAN,E9PJP3_HUMAN	UPI000013D6B1	.	deleterious(0)	probably_damaging(0.998)	10/14	.	Superfamily_domains:SSF47473,Gene3D:1.10.238.10,Pfam_domain:PF13499,hmmpanther:PTHR19237:SF22,hmmpanther:PTHR19237,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGATATG	.	5	ESCA
DCDC1	0	.	GRCh37	11	30946948	30946948	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2905G>T	p.Glu969Ter	p.E969*	ENST00000597505	21/36	23	7	16	32	32	0	DCDC1,stop_gained,p.Glu969Ter,ENST00000597505,;DCDC1,stop_gained,p.Glu48Ter,ENST00000339794,;DCDC1,5_prime_UTR_variant,,ENST00000406071,;DCDC1,stop_gained,p.Glu4Ter,ENST00000444572,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,;	A	ENSG00000170959	ENST00000597505	Transcript	stop_gained	2905	2905	969	E/*	Gag/Tag	.	.	.	-1	DCDC1	HGNC	20625	protein_coding	.	.	ENSP00000472625	.	M0R2J8_HUMAN	UPI0002A47319	.	.	.	21/36	.	PROSITE_profiles:PS50309,hmmpanther:PTHR14958:SF19,hmmpanther:PTHR14958,Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTCAGTGC	.	5	ESCA
AMBRA1	0	.	GRCh37	11	46430144	46430144	+	Missense_Mutation	SNP	C	C	A	rs757761674	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3052G>T	p.Ala1018Ser	p.A1018S	ENST00000314845	18/19	61	42	18	30	30	0	AMBRA1,missense_variant,p.Ala66Ser,ENST00000526545,;AMBRA1,missense_variant,p.Ala1048Ser,ENST00000534300,;AMBRA1,missense_variant,p.Ala989Ser,ENST00000533727,;AMBRA1,missense_variant,p.Ala1079Ser,ENST00000426438,;AMBRA1,missense_variant,p.Ala1048Ser,ENST00000298834,;AMBRA1,missense_variant,p.Ala1018Ser,ENST00000314845,;AMBRA1,missense_variant,p.Ala1079Ser,ENST00000528950,;AMBRA1,missense_variant,p.Ala1108Ser,ENST00000458649,;	A	ENSG00000110497	ENST00000314845	Transcript	missense_variant	3412	3052	1018	A/S	Gcc/Tcc	rs757761674	.	.	-1	AMBRA1	HGNC	25990	protein_coding	YES	CCDS31475.1	ENSP00000318313	AMRA1_HUMAN	E9PL55_HUMAN	UPI0000237851	.	tolerated_low_confidence(0.21)	possibly_damaging(0.783)	18/19	.	hmmpanther:PTHR22874:SF1,hmmpanther:PTHR22874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGGCCAGAG	byFrequency	5	ESCA
OR8K5	0	.	GRCh37	11	55927473	55927473	+	Missense_Mutation	SNP	G	G	C	rs267602995	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321C>G	p.Phe107Leu	p.F107L	ENST00000313447	1/1	42	21	21	26	26	0	OR8K5,missense_variant,p.Phe107Leu,ENST00000313447,;	C	ENSG00000181752	ENST00000313447	Transcript	missense_variant	321	321	107	F/L	ttC/ttG	rs267602995	.	.	-1	OR8K5	HGNC	15315	protein_coding	YES	CCDS31521.1	ENSP00000323853	OR8K5_HUMAN	.	UPI000004B231	.	deleterious_low_confidence(0.04)	probably_damaging(0.993)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF60,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	not_provided	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAATGAACAT	.	5	ESCA
OR5T2	0	.	GRCh37	11	56000131	56000131	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531C>G	p.%3D	p.P177P	ENST00000313264	1/1	107	62	44	69	69	0	OR5T2,synonymous_variant,p.%3D,ENST00000313264,;	C	ENSG00000181718	ENST00000313264	Transcript	synonymous_variant	607	531	177	P	ccC/ccG	.	.	.	-1	OR5T2	HGNC	15296	protein_coding	YES	CCDS31523.1	ENSP00000323688	OR5T2_HUMAN	.	UPI0000061E97	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF79,hmmpanther:PTHR24247,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTGGGTGA	.	5	ESCA
PTGDR2	0	.	GRCh37	11	60620689	60620689	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507C>T	p.%3D	p.F169F	ENST00000332539	2/2	18	4	14	37	37	0	PTGDR2,synonymous_variant,p.%3D,ENST00000332539,;CCDC86,downstream_gene_variant,,ENST00000227520,;CCDC86,downstream_gene_variant,,ENST00000545580,;RP11-804A23.4,upstream_gene_variant,,ENST00000538705,;CCDC86,downstream_gene_variant,,ENST00000535217,;	A	ENSG00000183134	ENST00000332539	Transcript	synonymous_variant	619	507	169	F	ttC/ttT	.	.	.	-1	PTGDR2	HGNC	4502	protein_coding	YES	CCDS7994.1	ENSP00000332812	PD2R2_HUMAN	.	UPI00001B011A	.	.	.	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF8,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGGAACAC	.	5	ESCA
CD6	0	.	GRCh37	11	60785799	60785799	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1876G>A	p.Gly626Arg	p.G626R	ENST00000313421	12/13	28	1	27	52	52	0	CD6,missense_variant,p.Gly553Arg,ENST00000346437,;CD6,missense_variant,p.Gly626Arg,ENST00000313421,;CD6,missense_variant,p.Gly594Arg,ENST00000344028,;CD6,intron_variant,,ENST00000452451,;CD6,intron_variant,,ENST00000352009,;CD6,downstream_gene_variant,,ENST00000433107,;CD6,downstream_gene_variant,,ENST00000542157,;CD6,downstream_gene_variant,,ENST00000538611,;CD6,downstream_gene_variant,,ENST00000545105,;CD6,non_coding_transcript_exon_variant,,ENST00000505761,;CD6,intron_variant,,ENST00000344931,;CD6,downstream_gene_variant,,ENST00000419282,;	A	ENSG00000013725	ENST00000313421	Transcript	missense_variant	2062	1876	626	G/R	Ggg/Agg	.	.	.	1	CD6	HGNC	1691	protein_coding	YES	CCDS7999.1	ENSP00000323280	CD6_HUMAN	.	UPI000013F532	.	deleterious(0)	probably_damaging(1)	12/13	.	hmmpanther:PTHR19331:SF252,hmmpanther:PTHR19331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCGGGGAG	.	5	ESCA
MALAT1	0	.	GRCh37	11	65266761	65266761	+	RNA	SNP	C	C	G	rs574680301	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1529C>G	.	.	ENST00000534336	1/1	61	57	4	48	48	0	MALAT1,non_coding_transcript_exon_variant,,ENST00000534336,;MALAT1,non_coding_transcript_exon_variant,,ENST00000544868,;AP000769.7,upstream_gene_variant,,ENST00000602344,;MALAT1,upstream_gene_variant,,ENST00000508832,;	G	ENSG00000251562	ENST00000534336	Transcript	non_coding_transcript_exon_variant	1529	.	.	.	.	rs574680301	.	.	1	MALAT1	HGNC	29665	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTTCTAAAA	by1000G	2	ESCA
CFL1	0	.	GRCh37	11	65625940	65625940	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-370G>T	.	.	ENST00000525451	2/5	8	4	4	14	14	0	CFL1,5_prime_UTR_variant,,ENST00000525451,;CFL1,intron_variant,,ENST00000534769,;MUS81,intron_variant,,ENST00000529857,;CFL1,intron_variant,,ENST00000526975,;CFL1,intron_variant,,ENST00000532134,;CFL1,intron_variant,,ENST00000531413,;MUS81,upstream_gene_variant,,ENST00000533035,;SNX32,downstream_gene_variant,,ENST00000308342,;CFL1,upstream_gene_variant,,ENST00000531407,;CFL1,upstream_gene_variant,,ENST00000308162,;CFL1,upstream_gene_variant,,ENST00000530413,;CFL1,upstream_gene_variant,,ENST00000527344,;MUS81,upstream_gene_variant,,ENST00000525768,;CFL1,upstream_gene_variant,,ENST00000534784,;MUS81,upstream_gene_variant,,ENST00000530111,;CFL1,upstream_gene_variant,,ENST00000524553,;MUS81,upstream_gene_variant,,ENST00000308110,;MUS81,upstream_gene_variant,,ENST00000529374,;CFL1,upstream_gene_variant,,ENST00000527752,;SNX32,downstream_gene_variant,,ENST00000530101,;CFL1,upstream_gene_variant,,ENST00000530945,;MUS81,upstream_gene_variant,,ENST00000530928,;MUS81,upstream_gene_variant,,ENST00000531905,;MUS81,upstream_gene_variant,,ENST00000524647,;MUS81,upstream_gene_variant,,ENST00000533555,;	A	ENSG00000172757	ENST00000525451	Transcript	5_prime_UTR_variant	347	.	.	.	.	.	.	.	-1	CFL1	HGNC	1874	protein_coding	YES	CCDS8114.1	ENSP00000432660	COF1_HUMAN	G3V1A4_HUMAN,E9PS23_HUMAN,E9PQB7_HUMAN,E9PP50_HUMAN,E9PLJ3_HUMAN	UPI0000127E2C	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGACCCGAAA	.	2	ESCA
CCDC87	0	.	GRCh37	11	66358083	66358083	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2404G>T	p.Gly802Trp	p.G802W	ENST00000333861	1/1	26	19	6	21	21	0	CCDC87,missense_variant,p.Gly802Trp,ENST00000333861,;CCS,upstream_gene_variant,,ENST00000310190,;CCS,upstream_gene_variant,,ENST00000533244,;CCS,upstream_gene_variant,,ENST00000530961,;CCS,upstream_gene_variant,,ENST00000526058,;CCS,upstream_gene_variant,,ENST00000526066,;CCS,upstream_gene_variant,,ENST00000530384,;CCS,upstream_gene_variant,,ENST00000531990,;	A	ENSG00000182791	ENST00000333861	Transcript	missense_variant	2472	2404	802	G/W	Ggg/Tgg	.	.	.	-1	CCDC87	HGNC	25579	protein_coding	YES	CCDS8145.1	ENSP00000328487	CCD87_HUMAN	.	UPI000013EFC2	.	deleterious(0)	probably_damaging(1)	1/1	.	hmmpanther:PTHR16078,hmmpanther:PTHR16078:SF1,Pfam_domain:PF03999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCCCCTTGA	.	5	ESCA
PPP1CA	0	.	GRCh37	11	67168163	67168163	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448G>T	p.Glu150Ter	p.E150*	ENST00000312989	3/7	117	99	17	27	27	0	PPP1CA,stop_gained,p.Glu95Ter,ENST00000358239,;PPP1CA,stop_gained,p.Glu139Ter,ENST00000376745,;PPP1CA,stop_gained,p.Glu139Ter,ENST00000527663,;PPP1CA,stop_gained,p.Glu150Ter,ENST00000312989,;PPP1CA,downstream_gene_variant,,ENST00000542876,;RAD9A,downstream_gene_variant,,ENST00000544620,;TBC1D10C,upstream_gene_variant,,ENST00000542590,;PPP1CA,downstream_gene_variant,,ENST00000546202,;RAD9A,downstream_gene_variant,,ENST00000307980,;TBC1D10C,upstream_gene_variant,,ENST00000526387,;TBC1D10C,upstream_gene_variant,,ENST00000312390,;PPP1CA,non_coding_transcript_exon_variant,,ENST00000532446,;PPP1CA,non_coding_transcript_exon_variant,,ENST00000537694,;PPP1CA,upstream_gene_variant,,ENST00000532279,;RAD9A,downstream_gene_variant,,ENST00000529100,;RAD9A,downstream_gene_variant,,ENST00000535644,;RAD9A,downstream_gene_variant,,ENST00000543808,;PPP1CA,downstream_gene_variant,,ENST00000529724,;PPP1CA,non_coding_transcript_exon_variant,,ENST00000526510,;RAD9A,downstream_gene_variant,,ENST00000530934,;TBC1D10C,upstream_gene_variant,,ENST00000526474,;TBC1D10C,upstream_gene_variant,,ENST00000530967,;TBC1D10C,upstream_gene_variant,,ENST00000533745,;TBC1D10C,upstream_gene_variant,,ENST00000529132,;TBC1D10C,upstream_gene_variant,,ENST00000529635,;RAD9A,downstream_gene_variant,,ENST00000538013,;RAD9A,downstream_gene_variant,,ENST00000542139,;	A	ENSG00000172531	ENST00000312989	Transcript	stop_gained	459	448	150	E/*	Gag/Tag	.	.	.	-1	PPP1CA	HGNC	9281	protein_coding	YES	CCDS31618.1	ENSP00000326031	PP1A_HUMAN	C4TNW6_HUMAN,C4TNW5_HUMAN,C0STL0_HUMAN	UPI0000070A42	.	.	.	3/7	.	hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF207,Pfam_domain:PF00149,Gene3D:3.60.21.10,SMART_domains:SM00156,Superfamily_domains:SSF56300,Prints_domain:PR00114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACTCATCGT	.	4	ESCA
SHANK2	0	.	GRCh37	11	70332808	70332808	+	Missense_Mutation	SNP	C	C	G	rs782355465	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3593G>C	p.Gly1198Ala	p.G1198A	ENST00000338508	32/33	152	137	15	40	40	0	SHANK2,missense_variant,p.Gly601Ala,ENST00000409161,;SHANK2,missense_variant,p.Gly476Ala,ENST00000424924,;SHANK2,missense_variant,p.Gly818Ala,ENST00000423696,;SHANK2,missense_variant,p.Gly821Ala,ENST00000294018,;SHANK2,missense_variant,p.Gly1198Ala,ENST00000338508,;SHANK2,missense_variant,p.Gly602Ala,ENST00000449833,;SHANK2,intron_variant,,ENST00000412252,;SHANK2,downstream_gene_variant,,ENST00000409530,;SHANK2,downstream_gene_variant,,ENST00000357171,;SHANK2,downstream_gene_variant,,ENST00000449116,;	G	ENSG00000162105	ENST00000338508	Transcript	missense_variant	3593	3593	1198	G/A	gGc/gCc	rs782355465	.	.	-1	SHANK2	HGNC	14295	protein_coding	YES	.	ENSP00000345193	.	C9JFP8_HUMAN,A6NHU9_HUMAN	UPI00020653A9	.	tolerated(0.3)	benign(0.001)	32/33	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGGGCCGGCT	.	4	ESCA
KRTAP5-11	0	.	GRCh37	11	71293036	71293036	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*377C>A	.	.	ENST00000398530	1/1	37	13	23	10	10	0	KRTAP5-11,3_prime_UTR_variant,,ENST00000398530,;AP000867.1,3_prime_UTR_variant,,ENST00000343767,;KRTAP5-11,non_coding_transcript_exon_variant,,ENST00000526239,;KRTAP5-14P,upstream_gene_variant,,ENST00000502328,;	T	ENSG00000204571	ENST00000398530	Transcript	3_prime_UTR_variant	886	.	.	.	.	.	.	.	-1	KRTAP5-11	HGNC	23606	protein_coding	YES	CCDS41685.1	ENSP00000381541	KR511_HUMAN	.	UPI0000376063	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGGACCCA	.	5	ESCA
P2RY6	0	.	GRCh37	11	73007949	73007949	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.386G>T	p.Cys129Phe	p.C129F	ENST00000393590	2/2	59	42	17	25	24	1	P2RY6,missense_variant,p.Cys129Phe,ENST00000538328,;P2RY6,missense_variant,p.Cys129Phe,ENST00000540342,;P2RY6,missense_variant,p.Cys129Phe,ENST00000349767,;P2RY6,missense_variant,p.Cys129Phe,ENST00000540124,;P2RY6,missense_variant,p.Cys129Phe,ENST00000542092,;P2RY6,missense_variant,p.Cys129Phe,ENST00000393592,;P2RY6,missense_variant,p.Cys129Phe,ENST00000535931,;P2RY6,missense_variant,p.Cys129Phe,ENST00000393591,;P2RY6,missense_variant,p.Cys129Phe,ENST00000393590,;P2RY6,intron_variant,,ENST00000536225,;P2RY6,downstream_gene_variant,,ENST00000544437,;	T	ENSG00000171631	ENST00000393590	Transcript	missense_variant	685	386	129	C/F	tGc/tTc	.	.	.	1	P2RY6	HGNC	8543	protein_coding	YES	CCDS8220.1	ENSP00000377215	P2RY6_HUMAN	F5GYF3_HUMAN,F5GX90_HUMAN	UPI000005041C	.	deleterious(0)	probably_damaging(1)	2/2	.	Prints_domain:PR01157,Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF16,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CATCTGCCACC	.	2	ESCA
TENM4	0	.	GRCh37	11	78383285	78383285	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5586G>T	p.%3D	p.R1862R	ENST00000278550	31/34	118	88	29	36	36	0	TENM4,synonymous_variant,p.%3D,ENST00000278550,;TENM4,synonymous_variant,p.%3D,ENST00000530738,;	A	ENSG00000149256	ENST00000278550	Transcript	synonymous_variant	6049	5586	1862	R	cgG/cgT	.	.	.	-1	TENM4	HGNC	29945	protein_coding	YES	CCDS44688.1	ENSP00000278550	TEN4_HUMAN	G3CAT1_HUMAN	UPI0000DD8112	.	.	.	31/34	.	hmmpanther:PTHR11219:SF9,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAATCCGAAG	.	5	ESCA
TENM4	0	.	GRCh37	11	78383286	78383286	+	Missense_Mutation	SNP	C	C	A	rs368379990	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5585G>T	p.Arg1862Leu	p.R1862L	ENST00000278550	31/34	122	93	29	36	36	0	TENM4,missense_variant,p.Arg1862Leu,ENST00000278550,;TENM4,missense_variant,p.Arg326Leu,ENST00000530738,;	A	ENSG00000149256	ENST00000278550	Transcript	missense_variant	6048	5585	1862	R/L	cGg/cTg	rs368379990,COSM4036960,COSM4036961	.	.	-1	TENM4	HGNC	29945	protein_coding	YES	CCDS44688.1	ENSP00000278550	TEN4_HUMAN	G3CAT1_HUMAN	UPI0000DD8112	.	deleterious(0.01)	benign(0.082)	31/34	.	hmmpanther:PTHR11219:SF9,hmmpanther:PTHR11219	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCCGAAGG	byFrequency|byCluster	5	ESCA
CUX2	0	.	GRCh37	12	111749974	111749974	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1971G>T	p.Gln657His	p.Q657H	ENST00000261726	16/22	15	8	7	8	8	0	CUX2,missense_variant,p.Gln657His,ENST00000261726,;	T	ENSG00000111249	ENST00000261726	Transcript	missense_variant	2125	1971	657	Q/H	caG/caT	.	.	.	1	CUX2	HGNC	19347	protein_coding	YES	CCDS41837.1	ENSP00000261726	CUX2_HUMAN	Q9BZX3_HUMAN,Q9BZV4_HUMAN	UPI00001FBB07	.	deleterious(0.03)	benign(0.414)	16/22	.	hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGCAGGCCAA	.	3	ESCA
HECTD4	0	.	GRCh37	12	112673435	112673435	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5160A>T	p.%3D	p.G1720G	ENST00000550722	36/76	35	19	16	26	26	0	HECTD4,synonymous_variant,p.%3D,ENST00000430131,;HECTD4,synonymous_variant,p.%3D,ENST00000550722,;HECTD4,synonymous_variant,p.%3D,ENST00000377560,;HECTD4,upstream_gene_variant,,ENST00000547519,;	A	ENSG00000173064	ENST00000550722	Transcript	synonymous_variant	5556	5160	1720	G	ggA/ggT	.	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	.	36/76	.	hmmpanther:PTHR11254:SF286,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGTTTCCACA	.	5	ESCA
TAOK3	0	.	GRCh37	12	118627865	118627865	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1195-119G>A	.	.	ENST00000392533	.	41	19	21	29	29	0	TAOK3,5_prime_UTR_variant,,ENST00000537952,;TAOK3,intron_variant,,ENST00000392533,;TAOK3,intron_variant,,ENST00000537822,;TAOK3,intron_variant,,ENST00000540561,;TAOK3,intron_variant,,ENST00000419821,;TAOK3,intron_variant,,ENST00000537305,;	T	ENSG00000135090	ENST00000392533	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TAOK3	HGNC	18133	protein_coding	YES	CCDS9188.1	ENSP00000376317	TAOK3_HUMAN	G3V1Q8_HUMAN,F5H7G4_HUMAN,F5H5E0_HUMAN,F5H5C7_HUMAN,F5H3L7_HUMAN,F5H005_HUMAN,F5GY38_HUMAN,F5GX96_HUMAN,F5GWV8_HUMAN	UPI000007231B	.	.	.	.	13/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCTGCTA	.	5	ESCA
C12orf43	0	.	GRCh37	12	121442237	121442237	+	Missense_Mutation	SNP	C	C	A	rs200371786	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.508G>T	p.Asp170Tyr	p.D170Y	ENST00000288757	6/6	41	19	22	47	47	0	C12orf43,missense_variant,p.Asp108Tyr,ENST00000538296,;C12orf43,missense_variant,p.Asp170Tyr,ENST00000288757,;C12orf43,missense_variant,p.Asp124Tyr,ENST00000546272,;C12orf43,missense_variant,p.Asp160Tyr,ENST00000539736,;C12orf43,missense_variant,p.Asp140Tyr,ENST00000445832,;C12orf43,missense_variant,p.Asp125Tyr,ENST00000535367,;C12orf43,missense_variant,p.Asp129Tyr,ENST00000366211,;C12orf43,missense_variant,p.Asp171Tyr,ENST00000537817,;C12orf43,intron_variant,,ENST00000536407,;HNF1A,downstream_gene_variant,,ENST00000544413,;HNF1A,downstream_gene_variant,,ENST00000541395,;HNF1A,downstream_gene_variant,,ENST00000257555,;RP11-216P16.2,upstream_gene_variant,,ENST00000606238,;C12orf43,3_prime_UTR_variant,,ENST00000539088,;C12orf43,non_coding_transcript_exon_variant,,ENST00000502891,;HNF1A,downstream_gene_variant,,ENST00000560968,;C12orf43,downstream_gene_variant,,ENST00000508193,;HNF1A,downstream_gene_variant,,ENST00000540108,;	A	ENSG00000157895	ENST00000288757	Transcript	missense_variant	531	508	170	D/Y	Gac/Tac	rs200371786,COSM1706378	.	.	-1	C12orf43	HGNC	25719	protein_coding	YES	CCDS9210.1	ENSP00000288757	CL043_HUMAN	E7ENF1_HUMAN	UPI000006ED81	.	deleterious(0)	probably_damaging(0.966)	6/6	.	hmmpanther:PTHR14482:SF0,hmmpanther:PTHR14482	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGTCGGACG	byFrequency|byCluster	5	ESCA
WDR66	0	.	GRCh37	12	122437781	122437781	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3166G>C	p.Gly1056Arg	p.G1056R	ENST00000288912	20/22	30	14	16	23	23	0	WDR66,missense_variant,p.Gly1056Arg,ENST00000288912,;WDR66,upstream_gene_variant,,ENST00000545988,;WDR66,non_coding_transcript_exon_variant,,ENST00000428465,;	C	ENSG00000158023	ENST00000288912	Transcript	missense_variant	4020	3166	1056	G/R	Ggt/Cgt	COSM3398457	.	.	1	WDR66	HGNC	28506	protein_coding	YES	CCDS41853.1	ENSP00000288912	WDR66_HUMAN	.	UPI00001AEB2C	.	deleterious(0)	probably_damaging(0.957)	20/22	.	hmmpanther:PTHR13720:SF13,hmmpanther:PTHR13720,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTCGGTTAT	.	5	ESCA
POLE	0	.	GRCh37	12	133201572	133201572	+	Silent	SNP	C	C	A	rs777438368	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6666G>T	p.%3D	p.L2222L	ENST00000320574	48/49	28	14	14	28	28	0	POLE,synonymous_variant,p.%3D,ENST00000535270,;POLE,synonymous_variant,p.%3D,ENST00000320574,;P2RX2,downstream_gene_variant,,ENST00000542301,;P2RX2,downstream_gene_variant,,ENST00000352418,;P2RX2,downstream_gene_variant,,ENST00000343948,;P2RX2,downstream_gene_variant,,ENST00000389110,;P2RX2,downstream_gene_variant,,ENST00000536121,;P2RX2,downstream_gene_variant,,ENST00000350048,;P2RX2,downstream_gene_variant,,ENST00000348800,;P2RX2,downstream_gene_variant,,ENST00000351222,;P2RX2,downstream_gene_variant,,ENST00000535910,;P2RX2,downstream_gene_variant,,ENST00000449132,;POLE,downstream_gene_variant,,ENST00000544870,;POLE,downstream_gene_variant,,ENST00000538196,;POLE,3_prime_UTR_variant,,ENST00000537064,;POLE,non_coding_transcript_exon_variant,,ENST00000541627,;POLE,non_coding_transcript_exon_variant,,ENST00000534922,;POLE,non_coding_transcript_exon_variant,,ENST00000544692,;POLE,downstream_gene_variant,,ENST00000543516,;	A	ENSG00000177084	ENST00000320574	Transcript	synonymous_variant	6710	6666	2222	L	ctG/ctT	rs777438368,COSM692201	.	.	-1	POLE	HGNC	9177	protein_coding	YES	CCDS9278.1	ENSP00000322570	DPOE1_HUMAN	Q9UNE8_HUMAN,Q96IE1_HUMAN,Q8WU23_HUMAN,F5H7H6_HUMAN,F5H5Q5_HUMAN,F5H3W5_HUMAN,F5H0H8_HUMAN,D3DXI9_HUMAN	UPI00001FBF97	.	.	.	48/49	.	hmmpanther:PTHR10670,hmmpanther:PTHR10670:SF0	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTTCAGGCA	byFrequency	5	ESCA
GRIN2B	0	.	GRCh37	12	13716394	13716394	+	Silent	SNP	G	G	A	rs200902451	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3778C>T	p.%3D	p.L1260L	ENST00000609686	13/13	33	14	19	29	29	0	GRIN2B,synonymous_variant,p.%3D,ENST00000609686,;	A	ENSG00000273079	ENST00000609686	Transcript	synonymous_variant	3988	3778	1260	L	Ctg/Ttg	rs200902451	.	.	-1	GRIN2B	HGNC	4586	protein_coding	YES	CCDS8662.1	ENSP00000477455	NMDE2_HUMAN	Q59HA9_HUMAN	UPI000013026C	.	.	.	13/13	.	Pfam_domain:PF10565	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGGGAGT	.	5	ESCA
PLCZ1	0	.	GRCh37	12	18889200	18889200	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90A>T	p.Lys30Asn	p.K30N	ENST00000266505	3/15	69	36	33	60	60	0	PLCZ1,missense_variant,p.Lys28Asn,ENST00000447925,;PLCZ1,missense_variant,p.Lys28Asn,ENST00000435379,;PLCZ1,missense_variant,p.Lys30Asn,ENST00000266505,;PLCZ1,missense_variant,p.Lys50Asn,ENST00000539072,;PLCZ1,missense_variant,p.Lys30Asn,ENST00000539875,;PLCZ1,5_prime_UTR_variant,,ENST00000541966,;PLCZ1,5_prime_UTR_variant,,ENST00000543242,;CAPZA3,upstream_gene_variant,,ENST00000317658,;RP11-361I14.2,intron_variant,,ENST00000536931,;PLCZ1,non_coding_transcript_exon_variant,,ENST00000541109,;PLCZ1,non_coding_transcript_exon_variant,,ENST00000545129,;PLCZ1,missense_variant,p.Lys30Asn,ENST00000318197,;PLCZ1,missense_variant,p.Lys30Asn,ENST00000539207,;PLCZ1,missense_variant,p.Lys30Asn,ENST00000535429,;PLCZ1,non_coding_transcript_exon_variant,,ENST00000544849,;	A	ENSG00000139151	ENST00000266505	Transcript	missense_variant	354	90	30	K/N	aaA/aaT	.	.	.	-1	PLCZ1	HGNC	19218	protein_coding	YES	CCDS8680.1	ENSP00000266505	PLCZ1_HUMAN	F5H828_HUMAN,F5H474_HUMAN,F5H3L4_HUMAN,F5H2Y6_HUMAN,F5GZK3_HUMAN	UPI000000D7E3	.	tolerated(0.16)	possibly_damaging(0.52)	3/15	.	hmmpanther:PTHR10336:SF29,hmmpanther:PTHR10336,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTAATTTTTC	.	5	ESCA
SLCO1C1	0	.	GRCh37	12	20876174	20876174	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1172C>A	p.Ala391Asp	p.A391D	ENST00000381552	9/15	58	33	25	58	58	0	SLCO1C1,missense_variant,p.Ala391Asp,ENST00000381552,;SLCO1C1,missense_variant,p.Ala391Asp,ENST00000545604,;SLCO1C1,missense_variant,p.Ala273Asp,ENST00000545102,;SLCO1C1,missense_variant,p.Ala391Asp,ENST00000266509,;SLCO1C1,missense_variant,p.Ala342Asp,ENST00000540354,;SLCO1C1,3_prime_UTR_variant,,ENST00000539415,;	A	ENSG00000139155	ENST00000381552	Transcript	missense_variant	1540	1172	391	A/D	gCc/gAc	.	.	.	1	SLCO1C1	HGNC	13819	protein_coding	YES	CCDS53757.1	ENSP00000370964	SO1C1_HUMAN	.	UPI00004C3E1B	.	deleterious(0)	probably_damaging(0.984)	9/15	.	hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF18,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Pfam_domain:PF03137,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCCAACT	.	5	ESCA
ABCC9	0	.	GRCh37	12	22012598	22012598	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2427C>A	p.%3D	p.G809G	ENST00000261200	20/38	39	23	16	12	12	0	ABCC9,synonymous_variant,p.%3D,ENST00000345162,;ABCC9,synonymous_variant,p.%3D,ENST00000261201,;ABCC9,synonymous_variant,p.%3D,ENST00000544039,;ABCC9,synonymous_variant,p.%3D,ENST00000261200,;RP11-729I10.2,intron_variant,,ENST00000539874,;	T	ENSG00000069431	ENST00000261200	Transcript	synonymous_variant	2427	2427	809	G	ggC/ggA	.	.	.	-1	ABCC9	HGNC	60	protein_coding	YES	CCDS8693.1	ENSP00000261200	ABCC9_HUMAN	Q8N9N1_HUMAN	UPI000013D13F	.	.	.	20/38	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Gene3D:3.40.50.300,Pfam_domain:PF00005,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,PROSITE_profiles:PS50893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATGCCCTA	.	5	ESCA
OVCH1	0	.	GRCh37	12	29617440	29617440	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2125G>T	p.Asp709Tyr	p.D709Y	ENST00000318184	18/28	48	19	28	35	35	0	OVCH1,missense_variant,p.Asp709Tyr,ENST00000318184,;OVCH1-AS1,3_prime_UTR_variant,,ENST00000550906,;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,;	A	ENSG00000187950	ENST00000318184	Transcript	missense_variant	2125	2125	709	D/Y	Gat/Tat	.	.	.	-1	OVCH1	HGNC	23080	protein_coding	YES	.	ENSP00000326708	OVCH1_HUMAN	.	UPI000040640A	.	deleterious(0.01)	probably_damaging(0.943)	18/28	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24259,hmmpanther:PTHR24259:SF64,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTTACCTGCAC	.	4	ESCA
SMARCD1	0	.	GRCh37	12	50492592	50492592	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1488C>T	p.%3D	p.Y496Y	ENST00000394963	12/13	74	43	30	55	55	0	SMARCD1,synonymous_variant,p.%3D,ENST00000394963,;SMARCD1,synonymous_variant,p.%3D,ENST00000548573,;SMARCD1,synonymous_variant,p.%3D,ENST00000381513,;SMARCD1,upstream_gene_variant,,ENST00000549526,;SMARCD1,synonymous_variant,p.%3D,ENST00000549274,;SMARCD1,non_coding_transcript_exon_variant,,ENST00000551352,;SMARCD1,non_coding_transcript_exon_variant,,ENST00000550280,;	T	ENSG00000066117	ENST00000394963	Transcript	synonymous_variant	1886	1488	496	Y	taC/taT	.	.	.	1	SMARCD1	HGNC	11106	protein_coding	YES	CCDS8797.2	ENSP00000378414	SMRD1_HUMAN	F8VW95_HUMAN	UPI00001A92EC	.	.	.	12/13	.	hmmpanther:PTHR13844,hmmpanther:PTHR13844:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTACTCCAA	.	5	ESCA
KCNA5	0	.	GRCh37	12	5155214	5155214	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*59G>T	.	.	ENST00000252321	1/1	72	40	31	53	53	0	KCNA5,3_prime_UTR_variant,,ENST00000252321,;	T	ENSG00000130037	ENST00000252321	Transcript	3_prime_UTR_variant	2130	.	.	.	.	.	.	.	1	KCNA5	HGNC	6224	protein_coding	YES	CCDS8536.1	ENSP00000252321	KCNA5_HUMAN	.	UPI000013CD56	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATGGATAT	.	5	ESCA
OR6C65	0	.	GRCh37	12	55794493	55794493	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181C>T	p.Leu61Phe	p.L61F	ENST00000379665	1/1	30	20	10	21	21	0	OR6C65,missense_variant,p.Leu61Phe,ENST00000379665,;OR6C73P,downstream_gene_variant,,ENST00000546432,;	T	ENSG00000205328	ENST00000379665	Transcript	missense_variant	280	181	61	L/F	Ctc/Ttc	.	.	.	1	OR6C65	HGNC	31295	protein_coding	YES	CCDS31821.1	ENSP00000368986	O6C65_HUMAN	.	UPI000044D410	.	deleterious_low_confidence(0)	probably_damaging(0.982)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF15,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCCTCAGG	.	5	ESCA
INHBE	0	.	GRCh37	12	57850479	57850479	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.901C>T	p.Leu301Phe	p.L301F	ENST00000266646	2/2	21	12	9	17	17	0	INHBE,missense_variant,p.Leu301Phe,ENST00000266646,;INHBE,missense_variant,p.Leu246Phe,ENST00000547970,;GLI1,upstream_gene_variant,,ENST00000228682,;GLI1,upstream_gene_variant,,ENST00000546141,;GLI1,upstream_gene_variant,,ENST00000528432,;GLI1,upstream_gene_variant,,ENST00000532291,;GLI1,upstream_gene_variant,,ENST00000543426,;INHBE,non_coding_transcript_exon_variant,,ENST00000551553,;INHBE,downstream_gene_variant,,ENST00000553033,;GLI1,upstream_gene_variant,,ENST00000530789,;	T	ENSG00000139269	ENST00000266646	Transcript	missense_variant	1117	901	301	L/F	Ctc/Ttc	.	.	.	1	INHBE	HGNC	24029	protein_coding	YES	CCDS8939.1	ENSP00000266646	INHBE_HUMAN	.	UPI000012D42C	.	deleterious(0.03)	probably_damaging(0.999)	2/2	.	PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF6,hmmpanther:PTHR11848,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGCCTCCTC	.	5	ESCA
FAM19A2	0	.	GRCh37	12	62103999	62103999	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*188C>A	.	.	ENST00000416284	5/5	22	8	14	10	10	0	FAM19A2,3_prime_UTR_variant,,ENST00000550003,;FAM19A2,3_prime_UTR_variant,,ENST00000416284,;FAM19A2,3_prime_UTR_variant,,ENST00000551619,;FAM19A2,3_prime_UTR_variant,,ENST00000551449,;FAM19A2,3_prime_UTR_variant,,ENST00000549379,;	T	ENSG00000198673	ENST00000416284	Transcript	3_prime_UTR_variant	2169	.	.	.	.	.	.	.	-1	FAM19A2	HGNC	21589	protein_coding	YES	CCDS8962.1	ENSP00000393987	F19A2_HUMAN	.	UPI000006F642	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GACATGCAAGT	.	4	ESCA
SLC2A14	0	.	GRCh37	12	7966711	7966711	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*201C>A	.	.	ENST00000543909	16/16	11	4	6	20	20	0	SLC2A14,3_prime_UTR_variant,,ENST00000535295,;SLC2A14,3_prime_UTR_variant,,ENST00000396589,;SLC2A14,3_prime_UTR_variant,,ENST00000431042,;SLC2A14,3_prime_UTR_variant,,ENST00000542546,;SLC2A14,3_prime_UTR_variant,,ENST00000542505,;SLC2A14,3_prime_UTR_variant,,ENST00000340749,;SLC2A14,3_prime_UTR_variant,,ENST00000539924,;SLC2A14,3_prime_UTR_variant,,ENST00000543909,;	T	ENSG00000173262	ENST00000543909	Transcript	3_prime_UTR_variant	2524	.	.	.	.	.	.	.	-1	SLC2A14	HGNC	18301	protein_coding	YES	CCDS8585.1	ENSP00000440480	GTR14_HUMAN	F5H6F6_HUMAN,F5GXP7_HUMAN	UPI000006D325	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGAGGATGTC	.	2	ESCA
OTOGL	0	.	GRCh37	12	80615872	80615872	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.309C>T	p.%3D	p.I103I	ENST00000458043	6/58	27	14	13	11	11	0	OTOGL,synonymous_variant,p.%3D,ENST00000458043,;OTOGL,synonymous_variant,p.%3D,ENST00000547103,;	T	ENSG00000165899	ENST00000458043	Transcript	synonymous_variant	315	309	103	I	atC/atT	.	.	.	1	OTOGL	HGNC	26901	protein_coding	YES	.	ENSP00000400895	.	E2QRK2_HUMAN	UPI0001D089C5	.	.	.	6/58	.	hmmpanther:PTHR11339:SF225,hmmpanther:PTHR11339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGTCCCAAA	.	5	ESCA
MYF6	0	.	GRCh37	12	81102703	81102704	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696dupA	p.Leu233ThrfsTer37	p.L233Tfs*37	ENST00000228641	3/3	122	79	43	60	60	0	MYF6,frameshift_variant,p.Leu233ThrfsTer37,ENST00000228641,;	A	ENSG00000111046	ENST00000228641	Transcript	frameshift_variant	915-916	693-694	231-232	-/X	-/A	.	.	.	1	MYF6	HGNC	7566	protein_coding	YES	CCDS9019.1	ENSP00000228641	MYF6_HUMAN	.	UPI0000001050	.	.	.	3/3	.	hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAACGCAAACT	.	3	ESCA
C12orf50	0	.	GRCh37	12	88390397	88390397	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.316C>A	p.Pro106Thr	p.P106T	ENST00000298699	5/13	44	25	18	32	32	0	C12orf50,missense_variant,p.Pro106Thr,ENST00000550553,;C12orf50,missense_variant,p.Pro106Thr,ENST00000298699,;C12orf50,downstream_gene_variant,,ENST00000551163,;C12orf50,non_coding_transcript_exon_variant,,ENST00000551944,;	T	ENSG00000165805	ENST00000298699	Transcript	missense_variant	497	316	106	P/T	Cct/Act	.	.	.	-1	C12orf50	HGNC	26665	protein_coding	YES	CCDS9031.1	ENSP00000298699	CL050_HUMAN	F8VXH4_HUMAN	UPI0000071382	.	tolerated(0.16)	benign(0.329)	5/13	.	hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGGGGTCT	.	5	ESCA
C12orf55	0	.	GRCh37	12	96983278	96983278	+	Missense_Mutation	SNP	C	C	T	rs561342804	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3149C>T	p.Ser1050Leu	p.S1050L	ENST00000524981	23/68	60	30	29	37	37	0	C12orf55,missense_variant,p.Ser1050Leu,ENST00000524981,;C12orf55,non_coding_transcript_exon_variant,,ENST00000554108,;	T	ENSG00000188596	ENST00000524981	Transcript	missense_variant	3172	3149	1050	S/L	tCg/tTg	rs561342804	.	.	1	C12orf55	HGNC	26456	protein_coding	YES	.	ENSP00000431759	.	R4GNI2_HUMAN,E9PJL5_HUMAN	UPI0001F77A4D	.	deleterious(0.01)	probably_damaging(0.954)	23/68	.	.	T:0.0022	T:0.0061	T:0.0014	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTCGCCAC	byFrequency|byCluster|by1000G	5	ESCA
KDELC1	0	.	GRCh37	13	103443452	103443452	+	Silent	SNP	C	C	A	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.882G>T	p.%3D	p.T294T	ENST00000376004	6/10	16	2	14	18	18	0	KDELC1,synonymous_variant,p.%3D,ENST00000376004,;KDELC1,non_coding_transcript_exon_variant,,ENST00000484943,;KDELC1,non_coding_transcript_exon_variant,,ENST00000460338,;KDELC1,downstream_gene_variant,,ENST00000486540,;	A	ENSG00000134901	ENST00000376004	Transcript	synonymous_variant	1219	882	294	T	acG/acT	COSM1365317	.	.	-1	KDELC1	HGNC	19350	protein_coding	YES	CCDS9504.1	ENSP00000365172	KDEL1_HUMAN	.	UPI000004C663	.	.	.	6/10	.	hmmpanther:PTHR12203:SF21,hmmpanther:PTHR12203,Pfam_domain:PF05686,SMART_domains:SM00672	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACCCGTGTT	.	5	ESCA
GRTP1	0	.	GRCh37	13	114009757	114009757	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221G>T	p.Arg74Leu	p.R74L	ENST00000375431	3/8	20	1	19	48	48	0	GRTP1,missense_variant,p.Arg74Leu,ENST00000375431,;GRTP1,missense_variant,p.Arg74Leu,ENST00000375430,;GRTP1,upstream_gene_variant,,ENST00000326039,;GRTP1-AS1,non_coding_transcript_exon_variant,,ENST00000419199,;GRTP1-AS1,intron_variant,,ENST00000423246,;GRTP1,downstream_gene_variant,,ENST00000476439,;	A	ENSG00000139835	ENST00000375431	Transcript	missense_variant	296	221	74	R/L	cGt/cTt	.	.	.	-1	GRTP1	HGNC	20310	protein_coding	YES	CCDS9534.2	ENSP00000364580	GRTP1_HUMAN	.	UPI00003E2A97	.	deleterious(0)	probably_damaging(1)	3/8	.	PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF232,Pfam_domain:PF00566,Gene3D:2qq8A02,SMART_domains:SM00164,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCACGGTGC	.	5	ESCA
RNF17	0	.	GRCh37	13	25367319	25367319	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1075C>A	p.Pro359Thr	p.P359T	ENST00000255324	10/36	46	27	19	35	35	0	RNF17,missense_variant,p.Pro359Thr,ENST00000255324,;RNF17,missense_variant,p.Pro359Thr,ENST00000381921,;RNF17,missense_variant,p.Pro359Thr,ENST00000255325,;RNF17,non_coding_transcript_exon_variant,,ENST00000255326,;	A	ENSG00000132972	ENST00000255324	Transcript	missense_variant	1127	1075	359	P/T	Cca/Aca	.	.	.	1	RNF17	HGNC	10060	protein_coding	YES	CCDS9308.2	ENSP00000255324	RNF17_HUMAN	.	UPI00001FC8BA	.	tolerated(0.25)	probably_damaging(0.981)	10/36	.	hmmpanther:PTHR16442	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCACCACCT	.	5	ESCA
MTUS2	0	.	GRCh37	13	30072650	30072650	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3804G>C	p.Lys1268Asn	p.K1268N	ENST00000431530	12/14	28	11	16	9	9	0	MTUS2,missense_variant,p.Lys237Asn,ENST00000380808,;MTUS2,missense_variant,p.Lys147Asn,ENST00000542829,;MTUS2,missense_variant,p.Lys1268Asn,ENST00000431530,;MTUS2,non_coding_transcript_exon_variant,,ENST00000400542,;MTUS2,downstream_gene_variant,,ENST00000467990,;	C	ENSG00000132938	ENST00000431530	Transcript	missense_variant	3862	3804	1268	K/N	aaG/aaC	COSM3468252,COSM3468251	.	.	1	MTUS2	HGNC	20595	protein_coding	YES	CCDS45022.1	ENSP00000392057	.	J3KQA9_HUMAN,B4DWQ4_HUMAN	UPI0000F734AC	.	deleterious(0.01)	probably_damaging(0.999)	12/14	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGAAGAT	.	4	ESCA
FREM2	0	.	GRCh37	13	39438592	39438592	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7832C>G	p.Pro2611Arg	p.P2611R	ENST00000280481	16/24	59	37	22	40	40	0	FREM2,missense_variant,p.Pro2611Arg,ENST00000280481,;	G	ENSG00000150893	ENST00000280481	Transcript	missense_variant	8048	7832	2611	P/R	cCt/cGt	.	.	.	1	FREM2	HGNC	25396	protein_coding	YES	CCDS31960.1	ENSP00000280481	FREM2_HUMAN	.	UPI00005520B9	.	deleterious(0)	probably_damaging(0.946)	16/24	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATCCTTACC	.	5	ESCA
LCP1	0	.	GRCh37	13	46718648	46718648	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182G>T	p.%3D	p.T394T	ENST00000398576	14/19	63	39	24	50	50	0	LCP1,synonymous_variant,p.%3D,ENST00000323076,;LCP1,synonymous_variant,p.%3D,ENST00000398576,;LCP1,upstream_gene_variant,,ENST00000435666,;LCP1,downstream_gene_variant,,ENST00000494531,;LCP1,downstream_gene_variant,,ENST00000469227,;	A	ENSG00000136167	ENST00000398576	Transcript	synonymous_variant	1571	1182	394	T	acG/acT	.	.	.	-1	LCP1	HGNC	6528	protein_coding	YES	CCDS9403.1	ENSP00000381581	PLSL_HUMAN	Q5TBN5_HUMAN,Q5TBN3_HUMAN	UPI0000070B5C	.	.	.	14/19	.	PROSITE_profiles:PS50021,hmmpanther:PTHR19961:SF34,hmmpanther:PTHR19961,Gene3D:1.10.418.10,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCGTCTC	.	5	ESCA
LRRC63	0	.	GRCh37	13	46808427	46808427	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933G>T	p.Met311Ile	p.M311I	ENST00000595396	4/9	56	30	26	35	35	0	LRRC63,missense_variant,p.Met311Ile,ENST00000446175,;LRRC63,missense_variant,p.Met311Ile,ENST00000595396,;snoU13,downstream_gene_variant,,ENST00000459016,;LRRC63,missense_variant,p.Met311Ile,ENST00000378805,;	T	ENSG00000173988	ENST00000595396	Transcript	missense_variant	933	933	311	M/I	atG/atT	COSM3813902,COSM3813901	.	.	1	LRRC63	HGNC	34296	protein_coding	YES	CCDS61325.1	ENSP00000469337	.	M0QXR7_HUMAN	UPI0002742DC2	.	deleterious(0.03)	possibly_damaging(0.693)	4/9	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATGACCAA	.	5	ESCA
PCDH9	0	.	GRCh37	13	66877566	66877566	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1221G>T	.	.	ENST00000544246	5/5	53	32	20	55	55	0	PCDH9,3_prime_UTR_variant,,ENST00000544246,;PCDH9,3_prime_UTR_variant,,ENST00000377865,;PCDH9,3_prime_UTR_variant,,ENST00000456367,;PCDH9,downstream_gene_variant,,ENST00000328454,;PCDH9-AS1,upstream_gene_variant,,ENST00000430861,;	A	ENSG00000184226	ENST00000544246	Transcript	3_prime_UTR_variant	5627	.	.	.	.	.	.	.	-1	PCDH9	HGNC	8661	protein_coding	YES	CCDS9444.1	ENSP00000442186	PCDH9_HUMAN	.	UPI00001FCE90	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACCCTACCT	.	5	ESCA
DACH1	0	.	GRCh37	13	72131182	72131182	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1550A>T	p.Glu517Val	p.E517V	ENST00000305425	6/11	21	2	19	28	28	0	DACH1,missense_variant,p.Glu517Val,ENST00000305425,;DACH1,missense_variant,p.Glu569Val,ENST00000359684,;DACH1,intron_variant,,ENST00000313174,;DACH1,intron_variant,,ENST00000354591,;	A	ENSG00000165659	ENST00000305425	Transcript	missense_variant	1973	1550	517	E/V	gAg/gTg	.	.	.	-1	DACH1	HGNC	2663	protein_coding	YES	CCDS41899.1	ENSP00000304994	DACH1_HUMAN	.	UPI00001FCE9E	.	.	benign(0.138)	6/11	.	hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGACTCATGT	.	5	ESCA
MYCBP2	0	.	GRCh37	13	77673124	77673124	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8051C>T	p.Ser2684Phe	p.S2684F	ENST00000544440	56/83	38	11	27	65	65	0	MYCBP2,missense_variant,p.Ser2684Phe,ENST00000544440,;MYCBP2,missense_variant,p.Ser2684Phe,ENST00000357337,;MYCBP2,missense_variant,p.Ser207Phe,ENST00000360084,;MYCBP2,missense_variant,p.Ser2722Phe,ENST00000407578,;MYCBP2-AS1,downstream_gene_variant,,ENST00000593933,;MYCBP2,non_coding_transcript_exon_variant,,ENST00000498073,;MYCBP2,non_coding_transcript_exon_variant,,ENST00000462987,;MYCBP2,non_coding_transcript_exon_variant,,ENST00000482517,;MYCBP2,upstream_gene_variant,,ENST00000485061,;	A	ENSG00000005810	ENST00000544440	Transcript	missense_variant	8069	8051	2684	S/F	tCt/tTt	.	.	.	-1	MYCBP2	HGNC	23386	protein_coding	YES	.	ENSP00000444596	MYCB2_HUMAN	.	UPI0000212757	.	.	benign(0.004)	56/83	.	hmmpanther:PTHR12846:SF14,hmmpanther:PTHR12846	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TAGAAGATGTT	.	4	ESCA
MIR770	0	.	GRCh37	14	101318813	101318813	+	RNA	SNP	G	G	T	rs768429501	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.87G>T	.	.	ENST00000390219	1/1	29	17	11	16	16	0	MIR770,non_coding_transcript_exon_variant,,ENST00000390219,;MEG3,intron_variant,,ENST00000522618,;MEG3,intron_variant,,ENST00000398474,;MEG3,intron_variant,,ENST00000554639,;MEG3,intron_variant,,ENST00000519709,;MEG3,intron_variant,,ENST00000521404,;MEG3,intron_variant,,ENST00000398518,;MEG3,intron_variant,,ENST00000524035,;MEG3,intron_variant,,ENST00000524131,;MEG3,intron_variant,,ENST00000556736,;MEG3,intron_variant,,ENST00000423456,;MEG3,intron_variant,,ENST00000412736,;MEG3,intron_variant,,ENST00000429159,;MEG3,intron_variant,,ENST00000555928,;MEG3,intron_variant,,ENST00000451743,;MEG3,intron_variant,,ENST00000398461,;MEG3,upstream_gene_variant,,ENST00000398460,;MEG3,downstream_gene_variant,,ENST00000522771,;MEG3,downstream_gene_variant,,ENST00000516892,;RP11-123M6.2,intron_variant,,ENST00000554041,;	T	ENSG00000211574	ENST00000390219	Transcript	non_coding_transcript_exon_variant	87	.	.	.	.	rs768429501	.	.	1	MIR770	HGNC	33143	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAGGGGTCT	.	5	ESCA
CDC42BPB	0	.	GRCh37	14	103435036	103435036	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2013G>T	p.%3D	p.R671R	ENST00000361246	15/37	20	12	7	13	13	0	CDC42BPB,synonymous_variant,p.%3D,ENST00000361246,;CDC42BPB,upstream_gene_variant,,ENST00000559043,;	A	ENSG00000198752	ENST00000361246	Transcript	synonymous_variant	2302	2013	671	R	cgG/cgT	.	.	.	-1	CDC42BPB	HGNC	1738	protein_coding	YES	CCDS9978.1	ENSP00000355237	MRCKB_HUMAN	.	UPI000013D27E	.	.	.	15/37	.	hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCCCGGCC	.	5	ESCA
IGHA1	0	.	GRCh37	14	106173779	106173779	+	Missense_Mutation	SNP	C	C	T	rs374415541	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.788G>A	p.Arg263His	p.R263H	ENST00000390547	3/3	54	35	19	53	53	0	IGHA1,missense_variant,p.Arg263His,ENST00000390547,;AL928768.3,upstream_gene_variant,,ENST00000497872,;AL901608.1,downstream_gene_variant,,ENST00000581070,;	T	ENSG00000211895	ENST00000390547	Transcript	missense_variant	788	788	263	R/H	cGc/cAc	rs374415541	.	.	-1	IGHA1	HGNC	5478	IG_C_gene	YES	.	ENSP00000374989	IGHA1_HUMAN	Q9UP60_HUMAN,Q96K68_HUMAN,Q8NCL6_HUMAN,Q6MZW0_HUMAN	UPI000004718D	.	tolerated(0.09)	benign(0.34)	3/3	.	Superfamily_domains:SSF48726,SMART_domains:SM00407,Gene3D:2.60.40.10,Pfam_domain:PF07654,hmmpanther:PTHR23266:SF68,hmmpanther:PTHR23266,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGCGAACC	byFrequency|byCluster	5	ESCA
SALL2	0	.	GRCh37	14	22005110	22005110	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-55C>G	.	.	ENST00000327430	1/2	37	19	17	35	35	0	SALL2,5_prime_UTR_variant,,ENST00000541965,;SALL2,5_prime_UTR_variant,,ENST00000327430,;SALL2,upstream_gene_variant,,ENST00000317492,;SALL2,upstream_gene_variant,,ENST00000546363,;	C	ENSG00000165821	ENST00000327430	Transcript	5_prime_UTR_variant	241	.	.	.	.	.	.	.	-1	SALL2	HGNC	10526	protein_coding	YES	CCDS32045.1	ENSP00000333537	SALL2_HUMAN	F5H1G6_HUMAN	UPI00001AF54D	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGGGGTGAC	.	5	ESCA
TRAV1-2	0	.	GRCh37	14	22111642	22111642	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.162A>C	p.Gln54His	p.Q54H	ENST00000390423	2/2	89	49	40	85	85	0	TRAV1-2,missense_variant,p.Gln54His,ENST00000390423,;	C	ENSG00000256553	ENST00000390423	Transcript	missense_variant	246	162	54	Q/H	caA/caC	.	.	.	1	TRAV1-2	HGNC	12102	TR_V_gene	YES	.	ENSP00000439668	.	.	UPI000002DA29	.	deleterious(0.04)	possibly_damaging(0.519)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19433:SF56,hmmpanther:PTHR19433,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAACATGC	.	5	ESCA
TRAV23DV6	0	.	GRCh37	14	22554771	22554771	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43C>G	p.Gln15Glu	p.Q15E	ENST00000390451	1/2	50	29	20	38	38	0	TRAV23DV6,missense_variant,p.Gln15Glu,ENST00000390451,;	G	ENSG00000211803	ENST00000390451	Transcript	missense_variant	88	43	15	Q/E	Caa/Gaa	.	.	.	1	TRAV23DV6	HGNC	12120	TR_V_gene	YES	.	ENSP00000451203	.	A0JD19_HUMAN	UPI000011D126	.	deleterious(0.03)	possibly_damaging(0.507)	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR19343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCAACTA	.	5	ESCA
NFATC4	0	.	GRCh37	14	24836196	24836196	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-65G>A	.	.	ENST00000413692	1/10	22	12	9	27	27	0	NFATC4,5_prime_UTR_variant,,ENST00000413692,;NFATC4,5_prime_UTR_variant,,ENST00000554591,;NFATC4,upstream_gene_variant,,ENST00000554050,;NFATC4,upstream_gene_variant,,ENST00000554779,;NFATC4,upstream_gene_variant,,ENST00000422617,;NFATC4,upstream_gene_variant,,ENST00000250373,;NFATC4,upstream_gene_variant,,ENST00000555590,;NFATC4,upstream_gene_variant,,ENST00000556169,;NFATC4,upstream_gene_variant,,ENST00000553469,;NFATC4,upstream_gene_variant,,ENST00000539237,;NFATC4,upstream_gene_variant,,ENST00000554661,;NFATC4,upstream_gene_variant,,ENST00000555453,;NFATC4,upstream_gene_variant,,ENST00000553708,;NFATC4,upstream_gene_variant,,ENST00000557451,;NFATC4,upstream_gene_variant,,ENST00000556279,;NFATC4,upstream_gene_variant,,ENST00000553879,;NFATC4,upstream_gene_variant,,ENST00000424781,;NFATC4,upstream_gene_variant,,ENST00000557674,;NFATC4,upstream_gene_variant,,ENST00000554966,;NFATC4,upstream_gene_variant,,ENST00000554903,;NFATC4,upstream_gene_variant,,ENST00000554344,;NFATC4,intron_variant,,ENST00000440487,;NFATC4,upstream_gene_variant,,ENST00000557028,;NFATC4,upstream_gene_variant,,ENST00000556957,;NFATC4,upstream_gene_variant,,ENST00000556302,;NFATC4,upstream_gene_variant,,ENST00000554655,;	A	ENSG00000100968	ENST00000413692	Transcript	5_prime_UTR_variant	80	.	.	.	.	.	.	.	1	NFATC4	HGNC	7778	protein_coding	YES	CCDS45089.1	ENSP00000388910	NFAC4_HUMAN	G3V4K1_HUMAN	UPI00017BD050	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCGGAGGGA	.	5	ESCA
FSCB	0	.	GRCh37	14	44974273	44974273	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1918G>C	p.Glu640Gln	p.E640Q	ENST00000340446	1/1	57	45	12	72	72	0	FSCB,missense_variant,p.Glu640Gln,ENST00000340446,;RP11-163M18.1,upstream_gene_variant,,ENST00000557465,;RP11-163M18.1,upstream_gene_variant,,ENST00000556228,;RP11-163M18.1,upstream_gene_variant,,ENST00000555433,;	G	ENSG00000189139	ENST00000340446	Transcript	missense_variant	2210	1918	640	E/Q	Gag/Cag	.	.	.	-1	FSCB	HGNC	20494	protein_coding	YES	CCDS9679.1	ENSP00000344579	FSCB_HUMAN	.	UPI00001FD466	.	deleterious(0.01)	unknown(0)	1/1	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CTCCTCAGCTG	.	2	ESCA
SYNE2	0	.	GRCh37	14	64421498	64421498	+	Missense_Mutation	SNP	G	G	A	rs370175849	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652G>A	p.Ala218Thr	p.A218T	ENST00000358025	8/116	18	7	11	17	17	0	SYNE2,missense_variant,p.Ala218Thr,ENST00000554584,;SYNE2,missense_variant,p.Ala218Thr,ENST00000356081,;SYNE2,missense_variant,p.Ala218Thr,ENST00000341472,;SYNE2,missense_variant,p.Ala218Thr,ENST00000358025,;SYNE2,missense_variant,p.Ala218Thr,ENST00000344113,;SYNE2,5_prime_UTR_variant,,ENST00000357395,;	A	ENSG00000054654	ENST00000358025	Transcript	missense_variant	882	652	218	A/T	Gcc/Acc	rs370175849	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	benign(0.059)	8/116	.	PROSITE_profiles:PS50021,hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGGCCATC	byFrequency|byCluster	5	ESCA
FAM71D	0	.	GRCh37	14	67675093	67675093	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1087G>A	p.Glu363Lys	p.E363K	ENST00000311864	6/9	37	20	16	32	32	0	FAM71D,missense_variant,p.Glu21Lys,ENST00000557671,;FAM71D,intron_variant,,ENST00000556117,;FAM71D,missense_variant,p.Glu341Lys,ENST00000534174,;FAM71D,missense_variant,p.Glu363Lys,ENST00000311864,;FAM71D,3_prime_UTR_variant,,ENST00000556046,;	A	ENSG00000172717	ENST00000311864	Transcript	missense_variant	1341	1087	363	E/K	Gag/Aag	.	.	.	1	FAM71D	HGNC	20101	nonsense_mediated_decay	YES	CCDS9778.1	ENSP00000431905	FA71D_HUMAN	E9PPX0_HUMAN,E9PM27_HUMAN	UPI000013F210	.	tolerated_low_confidence(0.05)	benign(0.051)	6/9	.	hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAGGAGATG	.	5	ESCA
ARG2	0	.	GRCh37	14	68113432	68113432	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594G>C	p.%3D	p.L198L	ENST00000261783	5/8	79	45	34	90	90	0	ARG2,synonymous_variant,p.%3D,ENST00000261783,;VTI1B,downstream_gene_variant,,ENST00000554636,;VTI1B,downstream_gene_variant,,ENST00000554659,;VTI1B,downstream_gene_variant,,ENST00000556461,;ARG2,non_coding_transcript_exon_variant,,ENST00000556491,;ARG2,non_coding_transcript_exon_variant,,ENST00000557319,;ARG2,non_coding_transcript_exon_variant,,ENST00000557120,;VTI1B,downstream_gene_variant,,ENST00000216456,;	C	ENSG00000081181	ENST00000261783	Transcript	synonymous_variant	774	594	198	L	ctG/ctC	.	.	.	1	ARG2	HGNC	664	protein_coding	YES	CCDS9785.1	ENSP00000261783	ARGI2_HUMAN	.	UPI0000125DF2	.	.	.	5/8	.	PROSITE_profiles:PS51409,hmmpanther:PTHR11358:SF18,hmmpanther:PTHR11358,Pfam_domain:PF00491,Gene3D:3.40.800.10,TIGRFAM_domain:TIGR01229,PIRSF_domain:PIRSF036979,Superfamily_domains:SSF52768,Prints_domain:PR00116	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGTCTGAGAGA	.	4	ESCA
NRXN3	0	.	GRCh37	14	80328302	80328302	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3181G>T	p.Val1061Leu	p.V1061L	ENST00000554719	17/17	10	6	4	10	10	0	NRXN3,missense_variant,p.Val1061Leu,ENST00000554719,;NRXN3,missense_variant,p.Val432Leu,ENST00000281127,;NRXN3,missense_variant,p.Val637Leu,ENST00000557594,;NRXN3,missense_variant,p.Val1061Leu,ENST00000335750,;NRXN3,missense_variant,p.Val459Leu,ENST00000428277,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556003,;NRXN3,3_prime_UTR_variant,,ENST00000555387,;NRXN3,3_prime_UTR_variant,,ENST00000554738,;	T	ENSG00000021645	ENST00000554719	Transcript	missense_variant	3672	3181	1061	V/L	Gtg/Ttg	COSM240928,COSM240929	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	deleterious(0)	benign(0.001)	17/17	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATTACGTGTAA	.	3	ESCA
SERPINA4	0	.	GRCh37	14	95030234	95030234	+	Missense_Mutation	SNP	G	G	A	rs539993882	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415G>A	p.Val139Met	p.V139M	ENST00000557004	2/5	54	31	22	32	32	0	SERPINA4,missense_variant,p.Val139Met,ENST00000555095,;SERPINA4,missense_variant,p.Val139Met,ENST00000298841,;SERPINA4,missense_variant,p.Val139Met,ENST00000557004,;SERPINA5,intron_variant,,ENST00000554220,;SERPINA5,intron_variant,,ENST00000553780,;	A	ENSG00000100665	ENST00000557004	Transcript	missense_variant	836	415	139	V/M	Gtg/Atg	rs539993882	.	.	1	SERPINA4	HGNC	8948	protein_coding	YES	CCDS9927.1	ENSP00000450838	KAIN_HUMAN	.	UPI000000CBEF	.	tolerated(0.92)	benign(0.167)	2/5	.	hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF157,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGCGTGGGC	by1000G	5	ESCA
MKRN3	0	.	GRCh37	15	23811871	23811871	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.942C>A	p.Cys314Ter	p.C314*	ENST00000314520	1/1	38	16	22	30	30	0	MKRN3,stop_gained,p.Cys314Ter,ENST00000314520,;MKRN3,intron_variant,,ENST00000564592,;MKRN3,intron_variant,,ENST00000568252,;MIR4508,upstream_gene_variant,,ENST00000584178,;RP11-73C9.1,downstream_gene_variant,,ENST00000563044,;MKRN3,intron_variant,,ENST00000568945,;MKRN3,intron_variant,,ENST00000570112,;	A	ENSG00000179455	ENST00000314520	Transcript	stop_gained	1418	942	314	C/*	tgC/tgA	.	.	.	1	MKRN3	HGNC	7114	protein_coding	YES	CCDS10013.1	ENSP00000313881	MKRN3_HUMAN	.	UPI000000DAA1	.	.	.	1/1	.	PROSITE_profiles:PS50089,hmmpanther:PTHR11224,hmmpanther:PTHR11224:SF38,Pfam_domain:PF00097,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGCATGGA	.	5	ESCA
MAGEL2	0	.	GRCh37	15	23889959	23889959	+	Silent	SNP	C	C	T	rs768824507	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1122G>A	p.%3D	p.R374R	ENST00000532292	1/1	13	8	5	11	11	0	MAGEL2,synonymous_variant,p.%3D,ENST00000532292,;AC124309.1,non_coding_transcript_exon_variant,,ENST00000314233,;	T	ENSG00000254585	ENST00000532292	Transcript	synonymous_variant	1217	1122	374	R	agG/agA	rs768824507	.	.	-1	MAGEL2	HGNC	6814	protein_coding	YES	.	ENSP00000433433	.	Q6P3U4_HUMAN,Q2M1Q7_HUMAN,Q05BN9_HUMAN,H0YDD5_HUMAN	UPI00005A89F6	.	.	.	1/1	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER	AGGGCCCTGGA	.	3	ESCA
NPAP1	0	.	GRCh37	15	24922115	24922115	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1101C>A	p.His367Gln	p.H367Q	ENST00000329468	1/1	20	11	8	17	17	0	NPAP1,missense_variant,p.His367Gln,ENST00000329468,;	A	ENSG00000185823	ENST00000329468	Transcript	missense_variant	1575	1101	367	H/Q	caC/caA	.	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	tolerated(0.26)	benign(0.091)	1/1	.	hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15,Pfam_domain:PF15229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACACACCTT	.	5	ESCA
SNORD115-27	0	.	GRCh37	15	25463800	25463800	+	5'Flank	SNP	A	A	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000364430	.	78	43	35	78	78	0	SNHG14,non_coding_transcript_exon_variant,,ENST00000365067,;SNORD115-27,upstream_gene_variant,,ENST00000364430,;SNORD115-24,downstream_gene_variant,,ENST00000363528,;SNORD115-28,upstream_gene_variant,,ENST00000363931,;SNORD115-25,downstream_gene_variant,,ENST00000362619,;SNORD115-29,upstream_gene_variant,,ENST00000362834,;SNHG14,non_coding_transcript_exon_variant,,ENST00000453082,;SNHG14,intron_variant,,ENST00000424208,;SNHG14,downstream_gene_variant,,ENST00000424333,;	C	ENSG00000201300	ENST00000364430	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1844	1	SNORD115-27	HGNC	33046	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAGAGGTGA	.	5	ESCA
FMN1	0	.	GRCh37	15	33261476	33261476	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1757G>A	p.Arg586Lys	p.R586K	ENST00000334528	4/17	73	43	30	64	64	0	FMN1,missense_variant,p.Arg809Lys,ENST00000559047,;FMN1,missense_variant,p.Arg711Lys,ENST00000561249,;FMN1,missense_variant,p.Arg586Lys,ENST00000334528,;SNORD77,upstream_gene_variant,,ENST00000391113,;	T	ENSG00000248905	ENST00000334528	Transcript	missense_variant	1757	1757	586	R/K	aGa/aAa	.	.	.	-1	FMN1	HGNC	3768	protein_coding	YES	CCDS45209.1	ENSP00000333950	FMN1_HUMAN	.	UPI00004086C3	.	deleterious(0)	unknown(0)	4/17	.	hmmpanther:PTHR13037,hmmpanther:PTHR13037:SF8,Prints_domain:PR00828	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCTGTCT	.	5	ESCA
RYR3	0	.	GRCh37	15	33895388	33895388	+	Missense_Mutation	SNP	G	G	A	rs750313484	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1987G>A	p.Glu663Lys	p.E663K	ENST00000389232	18/104	44	22	22	39	39	0	RYR3,missense_variant,p.Glu663Lys,ENST00000389232,;RYR3,missense_variant,p.Glu663Lys,ENST00000415757,;	A	ENSG00000198838	ENST00000389232	Transcript	missense_variant	2057	1987	663	E/K	Gag/Aag	rs750313484,COSM218472	.	.	1	RYR3	HGNC	10485	protein_coding	YES	CCDS45210.1	ENSP00000373884	RYR3_HUMAN	.	UPI0000E5B01A	.	.	probably_damaging(0.999)	18/104	.	Superfamily_domains:SSF49899,SMART_domains:SM00449,Pfam_domain:PF00622,hmmpanther:PTHR13715:SF16,hmmpanther:PTHR13715,PROSITE_profiles:PS50188	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E663K|c.1987G>A|3	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACTTCGAGCTG	byFrequency	4	ESCA
EXD1	0	.	GRCh37	15	41476502	41476502	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1172A>C	p.Asn391Thr	p.N391T	ENST00000314992	10/10	59	37	21	49	49	0	EXD1,missense_variant,p.Asn449Thr,ENST00000458580,;EXD1,missense_variant,p.Asn391Thr,ENST00000314992,;EXD1,non_coding_transcript_exon_variant,,ENST00000558881,;	G	ENSG00000178997	ENST00000314992	Transcript	missense_variant	1363	1172	391	N/T	aAt/aCt	.	.	.	-1	EXD1	HGNC	28507	protein_coding	YES	CCDS10072.1	ENSP00000321029	EXD1_HUMAN	.	UPI00001BBFD3	.	tolerated(0.42)	benign(0)	10/10	.	hmmpanther:PTHR12124:SF39,hmmpanther:PTHR12124	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGATTTGTA	.	5	ESCA
ATP8B4	0	.	GRCh37	15	50168486	50168486	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3016G>T	p.Val1006Phe	p.V1006F	ENST00000284509	25/28	38	19	19	30	30	0	ATP8B4,missense_variant,p.Val1006Phe,ENST00000559829,;ATP8B4,missense_variant,p.Val309Phe,ENST00000560479,;ATP8B4,missense_variant,p.Val1006Phe,ENST00000284509,;ATP8B4,missense_variant,p.Val97Phe,ENST00000558498,;CTD-2647E9.3,upstream_gene_variant,,ENST00000558150,;CTD-2647E9.3,upstream_gene_variant,,ENST00000560375,;ATP8B4,3_prime_UTR_variant,,ENST00000557955,;ATP8B4,3_prime_UTR_variant,,ENST00000558906,;ATP8B4,3_prime_UTR_variant,,ENST00000559726,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000558203,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000560354,;	A	ENSG00000104043	ENST00000284509	Transcript	missense_variant	3158	3016	1006	V/F	Gtc/Ttc	.	.	.	-1	ATP8B4	HGNC	13536	protein_coding	YES	CCDS32238.1	ENSP00000284509	AT8B4_HUMAN	H0YMB5_HUMAN	UPI0000055904	.	deleterious(0.01)	possibly_damaging(0.83)	25/28	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24092:SF46,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGACCACAA	.	5	ESCA
FAM81A	0	.	GRCh37	15	59808891	59808891	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.834C>A	p.%3D	p.A278A	ENST00000288228	8/9	13	7	6	18	18	0	FAM81A,synonymous_variant,p.%3D,ENST00000288228,;	A	ENSG00000157470	ENST00000288228	Transcript	synonymous_variant	1021	834	278	A	gcC/gcA	.	.	.	1	FAM81A	HGNC	28379	protein_coding	YES	CCDS45269.1	ENSP00000288228	FA81A_HUMAN	H0YN94_HUMAN,H0YN47_HUMAN,H0YMX7_HUMAN,H0YMW3_HUMAN,H0YMF2_HUMAN,H0YKW2_HUMAN,H0YKQ6_HUMAN	UPI000015DCFD	.	.	.	8/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22420:SF2,hmmpanther:PTHR22420	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TCAGCCAGGCT	.	4	ESCA
AGBL1	0	.	GRCh37	15	86791012	86791012	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499G>T	p.Gly167Cys	p.G167C	ENST00000441037	6/24	36	20	16	35	35	0	AGBL1,missense_variant,p.Gly167Cys,ENST00000441037,;AGBL1,missense_variant,p.Gly167Cys,ENST00000421325,;	T	ENSG00000166748	ENST00000441037	Transcript	missense_variant	594	499	167	G/C	Ggc/Tgc	.	.	.	1	AGBL1	HGNC	26504	protein_coding	YES	CCDS58398.1	ENSP00000413001	CBPC4_HUMAN	J3KQF5_HUMAN	UPI0000EC9CE0	.	deleterious(0)	possibly_damaging(0.778)	6/24	.	hmmpanther:PTHR12756:SF5,hmmpanther:PTHR12756,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGGGGCTTG	.	5	ESCA
AEN	0	.	GRCh37	15	89169568	89169568	+	Missense_Mutation	SNP	G	G	T	rs746830361	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128G>T	p.Arg43Leu	p.R43L	ENST00000332810	2/4	27	15	12	34	34	0	AEN,missense_variant,p.Arg43Leu,ENST00000559528,;AEN,missense_variant,p.Arg43Leu,ENST00000332810,;AEN,missense_variant,p.Arg43Leu,ENST00000379231,;AEN,non_coding_transcript_exon_variant,,ENST00000558327,;AEN,non_coding_transcript_exon_variant,,ENST00000557787,;AEN,upstream_gene_variant,,ENST00000557927,;AEN,downstream_gene_variant,,ENST00000560174,;	T	ENSG00000181026	ENST00000332810	Transcript	missense_variant	279	128	43	R/L	cGg/cTg	rs746830361	.	.	1	AEN	HGNC	25722	protein_coding	YES	CCDS10344.1	ENSP00000331944	AEN_HUMAN	Q8WYW8_HUMAN,H0YMJ6_HUMAN	UPI000013DF23	.	deleterious(0)	benign(0.253)	2/4	.	hmmpanther:PTHR12801,hmmpanther:PTHR12801:SF57	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCCGGAAGG	byCluster	5	ESCA
FES	0	.	GRCh37	15	91434332	91434332	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1441C>T	p.%3D	p.L481L	ENST00000328850	11/19	50	29	20	39	39	0	FES,synonymous_variant,p.%3D,ENST00000328850,;FES,synonymous_variant,p.%3D,ENST00000394300,;FES,intron_variant,,ENST00000394302,;FES,intron_variant,,ENST00000450438,;FES,intron_variant,,ENST00000444422,;FES,intron_variant,,ENST00000414248,;FES,downstream_gene_variant,,ENST00000452243,;FES,downstream_gene_variant,,ENST00000559355,;FES,downstream_gene_variant,,ENST00000448367,;FES,synonymous_variant,p.%3D,ENST00000464684,;FES,intron_variant,,ENST00000496379,;FES,downstream_gene_variant,,ENST00000462476,;FES,downstream_gene_variant,,ENST00000494259,;FES,downstream_gene_variant,,ENST00000497945,;FES,downstream_gene_variant,,ENST00000470152,;	T	ENSG00000182511	ENST00000328850	Transcript	synonymous_variant	1583	1441	481	L	Ctg/Ttg	.	.	.	1	FES	HGNC	3657	protein_coding	YES	CCDS10365.1	ENSP00000331504	FES_HUMAN	Q4JFK7_HUMAN,H0YNN8_HUMAN,E9PGC7_HUMAN,E7EMJ7_HUMAN,C9J3W6_HUMAN	UPI0000001C30	.	.	.	11/19	.	PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF197,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,PIRSF_domain:PIRSF000632,Superfamily_domains:SSF55550,Prints_domain:PR00401	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTCCTGGTG	.	5	ESCA
RHBDF1	0	.	GRCh37	16	109825	109825	+	Splice_Site	SNP	C	C	A	rs376515962	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1723-1G>T	.	p.X575_splice	ENST00000262316	.	38	21	17	27	27	0	RHBDF1,splice_acceptor_variant,,ENST00000262316,;RHBDF1,downstream_gene_variant,,ENST00000454039,;SNRNP25,downstream_gene_variant,,ENST00000383018,;RHBDF1,upstream_gene_variant,,ENST00000448893,;RHBDF1,downstream_gene_variant,,ENST00000419764,;SNRNP25,downstream_gene_variant,,ENST00000417493,;RHBDF1,downstream_gene_variant,,ENST00000450643,;SNRNP25,downstream_gene_variant,,ENST00000293861,;SNRNP25,downstream_gene_variant,,ENST00000493672,;RHBDF1,splice_acceptor_variant,,ENST00000428730,;RHBDF1,non_coding_transcript_exon_variant,,ENST00000493647,;RHBDF1,non_coding_transcript_exon_variant,,ENST00000486045,;RHBDF1,downstream_gene_variant,,ENST00000487201,;SNRNP25,downstream_gene_variant,,ENST00000397876,;SNRNP25,downstream_gene_variant,,ENST00000481947,;RHBDF1,downstream_gene_variant,,ENST00000417043,;RHBDF1,downstream_gene_variant,,ENST00000482904,;RHBDF1,downstream_gene_variant,,ENST00000472390,;SNRNP25,downstream_gene_variant,,ENST00000466183,;	A	ENSG00000007384	ENST00000262316	Transcript	splice_acceptor_variant	.	.	.	.	.	rs376515962	.	.	-1	RHBDF1	HGNC	20561	protein_coding	YES	CCDS32344.1	ENSP00000262316	RHDF1_HUMAN	A2IDA2_HUMAN	UPI00001A5206	.	.	.	.	13/17	.	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATCTGGGT	byFrequency|byCluster	5	ESCA
RHBDF1	0	.	GRCh37	16	112579	112579	+	Missense_Mutation	SNP	C	C	G	rs769452521	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.910G>C	p.Gly304Arg	p.G304R	ENST00000262316	7/18	53	23	29	47	47	0	RHBDF1,missense_variant,p.Gly304Arg,ENST00000262316,;RHBDF1,missense_variant,p.Gly304Arg,ENST00000454039,;SNRNP25,downstream_gene_variant,,ENST00000383018,;RHBDF1,upstream_gene_variant,,ENST00000448893,;RHBDF1,downstream_gene_variant,,ENST00000450643,;RHBDF1,downstream_gene_variant,,ENST00000419764,;SNRNP25,downstream_gene_variant,,ENST00000293861,;RHBDF1,3_prime_UTR_variant,,ENST00000428730,;RHBDF1,downstream_gene_variant,,ENST00000417043,;RHBDF1,downstream_gene_variant,,ENST00000487201,;RHBDF1,upstream_gene_variant,,ENST00000482904,;RHBDF1,upstream_gene_variant,,ENST00000493647,;RHBDF1,upstream_gene_variant,,ENST00000486045,;RHBDF1,downstream_gene_variant,,ENST00000472390,;	G	ENSG00000007384	ENST00000262316	Transcript	missense_variant	1053	910	304	G/R	Ggg/Cgg	rs769452521	.	.	-1	RHBDF1	HGNC	20561	protein_coding	YES	CCDS32344.1	ENSP00000262316	RHDF1_HUMAN	A2IDA2_HUMAN	UPI00001A5206	.	tolerated(0.19)	probably_damaging(0.935)	7/18	.	hmmpanther:PTHR22936:SF6,hmmpanther:PTHR22936,Pfam_domain:PF12595	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCCCGCCGG	byFrequency	5	ESCA
ABCC6	0	.	GRCh37	16	16276745	16276745	+	Silent	SNP	G	G	T	rs760798025	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1986C>A	p.%3D	p.V662V	ENST00000205557	16/31	50	30	19	42	42	0	ABCC6,synonymous_variant,p.%3D,ENST00000205557,;ABCC6,intron_variant,,ENST00000574094,;ABCC6,synonymous_variant,p.%3D,ENST00000456970,;	T	ENSG00000091262	ENST00000205557	Transcript	synonymous_variant	2016	1986	662	V	gtC/gtA	rs760798025	.	.	-1	ABCC6	HGNC	57	protein_coding	YES	CCDS10568.1	ENSP00000205557	MRP6_HUMAN	.	UPI00001AE5CA	.	.	.	16/31	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Pfam_domain:PF00005,TIGRFAM_domain:TIGR00957,Gene3D:3.40.50.300,hmmpanther:PTHR24223:SF63,hmmpanther:PTHR24223,PROSITE_profiles:PS50893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACCGACAAC	byFrequency	5	ESCA
ACSM2B	0	.	GRCh37	16	20556566	20556566	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1194G>T	p.Lys398Asn	p.K398N	ENST00000329697	10/14	55	24	31	32	32	0	ACSM2B,missense_variant,p.Lys398Asn,ENST00000565232,;ACSM2B,missense_variant,p.Lys398Asn,ENST00000329697,;ACSM2B,missense_variant,p.Lys398Asn,ENST00000567001,;ACSM2B,missense_variant,p.Lys319Asn,ENST00000565322,;ACSM2B,upstream_gene_variant,,ENST00000568098,;ACSM2B,downstream_gene_variant,,ENST00000569163,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000567288,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569131,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000566998,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000563943,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569364,;ACSM2B,downstream_gene_variant,,ENST00000569327,;ACSM2B,upstream_gene_variant,,ENST00000564849,;	A	ENSG00000066813	ENST00000329697	Transcript	missense_variant	1363	1194	398	K/N	aaG/aaT	.	.	.	-1	ACSM2B	HGNC	30931	protein_coding	YES	CCDS10586.1	ENSP00000327453	ACS2B_HUMAN	H3BTX9_HUMAN,H3BQ84_HUMAN,H3BP79_HUMAN,H3BM61_HUMAN	UPI00001AFAA7	.	tolerated(1)	benign(0.048)	10/14	.	Superfamily_domains:SSF56801,Gene3D:2.30.38.10,Pfam_domain:PF00501,hmmpanther:PTHR24095:SF140,hmmpanther:PTHR24095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCCCTTATC	.	5	ESCA
UQCRC2	0	.	GRCh37	16	21964769	21964769	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25T>A	p.Ser9Thr	p.S9T	ENST00000268379	1/14	31	11	20	27	27	0	UQCRC2,missense_variant,p.Ser9Thr,ENST00000565331,;UQCRC2,missense_variant,p.Ser9Thr,ENST00000561553,;UQCRC2,missense_variant,p.Ser9Thr,ENST00000268379,;UQCRC2,missense_variant,p.Ser9Thr,ENST00000564095,;UQCRC2,missense_variant,p.Ser9Thr,ENST00000563898,;UQCRC2,missense_variant,p.Ser9Thr,ENST00000565464,;UQCRC2,non_coding_transcript_exon_variant,,ENST00000567757,;	A	ENSG00000140740	ENST00000268379	Transcript	missense_variant	789	25	9	S/T	Tct/Act	.	.	.	1	UQCRC2	HGNC	12586	protein_coding	YES	CCDS10601.1	ENSP00000268379	QCR2_HUMAN	.	UPI0000137A45	.	tolerated_low_confidence(0.33)	benign(0.002)	1/14	.	hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGCTCTTTC	.	5	ESCA
COG7	0	.	GRCh37	16	23464262	23464262	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54T>C	p.%3D	p.N18N	ENST00000307149	1/17	20	11	9	48	48	0	COG7,synonymous_variant,p.%3D,ENST00000307149,;CTD-2270L9.4,non_coding_transcript_exon_variant,,ENST00000570080,;CTD-2270L9.4,upstream_gene_variant,,ENST00000562842,;CTD-2270L9.4,upstream_gene_variant,,ENST00000565747,;	G	ENSG00000168434	ENST00000307149	Transcript	synonymous_variant	240	54	18	N	aaT/aaC	.	.	.	-1	COG7	HGNC	18622	protein_coding	YES	CCDS10610.1	ENSP00000305442	COG7_HUMAN	.	UPI0000127E42	.	.	.	1/17	.	hmmpanther:PTHR21443,Pfam_domain:PF10191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCATTGAT	.	5	ESCA
PRKCB	0	.	GRCh37	16	24135161	24135161	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.924C>A	p.%3D	p.A308A	ENST00000303531	9/17	77	48	29	82	82	0	PRKCB,synonymous_variant,p.%3D,ENST00000303531,;PRKCB,synonymous_variant,p.%3D,ENST00000321728,;	A	ENSG00000166501	ENST00000303531	Transcript	synonymous_variant	1076	924	308	A	gcC/gcA	.	.	.	1	PRKCB	HGNC	9395	protein_coding	YES	CCDS10619.1	ENSP00000305355	KPCB_HUMAN	I3L1Z0_HUMAN	UPI000002ACF9	.	.	.	9/17	.	hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF63,PIRSF_domain:PIRSF000550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCCAAGAT	.	5	ESCA
SEZ6L2	0	.	GRCh37	16	29909173	29909173	+	Splice_Site	SNP	C	C	G	rs775175142	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211+1G>C	.	p.X71_splice	ENST00000308713	.	21	11	10	20	20	0	SEZ6L2,splice_donor_variant,,ENST00000308713,;SEZ6L2,splice_donor_variant,,ENST00000346932,;SEZ6L2,splice_donor_variant,,ENST00000350527,;SEZ6L2,intron_variant,,ENST00000537485,;SEZ6L2,intron_variant,,ENST00000568380,;ASPHD1,upstream_gene_variant,,ENST00000308748,;ASPHD1,upstream_gene_variant,,ENST00000483405,;ASPHD1,upstream_gene_variant,,ENST00000563177,;SEZ6L2,splice_donor_variant,,ENST00000562159,;ASPHD1,upstream_gene_variant,,ENST00000566693,;ASPHD1,upstream_gene_variant,,ENST00000414952,;	G	ENSG00000174938	ENST00000308713	Transcript	splice_donor_variant	.	.	.	.	.	rs775175142	.	.	-1	SEZ6L2	HGNC	30844	protein_coding	YES	CCDS10659.1	ENSP00000312550	SE6L2_HUMAN	B3KNF3_HUMAN	UPI0000366B1B	.	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCACCTGGC	.	5	ESCA
ITGAD	0	.	GRCh37	16	31426246	31426246	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2217C>G	p.%3D	p.P739P	ENST00000389202	18/30	42	23	18	38	38	0	ITGAD,synonymous_variant,p.%3D,ENST00000389202,;	G	ENSG00000156886	ENST00000389202	Transcript	synonymous_variant	2266	2217	739	P	ccC/ccG	.	.	.	1	ITGAD	HGNC	6146	protein_coding	YES	CCDS32438.1	ENSP00000373854	ITAD_HUMAN	Q59H14_HUMAN	UPI000004B27A	.	.	.	18/30	.	Superfamily_domains:SSF69179,Pfam_domain:PF08441,Gene3D:1jv2A02,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCCATCCC	.	5	ESCA
ZNF200	0	.	GRCh37	16	3283513	3283513	+	Silent	SNP	C	C	T	rs759662741	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.243G>A	p.%3D	p.Q81Q	ENST00000431561	2/5	47	44	3	43	43	0	ZNF200,synonymous_variant,p.%3D,ENST00000414144,;ZNF200,synonymous_variant,p.%3D,ENST00000575948,;ZNF200,synonymous_variant,p.%3D,ENST00000431561,;ZNF200,synonymous_variant,p.%3D,ENST00000396870,;ZNF200,synonymous_variant,p.%3D,ENST00000396868,;ZNF200,synonymous_variant,p.%3D,ENST00000396871,;ZNF200,downstream_gene_variant,,ENST00000575617,;ZNF200,non_coding_transcript_exon_variant,,ENST00000575630,;ZNF200,downstream_gene_variant,,ENST00000577015,;	T	ENSG00000010539	ENST00000431561	Transcript	synonymous_variant	856	243	81	Q	caG/caA	rs759662741	.	.	-1	ZNF200	HGNC	12993	protein_coding	YES	CCDS10497.1	ENSP00000395723	ZN200_HUMAN	I3L1E4_HUMAN	UPI00001D89D6	.	.	.	2/5	.	hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTTCTGAAG	.	2	ESCA
ZNF500	0	.	GRCh37	16	4803036	4803036	+	Missense_Mutation	SNP	C	C	A	rs142409847	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.784G>T	p.Gly262Cys	p.G262C	ENST00000219478	6/6	42	18	24	35	35	0	ZNF500,missense_variant,p.Gly262Cys,ENST00000545009,;ZNF500,missense_variant,p.Gly262Cys,ENST00000219478,;ZNF500,5_prime_UTR_variant,,ENST00000592425,;C16orf71,downstream_gene_variant,,ENST00000590191,;C16orf71,downstream_gene_variant,,ENST00000299320,;ZNF500,upstream_gene_variant,,ENST00000588942,;ZNF500,non_coding_transcript_exon_variant,,ENST00000591026,;RP11-127I20.7,upstream_gene_variant,,ENST00000588099,;ZNF500,3_prime_UTR_variant,,ENST00000589422,;C16orf71,downstream_gene_variant,,ENST00000586256,;	A	ENSG00000103199	ENST00000219478	Transcript	missense_variant	1084	784	262	G/C	Ggc/Tgc	rs142409847	.	.	-1	ZNF500	HGNC	23716	protein_coding	YES	CCDS32383.1	ENSP00000219478	ZN500_HUMAN	Q0VAL1_HUMAN,K7ERS9_HUMAN,K7EPZ1_HUMAN,K7EIH1_HUMAN	UPI00001C1FB0	.	deleterious(0)	probably_damaging(0.969)	6/6	.	hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF53	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGCCGTCCT	byCluster	5	ESCA
SNX20	0	.	GRCh37	16	50707505	50707505	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763C>G	p.Gln255Glu	p.Q255E	ENST00000330943	4/4	31	17	14	28	28	0	SNX20,missense_variant,p.Gln255Glu,ENST00000330943,;SNX20,intron_variant,,ENST00000423026,;SNX20,intron_variant,,ENST00000300590,;RP11-401P9.5,downstream_gene_variant,,ENST00000570167,;RP11-401P9.5,downstream_gene_variant,,ENST00000570241,;SNX20,intron_variant,,ENST00000568993,;	C	ENSG00000167208	ENST00000330943	Transcript	missense_variant	935	763	255	Q/E	Cag/Gag	.	.	.	-1	SNX20	HGNC	30390	protein_coding	YES	CCDS10745.1	ENSP00000332062	SNX20_HUMAN	.	UPI000004348D	.	tolerated(1)	benign(0.002)	4/4	.	hmmpanther:PTHR20939:SF1,hmmpanther:PTHR20939,Gene3D:1.25.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCTGCAGGG	.	5	ESCA
LPCAT2	0	.	GRCh37	16	55616969	55616969	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594G>C	p.Glu532Gln	p.E532Q	ENST00000262134	14/14	27	16	10	31	31	0	LPCAT2,missense_variant,p.Glu532Gln,ENST00000262134,;LPCAT2,downstream_gene_variant,,ENST00000565056,;LPCAT2,non_coding_transcript_exon_variant,,ENST00000562299,;LPCAT2,non_coding_transcript_exon_variant,,ENST00000566915,;	C	ENSG00000087253	ENST00000262134	Transcript	missense_variant	1778	1594	532	E/Q	Gaa/Caa	.	.	.	1	LPCAT2	HGNC	26032	protein_coding	YES	CCDS10753.1	ENSP00000262134	PCAT2_HUMAN	.	UPI00001BD900	.	tolerated(0.06)	benign(0.046)	14/14	.	hmmpanther:PTHR23063:SF12,hmmpanther:PTHR23063	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTGAAAAG	.	5	ESCA
CES1P1	0	.	GRCh37	16	55806303	55806303	+	RNA	SNP	G	G	T	rs780006447	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.605G>T	.	.	ENST00000571348	5/6	59	24	35	20	20	0	CES1P1,non_coding_transcript_exon_variant,,ENST00000573705,;CES1P1,non_coding_transcript_exon_variant,,ENST00000571348,;CES1P1,non_coding_transcript_exon_variant,,ENST00000574030,;CES1P1,non_coding_transcript_exon_variant,,ENST00000421606,;	T	ENSG00000228695	ENST00000571348	Transcript	non_coding_transcript_exon_variant	605	.	.	.	.	rs780006447	.	.	1	CES1P1	HGNC	18546	processed_transcript	YES	.	.	.	.	.	.	.	.	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCGGGGAAC	.	5	ESCA
TANGO6	0	.	GRCh37	16	69007950	69007950	+	Silent	SNP	C	C	T	rs759364664,rs775553124	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2721C>T	p.%3D	p.D907D	ENST00000261778	15/18	65	40	25	37	37	0	TANGO6,synonymous_variant,p.%3D,ENST00000261778,;TANGO6,non_coding_transcript_exon_variant,,ENST00000562000,;TANGO6,non_coding_transcript_exon_variant,,ENST00000568361,;	T	ENSG00000103047	ENST00000261778	Transcript	synonymous_variant	2733	2721	907	D	gaC/gaT	rs759364664,rs775553124	.	.	1	TANGO6	HGNC	25749	protein_coding	YES	CCDS45516.1	ENSP00000261778	TNG6_HUMAN	B3KTB6_HUMAN	UPI00001FF4A8	.	.	.	15/18	.	hmmpanther:PTHR20959:SF1,hmmpanther:PTHR20959,Pfam_domain:PF10363,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGACGTCTA	.	5	ESCA
HYDIN	0	.	GRCh37	16	70874024	70874024	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12986G>T	p.Gly4329Val	p.G4329V	ENST00000393567	76/86	38	20	18	30	30	0	HYDIN,missense_variant,p.Gly4329Val,ENST00000393567,;HYDIN,3_prime_UTR_variant,,ENST00000378856,;	A	ENSG00000157423	ENST00000393567	Transcript	missense_variant	13137	12986	4329	G/V	gGg/gTg	.	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	probably_damaging(0.988)	76/86	.	Gene3D:2.60.40.360,hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GCATCCCAGCT	.	3	ESCA
HYDIN	0	.	GRCh37	16	70891651	70891651	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12252C>A	p.%3D	p.I4084I	ENST00000393567	72/86	99	75	24	73	73	0	HYDIN,synonymous_variant,p.%3D,ENST00000393567,;RNU6ATAC25P,downstream_gene_variant,,ENST00000408798,;HYDIN,3_prime_UTR_variant,,ENST00000378856,;HYDIN,3_prime_UTR_variant,,ENST00000546257,;	T	ENSG00000157423	ENST00000393567	Transcript	synonymous_variant	12403	12252	4084	I	atC/atA	.	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	.	72/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGAGATGAG	.	5	ESCA
GLG1	0	.	GRCh37	16	74506261	74506261	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2101C>G	p.Gln701Glu	p.Q701E	ENST00000205061	14/27	102	55	47	82	82	0	GLG1,missense_variant,p.Gln701Glu,ENST00000422840,;GLG1,missense_variant,p.Gln701Glu,ENST00000205061,;GLG1,missense_variant,p.Gln690Glu,ENST00000447066,;GLG1,3_prime_UTR_variant,,ENST00000562090,;GLG1,3_prime_UTR_variant,,ENST00000567951,;GLG1,non_coding_transcript_exon_variant,,ENST00000566601,;GLG1,non_coding_transcript_exon_variant,,ENST00000563432,;GLG1,upstream_gene_variant,,ENST00000561481,;GLG1,downstream_gene_variant,,ENST00000567911,;	C	ENSG00000090863	ENST00000205061	Transcript	missense_variant	2121	2101	701	Q/E	Cag/Gag	COSM4151409	.	.	-1	GLG1	HGNC	4316	protein_coding	YES	CCDS32485.1	ENSP00000205061	GSLG1_HUMAN	Q6ZMF1_HUMAN,H3BQT1_HUMAN	UPI00001FFBD9	.	tolerated(0.43)	benign(0.108)	14/27	.	PROSITE_profiles:PS51289,hmmpanther:PTHR11884,hmmpanther:PTHR11884:SF1,Pfam_domain:PF00839	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTGAATTA	.	5	ESCA
CHST5	0	.	GRCh37	16	75562965	75562965	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*82G>A	.	.	ENST00000336257	3/3	13	5	8	10	10	0	CHST5,3_prime_UTR_variant,,ENST00000336257,;CHST5,downstream_gene_variant,,ENST00000565039,;CHST5,downstream_gene_variant,,ENST00000541075,;RP11-77K12.7,3_prime_UTR_variant,,ENST00000460606,;	T	ENSG00000135702	ENST00000336257	Transcript	3_prime_UTR_variant	2713	.	.	.	.	.	.	.	-1	CHST5	HGNC	1973	protein_coding	YES	CCDS10919.1	ENSP00000338783	CHST5_HUMAN	.	UPI000006EAEA	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CCATGCGCCCC	.	4	ESCA
KIAA0513	0	.	GRCh37	16	85122099	85122099	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*168C>G	.	.	ENST00000566428	13/13	21	10	10	11	11	0	KIAA0513,3_prime_UTR_variant,,ENST00000258180,;KIAA0513,3_prime_UTR_variant,,ENST00000566428,;KIAA0513,downstream_gene_variant,,ENST00000538274,;KIAA0513,downstream_gene_variant,,ENST00000562564,;KIAA0513,downstream_gene_variant,,ENST00000562580,;KIAA0513,non_coding_transcript_exon_variant,,ENST00000562388,;	G	ENSG00000135709	ENST00000566428	Transcript	3_prime_UTR_variant	2035	.	.	.	.	.	.	.	1	KIAA0513	HGNC	29058	protein_coding	YES	CCDS32499.1	ENSP00000457408	K0513_HUMAN	.	UPI0000139A26	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCTCCTC	.	5	ESCA
GSE1	0	.	GRCh37	16	85697186	85697186	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2610C>T	p.%3D	p.F870F	ENST00000253458	11/16	48	23	24	41	41	0	GSE1,synonymous_variant,p.%3D,ENST00000253458,;GSE1,synonymous_variant,p.%3D,ENST00000405402,;GSE1,synonymous_variant,p.%3D,ENST00000438180,;GSE1,synonymous_variant,p.%3D,ENST00000412692,;GSE1,synonymous_variant,p.%3D,ENST00000393243,;RN7SL381P,downstream_gene_variant,,ENST00000577658,;GSE1,non_coding_transcript_exon_variant,,ENST00000469381,;GSE1,upstream_gene_variant,,ENST00000495192,;GSE1,upstream_gene_variant,,ENST00000562659,;GSE1,downstream_gene_variant,,ENST00000479488,;	T	ENSG00000131149	ENST00000253458	Transcript	synonymous_variant	2786	2610	870	F	ttC/ttT	.	.	.	1	GSE1	HGNC	28979	protein_coding	YES	CCDS10952.1	ENSP00000253458	GSE1_HUMAN	C9JLW9_HUMAN	UPI0000185F04	.	.	.	11/16	.	Pfam_domain:PF12540,hmmpanther:PTHR17608:SF3,hmmpanther:PTHR17608	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCAACCT	.	5	ESCA
CBFA2T3	0	.	GRCh37	16	88947724	88947724	+	Silent	SNP	G	G	A	rs2272437	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1377C>T	p.%3D	p.S459S	ENST00000268679	9/12	15	10	5	20	20	0	CBFA2T3,synonymous_variant,p.%3D,ENST00000569464,;CBFA2T3,synonymous_variant,p.%3D,ENST00000360302,;CBFA2T3,synonymous_variant,p.%3D,ENST00000436887,;CBFA2T3,synonymous_variant,p.%3D,ENST00000327483,;CBFA2T3,synonymous_variant,p.%3D,ENST00000268679,;CBFA2T3,synonymous_variant,p.%3D,ENST00000448839,;RP11-830F9.5,non_coding_transcript_exon_variant,,ENST00000562574,;RP11-830F9.5,intron_variant,,ENST00000562405,;RP11-830F9.5,upstream_gene_variant,,ENST00000569249,;RP11-830F9.5,upstream_gene_variant,,ENST00000565053,;CBFA2T3,upstream_gene_variant,,ENST00000563856,;CBFA2T3,upstream_gene_variant,,ENST00000563920,;CBFA2T3,upstream_gene_variant,,ENST00000566868,;	A	ENSG00000129993	ENST00000268679	Transcript	synonymous_variant	1774	1377	459	S	tcC/tcT	rs2272437,COSM3957925	.	.	-1	CBFA2T3	HGNC	1537	protein_coding	YES	CCDS10972.1	ENSP00000268679	MTG16_HUMAN	H3BSI4_HUMAN,H3BR72_HUMAN,H3BMZ0_HUMAN,B3KR45_HUMAN	UPI0000167F93	.	.	.	9/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF6,Prints_domain:PR01878	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CCGGCGGAGCT	byCluster|byHapMap	2	ESCA
MYH13	0	.	GRCh37	17	10219245	10219245	+	Missense_Mutation	SNP	A	A	T	rs773824073	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3836T>A	p.Met1279Lys	p.M1279K	ENST00000418404	27/41	56	28	28	64	64	0	MYH13,missense_variant,p.Met1279Lys,ENST00000418404,;MYH13,missense_variant,p.Met1279Lys,ENST00000252172,;RP11-401O9.4,intron_variant,,ENST00000609088,;RP11-401O9.3,upstream_gene_variant,,ENST00000577743,;	T	ENSG00000006788	ENST00000418404	Transcript	missense_variant	4000	3836	1279	M/K	aTg/aAg	rs773824073	.	.	-1	MYH13	HGNC	7571	protein_coding	YES	CCDS45613.1	ENSP00000404570	MYH13_HUMAN	.	UPI0000DB39EA	.	tolerated(0.07)	benign(0.016)	27/41	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF267,Pfam_domain:PF01576,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGCATGTTC	byFrequency	5	ESCA
ARHGAP44	0	.	GRCh37	17	12894923	12894923	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1435C>T	.	.	ENST00000379672	21/21	32	19	13	38	38	0	ARHGAP44,3_prime_UTR_variant,,ENST00000340825,;ARHGAP44,3_prime_UTR_variant,,ENST00000379672,;ELAC2,downstream_gene_variant,,ENST00000584650,;ARHGAP44,downstream_gene_variant,,ENST00000262444,;ELAC2,downstream_gene_variant,,ENST00000426905,;ELAC2,downstream_gene_variant,,ENST00000338034,;ELAC2,downstream_gene_variant,,ENST00000395962,;RP11-597M12.1,upstream_gene_variant,,ENST00000582915,;ARHGAP44,3_prime_UTR_variant,,ENST00000580768,;ELAC2,downstream_gene_variant,,ENST00000491478,;ELAC2,downstream_gene_variant,,ENST00000484122,;ARHGAP44,downstream_gene_variant,,ENST00000584974,;ELAC2,downstream_gene_variant,,ENST00000480891,;ELAC2,downstream_gene_variant,,ENST00000492559,;ARHGAP44,downstream_gene_variant,,ENST00000544416,;ELAC2,downstream_gene_variant,,ENST00000487229,;ELAC2,downstream_gene_variant,,ENST00000465825,;	T	ENSG00000006740	ENST00000379672	Transcript	3_prime_UTR_variant	4192	.	.	.	.	.	.	.	1	ARHGAP44	HGNC	29096	protein_coding	YES	CCDS45616.1	ENSP00000368994	RHG44_HUMAN	J3QQU7_HUMAN	UPI0000252116	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTCAAAAG	.	5	ESCA
EVPLL	0	.	GRCh37	17	18284783	18284783	+	Missense_Mutation	SNP	G	G	A	rs745539671	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166G>A	p.Val56Met	p.V56M	ENST00000399134	3/11	80	37	43	75	75	0	EVPLL,missense_variant,p.Val56Met,ENST00000399134,;RP1-37N7.1,non_coding_transcript_exon_variant,,ENST00000579352,;EVPLL,upstream_gene_variant,,ENST00000583003,;	A	ENSG00000214860	ENST00000399134	Transcript	missense_variant	524	166	56	V/M	Gtg/Atg	rs745539671	.	.	1	EVPLL	HGNC	35236	protein_coding	YES	CCDS45626.1	ENSP00000382086	EVPLL_HUMAN	.	UPI00001C1FE2	.	deleterious(0.05)	benign(0.018)	3/11	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23169:SF8,hmmpanther:PTHR23169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACGTGGAC	.	5	ESCA
ARHGAP23	0	.	GRCh37	17	36667229	36667229	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*21C>T	.	.	ENST00000431231	24/24	21	8	12	26	26	0	ARHGAP23,3_prime_UTR_variant,,ENST00000431231,;ARHGAP23,3_prime_UTR_variant,,ENST00000443378,;ARHGAP23,downstream_gene_variant,,ENST00000548703,;ARHGAP23,downstream_gene_variant,,ENST00000437668,;ARHGAP23,downstream_gene_variant,,ENST00000583703,;	T	ENSG00000225485	ENST00000431231	Transcript	3_prime_UTR_variant	4565	.	.	.	.	.	.	.	1	ARHGAP23	HGNC	29293	protein_coding	YES	CCDS56027.1	ENSP00000393539	RHG23_HUMAN	H0YHF3_HUMAN,F8W040_HUMAN,C9JVU9_HUMAN	UPI0000F3BE51	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCTCGGGCG	.	5	ESCA
MEOX1	0	.	GRCh37	17	41738714	41738714	+	Silent	SNP	T	T	A	rs367782056	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189A>T	p.%3D	p.S63S	ENST00000318579	1/3	59	27	31	50	50	0	MEOX1,missense_variant,p.Gln34Leu,ENST00000549132,;MEOX1,synonymous_variant,p.%3D,ENST00000318579,;MEOX1,synonymous_variant,p.%3D,ENST00000329168,;MEOX1,5_prime_UTR_variant,,ENST00000393661,;	A	ENSG00000005102	ENST00000318579	Transcript	synonymous_variant	609	189	63	S	tcA/tcT	rs367782056	.	.	-1	MEOX1	HGNC	7013	protein_coding	YES	CCDS11466.1	ENSP00000321684	MEOX1_HUMAN	.	UPI000012F410	.	.	.	1/3	.	hmmpanther:PTHR24328:SF8,hmmpanther:PTHR24328	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCTGAGAA	byCluster|by1000G	5	ESCA
HSF5	0	.	GRCh37	17	56499659	56499659	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62C>G	.	.	ENST00000323777	6/6	29	19	10	31	31	0	HSF5,3_prime_UTR_variant,,ENST00000323777,;RNF43,upstream_gene_variant,,ENST00000584437,;RNF43,upstream_gene_variant,,ENST00000577716,;RNF43,upstream_gene_variant,,ENST00000407977,;RNF43,upstream_gene_variant,,ENST00000580014,;	C	ENSG00000176160	ENST00000323777	Transcript	3_prime_UTR_variant	1963	.	.	.	.	.	.	.	-1	HSF5	HGNC	26862	protein_coding	YES	CCDS32690.1	ENSP00000313243	HSF5_HUMAN	.	UPI0000161929	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCATGTGCAA	.	5	ESCA
SMG8	0	.	GRCh37	17	57289759	57289759	+	Missense_Mutation	SNP	G	G	T	rs369051063	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1817G>T	p.Arg606Leu	p.R606L	ENST00000543872	3/5	53	27	25	35	35	0	SMG8,missense_variant,p.Arg606Leu,ENST00000543872,;SMG8,missense_variant,p.Arg149Leu,ENST00000582469,;SMG8,missense_variant,p.Arg606Leu,ENST00000300917,;CTD-2510F5.6,intron_variant,,ENST00000577660,;SMG8,downstream_gene_variant,,ENST00000578922,;SMG8,non_coding_transcript_exon_variant,,ENST00000580498,;SMG8,3_prime_UTR_variant,,ENST00000580798,;	T	ENSG00000167447	ENST00000543872	Transcript	missense_variant	2081	1817	606	R/L	cGa/cTa	rs369051063	.	.	1	SMG8	HGNC	25551	protein_coding	YES	CCDS11615.1	ENSP00000438748	SMG8_HUMAN	.	UPI000006CCB5	.	deleterious(0)	probably_damaging(0.988)	3/5	.	hmmpanther:PTHR13091,hmmpanther:PTHR13091:SF0,Pfam_domain:PF10220	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCGATCTA	byFrequency|byCluster	5	ESCA
LRRC37A3	0	.	GRCh37	17	62856576	62856576	+	Missense_Mutation	SNP	C	C	G	rs756384249	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3688G>C	p.Ala1230Pro	p.A1230P	ENST00000584306	11/14	82	57	24	58	58	0	LRRC37A3,missense_variant,p.Ala1230Pro,ENST00000319651,;LRRC37A3,missense_variant,p.Ala1230Pro,ENST00000584306,;LRRC37A3,missense_variant,p.Ala268Pro,ENST00000400877,;LRRC37A3,missense_variant,p.Ala207Pro,ENST00000334962,;LRRC37A3,missense_variant,p.Ala348Pro,ENST00000339474,;LRRC37A3,downstream_gene_variant,,ENST00000581368,;LRRC37A3,downstream_gene_variant,,ENST00000584788,;LRRC37A3,upstream_gene_variant,,ENST00000583510,;LRRC37A3,downstream_gene_variant,,ENST00000579305,;	G	ENSG00000176809	ENST00000584306	Transcript	missense_variant	4219	3688	1230	A/P	Gcc/Ccc	rs756384249,COSM2796458	.	.	-1	LRRC37A3	HGNC	32427	protein_coding	YES	CCDS32708.1	ENSP00000464535	L37A3_HUMAN	F8W7X0_HUMAN,B4DSF2_HUMAN	UPI00005B2F0A	.	deleterious(0.03)	benign(0.027)	11/14	.	hmmpanther:PTHR23045	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGGCGTTTC	byFrequency	5	ESCA
JMJD6	0	.	GRCh37	17	74714728	74714728	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1208+87G>A	.	.	ENST00000445478	.	49	39	9	28	28	0	JMJD6,missense_variant,p.Asp386Asn,ENST00000585429,;JMJD6,3_prime_UTR_variant,,ENST00000397625,;JMJD6,intron_variant,,ENST00000445478,;JMJD6,3_prime_UTR_variant,,ENST00000542934,;JMJD6,3_prime_UTR_variant,,ENST00000303996,;JMJD6,non_coding_transcript_exon_variant,,ENST00000591460,;JMJD6,downstream_gene_variant,,ENST00000589982,;	T	ENSG00000070495	ENST00000445478	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	JMJD6	HGNC	19355	protein_coding	YES	CCDS42383.1	ENSP00000394085	JMJD6_HUMAN	.	UPI00003DFD0B	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTCTGCAG	.	5	ESCA
JMJD6	0	.	GRCh37	17	74714927	74714927	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096G>C	p.Glu366Gln	p.E366Q	ENST00000445478	6/7	122	87	35	57	57	0	JMJD6,missense_variant,p.Glu366Gln,ENST00000445478,;JMJD6,missense_variant,p.Glu366Gln,ENST00000397625,;JMJD6,synonymous_variant,p.%3D,ENST00000585429,;JMJD6,3_prime_UTR_variant,,ENST00000542934,;JMJD6,3_prime_UTR_variant,,ENST00000303996,;JMJD6,non_coding_transcript_exon_variant,,ENST00000591460,;JMJD6,non_coding_transcript_exon_variant,,ENST00000589982,;	G	ENSG00000070495	ENST00000445478	Transcript	missense_variant	1300	1096	366	E/Q	Gag/Cag	.	.	.	-1	JMJD6	HGNC	19355	protein_coding	YES	CCDS42383.1	ENSP00000394085	JMJD6_HUMAN	.	UPI00003DFD0B	.	tolerated(0.26)	benign(0.257)	6/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12480:SF5,hmmpanther:PTHR12480	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGGATC	.	5	ESCA
TP53	0	.	GRCh37	17	7577114	7577114	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	8/11	342	179	162	295	295	0	TP53,missense_variant,p.Cys275Phe,ENST00000420246,;TP53,missense_variant,p.Cys275Phe,ENST00000269305,;TP53,missense_variant,p.Cys143Phe,ENST00000509690,;TP53,missense_variant,p.Cys275Phe,ENST00000359597,;TP53,missense_variant,p.Cys275Phe,ENST00000445888,;TP53,missense_variant,p.Cys275Phe,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1014	824	275	C/F	tGt/tTt	CM951234,CM076568,TP53_g.13804G>A,TP53_g.13804del,TP53_g.13804G>C,TP53_g.13804G>T,COSM10701,COSM10893,COSM45413,COSM44178,COSM165084,COSM99932,COSM1167915,COSM318164,COSM3403255,COSM3723938,COSM1637959,COSM2744531,COSM1728541	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.983)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.C275F|c.824G>T|10,SITE|p.C275F|c.824G>T|43,SITE|p.C275F|c.824G>T|5,CODON|p.0?|c.1_1182del1182|6,CODON|p.C275C|c.825T>C|4,CODON|p.C275W|c.825T>G|8,CODON|p.C275*|c.825T>A|3,CODON|p.C275S|c.824G>C|4,CODON|p.C275Y|c.824G>A|5,CODON|p.C275Y|c.824G>A|54,CODON|p.C275Y|c.824G>A|5,CODON|p.C275Y|c.824G>A|11,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278fs*67|c.833delC|3,BUFFER|p.P278F|c.832_833CC>TT|3,BUFFER|p.P278H|c.833C>A|15,BUFFER|p.P278R|c.833C>G|5,BUFFER|p.P278R|c.833C>G|30,BUFFER|p.P278R|c.833C>G|3,BUFFER|p.P278H|c.833C>A|3,BUFFER|p.P278L|c.833C>T|3,BUFFER|p.P278L|c.833C>T|11,BUFFER|p.P278L|c.833C>T|65,BUFFER|p.P278L|c.833C>T|8,BUFFER|p.P278fs*67|c.832delC|3,BUFFER|p.P278T|c.832C>A|29,BUFFER|p.P278A|c.832C>G|25,BUFFER|p.P278T|c.832C>A|8,BUFFER|p.P278A|c.832C>G|4,BUFFER|p.P278A|c.832C>G|10,BUFFER|p.P278S|c.832C>T|4,BUFFER|p.P278S|c.832C>T|3,BUFFER|p.P278S|c.832C>T|8,BUFFER|p.P278S|c.832C>T|55,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273L|c.818G>T|98,BUFFER|p.R273P|c.818G>C|4,BUFFER|p.R273H|c.818G>A|116,BUFFER|p.R273H|c.818G>A|64,BUFFER|p.R273H|c.818G>A|588,BUFFER|p.R273L|c.818G>T|5,BUFFER|p.R273H|c.818G>A|83,BUFFER|p.R273P|c.818G>C|29,BUFFER|p.R273L|c.818G>T|18,BUFFER|p.R273L|c.818G>T|12,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCACAAACA	.	5	ESCA
TP53	0	.	GRCh37	17	7577547	7577547	+	Missense_Mutation	SNP	C	C	A	rs121912656	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	7/11	234	125	109	195	195	0	TP53,missense_variant,p.Gly245Val,ENST00000413465,;TP53,missense_variant,p.Gly245Val,ENST00000420246,;TP53,missense_variant,p.Gly245Val,ENST00000269305,;TP53,missense_variant,p.Gly113Val,ENST00000509690,;TP53,missense_variant,p.Gly245Val,ENST00000359597,;TP53,missense_variant,p.Gly152Val,ENST00000514944,;TP53,missense_variant,p.Gly245Val,ENST00000445888,;TP53,missense_variant,p.Gly245Val,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	924	734	245	G/V	gGc/gTc	CM010464,CM900209,rs121912656,TP53_g.13371G>C,TP53_g.13371del,TP53_g.13371G>A,TP53_g.13371G>T,COSM43606,COSM11196,COSM43965,COSM45770,COSM179806,COSM131475,COSM3388184,COSM179805,COSM3388187,COSM131476,COSM3388189,COSM3717638,COSM3388186,COSM1640832,COSM3388185,COSM1646856,COSM179807,COSM131477,COSM3388188	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G245V|c.734G>T|3,SITE|p.G152V|c.455G>T|15,SITE|p.G245V|c.734G>T|10,SITE|p.G245V|c.734G>T|15,SITE|p.G245V|c.734G>T|69,SITE|p.G245V|c.734G>T|15,CODON|p.0?|c.1_1182del1182|6,CODON|p.G245G|c.735C>T|5,CODON|p.G245D|c.734G>A|10,CODON|p.G245D|c.734G>A|23,CODON|p.G245A|c.734G>C|8,CODON|p.G152D|c.455G>A|23,CODON|p.G245D|c.734G>A|23,CODON|p.G245D|c.734G>A|119,CODON|p.G245D|c.734G>A|7,BUFFER|p.R248Q|c.743_744GG>AA|5,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248R|c.744G>A|5,BUFFER|p.R248W|c.741_742CC>TT|15,BUFFER|p.R248Q|c.743G>A|113,BUFFER|p.R248Q|c.743G>A|633,BUFFER|p.R248L|c.743G>T|7,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|64,BUFFER|p.R155L|c.464G>T|12,BUFFER|p.R155P|c.464G>C|5,BUFFER|p.R248P|c.743G>C|17,BUFFER|p.R248L|c.743G>T|12,BUFFER|p.R248Q|c.743G>A|42,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248L|c.743G>T|74,BUFFER|p.R155Q|c.464G>A|114,BUFFER|p.R248P|c.743G>C|5,BUFFER|p.R248Q|c.743G>A|110,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87,BUFFER|p.N247N|c.741C>T|10,BUFFER|p.N247I|c.740A>T|7,BUFFER|p.N154I|c.461A>T|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247T|c.740A>C|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247S|c.740A>G|7,BUFFER|p.N247D|c.739A>G|5,BUFFER|p.N247Y|c.739A>T|3,BUFFER|p.M153I|c.459G>C|3,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>A|21,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>C|4,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246R|c.737T>G|12,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246T|c.737T>C|8,BUFFER|p.M153R|c.458T>G|3,BUFFER|p.M246K|c.737T>A|7,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246L|c.736A>T|3,BUFFER|p.M153V|c.457A>G|7,BUFFER|p.M246V|c.736A>G|3,BUFFER|p.M246V|c.736A>G|35,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246V|c.736A>G|4,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245R|c.733G>C|14,BUFFER|p.G245S|c.733G>A|22,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152S|c.454G>A|56,BUFFER|p.G245C|c.733G>T|4,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245S|c.733G>A|340,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245C|c.733G>T|50,BUFFER|p.G245S|c.733G>A|39,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152C|c.454G>T|6,BUFFER|p.G152R|c.454G>C|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G151G|c.453C>T|3,BUFFER|p.G244G|c.732C>T|8,BUFFER|p.G244G|c.732C>A|6,BUFFER|p.G244fs*3|c.730delG|4,BUFFER|p.G151D|c.452G>A|8,BUFFER|p.G244D|c.731G>A|42,BUFFER|p.G244D|c.731G>A|3,BUFFER|p.G244D|c.731G>A|8,BUFFER|p.G244A|c.731G>C|8,BUFFER|p.G244D|c.731G>A|8,BUFFER|p.G244V|c.731G>T|15,BUFFER|p.G244C|c.730G>T|43,BUFFER|p.G244S|c.730G>A|6,BUFFER|p.G244C|c.730G>T|3,BUFFER|p.G244S|c.730G>A|5,BUFFER|p.G244C|c.730G>T|9,BUFFER|p.G244R|c.730G>C|5,BUFFER|p.G244C|c.730G>T|9,BUFFER|p.G244S|c.730G>A|9,BUFFER|p.G244S|c.730G>A|42,BUFFER|p.G151C|c.451G>T|9,BUFFER|p.G151S|c.451G>A|9,BUFFER|p.G244S|c.730G>A|8,BUFFER|p.G244C|c.730G>T|6,BUFFER|p.M243I|c.729G>A|5,BUFFER|p.M243T|c.728T>C|5,BUFFER|p.N239_C242delNSSC|c.715_726del12|3,BUFFER|p.M243L|c.727A>C|4,BUFFER|p.M243V|c.727A>G|3,BUFFER|p.M243L|c.727A>T|6,BUFFER|p.C242W|c.726C>G|3,BUFFER|p.C242*|c.726C>A|3,BUFFER|p.C242W|c.726C>G|3,BUFFER|p.C242W|c.726C>G|9,BUFFER|p.C149W|c.447C>G|3,BUFFER|p.C242S|c.725G>C|3,BUFFER|p.C242Y|c.725G>A|4,BUFFER|p.C242S|c.725G>C|4,BUFFER|p.C242Y|c.725G>A|42,BUFFER|p.C242Y|c.725G>A|4,BUFFER|p.C242F|c.725G>T|11,BUFFER|p.C149Y|c.446G>A|4,BUFFER|p.C242F|c.725G>T|11,BUFFER|p.C242S|c.725G>C|3,BUFFER|p.C242F|c.725G>T|71,BUFFER|p.C149S|c.446G>C|4,BUFFER|p.C149F|c.446G>T|11,BUFFER|p.C242F|c.725G>T|4,BUFFER|p.C242S|c.725G>C|20,BUFFER|p.C242S|c.725G>C|4,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.C149fs*5|c.444delC|5,BUFFER|p.C242fs*5|c.723delC|12,BUFFER|p.S241delS|c.721_723delTCC|3,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.S241F|c.722_723CC>TT|5,BUFFER|p.C242G|c.724T>G|6,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C149G|c.445T>G|3,BUFFER|p.C242S|c.724T>A|11,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242R|c.724T>C|12,BUFFER|p.C242fs*5|c.722delC|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATGCCGCCC	byCluster	5	ESCA
TBC1D16	0	.	GRCh37	17	77916004	77916004	+	Missense_Mutation	SNP	G	G	T	rs368445644	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1910C>A	p.Thr637Lys	p.T637K	ENST00000310924	11/12	48	11	37	12	12	0	TBC1D16,missense_variant,p.Thr275Lys,ENST00000340848,;TBC1D16,missense_variant,p.Thr262Lys,ENST00000576768,;TBC1D16,missense_variant,p.Thr637Lys,ENST00000310924,;TBC1D16,downstream_gene_variant,,ENST00000570373,;TBC1D16,downstream_gene_variant,,ENST00000572862,;	T	ENSG00000167291	ENST00000310924	Transcript	missense_variant	2026	1910	637	T/K	aCg/aAg	rs368445644	.	.	-1	TBC1D16	HGNC	28356	protein_coding	YES	CCDS11766.1	ENSP00000309794	TBC16_HUMAN	I3L0U9_HUMAN,B9A6L7_HUMAN	UPI000006DDA6	.	deleterious(0)	probably_damaging(0.991)	11/12	.	Superfamily_domains:SSF47923,SMART_domains:SM00164,Pfam_domain:PF00566,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF191	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCCGTCTGT	byFrequency|byCluster	5	ESCA
ALOX15B	0	.	GRCh37	17	7942415	7942415	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-59G>T	.	.	ENST00000380183	1/14	25	16	9	22	22	0	ALOX15B,5_prime_UTR_variant,,ENST00000380183,;ALOX15B,5_prime_UTR_variant,,ENST00000572022,;ALOX15B,5_prime_UTR_variant,,ENST00000380173,;ALOX15B,upstream_gene_variant,,ENST00000573359,;snoU13,upstream_gene_variant,,ENST00000459145,;ALOX15B,upstream_gene_variant,,ENST00000571240,;	T	ENSG00000179593	ENST00000380183	Transcript	5_prime_UTR_variant	81	.	.	.	.	.	.	.	1	ALOX15B	HGNC	434	protein_coding	YES	CCDS11128.1	ENSP00000369530	LX15B_HUMAN	.	UPI0000140991	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCCAGGGGGG	.	3	ESCA
VAMP2	0	.	GRCh37	17	8063738	8063738	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*435C>T	.	.	ENST00000316509	5/5	20	12	8	20	20	0	VAMP2,3_prime_UTR_variant,,ENST00000316509,;VAMP2,3_prime_UTR_variant,,ENST00000404970,;RP11-599B13.6,intron_variant,,ENST00000498285,;VAMP2,downstream_gene_variant,,ENST00000488857,;PER1,upstream_gene_variant,,ENST00000354903,;PER1,upstream_gene_variant,,ENST00000584202,;VAMP2,downstream_gene_variant,,ENST00000481878,;PER1,upstream_gene_variant,,ENST00000577253,;PER1,upstream_gene_variant,,ENST00000581395,;	A	ENSG00000220205	ENST00000316509	Transcript	3_prime_UTR_variant	882	.	.	.	.	.	.	.	-1	VAMP2	HGNC	12643	protein_coding	YES	CCDS32561.1	ENSP00000314214	VAMP2_HUMAN	.	UPI00000527F8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGAGGGAGC	.	2	ESCA
ZNF750	0	.	GRCh37	17	80789738	80789738	+	Nonsense_Mutation	SNP	G	G	T	rs750618427	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.593C>A	p.Ser198Ter	p.S198*	ENST00000269394	2/3	16	3	12	24	24	0	ZNF750,stop_gained,p.Ser198Ter,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	T	ENSG00000141579	ENST00000269394	Transcript	stop_gained	1427	593	198	S/*	tCg/tAg	rs750618427	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCCGACTTG	byFrequency	5	ESCA
PIK3R6	0	.	GRCh37	17	8736255	8736255	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753G>A	p.%3D	p.L251L	ENST00000311434	9/21	36	18	17	57	57	0	PIK3R6,synonymous_variant,p.%3D,ENST00000311434,;PIK3R6,non_coding_transcript_exon_variant,,ENST00000434064,;PIK3R6,3_prime_UTR_variant,,ENST00000583984,;PIK3R6,intron_variant,,ENST00000452122,;	T	ENSG00000174083	ENST00000311434	Transcript	synonymous_variant	993	753	251	L	ctG/ctA	.	.	.	-1	PIK3R6	HGNC	27101	protein_coding	YES	.	ENSP00000475670	PI3R6_HUMAN	U3KQ99_HUMAN	UPI00015DFB1F	.	.	.	9/21	.	hmmpanther:PTHR15593,hmmpanther:PTHR15593:SF1,Pfam_domain:PF10486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCCAGCCT	.	5	ESCA
USP43	0	.	GRCh37	17	9604869	9604869	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1863G>A	p.%3D	p.Q621Q	ENST00000285199	12/15	18	9	8	16	16	0	USP43,synonymous_variant,p.%3D,ENST00000574408,;USP43,synonymous_variant,p.%3D,ENST00000570475,;USP43,synonymous_variant,p.%3D,ENST00000285199,;USP43,synonymous_variant,p.%3D,ENST00000573955,;USP43,non_coding_transcript_exon_variant,,ENST00000570827,;	A	ENSG00000154914	ENST00000285199	Transcript	synonymous_variant	1959	1863	621	Q	caG/caA	.	.	.	1	USP43	HGNC	20072	protein_coding	YES	CCDS45610.1	ENSP00000285199	UBP43_HUMAN	.	UPI0000047AFB	.	.	.	12/15	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF408,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCAGAGAAG	.	5	ESCA
CXADRP3	0	.	GRCh37	18	14478919	14478919	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.990C>A	.	.	ENST00000581457	4/4	49	26	22	23	23	0	CXADRP3,non_coding_transcript_exon_variant,,ENST00000581457,;	T	ENSG00000265766	ENST00000581457	Transcript	non_coding_transcript_exon_variant	990	.	.	.	.	.	.	.	-1	CXADRP3	HGNC	33974	lincRNA	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGTGCCAAT	.	5	ESCA
GREB1L	0	.	GRCh37	18	19020304	19020304	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>T	p.Gly342Cys	p.G342C	ENST00000580732	9/33	82	41	40	47	47	0	GREB1L,missense_variant,p.Gly342Cys,ENST00000269218,;GREB1L,missense_variant,p.Gly342Cys,ENST00000424526,;GREB1L,missense_variant,p.Gly342Cys,ENST00000400483,;GREB1L,missense_variant,p.Gly342Cys,ENST00000580732,;GREB1L,missense_variant,p.Gly342Cys,ENST00000431264,;GREB1L,missense_variant,p.Gly183Cys,ENST00000579454,;RP11-296E23.1,intron_variant,,ENST00000584611,;GREB1L,non_coding_transcript_exon_variant,,ENST00000578368,;GREB1L,non_coding_transcript_exon_variant,,ENST00000584446,;	T	ENSG00000141449	ENST00000580732	Transcript	missense_variant	1405	1024	342	G/C	Ggc/Tgc	.	.	.	1	GREB1L	HGNC	31042	protein_coding	YES	CCDS45836.1	ENSP00000464162	GRB1L_HUMAN	.	UPI0001642876	.	deleterious(0)	possibly_damaging(0.678)	9/33	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15720:SF12,hmmpanther:PTHR15720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCTGGCTTA	.	5	ESCA
CDH2	0	.	GRCh37	18	25543357	25543357	+	Silent	SNP	G	G	T	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2478C>A	p.%3D	p.A826A	ENST00000269141	15/16	26	23	3	29	29	0	CDH2,synonymous_variant,p.%3D,ENST00000399380,;CDH2,synonymous_variant,p.%3D,ENST00000269141,;AC015933.2,non_coding_transcript_exon_variant,,ENST00000423367,;	T	ENSG00000170558	ENST00000269141	Transcript	synonymous_variant	2902	2478	826	A	gcC/gcA	COSM127596	.	.	-1	CDH2	HGNC	1759	protein_coding	YES	CCDS11891.1	ENSP00000269141	CADH2_HUMAN	C9JMH2_HUMAN,C9J126_HUMAN	UPI000013D7FD	.	.	.	15/16	.	hmmpanther:PTHR24027:SF79,hmmpanther:PTHR24027,Gene3D:4.10.900.10,Pfam_domain:PF01049	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGTGGGGCTGC	.	3	ESCA
NDC80	0	.	GRCh37	18	2590098	2590098	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.952G>T	p.Glu318Ter	p.E318*	ENST00000261597	10/17	49	34	15	32	32	0	NDC80,stop_gained,p.Glu318Ter,ENST00000261597,;KATNBL1P3,downstream_gene_variant,,ENST00000443475,;	T	ENSG00000080986	ENST00000261597	Transcript	stop_gained	1134	952	318	E/*	Gag/Tag	.	.	.	1	NDC80	HGNC	16909	protein_coding	YES	CCDS11827.1	ENSP00000261597	NDC80_HUMAN	A8K031_HUMAN	UPI0000073C92	.	.	.	10/17	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10643:SF2,hmmpanther:PTHR10643	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTGGAGTCT	.	5	ESCA
SETBP1	0	.	GRCh37	18	42456562	42456562	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.540+7314G>A	.	.	ENST00000282030	.	55	6	48	87	87	0	SETBP1,synonymous_variant,p.%3D,ENST00000426838,;SETBP1,intron_variant,,ENST00000282030,;	A	ENSG00000152217	ENST00000282030	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SETBP1	HGNC	15573	protein_coding	YES	CCDS11923.2	ENSP00000282030	SETBP_HUMAN	K7ES17_HUMAN	UPI0000201C54	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAAGAGAAG	.	5	ESCA
LOXHD1	0	.	GRCh37	18	44125297	44125297	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.269G>C	p.Gly90Ala	p.G90A	ENST00000300591	5/24	38	8	30	72	72	0	LOXHD1,missense_variant,p.Gly90Ala,ENST00000582408,;LOXHD1,missense_variant,p.Gly90Ala,ENST00000300591,;LOXHD1,missense_variant,p.Gly995Ala,ENST00000441551,;LOXHD1,missense_variant,p.Gly134Ala,ENST00000441893,;LOXHD1,missense_variant,p.Gly1201Ala,ENST00000536736,;LOXHD1,missense_variant,p.Gly923Ala,ENST00000398722,;LOXHD1,5_prime_UTR_variant,,ENST00000579038,;LOXHD1,downstream_gene_variant,,ENST00000419859,;LOXHD1,missense_variant,p.Gly103Ala,ENST00000536111,;LOXHD1,non_coding_transcript_exon_variant,,ENST00000335730,;	G	ENSG00000167210	ENST00000300591	Transcript	missense_variant	683	269	90	G/A	gGc/gCc	.	.	.	-1	LOXHD1	HGNC	26521	protein_coding	YES	CCDS45861.1	ENSP00000300591	LOXH1_HUMAN	C9J269_HUMAN,C9IYQ1_HUMAN	UPI0000456B8D	.	deleterious(0)	probably_damaging(1)	5/24	.	PROSITE_profiles:PS50095,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF110,Gene3D:2.60.60.20,Pfam_domain:PF01477,SMART_domains:SM00308,Superfamily_domains:SSF49723	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGCCAAAG	.	5	ESCA
DHPS	0	.	GRCh37	19	12792434	12792434	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147C>A	p.Phe49Leu	p.F49L	ENST00000210060	1/9	50	27	23	45	45	0	DHPS,missense_variant,p.Phe49Leu,ENST00000210060,;DHPS,missense_variant,p.Phe49Leu,ENST00000351660,;DHPS,upstream_gene_variant,,ENST00000594424,;DHPS,upstream_gene_variant,,ENST00000597152,;DHPS,upstream_gene_variant,,ENST00000600864,;DHPS,upstream_gene_variant,,ENST00000598246,;DHPS,upstream_gene_variant,,ENST00000596162,;CTD-2192J16.26,downstream_gene_variant,,ENST00000593554,;DHPS,upstream_gene_variant,,ENST00000599481,;DHPS,missense_variant,p.Phe49Leu,ENST00000595912,;DHPS,missense_variant,p.Phe49Leu,ENST00000601639,;DHPS,missense_variant,p.Phe49Leu,ENST00000595100,;DHPS,missense_variant,p.Phe49Leu,ENST00000601537,;DHPS,non_coding_transcript_exon_variant,,ENST00000593473,;DHPS,upstream_gene_variant,,ENST00000598850,;DHPS,upstream_gene_variant,,ENST00000593400,;DHPS,upstream_gene_variant,,ENST00000593432,;DHPS,upstream_gene_variant,,ENST00000600510,;DHPS,upstream_gene_variant,,ENST00000596847,;DHPS,upstream_gene_variant,,ENST00000600451,;DHPS,upstream_gene_variant,,ENST00000593423,;DHPS,upstream_gene_variant,,ENST00000595844,;	T	ENSG00000095059	ENST00000210060	Transcript	missense_variant	283	147	49	F/L	ttC/ttA	COSM3796641,COSM3822008,COSM3822009	.	.	-1	DHPS	HGNC	2869	protein_coding	YES	CCDS12276.1	ENSP00000210060	DHYS_HUMAN	M0R1T2_HUMAN	UPI00001293B4	.	tolerated(0.28)	benign(0.004)	1/9	.	hmmpanther:PTHR11703,Pfam_domain:PF01916,Gene3D:1rozA00,TIGRFAM_domain:TIGR00321,Superfamily_domains:SSF52467	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCGAAGGC	.	5	ESCA
EMR3	0	.	GRCh37	19	14740853	14740853	+	Missense_Mutation	SNP	G	G	T	rs550899495	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1810C>A	p.Gln604Lys	p.Q604K	ENST00000253673	14/16	28	13	15	23	23	0	EMR3,missense_variant,p.Gln604Lys,ENST00000253673,;EMR3,missense_variant,p.Gln389Lys,ENST00000599900,;EMR3,missense_variant,p.Gln552Lys,ENST00000344373,;EMR3,missense_variant,p.Gln478Lys,ENST00000443157,;	T	ENSG00000131355	ENST00000253673	Transcript	missense_variant	1911	1810	604	Q/K	Cag/Aag	rs550899495	.	.	-1	EMR3	HGNC	23647	protein_coding	YES	CCDS12315.1	ENSP00000253673	EMR3_HUMAN	M0R1G2_HUMAN	UPI0000456C29	.	deleterious(0.02)	probably_damaging(0.993)	14/16	.	Superfamily_domains:SSF81321,PROSITE_patterns:PS00650,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF178	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTGCTGGC	by1000G	5	ESCA
NOTCH3	0	.	GRCh37	19	15285174	15285174	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4441G>T	p.Asp1481Tyr	p.D1481Y	ENST00000263388	25/33	35	22	12	28	28	0	NOTCH3,missense_variant,p.Asp1481Tyr,ENST00000263388,;NOTCH3,downstream_gene_variant,,ENST00000601011,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,;NOTCH3,upstream_gene_variant,,ENST00000595514,;	A	ENSG00000074181	ENST00000263388	Transcript	missense_variant	4517	4441	1481	D/Y	Gac/Tac	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	deleterious(0)	probably_damaging(0.997)	25/33	.	Superfamily_domains:0042228,SMART_domains:SM00004,PIRSF_domain:PIRSF002279,Pfam_domain:PF00066,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50258	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGTCGGCAA	.	5	ESCA
IL12RB1	0	.	GRCh37	19	18170809	18170809	+	Silent	SNP	G	G	T	rs772945592	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1878C>A	p.%3D	p.G626G	ENST00000600835	17/18	32	22	10	23	23	0	IL12RB1,synonymous_variant,p.%3D,ENST00000593993,;IL12RB1,synonymous_variant,p.%3D,ENST00000600835,;	T	ENSG00000096996	ENST00000600835	Transcript	synonymous_variant	2177	1878	626	G	ggC/ggA	rs772945592	.	.	-1	IL12RB1	HGNC	5971	protein_coding	YES	CCDS54232.1	ENSP00000470788	I12R1_HUMAN	M0R382_HUMAN,M0QX06_HUMAN	UPI00000502CE	.	.	.	17/18	.	hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	CTCTCGCCTTT	byFrequency	3	ESCA
THOP1	0	.	GRCh37	19	2810172	2810172	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1456-130G>T	.	.	ENST00000307741	.	20	8	12	8	8	0	THOP1,5_prime_UTR_variant,,ENST00000395212,;THOP1,5_prime_UTR_variant,,ENST00000587468,;THOP1,intron_variant,,ENST00000590970,;THOP1,intron_variant,,ENST00000307741,;THOP1,intron_variant,,ENST00000587401,;THOP1,intron_variant,,ENST00000586677,;THOP1,intron_variant,,ENST00000591363,;THOP1,intron_variant,,ENST00000591149,;THOP1,intron_variant,,ENST00000592639,;THOP1,intron_variant,,ENST00000590533,;THOP1,intron_variant,,ENST00000589087,;	T	ENSG00000172009	ENST00000307741	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	THOP1	HGNC	11793	protein_coding	YES	CCDS12095.1	ENSP00000304467	THOP1_HUMAN	Q9BW75_HUMAN,K7EKB6_HUMAN,K7EIK4_HUMAN	UPI0000000C3E	.	.	.	.	9/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGTGGGAGG	.	2	ESCA
SYCN	0	.	GRCh37	19	39694850	39694850	+	Silent	SNP	G	G	A	rs374627027	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45C>T	p.%3D	p.S15S	ENST00000318438	1/2	19	12	7	15	15	0	SYCN,synonymous_variant,p.%3D,ENST00000318438,;NCCRP1,downstream_gene_variant,,ENST00000339852,;	A	ENSG00000179751	ENST00000318438	Transcript	synonymous_variant	57	45	15	S	tcC/tcT	rs374627027	.	.	-1	SYCN	HGNC	18442	protein_coding	YES	CCDS46070.1	ENSP00000325564	SYCN_HUMAN	.	UPI000022A840	.	.	.	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR17503,hmmpanther:PTHR17503:SF0	C:0.0032	C:0	C:0.0014	.	C:0.0129	C:0	C:0.002	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCACGGAGGC	byFrequency|byCluster|by1000G	5	ESCA
ZNF780A	0	.	GRCh37	19	40581754	40581754	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598G>T	p.Gly200Trp	p.G200W	ENST00000455521	6/6	70	39	31	53	53	0	ZNF780A,missense_variant,p.Gly200Trp,ENST00000594395,;ZNF780A,missense_variant,p.Gly199Trp,ENST00000340963,;ZNF780A,missense_variant,p.Gly165Trp,ENST00000450241,;ZNF780A,missense_variant,p.Gly199Trp,ENST00000595687,;ZNF780A,missense_variant,p.Gly200Trp,ENST00000455521,;ZNF780A,intron_variant,,ENST00000414720,;ZNF780A,downstream_gene_variant,,ENST00000595773,;ZNF780A,downstream_gene_variant,,ENST00000599972,;AC005614.5,intron_variant,,ENST00000595508,;ZNF780A,downstream_gene_variant,,ENST00000601688,;ZNF780A,downstream_gene_variant,,ENST00000601715,;ZNF780A,downstream_gene_variant,,ENST00000599368,;	A	ENSG00000197782	ENST00000455521	Transcript	missense_variant	746	598	200	G/W	Ggg/Tgg	.	.	.	-1	ZNF780A	HGNC	27603	protein_coding	YES	CCDS46079.1	ENSP00000400997	Z780A_HUMAN	.	UPI0001881B53	.	deleterious(0.02)	probably_damaging(0.999)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF124,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCCACACT	.	5	ESCA
SPTBN4	0	.	GRCh37	19	41025381	41025381	+	Missense_Mutation	SNP	G	G	T	rs756914383	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2977G>T	p.Val993Leu	p.V993L	ENST00000352632	16/36	47	21	25	56	56	0	SPTBN4,missense_variant,p.Val993Leu,ENST00000338932,;SPTBN4,missense_variant,p.Val993Leu,ENST00000352632,;SPTBN4,missense_variant,p.Val993Leu,ENST00000598249,;SPTBN4,missense_variant,p.Val993Leu,ENST00000595535,;SPTBN4,missense_variant,p.Val993Leu,ENST00000344104,;SPTBN4,missense_variant,p.Val385Leu,ENST00000597389,;	T	ENSG00000160460	ENST00000352632	Transcript	missense_variant	3063	2977	993	V/L	Gtg/Ttg	rs756914383	.	.	1	SPTBN4	HGNC	14896	protein_coding	YES	CCDS12559.1	ENSP00000263373	SPTN4_HUMAN	.	UPI0000135DBB	.	tolerated(0.66)	benign(0.019)	16/36	.	hmmpanther:PTHR11915:SF232,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002297,SMART_domains:SM00150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCACGTGCTG	byFrequency	5	ESCA
CYP2A13	0	.	GRCh37	19	41601712	41601712	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351C>G	p.Leu451Val	p.L451V	ENST00000330436	9/9	112	104	7	84	84	0	CYP2A13,missense_variant,p.Leu451Val,ENST00000330436,;	G	ENSG00000197838	ENST00000330436	Transcript	missense_variant	1351	1351	451	L/V	Ctc/Gtc	.	.	.	1	CYP2A13	HGNC	2608	protein_coding	YES	CCDS12571.1	ENSP00000332679	CP2AD_HUMAN	.	UPI000013E07A	.	deleterious(0.01)	benign(0.029)	9/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF96,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTTCTCTTC	.	2	ESCA
ATP1A3	0	.	GRCh37	19	42474551	42474551	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2446G>T	p.Gly816Cys	p.G816C	ENST00000545399	17/23	56	44	12	55	55	0	ATP1A3,missense_variant,p.Gly773Cys,ENST00000602133,;ATP1A3,missense_variant,p.Gly816Cys,ENST00000545399,;ATP1A3,missense_variant,p.Gly814Cys,ENST00000543770,;ATP1A3,missense_variant,p.Gly803Cys,ENST00000302102,;ATP1A3,missense_variant,p.Gly803Cys,ENST00000441343,;	A	ENSG00000105409	ENST00000545399	Transcript	missense_variant	2600	2446	816	G/C	Ggc/Tgc	.	.	.	-1	ATP1A3	HGNC	801	protein_coding	YES	CCDS58664.1	ENSP00000444688	AT1A3_HUMAN	Q58I21_HUMAN,M0R116_HUMAN,M0QXF2_HUMAN	UPI0001914BDE	.	deleterious(0.05)	probably_damaging(0.986)	17/23	.	Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00689,TIGRFAM_domain:TIGR01106,hmmpanther:PTHR24093:SF259,hmmpanther:PTHR24093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCCCAGAT	.	5	ESCA
PSG11	0	.	GRCh37	19	43514191	43514191	+	Missense_Mutation	SNP	G	G	T	rs201797073	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967C>A	p.Pro323Thr	p.P323T	ENST00000401740	5/6	43	21	22	32	31	1	PSG11,missense_variant,p.Pro201Thr,ENST00000306322,;PSG11,missense_variant,p.Pro201Thr,ENST00000403486,;PSG11,missense_variant,p.Pro323Thr,ENST00000401740,;PSG11,missense_variant,p.Pro323Thr,ENST00000320078,;PSG11,downstream_gene_variant,,ENST00000599976,;PSG11,splice_region_variant,,ENST00000593983,;PSG11,non_coding_transcript_exon_variant,,ENST00000593994,;PSG11,downstream_gene_variant,,ENST00000595138,;PSG11,downstream_gene_variant,,ENST00000594655,;	T	ENSG00000243130	ENST00000401740	Transcript	missense_variant	1071	967	323	P/T	Cct/Act	rs201797073,COSM1712444	.	.	-1	PSG11	HGNC	9516	protein_coding	YES	CCDS12614.2	ENSP00000384995	PSG11_HUMAN	.	UPI000004EE8C	.	tolerated(0.09)	benign(0.028)	5/6	.	Superfamily_domains:SSF48726,Gene3D:2.60.40.10,hmmpanther:PTHR19955,hmmpanther:PTHR19955:SF108	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TGGAGGAGCTG	byCluster|by1000G	2	ESCA
CRX	0	.	GRCh37	19	48342913	48342913	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.589C>A	p.Pro197Thr	p.P197T	ENST00000221996	4/4	19	5	13	39	39	0	CRX,missense_variant,p.Pro197Thr,ENST00000539067,;CRX,missense_variant,p.Pro197Thr,ENST00000221996,;TPRX2P,intron_variant,,ENST00000535362,;CRX,downstream_gene_variant,,ENST00000566686,;CRX,upstream_gene_variant,,ENST00000602001,;CRX,downstream_gene_variant,,ENST00000556527,;	A	ENSG00000105392	ENST00000221996	Transcript	missense_variant	795	589	197	P/T	Ccg/Acg	.	.	.	1	CRX	HGNC	2383	protein_coding	YES	CCDS12706.1	ENSP00000221996	CRX_HUMAN	Q0QD45_HUMAN,H3BUU7_HUMAN,A4GUB7_HUMAN	UPI00001284E0	.	tolerated(0.39)	possibly_damaging(0.696)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF271,Pfam_domain:PF03529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCCCCGGCC	.	5	ESCA
LRRC4B	0	.	GRCh37	19	51021614	51021614	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1356C>G	p.Asn452Lys	p.N452K	ENST00000599957	3/3	42	13	28	46	46	0	LRRC4B,missense_variant,p.Asn452Lys,ENST00000599957,;LRRC4B,missense_variant,p.Asn452Lys,ENST00000389201,;LRRC4B,downstream_gene_variant,,ENST00000600381,;ASPDH,upstream_gene_variant,,ENST00000601207,;ASPDH,upstream_gene_variant,,ENST00000598657,;ASPDH,upstream_gene_variant,,ENST00000376916,;ASPDH,upstream_gene_variant,,ENST00000389208,;ASPDH,upstream_gene_variant,,ENST00000597030,;ASPDH,upstream_gene_variant,,ENST00000593569,;ASPDH,upstream_gene_variant,,ENST00000601287,;	C	ENSG00000131409	ENST00000599957	Transcript	missense_variant	1554	1356	452	N/K	aaC/aaG	.	.	.	-1	LRRC4B	HGNC	25042	protein_coding	YES	CCDS42595.1	ENSP00000471502	LRC4B_HUMAN	M0R2G0_HUMAN,A0PJJ4_HUMAN	UPI00000497E7	.	deleterious(0.03)	probably_damaging(0.999)	3/3	.	PROSITE_profiles:PS50835,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF7,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACGTTGAG	.	5	ESCA
SYT3	0	.	GRCh37	19	51133168	51133168	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.935G>C	p.Gly312Ala	p.G312A	ENST00000338916	3/9	60	34	26	67	67	0	SYT3,missense_variant,p.Gly312Ala,ENST00000593901,;SYT3,missense_variant,p.Gly312Ala,ENST00000600079,;SYT3,missense_variant,p.Gly312Ala,ENST00000544769,;SYT3,missense_variant,p.Gly312Ala,ENST00000338916,;SYT3,downstream_gene_variant,,ENST00000598997,;SYT3,upstream_gene_variant,,ENST00000595117,;SYT3,upstream_gene_variant,,ENST00000595557,;	G	ENSG00000213023	ENST00000338916	Transcript	missense_variant	1569	935	312	G/A	gGc/gCc	.	.	.	-1	SYT3	HGNC	11511	protein_coding	YES	CCDS12798.1	ENSP00000340914	SYT3_HUMAN	M0QY70_HUMAN	UPI0000047AEB	.	tolerated(0.15)	benign(0.001)	3/9	.	hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF176,Gene3D:2.60.40.150,Superfamily_domains:SSF49562,Prints_domain:PR00399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGAGCCATAG	.	5	ESCA
ZNF528	0	.	GRCh37	19	52919741	52919741	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1636G>A	p.Glu546Lys	p.E546K	ENST00000360465	7/7	47	20	27	32	32	0	ZNF528,missense_variant,p.Glu546Lys,ENST00000360465,;ZNF528,3_prime_UTR_variant,,ENST00000391788,;ZNF528,downstream_gene_variant,,ENST00000448954,;ZNF528,non_coding_transcript_exon_variant,,ENST00000598479,;ZNF528,downstream_gene_variant,,ENST00000479718,;	A	ENSG00000167555	ENST00000360465	Transcript	missense_variant	2062	1636	546	E/K	Gag/Aag	COSM713016	.	.	1	ZNF528	HGNC	29384	protein_coding	YES	CCDS33091.1	ENSP00000353652	ZN528_HUMAN	C9K0H2_HUMAN	UPI00001B6535	.	deleterious(0.01)	possibly_damaging(0.854)	7/7	.	Superfamily_domains:SSF57667,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24377:SF143,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGAGAGG	.	5	ESCA
ZNF578	0	.	GRCh37	19	52954467	52954467	+	5'Flank	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000421239	.	49	16	32	22	22	0	ZNF534,missense_variant,p.Arg100Leu,ENST00000301085,;ZNF534,missense_variant,p.Arg57Leu,ENST00000432303,;ZNF578,upstream_gene_variant,,ENST00000421239,;ZNF578,upstream_gene_variant,,ENST00000596674,;ZNF578,upstream_gene_variant,,ENST00000596382,;ZNF578,upstream_gene_variant,,ENST00000602221,;ZNF578,upstream_gene_variant,,ENST00000594118,;	T	ENSG00000258405	ENST00000421239	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2362	1	ZNF578	HGNC	26449	protein_coding	YES	CCDS54310.1	ENSP00000459216	ZN578_HUMAN	M0QZV4_HUMAN	UPI000048A457	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGCGCGTCT	.	5	ESCA
ZNF415	0	.	GRCh37	19	53619674	53619674	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.28G>T	p.Asp10Tyr	p.D10Y	ENST00000500065	3/4	55	25	29	29	29	0	ZNF415,missense_variant,p.Asp10Tyr,ENST00000596051,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000595813,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000600574,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000601110,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000500065,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000243643,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000594011,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000597503,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000595193,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000599261,;ZNF415,missense_variant,p.Asp56Tyr,ENST00000595174,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000597748,;ZNF415,5_prime_UTR_variant,,ENST00000440291,;ZNF415,5_prime_UTR_variant,,ENST00000455735,;ZNF415,5_prime_UTR_variant,,ENST00000448501,;ZNF415,5_prime_UTR_variant,,ENST00000421033,;ZNF415,intron_variant,,ENST00000601215,;ZNF415,intron_variant,,ENST00000601493,;ZNF415,non_coding_transcript_exon_variant,,ENST00000602110,;ZNF415,non_coding_transcript_exon_variant,,ENST00000596683,;ZNF415,non_coding_transcript_exon_variant,,ENST00000596106,;ZNF415,non_coding_transcript_exon_variant,,ENST00000594286,;ZNF415,intron_variant,,ENST00000595359,;ZNF415,intron_variant,,ENST00000602024,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000600120,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000598578,;ZNF415,missense_variant,p.Asp10Tyr,ENST00000598024,;ZNF415,3_prime_UTR_variant,,ENST00000597877,;ZNF415,non_coding_transcript_exon_variant,,ENST00000600098,;	A	ENSG00000170954	ENST00000500065	Transcript	missense_variant	362	28	10	D/Y	Gac/Tac	.	.	.	-1	ZNF415	HGNC	20636	protein_coding	YES	CCDS54313.1	ENSP00000439435	ZN415_HUMAN	.	UPI0000E04BC1	.	deleterious(0)	probably_damaging(0.979)	3/4	.	Superfamily_domains:0044637,SMART_domains:SM00349,Pfam_domain:PF01352,hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGTCCCTGA	.	5	ESCA
NLRP12	0	.	GRCh37	19	54297247	54297247	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*56G>A	.	.	ENST00000324134	10/10	44	23	21	40	40	0	NLRP12,3_prime_UTR_variant,,ENST00000391772,;NLRP12,3_prime_UTR_variant,,ENST00000345770,;NLRP12,3_prime_UTR_variant,,ENST00000351894,;NLRP12,3_prime_UTR_variant,,ENST00000535162,;NLRP12,3_prime_UTR_variant,,ENST00000391775,;NLRP12,3_prime_UTR_variant,,ENST00000354278,;NLRP12,3_prime_UTR_variant,,ENST00000324134,;NLRP12,3_prime_UTR_variant,,ENST00000391773,;AC008753.4,downstream_gene_variant,,ENST00000597420,;NLRP12,non_coding_transcript_exon_variant,,ENST00000492915,;	T	ENSG00000142405	ENST00000324134	Transcript	3_prime_UTR_variant	3411	.	.	.	.	.	.	.	-1	NLRP12	HGNC	22938	protein_coding	YES	CCDS12864.1	ENSP00000319377	NAL12_HUMAN	.	UPI00001412CE	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAGCACCCT	.	5	ESCA
LILRB1	0	.	GRCh37	19	55144634	55144634	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1126C>G	p.Gln376Glu	p.Q376E	ENST00000324602	7/15	78	73	5	63	63	0	LILRB1,missense_variant,p.Gln376Glu,ENST00000396317,;LILRB1,missense_variant,p.Gln376Glu,ENST00000448689,;LILRB1,missense_variant,p.Gln376Glu,ENST00000396331,;LILRB1,missense_variant,p.Gln376Glu,ENST00000396315,;LILRB1,missense_variant,p.Gln412Glu,ENST00000427581,;LILRB1,missense_variant,p.Gln376Glu,ENST00000396327,;LILRB1,missense_variant,p.Gln376Glu,ENST00000418536,;LILRB1,missense_variant,p.Gln376Glu,ENST00000434867,;LILRB1,missense_variant,p.Gln376Glu,ENST00000324602,;LILRB1,missense_variant,p.Gln376Glu,ENST00000396332,;LILRB1,missense_variant,p.Gln376Glu,ENST00000396321,;AC009892.10,downstream_gene_variant,,ENST00000456337,;AC009892.1,upstream_gene_variant,,ENST00000578908,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,non_coding_transcript_exon_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,missense_variant,p.Gln376Glu,ENST00000421584,;LILRB1,upstream_gene_variant,,ENST00000480375,;LILRB1,upstream_gene_variant,,ENST00000487425,;	G	ENSG00000104972	ENST00000324602	Transcript	missense_variant	1351	1126	376	Q/E	Caa/Gaa	.	.	.	1	LILRB1	HGNC	6605	protein_coding	YES	CCDS42614.1	ENSP00000315997	LIRB1_HUMAN	.	UPI0000034BFC	.	tolerated(0.31)	benign(0.002)	7/15	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF89,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCTCAAAAA	.	2	ESCA
SUV420H2	0	.	GRCh37	19	55858816	55858816	+	Nonstop_Mutation	SNP	G	G	T	rs557988704	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1388G>T	p.Ter463LeuextTer33	p.*463Lext*33	ENST00000255613	9/9	12	4	8	15	15	0	SUV420H2,stop_lost,p.Ter463LeuextTer33,ENST00000255613,;COX6B2,downstream_gene_variant,,ENST00000326529,;COX6B2,downstream_gene_variant,,ENST00000590900,;COX6B2,downstream_gene_variant,,ENST00000593184,;AC020922.1,downstream_gene_variant,,ENST00000539076,;COX6B2,downstream_gene_variant,,ENST00000588572,;SUV420H2,downstream_gene_variant,,ENST00000402499,;SUV420H2,downstream_gene_variant,,ENST00000460956,;COX6B2,downstream_gene_variant,,ENST00000586191,;SUV420H2,downstream_gene_variant,,ENST00000587442,;COX6B2,downstream_gene_variant,,ENST00000589879,;COX6B2,downstream_gene_variant,,ENST00000588586,;SUV420H2,3_prime_UTR_variant,,ENST00000445196,;SUV420H2,downstream_gene_variant,,ENST00000592631,;SUV420H2,downstream_gene_variant,,ENST00000474492,;SUV420H2,downstream_gene_variant,,ENST00000464185,;SUV420H2,downstream_gene_variant,,ENST00000589338,;SUV420H2,downstream_gene_variant,,ENST00000498738,;CTD-2105E13.6,downstream_gene_variant,,ENST00000591954,;SUV420H2,downstream_gene_variant,,ENST00000468951,;	T	ENSG00000133247	ENST00000255613	Transcript	stop_lost	1636	1388	463	*/L	tGa/tTa	rs557988704	.	.	1	SUV420H2	HGNC	28405	protein_coding	YES	CCDS12922.1	ENSP00000255613	SV422_HUMAN	.	UPI000000DABC	.	.	.	9/9	.	.	A:0.0008	A:0	A:0.0058	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTGTGACAGG	byFrequency|by1000G	3	ESCA
ZNF551	0	.	GRCh37	19	58198238	58198238	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595A>G	p.Thr199Ala	p.T199A	ENST00000282296	3/3	24	8	16	18	18	0	ZNF551,missense_variant,p.Thr199Ala,ENST00000282296,;ZNF551,missense_variant,p.Thr171Ala,ENST00000601064,;ZNF551,missense_variant,p.Thr183Ala,ENST00000356715,;AC003006.7,intron_variant,,ENST00000594684,;ZNF551,intron_variant,,ENST00000596085,;AC003006.7,intron_variant,,ENST00000599221,;ZNF551,downstream_gene_variant,,ENST00000599402,;	G	ENSG00000204519	ENST00000282296	Transcript	missense_variant	780	595	199	T/A	Act/Gct	.	.	.	1	ZNF551	HGNC	25108	protein_coding	YES	CCDS12959.2	ENSP00000282296	ZN551_HUMAN	M0R2M4_HUMAN	UPI000059D7C6	.	tolerated(0.13)	benign(0.005)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF212,hmmpanther:PTHR24387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCCACTCCC	.	5	ESCA
ZSCAN18	0	.	GRCh37	19	58601532	58601532	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271G>T	p.Glu91Ter	p.E91*	ENST00000600404	2/7	37	16	20	28	27	1	ZSCAN18,stop_gained,p.Glu35Ter,ENST00000601144,;ZSCAN18,stop_gained,p.Glu35Ter,ENST00000240727,;ZSCAN18,stop_gained,p.Glu35Ter,ENST00000600897,;ZSCAN18,stop_gained,p.Glu35Ter,ENST00000600845,;ZSCAN18,stop_gained,p.Glu91Ter,ENST00000600404,;ZSCAN18,intron_variant,,ENST00000421612,;ZSCAN18,downstream_gene_variant,,ENST00000595721,;ZSCAN18,upstream_gene_variant,,ENST00000600522,;ZSCAN18,downstream_gene_variant,,ENST00000601063,;ZSCAN18,upstream_gene_variant,,ENST00000433686,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000598497,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000594191,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000600318,;ZNF135,downstream_gene_variant,,ENST00000515535,;ZSCAN18,upstream_gene_variant,,ENST00000596372,;ZSCAN18,upstream_gene_variant,,ENST00000595784,;	A	ENSG00000121413	ENST00000600404	Transcript	stop_gained	301	271	91	E/*	Gag/Tag	COSM1002654,COSM1590348	.	.	-1	ZSCAN18	HGNC	21037	protein_coding	YES	CCDS46214.1	ENSP00000470123	ZSC18_HUMAN	Q69Z04_HUMAN,M0R1U9_HUMAN	UPI00017A6DAF	.	.	.	2/7	.	hmmpanther:PTHR10032:SF6,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGTCTCGGGTT	.	2	ESCA
CCL25	0	.	GRCh37	19	8127175	8127175	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66C>A	.	.	ENST00000390669	5/5	28	15	13	21	21	0	CCL25,3_prime_UTR_variant,,ENST00000253451,;CCL25,3_prime_UTR_variant,,ENST00000390669,;FBN3,downstream_gene_variant,,ENST00000600128,;CCL25,downstream_gene_variant,,ENST00000315626,;FBN3,downstream_gene_variant,,ENST00000601739,;FBN3,downstream_gene_variant,,ENST00000270509,;CCL25,3_prime_UTR_variant,,ENST00000458625,;	A	ENSG00000131142	ENST00000390669	Transcript	3_prime_UTR_variant	569	.	.	.	.	.	.	.	1	CCL25	HGNC	10624	protein_coding	YES	CCDS12194.1	ENSP00000375086	CCL25_HUMAN	.	UPI000013CDD5	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCGCCCTACA	.	5	ESCA
FBN3	0	.	GRCh37	19	8161811	8161811	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5367C>A	p.Cys1789Ter	p.C1789*	ENST00000600128	43/64	15	6	8	19	19	0	FBN3,stop_gained,p.Cys1789Ter,ENST00000600128,;FBN3,stop_gained,p.Cys1789Ter,ENST00000601739,;FBN3,stop_gained,p.Cys1789Ter,ENST00000270509,;FBN3,stop_gained,p.Cys50Ter,ENST00000602121,;	T	ENSG00000142449	ENST00000600128	Transcript	stop_gained	5782	5367	1789	C/*	tgC/tgA	.	.	.	-1	FBN3	HGNC	18794	protein_coding	YES	CCDS12196.1	ENSP00000470498	FBN3_HUMAN	.	UPI000013D88F	.	.	.	43/64	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF0,PROSITE_patterns:PS01186,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,Pfam_domain:PF07645,Gene3D:2.10.25.10,SMART_domains:SM00181,PIRSF_domain:PIRSF036312,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTGCAGCG	.	5	ESCA
MYO1F	0	.	GRCh37	19	8601439	8601439	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1842C>A	p.%3D	p.I614I	ENST00000338257	18/28	61	30	31	56	56	0	MYO1F,synonymous_variant,p.%3D,ENST00000338257,;MYO1F,missense_variant,p.Gln109Lys,ENST00000598005,;MYO1F,non_coding_transcript_exon_variant,,ENST00000597222,;MYO1F,downstream_gene_variant,,ENST00000602136,;	T	ENSG00000142347	ENST00000338257	Transcript	synonymous_variant	2110	1842	614	I	atC/atA	.	.	.	-1	MYO1F	HGNC	7600	protein_coding	YES	CCDS42494.1	ENSP00000344871	MYO1F_HUMAN	Q14779_HUMAN,M0QXU2_HUMAN	UPI00001678F0	.	.	.	18/28	.	Superfamily_domains:SSF52540,SMART_domains:SM00242,Pfam_domain:PF00063,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF288,PROSITE_profiles:PS51456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTGATGTT	.	5	ESCA
PTCHD2	0	.	GRCh37	1	11580782	11580782	+	Missense_Mutation	SNP	G	G	T	rs527845484	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2239G>T	p.Ala747Ser	p.A747S	ENST00000294484	10/21	18	8	9	21	21	0	PTCHD2,missense_variant,p.Ala747Ser,ENST00000389575,;PTCHD2,missense_variant,p.Ala747Ser,ENST00000294484,;	T	ENSG00000204624	ENST00000294484	Transcript	missense_variant	2377	2239	747	A/S	Gcc/Tcc	rs527845484	.	.	1	PTCHD2	HGNC	29251	protein_coding	YES	CCDS41247.1	ENSP00000294484	PTHD2_HUMAN	.	UPI00001C1D7A	.	tolerated(0.06)	possibly_damaging(0.731)	10/21	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10796:SF49,hmmpanther:PTHR10796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCGCCAGC	byCluster	5	ESCA
SPAG17	0	.	GRCh37	1	118584486	118584486	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2994C>A	p.%3D	p.V998V	ENST00000336338	21/49	99	57	42	82	82	0	SPAG17,synonymous_variant,p.%3D,ENST00000336338,;SPAG17,upstream_gene_variant,,ENST00000486589,;SPAG17,upstream_gene_variant,,ENST00000470550,;	T	ENSG00000155761	ENST00000336338	Transcript	synonymous_variant	3060	2994	998	V	gtC/gtA	.	.	.	-1	SPAG17	HGNC	26620	protein_coding	YES	CCDS899.1	ENSP00000337804	SPG17_HUMAN	A7LBF9_HUMAN	UPI00001601FD	.	.	.	21/49	.	hmmpanther:PTHR21963	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTGACTTG	.	5	ESCA
HNRNPCL1	0	.	GRCh37	1	12908313	12908313	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-171G>A	.	.	ENST00000317869	2/2	44	38	6	17	17	0	HNRNPCL1,5_prime_UTR_variant,,ENST00000317869,;	T	ENSG00000179172	ENST00000317869	Transcript	5_prime_UTR_variant	56	.	.	.	.	.	.	.	-1	HNRNPCL1	HGNC	29295	protein_coding	YES	CCDS30591.1	ENSP00000365370	HNRCL_HUMAN	.	UPI0000134525	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCCCAACAA	.	2	ESCA
MCL1	0	.	GRCh37	1	150550893	150550893	+	Missense_Mutation	SNP	T	T	G	rs770153208	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763A>C	p.Ser255Arg	p.S255R	ENST00000369026	2/3	31	19	12	38	38	0	MCL1,missense_variant,p.Ser255Arg,ENST00000369026,;MCL1,intron_variant,,ENST00000307940,;MCL1,non_coding_transcript_exon_variant,,ENST00000464132,;	G	ENSG00000143384	ENST00000369026	Transcript	missense_variant	823	763	255	S/R	Agc/Cgc	rs770153208	.	.	-1	MCL1	HGNC	6943	protein_coding	YES	CCDS957.1	ENSP00000358022	MCL1_HUMAN	B4DG83_HUMAN	UPI000006D775	.	tolerated(0.17)	benign(0.126)	2/3	.	PROSITE_profiles:PS50062,hmmpanther:PTHR11256:SF6,hmmpanther:PTHR11256,PROSITE_patterns:PS01080,Pfam_domain:PF00452,Gene3D:1.10.437.10,SMART_domains:SM00337,Superfamily_domains:SSF56854,Prints_domain:PR01866,Prints_domain:PR01862	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCGCTGAAAA	.	5	ESCA
FLG	0	.	GRCh37	1	152280796	152280796	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6566C>A	p.Ala2189Glu	p.A2189E	ENST00000368799	3/3	232	153	79	186	186	0	FLG,missense_variant,p.Ala2189Glu,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	T	ENSG00000143631	ENST00000368799	Transcript	missense_variant	6602	6566	2189	A/E	gCa/gAa	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	possibly_damaging(0.587)	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S2188R|c.6562A>C|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTGCACTT	.	5	ESCA
SYT11	0	.	GRCh37	1	155829509	155829509	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-44C>A	.	.	ENST00000368324	1/4	44	23	21	38	38	0	SYT11,5_prime_UTR_variant,,ENST00000539162,;SYT11,5_prime_UTR_variant,,ENST00000368324,;GON4L,upstream_gene_variant,,ENST00000437809,;GON4L,upstream_gene_variant,,ENST00000361040,;GON4L,upstream_gene_variant,,ENST00000368331,;GON4L,upstream_gene_variant,,ENST00000271883,;GON4L,upstream_gene_variant,,ENST00000471341,;	A	ENSG00000132718	ENST00000368324	Transcript	5_prime_UTR_variant	210	.	.	.	.	.	.	.	1	SYT11	HGNC	19239	protein_coding	YES	CCDS1122.1	ENSP00000357307	SYT11_HUMAN	B4DK40_HUMAN	UPI00002049CC	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGTCTCACC	.	5	ESCA
KIAA0907	0	.	GRCh37	1	155884149	155884149	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1646-38G>T	.	.	ENST00000368321	.	33	15	18	15	15	0	KIAA0907,3_prime_UTR_variant,,ENST00000368320,;KIAA0907,intron_variant,,ENST00000368321,;RIT1,upstream_gene_variant,,ENST00000368323,;RIT1,upstream_gene_variant,,ENST00000609492,;RIT1,upstream_gene_variant,,ENST00000539040,;RIT1,upstream_gene_variant,,ENST00000368322,;KIAA0907,intron_variant,,ENST00000478002,;KIAA0907,downstream_gene_variant,,ENST00000465953,;KIAA0907,downstream_gene_variant,,ENST00000466520,;RIT1,upstream_gene_variant,,ENST00000461050,;RIT1,upstream_gene_variant,,ENST00000462687,;	A	ENSG00000132680	ENST00000368321	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KIAA0907	HGNC	29145	protein_coding	YES	CCDS30885.1	ENSP00000357304	K0907_HUMAN	.	UPI00001A36E0	.	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCGCCAAGG	.	5	ESCA
FCRL3	0	.	GRCh37	1	157659609	157659609	+	Missense_Mutation	SNP	C	C	G	rs142711385	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1789G>C	p.Ala597Pro	p.A597P	ENST00000368184	10/15	31	20	10	51	51	0	FCRL3,missense_variant,p.Ala597Pro,ENST00000368186,;FCRL3,missense_variant,p.Ala597Pro,ENST00000368184,;RP11-367J7.3,upstream_gene_variant,,ENST00000453692,;FCRL3,non_coding_transcript_exon_variant,,ENST00000494724,;FCRL3,non_coding_transcript_exon_variant,,ENST00000473231,;FCRL3,non_coding_transcript_exon_variant,,ENST00000468507,;FCRL3,non_coding_transcript_exon_variant,,ENST00000480682,;FCRL3,missense_variant,p.Ala597Pro,ENST00000485028,;FCRL3,missense_variant,p.Ala502Pro,ENST00000477837,;FCRL3,missense_variant,p.Ala603Pro,ENST00000492769,;	G	ENSG00000160856	ENST00000368184	Transcript	missense_variant	2081	1789	597	A/P	Gcc/Ccc	rs142711385	.	.	-1	FCRL3	HGNC	18506	protein_coding	YES	CCDS1167.1	ENSP00000357167	FCRL3_HUMAN	R4GNJ6_HUMAN	UPI000006D60E	.	deleterious(0.03)	possibly_damaging(0.643)	10/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF35	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGCGTAAT	byCluster	5	ESCA
FCRL3	0	.	GRCh37	1	157665953	157665953	+	Missense_Mutation	SNP	G	G	T	rs754226096	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009C>A	p.Arg337Ser	p.R337S	ENST00000368184	7/15	31	16	15	50	50	0	FCRL3,missense_variant,p.Arg337Ser,ENST00000368186,;FCRL3,missense_variant,p.Arg337Ser,ENST00000368184,;FCRL3,downstream_gene_variant,,ENST00000496769,;RP11-367J7.3,non_coding_transcript_exon_variant,,ENST00000453692,;FCRL3,non_coding_transcript_exon_variant,,ENST00000494724,;FCRL3,non_coding_transcript_exon_variant,,ENST00000473231,;FCRL3,non_coding_transcript_exon_variant,,ENST00000480682,;FCRL3,downstream_gene_variant,,ENST00000478179,;FCRL3,missense_variant,p.Arg337Ser,ENST00000485028,;FCRL3,missense_variant,p.Arg242Ser,ENST00000477837,;FCRL3,missense_variant,p.Arg337Ser,ENST00000492769,;	T	ENSG00000160856	ENST00000368184	Transcript	missense_variant	1301	1009	337	R/S	Cgt/Agt	rs754226096	.	.	-1	FCRL3	HGNC	18506	protein_coding	YES	CCDS1167.1	ENSP00000357167	FCRL3_HUMAN	R4GNJ6_HUMAN	UPI000006D60E	.	tolerated(0.07)	possibly_damaging(0.626)	7/15	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF35,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAACGCTGGG	byFrequency	5	ESCA
FCRL2	0	.	GRCh37	1	157738276	157738276	+	Missense_Mutation	SNP	C	C	A	rs749857247	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811G>T	p.Gly271Cys	p.G271C	ENST00000361516	5/12	35	22	12	27	27	0	FCRL2,missense_variant,p.Gly271Cys,ENST00000361516,;FCRL2,missense_variant,p.Gly271Cys,ENST00000392274,;FCRL2,intron_variant,,ENST00000368181,;FCRL2,upstream_gene_variant,,ENST00000469986,;FCRL2,non_coding_transcript_exon_variant,,ENST00000368178,;FCRL2,downstream_gene_variant,,ENST00000462774,;	A	ENSG00000132704	ENST00000361516	Transcript	missense_variant	860	811	271	G/C	Ggc/Tgc	rs749857247,COSM168238	.	.	-1	FCRL2	HGNC	14875	protein_coding	YES	CCDS1168.1	ENSP00000355157	FCRL2_HUMAN	.	UPI000006E1F3	.	deleterious(0)	probably_damaging(1)	5/12	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR11481:SF41,hmmpanther:PTHR11481,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGCCGGCAT	byFrequency	5	ESCA
RP5-1182A14.5	0	.	GRCh37	1	16945480	16945480	+	3'Flank	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000607700	.	147	127	19	130	130	0	CROCCP2,non_coding_transcript_exon_variant,,ENST00000540383,;CROCCP2,non_coding_transcript_exon_variant,,ENST00000412962,;RP5-1182A14.5,downstream_gene_variant,,ENST00000607700,;	A	ENSG00000271732	ENST00000607700	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1256	1	RP5-1182A14.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGCCGGCTC	.	4	ESCA
DARS2	0	.	GRCh37	1	173808541	173808541	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.877A>G	p.Ile293Val	p.I293V	ENST00000361951	10/17	38	35	3	45	45	0	DARS2,missense_variant,p.Ile293Val,ENST00000361951,;DARS2,5_prime_UTR_variant,,ENST00000239457,;DARS2,upstream_gene_variant,,ENST00000471476,;	G	ENSG00000117593	ENST00000361951	Transcript	missense_variant	1604	877	293	I/V	Atc/Gtc	.	.	.	1	DARS2	HGNC	25538	protein_coding	YES	CCDS1311.1	ENSP00000355086	SYDM_HUMAN	Q9H9J7_HUMAN	UPI00001C1D5B	.	tolerated(0.28)	benign(0.047)	10/17	.	PROSITE_profiles:PS50862,hmmpanther:PTHR22594,hmmpanther:PTHR22594:SF5,Pfam_domain:PF00152,Gene3D:3.30.930.10,TIGRFAM_domain:TIGR00459,Superfamily_domains:SSF55681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTGGGATCCAG	.	3	ESCA
CACNA1E	0	.	GRCh37	1	181685207	181685207	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1257G>T	p.%3D	p.R419R	ENST00000367573	10/48	52	23	29	36	36	0	CACNA1E,synonymous_variant,p.%3D,ENST00000367567,;CACNA1E,synonymous_variant,p.%3D,ENST00000360108,;CACNA1E,synonymous_variant,p.%3D,ENST00000524607,;CACNA1E,synonymous_variant,p.%3D,ENST00000358338,;CACNA1E,synonymous_variant,p.%3D,ENST00000357570,;CACNA1E,synonymous_variant,p.%3D,ENST00000526775,;CACNA1E,synonymous_variant,p.%3D,ENST00000367570,;CACNA1E,synonymous_variant,p.%3D,ENST00000367573,;	T	ENSG00000198216	ENST00000367573	Transcript	synonymous_variant	1257	1257	419	R	cgG/cgT	.	.	.	1	CACNA1E	HGNC	1392	protein_coding	YES	CCDS55664.1	ENSP00000356545	CAC1E_HUMAN	Q9UN68_HUMAN,Q9NYZ6_HUMAN,Q9NY05_HUMAN,E9PIE8_HUMAN	UPI00004588C2	.	.	.	10/48	.	hmmpanther:PTHR10037:SF57,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGGACAGA	.	5	ESCA
CACNA1E	0	.	GRCh37	1	181688895	181688895	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1647G>A	p.%3D	p.V549V	ENST00000367573	13/48	55	32	23	37	37	0	CACNA1E,synonymous_variant,p.%3D,ENST00000367567,;CACNA1E,synonymous_variant,p.%3D,ENST00000360108,;CACNA1E,synonymous_variant,p.%3D,ENST00000358338,;CACNA1E,synonymous_variant,p.%3D,ENST00000357570,;CACNA1E,synonymous_variant,p.%3D,ENST00000526775,;CACNA1E,synonymous_variant,p.%3D,ENST00000367570,;CACNA1E,synonymous_variant,p.%3D,ENST00000367573,;CACNA1E,downstream_gene_variant,,ENST00000524607,;	A	ENSG00000198216	ENST00000367573	Transcript	synonymous_variant	1647	1647	549	V	gtG/gtA	.	.	.	1	CACNA1E	HGNC	1392	protein_coding	YES	CCDS55664.1	ENSP00000356545	CAC1E_HUMAN	Q9UN68_HUMAN,Q9NYZ6_HUMAN,Q9NY05_HUMAN,E9PIE8_HUMAN	UPI00004588C2	.	.	.	13/48	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,Gene3D:1.20.120.350,hmmpanther:PTHR10037:SF57,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGTGGGCAG	.	5	ESCA
HMCN1	0	.	GRCh37	1	186135324	186135324	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15328G>A	p.Glu5110Lys	p.E5110K	ENST00000271588	99/107	63	42	21	53	53	0	HMCN1,missense_variant,p.Glu5110Lys,ENST00000367492,;HMCN1,missense_variant,p.Glu5110Lys,ENST00000271588,;HMCN1,intron_variant,,ENST00000475585,;	A	ENSG00000143341	ENST00000271588	Transcript	missense_variant	15557	15328	5110	E/K	Gaa/Aaa	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	benign(0.011)	99/107	.	PROSITE_profiles:PS50026,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGAATGT	.	5	ESCA
IGFN1	0	.	GRCh37	1	201187684	201187684	+	Silent	SNP	C	C	A	rs775262317	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9796C>A	p.%3D	p.R3266R	ENST00000335211	18/24	37	6	31	59	59	0	IGFN1,synonymous_variant,p.%3D,ENST00000295591,;IGFN1,synonymous_variant,p.%3D,ENST00000412892,;IGFN1,synonymous_variant,p.%3D,ENST00000335211,;IGFN1,downstream_gene_variant,,ENST00000451870,;RP11-567E21.3,downstream_gene_variant,,ENST00000453155,;IGFN1,3_prime_UTR_variant,,ENST00000437879,;IGFN1,non_coding_transcript_exon_variant,,ENST00000473483,;	A	ENSG00000163395	ENST00000335211	Transcript	synonymous_variant	9926	9796	3266	R	Cgg/Agg	rs775262317	.	.	1	IGFN1	HGNC	24607	protein_coding	YES	CCDS53455.1	ENSP00000334714	IGFN1_HUMAN	.	UPI0001B300F4	.	.	.	18/24	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,Pfam_domain:PF00041,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF145,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGTGCGGCAG	.	5	ESCA
NUAK2	0	.	GRCh37	1	205275371	205275371	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.635G>C	p.Ser212Thr	p.S212T	ENST00000367157	5/7	29	4	25	47	47	0	NUAK2,missense_variant,p.Ser212Thr,ENST00000367157,;	G	ENSG00000163545	ENST00000367157	Transcript	missense_variant	762	635	212	S/T	aGc/aCc	.	.	.	-1	NUAK2	HGNC	29558	protein_coding	YES	CCDS1453.1	ENSP00000356125	NUAK2_HUMAN	Q68E04_HUMAN,B4E0Y5_HUMAN	UPI0000037D77	.	deleterious(0)	probably_damaging(0.997)	5/7	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24343:SF133,hmmpanther:PTHR24343,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGGGGCTCCCA	.	4	ESCA
KIF17	0	.	GRCh37	1	20990952	20990952	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*125C>G	.	.	ENST00000247986	15/15	22	13	9	18	18	0	KIF17,3_prime_UTR_variant,,ENST00000247986,;KIF17,3_prime_UTR_variant,,ENST00000375044,;KIF17,3_prime_UTR_variant,,ENST00000400463,;DDOST,upstream_gene_variant,,ENST00000464364,;DDOST,upstream_gene_variant,,ENST00000375048,;DDOST,upstream_gene_variant,,ENST00000415136,;DDOST,upstream_gene_variant,,ENST00000602624,;KIF17,non_coding_transcript_exon_variant,,ENST00000493818,;KIF17,non_coding_transcript_exon_variant,,ENST00000490034,;KIF17,non_coding_transcript_exon_variant,,ENST00000477167,;KIF17,downstream_gene_variant,,ENST00000462858,;DDOST,upstream_gene_variant,,ENST00000477229,;	C	ENSG00000117245	ENST00000247986	Transcript	3_prime_UTR_variant	3526	.	.	.	.	.	.	.	-1	KIF17	HGNC	19167	protein_coding	YES	CCDS213.1	ENSP00000247986	KIF17_HUMAN	.	UPI0000185F1A	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGGCTGAG	.	5	ESCA
OBSCN	0	.	GRCh37	1	228470840	228470840	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9879G>T	p.Lys3293Asn	p.K3293N	ENST00000570156	37/116	20	8	12	36	36	0	OBSCN,missense_variant,p.Lys140Asn,ENST00000483539,;OBSCN,missense_variant,p.Lys2864Asn,ENST00000284548,;OBSCN,missense_variant,p.Lys1711Asn,ENST00000359599,;OBSCN,missense_variant,p.Lys712Asn,ENST00000366706,;OBSCN,missense_variant,p.Lys3293Asn,ENST00000570156,;OBSCN,missense_variant,p.Lys2864Asn,ENST00000422127,;OBSCN,5_prime_UTR_variant,,ENST00000366707,;OBSCN,5_prime_UTR_variant,,ENST00000366709,;OBSCN,non_coding_transcript_exon_variant,,ENST00000366704,;	T	ENSG00000154358	ENST00000570156	Transcript	missense_variant	9953	9879	3293	K/N	aaG/aaT	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	probably_damaging(0.999)	37/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAGGCCAT	.	5	ESCA
OR2T2	0	.	GRCh37	1	248617052	248617052	+	Silent	SNP	G	G	T	rs200152335	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.954G>T	p.%3D	p.A318A	ENST00000342927	1/1	36	9	27	58	58	0	OR2T2,synonymous_variant,p.%3D,ENST00000342927,;	T	ENSG00000196240	ENST00000342927	Transcript	synonymous_variant	976	954	318	A	gcG/gcT	rs200152335	.	.	1	OR2T2	HGNC	14725	protein_coding	YES	CCDS31116.1	ENSP00000343062	OR2T2_HUMAN	.	UPI0000048DB0	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCGACTGT	byCluster	5	ESCA
LYPD8	0	.	GRCh37	1	248902960	248902960	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.191C>T	p.%3D	p.L64L	ENST00000590317	1/1	42	38	4	59	59	0	LYPD8,synonymous_variant,p.%3D,ENST00000590317,;	A	ENSG00000266949	ENST00000590317	Transcript	synonymous_variant	191	192	64	L	ctC/ctT	.	.	.	-1	LYPD8	HGNC	44208	protein_coding	YES	.	ENSP00000466070	.	.	UPI0002841284	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR20914,hmmpanther:PTHR20914:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTAGAGGGA	.	2	ESCA
PEF1	0	.	GRCh37	1	32098083	32098083	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.625+13G>T	.	.	ENST00000373703	.	41	21	19	39	39	0	HCRTR1,synonymous_variant,p.%3D,ENST00000373705,;PEF1,intron_variant,,ENST00000373703,;PEF1,downstream_gene_variant,,ENST00000440872,;PEF1,intron_variant,,ENST00000461006,;PEF1,intron_variant,,ENST00000489164,;PEF1,intron_variant,,ENST00000478502,;PEF1,downstream_gene_variant,,ENST00000472443,;PEF1,downstream_gene_variant,,ENST00000492061,;HCRTR1,downstream_gene_variant,,ENST00000468521,;PEF1,downstream_gene_variant,,ENST00000471219,;PEF1,downstream_gene_variant,,ENST00000496805,;	A	ENSG00000162517	ENST00000373703	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PEF1	HGNC	30009	protein_coding	YES	CCDS345.1	ENSP00000362807	PEF1_HUMAN	.	UPI00000389E4	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGGCCATGA	.	5	ESCA
CSF3R	0	.	GRCh37	1	36937913	36937913	+	Missense_Mutation	SNP	C	C	G	rs148747030	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.923G>C	p.Arg308Pro	p.R308P	ENST00000373103	8/17	75	40	35	78	78	0	CSF3R,missense_variant,p.Arg308Pro,ENST00000373106,;CSF3R,missense_variant,p.Arg308Pro,ENST00000331941,;CSF3R,missense_variant,p.Arg308Pro,ENST00000361632,;CSF3R,missense_variant,p.Arg308Pro,ENST00000373104,;CSF3R,missense_variant,p.Arg308Pro,ENST00000418048,;CSF3R,missense_variant,p.Arg308Pro,ENST00000338937,;CSF3R,missense_variant,p.Arg308Pro,ENST00000373103,;CSF3R,missense_variant,p.Arg308Pro,ENST00000440588,;CSF3R,upstream_gene_variant,,ENST00000464465,;CSF3R,non_coding_transcript_exon_variant,,ENST00000487540,;CSF3R,downstream_gene_variant,,ENST00000526980,;CSF3R,non_coding_transcript_exon_variant,,ENST00000464365,;CSF3R,non_coding_transcript_exon_variant,,ENST00000480825,;CSF3R,upstream_gene_variant,,ENST00000466138,;CSF3R,upstream_gene_variant,,ENST00000484762,;CSF3R,downstream_gene_variant,,ENST00000469380,;	G	ENSG00000119535	ENST00000373103	Transcript	missense_variant	1471	923	308	R/P	cGc/cCc	rs148747030	.	.	-1	CSF3R	HGNC	2439	protein_coding	YES	CCDS414.1	ENSP00000362195	CSF3R_HUMAN	E9PK56_HUMAN	UPI000002AA5A	.	deleterious(0)	probably_damaging(1)	8/17	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,hmmpanther:PTHR23036:SF75,hmmpanther:PTHR23036,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGCGTATC	byCluster	5	ESCA
POU3F1	0	.	GRCh37	1	38510141	38510141	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*919C>A	.	.	ENST00000373012	1/1	23	13	9	18	18	0	POU3F1,3_prime_UTR_variant,,ENST00000373012,;RP5-884C9.2,upstream_gene_variant,,ENST00000432922,;RP5-884C9.2,upstream_gene_variant,,ENST00000428151,;	T	ENSG00000185668	ENST00000373012	Transcript	3_prime_UTR_variant	2310	.	.	.	.	.	.	.	-1	POU3F1	HGNC	9214	protein_coding	YES	CCDS30679.1	ENSP00000362103	PO3F1_HUMAN	.	UPI00001606D2	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCTGCAGCA	.	5	ESCA
SLC6A9	0	.	GRCh37	1	44476525	44476525	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279G>A	p.%3D	p.K93K	ENST00000360584	3/14	66	60	6	58	58	0	SLC6A9,synonymous_variant,p.%3D,ENST00000357730,;SLC6A9,synonymous_variant,p.%3D,ENST00000372306,;SLC6A9,synonymous_variant,p.%3D,ENST00000528803,;SLC6A9,synonymous_variant,p.%3D,ENST00000466926,;SLC6A9,synonymous_variant,p.%3D,ENST00000372310,;SLC6A9,synonymous_variant,p.%3D,ENST00000360584,;SLC6A9,5_prime_UTR_variant,,ENST00000372307,;SLC6A9,intron_variant,,ENST00000537678,;SLC6A9,intron_variant,,ENST00000475075,;SLC6A9,non_coding_transcript_exon_variant,,ENST00000492434,;SLC6A9,downstream_gene_variant,,ENST00000533007,;SLC6A9,non_coding_transcript_exon_variant,,ENST00000489764,;	T	ENSG00000196517	ENST00000360584	Transcript	synonymous_variant	471	279	93	K	aaG/aaA	.	.	.	-1	SLC6A9	HGNC	11056	protein_coding	YES	CCDS41317.1	ENSP00000353791	SC6A9_HUMAN	B7Z589_HUMAN	UPI000053030B	.	.	.	3/14	.	hmmpanther:PTHR11616:SF110,hmmpanther:PTHR11616,Prints_domain:PR01204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCCTCTTGGT	.	3	ESCA
MROH7	0	.	GRCh37	1	55118958	55118958	+	Missense_Mutation	SNP	G	G	A	rs531104510	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359G>A	p.Arg120His	p.R120H	ENST00000421030	3/24	21	12	9	19	19	0	MROH7,missense_variant,p.Arg120His,ENST00000395690,;MROH7,missense_variant,p.Arg120His,ENST00000421030,;MROH7,missense_variant,p.Arg120His,ENST00000339553,;MROH7,intron_variant,,ENST00000454855,;MROH7,intron_variant,,ENST00000409996,;MROH7,intron_variant,,ENST00000545244,;MROH7,non_coding_transcript_exon_variant,,ENST00000472987,;MROH7,intron_variant,,ENST00000478097,;MROH7-TTC4,missense_variant,p.Arg120His,ENST00000414150,;MROH7,missense_variant,p.Arg120His,ENST00000438846,;MROH7,missense_variant,p.Arg120His,ENST00000413188,;MROH7-TTC4,missense_variant,p.Arg120His,ENST00000425300,;MROH7,missense_variant,p.Arg120His,ENST00000422659,;MROH7,missense_variant,p.Arg120His,ENST00000440047,;MROH7-TTC4,missense_variant,p.Arg120His,ENST00000606515,;MROH7,upstream_gene_variant,,ENST00000440217,;	A	ENSG00000184313	ENST00000421030	Transcript	missense_variant	644	359	120	R/H	cGc/cAc	rs531104510	.	.	1	MROH7	HGNC	24802	protein_coding	YES	CCDS41342.2	ENSP00000396622	MROH7_HUMAN	C9K0L2_HUMAN,B7ZBM2_HUMAN	UPI000198C4E2	.	tolerated_low_confidence(0.13)	benign(0.001)	3/24	.	.	A:0.0004	A:0	A:0	.	A:0.001	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCGCCTCT	byFrequency|by1000G	5	ESCA
PLEKHG5	0	.	GRCh37	1	6534123	6534123	+	Missense_Mutation	SNP	C	C	A	rs527341275	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778G>T	p.Ala260Ser	p.A260S	ENST00000537245	8/22	24	14	10	32	32	0	PLEKHG5,missense_variant,p.Ala181Ser,ENST00000544978,;PLEKHG5,missense_variant,p.Ala181Ser,ENST00000377725,;PLEKHG5,missense_variant,p.Ala181Ser,ENST00000400913,;PLEKHG5,missense_variant,p.Ala258Ser,ENST00000377748,;PLEKHG5,missense_variant,p.Ala250Ser,ENST00000535355,;PLEKHG5,missense_variant,p.Ala258Ser,ENST00000377740,;PLEKHG5,missense_variant,p.Ala181Ser,ENST00000340850,;PLEKHG5,missense_variant,p.Ala237Ser,ENST00000400915,;PLEKHG5,missense_variant,p.Ala181Ser,ENST00000377728,;PLEKHG5,missense_variant,p.Ala218Ser,ENST00000377732,;PLEKHG5,missense_variant,p.Ala181Ser,ENST00000377737,;PLEKHG5,missense_variant,p.Ala260Ser,ENST00000537245,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000489097,;PLEKHG5,upstream_gene_variant,,ENST00000487949,;	A	ENSG00000171680	ENST00000537245	Transcript	missense_variant	843	778	260	A/S	Gcc/Tcc	rs527341275	.	.	-1	PLEKHG5	HGNC	29105	protein_coding	YES	CCDS57969.1	ENSP00000439625	PKHG5_HUMAN	B3KR92_HUMAN	UPI000206539E	.	tolerated(0.47)	benign(0.006)	8/22	.	hmmpanther:PTHR13217,hmmpanther:PTHR13217:SF6	T:0.0010	T:0.0008	T:0	.	T:0	T:0	T:0.0041	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGCGGGGG	byFrequency|by1000G	5	ESCA
NEGR1	0	.	GRCh37	1	72241972	72241972	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418A>C	p.Lys140Gln	p.K140Q	ENST00000357731	3/7	27	11	16	31	31	0	NEGR1,missense_variant,p.Lys140Gln,ENST00000357731,;NEGR1,missense_variant,p.Lys12Gln,ENST00000306821,;NEGR1,missense_variant,p.Lys138Gln,ENST00000434200,;NEGR1,non_coding_transcript_exon_variant,,ENST00000467479,;	G	ENSG00000172260	ENST00000357731	Transcript	missense_variant	658	418	140	K/Q	Aag/Cag	.	.	.	-1	NEGR1	HGNC	17302	protein_coding	YES	CCDS661.1	ENSP00000350364	NEGR1_HUMAN	Q8N440_HUMAN,Q68DZ8_HUMAN	UPI00000477EE	.	tolerated(0.2)	possibly_damaging(0.733)	3/7	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19831:SF11,hmmpanther:PTHR19831,Gene3D:2.60.40.10,Pfam_domain:PF07679,Superfamily_domains:SSF48726,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTTAGGAG	.	5	ESCA
GCLM	0	.	GRCh37	1	94354354	94354354	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*192G>T	.	.	ENST00000370238	7/7	34	18	16	28	28	0	GCLM,3_prime_UTR_variant,,ENST00000370238,;	A	ENSG00000023909	ENST00000370238	Transcript	3_prime_UTR_variant	1264	.	.	.	.	.	.	.	-1	GCLM	HGNC	4312	protein_coding	YES	CCDS746.1	ENSP00000359258	GSH0_HUMAN	M5A959_HUMAN,D3DT44_HUMAN	UPI000000D9B9	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATACAGAGG	.	5	ESCA
TASP1	0	.	GRCh37	20	13539707	13539707	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.623G>T	p.Arg208Met	p.R208M	ENST00000337743	8/14	27	4	23	35	35	0	TASP1,missense_variant,p.Arg208Met,ENST00000337743,;TASP1,missense_variant,p.Arg185Met,ENST00000455532,;TASP1,intron_variant,,ENST00000539805,;TASP1,non_coding_transcript_exon_variant,,ENST00000480436,;TASP1,intron_variant,,ENST00000465381,;	A	ENSG00000089123	ENST00000337743	Transcript	missense_variant	744	623	208	R/M	aGg/aTg	.	.	.	-1	TASP1	HGNC	15859	protein_coding	YES	CCDS13116.1	ENSP00000338624	TASP1_HUMAN	.	UPI00000382E5	.	deleterious(0.01)	benign(0.006)	8/14	.	hmmpanther:PTHR10188,hmmpanther:PTHR10188:SF8,Pfam_domain:PF01112,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCACCCTTTCT	.	3	ESCA
TASP1	0	.	GRCh37	20	13539717	13539717	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.613C>G	p.Leu205Val	p.L205V	ENST00000337743	8/14	27	5	22	36	36	0	TASP1,missense_variant,p.Leu205Val,ENST00000337743,;TASP1,missense_variant,p.Leu182Val,ENST00000455532,;TASP1,intron_variant,,ENST00000539805,;TASP1,non_coding_transcript_exon_variant,,ENST00000480436,;TASP1,intron_variant,,ENST00000465381,;	C	ENSG00000089123	ENST00000337743	Transcript	missense_variant	734	613	205	L/V	Ctg/Gtg	.	.	.	-1	TASP1	HGNC	15859	protein_coding	YES	CCDS13116.1	ENSP00000338624	TASP1_HUMAN	.	UPI00000382E5	.	tolerated(0.09)	benign(0.18)	8/14	.	hmmpanther:PTHR10188,hmmpanther:PTHR10188:SF8,Pfam_domain:PF01112,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCCAGCTCTA	.	3	ESCA
XKR7	0	.	GRCh37	20	30585278	30585278	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*18C>T	.	.	ENST00000562532	3/3	17	11	6	15	15	0	XKR7,3_prime_UTR_variant,,ENST00000562532,;	T	ENSG00000260903	ENST00000562532	Transcript	3_prime_UTR_variant	1932	.	.	.	.	.	.	.	1	XKR7	HGNC	23062	protein_coding	YES	CCDS33459.1	ENSP00000477059	XKR7_HUMAN	.	UPI00004C7A9E	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCACAAAAG	.	5	ESCA
ACTL10	0	.	GRCh37	20	32254766	32254766	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-538G>A	.	.	ENST00000330271	1/1	22	14	8	19	19	0	ACTL10,5_prime_UTR_variant,,ENST00000330271,;NECAB3,intron_variant,,ENST00000375238,;NECAB3,intron_variant,,ENST00000439478,;NECAB3,intron_variant,,ENST00000606690,;NECAB3,intron_variant,,ENST00000246190,;NECAB3,upstream_gene_variant,,ENST00000480994,;NECAB3,downstream_gene_variant,,ENST00000473892,;C20orf144,downstream_gene_variant,,ENST00000375222,;NECAB3,intron_variant,,ENST00000494174,;NECAB3,upstream_gene_variant,,ENST00000498353,;NECAB3,upstream_gene_variant,,ENST00000463246,;NECAB3,upstream_gene_variant,,ENST00000606106,;NECAB3,upstream_gene_variant,,ENST00000485976,;NECAB3,upstream_gene_variant,,ENST00000478237,;NECAB3,upstream_gene_variant,,ENST00000483813,;NECAB3,upstream_gene_variant,,ENST00000606525,;NECAB3,intron_variant,,ENST00000606699,;NECAB3,intron_variant,,ENST00000485399,;NECAB3,intron_variant,,ENST00000607805,;NECAB3,intron_variant,,ENST00000493590,;NECAB3,intron_variant,,ENST00000488489,;NECAB3,downstream_gene_variant,,ENST00000484824,;C20orf144,downstream_gene_variant,,ENST00000607738,;	A	ENSG00000182584	ENST00000330271	Transcript	5_prime_UTR_variant	463	.	.	.	.	.	.	.	1	ACTL10	HGNC	16127	protein_coding	YES	CCDS33463.1	ENSP00000329647	ACL10_HUMAN	.	UPI0000470AC1	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCGGAGGCA	.	5	ESCA
NCOA3	0	.	GRCh37	20	46256687	46256687	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743G>T	p.Cys248Phe	p.C248F	ENST00000371998	8/23	30	14	15	20	20	0	NCOA3,missense_variant,p.Cys248Phe,ENST00000371997,;NCOA3,missense_variant,p.Cys248Phe,ENST00000372004,;NCOA3,missense_variant,p.Cys248Phe,ENST00000341724,;NCOA3,missense_variant,p.Cys248Phe,ENST00000371998,;NCOA3,non_coding_transcript_exon_variant,,ENST00000497292,;NCOA3,downstream_gene_variant,,ENST00000490248,;RP5-1049G16.4,downstream_gene_variant,,ENST00000448675,;	T	ENSG00000124151	ENST00000371998	Transcript	missense_variant	934	743	248	C/F	tGt/tTt	.	.	.	1	NCOA3	HGNC	7670	protein_coding	YES	CCDS13407.1	ENSP00000361066	NCOA3_HUMAN	Q569F6_HUMAN,B4DYT5_HUMAN	UPI000012FE45	.	deleterious(0)	possibly_damaging(0.883)	8/23	.	hmmpanther:PTHR10684:SF3,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTGTGTGG	.	5	ESCA
LAMA5	0	.	GRCh37	20	60895671	60895671	+	Missense_Mutation	SNP	C	C	A	rs763195870	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6703G>T	p.Val2235Leu	p.V2235L	ENST00000252999	50/80	15	11	3	20	20	0	LAMA5,missense_variant,p.Val2235Leu,ENST00000252999,;LAMA5,downstream_gene_variant,,ENST00000497363,;LAMA5,downstream_gene_variant,,ENST00000464134,;LAMA5,upstream_gene_variant,,ENST00000481120,;LAMA5,upstream_gene_variant,,ENST00000471042,;	A	ENSG00000130702	ENST00000252999	Transcript	missense_variant	6770	6703	2235	V/L	Gtg/Ttg	rs763195870	.	.	-1	LAMA5	HGNC	6485	protein_coding	YES	CCDS33502.1	ENSP00000252999	LAMA5_HUMAN	O75079_HUMAN	UPI0000161FDC	.	.	benign(0.001)	50/80	.	hmmpanther:PTHR10574:SF261,hmmpanther:PTHR10574,Pfam_domain:PF06008	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CAGCACCTCCA	byFrequency	4	ESCA
C20orf166	0	.	GRCh37	20	61150722	61150722	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-143C>T	.	.	ENST00000370527	2/4	30	13	16	39	39	0	C20orf166,5_prime_UTR_variant,,ENST00000370524,;C20orf166,5_prime_UTR_variant,,ENST00000370527,;C20orf166,upstream_gene_variant,,ENST00000370523,;MIR1-1,upstream_gene_variant,,ENST00000362147,;C20orf166-AS1,upstream_gene_variant,,ENST00000412495,;C20orf166-AS1,upstream_gene_variant,,ENST00000475015,;C20orf166-AS1,upstream_gene_variant,,ENST00000436101,;	T	ENSG00000174407	ENST00000370527	Transcript	5_prime_UTR_variant	637	.	.	.	.	.	.	.	1	C20orf166	HGNC	16159	protein_coding	YES	CCDS46627.1	ENSP00000359558	CT166_HUMAN	.	UPI000012861B	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGATCCTGAC	.	5	ESCA
BIRC7	0	.	GRCh37	20	61870155	61870155	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.577+189C>T	.	.	ENST00000217169	.	9	5	3	8	8	0	BIRC7,intron_variant,,ENST00000395306,;BIRC7,intron_variant,,ENST00000217169,;BIRC7,intron_variant,,ENST00000342412,;NKAIN4,downstream_gene_variant,,ENST00000370307,;NKAIN4,downstream_gene_variant,,ENST00000370317,;NKAIN4,downstream_gene_variant,,ENST00000370313,;NKAIN4,downstream_gene_variant,,ENST00000370316,;MIR3196,mature_miRNA_variant,,ENST00000579556,;NKAIN4,downstream_gene_variant,,ENST00000466885,;NKAIN4,downstream_gene_variant,,ENST00000470246,;	T	ENSG00000101197	ENST00000217169	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	BIRC7	HGNC	13702	protein_coding	YES	CCDS13513.1	ENSP00000217169	BIRC7_HUMAN	.	UPI00001269A6	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGCCTCCCC	.	2	ESCA
ARFGAP1	0	.	GRCh37	20	61917478	61917478	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.865-246G>C	.	.	ENST00000353546	.	19	11	8	20	20	0	ARFGAP1,synonymous_variant,p.%3D,ENST00000370275,;ARFGAP1,intron_variant,,ENST00000523460,;ARFGAP1,intron_variant,,ENST00000370283,;ARFGAP1,intron_variant,,ENST00000518601,;ARFGAP1,intron_variant,,ENST00000519604,;ARFGAP1,intron_variant,,ENST00000547204,;ARFGAP1,intron_variant,,ENST00000549047,;ARFGAP1,intron_variant,,ENST00000353546,;ARFGAP1,intron_variant,,ENST00000519273,;ARFGAP1,upstream_gene_variant,,ENST00000549076,;ARFGAP1,downstream_gene_variant,,ENST00000522403,;MIR4326,upstream_gene_variant,,ENST00000582203,;ARFGAP1,intron_variant,,ENST00000468975,;ARFGAP1,intron_variant,,ENST00000518618,;ARFGAP1,intron_variant,,ENST00000518794,;ARFGAP1,non_coding_transcript_exon_variant,,ENST00000395285,;ARFGAP1,non_coding_transcript_exon_variant,,ENST00000518691,;ARFGAP1,intron_variant,,ENST00000520485,;ARFGAP1,downstream_gene_variant,,ENST00000520022,;ARFGAP1,downstream_gene_variant,,ENST00000519531,;	C	ENSG00000101199	ENST00000353546	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ARFGAP1	HGNC	15852	protein_coding	YES	CCDS13516.1	ENSP00000314615	ARFG1_HUMAN	F8VWH9_HUMAN,F8VWB3_HUMAN,E5RIU2_HUMAN	UPI000002A3F2	.	.	.	.	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTGGGAGC	.	5	ESCA
BTG3	0	.	GRCh37	21	18981448	18981448	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15T>C	p.%3D	p.I5I	ENST00000339775	2/6	40	23	17	33	33	0	BTG3,synonymous_variant,p.%3D,ENST00000348354,;BTG3,synonymous_variant,p.%3D,ENST00000339775,;BTG3,synonymous_variant,p.%3D,ENST00000457956,;BTG3,non_coding_transcript_exon_variant,,ENST00000464058,;BTG3,upstream_gene_variant,,ENST00000496601,;	G	ENSG00000154640	ENST00000339775	Transcript	synonymous_variant	169	15	5	I	atT/atC	.	.	.	-1	BTG3	HGNC	1132	protein_coding	YES	CCDS46636.1	ENSP00000344609	BTG3_HUMAN	Q9UHB2_HUMAN,C9JLA2_HUMAN	UPI000002A504	.	.	.	2/6	.	hmmpanther:PTHR22978,hmmpanther:PTHR22978:SF24,Pfam_domain:PF07742,SMART_domains:SM00099,Superfamily_domains:SSF160696	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCAATTTC	.	5	ESCA
TFF3	0	.	GRCh37	21	43735501	43735501	+	Missense_Mutation	SNP	G	G	C	rs561102941	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26C>G	p.Pro9Arg	p.P9R	ENST00000518498	1/3	70	33	37	82	82	0	TFF3,missense_variant,p.Pro9Arg,ENST00000518498,;TFF3,missense_variant,p.Pro45Arg,ENST00000291525,;TFF3,upstream_gene_variant,,ENST00000398431,;TFF3,upstream_gene_variant,,ENST00000489676,;	C	ENSG00000160180	ENST00000518498	Transcript	missense_variant	261	26	9	P/R	cCg/cGg	rs561102941	.	.	-1	TFF3	HGNC	11757	protein_coding	YES	CCDS33565.2	ENSP00000430690	TFF3_HUMAN	.	UPI0000206BD4	.	deleterious_low_confidence(0.02)	benign(0.041)	1/3	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR13826:SF5,hmmpanther:PTHR13826	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCGGGACG	by1000G	5	ESCA
PKNOX1	0	.	GRCh37	21	44450342	44450342	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*131G>T	.	.	ENST00000291547	11/11	19	15	4	13	13	0	PKNOX1,3_prime_UTR_variant,,ENST00000432907,;PKNOX1,3_prime_UTR_variant,,ENST00000291547,;PKNOX1,downstream_gene_variant,,ENST00000607150,;PKNOX1,downstream_gene_variant,,ENST00000557820,;PKNOX1,3_prime_UTR_variant,,ENST00000560448,;PKNOX1,downstream_gene_variant,,ENST00000558955,;PKNOX1,downstream_gene_variant,,ENST00000474336,;PKNOX1,downstream_gene_variant,,ENST00000607049,;	T	ENSG00000160199	ENST00000291547	Transcript	3_prime_UTR_variant	1653	.	.	.	.	.	.	.	1	PKNOX1	HGNC	9022	protein_coding	YES	CCDS13692.1	ENSP00000291547	PKNX1_HUMAN	Q96I87_HUMAN,E7EPN6_HUMAN	UPI000000D8D4	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCGCGTCTTT	.	5	ESCA
TSPEAR	0	.	GRCh37	21	45950950	45950950	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609G>T	p.%3D	p.R203R	ENST00000323084	4/12	53	35	17	40	40	0	TSPEAR,synonymous_variant,p.%3D,ENST00000397916,;TSPEAR,synonymous_variant,p.%3D,ENST00000323084,;	A	ENSG00000175894	ENST00000323084	Transcript	synonymous_variant	675	609	203	R	cgG/cgT	.	.	.	-1	TSPEAR	HGNC	1268	protein_coding	YES	CCDS13712.1	ENSP00000321987	TSEAR_HUMAN	.	UPI0000137746	.	.	.	4/12	.	Superfamily_domains:SSF49899,SMART_domains:SM00210,hmmpanther:PTHR15261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCCGGCT	.	5	ESCA
PCNT	0	.	GRCh37	21	47775526	47775526	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1921G>T	p.Glu641Ter	p.E641*	ENST00000359568	12/47	29	14	14	26	26	0	PCNT,stop_gained,p.Glu641Ter,ENST00000359568,;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,;PCNT,downstream_gene_variant,,ENST00000466474,;PCNT,downstream_gene_variant,,ENST00000483844,;	T	ENSG00000160299	ENST00000359568	Transcript	stop_gained	2028	1921	641	E/*	Gaa/Taa	.	.	.	1	PCNT	HGNC	16068	protein_coding	YES	CCDS33592.1	ENSP00000352572	PCNT_HUMAN	.	UPI00001AEB88	.	.	.	12/47	.	hmmpanther:PTHR18932:SF11,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCTGAAGGG	.	3	ESCA
PCNT	0	.	GRCh37	21	47775529	47775529	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1924G>A	p.Gly642Arg	p.G642R	ENST00000359568	12/47	28	15	13	24	24	0	PCNT,missense_variant,p.Gly642Arg,ENST00000359568,;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,;PCNT,downstream_gene_variant,,ENST00000466474,;PCNT,downstream_gene_variant,,ENST00000483844,;	A	ENSG00000160299	ENST00000359568	Transcript	missense_variant	2031	1924	642	G/R	Ggg/Agg	.	.	.	1	PCNT	HGNC	16068	protein_coding	YES	CCDS33592.1	ENSP00000352572	PCNT_HUMAN	.	UPI00001AEB88	.	.	probably_damaging(0.979)	12/47	.	hmmpanther:PTHR18932:SF11,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGAAGGGCAC	.	3	ESCA
IGLV2-18	0	.	GRCh37	22	23077381	23077381	+	Missense_Mutation	SNP	G	G	T	rs753509043	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.158G>T	p.Arg53Leu	p.R53L	ENST00000390310	2/2	63	36	27	53	53	0	IGLV2-18,missense_variant,p.Arg53Leu,ENST00000390310,;D87007.1,downstream_gene_variant,,ENST00000579613,;IGLV3-17,upstream_gene_variant,,ENST00000519099,;	T	ENSG00000211664	ENST00000390310	Transcript	missense_variant	171	158	53	R/L	cGt/cTt	rs753509043	.	.	1	IGLV2-18	HGNC	5889	IG_V_gene	YES	.	ENSP00000374845	.	Q5NV65_HUMAN	UPI0000EE5A3B	.	tolerated_low_confidence(0.44)	benign(0.001)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF138,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAACCGTGTCT	.	3	ESCA
SPECC1L	0	.	GRCh37	22	24718230	24718230	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1282A>G	p.Thr428Ala	p.T428A	ENST00000314328	5/17	33	14	19	25	25	0	SPECC1L,missense_variant,p.Thr428Ala,ENST00000541492,;SPECC1L,missense_variant,p.Thr428Ala,ENST00000314328,;SPECC1L,missense_variant,p.Thr428Ala,ENST00000421374,;SPECC1L,missense_variant,p.Thr428Ala,ENST00000437398,;SPECC1L,downstream_gene_variant,,ENST00000440893,;SPECC1L,intron_variant,,ENST00000416735,;SPECC1L-ADORA2A,missense_variant,p.Thr428Ala,ENST00000358654,;	G	ENSG00000100014	ENST00000314328	Transcript	missense_variant	1567	1282	428	T/A	Acc/Gcc	.	.	.	1	SPECC1L	HGNC	29022	protein_coding	YES	CCDS33619.1	ENSP00000325785	CYTSA_HUMAN	C9JLY8_HUMAN,C9J8U1_HUMAN	UPI00001B64E9	.	tolerated(0.08)	possibly_damaging(0.591)	5/17	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23167:SF18,hmmpanther:PTHR23167	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTACCCAG	.	5	ESCA
TFIP11	0	.	GRCh37	22	26902835	26902835	+	Missense_Mutation	SNP	G	G	A	rs113203306	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.269C>T	p.Ala90Val	p.A90V	ENST00000407690	5/15	21	12	8	14	14	0	TFIP11,missense_variant,p.Ala90Val,ENST00000407431,;TFIP11,missense_variant,p.Ala90Val,ENST00000407148,;TFIP11,missense_variant,p.Ala90Val,ENST00000407690,;TFIP11,missense_variant,p.Ala90Val,ENST00000405938,;TFIP11,missense_variant,p.Ala90Val,ENST00000455080,;TFIP11,downstream_gene_variant,,ENST00000418876,;TFIP11,downstream_gene_variant,,ENST00000440258,;TFIP11,downstream_gene_variant,,ENST00000420242,;TFIP11,upstream_gene_variant,,ENST00000450493,;TFIP11,upstream_gene_variant,,ENST00000496523,;TFIP11,non_coding_transcript_exon_variant,,ENST00000472918,;TFIP11,non_coding_transcript_exon_variant,,ENST00000479489,;TFIP11,upstream_gene_variant,,ENST00000493698,;TFIP11,downstream_gene_variant,,ENST00000464449,;	A	ENSG00000100109	ENST00000407690	Transcript	missense_variant	553	269	90	A/V	gCg/gTg	rs113203306	.	.	-1	TFIP11	HGNC	17165	protein_coding	YES	CCDS13838.1	ENSP00000384421	TFP11_HUMAN	F6XM96_HUMAN,F6UQ07_HUMAN,F6UKU9_HUMAN,F6SQZ1_HUMAN	UPI0000137191	.	tolerated(0.12)	possibly_damaging(0.701)	5/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23329,hmmpanther:PTHR23329:SF1,Pfam_domain:PF12457,PIRSF_domain:PIRSF017706	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCGCTGCC	byFrequency|byCluster|by1000G	4	ESCA
MTMR3	0	.	GRCh37	22	30414035	30414035	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1794C>T	p.%3D	p.T598T	ENST00000401950	16/20	51	37	14	61	61	0	MTMR3,synonymous_variant,p.%3D,ENST00000406629,;MTMR3,synonymous_variant,p.%3D,ENST00000333027,;MTMR3,synonymous_variant,p.%3D,ENST00000351488,;MTMR3,synonymous_variant,p.%3D,ENST00000401950,;MTMR3,synonymous_variant,p.%3D,ENST00000323630,;CTA-85E5.10,intron_variant,,ENST00000429350,;CTA-85E5.10,downstream_gene_variant,,ENST00000453743,;MTMR3,non_coding_transcript_exon_variant,,ENST00000492087,;MTMR3,upstream_gene_variant,,ENST00000491251,;	T	ENSG00000100330	ENST00000401950	Transcript	synonymous_variant	2136	1794	598	T	acC/acT	.	.	.	1	MTMR3	HGNC	7451	protein_coding	YES	CCDS13870.1	ENSP00000384651	MTMR3_HUMAN	Q9UPM2_HUMAN,G5E953_HUMAN,C9JLU3_HUMAN	UPI0000073EF2	.	.	.	16/20	.	hmmpanther:PTHR10807:SF66,hmmpanther:PTHR10807	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCACCAGCCC	.	5	ESCA
GATSL3	0	.	GRCh37	22	30681332	30681332	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*277C>T	.	.	ENST00000407689	9/9	12	6	6	8	8	0	GATSL3,3_prime_UTR_variant,,ENST00000404953,;GATSL3,3_prime_UTR_variant,,ENST00000407689,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000434291,;GATSL3,non_coding_transcript_exon_variant,,ENST00000459785,;GATSL3,downstream_gene_variant,,ENST00000498572,;GATSL3,downstream_gene_variant,,ENST00000464854,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000434987,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000447976,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000330168,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000418047,;GATSL3,downstream_gene_variant,,ENST00000492159,;GATSL3,downstream_gene_variant,,ENST00000471480,;GATSL3,downstream_gene_variant,,ENST00000463795,;GATSL3,downstream_gene_variant,,ENST00000415484,;GATSL3,downstream_gene_variant,,ENST00000497605,;GATSL3,downstream_gene_variant,,ENST00000440704,;GATSL3,downstream_gene_variant,,ENST00000425691,;GATSL3,downstream_gene_variant,,ENST00000421236,;GATSL3,downstream_gene_variant,,ENST00000440839,;	A	ENSG00000239282	ENST00000407689	Transcript	3_prime_UTR_variant	1397	.	.	.	.	.	.	.	-1	GATSL3	HGNC	34423	protein_coding	YES	CCDS43001.1	ENSP00000384183	GATL3_HUMAN	.	UPI0000071943	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGCGCAGGG	.	2	ESCA
BPIFC	0	.	GRCh37	22	32843205	32843205	+	Missense_Mutation	SNP	G	G	T	rs141691558	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.368C>A	p.Pro123Gln	p.P123Q	ENST00000397452	4/16	61	32	29	56	56	0	BPIFC,missense_variant,p.Pro123Gln,ENST00000397452,;BPIFC,missense_variant,p.Pro123Gln,ENST00000300399,;BPIFC,5_prime_UTR_variant,,ENST00000534972,;BPIFC,5_prime_UTR_variant,,ENST00000432451,;	T	ENSG00000184459	ENST00000397452	Transcript	missense_variant	479	368	123	P/Q	cCa/cAa	rs141691558,COSM108200	.	.	-1	BPIFC	HGNC	16503	protein_coding	YES	CCDS13906.1	ENSP00000380594	BPIFC_HUMAN	F5H3G0_HUMAN	UPI0000071B53	.	tolerated(0.16)	probably_damaging(0.983)	4/16	.	hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF17,Gene3D:1ewfA01,Pfam_domain:PF01273,SMART_domains:SM00328,Superfamily_domains:SSF55394	.	.	.	.	.	.	.	.	.	not_provided	1,1	21499247	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTGGAGAC	.	5	ESCA
TMPRSS6	0	.	GRCh37	22	37485698	37485698	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783G>T	p.%3D	p.L261L	ENST00000346753	7/18	69	35	34	94	94	0	TMPRSS6,synonymous_variant,p.%3D,ENST00000406725,;TMPRSS6,synonymous_variant,p.%3D,ENST00000406856,;TMPRSS6,synonymous_variant,p.%3D,ENST00000346753,;TMPRSS6,synonymous_variant,p.%3D,ENST00000381792,;TMPRSS6,synonymous_variant,p.%3D,ENST00000442782,;TMPRSS6,upstream_gene_variant,,ENST00000429068,;	A	ENSG00000187045	ENST00000346753	Transcript	synonymous_variant	900	783	261	L	ctG/ctT	.	.	.	-1	TMPRSS6	HGNC	16517	protein_coding	YES	CCDS13941.1	ENSP00000334962	TMPS6_HUMAN	B0QYB6_HUMAN	UPI00000747C8	.	.	.	7/18	.	Superfamily_domains:SSF49854,PIRSF_domain:PIRSF037135,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF96	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTCCAGCCG	.	5	ESCA
NOL12	0	.	GRCh37	22	38083951	38083951	+	Nonsense_Mutation	SNP	G	G	T	rs376416869	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118G>T	p.Glu40Ter	p.E40*	ENST00000359114	2/6	48	26	22	34	34	0	NOL12,stop_gained,p.Glu40Ter,ENST00000359114,;NOL12,non_coding_transcript_exon_variant,,ENST00000493862,;NOL12,stop_gained,p.Glu33Ter,ENST00000455236,;NOL12,stop_gained,p.Glu40Ter,ENST00000438329,;NOL12,non_coding_transcript_exon_variant,,ENST00000474032,;NOL12,non_coding_transcript_exon_variant,,ENST00000484650,;NOL12,non_coding_transcript_exon_variant,,ENST00000468597,;	T	ENSG00000100101	ENST00000359114	Transcript	stop_gained	188	118	40	E/*	Gag/Tag	rs376416869	.	.	1	NOL12	HGNC	28585	protein_coding	YES	CCDS13955.1	ENSP00000352021	NOL12_HUMAN	B4DGP7_HUMAN	UPI0000073B12	.	.	.	2/6	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14577:SF0,hmmpanther:PTHR14577,Pfam_domain:PF09805	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTCGAGCGA	byFrequency|byCluster	5	ESCA
PHF21B	0	.	GRCh37	22	45309806	45309806	+	Missense_Mutation	SNP	C	C	G	rs368576969	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.727G>C	p.Glu243Gln	p.E243Q	ENST00000313237	5/13	84	52	31	64	64	0	PHF21B,missense_variant,p.Glu189Gln,ENST00000420689,;PHF21B,missense_variant,p.Glu189Gln,ENST00000447824,;PHF21B,missense_variant,p.Glu201Gln,ENST00000396103,;PHF21B,missense_variant,p.Glu243Gln,ENST00000313237,;PHF21B,missense_variant,p.Glu39Gln,ENST00000414269,;PHF21B,missense_variant,p.Glu39Gln,ENST00000403565,;PHF21B,missense_variant,p.Glu189Gln,ENST00000404079,;PHF21B,downstream_gene_variant,,ENST00000460507,;PHF21B,downstream_gene_variant,,ENST00000490679,;PHF21B,downstream_gene_variant,,ENST00000474327,;	G	ENSG00000056487	ENST00000313237	Transcript	missense_variant	878	727	243	E/Q	Gag/Cag	rs368576969,COSM322622	.	.	-1	PHF21B	HGNC	25161	protein_coding	YES	CCDS14061.1	ENSP00000324403	PF21B_HUMAN	B3KTL5_HUMAN	UPI0000072111	.	tolerated(0.09)	benign(0.116)	5/13	.	hmmpanther:PTHR24102:SF1,hmmpanther:PTHR24102	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCGGGCT	byFrequency|byCluster	5	ESCA
ATXN10	0	.	GRCh37	22	46136258	46136258	+	Missense_Mutation	SNP	G	G	C	rs766922978	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1013G>C	p.Arg338Pro	p.R338P	ENST00000252934	9/12	54	29	25	35	35	0	ATXN10,missense_variant,p.Arg38Pro,ENST00000451241,;ATXN10,missense_variant,p.Arg90Pro,ENST00000435026,;ATXN10,missense_variant,p.Arg338Pro,ENST00000252934,;ATXN10,missense_variant,p.Arg274Pro,ENST00000381061,;ATXN10,non_coding_transcript_exon_variant,,ENST00000493643,;ATXN10,upstream_gene_variant,,ENST00000464482,;ATXN10,downstream_gene_variant,,ENST00000476998,;ATXN10,non_coding_transcript_exon_variant,,ENST00000483549,;	C	ENSG00000130638	ENST00000252934	Transcript	missense_variant	1278	1013	338	R/P	cGg/cCg	rs766922978	.	.	1	ATXN10	HGNC	10549	protein_coding	YES	CCDS14070.1	ENSP00000252934	ATX10_HUMAN	Q9NTC6_HUMAN	UPI0000052A56	.	deleterious(0)	possibly_damaging(0.88)	9/12	.	hmmpanther:PTHR13255,hmmpanther:PTHR13255:SF0,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGCGGGTGA	byFrequency	5	ESCA
FLJ27365	0	.	GRCh37	22	46493817	46493817	+	Missense_Mutation	SNP	G	G	T	rs149867851	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11G>T	p.Arg4Leu	p.R4L	ENST00000360737	2/5	29	16	13	30	30	0	FLJ27365,missense_variant,p.Arg4Leu,ENST00000381051,;FLJ27365,missense_variant,p.Arg4Leu,ENST00000443490,;FLJ27365,missense_variant,p.Arg4Leu,ENST00000360737,;FLJ27365,missense_variant,p.Arg4Leu,ENST00000435439,;	T	ENSG00000197182	ENST00000360737	Transcript	missense_variant	170	11	4	R/L	cGt/cTt	rs149867851	.	.	1	FLJ27365	Uniprot_gn	.	protein_coding	YES	.	ENSP00000353966	.	Q6ZNQ0_HUMAN,B1AKH8_HUMAN	UPI00001C11DA	.	tolerated_low_confidence(0.35)	benign(0.433)	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGTCCCA	byFrequency|by1000G	5	ESCA
AFF3	0	.	GRCh37	2	100163853	100163853	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4083C>T	.	.	ENST00000356421	24/24	23	1	22	35	35	0	AFF3,3_prime_UTR_variant,,ENST00000356421,;AFF3,3_prime_UTR_variant,,ENST00000317233,;AFF3,3_prime_UTR_variant,,ENST00000409236,;AFF3,downstream_gene_variant,,ENST00000409579,;	A	ENSG00000144218	ENST00000356421	Transcript	3_prime_UTR_variant	7983	.	.	.	.	.	.	.	-1	AFF3	HGNC	6473	protein_coding	YES	CCDS33258.1	ENSP00000348793	AFF3_HUMAN	.	UPI000041098C	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACATGCATTA	.	5	ESCA
RFX8	0	.	GRCh37	2	102029526	102029526	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569G>C	p.Arg190Pro	p.R190P	ENST00000428343	8/12	62	16	45	28	28	0	RFX8,missense_variant,p.Arg303Pro,ENST00000376826,;RFX8,missense_variant,p.Arg190Pro,ENST00000428343,;RFX8,3_prime_UTR_variant,,ENST00000481179,;	G	ENSG00000196460	ENST00000428343	Transcript	missense_variant	689	569	190	R/P	cGa/cCa	.	.	.	-1	RFX8	HGNC	37253	protein_coding	YES	CCDS46376.1	ENSP00000401536	RFX8_HUMAN	.	UPI0001AE76D5	.	deleterious(0)	probably_damaging(0.954)	8/12	.	hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATTCGCATA	.	5	ESCA
EPB41L5	0	.	GRCh37	2	120922456	120922456	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1932G>A	p.%3D	p.E644E	ENST00000263713	22/25	18	3	15	37	37	0	EPB41L5,synonymous_variant,p.%3D,ENST00000443902,;EPB41L5,synonymous_variant,p.%3D,ENST00000263713,;EPB41L5,synonymous_variant,p.%3D,ENST00000452780,;EPB41L5,non_coding_transcript_exon_variant,,ENST00000488691,;	A	ENSG00000115109	ENST00000263713	Transcript	synonymous_variant	2146	1932	644	E	gaG/gaA	.	.	.	1	EPB41L5	HGNC	19819	protein_coding	YES	CCDS2130.1	ENSP00000263713	E41L5_HUMAN	Q53RT1_HUMAN,Q4ZG32_HUMAN	UPI00001B078A	.	.	.	22/25	.	hmmpanther:PTHR23280:SF15,hmmpanther:PTHR23280	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGAGAATCT	.	5	ESCA
UGGT1	0	.	GRCh37	2	128877948	128877948	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.891G>T	p.%3D	p.L297L	ENST00000259253	9/41	20	3	17	48	48	0	UGGT1,synonymous_variant,p.%3D,ENST00000259253,;UGGT1,synonymous_variant,p.%3D,ENST00000375990,;RN7SL206P,upstream_gene_variant,,ENST00000580933,;UGGT1,3_prime_UTR_variant,,ENST00000376723,;UGGT1,3_prime_UTR_variant,,ENST00000438277,;	T	ENSG00000136731	ENST00000259253	Transcript	synonymous_variant	938	891	297	L	ctG/ctT	.	.	.	1	UGGT1	HGNC	15663	protein_coding	YES	CCDS2154.1	ENSP00000259253	UGGG1_HUMAN	.	UPI00000707D8	.	.	.	9/41	.	hmmpanther:PTHR11226:SF3,hmmpanther:PTHR11226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCTGGAGGG	.	5	ESCA
UGGT1	0	.	GRCh37	2	128914889	128914889	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2324G>T	p.Arg775Leu	p.R775L	ENST00000259253	22/41	59	11	48	97	97	0	UGGT1,missense_variant,p.Arg775Leu,ENST00000259253,;UGGT1,missense_variant,p.Arg751Leu,ENST00000375990,;UGGT1,3_prime_UTR_variant,,ENST00000376723,;UGGT1,3_prime_UTR_variant,,ENST00000438277,;UGGT1,non_coding_transcript_exon_variant,,ENST00000488439,;	T	ENSG00000136731	ENST00000259253	Transcript	missense_variant	2371	2324	775	R/L	cGg/cTg	.	.	.	1	UGGT1	HGNC	15663	protein_coding	YES	CCDS2154.1	ENSP00000259253	UGGG1_HUMAN	.	UPI00000707D8	.	deleterious(0)	possibly_damaging(0.795)	22/41	.	hmmpanther:PTHR11226:SF3,hmmpanther:PTHR11226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACGGCAGT	.	5	ESCA
LRP1B	0	.	GRCh37	2	141816620	141816620	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1240A>T	p.Arg414Ter	p.R414*	ENST00000389484	9/91	10	3	7	15	15	0	LRP1B,stop_gained,p.Arg414Ter,ENST00000389484,;LRP1B,intron_variant,,ENST00000434794,;	A	ENSG00000168702	ENST00000389484	Transcript	stop_gained	2212	1240	414	R/*	Aga/Tga	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	9/91	.	PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTCTAACCT	.	2	ESCA
GPD2	0	.	GRCh37	2	157442767	157442767	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3337G>A	.	.	ENST00000310454	17/17	8	1	7	17	17	0	GPD2,3_prime_UTR_variant,,ENST00000310454,;GPD2,downstream_gene_variant,,ENST00000409674,;GPD2,downstream_gene_variant,,ENST00000438166,;GPD2,downstream_gene_variant,,ENST00000540309,;GPD2,downstream_gene_variant,,ENST00000409125,;GPD2,downstream_gene_variant,,ENST00000496190,;GPD2,downstream_gene_variant,,ENST00000492005,;GPD2,intron_variant,,ENST00000409861,;GPD2,downstream_gene_variant,,ENST00000464846,;	A	ENSG00000115159	ENST00000310454	Transcript	3_prime_UTR_variant	5893	.	.	.	.	.	.	.	1	GPD2	HGNC	4456	protein_coding	YES	CCDS2202.1	ENSP00000308610	GPDM_HUMAN	Q53T76_HUMAN,Q53RD0_HUMAN,F8W6E4_HUMAN,F5GYK7_HUMAN,E7EM56_HUMAN	UPI000013F012	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGATGACACA	.	2	ESCA
HOXD3	0	.	GRCh37	2	177034035	177034035	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193G>T	p.Gly65Cys	p.G65C	ENST00000468418	3/4	34	4	30	44	44	0	HOXD3,missense_variant,p.Gly65Cys,ENST00000249440,;HOXD3,missense_variant,p.Gly65Cys,ENST00000432796,;HOXD3,missense_variant,p.Gly65Cys,ENST00000410016,;HOXD3,missense_variant,p.Gly65Cys,ENST00000468418,;HOXD-AS1,downstream_gene_variant,,ENST00000416928,;RP11-387A1.5,upstream_gene_variant,,ENST00000608941,;	T	ENSG00000128652	ENST00000468418	Transcript	missense_variant	2283	193	65	G/C	Ggt/Tgt	.	.	.	1	HOXD3	HGNC	5137	protein_coding	YES	CCDS2270.1	ENSP00000424734	HXD3_HUMAN	C9J1M3_HUMAN	UPI000013CC84	.	deleterious(0.02)	possibly_damaging(0.574)	3/4	.	hmmpanther:PTHR24326:SF4,hmmpanther:PTHR24326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCAGGTTCT	.	5	ESCA
TTN	0	.	GRCh37	2	179470053	179470053	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53882-31G>T	.	.	ENST00000589042	.	24	3	21	33	33	0	TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000591111,;TTN,intron_variant,,ENST00000589042,;TTN,intron_variant,,ENST00000342992,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000586452,;	A	ENSG00000155657	ENST00000589042	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	.	279/362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAACAAAGT	.	5	ESCA
TTN	0	.	GRCh37	2	179579779	179579779	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26134G>T	p.Glu8712Ter	p.E8712*	ENST00000589042	90/363	23	2	21	25	25	0	TTN,stop_gained,p.Glu7468Ter,ENST00000342992,;TTN,stop_gained,p.Glu8712Ter,ENST00000589042,;TTN,stop_gained,p.Glu8395Ter,ENST00000591111,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,downstream_gene_variant,,ENST00000592630,;TTN-AS1,downstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000589830,;	A	ENSG00000155657	ENST00000589042	Transcript	stop_gained	26359	26134	8712	E/*	Gaa/Taa	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	90/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCCCCAA	.	5	ESCA
TTN	0	.	GRCh37	2	179631333	179631333	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9478G>A	p.Glu3160Lys	p.E3160K	ENST00000589042	41/363	15	4	11	18	18	0	TTN,missense_variant,p.Glu3160Lys,ENST00000360870,;TTN,missense_variant,p.Glu3114Lys,ENST00000359218,;TTN,missense_variant,p.Glu3160Lys,ENST00000342992,;TTN,missense_variant,p.Glu3114Lys,ENST00000342175,;TTN,missense_variant,p.Glu3160Lys,ENST00000589042,;TTN,missense_variant,p.Glu3160Lys,ENST00000591111,;TTN,missense_variant,p.Glu3114Lys,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000610005,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,downstream_gene_variant,,ENST00000578746,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	9703	9478	3160	E/K	Gag/Aag	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	41/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTCTCAATGA	.	3	ESCA
STAT4	0	.	GRCh37	2	191894549	191894549	+	3'UTR	SNP	C	C	T	rs376543078	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*17G>A	.	.	ENST00000392320	24/24	35	4	31	52	52	0	STAT4,3_prime_UTR_variant,,ENST00000358470,;STAT4,3_prime_UTR_variant,,ENST00000392320,;AC067945.4,intron_variant,,ENST00000456176,;AC067945.4,upstream_gene_variant,,ENST00000429796,;STAT4,downstream_gene_variant,,ENST00000463951,;STAT4,downstream_gene_variant,,ENST00000495849,;	T	ENSG00000138378	ENST00000392320	Transcript	3_prime_UTR_variant	2579	.	.	.	.	rs376543078	.	.	-1	STAT4	HGNC	11365	protein_coding	YES	CCDS2310.1	ENSP00000376134	STAT4_HUMAN	Q53S87_HUMAN,Q53RU2_HUMAN,E9PBE2_HUMAN,C9JM11_HUMAN,C9JFG0_HUMAN,B7SIX5_HUMAN	UPI00000015F2	.	.	.	24/24	.	.	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGCGTCAG	byFrequency|byCluster	5	ESCA
SMARCAL1	0	.	GRCh37	2	217280027	217280027	+	Silent	SNP	G	G	A	rs530505647	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600G>A	p.%3D	p.S200S	ENST00000357276	3/18	48	28	19	23	23	0	SMARCAL1,synonymous_variant,p.%3D,ENST00000357276,;SMARCAL1,synonymous_variant,p.%3D,ENST00000358207,;SMARCAL1,synonymous_variant,p.%3D,ENST00000427645,;SMARCAL1,synonymous_variant,p.%3D,ENST00000392128,;SMARCAL1,downstream_gene_variant,,ENST00000425815,;SMARCAL1,downstream_gene_variant,,ENST00000434435,;SMARCAL1,upstream_gene_variant,,ENST00000412913,;SMARCAL1,downstream_gene_variant,,ENST00000444508,;SMARCAL1,downstream_gene_variant,,ENST00000430374,;AC098820.2,upstream_gene_variant,,ENST00000457694,;SMARCAL1,downstream_gene_variant,,ENST00000496037,;	A	ENSG00000138375	ENST00000357276	Transcript	synonymous_variant	930	600	200	S	tcG/tcA	rs530505647	.	.	1	SMARCAL1	HGNC	11102	protein_coding	YES	CCDS2403.1	ENSP00000349823	SMAL1_HUMAN	C9JP32_HUMAN,C9JHQ1_HUMAN,C9J8F8_HUMAN,C9J6I8_HUMAN	UPI000000DA30	.	.	.	3/18	.	hmmpanther:PTHR10799:SF571,hmmpanther:PTHR10799	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCGGGGCA	by1000G	5	ESCA
SP140L	0	.	GRCh37	2	231249995	231249995	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.760C>G	p.Leu254Val	p.L254V	ENST00000415673	9/19	51	25	25	23	23	0	SP140L,missense_variant,p.Leu254Val,ENST00000444636,;SP140L,missense_variant,p.Leu254Val,ENST00000415673,;SP140L,missense_variant,p.Leu254Val,ENST00000396563,;SP140L,missense_variant,p.Leu254Val,ENST00000243810,;SP140L,non_coding_transcript_exon_variant,,ENST00000462156,;SP140L,non_coding_transcript_exon_variant,,ENST00000483728,;	G	ENSG00000185404	ENST00000415673	Transcript	missense_variant	846	760	254	L/V	Ctg/Gtg	.	.	.	1	SP140L	HGNC	25105	protein_coding	YES	CCDS46538.1	ENSP00000397911	SP14L_HUMAN	.	UPI000020974D	.	tolerated(0.08)	possibly_damaging(0.889)	9/19	.	hmmpanther:PTHR13711:SF156,hmmpanther:PTHR13711	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCTGAAA	.	5	ESCA
SNX17	0	.	GRCh37	2	27599346	27599346	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1258G>C	p.Glu420Gln	p.E420Q	ENST00000233575	14/15	72	30	42	46	46	0	SNX17,missense_variant,p.Glu395Gln,ENST00000537606,;SNX17,missense_variant,p.Glu206Gln,ENST00000542478,;SNX17,missense_variant,p.Glu206Gln,ENST00000543024,;SNX17,missense_variant,p.Glu420Gln,ENST00000233575,;PPM1G,downstream_gene_variant,,ENST00000344034,;ZNF513,downstream_gene_variant,,ENST00000407879,;ZNF513,downstream_gene_variant,,ENST00000323703,;ZNF513,downstream_gene_variant,,ENST00000436006,;PPM1G,downstream_gene_variant,,ENST00000350803,;ZNF513,downstream_gene_variant,,ENST00000491924,;SNX17,splice_region_variant,,ENST00000453453,;SNX17,splice_region_variant,,ENST00000440760,;SNX17,splice_region_variant,,ENST00000427123,;SNX17,downstream_gene_variant,,ENST00000493711,;SNX17,downstream_gene_variant,,ENST00000484886,;SNX17,downstream_gene_variant,,ENST00000464279,;PPM1G,downstream_gene_variant,,ENST00000472077,;SNX17,downstream_gene_variant,,ENST00000494893,;SNX17,downstream_gene_variant,,ENST00000489402,;	C	ENSG00000115234	ENST00000233575	Transcript	missense_variant	1480	1258	420	E/Q	Gag/Cag	.	.	.	1	SNX17	HGNC	14979	protein_coding	YES	CCDS1750.1	ENSP00000233575	SNX17_HUMAN	B4DTB8_HUMAN,B4DLL7_HUMAN,B4DDM3_HUMAN	UPI0000135B4E	.	tolerated(0.32)	benign(0.322)	14/15	.	hmmpanther:PTHR12431,hmmpanther:PTHR12431:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAGGAGTCA	.	5	ESCA
RASGRP3	0	.	GRCh37	2	33764169	33764169	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1170C>A	p.%3D	p.T390T	ENST00000403687	12/18	40	20	19	23	23	0	RASGRP3,synonymous_variant,p.%3D,ENST00000407811,;RASGRP3,synonymous_variant,p.%3D,ENST00000402538,;RASGRP3,synonymous_variant,p.%3D,ENST00000403687,;RASGRP3,upstream_gene_variant,,ENST00000482731,;RASGRP3,synonymous_variant,p.%3D,ENST00000419772,;RASGRP3,non_coding_transcript_exon_variant,,ENST00000468856,;RASGRP3,non_coding_transcript_exon_variant,,ENST00000490150,;	A	ENSG00000152689	ENST00000403687	Transcript	synonymous_variant	1910	1170	390	T	acC/acA	.	.	.	1	RASGRP3	HGNC	14545	protein_coding	YES	CCDS46256.1	ENSP00000384192	GRP3_HUMAN	C9K0P4_HUMAN,C9JWP0_HUMAN,C9JSS2_HUMAN,C9J9C9_HUMAN,C9IYA5_HUMAN	UPI0000074694	.	.	.	12/18	.	Superfamily_domains:0041591,hmmpanther:PTHR23113:SF178,hmmpanther:PTHR23113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTACCTCCCC	.	5	ESCA
AC009499.1	0	.	GRCh37	2	33952528	33952528	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.68+20508G>T	.	.	ENST00000366209	.	51	20	30	23	23	0	AC009499.1,intron_variant,,ENST00000442026,;AC009499.1,intron_variant,,ENST00000366209,;MYADML,non_coding_transcript_exon_variant,,ENST00000474610,;MYADML,non_coding_transcript_exon_variant,,ENST00000490394,;MYADML,non_coding_transcript_exon_variant,,ENST00000491596,;MYADML,non_coding_transcript_exon_variant,,ENST00000322472,;	T	ENSG00000203386	ENST00000366209	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	AC009499.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACGAAGGT	.	5	ESCA
TRAPPC12	0	.	GRCh37	2	3425669	3425669	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182G>T	p.Arg394Ser	p.R394S	ENST00000324266	4/12	32	20	12	23	23	0	TRAPPC12,missense_variant,p.Arg394Ser,ENST00000382110,;TRAPPC12,missense_variant,p.Arg394Ser,ENST00000324266,;TRAPPC12,missense_variant,p.Arg74Ser,ENST00000441983,;TRAPPC12,upstream_gene_variant,,ENST00000469147,;TRAPPC12,missense_variant,p.Arg6Ser,ENST00000417243,;TRAPPC12,3_prime_UTR_variant,,ENST00000457845,;TRAPPC12,3_prime_UTR_variant,,ENST00000411973,;TRAPPC12,upstream_gene_variant,,ENST00000441099,;	T	ENSG00000171853	ENST00000324266	Transcript	missense_variant	1377	1182	394	R/S	agG/agT	.	.	.	1	TRAPPC12	HGNC	24284	protein_coding	YES	CCDS1652.1	ENSP00000324318	TPC12_HUMAN	Q53S18_HUMAN,Q53QD4_HUMAN	UPI000014132D	.	deleterious(0)	probably_damaging(0.969)	4/12	.	hmmpanther:PTHR21581:SF1,hmmpanther:PTHR21581	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGGGCAGC	.	5	ESCA
SOCS5	0	.	GRCh37	2	46986133	46986133	+	Missense_Mutation	SNP	G	G	C	rs760457146	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464G>C	p.Arg155Pro	p.R155P	ENST00000306503	2/2	54	34	20	37	37	0	SOCS5,missense_variant,p.Arg155Pro,ENST00000394861,;SOCS5,missense_variant,p.Arg155Pro,ENST00000306503,;	C	ENSG00000171150	ENST00000306503	Transcript	missense_variant	636	464	155	R/P	cGc/cCc	rs760457146	.	.	1	SOCS5	HGNC	16852	protein_coding	YES	CCDS1830.1	ENSP00000305133	SOCS5_HUMAN	B4DL10_HUMAN	UPI0000135B69	.	deleterious(0.04)	probably_damaging(0.998)	2/2	.	hmmpanther:PTHR10385,hmmpanther:PTHR10385:SF28,Pfam_domain:PF12610	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGCGCTACG	.	5	ESCA
NRXN1	0	.	GRCh37	2	50280637	50280637	+	Silent	SNP	C	C	A	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4020G>T	p.%3D	p.L1340L	ENST00000404971	22/24	78	52	26	41	41	0	NRXN1,synonymous_variant,p.%3D,ENST00000405472,;NRXN1,synonymous_variant,p.%3D,ENST00000401710,;NRXN1,synonymous_variant,p.%3D,ENST00000404971,;NRXN1,synonymous_variant,p.%3D,ENST00000406316,;NRXN1,synonymous_variant,p.%3D,ENST00000401669,;NRXN1,synonymous_variant,p.%3D,ENST00000342183,;NRXN1,synonymous_variant,p.%3D,ENST00000406859,;NRXN1,synonymous_variant,p.%3D,ENST00000402717,;	A	ENSG00000179915	ENST00000404971	Transcript	synonymous_variant	5360	4020	1340	L	ctG/ctT	COSM378725,COSM378727,COSM378726	.	.	-1	NRXN1	HGNC	8008	protein_coding	YES	CCDS46282.1	ENSP00000385142	NRX1A_HUMAN	Q08AH0_HUMAN	UPI00015A218A	.	.	.	22/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTACAGCCC	.	5	ESCA
COMMD1	0	.	GRCh37	2	62363038	62363038	+	Missense_Mutation	SNP	G	G	C	rs777579603	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535G>C	p.Glu179Gln	p.E179Q	ENST00000311832	3/3	99	40	58	75	75	0	COMMD1,missense_variant,p.Glu27Gln,ENST00000427417,;COMMD1,missense_variant,p.Glu21Gln,ENST00000444166,;COMMD1,missense_variant,p.Glu179Gln,ENST00000311832,;COMMD1,missense_variant,p.Glu27Gln,ENST00000458337,;AC018462.2,intron_variant,,ENST00000421323,;AC018462.2,intron_variant,,ENST00000425966,;COMMD1,non_coding_transcript_exon_variant,,ENST00000472729,;	C	ENSG00000173163	ENST00000311832	Transcript	missense_variant	567	535	179	E/Q	Gaa/Caa	rs777579603	.	.	1	COMMD1	HGNC	23024	protein_coding	YES	CCDS1869.1	ENSP00000308236	COMD1_HUMAN	Q53SJ8_HUMAN,Q53QP8_HUMAN,Q53Q75_HUMAN	UPI0000035FF0	.	tolerated(0.43)	probably_damaging(0.991)	3/3	.	PROSITE_profiles:PS51269,hmmpanther:PTHR21199,Pfam_domain:PF07258	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTAGAAGAA	.	5	ESCA
EXOC6B	0	.	GRCh37	2	72606863	72606863	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2117G>T	p.Cys706Phe	p.C706F	ENST00000272427	19/22	32	16	15	28	28	0	EXOC6B,missense_variant,p.Cys706Phe,ENST00000272427,;EXOC6B,downstream_gene_variant,,ENST00000464347,;	A	ENSG00000144036	ENST00000272427	Transcript	missense_variant	2248	2117	706	C/F	tGt/tTt	.	.	.	-1	EXOC6B	HGNC	17085	protein_coding	YES	CCDS46333.1	ENSP00000272427	EXC6B_HUMAN	Q9H8D6_HUMAN	UPI000046995C	.	deleterious(0.02)	probably_damaging(0.998)	19/22	.	hmmpanther:PTHR12702,hmmpanther:PTHR12702:SF3,Pfam_domain:PF04091,PIRSF_domain:PIRSF025007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCACATTCT	.	5	ESCA
FUNDC2P2	0	.	GRCh37	2	84518478	84518478	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.673C>T	.	.	ENST00000538499	1/1	41	23	17	39	39	0	FUNDC2P2,non_coding_transcript_exon_variant,,ENST00000331369,;FUNDC2P2,non_coding_transcript_exon_variant,,ENST00000538499,;FUNDC2P2,downstream_gene_variant,,ENST00000443452,;	T	ENSG00000182814	ENST00000538499	Transcript	non_coding_transcript_exon_variant	673	.	.	.	.	.	.	.	1	FUNDC2P2	HGNC	17247	transcribed_processed_pseudogene	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTCCTCCT	.	5	ESCA
SMYD1	0	.	GRCh37	2	88383991	88383991	+	Missense_Mutation	SNP	G	G	T	rs368545680	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.294G>T	p.Lys98Asn	p.K98N	ENST00000419482	2/10	41	19	22	36	36	0	SMYD1,missense_variant,p.Lys98Asn,ENST00000444564,;SMYD1,missense_variant,p.Lys98Asn,ENST00000438570,;SMYD1,missense_variant,p.Lys98Asn,ENST00000419482,;MIR4780,upstream_gene_variant,,ENST00000584268,;SMYD1,non_coding_transcript_exon_variant,,ENST00000468008,;	T	ENSG00000115593	ENST00000419482	Transcript	missense_variant	379	294	98	K/N	aaG/aaT	rs368545680	.	.	1	SMYD1	HGNC	20986	protein_coding	YES	CCDS33240.1	ENSP00000393453	SMYD1_HUMAN	Q5GJ33_HUMAN	UPI000006EB68	.	deleterious(0.04)	possibly_damaging(0.799)	2/10	.	PROSITE_profiles:PS50280,hmmpanther:PTHR12197:SF16,hmmpanther:PTHR12197,Pfam_domain:PF00856,SMART_domains:SM00317,Superfamily_domains:SSF82199	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAGGTGCC	byFrequency|byCluster	5	ESCA
IGKV2-24	0	.	GRCh37	2	89475972	89475972	+	Missense_Mutation	SNP	T	T	C	rs760944505	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200A>G	p.Gln67Arg	p.Q67R	ENST00000484817	2/2	75	51	24	71	71	0	IGKV2-24,missense_variant,p.Gln67Arg,ENST00000484817,;IGKV2-23,upstream_gene_variant,,ENST00000518729,;	C	ENSG00000241294	ENST00000484817	Transcript	missense_variant	230	200	67	Q/R	cAg/cGg	rs760944505	.	.	-1	IGKV2-24	HGNC	5781	IG_V_gene	YES	.	ENSP00000419300	.	.	UPI0000115DCF	.	deleterious(0.01)	benign(0.195)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF128,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCTGGCCT	.	5	ESCA
IGKV2-24	0	.	GRCh37	2	89475973	89475973	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199C>G	p.Gln67Glu	p.Q67E	ENST00000484817	2/2	73	49	24	72	72	0	IGKV2-24,missense_variant,p.Gln67Glu,ENST00000484817,;IGKV2-23,upstream_gene_variant,,ENST00000518729,;	C	ENSG00000241294	ENST00000484817	Transcript	missense_variant	229	199	67	Q/E	Cag/Gag	.	.	.	-1	IGKV2-24	HGNC	5781	IG_V_gene	YES	.	ENSP00000419300	.	.	UPI0000115DCF	.	deleterious(0.02)	benign(0.099)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF128,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCTGGCCTG	.	5	ESCA
IGKV2-24	0	.	GRCh37	2	89475974	89475974	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198C>A	p.%3D	p.G66G	ENST00000484817	2/2	72	48	24	72	72	0	IGKV2-24,synonymous_variant,p.%3D,ENST00000484817,;IGKV2-23,upstream_gene_variant,,ENST00000518729,;	T	ENSG00000241294	ENST00000484817	Transcript	synonymous_variant	228	198	66	G	ggC/ggA	.	.	.	-1	IGKV2-24	HGNC	5781	IG_V_gene	YES	.	ENSP00000419300	.	.	UPI0000115DCF	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF128,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGGCCTGG	.	5	ESCA
ANKRD20A8P	0	.	GRCh37	2	95481484	95481484	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1877C>T	.	.	ENST00000432432	15/15	126	76	50	111	111	0	ANKRD20A8P,non_coding_transcript_exon_variant,,ENST00000432432,;ANKRD20A8P,non_coding_transcript_exon_variant,,ENST00000590226,;ANKRD20A8P,non_coding_transcript_exon_variant,,ENST00000446135,;	A	ENSG00000229089	ENST00000432432	Transcript	non_coding_transcript_exon_variant	1877	.	.	.	.	.	.	.	-1	ANKRD20A8P	HGNC	23666	processed_transcript	YES	.	.	.	.	.	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATTGAGCCT	.	4	ESCA
NCAPH	0	.	GRCh37	2	97008912	97008912	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.465G>T	p.%3D	p.A155A	ENST00000240423	5/18	44	25	18	40	40	0	NCAPH,synonymous_variant,p.%3D,ENST00000435975,;NCAPH,synonymous_variant,p.%3D,ENST00000455200,;NCAPH,synonymous_variant,p.%3D,ENST00000427946,;NCAPH,synonymous_variant,p.%3D,ENST00000240423,;NCAPH,intron_variant,,ENST00000456906,;NCAPH,non_coding_transcript_exon_variant,,ENST00000477409,;	T	ENSG00000121152	ENST00000240423	Transcript	synonymous_variant	508	465	155	A	gcG/gcT	.	.	.	1	NCAPH	HGNC	1112	protein_coding	YES	CCDS2021.1	ENSP00000240423	CND2_HUMAN	E9PHA2_HUMAN,B4E189_HUMAN	UPI0000163F72	.	.	.	5/18	.	hmmpanther:PTHR13108,Pfam_domain:PF05786,PIRSF_domain:PIRSF017126	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCGGGTAC	.	5	ESCA
ATP2B2	0	.	GRCh37	3	10392245	10392245	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2153G>T	p.Arg718Leu	p.R718L	ENST00000360273	15/23	23	1	22	33	33	0	ATP2B2,missense_variant,p.Arg704Leu,ENST00000343816,;ATP2B2,missense_variant,p.Arg718Leu,ENST00000360273,;ATP2B2,missense_variant,p.Arg673Leu,ENST00000383800,;ATP2B2,missense_variant,p.Arg718Leu,ENST00000352432,;ATP2B2,missense_variant,p.Arg673Leu,ENST00000397077,;ATP2B2,missense_variant,p.Arg574Leu,ENST00000452124,;ATP2B2,missense_variant,p.Arg673Leu,ENST00000460129,;	A	ENSG00000157087	ENST00000360273	Transcript	missense_variant	2592	2153	718	R/L	cGc/cTc	.	.	.	-1	ATP2B2	HGNC	815	protein_coding	YES	CCDS33701.1	ENSP00000353414	AT2B2_HUMAN	Q4J699_HUMAN,Q4J696_HUMAN	UPI00001261EF	.	tolerated(0.16)	benign(0.019)	15/23	.	hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF247,TIGRFAM_domain:TIGR01517,Pfam_domain:PF00702,Gene3D:1.20.1110.10,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTGCGGATG	.	5	ESCA
TMEM39A	0	.	GRCh37	3	119156763	119156763	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763G>A	p.Ala255Thr	p.A255T	ENST00000319172	6/9	25	1	24	45	45	0	TMEM39A,missense_variant,p.Ala255Thr,ENST00000319172,;TMEM39A,missense_variant,p.Ala101Thr,ENST00000491685,;TMEM39A,downstream_gene_variant,,ENST00000486159,;TMEM39A,3_prime_UTR_variant,,ENST00000438581,;TMEM39A,non_coding_transcript_exon_variant,,ENST00000468545,;TMEM39A,upstream_gene_variant,,ENST00000473684,;	T	ENSG00000176142	ENST00000319172	Transcript	missense_variant	1184	763	255	A/T	Gcc/Acc	.	.	.	-1	TMEM39A	HGNC	25600	protein_coding	YES	CCDS2987.1	ENSP00000326063	TM39A_HUMAN	C9JYN8_HUMAN,C9JUZ6_HUMAN,C9IYN1_HUMAN	UPI00000715E5	.	tolerated(0.68)	benign(0.001)	6/9	.	hmmpanther:PTHR12995:SF3,hmmpanther:PTHR12995,Pfam_domain:PF10271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGGCATTAT	.	5	ESCA
MYLK	0	.	GRCh37	3	123419172	123419172	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3143A>G	p.Lys1048Arg	p.K1048R	ENST00000360304	18/34	24	10	14	46	46	0	MYLK,missense_variant,p.Lys1048Arg,ENST00000360304,;MYLK,missense_variant,p.Lys979Arg,ENST00000346322,;MYLK,missense_variant,p.Lys1048Arg,ENST00000360772,;MYLK,missense_variant,p.Lys1048Arg,ENST00000475616,;MYLK,missense_variant,p.Lys1048Arg,ENST00000359169,;MYLK,upstream_gene_variant,,ENST00000510775,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,non_coding_transcript_exon_variant,,ENST00000504946,;	C	ENSG00000065534	ENST00000360304	Transcript	missense_variant	3425	3143	1048	K/R	aAg/aGg	.	.	.	-1	MYLK	HGNC	7590	protein_coding	YES	CCDS46896.1	ENSP00000353452	MYLK_HUMAN	Q06S79_HUMAN,Q05B98_HUMAN,Q05B97_HUMAN,D6R9C2_HUMAN,B4DUE3_HUMAN	UPI000020A0AE	.	tolerated(0.19)	benign(0.186)	18/34	.	hmmpanther:PTHR22964,hmmpanther:PTHR22964:SF44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCTTCAGG	.	5	ESCA
PLXND1	0	.	GRCh37	3	129288754	129288754	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3797G>C	p.Gly1266Ala	p.G1266A	ENST00000324093	20/36	8	2	6	16	16	0	PLXND1,missense_variant,p.Gly1266Ala,ENST00000324093,;PLXND1,missense_variant,p.Gly1266Ala,ENST00000393239,;PLXND1,non_coding_transcript_exon_variant,,ENST00000514990,;PLXND1,upstream_gene_variant,,ENST00000512744,;PLXND1,upstream_gene_variant,,ENST00000503166,;PLXND1,downstream_gene_variant,,ENST00000504767,;PLXND1,downstream_gene_variant,,ENST00000511018,;PLXND1,downstream_gene_variant,,ENST00000515191,;PLXND1,downstream_gene_variant,,ENST00000505505,;	G	ENSG00000004399	ENST00000324093	Transcript	missense_variant	3976	3797	1266	G/A	gGg/gCg	.	.	.	-1	PLXND1	HGNC	9107	protein_coding	YES	CCDS33854.1	ENSP00000317128	PLXD1_HUMAN	Q6P657_HUMAN	UPI00003671AD	.	tolerated(0.06)	benign(0.188)	20/36	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCCCCCAGC	.	2	ESCA
COL6A5	0	.	GRCh37	3	130116450	130116450	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3592G>T	p.Gly1198Trp	p.G1198W	ENST00000265379	9/42	11	1	10	20	20	0	COL6A5,missense_variant,p.Gly1198Trp,ENST00000432398,;COL6A5,missense_variant,p.Gly1198Trp,ENST00000265379,;COL6A5,missense_variant,p.Gly1198Trp,ENST00000312481,;	T	ENSG00000172752	ENST00000265379	Transcript	missense_variant	4086	3592	1198	G/W	Ggg/Tgg	.	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	deleterious(0)	probably_damaging(0.999)	9/42	.	hmmpanther:PTHR22992:SF93,hmmpanther:PTHR22992,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGGTTGGGTTT	.	3	ESCA
PRR23A	0	.	GRCh37	3	138724356	138724356	+	Missense_Mutation	SNP	G	G	T	rs780074059	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.755C>A	p.Pro252Gln	p.P252Q	ENST00000383163	1/1	75	23	52	38	38	0	PRR23A,missense_variant,p.Pro252Gln,ENST00000383163,;MRPS22,upstream_gene_variant,,ENST00000495075,;	T	ENSG00000206260	ENST00000383163	Transcript	missense_variant	755	755	252	P/Q	cCg/cAg	rs780074059	.	.	-1	PRR23A	HGNC	37172	protein_coding	YES	CCDS46923.1	ENSP00000372649	PR23A_HUMAN	.	UPI00003671C1	.	deleterious(0.01)	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31813:SF2,hmmpanther:PTHR31813,Pfam_domain:PF10630	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTCGGGAGC	byFrequency	5	ESCA
PLS1	0	.	GRCh37	3	142395088	142395088	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454G>A	p.Asp152Asn	p.D152N	ENST00000337777	5/16	67	55	12	36	36	0	PLS1,missense_variant,p.Asp152Asn,ENST00000337777,;PLS1,missense_variant,p.Asp152Asn,ENST00000457734,;PLS1,missense_variant,p.Asp152Asn,ENST00000497002,;PLS1,missense_variant,p.Asp73Asn,ENST00000476044,;RN7SKP25,downstream_gene_variant,,ENST00000362449,;	A	ENSG00000120756	ENST00000337777	Transcript	missense_variant	667	454	152	D/N	Gat/Aat	.	.	.	1	PLS1	HGNC	9090	protein_coding	YES	CCDS3125.1	ENSP00000336831	PLSI_HUMAN	C9JYI1_HUMAN,C9JVY2_HUMAN,C9JU08_HUMAN,C9JAM8_HUMAN,C9JAM3_HUMAN,C9J359_HUMAN,C9J0F3_HUMAN	UPI000013D59A	.	tolerated(0.5)	benign(0.044)	5/16	.	PROSITE_profiles:PS50021,hmmpanther:PTHR19961:SF27,hmmpanther:PTHR19961,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAATGATGAT	.	5	ESCA
PLSCR1	0	.	GRCh37	3	146239439	146239456	+	In_Frame_Del	DEL	CCAAGTCTGAATAACATA	CCAAGTCTGAATAACATA	-	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	CCAAGTCTGAATAACATA	CCAAGTCTGAATAACATA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.613_630delTATGTTATTCAGACTTGG	p.Tyr205_Trp210del	p.Y205_W210del	ENST00000342435	7/9	83	70	13	29	29	0	PLSCR1,inframe_deletion,p.Tyr181_Trp186del,ENST00000462666,;PLSCR1,inframe_deletion,p.Tyr72_Trp77del,ENST00000483300,;PLSCR1,inframe_deletion,p.Tyr198_Trp203del,ENST00000487389,;PLSCR1,inframe_deletion,p.Tyr205_Trp210del,ENST00000472349,;PLSCR1,inframe_deletion,p.Tyr124_Trp129del,ENST00000486631,;PLSCR1,inframe_deletion,p.Tyr124_Trp129del,ENST00000448787,;PLSCR1,inframe_deletion,p.Tyr205_Trp210del,ENST00000342435,;PLSCR1,intron_variant,,ENST00000448205,;PLSCR1,non_coding_transcript_exon_variant,,ENST00000470496,;PLSCR1,upstream_gene_variant,,ENST00000484560,;PLSCR1,3_prime_UTR_variant,,ENST00000489775,;PLSCR1,3_prime_UTR_variant,,ENST00000468985,;PLSCR1,3_prime_UTR_variant,,ENST00000478267,;PLSCR1,3_prime_UTR_variant,,ENST00000488253,;PLSCR1,intron_variant,,ENST00000463777,;PLSCR1,intron_variant,,ENST00000493432,;PLSCR1,downstream_gene_variant,,ENST00000490745,;PLSCR1,downstream_gene_variant,,ENST00000494568,;	-	ENSG00000188313	ENST00000342435	Transcript	inframe_deletion	1024-1041	613-630	205-210	YVIQTW/-	TATGTTATTCAGACTTGG/-	.	.	.	-1	PLSCR1	HGNC	9092	protein_coding	YES	CCDS3135.1	ENSP00000345494	PLS1_HUMAN	C9JSI9_HUMAN,C9JE06_HUMAN,C9J7K9_HUMAN	UPI0000001627	.	.	.	7/9	.	Pfam_domain:PF03803,hmmpanther:PTHR23248,hmmpanther:PTHR23248:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	TGGGTGCCAAGTCTGAATAACATAACCTA	.	2	ESCA
RFTN1	0	.	GRCh37	3	16419499	16419499	+	Silent	SNP	G	G	T	rs371329309	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552C>A	p.%3D	p.T184T	ENST00000334133	5/10	11	1	10	19	19	0	RFTN1,synonymous_variant,p.%3D,ENST00000432519,;RFTN1,synonymous_variant,p.%3D,ENST00000334133,;RFTN1,synonymous_variant,p.%3D,ENST00000451036,;RFTN1,downstream_gene_variant,,ENST00000449415,;RFTN1,downstream_gene_variant,,ENST00000441460,;RFTN1,non_coding_transcript_exon_variant,,ENST00000495666,;RFTN1,downstream_gene_variant,,ENST00000470458,;RFTN1,downstream_gene_variant,,ENST00000484752,;	T	ENSG00000131378	ENST00000334133	Transcript	synonymous_variant	825	552	184	T	acC/acA	rs371329309	.	.	-1	RFTN1	HGNC	30278	protein_coding	YES	CCDS33712.1	ENSP00000334153	RFTN1_HUMAN	C9JRN3_HUMAN,C9JWQ9_HUMAN,C9JHG2_HUMAN,B4E1H7_HUMAN	UPI00001C1DE7	.	.	.	5/10	.	hmmpanther:PTHR17601:SF3,hmmpanther:PTHR17601,Pfam_domain:PF15250	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCTCGGTGCT	byFrequency|byCluster	3	ESCA
PEX5L	0	.	GRCh37	3	179519471	179519471	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*145G>A	.	.	ENST00000467460	15/15	133	101	32	46	46	0	PEX5L,3_prime_UTR_variant,,ENST00000392649,;PEX5L,3_prime_UTR_variant,,ENST00000472994,;PEX5L,3_prime_UTR_variant,,ENST00000263962,;PEX5L,3_prime_UTR_variant,,ENST00000476138,;PEX5L,3_prime_UTR_variant,,ENST00000485199,;PEX5L,3_prime_UTR_variant,,ENST00000468741,;PEX5L,3_prime_UTR_variant,,ENST00000467460,;PEX5L,downstream_gene_variant,,ENST00000464614,;PEX5L,downstream_gene_variant,,ENST00000465751,;RP11-494H4.3,upstream_gene_variant,,ENST00000602704,;PEX5L,non_coding_transcript_exon_variant,,ENST00000467440,;	T	ENSG00000114757	ENST00000467460	Transcript	3_prime_UTR_variant	2357	.	.	.	.	.	.	.	-1	PEX5L	HGNC	30024	protein_coding	YES	CCDS3236.1	ENSP00000419975	PEX5R_HUMAN	C9JZE2_HUMAN,C9IZ09_HUMAN	UPI0000049CE2	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTCCACAG	.	5	ESCA
DVL3	0	.	GRCh37	3	183882071	183882071	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.248G>A	p.Gly83Asp	p.G83D	ENST00000313143	3/15	75	12	62	26	26	0	DVL3,missense_variant,p.Gly83Asp,ENST00000313143,;DVL3,missense_variant,p.Gly83Asp,ENST00000431765,;DVL3,5_prime_UTR_variant,,ENST00000423300,;EIF2B5,intron_variant,,ENST00000444495,;DVL3,non_coding_transcript_exon_variant,,ENST00000462665,;DVL3,3_prime_UTR_variant,,ENST00000435708,;DVL3,non_coding_transcript_exon_variant,,ENST00000478247,;DVL3,upstream_gene_variant,,ENST00000467873,;DVL3,upstream_gene_variant,,ENST00000478639,;	A	ENSG00000161202	ENST00000313143	Transcript	missense_variant	496	248	83	G/D	gGc/gAc	.	.	.	1	DVL3	HGNC	3087	protein_coding	YES	CCDS3253.1	ENSP00000316054	DVL3_HUMAN	Q8WVA8_HUMAN,C9K0P9_HUMAN	UPI00001299A9	.	deleterious(0.02)	benign(0.172)	3/15	.	hmmpanther:PTHR10878:SF6,hmmpanther:PTHR10878	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGGGCTCAC	.	5	ESCA
CHRD	0	.	GRCh37	3	184107319	184107319	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*109C>A	.	.	ENST00000204604	23/23	83	61	22	39	39	0	CHRD,3_prime_UTR_variant,,ENST00000204604,;CHRD,3_prime_UTR_variant,,ENST00000450923,;CHRD,3_prime_UTR_variant,,ENST00000348986,;CHRD,3_prime_UTR_variant,,ENST00000545352,;EIF2B5,intron_variant,,ENST00000444495,;CHRD,3_prime_UTR_variant,,ENST00000448472,;CHRD,3_prime_UTR_variant,,ENST00000420973,;CHRD,non_coding_transcript_exon_variant,,ENST00000460627,;CHRD,non_coding_transcript_exon_variant,,ENST00000470150,;CHRD,downstream_gene_variant,,ENST00000464833,;	A	ENSG00000090539	ENST00000204604	Transcript	3_prime_UTR_variant	3223	.	.	.	.	.	.	.	1	CHRD	HGNC	1949	protein_coding	YES	CCDS3266.1	ENSP00000204604	CHRD_HUMAN	Q8N2W7_HUMAN	UPI000013C64D	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTCCTCTGT	.	5	ESCA
EIF4A2	0	.	GRCh37	3	186507064	186507064	+	3'UTR	SNP	G	G	C	rs778652756	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6G>C	.	.	ENST00000323963	11/11	63	54	8	31	31	0	EIF4A2,3_prime_UTR_variant,,ENST00000323963,;EIF4A2,3_prime_UTR_variant,,ENST00000356531,;EIF4A2,3_prime_UTR_variant,,ENST00000440191,;RFC4,downstream_gene_variant,,ENST00000418288,;RFC4,downstream_gene_variant,,ENST00000296273,;RFC4,downstream_gene_variant,,ENST00000433496,;RFC4,downstream_gene_variant,,ENST00000447345,;EIF4A2,downstream_gene_variant,,ENST00000445596,;EIF4A2,downstream_gene_variant,,ENST00000441007,;EIF4A2,downstream_gene_variant,,ENST00000498746,;RFC4,downstream_gene_variant,,ENST00000392481,;RFC4,downstream_gene_variant,,ENST00000417876,;SNORA81,downstream_gene_variant,,ENST00000408493,;SNORA63,downstream_gene_variant,,ENST00000363548,;SNORD2,downstream_gene_variant,,ENST00000459163,;SNORA4,downstream_gene_variant,,ENST00000584302,;SNORA63,downstream_gene_variant,,ENST00000363450,;EIF4A2,3_prime_UTR_variant,,ENST00000426808,;EIF4A2,3_prime_UTR_variant,,ENST00000443963,;EIF4A2,3_prime_UTR_variant,,ENST00000425053,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000496382,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000485101,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000494445,;EIF4A2,downstream_gene_variant,,ENST00000465032,;EIF4A2,downstream_gene_variant,,ENST00000465222,;EIF4A2,downstream_gene_variant,,ENST00000497177,;EIF4A2,downstream_gene_variant,,ENST00000475409,;EIF4A2,downstream_gene_variant,,ENST00000491473,;EIF4A2,downstream_gene_variant,,ENST00000495049,;EIF4A2,downstream_gene_variant,,ENST00000465267,;EIF4A2,downstream_gene_variant,,ENST00000486805,;EIF4A2,downstream_gene_variant,,ENST00000475653,;RFC4,downstream_gene_variant,,ENST00000460408,;RFC4,downstream_gene_variant,,ENST00000479307,;EIF4A2,downstream_gene_variant,,ENST00000468362,;EIF4A2,downstream_gene_variant,,ENST00000467585,;EIF4A2,downstream_gene_variant,,ENST00000465792,;EIF4A2,downstream_gene_variant,,ENST00000429589,;EIF4A2,downstream_gene_variant,,ENST00000466362,;EIF4A2,downstream_gene_variant,,ENST00000492144,;EIF4A2,downstream_gene_variant,,ENST00000461021,;RFC4,downstream_gene_variant,,ENST00000494047,;RFC4,downstream_gene_variant,,ENST00000449502,;	C	ENSG00000156976	ENST00000323963	Transcript	3_prime_UTR_variant	1294	.	.	.	.	rs778652756	.	.	1	EIF4A2	HGNC	3284	protein_coding	YES	CCDS3282.1	ENSP00000326381	IF4A2_HUMAN	Q96B07_HUMAN,J3KSN7_HUMAN,E7EMV8_HUMAN,C9JUF0_HUMAN	UPI0000000DD2	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTGGGATG	.	4	ESCA
MASP1	0	.	GRCh37	3	186947631	186947631	+	3'Flank	SNP	C	C	T	rs150028177	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000296280	.	90	70	19	28	28	0	MASP1,missense_variant,p.Arg453His,ENST00000337774,;MASP1,downstream_gene_variant,,ENST00000392472,;MASP1,downstream_gene_variant,,ENST00000296280,;MASP1,non_coding_transcript_exon_variant,,ENST00000468121,;MASP1,downstream_gene_variant,,ENST00000480349,;	T	ENSG00000127241	ENST00000296280	Transcript	downstream_gene_variant	.	.	.	.	.	rs150028177	.	4239	-1	MASP1	HGNC	6901	protein_coding	YES	CCDS33908.1	ENSP00000296280	MASP1_HUMAN	Q9NSY8_HUMAN,C9JLU5_HUMAN	UPI000007256E	.	.	.	.	.	.	T:0.0014	T:0.0038	T:0.0014	.	T:0	T:0	T:0.001	T:0.0011	T:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCGTCCA	byFrequency|byCluster|by1000G	5	ESCA
ZNF445	0	.	GRCh37	3	44491967	44491967	+	Silent	SNP	C	C	A	rs753760112	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792G>T	p.%3D	p.L264L	ENST00000425708	5/7	43	10	33	57	57	0	ZNF445,synonymous_variant,p.%3D,ENST00000425708,;ZNF445,synonymous_variant,p.%3D,ENST00000396077,;ZNF445,non_coding_transcript_exon_variant,,ENST00000460529,;ZNF445,downstream_gene_variant,,ENST00000474600,;	A	ENSG00000185219	ENST00000425708	Transcript	synonymous_variant	1134	792	264	L	ctG/ctT	rs753760112	.	.	-1	ZNF445	HGNC	21018	protein_coding	YES	CCDS2713.1	ENSP00000413073	ZN445_HUMAN	B7ZKX2_HUMAN	UPI000019AD12	.	.	.	5/7	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24385:SF48,hmmpanther:PTHR24385,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCCAGCAT	.	5	ESCA
DNAH12	0	.	GRCh37	3	57431006	57431006	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4251C>T	p.%3D	p.L1417L	ENST00000351747	28/59	38	2	36	36	36	0	DNAH12,synonymous_variant,p.%3D,ENST00000351747,;DNAH12,synonymous_variant,p.%3D,ENST00000495027,;	A	ENSG00000174844	ENST00000351747	Transcript	synonymous_variant	4432	4251	1417	L	ctC/ctT	.	.	.	-1	DNAH12	HGNC	2943	protein_coding	.	.	ENSP00000295937	DYH12_HUMAN	O15436_HUMAN	UPI00017AA3A8	.	.	.	28/59	.	hmmpanther:PTHR10676:SF250,hmmpanther:PTHR10676,Pfam_domain:PF12774,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGAGAGCTG	.	5	ESCA
GRM7	0	.	GRCh37	3	7188296	7188296	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.677C>A	p.Ser226Ter	p.S226*	ENST00000357716	2/10	31	5	26	37	37	0	GRM7,stop_gained,p.Ser226Ter,ENST00000402647,;GRM7,stop_gained,p.Ser226Ter,ENST00000486284,;GRM7,stop_gained,p.Ser18Ter,ENST00000448328,;GRM7,stop_gained,p.Ser226Ter,ENST00000389336,;GRM7,stop_gained,p.Ser226Ter,ENST00000357716,;GRM7,stop_gained,p.Ser226Ter,ENST00000403881,;GRM7,stop_gained,p.Ser226Ter,ENST00000389335,;GRM7,stop_gained,p.Ser226Ter,ENST00000467425,;GRM7,stop_gained,p.Ser226Ter,ENST00000440923,;GRM7,3_prime_UTR_variant,,ENST00000443259,;GRM7,3_prime_UTR_variant,,ENST00000435689,;	A	ENSG00000196277	ENST00000357716	Transcript	stop_gained	951	677	226	S/*	tCg/tAg	.	.	.	1	GRM7	HGNC	4599	protein_coding	YES	CCDS43042.1	ENSP00000350348	GRM7_HUMAN	C9JU97_HUMAN	UPI000004A7E3	.	.	.	2/10	.	hmmpanther:PTHR24060:SF104,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCATCGGAAG	.	5	ESCA
GRM7	0	.	GRCh37	3	7456848	7456848	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1172C>A	p.Thr391Lys	p.T391K	ENST00000357716	5/10	33	4	29	52	52	0	GRM7,missense_variant,p.Thr391Lys,ENST00000402647,;GRM7,missense_variant,p.Thr391Lys,ENST00000486284,;GRM7,missense_variant,p.Thr48Lys,ENST00000445087,;GRM7,missense_variant,p.Thr391Lys,ENST00000389336,;GRM7,missense_variant,p.Thr391Lys,ENST00000357716,;GRM7,missense_variant,p.Thr391Lys,ENST00000403881,;GRM7,missense_variant,p.Thr391Lys,ENST00000389335,;GRM7,missense_variant,p.Thr391Lys,ENST00000467425,;GRM7,missense_variant,p.Thr391Lys,ENST00000440923,;GRM7,splice_region_variant,,ENST00000463676,;GRM7,non_coding_transcript_exon_variant,,ENST00000461677,;	A	ENSG00000196277	ENST00000357716	Transcript	missense_variant	1446	1172	391	T/K	aCa/aAa	.	.	.	1	GRM7	HGNC	4599	protein_coding	YES	CCDS43042.1	ENSP00000350348	GRM7_HUMAN	C9JU97_HUMAN	UPI000004A7E3	.	deleterious(0.05)	possibly_damaging(0.824)	5/10	.	hmmpanther:PTHR24060:SF104,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCACAGGTA	.	5	ESCA
PRRT3	0	.	GRCh37	3	9991025	9991025	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775G>A	p.Glu259Lys	p.E259K	ENST00000412055	2/4	16	3	13	23	23	0	PRRT3,missense_variant,p.Glu259Lys,ENST00000411976,;PRRT3,missense_variant,p.Glu259Lys,ENST00000412055,;CRELD1,downstream_gene_variant,,ENST00000435417,;CRELD1,downstream_gene_variant,,ENST00000452070,;CRELD1,downstream_gene_variant,,ENST00000383811,;CRELD1,downstream_gene_variant,,ENST00000326434,;CRELD1,downstream_gene_variant,,ENST00000397170,;PRRT3-AS1,intron_variant,,ENST00000431558,;CRELD1,downstream_gene_variant,,ENST00000489674,;PRRT3,missense_variant,p.Glu259Lys,ENST00000295984,;CRELD1,downstream_gene_variant,,ENST00000482691,;	T	ENSG00000163704	ENST00000412055	Transcript	missense_variant	905	775	259	E/K	Gag/Aag	.	.	.	-1	PRRT3	HGNC	26591	protein_coding	YES	CCDS43049.1	ENSP00000392511	PRRT3_HUMAN	.	UPI000019962A	.	tolerated_low_confidence(0.12)	benign(0.016)	2/4	.	hmmpanther:PTHR21712,hmmpanther:PTHR21712:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCAACTG	.	5	ESCA
BANK1	0	.	GRCh37	4	102951371	102951371	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1849C>T	p.Arg617Ter	p.R617*	ENST00000322953	10/17	32	6	26	38	38	0	BANK1,stop_gained,p.Arg484Ter,ENST00000508653,;BANK1,stop_gained,p.Arg484Ter,ENST00000428908,;BANK1,stop_gained,p.Arg602Ter,ENST00000504592,;BANK1,stop_gained,p.Arg587Ter,ENST00000444316,;BANK1,stop_gained,p.Arg617Ter,ENST00000322953,;RP11-498M5.2,intron_variant,,ENST00000505091,;BANK1,downstream_gene_variant,,ENST00000510950,;	T	ENSG00000153064	ENST00000322953	Transcript	stop_gained	2123	1849	617	R/*	Cga/Tga	.	.	.	1	BANK1	HGNC	18233	protein_coding	YES	CCDS34038.1	ENSP00000320509	BANK1_HUMAN	.	UPI0000D6159D	.	.	.	10/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCCGACCC	.	5	ESCA
UGT8	0	.	GRCh37	4	115585172	115585172	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844G>T	p.Gly282Cys	p.G282C	ENST00000310836	3/6	42	25	16	30	30	0	UGT8,missense_variant,p.Gly282Cys,ENST00000310836,;UGT8,missense_variant,p.Gly282Cys,ENST00000394511,;	T	ENSG00000174607	ENST00000310836	Transcript	missense_variant	1366	844	282	G/C	Ggt/Tgt	.	.	.	1	UGT8	HGNC	12555	protein_coding	YES	CCDS3705.1	ENSP00000311648	CGT_HUMAN	D6RFW2_HUMAN	UPI000013F094	.	deleterious(0.03)	possibly_damaging(0.907)	3/6	.	Superfamily_domains:SSF53756,Pfam_domain:PF00201,Gene3D:3.40.50.2000,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAATGGTGCT	.	5	ESCA
MAB21L2	0	.	GRCh37	4	151504491	151504491	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310G>A	p.Asp104Asn	p.D104N	ENST00000317605	1/1	25	10	14	30	30	0	MAB21L2,missense_variant,p.Asp104Asn,ENST00000317605,;LRBA,intron_variant,,ENST00000510413,;LRBA,intron_variant,,ENST00000509835,;LRBA,intron_variant,,ENST00000535741,;LRBA,intron_variant,,ENST00000357115,;LRBA,intron_variant,,ENST00000507224,;RP11-1336O20.2,downstream_gene_variant,,ENST00000507934,;LRBA,intron_variant,,ENST00000513021,;LRBA,upstream_gene_variant,,ENST00000503716,;	A	ENSG00000181541	ENST00000317605	Transcript	missense_variant	1415	310	104	D/N	Gat/Aat	.	.	.	1	MAB21L2	HGNC	6758	protein_coding	YES	CCDS3774.1	ENSP00000324701	MB212_HUMAN	.	UPI000007290D	.	tolerated(0.1)	probably_damaging(0.99)	1/1	.	Pfam_domain:PF03281,hmmpanther:PTHR10656:SF37,hmmpanther:PTHR10656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGCGATGGG	.	5	ESCA
PDGFC	0	.	GRCh37	4	157732016	157732016	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.468C>T	p.%3D	p.F156F	ENST00000502773	3/6	41	22	18	24	24	0	PDGFC,synonymous_variant,p.%3D,ENST00000502773,;PDGFC,synonymous_variant,p.%3D,ENST00000422544,;PDGFC,5_prime_UTR_variant,,ENST00000541126,;PDGFC,5_prime_UTR_variant,,ENST00000542208,;PDGFC,non_coding_transcript_exon_variant,,ENST00000511985,;PDGFC,intron_variant,,ENST00000512711,;PDGFC,synonymous_variant,p.%3D,ENST00000506880,;PDGFC,3_prime_UTR_variant,,ENST00000274071,;	A	ENSG00000145431	ENST00000502773	Transcript	synonymous_variant	959	468	156	F	ttC/ttT	.	.	.	-1	PDGFC	HGNC	8801	protein_coding	YES	CCDS3795.1	ENSP00000422464	PDGFC_HUMAN	.	UPI0000034814	.	.	.	3/6	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF570,hmmpanther:PTHR10127,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCAGAACCC	.	5	ESCA
GLRA3	0	.	GRCh37	4	175565081	175565081	+	Missense_Mutation	SNP	C	C	G	rs748223691	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1251G>C	p.Met417Ile	p.M417I	ENST00000274093	10/10	52	28	23	39	39	0	GLRA3,missense_variant,p.Met417Ile,ENST00000274093,;GLRA3,missense_variant,p.Met402Ile,ENST00000340217,;	G	ENSG00000145451	ENST00000274093	Transcript	missense_variant	1754	1251	417	M/I	atG/atC	rs748223691	.	.	-1	GLRA3	HGNC	4328	protein_coding	YES	CCDS3822.1	ENSP00000274093	GLRA3_HUMAN	Q9UPF3_HUMAN,Q4W595_HUMAN	UPI0000001C50	.	tolerated(0.43)	benign(0.003)	10/10	.	hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF455,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCATTTC	.	5	ESCA
TRIML2	0	.	GRCh37	4	189026335	189026335	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38G>T	p.Arg13Met	p.R13M	ENST00000512729	1/7	61	34	27	46	46	0	TRIML2,missense_variant,p.Arg13Met,ENST00000326754,;TRIML2,missense_variant,p.Arg63Met,ENST00000536972,;TRIML2,missense_variant,p.Arg13Met,ENST00000512729,;TRIML2,downstream_gene_variant,,ENST00000394461,;TRIML2,downstream_gene_variant,,ENST00000502707,;TRIML2,splice_region_variant,,ENST00000511771,;TRIML2,upstream_gene_variant,,ENST00000503475,;TRIML2,upstream_gene_variant,,ENST00000503141,;RP11-713C19.1,upstream_gene_variant,,ENST00000464002,;	A	ENSG00000179046	ENST00000512729	Transcript	missense_variant	413	38	13	R/M	aGg/aTg	.	.	.	-1	TRIML2	HGNC	26378	protein_coding	YES	CCDS3850.1	ENSP00000422581	TRIMM_HUMAN	.	UPI000007300A	.	deleterious(0)	probably_damaging(0.91)	1/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103:SF267,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACCCTGTAA	.	5	ESCA
ZNF595	0	.	GRCh37	4	53332	53332	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-51G>A	.	.	ENST00000526473	1/4	196	167	28	317	317	0	ZNF595,5_prime_UTR_variant,,ENST00000526473,;ZNF595,5_prime_UTR_variant,,ENST00000509152,;ZNF595,non_coding_transcript_exon_variant,,ENST00000339368,;ZNF595,non_coding_transcript_exon_variant,,ENST00000512065,;ZNF595,non_coding_transcript_exon_variant,,ENST00000507368,;Z95704.4,upstream_gene_variant,,ENST00000596885,;ZNF595,non_coding_transcript_exon_variant,,ENST00000502981,;Z95704.4,upstream_gene_variant,,ENST00000503774,;	A	ENSG00000197701	ENST00000526473	Transcript	5_prime_UTR_variant	123	.	.	.	.	.	.	.	1	ZNF595	HGNC	27196	protein_coding	YES	.	ENSP00000437878	.	F5H663_HUMAN	UPI00020651F4	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGAGGGTAT	.	4	ESCA
PDGFRA	0	.	GRCh37	4	55164039	55164039	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2600G>C	.	.	ENST00000257290	23/23	58	37	21	36	36	0	PDGFRA,3_prime_UTR_variant,,ENST00000257290,;FIP1L1,downstream_gene_variant,,ENST00000507166,;	C	ENSG00000134853	ENST00000257290	Transcript	3_prime_UTR_variant	6201	.	.	.	.	.	.	.	1	PDGFRA	HGNC	8803	protein_coding	YES	CCDS3495.1	ENSP00000257290	PGFRA_HUMAN	D6RIG5_HUMAN,D6RG11_HUMAN,D6RDX0_HUMAN	UPI0000131793	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAGAGGGA	.	5	ESCA
JAKMIP1	0	.	GRCh37	4	6050609	6050609	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2003G>T	p.Gly668Val	p.G668V	ENST00000409021	16/21	27	3	23	51	51	0	JAKMIP1,missense_variant,p.Gly668Val,ENST00000409021,;JAKMIP1,missense_variant,p.Gly483Val,ENST00000409371,;JAKMIP1,downstream_gene_variant,,ENST00000409831,;JAKMIP1,downstream_gene_variant,,ENST00000282924,;JAKMIP1,downstream_gene_variant,,ENST00000410077,;JAKMIP1,downstream_gene_variant,,ENST00000473053,;	A	ENSG00000152969	ENST00000409021	Transcript	missense_variant	2453	2003	668	G/V	gGa/gTa	COSM339174	.	.	-1	JAKMIP1	HGNC	26460	protein_coding	YES	CCDS47005.1	ENSP00000386711	JKIP1_HUMAN	F2Z2K5_HUMAN	UPI00015734C1	.	tolerated(0.09)	probably_damaging(0.999)	16/21	.	hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCCAGCT	.	5	ESCA
JAKMIP1	0	.	GRCh37	4	6050610	6050610	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2002G>T	p.Gly668Ter	p.G668*	ENST00000409021	16/21	26	3	22	52	52	0	JAKMIP1,stop_gained,p.Gly668Ter,ENST00000409021,;JAKMIP1,stop_gained,p.Gly483Ter,ENST00000409371,;JAKMIP1,downstream_gene_variant,,ENST00000409831,;JAKMIP1,downstream_gene_variant,,ENST00000282924,;JAKMIP1,downstream_gene_variant,,ENST00000410077,;JAKMIP1,downstream_gene_variant,,ENST00000473053,;	A	ENSG00000152969	ENST00000409021	Transcript	stop_gained	2452	2002	668	G/*	Gga/Tga	.	.	.	-1	JAKMIP1	HGNC	26460	protein_coding	YES	CCDS47005.1	ENSP00000386711	JKIP1_HUMAN	F2Z2K5_HUMAN	UPI00015734C1	.	.	.	16/21	.	hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTCCAGCTT	.	5	ESCA
YTHDC1	0	.	GRCh37	4	69179699	69179699	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*118G>C	.	.	ENST00000344157	17/17	29	13	15	19	19	0	YTHDC1,3_prime_UTR_variant,,ENST00000355665,;YTHDC1,3_prime_UTR_variant,,ENST00000579690,;YTHDC1,3_prime_UTR_variant,,ENST00000344157,;YTHDC1,downstream_gene_variant,,ENST00000507529,;	G	ENSG00000083896	ENST00000344157	Transcript	3_prime_UTR_variant	2638	.	.	.	.	.	.	.	-1	YTHDC1	HGNC	30626	protein_coding	YES	CCDS33992.1	ENSP00000339245	YTDC1_HUMAN	J3KS01_HUMAN	UPI000020B86D	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTCTACAC	.	5	ESCA
UGT2B15	0	.	GRCh37	4	69535727	69535727	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>A	p.Asp204Asn	p.D204N	ENST00000338206	1/6	89	59	30	68	68	0	UGT2B15,missense_variant,p.Asp204Asn,ENST00000338206,;	T	ENSG00000196620	ENST00000338206	Transcript	missense_variant	620	610	204	D/N	Gat/Aat	.	.	.	-1	UGT2B15	HGNC	12546	protein_coding	YES	CCDS3524.1	ENSP00000341045	UDB15_HUMAN	.	UPI000045721A	.	deleterious(0.02)	probably_damaging(0.958)	1/6	.	Superfamily_domains:SSF53756,Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF178	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATCACTTA	.	5	ESCA
UGT2A1	0	.	GRCh37	4	70461989	70461989	+	Silent	SNP	G	G	T	rs149416008	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.975C>A	p.%3D	p.A325A	ENST00000503640	3/6	45	23	21	51	51	0	UGT2A1,synonymous_variant,p.%3D,ENST00000503640,;UGT2A2,synonymous_variant,p.%3D,ENST00000457664,;UGT2A2,synonymous_variant,p.%3D,ENST00000604629,;UGT2A1,intron_variant,,ENST00000286604,;UGT2A1,intron_variant,,ENST00000514019,;UGT2A2,intron_variant,,ENST00000604021,;UGT2A1,intron_variant,,ENST00000512704,;UGT2A1,intron_variant,,ENST00000502343,;UGT2A1,downstream_gene_variant,,ENST00000514341,;	T	ENSG00000173610	ENST00000503640	Transcript	synonymous_variant	1031	975	325	A	gcC/gcA	rs149416008	.	.	-1	UGT2A1	HGNC	12542	protein_coding	YES	CCDS3529.1	ENSP00000424478	UD2A1_HUMAN	D6RHF3_HUMAN	UPI000013DE58	.	.	.	3/6	.	hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF116,Gene3D:3.40.50.2000,Pfam_domain:PF00201,Superfamily_domains:SSF53756	A:0.0016	A:0.0061	A:0	.	A:0	A:0	A:0	A:0.003	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAGGGCTGA	byFrequency|byCluster|by1000G	4	ESCA
MOB1B	0	.	GRCh37	4	71853520	71853520	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5746A>T	.	.	ENST00000309395	6/6	24	13	11	14	14	0	MOB1B,3_prime_UTR_variant,,ENST00000309395,;DCK,upstream_gene_variant,,ENST00000509617,;MOB1B,intron_variant,,ENST00000511449,;	T	ENSG00000173542	ENST00000309395	Transcript	3_prime_UTR_variant	6598	.	.	.	.	.	.	.	1	MOB1B	HGNC	29801	protein_coding	.	CCDS34002.1	ENSP00000310189	MOB1B_HUMAN	Q4W5E0_HUMAN	UPI00000742E9	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATTGAGAAGA	.	2	ESCA
MOB1B	0	.	GRCh37	4	71853521	71853521	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5747G>A	.	.	ENST00000309395	6/6	24	13	11	14	14	0	MOB1B,3_prime_UTR_variant,,ENST00000309395,;DCK,upstream_gene_variant,,ENST00000509617,;MOB1B,intron_variant,,ENST00000511449,;	A	ENSG00000173542	ENST00000309395	Transcript	3_prime_UTR_variant	6599	.	.	.	.	.	.	.	1	MOB1B	HGNC	29801	protein_coding	.	CCDS34002.1	ENSP00000310189	MOB1B_HUMAN	Q4W5E0_HUMAN	UPI00000742E9	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTGAGAAGAG	.	2	ESCA
GC	0	.	GRCh37	4	72669693	72669693	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-30G>T	.	.	ENST00000504199	1/14	39	23	16	20	20	0	GC,5_prime_UTR_variant,,ENST00000504199,;	A	ENSG00000145321	ENST00000504199	Transcript	5_prime_UTR_variant	66	.	.	.	.	.	.	.	-1	GC	HGNC	4187	protein_coding	YES	CCDS56332.1	ENSP00000421725	VTDB_HUMAN	D6RF20_HUMAN	UPI0001D3B4EE	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCATCACCAG	.	5	ESCA
ART3	0	.	GRCh37	4	77018807	77018807	+	Silent	SNP	C	C	A	rs746991811	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792C>A	p.%3D	p.T264T	ENST00000355810	4/12	67	40	27	51	50	0	ART3,synonymous_variant,p.%3D,ENST00000349321,;ART3,synonymous_variant,p.%3D,ENST00000355810,;ART3,synonymous_variant,p.%3D,ENST00000341029,;ART3,synonymous_variant,p.%3D,ENST00000511188,;AC112719.1,downstream_gene_variant,,ENST00000582318,;ART3,non_coding_transcript_exon_variant,,ENST00000510669,;ART3,non_coding_transcript_exon_variant,,ENST00000513494,;ART3,non_coding_transcript_exon_variant,,ENST00000504112,;ART3,intron_variant,,ENST00000506313,;ART3,intron_variant,,ENST00000395688,;ART3,intron_variant,,ENST00000506667,;	A	ENSG00000156219	ENST00000355810	Transcript	synonymous_variant	911	792	264	T	acC/acA	rs746991811,COSM3975028,COSM3975027	.	.	1	ART3	HGNC	725	protein_coding	YES	CCDS47079.1	ENSP00000348064	NAR3_HUMAN	Q5J1Q0_HUMAN,Q5J1P8_HUMAN,Q5J1K8_HUMAN,Q5J1K7_HUMAN,E9PGR5_HUMAN,E7EX61_HUMAN,E7ESB3_HUMAN,E7ER42_HUMAN	UPI000012FD7B	.	.	.	4/12	.	hmmpanther:PTHR10339:SF4,hmmpanther:PTHR10339	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAACCGAAAA	.	5	ESCA
NAA11	0	.	GRCh37	4	80246777	80246777	+	Silent	SNP	G	G	T	rs768813512	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255C>A	p.%3D	p.G85G	ENST00000286794	1/2	26	16	10	35	35	0	NAA11,synonymous_variant,p.%3D,ENST00000286794,;NAA11,upstream_gene_variant,,ENST00000513733,;NAA11,upstream_gene_variant,,ENST00000511542,;	T	ENSG00000156269	ENST00000286794	Transcript	synonymous_variant	428	255	85	G	ggC/ggA	rs768813512	.	.	-1	NAA11	HGNC	28125	protein_coding	YES	CCDS47084.1	ENSP00000286794	NAA11_HUMAN	H0Y8T0_HUMAN	UPI00000467CA	.	.	.	1/2	.	Superfamily_domains:SSF55729,Gene3D:3.40.630.30,Pfam_domain:PF00583,hmmpanther:PTHR23091,hmmpanther:PTHR23091:SF205,PROSITE_profiles:PS51186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGGCCGAG	.	5	ESCA
CCT5	0	.	GRCh37	5	10250452	10250452	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1C>T	.	.	ENST00000280326	1/11	73	29	44	51	51	0	CCT5,5_prime_UTR_variant,,ENST00000280326,;CCT5,5_prime_UTR_variant,,ENST00000515390,;CCT5,intron_variant,,ENST00000503026,;FAM173B,upstream_gene_variant,,ENST00000511437,;FAM173B,upstream_gene_variant,,ENST00000280330,;CCT5,upstream_gene_variant,,ENST00000506600,;FAM173B,upstream_gene_variant,,ENST00000510047,;CCT5,upstream_gene_variant,,ENST00000515676,;CTD-2256P15.1,downstream_gene_variant,,ENST00000509915,;FAM173B,upstream_gene_variant,,ENST00000510052,;CCT5,missense_variant,p.Pro33Leu,ENST00000511700,;CCT5,5_prime_UTR_variant,,ENST00000512975,;CCT5,non_coding_transcript_exon_variant,,ENST00000423695,;CCT5,non_coding_transcript_exon_variant,,ENST00000510326,;CCT5,non_coding_transcript_exon_variant,,ENST00000508451,;FAM173B,upstream_gene_variant,,ENST00000506108,;CCT5,upstream_gene_variant,,ENST00000503454,;FAM173B,upstream_gene_variant,,ENST00000504390,;FAM173B,upstream_gene_variant,,ENST00000508553,;	T	ENSG00000150753	ENST00000280326	Transcript	5_prime_UTR_variant	420	.	.	.	.	.	.	.	1	CCT5	HGNC	1618	protein_coding	YES	CCDS3877.1	ENSP00000280326	TCPE_HUMAN	Q9HB74_HUMAN,Q9BU08_HUMAN,Q96GI1_HUMAN,B7ZAR1_HUMAN	UPI0000001C34	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACCATGGC	.	5	ESCA
SLC6A19	0	.	GRCh37	5	1221849	1221849	+	Missense_Mutation	SNP	C	C	A	rs772229902	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735C>A	p.Pro579Thr	p.P579T	ENST00000304460	12/12	56	26	29	34	34	0	SLC6A19,missense_variant,p.Pro579Thr,ENST00000304460,;SLC6A18,upstream_gene_variant,,ENST00000324642,;SLC6A18,upstream_gene_variant,,ENST00000296821,;SLC6A19,3_prime_UTR_variant,,ENST00000515652,;SLC6A18,upstream_gene_variant,,ENST00000513607,;	A	ENSG00000174358	ENST00000304460	Transcript	missense_variant	1791	1735	579	P/T	Ccg/Acg	rs772229902	.	.	1	SLC6A19	HGNC	27960	protein_coding	YES	CCDS34130.1	ENSP00000305302	S6A19_HUMAN	B3KVZ8_HUMAN	UPI0000401AF8	.	deleterious(0)	probably_damaging(0.996)	12/12	.	PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF125,Pfam_domain:PF00209,Superfamily_domains:0053687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTACCCGAAC	.	5	ESCA
PCDHA2	0	.	GRCh37	5	140176748	140176748	+	Silent	SNP	G	G	A	rs146821058	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2199G>A	p.%3D	p.A733A	ENST00000526136	1/4	59	35	24	48	48	0	PCDHA2,synonymous_variant,p.%3D,ENST00000378132,;PCDHA2,synonymous_variant,p.%3D,ENST00000526136,;PCDHA2,synonymous_variant,p.%3D,ENST00000520672,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,upstream_gene_variant,,ENST00000532566,;PCDHA3,upstream_gene_variant,,ENST00000522353,;	A	ENSG00000204969	ENST00000526136	Transcript	synonymous_variant	2199	2199	733	A	gcG/gcA	rs146821058,COSM1433735,COSM1433734	.	.	1	PCDHA2	HGNC	8668	protein_coding	YES	CCDS54914.1	ENSP00000431748	PCDA2_HUMAN	.	UPI00001273C9	.	.	.	1/4	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60	T:0.0012	T:0.0045	T:0	.	T:0	T:0	T:0	T:0.0041	T:0	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R732H|c.2195G>A|3,BUFFER|p.R732H|c.2195G>A|3	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGCGCGCCAGG	byFrequency|byCluster|by1000G	4	ESCA
PCDHA9	0	.	GRCh37	5	140229769	140229769	+	Silent	SNP	G	G	C	rs782296330	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1689G>C	p.%3D	p.P563P	ENST00000532602	1/4	86	40	46	90	90	0	PCDHA9,synonymous_variant,p.%3D,ENST00000378122,;PCDHA9,synonymous_variant,p.%3D,ENST00000532602,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	C	ENSG00000204961	ENST00000532602	Transcript	synonymous_variant	2722	1689	563	P	ccG/ccC	rs782296330	.	.	1	PCDHA9	HGNC	8675	protein_coding	YES	CCDS54920.1	ENSP00000436042	PCDA9_HUMAN	.	UPI00001273D1	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCCGGCGCT	byFrequency	5	ESCA
PCDHAC2	0	.	GRCh37	5	140347251	140347251	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.900G>T	p.%3D	p.T300T	ENST00000289269	1/4	22	8	13	20	20	0	PCDHAC2,synonymous_variant,p.%3D,ENST00000289269,;PCDHAC1,intron_variant,,ENST00000253807,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA13,intron_variant,,ENST00000289272,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA13,intron_variant,,ENST00000409494,;	T	ENSG00000243232	ENST00000289269	Transcript	synonymous_variant	1432	900	300	T	acG/acT	.	.	.	1	PCDHAC2	HGNC	8677	protein_coding	YES	CCDS4242.1	ENSP00000289269	PCDC2_HUMAN	.	UPI0000127786	.	.	.	1/4	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF10,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACACGTCGGA	.	5	ESCA
PCDHAC1	0	.	GRCh37	5	140389716	140389716	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*194G>T	.	.	ENST00000253807	4/4	25	10	14	14	14	0	PCDHAC1,3_prime_UTR_variant,,ENST00000253807,;PCDHA1,3_prime_UTR_variant,,ENST00000504120,;PCDHA2,3_prime_UTR_variant,,ENST00000526136,;PCDHA10,3_prime_UTR_variant,,ENST00000506939,;PCDHA8,3_prime_UTR_variant,,ENST00000531613,;PCDHA6,3_prime_UTR_variant,,ENST00000529310,;PCDHA5,3_prime_UTR_variant,,ENST00000529859,;PCDHA11,3_prime_UTR_variant,,ENST00000398640,;PCDHA4,3_prime_UTR_variant,,ENST00000530339,;PCDHAC2,3_prime_UTR_variant,,ENST00000289269,;PCDHA12,3_prime_UTR_variant,,ENST00000398631,;PCDHA13,3_prime_UTR_variant,,ENST00000289272,;PCDHA1,3_prime_UTR_variant,,ENST00000394633,;PCDHA3,3_prime_UTR_variant,,ENST00000522353,;PCDHA7,3_prime_UTR_variant,,ENST00000525929,;PCDHA10,3_prime_UTR_variant,,ENST00000307360,;PCDHA9,3_prime_UTR_variant,,ENST00000532602,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA13,intron_variant,,ENST00000409494,;PCDHA6,downstream_gene_variant,,ENST00000527624,;	T	ENSG00000248383	ENST00000253807	Transcript	3_prime_UTR_variant	3086	.	.	.	.	.	.	.	1	PCDHAC1	HGNC	8676	protein_coding	YES	CCDS4241.1	ENSP00000253807	PCDC1_HUMAN	.	UPI000013CDF7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTGTTAAC	.	5	ESCA
PCDHB6	0	.	GRCh37	5	140531971	140531971	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2133G>T	p.%3D	p.L711L	ENST00000231136	1/1	127	77	50	132	132	0	PCDHB6,synonymous_variant,p.%3D,ENST00000543635,;PCDHB6,synonymous_variant,p.%3D,ENST00000231136,;PCDHB17,upstream_gene_variant,,ENST00000539533,;	T	ENSG00000113211	ENST00000231136	Transcript	synonymous_variant	2133	2133	711	L	ctG/ctT	.	.	.	1	PCDHB6	HGNC	8691	protein_coding	YES	CCDS4248.1	ENSP00000231136	PCDB6_HUMAN	F5H446_HUMAN	UPI00001273E2	.	.	.	1/1	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCTGTGCAG	.	5	ESCA
PCDHB7	0	.	GRCh37	5	140554449	140554449	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2033C>A	p.Pro678Gln	p.P678Q	ENST00000231137	1/1	113	70	43	110	110	0	PCDHB7,missense_variant,p.Pro678Gln,ENST00000231137,;PCDHB8,upstream_gene_variant,,ENST00000239444,;	A	ENSG00000113212	ENST00000231137	Transcript	missense_variant	2207	2033	678	P/Q	cCg/cAg	.	.	.	1	PCDHB7	HGNC	8692	protein_coding	YES	CCDS4249.1	ENSP00000231137	PCDB7_HUMAN	.	UPI00001273E3	.	tolerated_low_confidence(0.57)	benign(0.008)	1/1	.	hmmpanther:PTHR24028:SF69,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCCGGACC	.	5	ESCA
PCDHB13	0	.	GRCh37	5	140594187	140594187	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.492C>A	p.%3D	p.G164G	ENST00000341948	1/1	47	25	22	35	35	0	PCDHB13,synonymous_variant,p.%3D,ENST00000341948,;PCDHB12,downstream_gene_variant,,ENST00000541609,;PCDHB12,downstream_gene_variant,,ENST00000239450,;	A	ENSG00000187372	ENST00000341948	Transcript	synonymous_variant	679	492	164	G	ggC/ggA	.	.	.	1	PCDHB13	HGNC	8684	protein_coding	YES	CCDS4255.1	ENSP00000345491	PCDBD_HUMAN	.	UPI0000047816	.	.	.	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGGCCAAAA	.	5	ESCA
PCDHGC5	0	.	GRCh37	5	140869552	140869552	+	Missense_Mutation	SNP	G	G	T	rs761481986	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.745G>T	p.Val249Leu	p.V249L	ENST00000252087	1/4	42	24	18	49	49	0	PCDHGC5,missense_variant,p.Val249Leu,ENST00000252087,;PCDHGB6,intron_variant,,ENST00000520790,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGA10,intron_variant,,ENST00000398610,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA12,intron_variant,,ENST00000252085,;PCDHGA11,intron_variant,,ENST00000398587,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGC3,intron_variant,,ENST00000308177,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA11,intron_variant,,ENST00000518882,;PCDHGC4,intron_variant,,ENST00000306593,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGB7,intron_variant,,ENST00000398594,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;	T	ENSG00000240764	ENST00000252087	Transcript	missense_variant	745	745	249	V/L	Gtg/Ttg	rs761481986	.	.	1	PCDHGC5	HGNC	8718	protein_coding	YES	CCDS4263.1	ENSP00000252087	PCDGM_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006D689	.	deleterious(0.03)	possibly_damaging(0.686)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF80,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACGTGTGGGA	byFrequency	5	ESCA
ITK	0	.	GRCh37	5	156679678	156679678	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1853C>A	p.Ser618Ter	p.S618*	ENST00000422843	17/17	13	0	13	35	35	0	ITK,stop_gained,p.Ser618Ter,ENST00000422843,;ITK,non_coding_transcript_exon_variant,,ENST00000519749,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;	A	ENSG00000113263	ENST00000422843	Transcript	stop_gained	2005	1853	618	S/*	tCa/tAa	.	.	.	1	ITK	HGNC	6171	protein_coding	YES	CCDS4336.1	ENSP00000398655	ITK_HUMAN	Q7Z318_HUMAN,E5RFR5_HUMAN	UPI000004CADA	.	.	.	17/17	.	hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	AGAATCAGGAC	.	4	ESCA
SOX30	0	.	GRCh37	5	157075856	157075856	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000265007	2/5	58	26	31	62	62	0	SOX30,missense_variant,p.Arg339Gln,ENST00000311371,;SOX30,missense_variant,p.Arg339Gln,ENST00000265007,;SOX30,missense_variant,p.Arg34Gln,ENST00000519442,;	T	ENSG00000039600	ENST00000265007	Transcript	missense_variant	1358	1016	339	R/Q	cGa/cAa	.	.	.	-1	SOX30	HGNC	30635	protein_coding	YES	CCDS4339.1	ENSP00000265007	SOX30_HUMAN	.	UPI00001362BA	.	deleterious(0)	probably_damaging(1)	2/5	.	PROSITE_profiles:PS50118,hmmpanther:PTHR10270:SF10,hmmpanther:PTHR10270,Gene3D:1.10.30.10,Pfam_domain:PF00505,SMART_domains:SM00398,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGTCGCTTC	.	5	ESCA
CDH12	0	.	GRCh37	5	21751397	21751397	+	3'UTR	SNP	G	G	C	rs548167357	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*449C>G	.	.	ENST00000382254	15/15	166	114	52	117	117	0	CDH12,3_prime_UTR_variant,,ENST00000504376,;CDH12,3_prime_UTR_variant,,ENST00000382254,;CDH12,downstream_gene_variant,,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,downstream_gene_variant,,ENST00000521384,;CDH12,downstream_gene_variant,,ENST00000517378,;	C	ENSG00000154162	ENST00000382254	Transcript	3_prime_UTR_variant	3921	.	.	.	.	rs548167357	.	.	-1	CDH12	HGNC	1751	protein_coding	YES	CCDS3890.1	ENSP00000371689	CAD12_HUMAN	B3KRT0_HUMAN	UPI00000622EB	.	.	.	15/15	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCCGCAATA	by1000G	5	ESCA
NIPBL	0	.	GRCh37	5	37014784	37014784	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4561-1G>T	.	p.X1521_splice	ENST00000282516	.	40	28	12	22	22	0	NIPBL,splice_acceptor_variant,,ENST00000448238,;NIPBL,splice_acceptor_variant,,ENST00000282516,;	T	ENSG00000164190	ENST00000282516	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	NIPBL	HGNC	28862	protein_coding	YES	CCDS3920.1	ENSP00000282516	NIPBL_HUMAN	A2RRA7_HUMAN	UPI00003761B5	.	.	.	.	21/46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTAGATTGA	.	5	ESCA
PAPD7	0	.	GRCh37	5	6755387	6755387	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*329G>C	.	.	ENST00000230859	13/13	79	29	50	40	40	0	PAPD7,3_prime_UTR_variant,,ENST00000230859,;PAPD7,non_coding_transcript_exon_variant,,ENST00000514697,;PAPD7,downstream_gene_variant,,ENST00000514410,;PAPD7,downstream_gene_variant,,ENST00000505457,;	C	ENSG00000112941	ENST00000230859	Transcript	3_prime_UTR_variant	2087	.	.	.	.	.	.	.	1	PAPD7	HGNC	16705	protein_coding	YES	CCDS3871.1	ENSP00000230859	PAPD7_HUMAN	M1JCE6_HUMAN,D6RJD0_HUMAN,B7ZLL4_HUMAN,B4E0T3_HUMAN	UPI0000071E30	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGCGGTTTG	.	5	ESCA
MARVELD2	0	.	GRCh37	5	68715944	68715944	+	Silent	SNP	G	G	T	rs772911556	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732G>T	p.%3D	p.G244G	ENST00000325631	2/7	51	9	42	81	81	0	MARVELD2,synonymous_variant,p.%3D,ENST00000512803,;MARVELD2,synonymous_variant,p.%3D,ENST00000454295,;MARVELD2,synonymous_variant,p.%3D,ENST00000325631,;MARVELD2,splice_region_variant,,ENST00000436532,;MARVELD2,splice_region_variant,,ENST00000413223,;MARVELD2,downstream_gene_variant,,ENST00000515844,;	T	ENSG00000152939	ENST00000325631	Transcript	synonymous_variant	806	732	244	G	ggG/ggT	rs772911556	.	.	1	MARVELD2	HGNC	26401	protein_coding	YES	CCDS34175.1	ENSP00000323264	MALD2_HUMAN	D6RAH8_HUMAN,D6RA09_HUMAN	UPI00001416EB	.	.	.	2/7	.	Pfam_domain:PF01284,hmmpanther:PTHR23288,hmmpanther:PTHR23288:SF3,PROSITE_profiles:PS51225,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGGGGCTA	.	5	ESCA
C6orf183	0	.	GRCh37	6	109575736	109575736	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.574T>C	.	.	ENST00000453496	4/10	41	25	15	55	55	0	C6orf183,non_coding_transcript_exon_variant,,ENST00000453496,;	C	ENSG00000243587	ENST00000453496	Transcript	non_coding_transcript_exon_variant	574	.	.	.	.	.	.	.	1	C6orf183	HGNC	21562	processed_transcript	YES	.	.	.	.	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCGTGCACC	.	5	ESCA
MICAL1	0	.	GRCh37	6	109767598	109767598	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2322T>A	p.Ser774Arg	p.S774R	ENST00000358807	19/25	73	39	33	47	47	0	MICAL1,missense_variant,p.Ser774Arg,ENST00000358807,;MICAL1,missense_variant,p.Ser688Arg,ENST00000358577,;MICAL1,missense_variant,p.Ser793Arg,ENST00000368952,;SMPD2,downstream_gene_variant,,ENST00000258052,;SMPD2,downstream_gene_variant,,ENST00000458487,;MICAL1,downstream_gene_variant,,ENST00000433205,;MICAL1,non_coding_transcript_exon_variant,,ENST00000465904,;MICAL1,intron_variant,,ENST00000456101,;SMPD2,downstream_gene_variant,,ENST00000439615,;	T	ENSG00000135596	ENST00000358807	Transcript	missense_variant	2634	2322	774	S/R	agT/agA	.	.	.	-1	MICAL1	HGNC	20619	protein_coding	YES	CCDS5076.1	ENSP00000351664	MICA1_HUMAN	Q5TED7_HUMAN,H0UI45_HUMAN	UPI00000745D0	.	tolerated(0.32)	benign(0.004)	19/25	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCACTTGG	.	5	ESCA
CEP85L	0	.	GRCh37	6	118786703	118786703	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2292G>T	p.Glu764Asp	p.E764D	ENST00000368488	14/14	58	26	32	41	41	0	CEP85L,missense_variant,p.Glu764Asp,ENST00000368488,;CEP85L,missense_variant,p.Glu761Asp,ENST00000368491,;	A	ENSG00000111860	ENST00000368488	Transcript	missense_variant	2359	2292	764	E/D	gaG/gaT	.	.	.	-1	CEP85L	HGNC	21638	protein_coding	YES	CCDS55052.1	ENSP00000357474	CE85L_HUMAN	A2A3P3_HUMAN	UPI0001D1E40A	.	tolerated(0.29)	benign(0.171)	14/14	.	hmmpanther:PTHR31075,hmmpanther:PTHR31075:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATTCTCAGT	.	5	ESCA
RAET1K	0	.	GRCh37	6	150321319	150321319	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.900C>G	.	.	ENST00000533735	3/4	86	76	10	82	82	0	RAET1K,non_coding_transcript_exon_variant,,ENST00000533735,;RAET1K,non_coding_transcript_exon_variant,,ENST00000403651,;	C	ENSG00000218358	ENST00000533735	Transcript	non_coding_transcript_exon_variant	900	.	.	.	.	.	.	.	-1	RAET1K	HGNC	16797	processed_transcript	YES	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCAGAGAGG	.	4	ESCA
TULP4	0	.	GRCh37	6	158922786	158922786	+	Silent	SNP	G	G	A	rs750680160	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2091G>A	p.%3D	p.S697S	ENST00000367097	13/14	41	20	20	43	43	0	TULP4,synonymous_variant,p.%3D,ENST00000367097,;TULP4,intron_variant,,ENST00000367094,;	A	ENSG00000130338	ENST00000367097	Transcript	synonymous_variant	3448	2091	697	S	tcG/tcA	rs750680160	.	.	1	TULP4	HGNC	15530	protein_coding	YES	CCDS34561.1	ENSP00000356064	TULP4_HUMAN	.	UPI000013CD76	.	.	.	13/14	.	hmmpanther:PTHR16517,hmmpanther:PTHR16517:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCGGCTCA	.	5	ESCA
SLC22A1	0	.	GRCh37	6	160575942	160575942	+	Missense_Mutation	SNP	G	G	C	rs777622481	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498G>C	p.Ala500Pro	p.A500P	ENST00000366963	9/11	73	37	35	77	77	0	SLC22A1,missense_variant,p.Ala500Pro,ENST00000366963,;SLC22A1,intron_variant,,ENST00000324965,;SLC22A1,intron_variant,,ENST00000457470,;SLC22A1,splice_region_variant,,ENST00000539263,;SLC22A1,splice_region_variant,,ENST00000460902,;SLC22A1,upstream_gene_variant,,ENST00000478607,;	C	ENSG00000175003	ENST00000366963	Transcript	missense_variant	1645	1498	500	A/P	Gcg/Ccg	rs777622481	.	.	1	SLC22A1	HGNC	10963	protein_coding	YES	CCDS5274.1	ENSP00000355930	S22A1_HUMAN	F5GY86_HUMAN	UPI0000070FB1	.	deleterious(0.01)	possibly_damaging(0.827)	9/11	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00898,Pfam_domain:PF00083,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF214,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTGGTAAG	byFrequency	5	ESCA
THBS2	0	.	GRCh37	6	169617510	169617510	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*407A>G	.	.	ENST00000366787	23/23	12	5	6	16	16	0	THBS2,3_prime_UTR_variant,,ENST00000366787,;XXyac-YX65C7_A.2,intron_variant,,ENST00000444188,;THBS2,downstream_gene_variant,,ENST00000488355,;	C	ENSG00000186340	ENST00000366787	Transcript	3_prime_UTR_variant	4176	.	.	.	.	.	.	.	-1	THBS2	HGNC	11786	protein_coding	YES	CCDS34574.1	ENSP00000355751	TSP2_HUMAN	Q6MZL6_HUMAN,Q5RI53_HUMAN	UPI0000231C7F	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AATATTTTTCA	.	3	ESCA
NHLRC1	0	.	GRCh37	6	18121616	18121616	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*34T>A	.	.	ENST00000340650	1/1	28	19	8	27	27	0	NHLRC1,3_prime_UTR_variant,,ENST00000340650,;	T	ENSG00000187566	ENST00000340650	Transcript	3_prime_UTR_variant	1236	.	.	.	.	.	.	.	-1	NHLRC1	HGNC	21576	protein_coding	YES	CCDS4542.1	ENSP00000345464	NHLC1_HUMAN	.	UPI0000198CE1	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACTAGTGCT	.	5	ESCA
FAM65B	0	.	GRCh37	6	24875925	24875925	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.95G>T	p.Arg32Leu	p.R32L	ENST00000259698	2/23	42	27	15	20	20	0	FAM65B,missense_variant,p.Arg61Leu,ENST00000538035,;FAM65B,missense_variant,p.Arg32Leu,ENST00000378023,;FAM65B,missense_variant,p.Arg32Leu,ENST00000540914,;FAM65B,missense_variant,p.Arg32Leu,ENST00000259698,;FAM65B,missense_variant,p.Arg66Leu,ENST00000510784,;	A	ENSG00000111913	ENST00000259698	Transcript	missense_variant	271	95	32	R/L	cGa/cTa	.	.	.	-1	FAM65B	HGNC	13872	protein_coding	YES	CCDS47383.1	ENSP00000259698	FA65B_HUMAN	H3BP45_HUMAN	UPI0000EE554D	.	deleterious(0.01)	probably_damaging(0.93)	2/23	.	hmmpanther:PTHR15829,hmmpanther:PTHR15829:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATCGCCTT	.	5	ESCA
SLC17A4	0	.	GRCh37	6	25773853	25773853	+	Missense_Mutation	SNP	C	C	G	rs374082636	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938C>G	p.Ala313Gly	p.A313G	ENST00000377905	8/12	121	93	27	65	65	0	SLC17A4,missense_variant,p.Ala83Gly,ENST00000397076,;SLC17A4,missense_variant,p.Ala313Gly,ENST00000377905,;SLC17A4,intron_variant,,ENST00000439485,;	G	ENSG00000146039	ENST00000377905	Transcript	missense_variant	1057	938	313	A/G	gCg/gGg	rs374082636	.	.	1	SLC17A4	HGNC	10932	protein_coding	YES	CCDS4564.1	ENSP00000367137	S17A4_HUMAN	.	UPI0000073585	.	tolerated(0.23)	benign(0.114)	8/12	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF25,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGCGTACA	byFrequency|byCluster	5	ESCA
HIST1H1A	0	.	GRCh37	6	26017517	26017517	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444G>C	p.Lys148Asn	p.K148N	ENST00000244573	1/1	77	54	23	42	42	0	HIST1H1A,missense_variant,p.Lys148Asn,ENST00000244573,;HIST1H4A,upstream_gene_variant,,ENST00000359907,;HIST1H3A,upstream_gene_variant,,ENST00000357647,;U91328.22,downstream_gene_variant,,ENST00000608919,;HIST1H1PS2,downstream_gene_variant,,ENST00000437528,;	G	ENSG00000124610	ENST00000244573	Transcript	missense_variant	524	444	148	K/N	aaG/aaC	COSM461843	.	.	-1	HIST1H1A	HGNC	4715	protein_coding	YES	CCDS4569.1	ENSP00000244573	H11_HUMAN	.	UPI0000001BD8	.	tolerated(0.06)	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11467:SF25,hmmpanther:PTHR11467	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCTCTTTTT	.	5	ESCA
HIST1H2BE	0	.	GRCh37	6	26184245	26184245	+	Silent	SNP	C	C	T	rs769608700	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.222C>T	p.%3D	p.I74I	ENST00000356530	1/1	87	51	35	92	92	0	HIST1H2BE,synonymous_variant,p.%3D,ENST00000356530,;HIST1H4D,downstream_gene_variant,,ENST00000340756,;	T	ENSG00000197697	ENST00000356530	Transcript	synonymous_variant	288	222	74	I	atC/atT	rs769608700,COSM1311872	.	.	1	HIST1H2BE	HGNC	4753	protein_coding	YES	CCDS4588.1	ENSP00000348924	H2B1C_HUMAN	B2R4S9_HUMAN	UPI0000000C24	.	.	.	1/1	.	hmmpanther:PTHR23428,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCATCGCCGG	.	5	ESCA
OR2J2	0	.	GRCh37	6	29142185	29142185	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.773G>T	p.Cys258Phe	p.C258F	ENST00000377167	1/1	92	46	45	62	62	0	OR2J2,missense_variant,p.Cys258Phe,ENST00000377167,;	T	ENSG00000204700	ENST00000377167	Transcript	missense_variant	875	773	258	C/F	tGc/tTc	.	.	.	1	OR2J2	HGNC	8260	protein_coding	YES	CCDS43434.1	ENSP00000366372	OR2J2_HUMAN	.	UPI000004B9D1	.	tolerated(0.48)	benign(0.003)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF207,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGTGCATGT	.	5	ESCA
OR12D3	0	.	GRCh37	6	29342679	29342679	+	Missense_Mutation	SNP	C	C	T	rs766788643	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.386G>A	p.Arg129His	p.R129H	ENST00000396806	1/1	49	31	17	27	27	0	OR12D3,missense_variant,p.Arg129His,ENST00000396806,;OR5V1,intron_variant,,ENST00000377154,;	T	ENSG00000112462	ENST00000396806	Transcript	missense_variant	390	386	129	R/H	cGc/cAc	rs766788643	.	.	-1	OR12D3	HGNC	13963	protein_coding	YES	CCDS4658.1	ENSP00000380023	O12D3_HUMAN	D2XT27_HUMAN	UPI000000DCA9	.	tolerated(0.53)	benign(0.002)	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451:SF193,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAGCGAAGA	.	5	ESCA
HLA-DPB1	0	.	GRCh37	6	33048746	33048746	+	Intron	SNP	C	C	A	rs774625599	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364+34C>A	.	.	ENST00000418931	.	31	15	15	32	32	0	HLA-DPB1,3_prime_UTR_variant,,ENST00000535465,;HLA-DPB1,intron_variant,,ENST00000418931,;HLA-DPB1,intron_variant,,ENST00000416804,;HLA-DPB1,intron_variant,,ENST00000428835,;HLA-DPA1,upstream_gene_variant,,ENST00000453337,;HLA-DPA1,upstream_gene_variant,,ENST00000417724,;HLA-DPA1,upstream_gene_variant,,ENST00000419277,;HLA-DPB1,non_coding_transcript_exon_variant,,ENST00000478189,;HLA-DPB1,intron_variant,,ENST00000488575,;HLA-DPB1,intron_variant,,ENST00000471184,;HLA-DPB1,intron_variant,,ENST00000498038,;HLA-DPA1,upstream_gene_variant,,ENST00000476642,;HLA-DPB1,non_coding_transcript_exon_variant,,ENST00000469120,;RPL32P1,downstream_gene_variant,,ENST00000439737,;	A	ENSG00000223865	ENST00000418931	Transcript	intron_variant	.	.	.	.	.	rs774625599	.	.	1	HLA-DPB1	HGNC	4940	protein_coding	YES	CCDS4765.1	ENSP00000408146	DPB1_HUMAN	T2KSN6_HUMAN,S4T765_HUMAN,S4T728_HUMAN,S4T726_HUMAN,S4T6V7_HUMAN,S4T6S0_HUMAN,N0A2U5_HUMAN,Q7YQ09_HUMAN,Q67AT7_HUMAN,Q67AT3_HUMAN,Q67AT0_HUMAN,Q67AS6_HUMAN,Q67AS4_HUMAN,Q67AS1_HUMAN,Q67AQ5_HUMAN,Q67AQ4_HUMAN,Q67AQ3_HUMAN,Q67AQ2_HUMAN,Q67AQ1_HUMAN,Q67AQ0_HUMAN,Q67AP9_HUMAN,Q67AP8_HUMAN,Q67AP7_HUMAN,Q67AP5_HUMAN,Q67AP4_HUMAN,Q67AP3_HUMAN,Q67AP1_HUMAN,Q49U72_HUMAN,Q49U70_HUMAN,Q49U66_HUMAN,Q49U64_HUMAN,Q49U62_HUMAN,Q49U58_HUMAN,Q49U56_HUMAN,Q49U54_HUMAN,Q49U52_HUMAN,Q49U50_HUMAN,Q49U48_HUMAN,Q49U46_HUMAN,Q49U44_HUMAN,Q49U42_HUMAN,Q49U38_HUMAN,Q49U34_HUMAN,Q49U32_HUMAN,Q49U30_HUMAN,Q49U28_HUMAN,O19686_HUMAN,O19628_HUMAN,L0BXX2_HUMAN,L0BXH6_HUMAN,I4EC15_HUMAN,H2A3H7_HUMAN,E9NVG1_HUMAN,A1YAC1_HUMAN	UPI000004494C	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAGGGCAGCCC	byFrequency	4	ESCA
TULP1	0	.	GRCh37	6	35471401	35471401	+	Missense_Mutation	SNP	G	G	C	rs551519696	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1258C>G	p.Arg420Gly	p.R420G	ENST00000229771	13/15	32	15	16	27	27	0	TULP1,missense_variant,p.Arg420Gly,ENST00000229771,;TULP1,missense_variant,p.Arg367Gly,ENST00000322263,;TULP1,non_coding_transcript_exon_variant,,ENST00000496434,;TULP1,non_coding_transcript_exon_variant,,ENST00000495781,;TULP1,downstream_gene_variant,,ENST00000373892,;	C	ENSG00000112041	ENST00000229771	Transcript	missense_variant	1338	1258	420	R/G	Cgc/Ggc	rs551519696	.	.	-1	TULP1	HGNC	12423	protein_coding	YES	CCDS4807.1	ENSP00000229771	TULP1_HUMAN	Q0QD38_HUMAN	UPI000045742A	.	deleterious(0)	probably_damaging(0.979)	13/15	.	hmmpanther:PTHR16517,hmmpanther:PTHR16517:SF12,Gene3D:3c5nA00,Pfam_domain:PF01167,Superfamily_domains:SSF54518,Prints_domain:PR01573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGCGCCGGG	byCluster	5	ESCA
CDKN1A	0	.	GRCh37	6	36653769	36653769	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*192G>T	.	.	ENST00000405375	3/3	23	13	9	21	21	0	CDKN1A,3_prime_UTR_variant,,ENST00000244741,;CDKN1A,3_prime_UTR_variant,,ENST00000448526,;CDKN1A,3_prime_UTR_variant,,ENST00000405375,;CDKN1A,downstream_gene_variant,,ENST00000373711,;CDKN1A,downstream_gene_variant,,ENST00000459970,;CDKN1A,downstream_gene_variant,,ENST00000478800,;	T	ENSG00000124762	ENST00000405375	Transcript	3_prime_UTR_variant	922	.	.	.	.	.	.	.	1	CDKN1A	HGNC	1784	protein_coding	YES	CCDS4824.1	ENSP00000384849	CDN1A_HUMAN	.	UPI0000048F7B	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTAGGCGGT	.	5	ESCA
POLR1C	0	.	GRCh37	6	43484854	43484854	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7G>T	p.Ala3Ser	p.A3S	ENST00000372389	1/9	48	20	27	29	29	0	POLR1C,missense_variant,p.Ala3Ser,ENST00000372389,;POLR1C,missense_variant,p.Ala3Ser,ENST00000372344,;POLR1C,missense_variant,p.Ala3Ser,ENST00000304004,;POLR1C,missense_variant,p.Ala3Ser,ENST00000423780,;POLR1C,intron_variant,,ENST00000428025,;YIPF3,upstream_gene_variant,,ENST00000506469,;YIPF3,upstream_gene_variant,,ENST00000503972,;YIPF3,upstream_gene_variant,,ENST00000372422,;YIPF3,upstream_gene_variant,,ENST00000500090,;YIPF3,upstream_gene_variant,,ENST00000511831,;RP3-337H4.9,downstream_gene_variant,,ENST00000607571,;POLR1C,non_coding_transcript_exon_variant,,ENST00000488601,;POLR1C,non_coding_transcript_exon_variant,,ENST00000481352,;POLR1C,non_coding_transcript_exon_variant,,ENST00000512472,;YIPF3,upstream_gene_variant,,ENST00000488966,;POLR1C,upstream_gene_variant,,ENST00000455605,;YIPF3,upstream_gene_variant,,ENST00000503147,;YIPF3,upstream_gene_variant,,ENST00000460903,;YIPF3,upstream_gene_variant,,ENST00000502714,;YIPF3,upstream_gene_variant,,ENST00000512713,;YIPF3,upstream_gene_variant,,ENST00000490447,;YIPF3,upstream_gene_variant,,ENST00000510102,;YIPF3,upstream_gene_variant,,ENST00000455768,;YIPF3,upstream_gene_variant,,ENST00000514627,;YIPF3,upstream_gene_variant,,ENST00000372417,;YIPF3,upstream_gene_variant,,ENST00000416380,;YIPF3,upstream_gene_variant,,ENST00000460547,;	T	ENSG00000171453	ENST00000372389	Transcript	missense_variant	95	7	3	A/S	Gct/Tct	.	.	.	1	POLR1C	HGNC	20194	protein_coding	YES	CCDS4901.1	ENSP00000361465	RPAC1_HUMAN	Q96HT3_HUMAN,D6RDJ3_HUMAN	UPI00001345BC	.	tolerated(0.28)	benign(0.007)	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCGGCTTCT	.	5	ESCA
HCRTR2	0	.	GRCh37	6	55128601	55128601	+	Missense_Mutation	SNP	G	G	T	rs199660644	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743G>T	p.Arg248Leu	p.R248L	ENST00000370862	4/7	31	19	11	36	36	0	HCRTR2,missense_variant,p.Arg248Leu,ENST00000370862,;	T	ENSG00000137252	ENST00000370862	Transcript	missense_variant	1079	743	248	R/L	cGc/cTc	rs199660644,COSM1445245	.	.	1	HCRTR2	HGNC	4849	protein_coding	YES	CCDS4956.1	ENSP00000359899	OX2R_HUMAN	S4X0W3_HUMAN,A6N9G8_HUMAN	UPI000013D07A	.	deleterious(0.01)	benign(0.434)	4/7	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF56,hmmpanther:PTHR24241,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01064	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R248C|c.742C>T|6,CODON|p.R248H|c.743G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCGCAAAC	byCluster|by1000G	5	ESCA
PRIM2	0	.	GRCh37	6	57372336	57372336	+	Missense_Mutation	SNP	C	C	A	rs761743105	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.742C>A	p.Pro248Thr	p.P248T	ENST00000607273	8/14	81	68	13	64	64	0	PRIM2,missense_variant,p.Pro248Thr,ENST00000607273,;PRIM2,non_coding_transcript_exon_variant,,ENST00000470638,;PRIM2,non_coding_transcript_exon_variant,,ENST00000389488,;	A	ENSG00000146143	ENST00000607273	Transcript	missense_variant	829	742	248	P/T	Cct/Act	rs761743105,COSM3629092	.	.	1	PRIM2	HGNC	9370	protein_coding	YES	.	ENSP00000475738	.	U3KQB9_HUMAN,I0CMK6_HUMAN,I0CMJ8_HUMAN,H9XFA6_HUMAN	UPI00004588DE	.	tolerated(0.06)	probably_damaging(0.945)	8/14	.	hmmpanther:PTHR10537:SF3,hmmpanther:PTHR10537,Pfam_domain:PF04104	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGCCTCTG	byFrequency	5	ESCA
EYS	0	.	GRCh37	6	65301594	65301594	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4166C>A	p.Ala1389Glu	p.A1389E	ENST00000503581	26/43	44	20	24	34	34	0	EYS,missense_variant,p.Ala1389Glu,ENST00000370616,;EYS,missense_variant,p.Ala1389Glu,ENST00000370621,;EYS,missense_variant,p.Ala1389Glu,ENST00000503581,;EYS,downstream_gene_variant,,ENST00000330816,;	T	ENSG00000188107	ENST00000503581	Transcript	missense_variant	4704	4166	1389	A/E	gCa/gAa	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	tolerated(1)	benign(0)	26/43	.	hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTGCTCTC	.	5	ESCA
BAI3	0	.	GRCh37	6	69665947	69665947	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1227G>T	p.Trp409Cys	p.W409C	ENST00000370598	7/32	70	36	33	39	39	0	BAI3,missense_variant,p.Trp409Cys,ENST00000370598,;	T	ENSG00000135298	ENST00000370598	Transcript	missense_variant	2048	1227	409	W/C	tgG/tgT	.	.	.	1	BAI3	HGNC	945	protein_coding	YES	CCDS4968.1	ENSP00000359630	BAI3_HUMAN	S4R3D0_HUMAN,B7Z1K0_HUMAN	UPI00001AE6A9	.	deleterious(0)	probably_damaging(0.999)	7/32	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50092,hmmpanther:PTHR12011:SF40,hmmpanther:PTHR12011,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S408L|c.1223C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTGGAGCCA	.	5	ESCA
BAI3	0	.	GRCh37	6	70049228	70049228	+	Silent	SNP	G	G	T	rs777094686	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3291G>T	p.%3D	p.A1097A	ENST00000370598	26/32	74	40	33	67	67	0	BAI3,synonymous_variant,p.%3D,ENST00000546190,;BAI3,synonymous_variant,p.%3D,ENST00000238918,;BAI3,synonymous_variant,p.%3D,ENST00000370598,;	T	ENSG00000135298	ENST00000370598	Transcript	synonymous_variant	4112	3291	1097	A	gcG/gcT	rs777094686	.	.	1	BAI3	HGNC	945	protein_coding	YES	CCDS4968.1	ENSP00000359630	BAI3_HUMAN	S4R3D0_HUMAN,B7Z1K0_HUMAN	UPI00001AE6A9	.	.	.	26/32	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF40,hmmpanther:PTHR12011,Pfam_domain:PF00002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCGTCTCT	byFrequency|byCluster	5	ESCA
IMPG1	0	.	GRCh37	6	76640719	76640719	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2194C>A	p.Pro732Thr	p.P732T	ENST00000369950	15/17	44	28	15	43	43	0	IMPG1,missense_variant,p.Pro732Thr,ENST00000369950,;IMPG1,missense_variant,p.Pro93Thr,ENST00000369952,;IMPG1,3_prime_UTR_variant,,ENST00000369963,;Y_RNA,downstream_gene_variant,,ENST00000363170,;	T	ENSG00000112706	ENST00000369950	Transcript	missense_variant	2384	2194	732	P/T	Cct/Act	.	.	.	-1	IMPG1	HGNC	6055	protein_coding	YES	CCDS4985.1	ENSP00000358966	IMPG1_HUMAN	H0UI08_HUMAN	UPI0000073F12	.	deleterious(0.04)	possibly_damaging(0.743)	15/17	.	hmmpanther:PTHR12199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGGGCCAC	.	5	ESCA
PRSS35	0	.	GRCh37	6	84233745	84233745	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.585T>A	p.Ser195Arg	p.S195R	ENST00000536636	3/3	36	20	16	37	37	0	PRSS35,missense_variant,p.Ser195Arg,ENST00000369700,;PRSS35,missense_variant,p.Ser195Arg,ENST00000536636,;	A	ENSG00000146250	ENST00000536636	Transcript	missense_variant	930	585	195	S/R	agT/agA	.	.	.	1	PRSS35	HGNC	21387	protein_coding	YES	CCDS4999.1	ENSP00000440870	PRS35_HUMAN	.	UPI000006D2C7	.	tolerated(0.57)	benign(0)	3/3	.	Low_complexity_(Seg):seg,Pfam_domain:PF00089,hmmpanther:PTHR15462:SF7,hmmpanther:PTHR15462	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGTGGAGG	.	5	ESCA
PNPLA8	0	.	GRCh37	7	108112732	108112732	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*113G>C	.	.	ENST00000422087	12/12	12	3	9	22	22	0	PNPLA8,3_prime_UTR_variant,,ENST00000453144,;PNPLA8,3_prime_UTR_variant,,ENST00000257694,;PNPLA8,3_prime_UTR_variant,,ENST00000388728,;PNPLA8,3_prime_UTR_variant,,ENST00000426128,;PNPLA8,3_prime_UTR_variant,,ENST00000422087,;PNPLA8,3_prime_UTR_variant,,ENST00000436062,;PNPLA8,downstream_gene_variant,,ENST00000453085,;	G	ENSG00000135241	ENST00000422087	Transcript	3_prime_UTR_variant	2869	.	.	.	.	.	.	.	-1	PNPLA8	HGNC	28900	protein_coding	YES	CCDS34733.1	ENSP00000410804	PLPL8_HUMAN	C9JAX4_HUMAN,C9J9W9_HUMAN	UPI0000073D34	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATTCTCCAGAA	.	3	ESCA
DOCK4	0	.	GRCh37	7	111428763	111428763	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3356C>T	p.Ser1119Leu	p.S1119L	ENST00000437633	32/52	314	15	299	46	46	0	DOCK4,missense_variant,p.Ser1119Leu,ENST00000428084,;DOCK4,missense_variant,p.Ser571Leu,ENST00000423057,;DOCK4,missense_variant,p.Ser1119Leu,ENST00000437633,;DOCK4,missense_variant,p.Ser17Leu,ENST00000417165,;DOCK4,missense_variant,p.Ser1143Leu,ENST00000445943,;DOCK4,upstream_gene_variant,,ENST00000437129,;DOCK4,upstream_gene_variant,,ENST00000494651,;DOCK4,upstream_gene_variant,,ENST00000450156,;DOCK4,non_coding_transcript_exon_variant,,ENST00000492436,;DOCK4,non_coding_transcript_exon_variant,,ENST00000464338,;DOCK4,non_coding_transcript_exon_variant,,ENST00000469898,;DOCK4,upstream_gene_variant,,ENST00000428053,;	A	ENSG00000128512	ENST00000437633	Transcript	missense_variant	3613	3356	1119	S/L	tCa/tTa	.	.	.	-1	DOCK4	HGNC	19192	protein_coding	YES	CCDS47688.1	ENSP00000404179	DOCK4_HUMAN	Q75MU6_HUMAN	UPI0000D5BB0D	.	deleterious(0)	probably_damaging(0.999)	32/52	.	hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTGACATC	.	5	ESCA
GRM8	0	.	GRCh37	7	126883165	126883165	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94C>T	p.His32Tyr	p.H32Y	ENST00000339582	2/11	34	20	14	20	20	0	GRM8,missense_variant,p.His32Tyr,ENST00000358373,;GRM8,missense_variant,p.His32Tyr,ENST00000444921,;GRM8,missense_variant,p.His32Tyr,ENST00000339582,;GRM8,missense_variant,p.His32Tyr,ENST00000457830,;GRM8,missense_variant,p.His32Tyr,ENST00000405249,;GRM8,downstream_gene_variant,,ENST00000412160,;GRM8,missense_variant,p.His32Tyr,ENST00000472701,;GRM8,missense_variant,p.His32Tyr,ENST00000341617,;	A	ENSG00000179603	ENST00000339582	Transcript	missense_variant	903	94	32	H/Y	Cac/Tac	.	.	.	-1	GRM8	HGNC	4600	protein_coding	YES	CCDS5794.1	ENSP00000344173	GRM8_HUMAN	E7ETK3_HUMAN,C9J7I1_HUMAN	UPI000012F085	.	tolerated(0.1)	benign(0)	2/11	.	hmmpanther:PTHR24060:SF26,hmmpanther:PTHR24060,Prints_domain:PR01058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R30I|c.89G>T|4,BUFFER|p.R30I|c.89G>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGTGAGTTC	.	5	ESCA
ARL4A	0	.	GRCh37	7	12729422	12729422	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*940C>G	.	.	ENST00000396663	2/2	41	19	21	31	31	0	ARL4A,3_prime_UTR_variant,,ENST00000396663,;ARL4A,downstream_gene_variant,,ENST00000404894,;ARL4A,downstream_gene_variant,,ENST00000396664,;ARL4A,downstream_gene_variant,,ENST00000396662,;ARL4A,downstream_gene_variant,,ENST00000439721,;ARL4A,downstream_gene_variant,,ENST00000356797,;CTD-2320J21.1,downstream_gene_variant,,ENST00000604949,;	G	ENSG00000122644	ENST00000396663	Transcript	3_prime_UTR_variant	2025	.	.	.	.	.	.	.	1	ARL4A	HGNC	695	protein_coding	YES	CCDS5359.1	ENSP00000379898	ARL4A_HUMAN	C9J7Q9_HUMAN	UPI000005273E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTACAAGAT	.	5	ESCA
CALU	0	.	GRCh37	7	128388853	128388853	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240G>T	p.Arg80Ser	p.R80S	ENST00000542996	3/8	24	21	3	12	12	0	CALU,missense_variant,p.Arg72Ser,ENST00000449187,;CALU,missense_variant,p.Arg80Ser,ENST00000535623,;CALU,missense_variant,p.Arg80Ser,ENST00000479257,;CALU,missense_variant,p.Arg80Ser,ENST00000542996,;CALU,missense_variant,p.Arg72Ser,ENST00000249364,;CALU,missense_variant,p.Arg72Ser,ENST00000535011,;CALU,intron_variant,,ENST00000538546,;	T	ENSG00000128595	ENST00000542996	Transcript	missense_variant	1183	240	80	R/S	agG/agT	.	.	.	1	CALU	HGNC	1458	protein_coding	YES	CCDS56507.1	ENSP00000438248	CALU_HUMAN	.	UPI0001D27CDB	.	deleterious(0)	probably_damaging(0.999)	3/8	.	PROSITE_profiles:PS50222,hmmpanther:PTHR10827:SF34,hmmpanther:PTHR10827,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GAAAGGCTTGG	.	2	ESCA
DGKI	0	.	GRCh37	7	137172381	137172381	+	Missense_Mutation	SNP	C	C	G	rs753459372	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2357G>C	p.Arg786Pro	p.R786P	ENST00000288490	23/34	21	12	8	16	16	0	DGKI,missense_variant,p.Arg786Pro,ENST00000288490,;DGKI,missense_variant,p.Arg789Pro,ENST00000424189,;DGKI,missense_variant,p.Arg486Pro,ENST00000453654,;DGKI,missense_variant,p.Arg768Pro,ENST00000446122,;DGKI,non_coding_transcript_exon_variant,,ENST00000460662,;	G	ENSG00000157680	ENST00000288490	Transcript	missense_variant	2358	2357	786	R/P	cGt/cCt	rs753459372	.	.	-1	DGKI	HGNC	2855	protein_coding	YES	CCDS5845.1	ENSP00000288490	DGKI_HUMAN	B3KR69_HUMAN	UPI000012DD23	.	deleterious(0)	probably_damaging(0.999)	23/34	.	hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATACGGCAA	byFrequency	5	ESCA
DGKI	0	.	GRCh37	7	137284581	137284581	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1238G>T	p.Gly413Val	p.G413V	ENST00000288490	11/34	20	8	11	15	15	0	DGKI,missense_variant,p.Gly413Val,ENST00000288490,;DGKI,missense_variant,p.Gly413Val,ENST00000424189,;DGKI,missense_variant,p.Gly113Val,ENST00000453654,;DGKI,missense_variant,p.Gly413Val,ENST00000446122,;DGKI,intron_variant,,ENST00000470895,;	A	ENSG00000157680	ENST00000288490	Transcript	missense_variant	1239	1238	413	G/V	gGg/gTg	.	.	.	-1	DGKI	HGNC	2855	protein_coding	YES	CCDS5845.1	ENSP00000288490	DGKI_HUMAN	B3KR69_HUMAN	UPI000012DD23	.	deleterious(0)	probably_damaging(1)	11/34	.	PROSITE_profiles:PS50146,hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41,Pfam_domain:PF00781,SMART_domains:SM00046,Superfamily_domains:SSF111331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCCCTTCC	.	5	ESCA
ZNF425	0	.	GRCh37	7	148800755	148800755	+	Silent	SNP	C	C	A	rs773536439	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2208G>T	p.%3D	p.A736A	ENST00000378061	4/4	21	4	17	29	29	0	ZNF425,synonymous_variant,p.%3D,ENST00000378061,;ZNF425,downstream_gene_variant,,ENST00000483014,;ZNF425,downstream_gene_variant,,ENST00000495685,;	A	ENSG00000204947	ENST00000378061	Transcript	synonymous_variant	2341	2208	736	A	gcG/gcT	rs773536439,COSM1488345	.	.	-1	ZNF425	HGNC	20690	protein_coding	YES	CCDS34773.1	ENSP00000367300	ZN425_HUMAN	.	UPI00001B64B9	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF120,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAGCGCCCC	byFrequency	5	ESCA
DPP6	0	.	GRCh37	7	154237656	154237656	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.497G>T	p.Arg166Ile	p.R166I	ENST00000377770	4/26	12	2	9	11	11	0	DPP6,missense_variant,p.Arg104Ile,ENST00000427557,;DPP6,missense_variant,p.Arg166Ile,ENST00000377770,;DPP6,missense_variant,p.Arg166Ile,ENST00000406326,;DPP6,missense_variant,p.Arg104Ile,ENST00000332007,;DPP6,missense_variant,p.Arg102Ile,ENST00000404039,;DPP6,non_coding_transcript_exon_variant,,ENST00000496611,;	T	ENSG00000130226	ENST00000377770	Transcript	missense_variant	638	497	166	R/I	aGa/aTa	.	.	.	1	DPP6	HGNC	3010	protein_coding	YES	.	ENSP00000367001	DPP6_HUMAN	Q75MI8_HUMAN,Q75MI7_HUMAN,Q75MF0_HUMAN	UPI00001AE746	.	tolerated(1)	benign(0)	4/26	.	Superfamily_domains:SSF82171,Gene3D:2.140.10.30,hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTGAGACTGT	.	3	ESCA
PAXIP1	0	.	GRCh37	7	154785468	154785468	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228G>A	p.%3D	p.V76V	ENST00000404141	3/21	10	2	8	16	16	0	PAXIP1,synonymous_variant,p.%3D,ENST00000404141,;PAXIP1,synonymous_variant,p.%3D,ENST00000397192,;PAXIP1,intron_variant,,ENST00000419436,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000473219,;PAXIP1,synonymous_variant,p.%3D,ENST00000457196,;	T	ENSG00000157212	ENST00000404141	Transcript	synonymous_variant	383	228	76	V	gtG/gtA	.	.	.	-1	PAXIP1	HGNC	8624	protein_coding	YES	CCDS47753.1	ENSP00000384048	PAXI1_HUMAN	.	UPI00004166F9	.	.	.	3/21	.	PROSITE_profiles:PS50172,hmmpanther:PTHR23196:SF1,hmmpanther:PTHR23196,Gene3D:3.40.50.10190,Superfamily_domains:SSF52113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGAATCACCCA	.	3	ESCA
PRR15	0	.	GRCh37	7	29606258	29606258	+	Missense_Mutation	SNP	G	G	T	rs764136558	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313G>T	p.Ala105Ser	p.A105S	ENST00000319694	2/2	13	3	10	26	26	0	PRR15,missense_variant,p.Ala105Ser,ENST00000319694,;PRR15,downstream_gene_variant,,ENST00000450427,;AC007255.8,upstream_gene_variant,,ENST00000450540,;AC007255.8,upstream_gene_variant,,ENST00000447171,;	T	ENSG00000176532	ENST00000319694	Transcript	missense_variant	1025	313	105	A/S	Gcc/Tcc	rs764136558	.	.	1	PRR15	HGNC	22310	protein_coding	YES	CCDS5421.1	ENSP00000317836	PRR15_HUMAN	C9JQ22_HUMAN,A4D1A1_HUMAN	UPI0000074699	.	deleterious(0.03)	probably_damaging(0.963)	2/2	.	hmmpanther:PTHR14581:SF4,hmmpanther:PTHR14581,Pfam_domain:PF15321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCGCGCCACG	byFrequency	3	ESCA
TRGC2	0	.	GRCh37	7	38289146	38289146	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.28C>G	p.Pro10Arg	p.P10R	ENST00000436911	1/4	47	35	12	31	31	0	TRGC2,missense_variant,p.Pro10Arg,ENST00000436911,;TRGJ2,downstream_gene_variant,,ENST00000390333,;	C	ENSG00000227191	ENST00000436911	Transcript	missense_variant	28	29	10	P/R	cCc/cGc	.	.	.	-1	TRGC2	HGNC	12276	TR_C_gene	YES	.	ENSP00000413437	.	.	UPI0000F30369	.	deleterious(0)	probably_damaging(1)	1/4	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19256,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTTGGGGGAA	.	3	ESCA
AEBP1	0	.	GRCh37	7	44153426	44153440	+	In_Frame_Del	DEL	CAGCGACGCCTGCAG	CAGCGACGCCTGCAG	-	rs755132794	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	CAGCGACGCCTGCAG	CAGCGACGCCTGCAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3054_3068delGCAGCAGCGACGCCT	p.Gln1020_Gln1024del	p.Q1020_Q1024del	ENST00000223357	21/21	53	42	11	40	40	0	AEBP1,inframe_deletion,p.Gln1020_Gln1024del,ENST00000223357,;AEBP1,inframe_deletion,p.Gln595_Gln599del,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000406581,;POLD2,downstream_gene_variant,,ENST00000223361,;POLD2,downstream_gene_variant,,ENST00000433715,;AEBP1,downstream_gene_variant,,ENST00000455443,;POLD2,downstream_gene_variant,,ENST00000436400,;POLD2,downstream_gene_variant,,ENST00000456038,;POLD2,downstream_gene_variant,,ENST00000452185,;POLD2,downstream_gene_variant,,ENST00000418438,;POLD2,downstream_gene_variant,,ENST00000436844,;MIR4649,downstream_gene_variant,,ENST00000582839,;AEBP1,downstream_gene_variant,,ENST00000454218,;AEBP1,3_prime_UTR_variant,,ENST00000413907,;POLD2,downstream_gene_variant,,ENST00000481104,;POLD2,downstream_gene_variant,,ENST00000463464,;AEBP1,downstream_gene_variant,,ENST00000434445,;POLD2,downstream_gene_variant,,ENST00000496539,;AEBP1,downstream_gene_variant,,ENST00000431035,;POLD2,downstream_gene_variant,,ENST00000467469,;POLD2,downstream_gene_variant,,ENST00000470867,;POLD2,downstream_gene_variant,,ENST00000461116,;POLD2,downstream_gene_variant,,ENST00000464871,;AEBP1,downstream_gene_variant,,ENST00000453052,;POLD2,downstream_gene_variant,,ENST00000489883,;	-	ENSG00000106624	ENST00000223357	Transcript	inframe_deletion	3348-3362	3043-3057	1015-1019	QRRLQ/-	CAGCGACGCCTGCAG/-	rs755132794	.	.	1	AEBP1	HGNC	303	protein_coding	YES	CCDS5476.1	ENSP00000223357	AEBP1_HUMAN	B4DJB3_HUMAN	UPI00000746E2	.	.	.	21/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11532:SF48,hmmpanther:PTHR11532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	11	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCCCAACAGCGACGCCTGCAGCAGCG	.	2	ESCA
RADIL	0	.	GRCh37	7	4874577	4874577	+	Silent	SNP	C	C	A	rs775315249	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1077G>T	p.%3D	p.A359A	ENST00000399583	4/15	22	13	9	22	22	0	RADIL,synonymous_variant,p.%3D,ENST00000399583,;RADIL,synonymous_variant,p.%3D,ENST00000536091,;RADIL,synonymous_variant,p.%3D,ENST00000538469,;RADIL,missense_variant,p.Ala358Ser,ENST00000445392,;RADIL,upstream_gene_variant,,ENST00000473130,;RADIL,upstream_gene_variant,,ENST00000484211,;	A	ENSG00000157927	ENST00000399583	Transcript	synonymous_variant	1265	1077	359	A	gcG/gcT	rs775315249	.	.	-1	RADIL	HGNC	22226	protein_coding	YES	CCDS43544.1	ENSP00000382492	RADIL_HUMAN	F5H6X3_HUMAN,C9J7G0_HUMAN	UPI0000E0A787	.	.	.	4/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGCGCGGG	byFrequency	5	ESCA
POM121L12	0	.	GRCh37	7	53103352	53103352	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13C>A	.	.	ENST00000408890	1/1	81	32	48	45	45	0	POM121L12,5_prime_UTR_variant,,ENST00000408890,;	A	ENSG00000221900	ENST00000408890	Transcript	5_prime_UTR_variant	4	.	.	.	.	.	.	.	1	POM121L12	HGNC	25369	protein_coding	YES	CCDS43584.1	ENSP00000386133	P1L12_HUMAN	.	UPI00001B6540	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAACGGTCC	.	5	ESCA
HIP1	0	.	GRCh37	7	75186055	75186055	+	Nonsense_Mutation	SNP	C	C	A	rs781891906	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1642G>T	p.Glu548Ter	p.E548*	ENST00000336926	17/31	17	5	11	22	22	0	HIP1,stop_gained,p.Glu548Ter,ENST00000434438,;HIP1,stop_gained,p.Glu548Ter,ENST00000336926,;HIP1,downstream_gene_variant,,ENST00000404944,;	A	ENSG00000127946	ENST00000336926	Transcript	stop_gained	1669	1642	548	E/*	Gag/Tag	rs781891906	.	.	-1	HIP1	HGNC	4913	protein_coding	YES	CCDS34669.1	ENSP00000336747	HIP1_HUMAN	Q8TDA4_HUMAN,B4DYD7_HUMAN,B4DK46_HUMAN	UPI000013D65F	.	.	.	17/31	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10407:SF14,hmmpanther:PTHR10407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTCCCGTT	.	5	ESCA
UPK3B	0	.	GRCh37	7	76178978	76178978	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*205+34205G>C	.	.	ENST00000419923	.	15	3	12	15	15	0	UPK3B,intron_variant,,ENST00000419923,;UPK3B,intron_variant,,ENST00000443097,;AC004980.7,splice_region_variant,,ENST00000423084,;AC004980.7,non_coding_transcript_exon_variant,,ENST00000450661,;AC004980.7,non_coding_transcript_exon_variant,,ENST00000418663,;AC004980.7,non_coding_transcript_exon_variant,,ENST00000429707,;	C	ENSG00000243566	ENST00000419923	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	UPK3B	HGNC	21444	protein_coding	YES	CCDS5588.1	ENSP00000441602	UPK3B_HUMAN	.	UPI00001AE7A4	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGAGCCCCA	.	5	ESCA
MAGI2	0	.	GRCh37	7	77797398	77797398	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2431G>T	p.Gly811Cys	p.G811C	ENST00000354212	15/22	72	37	35	70	70	0	MAGI2,missense_variant,p.Gly811Cys,ENST00000354212,;MAGI2,missense_variant,p.Gly797Cys,ENST00000419488,;MAGI2,missense_variant,p.Gly811Cys,ENST00000522391,;MAGI2,non_coding_transcript_exon_variant,,ENST00000522342,;MAGI2,non_coding_transcript_exon_variant,,ENST00000519748,;MAGI2,upstream_gene_variant,,ENST00000524268,;	A	ENSG00000187391	ENST00000354212	Transcript	missense_variant	2685	2431	811	G/C	Ggc/Tgc	.	.	.	-1	MAGI2	HGNC	18957	protein_coding	YES	CCDS5594.1	ENSP00000346151	MAGI2_HUMAN	.	UPI00001615D2	.	deleterious(0)	possibly_damaging(0.907)	15/22	.	PROSITE_profiles:PS50106,hmmpanther:PTHR10316:SF27,hmmpanther:PTHR10316,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGCCCATGG	.	5	ESCA
KIAA1324L	0	.	GRCh37	7	86548612	86548612	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1414G>A	p.Gly472Arg	p.G472R	ENST00000450689	11/22	39	12	26	13	13	0	KIAA1324L,missense_variant,p.Gly472Arg,ENST00000444627,;KIAA1324L,missense_variant,p.Gly433Arg,ENST00000423294,;KIAA1324L,missense_variant,p.Gly472Arg,ENST00000450689,;KIAA1324L,missense_variant,p.Gly232Arg,ENST00000297222,;KIAA1324L,missense_variant,p.Gly305Arg,ENST00000416314,;KIAA1324L,non_coding_transcript_exon_variant,,ENST00000474609,;KIAA1324L,non_coding_transcript_exon_variant,,ENST00000490995,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;	T	ENSG00000164659	ENST00000450689	Transcript	missense_variant	1600	1414	472	G/R	Gga/Aga	.	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	deleterious(0.02)	possibly_damaging(0.801)	11/22	.	hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCCAGCCA	.	5	ESCA
KIAA1324L	0	.	GRCh37	7	86577054	86577054	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495C>G	p.Asp165Glu	p.D165E	ENST00000450689	3/22	21	11	10	16	16	0	KIAA1324L,missense_variant,p.Asp51Glu,ENST00000398276,;KIAA1324L,missense_variant,p.Asp51Glu,ENST00000425689,;KIAA1324L,missense_variant,p.Asp165Glu,ENST00000444627,;KIAA1324L,missense_variant,p.Asp126Glu,ENST00000423294,;KIAA1324L,missense_variant,p.Asp165Glu,ENST00000450689,;KIAA1324L,intron_variant,,ENST00000416314,;KIAA1324L,upstream_gene_variant,,ENST00000394714,;	C	ENSG00000164659	ENST00000450689	Transcript	missense_variant	681	495	165	D/E	gaC/gaG	.	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	tolerated(1)	benign(0.001)	3/22	.	hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCGTCTGG	.	5	ESCA
ABCB1	0	.	GRCh37	7	87196171	87196171	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460G>T	p.Ala154Ser	p.A154S	ENST00000265724	7/29	212	31	181	41	41	0	ABCB1,missense_variant,p.Ala154Ser,ENST00000265724,;ABCB1,intron_variant,,ENST00000543898,;	A	ENSG00000085563	ENST00000265724	Transcript	missense_variant	878	460	154	A/S	Gct/Tct	.	.	.	-1	ABCB1	HGNC	40	protein_coding	YES	CCDS5608.1	ENSP00000265724	MDR1_HUMAN	Q6TBL4_HUMAN,E7EWT8_HUMAN,B5U2G4_HUMAN,A4D1D2_HUMAN	UPI000013D66C	.	tolerated(0.67)	benign(0.149)	7/29	.	PROSITE_profiles:PS50929,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAGCATGAA	.	5	ESCA
TRRAP	0	.	GRCh37	7	98609934	98609934	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11536G>A	p.Asp3846Asn	p.D3846N	ENST00000359863	72/72	327	315	11	43	43	0	TRRAP,missense_variant,p.Asp3817Asn,ENST00000355540,;TRRAP,missense_variant,p.Asp3835Asn,ENST00000446306,;TRRAP,missense_variant,p.Asp3575Asn,ENST00000456197,;TRRAP,missense_variant,p.Asp3846Asn,ENST00000359863,;AC004893.11,upstream_gene_variant,,ENST00000360902,;	A	ENSG00000196367	ENST00000359863	Transcript	missense_variant	11745	11536	3846	D/N	Gac/Aac	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	possibly_damaging(0.465)	72/72	.	PROSITE_profiles:PS51190,hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTGGACAAT	.	2	ESCA
CSMD3	0	.	GRCh37	8	113569036	113569036	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4190C>T	p.Thr1397Ile	p.T1397I	ENST00000297405	25/71	60	33	26	43	43	0	CSMD3,missense_variant,p.Thr1397Ile,ENST00000352409,;CSMD3,missense_variant,p.Thr1293Ile,ENST00000455883,;CSMD3,missense_variant,p.Thr1397Ile,ENST00000297405,;CSMD3,missense_variant,p.Thr737Ile,ENST00000339701,;CSMD3,missense_variant,p.Thr1357Ile,ENST00000343508,;	A	ENSG00000164796	ENST00000297405	Transcript	missense_variant	4435	4190	1397	T/I	aCa/aTa	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	deleterious(0.01)	probably_damaging(0.964)	25/71	.	PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTGTCATG	.	5	ESCA
DEFB136	0	.	GRCh37	8	11831522	11831522	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161G>T	p.Cys54Phe	p.C54F	ENST00000382209	2/2	21	4	17	30	30	0	DEFB136,missense_variant,p.Cys54Phe,ENST00000382209,;	A	ENSG00000205884	ENST00000382209	Transcript	missense_variant	161	161	54	C/F	tGc/tTc	.	.	.	-1	DEFB136	HGNC	34433	protein_coding	YES	CCDS43709.1	ENSP00000371644	DB136_HUMAN	.	UPI0000591BA5	.	deleterious(0.03)	probably_damaging(0.955)	2/2	.	Superfamily_domains:SSF57392	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGGCAGAAC	.	5	ESCA
PTP4A3	0	.	GRCh37	8	142444981	142444981	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000521578	.	61	31	30	71	71	0	PTP4A3,downstream_gene_variant,,ENST00000521578,;PTP4A3,downstream_gene_variant,,ENST00000329397,;PTP4A3,downstream_gene_variant,,ENST00000520105,;PTP4A3,downstream_gene_variant,,ENST00000349124,;PTP4A3,downstream_gene_variant,,ENST00000524028,;CTD-3064M3.7,non_coding_transcript_exon_variant,,ENST00000606664,;MROH5,3_prime_UTR_variant,,ENST00000521053,;MROH5,intron_variant,,ENST00000523857,;MROH5,missense_variant,p.Leu1242Phe,ENST00000430863,;	A	ENSG00000184489	ENST00000521578	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3587	1	PTP4A3	HGNC	9636	protein_coding	YES	CCDS6383.1	ENSP00000428976	TP4A3_HUMAN	E5RGR3_HUMAN	UPI000004981B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGAGGGCCT	.	5	ESCA
ARC	0	.	GRCh37	8	143695284	143695284	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349C>A	p.Arg117Ser	p.R117S	ENST00000356613	1/3	11	7	4	13	13	0	ARC,missense_variant,p.Arg117Ser,ENST00000356613,;ARC,upstream_gene_variant,,ENST00000581404,;	T	ENSG00000198576	ENST00000356613	Transcript	missense_variant	1550	349	117	R/S	Cgc/Agc	.	.	.	-1	ARC	HGNC	648	protein_coding	YES	CCDS34950.1	ENSP00000349022	ARC_HUMAN	.	UPI0000163B0F	.	deleterious_low_confidence(0)	probably_damaging(0.94)	1/3	.	hmmpanther:PTHR15962,Prints_domain:PR02027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCGCGCCACA	.	3	ESCA
GML	0	.	GRCh37	8	143921846	143921846	+	5'UTR	SNP	G	G	T	rs375561355	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-8G>T	.	.	ENST00000220940	2/4	34	17	17	44	44	0	GML,5_prime_UTR_variant,,ENST00000220940,;GML,5_prime_UTR_variant,,ENST00000522728,;	T	ENSG00000104499	ENST00000220940	Transcript	5_prime_UTR_variant	83	.	.	.	.	rs375561355	.	.	1	GML	HGNC	4375	protein_coding	YES	CCDS6391.1	ENSP00000220940	GML_HUMAN	.	UPI000012B8B1	.	.	.	2/4	.	.	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTGCGTGAAG	byFrequency|byCluster	3	ESCA
PYCRL	0	.	GRCh37	8	144688255	144688255	+	Missense_Mutation	SNP	G	G	A	rs375718982	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.655C>T	p.Arg219Cys	p.R219C	ENST00000220966	5/6	71	42	29	85	85	0	PYCRL,missense_variant,p.Arg70Cys,ENST00000377579,;PYCRL,missense_variant,p.Arg219Cys,ENST00000220966,;PYCRL,missense_variant,p.Arg194Cys,ENST00000433751,;RP11-661A12.14,downstream_gene_variant,,ENST00000606452,;PYCRL,non_coding_transcript_exon_variant,,ENST00000495276,;PYCRL,downstream_gene_variant,,ENST00000462036,;PYCRL,3_prime_UTR_variant,,ENST00000447926,;PYCRL,downstream_gene_variant,,ENST00000482616,;	A	ENSG00000104524	ENST00000220966	Transcript	missense_variant	685	655	219	R/C	Cgc/Tgc	rs375718982	.	.	-1	PYCRL	HGNC	25846	protein_coding	YES	CCDS6407.2	ENSP00000220966	P5CR3_HUMAN	B5MD87_HUMAN	UPI0000492870	.	deleterious(0)	probably_damaging(0.947)	5/6	.	hmmpanther:PTHR11645,TIGRFAM_domain:TIGR00112,Pfam_domain:PF14748,Gene3D:2ahrA02,PIRSF_domain:PIRSF000193,Superfamily_domains:SSF48179	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGCGGTGGG	byFrequency|byCluster	5	ESCA
EPPK1	0	.	GRCh37	8	144947157	144947157	+	Silent	SNP	G	G	T	rs782220071	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.265C>A	p.%3D	p.R89R	ENST00000525985	2/2	80	48	32	62	62	0	EPPK1,synonymous_variant,p.%3D,ENST00000525985,;	T	ENSG00000227184	ENST00000525985	Transcript	synonymous_variant	337	265	89	R	Cgg/Agg	rs782220071	.	.	-1	EPPK1	HGNC	15577	protein_coding	YES	.	ENSP00000436337	.	E9PPU0_HUMAN	UPI00006C0DF1	.	.	.	2/2	.	Superfamily_domains:SSF75399,SMART_domains:SM00250,Gene3D:3.90.1290.10,Pfam_domain:PF00681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGGGCGA	byFrequency	5	ESCA
ADRA1A	0	.	GRCh37	8	26627766	26627766	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269+32G>T	.	.	ENST00000380586	.	40	6	34	74	74	0	ADRA1A,missense_variant,p.Cys434Phe,ENST00000380573,;ADRA1A,missense_variant,p.Cys434Phe,ENST00000276393,;ADRA1A,intron_variant,,ENST00000380586,;ADRA1A,intron_variant,,ENST00000354550,;ADRA1A,intron_variant,,ENST00000380587,;ADRA1A,intron_variant,,ENST00000380581,;ADRA1A,intron_variant,,ENST00000380582,;ADRA1A,intron_variant,,ENST00000519229,;ADRA1A,non_coding_transcript_exon_variant,,ENST00000518621,;ADRA1A,intron_variant,,ENST00000521711,;ADRA1A,intron_variant,,ENST00000519096,;RP11-384C12.1,upstream_gene_variant,,ENST00000486251,;	A	ENSG00000120907	ENST00000380586	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ADRA1A	HGNC	277	protein_coding	YES	CCDS34869.1	ENSP00000369960	ADA1A_HUMAN	Q7KYZ9_HUMAN,B0ZBD3_HUMAN	UPI000066DA42	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAGCAGCAG	.	5	ESCA
BRF2	0	.	GRCh37	8	37702674	37702674	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594G>A	p.%3D	p.E198E	ENST00000220659	4/4	127	105	22	26	26	0	BRF2,synonymous_variant,p.%3D,ENST00000220659,;BRF2,3_prime_UTR_variant,,ENST00000520601,;BRF2,downstream_gene_variant,,ENST00000521170,;GPR124,downstream_gene_variant,,ENST00000412232,;GPR124,downstream_gene_variant,,ENST00000315215,;BRF2,downstream_gene_variant,,ENST00000522539,;	T	ENSG00000104221	ENST00000220659	Transcript	synonymous_variant	715	594	198	E	gaG/gaA	.	.	.	-1	BRF2	HGNC	17298	protein_coding	YES	CCDS6098.1	ENSP00000220659	BRF2_HUMAN	.	UPI000006D405	.	.	.	4/4	.	hmmpanther:PTHR11618:SF5,hmmpanther:PTHR11618	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCTCTTT	.	5	ESCA
TACC1	0	.	GRCh37	8	38708334	38708334	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2793G>A	.	.	ENST00000317827	13/13	45	12	32	10	10	0	TACC1,3_prime_UTR_variant,,ENST00000317827,;TACC1,3_prime_UTR_variant,,ENST00000379931,;TACC1,3_prime_UTR_variant,,ENST00000348567,;TACC1,3_prime_UTR_variant,,ENST00000330691,;TACC1,3_prime_UTR_variant,,ENST00000276520,;TACC1,downstream_gene_variant,,ENST00000520615,;TACC1,downstream_gene_variant,,ENST00000520973,;TACC1,downstream_gene_variant,,ENST00000518809,;TACC1,downstream_gene_variant,,ENST00000443286,;TACC1,downstream_gene_variant,,ENST00000520611,;TACC1,downstream_gene_variant,,ENST00000519416,;TACC1,downstream_gene_variant,,ENST00000518415,;TACC1,downstream_gene_variant,,ENST00000521866,;RP11-723D22.3,upstream_gene_variant,,ENST00000459965,;TACC1,non_coding_transcript_exon_variant,,ENST00000519093,;TACC1,downstream_gene_variant,,ENST00000522548,;	A	ENSG00000147526	ENST00000317827	Transcript	3_prime_UTR_variant	5590	.	.	.	.	.	.	.	1	TACC1	HGNC	11522	protein_coding	YES	CCDS6109.1	ENSP00000321703	TACC1_HUMAN	E5RJU4_HUMAN,E5RJG6_HUMAN,E5RIP3_HUMAN,E5RI10_HUMAN	UPI000013DACE	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAAAGGAAAGT	.	4	ESCA
ADAM18	0	.	GRCh37	8	39502989	39502989	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1042G>C	p.Ala348Pro	p.A348P	ENST00000265707	11/20	87	68	19	30	30	0	ADAM18,missense_variant,p.Ala348Pro,ENST00000265707,;ADAM18,missense_variant,p.Ala324Pro,ENST00000379866,;ADAM18,5_prime_UTR_variant,,ENST00000541111,;ADAM18,3_prime_UTR_variant,,ENST00000520087,;	C	ENSG00000168619	ENST00000265707	Transcript	missense_variant	1087	1042	348	A/P	Gca/Cca	.	.	.	1	ADAM18	HGNC	196	protein_coding	YES	CCDS6113.1	ENSP00000265707	ADA18_HUMAN	Q0VAI3_HUMAN,E5RK96_HUMAN	UPI00001254D7	.	deleterious(0)	probably_damaging(0.991)	11/20	.	PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF28,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAAGCAGTG	.	5	ESCA
XKR4	0	.	GRCh37	8	56436366	56436366	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1533C>G	p.%3D	p.A511A	ENST00000327381	3/3	33	17	15	24	24	0	XKR4,synonymous_variant,p.%3D,ENST00000327381,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,;	G	ENSG00000206579	ENST00000327381	Transcript	synonymous_variant	1633	1533	511	A	gcC/gcG	.	.	.	1	XKR4	HGNC	29394	protein_coding	YES	CCDS34893.1	ENSP00000328326	XKR4_HUMAN	.	UPI000016098C	.	.	.	3/3	.	Pfam_domain:PF09815,hmmpanther:PTHR32129:SF14,hmmpanther:PTHR32129	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGCCTTCTT	.	5	ESCA
CHMP4C	0	.	GRCh37	8	82670388	82670388	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495G>T	p.Met165Ile	p.M165I	ENST00000297265	4/5	15	7	8	13	13	0	CHMP4C,missense_variant,p.Met165Ile,ENST00000297265,;	T	ENSG00000164695	ENST00000297265	Transcript	missense_variant	688	495	165	M/I	atG/atT	.	.	.	1	CHMP4C	HGNC	30599	protein_coding	YES	CCDS6233.1	ENSP00000297265	CHM4C_HUMAN	.	UPI000005032A	.	deleterious(0.02)	benign(0.291)	4/5	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22761,hmmpanther:PTHR22761:SF13,Pfam_domain:PF03357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATGGCAGA	.	5	ESCA
RALYL	0	.	GRCh37	8	85774568	85774568	+	Missense_Mutation	SNP	C	C	T	rs527942610	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490C>T	p.Arg164Cys	p.R164C	ENST00000517638	6/9	41	23	17	47	47	0	RALYL,missense_variant,p.Arg62Cys,ENST00000521376,;RALYL,missense_variant,p.Arg78Cys,ENST00000523850,;RALYL,missense_variant,p.Arg151Cys,ENST00000521695,;RALYL,missense_variant,p.Arg151Cys,ENST00000521268,;RALYL,missense_variant,p.Arg140Cys,ENST00000518566,;RALYL,missense_variant,p.Arg151Cys,ENST00000522455,;RALYL,missense_variant,p.Arg164Cys,ENST00000517638,;RP11-98H4.4,downstream_gene_variant,,ENST00000521595,;	T	ENSG00000184672	ENST00000517638	Transcript	missense_variant	614	490	164	R/C	Cgt/Tgt	rs527942610,COSM606284,COSM606285	.	.	1	RALYL	HGNC	27036	protein_coding	YES	CCDS55252.1	ENSP00000430128	.	G3V129_HUMAN,E5RIX9_HUMAN,E5RG71_HUMAN	UPI00002108E6	.	deleterious(0)	possibly_damaging(0.474)	6/9	.	hmmpanther:PTHR13968,PIRSF_domain:PIRSF037992	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R151H|c.452G>A|3,BUFFER|p.R151H|c.452G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCCGTGCA	by1000G	5	ESCA
REXO1L1P	0	.	GRCh37	8	86575214	86575214	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.513G>T	p.%3D	p.T171T	ENST00000379010	1/1	70	52	18	79	79	0	REXO1L1P,synonymous_variant,p.%3D,ENST00000379010,;	A	ENSG00000205176	ENST00000379010	Transcript	synonymous_variant	513	513	171	T	acG/acT	.	.	.	-1	REXO1L1P	HGNC	24660	protein_coding	YES	.	ENSP00000368295	GOR_HUMAN	.	UPI000057A11F	.	.	.	1/1	.	hmmpanther:PTHR12801:SF22,hmmpanther:PTHR12801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GACTCCGTCAC	.	2	ESCA
PALM2-AKAP2	0	.	GRCh37	9	112898644	112898644	+	Missense_Mutation	SNP	G	G	C	rs758182958	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820G>C	p.Glu274Gln	p.E274Q	ENST00000374530	8/11	26	4	22	37	37	0	PALM2-AKAP2,missense_variant,p.Glu274Gln,ENST00000374530,;AKAP2,missense_variant,p.Glu132Gln,ENST00000374525,;AKAP2,missense_variant,p.Glu43Gln,ENST00000259318,;AKAP2,missense_variant,p.Glu132Gln,ENST00000434623,;PALM2-AKAP2,missense_variant,p.Glu274Gln,ENST00000302798,;AKAP2,missense_variant,p.Glu274Gln,ENST00000510514,;AKAP2,missense_variant,p.Glu274Gln,ENST00000555236,;AKAP2,missense_variant,p.Glu92Gln,ENST00000480388,;PALM2-AKAP2,downstream_gene_variant,,ENST00000413420,;AKAP2,upstream_gene_variant,,ENST00000482335,;AKAP2,downstream_gene_variant,,ENST00000471798,;AKAP2,intron_variant,,ENST00000495980,;	C	ENSG00000157654	ENST00000374530	Transcript	missense_variant	1000	820	274	E/Q	Gaa/Caa	rs758182958	.	.	1	PALM2-AKAP2	HGNC	33529	protein_coding	YES	CCDS35100.1	ENSP00000363654	.	.	UPI0000125755	.	deleterious(0.03)	possibly_damaging(0.859)	8/11	.	hmmpanther:PTHR10498,hmmpanther:PTHR10498:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCACGAATCC	byFrequency	5	ESCA
PAPPA	0	.	GRCh37	9	118982241	118982241	+	Silent	SNP	G	G	T	rs140997586	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1944G>T	p.%3D	p.T648T	ENST00000328252	5/22	17	3	14	27	27	0	PAPPA,synonymous_variant,p.%3D,ENST00000328252,;PAPPA,intron_variant,,ENST00000534838,;	T	ENSG00000182752	ENST00000328252	Transcript	synonymous_variant	2313	1944	648	T	acG/acT	rs140997586	.	.	1	PAPPA	HGNC	8602	protein_coding	YES	CCDS6813.1	ENSP00000330658	PAPP1_HUMAN	Q5QFB7_HUMAN,F5GZ19_HUMAN	UPI00001E0589	.	.	.	5/22	.	hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347,Pfam_domain:PF05572	.	.	.	.	.	.	.	A:0.0002	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCACGCCCAA	byCluster	5	ESCA
CBWD1	0	.	GRCh37	9	121496	121496	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1159C>T	p.Arg387Cys	p.R387C	ENST00000356521	15/15	367	197	170	466	466	0	CBWD1,missense_variant,p.Arg368Cys,ENST00000382447,;CBWD1,missense_variant,p.Arg351Cys,ENST00000314367,;CBWD1,missense_variant,p.Arg339Cys,ENST00000377400,;CBWD1,missense_variant,p.Arg387Cys,ENST00000356521,;FOXD4,upstream_gene_variant,,ENST00000382500,;CBWD1,non_coding_transcript_exon_variant,,ENST00000465014,;CBWD1,non_coding_transcript_exon_variant,,ENST00000475990,;CBWD1,non_coding_transcript_exon_variant,,ENST00000487575,;CBWD1,non_coding_transcript_exon_variant,,ENST00000464198,;CBWD1,non_coding_transcript_exon_variant,,ENST00000495302,;CBWD1,downstream_gene_variant,,ENST00000475411,;CBWD1,downstream_gene_variant,,ENST00000462513,;	A	ENSG00000172785	ENST00000356521	Transcript	missense_variant	1248	1159	387	R/C	Cgt/Tgt	.	.	.	-1	CBWD1	HGNC	17134	protein_coding	YES	CCDS6438.1	ENSP00000348915	CBWD1_HUMAN	.	UPI000006EFDF	.	deleterious_low_confidence(0.02)	benign(0.001)	15/15	.	hmmpanther:PTHR13748,hmmpanther:PTHR13748:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAACGTGTTG	.	5	ESCA
OBP2A	0	.	GRCh37	9	138439805	138439805	+	Silent	SNP	G	G	C	rs749358777	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366G>C	p.%3D	p.L122L	ENST00000539850	4/7	12	2	10	15	15	0	OBP2A,missense_variant,p.Ala78Pro,ENST00000342114,;OBP2A,synonymous_variant,p.%3D,ENST00000340780,;OBP2A,synonymous_variant,p.%3D,ENST00000539850,;OBP2A,synonymous_variant,p.%3D,ENST00000371776,;OBP2A,missense_variant,p.Ala78Pro,ENST00000537747,;OBP2A,synonymous_variant,p.%3D,ENST00000471886,;	C	ENSG00000122136	ENST00000539850	Transcript	synonymous_variant	392	366	122	L	ctG/ctC	rs749358777	.	.	1	OBP2A	HGNC	23380	protein_coding	YES	CCDS6992.1	ENSP00000441028	OBP2A_HUMAN	.	UPI00000377BA	.	.	.	4/7	.	hmmpanther:PTHR11430,hmmpanther:PTHR11430:SF6,Pfam_domain:PF00061,Gene3D:2.40.128.20,Superfamily_domains:SSF50814	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCCTGCGCTA	byFrequency	3	ESCA
UNC13B	0	.	GRCh37	9	35398978	35398978	+	Silent	SNP	G	G	T	rs573780841	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3774G>T	p.%3D	p.A1258A	ENST00000378495	32/39	20	4	16	45	45	0	UNC13B,synonymous_variant,p.%3D,ENST00000378495,;UNC13B,synonymous_variant,p.%3D,ENST00000396787,;UNC13B,synonymous_variant,p.%3D,ENST00000378496,;UNC13B,non_coding_transcript_exon_variant,,ENST00000481299,;	T	ENSG00000198722	ENST00000378495	Transcript	synonymous_variant	3996	3774	1258	A	gcG/gcT	rs573780841,COSM1624941,COSM3664327	.	.	1	UNC13B	HGNC	12566	protein_coding	YES	CCDS6579.1	ENSP00000367756	UN13B_HUMAN	.	UPI0000211336	.	.	.	32/39	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10480	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGCGGCTCA	byFrequency|byCluster	5	ESCA
PCSK5	0	.	GRCh37	9	78547359	78547359	+	Missense_Mutation	SNP	C	C	G	rs771011461	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257C>G	p.Ser86Trp	p.S86W	ENST00000545128	2/37	37	5	32	48	48	0	PCSK5,missense_variant,p.Ser86Trp,ENST00000376767,;PCSK5,missense_variant,p.Ser86Trp,ENST00000376752,;PCSK5,missense_variant,p.Ser86Trp,ENST00000545128,;	G	ENSG00000099139	ENST00000545128	Transcript	missense_variant	795	257	86	S/W	tCg/tGg	rs771011461,COSM3658258,COSM3658259,COSM3658257	.	.	1	PCSK5	HGNC	8747	protein_coding	YES	CCDS55320.1	ENSP00000446280	PCSK5_HUMAN	I0EZ71_HUMAN	UPI0001DAD817	.	deleterious(0)	probably_damaging(0.986)	2/37	.	hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF327,Gene3D:1kn6A00,Superfamily_domains:SSF54897	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTCGAGCA	.	5	ESCA
PRUNE2	0	.	GRCh37	9	79270373	79270373	+	Silent	SNP	G	G	C	rs777562104	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8322C>G	p.%3D	p.G2774G	ENST00000376718	10/19	12	0	12	28	28	0	PRUNE2,synonymous_variant,p.%3D,ENST00000376717,;PRUNE2,synonymous_variant,p.%3D,ENST00000223609,;PRUNE2,synonymous_variant,p.%3D,ENST00000426088,;PRUNE2,synonymous_variant,p.%3D,ENST00000443509,;PRUNE2,synonymous_variant,p.%3D,ENST00000376718,;PRUNE2,synonymous_variant,p.%3D,ENST00000428286,;PRUNE2,upstream_gene_variant,,ENST00000424866,;PRUNE2,non_coding_transcript_exon_variant,,ENST00000466266,;PRUNE2,non_coding_transcript_exon_variant,,ENST00000488346,;PRUNE2,non_coding_transcript_exon_variant,,ENST00000480674,;	C	ENSG00000106772	ENST00000376718	Transcript	synonymous_variant	8446	8322	2774	G	ggC/ggG	rs777562104,COSM85165	.	.	-1	PRUNE2	HGNC	25209	protein_coding	YES	CCDS47982.1	ENSP00000365908	PRUN2_HUMAN	.	UPI0001612CC0	.	.	.	10/19	.	hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.G2774G|c.8322C>T|4	RADIA|MUTECT|MUSE	AGCACGCCCTC	byFrequency	3	ESCA
DAPK1	0	.	GRCh37	9	90296515	90296515	+	Missense_Mutation	SNP	C	C	A	rs770318110	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2198C>A	p.Pro733His	p.P733H	ENST00000408954	20/26	20	9	11	43	43	0	DAPK1,missense_variant,p.Pro733His,ENST00000408954,;DAPK1,missense_variant,p.Pro733His,ENST00000358077,;DAPK1,missense_variant,p.Pro733His,ENST00000491893,;DAPK1,missense_variant,p.Pro733His,ENST00000469640,;DAPK1,missense_variant,p.Pro733His,ENST00000472284,;DAPK1,downstream_gene_variant,,ENST00000497743,;DAPK1,3_prime_UTR_variant,,ENST00000489291,;	A	ENSG00000196730	ENST00000408954	Transcript	missense_variant	2533	2198	733	P/H	cCt/cAt	rs770318110	.	.	1	DAPK1	HGNC	2674	protein_coding	YES	CCDS43842.1	ENSP00000386135	DAPK1_HUMAN	.	UPI0000210C2F	.	tolerated(0.14)	benign(0.129)	20/26	.	hmmpanther:PTHR22964:SF54,hmmpanther:PTHR22964	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACCTTCAC	.	5	ESCA
IL1RAPL2	0	.	GRCh37	X	104992962	104992962	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058A>C	p.Tyr353Ser	p.Y353S	ENST00000372582	9/11	43	2	40	38	38	0	IL1RAPL2,missense_variant,p.Tyr353Ser,ENST00000344799,;IL1RAPL2,missense_variant,p.Tyr353Ser,ENST00000372582,;IL1RAPL2,non_coding_transcript_exon_variant,,ENST00000485671,;	C	ENSG00000189108	ENST00000372582	Transcript	missense_variant	1814	1058	353	Y/S	tAt/tCt	.	.	.	1	IL1RAPL2	HGNC	5997	protein_coding	YES	CCDS14517.1	ENSP00000361663	IRPL2_HUMAN	.	UPI0000073DF7	.	deleterious(0.02)	benign(0.259)	9/11	.	hmmpanther:PTHR11890:SF10,hmmpanther:PTHR11890	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTATAAAA	.	5	ESCA
NRK	0	.	GRCh37	X	105125725	105125725	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205C>G	p.Arg69Gly	p.R69G	ENST00000428173	4/29	50	8	41	48	48	0	NRK,missense_variant,p.Arg69Gly,ENST00000536164,;NRK,missense_variant,p.Arg69Gly,ENST00000428173,;NRK,missense_variant,p.Arg69Gly,ENST00000243300,;	G	ENSG00000123572	ENST00000428173	Transcript	missense_variant	508	205	69	R/G	Cga/Gga	COSM283374,COSM283375	.	.	1	NRK	HGNC	25391	protein_coding	YES	.	ENSP00000438378	.	F5H049_HUMAN,B7Z6I7_HUMAN	UPI00015E03BB	.	deleterious_low_confidence(0)	probably_damaging(0.988)	4/29	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF216,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGGCGAGTG	.	5	ESCA
RBMXL3	0	.	GRCh37	X	114424215	114424215	+	Missense_Mutation	SNP	G	G	T	rs781851586	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211G>T	p.Gly71Cys	p.G71C	ENST00000424776	1/1	12	0	12	10	10	0	RBMXL3,missense_variant,p.Gly71Cys,ENST00000424776,;LRCH2,intron_variant,,ENST00000538422,;LRCH2,intron_variant,,ENST00000317135,;	T	ENSG00000175718	ENST00000424776	Transcript	missense_variant	253	211	71	G/C	Ggc/Tgc	rs781851586	.	.	1	RBMXL3	HGNC	26859	protein_coding	YES	CCDS55478.1	ENSP00000417451	RMXL3_HUMAN	.	UPI0001932819	.	deleterious_low_confidence(0)	probably_damaging(1)	1/1	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF325,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGAACGGCAAG	byFrequency	3	ESCA
AGTR2	0	.	GRCh37	X	115305011	115305011	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*386T>G	.	.	ENST00000371906	3/3	40	1	38	27	27	0	AGTR2,3_prime_UTR_variant,,ENST00000371906,;	G	ENSG00000180772	ENST00000371906	Transcript	3_prime_UTR_variant	1668	.	.	.	.	.	.	.	1	AGTR2	HGNC	338	protein_coding	YES	CCDS14569.1	ENSP00000360973	AGTR2_HUMAN	Q6UVH2_HUMAN	UPI0000125687	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAACTCATTG	.	5	ESCA
AGTR2	0	.	GRCh37	X	115305310	115305310	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*685C>T	.	.	ENST00000371906	3/3	49	4	44	32	32	0	AGTR2,3_prime_UTR_variant,,ENST00000371906,;	T	ENSG00000180772	ENST00000371906	Transcript	3_prime_UTR_variant	1967	.	.	.	.	.	.	.	1	AGTR2	HGNC	338	protein_coding	YES	CCDS14569.1	ENSP00000360973	AGTR2_HUMAN	Q6UVH2_HUMAN	UPI0000125687	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTTCACTAA	.	5	ESCA
DCAF12L2	0	.	GRCh37	X	125299265	125299265	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.643G>T	p.Gly215Cys	p.G215C	ENST00000538699	2/2	41	3	37	64	64	0	DCAF12L2,missense_variant,p.Gly215Cys,ENST00000538699,;DCAF12L2,missense_variant,p.Gly215Cys,ENST00000360028,;	A	ENSG00000198354	ENST00000538699	Transcript	missense_variant	724	643	215	G/C	Ggc/Tgc	.	.	.	-1	DCAF12L2	HGNC	32950	protein_coding	YES	CCDS43991.1	ENSP00000441489	DC122_HUMAN	.	UPI0000197594	.	deleterious(0)	probably_damaging(1)	2/2	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF8,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGCCGTCGC	.	5	ESCA
MAGEA12	0	.	GRCh37	X	151899757	151899757	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99G>A	.	.	ENST00000393900	3/3	73	69	4	59	59	0	MAGEA12,3_prime_UTR_variant,,ENST00000393869,;MAGEA12,3_prime_UTR_variant,,ENST00000357916,;MAGEA12,3_prime_UTR_variant,,ENST00000393900,;CSAG1,upstream_gene_variant,,ENST00000370287,;CSAG1,upstream_gene_variant,,ENST00000452779,;CSAG1,upstream_gene_variant,,ENST00000370291,;CSAG4,intron_variant,,ENST00000361201,;CSAG1,upstream_gene_variant,,ENST00000361211,;CSAG4,upstream_gene_variant,,ENST00000583763,;CSAG4,upstream_gene_variant,,ENST00000535353,;	T	ENSG00000213401	ENST00000393900	Transcript	3_prime_UTR_variant	1398	.	.	.	.	.	.	.	-1	MAGEA12	HGNC	6799	protein_coding	YES	CCDS14710.1	ENSP00000377478	MAGAC_HUMAN	Q6FHH8_HUMAN	UPI0000000C51	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCTCATATC	.	2	ESCA
ASMT	0	.	GRCh37	X	1748728	1748728	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.458G>T	p.Arg153Leu	p.R153L	ENST00000381241	5/9	73	11	62	230	229	1	ASMT,missense_variant,p.Arg153Leu,ENST00000381229,;ASMT,missense_variant,p.Arg153Leu,ENST00000381241,;ASMT,missense_variant,p.Arg153Leu,ENST00000381233,;ASMT,intron_variant,,ENST00000509780,;	T	ENSG00000196433	ENST00000381241	Transcript	missense_variant	657	458	153	R/L	cGg/cTg	COSM4108410	.	.	1	ASMT	HGNC	750	protein_coding	YES	CCDS14117.1	ENSP00000370639	ASMT_HUMAN	.	UPI00001AEDD0	.	tolerated(1)	benign(0.01)	5/9	.	PROSITE_profiles:PS51683,hmmpanther:PTHR11746,hmmpanther:PTHR11746:SF71,Gene3D:3.40.50.150,Pfam_domain:PF00891,PIRSF_domain:PIRSF005739	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGCGGCTAC	.	5	ESCA
IL1RAPL1	0	.	GRCh37	X	29301329	29301329	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.357C>A	p.%3D	p.V119V	ENST00000378993	3/11	26	1	24	15	15	0	IL1RAPL1,synonymous_variant,p.%3D,ENST00000378993,;IL1RAPL1,synonymous_variant,p.%3D,ENST00000302196,;	A	ENSG00000169306	ENST00000378993	Transcript	synonymous_variant	1030	357	119	V	gtC/gtA	.	.	.	1	IL1RAPL1	HGNC	5996	protein_coding	YES	CCDS14218.1	ENSP00000368278	IRPL1_HUMAN	Q7Z2H0_HUMAN	UPI000006D1BF	.	.	.	3/11	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Gene3D:2.60.40.10,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF20,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGTCATCAG	.	5	ESCA
DMD	0	.	GRCh37	X	32490336	32490336	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2894C>A	p.Pro965His	p.P965H	ENST00000357033	22/79	34	4	29	29	29	0	DMD,missense_variant,p.Pro965His,ENST00000357033,;DMD,missense_variant,p.Pro961His,ENST00000378677,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000488902,;	T	ENSG00000198947	ENST00000357033	Transcript	missense_variant	3101	2894	965	P/H	cCt/cAt	.	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	benign(0.061)	22/79	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF261,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,PIRSF_domain:PIRSF002341	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGAGGTATG	.	5	ESCA
AKAP4	0	.	GRCh37	X	49958206	49958206	+	Missense_Mutation	SNP	G	G	C	rs112225746	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1158C>G	p.Cys386Trp	p.C386W	ENST00000358526	5/6	17	2	15	14	14	0	AKAP4,missense_variant,p.Cys386Trp,ENST00000358526,;AKAP4,missense_variant,p.Cys377Trp,ENST00000376056,;AKAP4,missense_variant,p.Cys377Trp,ENST00000376064,;AKAP4,intron_variant,,ENST00000448865,;AKAP4,intron_variant,,ENST00000376058,;AKAP4,downstream_gene_variant,,ENST00000437370,;AKAP4,non_coding_transcript_exon_variant,,ENST00000481402,;AKAP4,downstream_gene_variant,,ENST00000480926,;	C	ENSG00000147081	ENST00000358526	Transcript	missense_variant	1282	1158	386	C/W	tgC/tgG	rs112225746,COSM1468388	.	.	-1	AKAP4	HGNC	374	protein_coding	YES	CCDS14329.1	ENSP00000351327	AKAP4_HUMAN	.	UPI000013DA96	.	deleterious(0)	probably_damaging(0.999)	5/6	.	hmmpanther:PTHR10226:SF8,hmmpanther:PTHR10226,Pfam_domain:PF05716,SMART_domains:SM00807	A:0.0019	A:0.0053	A:0	.	A:0	A:0	A:0	A:0.007	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATGCAAGA	byFrequency|byCluster|by1000G	4	ESCA
TBX22	0	.	GRCh37	X	79282340	79282340	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.771C>A	p.%3D	p.T257T	ENST00000373294	5/8	17	1	16	24	24	0	TBX22,synonymous_variant,p.%3D,ENST00000373291,;TBX22,synonymous_variant,p.%3D,ENST00000373294,;TBX22,synonymous_variant,p.%3D,ENST00000442340,;TBX22,synonymous_variant,p.%3D,ENST00000373296,;TBX22,downstream_gene_variant,,ENST00000476373,;	A	ENSG00000122145	ENST00000373294	Transcript	synonymous_variant	799	771	257	T	acC/acA	.	.	.	1	TBX22	HGNC	11600	protein_coding	YES	CCDS14445.1	ENSP00000362390	TBX22_HUMAN	C3TX51_HUMAN	UPI00001377ED	.	.	.	5/8	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF97,Pfam_domain:PF00907,Gene3D:1h6fA00,SMART_domains:SM00425,Superfamily_domains:SSF49417,Prints_domain:PR00937	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCACCACAGT	.	5	ESCA
CPXCR1	0	.	GRCh37	X	88008707	88008707	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A49Y-01A-11D-A27G-09	TCGA-LN-A49Y-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292A>G	p.Arg98Gly	p.R98G	ENST00000276127	3/3	22	1	21	17	17	0	CPXCR1,missense_variant,p.Arg98Gly,ENST00000276127,;CPXCR1,missense_variant,p.Arg98Gly,ENST00000373111,;	G	ENSG00000147183	ENST00000276127	Transcript	missense_variant	551	292	98	R/G	Aga/Gga	.	.	.	1	CPXCR1	HGNC	2332	protein_coding	YES	CCDS14458.1	ENSP00000276127	CPXCR_HUMAN	.	UPI000007369F	.	tolerated(0.07)	possibly_damaging(0.765)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCAGAAAA	.	5	ESCA
CELF2	0	.	GRCh37	10	11378438	11378438	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6028A>T	.	.	ENST00000450189	15/15	73	47	26	82	82	0	CELF2,3_prime_UTR_variant,,ENST00000427450,;CELF2,3_prime_UTR_variant,,ENST00000379261,;CELF2,3_prime_UTR_variant,,ENST00000450189,;CELF2,3_prime_UTR_variant,,ENST00000315874,;CELF2,downstream_gene_variant,,ENST00000354440,;	T	ENSG00000048740	ENST00000450189	Transcript	3_prime_UTR_variant	7754	.	.	.	.	.	.	.	1	CELF2	HGNC	2550	protein_coding	YES	CCDS44355.1	ENSP00000389951	.	E9PC62_HUMAN,B4DIB6_HUMAN	UPI0000F58F21	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATCAGGAAC	.	5	ESCA
SEPHS1	0	.	GRCh37	10	13364865	13364865	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934C>G	p.Leu312Val	p.L312V	ENST00000327347	8/9	35	22	12	32	32	0	SEPHS1,missense_variant,p.Leu312Val,ENST00000545675,;SEPHS1,missense_variant,p.Leu245Val,ENST00000537130,;SEPHS1,missense_variant,p.Leu312Val,ENST00000327347,;SEPHS1,intron_variant,,ENST00000378614,;	C	ENSG00000086475	ENST00000327347	Transcript	missense_variant	1310	934	312	L/V	Ctc/Gtc	.	.	.	-1	SEPHS1	HGNC	19685	protein_coding	YES	CCDS7098.1	ENSP00000367893	SPS1_HUMAN	Q5T5U7_HUMAN,Q5T5U6_HUMAN	UPI0000135E82	.	deleterious(0)	probably_damaging(0.987)	8/9	.	Superfamily_domains:SSF56042,PIRSF_domain:PIRSF036407,Pfam_domain:PF02769,TIGRFAM_domain:TIGR00476,Gene3D:3.90.650.10,hmmpanther:PTHR10256,hmmpanther:PTHR10256:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGAGGCCGA	.	5	ESCA
ITGA8	0	.	GRCh37	10	15573108	15573108	+	Nonsense_Mutation	SNP	C	C	A	rs762605347	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2923G>T	p.Glu975Ter	p.E975*	ENST00000378076	28/30	27	15	12	32	32	0	ITGA8,stop_gained,p.Glu975Ter,ENST00000378076,;	A	ENSG00000077943	ENST00000378076	Transcript	stop_gained	3277	2923	975	E/*	Gaa/Taa	rs762605347	.	.	-1	ITGA8	HGNC	6144	protein_coding	YES	CCDS31155.1	ENSP00000367316	ITA8_HUMAN	.	UPI00001D80A0	.	.	.	28/30	.	hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Gene3D:1jv2A04,Superfamily_domains:SSF69179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTCAAAGG	byFrequency	5	ESCA
RP11-85G18.6	0	.	GRCh37	10	27537671	27537671	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.256-1316A>T	.	.	ENST00000574842	.	153	101	52	161	161	0	RP11-85G18.6,intron_variant,,ENST00000574842,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000284414,;LRRC37A6P,downstream_gene_variant,,ENST00000575554,;LRRC37A6P,downstream_gene_variant,,ENST00000574795,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000448648,;	T	ENSG00000262412	ENST00000574842	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RP11-85G18.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTAAATGA	.	5	ESCA
WAC	0	.	GRCh37	10	28900777	28900777	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1363A>T	p.Ile455Leu	p.I455L	ENST00000354911	10/14	61	37	24	41	40	0	WAC,missense_variant,p.Ile352Leu,ENST00000347934,;WAC,missense_variant,p.Ile410Leu,ENST00000375664,;WAC,missense_variant,p.Ile303Leu,ENST00000375646,;WAC,missense_variant,p.Ile455Leu,ENST00000354911,;WAC,downstream_gene_variant,,ENST00000428935,;WAC,3_prime_UTR_variant,,ENST00000439676,;WAC,non_coding_transcript_exon_variant,,ENST00000345541,;WAC,upstream_gene_variant,,ENST00000480474,;WAC,downstream_gene_variant,,ENST00000424454,;WAC,downstream_gene_variant,,ENST00000495268,;WAC,downstream_gene_variant,,ENST00000476046,;	T	ENSG00000095787	ENST00000354911	Transcript	missense_variant	1524	1363	455	I/L	Ata/Tta	.	.	.	1	WAC	HGNC	17327	protein_coding	YES	CCDS7159.1	ENSP00000346986	WAC_HUMAN	J3QTA0_HUMAN,E9PMZ7_HUMAN,C9JVK6_HUMAN,C9JMU2_HUMAN,C9JD58_HUMAN	UPI000013D398	.	tolerated(0.13)	benign(0.418)	10/14	.	hmmpanther:PTHR15911,hmmpanther:PTHR15911:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAAGAATAAGC	.	4	ESCA
ZNF485	0	.	GRCh37	10	44112021	44112021	+	Missense_Mutation	SNP	A	A	G	rs372395438	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530A>G	p.His177Arg	p.H177R	ENST00000361807	5/5	33	20	13	39	39	0	ZNF485,missense_variant,p.His86Arg,ENST00000374437,;ZNF485,missense_variant,p.His177Arg,ENST00000374435,;ZNF485,missense_variant,p.His177Arg,ENST00000361807,;ZNF485,downstream_gene_variant,,ENST00000430885,;	G	ENSG00000198298	ENST00000361807	Transcript	missense_variant	724	530	177	H/R	cAt/cGt	rs372395438,COSM1470268,COSM1470267	.	.	1	ZNF485	HGNC	23440	protein_coding	YES	CCDS7205.2	ENSP00000354694	ZN485_HUMAN	C9JV60_HUMAN,B4DSE6_HUMAN,B2R8D6_HUMAN	UPI00000717FE	.	tolerated(0.09)	benign(0.001)	5/5	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,hmmpanther:PTHR24376:SF14,hmmpanther:PTHR24376,PROSITE_profiles:PS50157	G:0.0004	G:0.0015	G:0	.	G:0	G:0	G:0	G:0	G:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCATAAGG	byFrequency|byCluster|by1000G	5	ESCA
FAM208B	0	.	GRCh37	10	5791064	5791064	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5680C>G	p.Pro1894Ala	p.P1894A	ENST00000328090	15/21	45	26	19	37	37	0	FAM208B,missense_variant,p.Pro1894Ala,ENST00000328090,;	G	ENSG00000108021	ENST00000328090	Transcript	missense_variant	6305	5680	1894	P/A	Cct/Gct	.	.	.	1	FAM208B	HGNC	23484	protein_coding	YES	CCDS41485.1	ENSP00000328426	F208B_HUMAN	.	UPI00004589BB	.	tolerated(0.18)	benign(0.021)	15/21	.	hmmpanther:PTHR16207,hmmpanther:PTHR16207:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCCCTCCC	.	5	ESCA
NR1H3	0	.	GRCh37	11	47282123	47282123	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396C>T	p.%3D	p.Y132Y	ENST00000467728	3/9	33	24	8	34	34	0	NR1H3,synonymous_variant,p.%3D,ENST00000436029,;NR1H3,synonymous_variant,p.%3D,ENST00000395397,;NR1H3,synonymous_variant,p.%3D,ENST00000441012,;NR1H3,synonymous_variant,p.%3D,ENST00000449369,;NR1H3,synonymous_variant,p.%3D,ENST00000407404,;NR1H3,synonymous_variant,p.%3D,ENST00000467728,;NR1H3,synonymous_variant,p.%3D,ENST00000527949,;NR1H3,synonymous_variant,p.%3D,ENST00000405576,;NR1H3,synonymous_variant,p.%3D,ENST00000444396,;NR1H3,synonymous_variant,p.%3D,ENST00000481889,;NR1H3,synonymous_variant,p.%3D,ENST00000436778,;NR1H3,synonymous_variant,p.%3D,ENST00000405853,;NR1H3,synonymous_variant,p.%3D,ENST00000412937,;NR1H3,intron_variant,,ENST00000531660,;NR1H3,downstream_gene_variant,,ENST00000437276,;NR1H3,downstream_gene_variant,,ENST00000457932,;NR1H3,non_coding_transcript_exon_variant,,ENST00000461778,;NR1H3,non_coding_transcript_exon_variant,,ENST00000530310,;NR1H3,non_coding_transcript_exon_variant,,ENST00000473222,;NR1H3,non_coding_transcript_exon_variant,,ENST00000476086,;NR1H3,non_coding_transcript_exon_variant,,ENST00000527464,;NR1H3,non_coding_transcript_exon_variant,,ENST00000529540,;NR1H3,intron_variant,,ENST00000525441,;NR1H3,intron_variant,,ENST00000532630,;NR1H3,downstream_gene_variant,,ENST00000495866,;NR1H3,3_prime_UTR_variant,,ENST00000420369,;NR1H3,non_coding_transcript_exon_variant,,ENST00000481020,;NR1H3,non_coding_transcript_exon_variant,,ENST00000483882,;NR1H3,intron_variant,,ENST00000487913,;NR1H3,downstream_gene_variant,,ENST00000486991,;NR1H3,downstream_gene_variant,,ENST00000498548,;NR1H3,downstream_gene_variant,,ENST00000419652,;	T	ENSG00000025434	ENST00000467728	Transcript	synonymous_variant	1634	396	132	Y	taC/taT	.	.	.	1	NR1H3	HGNC	7966	protein_coding	YES	CCDS7929.1	ENSP00000420656	NR1H3_HUMAN	F1D8N1_HUMAN,C9JTS4_HUMAN,C9JJ16_HUMAN,C9JEC2_HUMAN,C9JCS0_HUMAN,C9JBS2_HUMAN,C9J4R0_HUMAN,C9J2C8_HUMAN	UPI000013050C	.	.	.	3/9	.	PROSITE_profiles:PS51030,hmmpanther:PTHR24082:SF259,hmmpanther:PTHR24082,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTACATCTG	.	5	ESCA
CELF1	0	.	GRCh37	11	47496971	47496971	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1184A>G	p.Tyr395Cys	p.Y395C	ENST00000532048	13/16	32	18	14	36	36	0	CELF1,missense_variant,p.Tyr368Cys,ENST00000395290,;CELF1,missense_variant,p.Tyr366Cys,ENST00000361904,;CELF1,missense_variant,p.Tyr397Cys,ENST00000531165,;CELF1,missense_variant,p.Tyr365Cys,ENST00000310513,;CELF1,missense_variant,p.Tyr395Cys,ENST00000532048,;CELF1,missense_variant,p.Tyr369Cys,ENST00000358597,;CELF1,missense_variant,p.Tyr366Cys,ENST00000395292,;CELF1,non_coding_transcript_exon_variant,,ENST00000539455,;CELF1,non_coding_transcript_exon_variant,,ENST00000539254,;CELF1,downstream_gene_variant,,ENST00000422993,;CELF1,upstream_gene_variant,,ENST00000524648,;CELF1,downstream_gene_variant,,ENST00000534614,;	C	ENSG00000149187	ENST00000532048	Transcript	missense_variant	2078	1184	395	Y/C	tAt/tGt	COSM1628001,COSM3739075	.	.	-1	CELF1	HGNC	2549	protein_coding	YES	CCDS53623.1	ENSP00000435926	CELF1_HUMAN	F5H4Y5_HUMAN,F5H3J7_HUMAN,F5H0D8_HUMAN,E9PSH0_HUMAN,E9PQK4_HUMAN,E9PKU1_HUMAN,E9PKA1_HUMAN	UPI0000D9D8B2	.	deleterious(0)	probably_damaging(0.994)	13/16	.	hmmpanther:PTHR24622:SF179,hmmpanther:PTHR24622	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCATATTGC	.	5	ESCA
ASRGL1	0	.	GRCh37	11	62123886	62123886	+	Missense_Mutation	SNP	G	G	A	rs201870863	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280G>A	p.Ala94Thr	p.A94T	ENST00000415229	3/7	114	61	52	108	107	1	ASRGL1,missense_variant,p.Ala94Thr,ENST00000415229,;ASRGL1,missense_variant,p.Ala94Thr,ENST00000301776,;ASRGL1,intron_variant,,ENST00000535727,;ASRGL1,non_coding_transcript_exon_variant,,ENST00000526096,;ASRGL1,upstream_gene_variant,,ENST00000528206,;ASRGL1,non_coding_transcript_exon_variant,,ENST00000534571,;ASRGL1,intron_variant,,ENST00000534183,;ASRGL1,intron_variant,,ENST00000529226,;	A	ENSG00000162174	ENST00000415229	Transcript	missense_variant	495	280	94	A/T	Gca/Aca	rs201870863	.	.	1	ASRGL1	HGNC	16448	protein_coding	YES	CCDS8019.1	ENSP00000400057	ASGL1_HUMAN	Q9BRH2_HUMAN	UPI000004BF00	.	deleterious(0.04)	possibly_damaging(0.842)	3/7	.	hmmpanther:PTHR10188,hmmpanther:PTHR10188:SF18,Pfam_domain:PF01112,Superfamily_domains:SSF56235	T:0.0006	T:0	T:0	.	T:0	T:0	T:0.0031	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCCGCAGTC	byFrequency|byCluster|by1000G	5	ESCA
ROM1	0	.	GRCh37	11	62381901	62381901	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.762T>A	p.His254Gln	p.H254Q	ENST00000278833	2/3	19	8	11	23	23	0	ROM1,missense_variant,p.His254Gln,ENST00000278833,;ROM1,missense_variant,p.Met45Lys,ENST00000525801,;ROM1,missense_variant,p.Met45Lys,ENST00000534093,;ROM1,missense_variant,p.Met45Lys,ENST00000525947,;EML3,upstream_gene_variant,,ENST00000278845,;B3GAT3,downstream_gene_variant,,ENST00000534026,;B3GAT3,downstream_gene_variant,,ENST00000265471,;EML3,upstream_gene_variant,,ENST00000494176,;EML3,upstream_gene_variant,,ENST00000394773,;EML3,upstream_gene_variant,,ENST00000419857,;EML3,upstream_gene_variant,,ENST00000394776,;EML3,upstream_gene_variant,,ENST00000529309,;EML3,upstream_gene_variant,,ENST00000466671,;B3GAT3,downstream_gene_variant,,ENST00000531383,;EML3,upstream_gene_variant,,ENST00000466886,;B3GAT3,downstream_gene_variant,,ENST00000534715,;EML3,upstream_gene_variant,,ENST00000531557,;ROM1,downstream_gene_variant,,ENST00000529273,;B3GAT3,downstream_gene_variant,,ENST00000533303,;EML3,upstream_gene_variant,,ENST00000494448,;B3GAT3,downstream_gene_variant,,ENST00000532585,;	A	ENSG00000149489	ENST00000278833	Transcript	missense_variant	1303	762	254	H/Q	caT/caA	.	.	.	1	ROM1	HGNC	10254	protein_coding	YES	CCDS8024.1	ENSP00000278833	ROM1_HUMAN	.	UPI000013DB95	.	deleterious(0.02)	probably_damaging(0.998)	2/3	.	Superfamily_domains:0037997,Pfam_domain:PF00335,hmmpanther:PTHR19282:SF188,hmmpanther:PTHR19282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCATGAGGT	.	5	ESCA
EHD1	0	.	GRCh37	11	64627509	64627509	+	Missense_Mutation	SNP	G	G	A	rs145274478	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.802C>T	p.Arg268Cys	p.R268C	ENST00000320631	3/5	59	39	20	64	64	0	EHD1,missense_variant,p.Arg268Cys,ENST00000359393,;EHD1,missense_variant,p.Arg132Cys,ENST00000421510,;EHD1,missense_variant,p.Arg268Cys,ENST00000320631,;EHD1,missense_variant,p.Arg282Cys,ENST00000433803,;EHD1,missense_variant,p.Arg132Cys,ENST00000455148,;EHD1,upstream_gene_variant,,ENST00000488711,;EHD1,non_coding_transcript_exon_variant,,ENST00000466015,;EHD1,non_coding_transcript_exon_variant,,ENST00000498472,;EHD1,upstream_gene_variant,,ENST00000484846,;	A	ENSG00000110047	ENST00000320631	Transcript	missense_variant	1057	802	268	R/C	Cgc/Tgc	rs145274478	.	.	-1	EHD1	HGNC	3242	protein_coding	YES	CCDS8084.1	ENSP00000320516	EHD1_HUMAN	C9JIJ3_HUMAN,C9JDQ8_HUMAN,C9J2Z4_HUMAN,C9IZH1_HUMAN,B2R5U3_HUMAN	UPI0000129E22	.	deleterious(0.01)	possibly_damaging(0.841)	3/5	.	PROSITE_profiles:PS51718,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF60,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCGGTTGT	byCluster	5	ESCA
EHD1	0	.	GRCh37	11	64627713	64627713	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598T>C	p.Phe200Leu	p.F200L	ENST00000320631	3/5	46	22	24	35	35	0	EHD1,missense_variant,p.Phe200Leu,ENST00000359393,;EHD1,missense_variant,p.Phe64Leu,ENST00000421510,;EHD1,missense_variant,p.Phe200Leu,ENST00000320631,;EHD1,missense_variant,p.Phe214Leu,ENST00000433803,;EHD1,missense_variant,p.Phe64Leu,ENST00000455148,;EHD1,non_coding_transcript_exon_variant,,ENST00000466015,;EHD1,upstream_gene_variant,,ENST00000484846,;EHD1,upstream_gene_variant,,ENST00000498472,;	G	ENSG00000110047	ENST00000320631	Transcript	missense_variant	853	598	200	F/L	Ttc/Ctc	.	.	.	-1	EHD1	HGNC	3242	protein_coding	YES	CCDS8084.1	ENSP00000320516	EHD1_HUMAN	C9JIJ3_HUMAN,C9JDQ8_HUMAN,C9J2Z4_HUMAN,C9IZH1_HUMAN,B2R5U3_HUMAN	UPI0000129E22	.	tolerated(0.08)	benign(0.387)	3/5	.	PROSITE_profiles:PS51718,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF60,Pfam_domain:PF00350,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGAACTCAT	.	5	ESCA
CORO1B	0	.	GRCh37	11	67208477	67208477	+	Intron	SNP	G	G	A	rs780078116	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756+119C>T	.	.	ENST00000393893	.	27	22	5	29	29	0	CORO1B,3_prime_UTR_variant,,ENST00000453768,;CORO1B,intron_variant,,ENST00000341356,;CORO1B,intron_variant,,ENST00000393893,;PTPRCAP,upstream_gene_variant,,ENST00000326294,;CORO1B,downstream_gene_variant,,ENST00000545016,;CORO1B,upstream_gene_variant,,ENST00000539970,;CORO1B,downstream_gene_variant,,ENST00000537010,;CORO1B,downstream_gene_variant,,ENST00000545736,;CORO1B,upstream_gene_variant,,ENST00000539724,;CORO1B,intron_variant,,ENST00000537042,;	A	ENSG00000172725	ENST00000393893	Transcript	intron_variant	.	.	.	.	.	rs780078116	.	.	-1	CORO1B	HGNC	2253	protein_coding	YES	CCDS8164.1	ENSP00000377471	COR1B_HUMAN	.	UPI0000127C42	.	.	.	.	7/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGAGAGCCT	.	5	ESCA
INTS4	0	.	GRCh37	11	77690104	77690104	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.409A>G	p.Ile137Val	p.I137V	ENST00000534064	4/23	39	21	18	56	56	0	INTS4,missense_variant,p.Ile137Val,ENST00000529807,;INTS4,missense_variant,p.Ile137Val,ENST00000534064,;INTS4,3_prime_UTR_variant,,ENST00000534408,;INTS4,intron_variant,,ENST00000433818,;INTS4,downstream_gene_variant,,ENST00000524766,;	C	ENSG00000149262	ENST00000534064	Transcript	missense_variant	444	409	137	I/V	Att/Gtt	.	.	.	-1	INTS4	HGNC	25048	protein_coding	YES	CCDS31644.1	ENSP00000434466	INT4_HUMAN	.	UPI00001FB00A	.	tolerated(0.4)	possibly_damaging(0.839)	4/23	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR20938,hmmpanther:PTHR20938:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAATTGCAA	.	5	ESCA
MAML2	0	.	GRCh37	11	95724824	95724825	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2202dupT	p.Pro735SerfsTer46	p.P735Sfs*46	ENST00000524717	3/5	77	50	27	66	66	0	MAML2,frameshift_variant,p.Pro735SerfsTer46,ENST00000524717,;	A	ENSG00000184384	ENST00000524717	Transcript	frameshift_variant	3487-3488	2202-2203	734-735	-/X	-/T	.	.	.	-1	MAML2	HGNC	16259	protein_coding	YES	CCDS44714.1	ENSP00000434552	MAML2_HUMAN	.	UPI00001B4EFC	.	.	.	3/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTTGGATTTG	.	3	ESCA
SART3	0	.	GRCh37	12	108923976	108923976	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1858C>T	p.Pro620Ser	p.P620S	ENST00000228284	15/19	22	5	17	28	28	0	SART3,missense_variant,p.Pro620Ser,ENST00000228284,;SART3,missense_variant,p.Pro584Ser,ENST00000431469,;SART3,missense_variant,p.Pro638Ser,ENST00000546815,;FICD,downstream_gene_variant,,ENST00000549641,;SART3,upstream_gene_variant,,ENST00000547397,;FICD,downstream_gene_variant,,ENST00000546448,;SART3,3_prime_UTR_variant,,ENST00000546728,;SART3,downstream_gene_variant,,ENST00000547528,;SART3,downstream_gene_variant,,ENST00000546808,;SART3,downstream_gene_variant,,ENST00000548077,;SART3,downstream_gene_variant,,ENST00000547196,;SART3,downstream_gene_variant,,ENST00000548582,;	A	ENSG00000075856	ENST00000228284	Transcript	missense_variant	2093	1858	620	P/S	Cca/Tca	.	.	.	-1	SART3	HGNC	16860	protein_coding	YES	CCDS9117.1	ENSP00000228284	SART3_HUMAN	H0YHU8_HUMAN,F8VZM2_HUMAN,F8VVK9_HUMAN	UPI000006D72B	.	tolerated(0.73)	benign(0.001)	15/19	.	hmmpanther:PTHR23269,hmmpanther:PTHR23269:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGGGCCTC	.	5	ESCA
TAS2R7	0	.	GRCh37	12	10954348	10954348	+	Silent	SNP	A	A	T	rs558100889	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822T>A	p.%3D	p.A274A	ENST00000240687	1/1	28	24	4	32	32	0	TAS2R7,synonymous_variant,p.%3D,ENST00000240687,;TAS2R8,downstream_gene_variant,,ENST00000240615,;	T	ENSG00000121377	ENST00000240687	Transcript	synonymous_variant	879	822	274	A	gcT/gcA	rs558100889	.	.	-1	TAS2R7	HGNC	14913	protein_coding	YES	CCDS8631.1	ENSP00000240687	TA2R7_HUMAN	Q50KV7_HUMAN,Q50KV5_HUMAN	UPI0000038B0F	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11394:SF58,hmmpanther:PTHR11394,Gene3D:1.20.1070.10,Pfam_domain:PF05296,Superfamily_domains:SSF81321	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTAGAGCTAT	by1000G	4	ESCA
P2RX4	0	.	GRCh37	12	121647986	121647986	+	Missense_Mutation	SNP	G	G	T	rs754311085	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19G>T	p.Ala7Ser	p.A7S	ENST00000359949	1/13	12	4	7	16	16	0	P2RX4,missense_variant,p.Ala7Ser,ENST00000538701,;P2RX4,missense_variant,p.Ala7Ser,ENST00000337233,;P2RX4,missense_variant,p.Ala7Ser,ENST00000359949,;P2RX4,missense_variant,p.Ala7Ser,ENST00000542067,;P2RX4,missense_variant,p.Ala7Ser,ENST00000541532,;P2RX4,5_prime_UTR_variant,,ENST00000543171,;P2RX4,non_coding_transcript_exon_variant,,ENST00000540930,;P2RX4,missense_variant,p.Ala7Ser,ENST00000543318,;P2RX4,missense_variant,p.Ala7Ser,ENST00000543984,;P2RX4,non_coding_transcript_exon_variant,,ENST00000543430,;P2RX4,non_coding_transcript_exon_variant,,ENST00000541187,;P2RX4,non_coding_transcript_exon_variant,,ENST00000499638,;P2RX4,upstream_gene_variant,,ENST00000538417,;P2RX4,upstream_gene_variant,,ENST00000314442,;	T	ENSG00000135124	ENST00000359949	Transcript	missense_variant	119	19	7	A/S	Gcg/Tcg	rs754311085	.	.	1	P2RX4	HGNC	8535	protein_coding	YES	CCDS58282.1	ENSP00000353032	.	K4KBD6_HUMAN,F5CTF4_HUMAN,E7EPF7_HUMAN,B7Z4R5_HUMAN	UPI0000D4DAF5	.	tolerated(0.61)	benign(0.005)	1/13	.	Prints_domain:PR01311,TIGRFAM_domain:TIGR00863,hmmpanther:PTHR10125:SF18,hmmpanther:PTHR10125,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCGCCGCGCTG	.	3	ESCA
ARID2	0	.	GRCh37	12	46299425	46299425	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*564A>G	.	.	ENST00000334344	21/21	38	26	11	53	53	0	ARID2,3_prime_UTR_variant,,ENST00000334344,;ARID2,3_prime_UTR_variant,,ENST00000444670,;ARID2,3_prime_UTR_variant,,ENST00000457135,;ARID2,non_coding_transcript_exon_variant,,ENST00000479608,;	G	ENSG00000189079	ENST00000334344	Transcript	3_prime_UTR_variant	6244	.	.	.	.	.	.	.	1	ARID2	HGNC	18037	protein_coding	YES	CCDS31783.1	ENSP00000335044	ARID2_HUMAN	Q96SQ4_HUMAN,F8WCU9_HUMAN	UPI00001D7973	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATATTTTC	.	5	ESCA
KMT2D	0	.	GRCh37	12	49443467	49443471	+	Frame_Shift_Del	DEL	GTTTG	GTTTG	-	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	GTTTG	GTTTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3900_3904delCAAAC	p.Lys1301GlyfsTer22	p.K1301Gfs*22	ENST00000301067	11/54	27	16	11	31	31	0	KMT2D,frameshift_variant,p.Lys1301GlyfsTer22,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000547610,;	-	ENSG00000167548	ENST00000301067	Transcript	frameshift_variant	3900-3904	3900-3904	1300-1302	IKQ/IX	atCAAACag/atag	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	11/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCACCTGTTTGATGCG	.	3	ESCA
KCNA1	0	.	GRCh37	12	5022461	5022461	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*429C>G	.	.	ENST00000382545	2/2	28	18	10	29	29	0	KCNA1,3_prime_UTR_variant,,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	G	ENSG00000111262	ENST00000382545	Transcript	3_prime_UTR_variant	3024	.	.	.	.	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACATCTTTGC	.	5	ESCA
KRT81	0	.	GRCh37	12	52681102	52681102	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1031C>G	p.Ser344Cys	p.S344C	ENST00000327741	7/9	31	23	7	30	30	0	KRT81,missense_variant,p.Ser344Cys,ENST00000327741,;KRT86,intron_variant,,ENST00000423955,;KRT86,intron_variant,,ENST00000544024,;KRT86,intron_variant,,ENST00000553310,;	C	ENSG00000205426	ENST00000327741	Transcript	missense_variant	1100	1031	344	S/C	tCc/tGc	.	.	.	-1	KRT81	HGNC	6458	protein_coding	YES	CCDS31805.1	ENSP00000369349	KRT81_HUMAN	Q8NFV1_HUMAN,Q8N120_HUMAN	UPI0000DBEEF8	.	tolerated(0.65)	benign(0.008)	7/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF143,hmmpanther:PTHR23239,Pfam_domain:PF00038,Gene3D:1.20.5.170,Superfamily_domains:SSF64593	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTGGAGTTC	.	5	ESCA
SP1	0	.	GRCh37	12	53800472	53800472	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1779C>T	p.%3D	p.P593P	ENST00000327443	4/6	42	22	20	43	43	0	SP1,synonymous_variant,p.%3D,ENST00000426431,;SP1,synonymous_variant,p.%3D,ENST00000327443,;	T	ENSG00000185591	ENST00000327443	Transcript	synonymous_variant	1877	1779	593	P	ccC/ccT	.	.	.	1	SP1	HGNC	11205	protein_coding	YES	CCDS8857.1	ENSP00000329357	SP1_HUMAN	G5E9M8_HUMAN,Q9NR52_HUMAN,H3BVI2_HUMAN,C4PGM0_HUMAN	UPI0000135D4E	.	.	.	4/6	.	hmmpanther:PTHR23235:SF4,hmmpanther:PTHR23235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACCCCAAGC	.	5	ESCA
PTPRR	0	.	GRCh37	12	71032196	71032196	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*768G>A	.	.	ENST00000283228	14/14	16	9	7	14	14	0	PTPRR,3_prime_UTR_variant,,ENST00000440835,;PTPRR,3_prime_UTR_variant,,ENST00000378778,;PTPRR,3_prime_UTR_variant,,ENST00000283228,;PTPRR,downstream_gene_variant,,ENST00000342084,;PTPRB,upstream_gene_variant,,ENST00000334414,;PTPRB,upstream_gene_variant,,ENST00000550358,;PTPRB,upstream_gene_variant,,ENST00000551525,;PTPRB,upstream_gene_variant,,ENST00000548122,;PTPRR,downstream_gene_variant,,ENST00000549308,;PTPRR,non_coding_transcript_exon_variant,,ENST00000537619,;PTPRR,non_coding_transcript_exon_variant,,ENST00000547752,;PTPRR,downstream_gene_variant,,ENST00000549107,;PTPRB,upstream_gene_variant,,ENST00000538174,;PTPRR,3_prime_UTR_variant,,ENST00000551219,;PTPRB,upstream_gene_variant,,ENST00000552253,;	T	ENSG00000153233	ENST00000283228	Transcript	3_prime_UTR_variant	3195	.	.	.	.	.	.	.	-1	PTPRR	HGNC	9680	protein_coding	YES	CCDS8998.1	ENSP00000283228	PTPRR_HUMAN	Q68CP6_HUMAN,F8VVE9_HUMAN	UPI000013DD2F	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTCCCTTT	.	2	ESCA
TPP2	0	.	GRCh37	13	103281862	103281862	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1047A>G	p.%3D	p.V349V	ENST00000376065	9/29	28	13	15	40	39	1	TPP2,synonymous_variant,p.%3D,ENST00000376052,;TPP2,synonymous_variant,p.%3D,ENST00000376065,;TPP2,non_coding_transcript_exon_variant,,ENST00000493770,;TPP2,downstream_gene_variant,,ENST00000496126,;	G	ENSG00000134900	ENST00000376065	Transcript	synonymous_variant	1083	1047	349	V	gtA/gtG	.	.	.	1	TPP2	HGNC	12016	protein_coding	YES	CCDS9502.1	ENSP00000365233	TPP2_HUMAN	.	UPI0000001C91	.	.	.	9/29	.	Superfamily_domains:SSF52743,Gene3D:3.40.50.200,Pfam_domain:PF00082,hmmpanther:PTHR10795	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCAGTATGGAA	.	4	ESCA
LIG4	0	.	GRCh37	13	108863310	108863310	+	Nonsense_Mutation	SNP	C	C	A	rs767537496	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.307G>T	p.Gly103Ter	p.G103*	ENST00000356922	2/2	20	15	5	35	35	0	LIG4,stop_gained,p.Gly103Ter,ENST00000405925,;LIG4,stop_gained,p.Gly103Ter,ENST00000356922,;LIG4,stop_gained,p.Gly103Ter,ENST00000442234,;	A	ENSG00000174405	ENST00000356922	Transcript	stop_gained	580	307	103	G/*	Gga/Tga	rs767537496	.	.	-1	LIG4	HGNC	6601	protein_coding	YES	CCDS9508.1	ENSP00000349393	DNLI4_HUMAN	.	UPI00000742BF	.	.	.	2/2	.	hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF7,Gene3D:1x9nA01,Pfam_domain:PF04675,TIGRFAM_domain:TIGR00574,Superfamily_domains:0050884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCCATCTC	byCluster	5	ESCA
PDS5B	0	.	GRCh37	13	33338643	33338643	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3535A>G	p.Met1179Val	p.M1179V	ENST00000315596	31/35	72	44	27	51	51	0	PDS5B,missense_variant,p.Met133Val,ENST00000447833,;PDS5B,missense_variant,p.Met1179Val,ENST00000315596,;RNY1P4,upstream_gene_variant,,ENST00000384595,;PDS5B,missense_variant,p.Met1179Val,ENST00000450460,;	G	ENSG00000083642	ENST00000315596	Transcript	missense_variant	3721	3535	1179	M/V	Atg/Gtg	.	.	.	1	PDS5B	HGNC	20418	protein_coding	YES	CCDS41878.1	ENSP00000313851	PDS5B_HUMAN	.	UPI000006D4A9	.	tolerated(1)	benign(0.005)	31/35	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAATGGAT	.	5	ESCA
KLF5	0	.	GRCh37	13	73650715	73650715	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*691A>G	.	.	ENST00000377687	4/4	9	4	5	11	11	0	KLF5,3_prime_UTR_variant,,ENST00000377687,;KLF5,downstream_gene_variant,,ENST00000539231,;KLF5,downstream_gene_variant,,ENST00000464404,;	G	ENSG00000102554	ENST00000377687	Transcript	3_prime_UTR_variant	2601	.	.	.	.	.	.	.	1	KLF5	HGNC	6349	protein_coding	YES	CCDS9448.1	ENSP00000366915	KLF5_HUMAN	Q5T6X2_HUMAN,B4DL96_HUMAN,A2TJX0_HUMAN	UPI0000000C89	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAAAATCATT	.	2	ESCA
BRF1	0	.	GRCh37	14	105676789	105676789	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99C>T	.	.	ENST00000546474	18/18	52	48	3	57	57	0	BRF1,3_prime_UTR_variant,,ENST00000446501,;BRF1,3_prime_UTR_variant,,ENST00000379937,;BRF1,3_prime_UTR_variant,,ENST00000547530,;BRF1,3_prime_UTR_variant,,ENST00000546474,;BRF1,3_prime_UTR_variant,,ENST00000327359,;BRF1,3_prime_UTR_variant,,ENST00000440513,;BRF1,3_prime_UTR_variant,,ENST00000392557,;BRF1,intron_variant,,ENST00000551787,;BRF1,intron_variant,,ENST00000379932,;BRF1,non_coding_transcript_exon_variant,,ENST00000547374,;BRF1,non_coding_transcript_exon_variant,,ENST00000546997,;	A	ENSG00000185024	ENST00000546474	Transcript	3_prime_UTR_variant	17093	.	.	.	.	.	.	.	-1	BRF1	HGNC	11551	protein_coding	YES	CCDS10001.1	ENSP00000448323	TF3B_HUMAN	F8VXJ4_HUMAN,F8VWY1_HUMAN,F8VWT8_HUMAN,F8VQ19_HUMAN,B3KWA2_HUMAN	UPI0000136C55	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCTCGGCGCT	.	2	ESCA
OR4K5	0	.	GRCh37	14	20389443	20389443	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.678G>T	p.Trp226Cys	p.W226C	ENST00000315915	1/1	60	46	14	78	78	0	OR4K5,missense_variant,p.Trp226Cys,ENST00000315915,;	T	ENSG00000176281	ENST00000315915	Transcript	missense_variant	703	678	226	W/C	tgG/tgT	.	.	.	1	OR4K5	HGNC	14745	protein_coding	YES	CCDS32024.1	ENSP00000319511	OR4K5_HUMAN	.	UPI0000061E9E	.	deleterious(0.05)	benign(0.005)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF46,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTGGCTCAA	.	5	ESCA
OR4K5	0	.	GRCh37	14	20389444	20389444	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679C>T	p.Leu227Phe	p.L227F	ENST00000315915	1/1	60	46	14	79	79	0	OR4K5,missense_variant,p.Leu227Phe,ENST00000315915,;	T	ENSG00000176281	ENST00000315915	Transcript	missense_variant	704	679	227	L/F	Ctc/Ttc	.	.	.	1	OR4K5	HGNC	14745	protein_coding	YES	CCDS32024.1	ENSP00000319511	OR4K5_HUMAN	.	UPI0000061E9E	.	tolerated(0.52)	benign(0.002)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF46,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGGCTCAAG	.	5	ESCA
FITM1	0	.	GRCh37	14	24601457	24601457	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304T>C	p.Phe102Leu	p.F102L	ENST00000267426	2/2	29	22	6	30	30	0	FITM1,missense_variant,p.Phe102Leu,ENST00000267426,;FITM1,5_prime_UTR_variant,,ENST00000559294,;PSME1,upstream_gene_variant,,ENST00000206451,;RP11-468E2.6,downstream_gene_variant,,ENST00000558325,;PSME1,upstream_gene_variant,,ENST00000559123,;PSME1,upstream_gene_variant,,ENST00000382708,;PSME1,upstream_gene_variant,,ENST00000561435,;PSME1,upstream_gene_variant,,ENST00000470718,;PSME1,upstream_gene_variant,,ENST00000561059,;PSME1,upstream_gene_variant,,ENST00000561142,;	C	ENSG00000139914	ENST00000267426	Transcript	missense_variant	593	304	102	F/L	Ttc/Ctc	COSM161077	.	.	1	FITM1	HGNC	33714	protein_coding	YES	CCDS9611.1	ENSP00000267426	FITM1_HUMAN	.	UPI000016146D	.	tolerated(0.81)	benign(0.027)	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR23129:SF3,hmmpanther:PTHR23129,Pfam_domain:PF10261	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACTTTCTTA	.	5	ESCA
TMEM260	0	.	GRCh37	14	57113980	57113980	+	Missense_Mutation	SNP	A	A	G	rs61739407	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1889A>G	p.Tyr630Cys	p.Y630C	ENST00000261556	16/16	18	11	7	26	26	0	TMEM260,missense_variant,p.Tyr630Cys,ENST00000261556,;TMEM260,missense_variant,p.Tyr164Cys,ENST00000536419,;TMEM260,intron_variant,,ENST00000555046,;RP11-1085N6.3,downstream_gene_variant,,ENST00000554597,;RP11-1085N6.2,intron_variant,,ENST00000553800,;RP11-1085N6.2,intron_variant,,ENST00000555924,;TMEM260,3_prime_UTR_variant,,ENST00000556422,;TMEM260,3_prime_UTR_variant,,ENST00000555497,;TMEM260,3_prime_UTR_variant,,ENST00000539559,;TMEM260,non_coding_transcript_exon_variant,,ENST00000556648,;	G	ENSG00000070269	ENST00000261556	Transcript	missense_variant	2011	1889	630	Y/C	tAt/tGt	rs61739407	.	.	1	TMEM260	HGNC	20185	protein_coding	YES	CCDS9727.2	ENSP00000261556	TM260_HUMAN	G3V4Y3_HUMAN,B3KN73_HUMAN	UPI00001FD5D2	.	tolerated(0.06)	benign(0.43)	16/16	.	hmmpanther:PTHR16214	G:0.0008	G:0.003	G:0	.	G:0	G:0	G:0	G:0.0016	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTATTTAC	byFrequency|byCluster|by1000G	5	ESCA
PCNXL4	0	.	GRCh37	14	60574805	60574805	+	Intron	SNP	C	C	T	rs557916204	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13-6613C>T	.	.	ENST00000317623	.	26	14	11	40	40	0	PCNXL4,missense_variant,p.Ala150Val,ENST00000406854,;PCNXL4,missense_variant,p.Ala150Val,ENST00000404681,;PCNXL4,missense_variant,p.Ala150Val,ENST00000391611,;PCNXL4,intron_variant,,ENST00000317623,;PCNXL4,intron_variant,,ENST00000406949,;PCNXL4,intron_variant,,ENST00000556907,;PCNXL4,intron_variant,,ENST00000555569,;	T	ENSG00000126773	ENST00000317623	Transcript	intron_variant	.	.	.	.	.	rs557916204	.	.	1	PCNXL4	HGNC	20349	protein_coding	YES	.	ENSP00000317396	.	B6ZDM2_HUMAN	UPI00014F7B83	.	.	.	.	1/9	.	T:0.0008	T:0	T:0	.	T:0	T:0	T:0.0041	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTAGCGTGTG	byFrequency|by1000G	5	ESCA
PLEKHH1	0	.	GRCh37	14	68038605	68038605	+	Missense_Mutation	SNP	G	G	A	rs573848643	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1571G>A	p.Arg524Gln	p.R524Q	ENST00000329153	10/29	31	22	9	20	20	0	PLEKHH1,missense_variant,p.Arg524Gln,ENST00000329153,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000557971,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000558386,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000561456,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000561135,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000558981,;	A	ENSG00000054690	ENST00000329153	Transcript	missense_variant	1703	1571	524	R/Q	cGg/cAg	rs573848643	.	.	1	PLEKHH1	HGNC	17733	protein_coding	YES	CCDS45128.1	ENSP00000330278	PKHH1_HUMAN	B3KWD2_HUMAN	UPI00001C1F64	.	deleterious(0.02)	probably_damaging(0.963)	10/29	.	hmmpanther:PTHR22903:SF4,hmmpanther:PTHR22903,Superfamily_domains:SSF50729	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCCGGGCCA	byFrequency|byCluster|by1000G	5	ESCA
NRXN3	0	.	GRCh37	14	79111726	79111726	+	5'UTR	SNP	G	G	A	rs201052888	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-99G>A	.	.	ENST00000554719	2/17	33	26	7	43	43	0	NRXN3,missense_variant,p.Ala106Thr,ENST00000553363,;NRXN3,5_prime_UTR_variant,,ENST00000554719,;NRXN3,5_prime_UTR_variant,,ENST00000335750,;NRXN3,intron_variant,,ENST00000553631,;NRXN3,missense_variant,p.Ala339Thr,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556088,;	A	ENSG00000021645	ENST00000554719	Transcript	5_prime_UTR_variant	393	.	.	.	.	rs201052888	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	2/17	.	.	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAACGCCTGG	byFrequency|byCluster|by1000G	5	ESCA
CCDC88C	0	.	GRCh37	14	91804354	91804354	+	Missense_Mutation	SNP	T	T	C	rs572844946	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1045A>G	p.Met349Val	p.M349V	ENST00000389857	10/30	35	23	11	35	35	0	CCDC88C,missense_variant,p.Met349Val,ENST00000389857,;AL133153.1,downstream_gene_variant,,ENST00000581346,;CCDC88C,downstream_gene_variant,,ENST00000554051,;CCDC88C,downstream_gene_variant,,ENST00000553437,;CCDC88C,downstream_gene_variant,,ENST00000554872,;	C	ENSG00000015133	ENST00000389857	Transcript	missense_variant	1132	1045	349	M/V	Atg/Gtg	rs572844946	.	.	-1	CCDC88C	HGNC	19967	protein_coding	YES	CCDS45151.1	ENSP00000374507	DAPLE_HUMAN	B4DZB8_HUMAN	UPI00006C1440	.	tolerated(0.88)	possibly_damaging(0.728)	10/30	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF31,Pfam_domain:PF05622	C:0.0004	C:0.0015	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCATGCGGG	byFrequency|by1000G	5	ESCA
SYNE3	0	.	GRCh37	14	95932472	95932472	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.423G>T	p.Glu141Asp	p.E141D	ENST00000334258	3/17	51	35	16	54	54	0	SYNE3,missense_variant,p.Glu141Asp,ENST00000334258,;SYNE3,missense_variant,p.Glu141Asp,ENST00000557275,;SYNE3,missense_variant,p.Glu141Asp,ENST00000553340,;SYNE3,non_coding_transcript_exon_variant,,ENST00000555759,;	A	ENSG00000176438	ENST00000334258	Transcript	missense_variant	438	423	141	E/D	gaG/gaT	.	.	.	-1	SYNE3	HGNC	19861	protein_coding	YES	CCDS9935.1	ENSP00000334308	SYNE3_HUMAN	.	UPI0000246F54	.	deleterious(0)	probably_damaging(0.921)	3/17	.	Superfamily_domains:SSF46966,Gene3D:1.20.58.60,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGCTCGAT	.	5	ESCA
CHEK2P2	0	.	GRCh37	15	20490509	20490509	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.489G>A	.	.	ENST00000555186	4/6	276	230	45	404	404	0	CHEK2P2,non_coding_transcript_exon_variant,,ENST00000566448,;CHEK2P2,non_coding_transcript_exon_variant,,ENST00000555186,;CHEK2P2,non_coding_transcript_exon_variant,,ENST00000554701,;	A	ENSG00000259156	ENST00000555186	Transcript	non_coding_transcript_exon_variant	489	.	.	.	.	.	.	.	1	CHEK2P2	HGNC	43578	processed_transcript	YES	.	.	.	.	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTGGACCTT	.	4	ESCA
GOLGA6B	0	.	GRCh37	15	72958352	72958352	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1837C>T	p.Leu613Phe	p.L613F	ENST00000421285	17/18	82	68	14	158	158	0	GOLGA6B,missense_variant,p.Leu613Phe,ENST00000421285,;RN7SL853P,downstream_gene_variant,,ENST00000477951,;	T	ENSG00000215186	ENST00000421285	Transcript	missense_variant	1837	1837	613	L/F	Ctt/Ttt	.	.	.	1	GOLGA6B	HGNC	32205	protein_coding	YES	CCDS10245.2	ENSP00000408132	GOG6B_HUMAN	.	UPI0000D74C4D	.	tolerated(0.08)	possibly_damaging(0.716)	17/18	.	Low_complexity_(Seg):seg,Pfam_domain:PF15070,hmmpanther:PTHR10881	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TGCCCCTTGTG	.	2	ESCA
KIAA1199	0	.	GRCh37	15	81235410	81235410	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3824delA	p.Gln1275ArgfsTer14	p.Q1275Rfs*14	ENST00000394685	28/30	40	27	13	58	58	0	KIAA1199,frameshift_variant,p.Gln1275ArgfsTer14,ENST00000356249,;KIAA1199,frameshift_variant,p.Gln1275ArgfsTer14,ENST00000220244,;KIAA1199,frameshift_variant,p.Gln1275ArgfsTer14,ENST00000394685,;KIAA1199,downstream_gene_variant,,ENST00000560027,;RP11-351M8.2,intron_variant,,ENST00000560873,;KIAA1199,upstream_gene_variant,,ENST00000559966,;MESDC2,downstream_gene_variant,,ENST00000561312,;KIAA1199,downstream_gene_variant,,ENST00000495041,;	-	ENSG00000103888	ENST00000394685	Transcript	frameshift_variant	4243	3824	1275	Q/X	cAg/cg	.	.	.	1	KIAA1199	HGNC	29213	protein_coding	YES	CCDS10315.1	ENSP00000378177	K1199_HUMAN	.	UPI00001D7799	.	.	.	28/30	.	hmmpanther:PTHR15535,hmmpanther:PTHR15535:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATGGCAGCTTT	.	3	ESCA
ZNF592	0	.	GRCh37	15	85345259	85345259	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3439C>G	p.Gln1147Glu	p.Q1147E	ENST00000299927	8/8	46	14	31	83	83	0	ZNF592,missense_variant,p.Gln1147Glu,ENST00000299927,;ZNF592,missense_variant,p.Gln1147Glu,ENST00000560079,;ZNF592,3_prime_UTR_variant,,ENST00000559607,;	G	ENSG00000166716	ENST00000299927	Transcript	missense_variant	3461	3439	1147	Q/E	Cag/Gag	.	.	.	1	ZNF592	HGNC	28986	protein_coding	YES	CCDS32317.1	ENSP00000299927	ZN592_HUMAN	.	UPI000013E5FC	.	deleterious(0.01)	benign(0.243)	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCACCAGGTG	.	5	ESCA
IGF1R	0	.	GRCh37	15	99501298	99501298	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*627G>A	.	.	ENST00000268035	21/21	14	3	11	40	40	0	IGF1R,3_prime_UTR_variant,,ENST00000558762,;IGF1R,3_prime_UTR_variant,,ENST00000268035,;RP11-654A16.3,intron_variant,,ENST00000559468,;IGF1R,downstream_gene_variant,,ENST00000558751,;	A	ENSG00000140443	ENST00000268035	Transcript	3_prime_UTR_variant	5342	.	.	.	.	.	.	.	1	IGF1R	HGNC	5465	protein_coding	YES	CCDS10378.1	ENSP00000268035	IGF1R_HUMAN	H0YNR0_HUMAN,H0YMJ5_HUMAN	UPI000012D3EA	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	GCGCTGATTCC	.	4	ESCA
ABCA17P	0	.	GRCh37	16	2415790	2415790	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.646A>G	.	.	ENST00000469908	3/17	54	31	22	37	37	0	ABCA17P,non_coding_transcript_exon_variant,,ENST00000469908,;ABCA17P,downstream_gene_variant,,ENST00000466730,;ABCA17P,downstream_gene_variant,,ENST00000512848,;ABCA17P,downstream_gene_variant,,ENST00000482286,;ABCA17P,non_coding_transcript_exon_variant,,ENST00000494925,;	G	ENSG00000238098	ENST00000469908	Transcript	non_coding_transcript_exon_variant	646	.	.	.	.	.	.	.	1	ABCA17P	HGNC	32972	processed_transcript	YES	.	.	.	.	.	.	.	.	3/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCAATGGAT	.	5	ESCA
AXIN1	0	.	GRCh37	16	396856	396856	+	Missense_Mutation	SNP	G	G	C	rs574168909	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.170C>G	p.Ser57Trp	p.S57W	ENST00000262320	2/11	31	20	11	27	27	0	AXIN1,missense_variant,p.Ser57Trp,ENST00000262320,;AXIN1,missense_variant,p.Ser57Trp,ENST00000354866,;AXIN1,intron_variant,,ENST00000481769,;AXIN1,upstream_gene_variant,,ENST00000461023,;	C	ENSG00000103126	ENST00000262320	Transcript	missense_variant	542	170	57	S/W	tCg/tGg	rs574168909	.	.	-1	AXIN1	HGNC	903	protein_coding	YES	CCDS10405.1	ENSP00000262320	AXIN1_HUMAN	.	UPI000012669E	.	deleterious(0.04)	probably_damaging(0.998)	2/11	.	hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF11	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTCGAAGTC	by1000G	5	ESCA
SALL1	0	.	GRCh37	16	51173964	51173964	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2169G>T	p.Met723Ile	p.M723I	ENST00000251020	2/3	35	14	21	68	68	0	SALL1,missense_variant,p.Met723Ile,ENST00000251020,;SALL1,missense_variant,p.Met626Ile,ENST00000570206,;SALL1,missense_variant,p.Met626Ile,ENST00000440970,;SALL1,intron_variant,,ENST00000541611,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,;	A	ENSG00000103449	ENST00000251020	Transcript	missense_variant	2203	2169	723	M/I	atG/atT	.	.	.	-1	SALL1	HGNC	10524	protein_coding	YES	CCDS10747.1	ENSP00000251020	SALL1_HUMAN	H3BSM9_HUMAN	UPI000013CCD8	.	deleterious(0.01)	probably_damaging(0.999)	2/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L721L|c.2163G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTGCATTTT	.	5	ESCA
HSF4	0	.	GRCh37	16	67203680	67203680	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1471T>C	p.Ser491Pro	p.S491P	ENST00000264009	15/15	45	41	3	51	51	0	HSF4,missense_variant,p.Ser491Pro,ENST00000264009,;HSF4,missense_variant,p.Ser223Pro,ENST00000519601,;HSF4,missense_variant,p.Ser415Pro,ENST00000517685,;HSF4,missense_variant,p.Ser461Pro,ENST00000584272,;HSF4,missense_variant,p.Ser491Pro,ENST00000521374,;HSF4,missense_variant,p.Ser461Pro,ENST00000421453,;HSF4,synonymous_variant,p.%3D,ENST00000520304,;HSF4,3_prime_UTR_variant,,ENST00000521916,;NOL3,upstream_gene_variant,,ENST00000563439,;NOL3,upstream_gene_variant,,ENST00000432069,;NOL3,upstream_gene_variant,,ENST00000268605,;NOL3,upstream_gene_variant,,ENST00000563258,;HSF4,downstream_gene_variant,,ENST00000517729,;NOL3,upstream_gene_variant,,ENST00000566871,;HSF4,downstream_gene_variant,,ENST00000517750,;NOL3,upstream_gene_variant,,ENST00000564053,;NOL3,upstream_gene_variant,,ENST00000568146,;NOL3,upstream_gene_variant,,ENST00000565560,;NOL3,upstream_gene_variant,,ENST00000564992,;NOL3,upstream_gene_variant,,ENST00000568199,;RP11-5A19.5,downstream_gene_variant,,ENST00000523360,;NOL3,upstream_gene_variant,,ENST00000565645,;HSF4,downstream_gene_variant,,ENST00000517867,;HSF4,3_prime_UTR_variant,,ENST00000522295,;HSF4,3_prime_UTR_variant,,ENST00000520528,;HSF4,3_prime_UTR_variant,,ENST00000521314,;HSF4,3_prime_UTR_variant,,ENST00000521624,;HSF4,3_prime_UTR_variant,,ENST00000434833,;HSF4,3_prime_UTR_variant,,ENST00000523562,;HSF4,downstream_gene_variant,,ENST00000517680,;HSF4,downstream_gene_variant,,ENST00000522027,;NOL3,upstream_gene_variant,,ENST00000568086,;RP11-5A19.5,downstream_gene_variant,,ENST00000518227,;HSF4,downstream_gene_variant,,ENST00000519105,;HSF4,downstream_gene_variant,,ENST00000522870,;HSF4,downstream_gene_variant,,ENST00000522459,;HSF4,downstream_gene_variant,,ENST00000520247,;RP11-5A19.5,downstream_gene_variant,,ENST00000518753,;RP11-5A19.5,downstream_gene_variant,,ENST00000580114,;NOL3,upstream_gene_variant,,ENST00000568503,;HSF4,downstream_gene_variant,,ENST00000519224,;HSF4,downstream_gene_variant,,ENST00000520833,;HSF4,downstream_gene_variant,,ENST00000523077,;HSF4,downstream_gene_variant,,ENST00000522023,;	C	ENSG00000102878	ENST00000264009	Transcript	missense_variant	2436	1471	491	S/P	Tcc/Ccc	COSM3983871	.	.	1	HSF4	HGNC	5227	protein_coding	YES	CCDS42175.1	ENSP00000264009	HSF4_HUMAN	.	UPI0000366B51	.	deleterious_low_confidence(0.05)	possibly_damaging(0.724)	15/15	.	hmmpanther:PTHR10015:SF43,hmmpanther:PTHR10015	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCCTCCCCC	.	2	ESCA
EDC4	0	.	GRCh37	16	67911274	67911274	+	Silent	SNP	C	C	T	rs368076076	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606C>T	p.%3D	p.F202F	ENST00000358933	5/29	67	28	39	98	98	0	EDC4,synonymous_variant,p.%3D,ENST00000358933,;NUTF2,downstream_gene_variant,,ENST00000219169,;AC040162.1,upstream_gene_variant,,ENST00000408599,;EDC4,non_coding_transcript_exon_variant,,ENST00000574770,;EDC4,non_coding_transcript_exon_variant,,ENST00000536072,;EDC4,non_coding_transcript_exon_variant,,ENST00000572221,;EDC4,upstream_gene_variant,,ENST00000577028,;EDC4,upstream_gene_variant,,ENST00000576972,;NUTF2,downstream_gene_variant,,ENST00000587481,;EDC4,upstream_gene_variant,,ENST00000573992,;EDC4,upstream_gene_variant,,ENST00000572724,;EDC4,upstream_gene_variant,,ENST00000572031,;EDC4,upstream_gene_variant,,ENST00000575507,;EDC4,upstream_gene_variant,,ENST00000575514,;	T	ENSG00000038358	ENST00000358933	Transcript	synonymous_variant	845	606	202	F	ttC/ttT	rs368076076,COSM558626	.	.	1	EDC4	HGNC	17157	protein_coding	YES	CCDS10849.1	ENSP00000351811	EDC4_HUMAN	.	UPI0000141377	.	.	.	5/29	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR15598	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTCGTGTG	byFrequency|byCluster	5	ESCA
GAN	0	.	GRCh37	16	81411245	81411245	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*44A>G	.	.	ENST00000568107	11/11	48	15	33	63	63	0	GAN,3_prime_UTR_variant,,ENST00000568107,;	G	ENSG00000261609	ENST00000568107	Transcript	3_prime_UTR_variant	2000	.	.	.	.	.	.	.	1	GAN	HGNC	4137	protein_coding	YES	CCDS10935.1	ENSP00000476795	GAN_HUMAN	.	UPI000000DAB6	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCATAACA	.	5	ESCA
ZC3H18	0	.	GRCh37	16	88694049	88694049	+	Missense_Mutation	SNP	G	G	A	rs370561351	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2128G>A	p.Val710Ile	p.V710I	ENST00000301011	14/18	46	23	22	61	61	0	ZC3H18,missense_variant,p.Val734Ile,ENST00000452588,;ZC3H18,missense_variant,p.Val710Ile,ENST00000301011,;ZC3H18,intron_variant,,ENST00000564341,;ZC3H18,downstream_gene_variant,,ENST00000567085,;ZC3H18,upstream_gene_variant,,ENST00000565583,;ZC3H18,non_coding_transcript_exon_variant,,ENST00000566496,;ZC3H18,downstream_gene_variant,,ENST00000563382,;ZC3H18,downstream_gene_variant,,ENST00000564161,;ZC3H18,upstream_gene_variant,,ENST00000566660,;ZC3H18,upstream_gene_variant,,ENST00000566317,;	A	ENSG00000158545	ENST00000301011	Transcript	missense_variant	2328	2128	710	V/I	Gtc/Atc	rs370561351	.	.	1	ZC3H18	HGNC	25091	protein_coding	YES	CCDS10967.1	ENSP00000301011	ZCH18_HUMAN	H3BRH3_HUMAN,B3KRL4_HUMAN	UPI00001FF676	.	tolerated_low_confidence(0.09)	unknown(0)	14/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12506,hmmpanther:PTHR12506:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGTCTCC	.	5	ESCA
AOC3	0	.	GRCh37	17	41004906	41004906	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1546C>G	p.Leu516Val	p.L516V	ENST00000308423	1/4	16	5	11	39	39	0	AOC3,missense_variant,p.Leu516Val,ENST00000308423,;AOC3,upstream_gene_variant,,ENST00000591562,;AOC3,upstream_gene_variant,,ENST00000588033,;AOC2,downstream_gene_variant,,ENST00000253799,;AOC3,upstream_gene_variant,,ENST00000592999,;AOC2,downstream_gene_variant,,ENST00000452774,;AOC3,missense_variant,p.Leu47Val,ENST00000587330,;	G	ENSG00000131471	ENST00000308423	Transcript	missense_variant	1706	1546	516	L/V	Ctg/Gtg	.	.	.	1	AOC3	HGNC	550	protein_coding	YES	CCDS11444.1	ENSP00000312326	AOC3_HUMAN	Q9UEU7_HUMAN,K7ESB3_HUMAN,K7EQZ5_HUMAN,K7EL47_HUMAN	UPI00000009FC	.	deleterious(0)	probably_damaging(0.963)	1/4	.	Superfamily_domains:SSF49998,Pfam_domain:PF01179,Gene3D:2.70.98.20,hmmpanther:PTHR10638,hmmpanther:PTHR10638:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCCTGGGC	.	5	ESCA
CA10	0	.	GRCh37	17	49825063	49825063	+	Missense_Mutation	SNP	C	C	T	rs766628041	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.395G>A	p.Arg132Gln	p.R132Q	ENST00000451037	4/9	55	48	7	88	88	0	CA10,missense_variant,p.Arg29Gln,ENST00000575097,;CA10,missense_variant,p.Arg132Gln,ENST00000285273,;CA10,missense_variant,p.Arg57Gln,ENST00000570565,;CA10,missense_variant,p.Arg138Gln,ENST00000340813,;CA10,missense_variant,p.Arg132Gln,ENST00000575181,;CA10,missense_variant,p.Arg132Gln,ENST00000451037,;CA10,missense_variant,p.Arg132Gln,ENST00000442502,;CA10,non_coding_transcript_exon_variant,,ENST00000571918,;CA10,3_prime_UTR_variant,,ENST00000571371,;	T	ENSG00000154975	ENST00000451037	Transcript	missense_variant	1336	395	132	R/Q	cGa/cAa	rs766628041	.	.	-1	CA10	HGNC	1369	protein_coding	YES	CCDS32684.1	ENSP00000405388	CAH10_HUMAN	I3L375_HUMAN,B4DGL6_HUMAN	UPI000000167C	.	tolerated(0.08)	probably_damaging(0.998)	4/9	.	PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF91,Gene3D:3.10.200.10,Pfam_domain:PF00194,SMART_domains:SM01057,Superfamily_domains:SSF51069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAGTCGGATC	.	4	ESCA
LRRC37A3	0	.	GRCh37	17	62892916	62892916	+	Missense_Mutation	SNP	G	G	T	rs763629368	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460C>A	p.Pro154Thr	p.P154T	ENST00000584306	3/14	66	40	25	76	76	0	LRRC37A3,missense_variant,p.Pro154Thr,ENST00000319651,;LRRC37A3,missense_variant,p.Pro154Thr,ENST00000584306,;LRRC37A3,intron_variant,,ENST00000581368,;LRRC37A3,intron_variant,,ENST00000400877,;LRRC37A3,intron_variant,,ENST00000339474,;LRRC37A3,upstream_gene_variant,,ENST00000584788,;LRRC37A3,upstream_gene_variant,,ENST00000580464,;RP11-927P21.1,intron_variant,,ENST00000584131,;RP11-927P21.1,intron_variant,,ENST00000584959,;RP11-927P21.2,upstream_gene_variant,,ENST00000581622,;RP11-927P21.1,downstream_gene_variant,,ENST00000577938,;LRRC37A3,downstream_gene_variant,,ENST00000577487,;LRRC37A3,downstream_gene_variant,,ENST00000580439,;RP11-927P21.9,downstream_gene_variant,,ENST00000607347,;	T	ENSG00000176809	ENST00000584306	Transcript	missense_variant	991	460	154	P/T	Cca/Aca	rs763629368	.	.	-1	LRRC37A3	HGNC	32427	protein_coding	YES	CCDS32708.1	ENSP00000464535	L37A3_HUMAN	F8W7X0_HUMAN,B4DSF2_HUMAN	UPI00005B2F0A	.	tolerated(0.15)	benign(0.004)	3/14	.	hmmpanther:PTHR23045	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGGATCTT	byFrequency	5	ESCA
C17orf58	0	.	GRCh37	17	65989212	65989213	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50dupT	p.Met17IlefsTer11	p.M17Ifs*11	ENST00000449250	2/3	111	62	49	44	44	0	C17orf58,frameshift_variant,p.Met17IlefsTer11,ENST00000449250,;C17orf58,frameshift_variant,p.Met17IlefsTer11,ENST00000334461,;C17orf58,frameshift_variant,p.Met17IlefsTer11,ENST00000536693,;RP11-855A2.5,downstream_gene_variant,,ENST00000580729,;	A	ENSG00000186665	ENST00000449250	Transcript	frameshift_variant	240-241	50-51	17	M/IX	atg/atTg	.	.	.	-1	C17orf58	HGNC	27568	protein_coding	YES	CCDS45765.1	ENSP00000402020	CQ058_HUMAN	.	UPI0000160F31	.	.	.	2/3	.	Gene3D:2.40.50.120,Superfamily_domains:SSF50242	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTAACATGTG	.	3	ESCA
ABCA9	0	.	GRCh37	17	67016582	67016582	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2547A>G	p.Ile849Met	p.I849M	ENST00000340001	19/39	15	7	8	27	27	0	ABCA9,missense_variant,p.Ile849Met,ENST00000370732,;ABCA9,missense_variant,p.Ile849Met,ENST00000453985,;ABCA9,missense_variant,p.Ile849Met,ENST00000340001,;ABCA9-AS1,downstream_gene_variant,,ENST00000458677,;ABCA9,upstream_gene_variant,,ENST00000492580,;	C	ENSG00000154258	ENST00000340001	Transcript	missense_variant	2759	2547	849	I/M	atA/atG	.	.	.	-1	ABCA9	HGNC	39	protein_coding	YES	CCDS11681.1	ENSP00000342216	ABCA9_HUMAN	K7EJJ0_HUMAN	UPI00000747B1	.	tolerated(0.46)	benign(0.069)	19/39	.	hmmpanther:PTHR19229:SF11,hmmpanther:PTHR19229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGCTATTGC	.	5	ESCA
TP53	0	.	GRCh37	17	7578457	7578457	+	Missense_Mutation	SNP	C	C	A	rs587782144	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	5/11	333	145	188	389	389	0	TP53,missense_variant,p.Arg158Leu,ENST00000508793,;TP53,missense_variant,p.Arg158Leu,ENST00000413465,;TP53,missense_variant,p.Arg158Leu,ENST00000420246,;TP53,missense_variant,p.Arg158Leu,ENST00000269305,;TP53,missense_variant,p.Arg26Leu,ENST00000509690,;TP53,missense_variant,p.Arg158Leu,ENST00000359597,;TP53,missense_variant,p.Arg65Leu,ENST00000514944,;TP53,missense_variant,p.Arg158Leu,ENST00000445888,;TP53,missense_variant,p.Arg158Leu,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	663	473	158	R/L	cGc/cTc	rs587782144,CM994513,CM102353,TP53_g.12461G>A,TP53_g.12461G>T,TP53_g.12461G>C,COSM10690,COSM43615,COSM10714,COSM99678,COSM220779,COSM1649375,COSM220778,COSM1649377,COSM99675,COSM220780,COSM99676,COSM1649379,COSM3378357,COSM3958835,COSM1640853,COSM1649374,COSM1649376,COSM220781,COSM1649378,COSM99677	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.986)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R158L|c.473G>T|14,SITE|p.R158L|c.473G>T|63,SITE|p.R158L|c.473G>T|5,SITE|p.R158L|c.473G>T|14,SITE|p.R26L|c.77G>T|19,SITE|p.R65L|c.194G>T|14,CODON|p.0?|c.1_1182del1182|6,CODON|p.R158fs*11|c.472_475delCGCG|3,CODON|p.R158_A159insX|c.473_474insNNN|4,CODON|p.R158R|c.474C>T|6,CODON|p.R158H|c.473G>A|24,CODON|p.R158H|c.473G>A|24,CODON|p.R158H|c.473G>A|78,CODON|p.R158H|c.473G>A|7,CODON|p.R158H|c.473G>A|11,CODON|p.R158P|c.473G>C|10,CODON|p.R65H|c.194G>A|24,CODON|p.R26H|c.77G>A|25,CODON|p.R158C|c.471_472CC>TT|6,CODON|p.R158fs*12|c.472delC|6,BUFFER|p.I162V|c.484A>G|5,BUFFER|p.I162F|c.484A>T|11,BUFFER|p.A161A|c.483C>T|5,BUFFER|p.A161fs*9|c.481delG|3,BUFFER|p.A161V|c.482C>T|9,BUFFER|p.A161D|c.482C>A|9,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A29T|c.85G>A|10,BUFFER|p.A161T|c.481G>A|52,BUFFER|p.A68T|c.202G>A|10,BUFFER|p.A161S|c.481G>T|3,BUFFER|p.M160I|c.480G>T|4,BUFFER|p.M160I|c.480G>A|3,BUFFER|p.M160K|c.479T>A|4,BUFFER|p.M160L|c.478A>C|3,BUFFER|p.M160V|c.478A>G|5,BUFFER|p.A159A|c.477C>T|8,BUFFER|p.A159fs*11|c.475delG|4,BUFFER|p.A159V|c.476C>T|9,BUFFER|p.A66V|c.197C>T|9,BUFFER|p.A27V|c.80C>T|9,BUFFER|p.A159V|c.476C>T|39,BUFFER|p.A159V|c.476C>T|9,BUFFER|p.A159D|c.476C>A|6,BUFFER|p.A159S|c.475G>T|5,BUFFER|p.A159P|c.475G>C|3,BUFFER|p.A159P|c.475G>C|5,BUFFER|p.A159T|c.475G>A|7,BUFFER|p.A66P|c.196G>C|5,BUFFER|p.A159P|c.475G>C|20,BUFFER|p.A159P|c.475G>C|5,BUFFER|p.A27P|c.79G>C|5,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R158C|c.472C>T|17,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R26C|c.76C>T|7,BUFFER|p.R65C|c.193C>T|7,BUFFER|p.R158G|c.472C>G|12,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R65G|c.193C>G|3,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R26G|c.76C>G|4,BUFFER|p.V157V|c.471C>A|3,BUFFER|p.V157G|c.470T>G|9,BUFFER|p.V157D|c.470T>A|8,BUFFER|p.V157F|c.469G>T|7,BUFFER|p.V157F|c.469G>T|8,BUFFER|p.V157L|c.469G>C|6,BUFFER|p.V157F|c.469G>T|22,BUFFER|p.V157F|c.469G>T|162,BUFFER|p.V157I|c.469G>A|10,BUFFER|p.V157F|c.469G>T|22,BUFFER|p.V25F|c.73G>T|25,BUFFER|p.V64F|c.190G>T|22,BUFFER|p.V157fs*13|c.468delC|3,BUFFER|p.R156P|c.467G>C|26,BUFFER|p.R63P|c.188G>C|4,BUFFER|p.R156H|c.467G>A|11,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R24P|c.71G>C|4,BUFFER|p.R156L|c.467G>T|3,BUFFER|p.P152fs*14|c.454_466del13|5,BUFFER|p.R156fs*14|c.466delC|9,BUFFER|p.R156S|c.466C>A|3,BUFFER|p.R156G|c.466C>G|3,BUFFER|p.R156C|c.466C>T|4,BUFFER|p.T155T|c.465C>T|4,BUFFER|p.T155N|c.464C>A|4,BUFFER|p.T155N|c.464C>A|5,BUFFER|p.T62N|c.185C>A|6,BUFFER|p.T155N|c.464C>A|25,BUFFER|p.T155I|c.464C>T|15,BUFFER|p.T23N|c.68C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.T62P|c.184A>C|3,BUFFER|p.T155P|c.463A>C|16,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T23P|c.67A>C|4,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T155A|c.463A>G|8,BUFFER|p.G154I|c.460_461GG>AT|3,BUFFER|p.G154G|c.462C>T|9	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCGCGGACG	byCluster	5	ESCA
RAVER1	0	.	GRCh37	19	10439506	10439506	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619A>C	p.Lys207Gln	p.K207Q	ENST00000293677	3/13	128	74	54	164	164	0	RAVER1,missense_variant,p.Lys207Gln,ENST00000293677,;ICAM3,downstream_gene_variant,,ENST00000592945,;ICAM3,downstream_gene_variant,,ENST00000589261,;ICAM3,downstream_gene_variant,,ENST00000160262,;RAVER1,3_prime_UTR_variant,,ENST00000591969,;RAVER1,non_coding_transcript_exon_variant,,ENST00000592208,;ICAM3,downstream_gene_variant,,ENST00000587992,;ICAM3,downstream_gene_variant,,ENST00000589900,;	G	ENSG00000161847	ENST00000293677	Transcript	missense_variant	701	619	207	K/Q	Aag/Cag	.	.	.	-1	RAVER1	HGNC	30296	protein_coding	YES	CCDS45960.1	ENSP00000293677	.	K7EQG2_HUMAN,E9PAU2_HUMAN	UPI0000E042A4	.	deleterious(0.01)	probably_damaging(0.997)	3/13	.	PROSITE_profiles:PS50102,hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF46,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGACTTGGCAC	.	5	ESCA
PRDX2	0	.	GRCh37	19	12910723	12910723	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.461A>T	p.Glu154Val	p.E154V	ENST00000301522	5/6	40	22	17	66	66	0	PRDX2,missense_variant,p.Glu154Val,ENST00000301522,;PRDX2,intron_variant,,ENST00000334482,;PRDX2,downstream_gene_variant,,ENST00000435703,;CTD-2659N19.10,intron_variant,,ENST00000585496,;HOOK2,intron_variant,,ENST00000589765,;PRDX2,non_coding_transcript_exon_variant,,ENST00000498785,;PRDX2,non_coding_transcript_exon_variant,,ENST00000478908,;PRDX2,non_coding_transcript_exon_variant,,ENST00000466174,;PRDX2,downstream_gene_variant,,ENST00000477555,;	A	ENSG00000167815	ENST00000301522	Transcript	missense_variant	590	461	154	E/V	gAg/gTg	.	.	.	-1	PRDX2	HGNC	9353	protein_coding	YES	CCDS12281.1	ENSP00000301522	PRDX2_HUMAN	.	UPI0000001C80	.	deleterious(0)	possibly_damaging(0.865)	5/6	.	PROSITE_profiles:PS51352,hmmpanther:PTHR10681:SF43,hmmpanther:PTHR10681,Gene3D:3.40.30.10,PIRSF_domain:PIRSF000239,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCCTCATCC	.	5	ESCA
SCAMP4	0	.	GRCh37	19	1925459	1925459	+	3'UTR	SNP	G	G	A	rs200424152	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1176G>A	.	.	ENST00000316097	7/7	41	28	13	43	43	0	SCAMP4,3_prime_UTR_variant,,ENST00000316097,;SCAMP4,3_prime_UTR_variant,,ENST00000409472,;SCAMP4,downstream_gene_variant,,ENST00000585335,;SCAMP4,downstream_gene_variant,,ENST00000489554,;SCAMP4,downstream_gene_variant,,ENST00000414057,;SCAMP4,non_coding_transcript_exon_variant,,ENST00000472442,;AC012615.1,non_coding_transcript_exon_variant,,ENST00000367461,;	A	ENSG00000227500	ENST00000316097	Transcript	3_prime_UTR_variant	2133	.	.	.	.	rs200424152	.	.	1	SCAMP4	HGNC	30385	protein_coding	YES	CCDS45903.1	ENSP00000316007	SCAM4_HUMAN	K7EJJ4_HUMAN,C9JWM2_HUMAN	UPI000006F786	.	.	.	7/7	.	.	A:0.0008	A:0.0023	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGGCCAC	byFrequency|byCluster|by1000G	5	ESCA
CLIP3	0	.	GRCh37	19	36507004	36507004	+	3'UTR	SNP	C	C	G	rs372057691	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*56G>C	.	.	ENST00000360535	14/14	46	22	24	76	76	0	CLIP3,3_prime_UTR_variant,,ENST00000593074,;CLIP3,3_prime_UTR_variant,,ENST00000360535,;ALKBH6,upstream_gene_variant,,ENST00000378875,;ALKBH6,upstream_gene_variant,,ENST00000252984,;ALKBH6,upstream_gene_variant,,ENST00000485128,;ALKBH6,upstream_gene_variant,,ENST00000486389,;AC002116.7,intron_variant,,ENST00000586962,;ALKBH6,upstream_gene_variant,,ENST00000495116,;ALKBH6,upstream_gene_variant,,ENST00000392183,;ALKBH6,upstream_gene_variant,,ENST00000590666,;ALKBH6,upstream_gene_variant,,ENST00000466196,;ALKBH6,upstream_gene_variant,,ENST00000490986,;ALKBH6,upstream_gene_variant,,ENST00000475223,;ALKBH6,upstream_gene_variant,,ENST00000461668,;ALKBH6,upstream_gene_variant,,ENST00000490483,;ALKBH6,upstream_gene_variant,,ENST00000468004,;ALKBH6,upstream_gene_variant,,ENST00000470859,;ALKBH6,upstream_gene_variant,,ENST00000471323,;ALKBH6,upstream_gene_variant,,ENST00000462793,;ALKBH6,upstream_gene_variant,,ENST00000497999,;ALKBH6,upstream_gene_variant,,ENST00000592353,;AC002116.8,upstream_gene_variant,,ENST00000473572,;ALKBH6,upstream_gene_variant,,ENST00000481257,;	G	ENSG00000105270	ENST00000360535	Transcript	3_prime_UTR_variant	1928	.	.	.	.	rs372057691	.	.	-1	CLIP3	HGNC	24314	protein_coding	YES	CCDS12486.1	ENSP00000353732	CLIP3_HUMAN	K7ESF3_HUMAN,B3KR09_HUMAN,B3KP03_HUMAN	UPI0000044718	.	.	.	14/14	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0007	T:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCGGGTG	byCluster|by1000G	5	ESCA
TFPT	0	.	GRCh37	19	54617971	54617971	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.133G>A	p.Val45Met	p.V45M	ENST00000391759	2/6	24	11	13	32	32	0	TFPT,missense_variant,p.Val45Met,ENST00000391757,;TFPT,missense_variant,p.Val36Met,ENST00000391758,;TFPT,missense_variant,p.Val45Met,ENST00000391759,;PRPF31,upstream_gene_variant,,ENST00000391755,;PRPF31,upstream_gene_variant,,ENST00000445124,;PRPF31,upstream_gene_variant,,ENST00000419967,;PRPF31,upstream_gene_variant,,ENST00000321030,;PRPF31,upstream_gene_variant,,ENST00000447810,;PRPF31,upstream_gene_variant,,ENST00000445811,;AC012314.8,downstream_gene_variant,,ENST00000452097,;PRPF31,upstream_gene_variant,,ENST00000498612,;TFPT,missense_variant,p.Val45Met,ENST00000420715,;PRPF31,upstream_gene_variant,,ENST00000467851,;PRPF31,upstream_gene_variant,,ENST00000466404,;	T	ENSG00000105619	ENST00000391759	Transcript	missense_variant	539	133	45	V/M	Gtg/Atg	.	.	.	-1	TFPT	HGNC	13630	protein_coding	YES	CCDS12878.1	ENSP00000375639	TFPT_HUMAN	G5E9B5_HUMAN	UPI000006CFD4	.	deleterious(0)	probably_damaging(0.977)	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCACTTCCG	.	5	ESCA
ZNF211	0	.	GRCh37	19	58153099	58153099	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1440C>A	p.His480Gln	p.H480Q	ENST00000299871	5/5	25	8	17	50	50	0	ZNF211,missense_variant,p.His406Gln,ENST00000254182,;ZNF211,missense_variant,p.His419Gln,ENST00000420680,;ZNF211,missense_variant,p.His428Gln,ENST00000240731,;ZNF211,missense_variant,p.His427Gln,ENST00000544273,;ZNF211,missense_variant,p.His406Gln,ENST00000541801,;ZNF211,missense_variant,p.His480Gln,ENST00000299871,;ZNF211,missense_variant,p.His415Gln,ENST00000347302,;ZNF211,missense_variant,p.His354Gln,ENST00000391703,;ZNF211,missense_variant,p.His419Gln,ENST00000407202,;ZNF211,3_prime_UTR_variant,,ENST00000540556,;ZNF211,3_prime_UTR_variant,,ENST00000535785,;	A	ENSG00000121417	ENST00000299871	Transcript	missense_variant	1571	1440	480	H/Q	caC/caA	.	.	.	1	ZNF211	HGNC	13003	protein_coding	YES	CCDS58686.1	ENSP00000299871	ZN211_HUMAN	.	UPI0000D4CB1A	.	deleterious(0)	benign(0.213)	5/5	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF201,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCACCGGAG	.	5	ESCA
PNPLA6	0	.	GRCh37	19	7622121	7622121	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3378C>T	p.%3D	p.P1126P	ENST00000414982	29/34	75	40	34	84	84	0	PNPLA6,synonymous_variant,p.%3D,ENST00000450331,;PNPLA6,synonymous_variant,p.%3D,ENST00000600737,;PNPLA6,synonymous_variant,p.%3D,ENST00000545201,;PNPLA6,synonymous_variant,p.%3D,ENST00000221249,;PNPLA6,synonymous_variant,p.%3D,ENST00000414982,;PNPLA6,upstream_gene_variant,,ENST00000599947,;PNPLA6,non_coding_transcript_exon_variant,,ENST00000595352,;PNPLA6,downstream_gene_variant,,ENST00000599951,;PNPLA6,upstream_gene_variant,,ENST00000597202,;	T	ENSG00000032444	ENST00000414982	Transcript	synonymous_variant	3573	3378	1126	P	ccC/ccT	.	.	.	1	PNPLA6	HGNC	16268	protein_coding	YES	CCDS54206.1	ENSP00000407509	PLPL6_HUMAN	.	UPI0001AE63FF	.	.	.	29/34	.	Superfamily_domains:SSF52151,Gene3D:3.40.1090.10,Pfam_domain:PF01734,hmmpanther:PTHR14226:SF26,hmmpanther:PTHR14226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCCCAAGGA	.	5	ESCA
CASZ1	0	.	GRCh37	1	10715742	10715742	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1629C>T	p.%3D	p.H543H	ENST00000377022	9/21	40	26	13	55	55	0	CASZ1,synonymous_variant,p.%3D,ENST00000344008,;CASZ1,synonymous_variant,p.%3D,ENST00000377022,;RP4-734G22.3,downstream_gene_variant,,ENST00000606802,;CASZ1,non_coding_transcript_exon_variant,,ENST00000496432,;CASZ1,downstream_gene_variant,,ENST00000492173,;CASZ1,upstream_gene_variant,,ENST00000490176,;	A	ENSG00000130940	ENST00000377022	Transcript	synonymous_variant	1947	1629	543	H	caC/caT	.	.	.	-1	CASZ1	HGNC	26002	protein_coding	YES	CCDS41246.1	ENSP00000366221	CASZ1_HUMAN	.	UPI0000EBB7D6	.	.	.	9/21	.	hmmpanther:PTHR12451	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGGTGGCA	.	5	ESCA
KIAA2013	0	.	GRCh37	1	11980144	11980144	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*228A>G	.	.	ENST00000376572	3/3	11	7	4	15	15	0	KIAA2013,3_prime_UTR_variant,,ENST00000376572,;KIAA2013,downstream_gene_variant,,ENST00000376576,;	C	ENSG00000116685	ENST00000376572	Transcript	3_prime_UTR_variant	2319	.	.	.	.	.	.	.	-1	KIAA2013	HGNC	28513	protein_coding	YES	CCDS141.1	ENSP00000365756	K2013_HUMAN	.	UPI00000741FB	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTTATTGAGT	.	3	ESCA
S100A11	0	.	GRCh37	1	152005018	152005018	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120A>G	.	.	ENST00000271638	3/3	36	31	5	31	31	0	S100A11,3_prime_UTR_variant,,ENST00000271638,;NBPF18P,intron_variant,,ENST00000432386,;S100A11,non_coding_transcript_exon_variant,,ENST00000478109,;	C	ENSG00000163191	ENST00000271638	Transcript	3_prime_UTR_variant	558	.	.	.	.	.	.	.	-1	S100A11	HGNC	10488	protein_coding	YES	CCDS1009.1	ENSP00000271638	S10AB_HUMAN	.	UPI0000034180	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTATTGGCA	.	5	ESCA
CHTOP	0	.	GRCh37	1	153610909	153610909	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204A>G	p.%3D	p.A68A	ENST00000368694	3/6	30	25	5	32	32	0	CHTOP,synonymous_variant,p.%3D,ENST00000368686,;CHTOP,synonymous_variant,p.%3D,ENST00000368690,;CHTOP,synonymous_variant,p.%3D,ENST00000368687,;CHTOP,synonymous_variant,p.%3D,ENST00000403433,;CHTOP,synonymous_variant,p.%3D,ENST00000368694,;S100A13,upstream_gene_variant,,ENST00000368699,;RP1-178F15.4,upstream_gene_variant,,ENST00000469931,;CHTOP,non_coding_transcript_exon_variant,,ENST00000495554,;RP1-178F15.5,upstream_gene_variant,,ENST00000484413,;RP1-178F15.5,upstream_gene_variant,,ENST00000472233,;RP1-178F15.5,upstream_gene_variant,,ENST00000497086,;	G	ENSG00000160679	ENST00000368694	Transcript	synonymous_variant	516	204	68	A	gcA/gcG	.	.	.	1	CHTOP	HGNC	24511	protein_coding	YES	CCDS1048.1	ENSP00000357683	CHTOP_HUMAN	.	UPI00000467F6	.	.	.	3/6	.	hmmpanther:PTHR19965,hmmpanther:PTHR19965:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCATTAAA	.	2	ESCA
CEP350	0	.	GRCh37	1	180082049	180082049	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1753A>T	.	.	ENST00000367607	38/38	93	77	16	115	114	0	CEP350,3_prime_UTR_variant,,ENST00000429851,;CEP350,3_prime_UTR_variant,,ENST00000417046,;CEP350,3_prime_UTR_variant,,ENST00000367607,;RP11-502H18.2,downstream_gene_variant,,ENST00000566904,;CEP350,downstream_gene_variant,,ENST00000490141,;CEP350,downstream_gene_variant,,ENST00000496440,;	T	ENSG00000135837	ENST00000367607	Transcript	3_prime_UTR_variant	11525	.	.	.	.	.	.	.	1	CEP350	HGNC	24238	protein_coding	YES	CCDS1336.1	ENSP00000356579	CE350_HUMAN	Q5T2X4_HUMAN	UPI000013CFC5	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGTATGATA	.	5	ESCA
UBXN10	0	.	GRCh37	1	20519588	20519588	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1691A>G	.	.	ENST00000375099	2/2	21	12	9	27	27	0	UBXN10,3_prime_UTR_variant,,ENST00000375099,;	G	ENSG00000162543	ENST00000375099	Transcript	3_prime_UTR_variant	2618	.	.	.	.	.	.	.	1	UBXN10	HGNC	26354	protein_coding	YES	CCDS205.1	ENSP00000364240	UBX10_HUMAN	.	UPI000000DBEB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AGCAGACAGAA	.	4	ESCA
CR1L	0	.	GRCh37	1	207872577	207872577	+	Nonsense_Mutation	SNP	G	G	T	rs757271882	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1186G>T	p.Gly396Ter	p.G396*	ENST00000508064	8/12	152	87	65	215	215	0	CR1L,stop_gained,p.Gly396Ter,ENST00000508064,;CR1L,intron_variant,,ENST00000530905,;CR1L,stop_gained,p.Gly340Ter,ENST00000294997,;	T	ENSG00000197721	ENST00000508064	Transcript	stop_gained	1246	1186	396	G/*	Gga/Tga	rs757271882	.	.	1	CR1L	HGNC	2335	protein_coding	YES	CCDS44310.1	ENSP00000421736	CR1L_HUMAN	.	UPI0000DD792A	.	.	.	8/12	.	Superfamily_domains:SSF57535,SMART_domains:SM00032,Pfam_domain:PF00084,Gene3D:2.10.70.10,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF322,PROSITE_profiles:PS50923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTGGAATG	byFrequency	5	ESCA
MARC2	0	.	GRCh37	1	220936256	220936256	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614C>T	p.Ala205Val	p.A205V	ENST00000366913	4/8	54	27	26	75	75	0	MARC2,missense_variant,p.Ala106Val,ENST00000425560,;MARC2,missense_variant,p.Ala205Val,ENST00000366913,;MARC2,missense_variant,p.Ala205Val,ENST00000359316,;MARC2,downstream_gene_variant,,ENST00000496078,;	T	ENSG00000117791	ENST00000366913	Transcript	missense_variant	812	614	205	A/V	gCc/gTc	.	.	.	1	MARC2	HGNC	26064	protein_coding	YES	CCDS1525.1	ENSP00000355880	MOSC2_HUMAN	.	UPI000003ED29	.	tolerated(0.05)	probably_damaging(0.971)	4/8	.	Pfam_domain:PF03473,hmmpanther:PTHR14237:SF17,hmmpanther:PTHR14237,PROSITE_profiles:PS51340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGGCCTACC	.	5	ESCA
HTR1D	0	.	GRCh37	1	23519984	23519984	+	Missense_Mutation	SNP	G	G	C	rs755360447	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729C>G	p.His243Gln	p.H243Q	ENST00000374619	1/1	55	44	11	52	52	0	HTR1D,missense_variant,p.His243Gln,ENST00000314113,;HTR1D,missense_variant,p.His243Gln,ENST00000374619,;	C	ENSG00000179546	ENST00000374619	Transcript	missense_variant	1239	729	243	H/Q	caC/caG	rs755360447	.	.	-1	HTR1D	HGNC	5289	protein_coding	YES	CCDS231.1	ENSP00000363748	5HT1D_HUMAN	.	UPI00000503DE	.	tolerated(0.73)	benign(0.004)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF17,hmmpanther:PTHR24247,Pfam_domain:PF00001,Prints_domain:PR00514	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAGGTGGGC	.	5	ESCA
HEATR1	0	.	GRCh37	1	236730087	236730087	+	Missense_Mutation	SNP	G	G	C	rs143307751	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4167C>G	p.His1389Gln	p.H1389Q	ENST00000366582	30/45	15	7	8	21	21	0	HEATR1,missense_variant,p.His1308Gln,ENST00000366581,;HEATR1,missense_variant,p.His1389Gln,ENST00000366582,;	C	ENSG00000119285	ENST00000366582	Transcript	missense_variant	4282	4167	1389	H/Q	caC/caG	rs143307751	.	.	-1	HEATR1	HGNC	25517	protein_coding	YES	CCDS31066.1	ENSP00000355541	HEAT1_HUMAN	Q6P664_HUMAN	UPI000013D4D4	.	deleterious(0)	probably_damaging(0.995)	30/45	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR13457:SF1,hmmpanther:PTHR13457	A:0.0024	A:0.0091	A:0	.	A:0	A:0	A:0	A:0.0025	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	GGGACGTGTGG	byFrequency|byCluster|by1000G	2	ESCA
LINC00982	0	.	GRCh37	1	2979294	2979294	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1057G>A	.	.	ENST00000321399	1/6	93	78	15	73	73	0	LINC00982,non_coding_transcript_exon_variant,,ENST00000445317,;LINC00982,non_coding_transcript_exon_variant,,ENST00000321399,;LINC00982,intron_variant,,ENST00000415573,;LINC00982,upstream_gene_variant,,ENST00000606861,;LINC00982,upstream_gene_variant,,ENST00000413472,;LINC00982,downstream_gene_variant,,ENST00000321336,;LINC00982,upstream_gene_variant,,ENST00000453118,;AL008733.1,upstream_gene_variant,,ENST00000420957,;	T	ENSG00000177133	ENST00000321399	Transcript	non_coding_transcript_exon_variant	1057	.	.	.	.	.	.	.	-1	LINC00982	HGNC	48664	antisense	YES	.	.	.	.	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGCTCCCC	.	5	ESCA
EXO5	0	.	GRCh37	1	40981183	40981183	+	Missense_Mutation	SNP	A	A	G	rs145178039	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967A>G	p.Met323Val	p.M323V	ENST00000372703	2/2	22	13	9	19	19	0	EXO5,missense_variant,p.Met323Val,ENST00000296380,;EXO5,missense_variant,p.Met323Val,ENST00000358527,;EXO5,missense_variant,p.Met323Val,ENST00000372703,;EXO5,downstream_gene_variant,,ENST00000419161,;EXO5,downstream_gene_variant,,ENST00000415550,;EXO5,downstream_gene_variant,,ENST00000420209,;EXO5,downstream_gene_variant,,ENST00000432259,;EXO5,downstream_gene_variant,,ENST00000418186,;EXO5,downstream_gene_variant,,ENST00000443729,;RP11-656D10.6,downstream_gene_variant,,ENST00000437060,;RP11-656D10.5,upstream_gene_variant,,ENST00000453437,;EXO5,downstream_gene_variant,,ENST00000471429,;	G	ENSG00000164002	ENST00000372703	Transcript	missense_variant	2041	967	323	M/V	Atg/Gtg	rs145178039	.	.	1	EXO5	HGNC	26115	protein_coding	YES	CCDS453.1	ENSP00000361788	EXO5_HUMAN	.	UPI00000722CF	.	tolerated(0.34)	benign(0.002)	2/2	.	hmmpanther:PTHR14464,Pfam_domain:PF09810	G:0.0002	G:0	G:0.0014	.	G:0	G:0	G:0	G:0	G:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTATATGGCC	byCluster|by1000G	4	ESCA
KCNQ4	0	.	GRCh37	1	41300749	41300749	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1724G>A	p.Arg575Gln	p.R575Q	ENST00000347132	12/14	39	34	4	52	52	0	KCNQ4,missense_variant,p.Arg521Gln,ENST00000509682,;KCNQ4,missense_variant,p.Arg436Gln,ENST00000443478,;KCNQ4,missense_variant,p.Arg575Gln,ENST00000347132,;KCNQ4,non_coding_transcript_exon_variant,,ENST00000506017,;	A	ENSG00000117013	ENST00000347132	Transcript	missense_variant	1806	1724	575	R/Q	cGg/cAg	.	.	.	1	KCNQ4	HGNC	6298	protein_coding	YES	CCDS456.1	ENSP00000262916	KCNQ4_HUMAN	.	UPI000013D35B	.	deleterious(0)	probably_damaging(0.999)	12/14	.	Pfam_domain:PF03520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGCCGGATCA	.	4	ESCA
ECHDC2	0	.	GRCh37	1	53372051	53372051	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457+140A>G	.	.	ENST00000371522	.	27	15	11	32	32	0	ECHDC2,3_prime_UTR_variant,,ENST00000541281,;ECHDC2,intron_variant,,ENST00000467988,;ECHDC2,intron_variant,,ENST00000358358,;ECHDC2,intron_variant,,ENST00000536120,;ECHDC2,intron_variant,,ENST00000371522,;ECHDC2,intron_variant,,ENST00000543419,;ECHDC2,intron_variant,,ENST00000479593,;ECHDC2,intron_variant,,ENST00000487851,;ECHDC2,intron_variant,,ENST00000486170,;ECHDC2,downstream_gene_variant,,ENST00000495920,;ECHDC2,non_coding_transcript_exon_variant,,ENST00000460612,;ECHDC2,intron_variant,,ENST00000476477,;ECHDC2,intron_variant,,ENST00000463923,;ECHDC2,intron_variant,,ENST00000487866,;ECHDC2,intron_variant,,ENST00000371520,;ECHDC2,downstream_gene_variant,,ENST00000544365,;ECHDC2,upstream_gene_variant,,ENST00000479183,;ECHDC2,upstream_gene_variant,,ENST00000498544,;ECHDC2,upstream_gene_variant,,ENST00000539680,;ECHDC2,downstream_gene_variant,,ENST00000492992,;ECHDC2,downstream_gene_variant,,ENST00000488268,;	C	ENSG00000121310	ENST00000371522	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ECHDC2	HGNC	23408	protein_coding	YES	CCDS55600.1	ENSP00000360577	ECHD2_HUMAN	Q8WY60_HUMAN,B7Z7N0_HUMAN	UPI0000204369	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCTCTGTG	.	5	ESCA
RAVER2	0	.	GRCh37	1	65268698	65268698	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1145A>G	p.Asn382Ser	p.N382S	ENST00000371072	6/12	31	22	8	52	52	0	RAVER2,missense_variant,p.Asn382Ser,ENST00000294428,;RAVER2,missense_variant,p.Asn88Ser,ENST00000430964,;RAVER2,missense_variant,p.Asn382Ser,ENST00000371072,;RAVER2,missense_variant,p.Asn88Ser,ENST00000418058,;	G	ENSG00000162437	ENST00000371072	Transcript	missense_variant	1223	1145	382	N/S	aAt/aGt	.	.	.	1	RAVER2	HGNC	25577	protein_coding	YES	CCDS41345.1	ENSP00000360112	RAVR2_HUMAN	.	UPI000043DED2	.	tolerated(0.23)	benign(0.031)	6/12	.	hmmpanther:PTHR23189:SF6,hmmpanther:PTHR23189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAATCCAT	.	5	ESCA
SRSF11	0	.	GRCh37	1	70716996	70716996	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*508A>G	.	.	ENST00000370950	13/13	55	40	15	87	87	0	SRSF11,3_prime_UTR_variant,,ENST00000370951,;SRSF11,3_prime_UTR_variant,,ENST00000370949,;SRSF11,3_prime_UTR_variant,,ENST00000370950,;SRSF11,downstream_gene_variant,,ENST00000405432,;SRSF11,downstream_gene_variant,,ENST00000395136,;SRSF11,non_coding_transcript_exon_variant,,ENST00000461935,;SRSF11,non_coding_transcript_exon_variant,,ENST00000484162,;SRSF11,downstream_gene_variant,,ENST00000460795,;SRSF11,downstream_gene_variant,,ENST00000463859,;SRSF11,downstream_gene_variant,,ENST00000489188,;	G	ENSG00000116754	ENST00000370950	Transcript	3_prime_UTR_variant	2045	.	.	.	.	.	.	.	1	SRSF11	HGNC	10782	protein_coding	YES	CCDS647.1	ENSP00000359988	SRS11_HUMAN	Q6N079_HUMAN	UPI00001358C5	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTACATCTGG	.	5	ESCA
FLRT3	0	.	GRCh37	20	14306311	14306311	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1842A>G	p.Ile614Met	p.I614M	ENST00000378053	2/2	72	55	16	95	95	0	FLRT3,missense_variant,p.Ile614Met,ENST00000378053,;FLRT3,missense_variant,p.Ile614Met,ENST00000341420,;MACROD2,intron_variant,,ENST00000217246,;MACROD2,intron_variant,,ENST00000310348,;MACROD2,intron_variant,,ENST00000490428,;MACROD2,intron_variant,,ENST00000494602,;MACROD2,intron_variant,,ENST00000477147,;FLRT3,downstream_gene_variant,,ENST00000462077,;	C	ENSG00000125848	ENST00000378053	Transcript	missense_variant	2099	1842	614	I/M	atA/atG	.	.	.	-1	FLRT3	HGNC	3762	protein_coding	YES	CCDS13121.1	ENSP00000367292	FLRT3_HUMAN	.	UPI0000001BE7	.	deleterious(0)	probably_damaging(0.984)	2/2	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAATATGGT	.	5	ESCA
RRBP1	0	.	GRCh37	20	17639256	17639256	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607A>T	p.Lys203Ter	p.K203*	ENST00000377807	4/26	46	23	23	64	64	0	RRBP1,stop_gained,p.Lys633Ter,ENST00000246043,;RRBP1,stop_gained,p.Lys203Ter,ENST00000360807,;RRBP1,stop_gained,p.Lys633Ter,ENST00000377813,;RRBP1,stop_gained,p.Lys203Ter,ENST00000377807,;RRBP1,intron_variant,,ENST00000455029,;RRBP1,downstream_gene_variant,,ENST00000398782,;RRBP1,stop_gained,p.Lys108Ter,ENST00000495501,;	A	ENSG00000125844	ENST00000377807	Transcript	stop_gained	961	607	203	K/*	Aaa/Taa	.	.	.	-1	RRBP1	HGNC	10448	protein_coding	YES	CCDS13128.1	ENSP00000367038	RRBP1_HUMAN	F8W7S5_HUMAN	UPI000002B2C0	.	.	.	4/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR18939:SF4,hmmpanther:PTHR18939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTTCTTTG	.	5	ESCA
MYH7B	0	.	GRCh37	20	33567245	33567245	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.270G>A	p.%3D	p.E90E	ENST00000262873	4/43	47	36	10	47	47	0	MYH7B,synonymous_variant,p.%3D,ENST00000262873,;MYH7B,upstream_gene_variant,,ENST00000481922,;MYH7B,non_coding_transcript_exon_variant,,ENST00000470929,;	A	ENSG00000078814	ENST00000262873	Transcript	synonymous_variant	362	270	90	E	gaG/gaA	.	.	.	1	MYH7B	HGNC	15906	protein_coding	YES	CCDS42869.1	ENSP00000262873	MYH7B_HUMAN	.	UPI0000253BD4	.	.	.	4/43	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF310,Pfam_domain:PF02736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGAGGTCAA	.	4	ESCA
RPN2	0	.	GRCh37	20	35827502	35827502	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.353A>T	p.Glu118Val	p.E118V	ENST00000237530	4/17	56	31	24	51	51	0	RPN2,missense_variant,p.Glu118Val,ENST00000373632,;RPN2,missense_variant,p.Glu118Val,ENST00000237530,;RPN2,missense_variant,p.Glu86Val,ENST00000373622,;RPN2,intron_variant,,ENST00000456102,;RPN2,intron_variant,,ENST00000462163,;	T	ENSG00000118705	ENST00000237530	Transcript	missense_variant	664	353	118	E/V	gAg/gTg	.	.	.	1	RPN2	HGNC	10382	protein_coding	YES	CCDS13291.1	ENSP00000237530	RPN2_HUMAN	.	UPI0000000C52	.	deleterious(0)	probably_damaging(0.962)	4/17	.	hmmpanther:PTHR12640:SF0,hmmpanther:PTHR12640,Pfam_domain:PF05817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTGAGGACT	.	5	ESCA
BLCAP	0	.	GRCh37	20	36146397	36146397	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*916C>A	.	.	ENST00000414542	3/3	13	9	4	24	24	0	BLCAP,3_prime_UTR_variant,,ENST00000397137,;BLCAP,3_prime_UTR_variant,,ENST00000373537,;BLCAP,3_prime_UTR_variant,,ENST00000414542,;BLCAP,downstream_gene_variant,,ENST00000445723,;NNAT,upstream_gene_variant,,ENST00000062104,;BLCAP,downstream_gene_variant,,ENST00000397131,;BLCAP,downstream_gene_variant,,ENST00000432507,;BLCAP,downstream_gene_variant,,ENST00000456058,;BLCAP,downstream_gene_variant,,ENST00000414080,;NNAT,upstream_gene_variant,,ENST00000346199,;BLCAP,downstream_gene_variant,,ENST00000397135,;BLCAP,downstream_gene_variant,,ENST00000397134,;BLCAP,intron_variant,,ENST00000467603,;	T	ENSG00000166619	ENST00000414542	Transcript	3_prime_UTR_variant	1628	.	.	.	.	.	.	.	-1	BLCAP	HGNC	1055	protein_coding	YES	CCDS13295.1	ENSP00000397172	BLCAP_HUMAN	A2A2K9_HUMAN,A2A2K8_HUMAN	UPI0000000D02	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACAGGGCACA	.	2	ESCA
HNF4A	0	.	GRCh37	20	43052981	43052981	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129+87T>C	.	.	ENST00000316099	.	12	8	4	16	16	0	HNF4A,synonymous_variant,p.%3D,ENST00000443598,;HNF4A,synonymous_variant,p.%3D,ENST00000609795,;HNF4A,intron_variant,,ENST00000415691,;HNF4A,intron_variant,,ENST00000316099,;HNF4A,intron_variant,,ENST00000316673,;HNF4A,intron_variant,,ENST00000457232,;AL132772.1,downstream_gene_variant,,ENST00000581483,;HNF4A,intron_variant,,ENST00000372920,;	C	ENSG00000101076	ENST00000316099	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	HNF4A	HGNC	5024	protein_coding	YES	CCDS13330.1	ENSP00000312987	HNF4A_HUMAN	F1D8T1_HUMAN	UPI000016A0BA	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	GCTCCTTGGCT	.	3	ESCA
KCNB1	0	.	GRCh37	20	47991182	47991182	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915C>T	p.%3D	p.L305L	ENST00000371741	2/2	30	21	9	20	20	0	KCNB1,synonymous_variant,p.%3D,ENST00000371741,;	A	ENSG00000158445	ENST00000371741	Transcript	synonymous_variant	1082	915	305	L	ctC/ctT	COSM3547582	.	.	-1	KCNB1	HGNC	6231	protein_coding	YES	CCDS13418.1	ENSP00000360806	KCNB1_HUMAN	.	UPI000012DC80	.	.	.	2/2	.	Prints_domain:PR00169,Superfamily_domains:SSF81324,Pfam_domain:PF00520,Gene3D:1.20.120.350,hmmpanther:PTHR11537:SF63,hmmpanther:PTHR11537	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.R303Q|c.908G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCGGAGAAT	.	5	ESCA
CDH4	0	.	GRCh37	20	60498649	60498649	+	Silent	SNP	C	C	A	rs777016060	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1515C>A	p.%3D	p.P505P	ENST00000360469	10/16	32	27	5	36	36	0	CDH4,synonymous_variant,p.%3D,ENST00000543233,;CDH4,synonymous_variant,p.%3D,ENST00000360469,;	A	ENSG00000179242	ENST00000360469	Transcript	synonymous_variant	1603	1515	505	P	ccC/ccA	rs777016060	.	.	1	CDH4	HGNC	1763	protein_coding	YES	CCDS13488.1	ENSP00000353656	CADH4_HUMAN	Q8ND09_HUMAN	UPI000015FE86	.	.	.	10/16	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCTCCCTACTT	.	3	ESCA
HELZ2	0	.	GRCh37	20	62196935	62196935	+	Silent	SNP	G	G	A	rs758579604	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3240C>T	p.%3D	p.D1080D	ENST00000467148	8/19	15	11	4	15	15	0	HELZ2,synonymous_variant,p.%3D,ENST00000467148,;HELZ2,synonymous_variant,p.%3D,ENST00000427522,;HELZ2,downstream_gene_variant,,ENST00000479540,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,upstream_gene_variant,,ENST00000478861,;HELZ2,downstream_gene_variant,,ENST00000370082,;	A	ENSG00000130589	ENST00000467148	Transcript	synonymous_variant	3310	3240	1080	D	gaC/gaT	rs758579604	.	.	-1	HELZ2	HGNC	30021	protein_coding	YES	CCDS33508.1	ENSP00000417401	HELZ2_HUMAN	Q3C1U4_HUMAN	UPI0000246BF7	.	.	.	8/19	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF332	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTCTCGTCCAG	.	4	ESCA
GGT5	0	.	GRCh37	22	24627486	24627486	+	Missense_Mutation	SNP	G	G	T	rs768749416	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767C>A	p.Thr256Lys	p.T256K	ENST00000398292	6/12	46	33	12	36	36	0	GGT5,missense_variant,p.Thr256Lys,ENST00000398292,;GGT5,missense_variant,p.Thr224Lys,ENST00000263112,;GGT5,missense_variant,p.Thr179Lys,ENST00000418439,;GGT5,missense_variant,p.Thr256Lys,ENST00000327365,;GGT5,downstream_gene_variant,,ENST00000424217,;	T	ENSG00000099998	ENST00000398292	Transcript	missense_variant	1101	767	256	T/K	aCg/aAg	rs768749416	.	.	-1	GGT5	HGNC	4260	protein_coding	YES	CCDS42990.1	ENSP00000381340	GGT5_HUMAN	.	UPI00003B5CB9	.	deleterious(0.04)	probably_damaging(0.95)	6/12	.	Prints_domain:PR01210,Superfamily_domains:SSF56235,Pfam_domain:PF01019,hmmpanther:PTHR11686,hmmpanther:PTHR11686:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGTCAGC	byFrequency	5	ESCA
CRYBB1	0	.	GRCh37	22	27008042	27008042	+	Missense_Mutation	SNP	G	G	A	rs144372140	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.293C>T	p.Ala98Val	p.A98V	ENST00000215939	3/6	60	50	10	69	69	0	CRYBB1,missense_variant,p.Ala98Val,ENST00000215939,;	A	ENSG00000100122	ENST00000215939	Transcript	missense_variant	424	293	98	A/V	gCg/gTg	rs144372140,COSM243859	.	.	-1	CRYBB1	HGNC	2397	protein_coding	YES	CCDS13840.1	ENSP00000215939	CRBB1_HUMAN	.	UPI000000165D	.	deleterious(0.02)	benign(0.007)	3/6	.	PROSITE_profiles:PS50915,hmmpanther:PTHR11818:SF12,hmmpanther:PTHR11818,Gene3D:2.60.20.10,Pfam_domain:PF00030,SMART_domains:SM00247,Superfamily_domains:SSF49695,Prints_domain:PR01367	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCGCGGAG	byCluster|by1000G	5	ESCA
MYH9	0	.	GRCh37	22	36690174	36690174	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3801G>A	p.%3D	p.V1267V	ENST00000216181	28/41	22	12	9	24	24	0	MYH9,synonymous_variant,p.%3D,ENST00000216181,;MYH9,downstream_gene_variant,,ENST00000459960,;	T	ENSG00000100345	ENST00000216181	Transcript	synonymous_variant	4032	3801	1267	V	gtG/gtA	.	.	.	-1	MYH9	HGNC	7579	protein_coding	YES	CCDS13927.1	ENSP00000216181	MYH9_HUMAN	Q9UMJ0_HUMAN,B1AH99_HUMAN	UPI000012FB80	.	.	.	28/41	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF317,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCGCACGCG	.	5	ESCA
TNRC6B	0	.	GRCh37	22	40662289	40662289	+	Silent	SNP	C	C	T	rs748158394	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2055C>T	p.%3D	p.A685A	ENST00000454349	5/23	15	10	4	14	14	0	TNRC6B,synonymous_variant,p.%3D,ENST00000454349,;TNRC6B,synonymous_variant,p.%3D,ENST00000446273,;TNRC6B,synonymous_variant,p.%3D,ENST00000335727,;TNRC6B,intron_variant,,ENST00000402203,;TNRC6B,intron_variant,,ENST00000301923,;	T	ENSG00000100354	ENST00000454349	Transcript	synonymous_variant	2266	2055	685	A	gcC/gcT	rs748158394	.	.	1	TNRC6B	HGNC	29190	protein_coding	YES	CCDS54533.1	ENSP00000401946	TNR6B_HUMAN	.	UPI00017A6F19	.	.	.	5/23	.	hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCCTCTAC	byFrequency	5	ESCA
CNTNAP5	0	.	GRCh37	2	125284959	125284959	+	Missense_Mutation	SNP	C	C	A	rs758855163	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1572C>A	p.Asp524Glu	p.D524E	ENST00000431078	10/24	57	29	28	81	81	0	CNTNAP5,missense_variant,p.Asp524Glu,ENST00000431078,;	A	ENSG00000155052	ENST00000431078	Transcript	missense_variant	1936	1572	524	D/E	gaC/gaA	rs758855163	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	deleterious(0)	probably_damaging(0.997)	10/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Gene3D:2.60.120.200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGACCTCAT	.	5	ESCA
SAP130	0	.	GRCh37	2	128712725	128712725	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2335A>G	p.Ile779Val	p.I779V	ENST00000357702	16/21	49	35	14	42	42	0	SAP130,missense_variant,p.Ile744Val,ENST00000259235,;SAP130,missense_variant,p.Ile752Val,ENST00000259234,;SAP130,missense_variant,p.Ile779Val,ENST00000357702,;	C	ENSG00000136715	ENST00000357702	Transcript	missense_variant	2467	2335	779	I/V	Att/Gtt	.	.	.	-1	SAP130	HGNC	29813	protein_coding	YES	CCDS54397.1	ENSP00000350333	SP130_HUMAN	Q96DP1_HUMAN,C9J683_HUMAN	UPI00005989D6	.	tolerated_low_confidence(0.33)	unknown(0)	16/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13497	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAATGGTTG	.	5	ESCA
STK39	0	.	GRCh37	2	168811130	168811130	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*876A>C	.	.	ENST00000355999	18/18	24	10	13	27	27	0	STK39,3_prime_UTR_variant,,ENST00000355999,;STK39,non_coding_transcript_exon_variant,,ENST00000487143,;	G	ENSG00000198648	ENST00000355999	Transcript	3_prime_UTR_variant	3220	.	.	.	.	.	.	.	-1	STK39	HGNC	17717	protein_coding	YES	CCDS42770.1	ENSP00000348278	STK39_HUMAN	.	UPI000013D46D	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAACTTAACA	.	5	ESCA
LRP2	0	.	GRCh37	2	170027101	170027101	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11340T>C	p.%3D	p.H3780H	ENST00000263816	59/79	43	13	29	64	64	0	LRP2,synonymous_variant,p.%3D,ENST00000263816,;	G	ENSG00000081479	ENST00000263816	Transcript	synonymous_variant	11626	11340	3780	H	caT/caC	.	.	.	-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	LRP2_HUMAN	Q9NP34_HUMAN,Q53TL0_HUMAN,Q4ZG84_HUMAN	UPI0000141BA5	.	.	.	59/79	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF220,PROSITE_patterns:PS01209,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTAATGGTC	.	5	ESCA
CYBRD1	0	.	GRCh37	2	172378944	172378944	+	5'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-112A>C	.	.	ENST00000321348	1/4	17	8	9	28	28	0	CYBRD1,5_prime_UTR_variant,,ENST00000321348,;CYBRD1,intron_variant,,ENST00000409484,;CYBRD1,upstream_gene_variant,,ENST00000375252,;CYBRD1,upstream_gene_variant,,ENST00000445146,;CYBRD1,non_coding_transcript_exon_variant,,ENST00000468308,;CYBRD1,upstream_gene_variant,,ENST00000494587,;CYBRD1,upstream_gene_variant,,ENST00000474182,;AC007969.5,upstream_gene_variant,,ENST00000433675,;AC007969.5,upstream_gene_variant,,ENST00000397084,;	C	ENSG00000071967	ENST00000321348	Transcript	5_prime_UTR_variant	87	.	.	.	.	.	.	.	1	CYBRD1	HGNC	20797	protein_coding	YES	CCDS2244.1	ENSP00000319141	CYBR1_HUMAN	.	UPI0000140B22	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGGAGACAG	.	5	ESCA
PLEKHA3	0	.	GRCh37	2	179345554	179345554	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-43C>A	.	.	ENST00000234453	1/8	33	26	7	13	13	0	PLEKHA3,5_prime_UTR_variant,,ENST00000234453,;FKBP7,upstream_gene_variant,,ENST00000434643,;FKBP7,upstream_gene_variant,,ENST00000424785,;FKBP7,upstream_gene_variant,,ENST00000470945,;PLEKHA3,upstream_gene_variant,,ENST00000461474,;FKBP7,upstream_gene_variant,,ENST00000464248,;PLEKHA3,5_prime_UTR_variant,,ENST00000453653,;FKBP7,upstream_gene_variant,,ENST00000412612,;FKBP7,upstream_gene_variant,,ENST00000233092,;FKBP7,upstream_gene_variant,,ENST00000419184,;FKBP7,upstream_gene_variant,,ENST00000435079,;	A	ENSG00000116095	ENST00000234453	Transcript	5_prime_UTR_variant	360	.	.	.	.	.	.	.	1	PLEKHA3	HGNC	14338	protein_coding	YES	CCDS33336.1	ENSP00000234453	PKHA3_HUMAN	.	UPI000000DA8A	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCGGCCGGCG	.	5	ESCA
ALS2	0	.	GRCh37	2	202593784	202593784	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2703A>G	p.%3D	p.G901G	ENST00000264276	14/34	50	22	27	37	37	0	ALS2,synonymous_variant,p.%3D,ENST00000264276,;ALS2,synonymous_variant,p.%3D,ENST00000457679,;ALS2,non_coding_transcript_exon_variant,,ENST00000494017,;ALS2,non_coding_transcript_exon_variant,,ENST00000483703,;ALS2,upstream_gene_variant,,ENST00000489440,;ALS2,synonymous_variant,p.%3D,ENST00000439495,;ALS2,non_coding_transcript_exon_variant,,ENST00000482891,;	C	ENSG00000003393	ENST00000264276	Transcript	synonymous_variant	3076	2703	901	G	ggA/ggG	.	.	.	-1	ALS2	HGNC	443	protein_coding	YES	CCDS42800.1	ENSP00000264276	ALS2_HUMAN	J3KQ43_HUMAN,J3KQ33_HUMAN,A8K4R4_HUMAN	UPI0000231C77	.	.	.	14/34	.	hmmpanther:PTHR22870,hmmpanther:PTHR22870:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTTCCGGG	.	5	ESCA
BMPR2	0	.	GRCh37	2	203420310	203420310	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1922A>G	p.His641Arg	p.H641R	ENST00000374580	12/13	10	7	3	21	21	0	BMPR2,missense_variant,p.His641Arg,ENST00000374580,;BMPR2,intron_variant,,ENST00000374574,;	G	ENSG00000204217	ENST00000374580	Transcript	missense_variant	2461	1922	641	H/R	cAt/cGt	.	.	.	1	BMPR2	HGNC	1078	protein_coding	YES	CCDS33361.1	ENSP00000363708	BMPR2_HUMAN	.	UPI0000126A3B	.	tolerated(0.48)	benign(0.055)	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGCATACCA	.	2	ESCA
YIPF4	0	.	GRCh37	2	32531489	32531489	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*794T>G	.	.	ENST00000238831	6/6	19	12	7	32	32	0	YIPF4,3_prime_UTR_variant,,ENST00000238831,;YIPF4,intron_variant,,ENST00000441084,;YIPF4,downstream_gene_variant,,ENST00000437765,;	G	ENSG00000119820	ENST00000238831	Transcript	3_prime_UTR_variant	1775	.	.	.	.	.	.	.	1	YIPF4	HGNC	28145	protein_coding	YES	CCDS1781.1	ENSP00000238831	YIPF4_HUMAN	.	UPI0000073BBE	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTTACTAT	.	5	ESCA
PAPOLG	0	.	GRCh37	2	61009902	61009902	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109A>G	p.Tyr370Cys	p.Y370C	ENST00000238714	12/22	33	21	11	31	31	0	PAPOLG,missense_variant,p.Tyr38Cys,ENST00000412217,;PAPOLG,missense_variant,p.Tyr370Cys,ENST00000238714,;PAPOLG,non_coding_transcript_exon_variant,,ENST00000483370,;PAPOLG,3_prime_UTR_variant,,ENST00000414060,;PAPOLG,3_prime_UTR_variant,,ENST00000453839,;PAPOLG,non_coding_transcript_exon_variant,,ENST00000496283,;	G	ENSG00000115421	ENST00000238714	Transcript	missense_variant	1358	1109	370	Y/C	tAt/tGt	.	.	.	1	PAPOLG	HGNC	14982	protein_coding	YES	CCDS1863.1	ENSP00000238714	PAPOG_HUMAN	Q9H968_HUMAN,Q53T81_HUMAN,Q53T17_HUMAN,Q2TAI9_HUMAN,F8WAT4_HUMAN	UPI00000704EB	.	deleterious(0)	probably_damaging(0.975)	12/22	.	hmmpanther:PTHR10682:SF6,hmmpanther:PTHR10682,Pfam_domain:PF04926,Gene3D:3.30.70.590,PIRSF_domain:PIRSF018425,Superfamily_domains:SSF55003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGTATAGGT	.	5	ESCA
REL	0	.	GRCh37	2	61149071	61149071	+	Missense_Mutation	SNP	C	C	T	rs772899527	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1261C>T	p.Arg421Cys	p.R421C	ENST00000295025	11/11	39	26	13	36	36	0	REL,missense_variant,p.Arg389Cys,ENST00000394479,;REL,missense_variant,p.Arg421Cys,ENST00000295025,;RP11-373L24.1,upstream_gene_variant,,ENST00000589496,;	T	ENSG00000162924	ENST00000295025	Transcript	missense_variant	1581	1261	421	R/C	Cgc/Tgc	rs772899527,COSM193314	.	.	1	REL	HGNC	9954	protein_coding	YES	CCDS1864.1	ENSP00000295025	REL_HUMAN	.	UPI000013367B	.	tolerated_low_confidence(0.23)	benign(0.007)	11/11	.	hmmpanther:PTHR24169,hmmpanther:PTHR24169:SF4	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCACGCTCA	byFrequency	5	ESCA
EHBP1	0	.	GRCh37	2	62998478	62998478	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263C>A	p.Pro88His	p.P88H	ENST00000263991	5/25	121	80	41	113	113	0	EHBP1,missense_variant,p.Pro88His,ENST00000405482,;EHBP1,missense_variant,p.Pro88His,ENST00000263991,;EHBP1,missense_variant,p.Pro88His,ENST00000405289,;EHBP1,missense_variant,p.Pro88His,ENST00000405015,;EHBP1,missense_variant,p.Pro88His,ENST00000431489,;EHBP1,missense_variant,p.Pro56His,ENST00000413434,;EHBP1,missense_variant,p.Pro88His,ENST00000354487,;EHBP1,5_prime_UTR_variant,,ENST00000426940,;EHBP1,intron_variant,,ENST00000449820,;EHBP1,non_coding_transcript_exon_variant,,ENST00000472809,;EHBP1,non_coding_transcript_exon_variant,,ENST00000494958,;	A	ENSG00000115504	ENST00000263991	Transcript	missense_variant	745	263	88	P/H	cCt/cAt	.	.	.	1	EHBP1	HGNC	29144	protein_coding	YES	CCDS1872.1	ENSP00000263991	EHBP1_HUMAN	C9K0H9_HUMAN,C9JEP1_HUMAN,C9J268_HUMAN,B3KM32_HUMAN	UPI000013D49A	.	deleterious(0)	probably_damaging(0.999)	5/25	.	hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF124,Pfam_domain:PF10358	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATCCTCATG	.	5	ESCA
REG3G	0	.	GRCh37	2	79253229	79253229	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10C>G	p.Pro4Ala	p.P4A	ENST00000272324	2/6	79	48	31	95	95	0	REG3G,missense_variant,p.Pro4Ala,ENST00000393897,;REG3G,missense_variant,p.Pro4Ala,ENST00000409471,;REG3G,missense_variant,p.Pro4Ala,ENST00000272324,;REG3G,non_coding_transcript_exon_variant,,ENST00000490944,;REG3G,non_coding_transcript_exon_variant,,ENST00000498312,;	G	ENSG00000143954	ENST00000272324	Transcript	missense_variant	194	10	4	P/A	Ccc/Gcc	.	.	.	1	REG3G	HGNC	29595	protein_coding	YES	CCDS1962.1	ENSP00000272324	REG3G_HUMAN	.	UPI0000048F1E	.	tolerated(0.11)	benign(0.005)	2/6	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCCCATG	.	5	ESCA
REG3G	0	.	GRCh37	2	79253939	79253939	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177A>T	p.Lys59Asn	p.K59N	ENST00000272324	3/6	41	22	19	42	42	0	REG3G,missense_variant,p.Lys59Asn,ENST00000393897,;REG3G,missense_variant,p.Lys59Asn,ENST00000409471,;REG3G,missense_variant,p.Lys59Asn,ENST00000272324,;REG3G,non_coding_transcript_exon_variant,,ENST00000490944,;REG3G,non_coding_transcript_exon_variant,,ENST00000498312,;	T	ENSG00000143954	ENST00000272324	Transcript	missense_variant	361	177	59	K/N	aaA/aaT	.	.	.	1	REG3G	HGNC	29595	protein_coding	YES	CCDS1962.1	ENSP00000272324	REG3G_HUMAN	.	UPI0000048F1E	.	deleterious(0.01)	probably_damaging(0.988)	3/6	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF29,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAAATCCTG	.	5	ESCA
MRPL35	0	.	GRCh37	2	86440334	86440334	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2543A>G	.	.	ENST00000337109	4/4	9	6	3	11	11	0	MRPL35,3_prime_UTR_variant,,ENST00000337109,;MRPL35,intron_variant,,ENST00000409180,;REEP1,downstream_gene_variant,,ENST00000538924,;REEP1,downstream_gene_variant,,ENST00000541910,;REEP1,downstream_gene_variant,,ENST00000535845,;REEP1,downstream_gene_variant,,ENST00000540790,;MRPL35,downstream_gene_variant,,ENST00000605125,;REEP1,downstream_gene_variant,,ENST00000165698,;MRPL35,downstream_gene_variant,,ENST00000254644,;	G	ENSG00000132313	ENST00000337109	Transcript	3_prime_UTR_variant	3144	.	.	.	.	.	.	.	1	MRPL35	HGNC	14489	protein_coding	YES	CCDS1988.1	ENSP00000338389	RM35_HUMAN	.	UPI000004A028	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTAAATAAAC	.	2	ESCA
PROM2	0	.	GRCh37	2	95940353	95940353	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20T>A	p.Leu7Gln	p.L7Q	ENST00000317620	1/24	72	55	16	70	70	0	PROM2,missense_variant,p.Leu7Gln,ENST00000317620,;PROM2,missense_variant,p.Leu7Gln,ENST00000542147,;PROM2,missense_variant,p.Leu7Gln,ENST00000403131,;PROM2,missense_variant,p.Leu7Gln,ENST00000317668,;PROM2,non_coding_transcript_exon_variant,,ENST00000463580,;PROM2,upstream_gene_variant,,ENST00000477767,;PROM2,missense_variant,p.Leu7Gln,ENST00000431567,;PROM2,non_coding_transcript_exon_variant,,ENST00000487138,;PROM2,upstream_gene_variant,,ENST00000478295,;	A	ENSG00000155066	ENST00000317620	Transcript	missense_variant	153	20	7	L/Q	cTg/cAg	.	.	.	1	PROM2	HGNC	20685	protein_coding	YES	CCDS2012.1	ENSP00000318270	PROM2_HUMAN	.	UPI0000071157	.	deleterious_low_confidence(0)	possibly_damaging(0.766)	1/24	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22730:SF6,hmmpanther:PTHR22730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCTGCTGG	.	5	ESCA
PIK3CB	0	.	GRCh37	3	138400822	138400822	+	Missense_Mutation	SNP	C	C	T	rs764933219	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2491G>A	p.Gly831Ser	p.G831S	ENST00000477593	18/23	46	41	5	38	38	0	PIK3CB,missense_variant,p.Gly463Ser,ENST00000493568,;PIK3CB,missense_variant,p.Gly831Ser,ENST00000477593,;PIK3CB,missense_variant,p.Gly282Ser,ENST00000544716,;PIK3CB,missense_variant,p.Gly831Ser,ENST00000289153,;PIK3CB,3_prime_UTR_variant,,ENST00000462898,;PIK3CB,3_prime_UTR_variant,,ENST00000469284,;PIK3CB,non_coding_transcript_exon_variant,,ENST00000481749,;PIK3CB,downstream_gene_variant,,ENST00000473435,;PIK3CB,downstream_gene_variant,,ENST00000485060,;	T	ENSG00000051382	ENST00000477593	Transcript	missense_variant	2565	2491	831	G/S	Ggt/Agt	rs764933219	.	.	-1	PIK3CB	HGNC	8976	protein_coding	YES	CCDS3104.1	ENSP00000418143	PK3CB_HUMAN	Q9BTS4_HUMAN,Q6PJ60_HUMAN,C9JYX0_HUMAN,C9JNF6_HUMAN,C9J345_HUMAN	UPI0000046842	.	deleterious(0)	benign(0.314)	18/23	.	PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF33,hmmpanther:PTHR10048,Gene3D:3.30.1010.10,Pfam_domain:PF00454,SMART_domains:SM00146,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L832W|c.2495T>G|5	RADIA|MUTECT|MUSE|VARSCANS	CAAACCAGCTT	byFrequency	4	ESCA
PRR23A	0	.	GRCh37	3	138724597	138724597	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514G>A	p.Ala172Thr	p.A172T	ENST00000383163	1/1	35	23	11	31	31	0	PRR23A,missense_variant,p.Ala172Thr,ENST00000383163,;MRPS22,upstream_gene_variant,,ENST00000495075,;	T	ENSG00000206260	ENST00000383163	Transcript	missense_variant	514	514	172	A/T	Gca/Aca	.	.	.	-1	PRR23A	HGNC	37172	protein_coding	YES	CCDS46923.1	ENSP00000372649	PR23A_HUMAN	.	UPI00003671C1	.	tolerated(0.22)	possibly_damaging(0.532)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31813:SF2,hmmpanther:PTHR31813,Pfam_domain:PF10630	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTGCGGAGT	.	5	ESCA
XRN1	0	.	GRCh37	3	142028884	142028884	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1469A>T	.	.	ENST00000264951	42/42	31	14	17	32	32	0	XRN1,3_prime_UTR_variant,,ENST00000498077,;XRN1,3_prime_UTR_variant,,ENST00000264951,;XRN1,downstream_gene_variant,,ENST00000392981,;	A	ENSG00000114127	ENST00000264951	Transcript	3_prime_UTR_variant	6708	.	.	.	.	.	.	.	-1	XRN1	HGNC	30654	protein_coding	YES	CCDS3123.1	ENSP00000264951	XRN1_HUMAN	C9JCZ8_HUMAN	UPI0000074113	.	.	.	42/42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGATAATGA	.	5	ESCA
MBNL1	0	.	GRCh37	3	152181097	152181097	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*942A>G	.	.	ENST00000282486	10/10	19	14	5	14	14	0	MBNL1,3_prime_UTR_variant,,ENST00000545754,;MBNL1,3_prime_UTR_variant,,ENST00000282486,;MBNL1,3_prime_UTR_variant,,ENST00000324196,;MBNL1,3_prime_UTR_variant,,ENST00000498502,;MBNL1,3_prime_UTR_variant,,ENST00000493459,;MBNL1,3_prime_UTR_variant,,ENST00000357472,;MBNL1,3_prime_UTR_variant,,ENST00000463374,;MBNL1,3_prime_UTR_variant,,ENST00000282488,;MBNL1,3_prime_UTR_variant,,ENST00000324210,;MBNL1,3_prime_UTR_variant,,ENST00000355460,;MBNL1,3_prime_UTR_variant,,ENST00000485910,;MBNL1,downstream_gene_variant,,ENST00000478535,;MBNL1,downstream_gene_variant,,ENST00000485509,;MBNL1,downstream_gene_variant,,ENST00000465907,;MBNL1,downstream_gene_variant,,ENST00000492948,;MBNL1,downstream_gene_variant,,ENST00000464596,;RP11-362A9.3,intron_variant,,ENST00000463255,;MBNL1,non_coding_transcript_exon_variant,,ENST00000497971,;	G	ENSG00000152601	ENST00000282486	Transcript	3_prime_UTR_variant	3951	.	.	.	.	.	.	.	1	MBNL1	HGNC	6923	protein_coding	YES	CCDS3165.1	ENSP00000282486	MBNL1_HUMAN	C9JCX1_HUMAN,C9J7P7_HUMAN	UPI000003B440	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAATATTTAT	.	5	ESCA
BCHE	0	.	GRCh37	3	165548781	165548781	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.41T>A	p.Phe14Tyr	p.F14Y	ENST00000264381	2/4	42	34	7	36	36	0	BCHE,missense_variant,p.Phe14Tyr,ENST00000264381,;BCHE,intron_variant,,ENST00000540653,;BCHE,intron_variant,,ENST00000479451,;BCHE,intron_variant,,ENST00000488954,;BCHE,missense_variant,p.Phe14Tyr,ENST00000482958,;BCHE,missense_variant,p.Phe14Tyr,ENST00000497011,;	T	ENSG00000114200	ENST00000264381	Transcript	missense_variant	208	41	14	F/Y	tTt/tAt	.	.	.	-1	BCHE	HGNC	983	protein_coding	YES	CCDS3198.1	ENSP00000264381	CHLE_HUMAN	Q96HL2_HUMAN,F8WF14_HUMAN,D3DNN4_HUMAN	UPI0000127866	.	tolerated(0.39)	benign(0.079)	2/4	.	Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-TM,Pfam_domain:PF00135,hmmpanther:PTHR11559:SF154,hmmpanther:PTHR11559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACCAAAAGAGA	.	4	ESCA
CPN2	0	.	GRCh37	3	194061764	194061764	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*30G>A	.	.	ENST00000323830	2/2	37	19	17	31	31	0	CPN2,3_prime_UTR_variant,,ENST00000323830,;CPN2,3_prime_UTR_variant,,ENST00000429275,;	T	ENSG00000178772	ENST00000323830	Transcript	3_prime_UTR_variant	1758	.	.	.	.	.	.	.	-1	CPN2	HGNC	2313	protein_coding	YES	CCDS33920.1	ENSP00000319464	CPN2_HUMAN	.	UPI0001AE76B7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGCCCCCTT	.	5	ESCA
SCAP	0	.	GRCh37	3	47469124	47469124	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444G>A	p.%3D	p.L148L	ENST00000265565	5/23	28	24	4	43	43	0	SCAP,synonymous_variant,p.%3D,ENST00000265565,;SCAP,intron_variant,,ENST00000545718,;SCAP,intron_variant,,ENST00000441517,;SCAP,downstream_gene_variant,,ENST00000416847,;SCAP,downstream_gene_variant,,ENST00000495603,;SCAP,upstream_gene_variant,,ENST00000468965,;SCAP,downstream_gene_variant,,ENST00000420588,;SCAP,intron_variant,,ENST00000428413,;SCAP,intron_variant,,ENST00000416208,;SCAP,intron_variant,,ENST00000320017,;SCAP,upstream_gene_variant,,ENST00000494938,;SCAP,downstream_gene_variant,,ENST00000487942,;	T	ENSG00000114650	ENST00000265565	Transcript	synonymous_variant	857	444	148	L	ctG/ctA	.	.	.	-1	SCAP	HGNC	30634	protein_coding	YES	CCDS2755.2	ENSP00000265565	SCAP_HUMAN	D6RA39_HUMAN,C9JQ35_HUMAN	UPI0000135624	.	.	.	5/23	.	hmmpanther:PTHR10796:SF53,hmmpanther:PTHR10796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	ACTTGCAGACA	.	2	ESCA
CRYBG3	0	.	GRCh37	3	97592034	97592034	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1996C>G	p.Leu666Val	p.L666V	ENST00000419587	4/4	19	15	4	20	20	0	CRYBG3,missense_variant,p.Leu666Val,ENST00000419587,;CRYBG3,upstream_gene_variant,,ENST00000182096,;	G	ENSG00000233280	ENST00000419587	Transcript	missense_variant	2163	1996	666	L/V	Ctg/Gtg	.	.	.	1	CRYBG3	Uniprot_gn	34427	protein_coding	YES	.	ENSP00000391551	.	B4DLE8_HUMAN	UPI00017A74DC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGCTGAGC	.	5	ESCA
CASP6	0	.	GRCh37	4	110624546	110624546	+	Silent	SNP	G	G	A	rs777518317	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6C>T	p.%3D	p.S2S	ENST00000265164	1/7	32	16	15	33	33	0	CASP6,synonymous_variant,p.%3D,ENST00000265164,;CASP6,synonymous_variant,p.%3D,ENST00000352981,;CASP6,synonymous_variant,p.%3D,ENST00000505486,;CASP6,upstream_gene_variant,,ENST00000503684,;	A	ENSG00000138794	ENST00000265164	Transcript	synonymous_variant	84	6	2	S	agC/agT	rs777518317	.	.	-1	CASP6	HGNC	1507	protein_coding	YES	CCDS3684.1	ENSP00000265164	CASP6_HUMAN	D6RHU3_HUMAN	UPI00000622E4	.	.	.	1/7	.	hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF144	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGAGCTCAT	byFrequency	5	ESCA
KIAA1109	0	.	GRCh37	4	123258086	123258086	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12061A>G	p.Met4021Val	p.M4021V	ENST00000264501	71/86	33	13	20	31	31	0	KIAA1109,missense_variant,p.Met397Val,ENST00000306802,;KIAA1109,missense_variant,p.Met690Val,ENST00000438707,;KIAA1109,missense_variant,p.Met4021Val,ENST00000264501,;KIAA1109,missense_variant,p.Met4021Val,ENST00000388738,;KIAA1109,upstream_gene_variant,,ENST00000442707,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000483357,;KIAA1109,downstream_gene_variant,,ENST00000480651,;	G	ENSG00000138688	ENST00000264501	Transcript	missense_variant	12434	12061	4021	M/V	Atg/Gtg	.	.	.	1	KIAA1109	HGNC	26953	protein_coding	YES	CCDS43267.1	ENSP00000264501	K1109_HUMAN	B3KN93_HUMAN	UPI0000DD87B4	.	.	benign(0.004)	71/86	.	hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTATGGAA	.	5	ESCA
LRAT	0	.	GRCh37	4	155665738	155665738	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.260G>A	p.Arg87His	p.R87H	ENST00000336356	2/3	10	2	8	19	19	0	LRAT,missense_variant,p.Arg87His,ENST00000507827,;LRAT,missense_variant,p.Arg87His,ENST00000336356,;LRAT,downstream_gene_variant,,ENST00000502525,;LRAT,intron_variant,,ENST00000499392,;LRAT,upstream_gene_variant,,ENST00000502474,;LRAT,upstream_gene_variant,,ENST00000510919,;LRAT,non_coding_transcript_exon_variant,,ENST00000510733,;	A	ENSG00000121207	ENST00000336356	Transcript	missense_variant	513	260	87	R/H	cGc/cAc	COSM4122971	.	.	1	LRAT	HGNC	6685	protein_coding	YES	CCDS3789.1	ENSP00000337224	LRAT_HUMAN	D6RC94_HUMAN	UPI0000072711	.	tolerated(0.58)	benign(0.025)	2/3	.	hmmpanther:PTHR13943:SF1,hmmpanther:PTHR13943,Pfam_domain:PF04970	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	GGGGCGCACGC	.	3	ESCA
ATP8A1	0	.	GRCh37	4	42425657	42425657	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3189G>C	p.%3D	p.L1063L	ENST00000381668	34/37	20	5	15	27	27	0	ATP8A1,synonymous_variant,p.%3D,ENST00000381668,;ATP8A1,synonymous_variant,p.%3D,ENST00000264449,;ATP8A1,3_prime_UTR_variant,,ENST00000506602,;ATP8A1,3_prime_UTR_variant,,ENST00000514372,;	G	ENSG00000124406	ENST00000381668	Transcript	synonymous_variant	3421	3189	1063	L	ctG/ctC	.	.	.	-1	ATP8A1	HGNC	13531	protein_coding	YES	CCDS3466.1	ENSP00000371084	AT8A1_HUMAN	H0YAJ4_HUMAN	UPI0000125063	.	.	.	34/37	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF56,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAGCAGAGA	.	5	ESCA
COX7B2	0	.	GRCh37	4	46736923	46736923	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*41A>G	.	.	ENST00000396533	4/4	51	20	30	76	76	0	COX7B2,3_prime_UTR_variant,,ENST00000543208,;COX7B2,3_prime_UTR_variant,,ENST00000355591,;COX7B2,3_prime_UTR_variant,,ENST00000302930,;COX7B2,3_prime_UTR_variant,,ENST00000396533,;COX7B2,downstream_gene_variant,,ENST00000505102,;	C	ENSG00000170516	ENST00000396533	Transcript	3_prime_UTR_variant	538	.	.	.	.	.	.	.	-1	COX7B2	HGNC	24381	protein_coding	YES	CCDS3472.2	ENSP00000379784	CX7B2_HUMAN	D6R9N1_HUMAN	UPI000005034B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGTTGGTTT	.	5	ESCA
TMPRSS11A	0	.	GRCh37	4	68812229	68812229	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72T>C	p.%3D	p.I24I	ENST00000334830	2/10	12	8	4	31	31	0	TMPRSS11A,synonymous_variant,p.%3D,ENST00000508048,;TMPRSS11A,synonymous_variant,p.%3D,ENST00000334830,;TMPRSS11A,synonymous_variant,p.%3D,ENST00000513536,;TMPRSS11A,synonymous_variant,p.%3D,ENST00000396188,;UBA6-AS1,intron_variant,,ENST00000500538,;	G	ENSG00000187054	ENST00000334830	Transcript	synonymous_variant	819	72	24	I	atT/atC	.	.	.	-1	TMPRSS11A	HGNC	27954	protein_coding	YES	CCDS3519.1	ENSP00000334611	TM11A_HUMAN	.	UPI0000457217	.	.	.	2/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24256:SF37,hmmpanther:PTHR24256,PIRSF_domain:PIRSF037941	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AACACAATGAG	.	3	ESCA
PPP2CA	0	.	GRCh37	5	133537546	133537546	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479A>G	p.Asp160Gly	p.D160G	ENST00000481195	3/7	51	35	15	40	40	0	PPP2CA,missense_variant,p.Asp160Gly,ENST00000481195,;PPP2CA,missense_variant,p.Asp95Gly,ENST00000522385,;CTD-2410N18.5,intron_variant,,ENST00000519718,;CDKL3,downstream_gene_variant,,ENST00000609383,;CDKL3,downstream_gene_variant,,ENST00000609654,;PPP2CA,downstream_gene_variant,,ENST00000523082,;PPP2CA,downstream_gene_variant,,ENST00000231504,;CTD-2410N18.4,downstream_gene_variant,,ENST00000518409,;PPP2CA,non_coding_transcript_exon_variant,,ENST00000495833,;PPP2CA,upstream_gene_variant,,ENST00000472253,;CTD-2410N18.4,downstream_gene_variant,,ENST00000520515,;	C	ENSG00000113575	ENST00000481195	Transcript	missense_variant	760	479	160	D/G	gAt/gGt	.	.	.	-1	PPP2CA	HGNC	9299	protein_coding	YES	CCDS4173.1	ENSP00000418447	PP2AA_HUMAN	E5RHP4_HUMAN,B3KUN1_HUMAN,B3KQ51_HUMAN	UPI0000000C15	.	tolerated(0.05)	benign(0.035)	3/7	.	hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF216,Gene3D:3.60.21.10,Pfam_domain:PF00149,SMART_domains:SM00156,Superfamily_domains:SSF56300,Prints_domain:PR00114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCATCCACC	.	5	ESCA
DNAH5	0	.	GRCh37	5	13700767	13700767	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13705A>T	p.Ile4569Phe	p.I4569F	ENST00000265104	78/79	25	17	7	21	21	0	DNAH5,missense_variant,p.Ile4569Phe,ENST00000265104,;	A	ENSG00000039139	ENST00000265104	Transcript	missense_variant	13810	13705	4569	I/F	Att/Ttt	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	possibly_damaging(0.537)	78/79	.	Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAAATCCTTA	.	5	ESCA
SLC6A3	0	.	GRCh37	5	1393616	1393616	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1234C>T	.	.	ENST00000270349	15/15	101	61	39	80	80	0	SLC6A3,3_prime_UTR_variant,,ENST00000270349,;SLC6A3,downstream_gene_variant,,ENST00000512002,;SLC6A3,downstream_gene_variant,,ENST00000453492,;	A	ENSG00000142319	ENST00000270349	Transcript	3_prime_UTR_variant	3225	.	.	.	.	.	.	.	-1	SLC6A3	HGNC	11049	protein_coding	YES	CCDS3863.1	ENSP00000270349	SC6A3_HUMAN	Q6LC27_HUMAN,H0YBA7_HUMAN	UPI000013548F	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGAGAGAAA	.	5	ESCA
PCDHA1	0	.	GRCh37	5	140168121	140168121	+	Nonsense_Mutation	SNP	C	C	A	rs782539814	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2246C>A	p.Ser749Ter	p.S749*	ENST00000504120	1/4	55	34	21	57	57	0	PCDHA1,stop_gained,p.Ser749Ter,ENST00000504120,;PCDHA1,stop_gained,p.Ser749Ter,ENST00000378133,;PCDHA1,intron_variant,,ENST00000394633,;	A	ENSG00000204970	ENST00000504120	Transcript	stop_gained	2246	2246	749	S/*	tCg/tAg	rs782539814	.	.	1	PCDHA1	HGNC	8663	protein_coding	YES	CCDS54913.1	ENSP00000420840	PCDA1_HUMAN	.	UPI00001273C7	.	.	.	1/4	.	hmmpanther:PTHR24028:SF92,hmmpanther:PTHR24028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTCGAACT	.	5	ESCA
PPAP2A	0	.	GRCh37	5	54771153	54771153	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214-7176A>G	.	.	ENST00000264775	.	19	10	8	41	41	0	PPAP2A,missense_variant,p.Ile62Val,ENST00000307259,;PPAP2A,intron_variant,,ENST00000264775,;PPAP2A,intron_variant,,ENST00000515132,;PPAP2A,3_prime_UTR_variant,,ENST00000509667,;	C	ENSG00000067113	ENST00000264775	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PPAP2A	HGNC	9228	protein_coding	YES	CCDS34160.1	ENSP00000264775	LPP1_HUMAN	.	UPI0000150635	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTATTCCAC	.	5	ESCA
DDX4	0	.	GRCh37	5	55110956	55110956	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1943C>T	p.Ser648Leu	p.S648L	ENST00000505374	20/22	94	65	29	84	84	0	DDX4,missense_variant,p.Ser628Leu,ENST00000514278,;DDX4,missense_variant,p.Ser614Leu,ENST00000353507,;DDX4,missense_variant,p.Ser499Leu,ENST00000511853,;DDX4,missense_variant,p.Ser614Leu,ENST00000354991,;DDX4,missense_variant,p.Ser648Leu,ENST00000505374,;DDX4,3_prime_UTR_variant,,ENST00000503129,;	T	ENSG00000152670	ENST00000505374	Transcript	missense_variant	2035	1943	648	S/L	tCg/tTg	.	.	.	1	DDX4	HGNC	18700	protein_coding	YES	CCDS3969.1	ENSP00000424838	DDX4_HUMAN	D6RBL3_HUMAN,D6RAF5_HUMAN	UPI00001290D3	.	deleterious(0.02)	benign(0.409)	20/22	.	PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF168,hmmpanther:PTHR24031,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCGGATA	.	5	ESCA
CMYA5	0	.	GRCh37	5	79095254	79095254	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12025G>C	p.Val4009Leu	p.V4009L	ENST00000446378	13/13	68	44	24	74	74	0	CMYA5,missense_variant,p.Val4009Leu,ENST00000446378,;CTC-431G16.2,intron_variant,,ENST00000421252,;CMYA5,non_coding_transcript_exon_variant,,ENST00000506603,;	C	ENSG00000164309	ENST00000446378	Transcript	missense_variant	12056	12025	4009	V/L	Gtg/Ctg	.	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	probably_damaging(0.98)	13/13	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7,Pfam_domain:PF00622,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGAGTGGGC	.	5	ESCA
GPR98	0	.	GRCh37	5	89948338	89948338	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000405460	19/90	21	14	7	33	33	0	GPR98,missense_variant,p.Glu1198Lys,ENST00000405460,;GPR98,missense_variant,p.Glu787Lys,ENST00000504142,;	A	ENSG00000164199	ENST00000405460	Transcript	missense_variant	3688	3592	1198	E/K	Gaa/Aaa	.	.	.	1	GPR98	HGNC	17416	protein_coding	YES	CCDS47246.1	ENSP00000384582	GPR98_HUMAN	.	UPI00002127A7	.	.	possibly_damaging(0.636)	19/90	.	Superfamily_domains:SSF141072,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTCCTGAATTC	.	2	ESCA
ANKRD32	0	.	GRCh37	5	93990336	93990336	+	Missense_Mutation	SNP	A	A	G	rs759771028	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1034A>G	p.Lys345Arg	p.K345R	ENST00000265140	9/21	47	42	5	59	59	0	ANKRD32,missense_variant,p.Lys345Arg,ENST00000265140,;ANKRD32,splice_region_variant,,ENST00000508130,;ANKRD32,intron_variant,,ENST00000466957,;	G	ENSG00000133302	ENST00000265140	Transcript	missense_variant	1453	1034	345	K/R	aAa/aGa	rs759771028	.	.	1	ANKRD32	HGNC	25408	protein_coding	YES	CCDS4071.2	ENSP00000265140	ANR32_HUMAN	I6L9F1_HUMAN,D6RED9_HUMAN	UPI000066D9F9	.	tolerated(0.18)	possibly_damaging(0.467)	9/21	.	hmmpanther:PTHR13561,hmmpanther:PTHR13561:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGAAAGAAA	.	2	ESCA
CAST	0	.	GRCh37	5	96098065	96098065	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1798C>T	p.Arg600Cys	p.R600C	ENST00000395812	23/30	38	28	10	35	35	0	CAST,missense_variant,p.Arg604Cys,ENST00000508608,;CAST,missense_variant,p.Arg641Cys,ENST00000395813,;CAST,missense_variant,p.Arg544Cys,ENST00000511049,;CAST,missense_variant,p.Arg273Cys,ENST00000508579,;CAST,missense_variant,p.Arg641Cys,ENST00000508830,;CAST,missense_variant,p.Arg606Cys,ENST00000325674,;CAST,missense_variant,p.Arg619Cys,ENST00000510756,;CAST,missense_variant,p.Arg544Cys,ENST00000511782,;CAST,missense_variant,p.Arg558Cys,ENST00000510156,;CAST,missense_variant,p.Arg622Cys,ENST00000359176,;CAST,missense_variant,p.Arg600Cys,ENST00000395812,;CAST,missense_variant,p.Arg536Cys,ENST00000309190,;CAST,missense_variant,p.Arg523Cys,ENST00000509903,;CAST,missense_variant,p.Arg558Cys,ENST00000341926,;CAST,missense_variant,p.Arg316Cys,ENST00000510500,;CAST,missense_variant,p.Arg545Cys,ENST00000338252,;CAST,missense_variant,p.Arg310Cys,ENST00000437034,;CAST,missense_variant,p.Arg281Cys,ENST00000515663,;CAST,missense_variant,p.Arg486Cys,ENST00000504465,;ERAP1,3_prime_UTR_variant,,ENST00000296754,;CAST,non_coding_transcript_exon_variant,,ENST00000348386,;CAST,missense_variant,p.Arg301Cys,ENST00000484552,;CAST,missense_variant,p.Arg53Cys,ENST00000510098,;	T	ENSG00000153113	ENST00000395812	Transcript	missense_variant	1984	1798	600	R/C	Cgt/Tgt	.	.	.	1	CAST	HGNC	1515	protein_coding	YES	CCDS54882.1	ENSP00000379157	ICAL_HUMAN	E7EQ12_HUMAN	UPI0000DA4C59	.	deleterious(0)	possibly_damaging(0.84)	23/30	.	hmmpanther:PTHR10077,hmmpanther:PTHR10077:SF0,Pfam_domain:PF00748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCCGTGAT	.	5	ESCA
ROS1	0	.	GRCh37	6	117609724	117609724	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6975T>A	p.%3D	p.P2325P	ENST00000368508	43/43	72	55	17	103	103	0	ROS1,synonymous_variant,p.%3D,ENST00000368507,;ROS1,synonymous_variant,p.%3D,ENST00000368508,;	T	ENSG00000047936	ENST00000368508	Transcript	synonymous_variant	7174	6975	2325	P	ccT/ccA	.	.	.	-1	ROS1	HGNC	10261	protein_coding	YES	CCDS5116.1	ENSP00000357494	ROS1_HUMAN	.	UPI000013D467	.	.	.	43/43	.	hmmpanther:PTHR24416:SF304,hmmpanther:PTHR24416	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGAAGGGCA	.	5	ESCA
PLG	0	.	GRCh37	6	161152209	161152209	+	Silent	SNP	T	T	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1383T>G	p.%3D	p.V461V	ENST00000308192	11/19	38	30	8	51	51	0	PLG,synonymous_variant,p.%3D,ENST00000308192,;PLG,non_coding_transcript_exon_variant,,ENST00000297289,;PLG,non_coding_transcript_exon_variant,,ENST00000493435,;	G	ENSG00000122194	ENST00000308192	Transcript	synonymous_variant	1446	1383	461	V	gtT/gtG	.	.	.	1	PLG	HGNC	9071	protein_coding	YES	CCDS5279.1	ENSP00000308938	PLMN_HUMAN	Q9UMI2_HUMAN,Q68DS2_HUMAN,Q5TEH5_HUMAN,B4DPH4_HUMAN	UPI000000D8B8	.	.	.	11/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24259,hmmpanther:PTHR24259:SF70,PIRSF_domain:PIRSF001150,Superfamily_domains:SSF57440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGTTGTAGC	.	5	ESCA
ERMARD	0	.	GRCh37	6	170154006	170154006	+	Missense_Mutation	SNP	A	A	G	rs758842196	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53A>G	p.Tyr18Cys	p.Y18C	ENST00000366773	2/18	36	18	18	52	52	0	ERMARD,missense_variant,p.Tyr18Cys,ENST00000586341,;ERMARD,missense_variant,p.Tyr18Cys,ENST00000366773,;ERMARD,missense_variant,p.Tyr18Cys,ENST00000418781,;ERMARD,missense_variant,p.Tyr18Cys,ENST00000366772,;ERMARD,5_prime_UTR_variant,,ENST00000592745,;ERMARD,5_prime_UTR_variant,,ENST00000588437,;ERMARD,5_prime_UTR_variant,,ENST00000592367,;ERMARD,5_prime_UTR_variant,,ENST00000588451,;ERMARD,intron_variant,,ENST00000392095,;ERMARD,intron_variant,,ENST00000590711,;TCTE3,upstream_gene_variant,,ENST00000366774,;ERMARD,missense_variant,p.Tyr18Cys,ENST00000592315,;ERMARD,missense_variant,p.Tyr3Cys,ENST00000590017,;ERMARD,non_coding_transcript_exon_variant,,ENST00000592580,;	G	ENSG00000130023	ENST00000366773	Transcript	missense_variant	86	53	18	Y/C	tAt/tGt	rs758842196	.	.	1	ERMARD	HGNC	21056	protein_coding	YES	CCDS34576.1	ENSP00000355735	EMARD_HUMAN	K7EMW5_HUMAN,K7EME8_HUMAN,F8WAF1_HUMAN	UPI000020DF6E	.	deleterious(0)	probably_damaging(0.935)	2/18	.	hmmpanther:PTHR31701,hmmpanther:PTHR31701:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGTATGATA	.	5	ESCA
KIF13A	0	.	GRCh37	6	17781431	17781431	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3646A>G	p.Ile1216Val	p.I1216V	ENST00000259711	30/39	40	34	6	37	37	0	KIF13A,missense_variant,p.Ile1203Val,ENST00000378814,;KIF13A,missense_variant,p.Ile220Val,ENST00000502297,;KIF13A,missense_variant,p.Ile1216Val,ENST00000259711,;KIF13A,missense_variant,p.Ile1216Val,ENST00000378826,;KIF13A,missense_variant,p.Ile610Val,ENST00000358380,;KIF13A,missense_variant,p.Ile214Val,ENST00000506044,;KIF13A,missense_variant,p.Ile1203Val,ENST00000378843,;KIF13A,missense_variant,p.Ile1216Val,ENST00000378816,;KIF13A,downstream_gene_variant,,ENST00000514714,;	C	ENSG00000137177	ENST00000259711	Transcript	missense_variant	3752	3646	1216	I/V	Atc/Gtc	.	.	.	-1	KIF13A	HGNC	14566	protein_coding	YES	CCDS47381.1	ENSP00000259711	KI13A_HUMAN	.	UPI0000E20DA3	.	deleterious(0.01)	probably_damaging(0.996)	30/39	.	Pfam_domain:PF12473,hmmpanther:PTHR24115:SF289,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATGATGGGCA	.	4	ESCA
TRIM38	0	.	GRCh37	6	25983525	25983525	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1008C>G	p.%3D	p.V336V	ENST00000357085	8/8	76	53	23	110	110	0	TRIM38,synonymous_variant,p.%3D,ENST00000357085,;TRIM38,synonymous_variant,p.%3D,ENST00000349458,;U91328.21,downstream_gene_variant,,ENST00000608931,;	G	ENSG00000112343	ENST00000357085	Transcript	synonymous_variant	1484	1008	336	V	gtC/gtG	.	.	.	1	TRIM38	HGNC	10059	protein_coding	YES	CCDS4568.1	ENSP00000349596	TRI38_HUMAN	.	UPI000013431A	.	.	.	8/8	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF47,hmmpanther:PTHR24103,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTCTTGGG	.	5	ESCA
ZNF165	0	.	GRCh37	6	28056940	28056954	+	In_Frame_Del	DEL	AGCTCAGATCTTACT	AGCTCAGATCTTACT	-	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	AGCTCAGATCTTACT	AGCTCAGATCTTACT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1152_1166delCTCAGATCTTACTAG	p.Ser384_Thr388del	p.S384_T388del	ENST00000377325	4/4	40	24	16	48	48	0	ZNF165,inframe_deletion,p.Ser384_Thr388del,ENST00000377325,;ZSCAN12P1,upstream_gene_variant,,ENST00000529104,;ZSCAN12P1,upstream_gene_variant,,ENST00000406489,;	-	ENSG00000197279	ENST00000377325	Transcript	inframe_deletion	1706-1720	1150-1164	384-388	SSDLT/-	AGCTCAGATCTTACT/-	.	.	.	1	ZNF165	HGNC	12953	protein_coding	YES	CCDS4643.1	ENSP00000366542	ZN165_HUMAN	Q53Z40_HUMAN	UPI000000129B	.	.	.	4/4	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF61,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCAGAGAGCTCAGATCTTACTAGACA	.	3	ESCA
RGL2	0	.	GRCh37	6	33264024	33264024	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549C>G	p.Asp183Glu	p.D183E	ENST00000497454	6/18	38	21	17	52	52	0	RGL2,missense_variant,p.Asp101Glu,ENST00000444031,;RGL2,missense_variant,p.Asp183Glu,ENST00000497454,;PFDN6,intron_variant,,ENST00000463584,;TAPBP,downstream_gene_variant,,ENST00000434618,;RGL2,downstream_gene_variant,,ENST00000425946,;RGL2,non_coding_transcript_exon_variant,,ENST00000437840,;RGL2,non_coding_transcript_exon_variant,,ENST00000485077,;RGL2,intron_variant,,ENST00000491168,;RGL2,upstream_gene_variant,,ENST00000471319,;RGL2,non_coding_transcript_exon_variant,,ENST00000478610,;RGL2,non_coding_transcript_exon_variant,,ENST00000460988,;RGL2,non_coding_transcript_exon_variant,,ENST00000494550,;RGL2,non_coding_transcript_exon_variant,,ENST00000483151,;RGL2,upstream_gene_variant,,ENST00000476616,;	C	ENSG00000237441	ENST00000497454	Transcript	missense_variant	1045	549	183	D/E	gaC/gaG	.	.	.	-1	RGL2	HGNC	9769	protein_coding	YES	CCDS4774.1	ENSP00000420211	RGL2_HUMAN	Q9BSI0_HUMAN,Q54AJ0_HUMAN,A2AB89_HUMAN	UPI0000001621	.	tolerated(1)	probably_damaging(0.937)	6/18	.	PROSITE_profiles:PS50212,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF159,Gene3D:2ii0A01,Pfam_domain:PF00618,SMART_domains:SM00229,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGGTCAAG	.	5	ESCA
KIFC1	0	.	GRCh37	6	33367865	33367865	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250+1701T>C	.	.	ENST00000428849	.	32	25	7	36	36	0	KIFC1,intron_variant,,ENST00000450504,;KIFC1,intron_variant,,ENST00000428849,;KIFC1,upstream_gene_variant,,ENST00000486695,;RPL12P1,non_coding_transcript_exon_variant,,ENST00000374520,;	C	ENSG00000237649	ENST00000428849	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KIFC1	HGNC	6389	protein_coding	YES	CCDS34430.1	ENSP00000393963	KIFC1_HUMAN	.	UPI000012DDB8	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACTGTTGA	.	5	ESCA
ITPR3	0	.	GRCh37	6	33663775	33663775	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*218T>C	.	.	ENST00000374316	59/59	34	20	14	40	40	0	ITPR3,3_prime_UTR_variant,,ENST00000374316,;ITPR3,3_prime_UTR_variant,,ENST00000605930,;UQCC2,intron_variant,,ENST00000374231,;UQCC2,downstream_gene_variant,,ENST00000374214,;UQCC2,downstream_gene_variant,,ENST00000607484,;SBP1,upstream_gene_variant,,ENST00000594414,;MIR3934,upstream_gene_variant,,ENST00000579806,;UQCC2,non_coding_transcript_exon_variant,,ENST00000606961,;	C	ENSG00000096433	ENST00000374316	Transcript	3_prime_UTR_variant	9294	.	.	.	.	.	.	.	1	ITPR3	HGNC	6182	protein_coding	YES	CCDS4783.1	ENSP00000363435	ITPR3_HUMAN	A6H8K3_HUMAN	UPI000013CB74	.	.	.	59/59	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGTTCACT	.	5	ESCA
GLTSCR1L	0	.	GRCh37	6	42824919	42824919	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2199G>T	p.%3D	p.L733L	ENST00000314073	10/13	37	22	15	25	25	0	GLTSCR1L,synonymous_variant,p.%3D,ENST00000394168,;GLTSCR1L,synonymous_variant,p.%3D,ENST00000314073,;	T	ENSG00000112624	ENST00000314073	Transcript	synonymous_variant	2375	2199	733	L	ctG/ctT	.	.	.	1	GLTSCR1L	HGNC	21111	protein_coding	YES	CCDS34451.1	ENSP00000313933	GSC1L_HUMAN	.	UPI0000161939	.	.	.	10/13	.	hmmpanther:PTHR15572:SF2,hmmpanther:PTHR15572,Pfam_domain:PF15249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTGCTCTC	.	5	ESCA
GLTSCR1L	0	.	GRCh37	6	42824920	42824920	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2200C>T	p.Leu734Phe	p.L734F	ENST00000314073	10/13	37	21	15	25	25	0	GLTSCR1L,missense_variant,p.Leu734Phe,ENST00000394168,;GLTSCR1L,missense_variant,p.Leu734Phe,ENST00000314073,;	T	ENSG00000112624	ENST00000314073	Transcript	missense_variant	2376	2200	734	L/F	Ctc/Ttc	.	.	.	1	GLTSCR1L	HGNC	21111	protein_coding	YES	CCDS34451.1	ENSP00000313933	GSC1L_HUMAN	.	UPI0000161939	.	deleterious(0)	probably_damaging(0.91)	10/13	.	hmmpanther:PTHR15572:SF2,hmmpanther:PTHR15572,Pfam_domain:PF15249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGCTCTCC	.	5	ESCA
SLC29A1	0	.	GRCh37	6	44199101	44199101	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767G>T	p.Gly256Val	p.G256V	ENST00000393841	10/14	69	41	28	120	120	0	SLC29A1,missense_variant,p.Gly256Val,ENST00000371740,;SLC29A1,missense_variant,p.Gly256Val,ENST00000371731,;SLC29A1,missense_variant,p.Gly335Val,ENST00000313248,;SLC29A1,missense_variant,p.Gly256Val,ENST00000371713,;SLC29A1,missense_variant,p.Gly256Val,ENST00000371755,;SLC29A1,missense_variant,p.Gly256Val,ENST00000393844,;SLC29A1,missense_variant,p.Gly256Val,ENST00000371724,;SLC29A1,missense_variant,p.Gly256Val,ENST00000393841,;SLC29A1,missense_variant,p.Gly256Val,ENST00000427851,;SLC29A1,missense_variant,p.Gly256Val,ENST00000371708,;SLC29A1,splice_region_variant,,ENST00000472176,;	T	ENSG00000112759	ENST00000393841	Transcript	missense_variant	1258	767	256	G/V	gGa/gTa	.	.	.	1	SLC29A1	HGNC	11003	protein_coding	YES	CCDS4908.1	ENSP00000377424	S29A1_HUMAN	C8KHU2_HUMAN,C8KHU1_HUMAN	UPI0000001BCC	.	tolerated(0.08)	possibly_damaging(0.869)	10/14	.	hmmpanther:PTHR10332,hmmpanther:PTHR10332:SF9,Pfam_domain:PF01733,TIGRFAM_domain:TIGR00939,PIRSF_domain:PIRSF016379	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCAGGAGAGG	.	5	ESCA
FAM83B	0	.	GRCh37	6	54735248	54735248	+	Silent	SNP	C	C	G	rs756319912	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204C>G	p.%3D	p.V68V	ENST00000306858	2/5	24	11	12	46	46	0	FAM83B,synonymous_variant,p.%3D,ENST00000306858,;	G	ENSG00000168143	ENST00000306858	Transcript	synonymous_variant	320	204	68	V	gtC/gtG	rs756319912	.	.	1	FAM83B	HGNC	21357	protein_coding	YES	CCDS34479.1	ENSP00000304078	FA83B_HUMAN	.	UPI00001D81EC	.	.	.	2/5	.	hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF4,Pfam_domain:PF07894	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGTCCAGAA	.	5	ESCA
KCNQ5	0	.	GRCh37	6	73904443	73904443	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2162T>C	p.Phe721Ser	p.F721S	ENST00000342056	15/15	16	12	4	31	31	0	KCNQ5,missense_variant,p.Phe721Ser,ENST00000342056,;KCNQ5,missense_variant,p.Phe712Ser,ENST00000402622,;KCNQ5,missense_variant,p.Phe702Ser,ENST00000355194,;KCNQ5,missense_variant,p.Phe702Ser,ENST00000370398,;KCNQ5,missense_variant,p.Phe592Ser,ENST00000414165,;KCNQ5,missense_variant,p.Phe703Ser,ENST00000355635,;KCNQ5,missense_variant,p.Phe693Ser,ENST00000403813,;	C	ENSG00000185760	ENST00000342056	Transcript	missense_variant	2560	2162	721	F/S	tTc/tCc	.	.	.	1	KCNQ5	HGNC	6299	protein_coding	YES	CCDS55034.1	ENSP00000345055	.	A6PVT6_HUMAN	UPI000155D644	.	tolerated(0.4)	benign(0.008)	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A704V|c.2111C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTTCTACG	.	5	ESCA
ASB15	0	.	GRCh37	7	123264623	123264623	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452C>A	p.Ala151Asp	p.A151D	ENST00000451558	10/14	18	3	15	34	34	0	ASB15,missense_variant,p.Ala151Asp,ENST00000275699,;ASB15,missense_variant,p.Ala151Asp,ENST00000540573,;ASB15,missense_variant,p.Ala151Asp,ENST00000434204,;ASB15,missense_variant,p.Ala151Asp,ENST00000451558,;ASB15,missense_variant,p.Ala151Asp,ENST00000451215,;ASB15,missense_variant,p.Ala151Asp,ENST00000447789,;RP11-390E23.3,non_coding_transcript_exon_variant,,ENST00000429396,;RP11-390E23.3,non_coding_transcript_exon_variant,,ENST00000418409,;RP11-390E23.3,non_coding_transcript_exon_variant,,ENST00000422401,;RP11-390E23.3,non_coding_transcript_exon_variant,,ENST00000451016,;RP11-390E23.3,intron_variant,,ENST00000440504,;	A	ENSG00000146809	ENST00000451558	Transcript	missense_variant	973	452	151	A/D	gCt/gAt	.	.	.	1	ASB15	HGNC	19767	protein_coding	YES	CCDS34742.1	ENSP00000397655	ASB15_HUMAN	C9J956_HUMAN	UPI000022D0FF	.	deleterious(0)	probably_damaging(0.983)	10/14	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24188:SF0,hmmpanther:PTHR24188,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAAGCTGTGA	.	5	ESCA
TAS2R5	0	.	GRCh37	7	141491086	141491086	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*25A>G	.	.	ENST00000247883	1/1	13	9	3	25	25	0	TAS2R5,3_prime_UTR_variant,,ENST00000247883,;SSBP1,downstream_gene_variant,,ENST00000465582,;TAS2R6,downstream_gene_variant,,ENST00000605022,;	G	ENSG00000127366	ENST00000247883	Transcript	3_prime_UTR_variant	1070	.	.	.	.	.	.	.	1	TAS2R5	HGNC	14912	protein_coding	YES	CCDS5869.1	ENSP00000247883	TA2R5_HUMAN	A4D1U0_HUMAN,Q50KW4_HUMAN	UPI0000038B0D	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TCAGGACACTC	.	4	ESCA
MGAM	0	.	GRCh37	7	141799444	141799444	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5093A>G	p.Lys1698Arg	p.K1698R	ENST00000549489	44/48	79	35	44	96	96	0	MGAM,missense_variant,p.Lys2594Arg,ENST00000475668,;MGAM,missense_variant,p.Lys1698Arg,ENST00000549489,;MGAM,downstream_gene_variant,,ENST00000485078,;	G	ENSG00000257335	ENST00000549489	Transcript	missense_variant	5188	5093	1698	K/R	aAg/aGg	.	.	.	1	MGAM	HGNC	7043	protein_coding	YES	CCDS47727.1	ENSP00000447378	MGA_HUMAN	Q8TE25_HUMAN,E9PEQ5_HUMAN,E7EW87_HUMAN	UPI000183CB7B	.	tolerated(0.6)	benign(0.003)	44/48	.	Superfamily_domains:SSF51011,Pfam_domain:PF01055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAAGACCT	.	5	ESCA
CTAGE6	0	.	GRCh37	7	143453646	143453646	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1106A>G	p.Glu369Gly	p.E369G	ENST00000470691	1/1	205	192	12	362	362	0	CTAGE6,missense_variant,p.Glu369Gly,ENST00000470691,;RNU6-267P,upstream_gene_variant,,ENST00000516714,;RP11-61L23.2,intron_variant,,ENST00000450076,;FAM115D,intron_variant,,ENST00000456362,;RP11-61L23.2,intron_variant,,ENST00000422705,;RP11-61L23.2,intron_variant,,ENST00000427403,;	C	ENSG00000271321	ENST00000470691	Transcript	missense_variant	1144	1106	369	E/G	gAa/gGa	.	.	.	-1	CTAGE6	HGNC	28644	protein_coding	YES	CCDS64790.1	ENSP00000474388	CTGE6_HUMAN	.	UPI0000199826	.	deleterious(0.01)	probably_damaging(0.929)	1/1	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTTTCTGAT	.	2	ESCA
ZNF467	0	.	GRCh37	7	149468160	149468160	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39C>G	.	.	ENST00000302017	2/5	22	15	7	27	27	0	ZNF467,5_prime_UTR_variant,,ENST00000302017,;ZNF467,5_prime_UTR_variant,,ENST00000484747,;SSPO,upstream_gene_variant,,ENST00000378016,;SSPO,upstream_gene_variant,,ENST00000262089,;	C	ENSG00000181444	ENST00000302017	Transcript	5_prime_UTR_variant	376	.	.	.	.	.	.	.	-1	ZNF467	HGNC	23154	protein_coding	YES	CCDS5899.1	ENSP00000304769	ZN467_HUMAN	.	UPI0000160B41	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAGAACCT	.	5	ESCA
CHST12	0	.	GRCh37	7	2473654	2473655	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*137dupT	.	.	ENST00000258711	2/2	55	43	12	34	34	0	CHST12,3_prime_UTR_variant,,ENST00000258711,;CHST12,downstream_gene_variant,,ENST00000432336,;AC004840.9,upstream_gene_variant,,ENST00000313156,;	T	ENSG00000136213	ENST00000258711	Transcript	3_prime_UTR_variant	1515-1516	.	.	.	.	.	.	.	1	CHST12	HGNC	17423	protein_coding	YES	CCDS5333.1	ENSP00000258711	CHSTC_HUMAN	C9J991_HUMAN	UPI000004C65C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCGATATTGTT	.	3	ESCA
GARS	0	.	GRCh37	7	30661051	30661051	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1402G>T	p.Asp468Tyr	p.D468Y	ENST00000389266	11/17	42	29	13	39	39	0	GARS,missense_variant,p.Asp468Tyr,ENST00000389266,;GARS,non_coding_transcript_exon_variant,,ENST00000478124,;GARS,non_coding_transcript_exon_variant,,ENST00000484093,;GARS,upstream_gene_variant,,ENST00000470392,;GARS,upstream_gene_variant,,ENST00000444666,;	T	ENSG00000106105	ENST00000389266	Transcript	missense_variant	1643	1402	468	D/Y	Gac/Tac	COSM1731138	.	.	1	GARS	HGNC	4162	protein_coding	YES	CCDS43564.1	ENSP00000373918	SYG_HUMAN	Q75MN1_HUMAN	UPI00005A885C	.	deleterious(0)	probably_damaging(0.923)	11/17	.	Superfamily_domains:SSF55681,Gene3D:3.30.930.10,TIGRFAM_domain:TIGR00389,hmmpanther:PTHR10745,hmmpanther:PTHR10745:SF0,PROSITE_profiles:PS50862	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTATGACCTC	.	5	ESCA
ADCYAP1R1	0	.	GRCh37	7	31121353	31121353	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312C>G	p.Asn104Lys	p.N104K	ENST00000396211	5/16	93	66	27	59	59	0	ADCYAP1R1,missense_variant,p.Asn104Lys,ENST00000409489,;ADCYAP1R1,missense_variant,p.Asn104Lys,ENST00000304166,;ADCYAP1R1,missense_variant,p.Asn104Lys,ENST00000396211,;ADCYAP1R1,intron_variant,,ENST00000409363,;ADCYAP1R1,downstream_gene_variant,,ENST00000431811,;	G	ENSG00000078549	ENST00000396211	Transcript	missense_variant	383	312	104	N/K	aaC/aaG	.	.	.	1	ADCYAP1R1	HGNC	242	protein_coding	YES	CCDS56480.1	ENSP00000379514	PACR_HUMAN	Q6S991_HUMAN,Q6RKA2_HUMAN,C9JVH3_HUMAN	UPI0000DA58BA	.	tolerated(0.64)	benign(0.003)	5/16	.	PROSITE_profiles:PS50227,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF228,Pfam_domain:PF02793,SMART_domains:SM00008,Superfamily_domains:SSF111418,Prints_domain:PR01156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAACTCCTT	.	5	ESCA
FAM183B	0	.	GRCh37	7	38725392	38725392	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214C>A	p.His72Asn	p.H72N	ENST00000409072	2/2	78	49	28	74	74	0	FAM183B,missense_variant,p.His72Asn,ENST00000409072,;	T	ENSG00000164556	ENST00000409072	Transcript	missense_variant	1149	214	72	H/N	Cac/Aac	.	.	.	-1	FAM183B	HGNC	34511	protein_coding	YES	.	ENSP00000386657	F183B_HUMAN	.	UPI000020EE1E	.	deleterious(0.01)	possibly_damaging(0.873)	2/2	.	Pfam_domain:PF14886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGTGAATGA	.	5	ESCA
ZNF727	0	.	GRCh37	7	63537695	63537695	+	Missense_Mutation	SNP	G	G	A	rs372078057	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268G>A	p.Asp90Asn	p.D90N	ENST00000550760	4/4	33	21	12	22	22	0	ZNF727,missense_variant,p.Asp90Asn,ENST00000550760,;RP11-3N2.13,non_coding_transcript_exon_variant,,ENST00000445978,;RP11-3N2.13,non_coding_transcript_exon_variant,,ENST00000456806,;RP11-3N2.13,upstream_gene_variant,,ENST00000430271,;	A	ENSG00000257482	ENST00000550760	Transcript	missense_variant	447	268	90	D/N	Gac/Aac	rs372078057	.	.	1	ZNF727	HGNC	22785	protein_coding	YES	CCDS55113.1	ENSP00000447987	ZN727_HUMAN	.	UPI0001A23134	.	tolerated(0.42)	probably_damaging(0.959)	4/4	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF79	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0022	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGCACGACATA	byCluster|by1000G	4	ESCA
RPA3	0	.	GRCh37	7	7713025	7713025	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-758+12436G>T	.	.	ENST00000223129	.	106	76	29	90	90	0	RPA3,intron_variant,,ENST00000223129,;RPA3-AS1,non_coding_transcript_exon_variant,,ENST00000469183,;RPA3-AS1,non_coding_transcript_exon_variant,,ENST00000482067,;RPA3-AS1,non_coding_transcript_exon_variant,,ENST00000463725,;RPA3-AS1,non_coding_transcript_exon_variant,,ENST00000493246,;RPA3-AS1,non_coding_transcript_exon_variant,,ENST00000471760,;RPA3-AS1,non_coding_transcript_exon_variant,,ENST00000468567,;	A	ENSG00000106399	ENST00000223129	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RPA3	HGNC	10291	protein_coding	YES	CCDS5356.1	ENSP00000223129	RFA3_HUMAN	B5MC59_HUMAN,A4D105_HUMAN	UPI00001122E6	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGCCTCCGG	.	5	ESCA
PCLO	0	.	GRCh37	7	82580258	82580258	+	Missense_Mutation	SNP	A	A	C	rs750254988	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9646T>G	p.Leu3216Val	p.L3216V	ENST00000333891	6/25	33	19	13	32	32	0	PCLO,missense_variant,p.Leu3216Val,ENST00000333891,;PCLO,missense_variant,p.Leu3216Val,ENST00000423517,;PCLO,upstream_gene_variant,,ENST00000437081,;	C	ENSG00000186472	ENST00000333891	Transcript	missense_variant	9984	9646	3216	L/V	Ttg/Gtg	rs750254988	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	6/25	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCAAGTCTA	.	5	ESCA
SEMA3D	0	.	GRCh37	7	84670056	84670056	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.979G>C	p.Asp327His	p.D327H	ENST00000284136	9/17	35	27	8	46	46	0	SEMA3D,missense_variant,p.Asp327His,ENST00000284136,;SEMA3D,splice_region_variant,,ENST00000484038,;SEMA3D,downstream_gene_variant,,ENST00000463315,;	G	ENSG00000153993	ENST00000284136	Transcript	missense_variant	1023	979	327	D/H	Gat/Cat	.	.	.	-1	SEMA3D	HGNC	10726	protein_coding	YES	CCDS34676.1	ENSP00000284136	SEM3D_HUMAN	.	UPI0000135A66	.	deleterious(0)	probably_damaging(1)	9/17	.	Superfamily_domains:SSF101912,SMART_domains:SM00630,Gene3D:2.130.10.10,Pfam_domain:PF01403,hmmpanther:PTHR11036:SF36,hmmpanther:PTHR11036,PROSITE_profiles:PS51004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AATATCTTCTA	.	4	ESCA
ERVW-1	0	.	GRCh37	7	92099372	92099372	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.324C>T	p.%3D	p.Y108Y	ENST00000493463	1/1	44	29	14	31	31	0	ERVW-1,synonymous_variant,p.%3D,ENST00000603053,;ERVW-1,synonymous_variant,p.%3D,ENST00000493463,;AC007566.10,intron_variant,,ENST00000427458,;ERVW-1,intron_variant,,ENST00000603704,;ERVW-1,intron_variant,,ENST00000604270,;ERVW-1,downstream_gene_variant,,ENST00000603252,;	A	ENSG00000242950	ENST00000493463	Transcript	synonymous_variant	1248	324	108	Y	taC/taT	.	.	.	-1	ERVW-1	HGNC	13525	protein_coding	YES	CCDS5626.1	ENSP00000419945	ENW1_HUMAN	Q9UQF1_HUMAN,Q96TB5_HUMAN,D0EYG5_HUMAN	UPI00000389BB	.	.	.	1/1	.	Pfam_domain:PF00429	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAGTAAGT	.	5	ESCA
FAM133B	0	.	GRCh37	7	92206427	92206427	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455C>T	p.Ser152Leu	p.S152L	ENST00000445716	7/11	45	23	22	23	23	0	FAM133B,missense_variant,p.Ser152Leu,ENST00000445716,;FAM133B,missense_variant,p.Ser142Leu,ENST00000438306,;FAM133B,missense_variant,p.Ser142Leu,ENST00000427372,;FAM133B,missense_variant,p.Ser49Leu,ENST00000494079,;FAM133B,downstream_gene_variant,,ENST00000456502,;FAM133B,3_prime_UTR_variant,,ENST00000415397,;FAM133B,non_coding_transcript_exon_variant,,ENST00000481407,;FAM133B,non_coding_transcript_exon_variant,,ENST00000490747,;FAM133B,downstream_gene_variant,,ENST00000492686,;FAM133B,upstream_gene_variant,,ENST00000468931,;FAM133B,downstream_gene_variant,,ENST00000480397,;	A	ENSG00000234545	ENST00000445716	Transcript	missense_variant	558	455	152	S/L	tCa/tTa	.	.	.	-1	FAM133B	HGNC	28629	protein_coding	YES	CCDS47640.1	ENSP00000398401	F133B_HUMAN	C9JUX2_HUMAN	UPI000004471D	.	tolerated_low_confidence(0.06)	unknown(0)	7/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31911,hmmpanther:PTHR31911:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTGATTCA	.	5	ESCA
GAL3ST4	0	.	GRCh37	7	99758410	99758410	+	Missense_Mutation	SNP	C	C	T	rs146874152	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.602G>A	p.Arg201His	p.R201H	ENST00000360039	4/4	36	33	3	32	32	0	GAL3ST4,missense_variant,p.Arg201His,ENST00000413800,;GAL3ST4,missense_variant,p.Val100Met,ENST00000423751,;GAL3ST4,missense_variant,p.Arg201His,ENST00000360039,;GAL3ST4,missense_variant,p.Arg139His,ENST00000426974,;GAL3ST4,missense_variant,p.Val100Met,ENST00000411994,;C7orf43,upstream_gene_variant,,ENST00000456769,;C7orf43,upstream_gene_variant,,ENST00000419841,;C7orf43,upstream_gene_variant,,ENST00000457641,;C7orf43,upstream_gene_variant,,ENST00000394035,;C7orf43,upstream_gene_variant,,ENST00000316937,;MIR4658,upstream_gene_variant,,ENST00000584344,;GAL3ST4,non_coding_transcript_exon_variant,,ENST00000498000,;C7orf43,upstream_gene_variant,,ENST00000498638,;C7orf43,upstream_gene_variant,,ENST00000472061,;LAMTOR4,downstream_gene_variant,,ENST00000490633,;GAL3ST4,non_coding_transcript_exon_variant,,ENST00000495882,;C7orf43,upstream_gene_variant,,ENST00000419037,;C7orf43,upstream_gene_variant,,ENST00000448720,;	T	ENSG00000197093	ENST00000360039	Transcript	missense_variant	995	602	201	R/H	cGt/cAt	rs146874152	.	.	-1	GAL3ST4	HGNC	24145	protein_coding	YES	CCDS5688.1	ENSP00000353142	G3ST4_HUMAN	.	UPI0000070C68	.	deleterious(0.02)	benign(0.049)	4/4	.	hmmpanther:PTHR14647:SF57,hmmpanther:PTHR14647,Pfam_domain:PF06990,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCCACGGGCC	byCluster	2	ESCA
PKHD1L1	0	.	GRCh37	8	110466969	110466969	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6762C>T	p.%3D	p.S2254S	ENST00000378402	45/78	105	99	6	64	64	0	PKHD1L1,synonymous_variant,p.%3D,ENST00000378402,;	T	ENSG00000205038	ENST00000378402	Transcript	synonymous_variant	6866	6762	2254	S	tcC/tcT	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	.	.	45/78	.	PROSITE_profiles:PS51484,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF213,Pfam_domain:PF10162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATCCCCATT	.	2	ESCA
CYP11B2	0	.	GRCh37	8	143998573	143998573	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297G>A	p.%3D	p.K99K	ENST00000323110	2/9	50	45	5	25	25	0	CYP11B2,synonymous_variant,p.%3D,ENST00000323110,;GML,downstream_gene_variant,,ENST00000522728,;	T	ENSG00000179142	ENST00000323110	Transcript	synonymous_variant	300	297	99	K	aaG/aaA	.	.	.	-1	CYP11B2	HGNC	2592	protein_coding	YES	CCDS6393.1	ENSP00000325822	C11B2_HUMAN	Q14098_HUMAN	UPI00001282CF	.	.	.	2/9	.	hmmpanther:PTHR24279:SF46,hmmpanther:PTHR24279,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|VARSCANS	TGCAGCTTCTC	.	2	ESCA
HR	0	.	GRCh37	8	21977925	21977925	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2706C>G	p.Ser902Arg	p.S902R	ENST00000381418	12/19	18	9	8	30	30	0	HR,missense_variant,p.Ser125Arg,ENST00000517699,;HR,missense_variant,p.Ser902Arg,ENST00000381418,;HR,missense_variant,p.Ser902Arg,ENST00000312841,;HR,upstream_gene_variant,,ENST00000522039,;HR,downstream_gene_variant,,ENST00000518461,;HR,upstream_gene_variant,,ENST00000522016,;	C	ENSG00000168453	ENST00000381418	Transcript	missense_variant	4187	2706	902	S/R	agC/agG	.	.	.	-1	HR	HGNC	5172	protein_coding	YES	CCDS6022.1	ENSP00000370826	HAIR_HUMAN	E5RK80_HUMAN	UPI000013EB0B	.	tolerated(0.16)	benign(0.104)	12/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12549:SF4,hmmpanther:PTHR12549,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGGCTCAG	.	5	ESCA
ADAM9	0	.	GRCh37	8	38871570	38871570	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333+8A>G	.	.	ENST00000487273	.	18	9	9	33	33	0	ADAM9,missense_variant,p.Tyr114Cys,ENST00000481513,;ADAM9,splice_region_variant,,ENST00000487273,;ADAM9,splice_region_variant,,ENST00000466936,;SNORD38,downstream_gene_variant,,ENST00000384470,;ADAM9,splice_region_variant,,ENST00000468065,;ADAM9,splice_region_variant,,ENST00000379917,;ADAM9,splice_region_variant,,ENST00000481873,;ADAM9,upstream_gene_variant,,ENST00000481058,;	G	ENSG00000168615	ENST00000487273	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	ADAM9	HGNC	216	protein_coding	YES	CCDS6112.1	ENSP00000419446	ADAM9_HUMAN	B4DDM8_HUMAN	UPI0000048D87	.	.	.	.	4/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGTATTTTT	.	5	ESCA
RUNX1T1	0	.	GRCh37	8	93017523	93017523	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>A	p.%3D	p.A198A	ENST00000436581	5/11	29	22	7	24	24	0	RUNX1T1,synonymous_variant,p.%3D,ENST00000518992,;RUNX1T1,synonymous_variant,p.%3D,ENST00000436581,;RUNX1T1,synonymous_variant,p.%3D,ENST00000265814,;RUNX1T1,synonymous_variant,p.%3D,ENST00000521054,;RUNX1T1,synonymous_variant,p.%3D,ENST00000518844,;RUNX1T1,synonymous_variant,p.%3D,ENST00000523629,;RUNX1T1,synonymous_variant,p.%3D,ENST00000360348,;RUNX1T1,synonymous_variant,p.%3D,ENST00000521553,;RUNX1T1,synonymous_variant,p.%3D,ENST00000520724,;RUNX1T1,synonymous_variant,p.%3D,ENST00000396218,;RUNX1T1,synonymous_variant,p.%3D,ENST00000422361,;RUNX1T1,splice_region_variant,,ENST00000522316,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000520047,;RUNX1T1,downstream_gene_variant,,ENST00000523290,;RUNX1T1,upstream_gene_variant,,ENST00000518361,;RUNX1T1,upstream_gene_variant,,ENST00000520978,;	T	ENSG00000079102	ENST00000436581	Transcript	synonymous_variant	605	594	198	A	gcC/gcA	.	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	.	.	5/11	.	PROSITE_profiles:PS51119,hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF5,Pfam_domain:PF07531,SMART_domains:SM00549,Superfamily_domains:SSF158553,Prints_domain:PR01875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTGGCCTG	.	5	ESCA
GPR107	0	.	GRCh37	9	132816283	132816283	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72C>T	p.%3D	p.L24L	ENST00000372406	1/20	15	11	4	15	15	0	GPR107,synonymous_variant,p.%3D,ENST00000372406,;GPR107,synonymous_variant,p.%3D,ENST00000372410,;GPR107,synonymous_variant,p.%3D,ENST00000347136,;GPR107,synonymous_variant,p.%3D,ENST00000493417,;	T	ENSG00000148358	ENST00000372406	Transcript	synonymous_variant	579	72	24	L	ctC/ctT	.	.	.	1	GPR107	HGNC	17830	protein_coding	YES	CCDS48041.1	ENSP00000361483	GP107_HUMAN	B7ZL93_HUMAN	UPI00004589E0	.	.	.	1/20	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR21229:SF12,hmmpanther:PTHR21229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	CTGCTCCCAAT	.	2	ESCA
NOTCH1	0	.	GRCh37	9	139407900	139407900	+	Missense_Mutation	SNP	C	C	G	rs374434131	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2297G>C	p.Gly766Ala	p.G766A	ENST00000277541	14/34	30	15	15	64	64	0	NOTCH1,missense_variant,p.Gly766Ala,ENST00000277541,;	G	ENSG00000148400	ENST00000277541	Transcript	missense_variant	2373	2297	766	G/A	gGc/gCc	rs374434131	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	tolerated(0.08)	probably_damaging(0.997)	14/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,Pfam_domain:PF00008,Gene3D:2gy5A03,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGCCGCCG	byFrequency|byCluster	5	ESCA
NOTCH1	0	.	GRCh37	9	139407924	139407925	+	Frame_Shift_Del	DEL	TC	TC	-	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	TC	TC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2272_2273delGA	p.Glu758IlefsTer50	p.E758Ifs*50	ENST00000277541	14/34	41	26	15	68	68	0	NOTCH1,frameshift_variant,p.Glu758IlefsTer50,ENST00000277541,;	-	ENSG00000148400	ENST00000277541	Transcript	frameshift_variant	2348-2349	2272-2273	758	E/X	GAa/a	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	14/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,Pfam_domain:PF00008,Gene3D:2gy5A03,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TTGGATTCACACT	.	2	ESCA
CLIC3	0	.	GRCh37	9	139890207	139890207	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36G>C	p.%3D	p.A12A	ENST00000494426	2/6	30	8	22	27	27	0	CLIC3,synonymous_variant,p.%3D,ENST00000494426,;C9orf142,downstream_gene_variant,,ENST00000371620,;CLIC3,splice_region_variant,,ENST00000473911,;C9orf142,downstream_gene_variant,,ENST00000492564,;C9orf142,downstream_gene_variant,,ENST00000463765,;C9orf142,downstream_gene_variant,,ENST00000481187,;CLIC3,upstream_gene_variant,,ENST00000480181,;C9orf142,downstream_gene_variant,,ENST00000498095,;C9orf142,downstream_gene_variant,,ENST00000483807,;C9orf142,downstream_gene_variant,,ENST00000493968,;C9orf142,downstream_gene_variant,,ENST00000467845,;C9orf142,downstream_gene_variant,,ENST00000468484,;C9orf142,downstream_gene_variant,,ENST00000488678,;	G	ENSG00000169583	ENST00000494426	Transcript	synonymous_variant	296	36	12	A	gcG/gcC	.	.	.	-1	CLIC3	HGNC	2064	protein_coding	YES	CCDS7021.1	ENSP00000419378	CLIC3_HUMAN	Q6FGP1_HUMAN,Q5SQ17_HUMAN	UPI00001AE551	.	.	.	2/6	.	hmmpanther:PTHR11260,hmmpanther:PTHR11260:SF129,Gene3D:3.40.30.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTCGCCTG	.	5	ESCA
NPR2	0	.	GRCh37	9	35807138	35807138	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2638A>T	p.Met880Leu	p.M880L	ENST00000342694	17/22	17	8	8	20	20	0	NPR2,missense_variant,p.Met139Leu,ENST00000447210,;NPR2,missense_variant,p.Met227Leu,ENST00000421267,;NPR2,missense_variant,p.Met880Leu,ENST00000342694,;SPAG8,downstream_gene_variant,,ENST00000497810,;SPAG8,downstream_gene_variant,,ENST00000340291,;SPAG8,downstream_gene_variant,,ENST00000484764,;SPAG8,downstream_gene_variant,,ENST00000396638,;AL133410.1,downstream_gene_variant,,ENST00000582432,;SPAG8,downstream_gene_variant,,ENST00000463889,;SPAG8,downstream_gene_variant,,ENST00000489063,;SPAG8,downstream_gene_variant,,ENST00000479751,;NPR2,missense_variant,p.Met43Leu,ENST00000448821,;NPR2,non_coding_transcript_exon_variant,,ENST00000464810,;SPAG8,downstream_gene_variant,,ENST00000471631,;SPAG8,downstream_gene_variant,,ENST00000495667,;SPAG8,downstream_gene_variant,,ENST00000460836,;SPAG8,downstream_gene_variant,,ENST00000475644,;SPAG8,downstream_gene_variant,,ENST00000472605,;NPR2,upstream_gene_variant,,ENST00000469249,;	T	ENSG00000159899	ENST00000342694	Transcript	missense_variant	2893	2638	880	M/L	Atg/Ttg	.	.	.	1	NPR2	HGNC	7944	protein_coding	YES	CCDS6590.1	ENSP00000341083	ANPRB_HUMAN	.	UPI0000125B42	.	tolerated(0.69)	benign(0.034)	17/22	.	PROSITE_profiles:PS50125,hmmpanther:PTHR11920:SF231,hmmpanther:PTHR11920,Gene3D:3.30.70.1230,Pfam_domain:PF00211,SMART_domains:SM00044,Superfamily_domains:SSF55073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCCCCATGCAG	.	4	ESCA
KDM4C	0	.	GRCh37	9	6986499	6986499	+	Missense_Mutation	SNP	G	G	A	rs774702584	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1510G>A	p.Glu504Lys	p.E504K	ENST00000381309	11/22	29	10	18	60	60	0	KDM4C,missense_variant,p.Glu504Lys,ENST00000381306,;KDM4C,missense_variant,p.Glu504Lys,ENST00000381309,;KDM4C,missense_variant,p.Glu526Lys,ENST00000535193,;KDM4C,missense_variant,p.Glu504Lys,ENST00000543771,;KDM4C,missense_variant,p.Glu323Lys,ENST00000536108,;KDM4C,missense_variant,p.Glu191Lys,ENST00000428870,;KDM4C,missense_variant,p.Glu323Lys,ENST00000442236,;KDM4C,non_coding_transcript_exon_variant,,ENST00000494570,;KDM4C,3_prime_UTR_variant,,ENST00000438023,;	A	ENSG00000107077	ENST00000381309	Transcript	missense_variant	2075	1510	504	E/K	Gag/Aag	rs774702584	.	.	1	KDM4C	HGNC	17071	protein_coding	YES	CCDS6471.1	ENSP00000370710	KDM4C_HUMAN	C9J879_HUMAN	UPI0000367602	.	tolerated(1)	benign(0)	11/22	.	hmmpanther:PTHR10694:SF32,hmmpanther:PTHR10694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCGAGCTT	byFrequency	5	ESCA
TMEM164	0	.	GRCh37	X	109419275	109419275	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2596T>C	.	.	ENST00000372073	7/7	35	7	28	24	24	0	TMEM164,3_prime_UTR_variant,,ENST00000372072,;TMEM164,3_prime_UTR_variant,,ENST00000372073,;TMEM164,3_prime_UTR_variant,,ENST00000288381,;TMEM164,3_prime_UTR_variant,,ENST00000372068,;TMEM164,intron_variant,,ENST00000464177,;TMEM164,downstream_gene_variant,,ENST00000461715,;	C	ENSG00000157600	ENST00000372073	Transcript	3_prime_UTR_variant	3826	.	.	.	.	.	.	.	1	TMEM164	HGNC	26217	protein_coding	YES	CCDS14550.2	ENSP00000361143	TM164_HUMAN	.	UPI00004560FF	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCTGTCAG	.	5	ESCA
CSF2RA	0	.	GRCh37	X	1409389	1409389	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633C>G	p.Asp211Glu	p.D211E	ENST00000417535	5/12	79	66	13	96	96	0	CSF2RA,missense_variant,p.Asp211Glu,ENST00000381524,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000381529,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000355432,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000355805,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000432318,;CSF2RA,missense_variant,p.Asp78Glu,ENST00000501036,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000361536,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000417535,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000412290,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000381500,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000381509,;CSF2RA,intron_variant,,ENST00000494969,;CSF2RA,downstream_gene_variant,,ENST00000419094,;BX649553.1,upstream_gene_variant,,ENST00000583047,;BX649553.2,upstream_gene_variant,,ENST00000578699,;MIR3690,upstream_gene_variant,,ENST00000580266,;BX649553.4,upstream_gene_variant,,ENST00000580687,;BX649553.3,upstream_gene_variant,,ENST00000581137,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000493312,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000475259,;CSF2RA,downstream_gene_variant,,ENST00000477940,;CSF2RA,upstream_gene_variant,,ENST00000498153,;CSF2RA,downstream_gene_variant,,ENST00000478256,;CSF2RA,upstream_gene_variant,,ENST00000491683,;CSF2RA,missense_variant,p.Asp211Glu,ENST00000486791,;	G	ENSG00000198223	ENST00000417535	Transcript	missense_variant	659	633	211	D/E	gaC/gaG	.	.	.	1	CSF2RA	HGNC	2435	protein_coding	YES	CCDS55359.1	ENSP00000394227	CSF2R_HUMAN	J3JS74_HUMAN,J3JS73_HUMAN	UPI000159C3E4	.	tolerated(0.29)	possibly_damaging(0.569)	5/12	.	hmmpanther:PTHR23036:SF84,hmmpanther:PTHR23036,Pfam_domain:PF09240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGACACAAA	.	5	ESCA
VSIG4	0	.	GRCh37	X	65259808	65259808	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33G>A	p.%3D	p.G11G	ENST00000374737	1/8	31	6	25	31	31	0	VSIG4,synonymous_variant,p.%3D,ENST00000455586,;VSIG4,synonymous_variant,p.%3D,ENST00000412866,;VSIG4,synonymous_variant,p.%3D,ENST00000374737,;	T	ENSG00000155659	ENST00000374737	Transcript	synonymous_variant	142	33	11	G	ggG/ggA	.	.	.	-1	VSIG4	HGNC	17032	protein_coding	YES	CCDS14383.1	ENSP00000363869	VSIG4_HUMAN	.	UPI000006F146	.	.	.	1/8	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR15466:SF1,hmmpanther:PTHR15466	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGCCCCAG	.	5	ESCA
KIF4A	0	.	GRCh37	X	69594099	69594099	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1773A>T	p.Gln591His	p.Q591H	ENST00000374403	16/31	19	7	12	17	17	0	KIF4A,missense_variant,p.Gln591His,ENST00000374403,;KIF4A,missense_variant,p.Gln591His,ENST00000374388,;	T	ENSG00000090889	ENST00000374403	Transcript	missense_variant	1855	1773	591	Q/H	caA/caT	.	.	.	1	KIF4A	HGNC	13339	protein_coding	YES	CCDS14401.1	ENSP00000363524	KIF4A_HUMAN	.	UPI000013D32A	.	deleterious(0.01)	benign(0.077)	16/31	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCAAGCCAA	.	5	ESCA
SATL1	0	.	GRCh37	X	84363348	84363348	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.627C>A	p.Ser209Arg	p.S209R	ENST00000509231	1/5	70	32	38	64	64	0	SATL1,missense_variant,p.Ser209Arg,ENST00000509231,;SATL1,missense_variant,p.Ser22Arg,ENST00000332921,;SATL1,missense_variant,p.Ser22Arg,ENST00000395409,;	T	ENSG00000184788	ENST00000509231	Transcript	missense_variant	707	627	209	S/R	agC/agA	.	.	.	-1	SATL1	HGNC	27992	protein_coding	YES	CCDS35343.2	ENSP00000425421	.	E9PB72_HUMAN	UPI000041ABBC	.	deleterious(0.02)	possibly_damaging(0.504)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTGGCTTGG	.	5	ESCA
SATL1	0	.	GRCh37	X	84363349	84363349	+	Missense_Mutation	SNP	C	C	T	rs190908833	.	TCGA-LN-A4A1-01A-21D-A27G-09	TCGA-LN-A4A1-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626G>A	p.Ser209Asn	p.S209N	ENST00000509231	1/5	69	32	37	64	64	0	SATL1,missense_variant,p.Ser209Asn,ENST00000509231,;SATL1,missense_variant,p.Ser22Asn,ENST00000332921,;SATL1,missense_variant,p.Ser22Asn,ENST00000395409,;	T	ENSG00000184788	ENST00000509231	Transcript	missense_variant	706	626	209	S/N	aGc/aAc	rs190908833	.	.	-1	SATL1	HGNC	27992	protein_coding	YES	CCDS35343.2	ENSP00000425421	.	E9PB72_HUMAN	UPI000041ABBC	.	tolerated(0.23)	benign(0.383)	1/5	.	.	T:0.0003	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0003	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGCTTGGG	byCluster|by1000G	5	ESCA
OAT	0	.	GRCh37	10	126097158	126097158	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473A>G	p.Tyr158Cys	p.Y158C	ENST00000368845	4/10	53	38	15	59	59	0	OAT,missense_variant,p.Tyr20Cys,ENST00000539214,;OAT,missense_variant,p.Tyr158Cys,ENST00000368845,;OAT,non_coding_transcript_exon_variant,,ENST00000476917,;OAT,non_coding_transcript_exon_variant,,ENST00000467675,;OAT,downstream_gene_variant,,ENST00000492376,;OAT,upstream_gene_variant,,ENST00000483711,;OAT,downstream_gene_variant,,ENST00000490096,;	C	ENSG00000065154	ENST00000368845	Transcript	missense_variant	566	473	158	Y/C	tAt/tGt	.	.	.	-1	OAT	HGNC	8091	protein_coding	YES	CCDS7639.1	ENSP00000357838	OAT_HUMAN	.	UPI0000000C1B	.	tolerated(0.06)	benign(0.343)	4/10	.	hmmpanther:PTHR11986:SF18,hmmpanther:PTHR11986,Pfam_domain:PF00202,Gene3D:3.40.640.10,TIGRFAM_domain:TIGR01885,PIRSF_domain:PIRSF000521,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTATAGCCC	.	5	ESCA
FXYD4	0	.	GRCh37	10	43869150	43869150	+	5'UTR	SNP	G	G	A	rs546355644	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-45G>A	.	.	ENST00000476166	3/9	45	31	14	44	44	0	FXYD4,5_prime_UTR_variant,,ENST00000476166,;FXYD4,intron_variant,,ENST00000480834,;FXYD4,upstream_gene_variant,,ENST00000479189,;	A	ENSG00000150201	ENST00000476166	Transcript	5_prime_UTR_variant	290	.	.	.	.	rs546355644	.	.	1	FXYD4	HGNC	4028	protein_coding	YES	CCDS7203.1	ENSP00000473361	FXYD4_HUMAN	.	UPI0000160F0C	.	.	.	3/9	.	.	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCCCCGCCCCA	byFrequency|by1000G	4	ESCA
AGAP4	0	.	GRCh37	10	46322367	46322367	+	Missense_Mutation	SNP	T	T	C	rs559818160	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.988A>G	p.Thr330Ala	p.T330A	ENST00000448048	7/7	71	47	24	128	127	0	AGAP4,missense_variant,p.Thr330Ala,ENST00000448048,;AGAP4,downstream_gene_variant,,ENST00000492347,;AGAP4,downstream_gene_variant,,ENST00000430779,;	C	ENSG00000188234	ENST00000448048	Transcript	missense_variant	1114	988	330	T/A	Aca/Gca	rs559818160	.	.	-1	AGAP4	HGNC	23459	protein_coding	YES	CCDS7215.1	ENSP00000392513	AGAP4_HUMAN	.	UPI000013ED67	.	tolerated(1)	benign(0.001)	7/7	.	SMART_domains:SM00233,Pfam_domain:PF00169,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213,PROSITE_profiles:PS50003	C:0.0004	C:0	C:0	.	C:0.002	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTGTGCAGG	byFrequency|by1000G	5	ESCA
NCOA4	0	.	GRCh37	10	51584855	51584855	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1002G>C	p.Glu334Asp	p.E334D	ENST00000452682	9/12	60	48	12	55	55	0	NCOA4,missense_variant,p.Glu318Asp,ENST00000374082,;NCOA4,missense_variant,p.Glu218Asp,ENST00000430396,;NCOA4,missense_variant,p.Glu334Asp,ENST00000452682,;NCOA4,missense_variant,p.Glu152Asp,ENST00000414907,;NCOA4,missense_variant,p.Glu318Asp,ENST00000344348,;NCOA4,missense_variant,p.Glu318Asp,ENST00000443446,;NCOA4,missense_variant,p.Glu234Asp,ENST00000431200,;NCOA4,missense_variant,p.Glu318Asp,ENST00000374087,;NCOA4,missense_variant,p.Glu334Asp,ENST00000438493,;NCOA4,downstream_gene_variant,,ENST00000498586,;	C	ENSG00000138293	ENST00000452682	Transcript	missense_variant	1254	1002	334	E/D	gaG/gaC	.	.	.	1	NCOA4	HGNC	7671	protein_coding	YES	CCDS44394.1	ENSP00000395465	NCOA4_HUMAN	.	UPI0001932817	.	tolerated(0.15)	possibly_damaging(0.74)	9/12	.	hmmpanther:PTHR17085,hmmpanther:PTHR17085:SF2,Pfam_domain:PF12489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGAGAATGG	.	5	ESCA
VCL	0	.	GRCh37	10	75758009	75758009	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44C>T	p.Pro15Leu	p.P15L	ENST00000211998	1/22	48	35	13	78	78	0	VCL,missense_variant,p.Pro15Leu,ENST00000211998,;VCL,missense_variant,p.Pro15Leu,ENST00000417648,;VCL,missense_variant,p.Pro15Leu,ENST00000372755,;VCL,non_coding_transcript_exon_variant,,ENST00000478896,;	T	ENSG00000035403	ENST00000211998	Transcript	missense_variant	138	44	15	P/L	cCg/cTg	.	.	.	1	VCL	HGNC	12665	protein_coding	YES	CCDS7341.1	ENSP00000211998	VINC_HUMAN	Q5JQ13_HUMAN	UPI0000167B54	.	deleterious(0)	probably_damaging(1)	1/22	.	hmmpanther:PTHR18914:SF22,hmmpanther:PTHR18914,Pfam_domain:PF01044,Gene3D:1.20.1490.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGAGCCGGTGG	.	4	ESCA
DDX6	0	.	GRCh37	11	118661613	118661613	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-268+194G>A	.	.	ENST00000264018	.	56	41	15	87	87	0	DDX6,5_prime_UTR_variant,,ENST00000526070,;DDX6,intron_variant,,ENST00000264018,;DDX6,upstream_gene_variant,,ENST00000534980,;DDX6,intron_variant,,ENST00000525082,;DDX6,intron_variant,,ENST00000533239,;DDX6,upstream_gene_variant,,ENST00000531971,;	T	ENSG00000110367	ENST00000264018	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DDX6	HGNC	2747	protein_coding	YES	CCDS44751.1	ENSP00000264018	DDX6_HUMAN	B2R858_HUMAN	UPI000013D4A2	.	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGCTCGGC	.	5	ESCA
LIN7C	0	.	GRCh37	11	27523398	27523398	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.107A>G	p.Gln36Arg	p.Q36R	ENST00000278193	2/5	58	54	4	61	61	0	LIN7C,missense_variant,p.Gln36Arg,ENST00000524596,;LIN7C,missense_variant,p.Gln36Arg,ENST00000278193,;BDNF-AS,upstream_gene_variant,,ENST00000530686,;BDNF-AS,upstream_gene_variant,,ENST00000532965,;	C	ENSG00000148943	ENST00000278193	Transcript	missense_variant	128	107	36	Q/R	cAg/cGg	.	.	.	-1	LIN7C	HGNC	17789	protein_coding	YES	CCDS7864.1	ENSP00000278193	LIN7C_HUMAN	.	UPI000000BB45	.	tolerated(0.19)	benign(0.428)	2/5	.	PROSITE_profiles:PS51022,hmmpanther:PTHR14063,Pfam_domain:PF02828,SMART_domains:SM00569,Superfamily_domains:SSF101288,PIRSF_domain:PIRSF038039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCCTGAAGT	.	2	ESCA
OR4A16	0	.	GRCh37	11	55110883	55110883	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207C>A	p.%3D	p.A69A	ENST00000314721	1/1	46	39	7	44	44	0	OR4A16,synonymous_variant,p.%3D,ENST00000314721,;	A	ENSG00000181961	ENST00000314721	Transcript	synonymous_variant	257	207	69	A	gcC/gcA	.	.	.	1	OR4A16	HGNC	15153	protein_coding	YES	CCDS31499.1	ENSP00000325128	O4A16_HUMAN	.	UPI0000061EB2	.	.	.	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451:SF153,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGCCATATA	.	5	ESCA
PRG3	0	.	GRCh37	11	57147010	57147010	+	Missense_Mutation	SNP	C	C	T	rs779423526	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.332G>A	p.Arg111His	p.R111H	ENST00000287143	3/6	46	35	11	59	59	0	PRG3,missense_variant,p.Arg111His,ENST00000287143,;	T	ENSG00000156575	ENST00000287143	Transcript	missense_variant	442	332	111	R/H	cGc/cAc	rs779423526,COSM1354762	.	.	-1	PRG3	HGNC	9363	protein_coding	YES	CCDS7954.1	ENSP00000287143	PRG3_HUMAN	.	UPI000013DE94	.	tolerated(0.54)	benign(0.001)	3/6	.	SMART_domains:SM00034,Gene3D:3.10.100.10,hmmpanther:PTHR10068:SF8,hmmpanther:PTHR10068	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTAGCGGCAG	byFrequency	5	ESCA
OR5B3	0	.	GRCh37	11	58170410	58170410	+	Missense_Mutation	SNP	G	G	A	rs77702214	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473C>T	p.Thr158Ile	p.T158I	ENST00000309403	1/1	71	59	12	64	64	0	OR5B3,missense_variant,p.Thr158Ile,ENST00000309403,;	A	ENSG00000172769	ENST00000309403	Transcript	missense_variant	473	473	158	T/I	aCt/aTt	rs77702214	.	.	-1	OR5B3	HGNC	8324	protein_coding	YES	CCDS31549.1	ENSP00000308270	OR5B3_HUMAN	.	UPI0000041DD0	.	tolerated_low_confidence(0.46)	benign(0.03)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF15,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCCAGTGTGG	byFrequency|byCluster|by1000G	3	ESCA
OR52L1	0	.	GRCh37	11	6007674	6007674	+	Missense_Mutation	SNP	C	C	T	rs769350807	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.487G>A	p.Gly163Arg	p.G163R	ENST00000332249	1/1	39	27	11	63	63	0	OR52L1,missense_variant,p.Gly163Arg,ENST00000332249,;	T	ENSG00000183313	ENST00000332249	Transcript	missense_variant	542	487	163	G/R	Gga/Aga	rs769350807	.	.	-1	OR52L1	HGNC	14785	protein_coding	YES	CCDS44529.1	ENSP00000330338	O52L1_HUMAN	.	UPI00001B006D	.	deleterious(0)	probably_damaging(0.989)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF96,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTCCGATGC	.	5	ESCA
CDHR5	0	.	GRCh37	11	617432	617432	+	Silent	SNP	G	G	A	rs764911557	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2457C>T	p.%3D	p.S819S	ENST00000358353	16/16	25	19	6	41	41	0	CDHR5,synonymous_variant,p.%3D,ENST00000397542,;CDHR5,synonymous_variant,p.%3D,ENST00000349570,;CDHR5,synonymous_variant,p.%3D,ENST00000358353,;IRF7,upstream_gene_variant,,ENST00000330243,;IRF7,upstream_gene_variant,,ENST00000397566,;IRF7,upstream_gene_variant,,ENST00000348655,;IRF7,upstream_gene_variant,,ENST00000525445,;CDHR5,downstream_gene_variant,,ENST00000534311,;IRF7,upstream_gene_variant,,ENST00000397570,;CDHR5,downstream_gene_variant,,ENST00000526077,;IRF7,upstream_gene_variant,,ENST00000397562,;CDHR5,downstream_gene_variant,,ENST00000531088,;IRF7,upstream_gene_variant,,ENST00000397574,;CDHR5,downstream_gene_variant,,ENST00000532949,;CDHR5,3_prime_UTR_variant,,ENST00000531177,;IRF7,upstream_gene_variant,,ENST00000527160,;IRF7,upstream_gene_variant,,ENST00000532326,;IRF7,upstream_gene_variant,,ENST00000531912,;IRF7,upstream_gene_variant,,ENST00000528413,;IRF7,upstream_gene_variant,,ENST00000532096,;IRF7,upstream_gene_variant,,ENST00000532788,;IRF7,upstream_gene_variant,,ENST00000469048,;IRF7,upstream_gene_variant,,ENST00000533182,;CDHR5,downstream_gene_variant,,ENST00000531899,;IRF7,upstream_gene_variant,,ENST00000525750,;IRF7,upstream_gene_variant,,ENST00000533190,;	A	ENSG00000099834	ENST00000358353	Transcript	synonymous_variant	2780	2457	819	S	tcC/tcT	rs764911557	.	.	-1	CDHR5	HGNC	7521	protein_coding	YES	CCDS7707.1	ENSP00000351118	CDHR5_HUMAN	.	UPI0000456444	.	.	.	16/16	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGGAGTC	byFrequency	5	ESCA
CCND1	0	.	GRCh37	11	69467865	69467865	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1815T>C	.	.	ENST00000227507	5/5	577	549	28	44	44	0	CCND1,3_prime_UTR_variant,,ENST00000227507,;ORAOV1,downstream_gene_variant,,ENST00000538554,;CCND1,downstream_gene_variant,,ENST00000536559,;ORAOV1,non_coding_transcript_exon_variant,,ENST00000542515,;ORAOV1,downstream_gene_variant,,ENST00000569105,;CCND1,downstream_gene_variant,,ENST00000542367,;CCND1,downstream_gene_variant,,ENST00000545484,;	C	ENSG00000110092	ENST00000227507	Transcript	3_prime_UTR_variant	2930	.	.	.	.	.	.	.	1	CCND1	HGNC	1582	protein_coding	YES	CCDS8191.1	ENSP00000227507	CCND1_HUMAN	Q9H014_HUMAN,Q6FI00_HUMAN,Q5MGB2_HUMAN	UPI0000001285	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTATTTAGG	.	2	ESCA
SERPINH1	0	.	GRCh37	11	75277524	75277524	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.130G>A	p.Ala44Thr	p.A44T	ENST00000524558	2/5	37	23	13	49	49	0	SERPINH1,missense_variant,p.Ala44Thr,ENST00000530284,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000528760,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000533449,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000528990,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000524558,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000533603,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000526397,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000532356,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000525611,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000358171,;SERPINH1,missense_variant,p.Ala19Thr,ENST00000526242,;SERPINH1,missense_variant,p.Ala44Thr,ENST00000529643,;SERPINH1,intron_variant,,ENST00000525492,;SERPINH1,upstream_gene_variant,,ENST00000525876,;	A	ENSG00000149257	ENST00000524558	Transcript	missense_variant	1565	130	44	A/T	Gcc/Acc	.	.	.	1	SERPINH1	HGNC	1546	protein_coding	YES	CCDS8239.1	ENSP00000434412	SERPH_HUMAN	Q9NPA9_HUMAN,E9PRS3_HUMAN,E9PR70_HUMAN,E9PNX1_HUMAN,E9PMI5_HUMAN,E9PKH2_HUMAN,E9PK86_HUMAN,E9PJH8_HUMAN,E9PIG2_HUMAN,B4DN87_HUMAN	UPI00001271B6	.	deleterious(0.02)	probably_damaging(0.96)	2/5	.	Superfamily_domains:SSF56574,Gene3D:3.30.497.10,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTTGCCGAG	.	5	ESCA
OAS2	0	.	GRCh37	12	113440810	113440810	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1082G>C	p.Cys361Ser	p.C361S	ENST00000342315	6/11	47	42	5	55	55	0	OAS2,missense_variant,p.Cys361Ser,ENST00000392583,;OAS2,missense_variant,p.Cys361Ser,ENST00000342315,;OAS2,downstream_gene_variant,,ENST00000552756,;RP1-71H24.1,intron_variant,,ENST00000552784,;OAS2,non_coding_transcript_exon_variant,,ENST00000548941,;OAS2,downstream_gene_variant,,ENST00000551603,;	C	ENSG00000111335	ENST00000342315	Transcript	missense_variant	1296	1082	361	C/S	tGc/tCc	COSM935343	.	.	1	OAS2	HGNC	8087	protein_coding	YES	CCDS31906.1	ENSP00000342278	OAS2_HUMAN	.	UPI000013CB0B	.	tolerated(0.77)	benign(0)	6/11	.	Superfamily_domains:SSF81301,Gene3D:3.30.460.10,hmmpanther:PTHR11258:SF3,hmmpanther:PTHR11258,PROSITE_profiles:PS50152	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAATGCTTCC	.	4	ESCA
ZCCHC8	0	.	GRCh37	12	122958783	122958783	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1385T>G	p.Phe462Cys	p.F462C	ENST00000336229	14/14	18	15	3	14	14	0	ZCCHC8,missense_variant,p.Phe73Cys,ENST00000542892,;ZCCHC8,missense_variant,p.Phe73Cys,ENST00000538116,;ZCCHC8,missense_variant,p.Phe224Cys,ENST00000543897,;ZCCHC8,missense_variant,p.Phe224Cys,ENST00000536306,;ZCCHC8,missense_variant,p.Phe462Cys,ENST00000336229,;ZCCHC8,downstream_gene_variant,,ENST00000536663,;ZCCHC8,downstream_gene_variant,,ENST00000544054,;	C	ENSG00000033030	ENST00000336229	Transcript	missense_variant	1516	1385	462	F/C	tTt/tGt	.	.	.	-1	ZCCHC8	HGNC	25265	protein_coding	YES	.	ENSP00000337313	ZCHC8_HUMAN	F5H803_HUMAN,F5H6J5_HUMAN,F5GYI9_HUMAN,F5GXQ6_HUMAN	UPI00001E0582	.	deleterious(0.01)	possibly_damaging(0.541)	14/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13316,hmmpanther:PTHR13316:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTGAAAACTT	.	2	ESCA
HIP1R	0	.	GRCh37	12	123346457	123346457	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*157G>A	.	.	ENST00000253083	32/32	26	21	4	13	13	0	HIP1R,3_prime_UTR_variant,,ENST00000535012,;HIP1R,3_prime_UTR_variant,,ENST00000253083,;VPS37B,downstream_gene_variant,,ENST00000267202,;RP11-463O12.3,upstream_gene_variant,,ENST00000537827,;HIP1R,non_coding_transcript_exon_variant,,ENST00000537322,;HIP1R,non_coding_transcript_exon_variant,,ENST00000536617,;HIP1R,downstream_gene_variant,,ENST00000541712,;HIP1R,downstream_gene_variant,,ENST00000452196,;HIP1R,downstream_gene_variant,,ENST00000538236,;HIP1R,downstream_gene_variant,,ENST00000535831,;	A	ENSG00000130787	ENST00000253083	Transcript	3_prime_UTR_variant	3489	.	.	.	.	.	.	.	1	HIP1R	HGNC	18415	protein_coding	YES	CCDS31922.1	ENSP00000253083	HIP1R_HUMAN	B3KN98_HUMAN	UPI000012C72C	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTGCAGGG	.	5	ESCA
SLC15A4	0	.	GRCh37	12	129278578	129278578	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*163G>A	.	.	ENST00000266771	8/8	32	26	5	62	62	0	SLC15A4,3_prime_UTR_variant,,ENST00000266771,;SLC15A4,3_prime_UTR_variant,,ENST00000545031,;SLC15A4,downstream_gene_variant,,ENST00000544112,;SLC15A4,3_prime_UTR_variant,,ENST00000376744,;	T	ENSG00000139370	ENST00000266771	Transcript	3_prime_UTR_variant	1937	.	.	.	.	.	.	.	-1	SLC15A4	HGNC	23090	protein_coding	YES	CCDS9264.1	ENSP00000266771	S15A4_HUMAN	F5GZQ7_HUMAN,B6ZDF2_HUMAN	UPI000006F120	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTACCAAGCT	.	5	ESCA
RECQL	0	.	GRCh37	12	21628683	21628683	+	Missense_Mutation	SNP	C	C	A	rs770714965	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1025G>T	p.Gly342Val	p.G342V	ENST00000444129	9/15	13	5	8	14	14	0	RECQL,missense_variant,p.Gly342Val,ENST00000421138,;RECQL,missense_variant,p.Gly342Val,ENST00000444129,;	A	ENSG00000004700	ENST00000444129	Transcript	missense_variant	1494	1025	342	G/V	gGt/gTt	rs770714965	.	.	-1	RECQL	HGNC	9948	protein_coding	YES	CCDS31756.1	ENSP00000416739	RECQ1_HUMAN	F8WD97_HUMAN,F8WA66_HUMAN,F5H4P4_HUMAN,F5H3W0_HUMAN,F5H2L2_HUMAN,F5GYB7_HUMAN	UPI0000167E2F	.	tolerated(0.1)	possibly_damaging(0.632)	9/15	.	Superfamily_domains:SSF52540,SMART_domains:SM00490,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00614,Pfam_domain:PF00271,hmmpanther:PTHR13710:SF72,hmmpanther:PTHR13710,PROSITE_profiles:PS51194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AAGCACCTGCA	byFrequency	4	ESCA
EFCAB4B	0	.	GRCh37	12	3757653	3757653	+	Intron	SNP	C	C	T	rs149287496	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118+55G>A	.	.	ENST00000440314	.	59	51	8	35	35	0	EFCAB4B,synonymous_variant,p.%3D,ENST00000252322,;EFCAB4B,intron_variant,,ENST00000444507,;EFCAB4B,intron_variant,,ENST00000535292,;EFCAB4B,intron_variant,,ENST00000440314,;EFCAB4B,synonymous_variant,p.%3D,ENST00000333750,;	T	ENSG00000130038	ENST00000440314	Transcript	intron_variant	.	.	.	.	.	rs149287496	.	.	-1	EFCAB4B	HGNC	28657	protein_coding	YES	CCDS44803.1	ENSP00000409382	EFC4B_HUMAN	.	UPI00017A8807	.	.	.	.	11/19	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTTCCGACCC	byCluster|by1000G	4	ESCA
KRT8	0	.	GRCh37	12	53292281	53292281	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1309A>T	p.Met437Leu	p.M437L	ENST00000552150	8/9	88	76	12	82	82	0	KRT8,missense_variant,p.Met409Leu,ENST00000546897,;KRT8,missense_variant,p.Met409Leu,ENST00000552551,;KRT8,missense_variant,p.Met409Leu,ENST00000293308,;KRT8,missense_variant,p.Met437Leu,ENST00000552150,;KRT8,downstream_gene_variant,,ENST00000546900,;KRT8,downstream_gene_variant,,ENST00000547176,;KRT8,downstream_gene_variant,,ENST00000546826,;KRT8,downstream_gene_variant,,ENST00000548998,;KRT8,downstream_gene_variant,,ENST00000547413,;KRT8,non_coding_transcript_exon_variant,,ENST00000550170,;KRT8,non_coding_transcript_exon_variant,,ENST00000547031,;KRT8,non_coding_transcript_exon_variant,,ENST00000546583,;KRT8,downstream_gene_variant,,ENST00000549176,;	A	ENSG00000170421	ENST00000552150	Transcript	missense_variant	1329	1309	437	M/L	Atg/Ttg	.	.	.	-1	KRT8	HGNC	6446	protein_coding	YES	CCDS58234.1	ENSP00000449404	K2C8_HUMAN	Q969I0_HUMAN,Q7L4M3_HUMAN,F8VUG2_HUMAN,F8VRG4_HUMAN,F8VP67_HUMAN	UPI0001892789	.	tolerated(0.31)	benign(0.018)	8/9	.	hmmpanther:PTHR23239:SF104,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCATGTTCT	.	5	ESCA
LINC00937	0	.	GRCh37	12	8542937	8542937	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1010G>T	.	.	ENST00000544461	2/5	50	41	9	25	25	0	LINC00937,non_coding_transcript_exon_variant,,ENST00000536539,;LINC00937,non_coding_transcript_exon_variant,,ENST00000538304,;LINC00937,non_coding_transcript_exon_variant,,ENST00000420040,;LINC00937,non_coding_transcript_exon_variant,,ENST00000544461,;LINC00937,upstream_gene_variant,,ENST00000536560,;LINC00937,upstream_gene_variant,,ENST00000539348,;	A	ENSG00000226091	ENST00000544461	Transcript	non_coding_transcript_exon_variant	1010	.	.	.	.	.	.	.	-1	LINC00937	HGNC	48629	lincRNA	YES	.	.	.	.	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCCTCGCAGT	.	4	ESCA
CLLU1	0	.	GRCh37	12	92818799	92818799	+	Missense_Mutation	SNP	C	C	A	rs761644797	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343C>A	p.Gln115Lys	p.Q115K	ENST00000378485	1/2	46	39	6	38	38	0	CLLU1,missense_variant,p.Gln115Lys,ENST00000378485,;CLLU1OS,intron_variant,,ENST00000378487,;CLLU1OS,intron_variant,,ENST00000538965,;RP11-693J15.4,intron_variant,,ENST00000508671,;CLLU1,intron_variant,,ENST00000512817,;CLLU1,intron_variant,,ENST00000472839,;CLLU1,non_coding_transcript_exon_variant,,ENST00000586526,;CLLU1,downstream_gene_variant,,ENST00000589406,;	A	ENSG00000257127	ENST00000378485	Transcript	missense_variant	1065	343	115	Q/K	Caa/Aaa	rs761644797	.	.	1	CLLU1	HGNC	29841	protein_coding	YES	.	ENSP00000367746	CLLU1_HUMAN	.	UPI00004A1179	.	.	benign(0.095)	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATTTCAACTG	.	4	ESCA
BRCA2	0	.	GRCh37	13	32954213	32954213	+	Missense_Mutation	SNP	C	C	T	rs80359176	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9187C>T	p.Pro3063Ser	p.P3063S	ENST00000544455	24/28	54	43	11	85	85	0	BRCA2,missense_variant,p.Pro3063Ser,ENST00000544455,;BRCA2,missense_variant,p.Pro3063Ser,ENST00000380152,;BRCA2,missense_variant,p.Pro49Ser,ENST00000470094,;BRCA2,downstream_gene_variant,,ENST00000528762,;IFIT1P1,upstream_gene_variant,,ENST00000400497,;	T	ENSG00000139618	ENST00000544455	Transcript	missense_variant	9414	9187	3063	P/S	Cca/Tca	rs80359176	.	.	1	BRCA2	HGNC	1101	protein_coding	YES	CCDS9344.1	ENSP00000439902	BRCA2_HUMAN	Q9H4L3_HUMAN,Q8IU82_HUMAN,Q8IU77_HUMAN,Q8IU64_HUMAN,K4K7W0_HUMAN,K4JXT6_HUMAN,K4JTT2_HUMAN,E9PIQ1_HUMAN	UPI00001FCBCC	.	deleterious(0.04)	benign(0.217)	24/28	.	hmmpanther:PTHR11289:SF0,hmmpanther:PTHR11289,Pfam_domain:PF09104,Gene3D:2.40.50.140,PIRSF_domain:PIRSF002397,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	uncertain_significance,not_provided	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATCCAGAC	byFrequency|byCluster	5	ESCA
AHNAK2	0	.	GRCh37	14	105404775	105404775	+	Silent	SNP	T	T	C	rs769793481	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17013A>G	p.%3D	p.R5671R	ENST00000333244	7/7	89	71	18	89	89	0	AHNAK2,synonymous_variant,p.%3D,ENST00000333244,;AHNAK2,synonymous_variant,p.%3D,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;	C	ENSG00000185567	ENST00000333244	Transcript	synonymous_variant	17133	17013	5671	R	agA/agG	rs769793481	.	.	-1	AHNAK2	HGNC	20125	protein_coding	YES	CCDS45177.1	ENSP00000353114	AHNK2_HUMAN	.	UPI00015BB2CA	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGATCTCTG	.	5	ESCA
OR4K14	0	.	GRCh37	14	20482510	20482510	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843A>G	p.%3D	p.P281P	ENST00000305045	1/1	19	13	5	27	27	0	OR4K14,synonymous_variant,p.%3D,ENST00000305045,;	C	ENSG00000169484	ENST00000305045	Transcript	synonymous_variant	843	843	281	P	ccA/ccG	.	.	.	-1	OR4K14	HGNC	15352	protein_coding	YES	CCDS32027.1	ENSP00000305011	OR4KE_HUMAN	.	UPI0000041CED	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF31,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGGAGTGGAGT	.	4	ESCA
FANCM	0	.	GRCh37	14	45644391	45644391	+	Missense_Mutation	SNP	C	C	G	rs773056258	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2434C>G	p.His812Asp	p.H812D	ENST00000267430	14/23	39	35	4	30	30	0	FANCM,missense_variant,p.His786Asp,ENST00000542564,;FANCM,missense_variant,p.His328Asp,ENST00000556250,;FANCM,missense_variant,p.His812Asp,ENST00000267430,;FANCM,upstream_gene_variant,,ENST00000554809,;	G	ENSG00000187790	ENST00000267430	Transcript	missense_variant	2519	2434	812	H/D	Cac/Gac	rs773056258	.	.	1	FANCM	HGNC	23168	protein_coding	YES	CCDS32070.1	ENSP00000267430	FANCM_HUMAN	.	UPI000059F032	.	tolerated(0.13)	benign(0.035)	14/23	.	hmmpanther:PTHR14025,hmmpanther:PTHR14025:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCACTCACAAG	.	3	ESCA
KLHDC2	0	.	GRCh37	14	50249303	50249303	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1088C>T	p.Ser363Phe	p.S363F	ENST00000298307	12/13	30	26	4	32	32	0	KLHDC2,missense_variant,p.Ser363Phe,ENST00000298307,;KLHDC2,intron_variant,,ENST00000554589,;KLHDC2,intron_variant,,ENST00000557247,;NEMF,downstream_gene_variant,,ENST00000555970,;NEMF,downstream_gene_variant,,ENST00000382135,;NEMF,downstream_gene_variant,,ENST00000298310,;NEMF,downstream_gene_variant,,ENST00000546046,;NEMF,downstream_gene_variant,,ENST00000545773,;NEMF,downstream_gene_variant,,ENST00000554275,;NEMF,downstream_gene_variant,,ENST00000556691,;KLHDC2,downstream_gene_variant,,ENST00000553538,;NEMF,downstream_gene_variant,,ENST00000556925,;KLHDC2,3_prime_UTR_variant,,ENST00000555443,;KLHDC2,3_prime_UTR_variant,,ENST00000555739,;KLHDC2,non_coding_transcript_exon_variant,,ENST00000554115,;KLHDC2,non_coding_transcript_exon_variant,,ENST00000553579,;NEMF,downstream_gene_variant,,ENST00000557193,;NEMF,downstream_gene_variant,,ENST00000556074,;KLHDC2,downstream_gene_variant,,ENST00000556559,;KLHDC2,downstream_gene_variant,,ENST00000557063,;	T	ENSG00000165516	ENST00000298307	Transcript	missense_variant	1949	1088	363	S/F	tCt/tTt	.	.	.	1	KLHDC2	HGNC	20231	protein_coding	YES	CCDS9693.1	ENSP00000298307	KLDC2_HUMAN	.	UPI00000372DF	.	deleterious(0)	probably_damaging(0.997)	12/13	.	hmmpanther:PTHR23244:SF261,hmmpanther:PTHR23244	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAATCTCTTG	.	4	ESCA
MAP3K9	0	.	GRCh37	14	71209128	71209128	+	Missense_Mutation	SNP	C	C	A	rs111385383	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1507G>T	p.Gly503Cys	p.G503C	ENST00000555993	6/13	59	45	14	50	50	0	MAP3K9,missense_variant,p.Gly197Cys,ENST00000553414,;MAP3K9,missense_variant,p.Gly240Cys,ENST00000554146,;MAP3K9,missense_variant,p.Gly503Cys,ENST00000381250,;MAP3K9,missense_variant,p.Gly503Cys,ENST00000555993,;MAP3K9,missense_variant,p.Gly503Cys,ENST00000554752,;	A	ENSG00000006432	ENST00000555993	Transcript	missense_variant	1870	1507	503	G/C	Ggc/Tgc	rs111385383	.	.	-1	MAP3K9	HGNC	6861	protein_coding	YES	CCDS32112.1	ENSP00000451263	M3K9_HUMAN	Q8NEB1_HUMAN,B4DSG3_HUMAN,B4DGF4_HUMAN,B3KRI5_HUMAN	UPI00001D7B5C	.	deleterious(0)	probably_damaging(0.988)	6/13	.	hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF401,PIRSF_domain:PIRSF000556	T:0.0004	T:0.0008	T:0	.	T:0	T:0.001	T:0	T:0.0002	T:0.0006	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGCCCTTGC	byFrequency|byCluster|by1000G	5	ESCA
ACOT6	0	.	GRCh37	14	74083849	74083849	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-30C>G	.	.	ENST00000381139	1/2	58	36	22	55	55	0	ACOT6,5_prime_UTR_variant,,ENST00000381139,;ACOT6,5_prime_UTR_variant,,ENST00000554229,;RP3-414A15.10,non_coding_transcript_exon_variant,,ENST00000555011,;RP3-414A15.10,downstream_gene_variant,,ENST00000555500,;	G	ENSG00000205669	ENST00000381139	Transcript	5_prime_UTR_variant	302	.	.	.	.	.	.	.	1	ACOT6	HGNC	33159	protein_coding	YES	CCDS32118.1	ENSP00000370531	ACOT6_HUMAN	G3V3W6_HUMAN	UPI00005BB7DB	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACATCTGGAG	.	5	ESCA
EML5	0	.	GRCh37	14	89124637	89124637	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3771C>T	p.%3D	p.G1257G	ENST00000554922	26/44	58	50	8	47	47	0	EML5,synonymous_variant,p.%3D,ENST00000352093,;EML5,synonymous_variant,p.%3D,ENST00000554922,;EML5,synonymous_variant,p.%3D,ENST00000380664,;EML5,3_prime_UTR_variant,,ENST00000553281,;EML5,3_prime_UTR_variant,,ENST00000553526,;	A	ENSG00000165521	ENST00000554922	Transcript	synonymous_variant	4020	3771	1257	G	ggC/ggT	.	.	.	-1	EML5	HGNC	18197	protein_coding	YES	CCDS45148.1	ENSP00000451998	EMAL5_HUMAN	.	UPI00001C0438	.	.	.	26/44	.	Superfamily_domains:SSF50998,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF16,PROSITE_profiles:PS50082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTACCGCCTAG	.	4	ESCA
AQR	0	.	GRCh37	15	35148927	35148927	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66A>G	.	.	ENST00000156471	35/35	28	24	4	41	41	0	AQR,3_prime_UTR_variant,,ENST00000156471,;AQR,3_prime_UTR_variant,,ENST00000543879,;AQR,non_coding_transcript_exon_variant,,ENST00000559090,;AQR,downstream_gene_variant,,ENST00000559767,;	C	ENSG00000021776	ENST00000156471	Transcript	3_prime_UTR_variant	4750	.	.	.	.	.	.	.	-1	AQR	HGNC	29513	protein_coding	YES	CCDS42013.1	ENSP00000156471	AQR_HUMAN	.	UPI00001C1F85	.	.	.	35/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAAATACAAA	.	4	ESCA
WDR76	0	.	GRCh37	15	44158510	44158510	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1801A>C	p.Met601Leu	p.M601L	ENST00000263795	13/13	146	118	27	158	158	0	WDR76,missense_variant,p.Met537Leu,ENST00000381246,;WDR76,missense_variant,p.Met601Leu,ENST00000263795,;FRMD5,downstream_gene_variant,,ENST00000417257,;FRMD5,downstream_gene_variant,,ENST00000402883,;Y_RNA,upstream_gene_variant,,ENST00000363521,;WDR76,non_coding_transcript_exon_variant,,ENST00000478130,;	C	ENSG00000092470	ENST00000263795	Transcript	missense_variant	1871	1801	601	M/L	Atg/Ctg	.	.	.	1	WDR76	HGNC	25773	protein_coding	YES	CCDS10106.1	ENSP00000263795	WDR76_HUMAN	C9JE56_HUMAN	UPI000013D462	.	tolerated(0.24)	benign(0.004)	13/13	.	hmmpanther:PTHR14773:SF0,hmmpanther:PTHR14773,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCCATGCAC	.	5	ESCA
EIF3J	0	.	GRCh37	15	44846786	44846786	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330A>G	p.%3D	p.P110P	ENST00000261868	5/8	54	41	12	55	55	0	EIF3J,synonymous_variant,p.%3D,ENST00000261868,;EIF3J,synonymous_variant,p.%3D,ENST00000535391,;EIF3J,synonymous_variant,p.%3D,ENST00000424492,;EIF3J,upstream_gene_variant,,ENST00000536248,;RP11-151N17.1,upstream_gene_variant,,ENST00000558006,;EIF3J,non_coding_transcript_exon_variant,,ENST00000558053,;EIF3J,downstream_gene_variant,,ENST00000558227,;EIF3J,upstream_gene_variant,,ENST00000558353,;	G	ENSG00000104131	ENST00000261868	Transcript	synonymous_variant	468	330	110	P	ccA/ccG	.	.	.	1	EIF3J	HGNC	3270	protein_coding	YES	CCDS10111.1	ENSP00000261868	EIF3J_HUMAN	.	UPI000012D2F9	.	.	.	5/8	.	HAMAP:MF_03009,hmmpanther:PTHR21681,Pfam_domain:PF08597	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCAGAAGA	.	5	ESCA
SIN3A	0	.	GRCh37	15	75692462	75692462	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1773G>T	p.Trp591Cys	p.W591C	ENST00000394947	12/21	30	23	6	18	18	0	SIN3A,missense_variant,p.Trp591Cys,ENST00000394949,;SIN3A,missense_variant,p.Trp591Cys,ENST00000394947,;SIN3A,missense_variant,p.Trp591Cys,ENST00000360439,;	A	ENSG00000169375	ENST00000394947	Transcript	missense_variant	2088	1773	591	W/C	tgG/tgT	.	.	.	-1	SIN3A	HGNC	19353	protein_coding	YES	CCDS10279.1	ENSP00000378402	SIN3A_HUMAN	H3BT34_HUMAN,H3BQ88_HUMAN,H3BQ76_HUMAN,H3BP90_HUMAN,H3BNZ3_HUMAN,H3BNA0_HUMAN	UPI000013EAD4	.	deleterious(0)	probably_damaging(1)	12/21	.	hmmpanther:PTHR12346,hmmpanther:PTHR12346:SF2,Pfam_domain:PF08295,SMART_domains:SM00761	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGACCACGA	.	5	ESCA
SNX29	0	.	GRCh37	16	12162928	12162928	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1258A>G	p.Ser420Gly	p.S420G	ENST00000566228	10/21	49	36	13	53	53	0	SNX29,missense_variant,p.Ser420Gly,ENST00000566228,;SNX29,missense_variant,p.Ser35Gly,ENST00000323433,;SNX29,missense_variant,p.Ser54Gly,ENST00000563308,;SNX29,missense_variant,p.Ser35Gly,ENST00000306030,;	G	ENSG00000048471	ENST00000566228	Transcript	missense_variant	1327	1258	420	S/G	Agc/Ggc	.	.	.	1	SNX29	HGNC	30542	protein_coding	YES	CCDS10553.2	ENSP00000456480	SNX29_HUMAN	J3KNF2_HUMAN	UPI00000382F9	.	deleterious(0.03)	benign(0.003)	10/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGAAGCCTG	.	5	ESCA
ERN2	0	.	GRCh37	16	23706340	23706340	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2044G>A	p.Val682Met	p.V682M	ENST00000256797	16/22	67	49	17	67	67	0	ERN2,missense_variant,p.Val582Met,ENST00000457008,;ERN2,missense_variant,p.Val682Met,ENST00000256797,;PLK1,downstream_gene_variant,,ENST00000300093,;ERN2,upstream_gene_variant,,ENST00000562458,;ERN2,intron_variant,,ENST00000562562,;PLK1,downstream_gene_variant,,ENST00000564794,;PLK1,downstream_gene_variant,,ENST00000562272,;	T	ENSG00000134398	ENST00000256797	Transcript	missense_variant	2213	2044	682	V/M	Gtg/Atg	.	.	.	-1	ERN2	HGNC	16942	protein_coding	YES	CCDS32407.1	ENSP00000256797	ERN2_HUMAN	.	UPI000041A8F8	.	deleterious(0)	probably_damaging(0.998)	16/22	.	PROSITE_profiles:PS50011,hmmpanther:PTHR13954:SF9,hmmpanther:PTHR13954,PROSITE_patterns:PS00108,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTACCTATGT	.	5	ESCA
C16orf82	0	.	GRCh37	16	27079902	27079902	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1875C>A	.	.	ENST00000505035	1/1	11	8	3	12	12	0	C16orf82,non_coding_transcript_exon_variant,,ENST00000505035,;C16orf82,non_coding_transcript_exon_variant,,ENST00000418886,;RP11-673P17.2,upstream_gene_variant,,ENST00000565783,;	A	ENSG00000234186	ENST00000505035	Transcript	non_coding_transcript_exon_variant	1875	.	.	.	.	.	.	.	1	C16orf82	HGNC	30755	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAGCAGCCA	.	2	ESCA
SULT1A1	0	.	GRCh37	16	28620538	28620538	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4-358C>G	.	.	ENST00000395609	.	57	50	7	74	74	0	SULT1A1,5_prime_UTR_variant,,ENST00000395607,;SULT1A1,intron_variant,,ENST00000566189,;SULT1A1,intron_variant,,ENST00000567512,;SULT1A1,intron_variant,,ENST00000314752,;SULT1A1,intron_variant,,ENST00000395609,;SULT1A1,intron_variant,,ENST00000350842,;SULT1A1,upstream_gene_variant,,ENST00000569554,;SULT1A1,non_coding_transcript_exon_variant,,ENST00000567998,;SULT1A1,intron_variant,,ENST00000564818,;SULT1A1,intron_variant,,ENST00000562058,;SULT1A1,intron_variant,,ENST00000563493,;	C	ENSG00000196502	ENST00000395609	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SULT1A1	HGNC	11453	protein_coding	YES	CCDS32420.1	ENSP00000378972	ST1A1_HUMAN	Q9UMT9_HUMAN,H3BRY5_HUMAN	UPI000013EA41	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTGCTGTCTCC	.	3	ESCA
MAPK3	0	.	GRCh37	16	30129094	30129094	+	Silent	SNP	C	C	T	rs763165244	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672G>A	p.%3D	p.K224K	ENST00000263025	5/9	31	24	7	38	38	0	MAPK3,synonymous_variant,p.%3D,ENST00000395202,;MAPK3,synonymous_variant,p.%3D,ENST00000263025,;MAPK3,synonymous_variant,p.%3D,ENST00000484663,;MAPK3,synonymous_variant,p.%3D,ENST00000322266,;MAPK3,synonymous_variant,p.%3D,ENST00000395200,;MAPK3,synonymous_variant,p.%3D,ENST00000395199,;MAPK3,synonymous_variant,p.%3D,ENST00000403394,;MAPK3,5_prime_UTR_variant,,ENST00000478356,;GDPD3,upstream_gene_variant,,ENST00000406256,;MAPK3,downstream_gene_variant,,ENST00000481230,;MAPK3,upstream_gene_variant,,ENST00000494643,;MAPK3,synonymous_variant,p.%3D,ENST00000466521,;MAPK3,synonymous_variant,p.%3D,ENST00000490298,;MAPK3,upstream_gene_variant,,ENST00000473431,;MAPK3,upstream_gene_variant,,ENST00000461737,;MAPK3,upstream_gene_variant,,ENST00000485579,;MAPK3,downstream_gene_variant,,ENST00000483869,;GDPD3,upstream_gene_variant,,ENST00000360688,;	T	ENSG00000102882	ENST00000263025	Transcript	synonymous_variant	757	672	224	K	aaG/aaA	rs763165244	.	.	-1	MAPK3	HGNC	6877	protein_coding	YES	CCDS10672.1	ENSP00000263025	MK03_HUMAN	Q9BWJ1_HUMAN,Q7Z3H5_HUMAN,L7RXH5_HUMAN,H0YEX6_HUMAN,H0YDH9_HUMAN,E9PRH7_HUMAN,B3KR49_HUMAN	UPI0000000DD7	.	.	.	5/9	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF111,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGACTTGGT	.	5	ESCA
SRCAP	0	.	GRCh37	16	30721919	30721919	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135-156A>T	.	.	ENST00000262518	.	54	43	11	41	41	0	SRCAP,intron_variant,,ENST00000262518,;SRCAP,intron_variant,,ENST00000344771,;SRCAP,intron_variant,,ENST00000395059,;SNORA30,non_coding_transcript_exon_variant,,ENST00000384028,;SRCAP,intron_variant,,ENST00000380361,;SRCAP,intron_variant,,ENST00000483083,;	T	ENSG00000080603	ENST00000262518	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SRCAP	HGNC	16974	protein_coding	YES	CCDS10689.2	ENSP00000262518	SRCAP_HUMAN	G1UI29_HUMAN,C9J4U4_HUMAN	UPI000059D368	.	.	.	.	8/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGAGAAAA	.	5	ESCA
ZNF646	0	.	GRCh37	16	31091869	31091869	+	Silent	SNP	G	G	A	rs369374909	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4224G>A	p.%3D	p.A1408A	ENST00000300850	2/3	85	57	27	96	96	0	ZNF646,synonymous_variant,p.%3D,ENST00000394979,;ZNF646,synonymous_variant,p.%3D,ENST00000300850,;PRSS53,downstream_gene_variant,,ENST00000280606,;ZNF646,downstream_gene_variant,,ENST00000428260,;ZNF646,downstream_gene_variant,,ENST00000564189,;RP11-196G11.1,downstream_gene_variant,,ENST00000533518,;PRSS53,downstream_gene_variant,,ENST00000486499,;	A	ENSG00000167395	ENST00000300850	Transcript	synonymous_variant	4513	4224	1408	A	gcG/gcA	rs369374909	.	.	1	ZNF646	HGNC	29004	protein_coding	YES	CCDS10702.1	ENSP00000300850	ZN646_HUMAN	H3BSD0_HUMAN,C9J3L0_HUMAN	UPI00001FFF54	.	.	.	2/3	.	hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF182	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCGAACCT	byCluster	5	ESCA
MYH1	0	.	GRCh37	17	10408304	10408304	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2514C>A	p.Phe838Leu	p.F838L	ENST00000226207	22/40	82	40	42	78	78	0	MYH1,missense_variant,p.Phe838Leu,ENST00000226207,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	T	ENSG00000109061	ENST00000226207	Transcript	missense_variant	2609	2514	838	F/L	ttC/ttA	COSM3513856	.	.	-1	MYH1	HGNC	7567	protein_coding	YES	CCDS11155.1	ENSP00000226207	MYH1_HUMAN	.	UPI000013C891	.	deleterious(0.01)	probably_damaging(0.997)	22/40	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF264,Gene3D:1wdcA00,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTGAAATA	.	5	ESCA
MAP2K4	0	.	GRCh37	17	11985228	11985228	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393+381C>T	.	.	ENST00000353533	.	42	36	6	35	35	0	MAP2K4,intron_variant,,ENST00000353533,;MAP2K4,intron_variant,,ENST00000415385,;MIR744,mature_miRNA_variant,,ENST00000578242,;MAP2K4,intron_variant,,ENST00000582897,;MAP2K4,intron_variant,,ENST00000579089,;MAP2K4,intron_variant,,ENST00000581941,;MAP2K4,intron_variant,,ENST00000602375,;MAP2K4,intron_variant,,ENST00000602811,;MAP2K4,intron_variant,,ENST00000582183,;MAP2K4,intron_variant,,ENST00000538465,;MAP2K4,intron_variant,,ENST00000602537,;MAP2K4,intron_variant,,ENST00000602686,;MAP2K4,intron_variant,,ENST00000602305,;	T	ENSG00000065559	ENST00000353533	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MAP2K4	HGNC	6844	protein_coding	YES	CCDS11162.1	ENSP00000262445	MP2K4_HUMAN	J3QQR2_HUMAN,J3KTI6_HUMAN	UPI000012F48E	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGTGCGGGGC	.	4	ESCA
DUSP14	0	.	GRCh37	17	35872295	35872295	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-80A>T	.	.	ENST00000487847	2/2	80	70	10	65	65	0	DUSP14,5_prime_UTR_variant,,ENST00000394386,;DUSP14,5_prime_UTR_variant,,ENST00000394389,;DUSP14,5_prime_UTR_variant,,ENST00000487847,;SYNRG,downstream_gene_variant,,ENST00000339208,;SYNRG,downstream_gene_variant,,ENST00000346661,;SYNRG,downstream_gene_variant,,ENST00000590102,;	T	ENSG00000161326	ENST00000487847	Transcript	5_prime_UTR_variant	899	.	.	.	.	.	.	.	1	DUSP14	HGNC	17007	protein_coding	YES	CCDS11320.1	ENSP00000466299	DUS14_HUMAN	Q6FI36_HUMAN	UPI0000129965	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCTAATTTT	.	4	ESCA
ZZEF1	0	.	GRCh37	17	3910023	3910023	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*161G>A	.	.	ENST00000381638	55/55	49	41	8	37	37	0	ZZEF1,3_prime_UTR_variant,,ENST00000381638,;ZZEF1,downstream_gene_variant,,ENST00000573536,;	T	ENSG00000074755	ENST00000381638	Transcript	3_prime_UTR_variant	9172	.	.	.	.	.	.	.	-1	ZZEF1	HGNC	29027	protein_coding	YES	CCDS11043.1	ENSP00000371051	ZZEF1_HUMAN	.	UPI00004569F7	.	.	.	55/55	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCACGGGAG	.	5	ESCA
CD300LG	0	.	GRCh37	17	41926113	41926113	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.231C>A	p.%3D	p.G77G	ENST00000317310	2/7	27	22	5	14	14	0	CD300LG,synonymous_variant,p.%3D,ENST00000317310,;CD300LG,synonymous_variant,p.%3D,ENST00000293396,;CD300LG,synonymous_variant,p.%3D,ENST00000588884,;CD300LG,synonymous_variant,p.%3D,ENST00000586233,;CD300LG,synonymous_variant,p.%3D,ENST00000377203,;CD300LG,synonymous_variant,p.%3D,ENST00000539718,;	A	ENSG00000161649	ENST00000317310	Transcript	synonymous_variant	272	231	77	G	ggC/ggA	.	.	.	1	CD300LG	HGNC	30455	protein_coding	YES	CCDS11470.1	ENSP00000321005	CLM9_HUMAN	.	UPI000013E104	.	.	.	2/7	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11860,hmmpanther:PTHR11860:SF42,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGGGCAGGGT	.	4	ESCA
RNF126P1	0	.	GRCh37	17	55123062	55123062	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.224G>A	.	.	ENST00000567452	1/1	64	56	8	75	75	0	RNF126P1,non_coding_transcript_exon_variant,,ENST00000567452,;RNF126P1,non_coding_transcript_exon_variant,,ENST00000569893,;	A	ENSG00000261192	ENST00000567452	Transcript	non_coding_transcript_exon_variant	224	.	.	.	.	.	.	.	1	RNF126P1	HGNC	30340	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCCGGCCGC	.	4	ESCA
MTMR4	0	.	GRCh37	17	56569953	56569953	+	Missense_Mutation	SNP	C	C	T	rs369998064	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3329G>A	p.Arg1110His	p.R1110H	ENST00000323456	18/19	46	33	12	40	40	0	MTMR4,missense_variant,p.Arg1110His,ENST00000323456,;MTMR4,missense_variant,p.Arg1053His,ENST00000579925,;HSF5,upstream_gene_variant,,ENST00000323777,;MTMR4,non_coding_transcript_exon_variant,,ENST00000578259,;	T	ENSG00000108389	ENST00000323456	Transcript	missense_variant	3454	3329	1110	R/H	cGc/cAc	rs369998064,COSM1197641	.	.	-1	MTMR4	HGNC	7452	protein_coding	YES	CCDS11608.1	ENSP00000325285	MTMR4_HUMAN	J3QRJ2_HUMAN	UPI00002010DE	.	deleterious(0)	probably_damaging(1)	18/19	.	hmmpanther:PTHR10807:SF64,hmmpanther:PTHR10807,Pfam_domain:PF01363,Gene3D:3.30.40.10,SMART_domains:SM00064,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAGCGAGTC	byCluster	5	ESCA
CLTC	0	.	GRCh37	17	57742246	57742246	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1620A>T	p.Glu540Asp	p.E540D	ENST00000269122	10/32	66	55	11	52	52	0	CLTC,missense_variant,p.Glu540Asp,ENST00000269122,;CLTC,missense_variant,p.Glu540Asp,ENST00000393043,;CLTC,intron_variant,,ENST00000579456,;CLTC,non_coding_transcript_exon_variant,,ENST00000466513,;CLTC,downstream_gene_variant,,ENST00000483176,;	T	ENSG00000141367	ENST00000269122	Transcript	missense_variant	1894	1620	540	E/D	gaA/gaT	.	.	.	1	CLTC	HGNC	2092	protein_coding	YES	CCDS32696.1	ENSP00000269122	CLH1_HUMAN	Q49AL0_HUMAN	UPI0000127ABD	.	tolerated(0.31)	possibly_damaging(0.73)	10/32	.	PROSITE_profiles:PS50236,hmmpanther:PTHR10292:SF7,hmmpanther:PTHR10292,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAAGAGCC	.	5	ESCA
BPTF	0	.	GRCh37	17	65905779	65905779	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2894C>T	p.Pro965Leu	p.P965L	ENST00000306378	10/28	32	27	4	44	44	0	BPTF,missense_variant,p.Pro965Leu,ENST00000306378,;BPTF,missense_variant,p.Pro1091Leu,ENST00000321892,;BPTF,missense_variant,p.Pro1028Leu,ENST00000544778,;BPTF,missense_variant,p.Pro1091Leu,ENST00000335221,;BPTF,missense_variant,p.Pro952Leu,ENST00000424123,;	T	ENSG00000171634	ENST00000306378	Transcript	missense_variant	2954	2894	965	P/L	cCt/cTt	.	.	.	1	BPTF	HGNC	3581	protein_coding	YES	CCDS11673.1	ENSP00000307208	BPTF_HUMAN	.	UPI00002263BF	.	.	benign(0.005)	10/28	.	hmmpanther:PTHR22880:SF5,hmmpanther:PTHR22880	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGCCTGATT	.	4	ESCA
ITGB4	0	.	GRCh37	17	73729646	73729654	+	In_Frame_Del	DEL	GCCGTGCTC	GCCGTGCTC	-	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	GCCGTGCTC	GCCGTGCTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1530_1538delGCCGTGCTC	p.Lys510_Ser513delinsAsn	p.K510_S513delinsN	ENST00000200181	13/40	85	73	12	71	71	0	ITGB4,inframe_deletion,p.Lys510_Ser513delinsAsn,ENST00000579662,;ITGB4,inframe_deletion,p.Lys510_Ser513delinsAsn,ENST00000450894,;ITGB4,inframe_deletion,p.Lys510_Ser513delinsAsn,ENST00000339591,;ITGB4,inframe_deletion,p.Lys510_Ser513delinsAsn,ENST00000449880,;ITGB4,inframe_deletion,p.Lys510_Ser513delinsAsn,ENST00000200181,;ITGB4,intron_variant,,ENST00000582629,;ITGB4,non_coding_transcript_exon_variant,,ENST00000584558,;ITGB4,non_coding_transcript_exon_variant,,ENST00000584374,;ITGB4,non_coding_transcript_exon_variant,,ENST00000580542,;	-	ENSG00000132470	ENST00000200181	Transcript	inframe_deletion	1717-1725	1530-1538	510-513	KPCS/N	aaGCCGTGCTCc/aac	.	.	.	1	ITGB4	HGNC	6158	protein_coding	YES	CCDS11727.1	ENSP00000200181	ITB4_HUMAN	.	UPI00001AE5C0	.	.	.	13/40	.	hmmpanther:PTHR10082:SF6,hmmpanther:PTHR10082,PROSITE_patterns:PS00243,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002513,Prints_domain:PR01186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGACAAGCCGTGCTCCGGCC	.	3	ESCA
TP53	0	.	GRCh37	17	7578457	7578457	+	Missense_Mutation	SNP	C	C	T	rs587782144	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473G>A	p.Arg158His	p.R158H	ENST00000269305	5/11	357	281	76	455	454	0	TP53,missense_variant,p.Arg158His,ENST00000508793,;TP53,missense_variant,p.Arg158His,ENST00000413465,;TP53,missense_variant,p.Arg158His,ENST00000420246,;TP53,missense_variant,p.Arg158His,ENST00000269305,;TP53,missense_variant,p.Arg26His,ENST00000509690,;TP53,missense_variant,p.Arg158His,ENST00000359597,;TP53,missense_variant,p.Arg65His,ENST00000514944,;TP53,missense_variant,p.Arg158His,ENST00000445888,;TP53,missense_variant,p.Arg158His,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	663	473	158	R/H	cGc/cAc	rs587782144,CM994513,CM102353,TP53_g.12461G>A,TP53_g.12461G>T,TP53_g.12461G>C,COSM10690,COSM43615,COSM10714,COSM99678,COSM220779,COSM1649375,COSM220778,COSM1649377,COSM99675,COSM220780,COSM99676,COSM1649379,COSM3378357,COSM3958835,COSM1640853,COSM1649374,COSM1649376,COSM220781,COSM1649378,COSM99677	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.1)	benign(0.438)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R158H|c.473G>A|24,SITE|p.R158H|c.473G>A|24,SITE|p.R158H|c.473G>A|78,SITE|p.R158H|c.473G>A|7,SITE|p.R158H|c.473G>A|11,SITE|p.R65H|c.194G>A|24,SITE|p.R26H|c.77G>A|25,CODON|p.0?|c.1_1182del1182|6,CODON|p.R158fs*11|c.472_475delCGCG|3,CODON|p.R158_A159insX|c.473_474insNNN|4,CODON|p.R158R|c.474C>T|6,CODON|p.R158L|c.473G>T|14,CODON|p.R158L|c.473G>T|63,CODON|p.R158P|c.473G>C|10,CODON|p.R158L|c.473G>T|5,CODON|p.R158L|c.473G>T|14,CODON|p.R26L|c.77G>T|19,CODON|p.R65L|c.194G>T|14,CODON|p.R158C|c.471_472CC>TT|6,CODON|p.R158fs*12|c.472delC|6,BUFFER|p.I162V|c.484A>G|5,BUFFER|p.I162F|c.484A>T|11,BUFFER|p.A161A|c.483C>T|5,BUFFER|p.A161fs*9|c.481delG|3,BUFFER|p.A161V|c.482C>T|9,BUFFER|p.A161D|c.482C>A|9,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A29T|c.85G>A|10,BUFFER|p.A161T|c.481G>A|52,BUFFER|p.A68T|c.202G>A|10,BUFFER|p.A161S|c.481G>T|3,BUFFER|p.M160I|c.480G>T|4,BUFFER|p.M160I|c.480G>A|3,BUFFER|p.M160K|c.479T>A|4,BUFFER|p.M160L|c.478A>C|3,BUFFER|p.M160V|c.478A>G|5,BUFFER|p.A159A|c.477C>T|8,BUFFER|p.A159fs*11|c.475delG|4,BUFFER|p.A159V|c.476C>T|9,BUFFER|p.A66V|c.197C>T|9,BUFFER|p.A27V|c.80C>T|9,BUFFER|p.A159V|c.476C>T|39,BUFFER|p.A159V|c.476C>T|9,BUFFER|p.A159D|c.476C>A|6,BUFFER|p.A159S|c.475G>T|5,BUFFER|p.A159P|c.475G>C|3,BUFFER|p.A159P|c.475G>C|5,BUFFER|p.A159T|c.475G>A|7,BUFFER|p.A66P|c.196G>C|5,BUFFER|p.A159P|c.475G>C|20,BUFFER|p.A159P|c.475G>C|5,BUFFER|p.A27P|c.79G>C|5,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R158C|c.472C>T|17,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R26C|c.76C>T|7,BUFFER|p.R65C|c.193C>T|7,BUFFER|p.R158G|c.472C>G|12,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R65G|c.193C>G|3,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R26G|c.76C>G|4,BUFFER|p.V157V|c.471C>A|3,BUFFER|p.V157G|c.470T>G|9,BUFFER|p.V157D|c.470T>A|8,BUFFER|p.V157F|c.469G>T|7,BUFFER|p.V157F|c.469G>T|8,BUFFER|p.V157L|c.469G>C|6,BUFFER|p.V157F|c.469G>T|22,BUFFER|p.V157F|c.469G>T|162,BUFFER|p.V157I|c.469G>A|10,BUFFER|p.V157F|c.469G>T|22,BUFFER|p.V25F|c.73G>T|25,BUFFER|p.V64F|c.190G>T|22,BUFFER|p.V157fs*13|c.468delC|3,BUFFER|p.R156P|c.467G>C|26,BUFFER|p.R63P|c.188G>C|4,BUFFER|p.R156H|c.467G>A|11,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R24P|c.71G>C|4,BUFFER|p.R156L|c.467G>T|3,BUFFER|p.P152fs*14|c.454_466del13|5,BUFFER|p.R156fs*14|c.466delC|9,BUFFER|p.R156S|c.466C>A|3,BUFFER|p.R156G|c.466C>G|3,BUFFER|p.R156C|c.466C>T|4,BUFFER|p.T155T|c.465C>T|4,BUFFER|p.T155N|c.464C>A|4,BUFFER|p.T155N|c.464C>A|5,BUFFER|p.T62N|c.185C>A|6,BUFFER|p.T155N|c.464C>A|25,BUFFER|p.T155I|c.464C>T|15,BUFFER|p.T23N|c.68C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.T62P|c.184A>C|3,BUFFER|p.T155P|c.463A>C|16,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T23P|c.67A>C|4,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T155A|c.463A>G|8,BUFFER|p.G154I|c.460_461GG>AT|3,BUFFER|p.G154G|c.462C>T|9	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCGCGGACG	byCluster	5	ESCA
TP53	0	.	GRCh37	17	7578556	7578556	+	Splice_Site	SNP	T	T	A	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376-2A>T	.	p.X126_splice	ENST00000269305	.	214	122	92	289	289	0	TP53,splice_acceptor_variant,,ENST00000508793,;TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000269305,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000503591,;TP53,splice_acceptor_variant,,ENST00000455263,;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	splice_acceptor_variant	.	.	.	.	.	CS114003,TP53_g.12362A>G,TP53_g.12362A>T,TP53_g.12362del,TP53_g.12362A>C,COSM45672,COSM46049,COSM45658,COSM21585,COSM562615,COSM318167,COSM3675526,COSM318166,COSM562616,COSM3675529,COSM3675528,COSM3388230,COSM3717681,COSM1649367,COSM1646843,COSM3675527,COSM318168,COSM3675530,COSM562617	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.376-2A>T|3,SITE|p.?|c.97-2A>T|3,SITE|p.?|c.376-2A>T|3,SITE|p.?|c.376-2A>T|3,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.Y126_K132delYSPALNK|c.376_396del21|6,BUFFER|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.P128L|c.383C>T|3,BUFFER|p.P128fs*42|c.382delC|3,BUFFER|p.P128S|c.382C>T|7,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S127Y|c.380C>A|10,BUFFER|p.S34F|c.101C>T|11,BUFFER|p.S127F|c.380C>T|4,BUFFER|p.S127F|c.380C>T|33,BUFFER|p.S127F|c.380C>T|3,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S34P|c.100T>C|4,BUFFER|p.S34T|c.100T>A|4,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.S127P|c.379T>C|8,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127T|c.379T>A|10,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>G|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>A|4,BUFFER|p.Y33*|c.99C>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y33C|c.98A>G|6,BUFFER|p.Y126C|c.377A>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y126C|c.377A>G|9,BUFFER|p.Y126S|c.377A>C|3,BUFFER|p.Y126C|c.377A>G|5,BUFFER|p.Y126N|c.376T>A|7,BUFFER|p.Y33D|c.97T>G|7,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.Y126D|c.376T>G|10,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.?|c.97-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|10,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.97-1G>A|20,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>T|9,BUFFER|p.?|c.376-2A>G|4,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.97-2A>G|10,BUFFER|p.?|c.376-2A>G|17,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.376-2A>G|6,BUFFER|p.?|c.376-2A>C|4,BUFFER|p.?|c.376-4A>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTACTGTAGG	.	5	ESCA
STRA13	0	.	GRCh37	17	79977072	79977072	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9G>A	.	.	ENST00000392359	5/5	102	85	17	92	92	0	STRA13,missense_variant,p.Ser129Asn,ENST00000584347,;STRA13,3_prime_UTR_variant,,ENST00000392359,;STRA13,3_prime_UTR_variant,,ENST00000580435,;STRA13,3_prime_UTR_variant,,ENST00000579520,;STRA13,3_prime_UTR_variant,,ENST00000306704,;STRA13,3_prime_UTR_variant,,ENST00000584600,;ASPSCR1,downstream_gene_variant,,ENST00000583744,;ASPSCR1,downstream_gene_variant,,ENST00000306739,;LRRC45,upstream_gene_variant,,ENST00000577638,;LRRC45,upstream_gene_variant,,ENST00000306688,;ASPSCR1,downstream_gene_variant,,ENST00000580534,;ASPSCR1,downstream_gene_variant,,ENST00000582355,;ASPSCR1,downstream_gene_variant,,ENST00000306729,;STRA13,non_coding_transcript_exon_variant,,ENST00000583767,;STRA13,non_coding_transcript_exon_variant,,ENST00000584514,;STRA13,non_coding_transcript_exon_variant,,ENST00000580090,;STRA13,non_coding_transcript_exon_variant,,ENST00000577379,;ASPSCR1,downstream_gene_variant,,ENST00000583142,;LRRC45,upstream_gene_variant,,ENST00000583383,;ASPSCR1,downstream_gene_variant,,ENST00000582404,;ASPSCR1,downstream_gene_variant,,ENST00000585140,;STRA13,non_coding_transcript_exon_variant,,ENST00000585091,;ASPSCR1,downstream_gene_variant,,ENST00000585274,;ASPSCR1,downstream_gene_variant,,ENST00000577733,;ASPSCR1,downstream_gene_variant,,ENST00000583693,;ASPSCR1,downstream_gene_variant,,ENST00000578236,;ASPSCR1,downstream_gene_variant,,ENST00000584454,;ASPSCR1,downstream_gene_variant,,ENST00000581608,;ASPSCR1,downstream_gene_variant,,ENST00000578361,;	T	ENSG00000169689	ENST00000392359	Transcript	3_prime_UTR_variant	312	.	.	.	.	.	.	.	-1	STRA13	HGNC	11422	protein_coding	YES	CCDS59303.1	ENSP00000376168	CENPX_HUMAN	.	UPI000015D192	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGGCTGAGA	.	5	ESCA
GLP2R	0	.	GRCh37	17	9760839	9760839	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.711C>T	p.%3D	p.N237N	ENST00000262441	6/13	78	64	13	88	88	0	GLP2R,synonymous_variant,p.%3D,ENST00000574745,;GLP2R,synonymous_variant,p.%3D,ENST00000304773,;GLP2R,synonymous_variant,p.%3D,ENST00000262441,;GLP2R,3_prime_UTR_variant,,ENST00000458005,;NPM1P45,upstream_gene_variant,,ENST00000583151,;	T	ENSG00000065325	ENST00000262441	Transcript	synonymous_variant	1224	711	237	N	aaC/aaT	.	.	.	1	GLP2R	HGNC	4325	protein_coding	YES	CCDS11150.1	ENSP00000262441	GLP2R_HUMAN	I3L151_HUMAN,I3L0P5_HUMAN,E9PC86_HUMAN	UPI0000050469	.	.	.	6/13	.	PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF269,Pfam_domain:PF00002,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAACTCTTA	.	5	ESCA
ANKRD30B	0	.	GRCh37	18	14784464	14784464	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1602T>A	p.%3D	p.P534P	ENST00000358984	14/36	133	111	22	130	130	0	ANKRD30B,synonymous_variant,p.%3D,ENST00000447268,;ANKRD30B,synonymous_variant,p.%3D,ENST00000358984,;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,synonymous_variant,p.%3D,ENST00000580206,;	A	ENSG00000180777	ENST00000358984	Transcript	synonymous_variant	1782	1602	534	P	ccT/ccA	.	.	.	1	ANKRD30B	HGNC	24165	protein_coding	YES	CCDS54182.1	ENSP00000351875	AN30B_HUMAN	.	UPI0000425FF7	.	.	.	14/36	.	hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCCTGCCGT	.	5	ESCA
USP14	0	.	GRCh37	18	211238	211238	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439A>G	p.Tyr480Cys	p.Y480C	ENST00000261601	16/16	46	38	8	35	35	0	USP14,missense_variant,p.Tyr480Cys,ENST00000261601,;USP14,missense_variant,p.Tyr434Cys,ENST00000383589,;USP14,missense_variant,p.Tyr445Cys,ENST00000582707,;USP14,missense_variant,p.Tyr469Cys,ENST00000400266,;THOC1,downstream_gene_variant,,ENST00000261600,;USP14,non_coding_transcript_exon_variant,,ENST00000578786,;USP14,non_coding_transcript_exon_variant,,ENST00000578942,;THOC1,downstream_gene_variant,,ENST00000579232,;THOC1,downstream_gene_variant,,ENST00000584470,;THOC1,downstream_gene_variant,,ENST00000580038,;THOC1,downstream_gene_variant,,ENST00000583228,;THOC1,downstream_gene_variant,,ENST00000585307,;THOC1,downstream_gene_variant,,ENST00000578529,;THOC1,downstream_gene_variant,,ENST00000577429,;	G	ENSG00000101557	ENST00000261601	Transcript	missense_variant	1530	1439	480	Y/C	tAt/tGt	.	.	.	1	USP14	HGNC	12612	protein_coding	YES	CCDS32780.1	ENSP00000261601	UBP14_HUMAN	J3KS55_HUMAN,D3DUG9_HUMAN	UPI0000163941	.	deleterious(0)	probably_damaging(0.952)	16/16	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF351,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTATGGGC	.	5	ESCA
KLHL14	0	.	GRCh37	18	30260215	30260215	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1505A>G	p.Gln502Arg	p.Q502R	ENST00000359358	7/9	49	38	10	50	50	0	KLHL14,missense_variant,p.Gln502Arg,ENST00000359358,;	C	ENSG00000197705	ENST00000359358	Transcript	missense_variant	1944	1505	502	Q/R	cAa/cGa	.	.	.	-1	KLHL14	HGNC	29266	protein_coding	YES	CCDS32813.1	ENSP00000352314	KLH14_HUMAN	.	UPI00001C1FF2	.	tolerated(0.06)	probably_damaging(0.932)	7/9	.	Superfamily_domains:0052715,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Pfam_domain:PF01344,Gene3D:1zgkA00,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D503H|c.1507G>C|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTTGTTTT	.	5	ESCA
ASXL3	0	.	GRCh37	18	31319646	31319646	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2278A>T	p.Ile760Leu	p.I760L	ENST00000269197	11/12	18	15	3	17	17	0	ASXL3,missense_variant,p.Ile760Leu,ENST00000269197,;ASXL3,3_prime_UTR_variant,,ENST00000592288,;	T	ENSG00000141431	ENST00000269197	Transcript	missense_variant	2278	2278	760	I/L	Ata/Tta	.	.	.	1	ASXL3	HGNC	29357	protein_coding	YES	CCDS45847.1	ENSP00000269197	ASXL3_HUMAN	K7EQY1_HUMAN	UPI000156D0F3	.	.	benign(0)	11/12	.	hmmpanther:PTHR13578:SF18,hmmpanther:PTHR13578	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCCATAAAT	.	2	ESCA
FHOD3	0	.	GRCh37	18	34298061	34298061	+	Missense_Mutation	SNP	C	C	T	rs373880183	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2275C>T	p.Arg759Trp	p.R759W	ENST00000257209	16/25	101	80	21	98	98	0	FHOD3,missense_variant,p.Arg721Trp,ENST00000445677,;FHOD3,missense_variant,p.Arg520Trp,ENST00000592930,;FHOD3,missense_variant,p.Arg759Trp,ENST00000257209,;FHOD3,missense_variant,p.Arg934Trp,ENST00000590592,;FHOD3,missense_variant,p.Arg742Trp,ENST00000359247,;FHOD3,intron_variant,,ENST00000591635,;FHOD3,upstream_gene_variant,,ENST00000592128,;FHOD3,downstream_gene_variant,,ENST00000587493,;	T	ENSG00000134775	ENST00000257209	Transcript	missense_variant	2397	2275	759	R/W	Cgg/Tgg	rs373880183	.	.	1	FHOD3	HGNC	26178	protein_coding	YES	CCDS32816.1	ENSP00000257209	FHOD3_HUMAN	.	UPI0000251DB7	.	deleterious(0)	probably_damaging(0.997)	16/25	.	hmmpanther:PTHR23213:SF213,hmmpanther:PTHR23213	.	.	.	.	.	.	.	G:0	G:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAATCGGGGC	byFrequency|byCluster	5	ESCA
KEAP1	0	.	GRCh37	19	10610154	10610154	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	2/6	19	16	3	22	22	0	KEAP1,missense_variant,p.Gly186Ser,ENST00000591419,;KEAP1,missense_variant,p.Gly186Ser,ENST00000591039,;KEAP1,missense_variant,p.Gly186Ser,ENST00000393623,;KEAP1,missense_variant,p.Gly186Ser,ENST00000171111,;KEAP1,missense_variant,p.Gly186Ser,ENST00000592055,;KEAP1,non_coding_transcript_exon_variant,,ENST00000588024,;KEAP1,3_prime_UTR_variant,,ENST00000585845,;	T	ENSG00000079999	ENST00000171111	Transcript	missense_variant	1104	556	186	G/S	Ggc/Agc	.	.	.	-1	KEAP1	HGNC	23177	protein_coding	YES	CCDS12239.1	ENSP00000171111	KEAP1_HUMAN	K7ESE0_HUMAN,K7EJD8_HUMAN,K7EJ49_HUMAN	UPI000007139C	.	deleterious(0)	probably_damaging(1)	2/6	.	hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF07707,SMART_domains:SM00875,PIRSF_domain:PIRSF037037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGCCGATGG	.	2	ESCA
CCDC151	0	.	GRCh37	19	11537524	11537524	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693G>T	p.%3D	p.L231L	ENST00000356392	5/13	28	15	12	49	49	0	CCDC151,synonymous_variant,p.%3D,ENST00000356392,;CCDC151,synonymous_variant,p.%3D,ENST00000586836,;CCDC151,synonymous_variant,p.%3D,ENST00000545100,;CCDC151,intron_variant,,ENST00000591179,;CCDC151,3_prime_UTR_variant,,ENST00000591345,;CCDC151,downstream_gene_variant,,ENST00000593281,;	A	ENSG00000198003	ENST00000356392	Transcript	synonymous_variant	781	693	231	L	ctG/ctT	.	.	.	-1	CCDC151	HGNC	28303	protein_coding	YES	CCDS42501.1	ENSP00000348757	CC151_HUMAN	K7EPK8_HUMAN,B7ZMB9_HUMAN	UPI000040CC83	.	.	.	5/13	.	hmmpanther:PTHR21694:SF1,hmmpanther:PTHR21694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.V229M|c.685G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGCAGGTA	.	5	ESCA
ZNF788	0	.	GRCh37	19	12222271	12222271	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-92G>T	.	.	ENST00000339302	3/3	28	22	6	50	50	0	ZNF788,5_prime_UTR_variant,,ENST00000339302,;ZNF788,3_prime_UTR_variant,,ENST00000596883,;ZNF788,3_prime_UTR_variant,,ENST00000430298,;ZNF20,intron_variant,,ENST00000600335,;ZNF788,upstream_gene_variant,,ENST00000397759,;RNA5SP467,downstream_gene_variant,,ENST00000391274,;ZNF788,intron_variant,,ENST00000601686,;	T	ENSG00000188474	ENST00000339302	Transcript	5_prime_UTR_variant	546	.	.	.	.	.	.	.	1	ZNF788	Uniprot_gn	33112	protein_coding	YES	.	ENSP00000342021	ZN788_HUMAN	.	UPI000041AACA	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGACAGACGCC	.	2	ESCA
KLF1	0	.	GRCh37	19	12995819	12995819	+	Silent	SNP	C	C	T	rs780786728	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.969G>A	p.%3D	p.S323S	ENST00000264834	3/3	40	34	6	53	53	0	KLF1,synonymous_variant,p.%3D,ENST00000264834,;DNASE2,upstream_gene_variant,,ENST00000538460,;DNASE2,upstream_gene_variant,,ENST00000592506,;DNASE2,upstream_gene_variant,,ENST00000222219,;CTD-2265O21.7,downstream_gene_variant,,ENST00000592400,;	T	ENSG00000105610	ENST00000264834	Transcript	synonymous_variant	1010	969	323	S	tcG/tcA	rs780786728	.	.	-1	KLF1	HGNC	6345	protein_coding	YES	CCDS12285.1	ENSP00000264834	KLF1_HUMAN	B9UZC3_HUMAN	UPI000012DED2	.	.	.	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23223,hmmpanther:PTHR23223:SF135,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGTCCGAGCG	.	4	ESCA
CPAMD8	0	.	GRCh37	19	17119359	17119359	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.656G>T	p.Gly219Val	p.G219V	ENST00000443236	7/42	36	30	6	39	39	0	CPAMD8,missense_variant,p.Gly172Val,ENST00000388925,;CPAMD8,missense_variant,p.Gly219Val,ENST00000443236,;CTD-2528A14.1,upstream_gene_variant,,ENST00000595134,;CPAMD8,missense_variant,p.Gly219Val,ENST00000291440,;	A	ENSG00000160111	ENST00000443236	Transcript	missense_variant	688	656	219	G/V	gGc/gTc	.	.	.	-1	CPAMD8	HGNC	23228	protein_coding	YES	CCDS42519.1	ENSP00000402505	CPMD8_HUMAN	.	UPI0000E8AC99	.	deleterious(0)	probably_damaging(0.972)	7/42	.	hmmpanther:PTHR11412:SF76,hmmpanther:PTHR11412,Pfam_domain:PF01835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAGCCTCGG	.	5	ESCA
ATP8B3	0	.	GRCh37	19	1809675	1809675	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369G>A	p.%3D	p.K123K	ENST00000310127	4/29	45	33	11	43	43	0	ATP8B3,synonymous_variant,p.%3D,ENST00000310127,;ATP8B3,synonymous_variant,p.%3D,ENST00000587160,;ATP8B3,synonymous_variant,p.%3D,ENST00000533993,;ATP8B3,synonymous_variant,p.%3D,ENST00000539485,;ATP8B3,synonymous_variant,p.%3D,ENST00000526092,;ATP8B3,synonymous_variant,p.%3D,ENST00000525591,;ATP8B3,missense_variant,p.Arg86Lys,ENST00000531925,;ATP8B3,upstream_gene_variant,,ENST00000533107,;	T	ENSG00000130270	ENST00000310127	Transcript	synonymous_variant	608	369	123	K	aaG/aaA	.	.	.	-1	ATP8B3	HGNC	13535	protein_coding	YES	CCDS45901.1	ENSP00000311336	AT8B3_HUMAN	.	UPI0000074660	.	.	.	4/29	.	hmmpanther:PTHR24092:SF44,hmmpanther:PTHR24092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACCTTCTC	.	5	ESCA
ELL	0	.	GRCh37	19	18553771	18553771	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1791C>T	.	.	ENST00000262809	12/12	21	15	6	26	26	0	ELL,3_prime_UTR_variant,,ENST00000262809,;ISYNA1,upstream_gene_variant,,ENST00000338128,;ISYNA1,upstream_gene_variant,,ENST00000581800,;ISYNA1,upstream_gene_variant,,ENST00000457269,;ELL,downstream_gene_variant,,ENST00000596124,;ISYNA1,upstream_gene_variant,,ENST00000317018,;ISYNA1,upstream_gene_variant,,ENST00000578352,;ISYNA1,upstream_gene_variant,,ENST00000545187,;ISYNA1,upstream_gene_variant,,ENST00000583534,;CTD-3137H5.1,intron_variant,,ENST00000594590,;ELL,3_prime_UTR_variant,,ENST00000594635,;ISYNA1,upstream_gene_variant,,ENST00000577820,;ISYNA1,upstream_gene_variant,,ENST00000582770,;ISYNA1,upstream_gene_variant,,ENST00000582811,;ELL,downstream_gene_variant,,ENST00000608165,;ELL,downstream_gene_variant,,ENST00000610152,;ISYNA1,upstream_gene_variant,,ENST00000577916,;AC010335.1,non_coding_transcript_exon_variant,,ENST00000541164,;	A	ENSG00000105656	ENST00000262809	Transcript	3_prime_UTR_variant	3729	.	.	.	.	.	.	.	-1	ELL	HGNC	23114	protein_coding	YES	CCDS12380.1	ENSP00000262809	ELL_HUMAN	Q75MS0_HUMAN	UPI0000062324	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTAGCTTCA	.	5	ESCA
HAPLN4	0	.	GRCh37	19	19368619	19368619	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7A>G	.	.	ENST00000291481	5/5	18	14	3	25	25	0	HAPLN4,3_prime_UTR_variant,,ENST00000291481,;AC138430.4,non_coding_transcript_exon_variant,,ENST00000586064,;HAPLN4,downstream_gene_variant,,ENST00000592862,;	C	ENSG00000187664	ENST00000291481	Transcript	3_prime_UTR_variant	1280	.	.	.	.	.	.	.	-1	HAPLN4	HGNC	31357	protein_coding	YES	CCDS12398.1	ENSP00000291481	HPLN4_HUMAN	.	UPI00000496C7	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTACTCCCAG	.	5	ESCA
ZNF714	0	.	GRCh37	19	21265121	21265121	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-210C>A	.	.	ENST00000596143	1/5	130	105	24	138	138	0	ZNF714,5_prime_UTR_variant,,ENST00000596143,;ZNF714,5_prime_UTR_variant,,ENST00000596367,;ZNF714,5_prime_UTR_variant,,ENST00000601416,;ZNF714,5_prime_UTR_variant,,ENST00000291770,;ZNF714,5_prime_UTR_variant,,ENST00000597424,;ZNF714,5_prime_UTR_variant,,ENST00000596053,;ZNF714,5_prime_UTR_variant,,ENST00000597086,;ZNF714,upstream_gene_variant,,ENST00000600535,;ZNF714,5_prime_UTR_variant,,ENST00000600770,;ZNF714,5_prime_UTR_variant,,ENST00000600435,;	A	ENSG00000160352	ENST00000596143	Transcript	5_prime_UTR_variant	116	.	.	.	.	.	.	.	1	ZNF714	HGNC	27124	protein_coding	YES	CCDS54239.1	ENSP00000472368	ZN714_HUMAN	M0R2G4_HUMAN,M0QYV9_HUMAN	UPI000059D6C5	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAGCTAAGA	.	5	ESCA
TLE2	0	.	GRCh37	19	3005571	3005571	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1760G>T	p.Gly587Val	p.G587V	ENST00000262953	17/20	19	15	4	33	33	0	TLE2,missense_variant,p.Gly254Val,ENST00000447365,;TLE2,missense_variant,p.Gly465Val,ENST00000455444,;TLE2,missense_variant,p.Gly601Val,ENST00000426948,;TLE2,missense_variant,p.Gly236Val,ENST00000589364,;TLE2,missense_variant,p.Gly465Val,ENST00000443826,;TLE2,missense_variant,p.Gly587Val,ENST00000262953,;TLE2,missense_variant,p.Gly588Val,ENST00000590536,;TLE2,missense_variant,p.Gly601Val,ENST00000591529,;TLE2,intron_variant,,ENST00000586422,;TLE2,downstream_gene_variant,,ENST00000586492,;TLE2,downstream_gene_variant,,ENST00000589205,;TLE2,downstream_gene_variant,,ENST00000587672,;	A	ENSG00000065717	ENST00000262953	Transcript	missense_variant	2023	1760	587	G/V	gGc/gTc	.	.	.	-1	TLE2	HGNC	11838	protein_coding	YES	CCDS45911.1	ENSP00000262953	TLE2_HUMAN	.	UPI0000137038	.	deleterious(0)	probably_damaging(0.998)	17/20	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR10814:SF4,hmmpanther:PTHR10814,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTGGCCCTGG	.	4	ESCA
CAPNS1	0	.	GRCh37	19	36632053	36632053	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.140G>A	p.Gly47Asp	p.G47D	ENST00000246533	2/11	19	12	6	18	18	0	CAPNS1,missense_variant,p.Gly47Asp,ENST00000588815,;CAPNS1,missense_variant,p.Gly47Asp,ENST00000587718,;CAPNS1,missense_variant,p.Gly47Asp,ENST00000588780,;CAPNS1,missense_variant,p.Gly47Asp,ENST00000592483,;CAPNS1,missense_variant,p.Gly47Asp,ENST00000246533,;CAPNS1,missense_variant,p.Gly47Asp,ENST00000591041,;CAPNS1,missense_variant,p.Gly47Asp,ENST00000590874,;CAPNS1,intron_variant,,ENST00000589146,;CAPNS1,upstream_gene_variant,,ENST00000590211,;CAPNS1,upstream_gene_variant,,ENST00000592354,;CAPNS1,upstream_gene_variant,,ENST00000586851,;CAPNS1,upstream_gene_variant,,ENST00000586963,;AD001527.7,downstream_gene_variant,,ENST00000604228,;CAPNS1,upstream_gene_variant,,ENST00000589162,;CAPNS1,upstream_gene_variant,,ENST00000590049,;	A	ENSG00000126247	ENST00000246533	Transcript	missense_variant	738	140	47	G/D	gGc/gAc	.	.	.	1	CAPNS1	HGNC	1481	protein_coding	YES	CCDS12489.1	ENSP00000246533	CPNS1_HUMAN	U3KPR7_HUMAN,K7ES78_HUMAN,K7EM73_HUMAN	UPI0000000E07	.	deleterious_low_confidence(0.03)	probably_damaging(0.931)	2/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10183:SF38,hmmpanther:PTHR10183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGGCGGCGGTG	.	4	ESCA
ZNF578	0	.	GRCh37	19	53014266	53014266	+	Missense_Mutation	SNP	A	A	T	rs763785937	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.632A>T	p.Asn211Ile	p.N211I	ENST00000421239	6/6	52	43	8	69	69	0	ZNF578,missense_variant,p.Asn211Ile,ENST00000421239,;ZNF578,missense_variant,p.Asn211Ile,ENST00000601120,;CTD-3099C6.5,downstream_gene_variant,,ENST00000599143,;	T	ENSG00000258405	ENST00000421239	Transcript	missense_variant	876	632	211	N/I	aAt/aTt	rs763785937	.	.	1	ZNF578	HGNC	26449	protein_coding	YES	CCDS54310.1	ENSP00000459216	ZN578_HUMAN	M0QZV4_HUMAN	UPI000048A457	.	tolerated(0.08)	possibly_damaging(0.885)	6/6	.	Superfamily_domains:SSF57667,hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATAATTTTT	byFrequency	5	ESCA
MYADM	0	.	GRCh37	19	54377333	54377333	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550G>T	p.Ala184Ser	p.A184S	ENST00000391769	3/3	34	24	10	50	50	0	MYADM,missense_variant,p.Ala184Ser,ENST00000391771,;MYADM,missense_variant,p.Ala184Ser,ENST00000391769,;MYADM,missense_variant,p.Ala184Ser,ENST00000391768,;MYADM,missense_variant,p.Ala184Ser,ENST00000439000,;MYADM,missense_variant,p.Ala184Ser,ENST00000448420,;MYADM,missense_variant,p.Ala184Ser,ENST00000336967,;MYADM,missense_variant,p.Ala184Ser,ENST00000421337,;MYADM,missense_variant,p.Ala184Ser,ENST00000391770,;MYADM,downstream_gene_variant,,ENST00000414489,;AC008753.6,upstream_gene_variant,,ENST00000455835,;AC008440.5,downstream_gene_variant,,ENST00000413496,;	T	ENSG00000179820	ENST00000391769	Transcript	missense_variant	830	550	184	A/S	Gcc/Tcc	.	.	.	1	MYADM	HGNC	7544	protein_coding	YES	CCDS12866.1	ENSP00000375649	MYADM_HUMAN	C9JZL8_HUMAN,C9JJV6_HUMAN,C9JC07_HUMAN,C9J5M0_HUMAN	UPI0000001BEF	.	deleterious(0)	probably_damaging(0.994)	3/3	.	Transmembrane_helices:TMhelix,Pfam_domain:PF01284,hmmpanther:PTHR17068:SF3,hmmpanther:PTHR17068,PROSITE_profiles:PS51225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTTGCCTGC	.	5	ESCA
ZNF749	0	.	GRCh37	19	57955022	57955022	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.506A>G	p.Gln169Arg	p.Q169R	ENST00000334181	3/3	33	25	8	41	41	0	ZNF749,missense_variant,p.Gln169Arg,ENST00000334181,;AC004076.9,intron_variant,,ENST00000596831,;ZNF749,downstream_gene_variant,,ENST00000415248,;	G	ENSG00000186230	ENST00000334181	Transcript	missense_variant	756	506	169	Q/R	cAg/cGg	.	.	.	1	ZNF749	HGNC	32783	protein_coding	YES	CCDS33132.2	ENSP00000333980	ZN749_HUMAN	C9J756_HUMAN	UPI0000237933	.	deleterious(0.05)	benign(0.403)	3/3	.	hmmpanther:PTHR24381:SF5,hmmpanther:PTHR24381	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCCAGCAAC	.	5	ESCA
TRIP10	0	.	GRCh37	19	6751205	6751205	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621C>T	p.Arg541Ter	p.R541*	ENST00000313285	14/14	28	21	6	33	33	0	TRIP10,stop_gained,p.Arg541Ter,ENST00000313285,;TRIP10,stop_gained,p.Arg433Ter,ENST00000600428,;TRIP10,stop_gained,p.Arg597Ter,ENST00000313244,;TRIP10,synonymous_variant,p.%3D,ENST00000596758,;SH2D3A,downstream_gene_variant,,ENST00000245908,;SH2D3A,downstream_gene_variant,,ENST00000597687,;SH2D3A,downstream_gene_variant,,ENST00000437152,;CTD-3128G10.6,intron_variant,,ENST00000594056,;SH2D3A,downstream_gene_variant,,ENST00000597254,;SH2D3A,downstream_gene_variant,,ENST00000599563,;SH2D3A,downstream_gene_variant,,ENST00000597168,;TRIP10,3_prime_UTR_variant,,ENST00000600677,;TRIP10,non_coding_transcript_exon_variant,,ENST00000595305,;SH2D3A,downstream_gene_variant,,ENST00000595681,;TRIP10,downstream_gene_variant,,ENST00000598843,;	T	ENSG00000125733	ENST00000313285	Transcript	stop_gained	1703	1621	541	R/*	Cga/Tga	.	.	.	1	TRIP10	HGNC	12304	protein_coding	YES	CCDS12172.1	ENSP00000320493	CIP4_HUMAN	M0R0F9_HUMAN,M0R070_HUMAN	UPI00001279E3	.	.	.	14/14	.	PROSITE_profiles:PS50002,hmmpanther:PTHR12602:SF7,hmmpanther:PTHR12602,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTCCGAGTC	.	5	ESCA
MUC16	0	.	GRCh37	19	9073177	9073177	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14269C>T	p.Pro4757Ser	p.P4757S	ENST00000397910	3/84	81	61	20	88	88	0	MUC16,missense_variant,p.Pro4757Ser,ENST00000397910,;	A	ENSG00000181143	ENST00000397910	Transcript	missense_variant	14473	14269	4757	P/S	Cct/Tct	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	3/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGGTAAGG	.	5	ESCA
OR7D4	0	.	GRCh37	19	9324685	9324685	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.829A>C	p.Met277Leu	p.M277L	ENST00000308682	1/1	37	31	6	52	52	0	OR7D4,missense_variant,p.Met277Leu,ENST00000308682,;	G	ENSG00000174667	ENST00000308682	Transcript	missense_variant	858	829	277	M/L	Atg/Ctg	.	.	.	-1	OR7D4	HGNC	8380	protein_coding	YES	CCDS32901.1	ENSP00000310488	OR7D4_HUMAN	.	UPI00000472B5	.	deleterious(0.05)	benign(0.107)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF131,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACATCACTG	.	5	ESCA
OLFM3	0	.	GRCh37	1	102312449	102312449	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70-9868A>T	.	.	ENST00000370103	.	84	64	20	93	93	0	OLFM3,synonymous_variant,p.%3D,ENST00000338858,;OLFM3,synonymous_variant,p.%3D,ENST00000359814,;OLFM3,intron_variant,,ENST00000370103,;OLFM3,non_coding_transcript_exon_variant,,ENST00000465523,;OLFM3,intron_variant,,ENST00000462354,;OLFM3,intron_variant,,ENST00000468901,;	A	ENSG00000118733	ENST00000370103	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	OLFM3	HGNC	17990	protein_coding	YES	CCDS30781.1	ENSP00000359121	NOE3_HUMAN	.	UPI000002AF6A	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGATGGGAG	.	5	ESCA
COL11A1	0	.	GRCh37	1	103354301	103354301	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4532delC	p.Pro1511GlnfsTer76	p.P1511Qfs*76	ENST00000370096	61/67	62	54	8	46	46	0	COL11A1,frameshift_variant,p.Pro1395GlnfsTer76,ENST00000512756,;COL11A1,frameshift_variant,p.Pro1472GlnfsTer76,ENST00000353414,;COL11A1,frameshift_variant,p.Pro1511GlnfsTer76,ENST00000370096,;COL11A1,frameshift_variant,p.Pro1523GlnfsTer76,ENST00000358392,;	-	ENSG00000060718	ENST00000370096	Transcript	frameshift_variant	4845	4532	1511	P/X	cCa/ca	COSM1953817,COSM1953818	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	.	61/67	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF42,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	deletion	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCCTTTGGGCCT	.	2	ESCA
MASP2	0	.	GRCh37	1	11105562	11105562	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.447G>A	p.%3D	p.A149A	ENST00000400897	4/11	128	101	26	133	133	0	MASP2,synonymous_variant,p.%3D,ENST00000400898,;MASP2,synonymous_variant,p.%3D,ENST00000400897,;MASP2,non_coding_transcript_exon_variant,,ENST00000480221,;MASP2,upstream_gene_variant,,ENST00000478645,;	T	ENSG00000009724	ENST00000400897	Transcript	synonymous_variant	463	447	149	A	gcG/gcA	.	.	.	-1	MASP2	HGNC	6902	protein_coding	YES	CCDS123.1	ENSP00000383690	MASP2_HUMAN	.	UPI0000161FB9	.	.	.	4/11	.	Superfamily_domains:SSF57196,PIRSF_domain:PIRSF001155,SMART_domains:SM00181,SMART_domains:SM00179,Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01187,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGGCGCCTC	.	5	ESCA
PLOD1	0	.	GRCh37	1	12008070	12008070	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114C>T	p.%3D	p.T38T	ENST00000196061	2/19	77	58	18	103	103	0	PLOD1,synonymous_variant,p.%3D,ENST00000429000,;PLOD1,synonymous_variant,p.%3D,ENST00000449038,;PLOD1,synonymous_variant,p.%3D,ENST00000376369,;PLOD1,synonymous_variant,p.%3D,ENST00000196061,;PLOD1,non_coding_transcript_exon_variant,,ENST00000485046,;PLOD1,non_coding_transcript_exon_variant,,ENST00000358133,;	T	ENSG00000083444	ENST00000196061	Transcript	synonymous_variant	141	114	38	T	acC/acT	.	.	.	1	PLOD1	HGNC	9081	protein_coding	YES	CCDS142.1	ENSP00000196061	PLOD1_HUMAN	Q9UL44_HUMAN	UPI000013C611	.	.	.	2/19	.	hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACCGAGGG	.	5	ESCA
GPR89A	0	.	GRCh37	1	145787778	145787778	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903T>G	p.Ile301Met	p.I301M	ENST00000313835	10/14	67	53	14	52	52	0	GPR89A,missense_variant,p.Ile276Met,ENST00000534502,;GPR89A,missense_variant,p.Ile301Met,ENST00000313835,;GPR89A,missense_variant,p.Ile181Met,ENST00000454423,;GPR89A,missense_variant,p.Ile276Met,ENST00000462900,;GPR89A,non_coding_transcript_exon_variant,,ENST00000478703,;GPR89A,3_prime_UTR_variant,,ENST00000460277,;GPR89A,non_coding_transcript_exon_variant,,ENST00000493684,;GPR89A,non_coding_transcript_exon_variant,,ENST00000465185,;GPR89A,downstream_gene_variant,,ENST00000528944,;GPR89A,downstream_gene_variant,,ENST00000492401,;GPR89A,downstream_gene_variant,,ENST00000466593,;	C	ENSG00000117262	ENST00000313835	Transcript	missense_variant	1047	903	301	I/M	atT/atG	.	.	.	-1	GPR89A	HGNC	31984	protein_coding	YES	CCDS41377.1	ENSP00000319673	GPHRA_HUMAN	.	UPI00000389CC	.	tolerated(0.24)	benign(0.078)	10/14	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15948,Pfam_domain:PF12430	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	ATGAAAATTTT	.	3	ESCA
FMO5	0	.	GRCh37	1	146658413	146658413	+	3'UTR	SNP	G	G	C	rs782485488	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66C>G	.	.	ENST00000254090	9/9	19	16	3	18	18	0	FMO5,3_prime_UTR_variant,,ENST00000254090,;FMO5,3_prime_UTR_variant,,ENST00000369272,;FMO5,intron_variant,,ENST00000441068,;RP11-337C18.8,intron_variant,,ENST00000606757,;RP11-337C18.8,intron_variant,,ENST00000607149,;RP11-337C18.10,intron_variant,,ENST00000606856,;FMO5,intron_variant,,ENST00000527849,;	C	ENSG00000131781	ENST00000254090	Transcript	3_prime_UTR_variant	2057	.	.	.	.	rs782485488	.	.	-1	FMO5	HGNC	3773	protein_coding	YES	CCDS926.1	ENSP00000254090	FMO5_HUMAN	E9PQ84_HUMAN,E9PP51_HUMAN	UPI000013CE15	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTCGTCAGA	.	2	ESCA
ARNT	0	.	GRCh37	1	150783607	150783607	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*890C>T	.	.	ENST00000358595	22/22	71	62	9	55	55	0	ARNT,3_prime_UTR_variant,,ENST00000358595,;ARNT,3_prime_UTR_variant,,ENST00000354396,;ARNT,downstream_gene_variant,,ENST00000505755,;ARNT,downstream_gene_variant,,ENST00000515192,;CTSK,upstream_gene_variant,,ENST00000271651,;CTSK,upstream_gene_variant,,ENST00000443913,;RNU6-1309P,downstream_gene_variant,,ENST00000363305,;CTSK,upstream_gene_variant,,ENST00000480670,;ARNT,3_prime_UTR_variant,,ENST00000471844,;	A	ENSG00000143437	ENST00000358595	Transcript	3_prime_UTR_variant	3461	.	.	.	.	.	.	.	-1	ARNT	HGNC	700	protein_coding	YES	CCDS970.1	ENSP00000351407	ARNT_HUMAN	.	UPI0000030984	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAATGTTTGC	.	4	ESCA
FLG	0	.	GRCh37	1	152281346	152281346	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6016G>A	p.Gly2006Arg	p.G2006R	ENST00000368799	3/3	501	460	40	459	458	1	FLG,missense_variant,p.Gly2006Arg,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	T	ENSG00000143631	ENST00000368799	Transcript	missense_variant	6052	6016	2006	G/R	Gga/Aga	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	probably_damaging(0.988)	3/3	.	Pfam_domain:PF03516	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGATCCATGTC	.	3	ESCA
CREB3L4	0	.	GRCh37	1	153945466	153945468	+	In_Frame_Del	DEL	AAG	AAG	-	rs778091329	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	AAG	AAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658_660delAAG	p.Lys220del	p.K220del	ENST00000368607	6/10	47	42	5	60	60	0	CREB3L4,inframe_deletion,p.Lys73del,ENST00000405694,;CREB3L4,inframe_deletion,p.Lys220del,ENST00000368603,;CREB3L4,inframe_deletion,p.Lys200del,ENST00000368600,;CREB3L4,inframe_deletion,p.Lys200del,ENST00000449724,;CREB3L4,inframe_deletion,p.Lys220del,ENST00000271889,;CREB3L4,inframe_deletion,p.Lys220del,ENST00000368607,;CREB3L4,3_prime_UTR_variant,,ENST00000368601,;JTB,downstream_gene_variant,,ENST00000356648,;JTB,downstream_gene_variant,,ENST00000271843,;JTB,downstream_gene_variant,,ENST00000368589,;CREB3L4,downstream_gene_variant,,ENST00000431292,;JTB,downstream_gene_variant,,ENST00000428469,;RP11-422P24.11,upstream_gene_variant,,ENST00000608236,;CREB3L4,non_coding_transcript_exon_variant,,ENST00000492729,;CREB3L4,non_coding_transcript_exon_variant,,ENST00000468845,;JTB,downstream_gene_variant,,ENST00000471173,;CREB3L4,downstream_gene_variant,,ENST00000473340,;CREB3L4,downstream_gene_variant,,ENST00000461688,;CREB3L4,downstream_gene_variant,,ENST00000477617,;JTB,downstream_gene_variant,,ENST00000461365,;CREB3L4,downstream_gene_variant,,ENST00000479010,;	-	ENSG00000143578	ENST00000368607	Transcript	inframe_deletion	921-923	655-657	219	K/-	AAG/-	rs778091329	.	.	1	CREB3L4	HGNC	18854	protein_coding	YES	CCDS1056.1	ENSP00000357596	CR3L4_HUMAN	B4DMZ9_HUMAN	UPI0000073CF0	.	.	.	6/10	.	Superfamily_domains:SSF57959,SMART_domains:SM00338,Pfam_domain:PF00170,Gene3D:1.20.5.170,hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF105,PROSITE_profiles:PS50217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GTCCTCAAGAAGGT	.	2	ESCA
MNDA	0	.	GRCh37	1	158815756	158815756	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.950C>A	p.Ser317Tyr	p.S317Y	ENST00000368141	5/7	102	76	26	68	68	0	MNDA,missense_variant,p.Ser23Tyr,ENST00000438394,;MNDA,missense_variant,p.Ser317Tyr,ENST00000368141,;MNDA,downstream_gene_variant,,ENST00000491210,;	A	ENSG00000163563	ENST00000368141	Transcript	missense_variant	1211	950	317	S/Y	tCt/tAt	.	.	.	1	MNDA	HGNC	7183	protein_coding	YES	CCDS1177.1	ENSP00000357123	MNDA_HUMAN	Q5VUU6_HUMAN	UPI0000001609	.	deleterious(0)	probably_damaging(0.993)	5/7	.	PROSITE_profiles:PS50834,hmmpanther:PTHR12200:SF18,hmmpanther:PTHR12200,Pfam_domain:PF02760,Gene3D:2.40.50.140,Superfamily_domains:SSF159141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATCTGGAA	.	5	ESCA
FAM78B	0	.	GRCh37	1	166039399	166039399	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*79A>G	.	.	ENST00000338353	3/3	46	32	14	32	32	0	FAM78B,3_prime_UTR_variant,,ENST00000354422,;FAM78B,3_prime_UTR_variant,,ENST00000338353,;FAM78B,3_prime_UTR_variant,,ENST00000441649,;FAM78B,3_prime_UTR_variant,,ENST00000435676,;FAM78B,3_prime_UTR_variant,,ENST00000456900,;	C	ENSG00000188859	ENST00000338353	Transcript	3_prime_UTR_variant	1455	.	.	.	.	.	.	.	-1	FAM78B	HGNC	13495	protein_coding	YES	CCDS30931.1	ENSP00000339681	FA78B_HUMAN	.	UPI00001612B4	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTGTTTGGC	.	5	ESCA
TNN	0	.	GRCh37	1	175066783	175066783	+	Nonsense_Mutation	SNP	C	C	T	rs762192072	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1819C>T	p.Arg607Ter	p.R607*	ENST00000239462	8/19	47	41	6	37	37	0	TNN,stop_gained,p.Arg607Ter,ENST00000239462,;	T	ENSG00000120332	ENST00000239462	Transcript	stop_gained	1932	1819	607	R/*	Cga/Tga	rs762192072	.	.	1	TNN	HGNC	22942	protein_coding	YES	CCDS30943.1	ENSP00000239462	TENN_HUMAN	.	UPI00001D7DA9	.	.	.	8/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF167,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGACCGAGAG	byFrequency	4	ESCA
RP11-568K15.1	0	.	GRCh37	1	178006918	178006918	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.73C>T	.	.	ENST00000476232	2/10	33	24	8	24	24	0	RP11-568K15.1,non_coding_transcript_exon_variant,,ENST00000512906,;RP11-568K15.1,non_coding_transcript_exon_variant,,ENST00000481349,;RP11-568K15.1,non_coding_transcript_exon_variant,,ENST00000476232,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000464428,;RP11-568K15.1,intron_variant,,ENST00000462729,;	A	ENSG00000242193	ENST00000476232	Transcript	non_coding_transcript_exon_variant	73	.	.	.	.	.	.	.	-1	RP11-568K15.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	2/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCCGCTGCC	.	5	ESCA
ADIPOR1	0	.	GRCh37	1	202913041	202913041	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650T>C	p.Met217Thr	p.M217T	ENST00000340990	6/8	29	26	3	28	28	0	ADIPOR1,missense_variant,p.Met217Thr,ENST00000436244,;ADIPOR1,missense_variant,p.Met217Thr,ENST00000340990,;ADIPOR1,missense_variant,p.Met217Thr,ENST00000417068,;ADIPOR1,intron_variant,,ENST00000367254,;ADIPOR1,downstream_gene_variant,,ENST00000426229,;ADIPOR1,non_coding_transcript_exon_variant,,ENST00000495562,;	G	ENSG00000159346	ENST00000340990	Transcript	missense_variant	949	650	217	M/T	aTg/aCg	.	.	.	-1	ADIPOR1	HGNC	24040	protein_coding	YES	CCDS1430.1	ENSP00000341785	ADR1_HUMAN	C9JNM5_HUMAN,C9J0W7_HUMAN	UPI000003779A	.	deleterious(0.02)	benign(0.223)	6/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR20855,hmmpanther:PTHR20855:SF40,Pfam_domain:PF03006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCCATAATT	.	4	ESCA
DDOST	0	.	GRCh37	1	20987472	20987472	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218A>T	p.Glu73Val	p.E73V	ENST00000375048	2/11	65	44	21	73	73	0	DDOST,missense_variant,p.Glu56Val,ENST00000464364,;DDOST,missense_variant,p.Glu73Val,ENST00000375048,;DDOST,missense_variant,p.Glu56Val,ENST00000602624,;DDOST,intron_variant,,ENST00000415136,;KIF17,downstream_gene_variant,,ENST00000247986,;KIF17,downstream_gene_variant,,ENST00000375044,;KIF17,downstream_gene_variant,,ENST00000400463,;DDOST,non_coding_transcript_exon_variant,,ENST00000477229,;KIF17,downstream_gene_variant,,ENST00000493818,;KIF17,downstream_gene_variant,,ENST00000490034,;KIF17,downstream_gene_variant,,ENST00000477167,;	A	ENSG00000244038	ENST00000375048	Transcript	missense_variant	324	218	73	E/V	gAg/gTg	.	.	.	-1	DDOST	HGNC	2728	protein_coding	YES	CCDS212.1	ENSP00000364188	OST48_HUMAN	.	UPI000013C9E0	.	tolerated(0.08)	benign(0.053)	2/11	.	hmmpanther:PTHR10830,hmmpanther:PTHR10830:SF0,Pfam_domain:PF03345	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGCTCAAAG	.	5	ESCA
SYT14	0	.	GRCh37	1	210334142	210334142	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1615C>T	p.Arg539Cys	p.R539C	ENST00000422431	10/10	41	33	8	41	41	0	SYT14,missense_variant,p.Arg475Cys,ENST00000472886,;SYT14,missense_variant,p.Arg501Cys,ENST00000534859,;SYT14,missense_variant,p.Arg539Cys,ENST00000422431,;SYT14,missense_variant,p.Arg437Cys,ENST00000367015,;SYT14,missense_variant,p.Arg494Cys,ENST00000367019,;SYT14,missense_variant,p.Arg437Cys,ENST00000537238,;SYT14,3_prime_UTR_variant,,ENST00000399639,;SYT14,non_coding_transcript_exon_variant,,ENST00000469604,;SYT14,non_coding_transcript_exon_variant,,ENST00000271745,;	T	ENSG00000143469	ENST00000422431	Transcript	missense_variant	1673	1615	539	R/C	Cgc/Tgc	.	.	.	1	SYT14	HGNC	23143	protein_coding	YES	CCDS53469.1	ENSP00000389039	SYT14_HUMAN	A1L3Y1_HUMAN	UPI0001639EBD	.	tolerated(0.24)	benign(0.347)	10/10	.	PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF209,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCCGCAGA	.	5	ESCA
RAP1GAP	0	.	GRCh37	1	21929326	21929326	+	Missense_Mutation	SNP	G	G	C	rs373868217	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1701C>G	p.Ile567Met	p.I567M	ENST00000290101	19/25	37	34	3	45	45	0	RAP1GAP,missense_variant,p.Ile529Met,ENST00000542643,;RAP1GAP,missense_variant,p.Ile534Met,ENST00000374761,;RAP1GAP,missense_variant,p.Ile567Met,ENST00000290101,;RAP1GAP,missense_variant,p.Ile503Met,ENST00000374765,;RAP1GAP,missense_variant,p.Ile588Met,ENST00000374763,;RAP1GAP,missense_variant,p.Ile503Met,ENST00000471600,;RAP1GAP,3_prime_UTR_variant,,ENST00000495204,;	C	ENSG00000076864	ENST00000290101	Transcript	missense_variant	1734	1701	567	I/M	atC/atG	rs373868217	.	.	-1	RAP1GAP	HGNC	9858	protein_coding	YES	CCDS53277.1	ENSP00000290101	RPGP1_HUMAN	Q5T3T1_HUMAN,Q5T3T0_HUMAN,Q5T3S6_HUMAN	UPI0000EE7109	.	tolerated(0.06)	probably_damaging(0.994)	19/25	.	hmmpanther:PTHR15711,hmmpanther:PTHR15711:SF3	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTCGATGCC	byFrequency|byCluster	2	ESCA
SNAP47	0	.	GRCh37	1	227935746	227935746	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444G>C	p.%3D	p.L148L	ENST00000366759	2/5	65	41	24	82	82	0	SNAP47,synonymous_variant,p.%3D,ENST00000366759,;SNAP47,synonymous_variant,p.%3D,ENST00000315781,;SNAP47,synonymous_variant,p.%3D,ENST00000426344,;SNAP47,intron_variant,,ENST00000366760,;SNAP47,intron_variant,,ENST00000418653,;SNAP47,upstream_gene_variant,,ENST00000606873,;SNAP47-AS1,upstream_gene_variant,,ENST00000413347,;SNAP47,non_coding_transcript_exon_variant,,ENST00000470038,;SNAP47,non_coding_transcript_exon_variant,,ENST00000475930,;SNAP47,intron_variant,,ENST00000491439,;SNAP47,upstream_gene_variant,,ENST00000478768,;	C	ENSG00000143740	ENST00000366759	Transcript	synonymous_variant	858	444	148	L	ctG/ctC	.	.	.	1	SNAP47	HGNC	30669	protein_coding	YES	CCDS1562.1	ENSP00000355721	SNP47_HUMAN	.	UPI000036662E	.	.	.	2/5	.	hmmpanther:PTHR19305:SF1,hmmpanther:PTHR19305,Gene3D:1.20.5.110,Superfamily_domains:SSF58038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGCTGTCTCA	.	3	ESCA
OBSCN	0	.	GRCh37	1	228434246	228434246	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4051G>T	p.Ala1351Ser	p.A1351S	ENST00000570156	14/116	73	58	14	69	69	0	OBSCN,missense_variant,p.Ala1259Ser,ENST00000284548,;OBSCN,missense_variant,p.Ala1259Ser,ENST00000422127,;OBSCN,missense_variant,p.Ala1351Ser,ENST00000570156,;OBSCN,5_prime_UTR_variant,,ENST00000366707,;OBSCN,5_prime_UTR_variant,,ENST00000366709,;	T	ENSG00000154358	ENST00000570156	Transcript	missense_variant	4125	4051	1351	A/S	Gcc/Tcc	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	probably_damaging(0.94)	14/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTGCCAAG	.	5	ESCA
SIPA1L2	0	.	GRCh37	1	232575095	232575095	+	Missense_Mutation	SNP	C	C	T	rs532670311	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3790G>A	p.Asp1264Asn	p.D1264N	ENST00000366630	14/22	99	85	14	70	70	0	SIPA1L2,missense_variant,p.Asp1264Asn,ENST00000366630,;SIPA1L2,missense_variant,p.Asp338Asn,ENST00000308942,;SIPA1L2,missense_variant,p.Asp1264Asn,ENST00000262861,;	T	ENSG00000116991	ENST00000366630	Transcript	missense_variant	4149	3790	1264	D/N	Gac/Aac	rs532670311	.	.	-1	SIPA1L2	HGNC	23800	protein_coding	YES	CCDS41474.1	ENSP00000355589	SI1L2_HUMAN	.	UPI00001D7D6A	.	deleterious(0)	possibly_damaging(0.703)	14/22	.	hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGTCGGTGG	by1000G	4	ESCA
FMN2	0	.	GRCh37	1	240370836	240370836	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2724G>T	p.%3D	p.L908L	ENST00000319653	5/18	53	45	7	44	44	0	FMN2,synonymous_variant,p.%3D,ENST00000319653,;FMN2,downstream_gene_variant,,ENST00000447095,;	T	ENSG00000155816	ENST00000319653	Transcript	synonymous_variant	2954	2724	908	L	ctG/ctT	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	.	5/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,SMART_domains:SM00498	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P1054fs*364|c.3157delC|3	RADIA|MUTECT|MUSE|VARSCANS	ATGCTGCCACC	.	4	ESCA
MAP1LC3C	0	.	GRCh37	1	242159683	242159683	+	Missense_Mutation	SNP	G	G	A	rs776473823	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226C>T	p.Arg76Cys	p.R76C	ENST00000357246	4/4	74	58	16	102	101	0	MAP1LC3C,missense_variant,p.Arg76Cys,ENST00000357246,;CFL1P4,downstream_gene_variant,,ENST00000451536,;	A	ENSG00000197769	ENST00000357246	Transcript	missense_variant	291	226	76	R/C	Cgc/Tgc	rs776473823,COSM906534	.	.	-1	MAP1LC3C	HGNC	13353	protein_coding	YES	CCDS31074.1	ENSP00000349785	MLP3C_HUMAN	.	UPI0000070E14	.	deleterious(0)	benign(0.19)	4/4	.	hmmpanther:PTHR10969:SF24,hmmpanther:PTHR10969,Gene3D:3.10.20.90,Pfam_domain:PF02991,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGCGGCTCC	byFrequency	5	ESCA
KIAA0319L	0	.	GRCh37	1	36020037	36020037	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.56A>G	p.Tyr19Cys	p.Y19C	ENST00000325722	2/21	39	28	11	43	43	0	KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000440579,;KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000325722,;KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000426982,;KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000469892,;KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000494948,;NCDN,upstream_gene_variant,,ENST00000373253,;NCDN,upstream_gene_variant,,ENST00000437806,;NCDN,upstream_gene_variant,,ENST00000356090,;NCDN,upstream_gene_variant,,ENST00000373243,;KIAA0319L,non_coding_transcript_exon_variant,,ENST00000476329,;KIAA0319L,intron_variant,,ENST00000492888,;NCDN,upstream_gene_variant,,ENST00000459931,;KIAA0319L,downstream_gene_variant,,ENST00000473465,;KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000478463,;KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000470388,;KIAA0319L,missense_variant,p.Tyr19Cys,ENST00000482929,;	C	ENSG00000142687	ENST00000325722	Transcript	missense_variant	291	56	19	Y/C	tAt/tGt	.	.	.	-1	KIAA0319L	HGNC	30071	protein_coding	YES	CCDS390.1	ENSP00000318406	K319L_HUMAN	E7EN73_HUMAN,C9JVB2_HUMAN,C9JQ56_HUMAN,C9J519_HUMAN,B1AN15_HUMAN	UPI000003F081	.	tolerated_low_confidence(0.14)	benign(0.115)	2/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAATATCCT	.	5	ESCA
AKR1A1	0	.	GRCh37	1	46035590	46035590	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.940G>T	p.Ala314Ser	p.A314S	ENST00000372070	10/10	31	26	5	42	42	0	AKR1A1,missense_variant,p.Ala314Ser,ENST00000372070,;AKR1A1,missense_variant,p.Ala314Ser,ENST00000351829,;AKR1A1,downstream_gene_variant,,ENST00000481885,;AKR1A1,downstream_gene_variant,,ENST00000471651,;AKR1A1,downstream_gene_variant,,ENST00000434299,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000495913,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000475985,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000487654,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000473038,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000475919,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000497973,;AKR1A1,downstream_gene_variant,,ENST00000496999,;AKR1A1,downstream_gene_variant,,ENST00000476957,;	T	ENSG00000117448	ENST00000372070	Transcript	missense_variant	1687	940	314	A/S	Gca/Tca	.	.	.	1	AKR1A1	HGNC	380	protein_coding	YES	CCDS523.1	ENSP00000361140	AK1A1_HUMAN	Q5T621_HUMAN	UPI000013D31D	.	tolerated(0.27)	benign(0.002)	10/10	.	PIRSF_domain:PIRSF000097,hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGATGCAGGG	.	5	ESCA
TAL1	0	.	GRCh37	1	47684909	47684909	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*483C>T	.	.	ENST00000294339	4/4	40	27	12	47	47	0	TAL1,3_prime_UTR_variant,,ENST00000294339,;TAL1,3_prime_UTR_variant,,ENST00000371883,;TAL1,3_prime_UTR_variant,,ENST00000371884,;TAL1,non_coding_transcript_exon_variant,,ENST00000459729,;TAL1,downstream_gene_variant,,ENST00000464796,;	A	ENSG00000162367	ENST00000294339	Transcript	3_prime_UTR_variant	2056	.	.	.	.	.	.	.	-1	TAL1	HGNC	11556	protein_coding	YES	CCDS547.1	ENSP00000294339	TAL1_HUMAN	Q9UE36_HUMAN	UPI00001368B2	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAGATGGG	.	5	ESCA
CYB5RL	0	.	GRCh37	1	54640384	54640384	+	Missense_Mutation	SNP	C	C	T	rs780876546	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.856G>A	p.Ala286Thr	p.A286T	ENST00000419823	7/7	61	45	15	54	54	0	CYB5RL,missense_variant,p.Ala286Thr,ENST00000534324,;CYB5RL,missense_variant,p.Ala218Thr,ENST00000537208,;CYB5RL,missense_variant,p.Ala286Thr,ENST00000542737,;CYB5RL,missense_variant,p.Ala286Thr,ENST00000419823,;CYB5RL,missense_variant,p.Ala218Thr,ENST00000287899,;CYB5RL,missense_variant,p.Ala138Thr,ENST00000401046,;CYB5RL,downstream_gene_variant,,ENST00000493530,;AL357673.1,upstream_gene_variant,,ENST00000536061,;RP11-446E24.4,upstream_gene_variant,,ENST00000525949,;CYB5RL,3_prime_UTR_variant,,ENST00000421415,;CYB5RL,3_prime_UTR_variant,,ENST00000528287,;CYB5RL,3_prime_UTR_variant,,ENST00000420054,;CYB5RL,non_coding_transcript_exon_variant,,ENST00000490863,;RP11-446E24.4,intron_variant,,ENST00000311841,;	T	ENSG00000215883	ENST00000419823	Transcript	missense_variant	1081	856	286	A/T	Gca/Aca	rs780876546,COSM274719	.	.	-1	CYB5RL	HGNC	32220	protein_coding	YES	CCDS44151.1	ENSP00000409075	NB5R5_HUMAN	.	UPI000019863E	.	tolerated(0.25)	benign(0.06)	7/7	.	Prints_domain:PR00406,Superfamily_domains:SSF52343,Gene3D:3.40.50.80,Pfam_domain:PF00175,hmmpanther:PTHR19370,hmmpanther:PTHR19370:SF81	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTGCGAATG	byFrequency	5	ESCA
OMA1	0	.	GRCh37	1	58993006	58993006	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1142A>G	p.Tyr381Cys	p.Y381C	ENST00000371226	7/9	49	40	9	56	56	0	OMA1,missense_variant,p.Tyr381Cys,ENST00000371226,;OMA1,missense_variant,p.Tyr223Cys,ENST00000421528,;OMA1,missense_variant,p.Tyr381Cys,ENST00000358603,;OMA1,splice_region_variant,,ENST00000476933,;OMA1,splice_region_variant,,ENST00000467509,;DAB1,splice_region_variant,,ENST00000485760,;	C	ENSG00000162600	ENST00000371226	Transcript	missense_variant	1256	1142	381	Y/C	tAt/tGt	COSM1218444	.	.	-1	OMA1	HGNC	29661	protein_coding	YES	CCDS608.1	ENSP00000360270	OMA1_HUMAN	S4R3A3_HUMAN	UPI000006D0C6	.	deleterious(0)	probably_damaging(0.928)	7/9	.	hmmpanther:PTHR22726,hmmpanther:PTHR22726:SF1,Pfam_domain:PF01435	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATATACTAA	.	5	ESCA
ICMT	0	.	GRCh37	1	6294509	6294509	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284+437C>T	.	.	ENST00000343813	.	43	30	13	37	37	0	ICMT,missense_variant,p.Pro116Leu,ENST00000362035,;ICMT,intron_variant,,ENST00000343813,;LINC00337,upstream_gene_variant,,ENST00000441724,;LINC00337,upstream_gene_variant,,ENST00000429480,;ICMT,missense_variant,p.Pro116Leu,ENST00000489498,;ICMT,intron_variant,,ENST00000474756,;	A	ENSG00000116237	ENST00000343813	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ICMT	HGNC	5350	protein_coding	YES	CCDS61.1	ENSP00000343552	ICMT_HUMAN	K7EQW0_HUMAN,B3KS61_HUMAN	UPI00000012C2	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAAGGGACT	.	5	ESCA
C1orf173	0	.	GRCh37	1	75038188	75038188	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3206C>G	p.Ser1069Cys	p.S1069C	ENST00000326665	14/15	86	68	17	99	99	0	C1orf173,missense_variant,p.Ser1069Cys,ENST00000326665,;C1orf173,non_coding_transcript_exon_variant,,ENST00000433746,;	C	ENSG00000178965	ENST00000326665	Transcript	missense_variant	3425	3206	1069	S/C	tCt/tGt	.	.	.	-1	C1orf173	HGNC	25346	protein_coding	YES	CCDS30755.1	ENSP00000322609	CA173_HUMAN	.	UPI0000237200	.	deleterious(0.01)	benign(0.247)	14/15	.	hmmpanther:PTHR23034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAGATGTT	.	5	ESCA
ACADM	0	.	GRCh37	1	76228511	76228511	+	3'Flank	SNP	A	A	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000420607	.	124	95	29	135	135	0	ACADM,3_prime_UTR_variant,,ENST00000370841,;ACADM,3_prime_UTR_variant,,ENST00000541113,;ACADM,3_prime_UTR_variant,,ENST00000370834,;ACADM,3_prime_UTR_variant,,ENST00000543667,;ACADM,downstream_gene_variant,,ENST00000420607,;ACADM,intron_variant,,ENST00000481374,;ACADM,3_prime_UTR_variant,,ENST00000526196,;ACADM,3_prime_UTR_variant,,ENST00000525808,;ACADM,non_coding_transcript_exon_variant,,ENST00000529059,;ACADM,intron_variant,,ENST00000528016,;ACADM,downstream_gene_variant,,ENST00000534334,;ACADM,downstream_gene_variant,,ENST00000526129,;ACADM,downstream_gene_variant,,ENST00000532207,;	T	ENSG00000117054	ENST00000420607	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	17	1	ACADM	HGNC	89	protein_coding	YES	CCDS44165.1	ENSP00000409612	ACADM_HUMAN	B4DVB1_HUMAN,B4DJE7_HUMAN	UPI0000EE3287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAAGAAAG	.	5	ESCA
IDH3B	0	.	GRCh37	20	2641145	2641145	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.623A>G	p.Lys208Arg	p.K208R	ENST00000380843	7/12	53	41	11	74	74	0	IDH3B,missense_variant,p.Lys208Arg,ENST00000380843,;IDH3B,missense_variant,p.Lys208Arg,ENST00000380851,;NOP56,downstream_gene_variant,,ENST00000329276,;NOP56,downstream_gene_variant,,ENST00000445139,;NOP56,downstream_gene_variant,,ENST00000415272,;SNORD86,downstream_gene_variant,,ENST00000391196,;SNORD57,downstream_gene_variant,,ENST00000448188,;SNORD56,downstream_gene_variant,,ENST00000413522,;RP4-686C3.7,upstream_gene_variant,,ENST00000418739,;IDH3B,non_coding_transcript_exon_variant,,ENST00000474315,;IDH3B,non_coding_transcript_exon_variant,,ENST00000462967,;IDH3B,non_coding_transcript_exon_variant,,ENST00000488299,;IDH3B,non_coding_transcript_exon_variant,,ENST00000479376,;IDH3B,upstream_gene_variant,,ENST00000477689,;NOP56,downstream_gene_variant,,ENST00000496775,;NOP56,downstream_gene_variant,,ENST00000462630,;NOP56,downstream_gene_variant,,ENST00000480992,;IDH3B,downstream_gene_variant,,ENST00000491065,;IDH3B,upstream_gene_variant,,ENST00000492240,;NOP56,downstream_gene_variant,,ENST00000490753,;NOP56,downstream_gene_variant,,ENST00000494697,;NOP56,downstream_gene_variant,,ENST00000480447,;NOP56,downstream_gene_variant,,ENST00000460258,;NOP56,downstream_gene_variant,,ENST00000467857,;IDH3B,upstream_gene_variant,,ENST00000466494,;NOP56,downstream_gene_variant,,ENST00000466447,;NOP56,downstream_gene_variant,,ENST00000471023,;NOP56,downstream_gene_variant,,ENST00000469588,;NOP56,downstream_gene_variant,,ENST00000492135,;IDH3B,upstream_gene_variant,,ENST00000466999,;NOP56,downstream_gene_variant,,ENST00000484998,;NOP56,downstream_gene_variant,,ENST00000467196,;	C	ENSG00000101365	ENST00000380843	Transcript	missense_variant	654	623	208	K/R	aAg/aGg	.	.	.	-1	IDH3B	HGNC	5385	protein_coding	YES	CCDS13032.1	ENSP00000370223	IDH3B_HUMAN	Q9UIC5_HUMAN,B4DU38_HUMAN	UPI000013CBC6	.	tolerated(0.06)	possibly_damaging(0.79)	7/12	.	hmmpanther:PTHR11835,hmmpanther:PTHR11835:SF39,TIGRFAM_domain:TIGR00175,Gene3D:3.40.718.10,Pfam_domain:PF00180,Superfamily_domains:SSF53659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCTTCTTG	.	5	ESCA
LZTS3	0	.	GRCh37	20	3143660	3143660	+	3'UTR	DEL	G	G	-	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1440delC	.	.	ENST00000329152	3/3	36	28	8	39	39	0	LZTS3,3_prime_UTR_variant,,ENST00000329152,;LZTS3,3_prime_UTR_variant,,ENST00000360342,;LZTS3,3_prime_UTR_variant,,ENST00000337576,;UBOX5,upstream_gene_variant,,ENST00000217173,;UBOX5,upstream_gene_variant,,ENST00000449731,;UBOX5,upstream_gene_variant,,ENST00000348031,;FASTKD5,upstream_gene_variant,,ENST00000380266,;	-	ENSG00000088899	ENST00000329152	Transcript	3_prime_UTR_variant	4860	.	.	.	.	.	.	.	-1	LZTS3	Uniprot_gn	.	protein_coding	YES	.	ENSP00000332123	LZTS3_HUMAN	.	UPI0000139A8C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	ATGGGAGGAGGC	.	2	ESCA
LBP	0	.	GRCh37	20	36982828	36982828	+	Silent	SNP	G	G	A	rs760833819	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.513G>A	p.%3D	p.S171S	ENST00000217407	4/15	28	23	5	25	25	0	LBP,synonymous_variant,p.%3D,ENST00000217407,;	A	ENSG00000129988	ENST00000217407	Transcript	synonymous_variant	674	513	171	S	tcG/tcA	rs760833819,COSM1565789	.	.	1	LBP	HGNC	6517	protein_coding	YES	CCDS13304.1	ENSP00000217407	LBP_HUMAN	.	UPI000013C728	.	.	.	4/15	.	hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF43,Gene3D:1ewfA01,Pfam_domain:PF01273,SMART_domains:SM00328,Superfamily_domains:SSF55394	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTCGGGAGA	byFrequency	2	ESCA
SNHG11	0	.	GRCh37	20	37076786	37076786	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.940-519A>T	.	.	ENST00000483342	.	114	98	16	115	115	0	SNHG11,non_coding_transcript_exon_variant,,ENST00000365032,;SNHG11,intron_variant,,ENST00000440918,;SNHG11,intron_variant,,ENST00000449351,;SNHG11,intron_variant,,ENST00000421599,;SNHG11,intron_variant,,ENST00000359074,;SNHG11,intron_variant,,ENST00000434729,;SNHG11,intron_variant,,ENST00000432153,;SNHG11,intron_variant,,ENST00000457218,;SNHG11,intron_variant,,ENST00000420006,;SNHG11,upstream_gene_variant,,ENST00000444816,;SNORA60,upstream_gene_variant,,ENST00000362396,;SNHG11,non_coding_transcript_exon_variant,,ENST00000400436,;SNHG11,intron_variant,,ENST00000437028,;SNHG11,intron_variant,,ENST00000453698,;SNHG11,intron_variant,,ENST00000483342,;SNHG11,intron_variant,,ENST00000442419,;SNHG11,downstream_gene_variant,,ENST00000418383,;	T	ENSG00000174365	ENST00000483342	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SNHG11	HGNC	25046	retained_intron	YES	.	.	.	.	.	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCAGAGGAAA	.	4	ESCA
PLCG1	0	.	GRCh37	20	39800921	39800922	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2897_2898insG	p.Asp966GlufsTer2	p.D966Efs*2	ENST00000373272	25/32	66	55	11	65	65	0	PLCG1,frameshift_variant,p.Asp966GlufsTer2,ENST00000373272,;PLCG1,frameshift_variant,p.Asp966GlufsTer2,ENST00000244007,;PLCG1,frameshift_variant,p.Asp966GlufsTer2,ENST00000373271,;PLCG1,upstream_gene_variant,,ENST00000609821,;PLCG1,upstream_gene_variant,,ENST00000608689,;PLCG1,intron_variant,,ENST00000599785,;PLCG1,upstream_gene_variant,,ENST00000609257,;PLCG1,upstream_gene_variant,,ENST00000608885,;PLCG1,downstream_gene_variant,,ENST00000483175,;PLCG1,downstream_gene_variant,,ENST00000477870,;PLCG1,upstream_gene_variant,,ENST00000461641,;PLCG1,upstream_gene_variant,,ENST00000607954,;	G	ENSG00000124181	ENST00000373272	Transcript	frameshift_variant	3302-3303	2897-2898	966	D/EX	gat/gaGt	.	.	.	1	PLCG1	HGNC	9065	protein_coding	YES	CCDS13313.1	ENSP00000362369	PLCG1_HUMAN	.	UPI00001B94DD	.	.	.	25/32	.	PROSITE_profiles:PS50008,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF52,Pfam_domain:PF00387,Gene3D:3.20.20.190,PIRSF_domain:PIRSF000952,SMART_domains:SM00149,Superfamily_domains:SSF51695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTTGATGAAG	.	3	ESCA
ELMO2	0	.	GRCh37	20	45017766	45017766	+	Missense_Mutation	SNP	C	C	G	rs770618795	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337G>C	p.Asp113His	p.D113H	ENST00000290246	7/22	79	64	15	40	40	0	ELMO2,missense_variant,p.Asp113His,ENST00000439931,;ELMO2,missense_variant,p.Asp25His,ENST00000372176,;ELMO2,missense_variant,p.Asp113His,ENST00000396391,;ELMO2,missense_variant,p.Asp113His,ENST00000450812,;ELMO2,missense_variant,p.Asp113His,ENST00000290246,;ELMO2,missense_variant,p.Asp113His,ENST00000352077,;ELMO2,5_prime_UTR_variant,,ENST00000445496,;ELMO2,upstream_gene_variant,,ENST00000425546,;ELMO2,non_coding_transcript_exon_variant,,ENST00000462593,;ELMO2,non_coding_transcript_exon_variant,,ENST00000497412,;ELMO2,non_coding_transcript_exon_variant,,ENST00000469801,;ELMO2,non_coding_transcript_exon_variant,,ENST00000460474,;ELMO2,non_coding_transcript_exon_variant,,ENST00000488853,;ELMO2,non_coding_transcript_exon_variant,,ENST00000487583,;ELMO2,upstream_gene_variant,,ENST00000480042,;ELMO2,upstream_gene_variant,,ENST00000462491,;	G	ENSG00000062598	ENST00000290246	Transcript	missense_variant	532	337	113	D/H	Gac/Cac	rs770618795	.	.	-1	ELMO2	HGNC	17233	protein_coding	YES	CCDS13398.1	ENSP00000290246	ELMO2_HUMAN	Q7Z5G9_HUMAN,Q5JVZ4_HUMAN,Q5BLP5_HUMAN,F5GZP8_HUMAN	UPI000013F6C4	.	deleterious(0)	probably_damaging(0.999)	7/22	.	hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF8,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGTCGGCAG	byFrequency	5	ESCA
ARFGEF2	0	.	GRCh37	20	47538534	47538534	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108C>T	p.%3D	p.C36C	ENST00000371917	1/39	69	56	12	53	53	0	ARFGEF2,synonymous_variant,p.%3D,ENST00000371917,;	T	ENSG00000124198	ENST00000371917	Transcript	synonymous_variant	108	108	36	C	tgC/tgT	.	.	.	1	ARFGEF2	HGNC	15853	protein_coding	YES	CCDS13411.1	ENSP00000360985	BIG2_HUMAN	Q59FR3_HUMAN	UPI000013D378	.	.	.	1/39	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF124	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTGCCAGGT	.	5	ESCA
PLCB1	0	.	GRCh37	20	8741066	8741066	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2669C>T	p.Ala890Val	p.A890V	ENST00000338037	25/32	57	48	9	61	61	0	PLCB1,missense_variant,p.Ala890Val,ENST00000378641,;PLCB1,missense_variant,p.Ala890Val,ENST00000338037,;PLCB1,missense_variant,p.Ala890Val,ENST00000378637,;PLCB1,non_coding_transcript_exon_variant,,ENST00000494924,;PLCB1,missense_variant,p.Ala631Val,ENST00000487210,;	T	ENSG00000182621	ENST00000338037	Transcript	missense_variant	2696	2669	890	A/V	gCa/gTa	.	.	.	1	PLCB1	HGNC	15917	protein_coding	YES	CCDS13102.1	ENSP00000338185	PLCB1_HUMAN	.	UPI0000131A8F	.	tolerated(0.17)	benign(0.001)	25/32	.	hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF12,PIRSF_domain:PIRSF000956	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGGCACCTG	.	5	ESCA
MORC3	0	.	GRCh37	21	37748463	37748463	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*869A>G	.	.	ENST00000400485	17/17	31	25	6	32	32	0	MORC3,3_prime_UTR_variant,,ENST00000400485,;MORC3,non_coding_transcript_exon_variant,,ENST00000487909,;MORC3,intron_variant,,ENST00000547657,;MORC3,intron_variant,,ENST00000551367,;MORC3,intron_variant,,ENST00000552581,;MORC3,intron_variant,,ENST00000551788,;MORC3,intron_variant,,ENST00000549948,;MORC3,intron_variant,,ENST00000546482,;	G	ENSG00000159256	ENST00000400485	Transcript	3_prime_UTR_variant	3765	.	.	.	.	.	.	.	1	MORC3	HGNC	23572	protein_coding	YES	CCDS42924.1	ENSP00000383333	MORC3_HUMAN	Q86YD6_HUMAN,H0YHQ4_HUMAN,B4DHJ4_HUMAN,A2RU29_HUMAN	UPI0000167F94	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTATATTACA	.	2	ESCA
TSPEAR	0	.	GRCh37	21	45949798	45949798	+	Missense_Mutation	SNP	C	C	T	rs146216896	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673G>A	p.Ala225Thr	p.A225T	ENST00000323084	5/12	53	45	7	38	38	0	TSPEAR,missense_variant,p.Ala157Thr,ENST00000397916,;TSPEAR,missense_variant,p.Ala225Thr,ENST00000323084,;C21orf90,downstream_gene_variant,,ENST00000465978,;	T	ENSG00000175894	ENST00000323084	Transcript	missense_variant	739	673	225	A/T	Gcc/Acc	rs146216896,COSM4101965	.	.	-1	TSPEAR	HGNC	1268	protein_coding	YES	CCDS13712.1	ENSP00000321987	TSEAR_HUMAN	.	UPI0000137746	.	deleterious(0)	possibly_damaging(0.9)	5/12	.	Superfamily_domains:SSF49899,hmmpanther:PTHR15261	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTGGCGTCTG	byCluster	4	ESCA
KLHL22	0	.	GRCh37	22	20819524	20819524	+	Missense_Mutation	SNP	G	G	A	rs747088998	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.733C>T	p.Arg245Trp	p.R245W	ENST00000328879	4/7	253	236	17	46	46	0	KLHL22,missense_variant,p.Arg277Trp,ENST00000444967,;KLHL22,missense_variant,p.Arg245Trp,ENST00000328879,;KLHL22,missense_variant,p.Arg102Trp,ENST00000440659,;KLHL22,missense_variant,p.Arg168Trp,ENST00000451553,;KLHL22,downstream_gene_variant,,ENST00000443285,;KLHL22,downstream_gene_variant,,ENST00000431430,;KLHL22,downstream_gene_variant,,ENST00000458248,;KLHL22,intron_variant,,ENST00000487090,;KLHL22,downstream_gene_variant,,ENST00000494929,;KLHL22,non_coding_transcript_exon_variant,,ENST00000479601,;	A	ENSG00000099910	ENST00000328879	Transcript	missense_variant	890	733	245	R/W	Cgg/Tgg	rs747088998,COSM3405521	.	.	-1	KLHL22	HGNC	25888	protein_coding	YES	CCDS13780.1	ENSP00000331682	KLH22_HUMAN	C9J2T1_HUMAN,C9J191_HUMAN,B7Z2G1_HUMAN	UPI0000072F37	.	deleterious(0)	probably_damaging(0.998)	4/7	.	hmmpanther:PTHR24412:SF180,hmmpanther:PTHR24412,Pfam_domain:PF07707,SMART_domains:SM00875,PIRSF_domain:PIRSF037037	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAACCGCACTG	byFrequency	2	ESCA
APOBEC3D	0	.	GRCh37	22	39428331	39428331	+	3'UTR	SNP	C	C	G	rs185523047	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10C>G	.	.	ENST00000216099	7/7	49	42	7	44	44	0	APOBEC3D,3_prime_UTR_variant,,ENST00000427494,;APOBEC3D,3_prime_UTR_variant,,ENST00000216099,;APOBEC3D,downstream_gene_variant,,ENST00000381568,;	G	ENSG00000243811	ENST00000216099	Transcript	3_prime_UTR_variant	1578	.	.	.	.	rs185523047	.	.	1	APOBEC3D	HGNC	17354	protein_coding	YES	CCDS46709.1	ENSP00000216099	ABC3D_HUMAN	B2CML4_HUMAN	UPI000006D7ED	.	.	.	7/7	.	.	A:0.0012	A:0.0045	A:0	.	A:0	A:0	A:0	A:0.0038	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTCCCTGGGC	byFrequency|byCluster|by1000G	4	ESCA
PKDREJ	0	.	GRCh37	22	46652641	46652641	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6579G>A	p.Met2193Ile	p.M2193I	ENST00000253255	1/1	24	11	13	28	28	0	PKDREJ,missense_variant,p.Met2193Ile,ENST00000253255,;	T	ENSG00000130943	ENST00000253255	Transcript	missense_variant	6579	6579	2193	M/I	atG/atA	.	.	.	-1	PKDREJ	HGNC	9015	protein_coding	YES	CCDS14073.1	ENSP00000253255	PKDRE_HUMAN	A6MW40_HUMAN	UPI0000031D01	.	tolerated(0.46)	benign(0.017)	1/1	.	hmmpanther:PTHR10877:SF113,hmmpanther:PTHR10877	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGTCATTGC	.	5	ESCA
GTSE1	0	.	GRCh37	22	46726517	46726517	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*490C>T	.	.	ENST00000454366	12/12	20	10	10	8	8	0	GTSE1,3_prime_UTR_variant,,ENST00000454366,;TRMU,upstream_gene_variant,,ENST00000290846,;TRMU,upstream_gene_variant,,ENST00000476901,;TRMU,upstream_gene_variant,,ENST00000486620,;TRMU,upstream_gene_variant,,ENST00000457572,;TRMU,upstream_gene_variant,,ENST00000456595,;TRMU,upstream_gene_variant,,ENST00000441818,;TRMU,upstream_gene_variant,,ENST00000453630,;GTSE1,downstream_gene_variant,,ENST00000479645,;GTSE1,downstream_gene_variant,,ENST00000466510,;GTSE1,downstream_gene_variant,,ENST00000491863,;TRMU,upstream_gene_variant,,ENST00000381021,;	T	ENSG00000075218	ENST00000454366	Transcript	3_prime_UTR_variant	2922	.	.	.	.	.	.	.	1	GTSE1	HGNC	13698	protein_coding	YES	CCDS14074.2	ENSP00000415430	GTSE1_HUMAN	.	UPI000021D19B	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTCCCGCCGC	.	3	ESCA
PLXNB2	0	.	GRCh37	22	50722580	50722589	+	Frame_Shift_Del	DEL	ATTCTTGCCG	ATTCTTGCCG	-	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	ATTCTTGCCG	ATTCTTGCCG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2235_2244delCGGCAAGAAT	p.Tyr745Ter	p.Y745*	ENST00000449103	13/37	127	50	77	158	158	0	PLXNB2,frameshift_variant,p.Tyr745Ter,ENST00000359337,;PLXNB2,frameshift_variant,p.Tyr745Ter,ENST00000449103,;PLXNB2,intron_variant,,ENST00000411680,;PLXNB2,upstream_gene_variant,,ENST00000427829,;PLXNB2,downstream_gene_variant,,ENST00000432455,;PLXNB2,downstream_gene_variant,,ENST00000434732,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000496720,;PLXNB2,upstream_gene_variant,,ENST00000479701,;PLXNB2,upstream_gene_variant,,ENST00000463165,;PLXNB2,upstream_gene_variant,,ENST00000492578,;	-	ENSG00000196576	ENST00000449103	Transcript	frameshift_variant	2376-2385	2235-2244	745-748	YGKN/X	taCGGCAAGAAT/ta	.	.	.	-1	PLXNB2	HGNC	9104	protein_coding	YES	CCDS43035.1	ENSP00000409171	PLXB2_HUMAN	Q2TBE4_HUMAN,E2PU09_HUMAN,A6QRH1_HUMAN	UPI000003812D	.	.	.	13/37	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCGATATTCTTGCCGTAAGA	.	3	ESCA
MYO7B	0	.	GRCh37	2	128370116	128370116	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3258C>T	p.%3D	p.P1086P	ENST00000428314	25/47	37	29	8	29	29	0	MYO7B,synonymous_variant,p.%3D,ENST00000389524,;MYO7B,synonymous_variant,p.%3D,ENST00000409816,;MYO7B,synonymous_variant,p.%3D,ENST00000428314,;MYO7B,downstream_gene_variant,,ENST00000563538,;	T	ENSG00000169994	ENST00000428314	Transcript	synonymous_variant	3311	3258	1086	P	ccC/ccT	.	.	.	1	MYO7B	HGNC	7607	protein_coding	YES	CCDS46405.1	ENSP00000415090	MYO7B_HUMAN	C9JC21_HUMAN,B9A063_HUMAN	UPI00006C04F0	.	.	.	25/47	.	PROSITE_profiles:PS51016,SMART_domains:SM00139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCCCATGTC	.	5	ESCA
LCT	0	.	GRCh37	2	136579638	136579638	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938G>A	p.Gly313Glu	p.G313E	ENST00000264162	5/17	60	49	11	73	73	0	LCT,missense_variant,p.Gly313Glu,ENST00000264162,;AC011893.3,non_coding_transcript_exon_variant,,ENST00000437007,;	T	ENSG00000115850	ENST00000264162	Transcript	missense_variant	949	938	313	G/E	gGg/gAg	.	.	.	-1	LCT	HGNC	6530	protein_coding	YES	CCDS2178.1	ENSP00000264162	LPH_HUMAN	.	UPI000013D4D2	.	deleterious(0)	probably_damaging(0.984)	5/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAACCCAATG	.	5	ESCA
XIRP2	0	.	GRCh37	2	168101152	168101152	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3250A>G	p.Arg1084Gly	p.R1084G	ENST00000409195	9/11	44	34	9	39	39	0	XIRP2,missense_variant,p.Arg862Gly,ENST00000409273,;XIRP2,missense_variant,p.Arg1084Gly,ENST00000409195,;XIRP2,missense_variant,p.Arg1084Gly,ENST00000295237,;XIRP2,intron_variant,,ENST00000409605,;XIRP2,intron_variant,,ENST00000420519,;XIRP2,intron_variant,,ENST00000409756,;XIRP2,intron_variant,,ENST00000409043,;XIRP2,intron_variant,,ENST00000409728,;	G	ENSG00000163092	ENST00000409195	Transcript	missense_variant	3339	3250	1084	R/G	Aga/Gga	.	.	.	1	XIRP2	HGNC	14303	protein_coding	YES	CCDS42769.1	ENSP00000386840	.	J3KNB1_HUMAN	UPI0000E9BBED	.	.	benign(0.043)	9/11	.	hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAACTAGAGAT	.	3	ESCA
TTN	0	.	GRCh37	2	179575994	179575994	+	Silent	SNP	G	G	T	rs773102635	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27969C>A	p.%3D	p.A9323A	ENST00000589042	97/363	66	57	9	64	64	0	TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000589830,;	T	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	28194	27969	9323	A	gcC/gcA	rs773102635	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	97/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTATGGCACA	byFrequency	4	ESCA
PMS1	0	.	GRCh37	2	190732645	190732645	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2463A>G	p.%3D	p.K821K	ENST00000441310	11/13	51	40	10	41	41	0	PMS1,synonymous_variant,p.%3D,ENST00000441310,;PMS1,synonymous_variant,p.%3D,ENST00000452382,;PMS1,synonymous_variant,p.%3D,ENST00000432292,;PMS1,synonymous_variant,p.%3D,ENST00000447232,;PMS1,synonymous_variant,p.%3D,ENST00000409823,;PMS1,synonymous_variant,p.%3D,ENST00000409593,;PMS1,synonymous_variant,p.%3D,ENST00000418224,;PMS1,downstream_gene_variant,,ENST00000424307,;PMS1,non_coding_transcript_exon_variant,,ENST00000483293,;PMS1,intron_variant,,ENST00000424059,;PMS1,downstream_gene_variant,,ENST00000421722,;PMS1,3_prime_UTR_variant,,ENST00000450931,;PMS1,3_prime_UTR_variant,,ENST00000342075,;	G	ENSG00000064933	ENST00000441310	Transcript	synonymous_variant	2696	2463	821	K	aaA/aaG	.	.	.	1	PMS1	HGNC	9121	protein_coding	YES	CCDS2302.1	ENSP00000406490	PMS1_HUMAN	Q5FBZ2_HUMAN,C9JKP0_HUMAN,C9JF76_HUMAN,C9J4L1_HUMAN,B7ZAA0_HUMAN	UPI00000405F5	.	.	.	11/13	.	hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAAATTGAT	.	5	ESCA
TMEFF2	0	.	GRCh37	2	192863843	192863843	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628G>T	p.Glu210Ter	p.E210*	ENST00000272771	6/10	130	106	23	92	92	0	TMEFF2,stop_gained,p.Glu210Ter,ENST00000272771,;TMEFF2,stop_gained,p.Glu210Ter,ENST00000392314,;AC098617.1,intron_variant,,ENST00000424116,;AC098617.1,intron_variant,,ENST00000428980,;TMEFF2,non_coding_transcript_exon_variant,,ENST00000487771,;	A	ENSG00000144339	ENST00000272771	Transcript	stop_gained	1813	628	210	E/*	Gaa/Taa	.	.	.	-1	TMEFF2	HGNC	11867	protein_coding	YES	CCDS2314.1	ENSP00000272771	TEFF2_HUMAN	.	UPI0000048F19	.	.	.	6/10	.	Superfamily_domains:SSF100895,SMART_domains:SM00280,Pfam_domain:PF07648,Gene3D:3.30.60.30,hmmpanther:PTHR10574,PROSITE_profiles:PS51465	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCTTTGA	.	5	ESCA
INO80D	0	.	GRCh37	2	206869439	206869439	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2737C>G	p.Leu913Val	p.L913V	ENST00000403263	11/11	63	55	7	60	59	0	INO80D,missense_variant,p.Leu913Val,ENST00000403263,;INO80D,downstream_gene_variant,,ENST00000424117,;Vault,downstream_gene_variant,,ENST00000516676,;AC007679.3,downstream_gene_variant,,ENST00000422116,;	C	ENSG00000114933	ENST00000403263	Transcript	missense_variant	3142	2737	913	L/V	Ctt/Gtt	.	.	.	-1	INO80D	HGNC	25997	protein_coding	YES	CCDS46500.1	ENSP00000384198	IN80D_HUMAN	C9JLZ4_HUMAN,C9JLV2_HUMAN	UPI0000EE35FC	.	deleterious_low_confidence(0)	probably_damaging(0.996)	11/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16198	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAAGATGTC	.	4	ESCA
KLF7	0	.	GRCh37	2	207988643	207988643	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588T>C	p.%3D	p.S196S	ENST00000309446	2/4	35	26	9	55	55	0	KLF7,synonymous_variant,p.%3D,ENST00000309446,;KLF7,synonymous_variant,p.%3D,ENST00000421199,;KLF7,synonymous_variant,p.%3D,ENST00000412414,;KLF7,synonymous_variant,p.%3D,ENST00000435602,;KLF7,intron_variant,,ENST00000458272,;KLF7,intron_variant,,ENST00000423015,;KLF7,downstream_gene_variant,,ENST00000426163,;KLF7,downstream_gene_variant,,ENST00000457962,;KLF7-IT1,upstream_gene_variant,,ENST00000428777,;KLF7,intron_variant,,ENST00000467833,;KLF7,downstream_gene_variant,,ENST00000451244,;	G	ENSG00000118263	ENST00000309446	Transcript	synonymous_variant	965	588	196	S	agT/agC	.	.	.	-1	KLF7	HGNC	6350	protein_coding	YES	CCDS2373.1	ENSP00000309570	KLF7_HUMAN	Q53TP3_HUMAN,Q4ZG79_HUMAN,E7EUU0_HUMAN,E7EQY2_HUMAN	UPI0000042958	.	.	.	2/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23223:SF2,hmmpanther:PTHR23223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCCACTCTT	.	5	ESCA
CPS1	0	.	GRCh37	2	211541847	211541847	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4409T>C	p.Leu1470Pro	p.L1470P	ENST00000430249	38/39	81	69	11	64	64	0	CPS1,missense_variant,p.Leu1470Pro,ENST00000430249,;CPS1,missense_variant,p.Leu1464Pro,ENST00000233072,;CPS1,missense_variant,p.Leu1013Pro,ENST00000451903,;CPS1,non_coding_transcript_exon_variant,,ENST00000479988,;	C	ENSG00000021826	ENST00000430249	Transcript	missense_variant	4464	4409	1470	L/P	cTc/cCc	.	.	.	1	CPS1	HGNC	2323	protein_coding	YES	CCDS46505.1	ENSP00000402608	CPSM_HUMAN	Q5R207_HUMAN,E7EWJ3_HUMAN,C9JTA4_HUMAN,B7ZAW0_HUMAN	UPI000166C19F	.	deleterious(0)	probably_damaging(0.929)	38/39	.	hmmpanther:PTHR11405:SF32,hmmpanther:PTHR11405,TIGRFAM_domain:TIGR01369,Pfam_domain:PF02142,Gene3D:3.40.50.1380,SMART_domains:SM00851,Superfamily_domains:SSF52335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCCTCACTA	.	5	ESCA
SLC11A1	0	.	GRCh37	2	219259680	219259680	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1575C>A	p.%3D	p.T525T	ENST00000233202	15/15	57	50	6	56	56	0	SLC11A1,synonymous_variant,p.%3D,ENST00000233202,;SLC11A1,synonymous_variant,p.%3D,ENST00000539932,;CTDSP1,upstream_gene_variant,,ENST00000273062,;CTDSP1,upstream_gene_variant,,ENST00000443891,;RP11-378A13.2,downstream_gene_variant,,ENST00000608367,;CTDSP1,upstream_gene_variant,,ENST00000491064,;CTDSP1,upstream_gene_variant,,ENST00000473420,;CTDSP1,upstream_gene_variant,,ENST00000492545,;CTDSP1,upstream_gene_variant,,ENST00000498160,;SLC11A1,3_prime_UTR_variant,,ENST00000354352,;SLC11A1,non_coding_transcript_exon_variant,,ENST00000468221,;SLC11A1,non_coding_transcript_exon_variant,,ENST00000465984,;SLC11A1,downstream_gene_variant,,ENST00000468721,;SLC11A1,downstream_gene_variant,,ENST00000490872,;SLC11A1,downstream_gene_variant,,ENST00000490536,;SLC11A1,downstream_gene_variant,,ENST00000494322,;	A	ENSG00000018280	ENST00000233202	Transcript	synonymous_variant	1915	1575	525	T	acC/acA	.	.	.	1	SLC11A1	HGNC	10907	protein_coding	YES	CCDS2415.1	ENSP00000233202	NRAM1_HUMAN	Q8NDV6_HUMAN	UPI0000130520	.	.	.	15/15	.	hmmpanther:PTHR11706:SF36,hmmpanther:PTHR11706	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCACCTTTCT	.	3	ESCA
RAB10	0	.	GRCh37	2	26350815	26350815	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514C>T	p.Arg172Ter	p.R172*	ENST00000264710	5/6	87	67	20	44	44	0	RAB10,stop_gained,p.Arg172Ter,ENST00000264710,;RAB10,non_coding_transcript_exon_variant,,ENST00000473035,;RAB10,non_coding_transcript_exon_variant,,ENST00000462003,;RAB10,non_coding_transcript_exon_variant,,ENST00000495146,;	T	ENSG00000084733	ENST00000264710	Transcript	stop_gained	1013	514	172	R/*	Cga/Tga	.	.	.	1	RAB10	HGNC	9759	protein_coding	YES	CCDS1720.1	ENSP00000264710	RAB10_HUMAN	Q9UL28_HUMAN,Q53T70_HUMAN,Q53SX4_HUMAN	UPI0000001263	.	.	.	5/6	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF358,hmmpanther:PTHR24073,Gene3D:3.40.50.300,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00177,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTCGAAAG	.	5	ESCA
WDR43	0	.	GRCh37	2	29150504	29150504	+	Missense_Mutation	SNP	A	A	G	rs780225617	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1243A>G	p.Ile415Val	p.I415V	ENST00000407426	10/18	75	55	20	57	57	0	WDR43,missense_variant,p.Ile415Val,ENST00000407426,;WDR43,downstream_gene_variant,,ENST00000296126,;WDR43,upstream_gene_variant,,ENST00000446643,;SNORD53,downstream_gene_variant,,ENST00000579969,;SNORD53_SNORD92,upstream_gene_variant,,ENST00000577887,;Y_RNA,upstream_gene_variant,,ENST00000410292,;WDR43,non_coding_transcript_exon_variant,,ENST00000466067,;	G	ENSG00000163811	ENST00000407426	Transcript	missense_variant	1299	1243	415	I/V	Atc/Gtc	rs780225617	.	.	1	WDR43	HGNC	28945	protein_coding	YES	CCDS46251.1	ENSP00000384302	WDR43_HUMAN	C9JH61_HUMAN,C9JEE7_HUMAN,C9IZK7_HUMAN	UPI00001C1DCD	.	tolerated(0.86)	benign(0.001)	10/18	.	hmmpanther:PTHR22847:SF406,hmmpanther:PTHR22847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTATCAAG	.	5	ESCA
CCDC142	0	.	GRCh37	2	74701784	74701784	+	Silent	SNP	C	C	T	rs768231556	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2121G>A	p.%3D	p.P707P	ENST00000290418	9/9	67	55	12	54	54	0	CCDC142,synonymous_variant,p.%3D,ENST00000393965,;CCDC142,synonymous_variant,p.%3D,ENST00000290418,;MRPL53,upstream_gene_variant,,ENST00000258105,;MRPL53,upstream_gene_variant,,ENST00000409710,;CCDC142,non_coding_transcript_exon_variant,,ENST00000473278,;CCDC142,intron_variant,,ENST00000454193,;CCDC142,downstream_gene_variant,,ENST00000497232,;MRPL53,upstream_gene_variant,,ENST00000468875,;MRPL53,upstream_gene_variant,,ENST00000467349,;CCDC142,downstream_gene_variant,,ENST00000486335,;	T	ENSG00000135637	ENST00000290418	Transcript	synonymous_variant	2280	2121	707	P	ccG/ccA	rs768231556	.	.	-1	CCDC142	HGNC	25889	protein_coding	YES	CCDS1945.1	ENSP00000290418	CC142_HUMAN	.	UPI000013CFB5	.	.	.	9/9	.	hmmpanther:PTHR21436,hmmpanther:PTHR21436:SF1,Pfam_domain:PF14923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCCGGGCT	.	5	ESCA
REG3A	0	.	GRCh37	2	79384410	79384410	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470G>T	p.Arg157Met	p.R157M	ENST00000393878	5/5	71	56	15	63	63	0	REG3A,missense_variant,p.Arg157Met,ENST00000305165,;REG3A,missense_variant,p.Arg157Met,ENST00000393878,;REG3A,missense_variant,p.Arg157Met,ENST00000409839,;AC011754.1,upstream_gene_variant,,ENST00000415201,;REG3A,downstream_gene_variant,,ENST00000464746,;REG3A,downstream_gene_variant,,ENST00000490901,;	A	ENSG00000172016	ENST00000393878	Transcript	missense_variant	725	470	157	R/M	aGg/aTg	.	.	.	-1	REG3A	HGNC	8601	protein_coding	YES	CCDS1965.1	ENSP00000377456	REG3A_HUMAN	Q53S56_HUMAN	UPI0000001C5B	.	deleterious(0.03)	benign(0.026)	5/5	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22801:SF29,hmmpanther:PTHR22801,PROSITE_patterns:PS00615,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACCTCAGA	.	5	ESCA
IGKV1D-43	0	.	GRCh37	2	90249310	90249310	+	Missense_Mutation	SNP	C	C	A	rs371291962	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.266C>A	p.Ser89Tyr	p.S89Y	ENST00000468879	2/2	257	217	40	189	189	0	IGKV1D-43,missense_variant,p.Ser89Tyr,ENST00000468879,;	A	ENSG00000242580	ENST00000468879	Transcript	missense_variant	447	266	89	S/Y	tCt/tAt	rs371291962	.	.	1	IGKV1D-43	HGNC	5758	IG_V_gene	YES	.	ENSP00000417961	.	.	UPI0000116191	.	deleterious(0.04)	benign(0.324)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF122,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGATCTGGGA	byFrequency|byCluster	4	ESCA
STARD7	0	.	GRCh37	2	96858916	96858916	+	Intron	SNP	C	C	A	rs751365389	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.661-18G>T	.	.	ENST00000337288	.	47	39	8	60	60	0	STARD7,intron_variant,,ENST00000337288,;STARD7,intron_variant,,ENST00000443962,;STARD7,non_coding_transcript_exon_variant,,ENST00000462501,;STARD7,non_coding_transcript_exon_variant,,ENST00000495687,;STARD7,downstream_gene_variant,,ENST00000488084,;	A	ENSG00000084090	ENST00000337288	Transcript	intron_variant	.	.	.	.	.	rs751365389	.	.	-1	STARD7	HGNC	18063	protein_coding	YES	CCDS2017.2	ENSP00000338030	STAR7_HUMAN	C9JTD3_HUMAN	UPI0000001C0C	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGCAGGAT	.	5	ESCA
CIAO1	0	.	GRCh37	2	96934312	96934312	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607G>C	p.Asp203His	p.D203H	ENST00000488633	5/7	66	56	10	47	47	0	CIAO1,missense_variant,p.Asp203His,ENST00000488633,;TMEM127,upstream_gene_variant,,ENST00000258439,;TMEM127,upstream_gene_variant,,ENST00000432959,;CIAO1,downstream_gene_variant,,ENST00000469320,;CIAO1,non_coding_transcript_exon_variant,,ENST00000272402,;CIAO1,downstream_gene_variant,,ENST00000491394,;	C	ENSG00000144021	ENST00000488633	Transcript	missense_variant	826	607	203	D/H	Gac/Cac	COSM384377	.	.	1	CIAO1	HGNC	14280	protein_coding	YES	CCDS2019.1	ENSP00000418287	CIAO1_HUMAN	.	UPI0000127987	.	deleterious(0.02)	probably_damaging(1)	5/7	.	HAMAP:MF_03037,PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR19920,hmmpanther:PTHR19920:SF0,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTGACCCG	.	5	ESCA
ATG3	0	.	GRCh37	3	112253120	112253120	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.859C>T	p.His287Tyr	p.H287Y	ENST00000283290	11/12	96	73	23	57	57	0	ATG3,missense_variant,p.His287Tyr,ENST00000402314,;ATG3,missense_variant,p.His287Tyr,ENST00000283290,;ATG3,downstream_gene_variant,,ENST00000492886,;ATG3,downstream_gene_variant,,ENST00000495756,;ATG3,non_coding_transcript_exon_variant,,ENST00000494571,;ATG3,downstream_gene_variant,,ENST00000496423,;ATG3,downstream_gene_variant,,ENST00000467275,;	A	ENSG00000144848	ENST00000283290	Transcript	missense_variant	1294	859	287	H/Y	Cat/Tat	.	.	.	-1	ATG3	HGNC	20962	protein_coding	YES	CCDS2966.1	ENSP00000283290	ATG3_HUMAN	C9JNW8_HUMAN	UPI0000073DB4	.	deleterious(0.02)	benign(0.33)	11/12	.	hmmpanther:PTHR12866:SF2,hmmpanther:PTHR12866,Pfam_domain:PF10381	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATATGAACTC	.	5	ESCA
WDR52	0	.	GRCh37	3	113025140	113025140	+	Nonsense_Mutation	SNP	G	G	A	rs749384603	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4666C>T	p.Arg1556Ter	p.R1556*	ENST00000393845	30/35	104	89	14	85	85	0	WDR52,stop_gained,p.Arg1556Ter,ENST00000393845,;WDR52,stop_gained,p.Arg693Ter,ENST00000465636,;WDR52,stop_gained,p.Arg159Ter,ENST00000308346,;WDR52,stop_gained,p.Arg177Ter,ENST00000461734,;WDR52,upstream_gene_variant,,ENST00000465510,;WDR52,upstream_gene_variant,,ENST00000489244,;	A	ENSG00000206530	ENST00000393845	Transcript	stop_gained	4733	4666	1556	R/*	Cga/Tga	rs749384603	.	.	-1	WDR52	HGNC	25631	protein_coding	YES	CCDS54624.1	ENSP00000377428	WDR52_HUMAN	C9K0A4_HUMAN	UPI0000367198	.	.	.	30/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTCGAAGGT	.	4	ESCA
ESYT3	0	.	GRCh37	3	138183220	138183220	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.949C>T	p.Gln317Ter	p.Q317*	ENST00000389567	9/23	34	28	6	34	34	0	ESYT3,stop_gained,p.Gln317Ter,ENST00000389567,;ESYT3,downstream_gene_variant,,ENST00000289135,;ESYT3,stop_gained,p.Gln317Ter,ENST00000490835,;ESYT3,non_coding_transcript_exon_variant,,ENST00000486831,;ESYT3,upstream_gene_variant,,ENST00000468103,;	T	ENSG00000158220	ENST00000389567	Transcript	stop_gained	1135	949	317	Q/*	Cag/Tag	.	.	.	1	ESYT3	HGNC	24295	protein_coding	YES	CCDS3101.2	ENSP00000374218	ESYT3_HUMAN	.	UPI0000251E45	.	.	.	9/23	.	PROSITE_profiles:PS50004,hmmpanther:PTHR10774:SF27,hmmpanther:PTHR10774,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGCAGCTG	.	5	ESCA
ECE2	0	.	GRCh37	3	184009973	184009973	+	Missense_Mutation	SNP	G	G	A	rs192602550	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2599G>A	p.Gly867Ser	p.G867S	ENST00000402825	19/19	69	59	10	68	68	0	ECE2,missense_variant,p.Gly720Ser,ENST00000359140,;ECE2,missense_variant,p.Gly795Ser,ENST00000357474,;ECE2,missense_variant,p.Gly749Ser,ENST00000404464,;ECE2,missense_variant,p.Gly867Ser,ENST00000402825,;EIF2B5,intron_variant,,ENST00000444495,;ECE2,downstream_gene_variant,,ENST00000430587,;ECE2,downstream_gene_variant,,ENST00000488401,;ECE2,downstream_gene_variant,,ENST00000490579,;	A	ENSG00000145194	ENST00000402825	Transcript	missense_variant	2599	2599	867	G/S	Ggc/Agc	rs192602550	.	.	1	ECE2	HGNC	13275	protein_coding	YES	CCDS3256.2	ENSP00000384223	ECE2_HUMAN	.	UPI0001596888	.	tolerated(0.56)	benign(0.027)	19/19	.	hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF122,Gene3D:3.40.390.10,Pfam_domain:PF01431,Superfamily_domains:SSF55486	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTTCGGCTGC	byFrequency|byCluster|by1000G	4	ESCA
GLB1	0	.	GRCh37	3	33060008	33060008	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1279A>C	p.Ser427Arg	p.S427R	ENST00000307363	13/16	65	51	14	85	85	0	GLB1,missense_variant,p.Ser397Arg,ENST00000399402,;GLB1,missense_variant,p.Ser427Arg,ENST00000307363,;GLB1,missense_variant,p.Ser296Arg,ENST00000307377,;GLB1,missense_variant,p.Ser475Arg,ENST00000445488,;GLB1,non_coding_transcript_exon_variant,,ENST00000497796,;GLB1,non_coding_transcript_exon_variant,,ENST00000461475,;GLB1,non_coding_transcript_exon_variant,,ENST00000467571,;GLB1,downstream_gene_variant,,ENST00000482097,;GLB1,downstream_gene_variant,,ENST00000473477,;	G	ENSG00000170266	ENST00000307363	Transcript	missense_variant	1424	1279	427	S/R	Agc/Cgc	.	.	.	-1	GLB1	HGNC	4298	protein_coding	YES	CCDS43061.1	ENSP00000306920	BGAL_HUMAN	C9JF15_HUMAN,C9J539_HUMAN	UPI0000E5A543	.	tolerated(0.48)	possibly_damaging(0.616)	13/16	.	PIRSF_domain:PIRSF006336,hmmpanther:PTHR23421,hmmpanther:PTHR23421:SF61	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGCTGCAAT	.	5	ESCA
LAMB2	0	.	GRCh37	3	49166737	49166737	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1539C>A	p.Ser513Arg	p.S513R	ENST00000418109	13/33	17	13	3	21	21	0	LAMB2,missense_variant,p.Ser513Arg,ENST00000305544,;LAMB2,missense_variant,p.Ser513Arg,ENST00000418109,;LAMB2,downstream_gene_variant,,ENST00000494831,;LAMB2,upstream_gene_variant,,ENST00000464891,;LAMB2,upstream_gene_variant,,ENST00000486298,;LAMB2,upstream_gene_variant,,ENST00000538659,;LAMB2,upstream_gene_variant,,ENST00000542580,;LAMB2,upstream_gene_variant,,ENST00000493571,;LAMB2,upstream_gene_variant,,ENST00000462930,;LAMB2,upstream_gene_variant,,ENST00000483321,;LAMB2,upstream_gene_variant,,ENST00000477701,;LAMB2,upstream_gene_variant,,ENST00000480640,;LAMB2,upstream_gene_variant,,ENST00000488638,;LAMB2,upstream_gene_variant,,ENST00000483057,;	T	ENSG00000172037	ENST00000418109	Transcript	missense_variant	1704	1539	513	S/R	agC/agA	.	.	.	-1	LAMB2	HGNC	6487	protein_coding	YES	CCDS2789.1	ENSP00000388325	LAMB2_HUMAN	F5H520_HUMAN	UPI000013EA62	.	deleterious(0)	probably_damaging(1)	13/33	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF36,hmmpanther:PTHR10574,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTGGCTCAG	.	5	ESCA
TRAIP	0	.	GRCh37	3	49867177	49867177	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109G>A	p.Gly370Asp	p.G370D	ENST00000331456	13/15	15	12	3	32	32	0	TRAIP,missense_variant,p.Gly215Asp,ENST00000469027,;TRAIP,missense_variant,p.Gly370Asp,ENST00000331456,;TRAIP,3_prime_UTR_variant,,ENST00000473195,;TRAIP,non_coding_transcript_exon_variant,,ENST00000491060,;TRAIP,downstream_gene_variant,,ENST00000475495,;	T	ENSG00000183763	ENST00000331456	Transcript	missense_variant	1223	1109	370	G/D	gGc/gAc	.	.	.	-1	TRAIP	HGNC	30764	protein_coding	YES	CCDS2806.1	ENSP00000328203	TRAIP_HUMAN	A4UCT7_HUMAN	UPI000006FE67	.	tolerated(0.66)	benign(0.048)	13/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGGCCACCC	.	2	ESCA
DOCK3	0	.	GRCh37	3	50927459	50927459	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165G>A	p.%3D	p.G55G	ENST00000266037	4/53	44	28	16	46	46	0	DOCK3,synonymous_variant,p.%3D,ENST00000266037,;	A	ENSG00000088538	ENST00000266037	Transcript	synonymous_variant	188	165	55	G	ggG/ggA	.	.	.	1	DOCK3	HGNC	2989	protein_coding	YES	CCDS46835.1	ENSP00000266037	DOCK3_HUMAN	.	UPI000007412C	.	.	.	4/53	.	PROSITE_profiles:PS50002,hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGGATCTT	.	5	ESCA
ANKRD50	0	.	GRCh37	4	125631531	125631531	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136A>G	p.Ser46Gly	p.S46G	ENST00000504087	2/5	46	36	9	68	68	0	ANKRD50,missense_variant,p.Ser46Gly,ENST00000504087,;ANKRD50,intron_variant,,ENST00000515641,;	C	ENSG00000151458	ENST00000504087	Transcript	missense_variant	1174	136	46	S/G	Agt/Ggt	.	.	.	-1	ANKRD50	HGNC	29223	protein_coding	YES	CCDS34060.1	ENSP00000425658	ANR50_HUMAN	Q8TB46_HUMAN	UPI00002377E8	.	tolerated_low_confidence(0.76)	benign(0)	2/5	.	hmmpanther:PTHR24151:SF1,hmmpanther:PTHR24151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCACTATTGC	.	5	ESCA
SPOCK3	0	.	GRCh37	4	167656208	167656208	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1175G>C	p.Ser392Thr	p.S392T	ENST00000357154	12/12	49	37	12	58	58	0	SPOCK3,missense_variant,p.Ser392Thr,ENST00000357154,;SPOCK3,missense_variant,p.Ser392Thr,ENST00000511531,;SPOCK3,missense_variant,p.Ser389Thr,ENST00000357545,;SPOCK3,missense_variant,p.Ser392Thr,ENST00000506886,;SPOCK3,missense_variant,p.Ser389Thr,ENST00000511269,;SPOCK3,missense_variant,p.Ser341Thr,ENST00000421836,;SPOCK3,missense_variant,p.Ser349Thr,ENST00000510741,;SPOCK3,missense_variant,p.Ser260Thr,ENST00000535728,;SPOCK3,missense_variant,p.Ser294Thr,ENST00000541637,;SPOCK3,missense_variant,p.Ser272Thr,ENST00000541354,;SPOCK3,missense_variant,p.Ser294Thr,ENST00000512681,;SPOCK3,missense_variant,p.Ser296Thr,ENST00000534949,;SPOCK3,missense_variant,p.Ser392Thr,ENST00000502330,;SPOCK3,missense_variant,p.Ser389Thr,ENST00000504953,;SPOCK3,non_coding_transcript_exon_variant,,ENST00000507137,;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,;	G	ENSG00000196104	ENST00000357154	Transcript	missense_variant	1313	1175	392	S/T	aGt/aCt	.	.	.	-1	SPOCK3	HGNC	13565	protein_coding	YES	CCDS54817.1	ENSP00000349677	TICN3_HUMAN	Q4W5S3_HUMAN,Q4W5E2_HUMAN,E7EMP8_HUMAN	UPI000004BA60	.	deleterious(0)	probably_damaging(0.995)	12/12	.	hmmpanther:PTHR12036,hmmpanther:PTHR12036:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCACTAGCA	.	5	ESCA
LRRC66	0	.	GRCh37	4	52861261	52861261	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1927G>A	p.Ala643Thr	p.A643T	ENST00000343457	4/4	44	34	9	40	40	0	LRRC66,missense_variant,p.Ala643Thr,ENST00000343457,;	T	ENSG00000188993	ENST00000343457	Transcript	missense_variant	1934	1927	643	A/T	Gca/Aca	.	.	.	-1	LRRC66	HGNC	34299	protein_coding	YES	CCDS43229.1	ENSP00000341944	LRC66_HUMAN	.	UPI0000425C5B	.	tolerated(0.17)	benign(0.22)	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTGCCCCGG	.	5	ESCA
ST8SIA4	0	.	GRCh37	5	100146563	100146563	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*988A>C	.	.	ENST00000231461	5/5	20	15	5	25	25	0	ST8SIA4,3_prime_UTR_variant,,ENST00000231461,;	G	ENSG00000113532	ENST00000231461	Transcript	3_prime_UTR_variant	2379	.	.	.	.	.	.	.	-1	ST8SIA4	HGNC	10871	protein_coding	YES	CCDS4091.1	ENSP00000231461	SIA8D_HUMAN	.	UPI0000135973	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTTTAGAG	.	5	ESCA
SLCO4C1	0	.	GRCh37	5	101583042	101583042	+	Silent	SNP	C	C	T	rs574597658	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1725G>A	p.%3D	p.A575A	ENST00000310954	10/13	43	34	9	71	71	0	SLCO4C1,synonymous_variant,p.%3D,ENST00000310954,;	T	ENSG00000173930	ENST00000310954	Transcript	synonymous_variant	2012	1725	575	A	gcG/gcA	rs574597658,COSM1642543	.	.	-1	SLCO4C1	HGNC	23612	protein_coding	YES	CCDS34205.1	ENSP00000309741	SO4C1_HUMAN	Q63HP3_HUMAN	UPI00001C10B6	.	.	.	10/13	.	Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,hmmpanther:PTHR11388:SF81,hmmpanther:PTHR11388,PROSITE_profiles:PS50850	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A575A|c.1725G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTCGCACA	by1000G	5	ESCA
DMXL1	0	.	GRCh37	5	118576136	118576136	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8611C>T	p.Leu2871Phe	p.L2871F	ENST00000311085	41/43	20	14	6	37	37	0	DMXL1,missense_variant,p.Leu2892Phe,ENST00000539542,;DMXL1,missense_variant,p.Leu2871Phe,ENST00000311085,;DMXL1,non_coding_transcript_exon_variant,,ENST00000505312,;DMXL1,downstream_gene_variant,,ENST00000511622,;DMXL1,non_coding_transcript_exon_variant,,ENST00000514595,;	T	ENSG00000172869	ENST00000311085	Transcript	missense_variant	8691	8611	2871	L/F	Ctt/Ttt	COSM3918492,COSM3918493	.	.	1	DMXL1	HGNC	2937	protein_coding	YES	CCDS4125.1	ENSP00000309690	DMXL1_HUMAN	F1T0K4_HUMAN,E7EMZ0_HUMAN	UPI000013F0EC	.	deleterious(0)	probably_damaging(0.999)	41/43	.	hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A2873A|c.8619A>C|3	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATACTCTTGTA	.	4	ESCA
KCNIP1	0	.	GRCh37	5	170163317	170163317	+	3'Flank	SNP	T	T	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000411494	.	30	22	8	38	38	0	KCNIP1,3_prime_UTR_variant,,ENST00000390656,;KCNIP1,3_prime_UTR_variant,,ENST00000328939,;KCNIP1,3_prime_UTR_variant,,ENST00000520740,;KCNIP1,downstream_gene_variant,,ENST00000411494,;KCNIP1,downstream_gene_variant,,ENST00000377360,;KCNIP1,downstream_gene_variant,,ENST00000434108,;	A	ENSG00000182132	ENST00000411494	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	507	1	KCNIP1	HGNC	15521	protein_coding	YES	CCDS34286.1	ENSP00000395323	KCIP1_HUMAN	.	UPI000004A27F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGATTGGGA	.	5	ESCA
STK10	0	.	GRCh37	5	171614953	171614953	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94C>A	p.Pro32Thr	p.P32T	ENST00000176763	1/19	47	32	14	81	81	0	STK10,missense_variant,p.Pro32Thr,ENST00000176763,;	T	ENSG00000072786	ENST00000176763	Transcript	missense_variant	438	94	32	P/T	Ccc/Acc	.	.	.	-1	STK10	HGNC	11388	protein_coding	YES	CCDS34290.1	ENSP00000176763	STK10_HUMAN	.	UPI0000136104	.	deleterious(0)	probably_damaging(0.996)	1/19	.	hmmpanther:PTHR24361:SF195,hmmpanther:PTHR24361,Gene3D:3.30.200.20,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGGGGTCCA	.	5	ESCA
DDX41	0	.	GRCh37	5	176940721	176940721	+	Missense_Mutation	SNP	C	C	T	rs778864620	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1063G>A	p.Glu355Lys	p.E355K	ENST00000507955	10/17	34	29	4	41	41	0	DDX41,missense_variant,p.Glu373Lys,ENST00000330503,;DDX41,missense_variant,p.Glu355Lys,ENST00000507955,;DOK3,upstream_gene_variant,,ENST00000312943,;DOK3,upstream_gene_variant,,ENST00000502885,;DOK3,upstream_gene_variant,,ENST00000510898,;DOK3,upstream_gene_variant,,ENST00000510380,;DOK3,upstream_gene_variant,,ENST00000510389,;DOK3,upstream_gene_variant,,ENST00000377112,;DOK3,upstream_gene_variant,,ENST00000509310,;DOK3,upstream_gene_variant,,ENST00000506493,;DOK3,upstream_gene_variant,,ENST00000501403,;DOK3,upstream_gene_variant,,ENST00000357198,;DDX41,downstream_gene_variant,,ENST00000506965,;DDX41,3_prime_UTR_variant,,ENST00000508279,;DDX41,non_coding_transcript_exon_variant,,ENST00000507900,;DDX41,non_coding_transcript_exon_variant,,ENST00000512027,;DDX41,non_coding_transcript_exon_variant,,ENST00000505081,;DDX41,non_coding_transcript_exon_variant,,ENST00000511040,;DDX41,non_coding_transcript_exon_variant,,ENST00000504807,;DDX41,non_coding_transcript_exon_variant,,ENST00000503078,;DDX41,non_coding_transcript_exon_variant,,ENST00000513562,;DOK3,upstream_gene_variant,,ENST00000500323,;DDX41,upstream_gene_variant,,ENST00000512334,;DDX41,downstream_gene_variant,,ENST00000509576,;DOK3,upstream_gene_variant,,ENST00000512660,;DDX41,downstream_gene_variant,,ENST00000512431,;DDX41,downstream_gene_variant,,ENST00000510171,;DOK3,upstream_gene_variant,,ENST00000502380,;DDX41,downstream_gene_variant,,ENST00000504781,;DDX41,downstream_gene_variant,,ENST00000515562,;	T	ENSG00000183258	ENST00000507955	Transcript	missense_variant	1587	1063	355	E/K	Gag/Aag	rs778864620,COSM1436357	.	.	-1	DDX41	HGNC	18674	protein_coding	YES	CCDS4427.1	ENSP00000422753	DDX41_HUMAN	B3KRK2_HUMAN	UPI0000125164	.	deleterious(0)	probably_damaging(0.996)	10/17	.	Superfamily_domains:SSF52540,Superfamily_domains:SSF52540,SMART_domains:SM00487,Gene3D:3.40.50.300,Pfam_domain:PF00270,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF20,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCCTCGAAGC	.	4	ESCA
PRDM9	0	.	GRCh37	5	23527403	23527403	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2206C>A	p.Leu736Ile	p.L736I	ENST00000296682	11/11	74	61	12	85	85	0	PRDM9,missense_variant,p.Leu736Ile,ENST00000296682,;	A	ENSG00000164256	ENST00000296682	Transcript	missense_variant	2388	2206	736	L/I	Ctc/Atc	.	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	tolerated(1)	probably_damaging(0.954)	11/11	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTCCTCAGA	.	4	ESCA
HCN1	0	.	GRCh37	5	45261002	45261002	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1021G>T	.	.	ENST00000303230	8/8	61	49	12	60	60	0	HCN1,3_prime_UTR_variant,,ENST00000303230,;	A	ENSG00000164588	ENST00000303230	Transcript	3_prime_UTR_variant	3752	.	.	.	.	.	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCCCCAG	.	5	ESCA
MAST4	0	.	GRCh37	5	66448651	66448651	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3482A>G	p.Tyr1161Cys	p.Y1161C	ENST00000403625	25/29	42	34	8	57	56	1	MAST4,missense_variant,p.Tyr972Cys,ENST00000403666,;MAST4,missense_variant,p.Tyr1164Cys,ENST00000404260,;MAST4,missense_variant,p.Tyr218Cys,ENST00000443808,;MAST4,missense_variant,p.Tyr967Cys,ENST00000261569,;MAST4,missense_variant,p.Tyr982Cys,ENST00000405643,;MAST4,missense_variant,p.Tyr1161Cys,ENST00000403625,;	G	ENSG00000069020	ENST00000403625	Transcript	missense_variant	3777	3482	1161	Y/C	tAt/tGt	.	.	.	1	MAST4	HGNC	19037	protein_coding	YES	CCDS54861.1	ENSP00000385727	.	J3QT34_HUMAN	UPI000173A2B0	.	.	probably_damaging(1)	25/29	.	Superfamily_domains:SSF50156,SMART_domains:SM00228,Gene3D:2.30.42.10,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF139,PROSITE_profiles:PS50106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GGTGTATGTGG	.	4	ESCA
TSPYL1	0	.	GRCh37	6	116600515	116600515	+	Missense_Mutation	SNP	C	C	A	rs745917630	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479G>T	p.Cys160Phe	p.C160F	ENST00000368608	1/1	87	64	23	149	149	0	TSPYL1,missense_variant,p.Cys160Phe,ENST00000368608,;DSE,intron_variant,,ENST00000540275,;DSE,intron_variant,,ENST00000430252,;DSE,upstream_gene_variant,,ENST00000452085,;RP1-93H18.1,upstream_gene_variant,,ENST00000453463,;RP1-93H18.1,upstream_gene_variant,,ENST00000449314,;DSE,non_coding_transcript_exon_variant,,ENST00000607094,;	A	ENSG00000189241	ENST00000368608	Transcript	missense_variant	552	479	160	C/F	tGc/tTc	rs745917630	.	.	-1	TSPYL1	HGNC	12382	protein_coding	YES	CCDS34518.1	ENSP00000357597	TSYL1_HUMAN	.	UPI000006EE16	.	tolerated(0.42)	benign(0.004)	1/1	.	hmmpanther:PTHR11875:SF57,hmmpanther:PTHR11875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCGCACTTT	.	5	ESCA
LAMA2	0	.	GRCh37	6	129475680	129475680	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058G>A	p.Cys353Tyr	p.C353Y	ENST00000421865	8/65	27	20	7	44	44	0	LAMA2,missense_variant,p.Cys353Tyr,ENST00000421865,;BMPR1APS1,downstream_gene_variant,,ENST00000403332,;	A	ENSG00000196569	ENST00000421865	Transcript	missense_variant	1107	1058	353	C/Y	tGc/tAc	.	.	.	1	LAMA2	HGNC	6482	protein_coding	YES	CCDS5138.1	ENSP00000400365	LAMA2_HUMAN	Q59H37_HUMAN	UPI00003673E0	.	deleterious(0)	probably_damaging(1)	8/65	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF106,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAATGCTATT	.	2	ESCA
VNN2	0	.	GRCh37	6	133072386	133072386	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1098C>T	p.%3D	p.C366C	ENST00000326499	5/7	27	18	9	36	36	0	VNN2,synonymous_variant,p.%3D,ENST00000525270,;VNN2,synonymous_variant,p.%3D,ENST00000326499,;VNN2,intron_variant,,ENST00000525289,;VNN2,downstream_gene_variant,,ENST00000524919,;VNN2,downstream_gene_variant,,ENST00000530536,;RP1-55C23.7,upstream_gene_variant,,ENST00000430895,;VNN2,downstream_gene_variant,,ENST00000526192,;VNN2,downstream_gene_variant,,ENST00000526157,;VNN2,missense_variant,p.Ala190Val,ENST00000532053,;VNN2,3_prime_UTR_variant,,ENST00000525674,;VNN2,3_prime_UTR_variant,,ENST00000418593,;VNN2,3_prime_UTR_variant,,ENST00000422400,;VNN2,3_prime_UTR_variant,,ENST00000533835,;VNN2,3_prime_UTR_variant,,ENST00000392389,;VNN2,intron_variant,,ENST00000528801,;VNN2,downstream_gene_variant,,ENST00000531279,;	A	ENSG00000112303	ENST00000326499	Transcript	synonymous_variant	1223	1098	366	C	tgC/tgT	.	.	.	-1	VNN2	HGNC	12706	protein_coding	YES	CCDS5161.1	ENSP00000322276	VNN2_HUMAN	E9PRD9_HUMAN,E9PL76_HUMAN,E9PK31_HUMAN	UPI000014194E	.	.	.	5/7	.	hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF5,PIRSF_domain:PIRSF011861	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACAGCAAAG	.	5	ESCA
HIST1H4L	0	.	GRCh37	6	27841109	27841109	+	Missense_Mutation	SNP	T	T	A	rs771307672	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180A>T	p.Lys60Asn	p.K60N	ENST00000355981	1/1	69	52	17	101	101	0	HIST1H4L,missense_variant,p.Lys60Asn,ENST00000355981,;HIST1H3I,upstream_gene_variant,,ENST00000328488,;	A	ENSG00000198558	ENST00000355981	Transcript	missense_variant	181	180	60	K/N	aaA/aaT	rs771307672	.	.	-1	HIST1H4L	HGNC	4791	protein_coding	YES	CCDS4637.1	ENSP00000348258	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	deleterious(0)	probably_damaging(0.974)	1/1	.	hmmpanther:PTHR10484,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00803,SMART_domains:SM00417,Superfamily_domains:SSF47113,Prints_domain:PR00623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACACTTTAAG	byFrequency	5	ESCA
HIST1H4L	0	.	GRCh37	6	27841110	27841110	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179A>G	p.Lys60Arg	p.K60R	ENST00000355981	1/1	69	52	16	98	98	0	HIST1H4L,missense_variant,p.Lys60Arg,ENST00000355981,;HIST1H3I,upstream_gene_variant,,ENST00000328488,;	C	ENSG00000198558	ENST00000355981	Transcript	missense_variant	180	179	60	K/R	aAa/aGa	.	.	.	-1	HIST1H4L	HGNC	4791	protein_coding	YES	CCDS4637.1	ENSP00000348258	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	tolerated(0.16)	benign(0.146)	1/1	.	hmmpanther:PTHR10484,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00803,SMART_domains:SM00417,Superfamily_domains:SSF47113,Prints_domain:PR00623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTTTAAGA	.	5	ESCA
SRF	0	.	GRCh37	6	43146938	43146938	+	3'UTR	SNP	C	C	T	rs370939499	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10C>T	.	.	ENST00000265354	7/7	86	52	33	74	74	0	SRF,3_prime_UTR_variant,,ENST00000457278,;SRF,3_prime_UTR_variant,,ENST00000265354,;CUL9,upstream_gene_variant,,ENST00000354495,;CUL9,upstream_gene_variant,,ENST00000372647,;CUL9,upstream_gene_variant,,ENST00000252050,;CUL9,upstream_gene_variant,,ENST00000451399,;CUL9,upstream_gene_variant,,ENST00000515773,;	T	ENSG00000112658	ENST00000265354	Transcript	3_prime_UTR_variant	1895	.	.	.	.	rs370939499	.	.	1	SRF	HGNC	11291	protein_coding	YES	CCDS4889.1	ENSP00000265354	SRF_HUMAN	F5H6V4_HUMAN	UPI0000135F3B	.	.	.	7/7	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGCCGCCCT	byFrequency|byCluster	5	ESCA
LGSN	0	.	GRCh37	6	63989979	63989979	+	Missense_Mutation	SNP	C	C	G	rs745357482	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1477G>C	p.Glu493Gln	p.E493Q	ENST00000370657	4/4	19	15	4	33	33	0	LGSN,missense_variant,p.Glu493Gln,ENST00000370657,;LGSN,3_prime_UTR_variant,,ENST00000370658,;LGSN,intron_variant,,ENST00000485906,;	G	ENSG00000146166	ENST00000370657	Transcript	missense_variant	1511	1477	493	E/Q	Gag/Cag	rs745357482	.	.	-1	LGSN	HGNC	21016	protein_coding	YES	CCDS4964.1	ENSP00000359691	LGSN_HUMAN	.	UPI000013DA35	.	deleterious(0.01)	possibly_damaging(0.517)	4/4	.	Superfamily_domains:SSF55931,Gene3D:3.30.590.10,hmmpanther:PTHR20852,hmmpanther:PTHR20852:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTCCAACT	byFrequency	5	ESCA
MDN1	0	.	GRCh37	6	90459388	90459388	+	Silent	SNP	C	C	T	rs764850569	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3489G>A	p.%3D	p.A1163A	ENST00000369393	25/102	17	10	7	36	36	0	MDN1,synonymous_variant,p.%3D,ENST00000369393,;MDN1,synonymous_variant,p.%3D,ENST00000428876,;MDN1,synonymous_variant,p.%3D,ENST00000439638,;	T	ENSG00000112159	ENST00000369393	Transcript	synonymous_variant	3605	3489	1163	A	gcG/gcA	rs764850569,COSM3178426	.	.	-1	MDN1	HGNC	18302	protein_coding	YES	CCDS5024.1	ENSP00000358400	MDN1_HUMAN	M0QXR3_HUMAN	UPI000013C4B8	.	.	.	25/102	.	hmmpanther:PTHR22908:SF58,hmmpanther:PTHR22908,Pfam_domain:PF07728,Gene3D:3.40.50.300,PIRSF_domain:PIRSF010340,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGCGCCTC	byFrequency	5	ESCA
RELN	0	.	GRCh37	7	103143467	103143467	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8485G>T	p.Gly2829Ter	p.G2829*	ENST00000428762	52/65	120	92	27	127	127	0	RELN,stop_gained,p.Gly2829Ter,ENST00000424685,;RELN,stop_gained,p.Gly2829Ter,ENST00000428762,;RELN,stop_gained,p.Gly2829Ter,ENST00000343529,;CTB-107G13.1,intron_variant,,ENST00000422488,;	A	ENSG00000189056	ENST00000428762	Transcript	stop_gained	8645	8485	2829	G/*	Gga/Tga	.	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	.	.	52/65	.	hmmpanther:PTHR11841	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCCCACTA	.	5	ESCA
KMT2E	0	.	GRCh37	7	104703927	104703927	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.316A>G	p.Ile106Val	p.I106V	ENST00000311117	5/27	58	47	11	36	36	0	KMT2E,missense_variant,p.Ile106Val,ENST00000495267,;KMT2E,missense_variant,p.Ile106Val,ENST00000257745,;KMT2E,missense_variant,p.Ile106Val,ENST00000476671,;KMT2E,missense_variant,p.Ile106Val,ENST00000311117,;KMT2E,missense_variant,p.Ile106Val,ENST00000334877,;KMT2E,5_prime_UTR_variant,,ENST00000334914,;KMT2E,intron_variant,,ENST00000478990,;KMT2E,downstream_gene_variant,,ENST00000474203,;KMT2E,missense_variant,p.Ile106Val,ENST00000482560,;KMT2E,missense_variant,p.Ile106Val,ENST00000334884,;KMT2E,non_coding_transcript_exon_variant,,ENST00000468607,;KMT2E,downstream_gene_variant,,ENST00000485619,;	G	ENSG00000005483	ENST00000311117	Transcript	missense_variant	861	316	106	I/V	Atc/Gtc	.	.	.	1	KMT2E	HGNC	18541	protein_coding	YES	CCDS34723.1	ENSP00000312379	KMT2E_HUMAN	O95038_HUMAN,C9JQ68_HUMAN,C9JNE1_HUMAN	UPI0000074133	.	tolerated(0.05)	benign(0.031)	5/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16286,hmmpanther:PTHR16286:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACAATCAGC	.	5	ESCA
EFCAB10	0	.	GRCh37	7	105206037	105206037	+	Missense_Mutation	SNP	C	C	T	rs777291719	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.409G>A	p.Glu137Lys	p.E137K	ENST00000485614	5/5	31	25	6	25	25	0	EFCAB10,missense_variant,p.Glu137Lys,ENST00000485614,;RINT1,missense_variant,p.Arg710Trp,ENST00000257700,;EFCAB10,intron_variant,,ENST00000480514,;EFCAB10,downstream_gene_variant,,ENST00000486180,;EFCAB10,downstream_gene_variant,,ENST00000460135,;EFCAB10,intron_variant,,ENST00000469099,;EFCAB10,downstream_gene_variant,,ENST00000490493,;RINT1,3_prime_UTR_variant,,ENST00000497979,;	T	ENSG00000185055	ENST00000485614	Transcript	missense_variant	442	409	137	E/K	Gag/Aag	rs777291719	.	.	-1	EFCAB10	HGNC	34531	protein_coding	YES	.	ENSP00000417841	.	J3KR52_HUMAN	UPI000020F8A0	.	tolerated_low_confidence(0.13)	possibly_damaging(0.807)	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACTCGGAAT	.	5	ESCA
COG5	0	.	GRCh37	7	106897227	106897227	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000297135	16/22	42	36	6	49	49	0	COG5,stop_gained,p.Gln598Ter,ENST00000393603,;COG5,stop_gained,p.Gln598Ter,ENST00000297135,;COG5,intron_variant,,ENST00000347053,;COG5,non_coding_transcript_exon_variant,,ENST00000468350,;COG5,non_coding_transcript_exon_variant,,ENST00000462342,;COG5,upstream_gene_variant,,ENST00000464542,;	A	ENSG00000164597	ENST00000297135	Transcript	stop_gained	2317	1792	598	Q/*	Cag/Tag	.	.	.	-1	COG5	HGNC	14857	protein_coding	YES	CCDS5742.1	ENSP00000297135	COG5_HUMAN	U3KQU7_HUMAN,B3KMW0_HUMAN	UPI0000246D05	.	.	.	16/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13228:SF3,hmmpanther:PTHR13228	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTCTGACTGG	.	3	ESCA
CAV1	0	.	GRCh37	7	116201111	116201111	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1770A>G	.	.	ENST00000341049	3/3	53	43	10	37	37	0	CAV1,3_prime_UTR_variant,,ENST00000341049,;CAV1,3_prime_UTR_variant,,ENST00000393467,;CAV1,3_prime_UTR_variant,,ENST00000405348,;CAV1,downstream_gene_variant,,ENST00000393470,;CAV1,downstream_gene_variant,,ENST00000456473,;CAV1,downstream_gene_variant,,ENST00000393468,;AC006159.4,downstream_gene_variant,,ENST00000421965,;CAV1,downstream_gene_variant,,ENST00000451122,;	G	ENSG00000105974	ENST00000341049	Transcript	3_prime_UTR_variant	2585	.	.	.	.	.	.	.	1	CAV1	HGNC	1527	protein_coding	YES	CCDS5767.1	ENSP00000339191	CAV1_HUMAN	Q2TNI1_HUMAN,C9JKI3_HUMAN	UPI00001270ED	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAAATCAAT	.	5	ESCA
TAS2R16	0	.	GRCh37	7	122635287	122635287	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402G>C	p.%3D	p.L134L	ENST00000249284	1/1	24	20	3	21	21	0	TAS2R16,synonymous_variant,p.%3D,ENST00000249284,;	G	ENSG00000128519	ENST00000249284	Transcript	synonymous_variant	468	402	134	L	ctG/ctC	.	.	.	-1	TAS2R16	HGNC	14921	protein_coding	YES	CCDS5785.1	ENSP00000249284	T2R16_HUMAN	Q50KN6_HUMAN	UPI0000038B18	.	.	.	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11394,Pfam_domain:PF05296,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCATCAGAGA	.	4	ESCA
IQUB	0	.	GRCh37	7	123097574	123097574	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2054C>G	p.Ser685Ter	p.S685*	ENST00000466202	12/13	66	61	5	44	44	0	IQUB,stop_gained,p.Ser685Ter,ENST00000324698,;IQUB,stop_gained,p.Ser685Ter,ENST00000466202,;RNU6-296P,downstream_gene_variant,,ENST00000384608,;RP11-332K15.1,non_coding_transcript_exon_variant,,ENST00000419832,;IQUB,3_prime_UTR_variant,,ENST00000484508,;IQUB,3_prime_UTR_variant,,ENST00000469057,;	C	ENSG00000164675	ENST00000466202	Transcript	stop_gained	2631	2054	685	S/*	tCa/tGa	.	.	.	-1	IQUB	HGNC	21995	protein_coding	YES	CCDS5787.1	ENSP00000417769	IQUB_HUMAN	.	UPI000013E3DF	.	.	.	12/13	.	hmmpanther:PTHR21074:SF0,hmmpanther:PTHR21074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGACTGACTGG	.	3	ESCA
GPR37	0	.	GRCh37	7	124386281	124386282	+	3'UTR	INS	-	-	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*297dupT	.	.	ENST00000303921	2/2	51	43	8	32	32	0	GPR37,3_prime_UTR_variant,,ENST00000303921,;	A	ENSG00000170775	ENST00000303921	Transcript	3_prime_UTR_variant	2790-2791	.	.	.	.	.	.	.	-1	GPR37	HGNC	4494	protein_coding	YES	CCDS5792.1	ENSP00000306449	GPR37_HUMAN	.	UPI0000001C92	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGAAGAAAAA	.	3	ESCA
TSPAN33	0	.	GRCh37	7	128802357	128802357	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283C>A	p.Gln95Lys	p.Q95K	ENST00000289407	3/8	49	37	12	60	60	0	TSPAN33,missense_variant,p.Gln95Lys,ENST00000289407,;Y_RNA,upstream_gene_variant,,ENST00000363759,;TSPAN33,non_coding_transcript_exon_variant,,ENST00000496963,;TSPAN33,upstream_gene_variant,,ENST00000486685,;	A	ENSG00000158457	ENST00000289407	Transcript	missense_variant	392	283	95	Q/K	Cag/Aag	.	.	.	1	TSPAN33	HGNC	28743	protein_coding	YES	CCDS5810.1	ENSP00000289407	TSN33_HUMAN	.	UPI000000DA83	.	tolerated(0.92)	benign(0.02)	3/8	.	Prints_domain:PR00259,PIRSF_domain:PIRSF002419,Pfam_domain:PF00335,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF154	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGCAGACG	.	5	ESCA
MGAM	0	.	GRCh37	7	141740561	141740561	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2413G>C	p.Glu805Gln	p.E805Q	ENST00000549489	21/48	60	48	11	54	54	0	MGAM,missense_variant,p.Glu805Gln,ENST00000475668,;MGAM,missense_variant,p.Glu805Gln,ENST00000549489,;MGAM,downstream_gene_variant,,ENST00000490593,;	C	ENSG00000257335	ENST00000549489	Transcript	missense_variant	2508	2413	805	E/Q	Gaa/Caa	COSM3634546,COSM3634545,COSM3634544	.	.	1	MGAM	HGNC	7043	protein_coding	YES	CCDS47727.1	ENSP00000447378	MGA_HUMAN	Q8TE25_HUMAN,E9PEQ5_HUMAN,E7EW87_HUMAN	UPI000183CB7B	.	tolerated(0.35)	benign(0.002)	21/48	.	Superfamily_domains:SSF51011,Pfam_domain:PF01055,hmmpanther:PTHR22762:SF63,hmmpanther:PTHR22762	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGGAACTT	.	5	ESCA
NME8	0	.	GRCh37	7	37934120	37934120	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1452G>T	p.Lys484Asn	p.K484N	ENST00000199447	16/18	68	57	10	43	43	0	NME8,missense_variant,p.Lys484Asn,ENST00000440017,;NME8,missense_variant,p.Lys484Asn,ENST00000199447,;EPDR1,intron_variant,,ENST00000476620,;NME8,upstream_gene_variant,,ENST00000476435,;	T	ENSG00000086288	ENST00000199447	Transcript	missense_variant	1824	1452	484	K/N	aaG/aaT	.	.	.	1	NME8	HGNC	16473	protein_coding	YES	CCDS5452.1	ENSP00000199447	TXND3_HUMAN	.	UPI00000700CB	.	deleterious(0.01)	probably_damaging(0.99)	16/18	.	hmmpanther:PTHR11349:SF45,hmmpanther:PTHR11349,Gene3D:3.30.70.141,Pfam_domain:PF00334,SMART_domains:SM00562,Superfamily_domains:SSF54919	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAGAAAAT	.	5	ESCA
ZNF679	0	.	GRCh37	7	63726929	63726929	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.918C>T	p.%3D	p.S306S	ENST00000421025	5/5	65	61	4	71	71	0	ZNF679,synonymous_variant,p.%3D,ENST00000255746,;ZNF679,synonymous_variant,p.%3D,ENST00000421025,;	T	ENSG00000197123	ENST00000421025	Transcript	synonymous_variant	1187	918	306	S	agC/agT	.	.	.	1	ZNF679	HGNC	28650	protein_coding	YES	CCDS47592.1	ENSP00000416809	ZN679_HUMAN	.	UPI000045756A	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF91,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTAGCTTATC	.	2	ESCA
ZNF117	0	.	GRCh37	7	64438393	64438393	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*104A>G	.	.	ENST00000282869	4/4	32	26	6	23	23	0	ZNF117,3_prime_UTR_variant,,ENST00000282869,;ZNF117,downstream_gene_variant,,ENST00000487644,;	C	ENSG00000152926	ENST00000282869	Transcript	3_prime_UTR_variant	2841	.	.	.	.	.	.	.	-1	ZNF117	HGNC	12897	protein_coding	YES	CCDS43593.1	ENSP00000282869	ZN117_HUMAN	.	UPI000049E07A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTTATGTTTA	.	4	ESCA
NPTX2	0	.	GRCh37	7	98256586	98256586	+	Missense_Mutation	SNP	G	G	A	rs753490696	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.998G>A	p.Gly333Asp	p.G333D	ENST00000265634	4/5	56	43	13	44	44	0	NPTX2,missense_variant,p.Gly333Asp,ENST00000265634,;NPTX2,downstream_gene_variant,,ENST00000466102,;	A	ENSG00000106236	ENST00000265634	Transcript	missense_variant	1163	998	333	G/D	gGc/gAc	rs753490696,COSM1453128	.	.	1	NPTX2	HGNC	7953	protein_coding	YES	CCDS5657.1	ENSP00000265634	NPTX2_HUMAN	.	UPI000013040F	.	deleterious(0)	probably_damaging(0.999)	4/5	.	hmmpanther:PTHR19277:SF1,hmmpanther:PTHR19277,Gene3D:2.60.120.200,Pfam_domain:PF00354,SMART_domains:SM00159,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCTGGGCACTG	byFrequency	4	ESCA
ZNF655	0	.	GRCh37	7	99170870	99170870	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1244A>G	p.Tyr415Cys	p.Y415C	ENST00000424881	4/4	27	18	9	30	30	0	ZNF655,missense_variant,p.Tyr415Cys,ENST00000493277,;ZNF655,missense_variant,p.Tyr415Cys,ENST00000424881,;ZNF655,missense_variant,p.Tyr380Cys,ENST00000252713,;ZNF655,missense_variant,p.Tyr380Cys,ENST00000394163,;ZNF655,3_prime_UTR_variant,,ENST00000425063,;ZNF655,downstream_gene_variant,,ENST00000422647,;ZNF655,downstream_gene_variant,,ENST00000449244,;ZNF655,downstream_gene_variant,,ENST00000422164,;ZNF655,downstream_gene_variant,,ENST00000427931,;ZNF655,downstream_gene_variant,,ENST00000454654,;ZNF655,non_coding_transcript_exon_variant,,ENST00000419215,;GS1-259H13.10,intron_variant,,ENST00000486324,;ZNF655,non_coding_transcript_exon_variant,,ENST00000494357,;GS1-259H13.10,intron_variant,,ENST00000455905,;ZNF655,downstream_gene_variant,,ENST00000412636,;ZNF655,downstream_gene_variant,,ENST00000493947,;	G	ENSG00000197343	ENST00000424881	Transcript	missense_variant	1464	1244	415	Y/C	tAt/tGt	COSM126472	.	.	1	ZNF655	HGNC	30899	protein_coding	YES	CCDS47655.1	ENSP00000393876	ZN655_HUMAN	Q68DU4_HUMAN,F8WEB1_HUMAN,C9JUB9_HUMAN,C9JS03_HUMAN,C9IYG2_HUMAN	UPI000020F66D	.	deleterious(0.02)	possibly_damaging(0.878)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF284,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTATACGT	.	5	ESCA
EIF3E	0	.	GRCh37	8	109229586	109229586	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.826G>A	p.Asp276Asn	p.D276N	ENST00000220849	8/13	83	46	36	51	51	0	EIF3E,missense_variant,p.Asp183Asn,ENST00000519030,;EIF3E,missense_variant,p.Asp276Asn,ENST00000220849,;EIF3E,missense_variant,p.Asp149Asn,ENST00000519627,;EIF3E,intron_variant,,ENST00000522352,;EIF3E,non_coding_transcript_exon_variant,,ENST00000519517,;EIF3E,non_coding_transcript_exon_variant,,ENST00000519413,;EIF3E,non_coding_transcript_exon_variant,,ENST00000521614,;EIF3E,downstream_gene_variant,,ENST00000522445,;	T	ENSG00000104408	ENST00000220849	Transcript	missense_variant	889	826	276	D/N	Gat/Aat	.	.	.	-1	EIF3E	HGNC	3277	protein_coding	YES	CCDS6308.1	ENSP00000220849	EIF3E_HUMAN	E5RIT4_HUMAN,E5RGA2_HUMAN,B3KW56_HUMAN	UPI0000000C92	.	deleterious(0.03)	benign(0.037)	8/13	.	Coiled-coils_(Ncoils):Coil,HAMAP:MF_03004,hmmpanther:PTHR10317,PIRSF_domain:PIRSF016255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATCTTTTA	.	5	ESCA
KCNQ3	0	.	GRCh37	8	133492507	133492507	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.273C>G	p.%3D	p.T91T	ENST00000388996	1/15	120	93	26	86	86	0	KCNQ3,synonymous_variant,p.%3D,ENST00000388996,;KCNQ3,synonymous_variant,p.%3D,ENST00000519445,;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,;	C	ENSG00000184156	ENST00000388996	Transcript	synonymous_variant	694	273	91	T	acC/acG	.	.	.	-1	KCNQ3	HGNC	6297	protein_coding	YES	CCDS34943.1	ENSP00000373648	KCNQ3_HUMAN	.	UPI00001279F0	.	.	.	1/15	.	hmmpanther:PTHR11537:SF5,hmmpanther:PTHR11537,Prints_domain:PR01462	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGGGGTCTT	.	5	ESCA
PARP10	0	.	GRCh37	8	145059977	145059977	+	Silent	SNP	C	C	G	rs201830961	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348G>C	p.%3D	p.S116S	ENST00000313028	3/11	34	28	5	27	27	0	PARP10,synonymous_variant,p.%3D,ENST00000528914,;PARP10,synonymous_variant,p.%3D,ENST00000525879,;PARP10,synonymous_variant,p.%3D,ENST00000529842,;PARP10,synonymous_variant,p.%3D,ENST00000313028,;PARP10,synonymous_variant,p.%3D,ENST00000524918,;PARP10,synonymous_variant,p.%3D,ENST00000528625,;PARP10,synonymous_variant,p.%3D,ENST00000531537,;PARP10,synonymous_variant,p.%3D,ENST00000528136,;PARP10,synonymous_variant,p.%3D,ENST00000525773,;PARP10,synonymous_variant,p.%3D,ENST00000525486,;PARP10,intron_variant,,ENST00000313059,;PARP10,downstream_gene_variant,,ENST00000529311,;GRINA,upstream_gene_variant,,ENST00000313269,;PARP10,downstream_gene_variant,,ENST00000532311,;GRINA,upstream_gene_variant,,ENST00000530898,;PARP10,downstream_gene_variant,,ENST00000531707,;PARP10,downstream_gene_variant,,ENST00000530478,;GRINA,upstream_gene_variant,,ENST00000395068,;GRINA,upstream_gene_variant,,ENST00000529301,;PARP10,non_coding_transcript_exon_variant,,ENST00000533665,;PARP10,downstream_gene_variant,,ENST00000534737,;PARP10,downstream_gene_variant,,ENST00000532660,;PARP10,synonymous_variant,p.%3D,ENST00000527262,;PARP10,non_coding_transcript_exon_variant,,ENST00000526985,;PARP10,upstream_gene_variant,,ENST00000526007,;PARP10,downstream_gene_variant,,ENST00000528580,;PARP10,upstream_gene_variant,,ENST00000528963,;	G	ENSG00000178685	ENST00000313028	Transcript	synonymous_variant	443	348	116	S	tcG/tcC	rs201830961	.	.	-1	PARP10	HGNC	25895	protein_coding	YES	CCDS34960.1	ENSP00000325618	PAR10_HUMAN	E9PSG8_HUMAN,E9PSE7_HUMAN,E9PQQ6_HUMAN,E9PPV8_HUMAN,E9PPU2_HUMAN,E9PM86_HUMAN,E9PLE8_HUMAN,E9PJI2_HUMAN,E9PIA6_HUMAN	UPI0000251FAB	.	.	.	3/11	.	.	T:0.0008	T:0	T:0.0029	.	T:0.002	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCCGAGGC	byFrequency|byCluster|by1000G	5	ESCA
WRN	0	.	GRCh37	8	30982124	30982124	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2717G>C	p.Ser906Thr	p.S906T	ENST00000298139	22/35	40	32	7	51	51	0	WRN,missense_variant,p.Ser906Thr,ENST00000298139,;WRN,non_coding_transcript_exon_variant,,ENST00000521620,;WRN,non_coding_transcript_exon_variant,,ENST00000520169,;	C	ENSG00000165392	ENST00000298139	Transcript	missense_variant	2966	2717	906	S/T	aGc/aCc	.	.	.	1	WRN	HGNC	12791	protein_coding	YES	CCDS6082.1	ENSP00000298139	WRN_HUMAN	.	UPI000013E49D	.	tolerated(0.27)	benign(0.022)	22/35	.	Gene3D:1.10.10.10,TIGRFAM_domain:TIGR00614,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF80	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTAGCAGAT	.	5	ESCA
RP1	0	.	GRCh37	8	55540391	55540391	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3949C>G	p.Gln1317Glu	p.Q1317E	ENST00000220676	4/4	114	89	25	125	125	0	RP1,missense_variant,p.Gln1317Glu,ENST00000220676,;	G	ENSG00000104237	ENST00000220676	Transcript	missense_variant	4097	3949	1317	Q/E	Caa/Gaa	.	.	.	1	RP1	HGNC	10263	protein_coding	YES	CCDS6160.1	ENSP00000220676	RP1_HUMAN	A0FDN2_HUMAN	UPI000013455B	.	tolerated(0.36)	benign(0.004)	4/4	.	hmmpanther:PTHR23005:SF4,hmmpanther:PTHR23005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCTCAAAAG	.	5	ESCA
TMEM68	0	.	GRCh37	8	56651457	56651457	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1234A>T	.	.	ENST00000334667	6/6	45	28	17	36	36	0	TMEM68,3_prime_UTR_variant,,ENST00000334667,;TMEM68,3_prime_UTR_variant,,ENST00000434581,;TMEM68,downstream_gene_variant,,ENST00000519780,;TMEM68,downstream_gene_variant,,ENST00000519784,;TMEM68,downstream_gene_variant,,ENST00000523073,;TMEM68,non_coding_transcript_exon_variant,,ENST00000519460,;TMEM68,intron_variant,,ENST00000522470,;TMEM68,downstream_gene_variant,,ENST00000517576,;	A	ENSG00000167904	ENST00000334667	Transcript	3_prime_UTR_variant	2261	.	.	.	.	.	.	.	-1	TMEM68	HGNC	26510	protein_coding	YES	CCDS6161.1	ENSP00000335416	TMM68_HUMAN	E5RJ96_HUMAN,E5RHI6_HUMAN,E5RGT2_HUMAN	UPI00000732CD	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCTGTTTA	.	5	ESCA
BHLHE22	0	.	GRCh37	8	65494794	65494794	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*301G>C	.	.	ENST00000321870	1/1	61	52	9	56	56	0	BHLHE22,3_prime_UTR_variant,,ENST00000321870,;RP11-21C4.1,upstream_gene_variant,,ENST00000517909,;RP11-21C4.1,upstream_gene_variant,,ENST00000520834,;	C	ENSG00000180828	ENST00000321870	Transcript	3_prime_UTR_variant	1981	.	.	.	.	.	.	.	1	BHLHE22	HGNC	11963	protein_coding	YES	CCDS6179.1	ENSP00000318799	BHE22_HUMAN	.	UPI0000070A3C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGTGGAATC	.	5	ESCA
COPS5	0	.	GRCh37	8	67971544	67971544	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280G>A	p.Asp94Asn	p.D94N	ENST00000357849	2/8	46	36	9	40	40	0	COPS5,missense_variant,p.Asp30Asn,ENST00000517736,;COPS5,missense_variant,p.Asp94Asn,ENST00000357849,;COPS5,missense_variant,p.Asp30Asn,ENST00000518747,;CSPP1,upstream_gene_variant,,ENST00000521919,;AC109335.1,downstream_gene_variant,,ENST00000578628,;COPS5,non_coding_transcript_exon_variant,,ENST00000517793,;COPS5,upstream_gene_variant,,ENST00000523086,;COPS5,downstream_gene_variant,,ENST00000519963,;COPS5,downstream_gene_variant,,ENST00000518768,;PPP1R42,upstream_gene_variant,,ENST00000517834,;COPS5,downstream_gene_variant,,ENST00000519057,;COPS5,3_prime_UTR_variant,,ENST00000523890,;COPS5,3_prime_UTR_variant,,ENST00000518374,;COPS5,non_coding_transcript_exon_variant,,ENST00000521509,;COPS5,non_coding_transcript_exon_variant,,ENST00000521386,;COPS5,downstream_gene_variant,,ENST00000517406,;	T	ENSG00000121022	ENST00000357849	Transcript	missense_variant	601	280	94	D/N	Gac/Aac	.	.	.	-1	COPS5	HGNC	2240	protein_coding	YES	CCDS6198.1	ENSP00000350512	CSN5_HUMAN	E5RHF2_HUMAN	UPI000006D7AB	.	deleterious(0)	probably_damaging(0.996)	2/8	.	Superfamily_domains:0048572,SMART_domains:SM00232,Gene3D:3.40.140.10,Pfam_domain:PF01398,hmmpanther:PTHR10410,hmmpanther:PTHR10410:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTCCATAA	.	5	ESCA
KIAA1429	0	.	GRCh37	8	95547194	95547194	+	Silent	SNP	A	A	G	rs771028941	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.357T>C	p.%3D	p.C119C	ENST00000297591	5/24	64	45	18	62	62	0	KIAA1429,synonymous_variant,p.%3D,ENST00000297591,;KIAA1429,synonymous_variant,p.%3D,ENST00000421249,;KIAA1429,synonymous_variant,p.%3D,ENST00000437199,;RP11-267M23.3,downstream_gene_variant,,ENST00000521010,;KIAA1429,intron_variant,,ENST00000519001,;	G	ENSG00000164944	ENST00000297591	Transcript	synonymous_variant	433	357	119	C	tgT/tgC	rs771028941	.	.	-1	KIAA1429	HGNC	24500	protein_coding	YES	CCDS34923.1	ENSP00000297591	VIR_HUMAN	.	UPI00001BBB23	.	.	.	5/24	.	hmmpanther:PTHR23185:SF0,hmmpanther:PTHR23185	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAGACAGTT	.	5	ESCA
TP53INP1	0	.	GRCh37	8	95942587	95942587	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120A>G	.	.	ENST00000342697	4/4	40	36	4	31	31	0	TP53INP1,3_prime_UTR_variant,,ENST00000342697,;TP53INP1,3_prime_UTR_variant,,ENST00000448464,;NDUFAF6,intron_variant,,ENST00000519136,;NDUFAF6,intron_variant,,ENST00000396113,;NDUFAF6,intron_variant,,ENST00000523378,;TP53INP1,downstream_gene_variant,,ENST00000378776,;	C	ENSG00000164938	ENST00000342697	Transcript	3_prime_UTR_variant	1251	.	.	.	.	.	.	.	-1	TP53INP1	HGNC	18022	protein_coding	YES	CCDS6265.1	ENSP00000344215	T53I1_HUMAN	.	UPI00000725F8	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ACTGATAAAAC	.	2	ESCA
SLC44A1	0	.	GRCh37	9	108127763	108127763	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1254-1G>C	.	p.X418_splice	ENST00000374720	.	87	56	31	90	90	0	SLC44A1,splice_acceptor_variant,,ENST00000374720,;SLC44A1,splice_acceptor_variant,,ENST00000374724,;SLC44A1,splice_acceptor_variant,,ENST00000343170,;SLC44A1,splice_acceptor_variant,,ENST00000374723,;SLC44A1,splice_acceptor_variant,,ENST00000470972,;	C	ENSG00000070214	ENST00000374720	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	SLC44A1	HGNC	18798	protein_coding	YES	CCDS6763.1	ENSP00000363852	CTL1_HUMAN	B3KMS7_HUMAN	UPI0000062328	.	.	.	.	10/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATAGGGATA	.	5	ESCA
LPAR1	0	.	GRCh37	9	113636395	113636395	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1306delT	.	.	ENST00000374431	5/5	69	56	13	33	33	0	LPAR1,3_prime_UTR_variant,,ENST00000374431,;LPAR1,3_prime_UTR_variant,,ENST00000541779,;LPAR1,3_prime_UTR_variant,,ENST00000374430,;LPAR1,downstream_gene_variant,,ENST00000538760,;LPAR1,downstream_gene_variant,,ENST00000358883,;	-	ENSG00000198121	ENST00000374431	Transcript	3_prime_UTR_variant	2785	.	.	.	.	.	.	.	-1	LPAR1	HGNC	3166	protein_coding	YES	CCDS6777.1	ENSP00000363553	LPAR1_HUMAN	Q6GPG7_HUMAN,Q5VZX0_HUMAN,B1AP63_HUMAN	UPI000011DBF9	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TTTTTTAAAAAA	.	2	ESCA
DFNB31	0	.	GRCh37	9	117168862	117168862	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2009C>T	p.Ala670Val	p.A670V	ENST00000362057	9/12	74	34	40	76	76	0	DFNB31,missense_variant,p.Ala670Val,ENST00000362057,;DFNB31,missense_variant,p.Ala287Val,ENST00000265134,;DFNB31,missense_variant,p.Ala319Val,ENST00000374059,;	A	ENSG00000095397	ENST00000362057	Transcript	missense_variant	2178	2009	670	A/V	gCc/gTc	.	.	.	-1	DFNB31	HGNC	16361	protein_coding	YES	CCDS6806.1	ENSP00000354623	WHRN_HUMAN	.	UPI00001C1EA6	.	tolerated(0.07)	benign(0.065)	9/12	.	hmmpanther:PTHR23116:SF31,hmmpanther:PTHR23116	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGGCCAGA	.	5	ESCA
NDUFA8	0	.	GRCh37	9	124914553	124914553	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186G>T	p.%3D	p.L62L	ENST00000373768	2/4	32	22	9	21	21	0	NDUFA8,synonymous_variant,p.%3D,ENST00000537618,;NDUFA8,synonymous_variant,p.%3D,ENST00000373768,;	A	ENSG00000119421	ENST00000373768	Transcript	synonymous_variant	328	186	62	L	ctG/ctT	.	.	.	-1	NDUFA8	HGNC	7692	protein_coding	YES	CCDS6835.1	ENSP00000362873	NDUA8_HUMAN	.	UPI000013CA3A	.	.	.	2/4	.	PIRSF_domain:PIRSF017016,hmmpanther:PTHR13344,hmmpanther:PTHR13344:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACCAGTTT	.	5	ESCA
SET	0	.	GRCh37	9	131457744	131457744	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*801G>T	.	.	ENST00000372692	8/8	83	69	14	65	65	0	SET,3_prime_UTR_variant,,ENST00000322030,;SET,3_prime_UTR_variant,,ENST00000372692,;SET,downstream_gene_variant,,ENST00000409104,;SET,downstream_gene_variant,,ENST00000372688,;SET,downstream_gene_variant,,ENST00000372686,;SET,downstream_gene_variant,,ENST00000466009,;SET,downstream_gene_variant,,ENST00000477806,;SET,downstream_gene_variant,,ENST00000480217,;SET,downstream_gene_variant,,ENST00000485056,;SET,downstream_gene_variant,,ENST00000480536,;	T	ENSG00000119335	ENST00000372692	Transcript	3_prime_UTR_variant	1915	.	.	.	.	.	.	.	1	SET	HGNC	10760	protein_coding	YES	CCDS48037.1	ENSP00000361777	SET_HUMAN	Q5VXV3_HUMAN,B2REB7_HUMAN	UPI000006D7FF	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATGATGCT	.	5	ESCA
FAM78A	0	.	GRCh37	9	134134513	134134513	+	3'UTR	SNP	C	C	T	rs541401038	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1696G>A	.	.	ENST00000372271	2/2	112	103	8	78	78	0	FAM78A,3_prime_UTR_variant,,ENST00000372269,;FAM78A,3_prime_UTR_variant,,ENST00000372271,;FAM78A,downstream_gene_variant,,ENST00000464831,;FAM78A,non_coding_transcript_exon_variant,,ENST00000247295,;	T	ENSG00000126882	ENST00000372271	Transcript	3_prime_UTR_variant	2916	.	.	.	.	rs541401038	.	.	-1	FAM78A	HGNC	25465	protein_coding	YES	CCDS6941.2	ENSP00000361345	FA78A_HUMAN	.	UPI000013F430	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGACGGTTT	.	2	ESCA
RAPGEF1	0	.	GRCh37	9	134501526	134501526	+	Silent	SNP	G	G	A	rs368148839	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1488C>T	p.%3D	p.Y496Y	ENST00000372190	10/24	56	39	17	59	59	0	RAPGEF1,synonymous_variant,p.%3D,ENST00000372190,;RAPGEF1,synonymous_variant,p.%3D,ENST00000372195,;RAPGEF1,synonymous_variant,p.%3D,ENST00000372189,;RAPGEF1,upstream_gene_variant,,ENST00000414781,;RAPGEF1,upstream_gene_variant,,ENST00000419442,;RAPGEF1,downstream_gene_variant,,ENST00000481260,;	A	ENSG00000107263	ENST00000372190	Transcript	synonymous_variant	1647	1488	496	Y	taC/taT	rs368148839	.	.	-1	RAPGEF1	HGNC	4568	protein_coding	YES	CCDS48048.1	ENSP00000361264	RPGF1_HUMAN	Q5JUE5_HUMAN	UPI0000074689	.	.	.	10/24	.	hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF40	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTCGTAGGA	byFrequency|byCluster|by1000G	5	ESCA
FAM69B	0	.	GRCh37	9	139621262	139621262	+	3'Flank	SNP	C	C	T	rs762878594	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000371692	.	37	30	7	49	49	0	FAM69B,downstream_gene_variant,,ENST00000371691,;FAM69B,downstream_gene_variant,,ENST00000371692,;SNHG7,non_coding_transcript_exon_variant,,ENST00000391185,;SNHG7,upstream_gene_variant,,ENST00000362567,;SNHG7,non_coding_transcript_exon_variant,,ENST00000447221,;SNHG7,intron_variant,,ENST00000416970,;SNHG7,intron_variant,,ENST00000414282,;SNHG7,upstream_gene_variant,,ENST00000436596,;	T	ENSG00000165716	ENST00000371692	Transcript	downstream_gene_variant	.	.	.	.	.	rs762878594	.	2760	1	FAM69B	HGNC	28290	protein_coding	YES	CCDS7004.1	ENSP00000360757	FA69B_HUMAN	.	UPI000013E4F3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTCTCTAA	.	4	ESCA
FAM205B	0	.	GRCh37	9	34832891	34832891	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3410G>C	.	.	ENST00000399773	4/4	92	65	26	124	124	0	FAM205B,non_coding_transcript_exon_variant,,ENST00000455647,;FAM205B,downstream_gene_variant,,ENST00000378786,;FAM205B,non_coding_transcript_exon_variant,,ENST00000399773,;	G	ENSG00000257198	ENST00000399773	Transcript	non_coding_transcript_exon_variant	3410	.	.	.	.	.	.	.	-1	FAM205B	HGNC	24504	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTCCTTCTC	.	5	ESCA
SPATA31A3	0	.	GRCh37	9	40705844	40705844	+	Missense_Mutation	SNP	C	C	G	rs745970967	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3501C>G	p.Ile1167Met	p.I1167M	ENST00000356699	4/4	89	69	20	113	113	0	SPATA31A3,missense_variant,p.Ile1167Met,ENST00000356699,;RP11-395E19.5,intron_variant,,ENST00000432614,;SPATA31A3,downstream_gene_variant,,ENST00000463536,;	G	ENSG00000147926	ENST00000356699	Transcript	missense_variant	3530	3501	1167	I/M	atC/atG	rs745970967	.	.	1	SPATA31A3	HGNC	32003	protein_coding	YES	CCDS47969.1	ENSP00000349132	S31A3_HUMAN	.	UPI00004588FC	.	tolerated(1)	probably_damaging(0.965)	4/4	.	hmmpanther:PTHR21859:SF9,hmmpanther:PTHR21859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATCAAGCA	.	5	ESCA
RLN2	0	.	GRCh37	9	5300025	5300025	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*73C>G	.	.	ENST00000381627	2/2	16	11	5	28	28	0	RLN2,3_prime_UTR_variant,,ENST00000416837,;RLN2,3_prime_UTR_variant,,ENST00000308420,;RLN2,3_prime_UTR_variant,,ENST00000381627,;	C	ENSG00000107014	ENST00000381627	Transcript	3_prime_UTR_variant	1020	.	.	.	.	.	.	.	-1	RLN2	HGNC	10027	protein_coding	YES	CCDS6460.1	ENSP00000371040	REL2_HUMAN	.	UPI000002C1A0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTGATAGA	.	2	ESCA
ANKRD20A4	0	.	GRCh37	9	69420323	69420323	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213G>T	p.Asp405Tyr	p.D405Y	ENST00000357336	13/15	147	128	19	128	128	0	ANKRD20A4,missense_variant,p.Asp405Tyr,ENST00000357336,;	T	ENSG00000172014	ENST00000357336	Transcript	missense_variant	1494	1213	405	D/Y	Gat/Tat	.	.	.	1	ANKRD20A4	HGNC	31982	protein_coding	YES	CCDS43828.1	ENSP00000349891	A20A4_HUMAN	.	UPI000051917A	.	deleterious(0.01)	benign(0.432)	13/15	.	hmmpanther:PTHR24147:SF1,hmmpanther:PTHR24147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TATGTGATAGT	.	2	ESCA
KANK1	0	.	GRCh37	9	712721	712721	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1955C>G	p.Thr652Ser	p.T652S	ENST00000382303	7/16	17	9	8	26	26	0	KANK1,missense_variant,p.Thr494Ser,ENST00000382293,;KANK1,missense_variant,p.Thr652Ser,ENST00000382303,;KANK1,missense_variant,p.Thr652Ser,ENST00000382297,;KANK1,non_coding_transcript_exon_variant,,ENST00000489369,;KANK1,non_coding_transcript_exon_variant,,ENST00000354485,;	G	ENSG00000107104	ENST00000382303	Transcript	missense_variant	2607	1955	652	T/S	aCt/aGt	COSM4138972,COSM4138973,COSM4138971	.	.	1	KANK1	HGNC	19309	protein_coding	YES	CCDS34976.1	ENSP00000371740	KANK1_HUMAN	Q8WUM7_HUMAN,Q53U93_HUMAN	UPI00001AF26E	.	deleterious(0.03)	probably_damaging(0.912)	7/16	.	hmmpanther:PTHR24168,hmmpanther:PTHR24168:SF19	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACACTGAGG	.	5	ESCA
TMC1	0	.	GRCh37	9	75404064	75404064	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1055C>A	p.Ala352Asp	p.A352D	ENST00000297784	15/24	13	5	8	8	8	0	TMC1,missense_variant,p.Ala352Asp,ENST00000297784,;TMC1,missense_variant,p.Ala352Asp,ENST00000340019,;TMC1,missense_variant,p.Ala352Asp,ENST00000396237,;TMC1,upstream_gene_variant,,ENST00000486417,;	A	ENSG00000165091	ENST00000297784	Transcript	missense_variant	1595	1055	352	A/D	gCc/gAc	.	.	.	1	TMC1	HGNC	16513	protein_coding	YES	CCDS6643.1	ENSP00000297784	TMC1_HUMAN	.	UPI0000161FA9	.	deleterious(0.04)	benign(0.101)	15/24	.	hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAGCCCAAG	.	2	ESCA
HNRNPK	0	.	GRCh37	9	86583502	86583502	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*820G>T	.	.	ENST00000376263	17/17	24	21	3	12	12	0	HNRNPK,3_prime_UTR_variant,,ENST00000376264,;HNRNPK,3_prime_UTR_variant,,ENST00000351839,;HNRNPK,3_prime_UTR_variant,,ENST00000376263,;HNRNPK,3_prime_UTR_variant,,ENST00000376281,;HNRNPK,downstream_gene_variant,,ENST00000481820,;HNRNPK,downstream_gene_variant,,ENST00000457156,;HNRNPK,downstream_gene_variant,,ENST00000360384,;MIR7-1,downstream_gene_variant,,ENST00000384871,;RP11-575L7.8,upstream_gene_variant,,ENST00000448389,;HNRNPK,downstream_gene_variant,,ENST00000493362,;HNRNPK,downstream_gene_variant,,ENST00000472778,;HNRNPK,downstream_gene_variant,,ENST00000376256,;HNRNPK,downstream_gene_variant,,ENST00000492865,;	A	ENSG00000165119	ENST00000376263	Transcript	3_prime_UTR_variant	2439	.	.	.	.	.	.	.	-1	HNRNPK	HGNC	5044	protein_coding	YES	CCDS6668.1	ENSP00000365439	HNRPK_HUMAN	Q6IBN1_HUMAN	UPI0000021C42	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTCCCCACC	.	2	ESCA
TMSB4X	0	.	GRCh37	X	12995192	12995192	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*262G>A	.	.	ENST00000380636	2/2	17	12	5	41	40	1	TMSB4X,3_prime_UTR_variant,,ENST00000380636,;TMSB4X,3_prime_UTR_variant,,ENST00000380633,;TMSB4X,3_prime_UTR_variant,,ENST00000451311,;TMSB4X,3_prime_UTR_variant,,ENST00000380635,;	A	ENSG00000205542	ENST00000380636	Transcript	3_prime_UTR_variant	1549	.	.	.	.	.	.	.	1	TMSB4X	HGNC	11881	protein_coding	YES	CCDS35202.1	ENSP00000370010	TYB4_HUMAN	A2VCK8_HUMAN,Q0P5U7_HUMAN,Q0P5T0_HUMAN,Q0P5Q0_HUMAN,Q0P5P4_HUMAN,Q0P5N8_HUMAN	UPI0000000CD7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GGGACGACAGT	.	2	ESCA
RAP2C	0	.	GRCh37	X	131337265	131337265	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2385A>G	.	.	ENST00000342983	4/4	50	31	18	42	42	0	RAP2C,3_prime_UTR_variant,,ENST00000342983,;RAP2C,downstream_gene_variant,,ENST00000370874,;RAP2C,downstream_gene_variant,,ENST00000460462,;	C	ENSG00000123728	ENST00000342983	Transcript	3_prime_UTR_variant	3684	.	.	.	.	.	.	.	-1	RAP2C	HGNC	21165	protein_coding	YES	CCDS14632.1	ENSP00000340274	RAP2C_HUMAN	.	UPI00000236AB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTATTTTAT	.	5	ESCA
MAGEC3	0	.	GRCh37	X	140985578	140985578	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1892C>A	p.Ala631Glu	p.A631E	ENST00000298296	8/8	62	42	20	53	53	0	MAGEC3,missense_variant,p.Ala631Glu,ENST00000298296,;MAGEC3,3_prime_UTR_variant,,ENST00000544766,;MAGEC3,3_prime_UTR_variant,,ENST00000409007,;MAGEC3,3_prime_UTR_variant,,ENST00000443323,;MAGEC3,3_prime_UTR_variant,,ENST00000536088,;MAGEC3,downstream_gene_variant,,ENST00000448920,;MAGEC3,downstream_gene_variant,,ENST00000483584,;	A	ENSG00000165509	ENST00000298296	Transcript	missense_variant	1892	1892	631	A/E	gCa/gAa	COSM1257110	.	.	1	MAGEC3	HGNC	23798	protein_coding	YES	CCDS14676.1	ENSP00000298296	MAGC3_HUMAN	.	UPI000006E09B	.	tolerated(0.07)	benign(0.043)	8/8	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF47	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTGCAAGCC	.	5	ESCA
DMD	0	.	GRCh37	X	32503127	32503127	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2712C>T	p.%3D	p.P904P	ENST00000357033	21/79	21	8	13	22	22	0	DMD,synonymous_variant,p.%3D,ENST00000357033,;DMD,synonymous_variant,p.%3D,ENST00000378677,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000488902,;	A	ENSG00000198947	ENST00000357033	Transcript	synonymous_variant	2919	2712	904	P	ccC/ccT	.	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	.	21/79	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF261,Pfam_domain:PF00435,SMART_domains:SM00150,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATGGGTCC	.	5	ESCA
DMD	0	.	GRCh37	X	32503128	32503128	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2711C>A	p.Pro904His	p.P904H	ENST00000357033	21/79	21	8	13	22	22	0	DMD,missense_variant,p.Pro904His,ENST00000357033,;DMD,missense_variant,p.Pro900His,ENST00000378677,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000488902,;	T	ENSG00000198947	ENST00000357033	Transcript	missense_variant	2918	2711	904	P/H	cCc/cAc	.	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	probably_damaging(0.99)	21/79	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF261,Pfam_domain:PF00435,SMART_domains:SM00150,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATGGGTCCT	.	5	ESCA
PCDH19	0	.	GRCh37	X	99661679	99661679	+	Missense_Mutation	SNP	C	C	A	rs762785195	.	TCGA-LN-A4A2-01A-31D-A27G-09	TCGA-LN-A4A2-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1917G>T	p.Glu639Asp	p.E639D	ENST00000373034	1/6	20	9	11	19	19	0	PCDH19,missense_variant,p.Glu639Asp,ENST00000420881,;PCDH19,missense_variant,p.Glu639Asp,ENST00000255531,;PCDH19,missense_variant,p.Glu639Asp,ENST00000373034,;	A	ENSG00000165194	ENST00000373034	Transcript	missense_variant	3593	1917	639	E/D	gaG/gaT	rs762785195	.	.	-1	PCDH19	HGNC	14270	protein_coding	YES	CCDS55462.1	ENSP00000362125	PCD19_HUMAN	.	UPI00001D7BCD	.	tolerated(0.14)	probably_damaging(0.956)	1/6	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF40,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAGCTCATA	.	5	ESCA
PPRC1	0	.	GRCh37	10	103901475	103901475	+	Silent	SNP	G	G	T	rs753532044	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3210G>T	p.%3D	p.V1070V	ENST00000278070	5/14	18	12	6	32	32	0	PPRC1,synonymous_variant,p.%3D,ENST00000413464,;PPRC1,synonymous_variant,p.%3D,ENST00000278070,;PPRC1,synonymous_variant,p.%3D,ENST00000370012,;PPRC1,upstream_gene_variant,,ENST00000489648,;PPRC1,upstream_gene_variant,,ENST00000462933,;	T	ENSG00000148840	ENST00000278070	Transcript	synonymous_variant	3249	3210	1070	V	gtG/gtT	rs753532044	.	.	1	PPRC1	HGNC	30025	protein_coding	YES	CCDS7529.1	ENSP00000278070	PPRC1_HUMAN	.	UPI000013DB5C	.	.	.	5/14	.	hmmpanther:PTHR15528:SF5,hmmpanther:PTHR15528	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGTGTCTGC	.	5	ESCA
WDR37	0	.	GRCh37	10	1142270	1142270	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726+84G>A	.	.	ENST00000358220	.	44	38	6	47	47	0	WDR37,3_prime_UTR_variant,,ENST00000381329,;WDR37,intron_variant,,ENST00000263150,;WDR37,intron_variant,,ENST00000358220,;WDR37,downstream_gene_variant,,ENST00000436154,;	A	ENSG00000047056	ENST00000358220	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	WDR37	HGNC	31406	protein_coding	YES	CCDS7057.1	ENSP00000350954	WDR37_HUMAN	A8K976_HUMAN	UPI000013D3B7	.	.	.	.	9/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGACGGAATG	.	4	ESCA
C10orf90	0	.	GRCh37	10	128192578	128192578	+	Missense_Mutation	SNP	G	G	T	rs764212114	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1191C>A	p.Ser397Arg	p.S397R	ENST00000284694	3/9	125	98	27	118	118	0	C10orf90,missense_variant,p.Ser350Arg,ENST00000356858,;C10orf90,missense_variant,p.Ser350Arg,ENST00000392694,;C10orf90,missense_variant,p.Ser37Arg,ENST00000424927,;C10orf90,missense_variant,p.Ser397Arg,ENST00000432642,;C10orf90,missense_variant,p.Ser397Arg,ENST00000284694,;C10orf90,missense_variant,p.Ser397Arg,ENST00000454341,;C10orf90,missense_variant,p.Ser494Arg,ENST00000544758,;C10orf90,downstream_gene_variant,,ENST00000488181,;C10orf90,non_coding_transcript_exon_variant,,ENST00000368674,;C10orf90,downstream_gene_variant,,ENST00000463082,;	T	ENSG00000154493	ENST00000284694	Transcript	missense_variant	1312	1191	397	S/R	agC/agA	rs764212114	.	.	-1	C10orf90	HGNC	26563	protein_coding	YES	CCDS31310.1	ENSP00000284694	CJ090_HUMAN	S4R3N7_HUMAN,Q5T025_HUMAN	UPI00001D808F	.	tolerated(0.34)	benign(0.022)	3/9	.	hmmpanther:PTHR21553:SF10,hmmpanther:PTHR21553	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATCGCTGGC	byFrequency	5	ESCA
MKI67	0	.	GRCh37	10	129902236	129902236	+	Missense_Mutation	SNP	G	G	A	rs368793936	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7868C>T	p.Thr2623Met	p.T2623M	ENST00000368654	13/15	117	86	31	110	110	0	MKI67,missense_variant,p.Thr2623Met,ENST00000368654,;MKI67,missense_variant,p.Thr2263Met,ENST00000368653,;MKI67,upstream_gene_variant,,ENST00000464771,;	A	ENSG00000148773	ENST00000368654	Transcript	missense_variant	8244	7868	2623	T/M	aCg/aTg	rs368793936	.	.	-1	MKI67	HGNC	7107	protein_coding	YES	CCDS7659.1	ENSP00000357643	KI67_HUMAN	.	UPI000013DB54	.	deleterious(0.02)	probably_damaging(0.995)	13/15	.	hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF3,Pfam_domain:PF08065	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCGTGAGC	byFrequency|byCluster	5	ESCA
GDF2	0	.	GRCh37	10	48413931	48413931	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937A>T	p.Thr313Ser	p.T313S	ENST00000249598	2/2	46	34	12	53	53	0	GDF2,missense_variant,p.Thr313Ser,ENST00000249598,;	A	ENSG00000128802	ENST00000249598	Transcript	missense_variant	1097	937	313	T/S	Act/Tct	.	.	.	-1	GDF2	HGNC	4217	protein_coding	YES	CCDS7219.1	ENSP00000249598	GDF2_HUMAN	.	UPI000012B394	.	tolerated(1)	benign(0)	2/2	.	hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF127	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAGTCGACC	.	5	ESCA
PRKG1	0	.	GRCh37	10	52834303	52834303	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-48A>T	.	.	ENST00000373980	1/18	127	95	31	125	125	0	PRKG1,5_prime_UTR_variant,,ENST00000373980,;PRKG1,intron_variant,,ENST00000401604,;PRKG1,intron_variant,,ENST00000373985,;	T	ENSG00000185532	ENST00000373980	Transcript	5_prime_UTR_variant	370	.	.	.	.	.	.	.	1	PRKG1	HGNC	9414	protein_coding	YES	CCDS7244.1	ENSP00000363092	KGP1_HUMAN	.	UPI000012DDCD	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCAAGACG	.	5	ESCA
NRBF2	0	.	GRCh37	10	64914115	64914115	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*137C>A	.	.	ENST00000277746	4/4	38	33	5	36	36	0	NRBF2,3_prime_UTR_variant,,ENST00000435510,;NRBF2,3_prime_UTR_variant,,ENST00000277746,;	A	ENSG00000148572	ENST00000277746	Transcript	3_prime_UTR_variant	1182	.	.	.	.	.	.	.	1	NRBF2	HGNC	19692	protein_coding	YES	CCDS7268.1	ENSP00000277746	NRBF2_HUMAN	.	UPI000006D398	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGAGGCATTGC	.	3	ESCA
KCNMA1	0	.	GRCh37	10	78644878	78644878	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000404857	.	27	22	5	32	32	0	KCNMA1,3_prime_UTR_variant,,ENST00000286628,;KCNMA1,3_prime_UTR_variant,,ENST00000286627,;KCNMA1,intron_variant,,ENST00000372408,;KCNMA1,intron_variant,,ENST00000372403,;KCNMA1,intron_variant,,ENST00000372440,;KCNMA1,intron_variant,,ENST00000604624,;KCNMA1,intron_variant,,ENST00000372437,;KCNMA1,intron_variant,,ENST00000457953,;KCNMA1,intron_variant,,ENST00000372443,;KCNMA1,intron_variant,,ENST00000434208,;KCNMA1,intron_variant,,ENST00000404771,;KCNMA1,intron_variant,,ENST00000372421,;KCNMA1,downstream_gene_variant,,ENST00000404857,;KCNMA1,downstream_gene_variant,,ENST00000406533,;KCNMA1,downstream_gene_variant,,ENST00000354353,;RP11-443A13.5,upstream_gene_variant,,ENST00000429850,;RP11-443A13.5,upstream_gene_variant,,ENST00000595702,;RP11-443A13.5,upstream_gene_variant,,ENST00000458661,;RP11-443A13.5,upstream_gene_variant,,ENST00000609102,;KCNMA1,downstream_gene_variant,,ENST00000468471,;	T	ENSG00000156113	ENST00000404857	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2146	-1	KCNMA1	HGNC	6284	protein_coding	YES	CCDS53545.1	ENSP00000385806	KCMA1_HUMAN	.	UPI00003519E8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	ATGTTCTGAGG	.	3	ESCA
TMPRSS4	0	.	GRCh37	11	117973848	117973848	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.190T>A	p.Cys64Ser	p.C64S	ENST00000437212	4/13	86	61	25	71	71	0	TMPRSS4,missense_variant,p.Cys64Ser,ENST00000437212,;TMPRSS4,missense_variant,p.Cys31Ser,ENST00000517544,;TMPRSS4,missense_variant,p.Cys24Ser,ENST00000523251,;TMPRSS4,missense_variant,p.Cys62Ser,ENST00000534111,;TMPRSS4,missense_variant,p.Cys64Ser,ENST00000522824,;TMPRSS4,5_prime_UTR_variant,,ENST00000522307,;TMPRSS4,intron_variant,,ENST00000522151,;TMPRSS4,missense_variant,p.Cys62Ser,ENST00000519236,;TMPRSS4,3_prime_UTR_variant,,ENST00000517483,;TMPRSS4,non_coding_transcript_exon_variant,,ENST00000519813,;TMPRSS4,non_coding_transcript_exon_variant,,ENST00000522462,;TMPRSS4,downstream_gene_variant,,ENST00000520063,;TMPRSS4,upstream_gene_variant,,ENST00000528118,;	A	ENSG00000137648	ENST00000437212	Transcript	missense_variant	404	190	64	C/S	Tgc/Agc	.	.	.	1	TMPRSS4	HGNC	11878	protein_coding	YES	CCDS31684.1	ENSP00000416037	TMPS4_HUMAN	.	UPI00001FA467	.	deleterious(0)	possibly_damaging(0.847)	4/13	.	Superfamily_domains:SSF57424,SMART_domains:SM00192,Gene3D:4.10.400.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCTGCGGG	.	5	ESCA
SLC37A2	0	.	GRCh37	11	124950542	124950542	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560A>C	p.His187Pro	p.H187P	ENST00000308074	7/19	31	27	3	51	51	0	SLC37A2,missense_variant,p.His187Pro,ENST00000308074,;SLC37A2,missense_variant,p.His187Pro,ENST00000403796,;SLC37A2,missense_variant,p.His187Pro,ENST00000407458,;SLC37A2,missense_variant,p.His187Pro,ENST00000298280,;SLC37A2,missense_variant,p.His150Pro,ENST00000532000,;SLC37A2,upstream_gene_variant,,ENST00000525837,;SLC37A2,non_coding_transcript_exon_variant,,ENST00000526405,;	C	ENSG00000134955	ENST00000308074	Transcript	missense_variant	592	560	187	H/P	cAc/cCc	.	.	.	1	SLC37A2	HGNC	20644	protein_coding	YES	CCDS31714.1	ENSP00000311833	SPX2_HUMAN	E9PRJ4_HUMAN,B7Z480_HUMAN	UPI000019AB60	.	deleterious(0)	probably_damaging(0.993)	7/19	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11662:SF163,hmmpanther:PTHR11662,Pfam_domain:PF07690,Gene3D:1.20.1250.20,PIRSF_domain:PIRSF002808,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCCACACAT	.	4	ESCA
ANO5	0	.	GRCh37	11	22297708	22297708	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2483T>C	p.Val828Ala	p.V828A	ENST00000324559	21/22	74	65	9	57	57	0	ANO5,missense_variant,p.Val828Ala,ENST00000324559,;ANO5,non_coding_transcript_exon_variant,,ENST00000532043,;	C	ENSG00000171714	ENST00000324559	Transcript	missense_variant	2800	2483	828	V/A	gTc/gCc	.	.	.	1	ANO5	HGNC	27337	protein_coding	YES	CCDS31444.1	ENSP00000315371	ANO5_HUMAN	.	UPI000035B19B	.	deleterious(0)	possibly_damaging(0.822)	21/22	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF23,Pfam_domain:PF04547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATGTCCTTG	.	4	ESCA
F2	0	.	GRCh37	11	46751011	46751011	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1554G>A	p.%3D	p.G518G	ENST00000311907	12/14	53	30	23	35	35	0	F2,synonymous_variant,p.%3D,ENST00000530231,;F2,synonymous_variant,p.%3D,ENST00000311907,;F2,downstream_gene_variant,,ENST00000442468,;F2,downstream_gene_variant,,ENST00000490274,;	A	ENSG00000180210	ENST00000311907	Transcript	synonymous_variant	1610	1554	518	G	ggG/ggA	.	.	.	1	F2	HGNC	3535	protein_coding	YES	CCDS31476.1	ENSP00000308541	THRB_HUMAN	Q8TD58_HUMAN,Q86WA1_HUMAN	UPI0000136ECD	.	.	.	12/14	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24254,hmmpanther:PTHR24254:SF8,Pfam_domain:PF00089,Gene3D:2.40.10.10,PIRSF_domain:PIRSF001149,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGGGCAGCC	.	5	ESCA
OR51T1	0	.	GRCh37	11	4904034	4904034	+	Missense_Mutation	SNP	G	G	A	rs151076376	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.986G>A	p.Arg329His	p.R329H	ENST00000380378	1/1	50	31	18	57	57	0	OR51T1,missense_variant,p.Arg329His,ENST00000380378,;OR51T1,missense_variant,p.Arg302His,ENST00000322049,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	A	ENSG00000176900	ENST00000380378	Transcript	missense_variant	986	986	329	R/H	cGc/cAc	rs151076376,COSM542920,COSM1737107,COSM1737106,COSM542919	.	.	1	OR51T1	HGNC	15205	protein_coding	YES	CCDS31363.1	ENSP00000369738	O51T1_HUMAN	.	UPI000015F1FF	.	deleterious(0.04)	benign(0.051)	1/1	.	hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF6,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	A:0	A:0.0006	.	0,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCCGCCAGG	byFrequency|byCluster	5	ESCA
OR51V1	0	.	GRCh37	11	5221161	5221161	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.770T>C	p.Val257Ala	p.V257A	ENST00000321255	1/1	58	53	5	77	77	0	OR51V1,missense_variant,p.Val257Ala,ENST00000321255,;	G	ENSG00000176742	ENST00000321255	Transcript	missense_variant	770	770	257	V/A	gTc/gCc	.	.	.	-1	OR51V1	HGNC	19597	protein_coding	YES	CCDS31375.1	ENSP00000321729	O51V1_HUMAN	.	UPI0000140ADA	.	deleterious(0)	possibly_damaging(0.868)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF67,hmmpanther:PTHR26450,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAAGGACAGCA	.	3	ESCA
GCN1L1	0	.	GRCh37	12	120569744	120569744	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7400A>G	p.Gln2467Arg	p.Q2467R	ENST00000300648	54/58	33	27	6	36	36	0	GCN1L1,missense_variant,p.Gln2467Arg,ENST00000300648,;GCN1L1,downstream_gene_variant,,ENST00000549815,;	C	ENSG00000089154	ENST00000300648	Transcript	missense_variant	7413	7400	2467	Q/R	cAg/cGg	.	.	.	-1	GCN1L1	HGNC	4199	protein_coding	YES	CCDS41847.1	ENSP00000300648	GCN1L_HUMAN	B4DM32_HUMAN	UPI00001FBC69	.	.	benign(0.003)	54/58	.	Superfamily_domains:SSF48371,Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGCTGTAGA	.	5	ESCA
TMEM132C	0	.	GRCh37	12	129153998	129153998	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1342A>G	p.Lys448Glu	p.K448E	ENST00000435159	5/9	47	42	5	71	71	0	TMEM132C,missense_variant,p.Lys64Glu,ENST00000315208,;TMEM132C,missense_variant,p.Lys448Glu,ENST00000435159,;AC107020.1,downstream_gene_variant,,ENST00000408822,;	G	ENSG00000181234	ENST00000435159	Transcript	missense_variant	1342	1342	448	K/E	Aag/Gag	.	.	.	1	TMEM132C	HGNC	25436	protein_coding	YES	.	ENSP00000410852	T132C_HUMAN	F5H439_HUMAN,E9PC33_HUMAN	UPI0001C0B37C	.	deleterious(0)	benign(0.381)	5/9	.	hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGGAAAGACA	.	3	ESCA
GLT1D1	0	.	GRCh37	12	129373274	129373274	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.308T>G	p.Val103Gly	p.V103G	ENST00000281703	3/8	54	51	3	53	53	0	GLT1D1,missense_variant,p.Val103Gly,ENST00000281703,;GLT1D1,missense_variant,p.Val103Gly,ENST00000442111,;GLT1D1,missense_variant,p.Val4Gly,ENST00000542193,;GLT1D1,missense_variant,p.Val92Gly,ENST00000537468,;GLT1D1,missense_variant,p.Val96Gly,ENST00000413816,;GLT1D1,missense_variant,p.Val103Gly,ENST00000441390,;GLT1D1,missense_variant,p.Val103Gly,ENST00000539044,;	G	ENSG00000151948	ENST00000281703	Transcript	missense_variant	354	308	103	V/G	gTt/gGt	.	.	.	1	GLT1D1	HGNC	26483	protein_coding	YES	CCDS9265.1	ENSP00000281703	GL1D1_HUMAN	.	UPI0000070E33	.	deleterious(0)	possibly_damaging(0.504)	3/8	.	hmmpanther:PTHR12526,hmmpanther:PTHR12526:SF331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGAGTTCTTG	.	2	ESCA
ALG10	0	.	GRCh37	12	34179678	34179678	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1250A>G	p.Tyr417Cys	p.Y417C	ENST00000266483	3/3	102	88	13	98	98	0	ALG10,missense_variant,p.Tyr417Cys,ENST00000266483,;ALG10,intron_variant,,ENST00000538927,;AC046130.1,downstream_gene_variant,,ENST00000401300,;RP11-847H18.2,intron_variant,,ENST00000501954,;ALG10,3_prime_UTR_variant,,ENST00000541875,;ALG10,downstream_gene_variant,,ENST00000541178,;	G	ENSG00000139133	ENST00000266483	Transcript	missense_variant	1569	1250	417	Y/C	tAc/tGc	.	.	.	1	ALG10	HGNC	23162	protein_coding	YES	CCDS41769.1	ENSP00000266483	AG10A_HUMAN	.	UPI000004E870	.	deleterious(0)	probably_damaging(1)	3/3	.	hmmpanther:PTHR12989,hmmpanther:PTHR12989:SF11,Pfam_domain:PF04922,PIRSF_domain:PIRSF028810	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R416C|c.1246C>T|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTTACTTCA	.	5	ESCA
TENC1	0	.	GRCh37	12	53453482	53453482	+	Missense_Mutation	SNP	C	C	A	rs771304396	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2087C>A	p.Ala696Asp	p.A696D	ENST00000314276	18/29	63	54	8	44	44	0	TENC1,missense_variant,p.Ala562Asp,ENST00000379902,;TENC1,missense_variant,p.Ala686Asp,ENST00000546602,;TENC1,missense_variant,p.Ala686Asp,ENST00000549700,;TENC1,missense_variant,p.Ala696Asp,ENST00000314276,;TENC1,missense_variant,p.Ala686Asp,ENST00000451358,;TENC1,missense_variant,p.Ala686Asp,ENST00000314250,;TENC1,missense_variant,p.Ala686Asp,ENST00000552570,;TENC1,downstream_gene_variant,,ENST00000602335,;SPRYD3,downstream_gene_variant,,ENST00000301463,;TENC1,non_coding_transcript_exon_variant,,ENST00000549311,;TENC1,upstream_gene_variant,,ENST00000551583,;TENC1,upstream_gene_variant,,ENST00000550660,;TENC1,downstream_gene_variant,,ENST00000549789,;TENC1,upstream_gene_variant,,ENST00000550048,;TENC1,upstream_gene_variant,,ENST00000552168,;TENC1,upstream_gene_variant,,ENST00000546772,;TENC1,downstream_gene_variant,,ENST00000547223,;TENC1,downstream_gene_variant,,ENST00000546759,;TENC1,downstream_gene_variant,,ENST00000549498,;TENC1,downstream_gene_variant,,ENST00000551693,;	A	ENSG00000111077	ENST00000314276	Transcript	missense_variant	2282	2087	696	A/D	gCc/gAc	rs771304396	.	.	1	TENC1	HGNC	19737	protein_coding	YES	CCDS8842.1	ENSP00000319756	TENC1_HUMAN	.	UPI000013F790	.	deleterious(0.01)	possibly_damaging(0.628)	18/29	.	hmmpanther:PTHR12583,hmmpanther:PTHR12583:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTGCCCTAT	byFrequency	4	ESCA
HOXC13	0	.	GRCh37	12	54339079	54339079	+	3'UTR	SNP	G	G	A	rs760321962	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39G>A	.	.	ENST00000243056	2/2	41	37	4	32	32	0	HOXC13,3_prime_UTR_variant,,ENST00000243056,;	A	ENSG00000123364	ENST00000243056	Transcript	3_prime_UTR_variant	1188	.	.	.	.	rs760321962	.	.	1	HOXC13	HGNC	5125	protein_coding	YES	CCDS8865.1	ENSP00000243056	HXC13_HUMAN	Q6LAM3_HUMAN	UPI000012CF7F	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TCTCCGCTTTG	.	2	ESCA
MON2	0	.	GRCh37	12	62936944	62936944	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2432T>A	p.Ile811Asn	p.I811N	ENST00000393632	20/35	64	58	5	103	103	0	MON2,missense_variant,p.Ile811Asn,ENST00000546600,;MON2,missense_variant,p.Ile811Asn,ENST00000393630,;MON2,missense_variant,p.Ile811Asn,ENST00000280379,;MON2,missense_variant,p.Ile811Asn,ENST00000552115,;MON2,missense_variant,p.Ile811Asn,ENST00000393629,;MON2,missense_variant,p.Ile811Asn,ENST00000393632,;MON2,missense_variant,p.Ile788Asn,ENST00000552738,;RNU6-399P,downstream_gene_variant,,ENST00000365164,;MON2,3_prime_UTR_variant,,ENST00000547095,;	A	ENSG00000061987	ENST00000393632	Transcript	missense_variant	2823	2432	811	I/N	aTt/aAt	.	.	.	1	MON2	HGNC	29177	protein_coding	YES	CCDS31849.1	ENSP00000377252	MON2_HUMAN	F8VZV1_HUMAN	UPI00001AEA4C	.	deleterious(0)	probably_damaging(0.947)	20/35	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF105,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAATTCTGT	.	2	ESCA
APAF1	0	.	GRCh37	12	99126322	99126322	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3725A>G	p.Tyr1242Cys	p.Y1242C	ENST00000551964	27/27	35	30	5	26	26	0	APAF1,missense_variant,p.Tyr1199Cys,ENST00000357310,;APAF1,missense_variant,p.Tyr1231Cys,ENST00000550527,;APAF1,missense_variant,p.Tyr1157Cys,ENST00000339433,;APAF1,missense_variant,p.Tyr1157Cys,ENST00000549007,;APAF1,missense_variant,p.Tyr1199Cys,ENST00000547045,;APAF1,missense_variant,p.Tyr1188Cys,ENST00000359972,;APAF1,missense_variant,p.Tyr1242Cys,ENST00000551964,;APAF1,3_prime_UTR_variant,,ENST00000333991,;APAF1,3_prime_UTR_variant,,ENST00000552268,;ANKS1B,downstream_gene_variant,,ENST00000547010,;ANKS1B,downstream_gene_variant,,ENST00000341752,;ANKS1B,downstream_gene_variant,,ENST00000329257,;ANKS1B,downstream_gene_variant,,ENST00000549558,;ANKS1B,downstream_gene_variant,,ENST00000547776,;APAF1,non_coding_transcript_exon_variant,,ENST00000552929,;ANKS1B,downstream_gene_variant,,ENST00000551212,;APAF1,upstream_gene_variant,,ENST00000547666,;ANKS1B,intron_variant,,ENST00000555119,;	G	ENSG00000120868	ENST00000551964	Transcript	missense_variant	4461	3725	1242	Y/C	tAt/tGt	.	.	.	1	APAF1	HGNC	576	protein_coding	YES	CCDS9069.1	ENSP00000448165	APAF_HUMAN	.	UPI0000036328	.	deleterious(0)	probably_damaging(0.958)	27/27	.	hmmpanther:PTHR22845:SF1,hmmpanther:PTHR22845,PIRSF_domain:PIRSF037646	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTATATATTT	.	4	ESCA
RP11-394A14.2	0	.	GRCh37	13	64415472	64415472	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.413G>T	.	.	ENST00000607822	2/5	11	4	7	14	14	0	RP11-394A14.2,non_coding_transcript_exon_variant,,ENST00000607822,;RP11-394A14.2,intron_variant,,ENST00000606050,;RP11-394A14.4,upstream_gene_variant,,ENST00000606894,;OR7E104P,downstream_gene_variant,,ENST00000400311,;	A	ENSG00000219926	ENST00000607822	Transcript	non_coding_transcript_exon_variant	413	.	.	.	.	.	.	.	-1	RP11-394A14.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CATGGCAGCGG	.	3	ESCA
CHRFAM7A	0	.	GRCh37	15	30653699	30653699	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000299847	.	60	55	5	84	84	0	CHRFAM7A,3_prime_UTR_variant,,ENST00000397827,;CHRFAM7A,downstream_gene_variant,,ENST00000299847,;CHRFAM7A,downstream_gene_variant,,ENST00000401522,;RP11-382B18.4,upstream_gene_variant,,ENST00000602453,;	A	ENSG00000166664	ENST00000299847	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	97	-1	CHRFAM7A	HGNC	15781	protein_coding	YES	CCDS32184.1	ENSP00000299847	CRFM7_HUMAN	Q693P7_HUMAN,H3BPP0_HUMAN	UPI000013E5F0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GTTCTGCAGAA	.	2	ESCA
SPG21	0	.	GRCh37	15	65267023	65267023	+	Missense_Mutation	SNP	G	G	T	rs763641808	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369C>A	p.His123Gln	p.H123Q	ENST00000204566	5/9	36	28	8	29	29	0	SPG21,missense_variant,p.His123Gln,ENST00000557795,;SPG21,missense_variant,p.His123Gln,ENST00000433215,;SPG21,missense_variant,p.His123Gln,ENST00000204566,;SPG21,missense_variant,p.His123Gln,ENST00000558765,;SPG21,missense_variant,p.His96Gln,ENST00000416889,;SPG21,5_prime_UTR_variant,,ENST00000559199,;SPG21,downstream_gene_variant,,ENST00000559677,;SPG21,non_coding_transcript_exon_variant,,ENST00000560564,;SPG21,intron_variant,,ENST00000561078,;	T	ENSG00000090487	ENST00000204566	Transcript	missense_variant	665	369	123	H/Q	caC/caA	rs763641808	.	.	-1	SPG21	HGNC	20373	protein_coding	YES	CCDS10198.1	ENSP00000204566	SPG21_HUMAN	H3BRR0_HUMAN,H0YML6_HUMAN,H0YMB7_HUMAN,H0YLW1_HUMAN,H0YLT5_HUMAN,H0YLD7_HUMAN,H0YKB0_HUMAN	UPI0000074012	.	tolerated(0.3)	benign(0.229)	5/9	.	hmmpanther:PTHR15913:SF0,hmmpanther:PTHR15913,Gene3D:3.40.50.1820,Pfam_domain:PF12697,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTGTGAGT	.	5	ESCA
SMG1	0	.	GRCh37	16	18858815	18858815	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5956G>A	p.Asp1986Asn	p.D1986N	ENST00000446231	38/63	44	39	5	36	36	0	SMG1,missense_variant,p.Asp1986Asn,ENST00000389467,;SMG1,missense_variant,p.Asp1876Asn,ENST00000565324,;SMG1,missense_variant,p.Asp1986Asn,ENST00000446231,;SMG1,non_coding_transcript_exon_variant,,ENST00000563448,;SMG1,downstream_gene_variant,,ENST00000562668,;	T	ENSG00000157106	ENST00000446231	Transcript	missense_variant	6369	5956	1986	D/N	Gat/Aat	.	.	.	-1	SMG1	HGNC	30045	protein_coding	YES	CCDS45430.1	ENSP00000402515	SMG1_HUMAN	H3BPS6_HUMAN	UPI00004F8E22	.	tolerated(0.16)	probably_damaging(0.958)	38/63	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF59,Gene3D:3.30.1010.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCATCTTCAA	.	4	ESCA
NPIPB7	0	.	GRCh37	16	28468188	28468188	+	Nonsense_Mutation	SNP	C	C	A	rs753247895	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.802G>T	p.Glu268Ter	p.E268*	ENST00000452313	7/7	132	90	42	149	149	0	NPIPB7,stop_gained,p.Glu268Ter,ENST00000452313,;RP11-57A19.5,upstream_gene_variant,,ENST00000602838,;	A	ENSG00000233232	ENST00000452313	Transcript	stop_gained	911	802	268	E/*	Gag/Tag	rs753247895	.	.	-1	NPIPB7	HGNC	33832	protein_coding	YES	.	ENSP00000405348	NPIB7_HUMAN	O60358_HUMAN	UPI0000E028CF	.	.	.	7/7	.	Low_complexity_(Seg):seg,Pfam_domain:PF06409,hmmpanther:PTHR15438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACTCGGGAG	.	5	ESCA
TBC1D10B	0	.	GRCh37	16	30370527	30370527	+	Silent	SNP	C	C	T	rs751167331	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1608G>A	p.%3D	p.S536S	ENST00000409939	7/9	43	40	3	27	27	0	TBC1D10B,synonymous_variant,p.%3D,ENST00000409939,;TBC1D10B,intron_variant,,ENST00000490703,;CD2BP2,upstream_gene_variant,,ENST00000305596,;CD2BP2,upstream_gene_variant,,ENST00000569466,;RP11-347C12.10,downstream_gene_variant,,ENST00000563252,;TBC1D10B,non_coding_transcript_exon_variant,,ENST00000566671,;TBC1D10B,non_coding_transcript_exon_variant,,ENST00000478158,;TBC1D10B,non_coding_transcript_exon_variant,,ENST00000475650,;TBC1D10B,intron_variant,,ENST00000475872,;CD2BP2,upstream_gene_variant,,ENST00000564525,;TBC1D10B,downstream_gene_variant,,ENST00000464644,;	T	ENSG00000169221	ENST00000409939	Transcript	synonymous_variant	1689	1608	536	S	tcG/tcA	rs751167331	.	.	-1	TBC1D10B	HGNC	24510	protein_coding	YES	CCDS10676.2	ENSP00000386538	TB10B_HUMAN	.	UPI000164FA1A	.	.	.	7/9	.	PROSITE_profiles:PS50086,hmmpanther:PTHR22957:SF207,hmmpanther:PTHR22957,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCACCGACGC	byFrequency	2	ESCA
ZSCAN32	0	.	GRCh37	16	3433044	3433044	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1266G>A	p.%3D	p.K422K	ENST00000304926	6/6	138	130	8	126	126	0	ZSCAN32,synonymous_variant,p.%3D,ENST00000396846,;ZSCAN32,synonymous_variant,p.%3D,ENST00000304926,;ZSCAN32,synonymous_variant,p.%3D,ENST00000439568,;ZSCAN32,synonymous_variant,p.%3D,ENST00000396852,;ZSCAN32,downstream_gene_variant,,ENST00000574940,;ZSCAN32,downstream_gene_variant,,ENST00000575350,;ZSCAN32,downstream_gene_variant,,ENST00000573327,;ZSCAN32,downstream_gene_variant,,ENST00000571906,;ZSCAN32,downstream_gene_variant,,ENST00000573830,;ZSCAN32,downstream_gene_variant,,ENST00000573719,;ZSCAN32,downstream_gene_variant,,ENST00000422427,;NAA60,intron_variant,,ENST00000576906,;ZSCAN32,3_prime_UTR_variant,,ENST00000576500,;ZSCAN32,non_coding_transcript_exon_variant,,ENST00000571285,;NAA60,intron_variant,,ENST00000575785,;ZSCAN32,downstream_gene_variant,,ENST00000574084,;	T	ENSG00000140987	ENST00000304926	Transcript	synonymous_variant	2068	1266	422	K	aaG/aaA	.	.	.	-1	ZSCAN32	HGNC	20812	protein_coding	YES	CCDS10503.1	ENSP00000302502	ZSC32_HUMAN	I3L1K0_HUMAN,B4DWL5_HUMAN	UPI00001A993A	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF210,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCACACTTGTA	.	2	ESCA
UBN1	0	.	GRCh37	16	4921188	4921188	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1592T>G	p.Leu531Arg	p.L531R	ENST00000396658	11/17	75	47	28	74	74	0	UBN1,missense_variant,p.Leu531Arg,ENST00000590769,;UBN1,missense_variant,p.Leu531Arg,ENST00000545171,;UBN1,missense_variant,p.Leu531Arg,ENST00000396658,;UBN1,missense_variant,p.Leu531Arg,ENST00000262376,;UBN1,intron_variant,,ENST00000586716,;UBN1,downstream_gene_variant,,ENST00000585857,;UBN1,upstream_gene_variant,,ENST00000589191,;UBN1,downstream_gene_variant,,ENST00000587027,;	G	ENSG00000118900	ENST00000396658	Transcript	missense_variant	2295	1592	531	L/R	cTg/cGg	.	.	.	1	UBN1	HGNC	12506	protein_coding	YES	CCDS10525.1	ENSP00000379894	UBN1_HUMAN	K7EQR1_HUMAN	UPI0000071469	.	deleterious(0)	probably_damaging(0.993)	11/17	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16426:SF14,hmmpanther:PTHR16426,Pfam_domain:PF14075	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAACTGGAGA	.	5	ESCA
CNOT1	0	.	GRCh37	16	58590827	58590827	+	Silent	SNP	G	G	A	rs751590881	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2403C>T	p.%3D	p.N801N	ENST00000317147	19/49	63	55	7	43	43	0	CNOT1,synonymous_variant,p.%3D,ENST00000317147,;CNOT1,synonymous_variant,p.%3D,ENST00000562046,;CNOT1,synonymous_variant,p.%3D,ENST00000569882,;CNOT1,synonymous_variant,p.%3D,ENST00000569240,;CNOT1,synonymous_variant,p.%3D,ENST00000441024,;SNORA50,downstream_gene_variant,,ENST00000384225,;CNOT1,non_coding_transcript_exon_variant,,ENST00000569732,;CNOT1,synonymous_variant,p.%3D,ENST00000567188,;	A	ENSG00000125107	ENST00000317147	Transcript	synonymous_variant	2736	2403	801	N	aaC/aaT	rs751590881	.	.	-1	CNOT1	HGNC	7877	protein_coding	YES	CCDS10799.1	ENSP00000320949	CNOT1_HUMAN	H3BUY8_HUMAN,H3BT18_HUMAN,H3BPF1_HUMAN,B7Z6X2_HUMAN,B3KS60_HUMAN	UPI00001FF2F6	.	.	.	19/49	.	hmmpanther:PTHR13162:SF8,hmmpanther:PTHR13162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTCGTTATT	byFrequency	4	ESCA
CDH11	0	.	GRCh37	16	64984804	64984804	+	Missense_Mutation	SNP	G	G	A	rs773287027	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1760C>T	p.Thr587Ile	p.T587I	ENST00000268603	12/13	60	54	6	48	48	0	CDH11,missense_variant,p.Thr587Ile,ENST00000394156,;CDH11,missense_variant,p.Thr587Ile,ENST00000268603,;CDH11,missense_variant,p.Thr461Ile,ENST00000566827,;	A	ENSG00000140937	ENST00000268603	Transcript	missense_variant	2376	1760	587	T/I	aCc/aTc	rs773287027	.	.	-1	CDH11	HGNC	1750	protein_coding	YES	CCDS10803.1	ENSP00000268603	CAD11_HUMAN	H3BUU9_HUMAN,H3BSM4_HUMAN,H3BR78_HUMAN,H3BQH2_HUMAN,H3BQB5_HUMAN,H3BPQ2_HUMAN,H3BP26_HUMAN	UPI000013D7C5	.	deleterious(0.01)	benign(0.356)	12/13	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF85,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGGGTGTTG	byFrequency	4	ESCA
SLC7A5	0	.	GRCh37	16	87868078	87868078	+	Silent	SNP	G	G	C	rs778987531	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1410C>G	p.%3D	p.P470P	ENST00000261622	9/10	62	46	15	60	60	0	SLC7A5,synonymous_variant,p.%3D,ENST00000261622,;SLC7A5,synonymous_variant,p.%3D,ENST00000565644,;RP4-536B24.2,upstream_gene_variant,,ENST00000563687,;SLC7A5,non_coding_transcript_exon_variant,,ENST00000563489,;	C	ENSG00000103257	ENST00000261622	Transcript	synonymous_variant	1476	1410	470	P	ccC/ccG	rs778987531,COSM3771241	.	.	-1	SLC7A5	HGNC	11063	protein_coding	YES	CCDS10964.1	ENSP00000261622	LAT1_HUMAN	.	UPI000000D9ED	.	.	.	9/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF232,TIGRFAM_domain:TIGR00911,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGACGGGCAG	byFrequency	5	ESCA
PIEZO1	0	.	GRCh37	16	88809254	88809254	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161-424G>A	.	.	ENST00000301015	.	14	10	4	13	13	0	PIEZO1,intron_variant,,ENST00000301015,;RP5-1142A6.8,non_coding_transcript_exon_variant,,ENST00000567588,;RP5-1142A6.8,non_coding_transcript_exon_variant,,ENST00000333666,;RP5-1142A6.7,downstream_gene_variant,,ENST00000566114,;RP5-1142A6.2,downstream_gene_variant,,ENST00000567968,;RP5-1142A6.2,downstream_gene_variant,,ENST00000440406,;	T	ENSG00000103335	ENST00000301015	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PIEZO1	HGNC	28993	protein_coding	YES	CCDS54058.1	ENSP00000301015	PIEZ1_HUMAN	.	UPI0001B300F3	.	.	.	.	2/50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CGGAGCGCCCC	.	4	ESCA
ELAC2	0	.	GRCh37	17	12898129	12898129	+	Missense_Mutation	SNP	C	C	G	rs747446525	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1981G>C	p.Val661Leu	p.V661L	ENST00000338034	21/24	13	9	4	22	22	0	ELAC2,missense_variant,p.Val461Leu,ENST00000584650,;ELAC2,missense_variant,p.Val621Leu,ENST00000426905,;ELAC2,missense_variant,p.Val661Leu,ENST00000338034,;ELAC2,missense_variant,p.Val642Leu,ENST00000395962,;ARHGAP44,downstream_gene_variant,,ENST00000340825,;ARHGAP44,downstream_gene_variant,,ENST00000262444,;ARHGAP44,downstream_gene_variant,,ENST00000379672,;ELAC2,downstream_gene_variant,,ENST00000446899,;RP11-597M12.1,upstream_gene_variant,,ENST00000582915,;ELAC2,non_coding_transcript_exon_variant,,ENST00000491478,;ELAC2,non_coding_transcript_exon_variant,,ENST00000484122,;ELAC2,non_coding_transcript_exon_variant,,ENST00000480891,;ELAC2,non_coding_transcript_exon_variant,,ENST00000487229,;ELAC2,non_coding_transcript_exon_variant,,ENST00000465825,;ARHGAP44,downstream_gene_variant,,ENST00000580768,;ELAC2,downstream_gene_variant,,ENST00000492559,;ELAC2,downstream_gene_variant,,ENST00000578991,;ARHGAP44,downstream_gene_variant,,ENST00000544416,;	G	ENSG00000006744	ENST00000338034	Transcript	missense_variant	2221	1981	661	V/L	Gtg/Ctg	rs747446525	.	.	-1	ELAC2	HGNC	14198	protein_coding	YES	CCDS11164.1	ENSP00000337445	RNZ2_HUMAN	Q9HAS7_HUMAN,J3QRS2_HUMAN,J3QL08_HUMAN,B4DT15_HUMAN	UPI000004A07E	.	tolerated(0.61)	benign(0.014)	21/24	.	hmmpanther:PTHR12553,hmmpanther:PTHR12553:SF44,Gene3D:3.60.15.10,Pfam_domain:PF12706,Superfamily_domains:SSF56281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCACTTTCC	.	2	ESCA
MYO1C	0	.	GRCh37	17	1378125	1378125	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1697T>C	p.Leu566Pro	p.L566P	ENST00000359786	16/32	43	23	20	38	38	0	MYO1C,missense_variant,p.Leu542Pro,ENST00000545534,;MYO1C,missense_variant,p.Leu547Pro,ENST00000438665,;MYO1C,missense_variant,p.Leu531Pro,ENST00000361007,;MYO1C,missense_variant,p.Leu531Pro,ENST00000575158,;MYO1C,missense_variant,p.Leu566Pro,ENST00000359786,;MYO1C,downstream_gene_variant,,ENST00000571851,;MYO1C,downstream_gene_variant,,ENST00000573198,;MYO1C,non_coding_transcript_exon_variant,,ENST00000571615,;MYO1C,upstream_gene_variant,,ENST00000575011,;MYO1C,downstream_gene_variant,,ENST00000573961,;MYO1C,upstream_gene_variant,,ENST00000572615,;MYO1C,upstream_gene_variant,,ENST00000575864,;MYO1C,upstream_gene_variant,,ENST00000574308,;	G	ENSG00000197879	ENST00000359786	Transcript	missense_variant	2022	1697	566	L/P	cTc/cCc	.	.	.	-1	MYO1C	HGNC	7597	protein_coding	YES	CCDS42226.1	ENSP00000352834	MYO1C_HUMAN	I3L4D4_HUMAN,I3L3Y6_HUMAN,I3L3F5_HUMAN,I3L204_HUMAN,I3L168_HUMAN	UPI0000200579	.	deleterious(0)	possibly_damaging(0.904)	16/32	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF255,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGAGAAGG	.	5	ESCA
PROCA1	0	.	GRCh37	17	27031779	27031779	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174T>C	p.%3D	p.C58C	ENST00000301039	2/4	54	44	10	38	38	0	PROCA1,synonymous_variant,p.%3D,ENST00000301039,;PROCA1,synonymous_variant,p.%3D,ENST00000439862,;PROCA1,5_prime_UTR_variant,,ENST00000415329,;PROCA1,intron_variant,,ENST00000581289,;SUPT6H,downstream_gene_variant,,ENST00000314616,;SUPT6H,downstream_gene_variant,,ENST00000347486,;PROCA1,non_coding_transcript_exon_variant,,ENST00000422880,;PROCA1,non_coding_transcript_exon_variant,,ENST00000584073,;PROCA1,non_coding_transcript_exon_variant,,ENST00000579650,;PROCA1,non_coding_transcript_exon_variant,,ENST00000578097,;PROCA1,synonymous_variant,p.%3D,ENST00000473751,;PROCA1,non_coding_transcript_exon_variant,,ENST00000495203,;SUPT6H,downstream_gene_variant,,ENST00000583340,;SUPT6H,downstream_gene_variant,,ENST00000581510,;	G	ENSG00000167525	ENST00000301039	Transcript	synonymous_variant	368	174	58	C	tgT/tgC	.	.	.	-1	PROCA1	HGNC	28600	protein_coding	YES	CCDS11239.1	ENSP00000301039	PRCA1_HUMAN	K7ESJ9_HUMAN	UPI000006D0EE	.	.	.	2/4	.	hmmpanther:PTHR12253:SF14,hmmpanther:PTHR12253,Gene3D:1.20.90.10,Superfamily_domains:SSF48619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGACACAGTC	.	5	ESCA
CCT6B	0	.	GRCh37	17	33255125	33255125	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1535C>T	p.Ala512Val	p.A512V	ENST00000314144	14/14	84	51	32	87	87	0	CCT6B,missense_variant,p.Ala512Val,ENST00000314144,;CCT6B,missense_variant,p.Ala467Val,ENST00000436961,;CCT6B,missense_variant,p.Ala475Val,ENST00000421975,;CCT6B,non_coding_transcript_exon_variant,,ENST00000577307,;	A	ENSG00000132141	ENST00000314144	Transcript	missense_variant	1651	1535	512	A/V	gCc/gTc	.	.	.	-1	CCT6B	HGNC	1621	protein_coding	YES	CCDS32617.1	ENSP00000327191	TCPW_HUMAN	J3KRI6_HUMAN	UPI000013F740	.	deleterious(0.04)	benign(0.368)	14/14	.	hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF58,TIGRFAM_domain:TIGR02347,Pfam_domain:PF00118,Gene3D:1.10.560.10,Superfamily_domains:SSF48592	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGGCAATC	.	5	ESCA
GAS2L2	0	.	GRCh37	17	34074204	34074204	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916C>A	p.Gln306Lys	p.Q306K	ENST00000254466	5/6	65	52	12	68	68	0	GAS2L2,missense_variant,p.Gln290Lys,ENST00000587565,;GAS2L2,missense_variant,p.Gln306Lys,ENST00000254466,;RASL10B,downstream_gene_variant,,ENST00000268864,;	T	ENSG00000132139	ENST00000254466	Transcript	missense_variant	944	916	306	Q/K	Cag/Aag	.	.	.	-1	GAS2L2	HGNC	24846	protein_coding	YES	CCDS11298.1	ENSP00000254466	GA2L2_HUMAN	.	UPI0000061E50	.	deleterious(0)	probably_damaging(0.996)	5/6	.	hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCTGGGTCT	.	5	ESCA
LUC7L3	0	.	GRCh37	17	48829869	48829869	+	3'UTR	SNP	C	C	G	rs189752694	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1847C>G	.	.	ENST00000505658	10/10	43	38	5	53	53	0	LUC7L3,3_prime_UTR_variant,,ENST00000505658,;LUC7L3,3_prime_UTR_variant,,ENST00000503728,;LUC7L3,3_prime_UTR_variant,,ENST00000240304,;LUC7L3,downstream_gene_variant,,ENST00000544170,;LUC7L3,downstream_gene_variant,,ENST00000511974,;LUC7L3,downstream_gene_variant,,ENST00000393227,;LUC7L3,downstream_gene_variant,,ENST00000513969,;LUC7L3,non_coding_transcript_exon_variant,,ENST00000503798,;LUC7L3,downstream_gene_variant,,ENST00000512549,;LUC7L3,downstream_gene_variant,,ENST00000508482,;LUC7L3,downstream_gene_variant,,ENST00000509487,;LUC7L3,downstream_gene_variant,,ENST00000504065,;	G	ENSG00000108848	ENST00000505658	Transcript	3_prime_UTR_variant	3335	.	.	.	.	rs189752694	.	.	1	LUC7L3	HGNC	24309	protein_coding	YES	CCDS11573.1	ENSP00000425092	LC7L3_HUMAN	U3KQT3_HUMAN,D6RHH0_HUMAN	UPI00000736F2	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAATCTTGGA	by1000G	4	ESCA
KCNH6	0	.	GRCh37	17	61613295	61613295	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1367G>A	p.Gly456Asp	p.G456D	ENST00000583023	6/14	81	72	8	69	69	0	KCNH6,missense_variant,p.Gly456Asp,ENST00000580652,;KCNH6,missense_variant,p.Gly456Asp,ENST00000583023,;KCNH6,missense_variant,p.Gly456Asp,ENST00000314672,;KCNH6,intron_variant,,ENST00000581784,;KCNH6,intron_variant,,ENST00000456941,;KCNH6,3_prime_UTR_variant,,ENST00000583465,;	A	ENSG00000173826	ENST00000583023	Transcript	missense_variant	1378	1367	456	G/D	gGc/gAc	.	.	.	1	KCNH6	HGNC	18862	protein_coding	YES	CCDS11638.1	ENSP00000463533	KCNH6_HUMAN	.	UPI000012DCAB	.	deleterious(0)	probably_damaging(0.999)	6/14	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,Gene3D:1.10.287.70,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCGGGCCCCT	.	4	ESCA
TP53	0	.	GRCh37	17	7577058	7577058	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	8/11	349	191	157	457	457	0	TP53,stop_gained,p.Glu294Ter,ENST00000420246,;TP53,stop_gained,p.Glu294Ter,ENST00000269305,;TP53,stop_gained,p.Glu162Ter,ENST00000509690,;TP53,stop_gained,p.Glu294Ter,ENST00000359597,;TP53,stop_gained,p.Glu294Ter,ENST00000445888,;TP53,stop_gained,p.Glu294Ter,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	1070	880	294	E/*	Gag/Tag	TP53_g.13860G>C,TP53_g.13860G>T,TP53_g.13860G>A,TP53_g.13860del,COSM10856,COSM44127,COSM6621,COSM45824,COSM126981,COSM318363,COSM3388169,COSM2744501	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Gene3D:2.60.40.720	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E294*|c.880G>T|50,SITE|p.E294*|c.880G>T|5,SITE|p.E294*|c.880G>T|12,SITE|p.E294*|c.880G>T|5,CODON|p.0?|c.1_1182del1182|6,CODON|p.K291fs*48|c.871_889del19|8,CODON|p.E294E|c.882G>A|4,CODON|p.E294fs*51|c.880delG|9,BUFFER|p.H297Y|c.889C>T|3,BUFFER|p.H296L|c.887A>T|4,BUFFER|p.H296Y|c.886C>T|4,BUFFER|p.P295P|c.885T>C|3,BUFFER|p.P295L|c.884C>T|4,BUFFER|p.E294fs*12|c.879_880insN|3,BUFFER|p.E294K|c.880G>A|3,BUFFER|p.G293G|c.879G>C|3,BUFFER|p.G293G|c.879G>A|4,BUFFER|p.E294fs*51|c.877delG|3,BUFFER|p.G293R|c.877G>A|4,BUFFER|p.G293fs*13|c.876_877insN|3,BUFFER|p.K292T|c.875A>C|4,BUFFER|p.K292R|c.875A>G|5,BUFFER|p.K292*|c.874A>T|5,BUFFER|p.K292*|c.874A>T|3,BUFFER|p.K291N|c.873G>C|3,BUFFER|p.N288fs*13|c.859_872del14|17,BUFFER|p.K291R|c.872A>G|3,BUFFER|p.K291T|c.872A>C|3,BUFFER|p.K291*|c.871A>T|6,BUFFER|p.R290L|c.869G>T|4,BUFFER|p.R290H|c.869G>A|19	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCTCCCCTT	.	5	ESCA
C18orf25	0	.	GRCh37	18	43846721	43846721	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3640A>T	.	.	ENST00000282059	5/5	43	36	7	48	48	0	C18orf25,3_prime_UTR_variant,,ENST00000321319,;C18orf25,3_prime_UTR_variant,,ENST00000282059,;	T	ENSG00000152242	ENST00000282059	Transcript	3_prime_UTR_variant	5226	.	.	.	.	.	.	.	1	C18orf25	HGNC	28172	protein_coding	YES	CCDS42430.1	ENSP00000282059	CR025_HUMAN	Q5BIX2_HUMAN,K7ER64_HUMAN,K7EQH1_HUMAN	UPI000013DCB6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTAATGTTT	.	5	ESCA
SOGA2	0	.	GRCh37	18	8825247	8825247	+	Missense_Mutation	SNP	C	C	T	rs781057852	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3739C>T	p.Arg1247Trp	p.R1247W	ENST00000359865	15/17	64	47	17	48	48	0	SOGA2,missense_variant,p.Arg572Trp,ENST00000518815,;SOGA2,missense_variant,p.Arg1247Trp,ENST00000359865,;SOGA2,missense_variant,p.Arg1206Trp,ENST00000517570,;SOGA2,missense_variant,p.Arg1206Trp,ENST00000400050,;SOGA2,missense_variant,p.Arg572Trp,ENST00000306285,;SOGA2,missense_variant,p.Arg1566Trp,ENST00000306329,;SOGA2,upstream_gene_variant,,ENST00000581670,;	T	ENSG00000168502	ENST00000359865	Transcript	missense_variant	3881	3739	1247	R/W	Cgg/Tgg	rs781057852,COSM1389925	.	.	1	SOGA2	HGNC	29121	protein_coding	YES	CCDS11841.1	ENSP00000352927	SOGA2_HUMAN	J3QLE1_HUMAN	UPI0000456B5B	.	deleterious(0)	probably_damaging(0.975)	15/17	.	hmmpanther:PTHR15742:SF3,hmmpanther:PTHR15742	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCCGGGAC	.	5	ESCA
COPE	0	.	GRCh37	19	19010510	19010510	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.905T>C	p.Leu302Pro	p.L302P	ENST00000262812	10/10	132	120	12	121	121	0	COPE,missense_variant,p.Leu250Pro,ENST00000349893,;COPE,missense_variant,p.Leu325Pro,ENST00000600932,;COPE,missense_variant,p.Leu302Pro,ENST00000262812,;COPE,missense_variant,p.Leu251Pro,ENST00000351079,;CERS1,upstream_gene_variant,,ENST00000429504,;CERS1,upstream_gene_variant,,ENST00000542296,;GDF1,upstream_gene_variant,,ENST00000247005,;CERS1,upstream_gene_variant,,ENST00000427170,;COPE,non_coding_transcript_exon_variant,,ENST00000600528,;COPE,non_coding_transcript_exon_variant,,ENST00000598969,;COPE,non_coding_transcript_exon_variant,,ENST00000595984,;COPE,downstream_gene_variant,,ENST00000593827,;	G	ENSG00000105669	ENST00000262812	Transcript	missense_variant	954	905	302	L/P	cTa/cCa	.	.	.	-1	COPE	HGNC	2234	protein_coding	YES	CCDS12387.1	ENSP00000262812	COPE_HUMAN	.	UPI000013D334	.	tolerated(0.27)	benign(0.432)	10/10	.	hmmpanther:PTHR10805:SF0,hmmpanther:PTHR10805,Pfam_domain:PF04733,PIRSF_domain:PIRSF016478	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGTAGCACC	.	4	ESCA
EID2	0	.	GRCh37	19	40030187	40030187	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.533G>A	p.Arg178His	p.R178H	ENST00000390658	1/1	38	34	4	61	61	0	EID2,missense_variant,p.Arg178His,ENST00000390658,;TDGF1P7,downstream_gene_variant,,ENST00000593394,;	T	ENSG00000176396	ENST00000390658	Transcript	missense_variant	684	533	178	R/H	cGc/cAc	.	.	.	-1	EID2	HGNC	28292	protein_coding	YES	CCDS12540.2	ENSP00000375073	EID2_HUMAN	.	UPI00001E052F	.	deleterious(0.01)	possibly_damaging(0.715)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15556,hmmpanther:PTHR15556:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCTGCGGCGT	.	3	ESCA
IRGC	0	.	GRCh37	19	44223370	44223370	+	Silent	SNP	G	G	A	rs369487767	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660G>A	p.%3D	p.P220P	ENST00000244314	2/2	19	15	4	11	11	0	IRGC,synonymous_variant,p.%3D,ENST00000596627,;IRGC,synonymous_variant,p.%3D,ENST00000244314,;	A	ENSG00000124449	ENST00000244314	Transcript	synonymous_variant	859	660	220	P	ccG/ccA	rs369487767	.	.	1	IRGC	HGNC	28835	protein_coding	YES	CCDS12629.1	ENSP00000244314	IIGP5_HUMAN	J7NNX4_HUMAN	UPI000011DFC0	.	.	.	2/2	.	PROSITE_profiles:PS51716,hmmpanther:PTHR32341:SF7,hmmpanther:PTHR32341,Pfam_domain:PF05049,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGCCGGCCCG	byFrequency|byCluster	4	ESCA
ZNF582	0	.	GRCh37	19	56895810	56895810	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.976T>G	p.Leu326Val	p.L326V	ENST00000301310	5/5	31	28	3	52	52	0	ZNF582,missense_variant,p.Leu326Val,ENST00000586929,;ZNF582,missense_variant,p.Leu326Val,ENST00000301310,;ZNF582,intron_variant,,ENST00000589143,;AC006116.12,upstream_gene_variant,,ENST00000589671,;ZNF542,downstream_gene_variant,,ENST00000467807,;ZNF542,downstream_gene_variant,,ENST00000495307,;ZNF542,downstream_gene_variant,,ENST00000490123,;ZNF582,downstream_gene_variant,,ENST00000593145,;ZNF582,downstream_gene_variant,,ENST00000587778,;SLC25A36P1,upstream_gene_variant,,ENST00000590111,;	C	ENSG00000018869	ENST00000301310	Transcript	missense_variant	1135	976	326	L/V	Ttg/Gtg	.	.	.	-1	ZNF582	HGNC	26421	protein_coding	YES	CCDS33121.1	ENSP00000301310	ZN582_HUMAN	B4DQZ9_HUMAN	UPI000006D278	.	deleterious(0.01)	probably_damaging(0.988)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF115,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCAACTGAG	.	2	ESCA
C3	0	.	GRCh37	19	6693004	6693004	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3321G>A	p.%3D	p.L1107L	ENST00000245907	26/41	46	33	12	70	70	0	C3,synonymous_variant,p.%3D,ENST00000245907,;C3,upstream_gene_variant,,ENST00000601008,;C3,non_coding_transcript_exon_variant,,ENST00000598805,;C3,downstream_gene_variant,,ENST00000594005,;C3,downstream_gene_variant,,ENST00000602053,;	T	ENSG00000125730	ENST00000245907	Transcript	synonymous_variant	3414	3321	1107	L	ctG/ctA	.	.	.	-1	C3	HGNC	1318	protein_coding	YES	CCDS32883.1	ENSP00000245907	CO3_HUMAN	Q6LDJ0_HUMAN,M0R1Q1_HUMAN	UPI000013EC9B	.	.	.	26/41	.	hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF81,Pfam_domain:PF07678,Gene3D:1.50.10.20,Superfamily_domains:SSF48239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATCAGCCA	.	5	ESCA
HIST2H2BF	0	.	GRCh37	1	149783891	149783891	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13T>C	.	.	ENST00000545683	1/2	79	62	17	91	91	0	HIST2H2BF,5_prime_UTR_variant,,ENST00000545683,;HIST2H2BF,5_prime_UTR_variant,,ENST00000369167,;HIST2H2BF,5_prime_UTR_variant,,ENST00000427880,;HIST2H3D,downstream_gene_variant,,ENST00000331491,;RP11-196G18.21,upstream_gene_variant,,ENST00000420462,;HIST2H2BF,non_coding_transcript_exon_variant,,ENST00000469483,;	G	ENSG00000203814	ENST00000545683	Transcript	5_prime_UTR_variant	38	.	.	.	.	.	.	.	-1	HIST2H2BF	HGNC	24700	protein_coding	YES	CCDS53359.1	ENSP00000445831	H2B2F_HUMAN	.	UPI00017A7443	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAAAAAAGAG	.	5	ESCA
HIST2H2BE	0	.	GRCh37	1	149858000	149858000	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.191A>G	p.Asn64Ser	p.N64S	ENST00000369155	1/1	190	182	8	142	142	0	HIST2H2BE,missense_variant,p.Asn64Ser,ENST00000369155,;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,;HIST2H2AC,upstream_gene_variant,,ENST00000331380,;	C	ENSG00000184678	ENST00000369155	Transcript	missense_variant	233	191	64	N/S	aAc/aGc	.	.	.	-1	HIST2H2BE	HGNC	4760	protein_coding	YES	CCDS936.1	ENSP00000358151	H2B2E_HUMAN	.	UPI0000000C6F	.	deleterious_low_confidence(0)	probably_damaging(0.999)	1/1	.	hmmpanther:PTHR23428,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAGTTCATG	.	2	ESCA
KIAA0907	0	.	GRCh37	1	155891416	155891416	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1016A>G	p.Tyr339Cys	p.Y339C	ENST00000368321	10/14	43	33	10	50	50	0	KIAA0907,missense_variant,p.Tyr339Cys,ENST00000368320,;KIAA0907,missense_variant,p.Tyr339Cys,ENST00000368321,;KIAA0907,intron_variant,,ENST00000368319,;SCARNA4,downstream_gene_variant,,ENST00000516999,;SNORA42,upstream_gene_variant,,ENST00000384744,;KIAA0907,non_coding_transcript_exon_variant,,ENST00000478002,;KIAA0907,intron_variant,,ENST00000482337,;KIAA0907,intron_variant,,ENST00000483237,;KIAA0907,downstream_gene_variant,,ENST00000466713,;KIAA0907,upstream_gene_variant,,ENST00000465953,;KIAA0907,upstream_gene_variant,,ENST00000466520,;	C	ENSG00000132680	ENST00000368321	Transcript	missense_variant	1040	1016	339	Y/C	tAt/tGt	.	.	.	-1	KIAA0907	HGNC	29145	protein_coding	YES	CCDS30885.1	ENSP00000357304	K0907_HUMAN	.	UPI00001A36E0	.	deleterious(0.03)	possibly_damaging(0.8)	10/14	.	hmmpanther:PTHR15744,hmmpanther:PTHR15744:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTATAGCCT	.	5	ESCA
DCAF8	0	.	GRCh37	1	160186913	160186913	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*469T>C	.	.	ENST00000368073	14/14	19	13	6	20	20	0	DCAF8,3_prime_UTR_variant,,ENST00000326837,;DCAF8,3_prime_UTR_variant,,ENST00000368073,;DCAF8,3_prime_UTR_variant,,ENST00000368074,;DCAF8,intron_variant,,ENST00000477163,;PEA15,downstream_gene_variant,,ENST00000360472,;PEA15,downstream_gene_variant,,ENST00000368077,;DCAF8,downstream_gene_variant,,ENST00000473382,;DCAF8,downstream_gene_variant,,ENST00000556710,;DCAF8,downstream_gene_variant,,ENST00000608310,;PEA15,downstream_gene_variant,,ENST00000368076,;PEA15,downstream_gene_variant,,ENST00000488858,;DCAF8,downstream_gene_variant,,ENST00000497354,;DCAF8,downstream_gene_variant,,ENST00000476033,;DCAF8,downstream_gene_variant,,ENST00000490368,;DCAF8,downstream_gene_variant,,ENST00000466253,;DCAF8,downstream_gene_variant,,ENST00000461888,;DCAF8,downstream_gene_variant,,ENST00000481831,;	G	ENSG00000132716	ENST00000368073	Transcript	3_prime_UTR_variant	2698	.	.	.	.	.	.	.	-1	DCAF8	HGNC	24891	protein_coding	YES	CCDS1200.1	ENSP00000357052	DCAF8_HUMAN	Q5TAQ8_HUMAN,Q5TAQ7_HUMAN,Q5TAQ6_HUMAN,Q5TAQ5_HUMAN,B7Z8C9_HUMAN	UPI0000141A39	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAAACTTTT	.	5	ESCA
C1orf192	0	.	GRCh37	1	161335367	161335368	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296dupA	p.Asn99LysfsTer3	p.N99Kfs*3	ENST00000367974	4/5	91	83	8	80	80	0	C1orf192,frameshift_variant,p.Asn99LysfsTer3,ENST00000367974,;SDHC,downstream_gene_variant,,ENST00000432287,;SDHC,downstream_gene_variant,,ENST00000392169,;SDHC,downstream_gene_variant,,ENST00000367975,;SDHC,downstream_gene_variant,,ENST00000513009,;SDHC,downstream_gene_variant,,ENST00000342751,;RP11-122G18.5,upstream_gene_variant,,ENST00000437833,;SDHC,downstream_gene_variant,,ENST00000470743,;SDHC,downstream_gene_variant,,ENST00000513700,;SDHC,downstream_gene_variant,,ENST00000504963,;	T	ENSG00000188931	ENST00000367974	Transcript	frameshift_variant	302-303	296-297	99	N/KX	aat/aaAt	.	.	.	-1	C1orf192	HGNC	32325	protein_coding	YES	CCDS30921.1	ENSP00000356951	CA192_HUMAN	.	UPI0000204C40	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCAGGATTTTT	.	2	ESCA
PLXNA2	0	.	GRCh37	1	208200421	208200421	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*167G>A	.	.	ENST00000367033	32/32	46	42	3	46	46	0	PLXNA2,3_prime_UTR_variant,,ENST00000367033,;PLXNA2,non_coding_transcript_exon_variant,,ENST00000483048,;PLXNA2,downstream_gene_variant,,ENST00000480053,;	T	ENSG00000076356	ENST00000367033	Transcript	3_prime_UTR_variant	6610	.	.	.	.	.	.	.	-1	PLXNA2	HGNC	9100	protein_coding	YES	CCDS31013.1	ENSP00000356000	PLXA2_HUMAN	.	UPI000022B239	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATGACGAAAC	.	2	ESCA
OBSCN	0	.	GRCh37	1	228467068	228467068	+	Missense_Mutation	SNP	G	G	A	rs547478529	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8606G>A	p.Arg2869Gln	p.R2869Q	ENST00000570156	32/116	178	165	13	116	116	0	OBSCN,missense_variant,p.Arg2440Gln,ENST00000284548,;OBSCN,missense_variant,p.Arg1287Gln,ENST00000359599,;OBSCN,missense_variant,p.Arg288Gln,ENST00000366706,;OBSCN,missense_variant,p.Arg2869Gln,ENST00000570156,;OBSCN,missense_variant,p.Arg2440Gln,ENST00000422127,;OBSCN,5_prime_UTR_variant,,ENST00000366707,;OBSCN,5_prime_UTR_variant,,ENST00000366709,;OBSCN,upstream_gene_variant,,ENST00000483539,;RP5-1139B12.2,upstream_gene_variant,,ENST00000602517,;RP5-1139B12.3,upstream_gene_variant,,ENST00000602529,;RP5-1139B12.3,upstream_gene_variant,,ENST00000602947,;OBSCN,upstream_gene_variant,,ENST00000366704,;	A	ENSG00000154358	ENST00000570156	Transcript	missense_variant	8680	8606	2869	R/Q	cGg/cAg	rs547478529	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	probably_damaging(0.964)	32/116	.	hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGGCGGACCT	by1000G	2	ESCA
ELOVL1	0	.	GRCh37	1	43830658	43830658	+	Missense_Mutation	SNP	T	T	A	rs112685758	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259A>T	p.Ser87Cys	p.S87C	ENST00000372458	4/8	25	16	9	26	26	0	ELOVL1,missense_variant,p.Ser87Cys,ENST00000372458,;ELOVL1,intron_variant,,ENST00000413844,;CDC20,downstream_gene_variant,,ENST00000310955,;CDC20,downstream_gene_variant,,ENST00000372462,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000468865,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000482302,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000465321,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000478481,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000496932,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000497050,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000487209,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000470769,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000479439,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000470968,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000479686,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000464204,;ELOVL1,non_coding_transcript_exon_variant,,ENST00000497569,;CDC20,downstream_gene_variant,,ENST00000482046,;CDC20,downstream_gene_variant,,ENST00000478882,;	A	ENSG00000066322	ENST00000372458	Transcript	missense_variant	377	259	87	S/C	Agc/Tgc	rs112685758	.	.	-1	ELOVL1	HGNC	14418	protein_coding	YES	CCDS485.1	ENSP00000361536	ELOV1_HUMAN	.	UPI00001196CE	.	tolerated(0.14)	possibly_damaging(0.726)	4/8	.	Pfam_domain:PF01151,hmmpanther:PTHR11157,hmmpanther:PTHR11157:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGCTCAGCC	.	5	ESCA
RP11-466L17.1	0	.	GRCh37	1	56197233	56197233	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.621T>C	.	.	ENST00000422374	3/3	23	16	7	11	11	0	RP11-466L17.1,non_coding_transcript_exon_variant,,ENST00000422374,;	C	ENSG00000234810	ENST00000422374	Transcript	non_coding_transcript_exon_variant	621	.	.	.	.	.	.	.	1	RP11-466L17.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTTTTTGC	.	5	ESCA
ZNF341	0	.	GRCh37	20	32377396	32377396	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2014+2T>A	.	p.X672_splice	ENST00000342427	.	55	31	24	48	48	0	ZNF341,splice_donor_variant,,ENST00000375200,;ZNF341,splice_donor_variant,,ENST00000342427,;RP4-553F4.6,intron_variant,,ENST00000439444,;RP4-553F4.6,intron_variant,,ENST00000443171,;RP4-553F4.6,intron_variant,,ENST00000423074,;ZNF341,splice_donor_variant,,ENST00000497876,;ZNF341,splice_donor_variant,,ENST00000483118,;ZNF341,splice_donor_variant,,ENST00000493497,;	A	ENSG00000131061	ENST00000342427	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	ZNF341	HGNC	15992	protein_coding	YES	CCDS13227.1	ENSP00000344308	ZN341_HUMAN	.	UPI000022B43D	.	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGGTAAGTG	.	5	ESCA
KCNQ2	0	.	GRCh37	20	62045497	62045497	+	Silent	SNP	G	G	A	rs528539094	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1575C>T	p.%3D	p.C525C	ENST00000359125	14/17	122	61	60	87	87	0	KCNQ2,synonymous_variant,p.%3D,ENST00000359689,;KCNQ2,synonymous_variant,p.%3D,ENST00000359125,;KCNQ2,synonymous_variant,p.%3D,ENST00000354587,;KCNQ2,synonymous_variant,p.%3D,ENST00000370224,;KCNQ2,synonymous_variant,p.%3D,ENST00000360480,;KCNQ2,synonymous_variant,p.%3D,ENST00000357249,;KCNQ2,synonymous_variant,p.%3D,ENST00000344462,;	A	ENSG00000075043	ENST00000359125	Transcript	synonymous_variant	1750	1575	525	C	tgC/tgT	rs528539094	.	.	-1	KCNQ2	HGNC	6296	protein_coding	YES	CCDS13520.1	ENSP00000352035	KCNQ2_HUMAN	.	UPI00001279ED	.	.	.	14/17	.	Pfam_domain:PF03520	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTCGCAGGG	by1000G	5	ESCA
RIPK4	0	.	GRCh37	21	43171399	43171399	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000332512	3/8	53	29	24	52	52	0	RIPK4,missense_variant,p.Asp161Tyr,ENST00000352483,;RIPK4,missense_variant,p.Asp98Tyr,ENST00000542057,;RIPK4,missense_variant,p.Asp98Tyr,ENST00000544709,;RIPK4,missense_variant,p.Asp161Tyr,ENST00000332512,;	A	ENSG00000183421	ENST00000332512	Transcript	missense_variant	546	481	161	D/Y	Gat/Tat	.	.	.	-1	RIPK4	HGNC	496	protein_coding	YES	CCDS13675.1	ENSP00000332454	RIPK4_HUMAN	B7ZAU7_HUMAN	UPI000002A3C9	.	deleterious(0)	probably_damaging(0.999)	3/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24198,hmmpanther:PTHR24198:SF18,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCAGAAA	.	5	ESCA
DGCR2	0	.	GRCh37	22	19048340	19048340	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.625+2375A>T	.	.	ENST00000263196	.	32	29	3	36	36	0	DGCR2,missense_variant,p.Arg249Trp,ENST00000545799,;DGCR2,intron_variant,,ENST00000263196,;DGCR2,intron_variant,,ENST00000537045,;DGCR2,intron_variant,,ENST00000608548,;DGCR2,intron_variant,,ENST00000473832,;DGCR2,5_prime_UTR_variant,,ENST00000389262,;DGCR2,upstream_gene_variant,,ENST00000467659,;AC004461.4,downstream_gene_variant,,ENST00000412461,;	A	ENSG00000070413	ENST00000263196	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DGCR2	HGNC	2845	protein_coding	YES	CCDS33598.1	ENSP00000263196	IDD_HUMAN	B7Z8B7_HUMAN,B7Z3C4_HUMAN	UPI0000001613	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCCTGGAGA	.	2	ESCA
IGLV4-60	0	.	GRCh37	22	22516622	22516622	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31C>T	p.Pro11Ser	p.P11S	ENST00000390284	1/2	31	19	12	25	25	0	IGLV4-60,missense_variant,p.Pro11Ser,ENST00000390284,;LL22NC03-30E12.11,downstream_gene_variant,,ENST00000440562,;	T	ENSG00000211639	ENST00000390284	Transcript	missense_variant	31	31	11	P/S	Cct/Tct	.	.	.	1	IGLV4-60	HGNC	5920	IG_V_gene	YES	.	ENSP00000374819	.	Q5NV79_HUMAN	UPI0001611017	.	tolerated(0.94)	benign(0.001)	1/2	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23267:SF9,hmmpanther:PTHR23267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTCCCTCTC	.	5	ESCA
CELSR1	0	.	GRCh37	22	46793652	46793652	+	Missense_Mutation	SNP	C	C	T	rs141922879	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5620G>A	p.Asp1874Asn	p.D1874N	ENST00000262738	12/35	88	71	17	106	106	0	CELSR1,missense_variant,p.Asp1874Asn,ENST00000262738,;	T	ENSG00000075275	ENST00000262738	Transcript	missense_variant	5620	5620	1874	D/N	Gac/Aac	rs141922879,COSM726816	.	.	-1	CELSR1	HGNC	1850	protein_coding	YES	CCDS14076.1	ENSP00000262738	CELR1_HUMAN	Q8NDT0_HUMAN	UPI0000040648	.	tolerated(0.65)	benign(0.008)	12/35	.	Superfamily_domains:SSF57196,SMART_domains:SM00179,Gene3D:2.60.120.200,hmmpanther:PTHR24026,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	T:0.0009	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTCGTCCA	byCluster	5	ESCA
NEB	0	.	GRCh37	2	152471049	152471049	+	Missense_Mutation	SNP	C	C	T	rs747898598	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11342G>A	p.Arg3781Gln	p.R3781Q	ENST00000397345	77/182	110	96	14	100	100	0	NEB,missense_variant,p.Arg3781Gln,ENST00000603639,;NEB,missense_variant,p.Arg3538Gln,ENST00000172853,;NEB,missense_variant,p.Arg3781Gln,ENST00000427231,;NEB,missense_variant,p.Arg3781Gln,ENST00000397345,;NEB,missense_variant,p.Arg3781Gln,ENST00000604864,;NEB,missense_variant,p.Arg3538Gln,ENST00000409198,;NEB,downstream_gene_variant,,ENST00000486320,;	T	ENSG00000183091	ENST00000397345	Transcript	missense_variant	11545	11342	3781	R/Q	cGg/cAg	rs747898598,COSM50690,COSM1400029,COSM1400026,COSM1400028,COSM1400027,COSM1400025	.	.	-1	NEB	HGNC	7720	protein_coding	YES	CCDS54407.1	ENSP00000380505	.	H7C2D0_HUMAN,F8WCL5_HUMAN	UPI0002065BA0	.	.	benign(0.106)	77/182	.	PROSITE_profiles:PS51216,hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R3538W|c.10612C>T|3,BUFFER|p.R3781W|c.11341C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TGTTCCGGGCC	byFrequency	4	ESCA
TFPI	0	.	GRCh37	2	188348894	188348894	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.585T>A	p.Asn195Lys	p.N195K	ENST00000233156	6/8	30	25	4	31	31	0	TFPI,missense_variant,p.Asn195Lys,ENST00000339091,;TFPI,missense_variant,p.Asn195Lys,ENST00000426055,;TFPI,missense_variant,p.Asn182Lys,ENST00000435414,;TFPI,missense_variant,p.Asn195Lys,ENST00000409676,;TFPI,missense_variant,p.Asn195Lys,ENST00000392365,;TFPI,missense_variant,p.Asn195Lys,ENST00000233156,;AC007319.1,intron_variant,,ENST00000453517,;AC007319.1,intron_variant,,ENST00000412276,;TFPI,non_coding_transcript_exon_variant,,ENST00000481389,;TFPI,non_coding_transcript_exon_variant,,ENST00000481132,;	T	ENSG00000003436	ENST00000233156	Transcript	missense_variant	880	585	195	N/K	aaT/aaA	.	.	.	-1	TFPI	HGNC	11760	protein_coding	YES	CCDS2294.1	ENSP00000233156	TFPI1_HUMAN	C9JT76_HUMAN,C9JQ14_HUMAN,C9JP39_HUMAN,C9JBB3_HUMAN,C9J103_HUMAN	UPI0000136C8F	.	deleterious(0.02)	benign(0.011)	6/8	.	hmmpanther:PTHR10083:SF204,hmmpanther:PTHR10083,PIRSF_domain:PIRSF001620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGTTATTCAC	.	4	ESCA
SH3YL1	0	.	GRCh37	2	262569	262569	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1+1415A>T	.	.	ENST00000356150	.	26	19	6	38	38	0	SH3YL1,intron_variant,,ENST00000415368,;SH3YL1,intron_variant,,ENST00000402632,;SH3YL1,intron_variant,,ENST00000454318,;SH3YL1,intron_variant,,ENST00000405430,;SH3YL1,intron_variant,,ENST00000356150,;SH3YL1,intron_variant,,ENST00000403712,;SH3YL1,intron_variant,,ENST00000403658,;ACP1,upstream_gene_variant,,ENST00000439645,;ACP1,upstream_gene_variant,,ENST00000272065,;ACP1,upstream_gene_variant,,ENST00000407983,;SH3YL1,upstream_gene_variant,,ENST00000403657,;ACP1,upstream_gene_variant,,ENST00000405233,;ACP1,upstream_gene_variant,,ENST00000272067,;SH3YL1,non_coding_transcript_exon_variant,,ENST00000468321,;SH3YL1,intron_variant,,ENST00000477707,;SH3YL1,intron_variant,,ENST00000475027,;SH3YL1,intron_variant,,ENST00000473104,;SH3YL1,intron_variant,,ENST00000488979,;SH3YL1,intron_variant,,ENST00000462719,;SH3YL1,intron_variant,,ENST00000472861,;SH3YL1,intron_variant,,ENST00000488044,;SH3YL1,intron_variant,,ENST00000465733,;SH3YL1,intron_variant,,ENST00000463865,;ACP1,upstream_gene_variant,,ENST00000484125,;ACP1,upstream_gene_variant,,ENST00000484464,;SH3YL1,upstream_gene_variant,,ENST00000605370,;SH3YL1,intron_variant,,ENST00000471948,;ACP1,upstream_gene_variant,,ENST00000453390,;ACP1,upstream_gene_variant,,ENST00000442386,;SH3YL1,upstream_gene_variant,,ENST00000479739,;ACP1,upstream_gene_variant,,ENST00000480874,;ACP1,upstream_gene_variant,,ENST00000405364,;ACP1,upstream_gene_variant,,ENST00000413140,;	A	ENSG00000035115	ENST00000356150	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SH3YL1	HGNC	29546	protein_coding	YES	CCDS42646.2	ENSP00000348471	SH3Y1_HUMAN	C9J4Z8_HUMAN	UPI0000072FAE	.	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTTAAAAA	.	5	ESCA
ZFP36L2	0	.	GRCh37	2	43452439	43452440	+	Frame_Shift_Ins	INS	-	-	CA	.	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502_503dupTG	p.Lys169AlafsTer19	p.K169Afs*19	ENST00000282388	2/2	107	96	11	69	69	0	ZFP36L2,frameshift_variant,p.Lys169AlafsTer19,ENST00000282388,;THADA,intron_variant,,ENST00000330266,;AC010883.5,upstream_gene_variant,,ENST00000423354,;	CA	ENSG00000152518	ENST00000282388	Transcript	frameshift_variant	797-798	503-504	168	C/CX	tgc/tgTGc	COSM1565568	.	.	-1	ZFP36L2	HGNC	1108	protein_coding	YES	CCDS1811.1	ENSP00000282388	TISD_HUMAN	.	UPI000013DCDA	.	.	.	2/2	.	PROSITE_profiles:PS50103,hmmpanther:PTHR12547,hmmpanther:PTHR12547:SF58,Pfam_domain:PF00642,Gene3D:1m9oA00,SMART_domains:SM00356,Superfamily_domains:SSF90229	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	insertion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TACTTGCACGT	.	3	ESCA
RP11-702L6.4	0	.	GRCh37	3	109136698	109136698	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.337C>T	.	.	ENST00000497996	2/5	50	46	4	47	47	0	RP11-702L6.4,non_coding_transcript_exon_variant,,ENST00000497996,;RP11-702L6.4,non_coding_transcript_exon_variant,,ENST00000489670,;	T	ENSG00000228980	ENST00000497996	Transcript	non_coding_transcript_exon_variant	337	.	.	.	.	.	.	.	1	RP11-702L6.4	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATTCAAGTC	.	2	ESCA
FXR1	0	.	GRCh37	3	180633301	180633301	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51+2777A>G	.	.	ENST00000357559	.	179	165	14	155	155	0	FXR1,5_prime_UTR_variant,,ENST00000484042,;FXR1,5_prime_UTR_variant,,ENST00000480918,;FXR1,intron_variant,,ENST00000491674,;FXR1,intron_variant,,ENST00000357559,;FXR1,intron_variant,,ENST00000491062,;FXR1,intron_variant,,ENST00000445140,;FXR1,intron_variant,,ENST00000484958,;FXR1,intron_variant,,ENST00000305586,;FXR1,intron_variant,,ENST00000468861,;FXR1,intron_variant,,ENST00000484790,;FXR1,intron_variant,,ENST00000465551,;FXR1,intron_variant,,ENST00000469882,;FXR1,intron_variant,,ENST00000479176,;FXR1,intron_variant,,ENST00000475315,;FXR1,intron_variant,,ENST00000472339,;	G	ENSG00000114416	ENST00000357559	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	FXR1	HGNC	4023	protein_coding	YES	CCDS3238.1	ENSP00000350170	FXR1_HUMAN	C9JZE0_HUMAN,C9JY20_HUMAN,C9J5B4_HUMAN,C9IZ22_HUMAN	UPI000013EA6E	.	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATAATACAT	.	2	ESCA
CHRD	0	.	GRCh37	3	184106703	184106703	+	Missense_Mutation	SNP	G	G	A	rs372347094	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2732G>A	p.Arg911Gln	p.R911Q	ENST00000204604	22/23	69	40	28	48	48	0	CHRD,missense_variant,p.Arg911Gln,ENST00000204604,;CHRD,missense_variant,p.Arg911Gln,ENST00000450923,;CHRD,missense_variant,p.Arg871Gln,ENST00000348986,;CHRD,missense_variant,p.Arg453Gln,ENST00000545352,;EIF2B5,intron_variant,,ENST00000444495,;CHRD,3_prime_UTR_variant,,ENST00000448472,;CHRD,3_prime_UTR_variant,,ENST00000420973,;CHRD,non_coding_transcript_exon_variant,,ENST00000460627,;CHRD,non_coding_transcript_exon_variant,,ENST00000470150,;CHRD,downstream_gene_variant,,ENST00000464833,;	A	ENSG00000090539	ENST00000204604	Transcript	missense_variant	2978	2732	911	R/Q	cGg/cAg	rs372347094,COSM730196	.	.	1	CHRD	HGNC	1949	protein_coding	YES	CCDS3266.1	ENSP00000204604	CHRD_HUMAN	Q8N2W7_HUMAN	UPI000013C64D	.	deleterious(0.02)	probably_damaging(0.996)	22/23	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF263,PIRSF_domain:PIRSF002496,SMART_domains:SM00214,Superfamily_domains:SSF57603	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGCGGGATG	byCluster	5	ESCA
MUC4	0	.	GRCh37	3	195505314	195505314	+	Missense_Mutation	SNP	G	G	A	rs142178516	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12803C>T	p.Pro4268Leu	p.P4268L	ENST00000463781	3/25	106	82	23	45	45	0	MUC4,missense_variant,p.Pro4268Leu,ENST00000463781,;MUC4,missense_variant,p.Pro32Leu,ENST00000346145,;MUC4,missense_variant,p.Pro4268Leu,ENST00000475231,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.Pro12Leu,ENST00000339251,;MUC4,missense_variant,p.Pro12Leu,ENST00000448861,;MUC4,missense_variant,p.Pro4268Leu,ENST00000470451,;MUC4,missense_variant,p.Pro12Leu,ENST00000308466,;MUC4,missense_variant,p.Pro12Leu,ENST00000415455,;MUC4,missense_variant,p.Pro4268Leu,ENST00000477086,;MUC4,missense_variant,p.Pro12Leu,ENST00000392407,;MUC4,missense_variant,p.Pro4268Leu,ENST00000466475,;MUC4,missense_variant,p.Pro4268Leu,ENST00000478156,;MUC4,missense_variant,p.Pro4268Leu,ENST00000479406,;MUC4,missense_variant,p.Pro4268Leu,ENST00000477756,;MUC4,missense_variant,p.Pro4268Leu,ENST00000462323,;MUC4,missense_variant,p.Pro4268Leu,ENST00000480843,;	A	ENSG00000145113	ENST00000463781	Transcript	missense_variant	13263	12803	4268	P/L	cCg/cTg	rs142178516	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	possibly_damaging(0.843)	3/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGACGGTGTT	byCluster	5	ESCA
TMF1	0	.	GRCh37	3	69088134	69088134	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1854G>A	p.%3D	p.E618E	ENST00000398559	7/17	19	16	3	33	33	0	TMF1,synonymous_variant,p.%3D,ENST00000398559,;TMF1,synonymous_variant,p.%3D,ENST00000543976,;CTD-2013N24.2,intron_variant,,ENST00000596523,;CTD-2013N24.2,intron_variant,,ENST00000597950,;CTD-2013N24.2,intron_variant,,ENST00000596732,;CTD-2013N24.2,intron_variant,,ENST00000598783,;CTD-2013N24.2,intron_variant,,ENST00000601735,;CTD-2013N24.2,intron_variant,,ENST00000595925,;CTD-2013N24.2,intron_variant,,ENST00000482368,;CTD-2013N24.2,intron_variant,,ENST00000596274,;CTD-2013N24.2,downstream_gene_variant,,ENST00000601511,;CTD-2013N24.2,downstream_gene_variant,,ENST00000599467,;TMF1,synonymous_variant,p.%3D,ENST00000488010,;TMF1,downstream_gene_variant,,ENST00000477872,;	T	ENSG00000144747	ENST00000398559	Transcript	synonymous_variant	2071	1854	618	E	gaG/gaA	.	.	.	-1	TMF1	HGNC	11870	protein_coding	YES	CCDS43105.1	ENSP00000381567	TMF1_HUMAN	.	UPI000013D9A7	.	.	.	7/17	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF285	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTTTCTCAAC	.	4	ESCA
ENPEP	0	.	GRCh37	4	111397731	111397731	+	Missense_Mutation	SNP	C	C	T	rs200528408	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161C>T	p.Ala54Val	p.A54V	ENST00000265162	1/20	26	20	6	25	25	0	ENPEP,missense_variant,p.Ala54Val,ENST00000265162,;ENPEP,intron_variant,,ENST00000510961,;	T	ENSG00000138792	ENST00000265162	Transcript	missense_variant	503	161	54	A/V	gCg/gTg	rs200528408	.	.	1	ENPEP	HGNC	3355	protein_coding	YES	CCDS3691.1	ENSP00000265162	AMPE_HUMAN	.	UPI000013D5C6	.	tolerated(0.16)	benign(0.003)	1/20	.	hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF165	T:0.0004	T:0	T:0	.	T:0	T:0.002	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGCGCCAG	byFrequency|byCluster|by1000G	5	ESCA
CTBP1	0	.	GRCh37	4	1208163	1208163	+	Silent	SNP	C	C	T	rs766411525	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.861G>A	p.%3D	p.A287A	ENST00000290921	6/9	230	215	15	203	203	0	CTBP1,synonymous_variant,p.%3D,ENST00000503594,;CTBP1,synonymous_variant,p.%3D,ENST00000290921,;CTBP1,synonymous_variant,p.%3D,ENST00000504092,;CTBP1,synonymous_variant,p.%3D,ENST00000382952,;CTBP1,downstream_gene_variant,,ENST00000506180,;CTBP1,downstream_gene_variant,,ENST00000505826,;CTBP1,downstream_gene_variant,,ENST00000514669,;CTBP1,synonymous_variant,p.%3D,ENST00000510739,;CTBP1,non_coding_transcript_exon_variant,,ENST00000511907,;CTBP1,upstream_gene_variant,,ENST00000514596,;CTBP1,upstream_gene_variant,,ENST00000382950,;	T	ENSG00000159692	ENST00000290921	Transcript	synonymous_variant	1043	861	287	A	gcG/gcA	rs766411525	.	.	-1	CTBP1	HGNC	2494	protein_coding	YES	CCDS3348.1	ENSP00000290921	CTBP1_HUMAN	.	UPI0000128637	.	.	.	6/9	.	hmmpanther:PTHR10996,hmmpanther:PTHR10996:SF128,Pfam_domain:PF00389,Pfam_domain:PF02826,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGCCGCGCC	byFrequency	2	ESCA
GPM6A	0	.	GRCh37	4	176555905	176555905	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*151G>A	.	.	ENST00000280187	8/8	54	47	7	73	73	0	GPM6A,3_prime_UTR_variant,,ENST00000280187,;GPM6A,3_prime_UTR_variant,,ENST00000515090,;GPM6A,3_prime_UTR_variant,,ENST00000506894,;GPM6A,3_prime_UTR_variant,,ENST00000393658,;GPM6A,non_coding_transcript_exon_variant,,ENST00000506219,;GPM6A,downstream_gene_variant,,ENST00000508323,;GPM6A,non_coding_transcript_exon_variant,,ENST00000507080,;	T	ENSG00000150625	ENST00000280187	Transcript	3_prime_UTR_variant	1034	.	.	.	.	.	.	.	-1	GPM6A	HGNC	4460	protein_coding	YES	CCDS3824.1	ENSP00000280187	GPM6A_HUMAN	Q49AH3_HUMAN,D6RIF4_HUMAN,D6RFZ3_HUMAN,D6RFY0_HUMAN,D6REJ8_HUMAN,D6RD95_HUMAN,D6RBM6_HUMAN,D6RBH3_HUMAN,D6RAE4_HUMAN,D6R9T7_HUMAN	UPI000012EAE1	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTAAACAACAA	.	4	ESCA
CLDN22	0	.	GRCh37	4	184239608	184239608	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1101G>A	.	.	ENST00000323319	1/1	54	51	3	64	64	0	CLDN22,3_prime_UTR_variant,,ENST00000323319,;WWC2,3_prime_UTR_variant,,ENST00000403733,;WWC2,downstream_gene_variant,,ENST00000504005,;WWC2,downstream_gene_variant,,ENST00000508747,;WWC2,downstream_gene_variant,,ENST00000513834,;CLDN24,downstream_gene_variant,,ENST00000514470,;WWC2,downstream_gene_variant,,ENST00000448232,;CLDN24,downstream_gene_variant,,ENST00000541814,;WWC2,3_prime_UTR_variant,,ENST00000427431,;WWC2,downstream_gene_variant,,ENST00000438543,;	T	ENSG00000177300	ENST00000323319	Transcript	3_prime_UTR_variant	2320	.	.	.	.	.	.	.	-1	CLDN22	HGNC	2044	protein_coding	YES	CCDS43286.1	ENSP00000318113	CLD22_HUMAN	.	UPI00001D76D6	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTTCCATGT	.	2	ESCA
WHSC1	0	.	GRCh37	4	1945980	1945980	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1881+4475T>C	.	.	ENST00000382895	.	40	36	4	52	52	0	WHSC1,3_prime_UTR_variant,,ENST00000398261,;WHSC1,3_prime_UTR_variant,,ENST00000503128,;WHSC1,intron_variant,,ENST00000508803,;WHSC1,intron_variant,,ENST00000382892,;WHSC1,intron_variant,,ENST00000382895,;WHSC1,intron_variant,,ENST00000382891,;WHSC1,intron_variant,,ENST00000514329,;WHSC1,downstream_gene_variant,,ENST00000420906,;WHSC1,downstream_gene_variant,,ENST00000514045,;WHSC1,intron_variant,,ENST00000513726,;WHSC1,intron_variant,,ENST00000502425,;WHSC1,intron_variant,,ENST00000482415,;WHSC1,intron_variant,,ENST00000511904,;WHSC1,intron_variant,,ENST00000353275,;WHSC1,intron_variant,,ENST00000312087,;	C	ENSG00000109685	ENST00000382895	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	WHSC1	HGNC	12766	protein_coding	YES	CCDS33940.1	ENSP00000372351	NSD2_HUMAN	D6RIS1_HUMAN,D6RFE7_HUMAN,D6R9V2_HUMAN	UPI0000073F57	.	.	.	.	11/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CCATCTCCTGG	.	3	ESCA
EPHA5	0	.	GRCh37	4	66213881	66213881	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2549T>G	p.Ile850Arg	p.I850R	ENST00000273854	15/18	36	30	6	51	51	0	EPHA5,missense_variant,p.Ile850Arg,ENST00000273854,;EPHA5,missense_variant,p.Ile851Arg,ENST00000511294,;EPHA5,missense_variant,p.Ile687Arg,ENST00000432638,;EPHA5,missense_variant,p.Ile828Arg,ENST00000354839,;	C	ENSG00000145242	ENST00000273854	Transcript	missense_variant	3150	2549	850	I/R	aTa/aGa	.	.	.	-1	EPHA5	HGNC	3389	protein_coding	YES	CCDS3513.1	ENSP00000273854	EPHA5_HUMAN	.	UPI000013D9D9	.	deleterious(0)	probably_damaging(0.995)	15/18	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF17,hmmpanther:PTHR24416,Pfam_domain:PF07714,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000666,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTATTGCT	.	5	ESCA
ADAMTS3	0	.	GRCh37	4	73169747	73169747	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2311G>C	p.Glu771Gln	p.E771Q	ENST00000286657	17/22	31	28	3	56	56	0	ADAMTS3,missense_variant,p.Glu771Gln,ENST00000286657,;ADAMTS3,non_coding_transcript_exon_variant,,ENST00000511274,;	G	ENSG00000156140	ENST00000286657	Transcript	missense_variant	2348	2311	771	E/Q	Gaa/Caa	.	.	.	-1	ADAMTS3	HGNC	219	protein_coding	YES	CCDS3553.1	ENSP00000286657	ATS3_HUMAN	Q96AY5_HUMAN	UPI00001AEAEA	.	tolerated(0.09)	benign(0.232)	17/22	.	hmmpanther:PTHR13723:SF158,hmmpanther:PTHR13723,Pfam_domain:PF05986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GGCTTCCTCCC	.	2	ESCA
RPS14	0	.	GRCh37	5	149827255	149827255	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42C>A	p.%3D	p.V14V	ENST00000401695	2/5	43	26	16	50	50	0	RPS14,synonymous_variant,p.%3D,ENST00000312037,;RPS14,synonymous_variant,p.%3D,ENST00000401695,;RPS14,synonymous_variant,p.%3D,ENST00000407193,;RPS14,synonymous_variant,p.%3D,ENST00000521466,;RPS14,upstream_gene_variant,,ENST00000519855,;RPS14,synonymous_variant,p.%3D,ENST00000518139,;RPS14,non_coding_transcript_exon_variant,,ENST00000519690,;	T	ENSG00000164587	ENST00000401695	Transcript	synonymous_variant	89	42	14	V	gtC/gtA	.	.	.	-1	RPS14	HGNC	10387	protein_coding	YES	CCDS4307.1	ENSP00000385958	RS14_HUMAN	.	UPI0000003F58	.	.	.	2/5	.	HAMAP:MF_01310,hmmpanther:PTHR11759,PIRSF_domain:PIRSF002131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATGACCTG	.	5	ESCA
HCN1	0	.	GRCh37	5	45261328	45261328	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*695C>T	.	.	ENST00000303230	8/8	72	67	4	64	64	0	HCN1,3_prime_UTR_variant,,ENST00000303230,;	A	ENSG00000164588	ENST00000303230	Transcript	3_prime_UTR_variant	3426	.	.	.	.	.	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TGATCGAGTCT	.	2	ESCA
FCHO2	0	.	GRCh37	5	72386096	72386096	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2179T>C	.	.	ENST00000430046	26/26	58	53	4	53	53	0	FCHO2,3_prime_UTR_variant,,ENST00000341845,;FCHO2,3_prime_UTR_variant,,ENST00000430046,;FCHO2,downstream_gene_variant,,ENST00000512348,;	C	ENSG00000157107	ENST00000430046	Transcript	3_prime_UTR_variant	4728	.	.	.	.	.	.	.	1	FCHO2	HGNC	25180	protein_coding	YES	CCDS47230.1	ENSP00000393776	FCHO2_HUMAN	B4DEU7_HUMAN	UPI000019971A	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCAATGGGAA	.	2	ESCA
RASGRF2	0	.	GRCh37	5	80382767	80382767	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1385G>A	p.Arg462His	p.R462H	ENST00000265080	9/27	27	24	3	41	41	0	RASGRF2,missense_variant,p.Arg462His,ENST00000265080,;RASGRF2,non_coding_transcript_exon_variant,,ENST00000502677,;RASGRF2,missense_variant,p.Arg462His,ENST00000503795,;	A	ENSG00000113319	ENST00000265080	Transcript	missense_variant	1452	1385	462	R/H	cGc/cAc	COSM3139297	.	.	1	RASGRF2	HGNC	9876	protein_coding	YES	CCDS4052.1	ENSP00000265080	RGRF2_HUMAN	Q68DX5_HUMAN	UPI0000047ABF	.	deleterious(0)	probably_damaging(0.945)	9/27	.	Superfamily_domains:SSF50729,SMART_domains:SM00233,Gene3D:2.30.29.30,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF187	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R462C|c.1384C>T|3	RADIA|MUTECT|VARSCANS	CATCCGCCAAG	.	3	ESCA
IGF2R	0	.	GRCh37	6	160471650	160471650	+	Missense_Mutation	SNP	C	C	T	rs752875889	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2660C>T	p.Thr887Met	p.T887M	ENST00000356956	19/48	38	28	10	53	53	0	IGF2R,missense_variant,p.Thr887Met,ENST00000356956,;	T	ENSG00000197081	ENST00000356956	Transcript	missense_variant	2808	2660	887	T/M	aCg/aTg	rs752875889	.	.	1	IGF2R	HGNC	5467	protein_coding	YES	CCDS5273.1	ENSP00000349437	MPRI_HUMAN	A0N9R7_HUMAN,A0N9R6_HUMAN	UPI0000072478	.	deleterious(0)	probably_damaging(0.989)	19/48	.	hmmpanther:PTHR10439:SF4,hmmpanther:PTHR10439,Gene3D:2.70.130.10,Pfam_domain:PF00878,Superfamily_domains:SSF50911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCACGAGGA	byFrequency	5	ESCA
CCNC	0	.	GRCh37	6	99990376	99990376	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1055T>C	.	.	ENST00000520429	12/12	14	10	4	27	27	0	CCNC,3_prime_UTR_variant,,ENST00000369220,;CCNC,3_prime_UTR_variant,,ENST00000520429,;CCNC,downstream_gene_variant,,ENST00000524049,;CCNC,downstream_gene_variant,,ENST00000523985,;CCNC,downstream_gene_variant,,ENST00000520371,;CCNC,downstream_gene_variant,,ENST00000518714,;CCNC,downstream_gene_variant,,ENST00000486428,;CCNC,downstream_gene_variant,,ENST00000523799,;CCNC,3_prime_UTR_variant,,ENST00000326298,;CCNC,downstream_gene_variant,,ENST00000523961,;CCNC,downstream_gene_variant,,ENST00000519617,;CCNC,downstream_gene_variant,,ENST00000484049,;	G	ENSG00000112237	ENST00000520429	Transcript	3_prime_UTR_variant	2353	.	.	.	.	.	.	.	-1	CCNC	HGNC	1581	protein_coding	YES	CCDS34502.1	ENSP00000428982	CCNC_HUMAN	Q7Z4L3_HUMAN,E5RIH8_HUMAN,E5RFX8_HUMAN	UPI0000169CFB	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATATCCTA	.	5	ESCA
HDAC9	0	.	GRCh37	7	18674352	18674352	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.899C>T	p.Thr300Ile	p.T300I	ENST00000441542	7/25	116	95	21	115	115	0	HDAC9,missense_variant,p.Thr256Ile,ENST00000401921,;HDAC9,missense_variant,p.Thr297Ile,ENST00000405010,;HDAC9,missense_variant,p.Thr253Ile,ENST00000428307,;HDAC9,missense_variant,p.Thr300Ile,ENST00000441542,;HDAC9,missense_variant,p.Thr295Ile,ENST00000417496,;HDAC9,missense_variant,p.Thr284Ile,ENST00000406072,;HDAC9,missense_variant,p.Thr297Ile,ENST00000406451,;HDAC9,missense_variant,p.Thr269Ile,ENST00000456174,;HDAC9,missense_variant,p.Thr297Ile,ENST00000432645,;HDAC9,missense_variant,p.Thr220Ile,ENST00000524023,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;	T	ENSG00000048052	ENST00000441542	Transcript	missense_variant	899	899	300	T/I	aCc/aTc	.	.	.	1	HDAC9	HGNC	14065	protein_coding	YES	CCDS47553.1	ENSP00000408617	HDAC9_HUMAN	Q8N926_HUMAN,Q75N15_HUMAN,Q75N14_HUMAN,Q75N10_HUMAN,C9JLX1_HUMAN,C9J835_HUMAN,C9J1W4_HUMAN,C9IZS0_HUMAN	UPI000019AB75	.	tolerated(0.25)	benign(0.012)	7/25	.	hmmpanther:PTHR10625:SF116,hmmpanther:PTHR10625,PIRSF_domain:PIRSF037911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTACCCCTC	.	5	ESCA
NFE2L3	0	.	GRCh37	7	26225269	26225269	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1951G>A	p.Asp651Asn	p.D651N	ENST00000056233	4/4	67	53	14	44	44	0	NFE2L3,missense_variant,p.Asp651Asn,ENST00000056233,;NFE2L3,downstream_gene_variant,,ENST00000607375,;HNRNPA2B1,downstream_gene_variant,,ENST00000354667,;HNRNPA2B1,downstream_gene_variant,,ENST00000476233,;NFE2L3,non_coding_transcript_exon_variant,,ENST00000606261,;HNRNPA2B1,downstream_gene_variant,,ENST00000360787,;HNRNPA2B1,downstream_gene_variant,,ENST00000463181,;	A	ENSG00000050344	ENST00000056233	Transcript	missense_variant	2210	1951	651	D/N	Gat/Aat	.	.	.	1	NFE2L3	HGNC	7783	protein_coding	YES	CCDS5396.1	ENSP00000056233	NF2L3_HUMAN	.	UPI000007206C	.	deleterious(0)	probably_damaging(1)	4/4	.	hmmpanther:PTHR24411:SF8,hmmpanther:PTHR24411	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGAGATGAC	.	5	ESCA
GLI3	0	.	GRCh37	7	42004063	42004063	+	Silent	SNP	G	G	A	rs776279429	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4608C>T	p.%3D	p.S1536S	ENST00000395925	15/15	70	46	24	60	60	0	GLI3,synonymous_variant,p.%3D,ENST00000395925,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,;	A	ENSG00000106571	ENST00000395925	Transcript	synonymous_variant	4693	4608	1536	S	tcC/tcT	rs776279429,COSM188291	.	.	-1	GLI3	HGNC	4319	protein_coding	YES	CCDS5465.1	ENSP00000379258	GLI3_HUMAN	C9J9N4_HUMAN	UPI000020EE4C	.	.	.	15/15	.	hmmpanther:PTHR19818:SF5,hmmpanther:PTHR19818	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCGGGAGGA	byFrequency	5	ESCA
ADCY8	0	.	GRCh37	8	131922004	131922004	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1590G>C	p.Trp530Cys	p.W530C	ENST00000286355	6/18	82	68	14	76	76	0	ADCY8,missense_variant,p.Trp530Cys,ENST00000286355,;ADCY8,missense_variant,p.Trp145Cys,ENST00000522949,;ADCY8,missense_variant,p.Trp530Cys,ENST00000377928,;	G	ENSG00000155897	ENST00000286355	Transcript	missense_variant	3683	1590	530	W/C	tgG/tgC	.	.	.	-1	ADCY8	HGNC	239	protein_coding	YES	CCDS6363.1	ENSP00000286355	ADCY8_HUMAN	E5RFR2_HUMAN	UPI000012887C	.	deleterious(0)	probably_damaging(1)	6/18	.	PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF229,PROSITE_patterns:PS00452,Pfam_domain:PF00211,Gene3D:3.30.70.1230,SMART_domains:SM00044,Superfamily_domains:SSF55073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAAGACCAGAC	.	3	ESCA
TRAPPC9	0	.	GRCh37	8	140743415	140743415	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3630A>T	p.%3D	p.G1210G	ENST00000389328	23/23	77	58	19	61	61	0	TRAPPC9,synonymous_variant,p.%3D,ENST00000520857,;TRAPPC9,synonymous_variant,p.%3D,ENST00000389327,;TRAPPC9,synonymous_variant,p.%3D,ENST00000389328,;TRAPPC9,synonymous_variant,p.%3D,ENST00000438773,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000521667,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000521700,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000522504,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000519482,;TRAPPC9,downstream_gene_variant,,ENST00000523777,;TRAPPC9,downstream_gene_variant,,ENST00000524162,;	A	ENSG00000167632	ENST00000389328	Transcript	synonymous_variant	3645	3630	1210	G	ggA/ggT	.	.	.	-1	TRAPPC9	HGNC	30832	protein_coding	YES	CCDS34946.1	ENSP00000373979	TPPC9_HUMAN	.	UPI0000DBEF2B	.	.	.	23/23	.	hmmpanther:PTHR21512,hmmpanther:PTHR21512:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCTCCCGT	.	5	ESCA
TSNARE1	0	.	GRCh37	8	143352650	143352650	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1446+3492G>A	.	.	ENST00000307180	.	23	18	5	11	11	0	TSNARE1,3_prime_UTR_variant,,ENST00000519651,;TSNARE1,intron_variant,,ENST00000524325,;TSNARE1,intron_variant,,ENST00000307180,;TSNARE1,intron_variant,,ENST00000520166,;TSNARE1,downstream_gene_variant,,ENST00000521825,;	T	ENSG00000171045	ENST00000307180	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TSNARE1	HGNC	26437	protein_coding	YES	CCDS6384.1	ENSP00000303437	TSNA1_HUMAN	E5RHW3_HUMAN,A0AVG3_HUMAN	UPI00001AEE5E	.	.	.	.	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACGCCATCG	.	5	ESCA
CHD7	0	.	GRCh37	8	61763057	61763057	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5410G>A	p.Glu1804Lys	p.E1804K	ENST00000423902	26/38	67	60	7	84	84	0	CHD7,missense_variant,p.Glu1804Lys,ENST00000423902,;CHD7,intron_variant,,ENST00000524602,;CHD7,upstream_gene_variant,,ENST00000527921,;CHD7,upstream_gene_variant,,ENST00000529472,;	A	ENSG00000171316	ENST00000423902	Transcript	missense_variant	5889	5410	1804	E/K	Gag/Aag	COSM606060,COSM606059	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	probably_damaging(0.986)	26/38	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF551	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTATGAGAAG	.	3	ESCA
ADHFE1	0	.	GRCh37	8	67372632	67372632	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1252G>C	p.Asp418His	p.D418H	ENST00000396623	13/14	59	40	18	54	54	0	ADHFE1,missense_variant,p.Asp370His,ENST00000415254,;ADHFE1,missense_variant,p.Asp418His,ENST00000396623,;C8orf46,non_coding_transcript_exon_variant,,ENST00000519702,;C8orf46,non_coding_transcript_exon_variant,,ENST00000482608,;ADHFE1,non_coding_transcript_exon_variant,,ENST00000480040,;ADHFE1,non_coding_transcript_exon_variant,,ENST00000496501,;ADHFE1,non_coding_transcript_exon_variant,,ENST00000466739,;ADHFE1,3_prime_UTR_variant,,ENST00000276576,;ADHFE1,3_prime_UTR_variant,,ENST00000424777,;ADHFE1,3_prime_UTR_variant,,ENST00000426810,;ADHFE1,3_prime_UTR_variant,,ENST00000419955,;	C	ENSG00000147576	ENST00000396623	Transcript	missense_variant	1283	1252	418	D/H	Gat/Cat	.	.	.	1	ADHFE1	HGNC	16354	protein_coding	YES	CCDS6190.2	ENSP00000379865	HOT_HUMAN	E5RFL4_HUMAN	UPI000004966C	.	deleterious(0.04)	possibly_damaging(0.537)	13/14	.	hmmpanther:PTHR11496:SF62,hmmpanther:PTHR11496,Pfam_domain:PF00465,Gene3D:1.20.1090.10,Superfamily_domains:SSF56796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATGATGGC	.	5	ESCA
KCNS2	0	.	GRCh37	8	99441892	99441892	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*251G>A	.	.	ENST00000287042	2/2	87	74	13	78	78	0	KCNS2,3_prime_UTR_variant,,ENST00000287042,;KCNS2,3_prime_UTR_variant,,ENST00000521839,;STK3,intron_variant,,ENST00000517832,;	A	ENSG00000156486	ENST00000287042	Transcript	3_prime_UTR_variant	2035	.	.	.	.	.	.	.	1	KCNS2	HGNC	6301	protein_coding	YES	CCDS6279.1	ENSP00000287042	KCNS2_HUMAN	.	UPI0000001653	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAAATGTTCAC	.	3	ESCA
RP11-383M4.6	0	.	GRCh37	9	84562614	84562614	+	Intron	SNP	G	G	A	rs774847304	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.943-1213C>T	.	.	ENST00000585776	.	31	28	3	54	54	0	RP11-383M4.6,intron_variant,,ENST00000592744,;RP11-383M4.6,intron_variant,,ENST00000585776,;SPATA31D3,non_coding_transcript_exon_variant,,ENST00000334208,;SPATA31D3,non_coding_transcript_exon_variant,,ENST00000445385,;	A	ENSG00000267559	ENST00000585776	Transcript	intron_variant	.	.	.	.	.	rs774847304	.	.	-1	RP11-383M4.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CAGGGGTGAGA	byFrequency	2	ESCA
MID1	0	.	GRCh37	X	10417677	10417677	+	Missense_Mutation	SNP	G	G	A	rs770539991	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735C>T	p.Arg579Cys	p.R579C	ENST00000317552	10/10	16	6	10	11	11	0	MID1,missense_variant,p.Arg579Cys,ENST00000380780,;MID1,missense_variant,p.Arg579Cys,ENST00000380787,;MID1,missense_variant,p.Arg579Cys,ENST00000380779,;MID1,missense_variant,p.Arg579Cys,ENST00000453318,;MID1,missense_variant,p.Arg579Cys,ENST00000380785,;MID1,missense_variant,p.Arg579Cys,ENST00000317552,;MID1,intron_variant,,ENST00000380782,;MID1,non_coding_transcript_exon_variant,,ENST00000479925,;	A	ENSG00000101871	ENST00000317552	Transcript	missense_variant	2136	1735	579	R/C	Cgc/Tgc	rs770539991	.	.	-1	MID1	HGNC	7095	protein_coding	YES	CCDS14138.1	ENSP00000312678	TRI18_HUMAN	C9JZJ7_HUMAN,C9J453_HUMAN	UPI000012F0E6	.	deleterious(0)	probably_damaging(1)	10/10	.	Superfamily_domains:SSF49899,SMART_domains:SM00449,Pfam_domain:PF00622,hmmpanther:PTHR24103:SF26,hmmpanther:PTHR24103,PROSITE_profiles:PS50188	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGGCAGA	byFrequency	5	ESCA
FRMPD3	0	.	GRCh37	X	106803587	106803587	+	Missense_Mutation	SNP	C	C	T	rs753103772	.	TCGA-LN-A4A3-01A-11D-A27G-09	TCGA-LN-A4A3-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.962C>T	p.Thr321Ile	p.T321I	ENST00000276185	10/16	16	10	6	14	14	0	FRMPD3,missense_variant,p.Thr321Ile,ENST00000276185,;FRMPD3,missense_variant,p.Thr269Ile,ENST00000439554,;	T	ENSG00000147234	ENST00000276185	Transcript	missense_variant	962	962	321	T/I	aCt/aTt	rs753103772	.	.	1	FRMPD3	HGNC	29382	protein_coding	YES	.	ENSP00000276185	FRPD3_HUMAN	.	UPI00006C1C33	.	deleterious(0.01)	possibly_damaging(0.905)	10/16	.	PROSITE_profiles:PS50057,hmmpanther:PTHR13436,hmmpanther:PTHR13436:SF6,Pfam_domain:PF00373,SMART_domains:SM00295,Superfamily_domains:SSF47031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AGCCACTCGAC	byFrequency	4	ESCA
RSU1	0	.	GRCh37	10	16859117	16859117	+	5'UTR	SNP	G	G	A	rs780971321	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-37C>T	.	.	ENST00000377921	1/8	41	28	12	24	24	0	RSU1,5_prime_UTR_variant,,ENST00000377921,;RSU1,intron_variant,,ENST00000602389,;RSU1,intron_variant,,ENST00000345264,;RSU1,intron_variant,,ENST00000377911,;RSU1,intron_variant,,ENST00000464074,;	A	ENSG00000148484	ENST00000377921	Transcript	5_prime_UTR_variant	266	.	.	.	.	rs780971321	.	.	-1	RSU1	HGNC	10464	protein_coding	YES	CCDS7112.1	ENSP00000367154	RSU1_HUMAN	.	UPI0000000C72	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGATGACAGC	byFrequency	5	ESCA
CUBN	0	.	GRCh37	10	16949507	16949507	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7705G>A	p.Val2569Met	p.V2569M	ENST00000377833	49/67	68	51	17	48	48	0	CUBN,missense_variant,p.Val2569Met,ENST00000377833,;	T	ENSG00000107611	ENST00000377833	Transcript	missense_variant	7771	7705	2569	V/M	Gtg/Atg	.	.	.	-1	CUBN	HGNC	2548	protein_coding	YES	CCDS7113.1	ENSP00000367064	CUBN_HUMAN	B3KQA6_HUMAN	UPI00001AE8F4	.	deleterious(0.01)	probably_damaging(0.954)	49/67	.	Gene3D:2.60.120.290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTACCTGCAT	.	5	ESCA
PCDH15	0	.	GRCh37	10	55892731	55892731	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1821A>G	p.%3D	p.P607P	ENST00000361849	15/34	50	31	19	57	57	0	PCDH15,synonymous_variant,p.%3D,ENST00000395433,;PCDH15,synonymous_variant,p.%3D,ENST00000395445,;PCDH15,synonymous_variant,p.%3D,ENST00000320301,;PCDH15,synonymous_variant,p.%3D,ENST00000409834,;PCDH15,synonymous_variant,p.%3D,ENST00000395432,;PCDH15,synonymous_variant,p.%3D,ENST00000373955,;PCDH15,synonymous_variant,p.%3D,ENST00000373957,;PCDH15,synonymous_variant,p.%3D,ENST00000361849,;PCDH15,synonymous_variant,p.%3D,ENST00000395438,;PCDH15,synonymous_variant,p.%3D,ENST00000395446,;PCDH15,synonymous_variant,p.%3D,ENST00000414778,;PCDH15,synonymous_variant,p.%3D,ENST00000373965,;PCDH15,synonymous_variant,p.%3D,ENST00000395430,;PCDH15,intron_variant,,ENST00000437009,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.His43Arg,ENST00000373956,;PCDH15,synonymous_variant,p.%3D,ENST00000448885,;PCDH15,intron_variant,,ENST00000414367,;	C	ENSG00000150275	ENST00000361849	Transcript	synonymous_variant	2216	1821	607	P	ccA/ccG	.	.	.	-1	PCDH15	HGNC	14674	protein_coding	YES	CCDS44404.1	ENSP00000354950	.	A2A3E7_HUMAN,A2A3D9_HUMAN	UPI0000EE048B	.	.	.	15/34	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGGTGGAAG	.	5	ESCA
BTAF1	0	.	GRCh37	10	93789866	93789866	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1176A>G	.	.	ENST00000265990	38/38	48	29	19	57	57	0	BTAF1,3_prime_UTR_variant,,ENST00000265990,;BTAF1,downstream_gene_variant,,ENST00000544642,;	G	ENSG00000095564	ENST00000265990	Transcript	3_prime_UTR_variant	7034	.	.	.	.	.	.	.	1	BTAF1	HGNC	17307	protein_coding	YES	CCDS7419.1	ENSP00000265990	BTAF1_HUMAN	Q8N6J1_HUMAN,Q2M1V9_HUMAN,B4E0W6_HUMAN	UPI0000136782	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTAATAAAC	.	5	ESCA
PCSK7	0	.	GRCh37	11	117076011	117076011	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*702C>A	.	.	ENST00000320934	17/17	19	7	11	21	21	0	PCSK7,3_prime_UTR_variant,,ENST00000320934,;PCSK7,3_prime_UTR_variant,,ENST00000540028,;TAGLN,downstream_gene_variant,,ENST00000525531,;TAGLN,downstream_gene_variant,,ENST00000529622,;TAGLN,downstream_gene_variant,,ENST00000530649,;TAGLN,downstream_gene_variant,,ENST00000529792,;TAGLN,downstream_gene_variant,,ENST00000532870,;TAGLN,downstream_gene_variant,,ENST00000278968,;TAGLN,downstream_gene_variant,,ENST00000392951,;PCSK7,downstream_gene_variant,,ENST00000533135,;PCSK7,downstream_gene_variant,,ENST00000529458,;PCSK7,non_coding_transcript_exon_variant,,ENST00000534529,;PCSK7,downstream_gene_variant,,ENST00000528973,;PCSK7,downstream_gene_variant,,ENST00000532810,;TAGLN,downstream_gene_variant,,ENST00000533863,;PCSK7,downstream_gene_variant,,ENST00000527037,;PCSK7,downstream_gene_variant,,ENST00000527861,;PCSK7,downstream_gene_variant,,ENST00000531573,;	T	ENSG00000160613	ENST00000320934	Transcript	3_prime_UTR_variant	3691	.	.	.	.	.	.	.	-1	PCSK7	HGNC	8748	protein_coding	YES	CCDS8382.1	ENSP00000325917	PCSK7_HUMAN	E9PMC0_HUMAN,E9PLM0_HUMAN,E9PIW7_HUMAN,B3KUH2_HUMAN	UPI0000070E4E	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGGGTGGTG	.	5	ESCA
DDX6	0	.	GRCh37	11	118620908	118620908	+	3'UTR	SNP	T	T	C	rs782094779	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1906A>G	.	.	ENST00000264018	14/14	26	21	4	64	63	1	DDX6,3_prime_UTR_variant,,ENST00000264018,;DDX6,downstream_gene_variant,,ENST00000526070,;DDX6,downstream_gene_variant,,ENST00000534980,;AP002954.4,intron_variant,,ENST00000526274,;DDX6,downstream_gene_variant,,ENST00000529162,;	C	ENSG00000110367	ENST00000264018	Transcript	3_prime_UTR_variant	3664	.	.	.	.	rs782094779	.	.	-1	DDX6	HGNC	2747	protein_coding	YES	CCDS44751.1	ENSP00000264018	DDX6_HUMAN	B2R858_HUMAN	UPI000013D4A2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TTTTTTCCCCC	.	4	ESCA
CBL	0	.	GRCh37	11	119077233	119077233	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.106C>T	p.His36Tyr	p.H36Y	ENST00000264033	1/16	24	7	17	20	20	0	CBL,missense_variant,p.His36Tyr,ENST00000264033,;	T	ENSG00000110395	ENST00000264033	Transcript	missense_variant	482	106	36	H/Y	Cac/Tac	.	.	.	1	CBL	HGNC	1541	protein_coding	YES	CCDS8418.1	ENSP00000264033	CBL_HUMAN	.	UPI000013D4A7	.	deleterious_low_confidence(0.04)	benign(0.152)	1/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23007:SF5,hmmpanther:PTHR23007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGCACCAC	.	5	ESCA
OR10S1	0	.	GRCh37	11	123847675	123847675	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724A>G	p.Ile242Val	p.I242V	ENST00000531945	1/1	16	8	8	21	21	0	OR10S1,missense_variant,p.Ile242Val,ENST00000531945,;	C	ENSG00000196248	ENST00000531945	Transcript	missense_variant	814	724	242	I/V	Atc/Gtc	.	.	.	-1	OR10S1	HGNC	14807	protein_coding	YES	CCDS31701.1	ENSP00000431914	O10S1_HUMAN	.	UPI00001A7787	.	deleterious(0)	possibly_damaging(0.469)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF205,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGATGCGCA	.	5	ESCA
OR10G8	0	.	GRCh37	11	123900746	123900746	+	Silent	SNP	G	G	T	rs540634723	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.417G>T	p.%3D	p.S139S	ENST00000431524	1/1	125	89	35	101	101	0	OR10G8,synonymous_variant,p.%3D,ENST00000431524,;	T	ENSG00000234560	ENST00000431524	Transcript	synonymous_variant	450	417	139	S	tcG/tcT	rs540634723	.	.	1	OR10G8	HGNC	14845	protein_coding	YES	CCDS31704.1	ENSP00000389072	O10G8_HUMAN	.	UPI0000040A8F	.	.	.	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF146,PROSITE_profiles:PS50262	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTCGTGTAC	by1000G	5	ESCA
OR8B12	0	.	GRCh37	11	124413294	124413294	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257C>G	p.Ser86Ter	p.S86*	ENST00000306842	1/1	24	9	14	27	27	0	OR8B12,stop_gained,p.Ser86Ter,ENST00000306842,;RP11-728D14.6,upstream_gene_variant,,ENST00000533869,;	C	ENSG00000170953	ENST00000306842	Transcript	stop_gained	282	257	86	S/*	tCa/tGa	.	.	.	-1	OR8B12	HGNC	15307	protein_coding	YES	CCDS31711.1	ENSP00000307159	OR8BC_HUMAN	.	UPI0000041E25	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF267,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R87R|c.261G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTGAGACA	.	5	ESCA
PANX3	0	.	GRCh37	11	124489477	124489477	+	Silent	SNP	C	C	A	rs765106995	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.825C>A	p.%3D	p.S275S	ENST00000284288	4/4	85	69	16	72	72	0	PANX3,synonymous_variant,p.%3D,ENST00000284288,;TBRG1,upstream_gene_variant,,ENST00000531667,;TBRG1,upstream_gene_variant,,ENST00000375005,;TBRG1,upstream_gene_variant,,ENST00000441174,;TBRG1,upstream_gene_variant,,ENST00000529543,;TBRG1,upstream_gene_variant,,ENST00000284290,;TBRG1,upstream_gene_variant,,ENST00000452080,;TBRG1,upstream_gene_variant,,ENST00000530731,;TBRG1,upstream_gene_variant,,ENST00000473629,;	A	ENSG00000154143	ENST00000284288	Transcript	synonymous_variant	892	825	275	S	tcC/tcA	rs765106995	.	.	1	PANX3	HGNC	20573	protein_coding	YES	CCDS8447.1	ENSP00000284288	PANX3_HUMAN	.	UPI0000131264	.	.	.	4/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF3,PROSITE_profiles:PS51013	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCCAGTGT	.	5	ESCA
ALKBH3	0	.	GRCh37	11	43904237	43904237	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35G>A	p.Gly12Glu	p.G12E	ENST00000302708	2/10	14	2	11	24	24	0	ALKBH3,missense_variant,p.Gly12Glu,ENST00000302708,;ALKBH3,missense_variant,p.Gly12Glu,ENST00000529366,;ALKBH3,missense_variant,p.Gly12Glu,ENST00000524742,;ALKBH3,missense_variant,p.Gly12Glu,ENST00000378840,;RP11-613D13.5,upstream_gene_variant,,ENST00000528765,;RP11-613D13.5,upstream_gene_variant,,ENST00000530450,;ALKBH3,non_coding_transcript_exon_variant,,ENST00000533200,;ALKBH3,upstream_gene_variant,,ENST00000532410,;ALKBH3,missense_variant,p.Gly12Glu,ENST00000534171,;ALKBH3,missense_variant,p.Gly12Glu,ENST00000532962,;ALKBH3,missense_variant,p.Gly12Glu,ENST00000530803,;ALKBH3,non_coding_transcript_exon_variant,,ENST00000527029,;ALKBH3,upstream_gene_variant,,ENST00000530754,;	A	ENSG00000166199	ENST00000302708	Transcript	missense_variant	446	35	12	G/E	gGa/gAa	.	.	.	1	ALKBH3	HGNC	30141	protein_coding	YES	CCDS7906.1	ENSP00000302232	ALKB3_HUMAN	E9PRD0_HUMAN	UPI0000039EA0	.	deleterious(0)	probably_damaging(1)	2/10	.	hmmpanther:PTHR31212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TCAGGGAGCCT	.	4	ESCA
GIF	0	.	GRCh37	11	59610015	59610015	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.412G>C	p.Ala138Pro	p.A138P	ENST00000257248	4/9	36	28	8	43	43	0	GIF,missense_variant,p.Ala138Pro,ENST00000257248,;GIF,missense_variant,p.Ala113Pro,ENST00000541311,;GIF,3_prime_UTR_variant,,ENST00000525058,;GIF,non_coding_transcript_exon_variant,,ENST00000532070,;GIF,upstream_gene_variant,,ENST00000533847,;	G	ENSG00000134812	ENST00000257248	Transcript	missense_variant	460	412	138	A/P	Gcg/Ccg	.	.	.	-1	GIF	HGNC	4268	protein_coding	YES	CCDS7977.1	ENSP00000257248	IF_HUMAN	.	UPI0000001C67	.	tolerated(0.23)	probably_damaging(0.976)	4/9	.	hmmpanther:PTHR10559,hmmpanther:PTHR10559:SF15,Pfam_domain:PF01122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCGCTAGAC	.	5	ESCA
EML3	0	.	GRCh37	11	62372637	62372638	+	Frame_Shift_Del	DEL	CA	CA	-	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1929_1930delTG	p.Ala644Ter	p.A644*	ENST00000394773	16/22	100	52	48	58	58	0	EML3,frameshift_variant,p.Ala645Ter,ENST00000278845,;EML3,frameshift_variant,p.Ala616Ter,ENST00000494176,;EML3,frameshift_variant,p.Ala644Ter,ENST00000394773,;EML3,frameshift_variant,p.Ala644Ter,ENST00000529309,;EML3,frameshift_variant,p.Ala638Ter,ENST00000394776,;EML3,frameshift_variant,p.Ala427Ter,ENST00000531557,;MTA2,upstream_gene_variant,,ENST00000527204,;MTA2,upstream_gene_variant,,ENST00000278823,;EML3,upstream_gene_variant,,ENST00000439994,;RP11-831H9.3,upstream_gene_variant,,ENST00000532626,;EML3,downstream_gene_variant,,ENST00000438258,;EML3,3_prime_UTR_variant,,ENST00000494448,;EML3,non_coding_transcript_exon_variant,,ENST00000460939,;EML3,non_coding_transcript_exon_variant,,ENST00000483199,;EML3,non_coding_transcript_exon_variant,,ENST00000533165,;EML3,non_coding_transcript_exon_variant,,ENST00000524518,;EML3,downstream_gene_variant,,ENST00000526116,;EML3,downstream_gene_variant,,ENST00000462626,;MTA2,upstream_gene_variant,,ENST00000532239,;MTA2,upstream_gene_variant,,ENST00000526844,;	-	ENSG00000149499	ENST00000394773	Transcript	frameshift_variant	2237-2238	1929-1930	643-644	CA/CX	tgTGct/tgct	.	.	.	-1	EML3	HGNC	26666	protein_coding	YES	CCDS8023.2	ENSP00000378254	EMAL3_HUMAN	G3V195_HUMAN,E9PJV5_HUMAN,C9J6V3_HUMAN	UPI0000228E33	.	.	.	16/22	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF15,Gene3D:2.130.10.10,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTCAGCACAGAG	.	3	ESCA
WSCD2	0	.	GRCh37	12	108643047	108643047	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*927G>T	.	.	ENST00000332082	10/10	35	23	12	26	26	0	WSCD2,3_prime_UTR_variant,,ENST00000549903,;WSCD2,3_prime_UTR_variant,,ENST00000332082,;WSCD2,3_prime_UTR_variant,,ENST00000547525,;WSCD2,3_prime_UTR_variant,,ENST00000261400,;	T	ENSG00000075035	ENST00000332082	Transcript	3_prime_UTR_variant	3443	.	.	.	.	.	.	.	1	WSCD2	HGNC	29117	protein_coding	YES	CCDS41828.1	ENSP00000331933	WSCD2_HUMAN	F8W030_HUMAN	UPI00001C1F3A	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGTGAGACA	.	5	ESCA
SH2B3	0	.	GRCh37	12	111889331	111889331	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3225T>G	.	.	ENST00000341259	8/8	110	96	14	80	80	0	SH2B3,3_prime_UTR_variant,,ENST00000341259,;ATXN2,downstream_gene_variant,,ENST00000542287,;ATXN2,downstream_gene_variant,,ENST00000389154,;ATXN2,downstream_gene_variant,,ENST00000608853,;ATXN2,downstream_gene_variant,,ENST00000377617,;ATXN2,downstream_gene_variant,,ENST00000535949,;ATXN2,downstream_gene_variant,,ENST00000475132,;ATXN2,downstream_gene_variant,,ENST00000389153,;ATXN2,downstream_gene_variant,,ENST00000550844,;ATXN2,downstream_gene_variant,,ENST00000550104,;SH2B3,downstream_gene_variant,,ENST00000538307,;ATXN2,downstream_gene_variant,,ENST00000550889,;ATXN2,downstream_gene_variant,,ENST00000484991,;ATXN2,downstream_gene_variant,,ENST00000483311,;ATXN2,downstream_gene_variant,,ENST00000551551,;ATXN2,downstream_gene_variant,,ENST00000482777,;ATXN2,downstream_gene_variant,,ENST00000468920,;	G	ENSG00000111252	ENST00000341259	Transcript	3_prime_UTR_variant	5310	.	.	.	.	.	.	.	1	SH2B3	HGNC	29605	protein_coding	YES	CCDS9153.1	ENSP00000345492	SH2B3_HUMAN	.	UPI000012E798	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTGTTTTATG	.	4	ESCA
KDM2B	0	.	GRCh37	12	121868348	121868348	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3830-76G>A	.	.	ENST00000377071	.	21	14	6	22	22	0	RNF34,3_prime_UTR_variant,,ENST00000392464,;KDM2B,intron_variant,,ENST00000536437,;KDM2B,intron_variant,,ENST00000542973,;KDM2B,intron_variant,,ENST00000377071,;KDM2B,intron_variant,,ENST00000377069,;KDM2B,intron_variant,,ENST00000543025,;KDM2B,intron_variant,,ENST00000538503,;	T	ENSG00000089094	ENST00000377071	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KDM2B	HGNC	13610	protein_coding	YES	CCDS41850.1	ENSP00000366271	KDM2B_HUMAN	F5H7T7_HUMAN,F5H6N6_HUMAN,F5H4A7_HUMAN,F5GXC2_HUMAN	UPI000006F36E	.	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACTCAGCAG	.	5	ESCA
LRP6	0	.	GRCh37	12	12312804	12312804	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2374C>T	p.Arg792Trp	p.R792W	ENST00000261349	11/23	82	70	11	55	55	0	LRP6,missense_variant,p.Arg792Trp,ENST00000543091,;LRP6,missense_variant,p.Arg792Trp,ENST00000261349,;LRP6,missense_variant,p.Arg657Trp,ENST00000538239,;BCL2L14,intron_variant,,ENST00000298566,;RP11-267J23.1,downstream_gene_variant,,ENST00000472093,;	A	ENSG00000070018	ENST00000261349	Transcript	missense_variant	2451	2374	792	R/W	Cgg/Tgg	.	.	.	-1	LRP6	HGNC	6698	protein_coding	YES	CCDS8647.1	ENSP00000261349	LRP6_HUMAN	F5H0Z3_HUMAN,B3KQA9_HUMAN	UPI00001FB66C	.	deleterious(0)	probably_damaging(1)	11/23	.	Superfamily_domains:SSF63825,SMART_domains:SM00135,PIRSF_domain:PIRSF036314,Gene3D:2.120.10.30,Pfam_domain:PF00058,hmmpanther:PTHR10529:SF109,hmmpanther:PTHR10529,PROSITE_profiles:PS51120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCCGCCCCA	.	4	ESCA
LINC00943	0	.	GRCh37	12	127229404	127229404	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.834T>C	.	.	ENST00000345111	2/3	117	91	25	105	105	0	LINC00943,non_coding_transcript_exon_variant,,ENST00000540250,;LINC00943,non_coding_transcript_exon_variant,,ENST00000535544,;LINC00943,non_coding_transcript_exon_variant,,ENST00000537374,;LINC00943,non_coding_transcript_exon_variant,,ENST00000345111,;LINC00944,intron_variant,,ENST00000540684,;LINC00943,intron_variant,,ENST00000539315,;LINC00943,downstream_gene_variant,,ENST00000535118,;LINC00943,downstream_gene_variant,,ENST00000541359,;LINC00944,downstream_gene_variant,,ENST00000542248,;	C	ENSG00000189238	ENST00000345111	Transcript	non_coding_transcript_exon_variant	834	.	.	.	.	.	.	.	1	LINC00943	HGNC	48639	lincRNA	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACATTGCCT	.	5	ESCA
ABCC9	0	.	GRCh37	12	22005402	22005402	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2543A>G	p.Asp848Gly	p.D848G	ENST00000261200	21/38	53	44	9	40	40	0	ABCC9,missense_variant,p.Asp812Gly,ENST00000345162,;ABCC9,missense_variant,p.Asp848Gly,ENST00000261201,;ABCC9,missense_variant,p.Asp475Gly,ENST00000544039,;ABCC9,missense_variant,p.Asp848Gly,ENST00000261200,;RP11-729I10.2,intron_variant,,ENST00000539874,;	C	ENSG00000069431	ENST00000261200	Transcript	missense_variant	2543	2543	848	D/G	gAt/gGt	.	.	.	-1	ABCC9	HGNC	60	protein_coding	YES	CCDS8693.1	ENSP00000261200	ABCC9_HUMAN	Q8N9N1_HUMAN	UPI000013D13F	.	tolerated(0.11)	benign(0.144)	21/38	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Gene3D:3.40.50.300,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,PROSITE_profiles:PS50893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGATCACTC	.	5	ESCA
NUP107	0	.	GRCh37	12	69127301	69127301	+	Missense_Mutation	SNP	A	A	G	rs780651405	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2171A>G	p.Tyr724Cys	p.Y724C	ENST00000229179	24/28	30	23	7	29	29	0	NUP107,missense_variant,p.Tyr724Cys,ENST00000229179,;NUP107,missense_variant,p.Tyr485Cys,ENST00000378905,;NUP107,missense_variant,p.Tyr695Cys,ENST00000539906,;NUP107,intron_variant,,ENST00000401003,;NUP107,3_prime_UTR_variant,,ENST00000538993,;NUP107,3_prime_UTR_variant,,ENST00000535718,;	G	ENSG00000111581	ENST00000229179	Transcript	missense_variant	2503	2171	724	Y/C	tAt/tGt	rs780651405	.	.	1	NUP107	HGNC	29914	protein_coding	YES	CCDS8985.1	ENSP00000229179	NU107_HUMAN	F5GY77_HUMAN	UPI000012FC0B	.	tolerated(0.06)	benign(0.128)	24/28	.	hmmpanther:PTHR13003,Pfam_domain:PF04121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTATAATC	.	5	ESCA
TSPAN8	0	.	GRCh37	12	71526592	71526592	+	Missense_Mutation	SNP	C	C	T	rs753825850	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457G>A	p.Gly153Ser	p.G153S	ENST00000393330	10/12	56	47	8	38	38	0	TSPAN8,missense_variant,p.Gly70Ser,ENST00000552128,;TSPAN8,missense_variant,p.Gly153Ser,ENST00000546561,;TSPAN8,missense_variant,p.Gly153Ser,ENST00000247829,;TSPAN8,missense_variant,p.Gly153Ser,ENST00000393330,;	T	ENSG00000127324	ENST00000393330	Transcript	missense_variant	1010	457	153	G/S	Ggt/Agt	rs753825850	.	.	-1	TSPAN8	HGNC	11855	protein_coding	YES	CCDS8999.1	ENSP00000377003	TSN8_HUMAN	.	UPI000003EE40	.	deleterious(0)	probably_damaging(1)	10/12	.	hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF33,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Superfamily_domains:0037997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAACCGCAGC	.	5	ESCA
TPP2	0	.	GRCh37	13	103330881	103330881	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000376065	.	39	24	14	26	26	0	TPP2,3_prime_UTR_variant,,ENST00000376052,;TPP2,downstream_gene_variant,,ENST00000376065,;RP11-29B2.5,upstream_gene_variant,,ENST00000602560,;TPP2,downstream_gene_variant,,ENST00000466153,;TPP2,downstream_gene_variant,,ENST00000482393,;	T	ENSG00000134900	ENST00000376065	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	70	1	TPP2	HGNC	12016	protein_coding	YES	CCDS9502.1	ENSP00000365233	TPP2_HUMAN	.	UPI0000001C91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCACATTGC	.	5	ESCA
ENOX1	0	.	GRCh37	13	43986993	43986993	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58A>T	p.Met20Leu	p.M20L	ENST00000261488	4/17	53	33	19	63	63	0	ENOX1,missense_variant,p.Met20Leu,ENST00000412891,;ENOX1,missense_variant,p.Met20Leu,ENST00000261488,;	A	ENSG00000120658	ENST00000261488	Transcript	missense_variant	636	58	20	M/L	Atg/Ttg	.	.	.	-1	ENOX1	HGNC	25474	protein_coding	YES	CCDS9389.1	ENSP00000261488	ENOX1_HUMAN	.	UPI0000071D6F	.	tolerated_low_confidence(0.98)	benign(0)	4/17	.	hmmpanther:PTHR16001:SF6,hmmpanther:PTHR16001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCATCTGAG	.	5	ESCA
ENOX1	0	.	GRCh37	13	43986994	43986994	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57G>T	p.Gln19His	p.Q19H	ENST00000261488	4/17	54	33	20	62	62	0	ENOX1,missense_variant,p.Gln19His,ENST00000412891,;ENOX1,missense_variant,p.Gln19His,ENST00000261488,;	A	ENSG00000120658	ENST00000261488	Transcript	missense_variant	635	57	19	Q/H	caG/caT	.	.	.	-1	ENOX1	HGNC	25474	protein_coding	YES	CCDS9389.1	ENSP00000261488	ENOX1_HUMAN	.	UPI0000071D6F	.	deleterious_low_confidence(0.03)	benign(0.216)	4/17	.	hmmpanther:PTHR16001:SF6,hmmpanther:PTHR16001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCATCTGAGG	.	5	ESCA
DACH1	0	.	GRCh37	13	72063217	72063217	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1640A>G	p.His547Arg	p.H547R	ENST00000305425	7/11	48	43	4	43	43	0	DACH1,missense_variant,p.His547Arg,ENST00000305425,;DACH1,missense_variant,p.His399Arg,ENST00000313174,;DACH1,missense_variant,p.His345Arg,ENST00000354591,;DACH1,missense_variant,p.His599Arg,ENST00000359684,;	C	ENSG00000165659	ENST00000305425	Transcript	missense_variant	2063	1640	547	H/R	cAt/cGt	.	.	.	-1	DACH1	HGNC	2663	protein_coding	YES	CCDS41899.1	ENSP00000304994	DACH1_HUMAN	.	UPI00001FCE9E	.	.	possibly_damaging(0.61)	7/11	.	hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCATGCCCA	.	2	ESCA
MIR411	0	.	GRCh37	14	101489664	101489664	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3G>T	.	.	ENST00000362239	1/1	124	80	44	93	93	0	MIR411,non_coding_transcript_exon_variant,,ENST00000362239,;MIR379,downstream_gene_variant,,ENST00000362218,;MIR329-1,upstream_gene_variant,,ENST00000385028,;MIR758,upstream_gene_variant,,ENST00000390227,;MIR329-2,upstream_gene_variant,,ENST00000385029,;MIR323A,upstream_gene_variant,,ENST00000362199,;MIR299,upstream_gene_variant,,ENST00000385016,;MIR1197,upstream_gene_variant,,ENST00000408818,;MIR380,downstream_gene_variant,,ENST00000362112,;	T	ENSG00000199109	ENST00000362239	Transcript	non_coding_transcript_exon_variant	3	.	.	.	.	.	.	.	1	MIR411	HGNC	32792	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTGGTACTT	.	5	ESCA
OR4K1	0	.	GRCh37	14	20404271	20404271	+	Nonsense_Mutation	SNP	G	G	A	rs778170531	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.446G>A	p.Trp149Ter	p.W149*	ENST00000285600	1/1	145	133	12	76	76	0	OR4K1,stop_gained,p.Trp149Ter,ENST00000285600,;	A	ENSG00000155249	ENST00000285600	Transcript	stop_gained	505	446	149	W/*	tGg/tAg	rs778170531	.	.	1	OR4K1	HGNC	14726	protein_coding	YES	CCDS32025.1	ENSP00000285600	OR4K1_HUMAN	.	UPI0000041B4A	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF182,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S148F|c.443C>T|4,BUFFER|p.A150V|c.449C>T|3,BUFFER|p.V153I|c.457G>A|3	MUTECT|MUSE	TTCCTGGGCGG	.	2	ESCA
ZFHX2	0	.	GRCh37	14	23999349	23999349	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2855A>G	p.Gln952Arg	p.Q952R	ENST00000419474	5/10	54	49	5	29	29	0	ZFHX2,missense_variant,p.Gln952Arg,ENST00000419474,;ZFHX2,downstream_gene_variant,,ENST00000555334,;ZFHX2,downstream_gene_variant,,ENST00000412565,;RP11-66N24.4,intron_variant,,ENST00000553985,;RP11-66N24.4,intron_variant,,ENST00000556354,;RP11-66N24.4,intron_variant,,ENST00000554403,;	C	ENSG00000136367	ENST00000419474	Transcript	missense_variant	3211	2855	952	Q/R	cAg/cGg	.	.	.	-1	ZFHX2	HGNC	20152	protein_coding	YES	CCDS55907.1	ENSP00000413418	ZFHX2_HUMAN	G3V3N5_HUMAN,C9JSX6_HUMAN	UPI000198D01B	.	.	benign(0.434)	5/10	.	hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF86	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTTCTGGGCA	.	3	ESCA
REC8	0	.	GRCh37	14	24641695	24641695	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-67C>G	.	.	ENST00000311457	2/20	51	46	5	32	32	0	REC8,splice_region_variant,,ENST00000557806,;REC8,5_prime_UTR_variant,,ENST00000311457,;REC8,5_prime_UTR_variant,,ENST00000559919,;REC8,upstream_gene_variant,,ENST00000560501,;REC8,non_coding_transcript_exon_variant,,ENST00000557979,;REC8,non_coding_transcript_exon_variant,,ENST00000560032,;REC8,upstream_gene_variant,,ENST00000558782,;REC8,upstream_gene_variant,,ENST00000558697,;	G	ENSG00000100918	ENST00000311457	Transcript	5_prime_UTR_variant	533	.	.	.	.	.	.	.	1	REC8	HGNC	16879	protein_coding	YES	CCDS41932.1	ENSP00000308699	REC8_HUMAN	H0YMV7_HUMAN,H0YM87_HUMAN,H0YLK4_HUMAN	UPI000013C70B	.	.	.	2/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGCCCTAAAG	.	3	ESCA
FAM177A1	0	.	GRCh37	14	35515698	35515698	+	Missense_Mutation	SNP	T	T	C	rs762757572	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29T>C	p.Leu10Pro	p.L10P	ENST00000280987	1/5	302	255	47	53	53	0	FAM177A1,missense_variant,p.Leu10Pro,ENST00000280987,;FAM177A1,intron_variant,,ENST00000396472,;FAM177A1,intron_variant,,ENST00000382406,;FAM177A1,intron_variant,,ENST00000555211,;FAM177A1,non_coding_transcript_exon_variant,,ENST00000554052,;FAM177A1,upstream_gene_variant,,ENST00000556858,;FAM177A1,upstream_gene_variant,,ENST00000553852,;FAM177A1,upstream_gene_variant,,ENST00000553955,;	C	ENSG00000151327	ENST00000280987	Transcript	missense_variant	90	29	10	L/P	cTc/cCc	rs762757572	.	.	1	FAM177A1	HGNC	19829	protein_coding	YES	CCDS9653.2	ENSP00000280987	F177A_HUMAN	G3V583_HUMAN,G3V3Z5_HUMAN	UPI00005A8F3C	.	deleterious_low_confidence(0)	benign(0.207)	1/5	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCCTCTTTC	.	4	ESCA
KTN1	0	.	GRCh37	14	56142634	56142634	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3853A>G	p.Lys1285Glu	p.K1285E	ENST00000395314	41/44	44	31	13	36	36	0	KTN1,missense_variant,p.Lys523Glu,ENST00000554507,;KTN1,missense_variant,p.Lys1234Glu,ENST00000395311,;KTN1,missense_variant,p.Lys1285Glu,ENST00000416613,;KTN1,missense_variant,p.Lys1234Glu,ENST00000395308,;KTN1,missense_variant,p.Lys1228Glu,ENST00000438792,;KTN1,missense_variant,p.Lys1234Glu,ENST00000413890,;KTN1,missense_variant,p.Lys1285Glu,ENST00000395309,;KTN1,missense_variant,p.Lys262Glu,ENST00000555573,;KTN1,missense_variant,p.Lys56Glu,ENST00000554294,;KTN1,missense_variant,p.Lys1285Glu,ENST00000395314,;KTN1,downstream_gene_variant,,ENST00000553624,;KTN1,missense_variant,p.Lys1285Glu,ENST00000459737,;KTN1,splice_region_variant,,ENST00000554831,;KTN1,splice_region_variant,,ENST00000556631,;KTN1,splice_region_variant,,ENST00000555172,;KTN1,splice_region_variant,,ENST00000334975,;KTN1,upstream_gene_variant,,ENST00000553710,;KTN1,downstream_gene_variant,,ENST00000555506,;	G	ENSG00000126777	ENST00000395314	Transcript	missense_variant	3921	3853	1285	K/E	Aag/Gag	.	.	.	1	KTN1	HGNC	6467	protein_coding	YES	CCDS41957.1	ENSP00000378725	KTN1_HUMAN	Q5GGW3_HUMAN,G3V5P0_HUMAN,G3V4L8_HUMAN,G3V475_HUMAN	UPI0000190F88	.	deleterious(0.03)	benign(0.399)	41/44	.	hmmpanther:PTHR18864	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCATAAGGTA	.	5	ESCA
TMEM260	0	.	GRCh37	14	57075997	57075997	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.810C>T	p.%3D	p.F270F	ENST00000261556	6/16	100	79	21	72	72	0	TMEM260,synonymous_variant,p.%3D,ENST00000261556,;TMEM260,synonymous_variant,p.%3D,ENST00000538838,;TMEM260,5_prime_UTR_variant,,ENST00000536419,;TMEM260,non_coding_transcript_exon_variant,,ENST00000553335,;TMEM260,synonymous_variant,p.%3D,ENST00000556422,;TMEM260,synonymous_variant,p.%3D,ENST00000555905,;TMEM260,synonymous_variant,p.%3D,ENST00000539559,;TMEM260,3_prime_UTR_variant,,ENST00000555497,;TMEM260,3_prime_UTR_variant,,ENST00000556929,;TMEM260,non_coding_transcript_exon_variant,,ENST00000557626,;TMEM260,non_coding_transcript_exon_variant,,ENST00000557657,;TMEM260,downstream_gene_variant,,ENST00000556079,;	T	ENSG00000070269	ENST00000261556	Transcript	synonymous_variant	932	810	270	F	ttC/ttT	.	.	.	1	TMEM260	HGNC	20185	protein_coding	YES	CCDS9727.2	ENSP00000261556	TM260_HUMAN	G3V4Y3_HUMAN,B3KN73_HUMAN	UPI00001FD5D2	.	.	.	6/16	.	hmmpanther:PTHR16214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCAGCCT	.	5	ESCA
C14orf37	0	.	GRCh37	14	58604975	58604975	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1102G>T	p.Gly368Trp	p.G368W	ENST00000267485	2/8	52	29	23	40	40	0	C14orf37,missense_variant,p.Gly368Trp,ENST00000267485,;C14orf37,non_coding_transcript_exon_variant,,ENST00000334342,;C14orf37,intron_variant,,ENST00000557175,;C14orf37,downstream_gene_variant,,ENST00000554218,;UBA52P3,upstream_gene_variant,,ENST00000491303,;	A	ENSG00000139971	ENST00000267485	Transcript	missense_variant	1297	1102	368	G/W	Ggg/Tgg	.	.	.	-1	C14orf37	HGNC	19846	protein_coding	YES	CCDS32089.1	ENSP00000267485	CN037_HUMAN	.	UPI000000CC37	.	deleterious(0)	benign(0.15)	2/8	.	hmmpanther:PTHR21585:SF0,hmmpanther:PTHR21585	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCCCAGAG	.	5	ESCA
LRRC57	0	.	GRCh37	15	42837391	42837391	+	Missense_Mutation	SNP	G	G	C	rs760414068	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562C>G	p.Leu188Val	p.L188V	ENST00000323443	4/5	37	25	11	38	38	0	LRRC57,missense_variant,p.Leu188Val,ENST00000323443,;LRRC57,missense_variant,p.Leu188Val,ENST00000563454,;LRRC57,missense_variant,p.Leu188Val,ENST00000397130,;SNAP23,missense_variant,p.Lys72Asn,ENST00000563873,;SNAP23,3_prime_UTR_variant,,ENST00000568841,;SNAP23,intron_variant,,ENST00000563830,;HAUS2,upstream_gene_variant,,ENST00000568846,;HAUS2,upstream_gene_variant,,ENST00000562398,;HAUS2,upstream_gene_variant,,ENST00000568876,;HAUS2,upstream_gene_variant,,ENST00000260372,;LRRC57,downstream_gene_variant,,ENST00000570160,;LRRC57,non_coding_transcript_exon_variant,,ENST00000569830,;LRRC57,non_coding_transcript_exon_variant,,ENST00000562868,;HAUS2,upstream_gene_variant,,ENST00000391623,;HAUS2,upstream_gene_variant,,ENST00000563479,;HAUS2,upstream_gene_variant,,ENST00000567640,;HAUS2,upstream_gene_variant,,ENST00000570178,;HAUS2,upstream_gene_variant,,ENST00000564279,;	C	ENSG00000180979	ENST00000323443	Transcript	missense_variant	930	562	188	L/V	Ctt/Gtt	rs760414068	.	.	-1	LRRC57	HGNC	26719	protein_coding	YES	CCDS10089.1	ENSP00000326817	LRC57_HUMAN	H3BSW0_HUMAN	UPI000004F8C8	.	deleterious(0.03)	probably_damaging(0.997)	4/5	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23155,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAAGACAAT	.	5	ESCA
SLC12A1	0	.	GRCh37	15	48500102	48500102	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186T>G	p.Phe62Leu	p.F62L	ENST00000396577	2/27	31	10	21	23	23	0	SLC12A1,missense_variant,p.Phe62Leu,ENST00000330289,;SLC12A1,missense_variant,p.Phe62Leu,ENST00000380993,;SLC12A1,missense_variant,p.Phe62Leu,ENST00000396577,;SLC12A1,missense_variant,p.Phe62Leu,ENST00000558405,;SLC12A1,missense_variant,p.Phe62Leu,ENST00000561031,;SLC12A1,intron_variant,,ENST00000559641,;CTXN2,downstream_gene_variant,,ENST00000417307,;SLC12A1,intron_variant,,ENST00000561127,;	G	ENSG00000074803	ENST00000396577	Transcript	missense_variant	401	186	62	F/L	ttT/ttG	.	.	.	1	SLC12A1	HGNC	10910	protein_coding	YES	CCDS53940.1	ENSP00000379822	.	O76030_HUMAN,E9PDW4_HUMAN	UPI000013C794	.	tolerated(0.18)	benign(0.103)	2/27	.	Prints_domain:PR01209	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTTAGGCC	.	5	ESCA
ACSM1	0	.	GRCh37	16	20702457	20702457	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54C>T	p.%3D	p.H18H	ENST00000307493	1/13	81	51	29	109	109	0	ACSM1,synonymous_variant,p.%3D,ENST00000523065,;ACSM1,synonymous_variant,p.%3D,ENST00000307493,;ACSM1,synonymous_variant,p.%3D,ENST00000520010,;ACSM1,5_prime_UTR_variant,,ENST00000219151,;ACSM3,intron_variant,,ENST00000561584,;ACSM3,intron_variant,,ENST00000568235,;ACSM3,intron_variant,,ENST00000501740,;ACSM1,synonymous_variant,p.%3D,ENST00000519745,;	A	ENSG00000166743	ENST00000307493	Transcript	synonymous_variant	122	54	18	H	caC/caT	.	.	.	-1	ACSM1	HGNC	18049	protein_coding	YES	CCDS10587.1	ENSP00000301956	ACSM1_HUMAN	E5RFK0_HUMAN	UPI00000558D0	.	.	.	1/13	.	hmmpanther:PTHR24095:SF150,hmmpanther:PTHR24095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTTGTGGAA	.	5	ESCA
CREBBP	0	.	GRCh37	16	3781439	3781439	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4926C>T	p.%3D	p.V1642V	ENST00000262367	30/31	18	13	5	14	14	0	CREBBP,synonymous_variant,p.%3D,ENST00000262367,;CREBBP,synonymous_variant,p.%3D,ENST00000382070,;CREBBP,downstream_gene_variant,,ENST00000571763,;CREBBP,downstream_gene_variant,,ENST00000576720,;	A	ENSG00000005339	ENST00000262367	Transcript	synonymous_variant	5736	4926	1642	V	gtC/gtT	.	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	.	30/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTGATGACAGG	.	3	ESCA
ABCC11	0	.	GRCh37	16	48209220	48209220	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3647C>A	p.Ser1216Tyr	p.S1216Y	ENST00000394747	25/29	52	25	27	36	36	0	ABCC11,missense_variant,p.Ser1216Tyr,ENST00000394747,;ABCC11,missense_variant,p.Ser1216Tyr,ENST00000394748,;ABCC11,missense_variant,p.Ser1216Tyr,ENST00000353782,;ABCC11,missense_variant,p.Ser1216Tyr,ENST00000356608,;ABCC11,non_coding_transcript_exon_variant,,ENST00000565329,;	T	ENSG00000121270	ENST00000394747	Transcript	missense_variant	3997	3647	1216	S/Y	tCc/tAc	.	.	.	-1	ABCC11	HGNC	14639	protein_coding	YES	CCDS10732.1	ENSP00000378230	ABCCB_HUMAN	H3BRJ2_HUMAN	UPI0000052711	.	deleterious(0)	probably_damaging(0.987)	25/29	.	PROSITE_profiles:PS50893,hmmpanther:PTHR24223:SF168,hmmpanther:PTHR24223,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTGGACCGC	.	5	ESCA
NLRC5	0	.	GRCh37	16	57104507	57104507	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4644G>C	p.%3D	p.G1548G	ENST00000262510	38/49	124	96	27	115	115	0	NLRC5,synonymous_variant,p.%3D,ENST00000308149,;NLRC5,synonymous_variant,p.%3D,ENST00000539144,;NLRC5,synonymous_variant,p.%3D,ENST00000262510,;NLRC5,3_prime_UTR_variant,,ENST00000436936,;NLRC5,synonymous_variant,p.%3D,ENST00000545349,;NLRC5,3_prime_UTR_variant,,ENST00000537056,;NLRC5,3_prime_UTR_variant,,ENST00000540182,;NLRC5,3_prime_UTR_variant,,ENST00000545081,;NLRC5,3_prime_UTR_variant,,ENST00000538453,;NLRC5,upstream_gene_variant,,ENST00000544189,;	C	ENSG00000140853	ENST00000262510	Transcript	synonymous_variant	4869	4644	1548	G	ggG/ggC	.	.	.	1	NLRC5	HGNC	29933	protein_coding	YES	CCDS10773.1	ENSP00000262510	NLRC5_HUMAN	F5H274_HUMAN,F5GYP0_HUMAN	UPI00001AEE94	.	.	.	38/49	.	hmmpanther:PTHR24106:SF69,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGGGAAATG	.	5	ESCA
GINS2	0	.	GRCh37	16	85712254	85712254	+	Silent	SNP	C	C	T	rs541558749	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.324G>A	p.%3D	p.P108P	ENST00000253462	4/5	10	7	3	10	10	0	GINS2,synonymous_variant,p.%3D,ENST00000596233,;GINS2,synonymous_variant,p.%3D,ENST00000595355,;GINS2,synonymous_variant,p.%3D,ENST00000253462,;GSE1,downstream_gene_variant,,ENST00000253458,;GSE1,downstream_gene_variant,,ENST00000412692,;GSE1,downstream_gene_variant,,ENST00000393243,;GSE1,downstream_gene_variant,,ENST00000469381,;	T	ENSG00000131153	ENST00000253462	Transcript	synonymous_variant	425	324	108	P	ccG/ccA	rs541558749,COSM974517	.	.	-1	GINS2	HGNC	24575	protein_coding	YES	CCDS10953.1	ENSP00000253462	PSF2_HUMAN	M0R043_HUMAN,M0QXS3_HUMAN	UPI000006D930	.	.	.	4/5	.	Superfamily_domains:SSF158573,PIRSF_domain:PIRSF028998,Pfam_domain:PF05916,hmmpanther:PTHR12772	G:0.0002	G:0	G:0.0014	.	G:0	G:0	G:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCCTTCGGGAT	by1000G	3	ESCA
MYOCD	0	.	GRCh37	17	12649386	12649386	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1122G>C	p.%3D	p.L374L	ENST00000425538	9/14	40	36	4	44	44	0	MYOCD,synonymous_variant,p.%3D,ENST00000343344,;MYOCD,synonymous_variant,p.%3D,ENST00000443061,;MYOCD,synonymous_variant,p.%3D,ENST00000425538,;AC005358.1,synonymous_variant,p.%3D,ENST00000609971,;MYOCD,non_coding_transcript_exon_variant,,ENST00000395988,;	C	ENSG00000141052	ENST00000425538	Transcript	synonymous_variant	1322	1122	374	L	ctG/ctC	.	.	.	1	MYOCD	HGNC	16067	protein_coding	YES	CCDS54091.1	ENSP00000401678	MYCD_HUMAN	.	UPI000022A2E2	.	.	.	9/14	.	Superfamily_domains:SSF68906,SMART_domains:SM00513,Gene3D:1.10.720.30,Pfam_domain:PF02037,hmmpanther:PTHR22793,hmmpanther:PTHR22793:SF11,PROSITE_profiles:PS50800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GATCTGAAGGT	.	2	ESCA
SLC47A2	0	.	GRCh37	17	19611088	19611088	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806T>A	p.Leu269Gln	p.L269Q	ENST00000325411	8/17	27	12	14	26	26	0	SLC47A2,missense_variant,p.Leu233Gln,ENST00000350657,;SLC47A2,missense_variant,p.Leu233Gln,ENST00000433844,;SLC47A2,missense_variant,p.Leu269Gln,ENST00000325411,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000463318,;SLC47A2,3_prime_UTR_variant,,ENST00000574239,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000467609,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000467379,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000574220,;	T	ENSG00000180638	ENST00000325411	Transcript	missense_variant	857	806	269	L/Q	cTg/cAg	.	.	.	-1	SLC47A2	HGNC	26439	protein_coding	YES	CCDS11211.1	ENSP00000326671	S47A2_HUMAN	.	UPI0000190813	.	tolerated(0.14)	benign(0.059)	8/17	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11206,hmmpanther:PTHR11206:SF81,TIGRFAM_domain:TIGR00797	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCAGCACA	.	5	ESCA
CACNG5	0	.	GRCh37	17	64876781	64876781	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391G>C	p.Ala131Pro	p.A131P	ENST00000533854	4/6	63	48	15	59	59	0	CACNG5,missense_variant,p.Ala131Pro,ENST00000169565,;CACNG5,missense_variant,p.Ala131Pro,ENST00000307139,;CACNG5,missense_variant,p.Ala131Pro,ENST00000533854,;	C	ENSG00000075429	ENST00000533854	Transcript	missense_variant	628	391	131	A/P	Gcc/Ccc	.	.	.	1	CACNG5	HGNC	1409	protein_coding	YES	CCDS11665.1	ENSP00000436836	CCG5_HUMAN	.	UPI0000001240	.	tolerated(0.13)	probably_damaging(0.976)	4/6	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12107:SF4,hmmpanther:PTHR12107,Pfam_domain:PF00822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTGGCCTTT	.	5	ESCA
YBX2	0	.	GRCh37	17	7193602	7193602	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712C>T	p.Pro238Ser	p.P238S	ENST00000007699	5/9	91	68	23	94	94	0	YBX2,missense_variant,p.Pro38Ser,ENST00000571464,;YBX2,missense_variant,p.Pro238Ser,ENST00000007699,;SLC2A4,downstream_gene_variant,,ENST00000317370,;SLC2A4,downstream_gene_variant,,ENST00000424875,;SLC2A4,downstream_gene_variant,,ENST00000571308,;YBX2,downstream_gene_variant,,ENST00000570627,;YBX2,non_coding_transcript_exon_variant,,ENST00000571485,;YBX2,non_coding_transcript_exon_variant,,ENST00000570720,;YBX2,non_coding_transcript_exon_variant,,ENST00000571834,;YBX2,downstream_gene_variant,,ENST00000571127,;SLC2A4,downstream_gene_variant,,ENST00000570783,;SLC2A4,downstream_gene_variant,,ENST00000572485,;	A	ENSG00000006047	ENST00000007699	Transcript	missense_variant	776	712	238	P/S	Ccc/Tcc	COSM3521674	.	.	-1	YBX2	HGNC	17948	protein_coding	YES	CCDS11098.1	ENSP00000007699	YBOX2_HUMAN	.	UPI000006E761	.	tolerated(0.1)	possibly_damaging(0.641)	5/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11544:SF41,hmmpanther:PTHR11544	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGGGGCCTC	.	5	ESCA
CD300A	0	.	GRCh37	17	72480172	72480172	+	Silent	SNP	G	G	A	rs772744436	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.807G>A	p.%3D	p.S269S	ENST00000360141	7/7	112	29	83	76	76	0	CD300A,synonymous_variant,p.%3D,ENST00000310828,;CD300A,synonymous_variant,p.%3D,ENST00000392625,;CD300A,synonymous_variant,p.%3D,ENST00000360141,;CD300A,synonymous_variant,p.%3D,ENST00000577511,;CD300A,synonymous_variant,p.%3D,ENST00000361933,;CD300A,non_coding_transcript_exon_variant,,ENST00000582319,;	A	ENSG00000167851	ENST00000360141	Transcript	synonymous_variant	1095	807	269	S	tcG/tcA	rs772744436	.	.	1	CD300A	HGNC	19319	protein_coding	YES	CCDS32720.1	ENSP00000353259	CLM8_HUMAN	J3QKQ4_HUMAN	UPI0000073EA9	.	.	.	7/7	.	hmmpanther:PTHR11860:SF40,hmmpanther:PTHR11860,Pfam_domain:PF15330	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCGGTGGT	.	5	ESCA
TP53	0	.	GRCh37	17	7577498	7577498	+	Splice_Site	SNP	C	C	T	.	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.782+1G>A	.	p.X261_splice	ENST00000269305	.	287	77	209	236	236	0	TP53,splice_donor_variant,,ENST00000413465,;TP53,splice_donor_variant,,ENST00000420246,;TP53,splice_donor_variant,,ENST00000269305,;TP53,splice_donor_variant,,ENST00000509690,;TP53,splice_donor_variant,,ENST00000359597,;TP53,splice_donor_variant,,ENST00000445888,;TP53,splice_donor_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,splice_donor_variant,,ENST00000504937,;TP53,splice_donor_variant,,ENST00000504290,;TP53,splice_donor_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	splice_donor_variant	.	.	.	.	.	TP53_g.13420G>C,TP53_g.13420G>A,TP53_g.13420G>T,COSM44640,COSM43571,COSM98254,COSM329756,COSM395657,COSM473430,COSM3937599,COSM395658,COSM3937602,COSM473431,COSM98255,COSM3717631,COSM3958806,COSM3937601,COSM2744561,COSM3717630,COSM3937600	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	7/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.782+1G>A|4,SITE|p.?|c.782+1G>A|15,SITE|p.?|c.782+1G>A|4,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.?|c.782+1G>T|12,BUFFER|p.?|c.782+1G>C|3,BUFFER|p.S261T|c.782G>C|3,BUFFER|p.S260_S261insX|c.780_781insNNN|3,BUFFER|p.S260S|c.780C>T|4,BUFFER|p.S260fs*85|c.778delT|3,BUFFER|p.S260C|c.779C>G|3,BUFFER|p.S260F|c.779C>T|3,BUFFER|p.D259E|c.777C>A|3,BUFFER|p.D259V|c.776A>T|17,BUFFER|p.D259V|c.776A>T|3,BUFFER|p.D259V|c.776A>T|3,BUFFER|p.D259G|c.776A>G|4,BUFFER|p.D259fs*86|c.775delG|3,BUFFER|p.D259N|c.775G>A|6,BUFFER|p.D259Y|c.775G>T|6,BUFFER|p.D259H|c.775G>C|3,BUFFER|p.D259Y|c.775G>T|23,BUFFER|p.D259Y|c.775G>T|4,BUFFER|p.D259Y|c.775G>T|6,BUFFER|p.E258D|c.774A>T|3,BUFFER|p.E258D|c.774A>C|3,BUFFER|p.E258D|c.774A>T|9,BUFFER|p.E258D|c.774A>T|3,BUFFER|p.E258G|c.773A>G|9,BUFFER|p.E258V|c.773A>T|10,BUFFER|p.E258A|c.773A>C|6,BUFFER|p.E258*|c.772G>T|20,BUFFER|p.E258K|c.772G>A|3,BUFFER|p.E258Q|c.772G>C|9,BUFFER|p.E258*|c.772G>T|8,BUFFER|p.E258*|c.772G>T|8,BUFFER|p.E258K|c.772G>A|43,BUFFER|p.E258K|c.772G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGACCTGGA	.	5	ESCA
AATK	0	.	GRCh37	17	79094681	79094681	+	Nonsense_Mutation	SNP	G	G	A	rs778316408	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3055C>T	p.Arg1019Ter	p.R1019*	ENST00000326724	11/14	41	17	24	40	40	0	AATK,stop_gained,p.Arg1019Ter,ENST00000326724,;AATK,stop_gained,p.Arg916Ter,ENST00000417379,;BAIAP2,downstream_gene_variant,,ENST00000428708,;BAIAP2,downstream_gene_variant,,ENST00000435091,;BAIAP2,downstream_gene_variant,,ENST00000321300,;BAIAP2,downstream_gene_variant,,ENST00000575245,;BAIAP2,downstream_gene_variant,,ENST00000392411,;BAIAP2,downstream_gene_variant,,ENST00000572498,;MIR657,downstream_gene_variant,,ENST00000385003,;MIR338,upstream_gene_variant,,ENST00000390137,;AATK,downstream_gene_variant,,ENST00000573441,;AATK,downstream_gene_variant,,ENST00000572339,;AATK,3_prime_UTR_variant,,ENST00000570932,;AATK,3_prime_UTR_variant,,ENST00000374792,;AATK,intron_variant,,ENST00000573469,;BAIAP2,downstream_gene_variant,,ENST00000576225,;	A	ENSG00000181409	ENST00000326724	Transcript	stop_gained	3080	3055	1019	R/*	Cga/Tga	rs778316408	.	.	-1	AATK	HGNC	21	protein_coding	YES	CCDS45807.1	ENSP00000324196	LMTK1_HUMAN	H7C175_HUMAN	UPI000041EA63	.	.	.	11/14	.	hmmpanther:PTHR24417:SF0,hmmpanther:PTHR24417	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCGGTCCC	byFrequency	5	ESCA
ANKRD30B	0	.	GRCh37	18	14778005	14778005	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351C>G	p.Gln451Glu	p.Q451E	ENST00000358984	10/36	19	9	10	16	16	0	ANKRD30B,missense_variant,p.Gln451Glu,ENST00000447268,;ANKRD30B,missense_variant,p.Gln451Glu,ENST00000358984,;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,missense_variant,p.Gln451Glu,ENST00000580206,;	G	ENSG00000180777	ENST00000358984	Transcript	missense_variant	1531	1351	451	Q/E	Cag/Gag	.	.	.	1	ANKRD30B	HGNC	24165	protein_coding	YES	CCDS54182.1	ENSP00000351875	AN30B_HUMAN	.	UPI0000425FF7	.	tolerated(0.2)	possibly_damaging(0.542)	10/36	.	hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCACAGAAT	.	5	ESCA
MYO5B	0	.	GRCh37	18	47431143	47431143	+	Missense_Mutation	SNP	G	G	A	rs777038090	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2470C>T	p.Arg824Cys	p.R824C	ENST00000285039	20/40	96	69	27	90	90	0	MYO5B,missense_variant,p.Arg824Cys,ENST00000285039,;MYO5B,upstream_gene_variant,,ENST00000324581,;MYO5B,upstream_gene_variant,,ENST00000592779,;	A	ENSG00000167306	ENST00000285039	Transcript	missense_variant	2770	2470	824	R/C	Cgc/Tgc	rs777038090	.	.	-1	MYO5B	HGNC	7603	protein_coding	YES	CCDS42436.1	ENSP00000285039	MYO5B_HUMAN	Q14782_HUMAN,Q0P656_HUMAN,K7EPI3_HUMAN	UPI00001D7B21	.	deleterious(0)	probably_damaging(0.982)	20/40	.	PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF356,Pfam_domain:PF00612,SMART_domains:SM00015,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGCGGTAAT	byFrequency	5	ESCA
L3MBTL4	0	.	GRCh37	18	6311610	6311610	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15C>T	p.%3D	p.N5N	ENST00000284898	3/20	58	40	17	55	55	0	L3MBTL4,synonymous_variant,p.%3D,ENST00000583054,;L3MBTL4,synonymous_variant,p.%3D,ENST00000284898,;L3MBTL4,synonymous_variant,p.%3D,ENST00000400105,;L3MBTL4,synonymous_variant,p.%3D,ENST00000317931,;L3MBTL4,synonymous_variant,p.%3D,ENST00000581231,;L3MBTL4,synonymous_variant,p.%3D,ENST00000583809,;L3MBTL4,synonymous_variant,p.%3D,ENST00000400104,;L3MBTL4,non_coding_transcript_exon_variant,,ENST00000580162,;	A	ENSG00000154655	ENST00000284898	Transcript	synonymous_variant	216	15	5	N	aaC/aaT	.	.	.	-1	L3MBTL4	HGNC	26677	protein_coding	YES	CCDS11839.2	ENSP00000284898	LMBL4_HUMAN	J3QLK8_HUMAN,J3KS41_HUMAN,J3KRN7_HUMAN	UPI000013DDC0	.	.	.	3/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTGTTGGG	.	5	ESCA
ZADH2	0	.	GRCh37	18	72914034	72914034	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471C>T	p.%3D	p.G157G	ENST00000322342	2/2	17	11	5	15	15	0	ZADH2,synonymous_variant,p.%3D,ENST00000581620,;ZADH2,synonymous_variant,p.%3D,ENST00000322342,;ZADH2,synonymous_variant,p.%3D,ENST00000537114,;ZADH2,synonymous_variant,p.%3D,ENST00000582437,;	A	ENSG00000180011	ENST00000322342	Transcript	synonymous_variant	761	471	157	G	ggC/ggT	.	.	.	-1	ZADH2	HGNC	28697	protein_coding	YES	CCDS12008.1	ENSP00000323678	ZADH2_HUMAN	J3QQQ7_HUMAN,J3KTQ8_HUMAN,B4DZ91_HUMAN	UPI00000350AF	.	.	.	2/2	.	hmmpanther:PTHR11695:SF264,hmmpanther:PTHR11695,Gene3D:3.90.180.10,SMART_domains:SM00829,Superfamily_domains:SSF50129,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTGCCACT	.	5	ESCA
ZADH2	0	.	GRCh37	18	72914035	72914035	+	Missense_Mutation	SNP	C	C	A	rs772466840	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470G>T	p.Gly157Val	p.G157V	ENST00000322342	2/2	18	12	5	15	15	0	ZADH2,missense_variant,p.Gly34Val,ENST00000581620,;ZADH2,missense_variant,p.Gly157Val,ENST00000322342,;ZADH2,missense_variant,p.Gly34Val,ENST00000537114,;ZADH2,missense_variant,p.Gly34Val,ENST00000582437,;	A	ENSG00000180011	ENST00000322342	Transcript	missense_variant	760	470	157	G/V	gGc/gTc	rs772466840	.	.	-1	ZADH2	HGNC	28697	protein_coding	YES	CCDS12008.1	ENSP00000323678	ZADH2_HUMAN	J3QQQ7_HUMAN,J3KTQ8_HUMAN,B4DZ91_HUMAN	UPI00000350AF	.	deleterious(0)	probably_damaging(0.98)	2/2	.	hmmpanther:PTHR11695:SF264,hmmpanther:PTHR11695,Gene3D:3.90.180.10,SMART_domains:SM00829,Superfamily_domains:SSF50129,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGCCACTT	byFrequency	5	ESCA
CNN2	0	.	GRCh37	19	1036240	1036408	+	Splice_Site	DEL	CTGCAGGTGGGCGACAGCTCCCCCAGCCCCAGGGACCACGGCATTGGGGGACCACGGTGTTGGGGGACAGCAGCATTGGGGGACAGCGGCATGGAGCCCTGTGGTCCCTCAATTTCAGGGAGGGACCGGAAGCTTGTTGGGTGCAGTCTGACCTCTCCCACGAACCTCC	CTGCAGGTGGGCGACAGCTCCCCCAGCCCCAGGGACCACGGCATTGGGGGACCACGGTGTTGGGGGACAGCAGCATTGGGGGACAGCGGCATGGAGCCCTGTGGTCCCTCAATTTCAGGGAGGGACCGGAAGCTTGTTGGGTGCAGTCTGACCTCTCCCACGAACCTCC	-	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	CTGCAGGTGGGCGACAGCTCCCCCAGCCCCAGGGACCACGGCATTGGGGGACCACGGTGTTGGGGGACAGCAGCATTGGGGGACAGCGGCATGGAGCCCTGTGGTCCCTCAATTTCAGGGAGGGACCGGAAGCTTGTTGGGTGCAGTCTGACCTCTCCCACGAACCTCC	CTGCAGGTGGGCGACAGCTCCCCCAGCCCCAGGGACCACGGCATTGGGGGACCACGGTGTTGGGGGACAGCAGCATTGGGGGACAGCGGCATGGAGCCCTGTGGTCCCTCAATTTCAGGGAGGGACCGGAAGCTTGTTGGGTGCAGTCTGACCTCTCCCACGAACCTCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.508-1_507+1delGTGGGCGACAGCTCCCCCAGCCCCAGGGACCACGGCATTGGGGGACCACGGTGTTGGGGGACAGCAGCATTGGGGGACAGCGGCATGGAGCCCTGTGGTCCCTCAATTTCAGGGAGGGACCGGAAGCTTGTTGGGTGCAGTCTGACCTCTCCCACGAACCTCCCTGCAG	.	p.X170_splice	ENST00000263097	5/7	40	36	4	46	46	0	CNN2,splice_donor_variant,,ENST00000263097,;CNN2,splice_donor_variant,,ENST00000562958,;CNN2,splice_donor_variant,,ENST00000568865,;CNN2,splice_donor_variant,,ENST00000565096,;CNN2,splice_region_variant,,ENST00000562075,;CNN2,splice_region_variant,,ENST00000607102,;CNN2,splice_region_variant,,ENST00000348419,;ABCA7,upstream_gene_variant,,ENST00000263094,;ABCA7,upstream_gene_variant,,ENST00000524850,;ABCA7,upstream_gene_variant,,ENST00000433129,;ABCA7,upstream_gene_variant,,ENST00000531467,;AC011558.5,downstream_gene_variant,,ENST00000585757,;CNN2,splice_region_variant,,ENST00000606983,;CNN2,downstream_gene_variant,,ENST00000562015,;CNN2,splice_donor_variant,,ENST00000566695,;CNN2,intron_variant,,ENST00000569352,;CNN2,upstream_gene_variant,,ENST00000564572,;ABCA7,upstream_gene_variant,,ENST00000526885,;ABCA7,upstream_gene_variant,,ENST00000530703,;ABCA7,upstream_gene_variant,,ENST00000525238,;ABCA7,upstream_gene_variant,,ENST00000527496,;	-	ENSG00000064666	ENST00000263097	Transcript	splice_donor_variant	865-?	502-?	168-?	.	.	.	.	.	1	CNN2	HGNC	2156	protein_coding	YES	CCDS12053.1	ENSP00000263097	CNN2_HUMAN	.	UPI0000127AF5	.	.	.	5/7	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA*|PINDEL|VARSCANS*	ATCGGGCTGCAGGTGGGCGACAGCTCCCCCAGCCCCAGGGACCACGGCATTGGGGGACCACGGTGTTGGGGGACAGCAGCATTGGGGGACAGCGGCATGGAGCCCTGTGGTCCCTCAATTTCAGGGAGGGACCGGAAGCTTGTTGGGTGCAGTCTGACCTCTCCCACGAACCTCCCTGCA	.	3	ESCA
SBNO2	0	.	GRCh37	19	1120003	1120003	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1169A>C	p.His390Pro	p.H390P	ENST00000361757	12/32	37	26	11	33	33	0	SBNO2,missense_variant,p.His333Pro,ENST00000438103,;SBNO2,missense_variant,p.His390Pro,ENST00000587024,;SBNO2,missense_variant,p.His390Pro,ENST00000361757,;SBNO2,non_coding_transcript_exon_variant,,ENST00000592222,;SBNO2,non_coding_transcript_exon_variant,,ENST00000590446,;	G	ENSG00000064932	ENST00000361757	Transcript	missense_variant	1407	1169	390	H/P	cAc/cCc	.	.	.	-1	SBNO2	HGNC	29158	protein_coding	YES	CCDS45894.1	ENSP00000354733	SBNO2_HUMAN	K7ERL2_HUMAN,K7ENA9_HUMAN	UPI0000140680	.	deleterious(0.01)	benign(0.25)	12/32	.	hmmpanther:PTHR12706:SF5,hmmpanther:PTHR12706,Gene3D:3.40.50.300,Pfam_domain:PF13872,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGTGACAC	.	5	ESCA
ZNF763	0	.	GRCh37	19	12090268	12090268	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*344A>C	.	.	ENST00000343949	4/4	35	31	3	46	46	0	ZNF763,3_prime_UTR_variant,,ENST00000343949,;ZNF763,3_prime_UTR_variant,,ENST00000545530,;ZNF763,downstream_gene_variant,,ENST00000538752,;ZNF763,downstream_gene_variant,,ENST00000586494,;ZNF763,downstream_gene_variant,,ENST00000481745,;ZNF763,downstream_gene_variant,,ENST00000590798,;ZNF763,downstream_gene_variant,,ENST00000591944,;ZNF763,downstream_gene_variant,,ENST00000592625,;ZNF763,downstream_gene_variant,,ENST00000358987,;ZNF763,downstream_gene_variant,,ENST00000591441,;ZNF763,downstream_gene_variant,,ENST00000586354,;	C	ENSG00000197054	ENST00000343949	Transcript	3_prime_UTR_variant	1693	.	.	.	.	.	.	.	1	ZNF763	HGNC	27614	protein_coding	YES	CCDS45982.1	ENSP00000369774	ZN763_HUMAN	K7EJF3_HUMAN,B4DRE7_HUMAN	UPI00001609E5	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAAAGACCTTA	.	3	ESCA
MAU2	0	.	GRCh37	19	19460171	19460171	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1474G>A	p.Glu492Lys	p.E492K	ENST00000392313	16/19	75	50	24	86	86	0	MAU2,missense_variant,p.Glu492Lys,ENST00000392313,;MAU2,missense_variant,p.Glu492Lys,ENST00000262815,;MAU2,downstream_gene_variant,,ENST00000609060,;MAU2,downstream_gene_variant,,ENST00000585823,;MAU2,non_coding_transcript_exon_variant,,ENST00000589947,;MAU2,non_coding_transcript_exon_variant,,ENST00000587638,;MAU2,non_coding_transcript_exon_variant,,ENST00000587709,;MAU2,non_coding_transcript_exon_variant,,ENST00000590882,;MAU2,non_coding_transcript_exon_variant,,ENST00000587938,;MAU2,non_coding_transcript_exon_variant,,ENST00000587362,;MAU2,non_coding_transcript_exon_variant,,ENST00000262816,;MAU2,upstream_gene_variant,,ENST00000499453,;	A	ENSG00000129933	ENST00000392313	Transcript	missense_variant	1653	1474	492	E/K	Gag/Aag	.	.	.	1	MAU2	HGNC	29140	protein_coding	YES	CCDS32969.2	ENSP00000376127	SCC4_HUMAN	.	UPI00001C200D	.	deleterious(0.01)	probably_damaging(1)	16/19	.	hmmpanther:PTHR21394,Gene3D:1.25.40.10,Pfam_domain:PF10345,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGAGGAC	.	5	ESCA
ZNF536	0	.	GRCh37	19	31039123	31039123	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2597C>G	p.Ser866Cys	p.S866C	ENST00000355537	4/5	31	24	7	33	33	0	ZNF536,missense_variant,p.Ser866Cys,ENST00000585628,;ZNF536,missense_variant,p.Ser866Cys,ENST00000355537,;ZNF536,upstream_gene_variant,,ENST00000592773,;	G	ENSG00000198597	ENST00000355537	Transcript	missense_variant	2744	2597	866	S/C	tCt/tGt	.	.	.	1	ZNF536	HGNC	29025	protein_coding	YES	CCDS32984.1	ENSP00000347730	ZN536_HUMAN	K7EKT4_HUMAN,K7EJP8_HUMAN	UPI000006ED3E	.	deleterious(0.01)	possibly_damaging(0.56)	4/5	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCTGGAG	.	5	ESCA
ZNF540	0	.	GRCh37	19	38102492	38102492	+	Missense_Mutation	SNP	T	T	C	rs745556311	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311T>C	p.Ile104Thr	p.I104T	ENST00000592533	5/5	24	18	5	26	26	0	ZNF540,stop_lost,p.Ter30GlnextTer1,ENST00000586792,;ZNF540,missense_variant,p.Ile104Thr,ENST00000316433,;ZNF540,missense_variant,p.Ile104Thr,ENST00000343599,;ZNF540,missense_variant,p.Ile72Thr,ENST00000589117,;ZNF540,missense_variant,p.Ile104Thr,ENST00000586134,;ZNF540,missense_variant,p.Ile104Thr,ENST00000592533,;ZNF540,downstream_gene_variant,,ENST00000590588,;ZFP30,downstream_gene_variant,,ENST00000589018,;ZNF540,non_coding_transcript_exon_variant,,ENST00000589857,;ZNF540,non_coding_transcript_exon_variant,,ENST00000589285,;	C	ENSG00000171817	ENST00000592533	Transcript	missense_variant	643	311	104	I/T	aTa/aCa	rs745556311	.	.	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	tolerated(0.18)	benign(0.002)	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24377:SF138,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTATAATAG	byFrequency	5	ESCA
EEF2	0	.	GRCh37	19	3982327	3982327	+	Silent	SNP	G	G	A	rs757277727	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.708C>T	p.%3D	p.F236F	ENST00000309311	5/15	25	22	3	43	43	0	EEF2,synonymous_variant,p.%3D,ENST00000309311,;EEF2,upstream_gene_variant,,ENST00000600794,;SNORD37,downstream_gene_variant,,ENST00000384048,;EEF2,downstream_gene_variant,,ENST00000600720,;EEF2,non_coding_transcript_exon_variant,,ENST00000598436,;EEF2,upstream_gene_variant,,ENST00000598182,;EEF2,upstream_gene_variant,,ENST00000596417,;EEF2,downstream_gene_variant,,ENST00000594885,;	A	ENSG00000167658	ENST00000309311	Transcript	synonymous_variant	797	708	236	F	ttC/ttT	rs757277727	.	.	-1	EEF2	HGNC	3214	protein_coding	YES	CCDS12117.1	ENSP00000307940	EF2_HUMAN	Q8TA90_HUMAN,B4DMC6_HUMAN	UPI00001649F3	.	.	.	5/15	.	hmmpanther:PTHR23115:SF103,hmmpanther:PTHR23115,Gene3D:1n0uA03,Pfam_domain:PF00009,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCGGCGAACTT	byFrequency	2	ESCA
GPR4	0	.	GRCh37	19	46094736	46094736	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389G>A	p.Arg130His	p.R130H	ENST00000323040	2/2	15	11	4	23	23	0	GPR4,missense_variant,p.Arg130His,ENST00000323040,;OPA3,intron_variant,,ENST00000544371,;GPR4,downstream_gene_variant,,ENST00000591614,;	T	ENSG00000177464	ENST00000323040	Transcript	missense_variant	1334	389	130	R/H	cGc/cAc	.	.	.	-1	GPR4	HGNC	4497	protein_coding	YES	CCDS12669.1	ENSP00000319744	GPR4_HUMAN	.	UPI0000050428	.	deleterious(0.01)	possibly_damaging(0.781)	2/2	.	Prints_domain:PR01147,Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,hmmpanther:PTHR24232:SF42,hmmpanther:PTHR24232,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACGCGGCGC	.	4	ESCA
NLRP2	0	.	GRCh37	19	55494687	55494687	+	Missense_Mutation	SNP	G	G	A	rs749931307	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621G>A	p.Gly541Arg	p.G541R	ENST00000543010	6/13	28	22	5	37	37	0	NLRP2,missense_variant,p.Gly519Arg,ENST00000537859,;NLRP2,missense_variant,p.Gly538Arg,ENST00000263437,;NLRP2,missense_variant,p.Gly517Arg,ENST00000391721,;NLRP2,missense_variant,p.Gly519Arg,ENST00000339757,;NLRP2,missense_variant,p.Gly541Arg,ENST00000543010,;NLRP2,missense_variant,p.Gly517Arg,ENST00000538819,;NLRP2,missense_variant,p.Gly541Arg,ENST00000448584,;NLRP2,missense_variant,p.Gly518Arg,ENST00000427260,;NLRP2,downstream_gene_variant,,ENST00000397169,;NLRP2,downstream_gene_variant,,ENST00000585500,;NLRP2,downstream_gene_variant,,ENST00000433772,;NLRP2,downstream_gene_variant,,ENST00000588619,;NLRP2,upstream_gene_variant,,ENST00000540005,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000543277,;NLRP2,downstream_gene_variant,,ENST00000539848,;NLRP2,upstream_gene_variant,,ENST00000381637,;	A	ENSG00000022556	ENST00000543010	Transcript	missense_variant	1764	1621	541	G/R	Gga/Aga	rs749931307	.	.	1	NLRP2	HGNC	22948	protein_coding	YES	CCDS12913.1	ENSP00000445135	NALP2_HUMAN	K7EPE6_HUMAN,K7ELX1_HUMAN,K7EJ90_HUMAN,F5H7Q5_HUMAN,F5H5B1_HUMAN	UPI000004C0CC	.	tolerated(0.42)	benign(0.002)	6/13	.	hmmpanther:PTHR24106:SF14,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCGGAGTA	byFrequency	5	ESCA
FUT5	0	.	GRCh37	19	5867206	5867206	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531C>T	p.%3D	p.D177D	ENST00000252675	5/5	37	30	7	43	43	0	FUT5,synonymous_variant,p.%3D,ENST00000252675,;FUT5,synonymous_variant,p.%3D,ENST00000588525,;AC024592.12,downstream_gene_variant,,ENST00000585661,;AC024592.12,downstream_gene_variant,,ENST00000586349,;AC024592.12,3_prime_UTR_variant,,ENST00000592091,;	A	ENSG00000130383	ENST00000252675	Transcript	synonymous_variant	1094	531	177	D	gaC/gaT	.	.	.	-1	FUT5	HGNC	4016	protein_coding	YES	CCDS12154.1	ENSP00000252675	FUT5_HUMAN	K7ENC0_HUMAN	UPI000013CD7B	.	.	.	5/5	.	hmmpanther:PTHR11929:SF137,hmmpanther:PTHR11929,Pfam_domain:PF00852,Superfamily_domains:SSF53756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGATGTCGGA	.	4	ESCA
TCHH	0	.	GRCh37	1	152082500	152082500	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3193G>A	p.Gly1065Arg	p.G1065R	ENST00000368804	2/2	102	68	34	102	102	0	TCHH,missense_variant,p.Gly1065Arg,ENST00000368804,;	T	ENSG00000159450	ENST00000368804	Transcript	missense_variant	3193	3193	1065	G/R	Gga/Aga	COSM2184241	.	.	-1	TCHH	HGNC	11791	protein_coding	YES	CCDS41396.1	ENSP00000357794	TRHY_HUMAN	Q5D861_HUMAN,A2RRS3_HUMAN	UPI0000458A5E	.	.	unknown(0)	2/2	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTCCCAGCA	.	5	ESCA
MPZ	0	.	GRCh37	1	161274579	161274579	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1087C>T	.	.	ENST00000533357	6/6	22	15	6	20	20	0	MPZ,3_prime_UTR_variant,,ENST00000360451,;MPZ,3_prime_UTR_variant,,ENST00000533357,;MPZ,3_prime_UTR_variant,,ENST00000491222,;MPZ,downstream_gene_variant,,ENST00000336559,;MPZ,downstream_gene_variant,,ENST00000526189,;MPZ,3_prime_UTR_variant,,ENST00000463290,;MPZ,downstream_gene_variant,,ENST00000488271,;MPZ,downstream_gene_variant,,ENST00000476410,;	A	ENSG00000158887	ENST00000533357	Transcript	3_prime_UTR_variant	1901	.	.	.	.	.	.	.	-1	MPZ	HGNC	7225	protein_coding	YES	CCDS1229.2	ENSP00000432943	MYP0_HUMAN	E9PL80_HUMAN	UPI000012FBB1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGAAATA	.	5	ESCA
FCGR3A	0	.	GRCh37	1	161519619	161519619	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16G>A	p.Gly6Arg	p.G6R	ENST00000367969	1/5	64	51	12	70	70	0	FCGR3A,missense_variant,p.Gly6Arg,ENST00000367969,;FCGR3A,missense_variant,p.Gly6Arg,ENST00000443193,;FCGR3A,intron_variant,,ENST00000540048,;FCGR3A,intron_variant,,ENST00000436743,;FCGR3A,intron_variant,,ENST00000442336,;FCGR3A,intron_variant,,ENST00000367967,;FCGR3A,upstream_gene_variant,,ENST00000426740,;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR3A,upstream_gene_variant,,ENST00000476031,;	T	ENSG00000203747	ENST00000367969	Transcript	missense_variant	200	16	6	G/R	Ggg/Agg	.	.	.	-1	FCGR3A	HGNC	3619	protein_coding	YES	CCDS1232.1	ENSP00000356946	.	M9MML0_HUMAN,Q9UN20_HUMAN	UPI000013E1BC	.	deleterious_low_confidence(0)	benign(0.145)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCCCAGCCC	.	5	ESCA
EPHA2	0	.	GRCh37	1	16460076	16460076	+	Silent	SNP	G	G	A	rs148209354	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1764C>T	p.%3D	p.Y588Y	ENST00000358432	10/17	46	23	22	36	36	0	EPHA2,synonymous_variant,p.%3D,ENST00000358432,;EPHA2,downstream_gene_variant,,ENST00000480202,;EPHA2,upstream_gene_variant,,ENST00000462805,;	A	ENSG00000142627	ENST00000358432	Transcript	synonymous_variant	1919	1764	588	Y	taC/taT	rs148209354	.	.	-1	EPHA2	HGNC	3386	protein_coding	YES	CCDS169.1	ENSP00000351209	EPHA2_HUMAN	Q96HF4_HUMAN,Q8IZL0_HUMAN	UPI00000731AB	.	.	.	10/17	.	hmmpanther:PTHR24416:SF306,hmmpanther:PTHR24416,Gene3D:3.30.200.20,Pfam_domain:PF14575,PIRSF_domain:PIRSF000666	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCACGTATGT	byCluster	5	ESCA
POGK	0	.	GRCh37	1	166822883	166822883	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3237G>C	.	.	ENST00000367875	5/5	19	13	5	32	32	0	POGK,3_prime_UTR_variant,,ENST00000367876,;POGK,3_prime_UTR_variant,,ENST00000367875,;TADA1,downstream_gene_variant,,ENST00000367874,;POGK,downstream_gene_variant,,ENST00000449930,;POGK,downstream_gene_variant,,ENST00000536514,;POGK,downstream_gene_variant,,ENST00000537173,;TADA1,downstream_gene_variant,,ENST00000467021,;	C	ENSG00000143157	ENST00000367875	Transcript	3_prime_UTR_variant	5427	.	.	.	.	.	.	.	1	POGK	HGNC	18800	protein_coding	YES	CCDS1254.1	ENSP00000356849	POGK_HUMAN	Q5TIJ2_HUMAN	UPI0000167816	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTGTGCTA	.	5	ESCA
CEP350	0	.	GRCh37	1	180064685	180064685	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8539C>T	p.Gln2847Ter	p.Q2847*	ENST00000367607	35/38	22	14	8	16	16	0	CEP350,stop_gained,p.Gln1022Ter,ENST00000429851,;CEP350,stop_gained,p.Gln311Ter,ENST00000417046,;CEP350,stop_gained,p.Gln2847Ter,ENST00000367607,;CEP350,non_coding_transcript_exon_variant,,ENST00000490141,;CEP350,non_coding_transcript_exon_variant,,ENST00000496440,;CEP350,downstream_gene_variant,,ENST00000484356,;	T	ENSG00000135837	ENST00000367607	Transcript	stop_gained	8957	8539	2847	Q/*	Cag/Tag	.	.	.	1	CEP350	HGNC	24238	protein_coding	YES	CCDS1336.1	ENSP00000356579	CE350_HUMAN	Q5T2X4_HUMAN	UPI000013CFC5	.	.	.	35/38	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13958	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGGCAGGAA	.	5	ESCA
RNF2	0	.	GRCh37	1	185069487	185069487	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*54A>G	.	.	ENST00000367510	7/7	40	24	16	60	60	0	RNF2,3_prime_UTR_variant,,ENST00000367509,;RNF2,3_prime_UTR_variant,,ENST00000367510,;RNF2,downstream_gene_variant,,ENST00000453650,;	G	ENSG00000121481	ENST00000367510	Transcript	3_prime_UTR_variant	1353	.	.	.	.	.	.	.	1	RNF2	HGNC	10061	protein_coding	YES	CCDS1365.1	ENSP00000356480	RING2_HUMAN	.	UPI000007131D	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATATTAAA	.	5	ESCA
PRELP	0	.	GRCh37	1	203452624	203452624	+	Silent	SNP	C	C	T	rs776957308	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312C>T	p.%3D	p.I104I	ENST00000343110	2/3	58	38	20	64	64	0	PRELP,synonymous_variant,p.%3D,ENST00000343110,;	T	ENSG00000188783	ENST00000343110	Transcript	synonymous_variant	439	312	104	I	atC/atT	rs776957308	.	.	1	PRELP	HGNC	9357	protein_coding	YES	CCDS1438.1	ENSP00000343924	PRELP_HUMAN	Q7Z4B2_HUMAN	UPI000013222E	.	.	.	2/3	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24371,hmmpanther:PTHR24371:SF15,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,SMART_domains:SM00013,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCATCCATTA	byFrequency	5	ESCA
SPATA17	0	.	GRCh37	1	217947781	217947781	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.625A>G	p.Lys209Glu	p.K209E	ENST00000366933	7/11	43	29	14	41	41	0	SPATA17,missense_variant,p.Lys209Glu,ENST00000366933,;SPATA17,non_coding_transcript_exon_variant,,ENST00000492747,;SPATA17,downstream_gene_variant,,ENST00000470448,;	G	ENSG00000162814	ENST00000366933	Transcript	missense_variant	680	625	209	K/E	Aag/Gag	.	.	.	1	SPATA17	HGNC	25184	protein_coding	YES	CCDS1519.1	ENSP00000355900	SPT17_HUMAN	R4GN71_HUMAN	UPI00000717C2	.	tolerated(0.84)	benign(0.001)	7/11	.	hmmpanther:PTHR22706	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGAAGGAC	.	5	ESCA
LGALS8	0	.	GRCh37	1	236704981	236704981	+	Silent	SNP	C	C	T	rs376845621	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493C>T	p.%3D	p.L165L	ENST00000526589	9/14	49	30	19	53	53	0	LGALS8,synonymous_variant,p.%3D,ENST00000454943,;LGALS8,synonymous_variant,p.%3D,ENST00000323938,;LGALS8,synonymous_variant,p.%3D,ENST00000527974,;LGALS8,synonymous_variant,p.%3D,ENST00000526634,;LGALS8,synonymous_variant,p.%3D,ENST00000366584,;LGALS8,synonymous_variant,p.%3D,ENST00000526589,;LGALS8,synonymous_variant,p.%3D,ENST00000406509,;LGALS8,synonymous_variant,p.%3D,ENST00000352231,;LGALS8,synonymous_variant,p.%3D,ENST00000341872,;LGALS8,synonymous_variant,p.%3D,ENST00000450372,;LGALS8,intron_variant,,ENST00000238181,;LGALS8,intron_variant,,ENST00000416919,;LGALS8,intron_variant,,ENST00000525042,;LGALS8,downstream_gene_variant,,ENST00000481485,;LGALS8,downstream_gene_variant,,ENST00000430527,;LGALS8,downstream_gene_variant,,ENST00000529489,;RP11-385F5.4,intron_variant,,ENST00000433131,;RP11-385F5.5,upstream_gene_variant,,ENST00000608547,;LGALS8,3_prime_UTR_variant,,ENST00000434231,;LGALS8,non_coding_transcript_exon_variant,,ENST00000528259,;LGALS8,non_coding_transcript_exon_variant,,ENST00000526652,;LGALS8,non_coding_transcript_exon_variant,,ENST00000366583,;LGALS8,intron_variant,,ENST00000442397,;LGALS8,intron_variant,,ENST00000528782,;LGALS8,upstream_gene_variant,,ENST00000532640,;LGALS8,upstream_gene_variant,,ENST00000489586,;LGALS8,downstream_gene_variant,,ENST00000532826,;LGALS8,upstream_gene_variant,,ENST00000529796,;LGALS8,upstream_gene_variant,,ENST00000525789,;	T	ENSG00000116977	ENST00000526589	Transcript	synonymous_variant	1013	493	165	L	Ctg/Ttg	rs376845621	.	.	1	LGALS8	HGNC	6569	protein_coding	YES	CCDS1611.1	ENSP00000435460	LEG8_HUMAN	Q5T3P9_HUMAN,E9PPL1_HUMAN,E9PJ77_HUMAN,B1ANM0_HUMAN	UPI0000169CE4	.	.	.	9/14	.	hmmpanther:PTHR11346,hmmpanther:PTHR11346:SF22	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAGTCTGGAA	byCluster	5	ESCA
CD164L2	0	.	GRCh37	1	27705891	27705891	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*646T>A	.	.	ENST00000374027	5/5	13	7	6	18	18	0	CD164L2,3_prime_UTR_variant,,ENST00000374027,;CD164L2,3_prime_UTR_variant,,ENST00000374030,;FCN3,upstream_gene_variant,,ENST00000354982,;FCN3,upstream_gene_variant,,ENST00000270879,;CD164L2,downstream_gene_variant,,ENST00000374025,;FCN3,upstream_gene_variant,,ENST00000481748,;	T	ENSG00000174950	ENST00000374027	Transcript	3_prime_UTR_variant	1232	.	.	.	.	.	.	.	-1	CD164L2	HGNC	32043	protein_coding	YES	CCDS302.1	ENSP00000363139	C16L2_HUMAN	.	UPI000004BA78	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CGGCCAGAGTT	.	4	ESCA
AHDC1	0	.	GRCh37	1	27875978	27875978	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2649G>A	p.%3D	p.R883R	ENST00000374011	6/7	41	19	21	40	40	0	AHDC1,synonymous_variant,p.%3D,ENST00000247087,;AHDC1,synonymous_variant,p.%3D,ENST00000374011,;AHDC1,downstream_gene_variant,,ENST00000490295,;AHDC1,downstream_gene_variant,,ENST00000487743,;	T	ENSG00000126705	ENST00000374011	Transcript	synonymous_variant	3618	2649	883	R	cgG/cgA	.	.	.	-1	AHDC1	HGNC	25230	protein_coding	YES	CCDS30652.1	ENSP00000363123	AHDC1_HUMAN	.	UPI0000418EA1	.	.	.	6/7	.	hmmpanther:PTHR15617,hmmpanther:PTHR15617:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCCCGCTG	.	5	ESCA
PTPRU	0	.	GRCh37	1	29606613	29606613	+	Missense_Mutation	SNP	G	G	A	rs747973212	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1828G>A	p.Val610Met	p.V610M	ENST00000345512	11/31	38	25	12	44	44	0	PTPRU,missense_variant,p.Val610Met,ENST00000373779,;PTPRU,missense_variant,p.Val610Met,ENST00000428026,;PTPRU,missense_variant,p.Val610Met,ENST00000460170,;PTPRU,missense_variant,p.Val610Met,ENST00000323874,;PTPRU,missense_variant,p.Val610Met,ENST00000356870,;PTPRU,missense_variant,p.Val610Met,ENST00000345512,;PTPRU,non_coding_transcript_exon_variant,,ENST00000415600,;PTPRU,downstream_gene_variant,,ENST00000527027,;PTPRU,upstream_gene_variant,,ENST00000531385,;	A	ENSG00000060656	ENST00000345512	Transcript	missense_variant	1957	1828	610	V/M	Gtg/Atg	rs747973212,COSM1579721,COSM1579723,COSM1579722	.	.	1	PTPRU	HGNC	9683	protein_coding	YES	CCDS334.1	ENSP00000334941	PTPRU_HUMAN	B3KT29_HUMAN	UPI000013C57E	.	deleterious(0)	probably_damaging(0.999)	11/31	.	hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF207	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCGTGCTG	.	5	ESCA
CCDC27	0	.	GRCh37	1	3677911	3677911	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778G>T	p.Glu260Ter	p.E260*	ENST00000294600	5/12	22	12	10	29	29	0	CCDC27,stop_gained,p.Glu260Ter,ENST00000294600,;CCDC27,3_prime_UTR_variant,,ENST00000462521,;	T	ENSG00000162592	ENST00000294600	Transcript	stop_gained	862	778	260	E/*	Gag/Tag	.	.	.	1	CCDC27	HGNC	26546	protein_coding	YES	CCDS50.1	ENSP00000294600	CCD27_HUMAN	.	UPI000013E186	.	.	.	5/12	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18853,hmmpanther:PTHR18853:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGGAGGAG	.	5	ESCA
NFYC	0	.	GRCh37	1	41220064	41220064	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387+1146G>T	.	.	ENST00000425457	.	46	22	23	52	52	0	NFYC,intron_variant,,ENST00000456393,;NFYC,intron_variant,,ENST00000372652,;NFYC,intron_variant,,ENST00000372651,;NFYC,intron_variant,,ENST00000425457,;NFYC,intron_variant,,ENST00000372653,;NFYC,intron_variant,,ENST00000447388,;NFYC,intron_variant,,ENST00000372669,;NFYC,intron_variant,,ENST00000427410,;NFYC,intron_variant,,ENST00000414185,;NFYC,intron_variant,,ENST00000416859,;NFYC,intron_variant,,ENST00000308733,;NFYC,intron_variant,,ENST00000440226,;NFYC,intron_variant,,ENST00000372654,;NFYC,intron_variant,,ENST00000525290,;NFYC,downstream_gene_variant,,ENST00000530965,;NFYC,downstream_gene_variant,,ENST00000453631,;NFYC,downstream_gene_variant,,ENST00000531464,;MIR30E,mature_miRNA_variant,,ENST00000362104,;MIR30C1,upstream_gene_variant,,ENST00000385227,;NFYC,intron_variant,,ENST00000467203,;NFYC,intron_variant,,ENST00000424419,;NFYC,upstream_gene_variant,,ENST00000525349,;	T	ENSG00000066136	ENST00000425457	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NFYC	HGNC	7806	protein_coding	YES	CCDS44120.1	ENSP00000396620	NFYC_HUMAN	Q5T6K7_HUMAN,Q14497_HUMAN,E9PQR2_HUMAN,E9PJA8_HUMAN	UPI0000D4DA2D	.	.	.	.	5/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAAGCTGTA	.	5	ESCA
TMEM59	0	.	GRCh37	1	54497595	54497595	+	3'UTR	SNP	T	T	A	rs376352704	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*228A>T	.	.	ENST00000234831	8/8	27	20	7	35	35	0	TMEM59,3_prime_UTR_variant,,ENST00000371344,;TMEM59,3_prime_UTR_variant,,ENST00000371348,;TMEM59,3_prime_UTR_variant,,ENST00000234831,;TMEM59,downstream_gene_variant,,ENST00000440019,;TMEM59,downstream_gene_variant,,ENST00000452421,;TMEM59,downstream_gene_variant,,ENST00000420738,;TMEM59,downstream_gene_variant,,ENST00000371341,;RP4-758J24.5,upstream_gene_variant,,ENST00000606641,;TMEM59,downstream_gene_variant,,ENST00000470395,;AL353898.2,downstream_gene_variant,,ENST00000327057,;	A	ENSG00000116209	ENST00000234831	Transcript	3_prime_UTR_variant	1450	.	.	.	.	rs376352704	.	.	-1	TMEM59	HGNC	1239	protein_coding	YES	CCDS586.1	ENSP00000234831	TMM59_HUMAN	Q5T6Z8_HUMAN	UPI0000001BF9	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAGCTACAGA	.	5	ESCA
IFI44L	0	.	GRCh37	1	79107493	79107493	+	Nonstop_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1358G>T	p.Ter453LeuextTer5	p.*453Lext*5	ENST00000370751	9/9	41	26	14	70	70	0	IFI44L,stop_lost,p.Ter195LeuextTer5,ENST00000342282,;IFI44L,stop_lost,p.Ter453LeuextTer5,ENST00000370751,;IFI44L,non_coding_transcript_exon_variant,,ENST00000476521,;IFI44L,downstream_gene_variant,,ENST00000476876,;IFI44L,downstream_gene_variant,,ENST00000459784,;IFI44L,non_coding_transcript_exon_variant,,ENST00000486882,;IFI44L,downstream_gene_variant,,ENST00000494910,;	T	ENSG00000137959	ENST00000370751	Transcript	stop_lost	1537	1358	453	*/L	tGa/tTa	.	.	.	1	IFI44L	HGNC	17817	protein_coding	YES	CCDS687.2	ENSP00000359787	IF44L_HUMAN	C9JPJ0_HUMAN,B4E019_HUMAN	UPI0000374C64	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTGAGATA	.	5	ESCA
GZF1	0	.	GRCh37	20	23345474	23345474	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454A>T	p.Ser152Cys	p.S152C	ENST00000338121	2/6	18	11	7	24	24	0	GZF1,missense_variant,p.Ser152Cys,ENST00000377051,;GZF1,missense_variant,p.Ser152Cys,ENST00000338121,;GZF1,intron_variant,,ENST00000544236,;GZF1,intron_variant,,ENST00000542987,;GZF1,downstream_gene_variant,,ENST00000424216,;GZF1,upstream_gene_variant,,ENST00000477239,;GZF1,upstream_gene_variant,,ENST00000461789,;	T	ENSG00000125812	ENST00000338121	Transcript	missense_variant	531	454	152	S/C	Agc/Tgc	.	.	.	1	GZF1	HGNC	15808	protein_coding	YES	CCDS13151.1	ENSP00000338290	GZF1_HUMAN	Q5JXG1_HUMAN,F5H2R0_HUMAN,B4DF58_HUMAN	UPI000013C35D	.	deleterious(0.01)	possibly_damaging(0.599)	2/6	.	hmmpanther:PTHR24402:SF170,hmmpanther:PTHR24402,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTGAGCAGT	.	5	ESCA
ENTPD6	0	.	GRCh37	20	25199221	25199221	+	Missense_Mutation	SNP	C	C	T	rs771320792	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.914C>T	p.Ala305Val	p.A305V	ENST00000376652	10/15	67	44	23	85	84	1	ENTPD6,missense_variant,p.Ala288Val,ENST00000354989,;ENTPD6,missense_variant,p.Ala129Val,ENST00000376666,;ENTPD6,missense_variant,p.Ala305Val,ENST00000376652,;ENTPD6,missense_variant,p.Ala304Val,ENST00000360031,;ENTPD6,missense_variant,p.Ala226Val,ENST00000433417,;ENTPD6,missense_variant,p.Ala305Val,ENST00000433259,;ENTPD6,missense_variant,p.Ala198Val,ENST00000447877,;ENTPD6,missense_variant,p.Ala257Val,ENST00000425813,;ENTPD6,missense_variant,p.Ala287Val,ENST00000439162,;ENTPD6,downstream_gene_variant,,ENST00000418890,;ENTPD6,downstream_gene_variant,,ENST00000417467,;ENTPD6,downstream_gene_variant,,ENST00000427553,;Y_RNA,downstream_gene_variant,,ENST00000365544,;ENTPD6,non_coding_transcript_exon_variant,,ENST00000471478,;ENTPD6,upstream_gene_variant,,ENST00000485936,;ENTPD6,upstream_gene_variant,,ENST00000481322,;	T	ENSG00000197586	ENST00000376652	Transcript	missense_variant	1077	914	305	A/V	gCg/gTg	rs771320792	.	.	1	ENTPD6	HGNC	3368	protein_coding	YES	CCDS13170.1	ENSP00000365840	ENTP6_HUMAN	.	UPI0000052B67	.	deleterious(0.01)	probably_damaging(0.945)	10/15	.	hmmpanther:PTHR11782,hmmpanther:PTHR11782:SF36,Pfam_domain:PF01150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGCGATCC	byFrequency	5	ESCA
PTPRT	0	.	GRCh37	20	41419951	41419951	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370G>A	p.Val124Met	p.V124M	ENST00000373187	3/31	43	11	32	49	49	0	PTPRT,missense_variant,p.Val124Met,ENST00000373201,;PTPRT,missense_variant,p.Val124Met,ENST00000356100,;PTPRT,missense_variant,p.Val124Met,ENST00000373198,;PTPRT,missense_variant,p.Val124Met,ENST00000373193,;PTPRT,missense_variant,p.Val124Met,ENST00000373184,;PTPRT,missense_variant,p.Val124Met,ENST00000373190,;PTPRT,missense_variant,p.Val124Met,ENST00000373187,;	T	ENSG00000196090	ENST00000373187	Transcript	missense_variant	370	370	124	V/M	Gtg/Atg	COSM287585	.	.	-1	PTPRT	HGNC	9682	protein_coding	YES	CCDS42874.1	ENSP00000362283	PTPRT_HUMAN	.	UPI0000246C03	.	deleterious(0)	possibly_damaging(0.844)	3/31	.	PROSITE_profiles:PS50060,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCACGTAGA	.	5	ESCA
SLC23A2	0	.	GRCh37	20	4848460	4848460	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1312T>C	p.Ser438Pro	p.S438P	ENST00000379333	13/17	35	31	4	22	22	0	SLC23A2,missense_variant,p.Ser195Pro,ENST00000423430,;SLC23A2,missense_variant,p.Ser438Pro,ENST00000379333,;SLC23A2,missense_variant,p.Ser324Pro,ENST00000424750,;SLC23A2,missense_variant,p.Ser438Pro,ENST00000338244,;SNORA31,upstream_gene_variant,,ENST00000516287,;SLC23A2,downstream_gene_variant,,ENST00000468355,;	G	ENSG00000089057	ENST00000379333	Transcript	missense_variant	1705	1312	438	S/P	Tct/Cct	.	.	.	-1	SLC23A2	HGNC	10973	protein_coding	YES	CCDS13085.1	ENSP00000368637	S23A2_HUMAN	Q4ZGM1_HUMAN	UPI0000136292	.	deleterious(0)	probably_damaging(0.996)	13/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11119,hmmpanther:PTHR11119:SF33,Pfam_domain:PF00860	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AGTAGAGCCAT	.	2	ESCA
SON	0	.	GRCh37	21	34926316	34926316	+	Silent	SNP	A	A	G	.	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4779A>G	p.%3D	p.L1593L	ENST00000356577	3/12	34	20	14	34	34	0	SON,synonymous_variant,p.%3D,ENST00000381679,;SON,synonymous_variant,p.%3D,ENST00000300278,;SON,synonymous_variant,p.%3D,ENST00000356577,;SON,synonymous_variant,p.%3D,ENST00000436227,;SON,synonymous_variant,p.%3D,ENST00000290239,;SON,intron_variant,,ENST00000381692,;SON,upstream_gene_variant,,ENST00000421541,;SON,synonymous_variant,p.%3D,ENST00000455528,;	G	ENSG00000159140	ENST00000356577	Transcript	synonymous_variant	5254	4779	1593	L	ctA/ctG	COSM238220,COSM238221	.	.	1	SON	HGNC	11183	protein_coding	YES	CCDS13629.1	ENSP00000348984	SON_HUMAN	.	UPI0000140BFD	.	.	.	3/12	.	hmmpanther:PTHR12813:SF26,hmmpanther:PTHR12813	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTATCTTC	.	5	ESCA
PPIL2	0	.	GRCh37	22	22043027	22043027	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1028A>T	p.Glu343Val	p.E343V	ENST00000412327	15/21	46	38	8	34	34	0	PPIL2,missense_variant,p.Glu343Val,ENST00000398831,;PPIL2,missense_variant,p.Glu343Val,ENST00000412327,;PPIL2,missense_variant,p.Glu343Val,ENST00000406385,;PPIL2,missense_variant,p.Glu322Val,ENST00000456792,;PPIL2,missense_variant,p.Glu343Val,ENST00000492445,;PPIL2,missense_variant,p.Glu343Val,ENST00000335025,;PPIL2,non_coding_transcript_exon_variant,,ENST00000446951,;PPIL2,downstream_gene_variant,,ENST00000484439,;PPIL2,3_prime_UTR_variant,,ENST00000417788,;	T	ENSG00000100023	ENST00000412327	Transcript	missense_variant	1144	1028	343	E/V	gAg/gTg	.	.	.	1	PPIL2	HGNC	9261	protein_coding	YES	CCDS46670.1	ENSP00000390427	PPIL2_HUMAN	.	UPI000002A7A2	.	deleterious(0.01)	benign(0.102)	15/21	.	PROSITE_profiles:PS50072,hmmpanther:PTHR11071,hmmpanther:PTHR11071:SF147,Pfam_domain:PF00160,Gene3D:2.40.100.10,Superfamily_domains:SSF50891	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGGAGTCAT	.	4	ESCA
TOP3B	0	.	GRCh37	22	22316801	22316801	+	Missense_Mutation	SNP	C	C	T	rs762892315	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1525G>A	p.Gly509Ser	p.G509S	ENST00000398793	13/18	61	55	6	66	66	0	TOP3B,missense_variant,p.Gly304Ser,ENST00000457270,;TOP3B,missense_variant,p.Gly238Ser,ENST00000413067,;TOP3B,missense_variant,p.Gly509Ser,ENST00000357179,;TOP3B,missense_variant,p.Gly509Ser,ENST00000398793,;TOP3B,splice_region_variant,,ENST00000436282,;TOP3B,splice_region_variant,,ENST00000444502,;TOP3B,splice_region_variant,,ENST00000457179,;TOP3B,non_coding_transcript_exon_variant,,ENST00000470338,;	T	ENSG00000100038	ENST00000398793	Transcript	missense_variant	1960	1525	509	G/S	Ggc/Agc	rs762892315	.	.	-1	TOP3B	HGNC	11993	protein_coding	YES	CCDS13797.1	ENSP00000381773	TOP3B_HUMAN	C9JTQ7_HUMAN,C9JT00_HUMAN,C9JKE2_HUMAN,C9JHR0_HUMAN,C9JEQ1_HUMAN,C9JEI7_HUMAN,C9J9X4_HUMAN	UPI00001371A1	.	deleterious(0)	probably_damaging(1)	13/18	.	Prints_domain:PR00417,Superfamily_domains:SSF56712,SMART_domains:SM00437,Pfam_domain:PF01131,Gene3D:1.10.460.10,hmmpanther:PTHR11390,hmmpanther:PTHR11390:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCACCGATGC	byFrequency	3	ESCA
TTN	0	.	GRCh37	2	179640736	179640736	+	Missense_Mutation	SNP	T	T	C	rs572691153	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5855A>G	p.His1952Arg	p.H1952R	ENST00000589042	28/363	43	31	12	47	47	0	TTN,missense_variant,p.His1952Arg,ENST00000360870,;TTN,missense_variant,p.His1906Arg,ENST00000359218,;TTN,missense_variant,p.His1952Arg,ENST00000342992,;TTN,missense_variant,p.His1906Arg,ENST00000342175,;TTN,missense_variant,p.His1952Arg,ENST00000589042,;TTN,missense_variant,p.His1952Arg,ENST00000591111,;TTN,missense_variant,p.His1906Arg,ENST00000460472,;TTN-AS1,downstream_gene_variant,,ENST00000610005,;TTN-AS1,downstream_gene_variant,,ENST00000585451,;RP11-88L24.4,upstream_gene_variant,,ENST00000582038,;TTN-AS1,downstream_gene_variant,,ENST00000584485,;	C	ENSG00000155657	ENST00000589042	Transcript	missense_variant	6080	5855	1952	H/R	cAt/cGt	rs572691153	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	28/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCATGTACG	by1000G	5	ESCA
ZNF804A	0	.	GRCh37	2	185804148	185804148	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*395C>G	.	.	ENST00000302277	4/4	68	47	21	65	65	0	ZNF804A,3_prime_UTR_variant,,ENST00000302277,;	G	ENSG00000170396	ENST00000302277	Transcript	3_prime_UTR_variant	4619	.	.	.	.	.	.	.	1	ZNF804A	HGNC	21711	protein_coding	YES	CCDS2291.1	ENSP00000303252	Z804A_HUMAN	.	UPI00001B4B18	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATCATGTT	.	5	ESCA
CASP8	0	.	GRCh37	2	202151220	202151220	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1520A>G	p.Tyr507Cys	p.Y507C	ENST00000358485	9/9	40	13	26	33	33	0	CASP8,missense_variant,p.Tyr433Cys,ENST00000323492,;CASP8,missense_variant,p.Tyr465Cys,ENST00000264275,;CASP8,missense_variant,p.Tyr507Cys,ENST00000358485,;CASP8,missense_variant,p.Tyr227Cys,ENST00000444430,;CASP8,missense_variant,p.Tyr433Cys,ENST00000392263,;CASP8,missense_variant,p.Tyr448Cys,ENST00000432109,;CASP8,missense_variant,p.Tyr364Cys,ENST00000264274,;CASP8,3_prime_UTR_variant,,ENST00000392266,;CASP8,3_prime_UTR_variant,,ENST00000392259,;ALS2CR12,downstream_gene_variant,,ENST00000415745,;ALS2CR12,downstream_gene_variant,,ENST00000405148,;ALS2CR12,downstream_gene_variant,,ENST00000392257,;CASP8,downstream_gene_variant,,ENST00000392258,;ALS2CR12,downstream_gene_variant,,ENST00000439709,;ALS2CR12,downstream_gene_variant,,ENST00000286190,;CASP8,downstream_gene_variant,,ENST00000424461,;CASP8,non_coding_transcript_exon_variant,,ENST00000339403,;ALS2CR12,downstream_gene_variant,,ENST00000494171,;ALS2CR12,downstream_gene_variant,,ENST00000494223,;	G	ENSG00000064012	ENST00000358485	Transcript	missense_variant	1716	1520	507	Y/C	tAt/tGt	.	.	.	1	CASP8	HGNC	1509	protein_coding	YES	CCDS42798.1	ENSP00000351273	CASP8_HUMAN	E7EVN1_HUMAN,E7ETB7_HUMAN,E7EQ01_HUMAN	UPI0000456ECD	.	tolerated(0.15)	possibly_damaging(0.841)	9/9	.	PROSITE_profiles:PS50207,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF141,Pfam_domain:PF00656,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTATGAAG	.	5	ESCA
NBEAL1	0	.	GRCh37	2	203991643	203991643	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3155A>G	p.Tyr1052Cys	p.Y1052C	ENST00000449802	22/55	81	60	21	96	96	0	NBEAL1,missense_variant,p.Tyr1052Cys,ENST00000449802,;	G	ENSG00000144426	ENST00000449802	Transcript	missense_variant	3488	3155	1052	Y/C	tAt/tGt	.	.	.	1	NBEAL1	HGNC	20681	protein_coding	YES	CCDS46495.1	ENSP00000399903	NBEL1_HUMAN	.	UPI000194EC27	.	deleterious(0.01)	benign(0.031)	22/55	.	hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTATTATG	.	5	ESCA
ZFAND2B	0	.	GRCh37	2	220073594	220073594	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657-105A>T	.	.	ENST00000289528	.	41	27	14	58	58	0	ZFAND2B,3_prime_UTR_variant,,ENST00000409206,;ZFAND2B,3_prime_UTR_variant,,ENST00000444522,;ZFAND2B,3_prime_UTR_variant,,ENST00000409594,;ZFAND2B,3_prime_UTR_variant,,ENST00000409097,;ZFAND2B,intron_variant,,ENST00000409336,;ZFAND2B,intron_variant,,ENST00000425849,;ZFAND2B,intron_variant,,ENST00000289528,;ZFAND2B,downstream_gene_variant,,ENST00000409319,;ABCB6,downstream_gene_variant,,ENST00000265316,;ZFAND2B,downstream_gene_variant,,ENST00000436556,;ZFAND2B,downstream_gene_variant,,ENST00000422255,;ABCB6,downstream_gene_variant,,ENST00000439002,;ZFAND2B,downstream_gene_variant,,ENST00000409217,;ZFAND2B,downstream_gene_variant,,ENST00000409412,;ABCB6,downstream_gene_variant,,ENST00000295750,;ZFAND2B,downstream_gene_variant,,ENST00000469596,;ZFAND2B,downstream_gene_variant,,ENST00000468301,;ZFAND2B,non_coding_transcript_exon_variant,,ENST00000486734,;ZFAND2B,non_coding_transcript_exon_variant,,ENST00000464902,;ZFAND2B,intron_variant,,ENST00000475533,;ABCB6,downstream_gene_variant,,ENST00000448398,;ABCB6,downstream_gene_variant,,ENST00000497882,;ABCB6,downstream_gene_variant,,ENST00000485773,;ABCB6,downstream_gene_variant,,ENST00000487380,;ZFAND2B,downstream_gene_variant,,ENST00000489197,;ABCB6,downstream_gene_variant,,ENST00000494639,;ZFAND2B,downstream_gene_variant,,ENST00000448496,;ABCB6,downstream_gene_variant,,ENST00000443805,;ZFAND2B,downstream_gene_variant,,ENST00000476713,;ABCB6,downstream_gene_variant,,ENST00000492543,;ATG9A,downstream_gene_variant,,ENST00000446716,;	T	ENSG00000158552	ENST00000289528	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZFAND2B	HGNC	25206	protein_coding	YES	CCDS2435.1	ENSP00000289528	ZFN2B_HUMAN	C9J1R6_HUMAN,B8ZZ56_HUMAN	UPI000004CC12	.	.	.	.	7/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAGATAATC	.	5	ESCA
DOCK10	0	.	GRCh37	2	225630329	225630329	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*109A>C	.	.	ENST00000258390	56/56	23	10	13	23	23	0	DOCK10,3_prime_UTR_variant,,ENST00000258390,;DOCK10,3_prime_UTR_variant,,ENST00000409592,;	G	ENSG00000135905	ENST00000258390	Transcript	3_prime_UTR_variant	6738	.	.	.	.	.	.	.	-1	DOCK10	HGNC	23479	protein_coding	YES	CCDS46528.1	ENSP00000258390	DOC10_HUMAN	Q4ZG60_HUMAN,Q3LIC8_HUMAN	UPI000021D2A7	.	.	.	56/56	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAATATTAA	.	5	ESCA
ALMS1	0	.	GRCh37	2	73827964	73827964	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11825C>T	p.Pro3942Leu	p.P3942L	ENST00000264448	18/23	34	26	8	38	38	0	ALMS1,missense_variant,p.Pro3900Leu,ENST00000409009,;ALMS1,missense_variant,p.Pro3942Leu,ENST00000264448,;ALMS1,non_coding_transcript_exon_variant,,ENST00000464408,;ALMS1,upstream_gene_variant,,ENST00000490821,;ALMS1,non_coding_transcript_exon_variant,,ENST00000484298,;	T	ENSG00000116127	ENST00000264448	Transcript	missense_variant	11936	11825	3942	P/L	cCt/cTt	.	.	.	1	ALMS1	HGNC	428	protein_coding	YES	CCDS42697.1	ENSP00000264448	ALMS1_HUMAN	A6NMY3_HUMAN	UPI0000212786	.	.	benign(0.003)	18/23	.	hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATCCTGAGG	.	5	ESCA
VAMP8	0	.	GRCh37	2	85808700	85808700	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.164C>T	p.Ser55Phe	p.S55F	ENST00000263864	3/3	90	64	26	60	60	0	VAMP8,missense_variant,p.Ser55Phe,ENST00000263864,;VAMP8,missense_variant,p.Ser29Phe,ENST00000432071,;VAMP8,synonymous_variant,p.%3D,ENST00000409760,;VAMP5,upstream_gene_variant,,ENST00000306384,;	T	ENSG00000118640	ENST00000263864	Transcript	missense_variant	320	164	55	S/F	tCt/tTt	.	.	.	1	VAMP8	HGNC	12647	protein_coding	YES	CCDS1979.1	ENSP00000263864	VAMP8_HUMAN	C9JXZ5_HUMAN	UPI000006F375	.	deleterious(0)	benign(0.414)	3/3	.	PROSITE_profiles:PS50892,hmmpanther:PTHR21136:SF75,hmmpanther:PTHR21136,Gene3D:2kogA00,Pfam_domain:PF00957,PIRSF_domain:PIRSF005409,Superfamily_domains:SSF58038,Prints_domain:PR00219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGTCTGAGC	.	5	ESCA
LMAN2L	0	.	GRCh37	2	97368755	97368755	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000377079	.	64	58	6	31	31	0	LMAN2L,downstream_gene_variant,,ENST00000426463,;LMAN2L,downstream_gene_variant,,ENST00000377079,;LMAN2L,downstream_gene_variant,,ENST00000537039,;LMAN2L,downstream_gene_variant,,ENST00000264963,;LMAN2L,downstream_gene_variant,,ENST00000534882,;FER1L5,non_coding_transcript_exon_variant,,ENST00000457909,;LMAN2L,downstream_gene_variant,,ENST00000440610,;LMAN2L,downstream_gene_variant,,ENST00000474494,;LMAN2L,downstream_gene_variant,,ENST00000449221,;LMAN2L,downstream_gene_variant,,ENST00000434524,;LMAN2L,downstream_gene_variant,,ENST00000434865,;LMAN2L,downstream_gene_variant,,ENST00000446780,;FER1L5,non_coding_transcript_exon_variant,,ENST00000424961,;FER1L5,non_coding_transcript_exon_variant,,ENST00000436930,;FER1L5,non_coding_transcript_exon_variant,,ENST00000414152,;FER1L5,non_coding_transcript_exon_variant,,ENST00000397978,;	T	ENSG00000114988	ENST00000377079	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3322	-1	LMAN2L	HGNC	19263	protein_coding	YES	CCDS46365.1	ENSP00000366280	LMA2L_HUMAN	B4DI83_HUMAN	UPI000044099B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTCCCAGCCC	.	4	ESCA
LYG1	0	.	GRCh37	2	99901179	99901179	+	Silent	SNP	T	T	G	rs112612184	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438A>C	p.%3D	p.P146P	ENST00000409448	7/8	46	30	16	31	31	0	LYG1,synonymous_variant,p.%3D,ENST00000409448,;LYG1,synonymous_variant,p.%3D,ENST00000308528,;C2orf15,intron_variant,,ENST00000424491,;	G	ENSG00000144214	ENST00000409448	Transcript	synonymous_variant	755	438	146	P	ccA/ccC	rs112612184	.	.	-1	LYG1	HGNC	27014	protein_coding	YES	CCDS2043.1	ENSP00000386923	LYG1_HUMAN	.	UPI0000036A47	.	.	.	7/8	.	Superfamily_domains:SSF53955,PIRSF_domain:PIRSF001065,Gene3D:1.10.530.10,hmmpanther:PTHR31698,hmmpanther:PTHR31698:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGTTGGAAA	.	5	ESCA
ATP2C1	0	.	GRCh37	3	130716559	130716559	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2455A>G	p.Ile819Val	p.I819V	ENST00000393221	24/28	87	44	42	78	78	0	ATP2C1,missense_variant,p.Ile785Val,ENST00000328560,;ATP2C1,missense_variant,p.Ile785Val,ENST00000508532,;ATP2C1,missense_variant,p.Ile785Val,ENST00000359644,;ATP2C1,missense_variant,p.Ile769Val,ENST00000504948,;ATP2C1,missense_variant,p.Ile303Val,ENST00000508660,;ATP2C1,missense_variant,p.Ile769Val,ENST00000507488,;ATP2C1,missense_variant,p.Ile780Val,ENST00000533801,;ATP2C1,missense_variant,p.Ile769Val,ENST00000505330,;ATP2C1,missense_variant,p.Ile739Val,ENST00000504612,;ATP2C1,missense_variant,p.Ile819Val,ENST00000393221,;ATP2C1,missense_variant,p.Ile785Val,ENST00000422190,;ATP2C1,missense_variant,p.Ile769Val,ENST00000513801,;ATP2C1,missense_variant,p.Ile785Val,ENST00000428331,;ATP2C1,missense_variant,p.Ile730Val,ENST00000504381,;ATP2C1,missense_variant,p.Ile785Val,ENST00000510168,;ATP2C1,3_prime_UTR_variant,,ENST00000507194,;ATP2C1,non_coding_transcript_exon_variant,,ENST00000514654,;ATP2C1,downstream_gene_variant,,ENST00000510774,;ATP2C1,downstream_gene_variant,,ENST00000504571,;	G	ENSG00000017260	ENST00000393221	Transcript	missense_variant	2670	2455	819	I/V	Atc/Gtc	.	.	.	1	ATP2C1	HGNC	13211	protein_coding	YES	CCDS56278.1	ENSP00000376914	AT2C1_HUMAN	D6RGE9_HUMAN,D6R9U9_HUMAN	UPI0000EE224C	.	tolerated(0.37)	benign(0.051)	24/28	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Superfamily_domains:0049473,Pfam_domain:PF00689,TIGRFAM_domain:TIGR01522,Gene3D:1.20.1110.10,hmmpanther:PTHR24093:SF214,hmmpanther:PTHR24093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATAATCATT	.	5	ESCA
SI	0	.	GRCh37	3	164727159	164727159	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4087C>A	p.Pro1363Thr	p.P1363T	ENST00000264382	35/48	56	45	11	47	47	0	SI,missense_variant,p.Pro1363Thr,ENST00000264382,;	T	ENSG00000090402	ENST00000264382	Transcript	missense_variant	4150	4087	1363	P/T	Cca/Aca	.	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	deleterious(0)	probably_damaging(0.998)	35/48	.	Superfamily_domains:SSF51445,Pfam_domain:PF01055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGGGAAAG	.	5	ESCA
MYNN	0	.	GRCh37	3	169496707	169496707	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418C>T	p.Gln140Ter	p.Q140*	ENST00000349841	3/8	64	57	6	46	46	0	MYNN,stop_gained,p.Gln140Ter,ENST00000356716,;MYNN,stop_gained,p.Gln140Ter,ENST00000392733,;MYNN,stop_gained,p.Gln140Ter,ENST00000349841,;MYNN,stop_gained,p.Gln140Ter,ENST00000544106,;RP11-362K14.5,non_coding_transcript_exon_variant,,ENST00000602342,;MYNN,3_prime_UTR_variant,,ENST00000602751,;MYNN,upstream_gene_variant,,ENST00000602391,;	T	ENSG00000085274	ENST00000349841	Transcript	stop_gained	1081	418	140	Q/*	Caa/Taa	.	.	.	1	MYNN	HGNC	14955	protein_coding	YES	CCDS3207.1	ENSP00000326240	MYNN_HUMAN	B4E2H9_HUMAN	UPI000000D72A	.	.	.	3/8	.	hmmpanther:PTHR24402:SF202,hmmpanther:PTHR24402	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAATCAACAG	.	4	ESCA
PIK3CA	0	.	GRCh37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	21/21	27	20	6	21	21	0	PIK3CA,missense_variant,p.His1047Arg,ENST00000263967,;RP11-245C23.3,downstream_gene_variant,,ENST00000609807,;	G	ENSG00000121879	ENST00000263967	Transcript	missense_variant	3297	3140	1047	H/R	cAt/cGt	rs121913279,COSM776,COSM775,COSM249874,COSM94987,COSM94986	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	tolerated(0.11)	possibly_damaging(0.529)	21/21	.	PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	pathogenic	0,1,1,1,1,1	25710561	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H1047R|c.3140A>G|1687,SITE|p.H1047R|c.3140A>G|242,CODON|p.H1047Y|c.3139C>T|8,CODON|p.H1047Y|c.3139C>T|54,CODON|p.H1047L|c.3140A>T|236,CODON|p.H1047L|c.3140A>T|45,BUFFER|p.M1043I|c.3129G>T|4,BUFFER|p.M1043I|c.3129G>A|8,BUFFER|p.M1043I|c.3129G>T|45,BUFFER|p.M1043I|c.3129G>A|22,BUFFER|p.M1043I|c.3129G>C|4,BUFFER|p.M1043I|c.3129G>C|6,BUFFER|p.N1044D|c.3130A>G|4,BUFFER|p.N1044Y|c.3130A>T|3,BUFFER|p.N1044S|c.3131A>G|5,BUFFER|p.N1044S|c.3131A>G|3,BUFFER|p.N1044K|c.3132T>G|5,BUFFER|p.N1044K|c.3132T>A|15,BUFFER|p.N1044K|c.3132T>A|7,BUFFER|p.D1045N|c.3133G>A|6,BUFFER|p.A1046T|c.3136G>A|6,BUFFER|p.A1046E|c.3137C>A|3,BUFFER|p.H1047Q|c.3141T>G|4,BUFFER|p.H1048R|c.3143A>G|6,BUFFER|p.H1048R|c.3143A>G|3,BUFFER|p.G1049S|c.3145G>A|16,BUFFER|p.G1049R|c.3145G>C|29,BUFFER|p.G1049R|c.3145G>C|5,BUFFER|p.G1049A|c.3146G>C|3,BUFFER|p.G1049D|c.3146G>A|4,BUFFER|p.G1049G|c.3147T>C|10,BUFFER|p.G1050S|c.3148G>A|3,BUFFER|p.G1050D|c.3149G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCACATCATG	byFrequency|byCluster	5	ESCA
ACAP2	0	.	GRCh37	3	195027311	195027311	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1045C>T	p.Arg349Cys	p.R349C	ENST00000326793	13/23	56	45	10	38	38	0	ACAP2,missense_variant,p.Arg224Cys,ENST00000439758,;ACAP2,missense_variant,p.Arg349Cys,ENST00000326793,;ACAP2,upstream_gene_variant,,ENST00000450200,;ACAP2,non_coding_transcript_exon_variant,,ENST00000484296,;ACAP2,upstream_gene_variant,,ENST00000475905,;	A	ENSG00000114331	ENST00000326793	Transcript	missense_variant	1276	1045	349	R/C	Cgc/Tgc	.	.	.	-1	ACAP2	HGNC	16469	protein_coding	YES	CCDS33924.1	ENSP00000324287	ACAP2_HUMAN	C9J8L1_HUMAN	UPI0000141A1A	.	deleterious(0.04)	benign(0.302)	13/23	.	PROSITE_profiles:PS50003,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF241,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGCAGCT	.	5	ESCA
KIF15	0	.	GRCh37	3	44882647	44882647	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3502G>C	p.Ala1168Pro	p.A1168P	ENST00000326047	29/35	24	10	14	28	28	0	KIF15,missense_variant,p.Ala803Pro,ENST00000425755,;KIF15,missense_variant,p.Ala1168Pro,ENST00000326047,;KIF15,3_prime_UTR_variant,,ENST00000438321,;KIF15,3_prime_UTR_variant,,ENST00000453693,;KIF15,upstream_gene_variant,,ENST00000422209,;	C	ENSG00000163808	ENST00000326047	Transcript	missense_variant	3651	3502	1168	A/P	Gcc/Ccc	.	.	.	1	KIF15	HGNC	17273	protein_coding	YES	CCDS33744.1	ENSP00000324020	KIF15_HUMAN	D6RCT7_HUMAN	UPI000006DB0E	.	deleterious(0.01)	possibly_damaging(0.888)	29/35	.	hmmpanther:PTHR24115:SF87,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAGCCTCT	.	5	ESCA
ITPR1	0	.	GRCh37	3	4888305	4888305	+	3'UTR	DEL	C	C	-	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*398delC	.	.	ENST00000302640	61/61	56	31	25	46	46	0	ITPR1,3_prime_UTR_variant,,ENST00000423119,;ITPR1,3_prime_UTR_variant,,ENST00000456211,;ITPR1,3_prime_UTR_variant,,ENST00000357086,;ITPR1,3_prime_UTR_variant,,ENST00000302640,;ITPR1,3_prime_UTR_variant,,ENST00000443694,;ITPR1,3_prime_UTR_variant,,ENST00000354582,;ITPR1,3_prime_UTR_variant,,ENST00000544951,;AC018816.3,intron_variant,,ENST00000441894,;AC018816.3,intron_variant,,ENST00000449914,;ITPR1,non_coding_transcript_exon_variant,,ENST00000463980,;AC018816.3,intron_variant,,ENST00000465436,;ITPR1,downstream_gene_variant,,ENST00000493491,;	-	ENSG00000150995	ENST00000302640	Transcript	3_prime_UTR_variant	8978	.	.	.	.	.	.	.	1	ITPR1	HGNC	6180	protein_coding	YES	CCDS54551.1	ENSP00000306253	ITPR1_HUMAN	.	UPI0000E5A461	.	.	.	61/61	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTAGCTCCCGAG	.	3	ESCA
RNF123	0	.	GRCh37	3	49739576	49739576	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1556G>C	p.Gly519Ala	p.G519A	ENST00000327697	18/39	15	6	9	53	53	0	RNF123,missense_variant,p.Gly519Ala,ENST00000327697,;RNF123,missense_variant,p.Gly373Ala,ENST00000432042,;RNF123,downstream_gene_variant,,ENST00000454491,;RNF123,missense_variant,p.Gly519Ala,ENST00000457726,;RNF123,splice_region_variant,,ENST00000487805,;RNF123,splice_region_variant,,ENST00000486102,;RNF123,downstream_gene_variant,,ENST00000494005,;RNF123,downstream_gene_variant,,ENST00000443204,;	C	ENSG00000164068	ENST00000327697	Transcript	missense_variant	1700	1556	519	G/A	gGg/gCg	.	.	.	1	RNF123	HGNC	21148	protein_coding	YES	CCDS33758.1	ENSP00000328287	RN123_HUMAN	C9JN91_HUMAN	UPI00001D6A07	.	tolerated(0.46)	possibly_damaging(0.632)	18/39	.	hmmpanther:PTHR13363,hmmpanther:PTHR13363:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATGGGGTGA	.	5	ESCA
PTPRG	0	.	GRCh37	3	62278318	62278318	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4191+87T>A	.	.	ENST00000474889	.	9	4	5	12	12	0	PTPRG,intron_variant,,ENST00000295874,;PTPRG,intron_variant,,ENST00000474889,;PTPRG-AS1,non_coding_transcript_exon_variant,,ENST00000498655,;PTPRG-AS1,non_coding_transcript_exon_variant,,ENST00000475371,;PTPRG-AS1,non_coding_transcript_exon_variant,,ENST00000479018,;PTPRG-AS1,intron_variant,,ENST00000462497,;PTPRG-AS1,intron_variant,,ENST00000495542,;PTPRG-AS1,intron_variant,,ENST00000474795,;PTPRG-AS1,intron_variant,,ENST00000466893,;PTPRG-AS1,intron_variant,,ENST00000490916,;PTPRG,intron_variant,,ENST00000475012,;PTPRG-AS1,downstream_gene_variant,,ENST00000479588,;	A	ENSG00000144724	ENST00000474889	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PTPRG	HGNC	9671	protein_coding	YES	CCDS2895.1	ENSP00000418112	PTPRG_HUMAN	O60420_HUMAN	UPI00001AEBFB	.	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGGGTGATTT	.	3	ESCA
PROS1	0	.	GRCh37	3	93593135	93593135	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1985G>C	p.Arg662Thr	p.R662T	ENST00000394236	15/15	65	43	22	89	89	0	PROS1,missense_variant,p.Arg662Thr,ENST00000394236,;PROS1,missense_variant,p.Arg531Thr,ENST00000407433,;	G	ENSG00000184500	ENST00000394236	Transcript	missense_variant	2302	1985	662	R/T	aGa/aCa	.	.	.	-1	PROS1	HGNC	9456	protein_coding	YES	CCDS2923.1	ENSP00000377783	PROS_HUMAN	Q8IXD5_HUMAN,Q8IXD4_HUMAN,Q8IXD2_HUMAN,Q6J1N0_HUMAN,Q06F35_HUMAN,G5E9F8_HUMAN,C9K0R0_HUMAN,B4E1L6_HUMAN	UPI00001323E8	.	tolerated(0.61)	possibly_damaging(0.846)	15/15	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24040,hmmpanther:PTHR24040:SF0,Gene3D:2.60.120.200,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTCTAATA	.	5	ESCA
CISD2	0	.	GRCh37	4	103806549	103806549	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280A>T	p.Thr94Ser	p.T94S	ENST00000273986	2/3	50	33	16	48	48	0	CISD2,missense_variant,p.Thr94Ser,ENST00000273986,;CISD2,missense_variant,p.Thr104Ser,ENST00000503643,;SLC9B1,intron_variant,,ENST00000394789,;CISD2,3_prime_UTR_variant,,ENST00000574446,;SLC9B1,intron_variant,,ENST00000503584,;SLC9B1,intron_variant,,ENST00000514972,;	T	ENSG00000145354	ENST00000273986	Transcript	missense_variant	387	280	94	T/S	Act/Tct	.	.	.	1	CISD2	HGNC	24212	protein_coding	YES	CCDS34040.1	ENSP00000273986	CISD2_HUMAN	.	UPI0000071BCA	.	tolerated(0.15)	benign(0.055)	2/3	.	hmmpanther:PTHR13680:SF4,hmmpanther:PTHR13680,Pfam_domain:PF09360,SMART_domains:SM00704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTACTAAA	.	5	ESCA
CENPE	0	.	GRCh37	4	104116291	104116291	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457A>G	p.Ile153Val	p.I153V	ENST00000265148	5/49	39	12	26	23	23	0	CENPE,missense_variant,p.Ile153Val,ENST00000503705,;CENPE,missense_variant,p.Ile153Val,ENST00000380026,;CENPE,missense_variant,p.Ile153Val,ENST00000265148,;CENPE,intron_variant,,ENST00000514974,;	C	ENSG00000138778	ENST00000265148	Transcript	missense_variant	547	457	153	I/V	Att/Gtt	.	.	.	-1	CENPE	HGNC	1856	protein_coding	YES	CCDS34042.1	ENSP00000265148	CENPE_HUMAN	D6RBW0_HUMAN	UPI000020B28A	.	.	benign(0.006)	5/49	.	Superfamily_domains:SSF52540,SMART_domains:SM00129,Pfam_domain:PF00225,Gene3D:3.40.850.10,hmmpanther:PTHR24115:SF384,hmmpanther:PTHR24115,PROSITE_profiles:PS50067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATAATTAAAG	.	5	ESCA
DKK2	0	.	GRCh37	4	107845807	107845807	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.424C>G	p.Leu142Val	p.L142V	ENST00000285311	3/4	58	33	24	47	47	0	DKK2,missense_variant,p.Leu42Val,ENST00000513208,;DKK2,missense_variant,p.Leu142Val,ENST00000285311,;DKK2,missense_variant,p.Leu96Val,ENST00000510463,;DKK2,non_coding_transcript_exon_variant,,ENST00000510534,;	C	ENSG00000155011	ENST00000285311	Transcript	missense_variant	1130	424	142	L/V	Ctg/Gtg	.	.	.	-1	DKK2	HGNC	2892	protein_coding	YES	CCDS3675.1	ENSP00000285311	DKK2_HUMAN	D6RGF1_HUMAN	UPI0000048EF2	.	tolerated(0.91)	benign(0.333)	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCAGAGCCG	.	5	ESCA
ZNF827	0	.	GRCh37	4	146682287	146682287	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*502G>A	.	.	ENST00000379448	15/15	20	12	7	50	50	0	ZNF827,missense_variant,p.Gly178Ser,ENST00000503462,;ZNF827,3_prime_UTR_variant,,ENST00000508784,;ZNF827,3_prime_UTR_variant,,ENST00000379448,;ZNF827,3_prime_UTR_variant,,ENST00000513320,;ZNF827,downstream_gene_variant,,ENST00000511659,;C4orf51,intron_variant,,ENST00000510096,;ZNF827,downstream_gene_variant,,ENST00000515386,;	T	ENSG00000151612	ENST00000379448	Transcript	3_prime_UTR_variant	3800	.	.	.	.	.	.	.	-1	ZNF827	HGNC	27193	protein_coding	YES	CCDS34072.1	ENSP00000368761	ZN827_HUMAN	.	UPI000049DFF1	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGCCGGCCG	.	5	ESCA
TLL1	0	.	GRCh37	4	167023131	167023131	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1103C>A	.	.	ENST00000061240	21/21	12	9	3	23	23	0	TLL1,3_prime_UTR_variant,,ENST00000061240,;TLL1,3_prime_UTR_variant,,ENST00000507499,;TLL1,3_prime_UTR_variant,,ENST00000509505,;	A	ENSG00000038295	ENST00000061240	Transcript	3_prime_UTR_variant	4792	.	.	.	.	.	.	.	1	TLL1	HGNC	11843	protein_coding	YES	CCDS3811.1	ENSP00000061240	TLL1_HUMAN	D6RCE0_HUMAN	UPI0000072EED	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT	CTATTCCATAA	.	2	ESCA
TLL1	0	.	GRCh37	4	167023132	167023132	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1104C>A	.	.	ENST00000061240	21/21	12	9	3	23	23	0	TLL1,3_prime_UTR_variant,,ENST00000061240,;TLL1,3_prime_UTR_variant,,ENST00000507499,;TLL1,3_prime_UTR_variant,,ENST00000509505,;	A	ENSG00000038295	ENST00000061240	Transcript	3_prime_UTR_variant	4793	.	.	.	.	.	.	.	1	TLL1	HGNC	11843	protein_coding	YES	CCDS3811.1	ENSP00000061240	TLL1_HUMAN	D6RCE0_HUMAN	UPI0000072EED	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT	TATTCCATAAA	.	2	ESCA
VEGFC	0	.	GRCh37	4	177650746	177650746	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302C>G	p.Ser101Ter	p.S101*	ENST00000280193	2/7	75	44	31	82	82	0	VEGFC,stop_gained,p.Ser101Ter,ENST00000280193,;VEGFC,non_coding_transcript_exon_variant,,ENST00000507638,;	C	ENSG00000150630	ENST00000280193	Transcript	stop_gained	718	302	101	S/*	tCa/tGa	COSM733007	.	.	-1	VEGFC	HGNC	12682	protein_coding	YES	CCDS43285.1	ENSP00000280193	VEGFC_HUMAN	.	UPI000020B749	.	.	.	2/7	.	hmmpanther:PTHR12025,hmmpanther:PTHR12025:SF3	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTGAGTTG	.	5	ESCA
N4BP2	0	.	GRCh37	4	40103753	40103755	+	In_Frame_Del	DEL	ATC	ATC	-	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	ATC	ATC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291_293delATC	p.Ser99del	p.S99del	ENST00000261435	4/18	20	6	14	27	27	0	N4BP2,inframe_deletion,p.Ser19del,ENST00000515550,;N4BP2,inframe_deletion,p.Ser99del,ENST00000261435,;N4BP2,upstream_gene_variant,,ENST00000513269,;N4BP2,3_prime_UTR_variant,,ENST00000511480,;	-	ENSG00000078177	ENST00000261435	Transcript	inframe_deletion	704-706	288-290	96-97	ES/E	gaATCa/gaa	.	.	.	1	N4BP2	HGNC	29851	protein_coding	YES	CCDS3457.1	ENSP00000261435	N4BP2_HUMAN	D6R9J2_HUMAN	UPI00001A962C	.	.	.	4/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAAGAATCATCTT	.	2	ESCA
GPRIN3	0	.	GRCh37	4	90168959	90168959	+	Missense_Mutation	SNP	C	C	T	rs145667508	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2303G>A	p.Arg768His	p.R768H	ENST00000609438	2/2	22	7	15	39	39	0	GPRIN3,missense_variant,p.Arg768His,ENST00000609438,;GPRIN3,missense_variant,p.Arg768His,ENST00000333209,;	T	ENSG00000185477	ENST00000609438	Transcript	missense_variant	2822	2303	768	R/H	cGt/cAt	rs145667508	.	.	-1	GPRIN3	HGNC	27733	protein_coding	YES	CCDS34030.1	ENSP00000476603	.	.	UPI00001C1E20	.	tolerated(0.11)	probably_damaging(0.98)	2/2	.	hmmpanther:PTHR15718:SF2,hmmpanther:PTHR15718,Pfam_domain:PF15235	.	.	.	.	.	.	.	T:0.0005	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGACGGACG	byFrequency|byCluster	5	ESCA
PRR16	0	.	GRCh37	5	120021833	120021833	+	Missense_Mutation	SNP	C	C	T	rs773682575	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.275C>T	p.Thr92Met	p.T92M	ENST00000379551	3/3	25	14	11	32	32	0	PRR16,missense_variant,p.Thr115Met,ENST00000407149,;PRR16,missense_variant,p.Thr45Met,ENST00000446965,;PRR16,missense_variant,p.Thr45Met,ENST00000505123,;PRR16,missense_variant,p.Thr45Met,ENST00000509923,;PRR16,missense_variant,p.Thr92Met,ENST00000379551,;	T	ENSG00000184838	ENST00000379551	Transcript	missense_variant	632	275	92	T/M	aCg/aTg	rs773682575,COSM735935,COSM1647738	.	.	1	PRR16	HGNC	29654	protein_coding	YES	CCDS4127.1	ENSP00000368869	PRR16_HUMAN	D6RGF0_HUMAN	UPI0000073195	.	deleterious_low_confidence(0)	probably_damaging(0.999)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF0,Pfam_domain:PF15252	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCACGGTCC	.	5	ESCA
PCDHB18	0	.	GRCh37	5	140615791	140615791	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1854C>T	.	.	ENST00000526308	1/1	121	83	37	145	144	0	PCDHB18,non_coding_transcript_exon_variant,,ENST00000526308,;PCDHB18,non_coding_transcript_exon_variant,,ENST00000524813,;PCDHB19P,upstream_gene_variant,,ENST00000570871,;	T	ENSG00000146001	ENST00000526308	Transcript	non_coding_transcript_exon_variant	1854	.	.	.	.	.	.	.	1	PCDHB18	HGNC	14548	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAACGACAA	.	5	ESCA
PCDHGA6	0	.	GRCh37	5	140754632	140754632	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.982C>T	p.Arg328Ter	p.R328*	ENST00000517434	1/4	23	12	11	41	41	0	PCDHGA6,stop_gained,p.Arg328Ter,ENST00000517434,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB2,intron_variant,,ENST00000522605,;	T	ENSG00000253731	ENST00000517434	Transcript	stop_gained	982	982	328	R/*	Cga/Tga	.	.	.	1	PCDHGA6	HGNC	8704	protein_coding	YES	CCDS54926.1	ENSP00000429601	PCDG6_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI00000715C8	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF107,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCGAGAC	.	5	ESCA
NR3C1	0	.	GRCh37	5	142658828	142658828	+	3'Flank	SNP	C	C	T	rs115618248	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000231509	.	25	19	6	23	23	0	NR3C1,3_prime_UTR_variant,,ENST00000394464,;NR3C1,3_prime_UTR_variant,,ENST00000343796,;NR3C1,3_prime_UTR_variant,,ENST00000415690,;NR3C1,downstream_gene_variant,,ENST00000231509,;NR3C1,downstream_gene_variant,,ENST00000503201,;NR3C1,downstream_gene_variant,,ENST00000504572,;NR3C1,downstream_gene_variant,,ENST00000424646,;NR3C1,downstream_gene_variant,,ENST00000416954,;NR3C1,downstream_gene_variant,,ENST00000394466,;	T	ENSG00000113580	ENST00000231509	Transcript	downstream_gene_variant	.	.	.	.	.	rs115618248	.	1899	-1	NR3C1	HGNC	7978	protein_coding	YES	CCDS34258.1	ENSP00000231509	GCR_HUMAN	E5KQF6_HUMAN,Q3MSN4_HUMAN,D6RDA9_HUMAN	UPI000016A246	.	.	.	.	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTCGATGA	by1000G	5	ESCA
SLC36A2	0	.	GRCh37	5	150704916	150704916	+	Missense_Mutation	SNP	G	G	A	rs766086527	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941C>T	p.Ala314Val	p.A314V	ENST00000335244	8/10	42	25	16	54	54	0	SLC36A2,missense_variant,p.Ala38Val,ENST00000450886,;SLC36A2,missense_variant,p.Ala314Val,ENST00000521967,;SLC36A2,missense_variant,p.Ala314Val,ENST00000335244,;SLC36A2,missense_variant,p.Ala67Val,ENST00000523044,;SLC36A2,3_prime_UTR_variant,,ENST00000518280,;SLC36A2,3_prime_UTR_variant,,ENST00000518617,;	A	ENSG00000186335	ENST00000335244	Transcript	missense_variant	1071	941	314	A/V	gCg/gTg	rs766086527,COSM1567826	.	.	-1	SLC36A2	HGNC	18762	protein_coding	YES	CCDS4315.1	ENSP00000334223	S36A2_HUMAN	E5RGH8_HUMAN	UPI000020D008	.	deleterious(0)	benign(0.151)	8/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22950:SF185,hmmpanther:PTHR22950,Pfam_domain:PF01490	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.G317V|c.950G>T|13	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGCCATG	.	5	ESCA
PRDM9	0	.	GRCh37	5	23522919	23522919	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.807G>T	p.%3D	p.L269L	ENST00000296682	8/11	64	44	20	65	65	0	PRDM9,synonymous_variant,p.%3D,ENST00000296682,;	T	ENSG00000164256	ENST00000296682	Transcript	synonymous_variant	989	807	269	L	ctG/ctT	.	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	.	.	8/11	.	Superfamily_domains:SSF82199,Gene3D:2.170.270.10,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50280	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCTGGGTCT	.	5	ESCA
ANXA2R	0	.	GRCh37	5	43039891	43039891	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258G>A	p.%3D	p.A86A	ENST00000314890	2/2	60	39	21	59	59	0	ANXA2R,synonymous_variant,p.%3D,ENST00000314890,;CTD-2201E18.3,intron_variant,,ENST00000503152,;AC025171.1,upstream_gene_variant,,ENST00000505541,;AC025171.1,upstream_gene_variant,,ENST00000451894,;AC025171.1,upstream_gene_variant,,ENST00000508913,;AC025171.1,upstream_gene_variant,,ENST00000515108,;AC025171.1,upstream_gene_variant,,ENST00000399543,;	T	ENSG00000177721	ENST00000314890	Transcript	synonymous_variant	1678	258	86	A	gcG/gcA	.	.	.	-1	ANXA2R	HGNC	33463	protein_coding	YES	CCDS34153.1	ENSP00000315915	AX2R_HUMAN	.	UPI0000072CD4	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTCGCTGT	.	5	ESCA
MAP3K1	0	.	GRCh37	5	56174810	56174810	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1969A>G	p.Thr657Ala	p.T657A	ENST00000399503	11/20	39	30	8	44	44	0	MAP3K1,missense_variant,p.Thr657Ala,ENST00000399503,;	G	ENSG00000095015	ENST00000399503	Transcript	missense_variant	1969	1969	657	T/A	Aca/Gca	.	.	.	1	MAP3K1	HGNC	6848	protein_coding	YES	CCDS43318.1	ENSP00000382423	M3K1_HUMAN	.	UPI000015153B	.	tolerated(0.16)	benign(0.316)	11/20	.	hmmpanther:PTHR24361:SF255,hmmpanther:PTHR24361,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAAACATTG	.	5	ESCA
HSPA1B	0	.	GRCh37	6	31795842	31795842	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115C>T	p.Pro39Ser	p.P39S	ENST00000375650	1/1	22	9	13	33	33	0	HSPA1B,missense_variant,p.Pro39Ser,ENST00000375650,;HSPA1B,intron_variant,,ENST00000545241,;	T	ENSG00000204388	ENST00000375650	Transcript	missense_variant	331	115	39	P/S	Ccc/Tcc	.	.	.	1	HSPA1B	HGNC	5233	protein_coding	YES	CCDS34415.1	ENSP00000364801	HSP71_HUMAN	A8K5I0_HUMAN	UPI0000000C40	.	deleterious_low_confidence(0)	possibly_damaging(0.801)	1/1	.	Prints_domain:PR00301,Superfamily_domains:SSF53067,Pfam_domain:PF00012,Gene3D:3.30.420.40,hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCACCCCCAGC	.	3	ESCA
C6orf201	0	.	GRCh37	6	4099372	4099372	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224A>G	p.Lys75Arg	p.K75R	ENST00000380175	3/6	33	9	24	52	52	0	C6orf201,missense_variant,p.Lys78Arg,ENST00000333388,;C6orf201,missense_variant,p.Lys75Arg,ENST00000380175,;C6orf201,missense_variant,p.Lys75Arg,ENST00000430835,;C6orf201,non_coding_transcript_exon_variant,,ENST00000483580,;C6orf201,non_coding_transcript_exon_variant,,ENST00000360378,;C6orf201,missense_variant,p.Lys75Arg,ENST00000436110,;C6orf201,missense_variant,p.Lys75Arg,ENST00000451679,;C6orf201,missense_variant,p.Lys78Arg,ENST00000427996,;	G	ENSG00000185689	ENST00000380175	Transcript	missense_variant	989	224	75	K/R	aAg/aGg	.	.	.	1	C6orf201	HGNC	21620	protein_coding	YES	CCDS43419.1	ENSP00000420610	CF201_HUMAN	.	UPI00004573AE	.	tolerated(0.24)	possibly_damaging(0.765)	3/6	.	Pfam_domain:PF15023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAAGAAAT	.	5	ESCA
SH3BGRL2	0	.	GRCh37	6	80383498	80383498	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.213T>C	p.%3D	p.N71N	ENST00000369838	2/4	9	1	7	13	13	0	SH3BGRL2,synonymous_variant,p.%3D,ENST00000369838,;	C	ENSG00000198478	ENST00000369838	Transcript	synonymous_variant	392	213	71	N	aaT/aaC	.	.	.	1	SH3BGRL2	HGNC	15567	protein_coding	YES	CCDS4991.1	ENSP00000358853	SH3L2_HUMAN	.	UPI0000049FF7	.	.	.	2/4	.	hmmpanther:PTHR12232,hmmpanther:PTHR12232:SF4,Gene3D:3.40.30.10,Pfam_domain:PF04908,PIRSF_domain:PIRSF008142,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D73N|c.217G>A|3	MUTECT|MUSE	TTTAATGGCGA	.	2	ESCA
THSD7A	0	.	GRCh37	7	11675933	11675933	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.846A>C	p.Glu282Asp	p.E282D	ENST00000423059	2/28	103	68	35	72	71	0	THSD7A,missense_variant,p.Glu282Asp,ENST00000423059,;THSD7A,downstream_gene_variant,,ENST00000480061,;	G	ENSG00000005108	ENST00000423059	Transcript	missense_variant	1098	846	282	E/D	gaA/gaC	.	.	.	-1	THSD7A	HGNC	22207	protein_coding	YES	CCDS47543.1	ENSP00000406482	THS7A_HUMAN	.	UPI00006C0B74	.	tolerated(0.52)	benign(0.003)	2/28	.	hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGTTCTTT	.	5	ESCA
KCND2	0	.	GRCh37	7	120389403	120389403	+	3'UTR	SNP	C	C	T	rs569095934	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1491C>T	.	.	ENST00000331113	6/6	18	14	4	17	17	0	KCND2,3_prime_UTR_variant,,ENST00000331113,;KCND2,downstream_gene_variant,,ENST00000425288,;RP4-797C5.2,intron_variant,,ENST00000450480,;KCND2,downstream_gene_variant,,ENST00000473190,;	T	ENSG00000184408	ENST00000331113	Transcript	3_prime_UTR_variant	4349	.	.	.	.	rs569095934	.	.	1	KCND2	HGNC	6238	protein_coding	YES	CCDS5776.1	ENSP00000333496	KCND2_HUMAN	A4D0V9_HUMAN,Q75LS7_HUMAN	UPI0000073D37	.	.	.	6/6	.	.	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTACATTTA	byFrequency|by1000G	2	ESCA
SSBP1	0	.	GRCh37	7	141443477	141443477	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202G>A	p.Gly68Arg	p.G68R	ENST00000481508	4/7	41	37	4	53	53	0	SSBP1,missense_variant,p.Gly68Arg,ENST00000484178,;SSBP1,missense_variant,p.Gly68Arg,ENST00000498107,;SSBP1,missense_variant,p.Gly68Arg,ENST00000265304,;SSBP1,missense_variant,p.Gly68Arg,ENST00000481508,;SSBP1,missense_variant,p.Gly68Arg,ENST00000463093,;SSBP1,missense_variant,p.Gly68Arg,ENST00000467681,;SSBP1,missense_variant,p.Gly68Arg,ENST00000465582,;SSBP1,downstream_gene_variant,,ENST00000473783,;SSBP1,non_coding_transcript_exon_variant,,ENST00000469123,;SSBP1,non_coding_transcript_exon_variant,,ENST00000465167,;SSBP1,non_coding_transcript_exon_variant,,ENST00000489378,;SSBP1,downstream_gene_variant,,ENST00000461433,;SSBP1,downstream_gene_variant,,ENST00000468267,;SSBP1,downstream_gene_variant,,ENST00000496622,;	A	ENSG00000106028	ENST00000481508	Transcript	missense_variant	637	202	68	G/R	Ggg/Agg	.	.	.	1	SSBP1	HGNC	11317	protein_coding	YES	CCDS5866.1	ENSP00000419665	SSBP_HUMAN	E7EUY5_HUMAN,C9K0U8_HUMAN,C9J8J0_HUMAN,A4D1U3_HUMAN	UPI0000135FAA	.	tolerated_low_confidence(0.4)	benign(0.247)	4/7	.	Superfamily_domains:SSF50249,PIRSF_domain:PIRSF002070,TIGRFAM_domain:TIGR00621,Pfam_domain:PF00436,Gene3D:2.40.50.140,hmmpanther:PTHR10302,PROSITE_profiles:PS50935	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GATCAGGGGAT	.	3	ESCA
DNAH11	0	.	GRCh37	7	21730409	21730409	+	Missense_Mutation	SNP	C	C	T	rs761069549	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5972C>T	p.Thr1991Ile	p.T1991I	ENST00000328843	36/83	53	48	5	37	37	0	DNAH11,missense_variant,p.Thr1991Ile,ENST00000328843,;DNAH11,missense_variant,p.Thr1984Ile,ENST00000409508,;	T	ENSG00000105877	ENST00000328843	Transcript	missense_variant	6003	5972	1991	T/I	aCa/aTa	rs761069549,COSM3928964,COSM3928963	.	.	1	DNAH11	HGNC	2942	protein_coding	YES	.	ENSP00000330671	DYH11_HUMAN	Q75MY1_HUMAN,Q75KM7_HUMAN,O95705_HUMAN,O43352_HUMAN,O15433_HUMAN	UPI000041AC4D	.	.	benign(0.007)	36/83	.	hmmpanther:PTHR10676:SF227,hmmpanther:PTHR10676,Pfam_domain:PF12774,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TATCACACTGA	.	3	ESCA
DNAH11	0	.	GRCh37	7	21750323	21750323	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6855+2T>C	.	p.X2285_splice	ENST00000328843	.	80	66	14	41	41	0	DNAH11,splice_donor_variant,,ENST00000328843,;DNAH11,splice_donor_variant,,ENST00000409508,;	C	ENSG00000105877	ENST00000328843	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	DNAH11	HGNC	2942	protein_coding	YES	.	ENSP00000330671	DYH11_HUMAN	Q75MY1_HUMAN,Q75KM7_HUMAN,O95705_HUMAN,O43352_HUMAN,O15433_HUMAN	UPI000041AC4D	.	.	.	.	42/82	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGTGAATA	.	5	ESCA
CARD11	0	.	GRCh37	7	2963891	2963891	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1916T>A	p.Met639Lys	p.M639K	ENST00000396946	15/25	56	49	7	46	46	0	CARD11,missense_variant,p.Met639Lys,ENST00000396946,;CARD11,missense_variant,p.Met110Lys,ENST00000355508,;CARD11,upstream_gene_variant,,ENST00000480332,;	T	ENSG00000198286	ENST00000396946	Transcript	missense_variant	2320	1916	639	M/K	aTg/aAg	.	.	.	-1	CARD11	HGNC	16393	protein_coding	YES	CCDS5336.2	ENSP00000380150	CAR11_HUMAN	Q8TES3_HUMAN,E2QRC0_HUMAN	UPI00003FED38	.	tolerated(0.2)	benign(0.129)	15/25	.	hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAACATGAGG	.	4	ESCA
PSMA2	0	.	GRCh37	7	42961412	42961412	+	Intron	SNP	T	T	C	rs756914359	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530+45A>G	.	.	ENST00000223321	.	58	44	13	23	23	0	PSMA2,3_prime_UTR_variant,,ENST00000538645,;PSMA2,intron_variant,,ENST00000445517,;PSMA2,intron_variant,,ENST00000223321,;PSMA2,3_prime_UTR_variant,,ENST00000411875,;PSMA2,intron_variant,,ENST00000433579,;PSMA2,intron_variant,,ENST00000442788,;PSMA2,intron_variant,,ENST00000457444,;PSMA2,intron_variant,,ENST00000436986,;AC010132.11,downstream_gene_variant,,ENST00000295493,;	C	ENSG00000106588	ENST00000223321	Transcript	intron_variant	.	.	.	.	.	rs756914359	.	.	-1	PSMA2	HGNC	9531	protein_coding	YES	CCDS5467.1	ENSP00000223321	PSA2_HUMAN	Q6MZI6_HUMAN	UPI000004D00F	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCATAAAGT	.	5	ESCA
DBNL	0	.	GRCh37	7	44080441	44080441	+	5'Flank	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000468694	.	80	35	44	27	27	0	DBNL,upstream_gene_variant,,ENST00000448521,;DBNL,upstream_gene_variant,,ENST00000456905,;DBNL,upstream_gene_variant,,ENST00000494774,;DBNL,upstream_gene_variant,,ENST00000452943,;DBNL,upstream_gene_variant,,ENST00000490734,;DBNL,upstream_gene_variant,,ENST00000468694,;DBNL,upstream_gene_variant,,ENST00000440166,;LINC00957,non_coding_transcript_exon_variant,,ENST00000441052,;LINC00957,non_coding_transcript_exon_variant,,ENST00000416824,;RASA4CP,upstream_gene_variant,,ENST00000425524,;RASA4CP,upstream_gene_variant,,ENST00000446874,;DBNL,upstream_gene_variant,,ENST00000464762,;DBNL,upstream_gene_variant,,ENST00000458579,;DBNL,upstream_gene_variant,,ENST00000485932,;DBNL,upstream_gene_variant,,ENST00000441904,;DBNL,upstream_gene_variant,,ENST00000498733,;DBNL,upstream_gene_variant,,ENST00000423561,;DBNL,upstream_gene_variant,,ENST00000411855,;DBNL,upstream_gene_variant,,ENST00000429716,;DBNL,upstream_gene_variant,,ENST00000439815,;DBNL,upstream_gene_variant,,ENST00000439983,;DBNL,upstream_gene_variant,,ENST00000441840,;RASA4CP,intron_variant,,ENST00000424092,;RASA4CP,upstream_gene_variant,,ENST00000545716,;	G	ENSG00000136279	ENST00000468694	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3869	1	DBNL	HGNC	2696	protein_coding	YES	CCDS47579.1	ENSP00000417653	DBNL_HUMAN	F2Z2V3_HUMAN	UPI000007147D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCTCACA	.	5	ESCA
PURB	0	.	GRCh37	7	44920662	44920662	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3347G>A	.	.	ENST00000395699	1/1	31	27	4	32	32	0	PURB,3_prime_UTR_variant,,ENST00000395699,;MIR4657,downstream_gene_variant,,ENST00000578157,;RP4-673M15.1,upstream_gene_variant,,ENST00000608450,;	T	ENSG00000146676	ENST00000395699	Transcript	3_prime_UTR_variant	4299	.	.	.	.	.	.	.	-1	PURB	HGNC	9702	protein_coding	YES	CCDS5499.1	ENSP00000379051	PURB_HUMAN	.	UPI000006F6CE	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATCTCTTCAC	.	2	ESCA
MIOS	0	.	GRCh37	7	7634722	7634722	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2155C>T	p.His719Tyr	p.H719Y	ENST00000340080	10/13	86	74	12	65	65	0	MIOS,missense_variant,p.His719Tyr,ENST00000405785,;MIOS,missense_variant,p.His719Tyr,ENST00000340080,;MIOS,non_coding_transcript_exon_variant,,ENST00000493227,;	T	ENSG00000164654	ENST00000340080	Transcript	missense_variant	2576	2155	719	H/Y	Cac/Tac	.	.	.	1	MIOS	HGNC	21905	protein_coding	YES	CCDS43554.1	ENSP00000339881	MIO_HUMAN	C9JUE6_HUMAN,C9JTV2_HUMAN,C9JAQ1_HUMAN	UPI000020EB0B	.	tolerated(1)	benign(0.036)	10/13	.	hmmpanther:PTHR16453	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATTCACAGG	.	4	ESCA
TDH	0	.	GRCh37	8	11219212	11219212	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.541G>A	.	.	ENST00000534302	6/8	49	17	31	55	55	0	TDH,non_coding_transcript_exon_variant,,ENST00000525664,;TDH,non_coding_transcript_exon_variant,,ENST00000534302,;TDH,non_coding_transcript_exon_variant,,ENST00000525246,;TDH,non_coding_transcript_exon_variant,,ENST00000531764,;TDH,non_coding_transcript_exon_variant,,ENST00000326605,;	A	ENSG00000154316	ENST00000534302	Transcript	non_coding_transcript_exon_variant	541	.	.	.	.	.	.	.	1	TDH	HGNC	15547	processed_transcript	YES	.	.	.	.	.	.	.	.	6/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGGGCTTTT	.	5	ESCA
MTBP	0	.	GRCh37	8	121473471	121473471	+	Missense_Mutation	SNP	A	A	G	rs371337948	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.953A>G	p.Tyr318Cys	p.Y318C	ENST00000305949	9/22	58	44	13	54	54	0	MTBP,missense_variant,p.Tyr318Cys,ENST00000305949,;MTBP,missense_variant,p.Tyr318Cys,ENST00000523373,;MTBP,non_coding_transcript_exon_variant,,ENST00000522449,;	G	ENSG00000172167	ENST00000305949	Transcript	missense_variant	998	953	318	Y/C	tAt/tGt	rs371337948	.	.	1	MTBP	HGNC	7417	protein_coding	YES	CCDS6333.1	ENSP00000303398	MTBP_HUMAN	.	UPI00000703F0	.	deleterious(0)	probably_damaging(0.979)	9/22	.	hmmpanther:PTHR14382,hmmpanther:PTHR14382:SF1,Pfam_domain:PF14919	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTATATGT	byCluster	5	ESCA
ADCY8	0	.	GRCh37	8	132052018	132052018	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562C>A	p.Leu188Met	p.L188M	ENST00000286355	1/18	31	21	10	16	16	0	ADCY8,missense_variant,p.Leu188Met,ENST00000286355,;ADCY8,missense_variant,p.Leu188Met,ENST00000377928,;	T	ENSG00000155897	ENST00000286355	Transcript	missense_variant	2655	562	188	L/M	Ctg/Atg	.	.	.	-1	ADCY8	HGNC	239	protein_coding	YES	CCDS6363.1	ENSP00000286355	ADCY8_HUMAN	E5RFR2_HUMAN	UPI000012887C	.	deleterious(0.01)	possibly_damaging(0.878)	1/18	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCAGCACGT	.	5	ESCA
DOCK5	0	.	GRCh37	8	25190123	25190123	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2006T>C	p.Leu669Ser	p.L669S	ENST00000276440	20/52	43	28	14	43	43	0	DOCK5,missense_variant,p.Leu669Ser,ENST00000276440,;DOCK5,missense_variant,p.Leu441Ser,ENST00000444569,;DOCK5,missense_variant,p.Leu76Ser,ENST00000467709,;	C	ENSG00000147459	ENST00000276440	Transcript	missense_variant	2050	2006	669	L/S	tTg/tCg	.	.	.	1	DOCK5	HGNC	23476	protein_coding	YES	CCDS6047.1	ENSP00000276440	DOCK5_HUMAN	.	UPI000022D4F3	.	deleterious(0)	probably_damaging(0.989)	20/52	.	hmmpanther:PTHR23317:SF68,hmmpanther:PTHR23317,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTTGCAAG	.	5	ESCA
LYPLA1	0	.	GRCh37	8	54960378	54960378	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247C>G	.	.	ENST00000316963	9/9	18	13	5	14	14	0	LYPLA1,3_prime_UTR_variant,,ENST00000343231,;LYPLA1,3_prime_UTR_variant,,ENST00000316963,;LYPLA1,downstream_gene_variant,,ENST00000518546,;LYPLA1,downstream_gene_variant,,ENST00000521352,;LYPLA1,downstream_gene_variant,,ENST00000522007,;RP11-30L15.6,upstream_gene_variant,,ENST00000565668,;LYPLA1,non_coding_transcript_exon_variant,,ENST00000519272,;LYPLA1,downstream_gene_variant,,ENST00000520718,;LYPLA1,downstream_gene_variant,,ENST00000519891,;	C	ENSG00000120992	ENST00000316963	Transcript	3_prime_UTR_variant	1134	.	.	.	.	.	.	.	-1	LYPLA1	HGNC	6737	protein_coding	YES	CCDS6157.1	ENSP00000320043	LYPA1_HUMAN	Q6IAQ1_HUMAN,E5RJ48_HUMAN,B4DJV9_HUMAN	UPI0000072858	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAGAAGCT	.	5	ESCA
CNGB3	0	.	GRCh37	8	87641177	87641177	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1450G>A	p.Glu484Lys	p.E484K	ENST00000320005	12/18	88	74	14	80	80	0	CNGB3,missense_variant,p.Glu484Lys,ENST00000320005,;	T	ENSG00000170289	ENST00000320005	Transcript	missense_variant	1498	1450	484	E/K	Gaa/Aaa	.	.	.	-1	CNGB3	HGNC	2153	protein_coding	YES	CCDS6244.1	ENSP00000316605	CNGB3_HUMAN	.	UPI000014076F	.	deleterious(0.05)	benign(0.013)	12/18	.	hmmpanther:PTHR10217:SF385,hmmpanther:PTHR10217,Gene3D:3bpzA01,Superfamily_domains:SSF51206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCATACC	.	5	ESCA
DAB2IP	0	.	GRCh37	9	124535315	124535315	+	Silent	SNP	G	G	A	rs373684988	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2424G>A	p.%3D	p.A808A	ENST00000259371	12/17	18	11	6	13	13	0	DAB2IP,synonymous_variant,p.%3D,ENST00000408936,;DAB2IP,synonymous_variant,p.%3D,ENST00000259371,;DAB2IP,synonymous_variant,p.%3D,ENST00000373782,;DAB2IP,synonymous_variant,p.%3D,ENST00000309989,;DAB2IP,downstream_gene_variant,,ENST00000459906,;	A	ENSG00000136848	ENST00000259371	Transcript	synonymous_variant	2493	2424	808	A	gcG/gcA	rs373684988	.	.	1	DAB2IP	HGNC	17294	protein_coding	YES	CCDS6833.2	ENSP00000259371	DAB2P_HUMAN	H0Y3A3_HUMAN,F8WA47_HUMAN,F6R503_HUMAN,B3KW96_HUMAN	UPI0000D77E70	.	.	.	12/17	.	hmmpanther:PTHR10194:SF26,hmmpanther:PTHR10194,Pfam_domain:PF12004	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGCGGCTGG	byCluster	5	ESCA
ZBTB34	0	.	GRCh37	9	129646660	129646660	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3467A>G	.	.	ENST00000373452	1/1	33	15	18	21	21	0	ZBTB34,3_prime_UTR_variant,,ENST00000319119,;ZBTB34,3_prime_UTR_variant,,ENST00000373452,;	G	ENSG00000177125	ENST00000373452	Transcript	3_prime_UTR_variant	5034	.	.	.	.	.	.	.	1	ZBTB34	HGNC	31446	protein_coding	YES	CCDS48023.1	ENSP00000362551	ZBT34_HUMAN	.	UPI00004031FA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTATATGGAG	.	5	ESCA
LCNL1	0	.	GRCh37	9	139877754	139877754	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-285C>A	.	.	ENST00000408973	1/3	46	21	24	39	39	0	LCNL1,5_prime_UTR_variant,,ENST00000408973,;PTGDS,downstream_gene_variant,,ENST00000224167,;PTGDS,downstream_gene_variant,,ENST00000444903,;PTGDS,downstream_gene_variant,,ENST00000446677,;PTGDS,downstream_gene_variant,,ENST00000457950,;PTGDS,downstream_gene_variant,,ENST00000371625,;PTGDS,downstream_gene_variant,,ENST00000371623,;PTGDS,downstream_gene_variant,,ENST00000462514,;PTGDS,downstream_gene_variant,,ENST00000492068,;PTGDS,downstream_gene_variant,,ENST00000467871,;PTGDS,downstream_gene_variant,,ENST00000460340,;LCNL1,upstream_gene_variant,,ENST00000432827,;LCNL1,5_prime_UTR_variant,,ENST00000482657,;PTGDS,intron_variant,,ENST00000471521,;LCNL1,upstream_gene_variant,,ENST00000460177,;	A	ENSG00000214402	ENST00000408973	Transcript	5_prime_UTR_variant	310	.	.	.	.	.	.	.	1	LCNL1	HGNC	34436	protein_coding	YES	CCDS43908.1	ENSP00000386162	LCNL1_HUMAN	Q6ZSQ0_HUMAN,F2Z3E7_HUMAN	UPI0000251FB0	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACCCACCC	.	5	ESCA
CCDC171	0	.	GRCh37	9	15744551	15744551	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2330C>G	p.Ser777Ter	p.S777*	ENST00000380701	17/26	19	13	6	31	31	0	CCDC171,stop_gained,p.Ser777Ter,ENST00000297641,;CCDC171,stop_gained,p.Ser777Ter,ENST00000380701,;CCDC171,stop_gained,p.Ser17Ter,ENST00000449575,;	G	ENSG00000164989	ENST00000380701	Transcript	stop_gained	2658	2330	777	S/*	tCa/tGa	.	.	.	1	CCDC171	HGNC	29828	protein_coding	YES	CCDS6481.1	ENSP00000370077	CC171_HUMAN	Q8NCV3_HUMAN	UPI000021C44B	.	.	.	17/26	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCAACTG	.	5	ESCA
COL4A6	0	.	GRCh37	X	107431880	107431880	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1457G>A	p.Gly486Asp	p.G486D	ENST00000372216	21/45	19	9	10	25	25	0	COL4A6,missense_variant,p.Gly486Asp,ENST00000394872,;COL4A6,missense_variant,p.Gly486Asp,ENST00000372216,;COL4A6,missense_variant,p.Gly485Asp,ENST00000334504,;COL4A6,missense_variant,p.Gly485Asp,ENST00000545689,;COL4A6,missense_variant,p.Gly485Asp,ENST00000538570,;	T	ENSG00000197565	ENST00000372216	Transcript	missense_variant	1558	1457	486	G/D	gGt/gAt	.	.	.	-1	COL4A6	HGNC	2208	protein_coding	YES	CCDS14541.1	ENSP00000361290	CO4A6_HUMAN	B4DU54_HUMAN	UPI000049E122	.	.	probably_damaging(0.959)	21/45	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF164	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCACCGTCA	.	5	ESCA
HTATSF1	0	.	GRCh37	X	135594149	135594157	+	In_Frame_Del	DEL	GATGATGAT	GATGATGAT	-	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	GATGATGAT	GATGATGAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2247_2255delTGATGATGA	p.Asp751_Asp753del	p.D751_D753del	ENST00000535601	10/10	79	55	24	62	62	0	HTATSF1,inframe_deletion,p.Asp751_Asp753del,ENST00000218364,;HTATSF1,inframe_deletion,p.Asp751_Asp753del,ENST00000535601,;	-	ENSG00000102241	ENST00000535601	Transcript	inframe_deletion	2667-2675	2245-2253	749-751	DDD/-	GATGATGAT/-	.	.	.	1	HTATSF1	HGNC	5276	protein_coding	YES	CCDS14657.1	ENSP00000442699	HTSF1_HUMAN	Q5H919_HUMAN,Q5H918_HUMAN	UPI000006D876	.	.	.	10/10	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTAGCGATGATGATGACGA	.	3	ESCA
UBQLN2	0	.	GRCh37	X	56593245	56593245	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1064C>T	.	.	ENST00000338222	1/1	35	14	21	40	40	0	UBQLN2,3_prime_UTR_variant,,ENST00000338222,;	T	ENSG00000188021	ENST00000338222	Transcript	3_prime_UTR_variant	3220	.	.	.	.	.	.	.	1	UBQLN2	HGNC	12509	protein_coding	YES	CCDS14374.1	ENSP00000345195	UBQL2_HUMAN	.	UPI000004A059	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGTCATGTG	.	5	ESCA
TTTY5	0	.	GRCh37	Y	24443783	24443783	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A4A4-01A-11D-A27G-09	TCGA-LN-A4A4-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.724C>G	.	.	ENST00000400581	2/2	76	44	32	28	28	0	TTTY5,non_coding_transcript_exon_variant,,ENST00000400581,;	C	ENSG00000215560	ENST00000400581	Transcript	non_coding_transcript_exon_variant	724	.	.	.	.	.	.	.	-1	TTTY5	HGNC	16482	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCGGGGTCG	.	5	ESCA
TMEM236	0	.	GRCh37	10	18088835	18088836	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3346dupT	.	.	ENST00000480516	4/4	133	111	22	85	85	0	TMEM236,3_prime_UTR_variant,,ENST00000457860,;TMEM236,3_prime_UTR_variant,,ENST00000480516,;	T	ENSG00000184040	ENST00000480516	Transcript	3_prime_UTR_variant	4445-4446	.	.	.	.	.	.	.	1	TMEM236	Uniprot_gn	.	protein_coding	YES	.	ENSP00000417134	.	.	UPI000041A684	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACTTTATACAA	.	3	ESCA
RNLS	0	.	GRCh37	10	90045196	90045196	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.944G>T	p.Gly315Val	p.G315V	ENST00000331772	7/7	79	74	5	55	55	0	RNLS,missense_variant,p.Gly315Val,ENST00000331772,;RNLS,intron_variant,,ENST00000371947,;RNLS,intron_variant,,ENST00000437752,;	A	ENSG00000184719	ENST00000331772	Transcript	missense_variant	967	944	315	G/V	gGa/gTa	.	.	.	-1	RNLS	HGNC	25641	protein_coding	YES	CCDS31239.1	ENSP00000332530	RNLS_HUMAN	G9G138_HUMAN,G9G137_HUMAN	UPI00001AFF46	.	deleterious(0)	probably_damaging(0.998)	7/7	.	hmmpanther:PTHR23357,Gene3D:3.50.50.60,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCCTCCACAT	.	2	ESCA
APOA1	0	.	GRCh37	11	116706854	116706854	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474G>A	p.%3D	p.L158L	ENST00000236850	4/4	32	29	3	28	28	0	APOA1,synonymous_variant,p.%3D,ENST00000375329,;APOA1,synonymous_variant,p.%3D,ENST00000236850,;APOA1,synonymous_variant,p.%3D,ENST00000375320,;APOA1,synonymous_variant,p.%3D,ENST00000359492,;APOA1,synonymous_variant,p.%3D,ENST00000375323,;APOC3,downstream_gene_variant,,ENST00000375345,;APOC3,downstream_gene_variant,,ENST00000227667,;APOA1-AS,non_coding_transcript_exon_variant,,ENST00000444200,;	T	ENSG00000118137	ENST00000236850	Transcript	synonymous_variant	840	474	158	L	ctG/ctA	.	.	.	-1	APOA1	HGNC	600	protein_coding	YES	CCDS8378.1	ENSP00000236850	APOA1_HUMAN	.	UPI000002C911	.	.	.	4/4	.	Superfamily_domains:0053393,Pfam_domain:PF01442,Gene3D:1.20.120.20,hmmpanther:PTHR18976:SF11,hmmpanther:PTHR18976	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGTGCAGCTT	.	2	ESCA
SLC6A5	0	.	GRCh37	11	20623021	20623021	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.350C>T	p.Ala117Val	p.A117V	ENST00000525748	2/16	60	51	9	39	39	0	SLC6A5,missense_variant,p.Ala117Val,ENST00000525748,;SLC6A5,missense_variant,p.Ala117Val,ENST00000298923,;	T	ENSG00000165970	ENST00000525748	Transcript	missense_variant	623	350	117	A/V	gCg/gTg	.	.	.	1	SLC6A5	HGNC	11051	protein_coding	YES	CCDS7854.1	ENSP00000434364	SC6A5_HUMAN	.	UPI00004564A5	.	tolerated_low_confidence(0.71)	benign(0.051)	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L118L|c.352C>T|3	RADIA|MUTECT|MUSE	CAACGCGCTGC	.	3	ESCA
RCN1	0	.	GRCh37	11	32112966	32112966	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224T>A	p.Leu75His	p.L75H	ENST00000054950	1/6	243	234	8	169	169	0	RCN1,missense_variant,p.Leu75His,ENST00000054950,;RCN1,intron_variant,,ENST00000532942,;RCN1,intron_variant,,ENST00000530348,;RCN1,upstream_gene_variant,,ENST00000532721,;	A	ENSG00000049449	ENST00000054950	Transcript	missense_variant	517	224	75	L/H	cTc/cAc	.	.	.	1	RCN1	HGNC	9934	protein_coding	YES	CCDS7876.1	ENSP00000054950	RCN1_HUMAN	Q5J7V8_HUMAN,H0YDA4_HUMAN,E9PP27_HUMAN,E9PLM2_HUMAN	UPI0000000CA7	.	deleterious(0)	probably_damaging(0.997)	1/6	.	hmmpanther:PTHR10827,hmmpanther:PTHR10827:SF17,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGCTCACCC	.	2	ESCA
SPTBN2	0	.	GRCh37	11	66458874	66458874	+	Missense_Mutation	SNP	G	G	A	rs757668466	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5446C>T	p.Arg1816Trp	p.R1816W	ENST00000533211	27/38	61	48	12	27	27	0	SPTBN2,missense_variant,p.Arg1816Trp,ENST00000533211,;SPTBN2,missense_variant,p.Arg1816Trp,ENST00000529997,;SPTBN2,missense_variant,p.Arg1816Trp,ENST00000309996,;SPTBN2,upstream_gene_variant,,ENST00000532650,;SPTBN2,upstream_gene_variant,,ENST00000532902,;SPTBN2,upstream_gene_variant,,ENST00000530775,;SPTBN2,upstream_gene_variant,,ENST00000528051,;SPTBN2,downstream_gene_variant,,ENST00000530665,;	A	ENSG00000173898	ENST00000533211	Transcript	missense_variant	5778	5446	1816	R/W	Cgg/Tgg	rs757668466,COSM3452167,COSM3452168	.	.	-1	SPTBN2	HGNC	11276	protein_coding	YES	CCDS8150.1	ENSP00000432568	SPTN2_HUMAN	E9PJZ2_HUMAN,C1KC08_HUMAN	UPI000013EF83	.	tolerated(0.07)	benign(0.426)	27/38	.	PIRSF_domain:PIRSF002297,SMART_domains:SM00150,Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF205	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCGCGCCA	.	5	ESCA
GPR83	0	.	GRCh37	11	94126685	94126686	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612dupT	p.Ala205CysfsTer13	p.A205Cfs*13	ENST00000243673	3/4	99	80	19	63	63	0	GPR83,frameshift_variant,p.Ala163CysfsTer13,ENST00000539203,;GPR83,frameshift_variant,p.Ala205CysfsTer13,ENST00000243673,;	A	ENSG00000123901	ENST00000243673	Transcript	frameshift_variant	784-785	612-613	204-205	-/X	-/T	.	.	.	-1	GPR83	HGNC	4523	protein_coding	YES	CCDS8297.1	ENSP00000243673	GPR83_HUMAN	Q9H011_HUMAN	UPI000013CB3F	.	.	.	3/4	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF174,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATAGCATGTG	.	3	ESCA
COL2A1	0	.	GRCh37	12	48391685	48391685	+	Missense_Mutation	SNP	G	G	A	rs201234519	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398C>T	p.Pro133Leu	p.P133L	ENST00000380518	6/54	28	21	7	19	19	0	COL2A1,missense_variant,p.Pro133Leu,ENST00000380518,;COL2A1,missense_variant,p.Pro64Leu,ENST00000337299,;COL2A1,non_coding_transcript_exon_variant,,ENST00000474996,;COL2A1,downstream_gene_variant,,ENST00000466884,;COL2A1,downstream_gene_variant,,ENST00000465743,;COL2A1,downstream_gene_variant,,ENST00000490609,;	A	ENSG00000139219	ENST00000380518	Transcript	missense_variant	563	398	133	P/L	cCc/cTc	rs201234519	.	.	-1	COL2A1	HGNC	2200	protein_coding	YES	CCDS41778.1	ENSP00000369889	CO2A1_HUMAN	.	UPI0000D79713	.	.	unknown(0)	6/54	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF58,Pfam_domain:PF01391	.	.	.	.	.	.	.	T:0.0018	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	CTCTGGGTCCT	byFrequency|byCluster	3	ESCA
CERS5	0	.	GRCh37	12	50531578	50531578	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569A>G	p.Tyr190Cys	p.Y190C	ENST00000317551	6/10	36	28	8	34	34	0	CERS5,missense_variant,p.Tyr132Cys,ENST00000422340,;CERS5,missense_variant,p.Tyr190Cys,ENST00000317551,;CERS5,intron_variant,,ENST00000547800,;CERS5,intron_variant,,ENST00000550547,;CERS5,upstream_gene_variant,,ENST00000550919,;CERS5,upstream_gene_variant,,ENST00000553122,;CERS5,non_coding_transcript_exon_variant,,ENST00000547138,;RP4-605O3.4,intron_variant,,ENST00000548468,;CERS5,upstream_gene_variant,,ENST00000548942,;CERS5,downstream_gene_variant,,ENST00000548930,;CERS5,missense_variant,p.Tyr190Cys,ENST00000551697,;CERS5,missense_variant,p.Ile171Val,ENST00000542320,;CERS5,missense_variant,p.Ile155Val,ENST00000438450,;CERS5,missense_variant,p.Ile171Val,ENST00000380189,;CERS5,3_prime_UTR_variant,,ENST00000547787,;CERS5,non_coding_transcript_exon_variant,,ENST00000551005,;CERS5,non_coding_transcript_exon_variant,,ENST00000549089,;CERS5,upstream_gene_variant,,ENST00000550079,;CERS5,upstream_gene_variant,,ENST00000546676,;CERS5,upstream_gene_variant,,ENST00000546406,;CERS5,upstream_gene_variant,,ENST00000551757,;	C	ENSG00000139624	ENST00000317551	Transcript	missense_variant	694	569	190	Y/C	tAt/tGt	.	.	.	-1	CERS5	HGNC	23749	protein_coding	YES	CCDS8801.1	ENSP00000325485	CERS5_HUMAN	F8W1K4_HUMAN	UPI000007101F	.	deleterious(0)	probably_damaging(0.995)	6/10	.	PIRSF_domain:PIRSF005225,SMART_domains:SM00724,Pfam_domain:PF03798,hmmpanther:PTHR12560:SF8,hmmpanther:PTHR12560,PROSITE_profiles:PS50922	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAATAGTGA	.	5	ESCA
PCBP2	0	.	GRCh37	12	53873333	53873333	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*107A>C	.	.	ENST00000359462	15/15	77	54	22	73	73	0	PCBP2,3_prime_UTR_variant,,ENST00000455667,;PCBP2,3_prime_UTR_variant,,ENST00000547859,;PCBP2,3_prime_UTR_variant,,ENST00000359282,;PCBP2,3_prime_UTR_variant,,ENST00000546463,;PCBP2,3_prime_UTR_variant,,ENST00000552819,;PCBP2,3_prime_UTR_variant,,ENST00000552296,;PCBP2,3_prime_UTR_variant,,ENST00000562264,;PCBP2,3_prime_UTR_variant,,ENST00000359462,;PCBP2,3_prime_UTR_variant,,ENST00000437231,;PCBP2,3_prime_UTR_variant,,ENST00000439930,;PCBP2,3_prime_UTR_variant,,ENST00000447282,;PCBP2,3_prime_UTR_variant,,ENST00000548933,;PCBP2,3_prime_UTR_variant,,ENST00000549863,;PCBP2,3_prime_UTR_variant,,ENST00000603815,;MAP3K12,downstream_gene_variant,,ENST00000547035,;MAP3K12,downstream_gene_variant,,ENST00000267079,;MAP3K12,downstream_gene_variant,,ENST00000547488,;PCBP2,downstream_gene_variant,,ENST00000553064,;PCBP2,3_prime_UTR_variant,,ENST00000550585,;PCBP2,non_coding_transcript_exon_variant,,ENST00000550733,;PCBP2,non_coding_transcript_exon_variant,,ENST00000547048,;MAP3K12,downstream_gene_variant,,ENST00000551511,;MAP3K12,downstream_gene_variant,,ENST00000547020,;MAP3K12,downstream_gene_variant,,ENST00000552365,;	C	ENSG00000197111	ENST00000359462	Transcript	3_prime_UTR_variant	1531	.	.	.	.	.	.	.	1	PCBP2	HGNC	8648	protein_coding	YES	CCDS44900.1	ENSP00000352438	PCBP2_HUMAN	H3BSP4_HUMAN,F8W0G4_HUMAN,F8VTZ0_HUMAN	UPI0000161C69	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTAAATTTT	.	5	ESCA
ITGA7	0	.	GRCh37	12	56092633	56092633	+	Missense_Mutation	SNP	G	G	T	rs563941470	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.871C>A	p.Arg291Ser	p.R291S	ENST00000553804	6/25	42	34	8	31	31	0	ITGA7,missense_variant,p.Arg194Ser,ENST00000452168,;ITGA7,missense_variant,p.Arg287Ser,ENST00000257879,;ITGA7,missense_variant,p.Arg291Ser,ENST00000553804,;ITGA7,missense_variant,p.Arg331Ser,ENST00000257880,;ITGA7,missense_variant,p.Arg287Ser,ENST00000394229,;ITGA7,missense_variant,p.Arg291Ser,ENST00000394230,;ITGA7,missense_variant,p.Arg331Ser,ENST00000555728,;ITGA7,missense_variant,p.Arg129Ser,ENST00000557257,;ITGA7,missense_variant,p.Arg287Ser,ENST00000347027,;ITGA7,missense_variant,p.Arg45Ser,ENST00000556273,;ITGA7,non_coding_transcript_exon_variant,,ENST00000554543,;ITGA7,downstream_gene_variant,,ENST00000555687,;ITGA7,downstream_gene_variant,,ENST00000553737,;ITGA7,downstream_gene_variant,,ENST00000553276,;ITGA7,upstream_gene_variant,,ENST00000557058,;ITGA7,downstream_gene_variant,,ENST00000553893,;ITGA7,downstream_gene_variant,,ENST00000554724,;ITGA7,upstream_gene_variant,,ENST00000554327,;ITGA7,downstream_gene_variant,,ENST00000555809,;ITGA7,upstream_gene_variant,,ENST00000557488,;ITGA7,downstream_gene_variant,,ENST00000554359,;ITGA7,downstream_gene_variant,,ENST00000556371,;	T	ENSG00000135424	ENST00000553804	Transcript	missense_variant	890	871	291	R/S	Cgc/Agc	rs563941470,COSM4043350,COSM4043352,COSM4043351,COSM4043349	.	.	-1	ITGA7	HGNC	6143	protein_coding	YES	CCDS55832.1	ENSP00000452120	ITA7_HUMAN	.	UPI00003668CF	.	deleterious(0)	probably_damaging(0.951)	6/25	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF72,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318,Prints_domain:PR01185	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGCGGGGGG	.	5	ESCA
C12orf66	0	.	GRCh37	12	64609541	64609541	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438G>T	p.Met146Ile	p.M146I	ENST00000398055	2/3	77	65	12	57	57	0	C12orf66,missense_variant,p.Met93Ile,ENST00000544871,;C12orf66,missense_variant,p.Met146Ile,ENST00000311915,;C12orf66,missense_variant,p.Met146Ile,ENST00000398055,;	A	ENSG00000174206	ENST00000398055	Transcript	missense_variant	492	438	146	M/I	atG/atT	.	.	.	-1	C12orf66	HGNC	26517	protein_coding	YES	CCDS41803.1	ENSP00000381132	CL066_HUMAN	.	UPI000013F222	.	deleterious(0.05)	benign(0.006)	2/3	.	hmmpanther:PTHR31581,hmmpanther:PTHR31581:SF1,Pfam_domain:PF09404,Superfamily_domains:0053959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTACATCTT	.	5	ESCA
LEMD3	0	.	GRCh37	12	65564146	65564146	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.770A>T	p.Asn257Ile	p.N257I	ENST00000308330	1/13	28	23	5	14	14	0	LEMD3,missense_variant,p.Asn257Ile,ENST00000308330,;LEMD3,non_coding_transcript_exon_variant,,ENST00000541171,;	T	ENSG00000174106	ENST00000308330	Transcript	missense_variant	796	770	257	N/I	aAc/aTc	.	.	.	1	LEMD3	HGNC	28887	protein_coding	YES	CCDS8972.1	ENSP00000308369	MAN1_HUMAN	B4DI45_HUMAN	UPI000012EB75	.	deleterious_low_confidence(0.01)	benign(0.176)	1/13	.	hmmpanther:PTHR13428:SF9,hmmpanther:PTHR13428	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAAAACTATT	.	2	ESCA
MYH7	0	.	GRCh37	14	23898239	23898239	+	Silent	SNP	A	A	G	rs397516099	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1332T>C	p.%3D	p.N444N	ENST00000355349	14/40	75	60	15	52	52	0	MYH7,synonymous_variant,p.%3D,ENST00000355349,;	G	ENSG00000092054	ENST00000355349	Transcript	synonymous_variant	1495	1332	444	N	aaT/aaC	rs397516099	.	.	-1	MYH7	HGNC	7577	protein_coding	YES	CCDS9601.1	ENSP00000347507	MYH7_HUMAN	Q59EV3_HUMAN,L0L5E6_HUMAN,A8CLN2_HUMAN,A8CLL2_HUMAN,A6N931_HUMAN,A6N930_HUMAN	UPI000014019B	.	.	.	14/40	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF279,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	likely_benign	.	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTGGCATTGAT	.	3	ESCA
MYH7	0	.	GRCh37	14	23898270	23898270	+	Missense_Mutation	SNP	C	C	T	rs786205356	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1301G>A	p.Arg434Lys	p.R434K	ENST00000355349	14/40	88	71	17	51	51	0	MYH7,missense_variant,p.Arg434Lys,ENST00000355349,;	T	ENSG00000092054	ENST00000355349	Transcript	missense_variant	1464	1301	434	R/K	aGg/aAg	rs786205356,COSM1258465	.	.	-1	MYH7	HGNC	7577	protein_coding	YES	CCDS9601.1	ENSP00000347507	MYH7_HUMAN	Q59EV3_HUMAN,L0L5E6_HUMAN,A8CLN2_HUMAN,A8CLL2_HUMAN,A6N931_HUMAN,A6N930_HUMAN	UPI000014019B	.	tolerated(1)	benign(0.006)	14/40	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF279,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	benign	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACATCCTCTCA	.	3	ESCA
ESR2	0	.	GRCh37	14	64746800	64746800	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.434A>G	p.Asp145Gly	p.D145G	ENST00000341099	3/9	64	55	9	48	48	0	ESR2,missense_variant,p.Asp145Gly,ENST00000357782,;ESR2,missense_variant,p.Asp145Gly,ENST00000553796,;ESR2,missense_variant,p.Asp145Gly,ENST00000353772,;ESR2,missense_variant,p.Asp145Gly,ENST00000267525,;ESR2,missense_variant,p.Asp145Gly,ENST00000341099,;ESR2,missense_variant,p.Asp145Gly,ENST00000555278,;ESR2,missense_variant,p.Asp145Gly,ENST00000556275,;ESR2,missense_variant,p.Asp145Gly,ENST00000557772,;ESR2,missense_variant,p.Asp145Gly,ENST00000554572,;ESR2,missense_variant,p.Asp145Gly,ENST00000542956,;ESR2,missense_variant,p.Asp145Gly,ENST00000358599,;ESR2,non_coding_transcript_exon_variant,,ENST00000554520,;ESR2,intron_variant,,ENST00000555483,;ESR2,missense_variant,p.Asp145Gly,ENST00000344288,;	C	ENSG00000140009	ENST00000341099	Transcript	missense_variant	852	434	145	D/G	gAt/gGt	.	.	.	-1	ESR2	HGNC	3468	protein_coding	YES	CCDS9762.1	ENSP00000343925	ESR2_HUMAN	Q7LCB3_HUMAN,G3V5S2_HUMAN	UPI0000000964	.	deleterious(0.01)	benign(0.027)	3/9	.	hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF1,PIRSF_domain:PIRSF500102,PIRSF_domain:PIRSF002527	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCATCCCTC	.	4	ESCA
ZFP36L1	0	.	GRCh37	14	69259723	69259725	+	5'UTR	DEL	GCA	GCA	-	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	GCA	GCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-70_-68delTGC	.	.	ENST00000439696	1/2	70	55	15	49	49	0	ZFP36L1,inframe_deletion,p.Ala47del,ENST00000553375,;ZFP36L1,5_prime_UTR_variant,,ENST00000336440,;ZFP36L1,5_prime_UTR_variant,,ENST00000439696,;ZFP36L1,intron_variant,,ENST00000557022,;ZFP36L1,intron_variant,,ENST00000557086,;ZFP36L1,downstream_gene_variant,,ENST00000408913,;ZFP36L1,upstream_gene_variant,,ENST00000555997,;	-	ENSG00000185650	ENST00000439696	Transcript	5_prime_UTR_variant	233-235	.	.	.	.	.	.	.	-1	ZFP36L1	HGNC	1107	protein_coding	YES	CCDS9791.1	ENSP00000388402	TISB_HUMAN	G3V2D5_HUMAN,B4E1N3_HUMAN,B4DG15_HUMAN	UPI0000136FBC	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAGGCGCAGCCTC	.	3	ESCA
NRXN3	0	.	GRCh37	14	80328631	80328631	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*324C>A	.	.	ENST00000554719	17/17	27	22	5	23	23	0	NRXN3,3_prime_UTR_variant,,ENST00000554719,;NRXN3,3_prime_UTR_variant,,ENST00000281127,;NRXN3,3_prime_UTR_variant,,ENST00000557594,;NRXN3,3_prime_UTR_variant,,ENST00000428277,;NRXN3,downstream_gene_variant,,ENST00000335750,;NRXN3,downstream_gene_variant,,ENST00000556003,;NRXN3,3_prime_UTR_variant,,ENST00000555387,;NRXN3,downstream_gene_variant,,ENST00000554738,;	A	ENSG00000021645	ENST00000554719	Transcript	3_prime_UTR_variant	4001	.	.	.	.	.	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GGAAACTTCCT	.	4	ESCA
RP11-578F21.2	0	.	GRCh37	15	28929558	28929558	+	5'Flank	SNP	A	A	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000531834	.	61	49	12	46	46	0	HERC2P9,non_coding_transcript_exon_variant,,ENST00000528584,;HERC2P9,downstream_gene_variant,,ENST00000569226,;RP11-578F21.2,upstream_gene_variant,,ENST00000531834,;	G	ENSG00000254398	ENST00000531834	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2160	-1	RP11-578F21.2	Clone_based_vega_gene	.	unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCGACTACG	.	5	ESCA
BNIP2	0	.	GRCh37	15	59970196	59970196	+	Missense_Mutation	SNP	C	C	T	rs144319954	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.749G>A	p.Arg250His	p.R250H	ENST00000267859	5/10	45	37	7	32	32	0	BNIP2,missense_variant,p.Arg129His,ENST00000607373,;BNIP2,missense_variant,p.Arg250His,ENST00000267859,;BNIP2,missense_variant,p.Arg7His,ENST00000439052,;BNIP2,missense_variant,p.Arg191His,ENST00000415213,;BNIP2,downstream_gene_variant,,ENST00000417312,;BNIP2,3_prime_UTR_variant,,ENST00000448414,;BNIP2,non_coding_transcript_exon_variant,,ENST00000464390,;BNIP2,non_coding_transcript_exon_variant,,ENST00000560458,;BNIP2,downstream_gene_variant,,ENST00000477543,;BNIP2,downstream_gene_variant,,ENST00000557987,;PIGHP1,downstream_gene_variant,,ENST00000558833,;	T	ENSG00000140299	ENST00000267859	Transcript	missense_variant	843	749	250	R/H	cGc/cAc	rs144319954	.	.	-1	BNIP2	HGNC	1083	protein_coding	YES	CCDS10174.2	ENSP00000267859	.	J3KN59_HUMAN	UPI0000E59C57	.	tolerated(0.15)	benign(0.148)	5/10	.	hmmpanther:PTHR12112,hmmpanther:PTHR12112:SF12,Pfam_domain:PF12496	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGCGTCGT	byCluster	5	ESCA
TLN2	0	.	GRCh37	15	63042648	63042648	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4167C>G	p.%3D	p.L1389L	ENST00000561311	33/58	84	71	13	80	80	0	TLN2,synonymous_variant,p.%3D,ENST00000494733,;TLN2,synonymous_variant,p.%3D,ENST00000561311,;TLN2,synonymous_variant,p.%3D,ENST00000306829,;TLN2,non_coding_transcript_exon_variant,,ENST00000489129,;	G	ENSG00000171914	ENST00000561311	Transcript	synonymous_variant	4397	4167	1389	L	ctC/ctG	.	.	.	1	TLN2	HGNC	15447	protein_coding	YES	CCDS32261.1	ENSP00000453508	TLN2_HUMAN	.	UPI00001FE5FC	.	.	.	33/58	.	Gene3D:1.20.1440.10,hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCTCTCTTA	.	5	ESCA
GSDMA	0	.	GRCh37	17	38122104	38122104	+	Missense_Mutation	SNP	G	G	T	rs767159876	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.164G>T	p.Arg55Leu	p.R55L	ENST00000301659	2/12	44	36	8	35	35	0	GSDMA,missense_variant,p.Arg55Leu,ENST00000577447,;GSDMA,missense_variant,p.Arg55Leu,ENST00000301659,;	T	ENSG00000167914	ENST00000301659	Transcript	missense_variant	282	164	55	R/L	cGc/cTc	rs767159876	.	.	1	GSDMA	HGNC	13311	protein_coding	YES	CCDS45669.1	ENSP00000301659	GSDMA_HUMAN	J3KRG2_HUMAN	UPI0000140D2A	.	tolerated(0.13)	benign(0.373)	2/12	.	hmmpanther:PTHR16399,hmmpanther:PTHR16399:SF18,Pfam_domain:PF04598	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCCGCACCG	byFrequency	5	ESCA
TP53	0	.	GRCh37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	7/11	435	201	234	223	223	0	TP53,missense_variant,p.Arg248Gln,ENST00000413465,;TP53,missense_variant,p.Arg248Gln,ENST00000420246,;TP53,missense_variant,p.Arg248Gln,ENST00000269305,;TP53,missense_variant,p.Arg116Gln,ENST00000509690,;TP53,missense_variant,p.Arg248Gln,ENST00000359597,;TP53,missense_variant,p.Arg155Gln,ENST00000514944,;TP53,missense_variant,p.Arg248Gln,ENST00000445888,;TP53,missense_variant,p.Arg248Gln,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	933	743	248	R/Q	cGg/cAg	rs11540652,CM920675,TP53_g.13380G>A,TP53_g.13380G>C,TP53_g.13380G>T,TP53_g.13380del,COSM10662,COSM11491,COSM6549,COSM46135,COSM340105,COSM99602,COSM241995,COSM99020,COSM241994,COSM340106,COSM3356964,COSM3378346,COSM1640830,COSM1646857,COSM1646858,COSM99021,COSM241996,COSM340107	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25032700,20377871,18798306,15450681,25105660,21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R248Q|c.743G>A|113,SITE|p.R248Q|c.743G>A|633,SITE|p.R248Q|c.743G>A|64,SITE|p.R248Q|c.743G>A|42,SITE|p.R155Q|c.464G>A|114,SITE|p.R248Q|c.743G>A|110,CODON|p.0?|c.1_1182del1182|6,CODON|p.R248Q|c.743_744GG>AA|5,CODON|p.R248R|c.744G>A|5,CODON|p.R248W|c.741_742CC>TT|15,CODON|p.R248L|c.743G>T|7,CODON|p.R248L|c.743G>T|12,CODON|p.R155L|c.464G>T|12,CODON|p.R155P|c.464G>C|5,CODON|p.R248P|c.743G>C|17,CODON|p.R248L|c.743G>T|12,CODON|p.R248P|c.743G>C|5,CODON|p.R248L|c.743G>T|74,CODON|p.R248P|c.743G>C|5,BUFFER|p.L252_I254delLTI|c.754_762delCTCACCATC|4,BUFFER|p.L252_I254delLTI|c.751_759delATCCTCACC|4,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252delL|c.754_756delCTC|9,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252fs*93|c.754delC|5,BUFFER|p.L252F|c.754C>T|10,BUFFER|p.I251I|c.753C>A|3,BUFFER|p.I251N|c.752T>A|9,BUFFER|p.I251T|c.752T>C|6,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251S|c.752T>G|12,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251fs*94|c.751delA|6,BUFFER|p.I251L|c.751A>C|3,BUFFER|p.I251F|c.751A>T|8,BUFFER|p.P250P|c.750C>T|4,BUFFER|p.P250F|c.748_749CC>TT|3,BUFFER|p.I251fs*94|c.748delC|4,BUFFER|p.P250L|c.749C>T|49,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250L|c.749C>T|8,BUFFER|p.P250L|c.749C>T|6,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250S|c.748C>T|12,BUFFER|p.R249fs*96|c.746delG|4,BUFFER|p.R249S|c.747G>T|31,BUFFER|p.R249S|c.747G>C|22,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|15,BUFFER|p.R249R|c.747G>A|6,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|314,BUFFER|p.R249S|c.747G>T|30,BUFFER|p.R249T|c.746G>C|3,BUFFER|p.R249M|c.746G>T|8,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249K|c.746G>A|17,BUFFER|p.R249M|c.746G>T|4,BUFFER|p.R249T|c.746G>C|20,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249M|c.746G>T|35,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87,BUFFER|p.N247N|c.741C>T|10,BUFFER|p.N247I|c.740A>T|7,BUFFER|p.N154I|c.461A>T|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247T|c.740A>C|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247S|c.740A>G|7,BUFFER|p.N247D|c.739A>G|5,BUFFER|p.N247Y|c.739A>T|3,BUFFER|p.M153I|c.459G>C|3,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>A|21,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>C|4,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246R|c.737T>G|12,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246T|c.737T>C|8,BUFFER|p.M153R|c.458T>G|3,BUFFER|p.M246K|c.737T>A|7,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246L|c.736A>T|3,BUFFER|p.M153V|c.457A>G|7,BUFFER|p.M246V|c.736A>G|3,BUFFER|p.M246V|c.736A>G|35,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246V|c.736A>G|4,BUFFER|p.G245G|c.735C>T|5,BUFFER|p.G245D|c.734G>A|10,BUFFER|p.G245V|c.734G>T|3,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245A|c.734G>C|8,BUFFER|p.G152D|c.455G>A|23,BUFFER|p.G152V|c.455G>T|15,BUFFER|p.G245V|c.734G>T|10,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245D|c.734G>A|119,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245D|c.734G>A|7,BUFFER|p.G245V|c.734G>T|69,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245R|c.733G>C|14,BUFFER|p.G245S|c.733G>A|22,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152S|c.454G>A|56,BUFFER|p.G245C|c.733G>T|4,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245S|c.733G>A|340,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245C|c.733G>T|50,BUFFER|p.G245S|c.733G>A|39,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152C|c.454G>T|6,BUFFER|p.G152R|c.454G>C|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G151G|c.453C>T|3,BUFFER|p.G244G|c.732C>T|8,BUFFER|p.G244G|c.732C>A|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCCGGTTC	byFrequency|byCluster	5	ESCA
TMEM235	0	.	GRCh37	17	76227704	76227704	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000551068	.	47	43	4	47	47	0	TMEM235,synonymous_variant,p.%3D,ENST00000421688,;TMEM235,5_prime_UTR_variant,,ENST00000586400,;TMEM235,5_prime_UTR_variant,,ENST00000374946,;TMEM235,upstream_gene_variant,,ENST00000591033,;TMEM235,upstream_gene_variant,,ENST00000550981,;TMEM235,upstream_gene_variant,,ENST00000551068,;	A	ENSG00000204278	ENST00000551068	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	280	1	TMEM235	HGNC	27563	protein_coding	YES	CCDS56046.1	ENSP00000446514	TM235_HUMAN	.	UPI0000251E19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTCCTCCTC	.	2	ESCA
PIEZO2	0	.	GRCh37	18	10681730	10681730	+	Silent	SNP	G	G	A	rs112914683	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7368C>T	p.%3D	p.A2456A	ENST00000503781	47/52	35	30	5	38	38	0	PIEZO2,synonymous_variant,p.%3D,ENST00000285141,;PIEZO2,synonymous_variant,p.%3D,ENST00000503781,;PIEZO2,synonymous_variant,p.%3D,ENST00000538948,;PIEZO2,synonymous_variant,p.%3D,ENST00000580640,;PIEZO2,synonymous_variant,p.%3D,ENST00000302079,;PIEZO2,upstream_gene_variant,,ENST00000581680,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,;PIEZO2,upstream_gene_variant,,ENST00000579151,;	A	ENSG00000154864	ENST00000503781	Transcript	synonymous_variant	7368	7368	2456	A	gcC/gcT	rs112914683	.	.	-1	PIEZO2	HGNC	26270	protein_coding	YES	.	ENSP00000421377	PIEZ2_HUMAN	J3KSM7_HUMAN	UPI0001B3CB29	.	.	.	47/52	.	hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24,Pfam_domain:PF12166	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTGGGCACT	byCluster	2	ESCA
ASXL3	0	.	GRCh37	18	31323088	31323088	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3276G>A	p.%3D	p.E1092E	ENST00000269197	12/12	30	25	5	29	29	0	ASXL3,synonymous_variant,p.%3D,ENST00000269197,;ASXL3,3_prime_UTR_variant,,ENST00000592288,;	A	ENSG00000141431	ENST00000269197	Transcript	synonymous_variant	3276	3276	1092	E	gaG/gaA	COSM4071909,COSM4071908	.	.	1	ASXL3	HGNC	29357	protein_coding	YES	CCDS45847.1	ENSP00000269197	ASXL3_HUMAN	K7EQY1_HUMAN	UPI000156D0F3	.	.	.	12/12	.	hmmpanther:PTHR13578:SF18,hmmpanther:PTHR13578	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGAGGGTGG	.	5	ESCA
RP11-862L9.3	0	.	GRCh37	18	74696752	74696752	+	3'Flank	SNP	C	C	T	rs747036508	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000582546	.	63	55	8	57	57	0	MBP,missense_variant,p.Arg34His,ENST00000528160,;MBP,synonymous_variant,p.%3D,ENST00000397866,;MBP,synonymous_variant,p.%3D,ENST00000397865,;MBP,synonymous_variant,p.%3D,ENST00000382582,;MBP,synonymous_variant,p.%3D,ENST00000578193,;MBP,synonymous_variant,p.%3D,ENST00000359645,;MBP,synonymous_variant,p.%3D,ENST00000580402,;MBP,synonymous_variant,p.%3D,ENST00000447114,;MBP,synonymous_variant,p.%3D,ENST00000397875,;MBP,synonymous_variant,p.%3D,ENST00000355994,;MBP,synonymous_variant,p.%3D,ENST00000397869,;MBP,synonymous_variant,p.%3D,ENST00000526111,;MBP,3_prime_UTR_variant,,ENST00000585201,;MBP,intron_variant,,ENST00000354542,;MBP,intron_variant,,ENST00000527041,;MBP,intron_variant,,ENST00000579129,;MBP,downstream_gene_variant,,ENST00000578873,;RP11-862L9.3,downstream_gene_variant,,ENST00000582546,;RP11-862L9.3,downstream_gene_variant,,ENST00000580580,;RP11-862L9.3,downstream_gene_variant,,ENST00000582763,;MBP,non_coding_transcript_exon_variant,,ENST00000581179,;MBP,non_coding_transcript_exon_variant,,ENST00000580473,;MBP,non_coding_transcript_exon_variant,,ENST00000578715,;MBP,downstream_gene_variant,,ENST00000585216,;MBP,downstream_gene_variant,,ENST00000582282,;MBP,3_prime_UTR_variant,,ENST00000527975,;MBP,3_prime_UTR_variant,,ENST00000577755,;MBP,3_prime_UTR_variant,,ENST00000583474,;MBP,3_prime_UTR_variant,,ENST00000533278,;MBP,3_prime_UTR_variant,,ENST00000531144,;MBP,non_coding_transcript_exon_variant,,ENST00000397868,;MBP,non_coding_transcript_exon_variant,,ENST00000490319,;MBP,downstream_gene_variant,,ENST00000473302,;MBP,downstream_gene_variant,,ENST00000467108,;MBP,downstream_gene_variant,,ENST00000583118,;MBP,downstream_gene_variant,,ENST00000493623,;MBP,downstream_gene_variant,,ENST00000484548,;MBP,downstream_gene_variant,,ENST00000482445,;MBP,downstream_gene_variant,,ENST00000459948,;MBP,downstream_gene_variant,,ENST00000483025,;	T	ENSG00000266844	ENST00000582546	Transcript	downstream_gene_variant	.	.	.	.	.	rs747036508	.	714	1	RP11-862L9.3	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGCGTGCC	byFrequency	5	ESCA
QTRT1	0	.	GRCh37	19	10812295	10812295	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159C>T	p.%3D	p.T53T	ENST00000250237	1/10	59	46	12	74	74	0	QTRT1,synonymous_variant,p.%3D,ENST00000592254,;QTRT1,synonymous_variant,p.%3D,ENST00000250237,;QTRT1,non_coding_transcript_exon_variant,,ENST00000585885,;QTRT1,synonymous_variant,p.%3D,ENST00000421333,;QTRT1,synonymous_variant,p.%3D,ENST00000587599,;QTRT1,non_coding_transcript_exon_variant,,ENST00000590705,;QTRT1,non_coding_transcript_exon_variant,,ENST00000589488,;	T	ENSG00000213339	ENST00000250237	Transcript	synonymous_variant	169	159	53	T	acC/acT	.	.	.	1	QTRT1	HGNC	23797	protein_coding	YES	CCDS12248.1	ENSP00000250237	TGT_HUMAN	.	UPI000003B010	.	.	.	1/10	.	HAMAP:MF_00168,hmmpanther:PTHR11962,hmmpanther:PTHR11962:SF6,TIGRFAM_domain:TIGR00449,TIGRFAM_domain:TIGR00430,Gene3D:3.20.20.105,Superfamily_domains:SSF51713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCACCATGAA	.	5	ESCA
PRKACA	0	.	GRCh37	19	14208265	14208265	+	Missense_Mutation	SNP	G	G	T	rs34988264	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673C>A	p.Leu225Met	p.L225M	ENST00000308677	8/10	23	18	5	23	23	0	PRKACA,missense_variant,p.Leu225Met,ENST00000308677,;PRKACA,missense_variant,p.Leu180Met,ENST00000587372,;PRKACA,missense_variant,p.Leu217Met,ENST00000589994,;PRKACA,3_prime_UTR_variant,,ENST00000593092,;PRKACA,intron_variant,,ENST00000590853,;PRKACA,non_coding_transcript_exon_variant,,ENST00000350356,;PRKACA,non_coding_transcript_exon_variant,,ENST00000588209,;PRKACA,non_coding_transcript_exon_variant,,ENST00000536649,;PRKACA,non_coding_transcript_exon_variant,,ENST00000587533,;	T	ENSG00000072062	ENST00000308677	Transcript	missense_variant	870	673	225	L/M	Ctg/Atg	rs34988264	.	.	-1	PRKACA	HGNC	9380	protein_coding	YES	CCDS12304.1	ENSP00000309591	KAPCA_HUMAN	K7EMV1_HUMAN	UPI0000001C8D	.	deleterious(0.02)	possibly_damaging(0.851)	8/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24353:SF55,hmmpanther:PTHR24353,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCAGGGCCC	.	5	ESCA
ATP13A1	0	.	GRCh37	19	19758016	19758016	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3027A>T	p.%3D	p.G1009G	ENST00000357324	22/26	29	24	5	37	37	0	ATP13A1,synonymous_variant,p.%3D,ENST00000291503,;ATP13A1,synonymous_variant,p.%3D,ENST00000357324,;GMIP,upstream_gene_variant,,ENST00000587238,;GMIP,upstream_gene_variant,,ENST00000203556,;GMIP,upstream_gene_variant,,ENST00000587205,;GMIP,upstream_gene_variant,,ENST00000445806,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000469641,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000497556,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000473243,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000467160,;GMIP,upstream_gene_variant,,ENST00000588171,;GMIP,upstream_gene_variant,,ENST00000591047,;ATP13A1,downstream_gene_variant,,ENST00000491221,;	A	ENSG00000105726	ENST00000357324	Transcript	synonymous_variant	3054	3027	1009	G	ggA/ggT	.	.	.	-1	ATP13A1	HGNC	24215	protein_coding	YES	CCDS32970.2	ENSP00000349877	AT131_HUMAN	Q8N3E5_HUMAN	UPI0000126647	.	.	.	22/26	.	Superfamily_domains:0049473,TIGRFAM_domain:TIGR01657,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF82	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGACTCCCTC	.	4	ESCA
PIP5K1C	0	.	GRCh37	19	3644144	3644144	+	Missense_Mutation	SNP	C	C	T	rs778345965	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1451G>A	p.Arg484Gln	p.R484Q	ENST00000335312	12/18	69	55	14	56	56	0	PIP5K1C,missense_variant,p.Arg484Gln,ENST00000589578,;PIP5K1C,missense_variant,p.Arg484Gln,ENST00000539785,;PIP5K1C,missense_variant,p.Arg484Gln,ENST00000537021,;PIP5K1C,missense_variant,p.Arg484Gln,ENST00000335312,;PIP5K1C,non_coding_transcript_exon_variant,,ENST00000592530,;	T	ENSG00000186111	ENST00000335312	Transcript	missense_variant	1540	1451	484	R/Q	cGg/cAg	rs778345965	.	.	-1	PIP5K1C	HGNC	8996	protein_coding	YES	CCDS32872.1	ENSP00000335333	PI51C_HUMAN	Q7LE22_HUMAN	UPI000019C574	.	tolerated(0.11)	benign(0.033)	12/18	.	hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCCCGCTCG	byFrequency	5	ESCA
FUT5	0	.	GRCh37	19	5867038	5867038	+	Silent	SNP	G	G	A	rs763176772	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.699C>T	p.%3D	p.D233D	ENST00000252675	5/5	74	60	13	62	62	0	FUT5,synonymous_variant,p.%3D,ENST00000252675,;FUT5,synonymous_variant,p.%3D,ENST00000588525,;AC024592.12,downstream_gene_variant,,ENST00000585661,;AC024592.12,downstream_gene_variant,,ENST00000586349,;AC024592.12,3_prime_UTR_variant,,ENST00000592091,;	A	ENSG00000130383	ENST00000252675	Transcript	synonymous_variant	1262	699	233	D	gaC/gaT	rs763176772	.	.	-1	FUT5	HGNC	4016	protein_coding	YES	CCDS12154.1	ENSP00000252675	FUT5_HUMAN	K7ENC0_HUMAN	UPI000013CD7B	.	.	.	5/5	.	hmmpanther:PTHR11929:SF137,hmmpanther:PTHR11929,Pfam_domain:PF00852,Superfamily_domains:SSF53756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACACGTCCAC	byFrequency	5	ESCA
PALM	0	.	GRCh37	19	747876	747876	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1062G>A	.	.	ENST00000338448	9/9	18	13	4	22	22	0	PALM,3_prime_UTR_variant,,ENST00000338448,;PALM,3_prime_UTR_variant,,ENST00000264560,;MISP,upstream_gene_variant,,ENST00000215582,;PALM,downstream_gene_variant,,ENST00000592155,;PALM,downstream_gene_variant,,ENST00000587513,;PALM,downstream_gene_variant,,ENST00000593172,;PALM,downstream_gene_variant,,ENST00000590161,;	A	ENSG00000099864	ENST00000338448	Transcript	3_prime_UTR_variant	2272	.	.	.	.	.	.	.	1	PALM	HGNC	8594	protein_coding	YES	CCDS32857.1	ENSP00000341911	PALM_HUMAN	B7Z6Y8_HUMAN	UPI0000001616	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGGGCTTC	.	5	ESCA
MTOR	0	.	GRCh37	1	11292543	11292543	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2464A>G	p.Ile822Val	p.I822V	ENST00000361445	16/58	29	21	7	20	20	0	MTOR,missense_variant,p.Ile822Val,ENST00000361445,;RPL39P6,upstream_gene_variant,,ENST00000448289,;	C	ENSG00000198793	ENST00000361445	Transcript	missense_variant	2541	2464	822	I/V	Att/Gtt	.	.	.	-1	MTOR	HGNC	3942	protein_coding	YES	CCDS127.1	ENSP00000354558	MTOR_HUMAN	Q96QW8_HUMAN,B1AKQ2_HUMAN,B1AKP8_HUMAN	UPI000012ABD3	.	deleterious(0.01)	benign(0.008)	16/58	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF63,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATAATAAAAA	.	5	ESCA
ATAD3A	0	.	GRCh37	1	1458215	1458215	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.986A>T	p.Lys329Met	p.K329M	ENST00000378755	8/16	109	91	18	88	88	0	ATAD3A,missense_variant,p.Lys202Met,ENST00000536055,;ATAD3A,missense_variant,p.Lys281Met,ENST00000378756,;ATAD3A,missense_variant,p.Lys267Met,ENST00000339113,;ATAD3A,missense_variant,p.Lys329Met,ENST00000378755,;ATAD3A,upstream_gene_variant,,ENST00000400830,;ATAD3A,downstream_gene_variant,,ENST00000429957,;	T	ENSG00000197785	ENST00000378755	Transcript	missense_variant	1080	986	329	K/M	aAg/aTg	.	.	.	1	ATAD3A	HGNC	25567	protein_coding	YES	CCDS31.1	ENSP00000368030	ATD3A_HUMAN	.	UPI000013D456	.	deleterious(0)	probably_damaging(0.982)	8/16	.	hmmpanther:PTHR23075,hmmpanther:PTHR23075:SF4,Pfam_domain:PF12037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGAAGCCGT	.	4	ESCA
FLAD1	0	.	GRCh37	1	154960867	154960867	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659T>G	p.Leu220Arg	p.L220R	ENST00000292180	2/7	54	45	8	43	43	0	FLAD1,missense_variant,p.Leu123Arg,ENST00000315144,;FLAD1,missense_variant,p.Leu220Arg,ENST00000368433,;FLAD1,missense_variant,p.Leu121Arg,ENST00000405236,;FLAD1,missense_variant,p.Leu123Arg,ENST00000368432,;FLAD1,missense_variant,p.Leu121Arg,ENST00000368431,;FLAD1,missense_variant,p.Leu220Arg,ENST00000292180,;FLAD1,5_prime_UTR_variant,,ENST00000295530,;FLAD1,upstream_gene_variant,,ENST00000368428,;FLAD1,non_coding_transcript_exon_variant,,ENST00000487371,;FLAD1,upstream_gene_variant,,ENST00000489992,;FLAD1,upstream_gene_variant,,ENST00000477609,;FLAD1,downstream_gene_variant,,ENST00000492620,;FLAD1,upstream_gene_variant,,ENST00000481758,;	G	ENSG00000160688	ENST00000292180	Transcript	missense_variant	981	659	220	L/R	cTa/cGa	.	.	.	1	FLAD1	HGNC	24671	protein_coding	YES	CCDS1078.1	ENSP00000292180	FAD1_HUMAN	Q5T196_HUMAN,Q5T190_HUMAN	UPI00000735B2	.	deleterious(0)	probably_damaging(0.965)	2/7	.	Superfamily_domains:SSF53218,SMART_domains:SM00852,PIRSF_domain:PIRSF036620,Gene3D:3.40.980.10,Pfam_domain:PF00994,hmmpanther:PTHR23293,hmmpanther:PTHR23293:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCTATCAT	.	5	ESCA
SH2D2A	0	.	GRCh37	1	156779493	156779493	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.704C>T	p.Ala235Val	p.A235V	ENST00000392306	6/9	75	62	12	54	54	0	SH2D2A,missense_variant,p.Ala225Val,ENST00000368199,;SH2D2A,missense_variant,p.Ala207Val,ENST00000368198,;SH2D2A,missense_variant,p.Ala235Val,ENST00000392306,;SH2D2A,non_coding_transcript_exon_variant,,ENST00000468744,;SH2D2A,non_coding_transcript_exon_variant,,ENST00000486350,;SH2D2A,downstream_gene_variant,,ENST00000495306,;	A	ENSG00000027869	ENST00000392306	Transcript	missense_variant	844	704	235	A/V	gCc/gTc	.	.	.	-1	SH2D2A	HGNC	10821	protein_coding	YES	CCDS53381.1	ENSP00000376123	SH22A_HUMAN	.	UPI0000F534AC	.	tolerated(0.22)	benign(0.02)	6/9	.	hmmpanther:PTHR14388,hmmpanther:PTHR14388:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGGCTTGC	.	5	ESCA
SH2D2A	0	.	GRCh37	1	156779494	156779494	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703G>T	p.Ala235Ser	p.A235S	ENST00000392306	6/9	74	61	12	54	54	0	SH2D2A,missense_variant,p.Ala225Ser,ENST00000368199,;SH2D2A,missense_variant,p.Ala207Ser,ENST00000368198,;SH2D2A,missense_variant,p.Ala235Ser,ENST00000392306,;SH2D2A,non_coding_transcript_exon_variant,,ENST00000468744,;SH2D2A,non_coding_transcript_exon_variant,,ENST00000486350,;SH2D2A,downstream_gene_variant,,ENST00000495306,;	A	ENSG00000027869	ENST00000392306	Transcript	missense_variant	843	703	235	A/S	Gcc/Tcc	COSM4023411,COSM529513,COSM1138664,COSM4023410	.	.	-1	SH2D2A	HGNC	10821	protein_coding	YES	CCDS53381.1	ENSP00000376123	SH22A_HUMAN	.	UPI0000F534AC	.	tolerated(0.46)	benign(0.02)	6/9	.	hmmpanther:PTHR14388,hmmpanther:PTHR14388:SF2	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGCTTGCC	.	5	ESCA
SH2D1B	0	.	GRCh37	1	162367093	162367093	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000367929	4/4	31	25	6	24	24	0	SH2D1B,missense_variant,p.Asp126Tyr,ENST00000367929,;SH2D1B,missense_variant,p.Asp71Tyr,ENST00000359567,;	A	ENSG00000198574	ENST00000367929	Transcript	missense_variant	486	376	126	D/Y	Gat/Tat	COSM357467	.	.	-1	SH2D1B	HGNC	30416	protein_coding	YES	CCDS30928.1	ENSP00000356906	SH21B_HUMAN	.	UPI00000015D1	.	deleterious(0)	probably_damaging(0.977)	4/4	.	hmmpanther:PTHR11200	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAATCGCTGT	.	5	ESCA
BRINP2	0	.	GRCh37	1	177250911	177250911	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247C>A	.	.	ENST00000361539	8/8	58	48	9	35	35	0	BRINP2,3_prime_UTR_variant,,ENST00000361539,;BRINP2,non_coding_transcript_exon_variant,,ENST00000478325,;	A	ENSG00000198797	ENST00000361539	Transcript	3_prime_UTR_variant	2911	.	.	.	.	.	.	.	1	BRINP2	HGNC	13746	protein_coding	YES	CCDS1320.1	ENSP00000354481	BRNP2_HUMAN	.	UPI000006DF55	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATCTGTAA	.	5	ESCA
ASPM	0	.	GRCh37	1	197070956	197070956	+	Missense_Mutation	SNP	C	C	A	rs545567176	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7425G>T	p.Lys2475Asn	p.K2475N	ENST00000367409	18/28	111	95	15	81	81	0	ASPM,missense_variant,p.Lys2475Asn,ENST00000367409,;ASPM,intron_variant,,ENST00000367408,;ASPM,intron_variant,,ENST00000294732,;	A	ENSG00000066279	ENST00000367409	Transcript	missense_variant	7682	7425	2475	K/N	aaG/aaT	rs545567176	.	.	-1	ASPM	HGNC	19048	protein_coding	YES	CCDS1389.1	ENSP00000356379	ASPM_HUMAN	.	UPI0000458904	.	deleterious(0.02)	probably_damaging(0.967)	18/28	.	PROSITE_profiles:PS50096,hmmpanther:PTHR25069:SF115,hmmpanther:PTHR25069,Pfam_domain:PF00612,SMART_domains:SM00015,Superfamily_domains:SSF52540	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTTCTTCTT	by1000G	4	ESCA
WNT3A	0	.	GRCh37	1	228210523	228210523	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227A>T	p.Glu76Val	p.E76V	ENST00000284523	2/4	57	49	8	29	29	0	WNT3A,missense_variant,p.Glu76Val,ENST00000284523,;WNT3A,missense_variant,p.Glu76Val,ENST00000366753,;	T	ENSG00000154342	ENST00000284523	Transcript	missense_variant	305	227	76	E/V	gAg/gTg	.	.	.	1	WNT3A	HGNC	15983	protein_coding	YES	CCDS1564.1	ENSP00000284523	WNT3A_HUMAN	.	UPI000004F0E2	.	deleterious(0)	probably_damaging(0.998)	2/4	.	hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF88,Pfam_domain:PF00110,SMART_domains:SM00097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGGAGTGCC	.	4	ESCA
PTPRU	0	.	GRCh37	1	29647330	29647330	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3851C>A	p.Ser1284Tyr	p.S1284Y	ENST00000345512	27/31	63	53	9	42	42	0	PTPRU,missense_variant,p.Ser1274Tyr,ENST00000373779,;PTPRU,missense_variant,p.Ser1271Tyr,ENST00000428026,;PTPRU,missense_variant,p.Ser1280Tyr,ENST00000460170,;PTPRU,missense_variant,p.Ser1280Tyr,ENST00000323874,;PTPRU,missense_variant,p.Ser1280Tyr,ENST00000356870,;PTPRU,missense_variant,p.Ser1284Tyr,ENST00000345512,;PTPRU,non_coding_transcript_exon_variant,,ENST00000493601,;PTPRU,non_coding_transcript_exon_variant,,ENST00000465525,;PTPRU,upstream_gene_variant,,ENST00000492954,;	A	ENSG00000060656	ENST00000345512	Transcript	missense_variant	3980	3851	1284	S/Y	tCc/tAc	.	.	.	1	PTPRU	HGNC	9683	protein_coding	YES	CCDS334.1	ENSP00000334941	PTPRU_HUMAN	B3KT29_HUMAN	UPI000013C57E	.	tolerated(0.62)	probably_damaging(0.926)	27/31	.	PROSITE_profiles:PS50055,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACTCCGCCT	.	4	ESCA
PTPRU	0	.	GRCh37	1	29647331	29647331	+	Silent	SNP	C	C	A	rs772465677	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3852C>A	p.%3D	p.S1284S	ENST00000345512	27/31	62	52	9	42	42	0	PTPRU,synonymous_variant,p.%3D,ENST00000373779,;PTPRU,synonymous_variant,p.%3D,ENST00000428026,;PTPRU,synonymous_variant,p.%3D,ENST00000460170,;PTPRU,synonymous_variant,p.%3D,ENST00000323874,;PTPRU,synonymous_variant,p.%3D,ENST00000356870,;PTPRU,synonymous_variant,p.%3D,ENST00000345512,;PTPRU,non_coding_transcript_exon_variant,,ENST00000493601,;PTPRU,non_coding_transcript_exon_variant,,ENST00000465525,;PTPRU,upstream_gene_variant,,ENST00000492954,;	A	ENSG00000060656	ENST00000345512	Transcript	synonymous_variant	3981	3852	1284	S	tcC/tcA	rs772465677	.	.	1	PTPRU	HGNC	9683	protein_coding	YES	CCDS334.1	ENSP00000334941	PTPRU_HUMAN	B3KT29_HUMAN	UPI000013C57E	.	.	.	27/31	.	PROSITE_profiles:PS50055,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AACTCCGCCTG	byFrequency	4	ESCA
AGO4	0	.	GRCh37	1	36290920	36290920	+	Missense_Mutation	SNP	A	A	G	rs779332147	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313A>G	p.Met105Val	p.M105V	ENST00000373210	4/18	48	40	8	45	45	0	AGO4,missense_variant,p.Met105Val,ENST00000373210,;	G	ENSG00000134698	ENST00000373210	Transcript	missense_variant	558	313	105	M/V	Atg/Gtg	rs779332147	.	.	1	AGO4	HGNC	18424	protein_coding	YES	CCDS397.1	ENSP00000362306	AGO4_HUMAN	Q9NXV9_HUMAN	UPI00001684D9	.	tolerated(0.32)	benign(0)	4/18	.	HAMAP:MF_03033,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF26,Superfamily_domains:SSF101690	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGATATGGAG	byFrequency	5	ESCA
PTPRF	0	.	GRCh37	1	44019257	44019257	+	Silent	SNP	G	G	A	rs749879491	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186G>A	p.%3D	p.P62P	ENST00000359947	4/34	60	50	10	56	56	0	PTPRF,synonymous_variant,p.%3D,ENST00000438120,;PTPRF,synonymous_variant,p.%3D,ENST00000359947,;PTPRF,synonymous_variant,p.%3D,ENST00000372413,;PTPRF,synonymous_variant,p.%3D,ENST00000437607,;PTPRF,synonymous_variant,p.%3D,ENST00000372414,;PTPRF,non_coding_transcript_exon_variant,,ENST00000436724,;PTPRF,non_coding_transcript_exon_variant,,ENST00000372405,;PTPRF,downstream_gene_variant,,ENST00000481019,;PTPRF,downstream_gene_variant,,ENST00000496043,;	A	ENSG00000142949	ENST00000359947	Transcript	synonymous_variant	526	186	62	P	ccG/ccA	rs749879491	.	.	1	PTPRF	HGNC	9670	protein_coding	YES	CCDS489.2	ENSP00000353030	PTPRF_HUMAN	G1UI20_HUMAN	UPI0000470154	.	.	.	4/34	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R63H|c.188G>A|3	RADIA|MUTECT|MUSE|VARSCANS	AAGCCGCGCAT	byFrequency	4	ESCA
RBMXL1	0	.	GRCh37	1	89448692	89448692	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.818C>T	p.Ser273Leu	p.S273L	ENST00000399794	3/3	95	77	17	94	94	0	RBMXL1,missense_variant,p.Ser273Leu,ENST00000321792,;RBMXL1,missense_variant,p.Ser273Leu,ENST00000399794,;CCBL2,intron_variant,,ENST00000370485,;CCBL2,intron_variant,,ENST00000370486,;CCBL2,intron_variant,,ENST00000370491,;CCBL2,intron_variant,,ENST00000260508,;CCBL2,intron_variant,,ENST00000446900,;RBMXL1,downstream_gene_variant,,ENST00000413769,;	A	ENSG00000213516	ENST00000399794	Transcript	missense_variant	1534	818	273	S/L	tCa/tTa	.	.	.	-1	RBMXL1	HGNC	25073	protein_coding	YES	CCDS716.1	ENSP00000446099	RMXL1_HUMAN	Q2VIN3_HUMAN	UPI000006DA18	.	tolerated(0.22)	benign(0.022)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24012:SF303,hmmpanther:PTHR24012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTGAATAG	.	5	ESCA
SIRPG	0	.	GRCh37	20	1629949	1629949	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179C>G	p.Pro60Arg	p.P60R	ENST00000303415	2/6	86	77	9	59	59	0	SIRPG,missense_variant,p.Pro60Arg,ENST00000381583,;SIRPG,missense_variant,p.Pro27Arg,ENST00000381580,;SIRPG,missense_variant,p.Pro60Arg,ENST00000303415,;SIRPG,missense_variant,p.Pro60Arg,ENST00000216927,;SIRPG,missense_variant,p.Pro60Arg,ENST00000344103,;RP11-77C3.3,downstream_gene_variant,,ENST00000456177,;	C	ENSG00000089012	ENST00000303415	Transcript	missense_variant	244	179	60	P/R	cCc/cGc	.	.	.	-1	SIRPG	HGNC	15757	protein_coding	YES	CCDS13020.2	ENSP00000305529	SIRPG_HUMAN	.	UPI00001AE5FD	.	deleterious(0)	possibly_damaging(0.898)	2/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF6,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCACGGGAAGC	.	3	ESCA
GFRA4	0	.	GRCh37	20	3640428	3640428	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000319242	.	45	35	10	31	31	0	GFRA4,3_prime_UTR_variant,,ENST00000290417,;GFRA4,downstream_gene_variant,,ENST00000319242,;GFRA4,downstream_gene_variant,,ENST00000477160,;	A	ENSG00000125861	ENST00000319242	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	128	-1	GFRA4	HGNC	13821	protein_coding	YES	CCDS13056.1	ENSP00000313423	GFRA4_HUMAN	.	UPI0000070328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCGGAGTG	.	2	ESCA
TTI1	0	.	GRCh37	20	36640246	36640246	+	Missense_Mutation	SNP	T	T	A	rs745624497	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1973A>T	p.Glu658Val	p.E658V	ENST00000373448	3/9	59	48	11	37	37	0	TTI1,missense_variant,p.Glu658Val,ENST00000449821,;TTI1,missense_variant,p.Glu658Val,ENST00000373447,;TTI1,missense_variant,p.Glu658Val,ENST00000373448,;TTI1,non_coding_transcript_exon_variant,,ENST00000487362,;	A	ENSG00000101407	ENST00000373448	Transcript	missense_variant	2212	1973	658	E/V	gAg/gTg	rs745624497	.	.	-1	TTI1	HGNC	29029	protein_coding	YES	CCDS13300.1	ENSP00000362547	TTI1_HUMAN	D6W4K3_HUMAN	UPI000012DB27	.	deleterious(0)	probably_damaging(0.991)	3/9	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF005250,hmmpanther:PTHR18460	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCTCCAGT	.	5	ESCA
CDH22	0	.	GRCh37	20	44856175	44856175	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642G>T	p.Glu214Asp	p.E214D	ENST00000372262	3/11	50	39	11	39	39	0	CDH22,missense_variant,p.Glu214Asp,ENST00000372262,;CDH22,missense_variant,p.Glu214Asp,ENST00000537909,;	A	ENSG00000149654	ENST00000372262	Transcript	missense_variant	1043	642	214	E/D	gaG/gaT	.	.	.	-1	CDH22	HGNC	13251	protein_coding	YES	CCDS13395.1	ENSP00000361336	CAD22_HUMAN	Q49AS4_HUMAN	UPI0000126DC0	.	deleterious(0)	possibly_damaging(0.682)	3/11	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF88,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGCTCGCC	.	5	ESCA
LZTR1	0	.	GRCh37	22	21348236	21348236	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1377C>T	p.%3D	p.H459H	ENST00000215739	13/21	49	39	9	46	46	0	LZTR1,synonymous_variant,p.%3D,ENST00000215739,;LZTR1,synonymous_variant,p.%3D,ENST00000389355,;LZTR1,upstream_gene_variant,,ENST00000415817,;LZTR1,non_coding_transcript_exon_variant,,ENST00000479606,;LZTR1,downstream_gene_variant,,ENST00000497716,;LZTR1,downstream_gene_variant,,ENST00000480895,;LZTR1,non_coding_transcript_exon_variant,,ENST00000492480,;LZTR1,upstream_gene_variant,,ENST00000464807,;LZTR1,upstream_gene_variant,,ENST00000452988,;LZTR1,upstream_gene_variant,,ENST00000498649,;LZTR1,upstream_gene_variant,,ENST00000491432,;LZTR1,upstream_gene_variant,,ENST00000463909,;LZTR1,upstream_gene_variant,,ENST00000439171,;LZTR1,upstream_gene_variant,,ENST00000495142,;LZTR1,downstream_gene_variant,,ENST00000461510,;LZTR1,downstream_gene_variant,,ENST00000414985,;LZTR1,upstream_gene_variant,,ENST00000415354,;LZTR1,downstream_gene_variant,,ENST00000443265,;	T	ENSG00000099949	ENST00000215739	Transcript	synonymous_variant	1736	1377	459	H	caC/caT	.	.	.	1	LZTR1	HGNC	6742	protein_coding	YES	CCDS33606.1	ENSP00000215739	LZTR1_HUMAN	B2R8T5_HUMAN	UPI000013C695	.	.	.	13/21	.	PROSITE_profiles:PS50097,hmmpanther:PTHR23244:SF15,hmmpanther:PTHR23244,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCACGTAGC	.	5	ESCA
CBWD2	0	.	GRCh37	2	114195430	114195430	+	5'UTR	SNP	C	C	T	rs751837727	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16C>T	.	.	ENST00000259199	1/15	173	151	21	149	149	0	CBWD2,5_prime_UTR_variant,,ENST00000416503,;CBWD2,5_prime_UTR_variant,,ENST00000433343,;CBWD2,5_prime_UTR_variant,,ENST00000259199,;RP11-480C16.1,downstream_gene_variant,,ENST00000608834,;CBWD2,5_prime_UTR_variant,,ENST00000456188,;CBWD2,5_prime_UTR_variant,,ENST00000358604,;CBWD2,non_coding_transcript_exon_variant,,ENST00000490323,;CBWD2,non_coding_transcript_exon_variant,,ENST00000463627,;CBWD2,upstream_gene_variant,,ENST00000492566,;	T	ENSG00000136682	ENST00000259199	Transcript	5_prime_UTR_variant	163	.	.	.	.	rs751837727	.	.	1	CBWD2	HGNC	17907	protein_coding	YES	CCDS2116.1	ENSP00000259199	CBWD2_HUMAN	.	UPI000007478B	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGACGTGCT	.	4	ESCA
CIR1	0	.	GRCh37	2	175213649	175213649	+	Missense_Mutation	SNP	T	T	C	rs777532880	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.929A>G	p.Lys310Arg	p.K310R	ENST00000342016	10/10	33	29	4	32	32	0	CIR1,missense_variant,p.Lys310Arg,ENST00000342016,;CIR1,3_prime_UTR_variant,,ENST00000362053,;CIR1,downstream_gene_variant,,ENST00000464393,;	C	ENSG00000138433	ENST00000342016	Transcript	missense_variant	1022	929	310	K/R	aAg/aGg	rs777532880	.	.	-1	CIR1	HGNC	24217	protein_coding	YES	CCDS2256.1	ENSP00000339723	CIR1_HUMAN	.	UPI000000DB2A	.	tolerated_low_confidence(0.21)	benign(0.097)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCCTTCTCT	.	4	ESCA
TTN	0	.	GRCh37	2	179455006	179455006	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61446T>C	p.%3D	p.C20482C	ENST00000589042	304/363	100	79	21	64	64	0	TTN,synonymous_variant,p.%3D,ENST00000359218,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000342175,;TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000590743,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,upstream_gene_variant,,ENST00000589234,;	G	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	61671	61446	20482	C	tgT/tgC	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	304/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACGACAAGT	.	5	ESCA
MYT1L	0	.	GRCh37	2	2328454	2328454	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-521+6285G>T	.	.	ENST00000428368	.	44	38	6	33	33	0	MYT1L,intron_variant,,ENST00000399161,;MYT1L,intron_variant,,ENST00000428368,;MYT1L-AS1,non_coding_transcript_exon_variant,,ENST00000422175,;MYT1L-AS1,non_coding_transcript_exon_variant,,ENST00000448106,;MYT1L,intron_variant,,ENST00000460585,;MYT1L,intron_variant,,ENST00000476547,;MYT1L,upstream_gene_variant,,ENST00000479156,;	A	ENSG00000186487	ENST00000428368	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MYT1L	HGNC	7623	protein_coding	YES	CCDS46222.1	ENSP00000396103	MYT1L_HUMAN	.	UPI00004E55EA	.	.	.	.	1/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCCCGCCTG	.	5	ESCA
SNX17	0	.	GRCh37	2	27599187	27599187	+	Missense_Mutation	SNP	G	G	T	rs751199615	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1190G>T	p.Arg397Leu	p.R397L	ENST00000233575	13/15	31	26	4	14	14	0	SNX17,missense_variant,p.Arg372Leu,ENST00000537606,;SNX17,missense_variant,p.Arg183Leu,ENST00000542478,;SNX17,missense_variant,p.Arg183Leu,ENST00000543024,;SNX17,missense_variant,p.Arg397Leu,ENST00000233575,;PPM1G,downstream_gene_variant,,ENST00000344034,;ZNF513,downstream_gene_variant,,ENST00000407879,;ZNF513,downstream_gene_variant,,ENST00000323703,;ZNF513,downstream_gene_variant,,ENST00000436006,;PPM1G,downstream_gene_variant,,ENST00000350803,;ZNF513,downstream_gene_variant,,ENST00000491924,;SNX17,3_prime_UTR_variant,,ENST00000453453,;SNX17,3_prime_UTR_variant,,ENST00000440760,;SNX17,3_prime_UTR_variant,,ENST00000427123,;SNX17,downstream_gene_variant,,ENST00000493711,;SNX17,downstream_gene_variant,,ENST00000484886,;SNX17,downstream_gene_variant,,ENST00000464279,;PPM1G,downstream_gene_variant,,ENST00000472077,;SNX17,downstream_gene_variant,,ENST00000494893,;SNX17,downstream_gene_variant,,ENST00000489402,;	T	ENSG00000115234	ENST00000233575	Transcript	missense_variant	1412	1190	397	R/L	cGc/cTc	rs751199615	.	.	1	SNX17	HGNC	14979	protein_coding	YES	CCDS1750.1	ENSP00000233575	SNX17_HUMAN	B4DTB8_HUMAN,B4DLL7_HUMAN,B4DDM3_HUMAN	UPI0000135B4E	.	tolerated(0.16)	benign(0.312)	13/15	.	hmmpanther:PTHR12431,hmmpanther:PTHR12431:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGCGCCGGC	byFrequency	4	ESCA
CRIM1	0	.	GRCh37	2	36777211	36777211	+	3'UTR	SNP	C	C	T	rs529018725	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1367C>T	.	.	ENST00000280527	17/17	34	27	7	29	28	0	CRIM1,3_prime_UTR_variant,,ENST00000280527,;AC007401.2,intron_variant,,ENST00000406220,;FEZ2,downstream_gene_variant,,ENST00000305852,;FEZ2,downstream_gene_variant,,ENST00000441005,;FEZ2,downstream_gene_variant,,ENST00000379245,;FEZ2,downstream_gene_variant,,ENST00000405912,;FEZ2,downstream_gene_variant,,ENST00000487919,;FEZ2,downstream_gene_variant,,ENST00000487282,;FEZ2,downstream_gene_variant,,ENST00000432869,;FEZ2,downstream_gene_variant,,ENST00000414288,;FEZ2,downstream_gene_variant,,ENST00000451623,;FEZ2,downstream_gene_variant,,ENST00000475815,;FEZ2,downstream_gene_variant,,ENST00000413938,;	T	ENSG00000150938	ENST00000280527	Transcript	3_prime_UTR_variant	4845	.	.	.	.	rs529018725	.	.	1	CRIM1	HGNC	2359	protein_coding	YES	CCDS1783.1	ENSP00000280527	CRIM1_HUMAN	Q53TR0_HUMAN,Q53TH9_HUMAN,Q4ZG85_HUMAN,B4DUW0_HUMAN	UPI000004C628	.	.	.	17/17	.	.	T:0.0158	T:0.0363	T:0.0043	.	T:0.0159	T:0.004	T:0.0082	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTGTGCGCGCG	byFrequency|by1000G	2	ESCA
LRPPRC	0	.	GRCh37	2	44187730	44187730	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1532G>T	p.Gly511Val	p.G511V	ENST00000260665	13/38	68	55	12	51	51	0	LRPPRC,missense_variant,p.Gly511Val,ENST00000260665,;LRPPRC,missense_variant,p.Gly511Val,ENST00000409946,;LRPPRC,downstream_gene_variant,,ENST00000409659,;LRPPRC,non_coding_transcript_exon_variant,,ENST00000467058,;	A	ENSG00000138095	ENST00000260665	Transcript	missense_variant	1590	1532	511	G/V	gGa/gTa	.	.	.	-1	LRPPRC	HGNC	15714	protein_coding	YES	CCDS33189.1	ENSP00000260665	LPPRC_HUMAN	E5KNY5_HUMAN	UPI000019B4D2	.	tolerated(0.07)	benign(0)	13/38	.	hmmpanther:PTHR24015:SF0,hmmpanther:PTHR24015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATCCAGCT	.	5	ESCA
CALM2	0	.	GRCh37	2	47387412	47387412	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*503C>T	.	.	ENST00000272298	6/6	43	36	7	41	41	0	CALM2,3_prime_UTR_variant,,ENST00000272298,;C2orf61,upstream_gene_variant,,ENST00000445927,;C2orf61,upstream_gene_variant,,ENST00000294947,;CALM2,downstream_gene_variant,,ENST00000456319,;CALM2,downstream_gene_variant,,ENST00000409563,;CALM2,downstream_gene_variant,,ENST00000489742,;CALM2,downstream_gene_variant,,ENST00000484408,;CALM2,3_prime_UTR_variant,,ENST00000432899,;CALM2,non_coding_transcript_exon_variant,,ENST00000460218,;RP11-761B3.1,intron_variant,,ENST00000422269,;CALM2,downstream_gene_variant,,ENST00000482532,;	A	ENSG00000143933	ENST00000272298	Transcript	3_prime_UTR_variant	1111	.	.	.	.	.	.	.	-1	CALM2	HGNC	1445	protein_coding	YES	CCDS1832.1	ENSP00000272298	CALM_HUMAN	Q96HY3_HUMAN,G3V361_HUMAN,B4DJ51_HUMAN	UPI00000000C1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAGCAAGT	.	5	ESCA
CTNNA2	0	.	GRCh37	2	80085292	80085292	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452C>T	p.Ser151Phe	p.S151F	ENST00000466387	8/22	50	42	8	35	35	0	CTNNA2,missense_variant,p.Ser151Phe,ENST00000496558,;CTNNA2,missense_variant,p.Ser151Phe,ENST00000540488,;CTNNA2,missense_variant,p.Ser185Phe,ENST00000361291,;CTNNA2,missense_variant,p.Ser151Phe,ENST00000466387,;CTNNA2,missense_variant,p.Ser151Phe,ENST00000541047,;CTNNA2,missense_variant,p.Ser151Phe,ENST00000402739,;CTNNA2,downstream_gene_variant,,ENST00000409971,;	T	ENSG00000066032	ENST00000466387	Transcript	missense_variant	1176	452	151	S/F	tCc/tTc	COSM3583566,COSM3583567,COSM3583565	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	deleterious(0.03)	benign(0.056)	8/22	.	hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Pfam_domain:PF01044,Gene3D:1.20.120.230,Superfamily_domains:SSF47220	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATCCCATC	.	5	ESCA
ASTL	0	.	GRCh37	2	96789707	96789707	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1178C>T	p.Thr393Ile	p.T393I	ENST00000342380	9/9	38	32	6	36	36	0	ASTL,missense_variant,p.Thr393Ile,ENST00000342380,;	A	ENSG00000188886	ENST00000342380	Transcript	missense_variant	1178	1178	393	T/I	aCc/aTc	.	.	.	-1	ASTL	HGNC	31704	protein_coding	YES	CCDS33249.1	ENSP00000343674	ASTL_HUMAN	.	UPI0000161978	.	deleterious_low_confidence(0.02)	benign(0.07)	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTGGTGGAC	.	4	ESCA
MYH15	0	.	GRCh37	3	108127166	108127166	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4641A>T	p.Glu1547Asp	p.E1547D	ENST00000273353	33/42	82	76	6	54	54	0	MYH15,missense_variant,p.Glu1547Asp,ENST00000273353,;MYH15,non_coding_transcript_exon_variant,,ENST00000478998,;	A	ENSG00000144821	ENST00000273353	Transcript	missense_variant	4698	4641	1547	E/D	gaA/gaT	.	.	.	-1	MYH15	HGNC	31073	protein_coding	YES	CCDS43127.1	ENSP00000273353	MYH15_HUMAN	H9XFA0_HUMAN	UPI0000253B6F	.	tolerated(0.43)	benign(0.012)	33/42	.	Pfam_domain:PF01576,hmmpanther:PTHR13140:SF263,hmmpanther:PTHR13140,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTCTTCTTC	.	2	ESCA
MSL2	0	.	GRCh37	3	135871405	135871405	+	Silent	SNP	T	T	C	rs544521594	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318A>G	p.%3D	p.L106L	ENST00000309993	2/2	91	73	18	59	59	0	MSL2,synonymous_variant,p.%3D,ENST00000491050,;MSL2,synonymous_variant,p.%3D,ENST00000309993,;MSL2,synonymous_variant,p.%3D,ENST00000473093,;MSL2,synonymous_variant,p.%3D,ENST00000434835,;MSL2,synonymous_variant,p.%3D,ENST00000481989,;PPP2R3A,downstream_gene_variant,,ENST00000264977,;TDGF1P6,upstream_gene_variant,,ENST00000463873,;	C	ENSG00000174579	ENST00000309993	Transcript	synonymous_variant	1051	318	106	L	ctA/ctG	rs544521594	.	.	-1	MSL2	HGNC	25544	protein_coding	YES	CCDS33861.1	ENSP00000311827	MSL2_HUMAN	C9J5S2_HUMAN,C9IZG7_HUMAN,C9IZ03_HUMAN	UPI000020A2D7	.	.	.	2/2	.	hmmpanther:PTHR16048,hmmpanther:PTHR16048:SF2	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCATAGTTT	by1000G	5	ESCA
MCF2L2	0	.	GRCh37	3	182941140	182941140	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2295G>C	p.%3D	p.L765L	ENST00000328913	20/30	22	16	6	23	23	0	MCF2L2,synonymous_variant,p.%3D,ENST00000473233,;MCF2L2,synonymous_variant,p.%3D,ENST00000328913,;MCF2L2,downstream_gene_variant,,ENST00000447025,;MCF2L2,non_coding_transcript_exon_variant,,ENST00000488149,;	G	ENSG00000053524	ENST00000328913	Transcript	synonymous_variant	2593	2295	765	L	ctG/ctC	.	.	.	-1	MCF2L2	HGNC	30319	protein_coding	YES	CCDS3243.1	ENSP00000328118	MF2L2_HUMAN	C9J326_HUMAN	UPI00001A962F	.	.	.	20/30	.	PROSITE_profiles:PS50010,hmmpanther:PTHR22826:SF89,hmmpanther:PTHR22826,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCAACAGCAT	.	2	ESCA
FAM157A	0	.	GRCh37	3	197894637	197894637	+	RNA	SNP	C	C	G	rs568039668	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.798C>G	.	.	ENST00000437428	3/11	337	325	12	309	309	0	FAM157A,non_coding_transcript_exon_variant,,ENST00000437428,;FAM157A,non_coding_transcript_exon_variant,,ENST00000431569,;	G	ENSG00000236438	ENST00000437428	Transcript	non_coding_transcript_exon_variant	798	.	.	.	.	rs568039668	.	.	1	FAM157A	HGNC	34079	lincRNA	YES	.	.	.	.	.	.	.	.	3/11	.	.	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCGCGCGAT	by1000G	2	ESCA
FEZF2	0	.	GRCh37	3	62355953	62355953	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1185C>G	p.Asn395Lys	p.N395K	ENST00000283268	5/5	147	123	24	149	149	0	FEZF2,missense_variant,p.Asn395Lys,ENST00000283268,;FEZF2,missense_variant,p.Asn395Lys,ENST00000475839,;FEZF2,missense_variant,p.Asn395Lys,ENST00000486811,;PTPRG-AS1,upstream_gene_variant,,ENST00000490916,;PTPRG-AS1,upstream_gene_variant,,ENST00000495542,;	C	ENSG00000153266	ENST00000283268	Transcript	missense_variant	1480	1185	395	N/K	aaC/aaG	.	.	.	-1	FEZF2	HGNC	13506	protein_coding	YES	CCDS2897.1	ENSP00000283268	FEZF2_HUMAN	.	UPI0000071A13	.	deleterious(0.03)	benign(0.115)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23228:SF105,hmmpanther:PTHR23228,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTGTTGCA	.	5	ESCA
RYBP	0	.	GRCh37	3	72426977	72426977	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*559A>G	.	.	ENST00000477973	4/4	19	12	7	29	29	0	RYBP,3_prime_UTR_variant,,ENST00000477973,;	C	ENSG00000163602	ENST00000477973	Transcript	3_prime_UTR_variant	1511	.	.	.	.	.	.	.	-1	RYBP	HGNC	10480	protein_coding	YES	.	ENSP00000419494	RYBP_HUMAN	.	UPI0001B794AD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTATTCACT	.	5	ESCA
COL8A1	0	.	GRCh37	3	99514062	99514062	+	Missense_Mutation	SNP	G	G	T	rs369684623	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1317G>T	p.Lys439Asn	p.K439N	ENST00000261037	5/5	64	54	10	44	44	0	COL8A1,missense_variant,p.Lys439Asn,ENST00000261037,;COL8A1,missense_variant,p.Lys439Asn,ENST00000273342,;COL8A1,downstream_gene_variant,,ENST00000452013,;	T	ENSG00000144810	ENST00000261037	Transcript	missense_variant	1697	1317	439	K/N	aaG/aaT	rs369684623	.	.	1	COL8A1	HGNC	2215	protein_coding	YES	CCDS2934.1	ENSP00000261037	CO8A1_HUMAN	C9JTN9_HUMAN	UPI0000126D21	.	deleterious(0.04)	unknown(0)	5/5	.	hmmpanther:PTHR24022,hmmpanther:PTHR24022:SF61	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAAGCCAGG	byFrequency|byCluster	5	ESCA
C4orf21	0	.	GRCh37	4	113506828	113506828	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3970T>C	p.Ser1324Pro	p.S1324P	ENST00000505019	14/28	39	33	6	40	40	0	C4orf21,missense_variant,p.Ser1324Pro,ENST00000505019,;C4orf21,downstream_gene_variant,,ENST00000309071,;C4orf21,missense_variant,p.Ser222Pro,ENST00000445413,;C4orf21,3_prime_UTR_variant,,ENST00000473015,;	G	ENSG00000138658	ENST00000505019	Transcript	missense_variant	4096	3970	1324	S/P	Tca/Cca	.	.	.	-1	C4orf21	HGNC	25654	protein_coding	YES	CCDS3700.2	ENSP00000424737	CD021_HUMAN	I3L0G6_HUMAN,D6REN9_HUMAN	UPI0000EE2F8F	.	deleterious(0.01)	probably_damaging(0.977)	14/28	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF325	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGAAAGAG	.	5	ESCA
MAB21L2	0	.	GRCh37	4	151504688	151504688	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507A>T	p.Gln169His	p.Q169H	ENST00000317605	1/1	37	33	4	18	18	0	MAB21L2,missense_variant,p.Gln169His,ENST00000317605,;LRBA,intron_variant,,ENST00000510413,;LRBA,intron_variant,,ENST00000509835,;LRBA,intron_variant,,ENST00000535741,;LRBA,intron_variant,,ENST00000357115,;LRBA,intron_variant,,ENST00000507224,;RP11-1336O20.2,downstream_gene_variant,,ENST00000507934,;LRBA,intron_variant,,ENST00000513021,;LRBA,upstream_gene_variant,,ENST00000503716,;	T	ENSG00000181541	ENST00000317605	Transcript	missense_variant	1612	507	169	Q/H	caA/caT	.	.	.	1	MAB21L2	HGNC	6758	protein_coding	YES	CCDS3774.1	ENSP00000324701	MB212_HUMAN	.	UPI000007290D	.	deleterious(0.01)	benign(0.314)	1/1	.	Pfam_domain:PF03281,hmmpanther:PTHR10656:SF37,hmmpanther:PTHR10656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGCAAATCAC	.	4	ESCA
KIAA0922	0	.	GRCh37	4	154471245	154471245	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.260G>C	p.Ser87Thr	p.S87T	ENST00000409959	4/35	32	22	9	28	28	0	KIAA0922,missense_variant,p.Ser87Thr,ENST00000409663,;KIAA0922,missense_variant,p.Ser87Thr,ENST00000440693,;KIAA0922,missense_variant,p.Ser87Thr,ENST00000409959,;KIAA0922,stop_lost,p.Ter72TyrextTer32,ENST00000445960,;KIAA0922,upstream_gene_variant,,ENST00000462540,;	C	ENSG00000121210	ENST00000409959	Transcript	missense_variant	309	260	87	S/T	aGt/aCt	.	.	.	1	KIAA0922	HGNC	29146	protein_coding	YES	CCDS47148.1	ENSP00000386787	T131L_HUMAN	D3DP10_HUMAN	UPI00017BE9AB	.	tolerated(0.38)	benign(0.009)	4/35	.	hmmpanther:PTHR22050,hmmpanther:PTHR22050:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTAGTGGAA	.	5	ESCA
SORBS2	0	.	GRCh37	4	186605996	186605996	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15C>T	p.%3D	p.S5S	ENST00000355634	5/24	30	23	7	22	22	0	SORBS2,synonymous_variant,p.%3D,ENST00000420158,;SORBS2,synonymous_variant,p.%3D,ENST00000355634,;SORBS2,synonymous_variant,p.%3D,ENST00000451701,;SORBS2,synonymous_variant,p.%3D,ENST00000456060,;SORBS2,synonymous_variant,p.%3D,ENST00000457934,;SORBS2,synonymous_variant,p.%3D,ENST00000432655,;SORBS2,synonymous_variant,p.%3D,ENST00000419063,;SORBS2,synonymous_variant,p.%3D,ENST00000421639,;SORBS2,synonymous_variant,p.%3D,ENST00000421420,;SORBS2,splice_region_variant,,ENST00000449407,;SORBS2,splice_region_variant,,ENST00000452351,;SORBS2,5_prime_UTR_variant,,ENST00000415274,;SORBS2,5_prime_UTR_variant,,ENST00000431902,;SORBS2,5_prime_UTR_variant,,ENST00000435480,;SORBS2,5_prime_UTR_variant,,ENST00000429056,;SORBS2,5_prime_UTR_variant,,ENST00000414724,;SORBS2,5_prime_UTR_variant,,ENST00000431808,;SORBS2,5_prime_UTR_variant,,ENST00000444781,;SORBS2,5_prime_UTR_variant,,ENST00000319471,;SORBS2,intron_variant,,ENST00000448662,;SORBS2,intron_variant,,ENST00000457247,;SORBS2,intron_variant,,ENST00000439049,;SORBS2,intron_variant,,ENST00000445115,;SORBS2,intron_variant,,ENST00000284776,;SORBS2,intron_variant,,ENST00000393523,;SORBS2,intron_variant,,ENST00000450341,;SORBS2,intron_variant,,ENST00000428330,;SORBS2,intron_variant,,ENST00000451958,;SORBS2,intron_variant,,ENST00000319454,;SORBS2,intron_variant,,ENST00000445343,;SORBS2,intron_variant,,ENST00000439914,;SORBS2,intron_variant,,ENST00000437304,;SORBS2,intron_variant,,ENST00000444771,;SORBS2,intron_variant,,ENST00000425679,;SORBS2,intron_variant,,ENST00000430503,;SORBS2,intron_variant,,ENST00000393528,;SORBS2,intron_variant,,ENST00000456596,;SORBS2,non_coding_transcript_exon_variant,,ENST00000463104,;SORBS2,intron_variant,,ENST00000493709,;SORBS2,intron_variant,,ENST00000478249,;SORBS2,intron_variant,,ENST00000464975,;SORBS2,intron_variant,,ENST00000464819,;SORBS2,non_coding_transcript_exon_variant,,ENST00000470685,;	A	ENSG00000154556	ENST00000355634	Transcript	synonymous_variant	729	15	5	S	agC/agT	.	.	.	-1	SORBS2	HGNC	24098	protein_coding	YES	CCDS59482.1	ENSP00000347852	SRBS2_HUMAN	C9JZ60_HUMAN,C9JN77_HUMAN,C9JL62_HUMAN,C9JI79_HUMAN,C9JDX2_HUMAN,C9JBR8_HUMAN,C9JBB0_HUMAN,C9J8E3_HUMAN,C9J7Q5_HUMAN,C9J4Z9_HUMAN,C9J4K2_HUMAN,C9J3W4_HUMAN,C9J372_HUMAN,C9IZT7_HUMAN,C9IZ89_HUMAN	UPI000198C7F0	.	.	.	5/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCGCTATC	.	5	ESCA
ZNF876P	0	.	GRCh37	4	248026	248026	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.850A>G	.	.	ENST00000356347	2/2	27	23	4	29	29	0	ZNF876P,non_coding_transcript_exon_variant,,ENST00000356347,;ZNF876P,non_coding_transcript_exon_variant,,ENST00000398732,;	G	ENSG00000198155	ENST00000356347	Transcript	non_coding_transcript_exon_variant	850	.	.	.	.	.	.	.	1	ZNF876P	HGNC	32472	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACATAAGAAT	.	4	ESCA
MCC	0	.	GRCh37	5	112389443	112389444	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2426dupT	p.Met809IlefsTer47	p.M809Ifs*47	ENST00000408903	15/19	58	44	14	34	34	0	MCC,frameshift_variant,p.Met619IlefsTer47,ENST00000302475,;MCC,frameshift_variant,p.Met556IlefsTer47,ENST00000515367,;MCC,frameshift_variant,p.Met809IlefsTer47,ENST00000408903,;MCC,non_coding_transcript_exon_variant,,ENST00000514701,;	A	ENSG00000171444	ENST00000408903	Transcript	frameshift_variant	2842-2843	2426-2427	809	M/IX	atg/atTg	.	.	.	-1	MCC	HGNC	6935	protein_coding	YES	CCDS43351.1	ENSP00000386227	CRCM_HUMAN	D6REY2_HUMAN	UPI00015E06EA	.	.	.	15/19	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23347,hmmpanther:PTHR23347:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCTGCATAAG	.	3	ESCA
PROB1	0	.	GRCh37	5	138729546	138729546	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1225T>A	p.Cys409Ser	p.C409S	ENST00000434752	1/1	27	21	6	42	42	0	PROB1,missense_variant,p.Cys409Ser,ENST00000434752,;MZB1,upstream_gene_variant,,ENST00000412103,;SPATA24,downstream_gene_variant,,ENST00000512761,;SPATA24,downstream_gene_variant,,ENST00000514983,;SPATA24,downstream_gene_variant,,ENST00000450845,;SPATA24,downstream_gene_variant,,ENST00000302091,;MZB1,upstream_gene_variant,,ENST00000302125,;MZB1,upstream_gene_variant,,ENST00000457570,;MZB1,upstream_gene_variant,,ENST00000509591,;MZB1,upstream_gene_variant,,ENST00000503351,;MZB1,upstream_gene_variant,,ENST00000513389,;MZB1,upstream_gene_variant,,ENST00000417694,;MZB1,upstream_gene_variant,,ENST00000503481,;MZB1,upstream_gene_variant,,ENST00000503120,;	T	ENSG00000228672	ENST00000434752	Transcript	missense_variant	1340	1225	409	C/S	Tgc/Agc	.	.	.	-1	PROB1	HGNC	41906	protein_coding	YES	CCDS54909.1	ENSP00000416033	PROB1_HUMAN	.	UPI00001974A9	.	tolerated_low_confidence(0.06)	benign(0.08)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGCAGCGAG	.	5	ESCA
DPYSL3	0	.	GRCh37	5	146770589	146770589	+	3'UTR	DEL	T	T	-	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3009delA	.	.	ENST00000343218	14/14	37	34	3	21	21	0	DPYSL3,3_prime_UTR_variant,,ENST00000398514,;DPYSL3,3_prime_UTR_variant,,ENST00000343218,;DPYSL3,downstream_gene_variant,,ENST00000534907,;STK32A,downstream_gene_variant,,ENST00000397936,;DPYSL3,downstream_gene_variant,,ENST00000520473,;DPYSL3,downstream_gene_variant,,ENST00000507309,;DPYSL3,downstream_gene_variant,,ENST00000523458,;	-	ENSG00000113657	ENST00000343218	Transcript	3_prime_UTR_variant	5262	.	.	.	.	.	.	.	-1	DPYSL3	HGNC	3015	protein_coding	YES	CCDS56387.1	ENSP00000343690	DPYL3_HUMAN	F5GWI3_HUMAN	UPI000020CF0E	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CACCAGTTTTCA	.	2	ESCA
CDH12	0	.	GRCh37	5	21765084	21765084	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1515+3A>G	.	.	ENST00000382254	.	40	25	15	25	25	0	CDH12,splice_region_variant,,ENST00000522262,;CDH12,splice_region_variant,,ENST00000504376,;CDH12,splice_region_variant,,ENST00000382254,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,splice_region_variant,,ENST00000521384,;CDH12,splice_region_variant,,ENST00000517378,;	C	ENSG00000154162	ENST00000382254	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	CDH12	HGNC	1751	protein_coding	YES	CCDS3890.1	ENSP00000371689	CAD12_HUMAN	B3KRT0_HUMAN	UPI00000622EB	.	.	.	.	12/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGATACCTG	.	4	ESCA
WDR70	0	.	GRCh37	5	37725063	37725063	+	Missense_Mutation	SNP	C	C	T	rs756805874	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1625C>T	p.Pro542Leu	p.P542L	ENST00000265107	16/18	57	50	7	36	36	0	WDR70,missense_variant,p.Pro542Leu,ENST00000265107,;WDR70,non_coding_transcript_exon_variant,,ENST00000508730,;WDR70,non_coding_transcript_exon_variant,,ENST00000507136,;WDR70,non_coding_transcript_exon_variant,,ENST00000511906,;	T	ENSG00000082068	ENST00000265107	Transcript	missense_variant	1781	1625	542	P/L	cCc/cTc	rs756805874	.	.	1	WDR70	HGNC	25495	protein_coding	YES	CCDS34147.1	ENSP00000265107	WDR70_HUMAN	.	UPI0000049FC2	.	tolerated(0.2)	benign(0.065)	16/18	.	hmmpanther:PTHR16017,hmmpanther:PTHR16017:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGCCCCGCC	byFrequency	4	ESCA
CD164	0	.	GRCh37	6	109687925	109687925	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2129G>A	.	.	ENST00000310786	6/6	20	16	4	29	29	0	CD164,3_prime_UTR_variant,,ENST00000368961,;CD164,3_prime_UTR_variant,,ENST00000310786,;CD164,3_prime_UTR_variant,,ENST00000275080,;CD164,3_prime_UTR_variant,,ENST00000413644,;CD164,3_prime_UTR_variant,,ENST00000324953,;CD164,downstream_gene_variant,,ENST00000504373,;CD164,downstream_gene_variant,,ENST00000512821,;CD164,downstream_gene_variant,,ENST00000506649,;CD164,non_coding_transcript_exon_variant,,ENST00000415861,;CD164,downstream_gene_variant,,ENST00000499860,;	T	ENSG00000135535	ENST00000310786	Transcript	3_prime_UTR_variant	2789	.	.	.	.	.	.	.	-1	CD164	HGNC	1632	protein_coding	YES	CCDS5073.1	ENSP00000309376	MUC24_HUMAN	.	UPI000006EB36	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATACCTTCT	.	5	ESCA
HECA	0	.	GRCh37	6	139501876	139501876	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3634T>C	.	.	ENST00000367658	4/4	78	59	18	67	67	0	HECA,3_prime_UTR_variant,,ENST00000367658,;RP1-225E12.2,intron_variant,,ENST00000590219,;RP1-225E12.2,intron_variant,,ENST00000585447,;RP1-225E12.2,intron_variant,,ENST00000588529,;RP1-225E12.2,intron_variant,,ENST00000586229,;RP1-225E12.2,intron_variant,,ENST00000415194,;RP1-225E12.2,intron_variant,,ENST00000586266,;RP1-225E12.2,intron_variant,,ENST00000588638,;RP1-225E12.2,intron_variant,,ENST00000587577,;RP1-225E12.2,intron_variant,,ENST00000591102,;RP1-225E12.2,intron_variant,,ENST00000590679,;RP1-225E12.2,intron_variant,,ENST00000589192,;RP1-225E12.2,downstream_gene_variant,,ENST00000587814,;RP1-225E12.3,intron_variant,,ENST00000585874,;	C	ENSG00000112406	ENST00000367658	Transcript	3_prime_UTR_variant	5551	.	.	.	.	.	.	.	1	HECA	HGNC	21041	protein_coding	YES	CCDS5194.1	ENSP00000356630	HDC_HUMAN	.	UPI000006D0F2	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTGTGGTTT	.	5	ESCA
MTHFD1L	0	.	GRCh37	6	151247388	151247388	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1213A>G	p.Arg405Gly	p.R405G	ENST00000367321	11/28	44	35	8	66	66	0	MTHFD1L,missense_variant,p.Arg405Gly,ENST00000367321,;MTHFD1L,missense_variant,p.Arg76Gly,ENST00000441122,;MTHFD1L,downstream_gene_variant,,ENST00000367308,;	G	ENSG00000120254	ENST00000367321	Transcript	missense_variant	1487	1213	405	R/G	Agg/Ggg	.	.	.	1	MTHFD1L	HGNC	21055	protein_coding	YES	CCDS5228.1	ENSP00000356290	C1TM_HUMAN	Q5JYA8_HUMAN,Q5JYA3_HUMAN,B7ZM99_HUMAN,B2RD24_HUMAN	UPI00001CE513	.	deleterious(0)	probably_damaging(0.982)	11/28	.	HAMAP:MF_01543,hmmpanther:PTHR10025,hmmpanther:PTHR10025:SF14,Pfam_domain:PF01268,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGAAAGGTTA	.	5	ESCA
HIST1H2AH	0	.	GRCh37	6	27115407	27115407	+	3'Flank	SNP	G	G	A	rs765005492	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000377459	.	53	45	7	33	33	0	HIST1H2AH,downstream_gene_variant,,ENST00000377459,;HIST1H2BK,upstream_gene_variant,,ENST00000356950,;HIST1H2BK,upstream_gene_variant,,ENST00000396891,;MIR3143,non_coding_transcript_exon_variant,,ENST00000584253,;	A	ENSG00000184825	ENST00000377459	Transcript	downstream_gene_variant	.	.	.	.	.	rs765005492	.	90	1	HIST1H2AH	HGNC	13671	protein_coding	YES	CCDS4622.1	ENSP00000366679	H2A1H_HUMAN	A3KPC7_HUMAN	UPI0000073C8A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCTAGATAAC	.	4	ESCA
HIST1H2AK	0	.	GRCh37	6	27805782	27805783	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.335dupT	p.Gln113ProfsTer7	p.Q113Pfs*7	ENST00000330180	1/1	198	175	23	146	146	0	HIST1H2AK,frameshift_variant,p.Gln113ProfsTer7,ENST00000330180,;HIST1H2BN,upstream_gene_variant,,ENST00000396980,;HIST1H2BN,upstream_gene_variant,,ENST00000606613,;HIST1H2BN,upstream_gene_variant,,ENST00000449538,;	A	ENSG00000184348	ENST00000330180	Transcript	frameshift_variant	335-336	335-336	112	I/IX	atc/atTc	.	.	.	-1	HIST1H2AK	HGNC	4726	protein_coding	YES	CCDS4632.1	ENSP00000330307	H2A1_HUMAN	A4FTV9_HUMAN,A3KPC7_HUMAN	UPI0000000E01	.	.	.	1/1	.	hmmpanther:PTHR23430,hmmpanther:PTHR23430:SF24,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCTGGATATT	.	3	ESCA
MICA	0	.	GRCh37	6	31371370	31371370	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-40C>A	.	.	ENST00000449934	1/6	113	103	10	125	125	0	MICA,5_prime_UTR_variant,,ENST00000449934,;MICA,upstream_gene_variant,,ENST00000421350,;HCP5,intron_variant,,ENST00000414046,;Y_RNA,upstream_gene_variant,,ENST00000362462,;	A	ENSG00000204520	ENST00000449934	Transcript	5_prime_UTR_variant	15	.	.	.	.	.	.	.	1	MICA	HGNC	7090	protein_coding	YES	CCDS56412.1	ENSP00000413079	.	Q96QC4_HUMAN,P79540_HUMAN,P79539_HUMAN,P79533_HUMAN,P79531_HUMAN,P79530_HUMAN,P79527_HUMAN,P78551_HUMAN,L0L8F7_HUMAN,J9YLR7_HUMAN,F5CQ57_HUMAN,F5CIT5_HUMAN	UPI000006F0B0	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCGGCCACTG	.	3	ESCA
ZBTB22	0	.	GRCh37	6	33284415	33284415	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279C>T	p.%3D	p.S93S	ENST00000431845	2/2	58	47	11	48	48	0	ZBTB22,synonymous_variant,p.%3D,ENST00000431845,;ZBTB22,synonymous_variant,p.%3D,ENST00000441117,;ZBTB22,synonymous_variant,p.%3D,ENST00000418724,;TAPBP,upstream_gene_variant,,ENST00000489157,;DAXX,downstream_gene_variant,,ENST00000374542,;TAPBP,upstream_gene_variant,,ENST00000456592,;DAXX,downstream_gene_variant,,ENST00000453407,;DAXX,downstream_gene_variant,,ENST00000446403,;DAXX,downstream_gene_variant,,ENST00000414083,;TAPBP,upstream_gene_variant,,ENST00000467025,;TAPBP,upstream_gene_variant,,ENST00000426633,;TAPBP,upstream_gene_variant,,ENST00000434618,;TAPBP,upstream_gene_variant,,ENST00000475304,;DAXX,downstream_gene_variant,,ENST00000266000,;DAXX,downstream_gene_variant,,ENST00000468536,;DAXX,downstream_gene_variant,,ENST00000477370,;DAXX,downstream_gene_variant,,ENST00000477162,;TAPBP,upstream_gene_variant,,ENST00000476333,;TAPBP,upstream_gene_variant,,ENST00000437116,;TAPBP,upstream_gene_variant,,ENST00000480730,;DAXX,downstream_gene_variant,,ENST00000490173,;DAXX,downstream_gene_variant,,ENST00000498030,;	A	ENSG00000236104	ENST00000431845	Transcript	synonymous_variant	431	279	93	S	tcC/tcT	.	.	.	-1	ZBTB22	HGNC	13085	protein_coding	YES	CCDS4775.1	ENSP00000407545	ZBT22_HUMAN	A2AB93_HUMAN	UPI000013C34E	.	.	.	2/2	.	Superfamily_domains:SSF54695,SMART_domains:SM00225,Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR24414:SF4,hmmpanther:PTHR24414,PROSITE_profiles:PS50097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATGGAGGT	.	5	ESCA
MEOX2	0	.	GRCh37	7	15651647	15651647	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*365G>T	.	.	ENST00000262041	3/3	41	37	4	20	20	0	MEOX2,3_prime_UTR_variant,,ENST00000262041,;	A	ENSG00000106511	ENST00000262041	Transcript	3_prime_UTR_variant	1690	.	.	.	.	.	.	.	-1	MEOX2	HGNC	7014	protein_coding	YES	CCDS34605.1	ENSP00000262041	MEOX2_HUMAN	Q6FHY5_HUMAN,A4D127_HUMAN	UPI000013D247	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGTTCATCCT	.	3	ESCA
SPDYE1	0	.	GRCh37	7	44048550	44048550	+	3'UTR	SNP	T	T	C	rs375908533	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*330T>C	.	.	ENST00000258704	7/7	82	74	7	42	42	0	SPDYE1,3_prime_UTR_variant,,ENST00000258704,;AC004951.6,upstream_gene_variant,,ENST00000447643,;POLR2J4,intron_variant,,ENST00000422304,;RP5-1165K10.2,intron_variant,,ENST00000454572,;POLR2J4,intron_variant,,ENST00000427076,;POLR2J4,downstream_gene_variant,,ENST00000326391,;	C	ENSG00000136206	ENST00000258704	Transcript	3_prime_UTR_variant	1478	.	.	.	.	rs375908533	.	.	1	SPDYE1	HGNC	16408	protein_coding	YES	CCDS5475.1	ENSP00000258704	SPDE1_HUMAN	.	UPI000013CFF7	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGAATTCCAAC	.	3	ESCA
PCLO	0	.	GRCh37	7	82580258	82580258	+	Missense_Mutation	SNP	A	A	C	rs750254988	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9646T>G	p.Leu3216Val	p.L3216V	ENST00000333891	6/25	33	27	6	36	36	0	PCLO,missense_variant,p.Leu3216Val,ENST00000333891,;PCLO,missense_variant,p.Leu3216Val,ENST00000423517,;PCLO,upstream_gene_variant,,ENST00000437081,;	C	ENSG00000186472	ENST00000333891	Transcript	missense_variant	9984	9646	3216	L/V	Ttg/Gtg	rs750254988	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	6/25	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCAAGTCTA	.	4	ESCA
RNF19A	0	.	GRCh37	8	101300299	101300299	+	Missense_Mutation	SNP	T	T	C	rs761833362	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.104A>G	p.His35Arg	p.H35R	ENST00000519449	3/11	37	29	7	23	23	0	RNF19A,missense_variant,p.His35Arg,ENST00000519449,;RNF19A,missense_variant,p.His35Arg,ENST00000519527,;RNF19A,missense_variant,p.His35Arg,ENST00000523167,;RNF19A,missense_variant,p.His35Arg,ENST00000522369,;RNF19A,missense_variant,p.His4Arg,ENST00000517584,;RNF19A,missense_variant,p.His35Arg,ENST00000432381,;RNF19A,missense_variant,p.His35Arg,ENST00000341084,;RNF19A,downstream_gene_variant,,ENST00000523481,;	C	ENSG00000034677	ENST00000519449	Transcript	missense_variant	421	104	35	H/R	cAt/cGt	rs761833362	.	.	-1	RNF19A	HGNC	13432	protein_coding	YES	CCDS6286.1	ENSP00000428968	RN19A_HUMAN	E7ETB2_HUMAN,E7EQV8_HUMAN,E7EQ63_HUMAN,A3KCU8_HUMAN	UPI000013D5E6	.	deleterious_low_confidence(0.01)	benign(0.138)	3/11	.	hmmpanther:PTHR11685,hmmpanther:PTHR11685:SF111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGATGTAAA	.	5	ESCA
COL15A1	0	.	GRCh37	9	101811974	101811974	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2796C>T	p.%3D	p.G932G	ENST00000375001	29/42	57	36	21	53	53	0	COL15A1,synonymous_variant,p.%3D,ENST00000375001,;	T	ENSG00000204291	ENST00000375001	Transcript	synonymous_variant	3219	2796	932	G	ggC/ggT	.	.	.	1	COL15A1	HGNC	2192	protein_coding	YES	CCDS35081.1	ENSP00000364140	COFA1_HUMAN	.	UPI0000211506	.	.	.	29/42	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF398,hmmpanther:PTHR24023,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCCCACC	.	5	ESCA
TGFBR1	0	.	GRCh37	9	101915707	101915707	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4120A>C	.	.	ENST00000374994	9/9	13	9	4	10	10	0	TGFBR1,3_prime_UTR_variant,,ENST00000552516,;TGFBR1,3_prime_UTR_variant,,ENST00000374990,;TGFBR1,3_prime_UTR_variant,,ENST00000374994,;TGFBR1,downstream_gene_variant,,ENST00000550253,;TGFBR1,downstream_gene_variant,,ENST00000549766,;	C	ENSG00000106799	ENST00000374994	Transcript	3_prime_UTR_variant	5749	.	.	.	.	.	.	.	1	TGFBR1	HGNC	11772	protein_coding	YES	CCDS6738.1	ENSP00000364133	TGFR1_HUMAN	Q5T7S2_HUMAN,F8VVC4_HUMAN,B4DY26_HUMAN	UPI000011D62A	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGAAAATGTCC	.	3	ESCA
C9orf43	0	.	GRCh37	9	116186500	116186500	+	Missense_Mutation	SNP	G	G	T	rs781076077	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.711G>T	p.Leu237Phe	p.L237F	ENST00000288462	8/14	43	36	6	20	20	0	C9orf43,missense_variant,p.Leu237Phe,ENST00000288462,;C9orf43,missense_variant,p.Leu237Phe,ENST00000374165,;C9orf43,downstream_gene_variant,,ENST00000490544,;	T	ENSG00000157653	ENST00000288462	Transcript	missense_variant	1157	711	237	L/F	ttG/ttT	rs781076077	.	.	1	C9orf43	HGNC	23570	protein_coding	YES	CCDS6796.1	ENSP00000288462	CI043_HUMAN	.	UPI00000725EE	.	deleterious(0)	probably_damaging(0.998)	8/14	.	Pfam_domain:PF15504	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTGGCCAT	byFrequency	5	ESCA
DPP7	0	.	GRCh37	9	140007735	140007735	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626T>A	p.Phe209Tyr	p.F209Y	ENST00000371579	6/13	106	93	13	70	69	0	DPP7,missense_variant,p.Phe209Tyr,ENST00000371579,;MAN1B1,downstream_gene_variant,,ENST00000550113,;DPP7,upstream_gene_variant,,ENST00000463619,;MAN1B1,downstream_gene_variant,,ENST00000475449,;MAN1B1,downstream_gene_variant,,ENST00000474902,;DPP7,downstream_gene_variant,,ENST00000497375,;DPP7,downstream_gene_variant,,ENST00000473703,;MAN1B1,downstream_gene_variant,,ENST00000371589,;MAN1B1,downstream_gene_variant,,ENST00000540391,;DPP7,3_prime_UTR_variant,,ENST00000472306,;DPP7,non_coding_transcript_exon_variant,,ENST00000482088,;DPP7,non_coding_transcript_exon_variant,,ENST00000485456,;DPP7,non_coding_transcript_exon_variant,,ENST00000478597,;DPP7,intron_variant,,ENST00000473532,;DPP7,downstream_gene_variant,,ENST00000491807,;DPP7,upstream_gene_variant,,ENST00000483783,;MAN1B1,downstream_gene_variant,,ENST00000535028,;MAN1B1,downstream_gene_variant,,ENST00000536349,;DPP7,upstream_gene_variant,,ENST00000460830,;DPP7,upstream_gene_variant,,ENST00000470766,;MAN1B1,downstream_gene_variant,,ENST00000480100,;MAN1B1,downstream_gene_variant,,ENST00000544448,;	T	ENSG00000176978	ENST00000371579	Transcript	missense_variant	631	626	209	F/Y	tTt/tAt	.	.	.	-1	DPP7	HGNC	14892	protein_coding	YES	CCDS7030.1	ENSP00000360635	DPP2_HUMAN	.	UPI00001AF169	.	tolerated(0.1)	possibly_damaging(0.682)	6/13	.	hmmpanther:PTHR11010:SF29,hmmpanther:PTHR11010,Pfam_domain:PF05577,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTCAAAGTCC	.	3	ESCA
ZMYND19	0	.	GRCh37	9	140482271	140482271	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116G>A	p.Arg39Gln	p.R39Q	ENST00000298585	3/6	46	38	8	66	66	0	ZMYND19,missense_variant,p.Arg39Gln,ENST00000298585,;ZMYND19,non_coding_transcript_exon_variant,,ENST00000471957,;	T	ENSG00000165724	ENST00000298585	Transcript	missense_variant	343	116	39	R/Q	cGa/cAa	.	.	.	-1	ZMYND19	HGNC	21146	protein_coding	YES	CCDS7048.1	ENSP00000298585	ZMY19_HUMAN	.	UPI0000022A7D	.	tolerated(0.06)	benign(0.375)	3/6	.	hmmpanther:PTHR13244:SF5,hmmpanther:PTHR13244	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATTCGGGCC	.	4	ESCA
CAPN6	0	.	GRCh37	X	110495711	110495711	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523G>T	p.Glu175Ter	p.E175*	ENST00000324068	5/13	38	30	8	18	18	0	CAPN6,stop_gained,p.Glu175Ter,ENST00000324068,;CAPN6,intron_variant,,ENST00000541758,;	A	ENSG00000077274	ENST00000324068	Transcript	stop_gained	691	523	175	E/*	Gag/Tag	.	.	.	-1	CAPN6	HGNC	1483	protein_coding	YES	CCDS14555.1	ENSP00000317214	CAN6_HUMAN	F5GWQ6_HUMAN	UPI0000126EA1	.	.	.	5/13	.	PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF281,Pfam_domain:PF00648,SMART_domains:SM00230,Superfamily_domains:SSF54001,Prints_domain:PR00704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCATAAC	.	5	ESCA
HTR2C	0	.	GRCh37	X	113873947	113873947	+	Intron	SNP	C	C	A	rs377648254	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-80+25608C>A	.	.	ENST00000276198	.	30	21	9	25	25	0	HTR2C,intron_variant,,ENST00000371950,;HTR2C,intron_variant,,ENST00000276198,;HTR2C,intron_variant,,ENST00000371951,;MIR764,mature_miRNA_variant,,ENST00000390811,;AC007025.1,downstream_gene_variant,,ENST00000583829,;	A	ENSG00000147246	ENST00000276198	Transcript	intron_variant	.	.	.	.	.	rs377648254	.	.	1	HTR2C	HGNC	5295	protein_coding	YES	CCDS14564.1	ENSP00000276198	5HT2C_HUMAN	B3VRF0_HUMAN,B3VRE5_HUMAN,B3VRE0_HUMAN	UPI000000126F	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTCCTCCA	byCluster	5	ESCA
MBTPS2	0	.	GRCh37	X	21861336	21861336	+	Missense_Mutation	SNP	G	G	A	rs375900835	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>A	p.Gly42Arg	p.G42R	ENST00000379484	2/11	52	43	9	39	39	0	MBTPS2,missense_variant,p.Gly42Arg,ENST00000365779,;MBTPS2,missense_variant,p.Gly42Arg,ENST00000379484,;MBTPS2,non_coding_transcript_exon_variant,,ENST00000465888,;	A	ENSG00000012174	ENST00000379484	Transcript	missense_variant	223	124	42	G/R	Gga/Aga	rs375900835	.	.	1	MBTPS2	HGNC	15455	protein_coding	YES	CCDS14201.1	ENSP00000368798	MBTP2_HUMAN	.	UPI000012F5A0	.	deleterious(0)	probably_damaging(0.998)	2/11	.	hmmpanther:PTHR13325:SF2,hmmpanther:PTHR13325	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAACGGACTG	byCluster	5	ESCA
HUWE1	0	.	GRCh37	X	53573489	53573489	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10823T>G	p.Leu3608Arg	p.L3608R	ENST00000342160	69/83	18	13	5	11	11	0	HUWE1,missense_variant,p.Leu3608Arg,ENST00000342160,;HUWE1,missense_variant,p.Leu3608Arg,ENST00000262854,;HUWE1,missense_variant,p.Leu2642Arg,ENST00000427052,;HUWE1,missense_variant,p.Leu446Arg,ENST00000426907,;HUWE1,non_coding_transcript_exon_variant,,ENST00000474288,;HUWE1,non_coding_transcript_exon_variant,,ENST00000468322,;HUWE1,upstream_gene_variant,,ENST00000463852,;	C	ENSG00000086758	ENST00000342160	Transcript	missense_variant	11281	10823	3608	L/R	cTc/cGc	.	.	.	-1	HUWE1	HGNC	30892	protein_coding	YES	CCDS35301.1	ENSP00000340648	HUWE1_HUMAN	Q5H963_HUMAN	UPI00004A0DAC	.	.	unknown(0)	69/83	.	hmmpanther:PTHR11254:SF67,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGAGAGCTGC	.	4	ESCA
OGT	0	.	GRCh37	X	70783039	70783039	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A5-01A-21D-A27G-09	TCGA-LN-A4A5-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2208G>C	p.%3D	p.L736L	ENST00000373719	17/22	28	24	4	30	30	0	OGT,synonymous_variant,p.%3D,ENST00000373701,;OGT,synonymous_variant,p.%3D,ENST00000373719,;OGT,non_coding_transcript_exon_variant,,ENST00000488174,;OGT,upstream_gene_variant,,ENST00000474633,;	C	ENSG00000147162	ENST00000373719	Transcript	synonymous_variant	2425	2208	736	L	ctG/ctC	.	.	.	1	OGT	HGNC	8127	protein_coding	YES	CCDS14414.1	ENSP00000362824	OGT1_HUMAN	C9JZL3_HUMAN	UPI0000073C9F	.	.	.	17/22	.	hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF369,Pfam_domain:PF13844	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTCTGAATGG	.	4	ESCA
USP6NL	0	.	GRCh37	10	11502820	11502820	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1620C>G	.	.	ENST00000277575	14/14	33	19	14	19	19	0	USP6NL,3_prime_UTR_variant,,ENST00000609104,;USP6NL,3_prime_UTR_variant,,ENST00000379237,;USP6NL,3_prime_UTR_variant,,ENST00000277575,;	C	ENSG00000148429	ENST00000277575	Transcript	3_prime_UTR_variant	4201	.	.	.	.	.	.	.	-1	USP6NL	HGNC	16858	protein_coding	YES	CCDS44357.1	ENSP00000277575	US6NL_HUMAN	.	UPI0000251ED1	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCAGCTTCC	.	5	ESCA
SLC18A2	0	.	GRCh37	10	119027194	119027195	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1139dupA	p.Asn380LysfsTer81	p.N380Kfs*81	ENST00000298472	13/16	71	52	19	52	52	0	SLC18A2,frameshift_variant,p.Asn380LysfsTer81,ENST00000298472,;SLC18A2,non_coding_transcript_exon_variant,,ENST00000497497,;	A	ENSG00000165646	ENST00000298472	Transcript	frameshift_variant	1276-1277	1133-1134	378	A/AX	gca/gcAa	.	.	.	1	SLC18A2	HGNC	10935	protein_coding	YES	CCDS7599.1	ENSP00000298472	VMAT2_HUMAN	.	UPI00001389DE	.	.	.	13/16	.	PROSITE_profiles:PS50850,hmmpanther:PTHR24004,hmmpanther:PTHR24004:SF63,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATTTGCAAAAA	.	3	ESCA
EBF3	0	.	GRCh37	10	131635360	131635360	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*833T>A	.	.	ENST00000368648	16/16	18	12	6	19	19	0	EBF3,3_prime_UTR_variant,,ENST00000355311,;EBF3,3_prime_UTR_variant,,ENST00000368648,;EBF3,downstream_gene_variant,,ENST00000440978,;	T	ENSG00000108001	ENST00000368648	Transcript	3_prime_UTR_variant	2562	.	.	.	.	.	.	.	-1	EBF3	HGNC	19087	protein_coding	YES	CCDS31314.1	ENSP00000357637	COE3_HUMAN	Q658Y5_HUMAN	UPI000002A6FB	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACAATTTCT	.	5	ESCA
PRPF18	0	.	GRCh37	10	13629084	13629084	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3G>A	.	.	ENST00000378572	1/10	83	68	14	61	61	0	PRPF18,5_prime_UTR_variant,,ENST00000417658,;PRPF18,5_prime_UTR_variant,,ENST00000378572,;PRPF18,5_prime_UTR_variant,,ENST00000320054,;RP11-295P9.2,downstream_gene_variant,,ENST00000445338,;	A	ENSG00000165630	ENST00000378572	Transcript	5_prime_UTR_variant	158	.	.	.	.	.	.	.	1	PRPF18	HGNC	17351	protein_coding	YES	CCDS7100.1	ENSP00000367835	PRP18_HUMAN	M0QXX3_HUMAN	UPI0000070C82	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGCGAGATG	.	5	ESCA
KIF20B	0	.	GRCh37	10	91478561	91478561	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1366A>G	p.Ile456Val	p.I456V	ENST00000260753	12/33	33	14	18	34	34	0	KIF20B,missense_variant,p.Ile456Val,ENST00000371728,;KIF20B,missense_variant,p.Ile456Val,ENST00000416354,;KIF20B,missense_variant,p.Ile456Val,ENST00000260753,;KIF20B,missense_variant,p.Ile456Val,ENST00000394289,;KIF20B,upstream_gene_variant,,ENST00000478929,;	G	ENSG00000138182	ENST00000260753	Transcript	missense_variant	1438	1366	456	I/V	Atc/Gtc	.	.	.	1	KIF20B	HGNC	7212	protein_coding	YES	CCDS7407.1	ENSP00000260753	KI20B_HUMAN	.	UPI00001F9377	.	tolerated(0.1)	probably_damaging(0.949)	12/33	.	PROSITE_profiles:PS50067,hmmpanther:PTHR23165,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATATCAGC	.	5	ESCA
CNTN5	0	.	GRCh37	11	100170076	100170076	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2568T>G	p.Asn856Lys	p.N856K	ENST00000524871	20/25	21	16	5	24	24	0	CNTN5,missense_variant,p.Asn856Lys,ENST00000279463,;CNTN5,missense_variant,p.Asn856Lys,ENST00000524871,;CNTN5,missense_variant,p.Asn856Lys,ENST00000528682,;CNTN5,missense_variant,p.Asn856Lys,ENST00000527185,;CNTN5,missense_variant,p.Asn782Lys,ENST00000418526,;CNTN5,non_coding_transcript_exon_variant,,ENST00000524560,;	G	ENSG00000149972	ENST00000524871	Transcript	missense_variant	2858	2568	856	N/K	aaT/aaG	.	.	.	1	CNTN5	HGNC	2175	protein_coding	YES	CCDS53696.1	ENSP00000435637	CNTN5_HUMAN	B4DGP0_HUMAN	UPI000006DAB0	.	deleterious(0.02)	probably_damaging(1)	20/25	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V853I|c.2557G>A|4,BUFFER|p.V853I|c.2557G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAATAAAGG	.	5	ESCA
CASP5	0	.	GRCh37	11	104879584	104879584	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.170C>A	p.Ser57Tyr	p.S57Y	ENST00000393141	2/10	84	69	15	97	97	0	CASP5,missense_variant,p.Ser28Tyr,ENST00000456094,;CASP5,missense_variant,p.Ser11Tyr,ENST00000393139,;CASP5,missense_variant,p.Ser44Tyr,ENST00000260315,;CASP5,missense_variant,p.Ser57Tyr,ENST00000393141,;CASP5,missense_variant,p.Ser57Tyr,ENST00000526056,;CASP5,intron_variant,,ENST00000531367,;CASP5,intron_variant,,ENST00000444749,;CASP5,intron_variant,,ENST00000418434,;CASP5,intron_variant,,ENST00000456200,;	T	ENSG00000137757	ENST00000393141	Transcript	missense_variant	202	170	57	S/Y	tCt/tAt	.	.	.	-1	CASP5	HGNC	1506	protein_coding	YES	CCDS44720.1	ENSP00000376849	CASP5_HUMAN	C9JF14_HUMAN	UPI0001824645	.	tolerated_low_confidence(0.12)	benign(0.307)	2/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATAGATGTT	.	5	ESCA
PSMA1	0	.	GRCh37	11	14526711	14526711	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*27A>G	.	.	ENST00000418988	11/11	36	16	20	27	27	0	PSMA1,3_prime_UTR_variant,,ENST00000396393,;PSMA1,3_prime_UTR_variant,,ENST00000418988,;PSMA1,3_prime_UTR_variant,,ENST00000530457,;PSMA1,3_prime_UTR_variant,,ENST00000396394,;PSMA1,3_prime_UTR_variant,,ENST00000419365,;PSMA1,non_coding_transcript_exon_variant,,ENST00000524606,;PSMA1,3_prime_UTR_variant,,ENST00000555531,;PSMA1,non_coding_transcript_exon_variant,,ENST00000528307,;PSMA1,downstream_gene_variant,,ENST00000527632,;	C	ENSG00000129084	ENST00000418988	Transcript	3_prime_UTR_variant	1165	.	.	.	.	.	.	.	-1	PSMA1	HGNC	9530	protein_coding	YES	CCDS31431.1	ENSP00000414359	PSA1_HUMAN	F5GX11_HUMAN	UPI000002B1AC	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGATAATAC	.	5	ESCA
IGF2	0	.	GRCh37	11	2150629	2150629	+	3'Flank	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000434045	.	15	9	6	10	10	0	IGF2,3_prime_UTR_variant,,ENST00000381395,;IGF2,3_prime_UTR_variant,,ENST00000381406,;IGF2,3_prime_UTR_variant,,ENST00000416167,;IGF2,3_prime_UTR_variant,,ENST00000300632,;IGF2,downstream_gene_variant,,ENST00000381389,;IGF2,downstream_gene_variant,,ENST00000434045,;IGF2,downstream_gene_variant,,ENST00000381392,;IGF2,downstream_gene_variant,,ENST00000418738,;MIR483,downstream_gene_variant,,ENST00000385070,;AC132217.4,non_coding_transcript_exon_variant,,ENST00000430034,;INS-IGF2,downstream_gene_variant,,ENST00000356578,;	T	ENSG00000167244	ENST00000434045	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3101	-1	IGF2	HGNC	5466	protein_coding	YES	CCDS44517.1	ENSP00000391826	IGF2_HUMAN	E3UN46_HUMAN	UPI0001751501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCAGACAGG	.	5	ESCA
ANO3	0	.	GRCh37	11	26569083	26569083	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1275T>A	p.Asn425Lys	p.N425K	ENST00000256737	12/27	37	22	15	57	57	0	ANO3,missense_variant,p.Asn279Lys,ENST00000531568,;ANO3,missense_variant,p.Asn409Lys,ENST00000525139,;ANO3,missense_variant,p.Asn425Lys,ENST00000256737,;ANO3,missense_variant,p.Asn409Lys,ENST00000537978,;ANO3,non_coding_transcript_exon_variant,,ENST00000529242,;	A	ENSG00000134343	ENST00000256737	Transcript	missense_variant	2127	1275	425	N/K	aaT/aaA	.	.	.	1	ANO3	HGNC	14004	protein_coding	YES	CCDS31447.1	ENSP00000256737	ANO3_HUMAN	E9PQ79_HUMAN,B7Z3F5_HUMAN,B7Z3A8_HUMAN	UPI00001F9ED8	.	deleterious(0.04)	benign(0.309)	12/27	.	hmmpanther:PTHR12308:SF16,hmmpanther:PTHR12308,Pfam_domain:PF04547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAATAATAG	.	5	ESCA
ARL14EP	0	.	GRCh37	11	30352585	30352585	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90T>A	p.%3D	p.T30T	ENST00000282032	2/4	11	8	3	18	18	0	ARL14EP,synonymous_variant,p.%3D,ENST00000530909,;ARL14EP,synonymous_variant,p.%3D,ENST00000282032,;ARL14EP,upstream_gene_variant,,ENST00000533457,;ARL14EP,non_coding_transcript_exon_variant,,ENST00000532047,;	A	ENSG00000152219	ENST00000282032	Transcript	synonymous_variant	305	90	30	T	acT/acA	.	.	.	1	ARL14EP	HGNC	26798	protein_coding	YES	CCDS7869.1	ENSP00000282032	AL14E_HUMAN	E9PRK7_HUMAN	UPI000000DC5B	.	.	.	2/4	.	hmmpanther:PTHR23080,hmmpanther:PTHR23080:SF72	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	AAGACTTTGCA	.	2	ESCA
CKAP5	0	.	GRCh37	11	46810291	46810291	+	Silent	SNP	T	T	C	rs747829891	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1908A>G	p.%3D	p.P636P	ENST00000529230	16/44	23	14	9	22	22	0	CKAP5,synonymous_variant,p.%3D,ENST00000415402,;CKAP5,synonymous_variant,p.%3D,ENST00000354558,;CKAP5,synonymous_variant,p.%3D,ENST00000312055,;CKAP5,synonymous_variant,p.%3D,ENST00000529230,;CKAP5,upstream_gene_variant,,ENST00000528593,;	C	ENSG00000175216	ENST00000529230	Transcript	synonymous_variant	1955	1908	636	P	ccA/ccG	rs747829891	.	.	-1	CKAP5	HGNC	28959	protein_coding	YES	CCDS31477.1	ENSP00000432768	CKAP5_HUMAN	E9PQH5_HUMAN	UPI000013F21E	.	.	.	16/44	.	hmmpanther:PTHR12609:SF0,hmmpanther:PTHR12609,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCATGGCAT	byFrequency	5	ESCA
OR8H1	0	.	GRCh37	11	56058416	56058416	+	Silent	SNP	G	G	T	rs748211309	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>A	p.%3D	p.G41G	ENST00000313022	1/1	52	42	10	57	57	0	OR8H1,synonymous_variant,p.%3D,ENST00000313022,;	T	ENSG00000181693	ENST00000313022	Transcript	synonymous_variant	151	123	41	G	ggC/ggA	rs748211309	.	.	-1	OR8H1	HGNC	14824	protein_coding	YES	CCDS31526.1	ENSP00000323595	OR8H1_HUMAN	.	UPI0000041BC0	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTGCCCAG	byFrequency	5	ESCA
AHNAK	0	.	GRCh37	11	62297376	62297376	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4513G>A	p.Asp1505Asn	p.D1505N	ENST00000378024	5/5	103	79	24	92	92	0	AHNAK,missense_variant,p.Asp1505Asn,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000528508,;	T	ENSG00000124942	ENST00000378024	Transcript	missense_variant	4788	4513	1505	D/N	Gac/Aac	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	probably_damaging(0.998)	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTCTGGGC	.	5	ESCA
CDC42BPG	0	.	GRCh37	11	64609344	64609344	+	Missense_Mutation	SNP	G	G	A	rs753090372	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193C>T	p.Arg65Cys	p.R65C	ENST00000342711	2/37	18	14	4	19	19	0	CDC42BPG,missense_variant,p.Arg65Cys,ENST00000342711,;	A	ENSG00000171219	ENST00000342711	Transcript	missense_variant	193	193	65	R/C	Cgt/Tgt	rs753090372	.	.	-1	CDC42BPG	HGNC	29829	protein_coding	YES	CCDS31601.1	ENSP00000345133	MRCKG_HUMAN	.	UPI000047C9E2	.	deleterious(0.04)	benign(0.244)	2/37	.	hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGACGCAGTT	byFrequency	4	ESCA
MRGPRF	0	.	GRCh37	11	68773599	68773599	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179T>A	p.Val60Glu	p.V60E	ENST00000309099	3/3	153	143	9	51	51	0	MRGPRF,missense_variant,p.Val60Glu,ENST00000441623,;MRGPRF,missense_variant,p.Val60Glu,ENST00000309099,;MRGPRF,downstream_gene_variant,,ENST00000320913,;RP11-554A11.5,downstream_gene_variant,,ENST00000562506,;RP11-554A11.4,upstream_gene_variant,,ENST00000562276,;	T	ENSG00000172935	ENST00000309099	Transcript	missense_variant	562	179	60	V/E	gTg/gAg	.	.	.	-1	MRGPRF	HGNC	24828	protein_coding	YES	CCDS8188.1	ENSP00000309782	MRGRF_HUMAN	Q8N7J6_HUMAN	UPI000012F566	.	deleterious(0.01)	possibly_damaging(0.478)	3/3	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF3,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCCACCAGG	.	2	ESCA
KRTAP5-8	0	.	GRCh37	11	71249670	71249670	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5C>T	.	.	ENST00000398534	1/1	265	240	25	89	89	0	KRTAP5-8,3_prime_UTR_variant,,ENST00000398534,;	T	ENSG00000241233	ENST00000398534	Transcript	3_prime_UTR_variant	600	.	.	.	.	.	.	.	1	KRTAP5-8	HGNC	23603	protein_coding	YES	CCDS41683.1	ENSP00000420723	KRA58_HUMAN	.	UPI000013ECDA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGCTCTGCCT	.	3	ESCA
FOLR3	0	.	GRCh37	11	71850422	71850422	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.515T>G	p.Leu172Arg	p.L172R	ENST00000456237	4/5	132	111	21	62	62	0	FOLR3,missense_variant,p.Leu170Arg,ENST00000445078,;FOLR3,missense_variant,p.Leu172Arg,ENST00000456237,;FOLR3,missense_variant,p.Leu129Arg,ENST00000442948,;FOLR3,downstream_gene_variant,,ENST00000546166,;FOLR3,3_prime_UTR_variant,,ENST00000325101,;FOLR3,3_prime_UTR_variant,,ENST00000542161,;FOLR3,non_coding_transcript_exon_variant,,ENST00000545379,;	G	ENSG00000110203	ENST00000456237	Transcript	missense_variant	565	515	172	L/R	cTg/cGg	.	.	.	1	FOLR3	HGNC	3795	protein_coding	YES	.	ENSP00000399235	.	J3KQ90_HUMAN,E9PGT2_HUMAN	UPI0001AE6C07	.	deleterious(0.02)	possibly_damaging(0.665)	4/5	.	Pfam_domain:PF03024,hmmpanther:PTHR10517,hmmpanther:PTHR10517:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTCTGAACG	.	5	ESCA
COQ5	0	.	GRCh37	12	120960101	120960101	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268A>G	p.Ile90Val	p.I90V	ENST00000288532	2/7	33	21	12	25	25	0	COQ5,missense_variant,p.Ile9Val,ENST00000551769,;COQ5,missense_variant,p.Ile90Val,ENST00000445328,;COQ5,missense_variant,p.Ile64Val,ENST00000547736,;COQ5,missense_variant,p.Ile9Val,ENST00000552443,;COQ5,missense_variant,p.Ile90Val,ENST00000288532,;COQ5,intron_variant,,ENST00000547943,;COQ5,downstream_gene_variant,,ENST00000547448,;RPL29P24,downstream_gene_variant,,ENST00000465434,;	C	ENSG00000110871	ENST00000288532	Transcript	missense_variant	309	268	90	I/V	Atc/Gtc	.	.	.	-1	COQ5	HGNC	28722	protein_coding	YES	CCDS31912.1	ENSP00000288532	COQ5_HUMAN	F8VVX6_HUMAN,F8VP53_HUMAN	UPI00001592AF	.	tolerated(0.16)	benign(0.047)	2/7	.	PROSITE_profiles:PS51608,HAMAP:MF_01813,hmmpanther:PTHR10108:SF24,hmmpanther:PTHR10108,PROSITE_patterns:PS01183,Gene3D:3.40.50.150,Pfam_domain:PF01209,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGATACCAA	.	5	ESCA
TMEM132C	0	.	GRCh37	12	128899509	128899509	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318G>A	p.%3D	p.K106K	ENST00000435159	2/9	46	33	12	35	35	0	TMEM132C,synonymous_variant,p.%3D,ENST00000435159,;	A	ENSG00000181234	ENST00000435159	Transcript	synonymous_variant	318	318	106	K	aaG/aaA	.	.	.	1	TMEM132C	HGNC	25436	protein_coding	YES	.	ENSP00000410852	T132C_HUMAN	F5H439_HUMAN,E9PC33_HUMAN	UPI0001C0B37C	.	.	.	2/9	.	hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGGTTGT	.	5	ESCA
PXMP2	0	.	GRCh37	12	133277913	133277913	+	Missense_Mutation	SNP	G	G	T	rs758880810	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.477G>T	p.Trp159Cys	p.W159C	ENST00000317479	4/5	60	48	12	48	48	0	PXMP2,missense_variant,p.Asp31Tyr,ENST00000539093,;PXMP2,missense_variant,p.Trp159Cys,ENST00000317479,;PXMP2,missense_variant,p.Asp31Tyr,ENST00000545677,;RP13-672B3.2,missense_variant,p.Asp31Tyr,ENST00000537262,;PXMP2,missense_variant,p.Trp66Cys,ENST00000428960,;PXMP2,intron_variant,,ENST00000543589,;PXMP2,non_coding_transcript_exon_variant,,ENST00000454379,;	T	ENSG00000176894	ENST00000317479	Transcript	missense_variant	542	477	159	W/C	tgG/tgT	rs758880810	.	.	1	PXMP2	HGNC	9716	protein_coding	YES	CCDS9279.1	ENSP00000321271	PXMP2_HUMAN	.	UPI000016788C	.	deleterious(0)	probably_damaging(1)	4/5	.	hmmpanther:PTHR11266:SF7,hmmpanther:PTHR11266,Pfam_domain:PF04117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTGGACGCC	.	5	ESCA
SLCO1C1	0	.	GRCh37	12	20858911	20858911	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.300C>A	p.Ser100Arg	p.S100R	ENST00000381552	4/15	50	37	13	50	50	0	SLCO1C1,missense_variant,p.Ser100Arg,ENST00000381552,;SLCO1C1,missense_variant,p.Ser100Arg,ENST00000545604,;SLCO1C1,missense_variant,p.Ser100Arg,ENST00000266509,;SLCO1C1,missense_variant,p.Ser100Arg,ENST00000540354,;SLCO1C1,5_prime_UTR_variant,,ENST00000545102,;SLCO1C1,intron_variant,,ENST00000539415,;	A	ENSG00000139155	ENST00000381552	Transcript	missense_variant	668	300	100	S/R	agC/agA	.	.	.	1	SLCO1C1	HGNC	13819	protein_coding	YES	CCDS53757.1	ENSP00000370964	SO1C1_HUMAN	.	UPI00004C3E1B	.	deleterious(0)	probably_damaging(0.999)	4/15	.	hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF18,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTAGCTACTT	.	5	ESCA
TMTC2	0	.	GRCh37	12	83289683	83289683	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.741A>G	p.%3D	p.G247G	ENST00000321196	3/12	36	23	12	17	17	0	TMTC2,synonymous_variant,p.%3D,ENST00000548305,;TMTC2,synonymous_variant,p.%3D,ENST00000321196,;TMTC2,synonymous_variant,p.%3D,ENST00000549919,;TMTC2,3_prime_UTR_variant,,ENST00000546590,;TMTC2,non_coding_transcript_exon_variant,,ENST00000551915,;	G	ENSG00000179104	ENST00000321196	Transcript	synonymous_variant	1448	741	247	G	ggA/ggG	.	.	.	1	TMTC2	HGNC	25440	protein_coding	YES	CCDS9025.1	ENSP00000322300	TMTC2_HUMAN	.	UPI0000073F0F	.	.	.	3/12	.	hmmpanther:PTHR23083:SF390,hmmpanther:PTHR23083,Pfam_domain:PF08409	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGGAAACAA	.	5	ESCA
ZMYM2	0	.	GRCh37	13	20660806	20660806	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*652C>G	.	.	ENST00000382869	25/25	50	34	15	39	39	0	ZMYM2,3_prime_UTR_variant,,ENST00000382869,;ZMYM2,3_prime_UTR_variant,,ENST00000382871,;ZMYM2,3_prime_UTR_variant,,ENST00000382874,;ZMYM2,downstream_gene_variant,,ENST00000494061,;ZMYM2,downstream_gene_variant,,ENST00000490422,;ZMYM2,non_coding_transcript_exon_variant,,ENST00000382870,;	G	ENSG00000121741	ENST00000382869	Transcript	3_prime_UTR_variant	5037	.	.	.	.	.	.	.	1	ZMYM2	HGNC	12989	protein_coding	YES	CCDS45016.1	ENSP00000372322	ZMYM2_HUMAN	.	UPI000013C318	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTCCCCTTA	.	5	ESCA
RALGAPA1	0	.	GRCh37	14	36211602	36211603	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1420dupT	p.Ser474PhefsTer18	p.S474Ffs*18	ENST00000307138	11/40	33	26	7	23	23	0	RALGAPA1,frameshift_variant,p.Ser474PhefsTer18,ENST00000389698,;RALGAPA1,frameshift_variant,p.Ser474PhefsTer18,ENST00000553892,;RALGAPA1,frameshift_variant,p.Ser474PhefsTer18,ENST00000258840,;RALGAPA1,frameshift_variant,p.Ser474PhefsTer18,ENST00000382366,;RALGAPA1,frameshift_variant,p.Ser474PhefsTer18,ENST00000307138,;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000554704,;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000557069,;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000554652,;	A	ENSG00000174373	ENST00000307138	Transcript	frameshift_variant	1889-1890	1420-1421	474	S/FX	tca/tTca	.	.	.	-1	RALGAPA1	HGNC	17770	protein_coding	YES	CCDS32064.1	ENSP00000302647	RGPA1_HUMAN	Q9H984_HUMAN	UPI00003B5C51	.	.	.	11/40	.	hmmpanther:PTHR10063:SF3,hmmpanther:PTHR10063	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCATTGAAATA	.	2	ESCA
MAP4K5	0	.	GRCh37	14	50930823	50930823	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766A>G	p.Ile256Val	p.I256V	ENST00000013125	12/32	45	30	14	30	30	0	MAP4K5,missense_variant,p.Ile256Val,ENST00000013125,;Y_RNA,downstream_gene_variant,,ENST00000364703,;MAP4K5,downstream_gene_variant,,ENST00000557578,;MAP4K5,3_prime_UTR_variant,,ENST00000554091,;MAP4K5,non_coding_transcript_exon_variant,,ENST00000557210,;	C	ENSG00000012983	ENST00000013125	Transcript	missense_variant	1085	766	256	I/V	Ata/Gta	COSM3956071	.	.	-1	MAP4K5	HGNC	6867	protein_coding	YES	.	ENSP00000013125	M4K5_HUMAN	G3V5C6_HUMAN,G3V4T8_HUMAN,G3V3V7_HUMAN	UPI00015DFDAA	.	tolerated(1)	benign(0.001)	12/32	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF203,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF038172,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTATTTTGA	.	5	ESCA
ZNF410	0	.	GRCh37	14	74371780	74371780	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958C>T	p.His320Tyr	p.H320Y	ENST00000442160	8/14	29	24	5	32	32	0	ZNF410,missense_variant,p.His320Tyr,ENST00000442160,;ZNF410,missense_variant,p.His230Tyr,ENST00000540593,;ZNF410,missense_variant,p.His303Tyr,ENST00000324593,;ZNF410,missense_variant,p.His250Tyr,ENST00000334521,;ZNF410,missense_variant,p.His34Tyr,ENST00000554316,;ZNF410,missense_variant,p.His303Tyr,ENST00000555044,;RP5-1021I20.5,intron_variant,,ENST00000554009,;RP5-1021I20.6,upstream_gene_variant,,ENST00000602874,;Y_RNA,downstream_gene_variant,,ENST00000362602,;ZNF410,non_coding_transcript_exon_variant,,ENST00000412490,;ZNF410,non_coding_transcript_exon_variant,,ENST00000541357,;ZNF410,downstream_gene_variant,,ENST00000555602,;ZNF410,3_prime_UTR_variant,,ENST00000556396,;RP5-1021I20.4,3_prime_UTR_variant,,ENST00000556551,;ZNF410,3_prime_UTR_variant,,ENST00000398139,;ZNF410,non_coding_transcript_exon_variant,,ENST00000555620,;ZNF410,non_coding_transcript_exon_variant,,ENST00000557679,;ZNF410,downstream_gene_variant,,ENST00000554582,;	T	ENSG00000119725	ENST00000442160	Transcript	missense_variant	1152	958	320	H/Y	Cac/Tac	.	.	.	1	ZNF410	HGNC	20144	protein_coding	YES	CCDS55929.1	ENSP00000407130	ZN410_HUMAN	G3V4E6_HUMAN	UPI00017A6BE1	.	deleterious(0)	probably_damaging(1)	8/14	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR11389:SF363,hmmpanther:PTHR11389,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCCACACA	.	5	ESCA
TRPM7	0	.	GRCh37	15	50867083	50867083	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4985A>G	p.Tyr1662Cys	p.Y1662C	ENST00000313478	34/39	34	17	16	25	25	0	TRPM7,missense_variant,p.Tyr1661Cys,ENST00000560955,;TRPM7,missense_variant,p.Tyr1662Cys,ENST00000313478,;TRPM7,missense_variant,p.Tyr42Cys,ENST00000561267,;TRPM7,non_coding_transcript_exon_variant,,ENST00000561443,;TRPM7,downstream_gene_variant,,ENST00000558444,;TRPM7,downstream_gene_variant,,ENST00000560849,;TRPM7,non_coding_transcript_exon_variant,,ENST00000560516,;	C	ENSG00000092439	ENST00000313478	Transcript	missense_variant	5267	4985	1662	Y/C	tAc/tGc	.	.	.	-1	TRPM7	HGNC	17994	protein_coding	YES	CCDS42035.1	ENSP00000320239	TRPM7_HUMAN	.	UPI0000071CBA	.	deleterious(0)	probably_damaging(0.998)	34/39	.	Superfamily_domains:SSF56112,SMART_domains:SM00811,Pfam_domain:PF02816,Gene3D:3.30.200.20,hmmpanther:PTHR13800:SF8,hmmpanther:PTHR13800,PROSITE_profiles:PS51158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTGTAAATA	.	5	ESCA
CYP19A1	0	.	GRCh37	15	51504529	51504529	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1251T>C	p.%3D	p.N417N	ENST00000396402	9/10	51	22	28	27	27	0	CYP19A1,synonymous_variant,p.%3D,ENST00000559878,;CYP19A1,synonymous_variant,p.%3D,ENST00000396404,;CYP19A1,synonymous_variant,p.%3D,ENST00000559653,;CYP19A1,synonymous_variant,p.%3D,ENST00000396402,;CYP19A1,synonymous_variant,p.%3D,ENST00000260433,;CYP19A1,downstream_gene_variant,,ENST00000558328,;CYP19A1,downstream_gene_variant,,ENST00000561075,;RP11-108K3.1,intron_variant,,ENST00000559909,;CYP19A1,downstream_gene_variant,,ENST00000478421,;CYP19A1,non_coding_transcript_exon_variant,,ENST00000490076,;CYP19A1,downstream_gene_variant,,ENST00000558066,;CYP19A1,downstream_gene_variant,,ENST00000439712,;CYP19A1,downstream_gene_variant,,ENST00000557934,;	G	ENSG00000137869	ENST00000396402	Transcript	synonymous_variant	1405	1251	417	N	aaT/aaC	.	.	.	-1	CYP19A1	HGNC	2594	protein_coding	YES	CCDS10139.1	ENSP00000379683	CP19A_HUMAN	Q16449_HUMAN,H0YLS2_HUMAN,H0YLP1_HUMAN,H0YKN1_HUMAN,E9PGZ6_HUMAN,E7EQ08_HUMAN,E7EPL6_HUMAN	UPI000013D0D7	.	.	.	9/10	.	hmmpanther:PTHR24290,hmmpanther:PTHR24290:SF57,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAAATTTTC	.	5	ESCA
CGNL1	0	.	GRCh37	15	57730212	57730212	+	Silent	SNP	C	C	T	rs765549295	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15C>T	p.%3D	p.F5F	ENST00000281282	2/19	38	32	6	49	49	0	CGNL1,synonymous_variant,p.%3D,ENST00000281282,;CGNL1,non_coding_transcript_exon_variant,,ENST00000559194,;	T	ENSG00000128849	ENST00000281282	Transcript	synonymous_variant	93	15	5	F	ttC/ttT	rs765549295,COSM2219125	.	.	1	CGNL1	HGNC	25931	protein_coding	YES	CCDS10161.1	ENSP00000281282	CGNL1_HUMAN	.	UPI000019B4EF	.	.	.	2/19	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTTCGGTGA	byFrequency	4	ESCA
GCOM1	0	.	GRCh37	15	57921909	57921909	+	Missense_Mutation	SNP	G	G	C	rs745806929	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535G>C	p.Val179Leu	p.V179L	ENST00000380569	6/14	42	39	3	34	34	0	GCOM1,missense_variant,p.Val179Leu,ENST00000572390,;MYZAP,missense_variant,p.Val179Leu,ENST00000380565,;GCOM1,missense_variant,p.Val110Leu,ENST00000380560,;MYZAP,missense_variant,p.Val179Leu,ENST00000267853,;GCOM1,missense_variant,p.Val179Leu,ENST00000380568,;GCOM1,missense_variant,p.Val148Leu,ENST00000380561,;GCOM1,missense_variant,p.Val148Leu,ENST00000396180,;GCOM1,missense_variant,p.Val179Leu,ENST00000587652,;GCOM1,missense_variant,p.Val179Leu,ENST00000574161,;GCOM1,missense_variant,p.Val179Leu,ENST00000380569,;POLR2M,5_prime_UTR_variant,,ENST00000380563,;MYZAP,downstream_gene_variant,,ENST00000569089,;MYZAP,upstream_gene_variant,,ENST00000461709,;GCOM1,missense_variant,p.Val148Leu,ENST00000468886,;GCOM1,missense_variant,p.Val179Leu,ENST00000463717,;GCOM1,missense_variant,p.Val179Leu,ENST00000460962,;GCOM1,missense_variant,p.Val179Leu,ENST00000488175,;GCOM1,missense_variant,p.Val148Leu,ENST00000496101,;GCOM1,missense_variant,p.Val110Leu,ENST00000471563,;GCOM1,missense_variant,p.Val179Leu,ENST00000496627,;GCOM1,missense_variant,p.Val179Leu,ENST00000477282,;GCOM1,missense_variant,p.Val179Leu,ENST00000482814,;	C	ENSG00000137878	ENST00000380569	Transcript	missense_variant	662	535	179	V/L	Gtg/Ctg	rs745806929	.	.	1	GCOM1	HGNC	26424	protein_coding	YES	CCDS32247.1	ENSP00000369943	.	.	UPI0000375B72	.	tolerated(0.79)	benign(0.183)	6/14	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23171,hmmpanther:PTHR23171:SF2,Pfam_domain:PF15328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTCGTGGAT	byFrequency	2	ESCA
MAP2K1	0	.	GRCh37	15	66782848	66782848	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1080delT	p.Phe360LeufsTer74	p.F360Lfs*74	ENST00000307102	11/11	108	64	44	60	60	0	MAP2K1,frameshift_variant,p.Phe360LeufsTer74,ENST00000307102,;MAP2K1,frameshift_variant,p.Phe184LeufsTer74,ENST00000566326,;SNAPC5,3_prime_UTR_variant,,ENST00000395589,;SNAPC5,3_prime_UTR_variant,,ENST00000563480,;SNAPC5,downstream_gene_variant,,ENST00000307979,;SNAPC5,downstream_gene_variant,,ENST00000316634,;SNAPC5,downstream_gene_variant,,ENST00000566658,;CTD-3185P2.1,non_coding_transcript_exon_variant,,ENST00000565387,;CTD-3185P2.2,upstream_gene_variant,,ENST00000602360,;SNAPC5,downstream_gene_variant,,ENST00000568875,;SNAPC5,downstream_gene_variant,,ENST00000565465,;SNAPC5,downstream_gene_variant,,ENST00000562411,;	-	ENSG00000169032	ENST00000307102	Transcript	frameshift_variant	1608	1077	359	A/X	gcT/gc	.	.	.	1	MAP2K1	HGNC	6840	protein_coding	YES	CCDS10216.1	ENSP00000302486	MP2K1_HUMAN	A4QPA9_HUMAN	UPI000013EBC9	.	.	.	11/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24360,hmmpanther:PTHR24360:SF15,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCATGCTTTTAT	.	3	ESCA
MSRB1	0	.	GRCh37	16	1993105	1993105	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53C>A	p.Pro18His	p.P18H	ENST00000361871	1/4	24	21	3	26	26	0	MSRB1,missense_variant,p.Pro18His,ENST00000564908,;MSRB1,missense_variant,p.Leu8Met,ENST00000473663,;MSRB1,missense_variant,p.Pro18His,ENST00000399753,;MSRB1,missense_variant,p.Pro18His,ENST00000361871,;RPL3L,downstream_gene_variant,,ENST00000268661,;MSRB1,upstream_gene_variant,,ENST00000489198,;	T	ENSG00000198736	ENST00000361871	Transcript	missense_variant	223	53	18	P/H	cCt/cAt	.	.	.	-1	MSRB1	HGNC	14133	protein_coding	YES	CCDS42100.1	ENSP00000355084	MSRB1_HUMAN	D3DU81_HUMAN	UPI0000161C13	.	deleterious(0.01)	possibly_damaging(0.895)	1/4	.	Superfamily_domains:SSF51316,Gene3D:2.170.150.20,Pfam_domain:PF01641,hmmpanther:PTHR10173:SF11,hmmpanther:PTHR10173	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACCAGGTTCA	.	2	ESCA
CREBBP	0	.	GRCh37	16	3777568	3777568	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*151A>G	.	.	ENST00000262367	31/31	14	10	4	14	14	0	CREBBP,3_prime_UTR_variant,,ENST00000262367,;CREBBP,3_prime_UTR_variant,,ENST00000382070,;CREBBP,downstream_gene_variant,,ENST00000571763,;CREBBP,downstream_gene_variant,,ENST00000576720,;	C	ENSG00000005339	ENST00000262367	Transcript	3_prime_UTR_variant	8290	.	.	.	.	.	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AAATATATTCT	.	4	ESCA
SIAH1	0	.	GRCh37	16	48396037	48396037	+	Silent	SNP	C	C	T	rs768759254	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396G>A	p.%3D	p.A132A	ENST00000356721	2/2	79	60	18	57	57	0	SIAH1,synonymous_variant,p.%3D,ENST00000380006,;SIAH1,synonymous_variant,p.%3D,ENST00000394725,;SIAH1,synonymous_variant,p.%3D,ENST00000356721,;LONP2,3_prime_UTR_variant,,ENST00000565867,;LONP2,downstream_gene_variant,,ENST00000285737,;SIAH1,downstream_gene_variant,,ENST00000563745,;SIAH1,upstream_gene_variant,,ENST00000565620,;SIAH1,downstream_gene_variant,,ENST00000573005,;LONP2,downstream_gene_variant,,ENST00000564259,;SIAH1,synonymous_variant,p.%3D,ENST00000568007,;LONP2,non_coding_transcript_exon_variant,,ENST00000566719,;LONP2,downstream_gene_variant,,ENST00000565185,;	T	ENSG00000196470	ENST00000356721	Transcript	synonymous_variant	820	396	132	A	gcG/gcA	rs768759254	.	.	-1	SIAH1	HGNC	10857	protein_coding	YES	CCDS32444.1	ENSP00000349156	SIAH1_HUMAN	H3BU09_HUMAN	UPI0000074729	.	.	.	2/2	.	Superfamily_domains:SSF49599,Pfam_domain:PF03145,Gene3D:3.30.40.10,hmmpanther:PTHR10315,hmmpanther:PTHR10315:SF23,PROSITE_profiles:PS51081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGACGCATA	byFrequency	5	ESCA
SLC12A3	0	.	GRCh37	16	56924229	56924229	+	Missense_Mutation	SNP	C	C	T	rs748994629	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2329C>T	p.Arg777Trp	p.R777W	ENST00000438926	19/26	102	63	39	114	114	0	SLC12A3,missense_variant,p.Arg776Trp,ENST00000566786,;SLC12A3,missense_variant,p.Arg777Trp,ENST00000563236,;SLC12A3,missense_variant,p.Arg777Trp,ENST00000438926,;SLC12A3,missense_variant,p.Arg776Trp,ENST00000262502,;	T	ENSG00000070915	ENST00000438926	Transcript	missense_variant	2358	2329	777	R/W	Cgg/Tgg	rs748994629	.	.	1	SLC12A3	HGNC	10912	protein_coding	YES	CCDS10770.1	ENSP00000402152	S12A3_HUMAN	.	UPI00001FF243	.	deleterious(0)	possibly_damaging(0.663)	19/26	.	hmmpanther:PTHR11827:SF9,hmmpanther:PTHR11827,TIGRFAM_domain:TIGR00930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGCGGGAG	byFrequency	5	ESCA
DOK4	0	.	GRCh37	16	57506214	57506214	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1075G>A	.	.	ENST00000340099	9/9	27	18	9	21	21	0	DOK4,3_prime_UTR_variant,,ENST00000340099,;DOK4,3_prime_UTR_variant,,ENST00000566936,;POLR2C,downstream_gene_variant,,ENST00000219252,;DOK4,downstream_gene_variant,,ENST00000566588,;DOK4,downstream_gene_variant,,ENST00000564378,;DOK4,downstream_gene_variant,,ENST00000562737,;DOK4,downstream_gene_variant,,ENST00000567276,;DOK4,downstream_gene_variant,,ENST00000569010,;DOK4,downstream_gene_variant,,ENST00000569538,;DOK4,downstream_gene_variant,,ENST00000569548,;DOK4,downstream_gene_variant,,ENST00000567175,;DOK4,downstream_gene_variant,,ENST00000562008,;DOK4,downstream_gene_variant,,ENST00000569250,;DOK4,downstream_gene_variant,,ENST00000568617,;DOK4,downstream_gene_variant,,ENST00000566705,;DOK4,downstream_gene_variant,,ENST00000567214,;DOK4,downstream_gene_variant,,ENST00000561918,;POLR2C,downstream_gene_variant,,ENST00000564651,;DOK4,downstream_gene_variant,,ENST00000563483,;POLR2C,downstream_gene_variant,,ENST00000563589,;POLR2C,downstream_gene_variant,,ENST00000563115,;DOK4,downstream_gene_variant,,ENST00000561659,;POLR2C,downstream_gene_variant,,ENST00000567982,;POLR2C,downstream_gene_variant,,ENST00000562953,;POLR2C,downstream_gene_variant,,ENST00000562599,;	T	ENSG00000125170	ENST00000340099	Transcript	3_prime_UTR_variant	2428	.	.	.	.	.	.	.	-1	DOK4	HGNC	19868	protein_coding	YES	CCDS10783.1	ENSP00000344277	DOK4_HUMAN	H3BVB4_HUMAN,H3BV67_HUMAN,H3BTK2_HUMAN,H3BTI7_HUMAN,H3BTI4_HUMAN,H3BSK0_HUMAN,H3BS85_HUMAN,H3BPY9_HUMAN,H3BN90_HUMAN	UPI0000070AA4	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AACAACAAAAA	.	4	ESCA
EXOC3L1	0	.	GRCh37	16	67222636	67222636	+	Missense_Mutation	SNP	G	G	A	rs775635066	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415C>T	p.Arg139Trp	p.R139W	ENST00000314586	4/14	42	26	16	43	43	0	EXOC3L1,missense_variant,p.Arg139Trp,ENST00000564418,;EXOC3L1,missense_variant,p.Arg139Trp,ENST00000314586,;EXOC3L1,intron_variant,,ENST00000545725,;EXOC3L1,intron_variant,,ENST00000563889,;KIAA0895L,upstream_gene_variant,,ENST00000290881,;KIAA0895L,upstream_gene_variant,,ENST00000561621,;E2F4,upstream_gene_variant,,ENST00000379378,;KIAA0895L,upstream_gene_variant,,ENST00000563902,;EXOC3L1,intron_variant,,ENST00000562887,;KIAA0895L,upstream_gene_variant,,ENST00000564423,;E2F4,upstream_gene_variant,,ENST00000564718,;EXOC3L1,intron_variant,,ENST00000564324,;E2F4,upstream_gene_variant,,ENST00000561904,;E2F4,upstream_gene_variant,,ENST00000568839,;E2F4,upstream_gene_variant,,ENST00000566368,;E2F4,upstream_gene_variant,,ENST00000565849,;E2F4,upstream_gene_variant,,ENST00000563238,;E2F4,upstream_gene_variant,,ENST00000568485,;E2F4,upstream_gene_variant,,ENST00000569573,;E2F4,upstream_gene_variant,,ENST00000567007,;EXOC3L1,upstream_gene_variant,,ENST00000563536,;	A	ENSG00000179044	ENST00000314586	Transcript	missense_variant	656	415	139	R/W	Cgg/Tgg	rs775635066	.	.	-1	EXOC3L1	HGNC	27540	protein_coding	YES	CCDS10832.1	ENSP00000325674	EX3L1_HUMAN	H3BTH9_HUMAN	UPI000013F886	.	deleterious(0)	possibly_damaging(0.841)	4/14	.	hmmpanther:PTHR21292,hmmpanther:PTHR21292:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CAGCCGAGGCA	.	4	ESCA
CIRH1A	0	.	GRCh37	16	69194279	69194279	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1465C>G	p.Leu489Val	p.L489V	ENST00000314423	13/17	33	25	8	30	30	0	CIRH1A,missense_variant,p.Leu489Val,ENST00000314423,;CIRH1A,missense_variant,p.Leu113Val,ENST00000567500,;CIRH1A,missense_variant,p.Leu489Val,ENST00000563094,;CIRH1A,missense_variant,p.Leu374Val,ENST00000352319,;CIRH1A,missense_variant,p.Leu503Val,ENST00000562237,;	G	ENSG00000141076	ENST00000314423	Transcript	missense_variant	1642	1465	489	L/V	Ctt/Gtt	.	.	.	1	CIRH1A	HGNC	1983	protein_coding	YES	CCDS10872.1	ENSP00000327179	CIR1A_HUMAN	J3KTR0_HUMAN,J3KSE6_HUMAN,H3BPD7_HUMAN	UPI0000037300	.	deleterious(0.02)	benign(0.203)	13/17	.	hmmpanther:PTHR22841,hmmpanther:PTHR22841:SF4,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF82171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTCTTTTG	.	5	ESCA
RPA1	0	.	GRCh37	17	1802203	1802203	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1734G>T	.	.	ENST00000254719	17/17	27	18	8	11	11	0	RPA1,3_prime_UTR_variant,,ENST00000254719,;RPA1,3_prime_UTR_variant,,ENST00000574049,;RPA1,downstream_gene_variant,,ENST00000573994,;	T	ENSG00000132383	ENST00000254719	Transcript	3_prime_UTR_variant	3695	.	.	.	.	.	.	.	1	RPA1	HGNC	10289	protein_coding	YES	CCDS11014.1	ENSP00000254719	RFA1_HUMAN	I3L524_HUMAN,I3L2M5_HUMAN	UPI000013379A	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGGGAAGT	.	5	ESCA
VTN	0	.	GRCh37	17	26691418	26691418	+	3'Flank	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000226218	.	36	18	18	36	36	0	VTN,missense_variant,p.Pro174Thr,ENST00000438614,;VTN,missense_variant,p.Pro175Thr,ENST00000431468,;VTN,missense_variant,p.Pro174Thr,ENST00000536498,;CTB-96E2.2,3_prime_UTR_variant,,ENST00000555059,;TMEM199,intron_variant,,ENST00000509083,;TMEM199,downstream_gene_variant,,ENST00000292114,;VTN,downstream_gene_variant,,ENST00000226218,;TMEM199,downstream_gene_variant,,ENST00000395404,;MIR4723,downstream_gene_variant,,ENST00000585070,;CTB-96E2.7,upstream_gene_variant,,ENST00000577850,;SARM1,non_coding_transcript_exon_variant,,ENST00000379061,;CTB-96E2.3,intron_variant,,ENST00000591482,;TMEM199,downstream_gene_variant,,ENST00000581386,;TMEM199,downstream_gene_variant,,ENST00000580868,;VTN,downstream_gene_variant,,ENST00000539746,;TMEM199,downstream_gene_variant,,ENST00000555264,;TMEM199,downstream_gene_variant,,ENST00000483505,;TMEM199,downstream_gene_variant,,ENST00000585027,;TMEM199,downstream_gene_variant,,ENST00000577317,;	T	ENSG00000109072	ENST00000226218	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2879	-1	VTN	HGNC	12724	protein_coding	YES	CCDS11229.1	ENSP00000226218	VTNC_HUMAN	F5GX75_HUMAN,D9ZGG2_HUMAN	UPI0000138E65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATGGGGCTA	.	5	ESCA
TP53	0	.	GRCh37	17	7579358	7579358	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	4/11	292	132	159	243	243	0	TP53,missense_variant,p.Arg110Leu,ENST00000508793,;TP53,missense_variant,p.Arg110Leu,ENST00000413465,;TP53,missense_variant,p.Arg110Leu,ENST00000604348,;TP53,missense_variant,p.Arg110Leu,ENST00000420246,;TP53,missense_variant,p.Arg110Leu,ENST00000269305,;TP53,missense_variant,p.Arg110Leu,ENST00000359597,;TP53,missense_variant,p.Arg110Leu,ENST00000445888,;TP53,missense_variant,p.Arg110Leu,ENST00000503591,;TP53,missense_variant,p.Arg110Leu,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	519	329	110	R/L	cGt/cTt	CM984590,CM115383,TP53_g.11560G>A,TP53_g.11560G>T,TP53_g.11560del,TP53_g.11560G>C,COSM10716,COSM43805,COSM11250,COSM46115,COSM99929,COSM1166752,COSM2745016,COSM2745018,COSM99928,COSM1166753,COSM3723935,COSM3388234,COSM2745017,COSM1646883	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.04)	possibly_damaging(0.898)	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	T:0	T:0	.	T:0.003	T:0	T:0	.	.	.	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R110L|c.329G>T|27,SITE|p.R110L|c.329G>T|5,SITE|p.R110L|c.329G>T|8,SITE|p.R110L|c.329G>T|8,CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,CODON|p.R110fs*13|c.329delG|3,CODON|p.R110fs*13|c.328delC|4,CODON|p.R110P|c.329G>C|11,BUFFER|p.F113L|c.339C>G|4,BUFFER|p.F113C|c.338T>G|4,BUFFER|p.F113C|c.338T>G|8,BUFFER|p.F113S|c.338T>C|3,BUFFER|p.F113C|c.338T>G|4,BUFFER|p.F113V|c.337T>G|3,BUFFER|p.F113V|c.337T>G|3,BUFFER|p.F113V|c.337T>G|6,BUFFER|p.L111R|c.332T>G|5,BUFFER|p.L111Q|c.332T>A|7,BUFFER|p.L111P|c.332T>C|9,BUFFER|p.L111Q|c.332T>A|3,BUFFER|p.L111R|c.332T>G|10,BUFFER|p.L111Q|c.332T>A|3,BUFFER|p.L111P|c.332T>C|3,BUFFER|p.L111R|c.332T>G|5,BUFFER|p.L111P|c.332T>C|3,BUFFER|p.R110C|c.328C>T|6,BUFFER|p.F109C|c.326T>G|3,BUFFER|p.F109C|c.326T>G|4,BUFFER|p.F109C|c.326T>G|3,BUFFER|p.G108delG|c.322_324delGGT|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.Y107*|c.321C>A|6,BUFFER|p.Y107Y|c.321C>T|3,BUFFER|p.Y107*|c.321C>G|3,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|8,BUFFER|p.S106R|c.318C>G|3,BUFFER|p.S106R|c.318C>G|3,BUFFER|p.S106R|c.318C>G|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGACGGAAA	.	5	ESCA
ZNF519	0	.	GRCh37	18	14105961	14105961	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578C>G	p.Ser193Cys	p.S193C	ENST00000590202	3/3	28	16	12	20	20	0	ZNF519,missense_variant,p.Ser193Cys,ENST00000590202,;ZNF519,intron_variant,,ENST00000589498,;RP11-411B10.3,downstream_gene_variant,,ENST00000592926,;ZNF519,intron_variant,,ENST00000591393,;ZNF519,intron_variant,,ENST00000592345,;ZNF519,intron_variant,,ENST00000592411,;ZNF519,intron_variant,,ENST00000589203,;ZNF519,intron_variant,,ENST00000592049,;ZNF519,downstream_gene_variant,,ENST00000588435,;ZNF519,intron_variant,,ENST00000587419,;	C	ENSG00000175322	ENST00000590202	Transcript	missense_variant	731	578	193	S/C	tCc/tGc	.	.	.	-1	ZNF519	HGNC	30574	protein_coding	YES	CCDS32797.1	ENSP00000464872	ZN519_HUMAN	.	UPI0000201A41	.	tolerated(0.13)	benign(0.01)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF97,hmmpanther:PTHR24384,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGGATTGG	.	5	ESCA
ROCK1	0	.	GRCh37	18	18559913	18559913	+	Missense_Mutation	SNP	T	T	G	rs767267219	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2612A>C	p.Asn871Thr	p.N871T	ENST00000399799	22/33	63	47	16	47	47	0	ROCK1,missense_variant,p.Asn871Thr,ENST00000399799,;ROCK1,non_coding_transcript_exon_variant,,ENST00000583556,;	G	ENSG00000067900	ENST00000399799	Transcript	missense_variant	3553	2612	871	N/T	aAc/aCc	rs767267219,COSM1387931,COSM1711014	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	tolerated(0.44)	benign(0.003)	22/33	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF28,PIRSF_domain:PIRSF037568	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGTTTTTT	.	5	ESCA
LOXHD1	0	.	GRCh37	18	44057279	44057279	+	Intron	DEL	G	G	-	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3308-96delC	.	.	ENST00000300591	.	24	17	7	20	20	0	LOXHD1,3_prime_UTR_variant,,ENST00000582408,;LOXHD1,3_prime_UTR_variant,,ENST00000441893,;LOXHD1,3_prime_UTR_variant,,ENST00000536736,;LOXHD1,3_prime_UTR_variant,,ENST00000398686,;LOXHD1,intron_variant,,ENST00000300591,;LOXHD1,intron_variant,,ENST00000398705,;LOXHD1,intron_variant,,ENST00000579038,;LOXHD1,intron_variant,,ENST00000398722,;LOXHD1,downstream_gene_variant,,ENST00000441551,;	-	ENSG00000167210	ENST00000300591	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	LOXHD1	HGNC	26521	protein_coding	YES	CCDS45861.1	ENSP00000300591	LOXH1_HUMAN	C9J269_HUMAN,C9IYQ1_HUMAN	UPI0000456B8D	.	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAAACTGGGGGT	.	3	ESCA
ATP8B1	0	.	GRCh37	18	55334329	55334329	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2280T>C	p.%3D	p.D760D	ENST00000536015	20/28	27	21	6	18	18	0	ATP8B1,synonymous_variant,p.%3D,ENST00000283684,;ATP8B1,synonymous_variant,p.%3D,ENST00000536015,;RP11-35G9.3,intron_variant,,ENST00000599199,;RP11-35G9.5,intron_variant,,ENST00000588925,;RP11-35G9.3,intron_variant,,ENST00000591854,;RP11-35G9.3,intron_variant,,ENST00000592201,;	G	ENSG00000081923	ENST00000536015	Transcript	synonymous_variant	2400	2280	760	D	gaT/gaC	.	.	.	-1	ATP8B1	HGNC	3706	protein_coding	YES	CCDS11965.1	ENSP00000445359	AT8B1_HUMAN	K7ERI0_HUMAN,K7EQC4_HUMAN	UPI000013DD54	.	.	.	20/28	.	hmmpanther:PTHR24092:SF48,hmmpanther:PTHR24092,Pfam_domain:PF12710,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01652	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTAATATCCTC	.	3	ESCA
ZCCHC2	0	.	GRCh37	18	60241388	60241388	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2074C>T	p.Gln692Ter	p.Q692*	ENST00000269499	13/14	32	28	4	46	46	0	ZCCHC2,stop_gained,p.Gln371Ter,ENST00000586834,;ZCCHC2,stop_gained,p.Gln692Ter,ENST00000269499,;ZCCHC2,upstream_gene_variant,,ENST00000587612,;ZCCHC2,stop_gained,p.Gln612Ter,ENST00000585873,;ZCCHC2,non_coding_transcript_exon_variant,,ENST00000585949,;ZCCHC2,upstream_gene_variant,,ENST00000591145,;	T	ENSG00000141664	ENST00000269499	Transcript	stop_gained	2492	2074	692	Q/*	Caa/Taa	.	.	.	1	ZCCHC2	HGNC	22916	protein_coding	YES	CCDS45880.1	ENSP00000269499	ZCHC2_HUMAN	K7ERQ9_HUMAN,B2RPG6_HUMAN	UPI00016D385A	.	.	.	13/14	.	hmmpanther:PTHR16195,hmmpanther:PTHR16195:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGTTCAAATT	.	3	ESCA
MKNK2	0	.	GRCh37	19	2046658	2046658	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84A>T	p.%3D	p.L28L	ENST00000250896	3/14	58	52	6	59	59	0	MKNK2,synonymous_variant,p.%3D,ENST00000591601,;MKNK2,synonymous_variant,p.%3D,ENST00000309340,;MKNK2,synonymous_variant,p.%3D,ENST00000250896,;MKNK2,synonymous_variant,p.%3D,ENST00000589534,;MKNK2,synonymous_variant,p.%3D,ENST00000589509,;MKNK2,5_prime_UTR_variant,,ENST00000541165,;MKNK2,upstream_gene_variant,,ENST00000591588,;MKNK2,upstream_gene_variant,,ENST00000588014,;MKNK2,upstream_gene_variant,,ENST00000591142,;MKNK2,synonymous_variant,p.%3D,ENST00000586828,;MKNK2,non_coding_transcript_exon_variant,,ENST00000588346,;MKNK2,upstream_gene_variant,,ENST00000587416,;MKNK2,upstream_gene_variant,,ENST00000586620,;MKNK2,upstream_gene_variant,,ENST00000585667,;	A	ENSG00000099875	ENST00000250896	Transcript	synonymous_variant	329	84	28	L	ctA/ctT	.	.	.	-1	MKNK2	HGNC	7111	protein_coding	YES	CCDS12080.1	ENSP00000250896	MKNK2_HUMAN	K7EIN7_HUMAN,B4DEQ4_HUMAN,B3KS07_HUMAN,A4CYL7_HUMAN	UPI000006E9B4	.	.	.	3/14	.	hmmpanther:PTHR24349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTCTAGGGA	.	4	ESCA
ZNF99	0	.	GRCh37	19	22941211	22941211	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1500G>T	p.Lys500Asn	p.K500N	ENST00000596209	4/4	50	43	6	55	55	0	ZNF99,missense_variant,p.Lys409Asn,ENST00000397104,;ZNF99,missense_variant,p.Lys500Asn,ENST00000596209,;CTC-451A6.4,upstream_gene_variant,,ENST00000442497,;	A	ENSG00000213973	ENST00000596209	Transcript	missense_variant	1591	1500	500	K/N	aaG/aaT	COSM1234765	.	.	-1	ZNF99	HGNC	13175	protein_coding	YES	CCDS59369.1	ENSP00000472969	.	M0R335_HUMAN	UPI0000426011	.	deleterious(0.01)	probably_damaging(0.999)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24375:SF102,hmmpanther:PTHR24375,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTACCTTATG	.	4	ESCA
EIF3K	0	.	GRCh37	19	39123261	39123261	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442A>T	p.Ile148Phe	p.I148F	ENST00000248342	6/8	52	33	18	53	53	0	EIF3K,missense_variant,p.Ile115Phe,ENST00000591409,;EIF3K,missense_variant,p.Ile148Phe,ENST00000545173,;EIF3K,missense_variant,p.Ile61Phe,ENST00000538434,;EIF3K,missense_variant,p.Ile61Phe,ENST00000593149,;EIF3K,missense_variant,p.Ile148Phe,ENST00000248342,;EIF3K,intron_variant,,ENST00000588934,;EIF3K,intron_variant,,ENST00000592558,;EIF3K,downstream_gene_variant,,ENST00000586513,;EIF3K,downstream_gene_variant,,ENST00000589307,;EIF3K,downstream_gene_variant,,ENST00000593062,;EIF3K,non_coding_transcript_exon_variant,,ENST00000588299,;EIF3K,non_coding_transcript_exon_variant,,ENST00000590134,;	T	ENSG00000178982	ENST00000248342	Transcript	missense_variant	614	442	148	I/F	Atc/Ttc	.	.	.	1	EIF3K	HGNC	24656	protein_coding	YES	CCDS12517.1	ENSP00000248342	EIF3K_HUMAN	K7EK53_HUMAN	UPI000012D318	.	deleterious(0)	probably_damaging(0.98)	6/8	.	Superfamily_domains:SSF46785,Pfam_domain:PF10075,Gene3D:1.10.10.10,hmmpanther:PTHR13022,HAMAP:MF_03010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTATCACT	.	5	ESCA
ZNF780B	0	.	GRCh37	19	40542336	40542336	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.430A>G	p.Ile144Val	p.I144V	ENST00000434248	5/5	82	50	31	67	67	0	ZNF780B,missense_variant,p.Ile144Val,ENST00000434248,;ZNF780B,5_prime_UTR_variant,,ENST00000221355,;ZNF780B,downstream_gene_variant,,ENST00000598845,;ZNF780B,downstream_gene_variant,,ENST00000595995,;	C	ENSG00000128000	ENST00000434248	Transcript	missense_variant	496	430	144	I/V	Atc/Gtc	.	.	.	-1	ZNF780B	HGNC	33109	protein_coding	YES	CCDS46077.1	ENSP00000391641	Z780B_HUMAN	M0R0W9_HUMAN,C9JTJ1_HUMAN	UPI000007137F	.	tolerated(0.42)	benign(0.031)	5/5	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF203	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGATGATCT	.	5	ESCA
ZNF404	0	.	GRCh37	19	44378184	44378185	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181dupA	p.Arg61LysfsTer4	p.R61Kfs*4	ENST00000587539	3/3	17	9	8	20	20	0	ZNF404,frameshift_variant,p.Arg59LysfsTer4,ENST00000324394,;ZNF404,frameshift_variant,p.Arg61LysfsTer4,ENST00000587539,;	T	ENSG00000176222	ENST00000587539	Transcript	frameshift_variant	181-182	181-182	61	R/KX	aga/aAga	.	.	.	-1	ZNF404	HGNC	19417	protein_coding	YES	CCDS59394.1	ENSP00000466051	.	Q86WM5_HUMAN,K7ELF2_HUMAN	UPI00001D8172	.	.	.	3/3	.	SMART_domains:SM00349,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF53,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AATTTCTTTTT	.	2	ESCA
DMPK	0	.	GRCh37	19	46273048	46273048	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*698G>C	.	.	ENST00000343373	14/14	51	31	20	101	101	0	DMPK,3_prime_UTR_variant,,ENST00000291270,;DMPK,3_prime_UTR_variant,,ENST00000600757,;DMPK,3_prime_UTR_variant,,ENST00000447742,;DMPK,3_prime_UTR_variant,,ENST00000343373,;DMPK,downstream_gene_variant,,ENST00000593574,;DMPK,downstream_gene_variant,,ENST00000597660,;DMPK,downstream_gene_variant,,ENST00000458663,;SIX5,upstream_gene_variant,,ENST00000560160,;SIX5,upstream_gene_variant,,ENST00000560168,;SIX5,upstream_gene_variant,,ENST00000317578,;DMPK,downstream_gene_variant,,ENST00000354227,;AC074212.5,non_coding_transcript_exon_variant,,ENST00000592217,;AC074212.6,intron_variant,,ENST00000590076,;AC074212.6,upstream_gene_variant,,ENST00000591530,;AC074212.6,upstream_gene_variant,,ENST00000586498,;AC074212.6,upstream_gene_variant,,ENST00000586251,;AC074212.5,downstream_gene_variant,,ENST00000559756,;DMPK,3_prime_UTR_variant,,ENST00000588522,;DMPK,non_coding_transcript_exon_variant,,ENST00000596686,;DMPK,downstream_gene_variant,,ENST00000600370,;DMPK,downstream_gene_variant,,ENST00000598272,;	G	ENSG00000104936	ENST00000343373	Transcript	3_prime_UTR_variant	3162	.	.	.	.	.	.	.	-1	DMPK	HGNC	2933	protein_coding	YES	CCDS46119.1	ENSP00000345997	DMPK_HUMAN	E5KR08_HUMAN	UPI00001AF19C	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATACCGAGG	.	5	ESCA
CPT1C	0	.	GRCh37	19	50207991	50207991	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.718G>A	p.Val240Met	p.V240M	ENST00000392518	8/20	17	14	3	29	29	0	CPT1C,missense_variant,p.Val240Met,ENST00000598293,;CPT1C,missense_variant,p.Val240Met,ENST00000323446,;CPT1C,missense_variant,p.Val240Met,ENST00000392518,;CPT1C,missense_variant,p.Val240Met,ENST00000354199,;CPT1C,missense_variant,p.Val240Met,ENST00000598396,;CPT1C,missense_variant,p.Val240Met,ENST00000405931,;CPT1C,downstream_gene_variant,,ENST00000602019,;CPT1C,downstream_gene_variant,,ENST00000595969,;CPT1C,downstream_gene_variant,,ENST00000594587,;CPT1C,upstream_gene_variant,,ENST00000595031,;CPT1C,3_prime_UTR_variant,,ENST00000595568,;CPT1C,3_prime_UTR_variant,,ENST00000598259,;CPT1C,non_coding_transcript_exon_variant,,ENST00000599023,;CPT1C,non_coding_transcript_exon_variant,,ENST00000295404,;CPT1C,non_coding_transcript_exon_variant,,ENST00000596701,;CPT1C,non_coding_transcript_exon_variant,,ENST00000594431,;CPT1C,downstream_gene_variant,,ENST00000596922,;	A	ENSG00000169169	ENST00000392518	Transcript	missense_variant	1090	718	240	V/M	Gtg/Atg	.	.	.	1	CPT1C	HGNC	18540	protein_coding	YES	CCDS12779.1	ENSP00000376303	CPT1C_HUMAN	M0R2V3_HUMAN,M0R115_HUMAN,M0QZ13_HUMAN,B3KU49_HUMAN	UPI0000071C78	.	deleterious(0)	probably_damaging(0.975)	8/20	.	Superfamily_domains:SSF52777,Pfam_domain:PF00755,hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF55	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AATTTGTGTAC	.	3	ESCA
OVGP1	0	.	GRCh37	1	111968031	111968031	+	Silent	SNP	G	G	A	rs373255062	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.291C>T	p.%3D	p.I97I	ENST00000369732	4/11	93	63	29	94	94	0	OVGP1,synonymous_variant,p.%3D,ENST00000369732,;OVGP1,synonymous_variant,p.%3D,ENST00000540696,;OVGP1,upstream_gene_variant,,ENST00000481495,;	A	ENSG00000085465	ENST00000369732	Transcript	synonymous_variant	347	291	97	I	atC/atT	rs373255062	.	.	-1	OVGP1	HGNC	8524	protein_coding	YES	CCDS834.1	ENSP00000358747	OVGP1_HUMAN	Q9UJZ3_HUMAN	UPI0000130C53	.	.	.	4/11	.	hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF114,Gene3D:3.20.20.80,Pfam_domain:PF00704,SMART_domains:SM00636,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCCGATGGA	byCluster	5	ESCA
VTCN1	0	.	GRCh37	1	117699294	117699294	+	Missense_Mutation	SNP	C	C	T	rs767710032	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347G>A	p.Arg116Gln	p.R116Q	ENST00000369458	3/6	51	43	8	45	45	0	VTCN1,missense_variant,p.Arg119Gln,ENST00000359008,;VTCN1,missense_variant,p.Arg21Gln,ENST00000539893,;VTCN1,missense_variant,p.Arg116Gln,ENST00000369458,;VTCN1,intron_variant,,ENST00000328189,;VTCN1,non_coding_transcript_exon_variant,,ENST00000463461,;VTCN1,non_coding_transcript_exon_variant,,ENST00000488493,;	T	ENSG00000134258	ENST00000369458	Transcript	missense_variant	426	347	116	R/Q	cGg/cAg	rs767710032	.	.	-1	VTCN1	HGNC	28873	protein_coding	YES	CCDS894.1	ENSP00000358470	VTCN1_HUMAN	.	UPI00000389E3	.	tolerated(0.32)	benign(0.108)	3/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR24100:SF0,hmmpanther:PTHR24100,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCCGCAAA	byFrequency	5	ESCA
RP11-417J8.6	0	.	GRCh37	1	142620909	142620909	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.6575G>T	.	.	ENST00000610091	14/14	34	31	3	39	39	0	RP11-417J8.6,non_coding_transcript_exon_variant,,ENST00000369381,;RP11-417J8.6,non_coding_transcript_exon_variant,,ENST00000610091,;RP11-417J8.3,intron_variant,,ENST00000411746,;RP11-417J8.3,intron_variant,,ENST00000426408,;RP11-417J8.3,intron_variant,,ENST00000413650,;RP11-417J8.3,intron_variant,,ENST00000446205,;RP11-417J8.3,intron_variant,,ENST00000400755,;RP11-417J8.3,intron_variant,,ENST00000412092,;	A	ENSG00000203849	ENST00000610091	Transcript	non_coding_transcript_exon_variant	6575	.	.	.	.	.	.	.	-1	RP11-417J8.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCCCAGGTA	.	2	ESCA
TCHH	0	.	GRCh37	1	152082711	152082711	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2982G>A	p.%3D	p.E994E	ENST00000368804	2/2	67	55	12	55	55	0	TCHH,synonymous_variant,p.%3D,ENST00000368804,;	T	ENSG00000159450	ENST00000368804	Transcript	synonymous_variant	2982	2982	994	E	gaG/gaA	.	.	.	-1	TCHH	HGNC	11791	protein_coding	YES	CCDS41396.1	ENSP00000357794	TRHY_HUMAN	Q5D861_HUMAN,A2RRS3_HUMAN	UPI0000458A5E	.	.	.	2/2	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTCCTCTTC	.	5	ESCA
RAB13	0	.	GRCh37	1	153955990	153955990	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246+7A>G	.	.	ENST00000368575	.	79	64	15	82	82	0	RAB13,splice_region_variant,,ENST00000368575,;RP11-422P24.11,downstream_gene_variant,,ENST00000608236,;RAB13,splice_region_variant,,ENST00000495720,;RAB13,splice_region_variant,,ENST00000484297,;RAB13,non_coding_transcript_exon_variant,,ENST00000462680,;	C	ENSG00000143545	ENST00000368575	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	RAB13	HGNC	9762	protein_coding	YES	CCDS1058.1	ENSP00000357564	RAB13_HUMAN	Q504R6_HUMAN	UPI0000001264	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACTTCATA	.	5	ESCA
OR6K6	0	.	GRCh37	1	158725436	158725437	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837dupT	p.Gly280TrpfsTer39	p.G280Wfs*39	ENST00000368144	1/1	97	79	18	78	78	0	OR6K6,frameshift_variant,p.Gly280TrpfsTer39,ENST00000368144,;	T	ENSG00000180433	ENST00000368144	Transcript	frameshift_variant	927-928	831-832	277-278	-/X	-/T	.	.	.	1	OR6K6	HGNC	15033	protein_coding	YES	CCDS30904.1	ENSP00000357126	OR6K6_HUMAN	.	UPI000015F229	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF132,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTGCTATTTTT	.	2	ESCA
PIGC	0	.	GRCh37	1	172411232	172411232	+	Silent	SNP	T	T	C	rs756094179	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531A>G	p.%3D	p.L177L	ENST00000367728	1/1	32	21	10	29	29	0	PIGC,synonymous_variant,p.%3D,ENST00000367728,;PIGC,synonymous_variant,p.%3D,ENST00000258324,;PIGC,synonymous_variant,p.%3D,ENST00000344529,;C1orf105,intron_variant,,ENST00000367727,;C1orf105,upstream_gene_variant,,ENST00000488100,;PIGC,intron_variant,,ENST00000484368,;PIGC,downstream_gene_variant,,ENST00000478184,;	C	ENSG00000135845	ENST00000367728	Transcript	synonymous_variant	1995	531	177	L	ctA/ctG	rs756094179	.	.	-1	PIGC	HGNC	8960	protein_coding	YES	CCDS1302.1	ENSP00000356702	PIGC_HUMAN	.	UPI0000131AB1	.	.	.	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12982,Pfam_domain:PF06432,PIRSF_domain:PIRSF016104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGATAGTGT	.	5	ESCA
PRDX6	0	.	GRCh37	1	173454551	173454551	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304A>G	p.Ile102Val	p.I102V	ENST00000340385	3/5	75	45	30	72	72	0	PRDX6,missense_variant,p.Ile102Val,ENST00000340385,;PRDX6,non_coding_transcript_exon_variant,,ENST00000470017,;PRDX6,downstream_gene_variant,,ENST00000460950,;	G	ENSG00000117592	ENST00000340385	Transcript	missense_variant	436	304	102	I/V	Atc/Gtc	.	.	.	1	PRDX6	HGNC	16753	protein_coding	YES	CCDS1307.1	ENSP00000342026	PRDX6_HUMAN	.	UPI0000001C4B	.	deleterious(0.02)	benign(0.019)	3/5	.	PROSITE_profiles:PS51352,hmmpanther:PTHR10681,hmmpanther:PTHR10681:SF77,Pfam_domain:PF00578,Gene3D:3.40.30.10,PIRSF_domain:PIRSF000239,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCCATCATC	.	5	ESCA
PTPN14	0	.	GRCh37	1	214542917	214542918	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3153dupT	p.Ala1052CysfsTer25	p.A1052Cfs*25	ENST00000366956	17/19	95	78	17	67	67	0	PTPN14,frameshift_variant,p.Ala1052CysfsTer25,ENST00000366956,;PTPN14,3_prime_UTR_variant,,ENST00000543945,;PTPN14,downstream_gene_variant,,ENST00000473261,;	A	ENSG00000152104	ENST00000366956	Transcript	frameshift_variant	3348-3349	3153-3154	1051-1052	-/X	-/T	.	.	.	-1	PTPN14	HGNC	9647	protein_coding	YES	CCDS1514.1	ENSP00000355923	PTN14_HUMAN	.	UPI000013DCA6	.	.	.	17/19	.	Superfamily_domains:SSF52799,PIRSF_domain:PIRSF000934,SMART_domains:SM00194,Gene3D:3.90.190.10,Pfam_domain:PF00102,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF77,PROSITE_profiles:PS50055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTTGCATAGC	.	3	ESCA
USH2A	0	.	GRCh37	1	216258050	216258050	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5157C>T	p.%3D	p.F1719F	ENST00000307340	25/72	34	24	9	28	28	0	USH2A,synonymous_variant,p.%3D,ENST00000307340,;USH2A,synonymous_variant,p.%3D,ENST00000366943,;RP11-22M7.2,intron_variant,,ENST00000442606,;RP11-22M7.2,intron_variant,,ENST00000430890,;RP11-22M7.2,intron_variant,,ENST00000446411,;RP11-22M7.2,intron_variant,,ENST00000445619,;USH2A,non_coding_transcript_exon_variant,,ENST00000463147,;USH2A,non_coding_transcript_exon_variant,,ENST00000481786,;	A	ENSG00000042781	ENST00000307340	Transcript	synonymous_variant	5544	5157	1719	F	ttC/ttT	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	.	25/72	.	Superfamily_domains:SSF49899,Gene3D:2.60.120.200,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTAGGAACTG	.	5	ESCA
EPHB2	0	.	GRCh37	1	23191505	23191525	+	In_Frame_Del	DEL	GCCGGGGTGCCTGCACCCGCT	GCCGGGGTGCCTGCACCCGCT	-	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	GCCGGGGTGCCTGCACCCGCT	GCCGGGGTGCCTGCACCCGCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1105_1125delCGGGGTGCCTGCACCCGCTGC	p.Arg369_Cys375del	p.R369_C375del	ENST00000374632	5/16	29	16	13	36	36	0	EPHB2,inframe_deletion,p.Arg369_Cys375del,ENST00000544305,;EPHB2,inframe_deletion,p.Arg363_Cys369del,ENST00000374627,;EPHB2,inframe_deletion,p.Arg369_Cys375del,ENST00000400191,;EPHB2,inframe_deletion,p.Arg369_Cys375del,ENST00000374630,;EPHB2,inframe_deletion,p.Arg369_Cys375del,ENST00000374632,;MIR4253,upstream_gene_variant,,ENST00000581187,;EPHB2,non_coding_transcript_exon_variant,,ENST00000465676,;EPHB2,upstream_gene_variant,,ENST00000490436,;	-	ENSG00000133216	ENST00000374632	Transcript	inframe_deletion	1116-1136	1103-1123	368-375	GRGACTRC/G	gGCCGGGGTGCCTGCACCCGCTgc/ggc	.	.	.	1	EPHB2	HGNC	3393	protein_coding	YES	CCDS230.1	ENSP00000363763	EPHB2_HUMAN	.	UPI000016135C	.	.	.	5/16	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF123,Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,SMART_domains:SM00060,Superfamily_domains:SSF57184,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	GCTCGGGCCGGGGTGCCTGCACCCGCTGCGGG	.	2	ESCA
LYST	0	.	GRCh37	1	235972743	235972743	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1375G>C	p.Asp459His	p.D459H	ENST00000389794	5/53	16	13	3	25	25	0	LYST,missense_variant,p.Asp459His,ENST00000536965,;LYST,missense_variant,p.Asp459His,ENST00000389793,;LYST,missense_variant,p.Asp459His,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000489585,;LYST,non_coding_transcript_exon_variant,,ENST00000465349,;	G	ENSG00000143669	ENST00000389794	Transcript	missense_variant	1550	1375	459	D/H	Gat/Cat	.	.	.	-1	LYST	HGNC	1968	protein_coding	YES	CCDS31062.1	ENSP00000374444	LYST_HUMAN	.	UPI000020509E	.	deleterious(0.04)	possibly_damaging(0.602)	5/53	.	hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF60,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCATCTCTTA	.	2	ESCA
NID1	0	.	GRCh37	1	236187381	236187381	+	Missense_Mutation	SNP	C	C	T	rs759141799	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2117G>A	p.Arg706Gln	p.R706Q	ENST00000264187	9/20	38	20	17	24	24	0	NID1,missense_variant,p.Arg706Gln,ENST00000264187,;NID1,missense_variant,p.Arg706Gln,ENST00000366595,;	T	ENSG00000116962	ENST00000264187	Transcript	missense_variant	2200	2117	706	R/Q	cGa/cAa	rs759141799,COSM1340325	.	.	-1	NID1	HGNC	7821	protein_coding	YES	CCDS1608.1	ENSP00000264187	NID1_HUMAN	.	UPI000013D4D9	.	tolerated(0.12)	benign(0.014)	9/20	.	PROSITE_profiles:PS50026,hmmpanther:PTHR10529:SF107,hmmpanther:PTHR10529,PROSITE_patterns:PS01186,Pfam_domain:PF12947,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTCGCCCG	byFrequency	5	ESCA
TCEB3	0	.	GRCh37	1	24086135	24086135	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*72A>C	.	.	ENST00000418390	11/11	22	14	8	12	12	0	TCEB3,3_prime_UTR_variant,,ENST00000418390,;TCEB3,3_prime_UTR_variant,,ENST00000609199,;RP5-886K2.3,downstream_gene_variant,,ENST00000427796,;	C	ENSG00000011007	ENST00000418390	Transcript	3_prime_UTR_variant	2740	.	.	.	.	.	.	.	1	TCEB3	HGNC	11620	protein_coding	YES	CCDS239.2	ENSP00000395574	ELOA1_HUMAN	.	UPI000181BA17	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGAATTCTA	.	5	ESCA
SLC9A1	0	.	GRCh37	1	27432219	27432219	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1485+157G>A	.	.	ENST00000263980	.	26	22	4	26	26	0	SLC9A1,missense_variant,p.Ala548Thr,ENST00000374086,;SLC9A1,intron_variant,,ENST00000263980,;SLC9A1,intron_variant,,ENST00000545949,;SLC9A1,upstream_gene_variant,,ENST00000374089,;SLC9A1,upstream_gene_variant,,ENST00000447808,;	T	ENSG00000090020	ENST00000263980	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SLC9A1	HGNC	11071	protein_coding	YES	CCDS295.1	ENSP00000263980	SL9A1_HUMAN	B4DTZ6_HUMAN,B1ALD5_HUMAN	UPI000012FD1B	.	.	.	.	5/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGGCCCAGA	.	4	ESCA
TRNAU1AP	0	.	GRCh37	1	28897783	28897783	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000373830	7/9	50	32	17	30	30	0	TRNAU1AP,missense_variant,p.Tyr209Cys,ENST00000373830,;TRNAU1AP,non_coding_transcript_exon_variant,,ENST00000491577,;TRNAU1AP,non_coding_transcript_exon_variant,,ENST00000480930,;TRNAU1AP,non_coding_transcript_exon_variant,,ENST00000484775,;TRNAU1AP,downstream_gene_variant,,ENST00000495215,;	G	ENSG00000180098	ENST00000373830	Transcript	missense_variant	652	626	209	Y/C	tAt/tGt	.	.	.	1	TRNAU1AP	HGNC	30813	protein_coding	YES	CCDS324.1	ENSP00000362936	TSAP1_HUMAN	.	UPI00000437E6	.	deleterious(0)	probably_damaging(0.935)	7/9	.	hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF55	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTATGACC	.	5	ESCA
DPH2	0	.	GRCh37	1	44435941	44435941	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94G>A	p.Val32Met	p.V32M	ENST00000255108	1/6	23	18	5	22	22	0	DPH2,missense_variant,p.Val32Met,ENST00000396758,;DPH2,missense_variant,p.Val32Met,ENST00000255108,;DPH2,5_prime_UTR_variant,,ENST00000412950,;IPO13,downstream_gene_variant,,ENST00000372343,;IPO13,downstream_gene_variant,,ENST00000372339,;ATP6V0B,upstream_gene_variant,,ENST00000236067,;ATP6V0B,upstream_gene_variant,,ENST00000472505,;ATP6V0B,upstream_gene_variant,,ENST00000532642,;DPH2,upstream_gene_variant,,ENST00000459879,;ATP6V0B,upstream_gene_variant,,ENST00000471859,;ATP6V0B,upstream_gene_variant,,ENST00000472174,;DPH2,splice_region_variant,,ENST00000477294,;DPH2,non_coding_transcript_exon_variant,,ENST00000471934,;DPH2,non_coding_transcript_exon_variant,,ENST00000529729,;IPO13,downstream_gene_variant,,ENST00000486876,;ATP6V0B,upstream_gene_variant,,ENST00000472277,;DPH2,missense_variant,p.Val32Met,ENST00000532140,;DPH2,missense_variant,p.Val32Met,ENST00000492306,;DPH2,missense_variant,p.Val32Met,ENST00000524776,;DPH2,missense_variant,p.Val32Met,ENST00000476260,;DPH2,missense_variant,p.Val32Met,ENST00000495421,;DPH2,splice_region_variant,,ENST00000530988,;DPH2,non_coding_transcript_exon_variant,,ENST00000490861,;DPH2,non_coding_transcript_exon_variant,,ENST00000534786,;DPH2,non_coding_transcript_exon_variant,,ENST00000527567,;ATP6V0B,upstream_gene_variant,,ENST00000461670,;ATP6V0B,upstream_gene_variant,,ENST00000473485,;ATP6V0B,upstream_gene_variant,,ENST00000498208,;DPH2,upstream_gene_variant,,ENST00000534655,;ATP6V0B,upstream_gene_variant,,ENST00000496131,;DPH2,upstream_gene_variant,,ENST00000527319,;ATP6V0B,upstream_gene_variant,,ENST00000468183,;	A	ENSG00000132768	ENST00000255108	Transcript	missense_variant	266	94	32	V/M	Gtg/Atg	.	.	.	1	DPH2	HGNC	3004	protein_coding	YES	CCDS504.1	ENSP00000255108	DPH2_HUMAN	B3KRB8_HUMAN	UPI0000070CCB	.	tolerated(0.09)	benign(0.01)	1/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10762,hmmpanther:PTHR10762:SF2,TIGRFAM_domain:TIGR00272	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGGAGTGTAC	.	2	ESCA
JAK1	0	.	GRCh37	1	65349067	65349067	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98A>T	p.Glu33Val	p.E33V	ENST00000342505	3/25	52	43	8	29	29	0	JAK1,missense_variant,p.Glu33Val,ENST00000342505,;JAK1,upstream_gene_variant,,ENST00000467764,;	A	ENSG00000162434	ENST00000342505	Transcript	missense_variant	347	98	33	E/V	gAg/gTg	.	.	.	-1	JAK1	HGNC	6190	protein_coding	YES	CCDS41346.1	ENSP00000343204	JAK1_HUMAN	.	UPI0000054C7D	.	tolerated(0.29)	benign(0.013)	3/25	.	hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF67,SMART_domains:SM00295,PIRSF_domain:PIRSF000636	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGCTCAGGG	.	5	ESCA
ZNF326	0	.	GRCh37	1	90493112	90493112	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1601A>G	p.Asn534Ser	p.N534S	ENST00000340281	12/12	31	20	11	28	28	0	ZNF326,missense_variant,p.Asn328Ser,ENST00000455342,;ZNF326,missense_variant,p.Asn445Ser,ENST00000370447,;ZNF326,missense_variant,p.Asn534Ser,ENST00000340281,;ZNF326,3_prime_UTR_variant,,ENST00000394583,;	G	ENSG00000162664	ENST00000340281	Transcript	missense_variant	1744	1601	534	N/S	aAt/aGt	.	.	.	1	ZNF326	HGNC	14104	protein_coding	YES	CCDS727.1	ENSP00000340796	ZN326_HUMAN	.	UPI0000160AB2	.	tolerated_low_confidence(0.5)	unknown(0)	12/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12190:SF1,hmmpanther:PTHR12190	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAAATATAC	.	5	ESCA
CCDC18	0	.	GRCh37	1	93648967	93648967	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210A>G	p.Ser71Gly	p.S71G	ENST00000370276	2/29	25	20	5	22	22	0	CCDC18,missense_variant,p.Ser135Gly,ENST00000557479,;CCDC18,missense_variant,p.Ser17Gly,ENST00000401026,;CCDC18,missense_variant,p.Ser17Gly,ENST00000343253,;CCDC18,missense_variant,p.Ser71Gly,ENST00000370276,;CCDC18,missense_variant,p.Ser64Gly,ENST00000448243,;CCDC18,5_prime_UTR_variant,,ENST00000334652,;CCDC18,5_prime_UTR_variant,,ENST00000338949,;TMED5,upstream_gene_variant,,ENST00000370280,;TMED5,upstream_gene_variant,,ENST00000479918,;TMED5,upstream_gene_variant,,ENST00000370282,;CCDC18,non_coding_transcript_exon_variant,,ENST00000528942,;CCDC18,missense_variant,p.Ser56Gly,ENST00000481180,;CCDC18,missense_variant,p.Ser49Gly,ENST00000479653,;TMED5,upstream_gene_variant,,ENST00000370290,;	G	ENSG00000122483	ENST00000370276	Transcript	missense_variant	210	211	71	S/G	Agt/Ggt	.	.	.	1	CCDC18	HGNC	30370	protein_coding	YES	.	ENSP00000359299	.	.	UPI0001F78148	.	tolerated(0.3)	benign(0.281)	2/29	.	hmmpanther:PTHR18875:SF4,hmmpanther:PTHR18875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L136F|c.408G>T|3	MUTECT|MUSE	AGGAAAGTTTG	.	2	ESCA
JAG1	0	.	GRCh37	20	10618607	10618607	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1539C>T	.	.	ENST00000254958	26/26	25	17	7	22	22	0	JAG1,3_prime_UTR_variant,,ENST00000423891,;JAG1,3_prime_UTR_variant,,ENST00000254958,;SLX4IP,downstream_gene_variant,,ENST00000488816,;	A	ENSG00000101384	ENST00000254958	Transcript	3_prime_UTR_variant	5712	.	.	.	.	.	.	.	-1	JAG1	HGNC	6188	protein_coding	YES	CCDS13112.1	ENSP00000254958	JAG1_HUMAN	B7U6M8_HUMAN,B4DYR1_HUMAN	UPI00000498B5	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGAGGCC	.	5	ESCA
UBE2V1	0	.	GRCh37	20	48698866	48698866	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*439G>A	.	.	ENST00000340309	4/4	44	34	10	28	28	0	UBE2V1,3_prime_UTR_variant,,ENST00000371657,;UBE2V1,3_prime_UTR_variant,,ENST00000415862,;UBE2V1,3_prime_UTR_variant,,ENST00000371677,;TMEM189-UBE2V1,3_prime_UTR_variant,,ENST00000341698,;UBE2V1,3_prime_UTR_variant,,ENST00000340309,;TMEM189,3_prime_UTR_variant,,ENST00000557021,;UBE2V1,3_prime_UTR_variant,,ENST00000371674,;UBE2V1,3_prime_UTR_variant,,ENST00000420027,;UBE2V1,non_coding_transcript_exon_variant,,ENST00000396059,;UBE2V1,downstream_gene_variant,,ENST00000486653,;UBE2V1,downstream_gene_variant,,ENST00000472923,;UBE2V1,downstream_gene_variant,,ENST00000492371,;UBE2V1,downstream_gene_variant,,ENST00000432266,;UBE2V1,downstream_gene_variant,,ENST00000483534,;UBE2V1,downstream_gene_variant,,ENST00000493090,;UBE2V1,downstream_gene_variant,,ENST00000490555,;UBE2V1,downstream_gene_variant,,ENST00000467839,;	T	ENSG00000244687	ENST00000340309	Transcript	3_prime_UTR_variant	1331	.	.	.	.	.	.	.	-1	UBE2V1	HGNC	12494	protein_coding	YES	CCDS13426.1	ENSP00000340305	UB2V1_HUMAN	.	UPI000006CD68	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTAACAAGCC	.	5	ESCA
SYCP2	0	.	GRCh37	20	58495530	58495530	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181G>A	p.Glu61Lys	p.E61K	ENST00000357552	5/45	39	20	18	27	27	0	SYCP2,missense_variant,p.Glu61Lys,ENST00000446834,;SYCP2,missense_variant,p.Glu61Lys,ENST00000357552,;SYCP2,missense_variant,p.Glu61Lys,ENST00000371001,;SYCP2,missense_variant,p.Glu60Lys,ENST00000425931,;SYCP2,non_coding_transcript_exon_variant,,ENST00000476314,;SYCP2,upstream_gene_variant,,ENST00000471331,;	T	ENSG00000196074	ENST00000357552	Transcript	missense_variant	407	181	61	E/K	Gag/Aag	.	.	.	-1	SYCP2	HGNC	11490	protein_coding	YES	CCDS13482.1	ENSP00000350162	SYCP2_HUMAN	A2A341_HUMAN	UPI0000135683	.	tolerated(1)	benign(0)	5/45	.	hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCTTTAT	.	5	ESCA
SLC2A4RG	0	.	GRCh37	20	62374233	62374233	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1054A>T	p.Lys352Ter	p.K352*	ENST00000266077	8/8	41	34	7	24	24	0	SLC2A4RG,stop_gained,p.Lys352Ter,ENST00000266077,;ZBTB46,downstream_gene_variant,,ENST00000395104,;RP4-583P15.14,downstream_gene_variant,,ENST00000467211,;LIME1,downstream_gene_variant,,ENST00000493265,;ZBTB46,downstream_gene_variant,,ENST00000245663,;LIME1,downstream_gene_variant,,ENST00000309546,;ZBTB46,downstream_gene_variant,,ENST00000302995,;LIME1,downstream_gene_variant,,ENST00000444951,;RP4-583P15.10,upstream_gene_variant,,ENST00000433905,;RP4-583P15.10,upstream_gene_variant,,ENST00000447343,;SLC2A4RG,splice_region_variant,,ENST00000473157,;SLC2A4RG,splice_region_variant,,ENST00000493772,;SLC2A4RG,splice_region_variant,,ENST00000496425,;LIME1,downstream_gene_variant,,ENST00000490824,;SLC2A4RG,downstream_gene_variant,,ENST00000482718,;SLC2A4RG,downstream_gene_variant,,ENST00000485897,;LIME1,downstream_gene_variant,,ENST00000476183,;SLC2A4RG,downstream_gene_variant,,ENST00000491109,;LIME1,downstream_gene_variant,,ENST00000496820,;LIME1,downstream_gene_variant,,ENST00000465591,;RP4-583P15.14,downstream_gene_variant,,ENST00000476221,;LIME1,downstream_gene_variant,,ENST00000487026,;SLC2A4RG,downstream_gene_variant,,ENST00000474248,;LIME1,downstream_gene_variant,,ENST00000489212,;LIME1,downstream_gene_variant,,ENST00000480139,;LIME1,downstream_gene_variant,,ENST00000494776,;RP4-583P15.15,downstream_gene_variant,,ENST00000490623,;	T	ENSG00000125520	ENST00000266077	Transcript	stop_gained	1106	1054	352	K/*	Aag/Tag	.	.	.	1	SLC2A4RG	HGNC	15930	protein_coding	YES	CCDS13537.1	ENSP00000266077	S2A4R_HUMAN	Q2PHL5_HUMAN	UPI000013D6CE	.	.	.	8/8	.	hmmpanther:PTHR13006,hmmpanther:PTHR13006:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGAAGCCC	.	5	ESCA
SYNJ1	0	.	GRCh37	21	34038867	34038867	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1945C>T	p.Leu649Phe	p.L649F	ENST00000433931	16/32	28	13	14	29	29	0	SYNJ1,missense_variant,p.Leu649Phe,ENST00000382499,;SYNJ1,missense_variant,p.Leu605Phe,ENST00000429236,;SYNJ1,missense_variant,p.Leu605Phe,ENST00000382491,;SYNJ1,missense_variant,p.Leu610Phe,ENST00000322229,;SYNJ1,missense_variant,p.Leu649Phe,ENST00000433931,;SYNJ1,missense_variant,p.Leu610Phe,ENST00000357345,;	A	ENSG00000159082	ENST00000433931	Transcript	missense_variant	1953	1945	649	L/F	Ctc/Ttc	.	.	.	-1	SYNJ1	HGNC	11503	protein_coding	YES	CCDS33539.2	ENSP00000409667	.	J3KQV8_HUMAN,C9J1Z6_HUMAN	UPI0001A47572	.	deleterious(0.01)	probably_damaging(0.994)	16/32	.	Superfamily_domains:SSF56219,SMART_domains:SM00128,Gene3D:3.60.10.10,Pfam_domain:PF03372,hmmpanther:PTHR11200:SF126,hmmpanther:PTHR11200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGAGCTTCT	.	5	ESCA
SLC5A3	0	.	GRCh37	21	35477726	35477726	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8072C>A	.	.	ENST00000608209	2/2	30	21	8	43	43	0	SLC5A3,3_prime_UTR_variant,,ENST00000608209,;SLC5A3,3_prime_UTR_variant,,ENST00000381151,;MRPS6,intron_variant,,ENST00000399312,;MRPS6,intron_variant,,ENST00000477091,;MRPS6,intron_variant,,ENST00000488492,;AP000320.7,intron_variant,,ENST00000362077,;	A	ENSG00000272962	ENST00000608209	Transcript	3_prime_UTR_variant	10741	.	.	.	.	.	.	.	1	SLC5A3	Uniprot_gn	11038	protein_coding	YES	CCDS33549.1	ENSP00000477068	.	.	UPI00001359F3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTCATTTA	.	5	ESCA
PCBP3	0	.	GRCh37	21	47250070	47250070	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-125-19805C>T	.	.	ENST00000400314	.	25	19	6	26	26	0	PCBP3,intron_variant,,ENST00000400314,;AL592528.1,non_coding_transcript_exon_variant,,ENST00000380008,;	T	ENSG00000183570	ENST00000400314	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PCBP3	HGNC	8651	protein_coding	YES	CCDS42974.2	ENSP00000383168	PCBP3_HUMAN	.	UPI00005989D5	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAACCCTAGA	.	5	ESCA
CRKL	0	.	GRCh37	22	21272499	21272499	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277C>T	p.%3D	p.L93L	ENST00000354336	1/3	14	10	4	13	13	0	CRKL,synonymous_variant,p.%3D,ENST00000354336,;CRKL,synonymous_variant,p.%3D,ENST00000411769,;	T	ENSG00000099942	ENST00000354336	Transcript	synonymous_variant	786	277	93	L	Ctg/Ttg	.	.	.	1	CRKL	HGNC	2363	protein_coding	YES	CCDS13785.1	ENSP00000346300	CRKL_HUMAN	.	UPI000000DA57	.	.	.	1/3	.	PROSITE_profiles:PS50001,hmmpanther:PTHR19969,hmmpanther:PTHR19969:SF9,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTACCTGGAC	.	5	ESCA
PRAME	0	.	GRCh37	22	22899288	22899288	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-36G>A	.	.	ENST00000543184	2/5	29	24	5	16	16	0	PRAME,5_prime_UTR_variant,,ENST00000398743,;PRAME,5_prime_UTR_variant,,ENST00000420709,;PRAME,5_prime_UTR_variant,,ENST00000406503,;PRAME,5_prime_UTR_variant,,ENST00000398741,;PRAME,5_prime_UTR_variant,,ENST00000402697,;PRAME,5_prime_UTR_variant,,ENST00000439106,;PRAME,5_prime_UTR_variant,,ENST00000403441,;PRAME,5_prime_UTR_variant,,ENST00000543184,;PRAME,5_prime_UTR_variant,,ENST00000405655,;PRAME,upstream_gene_variant,,ENST00000438888,;PRAME,upstream_gene_variant,,ENST00000539862,;PRAME,upstream_gene_variant,,ENST00000424204,;LL22NC03-63E9.3,upstream_gene_variant,,ENST00000407120,;PRAME,intron_variant,,ENST00000476336,;PRAME,upstream_gene_variant,,ENST00000485532,;PRAME,5_prime_UTR_variant,,ENST00000442481,;PRAME,non_coding_transcript_exon_variant,,ENST00000492657,;	T	ENSG00000185686	ENST00000543184	Transcript	5_prime_UTR_variant	828	.	.	.	.	.	.	.	-1	PRAME	HGNC	9336	protein_coding	YES	CCDS13801.1	ENSP00000445675	PRAME_HUMAN	F5H4B1_HUMAN,E7EW99_HUMAN,E7EMH2_HUMAN,B7Z986_HUMAN,B5MD04_HUMAN,B5MCY4_HUMAN	UPI0000000DDA	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAACGCTTG	.	2	ESCA
SLC35E4	0	.	GRCh37	22	31042745	31042745	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.780C>T	p.%3D	p.L260L	ENST00000343605	2/2	61	43	17	66	66	0	SLC35E4,synonymous_variant,p.%3D,ENST00000343605,;SLC35E4,intron_variant,,ENST00000451479,;SLC35E4,intron_variant,,ENST00000300385,;SLC35E4,intron_variant,,ENST00000406566,;	T	ENSG00000100036	ENST00000343605	Transcript	synonymous_variant	1579	780	260	L	ctC/ctT	.	.	.	1	SLC35E4	HGNC	17058	protein_coding	YES	CCDS13882.1	ENSP00000339626	S35E4_HUMAN	.	UPI0000198650	.	.	.	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11132:SF41,hmmpanther:PTHR11132,Pfam_domain:PF03151,Superfamily_domains:0043518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCAGCTG	.	5	ESCA
XPNPEP3	0	.	GRCh37	22	41277988	41277988	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396C>A	p.Ser132Arg	p.S132R	ENST00000357137	3/10	59	54	4	39	39	0	XPNPEP3,missense_variant,p.Ser132Arg,ENST00000357137,;XPNPEP3,missense_variant,p.Ser132Arg,ENST00000414396,;XPNPEP3,missense_variant,p.Ser109Arg,ENST00000544094,;XPNPEP3,missense_variant,p.Ser132Arg,ENST00000541156,;XPNPEP3,downstream_gene_variant,,ENST00000465258,;XPNPEP3,3_prime_UTR_variant,,ENST00000428799,;	A	ENSG00000196236	ENST00000357137	Transcript	missense_variant	480	396	132	S/R	agC/agA	.	.	.	1	XPNPEP3	HGNC	28052	protein_coding	YES	CCDS14007.1	ENSP00000349658	XPP3_HUMAN	B7ZBB4_HUMAN	UPI00000401E0	.	deleterious(0)	probably_damaging(0.996)	3/10	.	hmmpanther:PTHR10804,Gene3D:3.40.350.10,Pfam_domain:PF05195,SMART_domains:SM01011,Superfamily_domains:SSF53092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAGCATTCT	.	2	ESCA
RANBP2	0	.	GRCh37	2	109347782	109347782	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257C>T	p.Ser86Leu	p.S86L	ENST00000283195	4/29	249	214	35	193	193	0	RANBP2,missense_variant,p.Ser86Leu,ENST00000283195,;RANBP2,stop_gained,p.Gln49Ter,ENST00000425282,;RANBP2,non_coding_transcript_exon_variant,,ENST00000495924,;	T	ENSG00000153201	ENST00000283195	Transcript	missense_variant	383	257	86	S/L	tCa/tTa	.	.	.	1	RANBP2	HGNC	9848	protein_coding	YES	CCDS2079.1	ENSP00000283195	RBP2_HUMAN	I1Z9D1_HUMAN	UPI0000207FB9	.	deleterious(0)	benign(0.011)	4/29	.	PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF8,Pfam_domain:PF00515,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGTTCAGTGG	.	4	ESCA
LYPD6	0	.	GRCh37	2	150329680	150329680	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2316T>A	.	.	ENST00000334166	5/5	16	12	4	16	16	0	LYPD6,3_prime_UTR_variant,,ENST00000409381,;LYPD6,3_prime_UTR_variant,,ENST00000334166,;LYPD6,downstream_gene_variant,,ENST00000392854,;LYPD6,downstream_gene_variant,,ENST00000418762,;	A	ENSG00000187123	ENST00000334166	Transcript	3_prime_UTR_variant	3089	.	.	.	.	.	.	.	1	LYPD6	HGNC	28751	protein_coding	YES	CCDS2188.1	ENSP00000334463	LYPD6_HUMAN	C9IYE7_HUMAN	UPI000000DB99	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAATAAGAA	.	5	ESCA
NRP2	0	.	GRCh37	2	206628610	206628610	+	Nonsense_Mutation	SNP	G	G	T	rs753078349	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2257G>T	p.Glu753Ter	p.E753*	ENST00000360409	13/17	38	31	7	41	41	0	NRP2,stop_gained,p.Glu753Ter,ENST00000360409,;NRP2,stop_gained,p.Glu753Ter,ENST00000357118,;NRP2,stop_gained,p.Glu753Ter,ENST00000540178,;NRP2,stop_gained,p.Glu753Ter,ENST00000357785,;NRP2,stop_gained,p.Glu753Ter,ENST00000540841,;NRP2,stop_gained,p.Glu753Ter,ENST00000412873,;NRP2,stop_gained,p.Glu753Ter,ENST00000272849,;AC007362.3,non_coding_transcript_exon_variant,,ENST00000598710,;AC007362.3,non_coding_transcript_exon_variant,,ENST00000596616,;AC007362.3,non_coding_transcript_exon_variant,,ENST00000423425,;NRP2,non_coding_transcript_exon_variant,,ENST00000485684,;NRP2,upstream_gene_variant,,ENST00000467850,;NRP2,non_coding_transcript_exon_variant,,ENST00000472299,;NRP2,downstream_gene_variant,,ENST00000468256,;NRP2,downstream_gene_variant,,ENST00000460987,;	T	ENSG00000118257	ENST00000360409	Transcript	stop_gained	3048	2257	753	E/*	Gag/Tag	rs753078349	.	.	1	NRP2	HGNC	8005	protein_coding	YES	CCDS2364.1	ENSP00000353582	NRP2_HUMAN	C9JH98_HUMAN	UPI000014020F	.	.	.	13/17	.	PROSITE_profiles:PS50060,Pfam_domain:PF00629,PIRSF_domain:PIRSF036960,SMART_domains:SM00137,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGCGAGTGG	.	5	ESCA
NYAP2	0	.	GRCh37	2	226447051	226447051	+	Silent	SNP	C	C	T	rs533815234	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.918C>T	p.%3D	p.F306F	ENST00000272907	4/6	24	17	6	12	12	0	NYAP2,synonymous_variant,p.%3D,ENST00000272907,;NYAP2,intron_variant,,ENST00000409269,;	T	ENSG00000144460	ENST00000272907	Transcript	synonymous_variant	1331	918	306	F	ttC/ttT	rs533815234,COSM3578339	.	.	1	NYAP2	HGNC	29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	NYAP2_HUMAN	.	UPI00001C1DB6	.	.	.	4/6	.	Pfam_domain:PF15439,hmmpanther:PTHR22633	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCGCCAA	by1000G	5	ESCA
KIF1A	0	.	GRCh37	2	241722519	241722519	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806C>T	p.Ala269Val	p.A269V	ENST00000498729	9/50	91	64	27	90	90	0	KIF1A,missense_variant,p.Ala77Val,ENST00000428768,;KIF1A,missense_variant,p.Ala269Val,ENST00000498729,;KIF1A,missense_variant,p.Ala269Val,ENST00000320389,;KIF1A,missense_variant,p.Ala269Val,ENST00000404283,;	A	ENSG00000130294	ENST00000498729	Transcript	missense_variant	1053	806	269	A/V	gCc/gTc	.	.	.	-1	KIF1A	HGNC	888	protein_coding	YES	CCDS58757.1	ENSP00000438388	KIF1A_HUMAN	G1UI30_HUMAN,C9JBH1_HUMAN	UPI0002065B81	.	deleterious(0)	benign(0.415)	9/50	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF361,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTGGCCCCC	.	5	ESCA
CEBPZ-AS1	0	.	GRCh37	2	37429056	37429056	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*54delA	.	.	ENST00000402297	5/5	17	11	6	14	14	0	CEBPZ-AS1,3_prime_UTR_variant,,ENST00000402297,;CEBPZ-AS1,3_prime_UTR_variant,,ENST00000397226,;CEBPZ-AS1,intron_variant,,ENST00000397064,;CEBPZ-AS1,intron_variant,,ENST00000392061,;CEBPZ,intron_variant,,ENST00000234170,;CEBPZ-AS1,intron_variant,,ENST00000406711,;CEBPZ,intron_variant,,ENST00000489306,;CEBPZ-AS1,downstream_gene_variant,,ENST00000470216,;	-	ENSG00000218739	ENST00000402297	Transcript	3_prime_UTR_variant	330	.	.	.	.	.	.	.	1	CEBPZ-AS1	HGNC	49288	protein_coding	YES	.	ENSP00000384331	.	A8MTT3_HUMAN	UPI000015D72B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGAGAGAAGAAG	.	2	ESCA
CDKL4	0	.	GRCh37	2	39417577	39417577	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.521G>A	p.Gly174Glu	p.G174E	ENST00000378803	5/8	52	37	14	23	23	0	CDKL4,missense_variant,p.Gly174Glu,ENST00000395035,;CDKL4,missense_variant,p.Gly174Glu,ENST00000378803,;CDKL4,upstream_gene_variant,,ENST00000451199,;	T	ENSG00000205111	ENST00000378803	Transcript	missense_variant	521	521	174	G/E	gGa/gAa	.	.	.	-1	CDKL4	HGNC	19287	protein_coding	YES	CCDS33184.1	ENSP00000368080	CDKL4_HUMAN	.	UPI00000398E1	.	deleterious(0)	probably_damaging(0.998)	5/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF120,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCTCCCACA	.	5	ESCA
KIDINS220	0	.	GRCh37	2	8919884	8919884	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2290C>T	p.Gln764Ter	p.Q764*	ENST00000256707	18/30	75	54	20	40	40	0	KIDINS220,stop_gained,p.Gln764Ter,ENST00000427284,;KIDINS220,stop_gained,p.Gln765Ter,ENST00000489024,;KIDINS220,stop_gained,p.Gln722Ter,ENST00000418530,;KIDINS220,stop_gained,p.Gln764Ter,ENST00000256707,;KIDINS220,stop_gained,p.Gln764Ter,ENST00000473731,;KIDINS220,stop_gained,p.Gln511Ter,ENST00000496383,;KIDINS220,stop_gained,p.Gln765Ter,ENST00000319688,;KIDINS220,3_prime_UTR_variant,,ENST00000488729,;	A	ENSG00000134313	ENST00000256707	Transcript	stop_gained	2472	2290	764	Q/*	Cag/Tag	COSM576271	.	.	-1	KIDINS220	HGNC	29508	protein_coding	YES	CCDS42650.1	ENSP00000256707	KDIS_HUMAN	F8WAY8_HUMAN	UPI0000208E08	.	.	.	18/30	.	hmmpanther:PTHR24116,hmmpanther:PTHR24116:SF5,Pfam_domain:PF07693	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTGAGTGA	.	5	ESCA
CNGA3	0	.	GRCh37	2	98994176	98994176	+	Missense_Mutation	SNP	C	C	T	rs367575427	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128C>T	p.Ser43Leu	p.S43L	ENST00000393504	3/8	21	17	4	22	22	0	CNGA3,missense_variant,p.Ser43Leu,ENST00000436404,;CNGA3,missense_variant,p.Ser43Leu,ENST00000393504,;CNGA3,missense_variant,p.Ser43Leu,ENST00000272602,;CNGA3,5_prime_UTR_variant,,ENST00000409937,;CNGA3,upstream_gene_variant,,ENST00000393503,;	T	ENSG00000144191	ENST00000393504	Transcript	missense_variant	545	128	43	S/L	tCg/tTg	rs367575427	.	.	1	CNGA3	HGNC	2150	protein_coding	YES	CCDS2034.1	ENSP00000377140	CNGA3_HUMAN	.	UPI000004717B	.	tolerated_low_confidence(0.08)	benign(0.004)	3/8	.	Low_complexity_(Seg):seg	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACATCGTCAG	byCluster|by1000G	4	ESCA
SENP7	0	.	GRCh37	3	101085489	101085489	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1103T>C	p.Leu368Pro	p.L368P	ENST00000394095	9/24	53	36	17	64	64	0	SENP7,missense_variant,p.Leu204Pro,ENST00000394091,;SENP7,missense_variant,p.Leu302Pro,ENST00000314261,;SENP7,missense_variant,p.Leu368Pro,ENST00000394095,;SENP7,missense_variant,p.Leu335Pro,ENST00000348610,;SENP7,missense_variant,p.Leu204Pro,ENST00000358203,;SENP7,missense_variant,p.Leu303Pro,ENST00000394094,;	G	ENSG00000138468	ENST00000394095	Transcript	missense_variant	1157	1103	368	L/P	cTa/cCa	.	.	.	-1	SENP7	HGNC	30402	protein_coding	YES	CCDS2941.2	ENSP00000377655	SENP7_HUMAN	.	UPI0000E56ED1	.	tolerated(0.37)	benign(0.005)	9/24	.	hmmpanther:PTHR12438,hmmpanther:PTHR12438:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATAGTTTA	.	5	ESCA
KPNA1	0	.	GRCh37	3	122143603	122143603	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2229A>G	.	.	ENST00000344337	14/14	22	16	6	27	27	0	KPNA1,3_prime_UTR_variant,,ENST00000344337,;RP11-299J3.8,intron_variant,,ENST00000608756,;RP11-299J3.8,intron_variant,,ENST00000608015,;RP11-299J3.8,intron_variant,,ENST00000609469,;RP11-299J3.8,intron_variant,,ENST00000608346,;RP11-299J3.8,downstream_gene_variant,,ENST00000608465,;KPNA1,downstream_gene_variant,,ENST00000470904,;KPNA1,downstream_gene_variant,,ENST00000466923,;KPNA1,downstream_gene_variant,,ENST00000494339,;KPNA1,downstream_gene_variant,,ENST00000485027,;	C	ENSG00000114030	ENST00000344337	Transcript	3_prime_UTR_variant	4023	.	.	.	.	.	.	.	-1	KPNA1	HGNC	6394	protein_coding	YES	CCDS3013.1	ENSP00000343701	IMA5_HUMAN	C9JYI4_HUMAN,C9JWD9_HUMAN,C9J4U1_HUMAN,B3KXZ2_HUMAN	UPI000013D524	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAATTTAAA	.	5	ESCA
COPG1	0	.	GRCh37	3	128984416	128984416	+	Missense_Mutation	SNP	A	A	G	rs762084251	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1249A>G	p.Ile417Val	p.I417V	ENST00000314797	14/24	35	27	8	23	23	0	COPG1,missense_variant,p.Ile417Val,ENST00000314797,;COPG1,upstream_gene_variant,,ENST00000509889,;COPG1,non_coding_transcript_exon_variant,,ENST00000513410,;COPG1,non_coding_transcript_exon_variant,,ENST00000504547,;COPG1,non_coding_transcript_exon_variant,,ENST00000515725,;	G	ENSG00000181789	ENST00000314797	Transcript	missense_variant	1353	1249	417	I/V	Atc/Gtc	rs762084251	.	.	1	COPG1	HGNC	2236	protein_coding	YES	CCDS33851.1	ENSP00000325002	COPG1_HUMAN	Q8WUI6_HUMAN	UPI000000095F	.	tolerated(0.36)	possibly_damaging(0.646)	14/24	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF037093,Pfam_domain:PF01602,Gene3D:1.25.10.10,hmmpanther:PTHR10261,hmmpanther:PTHR10261:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCTATCGTG	byFrequency	5	ESCA
CLDN18	0	.	GRCh37	3	137729265	137729265	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198T>A	p.Tyr66Ter	p.Y66*	ENST00000183605	1/5	56	33	23	50	50	0	CLDN18,stop_gained,p.Tyr66Ter,ENST00000183605,;CLDN18,intron_variant,,ENST00000343735,;CLDN18,stop_gained,p.Tyr66Ter,ENST00000479660,;	A	ENSG00000066405	ENST00000183605	Transcript	stop_gained	424	198	66	Y/*	taT/taA	.	.	.	1	CLDN18	HGNC	2039	protein_coding	YES	CCDS3095.1	ENSP00000183605	CLD18_HUMAN	.	UPI00000389FC	.	.	.	1/5	.	hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF9,Pfam_domain:PF00822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTATTTCAC	.	5	ESCA
LEKR1	0	.	GRCh37	3	156763371	156763371	+	Frame_Shift_Del	DEL	C	C	-	rs144318565	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1911delC	p.Val639CysfsTer58	p.V639Cfs*58	ENST00000356539	13/13	45	34	11	30	30	0	LEKR1,frameshift_variant,p.Val639CysfsTer58,ENST00000356539,;LEKR1,frameshift_variant,p.Val335CysfsTer58,ENST00000470811,;	-	ENSG00000197980	ENST00000356539	Transcript	frameshift_variant	2025	1911	637	R/X	cgC/cg	rs144318565,COSM3005323,COSM3005324	.	.	1	LEKR1	HGNC	33765	protein_coding	.	.	ENSP00000348936	.	J3KP02_HUMAN	UPI0001BB2D45	.	.	.	13/13	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTGCGCGGGGT	byCluster	3	ESCA
WDR49	0	.	GRCh37	3	167320050	167320050	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117T>A	p.%3D	p.I39I	ENST00000308378	3/15	52	44	8	30	30	0	WDR49,synonymous_variant,p.%3D,ENST00000472600,;WDR49,synonymous_variant,p.%3D,ENST00000453925,;WDR49,synonymous_variant,p.%3D,ENST00000308378,;WDR49,synonymous_variant,p.%3D,ENST00000479765,;WDR49,intron_variant,,ENST00000466760,;WDR49,3_prime_UTR_variant,,ENST00000460448,;	T	ENSG00000174776	ENST00000308378	Transcript	synonymous_variant	423	117	39	I	atT/atA	.	.	.	-1	WDR49	HGNC	26587	protein_coding	YES	CCDS3201.1	ENSP00000311343	WDR49_HUMAN	.	UPI00000746AD	.	.	.	3/15	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR22844:SF132,hmmpanther:PTHR22844,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTTAATGCC	.	4	ESCA
NCEH1	0	.	GRCh37	3	172351286	172351286	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1326G>A	p.%3D	p.K442K	ENST00000538775	5/5	176	133	43	136	136	0	NCEH1,synonymous_variant,p.%3D,ENST00000543711,;NCEH1,synonymous_variant,p.%3D,ENST00000538775,;NCEH1,synonymous_variant,p.%3D,ENST00000475381,;NCEH1,synonymous_variant,p.%3D,ENST00000273512,;NCEH1,downstream_gene_variant,,ENST00000424772,;NCEH1,downstream_gene_variant,,ENST00000470419,;NCEH1,downstream_gene_variant,,ENST00000421723,;	T	ENSG00000144959	ENST00000538775	Transcript	synonymous_variant	1464	1326	442	K	aaG/aaA	.	.	.	-1	NCEH1	HGNC	29260	protein_coding	YES	CCDS54682.1	ENSP00000442464	.	F5H7K4_HUMAN	UPI000199A4B7	.	.	.	5/5	.	Superfamily_domains:SSF53474,PIRSF_domain:PIRSF037251,Gene3D:3.40.50.1820,hmmpanther:PTHR23024:SF108,hmmpanther:PTHR23024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCACTTGAT	.	5	ESCA
SOX2	0	.	GRCh37	3	181431472	181431472	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*370A>G	.	.	ENST00000325404	1/1	35	31	4	39	39	0	SOX2,3_prime_UTR_variant,,ENST00000325404,;SOX2,downstream_gene_variant,,ENST00000431565,;SOX2-OT,intron_variant,,ENST00000498731,;SOX2-OT,intron_variant,,ENST00000595287,;SOX2-OT,intron_variant,,ENST00000593549,;SOX2-OT,intron_variant,,ENST00000597828,;SOX2-OT,intron_variant,,ENST00000493521,;SOX2-OT,intron_variant,,ENST00000593330,;SOX2-OT,intron_variant,,ENST00000477928,;SOX2-OT,intron_variant,,ENST00000600778,;SOX2-OT,intron_variant,,ENST00000596250,;SOX2-OT,intron_variant,,ENST00000600386,;SOX2-OT,intron_variant,,ENST00000598474,;SOX2-OT,intron_variant,,ENST00000476964,;SOX2-OT,intron_variant,,ENST00000492337,;SOX2-OT,intron_variant,,ENST00000466034,;SOX2-OT,intron_variant,,ENST00000491282,;SOX2-OT,intron_variant,,ENST00000498226,;SOX2-OT,intron_variant,,ENST00000599082,;SOX2-OT,intron_variant,,ENST00000469278,;SOX2-OT,intron_variant,,ENST00000600801,;SOX2-OT,intron_variant,,ENST00000597651,;SOX2-OT,downstream_gene_variant,,ENST00000600962,;SOX2-OT,downstream_gene_variant,,ENST00000476125,;	G	ENSG00000181449	ENST00000325404	Transcript	3_prime_UTR_variant	1751	.	.	.	.	.	.	.	1	SOX2	HGNC	11195	protein_coding	YES	CCDS3239.1	ENSP00000323588	SOX2_HUMAN	.	UPI000003F545	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGTACGGTA	.	2	ESCA
ETV5	0	.	GRCh37	3	185766490	185766490	+	Missense_Mutation	SNP	C	C	T	rs773704999	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1471G>A	p.Ala491Thr	p.A491T	ENST00000306376	13/13	66	40	25	52	52	0	ETV5,missense_variant,p.Ala533Thr,ENST00000537818,;ETV5,missense_variant,p.Ala491Thr,ENST00000306376,;ETV5,missense_variant,p.Ala491Thr,ENST00000434744,;ETV5,non_coding_transcript_exon_variant,,ENST00000480706,;ETV5,downstream_gene_variant,,ENST00000433149,;	T	ENSG00000244405	ENST00000306376	Transcript	missense_variant	1718	1471	491	A/T	Gct/Act	rs773704999	.	.	-1	ETV5	HGNC	3494	protein_coding	YES	CCDS33906.1	ENSP00000306894	ETV5_HUMAN	C9JMF0_HUMAN,C9J5A5_HUMAN,C9J0Z2_HUMAN	UPI000012A175	.	tolerated(0.23)	benign(0.001)	13/13	.	hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAGCGGGGC	byFrequency	5	ESCA
MUC4	0	.	GRCh37	3	195513768	195513768	+	Silent	SNP	T	T	C	rs376555437	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4683A>G	p.%3D	p.V1561V	ENST00000463781	2/25	445	406	38	356	356	0	MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000477086,;MUC4,synonymous_variant,p.%3D,ENST00000466475,;MUC4,synonymous_variant,p.%3D,ENST00000478156,;MUC4,synonymous_variant,p.%3D,ENST00000470451,;MUC4,synonymous_variant,p.%3D,ENST00000479406,;MUC4,synonymous_variant,p.%3D,ENST00000477756,;MUC4,synonymous_variant,p.%3D,ENST00000462323,;MUC4,synonymous_variant,p.%3D,ENST00000480843,;	C	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	5143	4683	1561	V	gtA/gtG	rs376555437	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGATACTGA	.	2	ESCA
PDCD6IP	0	.	GRCh37	3	33870378	33870378	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766A>G	p.Ile256Val	p.I256V	ENST00000457054	7/18	56	43	13	43	43	0	PDCD6IP,missense_variant,p.Ile251Val,ENST00000307296,;PDCD6IP,missense_variant,p.Ile256Val,ENST00000457054,;PDCD6IP,downstream_gene_variant,,ENST00000413073,;PDCD6IP,non_coding_transcript_exon_variant,,ENST00000482561,;PDCD6IP,downstream_gene_variant,,ENST00000477798,;PDCD6IP,downstream_gene_variant,,ENST00000484478,;PDCD6IP,missense_variant,p.Ile61Val,ENST00000412887,;PDCD6IP,non_coding_transcript_exon_variant,,ENST00000487821,;PDCD6IP,downstream_gene_variant,,ENST00000435909,;PDCD6IP,downstream_gene_variant,,ENST00000459659,;PDCD6IP,downstream_gene_variant,,ENST00000494810,;	G	ENSG00000170248	ENST00000457054	Transcript	missense_variant	921	766	256	I/V	Atc/Gtc	.	.	.	1	PDCD6IP	HGNC	8766	protein_coding	YES	CCDS54561.1	ENSP00000411825	PDC6I_HUMAN	.	UPI00004121D3	.	tolerated(0.96)	benign(0.009)	7/18	.	PROSITE_profiles:PS51180,hmmpanther:PTHR23030:SF19,hmmpanther:PTHR23030,Pfam_domain:PF03097,Gene3D:2xs1A01,SMART_domains:SM01041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTATCATG	.	5	ESCA
STAC	0	.	GRCh37	3	36534710	36534710	+	Missense_Mutation	SNP	G	G	T	rs558026131	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.755G>T	p.Arg252Leu	p.R252L	ENST00000273183	6/11	41	19	21	44	44	0	STAC,missense_variant,p.Arg180Leu,ENST00000434649,;STAC,missense_variant,p.Arg252Leu,ENST00000273183,;STAC,missense_variant,p.Arg191Leu,ENST00000457375,;STAC,non_coding_transcript_exon_variant,,ENST00000476388,;STAC,3_prime_UTR_variant,,ENST00000427486,;STAC,non_coding_transcript_exon_variant,,ENST00000473452,;	T	ENSG00000144681	ENST00000273183	Transcript	missense_variant	1055	755	252	R/L	cGc/cTc	rs558026131	.	.	1	STAC	HGNC	11353	protein_coding	YES	CCDS2662.1	ENSP00000273183	STAC_HUMAN	B4DZ13_HUMAN	UPI0000136081	.	tolerated(0.23)	possibly_damaging(0.644)	6/11	.	hmmpanther:PTHR15135:SF3,hmmpanther:PTHR15135	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R252C|c.754C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAACGCAGCA	by1000G	5	ESCA
CC2D2A	0	.	GRCh37	4	15562218	15562218	+	Missense_Mutation	SNP	T	T	C	rs754327317	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2987T>C	p.Ile996Thr	p.I996T	ENST00000424120	23/37	46	21	25	52	52	0	CC2D2A,missense_variant,p.Ile996Thr,ENST00000503292,;CC2D2A,missense_variant,p.Ile996Thr,ENST00000413206,;CC2D2A,missense_variant,p.Ile947Thr,ENST00000389652,;CC2D2A,missense_variant,p.Ile996Thr,ENST00000424120,;RP11-799M12.2,downstream_gene_variant,,ENST00000609724,;CC2D2A,missense_variant,p.Ile439Thr,ENST00000506643,;CC2D2A,downstream_gene_variant,,ENST00000512202,;	C	ENSG00000048342	ENST00000424120	Transcript	missense_variant	3241	2987	996	I/T	aTa/aCa	rs754327317	.	.	1	CC2D2A	HGNC	29253	protein_coding	YES	CCDS47026.1	ENSP00000403465	C2D2A_HUMAN	D6R9V3_HUMAN	UPI000023731A	.	deleterious(0)	benign(0.255)	23/37	.	hmmpanther:PTHR20837:SF4,hmmpanther:PTHR20837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGATAGTAG	.	5	ESCA
KLKB1	0	.	GRCh37	4	187178462	187178462	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1668A>T	p.Lys556Asn	p.K556N	ENST00000264690	14/15	42	29	13	41	41	0	KLKB1,missense_variant,p.Lys604Asn,ENST00000511608,;KLKB1,missense_variant,p.Lys556Asn,ENST00000264690,;KLKB1,intron_variant,,ENST00000513864,;KLKB1,non_coding_transcript_exon_variant,,ENST00000511406,;	T	ENSG00000164344	ENST00000264690	Transcript	missense_variant	1855	1668	556	K/N	aaA/aaT	.	.	.	1	KLKB1	HGNC	6371	protein_coding	YES	CCDS34120.1	ENSP00000264690	KLKB1_HUMAN	C9JCT1_HUMAN,C9J075_HUMAN,C9IYG8_HUMAN	UPI000050EC06	.	tolerated(0.15)	benign(0.12)	14/15	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24265,hmmpanther:PTHR24265:SF74,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.R560Q|c.1679G>A|3,BUFFER|p.R560Q|c.1679G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAAAATAAC	.	5	ESCA
PDS5A	0	.	GRCh37	4	39915248	39915248	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.975G>A	p.Trp325Ter	p.W325*	ENST00000303538	9/33	21	15	6	28	28	0	PDS5A,stop_gained,p.Trp325Ter,ENST00000503396,;PDS5A,stop_gained,p.Trp325Ter,ENST00000303538,;PDS5A,intron_variant,,ENST00000513798,;PDS5A,stop_gained,p.Trp33Ter,ENST00000512643,;PDS5A,non_coding_transcript_exon_variant,,ENST00000508625,;PDS5A,upstream_gene_variant,,ENST00000503867,;	T	ENSG00000121892	ENST00000303538	Transcript	stop_gained	1515	975	325	W/*	tgG/tgA	.	.	.	-1	PDS5A	HGNC	29088	protein_coding	YES	CCDS47045.1	ENSP00000303427	PDS5A_HUMAN	Q96DB6_HUMAN,G1UI16_HUMAN,B3KMN2_HUMAN	UPI00006C6A7E	.	.	.	9/33	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF2,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTGCCAAAG	.	5	ESCA
GABRA2	0	.	GRCh37	4	46314679	46314679	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310T>G	p.Phe104Val	p.F104V	ENST00000510861	5/10	74	70	4	72	72	0	GABRA2,missense_variant,p.Phe104Val,ENST00000503806,;GABRA2,missense_variant,p.Phe104Val,ENST00000510861,;GABRA2,missense_variant,p.Phe104Val,ENST00000515082,;GABRA2,missense_variant,p.Phe104Val,ENST00000506961,;GABRA2,missense_variant,p.Phe104Val,ENST00000356504,;GABRA2,missense_variant,p.Phe104Val,ENST00000507069,;GABRA2,missense_variant,p.Phe104Val,ENST00000381620,;GABRA2,missense_variant,p.Phe49Val,ENST00000540012,;GABRA2,missense_variant,p.Phe104Val,ENST00000514090,;GABRA2,missense_variant,p.Phe104Val,ENST00000510233,;GABRA2,3_prime_UTR_variant,,ENST00000514193,;GABRA2,3_prime_UTR_variant,,ENST00000513005,;	C	ENSG00000151834	ENST00000510861	Transcript	missense_variant	484	310	104	F/V	Ttt/Gtt	.	.	.	-1	GABRA2	HGNC	4076	protein_coding	YES	CCDS3471.1	ENSP00000421828	GBRA2_HUMAN	Q4W5L8_HUMAN,D6RBL7_HUMAN,D6RBK9_HUMAN,D6RB77_HUMAN	UPI000013DC88	.	deleterious(0)	probably_damaging(1)	5/10	.	hmmpanther:PTHR18945:SF218,hmmpanther:PTHR18945,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932,Prints_domain:PR01079,Prints_domain:PR00252	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTTAAATTTTA	.	2	ESCA
OCIAD1	0	.	GRCh37	4	48859371	48859372	+	Frame_Shift_Ins	INS	-	-	A	rs768679897	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696dupA	p.Glu233ArgfsTer13	p.E233Rfs*13	ENST00000381473	8/9	39	21	18	48	48	0	OCIAD1,frameshift_variant,p.Glu233ArgfsTer13,ENST00000513391,;OCIAD1,frameshift_variant,p.Glu233ArgfsTer13,ENST00000508293,;OCIAD1,frameshift_variant,p.Glu233ArgfsTer13,ENST00000264312,;OCIAD1,frameshift_variant,p.Glu179ArgfsTer?,ENST00000503016,;OCIAD1,frameshift_variant,p.Glu233ArgfsTer13,ENST00000381473,;OCIAD1,frameshift_variant,p.Glu206ArgfsTer13,ENST00000509122,;OCIAD1,intron_variant,,ENST00000425583,;OCIAD1,intron_variant,,ENST00000506801,;OCIAD1,intron_variant,,ENST00000396448,;OCIAD1,intron_variant,,ENST00000444354,;OCIAD1,downstream_gene_variant,,ENST00000505922,;OCIAD1-AS1,intron_variant,,ENST00000513576,;OCIAD1,intron_variant,,ENST00000508329,;OCIAD1,downstream_gene_variant,,ENST00000512981,;OCIAD1,non_coding_transcript_exon_variant,,ENST00000502972,;	A	ENSG00000109180	ENST00000381473	Transcript	frameshift_variant	1107-1108	689-690	230	P/PX	cca/ccAa	rs768679897	.	.	1	OCIAD1	HGNC	16074	protein_coding	YES	CCDS3484.1	ENSP00000370882	OCAD1_HUMAN	D6RIT9_HUMAN,D6RI08_HUMAN,D6RG39_HUMAN,D6RF07_HUMAN,D6RF01_HUMAN,D6RDK6_HUMAN,D6RDK1_HUMAN,D6RDI5_HUMAN,D6RC55_HUMAN,D6RBC5_HUMAN,D6RA54_HUMAN,D6R918_HUMAN	UPI0000073D7F	.	.	.	8/9	.	hmmpanther:PTHR13336:SF4,hmmpanther:PTHR13336	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGTGCCAAAAA	.	2	ESCA
TIGD2	0	.	GRCh37	4	90035968	90035968	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*265G>T	.	.	ENST00000317005	1/1	75	58	17	71	71	0	TIGD2,3_prime_UTR_variant,,ENST00000317005,;RP11-84C13.2,upstream_gene_variant,,ENST00000603220,;RP11-84C13.1,downstream_gene_variant,,ENST00000603357,;FAM13A,upstream_gene_variant,,ENST00000502459,;	T	ENSG00000180346	ENST00000317005	Transcript	3_prime_UTR_variant	2001	.	.	.	.	.	.	.	1	TIGD2	HGNC	18333	protein_coding	YES	CCDS3633.1	ENSP00000317170	TIGD2_HUMAN	.	UPI000013FF3C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTGTGCCT	.	5	ESCA
WDR36	0	.	GRCh37	5	110434486	110434486	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526A>G	p.Ile176Val	p.I176V	ENST00000506538	4/23	14	6	8	11	11	0	WDR36,missense_variant,p.Ile176Val,ENST00000513710,;WDR36,missense_variant,p.Ile176Val,ENST00000506538,;WDR36,missense_variant,p.Ile47Val,ENST00000504122,;WDR36,missense_variant,p.Ile120Val,ENST00000505303,;WDR36,downstream_gene_variant,,ENST00000515784,;	G	ENSG00000134987	ENST00000506538	Transcript	missense_variant	1099	526	176	I/V	Atc/Gtc	.	.	.	1	WDR36	HGNC	30696	protein_coding	YES	CCDS4102.1	ENSP00000423067	WDR36_HUMAN	D6RFM8_HUMAN	UPI000007018C	.	tolerated(0.23)	benign(0.338)	4/23	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13889,hmmpanther:PTHR13889:SF2,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTATCTCT	.	5	ESCA
GFRA3	0	.	GRCh37	5	137600203	137600203	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126C>T	p.%3D	p.N42N	ENST00000274721	2/8	69	60	9	66	66	0	GFRA3,synonymous_variant,p.%3D,ENST00000378362,;GFRA3,synonymous_variant,p.%3D,ENST00000274721,;RP11-166J22.1,downstream_gene_variant,,ENST00000515536,;	A	ENSG00000146013	ENST00000274721	Transcript	synonymous_variant	373	126	42	N	aaC/aaT	.	.	.	-1	GFRA3	HGNC	4245	protein_coding	YES	CCDS4201.1	ENSP00000274721	GFRA3_HUMAN	.	UPI0000030833	.	.	.	2/8	.	hmmpanther:PTHR10269:SF11,hmmpanther:PTHR10269,Prints_domain:PR01319	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCTGTTCAT	.	4	ESCA
DNAH5	0	.	GRCh37	5	13871845	13871845	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3426A>C	p.Lys1142Asn	p.K1142N	ENST00000265104	23/79	72	56	15	59	59	0	DNAH5,missense_variant,p.Lys1142Asn,ENST00000265104,;CTB-51A17.1,intron_variant,,ENST00000503244,;	G	ENSG00000039139	ENST00000265104	Transcript	missense_variant	3531	3426	1142	K/N	aaA/aaC	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.403)	23/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCGTTTGAA	.	5	ESCA
FAT2	0	.	GRCh37	5	150946655	150946655	+	Missense_Mutation	SNP	T	T	C	rs754186565	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1838A>G	p.Asn613Ser	p.N613S	ENST00000261800	1/23	39	17	21	36	36	0	FAT2,missense_variant,p.Asn613Ser,ENST00000261800,;	C	ENSG00000086570	ENST00000261800	Transcript	missense_variant	1851	1838	613	N/S	aAt/aGt	rs754186565	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	benign(0.392)	1/23	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGATTTAGA	.	5	ESCA
LARP1	0	.	GRCh37	5	154181697	154181697	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1616T>C	p.Met539Thr	p.M539T	ENST00000336314	11/19	45	39	5	38	38	0	LARP1,missense_variant,p.Met411Thr,ENST00000524248,;LARP1,missense_variant,p.Met616Thr,ENST00000518297,;LARP1,missense_variant,p.Met539Thr,ENST00000336314,;LARP1,downstream_gene_variant,,ENST00000518742,;LARP1,upstream_gene_variant,,ENST00000522272,;LARP1,upstream_gene_variant,,ENST00000518677,;LARP1,downstream_gene_variant,,ENST00000523163,;LARP1,upstream_gene_variant,,ENST00000519194,;LARP1,downstream_gene_variant,,ENST00000518595,;	C	ENSG00000155506	ENST00000336314	Transcript	missense_variant	1640	1616	539	M/T	aTg/aCg	.	.	.	1	LARP1	HGNC	29531	protein_coding	YES	CCDS4328.1	ENSP00000336721	LARP1_HUMAN	E5RHK4_HUMAN,E5RH50_HUMAN	UPI00001DFE1B	.	tolerated(0.15)	benign(0.364)	11/19	.	hmmpanther:PTHR22792:SF51,hmmpanther:PTHR22792	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAGATGGATG	.	3	ESCA
NSD1	0	.	GRCh37	5	176683973	176683973	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4787G>T	p.Cys1596Phe	p.C1596F	ENST00000439151	13/23	62	29	33	51	51	0	NSD1,missense_variant,p.Cys1493Phe,ENST00000361032,;NSD1,missense_variant,p.Cys1327Phe,ENST00000354179,;NSD1,missense_variant,p.Cys1596Phe,ENST00000439151,;NSD1,missense_variant,p.Cys1327Phe,ENST00000347982,;	T	ENSG00000165671	ENST00000439151	Transcript	missense_variant	4832	4787	1596	C/F	tGt/tTt	.	.	.	1	NSD1	HGNC	14234	protein_coding	YES	CCDS4412.1	ENSP00000395929	NSD1_HUMAN	Q9H6H8_HUMAN,Q9H6B5_HUMAN,Q96MN8_HUMAN,Q96DQ7_HUMAN,Q658U6_HUMAN,D6RE14_HUMAN,D6RBP3_HUMAN,D6RA90_HUMAN	UPI000006F9C6	.	deleterious(0)	probably_damaging(0.999)	13/23	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312,SMART_domains:SM00249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATGTAAGC	.	5	ESCA
ZNF354A	0	.	GRCh37	5	178139089	178139089	+	Missense_Mutation	SNP	T	T	C	rs775196494	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1790A>G	p.Tyr597Cys	p.Y597C	ENST00000335815	5/5	34	14	20	26	26	0	ZNF354A,missense_variant,p.Tyr597Cys,ENST00000335815,;ZNF354A,downstream_gene_variant,,ENST00000520331,;	C	ENSG00000169131	ENST00000335815	Transcript	missense_variant	1988	1790	597	Y/C	tAt/tGt	rs775196494	.	.	-1	ZNF354A	HGNC	11628	protein_coding	YES	CCDS4438.1	ENSP00000337122	Z354A_HUMAN	E5RHT5_HUMAN	UPI000013EB5E	.	tolerated(0.06)	benign(0.009)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF146,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTATAATGA	.	5	ESCA
C5orf42	0	.	GRCh37	5	37196019	37196019	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3752T>A	p.Phe1251Tyr	p.F1251Y	ENST00000425232	21/52	75	66	9	33	33	0	C5orf42,missense_variant,p.Phe132Tyr,ENST00000274258,;C5orf42,missense_variant,p.Phe1251Tyr,ENST00000508244,;C5orf42,missense_variant,p.Phe1251Tyr,ENST00000425232,;C5orf42,missense_variant,p.Phe299Tyr,ENST00000514429,;C5orf42,missense_variant,p.Phe256Tyr,ENST00000509849,;	T	ENSG00000197603	ENST00000425232	Transcript	missense_variant	3983	3752	1251	F/Y	tTt/tAt	.	.	.	-1	C5orf42	HGNC	25801	protein_coding	YES	CCDS34146.2	ENSP00000389014	CE042_HUMAN	.	UPI0001AAB3EA	.	deleterious(0.01)	probably_damaging(0.995)	21/52	.	hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.A131T|c.391G>A|3,BUFFER|p.A1250T|c.3748G>A|3	RADIA|MUTECT|MUSE|VARSCANS	TAAAAAATGCG	.	4	ESCA
MROH2B	0	.	GRCh37	5	41000790	41000790	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4340A>C	p.Lys1447Thr	p.K1447T	ENST00000399564	38/42	42	35	7	19	19	0	MROH2B,missense_variant,p.Lys1002Thr,ENST00000506092,;MROH2B,missense_variant,p.Lys1447Thr,ENST00000399564,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,;MROH2B,upstream_gene_variant,,ENST00000511934,;	G	ENSG00000171495	ENST00000399564	Transcript	missense_variant	4791	4340	1447	K/T	aAg/aCg	.	.	.	-1	MROH2B	HGNC	26857	protein_coding	YES	CCDS47202.1	ENSP00000382476	MRO2B_HUMAN	F5GZ06_HUMAN	UPI000020CA04	.	tolerated(0.19)	benign(0.026)	38/42	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF15,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATCTTGGGG	.	5	ESCA
SEMA5A	0	.	GRCh37	5	9042784	9042784	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*225G>T	.	.	ENST00000382496	23/23	51	48	3	37	37	0	SEMA5A,3_prime_UTR_variant,,ENST00000382496,;CTD-2215L10.1,intron_variant,,ENST00000506519,;	A	ENSG00000112902	ENST00000382496	Transcript	3_prime_UTR_variant	4116	.	.	.	.	.	.	.	-1	SEMA5A	HGNC	10736	protein_coding	YES	CCDS3875.1	ENSP00000371936	SEM5A_HUMAN	D6RAF4_HUMAN,B4DE33_HUMAN	UPI000004F25D	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTTCACACCCT	.	2	ESCA
VTA1	0	.	GRCh37	6	142510589	142510589	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438A>T	p.Arg146Ser	p.R146S	ENST00000367630	5/8	58	33	24	42	42	0	VTA1,missense_variant,p.Arg146Ser,ENST00000367630,;VTA1,missense_variant,p.Arg88Ser,ENST00000452973,;VTA1,missense_variant,p.Arg88Ser,ENST00000367621,;VTA1,non_coding_transcript_exon_variant,,ENST00000491881,;	T	ENSG00000009844	ENST00000367630	Transcript	missense_variant	496	438	146	R/S	agA/agT	.	.	.	1	VTA1	HGNC	20954	protein_coding	YES	CCDS5197.1	ENSP00000356602	VTA1_HUMAN	.	UPI0000034E19	.	tolerated(0.08)	benign(0.207)	5/8	.	hmmpanther:PTHR12741,Pfam_domain:PF04652,Gene3D:2rkkA01	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGATGGAA	.	5	ESCA
HIST1H3D	0	.	GRCh37	6	26197139	26197139	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340C>A	p.His114Asn	p.H114N	ENST00000377831	2/2	95	49	45	83	83	0	HIST1H3D,missense_variant,p.His114Asn,ENST00000377831,;HIST1H3D,missense_variant,p.His114Asn,ENST00000356476,;HIST1H2BF,upstream_gene_variant,,ENST00000359985,;HIST1H2AD,downstream_gene_variant,,ENST00000341023,;HIST1H1PS1,downstream_gene_variant,,ENST00000404269,;	T	ENSG00000197409	ENST00000377831	Transcript	missense_variant	794	340	114	H/N	Cac/Aac	.	.	.	-1	HIST1H3D	HGNC	4767	protein_coding	YES	CCDS4590.1	ENSP00000367062	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0)	probably_damaging(0.996)	2/2	.	hmmpanther:PTHR11426,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGTGAATGG	.	5	ESCA
MDC1	0	.	GRCh37	6	30680031	30680031	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1688T>A	p.Leu563His	p.L563H	ENST00000376406	5/15	42	18	24	22	22	0	MDC1,missense_variant,p.Leu563His,ENST00000376405,;MDC1,missense_variant,p.Leu563His,ENST00000376406,;MDC1,downstream_gene_variant,,ENST00000422266,;MDC1,downstream_gene_variant,,ENST00000425072,;MDC1,upstream_gene_variant,,ENST00000417033,;MDC1,downstream_gene_variant,,ENST00000416571,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000494654,;MDC1,upstream_gene_variant,,ENST00000492462,;	T	ENSG00000137337	ENST00000376406	Transcript	missense_variant	2336	1688	563	L/H	cTt/cAt	.	.	.	-1	MDC1	HGNC	21163	protein_coding	YES	CCDS34384.1	ENSP00000365588	MDC1_HUMAN	A2AB07_HUMAN,A2AB06_HUMAN,A2AB05_HUMAN,A1Z5I9_HUMAN,A1Z5I7_HUMAN	UPI00001AF453	.	deleterious(0.05)	benign(0.334)	5/15	.	hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAAGCAGC	.	5	ESCA
RP4-529N6.1	0	.	GRCh37	6	4610914	4610914	+	RNA	SNP	T	T	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.25T>G	.	.	ENST00000380106	1/2	25	15	9	17	17	0	RP4-529N6.1,non_coding_transcript_exon_variant,,ENST00000380106,;	G	ENSG00000205444	ENST00000380106	Transcript	non_coding_transcript_exon_variant	25	.	.	.	.	.	.	.	1	RP4-529N6.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GAAGTTTGCAG	.	4	ESCA
ANKRD66	0	.	GRCh37	6	46721477	46721477	+	Missense_Mutation	SNP	G	G	A	rs746184595	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347G>A	p.Arg116Gln	p.R116Q	ENST00000565422	4/5	43	18	25	44	44	0	ANKRD66,missense_variant,p.Arg116Gln,ENST00000565422,;ANKRD66,missense_variant,p.Arg87Gln,ENST00000536046,;ANKRD66,upstream_gene_variant,,ENST00000445060,;RP11-268F1.3,downstream_gene_variant,,ENST00000438738,;	A	ENSG00000230062	ENST00000565422	Transcript	missense_variant	352	347	116	R/Q	cGg/cAg	rs746184595	.	.	1	ANKRD66	HGNC	44669	protein_coding	YES	CCDS59024.1	ENSP00000454770	ANR66_HUMAN	.	UPI0001F7E3C7	.	tolerated(0.44)	benign(0.043)	4/5	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24193,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATACGGCTCC	.	5	ESCA
FAM46A	0	.	GRCh37	6	82456439	82456439	+	3'UTR	SNP	G	G	T	rs1044381	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2973C>A	.	.	ENST00000320172	3/3	22	16	6	22	22	0	FAM46A,3_prime_UTR_variant,,ENST00000369754,;FAM46A,3_prime_UTR_variant,,ENST00000320172,;FAM46A,3_prime_UTR_variant,,ENST00000369756,;FAM46A,intron_variant,,ENST00000412306,;FAM46A,downstream_gene_variant,,ENST00000423467,;	T	ENSG00000112773	ENST00000320172	Transcript	3_prime_UTR_variant	4617	.	.	.	.	rs1044381	.	.	-1	FAM46A	HGNC	18345	protein_coding	YES	CCDS34489.1	ENSP00000318298	FA46A_HUMAN	.	UPI000006E9BA	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAAAGGAAAC	.	2	ESCA
FUT9	0	.	GRCh37	6	96662685	96662685	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10574A>G	.	.	ENST00000302103	3/3	22	11	11	13	13	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	G	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	11980	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGAATCCTA	.	5	ESCA
CHRM2	0	.	GRCh37	7	136700551	136700551	+	Silent	SNP	C	C	T	rs774236034	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.939C>T	p.%3D	p.G313G	ENST00000445907	3/3	20	10	10	25	25	0	CHRM2,synonymous_variant,p.%3D,ENST00000320658,;CHRM2,synonymous_variant,p.%3D,ENST00000401861,;CHRM2,synonymous_variant,p.%3D,ENST00000397608,;CHRM2,synonymous_variant,p.%3D,ENST00000402486,;CHRM2,synonymous_variant,p.%3D,ENST00000453373,;CHRM2,synonymous_variant,p.%3D,ENST00000445907,;hsa-mir-490,intron_variant,,ENST00000597642,;hsa-mir-490,intron_variant,,ENST00000586239,;hsa-mir-490,intron_variant,,ENST00000425981,;hsa-mir-490,intron_variant,,ENST00000592183,;hsa-mir-490,intron_variant,,ENST00000593789,;hsa-mir-490,intron_variant,,ENST00000598184,;hsa-mir-490,intron_variant,,ENST00000439694,;	T	ENSG00000181072	ENST00000445907	Transcript	synonymous_variant	1467	939	313	G	ggC/ggT	rs774236034	.	.	1	CHRM2	HGNC	1951	protein_coding	YES	CCDS5843.1	ENSP00000399745	ACM2_HUMAN	Q96RH0_HUMAN,Q86SJ1_HUMAN,Q6SL56_HUMAN,A4D1Q0_HUMAN	UPI0000050410	.	.	.	3/3	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF57,Pfam_domain:PF00001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGCCATTC	.	5	ESCA
PPP1R17	0	.	GRCh37	7	31732094	31732094	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39A>T	p.%3D	p.S13S	ENST00000342032	2/5	94	66	28	74	74	0	PPP1R17,synonymous_variant,p.%3D,ENST00000342032,;PPP1R17,synonymous_variant,p.%3D,ENST00000409146,;PPP1R17,upstream_gene_variant,,ENST00000498609,;	T	ENSG00000106341	ENST00000342032	Transcript	synonymous_variant	667	39	13	S	tcA/tcT	.	.	.	1	PPP1R17	HGNC	16973	protein_coding	YES	CCDS5436.1	ENSP00000340125	PPR17_HUMAN	.	UPI000006D182	.	.	.	2/5	.	hmmpanther:PTHR15387:SF0,hmmpanther:PTHR15387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCAGAAGA	.	5	ESCA
DBNL	0	.	GRCh37	7	44098544	44098544	+	Missense_Mutation	SNP	G	G	C	rs751811504	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.824G>C	p.Arg275Thr	p.R275T	ENST00000468694	9/13	39	36	3	43	43	0	DBNL,missense_variant,p.Arg266Thr,ENST00000448521,;DBNL,missense_variant,p.Arg6Thr,ENST00000452661,;DBNL,missense_variant,p.Arg218Thr,ENST00000456905,;DBNL,missense_variant,p.Arg195Thr,ENST00000432854,;DBNL,missense_variant,p.Arg267Thr,ENST00000494774,;DBNL,missense_variant,p.Arg242Thr,ENST00000452943,;DBNL,missense_variant,p.Arg275Thr,ENST00000468694,;DBNL,missense_variant,p.Arg172Thr,ENST00000490734,;DBNL,missense_variant,p.Arg163Thr,ENST00000440166,;PGAM2,downstream_gene_variant,,ENST00000297283,;DBNL,non_coding_transcript_exon_variant,,ENST00000497184,;DBNL,3_prime_UTR_variant,,ENST00000441904,;DBNL,3_prime_UTR_variant,,ENST00000498733,;DBNL,3_prime_UTR_variant,,ENST00000429716,;DBNL,3_prime_UTR_variant,,ENST00000411855,;DBNL,3_prime_UTR_variant,,ENST00000441840,;DBNL,non_coding_transcript_exon_variant,,ENST00000449997,;DBNL,downstream_gene_variant,,ENST00000464762,;DBNL,downstream_gene_variant,,ENST00000458579,;DBNL,downstream_gene_variant,,ENST00000485932,;DBNL,downstream_gene_variant,,ENST00000423561,;DBNL,downstream_gene_variant,,ENST00000439815,;	C	ENSG00000136279	ENST00000468694	Transcript	missense_variant	851	824	275	R/T	aGg/aCg	rs751811504	.	.	1	DBNL	HGNC	2696	protein_coding	YES	CCDS47579.1	ENSP00000417653	DBNL_HUMAN	F2Z2V3_HUMAN	UPI000007147D	.	deleterious(0.01)	possibly_damaging(0.738)	9/13	.	hmmpanther:PTHR10829,hmmpanther:PTHR10829:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGAGGGCCA	.	2	ESCA
CCZ1	0	.	GRCh37	7	5942299	5942299	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.446A>G	p.Asn149Ser	p.N149S	ENST00000325974	6/15	106	80	26	67	67	0	CCZ1,missense_variant,p.Asn6Ser,ENST00000537980,;CCZ1,missense_variant,p.Asn149Ser,ENST00000325974,;CCZ1,non_coding_transcript_exon_variant,,ENST00000483394,;CCZ1,downstream_gene_variant,,ENST00000461592,;CCZ1,downstream_gene_variant,,ENST00000478672,;	G	ENSG00000122674	ENST00000325974	Transcript	missense_variant	512	446	149	N/S	aAt/aGt	.	.	.	1	CCZ1	HGNC	21691	protein_coding	YES	CCDS34597.1	ENSP00000325681	CCZ1_HUMAN	Q7L8P3_HUMAN,F5H553_HUMAN	UPI000006CEFF	.	tolerated(0.19)	possibly_damaging(0.9)	6/15	.	Pfam_domain:PF08217,hmmpanther:PTHR13056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTAATGGTA	.	5	ESCA
ERV3-1	0	.	GRCh37	7	64452815	64452815	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590G>T	p.Cys197Phe	p.C197F	ENST00000394323	2/2	30	25	5	30	30	0	ERV3-1,missense_variant,p.Cys197Phe,ENST00000394323,;ZNF117,upstream_gene_variant,,ENST00000282869,;ZNF117,intron_variant,,ENST00000487644,;	A	ENSG00000213462	ENST00000394323	Transcript	missense_variant	1091	590	197	C/F	tGc/tTc	.	.	.	-1	ERV3-1	HGNC	3454	protein_coding	YES	CCDS47595.1	ENSP00000391594	ENR1_HUMAN	.	UPI000023FEAF	.	deleterious(0.01)	benign(0.299)	2/2	.	hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTGCAAGTG	.	5	ESCA
ERV3-1	0	.	GRCh37	7	64452816	64452816	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.589T>C	p.Cys197Arg	p.C197R	ENST00000394323	2/2	31	25	5	30	30	0	ERV3-1,missense_variant,p.Cys197Arg,ENST00000394323,;ZNF117,upstream_gene_variant,,ENST00000282869,;ZNF117,intron_variant,,ENST00000487644,;	G	ENSG00000213462	ENST00000394323	Transcript	missense_variant	1090	589	197	C/R	Tgc/Cgc	.	.	.	-1	ERV3-1	HGNC	3454	protein_coding	YES	CCDS47595.1	ENSP00000391594	ENR1_HUMAN	.	UPI000023FEAF	.	deleterious(0.04)	benign(0.299)	2/2	.	hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGCAAGTGC	.	5	ESCA
GUSB	0	.	GRCh37	7	65444784	65444784	+	Missense_Mutation	SNP	C	C	T	rs746475728	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.511G>A	p.Ala171Thr	p.A171T	ENST00000304895	3/12	54	38	15	46	46	0	GUSB,missense_variant,p.Ala171Thr,ENST00000345660,;GUSB,missense_variant,p.Ala171Thr,ENST00000304895,;GUSB,intron_variant,,ENST00000421103,;GUSB,non_coding_transcript_exon_variant,,ENST00000478118,;GUSB,intron_variant,,ENST00000476486,;GUSB,intron_variant,,ENST00000475316,;GUSB,intron_variant,,ENST00000479038,;GUSB,upstream_gene_variant,,ENST00000465785,;GUSB,intron_variant,,ENST00000446111,;GUSB,intron_variant,,ENST00000430730,;GUSB,intron_variant,,ENST00000447929,;GUSB,upstream_gene_variant,,ENST00000462371,;GUSB,upstream_gene_variant,,ENST00000489482,;GUSB,upstream_gene_variant,,ENST00000466883,;	T	ENSG00000169919	ENST00000304895	Transcript	missense_variant	642	511	171	A/T	Gcc/Acc	rs746475728	.	.	-1	GUSB	HGNC	4696	protein_coding	YES	CCDS5530.1	ENSP00000302728	BGLR_HUMAN	.	UPI000013E9E0	.	deleterious(0.01)	possibly_damaging(0.827)	3/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10066:SF51,hmmpanther:PTHR10066,Pfam_domain:PF02837,Gene3D:2.60.120.260,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGGCGATAG	byFrequency	5	ESCA
GTF2I	0	.	GRCh37	7	74167460	74167460	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2592A>T	p.Lys864Asn	p.K864N	ENST00000324896	29/35	141	130	11	108	108	0	GTF2I,missense_variant,p.Lys864Asn,ENST00000324896,;GTF2I,missense_variant,p.Lys844Asn,ENST00000353920,;GTF2I,missense_variant,p.Lys843Asn,ENST00000346152,;GTF2I,missense_variant,p.Lys823Asn,ENST00000416070,;GTF2I,downstream_gene_variant,,ENST00000438130,;GTF2I,non_coding_transcript_exon_variant,,ENST00000482232,;GTF2I,upstream_gene_variant,,ENST00000464471,;GTF2I,downstream_gene_variant,,ENST00000476035,;GTF2I,upstream_gene_variant,,ENST00000473759,;GTF2I,upstream_gene_variant,,ENST00000460938,;STAG3L2,intron_variant,,ENST00000380775,;	T	ENSG00000077809	ENST00000324896	Transcript	missense_variant	2981	2592	864	K/N	aaA/aaT	.	.	.	1	GTF2I	HGNC	4659	protein_coding	YES	CCDS5573.1	ENSP00000322542	GTF2I_HUMAN	C9J6M0_HUMAN,B4DRA9_HUMAN,B4DM07_HUMAN,B4DH52_HUMAN	UPI0000001233	.	tolerated(0.14)	probably_damaging(0.996)	29/35	.	PROSITE_profiles:PS51139,Gene3D:1q60A00,PIRSF_domain:PIRSF016441,Superfamily_domains:0048894	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAAAAAGCTAG	.	3	ESCA
CACNA2D1	0	.	GRCh37	7	81591785	81591785	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2807G>C	p.Ser936Thr	p.S936T	ENST00000356860	35/39	53	42	10	42	42	0	CACNA2D1,missense_variant,p.Ser948Thr,ENST00000356253,;CACNA2D1,missense_variant,p.Ser936Thr,ENST00000356860,;CACNA2D1,missense_variant,p.Ser148Thr,ENST00000535308,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000469297,;CACNA2D1,downstream_gene_variant,,ENST00000486539,;	G	ENSG00000153956	ENST00000356860	Transcript	missense_variant	3146	2807	936	S/T	aGt/aCt	COSM69988	.	.	-1	CACNA2D1	HGNC	1399	protein_coding	YES	CCDS5598.1	ENSP00000349320	CA2D1_HUMAN	Q9UDU5_HUMAN,Q9UDQ3_HUMAN,Q9UDL7_HUMAN,O95026_HUMAN	UPI00003674CD	.	tolerated(0.23)	possibly_damaging(0.7)	35/39	.	hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAAACTCAAG	.	5	ESCA
PEG10	0	.	GRCh37	7	94297997	94297997	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4151A>G	.	.	ENST00000482108	2/2	29	23	6	19	19	0	PEG10,3_prime_UTR_variant,,ENST00000482108,;PEG10,downstream_gene_variant,,ENST00000488574,;PEG10,intron_variant,,ENST00000465184,;PEG10,intron_variant,,ENST00000493935,;	G	ENSG00000242265	ENST00000482108	Transcript	3_prime_UTR_variant	5608	.	.	.	.	.	.	.	1	PEG10	HGNC	14005	protein_coding	YES	CCDS55126.1	ENSP00000417587	PEG10_HUMAN	B4DSP0_HUMAN	UPI0000047FA3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACACAGAAAG	.	5	ESCA
GRHL2	0	.	GRCh37	8	102570829	102570829	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.467C>T	p.Thr156Met	p.T156M	ENST00000251808	4/16	38	32	6	35	35	0	GRHL2,missense_variant,p.Thr156Met,ENST00000251808,;GRHL2,missense_variant,p.Thr140Met,ENST00000395927,;KB-1562D12.3,downstream_gene_variant,,ENST00000524051,;	T	ENSG00000083307	ENST00000251808	Transcript	missense_variant	805	467	156	T/M	aCg/aTg	.	.	.	1	GRHL2	HGNC	2799	protein_coding	YES	CCDS34931.1	ENSP00000251808	GRHL2_HUMAN	.	UPI000013CD16	.	tolerated(0.15)	benign(0.017)	4/16	.	hmmpanther:PTHR11037:SF17,hmmpanther:PTHR11037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.I155T|c.464T>C|4	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AATCACGGTGG	.	4	ESCA
CSMD3	0	.	GRCh37	8	113299359	113299359	+	Missense_Mutation	SNP	G	G	A	rs754162249	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9265C>T	p.His3089Tyr	p.H3089Y	ENST00000297405	58/71	82	51	30	76	76	0	CSMD3,missense_variant,p.His3019Tyr,ENST00000352409,;CSMD3,missense_variant,p.His2920Tyr,ENST00000455883,;CSMD3,missense_variant,p.His3089Tyr,ENST00000297405,;CSMD3,missense_variant,p.His2359Tyr,ENST00000339701,;CSMD3,missense_variant,p.His3049Tyr,ENST00000343508,;	A	ENSG00000164796	ENST00000297405	Transcript	missense_variant	9510	9265	3089	H/Y	Cat/Tat	rs754162249,COSM387927,COSM4150457	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.56)	benign(0.004)	58/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATGAAGGA	.	5	ESCA
CSMD3	0	.	GRCh37	8	114290890	114290890	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.445T>G	p.Ser149Ala	p.S149A	ENST00000297405	3/71	53	48	4	28	28	0	CSMD3,missense_variant,p.Ser149Ala,ENST00000352409,;CSMD3,missense_variant,p.Ser149Ala,ENST00000455883,;CSMD3,missense_variant,p.Ser149Ala,ENST00000297405,;CSMD3,missense_variant,p.Ser109Ala,ENST00000343508,;CSMD3,non_coding_transcript_exon_variant,,ENST00000497026,;	C	ENSG00000164796	ENST00000297405	Transcript	missense_variant	690	445	149	S/A	Tct/Gct	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.11)	benign(0.004)	3/71	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CACAGATTTGG	.	3	ESCA
HHLA1	0	.	GRCh37	8	133112334	133112334	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295C>T	p.Leu99Phe	p.L99F	ENST00000434736	5/17	35	29	6	26	26	0	HHLA1,missense_variant,p.Leu99Phe,ENST00000434736,;HHLA1,missense_variant,p.Leu63Phe,ENST00000414222,;	A	ENSG00000132297	ENST00000434736	Transcript	missense_variant	381	295	99	L/F	Ctt/Ttt	.	.	.	-1	HHLA1	HGNC	4904	protein_coding	YES	.	ENSP00000407107	.	C9JY47_HUMAN	UPI00021CEF49	.	deleterious(0)	probably_damaging(0.978)	5/17	.	hmmpanther:PTHR15299	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAAGAAATG	.	5	ESCA
TOP1MT	0	.	GRCh37	8	144400203	144400203	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1200C>G	p.%3D	p.L400L	ENST00000329245	9/14	79	38	40	55	55	0	TOP1MT,synonymous_variant,p.%3D,ENST00000523676,;TOP1MT,synonymous_variant,p.%3D,ENST00000519148,;TOP1MT,synonymous_variant,p.%3D,ENST00000521193,;TOP1MT,synonymous_variant,p.%3D,ENST00000329245,;TOP1MT,synonymous_variant,p.%3D,ENST00000519139,;TOP1MT,upstream_gene_variant,,ENST00000519977,;AC087793.1,downstream_gene_variant,,ENST00000585120,;TOP1MT,3_prime_UTR_variant,,ENST00000518951,;	C	ENSG00000184428	ENST00000329245	Transcript	synonymous_variant	1235	1200	400	L	ctC/ctG	.	.	.	-1	TOP1MT	HGNC	29787	protein_coding	YES	CCDS6400.1	ENSP00000328835	TOP1M_HUMAN	E5KMK7_HUMAN,Q8TBP3_HUMAN,E5RJ95_HUMAN,E5RJ33_HUMAN,E5RFS0_HUMAN	UPI000013716D	.	.	.	9/14	.	hmmpanther:PTHR10290,Pfam_domain:PF01028,Gene3D:3.90.15.10,SMART_domains:SM00435,Superfamily_domains:SSF56349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGAAGAGGTC	.	5	ESCA
SLC7A2	0	.	GRCh37	8	17412103	17412103	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210A>G	p.Ile404Val	p.I404V	ENST00000004531	7/12	74	30	43	59	59	0	SLC7A2,missense_variant,p.Ile364Val,ENST00000522656,;SLC7A2,missense_variant,p.Ile364Val,ENST00000494857,;SLC7A2,missense_variant,p.Ile404Val,ENST00000004531,;SLC7A2,intron_variant,,ENST00000470360,;SLC7A2,intron_variant,,ENST00000398090,;	G	ENSG00000003989	ENST00000004531	Transcript	missense_variant	1258	1210	404	I/V	Atc/Gtc	.	.	.	1	SLC7A2	HGNC	11060	protein_coding	YES	CCDS55203.1	ENSP00000004531	CTR2_HUMAN	.	UPI0001A336A4	.	tolerated(0.15)	benign(0.026)	7/12	.	hmmpanther:PTHR11785:SF242,hmmpanther:PTHR11785,Pfam_domain:PF13520,TIGRFAM_domain:TIGR00906	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTAATCTAT	.	5	ESCA
NECAB1	0	.	GRCh37	8	91962044	91962044	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.870A>G	p.Ile290Met	p.I290M	ENST00000417640	11/13	58	34	24	70	70	0	NECAB1,missense_variant,p.Ile39Met,ENST00000521366,;NECAB1,missense_variant,p.Ile39Met,ENST00000522820,;NECAB1,missense_variant,p.Ile290Met,ENST00000417640,;	G	ENSG00000123119	ENST00000417640	Transcript	missense_variant	1207	870	290	I/M	atA/atG	.	.	.	1	NECAB1	HGNC	20983	protein_coding	YES	CCDS47889.1	ENSP00000387380	NECA1_HUMAN	.	UPI0000070EEA	.	deleterious(0.04)	possibly_damaging(0.828)	11/13	.	hmmpanther:PTHR12178:SF11,hmmpanther:PTHR12178,Pfam_domain:PF03992,Gene3D:3.30.70.900,Superfamily_domains:SSF54909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTATACAGAA	.	5	ESCA
RC3H2	0	.	GRCh37	9	125639797	125639797	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1278A>G	p.%3D	p.P426P	ENST00000373670	8/20	47	25	22	26	26	0	RC3H2,synonymous_variant,p.%3D,ENST00000373670,;RC3H2,synonymous_variant,p.%3D,ENST00000423239,;RC3H2,synonymous_variant,p.%3D,ENST00000373665,;RC3H2,synonymous_variant,p.%3D,ENST00000335387,;RC3H2,synonymous_variant,p.%3D,ENST00000357244,;SNORD90,downstream_gene_variant,,ENST00000391145,;RC3H2,synonymous_variant,p.%3D,ENST00000498479,;	C	ENSG00000056586	ENST00000373670	Transcript	synonymous_variant	1879	1278	426	P	ccA/ccG	.	.	.	-1	RC3H2	HGNC	21461	protein_coding	YES	CCDS43874.1	ENSP00000362774	RC3H2_HUMAN	.	UPI0000048D91	.	.	.	8/20	.	PROSITE_profiles:PS50103,hmmpanther:PTHR13139,hmmpanther:PTHR13139:SF2,Pfam_domain:PF00642,Gene3D:1m9oA00,SMART_domains:SM00356,Superfamily_domains:SSF90229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCGTGGACA	.	5	ESCA
SDCCAG3	0	.	GRCh37	9	139303480	139303480	+	Missense_Mutation	SNP	G	G	A	rs763112506	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.260C>T	p.Pro87Leu	p.P87L	ENST00000357365	3/10	20	15	5	34	34	0	SDCCAG3,missense_variant,p.Pro87Leu,ENST00000357365,;SDCCAG3,missense_variant,p.Pro37Leu,ENST00000371723,;SDCCAG3,intron_variant,,ENST00000446833,;SDCCAG3,intron_variant,,ENST00000298537,;SDCCAG3,intron_variant,,ENST00000371725,;SDCCAG3,upstream_gene_variant,,ENST00000417512,;PMPCA,upstream_gene_variant,,ENST00000371717,;PMPCA,upstream_gene_variant,,ENST00000399219,;PMPCA,upstream_gene_variant,,ENST00000371720,;SDCCAG3,upstream_gene_variant,,ENST00000468963,;SDCCAG3,upstream_gene_variant,,ENST00000466579,;SDCCAG3,upstream_gene_variant,,ENST00000486441,;SDCCAG3,upstream_gene_variant,,ENST00000461693,;SDCCAG3,upstream_gene_variant,,ENST00000481114,;	A	ENSG00000165689	ENST00000357365	Transcript	missense_variant	390	260	87	P/L	cCg/cTg	rs763112506	.	.	-1	SDCCAG3	HGNC	10667	protein_coding	YES	CCDS43904.1	ENSP00000349929	SDCG3_HUMAN	.	UPI00006C511A	.	tolerated_low_confidence(0.08)	benign(0.02)	3/10	.	hmmpanther:PTHR31259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACGGGCTC	byFrequency	5	ESCA
FRMPD3	0	.	GRCh37	X	106846540	106846540	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5370C>T	p.%3D	p.G1790G	ENST00000276185	16/16	25	16	9	26	26	0	FRMPD3,synonymous_variant,p.%3D,ENST00000276185,;FRMPD3,synonymous_variant,p.%3D,ENST00000439554,;	T	ENSG00000147234	ENST00000276185	Transcript	synonymous_variant	5370	5370	1790	G	ggC/ggT	.	.	.	1	FRMPD3	HGNC	29382	protein_coding	YES	.	ENSP00000276185	FRPD3_HUMAN	.	UPI00006C1C33	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGCTCCCC	.	5	ESCA
MAGEC3	0	.	GRCh37	X	140983065	140983065	+	Missense_Mutation	SNP	C	C	T	rs756867913	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.920C>T	p.Ala307Val	p.A307V	ENST00000298296	5/8	16	5	11	23	23	0	MAGEC3,missense_variant,p.Ala59Val,ENST00000448920,;MAGEC3,missense_variant,p.Ala307Val,ENST00000298296,;MAGEC3,5_prime_UTR_variant,,ENST00000544766,;MAGEC3,intron_variant,,ENST00000443323,;MAGEC3,intron_variant,,ENST00000536088,;MAGEC3,upstream_gene_variant,,ENST00000409007,;MAGEC3,non_coding_transcript_exon_variant,,ENST00000483584,;	T	ENSG00000165509	ENST00000298296	Transcript	missense_variant	920	920	307	A/V	gCc/gTc	rs756867913	.	.	1	MAGEC3	HGNC	23798	protein_coding	YES	CCDS14676.1	ENSP00000298296	MAGC3_HUMAN	.	UPI000006E09B	.	deleterious(0.03)	benign(0.002)	5/8	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTCAGCCTTGG	byFrequency	2	ESCA
MAGEC3	0	.	GRCh37	X	140985273	140985273	+	Splice_Site	SNP	G	G	C	rs763585428	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1728+1G>C	.	p.X576_splice	ENST00000298296	.	27	10	17	24	24	0	MAGEC3,splice_donor_variant,,ENST00000298296,;MAGEC3,missense_variant,p.Val279Leu,ENST00000544766,;MAGEC3,missense_variant,p.Val279Leu,ENST00000409007,;MAGEC3,missense_variant,p.Val199Leu,ENST00000443323,;MAGEC3,missense_variant,p.Val279Leu,ENST00000536088,;MAGEC3,downstream_gene_variant,,ENST00000448920,;MAGEC3,downstream_gene_variant,,ENST00000483584,;	C	ENSG00000165509	ENST00000298296	Transcript	splice_donor_variant	.	.	.	.	.	rs763585428	.	.	1	MAGEC3	HGNC	23798	protein_coding	YES	CCDS14676.1	ENSP00000298296	MAGC3_HUMAN	.	UPI000006E09B	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGGGTGTGT	.	5	ESCA
DHRSX	0	.	GRCh37	X	2184836	2184836	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.541G>A	p.Val181Ile	p.V181I	ENST00000334651	5/7	144	121	23	132	132	0	DHRSX,missense_variant,p.Val158Ile,ENST00000412516,;DHRSX,missense_variant,p.Val181Ile,ENST00000334651,;DHRSX,missense_variant,p.Val114Ile,ENST00000444280,;DHRSX,non_coding_transcript_exon_variant,,ENST00000464935,;DHRSX,downstream_gene_variant,,ENST00000441131,;	T	ENSG00000169084	ENST00000334651	Transcript	missense_variant	594	541	181	V/I	Gtc/Atc	COSM3800541	.	.	-1	DHRSX	HGNC	18399	protein_coding	YES	CCDS35195.1	ENSP00000334113	DHRSX_HUMAN	C9JRH1_HUMAN	UPI0000D61D1C	.	deleterious(0.03)	possibly_damaging(0.595)	5/7	.	hmmpanther:PTHR24319,hmmpanther:PTHR24319:SF30,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGACGGTGA	.	4	ESCA
MXRA5	0	.	GRCh37	X	3228543	3228543	+	Silent	SNP	C	C	T	rs761736143	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7701G>A	p.%3D	p.A2567A	ENST00000217939	7/7	26	22	4	20	20	0	MXRA5,synonymous_variant,p.%3D,ENST00000217939,;	T	ENSG00000101825	ENST00000217939	Transcript	synonymous_variant	7856	7701	2567	A	gcG/gcA	rs761736143	.	.	-1	MXRA5	HGNC	7539	protein_coding	YES	CCDS14124.1	ENSP00000217939	MXRA5_HUMAN	.	UPI000013C73B	.	.	.	7/7	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF582,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCCCCGCGGC	byFrequency	4	ESCA
PRRG1	0	.	GRCh37	X	37300914	37300914	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A4A6-01A-11D-A27G-09	TCGA-LN-A4A6-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172-11475G>T	.	.	ENST00000542554	.	23	8	15	29	29	0	PRRG1,3_prime_UTR_variant,,ENST00000463135,;PRRG1,intron_variant,,ENST00000466533,;TM4SF2,intron_variant,,ENST00000465127,;PRRG1,intron_variant,,ENST00000543642,;PRRG1,intron_variant,,ENST00000542554,;PRRG1,intron_variant,,ENST00000449135,;PRRG1,intron_variant,,ENST00000484460,;PRRG1,intron_variant,,ENST00000378628,;PRRG1,intron_variant,,ENST00000491253,;PRRG1,intron_variant,,ENST00000470290,;RP11-357K9.2,non_coding_transcript_exon_variant,,ENST00000413104,;	T	ENSG00000130962	ENST00000542554	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PRRG1	HGNC	9469	protein_coding	YES	CCDS14239.1	ENSP00000444278	TMG1_HUMAN	C9JNY5_HUMAN,C9J6P5_HUMAN	UPI0000137077	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATGCGGCC	.	5	ESCA
PLXDC2	0	.	GRCh37	10	20568836	20568836	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*88C>T	.	.	ENST00000377252	14/14	13	8	5	14	14	0	PLXDC2,3_prime_UTR_variant,,ENST00000377242,;PLXDC2,3_prime_UTR_variant,,ENST00000377252,;PLXDC2,non_coding_transcript_exon_variant,,ENST00000377238,;	T	ENSG00000120594	ENST00000377252	Transcript	3_prime_UTR_variant	2519	.	.	.	.	.	.	.	1	PLXDC2	HGNC	21013	protein_coding	YES	CCDS7132.1	ENSP00000366460	PXDC2_HUMAN	.	UPI0000048F2C	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	AAACACACACA	.	4	ESCA
PCDH15	0	.	GRCh37	10	56424015	56424015	+	Missense_Mutation	SNP	C	C	T	rs372085398	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8G>A	p.Arg3Gln	p.R3Q	ENST00000361849	2/34	19	6	12	33	33	0	PCDH15,missense_variant,p.Arg3Gln,ENST00000437009,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395433,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395445,;PCDH15,missense_variant,p.Arg3Gln,ENST00000320301,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395432,;PCDH15,missense_variant,p.Arg3Gln,ENST00000373955,;PCDH15,missense_variant,p.Arg3Gln,ENST00000373957,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395440,;PCDH15,missense_variant,p.Arg3Gln,ENST00000361849,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395438,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395446,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395442,;PCDH15,missense_variant,p.Arg3Gln,ENST00000414778,;PCDH15,missense_variant,p.Arg3Gln,ENST00000458638,;PCDH15,missense_variant,p.Arg3Gln,ENST00000373965,;PCDH15,missense_variant,p.Arg3Gln,ENST00000395430,;PCDH15,5_prime_UTR_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Arg3Gln,ENST00000448885,;PCDH15,missense_variant,p.Arg3Gln,ENST00000373956,;PCDH15,missense_variant,p.Arg3Gln,ENST00000414367,;	T	ENSG00000150275	ENST00000361849	Transcript	missense_variant	403	8	3	R/Q	cGa/cAa	rs372085398	.	.	-1	PCDH15	HGNC	14674	protein_coding	YES	CCDS44404.1	ENSP00000354950	.	A2A3E7_HUMAN,A2A3D9_HUMAN	UPI0000EE048B	.	tolerated_low_confidence(1)	benign(0.003)	2/34	.	Cleavage_site_(Signalp):SignalP-noTM	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTCGAAAC	byCluster|by1000G	5	ESCA
SEC24C	0	.	GRCh37	10	75526572	75526572	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1854A>T	p.%3D	p.V618V	ENST00000339365	14/24	54	37	17	43	43	0	SEC24C,synonymous_variant,p.%3D,ENST00000345254,;SEC24C,synonymous_variant,p.%3D,ENST00000411652,;SEC24C,synonymous_variant,p.%3D,ENST00000339365,;SEC24C,intron_variant,,ENST00000540668,;SEC24C,intron_variant,,ENST00000535742,;SEC24C,downstream_gene_variant,,ENST00000546025,;SEC24C,upstream_gene_variant,,ENST00000496827,;SEC24C,synonymous_variant,p.%3D,ENST00000465076,;	T	ENSG00000176986	ENST00000339365	Transcript	synonymous_variant	2016	1854	618	V	gtA/gtT	.	.	.	1	SEC24C	HGNC	10705	protein_coding	YES	CCDS7332.1	ENSP00000343405	SC24C_HUMAN	B4DZT4_HUMAN	UPI000013F621	.	.	.	14/24	.	hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF5,Pfam_domain:PF04811,Gene3D:3.40.50.410,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGTATTTGT	.	5	ESCA
YAP1	0	.	GRCh37	11	102098302	102098302	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1266G>C	p.Glu422Asp	p.E422D	ENST00000282441	8/9	58	34	24	77	77	0	YAP1,missense_variant,p.Glu368Asp,ENST00000526343,;YAP1,missense_variant,p.Glu176Asp,ENST00000529029,;YAP1,missense_variant,p.Glu410Asp,ENST00000537274,;YAP1,missense_variant,p.Glu406Asp,ENST00000531439,;YAP1,missense_variant,p.Glu422Asp,ENST00000282441,;YAP1,missense_variant,p.Glu244Asp,ENST00000524575,;YAP1,missense_variant,p.Glu372Asp,ENST00000345877,;RP11-864G5.3,downstream_gene_variant,,ENST00000526310,;YAP1,non_coding_transcript_exon_variant,,ENST00000528834,;	C	ENSG00000137693	ENST00000282441	Transcript	missense_variant	1654	1266	422	E/D	gaG/gaC	.	.	.	1	YAP1	HGNC	16262	protein_coding	YES	CCDS44716.1	ENSP00000282441	YAP1_HUMAN	.	UPI00000746D8	.	tolerated(0.14)	possibly_damaging(0.574)	8/9	.	hmmpanther:PTHR17616,hmmpanther:PTHR17616:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAGATGGA	.	5	ESCA
CAPN1	0	.	GRCh37	11	64978923	64978924	+	3'UTR	INS	-	-	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*167dupC	.	.	ENST00000527323	21/21	27	15	12	20	20	0	CAPN1,3_prime_UTR_variant,,ENST00000279247,;CAPN1,3_prime_UTR_variant,,ENST00000524773,;CAPN1,3_prime_UTR_variant,,ENST00000527323,;CAPN1,3_prime_UTR_variant,,ENST00000533129,;CAPN1,3_prime_UTR_variant,,ENST00000533820,;SLC22A20,upstream_gene_variant,,ENST00000529062,;SLC22A20,upstream_gene_variant,,ENST00000525437,;SLC22A20,upstream_gene_variant,,ENST00000525264,;CAPN1,downstream_gene_variant,,ENST00000530495,;CAPN1,non_coding_transcript_exon_variant,,ENST00000530567,;CAPN1,non_coding_transcript_exon_variant,,ENST00000528165,;CAPN1,downstream_gene_variant,,ENST00000533704,;CAPN1,downstream_gene_variant,,ENST00000525013,;SLC22A20,upstream_gene_variant,,ENST00000454680,;SLC22A20,upstream_gene_variant,,ENST00000530038,;	C	ENSG00000014216	ENST00000527323	Transcript	3_prime_UTR_variant	2551-2552	.	.	.	.	.	.	.	1	CAPN1	HGNC	1476	protein_coding	YES	CCDS44644.1	ENSP00000431984	CAN1_HUMAN	E9PSA6_HUMAN,E9PQB3_HUMAN,E9PMC6_HUMAN,E9PLX0_HUMAN,E9PLC9_HUMAN,E9PJJ3_HUMAN,E9PJA6_HUMAN,E9PIA9_HUMAN	UPI0000000E05	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CATCTGCTCCG	.	2	ESCA
ARRB1	0	.	GRCh37	11	74985232	74985232	+	Missense_Mutation	SNP	G	G	A	rs200557530	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.800C>T	p.Thr267Met	p.T267M	ENST00000420843	11/16	37	13	23	73	73	0	ARRB1,missense_variant,p.Thr267Met,ENST00000360025,;ARRB1,missense_variant,p.Thr267Met,ENST00000420843,;ARRB1,missense_variant,p.Thr92Met,ENST00000532447,;ARRB1,missense_variant,p.Thr267Met,ENST00000393505,;ARRB1,downstream_gene_variant,,ENST00000532525,;ARRB1,non_coding_transcript_exon_variant,,ENST00000529741,;ARRB1,non_coding_transcript_exon_variant,,ENST00000531012,;ARRB1,downstream_gene_variant,,ENST00000527385,;ARRB1,downstream_gene_variant,,ENST00000533609,;ARRB1,downstream_gene_variant,,ENST00000524400,;	A	ENSG00000137486	ENST00000420843	Transcript	missense_variant	898	800	267	T/M	aCg/aTg	rs200557530,COSM1676306	.	.	-1	ARRB1	HGNC	711	protein_coding	YES	CCDS44684.1	ENSP00000409581	ARRB1_HUMAN	.	UPI0000126076	.	deleterious(0.01)	possibly_damaging(0.863)	11/16	.	hmmpanther:PTHR11792:SF22,hmmpanther:PTHR11792,Pfam_domain:PF02752,Gene3D:1g4mB02,SMART_domains:SM01017,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACGTCGAG	.	5	ESCA
TMEM41B	0	.	GRCh37	11	9304976	9304976	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.871G>C	p.Glu291Gln	p.E291Q	ENST00000528080	7/7	70	65	5	61	61	0	TMEM41B,missense_variant,p.Glu291Gln,ENST00000528080,;TMEM41B,downstream_gene_variant,,ENST00000527813,;TMEM41B,missense_variant,p.Glu291Gln,ENST00000299596,;TMEM41B,3_prime_UTR_variant,,ENST00000524543,;TMEM41B,non_coding_transcript_exon_variant,,ENST00000533867,;	G	ENSG00000166471	ENST00000528080	Transcript	missense_variant	1210	871	291	E/Q	Gag/Cag	COSM415697	.	.	-1	TMEM41B	HGNC	28948	protein_coding	YES	CCDS31424.1	ENSP00000433126	TM41B_HUMAN	.	UPI00001C1EF6	.	tolerated(0.19)	benign(0.126)	7/7	.	hmmpanther:PTHR12677:SF15,hmmpanther:PTHR12677	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTACTCAAATT	.	2	ESCA
SWAP70	0	.	GRCh37	11	9749710	9749710	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753A>T	p.Lys251Asn	p.K251N	ENST00000318950	5/12	32	24	7	17	17	0	SWAP70,missense_variant,p.Lys193Asn,ENST00000447399,;SWAP70,missense_variant,p.Lys102Asn,ENST00000534662,;SWAP70,missense_variant,p.Lys251Asn,ENST00000318950,;SWAP70,3_prime_UTR_variant,,ENST00000534562,;SWAP70,non_coding_transcript_exon_variant,,ENST00000524817,;SWAP70,downstream_gene_variant,,ENST00000531814,;SWAP70,downstream_gene_variant,,ENST00000526358,;	T	ENSG00000133789	ENST00000318950	Transcript	missense_variant	856	753	251	K/N	aaA/aaT	.	.	.	1	SWAP70	HGNC	17070	protein_coding	YES	CCDS31426.1	ENSP00000315630	SWP70_HUMAN	E9PJM7_HUMAN	UPI0000073652	.	deleterious(0)	probably_damaging(0.928)	5/12	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF50729,SMART_domains:SM00233,Gene3D:2.30.29.30,Pfam_domain:PF00169,hmmpanther:PTHR14383,hmmpanther:PTHR14383:SF6,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAAGGAGA	.	5	ESCA
GIT2	0	.	GRCh37	12	110383086	110383086	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1710G>T	p.%3D	p.S570S	ENST00000355312	16/20	27	15	12	23	23	0	GIT2,synonymous_variant,p.%3D,ENST00000338373,;GIT2,synonymous_variant,p.%3D,ENST00000355312,;GIT2,synonymous_variant,p.%3D,ENST00000551209,;GIT2,synonymous_variant,p.%3D,ENST00000360185,;GIT2,intron_variant,,ENST00000361006,;GIT2,intron_variant,,ENST00000356259,;GIT2,intron_variant,,ENST00000457474,;GIT2,intron_variant,,ENST00000550186,;GIT2,intron_variant,,ENST00000553118,;GIT2,intron_variant,,ENST00000343646,;GIT2,intron_variant,,ENST00000354574,;GIT2,downstream_gene_variant,,ENST00000320063,;GIT2,downstream_gene_variant,,ENST00000547815,;TCHP,intron_variant,,ENST00000550780,;GIT2,upstream_gene_variant,,ENST00000548000,;GIT2,upstream_gene_variant,,ENST00000548655,;GIT2,intron_variant,,ENST00000549999,;TCHP,intron_variant,,ENST00000544838,;	A	ENSG00000139436	ENST00000355312	Transcript	synonymous_variant	1710	1710	570	S	tcG/tcT	.	.	.	-1	GIT2	HGNC	4273	protein_coding	YES	CCDS9138.1	ENSP00000347464	GIT2_HUMAN	.	UPI000012B4C5	.	.	.	16/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF215	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCCTCGACCA	.	3	ESCA
SLCO1A2	0	.	GRCh37	12	21448561	21448561	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1241C>T	p.Ser414Leu	p.S414L	ENST00000307378	11/16	60	53	7	39	39	0	SLCO1A2,missense_variant,p.Ser412Leu,ENST00000390670,;SLCO1A2,missense_variant,p.Ser414Leu,ENST00000307378,;SLCO1A2,missense_variant,p.Ser282Leu,ENST00000537524,;SLCO1A2,missense_variant,p.Ser414Leu,ENST00000452078,;SLCO1A2,missense_variant,p.Ser282Leu,ENST00000458504,;SLCO1A2,3_prime_UTR_variant,,ENST00000544020,;SLCO1A2,3_prime_UTR_variant,,ENST00000544290,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000480394,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000463718,;	A	ENSG00000084453	ENST00000307378	Transcript	missense_variant	1962	1241	414	S/L	tCa/tTa	.	.	.	-1	SLCO1A2	HGNC	10956	protein_coding	YES	CCDS8686.1	ENSP00000305974	SO1A2_HUMAN	C9K059_HUMAN,C9JUW6_HUMAN,C9JTF6_HUMAN,C9JHU9_HUMAN,C9JGK7_HUMAN,C9JG34_HUMAN,C9JCA7_HUMAN,B4DJE6_HUMAN	UPI0000037575	.	tolerated(0.17)	benign(0.008)	11/16	.	TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,hmmpanther:PTHR11388:SF16,hmmpanther:PTHR11388,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACTGAAGAA	.	4	ESCA
EFCAB4B	0	.	GRCh37	12	3736823	3736823	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1785C>T	p.%3D	p.A595A	ENST00000440314	16/20	200	190	10	42	42	0	EFCAB4B,synonymous_variant,p.%3D,ENST00000440314,;EFCAB4B,3_prime_UTR_variant,,ENST00000333750,;	A	ENSG00000130038	ENST00000440314	Transcript	synonymous_variant	2259	1785	595	A	gcC/gcT	.	.	.	-1	EFCAB4B	HGNC	28657	protein_coding	YES	CCDS44803.1	ENSP00000409382	EFC4B_HUMAN	.	UPI00017A8807	.	.	.	16/20	.	PROSITE_profiles:PS51419,hmmpanther:PTHR22621,hmmpanther:PTHR22621:SF2,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00177,SMART_domains:SM00174,SMART_domains:SM00176,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCAGGGCCAC	.	2	ESCA
ADCY6	0	.	GRCh37	12	49161441	49161441	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*933C>T	.	.	ENST00000307885	21/21	39	35	3	36	36	0	ADCY6,3_prime_UTR_variant,,ENST00000307885,;ADCY6,3_prime_UTR_variant,,ENST00000550422,;ADCY6,3_prime_UTR_variant,,ENST00000357869,;LINC00935,downstream_gene_variant,,ENST00000548380,;MIR4701,downstream_gene_variant,,ENST00000583094,;RP11-579D7.2,downstream_gene_variant,,ENST00000548742,;ADCY6,downstream_gene_variant,,ENST00000548351,;ADCY6,non_coding_transcript_exon_variant,,ENST00000547260,;LINC00935,downstream_gene_variant,,ENST00000548054,;ADCY6,downstream_gene_variant,,ENST00000552099,;	A	ENSG00000174233	ENST00000307885	Transcript	3_prime_UTR_variant	5135	.	.	.	.	.	.	.	-1	ADCY6	HGNC	237	protein_coding	YES	CCDS8767.1	ENSP00000311405	ADCY6_HUMAN	Q9NR74_HUMAN,Q6LCE1_HUMAN	UPI000003EC29	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAAGAGGAA	.	4	ESCA
ACVR1B	0	.	GRCh37	12	52380769	52380769	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1384+43A>T	.	.	ENST00000541224	.	69	30	39	63	63	0	ACVR1B,missense_variant,p.Asp435Val,ENST00000415850,;ACVR1B,intron_variant,,ENST00000426655,;ACVR1B,intron_variant,,ENST00000541224,;ACVR1B,intron_variant,,ENST00000257963,;ACVR1B,intron_variant,,ENST00000542485,;RNU6-574P,upstream_gene_variant,,ENST00000384265,;ACVR1B,intron_variant,,ENST00000563121,;	T	ENSG00000135503	ENST00000541224	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ACVR1B	HGNC	172	protein_coding	YES	CCDS44894.2	ENSP00000442656	ACV1B_HUMAN	F5H5Q2_HUMAN	UPI0001915052	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGATGCTG	.	5	ESCA
RBMS2	0	.	GRCh37	12	56965518	56965518	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.421A>G	p.Asn141Asp	p.N141D	ENST00000262031	5/14	43	17	26	30	30	0	RBMS2,missense_variant,p.Asn16Asp,ENST00000550726,;RBMS2,missense_variant,p.Asn141Asp,ENST00000262031,;RBMS2,missense_variant,p.Asn141Asp,ENST00000552247,;RBMS2,intron_variant,,ENST00000542360,;RBMS2,non_coding_transcript_exon_variant,,ENST00000552228,;RBMS2,downstream_gene_variant,,ENST00000549945,;RBMS2,3_prime_UTR_variant,,ENST00000551369,;RBMS2,3_prime_UTR_variant,,ENST00000552916,;	G	ENSG00000076067	ENST00000262031	Transcript	missense_variant	516	421	141	N/D	Aac/Gac	.	.	.	1	RBMS2	HGNC	9909	protein_coding	YES	CCDS8923.1	ENSP00000262031	RBMS2_HUMAN	F8VV01_HUMAN	UPI000006EEB0	.	deleterious(0)	benign(0.366)	5/14	.	Superfamily_domains:SSF54928,SMART_domains:SM00360,Pfam_domain:PF00076,Gene3D:3.30.70.330,hmmpanther:PTHR24011:SF257,hmmpanther:PTHR24011,PROSITE_profiles:PS50102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCAAACCTC	.	5	ESCA
VWF	0	.	GRCh37	12	6128641	6128641	+	Missense_Mutation	SNP	G	G	A	rs61749395	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3943C>T	p.Arg1315Cys	p.R1315C	ENST00000261405	28/52	697	636	61	92	92	0	VWF,missense_variant,p.Arg1315Cys,ENST00000261405,;VWF,intron_variant,,ENST00000538635,;VWF,downstream_gene_variant,,ENST00000539641,;	A	ENSG00000110799	ENST00000261405	Transcript	missense_variant	4198	3943	1315	R/C	Cgc/Tgc	rs61749395,CM941402,VWF_c.3943C>T,COSM1704940	.	.	-1	VWF	HGNC	12726	protein_coding	YES	CCDS8539.1	ENSP00000261405	VWF_HUMAN	H2DLA2_HUMAN	UPI00001AE7EE	.	deleterious(0)	probably_damaging(0.992)	28/52	.	PROSITE_profiles:PS50234,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF259,Gene3D:3.40.50.410,Pfam_domain:PF00092,PIRSF_domain:PIRSF002495,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	not_provided	0,0,0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CACGCGGACCC	.	3	ESCA
CD4	0	.	GRCh37	12	6924124	6924124	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.573G>A	p.%3D	p.K191K	ENST00000011653	5/10	52	45	6	33	33	0	CD4,synonymous_variant,p.%3D,ENST00000541982,;CD4,synonymous_variant,p.%3D,ENST00000011653,;CD4,non_coding_transcript_exon_variant,,ENST00000536563,;CD4,non_coding_transcript_exon_variant,,ENST00000538827,;CD4,downstream_gene_variant,,ENST00000536590,;CD4,downstream_gene_variant,,ENST00000536610,;CD4,non_coding_transcript_exon_variant,,ENST00000544344,;CD4,non_coding_transcript_exon_variant,,ENST00000437800,;CD4,downstream_gene_variant,,ENST00000543755,;	A	ENSG00000010610	ENST00000011653	Transcript	synonymous_variant	831	573	191	K	aaG/aaA	COSM3872318	.	.	1	CD4	HGNC	1678	protein_coding	YES	CCDS8562.1	ENSP00000011653	CD4_HUMAN	Q6LCP8_HUMAN,Q13969_HUMAN,F5GYA9_HUMAN,B4DT49_HUMAN	UPI0000001294	.	.	.	5/10	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00408,Gene3D:2.60.40.10,Pfam_domain:PF05790,hmmpanther:PTHR11422:SF0,hmmpanther:PTHR11422	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAAGAAGGT	.	4	ESCA
TBC1D15	0	.	GRCh37	12	72312261	72312261	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1583G>T	p.Cys528Phe	p.C528F	ENST00000550746	15/18	103	56	47	70	70	0	TBC1D15,missense_variant,p.Cys519Phe,ENST00000319106,;TBC1D15,missense_variant,p.Cys511Phe,ENST00000485960,;TBC1D15,missense_variant,p.Cys528Phe,ENST00000550746,;TBC1D15,missense_variant,p.Cys282Phe,ENST00000393309,;TBC1D15,non_coding_transcript_exon_variant,,ENST00000548679,;TBC1D15,3_prime_UTR_variant,,ENST00000462788,;TBC1D15,non_coding_transcript_exon_variant,,ENST00000546450,;TBC1D15,downstream_gene_variant,,ENST00000483828,;	T	ENSG00000121749	ENST00000550746	Transcript	missense_variant	1647	1583	528	C/F	tGc/tTc	.	.	.	1	TBC1D15	HGNC	25694	protein_coding	YES	CCDS31858.1	ENSP00000448182	TBC15_HUMAN	Q9NSR4_HUMAN,F8VV61_HUMAN,A8K8E1_HUMAN	UPI000049DD7C	.	deleterious(0)	probably_damaging(0.999)	15/18	.	PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF250,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTGCTTCA	.	5	ESCA
CD163	0	.	GRCh37	12	7649729	7649729	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.779A>G	p.Lys260Arg	p.K260R	ENST00000359156	5/17	165	131	34	65	65	0	CD163,missense_variant,p.Lys248Arg,ENST00000541972,;CD163,missense_variant,p.Lys260Arg,ENST00000432237,;CD163,missense_variant,p.Lys260Arg,ENST00000359156,;CD163,missense_variant,p.Lys260Arg,ENST00000396620,;CD163,splice_region_variant,,ENST00000537044,;	C	ENSG00000177575	ENST00000359156	Transcript	missense_variant	982	779	260	K/R	aAg/aGg	.	.	.	-1	CD163	HGNC	1631	protein_coding	YES	CCDS8578.1	ENSP00000352071	C163A_HUMAN	.	UPI00004565CC	.	tolerated(0.11)	benign(0.017)	5/17	.	hmmpanther:PTHR19331:SF268,hmmpanther:PTHR19331,Superfamily_domains:SSF56487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCTCTGTA	.	5	ESCA
NAV3	0	.	GRCh37	12	78400821	78400821	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1503A>G	p.%3D	p.K501K	ENST00000536525	8/39	30	20	10	14	14	0	NAV3,synonymous_variant,p.%3D,ENST00000266692,;NAV3,synonymous_variant,p.%3D,ENST00000549464,;NAV3,synonymous_variant,p.%3D,ENST00000536525,;NAV3,synonymous_variant,p.%3D,ENST00000397909,;NAV3,synonymous_variant,p.%3D,ENST00000228327,;NAV3,downstream_gene_variant,,ENST00000550503,;NAV3,downstream_gene_variant,,ENST00000547725,;NAV3,upstream_gene_variant,,ENST00000550673,;	G	ENSG00000067798	ENST00000536525	Transcript	synonymous_variant	1676	1503	501	K	aaA/aaG	.	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	.	.	8/39	.	hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAAAATTGC	.	5	ESCA
CCDC41	0	.	GRCh37	12	94772658	94772658	+	Missense_Mutation	SNP	T	T	A	rs35337948	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.710A>T	p.Glu237Val	p.E237V	ENST00000397809	7/17	88	46	41	63	63	0	CCDC41,missense_variant,p.Glu204Val,ENST00000397807,;CCDC41,missense_variant,p.Glu237Val,ENST00000397809,;CCDC41,missense_variant,p.Glu237Val,ENST00000339839,;CCDC41,missense_variant,p.Glu237Val,ENST00000547575,;CCDC41,non_coding_transcript_exon_variant,,ENST00000549352,;CCDC41,non_coding_transcript_exon_variant,,ENST00000551250,;CCDC41,missense_variant,p.Glu204Val,ENST00000547232,;	A	ENSG00000173588	ENST00000397809	Transcript	missense_variant	1260	710	237	E/V	gAa/gTa	rs35337948	.	.	-1	CCDC41	HGNC	17966	protein_coding	YES	CCDS41820.1	ENSP00000380911	.	J3KNW7_HUMAN,H0YHH5_HUMAN	UPI0000D4BD6F	.	deleterious(0)	probably_damaging(0.999)	7/17	.	hmmpanther:PTHR23170,hmmpanther:PTHR23170:SF2,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTTCAGCC	.	5	ESCA
HAL	0	.	GRCh37	12	96387577	96387577	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524G>C	p.Arg175Thr	p.R175T	ENST00000261208	7/21	44	39	5	29	29	0	HAL,missense_variant,p.Arg175Thr,ENST00000261208,;HAL,missense_variant,p.Arg85Thr,ENST00000546579,;HAL,missense_variant,p.Arg175Thr,ENST00000538703,;HAL,intron_variant,,ENST00000541929,;HAL,intron_variant,,ENST00000552509,;RP11-256L6.3,upstream_gene_variant,,ENST00000551849,;HAL,upstream_gene_variant,,ENST00000551562,;HAL,intron_variant,,ENST00000544080,;HAL,intron_variant,,ENST00000546999,;HAL,upstream_gene_variant,,ENST00000549376,;	G	ENSG00000084110	ENST00000261208	Transcript	missense_variant	893	524	175	R/T	aGa/aCa	.	.	.	-1	HAL	HGNC	4806	protein_coding	YES	CCDS9058.1	ENSP00000261208	HUTH_HUMAN	Q2PH61_HUMAN,Q2PH60_HUMAN,Q2PH56_HUMAN	UPI000012CE8E	.	tolerated(0.12)	benign(0.016)	7/21	.	Superfamily_domains:SSF48557,Pfam_domain:PF00221,Gene3D:1.10.275.10,TIGRFAM_domain:TIGR01225,hmmpanther:PTHR10362,hmmpanther:PTHR10362:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTTCTGGCA	.	4	ESCA
ANKS1B	0	.	GRCh37	12	99138763	99138763	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3672+6370G>T	.	.	ENST00000547776	.	45	30	14	19	19	0	ANKS1B,3_prime_UTR_variant,,ENST00000549493,;ANKS1B,3_prime_UTR_variant,,ENST00000550693,;ANKS1B,3_prime_UTR_variant,,ENST00000549025,;ANKS1B,intron_variant,,ENST00000547010,;ANKS1B,intron_variant,,ENST00000341752,;ANKS1B,intron_variant,,ENST00000329257,;ANKS1B,intron_variant,,ENST00000549558,;ANKS1B,intron_variant,,ENST00000547776,;ANKS1B,downstream_gene_variant,,ENST00000333732,;ANKS1B,downstream_gene_variant,,ENST00000550778,;ANKS1B,downstream_gene_variant,,ENST00000547446,;ANKS1B,downstream_gene_variant,,ENST00000546568,;ANKS1B,downstream_gene_variant,,ENST00000546960,;ANKS1B,downstream_gene_variant,,ENST00000332712,;ANKS1B,intron_variant,,ENST00000551212,;ANKS1B,intron_variant,,ENST00000555119,;ANKS1B,downstream_gene_variant,,ENST00000547362,;	A	ENSG00000185046	ENST00000547776	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ANKS1B	HGNC	24600	protein_coding	YES	CCDS55872.1	ENSP00000449629	ANS1B_HUMAN	R4GN73_HUMAN,R4GN70_HUMAN,R4GN07_HUMAN	UPI00003FE521	.	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AACATCCCTCG	.	3	ESCA
STARD13	0	.	GRCh37	13	33760148	33760148	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.170-18389C>A	.	.	ENST00000336934	.	28	15	13	27	27	0	STARD13,synonymous_variant,p.%3D,ENST00000255486,;STARD13,intron_variant,,ENST00000567873,;STARD13,intron_variant,,ENST00000336934,;STARD13,intron_variant,,ENST00000399365,;STARD13,intron_variant,,ENST00000498019,;STARD13,intron_variant,,ENST00000487412,;	T	ENSG00000133121	ENST00000336934	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	STARD13	HGNC	19164	protein_coding	YES	CCDS9348.1	ENSP00000338785	STA13_HUMAN	B3KT04_HUMAN,B2R789_HUMAN	UPI000006226E	.	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGAGGGTTC	.	5	ESCA
SLC25A15	0	.	GRCh37	13	41379274	41379274	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.335C>G	p.Ala112Gly	p.A112G	ENST00000338625	4/7	51	37	13	70	70	0	SLC25A15,missense_variant,p.Ala112Gly,ENST00000338625,;SLC25A15,intron_variant,,ENST00000417731,;SLC25A15,non_coding_transcript_exon_variant,,ENST00000478827,;SLC25A15,3_prime_UTR_variant,,ENST00000470509,;	G	ENSG00000102743	ENST00000338625	Transcript	missense_variant	571	335	112	A/G	gCc/gGc	.	.	.	1	SLC25A15	HGNC	10985	protein_coding	YES	CCDS9373.1	ENSP00000342267	ORNT1_HUMAN	F2Z354_HUMAN	UPI0000130E9D	.	deleterious(0)	probably_damaging(0.936)	4/7	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF192,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGCCGGTT	.	5	ESCA
HNRNPA1L2	0	.	GRCh37	13	53203463	53203463	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-334G>T	.	.	ENST00000342657	4/7	17	12	4	16	16	0	HNRNPA1L2,5_prime_UTR_variant,,ENST00000342657,;HNRNPA1L2,intron_variant,,ENST00000398039,;MRPS31P4,non_coding_transcript_exon_variant,,ENST00000509685,;	T	ENSG00000139675	ENST00000342657	Transcript	5_prime_UTR_variant	740	.	.	.	.	.	.	.	1	HNRNPA1L2	HGNC	27067	protein_coding	YES	CCDS31980.1	ENSP00000341285	RA1L2_HUMAN	.	UPI00001618EB	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTGGCCTG	.	5	ESCA
SLC15A1	0	.	GRCh37	13	99358508	99358508	+	Splice_Site	SNP	C	C	G	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150-1G>C	.	p.X384_splice	ENST00000376503	.	42	39	3	39	39	0	SLC15A1,splice_acceptor_variant,,ENST00000376503,;	G	ENSG00000088386	ENST00000376503	Transcript	splice_acceptor_variant	.	.	.	.	.	COSM1686696	.	.	-1	SLC15A1	HGNC	10920	protein_coding	YES	CCDS9489.1	ENSP00000365686	S15A1_HUMAN	B2CQT6_HUMAN	UPI000013166F	.	.	.	.	15/22	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTTCTGAGC	.	2	ESCA
JPH4	0	.	GRCh37	14	24041033	24041033	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1248G>A	p.%3D	p.L416L	ENST00000397118	5/7	32	28	4	52	52	0	JPH4,synonymous_variant,p.%3D,ENST00000544177,;JPH4,synonymous_variant,p.%3D,ENST00000356300,;JPH4,synonymous_variant,p.%3D,ENST00000397118,;AP1G2,upstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000397120,;AP1G2,upstream_gene_variant,,ENST00000308724,;AP1G2,upstream_gene_variant,,ENST00000556843,;RP11-66N24.3,downstream_gene_variant,,ENST00000555968,;AP1G2,upstream_gene_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000557619,;AP1G2,upstream_gene_variant,,ENST00000556943,;AP1G2,upstream_gene_variant,,ENST00000554069,;AP1G2,upstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000556743,;AP1G2,upstream_gene_variant,,ENST00000535852,;AP1G2,upstream_gene_variant,,ENST00000460049,;JPH4,downstream_gene_variant,,ENST00000553505,;AP1G2,upstream_gene_variant,,ENST00000554816,;AP1G2,upstream_gene_variant,,ENST00000555896,;AP1G2,upstream_gene_variant,,ENST00000553756,;AP1G2,upstream_gene_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000465445,;	T	ENSG00000092051	ENST00000397118	Transcript	synonymous_variant	2151	1248	416	L	ctG/ctA	.	.	.	-1	JPH4	HGNC	20156	protein_coding	YES	CCDS9603.1	ENSP00000380307	JPH4_HUMAN	.	UPI00001C1F68	.	.	.	5/7	.	PIRSF_domain:PIRSF037387,hmmpanther:PTHR23085:SF14,hmmpanther:PTHR23085	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTGCAGGTC	.	4	ESCA
NUBPL	0	.	GRCh37	14	32030697	32030723	+	In_Frame_Del	DEL	GGTGGCGGGGCCACTGCCCCGCTTGGG	GGTGGCGGGGCCACTGCCCCGCTTGGG	-	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	GGTGGCGGGGCCACTGCCCCGCTTGGG	GGTGGCGGGGCCACTGCCCCGCTTGGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54_80delTGGCGGGGCCACTGCCCCGCTTGGGGG	p.Gly19_Gly27del	p.G19_G27del	ENST00000281081	1/11	53	30	23	40	40	0	NUBPL,inframe_deletion,p.Gly19_Gly27del,ENST00000550649,;NUBPL,inframe_deletion,p.Gly19_Gly27del,ENST00000281081,;NUBPL,intron_variant,,ENST00000550005,;NUBPL,upstream_gene_variant,,ENST00000551314,;CTD-2213F21.3,upstream_gene_variant,,ENST00000548096,;CTD-2213F21.4,upstream_gene_variant,,ENST00000547093,;NUBPL,non_coding_transcript_exon_variant,,ENST00000548937,;NUBPL,non_coding_transcript_exon_variant,,ENST00000550355,;NUBPL,downstream_gene_variant,,ENST00000552814,;NUBPL,inframe_deletion,p.Gly19_Gly27del,ENST00000552489,;NUBPL,inframe_deletion,p.Gly19_Gly27del,ENST00000547839,;NUBPL,inframe_deletion,p.Gly7_Gly15del,ENST00000549838,;	-	ENSG00000151413	ENST00000281081	Transcript	inframe_deletion	97-123	52-78	18-26	GGGATAPLG/-	GGTGGCGGGGCCACTGCCCCGCTTGGG/-	.	.	.	1	NUBPL	HGNC	20278	protein_coding	YES	CCDS41940.1	ENSP00000281081	NUBPL_HUMAN	F8W061_HUMAN,B3KSK2_HUMAN	UPI00003669AB	.	.	.	1/11	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23264,hmmpanther:PTHR23264:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	CGGGCTGGTGGCGGGGCCACTGCCCCGCTTGGGGGAAG	.	2	ESCA
SPTSSA	0	.	GRCh37	14	34903750	34903750	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*657T>G	.	.	ENST00000298130	2/2	51	33	18	59	59	0	SPTSSA,3_prime_UTR_variant,,ENST00000298130,;EGLN3,intron_variant,,ENST00000551935,;	C	ENSG00000165389	ENST00000298130	Transcript	3_prime_UTR_variant	1022	.	.	.	.	.	.	.	-1	SPTSSA	HGNC	20361	protein_coding	YES	CCDS9647.2	ENSP00000298130	SPTSA_HUMAN	.	UPI000015D305	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAATATTTAA	.	5	ESCA
NID2	0	.	GRCh37	14	52471901	52471901	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*303T>C	.	.	ENST00000216286	22/22	20	14	5	15	15	0	NID2,3_prime_UTR_variant,,ENST00000541773,;NID2,3_prime_UTR_variant,,ENST00000216286,;C14orf166,downstream_gene_variant,,ENST00000553362,;NID2,downstream_gene_variant,,ENST00000556572,;C14orf166,downstream_gene_variant,,ENST00000261700,;C14orf166,downstream_gene_variant,,ENST00000556760,;C14orf166,downstream_gene_variant,,ENST00000555319,;NID2,downstream_gene_variant,,ENST00000553297,;NID2,downstream_gene_variant,,ENST00000555310,;C14orf166,downstream_gene_variant,,ENST00000557553,;NID2,downstream_gene_variant,,ENST00000556686,;C14orf166,downstream_gene_variant,,ENST00000553479,;	G	ENSG00000087303	ENST00000216286	Transcript	3_prime_UTR_variant	4431	.	.	.	.	.	.	.	-1	NID2	HGNC	13389	protein_coding	YES	CCDS9706.1	ENSP00000216286	NID2_HUMAN	.	UPI000013C6E1	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGAATGAAT	.	5	ESCA
MNAT1	0	.	GRCh37	14	61275047	61275047	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321C>T	p.%3D	p.F107F	ENST00000261245	4/8	41	36	5	56	56	0	MNAT1,synonymous_variant,p.%3D,ENST00000261245,;MNAT1,synonymous_variant,p.%3D,ENST00000554002,;MNAT1,synonymous_variant,p.%3D,ENST00000539616,;MNAT1,upstream_gene_variant,,ENST00000557134,;MNAT1,non_coding_transcript_exon_variant,,ENST00000556525,;MNAT1,non_coding_transcript_exon_variant,,ENST00000553354,;MNAT1,non_coding_transcript_exon_variant,,ENST00000556764,;MNAT1,upstream_gene_variant,,ENST00000554641,;	T	ENSG00000020426	ENST00000261245	Transcript	synonymous_variant	422	321	107	F	ttC/ttT	.	.	.	1	MNAT1	HGNC	7181	protein_coding	YES	CCDS9750.1	ENSP00000261245	MAT1_HUMAN	H0YJ92_HUMAN	UPI000002FC14	.	.	.	4/8	.	PIRSF_domain:PIRSF003338,TIGRFAM_domain:TIGR00570,Pfam_domain:PF06391,hmmpanther:PTHR12683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTTCAACTT	.	2	ESCA
WDR89	0	.	GRCh37	14	64066414	64066414	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>A	p.Asp83Asn	p.D83N	ENST00000394942	2/2	25	15	10	30	30	0	WDR89,missense_variant,p.Asp83Asn,ENST00000394942,;WDR89,missense_variant,p.Asp83Asn,ENST00000554717,;WDR89,missense_variant,p.Asp83Asn,ENST00000267522,;CTD-2302E22.2,downstream_gene_variant,,ENST00000553983,;CTD-2302E22.5,upstream_gene_variant,,ENST00000603606,;HSPE1P2,upstream_gene_variant,,ENST00000554777,;	T	ENSG00000140006	ENST00000394942	Transcript	missense_variant	336	247	83	D/N	Gac/Aac	.	.	.	-1	WDR89	HGNC	20489	protein_coding	YES	CCDS9759.1	ENSP00000378399	WDR89_HUMAN	G3V4B8_HUMAN	UPI000000CBD9	.	tolerated(0.31)	benign(0.033)	2/2	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR22889,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTCACAGG	.	5	ESCA
MAX	0	.	GRCh37	14	65542289	65542289	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*905A>G	.	.	ENST00000358664	5/5	22	13	9	16	16	0	MAX,3_prime_UTR_variant,,ENST00000284165,;MAX,3_prime_UTR_variant,,ENST00000555932,;MAX,3_prime_UTR_variant,,ENST00000358402,;MAX,3_prime_UTR_variant,,ENST00000358664,;MAX,intron_variant,,ENST00000341653,;MAX,downstream_gene_variant,,ENST00000556979,;MAX,downstream_gene_variant,,ENST00000556443,;MAX,downstream_gene_variant,,ENST00000557277,;MAX,downstream_gene_variant,,ENST00000556892,;MAX,downstream_gene_variant,,ENST00000557746,;MAX,downstream_gene_variant,,ENST00000555419,;MAX,downstream_gene_variant,,ENST00000555667,;MAX,3_prime_UTR_variant,,ENST00000394606,;MAX,downstream_gene_variant,,ENST00000553928,;MAX,downstream_gene_variant,,ENST00000553951,;	C	ENSG00000125952	ENST00000358664	Transcript	3_prime_UTR_variant	1519	.	.	.	.	.	.	.	-1	MAX	HGNC	6913	protein_coding	YES	CCDS9771.1	ENSP00000351490	MAX_HUMAN	G3V570_HUMAN	UPI0000000C63	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATCTGTCGC	.	5	ESCA
ELMSAN1	0	.	GRCh37	14	74181867	74181867	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4137C>G	.	.	ENST00000286523	12/12	34	28	6	32	32	0	ELMSAN1,3_prime_UTR_variant,,ENST00000286523,;ELMSAN1,3_prime_UTR_variant,,ENST00000394071,;ELMSAN1,downstream_gene_variant,,ENST00000435371,;PNMA1,upstream_gene_variant,,ENST00000316836,;ELMSAN1,downstream_gene_variant,,ENST00000423556,;ELMSAN1,non_coding_transcript_exon_variant,,ENST00000476562,;ELMSAN1,downstream_gene_variant,,ENST00000451078,;ELMSAN1,downstream_gene_variant,,ENST00000478847,;	C	ENSG00000156030	ENST00000286523	Transcript	3_prime_UTR_variant	8058	.	.	.	.	.	.	.	-1	ELMSAN1	HGNC	19853	protein_coding	YES	CCDS9819.1	ENSP00000286523	EMSA1_HUMAN	F6RU81_HUMAN,C9JYU7_HUMAN	UPI00001FD815	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACAGAAGAA	.	5	ESCA
YLPM1	0	.	GRCh37	14	75245163	75245163	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.887A>G	p.Tyr296Cys	p.Y296C	ENST00000325680	2/21	40	24	15	28	28	0	YLPM1,missense_variant,p.Tyr296Cys,ENST00000325680,;YLPM1,missense_variant,p.Tyr296Cys,ENST00000238571,;YLPM1,missense_variant,p.Tyr296Cys,ENST00000552421,;YLPM1,upstream_gene_variant,,ENST00000549293,;	G	ENSG00000119596	ENST00000325680	Transcript	missense_variant	1011	887	296	Y/C	tAt/tGt	.	.	.	1	YLPM1	HGNC	17798	protein_coding	YES	CCDS45135.1	ENSP00000324463	YLPM1_HUMAN	B4DMQ9_HUMAN	UPI00006C1433	.	.	unknown(0)	2/21	.	hmmpanther:PTHR13413:SF0,hmmpanther:PTHR13413	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTATTGGT	.	5	ESCA
YLPM1	0	.	GRCh37	14	75277108	75277108	+	Missense_Mutation	SNP	G	G	A	rs754951613	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5213G>A	p.Arg1738Gln	p.R1738Q	ENST00000325680	9/21	23	9	14	18	18	0	YLPM1,missense_variant,p.Arg147Gln,ENST00000547879,;YLPM1,missense_variant,p.Arg1738Gln,ENST00000325680,;YLPM1,missense_variant,p.Arg1543Gln,ENST00000238571,;YLPM1,missense_variant,p.Arg1032Gln,ENST00000552421,;YLPM1,missense_variant,p.Arg1291Gln,ENST00000549293,;	A	ENSG00000119596	ENST00000325680	Transcript	missense_variant	5337	5213	1738	R/Q	cGa/cAa	rs754951613	.	.	1	YLPM1	HGNC	17798	protein_coding	YES	CCDS45135.1	ENSP00000324463	YLPM1_HUMAN	B4DMQ9_HUMAN	UPI00006C1433	.	.	possibly_damaging(0.797)	9/21	.	hmmpanther:PTHR13413:SF0,hmmpanther:PTHR13413,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCCGACCCC	.	5	ESCA
RAB8B	0	.	GRCh37	15	63548779	63548779	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400G>C	p.Glu134Gln	p.E134Q	ENST00000321437	5/8	28	25	3	40	40	0	RAB8B,missense_variant,p.Glu134Gln,ENST00000559006,;RAB8B,missense_variant,p.Glu134Gln,ENST00000321437,;RAB8B,missense_variant,p.Glu134Gln,ENST00000448330,;RAB8B,3_prime_UTR_variant,,ENST00000558119,;RAB8B,3_prime_UTR_variant,,ENST00000558990,;RAB8B,3_prime_UTR_variant,,ENST00000559927,;	C	ENSG00000166128	ENST00000321437	Transcript	missense_variant	556	400	134	E/Q	Gaa/Caa	.	.	.	1	RAB8B	HGNC	30273	protein_coding	YES	CCDS10183.1	ENSP00000312734	RAB8B_HUMAN	.	UPI00000412A7	.	tolerated(0.05)	possibly_damaging(0.641)	5/8	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF22,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00177,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAAAGAAAGA	.	2	ESCA
CHD2	0	.	GRCh37	15	93515583	93515583	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2441C>G	p.Ser814Cys	p.S814C	ENST00000394196	19/39	54	50	4	26	26	0	CHD2,missense_variant,p.Ser814Cys,ENST00000557381,;CHD2,missense_variant,p.Ser814Cys,ENST00000394196,;CHD2,intron_variant,,ENST00000557116,;CHD2,non_coding_transcript_exon_variant,,ENST00000557340,;	G	ENSG00000173575	ENST00000394196	Transcript	missense_variant	3509	2441	814	S/C	tCt/tGt	.	.	.	1	CHD2	HGNC	1917	protein_coding	YES	CCDS10374.2	ENSP00000377747	CHD2_HUMAN	Q6AI05_HUMAN,Q3YLD6_HUMAN,Q3YLD5_HUMAN,G3V4S8_HUMAN,G3V418_HUMAN	UPI0000E8A85C	.	deleterious(0)	probably_damaging(0.972)	19/39	.	PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF538,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTTCTCTCAGA	.	2	ESCA
ERI2	0	.	GRCh37	16	20814939	20814939	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77G>C	p.Gly26Ala	p.G26A	ENST00000357967	2/9	25	21	4	17	17	0	ERI2,missense_variant,p.Gly26Ala,ENST00000569729,;ERI2,missense_variant,p.Gly26Ala,ENST00000357967,;ERI2,missense_variant,p.Gly26Ala,ENST00000300005,;ERI2,5_prime_UTR_variant,,ENST00000563117,;ERI2,5_prime_UTR_variant,,ENST00000389345,;ERI2,5_prime_UTR_variant,,ENST00000564349,;AC004381.6,upstream_gene_variant,,ENST00000568046,;AC004381.6,upstream_gene_variant,,ENST00000568647,;AC004381.6,upstream_gene_variant,,ENST00000564274,;AC004381.6,upstream_gene_variant,,ENST00000563068,;AC004381.6,upstream_gene_variant,,ENST00000566276,;AC004381.6,upstream_gene_variant,,ENST00000261377,;AC004381.6,upstream_gene_variant,,ENST00000568501,;AC004381.6,upstream_gene_variant,,ENST00000565340,;AC004381.6,upstream_gene_variant,,ENST00000563617,;AC004381.6,upstream_gene_variant,,ENST00000568894,;AC004381.6,upstream_gene_variant,,ENST00000348433,;ERI2,non_coding_transcript_exon_variant,,ENST00000563537,;ERI2,non_coding_transcript_exon_variant,,ENST00000565884,;ERI2,non_coding_transcript_exon_variant,,ENST00000566223,;ERI2,non_coding_transcript_exon_variant,,ENST00000567562,;ERI2,non_coding_transcript_exon_variant,,ENST00000562277,;ERI2,downstream_gene_variant,,ENST00000568251,;AC004381.6,upstream_gene_variant,,ENST00000568476,;AC004381.6,upstream_gene_variant,,ENST00000567297,;ERI2,missense_variant,p.Gly26Ala,ENST00000568805,;ERI2,non_coding_transcript_exon_variant,,ENST00000567859,;AC004381.6,upstream_gene_variant,,ENST00000566518,;AC004381.6,upstream_gene_variant,,ENST00000566993,;ERI2,upstream_gene_variant,,ENST00000562215,;ERI2,upstream_gene_variant,,ENST00000562987,;	G	ENSG00000196678	ENST00000357967	Transcript	missense_variant	120	77	26	G/A	gGa/gCa	.	.	.	-1	ERI2	HGNC	30541	protein_coding	YES	CCDS45436.1	ENSP00000350651	ERI2_HUMAN	.	UPI0000EE8210	.	tolerated(0.09)	benign(0.013)	2/9	.	hmmpanther:PTHR23044:SF30,hmmpanther:PTHR23044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCCGAGA	.	5	ESCA
PKD1	0	.	GRCh37	16	2161577	2161577	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3591G>A	p.%3D	p.V1197V	ENST00000262304	15/46	129	87	41	213	213	0	PKD1,synonymous_variant,p.%3D,ENST00000262304,;PKD1,synonymous_variant,p.%3D,ENST00000423118,;PKD1,intron_variant,,ENST00000483024,;PKD1,intron_variant,,ENST00000488185,;RP11-304L19.4,upstream_gene_variant,,ENST00000568795,;PKD1,intron_variant,,ENST00000468674,;PKD1,upstream_gene_variant,,ENST00000483558,;PKD1,upstream_gene_variant,,ENST00000473780,;PKD1,non_coding_transcript_exon_variant,,ENST00000469241,;PKD1,intron_variant,,ENST00000568591,;PKD1,intron_variant,,ENST00000565639,;PKD1,intron_variant,,ENST00000415938,;PKD1,intron_variant,,ENST00000483731,;PKD1,intron_variant,,ENST00000569983,;PKD1,upstream_gene_variant,,ENST00000486339,;PKD1,upstream_gene_variant,,ENST00000496574,;PKD1,upstream_gene_variant,,ENST00000487932,;	T	ENSG00000008710	ENST00000262304	Transcript	synonymous_variant	3800	3591	1197	V	gtG/gtA	.	.	.	-1	PKD1	HGNC	9008	protein_coding	YES	CCDS32369.1	ENSP00000262304	PKD1_HUMAN	O75276_HUMAN	UPI00001B0454	.	.	.	15/46	.	PROSITE_profiles:PS50093,hmmpanther:PTHR10877:SF123,hmmpanther:PTHR10877,Gene3D:2.60.40.670,TIGRFAM_domain:TIGR00864,Pfam_domain:PF00801,SMART_domains:SM00089,Superfamily_domains:SSF49299	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCTCACCGT	.	5	ESCA
IGSF6	0	.	GRCh37	16	21658708	21658708	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.173G>T	p.Cys58Phe	p.C58F	ENST00000268389	2/6	67	41	26	74	74	0	IGSF6,missense_variant,p.Cys58Phe,ENST00000569602,;IGSF6,missense_variant,p.Cys58Phe,ENST00000268389,;METTL9,intron_variant,,ENST00000396014,;METTL9,intron_variant,,ENST00000567404,;METTL9,intron_variant,,ENST00000358154,;METTL9,intron_variant,,ENST00000568826,;RNU6-196P,downstream_gene_variant,,ENST00000384315,;IGSF6,non_coding_transcript_exon_variant,,ENST00000565499,;METTL9,upstream_gene_variant,,ENST00000564733,;	A	ENSG00000140749	ENST00000268389	Transcript	missense_variant	235	173	58	C/F	tGc/tTc	.	.	.	-1	IGSF6	HGNC	5953	protein_coding	YES	CCDS10599.1	ENSP00000268389	IGSF6_HUMAN	.	UPI000013D7B4	.	deleterious(0)	probably_damaging(1)	2/6	.	Superfamily_domains:SSF48726,SMART_domains:SM00406,Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR15297:SF2,hmmpanther:PTHR15297,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGGCATCCG	.	5	ESCA
CCNF	0	.	GRCh37	16	2487242	2487242	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459C>G	p.Ile153Met	p.I153M	ENST00000397066	5/17	33	30	3	39	39	0	CCNF,missense_variant,p.Ile153Met,ENST00000397066,;CCNF,3_prime_UTR_variant,,ENST00000293968,;CCNF,non_coding_transcript_exon_variant,,ENST00000564333,;CCNF,downstream_gene_variant,,ENST00000569093,;	G	ENSG00000162063	ENST00000397066	Transcript	missense_variant	547	459	153	I/M	atC/atG	.	.	.	1	CCNF	HGNC	1591	protein_coding	YES	CCDS10467.1	ENSP00000380256	CCNF_HUMAN	.	UPI0000127595	.	deleterious(0)	probably_damaging(0.997)	5/17	.	hmmpanther:PTHR10177,hmmpanther:PTHR10177:SF183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCATCCGCCC	.	2	ESCA
C16orf93	0	.	GRCh37	16	30773091	30773091	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-22C>G	.	.	ENST00000543610	1/9	45	41	4	46	46	0	C16orf93,5_prime_UTR_variant,,ENST00000545825,;C16orf93,5_prime_UTR_variant,,ENST00000541260,;RNF40,5_prime_UTR_variant,,ENST00000563909,;C16orf93,5_prime_UTR_variant,,ENST00000543610,;RNF40,upstream_gene_variant,,ENST00000566811,;RNF40,upstream_gene_variant,,ENST00000563683,;RNF40,upstream_gene_variant,,ENST00000324685,;RNF40,upstream_gene_variant,,ENST00000402121,;RNF40,upstream_gene_variant,,ENST00000565931,;PHKG2,downstream_gene_variant,,ENST00000328273,;PHKG2,downstream_gene_variant,,ENST00000424889,;C16orf93,upstream_gene_variant,,ENST00000535476,;RNF40,upstream_gene_variant,,ENST00000565995,;RNF40,upstream_gene_variant,,ENST00000357890,;PHKG2,downstream_gene_variant,,ENST00000563588,;C16orf93,upstream_gene_variant,,ENST00000544613,;C16orf93,5_prime_UTR_variant,,ENST00000545809,;C16orf93,non_coding_transcript_exon_variant,,ENST00000544487,;C16orf93,non_coding_transcript_exon_variant,,ENST00000544643,;C16orf93,non_coding_transcript_exon_variant,,ENST00000543128,;C16orf93,non_coding_transcript_exon_variant,,ENST00000546006,;PHKG2,downstream_gene_variant,,ENST00000563913,;RNF40,upstream_gene_variant,,ENST00000493683,;RNF40,upstream_gene_variant,,ENST00000566703,;C16orf93,upstream_gene_variant,,ENST00000433909,;PHKG2,downstream_gene_variant,,ENST00000564838,;C16orf93,upstream_gene_variant,,ENST00000537986,;	C	ENSG00000196118	ENST00000543610	Transcript	5_prime_UTR_variant	941	.	.	.	.	.	.	.	-1	C16orf93	HGNC	28078	protein_coding	YES	CCDS32434.2	ENSP00000437532	CP093_HUMAN	.	UPI0000EA2A74	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCGCGAGGCG	.	2	ESCA
OR2C1	0	.	GRCh37	16	3406771	3406771	+	Missense_Mutation	SNP	C	C	G	rs772065321	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.831C>G	p.Phe277Leu	p.F277L	ENST00000304936	1/1	17	11	6	20	20	0	OR2C1,missense_variant,p.Phe277Leu,ENST00000304936,;	G	ENSG00000168158	ENST00000304936	Transcript	missense_variant	883	831	277	F/L	ttC/ttG	rs772065321	.	.	1	OR2C1	HGNC	8242	protein_coding	YES	CCDS10502.1	ENSP00000307726	OR2C1_HUMAN	.	UPI000013E9E9	.	deleterious(0.02)	probably_damaging(0.996)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF237,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTGTTCTACTC	byFrequency	4	ESCA
ABCC12	0	.	GRCh37	16	48180286	48180286	+	Missense_Mutation	SNP	C	C	A	rs372957171	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50G>T	p.Arg17Leu	p.R17L	ENST00000311303	1/29	55	31	24	48	48	0	ABCC12,missense_variant,p.Arg17Leu,ENST00000527640,;ABCC12,missense_variant,p.Arg17Leu,ENST00000416054,;ABCC12,missense_variant,p.Arg17Leu,ENST00000448542,;ABCC12,missense_variant,p.Arg17Leu,ENST00000311303,;ABCC12,missense_variant,p.Arg17Leu,ENST00000532494,;ABCC12,missense_variant,p.Arg17Leu,ENST00000529504,;ABCC12,missense_variant,p.Arg17Leu,ENST00000497206,;ABCC12,missense_variant,p.Arg17Leu,ENST00000533639,;ABCC12,missense_variant,p.Arg17Leu,ENST00000534418,;ABCC12,missense_variant,p.Arg17Leu,ENST00000529084,;ABCC12,non_coding_transcript_exon_variant,,ENST00000528693,;	A	ENSG00000140798	ENST00000311303	Transcript	missense_variant	396	50	17	R/L	cGg/cTg	rs372957171,COSM435298	.	.	-1	ABCC12	HGNC	14640	protein_coding	YES	CCDS10730.1	ENSP00000311030	MRP9_HUMAN	E9PHY2_HUMAN	UPI0000456987	.	tolerated(0.07)	benign(0.051)	1/29	.	hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF10	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCGCCGGCCT	byFrequency|byCluster	5	ESCA
ADCY7	0	.	GRCh37	16	50334758	50334758	+	Silent	SNP	C	C	T	rs748635962	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209C>T	p.%3D	p.N403N	ENST00000394697	9/26	41	37	3	63	63	0	ADCY7,synonymous_variant,p.%3D,ENST00000537579,;ADCY7,synonymous_variant,p.%3D,ENST00000254235,;ADCY7,synonymous_variant,p.%3D,ENST00000538642,;ADCY7,synonymous_variant,p.%3D,ENST00000394697,;ADCY7,synonymous_variant,p.%3D,ENST00000566433,;ADCY7,non_coding_transcript_exon_variant,,ENST00000568731,;ADCY7,downstream_gene_variant,,ENST00000563677,;ADCY7,downstream_gene_variant,,ENST00000564044,;ADCY7,synonymous_variant,p.%3D,ENST00000567277,;ADCY7,upstream_gene_variant,,ENST00000570187,;	T	ENSG00000121281	ENST00000394697	Transcript	synonymous_variant	1549	1209	403	N	aaC/aaT	rs748635962	.	.	1	ADCY7	HGNC	238	protein_coding	YES	CCDS10741.1	ENSP00000378187	ADCY7_HUMAN	I3L3Q5_HUMAN	UPI000004C5DB	.	.	.	9/26	.	Superfamily_domains:SSF55073,SMART_domains:SM00044,Pfam_domain:PF00211,Gene3D:3.30.70.1230,hmmpanther:PTHR11920:SF273,hmmpanther:PTHR11920,PROSITE_profiles:PS50125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAACCGGAT	byFrequency	2	ESCA
IRX5	0	.	GRCh37	16	54966749	54966749	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.589G>C	p.Glu197Gln	p.E197Q	ENST00000394636	2/3	54	39	15	76	76	0	IRX5,missense_variant,p.Glu131Gln,ENST00000558597,;IRX5,missense_variant,p.Glu197Gln,ENST00000320990,;IRX5,missense_variant,p.Glu197Gln,ENST00000394636,;IRX5,intron_variant,,ENST00000560154,;CRNDE,upstream_gene_variant,,ENST00000558952,;CTD-3032H12.2,upstream_gene_variant,,ENST00000560487,;CRNDE,upstream_gene_variant,,ENST00000559598,;CRNDE,upstream_gene_variant,,ENST00000560208,;CRNDE,upstream_gene_variant,,ENST00000502066,;CRNDE,upstream_gene_variant,,ENST00000501177,;CRNDE,upstream_gene_variant,,ENST00000559432,;CTD-3032H12.1,downstream_gene_variant,,ENST00000559802,;CRNDE,upstream_gene_variant,,ENST00000560912,;CRNDE,upstream_gene_variant,,ENST00000557792,;	C	ENSG00000176842	ENST00000394636	Transcript	missense_variant	926	589	197	E/Q	Gag/Cag	.	.	.	1	IRX5	HGNC	14361	protein_coding	YES	CCDS10751.1	ENSP00000378132	IRX5_HUMAN	.	UPI00001FF1CD	.	deleterious(0.01)	probably_damaging(0.932)	2/3	.	hmmpanther:PTHR11211:SF17,hmmpanther:PTHR11211,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGGAGAAG	.	5	ESCA
CMTM3	0	.	GRCh37	16	66642288	66642289	+	Frame_Shift_Ins	INS	-	-	CC	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.225_226dupCC	p.Leu76ProfsTer15	p.L76Pfs*15	ENST00000424011	3/6	22	18	4	31	31	0	CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000567572,;CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000562357,;CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000361909,;CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000564060,;CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000424011,;CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000562707,;CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000563672,;CMTM3,5_prime_UTR_variant,,ENST00000565666,;CMTM3,5_prime_UTR_variant,,ENST00000566121,;CMTM3,5_prime_UTR_variant,,ENST00000565003,;CMTM3,5_prime_UTR_variant,,ENST00000460097,;CMTM3,5_prime_UTR_variant,,ENST00000568477,;CMTM3,intron_variant,,ENST00000360086,;CMTM3,intron_variant,,ENST00000565922,;CMTM3,frameshift_variant,p.Leu76ProfsTer15,ENST00000566756,;CMTM3,upstream_gene_variant,,ENST00000564247,;	CC	ENSG00000140931	ENST00000424011	Transcript	frameshift_variant	750-751	224-225	75	F/FX	ttc/ttCCc	.	.	.	1	CMTM3	HGNC	19174	protein_coding	YES	CCDS10815.1	ENSP00000400482	CKLF3_HUMAN	H3BU39_HUMAN,H3BN06_HUMAN,B3KQJ8_HUMAN	UPI000000DC37	.	.	.	3/6	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS51225,hmmpanther:PTHR22776,hmmpanther:PTHR22776:SF3,Pfam_domain:PF01284	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAGTTCCTGC	.	3	ESCA
TANGO6	0	.	GRCh37	16	68901087	68901087	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958C>G	p.Gln320Glu	p.Q320E	ENST00000261778	4/18	48	44	4	55	55	0	TANGO6,missense_variant,p.Gln320Glu,ENST00000261778,;TANGO6,non_coding_transcript_exon_variant,,ENST00000564180,;TANGO6,downstream_gene_variant,,ENST00000561566,;	G	ENSG00000103047	ENST00000261778	Transcript	missense_variant	970	958	320	Q/E	Cag/Gag	.	.	.	1	TANGO6	HGNC	25749	protein_coding	YES	CCDS45516.1	ENSP00000261778	TNG6_HUMAN	B3KTB6_HUMAN	UPI00001FF4A8	.	deleterious(0.01)	benign(0.271)	4/18	.	hmmpanther:PTHR20959:SF1,hmmpanther:PTHR20959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGTTCAGGCA	.	2	ESCA
TERF2	0	.	GRCh37	16	69389602	69389602	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1199C>T	.	.	ENST00000603068	10/10	16	11	5	20	20	0	TERF2,3_prime_UTR_variant,,ENST00000603068,;TERF2,3_prime_UTR_variant,,ENST00000254942,;RP11-343C2.9,intron_variant,,ENST00000563634,;TERF2,downstream_gene_variant,,ENST00000566051,;TMED6,upstream_gene_variant,,ENST00000288025,;RP11-343C2.7,upstream_gene_variant,,ENST00000564737,;RP11-343C2.7,upstream_gene_variant,,ENST00000570293,;	A	ENSG00000132604	ENST00000603068	Transcript	3_prime_UTR_variant	2827	.	.	.	.	.	.	.	-1	TERF2	HGNC	11729	protein_coding	YES	.	ENSP00000474453	TERF2_HUMAN	.	UPI0000137364	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GTCCGGGAGAG	.	4	ESCA
STUB1	0	.	GRCh37	16	732067	732067	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660G>A	p.%3D	p.E220E	ENST00000219548	5/7	39	33	6	51	51	0	STUB1,synonymous_variant,p.%3D,ENST00000565677,;STUB1,synonymous_variant,p.%3D,ENST00000567173,;STUB1,synonymous_variant,p.%3D,ENST00000219548,;STUB1,synonymous_variant,p.%3D,ENST00000564316,;STUB1,synonymous_variant,p.%3D,ENST00000564370,;STUB1,synonymous_variant,p.%3D,ENST00000566408,;JMJD8,3_prime_UTR_variant,,ENST00000609261,;JMJD8,3_prime_UTR_variant,,ENST00000454700,;JMJD8,3_prime_UTR_variant,,ENST00000293882,;JMJD8,3_prime_UTR_variant,,ENST00000412368,;JMJD8,downstream_gene_variant,,ENST00000562111,;JMJD8,downstream_gene_variant,,ENST00000562824,;RHBDL1,downstream_gene_variant,,ENST00000352681,;RHBDL1,downstream_gene_variant,,ENST00000561556,;WDR24,downstream_gene_variant,,ENST00000293883,;RHBDL1,downstream_gene_variant,,ENST00000219551,;WDR24,downstream_gene_variant,,ENST00000248142,;LA16c-313D11.9,upstream_gene_variant,,ENST00000571933,;LA16c-313D11.9,upstream_gene_variant,,ENST00000567091,;STUB1,non_coding_transcript_exon_variant,,ENST00000566181,;JMJD8,non_coding_transcript_exon_variant,,ENST00000565302,;STUB1,non_coding_transcript_exon_variant,,ENST00000569248,;JMJD8,non_coding_transcript_exon_variant,,ENST00000568689,;JMJD8,non_coding_transcript_exon_variant,,ENST00000567120,;STUB1,upstream_gene_variant,,ENST00000565813,;JMJD8,downstream_gene_variant,,ENST00000565258,;JMJD8,downstream_gene_variant,,ENST00000569396,;JMJD8,downstream_gene_variant,,ENST00000563088,;RHBDL1,downstream_gene_variant,,ENST00000450775,;JMJD8,downstream_gene_variant,,ENST00000566199,;STUB1,downstream_gene_variant,,ENST00000563505,;JMJD8,downstream_gene_variant,,ENST00000568313,;JMJD8,downstream_gene_variant,,ENST00000570037,;WDR24,downstream_gene_variant,,ENST00000567014,;STUB1,downstream_gene_variant,,ENST00000567790,;JMJD8,downstream_gene_variant,,ENST00000569441,;JMJD8,downstream_gene_variant,,ENST00000564436,;JMJD8,downstream_gene_variant,,ENST00000567901,;	A	ENSG00000103266	ENST00000219548	Transcript	synonymous_variant	910	660	220	E	gaG/gaA	.	.	.	1	STUB1	HGNC	11427	protein_coding	YES	CCDS10419.1	ENSP00000219548	CHIP_HUMAN	.	UPI000006E1B4	.	.	.	5/7	.	hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF305,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAGAAGAG	.	5	ESCA
BCMO1	0	.	GRCh37	16	81324181	81324181	+	Nonstop_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1643G>C	p.Ter548SerextTer60	p.*548Sext*60	ENST00000258168	11/11	49	41	8	38	38	0	BCMO1,stop_lost,p.Ter479SerextTer?,ENST00000425577,;BCMO1,stop_lost,p.Ter548SerextTer60,ENST00000258168,;BCMO1,3_prime_UTR_variant,,ENST00000563804,;	C	ENSG00000135697	ENST00000258168	Transcript	stop_lost	2104	1643	548	*/S	tGa/tCa	.	.	.	1	BCMO1	HGNC	13815	protein_coding	YES	CCDS10934.1	ENSP00000258168	BCDO1_HUMAN	.	UPI0000049CF7	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTGATGGT	.	5	ESCA
ZCCHC14	0	.	GRCh37	16	87441560	87441560	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2326G>C	.	.	ENST00000268616	13/13	39	28	11	40	40	0	ZCCHC14,3_prime_UTR_variant,,ENST00000268616,;ZCCHC14,downstream_gene_variant,,ENST00000561928,;MAP1LC3B,downstream_gene_variant,,ENST00000268607,;MAP1LC3B,downstream_gene_variant,,ENST00000534986,;ZCCHC14,3_prime_UTR_variant,,ENST00000568020,;MAP1LC3B,downstream_gene_variant,,ENST00000570189,;MAP1LC3B,downstream_gene_variant,,ENST00000564844,;	G	ENSG00000140948	ENST00000268616	Transcript	3_prime_UTR_variant	5394	.	.	.	.	.	.	.	-1	ZCCHC14	HGNC	24134	protein_coding	YES	CCDS10961.1	ENSP00000268616	ZCH14_HUMAN	.	UPI00000705C4	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGATTCTCGAC	.	5	ESCA
MYH2	0	.	GRCh37	17	10451186	10451186	+	Nonsense_Mutation	SNP	G	G	A	rs769712128	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.52C>T	p.Arg18Ter	p.R18*	ENST00000245503	3/40	33	25	7	31	31	0	MYH2,stop_gained,p.Arg18Ter,ENST00000245503,;MYH2,stop_gained,p.Arg18Ter,ENST00000532183,;MYH2,stop_gained,p.Arg18Ter,ENST00000397183,;MYH2,stop_gained,p.Arg18Ter,ENST00000420805,;MYH2,upstream_gene_variant,,ENST00000578017,;CTC-297N7.11,intron_variant,,ENST00000587182,;	A	ENSG00000125414	ENST00000245503	Transcript	stop_gained	437	52	18	R/*	Cga/Tga	rs769712128	.	.	-1	MYH2	HGNC	7572	protein_coding	YES	CCDS11156.1	ENSP00000245503	MYH2_HUMAN	J3QLR0_HUMAN,E7EX84_HUMAN,C9JIX4_HUMAN	UPI000012FB6C	.	.	.	3/40	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF314	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTCGGAGGA	.	5	ESCA
STARD3	0	.	GRCh37	17	37814733	37814733	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505C>T	p.Leu169Phe	p.L169F	ENST00000336308	6/15	66	29	37	63	63	0	STARD3,missense_variant,p.Leu169Phe,ENST00000336308,;STARD3,missense_variant,p.Leu151Phe,ENST00000394250,;STARD3,missense_variant,p.Leu143Phe,ENST00000580611,;STARD3,missense_variant,p.Leu169Phe,ENST00000443521,;STARD3,synonymous_variant,p.%3D,ENST00000544210,;STARD3,downstream_gene_variant,,ENST00000577248,;STARD3,downstream_gene_variant,,ENST00000579479,;STARD3,downstream_gene_variant,,ENST00000581894,;STARD3,downstream_gene_variant,,ENST00000583419,;STARD3,downstream_gene_variant,,ENST00000580331,;STARD3,downstream_gene_variant,,ENST00000583718,;STARD3,non_coding_transcript_exon_variant,,ENST00000582874,;STARD3,non_coding_transcript_exon_variant,,ENST00000578232,;STARD3,upstream_gene_variant,,ENST00000583639,;STARD3,downstream_gene_variant,,ENST00000460894,;STARD3,downstream_gene_variant,,ENST00000578254,;STARD3,downstream_gene_variant,,ENST00000585214,;STARD3,synonymous_variant,p.%3D,ENST00000578577,;STARD3,non_coding_transcript_exon_variant,,ENST00000584850,;STARD3,non_coding_transcript_exon_variant,,ENST00000481171,;STARD3,non_coding_transcript_exon_variant,,ENST00000488876,;STARD3,non_coding_transcript_exon_variant,,ENST00000484773,;STARD3,non_coding_transcript_exon_variant,,ENST00000583582,;STARD3,non_coding_transcript_exon_variant,,ENST00000585269,;STARD3,upstream_gene_variant,,ENST00000578384,;STARD3,upstream_gene_variant,,ENST00000583884,;STARD3,downstream_gene_variant,,ENST00000580551,;STARD3,upstream_gene_variant,,ENST00000578686,;STARD3,upstream_gene_variant,,ENST00000471896,;	T	ENSG00000131748	ENST00000336308	Transcript	missense_variant	723	505	169	L/F	Ctt/Ttt	.	.	.	1	STARD3	HGNC	17579	protein_coding	YES	CCDS11341.1	ENSP00000337446	STAR3_HUMAN	J3QRG8_HUMAN,J3QLS1_HUMAN,J3KT87_HUMAN,J3KSL3_HUMAN,J3KSH0_HUMAN,C9J555_HUMAN,B3KVT4_HUMAN	UPI000013CE10	.	deleterious(0.02)	benign(0.35)	6/15	.	PROSITE_profiles:PS51439,hmmpanther:PTHR12136:SF51,hmmpanther:PTHR12136,Pfam_domain:PF10457	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCCTTGAC	.	5	ESCA
CCR10	0	.	GRCh37	17	40832242	40832242	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418G>T	p.Val140Leu	p.V140L	ENST00000332438	2/2	13	6	7	14	14	0	CCR10,missense_variant,p.Val140Leu,ENST00000332438,;CCR10,5_prime_UTR_variant,,ENST00000591765,;CCR10,5_prime_UTR_variant,,ENST00000591568,;PLEKHH3,upstream_gene_variant,,ENST00000412503,;PLEKHH3,upstream_gene_variant,,ENST00000587627,;PLEKHH3,upstream_gene_variant,,ENST00000591022,;CNTNAP1,upstream_gene_variant,,ENST00000264638,;PLEKHH3,upstream_gene_variant,,ENST00000293349,;CTD-3193K9.4,non_coding_transcript_exon_variant,,ENST00000593139,;CTD-3193K9.3,downstream_gene_variant,,ENST00000592440,;PLEKHH3,upstream_gene_variant,,ENST00000591544,;PLEKHH3,upstream_gene_variant,,ENST00000456950,;PLEKHH3,upstream_gene_variant,,ENST00000591196,;CNTNAP1,upstream_gene_variant,,ENST00000591662,;PLEKHH3,upstream_gene_variant,,ENST00000591490,;	A	ENSG00000184451	ENST00000332438	Transcript	missense_variant	438	418	140	V/L	Gtg/Ttg	.	.	.	-1	CCR10	HGNC	4474	protein_coding	YES	CCDS11435.1	ENSP00000332504	CCR10_HUMAN	K7ER70_HUMAN,K7EPC9_HUMAN	UPI0000212EE9	.	deleterious(0.04)	benign(0.022)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24227,hmmpanther:PTHR24227:SF72,PROSITE_patterns:PS00237,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCCACGTAGC	.	3	ESCA
EPX	0	.	GRCh37	17	56270195	56270195	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13C>T	.	.	ENST00000225371	1/13	20	10	9	31	31	0	EPX,5_prime_UTR_variant,,ENST00000225371,;	T	ENSG00000121053	ENST00000225371	Transcript	5_prime_UTR_variant	98	.	.	.	.	.	.	.	1	EPX	HGNC	3423	protein_coding	YES	CCDS11602.1	ENSP00000225371	PERE_HUMAN	.	UPI0000131629	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAGCCTCGC	.	5	ESCA
PRKAR1A	0	.	GRCh37	17	66508651	66508651	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-45C>G	.	.	ENST00000589228	1/11	41	25	16	63	63	0	PRKAR1A,5_prime_UTR_variant,,ENST00000589309,;PRKAR1A,5_prime_UTR_variant,,ENST00000588702,;PRKAR1A,5_prime_UTR_variant,,ENST00000589228,;PRKAR1A,5_prime_UTR_variant,,ENST00000392711,;PRKAR1A,5_prime_UTR_variant,,ENST00000536854,;PRKAR1A,intron_variant,,ENST00000358598,;PRKAR1A,intron_variant,,ENST00000589017,;PRKAR1A,intron_variant,,ENST00000585427,;PRKAR1A,upstream_gene_variant,,ENST00000589480,;PRKAR1A,upstream_gene_variant,,ENST00000588178,;PRKAR1A,upstream_gene_variant,,ENST00000585815,;PRKAR1A,upstream_gene_variant,,ENST00000585981,;PRKAR1A,upstream_gene_variant,,ENST00000588188,;PRKAR1A,upstream_gene_variant,,ENST00000586397,;RP11-120M18.2,intron_variant,,ENST00000590353,;PRKAR1A,5_prime_UTR_variant,,ENST00000392710,;PRKAR1A,5_prime_UTR_variant,,ENST00000585608,;PRKAR1A,non_coding_transcript_exon_variant,,ENST00000585460,;PRKAR1A,non_coding_transcript_exon_variant,,ENST00000592194,;	G	ENSG00000108946	ENST00000589228	Transcript	5_prime_UTR_variant	84	.	.	.	.	.	.	.	1	PRKAR1A	HGNC	9388	protein_coding	YES	CCDS11678.1	ENSP00000464977	KAP0_HUMAN	Q96P62_HUMAN,K7EQK3_HUMAN,K7EPR5_HUMAN,K7EPB2_HUMAN,K7ENR3_HUMAN,K7EMU2_HUMAN,K7EK41_HUMAN,K7EJ40_HUMAN,K7EIE5_HUMAN,K7EID3_HUMAN,B2R5T5_HUMAN	UPI0000001C57	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGCCTCGCACC	.	3	ESCA
PRKAR1A	0	.	GRCh37	17	66508665	66508665	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-31C>T	.	.	ENST00000589228	1/11	36	20	15	48	48	0	PRKAR1A,5_prime_UTR_variant,,ENST00000589309,;PRKAR1A,5_prime_UTR_variant,,ENST00000588702,;PRKAR1A,5_prime_UTR_variant,,ENST00000589228,;PRKAR1A,5_prime_UTR_variant,,ENST00000392711,;PRKAR1A,5_prime_UTR_variant,,ENST00000536854,;PRKAR1A,intron_variant,,ENST00000358598,;PRKAR1A,intron_variant,,ENST00000589017,;PRKAR1A,intron_variant,,ENST00000585427,;PRKAR1A,upstream_gene_variant,,ENST00000589480,;PRKAR1A,upstream_gene_variant,,ENST00000588178,;PRKAR1A,upstream_gene_variant,,ENST00000585815,;PRKAR1A,upstream_gene_variant,,ENST00000585981,;PRKAR1A,upstream_gene_variant,,ENST00000588188,;PRKAR1A,upstream_gene_variant,,ENST00000586397,;RP11-120M18.2,intron_variant,,ENST00000590353,;PRKAR1A,5_prime_UTR_variant,,ENST00000392710,;PRKAR1A,5_prime_UTR_variant,,ENST00000585608,;PRKAR1A,non_coding_transcript_exon_variant,,ENST00000585460,;PRKAR1A,non_coding_transcript_exon_variant,,ENST00000592194,;	T	ENSG00000108946	ENST00000589228	Transcript	5_prime_UTR_variant	98	.	.	.	.	.	.	.	1	PRKAR1A	HGNC	9388	protein_coding	YES	CCDS11678.1	ENSP00000464977	KAP0_HUMAN	Q96P62_HUMAN,K7EQK3_HUMAN,K7EPR5_HUMAN,K7EPB2_HUMAN,K7ENR3_HUMAN,K7EMU2_HUMAN,K7EK41_HUMAN,K7EJ40_HUMAN,K7EIE5_HUMAN,K7EID3_HUMAN,B2R5T5_HUMAN	UPI0000001C57	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGCCTCGCGCC	.	3	ESCA
ABCA8	0	.	GRCh37	17	66873731	66873731	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4008G>C	p.%3D	p.V1336V	ENST00000269080	31/38	89	48	41	97	97	0	ABCA8,synonymous_variant,p.%3D,ENST00000269080,;ABCA8,synonymous_variant,p.%3D,ENST00000430352,;ABCA8,synonymous_variant,p.%3D,ENST00000586539,;ABCA8,non_coding_transcript_exon_variant,,ENST00000588458,;ABCA8,non_coding_transcript_exon_variant,,ENST00000591459,;ABCA8,non_coding_transcript_exon_variant,,ENST00000586292,;ABCA8,downstream_gene_variant,,ENST00000589980,;	G	ENSG00000141338	ENST00000269080	Transcript	synonymous_variant	4146	4008	1336	V	gtG/gtC	.	.	.	-1	ABCA8	HGNC	38	protein_coding	YES	CCDS11680.1	ENSP00000269080	ABCA8_HUMAN	K7ELK9_HUMAN	UPI000004C4B7	.	.	.	31/38	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229:SF115,hmmpanther:PTHR19229,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCCTCACTGT	.	3	ESCA
ICT1	0	.	GRCh37	17	73008936	73008936	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.155C>G	p.Ser52Cys	p.S52C	ENST00000301585	1/6	13	6	6	22	22	0	ICT1,missense_variant,p.Ser52Cys,ENST00000301585,;ICT1,missense_variant,p.Ser52Cys,ENST00000584208,;ICT1,missense_variant,p.Ser36Cys,ENST00000580800,;	G	ENSG00000167862	ENST00000301585	Transcript	missense_variant	168	155	52	S/C	tCt/tGt	.	.	.	1	ICT1	HGNC	5359	protein_coding	YES	CCDS11711.1	ENSP00000301585	ICT1_HUMAN	.	UPI0000000DF2	.	deleterious(0)	possibly_damaging(0.855)	1/6	.	hmmpanther:PTHR11075	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CGAATCTCAGG	.	4	ESCA
TP53	0	.	GRCh37	17	7578394	7578394	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.536A>G	p.His179Arg	p.H179R	ENST00000269305	5/11	394	103	291	432	432	0	TP53,missense_variant,p.His179Arg,ENST00000413465,;TP53,missense_variant,p.His179Arg,ENST00000420246,;TP53,missense_variant,p.His179Arg,ENST00000269305,;TP53,missense_variant,p.His47Arg,ENST00000509690,;TP53,missense_variant,p.His179Arg,ENST00000359597,;TP53,missense_variant,p.His86Arg,ENST00000514944,;TP53,missense_variant,p.His179Arg,ENST00000445888,;TP53,missense_variant,p.His179Arg,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	726	536	179	H/R	cAt/cGt	TP53_g.12524A>G,TP53_g.12524A>C,TP53_g.12524del,TP53_g.12524A>T,COSM10889,COSM43635,COSM44218,COSM44627,COSM214223,COSM3958828,COSM129844,COSM214222,COSM129845,COSM3958831,COSM214224,COSM129847,COSM3958833,COSM3396280,COSM3958830,COSM3980298,COSM1645241,COSM1731642,COSM3958829,COSM3958832,COSM129846,COSM214225	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H179R|c.536A>G|17,SITE|p.H47R|c.140A>G|31,SITE|p.H86R|c.257A>G|30,SITE|p.H179R|c.536A>G|136,SITE|p.H179R|c.536A>G|30,SITE|p.H179R|c.536A>G|21,SITE|p.H179R|c.536A>G|30,CODON|p.0?|c.1_1182del1182|6,CODON|p.P177_C182delPHHERC|c.529_546del18|9,CODON|p.P177_C182delPHHERC|c.526_543del18|3,CODON|p.H179Q|c.537T>A|7,CODON|p.H179Q|c.537T>A|16,CODON|p.H179Q|c.537T>A|7,CODON|p.H179Q|c.537T>A|5,CODON|p.H86Q|c.258T>A|7,CODON|p.H47Q|c.141T>A|7,CODON|p.H179Q|c.537T>G|9,CODON|p.H179L|c.536A>T|40,CODON|p.H179L|c.536A>T|4,CODON|p.H179L|c.536A>T|7,CODON|p.H179L|c.536A>T|7,CODON|p.H47L|c.140A>T|9,CODON|p.H179P|c.536A>C|5,CODON|p.H86L|c.257A>T|7,CODON|p.H179Y|c.534_535CC>TT|8,BUFFER|p.S183P|c.547T>C|3,BUFFER|p.C182*|c.546C>A|5,BUFFER|p.C182S|c.544T>A|7,BUFFER|p.R181H|c.542G>A|24,BUFFER|p.R88H|c.263G>A|3,BUFFER|p.R49H|c.146G>A|3,BUFFER|p.R181P|c.542G>C|12,BUFFER|p.R181H|c.542G>A|3,BUFFER|p.R181H|c.542G>A|3,BUFFER|p.R181L|c.542G>T|3,BUFFER|p.R181C|c.541C>T|6,BUFFER|p.R88C|c.262C>T|6,BUFFER|p.R49C|c.145C>T|6,BUFFER|p.R181C|c.541C>T|4,BUFFER|p.R181C|c.541C>T|20,BUFFER|p.R181C|c.541C>T|6,BUFFER|p.E180D|c.540G>T|5,BUFFER|p.E48D|c.144G>T|3,BUFFER|p.E87D|c.261G>T|3,BUFFER|p.E180D|c.540G>T|3,BUFFER|p.E180D|c.540G>T|3,BUFFER|p.E180K|c.538G>A|6,BUFFER|p.E180*|c.538G>T|14,BUFFER|p.H179D|c.535C>G|12,BUFFER|p.H179Y|c.535C>T|4,BUFFER|p.H47Y|c.139C>T|15,BUFFER|p.H179Y|c.535C>T|5,BUFFER|p.H179Y|c.535C>T|88,BUFFER|p.H179N|c.535C>A|15,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H86Y|c.256C>T|14,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCATGGTGG	.	5	ESCA
ANKRD30B	0	.	GRCh37	18	14763720	14763720	+	Missense_Mutation	SNP	C	C	T	rs759291819	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.856C>T	p.Pro286Ser	p.P286S	ENST00000358984	7/36	52	34	18	67	67	0	ANKRD30B,missense_variant,p.Pro286Ser,ENST00000447268,;ANKRD30B,missense_variant,p.Pro286Ser,ENST00000358984,;RNU6-1210P,downstream_gene_variant,,ENST00000363775,;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,missense_variant,p.Pro286Ser,ENST00000580206,;	T	ENSG00000180777	ENST00000358984	Transcript	missense_variant	1036	856	286	P/S	Ccc/Tcc	rs759291819,COSM230344	.	.	1	ANKRD30B	HGNC	24165	protein_coding	YES	CCDS54182.1	ENSP00000351875	AN30B_HUMAN	.	UPI0000425FF7	.	deleterious(0.04)	benign(0.175)	7/36	.	hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTGCACCCTTG	byFrequency	4	ESCA
C18orf8	0	.	GRCh37	18	21111652	21111652	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1958G>A	p.Arg653Lys	p.R653K	ENST00000269221	20/20	26	20	6	25	25	0	C18orf8,missense_variant,p.Arg653Lys,ENST00000269221,;C18orf8,missense_variant,p.Arg605Lys,ENST00000590868,;NPC1,3_prime_UTR_variant,,ENST00000269228,;NPC1,intron_variant,,ENST00000586150,;NPC1,intron_variant,,ENST00000590723,;NPC1,intron_variant,,ENST00000591107,;NPC1,intron_variant,,ENST00000593280,;NPC1,downstream_gene_variant,,ENST00000591051,;NPC1,downstream_gene_variant,,ENST00000412552,;C18orf8,non_coding_transcript_exon_variant,,ENST00000591367,;C18orf8,3_prime_UTR_variant,,ENST00000589215,;C18orf8,3_prime_UTR_variant,,ENST00000590870,;C18orf8,non_coding_transcript_exon_variant,,ENST00000593081,;C18orf8,non_coding_transcript_exon_variant,,ENST00000589409,;C18orf8,downstream_gene_variant,,ENST00000592682,;NPC1,downstream_gene_variant,,ENST00000587163,;C18orf8,downstream_gene_variant,,ENST00000590387,;NPC1,downstream_gene_variant,,ENST00000588867,;	A	ENSG00000141452	ENST00000269221	Transcript	missense_variant	2068	1958	653	R/K	aGg/aAg	.	.	.	1	C18orf8	HGNC	24326	protein_coding	YES	CCDS32803.1	ENSP00000269221	MIC1_HUMAN	.	UPI000013D80D	.	tolerated_low_confidence(1)	benign(0)	20/20	.	hmmpanther:PTHR12897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AATGAGGCCTA	.	4	ESCA
RPL17	0	.	GRCh37	18	47017676	47017676	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81+99G>A	.	.	ENST00000418495	.	46	41	5	45	45	0	RPL17,intron_variant,,ENST00000583036,;RPL17,intron_variant,,ENST00000580210,;RPL17,intron_variant,,ENST00000578528,;RPL17-C18orf32,intron_variant,,ENST00000332968,;RPL17,intron_variant,,ENST00000580261,;RPL17,intron_variant,,ENST00000583637,;RPL17,intron_variant,,ENST00000581373,;RPL17,intron_variant,,ENST00000579408,;RPL17,intron_variant,,ENST00000418495,;RPL17,intron_variant,,ENST00000580387,;RPL17,intron_variant,,ENST00000578532,;RPL17,intron_variant,,ENST00000579248,;RPL17-C18orf32,intron_variant,,ENST00000584895,;C18orf32,upstream_gene_variant,,ENST00000579820,;C18orf32,upstream_gene_variant,,ENST00000582392,;C18orf32,upstream_gene_variant,,ENST00000318240,;SNORD58A,non_coding_transcript_exon_variant,,ENST00000383875,;SNORD58C,upstream_gene_variant,,ENST00000365223,;SNORD58B,downstream_gene_variant,,ENST00000607313,;MIR1539,downstream_gene_variant,,ENST00000410758,;MIR1539,intron_variant,,ENST00000581232,;RPL17,intron_variant,,ENST00000581091,;RPL17,non_coding_transcript_exon_variant,,ENST00000581305,;RPL17,non_coding_transcript_exon_variant,,ENST00000582782,;RPL17,non_coding_transcript_exon_variant,,ENST00000579495,;RPL17,non_coding_transcript_exon_variant,,ENST00000578966,;RPL17-C18orf32,intron_variant,,ENST00000577910,;RPL17,upstream_gene_variant,,ENST00000582935,;RPL17,upstream_gene_variant,,ENST00000581741,;RPL17,upstream_gene_variant,,ENST00000582588,;RPL17,upstream_gene_variant,,ENST00000584364,;SRP72P1,downstream_gene_variant,,ENST00000580060,;	T	ENSG00000265681	ENST00000418495	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RPL17	HGNC	10307	protein_coding	YES	CCDS45865.1	ENSP00000397798	RL17_HUMAN	J3QS96_HUMAN,J3QQT2_HUMAN,J3KSJ0_HUMAN,J3KRX5_HUMAN,J3KRB3_HUMAN	UPI0000049C48	.	.	.	.	3/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTTTCACGGT	.	3	ESCA
ZNF532	0	.	GRCh37	18	56651290	56651290	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3498G>A	p.%3D	p.L1166L	ENST00000336078	11/11	60	54	5	56	56	0	ZNF532,synonymous_variant,p.%3D,ENST00000591230,;ZNF532,synonymous_variant,p.%3D,ENST00000591808,;ZNF532,synonymous_variant,p.%3D,ENST00000589288,;ZNF532,synonymous_variant,p.%3D,ENST00000591083,;ZNF532,synonymous_variant,p.%3D,ENST00000336078,;ZNF532,downstream_gene_variant,,ENST00000586997,;ZNF532,non_coding_transcript_exon_variant,,ENST00000588956,;ZNF532,non_coding_transcript_exon_variant,,ENST00000592249,;ZNF532,non_coding_transcript_exon_variant,,ENST00000589131,;ZNF532,non_coding_transcript_exon_variant,,ENST00000590442,;ZNF532,downstream_gene_variant,,ENST00000586723,;ZNF532,downstream_gene_variant,,ENST00000585662,;	A	ENSG00000074657	ENST00000336078	Transcript	synonymous_variant	4274	3498	1166	L	ctG/ctA	.	.	.	1	ZNF532	HGNC	30940	protein_coding	YES	CCDS11969.1	ENSP00000338217	ZN532_HUMAN	K7ER18_HUMAN,K7EQW7_HUMAN,K7EPI7_HUMAN,K7EP49_HUMAN,K7EMF9_HUMAN,K7ELB7_HUMAN,K7EL14_HUMAN,K7EKV7_HUMAN,K7EJM2_HUMAN,B4DQV3_HUMAN	UPI000013D30C	.	.	.	11/11	.	hmmpanther:PTHR26374:SF163,hmmpanther:PTHR26374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGCTGAAAAT	.	3	ESCA
SERPINB2	0	.	GRCh37	18	61569754	61569754	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.795C>T	p.%3D	p.F265F	ENST00000457692	8/9	50	46	4	51	51	0	SERPINB2,synonymous_variant,p.%3D,ENST00000457692,;SERPINB10,synonymous_variant,p.%3D,ENST00000397996,;SERPINB10,synonymous_variant,p.%3D,ENST00000418725,;SERPINB2,synonymous_variant,p.%3D,ENST00000299502,;SERPINB2,downstream_gene_variant,,ENST00000413956,;SERPINB2,non_coding_transcript_exon_variant,,ENST00000482254,;	T	ENSG00000197632	ENST00000457692	Transcript	synonymous_variant	1128	795	265	F	ttC/ttT	.	.	.	1	SERPINB2	HGNC	8584	protein_coding	YES	CCDS11989.1	ENSP00000401645	PAI2_HUMAN	Q6LDR6_HUMAN,E9PDK7_HUMAN,E7ERB5_HUMAN,E7EPJ9_HUMAN	UPI000002BB06	.	.	.	8/9	.	Superfamily_domains:SSF56574,SMART_domains:SM00093,Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461:SF61,hmmpanther:PTHR11461	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ATGTTCTTGTT	.	2	ESCA
DNMT1	0	.	GRCh37	19	10270336	10270336	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1278C>T	p.%3D	p.F426F	ENST00000359526	17/41	41	38	3	45	45	0	DNMT1,synonymous_variant,p.%3D,ENST00000340748,;DNMT1,synonymous_variant,p.%3D,ENST00000540357,;DNMT1,synonymous_variant,p.%3D,ENST00000359526,;DNMT1,splice_region_variant,,ENST00000585843,;DNMT1,splice_region_variant,,ENST00000592705,;DNMT1,downstream_gene_variant,,ENST00000585920,;DNMT1,downstream_gene_variant,,ENST00000591764,;DNMT1,downstream_gene_variant,,ENST00000589349,;DNMT1,upstream_gene_variant,,ENST00000586799,;	A	ENSG00000130816	ENST00000359526	Transcript	synonymous_variant	1458	1278	426	F	ttC/ttT	.	.	.	-1	DNMT1	HGNC	2976	protein_coding	YES	CCDS45958.1	ENSP00000352516	DNMT1_HUMAN	K7ELB1_HUMAN,K7EKC3_HUMAN,I6L9H2_HUMAN,B3KVA0_HUMAN	UPI000002A823	.	.	.	17/41	.	hmmpanther:PTHR10629:SF11,hmmpanther:PTHR10629,Pfam_domain:PF12047,PIRSF_domain:PIRSF037404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TACCTGAAGCA	.	2	ESCA
KRI1	0	.	GRCh37	19	10666007	10666008	+	Frame_Shift_Ins	INS	-	-	AA	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1653_1654insTT	p.Lys552LeufsTer4	p.K552Lfs*4	ENST00000312962	17/19	83	57	26	68	68	0	KRI1,frameshift_variant,p.Lys552LeufsTer4,ENST00000312962,;KRI1,frameshift_variant,p.Lys548LeufsTer4,ENST00000361821,;ATG4D,downstream_gene_variant,,ENST00000586863,;ATG4D,downstream_gene_variant,,ENST00000540862,;ATG4D,downstream_gene_variant,,ENST00000585437,;ATG4D,downstream_gene_variant,,ENST00000309469,;KRI1,downstream_gene_variant,,ENST00000539027,;ATG4D,downstream_gene_variant,,ENST00000587256,;ATG4D,downstream_gene_variant,,ENST00000588972,;RNU7-140P,upstream_gene_variant,,ENST00000459546,;MIR1238,downstream_gene_variant,,ENST00000408483,;KRI1,non_coding_transcript_exon_variant,,ENST00000543842,;KRI1,non_coding_transcript_exon_variant,,ENST00000537433,;KRI1,non_coding_transcript_exon_variant,,ENST00000536689,;KRI1,non_coding_transcript_exon_variant,,ENST00000537363,;KRI1,non_coding_transcript_exon_variant,,ENST00000478863,;ATG4D,downstream_gene_variant,,ENST00000588667,;ATG4D,downstream_gene_variant,,ENST00000586417,;KRI1,downstream_gene_variant,,ENST00000432197,;ATG4D,downstream_gene_variant,,ENST00000589753,;KRI1,downstream_gene_variant,,ENST00000536714,;ATG4D,downstream_gene_variant,,ENST00000585752,;ATG4D,downstream_gene_variant,,ENST00000588857,;	AA	ENSG00000129347	ENST00000312962	Transcript	frameshift_variant	1673-1674	1653-1654	551-552	-/X	-/TT	.	.	.	-1	KRI1	HGNC	25769	protein_coding	YES	CCDS12242.1	ENSP00000320917	KRI1_HUMAN	.	UPI0000246DCC	.	.	.	17/19	.	hmmpanther:PTHR14490,Pfam_domain:PF12936	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCCTTATCGT	.	3	ESCA
ZNF302	0	.	GRCh37	19	35175973	35175973	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1031G>A	p.Arg344Lys	p.R344K	ENST00000505242	5/5	63	41	21	60	60	0	ZNF302,missense_variant,p.Arg344Lys,ENST00000457781,;ZNF302,missense_variant,p.Arg344Lys,ENST00000423823,;ZNF302,missense_variant,p.Arg388Lys,ENST00000446502,;ZNF302,missense_variant,p.Arg344Lys,ENST00000505242,;ZNF302,3_prime_UTR_variant,,ENST00000505365,;ZNF302,downstream_gene_variant,,ENST00000506901,;ZNF302,downstream_gene_variant,,ENST00000505163,;ZNF302,downstream_gene_variant,,ENST00000507959,;ZNF302,downstream_gene_variant,,ENST00000509528,;ZNF302,downstream_gene_variant,,ENST00000502743,;ZNF302,non_coding_transcript_exon_variant,,ENST00000509196,;ZNF302,downstream_gene_variant,,ENST00000512455,;ZNF302,downstream_gene_variant,,ENST00000510002,;	A	ENSG00000089335	ENST00000505242	Transcript	missense_variant	1525	1031	344	R/K	aGa/aAa	.	.	.	1	ZNF302	HGNC	13848	protein_coding	YES	CCDS46042.1	ENSP00000421028	ZN302_HUMAN	Q7Z4B9_HUMAN,D6RAM0_HUMAN	UPI0000001668	.	tolerated(1)	benign(0.007)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF110,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTAGAGAAT	.	5	ESCA
CIC	0	.	GRCh37	19	42790978	42790978	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>G	p.%3D	p.V41V	ENST00000575354	2/20	43	39	4	47	47	0	CIC,synonymous_variant,p.%3D,ENST00000575354,;CIC,synonymous_variant,p.%3D,ENST00000572681,;CIC,synonymous_variant,p.%3D,ENST00000160740,;CIC,non_coding_transcript_exon_variant,,ENST00000575839,;	G	ENSG00000079432	ENST00000575354	Transcript	synonymous_variant	163	123	41	V	gtC/gtG	.	.	.	1	CIC	HGNC	14214	protein_coding	YES	CCDS12601.1	ENSP00000458663	CIC_HUMAN	.	UPI000013C5A0	.	.	.	2/20	.	hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTAGTCCCCTT	.	2	ESCA
CIC	0	.	GRCh37	19	42793154	42793154	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1046C>T	p.Ser349Leu	p.S349L	ENST00000575354	7/20	20	16	4	33	33	0	CIC,missense_variant,p.Ser349Leu,ENST00000575354,;CIC,missense_variant,p.Ser1258Leu,ENST00000572681,;CIC,missense_variant,p.Ser349Leu,ENST00000160740,;CIC,upstream_gene_variant,,ENST00000576505,;CIC,upstream_gene_variant,,ENST00000573349,;CIC,downstream_gene_variant,,ENST00000575839,;CIC,upstream_gene_variant,,ENST00000575287,;	T	ENSG00000079432	ENST00000575354	Transcript	missense_variant	1086	1046	349	S/L	tCa/tTa	.	.	.	1	CIC	HGNC	14214	protein_coding	YES	CCDS12601.1	ENSP00000458663	CIC_HUMAN	.	UPI000013C5A0	.	.	possibly_damaging(0.514)	7/20	.	hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTCAGCCC	.	5	ESCA
MEGF8	0	.	GRCh37	19	42861130	42861130	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4626G>C	p.Glu1542Asp	p.E1542D	ENST00000334370	26/41	22	19	3	30	30	0	MEGF8,missense_variant,p.Glu1542Asp,ENST00000334370,;MEGF8,missense_variant,p.Glu1609Asp,ENST00000251268,;MEGF8,upstream_gene_variant,,ENST00000598762,;MEGF8,downstream_gene_variant,,ENST00000593840,;	C	ENSG00000105429	ENST00000334370	Transcript	missense_variant	5261	4626	1542	E/D	gaG/gaC	.	.	.	1	MEGF8	HGNC	3233	protein_coding	YES	CCDS12604.2	ENSP00000334219	MEGF8_HUMAN	.	UPI00003CF1A7	.	tolerated(0.26)	possibly_damaging(0.674)	26/41	.	hmmpanther:PTHR10574:SF241,hmmpanther:PTHR10574,Pfam_domain:PF13418,Gene3D:1zgkA00,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAGGAGAAGGT	.	2	ESCA
LYPD3	0	.	GRCh37	19	43969651	43969651	+	Missense_Mutation	SNP	G	G	C	rs748210378	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73C>G	p.Arg25Gly	p.R25G	ENST00000244333	1/5	78	66	11	96	96	0	LYPD3,missense_variant,p.Arg25Gly,ENST00000244333,;LYPD3,non_coding_transcript_exon_variant,,ENST00000597741,;LYPD3,non_coding_transcript_exon_variant,,ENST00000595970,;LYPD3,upstream_gene_variant,,ENST00000594326,;	C	ENSG00000124466	ENST00000244333	Transcript	missense_variant	162	73	25	R/G	Cgc/Ggc	rs748210378	.	.	-1	LYPD3	HGNC	24880	protein_coding	YES	CCDS12620.1	ENSP00000244333	LYPD3_HUMAN	B2RBR3_HUMAN	UPI000000D965	.	tolerated(0.32)	benign(0.001)	1/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10624:SF6,hmmpanther:PTHR10624	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCGCGAAGCA	.	4	ESCA
ZNF541	0	.	GRCh37	19	48048783	48048783	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003C>T	p.Pro335Ser	p.P335S	ENST00000314121	3/15	65	46	18	94	94	0	ZNF541,missense_variant,p.Pro335Ser,ENST00000314121,;ZNF541,missense_variant,p.Pro335Ser,ENST00000448976,;ZNF541,missense_variant,p.Pro335Ser,ENST00000391901,;ZNF541,upstream_gene_variant,,ENST00000263351,;ZNF541,upstream_gene_variant,,ENST00000595558,;ZNF541,upstream_gene_variant,,ENST00000487275,;	A	ENSG00000118156	ENST00000314121	Transcript	missense_variant	1003	1003	335	P/S	Ccc/Tcc	.	.	.	-1	ZNF541	HGNC	25294	protein_coding	YES	.	ENSP00000313258	ZN541_HUMAN	.	UPI0001837EA0	.	tolerated(0.19)	benign(0.091)	3/15	.	hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCGGGAAGCT	.	5	ESCA
EMP3	0	.	GRCh37	19	48833676	48833676	+	Silent	SNP	C	C	T	rs377482803	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441C>T	p.%3D	p.P147P	ENST00000270221	5/5	21	14	7	26	26	0	EMP3,missense_variant,p.Pro127Ser,ENST00000593437,;EMP3,synonymous_variant,p.%3D,ENST00000597279,;EMP3,synonymous_variant,p.%3D,ENST00000270221,;EMP3,synonymous_variant,p.%3D,ENST00000596315,;TMEM143,downstream_gene_variant,,ENST00000541566,;TMEM143,downstream_gene_variant,,ENST00000293261,;EMP3,downstream_gene_variant,,ENST00000594198,;EMP3,downstream_gene_variant,,ENST00000599704,;TMEM143,downstream_gene_variant,,ENST00000436660,;TMEM143,downstream_gene_variant,,ENST00000377431,;TMEM143,downstream_gene_variant,,ENST00000435956,;EMP3,3_prime_UTR_variant,,ENST00000599255,;EMP3,non_coding_transcript_exon_variant,,ENST00000597057,;TMEM143,downstream_gene_variant,,ENST00000600816,;EMP3,downstream_gene_variant,,ENST00000597529,;	T	ENSG00000142227	ENST00000270221	Transcript	synonymous_variant	742	441	147	P	ccC/ccT	rs377482803	.	.	1	EMP3	HGNC	3335	protein_coding	YES	CCDS12715.1	ENSP00000270221	EMP3_HUMAN	M0R1L9_HUMAN,M0QZ66_HUMAN,M0QXS0_HUMAN	UPI0000129EAB	.	.	.	5/5	.	Transmembrane_helices:TMhelix,Pfam_domain:PF00822,hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF8	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCCCCTCGC	byCluster	5	ESCA
CEACAM18	0	.	GRCh37	19	51986564	51986564	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150C>A	p.Pro384Thr	p.P384T	ENST00000451626	5/5	42	23	18	59	59	0	CEACAM18,missense_variant,p.Pro384Thr,ENST00000451626,;CEACAM18,intron_variant,,ENST00000396477,;	A	ENSG00000213822	ENST00000451626	Transcript	missense_variant	1150	1150	384	P/T	Cct/Act	.	.	.	1	CEACAM18	HGNC	31949	protein_coding	YES	.	ENSP00000402203	.	.	UPI0000DD8506	.	tolerated_low_confidence(0.1)	benign(0.073)	5/5	.	hmmpanther:PTHR19955,hmmpanther:PTHR19955:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCCTCCA	.	5	ESCA
ZNF578	0	.	GRCh37	19	53014448	53014448	+	Nonsense_Mutation	SNP	C	C	T	rs767983794	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814C>T	p.Arg272Ter	p.R272*	ENST00000421239	6/6	75	71	4	85	85	0	ZNF578,stop_gained,p.Arg272Ter,ENST00000421239,;ZNF578,downstream_gene_variant,,ENST00000601120,;CTD-3099C6.5,downstream_gene_variant,,ENST00000599143,;	T	ENSG00000258405	ENST00000421239	Transcript	stop_gained	1058	814	272	R/*	Cga/Tga	rs767983794,COSM1000574	.	.	1	ZNF578	HGNC	26449	protein_coding	YES	CCDS54310.1	ENSP00000459216	ZN578_HUMAN	M0QZV4_HUMAN	UPI000048A457	.	.	.	6/6	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF12,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGCGATAC	.	2	ESCA
LENG8	0	.	GRCh37	19	54973144	54973144	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1036G>A	.	.	ENST00000326764	16/16	34	22	11	60	60	0	LENG8,3_prime_UTR_variant,,ENST00000326764,;LENG9,3_prime_UTR_variant,,ENST00000333834,;LENG8,3_prime_UTR_variant,,ENST00000431846,;LENG8,downstream_gene_variant,,ENST00000421200,;LENG8,downstream_gene_variant,,ENST00000376526,;LENG8,downstream_gene_variant,,ENST00000376514,;CDC42EP5,downstream_gene_variant,,ENST00000301200,;	A	ENSG00000167615	ENST00000326764	Transcript	3_prime_UTR_variant	3918	.	.	.	.	.	.	.	1	LENG8	HGNC	15500	protein_coding	YES	CCDS12894.1	ENSP00000318374	LENG8_HUMAN	E7EWC7_HUMAN,C9J1N5_HUMAN,B0VJY8_HUMAN	UPI0000074196	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACTGAGCAC	.	5	ESCA
LENG9	0	.	GRCh37	19	54973717	54973717	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059C>T	p.%3D	p.N353N	ENST00000333834	1/1	67	50	17	74	74	0	LENG9,synonymous_variant,p.%3D,ENST00000333834,;LENG8,downstream_gene_variant,,ENST00000421200,;LENG8,downstream_gene_variant,,ENST00000326764,;LENG8,downstream_gene_variant,,ENST00000376526,;LENG8,downstream_gene_variant,,ENST00000376514,;CDC42EP5,downstream_gene_variant,,ENST00000301200,;LENG8,downstream_gene_variant,,ENST00000431846,;	A	ENSG00000182909	ENST00000333834	Transcript	synonymous_variant	1178	1059	353	N	aaC/aaT	.	.	.	-1	LENG9	HGNC	16306	protein_coding	YES	CCDS12895.2	ENSP00000331647	LENG9_HUMAN	.	UPI000059D7A2	.	.	.	1/1	.	hmmpanther:PTHR21495,hmmpanther:PTHR21495:SF39,Pfam_domain:PF10469,Gene3D:3.90.1140.10,Superfamily_domains:SSF55144	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAGTTGGC	.	5	ESCA
NLRP7	0	.	GRCh37	19	55452840	55452840	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240C>G	p.%3D	p.L80L	ENST00000588756	4/13	46	43	3	55	55	0	NLRP7,synonymous_variant,p.%3D,ENST00000590030,;NLRP7,synonymous_variant,p.%3D,ENST00000446217,;NLRP7,synonymous_variant,p.%3D,ENST00000588756,;NLRP7,synonymous_variant,p.%3D,ENST00000448121,;NLRP7,synonymous_variant,p.%3D,ENST00000328092,;NLRP7,synonymous_variant,p.%3D,ENST00000587844,;NLRP7,synonymous_variant,p.%3D,ENST00000592784,;NLRP7,synonymous_variant,p.%3D,ENST00000340844,;NLRP7,downstream_gene_variant,,ENST00000590659,;NLRP7,downstream_gene_variant,,ENST00000587103,;NLRP7,synonymous_variant,p.%3D,ENST00000586379,;	C	ENSG00000167634	ENST00000588756	Transcript	synonymous_variant	727	240	80	L	ctC/ctG	.	.	.	-1	NLRP7	HGNC	22947	protein_coding	YES	CCDS46183.1	ENSP00000467123	NALP7_HUMAN	K7ER92_HUMAN,K7EPY3_HUMAN,K7EP54_HUMAN	UPI000174C6C4	.	.	.	4/13	.	PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF87,hmmpanther:PTHR24106,Gene3D:1.10.533.10,Pfam_domain:PF02758,Superfamily_domains:SSF47986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TCCGTGAGATT	.	2	ESCA
ZNF460	0	.	GRCh37	19	57802468	57802468	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559G>C	p.Glu187Gln	p.E187Q	ENST00000360338	3/3	33	23	9	35	35	0	ZNF460,missense_variant,p.Glu146Gln,ENST00000537645,;ZNF460,missense_variant,p.Glu187Gln,ENST00000360338,;ZNF460,downstream_gene_variant,,ENST00000599602,;	C	ENSG00000197714	ENST00000360338	Transcript	missense_variant	881	559	187	E/Q	Gag/Cag	.	.	.	1	ZNF460	HGNC	21628	protein_coding	YES	CCDS12949.1	ENSP00000353491	ZN460_HUMAN	M0R0J6_HUMAN,B4DNX9_HUMAN	UPI0000202D11	.	tolerated(0.56)	possibly_damaging(0.649)	3/3	.	hmmpanther:PTHR24384:SF15,hmmpanther:PTHR24384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATGAGCAG	.	5	ESCA
PDE4DIP	0	.	GRCh37	1	144881578	144881578	+	Silent	SNP	C	C	T	rs199509148	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3618G>A	p.%3D	p.A1206A	ENST00000369356	25/44	91	77	14	86	86	0	PDE4DIP,synonymous_variant,p.%3D,ENST00000369354,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369359,;PDE4DIP,synonymous_variant,p.%3D,ENST00000530740,;PDE4DIP,synonymous_variant,p.%3D,ENST00000530592,;PDE4DIP,synonymous_variant,p.%3D,ENST00000313382,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369356,;AL138796.1,downstream_gene_variant,,ENST00000582173,;RP4-791M13.5,downstream_gene_variant,,ENST00000531288,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000524974,;PDE4DIP,intron_variant,,ENST00000530062,;PDE4DIP,intron_variant,,ENST00000525886,;	T	ENSG00000178104	ENST00000369356	Transcript	synonymous_variant	3909	3618	1206	A	gcG/gcA	rs199509148	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	MYOME_HUMAN	I1VE15_HUMAN	UPI0000458A81	.	.	.	25/44	.	hmmpanther:PTHR13895:SF2,hmmpanther:PTHR13895	T:0.0004	T:0	T:0	.	T:0.001	T:0	T:0.001	T:0.0002	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTAAACGCTGA	byFrequency|byCluster|by1000G	4	ESCA
VPS45	0	.	GRCh37	1	150039956	150039956	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42G>C	p.Met14Ile	p.M14I	ENST00000369130	1/15	82	75	7	83	82	1	VPS45,missense_variant,p.Met14Ile,ENST00000369130,;VPS45,missense_variant,p.Met14Ile,ENST00000419023,;VPS45,missense_variant,p.Met14Ile,ENST00000535106,;VPS45,intron_variant,,ENST00000369128,;VPS45,non_coding_transcript_exon_variant,,ENST00000497638,;VPS45,non_coding_transcript_exon_variant,,ENST00000460366,;VPS45,intron_variant,,ENST00000478999,;VPS45,intron_variant,,ENST00000462852,;	C	ENSG00000136631	ENST00000369130	Transcript	missense_variant	588	42	14	M/I	atG/atC	.	.	.	1	VPS45	HGNC	14579	protein_coding	YES	CCDS944.1	ENSP00000358126	VPS45_HUMAN	.	UPI00000015E6	.	tolerated(0.08)	probably_damaging(0.945)	1/15	.	hmmpanther:PTHR11679:SF3,hmmpanther:PTHR11679,Gene3D:3.40.50.2060,PIRSF_domain:PIRSF005715,Superfamily_domains:SSF56815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAATGATAGA	.	3	ESCA
APH1A	0	.	GRCh37	1	150238561	150238561	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767delA	p.Tyr256PhefsTer14	p.Y256Ffs*14	ENST00000369109	7/7	62	46	16	23	23	0	APH1A,frameshift_variant,p.Tyr186PhefsTer14,ENST00000414276,;APH1A,frameshift_variant,p.Tyr256PhefsTer14,ENST00000369109,;APH1A,3_prime_UTR_variant,,ENST00000360244,;APH1A,downstream_gene_variant,,ENST00000236017,;CA14,downstream_gene_variant,,ENST00000607082,;C1orf54,upstream_gene_variant,,ENST00000369102,;CA14,downstream_gene_variant,,ENST00000369111,;snoU13,downstream_gene_variant,,ENST00000458929,;APH1A,downstream_gene_variant,,ENST00000493092,;APH1A,downstream_gene_variant,,ENST00000461320,;APH1A,downstream_gene_variant,,ENST00000486308,;APH1A,downstream_gene_variant,,ENST00000476538,;APH1A,downstream_gene_variant,,ENST00000486720,;CA14,downstream_gene_variant,,ENST00000607751,;CA14,downstream_gene_variant,,ENST00000607652,;CA14,downstream_gene_variant,,ENST00000483993,;	-	ENSG00000117362	ENST00000369109	Transcript	frameshift_variant	956	767	256	Y/X	tAt/tt	.	.	.	-1	APH1A	HGNC	29509	protein_coding	YES	CCDS41390.1	ENSP00000358105	APH1A_HUMAN	.	UPI0000073CA3	.	.	.	7/7	.	hmmpanther:PTHR12889:SF2,hmmpanther:PTHR12889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCAGAATACACC	.	3	ESCA
RORC	0	.	GRCh37	1	151804259	151804259	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-19G>A	.	.	ENST00000318247	1/11	33	30	3	57	57	0	RORC,5_prime_UTR_variant,,ENST00000318247,;RORC,upstream_gene_variant,,ENST00000392697,;	T	ENSG00000143365	ENST00000318247	Transcript	5_prime_UTR_variant	90	.	.	.	.	.	.	.	-1	RORC	HGNC	10260	protein_coding	YES	CCDS1004.1	ENSP00000327025	RORG_HUMAN	Q6I9R9_HUMAN,D3DV25_HUMAN,B6ZGS6_HUMAN	UPI000006FBD8	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTGCCGTCC	.	4	ESCA
HCN3	0	.	GRCh37	1	155247568	155247568	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.187C>T	p.Arg63Trp	p.R63W	ENST00000368358	1/8	65	55	9	64	64	0	HCN3,missense_variant,p.Arg63Trp,ENST00000368358,;CLK2,upstream_gene_variant,,ENST00000361168,;CLK2,upstream_gene_variant,,ENST00000536801,;CLK2,upstream_gene_variant,,ENST00000355560,;CLK2,upstream_gene_variant,,ENST00000368361,;HCN3,non_coding_transcript_exon_variant,,ENST00000496230,;CLK2,intron_variant,,ENST00000471047,;CLK2,upstream_gene_variant,,ENST00000476983,;HCN3,upstream_gene_variant,,ENST00000467204,;	T	ENSG00000143630	ENST00000368358	Transcript	missense_variant	195	187	63	R/W	Cgg/Tgg	COSM1295169	.	.	1	HCN3	HGNC	19183	protein_coding	YES	CCDS1108.1	ENSP00000357342	HCN3_HUMAN	.	UPI00000559A6	.	deleterious(0)	probably_damaging(0.978)	1/8	.	hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF374,Pfam_domain:PF08412	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTCGGGTG	.	5	ESCA
BCAN	0	.	GRCh37	1	156618415	156618415	+	Silent	SNP	G	G	A	rs776798315	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.825G>A	p.%3D	p.A275A	ENST00000329117	6/14	44	30	13	55	54	0	BCAN,synonymous_variant,p.%3D,ENST00000361588,;BCAN,synonymous_variant,p.%3D,ENST00000424639,;BCAN,synonymous_variant,p.%3D,ENST00000329117,;BCAN,downstream_gene_variant,,ENST00000441358,;BCAN,downstream_gene_variant,,ENST00000457777,;RP11-284F21.7,intron_variant,,ENST00000448869,;RP11-284F21.10,upstream_gene_variant,,ENST00000605886,;BCAN,3_prime_UTR_variant,,ENST00000479949,;BCAN,3_prime_UTR_variant,,ENST00000491823,;	A	ENSG00000132692	ENST00000329117	Transcript	synonymous_variant	1161	825	275	A	gcG/gcA	rs776798315,COSM4023353,COSM4023354	.	.	1	BCAN	HGNC	23059	protein_coding	YES	CCDS1149.1	ENSP00000331210	PGCB_HUMAN	Q9NT67_HUMAN,Q5T3I8_HUMAN,Q5T3I7_HUMAN,Q59F90_HUMAN	UPI000006F0E9	.	.	.	6/14	.	PROSITE_profiles:PS50963,hmmpanther:PTHR22804,Pfam_domain:PF00193,Gene3D:3.10.100.10,SMART_domains:SM00445,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGCGTACTG	byFrequency|byCluster	5	ESCA
TNN	0	.	GRCh37	1	175096214	175096214	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3038C>T	p.Thr1013Ile	p.T1013I	ENST00000239462	13/19	103	97	6	82	82	0	TNN,missense_variant,p.Thr1013Ile,ENST00000239462,;	T	ENSG00000120332	ENST00000239462	Transcript	missense_variant	3151	3038	1013	T/I	aCa/aTa	.	.	.	1	TNN	HGNC	22942	protein_coding	YES	CCDS30943.1	ENSP00000239462	TENN_HUMAN	.	UPI00001D7DA9	.	deleterious(0.01)	possibly_damaging(0.694)	13/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF167,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCACAGTTA	.	2	ESCA
TPR	0	.	GRCh37	1	186280961	186280961	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2142A>G	.	.	ENST00000367478	51/51	25	16	9	17	17	0	TPR,3_prime_UTR_variant,,ENST00000367478,;PRG4,intron_variant,,ENST00000367486,;PRG4,intron_variant,,ENST00000367483,;PRG4,intron_variant,,ENST00000367485,;PRG4,intron_variant,,ENST00000367484,;PRG4,intron_variant,,ENST00000445192,;PRG4,downstream_gene_variant,,ENST00000367482,;RNU6-1240P,non_coding_transcript_exon_variant,,ENST00000365155,;	C	ENSG00000047410	ENST00000367478	Transcript	3_prime_UTR_variant	9531	.	.	.	.	.	.	.	-1	TPR	HGNC	12017	protein_coding	YES	CCDS41446.1	ENSP00000356448	TPR_HUMAN	Q9UE33_HUMAN	UPI000046FCF4	.	.	.	51/51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTCATTTACT	.	2	ESCA
KIF21B	0	.	GRCh37	1	200938777	200938777	+	3'Flank	SNP	T	T	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000422435	.	14	8	6	16	16	0	KIF21B,3_prime_UTR_variant,,ENST00000332129,;KIF21B,downstream_gene_variant,,ENST00000422435,;KIF21B,downstream_gene_variant,,ENST00000360529,;KIF21B,downstream_gene_variant,,ENST00000461742,;MROH3P,downstream_gene_variant,,ENST00000435735,;	A	ENSG00000116852	ENST00000422435	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4158	-1	KIF21B	HGNC	29442	protein_coding	YES	CCDS58056.1	ENSP00000411831	KI21B_HUMAN	.	UPI0000153E7C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTCTTCTCT	.	5	ESCA
ATP2B4	0	.	GRCh37	1	203669435	203669435	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.751G>A	p.Asp251Asn	p.D251N	ENST00000357681	5/21	56	52	3	50	50	0	ATP2B4,missense_variant,p.Asp251Asn,ENST00000341360,;ATP2B4,missense_variant,p.Asp251Asn,ENST00000367218,;ATP2B4,missense_variant,p.Asp251Asn,ENST00000391954,;ATP2B4,missense_variant,p.Asp251Asn,ENST00000367219,;ATP2B4,missense_variant,p.Asp251Asn,ENST00000357681,;	A	ENSG00000058668	ENST00000357681	Transcript	missense_variant	1874	751	251	D/N	Gac/Aac	.	.	.	1	ATP2B4	HGNC	817	protein_coding	YES	CCDS1440.1	ENSP00000350310	AT2B4_HUMAN	A1X4Q2_HUMAN	UPI000002A464	.	tolerated(0.15)	benign(0.423)	5/21	.	hmmpanther:PTHR24093:SF276,hmmpanther:PTHR24093,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01494,Gene3D:1.20.1110.10,Superfamily_domains:0049471	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTGGACAAA	.	2	ESCA
CDC42BPA	0	.	GRCh37	1	227181864	227181864	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*105G>A	.	.	ENST00000366769	36/36	35	27	7	23	23	0	CDC42BPA,3_prime_UTR_variant,,ENST00000366767,;CDC42BPA,3_prime_UTR_variant,,ENST00000442054,;CDC42BPA,3_prime_UTR_variant,,ENST00000366769,;CDC42BPA,3_prime_UTR_variant,,ENST00000448940,;CDC42BPA,3_prime_UTR_variant,,ENST00000334218,;CDC42BPA,3_prime_UTR_variant,,ENST00000366764,;CDC42BPA,3_prime_UTR_variant,,ENST00000366766,;CDC42BPA,downstream_gene_variant,,ENST00000366765,;CDC42BPA,downstream_gene_variant,,ENST00000535525,;RP5-1087E8.3,downstream_gene_variant,,ENST00000433837,;	T	ENSG00000143776	ENST00000366769	Transcript	3_prime_UTR_variant	6557	.	.	.	.	.	.	.	-1	CDC42BPA	HGNC	1737	protein_coding	YES	CCDS1558.1	ENSP00000355731	MRCKA_HUMAN	Q9NYF6_HUMAN	UPI000019097D	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCCCCTGGT	.	5	ESCA
ZNF678	0	.	GRCh37	1	227751338	227751338	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-251G>T	.	.	ENST00000343776	1/4	73	41	31	64	64	0	ZNF678,5_prime_UTR_variant,,ENST00000397097,;ZNF678,5_prime_UTR_variant,,ENST00000608949,;ZNF678,5_prime_UTR_variant,,ENST00000343776,;ZNF678,5_prime_UTR_variant,,ENST00000440339,;RNA5SP77,downstream_gene_variant,,ENST00000365394,;ZNF678,non_coding_transcript_exon_variant,,ENST00000465266,;	T	ENSG00000181450	ENST00000343776	Transcript	5_prime_UTR_variant	95	.	.	.	.	.	.	.	1	ZNF678	HGNC	28652	protein_coding	YES	.	ENSP00000344828	ZN678_HUMAN	.	UPI000019862A	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTGCTGCT	.	5	ESCA
OBSCN	0	.	GRCh37	1	228481268	228481268	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12369C>T	p.%3D	p.Y4123Y	ENST00000570156	46/116	40	37	3	48	48	0	OBSCN,synonymous_variant,p.%3D,ENST00000366707,;OBSCN,synonymous_variant,p.%3D,ENST00000366709,;OBSCN,synonymous_variant,p.%3D,ENST00000483539,;OBSCN,synonymous_variant,p.%3D,ENST00000284548,;OBSCN,synonymous_variant,p.%3D,ENST00000359599,;OBSCN,synonymous_variant,p.%3D,ENST00000570156,;OBSCN,synonymous_variant,p.%3D,ENST00000422127,;RP5-1139B12.4,downstream_gene_variant,,ENST00000602778,;OBSCN,upstream_gene_variant,,ENST00000494839,;	T	ENSG00000154358	ENST00000570156	Transcript	synonymous_variant	12443	12369	4123	Y	taC/taT	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	.	46/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTACCTGTG	.	2	ESCA
MYOM3	0	.	GRCh37	1	24408891	24408891	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2092+192G>A	.	.	ENST00000374434	.	18	11	7	10	10	0	MYOM3,intron_variant,,ENST00000374434,;MYOM3,intron_variant,,ENST00000329601,;MYOM3,intron_variant,,ENST00000330966,;RP11-293P20.4,intron_variant,,ENST00000429191,;RP11-293P20.2,intron_variant,,ENST00000439239,;MYOM3,non_coding_transcript_exon_variant,,ENST00000475306,;MYOM3,intron_variant,,ENST00000448831,;	T	ENSG00000142661	ENST00000374434	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MYOM3	HGNC	26679	protein_coding	YES	CCDS41281.1	ENSP00000363557	MYOM3_HUMAN	.	UPI0000203A5D	.	.	.	.	17/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGCCCCATC	.	5	ESCA
ZBTB18	0	.	GRCh37	1	244217284	244217284	+	Missense_Mutation	SNP	G	G	A	rs373838988	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.208G>A	p.Asp70Asn	p.D70N	ENST00000358704	2/2	33	27	5	22	22	0	ZBTB18,missense_variant,p.Asp70Asn,ENST00000358704,;	A	ENSG00000179456	ENST00000358704	Transcript	missense_variant	357	208	70	D/N	Gac/Aac	rs373838988	.	.	1	ZBTB18	HGNC	13030	protein_coding	YES	CCDS1622.1	ENSP00000351539	ZBT18_HUMAN	.	UPI000034ECE2	.	deleterious(0)	benign(0.057)	2/2	.	PROSITE_profiles:PS50097,hmmpanther:PTHR11389:SF358,hmmpanther:PTHR11389,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGACATT	byFrequency|byCluster	5	ESCA
OR2W5	0	.	GRCh37	1	247655131	247655131	+	RNA	SNP	G	G	T	rs764931441	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.762G>T	.	.	ENST00000530852	1/1	80	57	22	75	75	0	OR2W5,non_coding_transcript_exon_variant,,ENST00000522351,;OR2W5,non_coding_transcript_exon_variant,,ENST00000530852,;OR2W5,non_coding_transcript_exon_variant,,ENST00000366492,;	T	ENSG00000203664	ENST00000530852	Transcript	non_coding_transcript_exon_variant	762	.	.	.	.	rs764931441	.	.	1	OR2W5	HGNC	15424	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGCGAAAGA	.	5	ESCA
BAI2	0	.	GRCh37	1	32205214	32205214	+	Silent	SNP	G	G	C	rs140390564	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2190C>G	p.%3D	p.P730P	ENST00000373658	15/33	36	22	14	34	34	0	BAI2,synonymous_variant,p.%3D,ENST00000373658,;BAI2,synonymous_variant,p.%3D,ENST00000398547,;BAI2,synonymous_variant,p.%3D,ENST00000420125,;BAI2,synonymous_variant,p.%3D,ENST00000398542,;BAI2,synonymous_variant,p.%3D,ENST00000373655,;BAI2,synonymous_variant,p.%3D,ENST00000440175,;BAI2,synonymous_variant,p.%3D,ENST00000398538,;BAI2,synonymous_variant,p.%3D,ENST00000527361,;BAI2,synonymous_variant,p.%3D,ENST00000257070,;BAI2,synonymous_variant,p.%3D,ENST00000398556,;BAI2,downstream_gene_variant,,ENST00000533175,;BAI2,non_coding_transcript_exon_variant,,ENST00000530134,;BAI2,downstream_gene_variant,,ENST00000473952,;BAI2,upstream_gene_variant,,ENST00000484002,;BAI2,upstream_gene_variant,,ENST00000465256,;BAI2,downstream_gene_variant,,ENST00000468430,;BAI2,upstream_gene_variant,,ENST00000466109,;BAI2,upstream_gene_variant,,ENST00000530999,;BAI2,upstream_gene_variant,,ENST00000525655,;	C	ENSG00000121753	ENST00000373658	Transcript	synonymous_variant	2532	2190	730	P	ccC/ccG	rs140390564	.	.	-1	BAI2	HGNC	944	protein_coding	YES	CCDS346.2	ENSP00000362762	BAI2_HUMAN	.	UPI0000E2A42F	.	.	.	15/33	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF41,Pfam_domain:PF12003	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGACGGGCTC	byFrequency|byCluster	5	ESCA
ATP6V0B	0	.	GRCh37	1	44442966	44442966	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.591+78C>G	.	.	ENST00000472174	.	21	11	10	32	32	0	ATP6V0B,missense_variant,p.Cys223Trp,ENST00000532642,;ATP6V0B,intron_variant,,ENST00000498664,;ATP6V0B,intron_variant,,ENST00000236067,;ATP6V0B,intron_variant,,ENST00000471859,;ATP6V0B,intron_variant,,ENST00000472174,;B4GALT2,upstream_gene_variant,,ENST00000372324,;DPH2,downstream_gene_variant,,ENST00000396758,;ATP6V0B,downstream_gene_variant,,ENST00000472505,;B4GALT2,upstream_gene_variant,,ENST00000309519,;DPH2,downstream_gene_variant,,ENST00000459879,;B4GALT2,upstream_gene_variant,,ENST00000356836,;B4GALT2,upstream_gene_variant,,ENST00000434555,;DPH2,downstream_gene_variant,,ENST00000255108,;DPH2,downstream_gene_variant,,ENST00000412950,;B4GALT2,upstream_gene_variant,,ENST00000497866,;ATP6V0B,downstream_gene_variant,,ENST00000472277,;B4GALT2,upstream_gene_variant,,ENST00000485678,;B4GALT2,upstream_gene_variant,,ENST00000498543,;ATP6V0B,non_coding_transcript_exon_variant,,ENST00000468183,;ATP6V0B,intron_variant,,ENST00000473485,;ATP6V0B,downstream_gene_variant,,ENST00000496131,;DPH2,downstream_gene_variant,,ENST00000527319,;DPH2,downstream_gene_variant,,ENST00000524776,;ATP6V0B,downstream_gene_variant,,ENST00000461670,;ATP6V0B,downstream_gene_variant,,ENST00000532072,;ATP6V0B,downstream_gene_variant,,ENST00000498208,;DPH2,downstream_gene_variant,,ENST00000495421,;	G	ENSG00000117410	ENST00000472174	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ATP6V0B	HGNC	861	protein_coding	YES	CCDS505.1	ENSP00000431605	VATO_HUMAN	Q8NHD8_HUMAN,E9PMR1_HUMAN	UPI0000138204	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTGCTCTCC	.	2	ESCA
FOXE3	0	.	GRCh37	1	47883576	47883576	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*629C>G	.	.	ENST00000335071	1/1	50	37	13	54	54	0	FOXE3,3_prime_UTR_variant,,ENST00000335071,;	G	ENSG00000186790	ENST00000335071	Transcript	3_prime_UTR_variant	1833	.	.	.	.	.	.	.	1	FOXE3	HGNC	3808	protein_coding	YES	CCDS550.1	ENSP00000334472	FOXE3_HUMAN	.	UPI000012ADD3	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCAGACA	.	5	ESCA
ALG6	0	.	GRCh37	1	63894627	63894629	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1158_1160delCCT	p.Leu387del	p.L387del	ENST00000371108	14/15	23	15	8	8	8	0	ALG6,inframe_deletion,p.Leu389del,ENST00000263440,;ALG6,inframe_deletion,p.Leu387del,ENST00000371108,;ALG6,non_coding_transcript_exon_variant,,ENST00000462390,;ALG6,non_coding_transcript_exon_variant,,ENST00000465969,;ALG6,non_coding_transcript_exon_variant,,ENST00000494765,;ALG6,3_prime_UTR_variant,,ENST00000603108,;	-	ENSG00000088035	ENST00000371108	Transcript	inframe_deletion	1461-1463	1156-1158	386	L/-	CTC/-	.	.	.	1	ALG6	HGNC	23157	protein_coding	YES	CCDS30735.1	ENSP00000360149	ALG6_HUMAN	.	UPI00001E057D	.	.	.	14/15	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12413:SF1,hmmpanther:PTHR12413,Pfam_domain:PF03155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GATGAACTCCTAAT	.	2	ESCA
ANKRD13C	0	.	GRCh37	1	70819708	70819708	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.384C>G	p.%3D	p.L128L	ENST00000370944	1/13	55	45	10	50	50	0	ANKRD13C,synonymous_variant,p.%3D,ENST00000262346,;ANKRD13C,synonymous_variant,p.%3D,ENST00000370944,;HHLA3,upstream_gene_variant,,ENST00000370940,;HHLA3,upstream_gene_variant,,ENST00000531950,;HHLA3,upstream_gene_variant,,ENST00000359875,;HHLA3,upstream_gene_variant,,ENST00000361764,;HHLA3,upstream_gene_variant,,ENST00000432224,;HHLA3,upstream_gene_variant,,ENST00000486110,;HHLA3,upstream_gene_variant,,ENST00000463058,;HHLA3,upstream_gene_variant,,ENST00000525653,;	C	ENSG00000118454	ENST00000370944	Transcript	synonymous_variant	698	384	128	L	ctC/ctG	.	.	.	-1	ANKRD13C	HGNC	25374	protein_coding	YES	CCDS648.2	ENSP00000359982	AN13C_HUMAN	.	UPI0000140CE0	.	.	.	1/13	.	Superfamily_domains:SSF48403,Gene3D:1.25.40.20,Pfam_domain:PF12796,hmmpanther:PTHR12447:SF1,hmmpanther:PTHR12447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGAGAGTCT	.	5	ESCA
VAMP3	0	.	GRCh37	1	7839798	7839798	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*93C>G	.	.	ENST00000054666	5/5	22	14	8	31	31	0	VAMP3,3_prime_UTR_variant,,ENST00000470357,;VAMP3,3_prime_UTR_variant,,ENST00000054666,;PER3,upstream_gene_variant,,ENST00000377541,;PER3,upstream_gene_variant,,ENST00000377532,;PER3,upstream_gene_variant,,ENST00000361923,;RP3-467L1.6,downstream_gene_variant,,ENST00000602406,;VAMP3,downstream_gene_variant,,ENST00000487194,;	G	ENSG00000049245	ENST00000054666	Transcript	3_prime_UTR_variant	511	.	.	.	.	.	.	.	1	VAMP3	HGNC	12644	protein_coding	YES	CCDS88.1	ENSP00000054666	VAMP3_HUMAN	Q6FGG2_HUMAN,K7EKX0_HUMAN	UPI00001380F2	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTATCTCTAA	.	5	ESCA
RPAP2	0	.	GRCh37	1	92846387	92846387	+	Nonsense_Mutation	SNP	G	G	T	rs779999130	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1795G>T	p.Glu599Ter	p.E599*	ENST00000610020	12/13	54	30	24	52	52	0	RPAP2,stop_gained,p.Glu599Ter,ENST00000610020,;RPAP2,non_coding_transcript_exon_variant,,ENST00000477322,;	T	ENSG00000122484	ENST00000610020	Transcript	stop_gained	1904	1795	599	E/*	Gaa/Taa	rs779999130	.	.	1	RPAP2	HGNC	25791	protein_coding	YES	CCDS740.1	ENSP00000476948	RPAP2_HUMAN	.	UPI0000074323	.	.	.	12/13	.	hmmpanther:PTHR14732:SF0,hmmpanther:PTHR14732	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGAAAGT	.	5	ESCA
SLC24A3	0	.	GRCh37	20	19264910	19264910	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271+3179C>G	.	.	ENST00000328041	.	78	74	4	96	96	0	SLC24A3,intron_variant,,ENST00000328041,;RP5-1027G4.3,non_coding_transcript_exon_variant,,ENST00000319682,;	G	ENSG00000185052	ENST00000328041	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SLC24A3	HGNC	10977	protein_coding	YES	CCDS13140.1	ENSP00000333519	NCKX3_HUMAN	.	UPI00001A8BFD	.	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTTCTCTGC	.	2	ESCA
MATN4	0	.	GRCh37	20	43922341	43922341	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66C>T	.	.	ENST00000537548	11/11	33	21	12	33	33	0	MATN4,3_prime_UTR_variant,,ENST00000372756,;MATN4,3_prime_UTR_variant,,ENST00000372754,;MATN4,3_prime_UTR_variant,,ENST00000537548,;MATN4,3_prime_UTR_variant,,ENST00000353917,;MATN4,3_prime_UTR_variant,,ENST00000342716,;MATN4,3_prime_UTR_variant,,ENST00000360607,;MATN4,downstream_gene_variant,,ENST00000372751,;	A	ENSG00000124159	ENST00000537548	Transcript	3_prime_UTR_variant	2057	.	.	.	.	.	.	.	-1	MATN4	HGNC	6910	protein_coding	YES	CCDS13348.1	ENSP00000440328	MATN4_HUMAN	.	UPI000016054E	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCGATGGC	.	5	ESCA
RASSF2	0	.	GRCh37	20	4771185	4771185	+	Missense_Mutation	SNP	C	C	T	rs145104204	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.449G>A	p.Arg150His	p.R150H	ENST00000379400	7/12	12	5	7	23	23	0	RASSF2,missense_variant,p.Arg150His,ENST00000379376,;RASSF2,missense_variant,p.Arg150His,ENST00000379400,;RASSF2,non_coding_transcript_exon_variant,,ENST00000478553,;	T	ENSG00000101265	ENST00000379400	Transcript	missense_variant	645	449	150	R/H	cGt/cAt	rs145104204,COSM4099187	.	.	-1	RASSF2	HGNC	9883	protein_coding	YES	CCDS13083.1	ENSP00000368710	RASF2_HUMAN	.	UPI0000001C0A	.	tolerated(0.48)	benign(0.017)	7/12	.	hmmpanther:PTHR22738:SF14,hmmpanther:PTHR22738	T:0.0004	T:0.0008	T:0	.	T:0	T:0.001	T:0	T:0.0005	T:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GGCGACGCACC	byFrequency|byCluster|by1000G	2	ESCA
PARD6B	0	.	GRCh37	20	49366851	49366851	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.945G>C	p.Glu315Asp	p.E315D	ENST00000371610	3/3	30	20	10	45	45	0	PARD6B,missense_variant,p.Glu315Asp,ENST00000371610,;PARD6B,intron_variant,,ENST00000396039,;	C	ENSG00000124171	ENST00000371610	Transcript	missense_variant	1188	945	315	E/D	gaG/gaC	.	.	.	1	PARD6B	HGNC	16245	protein_coding	YES	CCDS33485.1	ENSP00000360672	PAR6B_HUMAN	.	UPI000006FA7C	.	tolerated_low_confidence(0.45)	benign(0.015)	3/3	.	hmmpanther:PTHR14102:SF4,hmmpanther:PTHR14102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGAGAGCCT	.	5	ESCA
PARD6B	0	.	GRCh37	20	49367006	49367006	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1100G>A	p.Gly367Glu	p.G367E	ENST00000371610	3/3	12	6	6	16	16	0	PARD6B,missense_variant,p.Gly367Glu,ENST00000371610,;PARD6B,intron_variant,,ENST00000396039,;	A	ENSG00000124171	ENST00000371610	Transcript	missense_variant	1343	1100	367	G/E	gGa/gAa	.	.	.	1	PARD6B	HGNC	16245	protein_coding	YES	CCDS33485.1	ENSP00000360672	PAR6B_HUMAN	.	UPI000006FA7C	.	deleterious_low_confidence(0)	benign(0.023)	3/3	.	hmmpanther:PTHR14102:SF4,hmmpanther:PTHR14102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATGGAACAA	.	2	ESCA
TCP10L	0	.	GRCh37	21	33951108	33951108	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394C>G	p.Leu132Val	p.L132V	ENST00000300258	4/5	142	137	5	134	134	0	TCP10L,missense_variant,p.Leu132Val,ENST00000582575,;TCP10L,missense_variant,p.Leu46Val,ENST00000472557,;TCP10L,missense_variant,p.Leu132Val,ENST00000300258,;AP000275.65,downstream_gene_variant,,ENST00000553001,;AP000275.65,downstream_gene_variant,,ENST00000431216,;LINC00846,upstream_gene_variant,,ENST00000334165,;TCP10L,missense_variant,p.Leu46Val,ENST00000491828,;	C	ENSG00000242220	ENST00000300258	Transcript	missense_variant	508	394	132	L/V	Ctg/Gtg	.	.	.	-1	TCP10L	HGNC	11657	protein_coding	YES	CCDS13616.1	ENSP00000300258	TCP1L_HUMAN	.	UPI0000136B0B	.	tolerated(0.15)	benign(0.164)	4/5	.	hmmpanther:PTHR10331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGACAGAGGTG	.	2	ESCA
IL17RA	0	.	GRCh37	22	17578725	17578725	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202C>T	p.%3D	p.L68L	ENST00000319363	3/13	47	30	17	59	59	0	IL17RA,synonymous_variant,p.%3D,ENST00000319363,;IL17RA,non_coding_transcript_exon_variant,,ENST00000477874,;IL17RA,downstream_gene_variant,,ENST00000459971,;AC006946.12,upstream_gene_variant,,ENST00000429106,;	T	ENSG00000177663	ENST00000319363	Transcript	synonymous_variant	335	202	68	L	Ctg/Ttg	.	.	.	1	IL17RA	HGNC	5985	protein_coding	YES	CCDS13739.1	ENSP00000320936	I17RA_HUMAN	F1JZ08_HUMAN	UPI000005031F	.	.	.	3/13	.	hmmpanther:PTHR15583:SF1,hmmpanther:PTHR15583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R66*|c.196C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAACCTGACC	.	5	ESCA
TXNRD2	0	.	GRCh37	22	19885562	19885562	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774G>T	p.Gln258His	p.Q258H	ENST00000400521	10/18	19	14	5	24	24	0	TXNRD2,missense_variant,p.Gln228His,ENST00000400518,;TXNRD2,missense_variant,p.Gln258His,ENST00000400521,;TXNRD2,missense_variant,p.Gln257His,ENST00000400519,;TXNRD2,missense_variant,p.Gln258His,ENST00000334363,;TXNRD2,missense_variant,p.Gln257His,ENST00000535882,;TXNRD2,missense_variant,p.Gln228His,ENST00000542719,;TXNRD2,splice_region_variant,,ENST00000475995,;TXNRD2,splice_region_variant,,ENST00000491939,;TXNRD2,splice_region_variant,,ENST00000474308,;TXNRD2,missense_variant,p.Gln235His,ENST00000400525,;TXNRD2,splice_region_variant,,ENST00000494454,;	A	ENSG00000184470	ENST00000400521	Transcript	missense_variant	781	774	258	Q/H	caG/caT	.	.	.	-1	TXNRD2	HGNC	18155	protein_coding	YES	CCDS42981.1	ENSP00000383365	TRXR2_HUMAN	.	UPI0000167BDD	.	deleterious(0)	probably_damaging(0.986)	10/18	.	hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF101,Pfam_domain:PF00070,Pfam_domain:PF07992,Gene3D:3.50.50.60,TIGRFAM_domain:TIGR01438,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTACCTGGTC	.	5	ESCA
ZNRF3	0	.	GRCh37	22	29450653	29450653	+	3'UTR	SNP	G	G	A	rs757207274	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1043G>A	.	.	ENST00000544604	9/9	35	19	15	34	34	0	ZNRF3,3_prime_UTR_variant,,ENST00000332811,;ZNRF3,3_prime_UTR_variant,,ENST00000544604,;C22orf31,downstream_gene_variant,,ENST00000216071,;ZNRF3,downstream_gene_variant,,ENST00000406323,;ZNRF3,downstream_gene_variant,,ENST00000402174,;	A	ENSG00000183579	ENST00000544604	Transcript	3_prime_UTR_variant	4029	.	.	.	.	rs757207274	.	.	1	ZNRF3	HGNC	18126	protein_coding	YES	CCDS56225.1	ENSP00000443824	ZNRF3_HUMAN	.	UPI0000EE5944	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCCGATGGG	.	5	ESCA
SFI1	0	.	GRCh37	22	31969041	31969041	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766-3C>T	.	.	ENST00000400288	.	95	63	32	74	74	0	SFI1,splice_region_variant,,ENST00000400288,;SFI1,splice_region_variant,,ENST00000400289,;SFI1,splice_region_variant,,ENST00000414585,;SFI1,splice_region_variant,,ENST00000432498,;SFI1,splice_region_variant,,ENST00000443011,;SFI1,splice_region_variant,,ENST00000540643,;SFI1,splice_region_variant,,ENST00000443326,;SFI1,splice_region_variant,,ENST00000524296,;SFI1,splice_region_variant,,ENST00000382162,;SFI1,non_coding_transcript_exon_variant,,ENST00000476010,;SFI1,non_coding_transcript_exon_variant,,ENST00000484806,;SFI1,upstream_gene_variant,,ENST00000478887,;SFI1,upstream_gene_variant,,ENST00000452250,;	T	ENSG00000198089	ENST00000400288	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	SFI1	HGNC	29064	protein_coding	YES	CCDS43004.1	ENSP00000383145	SFI1_HUMAN	.	UPI00004703B1	.	.	.	.	8/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GTTTTCAGGCT	.	2	ESCA
MYH9	0	.	GRCh37	22	36677427	36677427	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1287A>G	.	.	ENST00000216181	41/41	14	10	4	22	22	0	MYH9,3_prime_UTR_variant,,ENST00000216181,;MYH9,downstream_gene_variant,,ENST00000475726,;MYH9,downstream_gene_variant,,ENST00000486218,;	C	ENSG00000100345	ENST00000216181	Transcript	3_prime_UTR_variant	7401	.	.	.	.	.	.	.	-1	MYH9	HGNC	7579	protein_coding	YES	CCDS13927.1	ENSP00000216181	MYH9_HUMAN	Q9UMJ0_HUMAN,B1AH99_HUMAN	UPI000012FB80	.	.	.	41/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TATTATATAAA	.	3	ESCA
AFF3	0	.	GRCh37	2	100210147	100210147	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2051T>C	p.Val684Ala	p.V684A	ENST00000356421	14/24	31	22	9	33	33	0	AFF3,missense_variant,p.Val684Ala,ENST00000409579,;AFF3,missense_variant,p.Val684Ala,ENST00000356421,;AFF3,missense_variant,p.Val659Ala,ENST00000317233,;AFF3,missense_variant,p.Val659Ala,ENST00000409236,;	G	ENSG00000144218	ENST00000356421	Transcript	missense_variant	2195	2051	684	V/A	gTc/gCc	.	.	.	-1	AFF3	HGNC	6473	protein_coding	YES	CCDS33258.1	ENSP00000348793	AFF3_HUMAN	.	UPI000041098C	.	tolerated(0.46)	benign(0.007)	14/24	.	hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGGACGATC	.	5	ESCA
PCDP1	0	.	GRCh37	2	120395988	120395988	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2128C>T	p.His710Tyr	p.H710Y	ENST00000413369	20/24	37	34	3	50	50	0	PCDP1,missense_variant,p.His710Tyr,ENST00000413369,;PCDP1,missense_variant,p.His18Tyr,ENST00000434869,;PCDP1,missense_variant,p.His269Tyr,ENST00000443972,;PCDP1,missense_variant,p.His424Tyr,ENST00000602047,;PCDP1,3_prime_UTR_variant,,ENST00000295220,;PCDP1,intron_variant,,ENST00000600951,;	T	ENSG00000163075	ENST00000413369	Transcript	missense_variant	2215	2128	710	H/Y	Cac/Tac	.	.	.	1	PCDP1	Uniprot_gn	.	protein_coding	YES	CCDS33282.2	ENSP00000393222	PCDP1_HUMAN	.	UPI0001D322F9	.	deleterious(0)	benign(0.43)	20/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCATCACACG	.	2	ESCA
TMEM163	0	.	GRCh37	2	135213572	135213572	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*715T>C	.	.	ENST00000281924	8/8	35	22	13	44	44	0	TMEM163,3_prime_UTR_variant,,ENST00000281924,;MGAT5,downstream_gene_variant,,ENST00000409645,;TMEM163,non_coding_transcript_exon_variant,,ENST00000476823,;TMEM163,non_coding_transcript_exon_variant,,ENST00000467316,;AC013718.1,downstream_gene_variant,,ENST00000538722,;	G	ENSG00000152128	ENST00000281924	Transcript	3_prime_UTR_variant	1650	.	.	.	.	.	.	.	-1	TMEM163	HGNC	25380	protein_coding	YES	CCDS2172.1	ENSP00000281924	TM163_HUMAN	.	UPI000007217C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTTATTTAT	.	5	ESCA
LCT	0	.	GRCh37	2	136570212	136570212	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2022G>C	p.%3D	p.L674L	ENST00000264162	7/17	57	49	7	70	70	0	LCT,synonymous_variant,p.%3D,ENST00000264162,;Y_RNA,upstream_gene_variant,,ENST00000363794,;LCT,synonymous_variant,p.%3D,ENST00000452974,;	G	ENSG00000115850	ENST00000264162	Transcript	synonymous_variant	2033	2022	674	L	ctG/ctC	.	.	.	-1	LCT	HGNC	6530	protein_coding	YES	CCDS2178.1	ENSP00000264162	LPH_HUMAN	.	UPI000013D4D2	.	.	.	7/17	.	Gene3D:3.20.20.80,Pfam_domain:PF00232,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTCAGGAG	.	5	ESCA
TTN	0	.	GRCh37	2	179595754	179595754	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17638C>T	p.%3D	p.L5880L	ENST00000589042	60/363	65	41	23	68	68	0	TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,upstream_gene_variant,,ENST00000582847,;RP11-171I2.1,downstream_gene_variant,,ENST00000590024,;	A	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	17863	17638	5880	L	Ctg/Ttg	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	60/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCAGTATTG	.	5	ESCA
MFSD6	0	.	GRCh37	2	191366418	191366418	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1474G>A	.	.	ENST00000392328	8/8	18	15	3	13	13	0	MFSD6,3_prime_UTR_variant,,ENST00000434582,;MFSD6,3_prime_UTR_variant,,ENST00000392328,;MFSD6,3_prime_UTR_variant,,ENST00000281416,;TMEM194B,downstream_gene_variant,,ENST00000409150,;MFSD6,downstream_gene_variant,,ENST00000535751,;MFSD6,downstream_gene_variant,,ENST00000444317,;MFSD6,intron_variant,,ENST00000412482,;MFSD6,downstream_gene_variant,,ENST00000486123,;	A	ENSG00000151690	ENST00000392328	Transcript	3_prime_UTR_variant	4174	.	.	.	.	.	.	.	1	MFSD6	HGNC	24711	protein_coding	YES	CCDS2306.1	ENSP00000376141	MFSD6_HUMAN	C9JJH2_HUMAN,C9JAZ7_HUMAN,C9J134_HUMAN,C9IYL1_HUMAN,B7Z810_HUMAN,B7Z7Y2_HUMAN	UPI000022BD91	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTGGGATA	.	2	ESCA
RNF25	0	.	GRCh37	2	219529070	219529070	+	Silent	SNP	G	G	A	rs754094338	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990C>T	p.%3D	p.G330G	ENST00000295704	10/10	75	48	27	85	85	0	RNF25,synonymous_variant,p.%3D,ENST00000295704,;BCS1L,downstream_gene_variant,,ENST00000423377,;BCS1L,downstream_gene_variant,,ENST00000412366,;BCS1L,downstream_gene_variant,,ENST00000430322,;BCS1L,downstream_gene_variant,,ENST00000443791,;BCS1L,downstream_gene_variant,,ENST00000426649,;BCS1L,downstream_gene_variant,,ENST00000456050,;BCS1L,downstream_gene_variant,,ENST00000439945,;BCS1L,downstream_gene_variant,,ENST00000392109,;ZNF142,upstream_gene_variant,,ENST00000411696,;ZNF142,upstream_gene_variant,,ENST00000432460,;BCS1L,downstream_gene_variant,,ENST00000359273,;BCS1L,downstream_gene_variant,,ENST00000428880,;BCS1L,downstream_gene_variant,,ENST00000392111,;BCS1L,downstream_gene_variant,,ENST00000436603,;ZNF142,upstream_gene_variant,,ENST00000450560,;BCS1L,downstream_gene_variant,,ENST00000392110,;BCS1L,downstream_gene_variant,,ENST00000431802,;ZNF142,upstream_gene_variant,,ENST00000449707,;BCS1L,downstream_gene_variant,,ENST00000465706,;RNF25,non_coding_transcript_exon_variant,,ENST00000474339,;RNF25,non_coding_transcript_exon_variant,,ENST00000473034,;ZNF142,upstream_gene_variant,,ENST00000450765,;BCS1L,downstream_gene_variant,,ENST00000493376,;BCS1L,downstream_gene_variant,,ENST00000477422,;BCS1L,downstream_gene_variant,,ENST00000471576,;RNF25,downstream_gene_variant,,ENST00000497832,;BCS1L,downstream_gene_variant,,ENST00000460579,;BCS1L,downstream_gene_variant,,ENST00000490188,;ZNF142,upstream_gene_variant,,ENST00000433921,;RNF25,downstream_gene_variant,,ENST00000423170,;RNF25,downstream_gene_variant,,ENST00000463188,;	A	ENSG00000163481	ENST00000295704	Transcript	synonymous_variant	1431	990	330	G	ggC/ggT	rs754094338	.	.	-1	RNF25	HGNC	14662	protein_coding	YES	CCDS2420.1	ENSP00000295704	RNF25_HUMAN	.	UPI000013431F	.	.	.	10/10	.	hmmpanther:PTHR13198	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTCGCCCAA	.	5	ESCA
DOCK10	0	.	GRCh37	2	225658132	225658133	+	Frame_Shift_Ins	INS	-	-	CT	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5195_5196dupAG	p.Tyr1733SerfsTer3	p.Y1733Sfs*3	ENST00000258390	46/56	34	27	7	28	28	0	DOCK10,frameshift_variant,p.Tyr1733SerfsTer3,ENST00000258390,;DOCK10,frameshift_variant,p.Tyr1727SerfsTer3,ENST00000409592,;DOCK10,non_coding_transcript_exon_variant,,ENST00000492251,;	CT	ENSG00000135905	ENST00000258390	Transcript	frameshift_variant	5264-5265	5196-5197	1732-1733	-/X	-/AG	.	.	.	-1	DOCK10	HGNC	23479	protein_coding	YES	CCDS46528.1	ENSP00000258390	DOC10_HUMAN	Q4ZG60_HUMAN,Q3LIC8_HUMAN	UPI000021D2A7	.	.	.	46/56	.	PROSITE_profiles:PS51651,hmmpanther:PTHR23317:SF71,hmmpanther:PTHR23317	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGATACTCTG	.	3	ESCA
SPATA3	0	.	GRCh37	2	231860992	231860992	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44G>A	p.Arg15Gln	p.R15Q	ENST00000452881	1/9	62	41	21	58	58	0	SPATA3,missense_variant,p.Arg15Gln,ENST00000455816,;SPATA3,missense_variant,p.Arg15Gln,ENST00000424440,;SPATA3,missense_variant,p.Arg15Gln,ENST00000452881,;SPATA3,missense_variant,p.Arg15Gln,ENST00000433428,;SPATA3,upstream_gene_variant,,ENST00000423134,;SPATA3,upstream_gene_variant,,ENST00000440792,;SPATA3-AS1,upstream_gene_variant,,ENST00000426904,;SPATA3-AS1,upstream_gene_variant,,ENST00000418330,;SPATA3-AS1,upstream_gene_variant,,ENST00000457803,;SPATA3-AS1,upstream_gene_variant,,ENST00000434094,;SPATA3-AS1,upstream_gene_variant,,ENST00000414876,;SPATA3-AS1,upstream_gene_variant,,ENST00000446741,;SPATA3-AS1,upstream_gene_variant,,ENST00000441063,;SPATA3,upstream_gene_variant,,ENST00000409956,;SPATA3,intron_variant,,ENST00000454918,;	A	ENSG00000173699	ENST00000452881	Transcript	missense_variant	152	44	15	R/Q	cGa/cAa	.	.	.	1	SPATA3	HGNC	17884	protein_coding	YES	CCDS2481.1	ENSP00000388895	SPTA3_HUMAN	.	UPI000006E910	.	deleterious(0.05)	benign(0.417)	1/9	.	hmmpanther:PTHR22234	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCGAGACT	.	5	ESCA
PTMA	0	.	GRCh37	2	232577559	232577559	+	Nonstop_Mutation	SNP	T	T	C	rs762198164	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334T>C	p.Ter112GlnextTer9	p.*112Qext*9	ENST00000341369	5/5	24	21	3	21	21	0	PTMA,stop_lost,p.Ter137GlnextTer?,ENST00000410064,;PTMA,stop_lost,p.Ter112GlnextTer9,ENST00000341369,;PTMA,stop_lost,p.Ter149GlnextTer9,ENST00000412128,;PTMA,stop_lost,p.Ter111GlnextTer9,ENST00000409115,;PTMA,stop_lost,p.Ter132GlnextTer9,ENST00000409321,;PTMA,stop_lost,p.Ter108GlnextTer9,ENST00000409683,;PTMA,downstream_gene_variant,,ENST00000440384,;PTMA,non_coding_transcript_exon_variant,,ENST00000466801,;PTMA,3_prime_UTR_variant,,ENST00000448874,;PTMA,non_coding_transcript_exon_variant,,ENST00000481928,;PTMA,downstream_gene_variant,,ENST00000467816,;PTMA,downstream_gene_variant,,ENST00000468027,;	C	ENSG00000187514	ENST00000341369	Transcript	stop_lost	525	334	112	*/Q	Tag/Cag	rs762198164,COSM573838	.	.	1	PTMA	HGNC	9623	protein_coding	YES	CCDS42833.1	ENSP00000344547	PTMA_HUMAN	.	UPI0000047512	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGACTAGACA	byFrequency	2	ESCA
HDLBP	0	.	GRCh37	2	242207945	242207945	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-91A>G	.	.	ENST00000391975	2/28	52	39	12	44	44	0	HDLBP,5_prime_UTR_variant,,ENST00000310931,;HDLBP,5_prime_UTR_variant,,ENST00000427183,;HDLBP,5_prime_UTR_variant,,ENST00000420451,;HDLBP,5_prime_UTR_variant,,ENST00000425989,;HDLBP,5_prime_UTR_variant,,ENST00000430918,;HDLBP,5_prime_UTR_variant,,ENST00000449504,;HDLBP,5_prime_UTR_variant,,ENST00000427007,;HDLBP,5_prime_UTR_variant,,ENST00000391976,;HDLBP,5_prime_UTR_variant,,ENST00000417540,;HDLBP,5_prime_UTR_variant,,ENST00000441124,;HDLBP,5_prime_UTR_variant,,ENST00000444092,;HDLBP,5_prime_UTR_variant,,ENST00000458564,;HDLBP,5_prime_UTR_variant,,ENST00000426343,;HDLBP,5_prime_UTR_variant,,ENST00000422080,;HDLBP,5_prime_UTR_variant,,ENST00000452065,;HDLBP,5_prime_UTR_variant,,ENST00000422933,;HDLBP,5_prime_UTR_variant,,ENST00000428482,;HDLBP,5_prime_UTR_variant,,ENST00000413241,;HDLBP,5_prime_UTR_variant,,ENST00000442714,;HDLBP,5_prime_UTR_variant,,ENST00000391975,;HDLBP,5_prime_UTR_variant,,ENST00000423693,;HDLBP,5_prime_UTR_variant,,ENST00000449864,;HDLBP,non_coding_transcript_exon_variant,,ENST00000490697,;HDLBP,non_coding_transcript_exon_variant,,ENST00000462130,;HDLBP,downstream_gene_variant,,ENST00000496569,;	C	ENSG00000115677	ENST00000391975	Transcript	5_prime_UTR_variant	138	.	.	.	.	.	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	.	.	2/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCCTGCCAG	.	5	ESCA
FARP2	0	.	GRCh37	2	242407662	242407662	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2001G>C	p.Gln667His	p.Q667H	ENST00000264042	18/27	43	40	3	48	48	0	FARP2,missense_variant,p.Gln667His,ENST00000264042,;FARP2,downstream_gene_variant,,ENST00000422951,;FARP2,downstream_gene_variant,,ENST00000545004,;FARP2,downstream_gene_variant,,ENST00000373287,;FARP2,upstream_gene_variant,,ENST00000491425,;FARP2,non_coding_transcript_exon_variant,,ENST00000496470,;FARP2,downstream_gene_variant,,ENST00000473510,;FARP2,downstream_gene_variant,,ENST00000476799,;	C	ENSG00000006607	ENST00000264042	Transcript	missense_variant	2171	2001	667	Q/H	caG/caC	.	.	.	1	FARP2	HGNC	16460	protein_coding	YES	CCDS33424.1	ENSP00000264042	FARP2_HUMAN	C9JWM9_HUMAN,C9JVQ5_HUMAN	UPI0000073D5B	.	deleterious(0.03)	probably_damaging(1)	18/27	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF58,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCAGAAGGT	.	2	ESCA
DYSF	0	.	GRCh37	2	71753404	71753404	+	Silent	SNP	C	C	A	rs370775850	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1204C>A	p.%3D	p.R402R	ENST00000410020	13/56	30	23	6	32	32	0	DYSF,synonymous_variant,p.%3D,ENST00000409582,;DYSF,synonymous_variant,p.%3D,ENST00000410020,;DYSF,synonymous_variant,p.%3D,ENST00000409744,;DYSF,synonymous_variant,p.%3D,ENST00000429174,;DYSF,synonymous_variant,p.%3D,ENST00000409762,;DYSF,synonymous_variant,p.%3D,ENST00000410041,;DYSF,synonymous_variant,p.%3D,ENST00000409651,;DYSF,synonymous_variant,p.%3D,ENST00000394120,;DYSF,synonymous_variant,p.%3D,ENST00000409366,;DYSF,synonymous_variant,p.%3D,ENST00000413539,;DYSF,synonymous_variant,p.%3D,ENST00000258104,;	A	ENSG00000135636	ENST00000410020	Transcript	synonymous_variant	1345	1204	402	R	Cgg/Agg	rs370775850	.	.	1	DYSF	HGNC	3097	protein_coding	YES	CCDS46328.1	ENSP00000386881	DYSF_HUMAN	A0FK00_HUMAN	UPI000171F710	.	.	.	13/56	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF35,Pfam_domain:PF08151	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTCCGGCCC	byCluster	5	ESCA
DYSF	0	.	GRCh37	2	71892349	71892349	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5232C>T	p.%3D	p.F1744F	ENST00000410020	47/56	31	19	12	27	27	0	DYSF,synonymous_variant,p.%3D,ENST00000409582,;DYSF,synonymous_variant,p.%3D,ENST00000410020,;DYSF,synonymous_variant,p.%3D,ENST00000409744,;DYSF,synonymous_variant,p.%3D,ENST00000429174,;DYSF,synonymous_variant,p.%3D,ENST00000409762,;DYSF,synonymous_variant,p.%3D,ENST00000410041,;DYSF,synonymous_variant,p.%3D,ENST00000409651,;DYSF,synonymous_variant,p.%3D,ENST00000394120,;DYSF,synonymous_variant,p.%3D,ENST00000409366,;DYSF,synonymous_variant,p.%3D,ENST00000413539,;DYSF,synonymous_variant,p.%3D,ENST00000258104,;DYSF,non_coding_transcript_exon_variant,,ENST00000479049,;	T	ENSG00000135636	ENST00000410020	Transcript	synonymous_variant	5373	5232	1744	F	ttC/ttT	.	.	.	1	DYSF	HGNC	3097	protein_coding	YES	CCDS46328.1	ENSP00000386881	DYSF_HUMAN	A0FK00_HUMAN	UPI000171F710	.	.	.	47/56	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTCTGCCA	.	5	ESCA
DNAH6	0	.	GRCh37	2	84912583	84912583	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7050G>C	p.%3D	p.L2350L	ENST00000389394	43/77	36	31	5	38	38	0	DNAH6,synonymous_variant,p.%3D,ENST00000237449,;DNAH6,synonymous_variant,p.%3D,ENST00000389394,;DNAH6,intron_variant,,ENST00000602588,;DNAH6,intron_variant,,ENST00000398278,;	C	ENSG00000115423	ENST00000389394	Transcript	synonymous_variant	7187	7050	2350	L	ctG/ctC	.	.	.	1	DNAH6	HGNC	2951	protein_coding	YES	CCDS46348.1	ENSP00000374045	DYH6_HUMAN	B0I1R8_HUMAN	UPI000163AC9D	.	.	.	43/77	.	hmmpanther:PTHR10676:SF136,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTCTGACAGA	.	4	ESCA
UPK1B	0	.	GRCh37	3	118913174	118913174	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.577A>G	p.Met193Val	p.M193V	ENST00000264234	6/8	69	52	17	66	66	0	UPK1B,missense_variant,p.Met193Val,ENST00000264234,;UPK1B,missense_variant,p.Met185Val,ENST00000460625,;UPK1B,missense_variant,p.Met113Val,ENST00000497685,;UPK1B,downstream_gene_variant,,ENST00000494855,;UPK1B,downstream_gene_variant,,ENST00000479520,;	G	ENSG00000114638	ENST00000264234	Transcript	missense_variant	726	577	193	M/V	Atg/Gtg	.	.	.	1	UPK1B	HGNC	12578	protein_coding	YES	CCDS2985.1	ENSP00000264234	UPK1B_HUMAN	E7ETN9_HUMAN,C9J6N2_HUMAN,C9J027_HUMAN	UPI000013D4E8	.	tolerated(0.3)	benign(0.024)	6/8	.	hmmpanther:PTHR19282:SF24,hmmpanther:PTHR19282,Pfam_domain:PF00335,Superfamily_domains:0037997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTATGAAC	.	5	ESCA
STAG1	0	.	GRCh37	3	136141639	136141639	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1804G>C	p.Glu602Gln	p.E602Q	ENST00000383202	18/34	53	41	12	38	38	0	STAG1,missense_variant,p.Glu186Gln,ENST00000536929,;STAG1,missense_variant,p.Glu376Gln,ENST00000434713,;STAG1,missense_variant,p.Glu602Gln,ENST00000383202,;STAG1,missense_variant,p.Glu602Gln,ENST00000236698,;STAG1,downstream_gene_variant,,ENST00000492318,;STAG1,3_prime_UTR_variant,,ENST00000483235,;STAG1,3_prime_UTR_variant,,ENST00000487065,;	G	ENSG00000118007	ENST00000383202	Transcript	missense_variant	2061	1804	602	E/Q	Gaa/Caa	.	.	.	-1	STAG1	HGNC	11354	protein_coding	YES	CCDS3090.1	ENSP00000372689	STAG1_HUMAN	Q4LE48_HUMAN	UPI000020A2DE	.	deleterious(0.02)	possibly_damaging(0.501)	18/34	.	hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCTAAAT	.	5	ESCA
TFDP2	0	.	GRCh37	3	141811953	141811953	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.32C>T	p.Thr11Ile	p.T11I	ENST00000489671	3/13	69	64	5	48	48	0	TFDP2,missense_variant,p.Thr11Ile,ENST00000489671,;TFDP2,missense_variant,p.Thr11Ile,ENST00000467634,;TFDP2,5_prime_UTR_variant,,ENST00000467072,;TFDP2,5_prime_UTR_variant,,ENST00000499676,;TFDP2,5_prime_UTR_variant,,ENST00000317104,;TFDP2,intron_variant,,ENST00000475734,;TFDP2,intron_variant,,ENST00000494358,;TFDP2,upstream_gene_variant,,ENST00000488107,;TFDP2,non_coding_transcript_exon_variant,,ENST00000476617,;TFDP2,non_coding_transcript_exon_variant,,ENST00000495095,;TFDP2,intron_variant,,ENST00000464782,;TFDP2,missense_variant,p.Thr11Ile,ENST00000487734,;TFDP2,non_coding_transcript_exon_variant,,ENST00000491667,;	A	ENSG00000114126	ENST00000489671	Transcript	missense_variant	463	32	11	T/I	aCa/aTa	COSM3944944	.	.	-1	TFDP2	HGNC	11751	protein_coding	YES	CCDS54650.1	ENSP00000420616	TFDP2_HUMAN	C9JTZ9_HUMAN,C9JNB6_HUMAN,C9JCY5_HUMAN,C9J5D5_HUMAN,C9J461_HUMAN	UPI0000136B56	.	tolerated_low_confidence(0.07)	benign(0.001)	3/13	.	hmmpanther:PTHR12548,hmmpanther:PTHR12548:SF5,PIRSF_domain:PIRSF009404	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTGTGGAA	.	2	ESCA
ATR	0	.	GRCh37	3	142168307	142168307	+	Silent	SNP	T	T	A	rs147649584	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7899A>T	p.%3D	p.L2633L	ENST00000350721	47/47	59	50	8	63	63	0	ATR,synonymous_variant,p.%3D,ENST00000383101,;ATR,synonymous_variant,p.%3D,ENST00000350721,;ATR,3_prime_UTR_variant,,ENST00000513291,;XRN1,upstream_gene_variant,,ENST00000544157,;XRN1,upstream_gene_variant,,ENST00000463916,;XRN1,upstream_gene_variant,,ENST00000392981,;XRN1,upstream_gene_variant,,ENST00000264951,;XRN1,upstream_gene_variant,,ENST00000465074,;ATR,3_prime_UTR_variant,,ENST00000515810,;ATR,3_prime_UTR_variant,,ENST00000504521,;ATR,non_coding_transcript_exon_variant,,ENST00000515107,;XRN1,upstream_gene_variant,,ENST00000486211,;XRN1,upstream_gene_variant,,ENST00000470537,;ATR,downstream_gene_variant,,ENST00000511016,;RP11-383G6.4,upstream_gene_variant,,ENST00000481134,;	A	ENSG00000175054	ENST00000350721	Transcript	synonymous_variant	8021	7899	2633	L	ctA/ctT	rs147649584	.	.	-1	ATR	HGNC	882	protein_coding	YES	CCDS3124.1	ENSP00000343741	ATR_HUMAN	.	UPI0000031A31	.	.	.	47/47	.	PROSITE_profiles:PS50290,PROSITE_profiles:PS51190,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64,Pfam_domain:PF02260,Gene3D:1.10.1070.11,SMART_domains:SM00146	.	.	.	.	.	.	.	C:0	C:0.0003	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCATAGTAA	byCluster	5	ESCA
SLC33A1	0	.	GRCh37	3	155547652	155547652	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1307A>G	p.Asn436Ser	p.N436S	ENST00000392845	5/6	86	64	21	59	59	0	SLC33A1,missense_variant,p.Asn436Ser,ENST00000392845,;SLC33A1,missense_variant,p.Asn72Ser,ENST00000496772,;SLC33A1,missense_variant,p.Asn436Ser,ENST00000359479,;SLC33A1,missense_variant,p.Asn156Ser,ENST00000475842,;SLC33A1,3_prime_UTR_variant,,ENST00000468581,;	C	ENSG00000169359	ENST00000392845	Transcript	missense_variant	1688	1307	436	N/S	aAt/aGt	.	.	.	-1	SLC33A1	HGNC	95	protein_coding	YES	CCDS3173.1	ENSP00000376587	ACATN_HUMAN	.	UPI000006E3FD	.	tolerated(0.31)	benign(0.102)	5/6	.	Superfamily_domains:SSF103473,Pfam_domain:PF13000,TIGRFAM_domain:TIGR00901,hmmpanther:PTHR12778,hmmpanther:PTHR12778:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCATTGAAA	.	5	ESCA
FAM131A	0	.	GRCh37	3	184062689	184062689	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032A>T	p.Gln344His	p.Q344H	ENST00000383847	6/6	76	53	23	70	70	0	FAM131A,missense_variant,p.Gln259His,ENST00000340957,;FAM131A,missense_variant,p.Gln259His,ENST00000453072,;FAM131A,missense_variant,p.Gln344His,ENST00000383847,;FAM131A,missense_variant,p.Gln313His,ENST00000310585,;FAM131A,missense_variant,p.Gln259His,ENST00000450976,;FAM131A,intron_variant,,ENST00000418281,;EIF2B5,intron_variant,,ENST00000444495,;CLCN2,downstream_gene_variant,,ENST00000434054,;FAM131A,downstream_gene_variant,,ENST00000418768,;CLCN2,downstream_gene_variant,,ENST00000265593,;FAM131A,downstream_gene_variant,,ENST00000433578,;CLCN2,downstream_gene_variant,,ENST00000344937,;CLCN2,downstream_gene_variant,,ENST00000457512,;CLCN2,downstream_gene_variant,,ENST00000423355,;FAM131A,downstream_gene_variant,,ENST00000487702,;FAM131A,downstream_gene_variant,,ENST00000497070,;CLCN2,downstream_gene_variant,,ENST00000430397,;	T	ENSG00000175182	ENST00000383847	Transcript	missense_variant	1211	1032	344	Q/H	caA/caT	.	.	.	1	FAM131A	HGNC	28308	protein_coding	YES	CCDS3262.2	ENSP00000373360	F131A_HUMAN	C9JY59_HUMAN,C9JP51_HUMAN	UPI0000EE22AD	.	deleterious(0)	benign(0.264)	6/6	.	hmmpanther:PTHR15736:SF4,hmmpanther:PTHR15736,Pfam_domain:PF15010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCAAGCCTC	.	5	ESCA
RTP4	0	.	GRCh37	3	187086357	187086357	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128A>T	p.Lys43Met	p.K43M	ENST00000259030	1/2	19	13	6	16	16	0	RTP4,missense_variant,p.Lys43Met,ENST00000259030,;	T	ENSG00000136514	ENST00000259030	Transcript	missense_variant	238	128	43	K/M	aAg/aTg	.	.	.	1	RTP4	HGNC	23992	protein_coding	YES	CCDS33910.1	ENSP00000259030	RTP4_HUMAN	.	UPI000013D021	.	deleterious(0.05)	probably_damaging(0.971)	1/2	.	hmmpanther:PTHR14402:SF8,hmmpanther:PTHR14402	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAAGCAAT	.	5	ESCA
HRASLS	0	.	GRCh37	3	192980950	192980950	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.646G>C	p.Ala216Pro	p.A216P	ENST00000264735	3/4	83	64	19	64	64	0	HRASLS,missense_variant,p.Ala216Pro,ENST00000264735,;HRASLS,missense_variant,p.Ala111Pro,ENST00000602513,;HRASLS,missense_variant,p.Ala54Pro,ENST00000416012,;	C	ENSG00000127252	ENST00000264735	Transcript	missense_variant	740	646	216	A/P	Gcc/Ccc	.	.	.	1	HRASLS	HGNC	14922	protein_coding	YES	CCDS3303.2	ENSP00000264735	.	H7C3Y1_HUMAN	UPI0000E5AB93	.	tolerated(0.42)	benign(0.046)	3/4	.	hmmpanther:PTHR13943,hmmpanther:PTHR13943:SF35,Pfam_domain:PF04970	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGGCCTAT	.	5	ESCA
ZBTB47	0	.	GRCh37	3	42707811	42707811	+	3'Flank	SNP	A	A	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000232974	.	27	11	15	37	37	0	ZBTB47,3_prime_UTR_variant,,ENST00000457842,;ZBTB47,downstream_gene_variant,,ENST00000232974,;ZBTB47,downstream_gene_variant,,ENST00000505904,;	T	ENSG00000114853	ENST00000232974	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	465	1	ZBTB47	HGNC	26955	protein_coding	YES	CCDS46805.2	ENSP00000232974	.	H7BXD3_HUMAN,D6RDG5_HUMAN	UPI0001BB2D41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGAGAGAA	.	5	ESCA
AMT	0	.	GRCh37	3	49454779	49454779	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*194T>C	.	.	ENST00000273588	9/9	26	10	16	36	36	0	AMT,stop_lost,p.Ter385ArgextTer25,ENST00000427987,;AMT,stop_lost,p.Ter387ArgextTer25,ENST00000395338,;AMT,3_prime_UTR_variant,,ENST00000458307,;AMT,3_prime_UTR_variant,,ENST00000538581,;AMT,3_prime_UTR_variant,,ENST00000273588,;AMT,downstream_gene_variant,,ENST00000430521,;TCTA,downstream_gene_variant,,ENST00000273590,;AMT,downstream_gene_variant,,ENST00000546031,;AMT,non_coding_transcript_exon_variant,,ENST00000476226,;TCTA,downstream_gene_variant,,ENST00000493381,;TCTA,downstream_gene_variant,,ENST00000497786,;TCTA,downstream_gene_variant,,ENST00000487432,;AMT,downstream_gene_variant,,ENST00000485108,;AMT,downstream_gene_variant,,ENST00000493046,;TCTA,downstream_gene_variant,,ENST00000488385,;AMT,downstream_gene_variant,,ENST00000487589,;RHOA,upstream_gene_variant,,ENST00000265538,;AMT,downstream_gene_variant,,ENST00000462048,;AMT,downstream_gene_variant,,ENST00000480957,;TCTA,downstream_gene_variant,,ENST00000482193,;AMT,non_coding_transcript_exon_variant,,ENST00000465925,;AMT,downstream_gene_variant,,ENST00000476828,;AMT,downstream_gene_variant,,ENST00000476127,;AMT,downstream_gene_variant,,ENST00000461210,;AMT,downstream_gene_variant,,ENST00000495436,;AMT,downstream_gene_variant,,ENST00000473163,;AMT,downstream_gene_variant,,ENST00000498571,;AMT,downstream_gene_variant,,ENST00000399379,;AMT,downstream_gene_variant,,ENST00000478594,;AMT,downstream_gene_variant,,ENST00000491800,;	G	ENSG00000145020	ENST00000273588	Transcript	3_prime_UTR_variant	1709	.	.	.	.	.	.	.	-1	AMT	HGNC	473	protein_coding	YES	CCDS2797.1	ENSP00000273588	GCST_HUMAN	B4DGG9_HUMAN,B3KTU4_HUMAN	UPI000012B35E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCAGAAGC	.	5	ESCA
APEH	0	.	GRCh37	3	49714115	49714115	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.818G>T	p.Arg273Leu	p.R273L	ENST00000296456	8/22	85	38	46	171	171	0	APEH,missense_variant,p.Arg273Leu,ENST00000296456,;APEH,missense_variant,p.Arg172Leu,ENST00000449966,;APEH,missense_variant,p.Arg224Leu,ENST00000457042,;APEH,missense_variant,p.Arg273Leu,ENST00000438011,;APEH,missense_variant,p.Arg198Leu,ENST00000442186,;APEH,3_prime_UTR_variant,,ENST00000447436,;APEH,3_prime_UTR_variant,,ENST00000446089,;APEH,3_prime_UTR_variant,,ENST00000447541,;APEH,non_coding_transcript_exon_variant,,ENST00000463995,;APEH,non_coding_transcript_exon_variant,,ENST00000482301,;APEH,downstream_gene_variant,,ENST00000463616,;APEH,downstream_gene_variant,,ENST00000491799,;APEH,downstream_gene_variant,,ENST00000483715,;APEH,upstream_gene_variant,,ENST00000469362,;APEH,downstream_gene_variant,,ENST00000462439,;	T	ENSG00000164062	ENST00000296456	Transcript	missense_variant	1218	818	273	R/L	cGc/cTc	.	.	.	1	APEH	HGNC	586	protein_coding	YES	CCDS2801.1	ENSP00000296456	ACPH_HUMAN	C9JLK2_HUMAN	UPI00000735A1	.	tolerated(0.17)	benign(0.122)	8/22	.	hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF108,Gene3D:2.120.10.30,Superfamily_domains:SSF50993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCGCTTTT	.	5	ESCA
DENND6A	0	.	GRCh37	3	57619036	57619036	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1309C>T	p.Arg437Ter	p.R437*	ENST00000311128	15/20	44	22	21	58	58	0	DENND6A,stop_gained,p.Arg9Ter,ENST00000471531,;DENND6A,stop_gained,p.Arg437Ter,ENST00000311128,;DENND6A,downstream_gene_variant,,ENST00000477344,;RP11-755B10.2,intron_variant,,ENST00000470427,;DENND6A,upstream_gene_variant,,ENST00000480710,;	A	ENSG00000174839	ENST00000311128	Transcript	stop_gained	1380	1309	437	R/*	Cga/Tga	.	.	.	-1	DENND6A	HGNC	26635	protein_coding	YES	CCDS33773.1	ENSP00000311401	DEN6A_HUMAN	.	UPI00000744F6	.	.	.	15/20	.	hmmpanther:PTHR13677:SF1,hmmpanther:PTHR13677	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGTCGAAGAA	.	5	ESCA
OR5H15	0	.	GRCh37	3	97888442	97888442	+	Nonsense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.899C>G	p.Ser300Ter	p.S300*	ENST00000356526	1/1	43	38	5	36	36	0	OR5H15,stop_gained,p.Ser300Ter,ENST00000356526,;	G	ENSG00000233412	ENST00000356526	Transcript	stop_gained	899	899	300	S/*	tCa/tGa	COSM163157	.	.	1	OR5H15	HGNC	31287	protein_coding	YES	CCDS33799.1	ENSP00000373195	O5H15_HUMAN	.	UPI00001606CE	.	.	.	1/1	.	hmmpanther:PTHR26452:SF135,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTCATTCA	.	5	ESCA
FAT4	0	.	GRCh37	4	126239676	126239676	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2110G>A	p.Gly704Arg	p.G704R	ENST00000394329	1/17	33	20	12	38	38	0	FAT4,missense_variant,p.Gly704Arg,ENST00000394329,;	A	ENSG00000196159	ENST00000394329	Transcript	missense_variant	2123	2110	704	G/R	Gga/Aga	.	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	possibly_damaging(0.555)	1/17	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGCCTGGAGGT	.	4	ESCA
ARHGAP10	0	.	GRCh37	4	148887900	148887900	+	Silent	SNP	G	G	C	rs745901558	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1626G>C	p.%3D	p.L542L	ENST00000336498	18/23	56	48	7	54	54	0	ARHGAP10,synonymous_variant,p.%3D,ENST00000507661,;ARHGAP10,synonymous_variant,p.%3D,ENST00000336498,;ARHGAP10,synonymous_variant,p.%3D,ENST00000414545,;ARHGAP10,non_coding_transcript_exon_variant,,ENST00000506020,;ARHGAP10,non_coding_transcript_exon_variant,,ENST00000506054,;	C	ENSG00000071205	ENST00000336498	Transcript	synonymous_variant	1865	1626	542	L	ctG/ctC	rs745901558	.	.	1	ARHGAP10	HGNC	26099	protein_coding	YES	CCDS34075.1	ENSP00000336923	RHG10_HUMAN	Q8ND72_HUMAN,Q3KQX3_HUMAN	UPI000013EA63	.	.	.	18/23	.	PROSITE_profiles:PS50238,hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF5,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCTGATGAG	.	4	ESCA
NR3C2	0	.	GRCh37	4	148999989	148999989	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2506A>G	.	.	ENST00000358102	9/9	51	32	19	35	35	0	NR3C2,3_prime_UTR_variant,,ENST00000358102,;NR3C2,3_prime_UTR_variant,,ENST00000344721,;NR3C2,3_prime_UTR_variant,,ENST00000355292,;NR3C2,downstream_gene_variant,,ENST00000512865,;NR3C2,downstream_gene_variant,,ENST00000511528,;NR3C2,downstream_gene_variant,,ENST00000342437,;	C	ENSG00000151623	ENST00000358102	Transcript	3_prime_UTR_variant	5824	.	.	.	.	.	.	.	-1	NR3C2	HGNC	7979	protein_coding	YES	CCDS3772.1	ENSP00000350815	.	Q4W5E8_HUMAN,B0ZBF6_HUMAN	UPI000013DC6D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGATATAAA	.	5	ESCA
GUCY1A3	0	.	GRCh37	4	156632055	156632055	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.738G>T	p.Glu246Asp	p.E246D	ENST00000296518	6/10	40	21	18	29	29	0	GUCY1A3,missense_variant,p.Glu246Asp,ENST00000506455,;GUCY1A3,missense_variant,p.Glu246Asp,ENST00000455639,;GUCY1A3,missense_variant,p.Glu246Asp,ENST00000513574,;GUCY1A3,missense_variant,p.Glu246Asp,ENST00000296518,;GUCY1A3,missense_variant,p.Glu246Asp,ENST00000511507,;GUCY1A3,missense_variant,p.Glu246Asp,ENST00000511108,;GUCY1A3,5_prime_UTR_variant,,ENST00000393832,;GUCY1A3,downstream_gene_variant,,ENST00000515602,;GUCY1A3,3_prime_UTR_variant,,ENST00000443668,;GUCY1A3,non_coding_transcript_exon_variant,,ENST00000512983,;GUCY1A3,intron_variant,,ENST00000515201,;GUCY1A3,intron_variant,,ENST00000509901,;	T	ENSG00000164116	ENST00000296518	Transcript	missense_variant	947	738	246	E/D	gaG/gaT	.	.	.	1	GUCY1A3	HGNC	4685	protein_coding	YES	CCDS34085.1	ENSP00000296518	GCYA3_HUMAN	Q9NNW8_HUMAN,J3KPQ8_HUMAN	UPI0000033343	.	tolerated(0.39)	benign(0.002)	6/10	.	hmmpanther:PTHR11920:SF226,hmmpanther:PTHR11920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGAGTTTGT	.	5	ESCA
FSTL5	0	.	GRCh37	4	162306700	162306700	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*199C>A	.	.	ENST00000306100	16/16	10	5	5	10	10	0	FSTL5,3_prime_UTR_variant,,ENST00000379164,;FSTL5,3_prime_UTR_variant,,ENST00000306100,;FSTL5,downstream_gene_variant,,ENST00000536695,;FSTL5,downstream_gene_variant,,ENST00000427802,;RP11-234O6.2,intron_variant,,ENST00000508189,;	T	ENSG00000168843	ENST00000306100	Transcript	3_prime_UTR_variant	3180	.	.	.	.	.	.	.	-1	FSTL5	HGNC	21386	protein_coding	YES	CCDS3802.1	ENSP00000305334	FSTL5_HUMAN	Q4W5Q0_HUMAN,Q4W5K3_HUMAN,Q4W5F8_HUMAN	UPI000020B66B	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GTGCTGAGTAT	.	2	ESCA
TKTL2	0	.	GRCh37	4	164394764	164394764	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123G>A	p.%3D	p.S41S	ENST00000280605	1/1	39	20	19	37	37	0	TKTL2,synonymous_variant,p.%3D,ENST00000280605,;	T	ENSG00000151005	ENST00000280605	Transcript	synonymous_variant	284	123	41	S	tcG/tcA	COSM3335268	.	.	-1	TKTL2	HGNC	25313	protein_coding	YES	CCDS3805.1	ENSP00000280605	TKTL2_HUMAN	Q96LZ0_HUMAN,Q8ND81_HUMAN	UPI0000037C67	.	.	.	1/1	.	hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF49,Gene3D:3.40.50.970,Pfam_domain:PF00456,Superfamily_domains:SSF52518	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T40T|c.120G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCACGACGT	.	5	ESCA
CLCN3	0	.	GRCh37	4	170608906	170608906	+	Missense_Mutation	SNP	C	C	T	rs200318516	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.416C>T	p.Ser139Leu	p.S139L	ENST00000347613	4/14	131	122	9	107	107	0	CLCN3,missense_variant,p.Ser122Leu,ENST00000504131,;CLCN3,missense_variant,p.Ser139Leu,ENST00000347613,;CLCN3,missense_variant,p.Ser139Leu,ENST00000513761,;CLCN3,missense_variant,p.Ser139Leu,ENST00000511092,;CLCN3,missense_variant,p.Ser112Leu,ENST00000507875,;CLCN3,missense_variant,p.Ser139Leu,ENST00000360642,;CLCN3,incomplete_terminal_codon_variant,p.%3D,ENST00000512813,;	T	ENSG00000109572	ENST00000347613	Transcript	missense_variant	970	416	139	S/L	tCa/tTa	rs200318516,COSM3775697	.	.	1	CLCN3	HGNC	2021	protein_coding	YES	CCDS34100.1	ENSP00000261514	CLCN3_HUMAN	D6RIX3_HUMAN,D6RDZ6_HUMAN	UPI000015F952	.	deleterious(0.01)	probably_damaging(0.981)	4/14	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF63,Gene3D:1otsB00,Superfamily_domains:SSF81340	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCATCAGGTA	.	2	ESCA
LIMCH1	0	.	GRCh37	4	41648815	41648815	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1570C>G	p.Pro524Ala	p.P524A	ENST00000313860	12/27	38	34	3	33	33	0	LIMCH1,missense_variant,p.Pro524Ala,ENST00000512632,;LIMCH1,missense_variant,p.Pro512Ala,ENST00000512820,;LIMCH1,missense_variant,p.Pro909Ala,ENST00000503057,;LIMCH1,missense_variant,p.Pro524Ala,ENST00000508501,;LIMCH1,missense_variant,p.Pro524Ala,ENST00000313860,;LIMCH1,missense_variant,p.Pro353Ala,ENST00000513024,;LIMCH1,missense_variant,p.Pro370Ala,ENST00000396595,;LIMCH1,missense_variant,p.Pro365Ala,ENST00000514096,;LIMCH1,missense_variant,p.Pro358Ala,ENST00000509277,;LIMCH1,missense_variant,p.Pro359Ala,ENST00000508466,;LIMCH1,missense_variant,p.Pro365Ala,ENST00000511496,;LIMCH1,missense_variant,p.Pro358Ala,ENST00000381753,;LIMCH1,missense_variant,p.Pro524Ala,ENST00000512946,;	G	ENSG00000064042	ENST00000313860	Transcript	missense_variant	1624	1570	524	P/A	Cca/Gca	.	.	.	1	LIMCH1	HGNC	29191	protein_coding	YES	CCDS33977.1	ENSP00000316891	LIMC1_HUMAN	D6RJ93_HUMAN,D6RGH8_HUMAN,D6R8Y0_HUMAN	UPI0000D61554	.	deleterious(0)	probably_damaging(0.99)	12/27	.	hmmpanther:PTHR15551,hmmpanther:PTHR15551:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCTCCAAGC	.	4	ESCA
ANKRD17	0	.	GRCh37	4	74027042	74027042	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.571G>A	p.Asp191Asn	p.D191N	ENST00000358602	3/34	48	44	4	36	36	0	ANKRD17,missense_variant,p.Asp191Asn,ENST00000358602,;ANKRD17,missense_variant,p.Asp78Asn,ENST00000509867,;ANKRD17,missense_variant,p.Asp191Asn,ENST00000330838,;ANKRD17,missense_variant,p.Asp76Asn,ENST00000558247,;ANKRD17,intron_variant,,ENST00000561029,;ANKRD17,non_coding_transcript_exon_variant,,ENST00000559367,;ANKRD17,missense_variant,p.Asp9Asn,ENST00000560372,;	T	ENSG00000132466	ENST00000358602	Transcript	missense_variant	688	571	191	D/N	Gat/Aat	.	.	.	-1	ANKRD17	HGNC	23575	protein_coding	YES	CCDS34004.1	ENSP00000351416	ANR17_HUMAN	.	UPI00002263B0	.	.	benign(0.102)	3/34	.	hmmpanther:PTHR23206:SF1,hmmpanther:PTHR23206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCATCAGCCG	.	3	ESCA
CNOT6L	0	.	GRCh37	4	78652538	78652538	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024+3G>A	.	.	ENST00000264903	.	56	39	17	48	48	0	CNOT6L,splice_region_variant,,ENST00000505983,;CNOT6L,splice_region_variant,,ENST00000504123,;CNOT6L,splice_region_variant,,ENST00000264903,;CNOT6L,splice_region_variant,,ENST00000515506,;CNOT6L,splice_region_variant,,ENST00000512485,;CNOT6L,splice_region_variant,,ENST00000504804,;CNOT6L,splice_region_variant,,ENST00000508371,;	T	ENSG00000138767	ENST00000264903	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	CNOT6L	HGNC	18042	protein_coding	YES	CCDS47082.1	ENSP00000264903	CNO6L_HUMAN	D6RGK9_HUMAN	UPI0000E445DF	.	.	.	.	9/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACTCACCTG	.	4	ESCA
CPZ	0	.	GRCh37	4	8620227	8620227	+	Silent	SNP	C	C	G	rs760220072	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1575C>G	p.%3D	p.V525V	ENST00000360986	10/11	17	12	5	32	32	0	CPZ,synonymous_variant,p.%3D,ENST00000360986,;CPZ,synonymous_variant,p.%3D,ENST00000429646,;CPZ,synonymous_variant,p.%3D,ENST00000315782,;CPZ,synonymous_variant,p.%3D,ENST00000382480,;GPR78,3_prime_UTR_variant,,ENST00000514302,;CPZ,3_prime_UTR_variant,,ENST00000515606,;GPR78,non_coding_transcript_exon_variant,,ENST00000513120,;CPZ,non_coding_transcript_exon_variant,,ENST00000513486,;	G	ENSG00000109625	ENST00000360986	Transcript	synonymous_variant	1749	1575	525	V	gtC/gtG	rs760220072	.	.	1	CPZ	HGNC	2333	protein_coding	YES	CCDS33953.1	ENSP00000354255	CBPZ_HUMAN	.	UPI000020BCC5	.	.	.	10/11	.	Superfamily_domains:SSF49464,SMART_domains:SM00631,Pfam_domain:PF13620,Gene3D:2.60.40.1120,hmmpanther:PTHR11532:SF4,hmmpanther:PTHR11532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGTCAAAGG	.	5	ESCA
STPG2	0	.	GRCh37	4	99049692	99049692	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274C>T	p.Pro92Ser	p.P92S	ENST00000295268	3/11	46	41	5	39	39	0	STPG2,missense_variant,p.Pro92Ser,ENST00000295268,;	A	ENSG00000163116	ENST00000295268	Transcript	missense_variant	364	274	92	P/S	Cct/Tct	.	.	.	-1	STPG2	HGNC	28712	protein_coding	YES	CCDS3645.1	ENSP00000295268	STPG2_HUMAN	.	UPI00000734EC	.	deleterious(0)	possibly_damaging(0.838)	3/11	.	hmmpanther:PTHR21580,hmmpanther:PTHR21580:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGGAATTG	.	2	ESCA
NDST1	0	.	GRCh37	5	149901145	149901145	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329A>G	p.Lys110Arg	p.K110R	ENST00000261797	2/15	37	17	20	72	72	0	NDST1,missense_variant,p.Lys110Arg,ENST00000261797,;NDST1,missense_variant,p.Lys110Arg,ENST00000519157,;NDST1,missense_variant,p.Lys110Arg,ENST00000523767,;NDST1,downstream_gene_variant,,ENST00000518299,;NDST1,downstream_gene_variant,,ENST00000522491,;NDST1,downstream_gene_variant,,ENST00000518346,;NDST1,downstream_gene_variant,,ENST00000524161,;	G	ENSG00000070614	ENST00000261797	Transcript	missense_variant	831	329	110	K/R	aAa/aGa	.	.	.	1	NDST1	HGNC	7680	protein_coding	YES	CCDS34277.1	ENSP00000261797	NDST1_HUMAN	E5RGN9_HUMAN,E5RG58_HUMAN,E5RG24_HUMAN	UPI000012CDA5	.	tolerated(0.76)	benign(0.006)	2/15	.	hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF30,Pfam_domain:PF12062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCAAATACC	.	5	ESCA
CPEB4	0	.	GRCh37	5	173383260	173383260	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120A>G	.	.	ENST00000265085	10/10	46	24	22	47	47	0	CPEB4,3_prime_UTR_variant,,ENST00000522336,;CPEB4,3_prime_UTR_variant,,ENST00000334035,;CPEB4,3_prime_UTR_variant,,ENST00000517880,;CPEB4,3_prime_UTR_variant,,ENST00000265085,;CPEB4,downstream_gene_variant,,ENST00000519835,;CPEB4,downstream_gene_variant,,ENST00000520867,;CPEB4,non_coding_transcript_exon_variant,,ENST00000519467,;	G	ENSG00000113742	ENST00000265085	Transcript	3_prime_UTR_variant	3764	.	.	.	.	.	.	.	1	CPEB4	HGNC	21747	protein_coding	YES	CCDS4390.1	ENSP00000265085	CPEB4_HUMAN	.	UPI000020C179	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTATAGTA	.	5	ESCA
SLC34A1	0	.	GRCh37	5	176812703	176812703	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-40G>A	.	.	ENST00000324417	2/13	21	12	9	31	31	0	SLC34A1,5_prime_UTR_variant,,ENST00000504577,;SLC34A1,5_prime_UTR_variant,,ENST00000512593,;SLC34A1,5_prime_UTR_variant,,ENST00000324417,;SLC34A1,upstream_gene_variant,,ENST00000513614,;SLC34A1,non_coding_transcript_exon_variant,,ENST00000507685,;	A	ENSG00000131183	ENST00000324417	Transcript	5_prime_UTR_variant	52	.	.	.	.	.	.	.	1	SLC34A1	HGNC	11019	protein_coding	YES	CCDS4418.1	ENSP00000321424	NPT2A_HUMAN	Q05BP0_HUMAN,D6RCE5_HUMAN	UPI0000130408	.	.	.	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCTGAGACC	.	5	ESCA
CDH10	0	.	GRCh37	5	24488069	24488069	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2070T>C	p.%3D	p.I690I	ENST00000264463	12/12	27	11	15	28	28	0	CDH10,synonymous_variant,p.%3D,ENST00000264463,;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,;	G	ENSG00000040731	ENST00000264463	Transcript	synonymous_variant	2578	2070	690	I	atT/atC	.	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	.	.	12/12	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Pfam_domain:PF01049	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATAATATC	.	5	ESCA
TARS	0	.	GRCh37	5	33457431	33457431	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1006C>A	p.Pro336Thr	p.P336T	ENST00000455217	10/20	30	13	17	55	55	0	TARS,missense_variant,p.Pro303Thr,ENST00000502553,;TARS,missense_variant,p.Pro303Thr,ENST00000265112,;TARS,missense_variant,p.Pro199Thr,ENST00000541634,;TARS,missense_variant,p.Pro336Thr,ENST00000455217,;TARS,missense_variant,p.Pro182Thr,ENST00000414361,;TARS,downstream_gene_variant,,ENST00000514259,;TARS,upstream_gene_variant,,ENST00000509410,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,3_prime_UTR_variant,,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,non_coding_transcript_exon_variant,,ENST00000504698,;TARS,downstream_gene_variant,,ENST00000513066,;TARS,downstream_gene_variant,,ENST00000505012,;	A	ENSG00000113407	ENST00000455217	Transcript	missense_variant	1128	1006	336	P/T	Cca/Aca	.	.	.	1	TARS	HGNC	11572	protein_coding	YES	CCDS58943.1	ENSP00000387710	SYTC_HUMAN	D6RBR8_HUMAN	UPI00017A6D60	.	deleterious(0)	probably_damaging(0.959)	10/20	.	Superfamily_domains:SSF55186,Gene3D:1tkeA02,TIGRFAM_domain:TIGR00418,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF23,HAMAP:MF_00184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTCCCAGAT	.	5	ESCA
GRIK2	0	.	GRCh37	6	102376504	102376504	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2082C>G	p.Phe694Leu	p.F694L	ENST00000421544	13/16	26	22	4	24	24	0	GRIK2,missense_variant,p.Phe694Leu,ENST00000369138,;GRIK2,missense_variant,p.Phe694Leu,ENST00000413795,;GRIK2,missense_variant,p.Phe694Leu,ENST00000318991,;GRIK2,missense_variant,p.Phe694Leu,ENST00000421544,;GRIK2,missense_variant,p.Phe645Leu,ENST00000369134,;GRIK2,missense_variant,p.Phe618Leu,ENST00000369137,;GRIK2,non_coding_transcript_exon_variant,,ENST00000487161,;GRIK2,non_coding_transcript_exon_variant,,ENST00000487395,;	G	ENSG00000164418	ENST00000421544	Transcript	missense_variant	2572	2082	694	F/L	ttC/ttG	.	.	.	1	GRIK2	HGNC	4580	protein_coding	YES	CCDS5048.1	ENSP00000397026	GRIK2_HUMAN	Q9BZ15_HUMAN,Q6P3V6_HUMAN,H7C2P5_HUMAN,F8WEZ8_HUMAN,D7RWZ8_HUMAN	UPI000012B617	.	deleterious(0)	probably_damaging(0.999)	13/16	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,Pfam_domain:PF00060,Gene3D:1.10.287.70,SMART_domains:SM00079,Superfamily_domains:SSF53850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTTCAAGGT	.	4	ESCA
GJA1	0	.	GRCh37	6	121768356	121768356	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363C>T	p.%3D	p.V121V	ENST00000282561	2/2	70	46	23	59	59	0	GJA1,synonymous_variant,p.%3D,ENST00000282561,;	T	ENSG00000152661	ENST00000282561	Transcript	synonymous_variant	520	363	121	V	gtC/gtT	.	.	.	1	GJA1	HGNC	4274	protein_coding	YES	CCDS5123.1	ENSP00000282561	CXA1_HUMAN	B4DN50_HUMAN,B4DMC9_HUMAN,B4DI81_HUMAN	UPI000013DCEC	.	.	.	2/2	.	hmmpanther:PTHR11984:SF33,hmmpanther:PTHR11984,Gene3D:2zw3A00	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGTCAATGT	.	5	ESCA
KIAA1244	0	.	GRCh37	6	138607140	138607140	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2519C>G	p.Thr840Arg	p.T840R	ENST00000251691	15/34	53	37	16	41	41	0	KIAA1244,missense_variant,p.Thr840Arg,ENST00000251691,;	G	ENSG00000112379	ENST00000251691	Transcript	missense_variant	2685	2519	840	T/R	aCa/aGa	.	.	.	1	KIAA1244	HGNC	21213	protein_coding	YES	CCDS5189.2	ENSP00000251691	BIG3_HUMAN	C5NM88_HUMAN,B5MDV5_HUMAN	UPI000150AF4A	.	tolerated(0.58)	benign(0.031)	15/34	.	hmmpanther:PTHR10663:SF13,hmmpanther:PTHR10663	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTACAGAGT	.	5	ESCA
REPS1	0	.	GRCh37	6	139238693	139238693	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597A>G	p.Arg533Gly	p.R533G	ENST00000258062	13/20	63	37	26	52	52	0	REPS1,missense_variant,p.Arg492Gly,ENST00000529597,;REPS1,missense_variant,p.Arg533Gly,ENST00000258062,;REPS1,missense_variant,p.Arg534Gly,ENST00000450536,;REPS1,missense_variant,p.Arg507Gly,ENST00000415951,;REPS1,missense_variant,p.Arg507Gly,ENST00000367663,;REPS1,intron_variant,,ENST00000530255,;REPS1,intron_variant,,ENST00000409812,;REPS1,upstream_gene_variant,,ENST00000478483,;REPS1,splice_region_variant,,ENST00000483468,;REPS1,splice_region_variant,,ENST00000445570,;REPS1,downstream_gene_variant,,ENST00000431346,;REPS1,upstream_gene_variant,,ENST00000530370,;REPS1,downstream_gene_variant,,ENST00000414243,;REPS1,upstream_gene_variant,,ENST00000492787,;REPS1,upstream_gene_variant,,ENST00000529423,;REPS1,upstream_gene_variant,,ENST00000484164,;	C	ENSG00000135597	ENST00000258062	Transcript	missense_variant	2176	1597	533	R/G	Agg/Ggg	.	.	.	-1	REPS1	HGNC	15578	protein_coding	YES	CCDS5193.2	ENSP00000258062	REPS1_HUMAN	.	UPI000020E30A	.	deleterious(0.01)	probably_damaging(0.999)	13/20	.	hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACCTTTGAC	.	5	ESCA
ZC3H12D	0	.	GRCh37	6	149795653	149795653	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27C>T	p.%3D	p.F9F	ENST00000409806	2/6	25	21	4	31	31	0	ZC3H12D,synonymous_variant,p.%3D,ENST00000416573,;ZC3H12D,synonymous_variant,p.%3D,ENST00000542614,;ZC3H12D,synonymous_variant,p.%3D,ENST00000409806,;ZC3H12D,synonymous_variant,p.%3D,ENST00000409948,;ZC3H12D,synonymous_variant,p.%3D,ENST00000389942,;ZC3H12D,non_coding_transcript_exon_variant,,ENST00000462655,;	A	ENSG00000178199	ENST00000409806	Transcript	synonymous_variant	346	27	9	F	ttC/ttT	.	.	.	-1	ZC3H12D	HGNC	21175	protein_coding	YES	.	ENSP00000386616	ZC12D_HUMAN	.	UPI00002377F7	.	.	.	2/6	.	hmmpanther:PTHR12876:SF11,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TGGAAGAATTC	.	2	ESCA
NOX3	0	.	GRCh37	6	155764431	155764431	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462C>T	p.%3D	p.L154L	ENST00000159060	5/14	34	31	3	41	41	0	NOX3,synonymous_variant,p.%3D,ENST00000159060,;	A	ENSG00000074771	ENST00000159060	Transcript	synonymous_variant	565	462	154	L	ctC/ctT	.	.	.	-1	NOX3	HGNC	7890	protein_coding	YES	CCDS5250.1	ENSP00000159060	NOX3_HUMAN	.	UPI000006EC80	.	.	.	5/14	.	hmmpanther:PTHR11972:SF12,hmmpanther:PTHR11972,Pfam_domain:PF01794	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTTGAGGTA	.	2	ESCA
DACT2	0	.	GRCh37	6	168708169	168708169	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2268G>A	p.%3D	p.L756L	ENST00000366795	4/4	30	27	3	47	47	0	DACT2,synonymous_variant,p.%3D,ENST00000366795,;DACT2,synonymous_variant,p.%3D,ENST00000610183,;DACT2,synonymous_variant,p.%3D,ENST00000607983,;DACT2,intron_variant,,ENST00000366796,;	T	ENSG00000164488	ENST00000366795	Transcript	synonymous_variant	2357	2268	756	L	ctG/ctA	.	.	.	-1	DACT2	HGNC	21231	protein_coding	YES	CCDS47519.1	ENSP00000355760	DACT2_HUMAN	.	UPI00001D8145	.	.	.	4/4	.	hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF13,Pfam_domain:PF15268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTTCAGGGC	.	2	ESCA
DCDC2	0	.	GRCh37	6	24178761	24178761	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1123G>A	p.Glu375Lys	p.E375K	ENST00000378454	9/10	65	42	22	57	57	0	DCDC2,missense_variant,p.Glu128Lys,ENST00000378450,;DCDC2,missense_variant,p.Glu375Lys,ENST00000378454,;	T	ENSG00000146038	ENST00000378454	Transcript	missense_variant	1425	1123	375	E/K	Gag/Aag	.	.	.	-1	DCDC2	HGNC	18141	protein_coding	YES	CCDS4550.1	ENSP00000367715	DCDC2_HUMAN	.	UPI000013DA24	.	tolerated(0.1)	benign(0.05)	9/10	.	hmmpanther:PTHR23004:SF5,hmmpanther:PTHR23004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTTCAA	.	5	ESCA
HIST1H3C	0	.	GRCh37	6	26045930	26045930	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292G>A	p.Glu98Lys	p.E98K	ENST00000540144	1/1	81	77	4	105	105	0	HIST1H3C,missense_variant,p.Glu98Lys,ENST00000540144,;HIST1H2BB,upstream_gene_variant,,ENST00000357905,;U91328.2,downstream_gene_variant,,ENST00000454320,;	A	ENSG00000196532	ENST00000540144	Transcript	missense_variant	292	292	98	E/K	Gag/Aag	COSM3941674,COSM1311859	.	.	1	HIST1H3C	HGNC	4768	protein_coding	YES	CCDS4576.1	ENSP00000439493	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0.02)	probably_damaging(1)	1/1	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGTGAGGCC	.	2	ESCA
OR14J1	0	.	GRCh37	6	29274876	29274876	+	Missense_Mutation	SNP	G	G	A	rs753138884	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.410G>A	p.Arg137His	p.R137H	ENST00000377160	1/1	74	46	28	48	48	0	OR14J1,missense_variant,p.Arg137His,ENST00000377160,;	A	ENSG00000204695	ENST00000377160	Transcript	missense_variant	474	410	137	R/H	cGt/cAt	rs753138884	.	.	1	OR14J1	HGNC	13971	protein_coding	YES	CCDS34362.1	ENSP00000366365	O14J1_HUMAN	.	UPI0000041CEC	.	tolerated(0.05)	benign(0.013)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF42,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCGTGCCT	byFrequency	5	ESCA
RPP21	0	.	GRCh37	6	30312963	30312963	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15G>A	p.%3D	p.V5V	ENST00000433076	1/5	38	27	11	60	60	0	RPP21,synonymous_variant,p.%3D,ENST00000436442,;RPP21,synonymous_variant,p.%3D,ENST00000433076,;RPP21,synonymous_variant,p.%3D,ENST00000442966,;RPP21,synonymous_variant,p.%3D,ENST00000428040,;TRIM39-RPP21,intron_variant,,ENST00000513556,;TRIM39,downstream_gene_variant,,ENST00000420746,;TRIM39,downstream_gene_variant,,ENST00000396547,;TRIM39,downstream_gene_variant,,ENST00000376656,;TRIM39,downstream_gene_variant,,ENST00000376659,;TRIM39,downstream_gene_variant,,ENST00000540416,;TRIM39,downstream_gene_variant,,ENST00000396551,;TRIM39,downstream_gene_variant,,ENST00000396548,;RPP21,non_coding_transcript_exon_variant,,ENST00000489124,;RPP21,non_coding_transcript_exon_variant,,ENST00000466327,;RPP21,non_coding_transcript_exon_variant,,ENST00000491477,;RPP21,non_coding_transcript_exon_variant,,ENST00000473266,;RPP21,non_coding_transcript_exon_variant,,ENST00000498414,;	A	ENSG00000241370	ENST00000433076	Transcript	synonymous_variant	56	15	5	V	gtG/gtA	.	.	.	1	RPP21	HGNC	21300	protein_coding	YES	CCDS56409.1	ENSP00000409799	RPP21_HUMAN	.	UPI0000470276	.	.	.	1/5	.	hmmpanther:PTHR14742:SF0,hmmpanther:PTHR14742	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGTGAAGGA	.	5	ESCA
CPNE5	0	.	GRCh37	6	36730753	36730753	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.796G>T	p.Glu266Ter	p.E266*	ENST00000244751	12/21	24	10	13	41	41	0	CPNE5,stop_gained,p.Glu266Ter,ENST00000244751,;	A	ENSG00000124772	ENST00000244751	Transcript	stop_gained	1421	796	266	E/*	Gag/Tag	.	.	.	-1	CPNE5	HGNC	2318	protein_coding	YES	CCDS4825.1	ENSP00000244751	CPNE5_HUMAN	Q7Z6C8_HUMAN,Q658T3_HUMAN	UPI0000127C15	.	.	.	12/21	.	Superfamily_domains:SSF49562,SMART_domains:SM00239,Pfam_domain:PF00168,Gene3D:2.60.40.150,hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF8,PROSITE_profiles:PS50004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACTCCCCAA	.	5	ESCA
GTPBP2	0	.	GRCh37	6	43588627	43588627	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*724A>G	.	.	ENST00000307126	12/12	26	17	9	29	29	0	GTPBP2,3_prime_UTR_variant,,ENST00000307126,;GTPBP2,3_prime_UTR_variant,,ENST00000419497,;GTPBP2,3_prime_UTR_variant,,ENST00000432918,;GTPBP2,downstream_gene_variant,,ENST00000307114,;POLH,downstream_gene_variant,,ENST00000535400,;GTPBP2,downstream_gene_variant,,ENST00000452781,;GTPBP2,downstream_gene_variant,,ENST00000442748,;GTPBP2,non_coding_transcript_exon_variant,,ENST00000476510,;GTPBP2,downstream_gene_variant,,ENST00000480263,;GTPBP2,downstream_gene_variant,,ENST00000459959,;GTPBP2,intron_variant,,ENST00000496137,;	C	ENSG00000172432	ENST00000307126	Transcript	3_prime_UTR_variant	2533	.	.	.	.	.	.	.	-1	GTPBP2	HGNC	4670	protein_coding	YES	CCDS4903.1	ENSP00000303997	GTPB2_HUMAN	.	UPI0000070C45	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCTTTGGT	.	5	ESCA
FUT9	0	.	GRCh37	6	96660202	96660202	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8091C>T	.	.	ENST00000302103	3/3	43	26	17	32	31	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	T	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	9497	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGACTGTAA	.	5	ESCA
C7orf33	0	.	GRCh37	7	148312549	148312549	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*56C>G	.	.	ENST00000307003	3/3	51	46	5	30	30	0	C7orf33,3_prime_UTR_variant,,ENST00000307003,;	G	ENSG00000170279	ENST00000307003	Transcript	3_prime_UTR_variant	951	.	.	.	.	.	.	.	1	C7orf33	HGNC	21724	protein_coding	YES	CCDS5890.1	ENSP00000304071	CG033_HUMAN	.	UPI00000707BF	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCTCTTCTT	.	2	ESCA
KMT2C	0	.	GRCh37	7	151833719	151833719	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*198G>A	.	.	ENST00000262189	59/59	48	40	8	25	25	0	KMT2C,3_prime_UTR_variant,,ENST00000355193,;KMT2C,3_prime_UTR_variant,,ENST00000424877,;KMT2C,3_prime_UTR_variant,,ENST00000485655,;KMT2C,3_prime_UTR_variant,,ENST00000360104,;KMT2C,3_prime_UTR_variant,,ENST00000262189,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;	T	ENSG00000055609	ENST00000262189	Transcript	3_prime_UTR_variant	15153	.	.	.	.	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	.	59/59	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCAGGAA	.	5	ESCA
KMT2C	0	.	GRCh37	7	151846214	151846214	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12798A>G	p.%3D	p.Q4266Q	ENST00000262189	52/59	65	29	36	45	45	0	KMT2C,synonymous_variant,p.%3D,ENST00000355193,;KMT2C,synonymous_variant,p.%3D,ENST00000424877,;KMT2C,synonymous_variant,p.%3D,ENST00000360104,;KMT2C,synonymous_variant,p.%3D,ENST00000262189,;KMT2C,downstream_gene_variant,,ENST00000418061,;KMT2C,downstream_gene_variant,,ENST00000485241,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;	C	ENSG00000055609	ENST00000262189	Transcript	synonymous_variant	13017	12798	4266	Q	caA/caG	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	.	52/59	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGATTGTGG	.	5	ESCA
BZW2	0	.	GRCh37	7	16685805	16685805	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-132C>T	.	.	ENST00000433922	1/12	84	38	46	117	117	0	BZW2,5_prime_UTR_variant,,ENST00000433922,;BZW2,5_prime_UTR_variant,,ENST00000415365,;BZW2,5_prime_UTR_variant,,ENST00000258761,;ANKMY2,upstream_gene_variant,,ENST00000306999,;BZW2,upstream_gene_variant,,ENST00000405202,;BZW2,upstream_gene_variant,,ENST00000452975,;BZW2,non_coding_transcript_exon_variant,,ENST00000432311,;ANKMY2,upstream_gene_variant,,ENST00000421746,;BZW2,5_prime_UTR_variant,,ENST00000437745,;BZW2,5_prime_UTR_variant,,ENST00000436868,;ANKMY2,upstream_gene_variant,,ENST00000453623,;ANKMY2,upstream_gene_variant,,ENST00000447802,;	T	ENSG00000136261	ENST00000433922	Transcript	5_prime_UTR_variant	47	.	.	.	.	.	.	.	1	BZW2	HGNC	18808	protein_coding	YES	CCDS5362.1	ENSP00000397249	BZW2_HUMAN	Q75MG1_HUMAN,E7ETZ4_HUMAN,E7EMS9_HUMAN,C9JF98_HUMAN,B5MCH7_HUMAN,B5MCE7_HUMAN	UPI000003B445	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCACTCC	.	5	ESCA
SRRM3	0	.	GRCh37	7	75916517	75916517	+	3'UTR	SNP	G	G	A	rs555014493	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1524G>A	.	.	ENST00000326382	15/15	35	29	5	37	37	0	SRRM3,3_prime_UTR_variant,,ENST00000326382,;SRRM3,3_prime_UTR_variant,,ENST00000413003,;SRRM3,3_prime_UTR_variant,,ENST00000388802,;RN7SL212P,upstream_gene_variant,,ENST00000583729,;	A	ENSG00000177679	ENST00000326382	Transcript	3_prime_UTR_variant	3525	.	.	.	.	rs555014493	.	.	1	SRRM3	HGNC	26729	protein_coding	YES	.	ENSP00000325298	SRRM3_HUMAN	.	UPI0000E5ADAA	.	.	.	15/15	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGTCCGGGTTC	by1000G	4	ESCA
RP1L1	0	.	GRCh37	8	10466069	10466069	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5539G>C	p.Glu1847Gln	p.E1847Q	ENST00000382483	4/4	61	44	17	85	85	0	RP1L1,missense_variant,p.Glu1847Gln,ENST00000382483,;	G	ENSG00000183638	ENST00000382483	Transcript	missense_variant	5763	5539	1847	E/Q	Gag/Cag	.	.	.	-1	RP1L1	HGNC	15946	protein_coding	YES	CCDS43708.1	ENSP00000371923	.	A6NKC6_HUMAN	UPI00001AF9CC	.	.	unknown(0)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23005:SF3,hmmpanther:PTHR23005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTCTGGCT	.	5	ESCA
RP1L1	0	.	GRCh37	8	10466966	10466966	+	Missense_Mutation	SNP	G	G	T	rs574264133	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4642C>A	p.Gln1548Lys	p.Q1548K	ENST00000382483	4/4	51	39	12	45	45	0	RP1L1,missense_variant,p.Gln1548Lys,ENST00000382483,;	T	ENSG00000183638	ENST00000382483	Transcript	missense_variant	4866	4642	1548	Q/K	Cag/Aag	rs574264133	.	.	-1	RP1L1	HGNC	15946	protein_coding	YES	CCDS43708.1	ENSP00000371923	.	A6NKC6_HUMAN	UPI00001AF9CC	.	.	unknown(0)	4/4	.	hmmpanther:PTHR23005:SF3,hmmpanther:PTHR23005	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTGCAGGC	by1000G	5	ESCA
RNF139	0	.	GRCh37	8	125498688	125498688	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.798C>T	p.%3D	p.F266F	ENST00000303545	2/2	22	13	8	18	18	0	RNF139,synonymous_variant,p.%3D,ENST00000303545,;RNF139,downstream_gene_variant,,ENST00000517684,;TATDN1,downstream_gene_variant,,ENST00000522810,;TATDN1,downstream_gene_variant,,ENST00000519548,;TATDN1,downstream_gene_variant,,ENST00000276692,;RP11-158K1.3,upstream_gene_variant,,ENST00000518639,;TATDN1,downstream_gene_variant,,ENST00000523214,;TATDN1,downstream_gene_variant,,ENST00000522927,;TATDN1,downstream_gene_variant,,ENST00000523631,;	T	ENSG00000170881	ENST00000303545	Transcript	synonymous_variant	1170	798	266	F	ttC/ttT	COSM604219	.	.	1	RNF139	HGNC	17023	protein_coding	YES	CCDS6350.1	ENSP00000304051	RN139_HUMAN	E5RH85_HUMAN	UPI0000071331	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12477:SF75,hmmpanther:PTHR12477,Pfam_domain:PF13705	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCTTTAT	.	5	ESCA
KIAA0196	0	.	GRCh37	8	126062872	126062872	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2133G>C	p.Arg711Ser	p.R711S	ENST00000318410	18/29	32	28	4	31	31	0	KIAA0196,missense_variant,p.Arg563Ser,ENST00000517845,;KIAA0196,missense_variant,p.Arg711Ser,ENST00000318410,;KIAA0196,upstream_gene_variant,,ENST00000530856,;	G	ENSG00000164961	ENST00000318410	Transcript	missense_variant	2483	2133	711	R/S	agG/agC	.	.	.	-1	KIAA0196	HGNC	28984	protein_coding	YES	CCDS6355.1	ENSP00000318016	STRUM_HUMAN	Q53EL1_HUMAN,E7EQI7_HUMAN,E5RFU6_HUMAN	UPI000013943B	.	deleterious(0)	probably_damaging(1)	18/29	.	hmmpanther:PTHR15691,Pfam_domain:PF10266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTTCCTTAT	.	4	ESCA
PROSC	0	.	GRCh37	8	37620177	37620177	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1G>A	.	.	ENST00000328195	1/8	22	19	3	27	27	0	PROSC,5_prime_UTR_variant,,ENST00000523187,;PROSC,5_prime_UTR_variant,,ENST00000523358,;PROSC,5_prime_UTR_variant,,ENST00000328195,;ERLIN2,downstream_gene_variant,,ENST00000276461,;PROSC,upstream_gene_variant,,ENST00000523521,;PROSC,5_prime_UTR_variant,,ENST00000518036,;PROSC,non_coding_transcript_exon_variant,,ENST00000523994,;PROSC,non_coding_transcript_exon_variant,,ENST00000520073,;	A	ENSG00000147471	ENST00000328195	Transcript	5_prime_UTR_variant	67	.	.	.	.	.	.	.	1	PROSC	HGNC	9457	protein_coding	YES	CCDS6096.1	ENSP00000333551	PROSC_HUMAN	E5RG77_HUMAN,E5RFX7_HUMAN,D3DSW3_HUMAN	UPI0000131F89	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CGGGGGATGTG	.	2	ESCA
SNTG1	0	.	GRCh37	8	51569521	51569521	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.902G>T	p.Arg301Ile	p.R301I	ENST00000522124	14/19	26	18	8	33	33	0	SNTG1,missense_variant,p.Arg301Ile,ENST00000517473,;SNTG1,missense_variant,p.Arg301Ile,ENST00000518864,;SNTG1,missense_variant,p.Arg301Ile,ENST00000276467,;SNTG1,missense_variant,p.Arg301Ile,ENST00000522124,;SNTG1,missense_variant,p.Arg301Ile,ENST00000520825,;SNTG1,missense_variant,p.Arg75Ile,ENST00000524004,;	T	ENSG00000147481	ENST00000522124	Transcript	missense_variant	1563	902	301	R/I	aGa/aTa	.	.	.	1	SNTG1	HGNC	13740	protein_coding	YES	CCDS6147.1	ENSP00000429842	SNTG1_HUMAN	E5RIN0_HUMAN	UPI000004A0DD	.	deleterious(0)	benign(0.187)	14/19	.	PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACAGAGTGT	.	5	ESCA
PDP1	0	.	GRCh37	8	94937606	94937606	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1705G>A	.	.	ENST00000396200	3/3	25	17	8	16	16	0	PDP1,3_prime_UTR_variant,,ENST00000396200,;PDP1,3_prime_UTR_variant,,ENST00000297598,;PDP1,downstream_gene_variant,,ENST00000517764,;PDP1,downstream_gene_variant,,ENST00000521144,;PDP1,downstream_gene_variant,,ENST00000520614,;PDP1,downstream_gene_variant,,ENST00000520728,;PDP1,downstream_gene_variant,,ENST00000518827,;PDP1,downstream_gene_variant,,ENST00000518107,;PDP1,downstream_gene_variant,,ENST00000518573,;PDP1,downstream_gene_variant,,ENST00000523021,;	A	ENSG00000164951	ENST00000396200	Transcript	3_prime_UTR_variant	3670	.	.	.	.	.	.	.	1	PDP1	HGNC	9279	protein_coding	YES	CCDS55262.1	ENSP00000379503	PDP1_HUMAN	Q6P1N1_HUMAN,E5RIV4_HUMAN,E5RIE5_HUMAN,E5RI96_HUMAN,E5RHB9_HUMAN,E5RFL8_HUMAN,B4DYX8_HUMAN,B3KPZ7_HUMAN	UPI0000D4BFBD	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGGGAAAGG	.	5	ESCA
PALM2	0	.	GRCh37	9	112705193	112705193	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724C>A	p.Gln242Lys	p.Q242K	ENST00000314527	7/7	21	14	7	21	21	0	PALM2,missense_variant,p.Gln244Lys,ENST00000448454,;PALM2-AKAP2,missense_variant,p.Gln242Lys,ENST00000413420,;PALM2,missense_variant,p.Gln210Lys,ENST00000374531,;PALM2,missense_variant,p.Gln242Lys,ENST00000314527,;PALM2,missense_variant,p.Gln208Lys,ENST00000483909,;PALM2-AKAP2,intron_variant,,ENST00000374530,;PALM2-AKAP2,intron_variant,,ENST00000302798,;AKAP2,intron_variant,,ENST00000510514,;AKAP2,intron_variant,,ENST00000555236,;PALM2,downstream_gene_variant,,ENST00000497711,;	A	ENSG00000243444	ENST00000314527	Transcript	missense_variant	774	724	242	Q/K	Caa/Aaa	.	.	.	1	PALM2	HGNC	15845	protein_coding	YES	CCDS48002.2	ENSP00000323805	PALM2_HUMAN	.	UPI0000071924	.	deleterious(0.03)	possibly_damaging(0.625)	7/7	.	hmmpanther:PTHR10498:SF4,hmmpanther:PTHR10498,Pfam_domain:PF03285	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGACAATCA	.	5	ESCA
TRAF1	0	.	GRCh37	9	123688378	123688378	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25C>T	.	.	ENST00000373887	2/8	31	22	9	52	52	0	TRAF1,5_prime_UTR_variant,,ENST00000540010,;TRAF1,5_prime_UTR_variant,,ENST00000373887,;	A	ENSG00000056558	ENST00000373887	Transcript	5_prime_UTR_variant	2422	.	.	.	.	.	.	.	-1	TRAF1	HGNC	12031	protein_coding	YES	CCDS6825.1	ENSP00000362994	TRAF1_HUMAN	.	UPI0000001079	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAGGGCCTG	.	5	ESCA
LURAP1L	0	.	GRCh37	9	12775744	12775744	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.30A>T	p.Arg10Ser	p.R10S	ENST00000319264	1/2	50	20	29	76	76	0	LURAP1L,missense_variant,p.Arg10Ser,ENST00000319264,;RP11-3L8.3,intron_variant,,ENST00000417638,;LURAP1L,non_coding_transcript_exon_variant,,ENST00000489107,;	T	ENSG00000153714	ENST00000319264	Transcript	missense_variant	725	30	10	R/S	agA/agT	COSM1105126	.	.	1	LURAP1L	HGNC	31452	protein_coding	YES	CCDS6473.1	ENSP00000321026	LUR1L_HUMAN	.	UPI0000140566	.	deleterious(0)	benign(0.306)	1/2	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGAGACAT	.	5	ESCA
SH2D3C	0	.	GRCh37	9	130506980	130506980	+	Missense_Mutation	SNP	G	G	A	rs375337324	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1663C>T	p.Pro555Ser	p.P555S	ENST00000314830	7/12	38	23	15	41	41	0	SH2D3C,missense_variant,p.Pro397Ser,ENST00000420366,;SH2D3C,missense_variant,p.Pro398Ser,ENST00000373277,;SH2D3C,missense_variant,p.Pro201Ser,ENST00000429553,;SH2D3C,missense_variant,p.Pro555Ser,ENST00000314830,;SH2D3C,missense_variant,p.Pro395Ser,ENST00000373274,;SH2D3C,missense_variant,p.Pro487Ser,ENST00000373276,;SH2D3C,downstream_gene_variant,,ENST00000440630,;SH2D3C,downstream_gene_variant,,ENST00000414380,;SH2D3C,non_coding_transcript_exon_variant,,ENST00000484160,;SH2D3C,non_coding_transcript_exon_variant,,ENST00000468969,;SH2D3C,non_coding_transcript_exon_variant,,ENST00000471939,;SH2D3C,downstream_gene_variant,,ENST00000488685,;SH2D3C,downstream_gene_variant,,ENST00000464239,;	A	ENSG00000095370	ENST00000314830	Transcript	missense_variant	1777	1663	555	P/S	Ccg/Tcg	rs375337324	.	.	-1	SH2D3C	HGNC	16884	protein_coding	YES	CCDS6877.1	ENSP00000317817	SH2D3_HUMAN	B3KUE2_HUMAN	UPI000006EC87	.	deleterious(0)	possibly_damaging(0.81)	7/12	.	hmmpanther:PTHR14247:SF6,hmmpanther:PTHR14247	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCGGGTTGA	byCluster	5	ESCA
SET	0	.	GRCh37	9	131458086	131458086	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1143T>A	.	.	ENST00000372692	8/8	22	13	9	29	29	0	SET,3_prime_UTR_variant,,ENST00000322030,;SET,3_prime_UTR_variant,,ENST00000372692,;SET,downstream_gene_variant,,ENST00000409104,;SET,downstream_gene_variant,,ENST00000372688,;SET,downstream_gene_variant,,ENST00000372686,;SET,downstream_gene_variant,,ENST00000466009,;SET,downstream_gene_variant,,ENST00000477806,;SET,downstream_gene_variant,,ENST00000480217,;SET,downstream_gene_variant,,ENST00000485056,;SET,downstream_gene_variant,,ENST00000480536,;	A	ENSG00000119335	ENST00000372692	Transcript	3_prime_UTR_variant	2257	.	.	.	.	.	.	.	1	SET	HGNC	10760	protein_coding	YES	CCDS48037.1	ENSP00000361777	SET_HUMAN	Q5VXV3_HUMAN,B2REB7_HUMAN	UPI000006D7FF	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTACATTGTGC	.	2	ESCA
PRSS3	0	.	GRCh37	9	33797844	33797844	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389T>A	p.Leu130Gln	p.L130Q	ENST00000361005	3/5	42	36	6	84	84	0	PRSS3,missense_variant,p.Leu73Gln,ENST00000379405,;PRSS3,missense_variant,p.Leu87Gln,ENST00000342836,;PRSS3,missense_variant,p.Leu130Gln,ENST00000361005,;PRSS3,missense_variant,p.Leu66Gln,ENST00000429677,;PRSS3,missense_variant,p.Leu85Gln,ENST00000457896,;RP11-133O22.6,intron_variant,,ENST00000454429,;PRSS3,non_coding_transcript_exon_variant,,ENST00000477653,;PRSS3,non_coding_transcript_exon_variant,,ENST00000468152,;PRSS3,upstream_gene_variant,,ENST00000495682,;	A	ENSG00000010438	ENST00000361005	Transcript	missense_variant	389	389	130	L/Q	cTg/cAg	.	.	.	1	PRSS3	HGNC	9486	protein_coding	YES	CCDS47958.1	ENSP00000354280	TRY3_HUMAN	.	UPI000013C519	.	deleterious(0)	probably_damaging(0.999)	3/5	.	Superfamily_domains:SSF50494,SMART_domains:SM00020,Gene3D:2.40.10.10,Pfam_domain:PF00089,hmmpanther:PTHR24264:SF15,hmmpanther:PTHR24264,PROSITE_profiles:PS50240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGACTGGGAG	.	5	ESCA
AMOT	0	.	GRCh37	X	112065833	112065833	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.522G>C	p.Leu174Phe	p.L174F	ENST00000371959	1/11	22	18	4	17	17	0	AMOT,missense_variant,p.Leu174Phe,ENST00000371959,;AMOT,missense_variant,p.Leu174Phe,ENST00000524145,;AMOT,intron_variant,,ENST00000304758,;AMOT,upstream_gene_variant,,ENST00000371962,;AMOT,upstream_gene_variant,,ENST00000371958,;AMOT,downstream_gene_variant,,ENST00000462114,;	G	ENSG00000126016	ENST00000371959	Transcript	missense_variant	522	522	174	L/F	ttG/ttC	.	.	.	-1	AMOT	HGNC	17810	protein_coding	YES	CCDS48154.1	ENSP00000361027	AMOT_HUMAN	E7ERM3_HUMAN	UPI000050ED33	.	.	unknown(0)	1/11	.	hmmpanther:PTHR14826,hmmpanther:PTHR14826:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCACTCAAGGA	.	2	ESCA
SOWAHD	0	.	GRCh37	X	118893624	118893624	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*46G>A	.	.	ENST00000343905	1/1	53	23	29	65	65	0	SOWAHD,3_prime_UTR_variant,,ENST00000343905,;	A	ENSG00000187808	ENST00000343905	Transcript	3_prime_UTR_variant	1049	.	.	.	.	.	.	.	1	SOWAHD	HGNC	32960	protein_coding	YES	CCDS43984.1	ENSP00000340975	SWAHD_HUMAN	.	UPI0000197588	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCGATGGC	.	5	ESCA
AFF2	0	.	GRCh37	X	148072955	148072955	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*93G>C	.	.	ENST00000370460	21/21	63	21	42	72	72	0	AFF2,3_prime_UTR_variant,,ENST00000370460,;AFF2,3_prime_UTR_variant,,ENST00000342251,;AFF2,3_prime_UTR_variant,,ENST00000286437,;AFF2,3_prime_UTR_variant,,ENST00000370457,;	C	ENSG00000155966	ENST00000370460	Transcript	3_prime_UTR_variant	4508	.	.	.	.	.	.	.	1	AFF2	HGNC	3776	protein_coding	YES	CCDS14684.1	ENSP00000359489	AFF2_HUMAN	.	UPI000049E130	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAACGTTCTC	.	5	ESCA
SLC25A6	0	.	GRCh37	X	1506281	1506281	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630C>T	p.%3D	p.I210I	ENST00000381401	3/4	69	49	19	56	56	0	SLC25A6,synonymous_variant,p.%3D,ENST00000381401,;IL3RA,downstream_gene_variant,,ENST00000381469,;IL3RA,downstream_gene_variant,,ENST00000331035,;SLC25A6,non_coding_transcript_exon_variant,,ENST00000484026,;SLC25A6,non_coding_transcript_exon_variant,,ENST00000475167,;	A	ENSG00000169100	ENST00000381401	Transcript	synonymous_variant	1345	630	210	I	atC/atT	.	.	.	-1	SLC25A6	HGNC	10992	protein_coding	YES	CCDS14114.1	ENSP00000370808	ADT3_HUMAN	Q6I9V5_HUMAN,Q59EI9_HUMAN,I7HJJ0_HUMAN	UPI00000015FE	.	.	.	3/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24089:SF217,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACGATGTG	.	5	ESCA
GATA1	0	.	GRCh37	X	48650412	48650412	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382G>A	p.Gly128Ser	p.G128S	ENST00000376670	3/6	31	9	21	48	48	0	GATA1,missense_variant,p.Gly128Ser,ENST00000376670,;GATA1,missense_variant,p.Gly128Ser,ENST00000376665,;	A	ENSG00000102145	ENST00000376670	Transcript	missense_variant	493	382	128	G/S	Ggc/Agc	.	.	.	1	GATA1	HGNC	4170	protein_coding	YES	CCDS14305.1	ENSP00000365858	GATA1_HUMAN	.	UPI000012B0FA	.	tolerated(0.46)	benign(0.001)	3/6	.	hmmpanther:PTHR10071:SF150,hmmpanther:PTHR10071,PIRSF_domain:PIRSF003027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAAGGCAGC	.	5	ESCA
DACH2	0	.	GRCh37	X	85994844	85994844	+	Missense_Mutation	SNP	C	C	A	rs763149898	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1199C>A	p.Ser400Tyr	p.S400Y	ENST00000373125	7/12	20	5	14	17	17	0	DACH2,missense_variant,p.Ser181Tyr,ENST00000510272,;DACH2,missense_variant,p.Ser400Tyr,ENST00000373125,;DACH2,missense_variant,p.Ser55Tyr,ENST00000484479,;DACH2,missense_variant,p.Ser387Tyr,ENST00000373131,;DACH2,missense_variant,p.Ser233Tyr,ENST00000508860,;DACH2,missense_variant,p.Ser400Tyr,ENST00000461604,;DACH2,3_prime_UTR_variant,,ENST00000506327,;	A	ENSG00000126733	ENST00000373125	Transcript	missense_variant	1199	1199	400	S/Y	tCc/tAc	rs763149898	.	.	1	DACH2	HGNC	16814	protein_coding	YES	CCDS14455.1	ENSP00000362217	DACH2_HUMAN	.	UPI00000717B4	.	deleterious(0.03)	probably_damaging(0.976)	7/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGTGTCCAGCT	byFrequency	4	ESCA
DACH2	0	.	GRCh37	X	85994845	85994845	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A8-01A-32D-A27G-09	TCGA-LN-A4A8-10A-01D-A27G-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1200C>G	p.%3D	p.S400S	ENST00000373125	7/12	19	5	14	17	17	0	DACH2,synonymous_variant,p.%3D,ENST00000510272,;DACH2,synonymous_variant,p.%3D,ENST00000373125,;DACH2,synonymous_variant,p.%3D,ENST00000484479,;DACH2,synonymous_variant,p.%3D,ENST00000373131,;DACH2,synonymous_variant,p.%3D,ENST00000508860,;DACH2,synonymous_variant,p.%3D,ENST00000461604,;DACH2,3_prime_UTR_variant,,ENST00000506327,;	G	ENSG00000126733	ENST00000373125	Transcript	synonymous_variant	1200	1200	400	S	tcC/tcG	.	.	.	1	DACH2	HGNC	16814	protein_coding	YES	CCDS14455.1	ENSP00000362217	DACH2_HUMAN	.	UPI00000717B4	.	.	.	7/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTCCAGCTC	.	5	ESCA
TAF5	0	.	GRCh37	10	105127805	105127805	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>A	p.Pro20Gln	p.P20Q	ENST00000369839	1/11	35	9	26	20	20	0	TAF5,missense_variant,p.Pro20Gln,ENST00000351396,;TAF5,missense_variant,p.Pro20Gln,ENST00000369839,;	A	ENSG00000148835	ENST00000369839	Transcript	missense_variant	82	59	20	P/Q	cCg/cAg	.	.	.	1	TAF5	HGNC	11539	protein_coding	YES	CCDS7547.1	ENSP00000358854	TAF5_HUMAN	.	UPI000013DB5B	.	deleterious_low_confidence(0)	probably_damaging(0.975)	1/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR19879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGACCGCCAA	.	5	ESCA
NHLRC2	0	.	GRCh37	10	115618346	115618346	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.238A>G	p.Ile80Val	p.I80V	ENST00000369301	2/11	64	39	25	65	65	0	NHLRC2,missense_variant,p.Ile80Val,ENST00000369301,;DCLRE1A,upstream_gene_variant,,ENST00000361384,;DCLRE1A,upstream_gene_variant,,ENST00000369305,;DCLRE1A,upstream_gene_variant,,ENST00000476112,;NHLRC2,non_coding_transcript_exon_variant,,ENST00000468890,;	G	ENSG00000196865	ENST00000369301	Transcript	missense_variant	450	238	80	I/V	Ata/Gta	.	.	.	1	NHLRC2	HGNC	24731	protein_coding	YES	CCDS7585.1	ENSP00000358307	NHLC2_HUMAN	.	UPI0000071EAF	.	tolerated(1)	benign(0.006)	2/11	.	PROSITE_profiles:PS51352,hmmpanther:PTHR13833:SF13,hmmpanther:PTHR13833,Gene3D:3.40.30.10,Pfam_domain:PF13905,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAATAGTC	.	5	ESCA
DMBT1P1	0	.	GRCh37	10	124554869	124554869	+	RNA	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3229T>G	.	.	ENST00000439464	26/28	29	9	19	25	25	0	DMBT1P1,non_coding_transcript_exon_variant,,ENST00000439464,;DMBT1P1,upstream_gene_variant,,ENST00000605982,;	G	ENSG00000176584	ENST00000439464	Transcript	non_coding_transcript_exon_variant	3229	.	.	.	.	.	.	.	1	DMBT1P1	HGNC	49497	processed_transcript	YES	.	.	.	.	.	.	.	.	26/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGTTTTGTGC	.	3	ESCA
ARID5B	0	.	GRCh37	10	63661443	63661443	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-26G>C	.	.	ENST00000279873	1/10	32	23	9	29	29	0	ARID5B,5_prime_UTR_variant,,ENST00000279873,;	C	ENSG00000150347	ENST00000279873	Transcript	5_prime_UTR_variant	385	.	.	.	.	.	.	.	1	ARID5B	HGNC	17362	protein_coding	YES	CCDS31208.1	ENSP00000279873	ARI5B_HUMAN	.	UPI00001606F0	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTTGAGTTC	.	5	ESCA
LRRTM3	0	.	GRCh37	10	68858032	68858032	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*478T>G	.	.	ENST00000361320	3/3	46	30	16	56	56	0	LRRTM3,3_prime_UTR_variant,,ENST00000361320,;CTNNA3,intron_variant,,ENST00000433211,;CTNNA3,intron_variant,,ENST00000494580,;CTNNA3,intron_variant,,ENST00000373744,;LRRTM3,downstream_gene_variant,,ENST00000485868,;	G	ENSG00000198739	ENST00000361320	Transcript	3_prime_UTR_variant	2802	.	.	.	.	.	.	.	1	LRRTM3	HGNC	19410	protein_coding	YES	CCDS7270.1	ENSP00000355187	LRRT3_HUMAN	B4DFC3_HUMAN	UPI0000088C0F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGTTACTG	.	5	ESCA
NUTM2D	0	.	GRCh37	10	89117727	89117727	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-296G>A	.	.	ENST00000412718	1/7	62	51	11	55	55	0	NUTM2D,5_prime_UTR_variant,,ENST00000412718,;NUTM2D,5_prime_UTR_variant,,ENST00000381697,;LINC00863,downstream_gene_variant,,ENST00000439559,;	A	ENSG00000214562	ENST00000412718	Transcript	5_prime_UTR_variant	251	.	.	.	.	.	.	.	1	NUTM2D	HGNC	23447	protein_coding	YES	.	ENSP00000396080	NTM2D_HUMAN	.	UPI0000458AED	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTGTTGAAATT	.	2	ESCA
PAPSS2	0	.	GRCh37	10	89487163	89487163	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003G>A	p.Asp335Asn	p.D335N	ENST00000456849	9/13	22	15	6	26	26	0	PAPSS2,missense_variant,p.Asp334Asn,ENST00000427144,;PAPSS2,missense_variant,p.Asp335Asn,ENST00000456849,;PAPSS2,missense_variant,p.Asp330Asn,ENST00000361175,;	A	ENSG00000198682	ENST00000456849	Transcript	missense_variant	1266	1003	335	D/N	Gac/Aac	.	.	.	1	PAPSS2	HGNC	8604	protein_coding	YES	CCDS44453.1	ENSP00000406157	PAPS2_HUMAN	.	UPI000002B182	.	tolerated(1)	benign(0.003)	9/13	.	hmmpanther:PTHR11055,hmmpanther:PTHR11055:SF16,Gene3D:3.10.400.10,TIGRFAM_domain:TIGR00339,Pfam_domain:PF14306,Superfamily_domains:SSF88697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACGAGACGCT	.	5	ESCA
EXOC6	0	.	GRCh37	10	94694131	94694131	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1084G>A	p.Asp362Asn	p.D362N	ENST00000260762	11/22	28	20	7	29	29	0	EXOC6,missense_variant,p.Asp362Asn,ENST00000260762,;EXOC6,missense_variant,p.Asp378Asn,ENST00000371547,;EXOC6,missense_variant,p.Asp357Asn,ENST00000371552,;EXOC6,intron_variant,,ENST00000443748,;EXOC6,missense_variant,p.Asp39Asn,ENST00000495132,;	A	ENSG00000138190	ENST00000260762	Transcript	missense_variant	1098	1084	362	D/N	Gat/Aat	.	.	.	1	EXOC6	HGNC	23196	protein_coding	YES	CCDS7424.2	ENSP00000260762	EXOC6_HUMAN	Q9NTA6_HUMAN,H0Y5J8_HUMAN,B1AP46_HUMAN	UPI0000141914	.	deleterious(0.03)	benign(0.056)	11/22	.	hmmpanther:PTHR12702:SF2,hmmpanther:PTHR12702,PIRSF_domain:PIRSF025007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTGATGAA	.	5	ESCA
TRPC6	0	.	GRCh37	11	101323836	101323836	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2646G>T	p.%3D	p.G882G	ENST00000344327	13/13	26	18	8	34	34	0	TRPC6,synonymous_variant,p.%3D,ENST00000532133,;TRPC6,synonymous_variant,p.%3D,ENST00000348423,;TRPC6,synonymous_variant,p.%3D,ENST00000344327,;TRPC6,synonymous_variant,p.%3D,ENST00000360497,;TRPC6,downstream_gene_variant,,ENST00000532184,;	A	ENSG00000137672	ENST00000344327	Transcript	synonymous_variant	3071	2646	882	G	ggG/ggT	.	.	.	-1	TRPC6	HGNC	12338	protein_coding	YES	CCDS8311.1	ENSP00000340913	TRPC6_HUMAN	B3KNL3_HUMAN	UPI00001374BA	.	.	.	13/13	.	hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF7,TIGRFAM_domain:TIGR00870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTCCCCTTT	.	5	ESCA
NCAM1	0	.	GRCh37	11	113103878	113103878	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1679C>A	p.Ser560Tyr	p.S560Y	ENST00000524665	12/19	34	19	15	46	46	0	NCAM1,missense_variant,p.Ser546Tyr,ENST00000534015,;NCAM1,missense_variant,p.Ser560Tyr,ENST00000524665,;NCAM1,missense_variant,p.Ser510Tyr,ENST00000401611,;NCAM1,missense_variant,p.Ser383Tyr,ENST00000533760,;NCAM1,missense_variant,p.Ser501Tyr,ENST00000316851,;NCAM1,non_coding_transcript_exon_variant,,ENST00000527506,;NCAM1,non_coding_transcript_exon_variant,,ENST00000530543,;NCAM1,non_coding_transcript_exon_variant,,ENST00000533073,;NCAM1,non_coding_transcript_exon_variant,,ENST00000526322,;NCAM1,non_coding_transcript_exon_variant,,ENST00000397957,;NCAM1,non_coding_transcript_exon_variant,,ENST00000531044,;NCAM1,non_coding_transcript_exon_variant,,ENST00000531915,;NCAM1,non_coding_transcript_exon_variant,,ENST00000528590,;NCAM1,intron_variant,,ENST00000526427,;NCAM1,downstream_gene_variant,,ENST00000528742,;NCAM1,missense_variant,p.Ser11Tyr,ENST00000531817,;NCAM1,upstream_gene_variant,,ENST00000525355,;NCAM1,downstream_gene_variant,,ENST00000534046,;	A	ENSG00000149294	ENST00000524665	Transcript	missense_variant	1679	1679	560	S/Y	tCt/tAt	.	.	.	1	NCAM1	HGNC	7656	protein_coding	YES	.	ENSP00000474028	.	S4R389_HUMAN	UPI000333505F	.	deleterious(0)	probably_damaging(1)	12/19	.	Superfamily_domains:SSF49265,Superfamily_domains:SSF48726,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF34,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTCTTCAC	.	5	ESCA
NCAM1	0	.	GRCh37	11	113144552	113144552	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2604-1437G>A	.	.	ENST00000524665	.	26	7	19	23	23	0	NCAM1,intron_variant,,ENST00000524665,;NCAM1,intron_variant,,ENST00000316851,;NCAM1-AS1,non_coding_transcript_exon_variant,,ENST00000526229,;RP11-839D17.3,downstream_gene_variant,,ENST00000526487,;RP11-839D17.3,downstream_gene_variant,,ENST00000529416,;NCAM1-AS1,upstream_gene_variant,,ENST00000533638,;NCAM1,intron_variant,,ENST00000397957,;NCAM1,intron_variant,,ENST00000531044,;NCAM1,intron_variant,,ENST00000528158,;NCAM1,intron_variant,,ENST00000531915,;NCAM1,intron_variant,,ENST00000528590,;NCAM1,intron_variant,,ENST00000533073,;NCAM1,downstream_gene_variant,,ENST00000526427,;NCAM1,intron_variant,,ENST00000533226,;NCAM1,downstream_gene_variant,,ENST00000531927,;	A	ENSG00000149294	ENST00000524665	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NCAM1	HGNC	7656	protein_coding	YES	.	ENSP00000474028	.	S4R389_HUMAN	UPI000333505F	.	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTAGATGTG	.	5	ESCA
IGSF9B	0	.	GRCh37	11	133790066	133790066	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3554G>T	p.Arg1185Met	p.R1185M	ENST00000533871	18/20	118	31	86	104	104	0	IGSF9B,missense_variant,p.Arg1185Met,ENST00000533871,;IGSF9B,missense_variant,p.Arg1185Met,ENST00000321016,;IGSF9B,downstream_gene_variant,,ENST00000527648,;	A	ENSG00000080854	ENST00000533871	Transcript	missense_variant	3785	3554	1185	R/M	aGg/aTg	.	.	.	-1	IGSF9B	HGNC	32326	protein_coding	YES	CCDS61010.1	ENSP00000436552	.	G5EA26_HUMAN	UPI0002C439DB	.	deleterious_low_confidence(0)	probably_damaging(0.935)	18/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10489:SF575,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R1182W|c.3544C>T|3,BUFFER|p.R638W|c.1912C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGCCTGGCC	.	5	ESCA
GTF2H1	0	.	GRCh37	11	18361125	18361125	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528C>G	p.%3D	p.P176P	ENST00000265963	5/15	58	40	18	78	78	0	GTF2H1,synonymous_variant,p.%3D,ENST00000265963,;GTF2H1,synonymous_variant,p.%3D,ENST00000534641,;GTF2H1,synonymous_variant,p.%3D,ENST00000453096,;GTF2H1,5_prime_UTR_variant,,ENST00000524753,;GTF2H1,downstream_gene_variant,,ENST00000525831,;GTF2H1,downstream_gene_variant,,ENST00000531757,;GTF2H1,non_coding_transcript_exon_variant,,ENST00000543932,;GTF2H1,non_coding_transcript_exon_variant,,ENST00000418116,;GTF2H1,upstream_gene_variant,,ENST00000607664,;	G	ENSG00000110768	ENST00000265963	Transcript	synonymous_variant	688	528	176	P	ccC/ccG	.	.	.	1	GTF2H1	HGNC	4655	protein_coding	YES	CCDS7838.1	ENSP00000265963	TF2H1_HUMAN	F5H0Y9_HUMAN,E9PM51_HUMAN,E9PL58_HUMAN,B4DSG6_HUMAN,B3KXE0_HUMAN	UPI0000136C8A	.	.	.	5/15	.	hmmpanther:PTHR12856	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCCCCAAAC	.	5	ESCA
BDNF	0	.	GRCh37	11	27722334	27722334	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-59+184C>A	.	.	ENST00000438929	.	10	2	8	9	9	0	BDNF,5_prime_UTR_variant,,ENST00000530861,;BDNF,intron_variant,,ENST00000438929,;BDNF,intron_variant,,ENST00000532997,;BDNF,intron_variant,,ENST00000395981,;BDNF,intron_variant,,ENST00000420794,;BDNF,intron_variant,,ENST00000395983,;BDNF,intron_variant,,ENST00000395980,;BDNF,intron_variant,,ENST00000525950,;BDNF,intron_variant,,ENST00000395978,;BDNF,intron_variant,,ENST00000314915,;BDNF,upstream_gene_variant,,ENST00000533131,;BDNF,upstream_gene_variant,,ENST00000356660,;BDNF,upstream_gene_variant,,ENST00000418212,;BDNF,upstream_gene_variant,,ENST00000395986,;BDNF,upstream_gene_variant,,ENST00000533246,;RP11-587D21.4,intron_variant,,ENST00000530663,;BDNF-AS,downstream_gene_variant,,ENST00000502161,;BDNF-AS,downstream_gene_variant,,ENST00000499568,;BDNF-AS,downstream_gene_variant,,ENST00000500662,;BDNF,intron_variant,,ENST00000584049,;BDNF,intron_variant,,ENST00000530786,;	T	ENSG00000176697	ENST00000438929	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	BDNF	HGNC	1033	protein_coding	YES	CCDS44558.1	ENSP00000414303	BDNF_HUMAN	S5MI63_HUMAN,Q96TC2_HUMAN,Q969N8_HUMAN	UPI0001594492	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCCGGGGAA	.	2	ESCA
CARS	0	.	GRCh37	11	3050660	3050660	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.815A>T	p.Glu272Val	p.E272V	ENST00000380525	8/23	38	10	28	27	27	0	CARS,missense_variant,p.Glu189Val,ENST00000278224,;CARS,missense_variant,p.Glu189Val,ENST00000397111,;CARS,missense_variant,p.Glu272Val,ENST00000380525,;CARS,missense_variant,p.Glu179Val,ENST00000397114,;CARS,missense_variant,p.Glu202Val,ENST00000401769,;CARS-AS1,non_coding_transcript_exon_variant,,ENST00000499962,;CARS,upstream_gene_variant,,ENST00000465240,;CARS,3_prime_UTR_variant,,ENST00000529772,;CARS,3_prime_UTR_variant,,ENST00000439280,;CARS,3_prime_UTR_variant,,ENST00000531387,;CARS,non_coding_transcript_exon_variant,,ENST00000526890,;	A	ENSG00000110619	ENST00000380525	Transcript	missense_variant	885	815	272	E/V	gAa/gTa	.	.	.	-1	CARS	HGNC	1493	protein_coding	YES	CCDS41600.1	ENSP00000369897	SYCC_HUMAN	.	UPI00004C4152	.	tolerated(0.05)	benign(0.213)	8/23	.	HAMAP:MF_00041,hmmpanther:PTHR10890,hmmpanther:PTHR10890:SF3,Pfam_domain:PF01406,TIGRFAM_domain:TIGR00435	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTTCTTCC	.	5	ESCA
CAPRIN1	0	.	GRCh37	11	34118131	34118131	+	Missense_Mutation	SNP	A	A	G	rs763927685	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1811A>G	p.Tyr604Cys	p.Y604C	ENST00000341394	16/19	45	23	21	39	39	0	CAPRIN1,missense_variant,p.Tyr604Cys,ENST00000532820,;CAPRIN1,missense_variant,p.Tyr604Cys,ENST00000389645,;CAPRIN1,missense_variant,p.Tyr604Cys,ENST00000530820,;CAPRIN1,missense_variant,p.Tyr604Cys,ENST00000341394,;CAPRIN1,missense_variant,p.Tyr523Cys,ENST00000529307,;CAPRIN1,non_coding_transcript_exon_variant,,ENST00000531668,;CAPRIN1,non_coding_transcript_exon_variant,,ENST00000533562,;CAPRIN1,non_coding_transcript_exon_variant,,ENST00000528948,;CAPRIN1,non_coding_transcript_exon_variant,,ENST00000533657,;CAPRIN1,intron_variant,,ENST00000528856,;	G	ENSG00000135387	ENST00000341394	Transcript	missense_variant	2000	1811	604	Y/C	tAt/tGt	rs763927685	.	.	1	CAPRIN1	HGNC	6743	protein_coding	YES	CCDS31453.1	ENSP00000340329	CAPR1_HUMAN	G3V153_HUMAN,E9PLA9_HUMAN	UPI0000251DB5	.	deleterious(0)	probably_damaging(0.935)	16/19	.	hmmpanther:PTHR22922,hmmpanther:PTHR22922:SF3,Pfam_domain:PF12287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTATTACA	.	5	ESCA
DGKZ	0	.	GRCh37	11	46401663	46401663	+	3'UTR	SNP	C	C	G	rs77301402	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*166C>G	.	.	ENST00000454345	32/32	33	19	14	41	41	0	DGKZ,3_prime_UTR_variant,,ENST00000527911,;DGKZ,3_prime_UTR_variant,,ENST00000456247,;DGKZ,3_prime_UTR_variant,,ENST00000543978,;DGKZ,3_prime_UTR_variant,,ENST00000343674,;DGKZ,3_prime_UTR_variant,,ENST00000454345,;DGKZ,3_prime_UTR_variant,,ENST00000318201,;DGKZ,3_prime_UTR_variant,,ENST00000395574,;DGKZ,3_prime_UTR_variant,,ENST00000532868,;MDK,upstream_gene_variant,,ENST00000395565,;MDK,upstream_gene_variant,,ENST00000359803,;DGKZ,downstream_gene_variant,,ENST00000421244,;DGKZ,downstream_gene_variant,,ENST00000524869,;MDK,upstream_gene_variant,,ENST00000533952,;MDK,upstream_gene_variant,,ENST00000441869,;MDK,upstream_gene_variant,,ENST00000395566,;MDK,upstream_gene_variant,,ENST00000395569,;CHRM4,downstream_gene_variant,,ENST00000433765,;MDK,upstream_gene_variant,,ENST00000407067,;MDK,upstream_gene_variant,,ENST00000405308,;DGKZ,downstream_gene_variant,,ENST00000528615,;MIR4688,downstream_gene_variant,,ENST00000577966,;DGKZ,downstream_gene_variant,,ENST00000529660,;MDK,upstream_gene_variant,,ENST00000533283,;DGKZ,3_prime_UTR_variant,,ENST00000524984,;DGKZ,non_coding_transcript_exon_variant,,ENST00000534802,;DGKZ,non_coding_transcript_exon_variant,,ENST00000528173,;DGKZ,non_coding_transcript_exon_variant,,ENST00000527211,;DGKZ,downstream_gene_variant,,ENST00000532941,;MDK,upstream_gene_variant,,ENST00000481047,;DGKZ,downstream_gene_variant,,ENST00000531879,;DGKZ,downstream_gene_variant,,ENST00000529698,;MDK,upstream_gene_variant,,ENST00000489525,;MDK,upstream_gene_variant,,ENST00000490240,;	G	ENSG00000149091	ENST00000454345	Transcript	3_prime_UTR_variant	3645	.	.	.	.	rs77301402	.	.	1	DGKZ	HGNC	2857	protein_coding	YES	CCDS41640.1	ENSP00000412178	DGKZ_HUMAN	Q7Z5X8_HUMAN,E9PNL8_HUMAN	UPI000013DB71	.	.	.	32/32	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTCAGGAG	byCluster|by1000G	5	ESCA
RASGRP2	0	.	GRCh37	11	64511413	64511413	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-71-1004G>C	.	.	ENST00000354024	.	24	17	6	34	34	0	RASGRP2,5_prime_UTR_variant,,ENST00000394430,;RASGRP2,intron_variant,,ENST00000354024,;RASGRP2,intron_variant,,ENST00000394432,;RASGRP2,intron_variant,,ENST00000377489,;RASGRP2,intron_variant,,ENST00000377486,;RASGRP2,intron_variant,,ENST00000430645,;RASGRP2,intron_variant,,ENST00000377485,;RASGRP2,intron_variant,,ENST00000419843,;RASGRP2,intron_variant,,ENST00000377497,;RASGRP2,intron_variant,,ENST00000431822,;RASGRP2,intron_variant,,ENST00000377487,;RASGRP2,upstream_gene_variant,,ENST00000394429,;PYGM,downstream_gene_variant,,ENST00000377432,;RASGRP2,upstream_gene_variant,,ENST00000394428,;RASGRP2,upstream_gene_variant,,ENST00000377494,;PYGM,downstream_gene_variant,,ENST00000164139,;RASGRP2,intron_variant,,ENST00000480443,;RASGRP2,intron_variant,,ENST00000441258,;RASGRP2,intron_variant,,ENST00000421556,;RASGRP2,upstream_gene_variant,,ENST00000464324,;PYGM,downstream_gene_variant,,ENST00000483742,;RASGRP2,upstream_gene_variant,,ENST00000445445,;	G	ENSG00000068831	ENST00000354024	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RASGRP2	HGNC	9879	protein_coding	YES	CCDS31598.1	ENSP00000338864	GRP2_HUMAN	Q2YDB1_HUMAN,E7EM78_HUMAN,C9JZ82_HUMAN,A6NHE2_HUMAN	UPI0000161186	.	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCACACA	.	5	ESCA
EHD1	0	.	GRCh37	11	64622896	64622896	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.978C>G	p.Ser326Arg	p.S326R	ENST00000320631	4/5	31	24	7	37	37	0	EHD1,missense_variant,p.Ser326Arg,ENST00000359393,;EHD1,missense_variant,p.Ser190Arg,ENST00000421510,;EHD1,missense_variant,p.Ser326Arg,ENST00000320631,;EHD1,missense_variant,p.Ser340Arg,ENST00000433803,;EHD1,downstream_gene_variant,,ENST00000455148,;EHD1,upstream_gene_variant,,ENST00000488711,;EHD1,non_coding_transcript_exon_variant,,ENST00000484846,;EHD1,non_coding_transcript_exon_variant,,ENST00000498472,;EHD1,downstream_gene_variant,,ENST00000466015,;	C	ENSG00000110047	ENST00000320631	Transcript	missense_variant	1233	978	326	S/R	agC/agG	.	.	.	-1	EHD1	HGNC	3242	protein_coding	YES	CCDS8084.1	ENSP00000320516	EHD1_HUMAN	C9JIJ3_HUMAN,C9JDQ8_HUMAN,C9J2Z4_HUMAN,C9IZH1_HUMAN,B2R5U3_HUMAN	UPI0000129E22	.	tolerated(0.21)	benign(0.001)	4/5	.	hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTGCTCTC	.	5	ESCA
DEFB108B	0	.	GRCh37	11	71544281	71544281	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36C>G	p.Phe12Leu	p.F12L	ENST00000328698	1/2	44	30	14	67	67	0	DEFB108B,missense_variant,p.Phe12Leu,ENST00000328698,;DEFB108B,upstream_gene_variant,,ENST00000529157,;	G	ENSG00000184276	ENST00000328698	Transcript	missense_variant	36	36	12	F/L	ttC/ttG	.	.	.	1	DEFB108B	HGNC	29966	protein_coding	YES	CCDS31631.1	ENSP00000333234	D108B_HUMAN	.	UPI00001AF853	.	tolerated(0.64)	benign(0)	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TTCTTCTTTAT	.	4	ESCA
FOLR2	0	.	GRCh37	11	71931984	71931984	+	Missense_Mutation	SNP	G	G	A	rs141073907	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221G>A	p.Arg74His	p.R74H	ENST00000298223	3/5	25	11	13	44	44	0	FOLR2,missense_variant,p.Arg120His,ENST00000541003,;FOLR2,missense_variant,p.Arg74His,ENST00000298223,;FOLR2,missense_variant,p.Arg89His,ENST00000536778,;FOLR2,missense_variant,p.Arg33His,ENST00000454954,;FOLR2,missense_variant,p.Arg74His,ENST00000538353,;FOLR2,missense_variant,p.Arg85His,ENST00000539412,;FOLR2,missense_variant,p.Arg74His,ENST00000535625,;FOLR2,missense_variant,p.Arg87His,ENST00000321324,;FOLR2,missense_variant,p.Arg91His,ENST00000449475,;INPPL1,upstream_gene_variant,,ENST00000540973,;INPPL1,upstream_gene_variant,,ENST00000298229,;INPPL1,upstream_gene_variant,,ENST00000541756,;INPPL1,upstream_gene_variant,,ENST00000543234,;INPPL1,upstream_gene_variant,,ENST00000541544,;	A	ENSG00000165457	ENST00000298223	Transcript	missense_variant	408	221	74	R/H	cGc/cAc	rs141073907,COSM385651	.	.	1	FOLR2	HGNC	3793	protein_coding	YES	CCDS8212.1	ENSP00000298223	FOLR2_HUMAN	Q6GTE8_HUMAN,Q05CA5_HUMAN,F5H4Z6_HUMAN	UPI000013E4AD	.	tolerated(0.32)	benign(0.009)	3/5	.	Pfam_domain:PF03024,hmmpanther:PTHR10517,hmmpanther:PTHR10517:SF8	A:0.0014	A:0	A:0.0014	.	A:0.006	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCGCCTGT	byFrequency|byCluster|by1000G	5	ESCA
RNF169	0	.	GRCh37	11	74546963	74546963	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000299563	6/6	23	14	9	23	23	0	RNF169,stop_gained,p.Gln439Ter,ENST00000299563,;RNF169,upstream_gene_variant,,ENST00000527301,;XRRA1,downstream_gene_variant,,ENST00000321448,;XRRA1,downstream_gene_variant,,ENST00000340360,;XRRA1,intron_variant,,ENST00000530562,;	T	ENSG00000166439	ENST00000299563	Transcript	stop_gained	1328	1315	439	Q/*	Cag/Tag	.	.	.	1	RNF169	HGNC	26961	protein_coding	YES	CCDS41691.1	ENSP00000299563	RN169_HUMAN	.	UPI00001C1F15	.	.	.	6/6	.	hmmpanther:PTHR23328:SF2,hmmpanther:PTHR23328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCAGGAG	.	5	ESCA
MAP6	0	.	GRCh37	11	75298065	75298065	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39G>C	.	.	ENST00000304771	4/4	37	24	13	36	36	0	MAP6,3_prime_UTR_variant,,ENST00000526740,;MAP6,3_prime_UTR_variant,,ENST00000304771,;CTD-2530H12.4,intron_variant,,ENST00000527803,;MAP6,downstream_gene_variant,,ENST00000526689,;	G	ENSG00000171533	ENST00000304771	Transcript	3_prime_UTR_variant	3232	.	.	.	.	.	.	.	-1	MAP6	HGNC	6868	protein_coding	YES	CCDS31641.1	ENSP00000307093	MAP6_HUMAN	Q6ZWB8_HUMAN	UPI0000251E6A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTCACTGT	.	5	ESCA
CHID1	0	.	GRCh37	11	869903	869903	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1212C>T	p.%3D	p.I404I	ENST00000454838	13/13	58	37	21	47	47	0	CHID1,synonymous_variant,p.%3D,ENST00000449825,;CHID1,synonymous_variant,p.%3D,ENST00000529539,;CHID1,synonymous_variant,p.%3D,ENST00000323578,;CHID1,synonymous_variant,p.%3D,ENST00000528581,;CHID1,synonymous_variant,p.%3D,ENST00000323541,;CHID1,synonymous_variant,p.%3D,ENST00000336845,;CHID1,synonymous_variant,p.%3D,ENST00000436108,;CHID1,synonymous_variant,p.%3D,ENST00000454838,;CHID1,synonymous_variant,p.%3D,ENST00000429789,;TSPAN4,downstream_gene_variant,,ENST00000397396,;TSPAN4,downstream_gene_variant,,ENST00000525201,;TSPAN4,downstream_gene_variant,,ENST00000532375,;TSPAN4,downstream_gene_variant,,ENST00000409543,;TSPAN4,downstream_gene_variant,,ENST00000397411,;TSPAN4,downstream_gene_variant,,ENST00000525334,;TSPAN4,downstream_gene_variant,,ENST00000397397,;TSPAN4,downstream_gene_variant,,ENST00000346501,;TSPAN4,downstream_gene_variant,,ENST00000397404,;TSPAN4,downstream_gene_variant,,ENST00000397406,;TSPAN4,downstream_gene_variant,,ENST00000397408,;TSPAN4,downstream_gene_variant,,ENST00000527644,;TSPAN4,downstream_gene_variant,,ENST00000409531,;CHID1,downstream_gene_variant,,ENST00000528534,;CHID1,downstream_gene_variant,,ENST00000526714,;CHID1,synonymous_variant,p.%3D,ENST00000532909,;CHID1,synonymous_variant,p.%3D,ENST00000534207,;CHID1,non_coding_transcript_exon_variant,,ENST00000524538,;CHID1,downstream_gene_variant,,ENST00000528521,;TSPAN4,downstream_gene_variant,,ENST00000529566,;TSPAN4,downstream_gene_variant,,ENST00000468468,;TSPAN4,downstream_gene_variant,,ENST00000494815,;TSPAN4,downstream_gene_variant,,ENST00000464987,;	A	ENSG00000177830	ENST00000454838	Transcript	synonymous_variant	1319	1212	404	I	atC/atT	.	.	.	-1	CHID1	HGNC	28474	protein_coding	YES	CCDS44511.1	ENSP00000398722	CHID1_HUMAN	H0YDL6_HUMAN,E9PJL0_HUMAN,E9PJ91_HUMAN	UPI000003B0AE	.	.	.	13/13	.	hmmpanther:PTHR11177,Gene3D:3.20.20.80,Pfam_domain:PF00704,SMART_domains:SM00636,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCAGATAGA	.	5	ESCA
GPR83	0	.	GRCh37	11	94134350	94134350	+	Missense_Mutation	SNP	C	C	A	rs543076194	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64G>T	p.Gly22Cys	p.G22C	ENST00000243673	1/4	13	2	10	16	16	0	GPR83,missense_variant,p.Gly22Cys,ENST00000539203,;GPR83,missense_variant,p.Gly22Cys,ENST00000243673,;	A	ENSG00000123901	ENST00000243673	Transcript	missense_variant	236	64	22	G/C	Ggc/Tgc	rs543076194	.	.	-1	GPR83	HGNC	4523	protein_coding	YES	CCDS8297.1	ENSP00000243673	GPR83_HUMAN	Q9H011_HUMAN	UPI000013CB3F	.	deleterious_low_confidence(0.05)	benign(0.137)	1/4	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CCGGCCCTCGT	by1000G	4	ESCA
RAD52	0	.	GRCh37	12	1023153	1023164	+	In_Frame_Del	DEL	TCTGGGTCACCA	TCTGGGTCACCA	-	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	TCTGGGTCACCA	TCTGGGTCACCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1091_1102delTGGTGACCCAGA	p.Met364_Gln367del	p.M364_Q367del	ENST00000358495	11/12	56	34	22	58	58	0	RAD52,inframe_deletion,p.Met287_Gln290del,ENST00000539046,;RAD52,inframe_deletion,p.Met364_Gln367del,ENST00000358495,;RAD52,inframe_deletion,p.Met364_Gln367del,ENST00000430095,;WNK1,downstream_gene_variant,,ENST00000315939,;WNK1,downstream_gene_variant,,ENST00000340908,;WNK1,downstream_gene_variant,,ENST00000535572,;RAD52,downstream_gene_variant,,ENST00000536177,;WNK1,downstream_gene_variant,,ENST00000537687,;RAD52,non_coding_transcript_exon_variant,,ENST00000535376,;RAD52,non_coding_transcript_exon_variant,,ENST00000542297,;RAD52,downstream_gene_variant,,ENST00000542584,;RAD52,3_prime_UTR_variant,,ENST00000468231,;RAD52,3_prime_UTR_variant,,ENST00000543912,;RAD52,3_prime_UTR_variant,,ENST00000461568,;RAD52,non_coding_transcript_exon_variant,,ENST00000481052,;RAD52,non_coding_transcript_exon_variant,,ENST00000228345,;RAD52,non_coding_transcript_exon_variant,,ENST00000488642,;RAD52,non_coding_transcript_exon_variant,,ENST00000463750,;WNK1,downstream_gene_variant,,ENST00000540885,;	-	ENSG00000002016	ENST00000358495	Transcript	inframe_deletion	1230-1241	1091-1102	364-368	MVTQN/N	aTGGTGACCCAGAac/aac	.	.	.	-1	RAD52	HGNC	9824	protein_coding	YES	CCDS8507.2	ENSP00000351284	RAD52_HUMAN	Q9UHE1_HUMAN,Q5DR82_HUMAN,Q3MI84_HUMAN,F5H3Q1_HUMAN,F5GX95_HUMAN,D3DUP4_HUMAN	UPI0000133035	.	.	.	11/12	.	hmmpanther:PTHR12132,hmmpanther:PTHR12132:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCTGTTCTGGGTCACCATCTGG	.	3	ESCA
CHST11	0	.	GRCh37	12	104995745	104995745	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180G>T	p.%3D	p.L60L	ENST00000303694	2/3	44	29	15	41	41	0	CHST11,synonymous_variant,p.%3D,ENST00000547956,;CHST11,synonymous_variant,p.%3D,ENST00000549260,;CHST11,synonymous_variant,p.%3D,ENST00000549016,;CHST11,synonymous_variant,p.%3D,ENST00000546689,;CHST11,synonymous_variant,p.%3D,ENST00000303694,;	T	ENSG00000171310	ENST00000303694	Transcript	synonymous_variant	619	180	60	L	ctG/ctT	.	.	.	1	CHST11	HGNC	17422	protein_coding	YES	CCDS9099.1	ENSP00000305725	CHSTB_HUMAN	F8VXK3_HUMAN	UPI000004A091	.	.	.	2/3	.	hmmpanther:PTHR12137,hmmpanther:PTHR12137:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTGCAGGA	.	5	ESCA
NUAK1	0	.	GRCh37	12	106459585	106459585	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*995T>G	.	.	ENST00000261402	7/7	45	31	13	29	29	0	NUAK1,3_prime_UTR_variant,,ENST00000261402,;NUAK1,downstream_gene_variant,,ENST00000548902,;NUAK1,downstream_gene_variant,,ENST00000553094,;NUAK1,downstream_gene_variant,,ENST00000549704,;	C	ENSG00000074590	ENST00000261402	Transcript	3_prime_UTR_variant	4361	.	.	.	.	.	.	.	-1	NUAK1	HGNC	14311	protein_coding	YES	CCDS31892.1	ENSP00000261402	NUAK1_HUMAN	F8VZ96_HUMAN,F8VXF0_HUMAN,F8VSH4_HUMAN	UPI00000403BC	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACAAGTTGC	.	5	ESCA
CUX2	0	.	GRCh37	12	111748077	111748077	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1491C>T	p.%3D	p.F497F	ENST00000261726	15/22	17	5	12	13	13	0	CUX2,synonymous_variant,p.%3D,ENST00000261726,;	T	ENSG00000111249	ENST00000261726	Transcript	synonymous_variant	1645	1491	497	F	ttC/ttT	.	.	.	1	CUX2	HGNC	19347	protein_coding	YES	CCDS41837.1	ENSP00000261726	CUX2_HUMAN	Q9BZX3_HUMAN,Q9BZV4_HUMAN	UPI00001FBB07	.	.	.	15/22	.	hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCAAGGG	.	5	ESCA
HECTD4	0	.	GRCh37	12	112607445	112607445	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11632G>A	p.Glu3878Lys	p.E3878K	ENST00000550722	70/76	24	18	6	19	19	0	HECTD4,missense_variant,p.Glu3602Lys,ENST00000430131,;HECTD4,missense_variant,p.Glu3878Lys,ENST00000550722,;HECTD4,missense_variant,p.Glu3852Lys,ENST00000377560,;HECTD4,downstream_gene_variant,,ENST00000548588,;HECTD4,non_coding_transcript_exon_variant,,ENST00000547085,;HECTD4,upstream_gene_variant,,ENST00000548140,;	T	ENSG00000173064	ENST00000550722	Transcript	missense_variant	12028	11632	3878	E/K	Gaa/Aaa	.	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	benign(0.262)	70/76	.	hmmpanther:PTHR11254:SF286,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTCAGAAG	.	5	ESCA
HCAR2	0	.	GRCh37	12	123187417	123187417	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.414G>C	p.Lys138Asn	p.K138N	ENST00000328880	1/1	84	48	36	70	70	0	HCAR2,missense_variant,p.Lys138Asn,ENST00000328880,;HCAR1,intron_variant,,ENST00000356987,;RP11-324E6.6,intron_variant,,ENST00000543611,;	G	ENSG00000182782	ENST00000328880	Transcript	missense_variant	474	414	138	K/N	aaG/aaC	.	.	.	-1	HCAR2	HGNC	24827	protein_coding	YES	CCDS9235.1	ENSP00000375066	HCAR2_HUMAN	.	UPI000003BCD5	.	tolerated(0.07)	possibly_damaging(0.857)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF0,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGATCTTGTT	.	5	ESCA
TMEM132D	0	.	GRCh37	12	129559126	129559126	+	Missense_Mutation	SNP	T	T	G	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2594A>C	p.Lys865Thr	p.K865T	ENST00000422113	9/9	123	99	24	143	143	0	TMEM132D,missense_variant,p.Lys865Thr,ENST00000422113,;TMEM132D,missense_variant,p.Lys403Thr,ENST00000389441,;	G	ENSG00000151952	ENST00000422113	Transcript	missense_variant	2921	2594	865	K/T	aAg/aCg	COSM1268015	.	.	-1	TMEM132D	HGNC	29411	protein_coding	YES	CCDS9266.1	ENSP00000408581	T132D_HUMAN	.	UPI000023759C	.	tolerated(0.16)	benign(0.055)	9/9	.	hmmpanther:PTHR13388	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCTTCTTC	.	5	ESCA
P2RX2	0	.	GRCh37	12	133197878	133197878	+	Missense_Mutation	SNP	C	C	A	rs761180947	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.943C>A	p.Arg315Ser	p.R315S	ENST00000343948	9/10	62	36	25	52	52	0	P2RX2,missense_variant,p.Arg243Ser,ENST00000352418,;P2RX2,missense_variant,p.Arg315Ser,ENST00000343948,;P2RX2,missense_variant,p.Arg315Ser,ENST00000389110,;P2RX2,missense_variant,p.Arg291Ser,ENST00000350048,;P2RX2,missense_variant,p.Arg315Ser,ENST00000348800,;P2RX2,missense_variant,p.Arg223Ser,ENST00000351222,;P2RX2,missense_variant,p.Arg281Ser,ENST00000449132,;P2RX2,downstream_gene_variant,,ENST00000542301,;POLE,downstream_gene_variant,,ENST00000535270,;P2RX2,downstream_gene_variant,,ENST00000536121,;P2RX2,downstream_gene_variant,,ENST00000535910,;POLE,downstream_gene_variant,,ENST00000320574,;POLE,downstream_gene_variant,,ENST00000544870,;POLE,downstream_gene_variant,,ENST00000538196,;POLE,downstream_gene_variant,,ENST00000541627,;POLE,downstream_gene_variant,,ENST00000534922,;POLE,downstream_gene_variant,,ENST00000544692,;POLE,downstream_gene_variant,,ENST00000537064,;POLE,downstream_gene_variant,,ENST00000543516,;	A	ENSG00000187848	ENST00000343948	Transcript	missense_variant	943	943	315	R/S	Cgc/Agc	rs761180947	.	.	1	P2RX2	HGNC	15459	protein_coding	YES	CCDS31930.1	ENSP00000343339	P2RX2_HUMAN	.	UPI000002B04A	.	deleterious(0)	probably_damaging(1)	9/10	.	hmmpanther:PTHR10125,hmmpanther:PTHR10125:SF4,Pfam_domain:PF00864,TIGRFAM_domain:TIGR00863,Gene3D:3h9vA02	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCCGCACG	byFrequency|byCluster	5	ESCA
TEAD4	0	.	GRCh37	12	3104056	3104056	+	Missense_Mutation	SNP	G	G	T	rs763254392	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>T	p.Val42Leu	p.V42L	ENST00000359864	3/13	60	16	43	88	88	0	TEAD4,missense_variant,p.Val42Leu,ENST00000536826,;TEAD4,missense_variant,p.Val42Leu,ENST00000543035,;TEAD4,missense_variant,p.Val42Leu,ENST00000359864,;TEAD4,missense_variant,p.Val42Leu,ENST00000358409,;TEAD4,intron_variant,,ENST00000397122,;TEAD4,downstream_gene_variant,,ENST00000540314,;TEAD4,missense_variant,p.Val42Leu,ENST00000443986,;	T	ENSG00000197905	ENST00000359864	Transcript	missense_variant	314	124	42	V/L	Gtg/Ttg	rs763254392	.	.	1	TEAD4	HGNC	11717	protein_coding	YES	CCDS31729.1	ENSP00000352926	.	Q53GI4_HUMAN,H0YGS2_HUMAN,H0YFK0_HUMAN,H0YFF9_HUMAN,D3DUQ6_HUMAN	UPI000013FEB3	.	deleterious(0)	probably_damaging(0.997)	3/13	.	PROSITE_profiles:PS51088,hmmpanther:PTHR11834,hmmpanther:PTHR11834:SF2,Pfam_domain:PF01285,PIRSF_domain:PIRSF002603,SMART_domains:SM00426,PIRSF_domain:PIRSF500722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCGTGTGG	.	5	ESCA
KDM5A	0	.	GRCh37	12	419007	419007	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3340G>A	p.Glu1114Lys	p.E1114K	ENST00000399788	22/28	55	33	22	42	42	0	KDM5A,missense_variant,p.Glu1114Lys,ENST00000382815,;KDM5A,missense_variant,p.Glu1114Lys,ENST00000399788,;KDM5A,downstream_gene_variant,,ENST00000544760,;KDM5A,downstream_gene_variant,,ENST00000535269,;KDM5A,upstream_gene_variant,,ENST00000540156,;	T	ENSG00000073614	ENST00000399788	Transcript	missense_variant	3703	3340	1114	E/K	Gag/Aag	.	.	.	-1	KDM5A	HGNC	9886	protein_coding	YES	CCDS41736.1	ENSP00000382688	KDM5A_HUMAN	.	UPI0000DB2E73	.	deleterious(0.01)	benign(0.097)	22/28	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCCAGAT	.	5	ESCA
CCND2	0	.	GRCh37	12	4413723	4413723	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4548C>A	.	.	ENST00000261254	5/5	31	15	16	27	27	0	CCND2,3_prime_UTR_variant,,ENST00000261254,;	A	ENSG00000118971	ENST00000261254	Transcript	3_prime_UTR_variant	5687	.	.	.	.	.	.	.	1	CCND2	HGNC	1583	protein_coding	YES	CCDS8524.1	ENSP00000261254	CCND2_HUMAN	.	UPI00001275C5	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAACCCAGA	.	5	ESCA
TIMELESS	0	.	GRCh37	12	56827937	56827937	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18G>A	p.Met6Ile	p.M6I	ENST00000553532	2/29	39	23	16	35	35	0	TIMELESS,missense_variant,p.Met6Ile,ENST00000553532,;TIMELESS,missense_variant,p.Met6Ile,ENST00000554616,;TIMELESS,missense_variant,p.Met6Ile,ENST00000229201,;	T	ENSG00000111602	ENST00000553532	Transcript	missense_variant	169	18	6	M/I	atG/atA	.	.	.	-1	TIMELESS	HGNC	11813	protein_coding	YES	CCDS8918.1	ENSP00000450607	TIM_HUMAN	.	UPI000013C8EA	.	deleterious(0.01)	possibly_damaging(0.824)	2/29	.	hmmpanther:PTHR22940:SF4,hmmpanther:PTHR22940	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCATCAT	.	5	ESCA
RDH16	0	.	GRCh37	12	57348715	57348715	+	Missense_Mutation	SNP	C	C	A	rs572909088	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547G>T	p.Val183Leu	p.V183L	ENST00000398138	2/4	29	17	12	25	25	0	RDH16,missense_variant,p.Val183Leu,ENST00000398138,;RDH16,intron_variant,,ENST00000360752,;	A	ENSG00000139547	ENST00000398138	Transcript	missense_variant	1404	547	183	V/L	Gtg/Ttg	rs572909088	.	.	-1	RDH16	HGNC	29674	protein_coding	YES	CCDS41797.1	ENSP00000381206	RDH16_HUMAN	.	UPI000013D71C	.	tolerated(0.06)	benign(0.291)	2/4	.	hmmpanther:PTHR24316:SF295,hmmpanther:PTHR24316,PROSITE_patterns:PS00061,Pfam_domain:PF00106,Gene3D:3.40.50.720,Superfamily_domains:SSF51735,Prints_domain:PR00081,Prints_domain:PR00080	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCACGCCAT	byFrequency|byCluster	5	ESCA
GRIP1	0	.	GRCh37	12	66839162	66839162	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1325C>A	p.Thr442Lys	p.T442K	ENST00000398016	11/24	66	48	17	36	36	0	GRIP1,missense_variant,p.Thr262Lys,ENST00000543172,;GRIP1,missense_variant,p.Thr442Lys,ENST00000538211,;GRIP1,missense_variant,p.Thr309Lys,ENST00000538164,;GRIP1,missense_variant,p.Thr494Lys,ENST00000286445,;GRIP1,missense_variant,p.Thr334Lys,ENST00000536215,;GRIP1,missense_variant,p.Thr442Lys,ENST00000398016,;GRIP1,missense_variant,p.Thr494Lys,ENST00000359742,;GRIP1,missense_variant,p.Thr386Lys,ENST00000540433,;GRIP1,intron_variant,,ENST00000540854,;GRIP1,downstream_gene_variant,,ENST00000535002,;	T	ENSG00000155974	ENST00000398016	Transcript	missense_variant	1394	1325	442	T/K	aCa/aAa	.	.	.	-1	GRIP1	HGNC	18708	protein_coding	YES	CCDS41807.1	ENSP00000381098	GRIP1_HUMAN	F5H5I0_HUMAN,F5H4P8_HUMAN,F5H424_HUMAN	UPI0000DD8148	.	deleterious(0)	probably_damaging(0.963)	11/24	.	PROSITE_profiles:PS50106,hmmpanther:PTHR10316:SF39,hmmpanther:PTHR10316,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTGTGGCA	.	5	ESCA
FRS2	0	.	GRCh37	12	69973116	69973116	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4381A>G	.	.	ENST00000299293	10/10	127	117	9	98	98	0	FRS2,3_prime_UTR_variant,,ENST00000550389,;FRS2,3_prime_UTR_variant,,ENST00000397997,;FRS2,3_prime_UTR_variant,,ENST00000299293,;FRS2,downstream_gene_variant,,ENST00000549921,;	G	ENSG00000166225	ENST00000299293	Transcript	3_prime_UTR_variant	6418	.	.	.	.	.	.	.	1	FRS2	HGNC	16971	protein_coding	YES	CCDS41809.1	ENSP00000299293	FRS2_HUMAN	L7RTG7_HUMAN,F8VZI4_HUMAN,F8VZ12_HUMAN,F8VYZ7_HUMAN,F8VX65_HUMAN,F8VW66_HUMAN,F8VS98_HUMAN	UPI000003F143	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTGAATGTGC	.	2	ESCA
MYF6	0	.	GRCh37	12	81102768	81102768	+	3'UTR	SNP	G	G	A	rs759406297	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29G>A	.	.	ENST00000228641	3/3	62	29	32	54	54	0	MYF6,3_prime_UTR_variant,,ENST00000228641,;	A	ENSG00000111046	ENST00000228641	Transcript	3_prime_UTR_variant	980	.	.	.	.	rs759406297	.	.	1	MYF6	HGNC	7566	protein_coding	YES	CCDS9019.1	ENSP00000228641	MYF6_HUMAN	.	UPI0000001050	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCACGCAGCA	.	5	ESCA
A2M	0	.	GRCh37	12	9254052	9254052	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1485C>G	p.Phe495Leu	p.F495L	ENST00000318602	12/36	25	15	10	21	21	0	A2M,missense_variant,p.Phe495Leu,ENST00000318602,;A2M,intron_variant,,ENST00000545828,;A2M,missense_variant,p.Phe13Leu,ENST00000546069,;A2M,non_coding_transcript_exon_variant,,ENST00000472360,;	C	ENSG00000175899	ENST00000318602	Transcript	missense_variant	1793	1485	495	F/L	ttC/ttG	.	.	.	-1	A2M	HGNC	7	protein_coding	YES	CCDS44827.1	ENSP00000323929	A2MG_HUMAN	Q9BQ22_HUMAN,F8W7L3_HUMAN,F5H1E8_HUMAN	UPI000014038F	.	deleterious(0)	benign(0.14)	12/36	.	hmmpanther:PTHR11412:SF75,hmmpanther:PTHR11412,Pfam_domain:PF07703	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATAGAAGGA	.	5	ESCA
EEA1	0	.	GRCh37	12	93169819	93169819	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4204T>G	p.Cys1402Gly	p.C1402G	ENST00000322349	29/29	50	37	12	31	31	0	EEA1,missense_variant,p.Cys1402Gly,ENST00000322349,;PLEKHG7,downstream_gene_variant,,ENST00000344636,;	C	ENSG00000102189	ENST00000322349	Transcript	missense_variant	4469	4204	1402	C/G	Tgt/Ggt	.	.	.	-1	EEA1	HGNC	3185	protein_coding	YES	CCDS31874.1	ENSP00000317955	EEA1_HUMAN	.	UPI000013C754	.	deleterious(0)	probably_damaging(1)	29/29	.	PROSITE_profiles:PS50178,hmmpanther:PTHR23164:SF2,hmmpanther:PTHR23164,Pfam_domain:PF01363,Gene3D:3.30.40.10,SMART_domains:SM00064,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACAGACAC	.	5	ESCA
SNRPF	0	.	GRCh37	12	96259806	96259806	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218G>C	p.Arg73Thr	p.R73T	ENST00000266735	4/4	71	31	39	57	57	0	SNRPF,missense_variant,p.Arg73Thr,ENST00000266735,;SNRPF,intron_variant,,ENST00000552085,;SNRPF,intron_variant,,ENST00000553192,;CCDC38,downstream_gene_variant,,ENST00000344280,;SNRPF,non_coding_transcript_exon_variant,,ENST00000549580,;SNRPF,downstream_gene_variant,,ENST00000551316,;CCDC38,downstream_gene_variant,,ENST00000549876,;CCDC38,downstream_gene_variant,,ENST00000546816,;	C	ENSG00000139343	ENST00000266735	Transcript	missense_variant	364	218	73	R/T	aGa/aCa	.	.	.	1	SNRPF	HGNC	11162	protein_coding	YES	CCDS9055.1	ENSP00000266735	RUXF_HUMAN	.	UPI0000027DBC	.	deleterious(0.03)	possibly_damaging(0.612)	4/4	.	hmmpanther:PTHR11021,Gene3D:2.30.30.100,PIRSF_domain:PIRSF006609,SMART_domains:SM00651,Superfamily_domains:SSF50182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCAGAGGTG	.	5	ESCA
CCDC168	0	.	GRCh37	13	103384753	103384753	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4407G>C	p.Met1469Ile	p.M1469I	ENST00000322527	1/1	81	49	32	75	75	0	CCDC168,missense_variant,p.Met1469Ile,ENST00000322527,;	G	ENSG00000175820	ENST00000322527	Transcript	missense_variant	4407	4407	1469	M/I	atG/atC	.	.	.	-1	CCDC168	HGNC	26851	protein_coding	YES	.	ENSP00000320232	CC168_HUMAN	.	UPI0000DD81F0	.	tolerated(0.12)	unknown(0)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCATAGT	.	5	ESCA
BIVM-ERCC5	0	.	GRCh37	13	103483940	103483940	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841C>G	p.%3D	p.T281T	ENST00000602836	6/21	36	19	16	37	37	0	BIVM-ERCC5,synonymous_variant,p.%3D,ENST00000602836,;BIVM,synonymous_variant,p.%3D,ENST00000448849,;BIVM,synonymous_variant,p.%3D,ENST00000257336,;BIVM,intron_variant,,ENST00000419638,;BIVM,non_coding_transcript_exon_variant,,ENST00000490317,;	G	ENSG00000270181	ENST00000602836	Transcript	synonymous_variant	841	843	281	T	acC/acG	.	.	.	1	BIVM-ERCC5	HGNC	43690	protein_coding	YES	.	ENSP00000473384	.	.	UPI0002B83330	.	.	.	6/21	.	hmmpanther:PTHR16171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAACCCGTGG	.	5	ESCA
TUBA3C	0	.	GRCh37	13	19747964	19747964	+	3'UTR	SNP	G	G	T	rs756263503	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39C>A	.	.	ENST00000400113	5/5	48	29	19	50	50	0	TUBA3C,3_prime_UTR_variant,,ENST00000400113,;SMPD4P2,upstream_gene_variant,,ENST00000440167,;	T	ENSG00000198033	ENST00000400113	Transcript	3_prime_UTR_variant	1497	.	.	.	.	rs756263503	.	.	-1	TUBA3C	HGNC	12408	protein_coding	YES	CCDS9284.1	ENSP00000382982	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTGGGGGTG	byFrequency	5	ESCA
UTP14C	0	.	GRCh37	13	52606992	52606992	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1751C>T	.	.	ENST00000521776	2/2	26	17	9	25	25	0	UTP14C,3_prime_UTR_variant,,ENST00000521776,;ALG11,downstream_gene_variant,,ENST00000523764,;ALG11,downstream_gene_variant,,ENST00000521508,;ALG11,downstream_gene_variant,,ENST00000519151,;NEK5,downstream_gene_variant,,ENST00000529080,;NEK5,downstream_gene_variant,,ENST00000465811,;	T	ENSG00000253797	ENST00000521776	Transcript	3_prime_UTR_variant	4785	.	.	.	.	.	.	.	1	UTP14C	HGNC	20321	protein_coding	YES	CCDS31978.1	ENSP00000428619	UT14C_HUMAN	.	UPI000006DB4B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGTCACAAA	.	5	ESCA
VPS36	0	.	GRCh37	13	53001132	53001132	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Glu211Lys	p.E211K	ENST00000378060	8/14	82	47	35	82	82	0	VPS36,missense_variant,p.Glu211Lys,ENST00000378060,;VPS36,non_coding_transcript_exon_variant,,ENST00000492650,;	T	ENSG00000136100	ENST00000378060	Transcript	missense_variant	659	631	211	E/K	Gaa/Aaa	.	.	.	-1	VPS36	HGNC	20312	protein_coding	YES	CCDS9434.1	ENSP00000367299	VPS36_HUMAN	.	UPI000013CFE6	.	deleterious(0.01)	benign(0.127)	8/14	.	hmmpanther:PTHR13128:SF12,hmmpanther:PTHR13128,Pfam_domain:PF04157,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCTGTGA	.	5	ESCA
LMO7	0	.	GRCh37	13	76397973	76397973	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2214G>A	p.%3D	p.G738G	ENST00000465261	12/27	54	37	16	41	41	0	LMO7,synonymous_variant,p.%3D,ENST00000357063,;LMO7,synonymous_variant,p.%3D,ENST00000321797,;LMO7,synonymous_variant,p.%3D,ENST00000526202,;LMO7,synonymous_variant,p.%3D,ENST00000465261,;LMO7,synonymous_variant,p.%3D,ENST00000524651,;LMO7,synonymous_variant,p.%3D,ENST00000341547,;LMO7,synonymous_variant,p.%3D,ENST00000377534,;LMO7,synonymous_variant,p.%3D,ENST00000377499,;LMO7,synonymous_variant,p.%3D,ENST00000447038,;LMO7,downstream_gene_variant,,ENST00000489941,;LMO7,downstream_gene_variant,,ENST00000525373,;LMO7,non_coding_transcript_exon_variant,,ENST00000485987,;LMO7,downstream_gene_variant,,ENST00000532785,;LMO7,downstream_gene_variant,,ENST00000532377,;	A	ENSG00000136153	ENST00000465261	Transcript	synonymous_variant	2974	2214	738	G	ggG/ggA	.	.	.	1	LMO7	HGNC	6646	protein_coding	YES	CCDS53876.1	ENSP00000433352	.	E9PRJ0_HUMAN,E9PLH4_HUMAN	UPI0001929501	.	.	.	12/27	.	Superfamily_domains:SSF50156,hmmpanther:PTHR15551,hmmpanther:PTHR15551:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGGGGAAAT	.	5	ESCA
IGHV3-53	0	.	GRCh37	14	107048753	107048753	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267C>G	p.%3D	p.S89S	ENST00000390627	2/2	268	236	32	188	188	0	IGHV3-53,synonymous_variant,p.%3D,ENST00000390627,;	C	ENSG00000211967	ENST00000390627	Transcript	synonymous_variant	488	267	89	S	tcC/tcG	.	.	.	-1	IGHV3-53	HGNC	5610	IG_V_gene	YES	.	ENSP00000375036	.	.	UPI000011AAC7	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266:SF91,hmmpanther:PTHR23266,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTCTGGAGAT	.	4	ESCA
OR4N2	0	.	GRCh37	14	20296476	20296476	+	Missense_Mutation	SNP	G	G	A	rs770622276	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.869G>A	p.Arg290His	p.R290H	ENST00000315947	1/1	123	67	55	110	110	0	OR4N2,missense_variant,p.Arg290His,ENST00000315947,;OR4N2,3_prime_UTR_variant,,ENST00000568211,;OR4N2,downstream_gene_variant,,ENST00000557677,;OR4N2,downstream_gene_variant,,ENST00000557414,;	A	ENSG00000176294	ENST00000315947	Transcript	missense_variant	869	869	290	R/H	cGc/cAc	rs770622276,COSM954081	.	.	1	OR4N2	HGNC	14742	protein_coding	YES	CCDS32022.1	ENSP00000319601	OR4N2_HUMAN	H3BTD8_HUMAN,G3V4W1_HUMAN,G3V3W5_HUMAN	UPI000004A5DF	.	deleterious(0.02)	benign(0.032)	1/1	.	hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF155,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R290H|c.869G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCGCAACC	byFrequency	5	ESCA
TRAV16	0	.	GRCh37	14	22459118	22459118	+	Missense_Mutation	SNP	C	C	G	rs746743109	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.270C>G	p.His90Gln	p.H90Q	ENST00000390444	2/2	42	23	19	27	27	0	TRAV16,missense_variant,p.His90Gln,ENST00000390444,;	G	ENSG00000211796	ENST00000390444	Transcript	missense_variant	270	270	90	H/Q	caC/caG	rs746743109	.	.	1	TRAV16	HGNC	12112	TR_V_gene	YES	.	ENSP00000451359	.	.	UPI000011C713	.	deleterious(0.02)	benign(0.337)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19367,hmmpanther:PTHR19367:SF4,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCACCTGAA	.	5	ESCA
HAUS4	0	.	GRCh37	14	23415895	23415895	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.931C>G	p.His311Asp	p.H311D	ENST00000206474	10/10	35	22	12	34	34	0	HAUS4,missense_variant,p.His266Asp,ENST00000555986,;HAUS4,missense_variant,p.His311Asp,ENST00000206474,;HAUS4,missense_variant,p.His185Asp,ENST00000397409,;HAUS4,missense_variant,p.His185Asp,ENST00000347758,;HAUS4,missense_variant,p.His187Asp,ENST00000490506,;RP11-298I3.5,missense_variant,p.His141Asp,ENST00000555074,;HAUS4,missense_variant,p.His266Asp,ENST00000555367,;HAUS4,missense_variant,p.His266Asp,ENST00000342454,;HAUS4,missense_variant,p.His311Asp,ENST00000541587,;HAUS4,downstream_gene_variant,,ENST00000554406,;HAUS4,downstream_gene_variant,,ENST00000557591,;HAUS4,downstream_gene_variant,,ENST00000555040,;HAUS4,downstream_gene_variant,,ENST00000554516,;HAUS4,downstream_gene_variant,,ENST00000556915,;HAUS4,downstream_gene_variant,,ENST00000553420,;RP11-298I3.1,intron_variant,,ENST00000548322,;RP11-298I3.1,intron_variant,,ENST00000548819,;HAUS4,non_coding_transcript_exon_variant,,ENST00000554446,;HAUS4,downstream_gene_variant,,ENST00000553794,;HAUS4,downstream_gene_variant,,ENST00000554349,;HAUS4,downstream_gene_variant,,ENST00000554373,;HAUS4,downstream_gene_variant,,ENST00000554651,;HAUS4,3_prime_UTR_variant,,ENST00000553859,;HAUS4,non_coding_transcript_exon_variant,,ENST00000556421,;HAUS4,downstream_gene_variant,,ENST00000554063,;	C	ENSG00000092036	ENST00000206474	Transcript	missense_variant	1184	931	311	H/D	Cac/Gac	.	.	.	-1	HAUS4	HGNC	20163	protein_coding	YES	CCDS9580.1	ENSP00000206474	HAUS4_HUMAN	G3V5A5_HUMAN,G3V541_HUMAN,G3V4X7_HUMAN	UPI000006F422	.	tolerated(0.17)	benign(0.088)	10/10	.	Pfam_domain:PF14735,hmmpanther:PTHR16219,hmmpanther:PTHR16219:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGTGAATGG	.	5	ESCA
MYH6	0	.	GRCh37	14	23865995	23865995	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2200G>A	p.Glu734Lys	p.E734K	ENST00000405093	19/39	70	47	22	82	82	0	MYH6,missense_variant,p.Glu734Lys,ENST00000405093,;MYH6,missense_variant,p.Glu734Lys,ENST00000356287,;MYH6,downstream_gene_variant,,ENST00000557461,;	T	ENSG00000197616	ENST00000405093	Transcript	missense_variant	2271	2200	734	E/K	Gag/Aag	.	.	.	-1	MYH6	HGNC	7576	protein_coding	YES	CCDS9600.1	ENSP00000386041	MYH6_HUMAN	Q9UQV1_HUMAN,A8CLL2_HUMAN	UPI0000160969	.	tolerated(0.23)	possibly_damaging(0.655)	19/39	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF260,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTCAGGGA	.	5	ESCA
KLHDC1	0	.	GRCh37	14	50201373	50201373	+	Missense_Mutation	SNP	G	G	A	rs370596217	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.890G>A	p.Arg297Lys	p.R297K	ENST00000359332	10/13	24	18	6	12	12	0	KLHDC1,missense_variant,p.Arg168Lys,ENST00000557128,;KLHDC1,missense_variant,p.Arg297Lys,ENST00000359332,;KLHDC1,non_coding_transcript_exon_variant,,ENST00000554512,;KLHDC1,3_prime_UTR_variant,,ENST00000556392,;KLHDC1,3_prime_UTR_variant,,ENST00000555704,;	A	ENSG00000197776	ENST00000359332	Transcript	missense_variant	980	890	297	R/K	aGa/aAa	rs370596217	.	.	1	KLHDC1	HGNC	19836	protein_coding	YES	CCDS9692.1	ENSP00000352282	KLDC1_HUMAN	G3V5V5_HUMAN	UPI0000072D4D	.	tolerated(1)	benign(0.003)	10/13	.	Superfamily_domains:0052715,Gene3D:1zgkA00,hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF286	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAAGACCTA	byCluster	5	ESCA
NIN	0	.	GRCh37	14	51239778	51239778	+	Silent	SNP	G	G	A	rs369292594	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.702C>T	p.%3D	p.D234D	ENST00000382041	8/30	65	50	14	36	36	0	NIN,synonymous_variant,p.%3D,ENST00000389868,;NIN,synonymous_variant,p.%3D,ENST00000245441,;NIN,synonymous_variant,p.%3D,ENST00000324330,;NIN,synonymous_variant,p.%3D,ENST00000382041,;NIN,synonymous_variant,p.%3D,ENST00000382043,;NIN,synonymous_variant,p.%3D,ENST00000453196,;NIN,synonymous_variant,p.%3D,ENST00000453401,;NIN,synonymous_variant,p.%3D,ENST00000530997,;NIN,synonymous_variant,p.%3D,ENST00000476352,;NIN,upstream_gene_variant,,ENST00000474937,;	A	ENSG00000100503	ENST00000382041	Transcript	synonymous_variant	893	702	234	D	gaC/gaT	rs369292594	.	.	-1	NIN	HGNC	14906	protein_coding	YES	CCDS32079.1	ENSP00000371472	NIN_HUMAN	H7C162_HUMAN,E9PJH9_HUMAN	UPI0000DBEF14	.	.	.	8/30	.	Superfamily_domains:SSF47473,Gene3D:1.10.238.10,hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF11,PROSITE_profiles:PS50222	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACCGTCAGG	byFrequency|byCluster	5	ESCA
AKAP5	0	.	GRCh37	14	64936794	64936794	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*398C>G	.	.	ENST00000394718	2/2	94	66	28	74	74	0	AKAP5,3_prime_UTR_variant,,ENST00000394718,;ZBTB25,intron_variant,,ENST00000555424,;ZBTB25,intron_variant,,ENST00000555220,;AKAP5,downstream_gene_variant,,ENST00000320636,;	G	ENSG00000179841	ENST00000394718	Transcript	3_prime_UTR_variant	2060	.	.	.	.	.	.	.	1	AKAP5	HGNC	375	protein_coding	YES	CCDS9764.1	ENSP00000378207	AKAP5_HUMAN	.	UPI0000140927	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATCACATT	.	5	ESCA
ADAM20	0	.	GRCh37	14	70990362	70990362	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1263G>T	p.Lys421Asn	p.K421N	ENST00000256389	2/2	72	17	54	48	48	0	ADAM20,missense_variant,p.Lys421Asn,ENST00000256389,;RP11-486O13.4,intron_variant,,ENST00000556646,;	A	ENSG00000134007	ENST00000256389	Transcript	missense_variant	1508	1263	421	K/N	aaG/aaT	.	.	.	-1	ADAM20	HGNC	199	protein_coding	YES	CCDS32111.1	ENSP00000256389	ADA20_HUMAN	.	UPI0000183495	.	tolerated(0.53)	benign(0.001)	2/2	.	PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF133,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCACCTTTCT	.	5	ESCA
FLRT2	0	.	GRCh37	14	86092741	86092741	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2900C>T	.	.	ENST00000330753	2/2	44	35	9	28	28	0	FLRT2,3_prime_UTR_variant,,ENST00000330753,;FLRT2,downstream_gene_variant,,ENST00000554746,;FLRT2,downstream_gene_variant,,ENST00000553650,;	T	ENSG00000185070	ENST00000330753	Transcript	3_prime_UTR_variant	5650	.	.	.	.	.	.	.	1	FLRT2	HGNC	3761	protein_coding	YES	CCDS9877.1	ENSP00000332879	FLRT2_HUMAN	B4DM15_HUMAN	UPI0000049E10	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTCACTGG	.	5	ESCA
TTC7B	0	.	GRCh37	14	91110514	91110514	+	Missense_Mutation	SNP	C	C	A	rs756471648	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1629G>T	p.Gln543His	p.Q543H	ENST00000328459	15/20	58	26	32	45	45	0	TTC7B,missense_variant,p.Gln13His,ENST00000553972,;TTC7B,missense_variant,p.Gln543His,ENST00000328459,;TTC7B,missense_variant,p.Gln543His,ENST00000357056,;RP11-1078H9.5,intron_variant,,ENST00000557007,;RP11-1078H9.5,intron_variant,,ENST00000553826,;TTC7B,non_coding_transcript_exon_variant,,ENST00000554654,;TTC7B,non_coding_transcript_exon_variant,,ENST00000556490,;TTC7B,missense_variant,p.Ala103Ser,ENST00000555239,;TTC7B,missense_variant,p.Gln284His,ENST00000555005,;TTC7B,downstream_gene_variant,,ENST00000556749,;	A	ENSG00000165914	ENST00000328459	Transcript	missense_variant	1751	1629	543	Q/H	caG/caT	rs756471648	.	.	-1	TTC7B	HGNC	19858	protein_coding	YES	CCDS32140.1	ENSP00000336127	TTC7B_HUMAN	G3V3E4_HUMAN,B3KX34_HUMAN	UPI00001FD9F0	.	tolerated(0.12)	possibly_damaging(0.885)	15/20	.	Superfamily_domains:SSF48452,SMART_domains:SM00028,Gene3D:1.25.40.10,hmmpanther:PTHR23083:SF365,hmmpanther:PTHR23083,PROSITE_profiles:PS50293,PROSITE_profiles:PS50005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAGCTGAAG	byFrequency	5	ESCA
PPP1R14D	0	.	GRCh37	15	41108162	41108162	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486G>A	p.%3D	p.Q162Q	ENST00000427255	4/5	39	22	16	33	33	0	PPP1R14D,missense_variant,p.Glu124Lys,ENST00000299174,;PPP1R14D,synonymous_variant,p.%3D,ENST00000427255,;ZFYVE19,downstream_gene_variant,,ENST00000561617,;ZFYVE19,downstream_gene_variant,,ENST00000570108,;ZFYVE19,downstream_gene_variant,,ENST00000566407,;ZFYVE19,downstream_gene_variant,,ENST00000564258,;ZFYVE19,downstream_gene_variant,,ENST00000355341,;ZFYVE19,downstream_gene_variant,,ENST00000336455,;ZFYVE19,downstream_gene_variant,,ENST00000299173,;ZFYVE19,downstream_gene_variant,,ENST00000570162,;ZFYVE19,downstream_gene_variant,,ENST00000563497,;ZFYVE19,downstream_gene_variant,,ENST00000560078,;ZFYVE19,downstream_gene_variant,,ENST00000569057,;ZFYVE19,downstream_gene_variant,,ENST00000561768,;	T	ENSG00000166143	ENST00000427255	Transcript	synonymous_variant	554	486	162	Q	caG/caA	.	.	.	-1	PPP1R14D	HGNC	14953	protein_coding	YES	CCDS45230.1	ENSP00000398342	.	E9PAT1_HUMAN	UPI0000E59BD7	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCTGTGG	.	5	ESCA
CDAN1	0	.	GRCh37	15	43029216	43029216	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85T>G	p.Ser29Ala	p.S29A	ENST00000356231	1/28	55	20	35	61	61	0	CDAN1,missense_variant,p.Ser29Ala,ENST00000356231,;CDAN1,missense_variant,p.Ser13Ala,ENST00000563260,;TTBK2,downstream_gene_variant,,ENST00000267890,;CTD-2036P10.3,upstream_gene_variant,,ENST00000567456,;CTD-2036P10.3,upstream_gene_variant,,ENST00000500850,;	C	ENSG00000140326	ENST00000356231	Transcript	missense_variant	109	85	29	S/A	Tcg/Gcg	.	.	.	-1	CDAN1	HGNC	1713	protein_coding	YES	CCDS32209.1	ENSP00000348564	CDAN1_HUMAN	H3BM60_HUMAN	UPI0000229BCB	.	tolerated(0.5)	benign(0.268)	1/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCGAACCCT	.	5	ESCA
CTDSPL2	0	.	GRCh37	15	44792002	44792002	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.960C>A	p.%3D	p.V320V	ENST00000260327	8/13	17	13	3	17	17	0	CTDSPL2,synonymous_variant,p.%3D,ENST00000396780,;CTDSPL2,synonymous_variant,p.%3D,ENST00000558373,;CTDSPL2,synonymous_variant,p.%3D,ENST00000558966,;CTDSPL2,synonymous_variant,p.%3D,ENST00000260327,;CTDSPL2,non_coding_transcript_exon_variant,,ENST00000561189,;CTDSPL2,synonymous_variant,p.%3D,ENST00000560620,;	A	ENSG00000137770	ENST00000260327	Transcript	synonymous_variant	1523	960	320	V	gtC/gtA	.	.	.	1	CTDSPL2	HGNC	26936	protein_coding	YES	CCDS10110.1	ENSP00000260327	CTSL2_HUMAN	H0YNW9_HUMAN,H0YNU2_HUMAN,H0YMH7_HUMAN	UPI000004A0B3	.	.	.	8/13	.	PROSITE_profiles:PS50969,hmmpanther:PTHR12210,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR02251,Pfam_domain:PF03031,SMART_domains:SM00577,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGTCATTTA	.	5	ESCA
SLC12A1	0	.	GRCh37	15	48577319	48577319	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2502A>T	p.Leu834Phe	p.L834F	ENST00000396577	21/27	43	10	32	49	49	0	SLC12A1,missense_variant,p.Leu834Phe,ENST00000558405,;SLC12A1,missense_variant,p.Leu834Phe,ENST00000396577,;SLC12A1,missense_variant,p.Leu647Phe,ENST00000559641,;SLC12A1,missense_variant,p.Leu834Phe,ENST00000380993,;SLC12A1,non_coding_transcript_exon_variant,,ENST00000560692,;SLC12A1,non_coding_transcript_exon_variant,,ENST00000558252,;	T	ENSG00000074803	ENST00000396577	Transcript	missense_variant	2717	2502	834	L/F	ttA/ttT	.	.	.	1	SLC12A1	HGNC	10910	protein_coding	YES	CCDS53940.1	ENSP00000379822	.	O76030_HUMAN,E9PDW4_HUMAN	UPI000013C794	.	tolerated(0.71)	possibly_damaging(0.809)	21/27	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF45,TIGRFAM_domain:TIGR00930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTAGAACA	.	5	ESCA
USP3	0	.	GRCh37	15	63866552	63866552	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1046G>C	p.Arg349Thr	p.R349T	ENST00000380324	11/15	39	30	9	28	28	0	USP3,missense_variant,p.Arg349Thr,ENST00000380324,;USP3,missense_variant,p.Arg332Thr,ENST00000558285,;USP3,missense_variant,p.Arg305Thr,ENST00000540797,;USP3,missense_variant,p.Arg100Thr,ENST00000539772,;USP3,missense_variant,p.Arg260Thr,ENST00000559711,;USP3,missense_variant,p.Arg327Thr,ENST00000268049,;USP3,3_prime_UTR_variant,,ENST00000536001,;USP3-AS1,intron_variant,,ENST00000559357,;USP3-AS1,intron_variant,,ENST00000560350,;USP3-AS1,intron_variant,,ENST00000559861,;USP3,downstream_gene_variant,,ENST00000561326,;USP3,missense_variant,p.Arg272Thr,ENST00000559257,;USP3,3_prime_UTR_variant,,ENST00000559873,;USP3,3_prime_UTR_variant,,ENST00000538686,;USP3,3_prime_UTR_variant,,ENST00000559192,;USP3,3_prime_UTR_variant,,ENST00000558157,;	C	ENSG00000140455	ENST00000380324	Transcript	missense_variant	1175	1046	349	R/T	aGa/aCa	.	.	.	1	USP3	HGNC	12626	protein_coding	YES	CCDS32265.1	ENSP00000369681	UBP3_HUMAN	Q9Y2R8_HUMAN,H0YM72_HUMAN,B4DWJ6_HUMAN	UPI0000071F2D	.	tolerated(0.42)	probably_damaging(0.935)	11/15	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF356,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCAGAAGTA	.	5	ESCA
AKAP13	0	.	GRCh37	15	86269664	86269664	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6781G>A	p.Asp2261Asn	p.D2261N	ENST00000361243	27/37	48	29	18	46	46	0	AKAP13,missense_variant,p.Asp2257Asn,ENST00000394518,;AKAP13,missense_variant,p.Asp2261Asn,ENST00000361243,;AKAP13,missense_variant,p.Asp502Asn,ENST00000394510,;RP11-158M2.2,non_coding_transcript_exon_variant,,ENST00000561417,;AKAP13,non_coding_transcript_exon_variant,,ENST00000560676,;AKAP13,non_coding_transcript_exon_variant,,ENST00000560579,;AKAP13,non_coding_transcript_exon_variant,,ENST00000558644,;AKAP13,downstream_gene_variant,,ENST00000558009,;	A	ENSG00000170776	ENST00000361243	Transcript	missense_variant	6862	6781	2261	D/N	Gac/Aac	.	.	.	1	AKAP13	HGNC	371	protein_coding	YES	CCDS32320.1	ENSP00000354718	AKP13_HUMAN	H0YMI5_HUMAN,A8MYJ1_HUMAN	UPI00001A8BEB	.	deleterious(0)	probably_damaging(0.989)	27/37	.	PROSITE_profiles:PS50003,hmmpanther:PTHR13944:SF4,hmmpanther:PTHR13944,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTGACATT	.	5	ESCA
TICRR	0	.	GRCh37	15	90163009	90163009	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3090T>C	p.%3D	p.Y1030Y	ENST00000268138	18/22	75	40	35	53	53	0	TICRR,synonymous_variant,p.%3D,ENST00000560985,;TICRR,synonymous_variant,p.%3D,ENST00000268138,;KIF7,intron_variant,,ENST00000558928,;	C	ENSG00000140534	ENST00000268138	Transcript	synonymous_variant	3195	3090	1030	Y	taT/taC	.	.	.	1	TICRR	HGNC	28704	protein_coding	YES	CCDS10352.2	ENSP00000268138	TICRR_HUMAN	.	UPI0000D61399	.	.	.	18/22	.	hmmpanther:PTHR21556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTATTCTGT	.	5	ESCA
IL4R	0	.	GRCh37	16	27357918	27357918	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.492G>C	p.Trp164Cys	p.W164C	ENST00000395762	6/11	51	34	16	68	68	0	IL4R,missense_variant,p.Trp164Cys,ENST00000395762,;IL4R,missense_variant,p.Trp149Cys,ENST00000380922,;IL4R,missense_variant,p.Trp164Cys,ENST00000543915,;IL4R,missense_variant,p.Trp164Cys,ENST00000449195,;IL4R,missense_variant,p.Trp164Cys,ENST00000170630,;IL4R,downstream_gene_variant,,ENST00000562968,;IL4R,downstream_gene_variant,,ENST00000562142,;IL4R,downstream_gene_variant,,ENST00000566117,;IL4R,downstream_gene_variant,,ENST00000563002,;IL4R,3_prime_UTR_variant,,ENST00000568746,;IL4R,non_coding_transcript_exon_variant,,ENST00000565696,;IL4R,intron_variant,,ENST00000566318,;IL4R,downstream_gene_variant,,ENST00000563787,;IL4R,downstream_gene_variant,,ENST00000561946,;IL4R,downstream_gene_variant,,ENST00000563926,;	C	ENSG00000077238	ENST00000395762	Transcript	missense_variant	751	492	164	W/C	tgG/tgC	.	.	.	1	IL4R	HGNC	6015	protein_coding	YES	CCDS10629.1	ENSP00000379111	IL4RA_HUMAN	J9JII2_HUMAN,H3BTD9_HUMAN,A1Z2K8_HUMAN	UPI0000044371	.	deleterious(0.01)	possibly_damaging(0.582)	6/11	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF24,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTGGAGTGA	.	5	ESCA
PRSS21	0	.	GRCh37	16	2871496	2871496	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835G>C	p.Glu279Gln	p.E279Q	ENST00000005995	6/6	74	60	14	84	84	0	PRSS21,missense_variant,p.Glu279Gln,ENST00000005995,;PRSS21,missense_variant,p.Glu221Gln,ENST00000574265,;PRSS21,missense_variant,p.Glu265Gln,ENST00000450020,;PRSS21,missense_variant,p.Glu277Gln,ENST00000455114,;PRSS21,3_prime_UTR_variant,,ENST00000574813,;PRSS21,intron_variant,,ENST00000575739,;PRSS21,downstream_gene_variant,,ENST00000571141,;PRSS21,downstream_gene_variant,,ENST00000575199,;PRSS21,downstream_gene_variant,,ENST00000577043,;PRSS21,downstream_gene_variant,,ENST00000570629,;PRSS21,downstream_gene_variant,,ENST00000570594,;LA16c-352F10.1,downstream_gene_variant,,ENST00000572664,;	C	ENSG00000007038	ENST00000005995	Transcript	missense_variant	877	835	279	E/Q	Gag/Cag	.	.	.	1	PRSS21	HGNC	9485	protein_coding	YES	CCDS10478.1	ENSP00000005995	TEST_HUMAN	.	UPI000004813E	.	tolerated(0.43)	benign(0.026)	6/6	.	Superfamily_domains:SSF50494,SMART_domains:SM00020,Gene3D:2.40.10.10,Pfam_domain:PF00089,hmmpanther:PTHR24256:SF99,hmmpanther:PTHR24256,PROSITE_profiles:PS50240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACTTTGAGTGG	.	3	ESCA
SEPHS2	0	.	GRCh37	16	30456364	30456364	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.685G>C	p.Val229Leu	p.V229L	ENST00000500504	1/1	56	34	22	59	59	0	SEPHS2,missense_variant,p.Val229Leu,ENST00000500504,;SEPHS2,missense_variant,p.Val229Leu,ENST00000478753,;SEPHS2,missense_variant,p.Val172Leu,ENST00000542752,;	G	ENSG00000179918	ENST00000500504	Transcript	missense_variant	685	685	229	V/L	Gta/Cta	.	.	.	-1	SEPHS2	HGNC	19686	protein_coding	YES	CCDS42150.1	ENSP00000426234	SPS2_HUMAN	B4E093_HUMAN	UPI00001678A0	.	.	benign(0.067)	1/1	.	Superfamily_domains:SSF55326,TIGRFAM_domain:TIGR00476,hmmpanther:PTHR10256:SF1,hmmpanther:PTHR10256	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTACAGTGG	.	5	ESCA
RP11-196G11.1	0	.	GRCh37	16	31098169	31098169	+	3'Flank	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000529564	.	46	29	17	40	40	0	RP11-196G11.1,missense_variant,p.Gln75Pro,ENST00000532364,;PRSS53,missense_variant,p.Gln98Pro,ENST00000280606,;VKORC1,downstream_gene_variant,,ENST00000394975,;VKORC1,downstream_gene_variant,,ENST00000420057,;RP11-196G11.1,downstream_gene_variant,,ENST00000529564,;VKORC1,downstream_gene_variant,,ENST00000498155,;VKORC1,downstream_gene_variant,,ENST00000319788,;ZNF646,downstream_gene_variant,,ENST00000394979,;VKORC1,downstream_gene_variant,,ENST00000394971,;VKORC1,downstream_gene_variant,,ENST00000354895,;ZNF646,downstream_gene_variant,,ENST00000300850,;VKORC1,downstream_gene_variant,,ENST00000300851,;VKORC1,downstream_gene_variant,,ENST00000472468,;RP11-196G11.1,3_prime_UTR_variant,,ENST00000533518,;PRSS53,non_coding_transcript_exon_variant,,ENST00000486499,;PRSS53,non_coding_transcript_exon_variant,,ENST00000492427,;	G	ENSG00000255439	ENST00000529564	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	20	-1	RP11-196G11.1	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000431371	.	E9PLN8_HUMAN	UPI0001F782E8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGCTGCAGA	.	5	ESCA
SLC6A10P	0	.	GRCh37	16	32888910	32888910	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3726C>T	.	.	ENST00000330048	9/9	123	101	22	168	168	0	SLC6A10P,non_coding_transcript_exon_variant,,ENST00000330048,;SLC6A10P,downstream_gene_variant,,ENST00000431994,;	A	ENSG00000214617	ENST00000330048	Transcript	non_coding_transcript_exon_variant	3726	.	.	.	.	.	.	.	-1	SLC6A10P	HGNC	11043	processed_transcript	YES	.	.	.	.	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGGTGTCAGG	.	4	ESCA
TIGD7	0	.	GRCh37	16	3348998	3348998	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1617C>T	p.%3D	p.F539F	ENST00000396862	2/2	58	24	33	44	44	0	TIGD7,synonymous_variant,p.%3D,ENST00000268674,;TIGD7,synonymous_variant,p.%3D,ENST00000396862,;ZNF263,intron_variant,,ENST00000574674,;ZNF263,intron_variant,,ENST00000575332,;TIGD7,downstream_gene_variant,,ENST00000573608,;TIGD7,downstream_gene_variant,,ENST00000570634,;TIGD7,downstream_gene_variant,,ENST00000573695,;TIGD7,downstream_gene_variant,,ENST00000576104,;TIGD7,downstream_gene_variant,,ENST00000571748,;TIGD7,downstream_gene_variant,,ENST00000572297,;TIGD7,downstream_gene_variant,,ENST00000574598,;	A	ENSG00000140993	ENST00000396862	Transcript	synonymous_variant	3446	1617	539	F	ttC/ttT	.	.	.	-1	TIGD7	HGNC	18331	protein_coding	YES	CCDS10500.1	ENSP00000380071	TIGD7_HUMAN	I3L2A8_HUMAN	UPI0000072536	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTGAAGGA	.	5	ESCA
C16orf96	0	.	GRCh37	16	4625340	4625340	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.859G>C	p.Glu287Gln	p.E287Q	ENST00000444310	5/16	57	44	12	44	44	0	C16orf96,missense_variant,p.Glu287Gln,ENST00000444310,;	C	ENSG00000205832	ENST00000444310	Transcript	missense_variant	859	859	287	E/Q	Gag/Cag	.	.	.	1	C16orf96	HGNC	40031	protein_coding	YES	CCDS53986.1	ENSP00000415027	CP096_HUMAN	.	UPI0001929538	.	tolerated(0.43)	possibly_damaging(0.622)	5/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCCAGAGCTC	.	3	ESCA
PPL	0	.	GRCh37	16	4942146	4942146	+	Missense_Mutation	SNP	G	G	C	rs778557169	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1719C>G	p.Phe573Leu	p.F573L	ENST00000345988	15/22	64	45	18	54	54	0	PPL,missense_variant,p.Phe571Leu,ENST00000590782,;PPL,missense_variant,p.Phe573Leu,ENST00000345988,;PPL,intron_variant,,ENST00000592772,;PPL,non_coding_transcript_exon_variant,,ENST00000590093,;PPL,upstream_gene_variant,,ENST00000589090,;PPL,downstream_gene_variant,,ENST00000588556,;	C	ENSG00000118898	ENST00000345988	Transcript	missense_variant	1809	1719	573	F/L	ttC/ttG	rs778557169	.	.	-1	PPL	HGNC	9273	protein_coding	YES	CCDS10526.1	ENSP00000340510	PEPL_HUMAN	.	UPI00001AE832	.	deleterious(0.04)	probably_damaging(0.998)	15/22	.	hmmpanther:PTHR23169,SMART_domains:SM00150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGGATGAAGGC	.	3	ESCA
GINS3	0	.	GRCh37	16	58438692	58438692	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*59G>C	.	.	ENST00000426538	4/4	17	10	7	13	13	0	GINS3,3_prime_UTR_variant,,ENST00000328514,;GINS3,3_prime_UTR_variant,,ENST00000426538,;GINS3,3_prime_UTR_variant,,ENST00000318129,;GINS3,non_coding_transcript_exon_variant,,ENST00000567143,;	C	ENSG00000181938	ENST00000426538	Transcript	3_prime_UTR_variant	1035	.	.	.	.	.	.	.	1	GINS3	HGNC	25851	protein_coding	YES	CCDS45498.1	ENSP00000401018	PSF3_HUMAN	.	UPI00001FF2F1	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATAGGAGCT	.	5	ESCA
TANGO6	0	.	GRCh37	16	68900993	68900993	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864T>C	p.%3D	p.D288D	ENST00000261778	4/18	73	34	38	48	48	0	TANGO6,synonymous_variant,p.%3D,ENST00000261778,;TANGO6,non_coding_transcript_exon_variant,,ENST00000564180,;TANGO6,downstream_gene_variant,,ENST00000561566,;	C	ENSG00000103047	ENST00000261778	Transcript	synonymous_variant	876	864	288	D	gaT/gaC	.	.	.	1	TANGO6	HGNC	25749	protein_coding	YES	CCDS45516.1	ENSP00000261778	TNG6_HUMAN	B3KTB6_HUMAN	UPI00001FF4A8	.	.	.	4/18	.	hmmpanther:PTHR20959:SF1,hmmpanther:PTHR20959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGATGTGAA	.	5	ESCA
ADAD2	0	.	GRCh37	16	84228699	84228699	+	Missense_Mutation	SNP	G	G	A	rs568492054	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.848G>A	p.Arg283His	p.R283H	ENST00000268624	5/11	107	93	13	94	94	0	ADAD2,missense_variant,p.Arg211His,ENST00000315906,;ADAD2,missense_variant,p.Arg120His,ENST00000567685,;ADAD2,missense_variant,p.Arg283His,ENST00000268624,;RP11-486L19.2,non_coding_transcript_exon_variant,,ENST00000569834,;RP11-486L19.2,non_coding_transcript_exon_variant,,ENST00000565643,;RP11-486L19.2,non_coding_transcript_exon_variant,,ENST00000536986,;RP11-486L19.2,upstream_gene_variant,,ENST00000561900,;ADAD2,downstream_gene_variant,,ENST00000567413,;ADAD2,non_coding_transcript_exon_variant,,ENST00000566526,;ADAD2,non_coding_transcript_exon_variant,,ENST00000564169,;ADAD2,non_coding_transcript_exon_variant,,ENST00000564430,;ADAD2,upstream_gene_variant,,ENST00000563849,;ADAD2,downstream_gene_variant,,ENST00000569221,;	A	ENSG00000140955	ENST00000268624	Transcript	missense_variant	941	848	283	R/H	cGc/cAc	rs568492054,COSM3378005	.	.	1	ADAD2	HGNC	30714	protein_coding	YES	CCDS10944.1	ENSP00000268624	ADAD2_HUMAN	D3DUL6_HUMAN	UPI000013D7CA	.	tolerated(0.12)	possibly_damaging(0.596)	5/11	.	hmmpanther:PTHR10910:SF83,hmmpanther:PTHR10910,SMART_domains:SM00552	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R283H|c.848G>A|4	RADIA|MUTECT|MUSE|VARSCANS	GCAGCGCTGCG	by1000G	4	ESCA
ZNF469	0	.	GRCh37	16	88495087	88495087	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209G>C	p.Gln403His	p.Q403H	ENST00000437464	1/2	61	43	17	56	56	0	ZNF469,missense_variant,p.Gln403His,ENST00000565624,;ZNF469,missense_variant,p.Gln403His,ENST00000437464,;	C	ENSG00000225614	ENST00000437464	Transcript	missense_variant	1209	1209	403	Q/H	caG/caC	.	.	.	1	ZNF469	HGNC	23216	protein_coding	YES	CCDS45544.1	ENSP00000402343	ZN469_HUMAN	.	UPI0000DD837B	.	.	benign(0.265)	1/2	.	hmmpanther:PTHR21465,hmmpanther:PTHR21465:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCAGAGGCA	.	5	ESCA
TCF25	0	.	GRCh37	16	89952360	89952360	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534C>G	p.%3D	p.L178L	ENST00000263346	4/18	81	53	28	56	56	0	TCF25,synonymous_variant,p.%3D,ENST00000565404,;TCF25,synonymous_variant,p.%3D,ENST00000568412,;TCF25,synonymous_variant,p.%3D,ENST00000565196,;TCF25,synonymous_variant,p.%3D,ENST00000562256,;TCF25,synonymous_variant,p.%3D,ENST00000263346,;TCF25,synonymous_variant,p.%3D,ENST00000561958,;TCF25,5_prime_UTR_variant,,ENST00000263347,;TCF25,upstream_gene_variant,,ENST00000568409,;TCF25,non_coding_transcript_exon_variant,,ENST00000566751,;TCF25,downstream_gene_variant,,ENST00000563406,;TCF25,3_prime_UTR_variant,,ENST00000564652,;TCF25,downstream_gene_variant,,ENST00000561585,;	G	ENSG00000141002	ENST00000263346	Transcript	synonymous_variant	590	534	178	L	ctC/ctG	.	.	.	1	TCF25	HGNC	29181	protein_coding	YES	CCDS10987.1	ENSP00000263346	TCF25_HUMAN	.	UPI000012A80B	.	.	.	4/18	.	hmmpanther:PTHR22684:SF0,hmmpanther:PTHR22684	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTTCTCTACGT	.	3	ESCA
DNAH9	0	.	GRCh37	17	11659960	11659960	+	Missense_Mutation	SNP	C	C	G	rs139421775	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6814C>G	p.Arg2272Gly	p.R2272G	ENST00000262442	34/69	51	18	32	45	45	0	DNAH9,missense_variant,p.Arg2272Gly,ENST00000454412,;DNAH9,missense_variant,p.Arg2272Gly,ENST00000262442,;	G	ENSG00000007174	ENST00000262442	Transcript	missense_variant	6882	6814	2272	R/G	Cgc/Ggc	rs139421775,COSM1238700	.	.	1	DNAH9	HGNC	2953	protein_coding	YES	CCDS11160.1	ENSP00000262442	DYH9_HUMAN	Q92865_HUMAN	UPI0000141BA2	.	.	possibly_damaging(0.72)	34/69	.	hmmpanther:PTHR10676:SF36,hmmpanther:PTHR10676,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGCGCACA	byCluster	5	ESCA
NCOR1	0	.	GRCh37	17	16004598	16004598	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2656G>A	p.Asp886Asn	p.D886N	ENST00000268712	20/46	78	47	31	81	81	0	NCOR1,missense_variant,p.Asp793Asn,ENST00000395848,;NCOR1,missense_variant,p.Asp902Asn,ENST00000395851,;NCOR1,missense_variant,p.Asp886Asn,ENST00000268712,;RNU6-314P,downstream_gene_variant,,ENST00000516574,;NCOR1,downstream_gene_variant,,ENST00000583226,;	T	ENSG00000141027	ENST00000268712	Transcript	missense_variant	2914	2656	886	D/N	Gat/Aat	.	.	.	-1	NCOR1	HGNC	7672	protein_coding	YES	CCDS11175.1	ENSP00000268712	NCOR1_HUMAN	Q9NSZ0_HUMAN,C9JAP0_HUMAN,B4DJ25_HUMAN	UPI000013D7D5	.	.	possibly_damaging(0.905)	20/46	.	hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCAGCGC	.	5	ESCA
RPA1	0	.	GRCh37	17	1800569	1800569	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*100G>A	.	.	ENST00000254719	17/17	9	4	5	14	14	0	RPA1,3_prime_UTR_variant,,ENST00000254719,;RPA1,3_prime_UTR_variant,,ENST00000574049,;RPA1,non_coding_transcript_exon_variant,,ENST00000573994,;	A	ENSG00000132383	ENST00000254719	Transcript	3_prime_UTR_variant	2061	.	.	.	.	.	.	.	1	RPA1	HGNC	10289	protein_coding	YES	CCDS11014.1	ENSP00000254719	RFA1_HUMAN	I3L524_HUMAN,I3L2M5_HUMAN	UPI000013379A	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCAGAGGCT	.	2	ESCA
LIG3	0	.	GRCh37	17	33318128	33318128	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1036G>A	p.Glu346Lys	p.E346K	ENST00000378526	5/20	31	23	8	34	34	0	LIG3,missense_variant,p.Glu75Lys,ENST00000585740,;LIG3,missense_variant,p.Glu346Lys,ENST00000378526,;LIG3,missense_variant,p.Glu346Lys,ENST00000262327,;LIG3,missense_variant,p.Glu355Lys,ENST00000585941,;LIG3,downstream_gene_variant,,ENST00000592690,;LIG3,downstream_gene_variant,,ENST00000586407,;LIG3,non_coding_transcript_exon_variant,,ENST00000586435,;LIG3,upstream_gene_variant,,ENST00000588713,;LIG3,downstream_gene_variant,,ENST00000588109,;LIG3,downstream_gene_variant,,ENST00000590181,;LIG3,upstream_gene_variant,,ENST00000590630,;LIG3,upstream_gene_variant,,ENST00000586058,;	A	ENSG00000005156	ENST00000378526	Transcript	missense_variant	1169	1036	346	E/K	Gag/Aag	.	.	.	1	LIG3	HGNC	6600	protein_coding	YES	CCDS11284.2	ENSP00000367787	DNLI3_HUMAN	E5KLB5_HUMAN,K7EQB6_HUMAN,K7ENR9_HUMAN,C4B7Q3_HUMAN,B7Z6I3_HUMAN	UPI0000350B71	.	deleterious(0.03)	possibly_damaging(0.9)	5/20	.	hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF11,Gene3D:1x9nA01,TIGRFAM_domain:TIGR00574,Pfam_domain:PF04675,Superfamily_domains:0050884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTAGAGCAG	.	5	ESCA
PEX12	0	.	GRCh37	17	33905081	33905081	+	5'UTR	SNP	C	C	G	rs368400940	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-41G>C	.	.	ENST00000225873	1/3	45	23	22	52	52	0	PEX12,5_prime_UTR_variant,,ENST00000225873,;AP2B1,5_prime_UTR_variant,,ENST00000589774,;PEX12,5_prime_UTR_variant,,ENST00000585380,;RP11-1094M14.11,downstream_gene_variant,,ENST00000592381,;SNORD7,downstream_gene_variant,,ENST00000384567,;PEX12,5_prime_UTR_variant,,ENST00000586663,;	G	ENSG00000108733	ENST00000225873	Transcript	5_prime_UTR_variant	568	.	.	.	.	rs368400940	.	.	-1	PEX12	HGNC	8854	protein_coding	YES	CCDS11296.1	ENSP00000225873	PEX12_HUMAN	K7ELY8_HUMAN	UPI0000131703	.	.	.	1/3	.	.	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTCTCTCG	byCluster	5	ESCA
GGNBP2	0	.	GRCh37	17	34916662	34916662	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.478A>T	p.Lys160Ter	p.K160*	ENST00000304718	5/14	47	11	35	60	60	0	GGNBP2,stop_gained,p.Lys160Ter,ENST00000304718,;GGNBP2,downstream_gene_variant,,ENST00000593016,;GGNBP2,non_coding_transcript_exon_variant,,ENST00000486208,;GGNBP2,non_coding_transcript_exon_variant,,ENST00000495023,;	T	ENSG00000005955	ENST00000304718	Transcript	stop_gained	794	478	160	K/*	Aag/Tag	.	.	.	1	GGNBP2	HGNC	19357	protein_coding	YES	CCDS11314.1	ENSP00000307617	GGNB2_HUMAN	K7ELA8_HUMAN,B4DWN7_HUMAN	UPI00000728CB	.	.	.	5/14	.	hmmpanther:PTHR13601	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGAATAAGAGA	.	3	ESCA
GGNBP2	0	.	GRCh37	17	34916664	34916664	+	Missense_Mutation	SNP	G	G	T	rs527456793	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.480G>T	p.Lys160Asn	p.K160N	ENST00000304718	5/14	47	11	35	58	58	0	GGNBP2,missense_variant,p.Lys160Asn,ENST00000304718,;GGNBP2,downstream_gene_variant,,ENST00000593016,;GGNBP2,non_coding_transcript_exon_variant,,ENST00000486208,;GGNBP2,non_coding_transcript_exon_variant,,ENST00000495023,;	T	ENSG00000005955	ENST00000304718	Transcript	missense_variant	796	480	160	K/N	aaG/aaT	rs527456793	.	.	1	GGNBP2	HGNC	19357	protein_coding	YES	CCDS11314.1	ENSP00000307617	GGNB2_HUMAN	K7ELA8_HUMAN,B4DWN7_HUMAN	UPI00000728CB	.	deleterious(0.04)	benign(0.028)	5/14	.	hmmpanther:PTHR13601	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AATAAGAGATG	by1000G	3	ESCA
ARHGAP23	0	.	GRCh37	17	36633860	36633860	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2159C>T	p.Ala720Val	p.A720V	ENST00000431231	12/24	49	28	21	52	52	0	ARHGAP23,missense_variant,p.Ala720Val,ENST00000431231,;ARHGAP23,missense_variant,p.Ala626Val,ENST00000443378,;ARHGAP23,missense_variant,p.Ala720Val,ENST00000437668,;ARHGAP23,intron_variant,,ENST00000581782,;ARHGAP23,missense_variant,p.Ala100Val,ENST00000548333,;ARHGAP23,upstream_gene_variant,,ENST00000578665,;	T	ENSG00000225485	ENST00000431231	Transcript	missense_variant	2227	2159	720	A/V	gCc/gTc	.	.	.	1	ARHGAP23	HGNC	29293	protein_coding	YES	CCDS56027.1	ENSP00000393539	RHG23_HUMAN	H0YHF3_HUMAN,F8W040_HUMAN,C9JVU9_HUMAN	UPI0000F3BE51	.	tolerated(0.33)	possibly_damaging(0.622)	12/24	.	PROSITE_profiles:PS50003,hmmpanther:PTHR23175,hmmpanther:PTHR23175:SF5,Pfam_domain:PF15410,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACGCCGCGC	.	5	ESCA
ANKFY1	0	.	GRCh37	17	4068170	4068170	+	3'Flank	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000570535	.	29	21	7	45	45	0	ANKFY1,3_prime_UTR_variant,,ENST00000341657,;CYB5D2,intron_variant,,ENST00000573984,;ANKFY1,downstream_gene_variant,,ENST00000574367,;ANKFY1,downstream_gene_variant,,ENST00000570535,;RP11-810M2.2,downstream_gene_variant,,ENST00000573371,;ANKFY1,downstream_gene_variant,,ENST00000572412,;ANKFY1,downstream_gene_variant,,ENST00000575298,;	C	ENSG00000185722	ENST00000570535	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	198	-1	ANKFY1	HGNC	20763	protein_coding	YES	CCDS58502.1	ENSP00000459943	ANFY1_HUMAN	I3L1Z9_HUMAN	UPI00003FECB0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTAGAGGAC	.	5	ESCA
ANKFY1	0	.	GRCh37	17	4069759	4069759	+	3'UTR	SNP	G	G	C	rs558820775	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1314C>G	.	.	ENST00000570535	25/25	42	25	16	50	50	0	ANKFY1,3_prime_UTR_variant,,ENST00000574367,;ANKFY1,3_prime_UTR_variant,,ENST00000341657,;ANKFY1,3_prime_UTR_variant,,ENST00000570535,;CYB5D2,intron_variant,,ENST00000573984,;RP11-810M2.2,downstream_gene_variant,,ENST00000573371,;ANKFY1,downstream_gene_variant,,ENST00000572412,;ANKFY1,downstream_gene_variant,,ENST00000575298,;	C	ENSG00000185722	ENST00000570535	Transcript	3_prime_UTR_variant	5067	.	.	.	.	rs558820775	.	.	-1	ANKFY1	HGNC	20763	protein_coding	YES	CCDS58502.1	ENSP00000459943	ANFY1_HUMAN	I3L1Z9_HUMAN	UPI00003FECB0	.	.	.	25/25	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATGTGCAT	by1000G	5	ESCA
ANKFY1	0	.	GRCh37	17	4070194	4070194	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*879C>G	.	.	ENST00000570535	25/25	21	16	5	12	12	0	ANKFY1,3_prime_UTR_variant,,ENST00000574367,;ANKFY1,3_prime_UTR_variant,,ENST00000341657,;ANKFY1,3_prime_UTR_variant,,ENST00000570535,;CYB5D2,intron_variant,,ENST00000573984,;RP11-810M2.2,downstream_gene_variant,,ENST00000573371,;ANKFY1,downstream_gene_variant,,ENST00000572412,;ANKFY1,downstream_gene_variant,,ENST00000575298,;	C	ENSG00000185722	ENST00000570535	Transcript	3_prime_UTR_variant	4632	.	.	.	.	.	.	.	-1	ANKFY1	HGNC	20763	protein_coding	YES	CCDS58502.1	ENSP00000459943	ANFY1_HUMAN	I3L1Z9_HUMAN	UPI00003FECB0	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CATTAGAATCA	.	4	ESCA
TOB1	0	.	GRCh37	17	48941282	48941282	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>C	p.Glu33Gln	p.E33Q	ENST00000499247	2/2	47	34	12	38	38	0	TOB1,missense_variant,p.Glu33Gln,ENST00000499247,;TOB1,missense_variant,p.Glu33Gln,ENST00000268957,;TOB1-AS1,upstream_gene_variant,,ENST00000416263,;TOB1-AS1,upstream_gene_variant,,ENST00000514358,;TOB1-AS1,upstream_gene_variant,,ENST00000523470,;TOB1,non_coding_transcript_exon_variant,,ENST00000509385,;	G	ENSG00000141232	ENST00000499247	Transcript	missense_variant	531	97	33	E/Q	Gaa/Caa	.	.	.	-1	TOB1	HGNC	11979	protein_coding	YES	CCDS11576.1	ENSP00000427695	TOB1_HUMAN	.	UPI00001370FB	.	deleterious(0.04)	possibly_damaging(0.795)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR17537,hmmpanther:PTHR17537:SF6,Pfam_domain:PF07742,SMART_domains:SM00099,Superfamily_domains:SSF160696,Prints_domain:PR00310	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCAAGTT	.	5	ESCA
NUP88	0	.	GRCh37	17	5289551	5289551	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2201A>G	p.Asp734Gly	p.D734G	ENST00000573584	17/17	72	47	25	92	92	0	NUP88,missense_variant,p.Asp689Gly,ENST00000225696,;NUP88,missense_variant,p.Asp734Gly,ENST00000573584,;RABEP1,downstream_gene_variant,,ENST00000408982,;RABEP1,downstream_gene_variant,,ENST00000262477,;RABEP1,downstream_gene_variant,,ENST00000572250,;RABEP1,downstream_gene_variant,,ENST00000341923,;RABEP1,downstream_gene_variant,,ENST00000537505,;RABEP1,downstream_gene_variant,,ENST00000546142,;NUP88,upstream_gene_variant,,ENST00000573169,;NUP88,non_coding_transcript_exon_variant,,ENST00000574855,;NUP88,intron_variant,,ENST00000576708,;NUP88,downstream_gene_variant,,ENST00000574867,;NUP88,downstream_gene_variant,,ENST00000576862,;NUP88,downstream_gene_variant,,ENST00000575976,;NUP88,downstream_gene_variant,,ENST00000574087,;	C	ENSG00000108559	ENST00000573584	Transcript	missense_variant	2711	2201	734	D/G	gAt/gGt	.	.	.	-1	NUP88	HGNC	8067	protein_coding	YES	CCDS11070.1	ENSP00000458954	NUP88_HUMAN	I3L245_HUMAN	UPI0000130894	.	deleterious(0.02)	possibly_damaging(0.595)	17/17	.	hmmpanther:PTHR13257:SF0,hmmpanther:PTHR13257,Pfam_domain:PF10168	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATATCATTG	.	5	ESCA
GH1	0	.	GRCh37	17	61994789	61994789	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534C>T	p.%3D	p.N178N	ENST00000323322	5/5	342	69	272	316	316	0	GH1,synonymous_variant,p.%3D,ENST00000342364,;GH1,synonymous_variant,p.%3D,ENST00000323322,;GH1,synonymous_variant,p.%3D,ENST00000458650,;GH1,synonymous_variant,p.%3D,ENST00000351388,;CSHL1,intron_variant,,ENST00000392824,;GH1,downstream_gene_variant,,ENST00000579711,;	A	ENSG00000259384	ENST00000323322	Transcript	synonymous_variant	577	534	178	N	aaC/aaT	.	.	.	-1	GH1	HGNC	4261	protein_coding	YES	CCDS11653.1	ENSP00000312673	SOMA_HUMAN	B1A4G6_HUMAN	UPI000002B7EE	.	.	.	5/5	.	hmmpanther:PTHR11417:SF38,hmmpanther:PTHR11417,Gene3D:1.20.1250.10,Pfam_domain:PF00103,Superfamily_domains:SSF47266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATCGTTGTG	.	5	ESCA
TEX2	0	.	GRCh37	17	62225034	62225055	+	3'UTR	DEL	AATGGTCAAACAATTTAAGTCA	AATGGTCAAACAATTTAAGTCA	-	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	AATGGTCAAACAATTTAAGTCA	AATGGTCAAACAATTTAAGTCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1274_*1295delTGACTTAAATTGTTTGACCATT	.	.	ENST00000258991	12/12	40	17	23	40	40	0	TEX2,3_prime_UTR_variant,,ENST00000584379,;TEX2,3_prime_UTR_variant,,ENST00000258991,;TEX2,3_prime_UTR_variant,,ENST00000583097,;TEX2,downstream_gene_variant,,ENST00000583501,;SNORA76,downstream_gene_variant,,ENST00000408535,;SNORD104,downstream_gene_variant,,ENST00000362883,;SNORA76,downstream_gene_variant,,ENST00000580828,;SNORA76,downstream_gene_variant,,ENST00000582965,;TEX2,downstream_gene_variant,,ENST00000581812,;TEX2,non_coding_transcript_exon_variant,,ENST00000584498,;	-	ENSG00000136478	ENST00000258991	Transcript	3_prime_UTR_variant	4764-4785	.	.	.	.	.	.	.	-1	TEX2	HGNC	30884	protein_coding	YES	CCDS11658.1	ENSP00000258991	TEX2_HUMAN	Q9NX99_HUMAN,J3QKY0_HUMAN,J3KRY2_HUMAN	UPI00001AE7BC	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AACTGGAATGGTCAAACAATTTAAGTCAAATGT	.	3	ESCA
HELZ	0	.	GRCh37	17	65072242	65072242	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2126G>A	.	.	ENST00000358691	33/33	19	16	3	23	23	0	HELZ,3_prime_UTR_variant,,ENST00000358691,;HELZ,downstream_gene_variant,,ENST00000580168,;HELZ,downstream_gene_variant,,ENST00000579953,;	T	ENSG00000198265	ENST00000358691	Transcript	3_prime_UTR_variant	8122	.	.	.	.	.	.	.	-1	HELZ	HGNC	16878	protein_coding	YES	CCDS42374.1	ENSP00000351524	HELZ_HUMAN	J3KT20_HUMAN,J3KS59_HUMAN	UPI000013D7F5	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTATCAGATT	.	2	ESCA
SDK2	0	.	GRCh37	17	71334666	71334666	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*60C>G	.	.	ENST00000392650	45/45	110	81	28	90	90	0	SDK2,3_prime_UTR_variant,,ENST00000424778,;SDK2,3_prime_UTR_variant,,ENST00000388726,;SDK2,3_prime_UTR_variant,,ENST00000392650,;SDK2,non_coding_transcript_exon_variant,,ENST00000410094,;	C	ENSG00000069188	ENST00000392650	Transcript	3_prime_UTR_variant	6580	.	.	.	.	.	.	.	-1	SDK2	HGNC	19308	protein_coding	YES	CCDS45769.1	ENSP00000376421	SDK2_HUMAN	.	UPI0000E5A088	.	.	.	45/45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGAGAGGAG	.	5	ESCA
FBF1	0	.	GRCh37	17	73915772	73915772	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2070G>T	p.Met690Ile	p.M690I	ENST00000319129	19/29	109	22	87	87	87	0	FBF1,missense_variant,p.Met690Ile,ENST00000319129,;FBF1,missense_variant,p.Met705Ile,ENST00000592193,;FBF1,missense_variant,p.Met691Ile,ENST00000389570,;FBF1,missense_variant,p.Met691Ile,ENST00000586717,;FBF1,non_coding_transcript_exon_variant,,ENST00000585990,;RP11-552F3.12,non_coding_transcript_exon_variant,,ENST00000593156,;FBF1,upstream_gene_variant,,ENST00000588283,;FBF1,downstream_gene_variant,,ENST00000586838,;FBF1,upstream_gene_variant,,ENST00000593076,;	A	ENSG00000188878	ENST00000319129	Transcript	missense_variant	2344	2070	690	M/I	atG/atT	.	.	.	-1	FBF1	HGNC	24674	protein_coding	YES	CCDS45779.1	ENSP00000324292	FBF1_HUMAN	K7ESG2_HUMAN	UPI0000DD841F	.	tolerated(0.14)	benign(0.022)	19/29	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTCCATTTC	.	5	ESCA
EXOC7	0	.	GRCh37	17	74077223	74077223	+	3'Flank	SNP	C	C	A	rs758571383	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000335146	.	27	6	20	23	23	0	EXOC7,3_prime_UTR_variant,,ENST00000589210,;EXOC7,3_prime_UTR_variant,,ENST00000332065,;EXOC7,3_prime_UTR_variant,,ENST00000607838,;ZACN,intron_variant,,ENST00000334586,;ZACN,downstream_gene_variant,,ENST00000392503,;EXOC7,downstream_gene_variant,,ENST00000357231,;GALR2,downstream_gene_variant,,ENST00000329003,;EXOC7,downstream_gene_variant,,ENST00000335146,;EXOC7,downstream_gene_variant,,ENST00000467929,;EXOC7,downstream_gene_variant,,ENST00000411744,;EXOC7,downstream_gene_variant,,ENST00000405575,;EXOC7,non_coding_transcript_exon_variant,,ENST00000591724,;EXOC7,non_coding_transcript_exon_variant,,ENST00000465252,;ZACN,non_coding_transcript_exon_variant,,ENST00000590045,;ZACN,intron_variant,,ENST00000421794,;ZACN,intron_variant,,ENST00000425015,;EXOC7,downstream_gene_variant,,ENST00000494787,;EXOC7,downstream_gene_variant,,ENST00000467586,;EXOC7,downstream_gene_variant,,ENST00000592559,;ZACN,downstream_gene_variant,,ENST00000591500,;ZACN,downstream_gene_variant,,ENST00000524242,;EXOC7,downstream_gene_variant,,ENST00000460476,;	A	ENSG00000182473	ENST00000335146	Transcript	downstream_gene_variant	.	.	.	.	.	rs758571383	.	1249	-1	EXOC7	HGNC	23214	protein_coding	YES	CCDS45782.1	ENSP00000334100	EXOC7_HUMAN	C9JME6_HUMAN,C9JKC2_HUMAN	UPI00001AFC78	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATCGGTTT	.	5	ESCA
TP53	0	.	GRCh37	17	7578528	7578528	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	5/11	46	12	33	39	39	0	TP53,missense_variant,p.Phe134Leu,ENST00000508793,;TP53,missense_variant,p.Phe134Leu,ENST00000413465,;TP53,missense_variant,p.Phe127Leu,ENST00000604348,;TP53,missense_variant,p.Phe134Leu,ENST00000420246,;TP53,missense_variant,p.Phe134Leu,ENST00000269305,;TP53,missense_variant,p.Phe2Leu,ENST00000509690,;TP53,missense_variant,p.Phe134Leu,ENST00000359597,;TP53,missense_variant,p.Phe41Leu,ENST00000514944,;TP53,missense_variant,p.Phe134Leu,ENST00000445888,;TP53,missense_variant,p.Phe134Leu,ENST00000455263,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	592	402	134	F/L	ttT/ttA	TP53_g.12390T>C,TP53_g.12390T>A,TP53_g.12390T>G,COSM11319,COSM44088,COSM45167	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.C135fs*35|c.400delT|6,CODON|p.F134S|c.401T>C|4,CODON|p.F134C|c.401T>G|9,BUFFER|p.A138fs*32|c.412delG|5,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A6V|c.17C>T|4,BUFFER|p.A45V|c.134C>T|4,BUFFER|p.A138V|c.413C>T|21,BUFFER|p.A138P|c.412G>C|14,BUFFER|p.A138T|c.412G>A|5,BUFFER|p.A138fs*11|c.411_412insN|3,BUFFER|p.L137L|c.411G>A|3,BUFFER|p.L137P|c.410T>C|3,BUFFER|p.L137Q|c.410T>A|3,BUFFER|p.Q136H|c.408A>C|5,BUFFER|p.Q136Q|c.408A>G|4,BUFFER|p.Q136P|c.407A>C|3,BUFFER|p.Q136E|c.406C>G|9,BUFFER|p.Q136*|c.406C>T|35,BUFFER|p.Q4*|c.10C>T|5,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q43*|c.127C>T|5,BUFFER|p.Q4E|c.10C>G|6,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q136E|c.406C>G|4,BUFFER|p.Q136E|c.406C>G|5,BUFFER|p.Q43E|c.127C>G|6,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|3,BUFFER|p.C3W|c.9C>G|4,BUFFER|p.C42W|c.126C>G|3,BUFFER|p.C135W|c.405C>G|3,BUFFER|p.C135W|c.405C>G|3,BUFFER|p.C135C|c.405C>T|5,BUFFER|p.C135*|c.405C>A|8,BUFFER|p.C135W|c.405C>G|24,BUFFER|p.C135F|c.404G>T|6,BUFFER|p.C3S|c.8G>C|3,BUFFER|p.C135S|c.404G>C|3,BUFFER|p.C3F|c.8G>T|13,BUFFER|p.C135S|c.404G>C|3,BUFFER|p.C42F|c.125G>T|13,BUFFER|p.C42S|c.125G>C|3,BUFFER|p.C135F|c.404G>T|6,BUFFER|p.C135Y|c.404G>A|8,BUFFER|p.C135Y|c.404G>A|54,BUFFER|p.C135S|c.404G>C|9,BUFFER|p.C135Y|c.404G>A|3,BUFFER|p.C42Y|c.125G>A|8,BUFFER|p.C135Y|c.404G>A|3,BUFFER|p.C135F|c.404G>T|13,BUFFER|p.C135F|c.404G>T|13,BUFFER|p.C135F|c.404G>T|49,BUFFER|p.C135Y|c.404G>A|8,BUFFER|p.C3Y|c.8G>A|8,BUFFER|p.C135fs*35|c.403delT|5,BUFFER|p.C135G|c.403T>G|8,BUFFER|p.C135S|c.403T>A|4,BUFFER|p.C135R|c.403T>C|11,BUFFER|p.F134V|c.400T>G|11,BUFFER|p.F41L|c.121T>C|4,BUFFER|p.F134L|c.400T>C|3,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F2L|c.4T>C|4,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F134L|c.400T>C|18,BUFFER|p.M133T|c.398T>C|5,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M40T|c.119T>C|3,BUFFER|p.M1T|c.2T>C|3,BUFFER|p.M1R|c.2T>G|3,BUFFER|p.M133R|c.398T>G|7,BUFFER|p.M133K|c.398T>A|12,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M40R|c.119T>G|3,BUFFER|p.Y126_K132delYSPALNK|c.376_396del21|6,BUFFER|p.K132N|c.396G>C|29,BUFFER|p.K132N|c.396G>T|3,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>C|5,BUFFER|p.K132N|c.396G>T|24,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>T|6,BUFFER|p.N131delN|c.393_395delCAA|4,BUFFER|p.K132R|c.395A>G|5,BUFFER|p.K132T|c.395A>C|7,BUFFER|p.K39T|c.116A>C|3,BUFFER|p.K132R|c.395A>G|39,BUFFER|p.K132M|c.395A>T|10,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K39R|c.116A>G|7,BUFFER|p.K132Q|c.394A>C|13,BUFFER|p.K39E|c.115A>G|3,BUFFER|p.K132*|c.394A>T|5,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|19,BUFFER|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.N131delN|c.391_393delAAC|8,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131I|c.392A>T|7,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131S|c.392A>G|5,BUFFER|p.N38I|c.113A>T|3,BUFFER|p.N131Y|c.391A>T|8	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCAAAACAT	.	5	ESCA
DNAH17-AS1	0	.	GRCh37	17	76496578	76496578	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*15G>A	.	.	ENST00000598378	1/1	18	12	6	10	10	0	DNAH17-AS1,3_prime_UTR_variant,,ENST00000598378,;DNAH17,intron_variant,,ENST00000585328,;DNAH17,intron_variant,,ENST00000389840,;RP11-559N14.5,downstream_gene_variant,,ENST00000591373,;DNAH17,downstream_gene_variant,,ENST00000587177,;	A	ENSG00000268470	ENST00000598378	Transcript	3_prime_UTR_variant	1668	.	.	.	.	.	.	.	1	DNAH17-AS1	HGNC	48594	protein_coding	YES	.	ENSP00000472049	.	M0R1Q4_HUMAN	UPI0000D623A2	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCGACCCC	.	5	ESCA
ZNF750	0	.	GRCh37	17	80789643	80789643	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.688delG	p.Ala230ProfsTer136	p.A230Pfs*136	ENST00000269394	2/3	173	87	86	72	72	0	ZNF750,frameshift_variant,p.Ala230ProfsTer136,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	-	ENSG00000141579	ENST00000269394	Transcript	frameshift_variant	1522	688	230	A/X	Gcc/cc	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAATGGCCCCAA	.	3	ESCA
EPG5	0	.	GRCh37	18	43427740	43427740	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4692A>G	.	.	ENST00000282041	44/44	33	17	15	41	41	0	EPG5,3_prime_UTR_variant,,ENST00000282041,;EPG5,3_prime_UTR_variant,,ENST00000590854,;SIGLEC15,downstream_gene_variant,,ENST00000593178,;	C	ENSG00000152223	ENST00000282041	Transcript	3_prime_UTR_variant	12467	.	.	.	.	.	.	.	-1	EPG5	HGNC	29331	protein_coding	YES	CCDS11926.2	ENSP00000282041	EPG5_HUMAN	Q9BYJ3_HUMAN,Q9BTI0_HUMAN	UPI00004F6F8A	.	.	.	44/44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTGTGGTTT	.	5	ESCA
PPP4R1	0	.	GRCh37	18	9550118	9550118	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2479G>C	p.Glu827Gln	p.E827Q	ENST00000400556	18/20	71	51	20	83	83	0	PPP4R1,missense_variant,p.Glu810Gln,ENST00000400555,;PPP4R1,missense_variant,p.Glu827Gln,ENST00000400556,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000579609,;PPP4R1,downstream_gene_variant,,ENST00000584754,;PPP4R1,3_prime_UTR_variant,,ENST00000285124,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000582594,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000578329,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000578010,;	G	ENSG00000154845	ENST00000400556	Transcript	missense_variant	2553	2479	827	E/Q	Gag/Cag	.	.	.	-1	PPP4R1	HGNC	9320	protein_coding	YES	CCDS42412.1	ENSP00000383402	PP4R1_HUMAN	J3QLA6_HUMAN,J3QL26_HUMAN,J3KSB0_HUMAN,J3KRU1_HUMAN,B4DID3_HUMAN	UPI000006D6DE	.	deleterious(0)	possibly_damaging(0.558)	18/20	.	hmmpanther:PTHR10648:SF8,hmmpanther:PTHR10648,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTCATTGA	.	5	ESCA
ABCA7	0	.	GRCh37	19	1044587	1044587	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059G>C	p.Gln353His	p.Q353H	ENST00000263094	11/47	78	52	26	87	87	0	ABCA7,missense_variant,p.Gln353His,ENST00000433129,;ABCA7,missense_variant,p.Gln353His,ENST00000263094,;ABCA7,missense_variant,p.Gln215His,ENST00000435683,;ABCA7,downstream_gene_variant,,ENST00000531467,;ABCA7,downstream_gene_variant,,ENST00000524850,;ABCA7,upstream_gene_variant,,ENST00000533574,;ABCA7,downstream_gene_variant,,ENST00000525238,;ABCA7,downstream_gene_variant,,ENST00000526885,;ABCA7,downstream_gene_variant,,ENST00000527496,;ABCA7,downstream_gene_variant,,ENST00000530703,;	C	ENSG00000064687	ENST00000263094	Transcript	missense_variant	1290	1059	353	Q/H	caG/caC	.	.	.	1	ABCA7	HGNC	37	protein_coding	YES	CCDS12055.1	ENSP00000263094	ABCA7_HUMAN	E9PL63_HUMAN	UPI000013D3A4	.	tolerated(0.1)	benign(0.001)	11/47	.	hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGATGCA	.	5	ESCA
ZNF653	0	.	GRCh37	19	11598622	11598622	+	Missense_Mutation	SNP	G	G	A	rs373230491	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.656C>T	p.Ala219Val	p.A219V	ENST00000293771	4/9	30	19	11	23	23	0	ZNF653,missense_variant,p.Ala219Val,ENST00000293771,;ZNF653,upstream_gene_variant,,ENST00000592756,;ZNF653,upstream_gene_variant,,ENST00000589051,;ZNF653,upstream_gene_variant,,ENST00000590296,;ZNF653,non_coding_transcript_exon_variant,,ENST00000590548,;CTC-398G3.6,intron_variant,,ENST00000585656,;	A	ENSG00000161914	ENST00000293771	Transcript	missense_variant	793	656	219	A/V	gCg/gTg	rs373230491	.	.	-1	ZNF653	HGNC	25196	protein_coding	YES	CCDS12261.1	ENSP00000293771	ZN653_HUMAN	.	UPI000006FAFC	.	tolerated(0.37)	benign(0.002)	4/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11389:SF353,hmmpanther:PTHR11389	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGCCGCAGCC	.	3	ESCA
ZNF653	0	.	GRCh37	19	11598670	11598670	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608C>T	p.Ser203Phe	p.S203F	ENST00000293771	4/9	19	14	5	15	15	0	ZNF653,missense_variant,p.Ser203Phe,ENST00000293771,;ZNF653,upstream_gene_variant,,ENST00000592756,;ZNF653,upstream_gene_variant,,ENST00000589051,;ZNF653,upstream_gene_variant,,ENST00000590296,;ZNF653,non_coding_transcript_exon_variant,,ENST00000590548,;CTC-398G3.6,intron_variant,,ENST00000585656,;	A	ENSG00000161914	ENST00000293771	Transcript	missense_variant	745	608	203	S/F	tCt/tTt	.	.	.	-1	ZNF653	HGNC	25196	protein_coding	YES	CCDS12261.1	ENSP00000293771	ZN653_HUMAN	.	UPI000006FAFC	.	deleterious(0)	possibly_damaging(0.541)	4/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11389:SF353,hmmpanther:PTHR11389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGCAGAGCCA	.	3	ESCA
ZNF625	0	.	GRCh37	19	12256319	12256319	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912A>C	p.Glu304Asp	p.E304D	ENST00000439556	4/4	63	32	31	81	81	0	ZNF625,missense_variant,p.Glu238Asp,ENST00000542938,;ZNF625,missense_variant,p.Glu304Asp,ENST00000439556,;ZNF625,missense_variant,p.Glu238Asp,ENST00000355738,;ZNF625,3_prime_UTR_variant,,ENST00000455799,;ZNF625,intron_variant,,ENST00000414892,;CTC-359D24.3,upstream_gene_variant,,ENST00000472362,;ZNF625-ZNF20,3_prime_UTR_variant,,ENST00000434822,;ZNF625-ZNF20,intron_variant,,ENST00000430024,;CTC-359D24.3,upstream_gene_variant,,ENST00000486612,;	G	ENSG00000257591	ENST00000439556	Transcript	missense_variant	1083	912	304	E/D	gaA/gaC	.	.	.	-1	ZNF625	HGNC	30571	protein_coding	YES	CCDS12269.2	ENSP00000394380	ZN625_HUMAN	.	UPI0000EE608F	.	deleterious(0.03)	probably_damaging(0.953)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF73,hmmpanther:PTHR24402,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACATTCATA	.	5	ESCA
MUM1	0	.	GRCh37	19	1373090	1373090	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2009C>G	p.Ser670Cys	p.S670C	ENST00000344663	13/14	54	35	18	43	43	0	MUM1,missense_variant,p.Ser670Cys,ENST00000591806,;MUM1,missense_variant,p.Ser670Cys,ENST00000344663,;MUM1,missense_variant,p.Ser601Cys,ENST00000311401,;MUM1,synonymous_variant,p.%3D,ENST00000415183,;AC004623.2,downstream_gene_variant,,ENST00000589673,;AC004623.2,downstream_gene_variant,,ENST00000587059,;MUM1,non_coding_transcript_exon_variant,,ENST00000591453,;MUM1,non_coding_transcript_exon_variant,,ENST00000586067,;MUM1,upstream_gene_variant,,ENST00000588888,;MUM1,3_prime_UTR_variant,,ENST00000587460,;MUM1,non_coding_transcript_exon_variant,,ENST00000591627,;MUM1,downstream_gene_variant,,ENST00000585399,;MUM1,downstream_gene_variant,,ENST00000591433,;	G	ENSG00000160953	ENST00000344663	Transcript	missense_variant	2110	2009	670	S/C	tCt/tGt	.	.	.	1	MUM1	HGNC	29641	protein_coding	YES	CCDS12062.1	ENSP00000345789	.	K7EP97_HUMAN,K7END0_HUMAN,J3KNX4_HUMAN	UPI00001A95DB	.	deleterious(0)	probably_damaging(0.938)	13/14	.	hmmpanther:PTHR31333,hmmpanther:PTHR31333:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTCTGCGG	.	5	ESCA
GIPC1	0	.	GRCh37	19	14588916	14588916	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*312C>T	.	.	ENST00000393033	9/9	9	5	4	19	19	0	GIPC1,3_prime_UTR_variant,,ENST00000393033,;GIPC1,3_prime_UTR_variant,,ENST00000393029,;GIPC1,3_prime_UTR_variant,,ENST00000393028,;GIPC1,3_prime_UTR_variant,,ENST00000589631,;GIPC1,3_prime_UTR_variant,,ENST00000345425,;GIPC1,downstream_gene_variant,,ENST00000591349,;GIPC1,downstream_gene_variant,,ENST00000591245,;GIPC1,downstream_gene_variant,,ENST00000587210,;PTGER1,upstream_gene_variant,,ENST00000292513,;GIPC1,downstream_gene_variant,,ENST00000587969,;GIPC1,downstream_gene_variant,,ENST00000587934,;GIPC1,downstream_gene_variant,,ENST00000586027,;GIPC1,non_coding_transcript_exon_variant,,ENST00000585606,;GIPC1,downstream_gene_variant,,ENST00000589497,;GIPC1,downstream_gene_variant,,ENST00000587811,;	A	ENSG00000123159	ENST00000393033	Transcript	3_prime_UTR_variant	1584	.	.	.	.	.	.	.	-1	GIPC1	HGNC	1226	protein_coding	YES	CCDS12310.1	ENSP00000376753	GIPC1_HUMAN	K7ESN1_HUMAN,K7ELJ2_HUMAN,K7EIT0_HUMAN	UPI000012B4BB	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTGATGGT	.	2	ESCA
MYO9B	0	.	GRCh37	19	17264866	17264866	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1088A>T	p.Tyr363Phe	p.Y363F	ENST00000595618	5/40	39	20	18	33	33	0	MYO9B,missense_variant,p.Tyr363Phe,ENST00000595641,;MYO9B,missense_variant,p.Tyr363Phe,ENST00000397274,;MYO9B,missense_variant,p.Tyr363Phe,ENST00000595618,;MYO9B,missense_variant,p.Tyr363Phe,ENST00000594824,;CTD-3032J10.2,intron_variant,,ENST00000599360,;CTD-3032J10.2,intron_variant,,ENST00000597216,;	T	ENSG00000099331	ENST00000595618	Transcript	missense_variant	1240	1088	363	Y/F	tAc/tTc	.	.	.	1	MYO9B	HGNC	7609	protein_coding	YES	CCDS46010.1	ENSP00000471457	MYO9B_HUMAN	Q4LE74_HUMAN	UPI000020367C	.	deleterious(0.01)	probably_damaging(0.995)	5/40	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF306,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTACCTCA	.	5	ESCA
MAST3	0	.	GRCh37	19	18234138	18234138	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.424G>A	p.Glu142Lys	p.E142K	ENST00000262811	6/27	22	16	6	31	31	0	MAST3,missense_variant,p.Glu142Lys,ENST00000262811,;MAST3,non_coding_transcript_exon_variant,,ENST00000608648,;MAST3,upstream_gene_variant,,ENST00000601226,;	A	ENSG00000099308	ENST00000262811	Transcript	missense_variant	424	424	142	E/K	Gaa/Aaa	.	.	.	1	MAST3	HGNC	19036	protein_coding	YES	CCDS46014.1	ENSP00000262811	MAST3_HUMAN	.	UPI00001D8275	.	deleterious(0.01)	possibly_damaging(0.472)	6/27	.	hmmpanther:PTHR24356:SF140,hmmpanther:PTHR24356,Pfam_domain:PF08926	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAGGAAGGC	.	5	ESCA
ZNF431	0	.	GRCh37	19	21365524	21365524	+	Missense_Mutation	SNP	G	G	C	rs181764553	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418G>C	p.Glu140Gln	p.E140Q	ENST00000311048	5/5	83	60	22	79	79	0	ZNF431,missense_variant,p.Glu180Gln,ENST00000598331,;ZNF431,missense_variant,p.Glu140Gln,ENST00000311048,;ZNF431,3_prime_UTR_variant,,ENST00000600692,;ZNF431,intron_variant,,ENST00000594425,;ZNF431,downstream_gene_variant,,ENST00000599296,;ZNF431,upstream_gene_variant,,ENST00000594821,;ZNF431,upstream_gene_variant,,ENST00000593426,;	C	ENSG00000196705	ENST00000311048	Transcript	missense_variant	562	418	140	E/Q	Gag/Cag	rs181764553,COSM1304269	.	.	1	ZNF431	HGNC	20809	protein_coding	YES	CCDS32979.1	ENSP00000308578	ZN431_HUMAN	.	UPI0000191EAC	.	deleterious(0.05)	possibly_damaging(0.673)	5/5	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF118	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATGAGAAT	byCluster|by1000G	5	ESCA
ZNF100	0	.	GRCh37	19	21909980	21909980	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1134T>C	p.%3D	p.C378C	ENST00000358296	5/5	35	24	11	48	48	0	ZNF100,synonymous_variant,p.%3D,ENST00000305570,;ZNF100,synonymous_variant,p.%3D,ENST00000358296,;ZNF100,downstream_gene_variant,,ENST00000594401,;	G	ENSG00000197020	ENST00000358296	Transcript	synonymous_variant	1333	1134	378	C	tgT/tgC	.	.	.	-1	ZNF100	HGNC	12880	protein_coding	YES	CCDS42538.1	ENSP00000351042	ZN100_HUMAN	Q6MZN6_HUMAN	UPI00001614AC	.	.	.	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF78,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TTGCCACATTC	.	3	ESCA
TLE6	0	.	GRCh37	19	2987362	2987362	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550C>T	p.Pro184Ser	p.P184S	ENST00000246112	8/17	28	17	10	21	21	0	TLE6,missense_variant,p.Pro184Ser,ENST00000246112,;TLE6,missense_variant,p.Pro61Ser,ENST00000452088,;TLE6,downstream_gene_variant,,ENST00000453329,;TLE6,non_coding_transcript_exon_variant,,ENST00000468176,;TLE6,non_coding_transcript_exon_variant,,ENST00000478073,;TLE6,downstream_gene_variant,,ENST00000591953,;TLE6,non_coding_transcript_exon_variant,,ENST00000474207,;TLE6,upstream_gene_variant,,ENST00000469572,;TLE6,upstream_gene_variant,,ENST00000497878,;	T	ENSG00000104953	ENST00000246112	Transcript	missense_variant	751	550	184	P/S	Cca/Tca	.	.	.	1	TLE6	HGNC	30788	protein_coding	YES	CCDS45910.1	ENSP00000246112	TLE6_HUMAN	K7ENW8_HUMAN,C9J532_HUMAN	UPI000059D62B	.	tolerated(0.2)	benign(0.174)	8/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCACCAGGC	.	5	ESCA
ANKRD27	0	.	GRCh37	19	33134334	33134334	+	Intron	SNP	C	C	T	rs777772865	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639+3G>A	.	.	ENST00000306065	.	38	23	14	26	26	0	ANKRD27,splice_region_variant,,ENST00000306065,;ANKRD27,splice_region_variant,,ENST00000587352,;ANKRD27,intron_variant,,ENST00000586463,;ANKRD27,downstream_gene_variant,,ENST00000590519,;ANKRD27,downstream_gene_variant,,ENST00000586693,;ANKRD27,upstream_gene_variant,,ENST00000591100,;ANKRD27,splice_region_variant,,ENST00000593232,;ANKRD27,splice_region_variant,,ENST00000588700,;	T	ENSG00000105186	ENST00000306065	Transcript	splice_region_variant	.	.	.	.	.	rs777772865	.	.	-1	ANKRD27	HGNC	25310	protein_coding	YES	CCDS32986.1	ENSP00000304292	ANR27_HUMAN	K7EPM2_HUMAN,K7EIN0_HUMAN,K7EIH4_HUMAN	UPI000004FDE9	.	.	.	.	7/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTCACCTC	.	4	ESCA
KMT2B	0	.	GRCh37	19	36212661	36212661	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2412C>G	p.Phe804Leu	p.F804L	ENST00000222270	3/37	29	17	12	41	41	0	KMT2B,missense_variant,p.Phe804Leu,ENST00000222270,;KMT2B,missense_variant,p.Phe804Leu,ENST00000420124,;ZBTB32,downstream_gene_variant,,ENST00000392197,;ZBTB32,downstream_gene_variant,,ENST00000262630,;KMT2B,downstream_gene_variant,,ENST00000341701,;KMT2B,non_coding_transcript_exon_variant,,ENST00000607650,;KMT2B,downstream_gene_variant,,ENST00000606995,;ZBTB32,downstream_gene_variant,,ENST00000481182,;	G	ENSG00000272333	ENST00000222270	Transcript	missense_variant	2412	2412	804	F/L	ttC/ttG	.	.	.	1	KMT2B	Uniprot_gn	15840	protein_coding	YES	CCDS46055.1	ENSP00000222270	KMT2B_HUMAN	.	UPI00001376B5	.	.	benign(0.017)	3/37	.	hmmpanther:PTHR22884:SF280,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTATTCAAGAT	.	2	ESCA
PIP5K1C	0	.	GRCh37	19	3656454	3656454	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570C>T	p.%3D	p.V190V	ENST00000335312	6/18	60	40	19	65	65	0	PIP5K1C,synonymous_variant,p.%3D,ENST00000589578,;PIP5K1C,synonymous_variant,p.%3D,ENST00000539785,;PIP5K1C,synonymous_variant,p.%3D,ENST00000537021,;PIP5K1C,synonymous_variant,p.%3D,ENST00000335312,;PIP5K1C,non_coding_transcript_exon_variant,,ENST00000587482,;	A	ENSG00000186111	ENST00000335312	Transcript	synonymous_variant	659	570	190	V	gtC/gtT	.	.	.	-1	PIP5K1C	HGNC	8996	protein_coding	YES	CCDS32872.1	ENSP00000335333	PI51C_HUMAN	Q7LE22_HUMAN	UPI000019C574	.	.	.	6/18	.	PROSITE_profiles:PS51455,hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF26,Gene3D:2gk9B01,Pfam_domain:PF01504,SMART_domains:SM00330,Superfamily_domains:SSF56104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCATGACGGT	.	5	ESCA
IFNL2	0	.	GRCh37	19	39759317	39759317	+	Missense_Mutation	SNP	A	A	G	rs778693588	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11A>G	p.Asp4Gly	p.D4G	ENST00000331982	2/6	59	34	25	63	63	0	IFNL2,missense_variant,p.Asp4Gly,ENST00000331982,;IFNL4P1,downstream_gene_variant,,ENST00000607083,;	G	ENSG00000183709	ENST00000331982	Transcript	missense_variant	66	11	4	D/G	gAc/gGc	rs778693588	.	.	1	IFNL2	HGNC	18364	protein_coding	YES	CCDS42567.1	ENSP00000333639	IFNL2_HUMAN	Q45KQ8_HUMAN	UPI0000074102	.	tolerated_low_confidence(0.11)	benign(0.001)	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAGACATGA	.	5	ESCA
PRX	0	.	GRCh37	19	40904703	40904703	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205C>G	p.Arg69Gly	p.R69G	ENST00000324001	6/7	13	8	5	22	22	0	PRX,missense_variant,p.Arg69Gly,ENST00000324001,;PRX,missense_variant,p.Arg69Gly,ENST00000291825,;	C	ENSG00000105227	ENST00000324001	Transcript	missense_variant	476	205	69	R/G	Cga/Gga	.	.	.	-1	PRX	HGNC	13797	protein_coding	YES	CCDS33028.1	ENSP00000326018	PRAX_HUMAN	.	UPI000044CC1A	.	deleterious(0)	benign(0.433)	6/7	.	PROSITE_profiles:PS50106,hmmpanther:PTHR23348:SF39,hmmpanther:PTHR23348,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CACTCGGGCAC	.	2	ESCA
C19orf54	0	.	GRCh37	19	41247442	41247442	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*896G>A	.	.	ENST00000378313	6/6	12	7	5	11	11	0	C19orf54,3_prime_UTR_variant,,ENST00000470681,;C19orf54,3_prime_UTR_variant,,ENST00000378313,;C19orf54,intron_variant,,ENST00000596940,;C19orf54,intron_variant,,ENST00000598485,;ITPKC,downstream_gene_variant,,ENST00000263370,;C19orf54,downstream_gene_variant,,ENST00000598352,;C19orf54,downstream_gene_variant,,ENST00000598729,;C19orf54,downstream_gene_variant,,ENST00000600139,;C19orf54,downstream_gene_variant,,ENST00000339153,;C19orf54,non_coding_transcript_exon_variant,,ENST00000594163,;C19orf54,intron_variant,,ENST00000469741,;C19orf54,downstream_gene_variant,,ENST00000597507,;C19orf54,downstream_gene_variant,,ENST00000596809,;ITPKC,downstream_gene_variant,,ENST00000597003,;	T	ENSG00000188493	ENST00000378313	Transcript	3_prime_UTR_variant	2072	.	.	.	.	.	.	.	-1	C19orf54	HGNC	24758	protein_coding	YES	CCDS12564.2	ENSP00000367564	CS054_HUMAN	.	UPI00001B64AB	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCTTCAGAGT	.	3	ESCA
CEACAM21	0	.	GRCh37	19	42082640	42082640	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14C>T	p.Ser5Leu	p.S5L	ENST00000401445	1/7	72	49	23	69	69	0	CEACAM21,missense_variant,p.Ser5Leu,ENST00000401445,;CEACAM21,missense_variant,p.Ser5Leu,ENST00000187608,;CEACAM21,intron_variant,,ENST00000407170,;CEACAM21,intron_variant,,ENST00000482870,;CEACAM21,missense_variant,p.Ser5Leu,ENST00000457737,;	T	ENSG00000007129	ENST00000401445	Transcript	missense_variant	40	14	5	S/L	tCa/tTa	.	.	.	1	CEACAM21	HGNC	28834	protein_coding	YES	CCDS46086.1	ENSP00000385739	CEA21_HUMAN	.	UPI0000D617B1	.	deleterious(0.03)	probably_damaging(0.98)	1/7	.	hmmpanther:PTHR19955:SF124,hmmpanther:PTHR19955	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTCAGCTT	.	5	ESCA
CIC	0	.	GRCh37	19	42796614	42796614	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3171C>T	p.%3D	p.L1057L	ENST00000575354	13/20	21	16	5	17	17	0	CIC,synonymous_variant,p.%3D,ENST00000575354,;CIC,synonymous_variant,p.%3D,ENST00000572681,;CIC,synonymous_variant,p.%3D,ENST00000160740,;PAFAH1B3,downstream_gene_variant,,ENST00000262890,;CIC,upstream_gene_variant,,ENST00000576505,;CIC,upstream_gene_variant,,ENST00000573349,;PAFAH1B3,downstream_gene_variant,,ENST00000538771,;PAFAH1B3,downstream_gene_variant,,ENST00000595530,;PAFAH1B3,downstream_gene_variant,,ENST00000596265,;PAFAH1B3,downstream_gene_variant,,ENST00000594989,;CIC,upstream_gene_variant,,ENST00000575287,;CIC,upstream_gene_variant,,ENST00000571033,;	T	ENSG00000079432	ENST00000575354	Transcript	synonymous_variant	3211	3171	1057	L	ctC/ctT	.	.	.	1	CIC	HGNC	14214	protein_coding	YES	CCDS12601.1	ENSP00000458663	CIC_HUMAN	.	UPI000013C5A0	.	.	.	13/20	.	hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTCTCAGG	.	5	ESCA
PVR	0	.	GRCh37	19	45150678	45150678	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263A>T	p.Glu88Val	p.E88V	ENST00000425690	2/8	63	49	14	60	60	0	PVR,missense_variant,p.Glu88Val,ENST00000406449,;PVR,missense_variant,p.Glu88Val,ENST00000425690,;PVR,missense_variant,p.Glu88Val,ENST00000344956,;PVR,missense_variant,p.Glu88Val,ENST00000403059,;PVR,upstream_gene_variant,,ENST00000587785,;CTB-171A8.1,intron_variant,,ENST00000590796,;PVR,3_prime_UTR_variant,,ENST00000187830,;	T	ENSG00000073008	ENST00000425690	Transcript	missense_variant	562	263	88	E/V	gAg/gTg	.	.	.	1	PVR	HGNC	9705	protein_coding	YES	CCDS12640.1	ENSP00000402060	PVR_HUMAN	.	UPI000004A2C1	.	deleterious(0.01)	probably_damaging(0.964)	2/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF54,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGGAGTCCA	.	5	ESCA
CEACAM16	0	.	GRCh37	19	45213942	45213942	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*164G>T	.	.	ENST00000587331	7/7	10	4	6	14	14	0	CEACAM16,3_prime_UTR_variant,,ENST00000587331,;CEACAM16,3_prime_UTR_variant,,ENST00000405314,;CTB-171A8.1,intron_variant,,ENST00000590796,;CTB-171A8.1,downstream_gene_variant,,ENST00000591312,;	T	ENSG00000213892	ENST00000587331	Transcript	3_prime_UTR_variant	1657	.	.	.	.	.	.	.	1	CEACAM16	HGNC	31948	protein_coding	YES	CCDS54278.1	ENSP00000466561	CEA16_HUMAN	.	UPI00001D8176	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCCTCGCTGAG	.	2	ESCA
SLC8A2	0	.	GRCh37	19	47932511	47932511	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*835A>G	.	.	ENST00000236877	10/10	28	16	12	28	28	0	SLC8A2,3_prime_UTR_variant,,ENST00000236877,;SLC8A2,downstream_gene_variant,,ENST00000539381,;SLC8A2,downstream_gene_variant,,ENST00000542837,;SLC8A2,downstream_gene_variant,,ENST00000601757,;SLC8A2,downstream_gene_variant,,ENST00000600576,;	C	ENSG00000118160	ENST00000236877	Transcript	3_prime_UTR_variant	3997	.	.	.	.	.	.	.	-1	SLC8A2	HGNC	11069	protein_coding	YES	CCDS33065.1	ENSP00000236877	NAC2_HUMAN	M0R211_HUMAN,M0R1Z4_HUMAN,F5H6L7_HUMAN,F5GYS4_HUMAN	UPI000012FC49	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTTTTCCC	.	5	ESCA
CYTH2	0	.	GRCh37	19	48976633	48976633	+	Silent	SNP	C	C	T	rs758032912	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432C>T	p.%3D	p.L144L	ENST00000452733	5/12	40	29	11	52	52	0	CYTH2,synonymous_variant,p.%3D,ENST00000427476,;CYTH2,synonymous_variant,p.%3D,ENST00000595765,;CYTH2,synonymous_variant,p.%3D,ENST00000325139,;CYTH2,synonymous_variant,p.%3D,ENST00000452733,;CTC-273B12.7,downstream_gene_variant,,ENST00000595676,;CTC-273B12.5,upstream_gene_variant,,ENST00000593476,;CTC-273B12.5,upstream_gene_variant,,ENST00000600650,;CTC-273B12.5,upstream_gene_variant,,ENST00000596497,;CYTH2,synonymous_variant,p.%3D,ENST00000391881,;CYTH2,splice_region_variant,,ENST00000493260,;CYTH2,splice_region_variant,,ENST00000474209,;CYTH2,splice_region_variant,,ENST00000460595,;CYTH2,non_coding_transcript_exon_variant,,ENST00000467412,;CYTH2,downstream_gene_variant,,ENST00000462117,;CYTH2,downstream_gene_variant,,ENST00000474049,;	T	ENSG00000105443	ENST00000452733	Transcript	synonymous_variant	908	432	144	L	ctC/ctT	rs758032912	.	.	1	CYTH2	HGNC	9502	protein_coding	YES	CCDS12722.1	ENSP00000408236	CYH2_HUMAN	M0QZ92_HUMAN	UPI000000009E	.	.	.	5/12	.	PROSITE_profiles:PS50190,hmmpanther:PTHR10663:SF123,hmmpanther:PTHR10663,Pfam_domain:PF01369,Gene3D:1.10.1000.11,SMART_domains:SM00222,Superfamily_domains:SSF48425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCAGGTG	.	5	ESCA
ZNF534	0	.	GRCh37	19	52941164	52941164	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490A>C	p.Ser164Arg	p.S164R	ENST00000332323	4/4	12	8	4	12	12	0	ZNF534,missense_variant,p.Ser164Arg,ENST00000332323,;ZNF534,missense_variant,p.Ser151Arg,ENST00000433050,;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000432303,;	C	ENSG00000198633	ENST00000332323	Transcript	missense_variant	551	490	164	S/R	Agt/Cgt	COSM567662	.	.	1	ZNF534	HGNC	26337	protein_coding	YES	CCDS46165.1	ENSP00000327538	ZN534_HUMAN	.	UPI0000351984	.	tolerated(0.08)	benign(0.193)	4/4	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	AAATAAGTTTT	.	4	ESCA
ZNF160	0	.	GRCh37	19	53576419	53576419	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271+974G>T	.	.	ENST00000429604	.	15	12	3	13	13	0	ZNF160,3_prime_UTR_variant,,ENST00000355147,;ZNF160,intron_variant,,ENST00000429604,;ZNF160,intron_variant,,ENST00000418871,;ZNF160,intron_variant,,ENST00000599247,;ZNF160,intron_variant,,ENST00000601982,;ZNF160,intron_variant,,ENST00000601421,;ZNF160,intron_variant,,ENST00000599056,;ZNF160,downstream_gene_variant,,ENST00000599637,;ZNF160,downstream_gene_variant,,ENST00000599729,;	A	ENSG00000170949	ENST00000429604	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ZNF160	HGNC	12948	protein_coding	YES	CCDS12859.1	ENSP00000406201	ZN160_HUMAN	M0QZI7_HUMAN,M0QZ49_HUMAN,M0QXU9_HUMAN	UPI0000202B37	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTACTCTTTGC	.	2	ESCA
LILRB2	0	.	GRCh37	19	54784380	54784380	+	5'UTR	SNP	G	G	T	rs770078885	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-29C>A	.	.	ENST00000391749	2/14	144	96	48	124	124	0	LILRB2,5_prime_UTR_variant,,ENST00000434421,;LILRB2,5_prime_UTR_variant,,ENST00000314446,;LILRB2,5_prime_UTR_variant,,ENST00000391748,;LILRB2,5_prime_UTR_variant,,ENST00000391749,;LILRB2,upstream_gene_variant,,ENST00000391746,;MIR4752,upstream_gene_variant,,ENST00000579672,;LILRB2,upstream_gene_variant,,ENST00000471216,;LILRB2,non_coding_transcript_exon_variant,,ENST00000493242,;LILRB2,upstream_gene_variant,,ENST00000455108,;	T	ENSG00000131042	ENST00000391749	Transcript	5_prime_UTR_variant	244	.	.	.	.	rs770078885	.	.	-1	LILRB2	HGNC	6606	protein_coding	YES	CCDS12886.1	ENSP00000375629	LIRB2_HUMAN	C9JF29_HUMAN	UPI00000707E4	.	.	.	2/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGCGGATGG	byFrequency	5	ESCA
NLRP2	0	.	GRCh37	19	55501422	55501422	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2399G>T	p.Trp800Leu	p.W800L	ENST00000543010	9/13	26	18	8	29	29	0	NLRP2,missense_variant,p.Trp778Leu,ENST00000537859,;NLRP2,missense_variant,p.Trp797Leu,ENST00000263437,;NLRP2,missense_variant,p.Trp776Leu,ENST00000391721,;NLRP2,missense_variant,p.Trp778Leu,ENST00000339757,;NLRP2,missense_variant,p.Trp800Leu,ENST00000543010,;NLRP2,missense_variant,p.Trp776Leu,ENST00000538819,;NLRP2,missense_variant,p.Trp800Leu,ENST00000448584,;NLRP2,missense_variant,p.Trp777Leu,ENST00000427260,;NLRP2,downstream_gene_variant,,ENST00000540005,;NLRP2,upstream_gene_variant,,ENST00000586512,;NLRP2,missense_variant,p.Trp48Leu,ENST00000543277,;NLRP2,3_prime_UTR_variant,,ENST00000381637,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000542755,;	T	ENSG00000022556	ENST00000543010	Transcript	missense_variant	2542	2399	800	W/L	tGg/tTg	.	.	.	1	NLRP2	HGNC	22948	protein_coding	YES	CCDS12913.1	ENSP00000445135	NALP2_HUMAN	K7EPE6_HUMAN,K7ELX1_HUMAN,K7EJ90_HUMAN,F5H7Q5_HUMAN,F5H5B1_HUMAN	UPI000004C0CC	.	tolerated(0.07)	benign(0.128)	9/13	.	hmmpanther:PTHR24106:SF14,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTGGGCTG	.	5	ESCA
ZNF579	0	.	GRCh37	19	56089494	56089494	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1512C>A	p.%3D	p.L504L	ENST00000325421	2/2	46	37	9	52	52	0	ZNF579,synonymous_variant,p.%3D,ENST00000325421,;ZNF579,downstream_gene_variant,,ENST00000592239,;CTD-2537I9.5,upstream_gene_variant,,ENST00000589396,;	T	ENSG00000218891	ENST00000325421	Transcript	synonymous_variant	1541	1512	504	L	ctC/ctA	.	.	.	-1	ZNF579	HGNC	26646	protein_coding	YES	CCDS12927.1	ENSP00000320188	ZN579_HUMAN	.	UPI0000141657	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTGCGAGGGG	.	2	ESCA
TRIM33	0	.	GRCh37	1	114940051	114940051	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*219C>G	.	.	ENST00000358465	20/20	16	4	11	28	28	0	TRIM33,3_prime_UTR_variant,,ENST00000358465,;TRIM33,downstream_gene_variant,,ENST00000369543,;TRIM33,downstream_gene_variant,,ENST00000448034,;TRIM33,downstream_gene_variant,,ENST00000450349,;TRIM33,intron_variant,,ENST00000492227,;TRIM33,downstream_gene_variant,,ENST00000478032,;	C	ENSG00000197323	ENST00000358465	Transcript	3_prime_UTR_variant	3687	.	.	.	.	.	.	.	-1	TRIM33	HGNC	16290	protein_coding	YES	CCDS872.1	ENSP00000351250	TRI33_HUMAN	.	UPI000013D8CD	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTTGAAACT	.	5	ESCA
CSDE1	0	.	GRCh37	1	115260085	115260085	+	3'UTR	SNP	A	A	C	rs371539180	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*705T>G	.	.	ENST00000438362	20/20	23	17	6	26	26	0	CSDE1,3_prime_UTR_variant,,ENST00000369530,;CSDE1,3_prime_UTR_variant,,ENST00000261443,;CSDE1,3_prime_UTR_variant,,ENST00000358528,;CSDE1,3_prime_UTR_variant,,ENST00000339438,;CSDE1,3_prime_UTR_variant,,ENST00000530886,;CSDE1,3_prime_UTR_variant,,ENST00000438362,;NRAS,upstream_gene_variant,,ENST00000369535,;CSDE1,downstream_gene_variant,,ENST00000534699,;CSDE1,downstream_gene_variant,,ENST00000483407,;CSDE1,downstream_gene_variant,,ENST00000483030,;CSDE1,downstream_gene_variant,,ENST00000530784,;	C	ENSG00000009307	ENST00000438362	Transcript	3_prime_UTR_variant	3619	.	.	.	.	rs371539180	.	.	-1	CSDE1	HGNC	29905	protein_coding	YES	CCDS55626.1	ENSP00000407724	.	Q9UG93_HUMAN,G5E9Q2_HUMAN,E9PLD4_HUMAN,E9PKN4_HUMAN	UPI0000D99B0F	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAAATTCTG	.	5	ESCA
ZNF687	0	.	GRCh37	1	151254324	151254324	+	5'Flank	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000324048	.	28	20	7	30	30	0	ZNF687,5_prime_UTR_variant,,ENST00000443959,;RP11-126K1.2,5_prime_UTR_variant,,ENST00000447795,;ZNF687,upstream_gene_variant,,ENST00000324048,;ZNF687,upstream_gene_variant,,ENST00000368879,;ZNF687,upstream_gene_variant,,ENST00000336715,;RP11-126K1.2,non_coding_transcript_exon_variant,,ENST00000494138,;ZNF687,upstream_gene_variant,,ENST00000449313,;	T	ENSG00000143373	ENST00000324048	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	464	1	ZNF687	HGNC	29277	protein_coding	YES	CCDS992.1	ENSP00000319829	ZN687_HUMAN	.	UPI00000721F7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCAGTGC	.	5	ESCA
KPRP	0	.	GRCh37	1	152734527	152734527	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*723C>G	.	.	ENST00000368773	2/2	77	47	30	96	96	0	KPRP,3_prime_UTR_variant,,ENST00000368773,;KPRP,3_prime_UTR_variant,,ENST00000606109,;	G	ENSG00000203786	ENST00000368773	Transcript	3_prime_UTR_variant	2521	.	.	.	.	.	.	.	1	KPRP	HGNC	31823	protein_coding	YES	CCDS30862.1	ENSP00000357762	KPRP_HUMAN	.	UPI0000199942	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACTCACTGC	.	5	ESCA
FCRL1	0	.	GRCh37	1	157772422	157772422	+	Missense_Mutation	SNP	G	G	C	rs144206423	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.352C>G	p.Gln118Glu	p.Q118E	ENST00000368176	4/11	42	23	18	32	32	0	FCRL1,missense_variant,p.Gln118Glu,ENST00000368176,;FCRL1,missense_variant,p.Gln118Glu,ENST00000358292,;FCRL1,missense_variant,p.Gln118Glu,ENST00000491942,;FCRL1,non_coding_transcript_exon_variant,,ENST00000368175,;FCRL1,non_coding_transcript_exon_variant,,ENST00000489998,;FCRL1,downstream_gene_variant,,ENST00000480310,;FCRL1,upstream_gene_variant,,ENST00000495126,;FCRL1,upstream_gene_variant,,ENST00000463001,;	C	ENSG00000163534	ENST00000368176	Transcript	missense_variant	420	352	118	Q/E	Cag/Gag	rs144206423	.	.	-1	FCRL1	HGNC	18509	protein_coding	YES	CCDS1170.1	ENSP00000357158	FCRL1_HUMAN	.	UPI000006E5BD	.	deleterious(0.04)	possibly_damaging(0.733)	4/11	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF56,hmmpanther:PTHR11481,Pfam_domain:PF13895,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0.0002	A:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTGAGTCT	byFrequency|byCluster	5	ESCA
OR6N2	0	.	GRCh37	1	158746611	158746611	+	Missense_Mutation	SNP	C	C	T	rs753611659	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.815G>A	p.Arg272Gln	p.R272Q	ENST00000339258	1/1	74	53	20	87	87	0	OR6N2,missense_variant,p.Arg272Gln,ENST00000339258,;	T	ENSG00000188340	ENST00000339258	Transcript	missense_variant	815	815	272	R/Q	cGa/cAa	rs753611659,COSM1986925	.	.	-1	OR6N2	HGNC	15035	protein_coding	YES	CCDS30906.1	ENSP00000344101	OR6N2_HUMAN	.	UPI0000041C8E	.	tolerated(0.08)	benign(0.133)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26451:SF68,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTCGGTCA	.	5	ESCA
FCRL6	0	.	GRCh37	1	159772228	159772228	+	Missense_Mutation	SNP	C	C	T	rs750496573	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14C>T	p.Thr5Met	p.T5M	ENST00000368106	1/10	84	53	30	86	86	0	FCRL6,missense_variant,p.Thr5Met,ENST00000392235,;FCRL6,missense_variant,p.Thr5Met,ENST00000339348,;FCRL6,missense_variant,p.Thr12Met,ENST00000321935,;FCRL6,missense_variant,p.Thr5Met,ENST00000368106,;FCRL6,intron_variant,,ENST00000536257,;FCRL6,non_coding_transcript_exon_variant,,ENST00000541729,;FCRL6,intron_variant,,ENST00000540741,;	T	ENSG00000181036	ENST00000368106	Transcript	missense_variant	15	14	5	T/M	aCg/aTg	rs750496573	.	.	1	FCRL6	HGNC	31910	protein_coding	YES	CCDS30912.1	ENSP00000357086	FCRL6_HUMAN	.	UPI0000D62020	.	tolerated_low_confidence(0.27)	benign(0.004)	1/10	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGACGGCTG	byFrequency	5	ESCA
ATP1A2	0	.	GRCh37	1	160093831	160093831	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.480G>A	p.%3D	p.K160K	ENST00000361216	5/23	108	60	48	96	96	0	ATP1A2,synonymous_variant,p.%3D,ENST00000361216,;ATP1A2,synonymous_variant,p.%3D,ENST00000392233,;ATP1A2,upstream_gene_variant,,ENST00000447527,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000468587,;ATP1A2,downstream_gene_variant,,ENST00000478587,;	A	ENSG00000018625	ENST00000361216	Transcript	synonymous_variant	569	480	160	K	aaG/aaA	.	.	.	1	ATP1A2	HGNC	800	protein_coding	YES	CCDS1196.1	ENSP00000354490	AT1A2_HUMAN	Q58I22_HUMAN	UPI0000124FC1	.	.	.	5/23	.	hmmpanther:PTHR24093:SF229,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01106,Gene3D:1bg5A03,Pfam_domain:PF00122,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAAGAACAT	.	5	ESCA
USP21	0	.	GRCh37	1	161133747	161133747	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1194T>G	p.Cys398Trp	p.C398W	ENST00000368002	9/14	78	47	31	74	74	0	USP21,missense_variant,p.Cys398Trp,ENST00000289865,;USP21,missense_variant,p.Cys398Trp,ENST00000368001,;USP21,missense_variant,p.Cys398Trp,ENST00000368002,;PPOX,upstream_gene_variant,,ENST00000367999,;PPOX,upstream_gene_variant,,ENST00000352210,;USP21,downstream_gene_variant,,ENST00000479344,;PPOX,upstream_gene_variant,,ENST00000537523,;PPOX,upstream_gene_variant,,ENST00000544598,;PPOX,upstream_gene_variant,,ENST00000432542,;USP21,downstream_gene_variant,,ENST00000492950,;PPOX,upstream_gene_variant,,ENST00000535223,;RP11-297K8.2,upstream_gene_variant,,ENST00000420498,;USP21,intron_variant,,ENST00000493054,;PPOX,upstream_gene_variant,,ENST00000462977,;PPOX,upstream_gene_variant,,ENST00000490768,;PPOX,upstream_gene_variant,,ENST00000497522,;PPOX,upstream_gene_variant,,ENST00000470607,;USP21,downstream_gene_variant,,ENST00000486299,;PPOX,upstream_gene_variant,,ENST00000494216,;PPOX,upstream_gene_variant,,ENST00000495483,;PPOX,upstream_gene_variant,,ENST00000460611,;PPOX,upstream_gene_variant,,ENST00000462866,;USP21,non_coding_transcript_exon_variant,,ENST00000485277,;USP21,non_coding_transcript_exon_variant,,ENST00000487163,;USP21,intron_variant,,ENST00000482385,;PPOX,upstream_gene_variant,,ENST00000468968,;PPOX,upstream_gene_variant,,ENST00000539753,;PPOX,upstream_gene_variant,,ENST00000479246,;	G	ENSG00000143258	ENST00000368002	Transcript	missense_variant	1571	1194	398	C/W	tgT/tgG	.	.	.	1	USP21	HGNC	12620	protein_coding	YES	CCDS30920.1	ENSP00000356981	UBP21_HUMAN	.	UPI00001379FD	.	tolerated(1)	probably_damaging(0.979)	9/14	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF365,Pfam_domain:PF00443,Gene3D:1nbfA02,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGTGACCT	.	5	ESCA
ILDR2	0	.	GRCh37	1	166888577	166888577	+	3'UTR	SNP	G	G	T	rs746348126	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*15C>A	.	.	ENST00000271417	10/10	72	54	17	55	55	0	ILDR2,missense_variant,p.Ser421Tyr,ENST00000469934,;ILDR2,3_prime_UTR_variant,,ENST00000526687,;ILDR2,3_prime_UTR_variant,,ENST00000529387,;ILDR2,3_prime_UTR_variant,,ENST00000271417,;ILDR2,3_prime_UTR_variant,,ENST00000525740,;ILDR2,3_prime_UTR_variant,,ENST00000529071,;ILDR2,3_prime_UTR_variant,,ENST00000528703,;	T	ENSG00000143195	ENST00000271417	Transcript	3_prime_UTR_variant	1991	.	.	.	.	rs746348126	.	.	-1	ILDR2	HGNC	18131	protein_coding	YES	CCDS1256.1	ENSP00000271417	ILDR2_HUMAN	.	UPI00002317DF	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGAGAAATG	.	5	ESCA
ILDR2	0	.	GRCh37	1	166888578	166888578	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*14T>A	.	.	ENST00000271417	10/10	71	54	17	55	55	0	ILDR2,missense_variant,p.Ser421Thr,ENST00000469934,;ILDR2,3_prime_UTR_variant,,ENST00000526687,;ILDR2,3_prime_UTR_variant,,ENST00000529387,;ILDR2,3_prime_UTR_variant,,ENST00000271417,;ILDR2,3_prime_UTR_variant,,ENST00000525740,;ILDR2,3_prime_UTR_variant,,ENST00000529071,;ILDR2,3_prime_UTR_variant,,ENST00000528703,;	T	ENSG00000143195	ENST00000271417	Transcript	3_prime_UTR_variant	1990	.	.	.	.	.	.	.	-1	ILDR2	HGNC	18131	protein_coding	YES	CCDS1256.1	ENSP00000271417	ILDR2_HUMAN	.	UPI00002317DF	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGAAATGT	.	5	ESCA
ANKRD45	0	.	GRCh37	1	173616057	173616057	+	Silent	SNP	G	G	T	rs117552597	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.424C>A	p.%3D	p.R142R	ENST00000333279	3/6	41	28	12	31	30	1	ANKRD45,synonymous_variant,p.%3D,ENST00000333279,;	T	ENSG00000183831	ENST00000333279	Transcript	synonymous_variant	485	424	142	R	Cgg/Agg	rs117552597	.	.	-1	ANKRD45	HGNC	24786	protein_coding	YES	CCDS1309.1	ENSP00000331268	ANR45_HUMAN	.	UPI000019851A	.	.	.	3/6	.	Superfamily_domains:SSF48403,Gene3D:1.25.40.20,hmmpanther:PTHR24180:SF12,hmmpanther:PTHR24180,PROSITE_profiles:PS50297	A:0.0010	A:0	A:0.0014	.	A:0.003	A:0	A:0.001	A:0.0002	A:0.0006	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TTCCCGGAAGT	byFrequency|byCluster|by1000G	2	ESCA
SOAT1	0	.	GRCh37	1	179304721	179304721	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258A>G	p.%3D	p.S86S	ENST00000367619	4/16	33	18	14	36	36	0	SOAT1,synonymous_variant,p.%3D,ENST00000540564,;SOAT1,synonymous_variant,p.%3D,ENST00000539888,;SOAT1,synonymous_variant,p.%3D,ENST00000367619,;SOAT1,synonymous_variant,p.%3D,ENST00000426956,;SOAT1,5_prime_UTR_variant,,ENST00000535686,;	G	ENSG00000057252	ENST00000367619	Transcript	synonymous_variant	401	258	86	S	tcA/tcG	.	.	.	1	SOAT1	HGNC	11177	protein_coding	YES	CCDS1330.1	ENSP00000356591	SOAT1_HUMAN	B4DFD8_HUMAN,B1APM4_HUMAN	UPI0000071233	.	.	.	4/16	.	hmmpanther:PTHR10408:SF6,hmmpanther:PTHR10408,PIRSF_domain:PIRSF000439,PIRSF_domain:PIRSF500230	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATCATTAGA	.	5	ESCA
RGSL1	0	.	GRCh37	1	182517507	182517507	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2725G>A	p.Glu909Lys	p.E909K	ENST00000294854	16/22	40	25	14	28	28	0	RGSL1,missense_variant,p.Glu909Lys,ENST00000294854,;RGSL1,missense_variant,p.Glu944Lys,ENST00000542961,;RGSL1,missense_variant,p.Glu944Lys,ENST00000443996,;RGSL1,3_prime_UTR_variant,,ENST00000415960,;RGSL1,non_coding_transcript_exon_variant,,ENST00000436031,;	A	ENSG00000121446	ENST00000294854	Transcript	missense_variant	2745	2725	909	E/K	Gag/Aag	.	.	.	1	RGSL1	HGNC	18636	protein_coding	YES	CCDS58049.1	ENSP00000457748	RGSL_HUMAN	H3BNQ0_HUMAN	UPI000156571A	.	tolerated(0.11)	benign(0.059)	16/22	.	hmmpanther:PTHR10845:SF137,hmmpanther:PTHR10845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAATGAGAAT	.	5	ESCA
PIGR	0	.	GRCh37	1	207102208	207102208	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1455C>A	.	.	ENST00000356495	11/11	45	29	16	57	57	0	PIGR,3_prime_UTR_variant,,ENST00000356495,;PIGR,downstream_gene_variant,,ENST00000487208,;	T	ENSG00000162896	ENST00000356495	Transcript	3_prime_UTR_variant	3934	.	.	.	.	.	.	.	-1	PIGR	HGNC	8968	protein_coding	YES	CCDS1474.1	ENSP00000348888	PIGR_HUMAN	.	UPI000007407E	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGCAGGGGCTC	.	4	ESCA
EPRS	0	.	GRCh37	1	220154793	220154793	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3380A>G	p.Tyr1127Cys	p.Y1127C	ENST00000366923	24/32	57	42	15	65	65	0	EPRS,missense_variant,p.Tyr1127Cys,ENST00000366923,;EPRS,downstream_gene_variant,,ENST00000485821,;	C	ENSG00000136628	ENST00000366923	Transcript	missense_variant	3650	3380	1127	Y/C	tAt/tGt	.	.	.	-1	EPRS	HGNC	3418	protein_coding	YES	CCDS31027.1	ENSP00000355890	SYEP_HUMAN	.	UPI0000205E8C	.	deleterious(0)	probably_damaging(0.977)	24/32	.	Superfamily_domains:SSF55681,Gene3D:3.30.930.10,TIGRFAM_domain:TIGR00408,Pfam_domain:PF00587,hmmpanther:PTHR10119:SF15,hmmpanther:PTHR10119,PROSITE_profiles:PS50862,HAMAP:MF_01571	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGATACATT	.	5	ESCA
PARP1	0	.	GRCh37	1	226576388	226576388	+	Missense_Mutation	SNP	T	T	A	rs535937365	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686A>T	p.Asp229Val	p.D229V	ENST00000366794	5/23	29	17	12	26	26	0	PARP1,missense_variant,p.Asp229Val,ENST00000366794,;PARP1,downstream_gene_variant,,ENST00000366792,;PARP1,downstream_gene_variant,,ENST00000366791,;PARP1,downstream_gene_variant,,ENST00000469663,;	A	ENSG00000143799	ENST00000366794	Transcript	missense_variant	830	686	229	D/V	gAc/gTc	rs535937365	.	.	-1	PARP1	HGNC	270	protein_coding	YES	CCDS1554.1	ENSP00000355759	PARP1_HUMAN	Q96P95_HUMAN	UPI000013D92D	.	tolerated(0.11)	benign(0.027)	5/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15447:SF13,hmmpanther:PTHR15447,PIRSF_domain:PIRSF000489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGTCTTTT	byCluster	5	ESCA
OBSCN	0	.	GRCh37	1	228487030	228487030	+	Missense_Mutation	SNP	A	A	C	rs562894992	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13281A>C	p.Gln4427His	p.Q4427H	ENST00000570156	50/116	90	62	28	80	80	0	OBSCN,missense_variant,p.Gln1117His,ENST00000366707,;OBSCN,missense_variant,p.Gln1274His,ENST00000483539,;OBSCN,missense_variant,p.Gln4427His,ENST00000570156,;OBSCN,3_prime_UTR_variant,,ENST00000359599,;OBSCN,intron_variant,,ENST00000366709,;OBSCN,intron_variant,,ENST00000284548,;OBSCN,intron_variant,,ENST00000422127,;RP5-1139B12.4,intron_variant,,ENST00000602778,;OBSCN,upstream_gene_variant,,ENST00000602685,;OBSCN,upstream_gene_variant,,ENST00000602832,;OBSCN,downstream_gene_variant,,ENST00000494839,;	C	ENSG00000154358	ENST00000570156	Transcript	missense_variant	13355	13281	4427	Q/H	caA/caC	rs562894992	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	benign(0.034)	50/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAATGTGA	by1000G	5	ESCA
URB2	0	.	GRCh37	1	229771466	229771466	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1106A>G	p.Asn369Ser	p.N369S	ENST00000258243	4/10	37	20	17	36	36	0	URB2,missense_variant,p.Asn369Ser,ENST00000258243,;	G	ENSG00000135763	ENST00000258243	Transcript	missense_variant	1242	1106	369	N/S	aAc/aGc	.	.	.	1	URB2	HGNC	28967	protein_coding	YES	CCDS31052.1	ENSP00000258243	URB2_HUMAN	Q5VYD0_HUMAN	UPI000013CFBD	.	tolerated(1)	benign(0.001)	4/10	.	hmmpanther:PTHR15682	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCAACAACA	.	5	ESCA
MAP10	0	.	GRCh37	1	232943711	232943711	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2942C>A	p.Ser981Tyr	p.S981Y	ENST00000418460	1/1	29	22	7	34	34	0	MAP10,missense_variant,p.Ser981Tyr,ENST00000418460,;	A	ENSG00000212916	ENST00000418460	Transcript	missense_variant	3069	2942	981	S/Y	tCt/tAt	.	.	.	1	MAP10	HGNC	29265	protein_coding	YES	CCDS44334.1	ENSP00000403208	MAP10_HUMAN	.	UPI0000418F25	.	deleterious(0.02)	possibly_damaging(0.907)	1/1	.	hmmpanther:PTHR21831,hmmpanther:PTHR21831:SF1,Pfam_domain:PF14925	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATCTTTAG	.	5	ESCA
OR14C36	0	.	GRCh37	1	248512820	248512820	+	Silent	SNP	C	C	T	rs142764213	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.744C>T	p.%3D	p.V248V	ENST00000317861	1/1	21	15	6	28	28	0	OR14C36,synonymous_variant,p.%3D,ENST00000317861,;	T	ENSG00000177174	ENST00000317861	Transcript	synonymous_variant	744	744	248	V	gtC/gtT	rs142764213	.	.	1	OR14C36	HGNC	15026	protein_coding	YES	CCDS31112.1	ENSP00000324534	O14CZ_HUMAN	.	UPI0000041CB1	.	.	.	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF180,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGTCTTCCT	byCluster	5	ESCA
STMN1	0	.	GRCh37	1	26228032	26228032	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.328G>A	p.Glu110Lys	p.E110K	ENST00000426559	4/5	42	23	19	52	52	0	STMN1,missense_variant,p.Glu110Lys,ENST00000399728,;STMN1,missense_variant,p.Glu110Lys,ENST00000426559,;STMN1,missense_variant,p.Glu110Lys,ENST00000374291,;STMN1,missense_variant,p.Glu110Lys,ENST00000357865,;STMN1,missense_variant,p.Glu110Lys,ENST00000455785,;STMN1,downstream_gene_variant,,ENST00000446334,;MIR3917,downstream_gene_variant,,ENST00000580971,;STMN1,non_coding_transcript_exon_variant,,ENST00000465604,;STMN1,non_coding_transcript_exon_variant,,ENST00000485226,;	T	ENSG00000117632	ENST00000426559	Transcript	missense_variant	468	328	110	E/K	Gag/Aag	.	.	.	-1	STMN1	HGNC	6510	protein_coding	YES	CCDS44090.1	ENSP00000410452	STMN1_HUMAN	A2A2D0_HUMAN	UPI000191512D	.	deleterious(0.01)	probably_damaging(0.925)	4/5	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51663,hmmpanther:PTHR10104,Pfam_domain:PF00836,PIRSF_domain:PIRSF002285,Superfamily_domains:0043535,Prints_domain:PR00345	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTCTTTAT	.	5	ESCA
MAP3K6	0	.	GRCh37	1	27687484	27687484	+	Silent	SNP	G	G	T	rs760381536	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1848C>A	p.%3D	p.I616I	ENST00000493901	15/30	9	5	4	12	12	0	MAP3K6,synonymous_variant,p.%3D,ENST00000374040,;MAP3K6,synonymous_variant,p.%3D,ENST00000357582,;MAP3K6,synonymous_variant,p.%3D,ENST00000472410,;MAP3K6,synonymous_variant,p.%3D,ENST00000493901,;MAP3K6,upstream_gene_variant,,ENST00000486046,;MAP3K6,upstream_gene_variant,,ENST00000470890,;MAP3K6,upstream_gene_variant,,ENST00000476509,;MAP3K6,upstream_gene_variant,,ENST00000495230,;	T	ENSG00000142733	ENST00000493901	Transcript	synonymous_variant	2088	1848	616	I	atC/atA	rs760381536,COSM1502555,COSM1502554	.	.	-1	MAP3K6	HGNC	6858	protein_coding	YES	CCDS299.1	ENSP00000419591	M3K6_HUMAN	Q32MQ5_HUMAN	UPI0000205587	.	.	.	15/30	.	hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF371	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCCTGGATCAG	byFrequency	3	ESCA
PABPC4	0	.	GRCh37	1	40027358	40027358	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*12C>T	.	.	ENST00000372858	15/16	138	112	26	24	24	0	PABPC4,splice_region_variant,,ENST00000372858,;PABPC4,splice_region_variant,,ENST00000372862,;PABPC4,splice_region_variant,,ENST00000372857,;PABPC4,splice_region_variant,,ENST00000372856,;PABPC4,3_prime_UTR_variant,,ENST00000530186,;PABPC4,intron_variant,,ENST00000437136,;PABPC4,downstream_gene_variant,,ENST00000527718,;PABPC4,downstream_gene_variant,,ENST00000421687,;RP11-69E11.8,upstream_gene_variant,,ENST00000415255,;PABPC4,splice_region_variant,,ENST00000492468,;PABPC4,splice_region_variant,,ENST00000482028,;PABPC4,non_coding_transcript_exon_variant,,ENST00000468476,;PABPC4,downstream_gene_variant,,ENST00000470443,;PABPC4,downstream_gene_variant,,ENST00000525045,;PABPC4,downstream_gene_variant,,ENST00000461578,;PABPC4,downstream_gene_variant,,ENST00000513632,;PABPC4,downstream_gene_variant,,ENST00000484555,;PABPC4,downstream_gene_variant,,ENST00000483770,;PABPC4,downstream_gene_variant,,ENST00000525669,;PABPC4,downstream_gene_variant,,ENST00000477556,;PPIEL,upstream_gene_variant,,ENST00000427240,;	A	ENSG00000090621	ENST00000372858	Transcript	splice_region_variant	2445	.	.	.	.	.	.	.	-1	PABPC4	HGNC	8557	protein_coding	YES	CCDS44115.1	ENSP00000361949	PABP4_HUMAN	B1ANR1_HUMAN	UPI00002057C5	.	.	.	15/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE	ATACGGTTTTT	.	3	ESCA
SLFNL1	0	.	GRCh37	1	41481743	41481743	+	3'UTR	SNP	G	G	C	rs753408231	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*35C>G	.	.	ENST00000359345	4/4	136	123	13	42	42	0	SLFNL1,3_prime_UTR_variant,,ENST00000302946,;SLFNL1,3_prime_UTR_variant,,ENST00000397197,;SLFNL1,3_prime_UTR_variant,,ENST00000372611,;SLFNL1,3_prime_UTR_variant,,ENST00000359345,;SLFNL1,3_prime_UTR_variant,,ENST00000372613,;SLFNL1,3_prime_UTR_variant,,ENST00000439569,;CTPS1,downstream_gene_variant,,ENST00000372616,;CTPS1,downstream_gene_variant,,ENST00000541520,;CTPS1,downstream_gene_variant,,ENST00000372621,;CTPS1,downstream_gene_variant,,ENST00000498694,;	C	ENSG00000171790	ENST00000359345	Transcript	3_prime_UTR_variant	3836	.	.	.	.	rs753408231	.	.	-1	SLFNL1	HGNC	26313	protein_coding	YES	CCDS460.1	ENSP00000352299	SLNL1_HUMAN	.	UPI000013E83F	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGAGAGTGC	byFrequency	4	ESCA
MPL	0	.	GRCh37	1	43804213	43804213	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.213G>A	p.%3D	p.R71R	ENST00000372470	3/12	110	96	14	49	49	0	MPL,synonymous_variant,p.%3D,ENST00000413998,;MPL,synonymous_variant,p.%3D,ENST00000372470,;	A	ENSG00000117400	ENST00000372470	Transcript	synonymous_variant	255	213	71	R	cgG/cgA	.	.	.	1	MPL	HGNC	7217	protein_coding	YES	CCDS483.1	ENSP00000361548	TPOR_HUMAN	.	UPI000002DB88	.	.	.	3/12	.	Superfamily_domains:SSF49265,Gene3D:2.60.40.10,Pfam_domain:PF09067,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACAGGGAGAA	.	4	ESCA
SZT2	0	.	GRCh37	1	43902856	43902856	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5878G>A	p.Glu1960Lys	p.E1960K	ENST00000562955	42/71	110	91	19	40	40	0	SZT2,missense_variant,p.Glu1118Lys,ENST00000372442,;SZT2,missense_variant,p.Glu1960Lys,ENST00000562955,;SZT2,upstream_gene_variant,,ENST00000471177,;SZT2,upstream_gene_variant,,ENST00000470897,;	A	ENSG00000198198	ENST00000562955	Transcript	missense_variant	5878	5878	1960	E/K	Gag/Aag	.	.	.	1	SZT2	HGNC	29040	protein_coding	YES	CCDS30694.2	ENSP00000457168	SZT2_HUMAN	.	UPI0001E24F46	.	deleterious(0.04)	probably_damaging(0.996)	42/71	.	hmmpanther:PTHR14918	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGATGAGAGC	.	5	ESCA
ATPAF1	0	.	GRCh37	1	47098595	47098595	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2853G>T	.	.	ENST00000576409	9/9	43	29	14	34	34	0	ATPAF1,3_prime_UTR_variant,,ENST00000371937,;ATPAF1,3_prime_UTR_variant,,ENST00000574428,;ATPAF1,3_prime_UTR_variant,,ENST00000576409,;ATPAF1,downstream_gene_variant,,ENST00000534216,;ATPAF1,downstream_gene_variant,,ENST00000542495,;ATPAF1,downstream_gene_variant,,ENST00000532925,;ATPAF1,downstream_gene_variant,,ENST00000492233,;ATPAF1,downstream_gene_variant,,ENST00000329231,;ATPAF1,downstream_gene_variant,,ENST00000526821,;ATPAF1,downstream_gene_variant,,ENST00000529214,;	A	ENSG00000123472	ENST00000576409	Transcript	3_prime_UTR_variant	3972	.	.	.	.	.	.	.	-1	ATPAF1	HGNC	18803	protein_coding	YES	CCDS541.2	ENSP00000460964	.	I3L448_HUMAN	UPI000222BB4E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCACTATGG	.	5	ESCA
FOXD2	0	.	GRCh37	1	47904390	47904390	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583C>T	p.Pro195Ser	p.P195S	ENST00000334793	1/1	140	108	32	128	128	0	FOXD2,missense_variant,p.Pro195Ser,ENST00000334793,;FOXD2-AS1,upstream_gene_variant,,ENST00000445551,;	T	ENSG00000186564	ENST00000334793	Transcript	missense_variant	2702	583	195	P/S	Ccg/Tcg	.	.	.	1	FOXD2	HGNC	3803	protein_coding	YES	CCDS30708.1	ENSP00000335493	FOXD2_HUMAN	.	UPI000014153E	.	deleterious(0.01)	probably_damaging(0.988)	1/1	.	PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF85,hmmpanther:PTHR11829,Pfam_domain:PF00250,Gene3D:1.10.10.10,SMART_domains:SM00339,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAACCCGGGC	.	5	ESCA
BEND5	0	.	GRCh37	1	49227056	49227056	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313G>T	p.Glu105Ter	p.E105*	ENST00000371833	2/6	95	73	21	83	83	0	BEND5,stop_gained,p.Glu105Ter,ENST00000371833,;AGBL4,intron_variant,,ENST00000371839,;AGBL4,intron_variant,,ENST00000416121,;AGBL4,intron_variant,,ENST00000371838,;BEND5,intron_variant,,ENST00000480399,;BEND5,upstream_gene_variant,,ENST00000476079,;BEND5,upstream_gene_variant,,ENST00000476096,;BEND5,non_coding_transcript_exon_variant,,ENST00000463562,;BEND5,non_coding_transcript_exon_variant,,ENST00000489956,;	A	ENSG00000162373	ENST00000371833	Transcript	stop_gained	400	313	105	E/*	Gag/Tag	.	.	.	-1	BEND5	HGNC	25668	protein_coding	YES	CCDS552.2	ENSP00000360899	BEND5_HUMAN	.	UPI00002042F4	.	.	.	2/6	.	hmmpanther:PTHR14628	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCTCTCCAT	.	5	ESCA
C8A	0	.	GRCh37	1	57378148	57378148	+	Missense_Mutation	SNP	C	C	A	rs370599466	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1453C>A	p.Arg485Ser	p.R485S	ENST00000361249	10/11	62	47	15	40	40	0	C8A,missense_variant,p.Arg485Ser,ENST00000361249,;	A	ENSG00000157131	ENST00000361249	Transcript	missense_variant	1549	1453	485	R/S	Cgc/Agc	rs370599466,COSM393977	.	.	1	C8A	HGNC	1352	protein_coding	YES	CCDS606.1	ENSP00000354458	CO8A_HUMAN	.	UPI0000127C5A	.	deleterious(0)	benign(0.296)	10/11	.	PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF338,hmmpanther:PTHR19325,Pfam_domain:PF01823,SMART_domains:SM00457,Prints_domain:PR00764	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R484C|c.1450C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGCCGCGCC	byFrequency|byCluster	5	ESCA
OMA1	0	.	GRCh37	1	59004831	59004831	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136A>G	p.Ile46Val	p.I46V	ENST00000371226	2/9	355	281	73	40	40	0	OMA1,missense_variant,p.Ile46Val,ENST00000482274,;OMA1,missense_variant,p.Ile46Val,ENST00000456980,;OMA1,missense_variant,p.Ile46Val,ENST00000426139,;OMA1,missense_variant,p.Ile46Val,ENST00000358603,;OMA1,missense_variant,p.Ile46Val,ENST00000371226,;OMA1,missense_variant,p.Ile46Val,ENST00000453710,;OMA1,missense_variant,p.Ile46Val,ENST00000419242,;OMA1,upstream_gene_variant,,ENST00000421528,;OMA1,intron_variant,,ENST00000467063,;DAB1,intron_variant,,ENST00000485760,;	C	ENSG00000162600	ENST00000371226	Transcript	missense_variant	250	136	46	I/V	Ata/Gta	.	.	.	-1	OMA1	HGNC	29661	protein_coding	YES	CCDS608.1	ENSP00000360270	OMA1_HUMAN	S4R3A3_HUMAN	UPI000006D0C6	.	tolerated_low_confidence(1)	benign(0.003)	2/9	.	hmmpanther:PTHR22726,hmmpanther:PTHR22726:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTATATGGT	.	5	ESCA
JUN	0	.	GRCh37	1	59247677	59247677	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*70G>C	.	.	ENST00000371222	1/1	143	130	13	42	42	0	JUN,3_prime_UTR_variant,,ENST00000371222,;LINC01135,upstream_gene_variant,,ENST00000544621,;LINC01135,upstream_gene_variant,,ENST00000419531,;	G	ENSG00000177606	ENST00000371222	Transcript	3_prime_UTR_variant	2109	.	.	.	.	.	.	.	-1	JUN	HGNC	6204	protein_coding	YES	CCDS610.1	ENSP00000360266	JUN_HUMAN	.	UPI000000D908	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTGTCAAGTT	.	3	ESCA
INADL	0	.	GRCh37	1	62253574	62253574	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.998C>T	p.Ser333Leu	p.S333L	ENST00000371158	8/43	177	161	15	43	43	0	INADL,missense_variant,p.Ser333Leu,ENST00000316485,;INADL,missense_variant,p.Ser333Leu,ENST00000371158,;INADL,non_coding_transcript_exon_variant,,ENST00000459752,;INADL,non_coding_transcript_exon_variant,,ENST00000484562,;	T	ENSG00000132849	ENST00000371158	Transcript	missense_variant	1112	998	333	S/L	tCa/tTa	.	.	.	1	INADL	HGNC	28881	protein_coding	YES	CCDS617.2	ENSP00000360200	INADL_HUMAN	.	UPI0000204487	.	tolerated(0.07)	benign(0.011)	8/43	.	hmmpanther:PTHR19964:SF11,hmmpanther:PTHR19964	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CATTTCAGTCA	.	3	ESCA
RPE65	0	.	GRCh37	1	68895504	68895504	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1557G>C	p.Glu519Asp	p.E519D	ENST00000262340	14/14	30	25	5	11	11	0	RPE65,missense_variant,p.Glu519Asp,ENST00000262340,;	G	ENSG00000116745	ENST00000262340	Transcript	missense_variant	1611	1557	519	E/D	gaG/gaC	.	.	.	-1	RPE65	HGNC	10294	protein_coding	YES	CCDS643.1	ENSP00000262340	RPE65_HUMAN	Q2EKB8_HUMAN,C7FEP0_HUMAN	UPI000004346C	.	tolerated(0.21)	benign(0)	14/14	.	hmmpanther:PTHR10543,hmmpanther:PTHR10543:SF7,Pfam_domain:PF03055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATCTCCAC	.	5	ESCA
ANKEF1	0	.	GRCh37	20	10030832	10030832	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1615G>C	p.Asp539His	p.D539H	ENST00000378380	6/10	42	35	6	46	46	0	ANKEF1,missense_variant,p.Asp539His,ENST00000378380,;ANKEF1,missense_variant,p.Asp539His,ENST00000378392,;SNAP25-AS1,intron_variant,,ENST00000603542,;SNAP25-AS1,intron_variant,,ENST00000421143,;ANKEF1,non_coding_transcript_exon_variant,,ENST00000488991,;	C	ENSG00000132623	ENST00000378380	Transcript	missense_variant	1944	1615	539	D/H	Gat/Cat	.	.	.	1	ANKEF1	HGNC	15803	protein_coding	YES	CCDS13108.1	ENSP00000367631	ANKE1_HUMAN	.	UPI0000125B51	.	deleterious(0.02)	possibly_damaging(0.872)	6/10	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24127,hmmpanther:PTHR24127:SF1,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATAGATGTG	.	5	ESCA
SYNDIG1	0	.	GRCh37	20	24524206	24524206	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473A>G	p.Glu158Gly	p.E158G	ENST00000376862	2/4	29	22	6	11	11	0	SYNDIG1,missense_variant,p.Glu158Gly,ENST00000376862,;	G	ENSG00000101463	ENST00000376862	Transcript	missense_variant	1106	473	158	E/G	gAg/gGg	.	.	.	1	SYNDIG1	HGNC	15885	protein_coding	YES	CCDS13164.1	ENSP00000366058	SYNG1_HUMAN	.	UPI00001285DC	.	deleterious(0.05)	possibly_damaging(0.804)	2/4	.	hmmpanther:PTHR14768,hmmpanther:PTHR14768:SF3,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGAGCTGG	.	5	ESCA
DEFB123	0	.	GRCh37	20	30037842	30037842	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69A>G	p.%3D	p.Q23Q	ENST00000376309	2/2	63	45	18	49	49	0	DEFB123,synonymous_variant,p.%3D,ENST00000376309,;	G	ENSG00000180424	ENST00000376309	Transcript	synonymous_variant	249	69	23	Q	caA/caG	.	.	.	1	DEFB123	HGNC	18103	protein_coding	YES	CCDS13180.1	ENSP00000365486	DB123_HUMAN	Q5GRF8_HUMAN	UPI0000128D96	.	.	.	2/2	.	hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCAAAGATG	.	5	ESCA
ZNF341	0	.	GRCh37	20	32341071	32341071	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583C>T	p.Gln195Ter	p.Q195*	ENST00000342427	5/15	64	53	11	29	29	0	ZNF341,stop_gained,p.Gln195Ter,ENST00000375200,;ZNF341,stop_gained,p.Gln195Ter,ENST00000342427,;ZNF341,stop_gained,p.Gln195Ter,ENST00000483118,;ZNF341,3_prime_UTR_variant,,ENST00000497876,;RPL31P2,upstream_gene_variant,,ENST00000413849,;	T	ENSG00000131061	ENST00000342427	Transcript	stop_gained	948	583	195	Q/*	Cag/Tag	.	.	.	1	ZNF341	HGNC	15992	protein_coding	YES	CCDS13227.1	ENSP00000344308	ZN341_HUMAN	.	UPI000022B43D	.	.	.	5/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCAGCCT	.	5	ESCA
HELZ2	0	.	GRCh37	20	62194954	62194954	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5221C>T	p.%3D	p.L1741L	ENST00000467148	8/19	20	11	9	31	31	0	HELZ2,synonymous_variant,p.%3D,ENST00000467148,;HELZ2,synonymous_variant,p.%3D,ENST00000427522,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,upstream_gene_variant,,ENST00000478861,;	A	ENSG00000130589	ENST00000467148	Transcript	synonymous_variant	5291	5221	1741	L	Ctg/Ttg	.	.	.	-1	HELZ2	HGNC	30021	protein_coding	YES	CCDS33508.1	ENSP00000417401	HELZ2_HUMAN	Q3C1U4_HUMAN	UPI0000246BF7	.	.	.	8/19	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF332	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCAGCTTGT	.	5	ESCA
APP	0	.	GRCh37	21	27462296	27462296	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318G>T	p.Lys106Asn	p.K106N	ENST00000346798	3/18	90	25	65	89	89	0	APP,missense_variant,p.Lys101Asn,ENST00000440126,;APP,missense_variant,p.Lys106Asn,ENST00000359726,;APP,missense_variant,p.Lys106Asn,ENST00000358918,;APP,missense_variant,p.Lys106Asn,ENST00000357903,;APP,missense_variant,p.Lys106Asn,ENST00000346798,;APP,missense_variant,p.Lys50Asn,ENST00000354192,;APP,missense_variant,p.Lys28Asn,ENST00000448850,;APP,missense_variant,p.Lys50Asn,ENST00000439274,;APP,missense_variant,p.Lys106Asn,ENST00000348990,;APP,missense_variant,p.Lys71Asn,ENST00000448388,;APP,non_coding_transcript_exon_variant,,ENST00000474136,;APP,non_coding_transcript_exon_variant,,ENST00000462267,;	A	ENSG00000142192	ENST00000346798	Transcript	missense_variant	352	318	106	K/N	aaG/aaT	.	.	.	-1	APP	HGNC	620	protein_coding	YES	CCDS13576.1	ENSP00000284981	A4_HUMAN	L7XE61_HUMAN,L7XCZ9_HUMAN,B7Z313_HUMAN	UPI000002DB1C	.	deleterious(0.02)	unknown(0)	3/18	.	Superfamily_domains:0041119,SMART_domains:SM00006,Pfam_domain:PF02177,Gene3D:1mwpA00,hmmpanther:PTHR23103:SF7,hmmpanther:PTHR23103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGTCTTGCA	.	5	ESCA
SLC5A3	0	.	GRCh37	21	35468056	35468056	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559C>G	p.Leu187Val	p.L187V	ENST00000608209	2/2	28	17	10	45	45	0	SLC5A3,missense_variant,p.Leu187Val,ENST00000608209,;SLC5A3,missense_variant,p.Leu187Val,ENST00000381151,;MRPS6,intron_variant,,ENST00000399312,;MRPS6,intron_variant,,ENST00000477091,;MRPS6,intron_variant,,ENST00000488492,;AP000320.7,intron_variant,,ENST00000362077,;	G	ENSG00000272962	ENST00000608209	Transcript	missense_variant	1071	559	187	L/V	Ctg/Gtg	COSM267453	.	.	1	SLC5A3	Uniprot_gn	11038	protein_coding	YES	CCDS33549.1	ENSP00000477068	.	.	UPI00001359F3	.	tolerated(0.23)	benign(0.192)	2/2	.	PROSITE_profiles:PS50283,hmmpanther:PTHR11819:SF123,hmmpanther:PTHR11819,TIGRFAM_domain:TIGR00813,Pfam_domain:PF00474	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTCTGCAG	.	5	ESCA
DYRK1A	0	.	GRCh37	21	38887441	38887441	+	3'Flank	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000398960	.	44	31	12	42	42	0	DYRK1A,3_prime_UTR_variant,,ENST00000339659,;DYRK1A,3_prime_UTR_variant,,ENST00000338785,;DYRK1A,downstream_gene_variant,,ENST00000455387,;DYRK1A,downstream_gene_variant,,ENST00000398956,;DYRK1A,downstream_gene_variant,,ENST00000398960,;AP001421.1,upstream_gene_variant,,ENST00000597817,;	T	ENSG00000157540	ENST00000398960	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2552	1	DYRK1A	HGNC	3091	protein_coding	YES	CCDS42925.1	ENSP00000381932	DYR1A_HUMAN	Q76N25_HUMAN,N0GVR9_HUMAN,F8WAP0_HUMAN,E7EMI5_HUMAN	UPI0000129A31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCATGCGGTC	.	5	ESCA
C21orf88	0	.	GRCh37	21	40978250	40978250	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.152+3260G>C	.	.	ENST00000380612	.	38	29	8	24	24	0	C21orf88,missense_variant,p.Lys59Asn,ENST00000329618,;B3GALT5,intron_variant,,ENST00000380620,;C21orf88,intron_variant,,ENST00000380604,;C21orf88,intron_variant,,ENST00000380612,;	G	ENSG00000184809	ENST00000380612	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	C21orf88	HGNC	16424	protein_coding	YES	.	ENSP00000369986	CU088_HUMAN	.	UPI00001AFA76	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGGCTTCCA	.	5	ESCA
ADARB1	0	.	GRCh37	21	46646029	46646029	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3917G>T	.	.	ENST00000539173	12/12	8	1	7	10	10	0	ADARB1,3_prime_UTR_variant,,ENST00000437626,;ADARB1,3_prime_UTR_variant,,ENST00000539173,;ADARB1,3_prime_UTR_variant,,ENST00000360697,;ADARB1,3_prime_UTR_variant,,ENST00000348831,;ADARB1,3_prime_UTR_variant,,ENST00000389863,;ADARB1,3_prime_UTR_variant,,ENST00000496664,;ADARB1,3_prime_UTR_variant,,ENST00000492414,;ADARB1,3_prime_UTR_variant,,ENST00000389861,;	T	ENSG00000197381	ENST00000539173	Transcript	3_prime_UTR_variant	6578	.	.	.	.	.	.	.	1	ADARB1	HGNC	226	protein_coding	YES	CCDS33589.1	ENSP00000441897	RED1_HUMAN	C9JUP4_HUMAN	UPI0000133622	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCTGTCTCT	.	2	ESCA
PRAMENP	0	.	GRCh37	22	22345724	22345724	+	RNA	SNP	C	C	G	rs544623916	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2811G>C	.	.	ENST00000337471	7/7	30	21	8	26	26	0	PRAMENP,non_coding_transcript_exon_variant,,ENST00000337471,;PRAMENP,non_coding_transcript_exon_variant,,ENST00000419303,;PRAMENP,non_coding_transcript_exon_variant,,ENST00000548391,;PRAMENP,non_coding_transcript_exon_variant,,ENST00000546598,;	G	ENSG00000197549	ENST00000337471	Transcript	non_coding_transcript_exon_variant	2811	.	.	.	.	rs544623916	.	.	-1	PRAMENP	HGNC	34302	processed_transcript	YES	.	.	.	.	.	.	.	.	7/7	.	.	T:0.0006	T:0.0023	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTCGTTCA	byFrequency|by1000G	5	ESCA
GSTT2B	0	.	GRCh37	22	24300541	24300541	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.456G>T	p.%3D	p.G152G	ENST00000290765	4/5	61	35	26	80	80	0	GSTT2B,synonymous_variant,p.%3D,ENST00000290765,;GSTT2B,synonymous_variant,p.%3D,ENST00000404172,;AP000350.8,downstream_gene_variant,,ENST00000440099,;	A	ENSG00000133433	ENST00000290765	Transcript	synonymous_variant	511	456	152	G	ggG/ggT	.	.	.	-1	GSTT2B	HGNC	33437	protein_coding	YES	CCDS33617.1	ENSP00000290765	GSTT2_HUMAN	G9J6Q5_HUMAN	UPI000011244D	.	.	.	4/5	.	PROSITE_profiles:PS50405,hmmpanther:PTHR11260:SF126,hmmpanther:PTHR11260,Gene3D:1.20.1050.10,Pfam_domain:PF00043,Superfamily_domains:SSF47616	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCCCCCAG	.	5	ESCA
SPECC1L	0	.	GRCh37	22	24807589	24807589	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3121A>G	p.Asn1041Asp	p.N1041D	ENST00000314328	15/17	50	30	19	41	41	0	SPECC1L,missense_variant,p.Asn1041Asp,ENST00000314328,;SPECC1L,missense_variant,p.Asn1041Asp,ENST00000437398,;SPECC1L,intron_variant,,ENST00000541492,;SPECC1L-ADORA2A,3_prime_UTR_variant,,ENST00000358654,;SPECC1L,upstream_gene_variant,,ENST00000472799,;	G	ENSG00000100014	ENST00000314328	Transcript	missense_variant	3406	3121	1041	N/D	Aat/Gat	COSM183348	.	.	1	SPECC1L	HGNC	29022	protein_coding	YES	CCDS33619.1	ENSP00000325785	CYTSA_HUMAN	C9JLY8_HUMAN,C9J8U1_HUMAN	UPI00001B64E9	.	deleterious(0.01)	probably_damaging(0.998)	15/17	.	PROSITE_profiles:PS50021,hmmpanther:PTHR23167:SF18,hmmpanther:PTHR23167,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGAATGAT	.	5	ESCA
MYO18B	0	.	GRCh37	22	26298604	26298604	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4848C>A	p.%3D	p.A1616A	ENST00000335473	30/44	78	55	23	68	68	0	MYO18B,synonymous_variant,p.%3D,ENST00000335473,;MYO18B,synonymous_variant,p.%3D,ENST00000536101,;MYO18B,synonymous_variant,p.%3D,ENST00000407587,;CTA-125H2.2,intron_variant,,ENST00000608257,;CTA-125H2.2,intron_variant,,ENST00000609889,;CTA-125H2.2,upstream_gene_variant,,ENST00000595093,;CTA-125H2.2,upstream_gene_variant,,ENST00000599792,;CTA-125H2.2,upstream_gene_variant,,ENST00000599080,;CTA-125H2.2,upstream_gene_variant,,ENST00000594542,;CTA-125H2.2,upstream_gene_variant,,ENST00000609275,;CTA-125H2.2,upstream_gene_variant,,ENST00000600211,;CTA-125H2.2,upstream_gene_variant,,ENST00000609157,;CTA-125H2.2,upstream_gene_variant,,ENST00000608115,;CTA-125H2.2,upstream_gene_variant,,ENST00000453457,;CTA-125H2.2,upstream_gene_variant,,ENST00000594856,;CTA-125H2.2,upstream_gene_variant,,ENST00000597284,;CTA-125H2.2,upstream_gene_variant,,ENST00000600903,;CTA-125H2.2,upstream_gene_variant,,ENST00000609570,;CTA-125H2.2,upstream_gene_variant,,ENST00000608507,;CTA-125H2.2,upstream_gene_variant,,ENST00000594585,;CTA-125H2.2,upstream_gene_variant,,ENST00000600269,;CTA-125H2.2,upstream_gene_variant,,ENST00000597548,;CTA-125H2.2,upstream_gene_variant,,ENST00000595102,;CTA-125H2.2,upstream_gene_variant,,ENST00000607895,;CTA-125H2.2,upstream_gene_variant,,ENST00000609823,;MYO18B,non_coding_transcript_exon_variant,,ENST00000536204,;MYO18B,non_coding_transcript_exon_variant,,ENST00000534908,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,;	A	ENSG00000133454	ENST00000335473	Transcript	synonymous_variant	5098	4848	1616	A	gcC/gcA	.	.	.	1	MYO18B	HGNC	18150	protein_coding	YES	CCDS54507.1	ENSP00000334563	.	Q8N903_HUMAN	UPI0000207402	.	.	.	30/44	.	hmmpanther:PTHR13140:SF254,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGCCCTAGG	.	5	ESCA
SEZ6L	0	.	GRCh37	22	26773696	26773696	+	Missense_Mutation	SNP	G	G	C	rs529920388	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3000G>C	p.Gln1000His	p.Q1000H	ENST00000248933	16/17	57	50	7	51	51	0	SEZ6L,missense_variant,p.Gln989His,ENST00000529632,;SEZ6L,missense_variant,p.Gln1000His,ENST00000248933,;SEZ6L,missense_variant,p.Gln925His,ENST00000360929,;SEZ6L,missense_variant,p.Gln696His,ENST00000403121,;SEZ6L,missense_variant,p.Gln999His,ENST00000404234,;SEZ6L,missense_variant,p.Gln924His,ENST00000343706,;SEZ6L,missense_variant,p.Gln772His,ENST00000402979,;SEZ6L,3_prime_UTR_variant,,ENST00000411842,;SEZ6L,downstream_gene_variant,,ENST00000494013,;	C	ENSG00000100095	ENST00000248933	Transcript	missense_variant	3095	3000	1000	Q/H	caG/caC	rs529920388	.	.	1	SEZ6L	HGNC	10763	protein_coding	YES	CCDS13833.1	ENSP00000248933	SE6L1_HUMAN	.	UPI0000136779	.	tolerated(0.23)	probably_damaging(0.998)	16/17	.	hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF81	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCAGATCAC	by1000G	4	ESCA
PMM1	0	.	GRCh37	22	41980059	41980059	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378A>G	p.%3D	p.G126G	ENST00000216259	5/8	39	29	9	36	36	0	PMM1,synonymous_variant,p.%3D,ENST00000216259,;PMM1,non_coding_transcript_exon_variant,,ENST00000466645,;PMM1,3_prime_UTR_variant,,ENST00000414636,;PMM1,non_coding_transcript_exon_variant,,ENST00000485648,;PMM1,non_coding_transcript_exon_variant,,ENST00000478337,;PMM1,non_coding_transcript_exon_variant,,ENST00000482178,;PMM1,non_coding_transcript_exon_variant,,ENST00000472620,;PMM1,upstream_gene_variant,,ENST00000463617,;PMM1,downstream_gene_variant,,ENST00000493389,;	C	ENSG00000100417	ENST00000216259	Transcript	synonymous_variant	463	378	126	G	ggA/ggG	.	.	.	-1	PMM1	HGNC	9114	protein_coding	YES	CCDS14020.1	ENSP00000216259	PMM1_HUMAN	.	UPI00000302B6	.	.	.	5/8	.	hmmpanther:PTHR10466,hmmpanther:PTHR10466:SF1,TIGRFAM_domain:TIGR01484,Pfam_domain:PF03332,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAGGTTCCACT	.	4	ESCA
MEI1	0	.	GRCh37	22	42180391	42180391	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3136A>T	p.Ser1046Cys	p.S1046C	ENST00000401548	25/31	58	33	25	55	55	0	MEI1,missense_variant,p.Ser54Cys,ENST00000300398,;MEI1,missense_variant,p.Ser54Cys,ENST00000403492,;MEI1,missense_variant,p.Ser1046Cys,ENST00000401548,;MEI1,missense_variant,p.Ser379Cys,ENST00000400107,;MEI1,downstream_gene_variant,,ENST00000540880,;MEI1,non_coding_transcript_exon_variant,,ENST00000484966,;MEI1,non_coding_transcript_exon_variant,,ENST00000476893,;MEI1,intron_variant,,ENST00000487535,;MEI1,downstream_gene_variant,,ENST00000462246,;MEI1,downstream_gene_variant,,ENST00000498456,;MEI1,downstream_gene_variant,,ENST00000462450,;MEI1,downstream_gene_variant,,ENST00000473736,;	T	ENSG00000167077	ENST00000401548	Transcript	missense_variant	3176	3136	1046	S/C	Agc/Tgc	.	.	.	1	MEI1	HGNC	28613	protein_coding	YES	CCDS46718.1	ENSP00000384115	MEI1_HUMAN	.	UPI00006E232C	.	tolerated(0.08)	probably_damaging(0.964)	25/31	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12044,hmmpanther:PTHR12044:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTCAGCTTT	.	5	ESCA
TCF20	0	.	GRCh37	22	42609304	42609304	+	Missense_Mutation	SNP	C	C	A	rs772027353	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2008G>T	p.Asp670Tyr	p.D670Y	ENST00000359486	1/5	80	54	25	79	79	0	TCF20,missense_variant,p.Asp670Tyr,ENST00000335626,;TCF20,missense_variant,p.Asp670Tyr,ENST00000359486,;TCF20,upstream_gene_variant,,ENST00000404876,;TCF20,downstream_gene_variant,,ENST00000515426,;	A	ENSG00000100207	ENST00000359486	Transcript	missense_variant	2145	2008	670	D/Y	Gat/Tat	rs772027353	.	.	-1	TCF20	HGNC	11631	protein_coding	YES	CCDS14033.1	ENSP00000352463	TCF20_HUMAN	I3L1M7_HUMAN	UPI00001A95D9	.	.	probably_damaging(0.959)	1/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14955,hmmpanther:PTHR14955:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTATCGCCAT	byFrequency	5	ESCA
GRAMD4	0	.	GRCh37	22	47022732	47022732	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36T>C	p.%3D	p.G12G	ENST00000406902	2/19	35	23	11	45	45	0	GRAMD4,synonymous_variant,p.%3D,ENST00000447351,;GRAMD4,synonymous_variant,p.%3D,ENST00000406902,;GRAMD4,synonymous_variant,p.%3D,ENST00000431155,;GRAMD4,synonymous_variant,p.%3D,ENST00000361034,;GRAMD4,upstream_gene_variant,,ENST00000490378,;	C	ENSG00000075240	ENST00000406902	Transcript	synonymous_variant	249	36	12	G	ggT/ggC	.	.	.	1	GRAMD4	HGNC	29113	protein_coding	YES	CCDS33672.1	ENSP00000385689	GRAM4_HUMAN	.	UPI0000161A59	.	.	.	2/19	.	hmmpanther:PTHR16122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGGTCACAA	.	5	ESCA
GRAMD4	0	.	GRCh37	22	47072525	47072525	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1592C>G	p.Ser531Ter	p.S531*	ENST00000406902	18/19	87	72	14	72	72	0	GRAMD4,stop_gained,p.Ser54Ter,ENST00000408031,;GRAMD4,stop_gained,p.Ser531Ter,ENST00000406902,;GRAMD4,stop_gained,p.Ser531Ter,ENST00000361034,;	G	ENSG00000075240	ENST00000406902	Transcript	stop_gained	1805	1592	531	S/*	tCa/tGa	.	.	.	1	GRAMD4	HGNC	29113	protein_coding	YES	CCDS33672.1	ENSP00000385689	GRAM4_HUMAN	.	UPI0000161A59	.	.	.	18/19	.	hmmpanther:PTHR16122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCTCAGGCA	.	5	ESCA
ZBED4	0	.	GRCh37	22	50280941	50280941	+	3'UTR	SNP	C	C	G	rs539760380	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*115C>G	.	.	ENST00000216268	2/2	42	36	6	24	24	0	ZBED4,3_prime_UTR_variant,,ENST00000216268,;	G	ENSG00000100426	ENST00000216268	Transcript	3_prime_UTR_variant	4108	.	.	.	.	rs539760380	.	.	1	ZBED4	HGNC	20721	protein_coding	YES	CCDS33677.1	ENSP00000216268	ZBED4_HUMAN	.	UPI000013C6DB	.	.	.	2/2	.	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTCAGGGC	by1000G	5	ESCA
TTL	0	.	GRCh37	2	113286627	113286627	+	3'UTR	SNP	G	G	A	rs540774000	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*255G>A	.	.	ENST00000233336	7/7	34	28	5	38	38	0	TTL,3_prime_UTR_variant,,ENST00000233336,;TTL,non_coding_transcript_exon_variant,,ENST00000460450,;	A	ENSG00000114999	ENST00000233336	Transcript	3_prime_UTR_variant	1580	.	.	.	.	rs540774000	.	.	1	TTL	HGNC	21586	protein_coding	YES	CCDS2096.1	ENSP00000233336	TTL_HUMAN	.	UPI000004FDE7	.	.	.	7/7	.	.	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGTGAGCAG	byFrequency|by1000G	4	ESCA
RABL2A	0	.	GRCh37	2	114399798	114399798	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*92C>T	.	.	ENST00000393167	9/9	32	22	10	28	28	0	RABL2A,3_prime_UTR_variant,,ENST00000409875,;RABL2A,3_prime_UTR_variant,,ENST00000393167,;RABL2A,3_prime_UTR_variant,,ENST00000409842,;RABL2A,intron_variant,,ENST00000376439,;RABL2A,intron_variant,,ENST00000393165,;RABL2A,intron_variant,,ENST00000393166,;RABL2A,downstream_gene_variant,,ENST00000413545,;RABL2A,non_coding_transcript_exon_variant,,ENST00000478880,;RABL2A,downstream_gene_variant,,ENST00000465711,;RABL2A,downstream_gene_variant,,ENST00000477218,;RABL2A,3_prime_UTR_variant,,ENST00000450954,;RABL2A,3_prime_UTR_variant,,ENST00000452831,;RABL2A,non_coding_transcript_exon_variant,,ENST00000409121,;RABL2A,non_coding_transcript_exon_variant,,ENST00000494909,;RABL2A,non_coding_transcript_exon_variant,,ENST00000486403,;	T	ENSG00000144134	ENST00000393167	Transcript	3_prime_UTR_variant	1004	.	.	.	.	.	.	.	1	RABL2A	HGNC	9799	protein_coding	YES	CCDS2118.1	ENSP00000376872	RBL2A_HUMAN	C9JFZ0_HUMAN,B7ZBD4_HUMAN	UPI00001331E4	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATCCCCTC	.	5	ESCA
EPB41L5	0	.	GRCh37	2	120925515	120925515	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2067A>G	p.%3D	p.G689G	ENST00000263713	24/25	91	59	32	85	85	0	EPB41L5,synonymous_variant,p.%3D,ENST00000263713,;EPB41L5,synonymous_variant,p.%3D,ENST00000452780,;EPB41L5,intron_variant,,ENST00000443902,;EPB41L5,non_coding_transcript_exon_variant,,ENST00000488691,;	G	ENSG00000115109	ENST00000263713	Transcript	synonymous_variant	2281	2067	689	G	ggA/ggG	.	.	.	1	EPB41L5	HGNC	19819	protein_coding	YES	CCDS2130.1	ENSP00000263713	E41L5_HUMAN	Q53RT1_HUMAN,Q4ZG32_HUMAN	UPI00001B078A	.	.	.	24/25	.	hmmpanther:PTHR23280:SF15,hmmpanther:PTHR23280	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGGACATGG	.	5	ESCA
WDR33	0	.	GRCh37	2	128471464	128471464	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3001G>A	p.Asp1001Asn	p.D1001N	ENST00000322313	18/22	82	51	31	93	93	0	WDR33,missense_variant,p.Asp1001Asn,ENST00000322313,;	T	ENSG00000136709	ENST00000322313	Transcript	missense_variant	3160	3001	1001	D/N	Gat/Aat	.	.	.	-1	WDR33	HGNC	25651	protein_coding	YES	CCDS2150.1	ENSP00000325377	WDR33_HUMAN	C9J8B4_HUMAN,B9A053_HUMAN	UPI000013D032	.	tolerated_low_confidence(0.12)	probably_damaging(0.956)	18/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22836	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTATCAGGGG	.	5	ESCA
CCNT2	0	.	GRCh37	2	135712333	135712333	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*115A>G	.	.	ENST00000264157	9/9	42	24	18	31	31	0	CCNT2,3_prime_UTR_variant,,ENST00000264157,;CCNT2,3_prime_UTR_variant,,ENST00000295238,;CCNT2,3_prime_UTR_variant,,ENST00000452521,;CCNT2,3_prime_UTR_variant,,ENST00000537343,;CCNT2,downstream_gene_variant,,ENST00000438691,;CCNT2,downstream_gene_variant,,ENST00000446247,;CCNT2,3_prime_UTR_variant,,ENST00000452839,;CCNT2,3_prime_UTR_variant,,ENST00000419781,;	G	ENSG00000082258	ENST00000264157	Transcript	3_prime_UTR_variant	2338	.	.	.	.	.	.	.	1	CCNT2	HGNC	1600	protein_coding	YES	CCDS2174.1	ENSP00000264157	CCNT2_HUMAN	.	UPI000013E228	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAATATTTGT	.	5	ESCA
LRP1B	0	.	GRCh37	2	141128844	141128844	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10779T>C	p.%3D	p.T3593T	ENST00000389484	70/91	29	19	10	29	29	0	LRP1B,synonymous_variant,p.%3D,ENST00000389484,;	G	ENSG00000168702	ENST00000389484	Transcript	synonymous_variant	11751	10779	3593	T	acT/acC	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	70/91	.	PROSITE_profiles:PS50068,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCAAGTAGG	.	5	ESCA
FIGN	0	.	GRCh37	2	164466828	164466828	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1514C>A	p.Pro505Gln	p.P505Q	ENST00000333129	3/3	55	34	21	62	62	0	FIGN,missense_variant,p.Pro505Gln,ENST00000333129,;FIGN,intron_variant,,ENST00000409634,;FIGN,downstream_gene_variant,,ENST00000482917,;	T	ENSG00000182263	ENST00000333129	Transcript	missense_variant	1829	1514	505	P/Q	cCa/cAa	COSM1400538	.	.	-1	FIGN	HGNC	13285	protein_coding	YES	CCDS2221.2	ENSP00000333836	FIGN_HUMAN	.	UPI000022BD13	.	deleterious(0)	probably_damaging(0.999)	3/3	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,hmmpanther:PTHR23074:SF14,hmmpanther:PTHR23074	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTGGCCAT	.	5	ESCA
ITGAV	0	.	GRCh37	2	187523819	187523819	+	Missense_Mutation	SNP	C	C	T	rs200949549	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1774C>T	p.Arg592Trp	p.R592W	ENST00000261023	18/30	35	10	25	38	38	0	ITGAV,missense_variant,p.Arg556Trp,ENST00000374907,;ITGAV,missense_variant,p.Arg592Trp,ENST00000261023,;ITGAV,missense_variant,p.Arg546Trp,ENST00000433736,;AC017101.10,intron_variant,,ENST00000453665,;	T	ENSG00000138448	ENST00000261023	Transcript	missense_variant	2048	1774	592	R/W	Cgg/Tgg	rs200949549,COSM4089536,COSM4089537	.	.	1	ITGAV	HGNC	6150	protein_coding	YES	CCDS2292.1	ENSP00000261023	ITAV_HUMAN	L7RXH0_HUMAN	UPI000013D12E	.	deleterious(0.02)	benign(0.009)	18/30	.	hmmpanther:PTHR23220:SF4,hmmpanther:PTHR23220,Gene3D:1jv2A02,Pfam_domain:PF08441,Superfamily_domains:SSF69179,Prints_domain:PR01185	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATCGGTTG	byCluster|by1000G	5	ESCA
GTF3C3	0	.	GRCh37	2	197664240	197664240	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96G>A	p.%3D	p.E32E	ENST00000263956	1/18	57	39	17	68	68	0	GTF3C3,synonymous_variant,p.%3D,ENST00000409364,;GTF3C3,synonymous_variant,p.%3D,ENST00000263956,;GTF3C3,synonymous_variant,p.%3D,ENST00000448539,;GTF3C3,synonymous_variant,p.%3D,ENST00000451088,;GTF3C3,upstream_gene_variant,,ENST00000455546,;	T	ENSG00000119041	ENST00000263956	Transcript	synonymous_variant	186	96	32	E	gaG/gaA	.	.	.	-1	GTF3C3	HGNC	4666	protein_coding	YES	CCDS2316.1	ENSP00000263956	TF3C3_HUMAN	.	UPI0000070C01	.	.	.	1/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTCTCGCG	.	5	ESCA
AOX1	0	.	GRCh37	2	201457904	201457904	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81G>C	p.%3D	p.L27L	ENST00000374700	2/35	111	68	43	97	97	0	AOX1,synonymous_variant,p.%3D,ENST00000454629,;AOX1,synonymous_variant,p.%3D,ENST00000374700,;	C	ENSG00000138356	ENST00000374700	Transcript	synonymous_variant	322	81	27	L	ctG/ctC	.	.	.	1	AOX1	HGNC	553	protein_coding	YES	CCDS33360.1	ENSP00000363832	ADO_HUMAN	C9J244_HUMAN,B4DNI5_HUMAN	UPI0000071863	.	.	.	2/35	.	PROSITE_profiles:PS51085,hmmpanther:PTHR11908,Gene3D:3.10.20.30,Pfam_domain:PF00111,TIGRFAM_domain:TIGR02969,PIRSF_domain:PIRSF000127,Superfamily_domains:SSF54292	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGTTGCC	.	5	ESCA
PRKAG3	0	.	GRCh37	2	219695486	219695486	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212C>T	p.Pro71Leu	p.P71L	ENST00000529249	3/13	90	27	63	106	106	0	PRKAG3,missense_variant,p.Pro71Leu,ENST00000392098,;PRKAG3,missense_variant,p.Pro71Leu,ENST00000430489,;PRKAG3,missense_variant,p.Pro46Leu,ENST00000439262,;PRKAG3,missense_variant,p.Pro71Leu,ENST00000529249,;PRKAG3,5_prime_UTR_variant,,ENST00000545803,;PRKAG3,missense_variant,p.Pro71Leu,ENST00000233944,;PRKAG3,missense_variant,p.Pro71Leu,ENST00000470307,;PRKAG3,non_coding_transcript_exon_variant,,ENST00000490971,;	A	ENSG00000115592	ENST00000529249	Transcript	missense_variant	528	212	71	P/L	cCa/cTa	COSM378331	.	.	-1	PRKAG3	HGNC	9387	protein_coding	YES	CCDS2424.1	ENSP00000436068	AAKG3_HUMAN	B4DT70_HUMAN	UPI0000043D98	.	tolerated_low_confidence(0.31)	benign(0.002)	3/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13780:SF31,hmmpanther:PTHR13780	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGTGGCTCC	.	5	ESCA
ING5	0	.	GRCh37	2	242662655	242662655	+	Missense_Mutation	SNP	G	G	T	rs762850893	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.649G>T	p.Val217Leu	p.V217L	ENST00000313552	7/8	129	30	99	147	147	0	ING5,missense_variant,p.Val217Leu,ENST00000406941,;ING5,missense_variant,p.Val217Leu,ENST00000313552,;AC114730.11,downstream_gene_variant,,ENST00000435195,;ING5,non_coding_transcript_exon_variant,,ENST00000493578,;ING5,upstream_gene_variant,,ENST00000486061,;ING5,downstream_gene_variant,,ENST00000482774,;ING5,upstream_gene_variant,,ENST00000474238,;ING5,downstream_gene_variant,,ENST00000445620,;ING5,downstream_gene_variant,,ENST00000489509,;	T	ENSG00000168395	ENST00000313552	Transcript	missense_variant	675	649	217	V/L	Gtg/Ttg	rs762850893	.	.	1	ING5	HGNC	19421	protein_coding	YES	CCDS33425.1	ENSP00000322142	ING5_HUMAN	.	UPI00000702CD	.	deleterious(0.03)	probably_damaging(0.999)	7/8	.	Superfamily_domains:SSF57903,SMART_domains:SM00249,Pfam_domain:PF00628,Gene3D:3.30.40.10,PROSITE_patterns:PS01359,hmmpanther:PTHR10333:SF41,hmmpanther:PTHR10333,PROSITE_profiles:PS50016	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCGTGGAC	.	5	ESCA
ASXL2	0	.	GRCh37	2	25972870	25972870	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555G>C	p.Glu519Gln	p.E519Q	ENST00000435504	12/13	74	49	24	74	74	0	ASXL2,missense_variant,p.Glu259Gln,ENST00000272341,;ASXL2,missense_variant,p.Glu491Gln,ENST00000336112,;ASXL2,missense_variant,p.Glu259Gln,ENST00000404843,;ASXL2,missense_variant,p.Glu519Gln,ENST00000435504,;	G	ENSG00000143970	ENST00000435504	Transcript	missense_variant	1849	1555	519	E/Q	Gaa/Caa	COSM3580283,COSM3580282	.	.	-1	ASXL2	HGNC	23805	protein_coding	YES	.	ENSP00000391447	ASXL2_HUMAN	.	UPI00001DFBE8	.	tolerated(0.21)	benign(0.022)	12/13	.	hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCTTGGC	.	5	ESCA
CGREF1	0	.	GRCh37	2	27324150	27324150	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.949G>T	p.Glu317Ter	p.E317*	ENST00000402394	6/6	58	43	14	55	55	0	CGREF1,stop_gained,p.Glu317Ter,ENST00000405600,;CGREF1,stop_gained,p.Glu300Ter,ENST00000260595,;CGREF1,stop_gained,p.Glu439Ter,ENST00000404694,;CGREF1,stop_gained,p.Glu317Ter,ENST00000312734,;CGREF1,stop_gained,p.Glu317Ter,ENST00000402394,;CGREF1,intron_variant,,ENST00000452318,;CGREF1,intron_variant,,ENST00000402550,;KHK,downstream_gene_variant,,ENST00000260599,;KHK,downstream_gene_variant,,ENST00000429697,;KHK,downstream_gene_variant,,ENST00000260598,;KHK,downstream_gene_variant,,ENST00000490823,;CGREF1,intron_variant,,ENST00000440612,;CGREF1,downstream_gene_variant,,ENST00000467539,;KHK,downstream_gene_variant,,ENST00000464371,;KHK,downstream_gene_variant,,ENST00000469936,;	A	ENSG00000138028	ENST00000402394	Transcript	stop_gained	1218	949	317	E/*	Gag/Tag	.	.	.	-1	CGREF1	HGNC	16962	protein_coding	YES	CCDS33162.2	ENSP00000385452	CGRE1_HUMAN	.	UPI000013D0EB	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTCATCAT	.	5	ESCA
EFEMP1	0	.	GRCh37	2	56145020	56145020	+	Silent	SNP	G	G	A	rs142637468	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297C>T	p.%3D	p.T99T	ENST00000394555	4/11	67	47	20	66	66	0	EFEMP1,synonymous_variant,p.%3D,ENST00000439193,;EFEMP1,synonymous_variant,p.%3D,ENST00000440439,;EFEMP1,synonymous_variant,p.%3D,ENST00000355426,;EFEMP1,synonymous_variant,p.%3D,ENST00000394554,;EFEMP1,synonymous_variant,p.%3D,ENST00000438672,;EFEMP1,synonymous_variant,p.%3D,ENST00000424836,;EFEMP1,synonymous_variant,p.%3D,ENST00000394555,;EFEMP1,downstream_gene_variant,,ENST00000452337,;EFEMP1,downstream_gene_variant,,ENST00000421664,;EFEMP1,downstream_gene_variant,,ENST00000424207,;EFEMP1,downstream_gene_variant,,ENST00000429909,;EFEMP1,non_coding_transcript_exon_variant,,ENST00000452161,;EFEMP1,downstream_gene_variant,,ENST00000497698,;EFEMP1,downstream_gene_variant,,ENST00000480016,;	A	ENSG00000115380	ENST00000394555	Transcript	synonymous_variant	733	297	99	T	acC/acT	rs142637468	.	.	-1	EFEMP1	HGNC	3218	protein_coding	YES	CCDS1857.1	ENSP00000378058	FBLN3_HUMAN	Q580Q6_HUMAN,Q53TA7_HUMAN,C9JUM4_HUMAN,C9JQX7_HUMAN,C9JPZ9_HUMAN,C9J8S9_HUMAN,C9J4J8_HUMAN,C9J4H7_HUMAN	UPI0000000C12	.	.	.	4/11	.	hmmpanther:PTHR24048:SF68,hmmpanther:PTHR24048	A:0.0004	A:0.0008	A:0.0014	.	A:0	A:0	A:0	A:0.002	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCCGGTGGT	byFrequency|byCluster|by1000G	5	ESCA
FBXO41	0	.	GRCh37	2	73491122	73491122	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1866G>C	p.Leu622Phe	p.L622F	ENST00000521871	7/13	74	42	31	62	62	0	FBXO41,missense_variant,p.Leu622Phe,ENST00000521871,;FBXO41,missense_variant,p.Leu622Phe,ENST00000520530,;FBXO41,missense_variant,p.Leu683Phe,ENST00000295133,;FBXO41,downstream_gene_variant,,ENST00000519873,;	G	ENSG00000163013	ENST00000521871	Transcript	missense_variant	2282	1866	622	L/F	ttG/ttC	.	.	.	-1	FBXO41	HGNC	29409	protein_coding	YES	CCDS46337.2	ENSP00000428646	FBX41_HUMAN	B3KXK3_HUMAN	UPI0000D611B7	.	deleterious(0)	probably_damaging(0.996)	7/13	.	hmmpanther:PTHR15739:SF4,hmmpanther:PTHR15739,Gene3D:3.80.10.10,Superfamily_domains:SSF81383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTCAAGTT	.	5	ESCA
LYG2	0	.	GRCh37	2	99858936	99858936	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530C>A	p.Ser177Ter	p.S177*	ENST00000333017	6/6	32	14	17	43	43	0	LYG2,stop_gained,p.Ser177Ter,ENST00000409238,;LYG2,stop_gained,p.Ser177Ter,ENST00000333017,;LYG2,3_prime_UTR_variant,,ENST00000423800,;LYG2,downstream_gene_variant,,ENST00000409679,;LYG2,downstream_gene_variant,,ENST00000423306,;C2orf15,intron_variant,,ENST00000424491,;	T	ENSG00000185674	ENST00000333017	Transcript	stop_gained	643	530	177	S/*	tCa/tAa	.	.	.	-1	LYG2	HGNC	29615	protein_coding	YES	CCDS2042.1	ENSP00000327533	LYG2_HUMAN	C9JBA4_HUMAN	UPI0000049D92	.	.	.	6/6	.	hmmpanther:PTHR31698:SF4,hmmpanther:PTHR31698,Pfam_domain:PF01464,Gene3D:1.10.530.10,PIRSF_domain:PIRSF001065,Superfamily_domains:SSF53955,Prints_domain:PR00749	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTGAGAGA	.	5	ESCA
TRMT10C	0	.	GRCh37	3	101284019	101284019	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394T>C	p.Tyr132His	p.Y132H	ENST00000309922	2/2	20	14	6	17	17	0	TRMT10C,missense_variant,p.Tyr132His,ENST00000495642,;TRMT10C,missense_variant,p.Tyr132His,ENST00000309922,;	C	ENSG00000174173	ENST00000309922	Transcript	missense_variant	548	394	132	Y/H	Tat/Cat	.	.	.	1	TRMT10C	HGNC	26022	protein_coding	YES	CCDS43122.1	ENSP00000312356	MRRP1_HUMAN	C9JVB6_HUMAN	UPI0000034E2A	.	deleterious(0)	probably_damaging(0.98)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13563,hmmpanther:PTHR13563:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.K131fs*3|c.384delA|13	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAATATTTA	.	5	ESCA
PVRL3	0	.	GRCh37	3	110852704	110852704	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1292G>A	p.Arg431Lys	p.R431K	ENST00000485303	6/6	60	40	20	38	38	0	PVRL3,missense_variant,p.Arg431Lys,ENST00000485303,;PVRL3,3_prime_UTR_variant,,ENST00000319792,;PVRL3,intron_variant,,ENST00000493615,;	A	ENSG00000177707	ENST00000485303	Transcript	missense_variant	1567	1292	431	R/K	aGa/aAa	COSM3585188	.	.	1	PVRL3	HGNC	17664	protein_coding	YES	CCDS2957.1	ENSP00000418070	PVRL3_HUMAN	.	UPI000004A2B6	.	tolerated(0.12)	benign(0.008)	6/6	.	Gene3D:1.20.5.100,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF10	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGACGGA	.	5	ESCA
PLA1A	0	.	GRCh37	3	119347680	119347680	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1254G>A	p.%3D	p.K418K	ENST00000273371	10/11	68	44	23	42	42	0	PLA1A,synonymous_variant,p.%3D,ENST00000488919,;PLA1A,synonymous_variant,p.%3D,ENST00000494440,;PLA1A,synonymous_variant,p.%3D,ENST00000273371,;PLA1A,synonymous_variant,p.%3D,ENST00000495992,;	A	ENSG00000144837	ENST00000273371	Transcript	synonymous_variant	1326	1254	418	K	aaG/aaA	.	.	.	1	PLA1A	HGNC	17661	protein_coding	YES	CCDS2991.1	ENSP00000273371	PLA1A_HUMAN	.	UPI0000073F97	.	.	.	10/11	.	PIRSF_domain:PIRSF000865,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF86	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAGTTCTG	.	5	ESCA
MAATS1	0	.	GRCh37	3	119426309	119426309	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.260C>G	p.Ser87Cys	p.S87C	ENST00000273390	3/18	60	50	10	28	28	0	MAATS1,missense_variant,p.Ser87Cys,ENST00000463700,;MAATS1,missense_variant,p.Ser87Cys,ENST00000273390,;MAATS1,3_prime_UTR_variant,,ENST00000482927,;MAATS1,3_prime_UTR_variant,,ENST00000482573,;MAATS1,non_coding_transcript_exon_variant,,ENST00000468630,;MAATS1,non_coding_transcript_exon_variant,,ENST00000483134,;MAATS1,non_coding_transcript_exon_variant,,ENST00000469659,;MAATS1,intron_variant,,ENST00000475093,;MAATS1,upstream_gene_variant,,ENST00000498167,;MAATS1,downstream_gene_variant,,ENST00000488533,;	G	ENSG00000183833	ENST00000273390	Transcript	missense_variant	337	260	87	S/C	tCt/tGt	COSM3120139,COSM3585780	.	.	1	MAATS1	HGNC	24010	protein_coding	YES	CCDS2994.1	ENSP00000273390	MAAT1_HUMAN	.	UPI00001C1DFE	.	deleterious(0.03)	benign(0.099)	3/18	.	hmmpanther:PTHR22455:SF10,hmmpanther:PTHR22455	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCTCTAT	.	5	ESCA
STXBP5L	0	.	GRCh37	3	120840538	120840538	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.656G>C	p.Arg219Thr	p.R219T	ENST00000273666	7/28	77	62	14	50	50	0	STXBP5L,missense_variant,p.Arg219Thr,ENST00000471262,;STXBP5L,missense_variant,p.Arg219Thr,ENST00000472879,;STXBP5L,missense_variant,p.Arg219Thr,ENST00000273666,;STXBP5L,missense_variant,p.Arg219Thr,ENST00000471454,;STXBP5L,missense_variant,p.Arg219Thr,ENST00000492541,;STXBP5L,missense_variant,p.Arg219Thr,ENST00000497029,;STXBP5L,3_prime_UTR_variant,,ENST00000461772,;	C	ENSG00000145087	ENST00000273666	Transcript	missense_variant	927	656	219	R/T	aGa/aCa	.	.	.	1	STXBP5L	HGNC	30757	protein_coding	YES	CCDS43137.1	ENSP00000273666	STB5L_HUMAN	C9JUZ7_HUMAN	UPI00001C1DEA	.	tolerated(0.4)	possibly_damaging(0.515)	7/28	.	PROSITE_profiles:PS50294,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAAGAGATG	.	5	ESCA
HCLS1	0	.	GRCh37	3	121356020	121356020	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538G>A	p.Glu180Lys	p.E180K	ENST00000314583	7/14	137	80	57	91	91	0	HCLS1,missense_variant,p.Glu180Lys,ENST00000314583,;HCLS1,intron_variant,,ENST00000428394,;HCLS1,non_coding_transcript_exon_variant,,ENST00000473883,;HCLS1,synonymous_variant,p.%3D,ENST00000495491,;HCLS1,3_prime_UTR_variant,,ENST00000464274,;	T	ENSG00000180353	ENST00000314583	Transcript	missense_variant	630	538	180	E/K	Gag/Aag	.	.	.	-1	HCLS1	HGNC	4844	protein_coding	YES	CCDS3003.1	ENSP00000320176	HCLS1_HUMAN	.	UPI000013F884	.	tolerated(0.66)	unknown(0)	7/14	.	PROSITE_profiles:PS51090,hmmpanther:PTHR10829:SF5,hmmpanther:PTHR10829,Pfam_domain:PF02218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCTCTCCCT	.	5	ESCA
UMPS	0	.	GRCh37	3	124459038	124459038	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150A>G	p.Arg384Gly	p.R384G	ENST00000232607	4/6	59	43	16	30	30	0	UMPS,missense_variant,p.Arg292Gly,ENST00000536109,;UMPS,missense_variant,p.Arg206Gly,ENST00000538242,;UMPS,missense_variant,p.Arg384Gly,ENST00000232607,;UMPS,intron_variant,,ENST00000413078,;UMPS,non_coding_transcript_exon_variant,,ENST00000495751,;UMPS,downstream_gene_variant,,ENST00000498715,;UMPS,3_prime_UTR_variant,,ENST00000474588,;UMPS,3_prime_UTR_variant,,ENST00000462091,;UMPS,3_prime_UTR_variant,,ENST00000479719,;UMPS,3_prime_UTR_variant,,ENST00000467167,;UMPS,3_prime_UTR_variant,,ENST00000460034,;UMPS,non_coding_transcript_exon_variant,,ENST00000487622,;UMPS,intron_variant,,ENST00000497791,;	G	ENSG00000114491	ENST00000232607	Transcript	missense_variant	1256	1150	384	R/G	Aga/Gga	.	.	.	1	UMPS	HGNC	12563	protein_coding	YES	CCDS3029.1	ENSP00000232607	UMPS_HUMAN	B5LY64_HUMAN,A8K5J1_HUMAN	UPI0000001223	.	tolerated(0.21)	benign(0.016)	4/6	.	hmmpanther:PTHR19278,hmmpanther:PTHR19278:SF9,TIGRFAM_domain:TIGR01740,Gene3D:3.20.20.70,Pfam_domain:PF00215,SMART_domains:SM00934,Superfamily_domains:SSF51366	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTAGAGCA	.	5	ESCA
H1FX	0	.	GRCh37	3	129034552	129034552	+	Missense_Mutation	SNP	G	G	C	rs750158697	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194C>G	p.Ser65Trp	p.S65W	ENST00000333762	1/1	44	36	7	30	30	0	H1FX,missense_variant,p.Ser65Trp,ENST00000333762,;H1FX-AS1,intron_variant,,ENST00000511998,;H1FX-AS1,intron_variant,,ENST00000433902,;H1FX-AS1,upstream_gene_variant,,ENST00000383461,;H1FX-AS1,upstream_gene_variant,,ENST00000537780,;H1FX-AS1,upstream_gene_variant,,ENST00000502789,;	C	ENSG00000184897	ENST00000333762	Transcript	missense_variant	569	194	65	S/W	tCg/tGg	rs750158697,COSM1732354	.	.	-1	H1FX	HGNC	4722	protein_coding	YES	CCDS3057.1	ENSP00000329662	H1X_HUMAN	.	UPI000012BF2F	.	deleterious(0.01)	probably_damaging(1)	1/1	.	PROSITE_profiles:PS51504,hmmpanther:PTHR11467:SF21,hmmpanther:PTHR11467,Pfam_domain:PF00538,Gene3D:1.10.10.10,SMART_domains:SM00526,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGACGAGCCG	byFrequency	5	ESCA
COL6A5	0	.	GRCh37	3	130098549	130098549	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956A>C	p.Asp319Ala	p.D319A	ENST00000265379	4/42	42	35	7	34	34	0	COL6A5,missense_variant,p.Asp319Ala,ENST00000432398,;COL6A5,missense_variant,p.Asp319Ala,ENST00000265379,;COL6A5,missense_variant,p.Asp319Ala,ENST00000312481,;	C	ENSG00000172752	ENST00000265379	Transcript	missense_variant	1450	956	319	D/A	gAt/gCt	.	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	tolerated(0.14)	benign(0.01)	4/42	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF93,hmmpanther:PTHR22992,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGATCAGA	.	5	ESCA
NUDT16	0	.	GRCh37	3	131102105	131102105	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*670C>A	.	.	ENST00000502852	2/2	99	70	28	62	62	0	NUDT16,missense_variant,p.Gln170Lys,ENST00000521288,;NUDT16,missense_variant,p.Gln137Lys,ENST00000359850,;NUDT16,missense_variant,p.Gln124Lys,ENST00000537561,;NUDT16,3_prime_UTR_variant,,ENST00000502852,;RP11-933H2.4,upstream_gene_variant,,ENST00000502521,;	A	ENSG00000198585	ENST00000502852	Transcript	3_prime_UTR_variant	1374	.	.	.	.	.	.	.	1	NUDT16	HGNC	26442	protein_coding	YES	CCDS54640.1	ENSP00000422375	NUD16_HUMAN	.	UPI0000E5A96C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAGCAGTTA	.	5	ESCA
DZIP1L	0	.	GRCh37	3	137822805	137822805	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9C>G	p.%3D	p.S3S	ENST00000327532	2/16	66	53	12	41	41	0	DZIP1L,synonymous_variant,p.%3D,ENST00000469243,;DZIP1L,synonymous_variant,p.%3D,ENST00000467030,;DZIP1L,synonymous_variant,p.%3D,ENST00000492010,;DZIP1L,synonymous_variant,p.%3D,ENST00000327532,;DZIP1L,upstream_gene_variant,,ENST00000490472,;KRT8P36,upstream_gene_variant,,ENST00000489121,;	C	ENSG00000158163	ENST00000327532	Transcript	synonymous_variant	372	9	3	S	tcC/tcG	.	.	.	-1	DZIP1L	HGNC	26551	protein_coding	YES	CCDS3096.1	ENSP00000332148	DZI1L_HUMAN	C9JRW2_HUMAN,C9JD19_HUMAN	UPI0000161A66	.	.	.	2/16	.	hmmpanther:PTHR21502:SF8,hmmpanther:PTHR21502	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGGGACTG	.	5	ESCA
LSM3	0	.	GRCh37	3	14220117	14220117	+	5'UTR	SNP	G	G	C	rs746341340	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-244G>C	.	.	ENST00000306024	1/4	55	31	23	77	77	0	LSM3,5_prime_UTR_variant,,ENST00000306024,;XPC,5_prime_UTR_variant,,ENST00000285021,;XPC,5_prime_UTR_variant,,ENST00000511155,;XPC,upstream_gene_variant,,ENST00000449060,;XPC,upstream_gene_variant,,ENST00000476581,;	C	ENSG00000170860	ENST00000306024	Transcript	5_prime_UTR_variant	260	.	.	.	.	rs746341340	.	.	1	LSM3	HGNC	17874	protein_coding	YES	CCDS2619.1	ENSP00000302160	LSM3_HUMAN	.	UPI0000003E6A	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCGATGCG	byFrequency	5	ESCA
C3orf20	0	.	GRCh37	3	14746055	14746055	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1090C>G	p.Gln364Glu	p.Q364E	ENST00000253697	7/17	82	55	27	104	104	0	C3orf20,missense_variant,p.Gln242Glu,ENST00000435614,;C3orf20,missense_variant,p.Gln242Glu,ENST00000412910,;C3orf20,missense_variant,p.Gln364Glu,ENST00000253697,;C3orf20,non_coding_transcript_exon_variant,,ENST00000495387,;	G	ENSG00000131379	ENST00000253697	Transcript	missense_variant	1542	1090	364	Q/E	Caa/Gaa	.	.	.	1	C3orf20	HGNC	25320	protein_coding	YES	CCDS33706.1	ENSP00000253697	CC020_HUMAN	.	UPI000013CDE9	.	tolerated(0.13)	possibly_damaging(0.716)	7/17	.	Pfam_domain:PF14977,hmmpanther:PTHR23093,hmmpanther:PTHR23093:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGTCAAGAG	.	5	ESCA
IFT80	0	.	GRCh37	3	160099401	160099401	+	Missense_Mutation	SNP	A	A	G	rs768189853	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.149T>C	p.Ile50Thr	p.I50T	ENST00000326448	3/20	75	65	10	43	43	0	IFT80,missense_variant,p.Ile50Thr,ENST00000326448,;IFT80,missense_variant,p.Ile50Thr,ENST00000489004,;IFT80,missense_variant,p.Ile50Thr,ENST00000478536,;IFT80,missense_variant,p.Ile50Thr,ENST00000498409,;IFT80,5_prime_UTR_variant,,ENST00000465537,;IFT80,5_prime_UTR_variant,,ENST00000483465,;IFT80,5_prime_UTR_variant,,ENST00000496589,;IFT80,intron_variant,,ENST00000468218,;IFT80,intron_variant,,ENST00000475677,;IFT80,intron_variant,,ENST00000478370,;IFT80,intron_variant,,ENST00000486856,;IFT80,splice_region_variant,,ENST00000465972,;IFT80,non_coding_transcript_exon_variant,,ENST00000477495,;IFT80,non_coding_transcript_exon_variant,,ENST00000468327,;IFT80,non_coding_transcript_exon_variant,,ENST00000498145,;IFT80,non_coding_transcript_exon_variant,,ENST00000472773,;IFT80,intron_variant,,ENST00000478460,;IFT80,downstream_gene_variant,,ENST00000466326,;IFT80,missense_variant,p.Ile50Thr,ENST00000482317,;IFT80,non_coding_transcript_exon_variant,,ENST00000487943,;RP11-432B6.3,intron_variant,,ENST00000483754,;IFT80,upstream_gene_variant,,ENST00000484963,;IFT80,downstream_gene_variant,,ENST00000467254,;	G	ENSG00000068885	ENST00000326448	Transcript	missense_variant	582	149	50	I/T	aTa/aCa	rs768189853	.	.	-1	IFT80	HGNC	29262	protein_coding	YES	CCDS3188.1	ENSP00000312778	IFT80_HUMAN	C9JUJ1_HUMAN,C9JUI1_HUMAN,C9JSB1_HUMAN,C9J6I5_HUMAN,C9J6G8_HUMAN,C9J627_HUMAN,C9IZR2_HUMAN	UPI0000160F16	.	deleterious(0.02)	benign(0.075)	3/20	.	hmmpanther:PTHR24098:SF8,hmmpanther:PTHR24098,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTATTTGA	.	5	ESCA
SERPINI2	0	.	GRCh37	3	167185064	167185064	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.257T>G	p.Phe86Cys	p.F86C	ENST00000476257	4/10	54	38	16	41	41	0	SERPINI2,missense_variant,p.Phe86Cys,ENST00000471111,;SERPINI2,missense_variant,p.Phe86Cys,ENST00000264677,;SERPINI2,missense_variant,p.Phe86Cys,ENST00000461846,;SERPINI2,missense_variant,p.Phe86Cys,ENST00000476257,;SERPINI2,missense_variant,p.Phe86Cys,ENST00000466903,;SERPINI2,intron_variant,,ENST00000467583,;SERPINI2,downstream_gene_variant,,ENST00000465031,;	C	ENSG00000114204	ENST00000476257	Transcript	missense_variant	556	257	86	F/C	tTt/tGt	.	.	.	-1	SERPINI2	HGNC	8945	protein_coding	YES	CCDS3200.1	ENSP00000420621	SPI2_HUMAN	C9J7N5_HUMAN	UPI0000135E26	.	deleterious(0)	probably_damaging(0.989)	4/10	.	hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF51,Pfam_domain:PF00079,Gene3D:3.30.497.10,SMART_domains:SM00093,Superfamily_domains:SSF56574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAAAAAATTCT	.	4	ESCA
ACTRT3	0	.	GRCh37	3	169486006	169486006	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333A>G	p.%3D	p.P111P	ENST00000330368	2/2	56	39	17	22	22	0	ACTRT3,synonymous_variant,p.%3D,ENST00000330368,;MYNN,upstream_gene_variant,,ENST00000392733,;MYNN,upstream_gene_variant,,ENST00000349841,;TERC,upstream_gene_variant,,ENST00000602385,;RP11-816J6.3,upstream_gene_variant,,ENST00000602879,;TERC,upstream_gene_variant,,ENST00000363312,;	C	ENSG00000184378	ENST00000330368	Transcript	synonymous_variant	708	333	111	P	ccA/ccG	.	.	.	-1	ACTRT3	HGNC	24022	protein_coding	YES	CCDS3206.1	ENSP00000333037	ACTT3_HUMAN	.	UPI000004EE04	.	.	.	2/2	.	hmmpanther:PTHR11937:SF159,hmmpanther:PTHR11937,PROSITE_patterns:PS01132,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGTGGGTT	.	5	ESCA
GHSR	0	.	GRCh37	3	172163075	172163076	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.976dupA	p.Met326AsnfsTer29	p.M326Nfs*29	ENST00000241256	2/2	110	76	34	51	51	0	GHSR,frameshift_variant,p.Met326AsnfsTer29,ENST00000241256,;GHSR,downstream_gene_variant,,ENST00000427970,;	T	ENSG00000121853	ENST00000241256	Transcript	frameshift_variant	1019-1020	976-977	326	M/NX	atg/aAtg	.	.	.	-1	GHSR	HGNC	4267	protein_coding	YES	CCDS3218.1	ENSP00000241256	GHSR_HUMAN	A2T3X1_HUMAN	UPI000003C2FA	.	.	.	2/2	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR24243:SF7,hmmpanther:PTHR24243	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGACATGATG	.	3	ESCA
DCUN1D1	0	.	GRCh37	3	182661815	182661815	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1067C>G	.	.	ENST00000292782	7/7	43	29	14	23	23	0	DCUN1D1,3_prime_UTR_variant,,ENST00000292782,;DCUN1D1,downstream_gene_variant,,ENST00000469954,;DCUN1D1,downstream_gene_variant,,ENST00000492563,;	C	ENSG00000043093	ENST00000292782	Transcript	3_prime_UTR_variant	2001	.	.	.	.	.	.	.	-1	DCUN1D1	HGNC	18184	protein_coding	YES	CCDS3240.1	ENSP00000292782	DCNL1_HUMAN	C9JVE2_HUMAN,C9JUW4_HUMAN,C9JRU6_HUMAN,C9J8R4_HUMAN,C9J0B2_HUMAN	UPI0000073D68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAAGAGCAG	.	5	ESCA
DCUN1D1	0	.	GRCh37	3	182662346	182662346	+	3'UTR	SNP	G	G	A	rs532370144	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*536C>T	.	.	ENST00000292782	7/7	39	28	11	23	22	0	DCUN1D1,3_prime_UTR_variant,,ENST00000292782,;DCUN1D1,downstream_gene_variant,,ENST00000469954,;DCUN1D1,downstream_gene_variant,,ENST00000492563,;	A	ENSG00000043093	ENST00000292782	Transcript	3_prime_UTR_variant	1470	.	.	.	.	rs532370144	.	.	-1	DCUN1D1	HGNC	18184	protein_coding	YES	CCDS3240.1	ENSP00000292782	DCNL1_HUMAN	C9JVE2_HUMAN,C9JUW4_HUMAN,C9JRU6_HUMAN,C9J8R4_HUMAN,C9J0B2_HUMAN	UPI0000073D68	.	.	.	7/7	.	.	-:0.0008	-:0.003	-:0	.	-:0	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TGCCAGGAAAA	byFrequency|by1000G	2	ESCA
DCUN1D1	0	.	GRCh37	3	182662347	182662347	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*535C>A	.	.	ENST00000292782	7/7	37	26	11	23	22	0	DCUN1D1,3_prime_UTR_variant,,ENST00000292782,;DCUN1D1,downstream_gene_variant,,ENST00000469954,;DCUN1D1,downstream_gene_variant,,ENST00000492563,;	T	ENSG00000043093	ENST00000292782	Transcript	3_prime_UTR_variant	1469	.	.	.	.	.	.	.	-1	DCUN1D1	HGNC	18184	protein_coding	YES	CCDS3240.1	ENSP00000292782	DCNL1_HUMAN	C9JVE2_HUMAN,C9JUW4_HUMAN,C9JRU6_HUMAN,C9J8R4_HUMAN,C9J0B2_HUMAN	UPI0000073D68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GCCAGGAAAAA	.	3	ESCA
DCUN1D1	0	.	GRCh37	3	182662686	182662686	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*196C>T	.	.	ENST00000292782	7/7	54	40	13	30	30	0	DCUN1D1,3_prime_UTR_variant,,ENST00000292782,;DCUN1D1,downstream_gene_variant,,ENST00000469954,;DCUN1D1,downstream_gene_variant,,ENST00000492563,;	A	ENSG00000043093	ENST00000292782	Transcript	3_prime_UTR_variant	1130	.	.	.	.	.	.	.	-1	DCUN1D1	HGNC	18184	protein_coding	YES	CCDS3240.1	ENSP00000292782	DCNL1_HUMAN	C9JVE2_HUMAN,C9JUW4_HUMAN,C9JRU6_HUMAN,C9J8R4_HUMAN,C9J0B2_HUMAN	UPI0000073D68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTAGAAGAC	.	5	ESCA
THPO	0	.	GRCh37	3	184090495	184090495	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.868C>T	p.Pro290Ser	p.P290S	ENST00000204615	6/6	70	42	28	39	39	0	THPO,missense_variant,p.Pro290Ser,ENST00000204615,;THPO,missense_variant,p.Pro286Ser,ENST00000445696,;THPO,missense_variant,p.Ala251Val,ENST00000421442,;EIF2B5,intron_variant,,ENST00000444495,;POLR2H,downstream_gene_variant,,ENST00000430783,;POLR2H,downstream_gene_variant,,ENST00000429568,;POLR2H,downstream_gene_variant,,ENST00000455712,;POLR2H,downstream_gene_variant,,ENST00000296223,;POLR2H,downstream_gene_variant,,ENST00000456318,;POLR2H,downstream_gene_variant,,ENST00000438240,;POLR2H,downstream_gene_variant,,ENST00000443489,;POLR2H,downstream_gene_variant,,ENST00000452961,;THPO,downstream_gene_variant,,ENST00000477594,;POLR2H,downstream_gene_variant,,ENST00000488213,;POLR2H,downstream_gene_variant,,ENST00000476003,;POLR2H,downstream_gene_variant,,ENST00000489043,;	A	ENSG00000090534	ENST00000204615	Transcript	missense_variant	1083	868	290	P/S	Cct/Tct	.	.	.	-1	THPO	HGNC	11795	protein_coding	YES	CCDS3265.1	ENSP00000204615	TPO_HUMAN	.	UPI000004A8D1	.	tolerated_low_confidence(0.18)	benign(0.018)	6/6	.	hmmpanther:PTHR10560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGGCTGGA	.	5	ESCA
TPRG1	0	.	GRCh37	3	188933129	188933129	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259G>C	p.Glu87Gln	p.E87Q	ENST00000345063	3/6	74	63	11	36	36	0	TPRG1,missense_variant,p.Glu15Gln,ENST00000425670,;TPRG1,missense_variant,p.Glu87Gln,ENST00000433971,;TPRG1,missense_variant,p.Glu87Gln,ENST00000456832,;TPRG1,missense_variant,p.Glu87Gln,ENST00000345063,;TPRG1,missense_variant,p.Glu87Gln,ENST00000412373,;TPRG1,non_coding_transcript_exon_variant,,ENST00000460613,;TPRG1,downstream_gene_variant,,ENST00000493725,;	C	ENSG00000188001	ENST00000345063	Transcript	missense_variant	426	259	87	E/Q	Gag/Cag	.	.	.	1	TPRG1	HGNC	24759	protein_coding	YES	CCDS3292.1	ENSP00000341031	TPRG1_HUMAN	C9JDW1_HUMAN	UPI00001C08BF	.	tolerated(0.45)	benign(0.012)	3/6	.	Pfam_domain:PF12456,hmmpanther:PTHR31108,hmmpanther:PTHR31108:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCTGAGACT	.	5	ESCA
SDHAP1	0	.	GRCh37	3	195711538	195711538	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.410A>G	.	.	ENST00000427841	4/17	298	238	60	239	239	0	SDHAP1,non_coding_transcript_exon_variant,,ENST00000427841,;SDHAP1,intron_variant,,ENST00000413474,;SDHAP1,intron_variant,,ENST00000435731,;SDHAP1,downstream_gene_variant,,ENST00000427415,;SDHAP1,non_coding_transcript_exon_variant,,ENST00000440850,;SDHAP1,non_coding_transcript_exon_variant,,ENST00000354937,;SDHAP1,intron_variant,,ENST00000538515,;SDHAP1,intron_variant,,ENST00000545003,;	C	ENSG00000185485	ENST00000427841	Transcript	non_coding_transcript_exon_variant	410	.	.	.	.	.	.	.	-1	SDHAP1	HGNC	32455	processed_transcript	YES	.	.	.	.	.	.	.	.	4/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCTTCACG	.	5	ESCA
RPL15	0	.	GRCh37	3	23959329	23959329	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-10-12T>C	.	.	ENST00000307839	.	53	33	19	36	36	0	RPL15,5_prime_UTR_variant,,ENST00000354811,;RPL15,intron_variant,,ENST00000456530,;RPL15,intron_variant,,ENST00000415719,;RPL15,intron_variant,,ENST00000434031,;NKIRAS1,intron_variant,,ENST00000421515,;RPL15,intron_variant,,ENST00000422218,;RPL15,intron_variant,,ENST00000307839,;RPL15,intron_variant,,ENST00000413699,;RPL15,intron_variant,,ENST00000412097,;RPL15,intron_variant,,ENST00000435882,;NKIRAS1,upstream_gene_variant,,ENST00000415901,;NKIRAS1,upstream_gene_variant,,ENST00000443659,;NKIRAS1,upstream_gene_variant,,ENST00000425478,;NKIRAS1,upstream_gene_variant,,ENST00000416026,;NKIRAS1,upstream_gene_variant,,ENST00000437230,;NKIRAS1,upstream_gene_variant,,ENST00000388759,;NKIRAS1,upstream_gene_variant,,ENST00000412028,;RPL15,non_coding_transcript_exon_variant,,ENST00000490223,;RPL15,intron_variant,,ENST00000465786,;RPL15,upstream_gene_variant,,ENST00000436146,;	C	ENSG00000174748	ENST00000307839	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RPL15	HGNC	10306	protein_coding	YES	CCDS2640.1	ENSP00000309334	RL15_HUMAN	Q76N55_HUMAN,E7EX53_HUMAN,E7EQV9_HUMAN	UPI0000003E34	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGTTTGATT	.	5	ESCA
CHL1	0	.	GRCh37	3	401982	401982	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1181G>A	p.Gly394Asp	p.G394D	ENST00000256509	12/28	58	55	3	57	57	0	CHL1,missense_variant,p.Gly378Asp,ENST00000397491,;CHL1,missense_variant,p.Gly394Asp,ENST00000256509,;CHL1-AS1,downstream_gene_variant,,ENST00000417612,;CHL1-AS1,downstream_gene_variant,,ENST00000608098,;CHL1,upstream_gene_variant,,ENST00000471332,;CHL1,3_prime_UTR_variant,,ENST00000453040,;	A	ENSG00000134121	ENST00000256509	Transcript	missense_variant	1823	1181	394	G/D	gGt/gAt	.	.	.	1	CHL1	HGNC	1939	protein_coding	YES	CCDS2556.1	ENSP00000256509	CHL1_HUMAN	C9JW79_HUMAN,C9JH37_HUMAN,C9JEY3_HUMAN,C9J905_HUMAN	UPI000013CF0F	.	tolerated(0.17)	possibly_damaging(0.628)	12/28	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF122,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTGGTGATG	.	2	ESCA
ITPR1	0	.	GRCh37	3	4687130	4687130	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.684T>C	p.%3D	p.D228D	ENST00000302640	9/61	62	45	17	69	69	0	ITPR1,synonymous_variant,p.%3D,ENST00000423119,;ITPR1,synonymous_variant,p.%3D,ENST00000456211,;ITPR1,synonymous_variant,p.%3D,ENST00000357086,;ITPR1,synonymous_variant,p.%3D,ENST00000302640,;ITPR1,synonymous_variant,p.%3D,ENST00000443694,;ITPR1,synonymous_variant,p.%3D,ENST00000354582,;ITPR1,synonymous_variant,p.%3D,ENST00000544951,;ITPR1,non_coding_transcript_exon_variant,,ENST00000477577,;ITPR1,non_coding_transcript_exon_variant,,ENST00000467056,;	C	ENSG00000150995	ENST00000302640	Transcript	synonymous_variant	1034	684	228	D	gaT/gaC	.	.	.	1	ITPR1	HGNC	6180	protein_coding	YES	CCDS54551.1	ENSP00000306253	ITPR1_HUMAN	.	UPI0000E5A461	.	.	.	9/61	.	hmmpanther:PTHR13715:SF52,hmmpanther:PTHR13715,Gene3D:2.80.10.50,Pfam_domain:PF08709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGATAACAA	.	5	ESCA
NCKIPSD	0	.	GRCh37	3	48711453	48711453	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*524G>C	.	.	ENST00000294129	13/13	44	30	14	44	44	0	NCKIPSD,3_prime_UTR_variant,,ENST00000294129,;NCKIPSD,3_prime_UTR_variant,,ENST00000416649,;NCKIPSD,intron_variant,,ENST00000341520,;NCKIPSD,downstream_gene_variant,,ENST00000413374,;RP11-572O6.1,downstream_gene_variant,,ENST00000607025,;RP11-148G20.1,downstream_gene_variant,,ENST00000421275,;NCKIPSD,downstream_gene_variant,,ENST00000470006,;	G	ENSG00000213672	ENST00000294129	Transcript	3_prime_UTR_variant	2813	.	.	.	.	.	.	.	-1	NCKIPSD	HGNC	15486	protein_coding	YES	CCDS2776.1	ENSP00000294129	SPN90_HUMAN	C9JMQ4_HUMAN,C9JC20_HUMAN	UPI0000135D86	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTTCAAAGC	.	5	ESCA
QARS	0	.	GRCh37	3	49133372	49133372	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*90C>G	.	.	ENST00000306125	24/24	50	38	12	47	47	0	QARS,3_prime_UTR_variant,,ENST00000453392,;QARS,3_prime_UTR_variant,,ENST00000306125,;QARS,3_prime_UTR_variant,,ENST00000414533,;QARS,downstream_gene_variant,,ENST00000420147,;QRICH1,upstream_gene_variant,,ENST00000424300,;QRICH1,upstream_gene_variant,,ENST00000357496,;QRICH1,upstream_gene_variant,,ENST00000430979,;QRICH1,upstream_gene_variant,,ENST00000437939,;QRICH1,upstream_gene_variant,,ENST00000395443,;QRICH1,upstream_gene_variant,,ENST00000411682,;QRICH1,upstream_gene_variant,,ENST00000450685,;QARS,non_coding_transcript_exon_variant,,ENST00000475599,;QARS,non_coding_transcript_exon_variant,,ENST00000487495,;QARS,downstream_gene_variant,,ENST00000466179,;QARS,downstream_gene_variant,,ENST00000482468,;QARS,downstream_gene_variant,,ENST00000470225,;QARS,3_prime_UTR_variant,,ENST00000430182,;QARS,non_coding_transcript_exon_variant,,ENST00000464962,;QARS,non_coding_transcript_exon_variant,,ENST00000497635,;QARS,non_coding_transcript_exon_variant,,ENST00000482248,;QARS,non_coding_transcript_exon_variant,,ENST00000494984,;QARS,downstream_gene_variant,,ENST00000478561,;QARS,downstream_gene_variant,,ENST00000459870,;QARS,downstream_gene_variant,,ENST00000494767,;QARS,downstream_gene_variant,,ENST00000494838,;QARS,downstream_gene_variant,,ENST00000470113,;	C	ENSG00000172053	ENST00000306125	Transcript	3_prime_UTR_variant	2756	.	.	.	.	.	.	.	-1	QARS	HGNC	9751	protein_coding	YES	CCDS2788.1	ENSP00000307567	SYQ_HUMAN	Q9H3A5_HUMAN,Q9BUZ3_HUMAN,B4DDN1_HUMAN	UPI000013661E	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGAGAATTT	.	5	ESCA
RHOA	0	.	GRCh37	3	49405948	49405948	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.190G>C	p.Glu64Gln	p.E64Q	ENST00000418115	3/5	28	14	14	41	41	0	RHOA,missense_variant,p.Glu64Gln,ENST00000422781,;RHOA,missense_variant,p.Glu64Gln,ENST00000445425,;RHOA,missense_variant,p.Glu64Gln,ENST00000418115,;RHOA,intron_variant,,ENST00000454011,;RHOA,downstream_gene_variant,,ENST00000431929,;RHOA-IT1,upstream_gene_variant,,ENST00000428083,;	G	ENSG00000067560	ENST00000418115	Transcript	missense_variant	575	190	64	E/Q	Gaa/Caa	.	.	.	-1	RHOA	HGNC	667	protein_coding	YES	CCDS2795.1	ENSP00000400175	RHOA_HUMAN	Q9BVT0_HUMAN,C9JNR4_HUMAN,B4DKN9_HUMAN	UPI0000046824	.	deleterious(0.02)	probably_damaging(0.95)	3/5	.	PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF100,hmmpanther:PTHR24072,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00173,SMART_domains:SM00175,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCCTGCC	.	5	ESCA
TKT	0	.	GRCh37	3	53264542	53264542	+	Silent	SNP	G	G	C	rs113369659	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1062C>G	p.%3D	p.T354T	ENST00000423516	9/15	134	34	100	144	144	0	TKT,synonymous_variant,p.%3D,ENST00000462138,;TKT,synonymous_variant,p.%3D,ENST00000423516,;TKT,synonymous_variant,p.%3D,ENST00000423525,;TKT,synonymous_variant,p.%3D,ENST00000296289,;TKT,non_coding_transcript_exon_variant,,ENST00000461139,;TKT,3_prime_UTR_variant,,ENST00000469678,;TKT,3_prime_UTR_variant,,ENST00000450814,;TKT,non_coding_transcript_exon_variant,,ENST00000460343,;TKT,downstream_gene_variant,,ENST00000472528,;TKT,downstream_gene_variant,,ENST00000487660,;TKT,downstream_gene_variant,,ENST00000494523,;TKT,downstream_gene_variant,,ENST00000466765,;TKT,upstream_gene_variant,,ENST00000460243,;	C	ENSG00000163931	ENST00000423516	Transcript	synonymous_variant	1142	1062	354	T	acC/acG	rs113369659	.	.	-1	TKT	HGNC	11834	protein_coding	YES	CCDS58834.1	ENSP00000391481	TKT_HUMAN	B3KPZ8_HUMAN	UPI0001AE759A	.	.	.	9/15	.	hmmpanther:PTHR11624:SF59,hmmpanther:PTHR11624,Gene3D:3.40.50.970,Pfam_domain:PF02779,SMART_domains:SM00861,Superfamily_domains:SSF52518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGGTGGA	byCluster	5	ESCA
CRYBG3	0	.	GRCh37	3	97591828	97591828	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1790C>T	p.Ser597Leu	p.S597L	ENST00000419587	4/4	48	38	10	18	18	0	CRYBG3,missense_variant,p.Ser597Leu,ENST00000419587,;CRYBG3,upstream_gene_variant,,ENST00000182096,;	T	ENSG00000233280	ENST00000419587	Transcript	missense_variant	1957	1790	597	S/L	tCa/tTa	.	.	.	1	CRYBG3	Uniprot_gn	34427	protein_coding	YES	.	ENSP00000391551	.	B4DLE8_HUMAN	UPI00017A74DC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCAGCAG	.	5	ESCA
RPL34	0	.	GRCh37	4	109546356	109546356	+	Missense_Mutation	SNP	G	G	C	rs1065701	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342G>C	p.Gln114His	p.Q114H	ENST00000394668	5/6	36	28	7	41	41	0	RPL34,missense_variant,p.Gln114His,ENST00000394665,;RPL34,missense_variant,p.Gln114His,ENST00000502534,;RPL34,missense_variant,p.Gln114His,ENST00000394668,;RPL34,missense_variant,p.Gln114His,ENST00000394667,;RPL34,missense_variant,p.Gln114His,ENST00000506397,;RPL34-AS1,upstream_gene_variant,,ENST00000510212,;RPL34-AS1,upstream_gene_variant,,ENST00000509984,;RPL34-AS1,upstream_gene_variant,,ENST00000506795,;RPL34-AS1,upstream_gene_variant,,ENST00000507248,;RPL34,downstream_gene_variant,,ENST00000503574,;RPL34,downstream_gene_variant,,ENST00000504231,;	C	ENSG00000109475	ENST00000394668	Transcript	missense_variant	408	342	114	Q/H	caG/caC	rs1065701	.	.	1	RPL34	HGNC	10340	protein_coding	YES	CCDS3680.1	ENSP00000378163	RL34_HUMAN	.	UPI000013C8A5	.	deleterious(0.02)	benign(0.007)	5/6	.	hmmpanther:PTHR10759,hmmpanther:PTHR10759:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCAGAAAGC	byHapMap	5	ESCA
NDST4	0	.	GRCh37	4	115997552	115997552	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.641C>T	p.Pro214Leu	p.P214L	ENST00000264363	2/14	42	34	8	24	24	0	NDST4,missense_variant,p.Pro214Leu,ENST00000264363,;NDST4,intron_variant,,ENST00000504854,;NDST4,intron_variant,,ENST00000514570,;	A	ENSG00000138653	ENST00000264363	Transcript	missense_variant	1320	641	214	P/L	cCt/cTt	.	.	.	-1	NDST4	HGNC	20779	protein_coding	YES	CCDS3706.1	ENSP00000264363	NDST4_HUMAN	.	UPI000006CED7	.	tolerated(0.29)	possibly_damaging(0.464)	2/14	.	Pfam_domain:PF12062,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAGGGCCT	.	5	ESCA
NAA15	0	.	GRCh37	4	140309613	140309613	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*375A>G	.	.	ENST00000296543	20/20	27	16	11	20	20	0	NAA15,3_prime_UTR_variant,,ENST00000296543,;NAA15,3_prime_UTR_variant,,ENST00000398947,;NAA15,intron_variant,,ENST00000515576,;NAA15,downstream_gene_variant,,ENST00000485905,;	G	ENSG00000164134	ENST00000296543	Transcript	3_prime_UTR_variant	3299	.	.	.	.	.	.	.	1	NAA15	HGNC	30782	protein_coding	YES	CCDS43270.1	ENSP00000296543	NAA15_HUMAN	.	UPI000004B631	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTATATCTCA	.	5	ESCA
NR3C2	0	.	GRCh37	4	149001812	149001812	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*683T>G	.	.	ENST00000358102	9/9	36	32	4	34	34	0	NR3C2,3_prime_UTR_variant,,ENST00000512865,;NR3C2,3_prime_UTR_variant,,ENST00000358102,;NR3C2,3_prime_UTR_variant,,ENST00000344721,;NR3C2,3_prime_UTR_variant,,ENST00000355292,;NR3C2,downstream_gene_variant,,ENST00000511528,;NR3C2,downstream_gene_variant,,ENST00000342437,;	C	ENSG00000151623	ENST00000358102	Transcript	3_prime_UTR_variant	4001	.	.	.	.	.	.	.	-1	NR3C2	HGNC	7979	protein_coding	YES	CCDS3772.1	ENSP00000350815	.	Q4W5E8_HUMAN,B0ZBF6_HUMAN	UPI000013DC6D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAAAAAATTA	.	4	ESCA
CPEB2	0	.	GRCh37	4	15069672	15069672	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1668G>C	.	.	ENST00000538197	12/12	24	14	10	36	36	0	CPEB2,3_prime_UTR_variant,,ENST00000541112,;CPEB2,3_prime_UTR_variant,,ENST00000382395,;CPEB2,3_prime_UTR_variant,,ENST00000259997,;CPEB2,3_prime_UTR_variant,,ENST00000382401,;CPEB2,3_prime_UTR_variant,,ENST00000538197,;CPEB2,3_prime_UTR_variant,,ENST00000442003,;CPEB2,downstream_gene_variant,,ENST00000507071,;CPEB2,downstream_gene_variant,,ENST00000345451,;CPEB2,downstream_gene_variant,,ENST00000509684,;RP11-665G4.1,intron_variant,,ENST00000502344,;RP11-665G4.1,intron_variant,,ENST00000513384,;	C	ENSG00000137449	ENST00000538197	Transcript	3_prime_UTR_variant	4773	.	.	.	.	.	.	.	1	CPEB2	HGNC	21745	protein_coding	YES	CCDS56325.1	ENSP00000443985	.	J3KN18_HUMAN,H0Y9D9_HUMAN,F5H160_HUMAN	UPI0001D0434B	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGAGTTACT	.	5	ESCA
TIGD4	0	.	GRCh37	4	153691031	153691032	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125dupT	p.Glu376Ter	p.E376*	ENST00000304337	2/2	82	64	18	56	56	0	TIGD4,frameshift_variant,p.Glu376Ter,ENST00000304337,;	A	ENSG00000169989	ENST00000304337	Transcript	frameshift_variant	1946-1947	1125-1126	375-376	-/X	-/T	.	.	.	-1	TIGD4	HGNC	18335	protein_coding	YES	CCDS34079.1	ENSP00000355162	TIGD4_HUMAN	.	UPI000013E966	.	.	.	2/2	.	hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCTTCATAGC	.	3	ESCA
TACC3	0	.	GRCh37	4	1732903	1732903	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1466G>C	p.Arg489Thr	p.R489T	ENST00000313288	6/16	48	34	14	49	49	0	TACC3,missense_variant,p.Arg156Thr,ENST00000470136,;TACC3,missense_variant,p.Arg489Thr,ENST00000313288,;TACC3,missense_variant,p.Arg129Thr,ENST00000485989,;TACC3,downstream_gene_variant,,ENST00000493975,;TACC3,downstream_gene_variant,,ENST00000458173,;TACC3,non_coding_transcript_exon_variant,,ENST00000466077,;TACC3,non_coding_transcript_exon_variant,,ENST00000484651,;TACC3,downstream_gene_variant,,ENST00000467746,;	C	ENSG00000013810	ENST00000313288	Transcript	missense_variant	1572	1466	489	R/T	aGa/aCa	.	.	.	1	TACC3	HGNC	11524	protein_coding	YES	CCDS3352.1	ENSP00000326550	TACC3_HUMAN	E7EMT0_HUMAN,C9JA91_HUMAN	UPI0000136869	.	tolerated(0.55)	benign(0.001)	6/16	.	hmmpanther:PTHR13924	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	GGAGAGAGCCT	.	3	ESCA
TACC3	0	.	GRCh37	4	1732910	1732910	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1473G>A	p.%3D	p.L491L	ENST00000313288	6/16	51	37	14	45	45	0	TACC3,synonymous_variant,p.%3D,ENST00000470136,;TACC3,synonymous_variant,p.%3D,ENST00000313288,;TACC3,synonymous_variant,p.%3D,ENST00000485989,;TACC3,downstream_gene_variant,,ENST00000493975,;TACC3,downstream_gene_variant,,ENST00000458173,;TACC3,non_coding_transcript_exon_variant,,ENST00000466077,;TACC3,non_coding_transcript_exon_variant,,ENST00000484651,;TACC3,downstream_gene_variant,,ENST00000467746,;	A	ENSG00000013810	ENST00000313288	Transcript	synonymous_variant	1579	1473	491	L	ttG/ttA	.	.	.	1	TACC3	HGNC	11524	protein_coding	YES	CCDS3352.1	ENSP00000326550	TACC3_HUMAN	E7EMT0_HUMAN,C9JA91_HUMAN	UPI0000136869	.	.	.	6/16	.	hmmpanther:PTHR13924	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	GCCTTGAACTC	.	3	ESCA
TACC3	0	.	GRCh37	4	1733001	1733001	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1564G>C	p.Glu522Gln	p.E522Q	ENST00000313288	6/16	18	13	5	35	35	0	TACC3,missense_variant,p.Glu522Gln,ENST00000313288,;TACC3,missense_variant,p.Glu162Gln,ENST00000485989,;TACC3,intron_variant,,ENST00000470136,;TACC3,downstream_gene_variant,,ENST00000493975,;TACC3,downstream_gene_variant,,ENST00000458173,;TACC3,non_coding_transcript_exon_variant,,ENST00000466077,;TACC3,non_coding_transcript_exon_variant,,ENST00000484651,;TACC3,downstream_gene_variant,,ENST00000467746,;	C	ENSG00000013810	ENST00000313288	Transcript	missense_variant	1670	1564	522	E/Q	Gag/Cag	COSM420117	.	.	1	TACC3	HGNC	11524	protein_coding	YES	CCDS3352.1	ENSP00000326550	TACC3_HUMAN	E7EMT0_HUMAN,C9JA91_HUMAN	UPI0000136869	.	tolerated(0.05)	possibly_damaging(0.758)	6/16	.	hmmpanther:PTHR13924	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAAGAGGAG	.	5	ESCA
FAT1	0	.	GRCh37	4	187524844	187524844	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10836C>G	p.%3D	p.L3612L	ENST00000441802	19/27	54	37	17	34	34	0	FAT1,synonymous_variant,p.%3D,ENST00000441802,;FAT1,upstream_gene_variant,,ENST00000512347,;FAT1,upstream_gene_variant,,ENST00000503253,;	C	ENSG00000083857	ENST00000441802	Transcript	synonymous_variant	11046	10836	3612	L	ctC/ctG	.	.	.	-1	FAT1	HGNC	3595	protein_coding	YES	CCDS47177.1	ENSP00000406229	FAT1_HUMAN	D6RCE4_HUMAN	UPI000051946B	.	.	.	19/27	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTGAGAAG	.	5	ESCA
ARAP2	0	.	GRCh37	4	36130237	36130237	+	Silent	SNP	C	C	G	rs771824573	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3558G>C	p.%3D	p.T1186T	ENST00000303965	21/33	46	21	24	48	48	0	ARAP2,synonymous_variant,p.%3D,ENST00000303965,;	G	ENSG00000047365	ENST00000303965	Transcript	synonymous_variant	4048	3558	1186	T	acG/acC	rs771824573,COSM3917706	.	.	-1	ARAP2	HGNC	16924	protein_coding	YES	CCDS3441.1	ENSP00000302895	ARAP2_HUMAN	D6RAD6_HUMAN	UPI000013E917	.	.	.	21/33	.	PROSITE_profiles:PS50238,hmmpanther:PTHR23180:SF228,hmmpanther:PTHR23180,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCCGTCAC	byFrequency	5	ESCA
KIAA1239	0	.	GRCh37	4	37448096	37448096	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4486T>C	p.Phe1496Leu	p.F1496L	ENST00000309447	7/7	54	37	16	49	49	0	KIAA1239,missense_variant,p.Phe1496Leu,ENST00000309447,;	C	ENSG00000174145	ENST00000309447	Transcript	missense_variant	5334	4486	1496	F/L	Ttt/Ctt	.	.	.	1	KIAA1239	HGNC	29229	protein_coding	YES	CCDS47040.1	ENSP00000309501	K1239_HUMAN	.	UPI00006C0875	.	tolerated(1)	benign(0.001)	7/7	.	hmmpanther:PTHR19857:SF18,hmmpanther:PTHR19857,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTGTTTATC	.	5	ESCA
LIAS	0	.	GRCh37	4	39465225	39465225	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393G>T	p.Met131Ile	p.M131I	ENST00000261434	4/11	54	34	20	45	45	0	LIAS,missense_variant,p.Met131Ile,ENST00000381846,;LIAS,missense_variant,p.Met131Ile,ENST00000261434,;LIAS,missense_variant,p.Met131Ile,ENST00000340169,;LIAS,intron_variant,,ENST00000513731,;RPL9,upstream_gene_variant,,ENST00000508595,;RPL9,upstream_gene_variant,,ENST00000504470,;RPL9,upstream_gene_variant,,ENST00000503040,;RPL9,upstream_gene_variant,,ENST00000295955,;RPL9,upstream_gene_variant,,ENST00000449470,;LIAS,splice_region_variant,,ENST00000515061,;LIAS,non_coding_transcript_exon_variant,,ENST00000509519,;LIAS,non_coding_transcript_exon_variant,,ENST00000424936,;RPL9,upstream_gene_variant,,ENST00000511075,;RPL9,upstream_gene_variant,,ENST00000514842,;RPL9,upstream_gene_variant,,ENST00000437992,;	T	ENSG00000121897	ENST00000261434	Transcript	missense_variant	511	393	131	M/I	atG/atT	.	.	.	1	LIAS	HGNC	16429	protein_coding	YES	CCDS3453.1	ENSP00000261434	LIAS_HUMAN	.	UPI000004EE9F	.	deleterious(0)	probably_damaging(0.973)	4/11	.	HAMAP:MF_00206,hmmpanther:PTHR10949:SF0,hmmpanther:PTHR10949,TIGRFAM_domain:TIGR00510,Gene3D:3.20.20.70,SMART_domains:SM00729,PIRSF_domain:PIRSF005963,Superfamily_domains:SSF102114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCATGGTAGG	.	5	ESCA
PDGFRA	0	.	GRCh37	4	55161840	55161840	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*401C>G	.	.	ENST00000257290	23/23	38	28	9	41	41	0	PDGFRA,3_prime_UTR_variant,,ENST00000257290,;FIP1L1,downstream_gene_variant,,ENST00000507166,;	G	ENSG00000134853	ENST00000257290	Transcript	3_prime_UTR_variant	4002	.	.	.	.	.	.	.	1	PDGFRA	HGNC	8803	protein_coding	YES	CCDS3495.1	ENSP00000257290	PGFRA_HUMAN	D6RIG5_HUMAN,D6RG11_HUMAN,D6RDX0_HUMAN	UPI0000131793	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTATCTTCTT	.	5	ESCA
HNRNPDL	0	.	GRCh37	4	83345509	83345509	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*550G>C	.	.	ENST00000295470	8/8	28	20	8	23	23	0	HNRNPDL,3_prime_UTR_variant,,ENST00000295470,;HNRNPDL,downstream_gene_variant,,ENST00000502762,;HNRNPDL,downstream_gene_variant,,ENST00000349655,;HNRNPDL,downstream_gene_variant,,ENST00000602300,;HNRNPDL,downstream_gene_variant,,ENST00000514511,;HNRNPDL,downstream_gene_variant,,ENST00000507721,;	G	ENSG00000152795	ENST00000295470	Transcript	3_prime_UTR_variant	1989	.	.	.	.	.	.	.	-1	HNRNPDL	HGNC	5037	protein_coding	YES	CCDS3593.1	ENSP00000295470	HNRDL_HUMAN	B4DGN3_HUMAN	UPI0000073377	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TATGTCTTCCT	.	2	ESCA
CPZ	0	.	GRCh37	4	8602970	8602970	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242T>G	p.Leu81Arg	p.L81R	ENST00000360986	3/11	100	62	38	122	122	0	CPZ,missense_variant,p.Leu81Arg,ENST00000360986,;CPZ,missense_variant,p.Leu70Arg,ENST00000315782,;CPZ,5_prime_UTR_variant,,ENST00000382480,;CPZ,upstream_gene_variant,,ENST00000429646,;CPZ,non_coding_transcript_exon_variant,,ENST00000504070,;CPZ,non_coding_transcript_exon_variant,,ENST00000506287,;GPR78,3_prime_UTR_variant,,ENST00000514302,;CPZ,3_prime_UTR_variant,,ENST00000515606,;CPZ,non_coding_transcript_exon_variant,,ENST00000514602,;GPR78,upstream_gene_variant,,ENST00000513120,;CPZ,downstream_gene_variant,,ENST00000514875,;	G	ENSG00000109625	ENST00000360986	Transcript	missense_variant	416	242	81	L/R	cTg/cGg	.	.	.	1	CPZ	HGNC	2333	protein_coding	YES	CCDS33953.1	ENSP00000354255	CBPZ_HUMAN	.	UPI000020BCC5	.	deleterious(0)	probably_damaging(0.999)	3/11	.	Superfamily_domains:SSF63501,SMART_domains:SM00063,Gene3D:1ijyA00,Pfam_domain:PF01392,hmmpanther:PTHR11532:SF4,hmmpanther:PTHR11532,PROSITE_profiles:PS50038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCCTGCTGA	.	5	ESCA
MMRN1	0	.	GRCh37	4	90874609	90874609	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*40A>T	.	.	ENST00000394980	9/9	17	11	6	20	19	0	MMRN1,3_prime_UTR_variant,,ENST00000394980,;MMRN1,3_prime_UTR_variant,,ENST00000264790,;MMRN1,3_prime_UTR_variant,,ENST00000394981,;MMRN1,downstream_gene_variant,,ENST00000508372,;MMRN1,downstream_gene_variant,,ENST00000506328,;	T	ENSG00000138722	ENST00000394980	Transcript	3_prime_UTR_variant	4046	.	.	.	.	.	.	.	1	MMRN1	HGNC	7178	protein_coding	YES	CCDS3635.1	ENSP00000378431	MMRN1_HUMAN	E7EPG1_HUMAN	UPI000013D570	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	GAAACAGCCAG	.	3	ESCA
KCNN2	0	.	GRCh37	5	113740169	113740169	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.617G>A	p.Arg206Lys	p.R206K	ENST00000512097	4/9	39	18	21	48	48	0	KCNN2,missense_variant,p.Arg206Lys,ENST00000512097,;KCNN2,missense_variant,p.Arg206Lys,ENST00000264773,;KCNN2,intron_variant,,ENST00000507750,;	A	ENSG00000080709	ENST00000512097	Transcript	missense_variant	1635	617	206	R/K	aGa/aAa	.	.	.	1	KCNN2	HGNC	6291	protein_coding	YES	CCDS4114.1	ENSP00000427120	KCNN2_HUMAN	.	UPI000013D56A	.	deleterious(0.01)	probably_damaging(0.92)	4/9	.	hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF21,Pfam_domain:PF03530,Gene3D:1.10.287.70	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGAATAG	.	5	ESCA
PRR16	0	.	GRCh37	5	120022569	120022569	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*165C>A	.	.	ENST00000379551	3/3	31	6	24	45	45	0	PRR16,3_prime_UTR_variant,,ENST00000407149,;PRR16,3_prime_UTR_variant,,ENST00000446965,;PRR16,3_prime_UTR_variant,,ENST00000505123,;PRR16,3_prime_UTR_variant,,ENST00000379551,;PRR16,downstream_gene_variant,,ENST00000509923,;	A	ENSG00000184838	ENST00000379551	Transcript	3_prime_UTR_variant	1368	.	.	.	.	.	.	.	1	PRR16	HGNC	29654	protein_coding	YES	CCDS4127.1	ENSP00000368869	PRR16_HUMAN	D6RGF0_HUMAN	UPI0000073195	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATATCCTGGG	.	5	ESCA
HNRNPA0	0	.	GRCh37	5	137089904	137089904	+	5'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-149T>G	.	.	ENST00000314940	1/1	19	6	12	23	23	0	HNRNPA0,5_prime_UTR_variant,,ENST00000314940,;	C	ENSG00000177733	ENST00000314940	Transcript	5_prime_UTR_variant	136	.	.	.	.	.	.	.	-1	HNRNPA0	HGNC	5030	protein_coding	YES	CCDS4193.1	ENSP00000316042	ROA0_HUMAN	.	UPI0000000C1D	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGAAGGGGA	.	5	ESCA
BRD8	0	.	GRCh37	5	137498825	137498825	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2081C>G	p.Ser694Ter	p.S694*	ENST00000254900	15/27	84	54	30	62	62	0	BRD8,stop_gained,p.Ser694Ter,ENST00000254900,;BRD8,stop_gained,p.Ser653Ter,ENST00000455658,;BRD8,stop_gained,p.Ser694Ter,ENST00000402931,;BRD8,stop_gained,p.Ser697Ter,ENST00000411594,;BRD8,stop_gained,p.Ser723Ter,ENST00000454473,;BRD8,stop_gained,p.Ser692Ter,ENST00000418329,;BRD8,stop_gained,p.Ser162Ter,ENST00000511898,;BRD8,stop_gained,p.Ser767Ter,ENST00000230901,;BRD8,stop_gained,p.Ser688Ter,ENST00000441656,;BRD8,downstream_gene_variant,,ENST00000453824,;BRD8,intron_variant,,ENST00000515014,;BRD8,3_prime_UTR_variant,,ENST00000512140,;BRD8,3_prime_UTR_variant,,ENST00000506167,;BRD8,downstream_gene_variant,,ENST00000471892,;BRD8,upstream_gene_variant,,ENST00000460746,;BRD8,downstream_gene_variant,,ENST00000483805,;BRD8,upstream_gene_variant,,ENST00000489351,;BRD8,downstream_gene_variant,,ENST00000428808,;BRD8,downstream_gene_variant,,ENST00000463620,;BRD8,upstream_gene_variant,,ENST00000472478,;	C	ENSG00000112983	ENST00000254900	Transcript	stop_gained	2453	2081	694	S/*	tCa/tGa	COSM3365845,COSM3365846	.	.	-1	BRD8	HGNC	19874	protein_coding	YES	CCDS4198.1	ENSP00000254900	BRD8_HUMAN	F8WDX5_HUMAN,F8WBH2_HUMAN	UPI0000246C01	.	.	.	15/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15398,hmmpanther:PTHR15398:SF1	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTGAAGAA	.	5	ESCA
ETF1	0	.	GRCh37	5	137843798	137843798	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*196C>A	.	.	ENST00000360541	11/11	43	26	17	48	48	0	ETF1,3_prime_UTR_variant,,ENST00000503014,;ETF1,3_prime_UTR_variant,,ENST00000360541,;ETF1,3_prime_UTR_variant,,ENST00000499810,;ETF1,downstream_gene_variant,,ENST00000572514,;ETF1,downstream_gene_variant,,ENST00000512198,;ETF1,downstream_gene_variant,,ENST00000506345,;ETF1,downstream_gene_variant,,ENST00000503183,;	T	ENSG00000120705	ENST00000360541	Transcript	3_prime_UTR_variant	1732	.	.	.	.	.	.	.	-1	ETF1	HGNC	3477	protein_coding	YES	CCDS4207.1	ENSP00000353741	ERF1_HUMAN	Q96CG1_HUMAN,I3L492_HUMAN,D6RJE8_HUMAN	UPI00001110CB	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCTGACACC	.	5	ESCA
PCDHA10	0	.	GRCh37	5	140237666	140237666	+	Missense_Mutation	SNP	C	C	T	rs782778779	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2033C>T	p.Ser678Leu	p.S678L	ENST00000307360	1/4	64	43	21	87	87	0	PCDHA10,missense_variant,p.Ser678Leu,ENST00000307360,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA9,intron_variant,,ENST00000532602,;AC005609.1,downstream_gene_variant,,ENST00000502505,;PCDHA9,downstream_gene_variant,,ENST00000378122,;PCDHA14,upstream_gene_variant,,ENST00000562220,;PCDHA14,upstream_gene_variant,,ENST00000506751,;	T	ENSG00000250120	ENST00000307360	Transcript	missense_variant	2033	2033	678	S/L	tCg/tTg	rs782778779	.	.	1	PCDHA10	HGNC	8664	protein_coding	YES	CCDS54921.1	ENSP00000304234	PCDAA_HUMAN	.	UPI00001273D3	.	tolerated_low_confidence(0.08)	benign(0.02)	1/4	.	hmmpanther:PTHR24028:SF76,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCGTCGC	.	5	ESCA
PCDHA13	0	.	GRCh37	5	140261985	140261985	+	Missense_Mutation	SNP	C	C	G	rs782194379	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132C>G	p.Phe44Leu	p.F44L	ENST00000289272	1/4	103	68	34	117	117	0	PCDHA13,missense_variant,p.Phe44Leu,ENST00000289272,;PCDHA13,missense_variant,p.Phe44Leu,ENST00000409494,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;	G	ENSG00000239389	ENST00000289272	Transcript	missense_variant	132	132	44	F/L	ttC/ttG	rs782194379	.	.	1	PCDHA13	HGNC	8667	protein_coding	YES	CCDS4240.1	ENSP00000289272	PCDAD_HUMAN	.	UPI00001273D6	.	deleterious_low_confidence(0.02)	benign(0.179)	1/4	.	Superfamily_domains:SSF49313,Pfam_domain:PF08266,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTCGTGGG	byFrequency	5	ESCA
PCDHGA8	0	.	GRCh37	5	140774532	140774532	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2152C>T	p.Arg718Cys	p.R718C	ENST00000398604	1/4	85	76	8	102	102	0	PCDHGA8,missense_variant,p.Arg718Cys,ENST00000398604,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB2,intron_variant,,ENST00000522605,;	T	ENSG00000253767	ENST00000398604	Transcript	missense_variant	2152	2152	718	R/C	Cgc/Tgc	.	.	.	1	PCDHGA8	HGNC	8706	protein_coding	YES	CCDS47291.1	ENSP00000381605	PCDG8_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006FC06	.	deleterious_low_confidence(0.03)	benign(0.177)	1/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF72	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGGCGCTGG	.	4	ESCA
C5orf60	0	.	GRCh37	5	179070016	179070016	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.537G>A	p.%3D	p.P179P	ENST00000448248	4/6	96	62	33	105	105	0	C5orf60,synonymous_variant,p.%3D,ENST00000448248,;C5orf60,non_coding_transcript_exon_variant,,ENST00000506142,;C5orf60,synonymous_variant,p.%3D,ENST00000512899,;C5orf60,3_prime_UTR_variant,,ENST00000513845,;C5orf60,non_coding_transcript_exon_variant,,ENST00000511063,;C5orf60,non_coding_transcript_exon_variant,,ENST00000514664,;C5orf60,downstream_gene_variant,,ENST00000503358,;C5orf60,downstream_gene_variant,,ENST00000513142,;	T	ENSG00000204661	ENST00000448248	Transcript	synonymous_variant	563	537	179	P	ccG/ccA	.	.	.	-1	C5orf60	HGNC	27753	protein_coding	YES	CCDS47353.1	ENSP00000404583	CE060_HUMAN	.	UPI00004191D3	.	.	.	4/6	.	hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTCGGGAC	.	5	ESCA
DROSHA	0	.	GRCh37	5	31401340	31401340	+	3'UTR	SNP	T	T	G	rs547345067	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*199A>C	.	.	ENST00000511367	35/35	29	4	25	32	32	0	DROSHA,3_prime_UTR_variant,,ENST00000442743,;DROSHA,3_prime_UTR_variant,,ENST00000511367,;DROSHA,3_prime_UTR_variant,,ENST00000513349,;DROSHA,3_prime_UTR_variant,,ENST00000344624,;DROSHA,non_coding_transcript_exon_variant,,ENST00000514927,;DROSHA,downstream_gene_variant,,ENST00000511778,;DROSHA,downstream_gene_variant,,ENST00000512166,;	G	ENSG00000113360	ENST00000511367	Transcript	3_prime_UTR_variant	4569	.	.	.	.	rs547345067	.	.	-1	DROSHA	HGNC	17904	protein_coding	YES	CCDS47195.1	ENSP00000425979	RNC_HUMAN	E5RHD1_HUMAN	UPI0000134351	.	.	.	35/35	.	.	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAATAGAAG	by1000G	5	ESCA
RAI14	0	.	GRCh37	5	34830933	34830933	+	3'Flank	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000515799	.	29	23	6	17	17	0	RAI14,3_prime_UTR_variant,,ENST00000265109,;RAI14,3_prime_UTR_variant,,ENST00000397449,;RAI14,3_prime_UTR_variant,,ENST00000428746,;RAI14,downstream_gene_variant,,ENST00000506376,;RAI14,downstream_gene_variant,,ENST00000515799,;RAI14,downstream_gene_variant,,ENST00000512629,;RAI14,downstream_gene_variant,,ENST00000503673,;RAI14,non_coding_transcript_exon_variant,,ENST00000507883,;RAI14,downstream_gene_variant,,ENST00000513772,;	A	ENSG00000039560	ENST00000515799	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	21	1	RAI14	HGNC	14873	protein_coding	YES	CCDS54839.1	ENSP00000427123	RAI14_HUMAN	B3KMZ9_HUMAN	UPI00001B296B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTCGGCAG	.	5	ESCA
LIFR	0	.	GRCh37	5	38478402	38478402	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3295G>C	.	.	ENST00000263409	20/20	10	4	6	8	8	0	LIFR,3_prime_UTR_variant,,ENST00000263409,;LIFR,downstream_gene_variant,,ENST00000453190,;	G	ENSG00000113594	ENST00000263409	Transcript	3_prime_UTR_variant	6752	.	.	.	.	.	.	.	-1	LIFR	HGNC	6597	protein_coding	YES	CCDS3927.1	ENSP00000263409	LIFR_HUMAN	D6RJ94_HUMAN,D6RF33_HUMAN	UPI000004CAC2	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TCTTTCAGATC	.	2	ESCA
SGTB	0	.	GRCh37	5	64965526	64965526	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*547C>A	.	.	ENST00000381007	11/11	22	14	8	23	23	0	SGTB,3_prime_UTR_variant,,ENST00000381007,;TRAPPC13,downstream_gene_variant,,ENST00000231526,;TRAPPC13,downstream_gene_variant,,ENST00000505553,;TRAPPC13,downstream_gene_variant,,ENST00000545191,;TRAPPC13,downstream_gene_variant,,ENST00000438419,;TRAPPC13,downstream_gene_variant,,ENST00000399438,;TRAPPC13,downstream_gene_variant,,ENST00000415825,;TRAPPC13,downstream_gene_variant,,ENST00000512009,;TRAPPC13,downstream_gene_variant,,ENST00000505108,;	T	ENSG00000197860	ENST00000381007	Transcript	3_prime_UTR_variant	1698	.	.	.	.	.	.	.	-1	SGTB	HGNC	23567	protein_coding	YES	CCDS3988.1	ENSP00000370395	SGTB_HUMAN	O75589_HUMAN,D6RFW1_HUMAN	UPI000004D24F	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTAAAGATAAC	.	2	ESCA
ERAP1	0	.	GRCh37	5	96132929	96132929	+	Missense_Mutation	SNP	G	G	T	rs138975720	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.747C>A	p.Phe249Leu	p.F249L	ENST00000296754	4/20	23	12	10	15	15	0	ERAP1,missense_variant,p.Phe249Leu,ENST00000443439,;ERAP1,missense_variant,p.Phe249Leu,ENST00000296754,;ERAP1,downstream_gene_variant,,ENST00000508227,;ERAP1,downstream_gene_variant,,ENST00000503921,;ERAP1,upstream_gene_variant,,ENST00000503311,;	T	ENSG00000164307	ENST00000296754	Transcript	missense_variant	1005	747	249	F/L	ttC/ttA	rs138975720	.	.	-1	ERAP1	HGNC	18173	protein_coding	YES	CCDS4085.1	ENSP00000296754	ERAP1_HUMAN	D6RAL9_HUMAN	UPI000045731D	.	deleterious(0.02)	benign(0.067)	4/20	.	hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF156,Pfam_domain:PF01433,Superfamily_domains:0038696,Prints_domain:PR00756	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATGAAGGC	byCluster	4	ESCA
AIM1	0	.	GRCh37	6	106999729	106999729	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4091G>C	p.Trp1364Ser	p.W1364S	ENST00000369066	12/20	27	17	10	42	42	0	AIM1,missense_variant,p.Trp183Ser,ENST00000457437,;AIM1,missense_variant,p.Trp1364Ser,ENST00000369066,;AIM1,missense_variant,p.Trp183Ser,ENST00000535438,;AIM1,splice_region_variant,,ENST00000487681,;	C	ENSG00000112297	ENST00000369066	Transcript	missense_variant	4578	4091	1364	W/S	tGg/tCg	.	.	.	1	AIM1	HGNC	356	protein_coding	YES	CCDS34506.1	ENSP00000358062	AIM1_HUMAN	B3KPT0_HUMAN	UPI000013C91D	.	deleterious(0)	probably_damaging(1)	12/20	.	PROSITE_profiles:PS50915,hmmpanther:PTHR11818:SF2,hmmpanther:PTHR11818,Pfam_domain:PF00030,Gene3D:2.60.20.10,SMART_domains:SM00247,Superfamily_domains:SSF49695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATGGGTAG	.	5	ESCA
SYCP2L	0	.	GRCh37	6	10930703	10930703	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1589C>A	p.Ser530Ter	p.S530*	ENST00000283141	19/30	30	23	7	23	23	0	SYCP2L,stop_gained,p.Ser530Ter,ENST00000283141,;SYCP2L,downstream_gene_variant,,ENST00000543878,;SYCP2L,3_prime_UTR_variant,,ENST00000341041,;SYCP2L,non_coding_transcript_exon_variant,,ENST00000474197,;RP11-637O19.3,downstream_gene_variant,,ENST00000480294,;	A	ENSG00000153157	ENST00000283141	Transcript	stop_gained	1885	1589	530	S/*	tCa/tAa	.	.	.	1	SYCP2L	HGNC	21537	protein_coding	YES	CCDS43423.1	ENSP00000283141	SYC2L_HUMAN	.	UPI000022CA18	.	.	.	19/30	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15607:SF14,hmmpanther:PTHR15607	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATCATATT	.	5	ESCA
GPRC6A	0	.	GRCh37	6	117113916	117113916	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2170A>C	p.Ile724Leu	p.I724L	ENST00000310357	6/6	31	20	11	35	35	0	GPRC6A,missense_variant,p.Ile724Leu,ENST00000310357,;GPRC6A,missense_variant,p.Ile653Leu,ENST00000368549,;GPRC6A,missense_variant,p.Ile549Leu,ENST00000530250,;	G	ENSG00000173612	ENST00000310357	Transcript	missense_variant	2192	2170	724	I/L	Atc/Ctc	.	.	.	-1	GPRC6A	HGNC	18510	protein_coding	YES	CCDS5112.1	ENSP00000309493	GPC6A_HUMAN	.	UPI000013EFF9	.	tolerated(0.26)	benign(0.042)	6/6	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24061:SF5,hmmpanther:PTHR24061,Pfam_domain:PF00003,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGATTAGCC	.	5	ESCA
PCMT1	0	.	GRCh37	6	150123514	150123514	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.848+9G>C	.	.	ENST00000367384	.	20	10	9	32	32	0	PCMT1,stop_lost,p.Ter286SerextTer78,ENST00000464889,;PCMT1,stop_lost,p.Ter193SerextTer?,ENST00000544496,;PCMT1,stop_lost,p.Ter228SerextTer78,ENST00000367380,;PCMT1,stop_lost,p.Ter286SerextTer22,ENST00000367378,;PCMT1,intron_variant,,ENST00000367384,;RP11-350J20.5,upstream_gene_variant,,ENST00000455607,;	C	ENSG00000120265	ENST00000367384	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PCMT1	HGNC	8728	protein_coding	YES	CCDS59041.1	ENSP00000356354	.	H7BY58_HUMAN,C9J0F2_HUMAN	UPI0001B7942B	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGTGATTTT	.	5	ESCA
RAET1E	0	.	GRCh37	6	150209742	150209742	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.684C>T	p.%3D	p.I228I	ENST00000357183	4/4	34	22	12	43	43	0	RAET1E,synonymous_variant,p.%3D,ENST00000367363,;RAET1E,synonymous_variant,p.%3D,ENST00000357183,;RAET1E,intron_variant,,ENST00000532335,;RAET1E,downstream_gene_variant,,ENST00000529948,;RAET1E,downstream_gene_variant,,ENST00000531073,;RP11-244K5.8,intron_variant,,ENST00000606915,;RAET1E-AS1,intron_variant,,ENST00000605899,;RAET1E-AS1,upstream_gene_variant,,ENST00000446954,;RAET1E,3_prime_UTR_variant,,ENST00000392270,;	A	ENSG00000164520	ENST00000357183	Transcript	synonymous_variant	817	684	228	I	atC/atT	.	.	.	-1	RAET1E	HGNC	16793	protein_coding	YES	CCDS5221.1	ENSP00000349709	N2DL4_HUMAN	I2GUA6_HUMAN,E9PKJ6_HUMAN	UPI0000071E77	.	.	.	4/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR16675:SF64,hmmpanther:PTHR16675	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGATGATCCA	.	3	ESCA
RBM24	0	.	GRCh37	6	17292855	17292855	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*505C>G	.	.	ENST00000379052	4/4	63	45	17	46	46	0	RBM24,3_prime_UTR_variant,,ENST00000509686,;RBM24,3_prime_UTR_variant,,ENST00000379052,;RBM24,3_prime_UTR_variant,,ENST00000318204,;RBM24,downstream_gene_variant,,ENST00000503965,;RBM24,downstream_gene_variant,,ENST00000425446,;RBM24,non_coding_transcript_exon_variant,,ENST00000508508,;RBM24,non_coding_transcript_exon_variant,,ENST00000510826,;RBM24,downstream_gene_variant,,ENST00000504055,;	G	ENSG00000112183	ENST00000379052	Transcript	3_prime_UTR_variant	1452	.	.	.	.	.	.	.	1	RBM24	HGNC	21539	protein_coding	YES	CCDS47378.1	ENSP00000368341	RBM24_HUMAN	A8KAI7_HUMAN	UPI000006E912	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTCAAGTC	.	5	ESCA
MDC1	0	.	GRCh37	6	30679848	30679848	+	Missense_Mutation	SNP	C	C	G	rs746258696	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1871G>C	p.Gly624Ala	p.G624A	ENST00000376406	5/15	64	41	23	75	75	0	MDC1,missense_variant,p.Gly624Ala,ENST00000376405,;MDC1,missense_variant,p.Gly624Ala,ENST00000376406,;MDC1,downstream_gene_variant,,ENST00000422266,;MDC1,downstream_gene_variant,,ENST00000425072,;MDC1,upstream_gene_variant,,ENST00000417033,;MDC1,downstream_gene_variant,,ENST00000416571,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000494654,;MDC1,upstream_gene_variant,,ENST00000492462,;	G	ENSG00000137337	ENST00000376406	Transcript	missense_variant	2519	1871	624	G/A	gGg/gCg	rs746258696	.	.	-1	MDC1	HGNC	21163	protein_coding	YES	CCDS34384.1	ENSP00000365588	MDC1_HUMAN	A2AB07_HUMAN,A2AB06_HUMAN,A2AB05_HUMAN,A1Z5I9_HUMAN,A1Z5I7_HUMAN	UPI00001AF453	.	tolerated(0.1)	possibly_damaging(0.549)	5/15	.	hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCCCCACC	.	5	ESCA
COL11A2	0	.	GRCh37	6	33147584	33147584	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1102-2A>G	.	p.X368_splice	ENST00000374708	.	44	32	12	47	47	0	COL11A2,splice_acceptor_variant,,ENST00000395197,;COL11A2,splice_acceptor_variant,,ENST00000374713,;COL11A2,splice_acceptor_variant,,ENST00000361917,;COL11A2,splice_acceptor_variant,,ENST00000374712,;COL11A2,splice_acceptor_variant,,ENST00000357486,;COL11A2,splice_acceptor_variant,,ENST00000374708,;COL11A2,splice_acceptor_variant,,ENST00000457788,;COL11A2,splice_acceptor_variant,,ENST00000341947,;COL11A2,splice_acceptor_variant,,ENST00000374714,;COL11A2,upstream_gene_variant,,ENST00000477772,;	C	ENSG00000204248	ENST00000374708	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	COL11A2	HGNC	2187	protein_coding	YES	CCDS43452.1	ENSP00000363840	.	Q6LCP7_HUMAN,Q4VXY6_HUMAN	UPI000013E9A5	.	.	.	.	10/63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAACTGAGGT	.	5	ESCA
PRPF4B	0	.	GRCh37	6	4061664	4061664	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*814T>G	.	.	ENST00000337659	15/15	79	60	19	65	65	0	PRPF4B,3_prime_UTR_variant,,ENST00000337659,;PRPF4B,downstream_gene_variant,,ENST00000538861,;FAM217A,intron_variant,,ENST00000469157,;PRPF4B,intron_variant,,ENST00000494674,;PRPF4B,intron_variant,,ENST00000490653,;PRPF4B,upstream_gene_variant,,ENST00000461612,;PRPF4B,downstream_gene_variant,,ENST00000466185,;PRPF4B,3_prime_UTR_variant,,ENST00000480058,;PRPF4B,intron_variant,,ENST00000463634,;PRPF4B,intron_variant,,ENST00000481109,;	G	ENSG00000112739	ENST00000337659	Transcript	3_prime_UTR_variant	3938	.	.	.	.	.	.	.	1	PRPF4B	HGNC	17346	protein_coding	YES	CCDS4488.1	ENSP00000337194	PRP4B_HUMAN	H0YDJ3_HUMAN,F5H2U2_HUMAN	UPI000013DD12	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTTGTTAA	.	5	ESCA
RCAN2	0	.	GRCh37	6	46293222	46293222	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226-76589G>A	.	.	ENST00000371374	.	13	8	5	15	15	0	RCAN2,5_prime_UTR_variant,,ENST00000330430,;RCAN2,intron_variant,,ENST00000371374,;RCAN2,intron_variant,,ENST00000405162,;RCAN2,intron_variant,,ENST00000306764,;	T	ENSG00000172348	ENST00000371374	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RCAN2	HGNC	3041	protein_coding	YES	CCDS59023.1	ENSP00000360425	RCAN2_HUMAN	.	UPI00001AEE48	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TCCCCCTTCTG	.	4	ESCA
TINAG	0	.	GRCh37	6	54173334	54173334	+	5'UTR	SNP	C	C	G	rs778508695	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-15C>G	.	.	ENST00000259782	1/11	20	13	7	19	19	0	TINAG,5_prime_UTR_variant,,ENST00000259782,;TINAG,intron_variant,,ENST00000370869,;TINAG,upstream_gene_variant,,ENST00000370864,;TINAG,intron_variant,,ENST00000486436,;	G	ENSG00000137251	ENST00000259782	Transcript	5_prime_UTR_variant	82	.	.	.	.	rs778508695	.	.	1	TINAG	HGNC	14599	protein_coding	YES	CCDS4955.1	ENSP00000259782	TINAG_HUMAN	B1AQ11_HUMAN	UPI000013D078	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATACCTGAC	byFrequency	5	ESCA
DST	0	.	GRCh37	6	56472397	56472397	+	Intron	SNP	G	G	C	rs766071070	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3672+2828C>G	.	.	ENST00000244364	.	51	31	20	55	55	0	DST,synonymous_variant,p.%3D,ENST00000439203,;DST,synonymous_variant,p.%3D,ENST00000446842,;DST,synonymous_variant,p.%3D,ENST00000370754,;DST,synonymous_variant,p.%3D,ENST00000361203,;DST,synonymous_variant,p.%3D,ENST00000370769,;DST,synonymous_variant,p.%3D,ENST00000312431,;DST,intron_variant,,ENST00000370788,;DST,intron_variant,,ENST00000244364,;DST,intron_variant,,ENST00000421834,;	C	ENSG00000151914	ENST00000244364	Transcript	intron_variant	.	.	.	.	.	rs766071070	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	.	25/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATATGAGACT	byFrequency	5	ESCA
BAI3	0	.	GRCh37	6	69640512	69640512	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.819A>T	p.Lys273Asn	p.K273N	ENST00000370598	4/32	33	17	15	27	27	0	BAI3,missense_variant,p.Lys273Asn,ENST00000370598,;	T	ENSG00000135298	ENST00000370598	Transcript	missense_variant	1640	819	273	K/N	aaA/aaT	.	.	.	1	BAI3	HGNC	945	protein_coding	YES	CCDS4968.1	ENSP00000359630	BAI3_HUMAN	S4R3D0_HUMAN,B7Z1K0_HUMAN	UPI00001AE6A9	.	tolerated(0.1)	benign(0.002)	4/32	.	hmmpanther:PTHR12011:SF40,hmmpanther:PTHR12011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAAAGGGT	.	5	ESCA
RIMS1	0	.	GRCh37	6	73043490	73043490	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4318G>T	p.Ala1440Ser	p.A1440S	ENST00000521978	29/34	57	35	22	64	64	0	RIMS1,missense_variant,p.Ala1263Ser,ENST00000491071,;RIMS1,missense_variant,p.Ala605Ser,ENST00000453976,;RIMS1,missense_variant,p.Ala246Ser,ENST00000538414,;RIMS1,missense_variant,p.Ala358Ser,ENST00000522211,;RIMS1,missense_variant,p.Ala1223Ser,ENST00000517960,;RIMS1,missense_variant,p.Ala786Ser,ENST00000517433,;RIMS1,missense_variant,p.Ala1289Ser,ENST00000264839,;RIMS1,missense_variant,p.Ala760Ser,ENST00000401910,;RIMS1,missense_variant,p.Ala1223Ser,ENST00000348717,;RIMS1,missense_variant,p.Ala1440Ser,ENST00000521978,;RIMS1,missense_variant,p.Ala488Ser,ENST00000370420,;RIMS1,intron_variant,,ENST00000517827,;RIMS1,intron_variant,,ENST00000522291,;RIMS1,intron_variant,,ENST00000520567,;RIMS1,intron_variant,,ENST00000518273,;RIMS1,intron_variant,,ENST00000523963,;RIMS1,intron_variant,,ENST00000425662,;RIMS1,intron_variant,,ENST00000463023,;	T	ENSG00000079841	ENST00000521978	Transcript	missense_variant	4318	4318	1440	A/S	Gcc/Tcc	.	.	.	1	RIMS1	HGNC	17282	protein_coding	YES	CCDS47449.1	ENSP00000428417	RIMS1_HUMAN	.	UPI00001908FB	.	deleterious(0.02)	possibly_damaging(0.873)	29/34	.	hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTTGCCATA	.	5	ESCA
USP45	0	.	GRCh37	6	99894129	99894129	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1519C>T	p.Pro507Ser	p.P507S	ENST00000327681	14/18	26	17	9	37	37	0	USP45,missense_variant,p.Pro187Ser,ENST00000392738,;USP45,missense_variant,p.Pro459Ser,ENST00000369233,;USP45,missense_variant,p.Pro507Ser,ENST00000500704,;USP45,missense_variant,p.Pro507Ser,ENST00000327681,;USP45,intron_variant,,ENST00000539675,;USP45,3_prime_UTR_variant,,ENST00000496518,;USP45,non_coding_transcript_exon_variant,,ENST00000513344,;	A	ENSG00000123552	ENST00000327681	Transcript	missense_variant	2052	1519	507	P/S	Cct/Tct	.	.	.	-1	USP45	HGNC	20080	protein_coding	YES	CCDS34501.1	ENSP00000333376	UBP45_HUMAN	F5H1L5_HUMAN,D6RE98_HUMAN	UPI0000253B80	.	tolerated(0.12)	benign(0.04)	14/18	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF346,hmmpanther:PTHR24006,Pfam_domain:PF00443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAGGCTCAC	.	5	ESCA
ZAN	0	.	GRCh37	7	100334441	100334441	+	Missense_Mutation	SNP	A	A	C	rs772332231	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263A>C	p.Tyr88Ser	p.Y88S	ENST00000546292	4/46	44	32	11	48	48	0	ZAN,missense_variant,p.Tyr88Ser,ENST00000546292,;ZAN,missense_variant,p.Tyr88Ser,ENST00000542585,;ZAN,missense_variant,p.Tyr88Ser,ENST00000538115,;ZAN,5_prime_UTR_variant,,ENST00000546213,;ZAN,missense_variant,p.Tyr88Ser,ENST00000421100,;ZAN,missense_variant,p.Tyr88Ser,ENST00000349350,;ZAN,missense_variant,p.Tyr88Ser,ENST00000427578,;ZAN,missense_variant,p.Tyr88Ser,ENST00000348028,;ZAN,missense_variant,p.Tyr88Ser,ENST00000449052,;ZAN,missense_variant,p.Tyr88Ser,ENST00000443370,;	C	ENSG00000146839	ENST00000546292	Transcript	missense_variant	411	263	88	Y/S	tAt/tCt	rs772332231	.	.	1	ZAN	HGNC	12857	protein_coding	YES	.	ENSP00000445943	.	F5H0T8_HUMAN	UPI00004575C6	.	.	probably_damaging(0.996)	4/46	.	Superfamily_domains:SSF49899,SMART_domains:SM00137,Pfam_domain:PF00629,PROSITE_profiles:PS50060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTATCTGC	.	5	ESCA
FBXL13	0	.	GRCh37	7	102453968	102453968	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2029C>G	p.Gln677Glu	p.Q677E	ENST00000313221	20/20	180	131	49	158	158	0	FBXL13,missense_variant,p.Gln395Glu,ENST00000379306,;FBXL13,missense_variant,p.Gln649Glu,ENST00000393772,;FBXL13,missense_variant,p.Gln395Glu,ENST00000456695,;FBXL13,missense_variant,p.Gln677Glu,ENST00000313221,;FBXL13,missense_variant,p.Gln632Glu,ENST00000455112,;FBXL13,missense_variant,p.Gln649Glu,ENST00000379305,;FBXL13,missense_variant,p.Gln677Glu,ENST00000436908,;FBXL13,missense_variant,p.Gln632Glu,ENST00000379308,;FAM185A,downstream_gene_variant,,ENST00000409231,;FBXL13,non_coding_transcript_exon_variant,,ENST00000480422,;FBXL13,3_prime_UTR_variant,,ENST00000448002,;FAM185A,downstream_gene_variant,,ENST00000442873,;FAM185A,downstream_gene_variant,,ENST00000420217,;	C	ENSG00000161040	ENST00000313221	Transcript	missense_variant	2456	2029	677	Q/E	Caa/Gaa	.	.	.	-1	FBXL13	HGNC	21658	protein_coding	YES	CCDS5726.1	ENSP00000321927	FXL13_HUMAN	.	UPI000020F830	.	tolerated(0.37)	benign(0.001)	20/20	.	hmmpanther:PTHR23125,hmmpanther:PTHR23125:SF219,Gene3D:3.80.10.10,SMART_domains:SM00367,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTGAGCTG	.	5	ESCA
ATXN7L1	0	.	GRCh37	7	105254708	105254708	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2073G>A	p.%3D	p.A691A	ENST00000419735	10/12	56	41	14	38	38	0	ATXN7L1,synonymous_variant,p.%3D,ENST00000477775,;ATXN7L1,synonymous_variant,p.%3D,ENST00000388807,;ATXN7L1,synonymous_variant,p.%3D,ENST00000472195,;ATXN7L1,synonymous_variant,p.%3D,ENST00000484475,;ATXN7L1,synonymous_variant,p.%3D,ENST00000419735,;ATXN7L1,3_prime_UTR_variant,,ENST00000474433,;	T	ENSG00000146776	ENST00000419735	Transcript	synonymous_variant	2119	2073	691	A	gcG/gcA	.	.	.	-1	ATXN7L1	HGNC	22210	protein_coding	YES	CCDS47682.1	ENSP00000410759	AT7L1_HUMAN	F8WDE7_HUMAN	UPI000162C85E	.	.	.	10/12	.	hmmpanther:PTHR15117:SF1,hmmpanther:PTHR15117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCCGCCTG	.	5	ESCA
POT1-AS1	0	.	GRCh37	7	124782801	124782801	+	RNA	SNP	T	T	G	rs548614026	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1433T>G	.	.	ENST00000453342	11/11	10	6	4	8	8	0	POT1-AS1,non_coding_transcript_exon_variant,,ENST00000449642,;POT1-AS1,non_coding_transcript_exon_variant,,ENST00000453342,;POT1-AS1,intron_variant,,ENST00000435452,;	G	ENSG00000224897	ENST00000453342	Transcript	non_coding_transcript_exon_variant	1433	.	.	.	.	rs548614026	.	.	1	POT1-AS1	HGNC	49459	antisense	YES	.	.	.	.	.	.	.	.	11/11	.	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAGTTGGAA	by1000G	2	ESCA
PODXL	0	.	GRCh37	7	131195718	131195718	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.575C>T	p.Pro192Leu	p.P192L	ENST00000378555	2/9	190	161	29	166	166	0	PODXL,missense_variant,p.Pro192Leu,ENST00000537928,;PODXL,missense_variant,p.Pro192Leu,ENST00000322985,;PODXL,missense_variant,p.Pro192Leu,ENST00000378555,;PODXL,missense_variant,p.Pro194Leu,ENST00000541194,;PODXL,downstream_gene_variant,,ENST00000465001,;PODXL,missense_variant,p.Pro192Leu,ENST00000446198,;PODXL,upstream_gene_variant,,ENST00000484346,;PODXL,upstream_gene_variant,,ENST00000487965,;PODXL,upstream_gene_variant,,ENST00000482581,;PODXL,upstream_gene_variant,,ENST00000490761,;	A	ENSG00000128567	ENST00000378555	Transcript	missense_variant	823	575	192	P/L	cCc/cTc	.	.	.	-1	PODXL	HGNC	9171	protein_coding	YES	CCDS34755.1	ENSP00000367817	PODXL_HUMAN	.	UPI000042467C	.	deleterious(0)	possibly_damaging(0.703)	2/9	.	PIRSF_domain:PIRSF038143,hmmpanther:PTHR12067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGTGGGTTGT	.	4	ESCA
KDM7A	0	.	GRCh37	7	139791832	139791832	+	Missense_Mutation	SNP	C	C	G	rs747849530	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2503G>C	p.Glu835Gln	p.E835Q	ENST00000397560	19/20	117	83	34	95	95	0	KDM7A,missense_variant,p.Glu835Gln,ENST00000397560,;KDM7A,downstream_gene_variant,,ENST00000006967,;Y_RNA,downstream_gene_variant,,ENST00000515919,;KDM7A,3_prime_UTR_variant,,ENST00000472616,;KDM7A,non_coding_transcript_exon_variant,,ENST00000478996,;	G	ENSG00000006459	ENST00000397560	Transcript	missense_variant	2601	2503	835	E/Q	Gaa/Caa	rs747849530	.	.	-1	KDM7A	HGNC	22224	protein_coding	YES	CCDS43658.1	ENSP00000380692	KDM7_HUMAN	.	UPI000045761B	.	deleterious_low_confidence(0.02)	benign(0.104)	19/20	.	hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTCTGATG	.	5	ESCA
AGK	0	.	GRCh37	7	141301071	141301071	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288T>A	p.%3D	p.T96T	ENST00000355413	5/16	50	37	12	27	27	0	AGK,synonymous_variant,p.%3D,ENST00000473247,;AGK,synonymous_variant,p.%3D,ENST00000355413,;AGK,synonymous_variant,p.%3D,ENST00000535825,;AGK,non_coding_transcript_exon_variant,,ENST00000496273,;AGK,downstream_gene_variant,,ENST00000495028,;AGK,synonymous_variant,p.%3D,ENST00000494688,;AGK,3_prime_UTR_variant,,ENST00000473884,;AGK,non_coding_transcript_exon_variant,,ENST00000465241,;AGK,downstream_gene_variant,,ENST00000496784,;	A	ENSG00000006530	ENST00000355413	Transcript	synonymous_variant	548	288	96	T	acT/acA	.	.	.	1	AGK	HGNC	21869	protein_coding	YES	CCDS5865.1	ENSP00000347581	AGK_HUMAN	A4D1U5_HUMAN	UPI000006E622	.	.	.	5/16	.	PROSITE_profiles:PS50146,hmmpanther:PTHR12358,hmmpanther:PTHR12358:SF7,Pfam_domain:PF00781,Gene3D:3.40.50.10330,SMART_domains:SM00046,Superfamily_domains:SSF111331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGACTATTGT	.	5	ESCA
PRSS58	0	.	GRCh37	7	141952041	141952041	+	Nonstop_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726A>T	p.Ter242CysextTer18	p.*242Cext*18	ENST00000552471	5/5	24	11	13	25	25	0	PRSS58,stop_lost,p.Ter242CysextTer18,ENST00000547058,;PRSS58,stop_lost,p.Ter242CysextTer18,ENST00000552471,;	A	ENSG00000258223	ENST00000552471	Transcript	stop_lost	1046	726	242	*/C	tgA/tgT	.	.	.	-1	PRSS58	HGNC	39125	protein_coding	YES	CCDS5871.1	ENSP00000446916	PRS58_HUMAN	.	UPI000004C649	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCTCAGTT	.	5	ESCA
TRBV6-6	0	.	GRCh37	7	142162146	142162146	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.129C>A	p.%3D	p.A43A	ENST00000390371	2/2	138	97	40	106	106	0	TRBV6-6,synonymous_variant,p.%3D,ENST00000390371,;TRBV7-5,upstream_gene_variant,,ENST00000390382,;	T	ENSG00000211724	ENST00000390371	Transcript	synonymous_variant	173	129	43	A	gcC/gcA	.	.	.	-1	TRBV6-6	HGNC	12231	TR_V_gene	YES	.	ENSP00000374894	.	.	UPI0001AE7162	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23268,hmmpanther:PTHR23268:SF18,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGGGCACA	.	5	ESCA
ZNF467	0	.	GRCh37	7	149462695	149462695	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.896C>T	p.Pro299Leu	p.P299L	ENST00000302017	5/5	76	60	15	68	68	0	ZNF467,missense_variant,p.Pro299Leu,ENST00000302017,;ZNF467,intron_variant,,ENST00000484747,;	A	ENSG00000181444	ENST00000302017	Transcript	missense_variant	1310	896	299	P/L	cCc/cTc	.	.	.	-1	ZNF467	HGNC	23154	protein_coding	YES	CCDS5899.1	ENSP00000304769	ZN467_HUMAN	.	UPI0000160B41	.	deleterious(0)	probably_damaging(1)	5/5	.	Superfamily_domains:SSF57667,Pfam_domain:PF13465,Gene3D:3.30.160.60,hmmpanther:PTHR24402:SF14,hmmpanther:PTHR24402,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAGGGCCTC	.	5	ESCA
RBM33	0	.	GRCh37	7	155570223	155570223	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2488G>C	.	.	ENST00000401878	18/18	13	9	4	18	18	0	RBM33,3_prime_UTR_variant,,ENST00000401878,;RBM33,3_prime_UTR_variant,,ENST00000341148,;RBM33,downstream_gene_variant,,ENST00000392755,;	C	ENSG00000184863	ENST00000401878	Transcript	3_prime_UTR_variant	6199	.	.	.	.	.	.	.	1	RBM33	HGNC	27223	protein_coding	YES	CCDS5941.2	ENSP00000384160	RBM33_HUMAN	C9J7M3_HUMAN	UPI00015743D7	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTTGGTATG	.	2	ESCA
IGF2BP3	0	.	GRCh37	7	23351085	23351085	+	3'UTR	SNP	G	G	A	rs2268742	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*896C>T	.	.	ENST00000258729	15/15	20	10	9	13	13	0	IGF2BP3,3_prime_UTR_variant,,ENST00000258729,;MALSU1,3_prime_UTR_variant,,ENST00000466681,;IGF2BP3,3_prime_UTR_variant,,ENST00000421467,;IGF2BP3,downstream_gene_variant,,ENST00000498363,;MALSU1,downstream_gene_variant,,ENST00000287543,;MALSU1,downstream_gene_variant,,ENST00000476623,;	A	ENSG00000136231	ENST00000258729	Transcript	3_prime_UTR_variant	2993	.	.	.	.	rs2268742	.	.	-1	IGF2BP3	HGNC	28868	protein_coding	YES	CCDS5382.1	ENSP00000258729	IF2B3_HUMAN	.	UPI0000117172	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCGACCAC	suspect|byHapMap	4	ESCA
GLI3	0	.	GRCh37	7	42017206	42017206	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1763C>G	p.Ser588Ter	p.S588*	ENST00000395925	12/15	180	131	49	157	157	0	GLI3,stop_gained,p.Ser588Ter,ENST00000395925,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,;GLI3,non_coding_transcript_exon_variant,,ENST00000464291,;	C	ENSG00000106571	ENST00000395925	Transcript	stop_gained	1848	1763	588	S/*	tCa/tGa	COSM3832781	.	.	-1	GLI3	HGNC	4319	protein_coding	YES	CCDS5465.1	ENSP00000379258	GLI3_HUMAN	C9J9N4_HUMAN	UPI000020EE4C	.	.	.	12/15	.	PROSITE_profiles:PS50157,hmmpanther:PTHR19818:SF5,hmmpanther:PTHR19818,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTGAGAAA	.	5	ESCA
NUDCD3	0	.	GRCh37	7	44530051	44530051	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.149G>T	p.Arg50Leu	p.R50L	ENST00000355451	1/6	34	11	22	39	39	0	NUDCD3,missense_variant,p.Arg50Leu,ENST00000355451,;NUDCD3,upstream_gene_variant,,ENST00000497978,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000464812,;	A	ENSG00000015676	ENST00000355451	Transcript	missense_variant	429	149	50	R/L	cGc/cTc	.	.	.	-1	NUDCD3	HGNC	22208	protein_coding	YES	CCDS5490.2	ENSP00000347626	NUDC3_HUMAN	A4D2J8_HUMAN	UPI000020EEEB	.	deleterious(0)	probably_damaging(0.926)	1/6	.	hmmpanther:PTHR12356:SF16,hmmpanther:PTHR12356,Pfam_domain:PF14050	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGCGGTCC	.	5	ESCA
ABCA13	0	.	GRCh37	7	48391999	48391999	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10603A>C	p.Ile3535Leu	p.I3535L	ENST00000435803	31/62	31	10	21	30	30	0	ABCA13,missense_variant,p.Ile3535Leu,ENST00000435803,;ABCA13,non_coding_transcript_exon_variant,,ENST00000484268,;	C	ENSG00000179869	ENST00000435803	Transcript	missense_variant	10627	10603	3535	I/L	Atc/Ctc	.	.	.	1	ABCA13	HGNC	14638	protein_coding	YES	CCDS47584.1	ENSP00000411096	ABCAD_HUMAN	.	UPI00001A95EA	.	.	probably_damaging(0.996)	31/62	.	Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCATCATT	.	5	ESCA
CALN1	0	.	GRCh37	7	71251946	71251946	+	3'UTR	DEL	T	T	-	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*814delA	.	.	ENST00000395275	7/7	117	75	42	63	63	0	CALN1,3_prime_UTR_variant,,ENST00000395276,;CALN1,3_prime_UTR_variant,,ENST00000395275,;CALN1,3_prime_UTR_variant,,ENST00000329008,;CALN1,downstream_gene_variant,,ENST00000431984,;CALN1,downstream_gene_variant,,ENST00000405452,;CALN1,downstream_gene_variant,,ENST00000412588,;	-	ENSG00000183166	ENST00000395275	Transcript	3_prime_UTR_variant	1989	.	.	.	.	.	.	.	-1	CALN1	HGNC	13248	protein_coding	YES	CCDS47603.1	ENSP00000378690	CABP8_HUMAN	Q86UM7_HUMAN,Q86UL5_HUMAN,Q75MW5_HUMAN,Q75MP5_HUMAN,Q75MI2_HUMAN,E9PFU3_HUMAN,A4D1Z1_HUMAN	UPI0000D4B903	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAAATATATATA	.	3	ESCA
EIF4H	0	.	GRCh37	7	73588738	73588738	+	Missense_Mutation	SNP	G	G	C	rs146609826	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25G>C	p.Asp9His	p.D9H	ENST00000265753	1/7	51	38	12	48	48	0	EIF4H,missense_variant,p.Asp9His,ENST00000265753,;EIF4H,missense_variant,p.Asp9His,ENST00000353999,;EIF4H,non_coding_transcript_exon_variant,,ENST00000489484,;EIF4H,non_coding_transcript_exon_variant,,ENST00000479338,;	C	ENSG00000106682	ENST00000265753	Transcript	missense_variant	164	25	9	D/H	Gat/Cat	rs146609826,COSM1452015	.	.	1	EIF4H	HGNC	12741	protein_coding	YES	CCDS5564.1	ENSP00000265753	IF4H_HUMAN	Q75MU2_HUMAN,Q75MU1_HUMAN,Q75MT8_HUMAN	UPI000012D373	.	deleterious_low_confidence(0.01)	probably_damaging(0.931)	1/7	.	hmmpanther:PTHR23236	.	.	.	.	.	.	.	A:0.0011	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGACGATCGG	byFrequency|byCluster	5	ESCA
HGF	0	.	GRCh37	7	81372751	81372751	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783C>T	p.%3D	p.R261R	ENST00000222390	7/18	84	45	39	46	46	0	HGF,synonymous_variant,p.%3D,ENST00000453411,;HGF,synonymous_variant,p.%3D,ENST00000457544,;HGF,synonymous_variant,p.%3D,ENST00000222390,;HGF,synonymous_variant,p.%3D,ENST00000444829,;	A	ENSG00000019991	ENST00000222390	Transcript	synonymous_variant	1010	783	261	R	cgC/cgT	.	.	.	-1	HGF	HGNC	4893	protein_coding	YES	CCDS5597.1	ENSP00000222390	HGF_HUMAN	C9JS80_HUMAN,C9JDP4_HUMAN	UPI000000D92B	.	.	.	7/18	.	PROSITE_profiles:PS50070,hmmpanther:PTHR24272:SF3,hmmpanther:PTHR24272,PROSITE_patterns:PS00021,Pfam_domain:PF00051,Gene3D:2.40.20.10,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,SMART_domains:SM00130,Superfamily_domains:SSF57440,Prints_domain:PR00018	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATTGCGGCA	.	5	ESCA
HGF	0	.	GRCh37	7	81372752	81372752	+	Missense_Mutation	SNP	C	C	A	rs768451705	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.782G>T	p.Arg261Leu	p.R261L	ENST00000222390	7/18	84	45	39	46	46	0	HGF,missense_variant,p.Arg256Leu,ENST00000453411,;HGF,missense_variant,p.Arg256Leu,ENST00000457544,;HGF,missense_variant,p.Arg261Leu,ENST00000222390,;HGF,missense_variant,p.Arg261Leu,ENST00000444829,;	A	ENSG00000019991	ENST00000222390	Transcript	missense_variant	1009	782	261	R/L	cGc/cTc	rs768451705,COSM3882616	.	.	-1	HGF	HGNC	4893	protein_coding	YES	CCDS5597.1	ENSP00000222390	HGF_HUMAN	C9JS80_HUMAN,C9JDP4_HUMAN	UPI000000D92B	.	deleterious(0)	probably_damaging(0.998)	7/18	.	PROSITE_profiles:PS50070,hmmpanther:PTHR24272:SF3,hmmpanther:PTHR24272,PROSITE_patterns:PS00021,Pfam_domain:PF00051,Gene3D:2.40.20.10,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,SMART_domains:SM00130,Superfamily_domains:SSF57440,Prints_domain:PR00018	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTGCGGCAA	.	5	ESCA
PON2	0	.	GRCh37	7	95039233	95039233	+	Missense_Mutation	SNP	G	G	C	rs528805572	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.675C>G	p.Ile225Met	p.I225M	ENST00000222572	6/9	52	42	10	25	25	0	PON2,missense_variant,p.Ile225Met,ENST00000222572,;PON2,missense_variant,p.Ile213Met,ENST00000433091,;PON2,missense_variant,p.Ile246Met,ENST00000536183,;PON2,non_coding_transcript_exon_variant,,ENST00000483292,;PON2,downstream_gene_variant,,ENST00000478801,;PON2,downstream_gene_variant,,ENST00000491069,;PON2,downstream_gene_variant,,ENST00000490778,;PON2,downstream_gene_variant,,ENST00000469926,;PON2,downstream_gene_variant,,ENST00000493290,;PON2,downstream_gene_variant,,ENST00000460873,;PON2,3_prime_UTR_variant,,ENST00000446142,;PON2,non_coding_transcript_exon_variant,,ENST00000459842,;PON2,intron_variant,,ENST00000455123,;	C	ENSG00000105854	ENST00000222572	Transcript	missense_variant	922	675	225	I/M	atC/atG	rs528805572	.	.	-1	PON2	HGNC	9205	protein_coding	YES	CCDS5640.1	ENSP00000222572	PON2_HUMAN	.	UPI000000D8F3	.	deleterious(0)	probably_damaging(0.999)	6/9	.	hmmpanther:PTHR11799:SF4,hmmpanther:PTHR11799,Gene3D:2.120.10.30,Pfam_domain:PF01731,Superfamily_domains:SSF63829	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTGATCCC	by1000G	5	ESCA
PKHD1L1	0	.	GRCh37	8	110376784	110376784	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.82C>A	p.Gln28Lys	p.Q28K	ENST00000378402	2/78	109	91	18	70	70	0	PKHD1L1,missense_variant,p.Gln28Lys,ENST00000378402,;	A	ENSG00000205038	ENST00000378402	Transcript	missense_variant	186	82	28	Q/K	Caa/Aaa	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	tolerated_low_confidence(1)	benign(0)	2/78	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCAAATA	.	5	ESCA
TRPS1	0	.	GRCh37	8	116635964	116635964	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-100A>G	.	.	ENST00000395715	2/7	50	38	12	28	28	0	TRPS1,5_prime_UTR_variant,,ENST00000395715,;TRPS1,5_prime_UTR_variant,,ENST00000451156,;TRPS1,5_prime_UTR_variant,,ENST00000422939,;TRPS1,5_prime_UTR_variant,,ENST00000519815,;TRPS1,5_prime_UTR_variant,,ENST00000395713,;TRPS1,intron_variant,,ENST00000520276,;TRPS1,intron_variant,,ENST00000519674,;TRPS1,intron_variant,,ENST00000220888,;TRPS1,intron_variant,,ENST00000517323,;TRPS1,upstream_gene_variant,,ENST00000519076,;	C	ENSG00000104447	ENST00000395715	Transcript	5_prime_UTR_variant	479	.	.	.	.	.	.	.	-1	TRPS1	HGNC	12340	protein_coding	YES	CCDS6318.2	ENSP00000379065	TRPS1_HUMAN	F8W8T0_HUMAN,E7EVN4_HUMAN,C9J6L7_HUMAN	UPI00002104B8	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACATTTTGA	.	5	ESCA
TAF2	0	.	GRCh37	8	120795769	120795769	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1964A>G	p.Tyr655Cys	p.Y655C	ENST00000378164	16/26	34	26	8	31	31	0	TAF2,missense_variant,p.Tyr655Cys,ENST00000378164,;TAF2,downstream_gene_variant,,ENST00000523904,;	C	ENSG00000064313	ENST00000378164	Transcript	missense_variant	2263	1964	655	Y/C	tAt/tGt	.	.	.	-1	TAF2	HGNC	11536	protein_coding	YES	CCDS34937.1	ENSP00000367406	TAF2_HUMAN	.	UPI0000210507	.	deleterious(0)	probably_damaging(0.993)	16/26	.	hmmpanther:PTHR15137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCATAGCGG	.	5	ESCA
KIAA0196	0	.	GRCh37	8	126071704	126071704	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1602G>A	p.Met534Ile	p.M534I	ENST00000318410	13/29	34	30	4	14	14	0	KIAA0196,missense_variant,p.Met386Ile,ENST00000517845,;KIAA0196,missense_variant,p.Met534Ile,ENST00000318410,;	T	ENSG00000164961	ENST00000318410	Transcript	missense_variant	1952	1602	534	M/I	atG/atA	.	.	.	-1	KIAA0196	HGNC	28984	protein_coding	YES	CCDS6355.1	ENSP00000318016	STRUM_HUMAN	Q53EL1_HUMAN,E7EQI7_HUMAN,E5RFU6_HUMAN	UPI000013943B	.	deleterious(0.02)	benign(0.086)	13/29	.	hmmpanther:PTHR15691,Pfam_domain:PF10266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGATCATTTG	.	4	ESCA
FAM135B	0	.	GRCh37	8	139164633	139164633	+	Silent	SNP	G	G	A	rs183117074	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2085C>T	p.%3D	p.V695V	ENST00000395297	13/20	41	14	27	30	30	0	FAM135B,synonymous_variant,p.%3D,ENST00000395297,;FAM135B,synonymous_variant,p.%3D,ENST00000276737,;FAM135B,synonymous_variant,p.%3D,ENST00000467365,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000395295,;	A	ENSG00000147724	ENST00000395297	Transcript	synonymous_variant	2256	2085	695	V	gtC/gtT	rs183117074,COSM3645501,COSM3645502	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	.	.	13/20	.	hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482	A:0.0004	A:0.0008	A:0	.	A:0	A:0	A:0.001	A:0.0003	A:0	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGCGACGGA	byFrequency|byCluster|by1000G	5	ESCA
PTP4A3	0	.	GRCh37	8	142437153	142437153	+	Missense_Mutation	SNP	G	G	T	rs762531825	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313G>T	p.Val105Leu	p.V105L	ENST00000521578	4/6	269	106	163	185	185	0	PTP4A3,missense_variant,p.Val105Leu,ENST00000349124,;PTP4A3,missense_variant,p.Val105Leu,ENST00000521578,;PTP4A3,missense_variant,p.Val105Leu,ENST00000329397,;PTP4A3,missense_variant,p.Val105Leu,ENST00000520105,;PTP4A3,intron_variant,,ENST00000524028,;PTP4A3,downstream_gene_variant,,ENST00000523147,;	T	ENSG00000184489	ENST00000521578	Transcript	missense_variant	1258	313	105	V/L	Gtg/Ttg	rs762531825,COSM1263345	.	.	1	PTP4A3	HGNC	9636	protein_coding	YES	CCDS6383.1	ENSP00000428976	TP4A3_HUMAN	E5RGR3_HUMAN	UPI000004981B	.	deleterious(0)	possibly_damaging(0.874)	4/6	.	PROSITE_profiles:PS50056,hmmpanther:PTHR23339,hmmpanther:PTHR23339:SF57,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00404,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGCGTGGCG	.	5	ESCA
TIGD5	0	.	GRCh37	8	144680307	144680307	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234C>G	p.Cys78Trp	p.C78W	ENST00000504548	1/1	16	11	5	9	9	0	TIGD5,missense_variant,p.Cys78Trp,ENST00000504548,;TIGD5,missense_variant,p.Cys29Trp,ENST00000321385,;EEF1D,intron_variant,,ENST00000533749,;EEF1D,upstream_gene_variant,,ENST00000423316,;EEF1D,upstream_gene_variant,,ENST00000528610,;EEF1D,upstream_gene_variant,,ENST00000531670,;EEF1D,upstream_gene_variant,,ENST00000534804,;EEF1D,upstream_gene_variant,,ENST00000528303,;EEF1D,upstream_gene_variant,,ENST00000529832,;EEF1D,upstream_gene_variant,,ENST00000525261,;EEF1D,upstream_gene_variant,,ENST00000533494,;EEF1D,upstream_gene_variant,,ENST00000530191,;EEF1D,upstream_gene_variant,,ENST00000529272,;EEF1D,upstream_gene_variant,,ENST00000534380,;EEF1D,upstream_gene_variant,,ENST00000526133,;EEF1D,upstream_gene_variant,,ENST00000419152,;EEF1D,upstream_gene_variant,,ENST00000526838,;EEF1D,upstream_gene_variant,,ENST00000534475,;EEF1D,upstream_gene_variant,,ENST00000532400,;EEF1D,upstream_gene_variant,,ENST00000524624,;EEF1D,upstream_gene_variant,,ENST00000530545,;EEF1D,upstream_gene_variant,,ENST00000531218,;EEF1D,upstream_gene_variant,,ENST00000532596,;EEF1D,upstream_gene_variant,,ENST00000532543,;EEF1D,upstream_gene_variant,,ENST00000530306,;EEF1D,upstream_gene_variant,,ENST00000395119,;EEF1D,upstream_gene_variant,,ENST00000526340,;EEF1D,upstream_gene_variant,,ENST00000317198,;EEF1D,upstream_gene_variant,,ENST00000531931,;EEF1D,upstream_gene_variant,,ENST00000531281,;EEF1D,upstream_gene_variant,,ENST00000529516,;EEF1D,upstream_gene_variant,,ENST00000531953,;EEF1D,upstream_gene_variant,,ENST00000533204,;EEF1D,upstream_gene_variant,,ENST00000534377,;EEF1D,upstream_gene_variant,,ENST00000531621,;EEF1D,upstream_gene_variant,,ENST00000524900,;EEF1D,upstream_gene_variant,,ENST00000526710,;EEF1D,upstream_gene_variant,,ENST00000442189,;RP11-661A12.14,upstream_gene_variant,,ENST00000606452,;EEF1D,upstream_gene_variant,,ENST00000531770,;EEF1D,upstream_gene_variant,,ENST00000526786,;EEF1D,upstream_gene_variant,,ENST00000525695,;EEF1D,upstream_gene_variant,,ENST00000530848,;EEF1D,upstream_gene_variant,,ENST00000529007,;EEF1D,upstream_gene_variant,,ENST00000524397,;EEF1D,upstream_gene_variant,,ENST00000533833,;EEF1D,upstream_gene_variant,,ENST00000534232,;	G	ENSG00000179886	ENST00000504548	Transcript	missense_variant	234	234	78	C/W	tgC/tgG	.	.	.	1	TIGD5	HGNC	18336	protein_coding	YES	CCDS6406.2	ENSP00000421489	TIGD5_HUMAN	.	UPI0001BAE24C	.	deleterious(0)	probably_damaging(0.989)	1/1	.	PROSITE_profiles:PS50960,hmmpanther:PTHR19303:SF210,hmmpanther:PTHR19303,Pfam_domain:PF04218,Gene3D:1.10.10.60,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGTGCCGCGA	.	3	ESCA
DLGAP2	0	.	GRCh37	8	1513881	1513881	+	Silent	SNP	C	C	T	rs374538901	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1023C>T	p.%3D	p.T341T	ENST00000421627	3/12	35	20	14	34	34	0	DLGAP2,synonymous_variant,p.%3D,ENST00000520901,;DLGAP2,synonymous_variant,p.%3D,ENST00000421627,;RP11-666I19.2,non_coding_transcript_exon_variant,,ENST00000518063,;	T	ENSG00000198010	ENST00000421627	Transcript	synonymous_variant	1157	1023	341	T	acC/acT	rs374538901	.	.	1	DLGAP2	HGNC	2906	protein_coding	YES	CCDS47760.1	ENSP00000400258	DLGP2_HUMAN	.	UPI000021BFBC	.	.	.	3/12	.	hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACCGGTGG	byFrequency|byCluster	5	ESCA
MYOM2	0	.	GRCh37	8	2020437	2020437	+	Missense_Mutation	SNP	C	C	G	rs202106832	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806C>G	p.Ser269Trp	p.S269W	ENST00000262113	9/37	85	47	38	83	83	0	MYOM2,missense_variant,p.Ser269Trp,ENST00000262113,;MYOM2,intron_variant,,ENST00000523438,;	G	ENSG00000036448	ENST00000262113	Transcript	missense_variant	947	806	269	S/W	tCg/tGg	rs202106832,COSM1097904	.	.	1	MYOM2	HGNC	7614	protein_coding	YES	CCDS5957.1	ENSP00000262113	MYOM2_HUMAN	E7EWH9_HUMAN	UPI000013D260	.	tolerated(0.13)	possibly_damaging(0.622)	9/37	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19900:SF48,hmmpanther:PTHR19900	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCATCGATGA	byFrequency|byCluster	5	ESCA
ZNF395	0	.	GRCh37	8	28206685	28206685	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1387C>T	p.His463Tyr	p.H463Y	ENST00000344423	9/10	26	12	14	26	26	0	ZNF395,missense_variant,p.His463Tyr,ENST00000344423,;ZNF395,missense_variant,p.His463Tyr,ENST00000523095,;ZNF395,missense_variant,p.His463Tyr,ENST00000523202,;ZNF395,intron_variant,,ENST00000520535,;FBXO16,3_prime_UTR_variant,,ENST00000521548,;ZNF395,downstream_gene_variant,,ENST00000517372,;	A	ENSG00000186918	ENST00000344423	Transcript	missense_variant	1519	1387	463	H/Y	Cat/Tat	.	.	.	-1	ZNF395	HGNC	18737	protein_coding	YES	CCDS6067.1	ENSP00000340494	ZN395_HUMAN	E5RH90_HUMAN,E5RGF1_HUMAN,E5RG59_HUMAN,E5RFV4_HUMAN	UPI0000073F08	.	deleterious(0)	probably_damaging(0.982)	9/10	.	hmmpanther:PTHR13006:SF6,hmmpanther:PTHR13006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATGAGATT	.	5	ESCA
KAT6A	0	.	GRCh37	8	41806773	41806773	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1707G>A	p.%3D	p.E569E	ENST00000396930	11/18	56	39	16	53	53	0	KAT6A,synonymous_variant,p.%3D,ENST00000396930,;KAT6A,synonymous_variant,p.%3D,ENST00000406337,;KAT6A,synonymous_variant,p.%3D,ENST00000485568,;KAT6A,synonymous_variant,p.%3D,ENST00000265713,;KAT6A,synonymous_variant,p.%3D,ENST00000418721,;	T	ENSG00000083168	ENST00000396930	Transcript	synonymous_variant	2251	1707	569	E	gaG/gaA	.	.	.	-1	KAT6A	HGNC	13013	protein_coding	YES	CCDS6124.1	ENSP00000380136	KAT6A_HUMAN	A5PKX7_HUMAN	UPI000013D666	.	.	.	11/18	.	hmmpanther:PTHR10615:SF26,hmmpanther:PTHR10615,Gene3D:3.40.630.30,Pfam_domain:PF01853,Superfamily_domains:SSF55729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATCTCATT	.	5	ESCA
ST18	0	.	GRCh37	8	53084980	53084980	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441A>G	p.%3D	p.E147E	ENST00000276480	10/26	64	40	23	39	39	0	ST18,synonymous_variant,p.%3D,ENST00000517580,;ST18,synonymous_variant,p.%3D,ENST00000276480,;ST18,downstream_gene_variant,,ENST00000520257,;ST18,synonymous_variant,p.%3D,ENST00000521582,;ST18,3_prime_UTR_variant,,ENST00000521824,;ST18,3_prime_UTR_variant,,ENST00000522251,;	C	ENSG00000147488	ENST00000276480	Transcript	synonymous_variant	1125	441	147	E	gaA/gaG	.	.	.	-1	ST18	HGNC	18695	protein_coding	YES	CCDS6149.1	ENSP00000276480	ST18_HUMAN	E5RHS3_HUMAN	UPI0000046C30	.	.	.	10/26	.	hmmpanther:PTHR10816:SF9,hmmpanther:PTHR10816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATTTTCACT	.	5	ESCA
SDR16C6P	0	.	GRCh37	8	57294613	57294613	+	RNA	SNP	A	A	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.599T>A	.	.	ENST00000524136	4/6	49	38	11	22	22	0	SDR16C6P,non_coding_transcript_exon_variant,,ENST00000517787,;SDR16C6P,non_coding_transcript_exon_variant,,ENST00000524136,;	T	ENSG00000253542	ENST00000524136	Transcript	non_coding_transcript_exon_variant	599	.	.	.	.	.	.	.	-1	SDR16C6P	HGNC	35413	unitary_pseudogene	YES	.	.	.	.	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGAGAGAT	.	5	ESCA
GGH	0	.	GRCh37	8	63948274	63948274	+	Silent	SNP	A	A	G	rs780111805	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165T>C	p.%3D	p.Y55Y	ENST00000260118	2/9	51	22	28	25	25	0	GGH,synonymous_variant,p.%3D,ENST00000260118,;GGH,non_coding_transcript_exon_variant,,ENST00000518966,;GGH,non_coding_transcript_exon_variant,,ENST00000520609,;GGH,non_coding_transcript_exon_variant,,ENST00000523788,;	G	ENSG00000137563	ENST00000260118	Transcript	synonymous_variant	568	165	55	Y	taT/taC	rs780111805	.	.	-1	GGH	HGNC	4248	protein_coding	YES	CCDS6177.1	ENSP00000260118	GGH_HUMAN	.	UPI000000127C	.	.	.	2/9	.	PROSITE_profiles:PS51275,hmmpanther:PTHR11315:SF2,hmmpanther:PTHR11315,Pfam_domain:PF07722,Gene3D:3.40.50.880,Superfamily_domains:SSF52317	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAATATAGTA	.	5	ESCA
REXO1L1P	0	.	GRCh37	8	86574539	86574539	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1188C>A	p.%3D	p.A396A	ENST00000379010	1/1	188	145	43	98	98	0	REXO1L1P,synonymous_variant,p.%3D,ENST00000379010,;	T	ENSG00000205176	ENST00000379010	Transcript	synonymous_variant	1188	1188	396	A	gcC/gcA	.	.	.	-1	REXO1L1P	HGNC	24660	protein_coding	YES	.	ENSP00000368295	GOR_HUMAN	.	UPI000057A11F	.	.	.	1/1	.	hmmpanther:PTHR12801:SF22,hmmpanther:PTHR12801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AGGACGGCGCC	.	2	ESCA
MMP16	0	.	GRCh37	8	89050748	89050748	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2941delT	.	.	ENST00000286614	10/10	61	47	13	40	40	0	MMP16,3_prime_UTR_variant,,ENST00000286614,;	-	ENSG00000156103	ENST00000286614	Transcript	3_prime_UTR_variant	5047	.	.	.	.	.	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TAGAGGAAAAAA	.	2	ESCA
PDP1	0	.	GRCh37	8	94935557	94935557	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1345A>G	p.Met449Val	p.M449V	ENST00000396200	3/3	269	211	58	150	150	0	PDP1,missense_variant,p.Met424Val,ENST00000517764,;PDP1,missense_variant,p.Met449Val,ENST00000396200,;PDP1,missense_variant,p.Met424Val,ENST00000520728,;PDP1,missense_variant,p.Met424Val,ENST00000297598,;PDP1,downstream_gene_variant,,ENST00000521144,;PDP1,downstream_gene_variant,,ENST00000520614,;PDP1,downstream_gene_variant,,ENST00000518827,;PDP1,downstream_gene_variant,,ENST00000518107,;PDP1,downstream_gene_variant,,ENST00000518573,;PDP1,downstream_gene_variant,,ENST00000523021,;	G	ENSG00000164951	ENST00000396200	Transcript	missense_variant	1621	1345	449	M/V	Atg/Gtg	.	.	.	1	PDP1	HGNC	9279	protein_coding	YES	CCDS55262.1	ENSP00000379503	PDP1_HUMAN	Q6P1N1_HUMAN,E5RIV4_HUMAN,E5RIE5_HUMAN,E5RI96_HUMAN,E5RHB9_HUMAN,E5RFL8_HUMAN,B4DYX8_HUMAN,B3KPZ7_HUMAN	UPI0000D4BFBD	.	tolerated(0.09)	benign(0.438)	3/3	.	hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF213,Gene3D:3.60.40.10,Pfam_domain:PF00481,SMART_domains:SM00332,Superfamily_domains:SSF81606	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACTATGCAT	.	5	ESCA
CCNE2	0	.	GRCh37	8	95893474	95893474	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*386G>C	.	.	ENST00000520509	12/12	42	27	15	34	34	0	CCNE2,3_prime_UTR_variant,,ENST00000308108,;INTS8,3_prime_UTR_variant,,ENST00000523731,;CCNE2,3_prime_UTR_variant,,ENST00000520509,;INTS8,downstream_gene_variant,,ENST00000520526,;CCNE2,downstream_gene_variant,,ENST00000524224,;CCNE2,downstream_gene_variant,,ENST00000396133,;INTS8,downstream_gene_variant,,ENST00000447247,;RP11-347C18.5,upstream_gene_variant,,ENST00000605911,;CCNE2,downstream_gene_variant,,ENST00000523476,;INTS8,downstream_gene_variant,,ENST00000343161,;INTS8,downstream_gene_variant,,ENST00000523998,;CCNE2,downstream_gene_variant,,ENST00000521809,;INTS8,downstream_gene_variant,,ENST00000524333,;INTS8,downstream_gene_variant,,ENST00000523206,;	G	ENSG00000175305	ENST00000520509	Transcript	3_prime_UTR_variant	1854	.	.	.	.	.	.	.	-1	CCNE2	HGNC	1590	protein_coding	YES	CCDS6264.1	ENSP00000429089	CCNE2_HUMAN	.	UPI00001275CF	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATCACTTA	.	5	ESCA
OSR2	0	.	GRCh37	8	99963089	99963089	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756+106G>C	.	.	ENST00000297565	.	112	85	26	67	67	0	OSR2,missense_variant,p.Asp288His,ENST00000523368,;OSR2,intron_variant,,ENST00000297565,;OSR2,intron_variant,,ENST00000457907,;OSR2,intron_variant,,ENST00000522510,;OSR2,intron_variant,,ENST00000435298,;OSR2,downstream_gene_variant,,ENST00000520951,;OSR2,downstream_gene_variant,,ENST00000518199,;OSR2,downstream_gene_variant,,ENST00000520791,;OSR2,downstream_gene_variant,,ENST00000520722,;OSR2,downstream_gene_variant,,ENST00000521044,;	C	ENSG00000164920	ENST00000297565	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	OSR2	HGNC	15830	protein_coding	YES	CCDS47901.1	ENSP00000297565	OSR2_HUMAN	E5RH47_HUMAN	UPI00001AEC4D	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTAGATTAG	.	5	ESCA
PALM2	0	.	GRCh37	9	112705216	112705216	+	Missense_Mutation	SNP	C	C	G	rs148645046	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.747C>G	p.His249Gln	p.H249Q	ENST00000314527	7/7	39	4	34	24	24	0	PALM2,missense_variant,p.His251Gln,ENST00000448454,;PALM2-AKAP2,missense_variant,p.His249Gln,ENST00000413420,;PALM2,missense_variant,p.His217Gln,ENST00000374531,;PALM2,missense_variant,p.His249Gln,ENST00000314527,;PALM2,missense_variant,p.His215Gln,ENST00000483909,;PALM2-AKAP2,intron_variant,,ENST00000374530,;PALM2-AKAP2,intron_variant,,ENST00000302798,;AKAP2,intron_variant,,ENST00000510514,;AKAP2,intron_variant,,ENST00000555236,;PALM2,downstream_gene_variant,,ENST00000497711,;	G	ENSG00000243444	ENST00000314527	Transcript	missense_variant	797	747	249	H/Q	caC/caG	rs148645046	.	.	1	PALM2	HGNC	15845	protein_coding	YES	CCDS48002.2	ENSP00000323805	PALM2_HUMAN	.	UPI0000071924	.	tolerated(0.58)	benign(0.007)	7/7	.	hmmpanther:PTHR10498:SF4,hmmpanther:PTHR10498,Pfam_domain:PF03285	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCACGTGTC	byCluster|by1000G	5	ESCA
ZNF883	0	.	GRCh37	9	115760042	115760042	+	RNA	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1772A>G	.	.	ENST00000427548	5/5	56	18	38	38	38	0	ZNF883,non_coding_transcript_exon_variant,,ENST00000427548,;	C	ENSG00000228623	ENST00000427548	Transcript	non_coding_transcript_exon_variant	1772	.	.	.	.	.	.	.	-1	ZNF883	HGNC	27271	lincRNA	YES	.	.	.	.	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTGTGTGCT	.	5	ESCA
TLR4	0	.	GRCh37	9	120475807	120475807	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1401C>A	p.Phe467Leu	p.F467L	ENST00000355622	3/3	50	10	40	37	37	0	TLR4,missense_variant,p.Phe467Leu,ENST00000355622,;TLR4,missense_variant,p.Phe427Leu,ENST00000394487,;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,;	A	ENSG00000136869	ENST00000355622	Transcript	missense_variant	1502	1401	467	F/L	ttC/ttA	.	.	.	1	TLR4	HGNC	11850	protein_coding	YES	CCDS6818.1	ENSP00000363089	TLR4_HUMAN	K9MSZ3_HUMAN,D0EWT7_HUMAN	UPI0000137057	.	deleterious(0)	probably_damaging(0.999)	3/3	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Pfam_domain:PF13855,Gene3D:3.80.10.10,PIRSF_domain:PIRSF037595,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCAATGG	.	5	ESCA
DENND1A	0	.	GRCh37	9	126176775	126176775	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1489-11006G>A	.	.	ENST00000373624	.	24	20	4	29	29	0	DENND1A,3_prime_UTR_variant,,ENST00000373618,;DENND1A,intron_variant,,ENST00000394219,;DENND1A,intron_variant,,ENST00000394215,;DENND1A,intron_variant,,ENST00000373624,;DENND1A,intron_variant,,ENST00000542603,;DENND1A,intron_variant,,ENST00000373620,;DENND1A,intron_variant,,ENST00000497135,;DENND1A,intron_variant,,ENST00000473039,;DENND1A,intron_variant,,ENST00000491650,;	T	ENSG00000119522	ENST00000373624	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DENND1A	HGNC	29324	protein_coding	YES	CCDS35133.1	ENSP00000362727	DEN1A_HUMAN	.	UPI00004589D2	.	.	.	.	19/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGACGCATT	.	4	ESCA
PTRH1	0	.	GRCh37	9	130478320	130478320	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-402C>G	.	.	ENST00000419060	2/6	118	87	31	66	66	0	PTRH1,5_prime_UTR_variant,,ENST00000419060,;PTRH1,upstream_gene_variant,,ENST00000423807,;C9orf117,downstream_gene_variant,,ENST00000373295,;PTRH1,upstream_gene_variant,,ENST00000543175,;TTC16,upstream_gene_variant,,ENST00000393748,;TTC16,upstream_gene_variant,,ENST00000373289,;C9orf117,downstream_gene_variant,,ENST00000373293,;PTRH1,non_coding_transcript_exon_variant,,ENST00000429848,;PTRH1,upstream_gene_variant,,ENST00000335223,;TTC16,upstream_gene_variant,,ENST00000488285,;TTC16,upstream_gene_variant,,ENST00000489226,;C9orf117,downstream_gene_variant,,ENST00000461104,;PTRH1,upstream_gene_variant,,ENST00000416214,;PTRH1,upstream_gene_variant,,ENST00000456267,;C9orf117,downstream_gene_variant,,ENST00000464092,;C9orf117,downstream_gene_variant,,ENST00000496009,;PTRH1,upstream_gene_variant,,ENST00000414832,;	C	ENSG00000187024	ENST00000419060	Transcript	5_prime_UTR_variant	1056	.	.	.	.	.	.	.	-1	PTRH1	HGNC	27039	protein_coding	YES	CCDS35147.1	ENSP00000418661	PTH_HUMAN	.	UPI000000DB98	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCAGAGGGG	.	5	ESCA
TTC16	0	.	GRCh37	9	130478440	130478440	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16G>A	p.Glu6Lys	p.E6K	ENST00000373289	1/14	102	75	26	67	67	0	TTC16,missense_variant,p.Glu6Lys,ENST00000373289,;TTC16,splice_region_variant,,ENST00000393748,;PTRH1,5_prime_UTR_variant,,ENST00000419060,;PTRH1,upstream_gene_variant,,ENST00000423807,;C9orf117,downstream_gene_variant,,ENST00000373295,;PTRH1,upstream_gene_variant,,ENST00000543175,;C9orf117,downstream_gene_variant,,ENST00000373293,;PTRH1,non_coding_transcript_exon_variant,,ENST00000429848,;PTRH1,upstream_gene_variant,,ENST00000335223,;TTC16,upstream_gene_variant,,ENST00000488285,;TTC16,upstream_gene_variant,,ENST00000489226,;C9orf117,downstream_gene_variant,,ENST00000461104,;PTRH1,upstream_gene_variant,,ENST00000416214,;PTRH1,upstream_gene_variant,,ENST00000456267,;C9orf117,downstream_gene_variant,,ENST00000464092,;C9orf117,downstream_gene_variant,,ENST00000496009,;PTRH1,upstream_gene_variant,,ENST00000414832,;	A	ENSG00000167094	ENST00000373289	Transcript	missense_variant	96	16	6	E/K	Gag/Aag	.	.	.	1	TTC16	HGNC	26536	protein_coding	YES	CCDS6875.1	ENSP00000362386	TTC16_HUMAN	.	UPI000006FE14	.	tolerated(0.26)	benign(0.012)	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGACGAGGTG	.	5	ESCA
PTRH1	0	.	GRCh37	9	130478996	130478996	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1078C>G	.	.	ENST00000419060	2/6	22	17	5	27	27	0	PTRH1,5_prime_UTR_variant,,ENST00000419060,;TTC16,intron_variant,,ENST00000393748,;TTC16,intron_variant,,ENST00000373289,;PTRH1,upstream_gene_variant,,ENST00000423807,;C9orf117,downstream_gene_variant,,ENST00000373295,;PTRH1,upstream_gene_variant,,ENST00000543175,;C9orf117,downstream_gene_variant,,ENST00000373293,;PTRH1,intron_variant,,ENST00000429848,;PTRH1,upstream_gene_variant,,ENST00000335223,;TTC16,upstream_gene_variant,,ENST00000488285,;TTC16,upstream_gene_variant,,ENST00000489226,;C9orf117,downstream_gene_variant,,ENST00000461104,;PTRH1,upstream_gene_variant,,ENST00000416214,;PTRH1,upstream_gene_variant,,ENST00000456267,;C9orf117,downstream_gene_variant,,ENST00000464092,;C9orf117,downstream_gene_variant,,ENST00000496009,;PTRH1,upstream_gene_variant,,ENST00000414832,;	C	ENSG00000187024	ENST00000419060	Transcript	5_prime_UTR_variant	380	.	.	.	.	.	.	.	-1	PTRH1	HGNC	27039	protein_coding	YES	CCDS35147.1	ENSP00000418661	PTH_HUMAN	.	UPI000000DB98	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCCCGAGTGG	.	2	ESCA
AL354898.1	0	.	GRCh37	9	133269907	133269907	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000277491	.	94	14	79	63	63	0	AL354898.1,upstream_gene_variant,,ENST00000277491,;HMCN2,non_coding_transcript_exon_variant,,ENST00000487727,;HMCN2,upstream_gene_variant,,ENST00000480829,;	A	ENSG00000215428	ENST00000277491	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4122	1	AL354898.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000277491	.	.	UPI0000073E91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGACCAGGC	.	5	ESCA
VAV2	0	.	GRCh37	9	136629169	136629169	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*15A>G	.	.	ENST00000371850	30/30	92	23	69	78	78	0	VAV2,3_prime_UTR_variant,,ENST00000371850,;VAV2,3_prime_UTR_variant,,ENST00000406606,;VAV2,3_prime_UTR_variant,,ENST00000371851,;AL590710.1,upstream_gene_variant,,ENST00000343203,;	C	ENSG00000160293	ENST00000371850	Transcript	3_prime_UTR_variant	2684	.	.	.	.	.	.	.	-1	VAV2	HGNC	12658	protein_coding	YES	CCDS48053.1	ENSP00000360916	VAV2_HUMAN	.	UPI000013E06E	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTGTCCACG	.	5	ESCA
FBXW5	0	.	GRCh37	9	139837916	139837916	+	Missense_Mutation	SNP	G	G	A	rs775883396	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236C>T	p.Thr79Met	p.T79M	ENST00000325285	3/9	72	50	21	63	63	0	FBXW5,missense_variant,p.Thr79Met,ENST00000443788,;FBXW5,missense_variant,p.Thr79Met,ENST00000325285,;FBXW5,missense_variant,p.Thr79Met,ENST00000428398,;FBXW5,upstream_gene_variant,,ENST00000433269,;C8G,upstream_gene_variant,,ENST00000224181,;C8G,upstream_gene_variant,,ENST00000371634,;FBXW5,non_coding_transcript_exon_variant,,ENST00000483559,;FBXW5,non_coding_transcript_exon_variant,,ENST00000491246,;FBXW5,non_coding_transcript_exon_variant,,ENST00000480818,;FBXW5,non_coding_transcript_exon_variant,,ENST00000459905,;C8G,upstream_gene_variant,,ENST00000465773,;C8G,upstream_gene_variant,,ENST00000484376,;FBXW5,upstream_gene_variant,,ENST00000487794,;	A	ENSG00000159069	ENST00000325285	Transcript	missense_variant	316	236	79	T/M	aCg/aTg	rs775883396	.	.	-1	FBXW5	HGNC	13613	protein_coding	YES	CCDS7014.1	ENSP00000313034	FBXW5_HUMAN	.	UPI000006EC75	.	tolerated(0.12)	benign(0.011)	3/9	.	hmmpanther:PTHR20995,hmmpanther:PTHR20995:SF15,Gene3D:1.20.1280.50,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACCGTGTCA	byFrequency	5	ESCA
MLLT3	0	.	GRCh37	9	20413721	20413721	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1123G>A	p.Asp375Asn	p.D375N	ENST00000380338	5/11	56	19	37	76	76	0	MLLT3,missense_variant,p.Asp372Asn,ENST00000429426,;MLLT3,missense_variant,p.Asp375Asn,ENST00000380338,;MLLT3,splice_region_variant,,ENST00000355930,;MIR4473,upstream_gene_variant,,ENST00000583731,;RNU4-26P,upstream_gene_variant,,ENST00000410270,;MLLT3,splice_region_variant,,ENST00000475957,;MLLT3,upstream_gene_variant,,ENST00000468513,;	T	ENSG00000171843	ENST00000380338	Transcript	missense_variant	1410	1123	375	D/N	Gat/Aat	.	.	.	-1	MLLT3	HGNC	7136	protein_coding	YES	CCDS6494.1	ENSP00000369695	AF9_HUMAN	Q6LEQ8_HUMAN,B1APT5_HUMAN	UPI00002111CB	.	deleterious(0)	benign(0.051)	5/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23195,hmmpanther:PTHR23195:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACATCAGATT	.	5	ESCA
VCP	0	.	GRCh37	9	35067938	35067938	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.252G>A	p.Met84Ile	p.M84I	ENST00000358901	3/17	65	44	20	52	52	0	VCP,missense_variant,p.Met39Ile,ENST00000417448,;VCP,missense_variant,p.Met39Ile,ENST00000448530,;VCP,missense_variant,p.Met84Ile,ENST00000358901,;VCP,non_coding_transcript_exon_variant,,ENST00000493886,;	T	ENSG00000165280	ENST00000358901	Transcript	missense_variant	1148	252	84	M/I	atG/atA	.	.	.	-1	VCP	HGNC	12666	protein_coding	YES	CCDS6573.1	ENSP00000351777	TERA_HUMAN	Q9NTC4_HUMAN,Q96IF9_HUMAN,Q0IIN5_HUMAN,C9JUP7_HUMAN,C9IZA5_HUMAN	UPI000005FB2E	.	tolerated(0.59)	benign(0.006)	3/17	.	Superfamily_domains:SSF50692,SMART_domains:SM01073,Pfam_domain:PF02359,TIGRFAM_domain:TIGR01243,Gene3D:2.40.40.20,hmmpanther:PTHR23077:SF69,hmmpanther:PTHR23077	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATTCATCCG	.	5	ESCA
INSL6	0	.	GRCh37	9	5185534	5185534	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69G>A	p.%3D	p.L23L	ENST00000381641	1/2	26	18	7	27	27	0	INSL6,synonymous_variant,p.%3D,ENST00000381641,;	T	ENSG00000120210	ENST00000381641	Transcript	synonymous_variant	135	69	23	L	ctG/ctA	.	.	.	-1	INSL6	HGNC	6089	protein_coding	YES	CCDS6458.1	ENSP00000371054	INSL6_HUMAN	.	UPI000012D681	.	.	.	1/2	.	Superfamily_domains:SSF56994,PIRSF_domain:PIRSF037062,hmmpanther:PTHR12004:SF1,hmmpanther:PTHR12004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCTCAGTTC	.	5	ESCA
S1PR3	0	.	GRCh37	9	91617467	91617467	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*215C>T	.	.	ENST00000375846	1/1	35	28	7	36	36	0	S1PR3,3_prime_UTR_variant,,ENST00000358157,;S1PR3,3_prime_UTR_variant,,ENST00000375846,;	T	ENSG00000213694	ENST00000375846	Transcript	3_prime_UTR_variant	6047	.	.	.	.	.	.	.	1	S1PR3	HGNC	3167	protein_coding	YES	CCDS6680.1	ENSP00000365006	S1PR3_HUMAN	.	UPI0000140B93	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCAGATG	.	5	ESCA
HIATL1	0	.	GRCh37	9	97222649	97222649	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*955A>G	.	.	ENST00000375344	12/12	88	18	70	91	91	0	HIATL1,3_prime_UTR_variant,,ENST00000375344,;HIATL1,downstream_gene_variant,,ENST00000428393,;	G	ENSG00000148110	ENST00000375344	Transcript	3_prime_UTR_variant	2745	.	.	.	.	.	.	.	1	HIATL1	HGNC	23376	protein_coding	YES	CCDS6710.2	ENSP00000364493	HIAL1_HUMAN	.	UPI000046FF5D	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCATCACA	.	5	ESCA
FANCC	0	.	GRCh37	9	97869387	97869387	+	Silent	SNP	A	A	T	rs76895298	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1494T>A	p.%3D	p.A498A	ENST00000289081	14/15	124	86	37	87	87	0	FANCC,synonymous_variant,p.%3D,ENST00000375305,;FANCC,synonymous_variant,p.%3D,ENST00000289081,;FANCC,non_coding_transcript_exon_variant,,ENST00000464627,;FANCC,downstream_gene_variant,,ENST00000477942,;FANCC,downstream_gene_variant,,ENST00000480712,;FANCC,downstream_gene_variant,,ENST00000490972,;	T	ENSG00000158169	ENST00000289081	Transcript	synonymous_variant	1749	1494	498	A	gcT/gcA	rs76895298,FANCC:c.1494T>G	.	.	-1	FANCC	HGNC	3584	protein_coding	YES	CCDS35071.1	ENSP00000289081	FANCC_HUMAN	B4E3W2_HUMAN,B1ALR7_HUMAN	UPI000000D910	.	.	.	14/15	.	Prints_domain:PR00494,PIRSF_domain:PIRSF018417,Pfam_domain:PF02106,hmmpanther:PTHR16798,hmmpanther:PTHR16798:SF0	G:0.0016	G:0	G:0	.	G:0.0079	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGAGCCCA	byFrequency|byCluster|by1000G	5	ESCA
WBP5	0	.	GRCh37	X	102611426	102611426	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-258G>A	.	.	ENST00000372661	1/3	14	7	6	27	27	0	WBP5,5_prime_UTR_variant,,ENST00000372656,;WBP5,5_prime_UTR_variant,,ENST00000372661,;	A	ENSG00000185222	ENST00000372661	Transcript	5_prime_UTR_variant	54	.	.	.	.	.	.	.	1	WBP5	HGNC	30084	protein_coding	YES	CCDS14507.1	ENSP00000361745	WBP5_HUMAN	.	UPI0000073C3F	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CAGAAGTCCTG	.	4	ESCA
UPF3B	0	.	GRCh37	X	118979254	118979254	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376G>A	p.Glu126Lys	p.E126K	ENST00000276201	4/11	23	10	12	25	25	0	UPF3B,missense_variant,p.Glu126Lys,ENST00000345865,;UPF3B,missense_variant,p.Glu126Lys,ENST00000276201,;UPF3B,upstream_gene_variant,,ENST00000478840,;	T	ENSG00000125351	ENST00000276201	Transcript	missense_variant	446	376	126	E/K	Gaa/Aaa	.	.	.	-1	UPF3B	HGNC	20439	protein_coding	YES	CCDS14588.1	ENSP00000276201	REN3B_HUMAN	I3XIE4_HUMAN	UPI000006D21C	.	deleterious(0)	possibly_damaging(0.895)	4/11	.	hmmpanther:PTHR13112,hmmpanther:PTHR13112:SF1,Pfam_domain:PF03467,Gene3D:3.30.70.330,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCCTGAC	.	5	ESCA
MAGEB4	0	.	GRCh37	X	30260669	30260669	+	Silent	SNP	C	C	T	rs776127502	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.417C>T	p.%3D	p.I139I	ENST00000378982	1/1	23	15	8	9	9	0	MAGEB4,synonymous_variant,p.%3D,ENST00000378982,;MAGEB1,upstream_gene_variant,,ENST00000397548,;MAGEB1,upstream_gene_variant,,ENST00000397550,;MAGEB1,upstream_gene_variant,,ENST00000378981,;	T	ENSG00000120289	ENST00000378982	Transcript	synonymous_variant	613	417	139	I	atC/atT	rs776127502	.	.	1	MAGEB4	HGNC	6811	protein_coding	YES	CCDS14221.1	ENSP00000368266	MAGB4_HUMAN	.	UPI000012F055	.	.	.	1/1	.	Pfam_domain:PF01454,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF75,PROSITE_profiles:PS50838	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCATCAGCAA	.	5	ESCA
BMP15	0	.	GRCh37	X	50654013	50654013	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.230C>G	p.Ser77Ter	p.S77*	ENST00000252677	1/2	27	19	8	17	17	0	BMP15,stop_gained,p.Ser77Ter,ENST00000252677,;	G	ENSG00000130385	ENST00000252677	Transcript	stop_gained	230	230	77	S/*	tCa/tGa	.	.	.	1	BMP15	HGNC	1068	protein_coding	YES	CCDS14334.1	ENSP00000252677	BMP15_HUMAN	.	UPI000013CD7C	.	.	.	1/2	.	hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGTTCAGCTG	.	5	ESCA
HDHD1	0	.	GRCh37	X	6995436	6995436	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404C>T	p.Ala135Val	p.A135V	ENST00000424830	4/5	92	11	80	65	65	0	HDHD1,missense_variant,p.Ala112Val,ENST00000540122,;HDHD1,missense_variant,p.Ala135Val,ENST00000424830,;HDHD1,missense_variant,p.Ala69Val,ENST00000412827,;HDHD1,missense_variant,p.Ala112Val,ENST00000486446,;HDHD1,missense_variant,p.Ala112Val,ENST00000381077,;	A	ENSG00000130021	ENST00000424830	Transcript	missense_variant	449	404	135	A/V	gCc/gTc	.	.	.	-1	HDHD1	HGNC	16818	protein_coding	YES	CCDS48076.1	ENSP00000396452	HDHD1_HUMAN	.	UPI0001818C59	.	deleterious(0)	possibly_damaging(0.638)	4/5	.	hmmpanther:PTHR18901,hmmpanther:PTHR18901:SF10,Pfam_domain:PF13419,TIGRFAM_domain:TIGR01509,Gene3D:3.40.50.1000,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTGGCCAGT	.	5	ESCA
TEX11	0	.	GRCh37	X	69964046	69964046	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.761T>C	p.Met254Thr	p.M254T	ENST00000395889	11/31	44	10	33	31	31	0	TEX11,missense_variant,p.Met239Thr,ENST00000374333,;TEX11,missense_variant,p.Met254Thr,ENST00000395889,;TEX11,missense_variant,p.Met254Thr,ENST00000344304,;	G	ENSG00000120498	ENST00000395889	Transcript	missense_variant	917	761	254	M/T	aTg/aCg	.	.	.	-1	TEX11	HGNC	11733	protein_coding	YES	CCDS35323.1	ENSP00000379226	TEX11_HUMAN	.	UPI000013CA89	.	tolerated(0.1)	benign(0.018)	11/31	.	hmmpanther:PTHR22904:SF291,hmmpanther:PTHR22904,Pfam_domain:PF08631	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCCATCTTC	.	5	ESCA
SATL1	0	.	GRCh37	X	84347377	84347377	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4A9-01A-11D-A28B-09	TCGA-LN-A4A9-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*168C>G	.	.	ENST00000509231	5/5	26	10	16	34	34	0	SATL1,3_prime_UTR_variant,,ENST00000509231,;SATL1,3_prime_UTR_variant,,ENST00000332921,;SATL1,3_prime_UTR_variant,,ENST00000395409,;APOOL,downstream_gene_variant,,ENST00000373173,;	C	ENSG00000184788	ENST00000509231	Transcript	3_prime_UTR_variant	2147	.	.	.	.	.	.	.	-1	SATL1	HGNC	27992	protein_coding	YES	CCDS35343.2	ENSP00000425421	.	E9PB72_HUMAN	UPI000041ABBC	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGATGAGTTG	.	5	ESCA
FAM170B	0	.	GRCh37	10	50339714	50339714	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.796G>A	p.Glu266Lys	p.E266K	ENST00000311787	2/2	51	33	18	70	70	0	FAM170B,missense_variant,p.Glu266Lys,ENST00000311787,;FAM170B-AS1,intron_variant,,ENST00000435809,;FAM170B-AS1,intron_variant,,ENST00000442525,;FAM170B-AS1,intron_variant,,ENST00000443389,;	T	ENSG00000172538	ENST00000311787	Transcript	missense_variant	886	796	266	E/K	Gaa/Aaa	.	.	.	-1	FAM170B	HGNC	19736	protein_coding	YES	CCDS53536.1	ENSP00000308292	F170B_HUMAN	.	UPI00001C1ED8	.	tolerated(0.26)	benign(0.038)	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTCGCTGT	.	5	ESCA
NCOA4	0	.	GRCh37	10	51590217	51590217	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1016C>T	.	.	ENST00000452682	12/12	108	58	50	95	95	0	NCOA4,3_prime_UTR_variant,,ENST00000374082,;NCOA4,3_prime_UTR_variant,,ENST00000452682,;NCOA4,3_prime_UTR_variant,,ENST00000344348,;NCOA4,3_prime_UTR_variant,,ENST00000443446,;NCOA4,3_prime_UTR_variant,,ENST00000374087,;NCOA4,3_prime_UTR_variant,,ENST00000438493,;TIMM23,downstream_gene_variant,,ENST00000374064,;NCOA4,downstream_gene_variant,,ENST00000430396,;TIMM23,downstream_gene_variant,,ENST00000260867,;NCOA4,downstream_gene_variant,,ENST00000414907,;TIMM23,downstream_gene_variant,,ENST00000374065,;TIMM23,downstream_gene_variant,,ENST00000444743,;TIMM23,downstream_gene_variant,,ENST00000485812,;TIMM23,downstream_gene_variant,,ENST00000476778,;TIMM23,downstream_gene_variant,,ENST00000469116,;	T	ENSG00000138293	ENST00000452682	Transcript	3_prime_UTR_variant	3221	.	.	.	.	.	.	.	1	NCOA4	HGNC	7671	protein_coding	YES	CCDS44394.1	ENSP00000395465	NCOA4_HUMAN	.	UPI0001932817	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTGCCTTGG	.	5	ESCA
PTEN	0	.	GRCh37	10	89692904	89692904	+	Nonsense_Mutation	SNP	C	C	T	rs121909224	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	5/9	80	72	7	87	87	0	PTEN,stop_gained,p.Arg130Ter,ENST00000371953,;PTEN,non_coding_transcript_exon_variant,,ENST00000498703,;	T	ENSG00000171862	ENST00000371953	Transcript	stop_gained	1745	388	130	R/*	Cga/Tga	CM971273,CM094223,rs121909224,COSM5329,COSM5219,COSM5152,COSM308347	.	.	1	PTEN	HGNC	9588	protein_coding	YES	CCDS31238.1	ENSP00000361021	PTEN_HUMAN	F6KD01_HUMAN,H6WA51_HUMAN,H6WA46_HUMAN	UPI00001328C5	.	.	.	5/9	.	PROSITE_profiles:PS51181,hmmpanther:PTHR12305,PROSITE_patterns:PS00383,Gene3D:3.90.190.10,Pfam_domain:PF00782,PIRSF_domain:PIRSF038025,SMART_domains:SM00404,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R130*|c.388C>T|69,CODON|p.0?|c.1_1212del1212|28,CODON|p.G129E|c.386G>A|3,CODON|p.G129V|c.386G>T|3,CODON|p.G129G|c.387A>G|4,BUFFER|p.A126V|c.377C>T|3,BUFFER|p.A126D|c.377C>A|4,BUFFER|p.G127R|c.379G>A|5,BUFFER|p.G127E|c.380G>A|5,BUFFER|p.G127G|c.381A>G|3,BUFFER|p.K128R|c.383A>G|6,BUFFER|p.K128N|c.384G>T|4,BUFFER|p.G129*|c.385G>T|4,BUFFER|p.G129R|c.385G>A|5,BUFFER|p.R130G|c.388C>G|107,BUFFER|p.R130fs*4|c.389delG|12,BUFFER|p.R130Q|c.389G>A|85,BUFFER|p.R130L|c.389G>T|17,BUFFER|p.R130P|c.389G>C|13,BUFFER|p.T131fs*3|c.391delA|3,BUFFER|p.G132S|c.394G>A|3,BUFFER|p.G132D|c.395G>A|7,BUFFER|p.G132V|c.395G>T|4	MUTECT|MUSE|VARSCANS	AGGGACGAACT	byCluster	3	ESCA
PTEN	0	.	GRCh37	10	89717762	89717762	+	Nonsense_Mutation	SNP	A	A	T	.	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787A>T	p.Lys263Ter	p.K263*	ENST00000371953	7/9	78	35	42	60	60	0	PTEN,stop_gained,p.Lys263Ter,ENST00000371953,;PTEN,non_coding_transcript_exon_variant,,ENST00000472832,;	T	ENSG00000171862	ENST00000371953	Transcript	stop_gained	2144	787	263	K/*	Aag/Tag	COSM43075	.	.	1	PTEN	HGNC	9588	protein_coding	YES	CCDS31238.1	ENSP00000361021	PTEN_HUMAN	F6KD01_HUMAN,H6WA51_HUMAN,H6WA46_HUMAN	UPI00001328C5	.	.	.	7/9	.	PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Gene3D:1d5rA02,Pfam_domain:PF10409,PIRSF_domain:PIRSF038025,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.K263*|c.787A>T|3,CODON|p.0?|c.1_1212del1212|28,BUFFER|p.Q261*|c.781C>T|3,BUFFER|p.K267fs*9|c.795delA|11	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAACAAGATG	.	5	ESCA
NUMA1	0	.	GRCh37	11	71726383	71726384	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2165dupA	p.Arg723AlafsTer16	p.R723Afs*16	ENST00000393695	15/27	31	16	15	15	15	0	NUMA1,frameshift_variant,p.Arg723AlafsTer16,ENST00000393695,;NUMA1,frameshift_variant,p.Arg723AlafsTer16,ENST00000542977,;NUMA1,frameshift_variant,p.Arg723AlafsTer16,ENST00000358965,;NUMA1,intron_variant,,ENST00000351960,;NUMA1,downstream_gene_variant,,ENST00000537930,;NUMA1,upstream_gene_variant,,ENST00000541584,;NUMA1,downstream_gene_variant,,ENST00000544129,;NUMA1,downstream_gene_variant,,ENST00000544238,;NUMA1,downstream_gene_variant,,ENST00000543009,;NUMA1,downstream_gene_variant,,ENST00000537217,;NUMA1,downstream_gene_variant,,ENST00000543937,;RP11-849H4.4,non_coding_transcript_exon_variant,,ENST00000502284,;NUMA1,downstream_gene_variant,,ENST00000540843,;NUMA1,downstream_gene_variant,,ENST00000534987,;NUMA1,downstream_gene_variant,,ENST00000536119,;NUMA1,upstream_gene_variant,,ENST00000545721,;NUMA1,upstream_gene_variant,,ENST00000540588,;	T	ENSG00000137497	ENST00000393695	Transcript	frameshift_variant	2497-2498	2165-2166	722	K/KX	aag/aaAg	.	.	.	-1	NUMA1	HGNC	8059	protein_coding	YES	CCDS31633.1	ENSP00000377298	NUMA1_HUMAN	Q9UPG3_HUMAN,Q9UNL7_HUMAN,Q86XH4_HUMAN,Q4LE64_HUMAN,G1UI36_HUMAN,F8W6T3_HUMAN,F5H7R5_HUMAN,F5H763_HUMAN,F5H6Y5_HUMAN,F5H4Y4_HUMAN,F5H4J1_HUMAN,F5H3L6_HUMAN,F5H2F3_HUMAN,F5H1L0_HUMAN,F5H0Z7_HUMAN,F5H073_HUMAN,F5H068_HUMAN,F5GZW1_HUMAN,F5GWK2_HUMAN,F5GWA2_HUMAN	UPI000013DB8B	.	.	.	15/27	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTGCGCTTCTC	.	2	ESCA
NAALAD2	0	.	GRCh37	11	89867841	89867847	+	5'UTR	DEL	GCCTCCT	GCCTCCT	-	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	GCCTCCT	GCCTCCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-83_-77delTCCTGCC	.	.	ENST00000534061	1/19	46	31	15	29	29	0	NAALAD2,5_prime_UTR_variant,,ENST00000534061,;NAALAD2,intron_variant,,ENST00000525497,;NAALAD2,upstream_gene_variant,,ENST00000526637,;NAALAD2,upstream_gene_variant,,ENST00000375944,;NAALAD2,upstream_gene_variant,,ENST00000525171,;NAALAD2,upstream_gene_variant,,ENST00000321955,;NAALAD2,5_prime_UTR_variant,,ENST00000527493,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000529090,;NAALAD2,upstream_gene_variant,,ENST00000524501,;	-	ENSG00000077616	ENST00000534061	Transcript	5_prime_UTR_variant	145-151	.	.	.	.	.	.	.	1	NAALAD2	HGNC	14526	protein_coding	YES	CCDS8288.1	ENSP00000432481	NALD2_HUMAN	E9PJ53_HUMAN,E9PII2_HUMAN	UPI0000031A85	.	.	.	1/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	CTCACAGCCTCCTGCCAG	.	2	ESCA
HCAR2	0	.	GRCh37	12	123187427	123187427	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404C>T	p.Ala135Val	p.A135V	ENST00000328880	1/1	175	133	42	78	78	0	HCAR2,missense_variant,p.Ala135Val,ENST00000328880,;HCAR1,intron_variant,,ENST00000356987,;RP11-324E6.6,intron_variant,,ENST00000543611,;	A	ENSG00000182782	ENST00000328880	Transcript	missense_variant	464	404	135	A/V	gCc/gTc	.	.	.	-1	HCAR2	HGNC	24827	protein_coding	YES	CCDS9235.1	ENSP00000375066	HCAR2_HUMAN	.	UPI000003BCD5	.	tolerated(0.59)	benign(0.005)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF0,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGGCGTGG	.	5	ESCA
ULK1	0	.	GRCh37	12	132407435	132407436	+	3'UTR	INS	-	-	CA	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1530_*1531dupCA	.	.	ENST00000321867	28/28	44	28	16	20	20	0	ULK1,3_prime_UTR_variant,,ENST00000321867,;ULK1,downstream_gene_variant,,ENST00000540647,;ULK1,downstream_gene_variant,,ENST00000541761,;RP11-417L19.4,downstream_gene_variant,,ENST00000539078,;ULK1,downstream_gene_variant,,ENST00000544718,;ULK1,downstream_gene_variant,,ENST00000540568,;	CA	ENSG00000177169	ENST00000321867	Transcript	3_prime_UTR_variant	5033-5034	.	.	.	.	.	.	.	1	ULK1	HGNC	12558	protein_coding	YES	CCDS9274.1	ENSP00000324560	ULK1_HUMAN	F5H4E9_HUMAN,F5H1S7_HUMAN,F5GZQ0_HUMAN	UPI00001FB0D9	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTGCTTCATGG	.	2	ESCA
GOLGA3	0	.	GRCh37	12	133360544	133360544	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3267+206G>A	.	.	ENST00000204726	.	33	28	5	11	11	0	GOLGA3,3_prime_UTR_variant,,ENST00000537452,;GOLGA3,3_prime_UTR_variant,,ENST00000545875,;GOLGA3,intron_variant,,ENST00000204726,;GOLGA3,intron_variant,,ENST00000450791,;GOLGA3,intron_variant,,ENST00000456883,;	T	ENSG00000090615	ENST00000204726	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	.	.	.	16/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGGCTGTAC	.	4	ESCA
ATF7IP	0	.	GRCh37	12	14518747	14518747	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-22C>T	.	.	ENST00000261168	1/15	61	55	6	37	37	0	ATF7IP,5_prime_UTR_variant,,ENST00000261168,;ATF7IP,5_prime_UTR_variant,,ENST00000545723,;ATF7IP,5_prime_UTR_variant,,ENST00000543189,;ATF7IP,5_prime_UTR_variant,,ENST00000538511,;ATF7IP,5_prime_UTR_variant,,ENST00000536444,;ATF7IP,upstream_gene_variant,,ENST00000534828,;ATF7IP,upstream_gene_variant,,ENST00000535132,;ATF7IP,upstream_gene_variant,,ENST00000542967,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000539659,;RPL30P11,upstream_gene_variant,,ENST00000509114,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000537653,;	T	ENSG00000171681	ENST00000261168	Transcript	5_prime_UTR_variant	132	.	.	.	.	.	.	.	1	ATF7IP	HGNC	20092	protein_coding	YES	CCDS8663.1	ENSP00000261168	MCAF1_HUMAN	F8WE35_HUMAN,F5H8I0_HUMAN,F5H6X8_HUMAN,F5H502_HUMAN,F5H3C4_HUMAN,F5H2W9_HUMAN,F5H2H9_HUMAN,F5H221_HUMAN,F5H1K9_HUMAN,F5GZ98_HUMAN,F5GZ10_HUMAN,F5GYR7_HUMAN,A8MV73_HUMAN	UPI00001FB6B1	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAGCTTCCG	.	4	ESCA
KCNA6	0	.	GRCh37	12	4921553	4921553	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*756G>C	.	.	ENST00000433855	1/2	77	69	8	69	69	0	KCNA6,3_prime_UTR_variant,,ENST00000433855,;KCNA6,3_prime_UTR_variant,,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,;	C	ENSG00000151079	ENST00000433855	Transcript	3_prime_UTR_variant	3212	.	.	.	.	.	.	.	1	KCNA6	HGNC	6225	protein_coding	YES	CCDS8534.1	ENSP00000408321	KCNA6_HUMAN	.	UPI00001279AD	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGAAGGTTCCT	.	3	ESCA
RARG	0	.	GRCh37	12	53621213	53621213	+	Silent	SNP	G	G	A	rs556025298	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117C>T	p.%3D	p.F39F	ENST00000425354	3/10	129	101	28	109	109	0	RARG,synonymous_variant,p.%3D,ENST00000425354,;RARG,synonymous_variant,p.%3D,ENST00000394426,;RARG,synonymous_variant,p.%3D,ENST00000546717,;RARG,intron_variant,,ENST00000327550,;RARG,downstream_gene_variant,,ENST00000551158,;RARG,downstream_gene_variant,,ENST00000550362,;RARG,intron_variant,,ENST00000543762,;RARG,downstream_gene_variant,,ENST00000546377,;RARG,downstream_gene_variant,,ENST00000551501,;RARG,downstream_gene_variant,,ENST00000552901,;RARG,downstream_gene_variant,,ENST00000550721,;RARG,downstream_gene_variant,,ENST00000550350,;RARG,downstream_gene_variant,,ENST00000549859,;	A	ENSG00000172819	ENST00000425354	Transcript	synonymous_variant	605	117	39	F	ttC/ttT	rs556025298	.	.	-1	RARG	HGNC	9866	protein_coding	YES	CCDS8850.1	ENSP00000388510	RARG_HUMAN	H3BMY6_HUMAN,H3BMK1_HUMAN,A8K3H3_HUMAN	UPI000000105D	.	.	.	3/10	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTCGAAAGG	by1000G	5	ESCA
SMARCC2	0	.	GRCh37	12	56574884	56574884	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.958C>T	p.Pro320Ser	p.P320S	ENST00000267064	11/28	114	88	26	82	82	0	SMARCC2,missense_variant,p.Pro320Ser,ENST00000267064,;SMARCC2,missense_variant,p.Pro320Ser,ENST00000550164,;SMARCC2,missense_variant,p.Pro320Ser,ENST00000394023,;SMARCC2,missense_variant,p.Pro320Ser,ENST00000347471,;RP11-977G19.5,intron_variant,,ENST00000553176,;SMARCC2,downstream_gene_variant,,ENST00000550859,;SMARCC2,splice_region_variant,,ENST00000552674,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000549757,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000548130,;SMARCC2,downstream_gene_variant,,ENST00000552627,;SMARCC2,downstream_gene_variant,,ENST00000550150,;SMARCC2,upstream_gene_variant,,ENST00000552566,;SMARCC2,downstream_gene_variant,,ENST00000547356,;SMARCC2,downstream_gene_variant,,ENST00000550519,;	A	ENSG00000139613	ENST00000267064	Transcript	missense_variant	1045	958	320	P/S	Ccc/Tcc	.	.	.	-1	SMARCC2	HGNC	11105	protein_coding	YES	CCDS8907.1	ENSP00000267064	SMRC2_HUMAN	F8VZW6_HUMAN	UPI0000071C4E	.	tolerated(0.22)	possibly_damaging(0.641)	11/28	.	hmmpanther:PTHR12802:SF38,hmmpanther:PTHR12802	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGGGACTGG	.	5	ESCA
RB1	0	.	GRCh37	13	48955516	48955516	+	Frame_Shift_Del	DEL	A	A	-	rs143948310	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1632delA	p.Glu545LysfsTer2	p.E545Kfs*2	ENST00000267163	17/27	77	42	35	31	31	0	RB1,frameshift_variant,p.Glu545LysfsTer2,ENST00000267163,;	-	ENSG00000139687	ENST00000267163	Transcript	frameshift_variant	1770	1632	544	R/X	agA/ag	rs143948310	.	.	1	RB1	HGNC	9884	protein_coding	YES	CCDS31973.1	ENSP00000267163	RB_HUMAN	Q7KZ61_HUMAN,Q7KZ60_HUMAN,Q6LE82_HUMAN,Q6LE81_HUMAN,Q6LE80_HUMAN,Q6LE79_HUMAN,Q6LE77_HUMAN,Q6LE65_HUMAN,Q6DUF0_HUMAN,P78495_HUMAN,B4DRB3_HUMAN	UPI0000001C79	.	.	.	17/27	.	hmmpanther:PTHR13742,Pfam_domain:PF01858,Gene3D:1.10.472.10,Superfamily_domains:SSF47954	G:0.0020	G:0.0076	G:0	.	G:0	G:0	G:0	G:0.0075	G:0.0001	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GACAAGAGAAAT	byFrequency|byCluster|by1000G	3	ESCA
NEK5	0	.	GRCh37	13	52649950	52649950	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1741T>A	p.Phe581Ile	p.F581I	ENST00000355568	20/22	56	41	14	35	35	0	NEK5,missense_variant,p.Phe581Ile,ENST00000355568,;NEK5,3_prime_UTR_variant,,ENST00000465811,;	T	ENSG00000197168	ENST00000355568	Transcript	missense_variant	1881	1741	581	F/I	Ttt/Att	.	.	.	-1	NEK5	HGNC	7748	protein_coding	YES	CCDS31979.1	ENSP00000347767	NEK5_HUMAN	.	UPI0000227E77	.	deleterious(0)	probably_damaging(0.999)	20/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAAATTTTA	.	5	ESCA
ARHGAP5	0	.	GRCh37	14	32561049	32561049	+	Missense_Mutation	SNP	A	A	G	rs372981423	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1174A>G	p.Ile392Val	p.I392V	ENST00000345122	2/7	35	24	10	21	21	0	ARHGAP5,missense_variant,p.Ile392Val,ENST00000432921,;ARHGAP5,missense_variant,p.Ile392Val,ENST00000539826,;ARHGAP5,missense_variant,p.Ile392Val,ENST00000345122,;ARHGAP5,missense_variant,p.Ile392Val,ENST00000556611,;ARHGAP5,intron_variant,,ENST00000554090,;ARHGAP5,intron_variant,,ENST00000396582,;ARHGAP5,intron_variant,,ENST00000433497,;ARHGAP5,downstream_gene_variant,,ENST00000556191,;ARHGAP5,downstream_gene_variant,,ENST00000555814,;ARHGAP5,upstream_gene_variant,,ENST00000557643,;	G	ENSG00000100852	ENST00000345122	Transcript	missense_variant	1489	1174	392	I/V	Ata/Gta	rs372981423	.	.	1	ARHGAP5	HGNC	675	protein_coding	YES	CCDS32062.1	ENSP00000371897	RHG05_HUMAN	G3V5I7_HUMAN,G3V444_HUMAN,G3V360_HUMAN	UPI000057B85C	.	tolerated(0.19)	benign(0.05)	2/7	.	PROSITE_profiles:PS51676,hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF4,SMART_domains:SM00441	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATATAGAC	byFrequency|byCluster	5	ESCA
FUT8	0	.	GRCh37	14	66190950	66190950	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1168T>A	p.Phe390Ile	p.F390I	ENST00000360689	9/11	43	34	9	42	42	0	FUT8,missense_variant,p.Phe390Ile,ENST00000394585,;FUT8,missense_variant,p.Phe227Ile,ENST00000557164,;FUT8,missense_variant,p.Phe390Ile,ENST00000360689,;FUT8,missense_variant,p.Phe261Ile,ENST00000358307,;FUT8,missense_variant,p.Phe390Ile,ENST00000394586,;FUT8,intron_variant,,ENST00000417683,;FUT8,downstream_gene_variant,,ENST00000554765,;FUT8,downstream_gene_variant,,ENST00000557536,;FUT8,intron_variant,,ENST00000342677,;	A	ENSG00000033170	ENST00000360689	Transcript	missense_variant	2895	1168	390	F/I	Ttt/Att	.	.	.	1	FUT8	HGNC	4019	protein_coding	YES	CCDS9775.1	ENSP00000353910	FUT8_HUMAN	Q546E0_HUMAN,G3V5Z4_HUMAN,G3V5E3_HUMAN,G3V530_HUMAN,G3V509_HUMAN,G3V4A8_HUMAN	UPI000000DCC9	.	deleterious(0)	possibly_damaging(0.546)	9/11	.	PROSITE_profiles:PS51659,hmmpanther:PTHR13132,PIRSF_domain:PIRSF000472	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATTTTCAG	.	5	ESCA
DLST	0	.	GRCh37	14	75369084	75369084	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*51C>A	.	.	ENST00000334220	15/15	180	173	6	99	99	0	DLST,3_prime_UTR_variant,,ENST00000334220,;DLST,3_prime_UTR_variant,,ENST00000334212,;RPS6KL1,downstream_gene_variant,,ENST00000553789,;RPS6KL1,downstream_gene_variant,,ENST00000555910,;RPS6KL1,downstream_gene_variant,,ENST00000553971,;RPS6KL1,downstream_gene_variant,,ENST00000358328,;RPS6KL1,downstream_gene_variant,,ENST00000555647,;RPS6KL1,downstream_gene_variant,,ENST00000557413,;RPS6KL1,downstream_gene_variant,,ENST00000556848,;RPS6KL1,downstream_gene_variant,,ENST00000553315,;RPS6KL1,downstream_gene_variant,,ENST00000354625,;DLST,downstream_gene_variant,,ENST00000554806,;DLST,downstream_gene_variant,,ENST00000555190,;DLST,3_prime_UTR_variant,,ENST00000554612,;DLST,3_prime_UTR_variant,,ENST00000238671,;RPS6KL1,downstream_gene_variant,,ENST00000553646,;RPS6KL1,downstream_gene_variant,,ENST00000555009,;RPS6KL1,downstream_gene_variant,,ENST00000555834,;DLST,downstream_gene_variant,,ENST00000555089,;	A	ENSG00000119689	ENST00000334220	Transcript	3_prime_UTR_variant	1474	.	.	.	.	.	.	.	1	DLST	HGNC	2911	protein_coding	YES	CCDS9833.1	ENSP00000335304	ODO2_HUMAN	.	UPI00000000C0	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGTCTTCTC	.	2	ESCA
ATG2B	0	.	GRCh37	14	96752289	96752289	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6040A>G	p.Thr2014Ala	p.T2014A	ENST00000359933	42/42	62	28	34	49	49	0	ATG2B,missense_variant,p.Thr2014Ala,ENST00000359933,;ATG2B,downstream_gene_variant,,ENST00000261834,;ATG2B,downstream_gene_variant,,ENST00000555263,;ATG2B,downstream_gene_variant,,ENST00000553643,;	C	ENSG00000066739	ENST00000359933	Transcript	missense_variant	6934	6040	2014	T/A	Act/Gct	.	.	.	-1	ATG2B	HGNC	20187	protein_coding	YES	CCDS9944.2	ENSP00000353010	ATG2B_HUMAN	.	UPI000155D51F	.	deleterious(0.04)	probably_damaging(0.931)	42/42	.	hmmpanther:PTHR13190:SF19,hmmpanther:PTHR13190,Pfam_domain:PF09333	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCAGTTTCAT	.	5	ESCA
SNRPN	0	.	GRCh37	15	25219597	25219597	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4A>G	.	.	ENST00000400100	7/13	132	127	5	127	127	0	SNRPN,5_prime_UTR_variant,,ENST00000400100,;SNRPN,5_prime_UTR_variant,,ENST00000400098,;SNRPN,5_prime_UTR_variant,,ENST00000584968,;SNURF,3_prime_UTR_variant,,ENST00000338094,;SNRPN,5_prime_UTR_variant,,ENST00000400097,;SNRPN,5_prime_UTR_variant,,ENST00000554227,;SNRPN,5_prime_UTR_variant,,ENST00000390687,;SNRPN,5_prime_UTR_variant,,ENST00000579070,;SNRPN,5_prime_UTR_variant,,ENST00000444203,;SNRPN,5_prime_UTR_variant,,ENST00000577565,;SNRPN,5_prime_UTR_variant,,ENST00000346403,;SNRPN,downstream_gene_variant,,ENST00000553597,;SNURF,intron_variant,,ENST00000551312,;SNURF,intron_variant,,ENST00000580062,;SNURF,intron_variant,,ENST00000557230,;SNHG14,upstream_gene_variant,,ENST00000557108,;	G	ENSG00000128739	ENST00000400100	Transcript	5_prime_UTR_variant	887	.	.	.	.	.	.	.	1	SNRPN	HGNC	11164	protein_coding	YES	CCDS10017.1	ENSP00000382972	RSMN_HUMAN	Q9UKR4_HUMAN,Q6LBS1_HUMAN,J3QLE5_HUMAN,J3KRY3_HUMAN	UPI000002948A	.	.	.	7/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACAGCAATCAT	.	2	ESCA
VPS13C	0	.	GRCh37	15	62256051	62256051	+	Missense_Mutation	SNP	G	G	A	rs780221902	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000261517	32/85	58	55	3	51	51	0	VPS13C,missense_variant,p.Ala1105Val,ENST00000261517,;VPS13C,missense_variant,p.Ala1105Val,ENST00000395896,;VPS13C,missense_variant,p.Ala1062Val,ENST00000249837,;VPS13C,missense_variant,p.Ala1062Val,ENST00000395898,;VPS13C,upstream_gene_variant,,ENST00000558088,;	A	ENSG00000129003	ENST00000261517	Transcript	missense_variant	3388	3314	1105	A/V	gCc/gTc	rs780221902	.	.	-1	VPS13C	HGNC	23594	protein_coding	YES	CCDS32257.1	ENSP00000261517	VP13C_HUMAN	B4E2S9_HUMAN,B3KW10_HUMAN	UPI000023B7D3	.	deleterious(0.01)	probably_damaging(0.947)	32/85	.	hmmpanther:PTHR16166:SF69,hmmpanther:PTHR16166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCGGCGATA	byFrequency	2	ESCA
VPS13C	0	.	GRCh37	15	62256052	62256052	+	Missense_Mutation	SNP	C	C	A	rs747305996	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3313G>T	p.Ala1105Ser	p.A1105S	ENST00000261517	32/85	57	54	3	51	51	0	VPS13C,missense_variant,p.Ala1105Ser,ENST00000261517,;VPS13C,missense_variant,p.Ala1105Ser,ENST00000395896,;VPS13C,missense_variant,p.Ala1062Ser,ENST00000249837,;VPS13C,missense_variant,p.Ala1062Ser,ENST00000395898,;VPS13C,upstream_gene_variant,,ENST00000558088,;	A	ENSG00000129003	ENST00000261517	Transcript	missense_variant	3387	3313	1105	A/S	Gcc/Tcc	rs747305996	.	.	-1	VPS13C	HGNC	23594	protein_coding	YES	CCDS32257.1	ENSP00000261517	VP13C_HUMAN	B4E2S9_HUMAN,B3KW10_HUMAN	UPI000023B7D3	.	tolerated(0.62)	probably_damaging(0.995)	32/85	.	hmmpanther:PTHR16166:SF69,hmmpanther:PTHR16166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCGGCGATAT	byFrequency	2	ESCA
SKOR1	0	.	GRCh37	15	68124644	68124644	+	Nonsense_Mutation	SNP	G	G	T	rs780493275	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2329G>T	p.Glu777Ter	p.E777*	ENST00000341418	12/15	43	35	8	25	25	0	SKOR1,stop_gained,p.Glu835Ter,ENST00000554240,;SKOR1,stop_gained,p.Glu846Ter,ENST00000554054,;SKOR1,stop_gained,p.Glu874Ter,ENST00000380035,;SKOR1,stop_gained,p.Glu777Ter,ENST00000341418,;SKOR1,stop_gained,p.Glu830Ter,ENST00000389002,;RP11-34F13.2,downstream_gene_variant,,ENST00000502156,;RP11-34F13.3,upstream_gene_variant,,ENST00000558889,;RP11-34F13.3,upstream_gene_variant,,ENST00000560577,;	T	ENSG00000188779	ENST00000341418	Transcript	stop_gained	2329	2329	777	E/*	Gag/Tag	rs780493275,COSM258014,COSM1517615	.	.	1	SKOR1	HGNC	21326	protein_coding	YES	CCDS58374.1	ENSP00000343200	SKOR1_HUMAN	.	UPI00001987EE	.	.	.	12/15	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10005,hmmpanther:PTHR10005:SF8	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATGGAGCTC	.	5	ESCA
TSC2	0	.	GRCh37	16	2126084	2126084	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2655C>T	p.%3D	p.I885I	ENST00000219476	24/42	162	144	18	147	147	0	TSC2,synonymous_variant,p.%3D,ENST00000439673,;TSC2,synonymous_variant,p.%3D,ENST00000219476,;TSC2,synonymous_variant,p.%3D,ENST00000568454,;TSC2,synonymous_variant,p.%3D,ENST00000401874,;TSC2,synonymous_variant,p.%3D,ENST00000353929,;TSC2,synonymous_variant,p.%3D,ENST00000350773,;TSC2,synonymous_variant,p.%3D,ENST00000382538,;TSC2,downstream_gene_variant,,ENST00000562474,;TSC2,upstream_gene_variant,,ENST00000568366,;TSC2,3_prime_UTR_variant,,ENST00000439117,;TSC2,downstream_gene_variant,,ENST00000568566,;TSC2,downstream_gene_variant,,ENST00000563346,;TSC2,upstream_gene_variant,,ENST00000483020,;TSC2,upstream_gene_variant,,ENST00000561695,;TSC2,downstream_gene_variant,,ENST00000488675,;TSC2,upstream_gene_variant,,ENST00000497886,;TSC2,downstream_gene_variant,,ENST00000463808,;TSC2,upstream_gene_variant,,ENST00000471143,;	T	ENSG00000103197	ENST00000219476	Transcript	synonymous_variant	3285	2655	885	I	atC/atT	COSM4059153,COSM4059154	.	.	1	TSC2	HGNC	12363	protein_coding	YES	CCDS10458.1	ENSP00000219476	TSC2_HUMAN	.	UPI000013C781	.	.	.	24/42	.	hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF1,Pfam_domain:PF03542,Prints_domain:PR01431	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACATCGTGTG	.	4	ESCA
NTN3	0	.	GRCh37	16	2521982	2521982	+	Missense_Mutation	SNP	C	C	T	rs749265175	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280C>T	p.Arg94Cys	p.R94C	ENST00000293973	1/6	55	44	11	49	49	0	NTN3,missense_variant,p.Arg94Cys,ENST00000293973,;TBC1D24,upstream_gene_variant,,ENST00000293970,;TBC1D24,upstream_gene_variant,,ENST00000567020,;RP11-715J22.2,upstream_gene_variant,,ENST00000563775,;RP11-715J22.6,upstream_gene_variant,,ENST00000561847,;	T	ENSG00000162068	ENST00000293973	Transcript	missense_variant	483	280	94	R/C	Cgc/Tgc	rs749265175	.	.	1	NTN3	HGNC	8030	protein_coding	YES	CCDS10469.1	ENSP00000293973	NET3_HUMAN	.	UPI000006ED30	.	deleterious(0.01)	possibly_damaging(0.904)	1/6	.	PROSITE_profiles:PS51117,hmmpanther:PTHR10574,Pfam_domain:PF00055,SMART_domains:SM00136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGCGCTCG	byFrequency	5	ESCA
PDPK1	0	.	GRCh37	16	2647916	2647916	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*148A>T	.	.	ENST00000342085	14/14	57	30	27	32	32	0	PDPK1,3_prime_UTR_variant,,ENST00000441549,;PDPK1,3_prime_UTR_variant,,ENST00000389224,;PDPK1,3_prime_UTR_variant,,ENST00000342085,;PDPK1,3_prime_UTR_variant,,ENST00000268673,;PDPK1,downstream_gene_variant,,ENST00000354836,;CTD-3126B10.1,non_coding_transcript_exon_variant,,ENST00000562166,;PDPK1,upstream_gene_variant,,ENST00000561962,;PDPK1,upstream_gene_variant,,ENST00000569721,;	T	ENSG00000140992	ENST00000342085	Transcript	3_prime_UTR_variant	1968	.	.	.	.	.	.	.	1	PDPK1	HGNC	8816	protein_coding	YES	CCDS10472.1	ENSP00000344220	PDPK1_HUMAN	Q9UPJ8_HUMAN,Q9UPJ7_HUMAN,H3BQ10_HUMAN,E9PER6_HUMAN	UPI00001314D4	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAAAAGAAG	.	5	ESCA
ZNF267	0	.	GRCh37	16	31927357	31927357	+	Missense_Mutation	SNP	G	G	A	rs757192362	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1787G>A	p.Arg596Gln	p.R596Q	ENST00000300870	4/4	33	20	13	40	40	0	ZNF267,missense_variant,p.Arg596Gln,ENST00000300870,;ZNF267,downstream_gene_variant,,ENST00000394846,;ZNF267,downstream_gene_variant,,ENST00000562971,;ZNF267,non_coding_transcript_exon_variant,,ENST00000575471,;ZNF267,downstream_gene_variant,,ENST00000561814,;ZNF267,downstream_gene_variant,,ENST00000566541,;	A	ENSG00000185947	ENST00000300870	Transcript	missense_variant	1996	1787	596	R/Q	cGa/cAa	rs757192362,COSM278276	.	.	1	ZNF267	HGNC	13060	protein_coding	YES	CCDS32440.1	ENSP00000300870	ZN267_HUMAN	H3BPW2_HUMAN	UPI000045696F	.	tolerated(0.3)	possibly_damaging(0.756)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF184,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R596Q|c.1787G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGCGAACTC	byFrequency	5	ESCA
PMP22	0	.	GRCh37	17	15134264	15134264	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453C>A	p.%3D	p.V151V	ENST00000395938	5/5	37	23	14	31	31	0	PMP22,missense_variant,p.His92Asn,ENST00000494511,;PMP22,synonymous_variant,p.%3D,ENST00000395938,;PMP22,synonymous_variant,p.%3D,ENST00000312280,;PMP22,3_prime_UTR_variant,,ENST00000395936,;PMP22,downstream_gene_variant,,ENST00000580584,;	T	ENSG00000109099	ENST00000395938	Transcript	synonymous_variant	648	453	151	V	gtC/gtA	.	.	.	-1	PMP22	HGNC	9118	protein_coding	YES	CCDS11168.1	ENSP00000379269	PMP22_HUMAN	Q6FH25_HUMAN,B4DUL1_HUMAN	UPI0000131C8E	.	.	.	5/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF7,Pfam_domain:PF00822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATGACACC	.	5	ESCA
IGF2BP1	0	.	GRCh37	17	47131354	47131354	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4548G>T	.	.	ENST00000290341	15/15	75	55	20	62	62	0	IGF2BP1,3_prime_UTR_variant,,ENST00000290341,;IGF2BP1,downstream_gene_variant,,ENST00000431824,;AC105030.1,downstream_gene_variant,,ENST00000578722,;	T	ENSG00000159217	ENST00000290341	Transcript	3_prime_UTR_variant	6616	.	.	.	.	.	.	.	1	IGF2BP1	HGNC	28866	protein_coding	YES	CCDS11543.1	ENSP00000290341	IF2B1_HUMAN	D3DTW3_HUMAN	UPI0000117170	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAAAGCCATT	.	5	ESCA
NXPH3	0	.	GRCh37	17	47656098	47656098	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.195C>T	p.%3D	p.L65L	ENST00000328741	2/2	87	66	21	89	89	0	NXPH3,synonymous_variant,p.%3D,ENST00000513748,;NXPH3,synonymous_variant,p.%3D,ENST00000328741,;RP5-1029K10.4,upstream_gene_variant,,ENST00000503624,;RP5-1029K10.2,upstream_gene_variant,,ENST00000514506,;NXPH3,non_coding_transcript_exon_variant,,ENST00000570453,;	T	ENSG00000182575	ENST00000328741	Transcript	synonymous_variant	557	195	65	L	ctC/ctT	.	.	.	1	NXPH3	HGNC	8077	protein_coding	YES	CCDS11550.1	ENSP00000329295	NXPH3_HUMAN	.	UPI00000389F1	.	.	.	2/2	.	hmmpanther:PTHR17103:SF12,hmmpanther:PTHR17103,Pfam_domain:PF06312,PIRSF_domain:PIRSF038019	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTCCTAGG	.	5	ESCA
SDK2	0	.	GRCh37	17	71375666	71375666	+	Nonsense_Mutation	SNP	G	G	C	rs141328074	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4785C>G	p.Tyr1595Ter	p.Y1595*	ENST00000392650	35/45	74	49	24	31	31	0	SDK2,stop_gained,p.Tyr752Ter,ENST00000424778,;SDK2,stop_gained,p.Tyr1576Ter,ENST00000388726,;SDK2,stop_gained,p.Tyr1595Ter,ENST00000392650,;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,;	C	ENSG00000069188	ENST00000392650	Transcript	stop_gained	4786	4785	1595	Y/*	taC/taG	rs141328074,COSM983865	.	.	-1	SDK2	HGNC	19308	protein_coding	YES	CCDS45769.1	ENSP00000376421	SDK2_HUMAN	.	UPI0000E5A088	.	.	.	35/45	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF37,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTCGTACCG	byCluster	5	ESCA
RHBDF2	0	.	GRCh37	17	74467981	74467981	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2305G>A	p.Asp769Asn	p.D769N	ENST00000313080	19/19	89	64	24	41	41	0	RHBDF2,missense_variant,p.Asp740Asn,ENST00000591885,;RHBDF2,missense_variant,p.Asp740Asn,ENST00000389760,;RHBDF2,missense_variant,p.Asp769Asn,ENST00000313080,;RHBDF2,3_prime_UTR_variant,,ENST00000591860,;AANAT,downstream_gene_variant,,ENST00000250615,;AANAT,downstream_gene_variant,,ENST00000585649,;AANAT,downstream_gene_variant,,ENST00000392492,;RHBDF2,non_coding_transcript_exon_variant,,ENST00000590168,;AANAT,downstream_gene_variant,,ENST00000587798,;RHBDF2,downstream_gene_variant,,ENST00000589582,;RHBDF2,downstream_gene_variant,,ENST00000587640,;	T	ENSG00000129667	ENST00000313080	Transcript	missense_variant	2579	2305	769	D/N	Gac/Aac	.	.	.	-1	RHBDF2	HGNC	20788	protein_coding	YES	CCDS32743.1	ENSP00000322775	RHDF2_HUMAN	K7EQT5_HUMAN,K7EPV3_HUMAN,K7ELA9_HUMAN,K7EJ10_HUMAN	UPI0000DBEF0D	.	deleterious(0.01)	probably_damaging(0.954)	19/19	.	hmmpanther:PTHR22936,hmmpanther:PTHR22936:SF10,Pfam_domain:PF01694,Gene3D:2xovA00,Superfamily_domains:SSF144091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTCGATCC	.	5	ESCA
TP53	0	.	GRCh37	17	7577566	7577568	+	In_Frame_Del	DEL	TAC	TAC	-	.	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	TAC	TAC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.713_715delGTA	p.Cys238_Asn239delinsTyr	p.C238_N239delinsY	ENST00000269305	7/11	89	26	63	66	66	0	TP53,inframe_deletion,p.Cys238_Asn239delinsTyr,ENST00000413465,;TP53,inframe_deletion,p.Cys238_Asn239delinsTyr,ENST00000420246,;TP53,inframe_deletion,p.Cys238_Asn239delinsTyr,ENST00000269305,;TP53,inframe_deletion,p.Cys106_Asn107delinsTyr,ENST00000509690,;TP53,inframe_deletion,p.Cys238_Asn239delinsTyr,ENST00000359597,;TP53,inframe_deletion,p.Cys145_Asn146delinsTyr,ENST00000514944,;TP53,inframe_deletion,p.Cys238_Asn239delinsTyr,ENST00000445888,;TP53,inframe_deletion,p.Cys238_Asn239delinsTyr,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	-	ENSG00000141510	ENST00000269305	Transcript	inframe_deletion	903-905	713-715	238-239	CN/Y	tGTAac/tac	TP53_g.13350_13352del	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.N239_C242delNSSC|c.715_726del12|3,CODON|p.S240C|c.718A>T|3,CODON|p.S240G|c.718A>G|16,CODON|p.N239K|c.717C>G|5,CODON|p.N146S|c.437A>G|6,CODON|p.N239T|c.716A>C|6,CODON|p.N239S|c.716A>G|3,CODON|p.N239S|c.716A>G|6,CODON|p.N239S|c.716A>G|4,CODON|p.N239S|c.716A>G|25,CODON|p.N239S|c.716A>G|5,CODON|p.N239D|c.715A>G|11,CODON|p.N239D|c.715A>G|13,CODON|p.N239D|c.715A>G|44,CODON|p.N146D|c.436A>G|14,CODON|p.N239Y|c.715A>T|6,CODON|p.N239D|c.715A>G|14,CODON|p.N239fs*1|c.714_715insT|3,CODON|p.N239fs*25|c.714_715insN|12,CODON|p.N239fs*1|c.714_715insT|4,CODON|p.N239fs*1|c.714_715insT|3,CODON|p.N146fs*1|c.435_436insT|3,CODON|p.C238*|c.714T>A|4,CODON|p.C238W|c.714T>G|3,BUFFER|p.M243L|c.727A>C|4,BUFFER|p.M243V|c.727A>G|3,BUFFER|p.M243L|c.727A>T|6,BUFFER|p.C242W|c.726C>G|3,BUFFER|p.C242*|c.726C>A|3,BUFFER|p.C242W|c.726C>G|3,BUFFER|p.C242W|c.726C>G|9,BUFFER|p.C149W|c.447C>G|3,BUFFER|p.C242S|c.725G>C|3,BUFFER|p.C242Y|c.725G>A|4,BUFFER|p.C242S|c.725G>C|4,BUFFER|p.C242Y|c.725G>A|42,BUFFER|p.C242Y|c.725G>A|4,BUFFER|p.C242F|c.725G>T|11,BUFFER|p.C149Y|c.446G>A|4,BUFFER|p.C242F|c.725G>T|11,BUFFER|p.C242S|c.725G>C|3,BUFFER|p.C242F|c.725G>T|71,BUFFER|p.C149S|c.446G>C|4,BUFFER|p.C149F|c.446G>T|11,BUFFER|p.C242F|c.725G>T|4,BUFFER|p.C242S|c.725G>C|20,BUFFER|p.C242S|c.725G>C|4,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.C149fs*5|c.444delC|5,BUFFER|p.C242fs*5|c.723delC|12,BUFFER|p.S241delS|c.721_723delTCC|3,BUFFER|p.C242fs*5|c.723delC|5,BUFFER|p.S241F|c.722_723CC>TT|5,BUFFER|p.C242G|c.724T>G|6,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C149G|c.445T>G|3,BUFFER|p.C242S|c.724T>A|11,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242G|c.724T>G|3,BUFFER|p.C242R|c.724T>C|12,BUFFER|p.C242fs*5|c.722delC|6,BUFFER|p.S241fs*6|c.721delT|9,BUFFER|p.S148F|c.443C>T|15,BUFFER|p.S241Y|c.722C>A|4,BUFFER|p.S241Y|c.722C>A|15,BUFFER|p.S241C|c.722C>G|28,BUFFER|p.S241C|c.722C>G|3,BUFFER|p.S148Y|c.443C>A|5,BUFFER|p.S241F|c.722C>T|15,BUFFER|p.S241F|c.722C>T|6,BUFFER|p.S241F|c.722C>T|83,BUFFER|p.S241C|c.722C>G|4,BUFFER|p.S241Y|c.722C>A|4,BUFFER|p.S241Y|c.722C>A|5,BUFFER|p.S241Y|c.722C>A|5,BUFFER|p.S148C|c.443C>G|4,BUFFER|p.S241F|c.722C>T|9,BUFFER|p.S241F|c.722C>T|14,BUFFER|p.S241T|c.721T>A|6,BUFFER|p.S241A|c.721T>G|10,BUFFER|p.S241P|c.721T>C|5,BUFFER|p.S240R|c.720T>A|4,BUFFER|p.S240R|c.720T>G|4,BUFFER|p.S240S|c.720T>C|3,BUFFER|p.S240I|c.719G>T|6,BUFFER|p.C238Y|c.713G>A|7,BUFFER|p.C238F|c.713G>T|12,BUFFER|p.C145F|c.434G>T|12,BUFFER|p.C238Y|c.713G>A|16,BUFFER|p.C238F|c.713G>T|11,BUFFER|p.C238Y|c.713G>A|15,BUFFER|p.C238Y|c.713G>A|65,BUFFER|p.C238F|c.713G>T|42,BUFFER|p.C238Y|c.713G>A|9,BUFFER|p.C238F|c.713G>T|6,BUFFER|p.C145Y|c.434G>A|16,BUFFER|p.C238F|c.713G>T|6,BUFFER|p.C238S|c.713G>C|8,BUFFER|p.C238G|c.712T>G|3,BUFFER|p.C145G|c.433T>G|3,BUFFER|p.C238G|c.712T>G|4,BUFFER|p.C238R|c.712T>C|17,BUFFER|p.C238G|c.712T>G|3,BUFFER|p.C238S|c.712T>A|12,BUFFER|p.M237I|c.711G>A|15,BUFFER|p.M237I|c.711G>T|7,BUFFER|p.M237I|c.711G>C|9,BUFFER|p.M237I|c.711G>A|78,BUFFER|p.M237I|c.711G>T|3,BUFFER|p.M237I|c.711G>A|10,BUFFER|p.M237I|c.711G>T|31,BUFFER|p.M144I|c.432G>T|7,BUFFER|p.M237I|c.711G>A|15,BUFFER|p.M237I|c.711G>T|6,BUFFER|p.M237I|c.711G>T|7,BUFFER|p.M144I|c.432G>A|15,BUFFER|p.M237I|c.711G>A|9,BUFFER|p.M237K|c.710T>A|9,BUFFER|p.M237R|c.710T>G|3,BUFFER|p.M237T|c.710T>C|3,BUFFER|p.M144T|c.431T>C|3,BUFFER|p.M237T|c.710T>C|3,BUFFER|p.M237T|c.710T>C|5,BUFFER|p.M144V|c.430A>G|3,BUFFER|p.M237V|c.709A>G|3,BUFFER|p.M237V|c.709A>G|3,BUFFER|p.M237L|c.709A>T|4,BUFFER|p.M237V|c.709A>G|10,BUFFER|p.Y236delY|c.706_708delTAC|4,BUFFER|p.Y236*|c.708C>G|3,BUFFER|p.Y143*|c.429C>A|4,BUFFER|p.Y236*|c.708C>A|4,BUFFER|p.Y236*|c.708C>A|4,BUFFER|p.Y236*|c.708C>A|11,BUFFER|p.Y236C|c.707A>G|5,BUFFER|p.Y236C|c.707A>G|4,BUFFER|p.Y236C|c.707A>G|11,BUFFER|p.Y236C|c.707A>G|55,BUFFER|p.Y143C|c.428A>G|12,BUFFER|p.Y236C|c.707A>G|11,BUFFER|p.Y236S|c.707A>C|4,BUFFER|p.Y236N|c.706T>A|3,BUFFER|p.Y236N|c.706T>A|16,BUFFER|p.Y236D|c.706T>G|7,BUFFER|p.Y236H|c.706T>C|10,BUFFER|p.Y143N|c.427T>A|3,BUFFER|p.Y236N|c.706T>A|3,BUFFER|p.N235T|c.704A>C|3,BUFFER|p.N235I|c.704A>T|4,BUFFER|p.N235S|c.704A>G|15,BUFFER|p.N235D|c.703A>G|7,BUFFER|p.Y234delY|c.700_702delTAC|3,BUFFER|p.Y234*|c.702C>A|4	INDELOCATOR*|VARSCANI*|PINDEL	AACTGTTACACATG	.	3	ESCA
EFNB3	0	.	GRCh37	17	7614656	7614656	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1762C>A	.	.	ENST00000226091	5/5	39	29	10	22	22	0	EFNB3,3_prime_UTR_variant,,ENST00000226091,;	A	ENSG00000108947	ENST00000226091	Transcript	3_prime_UTR_variant	3182	.	.	.	.	.	.	.	1	EFNB3	HGNC	3228	protein_coding	YES	CCDS11120.1	ENSP00000226091	EFNB3_HUMAN	.	UPI000000DA07	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAAACCAAAAA	.	4	ESCA
ASPSCR1	0	.	GRCh37	17	79974398	79974398	+	Missense_Mutation	SNP	C	C	T	rs575908489	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1682C>T	p.Pro561Leu	p.P561L	ENST00000306729	14/17	48	32	15	39	39	0	ASPSCR1,missense_variant,p.Pro74Leu,ENST00000583744,;ASPSCR1,missense_variant,p.Pro467Leu,ENST00000306739,;ASPSCR1,missense_variant,p.Pro415Leu,ENST00000580534,;ASPSCR1,missense_variant,p.Pro296Leu,ENST00000582355,;ASPSCR1,missense_variant,p.Pro561Leu,ENST00000306729,;STRA13,downstream_gene_variant,,ENST00000392359,;STRA13,downstream_gene_variant,,ENST00000580435,;STRA13,downstream_gene_variant,,ENST00000579520,;STRA13,downstream_gene_variant,,ENST00000306704,;STRA13,downstream_gene_variant,,ENST00000584347,;STRA13,downstream_gene_variant,,ENST00000584600,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000583142,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000582404,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000585140,;STRA13,downstream_gene_variant,,ENST00000583767,;STRA13,downstream_gene_variant,,ENST00000584514,;STRA13,downstream_gene_variant,,ENST00000580090,;STRA13,downstream_gene_variant,,ENST00000577379,;ASPSCR1,synonymous_variant,p.%3D,ENST00000584454,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000585274,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000577733,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000583693,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000578236,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000581608,;ASPSCR1,non_coding_transcript_exon_variant,,ENST00000578361,;STRA13,downstream_gene_variant,,ENST00000585091,;	T	ENSG00000169696	ENST00000306729	Transcript	missense_variant	1779	1682	561	P/L	cCg/cTg	rs575908489	.	.	1	ASPSCR1	HGNC	13825	protein_coding	YES	CCDS58611.1	ENSP00000306625	ASPC1_HUMAN	.	UPI000007263D	.	tolerated(0.07)	probably_damaging(0.96)	14/17	.	hmmpanther:PTHR23153:SF33,hmmpanther:PTHR23153	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGCCGGCAG	byFrequency|by1000G	5	ESCA
OR10H1	0	.	GRCh37	19	15918306	15918306	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542T>C	p.Val181Ala	p.V181A	ENST00000334920	1/1	177	164	13	133	133	0	OR10H1,missense_variant,p.Val181Ala,ENST00000334920,;	G	ENSG00000186723	ENST00000334920	Transcript	missense_variant	631	542	181	V/A	gTg/gCg	.	.	.	-1	OR10H1	HGNC	8172	protein_coding	YES	CCDS12335.1	ENSP00000335596	O10H1_HUMAN	.	UPI000004CA3D	.	deleterious(0.04)	benign(0.042)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF85,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGCACATGG	.	2	ESCA
ZNF506	0	.	GRCh37	19	19905342	19905342	+	3'UTR	SNP	G	G	A	rs547531723,rs780916362	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*19C>T	.	.	ENST00000443905	4/5	41	36	5	32	32	0	ZNF506,3_prime_UTR_variant,,ENST00000443905,;ZNF506,intron_variant,,ENST00000590766,;ZNF506,intron_variant,,ENST00000587461,;ZNF506,downstream_gene_variant,,ENST00000450683,;ZNF506,downstream_gene_variant,,ENST00000590319,;ZNF506,downstream_gene_variant,,ENST00000587452,;ZNF506,downstream_gene_variant,,ENST00000540806,;ZNF506,downstream_gene_variant,,ENST00000545006,;CTC-559E9.4,intron_variant,,ENST00000590274,;CTC-559E9.6,intron_variant,,ENST00000591884,;CTC-559E9.6,intron_variant,,ENST00000589657,;CTC-559E9.5,upstream_gene_variant,,ENST00000590697,;ZNF506,3_prime_UTR_variant,,ENST00000591639,;ZNF506,intron_variant,,ENST00000586260,;ZNF506,downstream_gene_variant,,ENST00000587822,;	A	ENSG00000081665	ENST00000443905	Transcript	3_prime_UTR_variant	1502	.	.	.	.	rs547531723,rs780916362	.	.	-1	ZNF506	HGNC	23780	protein_coding	YES	CCDS42531.1	ENSP00000393835	ZN506_HUMAN	K7ERD0_HUMAN	UPI00001B6472	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATACGGTTTC	byFrequency|byCluster	2	ESCA
ZNF431	0	.	GRCh37	19	21366096	21366096	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990C>T	p.%3D	p.T330T	ENST00000311048	5/5	44	36	7	54	54	0	ZNF431,synonymous_variant,p.%3D,ENST00000311048,;ZNF431,3_prime_UTR_variant,,ENST00000600692,;ZNF431,intron_variant,,ENST00000594425,;ZNF431,downstream_gene_variant,,ENST00000598331,;ZNF431,downstream_gene_variant,,ENST00000599296,;ZNF431,upstream_gene_variant,,ENST00000594821,;ZNF431,upstream_gene_variant,,ENST00000593426,;	T	ENSG00000196705	ENST00000311048	Transcript	synonymous_variant	1134	990	330	T	acC/acT	.	.	.	1	ZNF431	HGNC	20809	protein_coding	YES	CCDS32979.1	ENSP00000308578	ZN431_HUMAN	.	UPI0000191EAC	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF118,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAACCCTTAG	.	5	ESCA
ZNF77	0	.	GRCh37	19	2934253	2934253	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.872C>T	p.Thr291Ile	p.T291I	ENST00000314531	4/4	78	47	31	72	72	0	ZNF77,missense_variant,p.Thr291Ile,ENST00000314531,;	A	ENSG00000175691	ENST00000314531	Transcript	missense_variant	965	872	291	T/I	aCt/aTt	.	.	.	-1	ZNF77	HGNC	13150	protein_coding	YES	CCDS12099.1	ENSP00000319053	ZNF77_HUMAN	.	UPI0000160564	.	deleterious(0)	possibly_damaging(0.848)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF51,hmmpanther:PTHR24381,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCCAGTGTGT	.	3	ESCA
S1PR4	0	.	GRCh37	19	3180212	3180212	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*267C>T	.	.	ENST00000246115	1/1	61	52	9	44	44	0	S1PR4,3_prime_UTR_variant,,ENST00000246115,;S1PR4,downstream_gene_variant,,ENST00000591346,;	T	ENSG00000125910	ENST00000246115	Transcript	3_prime_UTR_variant	1477	.	.	.	.	.	.	.	1	S1PR4	HGNC	3170	protein_coding	YES	CCDS12105.1	ENSP00000246115	S1PR4_HUMAN	.	UPI0000050462	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCCCGCTTC	.	5	ESCA
SPTBN4	0	.	GRCh37	19	41071628	41071628	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6116G>A	p.Arg2039His	p.R2039H	ENST00000352632	29/36	110	104	5	86	86	0	SPTBN4,missense_variant,p.Arg2039His,ENST00000338932,;SPTBN4,missense_variant,p.Arg2039His,ENST00000352632,;SPTBN4,missense_variant,p.Arg2039His,ENST00000598249,;SPTBN4,missense_variant,p.Arg782His,ENST00000392025,;SPTBN4,downstream_gene_variant,,ENST00000392023,;SPTBN4,3_prime_UTR_variant,,ENST00000597389,;	A	ENSG00000160460	ENST00000352632	Transcript	missense_variant	6202	6116	2039	R/H	cGc/cAc	.	.	.	1	SPTBN4	HGNC	14896	protein_coding	YES	CCDS12559.1	ENSP00000263373	SPTN4_HUMAN	.	UPI0000135DBB	.	tolerated(0.07)	possibly_damaging(0.823)	29/36	.	hmmpanther:PTHR11915:SF232,hmmpanther:PTHR11915,Pfam_domain:PF00435,Gene3D:1.20.58.60,PIRSF_domain:PIRSF002297,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGACCGCCATT	.	2	ESCA
C19orf54	0	.	GRCh37	19	41248108	41248108	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*230C>G	.	.	ENST00000378313	6/6	42	25	17	21	21	0	C19orf54,3_prime_UTR_variant,,ENST00000470681,;C19orf54,3_prime_UTR_variant,,ENST00000378313,;C19orf54,intron_variant,,ENST00000596940,;C19orf54,intron_variant,,ENST00000598352,;C19orf54,intron_variant,,ENST00000598485,;C19orf54,intron_variant,,ENST00000339153,;ITPKC,downstream_gene_variant,,ENST00000263370,;C19orf54,downstream_gene_variant,,ENST00000598729,;C19orf54,downstream_gene_variant,,ENST00000600139,;C19orf54,upstream_gene_variant,,ENST00000594163,;C19orf54,intron_variant,,ENST00000469741,;C19orf54,intron_variant,,ENST00000597507,;C19orf54,intron_variant,,ENST00000596809,;ITPKC,downstream_gene_variant,,ENST00000597003,;	C	ENSG00000188493	ENST00000378313	Transcript	3_prime_UTR_variant	1406	.	.	.	.	.	.	.	-1	C19orf54	HGNC	24758	protein_coding	YES	CCDS12564.2	ENSP00000367564	CS054_HUMAN	.	UPI00001B64AB	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACAGACGAT	.	5	ESCA
CTB-60B18.6	0	.	GRCh37	19	49540113	49540113	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-358C>T	.	.	ENST00000591656	1/3	59	40	19	48	48	0	CTB-60B18.6,5_prime_UTR_variant,,ENST00000591656,;CTB-60B18.6,5_prime_UTR_variant,,ENST00000604577,;CGB1,5_prime_UTR_variant,,ENST00000601167,;CGB1,intron_variant,,ENST00000391869,;CGB1,upstream_gene_variant,,ENST00000301407,;CGB2,downstream_gene_variant,,ENST00000359342,;CGB2,downstream_gene_variant,,ENST00000474913,;NTF6B,downstream_gene_variant,,ENST00000591913,;	A	ENSG00000267335	ENST00000591656	Transcript	5_prime_UTR_variant	40	.	.	.	.	.	.	.	-1	CTB-60B18.6	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000466140	.	K7ELM3_HUMAN	UPI0002840D0E	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTGGCTGCT	.	5	ESCA
CTB-60B18.6	0	.	GRCh37	19	49540114	49540114	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-359G>T	.	.	ENST00000591656	1/3	59	40	19	46	46	0	CTB-60B18.6,5_prime_UTR_variant,,ENST00000591656,;CTB-60B18.6,5_prime_UTR_variant,,ENST00000604577,;CGB1,5_prime_UTR_variant,,ENST00000601167,;CGB1,intron_variant,,ENST00000391869,;CGB1,upstream_gene_variant,,ENST00000301407,;CGB2,downstream_gene_variant,,ENST00000359342,;CGB2,downstream_gene_variant,,ENST00000474913,;NTF6B,downstream_gene_variant,,ENST00000591913,;	A	ENSG00000267335	ENST00000591656	Transcript	5_prime_UTR_variant	39	.	.	.	.	.	.	.	-1	CTB-60B18.6	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000466140	.	K7ELM3_HUMAN	UPI0002840D0E	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGGCTGCTC	.	5	ESCA
KLK12	0	.	GRCh37	19	51532406	51532406	+	3'Flank	SNP	G	G	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000250351	.	54	47	6	45	45	0	KLK12,3_prime_UTR_variant,,ENST00000525263,;KLK12,3_prime_UTR_variant,,ENST00000250352,;KLK12,3_prime_UTR_variant,,ENST00000529888,;KLK12,3_prime_UTR_variant,,ENST00000319590,;KLK11,upstream_gene_variant,,ENST00000319720,;KLK11,upstream_gene_variant,,ENST00000453757,;KLK11,upstream_gene_variant,,ENST00000600362,;KLK11,upstream_gene_variant,,ENST00000594768,;KLK11,upstream_gene_variant,,ENST00000601671,;KLK12,downstream_gene_variant,,ENST00000250351,;KLK11,upstream_gene_variant,,ENST00000593681,;KLK11,upstream_gene_variant,,ENST00000391804,;KLK11,upstream_gene_variant,,ENST00000598799,;CTC-518B2.9,upstream_gene_variant,,ENST00000594910,;KLK11,upstream_gene_variant,,ENST00000594458,;KLK12,3_prime_UTR_variant,,ENST00000530943,;KLK12,3_prime_UTR_variant,,ENST00000531374,;KLK12,3_prime_UTR_variant,,ENST00000526824,;KLK11,upstream_gene_variant,,ENST00000594827,;KLK11,upstream_gene_variant,,ENST00000319756,;	T	ENSG00000186474	ENST00000250351	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	5	-1	KLK12	HGNC	6360	protein_coding	YES	CCDS12820.1	ENSP00000250351	KLK12_HUMAN	.	UPI000002ACDD	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCGTGGGTCT	.	4	ESCA
SPACA6P-AS	0	.	GRCh37	19	52195906	52195906	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.804T>C	.	.	ENST00000602324	1/2	188	142	46	147	146	0	SPACA6P-AS,non_coding_transcript_exon_variant,,ENST00000602324,;MIR99B,non_coding_transcript_exon_variant,,ENST00000384819,;MIRLET7E,upstream_gene_variant,,ENST00000362102,;SPACA6P,upstream_gene_variant,,ENST00000576093,;SPACA6P,upstream_gene_variant,,ENST00000573266,;MIR125A,upstream_gene_variant,,ENST00000385273,;SPACA6P,upstream_gene_variant,,ENST00000574072,;SPACA6P,upstream_gene_variant,,ENST00000576494,;SPACA6P,upstream_gene_variant,,ENST00000571328,;AC018755.2,upstream_gene_variant,,ENST00000331594,;	G	ENSG00000269959	ENST00000602324	Transcript	non_coding_transcript_exon_variant	804	.	.	.	.	.	.	.	-1	SPACA6P-AS	HGNC	49383	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCACACAA	.	5	ESCA
ZNF701	0	.	GRCh37	19	53086053	53086053	+	Silent	SNP	A	A	T	rs183892700	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.939A>T	p.%3D	p.V313V	ENST00000540331	5/5	110	94	15	72	72	0	ZNF701,synonymous_variant,p.%3D,ENST00000540331,;ZNF701,synonymous_variant,p.%3D,ENST00000391785,;ZNF701,synonymous_variant,p.%3D,ENST00000301093,;ZNF701,downstream_gene_variant,,ENST00000593941,;ZNF701,downstream_gene_variant,,ENST00000596514,;CTD-3099C6.7,intron_variant,,ENST00000599222,;	T	ENSG00000167562	ENST00000540331	Transcript	synonymous_variant	1164	939	313	V	gtA/gtT	rs183892700	.	.	1	ZNF701	HGNC	25597	protein_coding	YES	CCDS54311.1	ENSP00000444339	.	M0R085_HUMAN,F5GZM6_HUMAN	UPI0001C53D22	.	.	.	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,hmmpanther:PTHR24407:SF12,hmmpanther:PTHR24407,PROSITE_profiles:PS50157	G:0.0004	G:0.0015	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATGTATGCGG	byFrequency|byCluster|by1000G	4	ESCA
ZNF415	0	.	GRCh37	19	53619598	53619598	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.104T>C	p.Met35Thr	p.M35T	ENST00000500065	3/4	97	82	15	63	63	0	ZNF415,missense_variant,p.Met35Thr,ENST00000595813,;ZNF415,missense_variant,p.Met35Thr,ENST00000600574,;ZNF415,missense_variant,p.Met35Thr,ENST00000601110,;ZNF415,missense_variant,p.Met35Thr,ENST00000500065,;ZNF415,missense_variant,p.Met35Thr,ENST00000243643,;ZNF415,missense_variant,p.Met35Thr,ENST00000594011,;ZNF415,missense_variant,p.Met35Thr,ENST00000597503,;ZNF415,missense_variant,p.Met35Thr,ENST00000595193,;ZNF415,missense_variant,p.Met35Thr,ENST00000599261,;ZNF415,missense_variant,p.Met81Thr,ENST00000595174,;ZNF415,missense_variant,p.Met35Thr,ENST00000597748,;ZNF415,synonymous_variant,p.%3D,ENST00000455735,;ZNF415,synonymous_variant,p.%3D,ENST00000448501,;ZNF415,synonymous_variant,p.%3D,ENST00000421033,;ZNF415,5_prime_UTR_variant,,ENST00000440291,;ZNF415,intron_variant,,ENST00000601215,;ZNF415,intron_variant,,ENST00000601493,;ZNF415,downstream_gene_variant,,ENST00000596051,;ZNF415,non_coding_transcript_exon_variant,,ENST00000602110,;ZNF415,non_coding_transcript_exon_variant,,ENST00000596683,;ZNF415,non_coding_transcript_exon_variant,,ENST00000596106,;ZNF415,non_coding_transcript_exon_variant,,ENST00000594286,;ZNF415,intron_variant,,ENST00000595359,;ZNF415,intron_variant,,ENST00000602024,;ZNF415,missense_variant,p.Met35Thr,ENST00000600120,;ZNF415,missense_variant,p.Met35Thr,ENST00000598578,;ZNF415,missense_variant,p.Met35Thr,ENST00000598024,;ZNF415,3_prime_UTR_variant,,ENST00000597877,;ZNF415,non_coding_transcript_exon_variant,,ENST00000600098,;	G	ENSG00000170954	ENST00000500065	Transcript	missense_variant	438	104	35	M/T	aTg/aCg	.	.	.	-1	ZNF415	HGNC	20636	protein_coding	YES	CCDS54313.1	ENSP00000439435	ZN415_HUMAN	.	UPI0000E04BC1	.	deleterious(0)	benign(0.402)	3/4	.	Superfamily_domains:0044637,SMART_domains:SM00349,Pfam_domain:PF01352,hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAACATCACA	.	4	ESCA
NLRP11	0	.	GRCh37	19	56300637	56300637	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2642G>A	p.Cys881Tyr	p.C881Y	ENST00000443188	10/12	74	52	22	64	64	0	NLRP11,missense_variant,p.Cys881Tyr,ENST00000589093,;NLRP11,missense_variant,p.Cys782Tyr,ENST00000592953,;NLRP11,missense_variant,p.Cys827Tyr,ENST00000589824,;NLRP11,missense_variant,p.Cys827Tyr,ENST00000360133,;NLRP11,missense_variant,p.Cys881Tyr,ENST00000443188,;NLRP11,3_prime_UTR_variant,,ENST00000590409,;NLRP11,downstream_gene_variant,,ENST00000593244,;	T	ENSG00000179873	ENST00000443188	Transcript	missense_variant	3353	2642	881	C/Y	tGt/tAt	.	.	.	-1	NLRP11	HGNC	22945	protein_coding	YES	CCDS12935.1	ENSP00000409898	NAL11_HUMAN	K7ESF9_HUMAN	UPI000013ED9D	.	deleterious(0)	probably_damaging(0.987)	10/12	.	Superfamily_domains:SSF52047,SMART_domains:SM00368,Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF62	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCACATAGC	.	5	ESCA
PDE4DIP	0	.	GRCh37	1	144882552	144882552	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3467C>T	p.Ser1156Phe	p.S1156F	ENST00000369356	24/44	288	259	29	201	201	0	PDE4DIP,missense_variant,p.Ser1156Phe,ENST00000369354,;PDE4DIP,missense_variant,p.Ser1293Phe,ENST00000369359,;PDE4DIP,missense_variant,p.Ser1293Phe,ENST00000530740,;PDE4DIP,missense_variant,p.Ser51Phe,ENST00000530592,;PDE4DIP,missense_variant,p.Ser1156Phe,ENST00000369356,;PDE4DIP,intron_variant,,ENST00000313382,;RP4-791M13.5,downstream_gene_variant,,ENST00000531288,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000524974,;PDE4DIP,intron_variant,,ENST00000530062,;PDE4DIP,intron_variant,,ENST00000525886,;	A	ENSG00000178104	ENST00000369356	Transcript	missense_variant	3758	3467	1156	S/F	tCc/tTc	.	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	MYOME_HUMAN	I1VE15_HUMAN	UPI0000458A81	.	tolerated(0.49)	possibly_damaging(0.847)	24/44	.	hmmpanther:PTHR13895:SF2,hmmpanther:PTHR13895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGGGAACCA	.	4	ESCA
PTPRVP	0	.	GRCh37	1	202150797	202150797	+	Intron	SNP	G	G	A	rs150275149	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3128-1264G>A	.	.	ENST00000490225	.	119	101	18	84	84	0	PTPRVP,non_coding_transcript_exon_variant,,ENST00000482597,;PTPRVP,intron_variant,,ENST00000490225,;	A	ENSG00000243323	ENST00000490225	Transcript	intron_variant	.	.	.	.	.	rs150275149	.	.	1	PTPRVP	HGNC	13421	unitary_pseudogene	YES	.	.	.	.	.	.	.	.	.	13/28	.	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCGGTGTC	byFrequency|by1000G	5	ESCA
TAF1A	0	.	GRCh37	1	222753163	222753163	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343A>G	p.Met115Val	p.M115V	ENST00000350027	4/12	56	29	27	19	19	0	TAF1A,start_lost,p.Met1?,ENST00000391882,;TAF1A,start_lost,p.Met1?,ENST00000366890,;TAF1A,missense_variant,p.Met115Val,ENST00000352967,;TAF1A,missense_variant,p.Met115Val,ENST00000543857,;TAF1A,missense_variant,p.Met115Val,ENST00000350027,;TAF1A,intron_variant,,ENST00000391883,;TAF1A,non_coding_transcript_exon_variant,,ENST00000465263,;TAF1A,non_coding_transcript_exon_variant,,ENST00000487009,;	C	ENSG00000143498	ENST00000350027	Transcript	missense_variant	497	343	115	M/V	Atg/Gtg	.	.	.	-1	TAF1A	HGNC	11532	protein_coding	YES	CCDS1531.1	ENSP00000339976	TAF1A_HUMAN	.	UPI000006F49B	.	tolerated(1)	benign(0)	4/12	.	PIRSF_domain:PIRSF015161,Pfam_domain:PF14929,hmmpanther:PTHR32122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCATGTTGC	.	5	ESCA
RYR2	0	.	GRCh37	1	237801776	237801776	+	Silent	SNP	T	T	C	.	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6912T>C	p.%3D	p.F2304F	ENST00000366574	45/105	89	68	21	59	58	0	RYR2,synonymous_variant,p.%3D,ENST00000542537,;RYR2,synonymous_variant,p.%3D,ENST00000366574,;RYR2,synonymous_variant,p.%3D,ENST00000360064,;	C	ENSG00000198626	ENST00000366574	Transcript	synonymous_variant	7229	6912	2304	F	ttT/ttC	COSM679892	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	.	45/105	.	Pfam_domain:PF01365,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTTGCTGT	.	5	ESCA
PANK4	0	.	GRCh37	1	2441583	2441583	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1952G>T	p.Cys651Phe	p.C651F	ENST00000378466	17/19	56	36	20	41	41	0	PANK4,missense_variant,p.Cys612Phe,ENST00000435556,;PANK4,missense_variant,p.Cys651Phe,ENST00000378466,;PLCH2,downstream_gene_variant,,ENST00000419816,;PLCH2,downstream_gene_variant,,ENST00000278878,;PLCH2,downstream_gene_variant,,ENST00000449969,;PLCH2,downstream_gene_variant,,ENST00000378486,;PLCH2,downstream_gene_variant,,ENST00000378488,;PANK4,3_prime_UTR_variant,,ENST00000502512,;PANK4,3_prime_UTR_variant,,ENST00000505228,;PLCH2,downstream_gene_variant,,ENST00000343889,;PANK4,downstream_gene_variant,,ENST00000468002,;PANK4,downstream_gene_variant,,ENST00000487804,;PLCH2,downstream_gene_variant,,ENST00000462379,;PANK4,downstream_gene_variant,,ENST00000471361,;PANK4,downstream_gene_variant,,ENST00000515423,;PLCH2,downstream_gene_variant,,ENST00000473964,;	A	ENSG00000157881	ENST00000378466	Transcript	missense_variant	1965	1952	651	C/F	tGc/tTc	.	.	.	-1	PANK4	HGNC	19366	protein_coding	YES	CCDS42.1	ENSP00000367727	PANK4_HUMAN	.	UPI000000DA54	.	deleterious(0)	possibly_damaging(0.637)	17/19	.	hmmpanther:PTHR12280,Pfam_domain:PF01937,PIRSF_domain:PIRSF036939,Superfamily_domains:SSF111321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTGCACGCC	.	5	ESCA
SZT2	0	.	GRCh37	1	43916407	43916407	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*256C>T	.	.	ENST00000562955	71/71	24	20	4	16	16	0	SZT2,3_prime_UTR_variant,,ENST00000372442,;SZT2,3_prime_UTR_variant,,ENST00000562955,;HYI,downstream_gene_variant,,ENST00000487366,;HYI,downstream_gene_variant,,ENST00000372425,;HYI,downstream_gene_variant,,ENST00000486909,;HYI,downstream_gene_variant,,ENST00000583037,;HYI,downstream_gene_variant,,ENST00000372434,;HYI,downstream_gene_variant,,ENST00000372433,;HYI,downstream_gene_variant,,ENST00000470662,;HYI,downstream_gene_variant,,ENST00000372430,;HYI,downstream_gene_variant,,ENST00000372432,;HYI,downstream_gene_variant,,ENST00000372426,;SZT2-AS1,upstream_gene_variant,,ENST00000396885,;HYI-AS1,upstream_gene_variant,,ENST00000444386,;SZT2,non_coding_transcript_exon_variant,,ENST00000460536,;HYI,downstream_gene_variant,,ENST00000483618,;HYI,downstream_gene_variant,,ENST00000469587,;HYI,downstream_gene_variant,,ENST00000496142,;HYI,downstream_gene_variant,,ENST00000372427,;	T	ENSG00000198198	ENST00000562955	Transcript	3_prime_UTR_variant	10384	.	.	.	.	.	.	.	1	SZT2	HGNC	29040	protein_coding	YES	CCDS30694.2	ENSP00000457168	SZT2_HUMAN	.	UPI0001E24F46	.	.	.	71/71	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TTGGGCCCTTC	.	2	ESCA
TTLL7	0	.	GRCh37	1	84394840	84394840	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1121C>T	p.Ala374Val	p.A374V	ENST00000260505	10/21	94	67	27	77	77	0	TTLL7,missense_variant,p.Ala374Val,ENST00000260505,;TTLL7,non_coding_transcript_exon_variant,,ENST00000477524,;TTLL7,non_coding_transcript_exon_variant,,ENST00000472688,;TTLL7,non_coding_transcript_exon_variant,,ENST00000482783,;TTLL7,non_coding_transcript_exon_variant,,ENST00000488014,;TTLL7,missense_variant,p.Ala59Val,ENST00000474957,;TTLL7,missense_variant,p.Ala258Val,ENST00000485638,;TTLL7,missense_variant,p.Ala374Val,ENST00000480174,;	A	ENSG00000137941	ENST00000260505	Transcript	missense_variant	1499	1121	374	A/V	gCg/gTg	.	.	.	-1	TTLL7	HGNC	26242	protein_coding	YES	CCDS690.2	ENSP00000260505	TTLL7_HUMAN	.	UPI000020391D	.	deleterious(0)	possibly_damaging(0.558)	10/21	.	PROSITE_profiles:PS51221,hmmpanther:PTHR12241:SF11,hmmpanther:PTHR12241,Pfam_domain:PF03133	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAACGCATTT	.	5	ESCA
LZTS3	0	.	GRCh37	20	3147483	3147483	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327C>T	p.%3D	p.T109T	ENST00000329152	1/3	84	59	25	73	73	0	LZTS3,synonymous_variant,p.%3D,ENST00000329152,;LZTS3,synonymous_variant,p.%3D,ENST00000360342,;LZTS3,synonymous_variant,p.%3D,ENST00000337576,;	A	ENSG00000088899	ENST00000329152	Transcript	synonymous_variant	1725	327	109	T	acC/acT	.	.	.	-1	LZTS3	Uniprot_gn	.	protein_coding	YES	.	ENSP00000332123	LZTS3_HUMAN	.	UPI0000139A8C	.	.	.	1/3	.	hmmpanther:PTHR19354:SF6,hmmpanther:PTHR19354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATCGGTGTG	.	5	ESCA
EPB41L1	0	.	GRCh37	20	34797649	34797649	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1908C>T	p.%3D	p.F636F	ENST00000338074	15/22	45	25	19	36	36	0	EPB41L1,synonymous_variant,p.%3D,ENST00000338074,;EPB41L1,synonymous_variant,p.%3D,ENST00000373950,;EPB41L1,synonymous_variant,p.%3D,ENST00000373941,;EPB41L1,synonymous_variant,p.%3D,ENST00000202028,;EPB41L1,synonymous_variant,p.%3D,ENST00000441639,;EPB41L1,intron_variant,,ENST00000451082,;EPB41L1,intron_variant,,ENST00000454226,;EPB41L1,intron_variant,,ENST00000373946,;EPB41L1,upstream_gene_variant,,ENST00000432603,;EPB41L1,non_coding_transcript_exon_variant,,ENST00000479336,;	T	ENSG00000088367	ENST00000338074	Transcript	synonymous_variant	2069	1908	636	F	ttC/ttT	.	.	.	1	EPB41L1	HGNC	3378	protein_coding	YES	CCDS13271.1	ENSP00000337168	E41L1_HUMAN	Q4VXN8_HUMAN,Q4VXN7_HUMAN,Q4VXN6_HUMAN,Q4VXN5_HUMAN,Q4VXN2_HUMAN,Q4VXN1_HUMAN,Q4VXN0_HUMAN	UPI0000129AF8	.	.	.	15/22	.	hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF7,PIRSF_domain:PIRSF002304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTCTCCCG	.	5	ESCA
PREX1	0	.	GRCh37	20	47364399	47364399	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.238C>T	p.Arg80Trp	p.R80W	ENST00000371941	2/40	35	31	4	25	25	0	PREX1,missense_variant,p.Arg80Trp,ENST00000396220,;PREX1,missense_variant,p.Arg80Trp,ENST00000371941,;	A	ENSG00000124126	ENST00000371941	Transcript	missense_variant	261	238	80	R/W	Cgg/Tgg	.	.	.	-1	PREX1	HGNC	32594	protein_coding	YES	CCDS13410.1	ENSP00000361009	PREX1_HUMAN	.	UPI000013D375	.	deleterious(0)	probably_damaging(1)	2/40	.	PROSITE_profiles:PS50010,hmmpanther:PTHR22829,hmmpanther:PTHR22829:SF6,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R78H|c.233G>A|5,BUFFER|p.R78H|c.233G>A|5	RADIA|MUTECT|MUSE|VARSCANS	CTGCCGGATGC	.	4	ESCA
PTGIS	0	.	GRCh37	20	48130860	48130860	+	Missense_Mutation	SNP	G	G	A	rs745642215	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.928C>T	p.Arg310Cys	p.R310C	ENST00000244043	7/10	32	15	17	27	27	0	PTGIS,missense_variant,p.Arg310Cys,ENST00000244043,;PTGIS,non_coding_transcript_exon_variant,,ENST00000478971,;	A	ENSG00000124212	ENST00000244043	Transcript	missense_variant	958	928	310	R/C	Cgc/Tgc	rs745642215	.	.	-1	PTGIS	HGNC	9603	protein_coding	YES	CCDS13419.1	ENSP00000244043	PTGIS_HUMAN	Q6LEN0_HUMAN	UPI00001328DF	.	deleterious(0.01)	possibly_damaging(0.752)	7/10	.	hmmpanther:PTHR24306,hmmpanther:PTHR24306:SF4,Gene3D:1.10.630.10,Pfam_domain:PF00067,PIRSF_domain:PIRSF000047,PIRSF_domain:PIRSF500628,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGCGGACAG	byFrequency	5	ESCA
C21orf88	0	.	GRCh37	21	40969634	40969634	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435G>A	p.%3D	p.L145L	ENST00000380612	3/3	53	46	6	39	39	0	C21orf88,synonymous_variant,p.%3D,ENST00000380612,;B3GALT5,intron_variant,,ENST00000380620,;C21orf88,non_coding_transcript_exon_variant,,ENST00000489821,;	T	ENSG00000184809	ENST00000380612	Transcript	synonymous_variant	511	435	145	L	ctG/ctA	.	.	.	-1	C21orf88	HGNC	16424	protein_coding	YES	.	ENSP00000369986	CU088_HUMAN	.	UPI00001AFA76	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGTCACAGTGC	.	3	ESCA
MX1	0	.	GRCh37	21	42830713	42830713	+	3'UTR	SNP	G	G	C	rs777315672	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*28G>C	.	.	ENST00000398600	19/19	18	11	7	29	29	0	MX1,3_prime_UTR_variant,,ENST00000398600,;MX1,3_prime_UTR_variant,,ENST00000288383,;MX1,3_prime_UTR_variant,,ENST00000398598,;MX1,3_prime_UTR_variant,,ENST00000455164,;	C	ENSG00000157601	ENST00000398600	Transcript	3_prime_UTR_variant	3042	.	.	.	.	rs777315672	.	.	1	MX1	HGNC	7532	protein_coding	YES	CCDS13673.1	ENSP00000381601	MX1_HUMAN	H9KVD3_HUMAN,H9KVD0_HUMAN,H9KVC9_HUMAN,H9KVC7_HUMAN,H9KVC4_HUMAN,H9KVC3_HUMAN	UPI0000206F16	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GACGTGCACGC	.	4	ESCA
KRTAP10-7	0	.	GRCh37	21	46021807	46021807	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*158G>A	.	.	ENST00000380102	1/1	122	114	7	97	97	0	KRTAP10-7,3_prime_UTR_variant,,ENST00000380102,;TSPEAR,intron_variant,,ENST00000323084,;AL773602.1,downstream_gene_variant,,ENST00000339001,;	A	ENSG00000205441	ENST00000380102	Transcript	3_prime_UTR_variant	1311	.	.	.	.	.	.	.	1	KRTAP10-7	HGNC	22970	protein_coding	YES	.	ENSP00000369445	KR107_HUMAN	.	UPI000036709B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCAGCTCAG	.	2	ESCA
POLR3H	0	.	GRCh37	22	41923659	41923660	+	3'UTR	INS	-	-	TT	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1627_*1628insAA	.	.	ENST00000355209	6/6	17	11	6	11	11	0	POLR3H,3_prime_UTR_variant,,ENST00000396504,;POLR3H,3_prime_UTR_variant,,ENST00000355209,;ACO2,intron_variant,,ENST00000216254,;ACO2,intron_variant,,ENST00000396512,;POLR3H,downstream_gene_variant,,ENST00000407461,;POLR3H,downstream_gene_variant,,ENST00000337566,;POLR3H,downstream_gene_variant,,ENST00000420561,;POLR3H,downstream_gene_variant,,ENST00000442616,;POLR3H,downstream_gene_variant,,ENST00000431534,;POLR3H,downstream_gene_variant,,ENST00000432789,;	TT	ENSG00000100413	ENST00000355209	Transcript	3_prime_UTR_variant	2586-2587	.	.	.	.	.	.	.	-1	POLR3H	HGNC	30349	protein_coding	YES	CCDS14018.1	ENSP00000347345	RPC8_HUMAN	.	UPI0000073CE5	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGGACATGTGC	.	2	ESCA
SHANK3	0	.	GRCh37	22	51117786	51117786	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.815A>C	p.Tyr272Ser	p.Y272S	ENST00000262795	7/23	97	67	29	60	60	0	SHANK3,missense_variant,p.Tyr272Ser,ENST00000262795,;SHANK3,missense_variant,p.Tyr272Ser,ENST00000445220,;SHANK3,missense_variant,p.Tyr272Ser,ENST00000414786,;	C	ENSG00000251322	ENST00000262795	Transcript	missense_variant	815	815	272	Y/S	tAt/tCt	.	.	.	1	SHANK3	HGNC	14294	protein_coding	YES	.	ENSP00000442518	.	F8TCV3_HUMAN,F2Z3L0_HUMAN	UPI0000DD85FB	.	.	probably_damaging(0.997)	7/23	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24135:SF4,hmmpanther:PTHR24135,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTATGGGG	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098803	178098803	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242G>T	p.Gly81Val	p.G81V	ENST00000397062	2/5	163	107	56	114	114	0	NFE2L2,splice_donor_variant,,ENST00000449627,;NFE2L2,missense_variant,p.Gly65Val,ENST00000423513,;NFE2L2,missense_variant,p.Gly81Val,ENST00000397062,;NFE2L2,missense_variant,p.Gly65Val,ENST00000446151,;NFE2L2,missense_variant,p.Gly65Val,ENST00000588123,;NFE2L2,missense_variant,p.Gly80Val,ENST00000586532,;NFE2L2,missense_variant,p.Gly65Val,ENST00000421929,;NFE2L2,missense_variant,p.Gly65Val,ENST00000464747,;NFE2L2,missense_variant,p.Gly65Val,ENST00000448782,;NFE2L2,missense_variant,p.Gly65Val,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	A	ENSG00000116044	ENST00000397062	Transcript	missense_variant	797	242	81	G/V	gGt/gTt	COSM132961,COSM132957	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G81V|c.242G>T|7,CODON|p.G81D|c.242G>A|6,BUFFER|p.E82D|c.246A>C|3,BUFFER|p.E82D|c.246A>T|6,BUFFER|p.E82G|c.245A>G|7,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.G81S|c.241G>A|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79K|c.235G>A|10,BUFFER|p.E79Q|c.235G>C|11	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCACCTGTC	.	5	ESCA
TTN	0	.	GRCh37	2	179588345	179588345	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21482G>C	p.Arg7161Thr	p.R7161T	ENST00000589042	74/363	59	55	4	40	40	0	TTN,missense_variant,p.Arg5917Thr,ENST00000342992,;TTN,missense_variant,p.Arg6844Thr,ENST00000591111,;TTN,missense_variant,p.Arg7161Thr,ENST00000589042,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;RP11-171I2.1,non_coding_transcript_exon_variant,,ENST00000590024,;TTN-AS1,intron_variant,,ENST00000585451,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	21707	21482	7161	R/T	aGa/aCa	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	74/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCTAATA	.	2	ESCA
MAP2	0	.	GRCh37	2	210559468	210559468	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2574A>T	p.%3D	p.V858V	ENST00000360351	7/15	46	41	4	43	43	0	MAP2,synonymous_variant,p.%3D,ENST00000447185,;MAP2,synonymous_variant,p.%3D,ENST00000360351,;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000199940,;MAP2,intron_variant,,ENST00000392194,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000482864,;MAP2,intron_variant,,ENST00000471619,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,;MAP2,upstream_gene_variant,,ENST00000475600,;	T	ENSG00000078018	ENST00000360351	Transcript	synonymous_variant	3080	2574	858	V	gtA/gtT	.	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	.	.	7/15	.	hmmpanther:PTHR11501:SF15,hmmpanther:PTHR11501,Pfam_domain:PF08377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ATTGTAAAAAC	.	3	ESCA
C2orf57	0	.	GRCh37	2	232458874	232458874	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*24G>T	.	.	ENST00000313965	1/1	23	19	4	28	28	0	C2orf57,3_prime_UTR_variant,,ENST00000313965,;	T	ENSG00000177673	ENST00000313965	Transcript	3_prime_UTR_variant	1300	.	.	.	.	.	.	.	1	C2orf57	HGNC	28563	protein_coding	YES	CCDS2487.1	ENSP00000315557	CB057_HUMAN	.	UPI000013F6CA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGAAGGGCTG	.	4	ESCA
PPP1R7	0	.	GRCh37	2	242089045	242089045	+	5'Flank	SNP	G	G	T	rs550646731	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000234038	.	70	61	8	41	41	0	PPP1R7,5_prime_UTR_variant,,ENST00000402734,;PASK,5_prime_UTR_variant,,ENST00000405260,;PPP1R7,5_prime_UTR_variant,,ENST00000438799,;PPP1R7,5_prime_UTR_variant,,ENST00000423280,;PPP1R7,upstream_gene_variant,,ENST00000234038,;PPP1R7,upstream_gene_variant,,ENST00000450367,;PPP1R7,upstream_gene_variant,,ENST00000406106,;PPP1R7,upstream_gene_variant,,ENST00000404405,;PPP1R7,upstream_gene_variant,,ENST00000272983,;PASK,upstream_gene_variant,,ENST00000234040,;PPP1R7,upstream_gene_variant,,ENST00000439916,;PPP1R7,upstream_gene_variant,,ENST00000407025,;PASK,upstream_gene_variant,,ENST00000358649,;PASK,upstream_gene_variant,,ENST00000415234,;PASK,upstream_gene_variant,,ENST00000452907,;PPP1R7,upstream_gene_variant,,ENST00000427172,;PASK,upstream_gene_variant,,ENST00000403638,;PPP1R7,upstream_gene_variant,,ENST00000401987,;PASK,upstream_gene_variant,,ENST00000539818,;PASK,upstream_gene_variant,,ENST00000437780,;PPP1R7,upstream_gene_variant,,ENST00000498170,;PPP1R7,upstream_gene_variant,,ENST00000473017,;PPP1R7,upstream_gene_variant,,ENST00000493374,;	T	ENSG00000115685	ENST00000234038	Transcript	upstream_gene_variant	.	.	.	.	.	rs550646731	.	392	1	PPP1R7	HGNC	9295	protein_coding	YES	CCDS2546.1	ENSP00000234038	PP1R7_HUMAN	.	UPI000006E65A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTTCGGAGGAG	.	3	ESCA
FAM179A	0	.	GRCh37	2	29247111	29247111	+	Missense_Mutation	SNP	G	G	A	rs768497249	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1724G>A	p.Arg575His	p.R575H	ENST00000379558	13/20	67	56	10	49	49	0	FAM179A,missense_variant,p.Arg10His,ENST00000401723,;FAM179A,missense_variant,p.Arg70His,ENST00000440012,;FAM179A,missense_variant,p.Arg520His,ENST00000403861,;FAM179A,missense_variant,p.Arg575His,ENST00000379558,;FAM179A,non_coding_transcript_exon_variant,,ENST00000465300,;	A	ENSG00000189350	ENST00000379558	Transcript	missense_variant	2075	1724	575	R/H	cGc/cAc	rs768497249	.	.	1	FAM179A	HGNC	33715	protein_coding	YES	CCDS1769.2	ENSP00000368876	F179A_HUMAN	C9JLI7_HUMAN,C9JJW1_HUMAN,B5MCN5_HUMAN	UPI00014F7B81	.	deleterious(0)	probably_damaging(0.977)	13/20	.	hmmpanther:PTHR21567:SF31,hmmpanther:PTHR21567,Pfam_domain:PF12348,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCCGCTGCT	.	5	ESCA
ALLC	0	.	GRCh37	2	3743889	3743889	+	Missense_Mutation	SNP	C	C	T	rs369048525	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.692C>T	p.Ala231Val	p.A231V	ENST00000252505	9/12	111	106	5	85	85	0	ALLC,missense_variant,p.Ala231Val,ENST00000252505,;ALLC,non_coding_transcript_exon_variant,,ENST00000471711,;ALLC,non_coding_transcript_exon_variant,,ENST00000476389,;	T	ENSG00000151360	ENST00000252505	Transcript	missense_variant	854	692	231	A/V	gCg/gTg	rs369048525,COSM1734400	.	.	1	ALLC	HGNC	17377	protein_coding	YES	CCDS46223.1	ENSP00000252505	ALLC_HUMAN	B4DY77_HUMAN	UPI000050BBEF	.	tolerated(0.23)	benign(0.02)	9/12	.	hmmpanther:PTHR12045,Pfam_domain:PF03561,TIGRFAM_domain:TIGR02961,Gene3D:2.60.120.260,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	T:0.0003	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATGGCGGATG	byFrequency|byCluster	2	ESCA
USP34	0	.	GRCh37	2	61472421	61472421	+	Missense_Mutation	SNP	T	T	C	rs749963447	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6551A>G	p.Tyr2184Cys	p.Y2184C	ENST00000398571	51/80	43	29	13	33	33	0	USP34,missense_variant,p.Tyr462Cys,ENST00000453734,;USP34,missense_variant,p.Tyr2184Cys,ENST00000398571,;USP34,upstream_gene_variant,,ENST00000411912,;USP34,intron_variant,,ENST00000472706,;USP34,splice_region_variant,,ENST00000463046,;RP11-479F13.1,upstream_gene_variant,,ENST00000605372,;	C	ENSG00000115464	ENST00000398571	Transcript	missense_variant	6628	6551	2184	Y/C	tAt/tGt	rs749963447	.	.	-1	USP34	HGNC	20066	protein_coding	YES	CCDS42686.1	ENSP00000381577	UBP34_HUMAN	.	UPI0000410E09	.	deleterious(0)	probably_damaging(0.992)	51/80	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF97,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGATACCTA	.	5	ESCA
PLGLB2	0	.	GRCh37	2	88047674	88047674	+	Translation_Start_Site	SNP	T	T	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2T>C	p.Met1?	p.M1?	ENST00000359481	1/4	92	64	27	53	53	0	PLGLB2,start_lost,p.Met1?,ENST00000359481,;PLGLB2,start_lost,p.Met1?,ENST00000410086,;PLGLB2,upstream_gene_variant,,ENST00000465361,;	C	ENSG00000125551	ENST00000359481	Transcript	start_lost	69	2	1	M/T	aTg/aCg	.	.	.	1	PLGLB2	HGNC	9073	protein_coding	YES	CCDS1999.1	ENSP00000352458	PLGB_HUMAN	Q53QL7_HUMAN	UPI000013219F	.	deleterious(0)	probably_damaging(0.996)	1/4	.	Cleavage_site_(Signalp):SignalP-noTM,PIRSF_domain:PIRSF002483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CAAAATGGAAC	.	2	ESCA
SMYD1	0	.	GRCh37	2	88405895	88405895	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1033G>C	p.Asp345His	p.D345H	ENST00000419482	8/10	91	74	16	74	74	0	SMYD1,missense_variant,p.Asp332His,ENST00000444564,;SMYD1,missense_variant,p.Asp345His,ENST00000419482,;SMYD1,intron_variant,,ENST00000438570,;	C	ENSG00000115593	ENST00000419482	Transcript	missense_variant	1118	1033	345	D/H	Gac/Cac	.	.	.	1	SMYD1	HGNC	20986	protein_coding	YES	CCDS33240.1	ENSP00000393453	SMYD1_HUMAN	Q5GJ33_HUMAN	UPI000006EB68	.	deleterious(0)	possibly_damaging(0.592)	8/10	.	hmmpanther:PTHR12197:SF16,hmmpanther:PTHR12197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCTGACACC	.	5	ESCA
IRAK2	0	.	GRCh37	3	10255058	10255058	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696G>A	p.%3D	p.K232K	ENST00000256458	5/13	39	15	24	30	30	0	IRAK2,synonymous_variant,p.%3D,ENST00000256458,;RNU6-814P,upstream_gene_variant,,ENST00000410416,;	A	ENSG00000134070	ENST00000256458	Transcript	synonymous_variant	786	696	232	K	aaG/aaA	.	.	.	1	IRAK2	HGNC	6113	protein_coding	YES	CCDS33697.1	ENSP00000256458	IRAK2_HUMAN	.	UPI000020AB17	.	.	.	5/13	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24419,hmmpanther:PTHR24419:SF2,Pfam_domain:PF00069,Gene3D:3.30.200.20,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAGCCATT	.	5	ESCA
HRH1	0	.	GRCh37	3	11300956	11300956	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.233C>A	p.Ala78Asp	p.A78D	ENST00000397056	3/3	30	18	12	25	25	0	HRH1,missense_variant,p.Ala78Asp,ENST00000431010,;HRH1,missense_variant,p.Ala78Asp,ENST00000438284,;HRH1,missense_variant,p.Ala78Asp,ENST00000397056,;HRH1,downstream_gene_variant,,ENST00000413416,;	A	ENSG00000196639	ENST00000397056	Transcript	missense_variant	424	233	78	A/D	gCc/gAc	.	.	.	1	HRH1	HGNC	5182	protein_coding	YES	CCDS2604.1	ENSP00000380247	HRH1_HUMAN	.	UPI0000050401	.	deleterious(0)	probably_damaging(0.949)	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF244,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.I75I|c.225C>T|5	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGGTGCCGTCG	.	4	ESCA
UROC1	0	.	GRCh37	3	126211314	126211314	+	Missense_Mutation	SNP	G	G	A	rs201269614	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735C>T	p.Arg579Cys	p.R579C	ENST00000383579	17/21	76	62	14	42	42	0	UROC1,missense_variant,p.Arg579Cys,ENST00000383579,;UROC1,missense_variant,p.Arg519Cys,ENST00000290868,;	A	ENSG00000159650	ENST00000383579	Transcript	missense_variant	1769	1735	579	R/C	Cgc/Tgc	rs201269614	.	.	-1	UROC1	HGNC	26444	protein_coding	YES	CCDS54636.1	ENSP00000373073	HUTU_HUMAN	.	UPI0000480109	.	deleterious(0)	probably_damaging(0.987)	17/21	.	HAMAP:MF_00577,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Pfam_domain:PF01175,Gene3D:1x87B01,Superfamily_domains:SSF111326	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGCGGCCCT	byCluster	5	ESCA
IQSEC1	0	.	GRCh37	3	12977703	12977703	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855G>T	p.%3D	p.L285L	ENST00000273221	3/14	93	50	42	114	114	0	IQSEC1,synonymous_variant,p.%3D,ENST00000429247,;IQSEC1,synonymous_variant,p.%3D,ENST00000273221,;IQSEC1,synonymous_variant,p.%3D,ENST00000450726,;IQSEC1,downstream_gene_variant,,ENST00000473088,;	A	ENSG00000144711	ENST00000273221	Transcript	synonymous_variant	1072	855	285	L	ctG/ctT	.	.	.	-1	IQSEC1	HGNC	29112	protein_coding	YES	CCDS33703.1	ENSP00000273221	IQEC1_HUMAN	.	UPI00003E1F36	.	.	.	3/14	.	hmmpanther:PTHR10663:SF63,hmmpanther:PTHR10663	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTGCAGGGC	.	5	ESCA
FNDC3B	0	.	GRCh37	3	172115911	172115911	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*646A>T	.	.	ENST00000336824	26/26	183	162	21	78	78	0	FNDC3B,3_prime_UTR_variant,,ENST00000415807,;FNDC3B,3_prime_UTR_variant,,ENST00000336824,;FNDC3B,downstream_gene_variant,,ENST00000416957,;	T	ENSG00000075420	ENST00000336824	Transcript	3_prime_UTR_variant	4360	.	.	.	.	.	.	.	1	FNDC3B	HGNC	24670	protein_coding	YES	CCDS3217.1	ENSP00000338523	FND3B_HUMAN	.	UPI00001AE8B2	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAAATCAAG	.	4	ESCA
TP63	0	.	GRCh37	3	189612963	189612963	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*672A>G	.	.	ENST00000264731	14/14	32	25	7	17	17	0	TP63,3_prime_UTR_variant,,ENST00000354600,;TP63,3_prime_UTR_variant,,ENST00000264731,;TP63,3_prime_UTR_variant,,ENST00000382063,;TP63,downstream_gene_variant,,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000456148,;TP63,downstream_gene_variant,,ENST00000392460,;TP63,downstream_gene_variant,,ENST00000320472,;TP63,downstream_gene_variant,,ENST00000440651,;TP63,downstream_gene_variant,,ENST00000449992,;TP63,downstream_gene_variant,,ENST00000392463,;	G	ENSG00000073282	ENST00000264731	Transcript	3_prime_UTR_variant	2804	.	.	.	.	.	.	.	1	TP63	HGNC	15979	protein_coding	YES	CCDS3293.1	ENSP00000264731	P63_HUMAN	.	UPI0000073CF2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTATATTTTA	.	5	ESCA
MST1R	0	.	GRCh37	3	49933677	49933677	+	Missense_Mutation	SNP	C	C	G	rs761033628	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2600G>C	p.Ser867Thr	p.S867T	ENST00000296474	10/20	43	30	12	60	60	0	MST1R,missense_variant,p.Ser867Thr,ENST00000344206,;MST1R,missense_variant,p.Ser867Thr,ENST00000296474,;MST1R,upstream_gene_variant,,ENST00000440292,;MST1R,upstream_gene_variant,,ENST00000434765,;CTD-2330K9.2,upstream_gene_variant,,ENST00000435478,;MST1R,missense_variant,p.Ser867Thr,ENST00000411578,;MST1R,non_coding_transcript_exon_variant,,ENST00000468525,;MST1R,upstream_gene_variant,,ENST00000463789,;MST1R,downstream_gene_variant,,ENST00000497001,;MST1R,downstream_gene_variant,,ENST00000493535,;MST1R,upstream_gene_variant,,ENST00000467110,;MST1R,upstream_gene_variant,,ENST00000490053,;MST1R,downstream_gene_variant,,ENST00000485044,;	G	ENSG00000164078	ENST00000296474	Transcript	missense_variant	2628	2600	867	S/T	aGt/aCt	rs761033628	.	.	-1	MST1R	HGNC	7381	protein_coding	YES	CCDS2807.1	ENSP00000296474	RON_HUMAN	.	UPI000013E344	.	tolerated(0.21)	benign(0.006)	10/20	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF113,SMART_domains:SM00429,PIRSF_domain:PIRSF000617	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCACTGGGT	byFrequency	5	ESCA
ARF4	0	.	GRCh37	3	57563091	57563092	+	Frame_Shift_Ins	INS	-	-	CGAT	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281_282insATCG	p.Ser94ArgfsTer6	p.S94Rfs*6	ENST00000303436	4/6	37	23	14	45	45	0	ARF4,frameshift_variant,p.Ser94ArgfsTer6,ENST00000303436,;ARF4,frameshift_variant,p.Ser67ArgfsTer6,ENST00000496292,;ARF4,frameshift_variant,p.Ser94ArgfsTer6,ENST00000463880,;ARF4,5_prime_UTR_variant,,ENST00000489843,;ARF4,non_coding_transcript_exon_variant,,ENST00000483848,;ARF4,3_prime_UTR_variant,,ENST00000486310,;	CGAT	ENSG00000168374	ENST00000303436	Transcript	frameshift_variant	549-550	281-282	94	S/RSX	agc/agATCGc	.	.	.	-1	ARF4	HGNC	655	protein_coding	YES	CCDS2884.1	ENSP00000306010	ARF4_HUMAN	U3KQF2_HUMAN,C9JPM4_HUMAN,C9J6P1_HUMAN	UPI000013E89E	.	.	.	4/6	.	PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF110,Pfam_domain:PF00025,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00177,SMART_domains:SM00178,SMART_domains:SM00175,Superfamily_domains:SSF52540,Prints_domain:PR00328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCGTTGCTATC	.	3	ESCA
STOX2	0	.	GRCh37	4	184931510	184931510	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1519G>T	p.Gly507Trp	p.G507W	ENST00000308497	3/4	29	16	12	36	36	0	STOX2,missense_variant,p.Gly507Trp,ENST00000438269,;STOX2,missense_variant,p.Gly507Trp,ENST00000308497,;STOX2,intron_variant,,ENST00000513034,;STOX2,downstream_gene_variant,,ENST00000512520,;STOX2,upstream_gene_variant,,ENST00000506529,;	T	ENSG00000173320	ENST00000308497	Transcript	missense_variant	2954	1519	507	G/W	Ggg/Tgg	.	.	.	1	STOX2	HGNC	25450	protein_coding	YES	CCDS47167.1	ENSP00000311257	STOX2_HUMAN	D6RDA5_HUMAN	UPI00001C1E11	.	deleterious(0)	probably_damaging(0.999)	3/4	.	hmmpanther:PTHR22437:SF2,hmmpanther:PTHR22437	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTAGGGACG	.	5	ESCA
STOX2	0	.	GRCh37	4	184932024	184932024	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2033G>C	p.Gly678Ala	p.G678A	ENST00000308497	3/4	30	14	15	31	31	0	STOX2,missense_variant,p.Gly678Ala,ENST00000438269,;STOX2,missense_variant,p.Gly678Ala,ENST00000308497,;STOX2,intron_variant,,ENST00000513034,;STOX2,downstream_gene_variant,,ENST00000512520,;STOX2,missense_variant,p.Gly34Ala,ENST00000506529,;	C	ENSG00000173320	ENST00000308497	Transcript	missense_variant	3468	2033	678	G/A	gGa/gCa	.	.	.	1	STOX2	HGNC	25450	protein_coding	YES	CCDS47167.1	ENSP00000311257	STOX2_HUMAN	D6RDA5_HUMAN	UPI00001C1E11	.	tolerated_low_confidence(0.19)	benign(0.105)	3/4	.	hmmpanther:PTHR22437:SF2,hmmpanther:PTHR22437	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACGGACGCC	.	5	ESCA
CNGA1	0	.	GRCh37	4	47938770	47938770	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1948C>T	p.Leu650Phe	p.L650F	ENST00000402813	10/10	49	45	4	43	43	0	CNGA1,missense_variant,p.Leu581Phe,ENST00000358519,;CNGA1,missense_variant,p.Leu650Phe,ENST00000402813,;CNGA1,missense_variant,p.Leu581Phe,ENST00000544810,;CNGA1,missense_variant,p.Leu581Phe,ENST00000514170,;CNGA1,missense_variant,p.Leu581Phe,ENST00000420489,;NIPAL1,intron_variant,,ENST00000513724,;NIPAL1,intron_variant,,ENST00000500571,;	A	ENSG00000198515	ENST00000402813	Transcript	missense_variant	2091	1948	650	L/F	Ctc/Ttc	.	.	.	-1	CNGA1	HGNC	2148	protein_coding	YES	CCDS47050.1	ENSP00000384264	CNGA1_HUMAN	D6RCF1_HUMAN,D6R978_HUMAN	UPI0001881B54	.	deleterious(0)	probably_damaging(1)	10/10	.	PROSITE_profiles:PS50042,hmmpanther:PTHR10217:SF387,hmmpanther:PTHR10217,Gene3D:2.60.120.10,Pfam_domain:PF00027,SMART_domains:SM00100,Superfamily_domains:SSF51206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CATGAGGTCAT	.	3	ESCA
CYSTM1	0	.	GRCh37	5	139622995	139622995	+	Silent	SNP	G	G	A	rs370523896	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.293G>A	p.%3D	p.%3D	ENST00000261811	3/3	38	21	17	32	32	0	CYSTM1,stop_retained_variant,p.%3D,ENST00000261811,;PFDN1,downstream_gene_variant,,ENST00000510217,;PFDN1,downstream_gene_variant,,ENST00000261813,;PFDN1,downstream_gene_variant,,ENST00000524074,;CYSTM1,non_coding_transcript_exon_variant,,ENST00000509589,;CYSTM1,non_coding_transcript_exon_variant,,ENST00000504227,;CYSTM1,non_coding_transcript_exon_variant,,ENST00000509789,;PFDN1,downstream_gene_variant,,ENST00000514611,;PFDN1,downstream_gene_variant,,ENST00000512925,;PFDN1,downstream_gene_variant,,ENST00000512707,;	A	ENSG00000120306	ENST00000261811	Transcript	stop_retained_variant	957	293	98	*	tGa/tAa	rs370523896	.	.	1	CYSTM1	HGNC	30239	protein_coding	YES	CCDS4221.1	ENSP00000261811	CYTM1_HUMAN	.	UPI000004A7BE	.	.	.	3/3	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTGACCAG	.	5	ESCA
PCDHB14	0	.	GRCh37	5	140604553	140604553	+	Silent	SNP	G	G	A	rs782655623	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1476G>A	p.%3D	p.P492P	ENST00000239449	1/1	165	154	11	198	198	0	PCDHB14,synonymous_variant,p.%3D,ENST00000239449,;PCDHB14,synonymous_variant,p.%3D,ENST00000515856,;	A	ENSG00000120327	ENST00000239449	Transcript	synonymous_variant	1476	1476	492	P	ccG/ccA	rs782655623	.	.	1	PCDHB14	HGNC	8685	protein_coding	YES	CCDS4256.1	ENSP00000239449	PCDBE_HUMAN	B4DPE2_HUMAN	UPI00001273E7	.	.	.	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCCGCCCCA	byFrequency	2	ESCA
PCDHGA5	0	.	GRCh37	5	140745554	140745554	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1657C>T	p.%3D	p.L553L	ENST00000518069	1/4	81	75	6	80	80	0	PCDHGA5,synonymous_variant,p.%3D,ENST00000518069,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGB3,upstream_gene_variant,,ENST00000576222,;	T	ENSG00000253485	ENST00000518069	Transcript	synonymous_variant	1657	1657	553	L	Ctg/Ttg	.	.	.	1	PCDHGA5	HGNC	8703	protein_coding	YES	CCDS54925.1	ENSP00000429834	PCDG5_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006CD9F	.	.	.	1/4	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF105,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGTGCTGGAC	.	2	ESCA
NIPBL	0	.	GRCh37	5	37064653	37064653	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8074T>A	p.Ser2692Thr	p.S2692T	ENST00000282516	47/47	67	53	13	29	29	0	NIPBL,missense_variant,p.Ser2692Thr,ENST00000282516,;NIPBL,downstream_gene_variant,,ENST00000448238,;NIPBL,downstream_gene_variant,,ENST00000513819,;NIPBL,non_coding_transcript_exon_variant,,ENST00000514335,;	A	ENSG00000164190	ENST00000282516	Transcript	missense_variant	8573	8074	2692	S/T	Tca/Aca	.	.	.	1	NIPBL	HGNC	28862	protein_coding	YES	CCDS3920.1	ENSP00000282516	NIPBL_HUMAN	A2RRA7_HUMAN	UPI00003761B5	.	tolerated_low_confidence(0.08)	possibly_damaging(0.53)	47/47	.	hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATTCAGAC	.	5	ESCA
HCN1	0	.	GRCh37	5	45645478	45645478	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658A>C	p.Ser220Arg	p.S220R	ENST00000303230	2/8	86	80	5	50	50	0	HCN1,missense_variant,p.Ser220Arg,ENST00000303230,;	G	ENSG00000164588	ENST00000303230	Transcript	missense_variant	716	658	220	S/R	Agc/Cgc	.	.	.	-1	HCN1	HGNC	4845	protein_coding	YES	CCDS3952.1	ENSP00000307342	HCN1_HUMAN	.	UPI00001AED69	.	deleterious(0)	probably_damaging(0.996)	2/8	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,Gene3D:1.10.287.70,hmmpanther:PTHR10217:SF373,hmmpanther:PTHR10217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCAGCTTTTTA	.	2	ESCA
DDX4	0	.	GRCh37	5	55110775	55110775	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1762T>A	p.Phe588Ile	p.F588I	ENST00000505374	20/22	75	42	32	60	60	0	DDX4,missense_variant,p.Phe568Ile,ENST00000514278,;DDX4,missense_variant,p.Phe554Ile,ENST00000353507,;DDX4,missense_variant,p.Phe439Ile,ENST00000511853,;DDX4,missense_variant,p.Phe554Ile,ENST00000354991,;DDX4,missense_variant,p.Phe588Ile,ENST00000505374,;DDX4,3_prime_UTR_variant,,ENST00000503129,;	A	ENSG00000152670	ENST00000505374	Transcript	missense_variant	1854	1762	588	F/I	Ttt/Att	.	.	.	1	DDX4	HGNC	18700	protein_coding	YES	CCDS3969.1	ENSP00000424838	DDX4_HUMAN	D6RBL3_HUMAN,D6RAF5_HUMAN	UPI00001290D3	.	tolerated(0.1)	benign(0.063)	20/22	.	PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF168,hmmpanther:PTHR24031,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGCTTTGGA	.	5	ESCA
SAMD3	0	.	GRCh37	6	130535488	130535488	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263C>T	p.Ala88Val	p.A88V	ENST00000368134	6/14	82	77	4	95	94	1	SAMD3,missense_variant,p.Ala86Val,ENST00000529723,;SAMD3,missense_variant,p.Ala88Val,ENST00000531544,;SAMD3,missense_variant,p.Ala88Val,ENST00000532763,;SAMD3,missense_variant,p.Ala112Val,ENST00000457563,;SAMD3,missense_variant,p.Ala88Val,ENST00000437477,;SAMD3,missense_variant,p.Ala88Val,ENST00000532309,;SAMD3,missense_variant,p.Ala88Val,ENST00000368134,;SAMD3,missense_variant,p.Ala88Val,ENST00000324172,;SAMD3,missense_variant,p.Ala88Val,ENST00000439090,;SAMD3,non_coding_transcript_exon_variant,,ENST00000533296,;SAMD3,upstream_gene_variant,,ENST00000528422,;SAMD3,3_prime_UTR_variant,,ENST00000524930,;	A	ENSG00000164483	ENST00000368134	Transcript	missense_variant	872	263	88	A/V	gCt/gTt	.	.	.	-1	SAMD3	HGNC	21574	protein_coding	YES	CCDS34539.1	ENSP00000357116	SAMD3_HUMAN	E9PS85_HUMAN	UPI000006DCE7	.	tolerated_low_confidence(0.13)	benign(0.002)	6/14	.	hmmpanther:PTHR12844:SF18,hmmpanther:PTHR12844	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGAGCTGCT	.	2	ESCA
SUMO4	0	.	GRCh37	6	149721559	149721559	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.32A>T	p.Lys11Met	p.K11M	ENST00000326669	1/1	90	66	23	69	69	0	SUMO4,missense_variant,p.Lys11Met,ENST00000326669,;TAB2,intron_variant,,ENST00000538427,;TAB2,intron_variant,,ENST00000286332,;TAB2,intron_variant,,ENST00000536230,;TAB2,intron_variant,,ENST00000367456,;TAB2,intron_variant,,ENST00000484505,;TAB2,intron_variant,,ENST00000470466,;	T	ENSG00000177688	ENST00000326669	Transcript	missense_variant	65	32	11	K/M	aAg/aTg	.	.	.	1	SUMO4	HGNC	21181	protein_coding	YES	CCDS34549.1	ENSP00000318635	SUMO4_HUMAN	.	UPI0000072D67	.	deleterious(0)	possibly_damaging(0.685)	1/1	.	hmmpanther:PTHR10562,hmmpanther:PTHR10562:SF10,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCAAGACTG	.	5	ESCA
TTLL2	0	.	GRCh37	6	167754288	167754288	+	Silent	SNP	C	C	T	rs771651558	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.900C>T	p.%3D	p.S300S	ENST00000239587	3/3	73	68	4	52	52	0	TTLL2,synonymous_variant,p.%3D,ENST00000239587,;TTLL2,synonymous_variant,p.%3D,ENST00000515138,;TTLL2,downstream_gene_variant,,ENST00000512917,;	T	ENSG00000120440	ENST00000239587	Transcript	synonymous_variant	988	900	300	S	agC/agT	rs771651558	.	.	1	TTLL2	HGNC	21211	protein_coding	YES	CCDS5301.1	ENSP00000239587	TTLL2_HUMAN	.	UPI00001A3A8B	.	.	.	3/3	.	PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF90,Pfam_domain:PF03133	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACAGCAGCAT	.	2	ESCA
CDKAL1	0	.	GRCh37	6	21065322	21065322	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1099C>T	p.Pro367Ser	p.P367S	ENST00000274695	12/16	51	46	5	32	32	0	CDKAL1,missense_variant,p.Pro367Ser,ENST00000274695,;CDKAL1,missense_variant,p.Pro367Ser,ENST00000378610,;CDKAL1,missense_variant,p.Pro297Ser,ENST00000378624,;	T	ENSG00000145996	ENST00000274695	Transcript	missense_variant	1266	1099	367	P/S	Cct/Tct	.	.	.	1	CDKAL1	HGNC	21050	protein_coding	YES	CCDS4546.1	ENSP00000274695	CDKAL_HUMAN	.	UPI000013DA21	.	deleterious(0)	probably_damaging(0.999)	12/16	.	hmmpanther:PTHR11918,hmmpanther:PTHR11918:SF45,TIGRFAM_domain:TIGR00089,Pfam_domain:PF04055,Gene3D:2qgqB01,TIGRFAM_domain:TIGR01578,SMART_domains:SM00729,Superfamily_domains:SSF102114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTCCTGGA	.	4	ESCA
HIST1H4L	0	.	GRCh37	6	27840931	27840942	+	3'UTR	DEL	GGCCCTGAGAAG	GGCCCTGAGAAG	-	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	GGCCCTGAGAAG	GGCCCTGAGAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*35_*46delCTTCTCAGGGCC	.	.	ENST00000355981	1/1	87	66	21	62	62	0	HIST1H4L,3_prime_UTR_variant,,ENST00000355981,;HIST1H3I,upstream_gene_variant,,ENST00000328488,;	-	ENSG00000198558	ENST00000355981	Transcript	3_prime_UTR_variant	348-359	.	.	.	.	.	.	.	-1	HIST1H4L	HGNC	4791	protein_coding	YES	CCDS4637.1	ENSP00000348258	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGGGTGGCCCTGAGAAGGGCCT	.	3	ESCA
OR2B6	0	.	GRCh37	6	27925771	27925771	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753T>C	p.%3D	p.F251F	ENST00000244623	1/1	126	121	5	77	77	0	OR2B6,synonymous_variant,p.%3D,ENST00000244623,;	C	ENSG00000124657	ENST00000244623	Transcript	synonymous_variant	753	753	251	F	ttT/ttC	.	.	.	1	OR2B6	HGNC	8241	protein_coding	YES	CCDS4642.1	ENSP00000244623	OR2B6_HUMAN	.	UPI000003F061	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF202,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTTTTATAG	.	2	ESCA
MDC1	0	.	GRCh37	6	30680542	30680542	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1177A>G	p.Lys393Glu	p.K393E	ENST00000376406	5/15	73	66	7	48	48	0	MDC1,missense_variant,p.Lys393Glu,ENST00000376405,;MDC1,missense_variant,p.Lys393Glu,ENST00000376406,;MDC1,downstream_gene_variant,,ENST00000422266,;MDC1,downstream_gene_variant,,ENST00000425072,;MDC1,upstream_gene_variant,,ENST00000417033,;MDC1,downstream_gene_variant,,ENST00000416571,;MDC1-AS1,non_coding_transcript_exon_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000494654,;	C	ENSG00000137337	ENST00000376406	Transcript	missense_variant	1825	1177	393	K/E	Aaa/Gaa	.	.	.	-1	MDC1	HGNC	21163	protein_coding	YES	CCDS34384.1	ENSP00000365588	MDC1_HUMAN	A2AB07_HUMAN,A2AB06_HUMAN,A2AB05_HUMAN,A1Z5I9_HUMAN,A1Z5I7_HUMAN	UPI00001AF453	.	deleterious(0.03)	benign(0.054)	5/15	.	hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTTTTCTCCA	.	3	ESCA
VARS2	0	.	GRCh37	6	30894115	30894115	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128A>G	.	.	ENST00000541562	30/30	42	38	4	23	23	0	VARS2,3_prime_UTR_variant,,ENST00000321897,;VARS2,3_prime_UTR_variant,,ENST00000542001,;VARS2,3_prime_UTR_variant,,ENST00000541562,;VARS2,3_prime_UTR_variant,,ENST00000416670,;VARS2,non_coding_transcript_exon_variant,,ENST00000476162,;VARS2,non_coding_transcript_exon_variant,,ENST00000469358,;VARS2,non_coding_transcript_exon_variant,,ENST00000477288,;VARS2,non_coding_transcript_exon_variant,,ENST00000473916,;VARS2,downstream_gene_variant,,ENST00000477052,;	G	ENSG00000137411	ENST00000541562	Transcript	3_prime_UTR_variant	3491	.	.	.	.	.	.	.	1	VARS2	HGNC	21642	protein_coding	YES	CCDS54980.1	ENSP00000441000	SYVM_HUMAN	B7ZCJ6_HUMAN,A2ABL6_HUMAN	UPI0001BDAB0F	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAGGACACAG	.	2	ESCA
CDC5L	0	.	GRCh37	6	44394257	44394257	+	Silent	SNP	G	G	A	rs375237261	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1689G>A	p.%3D	p.P563P	ENST00000371477	13/16	60	47	13	22	22	0	CDC5L,synonymous_variant,p.%3D,ENST00000371477,;	A	ENSG00000096401	ENST00000371477	Transcript	synonymous_variant	1988	1689	563	P	ccG/ccA	rs375237261,COSM1079793	.	.	1	CDC5L	HGNC	1743	protein_coding	YES	CCDS4912.1	ENSP00000360532	CDC5L_HUMAN	.	UPI000006EE42	.	.	.	13/16	.	hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF17,Pfam_domain:PF11831	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACCGCCTTT	byFrequency|byCluster	5	ESCA
TRIM24	0	.	GRCh37	7	138264148	138264148	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2456G>A	p.Arg819Lys	p.R819K	ENST00000343526	15/19	48	45	3	45	45	0	TRIM24,missense_variant,p.Arg785Lys,ENST00000415680,;TRIM24,missense_variant,p.Arg819Lys,ENST00000343526,;	A	ENSG00000122779	ENST00000343526	Transcript	missense_variant	2671	2456	819	R/K	aGg/aAg	.	.	.	1	TRIM24	HGNC	11812	protein_coding	YES	CCDS5847.1	ENSP00000340507	TIF1A_HUMAN	B4DYZ9_HUMAN	UPI00000012CB	.	tolerated(0.99)	benign(0.304)	15/19	.	hmmpanther:PTHR24103:SF136,hmmpanther:PTHR24103,Gene3D:3.30.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACAAGGAAAG	.	2	ESCA
VPS41	0	.	GRCh37	7	38794506	38794506	+	Missense_Mutation	SNP	C	C	G	rs762720531	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1726G>C	p.Asp576His	p.D576H	ENST00000310301	20/29	29	20	8	21	21	0	VPS41,missense_variant,p.Asp576His,ENST00000310301,;VPS41,missense_variant,p.Asp551His,ENST00000395969,;VPS41,downstream_gene_variant,,ENST00000462429,;	G	ENSG00000006715	ENST00000310301	Transcript	missense_variant	1781	1726	576	D/H	Gat/Cat	rs762720531	.	.	-1	VPS41	HGNC	12713	protein_coding	YES	CCDS5457.1	ENSP00000309457	VPS41_HUMAN	Q75MS2_HUMAN,C9J2U9_HUMAN	UPI000000DAB7	.	deleterious(0)	possibly_damaging(0.815)	20/29	.	PROSITE_profiles:PS50236,hmmpanther:PTHR12616,Pfam_domain:PF00637,SMART_domains:SM00299,PIRSF_domain:PIRSF028921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATCTTCAT	byFrequency	5	ESCA
RNF216	0	.	GRCh37	7	5760759	5760759	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1549C>T	p.Arg517Ter	p.R517*	ENST00000389902	9/17	65	44	20	47	47	0	RNF216,stop_gained,p.Arg517Ter,ENST00000389902,;RNF216,stop_gained,p.Arg460Ter,ENST00000425013,;RNF216,3_prime_UTR_variant,,ENST00000389900,;	A	ENSG00000011275	ENST00000389902	Transcript	stop_gained	1817	1549	517	R/*	Cga/Tga	.	.	.	-1	RNF216	HGNC	21698	protein_coding	YES	CCDS34594.1	ENSP00000374552	RN216_HUMAN	C9JIV3_HUMAN	UPI000013F5B3	.	.	.	9/17	.	hmmpanther:PTHR22770:SF13,hmmpanther:PTHR22770	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTCGCTTAT	.	5	ESCA
SEMA3A	0	.	GRCh37	7	83589762	83589762	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*925C>T	.	.	ENST00000265362	17/17	9	5	4	9	9	0	SEMA3A,3_prime_UTR_variant,,ENST00000265362,;SEMA3A,downstream_gene_variant,,ENST00000436949,;	A	ENSG00000075213	ENST00000265362	Transcript	3_prime_UTR_variant	3556	.	.	.	.	.	.	.	-1	SEMA3A	HGNC	10723	protein_coding	YES	CCDS5599.1	ENSP00000265362	SEM3A_HUMAN	Q86UJ2_HUMAN,Q75MQ2_HUMAN,C9JD25_HUMAN,C9J9C4_HUMAN	UPI0000135A60	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGGGGAGG	.	2	ESCA
GRM3	0	.	GRCh37	7	86468866	86468866	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2036G>A	p.Arg679Lys	p.R679K	ENST00000361669	4/6	70	47	22	43	43	0	GRM3,missense_variant,p.Arg551Lys,ENST00000536043,;GRM3,missense_variant,p.Arg679Lys,ENST00000361669,;GRM3,missense_variant,p.Arg271Lys,ENST00000546348,;GRM3,intron_variant,,ENST00000439827,;GRM3,intron_variant,,ENST00000394720,;	A	ENSG00000198822	ENST00000361669	Transcript	missense_variant	3135	2036	679	R/K	aGg/aAg	COSM3721989	.	.	1	GRM3	HGNC	4595	protein_coding	YES	CCDS5600.1	ENSP00000355316	GRM3_HUMAN	C9JUH9_HUMAN,C9JIT1_HUMAN,A4D1D0_HUMAN	UPI0000153EFC	.	tolerated(0.31)	possibly_damaging(0.498)	4/6	.	PROSITE_profiles:PS50259,hmmpanther:PTHR24060,Pfam_domain:PF00003	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAGGCCAA	.	5	ESCA
ZNF394	0	.	GRCh37	7	99097549	99097549	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168T>G	p.%3D	p.A56A	ENST00000337673	1/3	53	40	13	49	49	0	ZNF394,synonymous_variant,p.%3D,ENST00000337673,;ZNF394,synonymous_variant,p.%3D,ENST00000426306,;ZNF789,intron_variant,,ENST00000493485,;ZKSCAN5,upstream_gene_variant,,ENST00000451158,;ZKSCAN5,upstream_gene_variant,,ENST00000326775,;ZNF394,intron_variant,,ENST00000394177,;ZNF789,intron_variant,,ENST00000494186,;ZNF394,upstream_gene_variant,,ENST00000462024,;ZNF394,non_coding_transcript_exon_variant,,ENST00000485576,;ZNF394,non_coding_transcript_exon_variant,,ENST00000481881,;ZNF394,upstream_gene_variant,,ENST00000464401,;	C	ENSG00000160908	ENST00000337673	Transcript	synonymous_variant	372	168	56	A	gcT/gcG	.	.	.	-1	ZNF394	HGNC	18832	protein_coding	YES	CCDS5666.1	ENSP00000337363	ZN394_HUMAN	.	UPI000006F498	.	.	.	1/3	.	hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGAAGCCGC	.	5	ESCA
FAM135B	0	.	GRCh37	8	139144969	139144969	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000395297	20/20	63	46	17	37	37	0	FAM135B,missense_variant,p.Arg1363Gln,ENST00000395297,;FAM135B,3_prime_UTR_variant,,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;	T	ENSG00000147724	ENST00000395297	Transcript	missense_variant	4259	4088	1363	R/Q	cGa/cAa	COSM3781384,COSM3781385	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	deleterious(0)	probably_damaging(0.999)	20/20	.	hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGTCGGATT	.	5	ESCA
ADAM28	0	.	GRCh37	8	24181426	24181426	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.800C>T	p.Pro267Leu	p.P267L	ENST00000265769	9/23	31	26	4	46	46	0	ADAM28,missense_variant,p.Pro267Leu,ENST00000437154,;ADAM28,missense_variant,p.Pro14Leu,ENST00000397649,;ADAM28,missense_variant,p.Pro34Leu,ENST00000540823,;ADAM28,missense_variant,p.Pro267Leu,ENST00000265769,;RP11-624C23.1,intron_variant,,ENST00000518988,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,;RP11-624C23.1,intron_variant,,ENST00000523700,;ADAM28,non_coding_transcript_exon_variant,,ENST00000518516,;ADAM28,upstream_gene_variant,,ENST00000521110,;ADAM28,3_prime_UTR_variant,,ENST00000520448,;	T	ENSG00000042980	ENST00000265769	Transcript	missense_variant	910	800	267	P/L	cCa/cTa	.	.	.	1	ADAM28	HGNC	206	protein_coding	YES	CCDS34865.1	ENSP00000265769	ADA28_HUMAN	E5RGY1_HUMAN	UPI000049E0B9	.	deleterious(0.01)	probably_damaging(0.909)	9/23	.	PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF22,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCCCAAATG	.	5	ESCA
PRKDC	0	.	GRCh37	8	48734271	48734271	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9002A>G	p.Tyr3001Cys	p.Y3001C	ENST00000314191	66/87	90	52	37	54	54	0	PRKDC,missense_variant,p.Tyr3001Cys,ENST00000338368,;PRKDC,missense_variant,p.Tyr3001Cys,ENST00000314191,;PRKDC,non_coding_transcript_exon_variant,,ENST00000518216,;PRKDC,non_coding_transcript_exon_variant,,ENST00000523565,;	C	ENSG00000253729	ENST00000314191	Transcript	missense_variant	9059	9002	3001	Y/C	tAc/tGc	.	.	.	-1	PRKDC	HGNC	9413	protein_coding	YES	.	ENSP00000313420	PRKDC_HUMAN	F5GX40_HUMAN	UPI000045790C	.	.	possibly_damaging(0.666)	66/87	.	PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTGTAACAG	.	5	ESCA
CA3	0	.	GRCh37	8	86357447	86357447	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507G>T	p.Lys169Asn	p.K169N	ENST00000285381	5/7	21	13	8	8	8	0	CA3,missense_variant,p.Lys169Asn,ENST00000285381,;CA3,downstream_gene_variant,,ENST00000520921,;RP11-317J10.2,intron_variant,,ENST00000521761,;RP11-317J10.2,intron_variant,,ENST00000517697,;CA3,downstream_gene_variant,,ENST00000522207,;	T	ENSG00000164879	ENST00000285381	Transcript	missense_variant	590	507	169	K/N	aaG/aaT	.	.	.	1	CA3	HGNC	1374	protein_coding	YES	CCDS6238.1	ENSP00000285381	CAH3_HUMAN	E5RHI4_HUMAN	UPI0000049C1A	.	deleterious(0)	probably_damaging(0.973)	5/7	.	PROSITE_profiles:PS51144,hmmpanther:PTHR18952:SF96,hmmpanther:PTHR18952,Gene3D:3.10.200.10,Pfam_domain:PF00194,SMART_domains:SM01057,Superfamily_domains:SSF51069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACAAAGGTAAA	.	3	ESCA
MMP16	0	.	GRCh37	8	89180161	89180161	+	Missense_Mutation	SNP	C	C	T	rs753769443	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.446G>A	p.Arg149His	p.R149H	ENST00000286614	4/10	86	60	26	63	63	0	MMP16,missense_variant,p.Arg149His,ENST00000286614,;MMP16,missense_variant,p.Arg166His,ENST00000522726,;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,;	T	ENSG00000156103	ENST00000286614	Transcript	missense_variant	728	446	149	R/H	cGt/cAt	rs753769443,COSM389664	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	tolerated(0.78)	benign(0.006)	4/10	.	hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,Gene3D:3.40.390.10,Pfam_domain:PF00413,SMART_domains:SM00235,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTACGAGTC	byFrequency	5	ESCA
ANKS6	0	.	GRCh37	9	101542596	101542596	+	Missense_Mutation	SNP	C	C	G	rs753258232	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1243G>C	p.Ala415Pro	p.A415P	ENST00000353234	6/15	66	60	6	54	54	0	ANKS6,missense_variant,p.Ala220Pro,ENST00000540940,;ANKS6,missense_variant,p.Ala114Pro,ENST00000375019,;ANKS6,missense_variant,p.Ala415Pro,ENST00000375018,;ANKS6,missense_variant,p.Ala415Pro,ENST00000353234,;ANKS6,upstream_gene_variant,,ENST00000444472,;ANKS6,downstream_gene_variant,,ENST00000486778,;ANKS6,downstream_gene_variant,,ENST00000466120,;	G	ENSG00000165138	ENST00000353234	Transcript	missense_variant	1291	1243	415	A/P	Gca/Cca	rs753258232	.	.	-1	ANKS6	HGNC	26724	protein_coding	YES	CCDS43856.1	ENSP00000297837	ANKS6_HUMAN	F5H7X9_HUMAN	UPI0000530317	.	deleterious(0)	probably_damaging(0.998)	6/15	.	PROSITE_profiles:PS50297,hmmpanther:PTHR10627,hmmpanther:PTHR10627:SF2,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGATGCCAGCA	.	3	ESCA
SETX	0	.	GRCh37	9	135173511	135173511	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5737G>C	p.Asp1913His	p.D1913H	ENST00000224140	13/26	50	41	8	29	29	0	SETX,missense_variant,p.Asp1913His,ENST00000372169,;SETX,missense_variant,p.Asp155His,ENST00000436441,;SETX,missense_variant,p.Asp1913His,ENST00000393220,;SETX,missense_variant,p.Asp1913His,ENST00000224140,;	G	ENSG00000107290	ENST00000224140	Transcript	missense_variant	5920	5737	1913	D/H	Gac/Cac	.	.	.	-1	SETX	HGNC	445	protein_coding	YES	CCDS6947.1	ENSP00000224140	SETX_HUMAN	.	UPI0000210D28	.	deleterious(0.01)	possibly_damaging(0.859)	13/26	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF336	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGTCCATAG	.	5	ESCA
ARRDC1	0	.	GRCh37	9	140508651	140508651	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.603G>A	p.%3D	p.V201V	ENST00000371421	5/8	77	23	54	40	40	0	ARRDC1,synonymous_variant,p.%3D,ENST00000419386,;ARRDC1,synonymous_variant,p.%3D,ENST00000371421,;EHMT1,upstream_gene_variant,,ENST00000334856,;ARRDC1,downstream_gene_variant,,ENST00000431925,;EHMT1,upstream_gene_variant,,ENST00000462484,;C9orf37,downstream_gene_variant,,ENST00000371417,;EHMT1,upstream_gene_variant,,ENST00000460843,;ARRDC1,non_coding_transcript_exon_variant,,ENST00000471125,;ARRDC1,non_coding_transcript_exon_variant,,ENST00000491911,;ARRDC1,non_coding_transcript_exon_variant,,ENST00000466367,;ARRDC1,non_coding_transcript_exon_variant,,ENST00000495220,;ARRDC1,non_coding_transcript_exon_variant,,ENST00000475658,;ARRDC1,non_coding_transcript_exon_variant,,ENST00000483563,;ARRDC1,non_coding_transcript_exon_variant,,ENST00000497877,;EHMT1,upstream_gene_variant,,ENST00000371394,;ARRDC1,downstream_gene_variant,,ENST00000468983,;C9orf37,downstream_gene_variant,,ENST00000496793,;ARRDC1,downstream_gene_variant,,ENST00000461627,;	A	ENSG00000197070	ENST00000371421	Transcript	synonymous_variant	667	603	201	V	gtG/gtA	.	.	.	1	ARRDC1	HGNC	28633	protein_coding	YES	CCDS7049.1	ENSP00000360475	ARRD1_HUMAN	.	UPI0000072A1F	.	.	.	5/8	.	Superfamily_domains:SSF81296,SMART_domains:SM01017,Pfam_domain:PF02752,hmmpanther:PTHR11188,hmmpanther:PTHR11188:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTGGCCAG	.	5	ESCA
MTMR1	0	.	GRCh37	X	149898659	149898659	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>A	p.Ala204Thr	p.A204T	ENST00000544228	6/15	41	15	26	28	28	0	MTMR1,missense_variant,p.Ala110Thr,ENST00000493995,;MTMR1,missense_variant,p.Ala204Thr,ENST00000542156,;MTMR1,missense_variant,p.Ala110Thr,ENST00000541925,;MTMR1,missense_variant,p.Ala204Thr,ENST00000451863,;MTMR1,missense_variant,p.Ala204Thr,ENST00000370390,;MTMR1,missense_variant,p.Ala91Thr,ENST00000538506,;MTMR1,missense_variant,p.Ala204Thr,ENST00000544228,;MTMR1,missense_variant,p.Ala212Thr,ENST00000445323,;MTMR1,downstream_gene_variant,,ENST00000429965,;MTMR1,downstream_gene_variant,,ENST00000438018,;MTMR1,downstream_gene_variant,,ENST00000490316,;MTMR1,downstream_gene_variant,,ENST00000439546,;MTMR1,downstream_gene_variant,,ENST00000436701,;MTMR1,downstream_gene_variant,,ENST00000434699,;MTMR1,missense_variant,p.Ala204Thr,ENST00000485376,;MTMR1,missense_variant,p.Ala103Thr,ENST00000488357,;MTMR1,non_coding_transcript_exon_variant,,ENST00000493480,;	A	ENSG00000063601	ENST00000544228	Transcript	missense_variant	731	610	204	A/T	Gca/Aca	.	.	.	1	MTMR1	HGNC	7449	protein_coding	YES	CCDS14695.1	ENSP00000440534	MTMR1_HUMAN	F8W8S8_HUMAN,F8W764_HUMAN,E9PIH9_HUMAN,B7Z3D5_HUMAN	UPI0000167F8A	.	deleterious(0.02)	possibly_damaging(0.489)	6/15	.	hmmpanther:PTHR10807:SF40,hmmpanther:PTHR10807,Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACATGCATTT	.	5	ESCA
GPR64	0	.	GRCh37	X	19007957	19007957	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1025C>T	.	.	ENST00000379869	29/29	31	19	12	27	27	0	GPR64,3_prime_UTR_variant,,ENST00000357544,;GPR64,3_prime_UTR_variant,,ENST00000379869,;GPR64,3_prime_UTR_variant,,ENST00000360279,;GPR64,3_prime_UTR_variant,,ENST00000379878,;GPR64,3_prime_UTR_variant,,ENST00000379876,;GPR64,3_prime_UTR_variant,,ENST00000379873,;GPR64,3_prime_UTR_variant,,ENST00000357991,;GPR64,3_prime_UTR_variant,,ENST00000356606,;GPR64,3_prime_UTR_variant,,ENST00000354791,;GPR64,downstream_gene_variant,,ENST00000340581,;	A	ENSG00000173698	ENST00000379869	Transcript	3_prime_UTR_variant	4243	.	.	.	.	.	.	.	-1	GPR64	HGNC	4516	protein_coding	YES	CCDS43923.1	ENSP00000369198	GPR64_HUMAN	.	UPI000021246C	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGGAATCC	.	5	ESCA
PPP2R3B	0	.	GRCh37	X	307473	307473	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.755A>G	p.Lys252Arg	p.K252R	ENST00000390665	5/13	75	32	42	71	71	0	PPP2R3B,missense_variant,p.Lys252Arg,ENST00000390665,;PPP2R3B,downstream_gene_variant,,ENST00000381625,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000475859,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000496630,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000445792,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000477110,;PPP2R3B,upstream_gene_variant,,ENST00000477636,;PPP2R3B,upstream_gene_variant,,ENST00000484364,;PPP2R3B,upstream_gene_variant,,ENST00000468169,;	C	ENSG00000167393	ENST00000390665	Transcript	missense_variant	774	755	252	K/R	aAg/aGg	.	.	.	-1	PPP2R3B	HGNC	13417	protein_coding	YES	CCDS14104.1	ENSP00000375080	P2R3B_HUMAN	Q96FD8_HUMAN	UPI00001BB8B8	.	tolerated(0.31)	benign(0.016)	5/13	.	hmmpanther:PTHR14095,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCTTCAGG	.	5	ESCA
BCOR	0	.	GRCh37	X	39911253	39911253	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*109C>G	.	.	ENST00000378444	15/15	37	11	26	26	26	0	BCOR,3_prime_UTR_variant,,ENST00000397354,;BCOR,3_prime_UTR_variant,,ENST00000442018,;BCOR,3_prime_UTR_variant,,ENST00000378444,;BCOR,3_prime_UTR_variant,,ENST00000427012,;BCOR,3_prime_UTR_variant,,ENST00000378455,;BCOR,3_prime_UTR_variant,,ENST00000342274,;BCOR,intron_variant,,ENST00000378463,;BCOR,intron_variant,,ENST00000413905,;	C	ENSG00000183337	ENST00000378444	Transcript	3_prime_UTR_variant	5606	.	.	.	.	.	.	.	-1	BCOR	HGNC	20893	protein_coding	YES	CCDS48093.1	ENSP00000367705	BCOR_HUMAN	H9A532_HUMAN,H7BZ37_HUMAN,C9JHP3_HUMAN,B3KTC2_HUMAN	UPI00002318CF	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAGATATT	.	5	ESCA
DGKK	0	.	GRCh37	X	50163452	50163452	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A4MQ-01A-11D-A28B-09	TCGA-LN-A4MQ-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.951G>T	.	.	ENST00000376025	4/28	42	36	6	26	26	0	DGKK,non_coding_transcript_exon_variant,,ENST00000376025,;DGKK,non_coding_transcript_exon_variant,,ENST00000546288,;	A	ENSG00000204466	ENST00000376025	Transcript	non_coding_transcript_exon_variant	951	.	.	.	.	.	.	.	-1	DGKK	HGNC	32395	processed_transcript	YES	.	.	.	.	.	.	.	.	4/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCCATGTC	.	5	ESCA
ADARB2	0	.	GRCh37	10	1229040	1229040	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*93A>G	.	.	ENST00000381312	10/10	29	21	8	35	35	0	ADARB2,3_prime_UTR_variant,,ENST00000381310,;ADARB2,3_prime_UTR_variant,,ENST00000381312,;ADARB2,downstream_gene_variant,,ENST00000381305,;ADARB2,non_coding_transcript_exon_variant,,ENST00000474762,;ADARB2,non_coding_transcript_exon_variant,,ENST00000490172,;	C	ENSG00000185736	ENST00000381312	Transcript	3_prime_UTR_variant	2639	.	.	.	.	.	.	.	-1	ADARB2	HGNC	227	protein_coding	YES	CCDS7058.1	ENSP00000370713	RED2_HUMAN	Q5VW43_HUMAN	UPI0000071776	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGAATGCAGG	.	5	ESCA
PTEN	0	.	GRCh37	10	89712008	89712008	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626G>C	p.Gly209Ala	p.G209A	ENST00000371953	6/9	15	11	4	18	18	0	PTEN,missense_variant,p.Gly209Ala,ENST00000371953,;PTEN,non_coding_transcript_exon_variant,,ENST00000472832,;	C	ENSG00000171862	ENST00000371953	Transcript	missense_variant	1983	626	209	G/A	gGa/gCa	.	.	.	1	PTEN	HGNC	9588	protein_coding	YES	CCDS31238.1	ENSP00000361021	PTEN_HUMAN	F6KD01_HUMAN,H6WA51_HUMAN,H6WA46_HUMAN	UPI00001328C5	.	tolerated(0.13)	benign(0.175)	6/9	.	PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Gene3D:1d5rA02,Pfam_domain:PF10409,PIRSF_domain:PIRSF038025,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.0?|c.1_1212del1212|28,CODON|p.G165fs*9|c.493_631del139|3	MUTECT|MUSE	TGGCGGAACTT	.	2	ESCA
TLL2	0	.	GRCh37	10	98136519	98136519	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2378C>A	p.Pro793His	p.P793H	ENST00000357947	18/21	50	24	26	66	66	0	TLL2,missense_variant,p.Pro793His,ENST00000357947,;TLL2,upstream_gene_variant,,ENST00000506028,;	T	ENSG00000095587	ENST00000357947	Transcript	missense_variant	2604	2378	793	P/H	cCt/cAt	.	.	.	-1	TLL2	HGNC	11844	protein_coding	YES	CCDS7449.1	ENSP00000350630	TLL2_HUMAN	.	UPI0000073AEE	.	deleterious(0)	probably_damaging(1)	18/21	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF613,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,PIRSF_domain:PIRSF001199,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCAGGCCAG	.	5	ESCA
DYNC2H1	0	.	GRCh37	11	103158284	103158284	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11066G>C	p.Arg3689Thr	p.R3689T	ENST00000398093	76/90	27	8	18	40	40	0	DYNC2H1,missense_variant,p.Arg3689Thr,ENST00000398093,;DYNC2H1,missense_variant,p.Arg3682Thr,ENST00000375735,;DYNC2H1,intron_variant,,ENST00000334267,;DYNC2H1,missense_variant,p.Arg75Thr,ENST00000528670,;DYNC2H1,non_coding_transcript_exon_variant,,ENST00000525306,;	C	ENSG00000187240	ENST00000398093	Transcript	missense_variant	11066	11066	3689	R/T	aGa/aCa	.	.	.	1	DYNC2H1	HGNC	2962	protein_coding	YES	CCDS44717.1	ENSP00000381167	DYHC2_HUMAN	.	UPI0000481AC7	.	.	probably_damaging(0.996)	76/90	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF34,Pfam_domain:PF03028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTAAGACCGG	.	5	ESCA
EIF4G2	0	.	GRCh37	11	10820915	10820915	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2381C>G	p.Ser794Cys	p.S794C	ENST00000526148	20/22	20	16	4	28	28	0	EIF4G2,missense_variant,p.Ser756Cys,ENST00000396525,;EIF4G2,missense_variant,p.Ser142Cys,ENST00000528839,;EIF4G2,missense_variant,p.Ser794Cys,ENST00000339995,;EIF4G2,missense_variant,p.Ser794Cys,ENST00000525681,;EIF4G2,missense_variant,p.Ser794Cys,ENST00000526148,;EIF4G2,downstream_gene_variant,,ENST00000532082,;EIF4G2,downstream_gene_variant,,ENST00000531416,;EIF4G2,downstream_gene_variant,,ENST00000527419,;EIF4G2,downstream_gene_variant,,ENST00000531180,;EIF4G2,downstream_gene_variant,,ENST00000524932,;SNORD97,downstream_gene_variant,,ENST00000459187,;RP11-685M7.5,intron_variant,,ENST00000532365,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000534272,;EIF4G2,intron_variant,,ENST00000532120,;EIF4G2,downstream_gene_variant,,ENST00000531507,;EIF4G2,downstream_gene_variant,,ENST00000525972,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000532383,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000525606,;EIF4G2,downstream_gene_variant,,ENST00000527015,;EIF4G2,downstream_gene_variant,,ENST00000532349,;EIF4G2,downstream_gene_variant,,ENST00000534605,;EIF4G2,downstream_gene_variant,,ENST00000530564,;EIF4G2,downstream_gene_variant,,ENST00000532152,;EIF4G2,downstream_gene_variant,,ENST00000531647,;EIF4G2,upstream_gene_variant,,ENST00000534470,;	C	ENSG00000110321	ENST00000526148	Transcript	missense_variant	2892	2381	794	S/C	tCc/tGc	.	.	.	-1	EIF4G2	HGNC	3297	protein_coding	YES	CCDS31428.1	ENSP00000433664	.	Q59G42_HUMAN,Q2TU89_HUMAN,H0YEN8_HUMAN,H0YEC5_HUMAN,H0YDC0_HUMAN,H0YD99_HUMAN,H0YD77_HUMAN,H0YCF8_HUMAN,D3DQV9_HUMAN,B4DZF2_HUMAN	UPI000013C8BE	.	tolerated(0.16)	possibly_damaging(0.619)	20/22	.	PROSITE_profiles:PS51363,hmmpanther:PTHR23253,Gene3D:1.25.40.180,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGGATGAA	.	5	ESCA
BACE1	0	.	GRCh37	11	117158124	117158124	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2158A>G	.	.	ENST00000313005	9/9	15	9	5	29	29	0	BACE1,3_prime_UTR_variant,,ENST00000528053,;BACE1,3_prime_UTR_variant,,ENST00000313005,;BACE1,3_prime_UTR_variant,,ENST00000392937,;BACE1,downstream_gene_variant,,ENST00000510630,;BACE1,downstream_gene_variant,,ENST00000445823,;BACE1,downstream_gene_variant,,ENST00000510915,;BACE1,downstream_gene_variant,,ENST00000428381,;RNF214,downstream_gene_variant,,ENST00000531452,;RNF214,downstream_gene_variant,,ENST00000531287,;RNF214,downstream_gene_variant,,ENST00000300650,;RNF214,downstream_gene_variant,,ENST00000530849,;BACE1,downstream_gene_variant,,ENST00000513780,;RNF214,downstream_gene_variant,,ENST00000524917,;RNF214,downstream_gene_variant,,ENST00000534709,;BACE1,downstream_gene_variant,,ENST00000530824,;BACE1,downstream_gene_variant,,ENST00000509916,;	C	ENSG00000186318	ENST00000313005	Transcript	3_prime_UTR_variant	4125	.	.	.	.	.	.	.	-1	BACE1	HGNC	933	protein_coding	YES	CCDS8383.1	ENSP00000318585	BACE1_HUMAN	U3KPS1_HUMAN,H0YDX0_HUMAN	UPI000013F419	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TATAATACATA	.	4	ESCA
CCDC34	0	.	GRCh37	11	27384468	27384468	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274G>A	p.Asp92Asn	p.D92N	ENST00000328697	1/6	35	25	10	38	38	0	CCDC34,missense_variant,p.Asp92Asn,ENST00000328697,;CCDC34,missense_variant,p.Asp92Asn,ENST00000317945,;LGR4,downstream_gene_variant,,ENST00000389858,;LGR4,downstream_gene_variant,,ENST00000379214,;	T	ENSG00000109881	ENST00000328697	Transcript	missense_variant	948	274	92	D/N	Gat/Aat	.	.	.	-1	CCDC34	HGNC	25079	protein_coding	YES	CCDS31448.1	ENSP00000330240	CCD34_HUMAN	.	UPI000050C095	.	tolerated(0.09)	benign(0.007)	1/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23247:SF1,hmmpanther:PTHR23247,Pfam_domain:PF13904	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATCATCCA	.	5	ESCA
KCNA4	0	.	GRCh37	11	30034490	30034490	+	5'UTR	SNP	C	C	T	rs557468064	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-265G>A	.	.	ENST00000328224	2/2	28	14	14	46	46	0	KCNA4,5_prime_UTR_variant,,ENST00000328224,;KCNA4,non_coding_transcript_exon_variant,,ENST00000526518,;	T	ENSG00000182255	ENST00000328224	Transcript	5_prime_UTR_variant	970	.	.	.	.	rs557468064	.	.	-1	KCNA4	HGNC	6222	protein_coding	YES	CCDS41629.1	ENSP00000328511	KCNA4_HUMAN	.	UPI00001649FF	.	.	.	2/2	.	.	T:0.0016	T:0	T:0	.	T:0.001	T:0	T:0.0072	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCCGAAAA	byFrequency|by1000G	5	ESCA
SLC1A2	0	.	GRCh37	11	35275000	35275000	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7441C>G	.	.	ENST00000278379	11/11	15	12	3	23	23	0	SLC1A2,3_prime_UTR_variant,,ENST00000395753,;SLC1A2,3_prime_UTR_variant,,ENST00000395750,;SLC1A2,3_prime_UTR_variant,,ENST00000278379,;SLC1A2,downstream_gene_variant,,ENST00000464522,;	C	ENSG00000110436	ENST00000278379	Transcript	3_prime_UTR_variant	9449	.	.	.	.	.	.	.	-1	SLC1A2	HGNC	10940	protein_coding	YES	CCDS31459.1	ENSP00000278379	EAA2_HUMAN	A2A2U1_HUMAN	UPI0000129B12	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTCTGATCTA	.	2	ESCA
SLC1A2	0	.	GRCh37	11	35275135	35275135	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7306C>G	.	.	ENST00000278379	11/11	33	21	11	50	50	0	SLC1A2,3_prime_UTR_variant,,ENST00000395753,;SLC1A2,3_prime_UTR_variant,,ENST00000395750,;SLC1A2,3_prime_UTR_variant,,ENST00000278379,;SLC1A2,downstream_gene_variant,,ENST00000464522,;	C	ENSG00000110436	ENST00000278379	Transcript	3_prime_UTR_variant	9314	.	.	.	.	.	.	.	-1	SLC1A2	HGNC	10940	protein_coding	YES	CCDS31459.1	ENSP00000278379	EAA2_HUMAN	A2A2U1_HUMAN	UPI0000129B12	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAAGATGAA	.	5	ESCA
F2	0	.	GRCh37	11	46749672	46749672	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1257G>A	p.%3D	p.E419E	ENST00000311907	10/14	38	24	14	38	38	0	F2,synonymous_variant,p.%3D,ENST00000530231,;F2,synonymous_variant,p.%3D,ENST00000311907,;F2,downstream_gene_variant,,ENST00000442468,;F2,downstream_gene_variant,,ENST00000490274,;	A	ENSG00000180210	ENST00000311907	Transcript	synonymous_variant	1313	1257	419	E	gaG/gaA	.	.	.	1	F2	HGNC	3535	protein_coding	YES	CCDS31476.1	ENSP00000308541	THRB_HUMAN	Q8TD58_HUMAN,Q86WA1_HUMAN	UPI0000136ECD	.	.	.	10/14	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24254,hmmpanther:PTHR24254:SF8,Pfam_domain:PF00089,Gene3D:2.40.10.10,PIRSF_domain:PIRSF001149,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR01505	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGAGAATGA	.	5	ESCA
SDHAF2	0	.	GRCh37	11	61205246	61205246	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186C>T	p.%3D	p.S62S	ENST00000301761	2/4	17	10	7	12	12	0	SDHAF2,synonymous_variant,p.%3D,ENST00000534878,;SDHAF2,synonymous_variant,p.%3D,ENST00000537782,;SDHAF2,synonymous_variant,p.%3D,ENST00000301761,;SDHAF2,synonymous_variant,p.%3D,ENST00000543265,;RP11-286N22.8,synonymous_variant,p.%3D,ENST00000541135,;SDHAF2,intron_variant,,ENST00000542074,;RP11-286N22.8,non_coding_transcript_exon_variant,,ENST00000544025,;RP11-286N22.8,non_coding_transcript_exon_variant,,ENST00000544880,;RP11-286N22.8,synonymous_variant,p.%3D,ENST00000544801,;RP11-286N22.8,synonymous_variant,p.%3D,ENST00000543044,;SDHAF2,synonymous_variant,p.%3D,ENST00000359614,;RP11-286N22.8,synonymous_variant,p.%3D,ENST00000538594,;SDHAF2,3_prime_UTR_variant,,ENST00000536250,;SDHAF2,3_prime_UTR_variant,,ENST00000542794,;RP11-286N22.8,non_coding_transcript_exon_variant,,ENST00000536670,;	T	ENSG00000167985	ENST00000301761	Transcript	synonymous_variant	260	186	62	S	tcC/tcT	.	.	.	1	SDHAF2	HGNC	26034	protein_coding	YES	CCDS8007.1	ENSP00000301761	SDHF2_HUMAN	F5GYJ5_HUMAN	UPI0000039E6D	.	.	.	2/4	.	HAMAP:MF_03057,hmmpanther:PTHR12469,hmmpanther:PTHR12469:SF2,Gene3D:1.10.150.250,Superfamily_domains:0042477	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAATCCATAGA	.	2	ESCA
TIGD3	0	.	GRCh37	11	65124656	65124656	+	Silent	SNP	C	C	T	rs750375970	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1377C>T	p.%3D	p.Y459Y	ENST00000309880	2/2	38	30	7	54	54	0	TIGD3,synonymous_variant,p.%3D,ENST00000309880,;DPF2,downstream_gene_variant,,ENST00000531989,;DPF2,downstream_gene_variant,,ENST00000252268,;DPF2,downstream_gene_variant,,ENST00000415073,;DPF2,downstream_gene_variant,,ENST00000528416,;DPF2,downstream_gene_variant,,ENST00000524666,;DPF2,downstream_gene_variant,,ENST00000532052,;	T	ENSG00000173825	ENST00000309880	Transcript	synonymous_variant	1584	1377	459	Y	taC/taT	rs750375970	.	.	1	TIGD3	HGNC	18334	protein_coding	YES	CCDS8101.1	ENSP00000308354	TIGD3_HUMAN	.	UPI000013EF51	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTACGACTG	.	5	ESCA
RBM4	0	.	GRCh37	11	66407134	66407134	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-49G>C	.	.	ENST00000409406	1/3	118	78	39	113	113	0	RBM4,5_prime_UTR_variant,,ENST00000409406,;RBM14-RBM4,intron_variant,,ENST00000412278,;RBM4,intron_variant,,ENST00000503028,;RBM4,intron_variant,,ENST00000398692,;RBM4,intron_variant,,ENST00000408993,;RBM4,intron_variant,,ENST00000506523,;RBM4,intron_variant,,ENST00000532968,;RBM4,intron_variant,,ENST00000510173,;RBM4,intron_variant,,ENST00000483858,;RBM4,intron_variant,,ENST00000396053,;RBM4,intron_variant,,ENST00000530235,;RBM4,intron_variant,,ENST00000514361,;RBM4,intron_variant,,ENST00000310092,;RBM4,intron_variant,,ENST00000578778,;RBM14-RBM4,intron_variant,,ENST00000500635,;RBM4,intron_variant,,ENST00000528039,;RBM14-RBM4,downstream_gene_variant,,ENST00000511114,;RBM4,upstream_gene_variant,,ENST00000515838,;RBM14-RBM4,intron_variant,,ENST00000421355,;	C	ENSG00000173933	ENST00000409406	Transcript	5_prime_UTR_variant	729	.	.	.	.	.	.	.	1	RBM4	HGNC	9901	protein_coding	YES	CCDS41676.1	ENSP00000386894	RBM4_HUMAN	.	UPI0000073FC1	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTGAGGTC	.	5	ESCA
RBM4	0	.	GRCh37	11	66407231	66407231	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.49G>C	p.Glu17Gln	p.E17Q	ENST00000409406	1/3	98	58	39	129	129	0	RBM4,missense_variant,p.Glu17Gln,ENST00000503028,;RBM4,missense_variant,p.Glu17Gln,ENST00000398692,;RBM4,missense_variant,p.Glu17Gln,ENST00000409406,;RBM4,missense_variant,p.Glu17Gln,ENST00000408993,;RBM4,missense_variant,p.Glu17Gln,ENST00000506523,;RBM4,missense_variant,p.Glu17Gln,ENST00000532968,;RBM4,missense_variant,p.Glu17Gln,ENST00000510173,;RBM4,missense_variant,p.Glu17Gln,ENST00000483858,;RBM4,missense_variant,p.Glu17Gln,ENST00000396053,;RBM4,missense_variant,p.Glu17Gln,ENST00000530235,;RBM4,missense_variant,p.Glu17Gln,ENST00000310092,;RBM4,missense_variant,p.Glu17Gln,ENST00000578778,;RBM14-RBM4,intron_variant,,ENST00000412278,;RBM4,intron_variant,,ENST00000514361,;RBM14-RBM4,intron_variant,,ENST00000500635,;RBM4,intron_variant,,ENST00000528039,;RBM14-RBM4,downstream_gene_variant,,ENST00000511114,;RBM4,upstream_gene_variant,,ENST00000515838,;RBM14-RBM4,missense_variant,p.Gly133Ala,ENST00000421355,;	C	ENSG00000173933	ENST00000409406	Transcript	missense_variant	826	49	17	E/Q	Gag/Cag	.	.	.	1	RBM4	HGNC	9901	protein_coding	YES	CCDS41676.1	ENSP00000386894	RBM4_HUMAN	.	UPI0000073FC1	.	deleterious(0)	possibly_damaging(0.692)	1/3	.	Superfamily_domains:SSF54928,SMART_domains:SM00360,Gene3D:3.30.70.330,Pfam_domain:PF00076,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF242,PROSITE_profiles:PS50102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGGAGATT	.	5	ESCA
FADD	0	.	GRCh37	11	70049577	70049577	+	Missense_Mutation	SNP	C	C	G	rs774870663	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12C>G	p.Phe4Leu	p.F4L	ENST00000301838	1/2	243	230	13	56	56	0	FADD,missense_variant,p.Phe4Leu,ENST00000301838,;RP11-805J14.5,downstream_gene_variant,,ENST00000527232,;RP11-805J14.5,downstream_gene_variant,,ENST00000526174,;	G	ENSG00000168040	ENST00000301838	Transcript	missense_variant	309	12	4	F/L	ttC/ttG	rs774870663	.	.	1	FADD	HGNC	3573	protein_coding	YES	CCDS8196.1	ENSP00000301838	FADD_HUMAN	Q6LCG1_HUMAN,Q6LCB0_HUMAN	UPI000012A4D1	.	deleterious(0)	benign(0.432)	1/2	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50168,hmmpanther:PTHR15077,Gene3D:1.10.533.10,Pfam_domain:PF01335,PIRSF_domain:PIRSF018586,SMART_domains:SM00031,Superfamily_domains:SSF47986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGTTCCTGGT	.	2	ESCA
FADD	0	.	GRCh37	11	70049640	70049640	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75C>T	p.%3D	p.F25F	ENST00000301838	1/2	316	295	21	64	64	0	FADD,synonymous_variant,p.%3D,ENST00000301838,;RP11-805J14.5,downstream_gene_variant,,ENST00000527232,;RP11-805J14.5,downstream_gene_variant,,ENST00000526174,;	T	ENSG00000168040	ENST00000301838	Transcript	synonymous_variant	372	75	25	F	ttC/ttT	.	.	.	1	FADD	HGNC	3573	protein_coding	YES	CCDS8196.1	ENSP00000301838	FADD_HUMAN	Q6LCG1_HUMAN,Q6LCB0_HUMAN	UPI000012A4D1	.	.	.	1/2	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50168,hmmpanther:PTHR15077,Gene3D:1.10.533.10,Pfam_domain:PF01335,PIRSF_domain:PIRSF018586,SMART_domains:SM00031,Superfamily_domains:SSF47986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTTCCTATG	.	2	ESCA
FADD	0	.	GRCh37	11	70049700	70049700	+	Silent	SNP	C	C	G	rs765079539	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.135C>G	p.%3D	p.L45L	ENST00000301838	1/2	210	200	10	41	41	0	FADD,synonymous_variant,p.%3D,ENST00000301838,;RP11-805J14.5,downstream_gene_variant,,ENST00000527232,;RP11-805J14.5,downstream_gene_variant,,ENST00000526174,;	G	ENSG00000168040	ENST00000301838	Transcript	synonymous_variant	432	135	45	L	ctC/ctG	rs765079539	.	.	1	FADD	HGNC	3573	protein_coding	YES	CCDS8196.1	ENSP00000301838	FADD_HUMAN	Q6LCG1_HUMAN,Q6LCB0_HUMAN	UPI000012A4D1	.	.	.	1/2	.	PROSITE_profiles:PS50168,hmmpanther:PTHR15077,Gene3D:1.10.533.10,Pfam_domain:PF01335,PIRSF_domain:PIRSF018586,SMART_domains:SM00031,Superfamily_domains:SSF47986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTCTTCTC	.	2	ESCA
CCDC67	0	.	GRCh37	11	93141459	93141459	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1389G>A	p.%3D	p.E463E	ENST00000298050	12/14	18	11	7	28	28	0	CCDC67,synonymous_variant,p.%3D,ENST00000534747,;CCDC67,synonymous_variant,p.%3D,ENST00000525646,;CCDC67,synonymous_variant,p.%3D,ENST00000298050,;CCDC67,upstream_gene_variant,,ENST00000529909,;AP004242.1,upstream_gene_variant,,ENST00000408638,;CCDC67,synonymous_variant,p.%3D,ENST00000531448,;CCDC67,3_prime_UTR_variant,,ENST00000530862,;	A	ENSG00000165325	ENST00000298050	Transcript	synonymous_variant	1489	1389	463	E	gaG/gaA	.	.	.	1	CCDC67	HGNC	26344	protein_coding	YES	CCDS44707.1	ENSP00000298050	CCD67_HUMAN	E9PIY2_HUMAN,E9PPB2_HUMAN,E9PIV7_HUMAN	UPI0000161951	.	.	.	12/14	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18875:SF5,hmmpanther:PTHR18875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGAGAATGA	.	5	ESCA
ACTR6	0	.	GRCh37	12	100603884	100603884	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.413A>G	p.Asp138Gly	p.D138G	ENST00000188312	5/11	39	32	6	48	48	0	ACTR6,missense_variant,p.Asp56Gly,ENST00000551617,;ACTR6,missense_variant,p.Asp150Gly,ENST00000551652,;ACTR6,missense_variant,p.Asp138Gly,ENST00000188312,;ACTR6,missense_variant,p.Asp138Gly,ENST00000552376,;ACTR6,missense_variant,p.Asp56Gly,ENST00000546902,;ACTR6,downstream_gene_variant,,ENST00000550813,;ACTR6,3_prime_UTR_variant,,ENST00000547458,;ACTR6,3_prime_UTR_variant,,ENST00000548180,;ACTR6,intron_variant,,ENST00000552064,;ACTR6,intron_variant,,ENST00000553038,;DEPDC4,intron_variant,,ENST00000378244,;ACTR6,downstream_gene_variant,,ENST00000551517,;ACTR6,downstream_gene_variant,,ENST00000551440,;ACTR6,downstream_gene_variant,,ENST00000549977,;	G	ENSG00000075089	ENST00000188312	Transcript	missense_variant	1178	413	138	D/G	gAt/gGt	.	.	.	1	ACTR6	HGNC	24025	protein_coding	YES	CCDS9074.1	ENSP00000188312	ARP6_HUMAN	Q7Z4D2_HUMAN,G3V1Y1_HUMAN	UPI0000044716	.	tolerated(0.09)	benign(0.005)	5/11	.	hmmpanther:PTHR11937:SF21,hmmpanther:PTHR11937,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGAGATAATC	.	5	ESCA
ANO4	0	.	GRCh37	12	101295550	101295550	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-14G>A	.	.	ENST00000392979	2/27	18	11	7	31	31	0	ANO4,missense_variant,p.Arg162Lys,ENST00000538618,;ANO4,5_prime_UTR_variant,,ENST00000299222,;ANO4,5_prime_UTR_variant,,ENST00000546991,;ANO4,5_prime_UTR_variant,,ENST00000392977,;ANO4,5_prime_UTR_variant,,ENST00000392979,;ANO4,downstream_gene_variant,,ENST00000551148,;ANO4,5_prime_UTR_variant,,ENST00000549155,;	A	ENSG00000151572	ENST00000392979	Transcript	5_prime_UTR_variant	348	.	.	.	.	.	.	.	1	ANO4	HGNC	23837	protein_coding	YES	CCDS31884.1	ENSP00000376705	ANO4_HUMAN	.	UPI0000198E2E	.	.	.	2/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGAAGGT	.	5	ESCA
CCDC62	0	.	GRCh37	12	123286164	123286164	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1471G>T	p.Glu491Ter	p.E491*	ENST00000253079	9/13	45	36	9	58	58	0	CCDC62,stop_gained,p.Glu252Ter,ENST00000537566,;CCDC62,stop_gained,p.Glu491Ter,ENST00000392441,;CCDC62,stop_gained,p.Glu491Ter,ENST00000253079,;CCDC62,stop_gained,p.Glu252Ter,ENST00000392440,;CCDC62,stop_gained,p.Glu491Ter,ENST00000341952,;	T	ENSG00000130783	ENST00000253079	Transcript	stop_gained	1815	1471	491	E/*	Gaa/Taa	.	.	.	1	CCDC62	HGNC	30723	protein_coding	YES	CCDS9238.1	ENSP00000253079	CCD62_HUMAN	.	UPI0000366924	.	.	.	9/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGGAAAGG	.	5	ESCA
GOLGA3	0	.	GRCh37	12	133351637	133351637	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4143+90C>A	.	.	ENST00000204726	.	10	5	5	22	22	0	GOLGA3,3_prime_UTR_variant,,ENST00000456883,;GOLGA3,intron_variant,,ENST00000204726,;GOLGA3,intron_variant,,ENST00000450791,;GOLGA3,intron_variant,,ENST00000541013,;	T	ENSG00000090615	ENST00000204726	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	.	.	.	22/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTATGTCTGA	.	3	ESCA
PLBD1	0	.	GRCh37	12	14659951	14659951	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1288T>G	p.Leu430Val	p.L430V	ENST00000240617	9/11	55	47	8	34	34	0	PLBD1,missense_variant,p.Leu430Val,ENST00000240617,;PLBD1,downstream_gene_variant,,ENST00000541800,;PLBD1,downstream_gene_variant,,ENST00000541618,;	C	ENSG00000121316	ENST00000240617	Transcript	missense_variant	1941	1288	430	L/V	Tta/Gta	.	.	.	-1	PLBD1	HGNC	26215	protein_coding	YES	CCDS31751.1	ENSP00000240617	PLBL1_HUMAN	F5H053_HUMAN	UPI00004565DA	.	deleterious(0.01)	possibly_damaging(0.648)	9/11	.	hmmpanther:PTHR12370,Pfam_domain:PF04916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTAAATCAT	.	5	ESCA
PTPRO	0	.	GRCh37	12	15739974	15739974	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3399C>T	p.%3D	p.I1133I	ENST00000281171	24/27	30	23	7	42	42	0	PTPRO,synonymous_variant,p.%3D,ENST00000348962,;PTPRO,synonymous_variant,p.%3D,ENST00000281171,;PTPRO,synonymous_variant,p.%3D,ENST00000544244,;PTPRO,synonymous_variant,p.%3D,ENST00000535322,;PTPRO,synonymous_variant,p.%3D,ENST00000445537,;PTPRO,synonymous_variant,p.%3D,ENST00000542557,;PTPRO,synonymous_variant,p.%3D,ENST00000442921,;	T	ENSG00000151490	ENST00000281171	Transcript	synonymous_variant	3729	3399	1133	I	atC/atT	.	.	.	1	PTPRO	HGNC	9678	protein_coding	YES	CCDS8675.1	ENSP00000281171	PTPRO_HUMAN	B4DS16_HUMAN	UPI000013DC62	.	.	.	24/27	.	PROSITE_profiles:PS50056,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF251,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00404,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATCATTCA	.	5	ESCA
SSPN	0	.	GRCh37	12	26383707	26383707	+	Frame_Shift_Del	DEL	G	G	-	rs374423870	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.430delG	p.Ala144ProfsTer38	p.A144Pfs*38	ENST00000242729	3/3	63	51	12	34	34	0	SSPN,frameshift_variant,p.Ala41ProfsTer38,ENST00000540266,;SSPN,frameshift_variant,p.Ala41ProfsTer38,ENST00000538142,;SSPN,frameshift_variant,p.Ala41ProfsTer38,ENST00000422622,;SSPN,frameshift_variant,p.Ala144ProfsTer38,ENST00000242729,;SSPN,intron_variant,,ENST00000535504,;RP11-283G6.4,intron_variant,,ENST00000540392,;RP11-283G6.5,downstream_gene_variant,,ENST00000540625,;RP11-283G6.5,downstream_gene_variant,,ENST00000537525,;RP11-283G6.5,downstream_gene_variant,,ENST00000541940,;SSPN,intron_variant,,ENST00000544231,;SSPN,intron_variant,,ENST00000534829,;	-	ENSG00000123096	ENST00000242729	Transcript	frameshift_variant	607	430	144	A/X	Gcc/cc	rs374423870	.	.	1	SSPN	HGNC	11322	protein_coding	YES	CCDS8707.1	ENSP00000242729	SSPN_HUMAN	F5H381_HUMAN	UPI0000135FF0	.	.	.	3/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15260,Pfam_domain:PF04103	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	T:0	T:0.0001	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTGCCGCCCAC	byCluster|by1000G	3	ESCA
ATN1	0	.	GRCh37	12	7046294	7046294	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1864G>C	p.Ala622Pro	p.A622P	ENST00000356654	5/10	44	18	26	28	28	0	ATN1,missense_variant,p.Ala622Pro,ENST00000396684,;ATN1,missense_variant,p.Ala622Pro,ENST00000356654,;ATN1,upstream_gene_variant,,ENST00000537488,;ATN1,upstream_gene_variant,,ENST00000541029,;	C	ENSG00000111676	ENST00000356654	Transcript	missense_variant	2101	1864	622	A/P	Gct/Cct	.	.	.	1	ATN1	HGNC	3033	protein_coding	YES	CCDS31734.1	ENSP00000349076	ATN1_HUMAN	Q86V38_HUMAN	UPI000006F554	.	.	probably_damaging(0.995)	5/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13859:SF9,hmmpanther:PTHR13859,Pfam_domain:PF03154	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTGGCTTCC	.	5	ESCA
TPTE2	0	.	GRCh37	13	19997096	19997096	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*106A>G	.	.	ENST00000400230	20/20	43	28	15	38	38	0	TPTE2,3_prime_UTR_variant,,ENST00000255310,;TPTE2,3_prime_UTR_variant,,ENST00000382978,;TPTE2,3_prime_UTR_variant,,ENST00000400103,;TPTE2,3_prime_UTR_variant,,ENST00000400230,;TPTE2,downstream_gene_variant,,ENST00000382977,;TPTE2,downstream_gene_variant,,ENST00000457266,;TPTE2,downstream_gene_variant,,ENST00000382975,;TPTE2,downstream_gene_variant,,ENST00000390680,;TPTE2,downstream_gene_variant,,ENST00000462409,;	C	ENSG00000132958	ENST00000400230	Transcript	3_prime_UTR_variant	1720	.	.	.	.	.	.	.	-1	TPTE2	HGNC	17299	protein_coding	YES	CCDS45014.1	ENSP00000383089	TPTE2_HUMAN	.	UPI000040738D	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGACTTAGGA	.	2	ESCA
SACS	0	.	GRCh37	13	23914586	23914586	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3429A>T	p.Gln1143His	p.Q1143H	ENST00000382298	10/10	37	25	12	26	26	0	SACS,missense_variant,p.Gln1143His,ENST00000382292,;SACS,missense_variant,p.Gln393His,ENST00000402364,;SACS,missense_variant,p.Gln1143His,ENST00000382298,;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,;	A	ENSG00000151835	ENST00000382298	Transcript	missense_variant	4018	3429	1143	Q/H	caA/caT	.	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	benign(0.002)	10/10	.	hmmpanther:PTHR15600:SF26,hmmpanther:PTHR15600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGATTGCAA	.	5	ESCA
PARP4	0	.	GRCh37	13	25058793	25058793	+	Silent	SNP	G	G	A	rs762180264	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1446C>T	p.%3D	p.L482L	ENST00000381989	12/34	81	60	21	84	84	0	PARP4,synonymous_variant,p.%3D,ENST00000381989,;TPTE2P6,intron_variant,,ENST00000445572,;	A	ENSG00000102699	ENST00000381989	Transcript	synonymous_variant	1552	1446	482	L	ctC/ctT	rs762180264	.	.	-1	PARP4	HGNC	271	protein_coding	YES	CCDS9307.1	ENSP00000371419	PARP4_HUMAN	.	UPI000013C76E	.	.	.	12/34	.	PROSITE_profiles:PS51059,Pfam_domain:PF00644,Gene3D:3.90.228.10,Superfamily_domains:SSF56399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCTGAGCGA	.	5	ESCA
RNF6	0	.	GRCh37	13	26788056	26788056	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1963C>G	p.His655Asp	p.H655D	ENST00000381588	5/5	20	8	12	32	32	0	RNF6,missense_variant,p.His655Asp,ENST00000346166,;RNF6,missense_variant,p.His655Asp,ENST00000381570,;RNF6,missense_variant,p.His655Asp,ENST00000381588,;RNF6,missense_variant,p.His299Asp,ENST00000399762,;RNF6,intron_variant,,ENST00000468480,;RNF6,downstream_gene_variant,,ENST00000498039,;	C	ENSG00000127870	ENST00000381588	Transcript	missense_variant	2716	1963	655	H/D	Cac/Gac	.	.	.	-1	RNF6	HGNC	10069	protein_coding	YES	CCDS9316.1	ENSP00000371000	RNF6_HUMAN	.	UPI0000000A0A	.	deleterious(0)	possibly_damaging(0.876)	5/5	.	Superfamily_domains:SSF57850,SMART_domains:SM00184,Gene3D:3.30.40.10,Pfam_domain:PF13639,hmmpanther:PTHR14155,hmmpanther:PTHR14155:SF4,PROSITE_profiles:PS50089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGTGAAATT	.	5	ESCA
FAM194B	0	.	GRCh37	13	46124142	46124142	+	Missense_Mutation	SNP	G	G	A	rs766375144	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1532C>T	p.Ala511Val	p.A511V	ENST00000298738	13/15	69	33	35	80	80	0	FAM194B,missense_variant,p.Ala511Val,ENST00000298738,;RNA5SP27,downstream_gene_variant,,ENST00000363839,;FAM194B,non_coding_transcript_exon_variant,,ENST00000504261,;FAM194B,non_coding_transcript_exon_variant,,ENST00000482992,;TIMM9P3,downstream_gene_variant,,ENST00000428659,;	A	ENSG00000165837	ENST00000298738	Transcript	missense_variant	1697	1532	511	A/V	gCg/gTg	rs766375144	.	.	-1	FAM194B	HGNC	26523	protein_coding	YES	CCDS45045.1	ENSP00000298738	F194B_HUMAN	.	UPI000013E513	.	tolerated(0.24)	benign(0.004)	13/15	.	hmmpanther:PTHR23093:SF12,hmmpanther:PTHR23093,Pfam_domain:PF14977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCGCATAT	.	5	ESCA
GUCY1B2	0	.	GRCh37	13	51594715	51594715	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1252C>A	.	.	ENST00000493639	10/17	61	28	33	62	61	1	GUCY1B2,non_coding_transcript_exon_variant,,ENST00000493639,;GUCY1B2,non_coding_transcript_exon_variant,,ENST00000389600,;GUCY1B2,non_coding_transcript_exon_variant,,ENST00000532104,;GUCY1B2,intron_variant,,ENST00000533288,;GUCY1B2,non_coding_transcript_exon_variant,,ENST00000531898,;GUCY1B2,non_coding_transcript_exon_variant,,ENST00000537462,;	T	ENSG00000123201	ENST00000493639	Transcript	non_coding_transcript_exon_variant	1252	.	.	.	.	.	.	.	-1	GUCY1B2	HGNC	4686	processed_transcript	YES	.	.	.	.	.	.	.	.	10/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAGGAGGAT	.	5	ESCA
RTL1	0	.	GRCh37	14	101347784	101347784	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3342G>T	p.%3D	p.R1114R	ENST00000534062	1/1	47	36	10	53	53	0	RTL1,synonymous_variant,p.%3D,ENST00000534062,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,upstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,;MIR127,upstream_gene_variant,,ENST00000384876,;MIR431,downstream_gene_variant,,ENST00000385266,;	A	ENSG00000254656	ENST00000534062	Transcript	synonymous_variant	3401	3342	1114	R	cgG/cgT	.	.	.	-1	RTL1	HGNC	14665	protein_coding	YES	CCDS53910.1	ENSP00000435342	RTL1_HUMAN	.	UPI00001D7B9E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCACCCGCAT	.	5	ESCA
TRAF3	0	.	GRCh37	14	103371584	103371584	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1170G>C	p.Gln390His	p.Q390H	ENST00000560371	11/11	59	33	26	62	62	0	TRAF3,missense_variant,p.Gln390His,ENST00000392745,;TRAF3,missense_variant,p.Gln390His,ENST00000560371,;TRAF3,missense_variant,p.Gln365His,ENST00000351691,;TRAF3,missense_variant,p.Gln218His,ENST00000559734,;TRAF3,missense_variant,p.Gln307His,ENST00000539721,;TRAF3,missense_variant,p.Gln365His,ENST00000347662,;	C	ENSG00000131323	ENST00000560371	Transcript	missense_variant	1387	1170	390	Q/H	caG/caC	.	.	.	1	TRAF3	HGNC	12033	protein_coding	YES	CCDS9975.1	ENSP00000454207	TRAF3_HUMAN	H0YMI8_HUMAN	UPI000000CBF9	.	tolerated(0.12)	benign(0.058)	11/11	.	hmmpanther:PTHR10131,hmmpanther:PTHR10131:SF72,PIRSF_domain:PIRSF015614,Superfamily_domains:SSF57953	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCAGATGCT	.	5	ESCA
SDR39U1	0	.	GRCh37	14	24909952	24909952	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472+37T>C	.	.	ENST00000399395	.	23	16	7	35	35	0	SDR39U1,5_prime_UTR_variant,,ENST00000555355,;KHNYN,3_prime_UTR_variant,,ENST00000251343,;SDR39U1,intron_variant,,ENST00000399390,;SDR39U1,intron_variant,,ENST00000556523,;SDR39U1,intron_variant,,ENST00000555225,;SDR39U1,intron_variant,,ENST00000554698,;SDR39U1,intron_variant,,ENST00000555365,;SDR39U1,intron_variant,,ENST00000556249,;SDR39U1,intron_variant,,ENST00000553343,;SDR39U1,intron_variant,,ENST00000538105,;SDR39U1,intron_variant,,ENST00000399395,;SDR39U1,intron_variant,,ENST00000553930,;KHNYN,downstream_gene_variant,,ENST00000556842,;KHNYN,downstream_gene_variant,,ENST00000553935,;KHNYN,downstream_gene_variant,,ENST00000554268,;SDR39U1,intron_variant,,ENST00000555561,;SDR39U1,downstream_gene_variant,,ENST00000555830,;SDR39U1,intron_variant,,ENST00000554947,;SDR39U1,intron_variant,,ENST00000553546,;SDR39U1,intron_variant,,ENST00000556548,;SDR39U1,intron_variant,,ENST00000556707,;SDR39U1,intron_variant,,ENST00000544691,;SDR39U1,intron_variant,,ENST00000556262,;KHNYN,downstream_gene_variant,,ENST00000556255,;SDR39U1,downstream_gene_variant,,ENST00000553937,;SDR39U1,downstream_gene_variant,,ENST00000556175,;SDR39U1,downstream_gene_variant,,ENST00000555778,;	G	ENSG00000100445	ENST00000399395	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SDR39U1	HGNC	20275	protein_coding	YES	CCDS45091.1	ENSP00000382327	D39U1_HUMAN	G3V4N6_HUMAN,G3V451_HUMAN,G3V3J5_HUMAN	UPI000059D223	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGACATTCCA	.	5	ESCA
FAM179B	0	.	GRCh37	14	45515859	45515859	+	Intron	SNP	A	A	G	rs749274192	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4154+1786A>G	.	.	ENST00000361577	.	52	34	18	42	42	0	FAM179B,missense_variant,p.Ile1422Met,ENST00000361462,;FAM179B,3_prime_UTR_variant,,ENST00000382233,;FAM179B,intron_variant,,ENST00000361577,;KLHL28,upstream_gene_variant,,ENST00000556239,;KLHL28,upstream_gene_variant,,ENST00000553817,;FAM179B,3_prime_UTR_variant,,ENST00000557423,;	G	ENSG00000198718	ENST00000361577	Transcript	intron_variant	.	.	.	.	.	rs749274192	.	.	1	FAM179B	HGNC	19959	protein_coding	YES	CCDS9681.1	ENSP00000355045	F179B_HUMAN	.	UPI00001C1F79	.	.	.	.	13/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGCATATTACC	.	3	ESCA
NIN	0	.	GRCh37	14	51224041	51224041	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3707A>T	p.Lys1236Met	p.K1236M	ENST00000382041	18/30	38	26	12	29	29	0	NIN,missense_variant,p.Lys1236Met,ENST00000245441,;NIN,missense_variant,p.Lys1236Met,ENST00000324330,;NIN,missense_variant,p.Lys1236Met,ENST00000382041,;NIN,missense_variant,p.Lys727Met,ENST00000389869,;NIN,missense_variant,p.Lys727Met,ENST00000530853,;NIN,missense_variant,p.Lys1236Met,ENST00000453196,;NIN,missense_variant,p.Lys1236Met,ENST00000530997,;NIN,intron_variant,,ENST00000389868,;NIN,intron_variant,,ENST00000382043,;NIN,missense_variant,p.Lys1236Met,ENST00000476352,;	A	ENSG00000100503	ENST00000382041	Transcript	missense_variant	3898	3707	1236	K/M	aAg/aTg	.	.	.	-1	NIN	HGNC	14906	protein_coding	YES	CCDS32079.1	ENSP00000371472	NIN_HUMAN	H7C162_HUMAN,E9PJH9_HUMAN	UPI0000DBEF14	.	deleterious(0)	probably_damaging(0.937)	18/30	.	hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCTTCAGT	.	5	ESCA
PTGER2	0	.	GRCh37	14	52782053	52782053	+	Missense_Mutation	SNP	C	C	G	rs746659837	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787C>G	p.Leu263Val	p.L263V	ENST00000245457	1/2	30	23	7	31	31	0	PTGER2,missense_variant,p.Leu8Val,ENST00000557436,;PTGER2,missense_variant,p.Leu263Val,ENST00000245457,;	G	ENSG00000125384	ENST00000245457	Transcript	missense_variant	941	787	263	L/V	Ctc/Gtc	rs746659837	.	.	1	PTGER2	HGNC	9594	protein_coding	YES	CCDS9708.1	ENSP00000245457	PE2R2_HUMAN	G3V2Y6_HUMAN	UPI000013CBA3	.	deleterious(0)	probably_damaging(0.986)	1/2	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF00001,hmmpanther:PTHR11866:SF8,hmmpanther:PTHR11866,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACCTCATT	.	5	ESCA
KTN1	0	.	GRCh37	14	56120290	56120290	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2777C>T	p.Ser926Leu	p.S926L	ENST00000395314	28/44	21	15	6	26	26	0	KTN1,missense_variant,p.Ser903Leu,ENST00000395308,;KTN1,missense_variant,p.Ser926Leu,ENST00000438792,;KTN1,missense_variant,p.Ser926Leu,ENST00000395309,;KTN1,missense_variant,p.Ser903Leu,ENST00000413890,;KTN1,missense_variant,p.Ser221Leu,ENST00000554507,;KTN1,missense_variant,p.Ser903Leu,ENST00000395311,;KTN1,missense_variant,p.Ser926Leu,ENST00000395314,;KTN1,missense_variant,p.Ser926Leu,ENST00000416613,;KTN1,upstream_gene_variant,,ENST00000554570,;KTN1,downstream_gene_variant,,ENST00000554890,;Y_RNA,downstream_gene_variant,,ENST00000363872,;KTN1,missense_variant,p.Ser926Leu,ENST00000459737,;KTN1,3_prime_UTR_variant,,ENST00000553360,;KTN1,non_coding_transcript_exon_variant,,ENST00000555164,;KTN1,upstream_gene_variant,,ENST00000554306,;	T	ENSG00000126777	ENST00000395314	Transcript	missense_variant	2845	2777	926	S/L	tCa/tTa	.	.	.	1	KTN1	HGNC	6467	protein_coding	YES	CCDS41957.1	ENSP00000378725	KTN1_HUMAN	Q5GGW3_HUMAN,G3V5P0_HUMAN,G3V4L8_HUMAN,G3V475_HUMAN	UPI0000190F88	.	tolerated(0.08)	benign(0.012)	28/44	.	hmmpanther:PTHR18864	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TGCATCACAGT	.	4	ESCA
DAAM1	0	.	GRCh37	14	59834304	59834304	+	Missense_Mutation	SNP	G	G	A	rs199742099	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3014G>A	p.Arg1005His	p.R1005H	ENST00000395125	24/25	33	20	13	23	23	0	DAAM1,missense_variant,p.Arg1005His,ENST00000351081,;DAAM1,missense_variant,p.Arg1005His,ENST00000395125,;DAAM1,missense_variant,p.Arg995His,ENST00000360909,;DAAM1,non_coding_transcript_exon_variant,,ENST00000553966,;DAAM1,downstream_gene_variant,,ENST00000557029,;DAAM1,non_coding_transcript_exon_variant,,ENST00000555651,;DAAM1,non_coding_transcript_exon_variant,,ENST00000553307,;DAAM1,downstream_gene_variant,,ENST00000553472,;DAAM1,downstream_gene_variant,,ENST00000557628,;	A	ENSG00000100592	ENST00000395125	Transcript	missense_variant	3037	3014	1005	R/H	cGc/cAc	rs199742099	.	.	1	DAAM1	HGNC	18142	protein_coding	YES	CCDS9737.1	ENSP00000378557	DAAM1_HUMAN	.	UPI0000161FAA	.	tolerated(0.08)	possibly_damaging(0.475)	24/25	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51444,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF181,SMART_domains:SM00498	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCGCATGG	byCluster	5	ESCA
SYNE2	0	.	GRCh37	14	64588838	64588838	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13267G>A	p.Glu4423Lys	p.E4423K	ENST00000358025	69/116	33	23	10	36	36	0	SYNE2,missense_variant,p.Glu4438Lys,ENST00000554584,;SYNE2,missense_variant,p.Glu808Lys,ENST00000394768,;SYNE2,missense_variant,p.Glu142Lys,ENST00000553455,;SYNE2,missense_variant,p.Glu4423Lys,ENST00000344113,;SYNE2,missense_variant,p.Glu808Lys,ENST00000357395,;SYNE2,missense_variant,p.Glu4423Lys,ENST00000358025,;SYNE2,missense_variant,p.Glu1057Lys,ENST00000555002,;ESR2,intron_variant,,ENST00000556275,;ESR2,intron_variant,,ENST00000542956,;	A	ENSG00000054654	ENST00000358025	Transcript	missense_variant	13497	13267	4423	E/K	Gaa/Aaa	.	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	benign(0.009)	69/116	.	hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAGGAATCA	.	5	ESCA
NPC2	0	.	GRCh37	14	74959998	74959998	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-21C>T	.	.	ENST00000555619	1/5	26	21	5	27	27	0	NPC2,5_prime_UTR_variant,,ENST00000555592,;NPC2,5_prime_UTR_variant,,ENST00000557510,;NPC2,5_prime_UTR_variant,,ENST00000434013,;NPC2,5_prime_UTR_variant,,ENST00000553490,;NPC2,5_prime_UTR_variant,,ENST00000555619,;NPC2,intron_variant,,ENST00000556009,;LTBP2,downstream_gene_variant,,ENST00000261978,;ISCA2,upstream_gene_variant,,ENST00000554924,;NPC2,upstream_gene_variant,,ENST00000238633,;ISCA2,upstream_gene_variant,,ENST00000298818,;ISCA2,upstream_gene_variant,,ENST00000556816,;NPC2,upstream_gene_variant,,ENST00000541064,;ISCA2,upstream_gene_variant,,ENST00000555139,;NPC2,upstream_gene_variant,,ENST00000554482,;	A	ENSG00000119655	ENST00000555619	Transcript	5_prime_UTR_variant	218	.	.	.	.	.	.	.	-1	NPC2	HGNC	14537	protein_coding	YES	CCDS32121.1	ENSP00000451112	NPC2_HUMAN	.	UPI0000062218	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAAGCTCGG	.	2	ESCA
RPS6KA5	0	.	GRCh37	14	91341668	91341668	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1873C>G	p.His625Asp	p.H625D	ENST00000261991	15/17	32	21	11	30	30	0	RPS6KA5,missense_variant,p.His625Asp,ENST00000261991,;RPS6KA5,missense_variant,p.His546Asp,ENST00000536315,;RPS6KA5,3_prime_UTR_variant,,ENST00000556178,;	C	ENSG00000100784	ENST00000261991	Transcript	missense_variant	2047	1873	625	H/D	Cat/Gat	.	.	.	-1	RPS6KA5	HGNC	10434	protein_coding	YES	CCDS9893.1	ENSP00000261991	KS6A5_HUMAN	Q9UG98_HUMAN,B7Z2Y5_HUMAN	UPI0000031C30	.	tolerated(0.62)	benign(0.002)	15/17	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,PIRSF_domain:PIRSF000606,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24351:SF42,hmmpanther:PTHR24351,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R627Q|c.1880G>A|3,BUFFER|p.R627Q|c.1880G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATGAGATT	.	5	ESCA
C14orf159	0	.	GRCh37	14	91691249	91691249	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*72C>G	.	.	ENST00000518868	17/17	18	11	6	21	21	0	C14orf159,3_prime_UTR_variant,,ENST00000523816,;C14orf159,3_prime_UTR_variant,,ENST00000518868,;C14orf159,3_prime_UTR_variant,,ENST00000521077,;C14orf159,3_prime_UTR_variant,,ENST00000520328,;C14orf159,3_prime_UTR_variant,,ENST00000428926,;C14orf159,3_prime_UTR_variant,,ENST00000522322,;C14orf159,3_prime_UTR_variant,,ENST00000523771,;C14orf159,3_prime_UTR_variant,,ENST00000256324,;C14orf159,3_prime_UTR_variant,,ENST00000525393,;C14orf159,3_prime_UTR_variant,,ENST00000412671,;C14orf159,downstream_gene_variant,,ENST00000522816,;C14orf159,downstream_gene_variant,,ENST00000523576,;C14orf159,3_prime_UTR_variant,,ENST00000523837,;C14orf159,3_prime_UTR_variant,,ENST00000523461,;C14orf159,3_prime_UTR_variant,,ENST00000517306,;	G	ENSG00000133943	ENST00000518868	Transcript	3_prime_UTR_variant	2628	.	.	.	.	.	.	.	1	C14orf159	HGNC	20498	protein_coding	YES	CCDS41979.1	ENSP00000428263	CN159_HUMAN	E5RK56_HUMAN,E5RK14_HUMAN,E5RJD1_HUMAN,E5RJ87_HUMAN,E5RJ62_HUMAN,E5RIU5_HUMAN,E5RIL4_HUMAN,E5RHG2_HUMAN,E5RGP9_HUMAN,E5RFT5_HUMAN	UPI000000CC60	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTCTGGCG	.	5	ESCA
AK7	0	.	GRCh37	14	96909064	96909064	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.691-3C>T	.	.	ENST00000267584	.	117	90	27	113	113	0	AK7,splice_region_variant,,ENST00000267584,;	T	ENSG00000140057	ENST00000267584	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	AK7	HGNC	20091	protein_coding	YES	CCDS9945.1	ENSP00000267584	KAD7_HUMAN	.	UPI00001FDB1D	.	.	.	.	6/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTCAGATG	.	4	ESCA
BCL11B	0	.	GRCh37	14	99635886	99635886	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4602A>G	.	.	ENST00000357195	4/4	14	10	4	11	11	0	BCL11B,3_prime_UTR_variant,,ENST00000345514,;BCL11B,3_prime_UTR_variant,,ENST00000357195,;BCL11B,downstream_gene_variant,,ENST00000443726,;	C	ENSG00000127152	ENST00000357195	Transcript	3_prime_UTR_variant	7297	.	.	.	.	.	.	.	-1	BCL11B	HGNC	13222	protein_coding	YES	CCDS9950.1	ENSP00000349723	BC11B_HUMAN	L8B7P7_HUMAN	UPI000006E083	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAAATACCAA	.	2	ESCA
DNM1P47	0	.	GRCh37	15	102299764	102299764	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.7810G>A	.	.	ENST00000561463	2/4	18	14	4	23	23	0	DNM1P47,non_coding_transcript_exon_variant,,ENST00000561463,;DNM1P47,non_coding_transcript_exon_variant,,ENST00000571780,;	A	ENSG00000259660	ENST00000561463	Transcript	non_coding_transcript_exon_variant	7810	.	.	.	.	.	.	.	1	DNM1P47	HGNC	35200	processed_transcript	YES	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GAGTCGGCAGA	.	2	ESCA
POTEB2	0	.	GRCh37	15	21071350	21071350	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.261C>T	p.%3D	p.D87D	ENST00000454856	1/11	74	64	10	81	81	0	POTEB2,synonymous_variant,p.%3D,ENST00000454856,;POTEB2,synonymous_variant,p.%3D,ENST00000438063,;	A	ENSG00000230031	ENST00000454856	Transcript	synonymous_variant	294	261	87	D	gaC/gaT	.	.	.	-1	POTEB2	HGNC	48327	protein_coding	YES	CCDS59248.1	ENSP00000456953	POTB2_HUMAN	.	UPI0001A5E771	.	.	.	1/11	.	hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF38,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTGTCGTCGTA	.	2	ESCA
NDN	0	.	GRCh37	15	23931422	23931422	+	Missense_Mutation	SNP	G	G	A	rs776854811	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.943C>T	p.Arg315Cys	p.R315C	ENST00000331837	1/1	33	24	8	37	37	0	NDN,missense_variant,p.Arg315Cys,ENST00000331837,;	A	ENSG00000182636	ENST00000331837	Transcript	missense_variant	1029	943	315	R/C	Cgc/Tgc	rs776854811	.	.	-1	NDN	HGNC	7675	protein_coding	YES	CCDS10014.1	ENSP00000332643	NECD_HUMAN	.	UPI000012FEF1	.	tolerated_low_confidence(0.11)	benign(0.014)	1/1	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCGAGGGT	.	5	ESCA
FMN1	0	.	GRCh37	15	33096524	33096524	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3269A>T	p.Glu1090Val	p.E1090V	ENST00000334528	14/17	35	29	6	62	62	0	FMN1,missense_variant,p.Glu1313Val,ENST00000559047,;FMN1,missense_variant,p.Glu1215Val,ENST00000561249,;FMN1,missense_variant,p.Glu1090Val,ENST00000334528,;FMN1,non_coding_transcript_exon_variant,,ENST00000558882,;	A	ENSG00000248905	ENST00000334528	Transcript	missense_variant	3269	3269	1090	E/V	gAg/gTg	.	.	.	-1	FMN1	HGNC	3768	protein_coding	YES	CCDS45209.1	ENSP00000333950	FMN1_HUMAN	.	UPI00004086C3	.	deleterious(0)	probably_damaging(0.982)	14/17	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51444,hmmpanther:PTHR13037,hmmpanther:PTHR13037:SF8,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATGCTCTTTT	.	4	ESCA
FMN1	0	.	GRCh37	15	33096525	33096525	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3268G>T	p.Glu1090Ter	p.E1090*	ENST00000334528	14/17	34	28	6	62	62	0	FMN1,stop_gained,p.Glu1313Ter,ENST00000559047,;FMN1,stop_gained,p.Glu1215Ter,ENST00000561249,;FMN1,stop_gained,p.Glu1090Ter,ENST00000334528,;FMN1,non_coding_transcript_exon_variant,,ENST00000558882,;	A	ENSG00000248905	ENST00000334528	Transcript	stop_gained	3268	3268	1090	E/*	Gag/Tag	.	.	.	-1	FMN1	HGNC	3768	protein_coding	YES	CCDS45209.1	ENSP00000333950	FMN1_HUMAN	.	UPI00004086C3	.	.	.	14/17	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51444,hmmpanther:PTHR13037,hmmpanther:PTHR13037:SF8,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGCTCTTTTT	.	4	ESCA
FBN1	0	.	GRCh37	15	48936865	48936865	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.102G>A	p.%3D	p.V34V	ENST00000316623	2/66	63	34	28	66	66	0	FBN1,synonymous_variant,p.%3D,ENST00000560355,;FBN1,synonymous_variant,p.%3D,ENST00000316623,;RP11-227D13.1,upstream_gene_variant,,ENST00000558061,;FBN1,non_coding_transcript_exon_variant,,ENST00000558230,;FBN1,synonymous_variant,p.%3D,ENST00000537463,;	T	ENSG00000166147	ENST00000316623	Transcript	synonymous_variant	558	102	34	V	gtG/gtA	.	.	.	-1	FBN1	HGNC	3603	protein_coding	YES	CCDS32232.1	ENSP00000325527	FBN1_HUMAN	Q75N89_HUMAN,Q75N88_HUMAN,H0YN80_HUMAN	UPI0000163B0B	.	.	.	2/66	.	hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,PIRSF_domain:PIRSF036312	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCACGTT	.	5	ESCA
UNC13C	0	.	GRCh37	15	54919647	54919647	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*336G>C	.	.	ENST00000260323	32/32	18	12	6	21	21	0	UNC13C,3_prime_UTR_variant,,ENST00000537900,;UNC13C,3_prime_UTR_variant,,ENST00000545554,;UNC13C,3_prime_UTR_variant,,ENST00000260323,;UNC13C,downstream_gene_variant,,ENST00000560537,;UNC13C,downstream_gene_variant,,ENST00000539562,;	C	ENSG00000137766	ENST00000260323	Transcript	3_prime_UTR_variant	6981	.	.	.	.	.	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AATGAGATTAT	.	4	ESCA
CORO2B	0	.	GRCh37	15	68987554	68987554	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292T>A	p.Phe98Ile	p.F98I	ENST00000566799	3/12	23	16	7	20	20	0	CORO2B,missense_variant,p.Phe98Ile,ENST00000566799,;CORO2B,missense_variant,p.Phe93Ile,ENST00000540068,;CORO2B,missense_variant,p.Phe93Ile,ENST00000261861,;CORO2B,missense_variant,p.Phe93Ile,ENST00000543950,;	A	ENSG00000103647	ENST00000566799	Transcript	missense_variant	321	292	98	F/I	Ttc/Atc	.	.	.	1	CORO2B	HGNC	2256	protein_coding	YES	CCDS10229.2	ENSP00000454783	COR2B_HUMAN	B3KWB4_HUMAN	UPI0000E59C95	.	deleterious(0.01)	probably_damaging(1)	3/12	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF17,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCCTTCATC	.	5	ESCA
ANKRD34C	0	.	GRCh37	15	79586906	79586906	+	Missense_Mutation	SNP	C	C	T	rs449340	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1280C>T	p.Pro427Leu	p.P427L	ENST00000421388	2/2	29	14	15	31	31	0	ANKRD34C,missense_variant,p.Pro427Leu,ENST00000421388,;ANKRD34C,missense_variant,p.Pro427Leu,ENST00000558647,;	T	ENSG00000235711	ENST00000421388	Transcript	missense_variant	1749	1280	427	P/L	cCt/cTt	rs449340	.	.	1	ANKRD34C	HGNC	33888	protein_coding	YES	CCDS53965.1	ENSP00000401089	AN34C_HUMAN	.	UPI0000160A7F	.	deleterious(0)	benign(0.22)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24157,hmmpanther:PTHR24157:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTACCTAGCA	byCluster|byHapMap	5	ESCA
SEMA4B	0	.	GRCh37	15	90768989	90768989	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1618G>T	p.Asp540Tyr	p.D540Y	ENST00000411539	12/14	88	59	29	82	82	0	SEMA4B,missense_variant,p.Asp58Tyr,ENST00000559247,;SEMA4B,missense_variant,p.Asp540Tyr,ENST00000332496,;SEMA4B,missense_variant,p.Asp118Tyr,ENST00000559983,;SEMA4B,missense_variant,p.Asp535Tyr,ENST00000379122,;SEMA4B,missense_variant,p.Asp259Tyr,ENST00000559074,;SEMA4B,missense_variant,p.Asp540Tyr,ENST00000411539,;SEMA4B,downstream_gene_variant,,ENST00000561085,;SEMA4B,downstream_gene_variant,,ENST00000558051,;CIB1,downstream_gene_variant,,ENST00000328649,;SEMA4B,3_prime_UTR_variant,,ENST00000560089,;SEMA4B,non_coding_transcript_exon_variant,,ENST00000558065,;SEMA4B,downstream_gene_variant,,ENST00000560993,;SEMA4B,downstream_gene_variant,,ENST00000561252,;SEMA4B,upstream_gene_variant,,ENST00000561321,;SEMA4B,downstream_gene_variant,,ENST00000558975,;	T	ENSG00000185033	ENST00000411539	Transcript	missense_variant	1878	1618	540	D/Y	Gac/Tac	.	.	.	1	SEMA4B	HGNC	10730	protein_coding	YES	CCDS45347.1	ENSP00000394720	.	Q4VBY2_HUMAN,J3KNP4_HUMAN,H0YMR1_HUMAN,H0YMD6_HUMAN,H0YLN3_HUMAN	UPI0000197391	.	deleterious(0)	probably_damaging(0.998)	12/14	.	hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF14,Pfam_domain:PF01437,Gene3D:3.30.1680.10,SMART_domains:SM00423,Superfamily_domains:SSF103575	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGGGACCCC	.	5	ESCA
CACNA1H	0	.	GRCh37	16	1261716	1261716	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4477G>A	p.Ala1493Thr	p.A1493T	ENST00000348261	24/35	45	40	5	33	33	0	CACNA1H,missense_variant,p.Ala235Thr,ENST00000562079,;CACNA1H,missense_variant,p.Ala1493Thr,ENST00000348261,;CACNA1H,missense_variant,p.Ala235Thr,ENST00000564231,;CACNA1H,missense_variant,p.Ala1493Thr,ENST00000565831,;CACNA1H,missense_variant,p.Ala1493Thr,ENST00000358590,;CACNA1H,missense_variant,p.Ala43Thr,ENST00000564927,;CACNA1H,missense_variant,p.Ala235Thr,ENST00000569107,;RP11-616M22.3,upstream_gene_variant,,ENST00000564700,;CACNA1H,downstream_gene_variant,,ENST00000569953,;	A	ENSG00000196557	ENST00000348261	Transcript	missense_variant	4725	4477	1493	A/T	Gcc/Acc	.	.	.	1	CACNA1H	HGNC	1395	protein_coding	YES	CCDS45375.1	ENSP00000334198	CAC1H_HUMAN	Q9NYY7_HUMAN,Q9NYY6_HUMAN	UPI000012727B	.	deleterious(0)	probably_damaging(0.982)	24/35	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCAGGCCCTG	.	3	ESCA
ERCC4	0	.	GRCh37	16	14029602	14029602	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1811+2C>A	.	p.X604_splice	ENST00000311895	.	28	24	4	40	40	0	ERCC4,splice_donor_variant,,ENST00000311895,;ERCC4,downstream_gene_variant,,ENST00000575156,;CTD-2135D7.2,upstream_gene_variant,,ENST00000575137,;CTD-2135D7.2,upstream_gene_variant,,ENST00000570663,;ERCC4,downstream_gene_variant,,ENST00000574781,;ERCC4,splice_donor_variant,,ENST00000389138,;ERCC4,upstream_gene_variant,,ENST00000462862,;ERCC4,downstream_gene_variant,,ENST00000573018,;ERCC4,downstream_gene_variant,,ENST00000574194,;	A	ENSG00000175595	ENST00000311895	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	ERCC4	HGNC	3436	protein_coding	YES	CCDS32390.1	ENSP00000310520	XPF_HUMAN	B4DXD8_HUMAN	UPI0000161BBF	.	.	.	.	8/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGAGGCAAGTT	.	3	ESCA
CDR2	0	.	GRCh37	16	22358728	22358728	+	Missense_Mutation	SNP	C	C	T	rs541082194	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.923G>A	p.Arg308His	p.R308H	ENST00000268383	5/5	51	46	4	42	42	0	CDR2,missense_variant,p.Arg308His,ENST00000268383,;CDR2,downstream_gene_variant,,ENST00000563573,;CDR2,downstream_gene_variant,,ENST00000564542,;CDR2,downstream_gene_variant,,ENST00000567010,;CDR2,downstream_gene_variant,,ENST00000567406,;CDR2,downstream_gene_variant,,ENST00000561630,;	T	ENSG00000140743	ENST00000268383	Transcript	missense_variant	1231	923	308	R/H	cGc/cAc	rs541082194	.	.	-1	CDR2	HGNC	1799	protein_coding	YES	CCDS32404.1	ENSP00000268383	CDR2_HUMAN	H3BU23_HUMAN,H3BTR1_HUMAN,H3BN65_HUMAN	UPI00001D7843	.	deleterious(0.03)	probably_damaging(0.995)	5/5	.	hmmpanther:PTHR19232:SF1,hmmpanther:PTHR19232	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCTGCGCTTG	by1000G	3	ESCA
ABCA3	0	.	GRCh37	16	2328323	2328323	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4684G>C	p.Glu1562Gln	p.E1562Q	ENST00000301732	30/33	55	44	10	56	56	0	ABCA3,missense_variant,p.Glu1504Gln,ENST00000382381,;ABCA3,missense_variant,p.Glu1562Gln,ENST00000301732,;MIR4717,downstream_gene_variant,,ENST00000584656,;MIR940,downstream_gene_variant,,ENST00000563734,;ABCA3,non_coding_transcript_exon_variant,,ENST00000566200,;ABCA3,downstream_gene_variant,,ENST00000569062,;	G	ENSG00000167972	ENST00000301732	Transcript	missense_variant	5385	4684	1562	E/Q	Gag/Cag	.	.	.	-1	ABCA3	HGNC	33	protein_coding	YES	CCDS10466.1	ENSP00000301732	ABCA3_HUMAN	.	UPI0000001232	.	deleterious(0.02)	benign(0.212)	30/33	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF98,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTCTCGGG	.	5	ESCA
GTF3C1	0	.	GRCh37	16	27481557	27481557	+	Silent	SNP	G	G	A	rs576044105	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4686C>T	p.%3D	p.D1562D	ENST00000356183	31/37	69	48	21	60	60	0	GTF3C1,synonymous_variant,p.%3D,ENST00000356183,;GTF3C1,synonymous_variant,p.%3D,ENST00000561623,;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,non_coding_transcript_exon_variant,,ENST00000567843,;GTF3C1,3_prime_UTR_variant,,ENST00000571886,;GTF3C1,non_coding_transcript_exon_variant,,ENST00000569394,;GTF3C1,downstream_gene_variant,,ENST00000564664,;GTF3C1,upstream_gene_variant,,ENST00000562609,;	A	ENSG00000077235	ENST00000356183	Transcript	synonymous_variant	4702	4686	1562	D	gaC/gaT	rs576044105,COSM3948416	.	.	-1	GTF3C1	HGNC	4664	protein_coding	YES	CCDS32414.1	ENSP00000348510	TF3C1_HUMAN	Q7Z7H4_HUMAN,I3L1Z3_HUMAN	UPI00001FF123	.	.	.	31/37	.	hmmpanther:PTHR15180	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCGTCCAG	byFrequency|byCluster	5	ESCA
TP53TG3D	0	.	GRCh37	16	32264978	32264978	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304C>T	p.Pro102Ser	p.P102S	ENST00000398664	1/2	165	135	30	182	182	0	TP53TG3D,missense_variant,p.Pro102Ser,ENST00000398664,;TP53TG3D,missense_variant,p.Pro102Ser,ENST00000354614,;TP53TG3D,intron_variant,,ENST00000569631,;RP11-56L13.7,intron_variant,,ENST00000562604,;TP53TG3D,upstream_gene_variant,,ENST00000564810,;TP53TG3D,missense_variant,p.Pro102Ser,ENST00000380148,;TP53TG3D,intron_variant,,ENST00000563025,;TP53TG3D,upstream_gene_variant,,ENST00000567978,;TP53TG3D,upstream_gene_variant,,ENST00000568044,;	T	ENSG00000205456	ENST00000398664	Transcript	missense_variant	939	304	102	P/S	Cct/Tct	.	.	.	1	TP53TG3D	HGNC	44657	protein_coding	YES	CCDS58456.1	ENSP00000455596	T53G3_HUMAN	.	UPI000006D8DD	.	tolerated_low_confidence(0.37)	possibly_damaging(0.803)	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGATACCTTGC	.	4	ESCA
NLRC3	0	.	GRCh37	16	3593431	3593431	+	Missense_Mutation	SNP	A	A	G	rs778451139	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3071T>C	p.Ile1024Thr	p.I1024T	ENST00000448023	16/19	46	35	11	52	52	0	NLRC3,missense_variant,p.Ile978Thr,ENST00000301749,;NLRC3,missense_variant,p.Ile949Thr,ENST00000359128,;NLRC3,missense_variant,p.Ile1024Thr,ENST00000448023,;CLUAP1,downstream_gene_variant,,ENST00000576634,;LA16c-390H2.4,upstream_gene_variant,,ENST00000573820,;NLRC3,non_coding_transcript_exon_variant,,ENST00000419350,;NLRC3,non_coding_transcript_exon_variant,,ENST00000603128,;NLRC3,downstream_gene_variant,,ENST00000604347,;NLRC3,synonymous_variant,p.%3D,ENST00000603507,;	G	ENSG00000167984	ENST00000448023	Transcript	missense_variant	3258	3071	1024	I/T	aTt/aCt	rs778451139	.	.	-1	NLRC3	HGNC	29889	protein_coding	YES	.	ENSP00000414415	.	C9JLH9_HUMAN	UPI0000246E58	.	tolerated(0.48)	benign(0.006)	16/19	.	Superfamily_domains:SSF52047,SMART_domains:SM00368,Pfam_domain:PF13516,Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGAATCTCC	byFrequency	5	ESCA
C16orf78	0	.	GRCh37	16	49430446	49430446	+	Missense_Mutation	SNP	G	G	C	rs374900464	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507G>C	p.Gln169His	p.Q169H	ENST00000299191	4/5	27	19	7	27	27	0	C16orf78,missense_variant,p.Gln169His,ENST00000299191,;	C	ENSG00000166152	ENST00000299191	Transcript	missense_variant	624	507	169	Q/H	caG/caC	rs374900464	.	.	1	C16orf78	HGNC	28479	protein_coding	YES	CCDS10738.1	ENSP00000299191	CP078_HUMAN	.	UPI0000071013	.	deleterious(0)	benign(0.001)	4/5	.	Pfam_domain:PF15472	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCAGAGGGC	byFrequency|byCluster|by1000G	5	ESCA
DOK4	0	.	GRCh37	16	57513551	57513551	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-132G>C	.	.	ENST00000340099	2/9	81	58	23	99	99	0	DOK4,5_prime_UTR_variant,,ENST00000566588,;DOK4,5_prime_UTR_variant,,ENST00000340099,;DOK4,5_prime_UTR_variant,,ENST00000564378,;DOK4,5_prime_UTR_variant,,ENST00000562737,;DOK4,5_prime_UTR_variant,,ENST00000566936,;DOK4,5_prime_UTR_variant,,ENST00000569010,;DOK4,5_prime_UTR_variant,,ENST00000567276,;DOK4,5_prime_UTR_variant,,ENST00000569548,;DOK4,5_prime_UTR_variant,,ENST00000569538,;DOK4,5_prime_UTR_variant,,ENST00000562008,;DOK4,5_prime_UTR_variant,,ENST00000567175,;DOK4,5_prime_UTR_variant,,ENST00000569250,;DOK4,5_prime_UTR_variant,,ENST00000568617,;DOK4,5_prime_UTR_variant,,ENST00000566705,;DOK4,5_prime_UTR_variant,,ENST00000567214,;DOK4,non_coding_transcript_exon_variant,,ENST00000561918,;DOK4,5_prime_UTR_variant,,ENST00000561659,;DOK4,upstream_gene_variant,,ENST00000563483,;	G	ENSG00000125170	ENST00000340099	Transcript	5_prime_UTR_variant	241	.	.	.	.	.	.	.	-1	DOK4	HGNC	19868	protein_coding	YES	CCDS10783.1	ENSP00000344277	DOK4_HUMAN	H3BVB4_HUMAN,H3BV67_HUMAN,H3BTK2_HUMAN,H3BTI7_HUMAN,H3BTI4_HUMAN,H3BSK0_HUMAN,H3BS85_HUMAN,H3BPY9_HUMAN,H3BN90_HUMAN	UPI0000070AA4	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCACCTC	.	5	ESCA
HYDIN	0	.	GRCh37	16	70841857	70841857	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14992G>A	p.Glu4998Lys	p.E4998K	ENST00000393567	86/86	32	17	15	55	55	0	HYDIN,missense_variant,p.Glu4998Lys,ENST00000393567,;HYDIN,3_prime_UTR_variant,,ENST00000378856,;	T	ENSG00000157423	ENST00000393567	Transcript	missense_variant	15143	14992	4998	E/K	Gag/Aag	.	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	possibly_damaging(0.801)	86/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCACCCA	.	5	ESCA
LLGL1	0	.	GRCh37	17	18133339	18133339	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166G>A	p.Gly56Arg	p.G56R	ENST00000316843	2/23	46	16	30	64	64	0	LLGL1,missense_variant,p.Gly56Arg,ENST00000316843,;LLGL1,upstream_gene_variant,,ENST00000479155,;	A	ENSG00000131899	ENST00000316843	Transcript	missense_variant	262	166	56	G/R	Ggg/Agg	.	.	.	1	LLGL1	HGNC	6628	protein_coding	YES	CCDS32586.1	ENSP00000321537	L2GL1_HUMAN	A0PJG1_HUMAN	UPI000049DE38	.	deleterious(0)	probably_damaging(1)	2/23	.	hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF21,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTGGGGCT	.	5	ESCA
PSMD11	0	.	GRCh37	17	30807535	30807535	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1155G>C	p.%3D	p.L385L	ENST00000261712	13/14	32	25	7	48	48	0	PSMD11,synonymous_variant,p.%3D,ENST00000457654,;PSMD11,synonymous_variant,p.%3D,ENST00000261712,;PSMD11,non_coding_transcript_exon_variant,,ENST00000585265,;PSMD11,non_coding_transcript_exon_variant,,ENST00000469475,;PSMD11,non_coding_transcript_exon_variant,,ENST00000493026,;PSMD11,downstream_gene_variant,,ENST00000584340,;PSMD11,downstream_gene_variant,,ENST00000578397,;	C	ENSG00000108671	ENST00000261712	Transcript	synonymous_variant	1418	1155	385	L	ctG/ctC	.	.	.	1	PSMD11	HGNC	9556	protein_coding	YES	CCDS11272.1	ENSP00000261712	PSD11_HUMAN	J3KSW3_HUMAN	UPI0000132791	.	.	.	13/14	.	hmmpanther:PTHR10678:SF4,hmmpanther:PTHR10678,Pfam_domain:PF01399,Gene3D:1.10.10.10,SMART_domains:SM00088,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTGATTAT	.	5	ESCA
CDK5R1	0	.	GRCh37	17	30817495	30817495	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1933C>T	.	.	ENST00000313401	2/2	44	33	11	45	45	0	CDK5R1,3_prime_UTR_variant,,ENST00000313401,;MYO1D,downstream_gene_variant,,ENST00000394649,;MYO1D,downstream_gene_variant,,ENST00000318217,;CDK5R1,downstream_gene_variant,,ENST00000584792,;MYO1D,downstream_gene_variant,,ENST00000577576,;CDK5R1,downstream_gene_variant,,ENST00000584716,;MYO1D,downstream_gene_variant,,ENST00000577352,;	T	ENSG00000176749	ENST00000313401	Transcript	3_prime_UTR_variant	3546	.	.	.	.	.	.	.	1	CDK5R1	HGNC	1775	protein_coding	YES	CCDS11273.1	ENSP00000318486	CD5R1_HUMAN	.	UPI000012738E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCGGAGG	.	5	ESCA
RFFL	0	.	GRCh37	17	33348699	33348699	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.282A>G	p.%3D	p.T94T	ENST00000315249	3/7	13	8	5	43	43	0	RFFL,synonymous_variant,p.%3D,ENST00000315249,;RFFL,synonymous_variant,p.%3D,ENST00000414419,;RFFL,synonymous_variant,p.%3D,ENST00000413582,;RFFL,synonymous_variant,p.%3D,ENST00000415395,;RFFL,synonymous_variant,p.%3D,ENST00000394597,;RFFL,synonymous_variant,p.%3D,ENST00000378516,;RFFL,synonymous_variant,p.%3D,ENST00000268850,;RFFL,synonymous_variant,p.%3D,ENST00000447669,;RFFL,synonymous_variant,p.%3D,ENST00000584655,;RAD51L3-RFFL,intron_variant,,ENST00000591723,;RFFL,intron_variant,,ENST00000582308,;RAD51L3-RFFL,intron_variant,,ENST00000593039,;RFFL,upstream_gene_variant,,ENST00000581039,;RAD51L3-RFFL,downstream_gene_variant,,ENST00000592181,;RFFL,intron_variant,,ENST00000584541,;RFFL,3_prime_UTR_variant,,ENST00000581265,;	C	ENSG00000092871	ENST00000315249	Transcript	synonymous_variant	505	282	94	T	acA/acG	.	.	.	-1	RFFL	HGNC	24821	protein_coding	YES	CCDS11286.1	ENSP00000326170	RFFL_HUMAN	J3QR17_HUMAN,C9JE27_HUMAN	UPI000006D6B9	.	.	.	3/7	.	hmmpanther:PTHR14879:SF2,hmmpanther:PTHR14879,Gene3D:3.30.40.10,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGGCTGTAGC	.	3	ESCA
PIGW	0	.	GRCh37	17	34893992	34893992	+	Missense_Mutation	SNP	A	A	G	rs754301297	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1042A>G	p.Ile348Val	p.I348V	ENST00000592983	2/2	35	27	8	43	43	0	PIGW,missense_variant,p.Ile348Val,ENST00000328396,;PIGW,missense_variant,p.Ile348Val,ENST00000592983,;MYO19,upstream_gene_variant,,ENST00000585818,;MYO19,upstream_gene_variant,,ENST00000544606,;MYO19,upstream_gene_variant,,ENST00000268852,;PIGW,downstream_gene_variant,,ENST00000429467,;MYO19,upstream_gene_variant,,ENST00000431794,;MYO19,upstream_gene_variant,,ENST00000586007,;MYO19,upstream_gene_variant,,ENST00000585719,;MYO19,upstream_gene_variant,,ENST00000589404,;MYO19,upstream_gene_variant,,ENST00000586886,;MYO19,intron_variant,,ENST00000586879,;MYO19,intron_variant,,ENST00000590081,;MYO19,upstream_gene_variant,,ENST00000592380,;MYO19,upstream_gene_variant,,ENST00000588664,;MYO19,upstream_gene_variant,,ENST00000591794,;MYO19,upstream_gene_variant,,ENST00000586908,;	G	ENSG00000184886	ENST00000592983	Transcript	missense_variant	1622	1042	348	I/V	Att/Gtt	rs754301297	.	.	1	PIGW	HGNC	23213	protein_coding	YES	CCDS11313.1	ENSP00000468778	PIGW_HUMAN	C9JLC8_HUMAN	UPI00001984EA	.	tolerated(0.73)	benign(0.009)	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR20661,Pfam_domain:PF06423,PIRSF_domain:PIRSF017321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTATTAGC	.	2	ESCA
MED1	0	.	GRCh37	17	37566025	37566025	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2449C>T	p.Gln817Ter	p.Q817*	ENST00000300651	17/17	46	35	10	67	67	0	MED1,stop_gained,p.Gln817Ter,ENST00000300651,;MED1,intron_variant,,ENST00000394287,;CTB-131K11.1,downstream_gene_variant,,ENST00000582842,;MED1,3_prime_UTR_variant,,ENST00000577831,;	A	ENSG00000125686	ENST00000300651	Transcript	stop_gained	2673	2449	817	Q/*	Cag/Tag	.	.	.	-1	MED1	HGNC	9234	protein_coding	YES	CCDS11336.1	ENSP00000300651	MED1_HUMAN	.	UPI0000167F57	.	.	.	17/17	.	hmmpanther:PTHR12881	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCTGAGAAT	.	5	ESCA
ZZEF1	0	.	GRCh37	17	3981250	3981250	+	Silent	SNP	T	T	C	rs754281701	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2916A>G	p.%3D	p.L972L	ENST00000381638	19/55	22	15	6	18	18	0	ZZEF1,synonymous_variant,p.%3D,ENST00000381638,;ZZEF1,non_coding_transcript_exon_variant,,ENST00000574474,;ZZEF1,upstream_gene_variant,,ENST00000572699,;	C	ENSG00000074755	ENST00000381638	Transcript	synonymous_variant	3041	2916	972	L	ctA/ctG	rs754281701	.	.	-1	ZZEF1	HGNC	29027	protein_coding	YES	CCDS11043.1	ENSP00000371051	ZZEF1_HUMAN	.	UPI00004569F7	.	.	.	19/55	.	hmmpanther:PTHR22772,hmmpanther:PTHR22772:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGATAGCAG	byFrequency	5	ESCA
AOC3	0	.	GRCh37	17	41006530	41006530	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1666G>C	p.Glu556Gln	p.E556Q	ENST00000308423	2/4	64	38	25	87	87	0	AOC3,missense_variant,p.Glu13Gln,ENST00000591562,;AOC3,missense_variant,p.Glu556Gln,ENST00000308423,;AOC3,missense_variant,p.Glu13Gln,ENST00000588033,;AOC3,missense_variant,p.Glu13Gln,ENST00000592999,;AOC2,downstream_gene_variant,,ENST00000253799,;AOC2,downstream_gene_variant,,ENST00000452774,;AOC3,intron_variant,,ENST00000587330,;	C	ENSG00000131471	ENST00000308423	Transcript	missense_variant	1826	1666	556	E/Q	Gag/Cag	.	.	.	1	AOC3	HGNC	550	protein_coding	YES	CCDS11444.1	ENSP00000312326	AOC3_HUMAN	Q9UEU7_HUMAN,K7ESB3_HUMAN,K7EQZ5_HUMAN,K7EL47_HUMAN	UPI00000009FC	.	tolerated(0.2)	benign(0.001)	2/4	.	Superfamily_domains:SSF49998,Pfam_domain:PF01179,Gene3D:2.70.98.20,hmmpanther:PTHR10638,hmmpanther:PTHR10638:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTGAGCAC	.	5	ESCA
HEATR6	0	.	GRCh37	17	58153567	58153567	+	Missense_Mutation	SNP	C	C	A	rs748737940	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.251G>T	p.Arg84Leu	p.R84L	ENST00000184956	2/20	25	11	14	24	24	0	HEATR6,missense_variant,p.Arg84Leu,ENST00000593228,;HEATR6,missense_variant,p.Arg84Leu,ENST00000585976,;HEATR6,missense_variant,p.Arg84Leu,ENST00000593097,;HEATR6,missense_variant,p.Arg84Leu,ENST00000184956,;CTD-2319I12.2,upstream_gene_variant,,ENST00000589740,;HEATR6,downstream_gene_variant,,ENST00000585712,;HEATR6,missense_variant,p.Arg84Leu,ENST00000592664,;HEATR6,missense_variant,p.Arg84Leu,ENST00000587003,;HEATR6,non_coding_transcript_exon_variant,,ENST00000591074,;HEATR6,upstream_gene_variant,,ENST00000590587,;	A	ENSG00000068097	ENST00000184956	Transcript	missense_variant	268	251	84	R/L	cGa/cTa	rs748737940	.	.	-1	HEATR6	HGNC	24076	protein_coding	YES	CCDS11623.1	ENSP00000184956	HEAT6_HUMAN	K7ELR8_HUMAN	UPI0000366C37	.	tolerated(0.14)	benign(0.089)	2/20	.	hmmpanther:PTHR13366	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTCGGCAA	byFrequency	5	ESCA
ABCA10	0	.	GRCh37	17	67193205	67193205	+	Missense_Mutation	SNP	C	C	T	rs760811449	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234G>A	p.Gly412Ser	p.G412S	ENST00000269081	12/40	32	22	9	43	43	0	ABCA10,missense_variant,p.Gly412Ser,ENST00000416101,;ABCA10,missense_variant,p.Gly412Ser,ENST00000269081,;ABCA10,missense_variant,p.Gly412Arg,ENST00000432313,;ABCA10,missense_variant,p.Gly412Arg,ENST00000522406,;ABCA10,missense_variant,p.Gly412Ser,ENST00000523419,;ABCA10,splice_region_variant,,ENST00000518929,;	T	ENSG00000154263	ENST00000269081	Transcript	missense_variant	2144	1234	412	G/S	Ggc/Agc	rs760811449	.	.	-1	ABCA10	HGNC	30	protein_coding	YES	CCDS11684.1	ENSP00000269081	ABCAA_HUMAN	K7ERP5_HUMAN	UPI000013D7F6	.	deleterious(0.01)	possibly_damaging(0.799)	12/40	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229:SF120,hmmpanther:PTHR19229,Pfam_domain:PF00005,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTACCTTGCA	byFrequency|byCluster	5	ESCA
NEURL4	0	.	GRCh37	17	7221920	7221920	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3758C>T	p.Ser1253Phe	p.S1253F	ENST00000399464	23/29	78	44	34	96	96	0	NEURL4,missense_variant,p.Ser1229Phe,ENST00000570460,;NEURL4,missense_variant,p.Ser1216Phe,ENST00000571887,;NEURL4,missense_variant,p.Ser1251Phe,ENST00000315614,;NEURL4,missense_variant,p.Ser1253Phe,ENST00000399464,;GPS2,upstream_gene_variant,,ENST00000573684,;GPS2,upstream_gene_variant,,ENST00000380728,;GPS2,upstream_gene_variant,,ENST00000570780,;GPS2,upstream_gene_variant,,ENST00000577040,;GPS2,upstream_gene_variant,,ENST00000391950,;GPS2,upstream_gene_variant,,ENST00000389167,;NEURL4,non_coding_transcript_exon_variant,,ENST00000574120,;RP11-542C16.2,missense_variant,p.Ser34Phe,ENST00000315601,;RP11-542C16.2,missense_variant,p.Ser67Phe,ENST00000575474,;NEURL4,synonymous_variant,p.%3D,ENST00000573186,;NEURL4,non_coding_transcript_exon_variant,,ENST00000576794,;NEURL4,non_coding_transcript_exon_variant,,ENST00000572029,;NEURL4,downstream_gene_variant,,ENST00000576485,;GPS2,upstream_gene_variant,,ENST00000571569,;GPS2,upstream_gene_variant,,ENST00000571697,;GPS2,upstream_gene_variant,,ENST00000571695,;GPS2,upstream_gene_variant,,ENST00000573059,;NEURL4,downstream_gene_variant,,ENST00000573651,;NEURL4,upstream_gene_variant,,ENST00000572680,;NEURL4,downstream_gene_variant,,ENST00000571508,;GPS2,upstream_gene_variant,,ENST00000572172,;GPS2,upstream_gene_variant,,ENST00000572707,;GPS2,upstream_gene_variant,,ENST00000573807,;GPS2,upstream_gene_variant,,ENST00000571098,;GPS2,upstream_gene_variant,,ENST00000572363,;GPS2,upstream_gene_variant,,ENST00000574201,;	A	ENSG00000215041	ENST00000399464	Transcript	missense_variant	3774	3758	1253	S/F	tCt/tTt	.	.	.	-1	NEURL4	HGNC	34410	protein_coding	YES	CCDS42251.1	ENSP00000382390	NEUL4_HUMAN	.	UPI000020081C	.	deleterious(0.02)	benign(0.054)	23/29	.	PROSITE_profiles:PS51065,hmmpanther:PTHR12429:SF2,hmmpanther:PTHR12429	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCAGAGCTG	.	5	ESCA
MYO15B	0	.	GRCh37	17	73611891	73611891	+	3'Flank	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000583560	.	44	41	3	64	63	1	MYO15B,downstream_gene_variant,,ENST00000578462,;MYO15B,downstream_gene_variant,,ENST00000583560,;MYO15B,non_coding_transcript_exon_variant,,ENST00000584723,;MYO15B,non_coding_transcript_exon_variant,,ENST00000584516,;MYO15B,non_coding_transcript_exon_variant,,ENST00000578382,;MYO15B,upstream_gene_variant,,ENST00000577342,;MYO15B,upstream_gene_variant,,ENST00000583140,;MYO15B,upstream_gene_variant,,ENST00000580096,;MYO15B,upstream_gene_variant,,ENST00000577785,;MYO15B,downstream_gene_variant,,ENST00000582012,;MYO15B,upstream_gene_variant,,ENST00000577296,;MYO15B,upstream_gene_variant,,ENST00000579052,;MYO15B,upstream_gene_variant,,ENST00000578005,;MYO15B,upstream_gene_variant,,ENST00000578300,;MYO15B,upstream_gene_variant,,ENST00000578960,;MYO15B,upstream_gene_variant,,ENST00000580176,;	C	ENSG00000266714	ENST00000583560	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4877	1	MYO15B	HGNC	14083	protein_coding	YES	.	ENSP00000463645	MY15B_HUMAN	J3QLP5_HUMAN	UPI000268B34F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCACCTCCAAG	.	2	ESCA
TP53	0	.	GRCh37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524G>A	p.Arg175His	p.R175H	ENST00000269305	5/11	25	11	14	29	29	0	TP53,missense_variant,p.Arg175His,ENST00000413465,;TP53,missense_variant,p.Arg175His,ENST00000420246,;TP53,missense_variant,p.Arg175His,ENST00000269305,;TP53,missense_variant,p.Arg43His,ENST00000509690,;TP53,missense_variant,p.Arg175His,ENST00000359597,;TP53,missense_variant,p.Arg82His,ENST00000514944,;TP53,missense_variant,p.Arg175His,ENST00000445888,;TP53,missense_variant,p.Arg175His,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	714	524	175	R/H	cGc/cAc	CM951224,rs28934578,CM062017,TP53_g.12512G>T,TP53_g.12512G>C,TP53_g.12512G>A,COSM10718,COSM10648,COSM45416,COSM99914,COSM1679508,COSM99022,COSM1679510,COSM99023,COSM1679512,COSM3355994,COSM1640851,COSM1679509,COSM99024,COSM1679511	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.11)	benign(0.308)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660,21264207,24929325,25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R175H|c.524G>A|181,SITE|p.R43H|c.128G>A|183,SITE|p.R82H|c.245G>A|183,SITE|p.R175H|c.524G>A|124,SITE|p.R175H|c.524G>A|180,SITE|p.R175H|c.524G>A|926,SITE|p.R175H|c.524G>A|88,CODON|p.0?|c.1_1182del1182|6,CODON|p.R175L|c.524G>T|20,CODON|p.R175P|c.524G>C|6,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R43L|c.128G>T|3,CODON|p.R82L|c.245G>T|3,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.P177_C182delPHHERC|c.526_543del18|3,BUFFER|p.H179Y|c.534_535CC>TT|8,BUFFER|p.H179D|c.535C>G|12,BUFFER|p.H179Y|c.535C>T|4,BUFFER|p.H47Y|c.139C>T|15,BUFFER|p.H179Y|c.535C>T|5,BUFFER|p.H179Y|c.535C>T|88,BUFFER|p.H179N|c.535C>A|15,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H86Y|c.256C>T|14,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R82G|c.244C>G|5,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43G|c.127C>G|8,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175G|c.523C>G|16,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R174K|c.521G>A|5,BUFFER|p.R174W|c.520A>T|11,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V172D|c.515T>A|11,BUFFER|p.V172A|c.515T>C|4,BUFFER|p.V172G|c.515T>G|4,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAGCGCCTC	byCluster	5	ESCA
ENDOV	0	.	GRCh37	17	78411315	78411315	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1372G>C	.	.	ENST00000518137	10/10	53	30	23	64	64	0	ENDOV,3_prime_UTR_variant,,ENST00000517795,;ENDOV,3_prime_UTR_variant,,ENST00000518907,;ENDOV,3_prime_UTR_variant,,ENST00000518901,;ENDOV,3_prime_UTR_variant,,ENST00000520367,;ENDOV,3_prime_UTR_variant,,ENST00000518137,;ENDOV,3_prime_UTR_variant,,ENST00000520284,;	C	ENSG00000173818	ENST00000518137	Transcript	3_prime_UTR_variant	2249	.	.	.	.	.	.	.	1	ENDOV	HGNC	26640	protein_coding	YES	CCDS54172.1	ENSP00000429190	ENDOV_HUMAN	I3L4V7_HUMAN,I3L1V3_HUMAN,E5RHX4_HUMAN	UPI0000072E31	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGAGAGTTG	.	5	ESCA
FAM195B	0	.	GRCh37	17	79782177	79782177	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113G>A	p.Arg38His	p.R38H	ENST00000576730	2/5	111	98	12	148	148	0	FAM195B,missense_variant,p.Arg59His,ENST00000575061,;FAM195B,missense_variant,p.Arg33His,ENST00000570507,;FAM195B,missense_variant,p.Arg38His,ENST00000574190,;FAM195B,missense_variant,p.Ala42Thr,ENST00000576679,;FAM195B,missense_variant,p.Arg38His,ENST00000576730,;FAM195B,missense_variant,p.Arg38His,ENST00000576431,;FAM195B,missense_variant,p.Arg38His,ENST00000455127,;FAM195B,missense_variant,p.Arg59His,ENST00000572645,;FAM195B,missense_variant,p.Arg38His,ENST00000538396,;FAM195B,missense_variant,p.Arg38His,ENST00000573478,;AC174470.1,3_prime_UTR_variant,,ENST00000457257,;FAM195B,upstream_gene_variant,,ENST00000575090,;	T	ENSG00000225663	ENST00000576730	Transcript	missense_variant	2269	113	38	R/H	cGc/cAc	.	.	.	-1	FAM195B	HGNC	28007	protein_coding	YES	CCDS45814.1	ENSP00000458707	F195B_HUMAN	.	UPI00002000D7	.	tolerated(0.07)	benign(0.07)	2/5	.	hmmpanther:PTHR19890:SF8,hmmpanther:PTHR19890,Pfam_domain:PF14799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAAGCGGACG	.	4	ESCA
ZNF788	0	.	GRCh37	19	12203239	12203239	+	5'UTR	SNP	C	C	G	rs760390142	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-44C>G	.	.	ENST00000596883	1/4	56	40	15	68	68	0	ZNF788,5_prime_UTR_variant,,ENST00000596883,;ZNF788,5_prime_UTR_variant,,ENST00000430298,;ZNF788,5_prime_UTR_variant,,ENST00000339302,;ZNF20,downstream_gene_variant,,ENST00000600335,;Y_RNA,upstream_gene_variant,,ENST00000362574,;ZNF788,non_coding_transcript_exon_variant,,ENST00000397755,;ZNF788,non_coding_transcript_exon_variant,,ENST00000596096,;ZNF788,non_coding_transcript_exon_variant,,ENST00000601686,;ZNF788,non_coding_transcript_exon_variant,,ENST00000595703,;RSL24D1P8,upstream_gene_variant,,ENST00000434442,;	G	ENSG00000214189	ENST00000596883	Transcript	5_prime_UTR_variant	44	.	.	.	.	rs760390142	.	.	1	ZNF788	HGNC	33112	protein_coding	YES	.	ENSP00000473243	.	M0R3I2_HUMAN	UPI0002A47478	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTCTAG	.	5	ESCA
ZNF443	0	.	GRCh37	19	12541042	12541042	+	Silent	SNP	T	T	C	rs2112851	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1944A>G	p.%3D	p.P648P	ENST00000301547	4/4	87	77	10	122	122	0	ZNF443,synonymous_variant,p.%3D,ENST00000301547,;CTD-3105H18.16,intron_variant,,ENST00000595562,;ZNF443,downstream_gene_variant,,ENST00000436821,;CTD-3105H18.18,downstream_gene_variant,,ENST00000598753,;	C	ENSG00000180855	ENST00000301547	Transcript	synonymous_variant	2142	1944	648	P	ccA/ccG	rs2112851	.	.	-1	ZNF443	HGNC	20878	protein_coding	YES	CCDS32918.1	ENSP00000301547	ZN443_HUMAN	F8WDY2_HUMAN	UPI000020344A	.	.	.	4/4	.	PROSITE_profiles:PS50157,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TCATATGGGTT	byCluster	2	ESCA
ZNF490	0	.	GRCh37	19	12721606	12721606	+	5'UTR	SNP	C	C	G	rs548566008	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-112G>C	.	.	ENST00000311437	1/5	13	9	4	17	17	0	ZNF490,5_prime_UTR_variant,,ENST00000311437,;ZNF791,upstream_gene_variant,,ENST00000600752,;ZNF791,upstream_gene_variant,,ENST00000343325,;ZNF791,upstream_gene_variant,,ENST00000540038,;ZNF791,upstream_gene_variant,,ENST00000458122,;ZNF791,upstream_gene_variant,,ENST00000446165,;ZNF490,intron_variant,,ENST00000465656,;ZNF791,upstream_gene_variant,,ENST00000498389,;ZNF490,5_prime_UTR_variant,,ENST00000414906,;ZNF791,upstream_gene_variant,,ENST00000597691,;ZNF791,upstream_gene_variant,,ENST00000598225,;	G	ENSG00000188033	ENST00000311437	Transcript	5_prime_UTR_variant	12	.	.	.	.	rs548566008	.	.	-1	ZNF490	HGNC	23705	protein_coding	YES	CCDS12272.1	ENSP00000311521	ZN490_HUMAN	.	UPI0000001C6F	.	.	.	1/5	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TCCCACCGGCG	by1000G	4	ESCA
BRD4	0	.	GRCh37	19	15367010	15367010	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1616A>G	p.Lys539Arg	p.K539R	ENST00000263377	9/20	79	50	29	77	77	0	BRD4,missense_variant,p.Lys539Arg,ENST00000594841,;BRD4,missense_variant,p.Lys539Arg,ENST00000371835,;BRD4,missense_variant,p.Lys539Arg,ENST00000263377,;BRD4,missense_variant,p.Lys539Arg,ENST00000360016,;BRD4,non_coding_transcript_exon_variant,,ENST00000602230,;BRD4,upstream_gene_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,;	C	ENSG00000141867	ENST00000263377	Transcript	missense_variant	1838	1616	539	K/R	aAg/aGg	.	.	.	-1	BRD4	HGNC	13575	protein_coding	YES	CCDS12328.1	ENSP00000263377	BRD4_HUMAN	Q96HN0_HUMAN,M0R0H4_HUMAN,M0QZD9_HUMAN	UPI0000126ACE	.	.	benign(0.292)	9/20	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF143,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCTTTTTC	.	5	ESCA
NWD1	0	.	GRCh37	19	16884031	16884031	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2505G>A	p.%3D	p.Q835Q	ENST00000524140	11/19	39	20	19	52	52	0	NWD1,synonymous_variant,p.%3D,ENST00000339803,;NWD1,synonymous_variant,p.%3D,ENST00000524140,;NWD1,synonymous_variant,p.%3D,ENST00000552788,;NWD1,synonymous_variant,p.%3D,ENST00000379808,;NWD1,synonymous_variant,p.%3D,ENST00000549814,;NWD1,synonymous_variant,p.%3D,ENST00000523826,;NWD1,3_prime_UTR_variant,,ENST00000438489,;NWD1,3_prime_UTR_variant,,ENST00000518676,;	A	ENSG00000188039	ENST00000524140	Transcript	synonymous_variant	2923	2505	835	Q	caG/caA	.	.	.	1	NWD1	HGNC	27619	protein_coding	YES	CCDS32945.2	ENSP00000428579	NWD1_HUMAN	.	UPI0000D6173E	.	.	.	11/19	.	hmmpanther:PTHR22847:SF273,hmmpanther:PTHR22847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCAGAGCTG	.	5	ESCA
KXD1	0	.	GRCh37	19	18672827	18672827	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-21-19C>T	.	.	ENST00000602094	.	24	19	5	45	45	0	KXD1,5_prime_UTR_variant,,ENST00000598830,;KXD1,5_prime_UTR_variant,,ENST00000595870,;KXD1,intron_variant,,ENST00000595073,;KXD1,intron_variant,,ENST00000602094,;KXD1,intron_variant,,ENST00000596785,;KXD1,intron_variant,,ENST00000600372,;KXD1,intron_variant,,ENST00000599000,;KXD1,intron_variant,,ENST00000539106,;KXD1,intron_variant,,ENST00000540691,;KXD1,intron_variant,,ENST00000601630,;KXD1,intron_variant,,ENST00000599319,;KXD1,intron_variant,,ENST00000222307,;KXD1,intron_variant,,ENST00000597438,;KXD1,intron_variant,,ENST00000596244,;KXD1,upstream_gene_variant,,ENST00000600099,;AC005253.2,upstream_gene_variant,,ENST00000597411,;KXD1,downstream_gene_variant,,ENST00000600796,;KXD1,intron_variant,,ENST00000600654,;	T	ENSG00000105700	ENST00000602094	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KXD1	HGNC	28420	protein_coding	YES	CCDS12381.1	ENSP00000472836	KXDL1_HUMAN	M0R228_HUMAN,M0QXP3_HUMAN,M0QXN9_HUMAN,M0QX74_HUMAN	UPI000013C7F8	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACTCTGTTC	.	4	ESCA
ATP13A1	0	.	GRCh37	19	19766338	19766338	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1395A>G	p.%3D	p.E465E	ENST00000357324	10/26	50	37	13	70	70	0	ATP13A1,synonymous_variant,p.%3D,ENST00000291503,;ATP13A1,synonymous_variant,p.%3D,ENST00000357324,;ATP13A1,downstream_gene_variant,,ENST00000455627,;ATP13A1,splice_region_variant,,ENST00000496082,;ATP13A1,downstream_gene_variant,,ENST00000487364,;ATP13A1,splice_region_variant,,ENST00000497762,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000473243,;ATP13A1,upstream_gene_variant,,ENST00000469641,;ATP13A1,upstream_gene_variant,,ENST00000497556,;ATP13A1,downstream_gene_variant,,ENST00000474955,;ATP13A1,upstream_gene_variant,,ENST00000491221,;ATP13A1,downstream_gene_variant,,ENST00000492774,;ATP13A1,upstream_gene_variant,,ENST00000497156,;ATP13A1,upstream_gene_variant,,ENST00000471063,;	C	ENSG00000105726	ENST00000357324	Transcript	synonymous_variant	1422	1395	465	E	gaA/gaG	.	.	.	-1	ATP13A1	HGNC	24215	protein_coding	YES	CCDS32970.2	ENSP00000349877	AT131_HUMAN	Q8N3E5_HUMAN	UPI0000126647	.	.	.	10/26	.	Superfamily_domains:0049473,TIGRFAM_domain:TIGR01494,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01657,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF82	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTACCTTCAAT	.	4	ESCA
ZNF429	0	.	GRCh37	19	21712490	21712490	+	Missense_Mutation	SNP	G	G	A	rs774747670	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34G>A	p.Glu12Lys	p.E12K	ENST00000358491	2/4	93	61	31	92	92	0	ZNF429,missense_variant,p.Glu12Lys,ENST00000597078,;ZNF429,missense_variant,p.Glu12Lys,ENST00000358491,;ZNF429,non_coding_transcript_exon_variant,,ENST00000594022,;ZNF429,downstream_gene_variant,,ENST00000596126,;	A	ENSG00000197013	ENST00000358491	Transcript	missense_variant	242	34	12	E/K	Gaa/Aaa	rs774747670,COSM3103009	.	.	1	ZNF429	HGNC	20817	protein_coding	YES	CCDS42537.1	ENSP00000351280	ZN429_HUMAN	.	UPI000022ABC2	.	deleterious(0.03)	possibly_damaging(0.615)	2/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24377:SF239,hmmpanther:PTHR24377,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATAGAATTC	.	5	ESCA
ZNF208	0	.	GRCh37	19	22157331	22157331	+	Nonsense_Mutation	SNP	C	C	A	rs148173796	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505G>T	p.Gly169Ter	p.G169*	ENST00000397126	4/4	130	104	26	152	152	0	ZNF208,stop_gained,p.Gly169Ter,ENST00000397126,;ZNF208,intron_variant,,ENST00000601773,;ZNF208,intron_variant,,ENST00000599916,;	A	ENSG00000160321	ENST00000397126	Transcript	stop_gained	654	505	169	G/*	Gga/Tga	rs148173796,COSM108489	.	.	-1	ZNF208	HGNC	12999	protein_coding	YES	CCDS54240.1	ENSP00000380315	ZN208_HUMAN	.	UPI0001B23C28	.	.	.	4/4	.	Superfamily_domains:SSF57667,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103	.	.	.	.	.	.	.	.	.	not_provided	1,1	21499247	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTTTCCAGTAT	.	3	ESCA
CD22	0	.	GRCh37	19	35828840	35828840	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.901A>G	p.Lys301Glu	p.K301E	ENST00000085219	5/14	45	40	5	52	52	0	CD22,missense_variant,p.Lys301Glu,ENST00000544992,;CD22,missense_variant,p.Lys181Glu,ENST00000270311,;CD22,missense_variant,p.Lys301Glu,ENST00000085219,;CD22,missense_variant,p.Lys301Glu,ENST00000536635,;CD22,missense_variant,p.Lys129Glu,ENST00000419549,;CD22,intron_variant,,ENST00000600424,;CD22,intron_variant,,ENST00000341773,;CD22,intron_variant,,ENST00000594250,;CD22,intron_variant,,ENST00000599811,;CD22,downstream_gene_variant,,ENST00000600131,;CD22,downstream_gene_variant,,ENST00000593867,;CD22,downstream_gene_variant,,ENST00000597916,;CD22,non_coding_transcript_exon_variant,,ENST00000601329,;CD22,non_coding_transcript_exon_variant,,ENST00000598028,;CD22,intron_variant,,ENST00000597433,;CD22,intron_variant,,ENST00000598815,;CD22,downstream_gene_variant,,ENST00000598138,;CD22,downstream_gene_variant,,ENST00000601732,;CD22,downstream_gene_variant,,ENST00000601414,;CD22,downstream_gene_variant,,ENST00000600905,;CD22,3_prime_UTR_variant,,ENST00000601769,;CD22,3_prime_UTR_variant,,ENST00000594349,;CD22,intron_variant,,ENST00000600655,;CD22,upstream_gene_variant,,ENST00000594125,;CD22,upstream_gene_variant,,ENST00000602123,;CD22,downstream_gene_variant,,ENST00000602224,;CD22,downstream_gene_variant,,ENST00000599717,;CD22,downstream_gene_variant,,ENST00000596492,;	G	ENSG00000012124	ENST00000085219	Transcript	missense_variant	967	901	301	K/E	Aag/Gag	.	.	.	1	CD22	HGNC	1643	protein_coding	YES	CCDS12457.1	ENSP00000085219	CD22_HUMAN	Q0EAF5_HUMAN,Q9UQB2_HUMAN,Q9UQB1_HUMAN,M0R3H1_HUMAN,M0R2M0_HUMAN,M0R1M2_HUMAN,M0QYP4_HUMAN	UPI000012733D	.	tolerated(0.08)	possibly_damaging(0.526)	5/14	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF39,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TGACCAAGGAC	.	3	ESCA
LIN37	0	.	GRCh37	19	36243179	36243179	+	Intron	SNP	G	G	A	rs375974881	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110+27G>A	.	.	ENST00000301159	.	26	19	7	58	58	0	LIN37,intron_variant,,ENST00000301159,;LIN37,downstream_gene_variant,,ENST00000587751,;HSPB6,downstream_gene_variant,,ENST00000004982,;LIN37,upstream_gene_variant,,ENST00000591163,;HSPB6,downstream_gene_variant,,ENST00000592984,;HSPB6,downstream_gene_variant,,ENST00000587965,;AC002398.11,non_coding_transcript_exon_variant,,ENST00000591091,;AC002398.12,upstream_gene_variant,,ENST00000587767,;AC002398.11,upstream_gene_variant,,ENST00000585365,;LIN37,downstream_gene_variant,,ENST00000591076,;AC002398.9,intron_variant,,ENST00000591613,;LIN37,intron_variant,,ENST00000595455,;LIN37,intron_variant,,ENST00000590706,;LIN37,intron_variant,,ENST00000587108,;LIN37,intron_variant,,ENST00000592871,;LIN37,upstream_gene_variant,,ENST00000590890,;	A	ENSG00000267796	ENST00000301159	Transcript	intron_variant	.	.	.	.	.	rs375974881	.	.	1	LIN37	HGNC	33234	protein_coding	YES	CCDS62642.1	ENSP00000301159	.	M0QYM3_HUMAN	UPI000013D2F3	.	.	.	.	2/8	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGCCGGGCAC	byCluster|by1000G	3	ESCA
ECH1	0	.	GRCh37	19	39322494	39322494	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-82C>G	.	.	ENST00000221418	1/10	19	8	11	31	31	0	ECH1,5_prime_UTR_variant,,ENST00000221418,;AC104534.3,intron_variant,,ENST00000602021,;AC104534.3,intron_variant,,ENST00000594769,;ECH1,upstream_gene_variant,,ENST00000595470,;ECH1,upstream_gene_variant,,ENST00000602115,;ECH1,upstream_gene_variant,,ENST00000597205,;ECH1,upstream_gene_variant,,ENST00000595567,;ECH1,upstream_gene_variant,,ENST00000601778,;HNRNPL,downstream_gene_variant,,ENST00000600873,;HNRNPL,downstream_gene_variant,,ENST00000601449,;HNRNPL,downstream_gene_variant,,ENST00000221419,;ECH1,upstream_gene_variant,,ENST00000601094,;ECH1,upstream_gene_variant,,ENST00000597805,;HNRNPL,downstream_gene_variant,,ENST00000595443,;HNRNPL,downstream_gene_variant,,ENST00000595164,;ECH1,upstream_gene_variant,,ENST00000597089,;ECH1,upstream_gene_variant,,ENST00000600178,;ECH1,upstream_gene_variant,,ENST00000594164,;HNRNPL,downstream_gene_variant,,ENST00000595804,;ECH1,upstream_gene_variant,,ENST00000598707,;HNRNPL,downstream_gene_variant,,ENST00000388749,;ECH1,upstream_gene_variant,,ENST00000596118,;HNRNPL,downstream_gene_variant,,ENST00000597731,;ECH1,upstream_gene_variant,,ENST00000601060,;ECH1,upstream_gene_variant,,ENST00000598316,;	C	ENSG00000104823	ENST00000221418	Transcript	5_prime_UTR_variant	152	.	.	.	.	.	.	.	-1	ECH1	HGNC	3149	protein_coding	YES	CCDS33014.1	ENSP00000221418	ECH1_HUMAN	M0QXS7_HUMAN	UPI0000071141	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTTGAGCGA	.	5	ESCA
SERTAD3	0	.	GRCh37	19	40947559	40947559	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429G>A	p.%3D	p.G143G	ENST00000322354	2/2	40	25	15	61	61	0	SERTAD3,synonymous_variant,p.%3D,ENST00000392028,;SERTAD3,synonymous_variant,p.%3D,ENST00000599706,;SERTAD3,synonymous_variant,p.%3D,ENST00000322354,;SERTAD3,downstream_gene_variant,,ENST00000596456,;CTC-492K19.4,upstream_gene_variant,,ENST00000599050,;SERTAD3,upstream_gene_variant,,ENST00000601217,;	T	ENSG00000167565	ENST00000322354	Transcript	synonymous_variant	926	429	143	G	ggG/ggA	.	.	.	-1	SERTAD3	HGNC	17931	protein_coding	YES	CCDS12558.1	ENSP00000325414	SRTD3_HUMAN	M0R352_HUMAN,M0QXL4_HUMAN	UPI0000072807	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15530,hmmpanther:PTHR15530:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCCCCCAA	.	5	ESCA
ADCK4	0	.	GRCh37	19	41206003	41206003	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1112C>A	p.Ala371Asp	p.A371D	ENST00000324464	12/15	22	18	4	33	33	0	ADCK4,missense_variant,p.Ala330Asp,ENST00000243583,;ADCK4,missense_variant,p.Ala371Asp,ENST00000324464,;ADCK4,missense_variant,p.Ala330Asp,ENST00000450541,;ADCK4,downstream_gene_variant,,ENST00000595254,;ADCK4,downstream_gene_variant,,ENST00000601967,;ADCK4,non_coding_transcript_exon_variant,,ENST00000593724,;ADCK4,downstream_gene_variant,,ENST00000601451,;ADCK4,downstream_gene_variant,,ENST00000601304,;ADCK4,downstream_gene_variant,,ENST00000599643,;ADCK4,downstream_gene_variant,,ENST00000596455,;	T	ENSG00000123815	ENST00000324464	Transcript	missense_variant	1414	1112	371	A/D	gCc/gAc	.	.	.	-1	ADCK4	HGNC	19041	protein_coding	YES	CCDS12562.1	ENSP00000315118	ADCK4_HUMAN	M0R3F7_HUMAN,M0R340_HUMAN,M0R307_HUMAN,M0R011_HUMAN,M0R001_HUMAN,M0QZZ2_HUMAN	UPI0000071B0F	.	deleterious(0)	possibly_damaging(0.889)	12/15	.	Superfamily_domains:SSF56112,hmmpanther:PTHR10566:SF22,hmmpanther:PTHR10566	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE	AGTTGGCCCAG	.	2	ESCA
CYP2B6	0	.	GRCh37	19	41515957	41515957	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.881C>T	p.Ser294Leu	p.S294L	ENST00000324071	6/9	106	53	53	110	110	0	CYP2B6,missense_variant,p.Ser294Leu,ENST00000324071,;CYP2B6,intron_variant,,ENST00000593831,;CYP2B6,intron_variant,,ENST00000330446,;CYP2B6,downstream_gene_variant,,ENST00000598834,;CYP2B6,non_coding_transcript_exon_variant,,ENST00000597612,;CYP2B6,downstream_gene_variant,,ENST00000594187,;	T	ENSG00000197408	ENST00000324071	Transcript	missense_variant	888	881	294	S/L	tCg/tTg	COSM1637593	.	.	1	CYP2B6	HGNC	2615	protein_coding	YES	CCDS12570.1	ENSP00000324648	CP2B6_HUMAN	Q9UNX8_HUMAN,F2X1B0_HUMAN	UPI000012823F	.	deleterious(0.01)	probably_damaging(0.995)	6/9	.	hmmpanther:PTHR24300:SF146,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTCGCTCT	.	5	ESCA
PSG2	0	.	GRCh37	19	43579505	43579505	+	Splice_Site	SNP	C	C	A	rs148538148	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.709+1G>T	.	p.X237_splice	ENST00000406487	.	215	174	41	222	222	0	PSG2,splice_donor_variant,,ENST00000329509,;PSG2,splice_donor_variant,,ENST00000406487,;PSG2,intron_variant,,ENST00000593482,;	A	ENSG00000242221	ENST00000406487	Transcript	splice_donor_variant	.	.	.	.	.	rs148538148,COSM3707195,COSM246829	.	.	-1	PSG2	HGNC	9519	protein_coding	YES	CCDS12616.1	ENSP00000385706	PSG2_HUMAN	.	UPI000013CCF5	.	.	.	.	3/5	.	T:0.0016	T:0.0053	T:0.0014	.	T:0	T:0	T:0	T:0.0009	T:0.0001	.	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCACGGAGG	byFrequency|byCluster|by1000G	5	ESCA
ZNF428	0	.	GRCh37	19	44112223	44112223	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113C>T	p.Ser38Leu	p.S38L	ENST00000300811	3/3	19	12	6	34	34	0	ZNF428,missense_variant,p.Ser71Leu,ENST00000598676,;ZNF428,missense_variant,p.Ser38Leu,ENST00000300811,;SRRM5,intron_variant,,ENST00000526798,;SRRM5,intron_variant,,ENST00000607544,;SRRM5,upstream_gene_variant,,ENST00000417606,;	A	ENSG00000131116	ENST00000300811	Transcript	missense_variant	560	113	38	S/L	tCa/tTa	.	.	.	-1	ZNF428	HGNC	20804	protein_coding	YES	CCDS12626.1	ENSP00000300811	ZN428_HUMAN	.	UPI00001BDA39	.	deleterious_low_confidence(0.01)	possibly_damaging(0.504)	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTGAGAGA	.	5	ESCA
APOE	0	.	GRCh37	19	45411884	45411884	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331C>A	p.Leu111Met	p.L111M	ENST00000252486	4/4	35	30	5	40	40	0	APOE,missense_variant,p.Leu111Met,ENST00000252486,;APOE,missense_variant,p.Leu111Met,ENST00000446996,;APOE,missense_variant,p.Leu111Met,ENST00000425718,;APOE,missense_variant,p.Leu137Met,ENST00000434152,;TOMM40,downstream_gene_variant,,ENST00000252487,;TOMM40,downstream_gene_variant,,ENST00000426677,;TOMM40,downstream_gene_variant,,ENST00000592434,;TOMM40,downstream_gene_variant,,ENST00000405636,;APOE,downstream_gene_variant,,ENST00000485628,;	A	ENSG00000130203	ENST00000252486	Transcript	missense_variant	442	331	111	L/M	Ctg/Atg	.	.	.	1	APOE	HGNC	613	protein_coding	YES	CCDS12647.1	ENSP00000252486	APOE_HUMAN	Q6LBZ1_HUMAN,Q6LA97_HUMAN,J9ZVQ3_HUMAN,E9PEV4_HUMAN,E7ERP7_HUMAN	UPI0000044948	.	deleterious(0.04)	possibly_damaging(0.729)	4/4	.	hmmpanther:PTHR18976:SF2,hmmpanther:PTHR18976,Pfam_domain:PF01442,Gene3D:1.20.120.20,Superfamily_domains:0053393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACGGCTGTCC	.	4	ESCA
BLOC1S3	0	.	GRCh37	19	45684142	45684142	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*979G>A	.	.	ENST00000433642	2/2	13	9	4	20	20	0	BLOC1S3,3_prime_UTR_variant,,ENST00000433642,;MARK4,intron_variant,,ENST00000587566,;BLOC1S3,intron_variant,,ENST00000592910,;TRAPPC6A,upstream_gene_variant,,ENST00000588062,;TRAPPC6A,upstream_gene_variant,,ENST00000592647,;TRAPPC6A,upstream_gene_variant,,ENST00000006275,;BLOC1S3,downstream_gene_variant,,ENST00000587722,;TRAPPC6A,upstream_gene_variant,,ENST00000585934,;BLOC1S3,intron_variant,,ENST00000588362,;AC005779.2,intron_variant,,ENST00000593083,;TRAPPC6A,upstream_gene_variant,,ENST00000587818,;AC005779.1,downstream_gene_variant,,ENST00000441087,;	A	ENSG00000189114	ENST00000433642	Transcript	3_prime_UTR_variant	1684	.	.	.	.	.	.	.	1	BLOC1S3	HGNC	20914	protein_coding	YES	CCDS12656.1	ENSP00000393840	BL1S3_HUMAN	K7EN58_HUMAN,K7ELZ0_HUMAN	UPI0000202628	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCACGCCTGG	.	5	ESCA
IGFL2	0	.	GRCh37	19	46664041	46664041	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277G>C	p.Asp93His	p.D93H	ENST00000434646	4/5	72	47	25	76	76	0	IGFL2,missense_variant,p.Asp82His,ENST00000377693,;IGFL2,missense_variant,p.Asp48His,ENST00000601052,;IGFL2,missense_variant,p.Asp93His,ENST00000434646,;AC007193.6,intron_variant,,ENST00000597989,;AC006262.4,downstream_gene_variant,,ENST00000599127,;IGFL2,non_coding_transcript_exon_variant,,ENST00000600243,;IGFL2,non_coding_transcript_exon_variant,,ENST00000593592,;	C	ENSG00000204866	ENST00000434646	Transcript	missense_variant	568	277	93	D/H	Gat/Cat	COSM389307,COSM1525635	.	.	1	IGFL2	HGNC	32929	protein_coding	YES	CCDS46122.1	ENSP00000395219	IGFL2_HUMAN	.	UPI00002026D9	.	deleterious(0)	possibly_damaging(0.694)	4/5	.	Pfam_domain:PF14653	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTGATTCC	.	5	ESCA
SIGLEC6	0	.	GRCh37	19	52032987	52032987	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003T>C	p.Phe335Leu	p.F335L	ENST00000425629	5/8	43	27	16	71	71	0	SIGLEC6,missense_variant,p.Phe283Leu,ENST00000436458,;SIGLEC6,missense_variant,p.Phe324Leu,ENST00000391797,;SIGLEC6,missense_variant,p.Phe346Leu,ENST00000359982,;SIGLEC6,missense_variant,p.Phe335Leu,ENST00000425629,;SIGLEC6,missense_variant,p.Phe335Leu,ENST00000343300,;SIGLEC6,missense_variant,p.Phe319Leu,ENST00000346477,;SIGLEC6,upstream_gene_variant,,ENST00000474054,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000489837,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000496422,;	G	ENSG00000105492	ENST00000425629	Transcript	missense_variant	1158	1003	335	F/L	Ttt/Ctt	.	.	.	-1	SIGLEC6	HGNC	10875	protein_coding	YES	CCDS12834.3	ENSP00000401502	SIGL6_HUMAN	.	UPI0000223FFD	.	tolerated(0.29)	benign(0.013)	5/8	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF07679,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAAAGAGAC	.	5	ESCA
ZNF350	0	.	GRCh37	19	52468501	52468501	+	Missense_Mutation	SNP	T	T	C	rs150778438	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1205A>G	p.Tyr402Cys	p.Y402C	ENST00000243644	5/5	47	29	18	73	73	0	ZNF350,missense_variant,p.Tyr402Cys,ENST00000243644,;ZNF350,downstream_gene_variant,,ENST00000593596,;ZNF350,downstream_gene_variant,,ENST00000594929,;ZNF350,downstream_gene_variant,,ENST00000601430,;ZNF350,downstream_gene_variant,,ENST00000597788,;HCCAT3,intron_variant,,ENST00000600253,;HCCAT3,intron_variant,,ENST00000595010,;ZNF350,downstream_gene_variant,,ENST00000600703,;ZNF350,downstream_gene_variant,,ENST00000598254,;	C	ENSG00000256683	ENST00000243644	Transcript	missense_variant	1433	1205	402	Y/C	tAt/tGt	rs150778438	.	.	-1	ZNF350	HGNC	16656	protein_coding	YES	CCDS12845.1	ENSP00000243644	ZN350_HUMAN	M0R1T8_HUMAN,M0R017_HUMAN,M0QYT6_HUMAN,M0QY52_HUMAN	UPI00000721F1	.	deleterious(0.01)	probably_damaging(0.983)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF11,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	C:0	C:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCATAGGGT	byCluster	5	ESCA
ZNF582	0	.	GRCh37	19	56895658	56895658	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1128T>A	p.Phe376Leu	p.F376L	ENST00000301310	5/5	33	18	15	33	33	0	ZNF582,missense_variant,p.Phe376Leu,ENST00000586929,;ZNF582,missense_variant,p.Phe376Leu,ENST00000301310,;ZNF582,intron_variant,,ENST00000589143,;AC006116.12,upstream_gene_variant,,ENST00000589671,;ZNF542,downstream_gene_variant,,ENST00000467807,;ZNF542,downstream_gene_variant,,ENST00000495307,;ZNF542,downstream_gene_variant,,ENST00000490123,;ZNF582,downstream_gene_variant,,ENST00000593145,;ZNF582,downstream_gene_variant,,ENST00000587778,;SLC25A36P1,upstream_gene_variant,,ENST00000590111,;	T	ENSG00000018869	ENST00000301310	Transcript	missense_variant	1287	1128	376	F/L	ttT/ttA	.	.	.	-1	ZNF582	HGNC	26421	protein_coding	YES	CCDS33121.1	ENSP00000301310	ZN582_HUMAN	B4DQZ9_HUMAN	UPI000006D278	.	deleterious(0)	probably_damaging(0.993)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF115,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCTAAAGGC	.	5	ESCA
BSG	0	.	GRCh37	19	577776	577776	+	Missense_Mutation	SNP	G	G	A	rs539913003	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70G>A	p.Gly24Ser	p.G24S	ENST00000333511	2/9	12	8	3	16	16	0	BSG,missense_variant,p.Gly24Ser,ENST00000333511,;BSG,intron_variant,,ENST00000353555,;BSG,intron_variant,,ENST00000573784,;BSG,intron_variant,,ENST00000545507,;BSG,intron_variant,,ENST00000576984,;BSG,intron_variant,,ENST00000573216,;BSG,intron_variant,,ENST00000346916,;BSG,splice_region_variant,,ENST00000574970,;BSG,splice_region_variant,,ENST00000590218,;BSG,intron_variant,,ENST00000572899,;BSG,intron_variant,,ENST00000576925,;BSG,upstream_gene_variant,,ENST00000571735,;	A	ENSG00000172270	ENST00000333511	Transcript	missense_variant	140	70	24	G/S	Ggc/Agc	rs539913003	.	.	1	BSG	HGNC	1116	protein_coding	YES	CCDS12033.1	ENSP00000333769	BASI_HUMAN	R4GN83_HUMAN,R4GMX5_HUMAN	UPI0000051E38	.	deleterious(0.03)	probably_damaging(0.994)	2/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10075,hmmpanther:PTHR10075:SF12	A:0.0006	A:0	A:0	.	A:0.003	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAGCCGGCTTC	byFrequency|by1000G	2	ESCA
ZNF772	0	.	GRCh37	19	57985077	57985077	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1035T>A	p.%3D	p.T345T	ENST00000343280	5/5	66	38	27	57	57	0	ZNF772,synonymous_variant,p.%3D,ENST00000427512,;ZNF772,synonymous_variant,p.%3D,ENST00000343280,;ZNF772,synonymous_variant,p.%3D,ENST00000356584,;ZNF772,3_prime_UTR_variant,,ENST00000425074,;ZNF772,intron_variant,,ENST00000600175,;ZNF772,intron_variant,,ENST00000601768,;AC004076.9,intron_variant,,ENST00000596831,;AC003005.2,upstream_gene_variant,,ENST00000595422,;AC003005.2,upstream_gene_variant,,ENST00000594562,;AC004076.9,intron_variant,,ENST00000415705,;ZNF772,downstream_gene_variant,,ENST00000450712,;	T	ENSG00000197128	ENST00000343280	Transcript	synonymous_variant	1296	1035	345	T	acT/acA	.	.	.	-1	ZNF772	HGNC	33106	protein_coding	YES	CCDS33133.1	ENSP00000341165	ZN772_HUMAN	.	UPI000022AA0A	.	.	.	5/5	.	Superfamily_domains:SSF57667,Gene3D:3.30.160.60,hmmpanther:PTHR24387:SF75,hmmpanther:PTHR24387,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCAGTGTG	.	5	ESCA
GTF2F1	0	.	GRCh37	19	6380476	6380476	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1370A>C	p.Asp457Ala	p.D457A	ENST00000394456	13/13	106	61	44	134	134	0	GTF2F1,missense_variant,p.Asp373Ala,ENST00000593678,;GTF2F1,missense_variant,p.Asp372Ala,ENST00000429701,;GTF2F1,missense_variant,p.Asp457Ala,ENST00000394456,;GTF2F1,downstream_gene_variant,,ENST00000595047,;PSPN,upstream_gene_variant,,ENST00000245810,;PSPN,upstream_gene_variant,,ENST00000597721,;GTF2F1,non_coding_transcript_exon_variant,,ENST00000594965,;GTF2F1,non_coding_transcript_exon_variant,,ENST00000594213,;	G	ENSG00000125651	ENST00000394456	Transcript	missense_variant	1835	1370	457	D/A	gAt/gCt	.	.	.	-1	GTF2F1	HGNC	4652	protein_coding	YES	CCDS12165.1	ENSP00000377969	T2FA_HUMAN	M0R0Z3_HUMAN	UPI000007323F	.	deleterious(0.01)	benign(0.11)	13/13	.	hmmpanther:PTHR13011,Gene3D:1.10.10.10,Pfam_domain:PF05793,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCATCCTCA	.	5	ESCA
C3	0	.	GRCh37	19	6697514	6697514	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2637G>A	p.%3D	p.K879K	ENST00000245907	21/41	106	67	38	97	97	0	C3,synonymous_variant,p.%3D,ENST00000245907,;C3,non_coding_transcript_exon_variant,,ENST00000594005,;C3,upstream_gene_variant,,ENST00000598805,;C3,downstream_gene_variant,,ENST00000602053,;	T	ENSG00000125730	ENST00000245907	Transcript	synonymous_variant	2730	2637	879	K	aaG/aaA	.	.	.	-1	C3	HGNC	1318	protein_coding	YES	CCDS32883.1	ENSP00000245907	CO3_HUMAN	Q6LDJ0_HUMAN,M0R1Q1_HUMAN	UPI000013EC9B	.	.	.	21/41	.	hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF81	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTCTTGGT	.	5	ESCA
PTBP1	0	.	GRCh37	19	811811	811811	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*985G>C	.	.	ENST00000356948	15/15	39	25	13	48	48	0	PTBP1,3_prime_UTR_variant,,ENST00000349038,;PTBP1,3_prime_UTR_variant,,ENST00000394601,;PTBP1,3_prime_UTR_variant,,ENST00000356948,;PTBP1,3_prime_UTR_variant,,ENST00000350092,;LPPR3,downstream_gene_variant,,ENST00000520876,;PTBP1,downstream_gene_variant,,ENST00000585956,;LPPR3,downstream_gene_variant,,ENST00000519502,;LPPR3,downstream_gene_variant,,ENST00000517665,;LPPR3,downstream_gene_variant,,ENST00000359894,;MIR3187,upstream_gene_variant,,ENST00000583431,;PTBP1,downstream_gene_variant,,ENST00000589770,;PTBP1,downstream_gene_variant,,ENST00000585932,;PTBP1,downstream_gene_variant,,ENST00000589883,;PTBP1,downstream_gene_variant,,ENST00000587191,;PTBP1,downstream_gene_variant,,ENST00000585856,;PTBP1,downstream_gene_variant,,ENST00000586944,;	C	ENSG00000011304	ENST00000356948	Transcript	3_prime_UTR_variant	3082	.	.	.	.	.	.	.	1	PTBP1	HGNC	9583	protein_coding	YES	CCDS42456.1	ENSP00000349428	PTBP1_HUMAN	.	UPI00000720B7	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTAGAAAAC	.	5	ESCA
OR1M1	0	.	GRCh37	19	9204692	9204692	+	Missense_Mutation	SNP	G	G	A	rs144608760	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772G>A	p.Val258Ile	p.V258I	ENST00000429566	1/1	42	34	7	45	45	0	OR1M1,missense_variant,p.Val258Ile,ENST00000429566,;	A	ENSG00000170929	ENST00000429566	Transcript	missense_variant	838	772	258	V/I	Gtc/Atc	rs144608760,COSM568523	.	.	1	OR1M1	HGNC	8220	protein_coding	YES	CCDS32896.1	ENSP00000401966	OR1M1_HUMAN	.	UPI0000041C29	.	deleterious(0.03)	probably_damaging(0.997)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF295,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGCGTCTAT	.	5	ESCA
RNPC3	0	.	GRCh37	1	104087666	104087666	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1149A>C	p.Glu383Asp	p.E383D	ENST00000533099	11/16	40	32	8	52	52	0	RNPC3,missense_variant,p.Glu382Asp,ENST00000524631,;RNPC3,missense_variant,p.Glu112Asp,ENST00000524641,;RNPC3,missense_variant,p.Glu383Asp,ENST00000533099,;RNPC3,missense_variant,p.Glu383Asp,ENST00000423855,;RNPC3,downstream_gene_variant,,ENST00000527062,;RNPC3,non_coding_transcript_exon_variant,,ENST00000533834,;RNPC3,upstream_gene_variant,,ENST00000525323,;	C	ENSG00000185946	ENST00000533099	Transcript	missense_variant	1385	1149	383	E/D	gaA/gaC	.	.	.	1	RNPC3	HGNC	18666	protein_coding	YES	CCDS781.1	ENSP00000432886	RBM40_HUMAN	E9PPV2_HUMAN	UPI000006E703	.	tolerated(0.58)	benign(0.002)	11/16	.	hmmpanther:PTHR16105:SF0,hmmpanther:PTHR16105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAAATGCC	.	5	ESCA
GPSM2	0	.	GRCh37	1	109472947	109472947	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*385G>A	.	.	ENST00000406462	16/16	25	20	5	27	27	0	GPSM2,3_prime_UTR_variant,,ENST00000406462,;CLCC1,3_prime_UTR_variant,,ENST00000415331,;CLCC1,3_prime_UTR_variant,,ENST00000369969,;GPSM2,3_prime_UTR_variant,,ENST00000264126,;CLCC1,3_prime_UTR_variant,,ENST00000369971,;CLCC1,3_prime_UTR_variant,,ENST00000369968,;CLCC1,3_prime_UTR_variant,,ENST00000369976,;CLCC1,3_prime_UTR_variant,,ENST00000356970,;AKNAD1,intron_variant,,ENST00000357393,;CLCC1,downstream_gene_variant,,ENST00000302500,;CLCC1,downstream_gene_variant,,ENST00000348264,;CLCC1,downstream_gene_variant,,ENST00000369970,;CLCC1,intron_variant,,ENST00000482889,;CLCC1,intron_variant,,ENST00000473062,;	A	ENSG00000121957	ENST00000406462	Transcript	3_prime_UTR_variant	3213	.	.	.	.	.	.	.	1	GPSM2	HGNC	29501	protein_coding	YES	CCDS792.2	ENSP00000385510	GPSM2_HUMAN	Q5T1N9_HUMAN,B4DIF1_HUMAN,B0QZD0_HUMAN,B0QZC9_HUMAN	UPI000013D4C2	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTAGTGGGA	.	5	ESCA
GPR89A	0	.	GRCh37	1	145811926	145811927	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.282dupT	p.Gly95TrpfsTer13	p.G95Wfs*13	ENST00000313835	4/14	68	57	11	48	48	0	GPR89A,frameshift_variant,p.Gly70TrpfsTer13,ENST00000534502,;GPR89A,frameshift_variant,p.Gly95TrpfsTer13,ENST00000313835,;GPR89A,frameshift_variant,p.Gly70TrpfsTer13,ENST00000462900,;GPR89A,5_prime_UTR_variant,,ENST00000454423,;GPR89A,non_coding_transcript_exon_variant,,ENST00000527989,;GPR89A,frameshift_variant,p.Gly95TrpfsTer369,ENST00000460277,;GPR89A,frameshift_variant,p.Gly95TrpfsTer54,ENST00000528944,;GPR89A,frameshift_variant,p.Gly75TrpfsTer13,ENST00000466593,;GPR89A,non_coding_transcript_exon_variant,,ENST00000532574,;GPR89A,downstream_gene_variant,,ENST00000524525,;	A	ENSG00000117262	ENST00000313835	Transcript	frameshift_variant	426-427	282-283	94-95	-/X	-/T	.	.	.	-1	GPR89A	HGNC	31984	protein_coding	YES	CCDS41377.1	ENSP00000319673	GPHRA_HUMAN	.	UPI00000389CC	.	.	.	4/14	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15948	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATAGCCAATGT	.	3	ESCA
CGN	0	.	GRCh37	1	151491113	151491113	+	Nonsense_Mutation	SNP	C	C	T	rs376940080	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118C>T	p.Arg40Ter	p.R40*	ENST00000271636	2/21	60	52	8	53	53	0	CGN,stop_gained,p.Arg40Ter,ENST00000271636,;CGN,stop_gained,p.Arg40Ter,ENST00000427934,;CGN,stop_gained,p.Arg40Ter,ENST00000505188,;CGN,stop_gained,p.Arg40Ter,ENST00000502442,;CGN,upstream_gene_variant,,ENST00000416743,;	T	ENSG00000143375	ENST00000271636	Transcript	stop_gained	251	118	40	R/*	Cga/Tga	rs376940080,COSM4022254	.	.	1	CGN	HGNC	17429	protein_coding	YES	CCDS999.1	ENSP00000271636	CING_HUMAN	A6PVU7_HUMAN,A2A3M4_HUMAN	UPI0000161C1E	.	.	.	2/21	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGACGACGC	byFrequency|byCluster	4	ESCA
SLC35E2B	0	.	GRCh37	1	1601102	1601102	+	Splice_Site	DEL	C	C	-	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.834+1delG	.	p.X278_splice	ENST00000378662	.	49	39	10	51	51	0	SLC35E2B,splice_donor_variant,,ENST00000234800,;SLC35E2B,splice_donor_variant,,ENST00000378662,;RP11-345P4.7,upstream_gene_variant,,ENST00000596308,;SLC35E2B,splice_donor_variant,,ENST00000480991,;SLC35E2B,downstream_gene_variant,,ENST00000481276,;RP11-345P4.6,upstream_gene_variant,,ENST00000597891,;	-	ENSG00000189339	ENST00000378662	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	SLC35E2B	HGNC	33941	protein_coding	YES	CCDS44041.1	ENSP00000367931	S352B_HUMAN	B3KRW7_HUMAN	UPI00001B6AFE	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AACCCACCGTAA	.	3	ESCA
PAPPA2	0	.	GRCh37	1	176564460	176564460	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1720A>C	p.Asn574His	p.N574H	ENST00000367662	3/23	49	36	13	62	62	0	PAPPA2,missense_variant,p.Asn574His,ENST00000367661,;PAPPA2,missense_variant,p.Asn574His,ENST00000367662,;	C	ENSG00000116183	ENST00000367662	Transcript	missense_variant	2884	1720	574	N/H	Aat/Cat	.	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	tolerated(0.06)	benign(0.349)	3/23	.	hmmpanther:PTHR19325:SF349,hmmpanther:PTHR19325,SMART_domains:SM00004,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACAATTCC	.	5	ESCA
HMCN1	0	.	GRCh37	1	186106700	186106700	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13653G>C	p.Lys4551Asn	p.K4551N	ENST00000271588	88/107	36	32	3	40	40	0	HMCN1,missense_variant,p.Lys4551Asn,ENST00000367492,;HMCN1,missense_variant,p.Lys4551Asn,ENST00000271588,;	C	ENSG00000143341	ENST00000271588	Transcript	missense_variant	13882	13653	4551	K/N	aaG/aaC	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	possibly_damaging(0.76)	88/107	.	PROSITE_profiles:PS50092,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAAAGAGGAG	.	4	ESCA
UBR4	0	.	GRCh37	1	19493660	19493660	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3965G>A	p.Ser1322Asn	p.S1322N	ENST00000375254	29/106	33	21	12	50	50	0	UBR4,missense_variant,p.Ser32Asn,ENST00000417040,;UBR4,missense_variant,p.Ser1322Asn,ENST00000375254,;UBR4,missense_variant,p.Ser1322Asn,ENST00000375217,;UBR4,missense_variant,p.Ser1322Asn,ENST00000375267,;UBR4,missense_variant,p.Ser1322Asn,ENST00000375226,;UBR4,non_coding_transcript_exon_variant,,ENST00000419533,;	T	ENSG00000127481	ENST00000375254	Transcript	missense_variant	3993	3965	1322	S/N	aGc/aAc	.	.	.	-1	UBR4	HGNC	30313	protein_coding	YES	CCDS189.1	ENSP00000364403	UBR4_HUMAN	Q96HY5_HUMAN	UPI000021276F	.	.	possibly_damaging(0.852)	29/106	.	Superfamily_domains:SSF48371,hmmpanther:PTHR21725,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTGCTTGAT	.	5	ESCA
RABIF	0	.	GRCh37	1	202858168	202858168	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>T	p.Ala20Val	p.A20V	ENST00000367262	1/2	20	12	8	20	20	0	RABIF,missense_variant,p.Ala20Val,ENST00000367262,;KLHL12,downstream_gene_variant,,ENST00000367261,;KLHL12,downstream_gene_variant,,ENST00000367259,;KLHL12,downstream_gene_variant,,ENST00000435533,;	A	ENSG00000183155	ENST00000367262	Transcript	missense_variant	96	59	20	A/V	gCg/gTg	.	.	.	-1	RABIF	HGNC	9797	protein_coding	YES	CCDS1428.1	ENSP00000356231	MSS4_HUMAN	.	UPI0000001C5E	.	tolerated(0.43)	benign(0.213)	1/2	.	Superfamily_domains:SSF51316,Pfam_domain:PF04421,Gene3D:2.170.150.10,hmmpanther:PTHR13276	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCGCCTTC	.	5	ESCA
C1QC	0	.	GRCh37	1	22974181	22974181	+	Missense_Mutation	SNP	G	G	A	rs750272291	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.643G>A	p.Glu215Lys	p.E215K	ENST00000374639	3/3	37	25	11	53	53	0	C1QC,missense_variant,p.Glu215Lys,ENST00000374640,;C1QC,missense_variant,p.Glu215Lys,ENST00000374637,;C1QC,missense_variant,p.Glu215Lys,ENST00000374639,;	A	ENSG00000159189	ENST00000374639	Transcript	missense_variant	761	643	215	E/K	Gag/Aag	rs750272291	.	.	1	C1QC	HGNC	1245	protein_coding	YES	CCDS227.1	ENSP00000363770	C1QC_HUMAN	.	UPI0000126BF3	.	deleterious(0.01)	benign(0.428)	3/3	.	PROSITE_profiles:PS50871,hmmpanther:PTHR24022,hmmpanther:PTHR24022:SF17,Gene3D:2.60.120.40,Pfam_domain:PF00386,SMART_domains:SM00110,Superfamily_domains:SSF49842,Prints_domain:PR00007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGCGAGGAG	.	5	ESCA
EXOC8	0	.	GRCh37	1	231472549	231472549	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.943G>A	p.Asp315Asn	p.D315N	ENST00000360394	1/1	52	39	13	45	45	0	EXOC8,missense_variant,p.Asp315Asn,ENST00000360394,;EXOC8,missense_variant,p.Asp311Asn,ENST00000366645,;SPRTN,upstream_gene_variant,,ENST00000008440,;SPRTN,upstream_gene_variant,,ENST00000366644,;SPRTN,upstream_gene_variant,,ENST00000295050,;SPRTN,upstream_gene_variant,,ENST00000391858,;SPRTN,upstream_gene_variant,,ENST00000492437,;	T	ENSG00000116903	ENST00000360394	Transcript	missense_variant	1030	943	315	D/N	Gac/Aac	COSM364944	.	.	-1	EXOC8	HGNC	24659	protein_coding	YES	CCDS1593.1	ENSP00000353564	EXOC8_HUMAN	.	UPI000006EA2C	.	tolerated(0.14)	benign(0.002)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21426	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCGTCATCCT	.	5	ESCA
LYST	0	.	GRCh37	1	235922855	235922855	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6298A>G	p.Met2100Val	p.M2100V	ENST00000389794	23/53	28	22	6	20	20	0	LYST,missense_variant,p.Met2100Val,ENST00000389793,;LYST,missense_variant,p.Met2100Val,ENST00000389794,;LYST,3_prime_UTR_variant,,ENST00000536965,;LYST,non_coding_transcript_exon_variant,,ENST00000489585,;	C	ENSG00000143669	ENST00000389794	Transcript	missense_variant	6473	6298	2100	M/V	Atg/Gtg	.	.	.	-1	LYST	HGNC	1968	protein_coding	YES	CCDS31062.1	ENSP00000374444	LYST_HUMAN	.	UPI000020509E	.	tolerated_low_confidence(0.53)	benign(0.003)	23/53	.	hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCATATGGG	.	5	ESCA
RYR2	0	.	GRCh37	1	237863703	237863703	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9303G>A	p.%3D	p.L3101L	ENST00000366574	65/105	61	48	13	50	50	0	RYR2,synonymous_variant,p.%3D,ENST00000542537,;RYR2,synonymous_variant,p.%3D,ENST00000366574,;RYR2,synonymous_variant,p.%3D,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,;	A	ENSG00000198626	ENST00000366574	Transcript	synonymous_variant	9620	9303	3101	L	ctG/ctA	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	.	65/105	.	hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTGCTGCC	.	5	ESCA
OR2M4	0	.	GRCh37	1	248402808	248402808	+	Missense_Mutation	SNP	C	C	A	rs374565024	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578C>A	p.Ser193Tyr	p.S193Y	ENST00000306687	1/1	86	61	24	75	75	0	OR2M4,missense_variant,p.Ser193Tyr,ENST00000306687,;	A	ENSG00000171180	ENST00000306687	Transcript	missense_variant	578	578	193	S/Y	tCt/tAt	rs374565024	.	.	1	OR2M4	HGNC	8270	protein_coding	YES	CCDS31108.1	ENSP00000306688	OR2M4_HUMAN	.	UPI000004B233	.	deleterious(0.02)	possibly_damaging(0.781)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF91,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACATCTGCAT	byFrequency|byCluster	5	ESCA
C1orf172	0	.	GRCh37	1	27278224	27278224	+	Nonsense_Mutation	SNP	G	G	C	rs772817105	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.648C>G	p.Tyr216Ter	p.Y216*	ENST00000320567	2/4	31	25	5	50	50	0	C1orf172,stop_gained,p.Tyr216Ter,ENST00000320567,;NUDC,downstream_gene_variant,,ENST00000321265,;	C	ENSG00000175707	ENST00000320567	Transcript	stop_gained	737	648	216	Y/*	taC/taG	rs772817105	.	.	-1	C1orf172	HGNC	26624	protein_coding	YES	CCDS293.1	ENSP00000319179	CA172_HUMAN	.	UPI00001408F3	.	.	.	2/4	.	Pfam_domain:PF15551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATAGTACTC	.	5	ESCA
HEYL	0	.	GRCh37	1	40092514	40092514	+	Nonsense_Mutation	SNP	G	G	A	rs753352796	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652C>T	p.Arg218Ter	p.R218*	ENST00000372852	5/5	63	36	27	68	68	0	HEYL,stop_gained,p.Arg218Ter,ENST00000372852,;HEYL,stop_gained,p.Arg190Ter,ENST00000535435,;	A	ENSG00000163909	ENST00000372852	Transcript	stop_gained	972	652	218	R/*	Cga/Tga	rs753352796,COSM426245	.	.	-1	HEYL	HGNC	4882	protein_coding	YES	CCDS439.1	ENSP00000361943	HEYL_HUMAN	F5H3V9_HUMAN	UPI000013E317	.	.	.	5/5	.	hmmpanther:PTHR10985:SF10,hmmpanther:PTHR10985	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCGGAGGG	.	5	ESCA
PTPRF	0	.	GRCh37	1	44072574	44072574	+	Silent	SNP	G	G	A	rs111705998	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3792G>A	p.%3D	p.V1264V	ENST00000359947	21/34	62	52	10	80	80	0	PTPRF,synonymous_variant,p.%3D,ENST00000372407,;PTPRF,synonymous_variant,p.%3D,ENST00000412568,;PTPRF,synonymous_variant,p.%3D,ENST00000414879,;PTPRF,synonymous_variant,p.%3D,ENST00000438120,;PTPRF,synonymous_variant,p.%3D,ENST00000359947,;PTPRF,synonymous_variant,p.%3D,ENST00000429895,;PTPRF,synonymous_variant,p.%3D,ENST00000372413,;PTPRF,synonymous_variant,p.%3D,ENST00000422171,;PTPRF,synonymous_variant,p.%3D,ENST00000372414,;PTPRF,non_coding_transcript_exon_variant,,ENST00000496447,;PTPRF,downstream_gene_variant,,ENST00000463041,;	A	ENSG00000142949	ENST00000359947	Transcript	synonymous_variant	4132	3792	1264	V	gtG/gtA	rs111705998	.	.	1	PTPRF	HGNC	9670	protein_coding	YES	CCDS489.2	ENSP00000353030	PTPRF_HUMAN	G1UI20_HUMAN	UPI0000470154	.	.	.	21/34	.	hmmpanther:PTHR19134:SF203,hmmpanther:PTHR19134,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTGACGGG	byCluster	5	ESCA
KIF2C	0	.	GRCh37	1	45228229	45228229	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870G>C	p.Glu624Gln	p.E624Q	ENST00000372224	19/21	26	20	6	31	31	0	KIF2C,missense_variant,p.Glu511Gln,ENST00000372222,;KIF2C,missense_variant,p.Glu570Gln,ENST00000372217,;KIF2C,missense_variant,p.Glu583Gln,ENST00000372218,;KIF2C,missense_variant,p.Glu624Gln,ENST00000372224,;KIF2C,missense_variant,p.Glu89Gln,ENST00000423289,;KIF2C,downstream_gene_variant,,ENST00000452259,;RP11-269F19.2,intron_variant,,ENST00000428791,;RP11-269F19.2,upstream_gene_variant,,ENST00000440985,;KIF2C,non_coding_transcript_exon_variant,,ENST00000472235,;KIF2C,downstream_gene_variant,,ENST00000493027,;	C	ENSG00000142945	ENST00000372224	Transcript	missense_variant	1983	1870	624	E/Q	Gag/Cag	.	.	.	1	KIF2C	HGNC	6393	protein_coding	YES	CCDS512.1	ENSP00000361298	KIF2C_HUMAN	Q8N5N1_HUMAN,B7Z7M6_HUMAN	UPI000012DDAD	.	tolerated(0.05)	benign(0.017)	19/21	.	hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGAGGAG	.	5	ESCA
AKR1A1	0	.	GRCh37	1	46035627	46035627	+	Silent	SNP	G	G	A	rs368164790	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.977G>A	p.%3D	p.%3D	ENST00000372070	10/10	43	31	11	47	47	0	AKR1A1,stop_retained_variant,p.%3D,ENST00000372070,;AKR1A1,stop_retained_variant,p.%3D,ENST00000351829,;AKR1A1,downstream_gene_variant,,ENST00000481885,;AKR1A1,downstream_gene_variant,,ENST00000471651,;AKR1A1,downstream_gene_variant,,ENST00000434299,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000495913,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000475985,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000487654,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000473038,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000475919,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000497973,;AKR1A1,downstream_gene_variant,,ENST00000496999,;AKR1A1,downstream_gene_variant,,ENST00000476957,;	A	ENSG00000117448	ENST00000372070	Transcript	stop_retained_variant	1724	977	326	*	tGa/tAa	rs368164790	.	.	1	AKR1A1	HGNC	380	protein_coding	YES	CCDS523.1	ENSP00000361140	AK1A1_HUMAN	Q5T621_HUMAN	UPI000013D31D	.	.	.	10/10	.	.	C:0.0008	C:0	C:0	.	C:0.004	C:0	C:0	C:0.0002	C:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACTGAGACC	byFrequency|byCluster|by1000G	5	ESCA
MAST2	0	.	GRCh37	1	46476523	46476523	+	Missense_Mutation	SNP	G	G	A	rs200211912	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000361297	10/29	41	31	10	39	39	0	MAST2,missense_variant,p.Arg367Gln,ENST00000361297,;MAST2,missense_variant,p.Arg252Gln,ENST00000372008,;MAST2,intron_variant,,ENST00000372009,;MAST2,non_coding_transcript_exon_variant,,ENST00000482881,;MAST2,downstream_gene_variant,,ENST00000488619,;	A	ENSG00000086015	ENST00000361297	Transcript	missense_variant	1383	1100	367	R/Q	cGa/cAa	rs200211912	.	.	1	MAST2	HGNC	19035	protein_coding	YES	CCDS41326.1	ENSP00000354671	MAST2_HUMAN	Q9NT11_HUMAN	UPI0000458AEB	.	deleterious_low_confidence(0)	probably_damaging(0.99)	10/29	.	hmmpanther:PTHR24356:SF136,hmmpanther:PTHR24356,Pfam_domain:PF08926,Gene3D:1v9vA01,Superfamily_domains:0050107	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCCGAGACT	byCluster|by1000G	5	ESCA
GLIS1	0	.	GRCh37	1	53972230	53972230	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62C>T	.	.	ENST00000312233	10/10	127	107	20	130	130	0	GLIS1,3_prime_UTR_variant,,ENST00000312233,;	A	ENSG00000174332	ENST00000312233	Transcript	3_prime_UTR_variant	2492	.	.	.	.	.	.	.	-1	GLIS1	HGNC	29525	protein_coding	YES	CCDS582.1	ENSP00000309653	GLIS1_HUMAN	.	UPI000013F293	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGCGACAGC	.	4	ESCA
CHD5	0	.	GRCh37	1	6202187	6202187	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2436+1G>A	.	p.X812_splice	ENST00000262450	.	29	15	14	37	37	0	CHD5,splice_donor_variant,,ENST00000378021,;CHD5,splice_donor_variant,,ENST00000262450,;CHD5,splice_donor_variant,,ENST00000496404,;CHD5,splice_donor_variant,,ENST00000462991,;	T	ENSG00000116254	ENST00000262450	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	CHD5	HGNC	16816	protein_coding	YES	CCDS57.1	ENSP00000262450	CHD5_HUMAN	.	UPI000006CD03	.	.	.	.	15/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCACCTTCA	.	5	ESCA
LEPR	0	.	GRCh37	1	66075661	66075661	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1784C>T	p.Ser595Phe	p.S595F	ENST00000349533	13/20	69	35	34	84	84	0	LEPR,missense_variant,p.Ser595Phe,ENST00000349533,;LEPR,missense_variant,p.Ser595Phe,ENST00000344610,;LEPR,missense_variant,p.Ser595Phe,ENST00000371060,;LEPR,missense_variant,p.Ser595Phe,ENST00000371058,;LEPR,missense_variant,p.Ser595Phe,ENST00000371059,;LEPR,intron_variant,,ENST00000406510,;LEPR,non_coding_transcript_exon_variant,,ENST00000462765,;	T	ENSG00000116678	ENST00000349533	Transcript	missense_variant	1969	1784	595	S/F	tCt/tTt	COSM3419404,COSM3419403,COSM3419402	.	.	1	LEPR	HGNC	6554	protein_coding	YES	CCDS631.1	ENSP00000330393	LEPR_HUMAN	L0I9J6_HUMAN,A2RRQ4_HUMAN	UPI000014C37B	.	tolerated(0.09)	benign(0.045)	13/20	.	PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF11,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCTGTCA	.	5	ESCA
SGIP1	0	.	GRCh37	1	67147594	67147594	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.857C>A	p.Pro286Gln	p.P286Q	ENST00000371037	15/25	33	23	10	47	47	0	SGIP1,missense_variant,p.Pro290Gln,ENST00000237247,;SGIP1,missense_variant,p.Pro286Gln,ENST00000371037,;SGIP1,intron_variant,,ENST00000371039,;SGIP1,intron_variant,,ENST00000371036,;SGIP1,intron_variant,,ENST00000371035,;SGIP1,downstream_gene_variant,,ENST00000424320,;AL139147.1,upstream_gene_variant,,ENST00000502413,;SGIP1,intron_variant,,ENST00000480548,;SGIP1,downstream_gene_variant,,ENST00000468286,;SGIP1,upstream_gene_variant,,ENST00000487507,;	A	ENSG00000118473	ENST00000371037	Transcript	missense_variant	934	857	286	P/Q	cCa/cAa	.	.	.	1	SGIP1	HGNC	25412	protein_coding	YES	CCDS30744.1	ENSP00000360076	SGIP1_HUMAN	.	UPI000045891B	.	deleterious_low_confidence(0)	probably_damaging(0.991)	15/25	.	hmmpanther:PTHR23065:SF5,hmmpanther:PTHR23065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTACCATCCA	.	5	ESCA
ENO1	0	.	GRCh37	1	8928111	8928111	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246G>A	p.%3D	p.L82L	ENST00000234590	5/12	38	32	6	47	47	0	ENO1,synonymous_variant,p.%3D,ENST00000497492,;ENO1,synonymous_variant,p.%3D,ENST00000234590,;ENO1,non_coding_transcript_exon_variant,,ENST00000464920,;ENO1,downstream_gene_variant,,ENST00000486051,;ENO1,downstream_gene_variant,,ENST00000492343,;	T	ENSG00000074800	ENST00000234590	Transcript	synonymous_variant	366	246	82	L	ctG/ctA	.	.	.	-1	ENO1	HGNC	3350	protein_coding	YES	CCDS97.1	ENSP00000234590	ENOA_HUMAN	Q9BT62_HUMAN,Q96GV1_HUMAN,K7EM90_HUMAN,E2DRY6_HUMAN,A4UCS8_HUMAN	UPI000013C9AF	.	.	.	5/12	.	HAMAP:MF_00318,hmmpanther:PTHR11902,TIGRFAM_domain:TIGR01060,Gene3D:3.30.390.10,Pfam_domain:PF03952,PIRSF_domain:PIRSF001400,Superfamily_domains:SSF54826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTTCAGTTT	.	5	ESCA
PLEKHN1	0	.	GRCh37	1	908636	908636	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1223G>A	p.Arg408Gln	p.R408Q	ENST00000379410	12/16	24	18	5	50	50	0	PLEKHN1,missense_variant,p.Arg460Gln,ENST00000379409,;PLEKHN1,missense_variant,p.Arg408Gln,ENST00000379410,;PLEKHN1,intron_variant,,ENST00000379407,;C1orf170,downstream_gene_variant,,ENST00000341290,;C1orf170,downstream_gene_variant,,ENST00000433179,;PLEKHN1,upstream_gene_variant,,ENST00000491024,;PLEKHN1,downstream_gene_variant,,ENST00000480267,;C1orf170,downstream_gene_variant,,ENST00000479361,;	A	ENSG00000187583	ENST00000379410	Transcript	missense_variant	1258	1223	408	R/Q	cGg/cAg	.	.	.	1	PLEKHN1	HGNC	25284	protein_coding	YES	CCDS4.1	ENSP00000368720	PKHN1_HUMAN	J3KSM5_HUMAN	UPI00001416D8	.	tolerated(0.1)	benign(0.041)	12/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22826:SF96,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CAGCCGGTCAC	.	4	ESCA
ACSS2	0	.	GRCh37	20	33515022	33515022	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5G>A	.	.	ENST00000253382	19/19	38	34	4	51	51	0	ACSS2,3_prime_UTR_variant,,ENST00000360596,;ACSS2,3_prime_UTR_variant,,ENST00000336325,;ACSS2,3_prime_UTR_variant,,ENST00000253382,;GSS,downstream_gene_variant,,ENST00000216951,;GSS,downstream_gene_variant,,ENST00000451957,;GSS,downstream_gene_variant,,ENST00000541098,;ACSS2,non_coding_transcript_exon_variant,,ENST00000476922,;ACSS2,3_prime_UTR_variant,,ENST00000481284,;ACSS2,3_prime_UTR_variant,,ENST00000477932,;ACSS2,downstream_gene_variant,,ENST00000491533,;ACSS2,downstream_gene_variant,,ENST00000480978,;ACSS2,downstream_gene_variant,,ENST00000494727,;ACSS2,downstream_gene_variant,,ENST00000470315,;	A	ENSG00000131069	ENST00000253382	Transcript	3_prime_UTR_variant	2182	.	.	.	.	.	.	.	1	ACSS2	HGNC	15814	protein_coding	YES	CCDS42868.2	ENSP00000253382	ACSA_HUMAN	F8WCJ4_HUMAN,B3KUV2_HUMAN	UPI00004709E0	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACATGATCCT	.	4	ESCA
PTPRT	0	.	GRCh37	20	41419957	41419957	+	Missense_Mutation	SNP	C	C	T	rs369230837	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364G>A	p.Val122Ile	p.V122I	ENST00000373187	3/31	38	34	3	37	37	0	PTPRT,missense_variant,p.Val122Ile,ENST00000373201,;PTPRT,missense_variant,p.Val122Ile,ENST00000356100,;PTPRT,missense_variant,p.Val122Ile,ENST00000373198,;PTPRT,missense_variant,p.Val122Ile,ENST00000373193,;PTPRT,missense_variant,p.Val122Ile,ENST00000373184,;PTPRT,missense_variant,p.Val122Ile,ENST00000373190,;PTPRT,missense_variant,p.Val122Ile,ENST00000373187,;	T	ENSG00000196090	ENST00000373187	Transcript	missense_variant	364	364	122	V/I	Gtc/Atc	rs369230837	.	.	-1	PTPRT	HGNC	9682	protein_coding	YES	CCDS42874.1	ENSP00000362283	PTPRT_HUMAN	.	UPI0000246C03	.	tolerated(0.32)	benign(0.297)	3/31	.	PROSITE_profiles:PS50060,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTAGACGTTCA	byCluster	2	ESCA
SERINC3	0	.	GRCh37	20	43135470	43135470	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.781C>T	p.Gln261Ter	p.Q261*	ENST00000342374	6/10	20	13	7	31	31	0	SERINC3,stop_gained,p.Gln206Ter,ENST00000541235,;SERINC3,stop_gained,p.Gln261Ter,ENST00000255175,;SERINC3,stop_gained,p.Gln261Ter,ENST00000342374,;SERINC3,upstream_gene_variant,,ENST00000411544,;	A	ENSG00000132824	ENST00000342374	Transcript	stop_gained	939	781	261	Q/*	Cag/Tag	.	.	.	-1	SERINC3	HGNC	11699	protein_coding	YES	CCDS13333.1	ENSP00000340243	SERC3_HUMAN	Q5H936_HUMAN,B4DUE9_HUMAN	UPI0000136B4D	.	.	.	6/10	.	Pfam_domain:PF03348,hmmpanther:PTHR10383,hmmpanther:PTHR10383:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTGAATTT	.	5	ESCA
C20orf166	0	.	GRCh37	20	61150778	61150778	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-87C>T	.	.	ENST00000370527	2/4	54	44	10	88	88	0	C20orf166,5_prime_UTR_variant,,ENST00000370524,;C20orf166,5_prime_UTR_variant,,ENST00000370523,;C20orf166,5_prime_UTR_variant,,ENST00000370527,;MIR1-1,upstream_gene_variant,,ENST00000362147,;C20orf166-AS1,upstream_gene_variant,,ENST00000412495,;C20orf166-AS1,upstream_gene_variant,,ENST00000475015,;C20orf166-AS1,upstream_gene_variant,,ENST00000436101,;	T	ENSG00000174407	ENST00000370527	Transcript	5_prime_UTR_variant	693	.	.	.	.	.	.	.	1	C20orf166	HGNC	16159	protein_coding	YES	CCDS46627.1	ENSP00000359558	CT166_HUMAN	.	UPI000012861B	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCATCTTCGG	.	5	ESCA
ZNF512B	0	.	GRCh37	20	62592679	62592679	+	Missense_Mutation	SNP	G	G	T	rs112150897	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2410C>A	p.Leu804Met	p.L804M	ENST00000450537	16/17	43	32	11	53	53	0	ZNF512B,missense_variant,p.Leu804Met,ENST00000450537,;ZNF512B,missense_variant,p.Leu804Met,ENST00000217130,;ZNF512B,missense_variant,p.Leu804Met,ENST00000369888,;UCKL1,upstream_gene_variant,,ENST00000354216,;UCKL1,upstream_gene_variant,,ENST00000358711,;UCKL1,upstream_gene_variant,,ENST00000369892,;UCKL1,upstream_gene_variant,,ENST00000483710,;	T	ENSG00000196700	ENST00000450537	Transcript	missense_variant	2471	2410	804	L/M	Ctg/Atg	rs112150897,COSM444241	.	.	-1	ZNF512B	HGNC	29212	protein_coding	YES	CCDS13548.1	ENSP00000393795	Z512B_HUMAN	.	UPI000013A290	.	tolerated(0.22)	probably_damaging(0.993)	16/17	.	PROSITE_profiles:PS50157,hmmpanther:PTHR22979,hmmpanther:PTHR22979:SF3,PROSITE_patterns:PS00028,Pfam_domain:PF13894,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCAGGATGT	.	5	ESCA
TPTE	0	.	GRCh37	21	10942941	10942941	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.646G>A	p.Glu216Lys	p.E216K	ENST00000361285	12/24	120	109	11	165	165	0	TPTE,missense_variant,p.Glu216Lys,ENST00000361285,;TPTE,missense_variant,p.Glu178Lys,ENST00000342420,;TPTE,missense_variant,p.Glu198Lys,ENST00000298232,;TPTE,non_coding_transcript_exon_variant,,ENST00000415664,;TPTE,non_coding_transcript_exon_variant,,ENST00000447568,;	T	ENSG00000166157	ENST00000361285	Transcript	missense_variant	976	646	216	E/K	Gaa/Aaa	.	.	.	-1	TPTE	HGNC	12023	protein_coding	YES	CCDS13560.2	ENSP00000355208	TPTE_HUMAN	.	UPI000016A18A	.	deleterious(0.04)	possibly_damaging(0.474)	12/24	.	hmmpanther:PTHR12305,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTTTCAAGTT	.	3	ESCA
CXADR	0	.	GRCh37	21	18938008	18938008	+	Nonstop_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096T>C	p.Ter366GlnextTer19	p.*366Qext*19	ENST00000284878	7/7	37	26	11	39	39	0	CXADR,stop_lost,p.Ter325GlnextTer?,ENST00000306618,;CXADR,stop_lost,p.Ter366GlnextTer19,ENST00000284878,;CXADR,3_prime_UTR_variant,,ENST00000400166,;CXADR,intron_variant,,ENST00000400169,;CXADR,downstream_gene_variant,,ENST00000356275,;CXADR,downstream_gene_variant,,ENST00000400165,;	C	ENSG00000154639	ENST00000284878	Transcript	stop_lost	1844	1096	366	*/Q	Tag/Cag	.	.	.	1	CXADR	HGNC	2559	protein_coding	YES	CCDS33519.1	ENSP00000284878	CXAR_HUMAN	.	UPI000004F892	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTATAGAGC	.	5	ESCA
AP000295.9	0	.	GRCh37	21	34638156	34638156	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.433-2543T>C	.	.	ENST00000433395	.	21	16	5	21	21	0	AP000295.9,intron_variant,,ENST00000433395,;IFNAR2,downstream_gene_variant,,ENST00000342136,;IFNAR2,downstream_gene_variant,,ENST00000413881,;IFNAR2,downstream_gene_variant,,ENST00000342101,;IL10RB,upstream_gene_variant,,ENST00000290200,;IFNAR2,downstream_gene_variant,,ENST00000404220,;IFNAR2,downstream_gene_variant,,ENST00000382241,;IFNAR2,downstream_gene_variant,,ENST00000443073,;IFNAR2,downstream_gene_variant,,ENST00000382264,;IL10RB-AS1,non_coding_transcript_exon_variant,,ENST00000411998,;AP000295.9,intron_variant,,ENST00000432231,;IFNAR2,downstream_gene_variant,,ENST00000417007,;IFNAR2,downstream_gene_variant,,ENST00000382238,;IL10RB,upstream_gene_variant,,ENST00000493295,;IL10RB,upstream_gene_variant,,ENST00000498371,;IL10RB,upstream_gene_variant,,ENST00000422891,;	C	ENSG00000249624	ENST00000433395	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	AP000295.9	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000388223	.	.	UPI0001D3B04A	.	.	.	.	3/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCGATGCCGT	.	2	ESCA
DIP2A	0	.	GRCh37	21	47970533	47970533	+	Silent	SNP	C	C	T	rs369236341	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2715C>T	p.%3D	p.L905L	ENST00000417564	23/38	41	28	12	63	63	0	DIP2A,synonymous_variant,p.%3D,ENST00000427143,;DIP2A,synonymous_variant,p.%3D,ENST00000318711,;DIP2A,synonymous_variant,p.%3D,ENST00000400274,;DIP2A,synonymous_variant,p.%3D,ENST00000417564,;DIP2A,downstream_gene_variant,,ENST00000435722,;DIP2A,downstream_gene_variant,,ENST00000457905,;DIP2A,downstream_gene_variant,,ENST00000466639,;DIP2A,upstream_gene_variant,,ENST00000481883,;DIP2A,upstream_gene_variant,,ENST00000472364,;DIP2A,downstream_gene_variant,,ENST00000494435,;DIP2A,downstream_gene_variant,,ENST00000480553,;	T	ENSG00000160305	ENST00000417564	Transcript	synonymous_variant	2736	2715	905	L	ctC/ctT	rs369236341	.	.	1	DIP2A	HGNC	17217	protein_coding	YES	CCDS46655.1	ENSP00000392066	DIP2A_HUMAN	Q9NSX6_HUMAN,Q96NX2_HUMAN	UPI00001B2E47	.	.	.	23/38	.	hmmpanther:PTHR22754:SF24,hmmpanther:PTHR22754,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTCGGAGG	byFrequency|byCluster	5	ESCA
TOM1	0	.	GRCh37	22	35734728	35734728	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1171G>T	p.Ala391Ser	p.A391S	ENST00000411850	12/15	87	70	16	110	110	0	TOM1,missense_variant,p.Ala391Ser,ENST00000449058,;TOM1,missense_variant,p.Ala391Ser,ENST00000411850,;TOM1,missense_variant,p.Ala346Ser,ENST00000425375,;TOM1,missense_variant,p.Ala353Ser,ENST00000436462,;TOM1,missense_variant,p.Ala358Ser,ENST00000447733,;TOM1,3_prime_UTR_variant,,ENST00000382034,;MIR3909,downstream_gene_variant,,ENST00000579518,;TOM1,3_prime_UTR_variant,,ENST00000404284,;TOM1,3_prime_UTR_variant,,ENST00000424387,;TOM1,non_coding_transcript_exon_variant,,ENST00000491987,;	T	ENSG00000100284	ENST00000411850	Transcript	missense_variant	1296	1171	391	A/S	Gca/Tca	.	.	.	1	TOM1	HGNC	11982	protein_coding	YES	CCDS46696.1	ENSP00000413697	TOM1_HUMAN	B0QY02_HUMAN	UPI000000DB48	.	deleterious(0.05)	possibly_damaging(0.61)	12/15	.	PIRSF_domain:PIRSF036948,hmmpanther:PTHR13856,hmmpanther:PTHR13856:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAAGCAACA	.	5	ESCA
TNRC6B	0	.	GRCh37	22	40661412	40661412	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1178G>A	p.Gly393Glu	p.G393E	ENST00000454349	5/23	21	17	4	27	27	0	TNRC6B,missense_variant,p.Gly393Glu,ENST00000454349,;TNRC6B,missense_variant,p.Gly136Glu,ENST00000446273,;TNRC6B,missense_variant,p.Gly393Glu,ENST00000335727,;TNRC6B,intron_variant,,ENST00000402203,;TNRC6B,intron_variant,,ENST00000301923,;	A	ENSG00000100354	ENST00000454349	Transcript	missense_variant	1389	1178	393	G/E	gGa/gAa	COSM1593066	.	.	1	TNRC6B	HGNC	29190	protein_coding	YES	CCDS54533.1	ENSP00000401946	TNR6B_HUMAN	.	UPI00017A6F19	.	tolerated(0.45)	probably_damaging(1)	5/23	.	hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF32	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAGGGAATGC	.	4	ESCA
NUP50	0	.	GRCh37	22	45583196	45583196	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2660C>T	.	.	ENST00000347635	8/8	24	20	4	11	11	0	NUP50,3_prime_UTR_variant,,ENST00000347635,;NUP50,downstream_gene_variant,,ENST00000396096,;KIAA0930,downstream_gene_variant,,ENST00000336156,;NUP50,downstream_gene_variant,,ENST00000407019,;NUP50,downstream_gene_variant,,ENST00000422489,;NUP50,downstream_gene_variant,,ENST00000425733,;NUP50,downstream_gene_variant,,ENST00000493456,;NUP50,downstream_gene_variant,,ENST00000469163,;	T	ENSG00000093000	ENST00000347635	Transcript	3_prime_UTR_variant	4533	.	.	.	.	.	.	.	1	NUP50	HGNC	8065	protein_coding	YES	CCDS14062.1	ENSP00000345895	NUP50_HUMAN	B4E2D3_HUMAN	UPI000013079E	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTTTCCATGG	.	3	ESCA
IL1B	0	.	GRCh37	2	113593181	113593181	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61G>A	p.Asp21Asn	p.D21N	ENST00000263341	3/7	39	19	19	68	68	0	IL1B,missense_variant,p.Asp21Asn,ENST00000418817,;IL1B,missense_variant,p.Asp21Asn,ENST00000432018,;IL1B,missense_variant,p.Asp21Asn,ENST00000263341,;IL1B,missense_variant,p.Asp21Asn,ENST00000416750,;IL1B,non_coding_transcript_exon_variant,,ENST00000491056,;IL1B,non_coding_transcript_exon_variant,,ENST00000477398,;IL1B,non_coding_transcript_exon_variant,,ENST00000496280,;IL1B,upstream_gene_variant,,ENST00000487639,;	T	ENSG00000125538	ENST00000263341	Transcript	missense_variant	272	61	21	D/N	Gac/Aac	.	.	.	-1	IL1B	HGNC	5992	protein_coding	YES	CCDS2102.1	ENSP00000263341	IL1B_HUMAN	C9JWV2_HUMAN,C9JVK0_HUMAN,C9JSC2_HUMAN,B5BUQ8_HUMAN	UPI0000054161	.	deleterious(0.04)	benign(0.16)	3/7	.	hmmpanther:PTHR10078,hmmpanther:PTHR10078:SF20,Pfam_domain:PF02394,Prints_domain:PR01359	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGTCATCCT	.	5	ESCA
IL1B	0	.	GRCh37	2	113593774	113593774	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33G>A	p.Met11Ile	p.M11I	ENST00000263341	2/7	21	12	9	31	31	0	IL1B,missense_variant,p.Met11Ile,ENST00000418817,;IL1B,missense_variant,p.Met11Ile,ENST00000432018,;IL1B,missense_variant,p.Met11Ile,ENST00000263341,;IL1B,missense_variant,p.Met11Ile,ENST00000416750,;IL1B,non_coding_transcript_exon_variant,,ENST00000491056,;IL1B,non_coding_transcript_exon_variant,,ENST00000477398,;IL1B,non_coding_transcript_exon_variant,,ENST00000496280,;IL1B,upstream_gene_variant,,ENST00000487639,;	T	ENSG00000125538	ENST00000263341	Transcript	missense_variant	244	33	11	M/I	atG/atA	COSM1398884,COSM3565392	.	.	-1	IL1B	HGNC	5992	protein_coding	YES	CCDS2102.1	ENSP00000263341	IL1B_HUMAN	C9JWV2_HUMAN,C9JVK0_HUMAN,C9JSC2_HUMAN,B5BUQ8_HUMAN	UPI0000054161	.	tolerated(0.17)	benign(0.055)	2/7	.	hmmpanther:PTHR10078,hmmpanther:PTHR10078:SF20,Pfam_domain:PF02394	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCATTTC	.	5	ESCA
MYO7B	0	.	GRCh37	2	128350402	128350402	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2026C>T	p.Arg676Ter	p.R676*	ENST00000428314	17/47	57	43	14	78	78	0	MYO7B,stop_gained,p.Arg676Ter,ENST00000389524,;MYO7B,stop_gained,p.Arg676Ter,ENST00000409816,;MYO7B,stop_gained,p.Arg676Ter,ENST00000428314,;	T	ENSG00000169994	ENST00000428314	Transcript	stop_gained	2079	2026	676	R/*	Cga/Tga	.	.	.	1	MYO7B	HGNC	7607	protein_coding	YES	CCDS46405.1	ENSP00000415090	MYO7B_HUMAN	C9JC21_HUMAN,B9A063_HUMAN	UPI00006C04F0	.	.	.	17/47	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF352,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGCGATAC	.	5	ESCA
CXCR4	0	.	GRCh37	2	136872988	136872988	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.522C>T	p.%3D	p.P174P	ENST00000409817	1/1	45	25	19	55	55	0	CXCR4,synonymous_variant,p.%3D,ENST00000241393,;CXCR4,synonymous_variant,p.%3D,ENST00000409817,;CXCR4,non_coding_transcript_exon_variant,,ENST00000466288,;	A	ENSG00000121966	ENST00000409817	Transcript	synonymous_variant	826	522	174	P	ccC/ccT	COSM1399596	.	.	-1	CXCR4	HGNC	2561	protein_coding	YES	CCDS33295.1	ENSP00000386884	CXCR4_HUMAN	Q5MIL4_HUMAN	UPI000002A5E3	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24227,hmmpanther:PTHR24227:SF7,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCGGGAAT	.	5	ESCA
ACVR1C	0	.	GRCh37	2	158390538	158390538	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1374G>A	p.%3D	p.G458G	ENST00000243349	9/9	20	15	5	33	33	0	ACVR1C,synonymous_variant,p.%3D,ENST00000348328,;ACVR1C,synonymous_variant,p.%3D,ENST00000409680,;ACVR1C,synonymous_variant,p.%3D,ENST00000243349,;ACVR1C,synonymous_variant,p.%3D,ENST00000335450,;	T	ENSG00000123612	ENST00000243349	Transcript	synonymous_variant	1735	1374	458	G	ggG/ggA	.	.	.	-1	ACVR1C	HGNC	18123	protein_coding	YES	CCDS2205.1	ENSP00000243349	ACV1C_HUMAN	Q53SF5_HUMAN	UPI000006CFAE	.	.	.	9/9	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF58,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTCCCCAT	.	5	ESCA
FAP	0	.	GRCh37	2	163031461	163031461	+	Missense_Mutation	SNP	C	C	T	rs141879753	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1885G>A	p.Val629Ile	p.V629I	ENST00000188790	22/26	29	24	4	47	47	0	FAP,missense_variant,p.Val604Ile,ENST00000443424,;FAP,missense_variant,p.Val629Ile,ENST00000188790,;AC007750.5,downstream_gene_variant,,ENST00000418968,;FAP,3_prime_UTR_variant,,ENST00000422436,;FAP,non_coding_transcript_exon_variant,,ENST00000461506,;FAP,non_coding_transcript_exon_variant,,ENST00000480044,;FAP,upstream_gene_variant,,ENST00000462608,;	T	ENSG00000078098	ENST00000188790	Transcript	missense_variant	2093	1885	629	V/I	Gtt/Att	rs141879753,COSM357865	.	.	-1	FAP	HGNC	3590	protein_coding	YES	CCDS33311.1	ENSP00000188790	SEPR_HUMAN	C9J131_HUMAN	UPI00000012A2	.	deleterious(0.03)	benign(0.014)	22/26	.	hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF111,PROSITE_patterns:PS00708,Pfam_domain:PF00326,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474	T:0.0004	T:0.0008	T:0.0014	.	T:0	T:0	T:0	T:0.0002	T:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TGAAACGTATC	byFrequency|byCluster|by1000G	4	ESCA
COBLL1	0	.	GRCh37	2	165559719	165559719	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1237C>T	p.Pro413Ser	p.P413S	ENST00000342193	9/14	39	27	11	36	36	0	COBLL1,missense_variant,p.Pro413Ser,ENST00000342193,;COBLL1,missense_variant,p.Pro451Ser,ENST00000392717,;COBLL1,missense_variant,p.Pro479Ser,ENST00000194871,;COBLL1,intron_variant,,ENST00000375458,;COBLL1,intron_variant,,ENST00000409184,;COBLL1,intron_variant,,ENST00000491126,;COBLL1,downstream_gene_variant,,ENST00000434366,;COBLL1,3_prime_UTR_variant,,ENST00000456171,;COBLL1,intron_variant,,ENST00000493868,;COBLL1,intron_variant,,ENST00000460238,;COBLL1,upstream_gene_variant,,ENST00000489955,;	A	ENSG00000082438	ENST00000342193	Transcript	missense_variant	1453	1237	413	P/S	Cct/Tct	.	.	.	-1	COBLL1	HGNC	23571	protein_coding	YES	CCDS2223.2	ENSP00000341360	COBL1_HUMAN	C9JWZ0_HUMAN,C9JAU3_HUMAN,B3KMG7_HUMAN	UPI000007132B	.	tolerated(0.07)	benign(0.091)	9/14	.	hmmpanther:PTHR21557:SF2,hmmpanther:PTHR21557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGGGTGAA	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098810	178098810	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	2/5	120	91	28	127	127	0	NFE2L2,missense_variant,p.Glu63Gln,ENST00000449627,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000423513,;NFE2L2,missense_variant,p.Glu79Gln,ENST00000397062,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000446151,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000588123,;NFE2L2,missense_variant,p.Glu78Gln,ENST00000586532,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000421929,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000464747,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000448782,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	G	ENSG00000116044	ENST00000397062	Transcript	missense_variant	790	235	79	E/Q	Gag/Cag	COSM132851,COSM120958,COSM1631472	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E79Q|c.235G>C|11,BUFFER|p.E82D|c.246A>C|3,BUFFER|p.E82D|c.246A>T|6,BUFFER|p.E82G|c.245A>G|7,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81D|c.242G>A|6,BUFFER|p.G81V|c.242G>T|7,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.G81S|c.241G>A|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79K|c.235G>A|10,BUFFER|p.D77V|c.230A>T|5,BUFFER|p.D77G|c.230A>G|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTCTTCAT	.	5	ESCA
TTN	0	.	GRCh37	2	179486627	179486627	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45022G>A	p.Glu15008Lys	p.E15008K	ENST00000589042	244/363	67	43	24	61	61	0	TTN,missense_variant,p.Glu6068Lys,ENST00000359218,;TTN,missense_variant,p.Glu13367Lys,ENST00000591111,;TTN,missense_variant,p.Glu15008Lys,ENST00000589042,;TTN,missense_variant,p.Glu12440Lys,ENST00000342992,;TTN,missense_variant,p.Glu6135Lys,ENST00000342175,;TTN,missense_variant,p.Glu5943Lys,ENST00000460472,;RP11-171I2.4,downstream_gene_variant,,ENST00000605334,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000604956,;TTN-AS1,downstream_gene_variant,,ENST00000592750,;TTN-AS1,downstream_gene_variant,,ENST00000456053,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	45247	45022	15008	E/K	Gaa/Aaa	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	244/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCATCAT	.	5	ESCA
HIBCH	0	.	GRCh37	2	191161574	191161574	+	Missense_Mutation	SNP	G	G	A	rs544400387	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.184C>T	p.Leu62Phe	p.L62F	ENST00000359678	3/14	71	56	14	83	83	0	HIBCH,missense_variant,p.Leu62Phe,ENST00000359678,;HIBCH,missense_variant,p.Leu62Phe,ENST00000392332,;HIBCH,missense_variant,p.Leu116Phe,ENST00000409934,;	A	ENSG00000198130	ENST00000359678	Transcript	missense_variant	479	184	62	L/F	Ctt/Ttt	rs544400387	.	.	-1	HIBCH	HGNC	4908	protein_coding	YES	CCDS2304.1	ENSP00000352706	HIBCH_HUMAN	B9A058_HUMAN	UPI000013F16E	.	tolerated(0.09)	benign(0.056)	3/14	.	hmmpanther:PTHR11941:SF53,hmmpanther:PTHR11941,Gene3D:3.90.226.10,Superfamily_domains:SSF52096	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTAAGAGTCA	byFrequency|byCluster|by1000G	5	ESCA
STK17B	0	.	GRCh37	2	197010768	197010768	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347G>A	p.Gly116Glu	p.G116E	ENST00000263955	4/8	19	12	6	27	27	0	STK17B,missense_variant,p.Gly116Glu,ENST00000263955,;STK17B,missense_variant,p.Gly116Glu,ENST00000409228,;	T	ENSG00000081320	ENST00000263955	Transcript	missense_variant	634	347	116	G/E	gGa/gAa	.	.	.	-1	STK17B	HGNC	11396	protein_coding	YES	CCDS2315.1	ENSP00000263955	ST17B_HUMAN	U3KQF8_HUMAN,Q53QE7_HUMAN,C9JZJ1_HUMAN	UPI0000035B5D	.	deleterious(0)	probably_damaging(1)	4/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24342,hmmpanther:PTHR24342:SF5,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCCACCT	.	5	ESCA
PGAP1	0	.	GRCh37	2	197744869	197744869	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1281A>G	p.%3D	p.T427T	ENST00000354764	13/27	24	10	14	24	23	1	PGAP1,synonymous_variant,p.%3D,ENST00000409475,;PGAP1,synonymous_variant,p.%3D,ENST00000354764,;PGAP1,non_coding_transcript_exon_variant,,ENST00000482051,;PGAP1,3_prime_UTR_variant,,ENST00000423035,;PGAP1,non_coding_transcript_exon_variant,,ENST00000470179,;	C	ENSG00000197121	ENST00000354764	Transcript	synonymous_variant	1396	1281	427	T	acA/acG	.	.	.	-1	PGAP1	HGNC	25712	protein_coding	YES	CCDS2318.1	ENSP00000346809	PGAP1_HUMAN	.	UPI000035154F	.	.	.	13/27	.	hmmpanther:PTHR15495,hmmpanther:PTHR15495:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CTTAATGTCAG	.	2	ESCA
SATB2	0	.	GRCh37	2	200246514	200246514	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376C>G	p.Leu126Val	p.L126V	ENST00000417098	4/11	28	24	4	40	40	0	SATB2,missense_variant,p.Leu126Val,ENST00000260926,;SATB2,missense_variant,p.Leu67Val,ENST00000443023,;SATB2,missense_variant,p.Leu126Val,ENST00000417098,;SATB2,missense_variant,p.Leu126Val,ENST00000457245,;SATB2,intron_variant,,ENST00000428695,;SATB2,non_coding_transcript_exon_variant,,ENST00000484124,;	C	ENSG00000119042	ENST00000417098	Transcript	missense_variant	1193	376	126	L/V	Ctc/Gtc	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	tolerated(1)	benign(0.001)	4/11	.	hmmpanther:PTHR15116,hmmpanther:PTHR15116:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGAGAGGGT	.	4	ESCA
CASP8	0	.	GRCh37	2	202149834	202149834	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1275G>T	p.Gln425His	p.Q425H	ENST00000358485	8/9	20	8	11	39	39	0	CASP8,missense_variant,p.Gln351His,ENST00000323492,;CASP8,missense_variant,p.Gln383His,ENST00000264275,;CASP8,missense_variant,p.Gln425His,ENST00000358485,;CASP8,missense_variant,p.Gln145His,ENST00000444430,;CASP8,missense_variant,p.Gln351His,ENST00000392263,;CASP8,missense_variant,p.Gln366His,ENST00000432109,;CASP8,missense_variant,p.Gln282His,ENST00000264274,;CASP8,3_prime_UTR_variant,,ENST00000392266,;CASP8,3_prime_UTR_variant,,ENST00000392259,;ALS2CR12,downstream_gene_variant,,ENST00000415745,;ALS2CR12,downstream_gene_variant,,ENST00000405148,;ALS2CR12,downstream_gene_variant,,ENST00000392257,;CASP8,downstream_gene_variant,,ENST00000392258,;ALS2CR12,downstream_gene_variant,,ENST00000439709,;ALS2CR12,downstream_gene_variant,,ENST00000286190,;CASP8,downstream_gene_variant,,ENST00000424461,;CASP8,non_coding_transcript_exon_variant,,ENST00000339403,;ALS2CR12,downstream_gene_variant,,ENST00000494171,;ALS2CR12,downstream_gene_variant,,ENST00000494223,;	T	ENSG00000064012	ENST00000358485	Transcript	missense_variant	1471	1275	425	Q/H	caG/caT	.	.	.	1	CASP8	HGNC	1509	protein_coding	YES	CCDS42798.1	ENSP00000351273	CASP8_HUMAN	E7EVN1_HUMAN,E7ETB7_HUMAN,E7EQ01_HUMAN	UPI0000456ECD	.	tolerated(0.3)	benign(0.078)	8/9	.	hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF141,Pfam_domain:PF00656,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCAGAAAGG	.	5	ESCA
CASP8	0	.	GRCh37	2	202149919	202149919	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360G>C	p.Asp454His	p.D454H	ENST00000358485	8/9	33	18	15	50	50	0	CASP8,missense_variant,p.Asp380His,ENST00000323492,;CASP8,missense_variant,p.Asp412His,ENST00000264275,;CASP8,missense_variant,p.Asp454His,ENST00000358485,;CASP8,missense_variant,p.Asp174His,ENST00000444430,;CASP8,missense_variant,p.Asp380His,ENST00000392263,;CASP8,missense_variant,p.Asp395His,ENST00000432109,;CASP8,missense_variant,p.Asp311His,ENST00000264274,;CASP8,3_prime_UTR_variant,,ENST00000392266,;CASP8,3_prime_UTR_variant,,ENST00000392259,;ALS2CR12,downstream_gene_variant,,ENST00000415745,;ALS2CR12,downstream_gene_variant,,ENST00000405148,;ALS2CR12,downstream_gene_variant,,ENST00000392257,;CASP8,downstream_gene_variant,,ENST00000392258,;ALS2CR12,downstream_gene_variant,,ENST00000439709,;ALS2CR12,downstream_gene_variant,,ENST00000286190,;CASP8,downstream_gene_variant,,ENST00000424461,;CASP8,non_coding_transcript_exon_variant,,ENST00000339403,;ALS2CR12,downstream_gene_variant,,ENST00000494171,;ALS2CR12,downstream_gene_variant,,ENST00000494223,;	C	ENSG00000064012	ENST00000358485	Transcript	missense_variant	1556	1360	454	D/H	Gat/Cat	COSM231953,COSM231954	.	.	1	CASP8	HGNC	1509	protein_coding	YES	CCDS42798.1	ENSP00000351273	CASP8_HUMAN	E7EVN1_HUMAN,E7ETB7_HUMAN,E7EQ01_HUMAN	UPI0000456ECD	.	deleterious(0)	benign(0.332)	8/9	.	PROSITE_profiles:PS50207,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF141,Pfam_domain:PF00656,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.P411L|c.1232C>T|3,CODON|p.P453L|c.1358C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCGGATGAG	.	5	ESCA
COL4A3	0	.	GRCh37	2	228111451	228111451	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438C>T	p.%3D	p.I146I	ENST00000396578	7/52	56	41	14	46	46	0	COL4A3,synonymous_variant,p.%3D,ENST00000396578,;AC097662.2,intron_variant,,ENST00000437673,;AC097662.2,intron_variant,,ENST00000606119,;AC097662.2,intron_variant,,ENST00000396588,;AC097662.2,intron_variant,,ENST00000439598,;	T	ENSG00000169031	ENST00000396578	Transcript	synonymous_variant	600	438	146	I	atC/atT	.	.	.	1	COL4A3	HGNC	2204	protein_coding	YES	CCDS42829.1	ENSP00000379823	CO4A3_HUMAN	Q548X1_HUMAN,A9QVI3_HUMAN	UPI000013E9F3	.	.	.	7/52	.	hmmpanther:PTHR24023:SF417,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGATCCCGGT	.	5	ESCA
NGEF	0	.	GRCh37	2	233752783	233752783	+	Missense_Mutation	SNP	C	C	T	rs572634482	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1307G>A	p.Arg436Gln	p.R436Q	ENST00000264051	9/15	88	66	22	85	85	0	NGEF,missense_variant,p.Arg344Gln,ENST00000373552,;NGEF,missense_variant,p.Arg436Gln,ENST00000264051,;NGEF,missense_variant,p.Arg28Gln,ENST00000424488,;NGEF,missense_variant,p.Arg159Gln,ENST00000416114,;NGEF,missense_variant,p.Arg159Gln,ENST00000539537,;NGEF,downstream_gene_variant,,ENST00000420650,;NGEF,downstream_gene_variant,,ENST00000458735,;NGEF,non_coding_transcript_exon_variant,,ENST00000461944,;NGEF,upstream_gene_variant,,ENST00000489127,;	T	ENSG00000066248	ENST00000264051	Transcript	missense_variant	1586	1307	436	R/Q	cGg/cAg	rs572634482	.	.	-1	NGEF	HGNC	7807	protein_coding	YES	CCDS2500.1	ENSP00000264051	NGEF_HUMAN	C9JTV7_HUMAN,B4DDI2_HUMAN	UPI000013D4AE	.	tolerated(0.06)	possibly_damaging(0.795)	9/15	.	PROSITE_profiles:PS50010,hmmpanther:PTHR12845:SF8,hmmpanther:PTHR12845,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCCGCTCA	byCluster|by1000G	5	ESCA
HDAC4	0	.	GRCh37	2	239975285	239975285	+	Missense_Mutation	SNP	C	C	G	rs754080436	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3086G>C	p.Arg1029Pro	p.R1029P	ENST00000345617	26/27	90	47	43	97	97	0	HDAC4,missense_variant,p.Arg613Pro,ENST00000543185,;HDAC4,missense_variant,p.Arg120Pro,ENST00000430200,;HDAC4,missense_variant,p.Arg1029Pro,ENST00000345617,;HDAC4,downstream_gene_variant,,ENST00000494800,;	G	ENSG00000068024	ENST00000345617	Transcript	missense_variant	3878	3086	1029	R/P	cGc/cCc	rs754080436	.	.	-1	HDAC4	HGNC	14063	protein_coding	YES	CCDS2529.1	ENSP00000264606	HDAC4_HUMAN	Q53SM2_HUMAN,Q53SB4_HUMAN,F5H0B1_HUMAN,F5GX36_HUMAN,C9J0X4_HUMAN	UPI000013D541	.	tolerated(0.23)	benign(0.002)	26/27	.	hmmpanther:PTHR10625:SF100,hmmpanther:PTHR10625,Gene3D:3.40.800.20,Pfam_domain:PF09757,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGCGCCAG	byFrequency	5	ESCA
OXER1	0	.	GRCh37	2	42990017	42990017	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*31G>A	.	.	ENST00000378661	1/1	20	16	3	31	31	0	OXER1,3_prime_UTR_variant,,ENST00000378661,;HAAO,downstream_gene_variant,,ENST00000294973,;HAAO,downstream_gene_variant,,ENST00000402698,;HAAO,downstream_gene_variant,,ENST00000406007,;HAAO,downstream_gene_variant,,ENST00000404451,;	T	ENSG00000162881	ENST00000378661	Transcript	3_prime_UTR_variant	1385	.	.	.	.	.	.	.	-1	OXER1	HGNC	24884	protein_coding	YES	CCDS1810.1	ENSP00000367930	OXER1_HUMAN	.	UPI000003BCC9	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTACCCCCAC	.	3	ESCA
STON1	0	.	GRCh37	2	48825535	48825535	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3094A>C	.	.	ENST00000309835	3/3	14	7	7	15	15	0	STON1,3_prime_UTR_variant,,ENST00000406226,;STON1,3_prime_UTR_variant,,ENST00000404752,;STON1,3_prime_UTR_variant,,ENST00000309835,;STON1-GTF2A1L,intron_variant,,ENST00000309827,;STON1-GTF2A1L,intron_variant,,ENST00000394754,;STON1-GTF2A1L,intron_variant,,ENST00000402114,;STON1-GTF2A1L,intron_variant,,ENST00000405008,;STON1-GTF2A1L,intron_variant,,ENST00000394751,;STON1,downstream_gene_variant,,ENST00000444932,;	C	ENSG00000243244	ENST00000309835	Transcript	3_prime_UTR_variant	5312	.	.	.	.	.	.	.	1	STON1	HGNC	17003	protein_coding	YES	CCDS1841.1	ENSP00000310969	STON1_HUMAN	.	UPI000006E627	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CTTAAAATACA	.	4	ESCA
ADD2	0	.	GRCh37	2	70890767	70890767	+	Silent	SNP	C	C	T	rs540699345	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1971G>A	p.%3D	p.T657T	ENST00000264436	16/16	51	38	12	53	53	0	ADD2,synonymous_variant,p.%3D,ENST00000264436,;ADD2,synonymous_variant,p.%3D,ENST00000407644,;ADD2,3_prime_UTR_variant,,ENST00000355733,;ADD2,synonymous_variant,p.%3D,ENST00000403045,;ADD2,non_coding_transcript_exon_variant,,ENST00000481675,;	T	ENSG00000075340	ENST00000264436	Transcript	synonymous_variant	2416	1971	657	T	acG/acA	rs540699345,COSM195311	.	.	-1	ADD2	HGNC	244	protein_coding	YES	CCDS1906.1	ENSP00000264436	ADDB_HUMAN	Q96HD4_HUMAN,C9J299_HUMAN,C9J080_HUMAN	UPI0000125503	.	.	.	16/16	.	hmmpanther:PTHR10672:SF6,hmmpanther:PTHR10672	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E660K|c.1978G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCCGTCTG	by1000G	5	ESCA
IGKV1D-16	0	.	GRCh37	2	90139466	90139466	+	Silent	SNP	G	G	T	rs757157192	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237G>T	p.%3D	p.G79G	ENST00000492446	2/2	143	88	54	178	178	0	IGKV1D-16,synonymous_variant,p.%3D,ENST00000492446,;AC073416.1,upstream_gene_variant,,ENST00000323194,;	T	ENSG00000241244	ENST00000492446	Transcript	synonymous_variant	264	237	79	G	ggG/ggT	rs757157192	.	.	1	IGKV1D-16	HGNC	5748	IG_V_gene	YES	.	ENSP00000418200	.	.	UPI0000116772	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF122,hmmpanther:PTHR23267,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGGGGTCCC	.	5	ESCA
TSGA10	0	.	GRCh37	2	99634813	99634813	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1923-1G>A	.	p.X641_splice	ENST00000393483	.	31	25	6	41	41	0	TSGA10,splice_acceptor_variant,,ENST00000410001,;TSGA10,splice_acceptor_variant,,ENST00000393482,;TSGA10,splice_acceptor_variant,,ENST00000409564,;TSGA10,splice_acceptor_variant,,ENST00000539964,;TSGA10,splice_acceptor_variant,,ENST00000355053,;TSGA10,splice_acceptor_variant,,ENST00000393483,;TSGA10,splice_acceptor_variant,,ENST00000489546,;	T	ENSG00000135951	ENST00000393483	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	TSGA10	HGNC	14927	protein_coding	YES	CCDS2037.1	ENSP00000377123	TSG10_HUMAN	F8WA32_HUMAN	UPI0000072CE3	.	.	.	.	19/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCTCCCTAAAG	.	4	ESCA
MORC1	0	.	GRCh37	3	108776315	108776315	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1050A>C	p.Arg350Ser	p.R350S	ENST00000232603	13/28	22	18	4	21	21	0	MORC1,missense_variant,p.Arg350Ser,ENST00000483760,;MORC1,missense_variant,p.Arg350Ser,ENST00000232603,;	G	ENSG00000114487	ENST00000232603	Transcript	missense_variant	1133	1050	350	R/S	agA/agC	.	.	.	-1	MORC1	HGNC	7198	protein_coding	YES	CCDS2955.1	ENSP00000232603	MORC1_HUMAN	.	UPI000013C964	.	deleterious(0)	benign(0.066)	13/28	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23337,hmmpanther:PTHR23337:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCGTTCTTGC	.	2	ESCA
EAF2	0	.	GRCh37	3	121591519	121591519	+	Missense_Mutation	SNP	C	C	G	rs200859609	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.620C>G	p.Ser207Cys	p.S207C	ENST00000273668	5/6	28	17	10	35	35	0	EAF2,missense_variant,p.Ser207Cys,ENST00000451944,;EAF2,missense_variant,p.Ser207Cys,ENST00000273668,;EAF2,3_prime_UTR_variant,,ENST00000490434,;	G	ENSG00000145088	ENST00000273668	Transcript	missense_variant	691	620	207	S/C	tCt/tGt	rs200859609	.	.	1	EAF2	HGNC	23115	protein_coding	YES	CCDS3006.1	ENSP00000273668	EAF2_HUMAN	F8WF04_HUMAN	UPI000000D7DA	.	deleterious(0.04)	possibly_damaging(0.707)	5/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15970,hmmpanther:PTHR15970:SF7	T:0.0016	T:0	T:0	.	T:0.0079	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTCTGATA	byFrequency|byCluster|by1000G	5	ESCA
CCDC58	0	.	GRCh37	3	122081851	122081851	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348G>A	p.%3D	p.L116L	ENST00000291458	4/5	59	40	18	71	71	0	CCDC58,synonymous_variant,p.%3D,ENST00000291458,;CCDC58,synonymous_variant,p.%3D,ENST00000479414,;CCDC58,synonymous_variant,p.%3D,ENST00000497726,;CCDC58,synonymous_variant,p.%3D,ENST00000479899,;CCDC58,non_coding_transcript_exon_variant,,ENST00000460810,;CCDC58,non_coding_transcript_exon_variant,,ENST00000466854,;CCDC58,downstream_gene_variant,,ENST00000498466,;	T	ENSG00000160124	ENST00000291458	Transcript	synonymous_variant	355	348	116	L	ctG/ctA	.	.	.	-1	CCDC58	HGNC	31136	protein_coding	YES	CCDS33838.1	ENSP00000291458	CCD58_HUMAN	.	UPI000020A069	.	.	.	4/5	.	hmmpanther:PTHR31905,Pfam_domain:PF09774	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTCAGTTC	.	5	ESCA
FAM162A	0	.	GRCh37	3	122121698	122121698	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126A>C	p.%3D	p.T42T	ENST00000477892	2/5	50	41	9	52	52	0	FAM162A,synonymous_variant,p.%3D,ENST00000477892,;FAM162A,synonymous_variant,p.%3D,ENST00000232125,;FAM162A,synonymous_variant,p.%3D,ENST00000469967,;	C	ENSG00000114023	ENST00000477892	Transcript	synonymous_variant	210	126	42	T	acA/acC	.	.	.	1	FAM162A	HGNC	17865	protein_coding	YES	CCDS43139.1	ENSP00000419088	F162A_HUMAN	.	UPI0000073F3F	.	.	.	2/5	.	Pfam_domain:PF06388,hmmpanther:PTHR13674:SF2,hmmpanther:PTHR13674	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACAAAACC	.	5	ESCA
PTPLB	0	.	GRCh37	3	123301073	123301073	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259G>A	p.Gly87Arg	p.G87R	ENST00000383657	2/7	20	14	6	17	17	0	PTPLB,missense_variant,p.Gly87Arg,ENST00000383657,;PTPLB,5_prime_UTR_variant,,ENST00000469317,;MYLK-AS1,upstream_gene_variant,,ENST00000463408,;MYLK-AS1,upstream_gene_variant,,ENST00000470449,;MYLK-AS1,upstream_gene_variant,,ENST00000485162,;	T	ENSG00000206527	ENST00000383657	Transcript	missense_variant	417	259	87	G/R	Gga/Aga	.	.	.	-1	PTPLB	HGNC	9640	protein_coding	YES	CCDS46895.1	ENSP00000373153	HACD2_HUMAN	C9JWG1_HUMAN	UPI0000160B26	.	tolerated(0.35)	possibly_damaging(0.827)	2/7	.	Pfam_domain:PF04387,hmmpanther:PTHR11035:SF17,hmmpanther:PTHR11035,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCCAGTTT	.	5	ESCA
PPP2R3A	0	.	GRCh37	3	135866361	135866361	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2353G>C	.	.	ENST00000264977	14/14	34	23	11	35	35	0	PPP2R3A,3_prime_UTR_variant,,ENST00000264977,;MSL2,downstream_gene_variant,,ENST00000434835,;MSL2,downstream_gene_variant,,ENST00000481989,;PPP2R3A,downstream_gene_variant,,ENST00000490467,;MSL2,downstream_gene_variant,,ENST00000491050,;MSL2,downstream_gene_variant,,ENST00000309993,;MSL2,downstream_gene_variant,,ENST00000473093,;PPP2R3A,downstream_gene_variant,,ENST00000334546,;	C	ENSG00000073711	ENST00000264977	Transcript	3_prime_UTR_variant	6423	.	.	.	.	.	.	.	1	PPP2R3A	HGNC	9307	protein_coding	YES	CCDS3087.1	ENSP00000264977	P2R3A_HUMAN	.	UPI0000124EAC	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTGAGGAA	.	5	ESCA
GFM1	0	.	GRCh37	3	158363966	158363966	+	Missense_Mutation	SNP	G	G	C	rs751861999	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>C	p.Asp83His	p.D83H	ENST00000486715	3/18	133	99	33	93	93	0	GFM1,missense_variant,p.Asp83His,ENST00000264263,;GFM1,missense_variant,p.Asp83His,ENST00000478576,;GFM1,missense_variant,p.Asp83His,ENST00000486715,;LXN,missense_variant,p.Ile132Met,ENST00000482640,;GFM1,missense_variant,p.Asp8His,ENST00000464732,;GFM1,missense_variant,p.Asp83His,ENST00000478254,;GFM1,upstream_gene_variant,,ENST00000478251,;	C	ENSG00000168827	ENST00000486715	Transcript	missense_variant	604	247	83	D/H	Gat/Cat	rs751861999	.	.	1	GFM1	HGNC	13780	protein_coding	YES	CCDS33885.1	ENSP00000419038	EFGM_HUMAN	E5KND5_HUMAN,C9JA25_HUMAN	UPI000006232D	.	deleterious(0)	probably_damaging(1)	3/18	.	Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00484,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00009,Gene3D:3.40.50.300,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF66,HAMAP:MF_00054_B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAAGATGGA	.	5	ESCA
B3GNT5	0	.	GRCh37	3	182987961	182987961	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375C>G	p.Ile125Met	p.I125M	ENST00000326505	2/2	41	27	14	31	31	0	B3GNT5,missense_variant,p.Ile125Met,ENST00000460419,;B3GNT5,missense_variant,p.Ile125Met,ENST00000326505,;B3GNT5,missense_variant,p.Ile125Met,ENST00000465010,;MCF2L2,intron_variant,,ENST00000328913,;MCF2L2,intron_variant,,ENST00000473233,;MCF2L2,intron_variant,,ENST00000447025,;B3GNT5,downstream_gene_variant,,ENST00000481531,;MCF2L2,downstream_gene_variant,,ENST00000414362,;B3GNT5,downstream_gene_variant,,ENST00000464191,;B3GNT5,downstream_gene_variant,,ENST00000464923,;B3GNT5,intron_variant,,ENST00000480551,;B3GNT5,downstream_gene_variant,,ENST00000496270,;B3GNT5,downstream_gene_variant,,ENST00000493370,;B3GNT5,downstream_gene_variant,,ENST00000488301,;B3GNT5,downstream_gene_variant,,ENST00000477699,;MCF2L2,intron_variant,,ENST00000488149,;	G	ENSG00000176597	ENST00000326505	Transcript	missense_variant	905	375	125	I/M	atC/atG	.	.	.	1	B3GNT5	HGNC	15684	protein_coding	YES	CCDS3244.1	ENSP00000316173	B3GN5_HUMAN	C9J5K2_HUMAN,C9J368_HUMAN,C9IYY0_HUMAN	UPI000003D75E	.	deleterious(0.02)	possibly_damaging(0.478)	2/2	.	hmmpanther:PTHR11214:SF21,hmmpanther:PTHR11214,Pfam_domain:PF01762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACATCAAAAC	.	5	ESCA
SENP2	0	.	GRCh37	3	185347753	185347753	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*121C>G	.	.	ENST00000296257	17/17	31	24	6	32	32	0	SENP2,3_prime_UTR_variant,,ENST00000545472,;SENP2,3_prime_UTR_variant,,ENST00000427465,;SENP2,3_prime_UTR_variant,,ENST00000296257,;SENP2,downstream_gene_variant,,ENST00000444509,;SENP2,3_prime_UTR_variant,,ENST00000413407,;	G	ENSG00000163904	ENST00000296257	Transcript	3_prime_UTR_variant	2131	.	.	.	.	.	.	.	1	SENP2	HGNC	23116	protein_coding	YES	CCDS33902.1	ENSP00000296257	SENP2_HUMAN	J3KQD2_HUMAN,B4E2S4_HUMAN	UPI000007452F	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTGTCAAAAG	.	3	ESCA
SENP2	0	.	GRCh37	3	185347774	185347774	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*142C>G	.	.	ENST00000296257	17/17	29	23	6	28	28	0	SENP2,3_prime_UTR_variant,,ENST00000545472,;SENP2,3_prime_UTR_variant,,ENST00000427465,;SENP2,3_prime_UTR_variant,,ENST00000296257,;SENP2,downstream_gene_variant,,ENST00000444509,;SENP2,3_prime_UTR_variant,,ENST00000413407,;	G	ENSG00000163904	ENST00000296257	Transcript	3_prime_UTR_variant	2152	.	.	.	.	.	.	.	1	SENP2	HGNC	23116	protein_coding	YES	CCDS33902.1	ENSP00000296257	SENP2_HUMAN	J3KQD2_HUMAN,B4E2S4_HUMAN	UPI000007452F	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCTCACTGT	.	3	ESCA
SENP2	0	.	GRCh37	3	185348476	185348476	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*844C>G	.	.	ENST00000296257	17/17	87	61	26	76	76	0	SENP2,3_prime_UTR_variant,,ENST00000296257,;SENP2,downstream_gene_variant,,ENST00000545472,;SENP2,downstream_gene_variant,,ENST00000444509,;SENP2,downstream_gene_variant,,ENST00000427465,;SENP2,downstream_gene_variant,,ENST00000413407,;	G	ENSG00000163904	ENST00000296257	Transcript	3_prime_UTR_variant	2854	.	.	.	.	.	.	.	1	SENP2	HGNC	23116	protein_coding	YES	CCDS33902.1	ENSP00000296257	SENP2_HUMAN	J3KQD2_HUMAN,B4E2S4_HUMAN	UPI000007452F	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAAATCTTCAT	.	3	ESCA
SENP2	0	.	GRCh37	3	185348488	185348488	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*856C>T	.	.	ENST00000296257	17/17	84	60	24	70	70	0	SENP2,3_prime_UTR_variant,,ENST00000296257,;SENP2,downstream_gene_variant,,ENST00000545472,;SENP2,downstream_gene_variant,,ENST00000444509,;SENP2,downstream_gene_variant,,ENST00000427465,;SENP2,downstream_gene_variant,,ENST00000413407,;	T	ENSG00000163904	ENST00000296257	Transcript	3_prime_UTR_variant	2866	.	.	.	.	.	.	.	1	SENP2	HGNC	23116	protein_coding	YES	CCDS33902.1	ENSP00000296257	SENP2_HUMAN	J3KQD2_HUMAN,B4E2S4_HUMAN	UPI000007452F	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTCATCCCAGA	.	3	ESCA
LPP	0	.	GRCh37	3	188593637	188593637	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1370G>C	.	.	ENST00000312675	11/11	27	17	10	18	18	0	LPP,3_prime_UTR_variant,,ENST00000312675,;LPP,3_prime_UTR_variant,,ENST00000543006,;	C	ENSG00000145012	ENST00000312675	Transcript	3_prime_UTR_variant	3455	.	.	.	.	.	.	.	1	LPP	HGNC	6679	protein_coding	YES	CCDS3291.1	ENSP00000318089	LPP_HUMAN	C9JT42_HUMAN,C9JIY7_HUMAN,C9JE51_HUMAN,C9J5C8_HUMAN,C9J4E3_HUMAN,C9J3U9_HUMAN,C9J2R5_HUMAN,C9J1K7_HUMAN,B7Z871_HUMAN	UPI000002E034	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGAGAGACA	.	5	ESCA
RBMS3	0	.	GRCh37	3	29941194	29941199	+	Splice_Site	DEL	AGGTCC	AGGTCC	-	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	AGGTCC	AGGTCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.889_894delGTCCAG	p.Val297_Gln298del	p.X297_splice	ENST00000383767	10/15	24	16	8	45	45	0	RBMS3,splice_acceptor_variant,p.Val297_Gln298del,ENST00000383767,;RBMS3,splice_acceptor_variant,p.Val296_Gln297del,ENST00000434693,;RBMS3,splice_acceptor_variant,p.Val297_Gln298del,ENST00000273139,;RBMS3,splice_acceptor_variant,p.Val297_Gln298del,ENST00000452462,;RBMS3,splice_acceptor_variant,p.Val310_Gln311del,ENST00000456853,;RBMS3,splice_acceptor_variant,p.Val310_Gln311del,ENST00000396583,;RBMS3,intron_variant,,ENST00000383766,;RBMS3,splice_acceptor_variant,,ENST00000497319,;	-	ENSG00000144642	ENST00000383767	Transcript	splice_acceptor_variant	?-1228	?-892	?-298	.	.	.	.	.	1	RBMS3	HGNC	13427	protein_coding	YES	CCDS33724.1	ENSP00000373277	RBMS3_HUMAN	C9J9B2_HUMAN	UPI000023FE75	.	.	.	10/15	9/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	ATGCATAGGTCCAGAGT	.	2	ESCA
TRAK1	0	.	GRCh37	3	42265157	42265157	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2790G>A	p.Met930Ile	p.M930I	ENST00000327628	16/16	23	12	11	41	41	0	TRAK1,missense_variant,p.Met872Ile,ENST00000396175,;TRAK1,missense_variant,p.Met930Ile,ENST00000327628,;RNU4-78P,downstream_gene_variant,,ENST00000410940,;TRAK1,non_coding_transcript_exon_variant,,ENST00000487159,;	A	ENSG00000182606	ENST00000327628	Transcript	missense_variant	3190	2790	930	M/I	atG/atA	.	.	.	1	TRAK1	HGNC	29947	protein_coding	YES	CCDS43072.1	ENSP00000328998	TRAK1_HUMAN	.	UPI0000139F52	.	deleterious(0.03)	probably_damaging(0.943)	16/16	.	hmmpanther:PTHR15751:SF11,hmmpanther:PTHR15751	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATGAAAGC	.	5	ESCA
ADAMTS9	0	.	GRCh37	3	64636815	64636815	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1341C>A	p.Asn447Lys	p.N447K	ENST00000498707	9/40	29	15	14	51	51	0	ADAMTS9,missense_variant,p.Asn419Lys,ENST00000295903,;ADAMTS9,missense_variant,p.Asn447Lys,ENST00000459780,;ADAMTS9,missense_variant,p.Asn447Lys,ENST00000498707,;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000467119,;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000475557,;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000482490,;ADAMTS9,downstream_gene_variant,,ENST00000494004,;	T	ENSG00000163638	ENST00000498707	Transcript	missense_variant	1684	1341	447	N/K	aaC/aaA	.	.	.	-1	ADAMTS9	HGNC	13202	protein_coding	YES	CCDS2903.1	ENSP00000418735	ATS9_HUMAN	B4E0E4_HUMAN	UPI00000463F0	.	deleterious(0)	benign(0.261)	9/40	.	PROSITE_profiles:PS50215,hmmpanther:PTHR13723:SF33,hmmpanther:PTHR13723,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTGTTGTC	.	5	ESCA
ROBO2	0	.	GRCh37	3	77681778	77681778	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3809-2243G>A	.	.	ENST00000487694	.	32	25	7	49	49	0	ROBO2,missense_variant,p.Arg1305Lys,ENST00000332191,;ROBO2,intron_variant,,ENST00000461745,;ROBO2,intron_variant,,ENST00000475334,;ROBO2,intron_variant,,ENST00000487694,;ROBO2,upstream_gene_variant,,ENST00000490534,;ROBO2,non_coding_transcript_exon_variant,,ENST00000470802,;ROBO2,intron_variant,,ENST00000473767,;	A	ENSG00000185008	ENST00000487694	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ROBO2	HGNC	10250	protein_coding	YES	CCDS54609.1	ENSP00000417335	ROBO2_HUMAN	H9XFA4_HUMAN	UPI0000D891EC	.	.	.	.	24/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTAGGCTGG	.	2	ESCA
CENPE	0	.	GRCh37	4	104065534	104065534	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5099T>C	p.Val1700Ala	p.V1700A	ENST00000265148	33/49	53	32	21	47	47	0	CENPE,missense_variant,p.Val1675Ala,ENST00000380026,;CENPE,missense_variant,p.Val1700Ala,ENST00000265148,;CENPE,downstream_gene_variant,,ENST00000515478,;	G	ENSG00000138778	ENST00000265148	Transcript	missense_variant	5189	5099	1700	V/A	gTa/gCa	.	.	.	-1	CENPE	HGNC	1856	protein_coding	YES	CCDS34042.1	ENSP00000265148	CENPE_HUMAN	D6RBW0_HUMAN	UPI000020B28A	.	.	benign(0.008)	33/49	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF384,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTACTTTG	.	5	ESCA
SETD7	0	.	GRCh37	4	140454373	140454373	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318C>T	p.%3D	p.F106F	ENST00000274031	3/8	101	55	45	118	118	0	SETD7,synonymous_variant,p.%3D,ENST00000404104,;SETD7,synonymous_variant,p.%3D,ENST00000506866,;SETD7,synonymous_variant,p.%3D,ENST00000274031,;SETD7,3_prime_UTR_variant,,ENST00000406354,;SETD7,downstream_gene_variant,,ENST00000608795,;	A	ENSG00000145391	ENST00000274031	Transcript	synonymous_variant	955	318	106	F	ttC/ttT	.	.	.	-1	SETD7	HGNC	30412	protein_coding	YES	CCDS3748.1	ENSP00000274031	SETD7_HUMAN	.	UPI0000135893	.	.	.	3/8	.	PROSITE_profiles:PS51577,hmmpanther:PTHR23084:SF129,hmmpanther:PTHR23084,Pfam_domain:PF02493,PIRSF_domain:PIRSF037249,Superfamily_domains:0038399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTGAAGAT	.	5	ESCA
NPY2R	0	.	GRCh37	4	156137685	156137685	+	3'UTR	DEL	T	T	-	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1448delT	.	.	ENST00000329476	2/2	57	49	8	38	38	0	NPY2R,3_prime_UTR_variant,,ENST00000506608,;NPY2R,3_prime_UTR_variant,,ENST00000329476,;	-	ENSG00000185149	ENST00000329476	Transcript	3_prime_UTR_variant	3083	.	.	.	.	.	.	.	1	NPY2R	HGNC	7957	protein_coding	YES	CCDS3791.1	ENSP00000332591	NPY2R_HUMAN	.	UPI000003B342	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCAACATGCATA	.	3	ESCA
CD38	0	.	GRCh37	4	15780234	15780234	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.197G>C	p.Arg66Pro	p.R66P	ENST00000226279	1/8	53	29	24	70	70	0	CD38,missense_variant,p.Arg66Pro,ENST00000226279,;CD38,missense_variant,p.Arg66Pro,ENST00000502843,;CD38,non_coding_transcript_exon_variant,,ENST00000511430,;CD38,non_coding_transcript_exon_variant,,ENST00000506191,;	C	ENSG00000004468	ENST00000226279	Transcript	missense_variant	334	197	66	R/P	cGa/cCa	COSM3373417	.	.	1	CD38	HGNC	1667	protein_coding	YES	CCDS3417.1	ENSP00000226279	CD38_HUMAN	Q4FCX6_HUMAN,B4DMR7_HUMAN	UPI00000739C2	.	deleterious(0)	probably_damaging(1)	1/8	.	hmmpanther:PTHR10912,hmmpanther:PTHR10912:SF5,Pfam_domain:PF02267,Gene3D:1.20.82.10,Superfamily_domains:SSF52309	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGCGATGCG	.	5	ESCA
FSTL5	0	.	GRCh37	4	162680564	162680564	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726C>G	p.Phe242Leu	p.F242L	ENST00000306100	6/16	43	33	10	38	38	0	FSTL5,missense_variant,p.Phe241Leu,ENST00000379164,;FSTL5,missense_variant,p.Phe241Leu,ENST00000536695,;FSTL5,missense_variant,p.Phe241Leu,ENST00000427802,;FSTL5,missense_variant,p.Phe242Leu,ENST00000306100,;	C	ENSG00000168843	ENST00000306100	Transcript	missense_variant	1163	726	242	F/L	ttC/ttG	.	.	.	-1	FSTL5	HGNC	21386	protein_coding	YES	CCDS3802.1	ENSP00000305334	FSTL5_HUMAN	Q4W5Q0_HUMAN,Q4W5K3_HUMAN,Q4W5F8_HUMAN	UPI000020B66B	.	deleterious(0.01)	probably_damaging(0.914)	6/16	.	Superfamily_domains:SSF47473,Gene3D:1.10.238.10,hmmpanther:PTHR10913:SF44,hmmpanther:PTHR10913	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACGGAATGC	.	5	ESCA
C4orf27	0	.	GRCh37	4	170652975	170652975	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.789G>C	p.Glu263Asp	p.E263D	ENST00000393381	7/8	82	57	25	57	57	0	C4orf27,missense_variant,p.Glu263Asp,ENST00000393381,;C4orf27,non_coding_transcript_exon_variant,,ENST00000515204,;	G	ENSG00000056050	ENST00000393381	Transcript	missense_variant	865	789	263	E/D	gaG/gaC	.	.	.	-1	C4orf27	HGNC	26051	protein_coding	YES	CCDS3813.1	ENSP00000406598	CD027_HUMAN	.	UPI000013D19D	.	tolerated(0.1)	benign(0.021)	7/8	.	hmmpanther:PTHR13386,hmmpanther:PTHR13386:SF1,Pfam_domain:PF10228	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCTCCTC	.	5	ESCA
SNCA	0	.	GRCh37	4	90647374	90647374	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*405C>T	.	.	ENST00000394986	6/6	26	21	5	50	50	0	SNCA,3_prime_UTR_variant,,ENST00000394989,;SNCA,3_prime_UTR_variant,,ENST00000420646,;SNCA,3_prime_UTR_variant,,ENST00000345009,;SNCA,3_prime_UTR_variant,,ENST00000394991,;SNCA,3_prime_UTR_variant,,ENST00000394986,;SNCA,3_prime_UTR_variant,,ENST00000336904,;SNCA,downstream_gene_variant,,ENST00000506244,;SNCA,downstream_gene_variant,,ENST00000508895,;SNCA,downstream_gene_variant,,ENST00000505199,;RP11-115D19.1,intron_variant,,ENST00000508021,;	A	ENSG00000145335	ENST00000394986	Transcript	3_prime_UTR_variant	1250	.	.	.	.	.	.	.	-1	SNCA	HGNC	11138	protein_coding	YES	CCDS3634.1	ENSP00000378437	SYUA_HUMAN	Q4W5L2_HUMAN,F6L6N6_HUMAN,D6RA31_HUMAN	UPI000003173B	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AATACGTCATT	.	2	ESCA
PDLIM5	0	.	GRCh37	4	95497125	95497125	+	Missense_Mutation	SNP	C	C	T	rs750811930	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.323C>T	p.Ser108Phe	p.S108F	ENST00000514743	4/16	25	20	5	35	35	0	PDLIM5,missense_variant,p.Ser217Phe,ENST00000317968,;PDLIM5,missense_variant,p.Ser76Phe,ENST00000513341,;PDLIM5,missense_variant,p.Ser108Phe,ENST00000380180,;PDLIM5,missense_variant,p.Ser108Phe,ENST00000503974,;PDLIM5,missense_variant,p.Ser108Phe,ENST00000450793,;PDLIM5,missense_variant,p.Ser108Phe,ENST00000437932,;PDLIM5,missense_variant,p.Ser108Phe,ENST00000514743,;PDLIM5,missense_variant,p.Ser95Phe,ENST00000542407,;PDLIM5,missense_variant,p.Ser108Phe,ENST00000508216,;PDLIM5,intron_variant,,ENST00000538141,;PDLIM5,intron_variant,,ENST00000318007,;PDLIM5,non_coding_transcript_exon_variant,,ENST00000508531,;PDLIM5,non_coding_transcript_exon_variant,,ENST00000514830,;PDLIM5,upstream_gene_variant,,ENST00000511586,;PDLIM5,downstream_gene_variant,,ENST00000510099,;PDLIM5,intron_variant,,ENST00000509357,;PDLIM5,downstream_gene_variant,,ENST00000509333,;	T	ENSG00000163110	ENST00000514743	Transcript	missense_variant	367	323	108	S/F	tCt/tTt	rs750811930	.	.	1	PDLIM5	HGNC	17468	protein_coding	YES	CCDS58916.1	ENSP00000424360	.	D6RB78_HUMAN	UPI000013E231	.	deleterious(0.01)	benign(0.105)	4/16	.	hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GACTTCTCAGG	byFrequency	3	ESCA
SLC12A7	0	.	GRCh37	5	1079523	1079523	+	Silent	SNP	C	C	T	rs762714893	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1386G>A	p.%3D	p.T462T	ENST00000264930	10/24	65	57	8	36	36	0	SLC12A7,synonymous_variant,p.%3D,ENST00000264930,;SLC12A7,upstream_gene_variant,,ENST00000513223,;SLC12A7,non_coding_transcript_exon_variant,,ENST00000510943,;SLC12A7,upstream_gene_variant,,ENST00000504576,;	T	ENSG00000113504	ENST00000264930	Transcript	synonymous_variant	1430	1386	462	T	acG/acA	rs762714893	.	.	-1	SLC12A7	HGNC	10915	protein_coding	YES	CCDS34129.1	ENSP00000264930	S12A7_HUMAN	.	UPI0000141815	.	.	.	10/24	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11827:SF47,hmmpanther:PTHR11827,Pfam_domain:PF00324,TIGRFAM_domain:TIGR00930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AAAGACGTCGT	byFrequency|byCluster	3	ESCA
HNRNPA0	0	.	GRCh37	5	137089438	137089438	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318A>G	p.%3D	p.K106K	ENST00000314940	1/1	32	14	17	25	25	0	HNRNPA0,synonymous_variant,p.%3D,ENST00000314940,;	C	ENSG00000177733	ENST00000314940	Transcript	synonymous_variant	602	318	106	K	aaA/aaG	.	.	.	-1	HNRNPA0	HGNC	5030	protein_coding	YES	CCDS4193.1	ENSP00000316042	ROA0_HUMAN	.	UPI0000000C1D	.	.	.	1/1	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF54928,SMART_domains:SM00360,Pfam_domain:PF00076,Gene3D:3.30.70.330,hmmpanther:PTHR24012,PROSITE_profiles:PS50102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCTTTAAG	.	5	ESCA
PCDHGA7	0	.	GRCh37	5	140764474	140764474	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2008G>A	p.Glu670Lys	p.E670K	ENST00000518325	1/4	61	25	35	107	107	0	PCDHGA7,missense_variant,p.Glu670Lys,ENST00000518325,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGB4,upstream_gene_variant,,ENST00000519479,;	A	ENSG00000253537	ENST00000518325	Transcript	missense_variant	2008	2008	670	E/K	Gaa/Aaa	.	.	.	1	PCDHGA7	HGNC	8705	protein_coding	YES	CCDS54927.1	ENSP00000430024	PCDG7_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000007146F	.	deleterious_low_confidence(0)	benign(0.158)	1/4	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF56,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCGAAGTC	.	5	ESCA
ARHGAP26	0	.	GRCh37	5	142513550	142513550	+	Missense_Mutation	SNP	G	G	T	rs775284912	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1717G>T	p.Asp573Tyr	p.D573Y	ENST00000274498	19/23	64	30	34	87	87	0	ARHGAP26,missense_variant,p.Asp573Tyr,ENST00000274498,;ARHGAP26,missense_variant,p.Asp145Tyr,ENST00000418236,;ARHGAP26,missense_variant,p.Asp192Tyr,ENST00000443674,;ARHGAP26,missense_variant,p.Asp573Tyr,ENST00000378004,;ARHGAP26,missense_variant,p.Asp18Tyr,ENST00000424007,;ARHGAP26,missense_variant,p.Asp19Tyr,ENST00000419676,;ARHGAP26,non_coding_transcript_exon_variant,,ENST00000489924,;	T	ENSG00000145819	ENST00000274498	Transcript	missense_variant	2095	1717	573	D/Y	Gat/Tat	rs775284912,COSM1063636	.	.	1	ARHGAP26	HGNC	17073	protein_coding	YES	CCDS4277.1	ENSP00000274498	RHG26_HUMAN	Q9HBW4_HUMAN,Q8NFJ1_HUMAN,C9J6V4_HUMAN	UPI0000130D6B	.	deleterious(0)	probably_damaging(0.92)	19/23	.	hmmpanther:PTHR12552:SF4,hmmpanther:PTHR12552,Gene3D:1.10.555.10	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGATATG	.	5	ESCA
CLINT1	0	.	GRCh37	5	157214829	157214829	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1757A>G	p.Asn586Ser	p.N586S	ENST00000523908	12/12	45	17	28	52	52	0	CLINT1,missense_variant,p.Asn568Ser,ENST00000523094,;CLINT1,missense_variant,p.Asn586Ser,ENST00000523908,;CLINT1,missense_variant,p.Asn568Ser,ENST00000530742,;CLINT1,missense_variant,p.Asn568Ser,ENST00000296951,;CLINT1,missense_variant,p.Asn568Ser,ENST00000411809,;CLINT1,3_prime_UTR_variant,,ENST00000522381,;CLINT1,downstream_gene_variant,,ENST00000521615,;CLINT1,3_prime_UTR_variant,,ENST00000521047,;CLINT1,non_coding_transcript_exon_variant,,ENST00000518855,;CLINT1,non_coding_transcript_exon_variant,,ENST00000524306,;CLINT1,downstream_gene_variant,,ENST00000530302,;	C	ENSG00000113282	ENST00000523908	Transcript	missense_variant	1930	1757	586	N/S	aAt/aGt	.	.	.	-1	CLINT1	HGNC	23186	protein_coding	YES	CCDS56389.1	ENSP00000429824	EPN4_HUMAN	.	UPI00003E6460	.	tolerated(0.58)	benign(0.003)	12/12	.	hmmpanther:PTHR12276:SF47,hmmpanther:PTHR12276	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTATTTCCA	.	5	ESCA
NPM1	0	.	GRCh37	5	170837816	170837816	+	3'UTR	SNP	G	G	A	rs1059683	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247G>A	.	.	ENST00000296930	11/11	27	15	12	22	22	0	NPM1,3_prime_UTR_variant,,ENST00000351986,;NPM1,3_prime_UTR_variant,,ENST00000517671,;NPM1,3_prime_UTR_variant,,ENST00000296930,;NPM1,downstream_gene_variant,,ENST00000393820,;NPM1,non_coding_transcript_exon_variant,,ENST00000524204,;	A	ENSG00000181163	ENST00000296930	Transcript	3_prime_UTR_variant	1433	.	.	.	.	rs1059683	.	.	1	NPM1	HGNC	7910	protein_coding	YES	CCDS4376.1	ENSP00000296930	NPM_HUMAN	Q9BTI9_HUMAN,E5RI98_HUMAN	UPI00001303ED	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGCGGTGGT	.	5	ESCA
NSD1	0	.	GRCh37	5	176719054	176719054	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6358G>T	p.Glu2120Ter	p.E2120*	ENST00000439151	22/23	31	16	15	45	45	0	NSD1,stop_gained,p.Glu2017Ter,ENST00000361032,;NSD1,stop_gained,p.Glu1851Ter,ENST00000354179,;NSD1,stop_gained,p.Glu2120Ter,ENST00000439151,;NSD1,stop_gained,p.Glu1851Ter,ENST00000347982,;NSD1,non_coding_transcript_exon_variant,,ENST00000513736,;	T	ENSG00000165671	ENST00000439151	Transcript	stop_gained	6403	6358	2120	E/*	Gag/Tag	.	.	.	1	NSD1	HGNC	14234	protein_coding	YES	CCDS4412.1	ENSP00000395929	NSD1_HUMAN	Q9H6H8_HUMAN,Q9H6B5_HUMAN,Q96MN8_HUMAN,Q96DQ7_HUMAN,Q658U6_HUMAN,D6RE14_HUMAN,D6RBP3_HUMAN,D6RA90_HUMAN	UPI000006F9C6	.	.	.	22/23	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312,Gene3D:3.30.40.10,SMART_domains:SM00249,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATGAGTGT	.	5	ESCA
KIAA0947	0	.	GRCh37	5	5473686	5473686	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6238G>A	p.Val2080Ile	p.V2080I	ENST00000296564	16/19	53	47	5	28	28	0	KIAA0947,missense_variant,p.Val2080Ile,ENST00000296564,;	A	ENSG00000164151	ENST00000296564	Transcript	missense_variant	6460	6238	2080	V/I	Gtt/Att	.	.	.	1	KIAA0947	HGNC	29154	protein_coding	YES	CCDS47187.1	ENSP00000296564	K0947_HUMAN	.	UPI00015542F9	.	deleterious(0.01)	probably_damaging(0.998)	16/19	.	hmmpanther:PTHR11852,hmmpanther:PTHR11852:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGATGTTGGC	.	4	ESCA
HAPLN1	0	.	GRCh37	5	82936972	82936972	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*343A>G	.	.	ENST00000274341	5/5	49	13	36	66	66	0	HAPLN1,3_prime_UTR_variant,,ENST00000274341,;HAPLN1,downstream_gene_variant,,ENST00000510978,;HAPLN1,downstream_gene_variant,,ENST00000508307,;HAPLN1,downstream_gene_variant,,ENST00000503117,;HAPLN1,downstream_gene_variant,,ENST00000504713,;	C	ENSG00000145681	ENST00000274341	Transcript	3_prime_UTR_variant	2259	.	.	.	.	.	.	.	-1	HAPLN1	HGNC	2380	protein_coding	YES	CCDS4061.1	ENSP00000274341	HPLN1_HUMAN	D6RG04_HUMAN,D6RC59_HUMAN,D6RBX9_HUMAN,D6RBS1_HUMAN	UPI0000131BFF	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCTCTGAG	.	5	ESCA
TFAP2A	0	.	GRCh37	6	10398177	10398177	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*473A>T	.	.	ENST00000379604	7/7	10	7	3	17	17	0	TFAP2A,3_prime_UTR_variant,,ENST00000379608,;TFAP2A,3_prime_UTR_variant,,ENST00000379613,;TFAP2A,3_prime_UTR_variant,,ENST00000319516,;TFAP2A,3_prime_UTR_variant,,ENST00000379604,;TFAP2A,intron_variant,,ENST00000461628,;TFAP2A,downstream_gene_variant,,ENST00000498450,;TFAP2A,downstream_gene_variant,,ENST00000475264,;TFAP2A,downstream_gene_variant,,ENST00000466073,;TFAP2A,downstream_gene_variant,,ENST00000482890,;TFAP2A,downstream_gene_variant,,ENST00000497266,;TFAP2A,3_prime_UTR_variant,,ENST00000488193,;TFAP2A,3_prime_UTR_variant,,ENST00000489805,;TFAP2A,downstream_gene_variant,,ENST00000478375,;	A	ENSG00000137203	ENST00000379604	Transcript	3_prime_UTR_variant	2039	.	.	.	.	.	.	.	-1	TFAP2A	HGNC	11742	protein_coding	YES	CCDS4510.1	ENSP00000368924	AP2A_HUMAN	.	UPI0000125BC5	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACAATCTGAA	.	2	ESCA
TBC1D32	0	.	GRCh37	6	121481218	121481218	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2711C>T	p.Ser904Leu	p.S904L	ENST00000398212	24/32	23	11	12	41	41	0	TBC1D32,missense_variant,p.Ser904Leu,ENST00000398212,;TBC1D32,missense_variant,p.Ser945Leu,ENST00000275159,;TBC1D32,non_coding_transcript_exon_variant,,ENST00000523345,;TBC1D32,non_coding_transcript_exon_variant,,ENST00000398197,;TBC1D32,3_prime_UTR_variant,,ENST00000464622,;TBC1D32,upstream_gene_variant,,ENST00000509492,;	A	ENSG00000146350	ENST00000398212	Transcript	missense_variant	2761	2711	904	S/L	tCa/tTa	COSM3620036	.	.	-1	TBC1D32	HGNC	21485	protein_coding	YES	CCDS43501.1	ENSP00000381270	BROMI_HUMAN	A2A304_HUMAN	UPI0000E67203	.	tolerated(0.12)	possibly_damaging(0.46)	24/32	.	hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3,Pfam_domain:PF14961	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATGAAAAC	.	5	ESCA
MAP3K5	0	.	GRCh37	6	137019722	137019722	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.711C>T	p.%3D	p.L237L	ENST00000359015	4/30	35	15	19	28	28	0	MAP3K5,synonymous_variant,p.%3D,ENST00000359015,;	A	ENSG00000197442	ENST00000359015	Transcript	synonymous_variant	1072	711	237	L	ctC/ctT	.	.	.	-1	MAP3K5	HGNC	6857	protein_coding	YES	CCDS5179.1	ENSP00000351908	M3K5_HUMAN	A6NIA0_HUMAN	UPI000012EAD5	.	.	.	4/30	.	hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF332,Pfam_domain:PF13281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCATGAGCTC	.	5	ESCA
ADGB	0	.	GRCh37	6	147123814	147123815	+	Intron	INS	-	-	A	rs542629056	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4818+673dupA	.	.	ENST00000397944	.	36	28	8	57	57	0	ADGB,intron_variant,,ENST00000367493,;ADGB,intron_variant,,ENST00000367490,;ADGB,intron_variant,,ENST00000367489,;ADGB,intron_variant,,ENST00000397944,;ADGB,intron_variant,,ENST00000367488,;ADGB,downstream_gene_variant,,ENST00000326916,;KATNBL1P6,non_coding_transcript_exon_variant,,ENST00000562413,;ADGB,intron_variant,,ENST00000493950,;ADGB,intron_variant,,ENST00000480328,;KATNBL1P6,downstream_gene_variant,,ENST00000453433,;	A	ENSG00000118492	ENST00000397944	Transcript	intron_variant	.	.	.	.	.	rs542629056	.	.	1	ADGB	HGNC	21212	protein_coding	YES	.	ENSP00000381036	ADGB_HUMAN	.	UPI000020E382	.	.	.	.	35/35	.	A:0.0046	A:0.0166	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAAAAGAAAAA	byFrequency|byCluster|by1000G	3	ESCA
MPC1	0	.	GRCh37	6	166778737	166778737	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*180A>G	.	.	ENST00000360961	5/5	17	8	9	34	34	0	MPC1,3_prime_UTR_variant,,ENST00000341756,;MPC1,3_prime_UTR_variant,,ENST00000360961,;MPC1,non_coding_transcript_exon_variant,,ENST00000487218,;MPC1,downstream_gene_variant,,ENST00000475708,;MPC1,non_coding_transcript_exon_variant,,ENST00000366868,;	C	ENSG00000060762	ENST00000360961	Transcript	3_prime_UTR_variant	632	.	.	.	.	.	.	.	-1	MPC1	HGNC	21606	protein_coding	YES	CCDS5293.1	ENSP00000354223	MPC1_HUMAN	Q5TI65_HUMAN	UPI000004F9EF	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAATACTTG	.	5	ESCA
E2F3	0	.	GRCh37	6	20490452	20490452	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1189C>G	p.Leu397Val	p.L397V	ENST00000346618	7/7	68	43	25	76	76	0	E2F3,missense_variant,p.Leu266Val,ENST00000535432,;E2F3,missense_variant,p.Leu397Val,ENST00000346618,;	G	ENSG00000112242	ENST00000346618	Transcript	missense_variant	1255	1189	397	L/V	Ctt/Gtt	.	.	.	1	E2F3	HGNC	3115	protein_coding	YES	CCDS4545.1	ENSP00000262904	E2F3_HUMAN	Q24JQ3_HUMAN	UPI0000129AC2	.	tolerated(0.15)	benign(0.055)	7/7	.	hmmpanther:PTHR12081:SF36,hmmpanther:PTHR12081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAACCTTTCT	.	5	ESCA
HIST1H3B	0	.	GRCh37	6	26031889	26031889	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400G>C	p.Glu134Gln	p.E134Q	ENST00000244661	1/1	46	34	11	59	59	0	HIST1H3B,missense_variant,p.Glu134Gln,ENST00000244661,;HIST1H2AB,downstream_gene_variant,,ENST00000259791,;HIST1H4B,upstream_gene_variant,,ENST00000377364,;	G	ENSG00000124693	ENST00000244661	Transcript	missense_variant	400	400	134	E/Q	Gaa/Caa	COSM3623430	.	.	-1	HIST1H3B	HGNC	4776	protein_coding	YES	CCDS4573.1	ENSP00000244661	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0.01)	probably_damaging(0.941)	1/1	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,SMART_domains:SM00428,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A136T|c.406G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCTCCGC	.	5	ESCA
C6orf25	0	.	GRCh37	6	31692520	31692520	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542-22C>T	.	.	ENST00000375806	.	25	16	9	33	33	0	C6orf25,splice_region_variant,,ENST00000375809,;C6orf25,splice_region_variant,,ENST00000375804,;C6orf25,splice_region_variant,,ENST00000375805,;C6orf25,splice_region_variant,,ENST00000375810,;C6orf25,intron_variant,,ENST00000375806,;C6orf25,intron_variant,,ENST00000375814,;C6orf25,intron_variant,,ENST00000480039,;DDAH2,downstream_gene_variant,,ENST00000375787,;DDAH2,downstream_gene_variant,,ENST00000375792,;DDAH2,downstream_gene_variant,,ENST00000375789,;DDAH2,downstream_gene_variant,,ENST00000437288,;LY6G6C,upstream_gene_variant,,ENST00000375819,;LY6G6C,upstream_gene_variant,,ENST00000495859,;DDAH2,downstream_gene_variant,,ENST00000416410,;DDAH2,downstream_gene_variant,,ENST00000436437,;DDAH2,downstream_gene_variant,,ENST00000483792,;DDAH2,downstream_gene_variant,,ENST00000480913,;C6orf25,splice_region_variant,,ENST00000485548,;C6orf25,non_coding_transcript_exon_variant,,ENST00000471545,;C6orf25,non_coding_transcript_exon_variant,,ENST00000460663,;DDAH2,downstream_gene_variant,,ENST00000488119,;C6orf25,downstream_gene_variant,,ENST00000466312,;DDAH2,downstream_gene_variant,,ENST00000469963,;	T	ENSG00000204420	ENST00000375806	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C6orf25	HGNC	13937	protein_coding	YES	CCDS4715.1	ENSP00000364964	G6B_HUMAN	.	UPI000006DE84	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TCCTTCAGCTC	.	2	ESCA
C6orf25	0	.	GRCh37	6	31692525	31692525	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542-17C>T	.	.	ENST00000375806	.	25	17	8	29	29	0	C6orf25,synonymous_variant,p.%3D,ENST00000375809,;C6orf25,synonymous_variant,p.%3D,ENST00000375804,;C6orf25,synonymous_variant,p.%3D,ENST00000375805,;C6orf25,synonymous_variant,p.%3D,ENST00000375810,;C6orf25,intron_variant,,ENST00000375806,;C6orf25,intron_variant,,ENST00000375814,;C6orf25,intron_variant,,ENST00000480039,;DDAH2,downstream_gene_variant,,ENST00000375787,;DDAH2,downstream_gene_variant,,ENST00000375792,;DDAH2,downstream_gene_variant,,ENST00000375789,;DDAH2,downstream_gene_variant,,ENST00000437288,;LY6G6C,upstream_gene_variant,,ENST00000375819,;LY6G6C,upstream_gene_variant,,ENST00000495859,;DDAH2,downstream_gene_variant,,ENST00000416410,;DDAH2,downstream_gene_variant,,ENST00000436437,;DDAH2,downstream_gene_variant,,ENST00000483792,;DDAH2,downstream_gene_variant,,ENST00000480913,;C6orf25,splice_region_variant,,ENST00000485548,;C6orf25,non_coding_transcript_exon_variant,,ENST00000471545,;C6orf25,non_coding_transcript_exon_variant,,ENST00000460663,;DDAH2,downstream_gene_variant,,ENST00000488119,;C6orf25,downstream_gene_variant,,ENST00000466312,;DDAH2,downstream_gene_variant,,ENST00000469963,;	T	ENSG00000204420	ENST00000375806	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C6orf25	HGNC	13937	protein_coding	YES	CCDS4715.1	ENSP00000364964	G6B_HUMAN	.	UPI000006DE84	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGCTCTGTCC	.	3	ESCA
DDAH2	0	.	GRCh37	6	31696815	31696815	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124C>T	p.Gln42Ter	p.Q42*	ENST00000375789	1/6	49	41	7	50	50	0	DDAH2,stop_gained,p.Gln42Ter,ENST00000375787,;DDAH2,stop_gained,p.Gln42Ter,ENST00000375792,;DDAH2,stop_gained,p.Gln42Ter,ENST00000375789,;DDAH2,stop_gained,p.Gln42Ter,ENST00000416410,;DDAH2,stop_gained,p.Gln42Ter,ENST00000436437,;CLIC1,downstream_gene_variant,,ENST00000395892,;C6orf25,downstream_gene_variant,,ENST00000375809,;C6orf25,downstream_gene_variant,,ENST00000375804,;CLIC1,downstream_gene_variant,,ENST00000375784,;DDAH2,upstream_gene_variant,,ENST00000437288,;C6orf25,downstream_gene_variant,,ENST00000375806,;C6orf25,downstream_gene_variant,,ENST00000375814,;C6orf25,downstream_gene_variant,,ENST00000480039,;C6orf25,downstream_gene_variant,,ENST00000375805,;CLIC1,downstream_gene_variant,,ENST00000375779,;CLIC1,downstream_gene_variant,,ENST00000375780,;C6orf25,downstream_gene_variant,,ENST00000375810,;DDAH2,intron_variant,,ENST00000483792,;DDAH2,intron_variant,,ENST00000480913,;DDAH2,non_coding_transcript_exon_variant,,ENST00000488119,;DDAH2,non_coding_transcript_exon_variant,,ENST00000469963,;C6orf25,downstream_gene_variant,,ENST00000471545,;C6orf25,downstream_gene_variant,,ENST00000485548,;C6orf25,downstream_gene_variant,,ENST00000460663,;C6orf25,downstream_gene_variant,,ENST00000466312,;	A	ENSG00000213722	ENST00000375789	Transcript	stop_gained	755	124	42	Q/*	Caa/Taa	.	.	.	-1	DDAH2	HGNC	2716	protein_coding	YES	CCDS4718.1	ENSP00000364945	DDAH2_HUMAN	Q5SSV3_HUMAN,Q5SRR8_HUMAN	UPI0000033BA3	.	.	.	1/6	.	hmmpanther:PTHR12737,hmmpanther:PTHR12737:SF16,Pfam_domain:PF02274,Gene3D:3.75.10.10,Superfamily_domains:SSF55909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTTTGAGCTT	.	4	ESCA
SYNGAP1	0	.	GRCh37	6	33421138	33421138	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1455C>A	.	.	ENST00000418600	19/19	28	18	9	33	33	0	SYNGAP1,3_prime_UTR_variant,,ENST00000418600,;ZBTB9,upstream_gene_variant,,ENST00000395064,;SYNGAP1,downstream_gene_variant,,ENST00000428982,;SYNGAP1,downstream_gene_variant,,ENST00000293748,;SYNGAP1,downstream_gene_variant,,ENST00000486399,;SYNGAP1,downstream_gene_variant,,ENST00000496374,;	A	ENSG00000197283	ENST00000418600	Transcript	3_prime_UTR_variant	5588	.	.	.	.	.	.	.	1	SYNGAP1	HGNC	11497	protein_coding	YES	CCDS34434.2	ENSP00000403636	SYGP1_HUMAN	.	UPI0000470C44	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCTTTGG	.	5	ESCA
DNAH8	0	.	GRCh37	6	38743696	38743696	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1280T>C	p.Leu427Ser	p.L427S	ENST00000359357	11/91	31	28	3	35	35	0	DNAH8,missense_variant,p.Leu427Ser,ENST00000359357,;DNAH8,missense_variant,p.Leu632Ser,ENST00000327475,;DNAH8,missense_variant,p.Leu427Ser,ENST00000441566,;DNAH8,missense_variant,p.Leu644Ser,ENST00000449981,;	C	ENSG00000124721	ENST00000359357	Transcript	missense_variant	1534	1280	427	L/S	tTa/tCa	.	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	benign(0.002)	11/91	.	Pfam_domain:PF08385,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TTTCTTAGATT	.	2	ESCA
RREB1	0	.	GRCh37	6	7250195	7250195	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*994C>G	.	.	ENST00000379938	13/13	60	42	18	62	62	0	RREB1,3_prime_UTR_variant,,ENST00000349384,;RREB1,3_prime_UTR_variant,,ENST00000334984,;RREB1,3_prime_UTR_variant,,ENST00000379938,;RREB1,downstream_gene_variant,,ENST00000379933,;	G	ENSG00000124782	ENST00000379938	Transcript	3_prime_UTR_variant	6760	.	.	.	.	.	.	.	1	RREB1	HGNC	10449	protein_coding	YES	CCDS34335.1	ENSP00000369270	RREB1_HUMAN	C9JU34_HUMAN,C9JPJ6_HUMAN,C9JE09_HUMAN	UPI000020E496	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCTACTG	.	5	ESCA
PLEKHA8	0	.	GRCh37	7	30118277	30118277	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1434G>C	p.Gln478His	p.Q478H	ENST00000449726	14/14	161	131	29	88	88	0	PLEKHA8,missense_variant,p.Gln504His,ENST00000440706,;PLEKHA8,missense_variant,p.Gln478His,ENST00000449726,;PLEKHA8,intron_variant,,ENST00000258679,;PLEKHA8,intron_variant,,ENST00000396257,;PLEKHA8,intron_variant,,ENST00000396259,;AC007285.7,upstream_gene_variant,,ENST00000433088,;	C	ENSG00000106086	ENST00000449726	Transcript	missense_variant	1784	1434	478	Q/H	caG/caC	.	.	.	1	PLEKHA8	HGNC	30037	protein_coding	YES	CCDS56473.1	ENSP00000397947	PKHA8_HUMAN	.	UPI000020ECE0	.	tolerated(0.23)	benign(0.01)	14/14	.	hmmpanther:PTHR10219,hmmpanther:PTHR10219:SF16,Gene3D:2i3fA00,Superfamily_domains:0043785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCAGAAAGA	.	5	ESCA
URGCP	0	.	GRCh37	7	43917445	43917445	+	Silent	SNP	C	C	T	rs753717943	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1617G>A	p.%3D	p.Q539Q	ENST00000453200	6/6	63	32	31	54	54	0	URGCP,synonymous_variant,p.%3D,ENST00000447717,;URGCP,synonymous_variant,p.%3D,ENST00000453200,;URGCP,synonymous_variant,p.%3D,ENST00000336086,;URGCP,synonymous_variant,p.%3D,ENST00000443736,;URGCP,synonymous_variant,p.%3D,ENST00000223341,;URGCP,synonymous_variant,p.%3D,ENST00000402306,;URGCP-MRPS24,intron_variant,,ENST00000603700,;URGCP,downstream_gene_variant,,ENST00000455877,;URGCP,downstream_gene_variant,,ENST00000426198,;URGCP,downstream_gene_variant,,ENST00000446958,;URGCP,non_coding_transcript_exon_variant,,ENST00000497914,;URGCP,downstream_gene_variant,,ENST00000467410,;URGCP,downstream_gene_variant,,ENST00000439702,;URGCP,downstream_gene_variant,,ENST00000474376,;	T	ENSG00000106608	ENST00000453200	Transcript	synonymous_variant	2111	1617	539	Q	caG/caA	rs753717943	.	.	-1	URGCP	HGNC	30890	protein_coding	YES	CCDS47578.1	ENSP00000396918	URGCP_HUMAN	C9JKA8_HUMAN,C9J0W2_HUMAN	UPI000020EE9D	.	.	.	6/6	.	hmmpanther:PTHR22796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTTCTGCTG	.	5	ESCA
PMS2	0	.	GRCh37	7	6026532	6026532	+	Missense_Mutation	SNP	T	T	A	rs370853512	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1864A>T	p.Met622Leu	p.M622L	ENST00000265849	11/15	84	33	51	63	63	0	PMS2,missense_variant,p.Met622Leu,ENST00000265849,;PMS2,missense_variant,p.Met516Leu,ENST00000441476,;PMS2,intron_variant,,ENST00000382321,;PMS2,intron_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000469652,;	A	ENSG00000122512	ENST00000265849	Transcript	missense_variant	1970	1864	622	M/L	Atg/Ttg	rs370853512	.	.	-1	PMS2	HGNC	9122	protein_coding	YES	CCDS5343.1	ENSP00000265849	PMS2_HUMAN	.	UPI000013D696	.	tolerated(0.55)	benign(0.004)	11/15	.	hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF9,Coiled-coils_(Ncoils):Coil	C:0.0010	C:0	C:0	.	C:0	C:0	C:0.0051	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCATAGAAA	byFrequency|byCluster|by1000G	5	ESCA
DBF4	0	.	GRCh37	7	87505953	87505953	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-95G>T	.	.	ENST00000265728	1/12	57	33	23	78	78	0	DBF4,5_prime_UTR_variant,,ENST00000265728,;SLC25A40,upstream_gene_variant,,ENST00000341119,;DBF4,5_prime_UTR_variant,,ENST00000413643,;DBF4,5_prime_UTR_variant,,ENST00000430279,;DBF4,5_prime_UTR_variant,,ENST00000431138,;DBF4,non_coding_transcript_exon_variant,,ENST00000495067,;DBF4,non_coding_transcript_exon_variant,,ENST00000486925,;SLC25A40,upstream_gene_variant,,ENST00000444363,;SLC25A40,upstream_gene_variant,,ENST00000491499,;	T	ENSG00000006634	ENST00000265728	Transcript	5_prime_UTR_variant	410	.	.	.	.	.	.	.	1	DBF4	HGNC	17364	protein_coding	YES	CCDS5611.1	ENSP00000265728	DBF4A_HUMAN	B7Z8C6_HUMAN,B3KMY2_HUMAN	UPI000000DC33	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCGGCCGTC	.	5	ESCA
AKAP9	0	.	GRCh37	7	91570243	91570243	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-171G>T	.	.	ENST00000356239	1/50	26	12	14	27	27	0	AKAP9,5_prime_UTR_variant,,ENST00000356239,;AKAP9,5_prime_UTR_variant,,ENST00000359028,;AKAP9,5_prime_UTR_variant,,ENST00000394564,;AKAP9,5_prime_UTR_variant,,ENST00000358100,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,;	T	ENSG00000127914	ENST00000356239	Transcript	5_prime_UTR_variant	63	.	.	.	.	.	.	.	1	AKAP9	HGNC	379	protein_coding	YES	CCDS5622.1	ENSP00000348573	AKAP9_HUMAN	Q8IW64_HUMAN	UPI000002A38D	.	.	.	1/50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGACGATCCG	.	3	ESCA
ZSCAN25	0	.	GRCh37	7	99226869	99226869	+	Silent	SNP	G	G	A	rs773315356	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.861G>A	p.%3D	p.A287A	ENST00000394152	8/8	25	16	8	44	44	0	ZSCAN25,synonymous_variant,p.%3D,ENST00000334715,;ZSCAN25,synonymous_variant,p.%3D,ENST00000262941,;ZSCAN25,synonymous_variant,p.%3D,ENST00000394152,;ZSCAN25,non_coding_transcript_exon_variant,,ENST00000493443,;ZSCAN25,intron_variant,,ENST00000466948,;ZSCAN25,3_prime_UTR_variant,,ENST00000394150,;ZSCAN25,non_coding_transcript_exon_variant,,ENST00000485586,;ZSCAN25,non_coding_transcript_exon_variant,,ENST00000481424,;ZSCAN25,downstream_gene_variant,,ENST00000473646,;	A	ENSG00000197037	ENST00000394152	Transcript	synonymous_variant	1188	861	287	A	gcG/gcA	rs773315356	.	.	1	ZSCAN25	HGNC	21961	protein_coding	YES	CCDS5671.2	ENSP00000377708	ZSC25_HUMAN	C9K079_HUMAN,B3KPY4_HUMAN	UPI000050D3F2	.	.	.	8/8	.	hmmpanther:PTHR23226:SF1,hmmpanther:PTHR23226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGCTGGT	.	5	ESCA
PARP10	0	.	GRCh37	8	145057845	145057845	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1912G>T	p.Glu638Ter	p.E638*	ENST00000313028	8/11	99	53	45	80	80	0	PARP10,stop_gained,p.Glu638Ter,ENST00000313028,;PARP10,stop_gained,p.Glu629Ter,ENST00000524918,;PARP10,stop_gained,p.Glu650Ter,ENST00000525773,;PARP10,downstream_gene_variant,,ENST00000528914,;PARP10,downstream_gene_variant,,ENST00000525879,;PARP10,downstream_gene_variant,,ENST00000529842,;PARP10,downstream_gene_variant,,ENST00000529311,;PARP10,downstream_gene_variant,,ENST00000528625,;PARP10,downstream_gene_variant,,ENST00000532311,;PARP10,downstream_gene_variant,,ENST00000531537,;PARP10,downstream_gene_variant,,ENST00000313059,;PARP10,downstream_gene_variant,,ENST00000528136,;PARP10,downstream_gene_variant,,ENST00000531707,;PARP10,downstream_gene_variant,,ENST00000525486,;PARP10,downstream_gene_variant,,ENST00000530478,;PARP10,downstream_gene_variant,,ENST00000534737,;PARP10,downstream_gene_variant,,ENST00000532660,;PARP10,downstream_gene_variant,,ENST00000533665,;PARP10,stop_gained,p.Glu638Ter,ENST00000527262,;PARP10,non_coding_transcript_exon_variant,,ENST00000526007,;PARP10,downstream_gene_variant,,ENST00000526985,;PARP10,downstream_gene_variant,,ENST00000528580,;PARP10,downstream_gene_variant,,ENST00000528963,;	A	ENSG00000178685	ENST00000313028	Transcript	stop_gained	2007	1912	638	E/*	Gag/Tag	.	.	.	-1	PARP10	HGNC	25895	protein_coding	YES	CCDS34960.1	ENSP00000325618	PAR10_HUMAN	E9PSG8_HUMAN,E9PSE7_HUMAN,E9PQQ6_HUMAN,E9PPV8_HUMAN,E9PPU2_HUMAN,E9PM86_HUMAN,E9PLE8_HUMAN,E9PJI2_HUMAN,E9PIA6_HUMAN	UPI0000251FAB	.	.	.	8/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14453,hmmpanther:PTHR14453:SF55	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGCTCCTCCT	.	3	ESCA
POLB	0	.	GRCh37	8	42196087	42196087	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-56G>C	.	.	ENST00000265421	1/14	68	40	28	109	109	0	POLB,5_prime_UTR_variant,,ENST00000538005,;POLB,5_prime_UTR_variant,,ENST00000520008,;POLB,5_prime_UTR_variant,,ENST00000532157,;POLB,5_prime_UTR_variant,,ENST00000518925,;POLB,5_prime_UTR_variant,,ENST00000265421,;POLB,non_coding_transcript_exon_variant,,ENST00000530566,;POLB,5_prime_UTR_variant,,ENST00000522610,;POLB,non_coding_transcript_exon_variant,,ENST00000519094,;POLB,non_coding_transcript_exon_variant,,ENST00000522297,;POLB,upstream_gene_variant,,ENST00000519771,;RPL5P23,downstream_gene_variant,,ENST00000496040,;	C	ENSG00000070501	ENST00000265421	Transcript	5_prime_UTR_variant	115	.	.	.	.	.	.	.	1	POLB	HGNC	9174	protein_coding	YES	CCDS6129.1	ENSP00000265421	DPOLB_HUMAN	Q6LBJ9_HUMAN,E5RJ55_HUMAN,E5RHZ4_HUMAN,B7Z1W5_HUMAN	UPI000013D61E	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGGGAGAGG	.	5	ESCA
GABBR2	0	.	GRCh37	9	101050547	101050547	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2319G>C	.	.	ENST00000259455	19/19	51	39	11	69	69	0	GABBR2,3_prime_UTR_variant,,ENST00000259455,;	G	ENSG00000136928	ENST00000259455	Transcript	3_prime_UTR_variant	5605	.	.	.	.	.	.	.	-1	GABBR2	HGNC	4507	protein_coding	YES	CCDS6736.1	ENSP00000259455	GABR2_HUMAN	H9NIL8_HUMAN	UPI0000035832	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCTTCAG	.	5	ESCA
STX17	0	.	GRCh37	9	102713526	102713526	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.374C>G	p.Thr125Ser	p.T125S	ENST00000259400	4/8	48	37	11	60	60	0	STX17,missense_variant,p.Thr125Ser,ENST00000534052,;STX17,missense_variant,p.Thr125Ser,ENST00000525640,;STX17,missense_variant,p.Thr125Ser,ENST00000259400,;STX17,downstream_gene_variant,,ENST00000531035,;STX17,non_coding_transcript_exon_variant,,ENST00000525847,;STX17,non_coding_transcript_exon_variant,,ENST00000525579,;STX17,missense_variant,p.Thr125Ser,ENST00000524405,;STX17,3_prime_UTR_variant,,ENST00000529340,;STX17,3_prime_UTR_variant,,ENST00000525342,;	G	ENSG00000136874	ENST00000259400	Transcript	missense_variant	510	374	125	T/S	aCt/aGt	.	.	.	1	STX17	HGNC	11432	protein_coding	YES	CCDS6745.1	ENSP00000259400	STX17_HUMAN	E9PJW1_HUMAN	UPI000013D04E	.	tolerated(0.71)	benign(0.001)	4/8	.	Superfamily_domains:SSF47661,hmmpanther:PTHR19957:SF81,hmmpanther:PTHR19957	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAACTTTGC	.	5	ESCA
PDCL	0	.	GRCh37	9	125582567	125582567	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703G>T	p.Ala235Ser	p.A235S	ENST00000259467	4/4	28	23	5	33	33	0	PDCL,missense_variant,p.Ala235Ser,ENST00000259467,;PDCL,intron_variant,,ENST00000436632,;PDCL,downstream_gene_variant,,ENST00000394285,;	A	ENSG00000136940	ENST00000259467	Transcript	missense_variant	869	703	235	A/S	Gcc/Tcc	.	.	.	-1	PDCL	HGNC	8770	protein_coding	YES	CCDS6845.1	ENSP00000259467	PHLP_HUMAN	Q9UNX2_HUMAN,Q9UNX1_HUMAN	UPI0000131988	.	deleterious(0.01)	probably_damaging(0.997)	4/4	.	Prints_domain:PR00677,Superfamily_domains:SSF52833,Pfam_domain:PF02114,Gene3D:3.40.30.10,hmmpanther:PTHR21148:SF21,hmmpanther:PTHR21148	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCAGGAA	.	5	ESCA
CIZ1	0	.	GRCh37	9	130931405	130931405	+	Missense_Mutation	SNP	C	C	T	rs767189940	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2221G>A	p.Glu741Lys	p.E741K	ENST00000393608	14/17	44	31	12	61	61	0	CIZ1,missense_variant,p.Glu712Lys,ENST00000325721,;CIZ1,missense_variant,p.Glu685Lys,ENST00000372948,;CIZ1,missense_variant,p.Glu713Lys,ENST00000357558,;CIZ1,missense_variant,p.Glu663Lys,ENST00000415526,;CIZ1,missense_variant,p.Glu767Lys,ENST00000538431,;CIZ1,missense_variant,p.Glu741Lys,ENST00000372938,;CIZ1,missense_variant,p.Glu640Lys,ENST00000541172,;CIZ1,missense_variant,p.Glu713Lys,ENST00000277465,;CIZ1,missense_variant,p.Glu741Lys,ENST00000393608,;CIZ1,missense_variant,p.Glu661Lys,ENST00000372954,;CIZ1,non_coding_transcript_exon_variant,,ENST00000471773,;CIZ1,non_coding_transcript_exon_variant,,ENST00000476727,;CIZ1,non_coding_transcript_exon_variant,,ENST00000471839,;CIZ1,upstream_gene_variant,,ENST00000491487,;CIZ1,upstream_gene_variant,,ENST00000485862,;CIZ1,upstream_gene_variant,,ENST00000461765,;CIZ1,upstream_gene_variant,,ENST00000485001,;CIZ1,non_coding_transcript_exon_variant,,ENST00000476541,;	T	ENSG00000148337	ENST00000393608	Transcript	missense_variant	2424	2221	741	E/K	Gag/Aag	rs767189940	.	.	-1	CIZ1	HGNC	16744	protein_coding	YES	CCDS6894.1	ENSP00000377232	CIZ1_HUMAN	Q9Y3F8_HUMAN,F6WSM2_HUMAN,F6VD24_HUMAN,B0EXJ7_HUMAN	UPI0000141722	.	tolerated(0.05)	possibly_damaging(0.509)	14/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15491:SF9,hmmpanther:PTHR15491	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCGAAGC	byFrequency	5	ESCA
DNM1	0	.	GRCh37	9	130996366	130996366	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1402G>A	p.Glu468Lys	p.E468K	ENST00000372923	11/22	36	22	13	58	58	0	DNM1,missense_variant,p.Glu468Lys,ENST00000341179,;DNM1,missense_variant,p.Glu468Lys,ENST00000372923,;DNM1,missense_variant,p.Glu468Lys,ENST00000486160,;DNM1,missense_variant,p.Glu468Lys,ENST00000475805,;DNM1,missense_variant,p.Glu468Lys,ENST00000393594,;DNM1,3_prime_UTR_variant,,ENST00000482638,;DNM1,non_coding_transcript_exon_variant,,ENST00000463998,;DNM1,non_coding_transcript_exon_variant,,ENST00000441149,;	A	ENSG00000106976	ENST00000372923	Transcript	missense_variant	1494	1402	468	E/K	Gag/Aag	.	.	.	1	DNM1	HGNC	2972	protein_coding	YES	CCDS6895.1	ENSP00000362014	DYN1_HUMAN	.	UPI000013CA31	.	tolerated(0.11)	probably_damaging(0.914)	11/22	.	hmmpanther:PTHR11566:SF32,hmmpanther:PTHR11566,Pfam_domain:PF01031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGCGAGGGC	.	5	ESCA
CACNA1B	0	.	GRCh37	9	141016131	141016131	+	Nonsense_Mutation	SNP	G	G	T	rs202111201	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6700G>T	p.Glu2234Ter	p.E2234*	ENST00000371372	47/47	26	15	11	50	50	0	CACNA1B,stop_gained,p.Glu2235Ter,ENST00000371355,;CACNA1B,stop_gained,p.Glu2233Ter,ENST00000371357,;CACNA1B,stop_gained,p.Glu1428Ter,ENST00000277549,;CACNA1B,stop_gained,p.Glu2232Ter,ENST00000371363,;CACNA1B,stop_gained,p.Glu2234Ter,ENST00000371372,;CACNA1B,synonymous_variant,p.%3D,ENST00000277551,;	T	ENSG00000148408	ENST00000371372	Transcript	stop_gained	6845	6700	2234	E/*	Gaa/Taa	rs202111201	.	.	1	CACNA1B	HGNC	1389	protein_coding	YES	CCDS59522.1	ENSP00000360423	CAC1B_HUMAN	Q9HBI3_HUMAN,Q9HBH4_HUMAN,Q9HBG3_HUMAN,Q9HBG2_HUMAN,Q9HAT5_HUMAN,Q9HAT4_HUMAN	UPI0000127267	.	.	.	47/47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCGAACAC	.	5	ESCA
RFX3	0	.	GRCh37	9	3395586	3395586	+	Translation_Start_Site	SNP	C	C	G	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3G>C	p.Met1?	p.M1?	ENST00000382004	3/18	41	30	11	46	46	0	RFX3,start_lost,p.Met1?,ENST00000381984,;RFX3,start_lost,p.Met1?,ENST00000457373,;RFX3,start_lost,p.Met1?,ENST00000302303,;RFX3,start_lost,p.Met1?,ENST00000449190,;RFX3,start_lost,p.Met1?,ENST00000382004,;RFX3,start_lost,p.Met1?,ENST00000358730,;RFX3,start_lost,p.Met1?,ENST00000451859,;	G	ENSG00000080298	ENST00000382004	Transcript	start_lost	315	3	1	M/I	atG/atC	.	.	.	-1	RFX3	HGNC	9984	protein_coding	YES	CCDS6449.1	ENSP00000371434	RFX3_HUMAN	F6XM74_HUMAN,F6USP3_HUMAN	UPI0000070BFB	.	deleterious_low_confidence(0)	possibly_damaging(0.69)	3/18	.	Pfam_domain:PF04589	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGCATGAT	.	5	ESCA
SUSD3	0	.	GRCh37	9	95847188	95847188	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*159G>C	.	.	ENST00000375472	5/5	10	5	5	20	20	0	SUSD3,3_prime_UTR_variant,,ENST00000375472,;SUSD3,3_prime_UTR_variant,,ENST00000375469,;SUSD3,3_prime_UTR_variant,,ENST00000471462,;SUSD3,downstream_gene_variant,,ENST00000465709,;	C	ENSG00000157303	ENST00000375472	Transcript	3_prime_UTR_variant	963	.	.	.	.	.	.	.	1	SUSD3	HGNC	28391	protein_coding	YES	CCDS6701.1	ENSP00000364621	SUSD3_HUMAN	.	UPI0000070B4A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAGCTGACATC	.	3	ESCA
GPR112	0	.	GRCh37	X	135429365	135429365	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3500C>T	p.Thr1167Ile	p.T1167I	ENST00000394143	6/26	36	29	7	36	36	0	GPR112,missense_variant,p.Thr1104Ile,ENST00000287534,;GPR112,missense_variant,p.Thr1167Ile,ENST00000370652,;GPR112,missense_variant,p.Thr1167Ile,ENST00000394143,;GPR112,missense_variant,p.Thr962Ile,ENST00000394141,;GPR112,missense_variant,p.Thr962Ile,ENST00000412101,;	T	ENSG00000156920	ENST00000394143	Transcript	missense_variant	3791	3500	1167	T/I	aCa/aTa	.	.	.	1	GPR112	HGNC	18992	protein_coding	YES	CCDS35409.1	ENSP00000377699	GP112_HUMAN	.	UPI00004CEC5B	.	tolerated(0.13)	benign(0.044)	6/26	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTACACCAG	.	5	ESCA
TMEM257	0	.	GRCh37	X	144910865	144910865	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1334G>T	.	.	ENST00000408967	1/1	21	9	12	18	18	0	TMEM257,3_prime_UTR_variant,,ENST00000408967,;SLITRK2,downstream_gene_variant,,ENST00000370490,;SLITRK2,downstream_gene_variant,,ENST00000434188,;SLITRK2,downstream_gene_variant,,ENST00000428560,;SLITRK2,downstream_gene_variant,,ENST00000413937,;SLITRK2,downstream_gene_variant,,ENST00000447897,;SLITRK2,downstream_gene_variant,,ENST00000335565,;	T	ENSG00000221870	ENST00000408967	Transcript	3_prime_UTR_variant	1938	.	.	.	.	.	.	.	1	TMEM257	HGNC	2562	protein_coding	YES	CCDS14681.1	ENSP00000386149	TM257_HUMAN	.	UPI0000128753	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATCGACTTT	.	5	ESCA
CFP	0	.	GRCh37	X	47486320	47486320	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792C>T	p.%3D	p.G264G	ENST00000247153	7/10	16	7	8	21	21	0	CFP,synonymous_variant,p.%3D,ENST00000377005,;CFP,synonymous_variant,p.%3D,ENST00000469388,;CFP,synonymous_variant,p.%3D,ENST00000247153,;CFP,synonymous_variant,p.%3D,ENST00000396992,;CFP,downstream_gene_variant,,ENST00000480317,;CFP,non_coding_transcript_exon_variant,,ENST00000485991,;CFP,upstream_gene_variant,,ENST00000478222,;	A	ENSG00000126759	ENST00000247153	Transcript	synonymous_variant	1034	792	264	G	ggC/ggT	.	.	.	-1	CFP	HGNC	8864	protein_coding	YES	CCDS14282.1	ENSP00000247153	PROP_HUMAN	E9PAQ1_HUMAN,C9J7V5_HUMAN	UPI0000132325	.	.	.	7/10	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50092,hmmpanther:PTHR22906,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGGCCCCA	.	5	ESCA
UBQLN2	0	.	GRCh37	X	56590987	56590987	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683delC	p.Pro228GlnfsTer3	p.P228Qfs*3	ENST00000338222	1/1	15	10	5	12	12	0	UBQLN2,frameshift_variant,p.Pro228GlnfsTer3,ENST00000338222,;	-	ENSG00000188021	ENST00000338222	Transcript	frameshift_variant	962	681	227	N/X	aaC/aa	.	.	.	1	UBQLN2	HGNC	12509	protein_coding	YES	CCDS14374.1	ENSP00000345195	UBQL2_HUMAN	.	UPI000004A059	.	.	.	1/1	.	Superfamily_domains:SSF48371,SMART_domains:SM00727,hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CAACAACCCAGA	.	2	ESCA
SPIN4	0	.	GRCh37	X	62570918	62570918	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-220G>A	.	.	ENST00000335144	1/1	42	27	14	37	37	0	SPIN4,5_prime_UTR_variant,,ENST00000335144,;SPIN4,5_prime_UTR_variant,,ENST00000374884,;RP11-357C3.3,intron_variant,,ENST00000610234,;RP11-357C3.3,intron_variant,,ENST00000610088,;SPIN4-AS1,intron_variant,,ENST00000451979,;	T	ENSG00000186767	ENST00000335144	Transcript	5_prime_UTR_variant	301	.	.	.	.	.	.	.	-1	SPIN4	HGNC	27040	protein_coding	YES	CCDS43964.1	ENSP00000334163	SPIN4_HUMAN	.	UPI000013FD3C	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTCCTCTC	.	5	ESCA
Y_RNA	0	.	GRCh37	X	70712092	70712092	+	5'Flank	SNP	G	G	C	novel	.	TCGA-LN-A4MR-01A-11D-A28B-09	TCGA-LN-A4MR-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000362881	.	20	12	8	26	26	0	Y_RNA,upstream_gene_variant,,ENST00000362881,;INGX,non_coding_transcript_exon_variant,,ENST00000489074,;TAF1,intron_variant,,ENST00000485087,;TAF1,intron_variant,,ENST00000468167,;TAF1,intron_variant,,ENST00000461764,;TAF1,intron_variant,,ENST00000467309,;TAF1,intron_variant,,ENST00000462588,;TAF1,upstream_gene_variant,,ENST00000497222,;TAF1,intron_variant,,ENST00000437147,;TAF1,intron_variant,,ENST00000373775,;INGX,non_coding_transcript_exon_variant,,ENST00000510256,;INGX,non_coding_transcript_exon_variant,,ENST00000359239,;	C	ENSG00000199751	ENST00000362881	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1075	-1	Y_RNA	RFAM	.	misc_RNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCGGATCAT	.	5	ESCA
OLAH	0	.	GRCh37	10	15091715	15091715	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114C>A	p.%3D	p.G38G	ENST00000378217	3/9	33	17	16	51	51	0	OLAH,synonymous_variant,p.%3D,ENST00000413672,;OLAH,synonymous_variant,p.%3D,ENST00000378217,;OLAH,synonymous_variant,p.%3D,ENST00000378225,;OLAH,synonymous_variant,p.%3D,ENST00000378228,;OLAH,synonymous_variant,p.%3D,ENST00000428897,;OLAH,synonymous_variant,p.%3D,ENST00000429028,;OLAH,upstream_gene_variant,,ENST00000493912,;DCLRE1CP1,intron_variant,,ENST00000378211,;	A	ENSG00000152463	ENST00000378217	Transcript	synonymous_variant	301	114	38	G	ggC/ggA	.	.	.	1	OLAH	HGNC	25625	protein_coding	YES	CCDS7106.1	ENSP00000367462	SAST_HUMAN	Q5VUC1_HUMAN	UPI000007139E	.	.	.	3/9	.	Gene3D:3.40.50.1820,hmmpanther:PTHR11487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGCTCCAC	.	5	ESCA
TECTA	0	.	GRCh37	11	120998865	120998865	+	Missense_Mutation	SNP	G	G	A	rs759694570	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2179G>A	p.Ala727Thr	p.A727T	ENST00000392793	9/24	34	25	9	34	34	0	TECTA,missense_variant,p.Ala727Thr,ENST00000264037,;TECTA,missense_variant,p.Ala727Thr,ENST00000392793,;	A	ENSG00000109927	ENST00000392793	Transcript	missense_variant	2450	2179	727	A/T	Gcc/Acc	rs759694570	.	.	1	TECTA	HGNC	11720	protein_coding	YES	CCDS8434.1	ENSP00000376543	TECTA_HUMAN	.	UPI000045659D	.	tolerated(0.38)	benign(0.01)	9/24	.	SMART_domains:SM00216,Pfam_domain:PF00094,hmmpanther:PTHR11339,PROSITE_profiles:PS51233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGCGCCTCC	.	5	ESCA
INSC	0	.	GRCh37	11	15260470	15260470	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1384C>A	p.Gln462Lys	p.Q462K	ENST00000379554	11/13	96	89	6	54	54	0	INSC,missense_variant,p.Gln462Lys,ENST00000379554,;INSC,missense_variant,p.Gln415Lys,ENST00000530161,;INSC,missense_variant,p.Gln415Lys,ENST00000379556,;INSC,missense_variant,p.Gln373Lys,ENST00000424273,;INSC,missense_variant,p.Gln415Lys,ENST00000528567,;INSC,missense_variant,p.Gln373Lys,ENST00000525218,;INSC,non_coding_transcript_exon_variant,,ENST00000526102,;INSC,non_coding_transcript_exon_variant,,ENST00000447214,;	A	ENSG00000188487	ENST00000379554	Transcript	missense_variant	1430	1384	462	Q/K	Cag/Aag	.	.	.	1	INSC	HGNC	33116	protein_coding	YES	CCDS41621.1	ENSP00000368872	INSC_HUMAN	.	UPI0000D63F1D	.	tolerated(0.49)	benign(0.117)	11/13	.	hmmpanther:PTHR21386,hmmpanther:PTHR21386:SF0,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTCCAGCTT	.	2	ESCA
PIK3C2A	0	.	GRCh37	11	17111318	17111318	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5028A>G	p.%3D	p.K1676K	ENST00000265970	32/32	55	42	13	29	29	0	PIK3C2A,synonymous_variant,p.%3D,ENST00000540361,;PIK3C2A,synonymous_variant,p.%3D,ENST00000265970,;PIK3C2A,intron_variant,,ENST00000531428,;	C	ENSG00000011405	ENST00000265970	Transcript	synonymous_variant	5028	5028	1676	K	aaA/aaG	.	.	.	-1	PIK3C2A	HGNC	8971	protein_coding	YES	CCDS7824.1	ENSP00000265970	P3C2A_HUMAN	L7RRS0_HUMAN,F5H2B0_HUMAN,E9PPP3_HUMAN	UPI000013D6B3	.	.	.	32/32	.	Superfamily_domains:SSF49562,SMART_domains:SM00239,Gene3D:2.60.40.150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCATTTAAC	.	5	ESCA
PRMT3	0	.	GRCh37	11	20529974	20529974	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*15C>A	.	.	ENST00000331079	16/16	18	14	4	9	9	0	PRMT3,3_prime_UTR_variant,,ENST00000437750,;PRMT3,3_prime_UTR_variant,,ENST00000331079,;PRMT3,3_prime_UTR_variant,,ENST00000330796,;PRMT3,non_coding_transcript_exon_variant,,ENST00000529592,;	A	ENSG00000185238	ENST00000331079	Transcript	3_prime_UTR_variant	1828	.	.	.	.	.	.	.	1	PRMT3	HGNC	30163	protein_coding	YES	CCDS7853.1	ENSP00000331879	ANM3_HUMAN	.	UPI0000198DED	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AAAAGCACACT	.	4	ESCA
UBXN1	0	.	GRCh37	11	62444034	62444035	+	3'UTR	INS	-	-	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*155dupG	.	.	ENST00000294119	8/8	111	79	32	83	83	0	UBXN1,frameshift_variant,p.Ter101Trp,ENST00000533000,;UBXN1,3_prime_UTR_variant,,ENST00000301935,;UBXN1,3_prime_UTR_variant,,ENST00000294119,;UBXN1,3_prime_UTR_variant,,ENST00000529640,;C11orf48,upstream_gene_variant,,ENST00000528862,;C11orf48,upstream_gene_variant,,ENST00000354588,;UBXN1,downstream_gene_variant,,ENST00000534176,;C11orf48,upstream_gene_variant,,ENST00000415855,;C11orf83,downstream_gene_variant,,ENST00000531323,;C11orf83,downstream_gene_variant,,ENST00000377953,;C11orf48,upstream_gene_variant,,ENST00000377954,;C11orf48,upstream_gene_variant,,ENST00000431002,;UBXN1,downstream_gene_variant,,ENST00000525004,;UBXN1,downstream_gene_variant,,ENST00000524762,;UBXN1,non_coding_transcript_exon_variant,,ENST00000532904,;UBXN1,non_coding_transcript_exon_variant,,ENST00000525717,;UBXN1,non_coding_transcript_exon_variant,,ENST00000533476,;C11orf48,upstream_gene_variant,,ENST00000524759,;UBXN1,downstream_gene_variant,,ENST00000531625,;UBXN1,downstream_gene_variant,,ENST00000531056,;UBXN1,downstream_gene_variant,,ENST00000528907,;UBXN1,downstream_gene_variant,,ENST00000527421,;UBXN1,downstream_gene_variant,,ENST00000436354,;UBXN1,downstream_gene_variant,,ENST00000533908,;C11orf48,upstream_gene_variant,,ENST00000527679,;UBXN1,downstream_gene_variant,,ENST00000526919,;	C	ENSG00000162191	ENST00000294119	Transcript	3_prime_UTR_variant	1226-1227	.	.	.	.	.	.	.	-1	UBXN1	HGNC	18402	protein_coding	YES	CCDS8029.1	ENSP00000294119	UBXN1_HUMAN	.	UPI000006DE59	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGGGTCACAG	.	3	ESCA
DNHD1	0	.	GRCh37	11	6580456	6580456	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9462C>T	p.%3D	p.H3154H	ENST00000254579	28/43	26	13	12	36	36	0	DNHD1,synonymous_variant,p.%3D,ENST00000527990,;DNHD1,synonymous_variant,p.%3D,ENST00000254579,;DNHD1,synonymous_variant,p.%3D,ENST00000524401,;DNHD1,non_coding_transcript_exon_variant,,ENST00000526027,;DNHD1,non_coding_transcript_exon_variant,,ENST00000531903,;DNHD1,non_coding_transcript_exon_variant,,ENST00000534210,;DNHD1,upstream_gene_variant,,ENST00000529821,;	T	ENSG00000179532	ENST00000254579	Transcript	synonymous_variant	10026	9462	3154	H	caC/caT	.	.	.	1	DNHD1	HGNC	26532	protein_coding	YES	CCDS44532.1	ENSP00000254579	DNHD1_HUMAN	.	UPI0001929529	.	.	.	28/43	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10676:SF244,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCACGGTAC	.	5	ESCA
NR1H4	0	.	GRCh37	12	100955761	100955761	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1207G>T	p.Val403Phe	p.V403F	ENST00000551379	8/9	28	19	9	27	27	0	NR1H4,missense_variant,p.Val393Phe,ENST00000392986,;NR1H4,missense_variant,p.Val389Phe,ENST00000548884,;NR1H4,missense_variant,p.Val403Phe,ENST00000551379,;NR1H4,missense_variant,p.Val342Phe,ENST00000549996,;NR1H4,missense_variant,p.Val399Phe,ENST00000188403,;NR1H4,3_prime_UTR_variant,,ENST00000321046,;	T	ENSG00000012504	ENST00000551379	Transcript	missense_variant	1235	1207	403	V/F	Gtt/Ttt	.	.	.	1	NR1H4	HGNC	7967	protein_coding	YES	CCDS55876.1	ENSP00000447149	NR1H4_HUMAN	B7Z423_HUMAN	UPI000006E701	.	deleterious(0)	probably_damaging(0.987)	8/9	.	hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF155,Pfam_domain:PF00104,Gene3D:1.10.565.10,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00546,Prints_domain:PR00398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAATTGTTATC	.	2	ESCA
H3F3C	0	.	GRCh37	12	31945089	31945089	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12C>G	p.%3D	p.T4T	ENST00000340398	1/1	90	68	21	75	75	0	H3F3C,synonymous_variant,p.%3D,ENST00000340398,;	C	ENSG00000188375	ENST00000340398	Transcript	synonymous_variant	87	12	4	T	acC/acG	.	.	.	-1	H3F3C	HGNC	33164	protein_coding	YES	CCDS31769.1	ENSP00000339835	H3C_HUMAN	.	UPI0000185FBF	.	.	.	1/1	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTGGTTCG	.	5	ESCA
KMT2D	0	.	GRCh37	12	49426916	49426916	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11572C>T	p.Gln3858Ter	p.Q3858*	ENST00000301067	39/54	100	50	49	45	45	0	KMT2D,stop_gained,p.Gln3858Ter,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	stop_gained	11572	11572	3858	Q/*	Cag/Tag	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	39/54	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTGCTGCT	.	5	ESCA
HOXC10	0	.	GRCh37	12	54383780	54383780	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*550C>T	.	.	ENST00000303460	2/2	40	31	9	43	43	0	HOXC10,3_prime_UTR_variant,,ENST00000303460,;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC6,upstream_gene_variant,,ENST00000509328,;HOXC6,upstream_gene_variant,,ENST00000504315,;HOXC10,downstream_gene_variant,,ENST00000515593,;MIR196A2,upstream_gene_variant,,ENST00000385189,;HOXC-AS3,upstream_gene_variant,,ENST00000514702,;HOXC-AS2,downstream_gene_variant,,ENST00000604081,;HOXC10,downstream_gene_variant,,ENST00000513413,;HOXC10,downstream_gene_variant,,ENST00000514415,;HOXC9,upstream_gene_variant,,ENST00000504557,;HOXC10,downstream_gene_variant,,ENST00000511575,;	T	ENSG00000180818	ENST00000303460	Transcript	3_prime_UTR_variant	1653	.	.	.	.	.	.	.	1	HOXC10	HGNC	5122	protein_coding	YES	CCDS8868.1	ENSP00000307321	HXC10_HUMAN	Q53XI4_HUMAN,D6RAG4_HUMAN	UPI000012CF7C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGCTTGAA	.	5	ESCA
OR6C2	0	.	GRCh37	12	55846702	55846702	+	Silent	SNP	C	C	T	rs182901840	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.705C>T	p.%3D	p.A235A	ENST00000322678	1/1	59	42	16	46	46	0	OR6C2,synonymous_variant,p.%3D,ENST00000322678,;RP11-110A12.2,intron_variant,,ENST00000555146,;RP11-110A12.2,intron_variant,,ENST00000556750,;RP11-110A12.2,intron_variant,,ENST00000554049,;RP11-110A12.2,intron_variant,,ENST00000555138,;	T	ENSG00000179695	ENST00000322678	Transcript	synonymous_variant	705	705	235	A	gcC/gcT	rs182901840	.	.	1	OR6C2	HGNC	15436	protein_coding	YES	CCDS31824.1	ENSP00000323606	OR6C2_HUMAN	.	UPI0000140EC9	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26454:SF48,hmmpanther:PTHR26454,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGCCTTTTC	by1000G	5	ESCA
BIVM-ERCC5	0	.	GRCh37	13	103524566	103524566	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3973T>C	p.%3D	p.A1325A	ENST00000602836	21/21	42	31	10	41	41	0	BIVM-ERCC5,synonymous_variant,p.%3D,ENST00000602836,;ERCC5,synonymous_variant,p.%3D,ENST00000355739,;ERCC5,synonymous_variant,p.%3D,ENST00000375954,;ERCC5,upstream_gene_variant,,ENST00000472247,;ERCC5,downstream_gene_variant,,ENST00000481099,;	C	ENSG00000270181	ENST00000602836	Transcript	synonymous_variant	3973	3975	1325	A	gcT/gcC	.	.	.	1	BIVM-ERCC5	HGNC	43690	protein_coding	YES	.	ENSP00000473384	.	.	UPI0002B83330	.	.	.	21/21	.	hmmpanther:PTHR16171,TIGRFAM_domain:TIGR00600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGCTCAAAA	.	5	ESCA
ARGLU1	0	.	GRCh37	13	107195790	107195790	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*554A>G	.	.	ENST00000400198	4/4	36	21	14	41	41	0	ARGLU1,3_prime_UTR_variant,,ENST00000400198,;ARGLU1,downstream_gene_variant,,ENST00000375926,;ARGLU1,downstream_gene_variant,,ENST00000472226,;	C	ENSG00000134884	ENST00000400198	Transcript	3_prime_UTR_variant	1621	.	.	.	.	.	.	.	-1	ARGLU1	HGNC	25482	protein_coding	YES	CCDS41906.1	ENSP00000383059	ARGL1_HUMAN	.	UPI00000373ED	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTATATATA	.	5	ESCA
AP1G2	0	.	GRCh37	14	24035227	24035227	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.568+46G>T	.	.	ENST00000308724	.	45	33	11	34	34	0	AP1G2,intron_variant,,ENST00000308724,;AP1G2,intron_variant,,ENST00000557189,;AP1G2,intron_variant,,ENST00000397120,;AP1G2,downstream_gene_variant,,ENST00000556843,;JPH4,downstream_gene_variant,,ENST00000544177,;AP1G2,upstream_gene_variant,,ENST00000554477,;JPH4,downstream_gene_variant,,ENST00000397118,;JPH4,downstream_gene_variant,,ENST00000356300,;RP11-66N24.3,non_coding_transcript_exon_variant,,ENST00000555968,;AP1G2,intron_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000555118,;AP1G2,upstream_gene_variant,,ENST00000555510,;AP1G2,non_coding_transcript_exon_variant,,ENST00000554069,;AP1G2,non_coding_transcript_exon_variant,,ENST00000554312,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556743,;AP1G2,non_coding_transcript_exon_variant,,ENST00000535852,;AP1G2,non_coding_transcript_exon_variant,,ENST00000460049,;AP1G2,non_coding_transcript_exon_variant,,ENST00000557619,;AP1G2,non_coding_transcript_exon_variant,,ENST00000555896,;AP1G2,non_coding_transcript_exon_variant,,ENST00000553629,;AP1G2,intron_variant,,ENST00000556943,;AP1G2,intron_variant,,ENST00000553756,;AP1G2,intron_variant,,ENST00000557482,;AP1G2,intron_variant,,ENST00000465445,;AP1G2,upstream_gene_variant,,ENST00000556741,;AP1G2,upstream_gene_variant,,ENST00000555789,;AP1G2,downstream_gene_variant,,ENST00000553685,;AP1G2,downstream_gene_variant,,ENST00000554816,;AP1G2,upstream_gene_variant,,ENST00000557132,;AP1G2,upstream_gene_variant,,ENST00000557162,;AP1G2,upstream_gene_variant,,ENST00000555974,;AP1G2,upstream_gene_variant,,ENST00000554977,;AP1G2,upstream_gene_variant,,ENST00000554554,;AP1G2,upstream_gene_variant,,ENST00000556966,;AP1G2,upstream_gene_variant,,ENST00000554982,;AP1G2,upstream_gene_variant,,ENST00000556152,;	A	ENSG00000213983	ENST00000308724	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AP1G2	HGNC	556	protein_coding	YES	CCDS9602.1	ENSP00000312442	AP1G2_HUMAN	Q86U41_HUMAN,Q86U03_HUMAN,G3V532_HUMAN,G3V3Z2_HUMAN,G3V2V9_HUMAN	UPI0000124FE8	.	.	.	.	4/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTGTCC	.	5	ESCA
STXBP6	0	.	GRCh37	14	25325274	25325274	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319G>T	p.Ala107Ser	p.A107S	ENST00000323944	4/6	32	22	10	27	27	0	STXBP6,missense_variant,p.Ala107Ser,ENST00000358326,;STXBP6,missense_variant,p.Ala107Ser,ENST00000550887,;STXBP6,missense_variant,p.Ala107Ser,ENST00000419632,;STXBP6,missense_variant,p.Ala107Ser,ENST00000396700,;STXBP6,missense_variant,p.Ala107Ser,ENST00000546511,;STXBP6,missense_variant,p.Ala107Ser,ENST00000323944,;STXBP6,missense_variant,p.Ala107Ser,ENST00000548724,;STXBP6,3_prime_UTR_variant,,ENST00000548182,;	A	ENSG00000168952	ENST00000323944	Transcript	missense_variant	771	319	107	A/S	Gct/Tct	.	.	.	-1	STXBP6	HGNC	19666	protein_coding	YES	CCDS9634.1	ENSP00000324302	STXB6_HUMAN	.	UPI000006DD7D	.	tolerated(0.1)	benign(0.04)	4/6	.	hmmpanther:PTHR16092,Pfam_domain:PF15277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGCATTTT	.	5	ESCA
TP53BP1	0	.	GRCh37	15	43748741	43748741	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2065A>C	p.Met689Leu	p.M689L	ENST00000382044	12/28	28	10	18	38	38	0	TP53BP1,missense_variant,p.Met684Leu,ENST00000263801,;TP53BP1,missense_variant,p.Met689Leu,ENST00000413546,;TP53BP1,missense_variant,p.Met689Leu,ENST00000382039,;TP53BP1,missense_variant,p.Met689Leu,ENST00000450115,;TP53BP1,missense_variant,p.Met689Leu,ENST00000382044,;TP53BP1,upstream_gene_variant,,ENST00000605155,;TP53BP1,upstream_gene_variant,,ENST00000414758,;TP53BP1,non_coding_transcript_exon_variant,,ENST00000572085,;TP53BP1,upstream_gene_variant,,ENST00000480860,;TP53BP1,upstream_gene_variant,,ENST00000411772,;	G	ENSG00000067369	ENST00000382044	Transcript	missense_variant	2193	2065	689	M/L	Atg/Ctg	.	.	.	-1	TP53BP1	HGNC	11999	protein_coding	YES	CCDS45250.1	ENSP00000371475	TP53B_HUMAN	B3KVT9_HUMAN	UPI0000D720ED	.	tolerated(0.28)	benign(0.001)	12/28	.	hmmpanther:PTHR15321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCATATTTT	.	5	ESCA
SKOR1	0	.	GRCh37	15	68122570	68122570	+	Missense_Mutation	SNP	G	G	A	rs749099614	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2158G>A	p.Glu720Lys	p.E720K	ENST00000341418	10/15	48	15	32	64	64	0	SKOR1,missense_variant,p.Glu778Lys,ENST00000554240,;SKOR1,missense_variant,p.Glu789Lys,ENST00000554054,;SKOR1,missense_variant,p.Glu817Lys,ENST00000380035,;SKOR1,missense_variant,p.Glu720Lys,ENST00000341418,;SKOR1,missense_variant,p.Glu773Lys,ENST00000389002,;RP11-34F13.2,downstream_gene_variant,,ENST00000502156,;RP11-34F13.3,upstream_gene_variant,,ENST00000558889,;RP11-34F13.3,upstream_gene_variant,,ENST00000560577,;	A	ENSG00000188779	ENST00000341418	Transcript	missense_variant	2158	2158	720	E/K	Gaa/Aaa	rs749099614	.	.	1	SKOR1	HGNC	21326	protein_coding	YES	CCDS58374.1	ENSP00000343200	SKOR1_HUMAN	.	UPI00001987EE	.	deleterious_low_confidence(0)	possibly_damaging(0.486)	10/15	.	hmmpanther:PTHR10005,hmmpanther:PTHR10005:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTGGAAACG	.	5	ESCA
TSC2	0	.	GRCh37	16	2111977	2111977	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1225G>T	p.Glu409Ter	p.E409*	ENST00000219476	12/42	77	54	23	83	83	0	TSC2,stop_gained,p.Glu372Ter,ENST00000439673,;TSC2,stop_gained,p.Glu409Ter,ENST00000219476,;TSC2,stop_gained,p.Glu409Ter,ENST00000353929,;TSC2,stop_gained,p.Glu409Ter,ENST00000350773,;TSC2,stop_gained,p.Glu420Ter,ENST00000568454,;TSC2,stop_gained,p.Glu360Ter,ENST00000382538,;TSC2,stop_gained,p.Glu409Ter,ENST00000401874,;TSC2,intron_variant,,ENST00000467949,;TSC2,upstream_gene_variant,,ENST00000562474,;TSC2,3_prime_UTR_variant,,ENST00000439117,;TSC2,non_coding_transcript_exon_variant,,ENST00000463601,;TSC2,upstream_gene_variant,,ENST00000488675,;TSC2,upstream_gene_variant,,ENST00000568238,;TSC2,upstream_gene_variant,,ENST00000568566,;TSC2,upstream_gene_variant,,ENST00000490108,;	T	ENSG00000103197	ENST00000219476	Transcript	stop_gained	1855	1225	409	E/*	Gaa/Taa	.	.	.	1	TSC2	HGNC	12363	protein_coding	YES	CCDS10458.1	ENSP00000219476	TSC2_HUMAN	.	UPI000013C781	.	.	.	12/42	.	hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF1,Pfam_domain:PF11864,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTGAACTG	.	5	ESCA
TAOK2	0	.	GRCh37	16	29998794	29998794	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3201C>A	p.%3D	p.G1067G	ENST00000308893	16/16	83	47	36	71	71	0	TAOK2,synonymous_variant,p.%3D,ENST00000416441,;TAOK2,synonymous_variant,p.%3D,ENST00000543033,;TAOK2,synonymous_variant,p.%3D,ENST00000308893,;TAOK2,intron_variant,,ENST00000279394,;HIRIP3,downstream_gene_variant,,ENST00000279392,;TAOK2,non_coding_transcript_exon_variant,,ENST00000566552,;TAOK2,upstream_gene_variant,,ENST00000570844,;	A	ENSG00000149930	ENST00000308893	Transcript	synonymous_variant	4244	3201	1067	G	ggC/ggA	.	.	.	1	TAOK2	HGNC	16835	protein_coding	YES	CCDS10663.1	ENSP00000310094	TAOK2_HUMAN	.	UPI000013EDDA	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGCAGATG	.	5	ESCA
DNASE1	0	.	GRCh37	16	3705487	3705487	+	Missense_Mutation	SNP	T	T	A	rs369619441	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113T>A	p.Met38Lys	p.M38K	ENST00000246949	2/9	116	110	6	97	97	0	DNASE1,missense_variant,p.Met38Lys,ENST00000407479,;DNASE1,missense_variant,p.Met38Lys,ENST00000246949,;DNASE1,5_prime_UTR_variant,,ENST00000414110,;TRAP1,downstream_gene_variant,,ENST00000575671,;DNASE1,upstream_gene_variant,,ENST00000570664,;DNASE1,upstream_gene_variant,,ENST00000575479,;DNASE1,upstream_gene_variant,,ENST00000576792,;TRAP1,downstream_gene_variant,,ENST00000538171,;TRAP1,downstream_gene_variant,,ENST00000246957,;RP11-461A8.4,upstream_gene_variant,,ENST00000570409,;DNASE1,downstream_gene_variant,,ENST00000570761,;DNASE1,missense_variant,p.Met38Lys,ENST00000576050,;DNASE1,missense_variant,p.Met38Lys,ENST00000571460,;DNASE1,missense_variant,p.Met38Lys,ENST00000570769,;DNASE1,missense_variant,p.Met38Lys,ENST00000570376,;DNASE1,non_coding_transcript_exon_variant,,ENST00000570520,;TRAP1,intron_variant,,ENST00000575707,;TRAP1,downstream_gene_variant,,ENST00000574494,;DNASE1,upstream_gene_variant,,ENST00000570807,;DNASE1,upstream_gene_variant,,ENST00000573804,;DNASE1,upstream_gene_variant,,ENST00000572237,;	A	ENSG00000213918	ENST00000246949	Transcript	missense_variant	3322	113	38	M/K	aTg/aAg	rs369619441	.	.	1	DNASE1	HGNC	2956	protein_coding	YES	CCDS10507.1	ENSP00000246949	DNAS1_HUMAN	.	UPI0000043698	.	tolerated(0.27)	probably_damaging(0.949)	2/9	.	hmmpanther:PTHR11371,hmmpanther:PTHR11371:SF27,Gene3D:3.60.10.10,PIRSF_domain:PIRSF000988,SMART_domains:SM00476,Superfamily_domains:SSF56219,Prints_domain:PR00130	.	.	.	.	.	.	.	C:0.0002	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAGATGTCCA	.	2	ESCA
SALL1	0	.	GRCh37	16	51174133	51174133	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2000C>T	p.Ser667Phe	p.S667F	ENST00000251020	2/3	47	29	18	59	59	0	SALL1,missense_variant,p.Ser667Phe,ENST00000251020,;SALL1,missense_variant,p.Ser570Phe,ENST00000570206,;SALL1,missense_variant,p.Ser570Phe,ENST00000440970,;SALL1,intron_variant,,ENST00000541611,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,;	A	ENSG00000103449	ENST00000251020	Transcript	missense_variant	2034	2000	667	S/F	tCc/tTc	.	.	.	-1	SALL1	HGNC	10524	protein_coding	YES	CCDS10747.1	ENSP00000251020	SALL1_HUMAN	H3BSM9_HUMAN	UPI000013CCD8	.	deleterious(0.01)	probably_damaging(0.971)	2/3	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCGGACATG	.	5	ESCA
ALG1	0	.	GRCh37	16	5121961	5121961	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111G>A	p.%3D	p.A37A	ENST00000262374	1/13	32	22	9	34	34	0	ALG1,synonymous_variant,p.%3D,ENST00000586840,;ALG1,synonymous_variant,p.%3D,ENST00000262374,;ALG1,intron_variant,,ENST00000588623,;ALG1,upstream_gene_variant,,ENST00000544428,;ALG1,upstream_gene_variant,,ENST00000591783,;ALG1,synonymous_variant,p.%3D,ENST00000591822,;ALG1,non_coding_transcript_exon_variant,,ENST00000592793,;	A	ENSG00000033011	ENST00000262374	Transcript	synonymous_variant	142	111	37	A	gcG/gcA	.	.	.	1	ALG1	HGNC	18294	protein_coding	YES	CCDS10528.1	ENSP00000262374	ALG1_HUMAN	K7EID2_HUMAN,B4DP08_HUMAN	UPI000003B09B	.	.	.	1/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13036,hmmpanther:PTHR13036:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGCGGTGGT	.	5	ESCA
CX3CL1	0	.	GRCh37	16	57416011	57416011	+	Silent	SNP	G	G	A	rs373682759	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.261G>A	p.%3D	p.Q87Q	ENST00000006053	3/3	75	41	34	54	54	0	CX3CL1,missense_variant,p.Ser47Asn,ENST00000564948,;CX3CL1,synonymous_variant,p.%3D,ENST00000006053,;CX3CL1,synonymous_variant,p.%3D,ENST00000565912,;CX3CL1,synonymous_variant,p.%3D,ENST00000563383,;	A	ENSG00000006210	ENST00000006053	Transcript	synonymous_variant	372	261	87	Q	caG/caA	rs373682759	.	.	1	CX3CL1	HGNC	10647	protein_coding	YES	CCDS10779.1	ENSP00000006053	X3CL1_HUMAN	J3QRA1_HUMAN,A0N0N7_HUMAN	UPI0000040685	.	.	.	3/3	.	Prints_domain:PR01721,Superfamily_domains:SSF54117,SMART_domains:SM00199,Gene3D:2.40.50.40,Pfam_domain:PF00048,hmmpanther:PTHR12015:SF81,hmmpanther:PTHR12015	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCAGCATCT	byFrequency|byCluster	5	ESCA
TEPP	0	.	GRCh37	16	58018605	58018605	+	Silent	SNP	G	G	A	rs759241646	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.516G>A	p.%3D	p.A172A	ENST00000290871	4/8	75	49	25	82	82	0	TEPP,synonymous_variant,p.%3D,ENST00000441824,;TEPP,synonymous_variant,p.%3D,ENST00000290871,;TEPP,non_coding_transcript_exon_variant,,ENST00000569996,;TEPP,upstream_gene_variant,,ENST00000562915,;	A	ENSG00000159648	ENST00000290871	Transcript	synonymous_variant	553	516	172	A	gcG/gcA	rs759241646,COSM3818171	.	.	1	TEPP	HGNC	33745	protein_coding	YES	CCDS10790.1	ENSP00000290871	TEPP_HUMAN	.	UPI0000366B4E	.	.	.	4/8	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGCGCCAGG	.	5	ESCA
PMFBP1	0	.	GRCh37	16	72154011	72154011	+	Intron	SNP	G	G	A	rs752745163	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2769-23C>T	.	.	ENST00000237353	.	73	48	25	76	76	0	PMFBP1,missense_variant,p.Arg791Cys,ENST00000355636,;PMFBP1,intron_variant,,ENST00000237353,;PMFBP1,intron_variant,,ENST00000537792,;PMFBP1,intron_variant,,ENST00000537465,;PMFBP1,3_prime_UTR_variant,,ENST00000379073,;PMFBP1,downstream_gene_variant,,ENST00000537392,;	A	ENSG00000118557	ENST00000237353	Transcript	intron_variant	.	.	.	.	.	rs752745163	.	.	-1	PMFBP1	HGNC	17728	protein_coding	YES	CCDS32483.1	ENSP00000237353	PMFBP_HUMAN	F5H4F8_HUMAN,F5H0H9_HUMAN,F5GYR2_HUMAN,F5GXW3_HUMAN	UPI0000141554	.	.	.	.	19/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGACGGGTTG	byFrequency	5	ESCA
PIEZO1	0	.	GRCh37	16	88801195	88801195	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1860C>A	p.Ser620Arg	p.S620R	ENST00000301015	15/51	70	54	16	86	85	1	PIEZO1,missense_variant,p.Ser620Arg,ENST00000301015,;RP5-1142A6.2,intron_variant,,ENST00000440406,;RP5-1142A6.2,upstream_gene_variant,,ENST00000567968,;PIEZO1,upstream_gene_variant,,ENST00000490756,;	T	ENSG00000103335	ENST00000301015	Transcript	missense_variant	2107	1860	620	S/R	agC/agA	.	.	.	-1	PIEZO1	HGNC	28993	protein_coding	YES	CCDS54058.1	ENSP00000301015	PIEZ1_HUMAN	.	UPI0001B300F3	.	deleterious(0.04)	possibly_damaging(0.851)	15/51	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAGGCTGTA	.	5	ESCA
TOP2A	0	.	GRCh37	17	38567403	38567403	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1161C>A	p.Ser387Arg	p.S387R	ENST00000423485	10/35	88	54	34	71	70	0	TOP2A,missense_variant,p.Ser387Arg,ENST00000423485,;TOP2A,downstream_gene_variant,,ENST00000581055,;	T	ENSG00000131747	ENST00000423485	Transcript	missense_variant	1320	1161	387	S/R	agC/agA	.	.	.	-1	TOP2A	HGNC	11989	protein_coding	YES	CCDS45672.1	ENSP00000411532	TOP2A_HUMAN	J3QR57_HUMAN,J3KTB7_HUMAN	UPI0000137195	.	deleterious(0)	benign(0.363)	10/35	.	hmmpanther:PTHR10169:SF33,hmmpanther:PTHR10169,Pfam_domain:PF00204,Gene3D:3.30.230.10,SMART_domains:SM00433,Superfamily_domains:SSF54211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAAGCTCTT	.	5	ESCA
TEX14	0	.	GRCh37	17	56663385	56663385	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2865G>T	p.Trp955Cys	p.W955C	ENST00000240361	18/33	32	21	11	50	50	0	TEX14,missense_variant,p.Trp949Cys,ENST00000349033,;TEX14,missense_variant,p.Trp949Cys,ENST00000389934,;TEX14,missense_variant,p.Trp955Cys,ENST00000240361,;TEX14,3_prime_UTR_variant,,ENST00000582740,;	A	ENSG00000121101	ENST00000240361	Transcript	missense_variant	2951	2865	955	W/C	tgG/tgT	.	.	.	-1	TEX14	HGNC	11737	protein_coding	YES	CCDS56042.1	ENSP00000240361	TEX14_HUMAN	.	UPI0000DAC9CA	.	tolerated(0.14)	probably_damaging(0.971)	18/33	.	hmmpanther:PTHR23060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATGCCAAGG	.	5	ESCA
ELP5	0	.	GRCh37	17	7156110	7156110	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116G>T	p.Arg39Leu	p.R39L	ENST00000396628	2/8	99	72	26	96	96	0	ELP5,missense_variant,p.Arg39Leu,ENST00000354429,;ELP5,missense_variant,p.Arg39Leu,ENST00000570500,;ELP5,missense_variant,p.Arg39Leu,ENST00000574993,;ELP5,missense_variant,p.Arg39Leu,ENST00000573513,;ELP5,missense_variant,p.Arg22Leu,ENST00000576496,;ELP5,missense_variant,p.Arg39Leu,ENST00000574255,;ELP5,missense_variant,p.Arg39Leu,ENST00000356683,;ELP5,missense_variant,p.Arg39Leu,ENST00000396628,;ELP5,missense_variant,p.Arg39Leu,ENST00000396627,;ELP5,missense_variant,p.Arg32Leu,ENST00000570322,;ELP5,missense_variant,p.Arg39Leu,ENST00000573657,;ELP5,missense_variant,p.Arg39Leu,ENST00000573699,;ELP5,5_prime_UTR_variant,,ENST00000574841,;CTDNEP1,upstream_gene_variant,,ENST00000576613,;CTDNEP1,upstream_gene_variant,,ENST00000575783,;CTDNEP1,upstream_gene_variant,,ENST00000574322,;CTDNEP1,upstream_gene_variant,,ENST00000572043,;CTDNEP1,upstream_gene_variant,,ENST00000571409,;CTDNEP1,upstream_gene_variant,,ENST00000573600,;CTDNEP1,upstream_gene_variant,,ENST00000318988,;ELP5,upstream_gene_variant,,ENST00000572104,;ELP5,missense_variant,p.Arg8Leu,ENST00000571146,;RP1-4G17.5,intron_variant,,ENST00000577138,;CTDNEP1,upstream_gene_variant,,ENST00000574205,;CTDNEP1,upstream_gene_variant,,ENST00000570380,;	T	ENSG00000170291	ENST00000396628	Transcript	missense_variant	333	116	39	R/L	cGc/cTc	.	.	.	1	ELP5	HGNC	30617	protein_coding	YES	CCDS11094.1	ENSP00000379869	ELP5_HUMAN	I3NI50_HUMAN,I3L3N8_HUMAN,I3L2T0_HUMAN,I3L1A8_HUMAN	UPI000013E7B7	.	deleterious(0)	probably_damaging(1)	2/8	.	hmmpanther:PTHR15641,hmmpanther:PTHR15641:SF1,Pfam_domain:PF10483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGCAGTC	.	5	ESCA
TP53	0	.	GRCh37	17	7577595	7577595	+	Frame_Shift_Del	DEL	C	C	-	.	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686delG	p.Cys229LeufsTer18	p.C229Lfs*18	ENST00000269305	7/11	202	108	94	70	70	0	TP53,frameshift_variant,p.Cys229LeufsTer18,ENST00000413465,;TP53,frameshift_variant,p.Cys229LeufsTer18,ENST00000420246,;TP53,frameshift_variant,p.Cys229LeufsTer18,ENST00000269305,;TP53,frameshift_variant,p.Cys97LeufsTer18,ENST00000509690,;TP53,frameshift_variant,p.Cys229LeufsTer18,ENST00000359597,;TP53,frameshift_variant,p.Cys136LeufsTer18,ENST00000514944,;TP53,frameshift_variant,p.Cys229LeufsTer18,ENST00000445888,;TP53,frameshift_variant,p.Cys229LeufsTer18,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	876	686	229	C/X	tGt/tt	TP53_g.13323G>T,TP53_g.13323G>C,TP53_g.13323G>A,COSM44313,COSM45974,COSM308322,COSM308324,COSM308323,COSM308325	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.C229fs*10|c.686_687delGT|9,CODON|p.C229fs*10|c.686_687delGT|3,CODON|p.C229fs*10|c.686_687delGT|3,CODON|p.C136fs*10|c.407_408delGT|3,CODON|p.T230P|c.688A>C|4,CODON|p.C229*|c.687T>A|3,CODON|p.C229fs*10|c.685_686delTG|5,BUFFER|p.H233L|c.698A>T|3,BUFFER|p.H233Y|c.697C>T|6,BUFFER|p.I232T|c.695T>C|8,BUFFER|p.I232S|c.695T>G|5,BUFFER|p.I232S|c.695T>G|5,BUFFER|p.I232N|c.695T>A|6,BUFFER|p.I139S|c.416T>G|5,BUFFER|p.I232S|c.695T>G|7,BUFFER|p.I232F|c.694A>T|11,BUFFER|p.I232V|c.694A>G|5,BUFFER|p.I232F|c.694A>T|4,BUFFER|p.I232F|c.694A>T|4,BUFFER|p.I139F|c.415A>T|4,BUFFER|p.T231T|c.693C>T|5,BUFFER|p.T231T|c.693C>A|3,BUFFER|p.T231I|c.692C>T|3,BUFFER|p.T231S|c.691A>T|3,BUFFER|p.T230I|c.689C>T|9,BUFFER|p.D228D|c.684C>T|3,BUFFER|p.D228E|c.684C>G|4,BUFFER|p.D228G|c.683A>G|5,BUFFER|p.D228Y|c.682G>T|3,BUFFER|p.D228N|c.682G>A|6,BUFFER|p.S227F|c.680C>T|8,BUFFER|p.S227P|c.679T>C|3,BUFFER|p.S134P|c.400T>C|3,BUFFER|p.S227P|c.679T>C|3,BUFFER|p.S227P|c.679T>C|3,BUFFER|p.G226D|c.677G>A|5,BUFFER|p.G226V|c.677G>T|4	INDELOCATOR*|VARSCANI*|PINDEL	GTGGTACAGTCA	.	3	ESCA
GAS7	0	.	GRCh37	17	9814245	9814245	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000432992	.	26	19	7	18	18	0	GAS7,3_prime_UTR_variant,,ENST00000437099,;GAS7,3_prime_UTR_variant,,ENST00000323816,;GAS7,downstream_gene_variant,,ENST00000432992,;GAS7,downstream_gene_variant,,ENST00000540214,;GAS7,downstream_gene_variant,,ENST00000585266,;	G	ENSG00000007237	ENST00000432992	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2922	-1	GAS7	HGNC	4169	protein_coding	YES	CCDS11152.1	ENSP00000407552	GAS7_HUMAN	J3QS26_HUMAN,J3QLH8_HUMAN,J3KTK6_HUMAN,J3KTB1_HUMAN,J3KS47_HUMAN,B7Z1Q2_HUMAN	UPI00001B4B17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CATGAAAAATG	.	4	ESCA
CXXC1	0	.	GRCh37	18	47810910	47810911	+	In_Frame_Ins	INS	-	-	GCC	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1052_1054dupGGC	p.Arg351dup	p.R351dup	ENST00000412036	9/15	24	12	12	38	38	0	CXXC1,inframe_insertion,p.Arg199dup,ENST00000591474,;CXXC1,inframe_insertion,p.Arg347dup,ENST00000285106,;CXXC1,inframe_insertion,p.Arg347dup,ENST00000589940,;CXXC1,inframe_insertion,p.Arg351dup,ENST00000412036,;MBD1,upstream_gene_variant,,ENST00000585595,;MBD1,upstream_gene_variant,,ENST00000590208,;CXXC1,downstream_gene_variant,,ENST00000586837,;CXXC1,downstream_gene_variant,,ENST00000589548,;MBD1,upstream_gene_variant,,ENST00000398493,;MBD1,upstream_gene_variant,,ENST00000436910,;MBD1,upstream_gene_variant,,ENST00000353909,;MBD1,upstream_gene_variant,,ENST00000349085,;MBD1,upstream_gene_variant,,ENST00000398488,;MBD1,upstream_gene_variant,,ENST00000587605,;MBD1,upstream_gene_variant,,ENST00000588937,;MBD1,upstream_gene_variant,,ENST00000269471,;MBD1,upstream_gene_variant,,ENST00000347968,;MBD1,upstream_gene_variant,,ENST00000269468,;MBD1,upstream_gene_variant,,ENST00000398495,;MBD1,upstream_gene_variant,,ENST00000591535,;MBD1,upstream_gene_variant,,ENST00000339998,;MBD1,upstream_gene_variant,,ENST00000585672,;MBD1,upstream_gene_variant,,ENST00000457839,;MBD1,upstream_gene_variant,,ENST00000382948,;MBD1,upstream_gene_variant,,ENST00000591416,;MBD1,upstream_gene_variant,,ENST00000424334,;CXXC1,downstream_gene_variant,,ENST00000587396,;CXXC1,non_coding_transcript_exon_variant,,ENST00000591190,;CXXC1,non_coding_transcript_exon_variant,,ENST00000590901,;CXXC1,non_coding_transcript_exon_variant,,ENST00000590234,;CXXC1,non_coding_transcript_exon_variant,,ENST00000592078,;CXXC1,upstream_gene_variant,,ENST00000586568,;CXXC1,downstream_gene_variant,,ENST00000586365,;MBD1,upstream_gene_variant,,ENST00000589758,;CXXC1,upstream_gene_variant,,ENST00000587170,;CXXC1,upstream_gene_variant,,ENST00000586502,;CXXC1,upstream_gene_variant,,ENST00000586144,;CXXC1,upstream_gene_variant,,ENST00000587342,;MBD1,upstream_gene_variant,,ENST00000586118,;MBD1,upstream_gene_variant,,ENST00000589867,;MBD1,upstream_gene_variant,,ENST00000590215,;	GCC	ENSG00000154832	ENST00000412036	Transcript	inframe_insertion	1101-1102	1054-1055	352	H/RH	cat/cGGCat	.	.	.	-1	CXXC1	HGNC	24343	protein_coding	YES	CCDS45866.1	ENSP00000390475	CXXC1_HUMAN	K7EJR0_HUMAN	UPI0000169F65	.	.	.	9/15	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12321:SF33,hmmpanther:PTHR12321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCGATGCCGC	.	3	ESCA
SBSN	0	.	GRCh37	19	36018071	36018071	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1113G>A	p.%3D	p.G371G	ENST00000452271	1/4	124	82	41	132	132	0	SBSN,synonymous_variant,p.%3D,ENST00000452271,;SBSN,intron_variant,,ENST00000518157,;SBSN,intron_variant,,ENST00000588674,;	T	ENSG00000189001	ENST00000452271	Transcript	synonymous_variant	1142	1113	371	G	ggG/ggA	.	.	.	-1	SBSN	HGNC	24950	protein_coding	YES	CCDS54253.1	ENSP00000430242	SBSN_HUMAN	.	UPI000059D6E7	.	.	.	1/4	.	hmmpanther:PTHR23243,hmmpanther:PTHR23243:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACCCCATG	.	5	ESCA
SUPT5H	0	.	GRCh37	19	39963105	39963105	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2007C>T	p.%3D	p.I669I	ENST00000599117	22/31	80	51	28	73	73	0	SUPT5H,synonymous_variant,p.%3D,ENST00000359191,;SUPT5H,synonymous_variant,p.%3D,ENST00000432763,;SUPT5H,synonymous_variant,p.%3D,ENST00000598725,;SUPT5H,synonymous_variant,p.%3D,ENST00000402194,;SUPT5H,synonymous_variant,p.%3D,ENST00000599117,;SUPT5H,non_coding_transcript_exon_variant,,ENST00000599335,;SUPT5H,upstream_gene_variant,,ENST00000600818,;SUPT5H,downstream_gene_variant,,ENST00000596208,;SUPT5H,downstream_gene_variant,,ENST00000598117,;	T	ENSG00000196235	ENST00000599117	Transcript	synonymous_variant	2374	2007	669	I	atC/atT	.	.	.	1	SUPT5H	HGNC	11469	protein_coding	YES	CCDS12536.1	ENSP00000470252	SPT5H_HUMAN	M0R2M5_HUMAN,M0R105_HUMAN,B4E0Q4_HUMAN,B4DZJ7_HUMAN	UPI000006D81A	.	.	.	22/31	.	hmmpanther:PTHR11125,PIRSF_domain:PIRSF036945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGATCAGCAG	.	5	ESCA
ZNF600	0	.	GRCh37	19	53282087	53282087	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-26C>T	.	.	ENST00000338230	2/3	83	56	26	77	77	0	ZNF600,5_prime_UTR_variant,,ENST00000338230,;ZNF600,downstream_gene_variant,,ENST00000598369,;ZNF600,downstream_gene_variant,,ENST00000594028,;ZNF600,downstream_gene_variant,,ENST00000597124,;ZNF600,downstream_gene_variant,,ENST00000599893,;	A	ENSG00000189190	ENST00000338230	Transcript	5_prime_UTR_variant	243	.	.	.	.	.	.	.	-1	ZNF600	HGNC	30951	protein_coding	YES	CCDS12856.1	ENSP00000344791	ZN600_HUMAN	.	UPI0000366E5E	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAGAGCCA	.	5	ESCA
C3	0	.	GRCh37	19	6690725	6690725	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3404A>G	p.Asn1135Ser	p.N1135S	ENST00000245907	27/41	52	29	22	62	62	0	C3,missense_variant,p.Asn1135Ser,ENST00000245907,;C3,upstream_gene_variant,,ENST00000601008,;C3,non_coding_transcript_exon_variant,,ENST00000598805,;C3,upstream_gene_variant,,ENST00000596238,;	C	ENSG00000125730	ENST00000245907	Transcript	missense_variant	3497	3404	1135	N/S	aAc/aGc	.	.	.	-1	C3	HGNC	1318	protein_coding	YES	CCDS32883.1	ENSP00000245907	CO3_HUMAN	Q6LDJ0_HUMAN,M0R1Q1_HUMAN	UPI000013EC9B	.	tolerated(0.38)	benign(0)	27/41	.	hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF81,Pfam_domain:PF07678,Gene3D:1.50.10.20,Superfamily_domains:SSF48239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTGTTCCGT	.	5	ESCA
FRRS1	0	.	GRCh37	1	100207810	100207810	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.353G>A	p.Arg118Lys	p.R118K	ENST00000287474	5/17	35	20	15	36	36	0	FRRS1,missense_variant,p.Arg118Lys,ENST00000414213,;FRRS1,missense_variant,p.Arg118Lys,ENST00000287474,;	T	ENSG00000156869	ENST00000287474	Transcript	missense_variant	955	353	118	R/K	aGa/aAa	.	.	.	-1	FRRS1	HGNC	27622	protein_coding	YES	CCDS30780.1	ENSP00000287474	FRRS1_HUMAN	.	UPI000042037B	.	tolerated(0.05)	benign(0.023)	5/17	.	PROSITE_profiles:PS51019,hmmpanther:PTHR23130:SF6,hmmpanther:PTHR23130,Pfam_domain:PF02014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTTCTGTGA	.	5	ESCA
DPH5	0	.	GRCh37	1	101456046	101456046	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.776delT	p.Ile259AsnfsTer9	p.I259Nfs*9	ENST00000370109	8/8	105	76	29	63	63	0	DPH5,frameshift_variant,p.Ile20AsnfsTer9,ENST00000427040,;DPH5,frameshift_variant,p.Ile259AsnfsTer9,ENST00000488176,;AC093157.1,frameshift_variant,p.Met14CysfsTer5,ENST00000593496,;DPH5,frameshift_variant,p.Ile258AsnfsTer9,ENST00000342173,;DPH5,frameshift_variant,p.Ile259AsnfsTer9,ENST00000370109,;RP11-421L21.2,upstream_gene_variant,,ENST00000414686,;DPH5,non_coding_transcript_exon_variant,,ENST00000488789,;DPH5,non_coding_transcript_exon_variant,,ENST00000498372,;DPH5,non_coding_transcript_exon_variant,,ENST00000481871,;DPH5,non_coding_transcript_exon_variant,,ENST00000370105,;DPH5,non_coding_transcript_exon_variant,,ENST00000477293,;DPH5,non_coding_transcript_exon_variant,,ENST00000490732,;DPH5,non_coding_transcript_exon_variant,,ENST00000492067,;DPH5,non_coding_transcript_exon_variant,,ENST00000466807,;DPH5,non_coding_transcript_exon_variant,,ENST00000464270,;	-	ENSG00000117543	ENST00000370109	Transcript	frameshift_variant	889	776	259	I/X	aTa/aa	.	.	.	-1	DPH5	HGNC	24270	protein_coding	YES	CCDS41358.1	ENSP00000359127	DPH5_HUMAN	Q96DC6_HUMAN,B3KWP1_HUMAN	UPI000003B000	.	.	.	8/8	.	HAMAP:MF_01084,hmmpanther:PTHR10882,hmmpanther:PTHR10882:SF0,Gene3D:3.30.950.10,TIGRFAM_domain:TIGR00522,PIRSF_domain:PIRSF036432,Superfamily_domains:SSF53790	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGATGTATGCTG	.	3	ESCA
FAM63A	0	.	GRCh37	1	150978596	150978596	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36G>A	p.%3D	p.T12T	ENST00000361738	2/11	69	65	4	67	67	0	FAM63A,synonymous_variant,p.%3D,ENST00000361738,;FAM63A,intron_variant,,ENST00000312210,;FAM63A,intron_variant,,ENST00000493834,;FAM63A,intron_variant,,ENST00000361936,;PRUNE,upstream_gene_variant,,ENST00000431193,;PRUNE,upstream_gene_variant,,ENST00000368936,;PRUNE,upstream_gene_variant,,ENST00000368935,;PRUNE,upstream_gene_variant,,ENST00000368937,;PRUNE,upstream_gene_variant,,ENST00000271619,;PRUNE,upstream_gene_variant,,ENST00000271620,;PRUNE,upstream_gene_variant,,ENST00000450884,;FAM63A,intron_variant,,ENST00000470877,;PRUNE,upstream_gene_variant,,ENST00000475722,;PRUNE,upstream_gene_variant,,ENST00000462440,;PRUNE,upstream_gene_variant,,ENST00000467771,;	T	ENSG00000143409	ENST00000361738	Transcript	synonymous_variant	256	36	12	T	acG/acA	.	.	.	-1	FAM63A	HGNC	25648	protein_coding	YES	CCDS53361.1	ENSP00000354669	FA63A_HUMAN	.	UPI0001AE7915	.	.	.	2/11	.	hmmpanther:PTHR18063:SF7,hmmpanther:PTHR18063	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTTCGTGCT	.	2	ESCA
PI4KB	0	.	GRCh37	1	151278723	151278723	+	Silent	SNP	G	G	A	rs764752078	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1335C>T	p.%3D	p.P445P	ENST00000368875	6/13	69	32	37	52	52	0	PI4KB,synonymous_variant,p.%3D,ENST00000368874,;PI4KB,synonymous_variant,p.%3D,ENST00000529142,;PI4KB,synonymous_variant,p.%3D,ENST00000368873,;PI4KB,synonymous_variant,p.%3D,ENST00000430800,;PI4KB,synonymous_variant,p.%3D,ENST00000368872,;PI4KB,synonymous_variant,p.%3D,ENST00000271657,;PI4KB,synonymous_variant,p.%3D,ENST00000368875,;PI4KB,downstream_gene_variant,,ENST00000489223,;PI4KB,non_coding_transcript_exon_variant,,ENST00000460323,;PI4KB,upstream_gene_variant,,ENST00000469239,;	A	ENSG00000143393	ENST00000368875	Transcript	synonymous_variant	1916	1335	445	P	ccC/ccT	rs764752078	.	.	-1	PI4KB	HGNC	8984	protein_coding	YES	CCDS993.1	ENSP00000357869	PI4KB_HUMAN	F8W860_HUMAN,E9PL47_HUMAN,E9PIH4_HUMAN	UPI000007161F	.	.	.	6/13	.	hmmpanther:PTHR10048:SF22,hmmpanther:PTHR10048	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTCGGGCAA	byFrequency	5	ESCA
RGL1	0	.	GRCh37	1	183867029	183867029	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1333A>G	p.Met445Val	p.M445V	ENST00000304685	11/19	40	30	10	33	33	0	RGL1,missense_variant,p.Met445Val,ENST00000304685,;RGL1,missense_variant,p.Met410Val,ENST00000539189,;RGL1,missense_variant,p.Met408Val,ENST00000536277,;RGL1,missense_variant,p.Met410Val,ENST00000360851,;	G	ENSG00000143344	ENST00000304685	Transcript	missense_variant	1782	1333	445	M/V	Atg/Gtg	.	.	.	1	RGL1	HGNC	30281	protein_coding	YES	CCDS1359.1	ENSP00000303192	RGL1_HUMAN	.	UPI000002B24C	.	deleterious(0.03)	possibly_damaging(0.785)	11/19	.	Superfamily_domains:0041591,SMART_domains:SM00147,Pfam_domain:PF00617,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF199,PROSITE_profiles:PS50009	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGACATGGTA	.	5	ESCA
TMCO4	0	.	GRCh37	1	20066381	20066381	+	Missense_Mutation	SNP	A	A	C	rs772635020	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1115T>G	p.Val372Gly	p.V372G	ENST00000294543	12/16	61	38	23	36	36	0	TMCO4,missense_variant,p.Val372Gly,ENST00000375127,;TMCO4,missense_variant,p.Val372Gly,ENST00000294543,;TMCO4,missense_variant,p.Val332Gly,ENST00000375122,;TMCO4,non_coding_transcript_exon_variant,,ENST00000489135,;TMCO4,upstream_gene_variant,,ENST00000489814,;	C	ENSG00000162542	ENST00000294543	Transcript	missense_variant	1357	1115	372	V/G	gTg/gGg	rs772635020	.	.	-1	TMCO4	HGNC	27393	protein_coding	YES	CCDS198.1	ENSP00000294543	TMCO4_HUMAN	Q6ZSC6_HUMAN	UPI0000197EC6	.	deleterious(0)	probably_damaging(0.999)	12/16	.	Pfam_domain:PF05277,hmmpanther:PTHR17920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACACCCCC	.	5	ESCA
DNAH14	0	.	GRCh37	1	225155192	225155192	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558C>A	p.%3D	p.S186S	ENST00000400952	6/11	42	30	11	40	40	0	DNAH14,synonymous_variant,p.%3D,ENST00000400952,;DNAH14,synonymous_variant,p.%3D,ENST00000430092,;DNAH14,synonymous_variant,p.%3D,ENST00000439375,;DNAH14,synonymous_variant,p.%3D,ENST00000366848,;DNAH14,synonymous_variant,p.%3D,ENST00000366849,;DNAH14,synonymous_variant,p.%3D,ENST00000366850,;DNAH14,synonymous_variant,p.%3D,ENST00000433124,;DNAH14,synonymous_variant,p.%3D,ENST00000445597,;DNAH14,non_coding_transcript_exon_variant,,ENST00000453375,;DNAH14,non_coding_transcript_exon_variant,,ENST00000486657,;DNAH14,upstream_gene_variant,,ENST00000474127,;	A	ENSG00000185842	ENST00000400952	Transcript	synonymous_variant	760	558	186	S	tcC/tcA	.	.	.	1	DNAH14	HGNC	2945	protein_coding	YES	CCDS44322.1	ENSP00000383737	DYH14_HUMAN	C9JU64_HUMAN	UPI0000203FC8	.	.	.	6/11	.	hmmpanther:PTHR22645:SF1,hmmpanther:PTHR22645	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATCCCTTTA	.	5	ESCA
SFPQ	0	.	GRCh37	1	35658710	35658710	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-60G>A	.	.	ENST00000357214	1/10	15	9	6	15	15	0	SFPQ,5_prime_UTR_variant,,ENST00000357214,;Y_RNA,upstream_gene_variant,,ENST00000364998,;SFPQ,upstream_gene_variant,,ENST00000470472,;	T	ENSG00000116560	ENST00000357214	Transcript	5_prime_UTR_variant	40	.	.	.	.	.	.	.	-1	SFPQ	HGNC	10774	protein_coding	YES	CCDS388.1	ENSP00000349748	SFPQ_HUMAN	Q9BSV4_HUMAN	UPI00001358B9	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGCCACCT	.	5	ESCA
MOB3C	0	.	GRCh37	1	47074494	47074494	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*833A>G	.	.	ENST00000271139	4/4	24	19	5	27	27	0	MOB3C,3_prime_UTR_variant,,ENST00000371940,;MOB3C,3_prime_UTR_variant,,ENST00000271139,;MOB3C,3_prime_UTR_variant,,ENST00000319928,;MKNK1,intron_variant,,ENST00000545730,;MKNK1,intron_variant,,ENST00000531769,;MKNK1,upstream_gene_variant,,ENST00000371945,;MKNK1,upstream_gene_variant,,ENST00000529170,;MKNK1,upstream_gene_variant,,ENST00000371946,;MKNK1,upstream_gene_variant,,ENST00000428112,;MKNK1,upstream_gene_variant,,ENST00000496619,;MKNK1,upstream_gene_variant,,ENST00000341183,;MKNK1,upstream_gene_variant,,ENST00000525888,;MOB3C,downstream_gene_variant,,ENST00000477318,;MKNK1,upstream_gene_variant,,ENST00000526513,;MKNK1,upstream_gene_variant,,ENST00000531355,;MKNK1,upstream_gene_variant,,ENST00000468852,;MKNK1,upstream_gene_variant,,ENST00000528077,;	C	ENSG00000142961	ENST00000271139	Transcript	3_prime_UTR_variant	1697	.	.	.	.	.	.	.	-1	MOB3C	HGNC	29800	protein_coding	YES	CCDS539.1	ENSP00000271139	.	.	UPI000034ECBB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAATACAGG	.	5	ESCA
SGIP1	0	.	GRCh37	1	67108534	67108534	+	Silent	SNP	C	C	T	rs766048418	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.270C>T	p.%3D	p.P90P	ENST00000371037	6/25	41	33	8	41	41	0	SGIP1,synonymous_variant,p.%3D,ENST00000424320,;SGIP1,synonymous_variant,p.%3D,ENST00000237247,;SGIP1,synonymous_variant,p.%3D,ENST00000371039,;SGIP1,synonymous_variant,p.%3D,ENST00000371037,;SGIP1,synonymous_variant,p.%3D,ENST00000371036,;SGIP1,synonymous_variant,p.%3D,ENST00000371035,;SGIP1,non_coding_transcript_exon_variant,,ENST00000483060,;SGIP1,non_coding_transcript_exon_variant,,ENST00000468286,;	T	ENSG00000118473	ENST00000371037	Transcript	synonymous_variant	347	270	90	P	ccC/ccT	rs766048418	.	.	1	SGIP1	HGNC	25412	protein_coding	YES	CCDS30744.1	ENSP00000360076	SGIP1_HUMAN	.	UPI000045891B	.	.	.	6/25	.	hmmpanther:PTHR23065:SF5,hmmpanther:PTHR23065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGACCCGAGGA	.	2	ESCA
RPE65	0	.	GRCh37	1	68906589	68906589	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590G>T	p.Gly197Val	p.G197V	ENST00000262340	6/14	18	10	8	27	27	0	RPE65,missense_variant,p.Gly197Val,ENST00000262340,;	A	ENSG00000116745	ENST00000262340	Transcript	missense_variant	644	590	197	G/V	gGa/gTa	.	.	.	-1	RPE65	HGNC	10294	protein_coding	YES	CCDS643.1	ENSP00000262340	RPE65_HUMAN	Q2EKB8_HUMAN,C7FEP0_HUMAN	UPI000004346C	.	tolerated(0.08)	probably_damaging(1)	6/14	.	hmmpanther:PTHR10543,hmmpanther:PTHR10543:SF7,Pfam_domain:PF03055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTCCAAAG	.	5	ESCA
KRTAP11-1	0	.	GRCh37	21	32253537	32253537	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.307C>A	p.Pro103Thr	p.P103T	ENST00000332378	1/1	37	21	15	21	21	0	KRTAP11-1,missense_variant,p.Pro103Thr,ENST00000332378,;	T	ENSG00000182591	ENST00000332378	Transcript	missense_variant	338	307	103	P/T	Ccg/Acg	.	.	.	-1	KRTAP11-1	HGNC	18922	protein_coding	YES	CCDS13608.1	ENSP00000330720	KR111_HUMAN	.	UPI000003B46F	.	deleterious(0.01)	probably_damaging(1)	1/1	.	hmmpanther:PTHR19051:SF14,hmmpanther:PTHR19051,Pfam_domain:PF05287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCGGCCGGC	.	5	ESCA
CTA-992D9.6	0	.	GRCh37	22	27445847	27445847	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.642G>A	.	.	ENST00000453934	2/2	25	17	8	22	22	0	CTA-992D9.6,non_coding_transcript_exon_variant,,ENST00000453934,;	T	ENSG00000236858	ENST00000453934	Transcript	non_coding_transcript_exon_variant	642	.	.	.	.	.	.	.	-1	CTA-992D9.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCACGATGA	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098924	178098944	+	In_Frame_Del	DEL	GACTGAAGTCAAATACTTCTC	GACTGAAGTCAAATACTTCTC	-	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	GACTGAAGTCAAATACTTCTC	GACTGAAGTCAAATACTTCTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.101_121delGAGAAGTATTTGACTTCAGTC	p.Arg34_Ser40del	p.R34_S40del	ENST00000397062	2/5	67	19	48	56	56	0	NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000449627,;NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000423513,;NFE2L2,inframe_deletion,p.Arg34_Ser40del,ENST00000397062,;NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000446151,;NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000588123,;NFE2L2,inframe_deletion,p.Arg33_Ser39del,ENST00000586532,;NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000421929,;NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000464747,;NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000448782,;NFE2L2,inframe_deletion,p.Arg18_Ser24del,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	-	ENSG00000116044	ENST00000397062	Transcript	inframe_deletion	656-676	101-121	34-41	REVFDFSQ/Q	cGAGAAGTATTTGACTTCAGTCag/cag	.	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	.	.	2/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R34P|c.101G>C|3,BUFFER|p.R34Q|c.101G>A|11,BUFFER|p.R34G|c.100C>G|11,BUFFER|p.G31E|c.92G>A|5,BUFFER|p.G31A|c.92G>C|7	INDELOCATOR*|VARSCANI*|PINDEL	GTCGCTGACTGAAGTCAAATACTTCTCGACTT	.	3	ESCA
TTN	0	.	GRCh37	2	179588638	179588638	+	Silent	SNP	G	G	A	rs750661972	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21348C>T	p.%3D	p.C7116C	ENST00000589042	73/363	32	27	5	31	31	0	TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;RP11-171I2.1,non_coding_transcript_exon_variant,,ENST00000590024,;TTN-AS1,intron_variant,,ENST00000585451,;	A	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	21573	21348	7116	C	tgC/tgT	rs750661972	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	73/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACGCATGT	.	5	ESCA
GULP1	0	.	GRCh37	2	189454467	189454467	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843+1791C>T	.	.	ENST00000409580	.	53	17	36	61	60	1	GULP1,missense_variant,p.Arg282Cys,ENST00000409843,;GULP1,3_prime_UTR_variant,,ENST00000451191,;GULP1,intron_variant,,ENST00000409805,;GULP1,intron_variant,,ENST00000409609,;GULP1,intron_variant,,ENST00000359135,;GULP1,intron_variant,,ENST00000409830,;GULP1,intron_variant,,ENST00000409580,;GULP1,intron_variant,,ENST00000433052,;GULP1,intron_variant,,ENST00000478306,;GULP1,downstream_gene_variant,,ENST00000495745,;GULP1,non_coding_transcript_exon_variant,,ENST00000496976,;	T	ENSG00000144366	ENST00000409580	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GULP1	HGNC	18649	protein_coding	YES	CCDS2295.1	ENSP00000386289	GULP1_HUMAN	B8ZZL1_HUMAN	UPI0000031CE3	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAGCGCCAG	.	5	ESCA
C2orf88	0	.	GRCh37	2	191066949	191066949	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2075T>C	.	.	ENST00000340623	2/2	16	3	13	17	17	0	C2orf88,3_prime_UTR_variant,,ENST00000340623,;HIBCH,intron_variant,,ENST00000399855,;HIBCH,downstream_gene_variant,,ENST00000359678,;C2orf88,downstream_gene_variant,,ENST00000409870,;HIBCH,downstream_gene_variant,,ENST00000392332,;C2orf88,downstream_gene_variant,,ENST00000443551,;C2orf88,downstream_gene_variant,,ENST00000450357,;C2orf88,downstream_gene_variant,,ENST00000409545,;HIBCH,downstream_gene_variant,,ENST00000410045,;C2orf88,downstream_gene_variant,,ENST00000396974,;HIBCH,downstream_gene_variant,,ENST00000486981,;C2orf88,downstream_gene_variant,,ENST00000490033,;	C	ENSG00000187699	ENST00000340623	Transcript	3_prime_UTR_variant	2774	.	.	.	.	.	.	.	1	C2orf88	HGNC	28191	protein_coding	YES	CCDS42792.1	ENSP00000345107	SMAKA_HUMAN	H7BZ15_HUMAN,C9JS57_HUMAN	UPI000013D122	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTATACTTT	.	5	ESCA
ABI2	0	.	GRCh37	2	204255850	204255850	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544G>T	p.Gly182Trp	p.G182W	ENST00000261017	4/10	34	6	28	35	35	0	ABI2,missense_variant,p.Gly182Trp,ENST00000261017,;ABI2,missense_variant,p.Gly182Trp,ENST00000430418,;ABI2,missense_variant,p.Gly188Trp,ENST00000422511,;ABI2,missense_variant,p.Gly54Trp,ENST00000451591,;ABI2,missense_variant,p.Gly188Trp,ENST00000417864,;ABI2,missense_variant,p.Gly137Trp,ENST00000261016,;ABI2,missense_variant,p.Gly23Trp,ENST00000261018,;ABI2,missense_variant,p.Gly188Trp,ENST00000295851,;ABI2,missense_variant,p.Gly182Trp,ENST00000424558,;ABI2,missense_variant,p.Gly29Trp,ENST00000454023,;RAPH1,downstream_gene_variant,,ENST00000457812,;ABI2,non_coding_transcript_exon_variant,,ENST00000422719,;ABI2,non_coding_transcript_exon_variant,,ENST00000411547,;ABI2,non_coding_transcript_exon_variant,,ENST00000430574,;ABI2,upstream_gene_variant,,ENST00000416396,;ABI2,3_prime_UTR_variant,,ENST00000441061,;ABI2,intron_variant,,ENST00000416001,;	T	ENSG00000138443	ENST00000261017	Transcript	missense_variant	779	544	182	G/W	Ggg/Tgg	.	.	.	1	ABI2	HGNC	24011	protein_coding	YES	CCDS2358.1	ENSP00000261017	ABI2_HUMAN	Q53SH3_HUMAN,Q53RS4_HUMAN,B7ZAM8_HUMAN	UPI0000070712	.	deleterious(0)	probably_damaging(0.999)	4/10	.	hmmpanther:PTHR10460:SF3,hmmpanther:PTHR10460	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCAGGGAAA	.	5	ESCA
IDH1	0	.	GRCh37	2	209106806	209106806	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.762G>A	p.Met254Ile	p.M254I	ENST00000415913	7/10	39	34	5	33	33	0	IDH1,missense_variant,p.Met254Ile,ENST00000415913,;IDH1,missense_variant,p.Met254Ile,ENST00000345146,;IDH1,missense_variant,p.Met254Ile,ENST00000446179,;IDH1,downstream_gene_variant,,ENST00000415282,;IDH1,upstream_gene_variant,,ENST00000484575,;	T	ENSG00000138413	ENST00000415913	Transcript	missense_variant	1144	762	254	M/I	atG/atA	.	.	.	-1	IDH1	HGNC	5382	protein_coding	YES	CCDS2381.1	ENSP00000390265	IDHC_HUMAN	Q6FHQ6_HUMAN,Q0QER2_HUMAN,C9JLU6_HUMAN,C9JJE5_HUMAN,C9J4N6_HUMAN,B4DXS4_HUMAN	UPI000012D1B4	.	deleterious_low_confidence(0)	possibly_damaging(0.906)	7/10	.	Superfamily_domains:SSF53659,PIRSF_domain:PIRSF000108,Pfam_domain:PF00180,Gene3D:3.40.718.10,TIGRFAM_domain:TIGR00127,hmmpanther:PTHR11822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCACCATGTC	.	4	ESCA
CTDSP1	0	.	GRCh37	2	219267102	219267102	+	Missense_Mutation	SNP	G	G	C	rs779217801	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.352G>C	p.Val118Leu	p.V118L	ENST00000273062	4/7	64	20	43	73	73	0	CTDSP1,missense_variant,p.Val103Leu,ENST00000452977,;CTDSP1,missense_variant,p.Val118Leu,ENST00000273062,;CTDSP1,missense_variant,p.Val187Leu,ENST00000431127,;CTDSP1,missense_variant,p.Val119Leu,ENST00000428361,;CTDSP1,missense_variant,p.Val117Leu,ENST00000443891,;MIR26B,upstream_gene_variant,,ENST00000362251,;RP11-378A13.2,upstream_gene_variant,,ENST00000608367,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000491064,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000464255,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000473420,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000498160,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000488627,;CTDSP1,downstream_gene_variant,,ENST00000496785,;CTDSP1,downstream_gene_variant,,ENST00000492545,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000482272,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000494067,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000497677,;	C	ENSG00000144579	ENST00000273062	Transcript	missense_variant	688	352	118	V/L	Gtg/Ctg	rs779217801	.	.	1	CTDSP1	HGNC	21614	protein_coding	YES	CCDS2416.1	ENSP00000273062	CTDS1_HUMAN	.	UPI000013007C	.	deleterious(0.01)	benign(0.092)	4/7	.	Superfamily_domains:SSF56784,SMART_domains:SM00577,Pfam_domain:PF03031,TIGRFAM_domain:TIGR02251,Gene3D:3.40.50.1000,hmmpanther:PTHR12210:SF41,hmmpanther:PTHR12210,PROSITE_profiles:PS50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTGTGGAG	.	5	ESCA
HTR3E	0	.	GRCh37	3	183818349	183818349	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189G>A	p.%3D	p.V63V	ENST00000440596	1/7	157	130	26	76	76	0	HTR3E,synonymous_variant,p.%3D,ENST00000425359,;HTR3E,synonymous_variant,p.%3D,ENST00000440596,;HTR3E,synonymous_variant,p.%3D,ENST00000335304,;HTR3E,synonymous_variant,p.%3D,ENST00000436361,;HTR3E,synonymous_variant,p.%3D,ENST00000415389,;HTR3E,5_prime_UTR_variant,,ENST00000431041,;HTR3E-AS1,intron_variant,,ENST00000431427,;	A	ENSG00000186038	ENST00000440596	Transcript	synonymous_variant	189	189	63	V	gtG/gtA	.	.	.	1	HTR3E	HGNC	24005	protein_coding	YES	CCDS58871.1	ENSP00000406050	5HT3E_HUMAN	.	UPI000198CB5D	.	.	.	1/7	.	hmmpanther:PTHR18945:SF378,hmmpanther:PTHR18945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGTGTTTAA	.	5	ESCA
STAB1	0	.	GRCh37	3	52551965	52551965	+	Nonsense_Mutation	SNP	C	C	A	rs375629208	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4707C>A	p.Cys1569Ter	p.C1569*	ENST00000321725	45/69	25	12	13	30	30	0	STAB1,stop_gained,p.Cys1569Ter,ENST00000321725,;STAB1,non_coding_transcript_exon_variant,,ENST00000461325,;STAB1,upstream_gene_variant,,ENST00000462741,;STAB1,upstream_gene_variant,,ENST00000462681,;STAB1,upstream_gene_variant,,ENST00000481626,;	A	ENSG00000010327	ENST00000321725	Transcript	stop_gained	4783	4707	1569	C/*	tgC/tgA	rs375629208,COSM3408795	.	.	1	STAB1	HGNC	18628	protein_coding	YES	CCDS33768.1	ENSP00000312946	STAB1_HUMAN	.	UPI0000140C12	.	.	.	45/69	.	Superfamily_domains:SSF57196,SMART_domains:SM00181,Gene3D:2.10.25.10,hmmpanther:PTHR24038:SF2,hmmpanther:PTHR24038,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGCGACAC	byFrequency|byCluster	5	ESCA
FILIP1L	0	.	GRCh37	3	99567929	99567929	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2591C>A	p.Pro864His	p.P864H	ENST00000354552	5/6	67	38	29	78	78	0	FILIP1L,missense_variant,p.Pro440His,ENST00000487087,;FILIP1L,missense_variant,p.Pro864His,ENST00000354552,;FILIP1L,missense_variant,p.Pro864His,ENST00000331335,;FILIP1L,missense_variant,p.Pro624His,ENST00000383694,;FILIP1L,missense_variant,p.Pro624His,ENST00000471562,;FILIP1L,missense_variant,p.Pro624His,ENST00000495625,;CMSS1,intron_variant,,ENST00000421999,;CMSS1,intron_variant,,ENST00000463526,;FILIP1L,upstream_gene_variant,,ENST00000477258,;FILIP1L,intron_variant,,ENST00000476723,;CMSS1,intron_variant,,ENST00000496116,;CMSS1,intron_variant,,ENST00000491299,;	T	ENSG00000168386	ENST00000354552	Transcript	missense_variant	3062	2591	864	P/H	cCc/cAc	.	.	.	-1	FILIP1L	HGNC	24589	protein_coding	YES	CCDS43117.1	ENSP00000346560	FIL1L_HUMAN	C9JYJ6_HUMAN	UPI00001B24B2	.	deleterious(0)	probably_damaging(0.986)	5/6	.	hmmpanther:PTHR23166,hmmpanther:PTHR23166:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGGGAATC	.	5	ESCA
NOP14	0	.	GRCh37	4	2952919	2952928	+	Frame_Shift_Del	DEL	TTTCTTAACA	TTTCTTAACA	-	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	TTTCTTAACA	TTTCTTAACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915_924delTGTTAAGAAA	p.Val306GlnfsTer9	p.V306Qfs*9	ENST00000416614	7/18	60	42	18	64	64	0	NOP14,frameshift_variant,p.Val306GlnfsTer9,ENST00000416614,;NOP14,frameshift_variant,p.Val306GlnfsTer9,ENST00000398071,;NOP14,frameshift_variant,p.Val306GlnfsTer9,ENST00000502735,;NOP14,frameshift_variant,p.Val306GlnfsTer9,ENST00000314262,;NOP14-AS1,intron_variant,,ENST00000503709,;NOP14-AS1,downstream_gene_variant,,ENST00000515194,;NOP14-AS1,downstream_gene_variant,,ENST00000507702,;NOP14-AS1,downstream_gene_variant,,ENST00000505731,;	-	ENSG00000087269	ENST00000416614	Transcript	frameshift_variant	981-990	915-924	305-308	NVKK/X	aaTGTTAAGAAA/aa	.	.	.	-1	NOP14	HGNC	16821	protein_coding	YES	CCDS33945.1	ENSP00000405068	NOP14_HUMAN	.	UPI00001A9472	.	.	.	7/18	.	hmmpanther:PTHR23183,hmmpanther:PTHR23183:SF0,Pfam_domain:PF04147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTGGTTTCTTAACATTTTC	.	3	ESCA
LRPAP1	0	.	GRCh37	4	3514590	3514590	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*111G>A	.	.	ENST00000500728	8/8	45	42	3	25	25	0	LRPAP1,3_prime_UTR_variant,,ENST00000500728,;AL590235.1,upstream_gene_variant,,ENST00000593823,;LRPAP1,downstream_gene_variant,,ENST00000296325,;LRPAP1,downstream_gene_variant,,ENST00000515119,;LRPAP1,downstream_gene_variant,,ENST00000509198,;	T	ENSG00000163956	ENST00000500728	Transcript	3_prime_UTR_variant	1332	.	.	.	.	.	.	.	-1	LRPAP1	HGNC	6701	protein_coding	YES	CCDS3371.1	ENSP00000421922	AMRP_HUMAN	.	UPI00000354C2	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACACCCGTGCC	.	2	ESCA
EPB41L4A	0	.	GRCh37	5	111540178	111540178	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1270T>C	p.Tyr424His	p.Y424H	ENST00000261486	15/23	65	36	29	50	50	0	EPB41L4A,missense_variant,p.Tyr424His,ENST00000261486,;CTC-459M5.2,non_coding_transcript_exon_variant,,ENST00000505825,;CTC-459M5.2,non_coding_transcript_exon_variant,,ENST00000506875,;EPB41L4A,non_coding_transcript_exon_variant,,ENST00000507810,;EPB41L4A,non_coding_transcript_exon_variant,,ENST00000513333,;EPB41L4A,non_coding_transcript_exon_variant,,ENST00000515047,;	G	ENSG00000129595	ENST00000261486	Transcript	missense_variant	1547	1270	424	Y/H	Tac/Cac	.	.	.	-1	EPB41L4A	HGNC	13278	protein_coding	YES	CCDS43350.1	ENSP00000261486	E41LA_HUMAN	Q8NEH8_HUMAN	UPI000020C3F8	.	deleterious(0)	probably_damaging(0.983)	15/23	.	hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTAGAGTC	.	5	ESCA
KCNN2	0	.	GRCh37	5	113698694	113698694	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.222C>G	p.Asn74Lys	p.N74K	ENST00000512097	2/9	48	31	17	41	41	0	KCNN2,missense_variant,p.Asn74Lys,ENST00000512097,;KCNN2,missense_variant,p.Asn74Lys,ENST00000264773,;KCNN2,upstream_gene_variant,,ENST00000507750,;	G	ENSG00000080709	ENST00000512097	Transcript	missense_variant	1240	222	74	N/K	aaC/aaG	.	.	.	1	KCNN2	HGNC	6291	protein_coding	YES	CCDS4114.1	ENSP00000427120	KCNN2_HUMAN	.	UPI000013D56A	.	tolerated_low_confidence(0.36)	benign(0.026)	2/9	.	hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAACAACTC	.	5	ESCA
TNIP1	0	.	GRCh37	5	150443229	150443229	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216G>T	p.%3D	p.L72L	ENST00000389378	3/18	107	65	41	89	89	0	TNIP1,synonymous_variant,p.%3D,ENST00000522100,;TNIP1,synonymous_variant,p.%3D,ENST00000518977,;TNIP1,synonymous_variant,p.%3D,ENST00000523200,;TNIP1,synonymous_variant,p.%3D,ENST00000523338,;TNIP1,synonymous_variant,p.%3D,ENST00000520931,;TNIP1,synonymous_variant,p.%3D,ENST00000524280,;TNIP1,synonymous_variant,p.%3D,ENST00000315050,;TNIP1,synonymous_variant,p.%3D,ENST00000522226,;TNIP1,synonymous_variant,p.%3D,ENST00000520695,;TNIP1,synonymous_variant,p.%3D,ENST00000389378,;TNIP1,synonymous_variant,p.%3D,ENST00000521001,;TNIP1,synonymous_variant,p.%3D,ENST00000521591,;TNIP1,synonymous_variant,p.%3D,ENST00000519339,;	A	ENSG00000145901	ENST00000389378	Transcript	synonymous_variant	805	216	72	L	ctG/ctT	.	.	.	-1	TNIP1	HGNC	16903	protein_coding	YES	CCDS34280.1	ENSP00000374029	TNIP1_HUMAN	E7EWG2_HUMAN,E7EW68_HUMAN,E7EW15_HUMAN,B7Z5B0_HUMAN,A4F1X2_HUMAN,A4F1W8_HUMAN	UPI000000DCDC	.	.	.	3/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31882:SF3,hmmpanther:PTHR31882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAGCAGCTC	.	5	ESCA
ENPP3	0	.	GRCh37	6	132054857	132054857	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2083C>G	p.Pro695Ala	p.P695A	ENST00000414305	22/26	49	35	13	29	29	0	ENPP3,missense_variant,p.Pro695Ala,ENST00000357639,;ENPP3,missense_variant,p.Pro695Ala,ENST00000414305,;ENPP3,intron_variant,,ENST00000358229,;	G	ENSG00000154269	ENST00000414305	Transcript	missense_variant	2411	2083	695	P/A	Cct/Gct	.	.	.	1	ENPP3	HGNC	3358	protein_coding	YES	CCDS5148.1	ENSP00000406261	ENPP3_HUMAN	Q9UNI4_HUMAN,Q9NQM9_HUMAN,Q9H515_HUMAN,F5GY67_HUMAN	UPI000013DD9F	.	deleterious(0)	probably_damaging(0.999)	22/26	.	hmmpanther:PTHR10151:SF55,hmmpanther:PTHR10151,Gene3D:1g8tA00,SMART_domains:SM00892,SMART_domains:SM00477,Superfamily_domains:SSF54060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTATCCTCCT	.	5	ESCA
SYNE1	0	.	GRCh37	6	152614873	152614873	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17862G>C	p.Lys5954Asn	p.K5954N	ENST00000367255	95/146	45	42	3	36	36	0	SYNE1,missense_variant,p.Lys478Asn,ENST00000356820,;SYNE1,missense_variant,p.Lys129Asn,ENST00000540663,;SYNE1,missense_variant,p.Lys5883Asn,ENST00000423061,;SYNE1,missense_variant,p.Lys5883Asn,ENST00000448038,;SYNE1,missense_variant,p.Lys176Asn,ENST00000537033,;SYNE1,missense_variant,p.Lys5954Asn,ENST00000367255,;SYNE1,missense_variant,p.Lys5566Asn,ENST00000341594,;SYNE1,missense_variant,p.Lys5954Asn,ENST00000265368,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,;SYNE1,non_coding_transcript_exon_variant,,ENST00000489156,;	G	ENSG00000131018	ENST00000367255	Transcript	missense_variant	18464	17862	5954	K/N	aaG/aaC	.	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	probably_damaging(0.959)	95/146	.	Superfamily_domains:SSF46966,Superfamily_domains:SSF46966,SMART_domains:SM00150,Gene3D:1.20.58.60,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCTGCTTCTC	.	2	ESCA
KIAA0319	0	.	GRCh37	6	24566850	24566850	+	Missense_Mutation	SNP	C	C	T	rs749156433	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2267G>A	p.Arg756Gln	p.R756Q	ENST00000378214	14/21	21	11	10	13	13	0	KIAA0319,missense_variant,p.Arg756Gln,ENST00000543707,;KIAA0319,missense_variant,p.Arg711Gln,ENST00000430948,;KIAA0319,missense_variant,p.Arg756Gln,ENST00000378214,;KIAA0319,missense_variant,p.Arg747Gln,ENST00000535378,;KIAA0319,missense_variant,p.Arg756Gln,ENST00000537886,;	T	ENSG00000137261	ENST00000378214	Transcript	missense_variant	2792	2267	756	R/Q	cGg/cAg	rs749156433,COSM1193400	.	.	-1	KIAA0319	HGNC	21580	protein_coding	YES	CCDS34348.1	ENSP00000367459	K0319_HUMAN	.	UPI000020D61A	.	deleterious(0)	probably_damaging(0.958)	14/21	.	Superfamily_domains:SSF49299,SMART_domains:SM00060,SMART_domains:SM00089,Gene3D:2.60.40.670,hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF194	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R756L|c.2267G>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCCCGGATC	.	5	ESCA
HIST1H2BH	0	.	GRCh37	6	26252252	26252252	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.374C>G	p.Ser125Cys	p.S125C	ENST00000356350	1/1	40	19	20	77	77	0	HIST1H2BH,missense_variant,p.Ser125Cys,ENST00000356350,;HIST1H4G,upstream_gene_variant,,ENST00000244537,;HIST1H3F,upstream_gene_variant,,ENST00000446824,;	G	ENSG00000197459	ENST00000356350	Transcript	missense_variant	374	374	125	S/C	tCc/tGc	.	.	.	1	HIST1H2BH	HGNC	4755	protein_coding	YES	CCDS4601.1	ENSP00000348706	H2B1H_HUMAN	.	UPI0000001BD4	.	deleterious_low_confidence(0)	probably_damaging(0.968)	1/1	.	hmmpanther:PTHR23428,Gene3D:1.10.20.10,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCCAAAT	.	5	ESCA
DPP6	0	.	GRCh37	7	153584641	153584641	+	5'UTR	DEL	T	T	-	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-120delT	.	.	ENST00000404039	1/26	19	13	6	25	25	0	DPP6,5_prime_UTR_variant,,ENST00000404039,;	-	ENSG00000130226	ENST00000404039	Transcript	5_prime_UTR_variant	460	.	.	.	.	.	.	.	1	DPP6	HGNC	3010	protein_coding	.	.	ENSP00000385578	.	Q75MI8_HUMAN,Q75MI7_HUMAN,Q75MF0_HUMAN,E9PF59_HUMAN	UPI000022D4BA	.	.	.	1/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGAAGATTTTTT	.	2	ESCA
POU6F2	0	.	GRCh37	7	39247015	39247015	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.307G>A	p.Ala103Thr	p.A103T	ENST00000403058	5/11	27	24	3	28	28	0	POU6F2,missense_variant,p.Ala95Thr,ENST00000520104,;POU6F2,missense_variant,p.Ala104Thr,ENST00000451021,;POU6F2,missense_variant,p.Ala103Thr,ENST00000403058,;POU6F2,missense_variant,p.Ala95Thr,ENST00000559001,;POU6F2,missense_variant,p.Ala95Thr,ENST00000524147,;POU6F2,missense_variant,p.Ala103Thr,ENST00000518318,;POU6F2,non_coding_transcript_exon_variant,,ENST00000517348,;	A	ENSG00000106536	ENST00000403058	Transcript	missense_variant	461	307	103	A/T	Gct/Act	.	.	.	1	POU6F2	HGNC	21694	protein_coding	YES	CCDS34620.2	ENSP00000384004	PO6F2_HUMAN	H0YL15_HUMAN	UPI0000480E81	.	deleterious(0.01)	probably_damaging(0.98)	5/11	.	hmmpanther:PTHR11636:SF68,hmmpanther:PTHR11636	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTTAGCTTCT	.	4	ESCA
CYTH3	0	.	GRCh37	7	6210543	6210543	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.629G>A	p.Arg210His	p.R210H	ENST00000350796	8/13	75	52	23	75	75	0	CYTH3,missense_variant,p.Arg125His,ENST00000396741,;CYTH3,missense_variant,p.Arg210His,ENST00000350796,;Y_RNA,downstream_gene_variant,,ENST00000458975,;CYTH3,non_coding_transcript_exon_variant,,ENST00000488964,;CYTH3,non_coding_transcript_exon_variant,,ENST00000461891,;CYTH3,non_coding_transcript_exon_variant,,ENST00000491641,;CYTH3,upstream_gene_variant,,ENST00000465320,;CYTH3,non_coding_transcript_exon_variant,,ENST00000466543,;CYTH3,non_coding_transcript_exon_variant,,ENST00000495176,;CYTH3,downstream_gene_variant,,ENST00000478541,;CYTH3,downstream_gene_variant,,ENST00000481329,;	T	ENSG00000008256	ENST00000350796	Transcript	missense_variant	766	629	210	R/H	cGt/cAt	.	.	.	-1	CYTH3	HGNC	9504	protein_coding	YES	CCDS5346.1	ENSP00000297044	CYH3_HUMAN	Q96HS5_HUMAN	UPI000002A7A1	.	deleterious(0)	probably_damaging(0.972)	8/13	.	PROSITE_profiles:PS50190,hmmpanther:PTHR10663:SF129,hmmpanther:PTHR10663,Pfam_domain:PF01369,Gene3D:1.10.1000.11,SMART_domains:SM00222,Superfamily_domains:SSF48425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCACGCACG	.	5	ESCA
FBXO43	0	.	GRCh37	8	101146049	101146049	+	Missense_Mutation	SNP	C	C	T	rs202056051	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2108G>A	p.Arg703Gln	p.R703Q	ENST00000428847	5/5	25	17	8	37	37	0	FBXO43,missense_variant,p.Arg703Gln,ENST00000428847,;RGS22,upstream_gene_variant,,ENST00000520117,;FBXO43,3_prime_UTR_variant,,ENST00000517806,;FBXO43,downstream_gene_variant,,ENST00000520987,;	T	ENSG00000156509	ENST00000428847	Transcript	missense_variant	2425	2108	703	R/Q	cGg/cAg	rs202056051,COSM1094274,COSM1094273,COSM1094272	.	.	-1	FBXO43	HGNC	28521	protein_coding	YES	CCDS47904.1	ENSP00000403293	FBX43_HUMAN	.	UPI000013DE8F	.	tolerated(0.06)	benign(0.337)	5/5	.	hmmpanther:PTHR15493:SF1,hmmpanther:PTHR15493	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTCCGCTTA	byCluster	5	ESCA
SLC7A2	0	.	GRCh37	8	17424379	17424379	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1724G>A	.	.	ENST00000004531	12/12	9	4	5	9	9	0	SLC7A2,3_prime_UTR_variant,,ENST00000494857,;SLC7A2,3_prime_UTR_variant,,ENST00000470360,;SLC7A2,3_prime_UTR_variant,,ENST00000398090,;SLC7A2,3_prime_UTR_variant,,ENST00000004531,;SLC7A2,downstream_gene_variant,,ENST00000522656,;	A	ENSG00000003989	ENST00000004531	Transcript	3_prime_UTR_variant	3869	.	.	.	.	.	.	.	1	SLC7A2	HGNC	11060	protein_coding	YES	CCDS55203.1	ENSP00000004531	CTR2_HUMAN	.	UPI0001A336A4	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCGTGTAATC	.	2	ESCA
PNOC	0	.	GRCh37	8	28196578	28196578	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148G>A	p.Glu50Lys	p.E50K	ENST00000301908	3/4	27	9	18	43	43	0	PNOC,missense_variant,p.Glu50Lys,ENST00000301908,;PNOC,missense_variant,p.Glu50Lys,ENST00000518479,;PNOC,5_prime_UTR_variant,,ENST00000522209,;RP11-380I10.4,non_coding_transcript_exon_variant,,ENST00000521731,;PNOC,non_coding_transcript_exon_variant,,ENST00000519592,;	A	ENSG00000168081	ENST00000301908	Transcript	missense_variant	356	148	50	E/K	Gag/Aag	.	.	.	1	PNOC	HGNC	9163	protein_coding	YES	CCDS6066.1	ENSP00000301908	PNOC_HUMAN	Q9BYY3_HUMAN,E7EVP0_HUMAN,B7Z749_HUMAN	UPI0000131D53	.	tolerated(0.11)	benign(0.029)	3/4	.	Prints_domain:PR01028,Prints_domain:PR01031,Pfam_domain:PF01160,PROSITE_patterns:PS01252,hmmpanther:PTHR11438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAGAGAAG	.	5	ESCA
UNC5D	0	.	GRCh37	8	35425616	35425616	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.323G>T	p.Gly108Val	p.G108V	ENST00000404895	3/17	49	27	21	56	56	0	UNC5D,missense_variant,p.Gly103Val,ENST00000453357,;UNC5D,missense_variant,p.Gly108Val,ENST00000416672,;UNC5D,missense_variant,p.Gly108Val,ENST00000404895,;UNC5D,missense_variant,p.Gly108Val,ENST00000287272,;UNC5D,missense_variant,p.Gly108Val,ENST00000420357,;	T	ENSG00000156687	ENST00000404895	Transcript	missense_variant	651	323	108	G/V	gGt/gTt	.	.	.	1	UNC5D	HGNC	18634	protein_coding	YES	CCDS6093.2	ENSP00000385143	UNC5D_HUMAN	.	UPI00001D6915	.	deleterious(0.01)	probably_damaging(0.999)	3/17	.	hmmpanther:PTHR12582:SF5,hmmpanther:PTHR12582,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCAGGTTTGA	.	5	ESCA
RAB2A	0	.	GRCh37	8	61496839	61496839	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259G>A	p.Asp87Asn	p.D87N	ENST00000262646	4/8	52	40	11	64	64	0	RAB2A,missense_variant,p.Asp87Asn,ENST00000529579,;RAB2A,missense_variant,p.Asp63Asn,ENST00000531289,;RAB2A,missense_variant,p.Asp87Asn,ENST00000262646,;RAB2A,upstream_gene_variant,,ENST00000452437,;RAB2A,non_coding_transcript_exon_variant,,ENST00000530071,;RAB2A,missense_variant,p.Arg103Gln,ENST00000466595,;RAB2A,3_prime_UTR_variant,,ENST00000534260,;RAB2A,non_coding_transcript_exon_variant,,ENST00000525529,;RAB2A,non_coding_transcript_exon_variant,,ENST00000429861,;	A	ENSG00000104388	ENST00000262646	Transcript	missense_variant	610	259	87	D/N	Gat/Aat	COSM606089	.	.	1	RAB2A	HGNC	9763	protein_coding	YES	CCDS6175.1	ENSP00000262646	RAB2A_HUMAN	.	UPI0000133168	.	deleterious(0)	probably_damaging(1)	4/8	.	Superfamily_domains:SSF52540,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00176,SMART_domains:SM00175,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF359,PROSITE_profiles:PS51419	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTACGATATT	.	5	ESCA
OR13C9	0	.	GRCh37	9	107379528	107379528	+	3'Flank	SNP	T	T	C	rs75210881	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000259362	.	128	94	34	88	88	0	OR13C9,downstream_gene_variant,,ENST00000259362,;	C	ENSG00000136839	ENST00000259362	Transcript	downstream_gene_variant	.	.	.	.	.	rs75210881	.	1	-1	OR13C9	HGNC	15104	protein_coding	YES	CCDS35093.1	ENSP00000259362	O13C9_HUMAN	Q8NGV4_HUMAN	UPI0000041D56	.	.	.	.	.	.	C:0.0004	C:0.0015	C:0	.	C:0	C:0	C:0	C:0	C:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCATTCACT	byFrequency|byCluster|by1000G	5	ESCA
FOXD4	0	.	GRCh37	9	117909	117909	+	Missense_Mutation	SNP	C	C	T	rs752872307	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211G>A	p.Glu71Lys	p.E71K	ENST00000382500	1/1	196	178	18	248	248	0	FOXD4,missense_variant,p.Glu71Lys,ENST00000382500,;CBWD1,downstream_gene_variant,,ENST00000382447,;CBWD1,downstream_gene_variant,,ENST00000314367,;CBWD1,downstream_gene_variant,,ENST00000377400,;CBWD1,downstream_gene_variant,,ENST00000356521,;RP11-143M1.4,upstream_gene_variant,,ENST00000416242,;CBWD1,downstream_gene_variant,,ENST00000475411,;CBWD1,downstream_gene_variant,,ENST00000465014,;CBWD1,downstream_gene_variant,,ENST00000475990,;CBWD1,downstream_gene_variant,,ENST00000487575,;CBWD1,downstream_gene_variant,,ENST00000464198,;CBWD1,downstream_gene_variant,,ENST00000462513,;CBWD1,downstream_gene_variant,,ENST00000495302,;	T	ENSG00000170122	ENST00000382500	Transcript	missense_variant	509	211	71	E/K	Gag/Aag	rs752872307	.	.	-1	FOXD4	HGNC	3805	protein_coding	YES	CCDS34975.1	ENSP00000371940	FOXD4_HUMAN	.	UPI00001AFF18	.	tolerated(0.06)	benign(0.174)	1/1	.	hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF149	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCCTCGATGT	.	3	ESCA
AK8	0	.	GRCh37	9	135702310	135702310	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.688A>G	p.Ile230Val	p.I230V	ENST00000298545	8/13	104	81	23	79	79	0	AK8,missense_variant,p.Ile230Val,ENST00000298545,;AK8,non_coding_transcript_exon_variant,,ENST00000477396,;AK8,non_coding_transcript_exon_variant,,ENST00000476719,;	C	ENSG00000165695	ENST00000298545	Transcript	missense_variant	1210	688	230	I/V	Att/Gtt	.	.	.	-1	AK8	HGNC	26526	protein_coding	YES	CCDS6954.1	ENSP00000298545	KAD8_HUMAN	.	UPI0000071236	.	tolerated(0.21)	benign(0.055)	8/13	.	hmmpanther:PTHR23359:SF64,hmmpanther:PTHR23359,Gene3D:3.40.50.300,Pfam_domain:PF00406,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAATGACCC	.	5	ESCA
AK8	0	.	GRCh37	9	135750508	135750508	+	Missense_Mutation	SNP	C	C	T	rs376201961	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163G>A	p.Asp55Asn	p.D55N	ENST00000298545	2/13	145	101	44	65	65	0	AK8,missense_variant,p.Asp55Asn,ENST00000298545,;C9orf9,upstream_gene_variant,,ENST00000372136,;C9orf9,upstream_gene_variant,,ENST00000350499,;C9orf9,upstream_gene_variant,,ENST00000356311,;AK8,non_coding_transcript_exon_variant,,ENST00000477396,;AK8,intron_variant,,ENST00000476719,;	T	ENSG00000165695	ENST00000298545	Transcript	missense_variant	685	163	55	D/N	Gac/Aac	rs376201961	.	.	-1	AK8	HGNC	26526	protein_coding	YES	CCDS6954.1	ENSP00000298545	KAD8_HUMAN	.	UPI0000071236	.	tolerated(0.06)	benign(0.008)	2/13	.	hmmpanther:PTHR23359:SF64,hmmpanther:PTHR23359,Gene3D:3.40.50.300	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTCGTTGT	byFrequency|byCluster	5	ESCA
EHMT1	0	.	GRCh37	9	140657246	140657246	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621A>C	p.Met541Leu	p.M541L	ENST00000460843	10/27	85	22	63	64	64	0	EHMT1,missense_variant,p.Met510Leu,ENST00000334856,;EHMT1,missense_variant,p.Met541Leu,ENST00000462484,;EHMT1,missense_variant,p.Met541Leu,ENST00000460843,;EHMT1,non_coding_transcript_exon_variant,,ENST00000465566,;EHMT1,non_coding_transcript_exon_variant,,ENST00000371394,;EHMT1,missense_variant,p.Met160Leu,ENST00000462942,;	C	ENSG00000181090	ENST00000460843	Transcript	missense_variant	1648	1621	541	M/L	Atg/Ctg	.	.	.	1	EHMT1	HGNC	24650	protein_coding	YES	CCDS7050.2	ENSP00000417980	EHMT1_HUMAN	Q71M33_HUMAN,A0PJE0_HUMAN	UPI000194EC2D	.	deleterious(0)	benign(0.066)	10/27	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCATGGCT	.	5	ESCA
LINGO2	0	.	GRCh37	9	27948528	27948529	+	3'UTR	INS	-	-	T	rs199562923	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*320dupA	.	.	ENST00000379992	6/6	19	4	15	20	20	0	LINGO2,3_prime_UTR_variant,,ENST00000379992,;LINGO2,downstream_gene_variant,,ENST00000308675,;RP11-438B23.2,upstream_gene_variant,,ENST00000566293,;	T	ENSG00000174482	ENST00000379992	Transcript	3_prime_UTR_variant	2591-2592	.	.	.	.	rs199562923	.	.	-1	LINGO2	HGNC	21207	protein_coding	YES	CCDS6524.1	ENSP00000369328	LIGO2_HUMAN	.	UPI000004C7CD	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTTTGTTTTT	byCluster|by1000G	2	ESCA
MAMDC2	0	.	GRCh37	9	72783711	72783711	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498G>C	p.Glu500Gln	p.E500Q	ENST00000377182	10/14	45	30	14	32	32	0	MAMDC2,missense_variant,p.Glu500Gln,ENST00000377182,;MAMDC2-AS1,intron_variant,,ENST00000591368,;MAMDC2-AS1,intron_variant,,ENST00000377178,;MAMDC2-AS1,downstream_gene_variant,,ENST00000448377,;MAMDC2-AS1,downstream_gene_variant,,ENST00000535188,;MAMDC2-AS1,downstream_gene_variant,,ENST00000420573,;MAMDC2,splice_region_variant,,ENST00000460688,;	C	ENSG00000165072	ENST00000377182	Transcript	missense_variant	2115	1498	500	E/Q	Gag/Cag	.	.	.	1	MAMDC2	HGNC	23673	protein_coding	YES	CCDS6631.1	ENSP00000366387	MAMC2_HUMAN	.	UPI000013E44F	.	tolerated(0.42)	benign(0.179)	10/14	.	hmmpanther:PTHR23282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCAGGTAAG	.	5	ESCA
TLE1	0	.	GRCh37	9	84268949	84268949	+	Silent	SNP	A	A	C	rs771286660	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237T>G	p.%3D	p.T79T	ENST00000376499	5/20	20	16	4	26	26	0	TLE1,synonymous_variant,p.%3D,ENST00000376499,;TLE1,synonymous_variant,p.%3D,ENST00000376463,;TLE1,synonymous_variant,p.%3D,ENST00000418319,;TLE1,splice_region_variant,,ENST00000376472,;	C	ENSG00000196781	ENST00000376499	Transcript	synonymous_variant	1302	237	79	T	acT/acG	rs771286660	.	.	-1	TLE1	HGNC	11837	protein_coding	YES	CCDS6661.1	ENSP00000365682	TLE1_HUMAN	.	UPI0000137034	.	.	.	5/20	.	Pfam_domain:PF03920,hmmpanther:PTHR10814	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCAGTCTA	.	5	ESCA
UBE2NL	0	.	GRCh37	X	142968056	142968056	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*392G>C	.	.	ENST00000370494	1/1	41	8	33	50	50	0	UBE2NL,3_prime_UTR_variant,,ENST00000370494,;	C	ENSG00000102069	ENST00000370494	Transcript	3_prime_UTR_variant	884	.	.	.	.	.	.	.	1	UBE2NL	HGNC	31710	protein_coding	YES	CCDS35420.1	ENSP00000359525	UE2NL_HUMAN	.	UPI0000070C39	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATGGGCTC	.	5	ESCA
MIR514A2	0	.	GRCh37	X	146363520	146363520	+	RNA	SNP	A	A	C	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.29T>G	.	.	ENST00000385131	1/1	28	14	14	22	22	0	MIR514A2,mature_miRNA_variant,,ENST00000385131,;MIR514A3,downstream_gene_variant,,ENST00000385132,;MIR514A1,upstream_gene_variant,,ENST00000385133,;	C	ENSG00000207866	ENST00000385131	Transcript	mature_miRNA_variant	29	.	.	.	.	.	.	.	-1	MIR514A2	HGNC	32149	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TTGTCACTCTC	.	3	ESCA
DMD	0	.	GRCh37	X	31139625	31139625	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A5U5-01A-21D-A28B-09	TCGA-LN-A5U5-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*411G>T	.	.	ENST00000357033	79/79	20	8	11	36	36	0	DMD,3_prime_UTR_variant,,ENST00000357033,;DMD,3_prime_UTR_variant,,ENST00000358062,;DMD,3_prime_UTR_variant,,ENST00000378723,;DMD,3_prime_UTR_variant,,ENST00000343523,;DMD,3_prime_UTR_variant,,ENST00000378707,;DMD,3_prime_UTR_variant,,ENST00000474231,;DMD,3_prime_UTR_variant,,ENST00000378677,;DMD,3_prime_UTR_variant,,ENST00000359836,;DMD,3_prime_UTR_variant,,ENST00000541735,;DMD,3_prime_UTR_variant,,ENST00000378702,;DMD,downstream_gene_variant,,ENST00000378680,;DMD,downstream_gene_variant,,ENST00000361471,;DMD,intron_variant,,ENST00000481143,;	A	ENSG00000198947	ENST00000357033	Transcript	3_prime_UTR_variant	11676	.	.	.	.	.	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	.	79/79	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAGCACACTTT	.	4	ESCA
SLK	0	.	GRCh37	10	105762560	105762560	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1624A>T	p.Ile542Phe	p.I542F	ENST00000369755	9/19	31	21	10	27	27	0	SLK,missense_variant,p.Ile542Phe,ENST00000369755,;SLK,missense_variant,p.Ile542Phe,ENST00000335753,;	T	ENSG00000065613	ENST00000369755	Transcript	missense_variant	2169	1624	542	I/F	Atc/Ttc	.	.	.	1	SLK	HGNC	11088	protein_coding	YES	CCDS7553.1	ENSP00000358770	SLK_HUMAN	.	UPI000004B6D3	.	deleterious(0.03)	benign(0.258)	9/19	.	hmmpanther:PTHR24361:SF53,hmmpanther:PTHR24361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGATCAGC	.	5	ESCA
FAM45A	0	.	GRCh37	10	120871395	120871395	+	Missense_Mutation	SNP	A	A	T	rs371713194	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287A>T	p.Asp96Val	p.D96V	ENST00000361432	3/9	26	22	3	33	33	0	FAM45A,missense_variant,p.Asp96Val,ENST00000535029,;FAM45A,missense_variant,p.Asp96Val,ENST00000361432,;FAM45A,5_prime_UTR_variant,,ENST00000544016,;FAM45A,non_coding_transcript_exon_variant,,ENST00000493766,;FAM45A,non_coding_transcript_exon_variant,,ENST00000487888,;FAM45A,intron_variant,,ENST00000448258,;FAM45A,upstream_gene_variant,,ENST00000489988,;FAM45A,downstream_gene_variant,,ENST00000497903,;	T	ENSG00000119979	ENST00000361432	Transcript	missense_variant	313	287	96	D/V	gAt/gTt	rs371713194,COSM465337	.	.	1	FAM45A	HGNC	31793	protein_coding	YES	CCDS7609.1	ENSP00000354688	FA45A_HUMAN	.	UPI0000071DBA	.	deleterious(0)	probably_damaging(0.955)	3/9	.	.	.	.	.	.	.	.	.	G:0	G:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAAAGATTTTA	byCluster	3	ESCA
ADAM12	0	.	GRCh37	10	127705709	127705709	+	3'UTR	SNP	C	C	T	rs557444468	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*139G>A	.	.	ENST00000368679	23/23	25	18	6	25	25	0	ADAM12,3_prime_UTR_variant,,ENST00000368679,;	T	ENSG00000148848	ENST00000368679	Transcript	3_prime_UTR_variant	3179	.	.	.	.	rs557444468	.	.	-1	ADAM12	HGNC	190	protein_coding	YES	CCDS7653.1	ENSP00000357668	ADA12_HUMAN	.	UPI000036672C	.	.	.	23/23	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGACGGCAG	by1000G	5	ESCA
SPRN	0	.	GRCh37	10	135278425	135278425	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16-41224T>C	.	.	ENST00000541506	.	28	17	10	36	36	0	SPRN,intron_variant,,ENST00000541506,;RP11-108K14.4,non_coding_transcript_exon_variant,,ENST00000488261,;RP11-108K14.4,non_coding_transcript_exon_variant,,ENST00000482993,;RP11-108K14.4,non_coding_transcript_exon_variant,,ENST00000462252,;RP11-108K14.4,intron_variant,,ENST00000463137,;RP11-108K14.4,upstream_gene_variant,,ENST00000475114,;RP11-108K14.4,non_coding_transcript_exon_variant,,ENST00000356567,;	G	ENSG00000203772	ENST00000541506	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SPRN	HGNC	16871	protein_coding	YES	CCDS53589.1	ENSP00000443979	SPRN_HUMAN	.	UPI0000251EE8	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATTACCTGT	.	5	ESCA
CYP2E1	0	.	GRCh37	10	135345740	135345740	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600G>T	p.Met200Ile	p.M200I	ENST00000463117	6/11	21	14	7	29	29	0	CYP2E1,missense_variant,p.Met63Ile,ENST00000418356,;CYP2E1,missense_variant,p.Met113Ile,ENST00000421586,;CYP2E1,missense_variant,p.Met200Ile,ENST00000463117,;CYP2E1,missense_variant,p.Met200Ile,ENST00000252945,;SPRN,intron_variant,,ENST00000541506,;CYP2E1,downstream_gene_variant,,ENST00000541261,;AL161645.2,upstream_gene_variant,,ENST00000599428,;CYP2E1,intron_variant,,ENST00000477500,;CYP2E1,downstream_gene_variant,,ENST00000480558,;CYP2E1,non_coding_transcript_exon_variant,,ENST00000368520,;CYP2E1,intron_variant,,ENST00000541080,;	T	ENSG00000130649	ENST00000463117	Transcript	missense_variant	872	600	200	M/I	atG/atT	.	.	.	1	CYP2E1	HGNC	2631	protein_coding	YES	CCDS7686.1	ENSP00000440689	CP2E1_HUMAN	Q4LBD0_HUMAN,F5H694_HUMAN	UPI0000128291	.	tolerated(0.38)	possibly_damaging(0.482)	6/11	.	hmmpanther:PTHR24300:SF19,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGATGTATTT	.	5	ESCA
ITIH5	0	.	GRCh37	10	7628031	7628031	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941C>A	p.Thr314Asn	p.T314N	ENST00000256861	8/14	100	66	33	59	59	0	ITIH5,missense_variant,p.Thr314Asn,ENST00000397146,;ITIH5,missense_variant,p.Thr96Asn,ENST00000446830,;ITIH5,missense_variant,p.Thr100Asn,ENST00000298441,;ITIH5,missense_variant,p.Thr314Asn,ENST00000256861,;ITIH5,missense_variant,p.Thr314Asn,ENST00000397145,;ITIH5,splice_region_variant,,ENST00000434980,;ITIH5,splice_region_variant,,ENST00000461751,;ITIH5,splice_region_variant,,ENST00000476417,;	T	ENSG00000123243	ENST00000256861	Transcript	missense_variant	1020	941	314	T/N	aCc/aAc	.	.	.	-1	ITIH5	HGNC	21449	protein_coding	YES	.	ENSP00000256861	ITIH5_HUMAN	.	UPI00001F8AF3	.	deleterious(0)	probably_damaging(0.918)	8/14	.	PROSITE_profiles:PS50234,hmmpanther:PTHR10338:SF62,hmmpanther:PTHR10338,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGGTCTAG	.	5	ESCA
OR10G7	0	.	GRCh37	11	123908903	123908903	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806G>C	p.Gly269Ala	p.G269A	ENST00000330487	1/1	99	46	52	105	105	0	OR10G7,missense_variant,p.Gly269Ala,ENST00000330487,;	G	ENSG00000182634	ENST00000330487	Transcript	missense_variant	815	806	269	G/A	gGg/gCg	.	.	.	-1	OR10G7	HGNC	14842	protein_coding	YES	CCDS31705.1	ENSP00000329689	O10G7_HUMAN	.	UPI0000040A84	.	tolerated(0.54)	benign(0.05)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF7,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACCCCATGC	.	5	ESCA
SERGEF	0	.	GRCh37	11	17809891	17809891	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118G>C	p.Trp373Ser	p.W373S	ENST00000265965	11/11	46	34	12	35	35	0	SERGEF,missense_variant,p.Trp237Ser,ENST00000529151,;SERGEF,missense_variant,p.Trp373Ser,ENST00000265965,;SERGEF,3_prime_UTR_variant,,ENST00000528200,;SERGEF,3_prime_UTR_variant,,ENST00000525920,;SERGEF,non_coding_transcript_exon_variant,,ENST00000528369,;SERGEF,non_coding_transcript_exon_variant,,ENST00000524589,;SERGEF,non_coding_transcript_exon_variant,,ENST00000531299,;SERGEF,non_coding_transcript_exon_variant,,ENST00000529440,;SERGEF,non_coding_transcript_exon_variant,,ENST00000531926,;SERGEF,3_prime_UTR_variant,,ENST00000527494,;SERGEF,3_prime_UTR_variant,,ENST00000525422,;SERGEF,3_prime_UTR_variant,,ENST00000532546,;	G	ENSG00000129158	ENST00000265965	Transcript	missense_variant	1270	1118	373	W/S	tGg/tCg	.	.	.	-1	SERGEF	HGNC	17499	protein_coding	YES	CCDS7828.1	ENSP00000265965	SRGEF_HUMAN	E9PS70_HUMAN,E9PR50_HUMAN	UPI000007326C	.	tolerated(0.24)	benign(0.173)	11/11	.	Superfamily_domains:SSF50985,Pfam_domain:PF00415,Gene3D:2.130.10.30,hmmpanther:PTHR22870,hmmpanther:PTHR22870:SF7,PROSITE_profiles:PS50012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCCAGACG	.	5	ESCA
MRGPRX1	0	.	GRCh37	11	18955619	18955619	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.713T>C	p.Leu238Pro	p.L238P	ENST00000302797	1/1	83	62	21	71	71	0	MRGPRX1,missense_variant,p.Leu238Pro,ENST00000302797,;RP11-583F24.8,upstream_gene_variant,,ENST00000528646,;MRGPRX1,downstream_gene_variant,,ENST00000526914,;	G	ENSG00000170255	ENST00000302797	Transcript	missense_variant	938	713	238	L/P	cTa/cCa	.	.	.	-1	MRGPRX1	HGNC	17962	protein_coding	YES	CCDS7846.1	ENSP00000305766	MRGX1_HUMAN	.	UPI000003BCCF	.	deleterious(0.02)	possibly_damaging(0.648)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF22,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F237F|c.711C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATAGGAAA	.	5	ESCA
NAV2	0	.	GRCh37	11	20066599	20066599	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3354C>A	p.%3D	p.G1118G	ENST00000396087	15/41	38	24	13	41	41	0	NAV2,synonymous_variant,p.%3D,ENST00000360655,;NAV2,synonymous_variant,p.%3D,ENST00000525322,;NAV2,synonymous_variant,p.%3D,ENST00000533917,;NAV2,synonymous_variant,p.%3D,ENST00000527559,;NAV2,synonymous_variant,p.%3D,ENST00000349880,;NAV2,synonymous_variant,p.%3D,ENST00000396087,;NAV2,synonymous_variant,p.%3D,ENST00000396085,;NAV2,synonymous_variant,p.%3D,ENST00000540292,;NAV2,synonymous_variant,p.%3D,ENST00000311043,;NAV2,downstream_gene_variant,,ENST00000530408,;NAV2-AS2,intron_variant,,ENST00000533767,;NAV2,downstream_gene_variant,,ENST00000526675,;NAV2,downstream_gene_variant,,ENST00000534299,;	A	ENSG00000166833	ENST00000396087	Transcript	synonymous_variant	3453	3354	1118	G	ggC/ggA	.	.	.	1	NAV2	HGNC	15997	protein_coding	YES	CCDS58126.1	ENSP00000379396	NAV2_HUMAN	.	UPI00001E0580	.	.	.	15/41	.	hmmpanther:PTHR12784:SF6,hmmpanther:PTHR12784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGCCGGAG	.	5	ESCA
OR5D13	0	.	GRCh37	11	55541412	55541412	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499G>A	p.Asp167Asn	p.D167N	ENST00000361760	1/1	54	43	10	48	48	0	OR5D13,missense_variant,p.Asp167Asn,ENST00000361760,;	A	ENSG00000198877	ENST00000361760	Transcript	missense_variant	499	499	167	D/N	Gac/Aac	.	.	.	1	OR5D13	HGNC	15280	protein_coding	YES	CCDS31507.1	ENSP00000354800	OR5DD_HUMAN	.	UPI0000041C36	.	tolerated(0.2)	benign(0)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF210,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTGACTTA	.	5	ESCA
ZFP91	0	.	GRCh37	11	58384886	58384886	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1420G>T	p.Asp474Tyr	p.D474Y	ENST00000316059	11/11	32	7	24	34	34	0	ZFP91,missense_variant,p.Asp474Tyr,ENST00000316059,;ZFP91-CNTF,missense_variant,p.Asp474Tyr,ENST00000389919,;ZFP91-CNTF,missense_variant,p.Asp301Tyr,ENST00000422974,;	T	ENSG00000186660	ENST00000316059	Transcript	missense_variant	1591	1420	474	D/Y	Gat/Tat	COSM295967,COSM295966	.	.	1	ZFP91	HGNC	14983	protein_coding	YES	CCDS31553.1	ENSP00000339030	ZFP91_HUMAN	B4DIN6_HUMAN	UPI0000070D45	.	deleterious_low_confidence(0)	possibly_damaging(0.898)	11/11	.	hmmpanther:PTHR11389:SF437,hmmpanther:PTHR11389	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACAGATATC	.	5	ESCA
IL18BP	0	.	GRCh37	11	71713012	71713012	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*105G>A	.	.	ENST00000404792	5/5	51	44	7	26	26	0	IL18BP,3_prime_UTR_variant,,ENST00000393705,;IL18BP,3_prime_UTR_variant,,ENST00000393707,;IL18BP,3_prime_UTR_variant,,ENST00000497194,;IL18BP,3_prime_UTR_variant,,ENST00000404792,;IL18BP,3_prime_UTR_variant,,ENST00000260049,;IL18BP,3_prime_UTR_variant,,ENST00000393703,;IL18BP,3_prime_UTR_variant,,ENST00000337131,;RNF121,downstream_gene_variant,,ENST00000361756,;NUMA1,downstream_gene_variant,,ENST00000393695,;RNF121,downstream_gene_variant,,ENST00000530137,;NUMA1,downstream_gene_variant,,ENST00000541584,;NUMA1,downstream_gene_variant,,ENST00000351960,;NUMA1,downstream_gene_variant,,ENST00000358965,;RNF121,downstream_gene_variant,,ENST00000545854,;IL18BP,downstream_gene_variant,,ENST00000531053,;RNF121,downstream_gene_variant,,ENST00000393713,;IL18BP,downstream_gene_variant,,ENST00000531777,;NUMA1,downstream_gene_variant,,ENST00000541262,;IL18BP,downstream_gene_variant,,ENST00000414358,;IL18BP,downstream_gene_variant,,ENST00000525932,;IL18BP,3_prime_UTR_variant,,ENST00000343898,;IL18BP,intron_variant,,ENST00000534583,;NUMA1,downstream_gene_variant,,ENST00000545721,;RNF121,downstream_gene_variant,,ENST00000526549,;NUMA1,downstream_gene_variant,,ENST00000540626,;	A	ENSG00000137496	ENST00000404792	Transcript	3_prime_UTR_variant	1612	.	.	.	.	.	.	.	1	IL18BP	HGNC	5987	protein_coding	YES	CCDS8206.2	ENSP00000384212	I18BP_HUMAN	Q9UNH2_HUMAN	UPI000000DA78	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATGCGCAACA	.	4	ESCA
DIP2B	0	.	GRCh37	12	51064999	51064999	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.458C>T	p.Ser153Phe	p.S153F	ENST00000301180	5/38	46	29	17	42	42	0	DIP2B,missense_variant,p.Ser153Phe,ENST00000301180,;DIP2B,non_coding_transcript_exon_variant,,ENST00000549620,;DIP2B,non_coding_transcript_exon_variant,,ENST00000546719,;	T	ENSG00000066084	ENST00000301180	Transcript	missense_variant	492	458	153	S/F	tCt/tTt	.	.	.	1	DIP2B	HGNC	29284	protein_coding	YES	CCDS31799.1	ENSP00000301180	DIP2B_HUMAN	Q96IB4_HUMAN	UPI0000406CA1	.	deleterious(0.01)	possibly_damaging(0.786)	5/38	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22754:SF22,hmmpanther:PTHR22754	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTCTCTGA	.	5	ESCA
CD9	0	.	GRCh37	12	6309666	6309667	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2dupT	p.Met1?	p.M1?	ENST00000382518	2/9	96	74	22	64	64	0	CD9,frameshift_variant,p.Met1?,ENST00000009180,;CD9,frameshift_variant,p.Met1?,ENST00000382518,;CD9,frameshift_variant,p.Met1?,ENST00000382519,;CD9,frameshift_variant,p.Met1?,ENST00000536586,;CD9,upstream_gene_variant,,ENST00000382515,;CD9,non_coding_transcript_exon_variant,,ENST00000538834,;CD9,non_coding_transcript_exon_variant,,ENST00000546073,;CD9,non_coding_transcript_exon_variant,,ENST00000538418,;CD9,intron_variant,,ENST00000543916,;	T	ENSG00000010278	ENST00000382518	Transcript	frameshift_variant	437-438	1-2	1	M/IX	atg/aTtg	.	.	.	1	CD9	HGNC	1709	protein_coding	YES	CCDS8540.1	ENSP00000371958	CD9_HUMAN	F5GXT1_HUMAN,B4DPP0_HUMAN,A6NNI4_HUMAN	UPI000003B45A	.	.	.	2/9	.	hmmpanther:PTHR19282:SF163,hmmpanther:PTHR19282,PIRSF_domain:PIRSF002419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCACCATGCCG	.	3	ESCA
ACSS3	0	.	GRCh37	12	81536947	81536947	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.842A>T	p.Gln281Leu	p.Q281L	ENST00000548058	5/16	51	31	20	59	59	0	ACSS3,missense_variant,p.Gln280Leu,ENST00000261206,;ACSS3,missense_variant,p.Gln281Leu,ENST00000548058,;ACSS3,non_coding_transcript_exon_variant,,ENST00000548387,;	T	ENSG00000111058	ENST00000548058	Transcript	missense_variant	1752	842	281	Q/L	cAg/cTg	.	.	.	1	ACSS3	HGNC	24723	protein_coding	YES	CCDS9022.1	ENSP00000449535	ACSS3_HUMAN	F8VZB4_HUMAN	UPI000007060A	.	tolerated(0.23)	benign(0.122)	5/16	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF0,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCAGTCAC	.	5	ESCA
RIMKLB	0	.	GRCh37	12	8904626	8904626	+	Silent	SNP	G	G	A	rs750088977	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.480G>A	p.%3D	p.T160T	ENST00000357529	5/7	92	69	23	100	100	0	RIMKLB,synonymous_variant,p.%3D,ENST00000357529,;RIMKLB,synonymous_variant,p.%3D,ENST00000535829,;RIMKLB,synonymous_variant,p.%3D,ENST00000538135,;RIMKLB,downstream_gene_variant,,ENST00000541044,;RIMKLB,downstream_gene_variant,,ENST00000539923,;RIMKLB,downstream_gene_variant,,ENST00000537189,;RIMKLB,non_coding_transcript_exon_variant,,ENST00000299673,;RIMKLB,synonymous_variant,p.%3D,ENST00000544257,;	A	ENSG00000166532	ENST00000357529	Transcript	synonymous_variant	1742	480	160	T	acG/acA	rs750088977,COSM1364735	.	.	1	RIMKLB	HGNC	29228	protein_coding	YES	CCDS41748.1	ENSP00000350136	RIMKB_HUMAN	F5H3V4_HUMAN,F5GZH5_HUMAN	UPI000013E5D1	.	.	.	5/7	.	PROSITE_profiles:PS50975,hmmpanther:PTHR21621,hmmpanther:PTHR21621:SF5,Pfam_domain:PF08443,TIGRFAM_domain:TIGR00768,Gene3D:3.30.1490.20,Superfamily_domains:SSF56059	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T160M|c.479C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATACGCGGGG	byFrequency	5	ESCA
BTG1	0	.	GRCh37	12	92539233	92539234	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78_79insT	p.Arg27SerfsTer27	p.R27Sfs*27	ENST00000256015	1/2	94	62	32	37	37	0	BTG1,frameshift_variant,p.Arg27SerfsTer27,ENST00000256015,;BTG1,upstream_gene_variant,,ENST00000552315,;C12orf79,upstream_gene_variant,,ENST00000549802,;C12orf79,upstream_gene_variant,,ENST00000551563,;C12orf79,upstream_gene_variant,,ENST00000546975,;RP11-796E2.4,upstream_gene_variant,,ENST00000501008,;RP11-796E2.4,upstream_gene_variant,,ENST00000499685,;C12orf79,upstream_gene_variant,,ENST00000551843,;C12orf79,upstream_gene_variant,,ENST00000553207,;C12orf79,upstream_gene_variant,,ENST00000552106,;C12orf79,upstream_gene_variant,,ENST00000548552,;	A	ENSG00000133639	ENST00000256015	Transcript	frameshift_variant	440-441	78-79	26-27	-/X	-/T	.	.	.	-1	BTG1	HGNC	1130	protein_coding	YES	CCDS9043.1	ENSP00000256015	BTG1_HUMAN	Q6IBC8_HUMAN,F8W0U7_HUMAN	UPI00000246C2	.	.	.	1/2	.	Prints_domain:PR00310,Superfamily_domains:SSF160696,SMART_domains:SM00099,Pfam_domain:PF07742,hmmpanther:PTHR22978:SF23,hmmpanther:PTHR22978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTGCGGAGAA	.	3	ESCA
NTN4	0	.	GRCh37	12	96180836	96180836	+	Missense_Mutation	SNP	G	G	A	rs748350808	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.466C>T	p.Pro156Ser	p.P156S	ENST00000343702	2/10	54	41	13	46	46	0	NTN4,missense_variant,p.Pro119Ser,ENST00000344911,;NTN4,missense_variant,p.Pro119Ser,ENST00000538383,;NTN4,missense_variant,p.Pro156Ser,ENST00000553059,;NTN4,missense_variant,p.Pro156Ser,ENST00000343702,;NTN4,missense_variant,p.Pro119Ser,ENST00000547980,;	A	ENSG00000074527	ENST00000343702	Transcript	missense_variant	915	466	156	P/S	Cct/Tct	rs748350808	.	.	-1	NTN4	HGNC	13658	protein_coding	YES	CCDS9054.1	ENSP00000340998	NET4_HUMAN	F8W0I7_HUMAN	UPI0000049824	.	deleterious(0.04)	possibly_damaging(0.61)	2/10	.	PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF260,Pfam_domain:PF00055,SMART_domains:SM00136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAGGCTTCC	byFrequency	5	ESCA
NTN4	0	.	GRCh37	12	96180837	96180837	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.465G>T	p.Lys155Asn	p.K155N	ENST00000343702	2/10	53	40	13	46	46	0	NTN4,missense_variant,p.Lys118Asn,ENST00000344911,;NTN4,missense_variant,p.Lys118Asn,ENST00000538383,;NTN4,missense_variant,p.Lys155Asn,ENST00000553059,;NTN4,missense_variant,p.Lys155Asn,ENST00000343702,;NTN4,missense_variant,p.Lys118Asn,ENST00000547980,;	A	ENSG00000074527	ENST00000343702	Transcript	missense_variant	914	465	155	K/N	aaG/aaT	.	.	.	-1	NTN4	HGNC	13658	protein_coding	YES	CCDS9054.1	ENSP00000340998	NET4_HUMAN	F8W0I7_HUMAN	UPI0000049824	.	deleterious(0.04)	possibly_damaging(0.456)	2/10	.	PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF260,Pfam_domain:PF00055,SMART_domains:SM00136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGGCTTCCA	.	5	ESCA
MYO16	0	.	GRCh37	13	109704676	109704676	+	Missense_Mutation	SNP	G	G	T	rs762837452	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2835G>T	p.Leu945Phe	p.L945F	ENST00000356711	25/35	67	57	10	31	31	0	MYO16,missense_variant,p.Leu457Phe,ENST00000457511,;MYO16,missense_variant,p.Leu945Phe,ENST00000356711,;MYO16,missense_variant,p.Leu945Phe,ENST00000357550,;MYO16,downstream_gene_variant,,ENST00000251041,;MYO16,non_coding_transcript_exon_variant,,ENST00000375857,;	T	ENSG00000041515	ENST00000356711	Transcript	missense_variant	2961	2835	945	L/F	ttG/ttT	rs762837452	.	.	1	MYO16	HGNC	29822	protein_coding	YES	CCDS32008.1	ENSP00000349145	MYO16_HUMAN	.	UPI0000160FF2	.	deleterious(0.01)	possibly_damaging(0.582)	25/35	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF345,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S948S|c.2844G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTGTTCCA	.	5	ESCA
RP11-556N21.1	0	.	GRCh37	13	25161430	25161430	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.954C>G	.	.	ENST00000453498	8/13	136	89	47	148	148	0	RP11-556N21.1,non_coding_transcript_exon_variant,,ENST00000453498,;TPTE2P6,non_coding_transcript_exon_variant,,ENST00000440905,;TPTE2P6,non_coding_transcript_exon_variant,,ENST00000450973,;TPTE2P6,non_coding_transcript_exon_variant,,ENST00000445572,;	G	ENSG00000243008	ENST00000453498	Transcript	non_coding_transcript_exon_variant	954	.	.	.	.	.	.	.	1	RP11-556N21.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	8/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACTCTTTAT	.	5	ESCA
MTUS2	0	.	GRCh37	13	29675068	29675068	+	Missense_Mutation	SNP	G	G	T	rs372355162	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2635G>T	p.Gly879Trp	p.G879W	ENST00000431530	3/14	81	51	29	38	38	0	MTUS2,missense_variant,p.Gly879Trp,ENST00000431530,;MTUS2,non_coding_transcript_exon_variant,,ENST00000255289,;	T	ENSG00000132938	ENST00000431530	Transcript	missense_variant	2693	2635	879	G/W	Ggg/Tgg	rs372355162	.	.	1	MTUS2	HGNC	20595	protein_coding	YES	CCDS45022.1	ENSP00000392057	.	J3KQA9_HUMAN,B4DWQ4_HUMAN	UPI0000F734AC	.	tolerated(0.12)	possibly_damaging(0.548)	3/14	.	hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCCGGGGAC	.	5	ESCA
ZAR1L	0	.	GRCh37	13	32877982	32877982	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*34C>T	.	.	ENST00000533490	6/6	24	17	7	31	31	0	ZAR1L,3_prime_UTR_variant,,ENST00000345108,;ZAR1L,3_prime_UTR_variant,,ENST00000533490,;	A	ENSG00000189167	ENST00000533490	Transcript	3_prime_UTR_variant	1419	.	.	.	.	.	.	.	-1	ZAR1L	HGNC	37116	protein_coding	YES	CCDS45023.1	ENSP00000437289	ZAR1L_HUMAN	.	UPI00006C1387	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAGCTCAG	.	5	ESCA
FREM2	0	.	GRCh37	13	39438423	39438423	+	Missense_Mutation	SNP	G	G	A	rs200997496	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7663G>A	p.Val2555Met	p.V2555M	ENST00000280481	16/24	28	23	4	37	37	0	FREM2,missense_variant,p.Val2555Met,ENST00000280481,;	A	ENSG00000150893	ENST00000280481	Transcript	missense_variant	7879	7663	2555	V/M	Gtg/Atg	rs200997496	.	.	1	FREM2	HGNC	25396	protein_coding	YES	CCDS31960.1	ENSP00000280481	FREM2_HUMAN	.	UPI00005520B9	.	deleterious(0.01)	benign(0.231)	16/24	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF19	T:0.0006	T:0	T:0	.	T:0	T:0	T:0.0031	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCGTGATC	byFrequency|byCluster|by1000G	5	ESCA
KLC1	0	.	GRCh37	14	104139456	104139456	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1093G>A	p.Ala365Thr	p.A365T	ENST00000452929	8/16	43	33	10	45	45	0	KLC1,missense_variant,p.Ala365Thr,ENST00000246489,;KLC1,missense_variant,p.Ala365Thr,ENST00000348520,;KLC1,missense_variant,p.Ala365Thr,ENST00000452929,;KLC1,missense_variant,p.Ala365Thr,ENST00000380038,;KLC1,missense_variant,p.Ala365Thr,ENST00000557575,;RP11-73M18.2,missense_variant,p.Ala537Thr,ENST00000472726,;KLC1,missense_variant,p.Ala363Thr,ENST00000445352,;KLC1,missense_variant,p.Ala365Thr,ENST00000553286,;KLC1,missense_variant,p.Ala365Thr,ENST00000557450,;KLC1,missense_variant,p.Ala365Thr,ENST00000554280,;KLC1,missense_variant,p.Ala365Thr,ENST00000555836,;KLC1,missense_variant,p.Ala365Thr,ENST00000347839,;KLC1,missense_variant,p.Ala365Thr,ENST00000334553,;KLC1,missense_variant,p.Ala365Thr,ENST00000389744,;KLC1,upstream_gene_variant,,ENST00000555856,;KLC1,upstream_gene_variant,,ENST00000537046,;KLC1,upstream_gene_variant,,ENST00000553325,;KLC1,upstream_gene_variant,,ENST00000553436,;KLC1,missense_variant,p.Ala365Thr,ENST00000554228,;	A	ENSG00000126214	ENST00000452929	Transcript	missense_variant	1348	1093	365	A/T	Gcc/Acc	.	.	.	1	KLC1	HGNC	6387	protein_coding	YES	CCDS45168.1	ENSP00000414982	KLC1_HUMAN	Q7Z5D5_HUMAN,G3V2P7_HUMAN	UPI0000E23AFA	.	deleterious(0)	probably_damaging(0.999)	8/16	.	PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR19959,hmmpanther:PTHR19959:SF129,PROSITE_patterns:PS01160,Gene3D:1.25.40.10,Pfam_domain:PF13424,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGAGCCCTC	.	5	ESCA
EXD2	0	.	GRCh37	14	69701701	69701701	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1002C>A	p.Asp334Glu	p.D334E	ENST00000409018	5/9	35	11	24	30	30	0	EXD2,missense_variant,p.Asp209Glu,ENST00000449989,;EXD2,missense_variant,p.Asp334Glu,ENST00000409018,;EXD2,missense_variant,p.Asp209Glu,ENST00000409014,;EXD2,missense_variant,p.Asp209Glu,ENST00000409949,;EXD2,missense_variant,p.Asp209Glu,ENST00000409242,;EXD2,missense_variant,p.Asp334Glu,ENST00000312994,;EXD2,missense_variant,p.Asp209Glu,ENST00000409675,;EXD2,downstream_gene_variant,,ENST00000413191,;RP11-363J20.2,downstream_gene_variant,,ENST00000556316,;EXD2,non_coding_transcript_exon_variant,,ENST00000492815,;EXD2,downstream_gene_variant,,ENST00000494629,;EXD2,downstream_gene_variant,,ENST00000489133,;EXD2,upstream_gene_variant,,ENST00000465286,;	A	ENSG00000081177	ENST00000409018	Transcript	missense_variant	1130	1002	334	D/E	gaC/gaA	.	.	.	1	EXD2	HGNC	20217	protein_coding	YES	CCDS53902.1	ENSP00000387331	EXD2_HUMAN	C9JLF4_HUMAN	UPI0000577ED7	.	tolerated(0.06)	possibly_damaging(0.55)	5/9	.	hmmpanther:PTHR13620:SF0,hmmpanther:PTHR13620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGACCCCAG	.	5	ESCA
SLC12A1	0	.	GRCh37	15	48595067	48595067	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3285G>C	p.Leu1095Phe	p.L1095F	ENST00000396577	27/27	36	26	10	47	47	0	SLC12A1,missense_variant,p.Leu1095Phe,ENST00000558405,;SLC12A1,missense_variant,p.Leu1095Phe,ENST00000396577,;SLC12A1,missense_variant,p.Leu1095Phe,ENST00000380993,;SLC12A1,non_coding_transcript_exon_variant,,ENST00000560692,;SLC12A1,non_coding_transcript_exon_variant,,ENST00000558252,;	C	ENSG00000074803	ENST00000396577	Transcript	missense_variant	3500	3285	1095	L/F	ttG/ttC	.	.	.	1	SLC12A1	HGNC	10910	protein_coding	YES	CCDS53940.1	ENSP00000379822	.	O76030_HUMAN,E9PDW4_HUMAN	UPI000013C794	.	deleterious(0)	probably_damaging(0.999)	27/27	.	hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF45,TIGRFAM_domain:TIGR00930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTGACATT	.	5	ESCA
IRX5	0	.	GRCh37	16	54967577	54967577	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1244A>G	p.Tyr415Cys	p.Y415C	ENST00000394636	3/3	69	62	7	85	85	0	IRX5,missense_variant,p.Tyr349Cys,ENST00000558597,;IRX5,missense_variant,p.Tyr414Cys,ENST00000320990,;IRX5,missense_variant,p.Tyr195Cys,ENST00000560154,;IRX5,missense_variant,p.Tyr415Cys,ENST00000394636,;CRNDE,upstream_gene_variant,,ENST00000558952,;CTD-3032H12.2,upstream_gene_variant,,ENST00000560487,;CRNDE,upstream_gene_variant,,ENST00000560208,;CRNDE,upstream_gene_variant,,ENST00000502066,;CTD-3032H12.1,downstream_gene_variant,,ENST00000558156,;CRNDE,upstream_gene_variant,,ENST00000559432,;CTD-3032H12.1,downstream_gene_variant,,ENST00000559802,;CRNDE,upstream_gene_variant,,ENST00000560912,;CRNDE,upstream_gene_variant,,ENST00000557792,;	G	ENSG00000176842	ENST00000394636	Transcript	missense_variant	1581	1244	415	Y/C	tAt/tGt	.	.	.	1	IRX5	HGNC	14361	protein_coding	YES	CCDS10751.1	ENSP00000378132	IRX5_HUMAN	.	UPI00001FF1CD	.	deleterious(0)	unknown(0)	3/3	.	hmmpanther:PTHR11211:SF17,hmmpanther:PTHR11211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACTATGGCT	.	4	ESCA
CYB5B	0	.	GRCh37	16	69458712	69458712	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126G>A	p.Trp42Ter	p.W42*	ENST00000307892	1/5	93	39	53	61	61	0	CYB5B,stop_gained,p.Trp42Ter,ENST00000307892,;CYB5B,stop_gained,p.Trp9Ter,ENST00000568237,;CYB5B,stop_gained,p.Trp38Ter,ENST00000561792,;CYB5B,stop_gained,p.Trp38Ter,ENST00000515314,;CYB5B,stop_gained,p.Trp38Ter,ENST00000512062,;CYB5B,non_coding_transcript_exon_variant,,ENST00000514123,;CYB5B,upstream_gene_variant,,ENST00000568342,;	A	ENSG00000103018	ENST00000307892	Transcript	stop_gained	215	126	42	W/*	tgG/tgA	.	.	.	1	CYB5B	HGNC	24374	protein_coding	YES	CCDS10880.2	ENSP00000308430	.	Q5HYD9_HUMAN,J3KNF8_HUMAN	UPI00000710AB	.	.	.	1/5	.	PROSITE_profiles:PS50255,hmmpanther:PTHR19359:SF16,hmmpanther:PTHR19359,Pfam_domain:PF00173,Gene3D:3.10.120.10,Superfamily_domains:SSF55856	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGGCTTGT	.	5	ESCA
CYB5B	0	.	GRCh37	16	69458713	69458713	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.127C>T	p.Leu43Phe	p.L43F	ENST00000307892	1/5	93	41	52	61	61	0	CYB5B,missense_variant,p.Leu43Phe,ENST00000307892,;CYB5B,missense_variant,p.Leu10Phe,ENST00000568237,;CYB5B,missense_variant,p.Leu39Phe,ENST00000561792,;CYB5B,missense_variant,p.Leu39Phe,ENST00000515314,;CYB5B,missense_variant,p.Leu39Phe,ENST00000512062,;CYB5B,non_coding_transcript_exon_variant,,ENST00000514123,;CYB5B,upstream_gene_variant,,ENST00000568342,;	T	ENSG00000103018	ENST00000307892	Transcript	missense_variant	216	127	43	L/F	Ctt/Ttt	.	.	.	1	CYB5B	HGNC	24374	protein_coding	YES	CCDS10880.2	ENSP00000308430	.	Q5HYD9_HUMAN,J3KNF8_HUMAN	UPI00000710AB	.	deleterious(0.04)	benign(0.059)	1/5	.	PROSITE_profiles:PS50255,hmmpanther:PTHR19359:SF16,hmmpanther:PTHR19359,Pfam_domain:PF00173,Gene3D:3.10.120.10,Superfamily_domains:SSF55856	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGGCTTGTG	.	5	ESCA
PHLPP2	0	.	GRCh37	16	71680883	71680883	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1910C>T	.	.	ENST00000568954	19/19	15	6	9	16	16	0	PHLPP2,3_prime_UTR_variant,,ENST00000356272,;PHLPP2,3_prime_UTR_variant,,ENST00000568954,;PHLPP2,3_prime_UTR_variant,,ENST00000393524,;PHLPP2,intron_variant,,ENST00000360429,;PHLPP2,intron_variant,,ENST00000540628,;PHLPP2,downstream_gene_variant,,ENST00000567016,;MARVELD3,downstream_gene_variant,,ENST00000561682,;PHLPP2,intron_variant,,ENST00000568004,;PHLPP2,intron_variant,,ENST00000564884,;	A	ENSG00000040199	ENST00000568954	Transcript	3_prime_UTR_variant	6261	.	.	.	.	.	.	.	-1	PHLPP2	HGNC	29149	protein_coding	YES	CCDS32479.1	ENSP00000457991	PHLP2_HUMAN	.	UPI0000229F5A	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	AAGATGAAGAC	.	4	ESCA
ZNRF1	0	.	GRCh37	16	75140446	75140446	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9C>T	.	.	ENST00000335325	4/5	68	55	13	37	37	0	ZNRF1,3_prime_UTR_variant,,ENST00000567962,;ZNRF1,3_prime_UTR_variant,,ENST00000335325,;ZNRF1,3_prime_UTR_variant,,ENST00000320619,;ZNRF1,intron_variant,,ENST00000568351,;ZNRF1,downstream_gene_variant,,ENST00000566250,;ZNRF1,downstream_gene_variant,,ENST00000568511,;RP11-252E2.1,downstream_gene_variant,,ENST00000499110,;ZNRF1,non_coding_transcript_exon_variant,,ENST00000564320,;ZNRF1,downstream_gene_variant,,ENST00000579084,;ZNRF1,non_coding_transcript_exon_variant,,ENST00000568844,;ZNRF1,non_coding_transcript_exon_variant,,ENST00000568494,;ZNRF1,non_coding_transcript_exon_variant,,ENST00000566244,;	T	ENSG00000186187	ENST00000335325	Transcript	3_prime_UTR_variant	1335	.	.	.	.	.	.	.	1	ZNRF1	HGNC	18452	protein_coding	YES	CCDS10912.1	ENSP00000335091	ZNRF1_HUMAN	J3KTB9_HUMAN	UPI0000037DAA	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGGCTTGCT	.	5	ESCA
DNAAF1	0	.	GRCh37	16	84203815	84203815	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1381G>A	p.Asp461Asn	p.D461N	ENST00000378553	8/12	150	106	44	109	109	0	DNAAF1,missense_variant,p.Asp461Asn,ENST00000378553,;DNAAF1,intron_variant,,ENST00000334315,;DNAAF1,non_coding_transcript_exon_variant,,ENST00000563818,;DNAAF1,downstream_gene_variant,,ENST00000567666,;DNAAF1,non_coding_transcript_exon_variant,,ENST00000570298,;DNAAF1,intron_variant,,ENST00000563093,;	A	ENSG00000154099	ENST00000378553	Transcript	missense_variant	1505	1381	461	D/N	Gat/Aat	.	.	.	1	DNAAF1	HGNC	30539	protein_coding	YES	CCDS10943.2	ENSP00000367815	DAAF1_HUMAN	H3BP51_HUMAN	UPI000059D3C9	.	tolerated(0.55)	benign(0.035)	8/12	.	hmmpanther:PTHR10588,hmmpanther:PTHR10588:SF208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGAGATCAA	.	5	ESCA
PIEZO1	0	.	GRCh37	16	88788401	88788401	+	Missense_Mutation	SNP	G	G	C	rs144994831	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5029C>G	p.Arg1677Gly	p.R1677G	ENST00000301015	37/51	79	55	24	61	61	0	PIEZO1,missense_variant,p.Arg1677Gly,ENST00000301015,;PIEZO1,upstream_gene_variant,,ENST00000327397,;PIEZO1,downstream_gene_variant,,ENST00000474606,;PIEZO1,upstream_gene_variant,,ENST00000466823,;RP5-1142A6.9,downstream_gene_variant,,ENST00000564984,;PIEZO1,upstream_gene_variant,,ENST00000419505,;PIEZO1,downstream_gene_variant,,ENST00000566414,;PIEZO1,upstream_gene_variant,,ENST00000484567,;PIEZO1,upstream_gene_variant,,ENST00000495568,;PIEZO1,downstream_gene_variant,,ENST00000475586,;PIEZO1,upstream_gene_variant,,ENST00000497793,;	C	ENSG00000103335	ENST00000301015	Transcript	missense_variant	5276	5029	1677	R/G	Cgg/Ggg	rs144994831	.	.	-1	PIEZO1	HGNC	28993	protein_coding	YES	CCDS54058.1	ENSP00000301015	PIEZ1_HUMAN	.	UPI0001B300F3	.	tolerated(0.08)	benign(0.062)	37/51	.	hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF40	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCCGCAGCA	by1000G	5	ESCA
DBNDD1	0	.	GRCh37	16	90072645	90072645	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*98G>A	.	.	ENST00000304733	4/4	146	109	36	115	115	0	DBNDD1,3_prime_UTR_variant,,ENST00000568838,;DBNDD1,3_prime_UTR_variant,,ENST00000392973,;DBNDD1,3_prime_UTR_variant,,ENST00000304733,;DBNDD1,3_prime_UTR_variant,,ENST00000002501,;DBNDD1,non_coding_transcript_exon_variant,,ENST00000568662,;AFG3L1P,downstream_gene_variant,,ENST00000454997,;DBNDD1,downstream_gene_variant,,ENST00000568330,;	T	ENSG00000003249	ENST00000304733	Transcript	3_prime_UTR_variant	709	.	.	.	.	.	.	.	-1	DBNDD1	HGNC	28455	protein_coding	YES	CCDS10991.2	ENSP00000306407	DBND1_HUMAN	D3DX86_HUMAN	UPI000037432A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTCGTGGG	.	5	ESCA
CPD	0	.	GRCh37	17	28758892	28758893	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2122dupT	p.Ser708PhefsTer11	p.S708Ffs*11	ENST00000225719	8/21	56	44	12	59	59	0	CPD,frameshift_variant,p.Ser461PhefsTer11,ENST00000543464,;CPD,frameshift_variant,p.Ser708PhefsTer11,ENST00000225719,;	T	ENSG00000108582	ENST00000225719	Transcript	frameshift_variant	2196-2197	2120-2121	707	Y/YX	tat/taTt	.	.	.	1	CPD	HGNC	2301	protein_coding	YES	CCDS11257.1	ENSP00000225719	CBPD_HUMAN	.	UPI000000DAF7	.	.	.	8/21	.	hmmpanther:PTHR11532:SF40,hmmpanther:PTHR11532,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTTATTCCA	.	3	ESCA
CA10	0	.	GRCh37	17	50235244	50235244	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-98G>A	.	.	ENST00000451037	1/9	20	10	10	29	29	0	CA10,5_prime_UTR_variant,,ENST00000285273,;CA10,5_prime_UTR_variant,,ENST00000575181,;CA10,5_prime_UTR_variant,,ENST00000340813,;CA10,5_prime_UTR_variant,,ENST00000451037,;CA10,5_prime_UTR_variant,,ENST00000442502,;CA10,intron_variant,,ENST00000570565,;CA10,non_coding_transcript_exon_variant,,ENST00000573294,;CA10,5_prime_UTR_variant,,ENST00000571371,;	T	ENSG00000154975	ENST00000451037	Transcript	5_prime_UTR_variant	844	.	.	.	.	.	.	.	-1	CA10	HGNC	1369	protein_coding	YES	CCDS32684.1	ENSP00000405388	CAH10_HUMAN	I3L375_HUMAN,B4DGL6_HUMAN	UPI000000167C	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTCCGAGCG	.	5	ESCA
EFCAB3	0	.	GRCh37	17	60484452	60484452	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.902T>C	p.Val301Ala	p.V301A	ENST00000450662	10/12	58	36	22	44	44	0	EFCAB3,missense_variant,p.Val301Ala,ENST00000450662,;EFCAB3,missense_variant,p.Val249Ala,ENST00000305286,;EFCAB3,downstream_gene_variant,,ENST00000520404,;	C	ENSG00000172421	ENST00000450662	Transcript	missense_variant	973	902	301	V/A	gTg/gCg	.	.	.	1	EFCAB3	HGNC	26379	protein_coding	YES	CCDS45751.1	ENSP00000403932	EFCB3_HUMAN	E5RJB7_HUMAN,E5RHB1_HUMAN	UPI0001929531	.	tolerated(0.2)	benign(0.384)	10/12	.	hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TAATGTGGATG	.	4	ESCA
TP53	0	.	GRCh37	17	7579497	7579498	+	Frame_Shift_Del	DEL	GA	GA	-	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	GA	GA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189_190delTC	p.Pro64GlnfsTer84	p.P64Qfs*84	ENST00000269305	4/11	57	19	38	45	45	0	TP53,frameshift_variant,p.Pro64GlnfsTer84,ENST00000508793,;TP53,frameshift_variant,p.Pro64GlnfsTer84,ENST00000413465,;TP53,frameshift_variant,p.Pro64GlnfsTer77,ENST00000604348,;TP53,frameshift_variant,p.Pro64GlnfsTer84,ENST00000420246,;TP53,frameshift_variant,p.Pro64GlnfsTer84,ENST00000269305,;TP53,frameshift_variant,p.Pro64GlnfsTer84,ENST00000359597,;TP53,frameshift_variant,p.Pro64GlnfsTer84,ENST00000445888,;TP53,frameshift_variant,p.Pro64GlnfsTer?,ENST00000503591,;TP53,frameshift_variant,p.Pro64GlnfsTer84,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	379-380	189-190	63-64	AP/AX	gcTCcc/gccc	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	4/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,CODON|p.R65*|c.193A>T|9,BUFFER|p.E68*|c.202G>T|11,BUFFER|p.E68*|c.202G>T|4,BUFFER|p.E68*|c.202G>T|8,BUFFER|p.E68*|c.202G>T|8,BUFFER|p.E68*|c.202G>T|3,BUFFER|p.P67S|c.199C>T|3,BUFFER|p.E62E|c.186A>G|3,BUFFER|p.E62*|c.184G>T|8,BUFFER|p.D61N|c.181G>A|4	INDELOCATOR*|VARSCANI*|PINDEL	TTCTGGGAGCTTC	.	3	ESCA
CHST9	0	.	GRCh37	18	24513588	24513588	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240+10705G>A	.	.	ENST00000284224	.	30	18	12	25	25	0	CHST9,intron_variant,,ENST00000581714,;CHST9,intron_variant,,ENST00000580774,;CHST9,intron_variant,,ENST00000284224,;AQP4-AS1,non_coding_transcript_exon_variant,,ENST00000568797,;AQP4-AS1,intron_variant,,ENST00000578701,;AQP4-AS1,downstream_gene_variant,,ENST00000582605,;AQP4-AS1,downstream_gene_variant,,ENST00000579964,;	T	ENSG00000154080	ENST00000284224	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CHST9	HGNC	19898	protein_coding	YES	CCDS42422.1	ENSP00000284224	CHST9_HUMAN	.	UPI000006EC67	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTACCTCAGC	.	5	ESCA
TRAPPC8	0	.	GRCh37	18	29522943	29522944	+	5'UTR	INS	-	-	GCGC	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-220_-217dupGCGC	.	.	ENST00000283351	1/29	82	72	10	53	53	0	TRAPPC8,5_prime_UTR_variant,,ENST00000582539,;TRAPPC8,5_prime_UTR_variant,,ENST00000582513,;TRAPPC8,5_prime_UTR_variant,,ENST00000283351,;TRAPPC8,upstream_gene_variant,,ENST00000578658,;RP11-326K13.4,non_coding_transcript_exon_variant,,ENST00000580420,;TRAPPC8,non_coding_transcript_exon_variant,,ENST00000584876,;TRAPPC8,intron_variant,,ENST00000577426,;TRAPPC8,intron_variant,,ENST00000580104,;	GCGC	ENSG00000153339	ENST00000283351	Transcript	5_prime_UTR_variant	120-121	.	.	.	.	.	.	.	-1	TRAPPC8	HGNC	29169	protein_coding	YES	CCDS11901.1	ENSP00000283351	TPPC8_HUMAN	J3QQJ5_HUMAN,J3QKL6_HUMAN	UPI0000052E22	.	.	.	1/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	TTCTCAGCGCT	.	2	ESCA
ASF1B	0	.	GRCh37	19	14236981	14237016	+	In_Frame_Del	DEL	CCGAGTCTAGGATCTGATCAAATTCCTCACTCTCAG	CCGAGTCTAGGATCTGATCAAATTCCTCACTCTCAG	-	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	CCGAGTCTAGGATCTGATCAAATTCCTCACTCTCAG	CCGAGTCTAGGATCTGATCAAATTCCTCACTCTCAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143_178delCTGAGAGTGAGGAATTTGATCAGATCCTAGACTCGG	p.Ala48_Ser59del	p.A48_S59del	ENST00000263382	2/4	52	20	32	75	75	0	ASF1B,inframe_deletion,p.Ala48_Ser59del,ENST00000592798,;ASF1B,inframe_deletion,p.Ala48_Ser59del,ENST00000263382,;ASF1B,inframe_deletion,p.Ala48_Ser59del,ENST00000474890,;ASF1B,inframe_deletion,p.Ala48_Ser59del,ENST00000590835,;ASF1B,intron_variant,,ENST00000589468,;	-	ENSG00000105011	ENST00000263382	Transcript	inframe_deletion	643-678	143-178	48-60	AESEEFDQILDSV/V	gCTGAGAGTGAGGAATTTGATCAGATCCTAGACTCGGtg/gtg	.	.	.	-1	ASF1B	HGNC	20996	protein_coding	YES	CCDS12306.1	ENSP00000263382	ASF1B_HUMAN	B4DXU6_HUMAN	UPI00000437D4	.	.	.	2/4	.	Superfamily_domains:SSF101546,Gene3D:1rocA00,Pfam_domain:PF04729,hmmpanther:PTHR12040,hmmpanther:PTHR12040:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAGCACCGAGTCTAGGATCTGATCAAATTCCTCACTCTCAGCCGAG	.	3	ESCA
DPY19L3	0	.	GRCh37	19	32927459	32927459	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436G>C	p.Val146Leu	p.V146L	ENST00000342179	5/19	61	43	17	74	74	0	DPY19L3,missense_variant,p.Val146Leu,ENST00000342179,;DPY19L3,missense_variant,p.Val146Leu,ENST00000392250,;DPY19L3,missense_variant,p.Val146Leu,ENST00000586987,;DPY19L3,downstream_gene_variant,,ENST00000586427,;DPY19L3,upstream_gene_variant,,ENST00000585597,;DPY19L3,upstream_gene_variant,,ENST00000588648,;	C	ENSG00000178904	ENST00000342179	Transcript	missense_variant	651	436	146	V/L	Gtt/Ctt	.	.	.	1	DPY19L3	HGNC	27120	protein_coding	YES	CCDS12422.1	ENSP00000344937	D19L3_HUMAN	K7ELG1_HUMAN	UPI00001C10BE	.	tolerated(0.52)	benign(0.001)	5/19	.	hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF4,Pfam_domain:PF10034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAGAGTTCTA	.	5	ESCA
ZNF571	0	.	GRCh37	19	38056953	38056953	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377C>T	p.Ser126Phe	p.S126F	ENST00000328550	4/5	72	23	49	61	61	0	ZNF571,missense_variant,p.Ser126Phe,ENST00000593133,;ZNF571,missense_variant,p.Ser126Phe,ENST00000358744,;ZNF571,missense_variant,p.Ser126Phe,ENST00000451802,;ZNF571,missense_variant,p.Ser126Phe,ENST00000328550,;ZNF571,intron_variant,,ENST00000590751,;ZNF540,intron_variant,,ENST00000592533,;ZNF571,downstream_gene_variant,,ENST00000590390,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000587121,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000591430,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000590838,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000586139,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000585578,;ZNF571-AS1,non_coding_transcript_exon_variant,,ENST00000592392,;ZNF571-AS1,intron_variant,,ENST00000586013,;ZNF571-AS1,intron_variant,,ENST00000589750,;ZNF571-AS1,intron_variant,,ENST00000589802,;ZNF571-AS1,upstream_gene_variant,,ENST00000591177,;	A	ENSG00000180479	ENST00000328550	Transcript	missense_variant	477	377	126	S/F	tCt/tTt	.	.	.	-1	ZNF571	HGNC	25000	protein_coding	YES	CCDS12505.1	ENSP00000333660	ZN571_HUMAN	.	UPI000020220A	.	tolerated(0.76)	benign(0.015)	4/5	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTAGAAGAG	.	5	ESCA
PRRG2	0	.	GRCh37	19	50093637	50093637	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600G>A	p.%3D	p.R200R	ENST00000246794	7/7	61	33	28	68	67	0	PRRG2,synonymous_variant,p.%3D,ENST00000246794,;NOSIP,upstream_gene_variant,,ENST00000599537,;PRR12,upstream_gene_variant,,ENST00000418929,;PRRG2,non_coding_transcript_exon_variant,,ENST00000596700,;PRRG2,3_prime_UTR_variant,,ENST00000597121,;PRRG2,non_coding_transcript_exon_variant,,ENST00000543867,;	A	ENSG00000126460	ENST00000246794	Transcript	synonymous_variant	769	600	200	R	agG/agA	.	.	.	1	PRRG2	HGNC	9470	protein_coding	YES	CCDS12773.1	ENSP00000246794	TMG2_HUMAN	M0QXL9_HUMAN	UPI0000137078	.	.	.	7/7	.	hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGGCCTCA	.	5	ESCA
ZNF525	0	.	GRCh37	19	53888325	53888325	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000474037	.	35	23	11	33	33	0	ZNF525,3_prime_UTR_variant,,ENST00000467003,;ZNF525,3_prime_UTR_variant,,ENST00000475179,;ZNF525,intron_variant,,ENST00000593918,;ZNF525,downstream_gene_variant,,ENST00000355326,;ZNF525,downstream_gene_variant,,ENST00000474037,;ZNF525,non_coding_transcript_exon_variant,,ENST00000601790,;ZNF525,downstream_gene_variant,,ENST00000600148,;ZNF765,upstream_gene_variant,,ENST00000504146,;CTD-3141N22.1,upstream_gene_variant,,ENST00000459631,;	G	ENSG00000203326	ENST00000474037	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	737	1	ZNF525	HGNC	29423	protein_coding	YES	.	ENSP00000417696	.	J3KR62_HUMAN,J3KR51_HUMAN	UPI0000EE700C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAACATTGAT	.	5	ESCA
MIR520D	0	.	GRCh37	19	54223358	54223358	+	RNA	SNP	T	T	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.9T>G	.	.	ENST00000385002	1/1	120	88	32	107	107	0	MIR520D,non_coding_transcript_exon_variant,,ENST00000385002,;MIR521-2,downstream_gene_variant,,ENST00000384818,;MIR517B,upstream_gene_variant,,ENST00000385102,;RNU6-803P,upstream_gene_variant,,ENST00000516034,;MIR520G,upstream_gene_variant,,ENST00000385064,;	G	ENSG00000207735	ENST00000385002	Transcript	non_coding_transcript_exon_variant	9	.	.	.	.	.	.	.	1	MIR520D	HGNC	32114	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGCTGTGAG	.	5	ESCA
ZNF579	0	.	GRCh37	19	56090160	56090160	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.846delC	p.Trp283GlyfsTer122	p.W283Gfs*122	ENST00000325421	2/2	16	11	5	13	13	0	ZNF579,frameshift_variant,p.Trp283GlyfsTer122,ENST00000325421,;ZNF579,downstream_gene_variant,,ENST00000592239,;CTD-2537I9.5,upstream_gene_variant,,ENST00000589396,;	-	ENSG00000218891	ENST00000325421	Transcript	frameshift_variant	875	846	282	P/X	ccC/cc	.	.	.	-1	ZNF579	HGNC	26646	protein_coding	YES	CCDS12927.1	ENSP00000320188	ZN579_HUMAN	.	UPI0000141657	.	.	.	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF8,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGACCAGGGCCT	.	2	ESCA
ZNF579	0	.	GRCh37	19	56090162	56090162	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844C>T	p.Pro282Ser	p.P282S	ENST00000325421	2/2	16	9	6	12	12	0	ZNF579,missense_variant,p.Pro282Ser,ENST00000325421,;ZNF579,downstream_gene_variant,,ENST00000592239,;CTD-2537I9.5,upstream_gene_variant,,ENST00000589396,;	A	ENSG00000218891	ENST00000325421	Transcript	missense_variant	873	844	282	P/S	Ccc/Tcc	.	.	.	-1	ZNF579	HGNC	26646	protein_coding	YES	CCDS12927.1	ENSP00000320188	ZN579_HUMAN	.	UPI0000141657	.	tolerated(0.07)	probably_damaging(0.966)	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF8,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CCAGGGCCTGG	.	2	ESCA
ZNF579	0	.	GRCh37	19	56090163	56090163	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843G>T	p.Arg281Ser	p.R281S	ENST00000325421	2/2	16	9	6	12	12	0	ZNF579,missense_variant,p.Arg281Ser,ENST00000325421,;ZNF579,downstream_gene_variant,,ENST00000592239,;CTD-2537I9.5,upstream_gene_variant,,ENST00000589396,;	A	ENSG00000218891	ENST00000325421	Transcript	missense_variant	872	843	281	R/S	agG/agT	.	.	.	-1	ZNF579	HGNC	26646	protein_coding	YES	CCDS12927.1	ENSP00000320188	ZN579_HUMAN	.	UPI0000141657	.	tolerated(0.1)	benign(0.443)	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF8,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CAGGGCCTGGC	.	2	ESCA
AMY2B	0	.	GRCh37	1	104116531	104116531	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715G>C	p.Ala239Pro	p.A239P	ENST00000361355	6/12	193	187	6	120	120	0	AMY2B,missense_variant,p.Ala239Pro,ENST00000361355,;AMY2B,downstream_gene_variant,,ENST00000435302,;AMY2B,downstream_gene_variant,,ENST00000453959,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,upstream_gene_variant,,ENST00000481821,;AMY2B,missense_variant,p.Ala239Pro,ENST00000477657,;ACTG1P4,downstream_gene_variant,,ENST00000425123,;	C	ENSG00000240038	ENST00000361355	Transcript	missense_variant	1331	715	239	A/P	Gca/Cca	.	.	.	1	AMY2B	HGNC	478	protein_coding	YES	CCDS782.1	ENSP00000354610	AMY2B_HUMAN	C9JWK7_HUMAN,C9J2Z5_HUMAN	UPI0000000CB1	.	tolerated(0.45)	benign(0.001)	6/12	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Gene3D:3.20.20.80,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCTGCAGGA	.	2	ESCA
RBM15	0	.	GRCh37	1	110882727	110882727	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.700G>T	p.Ala234Ser	p.A234S	ENST00000369784	1/3	80	54	25	59	59	0	RBM15,missense_variant,p.Ala234Ser,ENST00000602849,;RBM15,missense_variant,p.Ala234Ser,ENST00000369784,;RBM15,missense_variant,p.Ala234Ser,ENST00000487146,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,;	T	ENSG00000162775	ENST00000369784	Transcript	missense_variant	1600	700	234	A/S	Gcc/Tcc	.	.	.	1	RBM15	HGNC	14959	protein_coding	YES	CCDS822.1	ENSP00000358799	RBM15_HUMAN	.	UPI000013E1C5	.	tolerated(0.1)	probably_damaging(0.998)	1/3	.	PROSITE_profiles:PS50102,hmmpanther:PTHR23189:SF43,hmmpanther:PTHR23189,Pfam_domain:PF13893,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCATGCCAGA	.	5	ESCA
RBM15	0	.	GRCh37	1	110882728	110882728	+	Missense_Mutation	SNP	C	C	T	rs779388839	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.701C>T	p.Ala234Val	p.A234V	ENST00000369784	1/3	80	54	25	57	57	0	RBM15,missense_variant,p.Ala234Val,ENST00000602849,;RBM15,missense_variant,p.Ala234Val,ENST00000369784,;RBM15,missense_variant,p.Ala234Val,ENST00000487146,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,;	T	ENSG00000162775	ENST00000369784	Transcript	missense_variant	1601	701	234	A/V	gCc/gTc	rs779388839	.	.	1	RBM15	HGNC	14959	protein_coding	YES	CCDS822.1	ENSP00000358799	RBM15_HUMAN	.	UPI000013E1C5	.	deleterious(0)	probably_damaging(0.998)	1/3	.	PROSITE_profiles:PS50102,hmmpanther:PTHR23189:SF43,hmmpanther:PTHR23189,Pfam_domain:PF13893,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATGCCAGAG	.	5	ESCA
ATP5F1	0	.	GRCh37	1	112003655	112003655	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39C>A	.	.	ENST00000369722	7/7	19	14	5	30	30	0	ATP5F1,3_prime_UTR_variant,,ENST00000369722,;ATP5F1,downstream_gene_variant,,ENST00000483994,;ATP5F1,non_coding_transcript_exon_variant,,ENST00000468818,;ATP5F1,non_coding_transcript_exon_variant,,ENST00000369721,;ATP5F1,downstream_gene_variant,,ENST00000464154,;ATP5F1,downstream_gene_variant,,ENST00000493119,;	A	ENSG00000116459	ENST00000369722	Transcript	3_prime_UTR_variant	1416	.	.	.	.	.	.	.	1	ATP5F1	HGNC	840	protein_coding	YES	CCDS836.1	ENSP00000358737	AT5F1_HUMAN	Q08ET0_HUMAN	UPI0000126541	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTGACTGACT	.	2	ESCA
SYCP1	0	.	GRCh37	1	115537630	115537630	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2921T>A	p.Leu974Ter	p.L974*	ENST00000369522	32/32	26	21	5	29	29	0	SYCP1,stop_gained,p.Leu974Ter,ENST00000369518,;SYCP1,stop_gained,p.Leu974Ter,ENST00000369522,;SYCP1,non_coding_transcript_exon_variant,,ENST00000477590,;	A	ENSG00000198765	ENST00000369522	Transcript	stop_gained	3161	2921	974	L/*	tTa/tAa	.	.	.	1	SYCP1	HGNC	11487	protein_coding	YES	CCDS879.1	ENSP00000358535	SYCP1_HUMAN	Q5VXJ5_HUMAN	UPI00001CE3B9	.	.	.	32/32	.	hmmpanther:PTHR18878	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F975L|c.2925T>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTTATTTG	.	5	ESCA
TTF2	0	.	GRCh37	1	117632831	117632842	+	Splice_Site	DEL	GTAATCAAGTTT	GTAATCAAGTTT	-	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	GTAATCAAGTTT	GTAATCAAGTTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2496+4_2496+15delATCAAGTTTGTA	.	p.X832_splice	ENST00000369466	.	71	60	11	50	50	0	TTF2,splice_donor_variant,,ENST00000369466,;MIR942,upstream_gene_variant,,ENST00000401111,;TTF2,upstream_gene_variant,,ENST00000492682,;	-	ENSG00000116830	ENST00000369466	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	TTF2	HGNC	12398	protein_coding	YES	CCDS892.1	ENSP00000358478	TTF2_HUMAN	.	UPI000013CCE7	.	.	.	.	14/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTTTGGTAATCAAGTTTGTACC	.	3	ESCA
NTRK1	0	.	GRCh37	1	156837937	156837937	+	Missense_Mutation	SNP	G	G	A	rs141021604	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470G>A	p.Arg157His	p.R157H	ENST00000524377	5/17	70	32	38	51	51	0	NTRK1,missense_variant,p.Arg127His,ENST00000392302,;NTRK1,missense_variant,p.Arg157His,ENST00000524377,;NTRK1,missense_variant,p.Arg157His,ENST00000358660,;NTRK1,missense_variant,p.Arg157His,ENST00000368196,;NTRK1,intron_variant,,ENST00000489021,;NTRK1,missense_variant,p.Arg127His,ENST00000497019,;NTRK1,non_coding_transcript_exon_variant,,ENST00000530298,;NTRK1,downstream_gene_variant,,ENST00000533630,;	A	ENSG00000198400	ENST00000524377	Transcript	missense_variant	511	470	157	R/H	cGc/cAc	rs141021604	.	.	1	NTRK1	HGNC	8031	protein_coding	YES	CCDS1161.1	ENSP00000431418	NTRK1_HUMAN	.	UPI000013D5D3	.	tolerated(0.77)	benign(0)	5/17	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF133,Gene3D:3.80.10.10,SMART_domains:SM00082,Superfamily_domains:SSF52058	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0005	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCGCTGGC	byCluster|by1000G	5	ESCA
ARHGEF11	0	.	GRCh37	1	156914188	156914188	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3029G>A	p.Gly1010Glu	p.G1010E	ENST00000368194	31/41	38	24	13	44	44	0	ARHGEF11,missense_variant,p.Gly970Glu,ENST00000361409,;ARHGEF11,missense_variant,p.Gly386Glu,ENST00000315174,;ARHGEF11,missense_variant,p.Gly1010Glu,ENST00000368194,;ARHGEF11,non_coding_transcript_exon_variant,,ENST00000487682,;ARHGEF11,upstream_gene_variant,,ENST00000492592,;ARHGEF11,downstream_gene_variant,,ENST00000461678,;	T	ENSG00000132694	ENST00000368194	Transcript	missense_variant	4069	3029	1010	G/E	gGa/gAa	.	.	.	-1	ARHGEF11	HGNC	14580	protein_coding	YES	CCDS1163.1	ENSP00000357177	ARHGB_HUMAN	.	UPI00001D62A7	.	deleterious(0)	probably_damaging(0.999)	31/41	.	PROSITE_profiles:PS50003,hmmpanther:PTHR22825:SF5,hmmpanther:PTHR22825,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGTCCCTCA	.	5	ESCA
TNN	0	.	GRCh37	1	175054550	175054550	+	Missense_Mutation	SNP	C	C	T	rs763519873	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1244C>T	p.Pro415Leu	p.P415L	ENST00000239462	6/19	78	62	15	71	71	0	TNN,missense_variant,p.Pro415Leu,ENST00000239462,;	T	ENSG00000120332	ENST00000239462	Transcript	missense_variant	1357	1244	415	P/L	cCg/cTg	rs763519873,COSM4025308	.	.	1	TNN	HGNC	22942	protein_coding	YES	CCDS30943.1	ENSP00000239462	TENN_HUMAN	.	UPI00001D7DA9	.	tolerated(0.06)	probably_damaging(1)	6/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF167,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACCCGGGGA	.	5	ESCA
CEP350	0	.	GRCh37	1	179955361	179955361	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45G>C	p.Arg15Ser	p.R15S	ENST00000367607	2/38	82	57	25	63	62	1	CEP350,missense_variant,p.Arg15Ser,ENST00000357434,;CEP350,missense_variant,p.Arg15Ser,ENST00000367607,;CEP350,missense_variant,p.Glu29Gln,ENST00000491495,;	C	ENSG00000135837	ENST00000367607	Transcript	missense_variant	463	45	15	R/S	agG/agC	.	.	.	1	CEP350	HGNC	24238	protein_coding	YES	CCDS1336.1	ENSP00000356579	CE350_HUMAN	Q5T2X4_HUMAN	UPI000013CFC5	.	.	possibly_damaging(0.905)	2/38	.	hmmpanther:PTHR13958	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGGAACTC	.	5	ESCA
CD46	0	.	GRCh37	1	207930371	207930371	+	Missense_Mutation	SNP	A	A	T	rs766600746	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110A>T	p.Glu37Val	p.E37V	ENST00000322875	2/13	112	76	35	87	87	0	CD46,missense_variant,p.Glu37Val,ENST00000360212,;CD46,missense_variant,p.Glu37Val,ENST00000441839,;CD46,missense_variant,p.Glu37Val,ENST00000322918,;CD46,missense_variant,p.Glu37Val,ENST00000358170,;CD46,missense_variant,p.Glu37Val,ENST00000354848,;CD46,missense_variant,p.Glu37Val,ENST00000480003,;CD46,missense_variant,p.Glu37Val,ENST00000367042,;CD46,missense_variant,p.Glu37Val,ENST00000357714,;CD46,missense_variant,p.Glu37Val,ENST00000361067,;CD46,missense_variant,p.Glu37Val,ENST00000367041,;CD46,missense_variant,p.Glu37Val,ENST00000322875,;CD46,intron_variant,,ENST00000367047,;CD46,non_coding_transcript_exon_variant,,ENST00000493796,;CD46,non_coding_transcript_exon_variant,,ENST00000469535,;CD46,upstream_gene_variant,,ENST00000464082,;	T	ENSG00000117335	ENST00000322875	Transcript	missense_variant	266	110	37	E/V	gAg/gTg	rs766600746	.	.	1	CD46	HGNC	6953	protein_coding	YES	CCDS1482.1	ENSP00000313875	MCP_HUMAN	Q06C42_HUMAN	UPI000015FF6E	.	tolerated(0.05)	benign(0.064)	2/13	.	Superfamily_domains:SSF57535,SMART_domains:SM00032,PIRSF_domain:PIRSF037971,Gene3D:2.10.70.10,Pfam_domain:PF00084,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF50,PROSITE_profiles:PS50923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGGAGCCAC	.	5	ESCA
FMN2	0	.	GRCh37	1	240370785	240370785	+	Silent	SNP	G	G	T	rs763905334	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2673G>T	p.%3D	p.L891L	ENST00000319653	5/18	51	37	14	25	25	0	FMN2,synonymous_variant,p.%3D,ENST00000319653,;FMN2,downstream_gene_variant,,ENST00000447095,;	T	ENSG00000155816	ENST00000319653	Transcript	synonymous_variant	2903	2673	891	L	ctG/ctT	rs763905334	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	.	5/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,SMART_domains:SM00498,Prints_domain:PR01217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTGCCCAG	byFrequency	5	ESCA
PAFAH2	0	.	GRCh37	1	26299081	26299081	+	Missense_Mutation	SNP	C	C	T	rs778716854	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000374282	10/11	61	37	24	58	58	0	PAFAH2,missense_variant,p.Arg351Gln,ENST00000374282,;PAFAH2,missense_variant,p.Arg351Gln,ENST00000374284,;	T	ENSG00000158006	ENST00000374282	Transcript	missense_variant	1232	1052	351	R/Q	cGg/cAg	rs778716854	.	.	-1	PAFAH2	HGNC	8579	protein_coding	YES	CCDS270.1	ENSP00000363400	PAFA2_HUMAN	Q5SY01_HUMAN	UPI00001311EB	.	tolerated(0.32)	benign(0.026)	10/11	.	hmmpanther:PTHR10272:SF6,hmmpanther:PTHR10272,Pfam_domain:PF03403,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF018169,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCCGTACC	byFrequency	5	ESCA
STK40	0	.	GRCh37	1	36805394	36805394	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1962A>G	.	.	ENST00000373129	12/12	24	14	9	31	31	0	STK40,3_prime_UTR_variant,,ENST00000373132,;STK40,3_prime_UTR_variant,,ENST00000373129,;STK40,3_prime_UTR_variant,,ENST00000373130,;STK40,3_prime_UTR_variant,,ENST00000359297,;	C	ENSG00000196182	ENST00000373129	Transcript	3_prime_UTR_variant	3677	.	.	.	.	.	.	.	-1	STK40	HGNC	21373	protein_coding	YES	CCDS407.1	ENSP00000362221	STK40_HUMAN	.	UPI0000073E73	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCTTCACC	.	5	ESCA
PTCH2	0	.	GRCh37	1	45292310	45292310	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2826G>A	p.%3D	p.V942V	ENST00000372192	18/22	43	31	11	41	41	0	PTCH2,synonymous_variant,p.%3D,ENST00000447098,;PTCH2,synonymous_variant,p.%3D,ENST00000372192,;PTCH2,upstream_gene_variant,,ENST00000438067,;	T	ENSG00000117425	ENST00000372192	Transcript	synonymous_variant	2957	2826	942	V	gtG/gtA	.	.	.	-1	PTCH2	HGNC	9586	protein_coding	YES	CCDS516.1	ENSP00000361266	PTC2_HUMAN	.	UPI00001328B8	.	.	.	18/22	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF82866,Pfam_domain:PF02460,Gene3D:2j8sB01,TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF62	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGTGCACCCC	.	5	ESCA
ST6GALNAC3	0	.	GRCh37	1	77095055	77095055	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*564C>T	.	.	ENST00000328299	5/5	8	5	3	12	12	0	ST6GALNAC3,3_prime_UTR_variant,,ENST00000328299,;	T	ENSG00000184005	ENST00000328299	Transcript	3_prime_UTR_variant	1630	.	.	.	.	.	.	.	1	ST6GALNAC3	HGNC	19343	protein_coding	YES	CCDS672.1	ENSP00000329214	SIA7C_HUMAN	.	UPI000006F75A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAAGCCTCAG	.	2	ESCA
ST6GALNAC5	0	.	GRCh37	1	77529333	77529333	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*442T>C	.	.	ENST00000477717	5/5	56	42	13	51	51	0	ST6GALNAC5,3_prime_UTR_variant,,ENST00000477717,;RP4-564M11.2,upstream_gene_variant,,ENST00000454305,;ST6GALNAC5,3_prime_UTR_variant,,ENST00000318803,;	C	ENSG00000117069	ENST00000477717	Transcript	3_prime_UTR_variant	1688	.	.	.	.	.	.	.	1	ST6GALNAC5	HGNC	19342	protein_coding	YES	CCDS673.1	ENSP00000417583	SIA7E_HUMAN	B4DHB7_HUMAN	UPI0000001C9F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTGTAAAAA	.	5	ESCA
DNTTIP2	0	.	GRCh37	1	94338752	94338752	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1825A>G	p.Ile609Val	p.I609V	ENST00000436063	4/7	61	46	15	51	51	0	DNTTIP2,missense_variant,p.Ile609Val,ENST00000436063,;DNTTIP2,downstream_gene_variant,,ENST00000528680,;DNTTIP2,non_coding_transcript_exon_variant,,ENST00000496535,;DNTTIP2,downstream_gene_variant,,ENST00000496672,;DNTTIP2,downstream_gene_variant,,ENST00000460191,;DNTTIP2,synonymous_variant,p.%3D,ENST00000359208,;DNTTIP2,upstream_gene_variant,,ENST00000462746,;	C	ENSG00000067334	ENST00000436063	Transcript	missense_variant	1883	1825	609	I/V	Att/Gtt	.	.	.	-1	DNTTIP2	HGNC	24013	protein_coding	YES	CCDS44174.1	ENSP00000411010	TDIF2_HUMAN	.	UPI000006F063	.	deleterious(0.03)	benign(0.081)	4/7	.	hmmpanther:PTHR21686:SF12,hmmpanther:PTHR21686	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAATGACGG	.	5	ESCA
ITCH	0	.	GRCh37	20	33050008	33050008	+	Missense_Mutation	SNP	G	G	A	rs765813305	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1529G>A	p.Arg510His	p.R510H	ENST00000262650	15/26	52	37	14	46	46	0	ITCH,missense_variant,p.Arg469His,ENST00000374864,;ITCH,missense_variant,p.Arg359His,ENST00000535650,;ITCH,missense_variant,p.Arg510His,ENST00000262650,;MIR644A,upstream_gene_variant,,ENST00000385262,;ITCH,non_coding_transcript_exon_variant,,ENST00000483727,;	A	ENSG00000078747	ENST00000262650	Transcript	missense_variant	1665	1529	510	R/H	cGc/cAc	rs765813305,COSM2758045	.	.	1	ITCH	HGNC	13890	protein_coding	YES	CCDS58768.1	ENSP00000262650	ITCH_HUMAN	.	UPI00000731C2	.	deleterious(0)	probably_damaging(0.992)	15/26	.	Superfamily_domains:SSF51045,PIRSF_domain:PIRSF001569,SMART_domains:SM00456,Gene3D:2.20.70.10,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF66,PROSITE_profiles:PS50020	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R469H|c.1406G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCGCACAG	.	5	ESCA
ERG	0	.	GRCh37	21	39755332	39755332	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1454A>G	p.Tyr485Cys	p.Y485C	ENST00000417133	12/12	145	132	12	128	128	0	ERG,missense_variant,p.Tyr362Cys,ENST00000398897,;ERG,missense_variant,p.Tyr386Cys,ENST00000453032,;ERG,missense_variant,p.Tyr462Cys,ENST00000398910,;ERG,missense_variant,p.Tyr478Cys,ENST00000288319,;ERG,missense_variant,p.Tyr461Cys,ENST00000442448,;ERG,missense_variant,p.Tyr485Cys,ENST00000398919,;ERG,missense_variant,p.Tyr454Cys,ENST00000398905,;ERG,missense_variant,p.Tyr485Cys,ENST00000417133,;ERG,missense_variant,p.Tyr461Cys,ENST00000398911,;ERG,missense_variant,p.Tyr455Cys,ENST00000398907,;	C	ENSG00000157554	ENST00000417133	Transcript	missense_variant	1640	1454	485	Y/C	tAc/tGc	.	.	.	-1	ERG	HGNC	3446	protein_coding	YES	CCDS46648.1	ENSP00000414150	ERG_HUMAN	Q16031_HUMAN,B4DVX5_HUMAN	UPI000018681C	.	deleterious(0.02)	benign(0.366)	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTAGTAAGTG	.	2	ESCA
COL6A2	0	.	GRCh37	21	47552161	47552161	+	Missense_Mutation	SNP	G	G	A	rs372523558	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2755G>A	p.Ala919Thr	p.A919T	ENST00000300527	28/28	68	18	49	79	79	0	COL6A2,missense_variant,p.Ala919Thr,ENST00000300527,;FTCD,downstream_gene_variant,,ENST00000397746,;COL6A2,downstream_gene_variant,,ENST00000310645,;FTCD,downstream_gene_variant,,ENST00000291670,;FTCD,downstream_gene_variant,,ENST00000446405,;COL6A2,downstream_gene_variant,,ENST00000357838,;COL6A2,downstream_gene_variant,,ENST00000409416,;COL6A2,downstream_gene_variant,,ENST00000397763,;FTCD,downstream_gene_variant,,ENST00000359679,;FTCD,downstream_gene_variant,,ENST00000397743,;FTCD,downstream_gene_variant,,ENST00000355384,;FTCD,downstream_gene_variant,,ENST00000397748,;FTCD,downstream_gene_variant,,ENST00000483568,;FTCD,downstream_gene_variant,,ENST00000460011,;FTCD,downstream_gene_variant,,ENST00000498355,;FTCD,downstream_gene_variant,,ENST00000494498,;	A	ENSG00000142173	ENST00000300527	Transcript	missense_variant	2859	2755	919	A/T	Gca/Aca	rs372523558	.	.	1	COL6A2	HGNC	2212	protein_coding	YES	CCDS13728.1	ENSP00000300527	CO6A2_HUMAN	C9JH44_HUMAN	UPI00001AECE0	.	tolerated(0.49)	benign(0.003)	28/28	.	PROSITE_profiles:PS50234,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF119,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGCAGGC	byCluster|by1000G	5	ESCA
AP000349.1	0	.	GRCh37	22	24124522	24124522	+	Missense_Mutation	SNP	C	C	T	rs757559270	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.692G>A	p.Arg231Gln	p.R231Q	ENST00000598975	3/3	126	90	35	84	84	0	AP000349.1,missense_variant,p.Arg231Gln,ENST00000598975,;MMP11,synonymous_variant,p.%3D,ENST00000215743,;SMARCB1,upstream_gene_variant,,ENST00000407082,;SMARCB1,upstream_gene_variant,,ENST00000407422,;SMARCB1,upstream_gene_variant,,ENST00000263121,;SMARCB1,upstream_gene_variant,,ENST00000417137,;SMARCB1,upstream_gene_variant,,ENST00000344921,;MMP11,non_coding_transcript_exon_variant,,ENST00000488363,;MMP11,non_coding_transcript_exon_variant,,ENST00000480185,;MMP11,downstream_gene_variant,,ENST00000477567,;MMP11,downstream_gene_variant,,ENST00000460352,;MMP11,downstream_gene_variant,,ENST00000489582,;MMP11,3_prime_UTR_variant,,ENST00000434318,;MMP11,non_coding_transcript_exon_variant,,ENST00000465385,;MMP11,intron_variant,,ENST00000437086,;MMP11,downstream_gene_variant,,ENST00000428253,;MMP11,downstream_gene_variant,,ENST00000465730,;MMP11,downstream_gene_variant,,ENST00000493132,;MMP11,downstream_gene_variant,,ENST00000492464,;	T	ENSG00000267954	ENST00000598975	Transcript	missense_variant	692	692	231	R/Q	cGg/cAg	rs757559270	.	.	-1	AP000349.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000469183	.	Q71RC1_HUMAN,M0QXI1_HUMAN	UPI00015DF7BB	.	.	unknown(0)	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCCCGAGAA	byFrequency	5	ESCA
PLXNB2	0	.	GRCh37	22	50715316	50715316	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5216delT	p.Leu1739ArgfsTer32	p.L1739Rfs*32	ENST00000449103	34/37	127	89	38	41	41	0	PLXNB2,frameshift_variant,p.Leu1739ArgfsTer32,ENST00000359337,;PLXNB2,frameshift_variant,p.Leu1739ArgfsTer32,ENST00000449103,;AL022328.1,downstream_gene_variant,,ENST00000595015,;PLXNB2,downstream_gene_variant,,ENST00000427829,;PLXNB2,downstream_gene_variant,,ENST00000411680,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479818,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479701,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000463165,;PLXNB2,downstream_gene_variant,,ENST00000492578,;	-	ENSG00000196576	ENST00000449103	Transcript	frameshift_variant	5357	5216	1739	L/X	cTg/cg	.	.	.	-1	PLXNB2	HGNC	9104	protein_coding	YES	CCDS43035.1	ENSP00000409171	PLXB2_HUMAN	Q2TBE4_HUMAN,E2PU09_HUMAN,A6QRH1_HUMAN	UPI000003812D	.	.	.	34/37	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF9,Pfam_domain:PF08337,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TACAGCAGCTTG	.	3	ESCA
GCC2	0	.	GRCh37	2	109087996	109087996	+	Silent	SNP	G	G	A	rs759436302	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2211G>A	p.%3D	p.E737E	ENST00000309863	6/23	24	16	8	22	22	0	GCC2,synonymous_variant,p.%3D,ENST00000309863,;GCC2,synonymous_variant,p.%3D,ENST00000409896,;GCC2,upstream_gene_variant,,ENST00000492785,;GCC2,downstream_gene_variant,,ENST00000409821,;GCC2,upstream_gene_variant,,ENST00000462897,;GCC2,downstream_gene_variant,,ENST00000485546,;GCC2,downstream_gene_variant,,ENST00000478207,;GCC2,3_prime_UTR_variant,,ENST00000482325,;GCC2,upstream_gene_variant,,ENST00000447558,;	A	ENSG00000135968	ENST00000309863	Transcript	synonymous_variant	2925	2211	737	E	gaG/gaA	rs759436302	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	.	.	6/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAAGAGCAAGA	.	3	ESCA
GCC2	0	.	GRCh37	2	109087999	109087999	+	Missense_Mutation	SNP	A	A	T	rs769472880	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2214A>T	p.Gln738His	p.Q738H	ENST00000309863	6/23	25	16	9	24	24	0	GCC2,missense_variant,p.Gln738His,ENST00000309863,;GCC2,missense_variant,p.Gln701His,ENST00000409896,;GCC2,upstream_gene_variant,,ENST00000492785,;GCC2,downstream_gene_variant,,ENST00000409821,;GCC2,upstream_gene_variant,,ENST00000462897,;GCC2,downstream_gene_variant,,ENST00000485546,;GCC2,downstream_gene_variant,,ENST00000478207,;GCC2,3_prime_UTR_variant,,ENST00000482325,;GCC2,upstream_gene_variant,,ENST00000447558,;	T	ENSG00000135968	ENST00000309863	Transcript	missense_variant	2928	2214	738	Q/H	caA/caT	rs769472880	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	deleterious(0.01)	benign(0.084)	6/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAGCAAGATAA	byFrequency	3	ESCA
CCDC93	0	.	GRCh37	2	118698834	118698834	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1453A>G	p.Ile485Val	p.I485V	ENST00000376300	19/24	187	178	9	39	39	0	CCDC93,missense_variant,p.Ile485Val,ENST00000376300,;CCDC93,missense_variant,p.Ile484Val,ENST00000319432,;CCDC93,3_prime_UTR_variant,,ENST00000437999,;CCDC93,non_coding_transcript_exon_variant,,ENST00000466171,;CCDC93,upstream_gene_variant,,ENST00000470650,;	C	ENSG00000125633	ENST00000376300	Transcript	missense_variant	1591	1453	485	I/V	Att/Gtt	.	.	.	-1	CCDC93	HGNC	25611	protein_coding	YES	CCDS2121.2	ENSP00000365477	CCD93_HUMAN	.	UPI0000207DEC	.	deleterious(0.01)	benign(0.156)	19/24	.	hmmpanther:PTHR16441	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCAATCTTGC	.	2	ESCA
CCDC115	0	.	GRCh37	2	131099484	131099484	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.145A>T	p.Met49Leu	p.M49L	ENST00000259229	2/5	44	26	17	20	20	0	CCDC115,missense_variant,p.Met44Leu,ENST00000409127,;CCDC115,missense_variant,p.Met44Leu,ENST00000437688,;CCDC115,missense_variant,p.Met49Leu,ENST00000259229,;IMP4,upstream_gene_variant,,ENST00000259239,;IMP4,upstream_gene_variant,,ENST00000428740,;IMP4,upstream_gene_variant,,ENST00000409649,;IMP4,upstream_gene_variant,,ENST00000452955,;IMP4,upstream_gene_variant,,ENST00000409935,;CCDC115,missense_variant,p.Met49Leu,ENST00000442217,;CCDC115,non_coding_transcript_exon_variant,,ENST00000465315,;IMP4,upstream_gene_variant,,ENST00000462357,;IMP4,upstream_gene_variant,,ENST00000477375,;IMP4,upstream_gene_variant,,ENST00000475074,;IMP4,upstream_gene_variant,,ENST00000460766,;IMP4,upstream_gene_variant,,ENST00000462392,;IMP4,upstream_gene_variant,,ENST00000470672,;IMP4,upstream_gene_variant,,ENST00000490895,;IMP4,upstream_gene_variant,,ENST00000464432,;IMP4,upstream_gene_variant,,ENST00000473689,;IMP4,upstream_gene_variant,,ENST00000456713,;IMP4,upstream_gene_variant,,ENST00000495606,;IMP4,upstream_gene_variant,,ENST00000460100,;	A	ENSG00000136710	ENST00000259229	Transcript	missense_variant	369	145	49	M/L	Atg/Ttg	.	.	.	-1	CCDC115	HGNC	28178	protein_coding	YES	CCDS2159.1	ENSP00000259229	CC115_HUMAN	.	UPI000006E81C	.	deleterious(0)	possibly_damaging(0.799)	2/5	.	hmmpanther:PTHR31996,hmmpanther:PTHR31996:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCATCGCGT	.	5	ESCA
ZEB2	0	.	GRCh37	2	145156713	145156713	+	Missense_Mutation	SNP	C	C	G	rs769486815	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2041G>C	p.Val681Leu	p.V681L	ENST00000558170	8/10	83	37	45	69	69	0	ZEB2,missense_variant,p.Val681Leu,ENST00000427902,;ZEB2,missense_variant,p.Val657Leu,ENST00000539609,;ZEB2,missense_variant,p.Val681Leu,ENST00000409487,;ZEB2,missense_variant,p.Val681Leu,ENST00000303660,;ZEB2,missense_variant,p.Val681Leu,ENST00000558170,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000392861,;ZEB2,downstream_gene_variant,,ENST00000497268,;	G	ENSG00000169554	ENST00000558170	Transcript	missense_variant	3226	2041	681	V/L	Gtg/Ctg	rs769486815	.	.	-1	ZEB2	HGNC	14881	protein_coding	YES	CCDS2186.1	ENSP00000454157	ZEB2_HUMAN	U3KPV5_HUMAN,Q53TG0_HUMAN,Q53TD9_HUMAN,E7EUW9_HUMAN,E7ESP8_HUMAN,C9JUQ1_HUMAN,C9JU62_HUMAN,A0JP08_HUMAN	UPI00001359A2	.	deleterious(0.02)	possibly_damaging(0.581)	8/10	.	hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF2,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCACAGCAA	byFrequency	5	ESCA
SCN1A	0	.	GRCh37	2	166872165	166872165	+	Missense_Mutation	SNP	C	C	T	rs146374754	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3502G>A	p.Val1168Ile	p.V1168I	ENST00000303395	17/26	51	35	15	50	50	0	SCN1A,missense_variant,p.Val1140Ile,ENST00000409050,;SCN1A,missense_variant,p.Val1168Ile,ENST00000423058,;SCN1A,missense_variant,p.Val1168Ile,ENST00000303395,;SCN1A,missense_variant,p.Val1157Ile,ENST00000375405,;AC010127.3,non_coding_transcript_exon_variant,,ENST00000595647,;AC010127.3,non_coding_transcript_exon_variant,,ENST00000597623,;AC010127.3,upstream_gene_variant,,ENST00000595268,;	T	ENSG00000144285	ENST00000303395	Transcript	missense_variant	3502	3502	1168	V/I	Gta/Ata	rs146374754,COSM3312998,COSM3312997,COSM3971687	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	tolerated(0.22)	benign(0.018)	17/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF133,Pfam_domain:PF06512	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTACGGGCT	byCluster	5	ESCA
ITGA6	0	.	GRCh37	2	173338917	173338917	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.910G>C	p.Glu304Gln	p.E304Q	ENST00000409080	6/25	558	303	255	101	101	0	ITGA6,missense_variant,p.Glu343Gln,ENST00000264106,;ITGA6,missense_variant,p.Glu343Gln,ENST00000375221,;ITGA6,missense_variant,p.Glu299Gln,ENST00000343713,;ITGA6,missense_variant,p.Glu299Gln,ENST00000458358,;ITGA6,missense_variant,p.Glu190Gln,ENST00000412899,;ITGA6,missense_variant,p.Glu343Gln,ENST00000442250,;ITGA6,missense_variant,p.Glu304Gln,ENST00000264107,;ITGA6,missense_variant,p.Glu185Gln,ENST00000409532,;ITGA6,missense_variant,p.Glu304Gln,ENST00000409080,;ITGA6,downstream_gene_variant,,ENST00000497107,;	C	ENSG00000091409	ENST00000409080	Transcript	missense_variant	910	910	304	E/Q	Gag/Cag	.	.	.	1	ITGA6	HGNC	6142	protein_coding	YES	CCDS46451.1	ENSP00000386896	ITA6_HUMAN	C9JXX7_HUMAN	UPI0000EA87E5	.	tolerated(0.12)	probably_damaging(0.98)	6/25	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF9,hmmpanther:PTHR23220,Gene3D:3nigC00,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTGAGCAC	.	5	ESCA
SF3B1	0	.	GRCh37	2	198256808	198256808	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*219A>G	.	.	ENST00000335508	25/25	38	29	8	33	33	0	SF3B1,3_prime_UTR_variant,,ENST00000335508,;SF3B1,downstream_gene_variant,,ENST00000424674,;SF3B1,downstream_gene_variant,,ENST00000479532,;	C	ENSG00000115524	ENST00000335508	Transcript	3_prime_UTR_variant	4226	.	.	.	.	.	.	.	-1	SF3B1	HGNC	10768	protein_coding	YES	CCDS33356.1	ENSP00000335321	SF3B1_HUMAN	Q9NTB4_HUMAN,F8WC19_HUMAN	UPI000013D493	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTATAGTGT	.	5	ESCA
TNS1	0	.	GRCh37	2	218679706	218679706	+	Missense_Mutation	SNP	G	G	A	rs374445594	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4346C>T	p.Thr1449Met	p.T1449M	ENST00000171887	25/33	63	59	4	41	41	0	TNS1,missense_variant,p.Thr1449Met,ENST00000171887,;TNS1,missense_variant,p.Thr1428Met,ENST00000430930,;TNS1,missense_variant,p.Thr1436Met,ENST00000419504,;TNS1,missense_variant,p.Thr587Met,ENST00000446688,;TNS1,non_coding_transcript_exon_variant,,ENST00000495556,;TNS1,upstream_gene_variant,,ENST00000490566,;TNS1,upstream_gene_variant,,ENST00000480416,;	A	ENSG00000079308	ENST00000171887	Transcript	missense_variant	4799	4346	1449	T/M	aCg/aTg	rs374445594	.	.	-1	TNS1	HGNC	11973	protein_coding	YES	CCDS2407.1	ENSP00000171887	TENS1_HUMAN	Q9UFN8_HUMAN,Q9H757_HUMAN,C9JZT0_HUMAN,C9JI43_HUMAN,C9JFT7_HUMAN	UPI0000456EEB	.	deleterious(0)	benign(0.084)	25/33	.	hmmpanther:PTHR12305,hmmpanther:PTHR12305:SF40,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCGCGTCTCC	byFrequency|byCluster	2	ESCA
DOCK10	0	.	GRCh37	2	225710010	225710010	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2391C>G	p.His797Gln	p.H797Q	ENST00000258390	21/56	40	34	6	36	36	0	DOCK10,missense_variant,p.His797Gln,ENST00000258390,;DOCK10,missense_variant,p.His791Gln,ENST00000409592,;	C	ENSG00000135905	ENST00000258390	Transcript	missense_variant	2459	2391	797	H/Q	caC/caG	.	.	.	-1	DOCK10	HGNC	23479	protein_coding	YES	CCDS46528.1	ENSP00000258390	DOC10_HUMAN	Q4ZG60_HUMAN,Q3LIC8_HUMAN	UPI000021D2A7	.	tolerated(0.06)	benign(0.112)	21/56	.	PROSITE_profiles:PS51650,hmmpanther:PTHR23317:SF71,hmmpanther:PTHR23317,Pfam_domain:PF14429	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATCGTGTTT	.	5	ESCA
TRIP12	0	.	GRCh37	2	230693989	230693989	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1226G>C	p.Arg409Thr	p.R409T	ENST00000283943	7/41	31	22	9	13	13	0	TRIP12,missense_variant,p.Arg409Thr,ENST00000283943,;TRIP12,missense_variant,p.Arg112Thr,ENST00000389045,;TRIP12,missense_variant,p.Arg457Thr,ENST00000389044,;TRIP12,intron_variant,,ENST00000543084,;TRIP12,downstream_gene_variant,,ENST00000409677,;TRIP12,non_coding_transcript_exon_variant,,ENST00000479037,;	G	ENSG00000153827	ENST00000283943	Transcript	missense_variant	1405	1226	409	R/T	aGg/aCg	.	.	.	-1	TRIP12	HGNC	12306	protein_coding	YES	CCDS33391.1	ENSP00000283943	TRIPC_HUMAN	Q57Z94_HUMAN,F8W9P3_HUMAN,C9JSX9_HUMAN,C9JLJ5_HUMAN	UPI000013739D	.	deleterious(0)	probably_damaging(0.992)	7/41	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF73	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	GACCCCTTGCC	.	3	ESCA
C2orf72	0	.	GRCh37	2	231911623	231911623	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775C>A	p.Leu259Met	p.L259M	ENST00000373640	3/3	81	69	12	78	78	0	C2orf72,missense_variant,p.Leu259Met,ENST00000373640,;C2orf72,non_coding_transcript_exon_variant,,ENST00000477463,;C2orf72,non_coding_transcript_exon_variant,,ENST00000463834,;	A	ENSG00000204128	ENST00000373640	Transcript	missense_variant	851	775	259	L/M	Ctg/Atg	.	.	.	1	C2orf72	HGNC	27418	protein_coding	YES	CCDS46539.1	ENSP00000362743	CB072_HUMAN	.	UPI00004190AD	.	tolerated(0.18)	benign(0.422)	3/3	.	Pfam_domain:PF15443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGCTGCCA	.	5	ESCA
C2orf71	0	.	GRCh37	2	29294078	29294078	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3050G>A	p.Arg1017Lys	p.R1017K	ENST00000331664	1/2	41	32	9	25	25	0	C2orf71,missense_variant,p.Arg1017Lys,ENST00000331664,;	T	ENSG00000179270	ENST00000331664	Transcript	missense_variant	3050	3050	1017	R/K	aGa/aAa	.	.	.	-1	C2orf71	HGNC	34383	protein_coding	YES	CCDS42669.1	ENSP00000332809	CB071_HUMAN	.	UPI0000251DD8	.	tolerated(0.69)	benign(0.098)	1/2	.	hmmpanther:PTHR22017,Pfam_domain:PF15449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGTCTGTAA	.	5	ESCA
FOXN2	0	.	GRCh37	2	48602081	48602081	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.795A>C	p.Lys265Asn	p.K265N	ENST00000340553	7/7	39	30	9	29	29	0	FOXN2,missense_variant,p.Lys265Asn,ENST00000340553,;FOXN2,downstream_gene_variant,,ENST00000413569,;	C	ENSG00000170802	ENST00000340553	Transcript	missense_variant	1056	795	265	K/N	aaA/aaC	.	.	.	1	FOXN2	HGNC	5281	protein_coding	YES	CCDS1838.1	ENSP00000343633	FOXN2_HUMAN	Q6IS90_HUMAN,C9JTA7_HUMAN	UPI0000226321	.	tolerated(0.48)	benign(0.424)	7/7	.	hmmpanther:PTHR13962,hmmpanther:PTHR13962:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAAAACAGC	.	5	ESCA
MXD1	0	.	GRCh37	2	70168101	70168101	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2685C>G	.	.	ENST00000264444	6/6	29	12	17	26	26	0	MXD1,3_prime_UTR_variant,,ENST00000264444,;MXD1,downstream_gene_variant,,ENST00000540449,;MXD1,downstream_gene_variant,,ENST00000435990,;MXD1,intron_variant,,ENST00000465446,;MXD1,downstream_gene_variant,,ENST00000409442,;	G	ENSG00000059728	ENST00000264444	Transcript	3_prime_UTR_variant	3611	.	.	.	.	.	.	.	1	MXD1	HGNC	6761	protein_coding	YES	CCDS1896.1	ENSP00000264444	MAD1_HUMAN	C9JBE8_HUMAN,B7ZLI7_HUMAN	UPI0000035C7D	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAGTCTTTTT	.	5	ESCA
REG1B	0	.	GRCh37	2	79312718	79312718	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333G>T	p.Trp111Cys	p.W111C	ENST00000305089	5/6	69	65	4	29	29	0	REG1B,missense_variant,p.Trp62Cys,ENST00000454188,;REG1B,missense_variant,p.Trp111Cys,ENST00000305089,;REG1B,non_coding_transcript_exon_variant,,ENST00000479258,;REG1B,downstream_gene_variant,,ENST00000476554,;REG1B,downstream_gene_variant,,ENST00000469052,;	A	ENSG00000172023	ENST00000305089	Transcript	missense_variant	414	333	111	W/C	tgG/tgT	.	.	.	-1	REG1B	HGNC	9952	protein_coding	YES	CCDS1963.1	ENSP00000303206	REG1B_HUMAN	Q6ICS1_HUMAN	UPI00000012AB	.	deleterious(0)	probably_damaging(0.97)	5/6	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF31,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGTGCCAGCG	.	2	ESCA
IGKV1D-8	0	.	GRCh37	2	90260021	90260021	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124A>G	p.Thr42Ala	p.T42A	ENST00000471857	2/2	241	173	68	173	173	0	IGKV1D-8,missense_variant,p.Thr42Ala,ENST00000471857,;	G	ENSG00000239819	ENST00000471857	Transcript	missense_variant	305	124	42	T/A	Acc/Gcc	.	.	.	1	IGKV1D-8	HGNC	5759	IG_V_gene	YES	.	ENSP00000420285	.	.	UPI0000116192	.	deleterious(0.02)	benign(0.154)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267,hmmpanther:PTHR23267:SF122,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTCACCATC	.	5	ESCA
ADAM17	0	.	GRCh37	2	9630607	9630607	+	Missense_Mutation	SNP	C	C	T	rs147275585	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2174G>A	p.Arg725His	p.R725H	ENST00000310823	19/19	48	37	10	51	51	0	ADAM17,missense_variant,p.Arg725His,ENST00000310823,;IAH1,intron_variant,,ENST00000481367,;IAH1,intron_variant,,ENST00000545602,;IAH1,downstream_gene_variant,,ENST00000481688,;IAH1,downstream_gene_variant,,ENST00000470914,;IAH1,downstream_gene_variant,,ENST00000497473,;IAH1,downstream_gene_variant,,ENST00000482918,;IAH1,downstream_gene_variant,,ENST00000487850,;IAH1,downstream_gene_variant,,ENST00000489468,;IAH1,downstream_gene_variant,,ENST00000490621,;IAH1,downstream_gene_variant,,ENST00000484826,;IAH1,downstream_gene_variant,,ENST00000351760,;IAH1,downstream_gene_variant,,ENST00000492223,;IAH1,downstream_gene_variant,,ENST00000495050,;	T	ENSG00000151694	ENST00000310823	Transcript	missense_variant	2357	2174	725	R/H	cGc/cAc	rs147275585,COSM1181782	.	.	-1	ADAM17	HGNC	195	protein_coding	YES	CCDS1665.1	ENSP00000309968	ADA17_HUMAN	Q53S40_HUMAN,Q53RS1_HUMAN,Q53RF5_HUMAN,B2RNB2_HUMAN	UPI00001254D4	.	deleterious(0.01)	probably_damaging(0.999)	19/19	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF121	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATGCGAACC	byCluster	5	ESCA
MORC1	0	.	GRCh37	3	108751662	108751662	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1470T>G	p.%3D	p.L490L	ENST00000232603	16/28	47	39	7	27	27	0	MORC1,synonymous_variant,p.%3D,ENST00000483760,;MORC1,synonymous_variant,p.%3D,ENST00000232603,;	C	ENSG00000114487	ENST00000232603	Transcript	synonymous_variant	1553	1470	490	L	ctT/ctG	.	.	.	-1	MORC1	HGNC	7198	protein_coding	YES	CCDS2955.1	ENSP00000232603	MORC1_HUMAN	.	UPI000013C964	.	.	.	16/28	.	PROSITE_profiles:PS51050,hmmpanther:PTHR23337,hmmpanther:PTHR23337:SF6,Pfam_domain:PF07496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTAAGACA	.	5	ESCA
MAATS1	0	.	GRCh37	3	119452302	119452302	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1293T>A	p.%3D	p.G431G	ENST00000273390	10/18	74	33	41	63	63	0	MAATS1,synonymous_variant,p.%3D,ENST00000273390,;MAATS1,3_prime_UTR_variant,,ENST00000482927,;MAATS1,3_prime_UTR_variant,,ENST00000482573,;MAATS1,3_prime_UTR_variant,,ENST00000475093,;MAATS1,non_coding_transcript_exon_variant,,ENST00000468630,;MAATS1,non_coding_transcript_exon_variant,,ENST00000461322,;MAATS1,non_coding_transcript_exon_variant,,ENST00000483134,;	A	ENSG00000183833	ENST00000273390	Transcript	synonymous_variant	1370	1293	431	G	ggT/ggA	.	.	.	1	MAATS1	HGNC	24010	protein_coding	YES	CCDS2994.1	ENSP00000273390	MAAT1_HUMAN	.	UPI00001C1DFE	.	.	.	10/18	.	hmmpanther:PTHR22455:SF10,hmmpanther:PTHR22455	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGTTTTCT	.	5	ESCA
NR1I2	0	.	GRCh37	3	119530496	119530496	+	Missense_Mutation	SNP	C	C	T	rs780452746	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559C>T	p.Arg187Trp	p.R187W	ENST00000337940	4/9	69	50	18	64	64	0	NR1I2,missense_variant,p.Arg187Trp,ENST00000337940,;NR1I2,missense_variant,p.Arg148Trp,ENST00000466380,;NR1I2,missense_variant,p.Arg148Trp,ENST00000393716,;NR1I2,non_coding_transcript_exon_variant,,ENST00000493757,;NR1I2,downstream_gene_variant,,ENST00000474090,;	T	ENSG00000144852	ENST00000337940	Transcript	missense_variant	607	559	187	R/W	Cgg/Tgg	rs780452746	.	.	1	NR1I2	HGNC	7968	protein_coding	YES	CCDS2995.1	ENSP00000336528	NR1I2_HUMAN	J3KPQ3_HUMAN,F1DAL3_HUMAN,F1D8P9_HUMAN,B3KVM5_HUMAN	UPI000006EC88	.	tolerated(0.05)	benign(0)	4/9	.	hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF39,Superfamily_domains:SSF48508	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGCGGATG	byFrequency	5	ESCA
SI	0	.	GRCh37	3	164730787	164730787	+	Missense_Mutation	SNP	G	G	A	rs192640245	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4043C>T	p.Thr1348Met	p.T1348M	ENST00000264382	34/48	71	55	16	30	30	0	SI,missense_variant,p.Thr1348Met,ENST00000264382,;	A	ENSG00000090402	ENST00000264382	Transcript	missense_variant	4106	4043	1348	T/M	aCg/aTg	rs192640245,COSM2157201	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	deleterious(0.01)	probably_damaging(0.911)	34/48	.	Superfamily_domains:SSF51445,Pfam_domain:PF01055	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCGTTAGA	byCluster|by1000G	5	ESCA
BCHE	0	.	GRCh37	3	165548074	165548074	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.748C>T	p.%3D	p.L250L	ENST00000264381	2/4	111	92	18	44	44	0	BCHE,synonymous_variant,p.%3D,ENST00000264381,;BCHE,intron_variant,,ENST00000540653,;BCHE,intron_variant,,ENST00000479451,;BCHE,intron_variant,,ENST00000488954,;BCHE,synonymous_variant,p.%3D,ENST00000482958,;BCHE,synonymous_variant,p.%3D,ENST00000497011,;	A	ENSG00000114200	ENST00000264381	Transcript	synonymous_variant	915	748	250	L	Ctg/Ttg	.	.	.	-1	BCHE	HGNC	983	protein_coding	YES	CCDS3198.1	ENSP00000264381	CHLE_HUMAN	Q96HL2_HUMAN,F8WF14_HUMAN,D3DNN4_HUMAN	UPI0000127866	.	.	.	2/4	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559:SF154,hmmpanther:PTHR11559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAGAATGG	.	5	ESCA
MASP1	0	.	GRCh37	3	186944257	186944257	+	Missense_Mutation	SNP	G	G	A	rs551848961	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1493C>T	p.Pro498Leu	p.P498L	ENST00000337774	12/16	129	96	33	38	38	0	MASP1,missense_variant,p.Pro498Leu,ENST00000337774,;MASP1,non_coding_transcript_exon_variant,,ENST00000468121,;	A	ENSG00000127241	ENST00000337774	Transcript	missense_variant	1883	1493	498	P/L	cCg/cTg	rs551848961	.	.	-1	MASP1	HGNC	6901	protein_coding	.	CCDS33907.1	ENSP00000336792	MASP1_HUMAN	C9JLU5_HUMAN	UPI0000161FB8	.	tolerated(0.32)	benign(0.007)	12/16	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001155,SMART_domains:SM00020,Superfamily_domains:SSF50494	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCGGATCG	by1000G	5	ESCA
LPP	0	.	GRCh37	3	188594022	188594022	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1755A>G	.	.	ENST00000312675	11/11	105	70	35	61	61	0	LPP,3_prime_UTR_variant,,ENST00000312675,;LPP,3_prime_UTR_variant,,ENST00000543006,;	G	ENSG00000145012	ENST00000312675	Transcript	3_prime_UTR_variant	3840	.	.	.	.	.	.	.	1	LPP	HGNC	6679	protein_coding	YES	CCDS3291.1	ENSP00000318089	LPP_HUMAN	C9JT42_HUMAN,C9JIY7_HUMAN,C9JE51_HUMAN,C9J5C8_HUMAN,C9J4E3_HUMAN,C9J3U9_HUMAN,C9J2R5_HUMAN,C9J1K7_HUMAN,B7Z871_HUMAN	UPI000002E034	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTATTTTA	.	5	ESCA
TGFBR2	0	.	GRCh37	3	30713299	30713299	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.699G>A	p.%3D	p.K233K	ENST00000359013	5/8	18	14	4	25	25	0	TGFBR2,synonymous_variant,p.%3D,ENST00000295754,;TGFBR2,synonymous_variant,p.%3D,ENST00000359013,;	A	ENSG00000163513	ENST00000359013	Transcript	synonymous_variant	982	699	233	K	aaG/aaA	.	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	.	.	5/8	.	hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,PIRSF_domain:PIRSF037393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGAAGCTCAT	.	5	ESCA
NKTR	0	.	GRCh37	3	42659117	42659117	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114C>G	p.Asn38Lys	p.N38K	ENST00000232978	3/17	32	17	15	42	42	0	NKTR,missense_variant,p.Asn38Lys,ENST00000445842,;NKTR,missense_variant,p.Asn38Lys,ENST00000442970,;NKTR,missense_variant,p.Asn38Lys,ENST00000232978,;RP4-613B23.1,intron_variant,,ENST00000445452,;RP4-613B23.1,intron_variant,,ENST00000438017,;NKTR,missense_variant,p.Asn38Lys,ENST00000429888,;NKTR,non_coding_transcript_exon_variant,,ENST00000468735,;NKTR,non_coding_transcript_exon_variant,,ENST00000478488,;NKTR,non_coding_transcript_exon_variant,,ENST00000487466,;NKTR,upstream_gene_variant,,ENST00000465584,;NKTR,upstream_gene_variant,,ENST00000466553,;	G	ENSG00000114857	ENST00000232978	Transcript	missense_variant	302	114	38	N/K	aaC/aaG	.	.	.	1	NKTR	HGNC	7833	protein_coding	YES	CCDS2702.1	ENSP00000232978	NKTR_HUMAN	.	UPI00001301FD	.	deleterious_low_confidence(0)	unknown(0)	3/17	.	PROSITE_profiles:PS50072,hmmpanther:PTHR11071:SF30,hmmpanther:PTHR11071,Gene3D:2.40.100.10,Pfam_domain:PF00160,Superfamily_domains:SSF50891,Prints_domain:PR00153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAACTTCCT	.	5	ESCA
NDST3	0	.	GRCh37	4	119163246	119163246	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2341G>A	p.Asp781Asn	p.D781N	ENST00000296499	12/14	61	49	11	51	51	0	NDST3,missense_variant,p.Asp781Asn,ENST00000296499,;NDST3,downstream_gene_variant,,ENST00000433996,;	A	ENSG00000164100	ENST00000296499	Transcript	missense_variant	2744	2341	781	D/N	Gat/Aat	.	.	.	1	NDST3	HGNC	7682	protein_coding	YES	CCDS3708.1	ENSP00000296499	NDST3_HUMAN	.	UPI0000071C44	.	tolerated(0.45)	benign(0.064)	12/14	.	hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF15,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATGGATGAA	.	5	ESCA
SYNPO2	0	.	GRCh37	4	119978554	119978554	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3253-2A>C	.	p.X1085_splice	ENST00000307142	.	53	42	11	37	37	0	SYNPO2,splice_acceptor_variant,,ENST00000448416,;SYNPO2,splice_acceptor_variant,,ENST00000307142,;SYNPO2,splice_acceptor_variant,,ENST00000504178,;	C	ENSG00000172403	ENST00000307142	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	SYNPO2	HGNC	17732	protein_coding	YES	CCDS34054.1	ENSP00000306015	SYNP2_HUMAN	.	UPI00001D75EB	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTAGGAGA	.	5	ESCA
SPOCK3	0	.	GRCh37	4	167658627	167658627	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1132G>A	p.Ala378Thr	p.A378T	ENST00000357154	11/12	25	18	6	30	30	0	SPOCK3,missense_variant,p.Ala378Thr,ENST00000357154,;SPOCK3,missense_variant,p.Ala378Thr,ENST00000511531,;SPOCK3,missense_variant,p.Ala375Thr,ENST00000357545,;SPOCK3,missense_variant,p.Ala378Thr,ENST00000506886,;SPOCK3,missense_variant,p.Ala375Thr,ENST00000511269,;SPOCK3,missense_variant,p.Ala327Thr,ENST00000421836,;SPOCK3,missense_variant,p.Ala335Thr,ENST00000510741,;SPOCK3,missense_variant,p.Ala246Thr,ENST00000535728,;SPOCK3,missense_variant,p.Ala280Thr,ENST00000541637,;SPOCK3,missense_variant,p.Ala258Thr,ENST00000541354,;SPOCK3,missense_variant,p.Ala280Thr,ENST00000512681,;SPOCK3,missense_variant,p.Ala282Thr,ENST00000534949,;SPOCK3,missense_variant,p.Ala378Thr,ENST00000502330,;SPOCK3,missense_variant,p.Ala375Thr,ENST00000504953,;SPOCK3,non_coding_transcript_exon_variant,,ENST00000507137,;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,;	T	ENSG00000196104	ENST00000357154	Transcript	missense_variant	1270	1132	378	A/T	Gca/Aca	.	.	.	-1	SPOCK3	HGNC	13565	protein_coding	YES	CCDS54817.1	ENSP00000349677	TICN3_HUMAN	Q4W5S3_HUMAN,Q4W5E2_HUMAN,E7EMP8_HUMAN	UPI000004BA60	.	tolerated(0.29)	benign(0.068)	11/12	.	PROSITE_profiles:PS51162,hmmpanther:PTHR12036,hmmpanther:PTHR12036:SF4,Pfam_domain:PF00086,SMART_domains:SM00211,Superfamily_domains:SSF57610	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGCAACAC	.	5	ESCA
ZFP42	0	.	GRCh37	4	188925348	188925348	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*454T>C	.	.	ENST00000326866	4/4	40	26	13	35	35	0	ZFP42,3_prime_UTR_variant,,ENST00000326866,;ZFP42,3_prime_UTR_variant,,ENST00000509524,;	C	ENSG00000179059	ENST00000326866	Transcript	3_prime_UTR_variant	1795	.	.	.	.	.	.	.	1	ZFP42	HGNC	30949	protein_coding	YES	CCDS3849.1	ENSP00000317686	ZFP42_HUMAN	.	UPI0000049CA7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAATCCCAA	.	5	ESCA
MUC7	0	.	GRCh37	4	71346520	71346520	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59G>C	p.Ser20Thr	p.S20T	ENST00000413702	4/4	44	21	23	26	26	0	MUC7,missense_variant,p.Ser20Thr,ENST00000413702,;MUC7,missense_variant,p.Ser20Thr,ENST00000505411,;MUC7,missense_variant,p.Ser20Thr,ENST00000456088,;MUC7,missense_variant,p.Ser20Thr,ENST00000304887,;MUC7,non_coding_transcript_exon_variant,,ENST00000514512,;MUC7,non_coding_transcript_exon_variant,,ENST00000504482,;	C	ENSG00000171195	ENST00000413702	Transcript	missense_variant	347	59	20	S/T	aGt/aCt	COSM734837	.	.	1	MUC7	HGNC	7518	protein_coding	YES	CCDS3541.1	ENSP00000407422	MUC7_HUMAN	D6RHX1_HUMAN	UPI000013E9DD	.	deleterious(0.02)	possibly_damaging(0.801)	4/4	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCAGTGAAG	.	5	ESCA
FAM175A	0	.	GRCh37	4	84406270	84406270	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-45C>A	.	.	ENST00000321945	1/9	20	12	8	28	28	0	FAM175A,5_prime_UTR_variant,,ENST00000321945,;FAM175A,intron_variant,,ENST00000506553,;FAM175A,upstream_gene_variant,,ENST00000515303,;FAM175A,intron_variant,,ENST00000505489,;FAM175A,upstream_gene_variant,,ENST00000503217,;FAM175A,upstream_gene_variant,,ENST00000511801,;FAM175A,upstream_gene_variant,,ENST00000475656,;	T	ENSG00000163322	ENST00000321945	Transcript	5_prime_UTR_variant	65	.	.	.	.	.	.	.	-1	FAM175A	HGNC	25829	protein_coding	YES	CCDS3605.2	ENSP00000369857	F175A_HUMAN	D6REL5_HUMAN	UPI00005A8ABD	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGCGCGGAG	.	5	ESCA
FCHO2	0	.	GRCh37	5	72384732	72384732	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*815A>T	.	.	ENST00000430046	26/26	42	25	16	35	35	0	FCHO2,3_prime_UTR_variant,,ENST00000341845,;FCHO2,3_prime_UTR_variant,,ENST00000430046,;FCHO2,downstream_gene_variant,,ENST00000512348,;	T	ENSG00000157107	ENST00000430046	Transcript	3_prime_UTR_variant	3364	.	.	.	.	.	.	.	1	FCHO2	HGNC	25180	protein_coding	YES	CCDS47230.1	ENSP00000393776	FCHO2_HUMAN	B4DEU7_HUMAN	UPI000019971A	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTAATGTGC	.	5	ESCA
ERAP1	0	.	GRCh37	5	96098742	96098742	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*162T>C	.	.	ENST00000296754	20/20	30	9	21	30	30	0	ERAP1,3_prime_UTR_variant,,ENST00000296754,;CAST,intron_variant,,ENST00000508608,;CAST,intron_variant,,ENST00000395813,;CAST,intron_variant,,ENST00000511049,;CAST,intron_variant,,ENST00000508579,;CAST,intron_variant,,ENST00000508830,;CAST,intron_variant,,ENST00000325674,;CAST,intron_variant,,ENST00000510756,;CAST,intron_variant,,ENST00000511782,;CAST,intron_variant,,ENST00000510156,;CAST,intron_variant,,ENST00000359176,;CAST,intron_variant,,ENST00000395812,;CAST,intron_variant,,ENST00000309190,;CAST,intron_variant,,ENST00000509903,;CAST,intron_variant,,ENST00000341926,;CAST,intron_variant,,ENST00000510500,;CAST,intron_variant,,ENST00000338252,;CAST,intron_variant,,ENST00000437034,;CAST,intron_variant,,ENST00000515663,;CAST,intron_variant,,ENST00000504465,;CAST,intron_variant,,ENST00000348386,;CAST,intron_variant,,ENST00000484552,;CAST,intron_variant,,ENST00000510098,;	G	ENSG00000164307	ENST00000296754	Transcript	3_prime_UTR_variant	3267	.	.	.	.	.	.	.	-1	ERAP1	HGNC	18173	protein_coding	YES	CCDS4085.1	ENSP00000296754	ERAP1_HUMAN	D6RAL9_HUMAN	UPI000045731D	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAAAGGGAT	.	5	ESCA
NR2E1	0	.	GRCh37	6	108489319	108489319	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25+1325C>T	.	.	ENST00000368986	.	34	11	23	65	65	0	NR2E1,missense_variant,p.Pro30Leu,ENST00000368983,;NR2E1,intron_variant,,ENST00000368986,;OSTM1,upstream_gene_variant,,ENST00000440575,;NR2E1,upstream_gene_variant,,ENST00000426403,;OSTM1,upstream_gene_variant,,ENST00000492070,;	T	ENSG00000112333	ENST00000368986	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NR2E1	HGNC	7973	protein_coding	YES	CCDS5063.1	ENSP00000357982	NR2E1_HUMAN	B6ZGT9_HUMAN,A6PVF6_HUMAN	UPI0000130478	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCCTTTAG	.	5	ESCA
GJA1	0	.	GRCh37	6	121768609	121768609	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616A>G	p.Lys206Glu	p.K206E	ENST00000282561	2/2	107	74	33	125	124	0	GJA1,missense_variant,p.Lys206Glu,ENST00000282561,;	G	ENSG00000152661	ENST00000282561	Transcript	missense_variant	773	616	206	K/E	Aaa/Gaa	.	.	.	1	GJA1	HGNC	4274	protein_coding	YES	CCDS5123.1	ENSP00000282561	CXA1_HUMAN	B4DN50_HUMAN,B4DMC9_HUMAN,B4DI81_HUMAN	UPI000013DCEC	.	deleterious(0)	probably_damaging(0.999)	2/2	.	hmmpanther:PTHR11984:SF33,hmmpanther:PTHR11984,Pfam_domain:PF10582,Gene3D:2zw3A00,SMART_domains:SM01089,Prints_domain:PR00206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGAGAAAACC	.	5	ESCA
LATS1	0	.	GRCh37	6	149982764	149982764	+	3'UTR	SNP	T	T	C	rs367556235	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*101A>G	.	.	ENST00000543571	8/8	46	39	7	33	33	0	LATS1,3_prime_UTR_variant,,ENST00000253339,;LATS1,3_prime_UTR_variant,,ENST00000543571,;LATS1,downstream_gene_variant,,ENST00000441107,;	C	ENSG00000131023	ENST00000543571	Transcript	3_prime_UTR_variant	4042	.	.	.	.	rs367556235	.	.	-1	LATS1	HGNC	6514	protein_coding	YES	CCDS34551.1	ENSP00000437550	LATS1_HUMAN	.	UPI0000073DC2	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATATATAGC	.	4	ESCA
SYNE1	0	.	GRCh37	6	152751661	152751661	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4645G>A	p.Gly1549Arg	p.G1549R	ENST00000367255	35/146	45	35	9	40	40	0	SYNE1,missense_variant,p.Gly1556Arg,ENST00000423061,;SYNE1,missense_variant,p.Gly1556Arg,ENST00000448038,;SYNE1,missense_variant,p.Gly1549Arg,ENST00000367255,;SYNE1,missense_variant,p.Gly1549Arg,ENST00000367253,;SYNE1,missense_variant,p.Gly1619Arg,ENST00000341594,;SYNE1,missense_variant,p.Gly1549Arg,ENST00000265368,;SYNE1,downstream_gene_variant,,ENST00000367248,;SYNE1,downstream_gene_variant,,ENST00000413186,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,;	T	ENSG00000131018	ENST00000367255	Transcript	missense_variant	5247	4645	1549	G/R	Gga/Aga	.	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	possibly_damaging(0.516)	35/146	.	Superfamily_domains:SSF46966,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTCCCAGGA	.	5	ESCA
SLC17A3	0	.	GRCh37	6	25845682	25845682	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1425A>T	p.%3D	p.L475L	ENST00000397060	12/13	17	5	12	23	23	0	SLC17A3,synonymous_variant,p.%3D,ENST00000360657,;SLC17A3,synonymous_variant,p.%3D,ENST00000505420,;SLC17A3,synonymous_variant,p.%3D,ENST00000397060,;SLC17A3,synonymous_variant,p.%3D,ENST00000481949,;SLC17A3,synonymous_variant,p.%3D,ENST00000361703,;SLC17A3,downstream_gene_variant,,ENST00000503922,;SLC17A3,downstream_gene_variant,,ENST00000506105,;SLC17A3,downstream_gene_variant,,ENST00000509714,;	A	ENSG00000124564	ENST00000397060	Transcript	synonymous_variant	1535	1425	475	L	ctA/ctT	.	.	.	-1	SLC17A3	HGNC	10931	protein_coding	YES	CCDS47385.1	ENSP00000380250	NPT4_HUMAN	H0Y9F7_HUMAN	UPI0001536779	.	.	.	12/13	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF134,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAGTAGTCC	.	5	ESCA
HIST1H1A	0	.	GRCh37	6	26017677	26017677	+	Missense_Mutation	SNP	G	G	T	rs375118598	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.284C>A	p.Thr95Lys	p.T95K	ENST00000244573	1/1	63	22	40	84	84	0	HIST1H1A,missense_variant,p.Thr95Lys,ENST00000244573,;HIST1H4A,upstream_gene_variant,,ENST00000359907,;HIST1H3A,upstream_gene_variant,,ENST00000357647,;U91328.22,downstream_gene_variant,,ENST00000608919,;HIST1H1PS2,downstream_gene_variant,,ENST00000437528,;	T	ENSG00000124610	ENST00000244573	Transcript	missense_variant	364	284	95	T/K	aCg/aAg	rs375118598,COSM71060	.	.	-1	HIST1H1A	HGNC	4715	protein_coding	YES	CCDS4569.1	ENSP00000244573	H11_HUMAN	.	UPI0000001BD8	.	deleterious(0.01)	probably_damaging(0.999)	1/1	.	PROSITE_profiles:PS51504,hmmpanther:PTHR11467:SF25,hmmpanther:PTHR11467,Gene3D:1.10.10.10,Pfam_domain:PF00538,SMART_domains:SM00526,Superfamily_domains:SSF46785,Prints_domain:PR00624	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAACGTTCCC	byCluster	5	ESCA
SRSF3	0	.	GRCh37	6	36567835	36567835	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.341+1075C>A	.	.	ENST00000373715	.	41	10	30	84	84	0	SRSF3,3_prime_UTR_variant,,ENST00000339436,;SRSF3,intron_variant,,ENST00000373715,;SRSF3,3_prime_UTR_variant,,ENST00000477442,;	A	ENSG00000112081	ENST00000373715	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SRSF3	HGNC	10785	protein_coding	YES	CCDS4823.1	ENSP00000362820	SRSF3_HUMAN	B2R6F3_HUMAN	UPI0000004131	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTCCTGGC	.	5	ESCA
MUC17	0	.	GRCh37	7	100681041	100681041	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6344C>A	p.Ala2115Asp	p.A2115D	ENST00000306151	3/13	135	89	46	90	90	0	MUC17,missense_variant,p.Ala2115Asp,ENST00000306151,;MUC17,missense_variant,p.Ala2115Asp,ENST00000379439,;	A	ENSG00000169876	ENST00000306151	Transcript	missense_variant	6408	6344	2115	A/D	gCc/gAc	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	unknown(0)	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGCCAGTC	.	5	ESCA
CCDC136	0	.	GRCh37	7	128451963	128451963	+	Missense_Mutation	SNP	G	G	A	rs570468395	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2138G>A	p.Arg713Gln	p.R713Q	ENST00000297788	13/18	41	18	22	30	30	0	CCDC136,missense_variant,p.Arg713Gln,ENST00000297788,;CCDC136,missense_variant,p.Arg590Gln,ENST00000494552,;CCDC136,missense_variant,p.Arg304Gln,ENST00000464672,;CCDC136,intron_variant,,ENST00000464832,;CCDC136,intron_variant,,ENST00000487361,;CCDC136,intron_variant,,ENST00000378685,;CCDC136,upstream_gene_variant,,ENST00000471729,;CCDC136,non_coding_transcript_exon_variant,,ENST00000480137,;CCDC136,intron_variant,,ENST00000528772,;CCDC136,downstream_gene_variant,,ENST00000460941,;CCDC136,downstream_gene_variant,,ENST00000485832,;	A	ENSG00000128596	ENST00000297788	Transcript	missense_variant	2505	2138	713	R/Q	cGg/cAg	rs570468395	.	.	1	CCDC136	HGNC	22225	protein_coding	YES	CCDS47704.1	ENSP00000297788	CC136_HUMAN	C9JAD8_HUMAN,C9J884_HUMAN,C9IYI5_HUMAN	UPI0000E445DE	.	tolerated(0.12)	benign(0.35)	13/18	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18889:SF9,hmmpanther:PTHR18889	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGCGGAAGA	by1000G	5	ESCA
DGKI	0	.	GRCh37	7	137374666	137374666	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484G>T	p.Glu162Ter	p.E162*	ENST00000288490	2/34	30	20	10	18	18	0	DGKI,stop_gained,p.Glu162Ter,ENST00000288490,;DGKI,stop_gained,p.Glu162Ter,ENST00000424189,;DGKI,stop_gained,p.Glu162Ter,ENST00000446122,;DGKI,intron_variant,,ENST00000453654,;DGKI,non_coding_transcript_exon_variant,,ENST00000483619,;DGKI,non_coding_transcript_exon_variant,,ENST00000470895,;	A	ENSG00000157680	ENST00000288490	Transcript	stop_gained	485	484	162	E/*	Gag/Tag	.	.	.	-1	DGKI	HGNC	2855	protein_coding	YES	CCDS5845.1	ENSP00000288490	DGKI_HUMAN	B3KR69_HUMAN	UPI000012DD23	.	.	.	2/34	.	hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTCCTTGG	.	5	ESCA
ZNF775	0	.	GRCh37	7	150093612	150093612	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43G>T	p.Val15Leu	p.V15L	ENST00000329630	3/3	47	42	5	41	41	0	ZNF775,missense_variant,p.Val15Leu,ENST00000478789,;ZNF775,missense_variant,p.Val15Leu,ENST00000329630,;ZNF775,missense_variant,p.Val15Leu,ENST00000490973,;ZNF775,intron_variant,,ENST00000483664,;ZNF775,intron_variant,,ENST00000486297,;ZNF775,upstream_gene_variant,,ENST00000476489,;	T	ENSG00000196456	ENST00000329630	Transcript	missense_variant	150	43	15	V/L	Gtg/Ttg	.	.	.	1	ZNF775	HGNC	28501	protein_coding	YES	CCDS43678.1	ENSP00000330838	ZN775_HUMAN	C9JVG2_HUMAN,C9JAM7_HUMAN	UPI00001BDA25	.	tolerated_low_confidence(0.3)	benign(0.005)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTGGTGATG	.	4	ESCA
CHPF2	0	.	GRCh37	7	150934477	150934477	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1029G>A	p.%3D	p.L343L	ENST00000035307	4/4	57	45	12	41	41	0	CHPF2,synonymous_variant,p.%3D,ENST00000035307,;CHPF2,synonymous_variant,p.%3D,ENST00000495645,;CHPF2,downstream_gene_variant,,ENST00000482173,;SMARCD3,downstream_gene_variant,,ENST00000262188,;SMARCD3,downstream_gene_variant,,ENST00000392811,;SMARCD3,downstream_gene_variant,,ENST00000356800,;MIR671,upstream_gene_variant,,ENST00000390183,;RP4-548D19.3,upstream_gene_variant,,ENST00000607902,;SMARCD3,downstream_gene_variant,,ENST00000489503,;SMARCD3,downstream_gene_variant,,ENST00000477169,;SMARCD3,downstream_gene_variant,,ENST00000496530,;CHPF2,3_prime_UTR_variant,,ENST00000465601,;SMARCD3,downstream_gene_variant,,ENST00000470588,;SMARCD3,downstream_gene_variant,,ENST00000485592,;SMARCD3,downstream_gene_variant,,ENST00000472988,;SMARCD3,downstream_gene_variant,,ENST00000472103,;SMARCD3,downstream_gene_variant,,ENST00000469154,;SMARCD3,downstream_gene_variant,,ENST00000485610,;SMARCD3,downstream_gene_variant,,ENST00000472789,;	A	ENSG00000033100	ENST00000035307	Transcript	synonymous_variant	2542	1029	343	L	ctG/ctA	.	.	.	1	CHPF2	HGNC	29270	protein_coding	YES	CCDS34779.1	ENSP00000035307	CHPF2_HUMAN	.	UPI000003F537	.	.	.	4/4	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12369:SF14,hmmpanther:PTHR12369,Pfam_domain:PF05679	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCTGACCGT	.	5	ESCA
ITGB8	0	.	GRCh37	7	20451854	20451854	+	3'UTR	SNP	G	G	T	rs115227488	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2234G>T	.	.	ENST00000222573	14/14	26	21	5	20	20	0	ITGB8,3_prime_UTR_variant,,ENST00000222573,;ITGB8,downstream_gene_variant,,ENST00000537992,;	T	ENSG00000105855	ENST00000222573	Transcript	3_prime_UTR_variant	5228	.	.	.	.	rs115227488	.	.	1	ITGB8	HGNC	6163	protein_coding	YES	CCDS5370.1	ENSP00000222573	ITB8_HUMAN	B4DHD4_HUMAN	UPI000012DA14	.	.	.	14/14	.	.	T:0.0156	T:0.0567	T:0.0043	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTGCATTT	byFrequency|byCluster|by1000G	5	ESCA
CPVL	0	.	GRCh37	7	29152428	29152428	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180G>C	p.Leu60Phe	p.L60F	ENST00000409850	7/17	73	61	11	41	41	0	CPVL,missense_variant,p.Leu60Phe,ENST00000265394,;CPVL,missense_variant,p.Leu60Phe,ENST00000409850,;CPVL,missense_variant,p.Leu60Phe,ENST00000396276,;CPVL,5_prime_UTR_variant,,ENST00000447426,;CPVL,5_prime_UTR_variant,,ENST00000448959,;CPVL,non_coding_transcript_exon_variant,,ENST00000488891,;	G	ENSG00000106066	ENST00000409850	Transcript	missense_variant	827	180	60	L/F	ttG/ttC	.	.	.	-1	CPVL	HGNC	14399	protein_coding	YES	CCDS5419.1	ENSP00000387164	CPVL_HUMAN	Q75MM4_HUMAN,O75225_HUMAN,C9JZ94_HUMAN,C9JVI2_HUMAN,C9JLV0_HUMAN,C9JI22_HUMAN,C9J6L4_HUMAN	UPI0000048F1B	.	deleterious(0.04)	benign(0.316)	7/17	.	hmmpanther:PTHR11802	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACTCAATTC	.	4	ESCA
PGAM2	0	.	GRCh37	7	44104883	44104883	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246G>T	p.%3D	p.V82V	ENST00000297283	1/3	59	43	16	41	41	0	PGAM2,synonymous_variant,p.%3D,ENST00000297283,;DBNL,3_prime_UTR_variant,,ENST00000432854,;DBNL,downstream_gene_variant,,ENST00000448521,;DBNL,downstream_gene_variant,,ENST00000452661,;DBNL,downstream_gene_variant,,ENST00000456905,;DBNL,downstream_gene_variant,,ENST00000494774,;DBNL,downstream_gene_variant,,ENST00000452943,;DBNL,downstream_gene_variant,,ENST00000468694,;DBNL,downstream_gene_variant,,ENST00000490734,;DBNL,downstream_gene_variant,,ENST00000440166,;AC017116.11,non_coding_transcript_exon_variant,,ENST00000425727,;AC017116.11,non_coding_transcript_exon_variant,,ENST00000445938,;DBNL,downstream_gene_variant,,ENST00000497184,;DBNL,downstream_gene_variant,,ENST00000498733,;DBNL,downstream_gene_variant,,ENST00000449997,;DBNL,downstream_gene_variant,,ENST00000429716,;DBNL,downstream_gene_variant,,ENST00000411855,;DBNL,downstream_gene_variant,,ENST00000441840,;	A	ENSG00000164708	ENST00000297283	Transcript	synonymous_variant	304	246	82	V	gtG/gtT	.	.	.	-1	PGAM2	HGNC	8889	protein_coding	YES	CCDS34624.1	ENSP00000297283	PGAM2_HUMAN	.	UPI000013E3E8	.	.	.	1/3	.	HAMAP:MF_01039,hmmpanther:PTHR11931,hmmpanther:PTHR11931:SF8,TIGRFAM_domain:TIGR01258,Pfam_domain:PF00300,Gene3D:3.40.50.1240,SMART_domains:SM00855,Superfamily_domains:SSF53254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCGCACCAC	.	5	ESCA
VSTM2A	0	.	GRCh37	7	54617841	54617841	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612C>A	p.%3D	p.I204I	ENST00000407838	4/5	28	24	4	11	11	0	VSTM2A,synonymous_variant,p.%3D,ENST00000402026,;VSTM2A,synonymous_variant,p.%3D,ENST00000302287,;VSTM2A,synonymous_variant,p.%3D,ENST00000402613,;VSTM2A,synonymous_variant,p.%3D,ENST00000404951,;VSTM2A,synonymous_variant,p.%3D,ENST00000407838,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000466888,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000498834,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000469952,;VSTM2A,downstream_gene_variant,,ENST00000495904,;	A	ENSG00000170419	ENST00000407838	Transcript	synonymous_variant	1018	612	204	I	atC/atA	.	.	.	1	VSTM2A	HGNC	28499	protein_coding	YES	CCDS5512.2	ENSP00000384967	VTM2A_HUMAN	.	UPI0000EE7EC1	.	.	.	4/5	.	hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AAAATCCCCAA	.	3	ESCA
CALN1	0	.	GRCh37	7	71868318	71868318	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37G>A	p.Glu13Lys	p.E13K	ENST00000395275	2/7	143	110	33	95	95	0	CALN1,missense_variant,p.Glu13Lys,ENST00000395275,;CALN1,missense_variant,p.Glu13Lys,ENST00000412588,;CALN1,intron_variant,,ENST00000431984,;CALN1,intron_variant,,ENST00000395276,;	T	ENSG00000183166	ENST00000395275	Transcript	missense_variant	426	37	13	E/K	Gag/Aag	.	.	.	-1	CALN1	HGNC	13248	protein_coding	YES	CCDS47603.1	ENSP00000378690	CABP8_HUMAN	Q86UM7_HUMAN,Q86UL5_HUMAN,Q75MW5_HUMAN,Q75MP5_HUMAN,Q75MI2_HUMAN,E9PFU3_HUMAN,A4D1Z1_HUMAN	UPI0000D4B903	.	tolerated_low_confidence(0.3)	benign(0)	2/7	.	hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTCGGGCT	.	5	ESCA
MDH2	0	.	GRCh37	7	75684274	75684274	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193G>A	p.Ala65Thr	p.A65T	ENST00000315758	2/9	32	28	4	24	24	0	MDH2,missense_variant,p.Ala65Thr,ENST00000315758,;MDH2,missense_variant,p.Ala65Thr,ENST00000432020,;MDH2,intron_variant,,ENST00000443006,;MDH2,non_coding_transcript_exon_variant,,ENST00000490105,;MDH2,non_coding_transcript_exon_variant,,ENST00000492663,;MDH2,non_coding_transcript_exon_variant,,ENST00000461665,;	A	ENSG00000146701	ENST00000315758	Transcript	missense_variant	287	193	65	A/T	Gcc/Acc	.	.	.	1	MDH2	HGNC	6971	protein_coding	YES	CCDS5581.1	ENSP00000327070	MDHM_HUMAN	Q75MT9_HUMAN,Q0QF37_HUMAN,G3XAL0_HUMAN	UPI000013DA68	.	tolerated(0.09)	probably_damaging(0.971)	2/9	.	hmmpanther:PTHR11540:SF16,hmmpanther:PTHR11540,Pfam_domain:PF00056,TIGRFAM_domain:TIGR01772,Gene3D:3.40.50.720,PIRSF_domain:PIRSF000102,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTGGCCGCA	.	2	ESCA
MDH2	0	.	GRCh37	7	75684275	75684275	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194C>A	p.Ala65Asp	p.A65D	ENST00000315758	2/9	34	30	4	24	24	0	MDH2,missense_variant,p.Ala65Asp,ENST00000315758,;MDH2,missense_variant,p.Ala65Asp,ENST00000432020,;MDH2,intron_variant,,ENST00000443006,;MDH2,non_coding_transcript_exon_variant,,ENST00000490105,;MDH2,non_coding_transcript_exon_variant,,ENST00000492663,;MDH2,non_coding_transcript_exon_variant,,ENST00000461665,;	A	ENSG00000146701	ENST00000315758	Transcript	missense_variant	288	194	65	A/D	gCc/gAc	.	.	.	1	MDH2	HGNC	6971	protein_coding	YES	CCDS5581.1	ENSP00000327070	MDHM_HUMAN	Q75MT9_HUMAN,Q0QF37_HUMAN,G3XAL0_HUMAN	UPI000013DA68	.	deleterious(0)	probably_damaging(0.988)	2/9	.	hmmpanther:PTHR11540:SF16,hmmpanther:PTHR11540,Pfam_domain:PF00056,TIGRFAM_domain:TIGR01772,Gene3D:3.40.50.720,PIRSF_domain:PIRSF000102,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGGCCGCAG	.	2	ESCA
ADAM22	0	.	GRCh37	7	87778344	87778344	+	Missense_Mutation	SNP	G	G	A	rs200398630	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1538G>A	p.Arg513His	p.R513H	ENST00000265727	18/31	32	15	16	26	26	0	ADAM22,missense_variant,p.Arg513His,ENST00000398209,;ADAM22,missense_variant,p.Arg480His,ENST00000398203,;ADAM22,missense_variant,p.Arg513His,ENST00000315984,;ADAM22,missense_variant,p.Arg513His,ENST00000265727,;ADAM22,missense_variant,p.Arg513His,ENST00000398201,;ADAM22,missense_variant,p.Arg513His,ENST00000398204,;	A	ENSG00000008277	ENST00000265727	Transcript	missense_variant	1617	1538	513	R/H	cGt/cAt	rs200398630	.	.	1	ADAM22	HGNC	201	protein_coding	YES	CCDS47637.1	ENSP00000265727	ADA22_HUMAN	Q9UKK0_HUMAN,Q86UM2_HUMAN,Q75MS7_HUMAN,F8WAD8_HUMAN,D6W5P7_HUMAN	UPI00001254DC	.	deleterious(0.02)	benign(0.001)	18/31	.	PROSITE_profiles:PS50214,hmmpanther:PTHR11905:SF14,hmmpanther:PTHR11905,Gene3D:4.10.70.10,Pfam_domain:PF00200,SMART_domains:SM00050,Superfamily_domains:SSF57552	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTCGTGAAA	byCluster|by1000G	5	ESCA
ZNF804B	0	.	GRCh37	7	88964139	88964139	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1843A>G	p.Lys615Glu	p.K615E	ENST00000333190	4/4	38	26	11	27	27	0	ZNF804B,missense_variant,p.Lys615Glu,ENST00000333190,;	G	ENSG00000182348	ENST00000333190	Transcript	missense_variant	2452	1843	615	K/E	Aag/Gag	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	deleterious(0.01)	benign(0.055)	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGAAAGGCA	.	5	ESCA
TRRAP	0	.	GRCh37	7	98586521	98586521	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9535G>T	p.Ala3179Ser	p.A3179S	ENST00000359863	62/72	48	37	10	37	37	0	TRRAP,missense_variant,p.Ala3150Ser,ENST00000355540,;TRRAP,missense_variant,p.Ala3150Ser,ENST00000446306,;TRRAP,missense_variant,p.Ala2890Ser,ENST00000456197,;TRRAP,missense_variant,p.Ala3179Ser,ENST00000359863,;	T	ENSG00000196367	ENST00000359863	Transcript	missense_variant	9744	9535	3179	A/S	Gcc/Tcc	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	possibly_damaging(0.687)	62/72	.	PROSITE_profiles:PS51189,hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139,Pfam_domain:PF02259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTGCCATC	.	5	ESCA
TRMT12	0	.	GRCh37	8	125463784	125463784	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616A>G	p.Ile206Val	p.I206V	ENST00000328599	1/1	100	79	21	82	82	0	TRMT12,missense_variant,p.Ile206Val,ENST00000328599,;TRMT12,intron_variant,,ENST00000521443,;TRMT12,intron_variant,,ENST00000522518,;	G	ENSG00000183665	ENST00000328599	Transcript	missense_variant	737	616	206	I/V	Atc/Gtc	.	.	.	1	TRMT12	HGNC	26091	protein_coding	YES	CCDS6349.1	ENSP00000329858	TYW2_HUMAN	.	UPI0000140A61	.	deleterious(0.03)	possibly_damaging(0.805)	1/1	.	PROSITE_profiles:PS51684,hmmpanther:PTHR23245:SF33,hmmpanther:PTHR23245,Gene3D:3.40.50.150,Pfam_domain:PF02475,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGTATCCGT	.	5	ESCA
ADCY8	0	.	GRCh37	8	132051802	132051802	+	Missense_Mutation	SNP	C	C	G	rs529610958	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778G>C	p.Ala260Pro	p.A260P	ENST00000286355	1/18	65	58	7	36	36	0	ADCY8,missense_variant,p.Ala260Pro,ENST00000286355,;ADCY8,missense_variant,p.Ala260Pro,ENST00000377928,;	G	ENSG00000155897	ENST00000286355	Transcript	missense_variant	2871	778	260	A/P	Gca/Cca	rs529610958	.	.	-1	ADCY8	HGNC	239	protein_coding	YES	CCDS6363.1	ENSP00000286355	ADCY8_HUMAN	E5RFR2_HUMAN	UPI000012887C	.	deleterious(0.04)	possibly_damaging(0.483)	1/18	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF229	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTGCTGCCA	by1000G	4	ESCA
SLC26A7	0	.	GRCh37	8	92406495	92406495	+	Missense_Mutation	SNP	C	C	A	rs775261627	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1985C>A	p.Pro662Gln	p.P662Q	ENST00000309536	19/19	73	47	26	64	64	0	SLC26A7,missense_variant,p.Pro662Gln,ENST00000309536,;SLC26A7,intron_variant,,ENST00000276609,;SLC26A7,intron_variant,,ENST00000523719,;SLC26A7,intron_variant,,ENST00000520249,;SLC26A7,downstream_gene_variant,,ENST00000517930,;SLC26A7,intron_variant,,ENST00000522181,;	A	ENSG00000147606	ENST00000309536	Transcript	missense_variant	2205	1985	662	P/Q	cCg/cAg	rs775261627	.	.	1	SLC26A7	HGNC	14467	protein_coding	YES	CCDS6255.1	ENSP00000309504	S26A7_HUMAN	E5RFH2_HUMAN	UPI0000046B1C	.	.	probably_damaging(0.946)	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACCGCTCT	byFrequency	5	ESCA
TP53INP1	0	.	GRCh37	8	95940110	95940110	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2597G>A	.	.	ENST00000342697	4/4	24	16	8	29	29	0	TP53INP1,3_prime_UTR_variant,,ENST00000342697,;TP53INP1,3_prime_UTR_variant,,ENST00000448464,;NDUFAF6,intron_variant,,ENST00000519136,;NDUFAF6,intron_variant,,ENST00000396113,;NDUFAF6,intron_variant,,ENST00000523378,;TP53INP1,downstream_gene_variant,,ENST00000378776,;	T	ENSG00000164938	ENST00000342697	Transcript	3_prime_UTR_variant	3728	.	.	.	.	.	.	.	-1	TP53INP1	HGNC	18022	protein_coding	YES	CCDS6265.1	ENSP00000344215	T53I1_HUMAN	.	UPI00000725F8	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TAAAGCGCATT	.	4	ESCA
TNC	0	.	GRCh37	9	117838320	117838320	+	Missense_Mutation	SNP	C	C	T	rs139800185	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2941G>A	p.Ala981Thr	p.A981T	ENST00000350763	9/28	96	74	21	76	76	0	TNC,missense_variant,p.Ala981Thr,ENST00000345230,;TNC,missense_variant,p.Ala981Thr,ENST00000542877,;TNC,missense_variant,p.Ala981Thr,ENST00000346706,;TNC,missense_variant,p.Ala981Thr,ENST00000537320,;TNC,missense_variant,p.Ala981Thr,ENST00000341037,;TNC,missense_variant,p.Ala981Thr,ENST00000350763,;TNC,missense_variant,p.Ala981Thr,ENST00000535648,;TNC,missense_variant,p.Ala981Thr,ENST00000340094,;TNC,missense_variant,p.Ala981Thr,ENST00000423613,;TNC,upstream_gene_variant,,ENST00000473855,;TNC,upstream_gene_variant,,ENST00000498724,;	T	ENSG00000041982	ENST00000350763	Transcript	missense_variant	3353	2941	981	A/T	Gca/Aca	rs139800185	.	.	-1	TNC	HGNC	5318	protein_coding	YES	CCDS6811.1	ENSP00000265131	TENA_HUMAN	F5H5D6_HUMAN	UPI000013D5BD	.	deleterious(0.02)	possibly_damaging(0.509)	9/28	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF38,hmmpanther:PTHR19143,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTGCGTTGA	byFrequency|byCluster	5	ESCA
OR1J1	0	.	GRCh37	9	125239311	125239311	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895G>A	p.Gly299Arg	p.G299R	ENST00000259357	1/1	97	67	29	73	73	0	OR1J1,missense_variant,p.Gly299Arg,ENST00000259357,;RP11-542K23.9,downstream_gene_variant,,ENST00000412262,;	T	ENSG00000136834	ENST00000259357	Transcript	missense_variant	925	895	299	G/R	Gga/Aga	.	.	.	-1	OR1J1	HGNC	8208	protein_coding	YES	CCDS35120.1	ENSP00000259357	OR1J1_HUMAN	.	UPI0000061E79	.	tolerated_low_confidence(0.1)	possibly_damaging(0.655)	1/1	.	hmmpanther:PTHR26451:SF213,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCCCTTAA	.	5	ESCA
FCN2	0	.	GRCh37	9	137779104	137779104	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785A>C	p.Gln262Pro	p.Q262P	ENST00000291744	8/8	44	20	23	33	33	0	FCN2,missense_variant,p.Gln262Pro,ENST00000291744,;FCN2,missense_variant,p.Gln224Pro,ENST00000350339,;	C	ENSG00000160339	ENST00000291744	Transcript	missense_variant	795	785	262	Q/P	cAg/cCg	.	.	.	1	FCN2	HGNC	3624	protein_coding	YES	CCDS6983.1	ENSP00000291744	FCN2_HUMAN	.	UPI000013E075	.	deleterious(0.01)	benign(0.019)	8/8	.	Superfamily_domains:SSF56496,SMART_domains:SM00186,Gene3D:4.10.530.10,Pfam_domain:PF00147,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF179,PROSITE_profiles:PS51406	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTCAGGGAG	.	5	ESCA
NOTCH1	0	.	GRCh37	9	139418316	139418317	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255dupT	p.Ala86CysfsTer57	p.A86Cfs*57	ENST00000277541	3/34	154	80	74	98	98	0	NOTCH1,frameshift_variant,p.Ala86CysfsTer57,ENST00000277541,;MIR4673,upstream_gene_variant,,ENST00000584777,;NOTCH1,non_coding_transcript_exon_variant,,ENST00000491649,;	A	ENSG00000148400	ENST00000277541	Transcript	frameshift_variant	331-332	255-256	85-86	-/X	-/T	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	3/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,Pfam_domain:PF00008,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCAGGCATAGT	.	3	ESCA
FRMPD1	0	.	GRCh37	9	37740199	37740199	+	Missense_Mutation	SNP	G	G	T	rs761419639	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1674G>T	p.Gln558His	p.Q558H	ENST00000539465	15/16	47	13	34	32	32	0	FRMPD1,missense_variant,p.Gln380His,ENST00000536622,;FRMPD1,missense_variant,p.Gln558His,ENST00000539465,;FRMPD1,missense_variant,p.Gln558His,ENST00000377765,;FRMPD1,missense_variant,p.Gln427His,ENST00000541302,;RP11-613M10.9,intron_variant,,ENST00000540557,;	T	ENSG00000070601	ENST00000539465	Transcript	missense_variant	2267	1674	558	Q/H	caG/caT	rs761419639,COSM1555043	.	.	1	FRMPD1	HGNC	29159	protein_coding	YES	CCDS6612.1	ENSP00000444411	FRPD1_HUMAN	F5H0G3_HUMAN	UPI000013D2CC	.	tolerated(0.17)	benign(0.004)	15/16	.	hmmpanther:PTHR13436:SF4,hmmpanther:PTHR13436	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCAGCCTCC	byFrequency	5	ESCA
TLE4	0	.	GRCh37	9	82336710	82336710	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1893C>T	p.%3D	p.G631G	ENST00000376552	17/20	41	26	14	39	39	0	TLE4,synonymous_variant,p.%3D,ENST00000376534,;TLE4,synonymous_variant,p.%3D,ENST00000376552,;TLE4,synonymous_variant,p.%3D,ENST00000376537,;TLE4,synonymous_variant,p.%3D,ENST00000376544,;TLE4,synonymous_variant,p.%3D,ENST00000376520,;TLE4,synonymous_variant,p.%3D,ENST00000265284,;TLE4,downstream_gene_variant,,ENST00000496114,;TLE4,intron_variant,,ENST00000478290,;TLE4,3_prime_UTR_variant,,ENST00000462803,;TLE4,3_prime_UTR_variant,,ENST00000470872,;RP11-79D8.2,upstream_gene_variant,,ENST00000440700,;	T	ENSG00000106829	ENST00000376552	Transcript	synonymous_variant	2911	1893	631	G	ggC/ggT	.	.	.	1	TLE4	HGNC	11840	protein_coding	YES	CCDS43837.1	ENSP00000365735	TLE4_HUMAN	B3KQ29_HUMAN	UPI00001CE3BA	.	.	.	17/20	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR10814,hmmpanther:PTHR10814:SF21,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGGCACCAA	.	5	ESCA
KIF27	0	.	GRCh37	9	86451768	86451768	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*148T>C	.	.	ENST00000297814	18/18	13	9	4	10	10	0	KIF27,3_prime_UTR_variant,,ENST00000413982,;KIF27,3_prime_UTR_variant,,ENST00000334204,;KIF27,3_prime_UTR_variant,,ENST00000297814,;RP11-575L7.4,intron_variant,,ENST00000591217,;RP11-575L7.2,intron_variant,,ENST00000439378,;RP11-575L7.2,intron_variant,,ENST00000458016,;RP11-575L7.2,intron_variant,,ENST00000417672,;RP11-575L7.2,upstream_gene_variant,,ENST00000412069,;	G	ENSG00000165115	ENST00000297814	Transcript	3_prime_UTR_variant	4498	.	.	.	.	.	.	.	-1	KIF27	HGNC	18632	protein_coding	YES	CCDS6665.1	ENSP00000297814	KIF27_HUMAN	B4DMY5_HUMAN	UPI000018F32F	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACACATCTAT	.	2	ESCA
LRCH2	0	.	GRCh37	X	114422839	114422839	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444C>A	p.%3D	p.T148T	ENST00000317135	2/21	45	12	32	62	62	0	LRCH2,synonymous_variant,p.%3D,ENST00000538422,;LRCH2,synonymous_variant,p.%3D,ENST00000317135,;RBMXL3,upstream_gene_variant,,ENST00000424776,;	T	ENSG00000130224	ENST00000317135	Transcript	synonymous_variant	475	444	148	T	acC/acA	.	.	.	-1	LRCH2	HGNC	29292	protein_coding	YES	CCDS48155.1	ENSP00000325091	LRCH2_HUMAN	.	UPI000022DB30	.	.	.	2/21	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23155:SF409,hmmpanther:PTHR23155,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATGGTTTT	.	5	ESCA
L1CAM	0	.	GRCh37	X	153134086	153134086	+	Silent	SNP	G	G	A	rs150805225	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1476C>T	p.%3D	p.T492T	ENST00000370060	13/29	37	11	26	48	48	0	L1CAM,synonymous_variant,p.%3D,ENST00000538883,;L1CAM,synonymous_variant,p.%3D,ENST00000370055,;L1CAM,synonymous_variant,p.%3D,ENST00000361981,;L1CAM,synonymous_variant,p.%3D,ENST00000543994,;L1CAM,synonymous_variant,p.%3D,ENST00000370057,;L1CAM,synonymous_variant,p.%3D,ENST00000370060,;L1CAM,synonymous_variant,p.%3D,ENST00000361699,;L1CAM,downstream_gene_variant,,ENST00000407935,;L1CAM,downstream_gene_variant,,ENST00000420165,;L1CAM,upstream_gene_variant,,ENST00000455590,;L1CAM,downstream_gene_variant,,ENST00000458029,;L1CAM,downstream_gene_variant,,ENST00000439496,;L1CAM,upstream_gene_variant,,ENST00000370058,;L1CAM,non_coding_transcript_exon_variant,,ENST00000484652,;L1CAM,upstream_gene_variant,,ENST00000496122,;L1CAM,upstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000464967,;L1CAM,upstream_gene_variant,,ENST00000491983,;L1CAM,downstream_gene_variant,,ENST00000460553,;	A	ENSG00000198910	ENST00000370060	Transcript	synonymous_variant	1666	1476	492	T	acC/acT	rs150805225	.	.	-1	L1CAM	HGNC	6470	protein_coding	YES	CCDS14733.1	ENSP00000359077	L1CAM_HUMAN	Q86SE4_HUMAN,Q7Z3Z9_HUMAN,Q7Z2J9_HUMAN,Q7Z2J8_HUMAN,Q7Z2J6_HUMAN,Q7Z2J0_HUMAN,Q7Z2I3_HUMAN,Q7Z2H2_HUMAN,Q7Z2F9_HUMAN,E9PHJ4_HUMAN,E7EPI4_HUMAN	UPI0000126E89	.	.	.	13/29	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF42,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	A:0.0003	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0003	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCCGGTGTC	byCluster|by1000G	5	ESCA
MECP2	0	.	GRCh37	X	153295403	153295403	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000453960	.	37	7	30	23	23	0	MECP2,3_prime_UTR_variant,,ENST00000303391,;MECP2,downstream_gene_variant,,ENST00000407218,;MECP2,downstream_gene_variant,,ENST00000415944,;MECP2,downstream_gene_variant,,ENST00000453960,;MECP2,downstream_gene_variant,,ENST00000488293,;MECP2,downstream_gene_variant,,ENST00000460227,;MECP2,downstream_gene_variant,,ENST00000486506,;MECP2,downstream_gene_variant,,ENST00000496908,;MECP2,downstream_gene_variant,,ENST00000481807,;MECP2,downstream_gene_variant,,ENST00000463644,;MECP2,downstream_gene_variant,,ENST00000369957,;	A	ENSG00000169057	ENST00000453960	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	282	-1	MECP2	HGNC	6990	protein_coding	YES	CCDS48193.1	ENSP00000395535	MECP2_HUMAN	.	UPI0000253F1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGACGGGGCA	.	5	ESCA
SH3KBP1	0	.	GRCh37	X	19568147	19568147	+	Frame_Shift_Ins	INS	G	G	TC	.	.	TCGA-LN-A5U6-01A-11D-A28B-09	TCGA-LN-A5U6-10A-01D-A28E-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439delCinsGA	p.Thr480ArgfsTer26	p.T480Rfs*26	ENST00000397821	14/18	94	53	41	59	59	0	SH3KBP1,frameshift_variant,p.Thr443ArgfsTer26,ENST00000379698,;SH3KBP1,frameshift_variant,p.Thr480ArgfsTer26,ENST00000397821,;SH3KBP1,frameshift_variant,p.Thr460ArgfsTer26,ENST00000379726,;SH3KBP1,frameshift_variant,p.Thr219ArgfsTer26,ENST00000541422,;SH3KBP1,frameshift_variant,p.Thr242ArgfsTer26,ENST00000379716,;	TC	ENSG00000147010	ENST00000397821	Transcript	frameshift_variant	1730	1439	480	T/RX	aCc/aGAc	COSM3668661,COSM3668662	.	.	-1	SH3KBP1	HGNC	13867	protein_coding	YES	CCDS14193.1	ENSP00000380921	SH3K1_HUMAN	Q5JPT6_HUMAN,B7Z6E8_HUMAN	UPI000006CC82	.	.	.	14/18	.	hmmpanther:PTHR14167,hmmpanther:PTHR14167:SF6	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	substitution	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	CTTGTGGTCGGA	.	5	ESCA
NMT2	0	.	GRCh37	10	15183006	15183006	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246+415T>A	.	.	ENST00000378165	.	20	14	5	26	26	0	NMT2,missense_variant,p.Phe63Ile,ENST00000535341,;NMT2,missense_variant,p.Phe63Ile,ENST00000378150,;NMT2,intron_variant,,ENST00000378165,;NMT2,intron_variant,,ENST00000540259,;NMT2,non_coding_transcript_exon_variant,,ENST00000478580,;RPP38,downstream_gene_variant,,ENST00000451677,;	T	ENSG00000152465	ENST00000378165	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NMT2	HGNC	7858	protein_coding	YES	CCDS7109.1	ENSP00000367407	NMT2_HUMAN	B4DXS1_HUMAN	UPI0000130278	.	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAAATCTGC	.	5	ESCA
OTUD1	0	.	GRCh37	10	23730134	23730134	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*302T>C	.	.	ENST00000376495	1/1	49	9	40	53	53	0	OTUD1,3_prime_UTR_variant,,ENST00000376495,;	C	ENSG00000165312	ENST00000376495	Transcript	3_prime_UTR_variant	1937	.	.	.	.	.	.	.	1	OTUD1	HGNC	27346	protein_coding	YES	CCDS44366.1	ENSP00000365678	OTUD1_HUMAN	.	UPI0000458A32	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTCTATTTT	.	5	ESCA
ZMYND11	0	.	GRCh37	10	300299	300299	+	3'UTR	SNP	A	A	T	rs529301481	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1889A>T	.	.	ENST00000397962	15/15	23	10	12	23	23	0	ZMYND11,3_prime_UTR_variant,,ENST00000381607,;ZMYND11,3_prime_UTR_variant,,ENST00000402736,;ZMYND11,3_prime_UTR_variant,,ENST00000309776,;ZMYND11,3_prime_UTR_variant,,ENST00000397962,;ZMYND11,3_prime_UTR_variant,,ENST00000381591,;ZMYND11,downstream_gene_variant,,ENST00000545619,;ZMYND11,downstream_gene_variant,,ENST00000381584,;ZMYND11,downstream_gene_variant,,ENST00000397959,;ZMYND11,downstream_gene_variant,,ENST00000535374,;ZMYND11,downstream_gene_variant,,ENST00000381604,;ZMYND11,downstream_gene_variant,,ENST00000403354,;ZMYND11,downstream_gene_variant,,ENST00000602682,;	T	ENSG00000015171	ENST00000397962	Transcript	3_prime_UTR_variant	4126	.	.	.	.	rs529301481	.	.	1	ZMYND11	HGNC	16966	protein_coding	YES	CCDS7052.2	ENSP00000381053	ZMY11_HUMAN	.	UPI0000458A5F	.	.	.	15/15	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTAAAAAA	by1000G	5	ESCA
FBXO18	0	.	GRCh37	10	5955768	5955768	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1423A>G	p.Thr475Ala	p.T475A	ENST00000379999	8/22	57	33	24	98	98	0	FBXO18,missense_variant,p.Thr424Ala,ENST00000362091,;FBXO18,missense_variant,p.Thr475Ala,ENST00000379999,;FBXO18,5_prime_UTR_variant,,ENST00000397269,;FBXO18,downstream_gene_variant,,ENST00000470089,;FBXO18,upstream_gene_variant,,ENST00000489042,;FBXO18,upstream_gene_variant,,ENST00000460453,;FBXO18,downstream_gene_variant,,ENST00000469009,;FBXO18,downstream_gene_variant,,ENST00000494526,;	G	ENSG00000134452	ENST00000379999	Transcript	missense_variant	1527	1423	475	T/A	Aca/Gca	.	.	.	1	FBXO18	HGNC	13620	protein_coding	YES	CCDS7073.1	ENSP00000369335	FBX18_HUMAN	Q66K33_HUMAN,Q2TAK1_HUMAN	UPI000019AB6F	.	tolerated(0.59)	benign(0.001)	8/22	.	hmmpanther:PTHR11070:SF8,hmmpanther:PTHR11070	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCCACAAAA	.	5	ESCA
PPP2R1B	0	.	GRCh37	11	111635631	111635631	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.206-2A>T	.	p.X69_splice	ENST00000311129	.	10	6	4	8	8	0	PPP2R1B,splice_acceptor_variant,,ENST00000527614,;PPP2R1B,splice_acceptor_variant,,ENST00000393055,;PPP2R1B,splice_acceptor_variant,,ENST00000427203,;PPP2R1B,splice_acceptor_variant,,ENST00000311129,;PPP2R1B,splice_acceptor_variant,,ENST00000531373,;PPP2R1B,splice_acceptor_variant,,ENST00000341980,;PPP2R1B,intron_variant,,ENST00000426998,;RP11-108O10.2,downstream_gene_variant,,ENST00000534218,;RP11-108O10.2,downstream_gene_variant,,ENST00000529841,;PPP2R1B,splice_acceptor_variant,,ENST00000534521,;PPP2R1B,intron_variant,,ENST00000534500,;	A	ENSG00000137713	ENST00000311129	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	PPP2R1B	HGNC	9303	protein_coding	YES	CCDS8348.1	ENSP00000311344	2AAB_HUMAN	.	UPI000006CEE0	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTATCTGGAAG	.	2	ESCA
SLC37A2	0	.	GRCh37	11	124958034	124958034	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*49C>A	.	.	ENST00000308074	19/19	23	15	7	31	31	0	SLC37A2,3_prime_UTR_variant,,ENST00000308074,;SLC37A2,3_prime_UTR_variant,,ENST00000403796,;SLC37A2,3_prime_UTR_variant,,ENST00000298280,;SLC37A2,downstream_gene_variant,,ENST00000407458,;SLC37A2,downstream_gene_variant,,ENST00000525837,;SLC37A2,non_coding_transcript_exon_variant,,ENST00000526405,;AP001007.1,upstream_gene_variant,,ENST00000354617,;	A	ENSG00000134955	ENST00000308074	Transcript	3_prime_UTR_variant	1599	.	.	.	.	.	.	.	1	SLC37A2	HGNC	20644	protein_coding	YES	CCDS31714.1	ENSP00000311833	SPX2_HUMAN	E9PRJ4_HUMAN,B7Z480_HUMAN	UPI000019AB60	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCCCCAAT	.	5	ESCA
OR4S1	0	.	GRCh37	11	48328372	48328372	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598A>C	p.Asn200His	p.N200H	ENST00000319988	1/1	101	77	24	97	97	0	OR4S1,missense_variant,p.Asn200His,ENST00000319988,;	C	ENSG00000176555	ENST00000319988	Transcript	missense_variant	598	598	200	N/H	Aac/Cac	.	.	.	1	OR4S1	HGNC	14705	protein_coding	YES	CCDS31488.1	ENSP00000321447	OR4S1_HUMAN	.	UPI0000041B2E	.	deleterious(0)	probably_damaging(0.999)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF226,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCAACAGC	.	5	ESCA
OR4C15	0	.	GRCh37	11	55322499	55322499	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.717G>A	p.%3D	p.E239E	ENST00000314644	1/1	61	39	22	39	39	0	OR4C15,synonymous_variant,p.%3D,ENST00000314644,;	A	ENSG00000181939	ENST00000314644	Transcript	synonymous_variant	717	717	239	E	gaG/gaA	.	.	.	1	OR4C15	HGNC	15171	protein_coding	YES	CCDS31501.1	ENSP00000324958	OR4CF_HUMAN	.	UPI00003B288E	.	.	.	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26451:SF14,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGCTTGC	.	5	ESCA
SLC22A9	0	.	GRCh37	11	63176300	63176300	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1550C>T	p.Pro517Leu	p.P517L	ENST00000279178	9/10	66	48	17	57	57	0	SLC22A9,missense_variant,p.Pro517Leu,ENST00000279178,;SLC22A9,3_prime_UTR_variant,,ENST00000310969,;SLC22A9,intron_variant,,ENST00000536333,;	T	ENSG00000149742	ENST00000279178	Transcript	missense_variant	1799	1550	517	P/L	cCt/cTt	.	.	.	1	SLC22A9	HGNC	16261	protein_coding	YES	CCDS8043.1	ENSP00000279178	S22A9_HUMAN	A4PB24_HUMAN	UPI00000745FF	.	deleterious(0)	probably_damaging(0.978)	9/10	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF217,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCCTGAAA	.	5	ESCA
VPS51	0	.	GRCh37	11	64877263	64877263	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1746G>A	p.%3D	p.V582V	ENST00000279281	7/10	63	34	28	50	50	0	VPS51,synonymous_variant,p.%3D,ENST00000279281,;VPS51,synonymous_variant,p.%3D,ENST00000526856,;TM7SF2,upstream_gene_variant,,ENST00000530750,;TM7SF2,upstream_gene_variant,,ENST00000279263,;TM7SF2,upstream_gene_variant,,ENST00000526085,;TM7SF2,upstream_gene_variant,,ENST00000524986,;VPS51,upstream_gene_variant,,ENST00000530673,;TM7SF2,upstream_gene_variant,,ENST00000527968,;TM7SF2,upstream_gene_variant,,ENST00000345348,;TM7SF2,upstream_gene_variant,,ENST00000531321,;TM7SF2,upstream_gene_variant,,ENST00000528802,;TM7SF2,upstream_gene_variant,,ENST00000534371,;VPS51,downstream_gene_variant,,ENST00000530773,;VPS51,downstream_gene_variant,,ENST00000529180,;VPS51,downstream_gene_variant,,ENST00000526578,;TM7SF2,upstream_gene_variant,,ENST00000525385,;TM7SF2,upstream_gene_variant,,ENST00000529414,;VPS51,downstream_gene_variant,,ENST00000528588,;TM7SF2,upstream_gene_variant,,ENST00000526809,;TM7SF2,upstream_gene_variant,,ENST00000540748,;VPS51,downstream_gene_variant,,ENST00000534557,;AP003068.9,downstream_gene_variant,,ENST00000528887,;VPS51,non_coding_transcript_exon_variant,,ENST00000527646,;TM7SF2,upstream_gene_variant,,ENST00000531029,;TM7SF2,upstream_gene_variant,,ENST00000533646,;VPS51,3_prime_UTR_variant,,ENST00000533827,;VPS51,non_coding_transcript_exon_variant,,ENST00000531146,;VPS51,non_coding_transcript_exon_variant,,ENST00000534591,;TM7SF2,upstream_gene_variant,,ENST00000529601,;TM7SF2,upstream_gene_variant,,ENST00000533766,;TM7SF2,upstream_gene_variant,,ENST00000528026,;TM7SF2,upstream_gene_variant,,ENST00000529233,;TM7SF2,upstream_gene_variant,,ENST00000532328,;TM7SF2,upstream_gene_variant,,ENST00000529292,;TM7SF2,upstream_gene_variant,,ENST00000526048,;TM7SF2,upstream_gene_variant,,ENST00000527851,;VPS51,downstream_gene_variant,,ENST00000534124,;TM7SF2,upstream_gene_variant,,ENST00000524690,;TM7SF2,upstream_gene_variant,,ENST00000530650,;TM7SF2,upstream_gene_variant,,ENST00000530892,;VPS51,downstream_gene_variant,,ENST00000533656,;VPS51,downstream_gene_variant,,ENST00000533487,;TM7SF2,upstream_gene_variant,,ENST00000534667,;	A	ENSG00000149823	ENST00000279281	Transcript	synonymous_variant	1838	1746	582	V	gtG/gtA	.	.	.	1	VPS51	HGNC	1172	protein_coding	YES	CCDS8093.1	ENSP00000279281	VPS51_HUMAN	E9PMB6_HUMAN,E9PJ36_HUMAN	UPI000006D6D8	.	.	.	7/10	.	hmmpanther:PTHR15954:SF4,hmmpanther:PTHR15954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGTGCAGGG	.	5	ESCA
LRFN4	0	.	GRCh37	11	66627517	66627517	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1759G>A	p.Asp587Asn	p.D587N	ENST00000309602	2/2	42	30	12	65	65	0	LRFN4,missense_variant,p.Asp587Asn,ENST00000309602,;PC,intron_variant,,ENST00000393960,;PC,intron_variant,,ENST00000393958,;LRFN4,intron_variant,,ENST00000393952,;PC,intron_variant,,ENST00000393955,;PC,downstream_gene_variant,,ENST00000524491,;PC,downstream_gene_variant,,ENST00000355677,;PC,intron_variant,,ENST00000530187,;LRFN4,downstream_gene_variant,,ENST00000531590,;	A	ENSG00000173621	ENST00000309602	Transcript	missense_variant	2002	1759	587	D/N	Gac/Aac	.	.	.	1	LRFN4	HGNC	28456	protein_coding	YES	CCDS8153.1	ENSP00000312535	LRFN4_HUMAN	Q7L3C2_HUMAN	UPI0000001C10	.	deleterious_low_confidence(0.01)	benign(0.064)	2/2	.	hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTGGACCTG	.	5	ESCA
MAP6	0	.	GRCh37	11	75298556	75298556	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1990A>G	p.Met664Val	p.M664V	ENST00000304771	4/4	32	15	16	48	48	0	MAP6,missense_variant,p.Met335Val,ENST00000526740,;MAP6,missense_variant,p.Met664Val,ENST00000304771,;CTD-2530H12.4,intron_variant,,ENST00000527803,;MAP6,downstream_gene_variant,,ENST00000526689,;	C	ENSG00000171533	ENST00000304771	Transcript	missense_variant	2741	1990	664	M/V	Atg/Gtg	.	.	.	-1	MAP6	HGNC	6868	protein_coding	YES	CCDS31641.1	ENSP00000307093	MAP6_HUMAN	Q6ZWB8_HUMAN	UPI0000251E6A	.	tolerated_low_confidence(1)	benign(0)	4/4	.	hmmpanther:PTHR14759:SF2,hmmpanther:PTHR14759	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCATGGAAC	.	5	ESCA
PAK1	0	.	GRCh37	11	77054946	77054946	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916C>T	p.Gln306Ter	p.Q306*	ENST00000278568	10/16	31	15	15	49	49	0	PAK1,stop_gained,p.Gln306Ter,ENST00000278568,;PAK1,stop_gained,p.Gln306Ter,ENST00000356341,;PAK1,stop_gained,p.Gln306Ter,ENST00000530617,;PAK1,stop_gained,p.Gln28Ter,ENST00000533285,;PAK1,stop_gained,p.Gln208Ter,ENST00000528203,;PAK1,non_coding_transcript_exon_variant,,ENST00000525542,;PAK1,3_prime_UTR_variant,,ENST00000527535,;PAK1,non_coding_transcript_exon_variant,,ENST00000532991,;PAK1,non_coding_transcript_exon_variant,,ENST00000532711,;PAK1,intron_variant,,ENST00000527457,;	A	ENSG00000149269	ENST00000278568	Transcript	stop_gained	1446	916	306	Q/*	Cag/Tag	.	.	.	-1	PAK1	HGNC	8590	protein_coding	YES	CCDS44687.1	ENSP00000278568	PAK1_HUMAN	E9PRP6_HUMAN,E9PQW5_HUMAN,E9PMP2_HUMAN,E9PM17_HUMAN,E9PKH9_HUMAN,E9PJF8_HUMAN	UPI000013DB7F	.	.	.	10/16	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:3.30.200.20,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF250,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCTGCTGCT	.	5	ESCA
AAMDC	0	.	GRCh37	11	77583381	77583381	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*20T>G	.	.	ENST00000526415	5/5	19	9	9	25	25	0	AAMDC,3_prime_UTR_variant,,ENST00000525034,;AAMDC,3_prime_UTR_variant,,ENST00000526415,;AAMDC,3_prime_UTR_variant,,ENST00000533193,;AAMDC,3_prime_UTR_variant,,ENST00000393427,;AAMDC,3_prime_UTR_variant,,ENST00000525409,;AAMDC,intron_variant,,ENST00000304716,;AAMDC,intron_variant,,ENST00000532481,;AAMDC,intron_variant,,ENST00000527134,;RP11-91P24.7,upstream_gene_variant,,ENST00000525594,;RP11-91P24.6,upstream_gene_variant,,ENST00000530972,;AAMDC,intron_variant,,ENST00000526164,;AAMDC,upstream_gene_variant,,ENST00000529666,;RP11-91P24.1,upstream_gene_variant,,ENST00000495378,;	G	ENSG00000087884	ENST00000526415	Transcript	3_prime_UTR_variant	562	.	.	.	.	.	.	.	1	AAMDC	HGNC	30205	protein_coding	YES	CCDS8254.1	ENSP00000431808	AAMDC_HUMAN	.	UPI000007318D	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAATAAATC	.	5	ESCA
TRIM49	0	.	GRCh37	11	89536864	89536864	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507+2T>C	.	p.X169_splice	ENST00000329758	.	62	47	15	53	53	0	TRIM49,splice_donor_variant,,ENST00000532501,;TRIM49,splice_donor_variant,,ENST00000329758,;	G	ENSG00000168930	ENST00000329758	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	TRIM49	HGNC	13431	protein_coding	YES	CCDS8287.1	ENSP00000327604	TRI49_HUMAN	I1YAQ5_HUMAN	UPI000013431B	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GACTAACCTTC	.	3	ESCA
HCFC2	0	.	GRCh37	12	104458353	104458353	+	Silent	SNP	C	C	T	rs370124268	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15C>T	p.%3D	p.S5S	ENST00000229330	1/15	16	13	3	15	15	0	HCFC2,synonymous_variant,p.%3D,ENST00000229330,;HCFC2,upstream_gene_variant,,ENST00000550444,;GLT8D2,upstream_gene_variant,,ENST00000548660,;HCFC2,synonymous_variant,p.%3D,ENST00000544223,;	T	ENSG00000111727	ENST00000229330	Transcript	synonymous_variant	119	15	5	S	agC/agT	rs370124268	.	.	1	HCFC2	HGNC	24972	protein_coding	YES	CCDS9097.1	ENSP00000229330	HCFC2_HUMAN	F8VU09_HUMAN	UPI000006CF31	.	.	.	1/15	.	hmmpanther:PTHR23244:SF288,hmmpanther:PTHR23244	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCAGCCTCCT	.	2	ESCA
RFX4	0	.	GRCh37	12	107155486	107155486	+	3'Flank	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000357881	.	128	100	28	82	82	0	RFX4,3_prime_UTR_variant,,ENST00000392842,;RFX4,3_prime_UTR_variant,,ENST00000229387,;RP11-144F15.1,intron_variant,,ENST00000551505,;RFX4,downstream_gene_variant,,ENST00000357881,;RP11-144F15.1,intron_variant,,ENST00000549203,;	C	ENSG00000111783	ENST00000357881	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	49	1	RFX4	HGNC	9985	protein_coding	YES	CCDS55880.1	ENSP00000350552	RFX4_HUMAN	R4GMS3_HUMAN,F8VZC4_HUMAN	UPI00001FB460	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTGACTGT	.	5	ESCA
ACACB	0	.	GRCh37	12	109675106	109675106	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4583A>C	p.Lys1528Thr	p.K1528T	ENST00000338432	34/53	48	42	6	50	50	0	ACACB,missense_variant,p.Lys1458Thr,ENST00000377854,;ACACB,missense_variant,p.Lys1528Thr,ENST00000338432,;ACACB,missense_variant,p.Lys1528Thr,ENST00000377848,;ACACB,missense_variant,p.Lys194Thr,ENST00000543201,;ACACB,missense_variant,p.Lys195Thr,ENST00000538526,;ACACB,upstream_gene_variant,,ENST00000537347,;ACACB,upstream_gene_variant,,ENST00000534852,;ACACB,downstream_gene_variant,,ENST00000542524,;	C	ENSG00000076555	ENST00000338432	Transcript	missense_variant	4702	4583	1528	K/T	aAg/aCg	.	.	.	1	ACACB	HGNC	85	protein_coding	YES	CCDS31898.1	ENSP00000341044	ACACB_HUMAN	F5H5C3_HUMAN,E9PEW7_HUMAN	UPI0000DBEEFB	.	deleterious(0)	probably_damaging(0.923)	34/53	.	hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF84,Pfam_domain:PF08326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCAAGGTGA	.	4	ESCA
MLEC	0	.	GRCh37	12	121135110	121135111	+	3'UTR	INS	-	-	TTTG	rs3884201	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*778_*781dupGTTT	.	.	ENST00000228506	5/5	22	5	17	10	10	0	MLEC,3_prime_UTR_variant,,ENST00000228506,;MLEC,downstream_gene_variant,,ENST00000412616,;MLEC,downstream_gene_variant,,ENST00000535656,;MLEC,downstream_gene_variant,,ENST00000545525,;RP11-173P15.3,non_coding_transcript_exon_variant,,ENST00000541383,;RP11-173P15.3,downstream_gene_variant,,ENST00000535720,;MLEC,intron_variant,,ENST00000535413,;	TTTG	ENSG00000110917	ENST00000228506	Transcript	3_prime_UTR_variant	2069-2070	.	.	.	.	rs3884201	.	.	1	MLEC	HGNC	28973	protein_coding	YES	CCDS9206.1	ENSP00000228506	MLEC_HUMAN	F5H1S8_HUMAN	UPI000013938A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	19	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTCAGTTTTGT	byCluster|by1000G	2	ESCA
OASL	0	.	GRCh37	12	121476752	121476752	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.23A>G	p.Tyr8Cys	p.Y8C	ENST00000257570	1/6	22	16	5	26	26	0	OASL,missense_variant,p.Tyr8Cys,ENST00000339275,;OASL,missense_variant,p.Tyr8Cys,ENST00000257570,;OASL,upstream_gene_variant,,ENST00000543677,;	C	ENSG00000135114	ENST00000257570	Transcript	missense_variant	294	23	8	Y/C	tAt/tGt	COSM1605662	.	.	-1	OASL	HGNC	8090	protein_coding	YES	CCDS9211.1	ENSP00000257570	OASL_HUMAN	.	UPI000005339E	.	deleterious(0.01)	probably_damaging(0.935)	1/6	.	hmmpanther:PTHR11258:SF16,hmmpanther:PTHR11258,Gene3D:3.30.460.10,Superfamily_domains:SSF81301	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTATACAGT	.	2	ESCA
VPS37B	0	.	GRCh37	12	123351980	123351980	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.541C>T	p.Pro181Ser	p.P181S	ENST00000267202	4/4	49	9	39	48	48	0	VPS37B,missense_variant,p.Pro181Ser,ENST00000267202,;VPS37B,missense_variant,p.Pro179Ser,ENST00000535765,;VPS37B,missense_variant,p.Pro179Ser,ENST00000371248,;HIP1R,downstream_gene_variant,,ENST00000253083,;RP11-463O12.3,downstream_gene_variant,,ENST00000537827,;HIP1R,downstream_gene_variant,,ENST00000537322,;VPS37B,downstream_gene_variant,,ENST00000543590,;	A	ENSG00000139722	ENST00000267202	Transcript	missense_variant	923	541	181	P/S	Ccc/Tcc	.	.	.	-1	VPS37B	HGNC	25754	protein_coding	YES	CCDS9239.1	ENSP00000267202	VP37B_HUMAN	.	UPI000006ED3B	.	tolerated(0.09)	benign(0.004)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13678,hmmpanther:PTHR13678:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGGGCAGCC	.	5	ESCA
KCNA6	0	.	GRCh37	12	4922977	4922977	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2180T>A	.	.	ENST00000433855	1/2	16	12	4	28	28	0	KCNA6,3_prime_UTR_variant,,ENST00000433855,;GALNT8,intron_variant,,ENST00000542998,;KCNA6,downstream_gene_variant,,ENST00000280684,;GALNT8,upstream_gene_variant,,ENST00000541339,;	A	ENSG00000151079	ENST00000433855	Transcript	3_prime_UTR_variant	4636	.	.	.	.	.	.	.	1	KCNA6	HGNC	6225	protein_coding	YES	CCDS8534.1	ENSP00000408321	KCNA6_HUMAN	.	UPI00001279AD	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTTGAGAC	.	5	ESCA
INTS6	0	.	GRCh37	13	51995330	51995330	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429+9100G>A	.	.	ENST00000311234	.	34	25	9	25	25	0	INTS6,5_prime_UTR_variant,,ENST00000497989,;INTS6,intron_variant,,ENST00000425000,;INTS6,intron_variant,,ENST00000463928,;INTS6,intron_variant,,ENST00000398119,;INTS6,intron_variant,,ENST00000311234,;INTS6,intron_variant,,ENST00000491189,;INTS6,intron_variant,,ENST00000420668,;INTS6,non_coding_transcript_exon_variant,,ENST00000491723,;INTS6,non_coding_transcript_exon_variant,,ENST00000466784,;INTS6,intron_variant,,ENST00000486195,;INTS6,downstream_gene_variant,,ENST00000461515,;INTS6,3_prime_UTR_variant,,ENST00000469430,;INTS6,downstream_gene_variant,,ENST00000491997,;	T	ENSG00000102786	ENST00000311234	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	INTS6	HGNC	14879	protein_coding	YES	CCDS9428.1	ENSP00000310260	INT6_HUMAN	G5E9X1_HUMAN,C9K0V7_HUMAN,C9JVX2_HUMAN,C9J885_HUMAN,C9J0C6_HUMAN,B3KQH5_HUMAN	UPI0000030C84	.	.	.	.	4/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCCACGAT	.	5	ESCA
EDNRB	0	.	GRCh37	13	78472138	78472138	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*197G>A	.	.	ENST00000377211	8/8	114	95	18	50	50	0	EDNRB,3_prime_UTR_variant,,ENST00000377211,;EDNRB,3_prime_UTR_variant,,ENST00000334286,;EDNRB,intron_variant,,ENST00000446573,;	T	ENSG00000136160	ENST00000377211	Transcript	3_prime_UTR_variant	1949	.	.	.	.	.	.	.	-1	EDNRB	HGNC	3180	protein_coding	YES	CCDS55902.1	ENSP00000366416	EDNRB_HUMAN	.	UPI0000046D5C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCACTGATT	.	5	ESCA
IGHV1-24	0	.	GRCh37	14	106733166	106733166	+	Missense_Mutation	SNP	G	G	A	rs139845206	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329C>T	p.Thr110Met	p.T110M	ENST00000390610	2/2	93	29	63	86	86	0	IGHV1-24,missense_variant,p.Thr110Met,ENST00000390610,;	A	ENSG00000211950	ENST00000390610	Transcript	missense_variant	389	329	110	T/M	aCg/aTg	rs139845206	.	.	-1	IGHV1-24	HGNC	5551	IG_V_gene	YES	.	ENSP00000375019	.	.	UPI000011AAD6	.	tolerated(0.1)	possibly_damaging(0.678)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF73,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCCGTGTCC	byCluster|by1000G	5	ESCA
SALL2	0	.	GRCh37	14	21993601	21993620	+	Frame_Shift_Del	DEL	ATTGTGACCCTCAGGCCGGG	ATTGTGACCCTCAGGCCGGG	TTT	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	ATTGTGACCCTCAGGCCGGG	ATTGTGACCCTCAGGCCGGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242_261delCCCGGCCTGAGGGTCACAATinsAAA	p.Pro81GlnfsTer11	p.P81Qfs*11	ENST00000327430	2/2	30	27	3	44	44	0	SALL2,frameshift_variant,p.Pro79GlnfsTer11,ENST00000537235,;SALL2,frameshift_variant,p.Pro79GlnfsTer11,ENST00000538754,;SALL2,frameshift_variant,p.Pro81GlnfsTer11,ENST00000317492,;SALL2,frameshift_variant,p.Pro79GlnfsTer11,ENST00000450879,;SALL2,frameshift_variant,p.Pro19GlnfsTer11,ENST00000541965,;SALL2,frameshift_variant,p.Pro81GlnfsTer11,ENST00000327430,;SALL2,frameshift_variant,p.Pro75GlnfsTer11,ENST00000546363,;AE000658.22,downstream_gene_variant,,ENST00000535893,;	TTT	ENSG00000165821	ENST00000327430	Transcript	frameshift_variant	537-556	242-261	81-87	PRPEGHN/QX	cCCCGGCCTGAGGGTCACAAT/cAAA	.	.	.	-1	SALL2	HGNC	10526	protein_coding	YES	CCDS32045.1	ENSP00000333537	SALL2_HUMAN	F5H1G6_HUMAN	UPI00001AF54D	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23233:SF15,hmmpanther:PTHR23233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL|VARSCANS*	AGGATTATTGTGACCCTCAGGCCGGGGTTCA	.	3	ESCA
MPP5	0	.	GRCh37	14	67800651	67800651	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*978delA	.	.	ENST00000261681	15/15	46	38	8	33	33	0	MPP5,3_prime_UTR_variant,,ENST00000555925,;MPP5,3_prime_UTR_variant,,ENST00000261681,;ATP6V1D,downstream_gene_variant,,ENST00000553408,;ATP6V1D,downstream_gene_variant,,ENST00000555723,;ATP6V1D,downstream_gene_variant,,ENST00000555431,;ATP6V1D,downstream_gene_variant,,ENST00000554236,;ATP6V1D,downstream_gene_variant,,ENST00000555474,;ATP6V1D,downstream_gene_variant,,ENST00000216442,;ATP6V1D,intron_variant,,ENST00000553974,;ATP6V1D,intron_variant,,ENST00000554087,;ATP6V1D,downstream_gene_variant,,ENST00000555625,;	-	ENSG00000072415	ENST00000261681	Transcript	3_prime_UTR_variant	3667	.	.	.	.	.	.	.	1	MPP5	HGNC	18669	protein_coding	YES	CCDS9779.1	ENSP00000261681	MPP5_HUMAN	G3V2H1_HUMAN	UPI0000046FB9	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTATATATAGGT	.	3	ESCA
SPTLC2	0	.	GRCh37	14	78023490	78023490	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.851-1G>A	.	p.X284_splice	ENST00000216484	.	34	27	7	24	24	0	SPTLC2,splice_acceptor_variant,,ENST00000554901,;SPTLC2,splice_acceptor_variant,,ENST00000216484,;SPTLC2,upstream_gene_variant,,ENST00000556264,;SPTLC2,non_coding_transcript_exon_variant,,ENST00000554365,;SPTLC2,upstream_gene_variant,,ENST00000556607,;	T	ENSG00000100596	ENST00000216484	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	SPTLC2	HGNC	11278	protein_coding	YES	CCDS9865.1	ENSP00000216484	SPTC2_HUMAN	.	UPI0000000C6B	.	.	.	.	6/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATATCTACAG	.	5	ESCA
TRIP11	0	.	GRCh37	14	92471556	92471556	+	Missense_Mutation	SNP	G	G	C	rs775944391	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2764C>G	p.Gln922Glu	p.Q922E	ENST00000267622	11/21	85	43	42	64	64	0	TRIP11,missense_variant,p.Gln638Glu,ENST00000554357,;TRIP11,missense_variant,p.Gln922Glu,ENST00000267622,;	C	ENSG00000100815	ENST00000267622	Transcript	missense_variant	3138	2764	922	Q/E	Caa/Gaa	rs775944391	.	.	-1	TRIP11	HGNC	12305	protein_coding	YES	CCDS9899.1	ENSP00000267622	TRIPB_HUMAN	G3V4R7_HUMAN	UPI000013D767	.	deleterious(0)	possibly_damaging(0.624)	11/21	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18921:SF2,hmmpanther:PTHR18921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTGATCTT	byFrequency	5	ESCA
ITPK1	0	.	GRCh37	14	93534373	93534373	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.120+8567A>G	.	.	ENST00000267615	.	44	36	8	36	36	0	ITPK1,intron_variant,,ENST00000555553,;ITPK1,intron_variant,,ENST00000267615,;ITPK1,intron_variant,,ENST00000557309,;ITPK1,intron_variant,,ENST00000556603,;ITPK1,intron_variant,,ENST00000553452,;ITPK1,intron_variant,,ENST00000554999,;ITPK1,intron_variant,,ENST00000354313,;ITPK1,intron_variant,,ENST00000555495,;ITPK1,upstream_gene_variant,,ENST00000556185,;ITPK1-AS1,non_coding_transcript_exon_variant,,ENST00000553639,;	C	ENSG00000100605	ENST00000267615	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ITPK1	HGNC	6177	protein_coding	YES	CCDS9907.1	ENSP00000267615	ITPK1_HUMAN	G3V588_HUMAN,G3V4M9_HUMAN	UPI000006F88A	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTATATTCTCC	.	2	ESCA
OR4M2	0	.	GRCh37	15	22368839	22368839	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264G>A	p.%3D	p.E88E	ENST00000332663	1/1	95	86	9	122	122	0	OR4M2,synonymous_variant,p.%3D,ENST00000332663,;RP11-69H14.6,non_coding_transcript_exon_variant,,ENST00000560544,;RP11-69H14.6,intron_variant,,ENST00000560969,;RP11-69H14.6,intron_variant,,ENST00000558798,;RP11-69H14.6,intron_variant,,ENST00000559392,;RP11-69H14.6,intron_variant,,ENST00000558896,;RP11-69H14.6,intron_variant,,ENST00000558312,;	A	ENSG00000182974	ENST00000332663	Transcript	synonymous_variant	362	264	88	E	gaG/gaA	.	.	.	1	OR4M2	HGNC	15373	protein_coding	YES	CCDS32172.1	ENSP00000329467	OR4M2_HUMAN	.	UPI0000046191	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF53,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGGAGAGGAA	.	3	ESCA
SNORD115-33	0	.	GRCh37	15	25473974	25473974	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000363723	.	11	7	4	25	25	0	SNORD115-33,upstream_gene_variant,,ENST00000363723,;SNORD115-31,downstream_gene_variant,,ENST00000365318,;SNORD115-30,downstream_gene_variant,,ENST00000364117,;SNORD115-32,upstream_gene_variant,,ENST00000364079,;SNORD115-34,upstream_gene_variant,,ENST00000362441,;SNHG14,non_coding_transcript_exon_variant,,ENST00000453082,;	A	ENSG00000200593	ENST00000363723	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2011	1	SNORD115-33	HGNC	33052	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	CAGGCCAATGT	.	2	ESCA
TPSB2	0	.	GRCh37	16	1278443	1278443	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*207C>G	.	.	ENST00000430512	7/7	10	5	5	9	9	0	TPSB2,3_prime_UTR_variant,,ENST00000430512,;TPSG1,upstream_gene_variant,,ENST00000234798,;TPSB2,non_coding_transcript_exon_variant,,ENST00000606293,;TPSB2,intron_variant,,ENST00000339687,;TPSG1,upstream_gene_variant,,ENST00000564684,;TPSB2,downstream_gene_variant,,ENST00000445910,;	C	ENSG00000197253	ENST00000430512	Transcript	3_prime_UTR_variant	1084	.	.	.	.	.	.	.	-1	TPSB2	HGNC	14120	protein_coding	YES	.	ENSP00000412409	.	F8W8D0_HUMAN	UPI00015DFBB0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTAGGACAG	.	2	ESCA
RP11-1186N24.5	0	.	GRCh37	16	15200859	15200859	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2499+328C>G	.	.	ENST00000605794	.	29	3	26	18	18	0	PDXDC1,intron_variant,,ENST00000535621,;RP11-1186N24.5,intron_variant,,ENST00000605794,;RP11-72I8.1,non_coding_transcript_exon_variant,,ENST00000569858,;NPIPP1,intron_variant,,ENST00000534799,;RP11-1186N24.5,downstream_gene_variant,,ENST00000340301,;NPIPP1,downstream_gene_variant,,ENST00000448011,;NPIPP1,intron_variant,,ENST00000448014,;NPIPP1,intron_variant,,ENST00000358815,;NPIPP1,intron_variant,,ENST00000547107,;	C	ENSG00000270580	ENST00000605794	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RP11-1186N24.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	14/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	CTTTTGAAGGA	.	3	ESCA
SMG1	0	.	GRCh37	16	18937368	18937368	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-5A>G	.	.	ENST00000446231	1/63	21	12	9	26	26	0	SMG1,5_prime_UTR_variant,,ENST00000389467,;SMG1,5_prime_UTR_variant,,ENST00000532700,;SMG1,5_prime_UTR_variant,,ENST00000446231,;SMG1,upstream_gene_variant,,ENST00000569122,;AC092287.1,downstream_gene_variant,,ENST00000580939,;CTD-2288F12.1,upstream_gene_variant,,ENST00000565782,;SMG1,upstream_gene_variant,,ENST00000567737,;	C	ENSG00000157106	ENST00000446231	Transcript	5_prime_UTR_variant	409	.	.	.	.	.	.	.	-1	SMG1	HGNC	30045	protein_coding	YES	CCDS45430.1	ENSP00000402515	SMG1_HUMAN	H3BPS6_HUMAN	UPI00004F8E22	.	.	.	1/63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACCTTCCCC	.	5	ESCA
DOK4	0	.	GRCh37	16	57506953	57506954	+	3'UTR	INS	-	-	CC	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*334_*335dupGG	.	.	ENST00000340099	9/9	15	7	8	17	17	0	DOK4,3_prime_UTR_variant,,ENST00000340099,;DOK4,3_prime_UTR_variant,,ENST00000566936,;DOK4,3_prime_UTR_variant,,ENST00000569548,;POLR2C,downstream_gene_variant,,ENST00000219252,;DOK4,downstream_gene_variant,,ENST00000566588,;DOK4,downstream_gene_variant,,ENST00000564378,;DOK4,downstream_gene_variant,,ENST00000562737,;DOK4,downstream_gene_variant,,ENST00000567276,;DOK4,downstream_gene_variant,,ENST00000569010,;DOK4,downstream_gene_variant,,ENST00000569538,;DOK4,downstream_gene_variant,,ENST00000567175,;DOK4,downstream_gene_variant,,ENST00000562008,;DOK4,downstream_gene_variant,,ENST00000569250,;DOK4,downstream_gene_variant,,ENST00000568617,;DOK4,downstream_gene_variant,,ENST00000566705,;DOK4,downstream_gene_variant,,ENST00000567214,;DOK4,downstream_gene_variant,,ENST00000561918,;POLR2C,downstream_gene_variant,,ENST00000564651,;DOK4,downstream_gene_variant,,ENST00000563483,;POLR2C,downstream_gene_variant,,ENST00000563589,;POLR2C,downstream_gene_variant,,ENST00000563115,;DOK4,downstream_gene_variant,,ENST00000561659,;POLR2C,downstream_gene_variant,,ENST00000567982,;POLR2C,downstream_gene_variant,,ENST00000562953,;POLR2C,downstream_gene_variant,,ENST00000562599,;	CC	ENSG00000125170	ENST00000340099	Transcript	3_prime_UTR_variant	1688-1689	.	.	.	.	.	.	.	-1	DOK4	HGNC	19868	protein_coding	YES	CCDS10783.1	ENSP00000344277	DOK4_HUMAN	H3BVB4_HUMAN,H3BV67_HUMAN,H3BTK2_HUMAN,H3BTI7_HUMAN,H3BTI4_HUMAN,H3BSK0_HUMAN,H3BS85_HUMAN,H3BPY9_HUMAN,H3BN90_HUMAN	UPI0000070AA4	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCGTGGCCTGG	.	2	ESCA
LINC00922	0	.	GRCh37	16	65388165	65388165	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.666C>T	.	.	ENST00000569736	7/9	80	60	19	71	71	0	LINC00922,non_coding_transcript_exon_variant,,ENST00000564041,;LINC00922,non_coding_transcript_exon_variant,,ENST00000569736,;LINC00922,non_coding_transcript_exon_variant,,ENST00000568492,;RP11-256I9.3,intron_variant,,ENST00000562656,;	A	ENSG00000261742	ENST00000569736	Transcript	non_coding_transcript_exon_variant	666	.	.	.	.	.	.	.	-1	LINC00922	HGNC	27545	lincRNA	YES	.	.	.	.	.	.	.	.	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTGAATGT	.	5	ESCA
WFIKKN1	0	.	GRCh37	16	683045	683045	+	Missense_Mutation	SNP	G	G	A	rs146880296	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.635G>A	p.Arg212His	p.R212H	ENST00000319070	2/2	12	7	5	15	15	0	WFIKKN1,missense_variant,p.Arg212His,ENST00000319070,;RAB40C,downstream_gene_variant,,ENST00000538492,;C16orf13,downstream_gene_variant,,ENST00000397666,;C16orf13,downstream_gene_variant,,ENST00000301686,;RAB40C,downstream_gene_variant,,ENST00000539661,;C16orf13,downstream_gene_variant,,ENST00000565163,;C16orf13,downstream_gene_variant,,ENST00000397664,;C16orf13,downstream_gene_variant,,ENST00000338401,;C16orf13,downstream_gene_variant,,ENST00000397665,;RAB40C,downstream_gene_variant,,ENST00000535977,;C16orf13,downstream_gene_variant,,ENST00000568830,;C16orf13,downstream_gene_variant,,ENST00000568773,;RAB40C,downstream_gene_variant,,ENST00000248139,;WFIKKN1,non_coding_transcript_exon_variant,,ENST00000573440,;C16orf13,downstream_gene_variant,,ENST00000456420,;C16orf13,downstream_gene_variant,,ENST00000565799,;C16orf13,downstream_gene_variant,,ENST00000564039,;RAB40C,downstream_gene_variant,,ENST00000561781,;C16orf13,downstream_gene_variant,,ENST00000448973,;C16orf13,downstream_gene_variant,,ENST00000568077,;	A	ENSG00000127578	ENST00000319070	Transcript	missense_variant	957	635	212	R/H	cGc/cAc	rs146880296	.	.	1	WFIKKN1	HGNC	30912	protein_coding	YES	CCDS10414.1	ENSP00000324763	WFKN1_HUMAN	.	UPI0000043725	.	tolerated(0.31)	benign(0.053)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10083:SF87,hmmpanther:PTHR10083,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CGGCCGCCCGC	byCluster	2	ESCA
WDR90	0	.	GRCh37	16	710154	710154	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3281C>G	p.Ser1094Cys	p.S1094C	ENST00000293879	27/41	48	33	14	45	45	0	WDR90,missense_variant,p.Ser1094Cys,ENST00000549091,;WDR90,missense_variant,p.Ser77Cys,ENST00000550739,;WDR90,missense_variant,p.Ser1094Cys,ENST00000293879,;LA16c-349E10.1,upstream_gene_variant,,ENST00000573609,;WDR90,intron_variant,,ENST00000548844,;WDR90,upstream_gene_variant,,ENST00000547543,;WDR90,upstream_gene_variant,,ENST00000548603,;WDR90,downstream_gene_variant,,ENST00000552648,;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,;WDR90,non_coding_transcript_exon_variant,,ENST00000552943,;WDR90,non_coding_transcript_exon_variant,,ENST00000552683,;WDR90,non_coding_transcript_exon_variant,,ENST00000546516,;WDR90,intron_variant,,ENST00000552728,;WDR90,downstream_gene_variant,,ENST00000549648,;WDR90,upstream_gene_variant,,ENST00000549024,;WDR90,downstream_gene_variant,,ENST00000420061,;WDR90,upstream_gene_variant,,ENST00000550902,;WDR90,upstream_gene_variant,,ENST00000546923,;WDR90,upstream_gene_variant,,ENST00000553080,;WDR90,downstream_gene_variant,,ENST00000548859,;	G	ENSG00000161996	ENST00000293879	Transcript	missense_variant	3281	3281	1094	S/C	tCt/tGt	.	.	.	1	WDR90	HGNC	26960	protein_coding	YES	CCDS42092.1	ENSP00000293879	WDR90_HUMAN	.	UPI0000D67C48	.	deleterious(0.05)	benign(0.338)	27/41	.	hmmpanther:PTHR13720:SF10,hmmpanther:PTHR13720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTCTGCCA	.	5	ESCA
ATXN1L	0	.	GRCh37	16	71885540	71885540	+	Missense_Mutation	SNP	C	C	T	rs566942971	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1897C>T	p.Arg633Cys	p.R633C	ENST00000427980	3/3	22	12	10	17	17	0	ATXN1L,missense_variant,p.Arg633Cys,ENST00000427980,;IST1,intron_variant,,ENST00000568581,;ATXN1L,intron_variant,,ENST00000569119,;ATXN1L,downstream_gene_variant,,ENST00000565676,;	T	ENSG00000224470	ENST00000427980	Transcript	missense_variant	2190	1897	633	R/C	Cgt/Tgt	rs566942971	.	.	1	ATXN1L	HGNC	33279	protein_coding	YES	CCDS45523.1	ENSP00000415822	ATX1L_HUMAN	G1UI23_HUMAN	UPI0000198982	.	tolerated(0.08)	benign(0)	3/3	.	hmmpanther:PTHR13392,hmmpanther:PTHR13392:SF6	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCCGTGTG	by1000G	5	ESCA
ZNF821	0	.	GRCh37	16	71894143	71894143	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1017G>A	p.%3D	p.R339R	ENST00000425432	8/8	41	37	3	38	38	0	ZNF821,synonymous_variant,p.%3D,ENST00000425432,;ZNF821,synonymous_variant,p.%3D,ENST00000313565,;ZNF821,synonymous_variant,p.%3D,ENST00000568666,;ZNF821,synonymous_variant,p.%3D,ENST00000565601,;ZNF821,synonymous_variant,p.%3D,ENST00000446827,;ZNF821,3_prime_UTR_variant,,ENST00000564134,;IST1,intron_variant,,ENST00000568581,;ZNF821,downstream_gene_variant,,ENST00000568322,;ZNF821,downstream_gene_variant,,ENST00000562797,;ZNF821,downstream_gene_variant,,ENST00000565516,;ATXN1L,downstream_gene_variant,,ENST00000427980,;ZNF821,downstream_gene_variant,,ENST00000565843,;ATXN1L,intron_variant,,ENST00000569119,;ZNF821,downstream_gene_variant,,ENST00000564943,;ZNF821,3_prime_UTR_variant,,ENST00000568961,;ZNF821,3_prime_UTR_variant,,ENST00000562808,;ZNF821,3_prime_UTR_variant,,ENST00000566987,;ZNF821,downstream_gene_variant,,ENST00000569186,;ZNF821,downstream_gene_variant,,ENST00000563878,;ZNF821,downstream_gene_variant,,ENST00000562985,;ZNF821,downstream_gene_variant,,ENST00000563827,;	T	ENSG00000102984	ENST00000425432	Transcript	synonymous_variant	1397	1017	339	R	cgG/cgA	.	.	.	-1	ZNF821	HGNC	28043	protein_coding	YES	CCDS56006.1	ENSP00000398089	ZN821_HUMAN	H3BS68_HUMAN	UPI0000EE78C4	.	.	.	8/8	.	hmmpanther:PTHR24404:SF1,hmmpanther:PTHR24404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	GCCTGCCGCTT	.	2	ESCA
ALDH3A1	0	.	GRCh37	17	19646639	19646639	+	Silent	SNP	G	G	A	rs11554974	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.300C>T	p.%3D	p.I100I	ENST00000457500	2/10	26	20	6	29	29	0	ALDH3A1,synonymous_variant,p.%3D,ENST00000395555,;ALDH3A1,synonymous_variant,p.%3D,ENST00000574162,;ALDH3A1,synonymous_variant,p.%3D,ENST00000457500,;ALDH3A1,synonymous_variant,p.%3D,ENST00000225740,;ALDH3A1,synonymous_variant,p.%3D,ENST00000494157,;ALDH3A1,synonymous_variant,p.%3D,ENST00000444455,;ALDH3A1,synonymous_variant,p.%3D,ENST00000573368,;ALDH3A1,synonymous_variant,p.%3D,ENST00000439102,;ALDH3A1,synonymous_variant,p.%3D,ENST00000426645,;ALDH3A1,downstream_gene_variant,,ENST00000570414,;RP11-311F12.2,downstream_gene_variant,,ENST00000580884,;ALDH3A1,non_coding_transcript_exon_variant,,ENST00000485231,;ALDH3A1,synonymous_variant,p.%3D,ENST00000468746,;ALDH3A1,non_coding_transcript_exon_variant,,ENST00000575860,;ALDH3A1,non_coding_transcript_exon_variant,,ENST00000485472,;ALDH3A1,non_coding_transcript_exon_variant,,ENST00000479677,;ALDH3A1,upstream_gene_variant,,ENST00000487650,;ALDH3A1,downstream_gene_variant,,ENST00000575103,;	A	ENSG00000108602	ENST00000457500	Transcript	synonymous_variant	630	300	100	I	atC/atT	rs11554974	.	.	-1	ALDH3A1	HGNC	405	protein_coding	YES	CCDS11212.1	ENSP00000411821	AL3A1_HUMAN	I3L4E5_HUMAN,I3L3W9_HUMAN,I3L3I9_HUMAN,I3L1H6_HUMAN,C9JMC5_HUMAN	UPI000013C87C	.	.	.	2/10	.	hmmpanther:PTHR11699:SF105,hmmpanther:PTHR11699,Pfam_domain:PF00171,Gene3D:3.40.605.10,PIRSF_domain:PIRSF036492,Superfamily_domains:SSF53720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTGGATGTA	byCluster|byHapMap	5	ESCA
PHF12	0	.	GRCh37	17	27237002	27237002	+	Intron	SNP	G	G	A	rs186267238	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2359+242C>T	.	.	ENST00000332830	.	22	13	8	13	13	0	PHF12,3_prime_UTR_variant,,ENST00000577226,;PHF12,intron_variant,,ENST00000332830,;PHF12,downstream_gene_variant,,ENST00000579036,;PHF12,downstream_gene_variant,,ENST00000268756,;PHF12,downstream_gene_variant,,ENST00000579563,;PHF12,downstream_gene_variant,,ENST00000582655,;PHF12,non_coding_transcript_exon_variant,,ENST00000582436,;PHF12,intron_variant,,ENST00000589176,;PHF12,downstream_gene_variant,,ENST00000584822,;PHF12,downstream_gene_variant,,ENST00000583524,;PHF12,downstream_gene_variant,,ENST00000378879,;	A	ENSG00000109118	ENST00000332830	Transcript	intron_variant	.	.	.	.	.	rs186267238	.	.	-1	PHF12	HGNC	20816	protein_coding	YES	CCDS32598.1	ENSP00000329933	PHF12_HUMAN	K7ERZ4_HUMAN,K7ENU0_HUMAN,K7EMX6_HUMAN	UPI0000197E05	.	.	.	.	11/14	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTCGAAGTG	byCluster|by1000G	5	ESCA
KPNB1	0	.	GRCh37	17	45730174	45730174	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214A>G	p.Ile72Val	p.I72V	ENST00000290158	3/22	55	51	4	30	30	0	KPNB1,missense_variant,p.Ile72Val,ENST00000290158,;KPNB1,missense_variant,p.Ile72Val,ENST00000583648,;KPNB1,5_prime_UTR_variant,,ENST00000535458,;KPNB1,5_prime_UTR_variant,,ENST00000577875,;KPNB1,5_prime_UTR_variant,,ENST00000540627,;KPNB1,upstream_gene_variant,,ENST00000582097,;KPNB1,upstream_gene_variant,,ENST00000537679,;RP11-580I16.2,upstream_gene_variant,,ENST00000582389,;RP11-580I16.2,upstream_gene_variant,,ENST00000580045,;RP11-580I16.2,upstream_gene_variant,,ENST00000584391,;KPNB1,non_coding_transcript_exon_variant,,ENST00000577918,;	G	ENSG00000108424	ENST00000290158	Transcript	missense_variant	621	214	72	I/V	Atc/Gtc	.	.	.	1	KPNB1	HGNC	6400	protein_coding	YES	CCDS11513.1	ENSP00000290158	IMB1_HUMAN	J3QRG4_HUMAN,J3QR48_HUMAN,B7ZAV6_HUMAN	UPI0000001C21	.	tolerated(1)	benign(0)	3/22	.	PROSITE_profiles:PS50166,hmmpanther:PTHR10527:SF1,hmmpanther:PTHR10527,Pfam_domain:PF03810,SMART_domains:SM00913,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATATCAAG	.	2	ESCA
ZNF652	0	.	GRCh37	17	47373765	47373765	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2010G>C	.	.	ENST00000362063	6/6	121	77	43	77	77	0	ZNF652,3_prime_UTR_variant,,ENST00000362063,;ZNF652,3_prime_UTR_variant,,ENST00000430262,;ZNF652,intron_variant,,ENST00000508237,;	G	ENSG00000198740	ENST00000362063	Transcript	3_prime_UTR_variant	4150	.	.	.	.	.	.	.	-1	ZNF652	HGNC	29147	protein_coding	YES	CCDS32677.1	ENSP00000354686	ZN652_HUMAN	.	UPI000006D93D	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATCTCAAT	.	5	ESCA
ZNF594	0	.	GRCh37	17	5084962	5084962	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*166G>T	.	.	ENST00000399604	1/1	57	25	32	54	54	0	ZNF594,3_prime_UTR_variant,,ENST00000575779,;ZNF594,3_prime_UTR_variant,,ENST00000399604,;ZNF594,downstream_gene_variant,,ENST00000576772,;	A	ENSG00000180626	ENST00000399604	Transcript	3_prime_UTR_variant	2731	.	.	.	.	.	.	.	-1	ZNF594	HGNC	29392	protein_coding	YES	CCDS42241.1	ENSP00000382513	ZN594_HUMAN	I3L508_HUMAN	UPI00001C1FDF	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCTGGTG	.	5	ESCA
MFSD11	0	.	GRCh37	17	74774688	74774688	+	3'Flank	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000588460	.	73	60	13	38	38	0	MFSD11,3_prime_UTR_variant,,ENST00000336509,;MFSD11,3_prime_UTR_variant,,ENST00000355954,;MFSD11,3_prime_UTR_variant,,ENST00000593181,;MFSD11,3_prime_UTR_variant,,ENST00000586622,;MFSD11,3_prime_UTR_variant,,ENST00000590514,;MFSD11,intron_variant,,ENST00000585865,;MFSD11,downstream_gene_variant,,ENST00000588460,;MFSD11,downstream_gene_variant,,ENST00000585958,;MFSD11,downstream_gene_variant,,ENST00000590070,;MFSD11,downstream_gene_variant,,ENST00000585692,;MFSD11,downstream_gene_variant,,ENST00000588768,;MFSD11,downstream_gene_variant,,ENST00000588647,;	G	ENSG00000092931	ENST00000588460	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	34	1	MFSD11	HGNC	25458	protein_coding	YES	CCDS11750.1	ENSP00000464932	MFS11_HUMAN	K7ESK9_HUMAN,K7ELU3_HUMAN	UPI0000073F31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTATCTCAAT	.	5	ESCA
TP53	0	.	GRCh37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524G>A	p.Arg175His	p.R175H	ENST00000269305	5/11	24	2	22	15	15	0	TP53,missense_variant,p.Arg175His,ENST00000413465,;TP53,missense_variant,p.Arg175His,ENST00000420246,;TP53,missense_variant,p.Arg175His,ENST00000269305,;TP53,missense_variant,p.Arg43His,ENST00000509690,;TP53,missense_variant,p.Arg175His,ENST00000359597,;TP53,missense_variant,p.Arg82His,ENST00000514944,;TP53,missense_variant,p.Arg175His,ENST00000445888,;TP53,missense_variant,p.Arg175His,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	714	524	175	R/H	cGc/cAc	CM951224,rs28934578,CM062017,TP53_g.12512G>T,TP53_g.12512G>C,TP53_g.12512G>A,COSM10718,COSM10648,COSM45416,COSM99914,COSM1679508,COSM99022,COSM1679510,COSM99023,COSM1679512,COSM3355994,COSM1640851,COSM1679509,COSM99024,COSM1679511	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.11)	benign(0.308)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660,21264207,24929325,25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R175H|c.524G>A|181,SITE|p.R43H|c.128G>A|183,SITE|p.R82H|c.245G>A|183,SITE|p.R175H|c.524G>A|124,SITE|p.R175H|c.524G>A|180,SITE|p.R175H|c.524G>A|926,SITE|p.R175H|c.524G>A|88,CODON|p.0?|c.1_1182del1182|6,CODON|p.R175L|c.524G>T|20,CODON|p.R175P|c.524G>C|6,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R43L|c.128G>T|3,CODON|p.R82L|c.245G>T|3,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.P177_C182delPHHERC|c.526_543del18|3,BUFFER|p.H179Y|c.534_535CC>TT|8,BUFFER|p.H179D|c.535C>G|12,BUFFER|p.H179Y|c.535C>T|4,BUFFER|p.H47Y|c.139C>T|15,BUFFER|p.H179Y|c.535C>T|5,BUFFER|p.H179Y|c.535C>T|88,BUFFER|p.H179N|c.535C>A|15,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H179Y|c.535C>T|14,BUFFER|p.H86Y|c.256C>T|14,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R82G|c.244C>G|5,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43G|c.127C>G|8,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175G|c.523C>G|16,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R174K|c.521G>A|5,BUFFER|p.R174W|c.520A>T|11,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V172D|c.515T>A|11,BUFFER|p.V172A|c.515T>C|4,BUFFER|p.V172G|c.515T>G|4,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAGCGCCTC	byCluster	5	ESCA
CHD3	0	.	GRCh37	17	7803295	7803295	+	Missense_Mutation	SNP	C	C	T	rs780573521	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2803C>T	p.Arg935Cys	p.R935C	ENST00000380358	16/40	50	33	16	49	49	0	CHD3,missense_variant,p.Arg935Cys,ENST00000380358,;CHD3,missense_variant,p.Arg876Cys,ENST00000358181,;CHD3,missense_variant,p.Arg876Cys,ENST00000330494,;CHD3,downstream_gene_variant,,ENST00000452447,;CHD3,upstream_gene_variant,,ENST00000466233,;CHD3,upstream_gene_variant,,ENST00000473376,;CHD3,downstream_gene_variant,,ENST00000479080,;CHD3,upstream_gene_variant,,ENST00000470531,;	T	ENSG00000170004	ENST00000380358	Transcript	missense_variant	2804	2803	935	R/C	Cgc/Tgc	rs780573521	.	.	1	CHD3	HGNC	1918	protein_coding	YES	CCDS32553.2	ENSP00000369716	CHD3_HUMAN	Q2TAZ1_HUMAN	UPI00004DDA7C	.	.	possibly_damaging(0.898)	16/40	.	PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF544,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCCGCTGG	byFrequency	5	ESCA
AATK	0	.	GRCh37	17	79139525	79139525	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55+213G>A	.	.	ENST00000326724	.	43	34	9	31	31	0	AATK,intron_variant,,ENST00000326724,;AATK-AS1,non_coding_transcript_exon_variant,,ENST00000414089,;AATK-AS1,non_coding_transcript_exon_variant,,ENST00000571031,;AATK,non_coding_transcript_exon_variant,,ENST00000572798,;AATK,intron_variant,,ENST00000374792,;	T	ENSG00000181409	ENST00000326724	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AATK	HGNC	21	protein_coding	YES	CCDS45807.1	ENSP00000324196	LMTK1_HUMAN	H7C175_HUMAN	UPI000041EA63	.	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGACGCCAG	.	5	ESCA
TIMM22	0	.	GRCh37	17	900388	900388	+	Silent	SNP	G	G	A	rs774479973	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6G>A	p.%3D	p.A2A	ENST00000327158	1/4	26	19	6	10	10	0	TIMM22,synonymous_variant,p.%3D,ENST00000327158,;	A	ENSG00000177370	ENST00000327158	Transcript	synonymous_variant	32	6	2	A	gcG/gcA	rs774479973	.	.	1	TIMM22	HGNC	17317	protein_coding	YES	CCDS32521.1	ENSP00000320236	TIM22_HUMAN	.	UPI000012D5D5	.	.	.	1/4	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGCGGCGGC	byFrequency	5	ESCA
KCTD1	0	.	GRCh37	18	24034984	24034984	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*723C>G	.	.	ENST00000408011	5/5	51	37	13	38	38	0	KCTD1,3_prime_UTR_variant,,ENST00000579973,;KCTD1,3_prime_UTR_variant,,ENST00000317932,;KCTD1,3_prime_UTR_variant,,ENST00000417602,;KCTD1,3_prime_UTR_variant,,ENST00000408011,;KCTD1,downstream_gene_variant,,ENST00000580059,;KCTD1,downstream_gene_variant,,ENST00000580638,;KCTD1,downstream_gene_variant,,ENST00000580191,;KCTD1,downstream_gene_variant,,ENST00000578973,;KCTD1,downstream_gene_variant,,ENST00000582494,;KCTD1,downstream_gene_variant,,ENST00000577255,;	C	ENSG00000134504	ENST00000408011	Transcript	3_prime_UTR_variant	2057	.	.	.	.	.	.	.	-1	KCTD1	HGNC	18249	protein_coding	YES	CCDS11888.1	ENSP00000384367	KCTD1_HUMAN	J3KSG1_HUMAN	UPI00001CDFF1	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTGAAAAA	.	5	ESCA
SYT4	0	.	GRCh37	18	40853827	40853827	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567C>T	p.%3D	p.T189T	ENST00000255224	2/4	83	61	22	37	37	0	SYT4,synonymous_variant,p.%3D,ENST00000255224,;SYT4,synonymous_variant,p.%3D,ENST00000590752,;SYT4,intron_variant,,ENST00000596867,;SYT4,intron_variant,,ENST00000593720,;SYT4,intron_variant,,ENST00000586678,;SYT4,intron_variant,,ENST00000585604,;SYT4,downstream_gene_variant,,ENST00000591820,;SYT4,upstream_gene_variant,,ENST00000589479,;	A	ENSG00000132872	ENST00000255224	Transcript	synonymous_variant	936	567	189	T	acC/acT	.	.	.	-1	SYT4	HGNC	11512	protein_coding	YES	CCDS11922.1	ENSP00000255224	SYT4_HUMAN	M0QZF3_HUMAN,B4DMA9_HUMAN	UPI000013669E	.	.	.	2/4	.	PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF114,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAGGTCAT	.	5	ESCA
HDHD2	0	.	GRCh37	18	44639384	44639384	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640C>T	p.Gln214Ter	p.Q214*	ENST00000300605	6/7	177	155	22	33	33	0	HDHD2,stop_gained,p.Gln214Ter,ENST00000300605,;HDHD2,downstream_gene_variant,,ENST00000590815,;HDHD2,downstream_gene_variant,,ENST00000591480,;RP11-49K24.8,downstream_gene_variant,,ENST00000591183,;HDHD2,non_coding_transcript_exon_variant,,ENST00000587841,;HDHD2,3_prime_UTR_variant,,ENST00000588183,;HDHD2,downstream_gene_variant,,ENST00000586546,;HDHD2,upstream_gene_variant,,ENST00000588861,;	A	ENSG00000167220	ENST00000300605	Transcript	stop_gained	793	640	214	Q/*	Caa/Taa	.	.	.	-1	HDHD2	HGNC	25364	protein_coding	YES	CCDS32829.1	ENSP00000300605	HDHD2_HUMAN	K7ER15_HUMAN,K7EQD2_HUMAN	UPI0000037B93	.	.	.	6/7	.	hmmpanther:PTHR19288:SF36,hmmpanther:PTHR19288,TIGRFAM_domain:TIGR01460,Pfam_domain:PF13242,TIGRFAM_domain:TIGR01458,Gene3D:3.40.50.1000,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTTGAGCCC	.	4	ESCA
ONECUT2	0	.	GRCh37	18	55144761	55144761	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*806G>C	.	.	ENST00000491143	2/2	62	46	15	52	52	0	ONECUT2,3_prime_UTR_variant,,ENST00000491143,;ONECUT2,downstream_gene_variant,,ENST00000481727,;	C	ENSG00000119547	ENST00000491143	Transcript	3_prime_UTR_variant	2353	.	.	.	.	.	.	.	1	ONECUT2	HGNC	8139	protein_coding	YES	CCDS42440.1	ENSP00000419185	ONEC2_HUMAN	.	UPI0000201DC1	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGGGTTCA	.	5	ESCA
PHLPP1	0	.	GRCh37	18	60639791	60639791	+	Missense_Mutation	SNP	G	G	A	rs765622042	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3605G>A	p.Arg1202His	p.R1202H	ENST00000262719	15/17	44	28	16	45	45	0	PHLPP1,missense_variant,p.Arg690His,ENST00000400316,;PHLPP1,missense_variant,p.Arg1202His,ENST00000262719,;	A	ENSG00000081913	ENST00000262719	Transcript	missense_variant	3839	3605	1202	R/H	cGc/cAc	rs765622042	.	.	1	PHLPP1	HGNC	20610	protein_coding	YES	CCDS45881.2	ENSP00000262719	PHLP1_HUMAN	.	UPI000051AE2E	.	deleterious(0.05)	possibly_damaging(0.46)	15/17	.	Superfamily_domains:SSF81606,SMART_domains:SM00332,Gene3D:3.60.40.10,Pfam_domain:PF00481,hmmpanther:PTHR23155:SF252,hmmpanther:PTHR23155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACCGCGAAG	.	5	ESCA
PTPRM	0	.	GRCh37	18	7774252	7774252	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179A>T	p.Asp60Val	p.D60V	ENST00000580170	2/33	72	52	19	63	63	0	PTPRM,missense_variant,p.Asp60Val,ENST00000332175,;PTPRM,missense_variant,p.Asp60Val,ENST00000400060,;PTPRM,missense_variant,p.Asp60Val,ENST00000580170,;PTPRM,5_prime_UTR_variant,,ENST00000400053,;	T	ENSG00000173482	ENST00000580170	Transcript	missense_variant	1216	179	60	D/V	gAt/gTt	.	.	.	1	PTPRM	HGNC	9675	protein_coding	YES	CCDS58613.1	ENSP00000463325	PTPRM_HUMAN	Q49AC9_HUMAN	UPI00015CFC03	.	deleterious(0.02)	possibly_damaging(0.528)	2/33	.	Superfamily_domains:SSF49899,SMART_domains:SM00137,Pfam_domain:PF00629,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206,PROSITE_profiles:PS50060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGATCCAT	.	5	ESCA
DNAJB1	0	.	GRCh37	19	14628955	14628955	+	Silent	SNP	C	C	T	rs774882978	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207G>A	p.%3D	p.E69E	ENST00000254322	1/3	45	22	23	53	53	0	DNAJB1,synonymous_variant,p.%3D,ENST00000254322,;DNAJB1,5_prime_UTR_variant,,ENST00000596075,;DNAJB1,intron_variant,,ENST00000594099,;DNAJB1,intron_variant,,ENST00000598692,;DNAJB1,intron_variant,,ENST00000596853,;DNAJB1,intron_variant,,ENST00000396969,;DNAJB1,intron_variant,,ENST00000601533,;DNAJB1,intron_variant,,ENST00000595992,;DNAJB1,upstream_gene_variant,,ENST00000598235,;DNAJB1,upstream_gene_variant,,ENST00000595139,;TECR,intron_variant,,ENST00000600076,;	T	ENSG00000132002	ENST00000254322	Transcript	synonymous_variant	278	207	69	E	gaG/gaA	rs774882978	.	.	-1	DNAJB1	HGNC	5270	protein_coding	YES	CCDS12312.1	ENSP00000254322	DNJB1_HUMAN	Q6FHS4_HUMAN,M0R1D6_HUMAN,M0R128_HUMAN,M0R080_HUMAN,M0QZD0_HUMAN,M0QYT3_HUMAN,B4DX52_HUMAN	UPI0000000C3A	.	.	.	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24077:SF207,hmmpanther:PTHR24077,Gene3D:1.10.287.110,Superfamily_domains:SSF46565,Prints_domain:PR00625	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCCTCCCC	.	5	ESCA
OR10H4	0	.	GRCh37	19	16059901	16059901	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84G>C	p.Leu28Phe	p.L28F	ENST00000322107	1/1	122	102	20	86	86	0	OR10H4,missense_variant,p.Leu28Phe,ENST00000322107,;	C	ENSG00000176231	ENST00000322107	Transcript	missense_variant	84	84	28	L/F	ttG/ttC	.	.	.	1	OR10H4	HGNC	15388	protein_coding	YES	CCDS32941.1	ENSP00000318834	O10H4_HUMAN	.	UPI0000046194	.	tolerated(0.46)	benign(0.005)	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF78,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L25L|c.75G>C|3,BUFFER|p.F29F|c.87C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTGTTCCT	.	5	ESCA
ZNF493	0	.	GRCh37	19	21610041	21610041	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2255A>T	.	.	ENST00000392288	4/4	76	48	28	73	73	0	ZNF493,3_prime_UTR_variant,,ENST00000392288,;ZNF493,downstream_gene_variant,,ENST00000355504,;ZNF493,downstream_gene_variant,,ENST00000596302,;CTD-2561J22.3,intron_variant,,ENST00000600810,;ZNF493,downstream_gene_variant,,ENST00000598152,;	T	ENSG00000196268	ENST00000392288	Transcript	3_prime_UTR_variant	4689	.	.	.	.	.	.	.	1	ZNF493	HGNC	23708	protein_coding	YES	CCDS42536.1	ENSP00000376110	ZN493_HUMAN	.	UPI000022ABBF	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAATATTCTT	.	5	ESCA
ZNF429	0	.	GRCh37	19	21712542	21712542	+	Missense_Mutation	SNP	A	A	G	rs764139712	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86A>G	p.Tyr29Cys	p.Y29C	ENST00000358491	2/4	111	65	46	85	84	0	ZNF429,missense_variant,p.Tyr29Cys,ENST00000597078,;ZNF429,missense_variant,p.Tyr29Cys,ENST00000358491,;ZNF429,non_coding_transcript_exon_variant,,ENST00000594022,;ZNF429,downstream_gene_variant,,ENST00000596126,;	G	ENSG00000197013	ENST00000358491	Transcript	missense_variant	294	86	29	Y/C	tAt/tGt	rs764139712	.	.	1	ZNF429	HGNC	20817	protein_coding	YES	CCDS42537.1	ENSP00000351280	ZN429_HUMAN	.	UPI000022ABC2	.	deleterious(0)	probably_damaging(0.995)	2/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24377:SF239,hmmpanther:PTHR24377,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTATATAGAA	.	5	ESCA
ZNF43	0	.	GRCh37	19	22018895	22018895	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-55T>A	.	.	ENST00000354959	1/4	88	61	26	85	85	0	ZNF43,5_prime_UTR_variant,,ENST00000599906,;ZNF43,5_prime_UTR_variant,,ENST00000354959,;ZNF43,intron_variant,,ENST00000595461,;ZNF43,intron_variant,,ENST00000593551,;ZNF43,intron_variant,,ENST00000598288,;ZNF43,intron_variant,,ENST00000596899,;ZNF43,intron_variant,,ENST00000594012,;ZNF43,intron_variant,,ENST00000598381,;ZNF43,downstream_gene_variant,,ENST00000593886,;	T	ENSG00000198521	ENST00000354959	Transcript	5_prime_UTR_variant	116	.	.	.	.	.	.	.	-1	ZNF43	HGNC	13109	protein_coding	YES	CCDS12413.2	ENSP00000347045	ZNF43_HUMAN	M0R0T7_HUMAN,M0QYJ6_HUMAN,M0QXI2_HUMAN	UPI00001BD957	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGCAGGTCA	.	5	ESCA
C19orf35	0	.	GRCh37	19	2278932	2278932	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263G>C	p.Arg88Thr	p.R88T	ENST00000342063	3/4	107	69	37	51	51	0	C19orf35,missense_variant,p.Arg88Thr,ENST00000342063,;C19orf35,intron_variant,,ENST00000590316,;	G	ENSG00000188305	ENST00000342063	Transcript	missense_variant	357	263	88	R/T	aGa/aCa	.	.	.	-1	C19orf35	HGNC	24793	protein_coding	YES	CCDS12087.1	ENSP00000345102	CS035_HUMAN	.	UPI00001C0E91	.	deleterious(0.01)	possibly_damaging(0.545)	3/4	.	hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGTCTCCGA	.	5	ESCA
TMPRSS9	0	.	GRCh37	19	2418044	2418044	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1960G>A	p.Asp654Asn	p.D654N	ENST00000332578	12/17	29	22	7	26	26	0	TMPRSS9,missense_variant,p.Asp654Asn,ENST00000332578,;TMPRSS9,downstream_gene_variant,,ENST00000395264,;TMPRSS9,downstream_gene_variant,,ENST00000587863,;	A	ENSG00000178297	ENST00000332578	Transcript	missense_variant	1960	1960	654	D/N	Gac/Aac	.	.	.	1	TMPRSS9	HGNC	30079	protein_coding	YES	CCDS12088.1	ENSP00000330264	TMPS9_HUMAN	.	UPI00001B4EC6	.	tolerated(0.1)	probably_damaging(0.936)	12/17	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF108,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,PIRSF_domain:PIRSF037931,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATAGACCAG	.	5	ESCA
ZFR2	0	.	GRCh37	19	3808898	3808898	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2517G>C	p.Glu839Asp	p.E839D	ENST00000262961	17/19	20	16	4	20	20	0	ZFR2,missense_variant,p.Glu839Asp,ENST00000262961,;	G	ENSG00000105278	ENST00000262961	Transcript	missense_variant	2528	2517	839	E/D	gaG/gaC	.	.	.	-1	ZFR2	HGNC	29189	protein_coding	YES	CCDS45921.1	ENSP00000262961	ZFR2_HUMAN	.	UPI0000DD84BE	.	deleterious(0)	probably_damaging(0.999)	17/19	.	PROSITE_profiles:PS51703,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF85,Pfam_domain:PF07528,SMART_domains:SM00572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACGCACTCCAG	.	4	ESCA
ZNF540	0	.	GRCh37	19	38103939	38103939	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1758G>T	p.Lys586Asn	p.K586N	ENST00000592533	5/5	31	18	12	37	37	0	ZNF540,missense_variant,p.Lys586Asn,ENST00000316433,;ZNF540,missense_variant,p.Lys586Asn,ENST00000343599,;ZNF540,missense_variant,p.Lys554Asn,ENST00000589117,;ZNF540,missense_variant,p.Lys586Asn,ENST00000592533,;ZNF540,downstream_gene_variant,,ENST00000586134,;ZNF540,downstream_gene_variant,,ENST00000590588,;ZFP30,downstream_gene_variant,,ENST00000589018,;ZNF540,downstream_gene_variant,,ENST00000586792,;ZNF540,downstream_gene_variant,,ENST00000589857,;ZNF540,non_coding_transcript_exon_variant,,ENST00000589285,;	T	ENSG00000171817	ENST00000592533	Transcript	missense_variant	2090	1758	586	K/N	aaG/aaT	.	.	.	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	deleterious(0.03)	probably_damaging(0.996)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF138,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAGGCCTT	.	5	ESCA
SPTBN4	0	.	GRCh37	19	41029495	41029495	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3806G>A	p.Gly1269Asp	p.G1269D	ENST00000352632	17/36	26	23	3	39	39	0	SPTBN4,missense_variant,p.Gly1269Asp,ENST00000338932,;SPTBN4,missense_variant,p.Gly1269Asp,ENST00000352632,;SPTBN4,missense_variant,p.Gly1269Asp,ENST00000598249,;SPTBN4,missense_variant,p.Gly1269Asp,ENST00000595535,;SPTBN4,missense_variant,p.Gly1269Asp,ENST00000344104,;SPTBN4,upstream_gene_variant,,ENST00000392025,;SPTBN4,missense_variant,p.Gly661Asp,ENST00000597389,;	A	ENSG00000160460	ENST00000352632	Transcript	missense_variant	3892	3806	1269	G/D	gGc/gAc	.	.	.	1	SPTBN4	HGNC	14896	protein_coding	YES	CCDS12559.1	ENSP00000263373	SPTN4_HUMAN	.	UPI0000135DBB	.	tolerated(0.15)	benign(0.046)	17/36	.	hmmpanther:PTHR11915:SF232,hmmpanther:PTHR11915,Gene3D:1.20.58.60,PIRSF_domain:PIRSF002297,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GCAGGGCAACA	.	2	ESCA
LIPE	0	.	GRCh37	19	42914736	42914736	+	Missense_Mutation	SNP	C	C	T	rs141806189	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1142G>A	p.Arg381His	p.R381H	ENST00000244289	2/10	31	21	10	28	28	0	LIPE,missense_variant,p.Arg381His,ENST00000244289,;LIPE,missense_variant,p.Arg80His,ENST00000597001,;LIPE,missense_variant,p.Arg80His,ENST00000601189,;LIPE,missense_variant,p.Arg91His,ENST00000599211,;LIPE,missense_variant,p.Arg126His,ENST00000599783,;LIPE,upstream_gene_variant,,ENST00000597620,;LIPE,upstream_gene_variant,,ENST00000599918,;LIPE-AS1,intron_variant,,ENST00000597203,;LIPE-AS1,intron_variant,,ENST00000594624,;LIPE-AS1,downstream_gene_variant,,ENST00000593491,;LIPE-AS1,downstream_gene_variant,,ENST00000599276,;LIPE,intron_variant,,ENST00000602000,;LIPE,upstream_gene_variant,,ENST00000600224,;	T	ENSG00000079435	ENST00000244289	Transcript	missense_variant	1419	1142	381	R/H	cGc/cAc	rs141806189	.	.	-1	LIPE	HGNC	6621	protein_coding	YES	CCDS12607.1	ENSP00000244289	LIPS_HUMAN	M0QXM5_HUMAN,M0QXB1_HUMAN	UPI000013CB66	.	tolerated(0.08)	possibly_damaging(0.679)	2/10	.	hmmpanther:PTHR23025,hmmpanther:PTHR23025:SF3,Pfam_domain:PF06350	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGCGGGCT	.	5	ESCA
ZNF222	0	.	GRCh37	19	44536478	44536478	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.771A>G	p.%3D	p.K257K	ENST00000391960	4/4	48	29	19	49	49	0	ZNF222,synonymous_variant,p.%3D,ENST00000391960,;ZNF222,synonymous_variant,p.%3D,ENST00000187879,;ZNF222,downstream_gene_variant,,ENST00000587846,;ZNF222,downstream_gene_variant,,ENST00000590160,;ZNF223,intron_variant,,ENST00000591793,;	G	ENSG00000159885	ENST00000391960	Transcript	synonymous_variant	808	771	257	K	aaA/aaG	.	.	.	1	ZNF222	HGNC	13015	protein_coding	YES	CCDS46098.1	ENSP00000375822	ZN222_HUMAN	Q02387_HUMAN	UPI000014182E	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF163,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAAAGTTCA	.	5	ESCA
ZNF233	0	.	GRCh37	19	44777239	44777239	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426G>A	p.%3D	p.Q142Q	ENST00000391958	5/5	34	20	13	25	25	0	ZNF233,synonymous_variant,p.%3D,ENST00000391958,;ZNF233,synonymous_variant,p.%3D,ENST00000590668,;ZNF233,3_prime_UTR_variant,,ENST00000592581,;ZNF233,intron_variant,,ENST00000334152,;ZNF235,intron_variant,,ENST00000589799,;ZNF233,downstream_gene_variant,,ENST00000589522,;ZNF235,downstream_gene_variant,,ENST00000589248,;ZNF235,intron_variant,,ENST00000592844,;	A	ENSG00000159915	ENST00000391958	Transcript	synonymous_variant	553	426	142	Q	caG/caA	.	.	.	1	ZNF233	HGNC	30946	protein_coding	YES	CCDS33047.1	ENSP00000375820	ZN233_HUMAN	K7EN46_HUMAN	UPI000049DEBE	.	.	.	5/5	.	hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCAGGTGTG	.	5	ESCA
ZNF549	0	.	GRCh37	19	58046597	58046597	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.158A>T	p.His53Leu	p.H53L	ENST00000376233	3/4	74	41	32	78	78	0	ZNF549,missense_variant,p.His53Leu,ENST00000376233,;ZNF549,missense_variant,p.His40Leu,ENST00000240719,;ZNF549,missense_variant,p.His53Leu,ENST00000602149,;ZNF549,intron_variant,,ENST00000594943,;ZNF550,downstream_gene_variant,,ENST00000601415,;	T	ENSG00000121406	ENST00000376233	Transcript	missense_variant	339	158	53	H/L	cAt/cTt	.	.	.	1	ZNF549	HGNC	26632	protein_coding	YES	CCDS56106.1	ENSP00000365407	ZN549_HUMAN	.	UPI0000202D31	.	tolerated(0.75)	benign(0.066)	3/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF30,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATCATGATG	.	5	ESCA
ZNF587	0	.	GRCh37	19	58374323	58374323	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2815G>C	.	.	ENST00000339656	3/3	62	41	20	77	77	0	ZNF587,3_prime_UTR_variant,,ENST00000419854,;ZNF587,3_prime_UTR_variant,,ENST00000339656,;ZNF814,intron_variant,,ENST00000597342,;ZNF814,intron_variant,,ENST00000595295,;ZNF814,intron_variant,,ENST00000596604,;ZNF814,intron_variant,,ENST00000597832,;CTD-2583A14.10,downstream_gene_variant,,ENST00000598031,;ZNF814,downstream_gene_variant,,ENST00000595048,;ZNF587,downstream_gene_variant,,ENST00000423137,;CTD-2583A14.10,downstream_gene_variant,,ENST00000597134,;ZNF814,downstream_gene_variant,,ENST00000600634,;ZNF587B,downstream_gene_variant,,ENST00000316462,;CTD-2583A14.10,downstream_gene_variant,,ENST00000593873,;CTD-2583A14.10,downstream_gene_variant,,ENST00000596498,;CTD-2583A14.10,downstream_gene_variant,,ENST00000603271,;CTD-2583A14.8,downstream_gene_variant,,ENST00000597780,;ZNF587,downstream_gene_variant,,ENST00000596433,;CTD-2583A14.11,upstream_gene_variant,,ENST00000604665,;ZNF814,intron_variant,,ENST00000595894,;CTD-2583A14.10,downstream_gene_variant,,ENST00000604231,;ZNF814,downstream_gene_variant,,ENST00000597348,;ZNF814,upstream_gene_variant,,ENST00000596184,;	C	ENSG00000198466	ENST00000339656	Transcript	3_prime_UTR_variant	4725	.	.	.	.	.	.	.	1	ZNF587	HGNC	30955	protein_coding	YES	CCDS12964.1	ENSP00000345479	ZN587_HUMAN	M0R2A6_HUMAN,M0R178_HUMAN,M0R0V5_HUMAN,M0R0M6_HUMAN,M0QXF5_HUMAN,E7EP41_HUMAN	UPI0000073916	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTGGACACT	.	5	ESCA
INSR	0	.	GRCh37	19	7152788	7152788	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2180C>T	p.Ser727Leu	p.S727L	ENST00000302850	10/22	48	29	18	19	19	0	INSR,missense_variant,p.Ser727Leu,ENST00000302850,;INSR,missense_variant,p.Ser727Leu,ENST00000341500,;INSR,non_coding_transcript_exon_variant,,ENST00000598216,;	A	ENSG00000171105	ENST00000302850	Transcript	missense_variant	2323	2180	727	S/L	tCg/tTg	.	.	.	-1	INSR	HGNC	6091	protein_coding	YES	CCDS12176.1	ENSP00000303830	INSR_HUMAN	Q4U0V1_HUMAN,Q2PJC5_HUMAN,Q2PJC4_HUMAN,Q2PJC3_HUMAN,Q2PJC1_HUMAN,Q2MKP2_HUMAN,B4DTR7_HUMAN,A4ZPI8_HUMAN,A4ZPI7_HUMAN,A4ZPI5_HUMAN,A4ZPI3_HUMAN	UPI000020324D	.	tolerated(0.07)	benign(0.11)	10/22	.	hmmpanther:PTHR24416:SF140,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000620,SMART_domains:SM00060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAACGAGGAC	.	5	ESCA
RP11-458D21.5	0	.	GRCh37	1	145209276	145209276	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-205A>T	.	.	ENST00000468030	1/23	146	107	38	143	143	0	NOTCH2NL,5_prime_UTR_variant,,ENST00000362074,;NOTCH2NL,5_prime_UTR_variant,,ENST00000344859,;RP11-458D21.5,5_prime_UTR_variant,,ENST00000468030,;	T	ENSG00000255168	ENST00000468030	Transcript	5_prime_UTR_variant	132	.	.	.	.	.	.	.	1	RP11-458D21.5	Clone_based_vega_gene	.	nonsense_mediated_decay	YES	.	ENSP00000457682	.	E9PLD5_HUMAN	UPI0001F78571	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGAGAGTG	.	5	ESCA
POGZ	0	.	GRCh37	1	151400365	151400365	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1012delG	p.Val338TrpfsTer21	p.V338Wfs*21	ENST00000271715	7/19	45	26	19	36	36	0	POGZ,frameshift_variant,p.Val338TrpfsTer21,ENST00000271715,;POGZ,frameshift_variant,p.Val285TrpfsTer21,ENST00000392723,;POGZ,frameshift_variant,p.Val329TrpfsTer21,ENST00000409503,;POGZ,frameshift_variant,p.Val285TrpfsTer21,ENST00000361398,;POGZ,frameshift_variant,p.Val276TrpfsTer21,ENST00000531094,;POGZ,frameshift_variant,p.Val84TrpfsTer21,ENST00000594456,;POGZ,frameshift_variant,p.Val243TrpfsTer21,ENST00000368863,;POGZ,frameshift_variant,p.Val285TrpfsTer21,ENST00000491586,;POGZ,intron_variant,,ENST00000540984,;POGZ,downstream_gene_variant,,ENST00000533461,;POGZ,upstream_gene_variant,,ENST00000529669,;POGZ,downstream_gene_variant,,ENST00000533351,;POGZ,downstream_gene_variant,,ENST00000450842,;POGZ,frameshift_variant,p.Val32TrpfsTer21,ENST00000441516,;POGZ,non_coding_transcript_exon_variant,,ENST00000485040,;POGZ,non_coding_transcript_exon_variant,,ENST00000358476,;POGZ,upstream_gene_variant,,ENST00000482678,;POGZ,upstream_gene_variant,,ENST00000495253,;POGZ,downstream_gene_variant,,ENST00000467287,;	-	ENSG00000143442	ENST00000271715	Transcript	frameshift_variant	1327	1012	338	V/X	Gtg/tg	.	.	.	-1	POGZ	HGNC	18801	protein_coding	YES	CCDS997.1	ENSP00000271715	POGZ_HUMAN	F5H8H4_HUMAN,E9PJY9_HUMAN,E9PIR8_HUMAN	UPI000035895F	.	.	.	7/19	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACACCACCACTG	.	3	ESCA
FLG	0	.	GRCh37	1	152275131	152275131	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45C>A	.	.	ENST00000368799	3/3	34	21	12	30	30	0	FLG,3_prime_UTR_variant,,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	T	ENSG00000143631	ENST00000368799	Transcript	3_prime_UTR_variant	12267	.	.	.	.	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTTGCTTCA	.	5	ESCA
FLG	0	.	GRCh37	1	152284593	152284593	+	Silent	SNP	A	A	G	rs757865005	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2769T>C	p.%3D	p.S923S	ENST00000368799	3/3	198	146	52	179	179	0	FLG,synonymous_variant,p.%3D,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	G	ENSG00000143631	ENST00000368799	Transcript	synonymous_variant	2805	2769	923	S	tcT/tcC	rs757865005	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	.	3/3	.	hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF21,Pfam_domain:PF03516	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTAGAGAT	.	5	ESCA
OLFML2B	0	.	GRCh37	1	161953792	161953792	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1926C>G	p.Ser642Arg	p.S642R	ENST00000294794	8/8	47	36	10	47	47	0	OLFML2B,missense_variant,p.Ser643Arg,ENST00000367940,;OLFML2B,missense_variant,p.Ser642Arg,ENST00000294794,;OLFML2B,missense_variant,p.Ser125Arg,ENST00000367938,;OLFML2B,upstream_gene_variant,,ENST00000525589,;OLFML2B,upstream_gene_variant,,ENST00000533556,;	C	ENSG00000162745	ENST00000294794	Transcript	missense_variant	2350	1926	642	S/R	agC/agG	.	.	.	-1	OLFML2B	HGNC	24558	protein_coding	YES	CCDS1236.1	ENSP00000294794	OLM2B_HUMAN	H0YEW8_HUMAN,H0YE85_HUMAN	UPI00001D7DE0	.	tolerated(0.38)	possibly_damaging(0.719)	8/8	.	PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37,Pfam_domain:PF02191,SMART_domains:SM00284	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGGCTGAA	.	5	ESCA
GPR161	0	.	GRCh37	1	168066418	168066418	+	Missense_Mutation	SNP	G	G	A	rs768889642	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.487C>T	p.Arg163Trp	p.R163W	ENST00000537209	4/7	46	37	9	39	39	0	GPR161,missense_variant,p.Arg143Trp,ENST00000367835,;GPR161,missense_variant,p.Arg143Trp,ENST00000271357,;GPR161,missense_variant,p.Arg65Trp,ENST00000539777,;GPR161,missense_variant,p.Arg29Trp,ENST00000546300,;GPR161,missense_variant,p.Arg11Trp,ENST00000367836,;GPR161,missense_variant,p.Arg143Trp,ENST00000361697,;GPR161,missense_variant,p.Arg143Trp,ENST00000367838,;GPR161,missense_variant,p.Arg163Trp,ENST00000537209,;GPR161,non_coding_transcript_exon_variant,,ENST00000493800,;	A	ENSG00000143147	ENST00000537209	Transcript	missense_variant	736	487	163	R/W	Cgg/Tgg	rs768889642	.	.	-1	GPR161	HGNC	23694	protein_coding	YES	CCDS58043.1	ENSP00000441039	GP161_HUMAN	.	UPI0002065201	.	deleterious(0)	probably_damaging(1)	4/7	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF246,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCGGTTCC	byFrequency	5	ESCA
PAPPA2	0	.	GRCh37	1	176734869	176734869	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4219G>C	p.Val1407Leu	p.V1407L	ENST00000367662	15/23	62	45	17	57	57	0	PAPPA2,missense_variant,p.Val1407Leu,ENST00000367662,;	C	ENSG00000116183	ENST00000367662	Transcript	missense_variant	5383	4219	1407	V/L	Gtg/Ctg	.	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	tolerated(0.53)	benign(0.002)	15/23	.	hmmpanther:PTHR19325:SF349,hmmpanther:PTHR19325,SMART_domains:SM00032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGGTGAAC	.	5	ESCA
CAMSAP2	0	.	GRCh37	1	200827408	200827408	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*221C>T	.	.	ENST00000358823	17/17	18	12	6	28	28	0	CAMSAP2,3_prime_UTR_variant,,ENST00000358823,;CAMSAP2,3_prime_UTR_variant,,ENST00000236925,;CAMSAP2,downstream_gene_variant,,ENST00000413307,;CAMSAP2,downstream_gene_variant,,ENST00000475326,;CAMSAP2,downstream_gene_variant,,ENST00000447701,;	T	ENSG00000118200	ENST00000358823	Transcript	3_prime_UTR_variant	4928	.	.	.	.	.	.	.	1	CAMSAP2	HGNC	29188	protein_coding	YES	CCDS1404.1	ENSP00000351684	CAMP2_HUMAN	.	UPI000020470D	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATTCACAAA	.	5	ESCA
YOD1	0	.	GRCh37	1	207218511	207218511	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3854A>G	.	.	ENST00000315927	2/2	25	21	4	21	21	0	YOD1,3_prime_UTR_variant,,ENST00000315927,;YOD1,3_prime_UTR_variant,,ENST00000367084,;YOD1,3_prime_UTR_variant,,ENST00000391927,;PFKFB2,upstream_gene_variant,,ENST00000411990,;	C	ENSG00000180667	ENST00000315927	Transcript	3_prime_UTR_variant	4948	.	.	.	.	.	.	.	-1	YOD1	HGNC	25035	protein_coding	YES	CCDS31002.1	ENSP00000326813	OTU1_HUMAN	.	UPI0000458A05	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	TTCCTTATAAG	.	3	ESCA
KMO	0	.	GRCh37	1	241755423	241755423	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1429C>G	p.Leu477Val	p.L477V	ENST00000366559	15/15	45	28	17	25	25	0	KMO,missense_variant,p.Leu464Val,ENST00000366558,;KMO,missense_variant,p.Leu477Val,ENST00000366559,;KMO,missense_variant,p.Leu443Val,ENST00000366557,;KMO,missense_variant,p.Leu163Val,ENST00000366555,;OPN3,downstream_gene_variant,,ENST00000331838,;OPN3,downstream_gene_variant,,ENST00000366554,;OPN3,splice_acceptor_variant,,ENST00000462265,;OPN3,downstream_gene_variant,,ENST00000469376,;OPN3,downstream_gene_variant,,ENST00000478849,;OPN3,downstream_gene_variant,,ENST00000490673,;OPN3,downstream_gene_variant,,ENST00000463155,;	G	ENSG00000117009	ENST00000366559	Transcript	missense_variant	1740	1429	477	L/V	Cta/Gta	.	.	.	1	KMO	HGNC	6381	protein_coding	YES	CCDS1618.1	ENSP00000355517	KMO_HUMAN	.	UPI000045632A	.	deleterious_low_confidence(0.04)	benign(0.018)	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCCCTAGAA	.	5	ESCA
KMO	0	.	GRCh37	1	241755538	241755538	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*83G>A	.	.	ENST00000366559	15/15	17	12	4	13	13	0	KMO,3_prime_UTR_variant,,ENST00000366558,;KMO,3_prime_UTR_variant,,ENST00000366559,;KMO,3_prime_UTR_variant,,ENST00000366557,;KMO,intron_variant,,ENST00000366555,;OPN3,downstream_gene_variant,,ENST00000331838,;OPN3,downstream_gene_variant,,ENST00000366554,;OPN3,intron_variant,,ENST00000462265,;OPN3,downstream_gene_variant,,ENST00000469376,;OPN3,downstream_gene_variant,,ENST00000478849,;OPN3,downstream_gene_variant,,ENST00000490673,;OPN3,downstream_gene_variant,,ENST00000463155,;	A	ENSG00000117009	ENST00000366559	Transcript	3_prime_UTR_variant	1855	.	.	.	.	.	.	.	1	KMO	HGNC	6381	protein_coding	YES	CCDS1618.1	ENSP00000355517	KMO_HUMAN	.	UPI000045632A	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTGATTCA	.	5	ESCA
OR2M7	0	.	GRCh37	1	248487277	248487277	+	Silent	SNP	A	A	G	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594T>C	p.%3D	p.V198V	ENST00000317965	1/1	127	90	37	133	133	0	OR2M7,synonymous_variant,p.%3D,ENST00000317965,;	G	ENSG00000177186	ENST00000317965	Transcript	synonymous_variant	623	594	198	V	gtT/gtC	COSM907274	.	.	-1	OR2M7	HGNC	19594	protein_coding	YES	CCDS31111.1	ENSP00000324557	OR2M7_HUMAN	.	UPI000004B236	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF233,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATAACCTC	.	5	ESCA
ZSCAN20	0	.	GRCh37	1	33945122	33945122	+	Missense_Mutation	SNP	G	G	A	rs375588396	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.233G>A	p.Arg78His	p.R78H	ENST00000361328	2/8	17	9	8	16	16	0	ZSCAN20,missense_variant,p.Arg78His,ENST00000373413,;ZSCAN20,missense_variant,p.Arg78His,ENST00000361328,;ZSCAN20,non_coding_transcript_exon_variant,,ENST00000480917,;	A	ENSG00000121903	ENST00000361328	Transcript	missense_variant	386	233	78	R/H	cGt/cAt	rs375588396	.	.	1	ZSCAN20	HGNC	13093	protein_coding	YES	CCDS41300.1	ENSP00000355053	ZSC20_HUMAN	.	UPI0000D61EC5	.	tolerated(0.22)	benign(0.005)	2/8	.	PROSITE_profiles:PS50804,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCGTTGGC	byFrequency|byCluster	5	ESCA
NASP	0	.	GRCh37	1	46083885	46083885	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*72C>G	.	.	ENST00000350030	15/15	35	23	12	47	47	0	NASP,3_prime_UTR_variant,,ENST00000402363,;NASP,3_prime_UTR_variant,,ENST00000350030,;NASP,3_prime_UTR_variant,,ENST00000534450,;NASP,3_prime_UTR_variant,,ENST00000537798,;NASP,3_prime_UTR_variant,,ENST00000351223,;NASP,3_prime_UTR_variant,,ENST00000531612,;NASP,3_prime_UTR_variant,,ENST00000372052,;CCDC17,downstream_gene_variant,,ENST00000445048,;NASP,downstream_gene_variant,,ENST00000528238,;CCDC17,downstream_gene_variant,,ENST00000528266,;CCDC17,downstream_gene_variant,,ENST00000343901,;CCDC17,downstream_gene_variant,,ENST00000421127,;NASP,downstream_gene_variant,,ENST00000525515,;NASP,downstream_gene_variant,,ENST00000437901,;NASP,non_coding_transcript_exon_variant,,ENST00000530073,;CCDC17,downstream_gene_variant,,ENST00000464739,;NASP,non_coding_transcript_exon_variant,,ENST00000481782,;NASP,non_coding_transcript_exon_variant,,ENST00000472408,;CCDC17,downstream_gene_variant,,ENST00000525599,;NASP,downstream_gene_variant,,ENST00000437362,;NASP,downstream_gene_variant,,ENST00000527359,;NASP,downstream_gene_variant,,ENST00000527932,;CCDC17,downstream_gene_variant,,ENST00000372044,;CCDC17,downstream_gene_variant,,ENST00000479529,;NASP,downstream_gene_variant,,ENST00000453748,;CCDC17,downstream_gene_variant,,ENST00000482416,;CCDC17,downstream_gene_variant,,ENST00000491755,;	G	ENSG00000132780	ENST00000350030	Transcript	3_prime_UTR_variant	2526	.	.	.	.	.	.	.	1	NASP	HGNC	7644	protein_coding	YES	CCDS524.1	ENSP00000255120	NASP_HUMAN	Q9P1N1_HUMAN,B4DS57_HUMAN	UPI000012FDA0	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATTCTTTTT	.	5	ESCA
LRRC40	0	.	GRCh37	1	70671212	70671212	+	Silent	SNP	C	C	T	rs761124498	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12G>A	p.%3D	p.L4L	ENST00000370952	1/15	15	9	6	23	23	0	LRRC40,synonymous_variant,p.%3D,ENST00000370952,;SRSF11,upstream_gene_variant,,ENST00000454435,;SRSF11,upstream_gene_variant,,ENST00000405432,;SRSF11,upstream_gene_variant,,ENST00000370951,;SRSF11,upstream_gene_variant,,ENST00000370950,;SRSF11,upstream_gene_variant,,ENST00000463877,;	T	ENSG00000066557	ENST00000370952	Transcript	synonymous_variant	92	12	4	L	ctG/ctA	rs761124498	.	.	-1	LRRC40	HGNC	26004	protein_coding	YES	CCDS646.1	ENSP00000359990	LRC40_HUMAN	.	UPI000004A0A0	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CGCTTCAGGCG	.	4	ESCA
COL24A1	0	.	GRCh37	1	86289379	86289379	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3724C>G	p.Gln1242Glu	p.Q1242E	ENST00000370571	44/60	25	19	6	48	48	0	COL24A1,missense_variant,p.Gln1242Glu,ENST00000436319,;COL24A1,missense_variant,p.Gln1242Glu,ENST00000370571,;COL24A1,3_prime_UTR_variant,,ENST00000426639,;	C	ENSG00000171502	ENST00000370571	Transcript	missense_variant	4091	3724	1242	Q/E	Caa/Gaa	.	.	.	-1	COL24A1	HGNC	20821	protein_coding	YES	CCDS41353.1	ENSP00000359603	COOA1_HUMAN	E9PNK8_HUMAN	UPI000013E81F	.	tolerated(0.12)	probably_damaging(0.998)	44/60	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF360,Pfam_domain:PF01391,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTGTTGTC	.	5	ESCA
GBP1P1	0	.	GRCh37	1	89890100	89890100	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1626+90A>G	.	.	ENST00000394662	.	30	20	10	36	36	0	GBP1P1,non_coding_transcript_exon_variant,,ENST00000513638,;GBP1P1,intron_variant,,ENST00000394662,;	G	ENSG00000225492	ENST00000394662	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GBP1P1	HGNC	39561	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATGAAGCCC	.	5	ESCA
AGRN	0	.	GRCh37	1	982784	982784	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3466G>T	p.Asp1156Tyr	p.D1156Y	ENST00000379370	20/36	20	13	7	19	19	0	AGRN,missense_variant,p.Asp1156Tyr,ENST00000379370,;AGRN,upstream_gene_variant,,ENST00000419249,;AGRN,non_coding_transcript_exon_variant,,ENST00000466223,;AGRN,upstream_gene_variant,,ENST00000478677,;AGRN,downstream_gene_variant,,ENST00000479707,;AGRN,upstream_gene_variant,,ENST00000461111,;AGRN,upstream_gene_variant,,ENST00000492947,;	T	ENSG00000188157	ENST00000379370	Transcript	missense_variant	3516	3466	1156	D/Y	Gac/Tac	.	.	.	1	AGRN	HGNC	329	protein_coding	YES	CCDS30551.1	ENSP00000368678	AGRIN_HUMAN	Q5XG79_HUMAN	UPI00001D7C8B	.	deleterious(0)	probably_damaging(1)	20/36	.	Superfamily_domains:0047452,SMART_domains:SM00200,Pfam_domain:PF01390,Gene3D:1ivzA00,hmmpanther:PTHR10574:SF227,hmmpanther:PTHR10574,PROSITE_profiles:PS50024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTGACCCC	.	5	ESCA
C20orf194	0	.	GRCh37	20	3240608	3240608	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2940C>T	p.%3D	p.G980G	ENST00000252032	32/37	53	43	10	38	38	0	C20orf194,synonymous_variant,p.%3D,ENST00000252032,;C20orf194,3_prime_UTR_variant,,ENST00000453730,;	A	ENSG00000088854	ENST00000252032	Transcript	synonymous_variant	3008	2940	980	G	ggC/ggT	.	.	.	-1	C20orf194	HGNC	17721	protein_coding	YES	CCDS42851.1	ENSP00000252032	CT194_HUMAN	Q3KQR5_HUMAN	UPI0000470A8D	.	.	.	32/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACGGCCAAA	.	5	ESCA
RPRD1B	0	.	GRCh37	20	36718325	36718325	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*48G>C	.	.	ENST00000373433	7/7	19	10	9	23	23	0	RPRD1B,3_prime_UTR_variant,,ENST00000373433,;RPRD1B,downstream_gene_variant,,ENST00000449186,;RPRD1B,non_coding_transcript_exon_variant,,ENST00000471511,;RPRD1B,non_coding_transcript_exon_variant,,ENST00000484683,;RPRD1B,3_prime_UTR_variant,,ENST00000462548,;	C	ENSG00000101413	ENST00000373433	Transcript	3_prime_UTR_variant	1431	.	.	.	.	.	.	.	1	RPRD1B	HGNC	16209	protein_coding	YES	CCDS13301.1	ENSP00000362532	RPR1B_HUMAN	.	UPI00001285EB	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAGGGCAA	.	5	ESCA
SLC12A5	0	.	GRCh37	20	44686391	44686391	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000454036	.	27	15	11	13	13	0	SLC12A5,3_prime_UTR_variant,,ENST00000243964,;NCOA5,downstream_gene_variant,,ENST00000290231,;SLC12A5,downstream_gene_variant,,ENST00000454036,;	T	ENSG00000124140	ENST00000454036	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	50	1	SLC12A5	HGNC	13818	protein_coding	YES	CCDS46610.1	ENSP00000387694	S12A5_HUMAN	B7Z3I0_HUMAN	UPI00015F4605	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCACGCCTG	.	5	ESCA
PTPN1	0	.	GRCh37	20	49195772	49195772	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.770G>A	p.Arg257Gln	p.R257Q	ENST00000371621	7/10	65	32	32	46	46	0	PTPN1,missense_variant,p.Arg257Gln,ENST00000371621,;PTPN1,missense_variant,p.Arg184Gln,ENST00000541713,;RP4-530I15.9,upstream_gene_variant,,ENST00000431019,;	A	ENSG00000196396	ENST00000371621	Transcript	missense_variant	944	770	257	R/Q	cGg/cAg	.	.	.	1	PTPN1	HGNC	9642	protein_coding	YES	CCDS13430.1	ENSP00000360683	PTN1_HUMAN	B4DSN5_HUMAN,A8K3M3_HUMAN	UPI000011DD79	.	deleterious(0.02)	probably_damaging(1)	7/10	.	PROSITE_profiles:PS50056,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF239,Pfam_domain:PF00102,Gene3D:3.90.190.10,PIRSF_domain:PIRSF000926,SMART_domains:SM00404,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTCGGATGG	.	5	ESCA
TUBB1	0	.	GRCh37	20	57599009	57599009	+	Missense_Mutation	SNP	C	C	T	rs369101405	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.527C>T	p.Ser176Leu	p.S176L	ENST00000217133	4/4	44	40	3	44	44	0	TUBB1,missense_variant,p.Ser176Leu,ENST00000217133,;ATP5E,downstream_gene_variant,,ENST00000395663,;ATP5E,downstream_gene_variant,,ENST00000395659,;ATP5E,downstream_gene_variant,,ENST00000243997,;	T	ENSG00000101162	ENST00000217133	Transcript	missense_variant	796	527	176	S/L	tCg/tTg	rs369101405	.	.	1	TUBB1	HGNC	16257	protein_coding	YES	CCDS13475.1	ENSP00000217133	TBB1_HUMAN	.	UPI0000071B14	.	deleterious_low_confidence(0.01)	probably_damaging(0.996)	4/4	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF74,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGTGTCGGACA	byFrequency|byCluster	2	ESCA
TPTE	0	.	GRCh37	21	10906971	10906971	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1590T>G	p.Asp530Glu	p.D530E	ENST00000361285	24/24	181	153	28	247	247	0	TPTE,missense_variant,p.Asp530Glu,ENST00000361285,;TPTE,missense_variant,p.Asp492Glu,ENST00000342420,;TPTE,missense_variant,p.Asp512Glu,ENST00000298232,;TPTE,non_coding_transcript_exon_variant,,ENST00000415664,;TPTE,non_coding_transcript_exon_variant,,ENST00000447568,;	C	ENSG00000166157	ENST00000361285	Transcript	missense_variant	1920	1590	530	D/E	gaT/gaG	.	.	.	-1	TPTE	HGNC	12023	protein_coding	YES	CCDS13560.2	ENSP00000355208	TPTE_HUMAN	.	UPI000016A18A	.	tolerated(1)	benign(0.004)	24/24	.	PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Pfam_domain:PF10409,Gene3D:1d5rA02,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAAAATCTGA	.	4	ESCA
LTN1	0	.	GRCh37	21	30342970	30342971	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1216dupT	p.Tyr406LeufsTer40	p.Y406Lfs*40	ENST00000389194	8/30	62	38	24	54	54	0	LTN1,frameshift_variant,p.Tyr360LeufsTer40,ENST00000361371,;LTN1,frameshift_variant,p.Tyr406LeufsTer40,ENST00000389195,;LTN1,frameshift_variant,p.Tyr406LeufsTer40,ENST00000389194,;LTN1,frameshift_variant,p.Tyr289LeufsTer40,ENST00000483326,;	A	ENSG00000198862	ENST00000389194	Transcript	frameshift_variant	1222-1223	1216-1217	406	Y/LX	tat/tTat	.	.	.	-1	LTN1	HGNC	13082	protein_coding	YES	CCDS33527.2	ENSP00000373846	LTN1_HUMAN	G1UI34_HUMAN	UPI000049DF6C	.	.	.	8/30	.	Superfamily_domains:SSF48371,hmmpanther:PTHR12389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGGATATATG	.	3	ESCA
GART	0	.	GRCh37	21	34901225	34901225	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.742C>G	p.Leu248Val	p.L248V	ENST00000381831	8/22	49	26	23	61	61	0	GART,missense_variant,p.Leu248Val,ENST00000381831,;GART,missense_variant,p.Leu248Val,ENST00000381815,;GART,missense_variant,p.Leu248Val,ENST00000381839,;GART,missense_variant,p.Leu248Val,ENST00000361093,;GART,downstream_gene_variant,,ENST00000430874,;GART,downstream_gene_variant,,ENST00000426819,;GART,downstream_gene_variant,,ENST00000497313,;GART,upstream_gene_variant,,ENST00000460305,;GART,missense_variant,p.Leu248Val,ENST00000424203,;GART,3_prime_UTR_variant,,ENST00000366093,;GART,non_coding_transcript_exon_variant,,ENST00000466882,;GART,downstream_gene_variant,,ENST00000488791,;GART,downstream_gene_variant,,ENST00000476524,;GART,upstream_gene_variant,,ENST00000467575,;	C	ENSG00000159131	ENST00000381831	Transcript	missense_variant	1006	742	248	L/V	Cta/Gta	.	.	.	-1	GART	HGNC	4163	protein_coding	YES	CCDS13627.1	ENSP00000371253	PUR2_HUMAN	Q71VH3_HUMAN,C9JZG2_HUMAN,C9JTV6_HUMAN,C9JKQ7_HUMAN,C9JBJ1_HUMAN,B4DJ93_HUMAN	UPI0000132A2A	.	tolerated(0.19)	benign(0.001)	8/22	.	PROSITE_profiles:PS50975,HAMAP:MF_00138,hmmpanther:PTHR10520,hmmpanther:PTHR10520:SF10,TIGRFAM_domain:TIGR00877,Pfam_domain:PF01071,Gene3D:3.30.470.20,Superfamily_domains:SSF56059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTAGTAATA	.	5	ESCA
DSCAM	0	.	GRCh37	21	41496159	41496159	+	Missense_Mutation	SNP	C	C	T	rs755579756	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000400454	20/33	42	18	24	43	43	0	DSCAM,missense_variant,p.Arg972Gln,ENST00000404019,;DSCAM,missense_variant,p.Arg1220Gln,ENST00000400454,;	T	ENSG00000171587	ENST00000400454	Transcript	missense_variant	4137	3659	1220	R/Q	cGa/cAa	rs755579756	.	.	-1	DSCAM	HGNC	3039	protein_coding	YES	CCDS42929.1	ENSP00000383303	DSCAM_HUMAN	.	UPI00000422DF	.	deleterious(0.04)	probably_damaging(0.941)	20/33	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTTCGGATG	.	5	ESCA
CLTCL1	0	.	GRCh37	22	19207487	19207487	+	Silent	SNP	G	G	A	rs199728866	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2826C>T	p.%3D	p.S942S	ENST00000263200	18/33	92	37	55	56	56	0	CLTCL1,synonymous_variant,p.%3D,ENST00000427926,;CLTCL1,synonymous_variant,p.%3D,ENST00000263200,;CLTCL1,synonymous_variant,p.%3D,ENST00000353891,;CLTCL1,synonymous_variant,p.%3D,ENST00000505027,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000413132,;CLTCL1,downstream_gene_variant,,ENST00000458188,;	A	ENSG00000070371	ENST00000263200	Transcript	synonymous_variant	2899	2826	942	S	agC/agT	rs199728866	.	.	-1	CLTCL1	HGNC	2093	protein_coding	YES	CCDS46662.1	ENSP00000445677	CLH2_HUMAN	.	UPI0000127ABE	.	.	.	18/33	.	PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Pfam_domain:PF00637,SMART_domains:SM00299,PIRSF_domain:PIRSF002290,Superfamily_domains:SSF48371	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCGCTTTT	byCluster|by1000G	5	ESCA
CLTCL1	0	.	GRCh37	22	19209533	19209533	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2502G>C	p.Met834Ile	p.M834I	ENST00000263200	16/33	67	58	9	38	38	0	CLTCL1,missense_variant,p.Met834Ile,ENST00000427926,;CLTCL1,missense_variant,p.Met834Ile,ENST00000263200,;CLTCL1,missense_variant,p.Met834Ile,ENST00000353891,;CLTCL1,missense_variant,p.Met834Ile,ENST00000505027,;CLTCL1,3_prime_UTR_variant,,ENST00000458188,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000413132,;	G	ENSG00000070371	ENST00000263200	Transcript	missense_variant	2575	2502	834	M/I	atG/atC	.	.	.	-1	CLTCL1	HGNC	2093	protein_coding	YES	CCDS46662.1	ENSP00000445677	CLH2_HUMAN	.	UPI0000127ABE	.	tolerated(0.39)	benign(0.003)	16/33	.	PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Gene3D:1.25.40.10,SMART_domains:SM00299,PIRSF_domain:PIRSF002290,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGCCATGAT	.	4	ESCA
GUCD1	0	.	GRCh37	22	24944925	24944925	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88C>T	p.His30Tyr	p.H30Y	ENST00000407471	2/6	51	35	16	25	25	0	GUCD1,missense_variant,p.His86Tyr,ENST00000404664,;GUCD1,missense_variant,p.His30Tyr,ENST00000407973,;GUCD1,missense_variant,p.His30Tyr,ENST00000402766,;GUCD1,missense_variant,p.His30Tyr,ENST00000447813,;GUCD1,missense_variant,p.His30Tyr,ENST00000407471,;GUCD1,missense_variant,p.His30Tyr,ENST00000435822,;GUCD1,non_coding_transcript_exon_variant,,ENST00000490810,;GUCD1,upstream_gene_variant,,ENST00000490922,;GUCD1,upstream_gene_variant,,ENST00000493099,;GUCD1,missense_variant,p.His30Tyr,ENST00000398245,;GUCD1,non_coding_transcript_exon_variant,,ENST00000468170,;GUCD1,upstream_gene_variant,,ENST00000480272,;	A	ENSG00000138867	ENST00000407471	Transcript	missense_variant	279	88	30	H/Y	Cac/Tac	.	.	.	-1	GUCD1	HGNC	14237	protein_coding	YES	CCDS33621.1	ENSP00000386076	GUCD1_HUMAN	B5MCF3_HUMAN	UPI00003FF9EE	.	deleterious(0.01)	probably_damaging(0.915)	2/6	.	Pfam_domain:PF09778,hmmpanther:PTHR31400	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGTGGTAGA	.	5	ESCA
CHST10	0	.	GRCh37	2	101014417	101014417	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380C>A	p.Pro127His	p.P127H	ENST00000264249	5/7	34	23	10	25	25	0	CHST10,missense_variant,p.Pro127His,ENST00000420858,;CHST10,missense_variant,p.Pro127His,ENST00000409046,;CHST10,missense_variant,p.Pro175His,ENST00000542617,;CHST10,missense_variant,p.Pro127His,ENST00000264249,;CHST10,missense_variant,p.Pro127His,ENST00000409701,;CHST10,downstream_gene_variant,,ENST00000418201,;CHST10,downstream_gene_variant,,ENST00000448989,;CHST10,downstream_gene_variant,,ENST00000421474,;CHST10,non_coding_transcript_exon_variant,,ENST00000484382,;	T	ENSG00000115526	ENST00000264249	Transcript	missense_variant	766	380	127	P/H	cCc/cAc	.	.	.	-1	CHST10	HGNC	19650	protein_coding	YES	CCDS2047.1	ENSP00000264249	CHSTA_HUMAN	C9JUE4_HUMAN,C9JI33_HUMAN,C9JCK7_HUMAN,C9J5X0_HUMAN,B8ZZ48_HUMAN	UPI0000073357	.	deleterious(0)	probably_damaging(0.997)	5/7	.	Pfam_domain:PF03567,hmmpanther:PTHR12137,hmmpanther:PTHR12137:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGGGAGTC	.	5	ESCA
ST6GAL2	0	.	GRCh37	2	107450593	107450593	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.953A>G	p.Asp318Gly	p.D318G	ENST00000409382	3/6	37	22	15	22	22	0	ST6GAL2,missense_variant,p.Asp318Gly,ENST00000409087,;ST6GAL2,missense_variant,p.Asp318Gly,ENST00000409382,;ST6GAL2,missense_variant,p.Asp318Gly,ENST00000361686,;ST6GAL2,upstream_gene_variant,,ENST00000361803,;AC016994.2,upstream_gene_variant,,ENST00000425419,;	C	ENSG00000144057	ENST00000409382	Transcript	missense_variant	1564	953	318	D/G	gAt/gGt	.	.	.	-1	ST6GAL2	HGNC	10861	protein_coding	YES	CCDS2073.1	ENSP00000386942	SIAT2_HUMAN	C9JIK2_HUMAN,C4N9P8_HUMAN	UPI000007477B	.	.	possibly_damaging(0.651)	3/6	.	hmmpanther:PTHR13713:SF48,hmmpanther:PTHR13713,Pfam_domain:PF00777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCATCATGA	.	5	ESCA
THSD7B	0	.	GRCh37	2	137872828	137872828	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1334G>A	p.Ser445Asn	p.S445N	ENST00000272643	4/28	33	22	11	37	37	0	THSD7B,missense_variant,p.Ser445Asn,ENST00000409968,;THSD7B,missense_variant,p.Ser414Asn,ENST00000413152,;THSD7B,missense_variant,p.Ser445Asn,ENST00000272643,;THSD7B,intron_variant,,ENST00000543459,;	A	ENSG00000144229	ENST00000272643	Transcript	missense_variant	1334	1334	445	S/N	aGc/aAc	.	.	.	1	THSD7B	HGNC	29348	protein_coding	YES	.	ENSP00000272643	THS7B_HUMAN	.	UPI00015E0A18	.	tolerated(0.43)	benign(0.44)	4/28	.	PROSITE_profiles:PS50092,hmmpanther:PTHR11311:SF7,hmmpanther:PTHR11311	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGAGCGTAC	.	5	ESCA
THSD7B	0	.	GRCh37	2	137872829	137872829	+	Missense_Mutation	SNP	C	C	A	rs768714043	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1335C>A	p.Ser445Arg	p.S445R	ENST00000272643	4/28	33	22	11	36	36	0	THSD7B,missense_variant,p.Ser445Arg,ENST00000409968,;THSD7B,missense_variant,p.Ser414Arg,ENST00000413152,;THSD7B,missense_variant,p.Ser445Arg,ENST00000272643,;THSD7B,intron_variant,,ENST00000543459,;	A	ENSG00000144229	ENST00000272643	Transcript	missense_variant	1335	1335	445	S/R	agC/agA	rs768714043	.	.	1	THSD7B	HGNC	29348	protein_coding	YES	.	ENSP00000272643	THS7B_HUMAN	.	UPI00015E0A18	.	tolerated(0.42)	possibly_damaging(0.83)	4/28	.	PROSITE_profiles:PS50092,hmmpanther:PTHR11311:SF7,hmmpanther:PTHR11311	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGCGTACC	byFrequency	5	ESCA
OLA1	0	.	GRCh37	2	175087808	175087808	+	Missense_Mutation	SNP	G	G	A	rs768339153	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326C>T	p.Ala109Val	p.A109V	ENST00000284719	4/11	25	19	5	24	24	0	OLA1,missense_variant,p.Ala109Val,ENST00000428402,;OLA1,missense_variant,p.Ala109Val,ENST00000284719,;OLA1,missense_variant,p.Ala109Val,ENST00000427472,;OLA1,missense_variant,p.Ala129Val,ENST00000409546,;OLA1,5_prime_UTR_variant,,ENST00000344357,;	A	ENSG00000138430	ENST00000284719	Transcript	missense_variant	573	326	109	A/V	gCt/gTt	rs768339153	.	.	-1	OLA1	HGNC	28833	protein_coding	YES	CCDS2255.1	ENSP00000284719	OLA1_HUMAN	Q53SW9_HUMAN,Q53SQ6_HUMAN,C9JTK6_HUMAN,C9JCJ9_HUMAN	UPI00001328C1	.	deleterious(0.03)	benign(0.354)	4/11	.	PROSITE_profiles:PS51710,HAMAP:MF_00944,hmmpanther:PTHR23305,Pfam_domain:PF01926,TIGRFAM_domain:TIGR00092,Gene3D:3.40.50.300,PIRSF_domain:PIRSF006641,Superfamily_domains:SSF52540,Prints_domain:PR00326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAGCATTC	.	5	ESCA
OLA1	0	.	GRCh37	2	175087809	175087809	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.325G>T	p.Ala109Ser	p.A109S	ENST00000284719	4/11	24	19	4	23	23	0	OLA1,missense_variant,p.Ala109Ser,ENST00000428402,;OLA1,missense_variant,p.Ala109Ser,ENST00000284719,;OLA1,missense_variant,p.Ala109Ser,ENST00000427472,;OLA1,missense_variant,p.Ala129Ser,ENST00000409546,;OLA1,5_prime_UTR_variant,,ENST00000344357,;	A	ENSG00000138430	ENST00000284719	Transcript	missense_variant	572	325	109	A/S	Gct/Tct	.	.	.	-1	OLA1	HGNC	28833	protein_coding	YES	CCDS2255.1	ENSP00000284719	OLA1_HUMAN	Q53SW9_HUMAN,Q53SQ6_HUMAN,C9JTK6_HUMAN,C9JCJ9_HUMAN	UPI00001328C1	.	tolerated(0.07)	benign(0.266)	4/11	.	PROSITE_profiles:PS51710,HAMAP:MF_00944,hmmpanther:PTHR23305,Pfam_domain:PF01926,TIGRFAM_domain:TIGR00092,Gene3D:3.40.50.300,PIRSF_domain:PIRSF006641,Superfamily_domains:SSF52540,Prints_domain:PR00326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGCATTCC	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098960	178098961	+	In_Frame_Ins	INS	-	-	TAT	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.82_84dupATA	p.Ile28dup	p.I28dup	ENST00000397062	2/5	70	48	22	35	35	0	NFE2L2,inframe_insertion,p.Ile12dup,ENST00000449627,;NFE2L2,inframe_insertion,p.Ile12dup,ENST00000423513,;NFE2L2,inframe_insertion,p.Ile28dup,ENST00000397062,;NFE2L2,inframe_insertion,p.Ile12dup,ENST00000446151,;NFE2L2,inframe_insertion,p.Ile12dup,ENST00000588123,;NFE2L2,inframe_insertion,p.Ile27dup,ENST00000586532,;NFE2L2,inframe_insertion,p.Ile12dup,ENST00000421929,;NFE2L2,inframe_insertion,p.Ile12dup,ENST00000464747,;NFE2L2,inframe_insertion,p.Ile12dup,ENST00000448782,;NFE2L2,inframe_insertion,p.Ile12dup,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	TAT	ENSG00000116044	ENST00000397062	Transcript	inframe_insertion	639-640	84-85	28-29	-/I	-/ATA	.	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	.	.	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.D29G|c.86A>G|11,CODON|p.D29H|c.85G>C|12,CODON|p.D29N|c.85G>A|3,CODON|p.D29Y|c.85G>T|4,BUFFER|p.G31E|c.92G>A|5,BUFFER|p.G31A|c.92G>C|7,BUFFER|p.L30R|c.89T>G|7,BUFFER|p.L30F|c.88C>T|6,BUFFER|p.D27G|c.80A>G|3	INDELOCATOR*|VARSCANI*|PINDEL	AAGATCTATAT	.	3	ESCA
COL5A2	0	.	GRCh37	2	189933524	189933524	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245T>A	p.%3D	p.S415S	ENST00000374866	19/54	43	21	21	50	50	0	COL5A2,synonymous_variant,p.%3D,ENST00000374866,;	T	ENSG00000204262	ENST00000374866	Transcript	synonymous_variant	1520	1245	415	S	tcT/tcA	.	.	.	-1	COL5A2	HGNC	2210	protein_coding	YES	CCDS33350.1	ENSP00000364000	CO5A2_HUMAN	D3DPH5_HUMAN	UPI00006C511C	.	.	.	19/54	.	hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF481,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGAGAGCC	.	5	ESCA
MFSD6	0	.	GRCh37	2	191301211	191301211	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.456C>G	p.%3D	p.V152V	ENST00000392328	3/8	33	22	11	19	19	0	MFSD6,synonymous_variant,p.%3D,ENST00000281416,;MFSD6,synonymous_variant,p.%3D,ENST00000392328,;MFSD6,synonymous_variant,p.%3D,ENST00000445546,;MFSD6,upstream_gene_variant,,ENST00000434582,;MFSD6,downstream_gene_variant,,ENST00000417958,;MFSD6,downstream_gene_variant,,ENST00000432036,;	G	ENSG00000151690	ENST00000392328	Transcript	synonymous_variant	780	456	152	V	gtC/gtG	.	.	.	1	MFSD6	HGNC	24711	protein_coding	YES	CCDS2306.1	ENSP00000376141	MFSD6_HUMAN	C9JJH2_HUMAN,C9JAZ7_HUMAN,C9J134_HUMAN,C9IYL1_HUMAN,B7Z810_HUMAN,B7Z7Y2_HUMAN	UPI000022BD91	.	.	.	3/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR16172:SF2,hmmpanther:PTHR16172,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGTCAAACC	.	5	ESCA
PTH2R	0	.	GRCh37	2	209345817	209345817	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1004A>G	p.Asn335Ser	p.N335S	ENST00000272847	10/13	93	79	13	78	78	0	PTH2R,missense_variant,p.Asn335Ser,ENST00000272847,;AC019185.4,intron_variant,,ENST00000424628,;PTH2R,non_coding_transcript_exon_variant,,ENST00000413482,;	G	ENSG00000144407	ENST00000272847	Transcript	missense_variant	1217	1004	335	N/S	aAt/aGt	.	.	.	1	PTH2R	HGNC	9609	protein_coding	YES	CCDS2383.1	ENSP00000272847	PTH2R_HUMAN	Q53T35_HUMAN,Q53SF6_HUMAN,B4DFN8_HUMAN	UPI000005041E	.	deleterious(0.03)	probably_damaging(0.999)	10/13	.	Prints_domain:PR00249,Superfamily_domains:SSF81321,Pfam_domain:PF00002,hmmpanther:PTHR12011:SF69,hmmpanther:PTHR12011,PROSITE_profiles:PS50261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGAATACGG	.	5	ESCA
SPHKAP	0	.	GRCh37	2	228996765	228996765	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69A>G	p.%3D	p.E23E	ENST00000392056	2/12	30	17	12	45	45	0	SPHKAP,synonymous_variant,p.%3D,ENST00000344657,;SPHKAP,synonymous_variant,p.%3D,ENST00000392056,;	C	ENSG00000153820	ENST00000392056	Transcript	synonymous_variant	116	69	23	E	gaA/gaG	.	.	.	-1	SPHKAP	HGNC	30619	protein_coding	YES	CCDS46537.1	ENSP00000375909	SPKAP_HUMAN	.	UPI0000411D7E	.	.	.	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGGTTCCAA	.	5	ESCA
DNER	0	.	GRCh37	2	230312083	230312083	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1435C>T	p.His479Tyr	p.H479Y	ENST00000341772	8/13	42	33	9	30	30	0	DNER,missense_variant,p.His479Tyr,ENST00000341772,;	A	ENSG00000187957	ENST00000341772	Transcript	missense_variant	1570	1435	479	H/Y	Cat/Tat	COSM137377	.	.	-1	DNER	HGNC	24456	protein_coding	YES	CCDS33390.1	ENSP00000345229	DNER_HUMAN	B4E399_HUMAN	UPI0000048EB8	.	deleterious(0)	possibly_damaging(0.753)	8/13	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF58,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCATGAGCAC	.	4	ESCA
HADHA	0	.	GRCh37	2	26435399	26435399	+	Intron	SNP	C	C	T	rs375484761	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.975+40G>A	.	.	ENST00000380649	.	31	21	10	27	27	0	HADHA,missense_variant,p.Gly252Arg,ENST00000457468,;HADHA,intron_variant,,ENST00000380649,;HADHA,non_coding_transcript_exon_variant,,ENST00000471743,;	T	ENSG00000084754	ENST00000380649	Transcript	intron_variant	.	.	.	.	.	rs375484761	.	.	-1	HADHA	HGNC	4801	protein_coding	YES	CCDS1721.1	ENSP00000370023	ECHA_HUMAN	Q9UQC5_HUMAN,E9KL44_HUMAN,B4DDZ5_HUMAN	UPI0000129B6B	.	.	.	.	10/19	.	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCCTTTAA	byFrequency|byCluster	5	ESCA
C2orf16	0	.	GRCh37	2	27799403	27799403	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-37C>T	.	.	ENST00000408964	1/1	11	8	3	9	9	0	C2orf16,5_prime_UTR_variant,,ENST00000408964,;	T	ENSG00000221843	ENST00000408964	Transcript	5_prime_UTR_variant	15	.	.	.	.	.	.	.	1	C2orf16	HGNC	25275	protein_coding	YES	CCDS42666.1	ENSP00000386190	CB016_HUMAN	.	UPI0000D61179	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGCCTTTGC	.	2	ESCA
SPAST	0	.	GRCh37	2	32289128	32289128	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228G>T	p.%3D	p.V76V	ENST00000315285	1/17	51	30	21	47	47	0	SPAST,synonymous_variant,p.%3D,ENST00000315285,;SPAST,synonymous_variant,p.%3D,ENST00000345662,;	T	ENSG00000021574	ENST00000315285	Transcript	synonymous_variant	353	228	76	V	gtG/gtT	.	.	.	1	SPAST	HGNC	11233	protein_coding	YES	CCDS1778.1	ENSP00000320885	SPAST_HUMAN	E5KRP5_HUMAN	UPI0000038A6B	.	.	.	1/17	.	Transmembrane_helices:TMhelix,HAMAP:MF_03021,hmmpanther:PTHR23074:SF66,hmmpanther:PTHR23074,PIRSF_domain:PIRSF037338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGTGTGGCT	.	5	ESCA
BIRC6	0	.	GRCh37	2	32757250	32757250	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12291+632A>G	.	.	ENST00000421745	.	36	26	10	23	23	0	BIRC6,intron_variant,,ENST00000421745,;MIR558,non_coding_transcript_exon_variant,,ENST00000384920,;BIRC6,intron_variant,,ENST00000471232,;	G	ENSG00000115760	ENST00000421745	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	BIRC6	HGNC	13516	protein_coding	YES	CCDS33175.2	ENSP00000393596	BIRC6_HUMAN	.	UPI0001611442	.	.	.	.	61/73	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGTATAGTA	.	5	ESCA
B3GNT2	0	.	GRCh37	2	62449623	62449623	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268A>G	p.Ile90Val	p.I90V	ENST00000301998	2/2	11	8	3	10	10	0	B3GNT2,missense_variant,p.Ile90Val,ENST00000405767,;B3GNT2,missense_variant,p.Ile90Val,ENST00000301998,;	G	ENSG00000170340	ENST00000301998	Transcript	missense_variant	520	268	90	I/V	Ata/Gta	.	.	.	1	B3GNT2	HGNC	15629	protein_coding	YES	CCDS1870.1	ENSP00000305595	B3GN2_HUMAN	.	UPI00000009FB	.	tolerated(0.34)	benign(0)	2/2	.	hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCAATATAAGC	.	3	ESCA
WDR52	0	.	GRCh37	3	113085073	113085073	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2528C>G	p.Thr843Ser	p.T843S	ENST00000393845	19/35	60	52	8	42	42	0	WDR52,missense_variant,p.Thr843Ser,ENST00000393845,;WDR52,missense_variant,p.Thr843Ser,ENST00000295868,;WDR52,upstream_gene_variant,,ENST00000465636,;WDR52,intron_variant,,ENST00000488854,;WDR52,upstream_gene_variant,,ENST00000490481,;RP11-553D4.2,downstream_gene_variant,,ENST00000462549,;	C	ENSG00000206530	ENST00000393845	Transcript	missense_variant	2595	2528	843	T/S	aCc/aGc	.	.	.	-1	WDR52	HGNC	25631	protein_coding	YES	CCDS54624.1	ENSP00000377428	WDR52_HUMAN	C9K0A4_HUMAN	UPI0000367198	.	tolerated(0.55)	benign(0.004)	19/35	.	hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF18,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTGGTCAAT	.	5	ESCA
PLXNA1	0	.	GRCh37	3	126737237	126737237	+	Missense_Mutation	SNP	G	G	A	rs539016754	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3761G>A	p.Gly1254Asp	p.G1254D	ENST00000393409	19/31	83	67	16	49	49	0	PLXNA1,missense_variant,p.Gly1254Asp,ENST00000393409,;PLXNA1,missense_variant,p.Gly1231Asp,ENST00000251772,;	A	ENSG00000114554	ENST00000393409	Transcript	missense_variant	3761	3761	1254	G/D	gGt/gAt	rs539016754	.	.	1	PLXNA1	HGNC	9099	protein_coding	YES	CCDS33847.2	ENSP00000377061	PLXA1_HUMAN	Q9NSM6_HUMAN,F8VSZ4_HUMAN,B4DE20_HUMAN,B3KY38_HUMAN	UPI00001A7983	.	deleterious(0.04)	possibly_damaging(0.821)	19/31	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGGGTCTCC	by1000G	5	ESCA
PODXL2	0	.	GRCh37	3	127390276	127390276	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1426-1G>C	.	p.X476_splice	ENST00000342480	.	70	46	23	44	44	0	PODXL2,splice_acceptor_variant,,ENST00000342480,;ABTB1,upstream_gene_variant,,ENST00000232744,;ABTB1,upstream_gene_variant,,ENST00000393363,;ABTB1,upstream_gene_variant,,ENST00000453791,;ABTB1,upstream_gene_variant,,ENST00000468137,;ABTB1,upstream_gene_variant,,ENST00000466612,;ABTB1,upstream_gene_variant,,ENST00000467179,;ABTB1,upstream_gene_variant,,ENST00000491633,;ABTB1,upstream_gene_variant,,ENST00000479280,;ABTB1,upstream_gene_variant,,ENST00000483857,;ABTB1,upstream_gene_variant,,ENST00000464431,;ABTB1,upstream_gene_variant,,ENST00000475265,;ABTB1,upstream_gene_variant,,ENST00000475042,;ABTB1,upstream_gene_variant,,ENST00000493365,;	C	ENSG00000114631	ENST00000342480	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	PODXL2	HGNC	17936	protein_coding	YES	CCDS3044.1	ENSP00000345359	PDXL2_HUMAN	.	UPI000006FC4B	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTAGATTGG	.	5	ESCA
SEC61A1	0	.	GRCh37	3	127775657	127775657	+	Missense_Mutation	SNP	G	G	T	rs749579516	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326G>T	p.Arg109Leu	p.R109L	ENST00000243253	5/12	112	58	54	81	81	0	SEC61A1,missense_variant,p.Arg56Leu,ENST00000481210,;SEC61A1,missense_variant,p.Arg109Leu,ENST00000243253,;SEC61A1,missense_variant,p.Arg115Leu,ENST00000464451,;SEC61A1,intron_variant,,ENST00000424880,;SEC61A1,downstream_gene_variant,,ENST00000491668,;	T	ENSG00000058262	ENST00000243253	Transcript	missense_variant	510	326	109	R/L	cGa/cTa	rs749579516,COSM1037959	.	.	1	SEC61A1	HGNC	18276	protein_coding	YES	CCDS3046.1	ENSP00000243253	S61A1_HUMAN	B3KNG2_HUMAN,C9JXC6_HUMAN,B3KNF6_HUMAN,B3KME8_HUMAN	UPI00000041A9	.	deleterious(0)	possibly_damaging(0.723)	5/12	.	hmmpanther:PTHR10906,Gene3D:1.10.3370.10,TIGRFAM_domain:TIGR00967,Pfam_domain:PF00344,PIRSF_domain:PIRSF004557,Superfamily_domains:0043235	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCGAGCTC	.	5	ESCA
COL6A5	0	.	GRCh37	3	130134526	130134526	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4799G>A	p.Gly1600Glu	p.G1600E	ENST00000265379	23/42	37	31	6	16	16	0	COL6A5,missense_variant,p.Gly1600Glu,ENST00000432398,;COL6A5,missense_variant,p.Gly1600Glu,ENST00000265379,;COL6A5,missense_variant,p.Gly1600Glu,ENST00000312481,;	A	ENSG00000172752	ENST00000265379	Transcript	missense_variant	5293	4799	1600	G/E	gGa/gAa	.	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	deleterious(0.02)	probably_damaging(0.992)	23/42	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22992:SF93,hmmpanther:PTHR22992,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGGAAGCC	.	5	ESCA
COL6A6	0	.	GRCh37	3	130282064	130282064	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217G>T	p.Asp73Tyr	p.D73Y	ENST00000358511	2/36	70	47	22	46	46	0	COL6A6,missense_variant,p.Asp73Tyr,ENST00000453409,;COL6A6,missense_variant,p.Asp73Tyr,ENST00000358511,;	T	ENSG00000206384	ENST00000358511	Transcript	missense_variant	248	217	73	D/Y	Gat/Tat	.	.	.	1	COL6A6	HGNC	27023	protein_coding	YES	CCDS46911.1	ENSP00000351310	CO6A6_HUMAN	.	UPI00015B6548	.	deleterious(0)	probably_damaging(0.926)	2/36	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF86,hmmpanther:PTHR22992,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGTGATAAA	.	5	ESCA
NEK11	0	.	GRCh37	3	130947497	130947497	+	Missense_Mutation	SNP	G	G	A	rs756935996	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1525G>A	p.Glu509Lys	p.E509K	ENST00000383366	15/18	20	15	5	14	14	0	NEK11,missense_variant,p.Glu509Lys,ENST00000383366,;NEK11,missense_variant,p.Glu404Lys,ENST00000510769,;NEK11,missense_variant,p.Glu509Lys,ENST00000508196,;NEK11,missense_variant,p.Glu325Lys,ENST00000412440,;NEK11,missense_variant,p.Glu509Lys,ENST00000510688,;NEK11,missense_variant,p.Glu509Lys,ENST00000429253,;NEK11,3_prime_UTR_variant,,ENST00000514915,;NEK11,3_prime_UTR_variant,,ENST00000510474,;NEK11,downstream_gene_variant,,ENST00000510823,;	A	ENSG00000114670	ENST00000383366	Transcript	missense_variant	1818	1525	509	E/K	Gag/Aag	rs756935996	.	.	1	NEK11	HGNC	18593	protein_coding	YES	CCDS3069.1	ENSP00000372857	NEK11_HUMAN	.	UPI000013F25D	.	tolerated(0.27)	benign(0.014)	15/18	.	hmmpanther:PTHR24362:SF242,hmmpanther:PTHR24362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATGAGGGA	.	5	ESCA
ANKUB1	0	.	GRCh37	3	149498106	149498106	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.371T>C	p.Val124Ala	p.V124A	ENST00000446160	3/6	90	80	10	36	36	0	ANKUB1,missense_variant,p.Val124Ala,ENST00000462519,;ANKUB1,missense_variant,p.Val124Ala,ENST00000446160,;ANKUB1,missense_variant,p.Val124Ala,ENST00000383050,;RNU6-507P,upstream_gene_variant,,ENST00000516045,;ANKUB1,splice_donor_variant,,ENST00000474224,;ANKUB1,non_coding_transcript_exon_variant,,ENST00000481585,;ANKUB1,non_coding_transcript_exon_variant,,ENST00000462561,;ANKUB1,downstream_gene_variant,,ENST00000497728,;ANKUB1,splice_donor_variant,,ENST00000484019,;ANKUB1,non_coding_transcript_exon_variant,,ENST00000474404,;	G	ENSG00000206199	ENST00000446160	Transcript	missense_variant	828	371	124	V/A	gTg/gCg	.	.	.	-1	ANKUB1	HGNC	29642	protein_coding	YES	.	ENSP00000387907	.	E9PHT4_HUMAN	UPI0000DD7B6F	.	deleterious(0.02)	benign(0.345)	3/6	.	hmmpanther:PTHR10666,hmmpanther:PTHR10666:SF111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACTCACGGGG	.	4	ESCA
SIAH2	0	.	GRCh37	3	150459011	150459011	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*917T>G	.	.	ENST00000312960	2/2	117	90	26	50	50	0	SIAH2,3_prime_UTR_variant,,ENST00000312960,;SIAH2,downstream_gene_variant,,ENST00000482706,;	C	ENSG00000181788	ENST00000312960	Transcript	3_prime_UTR_variant	2420	.	.	.	.	.	.	.	-1	SIAH2	HGNC	10858	protein_coding	YES	CCDS3152.1	ENSP00000322457	SIAH2_HUMAN	C9J9D7_HUMAN	UPI0000071280	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTATAAAGCT	.	5	ESCA
RP11-379F4.4	0	.	GRCh37	3	158460573	158460573	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.279G>T	.	.	ENST00000477589	4/4	78	54	24	41	41	0	MFSD1,intron_variant,,ENST00000486568,;MFSD1,intron_variant,,ENST00000491804,;MFSD1,upstream_gene_variant,,ENST00000465739,;RP11-379F4.4,non_coding_transcript_exon_variant,,ENST00000496842,;RP11-379F4.4,non_coding_transcript_exon_variant,,ENST00000477589,;RP11-379F4.4,intron_variant,,ENST00000465477,;RP11-379F4.4,intron_variant,,ENST00000468242,;RP11-379F4.4,downstream_gene_variant,,ENST00000607426,;	T	ENSG00000240207	ENST00000477589	Transcript	non_coding_transcript_exon_variant	279	.	.	.	.	.	.	.	1	RP11-379F4.4	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGAGCCTGG	.	5	ESCA
KPNA4	0	.	GRCh37	3	160219689	160219689	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*203G>C	.	.	ENST00000334256	17/17	86	76	10	35	35	0	KPNA4,3_prime_UTR_variant,,ENST00000334256,;KPNA4,downstream_gene_variant,,ENST00000483437,;	G	ENSG00000186432	ENST00000334256	Transcript	3_prime_UTR_variant	2075	.	.	.	.	.	.	.	-1	KPNA4	HGNC	6397	protein_coding	YES	CCDS3191.1	ENSP00000334373	IMA3_HUMAN	.	UPI0000001648	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCATCTTGAC	.	4	ESCA
B3GALNT1	0	.	GRCh37	3	160804342	160804342	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201T>C	p.%3D	p.L67L	ENST00000392781	8/8	95	86	9	53	53	0	B3GALNT1,synonymous_variant,p.%3D,ENST00000392779,;B3GALNT1,synonymous_variant,p.%3D,ENST00000392780,;B3GALNT1,synonymous_variant,p.%3D,ENST00000473285,;B3GALNT1,synonymous_variant,p.%3D,ENST00000320474,;B3GALNT1,synonymous_variant,p.%3D,ENST00000468268,;B3GALNT1,synonymous_variant,p.%3D,ENST00000488170,;B3GALNT1,synonymous_variant,p.%3D,ENST00000392781,;B3GALNT1,intron_variant,,ENST00000417187,;B3GALNT1,downstream_gene_variant,,ENST00000460353,;B3GALNT1,downstream_gene_variant,,ENST00000492353,;B3GALNT1,downstream_gene_variant,,ENST00000473142,;B3GALNT1,downstream_gene_variant,,ENST00000498216,;B3GALNT1,downstream_gene_variant,,ENST00000484127,;B3GALNT1,downstream_gene_variant,,ENST00000494173,;B3GALNT1,downstream_gene_variant,,ENST00000496295,;B3GALNT1,downstream_gene_variant,,ENST00000478383,;B3GALNT1,downstream_gene_variant,,ENST00000476999,;	G	ENSG00000169255	ENST00000392781	Transcript	synonymous_variant	949	201	67	L	ctT/ctC	.	.	.	-1	B3GALNT1	HGNC	918	protein_coding	YES	CCDS3193.1	ENSP00000376532	B3GL1_HUMAN	R4X604_HUMAN,Q8TDY1_HUMAN,Q8NHI0_HUMAN,Q6RC01_HUMAN,Q6RBZ9_HUMAN,E7EVS2_HUMAN,C9JXR0_HUMAN,C9JRV6_HUMAN,C9JD16_HUMAN,C9J8U7_HUMAN,C9J0F8_HUMAN	UPI000000DC24	.	.	.	8/8	.	hmmpanther:PTHR11214:SF17,hmmpanther:PTHR11214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTCGAAGTGT	.	3	ESCA
SLC7A14	0	.	GRCh37	3	170219048	170219048	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391G>C	p.Val131Leu	p.V131L	ENST00000231706	3/8	68	57	11	27	27	0	SLC7A14,missense_variant,p.Val131Leu,ENST00000231706,;CLDN11,intron_variant,,ENST00000486975,;CLDN11,intron_variant,,ENST00000451576,;CLDN11,intron_variant,,ENST00000480067,;CLDN11,intron_variant,,ENST00000471373,;KRT8P13,downstream_gene_variant,,ENST00000463294,;	G	ENSG00000013293	ENST00000231706	Transcript	missense_variant	707	391	131	V/L	Gtg/Ctg	COSM1670695	.	.	-1	SLC7A14	HGNC	29326	protein_coding	YES	CCDS33892.1	ENSP00000231706	S7A14_HUMAN	.	UPI0000051F6B	.	deleterious(0.04)	possibly_damaging(0.53)	3/8	.	Transmembrane_helices:TMhelix,Pfam_domain:PF13520,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF250	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCACAAATT	.	5	ESCA
YEATS2	0	.	GRCh37	3	183476656	183476656	+	Missense_Mutation	SNP	C	C	T	rs748267661	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1559C>T	p.Pro520Leu	p.P520L	ENST00000305135	13/31	52	42	10	15	15	0	YEATS2,missense_variant,p.Pro520Leu,ENST00000305135,;	T	ENSG00000163872	ENST00000305135	Transcript	missense_variant	1754	1559	520	P/L	cCt/cTt	rs748267661,COSM729642	.	.	1	YEATS2	HGNC	25489	protein_coding	YES	CCDS43175.1	ENSP00000306983	YETS2_HUMAN	.	UPI00001BB2B9	.	deleterious_low_confidence(0)	possibly_damaging(0.776)	13/31	.	hmmpanther:PTHR23195,hmmpanther:PTHR23195:SF7	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTCCTACAA	.	5	ESCA
RP11-352G9.1	0	.	GRCh37	3	195638762	195638762	+	3'Flank	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000607976	.	51	45	5	26	26	0	TNK2,upstream_gene_variant,,ENST00000333602,;RP11-352G9.1,downstream_gene_variant,,ENST00000607976,;AC124944.3,upstream_gene_variant,,ENST00000424819,;AC124944.3,upstream_gene_variant,,ENST00000448113,;TNK2-AS1,downstream_gene_variant,,ENST00000458180,;TNK2,non_coding_transcript_exon_variant,,ENST00000468819,;	C	ENSG00000273009	ENST00000607976	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1187	-1	RP11-352G9.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGGAGACTGC	.	3	ESCA
NKTR	0	.	GRCh37	3	42687711	42687711	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*244A>T	.	.	ENST00000232978	17/17	16	2	14	21	21	0	NKTR,3_prime_UTR_variant,,ENST00000232978,;RP4-613B23.1,intron_variant,,ENST00000434363,;RP4-613B23.1,intron_variant,,ENST00000445452,;RP4-613B23.1,intron_variant,,ENST00000438017,;NKTR,3_prime_UTR_variant,,ENST00000429888,;NKTR,downstream_gene_variant,,ENST00000490189,;	T	ENSG00000114857	ENST00000232978	Transcript	3_prime_UTR_variant	4821	.	.	.	.	.	.	.	1	NKTR	HGNC	7833	protein_coding	YES	CCDS2702.1	ENSP00000232978	NKTR_HUMAN	.	UPI00001301FD	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGAATCAAG	.	5	ESCA
COL7A1	0	.	GRCh37	3	48624968	48624968	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2877C>A	p.Ser959Arg	p.S959R	ENST00000328333	22/118	17	1	15	18	18	0	COL7A1,missense_variant,p.Ser959Arg,ENST00000328333,;COL7A1,missense_variant,p.Ser959Arg,ENST00000454817,;COL7A1,upstream_gene_variant,,ENST00000487017,;	T	ENSG00000114270	ENST00000328333	Transcript	missense_variant	2985	2877	959	S/R	agC/agA	.	.	.	-1	COL7A1	HGNC	2214	protein_coding	YES	CCDS2773.1	ENSP00000332371	CO7A1_HUMAN	.	UPI0000126D20	.	.	unknown(0)	22/118	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24023,SMART_domains:SM00060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAATGCTTGG	.	5	ESCA
RBM6	0	.	GRCh37	3	50098935	50098935	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2394C>T	p.%3D	p.Y798Y	ENST00000266022	14/21	88	55	33	113	113	0	RBM6,synonymous_variant,p.%3D,ENST00000539992,;RBM6,synonymous_variant,p.%3D,ENST00000442092,;RBM6,synonymous_variant,p.%3D,ENST00000266022,;RBM6,synonymous_variant,p.%3D,ENST00000443081,;RBM6,synonymous_variant,p.%3D,ENST00000422955,;RBM6,synonymous_variant,p.%3D,ENST00000438912,;RBM6,downstream_gene_variant,,ENST00000446471,;RBM6,upstream_gene_variant,,ENST00000421682,;RBM6,non_coding_transcript_exon_variant,,ENST00000441115,;RBM6,downstream_gene_variant,,ENST00000464013,;RBM6,synonymous_variant,p.%3D,ENST00000454079,;RBM6,3_prime_UTR_variant,,ENST00000434592,;RBM6,3_prime_UTR_variant,,ENST00000419610,;RBM6,downstream_gene_variant,,ENST00000483350,;RBM6,downstream_gene_variant,,ENST00000425608,;RBM6,downstream_gene_variant,,ENST00000478026,;RBM6,downstream_gene_variant,,ENST00000466247,;	T	ENSG00000004534	ENST00000266022	Transcript	synonymous_variant	2653	2394	798	Y	taC/taT	.	.	.	1	RBM6	HGNC	9903	protein_coding	YES	CCDS2809.1	ENSP00000266022	RBM6_HUMAN	E9PGM9_HUMAN,C9JSL1_HUMAN,C9JMC8_HUMAN,C9JII0_HUMAN,B4DNY1_HUMAN	UPI000013D6C0	.	.	.	14/21	.	hmmpanther:PTHR13948:SF22,hmmpanther:PTHR13948	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTACTATTA	.	4	ESCA
PDZRN3	0	.	GRCh37	3	73432059	73432059	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*457G>A	.	.	ENST00000263666	10/10	40	7	32	52	52	0	PDZRN3,3_prime_UTR_variant,,ENST00000263666,;PDZRN3,3_prime_UTR_variant,,ENST00000494559,;PDZRN3,3_prime_UTR_variant,,ENST00000462146,;PDZRN3,3_prime_UTR_variant,,ENST00000535920,;PDZRN3,downstream_gene_variant,,ENST00000466780,;PDZRN3,downstream_gene_variant,,ENST00000479530,;PDZRN3,downstream_gene_variant,,ENST00000492909,;PDZRN3,downstream_gene_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000478209,;	T	ENSG00000121440	ENST00000263666	Transcript	3_prime_UTR_variant	3773	.	.	.	.	.	.	.	-1	PDZRN3	HGNC	17704	protein_coding	YES	CCDS33789.1	ENSP00000263666	PZRN3_HUMAN	E7ENB6_HUMAN	UPI00001C1DE6	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGTCACGCATA	.	4	ESCA
CADM2	0	.	GRCh37	3	86114860	86114860	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1175G>A	p.Arg392Gln	p.R392Q	ENST00000405615	9/10	41	5	35	63	63	0	CADM2,missense_variant,p.Arg390Gln,ENST00000407528,;CADM2,missense_variant,p.Arg359Gln,ENST00000383699,;CADM2,missense_variant,p.Arg392Gln,ENST00000405615,;	A	ENSG00000175161	ENST00000405615	Transcript	missense_variant	1175	1175	392	R/Q	cGa/cAa	COSM174597,COSM1693032	.	.	1	CADM2	HGNC	29849	protein_coding	YES	CCDS33792.1	ENSP00000384193	CADM2_HUMAN	G3XHN8_HUMAN	UPI000013F077	.	deleterious(0.01)	probably_damaging(0.987)	9/10	.	hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF56,SMART_domains:SM00294	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTCGATATC	.	5	ESCA
UVSSA	0	.	GRCh37	4	1369233	1369233	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1370C>G	p.Pro457Arg	p.P457R	ENST00000389851	9/14	86	56	29	71	71	0	UVSSA,missense_variant,p.Pro8Arg,ENST00000512728,;UVSSA,missense_variant,p.Pro457Arg,ENST00000507531,;UVSSA,missense_variant,p.Pro457Arg,ENST00000389851,;UVSSA,missense_variant,p.Pro457Arg,ENST00000511216,;UVSSA,missense_variant,p.Pro8Arg,ENST00000511563,;UVSSA,upstream_gene_variant,,ENST00000503548,;	G	ENSG00000163945	ENST00000389851	Transcript	missense_variant	1817	1370	457	P/R	cCc/cGc	.	.	.	1	UVSSA	HGNC	29304	protein_coding	YES	CCDS33938.1	ENSP00000374501	UVSSA_HUMAN	.	UPI00001C1E0C	.	deleterious(0)	probably_damaging(0.998)	9/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACCCCACCT	.	5	ESCA
OTUD4	0	.	GRCh37	4	146057331	146057331	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1251C>G	.	.	ENST00000454497	21/21	25	18	6	13	13	0	OTUD4,3_prime_UTR_variant,,ENST00000454497,;OTUD4,downstream_gene_variant,,ENST00000447906,;OTUD4,intron_variant,,ENST00000455611,;	C	ENSG00000164164	ENST00000454497	Transcript	3_prime_UTR_variant	4539	.	.	.	.	.	.	.	-1	OTUD4	HGNC	24949	protein_coding	YES	CCDS47139.1	ENSP00000409279	OTUD4_HUMAN	D6RA27_HUMAN	UPI0000DA6D4D	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATGAATGA	.	5	ESCA
RXFP1	0	.	GRCh37	4	159560459	159560459	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1091G>T	p.Arg364Ile	p.R364I	ENST00000307765	14/18	98	71	27	82	82	0	RXFP1,missense_variant,p.Arg259Ile,ENST00000448688,;RXFP1,missense_variant,p.Arg331Ile,ENST00000470033,;RXFP1,missense_variant,p.Arg364Ile,ENST00000307765,;RXFP1,missense_variant,p.Arg283Ile,ENST00000460056,;RXFP1,missense_variant,p.Arg316Ile,ENST00000343542,;RXFP1,3_prime_UTR_variant,,ENST00000471616,;RXFP1,3_prime_UTR_variant,,ENST00000342048,;	T	ENSG00000171509	ENST00000307765	Transcript	missense_variant	1342	1091	364	R/I	aGa/aTa	.	.	.	1	RXFP1	HGNC	19718	protein_coding	YES	CCDS43276.1	ENSP00000303248	RXFP1_HUMAN	Q4W5D9_HUMAN,E9PCA3_HUMAN	UPI000013EC4B	.	deleterious(0.03)	benign(0.005)	14/18	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF18,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTAGACCTC	.	5	ESCA
KIAA1430	0	.	GRCh37	4	186111979	186111979	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372A>G	p.%3D	p.V124V	ENST00000458385	2/5	61	26	35	63	63	0	KIAA1430,synonymous_variant,p.%3D,ENST00000514798,;KIAA1430,synonymous_variant,p.%3D,ENST00000503223,;KIAA1430,synonymous_variant,p.%3D,ENST00000458385,;KIAA1430,synonymous_variant,p.%3D,ENST00000296775,;	C	ENSG00000164323	ENST00000458385	Transcript	synonymous_variant	492	372	124	V	gtA/gtG	.	.	.	-1	KIAA1430	HGNC	29276	protein_coding	YES	CCDS47168.1	ENSP00000409964	K1430_HUMAN	D6RDU8_HUMAN	UPI00001971F9	.	.	.	2/5	.	hmmpanther:PTHR23035,hmmpanther:PTHR23035:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTTACAAT	.	5	ESCA
EVC	0	.	GRCh37	4	5743442	5743442	+	Splice_Site	SNP	G	G	A	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703-1G>A	.	p.X235_splice	ENST00000382674	.	22	12	10	31	31	0	EVC,splice_acceptor_variant,,ENST00000382674,;EVC,splice_acceptor_variant,,ENST00000264956,;EVC,splice_acceptor_variant,,ENST00000509451,;	A	ENSG00000072840	ENST00000382674	Transcript	splice_acceptor_variant	.	.	.	.	.	CS070372	.	.	1	EVC	HGNC	3497	protein_coding	YES	CCDS3383.1	ENSP00000372120	EVC_HUMAN	Q4W5F2_HUMAN,Q4W5A3_HUMAN	UPI000012A2A5	.	.	.	.	5/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATAGATGTT	.	5	ESCA
WDFY3	0	.	GRCh37	4	85594028	85594028	+	Missense_Mutation	SNP	T	T	G	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10574A>C	p.Asn3525Thr	p.N3525T	ENST00000295888	68/68	41	25	15	44	44	0	WDFY3,missense_variant,p.Asn3525Thr,ENST00000295888,;WDFY3,missense_variant,p.Asn3508Thr,ENST00000322366,;WDFY3,non_coding_transcript_exon_variant,,ENST00000425179,;	G	ENSG00000163625	ENST00000295888	Transcript	missense_variant	10982	10574	3525	N/T	aAt/aCt	COSM4165042	.	.	-1	WDFY3	HGNC	20751	protein_coding	YES	CCDS3609.1	ENSP00000295888	WDFY3_HUMAN	D6RJE4_HUMAN,A7E1Z6_HUMAN	UPI000013E2C7	.	deleterious_low_confidence(0)	probably_damaging(0.968)	68/68	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAATTTCGA	.	5	ESCA
KLHL8	0	.	GRCh37	4	88104481	88104481	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.826G>A	p.Val276Ile	p.V276I	ENST00000273963	4/10	25	14	11	39	39	0	KLHL8,missense_variant,p.Val276Ile,ENST00000512111,;KLHL8,missense_variant,p.Val200Ile,ENST00000498875,;KLHL8,missense_variant,p.Val276Ile,ENST00000273963,;KLHL8,missense_variant,p.Val93Ile,ENST00000425278,;KLHL8,intron_variant,,ENST00000545252,;KLHL8,intron_variant,,ENST00000504029,;KLHL8,intron_variant,,ENST00000505388,;KLHL8,intron_variant,,ENST00000506985,;	T	ENSG00000145332	ENST00000273963	Transcript	missense_variant	1168	826	276	V/I	Gtc/Atc	.	.	.	-1	KLHL8	HGNC	18644	protein_coding	YES	CCDS3617.1	ENSP00000273963	KLHL8_HUMAN	Q49A95_HUMAN	UPI00001AE9B8	.	tolerated(0.87)	benign(0.001)	4/10	.	hmmpanther:PTHR24412:SF138,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGACAATCT	.	5	ESCA
NAP1L5	0	.	GRCh37	4	89618288	89618288	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69C>T	.	.	ENST00000323061	1/1	64	39	25	63	63	0	NAP1L5,3_prime_UTR_variant,,ENST00000323061,;HERC3,intron_variant,,ENST00000402738,;HERC3,intron_variant,,ENST00000543130,;HERC3,intron_variant,,ENST00000264345,;	A	ENSG00000177432	ENST00000323061	Transcript	3_prime_UTR_variant	1099	.	.	.	.	.	.	.	-1	NAP1L5	HGNC	19968	protein_coding	YES	CCDS3632.1	ENSP00000320488	NP1L5_HUMAN	.	UPI000004A03B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCGATATT	.	5	ESCA
PJA2	0	.	GRCh37	5	108714946	108714946	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242C>G	p.Pro81Arg	p.P81R	ENST00000361189	4/10	21	14	6	27	27	0	PJA2,missense_variant,p.Pro81Arg,ENST00000361189,;PJA2,missense_variant,p.Pro81Arg,ENST00000361557,;PJA2,non_coding_transcript_exon_variant,,ENST00000511624,;PJA2,downstream_gene_variant,,ENST00000512822,;	C	ENSG00000198961	ENST00000361189	Transcript	missense_variant	482	242	81	P/R	cCt/cGt	.	.	.	-1	PJA2	HGNC	17481	protein_coding	YES	CCDS4099.1	ENSP00000354775	PJA2_HUMAN	.	UPI000013D192	.	deleterious(0.01)	possibly_damaging(0.885)	4/10	.	hmmpanther:PTHR15710,hmmpanther:PTHR15710:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCAAAGGACTG	.	4	ESCA
SMAD5	0	.	GRCh37	5	135518229	135518229	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5061A>G	.	.	ENST00000545279	9/9	62	10	52	63	63	0	SMAD5,3_prime_UTR_variant,,ENST00000545620,;SMAD5,3_prime_UTR_variant,,ENST00000545279,;SMAD5,non_coding_transcript_exon_variant,,ENST00000514641,;SMAD5,intron_variant,,ENST00000513418,;	G	ENSG00000113658	ENST00000545279	Transcript	3_prime_UTR_variant	6816	.	.	.	.	.	.	.	1	SMAD5	HGNC	6771	protein_coding	YES	.	ENSP00000441954	SMAD5_HUMAN	Q68DB7_HUMAN,F5GWU7_HUMAN,D6RIZ9_HUMAN,D6RBB4_HUMAN,D6R9D4_HUMAN	UPI000013C952	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTATTTGT	.	5	ESCA
PCDHB2	0	.	GRCh37	5	140476237	140476237	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1863G>A	p.%3D	p.A621A	ENST00000194155	1/1	114	53	60	107	107	0	PCDHB2,synonymous_variant,p.%3D,ENST00000194155,;PCDHB3,upstream_gene_variant,,ENST00000231130,;AC005754.7,downstream_gene_variant,,ENST00000607216,;	A	ENSG00000112852	ENST00000194155	Transcript	synonymous_variant	2011	1863	621	A	gcG/gcA	.	.	.	1	PCDHB2	HGNC	8687	protein_coding	YES	CCDS4244.1	ENSP00000194155	PCDB2_HUMAN	.	UPI00001273DC	.	.	.	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF77,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGCACAA	.	5	ESCA
C5orf54	0	.	GRCh37	5	159821568	159821568	+	Silent	SNP	T	T	C	rs757344812	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.930A>G	p.%3D	p.L310L	ENST00000408953	2/2	25	6	19	31	31	0	C5orf54,synonymous_variant,p.%3D,ENST00000408953,;C5orf54,synonymous_variant,p.%3D,ENST00000523213,;	C	ENSG00000221886	ENST00000408953	Transcript	synonymous_variant	1438	930	310	L	ctA/ctG	rs757344812	.	.	-1	C5orf54	HGNC	30804	protein_coding	YES	CCDS34283.1	ENSP00000386184	ZBED8_HUMAN	.	UPI00000741A3	.	.	.	2/2	.	Superfamily_domains:SSF53098,hmmpanther:PTHR11697:SF102,hmmpanther:PTHR11697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAATAGGCG	.	5	ESCA
ZNF454	0	.	GRCh37	5	178373440	178373440	+	Silent	SNP	G	G	C	rs767545892	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114G>C	p.%3D	p.L38L	ENST00000320129	3/5	55	36	19	58	58	0	ZNF454,synonymous_variant,p.%3D,ENST00000519564,;ZNF454,synonymous_variant,p.%3D,ENST00000320129,;ZNF454,non_coding_transcript_exon_variant,,ENST00000522827,;	C	ENSG00000178187	ENST00000320129	Transcript	synonymous_variant	417	114	38	L	ctG/ctC	rs767545892	.	.	1	ZNF454	HGNC	21200	protein_coding	YES	CCDS4441.1	ENSP00000326249	ZN454_HUMAN	.	UPI00001407C7	.	.	.	3/5	.	Superfamily_domains:0044637,SMART_domains:SM00349,Pfam_domain:PF01352,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF221,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTGTACAG	byFrequency	5	ESCA
RASGEF1C	0	.	GRCh37	5	179563528	179563528	+	Intron	SNP	G	G	A	rs201217573	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301-13C>T	.	.	ENST00000393371	.	59	45	14	72	72	0	RASGEF1C,5_prime_UTR_variant,,ENST00000522500,;RASGEF1C,intron_variant,,ENST00000361132,;RASGEF1C,intron_variant,,ENST00000393371,;RASGEF1C,upstream_gene_variant,,ENST00000519883,;RASGEF1C,5_prime_UTR_variant,,ENST00000520209,;	A	ENSG00000146090	ENST00000393371	Transcript	intron_variant	.	.	.	.	.	rs201217573	.	.	-1	RASGEF1C	HGNC	27400	protein_coding	YES	CCDS4452.1	ENSP00000377037	RGF1C_HUMAN	.	UPI0000037308	.	.	.	.	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGCGAGGGG	by1000G	5	ESCA
PRDM9	0	.	GRCh37	5	23527075	23527075	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1878C>G	p.His626Gln	p.H626Q	ENST00000296682	11/11	58	30	27	80	80	0	PRDM9,missense_variant,p.His626Gln,ENST00000296682,;	G	ENSG00000164256	ENST00000296682	Transcript	missense_variant	2060	1878	626	H/Q	caC/caG	.	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	deleterious(0)	probably_damaging(0.999)	11/11	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCACCAGAG	.	5	ESCA
GHR	0	.	GRCh37	5	42719319	42719319	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1710A>G	p.%3D	p.E570E	ENST00000230882	10/10	38	35	3	41	41	0	GHR,synonymous_variant,p.%3D,ENST00000230882,;GHR,synonymous_variant,p.%3D,ENST00000537449,;GHR,synonymous_variant,p.%3D,ENST00000357703,;GHR,downstream_gene_variant,,ENST00000513625,;GHR,3_prime_UTR_variant,,ENST00000511135,;	G	ENSG00000112964	ENST00000230882	Transcript	synonymous_variant	1900	1710	570	E	gaA/gaG	.	.	.	1	GHR	HGNC	4263	protein_coding	YES	CCDS3940.1	ENSP00000230882	GHR_HUMAN	Q9NRZ8_HUMAN,Q9HCW9_HUMAN,F5H7X2_HUMAN	UPI000012B416	.	.	.	10/10	.	Pfam_domain:PF12772,hmmpanther:PTHR23036:SF74,hmmpanther:PTHR23036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACAGAAAGCCT	.	2	ESCA
TRIM23	0	.	GRCh37	5	64885613	64885613	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1983C>A	.	.	ENST00000231524	11/11	36	23	12	67	67	0	TRIM23,3_prime_UTR_variant,,ENST00000231524,;PPWD1,downstream_gene_variant,,ENST00000261308,;PPWD1,downstream_gene_variant,,ENST00000535264,;TRIM23,downstream_gene_variant,,ENST00000381018,;PPWD1,downstream_gene_variant,,ENST00000538977,;TRIM23,downstream_gene_variant,,ENST00000274327,;PPWD1,downstream_gene_variant,,ENST00000515151,;PPWD1,downstream_gene_variant,,ENST00000511908,;PPWD1,downstream_gene_variant,,ENST00000510930,;PPWD1,downstream_gene_variant,,ENST00000513773,;	T	ENSG00000113595	ENST00000231524	Transcript	3_prime_UTR_variant	4080	.	.	.	.	.	.	.	-1	TRIM23	HGNC	660	protein_coding	YES	CCDS3987.1	ENSP00000231524	TRI23_HUMAN	D6R9E9_HUMAN	UPI0000125DB3	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACGGCTATA	.	5	ESCA
PDE8B	0	.	GRCh37	5	76633130	76633130	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787T>A	p.Phe263Ile	p.F263I	ENST00000264917	6/22	32	29	3	37	37	0	PDE8B,missense_variant,p.Phe263Ile,ENST00000333194,;PDE8B,missense_variant,p.Phe263Ile,ENST00000346042,;PDE8B,missense_variant,p.Phe25Ile,ENST00000503963,;PDE8B,missense_variant,p.Phe243Ile,ENST00000342343,;PDE8B,missense_variant,p.Phe263Ile,ENST00000264917,;PDE8B,missense_variant,p.Phe263Ile,ENST00000340978,;	A	ENSG00000113231	ENST00000264917	Transcript	missense_variant	832	787	263	F/I	Ttc/Atc	.	.	.	1	PDE8B	HGNC	8794	protein_coding	YES	CCDS4037.1	ENSP00000264917	PDE8B_HUMAN	Q3ZCR2_HUMAN,D6RH10_HUMAN,D6R9W0_HUMAN,B3KN77_HUMAN	UPI0000001BBE	.	tolerated(0.14)	possibly_damaging(0.77)	6/22	.	hmmpanther:PTHR11347:SF98,hmmpanther:PTHR11347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCCAGTTCAAA	.	2	ESCA
POLR3G	0	.	GRCh37	5	89781458	89781458	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.74A>G	p.Glu25Gly	p.E25G	ENST00000399107	2/8	64	45	18	74	74	0	POLR3G,missense_variant,p.Glu25Gly,ENST00000504930,;POLR3G,missense_variant,p.Glu25Gly,ENST00000505345,;POLR3G,missense_variant,p.Glu25Gly,ENST00000514483,;POLR3G,missense_variant,p.Glu25Gly,ENST00000503973,;POLR3G,missense_variant,p.Glu25Gly,ENST00000503373,;POLR3G,missense_variant,p.Glu25Gly,ENST00000399107,;POLR3G,missense_variant,p.Glu25Gly,ENST00000512239,;	G	ENSG00000113356	ENST00000399107	Transcript	missense_variant	274	74	25	E/G	gAa/gGa	.	.	.	1	POLR3G	HGNC	30075	protein_coding	YES	CCDS43337.1	ENSP00000382058	RPC7_HUMAN	D6RIT0_HUMAN,D6REQ0_HUMAN,D6R9U7_HUMAN	UPI000020CC53	.	tolerated(0.05)	probably_damaging(0.914)	2/8	.	hmmpanther:PTHR15367:SF3,hmmpanther:PTHR15367,Pfam_domain:PF11705	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTGAAAAGT	.	5	ESCA
ERAP1	0	.	GRCh37	5	96139172	96139172	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.458G>C	p.Gly153Ala	p.G153A	ENST00000296754	2/20	53	29	24	28	28	0	ERAP1,missense_variant,p.Gly153Ala,ENST00000443439,;ERAP1,missense_variant,p.Gly153Ala,ENST00000296754,;ERAP1,5_prime_UTR_variant,,ENST00000508227,;ERAP1,5_prime_UTR_variant,,ENST00000503921,;ERAP1,downstream_gene_variant,,ENST00000507154,;CTD-2260A17.3,upstream_gene_variant,,ENST00000606656,;CTD-2260A17.3,upstream_gene_variant,,ENST00000606346,;	G	ENSG00000164307	ENST00000296754	Transcript	missense_variant	716	458	153	G/A	gGc/gCc	.	.	.	-1	ERAP1	HGNC	18173	protein_coding	YES	CCDS4085.1	ENSP00000296754	ERAP1_HUMAN	D6RAL9_HUMAN	UPI000045731D	.	tolerated(1)	benign(0.011)	2/20	.	hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF156,Pfam_domain:PF01433,Superfamily_domains:0038696	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTGCCAGCA	.	5	ESCA
CDK19	0	.	GRCh37	6	110935627	110935627	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*111C>A	.	.	ENST00000368911	13/13	15	11	4	14	14	0	CDK19,3_prime_UTR_variant,,ENST00000413605,;CDK19,3_prime_UTR_variant,,ENST00000323817,;CDK19,3_prime_UTR_variant,,ENST00000368911,;	T	ENSG00000155111	ENST00000368911	Transcript	3_prime_UTR_variant	1800	.	.	.	.	.	.	.	-1	CDK19	HGNC	19338	protein_coding	YES	CCDS5085.1	ENSP00000357907	CDK19_HUMAN	Q5JQZ9_HUMAN	UPI0000070643	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	CATGTGTATGA	.	2	ESCA
SERINC1	0	.	GRCh37	6	122792867	122792867	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16G>C	p.Gly6Arg	p.G6R	ENST00000339697	1/10	18	8	10	21	21	0	SERINC1,missense_variant,p.Gly6Arg,ENST00000339697,;PKIB,upstream_gene_variant,,ENST00000392491,;PKIB,upstream_gene_variant,,ENST00000607474,;PKIB,upstream_gene_variant,,ENST00000608895,;	G	ENSG00000111897	ENST00000339697	Transcript	missense_variant	101	16	6	G/R	Ggg/Cgg	.	.	.	-1	SERINC1	HGNC	13464	protein_coding	YES	CCDS5125.1	ENSP00000342962	SERC1_HUMAN	.	UPI000004E6A2	.	deleterious(0.02)	benign(0.275)	1/10	.	Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-TM,hmmpanther:PTHR10383,hmmpanther:PTHR10383:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCCCAGGA	.	5	ESCA
TAAR8	0	.	GRCh37	6	132874111	132874111	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280G>T	p.Glu94Ter	p.E94*	ENST00000275200	1/1	50	26	23	72	72	0	TAAR8,stop_gained,p.Glu94Ter,ENST00000275200,;	T	ENSG00000146385	ENST00000275200	Transcript	stop_gained	280	280	94	E/*	Gag/Tag	.	.	.	1	TAAR8	HGNC	14964	protein_coding	YES	CCDS5154.1	ENSP00000275200	TAAR8_HUMAN	.	UPI000000D87F	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF253,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01830	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTGGAGAGC	.	5	ESCA
TAAR5	0	.	GRCh37	6	132910226	132910226	+	Missense_Mutation	SNP	C	C	A	rs757605842	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.600G>T	p.Trp200Cys	p.W200C	ENST00000258034	1/1	16	9	7	27	27	0	TAAR5,missense_variant,p.Trp200Cys,ENST00000258034,;	A	ENSG00000135569	ENST00000258034	Transcript	missense_variant	652	600	200	W/C	tgG/tgT	rs757605842	.	.	-1	TAAR5	HGNC	30236	protein_coding	YES	CCDS5156.1	ENSP00000258034	TAAR5_HUMAN	.	UPI000013CFAA	.	deleterious(0.02)	probably_damaging(1)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF00001,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF217,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCCCAAAA	.	5	ESCA
TDP2	0	.	GRCh37	6	24651204	24651204	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.901A>G	p.Met301Val	p.M301V	ENST00000378198	7/7	20	9	11	19	19	0	TDP2,missense_variant,p.Met243Val,ENST00000341060,;TDP2,missense_variant,p.Met331Val,ENST00000545995,;TDP2,missense_variant,p.Met301Val,ENST00000378198,;KIAA0319,upstream_gene_variant,,ENST00000430948,;KIAA0319,upstream_gene_variant,,ENST00000378214,;KIAA0319,upstream_gene_variant,,ENST00000535378,;KIAA0319,upstream_gene_variant,,ENST00000537886,;TDP2,downstream_gene_variant,,ENST00000478507,;TDP2,downstream_gene_variant,,ENST00000478285,;	C	ENSG00000111802	ENST00000378198	Transcript	missense_variant	1072	901	301	M/V	Atg/Gtg	.	.	.	-1	TDP2	HGNC	17768	protein_coding	YES	CCDS4557.1	ENSP00000367440	TYDP2_HUMAN	.	UPI0000032018	.	tolerated(0.35)	benign(0.002)	7/7	.	Superfamily_domains:SSF56219,Pfam_domain:PF03372,Gene3D:3.60.10.10,hmmpanther:PTHR15822,hmmpanther:PTHR15822:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCATTTGTG	.	5	ESCA
HIST1H2AC	0	.	GRCh37	6	26124702	26124702	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242C>A	p.Pro81Gln	p.P81Q	ENST00000602637	1/2	68	46	22	78	78	0	HIST1H2AC,missense_variant,p.Pro81Gln,ENST00000377791,;HIST1H2AC,missense_variant,p.Pro81Gln,ENST00000602637,;HIST1H2BC,upstream_gene_variant,,ENST00000314332,;HIST1H2BC,upstream_gene_variant,,ENST00000396984,;HIST1H2AC,missense_variant,p.Pro81Gln,ENST00000314088,;	A	ENSG00000180573	ENST00000602637	Transcript	missense_variant	272	242	81	P/Q	cCg/cAg	.	.	.	1	HIST1H2AC	HGNC	4733	protein_coding	YES	CCDS4585.1	ENSP00000473534	H2A1C_HUMAN	.	UPI0000000DB8	.	deleterious_low_confidence(0)	probably_damaging(1)	1/2	.	hmmpanther:PTHR23430,hmmpanther:PTHR23430:SF24,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCCCGCGCC	.	5	ESCA
HIST1H2BH	0	.	GRCh37	6	26252158	26252158	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280G>C	p.Glu94Gln	p.E94Q	ENST00000356350	1/1	49	36	13	60	60	0	HIST1H2BH,missense_variant,p.Glu94Gln,ENST00000356350,;HIST1H4G,upstream_gene_variant,,ENST00000244537,;HIST1H3F,upstream_gene_variant,,ENST00000446824,;	C	ENSG00000197459	ENST00000356350	Transcript	missense_variant	280	280	94	E/Q	Gag/Cag	.	.	.	1	HIST1H2BH	HGNC	4755	protein_coding	YES	CCDS4601.1	ENSP00000348706	H2B1H_HUMAN	.	UPI0000001BD4	.	deleterious_low_confidence(0)	probably_damaging(0.978)	1/1	.	hmmpanther:PTHR23428,PROSITE_patterns:PS00357,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGGAGATC	.	5	ESCA
LINC00951	0	.	GRCh37	6	40312262	40312262	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.375G>A	.	.	ENST00000373171	2/2	21	2	19	19	19	0	LINC00951,non_coding_transcript_exon_variant,,ENST00000373171,;TDRG1,intron_variant,,ENST00000451810,;TDRG1,intron_variant,,ENST00000448559,;	T	ENSG00000204092	ENST00000373171	Transcript	non_coding_transcript_exon_variant	375	.	.	.	.	.	.	.	-1	LINC00951	HGNC	48662	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGGCTCCAG	.	5	ESCA
TRERF1	0	.	GRCh37	6	42236020	42236020	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1309G>C	p.Ala437Pro	p.A437P	ENST00000372922	5/18	14	11	3	20	20	0	TRERF1,missense_variant,p.Ala437Pro,ENST00000541110,;TRERF1,missense_variant,p.Ala437Pro,ENST00000340840,;TRERF1,missense_variant,p.Ala437Pro,ENST00000372922,;TRERF1,missense_variant,p.Ala437Pro,ENST00000372917,;TRERF1,missense_variant,p.Ala437Pro,ENST00000354325,;	G	ENSG00000124496	ENST00000372922	Transcript	missense_variant	1872	1309	437	A/P	Gcg/Ccg	.	.	.	-1	TRERF1	HGNC	18273	protein_coding	YES	CCDS4867.1	ENSP00000362013	TREF1_HUMAN	.	UPI0000052952	.	tolerated_low_confidence(0.25)	possibly_damaging(0.665)	5/18	.	hmmpanther:PTHR16089:SF19,hmmpanther:PTHR16089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCGCTGGGT	.	2	ESCA
HMGCLL1	0	.	GRCh37	6	55443889	55443889	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-36T>A	.	.	ENST00000398661	1/10	59	53	5	31	31	0	HMGCLL1,5_prime_UTR_variant,,ENST00000274901,;HMGCLL1,5_prime_UTR_variant,,ENST00000308161,;HMGCLL1,5_prime_UTR_variant,,ENST00000358072,;HMGCLL1,5_prime_UTR_variant,,ENST00000398661,;HMGCLL1,5_prime_UTR_variant,,ENST00000370850,;HMGCLL1,5_prime_UTR_variant,,ENST00000508459,;HMGCLL1,upstream_gene_variant,,ENST00000428842,;HMGCLL1,5_prime_UTR_variant,,ENST00000370852,;HMGCLL1,5_prime_UTR_variant,,ENST00000515546,;	T	ENSG00000146151	ENST00000398661	Transcript	5_prime_UTR_variant	97	.	.	.	.	.	.	.	-1	HMGCLL1	HGNC	21359	protein_coding	YES	CCDS43475.1	ENSP00000381654	HMGC2_HUMAN	.	UPI000023780E	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GAGGGAGACTG	.	3	ESCA
MEPCE	0	.	GRCh37	7	100028402	100028402	+	Missense_Mutation	SNP	C	C	T	rs760505363	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.761C>T	p.Ser254Leu	p.S254L	ENST00000310512	1/4	45	38	7	11	11	0	MEPCE,missense_variant,p.Ser254Leu,ENST00000310512,;MEPCE,5_prime_UTR_variant,,ENST00000414441,;ZCWPW1,upstream_gene_variant,,ENST00000360951,;ZCWPW1,upstream_gene_variant,,ENST00000398027,;ZCWPW1,upstream_gene_variant,,ENST00000324725,;PPP1R35,downstream_gene_variant,,ENST00000292330,;ZCWPW1,upstream_gene_variant,,ENST00000472716,;RP11-758P17.2,upstream_gene_variant,,ENST00000492523,;PPP1R35,downstream_gene_variant,,ENST00000476185,;MEPCE,intron_variant,,ENST00000497759,;MEPCE,intron_variant,,ENST00000479201,;PPP1R35,downstream_gene_variant,,ENST00000487452,;PPP1R35,downstream_gene_variant,,ENST00000491407,;ZCWPW1,upstream_gene_variant,,ENST00000464510,;PPP1R35,downstream_gene_variant,,ENST00000470295,;	T	ENSG00000146834	ENST00000310512	Transcript	missense_variant	1149	761	254	S/L	tCg/tTg	rs760505363	.	.	1	MEPCE	HGNC	20247	protein_coding	YES	CCDS5693.1	ENSP00000308546	MEPCE_HUMAN	.	UPI0000227DFA	.	deleterious(0.04)	possibly_damaging(0.88)	1/4	.	hmmpanther:PTHR12315:SF0,hmmpanther:PTHR12315	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTTCGCCAC	byFrequency	4	ESCA
MUC17	0	.	GRCh37	7	100696700	100696700	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13346G>A	p.Gly4449Asp	p.G4449D	ENST00000306151	11/13	37	27	10	27	27	0	MUC17,missense_variant,p.Gly4449Asp,ENST00000306151,;RN7SKP54,upstream_gene_variant,,ENST00000410704,;MUC17,3_prime_UTR_variant,,ENST00000379439,;MUC17,non_coding_transcript_exon_variant,,ENST00000497859,;	A	ENSG00000169876	ENST00000306151	Transcript	missense_variant	13410	13346	4449	G/D	gGc/gAc	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	unknown(0)	11/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGGCTTTG	.	5	ESCA
THSD7A	0	.	GRCh37	7	11630185	11630185	+	Missense_Mutation	SNP	G	G	A	rs767811878	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355C>T	p.Thr452Met	p.T452M	ENST00000423059	4/28	43	35	7	54	54	0	THSD7A,missense_variant,p.Thr452Met,ENST00000423059,;	A	ENSG00000005108	ENST00000423059	Transcript	missense_variant	1607	1355	452	T/M	aCg/aTg	rs767811878,COSM1084364	.	.	-1	THSD7A	HGNC	22207	protein_coding	YES	CCDS47543.1	ENSP00000406482	THS7A_HUMAN	.	UPI00006C0B74	.	deleterious(0.01)	probably_damaging(0.978)	4/28	.	PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCGTCTGG	byFrequency	5	ESCA
KIAA1147	0	.	GRCh37	7	141366131	141366131	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.776T>C	p.Ile259Thr	p.I259T	ENST00000536163	5/9	27	17	9	44	44	0	KIAA1147,missense_variant,p.Ile155Thr,ENST00000482493,;KIAA1147,missense_variant,p.Ile259Thr,ENST00000536163,;RP5-894A10.6,upstream_gene_variant,,ENST00000602609,;	G	ENSG00000257093	ENST00000536163	Transcript	missense_variant	776	776	259	I/T	aTt/aCt	.	.	.	-1	KIAA1147	HGNC	29472	protein_coding	YES	CCDS47726.1	ENSP00000445768	LCHN_HUMAN	.	UPI0000251F74	.	deleterious(0)	probably_damaging(0.991)	5/9	.	Pfam_domain:PF09804,hmmpanther:PTHR31017,hmmpanther:PTHR31017:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAAATGCGC	.	5	ESCA
OR9A4	0	.	GRCh37	7	141619455	141619455	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.780G>A	p.%3D	p.V260V	ENST00000548136	1/1	27	18	9	23	23	0	OR9A4,synonymous_variant,p.%3D,ENST00000548136,;MGAM,intron_variant,,ENST00000465654,;MGAM,intron_variant,,ENST00000497554,;	A	ENSG00000258083	ENST00000548136	Transcript	synonymous_variant	839	780	260	V	gtG/gtA	.	.	.	1	OR9A4	HGNC	15095	protein_coding	YES	CCDS43661.1	ENSP00000448789	OR9A4_HUMAN	.	UPI0000041D24	.	.	.	1/1	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR24242:SF216,hmmpanther:PTHR24242,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACGTGAAACC	.	5	ESCA
NOS3	0	.	GRCh37	7	150695532	150695532	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670C>T	p.Leu224Phe	p.L224F	ENST00000297494	6/27	15	7	8	37	37	0	NOS3,missense_variant,p.Leu224Phe,ENST00000467517,;NOS3,missense_variant,p.Leu224Phe,ENST00000484524,;NOS3,missense_variant,p.Leu18Phe,ENST00000461406,;NOS3,missense_variant,p.Leu224Phe,ENST00000297494,;NOS3,upstream_gene_variant,,ENST00000460603,;	T	ENSG00000164867	ENST00000297494	Transcript	missense_variant	1027	670	224	L/F	Ctt/Ttt	.	.	.	1	NOS3	HGNC	7876	protein_coding	YES	CCDS5912.1	ENSP00000297494	NOS3_HUMAN	Q96P37_HUMAN,Q96J98_HUMAN,O14937_HUMAN,E7ESA7_HUMAN	UPI000013E417	.	deleterious(0)	possibly_damaging(0.615)	6/27	.	hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF66,Gene3D:3.90.340.10,Pfam_domain:PF02898,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAACCTTCGG	.	5	ESCA
DNAH11	0	.	GRCh37	7	21628842	21628842	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1990G>A	p.Asp664Asn	p.D664N	ENST00000328843	12/83	114	105	8	83	83	0	DNAH11,missense_variant,p.Asp664Asn,ENST00000328843,;DNAH11,missense_variant,p.Asp664Asn,ENST00000409508,;	A	ENSG00000105877	ENST00000328843	Transcript	missense_variant	2021	1990	664	D/N	Gat/Aat	.	.	.	1	DNAH11	HGNC	2942	protein_coding	YES	.	ENSP00000330671	DYH11_HUMAN	Q75MY1_HUMAN,Q75KM7_HUMAN,O95705_HUMAN,O43352_HUMAN,O15433_HUMAN	UPI000041AC4D	.	.	benign(0.258)	12/83	.	hmmpanther:PTHR10676:SF227,hmmpanther:PTHR10676,Pfam_domain:PF08385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCTGATCAC	.	2	ESCA
ZNF117	0	.	GRCh37	7	64439388	64439388	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.561T>G	p.His187Gln	p.H187Q	ENST00000282869	4/4	39	24	14	46	46	0	ZNF117,missense_variant,p.His187Gln,ENST00000282869,;ZNF117,downstream_gene_variant,,ENST00000487644,;	C	ENSG00000152926	ENST00000282869	Transcript	missense_variant	1846	561	187	H/Q	caT/caG	.	.	.	-1	ZNF117	HGNC	12897	protein_coding	YES	CCDS43593.1	ENSP00000282869	ZN117_HUMAN	.	UPI000049E07A	.	deleterious(0.01)	probably_damaging(0.959)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF120,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R185I|c.554G>T|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGTATGAAT	.	5	ESCA
ABCB4	0	.	GRCh37	7	87076347	87076347	+	Intron	SNP	T	T	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1005+3A>C	.	.	ENST00000265723	.	64	54	10	36	36	0	ABCB4,splice_region_variant,,ENST00000453593,;ABCB4,splice_region_variant,,ENST00000265723,;ABCB4,splice_region_variant,,ENST00000358400,;ABCB4,splice_region_variant,,ENST00000545634,;ABCB4,splice_region_variant,,ENST00000359206,;	G	ENSG00000005471	ENST00000265723	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	ABCB4	HGNC	45	protein_coding	YES	CCDS5606.1	ENSP00000265723	MDR3_HUMAN	Q75MQ5_HUMAN,I7D7J8_HUMAN,I7CY13_HUMAN,I7CAJ8_HUMAN,E7EQI1_HUMAN,A8HT68_HUMAN,A7J1S3_HUMAN,A7J1S1_HUMAN,A7J1Q4_HUMAN	UPI000013D66B	.	.	.	.	9/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACTTACTGT	.	4	ESCA
ASNS	0	.	GRCh37	7	97493669	97493669	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389A>G	p.Asn130Ser	p.N130S	ENST00000175506	5/14	48	23	25	28	28	0	ASNS,missense_variant,p.Asn130Ser,ENST00000394309,;ASNS,missense_variant,p.Asn130Ser,ENST00000442734,;ASNS,missense_variant,p.Asn47Ser,ENST00000437628,;ASNS,missense_variant,p.Asn130Ser,ENST00000175506,;ASNS,missense_variant,p.Asn130Ser,ENST00000437657,;ASNS,missense_variant,p.Asn47Ser,ENST00000455086,;ASNS,missense_variant,p.Asn109Ser,ENST00000444334,;ASNS,missense_variant,p.Asn130Ser,ENST00000394308,;ASNS,missense_variant,p.Asn109Ser,ENST00000422745,;ASNS,downstream_gene_variant,,ENST00000448127,;ASNS,downstream_gene_variant,,ENST00000414884,;ASNS,downstream_gene_variant,,ENST00000453600,;ASNS,downstream_gene_variant,,ENST00000451771,;ASNS,missense_variant,p.Asn130Ser,ENST00000454046,;ASNS,non_coding_transcript_exon_variant,,ENST00000495255,;	C	ENSG00000070669	ENST00000175506	Transcript	missense_variant	918	389	130	N/S	aAt/aGt	.	.	.	-1	ASNS	HGNC	753	protein_coding	YES	CCDS5652.1	ENSP00000175506	ASNS_HUMAN	C9JT45_HUMAN,C9JM09_HUMAN,C9JLA3_HUMAN,C9J605_HUMAN,C9J057_HUMAN	UPI0000169F55	.	tolerated(0.46)	benign(0.01)	5/14	.	PROSITE_profiles:PS51278,hmmpanther:PTHR11772:SF5,hmmpanther:PTHR11772,TIGRFAM_domain:TIGR01536,Gene3D:3.60.20.10,Pfam_domain:PF13537,PIRSF_domain:PIRSF001589,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTATTGGCA	.	5	ESCA
SPDYE3	0	.	GRCh37	7	99917260	99917260	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1419G>A	p.%3D	p.K473K	ENST00000332397	9/11	250	202	47	146	146	0	SPDYE3,synonymous_variant,p.%3D,ENST00000437326,;SPDYE3,synonymous_variant,p.%3D,ENST00000332397,;SPDYE3,non_coding_transcript_exon_variant,,ENST00000380765,;PMS2P1,downstream_gene_variant,,ENST00000431037,;	A	ENSG00000214300	ENST00000332397	Transcript	synonymous_variant	1603	1419	473	K	aaG/aaA	.	.	.	1	SPDYE3	HGNC	35462	protein_coding	YES	CCDS47658.2	ENSP00000329565	SPDE3_HUMAN	.	UPI00004193B6	.	.	.	9/11	.	hmmpanther:PTHR31156:SF10,hmmpanther:PTHR31156,Pfam_domain:PF11357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGAAGACCCA	.	4	ESCA
MAK16	0	.	GRCh37	8	33356668	33356668	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*521C>G	.	.	ENST00000360128	10/10	40	19	21	46	46	0	MAK16,3_prime_UTR_variant,,ENST00000360128,;TTI2,3_prime_UTR_variant,,ENST00000431156,;TTI2,3_prime_UTR_variant,,ENST00000520636,;TTI2,3_prime_UTR_variant,,ENST00000360742,;TTI2,intron_variant,,ENST00000519356,;MAK16,downstream_gene_variant,,ENST00000518389,;	G	ENSG00000198042	ENST00000360128	Transcript	3_prime_UTR_variant	1881	.	.	.	.	.	.	.	1	MAK16	HGNC	13703	protein_coding	YES	CCDS6089.1	ENSP00000353246	MAK16_HUMAN	.	UPI000019080B	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCCTCTTG	.	5	ESCA
DPY19L4	0	.	GRCh37	8	95774026	95774026	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.834C>T	p.%3D	p.F278F	ENST00000414645	8/19	82	58	24	59	59	0	DPY19L4,synonymous_variant,p.%3D,ENST00000414645,;DPY19L4,synonymous_variant,p.%3D,ENST00000523020,;	T	ENSG00000156162	ENST00000414645	Transcript	synonymous_variant	933	834	278	F	ttC/ttT	.	.	.	1	DPY19L4	HGNC	27829	protein_coding	YES	CCDS34924.1	ENSP00000389630	D19L4_HUMAN	.	UPI00001A9D7A	.	.	.	8/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31488:SF2,hmmpanther:PTHR31488,Pfam_domain:PF10034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATTCCTGCT	.	5	ESCA
CORO2A	0	.	GRCh37	9	100895438	100895438	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530G>A	p.Ser177Asn	p.S177N	ENST00000343933	5/12	82	57	25	63	63	0	CORO2A,missense_variant,p.Ser177Asn,ENST00000375077,;CORO2A,missense_variant,p.Ser177Asn,ENST00000343933,;	T	ENSG00000106789	ENST00000343933	Transcript	missense_variant	788	530	177	S/N	aGc/aAc	.	.	.	-1	CORO2A	HGNC	2255	protein_coding	YES	CCDS6735.1	ENSP00000343746	COR2A_HUMAN	.	UPI0000127C45	.	tolerated(0.12)	benign(0.003)	5/12	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF2,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GACAGCTAATC	.	3	ESCA
CERCAM	0	.	GRCh37	9	131196803	131196803	+	Silent	SNP	G	G	A	rs776951394	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1446G>A	p.%3D	p.A482A	ENST00000372838	11/13	22	17	4	28	28	0	CERCAM,synonymous_variant,p.%3D,ENST00000372842,;CERCAM,synonymous_variant,p.%3D,ENST00000372838,;RP11-339B21.10,downstream_gene_variant,,ENST00000610052,;CERCAM,intron_variant,,ENST00000487001,;CERCAM,downstream_gene_variant,,ENST00000472858,;CERCAM,non_coding_transcript_exon_variant,,ENST00000463535,;	A	ENSG00000167123	ENST00000372838	Transcript	synonymous_variant	1844	1446	482	A	gcG/gcA	rs776951394	.	.	1	CERCAM	HGNC	23723	protein_coding	YES	CCDS6901.2	ENSP00000361929	GT253_HUMAN	B7ZBT0_HUMAN,B7ZBS9_HUMAN,B7ZBS8_HUMAN	UPI000046FF85	.	.	.	11/13	.	Low_complexity_(Seg):seg,Pfam_domain:PF01755,hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGGGTGC	byFrequency	5	ESCA
MAMDC4	0	.	GRCh37	9	139753531	139753531	+	Missense_Mutation	SNP	C	C	T	rs752206848	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3031C>T	p.Arg1011Trp	p.R1011W	ENST00000317446	24/27	20	12	8	24	24	0	MAMDC4,missense_variant,p.Arg1090Trp,ENST00000445819,;MAMDC4,missense_variant,p.Arg1011Trp,ENST00000317446,;EDF1,downstream_gene_variant,,ENST00000371648,;EDF1,downstream_gene_variant,,ENST00000371649,;EDF1,downstream_gene_variant,,ENST00000224073,;MAMDC4,non_coding_transcript_exon_variant,,ENST00000485732,;MAMDC4,downstream_gene_variant,,ENST00000481327,;MAMDC4,3_prime_UTR_variant,,ENST00000479475,;	T	ENSG00000177943	ENST00000317446	Transcript	missense_variant	3081	3031	1011	R/W	Cgg/Tgg	rs752206848	.	.	1	MAMDC4	HGNC	24083	protein_coding	YES	CCDS7010.1	ENSP00000319388	AEGP_HUMAN	.	UPI0000237828	.	deleterious(0.02)	probably_damaging(0.972)	24/27	.	PROSITE_profiles:PS50060,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF63,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCGGCGGCAC	.	2	ESCA
SPATA31A6	0	.	GRCh37	9	43628646	43628646	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296C>A	p.Ser99Ter	p.S99*	ENST00000332857	3/4	138	95	43	114	114	0	SPATA31A6,stop_gained,p.Ser99Ter,ENST00000332857,;SPATA31A6,non_coding_transcript_exon_variant,,ENST00000496386,;	T	ENSG00000185775	ENST00000332857	Transcript	stop_gained	325	296	99	S/*	tCa/tAa	.	.	.	-1	SPATA31A6	HGNC	32006	protein_coding	YES	CCDS47973.1	ENSP00000329825	S31A6_HUMAN	.	UPI0000197F6E	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21859:SF9,hmmpanther:PTHR21859,Pfam_domain:PF15371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTGAAAGA	.	5	ESCA
ZFAND5	0	.	GRCh37	9	74970277	74970277	+	3'UTR	SNP	G	G	C	rs549304936	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*592C>G	.	.	ENST00000237937	6/6	13	10	3	24	24	0	ZFAND5,3_prime_UTR_variant,,ENST00000237937,;ZFAND5,3_prime_UTR_variant,,ENST00000376960,;ZFAND5,3_prime_UTR_variant,,ENST00000376962,;ZFAND5,downstream_gene_variant,,ENST00000343431,;ZFAND5,downstream_gene_variant,,ENST00000376956,;ZFAND5,non_coding_transcript_exon_variant,,ENST00000488164,;ZFAND5,downstream_gene_variant,,ENST00000471197,;	C	ENSG00000107372	ENST00000237937	Transcript	3_prime_UTR_variant	1792	.	.	.	.	rs549304936	.	.	-1	ZFAND5	HGNC	13008	protein_coding	YES	CCDS6642.1	ENSP00000237937	ZFAN5_HUMAN	.	UPI000013C322	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCACAGAATGT	byCluster	2	ESCA
ZFAND5	0	.	GRCh37	9	74970520	74970520	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*349C>A	.	.	ENST00000237937	6/6	38	27	11	29	29	0	ZFAND5,3_prime_UTR_variant,,ENST00000376962,;ZFAND5,3_prime_UTR_variant,,ENST00000237937,;ZFAND5,3_prime_UTR_variant,,ENST00000376960,;ZFAND5,downstream_gene_variant,,ENST00000343431,;ZFAND5,downstream_gene_variant,,ENST00000376956,;ZFAND5,non_coding_transcript_exon_variant,,ENST00000488164,;ZFAND5,downstream_gene_variant,,ENST00000471197,;ZFAND5,downstream_gene_variant,,ENST00000487330,;	T	ENSG00000107372	ENST00000237937	Transcript	3_prime_UTR_variant	1549	.	.	.	.	.	.	.	-1	ZFAND5	HGNC	13008	protein_coding	YES	CCDS6642.1	ENSP00000237937	ZFAN5_HUMAN	.	UPI000013C322	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCTTGATTAC	.	2	ESCA
UBE2A	0	.	GRCh37	X	118718122	118718122	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*904T>C	.	.	ENST00000371558	6/6	56	5	50	34	34	0	UBE2A,3_prime_UTR_variant,,ENST00000371569,;UBE2A,3_prime_UTR_variant,,ENST00000371558,;UBE2A,downstream_gene_variant,,ENST00000346330,;NKRF,downstream_gene_variant,,ENST00000304449,;NKRF,downstream_gene_variant,,ENST00000371527,;NKRF,downstream_gene_variant,,ENST00000542113,;NKRF,downstream_gene_variant,,ENST00000487600,;	C	ENSG00000077721	ENST00000371558	Transcript	3_prime_UTR_variant	1537	.	.	.	.	.	.	.	1	UBE2A	HGNC	12472	protein_coding	YES	CCDS14580.1	ENSP00000360613	UBE2A_HUMAN	Q8WXB3_HUMAN,B4DWT6_HUMAN	UPI00000043A0	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTATTGCTG	.	5	ESCA
ACTRT1	0	.	GRCh37	X	127185461	127185461	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725G>C	p.Arg242Thr	p.R242T	ENST00000371124	1/1	23	14	9	19	19	0	ACTRT1,missense_variant,p.Arg242Thr,ENST00000371124,;	G	ENSG00000123165	ENST00000371124	Transcript	missense_variant	922	725	242	R/T	aGa/aCa	COSM3557649	.	.	-1	ACTRT1	HGNC	24027	protein_coding	YES	CCDS14611.1	ENSP00000360165	ACTT1_HUMAN	.	UPI0000072276	.	tolerated(0.13)	benign(0.039)	1/1	.	hmmpanther:PTHR11937:SF153,hmmpanther:PTHR11937,Gene3D:3.90.640.10,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067,Prints_domain:PR00190	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTCTGTAT	.	5	ESCA
ATP11C	0	.	GRCh37	X	138864830	138864830	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1837A>G	p.Arg613Gly	p.R613G	ENST00000327569	18/30	53	8	45	45	45	0	ATP11C,missense_variant,p.Arg613Gly,ENST00000370543,;ATP11C,missense_variant,p.Arg613Gly,ENST00000361648,;ATP11C,missense_variant,p.Arg613Gly,ENST00000327569,;ATP11C,missense_variant,p.Arg610Gly,ENST00000370557,;ATP11C,missense_variant,p.Arg613Gly,ENST00000359686,;ATP11C,missense_variant,p.Arg165Gly,ENST00000422228,;ATP11C,non_coding_transcript_exon_variant,,ENST00000460773,;ATP11C,upstream_gene_variant,,ENST00000471746,;	C	ENSG00000101974	ENST00000327569	Transcript	missense_variant	1936	1837	613	R/G	Aga/Gga	.	.	.	-1	ATP11C	HGNC	13554	protein_coding	YES	CCDS14668.1	ENSP00000332756	AT11C_HUMAN	.	UPI000036777E	.	tolerated(0.4)	benign(0.065)	18/30	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF38,Pfam_domain:PF12710,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF81660,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTCTTTCAT	.	5	ESCA
SPRY3	0	.	GRCh37	X	155007365	155007365	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2965G>T	.	.	ENST00000302805	2/2	32	22	9	20	20	0	SPRY3,3_prime_UTR_variant,,ENST00000302805,;	T	ENSG00000168939	ENST00000302805	Transcript	3_prime_UTR_variant	4263	.	.	.	.	.	.	.	1	SPRY3	HGNC	11271	protein_coding	YES	CCDS14769.4	ENSP00000302978	SPY3_HUMAN	.	UPI0000135E98	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAAAGAACTC	.	5	ESCA
ARSE	0	.	GRCh37	X	2861176	2861176	+	Silent	SNP	C	C	T	rs187110605	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1056G>A	p.%3D	p.S352S	ENST00000381134	8/11	23	6	17	28	28	0	ARSE,synonymous_variant,p.%3D,ENST00000545496,;ARSE,synonymous_variant,p.%3D,ENST00000540563,;ARSE,synonymous_variant,p.%3D,ENST00000381134,;	T	ENSG00000157399	ENST00000381134	Transcript	synonymous_variant	1123	1056	352	S	tcG/tcA	rs187110605	.	.	-1	ARSE	HGNC	719	protein_coding	YES	CCDS14122.1	ENSP00000370526	ARSE_HUMAN	C9J5G7_HUMAN	UPI000049E10C	.	.	.	8/11	.	Superfamily_domains:SSF53649,Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF63	T:0.0005	T:0	T:0	.	T:0.002	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D353N|c.1057G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATCCGACGT	byFrequency|byCluster|by1000G	5	ESCA
CLCN5	0	.	GRCh37	X	49857291	49857291	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*415T>C	.	.	ENST00000376088	15/15	16	3	13	12	12	0	CLCN5,3_prime_UTR_variant,,ENST00000307367,;CLCN5,3_prime_UTR_variant,,ENST00000376088,;CLCN5,downstream_gene_variant,,ENST00000376091,;CLCN5,downstream_gene_variant,,ENST00000376108,;	C	ENSG00000171365	ENST00000376088	Transcript	3_prime_UTR_variant	3507	.	.	.	.	.	.	.	1	CLCN5	HGNC	2023	protein_coding	YES	CCDS48115.1	ENSP00000365256	CLCN5_HUMAN	.	UPI0000212052	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTACTGGAAG	.	5	ESCA
PCDH11X	0	.	GRCh37	X	91642780	91642780	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A5U7-01A-11D-A31U-09	TCGA-LN-A5U7-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3191G>A	p.Ser1064Asn	p.S1064N	ENST00000373094	5/7	24	11	13	27	27	0	PCDH11X,missense_variant,p.Ser1064Asn,ENST00000406881,;PCDH11X,missense_variant,p.Ser1054Asn,ENST00000373097,;PCDH11X,missense_variant,p.Ser1064Asn,ENST00000373094,;PCDH11X,missense_variant,p.Ser1027Asn,ENST00000373088,;PCDH11X,missense_variant,p.Ser1054Asn,ENST00000361655,;PCDH11X,missense_variant,p.Ser1027Asn,ENST00000298274,;PCDH11X,intron_variant,,ENST00000504220,;	A	ENSG00000102290	ENST00000373094	Transcript	missense_variant	4036	3191	1064	S/N	aGc/aAc	.	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	tolerated(0.14)	probably_damaging(0.995)	5/7	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAAGCAGCA	.	5	ESCA
KIAA1598	0	.	GRCh37	10	118689440	118689440	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932A>T	p.Glu311Val	p.E311V	ENST00000355371	10/17	33	30	3	58	58	0	KIAA1598,missense_variant,p.Glu311Val,ENST00000260777,;KIAA1598,missense_variant,p.Glu311Val,ENST00000392903,;KIAA1598,missense_variant,p.Glu251Val,ENST00000392901,;KIAA1598,missense_variant,p.Glu311Val,ENST00000355371,;KIAA1598,non_coding_transcript_exon_variant,,ENST00000497044,;	A	ENSG00000187164	ENST00000355371	Transcript	missense_variant	1430	932	311	E/V	gAg/gTg	.	.	.	-1	KIAA1598	HGNC	29319	protein_coding	YES	CCDS44482.1	ENSP00000347532	SHOT1_HUMAN	.	UPI0000404A8F	.	deleterious(0)	possibly_damaging(0.872)	10/17	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23213:SF179,hmmpanther:PTHR23213	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAGCTCCAGT	.	2	ESCA
ARHGAP12	0	.	GRCh37	10	32101634	32101634	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1951+1G>T	.	p.X651_splice	ENST00000344936	.	108	75	32	147	147	0	ARHGAP12,splice_donor_variant,,ENST00000344936,;ARHGAP12,splice_donor_variant,,ENST00000311380,;ARHGAP12,splice_donor_variant,,ENST00000375245,;ARHGAP12,splice_donor_variant,,ENST00000375250,;ARHGAP12,splice_donor_variant,,ENST00000396144,;ARHGAP12,splice_donor_variant,,ENST00000492028,;ARHGAP12,non_coding_transcript_exon_variant,,ENST00000497103,;ARHGAP12,upstream_gene_variant,,ENST00000497085,;ARHGAP12,upstream_gene_variant,,ENST00000493008,;	A	ENSG00000165322	ENST00000344936	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	ARHGAP12	HGNC	16348	protein_coding	YES	CCDS7170.1	ENSP00000345808	RHG12_HUMAN	D3DRX4_HUMAN	UPI000007445E	.	.	.	.	15/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAACCTTTA	.	5	ESCA
NCOA4	0	.	GRCh37	10	51586352	51586352	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1828T>C	p.Phe610Leu	p.F610L	ENST00000452682	10/12	63	44	18	72	72	0	NCOA4,missense_variant,p.Phe494Leu,ENST00000430396,;NCOA4,missense_variant,p.Phe610Leu,ENST00000452682,;NCOA4,missense_variant,p.Phe428Leu,ENST00000414907,;NCOA4,missense_variant,p.Phe594Leu,ENST00000344348,;NCOA4,missense_variant,p.Phe594Leu,ENST00000443446,;NCOA4,missense_variant,p.Phe594Leu,ENST00000374087,;NCOA4,missense_variant,p.Phe610Leu,ENST00000438493,;NCOA4,synonymous_variant,p.%3D,ENST00000374082,;NCOA4,downstream_gene_variant,,ENST00000431200,;NCOA4,downstream_gene_variant,,ENST00000498586,;	C	ENSG00000138293	ENST00000452682	Transcript	missense_variant	2080	1828	610	F/L	Ttt/Ctt	.	.	.	1	NCOA4	HGNC	7671	protein_coding	YES	CCDS44394.1	ENSP00000395465	NCOA4_HUMAN	.	UPI0001932817	.	deleterious(0)	probably_damaging(0.997)	10/12	.	hmmpanther:PTHR17085,hmmpanther:PTHR17085:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTCTTTGCC	.	5	ESCA
BMPR1A	0	.	GRCh37	10	88635670	88635670	+	5'UTR	SNP	C	C	A	rs531097871	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-106C>A	.	.	ENST00000372037	3/13	17	11	6	21	21	0	BMPR1A,5_prime_UTR_variant,,ENST00000372037,;BMPR1A,non_coding_transcript_exon_variant,,ENST00000480152,;	A	ENSG00000107779	ENST00000372037	Transcript	5_prime_UTR_variant	432	.	.	.	.	rs531097871	.	.	1	BMPR1A	HGNC	1076	protein_coding	YES	CCDS7378.1	ENSP00000361107	BMR1A_HUMAN	.	UPI000006EB08	.	.	.	3/13	.	.	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTGCGATCT	byFrequency|by1000G	5	ESCA
PTEN	0	.	GRCh37	10	89653835	89653835	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.133delG	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	2/9	75	53	22	72	72	0	PTEN,frameshift_variant,p.Val45TyrfsTer9,ENST00000371953,;PTEN,non_coding_transcript_exon_variant,,ENST00000462694,;	-	ENSG00000171862	ENST00000371953	Transcript	frameshift_variant	1490	133	45	V/X	Gta/ta	COSM1349477,COSM249824,COSM921065	.	.	1	PTEN	HGNC	9588	protein_coding	YES	CCDS31238.1	ENSP00000361021	PTEN_HUMAN	F6KD01_HUMAN,H6WA51_HUMAN,H6WA46_HUMAN	UPI00001328C5	.	.	.	2/9	.	PROSITE_profiles:PS51181,hmmpanther:PTHR12305,Gene3D:3.90.190.10,PIRSF_domain:PIRSF038025,SMART_domains:SM00404,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.0?|c.1_1212del1212|28,CODON|p.G44D|c.131G>A|4,BUFFER|p.L42R|c.125T>G|6,BUFFER|p.G44G|c.132C>T|4,BUFFER|p.R47G|c.139A>G|4,BUFFER|p.R47M|c.140G>T|3	INDELOCATOR*|VARSCANI*|PINDEL	GAAGGCGTATAC	.	3	ESCA
NXPE2	0	.	GRCh37	11	114577407	114577407	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1435C>G	p.Arg479Gly	p.R479G	ENST00000389586	6/6	86	82	4	85	85	0	NXPE2,missense_variant,p.Arg479Gly,ENST00000389586,;NXPE2,intron_variant,,ENST00000375475,;	G	ENSG00000204361	ENST00000389586	Transcript	missense_variant	1625	1435	479	R/G	Cga/Gga	.	.	.	1	NXPE2	HGNC	26331	protein_coding	YES	CCDS44738.1	ENSP00000374237	NXPE2_HUMAN	.	UPI0001662547	.	deleterious(0)	probably_damaging(0.97)	6/6	.	hmmpanther:PTHR16165:SF6,hmmpanther:PTHR16165	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTGCGAAGC	.	2	ESCA
KMT2A	0	.	GRCh37	11	118375390	118375390	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8783T>A	p.Leu2928Gln	p.L2928Q	ENST00000534358	27/36	51	24	27	52	52	0	KMT2A,missense_variant,p.Leu2925Gln,ENST00000389506,;KMT2A,missense_variant,p.Leu2887Gln,ENST00000354520,;KMT2A,missense_variant,p.Leu2928Gln,ENST00000534358,;KMT2A,upstream_gene_variant,,ENST00000534085,;KMT2A,downstream_gene_variant,,ENST00000528278,;	A	ENSG00000118058	ENST00000534358	Transcript	missense_variant	8806	8783	2928	L/Q	cTa/cAa	.	.	.	1	KMT2A	HGNC	7132	protein_coding	YES	CCDS55791.1	ENSP00000436786	KMT2A_HUMAN	Q9UPD0_HUMAN,Q9UM91_HUMAN,Q9HBJ4_HUMAN,B4DIJ7_HUMAN	UPI0001E5E732	.	.	probably_damaging(0.991)	27/36	.	hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCTAGAGC	.	5	ESCA
FAR1	0	.	GRCh37	11	13749173	13749173	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1328A>T	p.Lys443Met	p.K443M	ENST00000354817	11/12	59	29	30	79	79	0	FAR1,missense_variant,p.Lys443Met,ENST00000354817,;FAR1,missense_variant,p.Lys67Met,ENST00000532502,;	T	ENSG00000197601	ENST00000354817	Transcript	missense_variant	1472	1328	443	K/M	aAg/aTg	.	.	.	1	FAR1	HGNC	26222	protein_coding	YES	CCDS7813.1	ENSP00000346874	FACR1_HUMAN	E9PPB8_HUMAN	UPI00000477EF	.	tolerated(0.06)	probably_damaging(0.922)	11/12	.	hmmpanther:PTHR11011,Pfam_domain:PF03015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGAAGTACG	.	5	ESCA
SLC17A6	0	.	GRCh37	11	22387154	22387154	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.810G>A	p.%3D	p.K270K	ENST00000263160	7/12	113	73	39	108	108	0	SLC17A6,synonymous_variant,p.%3D,ENST00000263160,;CTD-2140G10.4,upstream_gene_variant,,ENST00000534543,;SLC17A6,downstream_gene_variant,,ENST00000534115,;	A	ENSG00000091664	ENST00000263160	Transcript	synonymous_variant	1247	810	270	K	aaG/aaA	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	7/12	.	PROSITE_profiles:PS50850,hmmpanther:PTHR11662:SF201,hmmpanther:PTHR11662,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAAGCATCC	.	5	ESCA
KCNQ1	0	.	GRCh37	11	2869032	2869032	+	Silent	SNP	C	C	A	rs774101297	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1830C>A	p.%3D	p.T610T	ENST00000155840	16/16	37	29	8	28	28	0	KCNQ1,synonymous_variant,p.%3D,ENST00000155840,;KCNQ1,synonymous_variant,p.%3D,ENST00000335475,;KCNQ1-AS1,intron_variant,,ENST00000440887,;KCNQ1,non_coding_transcript_exon_variant,,ENST00000526095,;	A	ENSG00000053918	ENST00000155840	Transcript	synonymous_variant	1938	1830	610	T	acC/acA	rs774101297,COSM1353360	.	.	1	KCNQ1	HGNC	6294	protein_coding	YES	CCDS7736.1	ENSP00000155840	KCNQ1_HUMAN	Q96AI9_HUMAN,A0FIK7_HUMAN	UPI000004662D	.	.	.	16/16	.	Coiled-coils_(Ncoils):Coil,Pfam_domain:PF03520,Prints_domain:PR01460	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACCGACAT	.	5	ESCA
PGAP2	0	.	GRCh37	11	3845137	3845137	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.373A>G	p.Ser125Gly	p.S125G	ENST00000278243	4/7	15	11	4	16	16	0	PGAP2,stop_lost,p.Ter137TrpextTer?,ENST00000532535,;PGAP2,missense_variant,p.Glu67Gly,ENST00000465307,;PGAP2,missense_variant,p.Ser95Gly,ENST00000459679,;PGAP2,missense_variant,p.Ser121Gly,ENST00000396986,;PGAP2,missense_variant,p.Ser64Gly,ENST00000463452,;PGAP2,missense_variant,p.Ser121Gly,ENST00000300730,;PGAP2,missense_variant,p.Ser155Gly,ENST00000464906,;PGAP2,missense_variant,p.Ser94Gly,ENST00000464261,;PGAP2,missense_variant,p.Glu82Gly,ENST00000532523,;PGAP2,missense_variant,p.Ser125Gly,ENST00000396991,;PGAP2,missense_variant,p.Ser125Gly,ENST00000278243,;PGAP2,missense_variant,p.Glu17Gly,ENST00000396993,;PGAP2,missense_variant,p.Ser64Gly,ENST00000493547,;PGAP2,missense_variant,p.Ser64Gly,ENST00000469307,;PGAP2,5_prime_UTR_variant,,ENST00000496834,;PGAP2,5_prime_UTR_variant,,ENST00000479072,;PGAP2,intron_variant,,ENST00000464441,;RHOG,downstream_gene_variant,,ENST00000396978,;RHOG,downstream_gene_variant,,ENST00000533217,;RHOG,downstream_gene_variant,,ENST00000351018,;RHOG,downstream_gene_variant,,ENST00000396979,;AC090587.2,downstream_gene_variant,,ENST00000507938,;PGAP2,non_coding_transcript_exon_variant,,ENST00000489571,;PGAP2,non_coding_transcript_exon_variant,,ENST00000532017,;PGAP2,stop_lost,p.Ter43TrpextTer65,ENST00000492246,;PGAP2,stop_lost,p.Ter35TrpextTer65,ENST00000490830,;PGAP2,stop_lost,p.Ter36TrpextTer65,ENST00000464229,;PGAP2,3_prime_UTR_variant,,ENST00000524661,;PGAP2,3_prime_UTR_variant,,ENST00000528216,;PGAP2,non_coding_transcript_exon_variant,,ENST00000495026,;PGAP2,non_coding_transcript_exon_variant,,ENST00000487112,;PGAP2,non_coding_transcript_exon_variant,,ENST00000529944,;PGAP2,non_coding_transcript_exon_variant,,ENST00000465237,;PGAP2,non_coding_transcript_exon_variant,,ENST00000525937,;PGAP2,non_coding_transcript_exon_variant,,ENST00000478773,;PGAP2,non_coding_transcript_exon_variant,,ENST00000527810,;PGAP2,non_coding_transcript_exon_variant,,ENST00000483829,;PGAP2,non_coding_transcript_exon_variant,,ENST00000464590,;PGAP2,non_coding_transcript_exon_variant,,ENST00000534498,;PGAP2,intron_variant,,ENST00000485602,;PGAP2,intron_variant,,ENST00000475884,;PGAP2,intron_variant,,ENST00000477358,;PGAP2,upstream_gene_variant,,ENST00000528526,;	G	ENSG00000148985	ENST00000278243	Transcript	missense_variant	574	373	125	S/G	Agc/Ggc	.	.	.	1	PGAP2	HGNC	17893	protein_coding	YES	CCDS7747.1	ENSP00000278243	PGAP2_HUMAN	E9PPF7_HUMAN	UPI000006E9EC	.	deleterious(0.01)	possibly_damaging(0.766)	4/7	.	hmmpanther:PTHR12892:SF11,hmmpanther:PTHR12892,Pfam_domain:PF10277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGTGAGCTCA	.	5	ESCA
OR1S1	0	.	GRCh37	11	57982300	57982300	+	Silent	SNP	G	G	T	rs139788490	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84G>T	p.%3D	p.L28L	ENST00000309433	1/1	94	71	23	117	117	0	OR1S1,synonymous_variant,p.%3D,ENST00000309433,;	T	ENSG00000172774	ENST00000309433	Transcript	synonymous_variant	84	84	28	L	ctG/ctT	rs139788490	.	.	1	OR1S1	HGNC	8227	protein_coding	YES	CCDS31546.1	ENSP00000311688	OR1S1_HUMAN	.	UPI0000041C51	.	.	.	1/1	.	hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF180,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	T:0.0004	T:0	T:0	.	T:0	T:0.002	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTGGGATT	byFrequency|byCluster|by1000G	5	ESCA
POLD3	0	.	GRCh37	11	74324010	74324010	+	Missense_Mutation	SNP	A	A	G	rs142882622	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347A>G	p.Asn116Ser	p.N116S	ENST00000263681	5/12	32	24	8	34	34	0	POLD3,missense_variant,p.Asn77Ser,ENST00000528481,;POLD3,missense_variant,p.Asn10Ser,ENST00000532497,;POLD3,missense_variant,p.Asn77Ser,ENST00000530511,;POLD3,missense_variant,p.Asn77Ser,ENST00000527458,;POLD3,missense_variant,p.Asn77Ser,ENST00000531615,;POLD3,missense_variant,p.Asn116Ser,ENST00000263681,;	G	ENSG00000077514	ENST00000263681	Transcript	missense_variant	476	347	116	N/S	aAt/aGt	rs142882622	.	.	1	POLD3	HGNC	20932	protein_coding	YES	CCDS8233.1	ENSP00000263681	DPOD3_HUMAN	Q32N00_HUMAN,Q32MZ9_HUMAN,E9PRK3_HUMAN,E9PNC0_HUMAN,E9PM91_HUMAN,B4DMA6_HUMAN	UPI000012973E	.	tolerated(0.34)	benign(0.093)	5/12	.	hmmpanther:PTHR17598,Pfam_domain:PF09507	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCAATACTG	byCluster|by1000G	5	ESCA
TSKU	0	.	GRCh37	11	76508883	76508883	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1161T>A	.	.	ENST00000527881	2/2	41	26	15	59	59	0	TSKU,3_prime_UTR_variant,,ENST00000333090,;TSKU,3_prime_UTR_variant,,ENST00000527881,;TSKU,downstream_gene_variant,,ENST00000533752,;TSKU,downstream_gene_variant,,ENST00000525167,;RP11-21L23.2,upstream_gene_variant,,ENST00000566747,;	A	ENSG00000182704	ENST00000527881	Transcript	3_prime_UTR_variant	3249	.	.	.	.	.	.	.	1	TSKU	HGNC	28850	protein_coding	YES	CCDS8246.1	ENSP00000434847	TSK_HUMAN	E9PN12_HUMAN,E9PLG7_HUMAN	UPI000006E7B7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTCTTCATT	.	5	ESCA
ZNF143	0	.	GRCh37	11	9534025	9534025	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1406A>G	p.Gln469Arg	p.Q469R	ENST00000396602	13/16	50	33	17	69	69	0	ZNF143,missense_variant,p.Gln438Arg,ENST00000396597,;ZNF143,missense_variant,p.Gln469Arg,ENST00000396602,;ZNF143,missense_variant,p.Gln468Arg,ENST00000530463,;ZNF143,missense_variant,p.Gln468Arg,ENST00000396604,;ZNF143,missense_variant,p.Gln441Arg,ENST00000299606,;ZNF143,upstream_gene_variant,,ENST00000447186,;	G	ENSG00000166478	ENST00000396602	Transcript	missense_variant	1525	1406	469	Q/R	cAg/cGg	.	.	.	1	ZNF143	HGNC	12928	protein_coding	YES	CCDS7799.2	ENSP00000379847	ZN143_HUMAN	E9PPB0_HUMAN,E9PJF2_HUMAN,C9JTC5_HUMAN,C9JCG1_HUMAN,C9J2G7_HUMAN	UPI00001F9D01	.	tolerated(0.56)	benign(0.012)	13/16	.	hmmpanther:PTHR11389:SF362,hmmpanther:PTHR11389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCCAGATTA	.	5	ESCA
CMKLR1	0	.	GRCh37	12	108686629	108686629	+	Missense_Mutation	SNP	C	C	A	rs776930995	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111G>T	p.Arg37Ser	p.R37S	ENST00000312143	3/3	37	31	6	47	47	0	CMKLR1,missense_variant,p.Arg37Ser,ENST00000312143,;CMKLR1,missense_variant,p.Arg37Ser,ENST00000550573,;CMKLR1,missense_variant,p.Arg37Ser,ENST00000549466,;CMKLR1,missense_variant,p.Arg35Ser,ENST00000397688,;CMKLR1,missense_variant,p.Arg35Ser,ENST00000552995,;CMKLR1,missense_variant,p.Arg37Ser,ENST00000412676,;CMKLR1,missense_variant,p.Arg37Ser,ENST00000550402,;	A	ENSG00000174600	ENST00000312143	Transcript	missense_variant	475	111	37	R/S	agG/agT	rs776930995	.	.	-1	CMKLR1	HGNC	2121	protein_coding	YES	CCDS44965.1	ENSP00000311733	CML1_HUMAN	F8VYN7_HUMAN,F8VSC8_HUMAN	UPI0000127BD4	.	tolerated(0.72)	benign(0.007)	3/3	.	Prints_domain:PR01126,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR24227:SF2,hmmpanther:PTHR24227	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCACCCTGGC	.	3	ESCA
TAS2R46	0	.	GRCh37	12	11214379	11214379	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.515T>C	p.Met172Thr	p.M172T	ENST00000533467	1/1	67	34	33	63	63	0	TAS2R46,missense_variant,p.Met172Thr,ENST00000533467,;TAS2R14,intron_variant,,ENST00000381852,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000546265,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;	G	ENSG00000226761	ENST00000533467	Transcript	missense_variant	515	515	172	M/T	aTg/aCg	.	.	.	-1	TAS2R46	HGNC	18877	protein_coding	YES	CCDS53748.1	ENSP00000436450	T2R46_HUMAN	Q50KH0_HUMAN	UPI000000D821	.	tolerated(0.47)	benign(0.002)	1/1	.	hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF48,Pfam_domain:PF05296,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTACATTGCA	.	5	ESCA
DTX1	0	.	GRCh37	12	113534587	113534587	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1706C>T	p.Thr569Met	p.T569M	ENST00000257600	9/9	66	40	26	85	85	0	DTX1,missense_variant,p.Thr569Met,ENST00000257600,;RASAL1,downstream_gene_variant,,ENST00000261729,;RASAL1,downstream_gene_variant,,ENST00000548055,;RASAL1,downstream_gene_variant,,ENST00000446861,;RASAL1,downstream_gene_variant,,ENST00000546530,;DTX1,non_coding_transcript_exon_variant,,ENST00000547974,;RASAL1,downstream_gene_variant,,ENST00000549444,;DTX1,downstream_gene_variant,,ENST00000553140,;DTX1,downstream_gene_variant,,ENST00000547730,;RASAL1,downstream_gene_variant,,ENST00000546727,;RASAL1,downstream_gene_variant,,ENST00000551051,;	T	ENSG00000135144	ENST00000257600	Transcript	missense_variant	2209	1706	569	T/M	aCg/aTg	.	.	.	1	DTX1	HGNC	3060	protein_coding	YES	CCDS9164.1	ENSP00000257600	DTX1_HUMAN	.	UPI000013CF71	.	deleterious(0)	probably_damaging(0.999)	9/9	.	hmmpanther:PTHR12622,hmmpanther:PTHR12622:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCACGGGCG	.	5	ESCA
CREBL2	0	.	GRCh37	12	12796243	12796243	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1311A>G	.	.	ENST00000228865	4/4	25	17	8	20	20	0	CREBL2,3_prime_UTR_variant,,ENST00000228865,;	G	ENSG00000111269	ENST00000228865	Transcript	3_prime_UTR_variant	1955	.	.	.	.	.	.	.	1	CREBL2	HGNC	2350	protein_coding	YES	CCDS8651.1	ENSP00000228865	CRBL2_HUMAN	.	UPI0000070749	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATATGATACAC	.	2	ESCA
PIK3C2G	0	.	GRCh37	12	18552628	18552628	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2039A>G	p.Tyr680Cys	p.Y680C	ENST00000433979	15/32	68	47	20	52	52	0	PIK3C2G,missense_variant,p.Tyr721Cys,ENST00000538779,;PIK3C2G,missense_variant,p.Tyr680Cys,ENST00000266497,;PIK3C2G,missense_variant,p.Tyr680Cys,ENST00000433979,;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,;	G	ENSG00000139144	ENST00000433979	Transcript	missense_variant	2155	2039	680	Y/C	tAt/tGt	.	.	.	1	PIK3C2G	HGNC	8973	protein_coding	YES	CCDS44839.1	ENSP00000404845	P3C2G_HUMAN	.	UPI000013D6EF	.	tolerated(0.1)	probably_damaging(0.971)	15/32	.	PROSITE_profiles:PS51545,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF29,Gene3D:1.25.40.70,Pfam_domain:PF00613,SMART_domains:SM00145,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTATCGCT	.	5	ESCA
CSRNP2	0	.	GRCh37	12	51458091	51458091	+	Missense_Mutation	SNP	C	C	A	rs763150966	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1070G>T	p.Gly357Val	p.G357V	ENST00000228515	5/5	38	30	7	43	43	0	CSRNP2,missense_variant,p.Gly357Val,ENST00000228515,;LETMD1,downstream_gene_variant,,ENST00000547008,;LETMD1,downstream_gene_variant,,ENST00000553043,;LETMD1,downstream_gene_variant,,ENST00000552739,;CSRNP2,downstream_gene_variant,,ENST00000548206,;LETMD1,downstream_gene_variant,,ENST00000418425,;LETMD1,downstream_gene_variant,,ENST00000551931,;LETMD1,downstream_gene_variant,,ENST00000550929,;LETMD1,downstream_gene_variant,,ENST00000262055,;LETMD1,downstream_gene_variant,,ENST00000547256,;LETMD1,downstream_gene_variant,,ENST00000380123,;LETMD1,downstream_gene_variant,,ENST00000547660,;LETMD1,downstream_gene_variant,,ENST00000548516,;LETMD1,downstream_gene_variant,,ENST00000549395,;LETMD1,downstream_gene_variant,,ENST00000546814,;LETMD1,downstream_gene_variant,,ENST00000552645,;LETMD1,downstream_gene_variant,,ENST00000550100,;LETMD1,downstream_gene_variant,,ENST00000550274,;LETMD1,downstream_gene_variant,,ENST00000547555,;LETMD1,downstream_gene_variant,,ENST00000380135,;LETMD1,downstream_gene_variant,,ENST00000547318,;LETMD1,downstream_gene_variant,,ENST00000547877,;LETMD1,downstream_gene_variant,,ENST00000549686,;	A	ENSG00000110925	ENST00000228515	Transcript	missense_variant	1368	1070	357	G/V	gGt/gTt	rs763150966	.	.	-1	CSRNP2	HGNC	16006	protein_coding	YES	CCDS8807.1	ENSP00000228515	CSRN2_HUMAN	F8W1G8_HUMAN,F8VZY2_HUMAN,F8VVN1_HUMAN,F8VTU0_HUMAN	UPI0000073111	.	deleterious(0)	probably_damaging(0.967)	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13580:SF6,hmmpanther:PTHR13580	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACACCCAGG	.	5	ESCA
PFDN5	0	.	GRCh37	12	53690058	53690058	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.206C>T	p.Ser69Phe	p.S69F	ENST00000551018	3/6	37	26	10	53	53	0	PFDN5,missense_variant,p.Ser69Phe,ENST00000334478,;PFDN5,missense_variant,p.Ser69Phe,ENST00000551018,;PFDN5,intron_variant,,ENST00000550846,;PFDN5,intron_variant,,ENST00000351500,;PFDN5,intron_variant,,ENST00000549759,;C12orf10,upstream_gene_variant,,ENST00000549488,;ESPL1,downstream_gene_variant,,ENST00000552462,;ESPL1,downstream_gene_variant,,ENST00000257934,;C12orf10,upstream_gene_variant,,ENST00000548632,;C12orf10,upstream_gene_variant,,ENST00000267103,;RP11-680A11.5,downstream_gene_variant,,ENST00000550263,;PFDN5,splice_region_variant,,ENST00000549995,;PFDN5,splice_region_variant,,ENST00000552548,;PFDN5,splice_region_variant,,ENST00000550513,;PFDN5,non_coding_transcript_exon_variant,,ENST00000547228,;PFDN5,non_coding_transcript_exon_variant,,ENST00000550069,;PFDN5,intron_variant,,ENST00000547130,;PFDN5,intron_variant,,ENST00000552341,;PFDN5,intron_variant,,ENST00000243040,;PFDN5,intron_variant,,ENST00000551223,;PFDN5,intron_variant,,ENST00000552742,;PFDN5,intron_variant,,ENST00000550880,;C12orf10,upstream_gene_variant,,ENST00000551670,;PFDN5,upstream_gene_variant,,ENST00000553171,;ESPL1,downstream_gene_variant,,ENST00000549154,;C12orf10,upstream_gene_variant,,ENST00000548845,;PFDN5,upstream_gene_variant,,ENST00000550964,;C12orf10,upstream_gene_variant,,ENST00000551131,;ESPL1,downstream_gene_variant,,ENST00000552671,;PFDN5,upstream_gene_variant,,ENST00000548984,;	T	ENSG00000123349	ENST00000551018	Transcript	missense_variant	483	206	69	S/F	tCt/tTt	.	.	.	1	PFDN5	HGNC	8869	protein_coding	YES	CCDS8853.1	ENSP00000447942	PFD5_HUMAN	.	UPI00000009FD	.	deleterious(0)	probably_damaging(0.988)	3/6	.	HAMAP:MF_00308,hmmpanther:PTHR12674,Pfam_domain:PF02996,Gene3D:1.10.287.370,TIGRFAM_domain:TIGR00293,Superfamily_domains:SSF46579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTTCTGTAT	.	5	ESCA
NOP9	0	.	GRCh37	14	24769638	24769638	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272A>G	p.Lys91Arg	p.K91R	ENST00000267425	2/10	49	27	22	80	79	0	NOP9,missense_variant,p.Lys91Arg,ENST00000267425,;NOP9,missense_variant,p.Lys91Arg,ENST00000396802,;DHRS1,upstream_gene_variant,,ENST00000288111,;CIDEB,downstream_gene_variant,,ENST00000554411,;CIDEB,downstream_gene_variant,,ENST00000336557,;NOP9,upstream_gene_variant,,ENST00000557362,;CIDEB,downstream_gene_variant,,ENST00000258807,;DHRS1,upstream_gene_variant,,ENST00000396813,;DHRS1,upstream_gene_variant,,ENST00000559483,;DHRS1,upstream_gene_variant,,ENST00000561273,;DHRS1,upstream_gene_variant,,ENST00000558114,;DHRS1,upstream_gene_variant,,ENST00000558340,;DHRS1,upstream_gene_variant,,ENST00000560991,;	G	ENSG00000196943	ENST00000267425	Transcript	missense_variant	365	272	91	K/R	aAg/aGg	.	.	.	1	NOP9	HGNC	19826	protein_coding	YES	CCDS9624.1	ENSP00000267425	NOP9_HUMAN	B3KVY3_HUMAN	UPI000000CBCF	.	tolerated(0.18)	possibly_damaging(0.723)	2/10	.	hmmpanther:PTHR13102,hmmpanther:PTHR13102:SF0,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGAAGGAAG	.	5	ESCA
HSPA2	0	.	GRCh37	14	65007517	65007517	+	5'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-51A>G	.	.	ENST00000247207	1/1	23	15	8	61	61	0	HSPA2,5_prime_UTR_variant,,ENST00000247207,;HSPA2,intron_variant,,ENST00000394709,;RP11-973N13.4,upstream_gene_variant,,ENST00000554918,;HSPA2,non_coding_transcript_exon_variant,,ENST00000554883,;RP11-973N13.5,upstream_gene_variant,,ENST00000555669,;	G	ENSG00000126803	ENST00000247207	Transcript	5_prime_UTR_variant	332	.	.	.	.	.	.	.	1	HSPA2	HGNC	5235	protein_coding	YES	CCDS9766.1	ENSP00000247207	HSP72_HUMAN	.	UPI000012CC6A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGGAGTTCA	.	5	ESCA
TLN2	0	.	GRCh37	15	63116186	63116186	+	Intron	SNP	T	T	G	rs777464613	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7002+3377T>G	.	.	ENST00000561311	.	55	38	17	47	47	0	TLN2,intron_variant,,ENST00000494733,;TLN2,intron_variant,,ENST00000561311,;TLN2,intron_variant,,ENST00000306829,;MIR190A,mature_miRNA_variant,,ENST00000388402,;TLN2,intron_variant,,ENST00000489129,;	G	ENSG00000171914	ENST00000561311	Transcript	intron_variant	.	.	.	.	.	rs777464613	.	.	1	TLN2	HGNC	15447	protein_coding	YES	CCDS32261.1	ENSP00000453508	TLN2_HUMAN	.	UPI00001FE5FC	.	.	.	.	53/57	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATATTAGGT	byFrequency	5	ESCA
IGDCC4	0	.	GRCh37	15	65681218	65681218	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2635G>A	p.Val879Met	p.V879M	ENST00000352385	15/20	35	23	11	51	51	0	IGDCC4,missense_variant,p.Val879Met,ENST00000352385,;IGDCC4,upstream_gene_variant,,ENST00000558048,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000559327,;IGDCC4,upstream_gene_variant,,ENST00000560319,;IGDCC4,upstream_gene_variant,,ENST00000561309,;	T	ENSG00000103742	ENST00000352385	Transcript	missense_variant	2845	2635	879	V/M	Gtg/Atg	.	.	.	-1	IGDCC4	HGNC	13770	protein_coding	YES	CCDS10206.1	ENSP00000319623	IGDC4_HUMAN	.	UPI000006F31C	.	deleterious(0.01)	probably_damaging(0.99)	15/20	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCACGATCT	.	5	ESCA
ANP32A	0	.	GRCh37	15	69079862	69079862	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217G>A	p.Asp73Asn	p.D73N	ENST00000465139	3/7	95	90	4	108	108	0	ANP32A,missense_variant,p.Asp73Asn,ENST00000560303,;ANP32A,missense_variant,p.Asp73Asn,ENST00000465139,;ANP32A,non_coding_transcript_exon_variant,,ENST00000495764,;ANP32A,non_coding_transcript_exon_variant,,ENST00000267918,;ANP32A,non_coding_transcript_exon_variant,,ENST00000483551,;ANP32A,non_coding_transcript_exon_variant,,ENST00000561430,;ANP32A,non_coding_transcript_exon_variant,,ENST00000495420,;ANP32A,intron_variant,,ENST00000409628,;ANP32A,upstream_gene_variant,,ENST00000480858,;	T	ENSG00000140350	ENST00000465139	Transcript	missense_variant	361	217	73	D/N	Gat/Aat	.	.	.	-1	ANP32A	HGNC	13233	protein_coding	YES	CCDS45292.1	ENSP00000417864	AN32A_HUMAN	Q08AJ6_HUMAN	UPI0000125027	.	deleterious(0.04)	benign(0.04)	3/7	.	PROSITE_profiles:PS51450,hmmpanther:PTHR11375:SF1,hmmpanther:PTHR11375,Pfam_domain:PF14580,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTATCGCTTA	.	2	ESCA
MYO9A	0	.	GRCh37	15	72192087	72192087	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3411A>G	p.%3D	p.E1137E	ENST00000356056	24/42	25	17	8	37	37	0	MYO9A,synonymous_variant,p.%3D,ENST00000424560,;MYO9A,synonymous_variant,p.%3D,ENST00000564571,;MYO9A,synonymous_variant,p.%3D,ENST00000566885,;MYO9A,synonymous_variant,p.%3D,ENST00000356056,;MYO9A,synonymous_variant,p.%3D,ENST00000444904,;MYO9A,upstream_gene_variant,,ENST00000561618,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563542,;MYO9A,downstream_gene_variant,,ENST00000566744,;MYO9A,upstream_gene_variant,,ENST00000568781,;	C	ENSG00000066933	ENST00000356056	Transcript	synonymous_variant	3884	3411	1137	E	gaA/gaG	.	.	.	-1	MYO9A	HGNC	7608	protein_coding	YES	CCDS10239.1	ENSP00000348349	MYO9A_HUMAN	H3BSU8_HUMAN,H3BMS3_HUMAN	UPI000013D213	.	.	.	24/42	.	PROSITE_profiles:PS50096,hmmpanther:PTHR13140:SF9,hmmpanther:PTHR13140,SMART_domains:SM00015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGTTCTTG	.	5	ESCA
NTRK3	0	.	GRCh37	15	88419991	88419991	+	3'Flank	SNP	T	T	C	rs182178380	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000360948	.	21	18	3	13	13	0	NTRK3,3_prime_UTR_variant,,ENST00000394480,;NTRK3,downstream_gene_variant,,ENST00000357724,;NTRK3,downstream_gene_variant,,ENST00000557856,;NTRK3,downstream_gene_variant,,ENST00000355254,;NTRK3,downstream_gene_variant,,ENST00000360948,;	C	ENSG00000140538	ENST00000360948	Transcript	downstream_gene_variant	.	.	.	.	.	rs182178380	.	31	-1	NTRK3	HGNC	8033	protein_coding	YES	CCDS32322.1	ENSP00000354207	NTRK3_HUMAN	R4GNH5_HUMAN	UPI000006DC82	.	.	.	.	.	.	A:0.0028	A:0.0098	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAGGGTTTTTT	byFrequency|byCluster|by1000G	2	ESCA
VWA3A	0	.	GRCh37	16	22128487	22128487	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.980C>A	p.Pro327Gln	p.P327Q	ENST00000389398	11/34	44	28	16	50	50	0	VWA3A,missense_variant,p.Pro327Gln,ENST00000568328,;VWA3A,missense_variant,p.Pro327Gln,ENST00000389398,;VWA3A,5_prime_UTR_variant,,ENST00000389397,;VWA3A,non_coding_transcript_exon_variant,,ENST00000566668,;VWA3A,upstream_gene_variant,,ENST00000299840,;	A	ENSG00000175267	ENST00000389398	Transcript	missense_variant	1076	980	327	P/Q	cCa/cAa	.	.	.	1	VWA3A	HGNC	27088	protein_coding	YES	CCDS45441.1	ENSP00000374049	VWA3A_HUMAN	H3BTX3_HUMAN	UPI0001663067	.	deleterious(0)	possibly_damaging(0.52)	11/34	.	hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF105,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCCAAAGA	.	5	ESCA
RNPS1	0	.	GRCh37	16	2303349	2303353	+	3'UTR	INS	TGACT	TGACT	ATGACC	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	TGACT	TGACT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*612_*616delAGTCAinsGGTCAT	.	.	ENST00000565678	8/8	32	17	15	22	22	0	RNPS1,3_prime_UTR_variant,,ENST00000565678,;RNPS1,3_prime_UTR_variant,,ENST00000320225,;RNPS1,3_prime_UTR_variant,,ENST00000561718,;RNPS1,3_prime_UTR_variant,,ENST00000566397,;RNPS1,3_prime_UTR_variant,,ENST00000566458,;RNPS1,3_prime_UTR_variant,,ENST00000397086,;RNPS1,downstream_gene_variant,,ENST00000568631,;ECI1,upstream_gene_variant,,ENST00000570258,;ECI1,upstream_gene_variant,,ENST00000562238,;RNPS1,downstream_gene_variant,,ENST00000567147,;ECI1,upstream_gene_variant,,ENST00000566379,;RNPS1,downstream_gene_variant,,ENST00000301730,;ECI1,upstream_gene_variant,,ENST00000301729,;RNPS1,downstream_gene_variant,,ENST00000569598,;AC009065.1,upstream_gene_variant,,ENST00000454671,;RNPS1,downstream_gene_variant,,ENST00000561518,;RNPS1,downstream_gene_variant,,ENST00000565870,;RNPS1,non_coding_transcript_exon_variant,,ENST00000562205,;RNPS1,downstream_gene_variant,,ENST00000565243,;ECI1,upstream_gene_variant,,ENST00000561688,;ECI1,upstream_gene_variant,,ENST00000563029,;RNPS1,downstream_gene_variant,,ENST00000564311,;	ATGACC	ENSG00000205937	ENST00000565678	Transcript	3_prime_UTR_variant	2076-2080	.	.	.	.	.	.	.	-1	RNPS1	HGNC	10080	protein_coding	YES	CCDS10465.1	ENSP00000457723	RNPS1_HUMAN	H3BUL0_HUMAN,H3BUG0_HUMAN,H3BTY0_HUMAN,H3BTV0_HUMAN,H3BTR6_HUMAN,H3BTC0_HUMAN,H3BRK4_HUMAN,H3BPG5_HUMAN,H3BNI3_HUMAN,H3BMM9_HUMAN,D3DU92_HUMAN	UPI00000245F5	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCGTGATGACTCCGCA	.	3	ESCA
SRCAP	0	.	GRCh37	16	30720962	30720962	+	Silent	SNP	A	A	G	rs764585756	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.762A>G	p.%3D	p.P254P	ENST00000262518	7/34	57	38	19	64	64	0	SRCAP,synonymous_variant,p.%3D,ENST00000262518,;SRCAP,synonymous_variant,p.%3D,ENST00000344771,;SRCAP,synonymous_variant,p.%3D,ENST00000395059,;SNORA30,upstream_gene_variant,,ENST00000384028,;SRCAP,synonymous_variant,p.%3D,ENST00000380361,;SRCAP,upstream_gene_variant,,ENST00000483083,;	G	ENSG00000080603	ENST00000262518	Transcript	synonymous_variant	1147	762	254	P	ccA/ccG	rs764585756	.	.	1	SRCAP	HGNC	16974	protein_coding	YES	CCDS10689.2	ENSP00000262518	SRCAP_HUMAN	G1UI29_HUMAN,C9J4U4_HUMAN	UPI000059D368	.	.	.	7/34	.	hmmpanther:PTHR10799:SF581,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCATTAAC	.	5	ESCA
ADCY9	0	.	GRCh37	16	4016561	4016561	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3277G>T	p.Asp1093Tyr	p.D1093Y	ENST00000294016	11/11	68	51	16	61	61	0	ADCY9,missense_variant,p.Asp1093Tyr,ENST00000294016,;ADCY9,intron_variant,,ENST00000576936,;	A	ENSG00000162104	ENST00000294016	Transcript	missense_variant	3816	3277	1093	D/Y	Gac/Tac	.	.	.	-1	ADCY9	HGNC	240	protein_coding	YES	CCDS32382.1	ENSP00000294016	ADCY9_HUMAN	.	UPI000012887F	.	deleterious(0)	probably_damaging(1)	11/11	.	PROSITE_profiles:PS50125,hmmpanther:PTHR11920:SF272,hmmpanther:PTHR11920,Gene3D:3.30.70.1230,Pfam_domain:PF00211,SMART_domains:SM00044,Superfamily_domains:SSF55073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGTCAAAGT	.	5	ESCA
ADORA2B	0	.	GRCh37	17	15878317	15878317	+	Missense_Mutation	SNP	C	C	G	rs775839247	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660C>G	p.Asp220Glu	p.D220E	ENST00000304222	2/2	24	11	12	40	40	0	ADORA2B,missense_variant,p.Asp220Glu,ENST00000304222,;ZSWIM7,downstream_gene_variant,,ENST00000486655,;ZSWIM7,downstream_gene_variant,,ENST00000399277,;ZSWIM7,downstream_gene_variant,,ENST00000472495,;ZSWIM7,downstream_gene_variant,,ENST00000475498,;ZSWIM7,downstream_gene_variant,,ENST00000497434,;ZSWIM7,downstream_gene_variant,,ENST00000497719,;ZSWIM7,downstream_gene_variant,,ENST00000495825,;ZSWIM7,downstream_gene_variant,,ENST00000399280,;ADORA2B,non_coding_transcript_exon_variant,,ENST00000582124,;ZSWIM7,downstream_gene_variant,,ENST00000491631,;ZSWIM7,downstream_gene_variant,,ENST00000585208,;ZSWIM7,downstream_gene_variant,,ENST00000579955,;ZSWIM7,downstream_gene_variant,,ENST00000476496,;ZSWIM7,downstream_gene_variant,,ENST00000486706,;ZSWIM7,downstream_gene_variant,,ENST00000460252,;ZSWIM7,downstream_gene_variant,,ENST00000474716,;ZSWIM7,downstream_gene_variant,,ENST00000490395,;ZSWIM7,downstream_gene_variant,,ENST00000460315,;ZSWIM7,downstream_gene_variant,,ENST00000584519,;	G	ENSG00000170425	ENST00000304222	Transcript	missense_variant	992	660	220	D/E	gaC/gaG	rs775839247	.	.	1	ADORA2B	HGNC	264	protein_coding	YES	CCDS11173.1	ENSP00000304501	AA2BR_HUMAN	Q2L7J7_HUMAN	UPI00000503E3	.	tolerated(1)	benign(0.01)	2/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24246,hmmpanther:PTHR24246:SF18,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00554	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGACCACTC	.	5	ESCA
SGSM2	0	.	GRCh37	17	2266426	2266426	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670G>A	p.Gly224Arg	p.G224R	ENST00000268989	6/24	20	13	6	33	33	0	SGSM2,missense_variant,p.Gly224Arg,ENST00000268989,;SGSM2,missense_variant,p.Gly224Arg,ENST00000426855,;SGSM2,missense_variant,p.Gly224Arg,ENST00000574563,;SGSM2,upstream_gene_variant,,ENST00000570431,;SGSM2,downstream_gene_variant,,ENST00000574650,;SGSM2,stop_gained,p.Trp251Ter,ENST00000573062,;SGSM2,upstream_gene_variant,,ENST00000575367,;SGSM2,upstream_gene_variant,,ENST00000574857,;SGSM2,downstream_gene_variant,,ENST00000572875,;	A	ENSG00000141258	ENST00000268989	Transcript	missense_variant	847	670	224	G/R	Ggg/Agg	.	.	.	1	SGSM2	HGNC	29026	protein_coding	YES	CCDS32526.1	ENSP00000268989	SGSM2_HUMAN	I3L1Y7_HUMAN	UPI0000160300	.	tolerated(0.34)	possibly_damaging(0.743)	6/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGGGGGTA	.	5	ESCA
SLC46A1	0	.	GRCh37	17	26729266	26729266	+	Missense_Mutation	SNP	C	C	G	rs782018017	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1155G>C	p.Glu385Asp	p.E385D	ENST00000440501	3/6	56	17	38	57	57	0	SLC46A1,missense_variant,p.Glu385Asp,ENST00000440501,;SLC46A1,intron_variant,,ENST00000321666,;SLC46A1,intron_variant,,ENST00000582735,;SLC46A1,downstream_gene_variant,,ENST00000581516,;SLC46A1,downstream_gene_variant,,ENST00000584995,;SLC46A1,downstream_gene_variant,,ENST00000584426,;SARM1,downstream_gene_variant,,ENST00000457710,;CTD-2350C19.1,non_coding_transcript_exon_variant,,ENST00000583956,;CTD-2350C19.2,upstream_gene_variant,,ENST00000580714,;SLC46A1,non_coding_transcript_exon_variant,,ENST00000584729,;SLC46A1,intron_variant,,ENST00000583295,;SLC46A1,downstream_gene_variant,,ENST00000578217,;SARM1,downstream_gene_variant,,ENST00000379061,;SLC46A1,downstream_gene_variant,,ENST00000582590,;SARM1,downstream_gene_variant,,ENST00000003834,;SLC46A1,upstream_gene_variant,,ENST00000582345,;	G	ENSG00000076351	ENST00000440501	Transcript	missense_variant	1251	1155	385	E/D	gaG/gaC	rs782018017	.	.	-1	SLC46A1	HGNC	30521	protein_coding	YES	.	ENSP00000395653	PCFT_HUMAN	K7EPJ7_HUMAN,J3QRF7_HUMAN,J3KTE6_HUMAN	UPI0000050394	.	tolerated(0.34)	benign(0.122)	3/6	.	PROSITE_profiles:PS50850,hmmpanther:PTHR23038,hmmpanther:PTHR23038:SF43,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGTCTCTCT	.	5	ESCA
ALDOC	0	.	GRCh37	17	26901517	26901517	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619G>C	p.Glu207Gln	p.E207Q	ENST00000226253	6/9	49	45	3	56	56	0	ALDOC,missense_variant,p.Glu207Gln,ENST00000226253,;ALDOC,missense_variant,p.Glu207Gln,ENST00000395321,;ALDOC,intron_variant,,ENST00000395319,;PIGS,upstream_gene_variant,,ENST00000395346,;ALDOC,downstream_gene_variant,,ENST00000581807,;SPAG5,downstream_gene_variant,,ENST00000321765,;PIGS,upstream_gene_variant,,ENST00000308360,;ALDOC,downstream_gene_variant,,ENST00000578590,;PIGS,upstream_gene_variant,,ENST00000543734,;ALDOC,downstream_gene_variant,,ENST00000460201,;SPAG5,downstream_gene_variant,,ENST00000582076,;ALDOC,downstream_gene_variant,,ENST00000584086,;ALDOC,downstream_gene_variant,,ENST00000435638,;RP11-192H23.5,downstream_gene_variant,,ENST00000585189,;PIGS,upstream_gene_variant,,ENST00000584413,;RP11-192H23.4,intron_variant,,ENST00000481916,;SPAG5,downstream_gene_variant,,ENST00000581133,;SPAG5,downstream_gene_variant,,ENST00000582175,;PIGS,upstream_gene_variant,,ENST00000584080,;SPAG5,downstream_gene_variant,,ENST00000580676,;PIGS,upstream_gene_variant,,ENST00000268758,;PIGS,upstream_gene_variant,,ENST00000582721,;SPAG5,downstream_gene_variant,,ENST00000580406,;SPAG5,downstream_gene_variant,,ENST00000577259,;PIGS,upstream_gene_variant,,ENST00000577594,;SPAG5,downstream_gene_variant,,ENST00000580377,;ALDOC,downstream_gene_variant,,ENST00000582381,;PIGS,upstream_gene_variant,,ENST00000583631,;SPAG5,downstream_gene_variant,,ENST00000580682,;	G	ENSG00000109107	ENST00000226253	Transcript	missense_variant	1095	619	207	E/Q	Gag/Cag	.	.	.	-1	ALDOC	HGNC	418	protein_coding	YES	CCDS11236.1	ENSP00000226253	ALDOC_HUMAN	K7EKH5_HUMAN,J3QKP5_HUMAN,J3QKK1_HUMAN,J3KSV6_HUMAN,C9J8F3_HUMAN,B7Z1N6_HUMAN	UPI0000000C53	.	deleterious(0.03)	possibly_damaging(0.552)	6/9	.	hmmpanther:PTHR11627,hmmpanther:PTHR11627:SF3,Pfam_domain:PF00274,Gene3D:3.20.20.70,Superfamily_domains:SSF51569	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCTCTGTAA	.	2	ESCA
CPD	0	.	GRCh37	17	28783319	28783319	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3383A>G	p.Asn1128Ser	p.N1128S	ENST00000225719	16/21	45	9	36	50	50	0	CPD,missense_variant,p.Asn1128Ser,ENST00000225719,;CPD,missense_variant,p.Asn881Ser,ENST00000543464,;CPD,intron_variant,,ENST00000584221,;CPD,non_coding_transcript_exon_variant,,ENST00000584051,;CPD,downstream_gene_variant,,ENST00000588977,;CPD,missense_variant,p.Asn72Ser,ENST00000579502,;CPD,3_prime_UTR_variant,,ENST00000584050,;CPD,non_coding_transcript_exon_variant,,ENST00000580396,;	G	ENSG00000108582	ENST00000225719	Transcript	missense_variant	3459	3383	1128	N/S	aAt/aGt	.	.	.	1	CPD	HGNC	2301	protein_coding	YES	CCDS11257.1	ENSP00000225719	CBPD_HUMAN	.	UPI000000DAF7	.	tolerated(0.81)	benign(0.07)	16/21	.	hmmpanther:PTHR11532:SF40,hmmpanther:PTHR11532,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAAATAATC	.	5	ESCA
PSMD3	0	.	GRCh37	17	38151522	38151522	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000264639	8/12	36	27	9	42	42	0	PSMD3,missense_variant,p.Arg259Gln,ENST00000541736,;PSMD3,missense_variant,p.Arg397Gln,ENST00000264639,;PSMD3,intron_variant,,ENST00000540504,;PSMD3,3_prime_UTR_variant,,ENST00000415039,;PSMD3,non_coding_transcript_exon_variant,,ENST00000485835,;	A	ENSG00000108344	ENST00000264639	Transcript	missense_variant	1364	1190	397	R/Q	cGg/cAg	COSM125645	.	.	1	PSMD3	HGNC	9560	protein_coding	YES	CCDS11356.1	ENSP00000264639	PSMD3_HUMAN	Q96N86_HUMAN,B3KNN7_HUMAN	UPI0000001062	.	deleterious(0)	probably_damaging(0.931)	8/12	.	hmmpanther:PTHR10758:SF2,hmmpanther:PTHR10758,Pfam_domain:PF01399,Gene3D:1.10.10.10,SMART_domains:SM00088	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCCGGCTGC	.	5	ESCA
KRT13	0	.	GRCh37	17	39659228	39659228	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.858G>A	p.%3D	p.E286E	ENST00000246635	4/8	40	37	3	41	41	0	KRT13,synonymous_variant,p.%3D,ENST00000246635,;KRT13,synonymous_variant,p.%3D,ENST00000587544,;KRT13,synonymous_variant,p.%3D,ENST00000336861,;KRT13,downstream_gene_variant,,ENST00000590425,;KRT13,downstream_gene_variant,,ENST00000587435,;AC019349.5,downstream_gene_variant,,ENST00000411759,;KRT13,downstream_gene_variant,,ENST00000587118,;KRT13,upstream_gene_variant,,ENST00000475217,;KRT13,3_prime_UTR_variant,,ENST00000464634,;KRT13,non_coding_transcript_exon_variant,,ENST00000468313,;	T	ENSG00000171401	ENST00000246635	Transcript	synonymous_variant	905	858	286	E	gaG/gaA	.	.	.	-1	KRT13	HGNC	6415	protein_coding	YES	CCDS11396.1	ENSP00000246635	K1C13_HUMAN	K7ERE3_HUMAN,K7EMD9_HUMAN	UPI000013CBF6	.	.	.	4/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF121,hmmpanther:PTHR23239,Pfam_domain:PF00038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCTCTGC	.	2	ESCA
TP53	0	.	GRCh37	17	7577106	7577106	+	Missense_Mutation	SNP	G	G	C	rs17849781	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	8/11	18	12	6	38	38	0	TP53,missense_variant,p.Pro278Ala,ENST00000420246,;TP53,missense_variant,p.Pro278Ala,ENST00000269305,;TP53,missense_variant,p.Pro146Ala,ENST00000509690,;TP53,missense_variant,p.Pro278Ala,ENST00000359597,;TP53,missense_variant,p.Pro278Ala,ENST00000445888,;TP53,missense_variant,p.Pro278Ala,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1022	832	278	P/A	Cct/Gct	CM052927,CX0910928,rs17849781,CM011015,TP53_g.13812C>G,TP53_g.13812C>A,TP53_g.13812del,TP53_g.13812C>T,COSM43697,COSM10939,COSM10814,COSM45178,COSM368635,COSM139044,COSM99725,COSM3421932,COSM3773297,COSM3717626,COSM1646810,COSM1646809,COSM3421931	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.01)	probably_damaging(1)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P278A|c.832C>G|25,SITE|p.P278A|c.832C>G|4,SITE|p.P278A|c.832C>G|10,CODON|p.0?|c.1_1182del1182|6,CODON|p.P278fs*67|c.833delC|3,CODON|p.P278F|c.832_833CC>TT|3,CODON|p.P278H|c.833C>A|15,CODON|p.P278R|c.833C>G|5,CODON|p.P278R|c.833C>G|30,CODON|p.P278R|c.833C>G|3,CODON|p.P278H|c.833C>A|3,CODON|p.P278L|c.833C>T|3,CODON|p.P278L|c.833C>T|11,CODON|p.P278L|c.833C>T|65,CODON|p.P278L|c.833C>T|8,CODON|p.P278fs*67|c.832delC|3,BUFFER|p.R282W|c.843_844CC>TT|10,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12,BUFFER|p.D281V|c.842A>T|5,BUFFER|p.D281G|c.842A>G|10,BUFFER|p.D281H|c.841G>C|6,BUFFER|p.D281H|c.841G>C|28,BUFFER|p.D281H|c.841G>C|3,BUFFER|p.D281H|c.841G>C|4,BUFFER|p.D281Y|c.841G>T|7,BUFFER|p.D281N|c.841G>A|7,BUFFER|p.D281N|c.841G>A|3,BUFFER|p.D281Y|c.841G>T|13,BUFFER|p.D281Y|c.841G>T|4,BUFFER|p.D281N|c.841G>A|27,BUFFER|p.R280R|c.840A>G|3,BUFFER|p.R280S|c.840A>T|11,BUFFER|p.R280S|c.840A>C|6,BUFFER|p.R280T|c.839G>C|63,BUFFER|p.R280T|c.839G>C|4,BUFFER|p.R280I|c.839G>T|17,BUFFER|p.R280K|c.839G>A|17,BUFFER|p.R280K|c.839G>A|6,BUFFER|p.R280I|c.839G>T|4,BUFFER|p.R280K|c.839G>A|57,BUFFER|p.R280I|c.839G>T|3,BUFFER|p.R280T|c.839G>C|10,BUFFER|p.R280K|c.839G>A|11,BUFFER|p.R280*|c.838A>T|12,BUFFER|p.R280G|c.838A>G|6,BUFFER|p.R280G|c.838A>G|3,BUFFER|p.R280G|c.838A>G|23,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279E|c.836G>A|4,BUFFER|p.G279E|c.836G>A|34,BUFFER|p.G279V|c.836G>T|3,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278T|c.832C>A|29,BUFFER|p.P278T|c.832C>A|8,BUFFER|p.P278S|c.832C>T|4,BUFFER|p.P278S|c.832C>T|3,BUFFER|p.P278S|c.832C>T|8,BUFFER|p.P278S|c.832C>T|55,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAGGACAGG	.	5	ESCA
TNRC6C	0	.	GRCh37	17	76027743	76027743	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-399C>G	.	.	ENST00000335749	2/21	31	25	6	65	65	0	TNRC6C,5_prime_UTR_variant,,ENST00000301624,;TNRC6C,5_prime_UTR_variant,,ENST00000335749,;TNRC6C,5_prime_UTR_variant,,ENST00000585438,;TNRC6C,5_prime_UTR_variant,,ENST00000588061,;TNRC6C,5_prime_UTR_variant,,ENST00000588847,;	G	ENSG00000078687	ENST00000335749	Transcript	5_prime_UTR_variant	171	.	.	.	.	.	.	.	1	TNRC6C	HGNC	29318	protein_coding	YES	CCDS45799.1	ENSP00000336783	.	K7ELY5_HUMAN,K7EKN9_HUMAN,G3XAB8_HUMAN	UPI0000EE5F80	.	.	.	2/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCTCGTGAG	.	5	ESCA
LGALS3BP	0	.	GRCh37	17	76967577	76967577	+	3'UTR	SNP	G	G	C	rs3191375	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*81C>G	.	.	ENST00000262776	6/6	19	6	13	36	36	0	LGALS3BP,3_prime_UTR_variant,,ENST00000591778,;LGALS3BP,3_prime_UTR_variant,,ENST00000262776,;LGALS3BP,downstream_gene_variant,,ENST00000589906,;LGALS3BP,downstream_gene_variant,,ENST00000585407,;LGALS3BP,downstream_gene_variant,,ENST00000589775,;LGALS3BP,downstream_gene_variant,,ENST00000591274,;LGALS3BP,downstream_gene_variant,,ENST00000589527,;LGALS3BP,3_prime_UTR_variant,,ENST00000587311,;LGALS3BP,3_prime_UTR_variant,,ENST00000587251,;LGALS3BP,3_prime_UTR_variant,,ENST00000586720,;LGALS3BP,downstream_gene_variant,,ENST00000588205,;LGALS3BP,downstream_gene_variant,,ENST00000588899,;LGALS3BP,downstream_gene_variant,,ENST00000588508,;LGALS3BP,downstream_gene_variant,,ENST00000592255,;LGALS3BP,downstream_gene_variant,,ENST00000588198,;LGALS3BP,downstream_gene_variant,,ENST00000587310,;LGALS3BP,downstream_gene_variant,,ENST00000588990,;LGALS3BP,downstream_gene_variant,,ENST00000588587,;	C	ENSG00000108679	ENST00000262776	Transcript	3_prime_UTR_variant	2148	.	.	.	.	rs3191375	.	.	-1	LGALS3BP	HGNC	6564	protein_coding	YES	CCDS11759.1	ENSP00000262776	LG3BP_HUMAN	K7ESM3_HUMAN,K7ES75_HUMAN,K7EP36_HUMAN,K7EKQ5_HUMAN,B4DVE1_HUMAN	UPI000006E64A	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGAGAGGAA	byCluster	5	ESCA
ZNF750	0	.	GRCh37	17	80790213	80790213	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118delC	p.Leu40PhefsTer5	p.L40Ffs*5	ENST00000269394	2/3	84	53	31	65	65	0	ZNF750,frameshift_variant,p.Leu40PhefsTer5,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	-	ENSG00000141579	ENST00000269394	Transcript	frameshift_variant	952	118	40	L/X	Ctt/tt	COSM3796262,COSM986189	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678,Pfam_domain:PF15269	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	deletion	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAAAAAGATGTG	.	3	ESCA
GNAL	0	.	GRCh37	18	11753862	11753862	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542T>C	p.Val181Ala	p.V181A	ENST00000334049	4/12	91	83	8	103	103	0	GNAL,missense_variant,p.Val104Ala,ENST00000535121,;GNAL,missense_variant,p.Val43Ala,ENST00000585642,;GNAL,missense_variant,p.Val104Ala,ENST00000423027,;GNAL,missense_variant,p.Val104Ala,ENST00000269162,;GNAL,missense_variant,p.Val181Ala,ENST00000334049,;GNAL,missense_variant,p.Val8Ala,ENST00000590228,;GNAL,non_coding_transcript_exon_variant,,ENST00000590972,;	C	ENSG00000141404	ENST00000334049	Transcript	missense_variant	1150	542	181	V/A	gTt/gCt	.	.	.	1	GNAL	HGNC	4388	protein_coding	YES	CCDS11851.1	ENSP00000334051	GNAL_HUMAN	Q8N2B4_HUMAN,K7EQ80_HUMAN,K7EPE2_HUMAN	UPI000017DF81	.	tolerated(0.15)	possibly_damaging(0.569)	4/12	.	hmmpanther:PTHR10218:SF131,hmmpanther:PTHR10218,Gene3D:1.10.400.10,Pfam_domain:PF00503,SMART_domains:SM00275,Superfamily_domains:SSF47895,Prints_domain:PR00443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCAGTTCCGC	.	3	ESCA
ANKRD30B	0	.	GRCh37	18	14852215	14852215	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3915A>G	p.%3D	p.Q1305Q	ENST00000358984	36/36	67	50	17	74	74	0	ANKRD30B,synonymous_variant,p.%3D,ENST00000358984,;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,;	G	ENSG00000180777	ENST00000358984	Transcript	synonymous_variant	4095	3915	1305	Q	caA/caG	.	.	.	1	ANKRD30B	HGNC	24165	protein_coding	YES	CCDS54182.1	ENSP00000351875	AN30B_HUMAN	.	UPI0000425FF7	.	.	.	36/36	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF14915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCAACTAGA	.	5	ESCA
DSG2	0	.	GRCh37	18	29126669	29126669	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3320T>C	p.Val1107Ala	p.V1107A	ENST00000261590	15/15	38	24	14	36	36	0	DSG2,missense_variant,p.Val1107Ala,ENST00000261590,;RP11-75N4.2,intron_variant,,ENST00000583706,;RP11-75N4.2,downstream_gene_variant,,ENST00000579251,;	C	ENSG00000046604	ENST00000261590	Transcript	missense_variant	3529	3320	1107	V/A	gTt/gCt	.	.	.	1	DSG2	HGNC	3049	protein_coding	YES	CCDS42423.1	ENSP00000261590	DSG2_HUMAN	.	UPI0000048E38	.	deleterious(0)	possibly_damaging(0.64)	15/15	.	hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGTTACCA	.	5	ESCA
SMAD7	0	.	GRCh37	18	46476341	46476341	+	Missense_Mutation	SNP	A	A	G	rs749074075	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454T>C	p.Ser152Pro	p.S152P	ENST00000262158	1/4	36	28	8	41	40	1	SMAD7,missense_variant,p.Ser152Pro,ENST00000262158,;SMAD7,missense_variant,p.Ser152Pro,ENST00000589634,;SMAD7,upstream_gene_variant,,ENST00000591805,;SMAD7,upstream_gene_variant,,ENST00000586093,;	G	ENSG00000101665	ENST00000262158	Transcript	missense_variant	741	454	152	S/P	Tcc/Ccc	rs749074075	.	.	-1	SMAD7	HGNC	6773	protein_coding	YES	CCDS11936.1	ENSP00000262158	SMAD7_HUMAN	K7EKF0_HUMAN	UPI0000135A83	.	tolerated_low_confidence(0.29)	benign(0.004)	1/4	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51075,hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF27,Pfam_domain:PF03165,Gene3D:1ozjA00,SMART_domains:SM00523,Superfamily_domains:0040928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	GTAGGACGAGG	.	3	ESCA
TCF4	0	.	GRCh37	18	52937190	52937190	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1100A>G	p.Tyr367Cys	p.Y367C	ENST00000398339	12/21	80	63	17	94	94	0	TCF4,missense_variant,p.Tyr135Cys,ENST00000570177,;TCF4,missense_variant,p.Tyr240Cys,ENST00000568740,;TCF4,missense_variant,p.Tyr265Cys,ENST00000565018,;TCF4,missense_variant,p.Tyr205Cys,ENST00000566279,;TCF4,missense_variant,p.Tyr241Cys,ENST00000568673,;TCF4,missense_variant,p.Tyr241Cys,ENST00000537578,;TCF4,missense_variant,p.Tyr194Cys,ENST00000544241,;TCF4,missense_variant,p.Tyr367Cys,ENST00000398339,;TCF4,missense_variant,p.Tyr271Cys,ENST00000564403,;TCF4,missense_variant,p.Tyr105Cys,ENST00000570287,;TCF4,missense_variant,p.Tyr223Cys,ENST00000543082,;TCF4,missense_variant,p.Tyr263Cys,ENST00000566286,;TCF4,missense_variant,p.Tyr205Cys,ENST00000567880,;TCF4,missense_variant,p.Tyr194Cys,ENST00000564228,;TCF4,missense_variant,p.Tyr135Cys,ENST00000537856,;TCF4,missense_variant,p.Tyr265Cys,ENST00000354452,;TCF4,missense_variant,p.Tyr241Cys,ENST00000540999,;TCF4,missense_variant,p.Tyr135Cys,ENST00000569012,;TCF4,missense_variant,p.Tyr105Cys,ENST00000561831,;TCF4,missense_variant,p.Tyr20Cys,ENST00000570146,;TCF4,missense_variant,p.Tyr269Cys,ENST00000568169,;TCF4,missense_variant,p.Tyr265Cys,ENST00000564999,;TCF4,missense_variant,p.Tyr241Cys,ENST00000566514,;TCF4,missense_variant,p.Tyr105Cys,ENST00000457482,;TCF4,missense_variant,p.Tyr265Cys,ENST00000356073,;TCF4,missense_variant,p.Tyr135Cys,ENST00000561992,;TCF4,non_coding_transcript_exon_variant,,ENST00000563760,;TCF4,non_coding_transcript_exon_variant,,ENST00000562680,;TCF4,non_coding_transcript_exon_variant,,ENST00000563686,;	C	ENSG00000196628	ENST00000398339	Transcript	missense_variant	1157	1100	367	Y/C	tAt/tGt	.	.	.	-1	TCF4	HGNC	11634	protein_coding	YES	CCDS58631.1	ENSP00000381382	.	K7ERJ0_HUMAN,H3BUQ3_HUMAN,H3BTM9_HUMAN,H3BTC3_HUMAN,H3BT24_HUMAN,H3BSX3_HUMAN,H3BRF7_HUMAN,H3BPG3_HUMAN,H3BP59_HUMAN,H3BNZ2_HUMAN,H3BNI2_HUMAN,H3BME8_HUMAN,H3BMC8_HUMAN,G0LNT8_HUMAN,G0LNT7_HUMAN,G0LNT4_HUMAN,G0LNT3_HUMAN,E9PH57_HUMAN	UPI000059D58C	.	deleterious(0.01)	probably_damaging(0.995)	12/21	.	hmmpanther:PTHR11793,hmmpanther:PTHR11793:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGATAGCTC	.	5	ESCA
MALT1	0	.	GRCh37	18	56411668	56411668	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1852A>G	p.Ile618Val	p.I618V	ENST00000348428	15/17	70	48	22	68	68	0	MALT1,missense_variant,p.Ile607Val,ENST00000345724,;MALT1,missense_variant,p.Ile618Val,ENST00000348428,;RP11-126O1.4,intron_variant,,ENST00000588835,;MALT1,non_coding_transcript_exon_variant,,ENST00000587438,;MALT1,non_coding_transcript_exon_variant,,ENST00000589873,;	G	ENSG00000172175	ENST00000348428	Transcript	missense_variant	2110	1852	618	I/V	Ata/Gta	.	.	.	1	MALT1	HGNC	6819	protein_coding	YES	CCDS11967.1	ENSP00000319279	MALT1_HUMAN	K7EP42_HUMAN	UPI000004D05E	.	tolerated(0.3)	benign(0.002)	15/17	.	hmmpanther:PTHR22576,hmmpanther:PTHR22576:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGTATAGTT	.	5	ESCA
CDH7	0	.	GRCh37	18	63525173	63525173	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357C>T	p.Leu453Phe	p.L453F	ENST00000397968	8/12	90	65	25	85	85	0	CDH7,missense_variant,p.Leu453Phe,ENST00000397968,;CDH7,missense_variant,p.Leu453Phe,ENST00000536984,;CDH7,missense_variant,p.Leu453Phe,ENST00000323011,;	T	ENSG00000081138	ENST00000397968	Transcript	missense_variant	1783	1357	453	L/F	Ctt/Ttt	COSM227912,COSM227913	.	.	1	CDH7	HGNC	1766	protein_coding	YES	CCDS11993.1	ENSP00000381058	CADH7_HUMAN	.	UPI000013D269	.	tolerated(0.18)	benign(0.098)	8/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTCCTTGCA	.	5	ESCA
ATP9B	0	.	GRCh37	18	76886355	76886355	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647A>G	p.Tyr216Cys	p.Y216C	ENST00000426216	5/30	60	41	18	74	74	0	ATP9B,missense_variant,p.Tyr216Cys,ENST00000426216,;ATP9B,missense_variant,p.Tyr216Cys,ENST00000307671,;ATP9B,missense_variant,p.Tyr158Cys,ENST00000586672,;ATP9B,non_coding_transcript_exon_variant,,ENST00000591464,;ATP9B,missense_variant,p.Tyr216Cys,ENST00000586366,;ATP9B,non_coding_transcript_exon_variant,,ENST00000590608,;ATP9B,non_coding_transcript_exon_variant,,ENST00000590271,;ATP9B,non_coding_transcript_exon_variant,,ENST00000490210,;	G	ENSG00000166377	ENST00000426216	Transcript	missense_variant	664	647	216	Y/C	tAt/tGt	.	.	.	1	ATP9B	HGNC	13541	protein_coding	YES	CCDS12014.1	ENSP00000398076	ATP9B_HUMAN	.	UPI00002371AF	.	deleterious(0.01)	possibly_damaging(0.802)	5/30	.	hmmpanther:PTHR24092:SF50,hmmpanther:PTHR24092,Pfam_domain:PF00122,Gene3D:2.70.150.10,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTATATAGCA	.	5	ESCA
LDLR	0	.	GRCh37	19	11222262	11222262	+	Missense_Mutation	SNP	A	A	G	rs730882098	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1133A>G	p.Gln378Arg	p.Q378R	ENST00000558518	8/18	35	30	5	44	44	0	LDLR,missense_variant,p.Gln378Arg,ENST00000558013,;LDLR,missense_variant,p.Gln251Arg,ENST00000545707,;LDLR,missense_variant,p.Gln337Arg,ENST00000535915,;LDLR,missense_variant,p.Gln210Arg,ENST00000455727,;LDLR,missense_variant,p.Gln463Arg,ENST00000252444,;LDLR,missense_variant,p.Gln378Arg,ENST00000558518,;LDLR,missense_variant,p.Gln205Arg,ENST00000560467,;LDLR,missense_variant,p.Gln378Arg,ENST00000557933,;LDLR,non_coding_transcript_exon_variant,,ENST00000560173,;LDLR,upstream_gene_variant,,ENST00000559340,;LDLR,downstream_gene_variant,,ENST00000558528,;	G	ENSG00000130164	ENST00000558518	Transcript	missense_variant	1320	1133	378	Q/R	cAg/cGg	CM983962,rs730882098	.	.	1	LDLR	HGNC	6547	protein_coding	YES	CCDS12254.1	ENSP00000454071	LDLR_HUMAN	Q6LCH2_HUMAN,E1B4S5_HUMAN	UPI00000015DF	.	deleterious(0.01)	benign(0.132)	8/18	.	PROSITE_profiles:PS50026,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF195,PROSITE_patterns:PS01186,PROSITE_patterns:PS00010,Pfam_domain:PF07645,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	not_provided	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGCCAGTGTG	byFrequency|byCluster	4	ESCA
STK11	0	.	GRCh37	19	1220644	1220644	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	5/10	11	7	4	22	22	0	STK11,missense_variant,p.Pro221Leu,ENST00000326873,;STK11,upstream_gene_variant,,ENST00000586243,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,3_prime_UTR_variant,,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,upstream_gene_variant,,ENST00000585465,;	T	ENSG00000118046	ENST00000326873	Transcript	missense_variant	1835	662	221	P/L	cCg/cTg	COSM377895	.	.	1	STK11	HGNC	11389	protein_coding	YES	CCDS45896.1	ENSP00000324856	STK11_HUMAN	Q9NS52_HUMAN	UPI0000136105	.	deleterious(0)	probably_damaging(0.999)	5/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF1,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.0?|c.1_1302del1302|16,BUFFER|p.Q220*|c.658C>T|4	RADIA|MUTECT|MUSE	CCAGCCGCCCG	.	3	ESCA
CCDC130	0	.	GRCh37	19	13869945	13869945	+	Silent	SNP	C	C	T	rs768115849	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432C>T	p.%3D	p.D144D	ENST00000586600	9/11	20	13	7	20	20	0	CCDC130,missense_variant,p.Arg117Cys,ENST00000588809,;CCDC130,synonymous_variant,p.%3D,ENST00000221554,;CCDC130,synonymous_variant,p.%3D,ENST00000585844,;CCDC130,synonymous_variant,p.%3D,ENST00000586666,;CCDC130,synonymous_variant,p.%3D,ENST00000586600,;CCDC130,3_prime_UTR_variant,,ENST00000589096,;CCDC130,upstream_gene_variant,,ENST00000589669,;CCDC130,non_coding_transcript_exon_variant,,ENST00000587019,;CCDC130,non_coding_transcript_exon_variant,,ENST00000588071,;CCDC130,non_coding_transcript_exon_variant,,ENST00000593174,;CCDC130,downstream_gene_variant,,ENST00000540216,;	T	ENSG00000104957	ENST00000586600	Transcript	synonymous_variant	935	432	144	D	gaC/gaT	rs768115849	.	.	1	CCDC130	HGNC	28118	protein_coding	YES	CCDS12296.1	ENSP00000465776	CC130_HUMAN	K7EPA5_HUMAN,K7ELI4_HUMAN	UPI0000071AFB	.	.	.	9/11	.	hmmpanther:PTHR12111:SF2,hmmpanther:PTHR12111,Pfam_domain:PF04502	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGACGCCAT	.	5	ESCA
ATP8B3	0	.	GRCh37	19	1785628	1785628	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3233T>C	p.Val1078Ala	p.V1078A	ENST00000310127	26/29	34	19	14	65	65	0	ATP8B3,missense_variant,p.Val1078Ala,ENST00000310127,;ATP8B3,missense_variant,p.Val1088Ala,ENST00000539485,;ATP8B3,missense_variant,p.Val1041Ala,ENST00000525591,;ONECUT3,downstream_gene_variant,,ENST00000382349,;ATP8B3,3_prime_UTR_variant,,ENST00000531925,;ATP8B3,3_prime_UTR_variant,,ENST00000526847,;	G	ENSG00000130270	ENST00000310127	Transcript	missense_variant	3472	3233	1078	V/A	gTc/gCc	.	.	.	-1	ATP8B3	HGNC	13535	protein_coding	YES	CCDS45901.1	ENSP00000311336	AT8B3_HUMAN	.	UPI0000074660	.	tolerated(0.62)	possibly_damaging(0.593)	26/29	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24092:SF44,hmmpanther:PTHR24092,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAAGACCCAG	.	5	ESCA
ADCK4	0	.	GRCh37	19	41216000	41216000	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331G>T	p.Ala111Ser	p.A111S	ENST00000324464	5/15	40	28	12	40	40	0	ADCK4,missense_variant,p.Ala111Ser,ENST00000243583,;ADCK4,missense_variant,p.Ala2Ser,ENST00000595254,;ADCK4,missense_variant,p.Ala111Ser,ENST00000600707,;ADCK4,missense_variant,p.Ala111Ser,ENST00000450541,;ADCK4,missense_variant,p.Ala111Ser,ENST00000594084,;ADCK4,missense_variant,p.Ala111Ser,ENST00000594720,;ADCK4,missense_variant,p.Ala2Ser,ENST00000600080,;ADCK4,missense_variant,p.Ala111Ser,ENST00000324464,;ADCK4,missense_variant,p.Ala111Ser,ENST00000601967,;ADCK4,incomplete_terminal_codon_variant,p.%3D,ENST00000596357,;ADCK4,intron_variant,,ENST00000594490,;ADCK4,downstream_gene_variant,,ENST00000593723,;RNU6-195P,upstream_gene_variant,,ENST00000411352,;ADCK4,3_prime_UTR_variant,,ENST00000601304,;ADCK4,non_coding_transcript_exon_variant,,ENST00000596455,;ADCK4,non_coding_transcript_exon_variant,,ENST00000601451,;ADCK4,non_coding_transcript_exon_variant,,ENST00000593544,;ADCK4,intron_variant,,ENST00000599643,;	A	ENSG00000123815	ENST00000324464	Transcript	missense_variant	633	331	111	A/S	Gct/Tct	.	.	.	-1	ADCK4	HGNC	19041	protein_coding	YES	CCDS12562.1	ENSP00000315118	ADCK4_HUMAN	M0R3F7_HUMAN,M0R340_HUMAN,M0R307_HUMAN,M0R011_HUMAN,M0R001_HUMAN,M0QZZ2_HUMAN	UPI0000071B0F	.	tolerated(0.06)	benign(0.297)	5/15	.	hmmpanther:PTHR10566:SF22,hmmpanther:PTHR10566	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAGCCATCT	.	5	ESCA
SULT2A1	0	.	GRCh37	19	48386900	48386900	+	Silent	SNP	T	T	C	rs781311827	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279A>G	p.%3D	p.P93P	ENST00000222002	2/6	127	120	7	136	136	0	SULT2A1,synonymous_variant,p.%3D,ENST00000222002,;	C	ENSG00000105398	ENST00000222002	Transcript	synonymous_variant	419	279	93	P	ccA/ccG	rs781311827	.	.	-1	SULT2A1	HGNC	11458	protein_coding	YES	CCDS12707.1	ENSP00000222002	ST2A1_HUMAN	A8K015_HUMAN	UPI000013C7E8	.	.	.	2/6	.	hmmpanther:PTHR11783:SF8,hmmpanther:PTHR11783,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T90M|c.269C>T|3	MUTECT|MUSE	AAACGTGGACT	.	2	ESCA
ZNF17	0	.	GRCh37	19	57932633	57932633	+	Missense_Mutation	SNP	T	T	A	rs61733518	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1773T>A	p.Phe591Leu	p.F591L	ENST00000601808	3/3	59	38	20	81	81	0	ZNF17,missense_variant,p.Phe593Leu,ENST00000307658,;ZNF17,missense_variant,p.Phe591Leu,ENST00000601808,;AC004076.7,intron_variant,,ENST00000597410,;AC003002.6,downstream_gene_variant,,ENST00000596400,;AC003002.6,downstream_gene_variant,,ENST00000596617,;ZNF17,downstream_gene_variant,,ENST00000597350,;ZNF17,downstream_gene_variant,,ENST00000595206,;ZNF17,downstream_gene_variant,,ENST00000599867,;ZNF17,non_coding_transcript_exon_variant,,ENST00000602050,;ZNF17,downstream_gene_variant,,ENST00000595162,;	A	ENSG00000186272	ENST00000601808	Transcript	missense_variant	1986	1773	591	F/L	ttT/ttA	rs61733518	.	.	1	ZNF17	HGNC	12958	protein_coding	YES	CCDS42636.1	ENSP00000471905	ZNF17_HUMAN	.	UPI00001D8198	.	deleterious(0.02)	benign(0.037)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF166,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	C:0.0028	C:0.0106	C:0	.	C:0	C:0	C:0	C:0.0082	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTTATGGA	byFrequency|byCluster|by1000G	4	ESCA
RPS5	0	.	GRCh37	19	58904399	58904399	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165G>T	p.%3D	p.R55R	ENST00000596046	2/5	35	28	6	46	46	0	RPS5,synonymous_variant,p.%3D,ENST00000196551,;RPS5,synonymous_variant,p.%3D,ENST00000596314,;RPS5,synonymous_variant,p.%3D,ENST00000601521,;RPS5,synonymous_variant,p.%3D,ENST00000598495,;RPS5,synonymous_variant,p.%3D,ENST00000596046,;RPS5,intron_variant,,ENST00000598098,;AC012313.1,upstream_gene_variant,,ENST00000601382,;RPS5,non_coding_transcript_exon_variant,,ENST00000598807,;RPS5,upstream_gene_variant,,ENST00000599232,;RPS5,downstream_gene_variant,,ENST00000599909,;	T	ENSG00000083845	ENST00000596046	Transcript	synonymous_variant	1014	165	55	R	cgG/cgT	.	.	.	1	RPS5	HGNC	10426	protein_coding	YES	CCDS12978.1	ENSP00000472985	RS5_HUMAN	M0R0F0_HUMAN	UPI0000135052	.	.	.	2/5	.	hmmpanther:PTHR11205,TIGRFAM_domain:TIGR01028,Pfam_domain:PF00177,Gene3D:1.10.455.10,Superfamily_domains:SSF47973	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGCGGTATGC	.	3	ESCA
C19orf59	0	.	GRCh37	19	7742575	7742575	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147C>G	p.Asp49Glu	p.D49E	ENST00000333598	2/7	49	46	3	50	50	0	C19orf59,missense_variant,p.Asp49Glu,ENST00000333598,;C19orf59,intron_variant,,ENST00000597445,;TRAPPC5,upstream_gene_variant,,ENST00000595985,;TRAPPC5,upstream_gene_variant,,ENST00000426877,;CTD-3214H19.16,upstream_gene_variant,,ENST00000597959,;TRAPPC5,upstream_gene_variant,,ENST00000317378,;TRAPPC5,upstream_gene_variant,,ENST00000596148,;C19orf59,upstream_gene_variant,,ENST00000598851,;	G	ENSG00000183019	ENST00000333598	Transcript	missense_variant	601	147	49	D/E	gaC/gaG	.	.	.	1	C19orf59	HGNC	27291	protein_coding	YES	CCDS12183.1	ENSP00000329920	MCEM1_HUMAN	.	UPI000007442E	.	tolerated(0.21)	possibly_damaging(0.866)	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGACCATGC	.	2	ESCA
HNRNPM	0	.	GRCh37	19	8550661	8550661	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1349T>G	p.Met450Arg	p.M450R	ENST00000325495	14/16	15	10	5	11	11	0	HNRNPM,missense_variant,p.Met450Arg,ENST00000325495,;HNRNPM,missense_variant,p.Met218Arg,ENST00000597270,;HNRNPM,missense_variant,p.Met411Arg,ENST00000348943,;HNRNPM,upstream_gene_variant,,ENST00000596295,;HNRNPM,downstream_gene_variant,,ENST00000594907,;HNRNPM,upstream_gene_variant,,ENST00000598999,;PRAM1,downstream_gene_variant,,ENST00000255612,;PRAM1,downstream_gene_variant,,ENST00000423345,;HNRNPM,downstream_gene_variant,,ENST00000600092,;HNRNPM,non_coding_transcript_exon_variant,,ENST00000597081,;HNRNPM,upstream_gene_variant,,ENST00000602219,;HNRNPM,3_prime_UTR_variant,,ENST00000600806,;PRAM1,downstream_gene_variant,,ENST00000599698,;HNRNPM,downstream_gene_variant,,ENST00000598603,;PRAM1,downstream_gene_variant,,ENST00000594696,;	G	ENSG00000099783	ENST00000325495	Transcript	missense_variant	1390	1349	450	M/R	aTg/aGg	.	.	.	1	HNRNPM	HGNC	5046	protein_coding	YES	CCDS12203.1	ENSP00000325376	HNRPM_HUMAN	Q8TCM5_HUMAN,Q7KYM9_HUMAN	UPI000006E7A2	.	tolerated(0.1)	benign(0.001)	14/16	.	hmmpanther:PTHR23003,hmmpanther:PTHR23003:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCATGGGCT	.	5	ESCA
ZNF561	0	.	GRCh37	19	9721697	9721697	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640A>T	p.Asn214Tyr	p.N214Y	ENST00000302851	6/6	66	42	24	76	76	0	ZNF561,missense_variant,p.Asn145Tyr,ENST00000424629,;ZNF561,missense_variant,p.Asn220Tyr,ENST00000444611,;ZNF561,missense_variant,p.Asn214Tyr,ENST00000302851,;ZNF561,missense_variant,p.Asn78Tyr,ENST00000354661,;ZNF561,3_prime_UTR_variant,,ENST00000326044,;ZNF561,non_coding_transcript_exon_variant,,ENST00000495503,;ZNF561,downstream_gene_variant,,ENST00000465974,;ZNF561,3_prime_UTR_variant,,ENST00000443819,;ZNF561,intron_variant,,ENST00000444802,;ZNF561,downstream_gene_variant,,ENST00000483768,;ZNF561,downstream_gene_variant,,ENST00000494276,;ZNF561,downstream_gene_variant,,ENST00000457965,;	A	ENSG00000171469	ENST00000302851	Transcript	missense_variant	1004	640	214	N/Y	Aat/Tat	.	.	.	-1	ZNF561	HGNC	28684	protein_coding	YES	CCDS12216.2	ENSP00000303915	ZN561_HUMAN	F8WAU2_HUMAN,C9JQP3_HUMAN,C9J7U2_HUMAN,B4E2Q8_HUMAN,A8KAD9_HUMAN	UPI000037525C	.	tolerated(0.07)	probably_damaging(0.999)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF11,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATTATCAA	.	5	ESCA
FRRS1	0	.	GRCh37	1	100174461	100174461	+	Missense_Mutation	SNP	C	C	A	rs146752240	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1874G>T	p.Cys625Phe	p.C625F	ENST00000287474	17/17	18	12	6	22	22	0	FRRS1,missense_variant,p.Cys625Phe,ENST00000287474,;FRRS1,3_prime_UTR_variant,,ENST00000414213,;FRRS1,downstream_gene_variant,,ENST00000489209,;FRRS1,downstream_gene_variant,,ENST00000492943,;	A	ENSG00000156869	ENST00000287474	Transcript	missense_variant	2476	1874	625	C/F	tGt/tTt	rs146752240	.	.	-1	FRRS1	HGNC	27622	protein_coding	YES	CCDS30780.1	ENSP00000287474	FRRS1_HUMAN	.	UPI000042037B	.	deleterious_low_confidence(0)	benign(0.106)	17/17	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAGACATGAC	byCluster	2	ESCA
DENND2C	0	.	GRCh37	1	115168298	115168298	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.308A>C	p.Asp103Ala	p.D103A	ENST00000393274	4/21	32	21	10	56	56	0	DENND2C,missense_variant,p.Asp103Ala,ENST00000393274,;DENND2C,missense_variant,p.Asp103Ala,ENST00000393277,;DENND2C,missense_variant,p.Asp103Ala,ENST00000393276,;DENND2C,downstream_gene_variant,,ENST00000493549,;DENND2C,upstream_gene_variant,,ENST00000481894,;	G	ENSG00000175984	ENST00000393274	Transcript	missense_variant	934	308	103	D/A	gAc/gCc	.	.	.	-1	DENND2C	HGNC	24748	protein_coding	YES	CCDS58018.1	ENSP00000376955	DEN2C_HUMAN	.	UPI000048AF71	.	tolerated(0.59)	benign(0.01)	4/21	.	hmmpanther:PTHR15288:SF6,hmmpanther:PTHR15288	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCGTCATAT	.	5	ESCA
INSRR	0	.	GRCh37	1	156821495	156821495	+	Missense_Mutation	SNP	C	C	A	rs767529375	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027G>T	p.Asp343Tyr	p.D343Y	ENST00000368195	4/22	46	41	5	43	43	0	INSRR,missense_variant,p.Asp343Tyr,ENST00000368195,;NTRK1,intron_variant,,ENST00000392302,;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,intron_variant,,ENST00000530298,;	A	ENSG00000027644	ENST00000368195	Transcript	missense_variant	1424	1027	343	D/Y	Gat/Tat	rs767529375	.	.	-1	INSRR	HGNC	6093	protein_coding	YES	CCDS1160.1	ENSP00000357178	INSRR_HUMAN	I6U4P1_HUMAN	UPI000012D8BD	.	deleterious(0.01)	possibly_damaging(0.502)	4/22	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF107,Gene3D:3.80.20.20,PIRSF_domain:PIRSF000620,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGATCCTGTG	byFrequency	3	ESCA
OR10X1	0	.	GRCh37	1	158549594	158549594	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96C>G	p.%3D	p.G32G	ENST00000368150	1/1	43	33	10	52	52	0	OR10X1,synonymous_variant,p.%3D,ENST00000368150,;	C	ENSG00000186400	ENST00000368150	Transcript	synonymous_variant	96	96	32	G	ggC/ggG	.	.	.	-1	OR10X1	HGNC	14995	protein_coding	YES	CCDS30900.1	ENSP00000357132	O10X1_HUMAN	.	UPI000004CA20	.	.	.	1/1	.	hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF195,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAAGCCAAC	.	5	ESCA
PLEKHM2	0	.	GRCh37	1	16053914	16053914	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1347G>A	p.%3D	p.P449P	ENST00000375799	9/20	30	14	16	47	47	0	PLEKHM2,synonymous_variant,p.%3D,ENST00000375793,;PLEKHM2,synonymous_variant,p.%3D,ENST00000375799,;RP11-288I21.1,intron_variant,,ENST00000453804,;PLEKHM2,upstream_gene_variant,,ENST00000477849,;	A	ENSG00000116786	ENST00000375799	Transcript	synonymous_variant	1574	1347	449	P	ccG/ccA	.	.	.	1	PLEKHM2	HGNC	29131	protein_coding	YES	CCDS44063.1	ENSP00000364956	PKHM2_HUMAN	.	UPI00001C1D9C	.	.	.	9/20	.	hmmpanther:PTHR22835:SF132,hmmpanther:PTHR22835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCCGCCGCT	.	5	ESCA
RCSD1	0	.	GRCh37	1	167666533	167666533	+	Silent	SNP	G	G	A	rs149253367	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672G>A	p.%3D	p.A224A	ENST00000367854	6/7	41	29	11	45	45	0	RCSD1,synonymous_variant,p.%3D,ENST00000537350,;RCSD1,synonymous_variant,p.%3D,ENST00000367854,;RCSD1,downstream_gene_variant,,ENST00000361496,;	A	ENSG00000198771	ENST00000367854	Transcript	synonymous_variant	1003	672	224	A	gcG/gcA	rs149253367	.	.	1	RCSD1	HGNC	28310	protein_coding	YES	CCDS1263.1	ENSP00000356828	CPZIP_HUMAN	.	UPI0000204CFA	.	.	.	6/7	.	hmmpanther:PTHR21669,hmmpanther:PTHR21669:SF2	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0009	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCGGGAGA	byCluster|by1000G	5	ESCA
TNN	0	.	GRCh37	1	175067617	175067617	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2005G>A	p.Glu669Lys	p.E669K	ENST00000239462	9/19	104	73	30	128	128	0	TNN,missense_variant,p.Glu669Lys,ENST00000239462,;	A	ENSG00000120332	ENST00000239462	Transcript	missense_variant	2118	2005	669	E/K	Gag/Aag	.	.	.	1	TNN	HGNC	22942	protein_coding	YES	CCDS30943.1	ENSP00000239462	TENN_HUMAN	.	UPI00001D7DA9	.	deleterious(0.02)	benign(0.41)	9/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF167,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGGAGCAG	.	5	ESCA
PKP1	0	.	GRCh37	1	201292259	201292259	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1685A>G	p.Asp562Gly	p.D562G	ENST00000263946	10/15	55	34	21	90	90	0	PKP1,missense_variant,p.Asp562Gly,ENST00000352845,;PKP1,missense_variant,p.Asp562Gly,ENST00000263946,;PKP1,missense_variant,p.Asp541Gly,ENST00000367324,;PKP1,downstream_gene_variant,,ENST00000475988,;	G	ENSG00000081277	ENST00000263946	Transcript	missense_variant	1936	1685	562	D/G	gAt/gGt	.	.	.	1	PKP1	HGNC	9023	protein_coding	YES	CCDS30966.1	ENSP00000263946	PKP1_HUMAN	B4DRX5_HUMAN	UPI0000131B86	.	deleterious(0.04)	probably_damaging(0.998)	10/15	.	hmmpanther:PTHR10372:SF3,hmmpanther:PTHR10372,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGATGCTA	.	5	ESCA
TBCE	0	.	GRCh37	1	235612062	235612062	+	Silent	SNP	A	A	G	rs758366722	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1569A>G	p.%3D	p.L523L	ENST00000366601	17/17	22	16	6	25	25	0	TBCE,synonymous_variant,p.%3D,ENST00000543662,;TBCE,synonymous_variant,p.%3D,ENST00000366601,;TBCE,synonymous_variant,p.%3D,ENST00000406207,;B3GALNT2,downstream_gene_variant,,ENST00000366600,;TBCE,non_coding_transcript_exon_variant,,ENST00000472011,;TBCE,downstream_gene_variant,,ENST00000465463,;	G	ENSG00000116957	ENST00000366601	Transcript	synonymous_variant	1745	1569	523	L	ctA/ctG	rs758366722	.	.	1	TBCE	HGNC	11582	protein_coding	YES	CCDS1605.1	ENSP00000355560	TBCE_HUMAN	.	UPI000006F791	.	.	.	17/17	.	Superfamily_domains:SSF54236,Pfam_domain:PF14560,Gene3D:3.10.20.90,hmmpanther:PTHR15140:SF6,hmmpanther:PTHR15140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTATTAGT	.	5	ESCA
OR2W3	0	.	GRCh37	1	248059198	248059198	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310T>C	p.Phe104Leu	p.F104L	ENST00000537741	3/3	43	37	5	42	42	0	OR2W3,missense_variant,p.Phe104Leu,ENST00000537741,;OR2W3,missense_variant,p.Phe104Leu,ENST00000360358,;	C	ENSG00000238243	ENST00000537741	Transcript	missense_variant	567	310	104	F/L	Ttc/Ctc	.	.	.	1	OR2W3	HGNC	15021	protein_coding	YES	CCDS31099.1	ENSP00000445853	OR2W3_HUMAN	.	UPI0000061EA8	.	tolerated(0.12)	benign(0.354)	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF223,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTGTTCCTG	.	4	ESCA
ADC	0	.	GRCh37	1	33585965	33585965	+	3'UTR	SNP	C	C	A	rs117064966	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*182C>A	.	.	ENST00000294517	12/12	97	84	12	99	99	0	ADC,3_prime_UTR_variant,,ENST00000294517,;ADC,3_prime_UTR_variant,,ENST00000373443,;ADC,3_prime_UTR_variant,,ENST00000398167,;ADC,downstream_gene_variant,,ENST00000373441,;ADC,non_coding_transcript_exon_variant,,ENST00000481886,;ADC,non_coding_transcript_exon_variant,,ENST00000484656,;ADC,non_coding_transcript_exon_variant,,ENST00000471119,;ADC,non_coding_transcript_exon_variant,,ENST00000475935,;ADC,non_coding_transcript_exon_variant,,ENST00000478204,;	A	ENSG00000142920	ENST00000294517	Transcript	3_prime_UTR_variant	2152	.	.	.	.	rs117064966	.	.	1	ADC	HGNC	29957	protein_coding	YES	CCDS375.1	ENSP00000294517	ADC_HUMAN	D3DPR0_HUMAN,B3KV62_HUMAN	UPI0000047152	.	.	.	12/12	.	.	A:0.0012	A:0	A:0	.	A:0.006	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGTTCAAGTA	byFrequency|byCluster|by1000G	4	ESCA
MYCBP	0	.	GRCh37	1	39330042	39330042	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*300T>C	.	.	ENST00000397572	5/5	20	17	3	19	19	0	MYCBP,3_prime_UTR_variant,,ENST00000397572,;RRAGC,upstream_gene_variant,,ENST00000373001,;GJA9,downstream_gene_variant,,ENST00000454994,;RP5-864K19.4,intron_variant,,ENST00000456813,;RP5-864K19.4,intron_variant,,ENST00000433671,;MYCBP,non_coding_transcript_exon_variant,,ENST00000495043,;MYCBP,non_coding_transcript_exon_variant,,ENST00000494695,;MYCBP,downstream_gene_variant,,ENST00000465771,;MYCBP,downstream_gene_variant,,ENST00000489803,;MYCBP,downstream_gene_variant,,ENST00000462027,;MYCBP,downstream_gene_variant,,ENST00000489575,;	G	ENSG00000214114	ENST00000397572	Transcript	3_prime_UTR_variant	1412	.	.	.	.	.	.	.	-1	MYCBP	HGNC	7554	protein_coding	YES	CCDS431.1	ENSP00000380702	MYCBP_HUMAN	.	UPI000013CDE0	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTAAAATACAA	.	2	ESCA
MACF1	0	.	GRCh37	1	39797646	39797646	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4629+4621G>A	.	.	ENST00000545844	.	21	11	10	31	31	0	MACF1,missense_variant,p.Asp236Asn,ENST00000289893,;MACF1,missense_variant,p.Asp1796Asn,ENST00000564288,;MACF1,missense_variant,p.Asp1801Asn,ENST00000372915,;MACF1,missense_variant,p.Asp1833Asn,ENST00000567887,;MACF1,intron_variant,,ENST00000372925,;MACF1,intron_variant,,ENST00000361689,;MACF1,intron_variant,,ENST00000530262,;MACF1,intron_variant,,ENST00000539005,;MACF1,intron_variant,,ENST00000317713,;MACF1,intron_variant,,ENST00000545844,;MACF1,intron_variant,,ENST00000476350,;MACF1,downstream_gene_variant,,ENST00000528611,;MACF1,downstream_gene_variant,,ENST00000496804,;	A	ENSG00000127603	ENST00000545844	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	.	.	36/93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATTGACCAA	.	5	ESCA
HPCAL4	0	.	GRCh37	1	40147797	40147797	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*411C>G	.	.	ENST00000372844	4/4	43	19	24	44	44	0	HPCAL4,3_prime_UTR_variant,,ENST00000372844,;	C	ENSG00000116983	ENST00000372844	Transcript	3_prime_UTR_variant	1379	.	.	.	.	.	.	.	-1	HPCAL4	HGNC	18212	protein_coding	YES	CCDS441.1	ENSP00000361935	HPCL4_HUMAN	B4DG51_HUMAN	UPI0000073F20	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTGGAGCCT	.	5	ESCA
NASP	0	.	GRCh37	1	46073188	46073188	+	Missense_Mutation	SNP	C	C	G	rs774670119	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.605C>G	p.Thr202Ser	p.T202S	ENST00000350030	6/15	75	35	39	78	78	0	NASP,missense_variant,p.Thr138Ser,ENST00000527470,;NASP,missense_variant,p.Thr204Ser,ENST00000402363,;NASP,missense_variant,p.Thr202Ser,ENST00000350030,;NASP,missense_variant,p.Thr138Ser,ENST00000537798,;NASP,missense_variant,p.Thr165Ser,ENST00000470768,;NASP,intron_variant,,ENST00000351223,;NASP,intron_variant,,ENST00000528238,;NASP,intron_variant,,ENST00000372052,;NASP,intron_variant,,ENST00000525515,;NASP,intron_variant,,ENST00000437901,;NASP,non_coding_transcript_exon_variant,,ENST00000534101,;NASP,upstream_gene_variant,,ENST00000530073,;NASP,3_prime_UTR_variant,,ENST00000453748,;NASP,intron_variant,,ENST00000437362,;NASP,intron_variant,,ENST00000527359,;NASP,downstream_gene_variant,,ENST00000529333,;NASP,downstream_gene_variant,,ENST00000531532,;NASP,downstream_gene_variant,,ENST00000528084,;NASP,upstream_gene_variant,,ENST00000481782,;NASP,downstream_gene_variant,,ENST00000464190,;	G	ENSG00000132780	ENST00000350030	Transcript	missense_variant	692	605	202	T/S	aCt/aGt	rs774670119	.	.	1	NASP	HGNC	7644	protein_coding	YES	CCDS524.1	ENSP00000255120	NASP_HUMAN	Q9P1N1_HUMAN,B4DS57_HUMAN	UPI000012FDA0	.	tolerated_low_confidence(0.07)	benign(0.219)	6/15	.	hmmpanther:PTHR15081:SF1,hmmpanther:PTHR15081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGACTCTAG	.	5	ESCA
DHCR24	0	.	GRCh37	1	55315495	55315495	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2411G>A	.	.	ENST00000371269	9/9	41	28	13	56	56	0	DHCR24,3_prime_UTR_variant,,ENST00000371269,;DHCR24,downstream_gene_variant,,ENST00000537443,;DHCR24,downstream_gene_variant,,ENST00000535035,;DHCR24,downstream_gene_variant,,ENST00000436604,;	T	ENSG00000116133	ENST00000371269	Transcript	3_prime_UTR_variant	4061	.	.	.	.	.	.	.	-1	DHCR24	HGNC	2859	protein_coding	YES	CCDS600.1	ENSP00000360316	DHC24_HUMAN	Q3LIE7_HUMAN,B7Z546_HUMAN	UPI00000335D4	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCCCTCCC	.	5	ESCA
HS2ST1	0	.	GRCh37	1	87538711	87538711	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.219C>T	p.%3D	p.D73D	ENST00000370550	2/7	66	59	7	90	90	0	HS2ST1,synonymous_variant,p.%3D,ENST00000370550,;RP5-1052I5.2,synonymous_variant,p.%3D,ENST00000370548,;HS2ST1,synonymous_variant,p.%3D,ENST00000591456,;HS2ST1,synonymous_variant,p.%3D,ENST00000356813,;HS2ST1,synonymous_variant,p.%3D,ENST00000370551,;	T	ENSG00000153936	ENST00000370550	Transcript	synonymous_variant	582	219	73	D	gaC/gaT	.	.	.	1	HS2ST1	HGNC	5193	protein_coding	YES	CCDS711.1	ENSP00000359581	HS2ST_HUMAN	K7EP71_HUMAN	UPI0000073F43	.	.	.	2/7	.	hmmpanther:PTHR12129:SF14,hmmpanther:PTHR12129,Pfam_domain:PF03567,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGACATGGT	.	4	ESCA
NECAB3	0	.	GRCh37	20	32247407	32247407	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775C>G	p.Pro259Ala	p.P259A	ENST00000246190	8/12	82	56	25	110	110	0	NECAB3,missense_variant,p.Pro259Ala,ENST00000246190,;NECAB3,intron_variant,,ENST00000480994,;NECAB3,intron_variant,,ENST00000375238,;NECAB3,intron_variant,,ENST00000439478,;NECAB3,intron_variant,,ENST00000606690,;C20orf144,upstream_gene_variant,,ENST00000375222,;RP1-63M2.6,downstream_gene_variant,,ENST00000607224,;NECAB3,non_coding_transcript_exon_variant,,ENST00000483813,;NECAB3,intron_variant,,ENST00000463246,;NECAB3,intron_variant,,ENST00000485976,;NECAB3,intron_variant,,ENST00000478237,;NECAB3,intron_variant,,ENST00000494174,;NECAB3,intron_variant,,ENST00000606525,;NECAB3,downstream_gene_variant,,ENST00000498353,;NECAB3,downstream_gene_variant,,ENST00000606106,;NECAB3,upstream_gene_variant,,ENST00000477778,;NECAB3,intron_variant,,ENST00000485399,;NECAB3,intron_variant,,ENST00000607805,;NECAB3,intron_variant,,ENST00000488489,;NECAB3,downstream_gene_variant,,ENST00000606699,;C20orf144,upstream_gene_variant,,ENST00000607738,;NECAB3,downstream_gene_variant,,ENST00000493590,;	C	ENSG00000125967	ENST00000246190	Transcript	missense_variant	831	775	259	P/A	Cca/Gca	.	.	.	-1	NECAB3	HGNC	15851	protein_coding	YES	CCDS42866.1	ENSP00000246190	NECA3_HUMAN	H0UI92_HUMAN	UPI0000125101	.	tolerated(0.22)	benign(0)	8/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12178,hmmpanther:PTHR12178:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTGGTGGAT	.	5	ESCA
RBPJL	0	.	GRCh37	20	43938331	43938331	+	Missense_Mutation	SNP	C	C	T	rs775667917	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256C>T	p.Arg86Trp	p.R86W	ENST00000343694	3/12	56	45	11	68	68	0	RBPJL,missense_variant,p.Arg86Trp,ENST00000372741,;RBPJL,missense_variant,p.Arg86Trp,ENST00000343694,;RBPJL,missense_variant,p.Arg86Trp,ENST00000372743,;MATN4,upstream_gene_variant,,ENST00000372754,;MATN4,upstream_gene_variant,,ENST00000537548,;MATN4,upstream_gene_variant,,ENST00000360607,;MATN4,upstream_gene_variant,,ENST00000372751,;MATN4,upstream_gene_variant,,ENST00000372756,;MATN4,upstream_gene_variant,,ENST00000353917,;MATN4,upstream_gene_variant,,ENST00000342716,;RBPJL,upstream_gene_variant,,ENST00000464504,;	T	ENSG00000124232	ENST00000343694	Transcript	missense_variant	328	256	86	R/W	Cgg/Tgg	rs775667917,COSM1412041	.	.	1	RBPJL	HGNC	13761	protein_coding	YES	CCDS13349.1	ENSP00000341243	RBPJL_HUMAN	.	UPI0000047297	.	deleterious(0)	probably_damaging(1)	3/12	.	hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2,Gene3D:2.60.40.1450,Pfam_domain:PF09271,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGCGGTAG	byCluster	5	ESCA
DNTTIP1	0	.	GRCh37	20	44433804	44433804	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.623A>G	p.Asn208Ser	p.N208S	ENST00000372622	9/13	68	47	21	85	85	0	DNTTIP1,missense_variant,p.Asn208Ser,ENST00000372622,;DNTTIP1,missense_variant,p.Asn159Ser,ENST00000456939,;DNTTIP1,missense_variant,p.Asn135Ser,ENST00000435014,;DNTTIP1,downstream_gene_variant,,ENST00000415790,;DNTTIP1,non_coding_transcript_exon_variant,,ENST00000467701,;	G	ENSG00000101457	ENST00000372622	Transcript	missense_variant	691	623	208	N/S	aAt/aGt	.	.	.	1	DNTTIP1	HGNC	16160	protein_coding	YES	CCDS13369.1	ENSP00000361705	TDIF1_HUMAN	F2Z2A4_HUMAN	UPI0000136B4E	.	tolerated(0.41)	benign(0.008)	9/13	.	hmmpanther:PTHR23399,hmmpanther:PTHR23399:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGAATGAAT	.	5	ESCA
LTN1	0	.	GRCh37	21	30302439	30302439	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*331A>C	.	.	ENST00000389194	30/30	23	20	3	25	25	0	LTN1,3_prime_UTR_variant,,ENST00000361371,;LTN1,3_prime_UTR_variant,,ENST00000389194,;	G	ENSG00000198862	ENST00000389194	Transcript	3_prime_UTR_variant	5776	.	.	.	.	.	.	.	-1	LTN1	HGNC	13082	protein_coding	YES	CCDS33527.2	ENSP00000373846	LTN1_HUMAN	G1UI34_HUMAN	UPI000049DF6C	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATAGTTGTGCA	.	3	ESCA
U2AF1	0	.	GRCh37	21	44513084	44513084	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128A>G	.	.	ENST00000291552	8/8	25	18	7	31	31	0	U2AF1,3_prime_UTR_variant,,ENST00000380276,;U2AF1,3_prime_UTR_variant,,ENST00000398137,;U2AF1,3_prime_UTR_variant,,ENST00000291552,;U2AF1,3_prime_UTR_variant,,ENST00000459639,;U2AF1,downstream_gene_variant,,ENST00000486519,;U2AF1,3_prime_UTR_variant,,ENST00000464750,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000478282,;U2AF1,non_coding_transcript_exon_variant,,ENST00000471250,;U2AF1,downstream_gene_variant,,ENST00000496462,;U2AF1,downstream_gene_variant,,ENST00000463599,;	C	ENSG00000160201	ENST00000291552	Transcript	3_prime_UTR_variant	944	.	.	.	.	.	.	.	-1	U2AF1	HGNC	12453	protein_coding	YES	CCDS13694.1	ENSP00000291552	U2AF1_HUMAN	.	UPI0000000C26	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAAATTTTAT	.	5	ESCA
TNRC6B	0	.	GRCh37	22	40722824	40722824	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3579A>G	.	.	ENST00000454349	23/23	38	29	9	59	59	0	TNRC6B,3_prime_UTR_variant,,ENST00000454349,;TNRC6B,3_prime_UTR_variant,,ENST00000301923,;TNRC6B,3_prime_UTR_variant,,ENST00000335727,;TNRC6B,downstream_gene_variant,,ENST00000402203,;	G	ENSG00000100354	ENST00000454349	Transcript	3_prime_UTR_variant	9292	.	.	.	.	.	.	.	1	TNRC6B	HGNC	29190	protein_coding	YES	CCDS54533.1	ENSP00000401946	TNR6B_HUMAN	.	UPI00017A6F19	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTAATGAAG	.	5	ESCA
PLXNB2	0	.	GRCh37	22	50717349	50717349	+	Frame_Shift_Del	DEL	A	A	-	.	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4481delT	p.Ile1494ThrfsTer38	p.I1494Tfs*38	ENST00000449103	28/37	40	34	6	39	39	0	PLXNB2,frameshift_variant,p.Ile1494ThrfsTer38,ENST00000359337,;PLXNB2,frameshift_variant,p.Ile1494ThrfsTer38,ENST00000449103,;PLXNB2,intron_variant,,ENST00000411680,;AL022328.1,downstream_gene_variant,,ENST00000595015,;PLXNB2,downstream_gene_variant,,ENST00000427829,;PLXNB2,downstream_gene_variant,,ENST00000496720,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479701,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000463165,;PLXNB2,upstream_gene_variant,,ENST00000479818,;PLXNB2,downstream_gene_variant,,ENST00000492578,;	-	ENSG00000196576	ENST00000449103	Transcript	frameshift_variant	4622	4481	1494	I/X	aTc/ac	COSM4164976	.	.	-1	PLXNB2	HGNC	9104	protein_coding	YES	CCDS43035.1	ENSP00000409171	PLXB2_HUMAN	Q2TBE4_HUMAN,E2PU09_HUMAN,A6QRH1_HUMAN	UPI000003812D	.	.	.	28/37	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF9,Pfam_domain:PF08337,Gene3D:3.10.20.90	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCAATGATCTTC	.	3	ESCA
ARSA	0	.	GRCh37	22	51065088	51065088	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785C>A	p.Thr262Asn	p.T262N	ENST00000216124	4/8	36	22	14	45	45	0	ARSA,missense_variant,p.Thr260Asn,ENST00000547805,;ARSA,missense_variant,p.Thr262Asn,ENST00000395619,;ARSA,missense_variant,p.Thr176Asn,ENST00000453344,;ARSA,missense_variant,p.Thr262Asn,ENST00000395621,;ARSA,missense_variant,p.Thr262Asn,ENST00000216124,;ARSA,missense_variant,p.Thr260Asn,ENST00000547307,;ARSA,missense_variant,p.Thr262Asn,ENST00000356098,;ARSA,upstream_gene_variant,,ENST00000610191,;ARSA,non_coding_transcript_exon_variant,,ENST00000551731,;ARSA,upstream_gene_variant,,ENST00000608497,;	T	ENSG00000100299	ENST00000216124	Transcript	missense_variant	1178	785	262	T/N	aCc/aAc	.	.	.	-1	ARSA	HGNC	713	protein_coding	YES	CCDS14100.2	ENSP00000216124	ARSA_HUMAN	.	UPI000013C6C4	.	tolerated(0.45)	benign(0.001)	4/8	.	hmmpanther:PTHR10342:SF22,hmmpanther:PTHR10342,Pfam_domain:PF00884,Gene3D:3.40.720.10,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGGGTCCCC	.	5	ESCA
GCC2	0	.	GRCh37	2	109124022	109124022	+	Missense_Mutation	SNP	A	A	G	rs745310946	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4991A>G	p.Glu1664Gly	p.E1664G	ENST00000309863	23/23	202	195	6	204	204	0	GCC2,missense_variant,p.Glu1664Gly,ENST00000309863,;AC012487.2,non_coding_transcript_exon_variant,,ENST00000322353,;AC012487.2,downstream_gene_variant,,ENST00000440975,;GCC2,3_prime_UTR_variant,,ENST00000482325,;GCC2,non_coding_transcript_exon_variant,,ENST00000480863,;	G	ENSG00000135968	ENST00000309863	Transcript	missense_variant	5705	4991	1664	E/G	gAa/gGa	rs745310946	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	deleterious(0)	possibly_damaging(0.522)	23/23	.	hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAGGAAGAAA	.	2	ESCA
IL37	0	.	GRCh37	2	113670654	113670654	+	Missense_Mutation	SNP	C	C	T	rs550494451	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.65C>T	p.Pro22Leu	p.P22L	ENST00000263326	1/5	78	57	21	78	78	0	IL37,missense_variant,p.Pro22Leu,ENST00000353225,;IL37,missense_variant,p.Pro22Leu,ENST00000349806,;IL37,missense_variant,p.Pro22Leu,ENST00000352179,;IL37,missense_variant,p.Pro22Leu,ENST00000263326,;IL37,upstream_gene_variant,,ENST00000311328,;	T	ENSG00000125571	ENST00000263326	Transcript	missense_variant	107	65	22	P/L	cCc/cTc	rs550494451	.	.	1	IL37	HGNC	15563	protein_coding	YES	CCDS2103.1	ENSP00000263326	IL37_HUMAN	.	UPI000003C9C6	.	tolerated(0.29)	benign(0.012)	1/5	.	hmmpanther:PTHR10078:SF9,hmmpanther:PTHR10078	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACCCCAGT	by1000G	5	ESCA
MARCO	0	.	GRCh37	2	119739003	119739003	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785G>A	p.Gly262Asp	p.G262D	ENST00000327097	9/17	72	43	29	70	70	0	MARCO,missense_variant,p.Gly262Asp,ENST00000327097,;MARCO,missense_variant,p.Gly184Asp,ENST00000541757,;	A	ENSG00000019169	ENST00000327097	Transcript	missense_variant	920	785	262	G/D	gGc/gAc	.	.	.	1	MARCO	HGNC	6895	protein_coding	YES	CCDS2124.1	ENSP00000318916	MARCO_HUMAN	Q4ZG40_HUMAN,C9JKT8_HUMAN,B4DW79_HUMAN,B4DLJ6_HUMAN	UPI0000000DF8	.	deleterious(0)	probably_damaging(0.998)	9/17	.	hmmpanther:PTHR24021:SF16,hmmpanther:PTHR24021,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGGCATGA	.	5	ESCA
MARS2	0	.	GRCh37	2	198572530	198572530	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*619A>T	.	.	ENST00000282276	1/1	55	32	22	110	110	0	MARS2,3_prime_UTR_variant,,ENST00000282276,;AC011997.1,intron_variant,,ENST00000409845,;	T	ENSG00000247626	ENST00000282276	Transcript	3_prime_UTR_variant	2444	.	.	.	.	.	.	.	1	MARS2	HGNC	25133	protein_coding	YES	CCDS33358.1	ENSP00000282276	SYMM_HUMAN	.	UPI00000492CE	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTAATCTCA	.	5	ESCA
COL6A3	0	.	GRCh37	2	238259800	238259800	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6789A>T	p.%3D	p.R2263R	ENST00000295550	27/44	30	27	3	54	54	0	COL6A3,synonymous_variant,p.%3D,ENST00000346358,;COL6A3,synonymous_variant,p.%3D,ENST00000347401,;COL6A3,synonymous_variant,p.%3D,ENST00000472056,;COL6A3,synonymous_variant,p.%3D,ENST00000353578,;COL6A3,synonymous_variant,p.%3D,ENST00000409809,;COL6A3,synonymous_variant,p.%3D,ENST00000295550,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;	A	ENSG00000163359	ENST00000295550	Transcript	synonymous_variant	7242	6789	2263	R	cgA/cgT	.	.	.	-1	COL6A3	HGNC	2213	protein_coding	YES	CCDS33412.1	ENSP00000295550	CO6A3_HUMAN	Q8N4Z1_HUMAN,D9ZGF2_HUMAN	UPI0000456F39	.	.	.	27/44	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22992,hmmpanther:PTHR22992:SF83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCCTCGTTC	.	2	ESCA
EHD3	0	.	GRCh37	2	31483423	31483423	+	Missense_Mutation	SNP	C	C	T	rs778088572	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550C>T	p.Arg184Cys	p.R184C	ENST00000322054	4/6	62	45	16	58	58	0	EHD3,missense_variant,p.Arg184Cys,ENST00000322054,;EHD3,intron_variant,,ENST00000541626,;	T	ENSG00000013016	ENST00000322054	Transcript	missense_variant	835	550	184	R/C	Cgc/Tgc	rs778088572	.	.	1	EHD3	HGNC	3244	protein_coding	YES	CCDS1774.1	ENSP00000327116	EHD3_HUMAN	.	UPI0000140D07	.	deleterious(0.01)	possibly_damaging(0.605)	4/6	.	PROSITE_profiles:PS51718,hmmpanther:PTHR11216:SF67,hmmpanther:PTHR11216,Pfam_domain:PF00350,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACCGCATC	.	5	ESCA
EML4	0	.	GRCh37	2	42557121	42557121	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2720A>G	p.Asn907Ser	p.N907S	ENST00000318522	23/23	34	26	7	19	19	0	EML4,missense_variant,p.Asn918Ser,ENST00000401738,;EML4,missense_variant,p.Asn907Ser,ENST00000318522,;EML4,missense_variant,p.Asn171Ser,ENST00000453191,;EML4,missense_variant,p.Asn849Ser,ENST00000402711,;COX7A2L,downstream_gene_variant,,ENST00000468711,;EML4,non_coding_transcript_exon_variant,,ENST00000406175,;	G	ENSG00000143924	ENST00000318522	Transcript	missense_variant	2982	2720	907	N/S	aAt/aGt	.	.	.	1	EML4	HGNC	1316	protein_coding	YES	CCDS1807.1	ENSP00000320663	EMAL4_HUMAN	F2Z2B5_HUMAN	UPI0000140350	.	tolerated_low_confidence(0.66)	benign(0.001)	23/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAAATGAGA	.	5	ESCA
UMPS	0	.	GRCh37	3	124451286	124451286	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.156+1812G>A	.	.	ENST00000232607	.	51	39	11	59	59	0	UMPS,intron_variant,,ENST00000536109,;UMPS,intron_variant,,ENST00000538242,;UMPS,intron_variant,,ENST00000232607,;UMPS,intron_variant,,ENST00000413078,;MIR544B,non_coding_transcript_exon_variant,,ENST00000582372,;UMPS,upstream_gene_variant,,ENST00000498715,;UMPS,intron_variant,,ENST00000474588,;UMPS,intron_variant,,ENST00000462091,;UMPS,intron_variant,,ENST00000479719,;UMPS,intron_variant,,ENST00000497791,;UMPS,intron_variant,,ENST00000467167,;UMPS,intron_variant,,ENST00000460034,;RP11-71H17.1,downstream_gene_variant,,ENST00000475510,;	A	ENSG00000114491	ENST00000232607	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	UMPS	HGNC	12563	protein_coding	YES	CCDS3029.1	ENSP00000232607	UMPS_HUMAN	B5LY64_HUMAN,A8K5J1_HUMAN	UPI0000001223	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGGGAATT	.	5	ESCA
COL6A6	0	.	GRCh37	3	130293213	130293213	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3391G>A	p.Asp1131Asn	p.D1131N	ENST00000358511	7/36	52	48	4	43	43	0	COL6A6,missense_variant,p.Asp1131Asn,ENST00000453409,;COL6A6,missense_variant,p.Asp1131Asn,ENST00000358511,;	A	ENSG00000206384	ENST00000358511	Transcript	missense_variant	3422	3391	1131	D/N	Gac/Aac	COSM1038237,COSM1593316	.	.	1	COL6A6	HGNC	27023	protein_coding	YES	CCDS46911.1	ENSP00000351310	CO6A6_HUMAN	.	UPI00015B6548	.	tolerated(0.98)	benign(0.021)	7/36	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF86,hmmpanther:PTHR22992,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTATCGACATC	.	3	ESCA
SLC33A1	0	.	GRCh37	3	155571332	155571332	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455G>C	p.Gly152Ala	p.G152A	ENST00000392845	1/6	65	54	11	64	64	0	SLC33A1,missense_variant,p.Gly152Ala,ENST00000392845,;SLC33A1,missense_variant,p.Gly152Ala,ENST00000359479,;SLC33A1,upstream_gene_variant,,ENST00000475842,;SLC33A1,upstream_gene_variant,,ENST00000460729,;SLC33A1,upstream_gene_variant,,ENST00000468581,;	G	ENSG00000169359	ENST00000392845	Transcript	missense_variant	836	455	152	G/A	gGa/gCa	.	.	.	-1	SLC33A1	HGNC	95	protein_coding	YES	CCDS3173.1	ENSP00000376587	ACATN_HUMAN	.	UPI000006E3FD	.	deleterious(0.04)	probably_damaging(0.923)	1/6	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,Pfam_domain:PF13000,TIGRFAM_domain:TIGR00901,hmmpanther:PTHR12778,hmmpanther:PTHR12778:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGTCCTAGT	.	5	ESCA
MYNN	0	.	GRCh37	3	169496700	169496700	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.411A>G	p.%3D	p.E137E	ENST00000349841	3/8	38	30	8	45	45	0	MYNN,synonymous_variant,p.%3D,ENST00000356716,;MYNN,synonymous_variant,p.%3D,ENST00000392733,;MYNN,synonymous_variant,p.%3D,ENST00000349841,;MYNN,synonymous_variant,p.%3D,ENST00000544106,;RP11-362K14.5,non_coding_transcript_exon_variant,,ENST00000602342,;MYNN,3_prime_UTR_variant,,ENST00000602751,;MYNN,upstream_gene_variant,,ENST00000602391,;	G	ENSG00000085274	ENST00000349841	Transcript	synonymous_variant	1074	411	137	E	gaA/gaG	.	.	.	1	MYNN	HGNC	14955	protein_coding	YES	CCDS3207.1	ENSP00000326240	MYNN_HUMAN	B4E2H9_HUMAN	UPI000000D72A	.	.	.	3/8	.	hmmpanther:PTHR24402:SF202,hmmpanther:PTHR24402	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGAATTGAA	.	5	ESCA
TBC1D5	0	.	GRCh37	3	17416137	17416137	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736C>T	p.%3D	p.L246L	ENST00000446818	12/24	52	49	3	83	83	0	TBC1D5,synonymous_variant,p.%3D,ENST00000429924,;TBC1D5,synonymous_variant,p.%3D,ENST00000446818,;TBC1D5,synonymous_variant,p.%3D,ENST00000429383,;TBC1D5,synonymous_variant,p.%3D,ENST00000253692,;TBC1D5,intron_variant,,ENST00000414318,;TBC1D5,upstream_gene_variant,,ENST00000465884,;	A	ENSG00000131374	ENST00000446818	Transcript	synonymous_variant	1000	736	246	L	Ctg/Ttg	.	.	.	-1	TBC1D5	HGNC	19166	protein_coding	YES	CCDS46770.1	ENSP00000402935	TBCD5_HUMAN	F2Z3C3_HUMAN,C9K0P2_HUMAN,C9JWX0_HUMAN,C9JW04_HUMAN,C9JNM0_HUMAN,C9JMP7_HUMAN,C9JIU4_HUMAN,C9JED7_HUMAN,C9JDR8_HUMAN,C9J397_HUMAN	UPI00017E10F6	.	.	.	12/24	.	PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF220,Pfam_domain:PF00566,Gene3D:2qq8A02,SMART_domains:SM00164	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCAGATACT	.	2	ESCA
ABCC5	0	.	GRCh37	3	183638532	183638532	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*556G>A	.	.	ENST00000334444	30/30	28	23	5	27	27	0	ABCC5,3_prime_UTR_variant,,ENST00000334444,;ABCC5,downstream_gene_variant,,ENST00000265586,;ABCC5,3_prime_UTR_variant,,ENST00000437205,;ABCC5,downstream_gene_variant,,ENST00000443497,;	T	ENSG00000114770	ENST00000334444	Transcript	3_prime_UTR_variant	5111	.	.	.	.	.	.	.	-1	ABCC5	HGNC	56	protein_coding	YES	CCDS43176.1	ENSP00000333926	MRP5_HUMAN	C9JZL5_HUMAN	UPI000004A33C	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGTCGGAGG	.	2	ESCA
TRA2B	0	.	GRCh37	3	185639916	185639916	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523-2A>G	.	p.X175_splice	ENST00000453386	.	36	26	10	38	38	0	TRA2B,splice_acceptor_variant,,ENST00000259043,;TRA2B,splice_acceptor_variant,,ENST00000453386,;TRA2B,splice_acceptor_variant,,ENST00000382191,;TRA2B,upstream_gene_variant,,ENST00000414862,;TRA2B,splice_acceptor_variant,,ENST00000465245,;TRA2B,downstream_gene_variant,,ENST00000471134,;TRA2B,splice_acceptor_variant,,ENST00000463328,;TRA2B,splice_acceptor_variant,,ENST00000487615,;TRA2B,splice_acceptor_variant,,ENST00000492417,;TRA2B,splice_acceptor_variant,,ENST00000456380,;TRA2B,non_coding_transcript_exon_variant,,ENST00000466832,;TRA2B,downstream_gene_variant,,ENST00000477939,;TRA2B,downstream_gene_variant,,ENST00000485530,;TRA2B,downstream_gene_variant,,ENST00000493864,;	C	ENSG00000136527	ENST00000453386	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	TRA2B	HGNC	10781	protein_coding	YES	CCDS33905.1	ENSP00000416959	TRA2B_HUMAN	.	UPI00000040A0	.	.	.	.	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCCTTCAAA	.	5	ESCA
MUC4	0	.	GRCh37	3	195512519	195512519	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5932T>C	p.Ser1978Pro	p.S1978P	ENST00000463781	2/25	526	507	19	465	465	0	MUC4,missense_variant,p.Ser1978Pro,ENST00000475231,;MUC4,missense_variant,p.Ser1978Pro,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.Ser1978Pro,ENST00000477086,;MUC4,missense_variant,p.Ser1978Pro,ENST00000466475,;MUC4,missense_variant,p.Ser1978Pro,ENST00000478156,;MUC4,missense_variant,p.Ser1978Pro,ENST00000470451,;MUC4,missense_variant,p.Ser1978Pro,ENST00000479406,;MUC4,missense_variant,p.Ser1978Pro,ENST00000477756,;MUC4,missense_variant,p.Ser1978Pro,ENST00000462323,;MUC4,missense_variant,p.Ser1978Pro,ENST00000480843,;	G	ENSG00000145113	ENST00000463781	Transcript	missense_variant	6392	5932	1978	S/P	Tcc/Ccc	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	unknown(0)	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTGGACACTG	.	2	ESCA
TRAK1	0	.	GRCh37	3	42244124	42244124	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1624G>A	p.Glu542Lys	p.E542K	ENST00000327628	13/16	45	41	3	107	107	0	TRAK1,missense_variant,p.Glu468Lys,ENST00000449246,;TRAK1,missense_variant,p.Glu484Lys,ENST00000396175,;TRAK1,missense_variant,p.Glu260Lys,ENST00000427771,;TRAK1,missense_variant,p.Glu484Lys,ENST00000341421,;TRAK1,missense_variant,p.Glu542Lys,ENST00000327628,;TRAK1,non_coding_transcript_exon_variant,,ENST00000487159,;TRAK1,non_coding_transcript_exon_variant,,ENST00000484786,;	A	ENSG00000182606	ENST00000327628	Transcript	missense_variant	2024	1624	542	E/K	Gag/Aag	.	.	.	1	TRAK1	HGNC	29947	protein_coding	YES	CCDS43072.1	ENSP00000328998	TRAK1_HUMAN	.	UPI0000139F52	.	deleterious(0.03)	possibly_damaging(0.626)	13/16	.	hmmpanther:PTHR15751:SF11,hmmpanther:PTHR15751,Pfam_domain:PF12448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACTGAGAGC	.	2	ESCA
TREX1	0	.	GRCh37	3	48508870	48508870	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.981T>C	p.%3D	p.D327D	ENST00000422277	1/1	17	11	6	56	56	0	TREX1,synonymous_variant,p.%3D,ENST00000444177,;TREX1,synonymous_variant,p.%3D,ENST00000296443,;TREX1,synonymous_variant,p.%3D,ENST00000433541,;TREX1,synonymous_variant,p.%3D,ENST00000422277,;TREX1,synonymous_variant,p.%3D,ENST00000436480,;TREX1,synonymous_variant,p.%3D,ENST00000456089,;ATRIP,downstream_gene_variant,,ENST00000320211,;SHISA5,downstream_gene_variant,,ENST00000296444,;SHISA5,downstream_gene_variant,,ENST00000442747,;ATRIP,downstream_gene_variant,,ENST00000357105,;SHISA5,downstream_gene_variant,,ENST00000444115,;SHISA5,downstream_gene_variant,,ENST00000417841,;ATRIP,downstream_gene_variant,,ENST00000346691,;ATRIP,downstream_gene_variant,,ENST00000412052,;SHISA5,downstream_gene_variant,,ENST00000426002,;SHISA5,downstream_gene_variant,,ENST00000443308,;SHISA5,downstream_gene_variant,,ENST00000486344,;SHISA5,downstream_gene_variant,,ENST00000466424,;TREX1,downstream_gene_variant,,ENST00000492235,;SHISA5,downstream_gene_variant,,ENST00000465449,;TREX1,non_coding_transcript_exon_variant,,ENST00000395677,;SHISA5,downstream_gene_variant,,ENST00000494854,;SHISA5,downstream_gene_variant,,ENST00000460758,;ATRIP,downstream_gene_variant,,ENST00000424906,;SHISA5,downstream_gene_variant,,ENST00000417962,;SHISA5,downstream_gene_variant,,ENST00000415268,;SHISA5,downstream_gene_variant,,ENST00000424965,;SHISA5,downstream_gene_variant,,ENST00000497863,;	C	ENSG00000213689	ENST00000422277	Transcript	synonymous_variant	1642	981	327	D	gaT/gaC	.	.	.	1	TREX1	HGNC	12269	protein_coding	YES	CCDS43086.1	ENSP00000390478	TREX1_HUMAN	Q5TZT0_HUMAN,C9J052_HUMAN	UPI00000411D8	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGATCTTCC	.	5	ESCA
LRBA	0	.	GRCh37	4	151935949	151935949	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-155C>T	.	.	ENST00000357115	2/58	27	23	4	59	59	0	LRBA,5_prime_UTR_variant,,ENST00000535741,;LRBA,5_prime_UTR_variant,,ENST00000507224,;LRBA,5_prime_UTR_variant,,ENST00000357115,;LRBA,5_prime_UTR_variant,,ENST00000510413,;LRBA,non_coding_transcript_exon_variant,,ENST00000510841,;LRBA,non_coding_transcript_exon_variant,,ENST00000514435,;	A	ENSG00000198589	ENST00000357115	Transcript	5_prime_UTR_variant	90	.	.	.	.	.	.	.	-1	LRBA	HGNC	1742	protein_coding	YES	CCDS3773.1	ENSP00000349629	LRBA_HUMAN	Q7KZN3_HUMAN	UPI000013E35C	.	.	.	2/58	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE	GCGTCGCCCTC	.	2	ESCA
DDX60L	0	.	GRCh37	4	169279318	169279318	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5101A>T	p.Ser1701Cys	p.S1701C	ENST00000260184	38/38	39	36	3	70	70	0	DDX60L,missense_variant,p.Ser1701Cys,ENST00000511577,;DDX60L,missense_variant,p.Ser1701Cys,ENST00000260184,;DDX60L,non_coding_transcript_exon_variant,,ENST00000510590,;DDX60L,non_coding_transcript_exon_variant,,ENST00000513103,;	A	ENSG00000181381	ENST00000260184	Transcript	missense_variant	5322	5101	1701	S/C	Agt/Tgt	.	.	.	-1	DDX60L	HGNC	26429	protein_coding	YES	CCDS47161.1	ENSP00000260184	DDX6L_HUMAN	D6RIU1_HUMAN,D6RBA2_HUMAN,D6RB62_HUMAN	UPI0001553B03	.	tolerated_low_confidence(0.19)	benign(0)	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTGACTCATTT	.	3	ESCA
RFC1	0	.	GRCh37	4	39306472	39306472	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2075A>T	p.Glu692Val	p.E692V	ENST00000381897	15/25	59	43	15	49	49	0	RFC1,missense_variant,p.Glu692Val,ENST00000381897,;RFC1,missense_variant,p.Glu154Val,ENST00000504554,;RFC1,missense_variant,p.Glu691Val,ENST00000349703,;RFC1,downstream_gene_variant,,ENST00000502706,;RFC1,upstream_gene_variant,,ENST00000505077,;	A	ENSG00000035928	ENST00000381897	Transcript	missense_variant	2209	2075	692	E/V	gAg/gTg	.	.	.	-1	RFC1	HGNC	9969	protein_coding	YES	CCDS56329.1	ENSP00000371321	RFC1_HUMAN	.	UPI0000167BB4	.	deleterious(0)	probably_damaging(0.978)	15/25	.	hmmpanther:PTHR11107,hmmpanther:PTHR11107:SF9,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,PIRSF_domain:PIRSF036578,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGACTCAGCA	.	5	ESCA
GRXCR1	0	.	GRCh37	4	42965026	42965026	+	Missense_Mutation	SNP	G	G	T	rs577521620	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502G>T	p.Val168Leu	p.V168L	ENST00000399770	2/4	118	87	30	112	112	0	GRXCR1,missense_variant,p.Val168Leu,ENST00000399770,;	T	ENSG00000215203	ENST00000399770	Transcript	missense_variant	502	502	168	V/L	Gta/Tta	rs577521620,COSM1055539	.	.	1	GRXCR1	HGNC	31673	protein_coding	YES	CCDS43225.1	ENSP00000382670	GRCR1_HUMAN	.	UPI00004191A5	.	deleterious(0.01)	possibly_damaging(0.489)	2/4	.	PROSITE_profiles:PS51354,hmmpanther:PTHR10168:SF65,hmmpanther:PTHR10168,Pfam_domain:PF00462,Gene3D:3.40.30.10,Superfamily_domains:SSF52833	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.V168I|c.502G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCGCGTAAAA	by1000G	5	ESCA
FRYL	0	.	GRCh37	4	48597637	48597637	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1218A>G	p.Ile406Met	p.I406M	ENST00000358350	15/64	37	33	4	52	52	0	FRYL,missense_variant,p.Ile112Met,ENST00000506685,;FRYL,missense_variant,p.Ile406Met,ENST00000358350,;FRYL,missense_variant,p.Ile406Met,ENST00000503238,;FRYL,missense_variant,p.Ile406Met,ENST00000507711,;FRYL,missense_variant,p.Ile406Met,ENST00000537810,;FRYL,5_prime_UTR_variant,,ENST00000264319,;	C	ENSG00000075539	ENST00000358350	Transcript	missense_variant	1823	1218	406	I/M	atA/atG	.	.	.	-1	FRYL	HGNC	29127	protein_coding	YES	CCDS43227.1	ENSP00000351113	FRYL_HUMAN	.	UPI0000EBC149	.	deleterious(0)	probably_damaging(0.995)	15/64	.	Pfam_domain:PF14222,hmmpanther:PTHR12295:SF9,hmmpanther:PTHR12295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAAATATATT	.	2	ESCA
UBA6	0	.	GRCh37	4	68544176	68544176	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334G>T	p.Val112Phe	p.V112F	ENST00000322244	5/33	36	25	11	51	51	0	UBA6,missense_variant,p.Val112Phe,ENST00000322244,;UBA6,missense_variant,p.Val112Phe,ENST00000420827,;UBA6,non_coding_transcript_exon_variant,,ENST00000429659,;UBA6,non_coding_transcript_exon_variant,,ENST00000506571,;	A	ENSG00000033178	ENST00000322244	Transcript	missense_variant	394	334	112	V/F	Gtt/Ttt	.	.	.	-1	UBA6	HGNC	25581	protein_coding	YES	CCDS3516.1	ENSP00000313454	UBA6_HUMAN	B3KSS1_HUMAN	UPI000004A4F7	.	deleterious(0)	benign(0.398)	5/33	.	hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF141,Gene3D:3.40.50.720,TIGRFAM_domain:TIGR01408,Pfam_domain:PF00899,Superfamily_domains:SSF69572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAACATCAT	.	5	ESCA
YTHDC2	0	.	GRCh37	5	112862420	112862420	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.613A>G	p.Ile205Val	p.I205V	ENST00000161863	4/30	55	31	23	116	116	0	YTHDC2,missense_variant,p.Ile205Val,ENST00000515883,;YTHDC2,missense_variant,p.Ile205Val,ENST00000161863,;YTHDC2,downstream_gene_variant,,ENST00000514720,;YTHDC2,intron_variant,,ENST00000503857,;	G	ENSG00000047188	ENST00000161863	Transcript	missense_variant	826	613	205	I/V	Ata/Gta	.	.	.	1	YTHDC2	HGNC	24721	protein_coding	YES	CCDS4113.1	ENSP00000161863	YTDC2_HUMAN	D6RA70_HUMAN	UPI0000367311	.	tolerated(1)	benign(0.05)	4/30	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF52540,SMART_domains:SM00487,Gene3D:3.40.50.300,Pfam_domain:PF00270,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF86,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAATAATT	.	5	ESCA
TNFAIP8	0	.	GRCh37	5	118604488	118604488	+	5'UTR	SNP	C	C	T	rs181428331	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-298C>T	.	.	ENST00000388882	1/3	9	4	5	12	12	0	TNFAIP8,5_prime_UTR_variant,,ENST00000388882,;TNFAIP8,5_prime_UTR_variant,,ENST00000274456,;	T	ENSG00000145779	ENST00000388882	Transcript	5_prime_UTR_variant	40	.	.	.	.	rs181428331	.	.	1	TNFAIP8	HGNC	17260	protein_coding	.	.	ENSP00000429432	.	E5RIJ3_HUMAN	UPI0001E8F1B0	.	.	.	1/3	.	.	T:0.0020	T:0	T:0	.	T:0.0099	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	ACCCGCGCTTG	byFrequency|by1000G	2	ESCA
FSTL4	0	.	GRCh37	5	132585213	132585213	+	Silent	SNP	G	G	A	rs375676940	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783C>T	p.%3D	p.T261T	ENST00000265342	7/16	14	10	3	20	20	0	FSTL4,synonymous_variant,p.%3D,ENST00000265342,;CTB-49A3.5,downstream_gene_variant,,ENST00000515122,;CTB-49A3.5,downstream_gene_variant,,ENST00000504312,;FSTL4,non_coding_transcript_exon_variant,,ENST00000507112,;	A	ENSG00000053108	ENST00000265342	Transcript	synonymous_variant	1033	783	261	T	acC/acT	rs375676940,COSM1433120	.	.	-1	FSTL4	HGNC	21389	protein_coding	YES	CCDS34238.1	ENSP00000265342	FSTL4_HUMAN	.	UPI000003AFB0	.	.	.	7/16	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50835,hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF9,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	CCCACGGTCAC	byCluster|by1000G	2	ESCA
C5orf54	0	.	GRCh37	5	159821723	159821723	+	Missense_Mutation	SNP	C	C	T	rs775463125	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775G>A	p.Val259Met	p.V259M	ENST00000408953	2/2	17	10	7	52	52	0	C5orf54,missense_variant,p.Val259Met,ENST00000408953,;C5orf54,missense_variant,p.Val259Met,ENST00000523213,;	T	ENSG00000221886	ENST00000408953	Transcript	missense_variant	1283	775	259	V/M	Gtg/Atg	rs775463125	.	.	-1	C5orf54	HGNC	30804	protein_coding	YES	CCDS34283.1	ENSP00000386184	ZBED8_HUMAN	.	UPI00000741A3	.	tolerated(0.12)	benign(0.01)	2/2	.	Superfamily_domains:SSF53098,hmmpanther:PTHR11697:SF102,hmmpanther:PTHR11697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCACGTAGG	byFrequency	2	ESCA
CHD1	0	.	GRCh37	5	98223851	98223851	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2437A>G	p.Met813Val	p.M813V	ENST00000284049	16/35	63	33	30	109	109	0	CHD1,missense_variant,p.Met813Val,ENST00000284049,;RNU6-402P,upstream_gene_variant,,ENST00000410678,;CHD1,non_coding_transcript_exon_variant,,ENST00000511628,;CHD1,upstream_gene_variant,,ENST00000505982,;	C	ENSG00000153922	ENST00000284049	Transcript	missense_variant	2587	2437	813	M/V	Atg/Gtg	.	.	.	-1	CHD1	HGNC	1915	protein_coding	YES	CCDS34204.1	ENSP00000284049	CHD1_HUMAN	.	UPI000013DD75	.	deleterious(0)	probably_damaging(0.998)	16/35	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,hmmpanther:PTHR10799:SF535,hmmpanther:PTHR10799,PROSITE_profiles:PS51194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCATTTGTG	.	5	ESCA
AIM1	0	.	GRCh37	6	106967345	106967345	+	Silent	SNP	C	C	G	rs761466918	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1038C>G	p.%3D	p.T346T	ENST00000369066	2/20	22	18	4	29	29	0	AIM1,synonymous_variant,p.%3D,ENST00000369066,;	G	ENSG00000112297	ENST00000369066	Transcript	synonymous_variant	1525	1038	346	T	acC/acG	rs761466918	.	.	1	AIM1	HGNC	356	protein_coding	YES	CCDS34506.1	ENSP00000358062	AIM1_HUMAN	B3KPT0_HUMAN	UPI000013C91D	.	.	.	2/20	.	hmmpanther:PTHR11818:SF2,hmmpanther:PTHR11818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTACCGTCTC	byFrequency	4	ESCA
HIVEP1	0	.	GRCh37	6	12161991	12161991	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6807G>A	p.%3D	p.R2269R	ENST00000379388	8/9	22	13	8	20	20	0	HIVEP1,synonymous_variant,p.%3D,ENST00000541134,;HIVEP1,synonymous_variant,p.%3D,ENST00000379388,;HIVEP1,synonymous_variant,p.%3D,ENST00000442081,;HIVEP1,3_prime_UTR_variant,,ENST00000399469,;	A	ENSG00000095951	ENST00000379388	Transcript	synonymous_variant	7139	6807	2269	R	agG/agA	.	.	.	1	HIVEP1	HGNC	4920	protein_coding	YES	CCDS43426.1	ENSP00000368698	ZEP1_HUMAN	C9JZF8_HUMAN,C9JAW2_HUMAN,C9J2N3_HUMAN	UPI000020D52B	.	.	.	8/9	.	hmmpanther:PTHR23233:SF48,hmmpanther:PTHR23233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAGGAAGAC	.	5	ESCA
TRDN	0	.	GRCh37	6	123892175	123892175	+	Missense_Mutation	SNP	G	G	A	rs371627659	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.125C>T	p.Thr42Met	p.T42M	ENST00000398178	2/41	74	39	35	67	67	0	TRDN,missense_variant,p.Thr42Met,ENST00000398178,;TRDN,missense_variant,p.Thr42Met,ENST00000334268,;TRDN,missense_variant,p.Thr42Met,ENST00000546248,;TRDN,missense_variant,p.Thr42Met,ENST00000542443,;	A	ENSG00000186439	ENST00000398178	Transcript	missense_variant	147	125	42	T/M	aCg/aTg	rs371627659	.	.	-1	TRDN	HGNC	12261	protein_coding	YES	CCDS55053.1	ENSP00000381240	TRDN_HUMAN	.	UPI0000D820CC	.	deleterious_low_confidence(0)	unknown(0)	2/41	.	hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGTCGTCACT	byFrequency|byCluster	5	ESCA
FAM120B	0	.	GRCh37	6	170627759	170627759	+	Missense_Mutation	SNP	G	G	T	rs763079839	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1281G>T	p.Met427Ile	p.M427I	ENST00000476287	2/11	199	102	96	161	161	0	FAM120B,missense_variant,p.Met427Ile,ENST00000476287,;FAM120B,missense_variant,p.Met450Ile,ENST00000537664,;FAM120B,missense_variant,p.Met439Ile,ENST00000540480,;FAM120B,intron_variant,,ENST00000252510,;	T	ENSG00000112584	ENST00000476287	Transcript	missense_variant	1389	1281	427	M/I	atG/atT	rs763079839	.	.	1	FAM120B	HGNC	21109	protein_coding	YES	CCDS5314.1	ENSP00000417970	F120B_HUMAN	B4DL34_HUMAN	UPI000006DC13	.	tolerated_low_confidence(0.1)	benign(0.003)	2/11	.	hmmpanther:PTHR15976,hmmpanther:PTHR15976:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATGTATAC	byFrequency	5	ESCA
ZNF391	0	.	GRCh37	6	27368437	27368437	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288A>C	p.Leu96Phe	p.L96F	ENST00000244576	3/3	52	39	12	60	60	0	ZNF391,missense_variant,p.Leu96Phe,ENST00000461521,;ZNF391,missense_variant,p.Leu96Phe,ENST00000244576,;RP1-153G14.4,downstream_gene_variant,,ENST00000607727,;ZNF391,downstream_gene_variant,,ENST00000477999,;	C	ENSG00000124613	ENST00000244576	Transcript	missense_variant	833	288	96	L/F	ttA/ttC	.	.	.	1	ZNF391	HGNC	18779	protein_coding	YES	CCDS43429.1	ENSP00000244576	ZN391_HUMAN	C9JUF8_HUMAN	UPI00001D81D5	.	tolerated(0.08)	benign(0.004)	3/3	.	hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTAATTAA	.	5	ESCA
SNRPC	0	.	GRCh37	6	34730402	34730402	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.82A>T	p.Arg28Trp	p.R28W	ENST00000244520	3/6	36	28	8	53	53	0	SNRPC,missense_variant,p.Arg28Trp,ENST00000244520,;SNRPC,missense_variant,p.Arg49Trp,ENST00000374017,;SNRPC,5_prime_UTR_variant,,ENST00000374018,;SNRPC,non_coding_transcript_exon_variant,,ENST00000474635,;	T	ENSG00000124562	ENST00000244520	Transcript	missense_variant	220	82	28	R/W	Agg/Tgg	.	.	.	1	SNRPC	HGNC	11157	protein_coding	YES	CCDS34436.1	ENSP00000244520	RU1C_HUMAN	Q5TAL4_HUMAN,Q5TAL2_HUMAN	UPI00001352E7	.	deleterious(0.01)	possibly_damaging(0.733)	3/6	.	HAMAP:MF_03153,PROSITE_profiles:PS50171,hmmpanther:PTHR31148,hmmpanther:PTHR31148:SF1,Pfam_domain:PF06220,SMART_domains:SM00451,PIRSF_domain:PIRSF037969,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGAAGGAAA	.	5	ESCA
TFAP2B	0	.	GRCh37	6	50815251	50815251	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4146A>G	.	.	ENST00000393655	7/7	60	37	22	66	66	0	TFAP2B,3_prime_UTR_variant,,ENST00000393655,;TFAP2B,3_prime_UTR_variant,,ENST00000263046,;	G	ENSG00000008196	ENST00000393655	Transcript	3_prime_UTR_variant	5698	.	.	.	.	.	.	.	1	TFAP2B	HGNC	11743	protein_coding	YES	CCDS4934.2	ENSP00000377265	AP2B_HUMAN	A8K557_HUMAN	UPI000020DE90	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTATGGTA	.	5	ESCA
DST	0	.	GRCh37	6	56504082	56504082	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1328A>G	p.Asn443Ser	p.N443S	ENST00000244364	8/84	35	24	10	57	57	0	DST,missense_variant,p.Asn443Ser,ENST00000439203,;DST,missense_variant,p.Asn947Ser,ENST00000370754,;DST,missense_variant,p.Asn769Ser,ENST00000370769,;DST,missense_variant,p.Asn769Ser,ENST00000312431,;DST,missense_variant,p.Asn769Ser,ENST00000421834,;DST,missense_variant,p.Asn443Ser,ENST00000446842,;DST,missense_variant,p.Asn443Ser,ENST00000244364,;DST,missense_variant,p.Asn769Ser,ENST00000370788,;DST,missense_variant,p.Asn809Ser,ENST00000520645,;DST,missense_variant,p.Asn769Ser,ENST00000361203,;DST,missense_variant,p.Asn443Ser,ENST00000370765,;DST,missense_variant,p.Asn443Ser,ENST00000518935,;DST,downstream_gene_variant,,ENST00000449297,;DST,non_coding_transcript_exon_variant,,ENST00000521104,;DST,non_coding_transcript_exon_variant,,ENST00000523967,;DST,downstream_gene_variant,,ENST00000518828,;	C	ENSG00000151914	ENST00000244364	Transcript	missense_variant	1536	1328	443	N/S	aAt/aGt	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	benign(0.023)	8/84	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF38,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGATTTTCT	.	5	ESCA
MUC17	0	.	GRCh37	7	100684551	100684551	+	Missense_Mutation	SNP	G	G	C	rs149757750	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9854G>C	p.Ser3285Thr	p.S3285T	ENST00000306151	3/13	125	110	14	112	112	0	MUC17,missense_variant,p.Ser3285Thr,ENST00000306151,;MUC17,missense_variant,p.Ser3285Thr,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,;	C	ENSG00000169876	ENST00000306151	Transcript	missense_variant	9918	9854	3285	S/T	aGt/aCt	rs149757750	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	possibly_damaging(0.777)	3/13	.	.	A:0.0046	A:0.0174	A:0	.	A:0	A:0	A:0	A:0.0132	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AACAAGTATGC	byFrequency|byCluster|by1000G	3	ESCA
ORAI2	0	.	GRCh37	7	102087506	102087506	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7G>A	.	.	ENST00000356387	4/4	20	10	9	20	20	0	ORAI2,3_prime_UTR_variant,,ENST00000403646,;ORAI2,3_prime_UTR_variant,,ENST00000473939,;ORAI2,3_prime_UTR_variant,,ENST00000478730,;ORAI2,3_prime_UTR_variant,,ENST00000356387,;ORAI2,downstream_gene_variant,,ENST00000495936,;ORAI2,downstream_gene_variant,,ENST00000468241,;ORAI2,downstream_gene_variant,,ENST00000498661,;ORAI2,downstream_gene_variant,,ENST00000488996,;	A	ENSG00000160991	ENST00000356387	Transcript	3_prime_UTR_variant	1007	.	.	.	.	.	.	.	1	ORAI2	HGNC	21667	protein_coding	YES	CCDS5722.1	ENSP00000348752	ORAI2_HUMAN	C9JUY6_HUMAN,C9JQR7_HUMAN,C9J5L2_HUMAN,C9J2H9_HUMAN,B4DUB4_HUMAN	UPI0000070E55	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCGAGGGC	.	5	ESCA
TRBV7-8	0	.	GRCh37	7	142099897	142099897	+	Silent	SNP	T	T	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42A>C	p.%3D	p.L14L	ENST00000390359	1/2	57	46	11	80	80	0	TRBV7-8,synonymous_variant,p.%3D,ENST00000390359,;TRBV6-9,downstream_gene_variant,,ENST00000390379,;	G	ENSG00000229200	ENST00000390359	Transcript	synonymous_variant	81	42	14	L	ctA/ctC	.	.	.	-1	TRBV7-8	HGNC	12242	TR_V_gene	YES	.	ENSP00000374882	.	A0A5A1_HUMAN	UPI00001140ED	.	.	.	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23268,hmmpanther:PTHR23268:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCCTAGGAA	.	5	ESCA
OR2A5	0	.	GRCh37	7	143747992	143747992	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.498G>T	p.%3D	p.L166L	ENST00000408906	1/1	74	53	21	93	93	0	OR2A5,synonymous_variant,p.%3D,ENST00000408906,;	T	ENSG00000221836	ENST00000408906	Transcript	synonymous_variant	532	498	166	L	ctG/ctT	.	.	.	1	OR2A5	HGNC	8232	protein_coding	YES	CCDS43668.1	ENSP00000386208	OR2A5_HUMAN	.	UPI0000061F52	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF232,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCTGCCCTT	.	5	ESCA
KMT2C	0	.	GRCh37	7	152012301	152012301	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.512A>G	p.Lys171Arg	p.K171R	ENST00000262189	4/59	55	36	18	83	83	0	KMT2C,missense_variant,p.Lys171Arg,ENST00000355193,;KMT2C,missense_variant,p.Lys171Arg,ENST00000262189,;KMT2C,downstream_gene_variant,,ENST00000452749,;KMT2C,missense_variant,p.Lys171Arg,ENST00000558084,;KMT2C,upstream_gene_variant,,ENST00000490130,;	C	ENSG00000055609	ENST00000262189	Transcript	missense_variant	731	512	171	K/R	aAg/aGg	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	benign(0.008)	4/59	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCCTTCTTG	.	5	ESCA
TBRG4	0	.	GRCh37	7	45143810	45143830	+	In_Frame_Del	DEL	GTGGCCAGGCGCTGGGACACC	GTGGCCAGGCGCTGGGACACC	-	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	GTGGCCAGGCGCTGGGACACC	GTGGCCAGGCGCTGGGACACC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933_953delGGTGTCCCAGCGCCTGGCCAC	p.Gln311_Thr318delinsHis	p.Q311_T318delinsH	ENST00000258770	5/11	28	20	8	59	59	0	TBRG4,inframe_deletion,p.Gln4_Thr11delinsHis,ENST00000483615,;TBRG4,inframe_deletion,p.Gln311_Thr318delinsHis,ENST00000258770,;TBRG4,inframe_deletion,p.Gln311_Thr318delinsHis,ENST00000494076,;TBRG4,inframe_deletion,p.Gln276_Thr283delinsHis,ENST00000478532,;TBRG4,intron_variant,,ENST00000361278,;TBRG4,intron_variant,,ENST00000395655,;TBRG4,downstream_gene_variant,,ENST00000475893,;TBRG4,downstream_gene_variant,,ENST00000495078,;TBRG4,downstream_gene_variant,,ENST00000482285,;TBRG4,downstream_gene_variant,,ENST00000461363,;SNORA5B,downstream_gene_variant,,ENST00000363786,;SNORA5A,downstream_gene_variant,,ENST00000384111,;SNORA5C,downstream_gene_variant,,ENST00000364902,;TBRG4,downstream_gene_variant,,ENST00000471142,;TBRG4,non_coding_transcript_exon_variant,,ENST00000484326,;TBRG4,non_coding_transcript_exon_variant,,ENST00000495973,;TBRG4,non_coding_transcript_exon_variant,,ENST00000488222,;TBRG4,downstream_gene_variant,,ENST00000477328,;TBRG4,upstream_gene_variant,,ENST00000478116,;TBRG4,upstream_gene_variant,,ENST00000482482,;	-	ENSG00000136270	ENST00000258770	Transcript	inframe_deletion	1055-1075	933-953	311-318	QVSQRLAT/H	caGGTGTCCCAGCGCCTGGCCACc/cac	.	.	.	-1	TBRG4	HGNC	17443	protein_coding	YES	CCDS5501.1	ENSP00000258770	TBRG4_HUMAN	D3DVL7_HUMAN,C9J7P5_HUMAN,C9J618_HUMAN,C9J5A2_HUMAN,C9J347_HUMAN,B4DU42_HUMAN,B3KRS4_HUMAN	UPI0000071F89	.	.	.	5/11	.	hmmpanther:PTHR21228:SF26,hmmpanther:PTHR21228	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGGTCGGTGGCCAGGCGCTGGGACACCTGGGT	.	3	ESCA
WBSCR17	0	.	GRCh37	7	70853300	70853300	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502A>T	p.Ile168Phe	p.I168F	ENST00000333538	3/11	34	26	8	41	41	0	WBSCR17,missense_variant,p.Ile168Phe,ENST00000333538,;WBSCR17,missense_variant,p.Ile146Phe,ENST00000447516,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;	T	ENSG00000185274	ENST00000333538	Transcript	missense_variant	1136	502	168	I/F	Atc/Ttc	.	.	.	1	WBSCR17	HGNC	16347	protein_coding	YES	CCDS5540.1	ENSP00000329654	GLTL3_HUMAN	Q68CW8_HUMAN,Q2L4S5_HUMAN,B3KRD2_HUMAN	UPI00000502D5	.	deleterious(0.01)	possibly_damaging(0.825)	3/11	.	hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Pfam_domain:PF00535,Gene3D:3.90.550.10,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTGATCCTG	.	5	ESCA
SEMA3D	0	.	GRCh37	7	84694822	84694822	+	Silent	SNP	A	A	G	rs776327910	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.636T>C	p.%3D	p.D212D	ENST00000284136	6/17	37	29	8	59	59	0	SEMA3D,synonymous_variant,p.%3D,ENST00000284136,;SEMA3D,synonymous_variant,p.%3D,ENST00000444867,;	G	ENSG00000153993	ENST00000284136	Transcript	synonymous_variant	680	636	212	D	gaT/gaC	rs776327910,COSM1132931	.	.	-1	SEMA3D	HGNC	10726	protein_coding	YES	CCDS34676.1	ENSP00000284136	SEM3D_HUMAN	.	UPI0000135A66	.	.	.	6/17	.	Superfamily_domains:SSF101912,SMART_domains:SM00630,Gene3D:2.130.10.10,Pfam_domain:PF01403,hmmpanther:PTHR11036:SF36,hmmpanther:PTHR11036,PROSITE_profiles:PS51004	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTATCTTT	byFrequency	5	ESCA
TECPR1	0	.	GRCh37	7	97875460	97875460	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2C>T	.	.	ENST00000447648	3/26	51	48	3	43	43	0	TECPR1,5_prime_UTR_variant,,ENST00000447648,;TECPR1,5_prime_UTR_variant,,ENST00000420697,;TECPR1,5_prime_UTR_variant,,ENST00000423128,;TECPR1,5_prime_UTR_variant,,ENST00000415086,;TECPR1,5_prime_UTR_variant,,ENST00000379795,;TECPR1,intron_variant,,ENST00000542604,;TECPR1,intron_variant,,ENST00000472845,;TECPR1,upstream_gene_variant,,ENST00000471397,;TECPR1,upstream_gene_variant,,ENST00000463648,;TECPR1,downstream_gene_variant,,ENST00000488667,;	A	ENSG00000205356	ENST00000447648	Transcript	5_prime_UTR_variant	299	.	.	.	.	.	.	.	-1	TECPR1	HGNC	22214	protein_coding	YES	CCDS47648.1	ENSP00000404923	TCPR1_HUMAN	C9JUV4_HUMAN	UPI0000161940	.	.	.	3/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCATGGCAGCG	.	2	ESCA
ZFPM2	0	.	GRCh37	8	106811047	106811047	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835G>A	p.Glu279Lys	p.E279K	ENST00000407775	7/8	61	50	11	53	53	0	ZFPM2,missense_variant,p.Glu147Lys,ENST00000517361,;ZFPM2,missense_variant,p.Glu10Lys,ENST00000378472,;ZFPM2,missense_variant,p.Glu147Lys,ENST00000520492,;ZFPM2,missense_variant,p.Glu279Lys,ENST00000407775,;RP11-152P17.2,intron_variant,,ENST00000524045,;RP11-152P17.2,intron_variant,,ENST00000509144,;RP11-152P17.2,intron_variant,,ENST00000521622,;RP11-152P17.2,intron_variant,,ENST00000520594,;RP11-152P17.2,intron_variant,,ENST00000520433,;RP11-152P17.2,intron_variant,,ENST00000518932,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;RP11-152P17.2,intron_variant,,ENST00000520078,;	A	ENSG00000169946	ENST00000407775	Transcript	missense_variant	1085	835	279	E/K	Gaa/Aaa	.	.	.	1	ZFPM2	HGNC	16700	protein_coding	YES	CCDS47908.1	ENSP00000384179	FOG2_HUMAN	Q9NPQ0_HUMAN,F5H542_HUMAN,E7ET52_HUMAN,E5RJX0_HUMAN	UPI000057A0B4	.	deleterious(0.04)	benign(0.113)	7/8	.	hmmpanther:PTHR12958:SF5,hmmpanther:PTHR12958	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGAAGCT	.	5	ESCA
MTMR9	0	.	GRCh37	8	11152762	11152762	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242T>G	p.Leu81Trp	p.L81W	ENST00000221086	2/10	62	55	7	76	76	0	MTMR9,missense_variant,p.Leu81Trp,ENST00000221086,;MTMR9,5_prime_UTR_variant,,ENST00000526292,;MTMR9,missense_variant,p.Leu81Trp,ENST00000530200,;MTMR9,non_coding_transcript_exon_variant,,ENST00000528389,;	G	ENSG00000104643	ENST00000221086	Transcript	missense_variant	715	242	81	L/W	tTg/tGg	.	.	.	1	MTMR9	HGNC	14596	protein_coding	YES	CCDS5979.1	ENSP00000221086	MTMR9_HUMAN	Q9Y4N6_HUMAN,B7Z291_HUMAN	UPI0000073CA7	.	deleterious(0)	probably_damaging(0.995)	2/10	.	hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF56,Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAGTTGGATA	.	4	ESCA
FGL1	0	.	GRCh37	8	17731947	17731947	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.328G>T	p.Val110Phe	p.V110F	ENST00000398056	6/10	44	28	16	50	50	0	FGL1,missense_variant,p.Val110Phe,ENST00000518650,;FGL1,missense_variant,p.Val110Phe,ENST00000522444,;FGL1,missense_variant,p.Val110Phe,ENST00000398056,;FGL1,missense_variant,p.Val110Phe,ENST00000398054,;FGL1,missense_variant,p.Val110Phe,ENST00000381841,;FGL1,missense_variant,p.Val110Phe,ENST00000381840,;FGL1,missense_variant,p.Val110Phe,ENST00000427924,;FGL1,non_coding_transcript_exon_variant,,ENST00000522636,;FGL1,non_coding_transcript_exon_variant,,ENST00000523097,;	A	ENSG00000104760	ENST00000398056	Transcript	missense_variant	1144	328	110	V/F	Gtt/Ttt	.	.	.	-1	FGL1	HGNC	3695	protein_coding	YES	CCDS6004.1	ENSP00000381133	FGL1_HUMAN	.	UPI0000169E8B	.	deleterious(0)	probably_damaging(0.969)	6/10	.	PROSITE_profiles:PS51406,hmmpanther:PTHR19143,Gene3D:3.90.215.10,Pfam_domain:PF00147,SMART_domains:SM00186,Superfamily_domains:SSF56496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATAAACAGAAA	.	3	ESCA
STC1	0	.	GRCh37	8	23699683	23699683	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2600T>C	.	.	ENST00000290271	4/4	52	39	13	48	48	0	STC1,3_prime_UTR_variant,,ENST00000290271,;STC1,downstream_gene_variant,,ENST00000524323,;	G	ENSG00000159167	ENST00000290271	Transcript	3_prime_UTR_variant	3628	.	.	.	.	.	.	.	-1	STC1	HGNC	11373	protein_coding	YES	CCDS6043.1	ENSP00000290271	STC1_HUMAN	Q71UE5_HUMAN,B4DN22_HUMAN	UPI00001360B4	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATATCATT	.	5	ESCA
DOCK5	0	.	GRCh37	8	25261196	25261196	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5049T>A	p.%3D	p.S1683S	ENST00000276440	48/52	85	63	22	92	92	0	DOCK5,synonymous_variant,p.%3D,ENST00000276440,;DOCK5,3_prime_UTR_variant,,ENST00000467709,;	A	ENSG00000147459	ENST00000276440	Transcript	synonymous_variant	5093	5049	1683	S	tcT/tcA	.	.	.	1	DOCK5	HGNC	23476	protein_coding	YES	CCDS6047.1	ENSP00000276440	DOCK5_HUMAN	.	UPI000022D4F3	.	.	.	48/52	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23317:SF68,hmmpanther:PTHR23317	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTCTTCAAA	.	5	ESCA
OR13C3	0	.	GRCh37	9	107298655	107298655	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.440T>A	p.Met147Lys	p.M147K	ENST00000374781	1/1	58	21	36	84	84	0	OR13C3,missense_variant,p.Met147Lys,ENST00000374781,;	T	ENSG00000204246	ENST00000374781	Transcript	missense_variant	483	440	147	M/K	aTg/aAg	.	.	.	-1	OR13C3	HGNC	14704	protein_coding	YES	CCDS35089.1	ENSP00000363913	O13C3_HUMAN	.	UPI000015F232	.	deleterious(0)	benign(0.15)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF34,hmmpanther:PTHR26453,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCATGCCA	.	5	ESCA
PTPN3	0	.	GRCh37	9	112219585	112219585	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.233C>T	p.Ser78Phe	p.S78F	ENST00000374541	3/26	44	40	4	63	63	0	PTPN3,missense_variant,p.Ser78Phe,ENST00000374541,;PTPN3,5_prime_UTR_variant,,ENST00000262539,;	A	ENSG00000070159	ENST00000374541	Transcript	missense_variant	338	233	78	S/F	tCc/tTc	.	.	.	-1	PTPN3	HGNC	9655	protein_coding	YES	CCDS6776.1	ENSP00000363667	PTN3_HUMAN	B7Z8K9_HUMAN	UPI000013D2D2	.	deleterious(0.01)	possibly_damaging(0.701)	3/26	.	PROSITE_profiles:PS50057,hmmpanther:PTHR19134:SF248,hmmpanther:PTHR19134,Gene3D:3.10.20.90,Pfam_domain:PF09379,SMART_domains:SM00295,PIRSF_domain:PIRSF000927,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCACGGAGTCG	.	3	ESCA
AL354898.1	0	.	GRCh37	9	133269131	133269133	+	5'Flank	DEL	CCC	CCC	-	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	CCC	CCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000277491	.	72	47	25	77	77	0	AL354898.1,upstream_gene_variant,,ENST00000277491,;HMCN2,splice_region_variant,,ENST00000487727,;HMCN2,upstream_gene_variant,,ENST00000480829,;	-	ENSG00000215428	ENST00000277491	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4896	1	AL354898.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000277491	.	.	UPI0000073E91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATAGTGCCCCCTGT	.	3	ESCA
ELAVL2	0	.	GRCh37	9	23690150	23690150	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2405T>C	.	.	ENST00000397312	7/7	14	6	8	21	21	0	ELAVL2,3_prime_UTR_variant,,ENST00000380110,;ELAVL2,3_prime_UTR_variant,,ENST00000397312,;ELAVL2,3_prime_UTR_variant,,ENST00000223951,;ELAVL2,3_prime_UTR_variant,,ENST00000544538,;ELAVL2,downstream_gene_variant,,ENST00000380117,;	G	ENSG00000107105	ENST00000397312	Transcript	3_prime_UTR_variant	3760	.	.	.	.	.	.	.	-1	ELAVL2	HGNC	3313	protein_coding	YES	CCDS6515.1	ENSP00000380479	ELAV2_HUMAN	C9JB16_HUMAN,B1AM48_HUMAN	UPI000013C83F	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAAAGAATC	.	5	ESCA
DOCK8	0	.	GRCh37	9	465079	465079	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*860G>T	.	.	ENST00000453981	48/48	60	31	29	82	82	0	DOCK8,3_prime_UTR_variant,,ENST00000432829,;DOCK8,3_prime_UTR_variant,,ENST00000453981,;DOCK8,3_prime_UTR_variant,,ENST00000382329,;DOCK8,downstream_gene_variant,,ENST00000469391,;RP11-165F24.3,intron_variant,,ENST00000586805,;RP11-165F24.3,intron_variant,,ENST00000589287,;RP11-165F24.3,intron_variant,,ENST00000588474,;RP11-165F24.3,intron_variant,,ENST00000415004,;RP11-165F24.3,intron_variant,,ENST00000588989,;RP11-165F24.3,intron_variant,,ENST00000608617,;RP11-165F24.3,intron_variant,,ENST00000590518,;RP11-165F24.3,intron_variant,,ENST00000591577,;RP11-165F24.3,intron_variant,,ENST00000589387,;RP11-165F24.3,intron_variant,,ENST00000593137,;RP11-165F24.3,intron_variant,,ENST00000585819,;RP11-165F24.3,intron_variant,,ENST00000592805,;RP11-165F24.3,upstream_gene_variant,,ENST00000590240,;RP11-165F24.3,upstream_gene_variant,,ENST00000585631,;DOCK8,non_coding_transcript_exon_variant,,ENST00000462618,;DOCK8,non_coding_transcript_exon_variant,,ENST00000495184,;	T	ENSG00000107099	ENST00000453981	Transcript	3_prime_UTR_variant	7272	.	.	.	.	.	.	.	1	DOCK8	HGNC	19191	protein_coding	YES	CCDS6440.2	ENSP00000408464	DOCK8_HUMAN	E2J6M5_HUMAN,C9J7A3_HUMAN,C9J613_HUMAN	UPI0000E0B9E5	.	.	.	48/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTGTGCTG	.	5	ESCA
DDX26B	0	.	GRCh37	X	134715018	134715018	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2427T>A	p.%3D	p.P809P	ENST00000370752	16/17	96	38	57	140	140	0	DDX26B,synonymous_variant,p.%3D,ENST00000370752,;DDX26B,non_coding_transcript_exon_variant,,ENST00000481429,;DDX26B,non_coding_transcript_exon_variant,,ENST00000481908,;DDX26B,non_coding_transcript_exon_variant,,ENST00000494957,;DDX26B,non_coding_transcript_exon_variant,,ENST00000493637,;RP11-432N13.2,downstream_gene_variant,,ENST00000439300,;	A	ENSG00000165359	ENST00000370752	Transcript	synonymous_variant	2761	2427	809	P	ccT/ccA	.	.	.	1	DDX26B	HGNC	27334	protein_coding	YES	CCDS35401.1	ENSP00000359788	DX26B_HUMAN	.	UPI00004A3AAF	.	.	.	16/17	.	hmmpanther:PTHR12957:SF22,hmmpanther:PTHR12957,Pfam_domain:PF15300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACCTCTGGA	.	5	ESCA
PTCHD1	0	.	GRCh37	X	23397967	23397967	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HV-01A-21D-A351-09	TCGA-LN-A7HV-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.611A>G	p.Lys204Arg	p.K204R	ENST00000379361	2/3	36	16	19	36	36	0	PTCHD1,missense_variant,p.Lys204Arg,ENST00000379361,;PTCHD1,intron_variant,,ENST00000456522,;	G	ENSG00000165186	ENST00000379361	Transcript	missense_variant	1471	611	204	K/R	aAa/aGa	.	.	.	1	PTCHD1	HGNC	26392	protein_coding	YES	CCDS35215.2	ENSP00000368666	PTHD1_HUMAN	.	UPI000059DAD8	.	tolerated(0.56)	benign(0.005)	2/3	.	Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGAAATCTG	.	5	ESCA
PSD	0	.	GRCh37	10	104176706	104176706	+	Silent	SNP	C	C	T	rs371738181	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90G>A	p.%3D	p.P30P	ENST00000020673	2/17	33	29	4	58	58	0	PSD,synonymous_variant,p.%3D,ENST00000020673,;PSD,synonymous_variant,p.%3D,ENST00000406432,;FBXL15,upstream_gene_variant,,ENST00000440407,;FBXL15,upstream_gene_variant,,ENST00000425536,;FBXL15,upstream_gene_variant,,ENST00000457067,;FBXL15,upstream_gene_variant,,ENST00000224862,;FBXL15,upstream_gene_variant,,ENST00000432590,;FBXL15,upstream_gene_variant,,ENST00000369956,;PSD,non_coding_transcript_exon_variant,,ENST00000472685,;PSD,non_coding_transcript_exon_variant,,ENST00000492902,;FBXL15,upstream_gene_variant,,ENST00000481808,;	T	ENSG00000059915	ENST00000020673	Transcript	synonymous_variant	617	90	30	P	ccG/ccA	rs371738181	.	.	-1	PSD	HGNC	9507	protein_coding	YES	CCDS31272.1	ENSP00000020673	PSD1_HUMAN	.	UPI0000404928	.	.	.	2/17	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF115	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GGCACCGGGCC	byFrequency|byCluster	2	ESCA
TECTB	0	.	GRCh37	10	114063043	114063043	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.963G>A	p.Met321Ile	p.M321I	ENST00000369422	10/10	85	37	48	139	139	0	TECTB,missense_variant,p.Met321Ile,ENST00000369422,;GUCY2GP,downstream_gene_variant,,ENST00000490269,;TECTB,downstream_gene_variant,,ENST00000494328,;GUCY2GP,downstream_gene_variant,,ENST00000479705,;	A	ENSG00000119913	ENST00000369422	Transcript	missense_variant	963	963	321	M/I	atG/atA	.	.	.	1	TECTB	HGNC	11721	protein_coding	YES	CCDS7571.1	ENSP00000358430	TECTB_HUMAN	.	UPI00000720CC	.	tolerated_low_confidence(0.18)	benign(0)	10/10	.	hmmpanther:PTHR22962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATGATGTT	.	5	ESCA
FAM160B1	0	.	GRCh37	10	116621445	116621445	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*146G>C	.	.	ENST00000369248	17/17	18	6	12	21	21	0	FAM160B1,3_prime_UTR_variant,,ENST00000369248,;FAM160B1,intron_variant,,ENST00000411414,;FAM160B1,intron_variant,,ENST00000369250,;	C	ENSG00000151553	ENST00000369248	Transcript	3_prime_UTR_variant	2779	.	.	.	.	.	.	.	1	FAM160B1	HGNC	29320	protein_coding	YES	CCDS31290.1	ENSP00000358251	F16B1_HUMAN	.	UPI0000160B10	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATTGAGTGG	.	5	ESCA
LINC00264	0	.	GRCh37	10	26880236	26880236	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.474-3C>G	.	.	ENST00000412114	.	69	48	21	63	62	0	LINC00264,splice_region_variant,,ENST00000412114,;	G	ENSG00000233261	ENST00000412114	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	LINC00264	HGNC	17776	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCAGGAC	.	4	ESCA
BMS1	0	.	GRCh37	10	43326619	43326619	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*75G>T	.	.	ENST00000374518	23/23	10	3	7	16	16	0	BMS1,3_prime_UTR_variant,,ENST00000374518,;RNU6-885P,downstream_gene_variant,,ENST00000516607,;	T	ENSG00000165733	ENST00000374518	Transcript	3_prime_UTR_variant	3987	.	.	.	.	.	.	.	1	BMS1	HGNC	23505	protein_coding	YES	CCDS7199.1	ENSP00000363642	BMS1_HUMAN	.	UPI0000126A3E	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCTGTGAATGA	.	2	ESCA
DDX50	0	.	GRCh37	10	70700818	70700818	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1758G>A	p.%3D	p.G586G	ENST00000373585	13/15	59	23	36	87	87	0	DDX50,synonymous_variant,p.%3D,ENST00000373585,;DDX50,splice_region_variant,,ENST00000466265,;	A	ENSG00000107625	ENST00000373585	Transcript	synonymous_variant	1865	1758	586	G	ggG/ggA	.	.	.	1	DDX50	HGNC	17906	protein_coding	YES	CCDS7283.1	ENSP00000362687	DDX50_HUMAN	Q9NTA9_HUMAN,B4DED6_HUMAN	UPI000006FBBF	.	.	.	13/15	.	hmmpanther:PTHR24031:SF227,hmmpanther:PTHR24031,Pfam_domain:PF08152,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGGGTTTGT	.	5	ESCA
MICALCL	0	.	GRCh37	11	12316029	12316029	+	Missense_Mutation	SNP	C	C	T	rs113400332	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1051C>T	p.Arg351Trp	p.R351W	ENST00000256186	3/9	75	26	48	141	140	1	MICALCL,missense_variant,p.Arg351Trp,ENST00000256186,;MICALCL,downstream_gene_variant,,ENST00000533534,;	T	ENSG00000133808	ENST00000256186	Transcript	missense_variant	1342	1051	351	R/W	Cgg/Tgg	rs113400332,COSM686772	.	.	1	MICALCL	HGNC	25933	protein_coding	YES	CCDS41620.1	ENSP00000256186	MICLK_HUMAN	E9PRG5_HUMAN	UPI0000228C2E	.	deleterious(0)	probably_damaging(0.981)	3/9	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF12	T:0.0016	T:0.0053	T:0	.	T:0	T:0.001	T:0	T:0.0028	T:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAATCGGCCA	byFrequency|byCluster|by1000G	5	ESCA
SLC17A6	0	.	GRCh37	11	22399782	22399782	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*496C>T	.	.	ENST00000263160	12/12	28	9	19	72	72	0	SLC17A6,3_prime_UTR_variant,,ENST00000263160,;	T	ENSG00000091664	ENST00000263160	Transcript	3_prime_UTR_variant	2682	.	.	.	.	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAACTATCA	.	5	ESCA
AGBL2	0	.	GRCh37	11	47727462	47727462	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240C>G	p.Ile80Met	p.I80M	ENST00000525123	5/19	146	98	47	139	139	0	AGBL2,missense_variant,p.Ile80Met,ENST00000528244,;AGBL2,missense_variant,p.Ile80Met,ENST00000357610,;AGBL2,missense_variant,p.Ile80Met,ENST00000298861,;AGBL2,missense_variant,p.Ile80Met,ENST00000525123,;AGBL2,missense_variant,p.Ile60Met,ENST00000530577,;AGBL2,missense_variant,p.Ile80Met,ENST00000529154,;AGBL2,intron_variant,,ENST00000532595,;AGBL2,non_coding_transcript_exon_variant,,ENST00000526331,;AGBL2,intron_variant,,ENST00000529712,;AGBL2,downstream_gene_variant,,ENST00000531835,;AGBL2,3_prime_UTR_variant,,ENST00000528632,;AGBL2,non_coding_transcript_exon_variant,,ENST00000532835,;	C	ENSG00000165923	ENST00000525123	Transcript	missense_variant	526	240	80	I/M	atC/atG	.	.	.	-1	AGBL2	HGNC	26296	protein_coding	YES	CCDS7944.1	ENSP00000435582	CBPC2_HUMAN	E9PJH3_HUMAN,E9PI49_HUMAN	UPI00001A95E3	.	tolerated_low_confidence(0.2)	benign(0.045)	5/19	.	hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTGATAGG	.	5	ESCA
RP11-707M1.1	0	.	GRCh37	11	49829204	49829204	+	Intron	SNP	C	C	G	rs537344366	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1398-3C>G	.	.	ENST00000527477	.	153	98	55	172	172	0	RP11-707M1.1,splice_region_variant,,ENST00000527477,;RP11-707M1.1,splice_region_variant,,ENST00000534201,;RP11-707M1.1,splice_region_variant,,ENST00000530858,;	G	ENSG00000205035	ENST00000527477	Transcript	splice_region_variant	.	.	.	.	.	rs537344366	.	.	1	RP11-707M1.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	.	4/6	.	T:0.0020	T:0.0061	T:0.0014	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTACAGGGT	byFrequency|by1000G	4	ESCA
CTNND1	0	.	GRCh37	11	57564314	57564314	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806G>C	p.Ser269Thr	p.S269T	ENST00000399050	6/21	76	40	35	84	84	0	CTNND1,missense_variant,p.Ser269Thr,ENST00000361796,;CTNND1,missense_variant,p.Ser168Thr,ENST00000532787,;CTNND1,missense_variant,p.Ser215Thr,ENST00000526357,;CTNND1,missense_variant,p.Ser269Thr,ENST00000428599,;CTNND1,missense_variant,p.Ser215Thr,ENST00000532649,;CTNND1,missense_variant,p.Ser168Thr,ENST00000528232,;CTNND1,missense_variant,p.Ser269Thr,ENST00000529919,;CTNND1,missense_variant,p.Ser215Thr,ENST00000529873,;CTNND1,missense_variant,p.Ser215Thr,ENST00000532844,;CTNND1,missense_variant,p.Ser168Thr,ENST00000532463,;CTNND1,missense_variant,p.Ser168Thr,ENST00000415361,;CTNND1,missense_variant,p.Ser168Thr,ENST00000530094,;CTNND1,missense_variant,p.Ser168Thr,ENST00000529986,;CTNND1,missense_variant,p.Ser168Thr,ENST00000532245,;CTNND1,missense_variant,p.Ser215Thr,ENST00000530748,;CTNND1,missense_variant,p.Ser215Thr,ENST00000528621,;CTNND1,missense_variant,p.Ser269Thr,ENST00000361391,;CTNND1,missense_variant,p.Ser269Thr,ENST00000399050,;CTNND1,missense_variant,p.Ser215Thr,ENST00000534579,;CTNND1,missense_variant,p.Ser269Thr,ENST00000526938,;CTNND1,missense_variant,p.Ser215Thr,ENST00000529526,;CTNND1,missense_variant,p.Ser269Thr,ENST00000399039,;CTNND1,missense_variant,p.Ser269Thr,ENST00000360682,;CTNND1,missense_variant,p.Ser269Thr,ENST00000524630,;CTNND1,missense_variant,p.Ser191Thr,ENST00000534647,;CTNND1,missense_variant,p.Ser269Thr,ENST00000358694,;CTNND1,missense_variant,p.Ser168Thr,ENST00000426142,;CTNND1,missense_variant,p.Ser269Thr,ENST00000361332,;CTNND1,intron_variant,,ENST00000533189,;CTNND1,intron_variant,,ENST00000533667,;CTNND1,intron_variant,,ENST00000531014,;CTNND1,intron_variant,,ENST00000527467,;CTNND1,intron_variant,,ENST00000526772,;CTNND1,intron_variant,,ENST00000525902,;CTNND1,downstream_gene_variant,,ENST00000530068,;RP11-691N7.6,downstream_gene_variant,,ENST00000531074,;	C	ENSG00000198561	ENST00000399050	Transcript	missense_variant	1342	806	269	S/T	aGc/aCc	.	.	.	1	CTNND1	HGNC	2515	protein_coding	YES	CCDS44604.1	ENSP00000382004	CTND1_HUMAN	E9PKY0_HUMAN,E9PKL1_HUMAN	UPI000012860B	.	tolerated(0.44)	benign(0.028)	6/21	.	hmmpanther:PTHR10372:SF6,hmmpanther:PTHR10372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCAGCGTGG	.	5	ESCA
EEF1G	0	.	GRCh37	11	62327763	62327763	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1021C>G	p.Leu341Val	p.L341V	ENST00000329251	8/10	74	63	11	68	68	0	EEF1G,missense_variant,p.Leu391Val,ENST00000378019,;EEF1G,missense_variant,p.Leu341Val,ENST00000329251,;AHNAK,upstream_gene_variant,,ENST00000530285,;MIR3654,3_prime_UTR_variant,,ENST00000496634,;MIR3654,non_coding_transcript_exon_variant,,ENST00000526409,;EEF1G,non_coding_transcript_exon_variant,,ENST00000525340,;	C	ENSG00000254772	ENST00000329251	Transcript	missense_variant	1152	1021	341	L/V	Ctc/Gtc	.	.	.	-1	EEF1G	HGNC	3213	protein_coding	YES	CCDS44626.1	ENSP00000331901	EF1G_HUMAN	Q53YD7_HUMAN,Q2F840_HUMAN	UPI00000012C3	.	deleterious(0)	possibly_damaging(0.848)	8/10	.	PROSITE_profiles:PS50040,hmmpanther:PTHR11260,hmmpanther:PTHR11260:SF161,Gene3D:1pbuA00,Pfam_domain:PF00647,Superfamily_domains:0048731	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATGAGATTGC	.	4	ESCA
FERMT3	0	.	GRCh37	11	63978612	63978612	+	Silent	SNP	C	C	G	rs781259522	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483C>G	p.%3D	p.L161L	ENST00000279227	4/15	21	18	3	23	23	0	FERMT3,synonymous_variant,p.%3D,ENST00000345728,;FERMT3,synonymous_variant,p.%3D,ENST00000279227,;FERMT3,synonymous_variant,p.%3D,ENST00000544997,;FERMT3,5_prime_UTR_variant,,ENST00000541252,;FERMT3,upstream_gene_variant,,ENST00000546255,;FERMT3,upstream_gene_variant,,ENST00000541326,;	G	ENSG00000149781	ENST00000279227	Transcript	synonymous_variant	578	483	161	L	ctC/ctG	rs781259522	.	.	1	FERMT3	HGNC	23151	protein_coding	YES	CCDS8060.1	ENSP00000279227	URP2_HUMAN	F5H3I6_HUMAN,F5H1C6_HUMAN	UPI000019270B	.	.	.	4/15	.	hmmpanther:PTHR16160:SF1,hmmpanther:PTHR16160,SMART_domains:SM00295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCTCTATGA	byFrequency	2	ESCA
CCDC88B	0	.	GRCh37	11	64108393	64108393	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221G>A	p.Arg74Gln	p.R74Q	ENST00000356786	3/27	92	47	45	86	86	0	CCDC88B,missense_variant,p.Arg74Gln,ENST00000356786,;CCDC88B,upstream_gene_variant,,ENST00000301897,;CCDC88B,non_coding_transcript_exon_variant,,ENST00000463837,;CCDC88B,upstream_gene_variant,,ENST00000494566,;CCDC88B,upstream_gene_variant,,ENST00000492980,;CCDC88B,upstream_gene_variant,,ENST00000494080,;	A	ENSG00000168071	ENST00000356786	Transcript	missense_variant	265	221	74	R/Q	cGa/cAa	.	.	.	1	CCDC88B	HGNC	26757	protein_coding	YES	CCDS8072.2	ENSP00000349238	CC88B_HUMAN	.	UPI00001FAAA6	.	tolerated(0.16)	benign(0.23)	3/27	.	Superfamily_domains:0050601,Pfam_domain:PF05622,hmmpanther:PTHR18947:SF29,hmmpanther:PTHR18947	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCGAGGGG	.	5	ESCA
PPP2R5B	0	.	GRCh37	11	64695604	64695604	+	Missense_Mutation	SNP	T	T	C	rs745568548	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565T>C	p.Tyr189His	p.Y189H	ENST00000164133	5/14	78	38	39	106	106	0	PPP2R5B,missense_variant,p.Tyr103His,ENST00000532850,;PPP2R5B,missense_variant,p.Tyr189His,ENST00000526559,;PPP2R5B,missense_variant,p.Tyr189His,ENST00000164133,;PPP2R5B,downstream_gene_variant,,ENST00000413292,;PPP2R5B,non_coding_transcript_exon_variant,,ENST00000528530,;	C	ENSG00000068971	ENST00000164133	Transcript	missense_variant	1187	565	189	Y/H	Tat/Cat	rs745568548,COSM930264	.	.	1	PPP2R5B	HGNC	9310	protein_coding	YES	CCDS8085.1	ENSP00000164133	2A5B_HUMAN	E9PQN5_HUMAN,E9PNY3_HUMAN	UPI000000DAF4	.	tolerated(0.07)	possibly_damaging(0.66)	5/14	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF028043,Pfam_domain:PF01603,hmmpanther:PTHR10257:SF4,hmmpanther:PTHR10257	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGATATGTG	.	5	ESCA
SIPA1	0	.	GRCh37	11	65417519	65417519	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2845G>A	p.Glu949Lys	p.E949K	ENST00000394224	13/16	100	76	24	110	110	0	SIPA1,missense_variant,p.Glu847Lys,ENST00000527525,;SIPA1,missense_variant,p.Glu949Lys,ENST00000394224,;SIPA1,missense_variant,p.Glu847Lys,ENST00000394227,;SIPA1,missense_variant,p.Glu949Lys,ENST00000534313,;RELA,downstream_gene_variant,,ENST00000532999,;RELA,downstream_gene_variant,,ENST00000525693,;RELA,downstream_gene_variant,,ENST00000406246,;RELA,downstream_gene_variant,,ENST00000308639,;MIR4489,downstream_gene_variant,,ENST00000578869,;SIPA1,non_coding_transcript_exon_variant,,ENST00000529725,;SIPA1,non_coding_transcript_exon_variant,,ENST00000531339,;SIPA1,downstream_gene_variant,,ENST00000530226,;RELA,downstream_gene_variant,,ENST00000526283,;RELA,downstream_gene_variant,,ENST00000531484,;SIPA1,upstream_gene_variant,,ENST00000528699,;	A	ENSG00000213445	ENST00000394224	Transcript	missense_variant	3141	2845	949	E/K	Gag/Aag	.	.	.	1	SIPA1	HGNC	10885	protein_coding	YES	CCDS8108.1	ENSP00000377771	SIPA1_HUMAN	E9PIB3_HUMAN	UPI0000135D8A	.	deleterious(0)	benign(0.309)	13/16	.	hmmpanther:PTHR15711,hmmpanther:PTHR15711:SF14,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGAGAGGGT	.	5	ESCA
SIPA1	0	.	GRCh37	11	65417876	65417876	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2908G>C	p.Glu970Gln	p.E970Q	ENST00000394224	15/16	86	66	19	88	88	0	SIPA1,missense_variant,p.Glu868Gln,ENST00000527525,;SIPA1,missense_variant,p.Glu970Gln,ENST00000394224,;SIPA1,missense_variant,p.Glu868Gln,ENST00000394227,;SIPA1,missense_variant,p.Glu970Gln,ENST00000534313,;RELA,downstream_gene_variant,,ENST00000532999,;RELA,downstream_gene_variant,,ENST00000525693,;RELA,downstream_gene_variant,,ENST00000406246,;RELA,downstream_gene_variant,,ENST00000308639,;MIR4489,downstream_gene_variant,,ENST00000578869,;SIPA1,non_coding_transcript_exon_variant,,ENST00000529725,;SIPA1,non_coding_transcript_exon_variant,,ENST00000531339,;SIPA1,non_coding_transcript_exon_variant,,ENST00000528699,;SIPA1,downstream_gene_variant,,ENST00000530226,;RELA,downstream_gene_variant,,ENST00000526283,;RELA,downstream_gene_variant,,ENST00000531484,;	C	ENSG00000213445	ENST00000394224	Transcript	missense_variant	3204	2908	970	E/Q	Gag/Cag	.	.	.	1	SIPA1	HGNC	10885	protein_coding	YES	CCDS8108.1	ENSP00000377771	SIPA1_HUMAN	E9PIB3_HUMAN	UPI0000135D8A	.	tolerated(0.19)	benign(0.003)	15/16	.	hmmpanther:PTHR15711,hmmpanther:PTHR15711:SF14,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCAGAGCCT	.	5	ESCA
CATSPER1	0	.	GRCh37	11	65793409	65793409	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442C>G	p.His148Asp	p.H148D	ENST00000312106	1/12	55	34	21	50	50	0	CATSPER1,missense_variant,p.His148Asp,ENST00000312106,;CATSPER1,upstream_gene_variant,,ENST00000529244,;	C	ENSG00000175294	ENST00000312106	Transcript	missense_variant	580	442	148	H/D	Cac/Gac	.	.	.	-1	CATSPER1	HGNC	17116	protein_coding	YES	CCDS8127.1	ENSP00000309052	CTSR1_HUMAN	.	UPI000045651C	.	tolerated(0.15)	benign(0.351)	1/12	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGTGAGACC	.	5	ESCA
LRTOMT	0	.	GRCh37	11	71806129	71806129	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21G>C	p.Lys7Asn	p.K7N	ENST00000435085	5/9	53	44	9	55	55	0	LRTOMT,missense_variant,p.Lys7Asn,ENST00000440313,;LRTOMT,missense_variant,p.Lys7Asn,ENST00000539271,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000289488,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000538478,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000439209,;LRTOMT,missense_variant,p.Lys7Asn,ENST00000435085,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000541614,;LRTOMT,missense_variant,p.Lys7Asn,ENST00000307198,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000447974,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000536917,;LRTOMT,missense_variant,p.Lys7Asn,ENST00000419228,;LRTOMT,missense_variant,p.Glu124Gln,ENST00000423494,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000324866,;LRTOMT,missense_variant,p.Lys7Asn,ENST00000539587,;LAMTOR1,intron_variant,,ENST00000545249,;LAMTOR1,intron_variant,,ENST00000535107,;LAMTOR1,downstream_gene_variant,,ENST00000278671,;LRTOMT,downstream_gene_variant,,ENST00000538413,;LRTOMT,downstream_gene_variant,,ENST00000542846,;LAMTOR1,downstream_gene_variant,,ENST00000544594,;LAMTOR1,downstream_gene_variant,,ENST00000538404,;LAMTOR1,downstream_gene_variant,,ENST00000539797,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000544409,;LRTOMT,missense_variant,p.Glu142Gln,ENST00000427369,;LRTOMT,3_prime_UTR_variant,,ENST00000535883,;LRTOMT,non_coding_transcript_exon_variant,,ENST00000412777,;LAMTOR1,downstream_gene_variant,,ENST00000535872,;LAMTOR1,downstream_gene_variant,,ENST00000541403,;	C	ENSG00000184154	ENST00000435085	Transcript	missense_variant	1113	21	7	K/N	aaG/aaC	.	.	.	1	LRTOMT	HGNC	25033	protein_coding	YES	CCDS44668.1	ENSP00000409789	TOMT_HUMAN	.	UPI00019150CB	.	tolerated_low_confidence(0.11)	benign(0.005)	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGAGAAA	.	5	ESCA
OR2AT4	0	.	GRCh37	11	74800003	74800003	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756C>A	p.%3D	p.V252V	ENST00000305159	1/1	58	41	16	44	44	0	OR2AT4,synonymous_variant,p.%3D,ENST00000305159,;	T	ENSG00000171561	ENST00000305159	Transcript	synonymous_variant	797	756	252	V	gtC/gtA	.	.	.	-1	OR2AT4	HGNC	19620	protein_coding	YES	CCDS31639.1	ENSP00000304846	O2AT4_HUMAN	.	UPI0000061FA5	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF15,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCACGACCAG	.	5	ESCA
RIC3	0	.	GRCh37	11	8190574	8190574	+	5'Flank	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000309737	.	55	17	38	86	86	0	RIC3,5_prime_UTR_variant,,ENST00000335425,;RIC3,5_prime_UTR_variant,,ENST00000343202,;RIC3,upstream_gene_variant,,ENST00000425599,;RIC3,upstream_gene_variant,,ENST00000539720,;RIC3,upstream_gene_variant,,ENST00000531450,;RIC3,upstream_gene_variant,,ENST00000309737,;RIC3,upstream_gene_variant,,ENST00000419822,;RP11-379P15.1,upstream_gene_variant,,ENST00000499752,;RIC3,5_prime_UTR_variant,,ENST00000526962,;RIC3,upstream_gene_variant,,ENST00000528463,;	A	ENSG00000166405	ENST00000309737	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	38	-1	RIC3	HGNC	30338	protein_coding	YES	CCDS55742.1	ENSP00000308820	RIC3_HUMAN	F5GZ89_HUMAN	UPI00001B3DB4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGGAACCG	.	5	ESCA
AMOTL1	0	.	GRCh37	11	94609168	94609168	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5208G>C	.	.	ENST00000433060	13/13	76	67	9	44	44	0	AMOTL1,3_prime_UTR_variant,,ENST00000317837,;AMOTL1,3_prime_UTR_variant,,ENST00000317829,;AMOTL1,3_prime_UTR_variant,,ENST00000433060,;RP11-856F16.2,intron_variant,,ENST00000545958,;	C	ENSG00000166025	ENST00000433060	Transcript	3_prime_UTR_variant	8220	.	.	.	.	.	.	.	1	AMOTL1	HGNC	17811	protein_coding	YES	CCDS44712.1	ENSP00000387739	AMOL1_HUMAN	.	UPI00000742C2	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCATGAAACT	.	2	ESCA
BRAP	0	.	GRCh37	12	112123540	112123540	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57C>T	p.%3D	p.P19P	ENST00000419234	1/12	39	23	16	35	35	0	BRAP,synonymous_variant,p.%3D,ENST00000419234,;ACAD10,upstream_gene_variant,,ENST00000392636,;ACAD10,upstream_gene_variant,,ENST00000549590,;ACAD10,upstream_gene_variant,,ENST00000515283,;ACAD10,upstream_gene_variant,,ENST00000313698,;ACAD10,upstream_gene_variant,,ENST00000514615,;BRAP,upstream_gene_variant,,ENST00000539060,;ACAD10,upstream_gene_variant,,ENST00000455480,;ACAD10,upstream_gene_variant,,ENST00000552965,;BRAP,upstream_gene_variant,,ENST00000327551,;ACAD10,upstream_gene_variant,,ENST00000413681,;ACAD10,upstream_gene_variant,,ENST00000509936,;ACAD10,upstream_gene_variant,,ENST00000507135,;ACAD10,upstream_gene_variant,,ENST00000511915,;	A	ENSG00000089234	ENST00000419234	Transcript	synonymous_variant	251	57	19	P	ccC/ccT	.	.	.	-1	BRAP	HGNC	1099	protein_coding	YES	CCDS9154.1	ENSP00000403524	BRAP_HUMAN	Q59H81_HUMAN,J3KNN7_HUMAN	UPI00001AF597	.	.	.	1/12	.	hmmpanther:PTHR24007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGCGGGGAC	.	5	ESCA
BAZ2A	0	.	GRCh37	12	57003984	57003984	+	Missense_Mutation	SNP	C	C	T	rs369013055	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1801G>A	p.Val601Met	p.V601M	ENST00000551812	9/29	52	16	36	81	81	0	BAZ2A,missense_variant,p.Val571Met,ENST00000379441,;BAZ2A,missense_variant,p.Val30Met,ENST00000547650,;BAZ2A,missense_variant,p.Arg256His,ENST00000551996,;BAZ2A,missense_variant,p.Val569Met,ENST00000179765,;BAZ2A,missense_variant,p.Val601Met,ENST00000551812,;BAZ2A,missense_variant,p.Val599Met,ENST00000549884,;BAZ2A,downstream_gene_variant,,ENST00000549327,;BAZ2A,downstream_gene_variant,,ENST00000547647,;BAZ2A,upstream_gene_variant,,ENST00000549763,;BAZ2A,upstream_gene_variant,,ENST00000551759,;BAZ2A,upstream_gene_variant,,ENST00000548578,;	T	ENSG00000076108	ENST00000551812	Transcript	missense_variant	1995	1801	601	V/M	Gtg/Atg	rs369013055	.	.	-1	BAZ2A	HGNC	962	protein_coding	YES	CCDS44924.1	ENSP00000446880	BAZ2A_HUMAN	F8W053_HUMAN,F8VWQ3_HUMAN,F8VU39_HUMAN	UPI0000D4FED1	.	tolerated(0.15)	probably_damaging(0.999)	9/29	.	PROSITE_profiles:PS50982,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF141,Gene3D:3.30.890.10,Pfam_domain:PF01429,SMART_domains:SM00391,Superfamily_domains:SSF54171	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCACGTTGC	byFrequency|byCluster	5	ESCA
CD4	0	.	GRCh37	12	6909240	6909240	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-65C>G	.	.	ENST00000011653	2/10	81	36	45	89	89	0	CD4,splice_region_variant,,ENST00000541982,;CD4,splice_region_variant,,ENST00000011653,;CD4,splice_region_variant,,ENST00000539492,;CD4,splice_region_variant,,ENST00000536590,;CD4,splice_region_variant,,ENST00000536610,;CD4,splice_region_variant,,ENST00000535466,;CD4,splice_region_variant,,ENST00000535707,;CD4,intron_variant,,ENST00000538827,;CD4,intron_variant,,ENST00000544344,;CD4,intron_variant,,ENST00000437800,;	G	ENSG00000010610	ENST00000011653	Transcript	splice_region_variant	194	.	.	.	.	.	.	.	1	CD4	HGNC	1678	protein_coding	YES	CCDS8562.1	ENSP00000011653	CD4_HUMAN	Q6LCP8_HUMAN,Q13969_HUMAN,F5GYA9_HUMAN,B4DT49_HUMAN	UPI0000001294	.	.	.	2/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CAGGCCCTGCC	.	4	ESCA
ZFC3H1	0	.	GRCh37	12	72057336	72057336	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55G>A	p.Glu19Lys	p.E19K	ENST00000378743	1/35	39	17	21	50	50	0	ZFC3H1,missense_variant,p.Glu19Lys,ENST00000552037,;ZFC3H1,missense_variant,p.Glu19Lys,ENST00000378743,;ZFC3H1,missense_variant,p.Glu19Lys,ENST00000548100,;THAP2,5_prime_UTR_variant,,ENST00000308086,;THAP2,upstream_gene_variant,,ENST00000551488,;THAP2,upstream_gene_variant,,ENST00000547843,;THAP2,upstream_gene_variant,,ENST00000551238,;ZFC3H1,intron_variant,,ENST00000550712,;ZFC3H1,upstream_gene_variant,,ENST00000549407,;ZFC3H1,missense_variant,p.Glu19Lys,ENST00000552994,;	T	ENSG00000133858	ENST00000378743	Transcript	missense_variant	414	55	19	E/K	Gaa/Aaa	.	.	.	-1	ZFC3H1	HGNC	28328	protein_coding	YES	CCDS41813.1	ENSP00000368017	ZC3H1_HUMAN	.	UPI00003668E9	.	deleterious_low_confidence(0.01)	benign(0.292)	1/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTCTTCCT	.	5	ESCA
POSTN	0	.	GRCh37	13	38166244	38166244	+	Missense_Mutation	SNP	G	G	C	rs764263003	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.276C>G	p.Cys92Trp	p.C92W	ENST00000379747	3/23	120	83	37	93	93	0	POSTN,missense_variant,p.Cys92Trp,ENST00000379747,;POSTN,missense_variant,p.Cys92Trp,ENST00000379749,;POSTN,missense_variant,p.Cys92Trp,ENST00000541481,;POSTN,missense_variant,p.Cys92Trp,ENST00000379743,;POSTN,missense_variant,p.Cys92Trp,ENST00000541179,;POSTN,missense_variant,p.Cys92Trp,ENST00000379742,;	C	ENSG00000133110	ENST00000379747	Transcript	missense_variant	394	276	92	C/W	tgC/tgG	rs764263003	.	.	-1	POSTN	HGNC	16953	protein_coding	YES	CCDS9364.1	ENSP00000369071	POSTN_HUMAN	.	UPI000013CEB8	.	deleterious(0)	probably_damaging(0.927)	3/23	.	Superfamily_domains:SSF82153,PIRSF_domain:PIRSF016553,hmmpanther:PTHR10900:SF12,hmmpanther:PTHR10900,PROSITE_profiles:PS51041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGGGCAGCC	byFrequency	5	ESCA
DIS3	0	.	GRCh37	13	73333933	73333933	+	Nonstop_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2877G>T	p.Ter959TyrextTer14	p.*959Yext*14	ENST00000377767	21/21	21	11	9	36	36	0	DIS3,stop_lost,p.Ter797TyrextTer14,ENST00000545453,;DIS3,stop_lost,p.Ter959TyrextTer14,ENST00000377767,;DIS3,stop_lost,p.Ter929TyrextTer14,ENST00000377780,;BORA,downstream_gene_variant,,ENST00000390667,;BORA,downstream_gene_variant,,ENST00000377815,;DIS3,intron_variant,,ENST00000469339,;DIS3,3_prime_UTR_variant,,ENST00000490646,;	A	ENSG00000083520	ENST00000377767	Transcript	stop_lost	2978	2877	959	*/Y	taG/taT	.	.	.	-1	DIS3	HGNC	20604	protein_coding	YES	CCDS9447.1	ENSP00000366997	RRP44_HUMAN	G3V1J5_HUMAN,B3KM83_HUMAN	UPI0000141B79	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAGCTATTT	.	5	ESCA
BCL2L2	0	.	GRCh37	14	23779833	23779833	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1659G>T	.	.	ENST00000250405	4/4	25	10	15	12	12	0	BCL2L2,3_prime_UTR_variant,,ENST00000250405,;BCL2L2-PABPN1,intron_variant,,ENST00000557008,;BCL2L2-PABPN1,intron_variant,,ENST00000553781,;BCL2L2,intron_variant,,ENST00000556599,;BCL2L2-PABPN1,intron_variant,,ENST00000556100,;BCL2L2,downstream_gene_variant,,ENST00000557579,;BCL2L2,downstream_gene_variant,,ENST00000554635,;BCL2L2,downstream_gene_variant,,ENST00000553824,;BCL2L2,downstream_gene_variant,,ENST00000557236,;	T	ENSG00000129473	ENST00000250405	Transcript	3_prime_UTR_variant	2470	.	.	.	.	.	.	.	1	BCL2L2	HGNC	995	protein_coding	YES	CCDS9591.1	ENSP00000250405	B2CL2_HUMAN	G3V5A9_HUMAN,G3V4B7_HUMAN,G3V3G8_HUMAN,G3V3B7_HUMAN	UPI000013CCB8	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTGTGAGT	.	5	ESCA
NOP9	0	.	GRCh37	14	24771499	24771499	+	Missense_Mutation	SNP	G	G	A	rs772136432	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1012G>A	p.Val338Met	p.V338M	ENST00000267425	5/10	69	37	32	84	84	0	NOP9,missense_variant,p.Val338Met,ENST00000267425,;NOP9,missense_variant,p.Val338Met,ENST00000396802,;LTB4R2,upstream_gene_variant,,ENST00000527924,;DHRS1,upstream_gene_variant,,ENST00000288111,;CIDEB,downstream_gene_variant,,ENST00000556756,;CIDEB,downstream_gene_variant,,ENST00000554411,;CIDEB,downstream_gene_variant,,ENST00000336557,;NOP9,upstream_gene_variant,,ENST00000557362,;CIDEB,downstream_gene_variant,,ENST00000258807,;DHRS1,upstream_gene_variant,,ENST00000396813,;DHRS1,upstream_gene_variant,,ENST00000559483,;DHRS1,upstream_gene_variant,,ENST00000561273,;DHRS1,upstream_gene_variant,,ENST00000558114,;DHRS1,upstream_gene_variant,,ENST00000558340,;DHRS1,upstream_gene_variant,,ENST00000560991,;	A	ENSG00000196943	ENST00000267425	Transcript	missense_variant	1105	1012	338	V/M	Gtg/Atg	rs772136432	.	.	1	NOP9	HGNC	19826	protein_coding	YES	CCDS9624.1	ENSP00000267425	NOP9_HUMAN	B3KVY3_HUMAN	UPI000000CBCF	.	deleterious(0.01)	probably_damaging(0.985)	5/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13102,hmmpanther:PTHR13102:SF0,Gene3D:1.25.10.10,SMART_domains:SM00025,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTGGTGTTG	byFrequency	5	ESCA
RP11-813I20.2	0	.	GRCh37	14	56233183	56233183	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.76-5166C>A	.	.	ENST00000554458	.	66	59	7	80	80	0	RP11-813I20.2,intron_variant,,ENST00000554458,;RPL13AP3,non_coding_transcript_exon_variant,,ENST00000494676,;RPL13AP3,non_coding_transcript_exon_variant,,ENST00000487479,;	A	ENSG00000258784	ENST00000554458	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RP11-813I20.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAGGCCATGC	.	4	ESCA
NAA30	0	.	GRCh37	14	57877794	57877794	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1560A>T	.	.	ENST00000556492	5/5	72	67	5	92	92	0	NAA30,3_prime_UTR_variant,,ENST00000298406,;NAA30,3_prime_UTR_variant,,ENST00000556492,;NAA30,downstream_gene_variant,,ENST00000555166,;NAA30,downstream_gene_variant,,ENST00000554703,;	T	ENSG00000139977	ENST00000556492	Transcript	3_prime_UTR_variant	2803	.	.	.	.	.	.	.	1	NAA30	HGNC	19844	protein_coding	YES	CCDS32088.1	ENSP00000452521	NAA30_HUMAN	B4DK34_HUMAN	UPI0000161013	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTAAAGGA	.	2	ESCA
PNMA1	0	.	GRCh37	14	74179414	74179414	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.929T>A	p.Leu310His	p.L310H	ENST00000316836	1/1	53	23	30	59	59	0	PNMA1,missense_variant,p.Leu310His,ENST00000316836,;ELMSAN1,downstream_gene_variant,,ENST00000286523,;ELMSAN1,downstream_gene_variant,,ENST00000394071,;ELMSAN1,downstream_gene_variant,,ENST00000476562,;	T	ENSG00000176903	ENST00000316836	Transcript	missense_variant	1715	929	310	L/H	cTt/cAt	.	.	.	-1	PNMA1	HGNC	9158	protein_coding	YES	CCDS9818.1	ENSP00000318914	PNMA1_HUMAN	.	UPI000003779C	.	deleterious(0)	probably_damaging(0.992)	1/1	.	hmmpanther:PTHR23095:SF17,hmmpanther:PTHR23095,Pfam_domain:PF14893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTAAGCCAC	.	5	ESCA
TRIP11	0	.	GRCh37	14	92470509	92470509	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3811A>T	p.Ile1271Phe	p.I1271F	ENST00000267622	11/21	72	49	23	73	73	0	TRIP11,missense_variant,p.Ile987Phe,ENST00000554357,;TRIP11,missense_variant,p.Ile1271Phe,ENST00000267622,;TRIP11,upstream_gene_variant,,ENST00000557017,;	A	ENSG00000100815	ENST00000267622	Transcript	missense_variant	4185	3811	1271	I/F	Atc/Ttc	.	.	.	-1	TRIP11	HGNC	12305	protein_coding	YES	CCDS9899.1	ENSP00000267622	TRIPB_HUMAN	G3V4R7_HUMAN	UPI000013D767	.	deleterious(0.04)	probably_damaging(0.988)	11/21	.	hmmpanther:PTHR18921:SF2,hmmpanther:PTHR18921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGATCAGGC	.	5	ESCA
UNC79	0	.	GRCh37	14	94004395	94004395	+	Missense_Mutation	SNP	C	C	A	rs377687253	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652C>A	p.Arg218Ser	p.R218S	ENST00000256339	12/50	58	48	10	48	48	0	UNC79,missense_variant,p.Arg395Ser,ENST00000393151,;UNC79,missense_variant,p.Arg218Ser,ENST00000256339,;UNC79,missense_variant,p.Arg395Ser,ENST00000553484,;UNC79,missense_variant,p.Arg395Ser,ENST00000555664,;	A	ENSG00000133958	ENST00000256339	Transcript	missense_variant	1307	652	218	R/S	Cgt/Agt	rs377687253,COSM198451	.	.	1	UNC79	HGNC	19966	protein_coding	YES	CCDS9911.2	ENSP00000256339	UNC79_HUMAN	.	UPI0000D62441	.	tolerated(0.37)	probably_damaging(0.997)	12/50	.	hmmpanther:PTHR21696:SF1,hmmpanther:PTHR21696,Pfam_domain:PF14776	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGTCGTCAC	byCluster	5	ESCA
DNM1P47	0	.	GRCh37	15	102297905	102297905	+	RNA	SNP	C	C	T	rs573971922	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.5951C>T	.	.	ENST00000561463	2/4	34	11	23	33	33	0	DNM1P47,non_coding_transcript_exon_variant,,ENST00000561463,;DNM1P47,non_coding_transcript_exon_variant,,ENST00000571780,;	T	ENSG00000259660	ENST00000561463	Transcript	non_coding_transcript_exon_variant	5951	.	.	.	.	rs573971922	.	.	1	DNM1P47	HGNC	35200	processed_transcript	YES	.	.	.	.	.	.	.	.	2/4	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTCGGCAG	by1000G	5	ESCA
DUOX1	0	.	GRCh37	15	45444575	45444575	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3285C>T	p.%3D	p.F1095F	ENST00000321429	26/35	86	48	38	94	94	0	DUOX1,synonymous_variant,p.%3D,ENST00000389037,;DUOX1,synonymous_variant,p.%3D,ENST00000561166,;DUOX1,synonymous_variant,p.%3D,ENST00000321429,;CTD-2651B20.1,downstream_gene_variant,,ENST00000558039,;DUOX1,upstream_gene_variant,,ENST00000559221,;DUOX1,3_prime_UTR_variant,,ENST00000561220,;DUOX1,non_coding_transcript_exon_variant,,ENST00000557893,;DUOX1,non_coding_transcript_exon_variant,,ENST00000559716,;DUOX1,upstream_gene_variant,,ENST00000558744,;DUOX1,downstream_gene_variant,,ENST00000559219,;DUOX1,downstream_gene_variant,,ENST00000558446,;	T	ENSG00000137857	ENST00000321429	Transcript	synonymous_variant	3692	3285	1095	F	ttC/ttT	COSM3816195,COSM3816196	.	.	1	DUOX1	HGNC	3062	protein_coding	YES	CCDS32221.1	ENSP00000317997	DUOX1_HUMAN	H0YNR5_HUMAN	UPI000006E50E	.	.	.	26/35	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF37,Pfam_domain:PF01794	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCATGTT	.	5	ESCA
UNC13C	0	.	GRCh37	15	54920744	54920744	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1433T>G	.	.	ENST00000260323	32/32	54	36	17	53	53	0	UNC13C,3_prime_UTR_variant,,ENST00000537900,;UNC13C,3_prime_UTR_variant,,ENST00000545554,;UNC13C,3_prime_UTR_variant,,ENST00000260323,;UNC13C,downstream_gene_variant,,ENST00000560537,;UNC13C,downstream_gene_variant,,ENST00000539562,;	G	ENSG00000137766	ENST00000260323	Transcript	3_prime_UTR_variant	8078	.	.	.	.	.	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCATAGTGT	.	5	ESCA
PKD1	0	.	GRCh37	16	2160143	2160143	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5025C>T	p.%3D	p.A1675A	ENST00000262304	15/46	115	47	68	144	144	0	PKD1,synonymous_variant,p.%3D,ENST00000262304,;PKD1,synonymous_variant,p.%3D,ENST00000423118,;PKD1,intron_variant,,ENST00000483024,;PKD1,intron_variant,,ENST00000488185,;PKD1,upstream_gene_variant,,ENST00000567946,;RP11-304L19.4,upstream_gene_variant,,ENST00000568795,;PKD1,intron_variant,,ENST00000468674,;PKD1,upstream_gene_variant,,ENST00000564865,;PKD1,upstream_gene_variant,,ENST00000483558,;PKD1,upstream_gene_variant,,ENST00000473780,;PKD1,upstream_gene_variant,,ENST00000561991,;PKD1,intron_variant,,ENST00000568591,;PKD1,intron_variant,,ENST00000565639,;PKD1,intron_variant,,ENST00000415938,;PKD1,intron_variant,,ENST00000483731,;PKD1,intron_variant,,ENST00000569983,;PKD1,upstream_gene_variant,,ENST00000486339,;PKD1,upstream_gene_variant,,ENST00000496574,;PKD1,downstream_gene_variant,,ENST00000469241,;PKD1,upstream_gene_variant,,ENST00000487932,;PKD1,upstream_gene_variant,,ENST00000564890,;	A	ENSG00000008710	ENST00000262304	Transcript	synonymous_variant	5234	5025	1675	A	gcC/gcT	.	.	.	-1	PKD1	HGNC	9008	protein_coding	YES	CCDS32369.1	ENSP00000262304	PKD1_HUMAN	O75276_HUMAN	UPI00001B0454	.	.	.	15/46	.	hmmpanther:PTHR10877:SF123,hmmpanther:PTHR10877,Gene3D:2.60.40.670,TIGRFAM_domain:TIGR00864,Pfam_domain:PF00801,SMART_domains:SM00089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGGGCCGG	.	5	ESCA
ZNF785	0	.	GRCh37	16	30594220	30594220	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.879C>T	p.%3D	p.F293F	ENST00000395216	3/3	153	140	12	153	153	0	ZNF785,synonymous_variant,p.%3D,ENST00000470110,;ZNF785,synonymous_variant,p.%3D,ENST00000395216,;ZNF785,downstream_gene_variant,,ENST00000567773,;AC002310.7,non_coding_transcript_exon_variant,,ENST00000492040,;RP11-146F11.5,upstream_gene_variant,,ENST00000563540,;AC002310.7,downstream_gene_variant,,ENST00000486926,;ZNF785,upstream_gene_variant,,ENST00000562128,;AC002310.17,downstream_gene_variant,,ENST00000564755,;	A	ENSG00000197162	ENST00000395216	Transcript	synonymous_variant	1039	879	293	F	ttC/ttT	.	.	.	-1	ZNF785	HGNC	26496	protein_coding	YES	CCDS10685.1	ENSP00000378642	ZN785_HUMAN	.	UPI0000074535	.	.	.	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF130,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGGCGAAACG	.	2	ESCA
BCL7C	0	.	GRCh37	16	30903911	30903911	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438G>A	p.%3D	p.E146E	ENST00000215115	4/6	42	33	9	33	33	0	BCL7C,synonymous_variant,p.%3D,ENST00000215115,;BCL7C,synonymous_variant,p.%3D,ENST00000572628,;BCL7C,synonymous_variant,p.%3D,ENST00000380317,;CTF1,upstream_gene_variant,,ENST00000279804,;CTF1,upstream_gene_variant,,ENST00000395019,;MIR762,upstream_gene_variant,,ENST00000390236,;MIR4519,intron_variant,,ENST00000564901,;AC106782.20,intron_variant,,ENST00000572471,;MIR4519,intron_variant,,ENST00000565573,;MIR4519,intron_variant,,ENST00000570025,;BCL7C,missense_variant,p.Arg99Lys,ENST00000574418,;	T	ENSG00000099385	ENST00000215115	Transcript	synonymous_variant	1454	438	146	E	gaG/gaA	.	.	.	-1	BCL7C	HGNC	1006	protein_coding	YES	CCDS10693.1	ENSP00000215115	BCL7C_HUMAN	.	UPI000006F931	.	.	.	4/6	.	hmmpanther:PTHR12767,hmmpanther:PTHR12767:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTCTCTTG	.	5	ESCA
CTCF	0	.	GRCh37	16	67672084	67672084	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*309T>G	.	.	ENST00000264010	12/12	56	39	17	84	84	0	CTCF,3_prime_UTR_variant,,ENST00000401394,;CTCF,3_prime_UTR_variant,,ENST00000264010,;	G	ENSG00000102974	ENST00000264010	Transcript	3_prime_UTR_variant	2937	.	.	.	.	.	.	.	1	CTCF	HGNC	13723	protein_coding	YES	CCDS10841.1	ENSP00000264010	CTCF_HUMAN	.	UPI0000000DDE	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGGTAAACC	.	5	ESCA
ESRP2	0	.	GRCh37	16	68265264	68265264	+	Missense_Mutation	SNP	C	C	T	rs374057525	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1528G>A	p.Asp510Asn	p.D510N	ENST00000473183	12/15	59	33	26	46	46	0	ESRP2,missense_variant,p.Asp510Asn,ENST00000473183,;ESRP2,missense_variant,p.Asp520Asn,ENST00000565858,;NFATC3,downstream_gene_variant,,ENST00000346183,;ESRP2,downstream_gene_variant,,ENST00000562724,;NFATC3,downstream_gene_variant,,ENST00000329524,;NFATC3,downstream_gene_variant,,ENST00000570212,;NFATC3,downstream_gene_variant,,ENST00000349223,;ESRP2,downstream_gene_variant,,ENST00000564382,;NFATC3,downstream_gene_variant,,ENST00000562926,;RP11-96D1.10,downstream_gene_variant,,ENST00000571975,;RP11-96D1.11,upstream_gene_variant,,ENST00000571197,;NFATC3,downstream_gene_variant,,ENST00000566301,;NFATC3,downstream_gene_variant,,ENST00000563288,;NFATC3,downstream_gene_variant,,ENST00000563796,;NFATC3,downstream_gene_variant,,ENST00000563319,;NFATC3,downstream_gene_variant,,ENST00000569766,;NFATC3,downstream_gene_variant,,ENST00000567152,;NFATC3,downstream_gene_variant,,ENST00000535127,;ESRP2,3_prime_UTR_variant,,ENST00000566774,;ESRP2,non_coding_transcript_exon_variant,,ENST00000251366,;ESRP2,downstream_gene_variant,,ENST00000562567,;ESRP2,downstream_gene_variant,,ENST00000564465,;ESRP2,downstream_gene_variant,,ENST00000563159,;ESRP2,downstream_gene_variant,,ENST00000569964,;ESRP2,downstream_gene_variant,,ENST00000562738,;ESRP2,downstream_gene_variant,,ENST00000565213,;	T	ENSG00000103067	ENST00000473183	Transcript	missense_variant	2067	1528	510	D/N	Gat/Aat	rs374057525	.	.	-1	ESRP2	HGNC	26152	protein_coding	YES	CCDS10863.1	ENSP00000418748	ESRP2_HUMAN	J3QQJ9_HUMAN,J3KRF2_HUMAN	UPI000006FB08	.	deleterious(0.03)	probably_damaging(0.996)	12/15	.	hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF30,Pfam_domain:PF14259,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATCGCCCG	.	5	ESCA
ATXN1L	0	.	GRCh37	16	71885915	71885915	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*202G>C	.	.	ENST00000427980	3/3	156	115	40	103	103	0	ATXN1L,3_prime_UTR_variant,,ENST00000427980,;IST1,intron_variant,,ENST00000568581,;ATXN1L,intron_variant,,ENST00000569119,;ATXN1L,downstream_gene_variant,,ENST00000565676,;	C	ENSG00000224470	ENST00000427980	Transcript	3_prime_UTR_variant	2565	.	.	.	.	.	.	.	1	ATXN1L	HGNC	33279	protein_coding	YES	CCDS45523.1	ENSP00000415822	ATX1L_HUMAN	G1UI23_HUMAN	UPI0000198982	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGAGGGTGT	.	5	ESCA
ATXN1L	0	.	GRCh37	16	71889948	71889948	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4235G>T	.	.	ENST00000427980	3/3	87	60	27	56	56	0	ATXN1L,3_prime_UTR_variant,,ENST00000427980,;IST1,intron_variant,,ENST00000568581,;ZNF821,downstream_gene_variant,,ENST00000562797,;ZNF821,downstream_gene_variant,,ENST00000425432,;ZNF821,downstream_gene_variant,,ENST00000565516,;ZNF821,downstream_gene_variant,,ENST00000313565,;ZNF821,downstream_gene_variant,,ENST00000568666,;ZNF821,downstream_gene_variant,,ENST00000565601,;ZNF821,downstream_gene_variant,,ENST00000446827,;ZNF821,downstream_gene_variant,,ENST00000564134,;ATXN1L,intron_variant,,ENST00000569119,;ZNF821,downstream_gene_variant,,ENST00000568961,;ZNF821,downstream_gene_variant,,ENST00000563878,;ZNF821,downstream_gene_variant,,ENST00000562808,;ZNF821,downstream_gene_variant,,ENST00000566987,;ZNF821,downstream_gene_variant,,ENST00000563827,;	T	ENSG00000224470	ENST00000427980	Transcript	3_prime_UTR_variant	6598	.	.	.	.	.	.	.	1	ATXN1L	HGNC	33279	protein_coding	YES	CCDS45523.1	ENSP00000415822	ATX1L_HUMAN	G1UI23_HUMAN	UPI0000198982	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGGTCTGT	.	5	ESCA
PIRT	0	.	GRCh37	17	10728609	10728609	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.354G>A	p.%3D	p.Q118Q	ENST00000580256	2/2	83	56	27	86	86	0	PIRT,synonymous_variant,p.%3D,ENST00000580256,;	T	ENSG00000233670	ENST00000580256	Transcript	synonymous_variant	993	354	118	Q	caG/caA	.	.	.	-1	PIRT	HGNC	37239	protein_coding	YES	CCDS45614.1	ENSP00000462046	PIRT_HUMAN	.	UPI00006C1760	.	.	.	2/2	.	Pfam_domain:PF15099,hmmpanther:PTHR16100,hmmpanther:PTHR16100:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCTGTTT	.	5	ESCA
DNAH9	0	.	GRCh37	17	11660984	11660984	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6970A>C	p.Thr2324Pro	p.T2324P	ENST00000262442	35/69	118	84	34	134	133	0	DNAH9,missense_variant,p.Thr2324Pro,ENST00000454412,;DNAH9,missense_variant,p.Thr2324Pro,ENST00000262442,;	C	ENSG00000007174	ENST00000262442	Transcript	missense_variant	7038	6970	2324	T/P	Acc/Ccc	.	.	.	1	DNAH9	HGNC	2953	protein_coding	YES	CCDS11160.1	ENSP00000262442	DYH9_HUMAN	Q92865_HUMAN	UPI0000141BA2	.	.	benign(0.001)	35/69	.	hmmpanther:PTHR10676:SF36,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCAACCTGC	.	5	ESCA
ARL4D	0	.	GRCh37	17	41477058	41477058	+	5'UTR	SNP	A	A	C	rs376575358	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-43A>C	.	.	ENST00000320033	2/2	34	25	9	23	23	0	ARL4D,5_prime_UTR_variant,,ENST00000320033,;RNU6-1137P,upstream_gene_variant,,ENST00000517073,;	C	ENSG00000175906	ENST00000320033	Transcript	5_prime_UTR_variant	165	.	.	.	.	rs376575358	.	.	1	ARL4D	HGNC	656	protein_coding	YES	CCDS11463.1	ENSP00000322628	ARL4D_HUMAN	.	UPI0000140783	.	.	.	2/2	.	.	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCAATTTC	byFrequency|byCluster	5	ESCA
RNF43	0	.	GRCh37	17	56432282	56432282	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*22C>G	.	.	ENST00000584437	9/9	46	30	15	33	33	0	RNF43,3_prime_UTR_variant,,ENST00000407977,;RNF43,3_prime_UTR_variant,,ENST00000584437,;RNF43,3_prime_UTR_variant,,ENST00000583753,;RNF43,3_prime_UTR_variant,,ENST00000577716,;RNF43,3_prime_UTR_variant,,ENST00000500597,;SUPT4H1,upstream_gene_variant,,ENST00000580947,;SUPT4H1,upstream_gene_variant,,ENST00000577396,;SUPT4H1,upstream_gene_variant,,ENST00000581540,;RNF43,downstream_gene_variant,,ENST00000581868,;RNF43,downstream_gene_variant,,ENST00000577625,;SUPT4H1,upstream_gene_variant,,ENST00000225504,;BZRAP1-AS1,intron_variant,,ENST00000583841,;BZRAP1-AS1,downstream_gene_variant,,ENST00000578334,;BZRAP1-AS1,downstream_gene_variant,,ENST00000583826,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580515,;BZRAP1-AS1,downstream_gene_variant,,ENST00000579527,;BZRAP1-AS1,downstream_gene_variant,,ENST00000578025,;BZRAP1-AS1,downstream_gene_variant,,ENST00000582348,;BZRAP1-AS1,downstream_gene_variant,,ENST00000585236,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580633,;BZRAP1-AS1,downstream_gene_variant,,ENST00000580022,;BZRAP1-AS1,downstream_gene_variant,,ENST00000579859,;SUPT4H1,upstream_gene_variant,,ENST00000579289,;SUPT4H1,upstream_gene_variant,,ENST00000581166,;	C	ENSG00000108375	ENST00000584437	Transcript	3_prime_UTR_variant	4330	.	.	.	.	.	.	.	-1	RNF43	HGNC	18505	protein_coding	YES	CCDS11607.1	ENSP00000463069	RNF43_HUMAN	.	UPI000022A469	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTGGTTGGA	.	5	ESCA
GDPD1	0	.	GRCh37	17	57351335	57351335	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*201G>A	.	.	ENST00000284116	10/10	107	79	28	128	128	0	GDPD1,3_prime_UTR_variant,,ENST00000284116,;GDPD1,intron_variant,,ENST00000581140,;GDPD1,downstream_gene_variant,,ENST00000581276,;GDPD1,intron_variant,,ENST00000579076,;GDPD1,downstream_gene_variant,,ENST00000579020,;GDPD1,downstream_gene_variant,,ENST00000578026,;	A	ENSG00000153982	ENST00000284116	Transcript	3_prime_UTR_variant	1283	.	.	.	.	.	.	.	1	GDPD1	HGNC	20883	protein_coding	YES	CCDS11616.1	ENSP00000284116	GDPD1_HUMAN	J3QRR6_HUMAN	UPI000019850B	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTTTGTAAAT	.	2	ESCA
RPS6KB1	0	.	GRCh37	17	58024338	58024338	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*189G>A	.	.	ENST00000225577	15/15	149	114	35	79	79	0	RPS6KB1,3_prime_UTR_variant,,ENST00000225577,;RPS6KB1,3_prime_UTR_variant,,ENST00000443572,;RPS6KB1,3_prime_UTR_variant,,ENST00000393021,;RP11-178C3.1,intron_variant,,ENST00000591035,;RPS6KB1,intron_variant,,ENST00000406116,;RPS6KB1,upstream_gene_variant,,ENST00000587061,;RPS6KB1,3_prime_UTR_variant,,ENST00000472940,;RPS6KB1,downstream_gene_variant,,ENST00000475155,;	A	ENSG00000108443	ENST00000225577	Transcript	3_prime_UTR_variant	1788	.	.	.	.	.	.	.	1	RPS6KB1	HGNC	10436	protein_coding	YES	CCDS11621.1	ENSP00000225577	KS6B1_HUMAN	K7EIM2_HUMAN,B4DLT4_HUMAN	UPI000013C873	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAAGCAAAA	.	5	ESCA
GGA3	0	.	GRCh37	17	73240711	73240711	+	Missense_Mutation	SNP	C	C	T	rs776432859	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.289G>A	p.Val97Ile	p.V97I	ENST00000245541	4/17	64	23	41	102	102	0	GGA3,missense_variant,p.Val25Ile,ENST00000582486,;GGA3,missense_variant,p.Val25Ile,ENST00000582717,;GGA3,missense_variant,p.Val97Ile,ENST00000245541,;GGA3,missense_variant,p.Val97Ile,ENST00000537686,;GGA3,intron_variant,,ENST00000578348,;GGA3,intron_variant,,ENST00000580799,;GGA3,intron_variant,,ENST00000351904,;GGA3,intron_variant,,ENST00000538886,;GGA3,non_coding_transcript_exon_variant,,ENST00000579743,;GGA3,missense_variant,p.Val97Ile,ENST00000584243,;GGA3,missense_variant,p.Val97Ile,ENST00000582376,;GGA3,missense_variant,p.Val97Ile,ENST00000584978,;GGA3,3_prime_UTR_variant,,ENST00000537584,;GGA3,non_coding_transcript_exon_variant,,ENST00000582200,;GGA3,intron_variant,,ENST00000582821,;GGA3,intron_variant,,ENST00000577435,;GGA3,upstream_gene_variant,,ENST00000578896,;GGA3,upstream_gene_variant,,ENST00000583667,;GGA3,upstream_gene_variant,,ENST00000578275,;GGA3,upstream_gene_variant,,ENST00000582232,;	T	ENSG00000125447	ENST00000245541	Transcript	missense_variant	506	289	97	V/I	Gtc/Atc	rs776432859	.	.	-1	GGA3	HGNC	17079	protein_coding	YES	CCDS11717.1	ENSP00000245541	GGA3_HUMAN	J3KSG3_HUMAN,B7Z456_HUMAN	UPI000012B3DF	.	tolerated(0.1)	possibly_damaging(0.714)	4/17	.	Superfamily_domains:SSF48464,SMART_domains:SM00288,Gene3D:1.25.40.90,Pfam_domain:PF00790,hmmpanther:PTHR13856:SF34,hmmpanther:PTHR13856,PROSITE_profiles:PS50179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGACGACTT	.	5	ESCA
TP53	0	.	GRCh37	17	7578266	7578266	+	Missense_Mutation	SNP	T	T	A	.	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	6/11	117	19	97	114	114	0	TP53,missense_variant,p.Ile195Phe,ENST00000413465,;TP53,missense_variant,p.Ile195Phe,ENST00000420246,;TP53,missense_variant,p.Ile195Phe,ENST00000269305,;TP53,missense_variant,p.Ile63Phe,ENST00000509690,;TP53,missense_variant,p.Ile195Phe,ENST00000359597,;TP53,missense_variant,p.Ile102Phe,ENST00000514944,;TP53,missense_variant,p.Ile195Phe,ENST00000445888,;TP53,missense_variant,p.Ile195Phe,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	773	583	195	I/F	Atc/Ttc	TP53_g.12652A>T,TP53_g.12652A>C,TP53_g.12652del,TP53_g.12652A>G,COSM44633,COSM45773,COSM44509,COSM129840,COSM129841,COSM129843,COSM3388199,COSM1731912,COSM129842	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.I195F|c.583A>T|6,SITE|p.I195F|c.583A>T|28,SITE|p.I195F|c.583A>T|9,SITE|p.I63F|c.187A>T|9,SITE|p.I102F|c.304A>T|9,SITE|p.I195F|c.583A>T|5,SITE|p.I195F|c.583A>T|9,CODON|p.0?|c.1_1182del1182|6,CODON|p.A189_V197delAPPQHLIRV|c.565_591del27|4,CODON|p.R196*|c.585_586CC>TT|7,CODON|p.I102N|c.305T>A|10,CODON|p.I102T|c.305T>C|21,CODON|p.I195N|c.584T>A|10,CODON|p.I63S|c.188T>G|3,CODON|p.I195T|c.584T>C|88,CODON|p.I195N|c.584T>A|4,CODON|p.I195T|c.584T>C|21,CODON|p.I63N|c.188T>A|10,CODON|p.I195T|c.584T>C|12,CODON|p.I63T|c.188T>C|21,CODON|p.I195T|c.584T>C|21,CODON|p.I195N|c.584T>A|10,CODON|p.I195N|c.584T>A|23,CODON|p.I195T|c.584T>C|10,CODON|p.I195N|c.584T>A|10,CODON|p.I195S|c.584T>G|7,BUFFER|p.E198*|c.592G>T|5,BUFFER|p.E198K|c.592G>A|5,BUFFER|p.E198*|c.592G>T|4,BUFFER|p.E105*|c.313G>T|9,BUFFER|p.E198*|c.592G>T|27,BUFFER|p.E198*|c.592G>T|9,BUFFER|p.E66*|c.196G>T|9,BUFFER|p.E198*|c.592G>T|9,BUFFER|p.V197G|c.590T>G|15,BUFFER|p.V197E|c.590T>A|8,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.V65L|c.193G>T|3,BUFFER|p.V197M|c.589G>A|12,BUFFER|p.V197L|c.589G>T|5,BUFFER|p.V104L|c.310G>T|3,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.R196R|c.588A>G|4,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R196P|c.587G>C|18,BUFFER|p.R64P|c.191G>C|7,BUFFER|p.R196Q|c.587G>A|4,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R103P|c.308G>C|7,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R64fs*>27|c.190delC|3,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R103fs*51|c.307delC|3,BUFFER|p.R196fs*51|c.586delC|7,BUFFER|p.R64*|c.190C>T|65,BUFFER|p.R196*|c.586C>T|45,BUFFER|p.R196*|c.586C>T|33,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R103*|c.307C>T|64,BUFFER|p.R196*|c.586C>T|180,BUFFER|p.L194L|c.582T>C|3,BUFFER|p.L62R|c.185T>G|17,BUFFER|p.L194R|c.581T>G|50,BUFFER|p.L194R|c.581T>G|11,BUFFER|p.L194H|c.581T>A|6,BUFFER|p.L194P|c.581T>C|9,BUFFER|p.L101R|c.302T>G|17,BUFFER|p.L194R|c.581T>G|9,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|19,BUFFER|p.L101F|c.301C>T|3,BUFFER|p.L62F|c.184C>T|3,BUFFER|p.H193fs*16|c.577_578insN|3,BUFFER|p.H193R|c.578A>G|8,BUFFER|p.H193L|c.578A>T|8,BUFFER|p.H193R|c.578A>G|89,BUFFER|p.H61P|c.182A>C|4,BUFFER|p.H100L|c.299A>T|8,BUFFER|p.H61R|c.182A>G|23,BUFFER|p.H193R|c.578A>G|21,BUFFER|p.H193L|c.578A>T|8,BUFFER|p.H193R|c.578A>G|22,BUFFER|p.H100R|c.299A>G|22,BUFFER|p.H100P|c.299A>C|4,BUFFER|p.H193P|c.578A>C|4,BUFFER|p.H193L|c.578A>T|3,BUFFER|p.H193L|c.578A>T|3,BUFFER|p.H193P|c.578A>C|16,BUFFER|p.H193R|c.578A>G|5,BUFFER|p.H193P|c.578A>C|3,BUFFER|p.H193L|c.578A>T|37,BUFFER|p.H61L|c.182A>T|10,BUFFER|p.H193N|c.577C>A|6,BUFFER|p.H193D|c.577C>G|8,BUFFER|p.H193Y|c.577C>T|5,BUFFER|p.H193Y|c.577C>T|40,BUFFER|p.H100Y|c.298C>T|15,BUFFER|p.H193Y|c.577C>T|15,BUFFER|p.H61Y|c.181C>T|15,BUFFER|p.H193Y|c.577C>T|15,BUFFER|p.H193Y|c.577C>T|3,BUFFER|p.Q192H|c.576G>T|3,BUFFER|p.Q192Q|c.576G>A|3,BUFFER|p.Q192R|c.575A>G|5,BUFFER|p.P191delP|c.572_574delCTC|3,BUFFER|p.P191delP|c.572_574delCTC|3,BUFFER|p.P191delP|c.572_574delCTC|5,BUFFER|p.P59delP|c.176_178delCTC|3,BUFFER|p.P98delP|c.293_295delCTC|3,BUFFER|p.Q192*|c.574C>T|6,BUFFER|p.Q99*|c.295C>T|17,BUFFER|p.Q192*|c.574C>T|10,BUFFER|p.Q192*|c.574C>T|17,BUFFER|p.Q192*|c.574C>T|86,BUFFER|p.Q192*|c.574C>T|17,BUFFER|p.Q60*|c.178C>T|17,BUFFER|p.P191fs*56|c.571delC|3,BUFFER|p.P191L|c.572C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGATAAGAT	.	5	ESCA
CHST9	0	.	GRCh37	18	24513645	24513645	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240+10648A>T	.	.	ENST00000284224	.	25	18	7	31	31	0	CHST9,intron_variant,,ENST00000581714,;CHST9,intron_variant,,ENST00000580774,;CHST9,intron_variant,,ENST00000284224,;AQP4-AS1,non_coding_transcript_exon_variant,,ENST00000568797,;AQP4-AS1,intron_variant,,ENST00000578701,;AQP4-AS1,downstream_gene_variant,,ENST00000582605,;AQP4-AS1,downstream_gene_variant,,ENST00000579964,;	A	ENSG00000154080	ENST00000284224	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CHST9	HGNC	19898	protein_coding	YES	CCDS42422.1	ENSP00000284224	CHST9_HUMAN	.	UPI000006EC67	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCTACTAT	.	5	ESCA
ASXL3	0	.	GRCh37	18	31326180	31326180	+	Missense_Mutation	SNP	C	C	G	rs772435969	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6368C>G	p.Ser2123Cys	p.S2123C	ENST00000269197	12/12	60	41	18	78	78	0	ASXL3,missense_variant,p.Ser2123Cys,ENST00000269197,;ASXL3,downstream_gene_variant,,ENST00000592288,;	G	ENSG00000141431	ENST00000269197	Transcript	missense_variant	6368	6368	2123	S/C	tCt/tGt	rs772435969	.	.	1	ASXL3	HGNC	29357	protein_coding	YES	CCDS45847.1	ENSP00000269197	ASXL3_HUMAN	K7EQY1_HUMAN	UPI000156D0F3	.	.	probably_damaging(0.998)	12/12	.	hmmpanther:PTHR13578:SF18,hmmpanther:PTHR13578	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCTTCCT	.	5	ESCA
DCC	0	.	GRCh37	18	50923684	50923684	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2695G>A	p.Asp899Asn	p.D899N	ENST00000442544	18/29	91	72	18	98	98	0	DCC,missense_variant,p.Asp534Asn,ENST00000581580,;DCC,missense_variant,p.Asp899Asn,ENST00000442544,;DCC,missense_variant,p.Asp727Asn,ENST00000412726,;DCC,missense_variant,p.Asp38Asn,ENST00000579941,;DCC,missense_variant,p.Arg755Lys,ENST00000304775,;	A	ENSG00000187323	ENST00000442544	Transcript	missense_variant	3311	2695	899	D/N	Gac/Aac	.	.	.	1	DCC	HGNC	2701	protein_coding	YES	CCDS11952.1	ENSP00000389140	DCC_HUMAN	J3QQJ6_HUMAN	UPI00001AEDC6	.	tolerated(1)	benign(0.016)	18/29	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF68,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265,Prints_domain:PR00014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGACACA	.	5	ESCA
ZNF788	0	.	GRCh37	19	12223836	12223836	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1474C>A	p.His492Asn	p.H492N	ENST00000339302	3/3	75	70	4	96	96	0	ZNF788,missense_variant,p.His492Asn,ENST00000339302,;ZNF788,missense_variant,p.His111Asn,ENST00000397759,;ZNF788,3_prime_UTR_variant,,ENST00000430298,;ZNF20,intron_variant,,ENST00000600335,;ZNF788,downstream_gene_variant,,ENST00000596883,;ZNF788,intron_variant,,ENST00000601686,;	A	ENSG00000188474	ENST00000339302	Transcript	missense_variant	2111	1474	492	H/N	Cat/Aat	.	.	.	1	ZNF788	Uniprot_gn	33112	protein_coding	YES	.	ENSP00000342021	ZN788_HUMAN	.	UPI000041AACA	.	deleterious(0)	probably_damaging(0.913)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF13,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAACACATGAA	.	2	ESCA
DCAF15	0	.	GRCh37	19	14070617	14070617	+	Silent	SNP	C	C	T	rs778091615	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1350C>T	p.%3D	p.F450F	ENST00000254337	9/13	71	38	32	43	43	0	DCAF15,synonymous_variant,p.%3D,ENST00000585468,;DCAF15,synonymous_variant,p.%3D,ENST00000587307,;DCAF15,synonymous_variant,p.%3D,ENST00000254337,;RFX1,downstream_gene_variant,,ENST00000254325,;DCAF15,non_coding_transcript_exon_variant,,ENST00000588523,;DCAF15,upstream_gene_variant,,ENST00000591385,;RFX1,downstream_gene_variant,,ENST00000588520,;	T	ENSG00000132017	ENST00000254337	Transcript	synonymous_variant	1371	1350	450	F	ttC/ttT	rs778091615	.	.	1	DCAF15	HGNC	25095	protein_coding	YES	CCDS32926.1	ENSP00000254337	DCA15_HUMAN	.	UPI0000203531	.	.	.	9/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCGAATA	.	5	ESCA
BRD4	0	.	GRCh37	19	15357913	15357913	+	Intron	SNP	T	T	C	rs565692731	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2159-2340A>G	.	.	ENST00000263377	.	167	105	61	145	145	0	BRD4,3_prime_UTR_variant,,ENST00000371835,;BRD4,intron_variant,,ENST00000263377,;BRD4,upstream_gene_variant,,ENST00000594066,;	C	ENSG00000141867	ENST00000263377	Transcript	intron_variant	.	.	.	.	.	rs565692731	.	.	-1	BRD4	HGNC	13575	protein_coding	YES	CCDS12328.1	ENSP00000263377	BRD4_HUMAN	Q96HN0_HUMAN,M0R0H4_HUMAN,M0QZD9_HUMAN	UPI0000126ACE	.	.	.	.	11/19	.	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAATTTCAT	byCluster|by1000G	5	ESCA
USHBP1	0	.	GRCh37	19	17373483	17373483	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520G>T	p.Ala174Ser	p.A174S	ENST00000252597	4/13	98	87	11	86	86	0	USHBP1,missense_variant,p.Ala174Ser,ENST00000252597,;USHBP1,missense_variant,p.Ala110Ser,ENST00000431146,;BABAM1,upstream_gene_variant,,ENST00000595632,;BABAM1,upstream_gene_variant,,ENST00000599057,;BABAM1,upstream_gene_variant,,ENST00000601043,;USHBP1,downstream_gene_variant,,ENST00000594190,;BABAM1,upstream_gene_variant,,ENST00000598188,;BABAM1,upstream_gene_variant,,ENST00000596335,;BABAM1,upstream_gene_variant,,ENST00000601436,;BABAM1,upstream_gene_variant,,ENST00000447614,;BABAM1,upstream_gene_variant,,ENST00000599474,;BABAM1,upstream_gene_variant,,ENST00000359435,;USHBP1,downstream_gene_variant,,ENST00000598309,;USHBP1,non_coding_transcript_exon_variant,,ENST00000598570,;BABAM1,upstream_gene_variant,,ENST00000448635,;USHBP1,downstream_gene_variant,,ENST00000595993,;USHBP1,missense_variant,p.Ala174Ser,ENST00000324554,;USHBP1,3_prime_UTR_variant,,ENST00000597928,;BABAM1,upstream_gene_variant,,ENST00000601171,;USHBP1,downstream_gene_variant,,ENST00000596436,;CTD-2278I10.6,upstream_gene_variant,,ENST00000596542,;USHBP1,downstream_gene_variant,,ENST00000600286,;BABAM1,upstream_gene_variant,,ENST00000594247,;BABAM1,upstream_gene_variant,,ENST00000595393,;	A	ENSG00000130307	ENST00000252597	Transcript	missense_variant	694	520	174	A/S	Gct/Tct	.	.	.	-1	USHBP1	HGNC	24058	protein_coding	YES	CCDS12353.1	ENSP00000252597	USBP1_HUMAN	M0R3B1_HUMAN,M0R172_HUMAN	UPI000006F7A8	.	deleterious(0.05)	possibly_damaging(0.452)	4/13	.	hmmpanther:PTHR23347:SF5,hmmpanther:PTHR23347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGAGCTGCCT	.	4	ESCA
GPATCH1	0	.	GRCh37	19	33609992	33609992	+	Silent	SNP	C	C	T	rs770047387	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2490C>T	p.%3D	p.F830F	ENST00000170564	17/20	36	23	13	35	35	0	GPATCH1,synonymous_variant,p.%3D,ENST00000170564,;GPATCH1,non_coding_transcript_exon_variant,,ENST00000592262,;	T	ENSG00000076650	ENST00000170564	Transcript	synonymous_variant	2804	2490	830	F	ttC/ttT	rs770047387	.	.	1	GPATCH1	HGNC	24658	protein_coding	YES	CCDS12428.1	ENSP00000170564	GPTC1_HUMAN	.	UPI000004EC71	.	.	.	17/20	.	hmmpanther:PTHR13384:SF19,hmmpanther:PTHR13384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTCGGCCC	.	5	ESCA
LTBP4	0	.	GRCh37	19	41111350	41111350	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683A>G	p.Gln228Arg	p.Q228R	ENST00000308370	6/34	99	64	35	141	141	0	LTBP4,missense_variant,p.Gln161Arg,ENST00000396819,;LTBP4,missense_variant,p.Gln191Arg,ENST00000204005,;LTBP4,missense_variant,p.Gln228Arg,ENST00000308370,;LTBP4,5_prime_UTR_variant,,ENST00000545697,;RN7SL758P,downstream_gene_variant,,ENST00000580450,;LTBP4,non_coding_transcript_exon_variant,,ENST00000602240,;LTBP4,non_coding_transcript_exon_variant,,ENST00000600509,;LTBP4,non_coding_transcript_exon_variant,,ENST00000599016,;LTBP4,non_coding_transcript_exon_variant,,ENST00000594537,;LTBP4,non_coding_transcript_exon_variant,,ENST00000601209,;LTBP4,upstream_gene_variant,,ENST00000598677,;LTBP4,downstream_gene_variant,,ENST00000600026,;LTBP4,intron_variant,,ENST00000598717,;LTBP4,downstream_gene_variant,,ENST00000593738,;LTBP4,upstream_gene_variant,,ENST00000598256,;LTBP4,upstream_gene_variant,,ENST00000595529,;LTBP4,upstream_gene_variant,,ENST00000546155,;	G	ENSG00000090006	ENST00000308370	Transcript	missense_variant	683	683	228	Q/R	cAg/cGg	.	.	.	1	LTBP4	HGNC	6717	protein_coding	YES	.	ENSP00000311905	LTBP4_HUMAN	.	UPI000179A7A0	.	deleterious(0.03)	possibly_damaging(0.899)	6/34	.	hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGCAGGAGG	.	5	ESCA
IRGQ	0	.	GRCh37	19	44096738	44096738	+	Missense_Mutation	SNP	C	C	T	rs750405377	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1312G>A	p.Gly438Arg	p.G438R	ENST00000422989	3/3	21	14	7	16	16	0	IRGQ,missense_variant,p.Gly438Arg,ENST00000422989,;IRGQ,missense_variant,p.Gly438Arg,ENST00000602269,;L34079.2,intron_variant,,ENST00000594374,;ZNF576,upstream_gene_variant,,ENST00000525771,;ZNF576,upstream_gene_variant,,ENST00000528387,;SRRM5,upstream_gene_variant,,ENST00000607544,;ZNF576,upstream_gene_variant,,ENST00000391965,;ZNF576,upstream_gene_variant,,ENST00000336564,;SRRM5,upstream_gene_variant,,ENST00000526798,;ZNF576,upstream_gene_variant,,ENST00000529930,;IRGQ,downstream_gene_variant,,ENST00000598324,;ZNF576,upstream_gene_variant,,ENST00000533118,;IRGQ,intron_variant,,ENST00000601520,;IRGQ,upstream_gene_variant,,ENST00000596409,;ZNF576,upstream_gene_variant,,ENST00000595041,;	T	ENSG00000167378	ENST00000422989	Transcript	missense_variant	1468	1312	438	G/R	Gga/Aga	rs750405377	.	.	-1	IRGQ	HGNC	24868	protein_coding	YES	CCDS33040.1	ENSP00000387535	IRGQ_HUMAN	M0QZP8_HUMAN	UPI000003FDB6	.	deleterious(0.01)	probably_damaging(1)	3/3	.	PROSITE_profiles:PS51716,hmmpanther:PTHR19364,hmmpanther:PTHR19364:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCCGCCAG	.	5	ESCA
NOVA2	0	.	GRCh37	19	46443970	46443970	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630C>G	p.%3D	p.L210L	ENST00000263257	4/4	56	38	18	49	49	0	NOVA2,synonymous_variant,p.%3D,ENST00000263257,;NOVA2,downstream_gene_variant,,ENST00000596784,;	C	ENSG00000104967	ENST00000263257	Transcript	synonymous_variant	825	630	210	L	ctC/ctG	.	.	.	-1	NOVA2	HGNC	7887	protein_coding	YES	CCDS12679.1	ENSP00000263257	NOVA2_HUMAN	Q9HDB7_HUMAN,M0R1A0_HUMAN	UPI000006EBE8	.	.	.	4/4	.	hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF141,Gene3D:3.30.1370.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTTGAGGCA	.	5	ESCA
PRKD2	0	.	GRCh37	19	47197277	47197277	+	Silent	SNP	G	G	A	rs763789755	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1431C>T	p.%3D	p.F477F	ENST00000433867	11/19	55	30	25	71	71	0	PRKD2,synonymous_variant,p.%3D,ENST00000595515,;PRKD2,synonymous_variant,p.%3D,ENST00000600194,;PRKD2,synonymous_variant,p.%3D,ENST00000601806,;PRKD2,synonymous_variant,p.%3D,ENST00000433867,;PRKD2,synonymous_variant,p.%3D,ENST00000291281,;PRKD2,downstream_gene_variant,,ENST00000601605,;RN7SL364P,upstream_gene_variant,,ENST00000473668,;PRKD2,non_coding_transcript_exon_variant,,ENST00000597589,;PRKD2,non_coding_transcript_exon_variant,,ENST00000599019,;PRKD2,upstream_gene_variant,,ENST00000597390,;PRKD2,upstream_gene_variant,,ENST00000599464,;PRKD2,upstream_gene_variant,,ENST00000602155,;	A	ENSG00000105287	ENST00000433867	Transcript	synonymous_variant	1909	1431	477	F	ttC/ttT	rs763789755	.	.	-1	PRKD2	HGNC	17293	protein_coding	YES	CCDS12689.1	ENSP00000393978	KPCD2_HUMAN	M0R346_HUMAN,M0R2R2_HUMAN,M0R012_HUMAN	UPI000013E03A	.	.	.	11/19	.	Superfamily_domains:SSF50729,PIRSF_domain:PIRSF000552,SMART_domains:SM00233,Pfam_domain:PF00169,Gene3D:2.30.29.30,hmmpanther:PTHR22968,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCACGAAGTA	.	5	ESCA
EMC10	0	.	GRCh37	19	50985908	50985908	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*392C>G	.	.	ENST00000334976	7/7	41	21	20	50	50	0	EMC10,missense_variant,p.His347Asp,ENST00000598585,;EMC10,3_prime_UTR_variant,,ENST00000334976,;EMC10,3_prime_UTR_variant,,ENST00000376918,;EMC10,downstream_gene_variant,,ENST00000597799,;EMC10,downstream_gene_variant,,ENST00000597426,;CTD-2545M3.8,downstream_gene_variant,,ENST00000595005,;CTD-2545M3.2,intron_variant,,ENST00000598194,;EMC10,3_prime_UTR_variant,,ENST00000601780,;EMC10,3_prime_UTR_variant,,ENST00000599293,;EMC10,downstream_gene_variant,,ENST00000594508,;	G	ENSG00000161671	ENST00000334976	Transcript	3_prime_UTR_variant	1227	.	.	.	.	.	.	.	1	EMC10	HGNC	27609	protein_coding	YES	CCDS12796.1	ENSP00000334037	EMC10_HUMAN	.	UPI0000036D2B	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCACCCT	.	5	ESCA
KLK15	0	.	GRCh37	19	51330300	51330300	+	Silent	SNP	G	G	A	rs369380000	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315C>T	p.%3D	p.N105N	ENST00000598239	3/5	41	27	14	51	51	0	KLK15,synonymous_variant,p.%3D,ENST00000326856,;KLK15,synonymous_variant,p.%3D,ENST00000598673,;KLK15,synonymous_variant,p.%3D,ENST00000598239,;KLK15,synonymous_variant,p.%3D,ENST00000301421,;KLK15,synonymous_variant,p.%3D,ENST00000596931,;KLK15,synonymous_variant,p.%3D,ENST00000416184,;KLK1,upstream_gene_variant,,ENST00000301420,;KLK1,upstream_gene_variant,,ENST00000448701,;AC011523.2,upstream_gene_variant,,ENST00000598079,;KLK15,synonymous_variant,p.%3D,ENST00000602114,;KLK15,non_coding_transcript_exon_variant,,ENST00000596531,;KLK15,non_coding_transcript_exon_variant,,ENST00000601680,;KLK1,upstream_gene_variant,,ENST00000593859,;KLK1,upstream_gene_variant,,ENST00000593325,;	A	ENSG00000174562	ENST00000598239	Transcript	synonymous_variant	346	315	105	N	aaC/aaT	rs369380000,COSM3404489	.	.	-1	KLK15	HGNC	20453	protein_coding	YES	CCDS12805.1	ENSP00000469315	KLK15_HUMAN	S5TEP0_HUMAN,M0R2F7_HUMAN	UPI000004CA04	.	.	.	3/5	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24259,hmmpanther:PTHR24259:SF68,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0.0002	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCGTTGCG	byCluster|by1000G	5	ESCA
CEACAM18	0	.	GRCh37	19	51983739	51983739	+	Missense_Mutation	SNP	G	G	A	rs371514477	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388G>A	p.Ala130Thr	p.A130T	ENST00000451626	3/5	97	64	33	88	88	0	CEACAM18,missense_variant,p.Ala130Thr,ENST00000451626,;CEACAM18,missense_variant,p.Ala69Thr,ENST00000396477,;	A	ENSG00000213822	ENST00000451626	Transcript	missense_variant	388	388	130	A/T	Gca/Aca	rs371514477,COSM272484,COSM272485	.	.	1	CEACAM18	HGNC	31949	protein_coding	YES	.	ENSP00000402203	.	.	UPI0000DD8506	.	tolerated(0.58)	benign(0.035)	3/5	.	hmmpanther:PTHR19955,hmmpanther:PTHR19955:SF6,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A69T|c.205G>A|3,SITE|p.A130T|c.388G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCGCAGGA	byFrequency|byCluster	5	ESCA
COL11A1	0	.	GRCh37	1	103342606	103342606	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*969G>C	.	.	ENST00000370096	67/67	34	16	18	55	55	0	COL11A1,3_prime_UTR_variant,,ENST00000353414,;COL11A1,3_prime_UTR_variant,,ENST00000370096,;COL11A1,3_prime_UTR_variant,,ENST00000358392,;COL11A1,downstream_gene_variant,,ENST00000512756,;COL11A1,downstream_gene_variant,,ENST00000470170,;	G	ENSG00000060718	ENST00000370096	Transcript	3_prime_UTR_variant	6703	.	.	.	.	.	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	.	67/67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTCCATCTT	.	5	ESCA
NBPF12	0	.	GRCh37	1	146398500	146398500	+	Silent	SNP	C	C	T	rs782276451	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486C>T	p.%3D	p.L162L	ENST00000442909	7/82	355	220	134	341	341	0	NBPF12,synonymous_variant,p.%3D,ENST00000309471,;NBPF12,synonymous_variant,p.%3D,ENST00000442909,;NBPF12,synonymous_variant,p.%3D,ENST00000446760,;	T	ENSG00000186275	ENST00000442909	Transcript	synonymous_variant	1322	486	162	L	ctC/ctT	rs782276451	.	.	1	NBPF12	HGNC	24297	protein_coding	YES	.	ENSP00000391116	NBPFC_HUMAN	S4R3H5_HUMAN,H7BZX4_HUMAN,H7BYX2_HUMAN,F8WEX1_HUMAN,F5GXN6_HUMAN	UPI0001B798CE	.	.	.	7/82	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTCAGCCC	byFrequency	5	ESCA
VANGL2	0	.	GRCh37	1	160389226	160389226	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.627G>A	p.%3D	p.E209E	ENST00000368061	4/8	55	39	15	34	34	0	VANGL2,synonymous_variant,p.%3D,ENST00000368061,;VANGL2,upstream_gene_variant,,ENST00000483408,;	A	ENSG00000162738	ENST00000368061	Transcript	synonymous_variant	1101	627	209	E	gaG/gaA	.	.	.	1	VANGL2	HGNC	15511	protein_coding	YES	CCDS30915.1	ENSP00000357040	VANG2_HUMAN	.	UPI00001C1D79	.	.	.	4/8	.	hmmpanther:PTHR20886,hmmpanther:PTHR20886:SF10,Pfam_domain:PF06638,PIRSF_domain:PIRSF007991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGAGCGCAG	.	5	ESCA
RGS16	0	.	GRCh37	1	182568892	182568892	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*535G>A	.	.	ENST00000367558	5/5	26	12	14	30	30	0	RGS16,3_prime_UTR_variant,,ENST00000367558,;	T	ENSG00000143333	ENST00000367558	Transcript	3_prime_UTR_variant	1293	.	.	.	.	.	.	.	-1	RGS16	HGNC	9997	protein_coding	YES	CCDS1348.1	ENSP00000356529	RGS16_HUMAN	.	UPI000013D8E9	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACTCTGGGC	.	5	ESCA
RGS8	0	.	GRCh37	1	182615830	182615830	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*40delT	.	.	ENST00000258302	6/6	106	83	23	69	69	0	RGS8,3_prime_UTR_variant,,ENST00000367557,;RGS8,3_prime_UTR_variant,,ENST00000258302,;RGS8,3_prime_UTR_variant,,ENST00000483095,;RGS8,downstream_gene_variant,,ENST00000367556,;RP11-317P15.5,upstream_gene_variant,,ENST00000570153,;	-	ENSG00000135824	ENST00000258302	Transcript	3_prime_UTR_variant	727	.	.	.	.	.	.	.	-1	RGS8	HGNC	16810	protein_coding	YES	CCDS1349.1	ENSP00000258302	RGS8_HUMAN	.	UPI0000038BF1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGTGGAGGGGA	.	3	ESCA
LGR6	0	.	GRCh37	1	202245493	202245493	+	Missense_Mutation	SNP	C	C	T	rs747408179	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.488C>T	p.Ser163Phe	p.S163F	ENST00000367278	5/18	62	44	17	30	30	0	LGR6,missense_variant,p.Ser111Phe,ENST00000255432,;LGR6,missense_variant,p.Ser163Phe,ENST00000367278,;LGR6,missense_variant,p.Ser89Phe,ENST00000423542,;LGR6,intron_variant,,ENST00000439764,;LGR6,non_coding_transcript_exon_variant,,ENST00000308543,;LGR6,non_coding_transcript_exon_variant,,ENST00000506931,;LGR6,missense_variant,p.Ser111Phe,ENST00000487787,;	T	ENSG00000133067	ENST00000367278	Transcript	missense_variant	577	488	163	S/F	tCc/tTc	rs747408179,COSM3481660,COSM3481661	.	.	1	LGR6	HGNC	19719	protein_coding	YES	CCDS30971.1	ENSP00000356247	LGR6_HUMAN	.	UPI0000161221	.	tolerated(0.06)	probably_damaging(0.981)	5/18	.	Superfamily_domains:SSF52058,SMART_domains:SM00365,SMART_domains:SM00369,Pfam_domain:PF13855,Gene3D:3.80.10.10,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF12,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTCCCTCC	.	5	ESCA
YOD1	0	.	GRCh37	1	207222508	207222510	+	In_Frame_Del	DEL	CTG	CTG	-	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	CTG	CTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.902_904delCAG	p.Ala301del	p.A301del	ENST00000315927	2/2	54	25	29	49	49	0	YOD1,inframe_deletion,p.Ala301del,ENST00000315927,;YOD1,inframe_deletion,p.Ala257del,ENST00000367084,;YOD1,inframe_deletion,p.Ala257del,ENST00000391927,;PFKFB2,upstream_gene_variant,,ENST00000367080,;PFKFB2,upstream_gene_variant,,ENST00000411990,;PFKFB2,upstream_gene_variant,,ENST00000367079,;PFKFB2,upstream_gene_variant,,ENST00000464777,;PFKFB2,upstream_gene_variant,,ENST00000468857,;	-	ENSG00000180667	ENST00000315927	Transcript	inframe_deletion	949-951	902-904	301-302	AD/D	gCAGat/gat	.	.	.	-1	YOD1	HGNC	25035	protein_coding	YES	CCDS31002.1	ENSP00000326813	OTU1_HUMAN	.	UPI0000458A05	.	.	.	2/2	.	hmmpanther:PTHR13312:SF0,hmmpanther:PTHR13312	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTCATCTGCTAAT	.	3	ESCA
USH2A	0	.	GRCh37	1	215987082	215987082	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9735A>G	p.%3D	p.L3245L	ENST00000307340	49/72	162	111	51	147	147	0	USH2A,synonymous_variant,p.%3D,ENST00000366943,;USH2A,synonymous_variant,p.%3D,ENST00000307340,;	C	ENSG00000042781	ENST00000307340	Transcript	synonymous_variant	10122	9735	3245	L	ctA/ctG	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	.	49/72	.	SMART_domains:SM00060,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGTAGAAT	.	5	ESCA
ENAH	0	.	GRCh37	1	225682660	225682660	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2817T>G	.	.	ENST00000366844	15/15	106	60	46	95	94	0	ENAH,3_prime_UTR_variant,,ENST00000366844,;ENAH,downstream_gene_variant,,ENST00000366843,;ENAH,downstream_gene_variant,,ENST00000284563,;ENAH,intron_variant,,ENST00000488523,;ENAH,downstream_gene_variant,,ENST00000498108,;ENAH,downstream_gene_variant,,ENST00000483952,;ENAH,downstream_gene_variant,,ENST00000358675,;	C	ENSG00000154380	ENST00000366844	Transcript	3_prime_UTR_variant	5045	.	.	.	.	.	.	.	-1	ENAH	HGNC	18271	protein_coding	YES	CCDS31041.1	ENSP00000355809	ENAH_HUMAN	.	UPI0000203FDB	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAGAATTCA	.	5	ESCA
CHRM3	0	.	GRCh37	1	240072316	240072316	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1565C>G	p.Pro522Arg	p.P522R	ENST00000255380	5/5	92	60	32	70	70	0	CHRM3,missense_variant,p.Pro522Arg,ENST00000255380,;CHRM3,downstream_gene_variant,,ENST00000448020,;	G	ENSG00000133019	ENST00000255380	Transcript	missense_variant	2344	1565	522	P/R	cCc/cGc	.	.	.	1	CHRM3	HGNC	1952	protein_coding	YES	CCDS1616.1	ENSP00000255380	ACM3_HUMAN	Q8NG01_HUMAN,B1AN12_HUMAN	UPI0000050453	.	deleterious(0.02)	probably_damaging(0.998)	5/5	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF61,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00243	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATACCCAAAA	.	5	ESCA
OMA1	0	.	GRCh37	1	59004813	59004813	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154G>T	p.Gly52Ter	p.G52*	ENST00000371226	2/9	38	8	29	47	47	0	OMA1,stop_gained,p.Gly52Ter,ENST00000482274,;OMA1,stop_gained,p.Gly52Ter,ENST00000456980,;OMA1,stop_gained,p.Gly52Ter,ENST00000426139,;OMA1,stop_gained,p.Gly52Ter,ENST00000358603,;OMA1,stop_gained,p.Gly52Ter,ENST00000371226,;OMA1,stop_gained,p.Gly52Ter,ENST00000453710,;OMA1,stop_gained,p.Gly52Ter,ENST00000419242,;OMA1,upstream_gene_variant,,ENST00000421528,;OMA1,intron_variant,,ENST00000467063,;DAB1,intron_variant,,ENST00000485760,;	A	ENSG00000162600	ENST00000371226	Transcript	stop_gained	268	154	52	G/*	Gga/Tga	.	.	.	-1	OMA1	HGNC	29661	protein_coding	YES	CCDS608.1	ENSP00000360270	OMA1_HUMAN	S4R3A3_HUMAN	UPI000006D0C6	.	.	.	2/9	.	hmmpanther:PTHR22726,hmmpanther:PTHR22726:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTCCCTGAT	.	5	ESCA
PKN2	0	.	GRCh37	1	89250469	89250469	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1133G>A	p.Gly378Glu	p.G378E	ENST00000370521	7/22	67	60	7	94	94	0	PKN2,missense_variant,p.Gly378Glu,ENST00000370513,;PKN2,missense_variant,p.Gly221Glu,ENST00000370505,;PKN2,missense_variant,p.Gly378Glu,ENST00000370521,;PKN2,missense_variant,p.Gly52Glu,ENST00000544045,;PKN2,missense_variant,p.Gly378Glu,ENST00000316005,;PKN2,intron_variant,,ENST00000436111,;	A	ENSG00000065243	ENST00000370521	Transcript	missense_variant	1492	1133	378	G/E	gGa/gAa	.	.	.	1	PKN2	HGNC	9406	protein_coding	YES	CCDS714.1	ENSP00000359552	PKN2_HUMAN	Q6P5W9_HUMAN	UPI000004D291	.	tolerated(0.12)	benign(0.027)	7/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24357:SF76,hmmpanther:PTHR24357,SMART_domains:SM00239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCGGAAGTA	.	4	ESCA
SUN5	0	.	GRCh37	20	31584143	31584143	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.412C>T	p.%3D	p.L138L	ENST00000356173	7/13	103	55	47	85	85	0	SUN5,synonymous_variant,p.%3D,ENST00000356173,;SUN5,synonymous_variant,p.%3D,ENST00000375523,;SUN5,downstream_gene_variant,,ENST00000375519,;SUN5,downstream_gene_variant,,ENST00000420875,;	A	ENSG00000167098	ENST00000356173	Transcript	synonymous_variant	505	412	138	L	Ctg/Ttg	.	.	.	-1	SUN5	HGNC	16252	protein_coding	YES	CCDS13209.1	ENSP00000348496	SUN5_HUMAN	.	UPI0000135D7C	.	.	.	7/13	.	hmmpanther:PTHR12911:SF19,hmmpanther:PTHR12911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGTGGAC	.	5	ESCA
E2F1	0	.	GRCh37	20	32264556	32264556	+	Silent	SNP	G	G	A	rs752347181	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1296C>T	p.%3D	p.L432L	ENST00000343380	7/7	142	82	59	144	144	0	E2F1,synonymous_variant,p.%3D,ENST00000343380,;NECAB3,upstream_gene_variant,,ENST00000439478,;NECAB3,upstream_gene_variant,,ENST00000606690,;NECAB3,upstream_gene_variant,,ENST00000246190,;NECAB3,upstream_gene_variant,,ENST00000375238,;RP1-63M2.5,downstream_gene_variant,,ENST00000606866,;NECAB3,upstream_gene_variant,,ENST00000606699,;NECAB3,upstream_gene_variant,,ENST00000493590,;NECAB3,upstream_gene_variant,,ENST00000485399,;NECAB3,upstream_gene_variant,,ENST00000484824,;NECAB3,upstream_gene_variant,,ENST00000607055,;NECAB3,upstream_gene_variant,,ENST00000607805,;NECAB3,upstream_gene_variant,,ENST00000488489,;	A	ENSG00000101412	ENST00000343380	Transcript	synonymous_variant	1436	1296	432	L	ctC/ctT	rs752347181	.	.	-1	E2F1	HGNC	3113	protein_coding	YES	CCDS13224.1	ENSP00000345571	E2F1_HUMAN	.	UPI000002EDEC	.	.	.	7/7	.	hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTGAGGTC	.	5	ESCA
E2F1	0	.	GRCh37	20	32264679	32264679	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1173C>G	p.Phe391Leu	p.F391L	ENST00000343380	7/7	65	34	31	51	51	0	E2F1,missense_variant,p.Phe391Leu,ENST00000343380,;NECAB3,upstream_gene_variant,,ENST00000439478,;NECAB3,upstream_gene_variant,,ENST00000606690,;NECAB3,upstream_gene_variant,,ENST00000246190,;NECAB3,upstream_gene_variant,,ENST00000375238,;RP1-63M2.5,downstream_gene_variant,,ENST00000606866,;NECAB3,upstream_gene_variant,,ENST00000606699,;NECAB3,upstream_gene_variant,,ENST00000493590,;NECAB3,upstream_gene_variant,,ENST00000485399,;NECAB3,upstream_gene_variant,,ENST00000484824,;NECAB3,upstream_gene_variant,,ENST00000607055,;NECAB3,upstream_gene_variant,,ENST00000607805,;NECAB3,upstream_gene_variant,,ENST00000488489,;	C	ENSG00000101412	ENST00000343380	Transcript	missense_variant	1313	1173	391	F/L	ttC/ttG	.	.	.	-1	E2F1	HGNC	3113	protein_coding	YES	CCDS13224.1	ENSP00000345571	E2F1_HUMAN	.	UPI000002EDEC	.	tolerated(0.28)	benign(0.042)	7/7	.	hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGAGAAGTC	.	5	ESCA
PXMP4	0	.	GRCh37	20	32307929	32307929	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85G>A	p.Val29Met	p.V29M	ENST00000409299	1/4	230	148	82	169	169	0	PXMP4,missense_variant,p.Val29Met,ENST00000217398,;PXMP4,missense_variant,p.Val29Met,ENST00000344022,;PXMP4,missense_variant,p.Val29Met,ENST00000409299,;	T	ENSG00000101417	ENST00000409299	Transcript	missense_variant	178	85	29	V/M	Gtg/Atg	.	.	.	-1	PXMP4	HGNC	15920	protein_coding	YES	CCDS13225.1	ENSP00000386385	PXMP4_HUMAN	B4DLI8_HUMAN	UPI000013C727	.	tolerated(0.3)	benign(0.045)	1/4	.	hmmpanther:PTHR15460,Pfam_domain:PF02466,PIRSF_domain:PIRSF013674	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCACGGCCA	.	5	ESCA
PIGT	0	.	GRCh37	20	44054363	44054363	+	Missense_Mutation	SNP	A	A	G	rs376655698	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1634A>G	p.Asn545Ser	p.N545S	ENST00000279036	12/12	96	59	36	84	84	0	PIGT,missense_variant,p.Asn390Ser,ENST00000535404,;PIGT,missense_variant,p.Asn283Ser,ENST00000545755,;PIGT,missense_variant,p.Asn443Ser,ENST00000279035,;PIGT,missense_variant,p.Asn489Ser,ENST00000543458,;PIGT,missense_variant,p.Asn478Ser,ENST00000372689,;PIGT,missense_variant,p.Asn351Ser,ENST00000341555,;PIGT,missense_variant,p.Asn545Ser,ENST00000279036,;PIGT,3_prime_UTR_variant,,ENST00000455050,;	G	ENSG00000124155	ENST00000279036	Transcript	missense_variant	1714	1634	545	N/S	aAt/aGt	rs376655698	.	.	1	PIGT	HGNC	14938	protein_coding	YES	CCDS13353.1	ENSP00000279036	PIGT_HUMAN	B7Z1N3_HUMAN	UPI000003B0D0	.	deleterious(0)	probably_damaging(0.999)	12/12	.	hmmpanther:PTHR12959:SF11,hmmpanther:PTHR12959,Pfam_domain:PF04113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	CTACAATCTCC	byFrequency|byCluster	3	ESCA
SPATA25	0	.	GRCh37	20	44515296	44515296	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544C>G	p.Gln182Glu	p.Q182E	ENST00000372519	2/2	73	39	33	66	66	0	SPATA25,missense_variant,p.Gln182Glu,ENST00000372519,;ZSWIM1,downstream_gene_variant,,ENST00000372523,;NEURL2,downstream_gene_variant,,ENST00000545238,;CTSA,upstream_gene_variant,,ENST00000372484,;CTSA,upstream_gene_variant,,ENST00000354880,;CTSA,upstream_gene_variant,,ENST00000372459,;ZSWIM1,downstream_gene_variant,,ENST00000372520,;NEURL2,downstream_gene_variant,,ENST00000372518,;CTSA,upstream_gene_variant,,ENST00000607482,;CTSA,upstream_gene_variant,,ENST00000191018,;CTSA,upstream_gene_variant,,ENST00000606788,;CTSA,upstream_gene_variant,,ENST00000606394,;CTSA,upstream_gene_variant,,ENST00000607841,;CTSA,upstream_gene_variant,,ENST00000607814,;CTSA,upstream_gene_variant,,ENST00000607212,;CTSA,upstream_gene_variant,,ENST00000606066,;	C	ENSG00000149634	ENST00000372519	Transcript	missense_variant	589	544	182	Q/E	Caa/Gaa	.	.	.	-1	SPATA25	HGNC	16158	protein_coding	YES	CCDS13383.1	ENSP00000361597	SPT25_HUMAN	.	UPI000012861A	.	deleterious_low_confidence(0.02)	probably_damaging(0.987)	2/2	.	Pfam_domain:PF15218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTGAGCGG	.	5	ESCA
MTG2	0	.	GRCh37	20	60775767	60775767	+	Silent	SNP	C	C	A	rs772798244	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855C>A	p.%3D	p.G285G	ENST00000370823	7/7	46	24	22	40	40	0	MTG2,synonymous_variant,p.%3D,ENST00000436421,;MTG2,synonymous_variant,p.%3D,ENST00000536470,;MTG2,synonymous_variant,p.%3D,ENST00000370823,;MTG2,downstream_gene_variant,,ENST00000448254,;MTG2,non_coding_transcript_exon_variant,,ENST00000472005,;MTG2,downstream_gene_variant,,ENST00000471352,;MTG2,downstream_gene_variant,,ENST00000466099,;MTG2,upstream_gene_variant,,ENST00000488748,;MTG2,downstream_gene_variant,,ENST00000461411,;MTG2,downstream_gene_variant,,ENST00000471962,;MTG2,3_prime_UTR_variant,,ENST00000467101,;	A	ENSG00000101181	ENST00000370823	Transcript	synonymous_variant	873	855	285	G	ggC/ggA	rs772798244	.	.	1	MTG2	HGNC	16239	protein_coding	YES	CCDS13492.1	ENSP00000359859	MTG2_HUMAN	Q5JXJ0_HUMAN,B4DR85_HUMAN	UPI000006EF41	.	.	.	7/7	.	PROSITE_profiles:PS51710,HAMAP:MF_01454,hmmpanther:PTHR11702,hmmpanther:PTHR11702:SF3,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR02729,TIGRFAM_domain:TIGR00231,Pfam_domain:PF01926,PIRSF_domain:PIRSF002401,Superfamily_domains:SSF52540,Prints_domain:PR00326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGGCGCCCA	.	5	ESCA
KRTAP20-1	0	.	GRCh37	21	31988818	31988818	+	Silent	SNP	G	G	T	rs750518775	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45G>T	p.%3D	p.G15G	ENST00000334664	1/1	131	43	87	178	178	0	KRTAP20-1,synonymous_variant,p.%3D,ENST00000334664,;KRTAP6-1,upstream_gene_variant,,ENST00000329122,;KRTAP20-4,upstream_gene_variant,,ENST00000382828,;	T	ENSG00000244624	ENST00000334664	Transcript	synonymous_variant	69	45	15	G	ggG/ggT	rs750518775	.	.	1	KRTAP20-1	HGNC	18943	protein_coding	YES	CCDS13603.1	ENSP00000335503	KR201_HUMAN	.	UPI00001A9E4F	.	.	.	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Pfam_domain:PF11759	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGGGCTTGG	.	5	ESCA
SON	0	.	GRCh37	21	34922690	34922690	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1153G>T	p.Gly385Trp	p.G385W	ENST00000356577	3/12	71	25	46	98	98	0	SON,missense_variant,p.Gly385Trp,ENST00000381679,;SON,missense_variant,p.Gly385Trp,ENST00000300278,;SON,missense_variant,p.Gly385Trp,ENST00000290239,;SON,missense_variant,p.Gly385Trp,ENST00000356577,;SON,intron_variant,,ENST00000381692,;SON,upstream_gene_variant,,ENST00000421541,;SON,upstream_gene_variant,,ENST00000436227,;SON,downstream_gene_variant,,ENST00000492229,;SON,missense_variant,p.Gly385Trp,ENST00000455528,;SON,downstream_gene_variant,,ENST00000475072,;	T	ENSG00000159140	ENST00000356577	Transcript	missense_variant	1628	1153	385	G/W	Ggg/Tgg	.	.	.	1	SON	HGNC	11183	protein_coding	YES	CCDS13629.1	ENSP00000348984	SON_HUMAN	.	UPI0000140BFD	.	.	probably_damaging(0.965)	3/12	.	hmmpanther:PTHR12813:SF26,hmmpanther:PTHR12813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCGGGGCCA	.	5	ESCA
ITSN1	0	.	GRCh37	21	35257404	35257404	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4736A>G	p.Lys1579Arg	p.K1579R	ENST00000381318	37/40	50	47	3	58	58	0	ITSN1,missense_variant,p.Lys259Arg,ENST00000381284,;ITSN1,missense_variant,p.Lys1579Arg,ENST00000381285,;ITSN1,missense_variant,p.Lys115Arg,ENST00000415023,;ITSN1,missense_variant,p.Lys1579Arg,ENST00000381318,;ITSN1,missense_variant,p.Lys1574Arg,ENST00000399367,;ITSN1,missense_variant,p.Lys1518Arg,ENST00000437442,;ITSN1,3_prime_UTR_variant,,ENST00000399326,;AP000304.12,intron_variant,,ENST00000429238,;ITSN1,3_prime_UTR_variant,,ENST00000420666,;	G	ENSG00000205726	ENST00000381318	Transcript	missense_variant	5024	4736	1579	K/R	aAg/aGg	.	.	.	1	ITSN1	HGNC	6183	protein_coding	YES	CCDS33545.1	ENSP00000370719	ITSN1_HUMAN	D6PAW2_HUMAN,C9JXS9_HUMAN,C9J1A4_HUMAN	UPI00001403C6	.	tolerated(0.09)	benign(0.019)	37/40	.	Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAAAGAAGC	.	2	ESCA
DGCR6L	0	.	GRCh37	22	20307414	20307414	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98A>G	p.Lys33Arg	p.K33R	ENST00000248879	1/5	51	26	24	47	47	0	DGCR6L,missense_variant,p.Lys33Arg,ENST00000405465,;DGCR6L,missense_variant,p.Lys33Arg,ENST00000248879,;XXbac-B444P24.14,upstream_gene_variant,,ENST00000609632,;XXbac-B444P24.13,upstream_gene_variant,,ENST00000608275,;DGCR6L,missense_variant,p.Lys33Arg,ENST00000443409,;	C	ENSG00000128185	ENST00000248879	Transcript	missense_variant	190	98	33	K/R	aAg/aGg	.	.	.	-1	DGCR6L	HGNC	18551	protein_coding	YES	CCDS13778.1	ENSP00000248879	DGC6L_HUMAN	.	UPI0000129216	.	tolerated(0.43)	benign(0.04)	1/5	.	Pfam_domain:PF07324,hmmpanther:PTHR13054:SF4,hmmpanther:PTHR13054	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCTTCACC	.	5	ESCA
CRYBA4	0	.	GRCh37	22	27026481	27026481	+	3'UTR	SNP	G	G	A	rs376812109	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*30G>A	.	.	ENST00000354760	6/6	46	35	11	49	49	0	CRYBA4,3_prime_UTR_variant,,ENST00000354760,;CRYBA4,non_coding_transcript_exon_variant,,ENST00000466315,;	A	ENSG00000196431	ENST00000354760	Transcript	3_prime_UTR_variant	656	.	.	.	.	rs376812109	.	.	1	CRYBA4	HGNC	2396	protein_coding	YES	CCDS13841.1	ENSP00000346805	CRBA4_HUMAN	.	UPI0000167B21	.	.	.	6/6	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGCGTGCTT	byFrequency|byCluster	5	ESCA
RASD2	0	.	GRCh37	22	35948086	35948086	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7G>A	.	.	ENST00000216127	3/3	63	38	25	40	40	0	RASD2,3_prime_UTR_variant,,ENST00000216127,;	A	ENSG00000100302	ENST00000216127	Transcript	3_prime_UTR_variant	1450	.	.	.	.	.	.	.	1	RASD2	HGNC	18229	protein_coding	YES	CCDS13916.1	ENSP00000216127	RHES_HUMAN	.	UPI000004980A	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGGGATGCT	.	5	ESCA
EP300	0	.	GRCh37	22	41576061	41576061	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1101A>G	.	.	ENST00000263253	31/31	71	47	24	84	84	0	EP300,3_prime_UTR_variant,,ENST00000263253,;RP1-85F18.5,intron_variant,,ENST00000420537,;RP1-85F18.6,intron_variant,,ENST00000415054,;	G	ENSG00000100393	ENST00000263253	Transcript	3_prime_UTR_variant	9565	.	.	.	.	.	.	.	1	EP300	HGNC	3373	protein_coding	YES	CCDS14010.1	ENSP00000263253	EP300_HUMAN	B5A250_HUMAN	UPI00001AE876	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTAAATAAAC	.	5	ESCA
SAMM50	0	.	GRCh37	22	44372658	44372658	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806C>G	p.Ser269Cys	p.S269C	ENST00000350028	9/15	76	45	31	95	95	0	SAMM50,missense_variant,p.Ser59Cys,ENST00000396202,;SAMM50,missense_variant,p.Ser269Cys,ENST00000350028,;SAMM50,downstream_gene_variant,,ENST00000493161,;SAMM50,non_coding_transcript_exon_variant,,ENST00000474323,;	G	ENSG00000100347	ENST00000350028	Transcript	missense_variant	963	806	269	S/C	tCt/tGt	.	.	.	1	SAMM50	HGNC	24276	protein_coding	YES	CCDS14055.1	ENSP00000345445	SAM50_HUMAN	A8MZI2_HUMAN	UPI000016A33D	.	deleterious(0.04)	benign(0.159)	9/15	.	Gene3D:2qdzA01,Pfam_domain:PF01103,hmmpanther:PTHR12815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTCTTCCA	.	5	ESCA
TMEM182	0	.	GRCh37	2	103414392	103414392	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402C>G	p.Ile134Met	p.I134M	ENST00000412401	4/5	73	44	29	54	54	0	TMEM182,missense_variant,p.Ile134Met,ENST00000412401,;TMEM182,missense_variant,p.Ile38Met,ENST00000409528,;TMEM182,missense_variant,p.Ile91Met,ENST00000409173,;TMEM182,downstream_gene_variant,,ENST00000454536,;TMEM182,non_coding_transcript_exon_variant,,ENST00000486293,;TMEM182,intron_variant,,ENST00000488134,;TMEM182,non_coding_transcript_exon_variant,,ENST00000484094,;	G	ENSG00000170417	ENST00000412401	Transcript	missense_variant	607	402	134	I/M	atC/atG	.	.	.	1	TMEM182	HGNC	26391	protein_coding	YES	CCDS2064.1	ENSP00000394178	TM182_HUMAN	.	UPI0000366F4E	.	tolerated(0.08)	probably_damaging(0.98)	4/5	.	Pfam_domain:PF13903,hmmpanther:PTHR32012,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGATCATCTG	.	5	ESCA
ROCK2	0	.	GRCh37	2	11332666	11332666	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3860C>T	p.Pro1287Leu	p.P1287L	ENST00000315872	31/33	89	53	36	68	68	0	ROCK2,missense_variant,p.Pro1287Leu,ENST00000315872,;ROCK2,missense_variant,p.Pro1044Leu,ENST00000401753,;ROCK2,downstream_gene_variant,,ENST00000493096,;ROCK2,downstream_gene_variant,,ENST00000460262,;	A	ENSG00000134318	ENST00000315872	Transcript	missense_variant	4309	3860	1287	P/L	cCt/cTt	.	.	.	-1	ROCK2	HGNC	10252	protein_coding	YES	CCDS42654.1	ENSP00000317985	ROCK2_HUMAN	Q14DU5_HUMAN,E9PF63_HUMAN	UPI000034ECB0	.	deleterious(0)	probably_damaging(0.998)	31/33	.	PROSITE_profiles:PS50003,PROSITE_profiles:PS50081,hmmpanther:PTHR22988:SF24,hmmpanther:PTHR22988,Gene3D:3.30.60.20,Pfam_domain:PF00169,SMART_domains:SM00109,SMART_domains:SM00233,PIRSF_domain:PIRSF037568,Superfamily_domains:SSF57889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGAGGCTTA	.	5	ESCA
LRP1B	0	.	GRCh37	2	141093318	141093318	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11982C>A	p.Phe3994Leu	p.F3994L	ENST00000389484	78/91	123	72	51	143	143	0	LRP1B,missense_variant,p.Phe3994Leu,ENST00000389484,;LRP1B,missense_variant,p.Phe226Leu,ENST00000437977,;	T	ENSG00000168702	ENST00000389484	Transcript	missense_variant	12954	11982	3994	F/L	ttC/ttA	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	benign(0.153)	78/91	.	Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTGAACCA	.	5	ESCA
SCN1A	0	.	GRCh37	2	166900237	166900237	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1985C>T	p.Ser662Leu	p.S662L	ENST00000303395	11/26	97	48	48	99	99	0	SCN1A,missense_variant,p.Ser662Leu,ENST00000423058,;SCN1A,missense_variant,p.Ser662Leu,ENST00000303395,;SCN1A,missense_variant,p.Ser662Leu,ENST00000375405,;SCN1A,intron_variant,,ENST00000409050,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000595268,;	A	ENSG00000144285	ENST00000303395	Transcript	missense_variant	1985	1985	662	S/L	tCg/tTg	CM104355,COSM137365	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	tolerated(0.3)	benign(0.025)	11/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF133,Pfam_domain:PF11933	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGCGATGTA	.	5	ESCA
ABCB11	0	.	GRCh37	2	169850332	169850332	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672G>A	p.Met224Ile	p.M224I	ENST00000263817	8/28	69	36	33	92	92	0	ABCB11,missense_variant,p.Met224Ile,ENST00000263817,;	T	ENSG00000073734	ENST00000263817	Transcript	missense_variant	797	672	224	M/I	atG/atA	.	.	.	-1	ABCB11	HGNC	42	protein_coding	YES	CCDS46444.1	ENSP00000263817	ABCBB_HUMAN	Q9UIL3_HUMAN,Q53S60_HUMAN,B4DYQ0_HUMAN	UPI0000163BFA	.	tolerated(0.61)	benign(0.002)	8/28	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGTCATGCG	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098953	178098953	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	2/5	44	23	21	53	53	0	NFE2L2,missense_variant,p.Gly15Ala,ENST00000449627,;NFE2L2,missense_variant,p.Gly15Ala,ENST00000423513,;NFE2L2,missense_variant,p.Gly31Ala,ENST00000397062,;NFE2L2,missense_variant,p.Gly15Ala,ENST00000446151,;NFE2L2,missense_variant,p.Gly15Ala,ENST00000588123,;NFE2L2,missense_variant,p.Gly30Ala,ENST00000586532,;NFE2L2,missense_variant,p.Gly15Ala,ENST00000421929,;NFE2L2,missense_variant,p.Gly15Ala,ENST00000464747,;NFE2L2,missense_variant,p.Gly15Ala,ENST00000448782,;NFE2L2,missense_variant,p.Gly15Ala,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	G	ENSG00000116044	ENST00000397062	Transcript	missense_variant	647	92	31	G/A	gGa/gCa	COSM132956,COSM1613738,COSM1259060	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0.02)	benign(0.318)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G31A|c.92G>C|7,CODON|p.G31E|c.92G>A|5,BUFFER|p.R34P|c.101G>C|3,BUFFER|p.R34Q|c.101G>A|11,BUFFER|p.R34G|c.100C>G|11,BUFFER|p.L30R|c.89T>G|7,BUFFER|p.L30F|c.88C>T|6,BUFFER|p.D29G|c.86A>G|11,BUFFER|p.D29H|c.85G>C|12,BUFFER|p.D29N|c.85G>A|3,BUFFER|p.D29Y|c.85G>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACTCCAAGA	.	5	ESCA
ZNF385B	0	.	GRCh37	2	180409561	180409561	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389T>A	p.Phe130Tyr	p.F130Y	ENST00000410066	4/10	66	49	17	73	73	0	ZNF385B,missense_variant,p.Phe28Tyr,ENST00000409692,;ZNF385B,missense_variant,p.Phe54Tyr,ENST00000409343,;ZNF385B,missense_variant,p.Phe130Tyr,ENST00000410066,;ZNF385B,missense_variant,p.Phe28Tyr,ENST00000336917,;ZNF385B,missense_variant,p.Phe48Tyr,ENST00000439340,;ZNF385B,missense_variant,p.Phe28Tyr,ENST00000457304,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000466398,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000469551,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000463918,;ZNF385B,intron_variant,,ENST00000475539,;	T	ENSG00000144331	ENST00000410066	Transcript	missense_variant	993	389	130	F/Y	tTt/tAt	.	.	.	-1	ZNF385B	HGNC	26332	protein_coding	YES	CCDS33339.1	ENSP00000386845	Z385B_HUMAN	Q53S82_HUMAN,Q53R81_HUMAN,C9JPH4_HUMAN,C9JKK0_HUMAN,C9J0U3_HUMAN	UPI00004F9C24	.	deleterious(0)	probably_damaging(0.995)	4/10	.	hmmpanther:PTHR23067:SF8,hmmpanther:PTHR23067,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P128Q|c.383C>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTAAAATTT	.	5	ESCA
HNRNPLL	0	.	GRCh37	2	38796385	38796385	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1291A>T	p.Asn431Tyr	p.N431Y	ENST00000409636	11/14	52	31	21	44	44	0	HNRNPLL,missense_variant,p.Asn402Tyr,ENST00000409328,;HNRNPLL,missense_variant,p.Asn43Tyr,ENST00000441689,;HNRNPLL,missense_variant,p.Asn436Tyr,ENST00000449105,;HNRNPLL,missense_variant,p.Asn402Tyr,ENST00000378915,;HNRNPLL,missense_variant,p.Asn431Tyr,ENST00000409636,;HNRNPLL,missense_variant,p.Asn436Tyr,ENST00000608859,;HNRNPLL,3_prime_UTR_variant,,ENST00000272249,;	A	ENSG00000143889	ENST00000409636	Transcript	missense_variant	1453	1291	431	N/Y	Aat/Tat	.	.	.	-1	HNRNPLL	HGNC	25127	protein_coding	YES	CCDS46261.1	ENSP00000387088	HNRLL_HUMAN	.	UPI000007462B	.	deleterious(0)	probably_damaging(1)	11/14	.	TIGRFAM_domain:TIGR01649,Gene3D:3.30.70.330,hmmpanther:PTHR11546:SF15,hmmpanther:PTHR11546	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGATTATTTT	.	5	ESCA
EPAS1	0	.	GRCh37	2	46587838	46587838	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.516G>A	p.Met172Ile	p.M172I	ENST00000263734	5/16	49	34	15	44	44	0	EPAS1,missense_variant,p.Met172Ile,ENST00000263734,;EPAS1,missense_variant,p.Met172Ile,ENST00000449347,;EPAS1,downstream_gene_variant,,ENST00000475822,;EPAS1,non_coding_transcript_exon_variant,,ENST00000463191,;	A	ENSG00000116016	ENST00000263734	Transcript	missense_variant	1026	516	172	M/I	atG/atA	.	.	.	1	EPAS1	HGNC	3374	protein_coding	YES	CCDS1825.1	ENSP00000263734	EPAS1_HUMAN	Q53SM6_HUMAN,C9J9N2_HUMAN,B3KW07_HUMAN	UPI000013D44F	.	deleterious(0)	benign(0.052)	5/16	.	hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF8,Gene3D:3.30.450.20,Superfamily_domains:SSF55785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGAAGTG	.	5	ESCA
SLC4A5	0	.	GRCh37	2	74531762	74531762	+	Missense_Mutation	SNP	T	T	A	rs752448602	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.125A>T	p.Gln42Leu	p.Q42L	ENST00000377634	7/31	113	74	39	112	112	0	SLC4A5,missense_variant,p.Gln42Leu,ENST00000377632,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000444570,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000425249,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000436454,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000423644,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000394019,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000346834,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000377634,;SLC4A5,missense_variant,p.Gln42Leu,ENST00000357822,;SLC4A5,intron_variant,,ENST00000359484,;SLC4A5,intron_variant,,ENST00000358683,;SLC4A5,intron_variant,,ENST00000483195,;RP11-287D1.3,3_prime_UTR_variant,,ENST00000451608,;KRT18P26,downstream_gene_variant,,ENST00000454475,;	A	ENSG00000188687	ENST00000377634	Transcript	missense_variant	525	125	42	Q/L	cAa/cTa	rs752448602	.	.	-1	SLC4A5	HGNC	18168	protein_coding	YES	CCDS1936.1	ENSP00000366861	S4A5_HUMAN	Q9UDR3_HUMAN,Q53S35_HUMAN,Q53QY5_HUMAN,C9JW32_HUMAN,C9JU12_HUMAN,C9JNL6_HUMAN	UPI000013C97B	.	deleterious_low_confidence(0.01)	benign(0.021)	7/31	.	hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTTGAGGG	.	5	ESCA
FER1L5	0	.	GRCh37	2	97355040	97355040	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.911C>T	.	.	ENST00000457909	8/35	136	84	52	99	99	0	FER1L5,non_coding_transcript_exon_variant,,ENST00000457909,;FER1L5,non_coding_transcript_exon_variant,,ENST00000436930,;FER1L5,non_coding_transcript_exon_variant,,ENST00000414152,;FER1L5,non_coding_transcript_exon_variant,,ENST00000424961,;	T	ENSG00000249715	ENST00000457909	Transcript	non_coding_transcript_exon_variant	911	.	.	.	.	.	.	.	1	FER1L5	HGNC	19044	retained_intron	.	.	.	.	.	.	.	.	.	8/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACCCTCCCC	.	5	ESCA
FAHD2B	0	.	GRCh37	2	97749938	97749938	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.762C>T	p.%3D	p.F254F	ENST00000414820	7/9	168	113	55	146	146	0	FAHD2B,synonymous_variant,p.%3D,ENST00000272610,;FAHD2B,synonymous_variant,p.%3D,ENST00000440566,;FAHD2B,synonymous_variant,p.%3D,ENST00000414820,;FAHD2B,downstream_gene_variant,,ENST00000468548,;FAHD2B,non_coding_transcript_exon_variant,,ENST00000474849,;FAHD2B,non_coding_transcript_exon_variant,,ENST00000463096,;AC018892.9,downstream_gene_variant,,ENST00000340118,;AC018892.9,downstream_gene_variant,,ENST00000445404,;	A	ENSG00000144199	ENST00000414820	Transcript	synonymous_variant	1033	762	254	F	ttC/ttT	.	.	.	-1	FAHD2B	HGNC	25318	protein_coding	YES	CCDS2030.1	ENSP00000410470	FAH2B_HUMAN	.	UPI000004D29E	.	.	.	7/9	.	hmmpanther:PTHR11820:SF77,hmmpanther:PTHR11820,Gene3D:3.90.850.10,Pfam_domain:PF01557,Superfamily_domains:SSF56529	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTGAATAC	.	5	ESCA
DPPA4	0	.	GRCh37	3	109046719	109046719	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*116G>A	.	.	ENST00000335658	7/7	32	26	6	41	41	0	DPPA4,3_prime_UTR_variant,,ENST00000335658,;DPPA4,downstream_gene_variant,,ENST00000477303,;DPPA4,non_coding_transcript_exon_variant,,ENST00000463966,;DPPA4,downstream_gene_variant,,ENST00000478791,;DPPA4,non_coding_transcript_exon_variant,,ENST00000475135,;DPPA4,downstream_gene_variant,,ENST00000487299,;DPPA4,downstream_gene_variant,,ENST00000495679,;	T	ENSG00000121570	ENST00000335658	Transcript	3_prime_UTR_variant	1086	.	.	.	.	.	.	.	-1	DPPA4	HGNC	19200	protein_coding	YES	CCDS33814.1	ENSP00000335306	DPPA4_HUMAN	C9J7A7_HUMAN	UPI000022C153	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGCATGGC	.	5	ESCA
KIAA2018	0	.	GRCh37	3	113379264	113379264	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1265G>T	p.Arg422Leu	p.R422L	ENST00000316407	7/7	40	16	24	62	62	0	KIAA2018,missense_variant,p.Arg422Leu,ENST00000478658,;KIAA2018,missense_variant,p.Arg422Leu,ENST00000316407,;KIAA2018,intron_variant,,ENST00000491165,;KIAA2018,non_coding_transcript_exon_variant,,ENST00000496826,;	A	ENSG00000176542	ENST00000316407	Transcript	missense_variant	1676	1265	422	R/L	cGa/cTa	.	.	.	-1	KIAA2018	HGNC	30494	protein_coding	YES	CCDS43133.1	ENSP00000320794	K2018_HUMAN	.	UPI00004800D8	.	.	probably_damaging(0.998)	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTCGTGTA	.	5	ESCA
C3orf72	0	.	GRCh37	3	138669212	138669212	+	Missense_Mutation	SNP	C	C	T	rs779660003	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326C>T	p.Ser109Leu	p.S109L	ENST00000383165	3/3	38	13	25	17	17	0	C3orf72,missense_variant,p.Ser109Leu,ENST00000383165,;FOXL2,upstream_gene_variant,,ENST00000330315,;C3orf72,3_prime_UTR_variant,,ENST00000470680,;C3orf72,non_coding_transcript_exon_variant,,ENST00000498709,;	T	ENSG00000206262	ENST00000383165	Transcript	missense_variant	457	326	109	S/L	tCg/tTg	rs779660003,COSM3380417	.	.	1	C3orf72	HGNC	34428	protein_coding	YES	CCDS43155.1	ENSP00000372651	CC072_HUMAN	.	UPI00001C0AE3	.	deleterious_low_confidence(0.02)	possibly_damaging(0.776)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTTCGCTAG	byFrequency	5	ESCA
PIK3CA	0	.	GRCh37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	10/21	256	155	101	115	115	0	PIK3CA,missense_variant,p.Glu545Lys,ENST00000263967,;PIK3CA,upstream_gene_variant,,ENST00000462255,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	1790	1633	545	E/K	Gag/Aag	rs104886003,COSM763,COSM27133,COSM125370,COSM295672	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	deleterious(0.02)	probably_damaging(0.959)	10/21	.	PROSITE_profiles:PS51545,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Pfam_domain:PF00613,Gene3D:1.25.40.70,SMART_domains:SM00145,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	not_provided,pathogenic	0,1,1,1,1	21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E545K|c.1633G>A|227,SITE|p.E545K|c.1633G>A|1153,CODON|p.T544N|c.1631C>A|3,BUFFER|p.E542Q|c.1624G>C|8,BUFFER|p.E542K|c.1624G>A|115,BUFFER|p.E542K|c.1624G>A|758,BUFFER|p.E542G|c.1625A>G|3,BUFFER|p.E542V|c.1625A>T|14,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.E542V|c.1625A>T|5,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.I543V|c.1627A>G|3,BUFFER|p.E545Q|c.1633G>C|30,BUFFER|p.E545Q|c.1633G>C|9,BUFFER|p.E545A|c.1634A>C|130,BUFFER|p.E545V|c.1634A>T|4,BUFFER|p.E545A|c.1634A>C|11,BUFFER|p.E545G|c.1634A>G|14,BUFFER|p.E545G|c.1634A>G|90,BUFFER|p.E545D|c.1635G>T|13,BUFFER|p.E545D|c.1635G>C|11,BUFFER|p.E545D|c.1635G>T|4,BUFFER|p.Q546K|c.1636C>A|119,BUFFER|p.Q546E|c.1636C>G|15,BUFFER|p.Q546K|c.1636C>A|18,BUFFER|p.Q546R|c.1637A>G|20,BUFFER|p.Q546P|c.1637A>C|22,BUFFER|p.Q546P|c.1637A>C|7,BUFFER|p.Q546L|c.1637A>T|8,BUFFER|p.Q546R|c.1637A>G|41,BUFFER|p.Q546H|c.1638G>T|7,BUFFER|p.E547K|c.1639G>A|11,BUFFER|p.E547G|c.1640A>G|5,BUFFER|p.E547G|c.1640A>G|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTGAGCAG	byCluster	5	ESCA
TP63	0	.	GRCh37	3	189612899	189612899	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*608C>A	.	.	ENST00000264731	14/14	81	62	18	39	39	0	TP63,3_prime_UTR_variant,,ENST00000354600,;TP63,3_prime_UTR_variant,,ENST00000264731,;TP63,3_prime_UTR_variant,,ENST00000382063,;TP63,downstream_gene_variant,,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000456148,;TP63,downstream_gene_variant,,ENST00000392460,;TP63,downstream_gene_variant,,ENST00000320472,;TP63,downstream_gene_variant,,ENST00000440651,;TP63,downstream_gene_variant,,ENST00000449992,;TP63,downstream_gene_variant,,ENST00000392463,;	A	ENSG00000073282	ENST00000264731	Transcript	3_prime_UTR_variant	2740	.	.	.	.	.	.	.	1	TP63	HGNC	15979	protein_coding	YES	CCDS3293.1	ENSP00000264731	P63_HUMAN	.	UPI0000073CF2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGATCCATTT	.	5	ESCA
CMTM7	0	.	GRCh37	3	32495940	32495940	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*194C>G	.	.	ENST00000334983	5/5	15	7	8	15	15	0	CMTM7,missense_variant,p.Pro137Ala,ENST00000465248,;CMTM7,3_prime_UTR_variant,,ENST00000349718,;CMTM7,3_prime_UTR_variant,,ENST00000334983,;CMTM7,3_prime_UTR_variant,,ENST00000487007,;CMTM7,non_coding_transcript_exon_variant,,ENST00000464689,;CMTM7,downstream_gene_variant,,ENST00000454304,;	G	ENSG00000153551	ENST00000334983	Transcript	3_prime_UTR_variant	958	.	.	.	.	.	.	.	1	CMTM7	HGNC	19178	protein_coding	YES	CCDS33730.1	ENSP00000335605	CKLF7_HUMAN	.	UPI00000343F1	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCCAGCC	.	5	ESCA
XYLB	0	.	GRCh37	3	38437017	38437017	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1313C>T	p.Ala438Val	p.A438V	ENST00000207870	16/19	40	37	3	64	63	1	XYLB,missense_variant,p.Ala438Val,ENST00000207870,;XYLB,missense_variant,p.Ala301Val,ENST00000542835,;XYLB,non_coding_transcript_exon_variant,,ENST00000472721,;XYLB,3_prime_UTR_variant,,ENST00000424034,;	T	ENSG00000093217	ENST00000207870	Transcript	missense_variant	1403	1313	438	A/V	gCc/gTc	.	.	.	1	XYLB	HGNC	12839	protein_coding	YES	CCDS2678.1	ENSP00000207870	XYLB_HUMAN	B4DDT2_HUMAN,B3KM56_HUMAN	UPI0000160544	.	tolerated(0.13)	benign(0.173)	16/19	.	Superfamily_domains:SSF53067,Gene3D:3.30.420.40,Pfam_domain:PF02782,hmmpanther:PTHR10196,hmmpanther:PTHR10196:SF57	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTGGCCACAG	.	2	ESCA
TRAK1	0	.	GRCh37	3	42243925	42243925	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1428-3C>T	.	.	ENST00000327628	.	73	28	44	93	93	0	TRAK1,splice_region_variant,,ENST00000449246,;TRAK1,splice_region_variant,,ENST00000396175,;TRAK1,splice_region_variant,,ENST00000427771,;TRAK1,splice_region_variant,,ENST00000341421,;TRAK1,splice_region_variant,,ENST00000327628,;TRAK1,splice_region_variant,,ENST00000487159,;TRAK1,splice_region_variant,,ENST00000484786,;	T	ENSG00000182606	ENST00000327628	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	TRAK1	HGNC	29947	protein_coding	YES	CCDS43072.1	ENSP00000328998	TRAK1_HUMAN	.	UPI0000139F52	.	.	.	.	12/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCCAGAAA	.	4	ESCA
BSN	0	.	GRCh37	3	49700504	49700504	+	Missense_Mutation	SNP	G	G	A	rs147167809	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10913G>A	p.Arg3638His	p.R3638H	ENST00000296452	7/12	35	18	17	40	40	0	BSN,missense_variant,p.Arg3638His,ENST00000296452,;	A	ENSG00000164061	ENST00000296452	Transcript	missense_variant	11027	10913	3638	R/H	cGc/cAc	rs147167809	.	.	1	BSN	HGNC	1117	protein_coding	YES	CCDS2800.1	ENSP00000296452	BSN_HUMAN	.	UPI000013E33C	.	.	unknown(0)	7/12	.	hmmpanther:PTHR14113:SF1,hmmpanther:PTHR14113	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCGCCATG	byFrequency|byCluster	5	ESCA
SPATA18	0	.	GRCh37	4	52926601	52926601	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.104A>G	p.Gln35Arg	p.Q35R	ENST00000295213	2/13	73	32	41	128	128	0	SPATA18,missense_variant,p.Gln35Arg,ENST00000295213,;SPATA18,missense_variant,p.Gln35Arg,ENST00000419395,;SPATA18,intron_variant,,ENST00000514670,;SPATA18,intron_variant,,ENST00000506829,;SPATA18,missense_variant,p.Gln35Arg,ENST00000505038,;SPATA18,missense_variant,p.Gln35Arg,ENST00000505320,;SPATA18,non_coding_transcript_exon_variant,,ENST00000511028,;SPATA18,intron_variant,,ENST00000503055,;SPATA18,intron_variant,,ENST00000508915,;	G	ENSG00000163071	ENST00000295213	Transcript	missense_variant	478	104	35	Q/R	cAa/cGa	.	.	.	1	SPATA18	HGNC	29579	protein_coding	YES	CCDS3489.1	ENSP00000295213	MIEAP_HUMAN	.	UPI000006FB0D	.	deleterious(0)	possibly_damaging(0.888)	2/13	.	hmmpanther:PTHR21771:SF0,hmmpanther:PTHR21771	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATCAAAATC	.	5	ESCA
MYL5	0	.	GRCh37	4	667962	667962	+	5'Flank	SNP	G	G	T	rs763951083	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000400159	.	73	26	47	103	103	0	MYL5,5_prime_UTR_variant,,ENST00000506838,;MYL5,intron_variant,,ENST00000505477,;ATP5I,intron_variant,,ENST00000304312,;PDE6B,downstream_gene_variant,,ENST00000429163,;MYL5,upstream_gene_variant,,ENST00000507804,;PDE6B,downstream_gene_variant,,ENST00000255622,;PDE6B,downstream_gene_variant,,ENST00000471824,;MYL5,upstream_gene_variant,,ENST00000511290,;PDE6B,downstream_gene_variant,,ENST00000461490,;PDE6B,downstream_gene_variant,,ENST00000496514,;MYL5,upstream_gene_variant,,ENST00000400159,;ATP5I,intron_variant,,ENST00000505852,;ATP5I,upstream_gene_variant,,ENST00000506525,;MYL5,upstream_gene_variant,,ENST00000502720,;ATP5I,upstream_gene_variant,,ENST00000515116,;MYL5,upstream_gene_variant,,ENST00000513662,;ATP5I,upstream_gene_variant,,ENST00000515202,;MYL5,upstream_gene_variant,,ENST00000503300,;	T	ENSG00000215375	ENST00000400159	Transcript	upstream_gene_variant	.	.	.	.	.	rs763951083	.	3749	1	MYL5	HGNC	7586	protein_coding	YES	CCDS43197.1	ENSP00000383023	MYL5_HUMAN	.	UPI000012F210	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGGCCCAG	byFrequency	5	ESCA
SDHA	0	.	GRCh37	5	233760	233760	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1064G>A	p.Arg355Lys	p.R355K	ENST00000264932	8/15	265	107	157	143	143	0	SDHA,missense_variant,p.Arg355Lys,ENST00000264932,;SDHA,missense_variant,p.Arg355Lys,ENST00000504309,;SDHA,missense_variant,p.Arg307Lys,ENST00000510361,;SDHA,upstream_gene_variant,,ENST00000515815,;SDHA,downstream_gene_variant,,ENST00000514233,;SDHA,splice_region_variant,,ENST00000514027,;SDHA,splice_region_variant,,ENST00000504824,;SDHA,splice_region_variant,,ENST00000505555,;SDHA,non_coding_transcript_exon_variant,,ENST00000512962,;SDHA,non_coding_transcript_exon_variant,,ENST00000515752,;SDHA,upstream_gene_variant,,ENST00000511810,;SDHA,downstream_gene_variant,,ENST00000509420,;	A	ENSG00000073578	ENST00000264932	Transcript	missense_variant	1179	1064	355	R/K	aGa/aAa	.	.	.	1	SDHA	HGNC	10680	protein_coding	YES	CCDS3853.1	ENSP00000264932	DHSA_HUMAN	Q0QF12_HUMAN,B3KT34_HUMAN	UPI0000000C2C	.	deleterious_low_confidence(0)	probably_damaging(1)	8/15	.	hmmpanther:PTHR11632,hmmpanther:PTHR11632:SF37,Gene3D:3.90.700.10,TIGRFAM_domain:TIGR01816,Pfam_domain:PF00890,TIGRFAM_domain:TIGR01812,Superfamily_domains:SSF56425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGGTGCG	.	5	ESCA
CDH10	0	.	GRCh37	5	24509822	24509822	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109T>C	p.Ile370Thr	p.I370T	ENST00000264463	7/12	134	108	25	86	86	0	CDH10,missense_variant,p.Ile370Thr,ENST00000264463,;CDH10,missense_variant,p.Ile370Thr,ENST00000510477,;	G	ENSG00000040731	ENST00000264463	Transcript	missense_variant	1617	1109	370	I/T	aTa/aCa	.	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	tolerated(1)	benign(0.001)	7/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTATGGTA	.	5	ESCA
BRIX1	0	.	GRCh37	5	34918517	34918517	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.208A>T	p.Ile70Leu	p.I70L	ENST00000336767	2/10	277	95	181	148	148	0	BRIX1,missense_variant,p.Ile70Leu,ENST00000336767,;RAD1,intron_variant,,ENST00000341754,;RAD1,upstream_gene_variant,,ENST00000382038,;BRIX1,intron_variant,,ENST00000506023,;BRIX1,non_coding_transcript_exon_variant,,ENST00000510834,;BRIX1,non_coding_transcript_exon_variant,,ENST00000515798,;BRIX1,non_coding_transcript_exon_variant,,ENST00000510960,;RAD1,upstream_gene_variant,,ENST00000511456,;RAD1,upstream_gene_variant,,ENST00000506311,;RAD1,upstream_gene_variant,,ENST00000325577,;RAD1,upstream_gene_variant,,ENST00000512192,;RAD1,upstream_gene_variant,,ENST00000513914,;	T	ENSG00000113460	ENST00000336767	Transcript	missense_variant	571	208	70	I/L	Ata/Tta	.	.	.	1	BRIX1	HGNC	24170	protein_coding	YES	CCDS34143.1	ENSP00000338862	BRX1_HUMAN	Q9NUW4_HUMAN	UPI000007186B	.	deleterious(0.03)	possibly_damaging(0.612)	2/10	.	PROSITE_profiles:PS50833,hmmpanther:PTHR13634,Pfam_domain:PF04427,SMART_domains:SM00879,Superfamily_domains:SSF52954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGAATAAAT	.	5	ESCA
HIVEP1	0	.	GRCh37	6	12164527	12164527	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7990C>T	p.%3D	p.L2664L	ENST00000379388	9/9	26	18	7	29	29	0	HIVEP1,synonymous_variant,p.%3D,ENST00000541134,;HIVEP1,synonymous_variant,p.%3D,ENST00000379388,;HIVEP1,downstream_gene_variant,,ENST00000442081,;HIVEP1,3_prime_UTR_variant,,ENST00000399469,;	T	ENSG00000095951	ENST00000379388	Transcript	synonymous_variant	8322	7990	2664	L	Ctg/Ttg	COSM3620057	.	.	1	HIVEP1	HGNC	4920	protein_coding	YES	CCDS43426.1	ENSP00000368698	ZEP1_HUMAN	C9JZF8_HUMAN,C9JAW2_HUMAN,C9J2N3_HUMAN	UPI000020D52B	.	.	.	9/9	.	hmmpanther:PTHR23233:SF48,hmmpanther:PTHR23233	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTCTGCTG	.	5	ESCA
PRL	0	.	GRCh37	6	22287656	22287656	+	Missense_Mutation	SNP	C	C	T	rs779422396	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659G>A	p.Arg220Gln	p.R220Q	ENST00000306482	5/5	46	29	17	69	69	0	PRL,missense_variant,p.Arg220Gln,ENST00000306482,;RP3-404K8.2,intron_variant,,ENST00000561912,;	T	ENSG00000172179	ENST00000306482	Transcript	missense_variant	1178	659	220	R/Q	cGa/cAa	rs779422396,COSM3784475	.	.	-1	PRL	HGNC	9445	protein_coding	YES	CCDS4548.1	ENSP00000302150	PRL_HUMAN	Q5THQ0_HUMAN,Q5I0G2_HUMAN	UPI0000001C13	.	tolerated(0.16)	possibly_damaging(0.523)	5/5	.	hmmpanther:PTHR11417:SF5,hmmpanther:PTHR11417,Pfam_domain:PF00103,Gene3D:1.20.1250.10,Superfamily_domains:SSF47266,Prints_domain:PR00836	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTCGGCAC	byFrequency	5	ESCA
HIST1H3G	0	.	GRCh37	6	26271357	26271357	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256C>T	p.Gln86Ter	p.Q86*	ENST00000305910	1/1	124	74	50	106	106	0	HIST1H3G,stop_gained,p.Gln86Ter,ENST00000305910,;HIST1H2BI,upstream_gene_variant,,ENST00000377733,;HIST1H2APS4,downstream_gene_variant,,ENST00000362070,;	A	ENSG00000256018	ENST00000305910	Transcript	stop_gained	256	256	86	Q/*	Cag/Tag	.	.	.	-1	HIST1H3G	HGNC	4772	protein_coding	YES	CCDS4602.1	ENSP00000439660	H31_HUMAN	.	UPI00000003C7	.	.	.	1/1	.	hmmpanther:PTHR11426,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCTGAAAGC	.	5	ESCA
STK38	0	.	GRCh37	6	36462204	36462204	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1357G>C	.	.	ENST00000229812	14/14	132	82	50	103	103	0	STK38,3_prime_UTR_variant,,ENST00000229812,;KCTD20,downstream_gene_variant,,ENST00000449081,;KCTD20,downstream_gene_variant,,ENST00000373731,;	G	ENSG00000112079	ENST00000229812	Transcript	3_prime_UTR_variant	3041	.	.	.	.	.	.	.	-1	STK38	HGNC	17847	protein_coding	YES	CCDS4822.1	ENSP00000229812	STK38_HUMAN	.	UPI0000047AC1	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTATCAAAAC	.	5	ESCA
IRF4	0	.	GRCh37	6	407912	407912	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*314G>A	.	.	ENST00000380956	9/9	16	10	6	23	23	0	IRF4,3_prime_UTR_variant,,ENST00000380956,;IRF4,downstream_gene_variant,,ENST00000493114,;	A	ENSG00000137265	ENST00000380956	Transcript	3_prime_UTR_variant	1796	.	.	.	.	.	.	.	1	IRF4	HGNC	6119	protein_coding	YES	CCDS4469.1	ENSP00000370343	IRF4_HUMAN	.	UPI000012D88B	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGTTGAGGAG	.	2	ESCA
MYO6	0	.	GRCh37	6	76591508	76591508	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2389C>G	p.Gln797Glu	p.Q797E	ENST00000369977	23/35	74	41	32	111	111	0	MYO6,missense_variant,p.Gln797Glu,ENST00000369985,;MYO6,missense_variant,p.Gln797Glu,ENST00000369977,;MYO6,missense_variant,p.Gln797Glu,ENST00000369981,;MYO6,missense_variant,p.Gln797Glu,ENST00000369975,;MYO6,non_coding_transcript_exon_variant,,ENST00000462633,;	G	ENSG00000196586	ENST00000369977	Transcript	missense_variant	2528	2389	797	Q/E	Cag/Gag	COSM1634935,COSM3703061	.	.	1	MYO6	HGNC	7605	protein_coding	YES	CCDS34487.1	ENSP00000358994	MYO6_HUMAN	Q14784_HUMAN	UPI00000727CF	.	deleterious(0.02)	unknown(0)	23/35	.	Superfamily_domains:SSF52540,hmmpanther:PTHR13140:SF346,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTCAGTGG	.	5	ESCA
KIAA1009	0	.	GRCh37	6	84872950	84872950	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2425A>C	p.Lys809Gln	p.K809Q	ENST00000403245	19/27	88	80	8	118	118	0	KIAA1009,missense_variant,p.Lys809Gln,ENST00000403245,;KIAA1009,missense_variant,p.Lys733Gln,ENST00000257766,;KIAA1009,non_coding_transcript_exon_variant,,ENST00000461137,;	G	ENSG00000135315	ENST00000403245	Transcript	missense_variant	2540	2425	809	K/Q	Aaa/Caa	.	.	.	-1	KIAA1009	HGNC	21107	protein_coding	YES	CCDS34494.2	ENSP00000385215	CE162_HUMAN	B3KN48_HUMAN	UPI0001533DAA	.	deleterious(0)	probably_damaging(0.999)	19/27	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTTTCAGTC	.	4	ESCA
PLXNA4	0	.	GRCh37	7	131908323	131908323	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2060C>T	p.Thr687Ile	p.T687I	ENST00000359827	9/32	84	47	37	84	84	0	PLXNA4,missense_variant,p.Thr687Ile,ENST00000321063,;PLXNA4,missense_variant,p.Thr687Ile,ENST00000359827,;	A	ENSG00000221866	ENST00000359827	Transcript	missense_variant	3023	2060	687	T/I	aCc/aTc	.	.	.	-1	PLXNA4	HGNC	9102	protein_coding	YES	CCDS43646.1	ENSP00000352882	PLXA4_HUMAN	.	UPI000004E55B	.	deleterious(0.01)	benign(0.381)	9/32	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,Pfam_domain:PF01437,SMART_domains:SM00423	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGGTCTTG	.	5	ESCA
TBXAS1	0	.	GRCh37	7	139653225	139653225	+	Missense_Mutation	SNP	C	C	T	rs775968061	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650C>T	p.Ala217Val	p.A217V	ENST00000416849	7/14	49	46	3	60	60	0	TBXAS1,missense_variant,p.Ala171Val,ENST00000436047,;TBXAS1,missense_variant,p.Ala171Val,ENST00000414508,;TBXAS1,missense_variant,p.Ala170Val,ENST00000411653,;TBXAS1,missense_variant,p.Ala216Val,ENST00000458722,;TBXAS1,missense_variant,p.Ala103Val,ENST00000425687,;TBXAS1,missense_variant,p.Ala170Val,ENST00000448866,;TBXAS1,missense_variant,p.Ala171Val,ENST00000263552,;TBXAS1,missense_variant,p.Ala170Val,ENST00000336425,;TBXAS1,missense_variant,p.Ala217Val,ENST00000416849,;TBXAS1,non_coding_transcript_exon_variant,,ENST00000462275,;TBXAS1,3_prime_UTR_variant,,ENST00000422328,;TBXAS1,non_coding_transcript_exon_variant,,ENST00000476637,;TBXAS1,upstream_gene_variant,,ENST00000494876,;TBXAS1,upstream_gene_variant,,ENST00000469630,;	T	ENSG00000059377	ENST00000416849	Transcript	missense_variant	885	650	217	A/V	gCg/gTg	rs775968061	.	.	1	TBXAS1	HGNC	11609	protein_coding	YES	CCDS55174.1	ENSP00000389414	.	F8WD37_HUMAN,E7EP08_HUMAN,C9JS68_HUMAN,C9J8N6_HUMAN	UPI0001AE7134	.	deleterious(0.01)	possibly_damaging(0.609)	7/14	.	Superfamily_domains:SSF48264,Pfam_domain:PF00067,Gene3D:1.10.630.10,hmmpanther:PTHR24301:SF2,hmmpanther:PTHR24301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTATGCGGAAT	byFrequency	2	ESCA
MGAM	0	.	GRCh37	7	141708393	141708393	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.215C>T	p.Thr72Ile	p.T72I	ENST00000549489	3/48	147	91	56	124	124	0	MGAM,missense_variant,p.Thr72Ile,ENST00000465654,;MGAM,missense_variant,p.Thr72Ile,ENST00000475668,;MGAM,missense_variant,p.Thr72Ile,ENST00000549489,;MGAM,missense_variant,p.Thr72Ile,ENST00000497673,;	T	ENSG00000257335	ENST00000549489	Transcript	missense_variant	310	215	72	T/I	aCa/aTa	.	.	.	1	MGAM	HGNC	7043	protein_coding	YES	CCDS47727.1	ENSP00000447378	MGA_HUMAN	Q8TE25_HUMAN,E9PEQ5_HUMAN,E7EW87_HUMAN	UPI000183CB7B	.	tolerated(0.4)	benign(0.004)	3/48	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22762:SF63,hmmpanther:PTHR22762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGACAACGG	.	5	ESCA
TRBV7-3	0	.	GRCh37	7	142247228	142247228	+	Silent	SNP	G	G	A	rs748818661	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228C>T	p.%3D	p.D76D	ENST00000390361	2/2	69	41	27	52	51	1	TRBV7-3,synonymous_variant,p.%3D,ENST00000390361,;TRBV5-3,upstream_gene_variant,,ENST00000390362,;TRBV6-4,downstream_gene_variant,,ENST00000390360,;TRBV8-2,upstream_gene_variant,,ENST00000475637,;	A	ENSG00000211714	ENST00000390361	Transcript	synonymous_variant	278	228	76	D	gaC/gaT	rs748818661	.	.	-1	TRBV7-3	HGNC	12237	TR_V_gene	YES	.	ENSP00000374884	.	.	UPI0001AE7167	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23268:SF20,hmmpanther:PTHR23268,Gene3D:2.60.40.10,Pfam_domain:PF07686,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	CCTGAGTCATC	byFrequency	3	ESCA
MEOX2	0	.	GRCh37	7	15651473	15651473	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*539C>T	.	.	ENST00000262041	3/3	23	17	6	15	15	0	MEOX2,3_prime_UTR_variant,,ENST00000262041,;	A	ENSG00000106511	ENST00000262041	Transcript	3_prime_UTR_variant	1864	.	.	.	.	.	.	.	-1	MEOX2	HGNC	7014	protein_coding	YES	CCDS34605.1	ENSP00000262041	MEOX2_HUMAN	Q6FHY5_HUMAN,A4D127_HUMAN	UPI000013D247	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACAGAGTTA	.	5	ESCA
TWISTNB	0	.	GRCh37	7	19748587	19748587	+	Missense_Mutation	SNP	G	G	C	rs146649877	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53C>G	p.Ser18Cys	p.S18C	ENST00000222567	1/4	36	23	12	35	35	0	TWISTNB,missense_variant,p.Ser18Cys,ENST00000222567,;MIR3146,upstream_gene_variant,,ENST00000580367,;	C	ENSG00000105849	ENST00000222567	Transcript	missense_variant	124	53	18	S/C	tCt/tGt	rs146649877	.	.	-1	TWISTNB	HGNC	18027	protein_coding	YES	CCDS34606.1	ENSP00000222567	RPA43_HUMAN	.	UPI000006CEF4	.	deleterious(0.01)	benign(0.258)	1/4	.	.	A:0.0014	A:0	A:0	.	A:0.006	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGAGACCCA	byFrequency|byCluster|by1000G	5	ESCA
CCDC146	0	.	GRCh37	7	76908384	76908384	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1660G>C	p.Glu554Gln	p.E554Q	ENST00000285871	13/19	117	68	49	139	139	0	CCDC146,missense_variant,p.Glu554Gln,ENST00000285871,;CCDC146,missense_variant,p.Glu268Gln,ENST00000431197,;CCDC146,non_coding_transcript_exon_variant,,ENST00000415740,;CCDC146,upstream_gene_variant,,ENST00000464021,;CCDC146,upstream_gene_variant,,ENST00000461259,;CCDC146,upstream_gene_variant,,ENST00000474733,;	C	ENSG00000135205	ENST00000285871	Transcript	missense_variant	1787	1660	554	E/Q	Gaa/Caa	.	.	.	1	CCDC146	HGNC	29296	protein_coding	YES	CCDS34671.1	ENSP00000285871	CC146_HUMAN	Q7Z4Q3_HUMAN	UPI000020F44F	.	deleterious(0.03)	probably_damaging(0.925)	13/19	.	hmmpanther:PTHR32083:SF23,hmmpanther:PTHR32083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTGAAATT	.	5	ESCA
DMTN	0	.	GRCh37	8	21925182	21925182	+	Missense_Mutation	SNP	C	C	T	rs781626631	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.238C>T	p.Arg80Cys	p.R80C	ENST00000523266	4/16	14	4	10	43	43	0	DMTN,missense_variant,p.Arg80Cys,ENST00000265800,;DMTN,missense_variant,p.Arg80Cys,ENST00000381470,;DMTN,missense_variant,p.Arg80Cys,ENST00000517804,;DMTN,missense_variant,p.Arg55Cys,ENST00000517600,;DMTN,missense_variant,p.Arg80Cys,ENST00000415253,;DMTN,missense_variant,p.Arg80Cys,ENST00000432128,;DMTN,missense_variant,p.Arg80Cys,ENST00000519907,;DMTN,missense_variant,p.Arg55Cys,ENST00000520174,;DMTN,missense_variant,p.Arg55Cys,ENST00000522148,;DMTN,missense_variant,p.Arg55Cys,ENST00000443491,;DMTN,missense_variant,p.Arg80Cys,ENST00000519850,;DMTN,missense_variant,p.Arg55Cys,ENST00000523300,;DMTN,missense_variant,p.Arg55Cys,ENST00000523623,;DMTN,missense_variant,p.Arg55Cys,ENST00000523782,;DMTN,missense_variant,p.Arg80Cys,ENST00000523266,;DMTN,missense_variant,p.Arg80Cys,ENST00000358242,;DMTN,missense_variant,p.Arg80Cys,ENST00000517418,;DMTN,missense_variant,p.Arg80Cys,ENST00000517305,;DMTN,non_coding_transcript_exon_variant,,ENST00000519333,;DMTN,non_coding_transcript_exon_variant,,ENST00000520856,;DMTN,non_coding_transcript_exon_variant,,ENST00000518816,;DMTN,downstream_gene_variant,,ENST00000522340,;DMTN,downstream_gene_variant,,ENST00000519959,;	T	ENSG00000158856	ENST00000523266	Transcript	missense_variant	700	238	80	R/C	Cgc/Tgc	rs781626631	.	.	1	DMTN	HGNC	3382	protein_coding	YES	CCDS6020.1	ENSP00000427866	DEMA_HUMAN	E5RJ61_HUMAN	UPI0000129189	.	deleterious(0.01)	possibly_damaging(0.88)	4/16	.	hmmpanther:PTHR24213	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCCTCGCAGC	byFrequency	3	ESCA
CDCA2	0	.	GRCh37	8	25340994	25340994	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1112A>G	p.Lys371Arg	p.K371R	ENST00000330560	9/15	100	35	64	160	160	0	CDCA2,missense_variant,p.Lys356Arg,ENST00000380665,;CDCA2,missense_variant,p.Lys371Arg,ENST00000330560,;CDCA2,non_coding_transcript_exon_variant,,ENST00000523454,;CDCA2,non_coding_transcript_exon_variant,,ENST00000521098,;	G	ENSG00000184661	ENST00000330560	Transcript	missense_variant	1589	1112	371	K/R	aAa/aGa	.	.	.	1	CDCA2	HGNC	14623	protein_coding	YES	CCDS6049.1	ENSP00000328228	CDCA2_HUMAN	.	UPI000013DF9A	.	tolerated(0.36)	benign(0.002)	9/15	.	hmmpanther:PTHR21603:SF2,hmmpanther:PTHR21603,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAAAGAAG	.	5	ESCA
PPP2R2A	0	.	GRCh37	8	26228342	26228343	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*420dupT	.	.	ENST00000315985	10/10	59	46	13	70	70	0	PPP2R2A,3_prime_UTR_variant,,ENST00000380737,;PPP2R2A,3_prime_UTR_variant,,ENST00000315985,;PPP2R2A,downstream_gene_variant,,ENST00000524169,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000517754,;PPP2R2A,downstream_gene_variant,,ENST00000518215,;PPP2R2A,downstream_gene_variant,,ENST00000518208,;PPP2R2A,downstream_gene_variant,,ENST00000518890,;	T	ENSG00000221914	ENST00000315985	Transcript	3_prime_UTR_variant	1818-1819	.	.	.	.	.	.	.	1	PPP2R2A	HGNC	9304	protein_coding	YES	CCDS55213.1	ENSP00000325074	2ABA_HUMAN	E5RFR9_HUMAN	UPI0000E219EC	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCCCCCTTTTT	.	2	ESCA
KIF13B	0	.	GRCh37	8	28980128	28980128	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3515T>C	p.Val1172Ala	p.V1172A	ENST00000524189	29/40	44	17	27	74	73	0	KIF13B,missense_variant,p.Val1172Ala,ENST00000524189,;CTD-2647L4.1,intron_variant,,ENST00000523661,;	G	ENSG00000197892	ENST00000524189	Transcript	missense_variant	3554	3515	1172	V/A	gTt/gCt	.	.	.	-1	KIF13B	HGNC	14405	protein_coding	YES	CCDS55217.1	ENSP00000427900	KI13B_HUMAN	.	UPI000035B257	.	deleterious(0.01)	possibly_damaging(0.54)	29/40	.	hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATAACAGGA	.	5	ESCA
C8orf4	0	.	GRCh37	8	40011816	40011816	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*444G>C	.	.	ENST00000315792	1/1	37	14	23	66	66	0	C8orf4,3_prime_UTR_variant,,ENST00000315792,;	C	ENSG00000176907	ENST00000315792	Transcript	3_prime_UTR_variant	828	.	.	.	.	.	.	.	1	C8orf4	HGNC	1357	protein_coding	YES	CCDS6115.1	ENSP00000319914	CH004_HUMAN	.	UPI000013FBD4	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGAGAGGGAGG	.	4	ESCA
OR13C3	0	.	GRCh37	9	107298339	107298339	+	Silent	SNP	G	G	C	rs535495429	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756C>G	p.%3D	p.L252L	ENST00000374781	1/1	77	52	24	60	60	0	OR13C3,synonymous_variant,p.%3D,ENST00000374781,;	C	ENSG00000204246	ENST00000374781	Transcript	synonymous_variant	799	756	252	L	ctC/ctG	rs535495429	.	.	-1	OR13C3	HGNC	14704	protein_coding	YES	CCDS35089.1	ENSP00000363913	O13C3_HUMAN	.	UPI000015F232	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF34,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTAGAGGAT	by1000G	5	ESCA
ZNF618	0	.	GRCh37	9	116811401	116811401	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1540G>A	p.Val514Met	p.V514M	ENST00000288466	14/14	25	16	9	19	19	0	ZNF618,missense_variant,p.Val514Met,ENST00000288466,;ZNF618,missense_variant,p.Val607Met,ENST00000374126,;ZNF618,non_coding_transcript_exon_variant,,ENST00000470105,;	A	ENSG00000157657	ENST00000288466	Transcript	missense_variant	1639	1540	514	V/M	Gtg/Atg	.	.	.	1	ZNF618	HGNC	29416	protein_coding	YES	CCDS48008.1	ENSP00000288466	ZN618_HUMAN	.	UPI0000D4BD81	.	deleterious(0.02)	probably_damaging(1)	14/14	.	hmmpanther:PTHR24383:SF12,hmmpanther:PTHR24383,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.F606F|c.1818C>T|3,CODON|p.F513F|c.1539C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTCGTGATG	.	5	ESCA
NUP188	0	.	GRCh37	9	131768007	131768007	+	Silent	SNP	C	C	T	rs755350781	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4821C>T	p.%3D	p.F1607F	ENST00000372577	41/44	83	46	36	104	104	0	NUP188,synonymous_variant,p.%3D,ENST00000372577,;SH3GLB2,downstream_gene_variant,,ENST00000372554,;SH3GLB2,downstream_gene_variant,,ENST00000372564,;SH3GLB2,downstream_gene_variant,,ENST00000416629,;SH3GLB2,downstream_gene_variant,,ENST00000417224,;SH3GLB2,downstream_gene_variant,,ENST00000372559,;RP11-167N5.5,upstream_gene_variant,,ENST00000594418,;SH3GLB2,downstream_gene_variant,,ENST00000461811,;SH3GLB2,downstream_gene_variant,,ENST00000455407,;SH3GLB2,downstream_gene_variant,,ENST00000479237,;NUP188,downstream_gene_variant,,ENST00000487952,;NUP188,downstream_gene_variant,,ENST00000477069,;SH3GLB2,downstream_gene_variant,,ENST00000483980,;	T	ENSG00000095319	ENST00000372577	Transcript	synonymous_variant	4842	4821	1607	F	ttC/ttT	rs755350781,COSM455443	.	.	1	NUP188	HGNC	17859	protein_coding	YES	CCDS35156.1	ENSP00000361658	NU188_HUMAN	.	UPI000041A60F	.	.	.	41/44	.	hmmpanther:PTHR31431,hmmpanther:PTHR31431:SF1	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCGGGAC	byFrequency	5	ESCA
GLDC	0	.	GRCh37	9	6532760	6532760	+	3'UTR	SNP	C	C	T	rs111326356	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*257G>A	.	.	ENST00000321612	25/25	46	14	32	80	80	0	GLDC,3_prime_UTR_variant,,ENST00000321612,;GLDC,downstream_gene_variant,,ENST00000477960,;	T	ENSG00000178445	ENST00000321612	Transcript	3_prime_UTR_variant	3471	.	.	.	.	rs111326356	.	.	-1	GLDC	HGNC	4313	protein_coding	YES	CCDS34987.1	ENSP00000370737	GCSP_HUMAN	.	UPI0000684276	.	.	.	25/25	.	.	T:0.0108	T:0.0371	T:0.0043	.	T:0	T:0.002	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTACGCAAA	byFrequency|byCluster|by1000G	5	ESCA
SECISBP2	0	.	GRCh37	9	91940893	91940893	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514A>G	p.Ile172Val	p.I172V	ENST00000375807	4/17	56	20	35	91	91	0	SECISBP2,missense_variant,p.Ile7Val,ENST00000425851,;SECISBP2,missense_variant,p.Ile104Val,ENST00000534113,;SECISBP2,missense_variant,p.Ile172Val,ENST00000375807,;SECISBP2,missense_variant,p.Ile99Val,ENST00000339901,;SECISBP2,non_coding_transcript_exon_variant,,ENST00000470305,;	G	ENSG00000187742	ENST00000375807	Transcript	missense_variant	585	514	172	I/V	Ata/Gta	.	.	.	1	SECISBP2	HGNC	30972	protein_coding	YES	CCDS6683.1	ENSP00000364965	SEBP2_HUMAN	Q9H948_HUMAN,Q7L1Z0_HUMAN,Q6AW84_HUMAN,F8W892_HUMAN	UPI00001AEA0A	.	tolerated(0.73)	benign(0.103)	4/17	.	hmmpanther:PTHR13284:SF9,hmmpanther:PTHR13284	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGATAAAA	.	5	ESCA
SRPK3	0	.	GRCh37	X	153047664	153047664	+	Splice_Site	SNP	G	G	A	rs782665626	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.475+1G>A	.	p.X159_splice	ENST00000370101	.	48	44	4	50	50	0	SRPK3,splice_donor_variant,,ENST00000370108,;SRPK3,splice_donor_variant,,ENST00000370100,;SRPK3,splice_donor_variant,,ENST00000430541,;SRPK3,splice_donor_variant,,ENST00000489426,;SRPK3,splice_donor_variant,,ENST00000393786,;SRPK3,splice_donor_variant,,ENST00000370104,;SRPK3,splice_donor_variant,,ENST00000370101,;IDH3G,downstream_gene_variant,,ENST00000454076,;PLXNB3,downstream_gene_variant,,ENST00000538966,;IDH3G,downstream_gene_variant,,ENST00000444450,;PLXNB3,downstream_gene_variant,,ENST00000448847,;IDH3G,downstream_gene_variant,,ENST00000427365,;IDH3G,downstream_gene_variant,,ENST00000370093,;SRPK3,upstream_gene_variant,,ENST00000458681,;PLXNB3,downstream_gene_variant,,ENST00000538776,;IDH3G,downstream_gene_variant,,ENST00000217901,;IDH3G,downstream_gene_variant,,ENST00000370092,;PLXNB3,downstream_gene_variant,,ENST00000361971,;IDH3G,downstream_gene_variant,,ENST00000444338,;PLXNB3,downstream_gene_variant,,ENST00000472415,;IDH3G,downstream_gene_variant,,ENST00000497043,;PLXNB3,downstream_gene_variant,,ENST00000485980,;PLXNB3,downstream_gene_variant,,ENST00000469190,;	A	ENSG00000184343	ENST00000370101	Transcript	splice_donor_variant	.	.	.	.	.	rs782665626	.	.	1	SRPK3	HGNC	11402	protein_coding	YES	CCDS35441.1	ENSP00000359119	SRPK3_HUMAN	.	UPI000050571A	.	.	.	.	5/14	.	A:0.0003	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTCCGTATCC	byCluster|by1000G	2	ESCA
TAB3	0	.	GRCh37	X	30848555	30848555	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*989A>G	.	.	ENST00000378933	8/8	51	18	32	70	70	0	TAB3,3_prime_UTR_variant,,ENST00000378930,;TAB3,3_prime_UTR_variant,,ENST00000288422,;TAB3,3_prime_UTR_variant,,ENST00000378932,;TAB3,3_prime_UTR_variant,,ENST00000378933,;TAB3-AS1,upstream_gene_variant,,ENST00000428263,;TAB3,downstream_gene_variant,,ENST00000467136,;	C	ENSG00000157625	ENST00000378933	Transcript	3_prime_UTR_variant	3306	.	.	.	.	.	.	.	-1	TAB3	HGNC	30681	protein_coding	YES	CCDS14226.1	ENSP00000368215	TAB3_HUMAN	.	UPI000013DF10	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTATCACAA	.	5	ESCA
PCDH11X	0	.	GRCh37	X	91518126	91518126	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HW-01A-22D-A351-09	TCGA-LN-A7HW-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3128G>A	p.Gly1043Glu	p.G1043E	ENST00000373094	4/7	120	32	88	128	128	0	PCDH11X,missense_variant,p.Gly1043Glu,ENST00000406881,;PCDH11X,missense_variant,p.Gly1043Glu,ENST00000373094,;PCDH11X,missense_variant,p.Gly1043Glu,ENST00000504220,;PCDH11X,intron_variant,,ENST00000373097,;PCDH11X,intron_variant,,ENST00000373088,;PCDH11X,intron_variant,,ENST00000361655,;PCDH11X,intron_variant,,ENST00000298274,;	A	ENSG00000102290	ENST00000373094	Transcript	missense_variant	3973	3128	1043	G/E	gGg/gAg	.	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	tolerated(0.24)	benign(0.011)	4/7	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAGGGAAAG	.	5	ESCA
CNNM2	0	.	GRCh37	10	104835858	104835858	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2249C>G	p.Pro750Arg	p.P750R	ENST00000369878	7/8	55	45	10	122	122	0	CNNM2,missense_variant,p.Pro750Arg,ENST00000369878,;CNNM2,missense_variant,p.Pro728Arg,ENST00000433628,;CNNM2,non_coding_transcript_exon_variant,,ENST00000475511,;	G	ENSG00000148842	ENST00000369878	Transcript	missense_variant	2437	2249	750	P/R	cCt/cGt	.	.	.	1	CNNM2	HGNC	103	protein_coding	YES	CCDS44474.1	ENSP00000358894	CNNM2_HUMAN	.	UPI0000231CA6	.	deleterious(0.01)	possibly_damaging(0.786)	7/8	.	hmmpanther:PTHR12064,hmmpanther:PTHR12064:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCCCTCCTC	.	5	ESCA
CTNNA3	0	.	GRCh37	10	68526045	68526045	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1258G>A	p.Glu420Lys	p.E420K	ENST00000433211	9/18	28	24	4	60	60	0	CTNNA3,missense_variant,p.Glu420Lys,ENST00000433211,;CTNNA3,missense_variant,p.Glu114Lys,ENST00000494580,;CTNNA3,missense_variant,p.Glu420Lys,ENST00000373744,;	T	ENSG00000183230	ENST00000433211	Transcript	missense_variant	1433	1258	420	E/K	Gaa/Aaa	.	.	.	-1	CTNNA3	HGNC	2511	protein_coding	YES	CCDS7269.1	ENSP00000389714	CTNA3_HUMAN	Q5SW23_HUMAN,A6NKP0_HUMAN	UPI000004A0E6	.	deleterious(0.04)	possibly_damaging(0.57)	9/18	.	hmmpanther:PTHR18914:SF21,hmmpanther:PTHR18914,Pfam_domain:PF01044,Gene3D:1.20.120.230,Superfamily_domains:SSF47220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|VARSCANS	GTGTTCATGAA	.	3	ESCA
VPS26A	0	.	GRCh37	10	70893327	70893327	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153+524A>G	.	.	ENST00000373382	.	41	19	22	74	74	0	VPS26A,synonymous_variant,p.%3D,ENST00000546041,;VPS26A,intron_variant,,ENST00000395098,;VPS26A,intron_variant,,ENST00000373382,;VPS26A,intron_variant,,ENST00000541711,;VPS26A,intron_variant,,ENST00000489794,;VPS26A,intron_variant,,ENST00000263559,;VPS26A,intron_variant,,ENST00000467852,;VPS26A,intron_variant,,ENST00000497564,;VPS26A,intron_variant,,ENST00000490696,;VPS26A,intron_variant,,ENST00000489656,;	G	ENSG00000122958	ENST00000373382	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	VPS26A	HGNC	12711	protein_coding	YES	CCDS7286.1	ENSP00000362480	VP26A_HUMAN	G3V1N8_HUMAN	UPI0000138BC6	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTATGCAT	.	5	ESCA
ZMIZ1	0	.	GRCh37	10	81072411	81072411	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3109C>G	p.Leu1037Val	p.L1037V	ENST00000334512	25/25	54	30	24	112	112	0	ZMIZ1,missense_variant,p.Leu1037Val,ENST00000334512,;ZMIZ1,missense_variant,p.Leu103Val,ENST00000446377,;	G	ENSG00000108175	ENST00000334512	Transcript	missense_variant	3681	3109	1037	L/V	Ctc/Gtc	.	.	.	1	ZMIZ1	HGNC	16493	protein_coding	YES	CCDS7357.1	ENSP00000334474	ZMIZ1_HUMAN	A0PJD4_HUMAN	UPI0000161744	.	.	probably_damaging(0.99)	25/25	.	hmmpanther:PTHR10782:SF7,hmmpanther:PTHR10782	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGAACTCACA	.	5	ESCA
SFTPA1	0	.	GRCh37	10	81372184	81372184	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334C>A	p.Pro112Thr	p.P112T	ENST00000419470	4/6	34	26	8	70	70	0	SFTPA1,missense_variant,p.Pro97Thr,ENST00000429958,;SFTPA1,missense_variant,p.Pro97Thr,ENST00000428376,;SFTPA1,missense_variant,p.Pro97Thr,ENST00000372308,;SFTPA1,missense_variant,p.Pro97Thr,ENST00000439264,;SFTPA1,missense_variant,p.Pro112Thr,ENST00000419470,;SFTPA1,missense_variant,p.Pro38Thr,ENST00000372313,;SFTPA1,missense_variant,p.Pro97Thr,ENST00000398636,;SFTPA1,downstream_gene_variant,,ENST00000486922,;	A	ENSG00000122852	ENST00000419470	Transcript	missense_variant	410	334	112	P/T	Cca/Aca	.	.	.	1	SFTPA1	HGNC	10798	protein_coding	YES	CCDS44444.2	ENSP00000397082	SFTA1_HUMAN	B7Z4Y4_HUMAN,J3KPA7_HUMAN,B4DNW5_HUMAN,B4DNR9_HUMAN	UPI00006C104C	.	deleterious(0)	benign(0.36)	4/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24024,hmmpanther:PTHR24024:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCCAGGT	.	4	ESCA
LARP4B	0	.	GRCh37	10	857401	857402	+	3'UTR	INS	-	-	ACT	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1462_*1464dupAGT	.	.	ENST00000316157	17/17	35	19	15	58	58	0	LARP4B,3_prime_UTR_variant,,ENST00000316157,;LARP4B,downstream_gene_variant,,ENST00000440895,;LARP4B,downstream_gene_variant,,ENST00000448368,;LARP4B,downstream_gene_variant,,ENST00000469487,;LARP4B,downstream_gene_variant,,ENST00000608970,;LARP4B,downstream_gene_variant,,ENST00000609318,;	ACT	ENSG00000107929	ENST00000316157	Transcript	3_prime_UTR_variant	3722-3723	.	.	.	.	.	.	.	-1	LARP4B	HGNC	28987	protein_coding	YES	CCDS31131.1	ENSP00000326128	LAR4B_HUMAN	B5MCU2_HUMAN	UPI00001F8C87	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACAAAAACTAC	.	2	ESCA
GRID1	0	.	GRCh37	10	88024517	88024517	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236-58112G>T	.	.	ENST00000327946	.	18	14	4	47	47	0	GRID1,intron_variant,,ENST00000327946,;MIR346,mature_miRNA_variant,,ENST00000362234,;GRID1,intron_variant,,ENST00000464741,;	A	ENSG00000182771	ENST00000327946	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	GRID1	HGNC	4575	protein_coding	YES	CCDS31236.1	ENSP00000330148	GRID1_HUMAN	B7Z7L0_HUMAN	UPI00001D8051	.	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	GCATGCGGGCA	.	3	ESCA
PLCE1	0	.	GRCh37	10	96022423	96022423	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3987C>G	p.%3D	p.L1329L	ENST00000371380	13/32	56	45	11	61	61	0	PLCE1,synonymous_variant,p.%3D,ENST00000371380,;PLCE1,synonymous_variant,p.%3D,ENST00000260766,;PLCE1,synonymous_variant,p.%3D,ENST00000371375,;PLCE1,synonymous_variant,p.%3D,ENST00000371385,;	G	ENSG00000138193	ENST00000371380	Transcript	synonymous_variant	4222	3987	1329	L	ctC/ctG	.	.	.	1	PLCE1	HGNC	17175	protein_coding	YES	CCDS41552.1	ENSP00000360431	PLCE1_HUMAN	B7ZM61_HUMAN	UPI00001F93EE	.	.	.	13/32	.	Superfamily_domains:SSF47473,Pfam_domain:PF09279,Gene3D:1.10.238.10,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCAACGA	.	5	ESCA
KDELC2	0	.	GRCh37	11	108352752	108352752	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.882C>G	p.%3D	p.L294L	ENST00000323468	4/8	29	13	16	65	65	0	KDELC2,synonymous_variant,p.%3D,ENST00000530318,;KDELC2,synonymous_variant,p.%3D,ENST00000323468,;KDELC2,synonymous_variant,p.%3D,ENST00000375648,;KDELC2,synonymous_variant,p.%3D,ENST00000434945,;KDELC2,intron_variant,,ENST00000532730,;KDELC2,downstream_gene_variant,,ENST00000524787,;KDELC2,synonymous_variant,p.%3D,ENST00000530529,;	C	ENSG00000178202	ENST00000323468	Transcript	synonymous_variant	948	882	294	L	ctC/ctG	.	.	.	-1	KDELC2	HGNC	28496	protein_coding	YES	CCDS41711.1	ENSP00000315386	KDEL2_HUMAN	B2R8W4_HUMAN	UPI0000456580	.	.	.	4/8	.	hmmpanther:PTHR12203:SF18,hmmpanther:PTHR12203,Pfam_domain:PF05686,SMART_domains:SM00672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAGAGAGGAG	.	5	ESCA
COPB1	0	.	GRCh37	11	14486508	14486508	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2359G>A	p.Ala787Thr	p.A787T	ENST00000249923	18/22	69	61	8	77	77	0	COPB1,missense_variant,p.Ala787Thr,ENST00000439561,;COPB1,missense_variant,p.Ala787Thr,ENST00000249923,;COPB1,upstream_gene_variant,,ENST00000526527,;COPB1,upstream_gene_variant,,ENST00000525214,;	T	ENSG00000129083	ENST00000249923	Transcript	missense_variant	2660	2359	787	A/T	Gct/Act	.	.	.	-1	COPB1	HGNC	2231	protein_coding	YES	CCDS7815.1	ENSP00000249923	COPB_HUMAN	E9PP63_HUMAN,E9PKQ1_HUMAN	UPI000000103D	.	tolerated(0.15)	probably_damaging(1)	18/22	.	hmmpanther:PTHR10635,Pfam_domain:PF07718,PIRSF_domain:PIRSF005727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTAGCTTTAA	.	3	ESCA
TSG101	0	.	GRCh37	11	18501963	18501964	+	3'UTR	INS	-	-	AT	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128_*129dupAT	.	.	ENST00000251968	10/10	70	58	12	90	90	0	TSG101,3_prime_UTR_variant,,ENST00000251968,;TSG101,3_prime_UTR_variant,,ENST00000357193,;TSG101,intron_variant,,ENST00000536719,;LDHAL6A,downstream_gene_variant,,ENST00000396213,;LDHAL6A,downstream_gene_variant,,ENST00000280706,;TSG101,intron_variant,,ENST00000584526,;TSG101,intron_variant,,ENST00000580814,;TSG101,downstream_gene_variant,,ENST00000543054,;TSG101,downstream_gene_variant,,ENST00000540555,;TSG101,downstream_gene_variant,,ENST00000545247,;	AT	ENSG00000074319	ENST00000251968	Transcript	3_prime_UTR_variant	1718-1719	.	.	.	.	.	.	.	-1	TSG101	HGNC	15971	protein_coding	YES	CCDS7842.1	ENSP00000251968	TS101_HUMAN	L0L6B6_HUMAN,J3QRU6_HUMAN,D3DQY6_HUMAN	UPI000004750C	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGAAAATATA	.	3	ESCA
DCDC1	0	.	GRCh37	11	31112992	31112992	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2185A>G	p.Lys729Glu	p.K729E	ENST00000597505	15/36	28	22	6	78	78	0	DCDC1,missense_variant,p.Lys729Glu,ENST00000597505,;DCDC1,non_coding_transcript_exon_variant,,ENST00000437348,;DCDC1,3_prime_UTR_variant,,ENST00000342355,;	C	ENSG00000170959	ENST00000597505	Transcript	missense_variant	2185	2185	729	K/E	Aag/Gag	.	.	.	-1	DCDC1	HGNC	20625	protein_coding	.	.	ENSP00000472625	.	M0R2J8_HUMAN	UPI0002A47319	.	tolerated(0.83)	benign(0.02)	15/36	.	PROSITE_profiles:PS50231,Superfamily_domains:SSF50370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTTGACTC	.	5	ESCA
DCDC1	0	.	GRCh37	11	31128366	31128366	+	Missense_Mutation	SNP	C	C	A	rs773544052	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1729G>T	p.Val577Phe	p.V577F	ENST00000597505	11/36	72	64	8	142	142	0	DCDC1,missense_variant,p.Val577Phe,ENST00000597505,;DCDC1,non_coding_transcript_exon_variant,,ENST00000437348,;DCDC1,downstream_gene_variant,,ENST00000534722,;DCDC1,3_prime_UTR_variant,,ENST00000342355,;	A	ENSG00000170959	ENST00000597505	Transcript	missense_variant	1729	1729	577	V/F	Gtc/Ttc	rs773544052	.	.	-1	DCDC1	HGNC	20625	protein_coding	.	.	ENSP00000472625	.	M0R2J8_HUMAN	UPI0002A47319	.	tolerated(0.07)	benign(0.028)	11/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGACCCAAA	.	4	ESCA
RAG1	0	.	GRCh37	11	36596307	36596307	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1453C>A	p.His485Asn	p.H485N	ENST00000299440	2/2	27	24	3	35	35	0	RAG1,missense_variant,p.His485Asn,ENST00000299440,;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.His485Asn,ENST00000534663,;	A	ENSG00000166349	ENST00000299440	Transcript	missense_variant	1565	1453	485	H/N	Cac/Aac	.	.	.	1	RAG1	HGNC	9831	protein_coding	YES	CCDS7902.1	ENSP00000299440	RAG1_HUMAN	.	UPI000013E5A0	.	deleterious_low_confidence(0)	possibly_damaging(0.838)	2/2	.	hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGTACCACAAG	.	3	ESCA
OR5M9	0	.	GRCh37	11	56230677	56230677	+	Silent	SNP	C	C	T	rs770156394	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201G>A	p.%3D	p.A67A	ENST00000279791	1/1	32	28	4	38	38	0	OR5M9,synonymous_variant,p.%3D,ENST00000279791,;	T	ENSG00000150269	ENST00000279791	Transcript	synonymous_variant	201	201	67	A	gcG/gcA	rs770156394	.	.	-1	OR5M9	HGNC	15294	protein_coding	YES	CCDS31531.1	ENSP00000279791	OR5M9_HUMAN	.	UPI0000061E81	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF13,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACGTCCGCAAA	.	3	ESCA
SLC22A24	0	.	GRCh37	11	62910850	62910850	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402G>C	p.Glu134Asp	p.E134D	ENST00000417740	1/10	54	46	8	83	83	0	SLC22A24,missense_variant,p.Glu134Asp,ENST00000326192,;SLC22A24,missense_variant,p.Glu134Asp,ENST00000417740,;SLC22A10,intron_variant,,ENST00000525620,;	G	ENSG00000197658	ENST00000417740	Transcript	missense_variant	844	402	134	E/D	gaG/gaC	.	.	.	-1	SLC22A24	HGNC	28542	protein_coding	YES	.	ENSP00000396586	.	C9JC66_HUMAN	UPI00016625C6	.	deleterious(0.03)	possibly_damaging(0.585)	1/10	.	PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF208,Pfam_domain:PF00083,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTATCTCAGT	.	4	ESCA
SMPD1	0	.	GRCh37	11	6413419	6413422	+	Intron	DEL	AAAG	AAAG	-	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	AAAG	AAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1091+37_1091+40delAAAG	.	.	ENST00000342245	.	22	12	10	48	48	0	SMPD1,splice_acceptor_variant,p.Lys365CysfsTer3,ENST00000356761,;SMPD1,frameshift_variant,p.Lys107CysfsTer3,ENST00000526280,;SMPD1,frameshift_variant,p.Lys377CysfsTer3,ENST00000299397,;SMPD1,intron_variant,,ENST00000527275,;SMPD1,intron_variant,,ENST00000342245,;APBB1,downstream_gene_variant,,ENST00000608704,;APBB1,downstream_gene_variant,,ENST00000608394,;APBB1,downstream_gene_variant,,ENST00000530885,;APBB1,downstream_gene_variant,,ENST00000609360,;APBB1,downstream_gene_variant,,ENST00000299402,;APBB1,downstream_gene_variant,,ENST00000389906,;APBB1,downstream_gene_variant,,ENST00000608645,;APBB1,downstream_gene_variant,,ENST00000609331,;APBB1,downstream_gene_variant,,ENST00000311051,;APBB1,downstream_gene_variant,,ENST00000608655,;APBB1,downstream_gene_variant,,ENST00000529519,;SMPD1,downstream_gene_variant,,ENST00000530395,;APBB1,downstream_gene_variant,,ENST00000526240,;SMPD1,downstream_gene_variant,,ENST00000533196,;SMPD1,frameshift_variant,p.Lys377IlefsTer268,ENST00000534405,;SMPD1,intron_variant,,ENST00000533123,;SMPD1,intron_variant,,ENST00000531303,;SMPD1,upstream_gene_variant,,ENST00000532367,;APBB1,downstream_gene_variant,,ENST00000608435,;SMPD1,upstream_gene_variant,,ENST00000531336,;APBB1,downstream_gene_variant,,ENST00000524626,;	-	ENSG00000166311	ENST00000342245	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SMPD1	HGNC	11120	protein_coding	YES	CCDS44531.1	ENSP00000340409	ASM_HUMAN	E9PL59_HUMAN	UPI000013E592	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGGGAAAAGAAAGG	.	3	ESCA
PPP2R5B	0	.	GRCh37	11	64697849	64697849	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778G>A	p.Gly260Arg	p.G260R	ENST00000164133	7/14	19	10	9	52	52	0	PPP2R5B,missense_variant,p.Gly260Arg,ENST00000164133,;PPP2R5B,downstream_gene_variant,,ENST00000532850,;GPHA2,downstream_gene_variant,,ENST00000533257,;PPP2R5B,downstream_gene_variant,,ENST00000526559,;GPHA2,downstream_gene_variant,,ENST00000532246,;GPHA2,downstream_gene_variant,,ENST00000279168,;PPP2R5B,downstream_gene_variant,,ENST00000528530,;	A	ENSG00000068971	ENST00000164133	Transcript	missense_variant	1400	778	260	G/R	Gga/Aga	.	.	.	1	PPP2R5B	HGNC	9310	protein_coding	YES	CCDS8085.1	ENSP00000164133	2A5B_HUMAN	E9PQN5_HUMAN,E9PNY3_HUMAN	UPI000000DAF4	.	deleterious(0)	possibly_damaging(0.716)	7/14	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF028043,Pfam_domain:PF01603,hmmpanther:PTHR10257:SF4,hmmpanther:PTHR10257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTAGGAAGG	.	5	ESCA
BBS1	0	.	GRCh37	11	66288790	66288790	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.773A>C	p.Asp258Ala	p.D258A	ENST00000318312	9/17	54	43	11	100	100	0	BBS1,missense_variant,p.Asp258Ala,ENST00000318312,;CTD-3074O7.11,missense_variant,p.Asp295Ala,ENST00000419755,;BBS1,missense_variant,p.Asp161Ala,ENST00000455748,;BBS1,missense_variant,p.Asp167Ala,ENST00000525809,;BBS1,missense_variant,p.Asp146Ala,ENST00000537537,;ZDHHC24,3_prime_UTR_variant,,ENST00000526986,;BBS1,intron_variant,,ENST00000393994,;BBS1,non_coding_transcript_exon_variant,,ENST00000529766,;BBS1,downstream_gene_variant,,ENST00000529953,;BBS1,3_prime_UTR_variant,,ENST00000533557,;BBS1,3_prime_UTR_variant,,ENST00000526035,;BBS1,3_prime_UTR_variant,,ENST00000524458,;BBS1,3_prime_UTR_variant,,ENST00000532908,;BBS1,3_prime_UTR_variant,,ENST00000533644,;BBS1,3_prime_UTR_variant,,ENST00000526760,;ZDHHC24,3_prime_UTR_variant,,ENST00000534073,;BBS1,non_coding_transcript_exon_variant,,ENST00000529955,;BBS1,non_coding_transcript_exon_variant,,ENST00000533430,;BBS1,upstream_gene_variant,,ENST00000524884,;BBS1,upstream_gene_variant,,ENST00000529895,;BBS1,downstream_gene_variant,,ENST00000524907,;BBS1,downstream_gene_variant,,ENST00000528543,;BBS1,downstream_gene_variant,,ENST00000527251,;BBS1,downstream_gene_variant,,ENST00000532283,;BBS1,upstream_gene_variant,,ENST00000527959,;	C	ENSG00000174483	ENST00000318312	Transcript	missense_variant	824	773	258	D/A	gAt/gCt	.	.	.	1	BBS1	HGNC	966	protein_coding	YES	CCDS8142.1	ENSP00000317469	BBS1_HUMAN	E9PQD9_HUMAN,E9PPR3_HUMAN	UPI0000073430	.	deleterious(0)	benign(0.244)	9/17	.	hmmpanther:PTHR20870:SF0,hmmpanther:PTHR20870,Gene3D:2.130.10.10,Pfam_domain:PF14779,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTGATGTTG	.	5	ESCA
NLRP14	0	.	GRCh37	11	7083694	7083694	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2935G>A	p.Asp979Asn	p.D979N	ENST00000299481	10/12	52	46	6	105	105	0	NLRP14,missense_variant,p.Asp979Asn,ENST00000299481,;	A	ENSG00000158077	ENST00000299481	Transcript	missense_variant	3281	2935	979	D/N	Gat/Aat	.	.	.	1	NLRP14	HGNC	22939	protein_coding	YES	CCDS7776.1	ENSP00000299481	NAL14_HUMAN	.	UPI0000167F6E	.	deleterious(0.01)	benign(0.428)	10/12	.	Superfamily_domains:SSF52047,SMART_domains:SM00368,Gene3D:3.80.10.10,hmmpanther:PTHR24106:SF82,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTGTGATGCT	.	4	ESCA
FAT3	0	.	GRCh37	11	92564908	92564910	+	In_Frame_Del	DEL	ACA	ACA	-	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	ACA	ACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9605_9607delACA	p.Asn3202del	p.N3202del	ENST00000298047	13/27	66	58	8	82	82	0	FAT3,inframe_deletion,p.Asn3202del,ENST00000298047,;FAT3,inframe_deletion,p.Asn3202del,ENST00000409404,;FAT3,inframe_deletion,p.Asn3052del,ENST00000525166,;	-	ENSG00000165323	ENST00000298047	Transcript	inframe_deletion	9619-9621	9602-9604	3201-3202	YN/Y	tACAac/tac	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	.	13/27	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTCGTACAACATC	.	3	ESCA
FUT4	0	.	GRCh37	11	94282611	94282611	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3719A>G	.	.	ENST00000358752	1/1	50	43	7	42	42	0	FUT4,3_prime_UTR_variant,,ENST00000358752,;RP11-867G2.8,intron_variant,,ENST00000536540,;RP11-867G2.8,intron_variant,,ENST00000537874,;PIWIL4,intron_variant,,ENST00000543336,;PIWIL4,intron_variant,,ENST00000446230,;	G	ENSG00000196371	ENST00000358752	Transcript	3_prime_UTR_variant	5595	.	.	.	.	.	.	.	1	FUT4	HGNC	4015	protein_coding	YES	CCDS8301.1	ENSP00000351602	FUT4_HUMAN	.	UPI000002CC7E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGCAAAATG	.	4	ESCA
FAM76B	0	.	GRCh37	11	95502352	95502352	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2373T>A	.	.	ENST00000358780	10/10	74	29	45	68	68	0	FAM76B,3_prime_UTR_variant,,ENST00000358780,;FAM76B,downstream_gene_variant,,ENST00000536839,;FAM76B,3_prime_UTR_variant,,ENST00000398187,;FAM76B,intron_variant,,ENST00000543641,;FAM76B,downstream_gene_variant,,ENST00000545813,;	T	ENSG00000077458	ENST00000358780	Transcript	3_prime_UTR_variant	3706	.	.	.	.	.	.	.	-1	FAM76B	HGNC	28492	protein_coding	YES	CCDS41700.1	ENSP00000351631	FA76B_HUMAN	.	UPI0000D62675	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTAATAGTG	.	5	ESCA
NOC4L	0	.	GRCh37	12	132629489	132629489	+	Nonsense_Mutation	SNP	C	C	T	rs768110580	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.208C>T	p.Gln70Ter	p.Q70*	ENST00000330579	2/15	20	16	4	50	50	0	NOC4L,stop_gained,p.Gln70Ter,ENST00000330579,;NOC4L,5_prime_UTR_variant,,ENST00000541954,;DDX51,upstream_gene_variant,,ENST00000397333,;NOC4L,upstream_gene_variant,,ENST00000535343,;DDX51,upstream_gene_variant,,ENST00000329073,;DDX51,upstream_gene_variant,,ENST00000462829,;DDX51,upstream_gene_variant,,ENST00000541489,;DDX51,upstream_gene_variant,,ENST00000545991,;DDX51,upstream_gene_variant,,ENST00000546058,;	T	ENSG00000184967	ENST00000330579	Transcript	stop_gained	249	208	70	Q/*	Cag/Tag	rs768110580	.	.	1	NOC4L	HGNC	28461	protein_coding	YES	CCDS9277.1	ENSP00000328854	NOC4L_HUMAN	F5H5K6_HUMAN	UPI00000723C4	.	.	.	2/15	.	hmmpanther:PTHR12455:SF0,hmmpanther:PTHR12455	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGCCAGCTG	byFrequency	4	ESCA
GOLGA3	0	.	GRCh37	12	133372506	133372506	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2401G>A	p.Glu801Lys	p.E801K	ENST00000204726	11/24	15	10	5	40	40	0	GOLGA3,missense_variant,p.Glu801Lys,ENST00000204726,;GOLGA3,missense_variant,p.Glu801Lys,ENST00000537452,;GOLGA3,missense_variant,p.Glu801Lys,ENST00000450791,;GOLGA3,missense_variant,p.Glu801Lys,ENST00000456883,;GOLGA3,missense_variant,p.Glu801Lys,ENST00000545875,;	T	ENSG00000090615	ENST00000204726	Transcript	missense_variant	2960	2401	801	E/K	Gaa/Aaa	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	deleterious(0.03)	possibly_damaging(0.874)	11/24	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902:SF20,hmmpanther:PTHR18902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTCTTCCA	.	5	ESCA
ANHX	0	.	GRCh37	12	133795907	133795907	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015T>G	p.Ser339Ala	p.S339A	ENST00000545940	7/8	21	10	11	32	32	0	ANHX,missense_variant,p.Ser339Ala,ENST00000419717,;ANHX,missense_variant,p.Ser339Ala,ENST00000545940,;AC226150.3,upstream_gene_variant,,ENST00000544259,;	C	ENSG00000227059	ENST00000545940	Transcript	missense_variant	2754	1015	339	S/A	Tct/Gct	.	.	.	-1	ANHX	HGNC	40024	protein_coding	YES	CCDS53855.1	ENSP00000439513	ANHX_HUMAN	.	UPI0001AE6BD3	.	tolerated(0.11)	benign(0.096)	7/8	.	hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAGACACAG	.	5	ESCA
MGP	0	.	GRCh37	12	15035090	15035090	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370C>T	p.Arg124Cys	p.R124C	ENST00000228938	5/5	44	36	8	62	62	0	MGP,missense_variant,p.Arg99Cys,ENST00000539261,;MGP,missense_variant,p.Arg124Cys,ENST00000228938,;MGP,synonymous_variant,p.%3D,ENST00000545199,;C12orf60,intron_variant,,ENST00000527783,;C12orf60,intron_variant,,ENST00000533472,;C12orf60,upstream_gene_variant,,ENST00000543822,;MGP,downstream_gene_variant,,ENST00000507170,;	A	ENSG00000111341	ENST00000228938	Transcript	missense_variant	436	370	124	R/C	Cgc/Tgc	.	.	.	-1	MGP	HGNC	7060	protein_coding	YES	CCDS53752.1	ENSP00000228938	MGP_HUMAN	.	UPI0001DB9553	.	deleterious_low_confidence(0)	probably_damaging(0.967)	5/5	.	hmmpanther:PTHR10109,hmmpanther:PTHR10109:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T102A|c.304A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGCGCTTCC	.	5	ESCA
CACNA2D4	0	.	GRCh37	12	1995148	1995148	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000382722	9/38	30	22	7	48	47	0	CACNA2D4,missense_variant,p.Asp267Tyr,ENST00000585732,;CACNA2D4,missense_variant,p.Asp351Tyr,ENST00000587995,;CACNA2D4,missense_variant,p.Asp351Tyr,ENST00000586184,;CACNA2D4,missense_variant,p.Asp351Tyr,ENST00000382722,;CACNA2D4,missense_variant,p.Asp287Tyr,ENST00000588077,;CACNA2D4,missense_variant,p.Asp287Tyr,ENST00000585708,;CACNA2D4,missense_variant,p.Asp351Tyr,ENST00000444595,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000280663,;CACNA2D4,upstream_gene_variant,,ENST00000590880,;	A	ENSG00000151062	ENST00000382722	Transcript	missense_variant	1414	1051	351	D/Y	Gac/Tac	.	.	.	-1	CACNA2D4	HGNC	20202	protein_coding	YES	CCDS44785.1	ENSP00000372169	CA2D4_HUMAN	.	UPI0000E593D9	.	deleterious(0)	possibly_damaging(0.771)	9/38	.	PROSITE_profiles:PS50234,hmmpanther:PTHR10166:SF26,hmmpanther:PTHR10166,Pfam_domain:PF13768,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGTCCGCCT	.	4	ESCA
ABCC9	0	.	GRCh37	12	22013930	22013930	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2399G>C	p.Gly800Ala	p.G800A	ENST00000261200	19/38	39	32	7	71	71	0	ABCC9,missense_variant,p.Gly764Ala,ENST00000345162,;ABCC9,missense_variant,p.Gly800Ala,ENST00000261201,;ABCC9,missense_variant,p.Gly427Ala,ENST00000544039,;ABCC9,missense_variant,p.Gly800Ala,ENST00000261200,;RP11-729I10.2,intron_variant,,ENST00000539874,;	G	ENSG00000069431	ENST00000261200	Transcript	missense_variant	2399	2399	800	G/A	gGa/gCa	.	.	.	-1	ABCC9	HGNC	60	protein_coding	YES	CCDS8693.1	ENSP00000261200	ABCC9_HUMAN	Q8N9N1_HUMAN	UPI000013D13F	.	deleterious(0.01)	probably_damaging(0.974)	19/38	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Gene3D:3.40.50.300,Pfam_domain:PF00005,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,PROSITE_profiles:PS50893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTCCAAAT	.	5	ESCA
CACNB3	0	.	GRCh37	12	49218100	49218100	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351C>T	p.%3D	p.F117F	ENST00000301050	4/13	84	71	12	151	151	0	CACNB3,synonymous_variant,p.%3D,ENST00000547392,;CACNB3,synonymous_variant,p.%3D,ENST00000548279,;CACNB3,synonymous_variant,p.%3D,ENST00000301050,;CACNB3,synonymous_variant,p.%3D,ENST00000536187,;CACNB3,synonymous_variant,p.%3D,ENST00000547230,;CACNB3,synonymous_variant,p.%3D,ENST00000540990,;CACNB3,5_prime_UTR_variant,,ENST00000550064,;CACNB3,5_prime_UTR_variant,,ENST00000547818,;CACNB3,intron_variant,,ENST00000550190,;CACNB3,non_coding_transcript_exon_variant,,ENST00000550168,;CACNB3,non_coding_transcript_exon_variant,,ENST00000552022,;CACNB3,downstream_gene_variant,,ENST00000549971,;CACNB3,synonymous_variant,p.%3D,ENST00000550391,;CACNB3,synonymous_variant,p.%3D,ENST00000550483,;CACNB3,3_prime_UTR_variant,,ENST00000551544,;CACNB3,non_coding_transcript_exon_variant,,ENST00000549226,;CACNB3,non_coding_transcript_exon_variant,,ENST00000548860,;CACNB3,intron_variant,,ENST00000548874,;CACNB3,upstream_gene_variant,,ENST00000552480,;CACNB3,downstream_gene_variant,,ENST00000551716,;CACNB3,downstream_gene_variant,,ENST00000552812,;CACNB3,downstream_gene_variant,,ENST00000547693,;CACNB3,downstream_gene_variant,,ENST00000550771,;	T	ENSG00000167535	ENST00000301050	Transcript	synonymous_variant	550	351	117	F	ttC/ttT	.	.	.	1	CACNB3	HGNC	1403	protein_coding	YES	CCDS8769.1	ENSP00000301050	CACB3_HUMAN	F8VUW8_HUMAN,F8VU10_HUMAN	UPI000000D9BA	.	.	.	4/13	.	hmmpanther:PTHR11824,Gene3D:2.30.30.40,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTTCATCCC	.	4	ESCA
PIP4K2C	0	.	GRCh37	12	57984966	57984966	+	5'Flank	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000354947	.	39	33	6	75	75	0	PIP4K2C,5_prime_UTR_variant,,ENST00000422156,;PIP4K2C,upstream_gene_variant,,ENST00000550465,;KIF5A,downstream_gene_variant,,ENST00000455537,;PIP4K2C,upstream_gene_variant,,ENST00000354947,;PIP4K2C,upstream_gene_variant,,ENST00000551772,;PIP4K2C,upstream_gene_variant,,ENST00000540759,;PIP4K2C,upstream_gene_variant,,ENST00000550360,;PIP4K2C,upstream_gene_variant,,ENST00000550095,;	G	ENSG00000166908	ENST00000354947	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	91	1	PIP4K2C	HGNC	23786	protein_coding	YES	CCDS8946.1	ENSP00000347032	PI42C_HUMAN	F8VU68_HUMAN	UPI000003F553	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGTCCGGCC	.	2	ESCA
HMGA2	0	.	GRCh37	12	66359464	66359464	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2392A>T	.	.	ENST00000403681	5/5	25	20	4	49	49	0	HMGA2,3_prime_UTR_variant,,ENST00000403681,;HMGA2,downstream_gene_variant,,ENST00000539662,;	T	ENSG00000149948	ENST00000403681	Transcript	3_prime_UTR_variant	3862	.	.	.	.	.	.	.	1	HMGA2	HGNC	5009	protein_coding	YES	CCDS44936.1	ENSP00000384026	HMGA2_HUMAN	Q8IZX8_HUMAN,B2KX87_HUMAN	UPI0000000CE6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTAGAAACCTC	.	4	ESCA
HELB	0	.	GRCh37	12	66716526	66716526	+	Missense_Mutation	SNP	G	G	A	rs772072453	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2260G>A	p.Asp754Asn	p.D754N	ENST00000247815	9/13	38	25	13	67	67	0	HELB,missense_variant,p.Asp754Asn,ENST00000247815,;HELB,missense_variant,p.Asp754Asn,ENST00000545134,;HELB,missense_variant,p.Asp754Asn,ENST00000542394,;HELB,3_prime_UTR_variant,,ENST00000440906,;HELB,non_coding_transcript_exon_variant,,ENST00000536862,;HELB,non_coding_transcript_exon_variant,,ENST00000545455,;	A	ENSG00000127311	ENST00000247815	Transcript	missense_variant	2319	2260	754	D/N	Gac/Aac	rs772072453	.	.	1	HELB	HGNC	17196	protein_coding	YES	CCDS8976.1	ENSP00000247815	HELB_HUMAN	.	UPI000013CC2D	.	deleterious(0.01)	benign(0.206)	9/13	.	Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATGACTGC	byFrequency	5	ESCA
MDM2	0	.	GRCh37	12	69233544	69233544	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1409G>A	p.Cys470Tyr	p.C470Y	ENST00000462284	11/11	68	53	14	120	120	0	MDM2,missense_variant,p.Cys269Tyr,ENST00000540827,;MDM2,missense_variant,p.Cys191Tyr,ENST00000393413,;MDM2,missense_variant,p.Cys191Tyr,ENST00000393412,;MDM2,missense_variant,p.Cys238Tyr,ENST00000348801,;MDM2,missense_variant,p.Cys103Tyr,ENST00000517852,;MDM2,missense_variant,p.Cys409Tyr,ENST00000258149,;MDM2,missense_variant,p.Cys415Tyr,ENST00000258148,;MDM2,missense_variant,p.Cys439Tyr,ENST00000350057,;MDM2,missense_variant,p.Cys216Tyr,ENST00000393410,;MDM2,missense_variant,p.Cys294Tyr,ENST00000299252,;MDM2,missense_variant,p.Cys470Tyr,ENST00000462284,;MDM2,missense_variant,p.Met62Ile,ENST00000544561,;MDM2,missense_variant,p.Cys269Tyr,ENST00000360430,;MDM2,missense_variant,p.Cys294Tyr,ENST00000356290,;MDM2,missense_variant,p.Cys243Tyr,ENST00000428863,;MDM2,3_prime_UTR_variant,,ENST00000545204,;MDM2,3_prime_UTR_variant,,ENST00000478070,;MDM2,downstream_gene_variant,,ENST00000393415,;CPM,downstream_gene_variant,,ENST00000551897,;MDM2,downstream_gene_variant,,ENST00000539479,;MDM2,downstream_gene_variant,,ENST00000543323,;MDM2,downstream_gene_variant,,ENST00000523991,;RP11-611O2.5,downstream_gene_variant,,ENST00000553141,;MDM2,upstream_gene_variant,,ENST00000400501,;MDM2,upstream_gene_variant,,ENST00000544125,;MDM2,upstream_gene_variant,,ENST00000540709,;MDM2,3_prime_UTR_variant,,ENST00000542502,;MDM2,3_prime_UTR_variant,,ENST00000537182,;MDM2,3_prime_UTR_variant,,ENST00000540352,;MDM2,3_prime_UTR_variant,,ENST00000311420,;MDM2,3_prime_UTR_variant,,ENST00000496959,;MDM2,3_prime_UTR_variant,,ENST00000481186,;MDM2,3_prime_UTR_variant,,ENST00000393417,;MDM2,3_prime_UTR_variant,,ENST00000536089,;MDM2,intron_variant,,ENST00000546048,;CPM,downstream_gene_variant,,ENST00000546556,;RP11-611O2.3,upstream_gene_variant,,ENST00000537570,;	A	ENSG00000135679	ENST00000462284	Transcript	missense_variant	1711	1409	470	C/Y	tGt/tAt	COSM1188548,COSM1188547	.	.	1	MDM2	HGNC	6973	protein_coding	YES	CCDS8986.2	ENSP00000417281	MDM2_HUMAN	Q546E6_HUMAN,A8WFP2_HUMAN,A7UKY0_HUMAN	UPI00006CA35C	.	deleterious(0)	probably_damaging(0.992)	11/11	.	PROSITE_profiles:PS50089,hmmpanther:PTHR10360,hmmpanther:PTHR10360:SF11,Gene3D:3.30.40.10,Pfam_domain:PF13920,PIRSF_domain:PIRSF500700,PIRSF_domain:PIRSF006748,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACATGTGCAA	.	5	ESCA
NAV3	0	.	GRCh37	12	78574660	78574660	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5461G>C	p.Glu1821Gln	p.E1821Q	ENST00000536525	29/39	39	33	6	50	50	0	NAV3,missense_variant,p.Glu1821Gln,ENST00000536525,;NAV3,missense_variant,p.Glu1843Gln,ENST00000397909,;NAV3,missense_variant,p.Glu443Gln,ENST00000550788,;NAV3,missense_variant,p.Glu1644Gln,ENST00000266692,;NAV3,missense_variant,p.Glu1821Gln,ENST00000228327,;NAV3,missense_variant,p.Glu716Gln,ENST00000552895,;NAV3,non_coding_transcript_exon_variant,,ENST00000552300,;NAV3,non_coding_transcript_exon_variant,,ENST00000548948,;	C	ENSG00000067798	ENST00000536525	Transcript	missense_variant	5634	5461	1821	E/Q	Gaa/Caa	.	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	deleterious(0)	probably_damaging(0.999)	29/39	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATTGAAATA	.	5	ESCA
LIN7A	0	.	GRCh37	12	81226363	81226363	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483+13146A>G	.	.	ENST00000552864	.	16	11	5	22	22	0	LIN7A,intron_variant,,ENST00000552864,;MIR617,non_coding_transcript_exon_variant,,ENST00000385030,;LIN7A,intron_variant,,ENST00000261203,;	C	ENSG00000111052	ENST00000552864	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	LIN7A	HGNC	17787	protein_coding	YES	CCDS9021.1	ENSP00000447488	LIN7A_HUMAN	.	UPI0000073ECD	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGTGGTAGGAA	.	3	ESCA
C13orf35	0	.	GRCh37	13	113333639	113333639	+	5'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-55T>G	.	.	ENST00000356049	2/3	202	8	193	50	50	0	C13orf35,5_prime_UTR_variant,,ENST00000356049,;	G	ENSG00000197595	ENST00000356049	Transcript	5_prime_UTR_variant	704	.	.	.	.	.	.	.	1	C13orf35	HGNC	33793	protein_coding	YES	CCDS9526.1	ENSP00000348337	CM035_HUMAN	.	UPI00001C1118	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTTGAGGC	.	5	ESCA
N4BP2L1	0	.	GRCh37	13	32978401	32978401	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473+57A>T	.	.	ENST00000380130	.	48	16	31	95	95	0	N4BP2L1,missense_variant,p.Gln135Leu,ENST00000380139,;N4BP2L1,intron_variant,,ENST00000530622,;N4BP2L1,intron_variant,,ENST00000343281,;N4BP2L1,intron_variant,,ENST00000495479,;N4BP2L1,intron_variant,,ENST00000380133,;N4BP2L1,intron_variant,,ENST00000380130,;BRCA2,downstream_gene_variant,,ENST00000544455,;N4BP2L1,intron_variant,,ENST00000459716,;N4BP2L1,downstream_gene_variant,,ENST00000472298,;	A	ENSG00000139597	ENST00000380130	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	N4BP2L1	HGNC	25037	protein_coding	YES	CCDS9345.2	ENSP00000369473	N42L1_HUMAN	Q9Y273_HUMAN,Q9UQP6_HUMAN	UPI000003CA35	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGTCTGAAAT	.	5	ESCA
RP11-248G5.8	0	.	GRCh37	13	52857389	52857389	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.317C>T	.	.	ENST00000451298	3/22	118	95	22	116	116	0	TPTE2P2,non_coding_transcript_exon_variant,,ENST00000605924,;RP11-248G5.8,non_coding_transcript_exon_variant,,ENST00000451298,;TPTE2P2,non_coding_transcript_exon_variant,,ENST00000403471,;	A	ENSG00000217576	ENST00000451298	Transcript	non_coding_transcript_exon_variant	317	.	.	.	.	.	.	.	-1	RP11-248G5.8	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	3/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTAAGAAACT	.	4	ESCA
MDGA2	0	.	GRCh37	14	47770688	47770688	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.346G>A	p.Glu116Lys	p.E116K	ENST00000439988	2/17	33	23	10	50	50	0	MDGA2,missense_variant,p.Glu71Lys,ENST00000486952,;MDGA2,missense_variant,p.Glu116Lys,ENST00000439988,;MDGA2,missense_variant,p.Glu47Lys,ENST00000399232,;MDGA2,5_prime_UTR_variant,,ENST00000357362,;MDGA2,5_prime_UTR_variant,,ENST00000426342,;MDGA2,non_coding_transcript_exon_variant,,ENST00000472499,;MDGA2,5_prime_UTR_variant,,ENST00000482848,;MDGA2,5_prime_UTR_variant,,ENST00000557238,;	T	ENSG00000272781	ENST00000439988	Transcript	missense_variant	346	346	116	E/K	Gaa/Aaa	.	.	.	-1	MDGA2	Uniprot_gn	19835	protein_coding	YES	.	ENSP00000400011	MDGA2_HUMAN	F8WE89_HUMAN	UPI0001DD21C1	.	deleterious(0)	probably_damaging(0.992)	2/17	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,SMART_domains:SM00409	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTCGGAGT	.	5	ESCA
AKAP5	0	.	GRCh37	14	64940331	64940331	+	3'UTR	DEL	T	T	-	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3939delT	.	.	ENST00000394718	2/2	52	41	11	67	67	0	AKAP5,3_prime_UTR_variant,,ENST00000394718,;ZBTB25,intron_variant,,ENST00000555424,;ZBTB25,intron_variant,,ENST00000555220,;ZBTB25,downstream_gene_variant,,ENST00000608382,;AKAP5,downstream_gene_variant,,ENST00000320636,;	-	ENSG00000179841	ENST00000394718	Transcript	3_prime_UTR_variant	5597	.	.	.	.	.	.	.	1	AKAP5	HGNC	375	protein_coding	YES	CCDS9764.1	ENSP00000378207	AKAP5_HUMAN	.	UPI0000140927	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAATGTTTTTC	.	3	ESCA
YLPM1	0	.	GRCh37	14	75265542	75265542	+	Missense_Mutation	SNP	A	A	G	rs748123589	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3542A>G	p.Tyr1181Cys	p.Y1181C	ENST00000325680	5/21	63	45	18	88	88	0	YLPM1,missense_variant,p.Tyr1181Cys,ENST00000325680,;YLPM1,missense_variant,p.Tyr986Cys,ENST00000238571,;YLPM1,intron_variant,,ENST00000552421,;YLPM1,missense_variant,p.Tyr734Cys,ENST00000549293,;	G	ENSG00000119596	ENST00000325680	Transcript	missense_variant	3666	3542	1181	Y/C	tAt/tGt	rs748123589	.	.	1	YLPM1	HGNC	17798	protein_coding	YES	CCDS45135.1	ENSP00000324463	YLPM1_HUMAN	B4DMQ9_HUMAN	UPI00006C1433	.	.	probably_damaging(0.935)	5/21	.	hmmpanther:PTHR13413:SF0,hmmpanther:PTHR13413	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGTATCCAT	byFrequency	5	ESCA
TGFB3	0	.	GRCh37	14	76425513	76425513	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*17G>C	.	.	ENST00000238682	7/7	46	35	10	89	89	0	TGFB3,3_prime_UTR_variant,,ENST00000238682,;TGFB3,downstream_gene_variant,,ENST00000556285,;TTLL5,downstream_gene_variant,,ENST00000298832,;TGFB3,downstream_gene_variant,,ENST00000557493,;TTLL5,downstream_gene_variant,,ENST00000554487,;TGFB3,downstream_gene_variant,,ENST00000556507,;TTLL5,downstream_gene_variant,,ENST00000554972,;TGFB3,non_coding_transcript_exon_variant,,ENST00000554980,;IFT43,intron_variant,,ENST00000555677,;	G	ENSG00000119699	ENST00000238682	Transcript	3_prime_UTR_variant	1554	.	.	.	.	.	.	.	-1	TGFB3	HGNC	11769	protein_coding	YES	CCDS9846.1	ENSP00000238682	TGFB3_HUMAN	Q8WV88_HUMAN,Q6TV16_HUMAN,Q6TV15_HUMAN,Q6TV14_HUMAN,Q6LDJ6_HUMAN,A5YM40_HUMAN	UPI000000D8EC	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCTGTCG	.	5	ESCA
CCNK	0	.	GRCh37	14	99969314	99969314	+	Missense_Mutation	SNP	G	G	A	rs759957278	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000389879	8/11	52	38	14	73	73	0	CCNK,missense_variant,p.Arg335Gln,ENST00000555049,;CCNK,missense_variant,p.Arg335Gln,ENST00000389879,;CCNK,downstream_gene_variant,,ENST00000557441,;CCNK,downstream_gene_variant,,ENST00000557165,;CCNK,non_coding_transcript_exon_variant,,ENST00000553865,;CCNK,downstream_gene_variant,,ENST00000556641,;	A	ENSG00000090061	ENST00000389879	Transcript	missense_variant	1127	1004	335	R/Q	cGa/cAa	rs759957278	.	.	1	CCNK	HGNC	1596	protein_coding	YES	CCDS45160.1	ENSP00000374529	CCNK_HUMAN	G3V2Q3_HUMAN,G3V235_HUMAN	UPI00001FDB50	.	tolerated(0.28)	unknown(0)	8/11	.	hmmpanther:PTHR10026,hmmpanther:PTHR10026:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGCGAGCCG	byFrequency	5	ESCA
TJP1	0	.	GRCh37	15	30058538	30058538	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520C>T	p.Arg174Trp	p.R174W	ENST00000346128	5/28	54	23	31	56	56	0	TJP1,missense_variant,p.Arg174Trp,ENST00000356107,;TJP1,missense_variant,p.Arg178Trp,ENST00000400011,;TJP1,missense_variant,p.Arg174Trp,ENST00000495972,;TJP1,missense_variant,p.Arg174Trp,ENST00000346128,;TJP1,missense_variant,p.Arg174Trp,ENST00000545208,;TJP1,downstream_gene_variant,,ENST00000558447,;	A	ENSG00000104067	ENST00000346128	Transcript	missense_variant	995	520	174	R/W	Cgg/Tgg	.	.	.	-1	TJP1	HGNC	11827	protein_coding	YES	CCDS42007.1	ENSP00000281537	ZO1_HUMAN	.	UPI000013DC83	.	deleterious(0)	probably_damaging(0.973)	5/28	.	hmmpanther:PTHR13865,hmmpanther:PTHR13865:SF25,Gene3D:2.30.42.10,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACCGCCTGT	.	5	ESCA
MAPKBP1	0	.	GRCh37	15	42106776	42106776	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027A>G	p.Arg343Gly	p.R343G	ENST00000456763	11/32	44	39	5	76	76	0	MAPKBP1,missense_variant,p.Arg225Gly,ENST00000260357,;MAPKBP1,missense_variant,p.Arg337Gly,ENST00000457542,;MAPKBP1,missense_variant,p.Arg343Gly,ENST00000456763,;MAPKBP1,missense_variant,p.Arg337Gly,ENST00000514566,;MAPKBP1,intron_variant,,ENST00000221214,;MAPKBP1,downstream_gene_variant,,ENST00000510535,;MAPKBP1,downstream_gene_variant,,ENST00000507762,;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000502292,;MAPKBP1,intron_variant,,ENST00000512970,;MAPKBP1,downstream_gene_variant,,ENST00000507147,;MAPKBP1,upstream_gene_variant,,ENST00000503526,;MAPKBP1,downstream_gene_variant,,ENST00000515164,;	G	ENSG00000137802	ENST00000456763	Transcript	missense_variant	1223	1027	343	R/G	Agg/Ggg	.	.	.	1	MAPKBP1	HGNC	29536	protein_coding	YES	CCDS45239.1	ENSP00000393099	MABP1_HUMAN	D6R9F7_HUMAN	UPI00002375CB	.	deleterious(0.01)	benign(0.042)	11/32	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR22847:SF326,hmmpanther:PTHR22847,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGCCAGGTAT	.	4	ESCA
SNX1	0	.	GRCh37	15	64430097	64430097	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1519-144A>G	.	.	ENST00000261889	.	121	87	34	132	132	0	SNX1,3_prime_UTR_variant,,ENST00000559844,;SNX1,3_prime_UTR_variant,,ENST00000560829,;SNX1,3_prime_UTR_variant,,ENST00000353874,;SNX1,intron_variant,,ENST00000560861,;SNX1,intron_variant,,ENST00000261889,;SNX1,intron_variant,,ENST00000558040,;SNX1,downstream_gene_variant,,ENST00000561026,;SNX1,3_prime_UTR_variant,,ENST00000380285,;SNX1,downstream_gene_variant,,ENST00000559401,;SNX1,downstream_gene_variant,,ENST00000560260,;SNX1,downstream_gene_variant,,ENST00000559961,;	G	ENSG00000028528	ENST00000261889	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SNX1	HGNC	11172	protein_coding	YES	CCDS58371.1	ENSP00000261889	SNX1_HUMAN	H0YKT3_HUMAN	UPI000217BDBB	.	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAAATACAA	.	5	ESCA
VPS33B	0	.	GRCh37	15	91549260	91549260	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.882C>T	p.%3D	p.F294F	ENST00000333371	12/23	31	27	4	20	20	0	VPS33B,synonymous_variant,p.%3D,ENST00000535843,;VPS33B,synonymous_variant,p.%3D,ENST00000535906,;VPS33B,synonymous_variant,p.%3D,ENST00000333371,;VPS33B,3_prime_UTR_variant,,ENST00000574755,;VPS33B,non_coding_transcript_exon_variant,,ENST00000556096,;VPS33B,upstream_gene_variant,,ENST00000557470,;VPS33B,downstream_gene_variant,,ENST00000554264,;	A	ENSG00000184056	ENST00000333371	Transcript	synonymous_variant	1236	882	294	F	ttC/ttT	.	.	.	-1	VPS33B	HGNC	12712	protein_coding	YES	CCDS10369.1	ENSP00000327650	VP33B_HUMAN	B3KQF6_HUMAN	UPI0000169A6E	.	.	.	12/23	.	hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF1,Pfam_domain:PF00995,Gene3D:3.40.50.1910,Superfamily_domains:SSF56815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|VARSCANS	TTGGAGAAGTG	.	3	ESCA
CACNA1H	0	.	GRCh37	16	1260600	1260600	+	Silent	SNP	C	C	T	rs770769436	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3987C>T	p.%3D	p.S1329S	ENST00000348261	20/35	45	33	12	98	98	0	CACNA1H,synonymous_variant,p.%3D,ENST00000562079,;CACNA1H,synonymous_variant,p.%3D,ENST00000348261,;CACNA1H,synonymous_variant,p.%3D,ENST00000564231,;CACNA1H,synonymous_variant,p.%3D,ENST00000565831,;CACNA1H,synonymous_variant,p.%3D,ENST00000358590,;CACNA1H,synonymous_variant,p.%3D,ENST00000569107,;CACNA1H,upstream_gene_variant,,ENST00000564927,;RP11-616M22.3,upstream_gene_variant,,ENST00000564700,;CACNA1H,non_coding_transcript_exon_variant,,ENST00000569953,;	T	ENSG00000196557	ENST00000348261	Transcript	synonymous_variant	4235	3987	1329	S	agC/agT	rs770769436,COSM1563258,COSM1563257	.	.	1	CACNA1H	HGNC	1395	protein_coding	YES	CCDS45375.1	ENSP00000334198	CAC1H_HUMAN	Q9NYY7_HUMAN,Q9NYY6_HUMAN	UPI000012727B	.	.	.	20/35	.	Superfamily_domains:SSF81324,Gene3D:1.20.120.350,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAGCGTCTC	.	5	ESCA
MRPS34	0	.	GRCh37	16	1822500	1822500	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.379G>C	p.Glu127Gln	p.E127Q	ENST00000397375	3/3	33	24	8	37	37	0	MRPS34,missense_variant,p.Glu127Gln,ENST00000397375,;MRPS34,missense_variant,p.Glu134Gln,ENST00000177742,;SPSB3,downstream_gene_variant,,ENST00000301717,;MAPK8IP3,downstream_gene_variant,,ENST00000356010,;EME2,upstream_gene_variant,,ENST00000568449,;NME3,upstream_gene_variant,,ENST00000564628,;SPSB3,downstream_gene_variant,,ENST00000566339,;MAPK8IP3,downstream_gene_variant,,ENST00000250894,;EME2,upstream_gene_variant,,ENST00000307394,;NME3,upstream_gene_variant,,ENST00000219302,;NME3,upstream_gene_variant,,ENST00000563498,;MRPS34,non_coding_transcript_exon_variant,,ENST00000569585,;NME3,upstream_gene_variant,,ENST00000567271,;NME3,upstream_gene_variant,,ENST00000568561,;SPSB3,downstream_gene_variant,,ENST00000567868,;NME3,upstream_gene_variant,,ENST00000566600,;NME3,upstream_gene_variant,,ENST00000561637,;EME2,upstream_gene_variant,,ENST00000564182,;NME3,upstream_gene_variant,,ENST00000563367,;SPSB3,downstream_gene_variant,,ENST00000564709,;SPSB3,downstream_gene_variant,,ENST00000563668,;NME3,upstream_gene_variant,,ENST00000563854,;SPSB3,downstream_gene_variant,,ENST00000563741,;MAPK8IP3,downstream_gene_variant,,ENST00000566064,;NME3,upstream_gene_variant,,ENST00000564252,;EME2,upstream_gene_variant,,ENST00000565326,;NME3,upstream_gene_variant,,ENST00000565379,;EME2,upstream_gene_variant,,ENST00000570069,;EME2,upstream_gene_variant,,ENST00000561903,;EME2,upstream_gene_variant,,ENST00000561564,;MAPK8IP3,downstream_gene_variant,,ENST00000563868,;SPSB3,downstream_gene_variant,,ENST00000569380,;MAPK8IP3,downstream_gene_variant,,ENST00000564868,;	G	ENSG00000074071	ENST00000397375	Transcript	missense_variant	415	379	127	E/Q	Gag/Cag	COSM3817343	.	.	-1	MRPS34	HGNC	16618	protein_coding	YES	CCDS10444.1	ENSP00000380531	RT34_HUMAN	.	UPI0000049FE2	.	tolerated(0.16)	benign(0.043)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCTCGCTCT	.	5	ESCA
DNAH3	0	.	GRCh37	16	20975118	20975118	+	Missense_Mutation	SNP	C	C	T	rs760740628	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10088G>A	p.Arg3363His	p.R3363H	ENST00000261383	53/62	51	37	14	72	72	0	DNAH3,missense_variant,p.Arg3363His,ENST00000261383,;DNAH3,3_prime_UTR_variant,,ENST00000415178,;	T	ENSG00000158486	ENST00000261383	Transcript	missense_variant	10088	10088	3363	R/H	cGt/cAt	rs760740628,COSM1708888,COSM1708887	.	.	-1	DNAH3	HGNC	2949	protein_coding	YES	CCDS10594.1	ENSP00000261383	DYH3_HUMAN	.	UPI00001100F2	.	deleterious(0)	probably_damaging(1)	53/62	.	hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V3361M|c.10081G>A|3,BUFFER|p.V3361M|c.10081G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAACGGCAC	byFrequency|byCluster	5	ESCA
ARHGAP17	0	.	GRCh37	16	24950906	24950906	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1503G>A	p.%3D	p.K501K	ENST00000289968	17/20	69	57	12	106	105	0	ARHGAP17,synonymous_variant,p.%3D,ENST00000289968,;ARHGAP17,3_prime_UTR_variant,,ENST00000441763,;ARHGAP17,intron_variant,,ENST00000303665,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000572314,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000575283,;ARHGAP17,downstream_gene_variant,,ENST00000575412,;ARHGAP17,upstream_gene_variant,,ENST00000570320,;ARHGAP17,downstream_gene_variant,,ENST00000570841,;	T	ENSG00000140750	ENST00000289968	Transcript	synonymous_variant	1573	1503	501	K	aaG/aaA	.	.	.	-1	ARHGAP17	HGNC	18239	protein_coding	YES	CCDS32409.1	ENSP00000289968	RHG17_HUMAN	I3L4P6_HUMAN	UPI00000433FD	.	.	.	17/20	.	hmmpanther:PTHR14130:SF3,hmmpanther:PTHR14130	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAGCTTCAC	.	5	ESCA
ZNF629	0	.	GRCh37	16	30793915	30793915	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1734C>T	p.%3D	p.F578F	ENST00000262525	3/3	23	17	6	42	42	0	ZNF629,synonymous_variant,p.%3D,ENST00000262525,;RP11-2C24.6,downstream_gene_variant,,ENST00000575562,;	A	ENSG00000102870	ENST00000262525	Transcript	synonymous_variant	1942	1734	578	F	ttC/ttT	.	.	.	-1	ZNF629	HGNC	29008	protein_coding	YES	CCDS45463.1	ENSP00000262525	ZN629_HUMAN	.	UPI00001C1FA5	.	.	.	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF286,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGTTGAAGCC	.	2	ESCA
NUDT21	0	.	GRCh37	16	56480535	56480535	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381+3A>G	.	.	ENST00000300291	.	72	53	19	124	124	0	NUDT21,splice_region_variant,,ENST00000568822,;NUDT21,splice_region_variant,,ENST00000300291,;NUDT21,splice_region_variant,,ENST00000566340,;OGFOD1,upstream_gene_variant,,ENST00000566157,;OGFOD1,upstream_gene_variant,,ENST00000568397,;OGFOD1,upstream_gene_variant,,ENST00000561646,;OGFOD1,upstream_gene_variant,,ENST00000562150,;OGFOD1,upstream_gene_variant,,ENST00000568172,;OGFOD1,upstream_gene_variant,,ENST00000569645,;OGFOD1,upstream_gene_variant,,ENST00000569802,;OGFOD1,upstream_gene_variant,,ENST00000563733,;OGFOD1,upstream_gene_variant,,ENST00000565682,;OGFOD1,upstream_gene_variant,,ENST00000336111,;NUDT21,downstream_gene_variant,,ENST00000567110,;	C	ENSG00000167005	ENST00000300291	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	NUDT21	HGNC	13870	protein_coding	YES	CCDS10760.1	ENSP00000300291	CPSF5_HUMAN	H3BV41_HUMAN,H3BND3_HUMAN	UPI0000073E79	.	.	.	.	3/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAATACCTC	.	4	ESCA
C16orf70	0	.	GRCh37	16	67180989	67180989	+	Frame_Shift_Del	DEL	C	C	-	rs751141757	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1230delC	p.Arg411GlyfsTer6	p.R411Gfs*6	ENST00000219139	16/16	29	25	4	38	38	0	C16orf70,frameshift_variant,p.Arg40AspfsTer25,ENST00000569277,;C16orf70,frameshift_variant,p.Arg411GlyfsTer6,ENST00000219139,;C16orf70,frameshift_variant,p.Arg411GlyfsTer6,ENST00000569600,;B3GNT9,downstream_gene_variant,,ENST00000449549,;C16orf70,downstream_gene_variant,,ENST00000563853,;C16orf70,downstream_gene_variant,,ENST00000567162,;	-	ENSG00000125149	ENST00000219139	Transcript	frameshift_variant	1412	1224	408	G/X	ggC/gg	rs751141757,COSM392149	.	.	1	C16orf70	HGNC	29564	protein_coding	YES	CCDS10828.1	ENSP00000219139	CP070_HUMAN	H3BSG0_HUMAN	UPI0000137911	.	.	.	16/16	.	hmmpanther:PTHR13465,Pfam_domain:PF03676	.	.	.	.	.	.	.	-:0.0005	-:0	.	0,1	.	.	.	.	.	HIGH	.	deletion	.	6	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GTATGGCCCCCC	.	2	ESCA
FHOD1	0	.	GRCh37	16	67265688	67265688	+	Missense_Mutation	SNP	C	C	T	rs774658881	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2237G>A	p.Arg746Gln	p.R746Q	ENST00000258201	15/22	25	16	9	38	38	0	FHOD1,missense_variant,p.Arg746Gln,ENST00000258201,;TMEM208,downstream_gene_variant,,ENST00000304800,;LRRC29,upstream_gene_variant,,ENST00000433915,;TMEM208,downstream_gene_variant,,ENST00000563953,;LRRC29,upstream_gene_variant,,ENST00000393992,;TMEM208,downstream_gene_variant,,ENST00000565201,;LRRC29,upstream_gene_variant,,ENST00000409509,;LRRC29,upstream_gene_variant,,ENST00000447579,;LRRC29,upstream_gene_variant,,ENST00000424285,;AC040160.1,upstream_gene_variant,,ENST00000454102,;LRRC29,upstream_gene_variant,,ENST00000341546,;TMEM208,downstream_gene_variant,,ENST00000563426,;LRRC29,upstream_gene_variant,,ENST00000485549,;LRRC29,upstream_gene_variant,,ENST00000462169,;FHOD1,synonymous_variant,p.%3D,ENST00000567509,;FHOD1,3_prime_UTR_variant,,ENST00000567561,;FHOD1,non_coding_transcript_exon_variant,,ENST00000567752,;FHOD1,downstream_gene_variant,,ENST00000561922,;TMEM208,downstream_gene_variant,,ENST00000564649,;TMEM208,downstream_gene_variant,,ENST00000563168,;FHOD1,downstream_gene_variant,,ENST00000568595,;TMEM208,downstream_gene_variant,,ENST00000564087,;TMEM208,downstream_gene_variant,,ENST00000566486,;FHOD1,upstream_gene_variant,,ENST00000566006,;TMEM208,downstream_gene_variant,,ENST00000567193,;FHOD1,downstream_gene_variant,,ENST00000562266,;FHOD1,downstream_gene_variant,,ENST00000569888,;TMEM208,downstream_gene_variant,,ENST00000562235,;TMEM208,downstream_gene_variant,,ENST00000561586,;TMEM208,downstream_gene_variant,,ENST00000563271,;FHOD1,upstream_gene_variant,,ENST00000569085,;	T	ENSG00000135723	ENST00000258201	Transcript	missense_variant	2485	2237	746	R/Q	cGg/cAg	rs774658881	.	.	-1	FHOD1	HGNC	17905	protein_coding	YES	CCDS10834.1	ENSP00000258201	FHOD1_HUMAN	.	UPI000013CFB9	.	tolerated(0.08)	benign(0.007)	15/22	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF189,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGCCGCTCT	byFrequency	5	ESCA
SYCE1L	0	.	GRCh37	16	77240393	77240393	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117G>A	p.%3D	p.Q39Q	ENST00000378644	2/11	35	27	8	78	78	0	SYCE1L,synonymous_variant,p.%3D,ENST00000378644,;MON1B,downstream_gene_variant,,ENST00000248248,;RP11-538I12.2,intron_variant,,ENST00000569032,;	A	ENSG00000205078	ENST00000378644	Transcript	synonymous_variant	172	117	39	Q	caG/caA	.	.	.	1	SYCE1L	HGNC	37236	protein_coding	YES	CCDS45533.1	ENSP00000367911	SYC1L_HUMAN	.	UPI000025210F	.	.	.	2/11	.	hmmpanther:PTHR21731:SF1,hmmpanther:PTHR21731	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGAAAGG	.	5	ESCA
SERPINF1	0	.	GRCh37	17	1674466	1674466	+	Missense_Mutation	SNP	G	G	C	rs548418598	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427G>C	p.Val143Leu	p.V143L	ENST00000254722	4/8	33	30	3	60	60	0	SERPINF1,missense_variant,p.Val143Leu,ENST00000254722,;SERPINF1,5_prime_UTR_variant,,ENST00000576406,;SERPINF1,upstream_gene_variant,,ENST00000572048,;SERPINF1,downstream_gene_variant,,ENST00000571149,;SERPINF1,downstream_gene_variant,,ENST00000571360,;SERPINF1,upstream_gene_variant,,ENST00000573763,;SERPINF1,downstream_gene_variant,,ENST00000570731,;SERPINF1,downstream_gene_variant,,ENST00000577053,;SERPINF1,non_coding_transcript_exon_variant,,ENST00000571870,;SERPINF1,3_prime_UTR_variant,,ENST00000573770,;SERPINF1,non_coding_transcript_exon_variant,,ENST00000570820,;	C	ENSG00000132386	ENST00000254722	Transcript	missense_variant	590	427	143	V/L	Gtc/Ctc	rs548418598	.	.	1	SERPINF1	HGNC	8824	protein_coding	YES	CCDS11012.1	ENSP00000254722	PEDF_HUMAN	I3L4F9_HUMAN,I3L425_HUMAN,I3L3Z3_HUMAN,I3L2R7_HUMAN,I3L107_HUMAN	UPI000013CE56	.	tolerated(0.4)	benign(0.009)	4/8	.	hmmpanther:PTHR11461:SF84,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:3.30.497.10,SMART_domains:SM00093,Superfamily_domains:SSF56574	A:0.0016	A:0	A:0	.	A:0.006	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGATCGTCTTT	byFrequency|by1000G	2	ESCA
RAP1GAP2	0	.	GRCh37	17	2923853	2923853	+	Missense_Mutation	SNP	C	C	T	rs781454135	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1715C>T	p.Thr572Met	p.T572M	ENST00000254695	19/25	37	33	4	88	88	0	RAP1GAP2,missense_variant,p.Thr553Met,ENST00000540393,;RAP1GAP2,missense_variant,p.Thr557Met,ENST00000366401,;RAP1GAP2,missense_variant,p.Thr572Met,ENST00000542807,;RAP1GAP2,missense_variant,p.Thr572Met,ENST00000254695,;RAP1GAP2,non_coding_transcript_exon_variant,,ENST00000575979,;	T	ENSG00000132359	ENST00000254695	Transcript	missense_variant	1805	1715	572	T/M	aCg/aTg	rs781454135	.	.	1	RAP1GAP2	HGNC	29176	protein_coding	YES	CCDS45573.1	ENSP00000254695	RPGP2_HUMAN	.	UPI0000D622A3	.	deleterious(0)	benign(0.047)	19/25	.	hmmpanther:PTHR15711:SF17,hmmpanther:PTHR15711	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GCACACGGGCT	byFrequency|byCluster	2	ESCA
KRT17	0	.	GRCh37	17	39785011	39785011	+	5'Flank	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000311208	.	56	44	11	128	128	0	JUP,intron_variant,,ENST00000540235,;KRT17,upstream_gene_variant,,ENST00000577817,;KRT17,upstream_gene_variant,,ENST00000311208,;KRT17,upstream_gene_variant,,ENST00000463128,;KRT42P,non_coding_transcript_exon_variant,,ENST00000438131,;KRT42P,intron_variant,,ENST00000398469,;KRT42P,downstream_gene_variant,,ENST00000587390,;KRT42P,downstream_gene_variant,,ENST00000589633,;KRT42P,non_coding_transcript_exon_variant,,ENST00000587335,;KRT17,upstream_gene_variant,,ENST00000491673,;KRT17,upstream_gene_variant,,ENST00000493253,;KRT42P,intron_variant,,ENST00000458343,;	A	ENSG00000128422	ENST00000311208	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4182	-1	KRT17	HGNC	6427	protein_coding	YES	CCDS11402.1	ENSP00000308452	K1C17_HUMAN	K7ESE1_HUMAN,B4E2P9_HUMAN	UPI0000148FD6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACCGGAGAT	.	5	ESCA
MAP3K14-AS1	0	.	GRCh37	17	43348439	43348439	+	3'Flank	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000585780	.	26	23	3	60	60	0	MAP3K14-AS1,downstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,downstream_gene_variant,,ENST00000591263,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585351,;MAP3K14-AS1,downstream_gene_variant,,ENST00000586450,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588504,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588160,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585346,;MAP3K14-AS1,downstream_gene_variant,,ENST00000592422,;MAP3K14-AS1,downstream_gene_variant,,ENST00000588698,;MAP3K14-AS1,downstream_gene_variant,,ENST00000585780,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000376926,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000587332,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000344686,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000586644,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000592267,;	A	ENSG00000267278	ENST00000585780	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3013	1	MAP3K14-AS1	HGNC	44359	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCGGCCCTC	.	2	ESCA
MINK1	0	.	GRCh37	17	4800902	4800902	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*320C>A	.	.	ENST00000355280	32/32	72	44	28	101	101	0	MINK1,3_prime_UTR_variant,,ENST00000347992,;MINK1,3_prime_UTR_variant,,ENST00000355280,;C17orf107,upstream_gene_variant,,ENST00000521575,;CHRNE,downstream_gene_variant,,ENST00000293780,;C17orf107,upstream_gene_variant,,ENST00000381365,;MINK1,downstream_gene_variant,,ENST00000576037,;MINK1,downstream_gene_variant,,ENST00000453408,;CHRNE,downstream_gene_variant,,ENST00000575637,;MINK1,3_prime_UTR_variant,,ENST00000574453,;MINK1,3_prime_UTR_variant,,ENST00000571207,;MINK1,non_coding_transcript_exon_variant,,ENST00000574871,;MINK1,non_coding_transcript_exon_variant,,ENST00000572330,;CHRNE,downstream_gene_variant,,ENST00000572438,;MINK1,downstream_gene_variant,,ENST00000572629,;MINK1,downstream_gene_variant,,ENST00000572304,;MINK1,downstream_gene_variant,,ENST00000575511,;MINK1,downstream_gene_variant,,ENST00000571526,;	A	ENSG00000141503	ENST00000355280	Transcript	3_prime_UTR_variant	4515	.	.	.	.	.	.	.	1	MINK1	HGNC	17565	protein_coding	YES	CCDS45588.1	ENSP00000347427	MINK1_HUMAN	Q9HBM9_HUMAN,Q8NG69_HUMAN	UPI00001678BB	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAACCCCTT	.	5	ESCA
KIF2B	0	.	GRCh37	17	51901127	51901127	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.733A>T	p.Met245Leu	p.M245L	ENST00000268919	1/1	32	27	4	58	58	0	KIF2B,missense_variant,p.Met245Leu,ENST00000268919,;	T	ENSG00000141200	ENST00000268919	Transcript	missense_variant	889	733	245	M/L	Atg/Ttg	.	.	.	1	KIF2B	HGNC	29443	protein_coding	YES	CCDS32685.1	ENSP00000268919	KIF2B_HUMAN	.	UPI000013D7E6	.	tolerated(0.5)	benign(0.046)	1/1	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF379,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTATGGTG	.	4	ESCA
LPO	0	.	GRCh37	17	56345434	56345434	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*79C>A	.	.	ENST00000262290	13/13	19	13	6	40	40	0	LPO,3_prime_UTR_variant,,ENST00000421678,;LPO,3_prime_UTR_variant,,ENST00000262290,;LPO,3_prime_UTR_variant,,ENST00000543544,;LPO,3_prime_UTR_variant,,ENST00000582328,;MPO,downstream_gene_variant,,ENST00000340482,;MPO,downstream_gene_variant,,ENST00000225275,;MPO,downstream_gene_variant,,ENST00000577220,;LPO,3_prime_UTR_variant,,ENST00000580890,;LPO,3_prime_UTR_variant,,ENST00000389576,;	A	ENSG00000167419	ENST00000262290	Transcript	3_prime_UTR_variant	2534	.	.	.	.	.	.	.	1	LPO	HGNC	6678	protein_coding	YES	CCDS32689.1	ENSP00000262290	PERL_HUMAN	J3QSD8_HUMAN,F5H386_HUMAN	UPI0000131631	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGAGCTCCAT	.	5	ESCA
MED13	0	.	GRCh37	17	60020268	60020268	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3561G>C	.	.	ENST00000397786	30/30	35	19	15	67	67	0	MED13,3_prime_UTR_variant,,ENST00000397786,;	G	ENSG00000108510	ENST00000397786	Transcript	3_prime_UTR_variant	10163	.	.	.	.	.	.	.	-1	MED13	HGNC	22474	protein_coding	YES	CCDS42366.1	ENSP00000380888	MED13_HUMAN	.	UPI0000D7D6F6	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAGCTTAAA	.	5	ESCA
MED13	0	.	GRCh37	17	60023404	60023404	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*425C>T	.	.	ENST00000397786	30/30	57	47	10	81	80	1	MED13,3_prime_UTR_variant,,ENST00000397786,;	A	ENSG00000108510	ENST00000397786	Transcript	3_prime_UTR_variant	7027	.	.	.	.	.	.	.	-1	MED13	HGNC	22474	protein_coding	YES	CCDS42366.1	ENSP00000380888	MED13_HUMAN	.	UPI0000D7D6F6	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGGCATTT	.	5	ESCA
MARCH10	0	.	GRCh37	17	60865948	60865948	+	Nonsense_Mutation	SNP	G	G	A	rs200814272	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103C>T	p.Arg35Ter	p.R35*	ENST00000311269	3/11	40	33	7	71	71	0	MARCH10,stop_gained,p.Arg35Ter,ENST00000583600,;MARCH10,stop_gained,p.Arg35Ter,ENST00000456609,;MARCH10,stop_gained,p.Arg35Ter,ENST00000311269,;MARCH10,stop_gained,p.Arg35Ter,ENST00000544856,;MARCH10,stop_gained,p.Arg35Ter,ENST00000583803,;MARCH10,non_coding_transcript_exon_variant,,ENST00000578346,;	A	ENSG00000173838	ENST00000311269	Transcript	stop_gained	378	103	35	R/*	Cga/Tga	rs200814272	.	.	-1	MARCH10	HGNC	26655	protein_coding	YES	CCDS11635.1	ENSP00000311496	MARHA_HUMAN	J3KTK3_HUMAN	UPI000013F13A	.	.	.	3/11	.	hmmpanther:PTHR14471,hmmpanther:PTHR14471:SF5	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTCGTCTCA	byCluster|by1000G	4	ESCA
CYB561	0	.	GRCh37	17	61514912	61514912	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4C>A	.	.	ENST00000392976	2/6	27	20	7	55	55	0	CYB561,synonymous_variant,p.%3D,ENST00000580592,;CYB561,synonymous_variant,p.%3D,ENST00000580691,;CYB561,synonymous_variant,p.%3D,ENST00000582997,;CYB561,synonymous_variant,p.%3D,ENST00000542042,;CYB561,5_prime_UTR_variant,,ENST00000581573,;CYB561,5_prime_UTR_variant,,ENST00000360793,;CYB561,5_prime_UTR_variant,,ENST00000448884,;CYB561,5_prime_UTR_variant,,ENST00000584291,;CYB561,5_prime_UTR_variant,,ENST00000392975,;CYB561,5_prime_UTR_variant,,ENST00000584031,;CYB561,5_prime_UTR_variant,,ENST00000392976,;CYB561,5_prime_UTR_variant,,ENST00000582297,;CYB561,5_prime_UTR_variant,,ENST00000578072,;CYB561,intron_variant,,ENST00000582034,;CYB561,upstream_gene_variant,,ENST00000585153,;CYB561,non_coding_transcript_exon_variant,,ENST00000578016,;CYB561,intron_variant,,ENST00000577989,;CYB561,upstream_gene_variant,,ENST00000581163,;CYB561,non_coding_transcript_exon_variant,,ENST00000583478,;CYB561,non_coding_transcript_exon_variant,,ENST00000577368,;CYB561,upstream_gene_variant,,ENST00000582143,;	T	ENSG00000008283	ENST00000392976	Transcript	5_prime_UTR_variant	297	.	.	.	.	.	.	.	-1	CYB561	HGNC	2571	protein_coding	YES	CCDS11636.1	ENSP00000376702	CY561_HUMAN	J3QS47_HUMAN	UPI0000126C79	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGAGGCA	.	5	ESCA
ABCA8	0	.	GRCh37	17	66878742	66878742	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000269080	28/38	45	36	9	71	71	0	ABCA8,missense_variant,p.Glu1236Lys,ENST00000269080,;ABCA8,missense_variant,p.Glu1276Lys,ENST00000430352,;ABCA8,missense_variant,p.Glu1276Lys,ENST00000586539,;ABCA8,splice_region_variant,,ENST00000589980,;ABCA8,splice_region_variant,,ENST00000586292,;ABCA8,upstream_gene_variant,,ENST00000588458,;ABCA8,downstream_gene_variant,,ENST00000541225,;ABCA8,upstream_gene_variant,,ENST00000591459,;	T	ENSG00000141338	ENST00000269080	Transcript	missense_variant	3844	3706	1236	E/K	Gag/Aag	.	.	.	-1	ABCA8	HGNC	38	protein_coding	YES	CCDS11680.1	ENSP00000269080	ABCA8_HUMAN	K7ELK9_HUMAN	UPI000004C4B7	.	deleterious(0)	possibly_damaging(0.521)	28/38	.	hmmpanther:PTHR19229:SF115,hmmpanther:PTHR19229,Gene3D:3.40.50.300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCATCAA	.	5	ESCA
UBE2O	0	.	GRCh37	17	74395935	74395935	+	Missense_Mutation	SNP	C	C	A	rs149178826	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1223G>T	p.Arg408Leu	p.R408L	ENST00000319380	9/18	17	12	5	43	43	0	UBE2O,missense_variant,p.Arg168Leu,ENST00000590658,;UBE2O,missense_variant,p.Arg408Leu,ENST00000319380,;UBE2O,upstream_gene_variant,,ENST00000587127,;UBE2O,upstream_gene_variant,,ENST00000587581,;UBE2O,non_coding_transcript_exon_variant,,ENST00000586409,;UBE2O,downstream_gene_variant,,ENST00000586505,;	A	ENSG00000175931	ENST00000319380	Transcript	missense_variant	1288	1223	408	R/L	cGg/cTg	rs149178826	.	.	-1	UBE2O	HGNC	29554	protein_coding	YES	CCDS32742.1	ENSP00000323687	UBE2O_HUMAN	.	UPI000020032F	.	tolerated(0.3)	benign(0.03)	9/18	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCCCGGGAA	byCluster	5	ESCA
TP53	0	.	GRCh37	17	7577124	7577124	+	Missense_Mutation	SNP	C	C	T	rs121912657	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814G>A	p.Val272Met	p.V272M	ENST00000269305	8/11	28	19	9	39	39	0	TP53,missense_variant,p.Val272Met,ENST00000420246,;TP53,missense_variant,p.Val272Met,ENST00000269305,;TP53,missense_variant,p.Val140Met,ENST00000509690,;TP53,missense_variant,p.Val272Met,ENST00000359597,;TP53,missense_variant,p.Val272Met,ENST00000445888,;TP53,missense_variant,p.Val272Met,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1004	814	272	V/M	Gtg/Atg	CM920676,rs121912657,TP53_g.13794G>T,TP53_g.13794del,TP53_g.13794G>C,TP53_g.13794G>A,COSM10859,COSM10891,COSM13421,COSM45898,COSM99950,COSM212313,COSM1177737,COSM3388172,COSM3773300,COSM1645249,COSM2744536	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.997)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	uncertain_significance,pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.V272M|c.814G>A|11,SITE|p.V272M|c.814G>A|84,SITE|p.V272M|c.814G>A|6,SITE|p.V272M|c.814G>A|22,CODON|p.0?|c.1_1182del1182|6,CODON|p.V272E|c.815T>A|9,CODON|p.V272G|c.815T>G|7,CODON|p.V272A|c.815T>C|7,CODON|p.V272fs*73|c.814delG|3,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273L|c.818G>T|98,BUFFER|p.R273P|c.818G>C|4,BUFFER|p.R273H|c.818G>A|116,BUFFER|p.R273H|c.818G>A|64,BUFFER|p.R273H|c.818G>A|588,BUFFER|p.R273L|c.818G>T|5,BUFFER|p.R273H|c.818G>A|83,BUFFER|p.R273P|c.818G>C|29,BUFFER|p.R273L|c.818G>T|18,BUFFER|p.R273L|c.818G>T|12,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3,BUFFER|p.E271Q|c.811G>C|4,BUFFER|p.E271K|c.811G>A|35,BUFFER|p.E271*|c.811G>T|16,BUFFER|p.E271*|c.811G>T|3,BUFFER|p.E271K|c.811G>A|13,BUFFER|p.E271K|c.811G>A|4,BUFFER|p.E271K|c.811G>A|8,BUFFER|p.F270L|c.810T>G|4,BUFFER|p.F270L|c.810T>A|5,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270Y|c.809T>A|5,BUFFER|p.F270C|c.809T>G|16,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270S|c.809T>C|14,BUFFER|p.F270S|c.809T>C|6,BUFFER|p.F270L|c.808T>C|16,BUFFER|p.F270I|c.808T>A|3,BUFFER|p.F270V|c.808T>G|8,BUFFER|p.F270L|c.808T>C|3,BUFFER|p.F270I|c.808T>A|6,BUFFER|p.S269S|c.807C>T|3,BUFFER|p.S269N|c.806G>A|4,BUFFER|p.S269C|c.805A>T|4,BUFFER|p.S269G|c.805A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCACCTCAA	byFrequency|byCluster	5	ESCA
TP53	0	.	GRCh37	17	7578410	7578410	+	Missense_Mutation	SNP	T	T	A	.	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	5/11	23	15	8	57	57	0	TP53,missense_variant,p.Arg174Trp,ENST00000413465,;TP53,missense_variant,p.Arg174Trp,ENST00000420246,;TP53,missense_variant,p.Arg174Trp,ENST00000269305,;TP53,missense_variant,p.Arg42Trp,ENST00000509690,;TP53,missense_variant,p.Arg174Trp,ENST00000359597,;TP53,missense_variant,p.Arg81Trp,ENST00000514944,;TP53,missense_variant,p.Arg174Trp,ENST00000445888,;TP53,missense_variant,p.Arg174Trp,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	710	520	174	R/W	Agg/Tgg	CM942119,TP53_g.12508del,TP53_g.12508A>G,TP53_g.12508A>T,TP53_g.12508A>C,COSM44782,COSM43763,COSM45316,COSM131454,COSM131455,COSM131457,COSM3773316,COSM3773315,COSM131456	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.997)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R174W|c.520A>T|11,CODON|p.0?|c.1_1182del1182|6,CODON|p.R174K|c.521G>A|5,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.P177_C182delPHHERC|c.526_543del18|3,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175L|c.524G>T|20,BUFFER|p.R175H|c.524G>A|181,BUFFER|p.R175P|c.524G>C|6,BUFFER|p.R43H|c.128G>A|183,BUFFER|p.R82H|c.245G>A|183,BUFFER|p.R175H|c.524G>A|124,BUFFER|p.R175L|c.524G>T|3,BUFFER|p.R175L|c.524G>T|3,BUFFER|p.R175H|c.524G>A|180,BUFFER|p.R175H|c.524G>A|926,BUFFER|p.R175L|c.524G>T|3,BUFFER|p.R175H|c.524G>A|88,BUFFER|p.R43L|c.128G>T|3,BUFFER|p.R82L|c.245G>T|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R82G|c.244C>G|5,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43G|c.127C>G|8,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R175G|c.523C>G|5,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175G|c.523C>G|16,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V172D|c.515T>A|11,BUFFER|p.V172A|c.515T>C|4,BUFFER|p.V172G|c.515T>G|4,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.E171G|c.512A>G|3,BUFFER|p.E78*|c.232G>T|4,BUFFER|p.E171*|c.511G>T|4,BUFFER|p.E171Q|c.511G>C|4,BUFFER|p.E39*|c.115G>T|4,BUFFER|p.E171*|c.511G>T|13,BUFFER|p.E171*|c.511G>T|4,BUFFER|p.E171K|c.511G>A|9,BUFFER|p.T170T|c.510G>A|6,BUFFER|p.T170M|c.509C>T|7	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCCTCACAA	.	5	ESCA
TMEM235	0	.	GRCh37	17	76227867	76227868	+	5'Flank	INS	-	-	CTTC	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000551068	.	41	25	16	83	83	0	TMEM235,frameshift_variant,p.Ser107PhefsTer145,ENST00000421688,;TMEM235,5_prime_UTR_variant,,ENST00000586400,;TMEM235,5_prime_UTR_variant,,ENST00000374946,;TMEM235,upstream_gene_variant,,ENST00000591033,;TMEM235,upstream_gene_variant,,ENST00000550981,;TMEM235,upstream_gene_variant,,ENST00000551068,;	CTTC	ENSG00000204278	ENST00000551068	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	116	1	TMEM235	HGNC	27563	protein_coding	YES	CCDS56046.1	ENSP00000446514	TM235_HUMAN	.	UPI0000251E19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTCGACTTCC	.	3	ESCA
ZNF750	0	.	GRCh37	17	80789490	80789490	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841C>T	p.Pro281Ser	p.P281S	ENST00000269394	2/3	74	38	36	142	142	0	ZNF750,missense_variant,p.Pro281Ser,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	A	ENSG00000141579	ENST00000269394	Transcript	missense_variant	1675	841	281	P/S	Ccg/Tcg	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	deleterious(0)	benign(0.003)	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCGGGTCTT	.	5	ESCA
APCDD1	0	.	GRCh37	18	10487902	10487902	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1412C>T	p.Pro471Leu	p.P471L	ENST00000355285	5/5	31	20	11	51	51	0	APCDD1,missense_variant,p.Pro471Leu,ENST00000355285,;APCDD1,downstream_gene_variant,,ENST00000578882,;APCDD1,downstream_gene_variant,,ENST00000579685,;APCDD1,downstream_gene_variant,,ENST00000582723,;APCDD1,downstream_gene_variant,,ENST00000423585,;	T	ENSG00000154856	ENST00000355285	Transcript	missense_variant	1766	1412	471	P/L	cCg/cTg	.	.	.	1	APCDD1	HGNC	15718	protein_coding	YES	CCDS11849.1	ENSP00000347433	APCD1_HUMAN	.	UPI000000D766	.	tolerated(0.11)	benign(0.01)	5/5	.	hmmpanther:PTHR31021,hmmpanther:PTHR31021:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGCCGAGGG	.	5	ESCA
PTPN2	0	.	GRCh37	18	12825906	12825906	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398A>T	p.Glu133Val	p.E133V	ENST00000309660	5/9	35	30	5	63	63	0	PTPN2,missense_variant,p.Glu34Val,ENST00000592059,;PTPN2,missense_variant,p.Glu133Val,ENST00000309660,;PTPN2,missense_variant,p.Glu133Val,ENST00000327283,;PTPN2,missense_variant,p.Glu104Val,ENST00000591497,;PTPN2,missense_variant,p.Glu133Val,ENST00000591115,;PTPN2,missense_variant,p.Glu133Val,ENST00000353319,;PTPN2,intron_variant,,ENST00000587703,;PTPN2,missense_variant,p.Glu133Val,ENST00000592776,;PTPN2,3_prime_UTR_variant,,ENST00000589216,;PTPN2,intron_variant,,ENST00000591305,;	A	ENSG00000175354	ENST00000309660	Transcript	missense_variant	492	398	133	E/V	gAg/gTg	.	.	.	-1	PTPN2	HGNC	9650	protein_coding	YES	CCDS11865.1	ENSP00000311857	PTN2_HUMAN	K7ER87_HUMAN,D3DUJ3_HUMAN	UPI000017284E	.	tolerated(0.09)	benign(0.007)	5/9	.	Superfamily_domains:SSF52799,PIRSF_domain:PIRSF000926,SMART_domains:SM00194,Gene3D:3.90.190.10,Pfam_domain:PF00102,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF200,PROSITE_profiles:PS50055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATCTCTTGG	.	4	ESCA
HDHD2	0	.	GRCh37	18	44634276	44634276	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*777A>G	.	.	ENST00000300605	7/7	43	38	5	90	90	0	HDHD2,3_prime_UTR_variant,,ENST00000300605,;RP11-49K24.8,non_coding_transcript_exon_variant,,ENST00000591183,;HDHD2,downstream_gene_variant,,ENST00000587841,;HDHD2,3_prime_UTR_variant,,ENST00000588183,;HDHD2,non_coding_transcript_exon_variant,,ENST00000588861,;	C	ENSG00000167220	ENST00000300605	Transcript	3_prime_UTR_variant	1710	.	.	.	.	.	.	.	-1	HDHD2	HGNC	25364	protein_coding	YES	CCDS32829.1	ENSP00000300605	HDHD2_HUMAN	K7ER15_HUMAN,K7EQD2_HUMAN	UPI0000037B93	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTCCTGTTAA	.	4	ESCA
FBXO15	0	.	GRCh37	18	71740731	71740731	+	Missense_Mutation	SNP	C	C	T	rs748658162	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498G>A	p.Ala500Thr	p.A500T	ENST00000419743	10/10	25	20	4	63	63	0	FBXO15,missense_variant,p.Ala500Thr,ENST00000419743,;FBXO15,missense_variant,p.Ala424Thr,ENST00000269500,;FBXO15,3_prime_UTR_variant,,ENST00000580088,;FBXO15,non_coding_transcript_exon_variant,,ENST00000580806,;FBXO15,non_coding_transcript_exon_variant,,ENST00000577575,;FBXO15,downstream_gene_variant,,ENST00000579108,;FBXO15,3_prime_UTR_variant,,ENST00000583443,;FBXO15,3_prime_UTR_variant,,ENST00000578399,;FBXO15,3_prime_UTR_variant,,ENST00000581214,;FBXO15,non_coding_transcript_exon_variant,,ENST00000584425,;	T	ENSG00000141665	ENST00000419743	Transcript	missense_variant	1578	1498	500	A/T	Gca/Aca	rs748658162,COSM195038	.	.	-1	FBXO15	HGNC	13617	protein_coding	YES	CCDS45884.1	ENSP00000393154	FBX15_HUMAN	J3QRE7_HUMAN	UPI00003CF23D	.	tolerated(0.4)	benign(0.054)	10/10	.	hmmpanther:PTHR20995:SF16,hmmpanther:PTHR20995	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTGCGATAC	.	4	ESCA
AC139100.2	0	.	GRCh37	18	77906059	77906059	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18G>C	p.%3D	p.L6L	ENST00000586421	1/3	25	17	7	46	46	0	AC139100.2,synonymous_variant,p.%3D,ENST00000585422,;AC139100.2,synonymous_variant,p.%3D,ENST00000586421,;AC139100.2,synonymous_variant,p.%3D,ENST00000588226,;AC139100.2,synonymous_variant,p.%3D,ENST00000587254,;AC139100.2,synonymous_variant,p.%3D,ENST00000589574,;ADNP2,downstream_gene_variant,,ENST00000561195,;	C	ENSG00000267270	ENST00000586421	Transcript	synonymous_variant	252	18	6	L	ctG/ctC	.	.	.	1	AC139100.2	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000467155	.	K7ENZ4_HUMAN	UPI000195170D	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCTGAGCTC	.	5	ESCA
ZNF626	0	.	GRCh37	19	20808428	20808428	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255T>G	p.%3D	p.L85L	ENST00000601440	4/4	41	27	13	110	110	0	ZNF626,synonymous_variant,p.%3D,ENST00000601440,;ZNF626,synonymous_variant,p.%3D,ENST00000595405,;CTC-513N18.7,intron_variant,,ENST00000595094,;	C	ENSG00000188171	ENST00000601440	Transcript	synonymous_variant	402	255	85	L	ctT/ctG	.	.	.	-1	ZNF626	HGNC	30461	protein_coding	YES	CCDS42535.1	ENSP00000469958	ZN626_HUMAN	M0QY39_HUMAN,I0CMK8_HUMAN	UPI000035E843	.	.	.	4/4	.	hmmpanther:PTHR24384:SF105,hmmpanther:PTHR24384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCAAAGGTC	.	5	ESCA
ZNF585B	0	.	GRCh37	19	37677429	37677429	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1010A>G	p.Asn337Ser	p.N337S	ENST00000532828	5/5	28	16	12	79	79	0	ZNF585B,missense_variant,p.Asn282Ser,ENST00000531805,;ZNF585B,missense_variant,p.Asn337Ser,ENST00000532828,;ZNF585B,5_prime_UTR_variant,,ENST00000312908,;ZNF585B,3_prime_UTR_variant,,ENST00000527838,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF585B,downstream_gene_variant,,ENST00000586320,;ZNF585B,downstream_gene_variant,,ENST00000591492,;CTC-454I21.3,intron_variant,,ENST00000585860,;CTC-454I21.3,intron_variant,,ENST00000590245,;ZNF585B,downstream_gene_variant,,ENST00000591273,;ZNF585B,downstream_gene_variant,,ENST00000392156,;ZNF585B,downstream_gene_variant,,ENST00000526705,;	C	ENSG00000245680	ENST00000532828	Transcript	missense_variant	1262	1010	337	N/S	aAt/aGt	.	.	.	-1	ZNF585B	HGNC	30948	protein_coding	YES	CCDS12500.1	ENSP00000433773	Z585B_HUMAN	E9PQH3_HUMAN,B3KRH5_HUMAN	UPI00001AF01B	.	tolerated(0.5)	benign(0.005)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF105,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTATTGCTG	.	5	ESCA
FBXO17	0	.	GRCh37	19	39443225	39443225	+	Intron	SNP	G	G	A	rs373927011	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-17-2249C>T	.	.	ENST00000292852	.	17	12	5	49	49	0	FBXO17,5_prime_UTR_variant,,ENST00000595329,;FBXO17,intron_variant,,ENST00000292852,;SARS2,upstream_gene_variant,,ENST00000448145,;CTC-360G5.8,upstream_gene_variant,,ENST00000599996,;FBXO17,upstream_gene_variant,,ENST00000599598,;FBXO17,intron_variant,,ENST00000596025,;FBXO17,upstream_gene_variant,,ENST00000601394,;	A	ENSG00000269190	ENST00000292852	Transcript	intron_variant	.	.	.	.	.	rs373927011	.	.	-1	FBXO17	HGNC	18754	protein_coding	YES	CCDS12526.1	ENSP00000292852	FBX17_HUMAN	.	UPI000012ADC1	.	.	.	.	1/5	.	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGCGTCATC	byFrequency|byCluster	5	ESCA
BCAT2	0	.	GRCh37	19	49299887	49299887	+	Missense_Mutation	SNP	G	G	A	rs772311929	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1013C>T	p.Ser338Leu	p.S338L	ENST00000316273	9/11	45	34	11	103	103	0	BCAT2,missense_variant,p.Ser298Leu,ENST00000402551,;BCAT2,missense_variant,p.Ser298Leu,ENST00000597011,;BCAT2,missense_variant,p.Ser246Leu,ENST00000599246,;BCAT2,missense_variant,p.Ser338Leu,ENST00000316273,;BCAT2,missense_variant,p.Ser338Leu,ENST00000598162,;BCAT2,missense_variant,p.Ser330Leu,ENST00000593515,;BCAT2,missense_variant,p.Ser246Leu,ENST00000545387,;BCAT2,downstream_gene_variant,,ENST00000601681,;RNU6-317P,upstream_gene_variant,,ENST00000384031,;BCAT2,non_coding_transcript_exon_variant,,ENST00000599510,;BCAT2,downstream_gene_variant,,ENST00000595376,;	A	ENSG00000105552	ENST00000316273	Transcript	missense_variant	1026	1013	338	S/L	tCg/tTg	rs772311929	.	.	-1	BCAT2	HGNC	977	protein_coding	YES	CCDS12735.1	ENSP00000322991	BCAT2_HUMAN	M0R2K7_HUMAN,B3KSI3_HUMAN	UPI00001267CC	.	deleterious(0)	probably_damaging(0.961)	9/11	.	Superfamily_domains:SSF56752,PIRSF_domain:PIRSF006468,TIGRFAM_domain:TIGR01123,Pfam_domain:PF01063,Gene3D:3.20.10.10,hmmpanther:PTHR11825:SF2,hmmpanther:PTHR11825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGCCCGAGCCA	byFrequency	4	ESCA
KLK12	0	.	GRCh37	19	51537306	51537306	+	Missense_Mutation	SNP	T	T	G	rs747067935	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.127A>C	p.Thr43Pro	p.T43P	ENST00000250351	3/7	53	29	23	102	101	1	KLK12,missense_variant,p.Thr43Pro,ENST00000529888,;KLK12,missense_variant,p.Thr43Pro,ENST00000250351,;KLK12,missense_variant,p.Thr43Pro,ENST00000525263,;KLK12,missense_variant,p.Thr43Pro,ENST00000319590,;KLK12,synonymous_variant,p.%3D,ENST00000250352,;CTC-518B2.9,non_coding_transcript_exon_variant,,ENST00000594910,;KLK12,missense_variant,p.Thr43Pro,ENST00000531374,;KLK12,3_prime_UTR_variant,,ENST00000530943,;KLK12,3_prime_UTR_variant,,ENST00000526824,;	G	ENSG00000186474	ENST00000250351	Transcript	missense_variant	244	127	43	T/P	Acc/Ccc	rs747067935	.	.	-1	KLK12	HGNC	6360	protein_coding	YES	CCDS12820.1	ENSP00000250351	KLK12_HUMAN	.	UPI000002ACDD	.	tolerated(0.3)	possibly_damaging(0.452)	3/7	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24275,hmmpanther:PTHR24275:SF21,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGTGCCCT	byFrequency	5	ESCA
AC018755.1	0	.	GRCh37	19	52096164	52096164	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514C>A	p.Pro172Thr	p.P172T	ENST00000301439	2/2	50	24	26	95	95	0	AC018755.1,missense_variant,p.Pro172Thr,ENST00000301439,;ZNF175,downstream_gene_variant,,ENST00000436511,;ZNF175,downstream_gene_variant,,ENST00000262259,;AC018755.16,upstream_gene_variant,,ENST00000598755,;	T	ENSG00000167765	ENST00000301439	Transcript	missense_variant	570	514	172	P/T	Cct/Act	.	.	.	-1	AC018755.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000301439	.	Q96NP5_HUMAN	UPI00000721AE	.	.	possibly_damaging(0.803)	2/2	.	hmmpanther:PTHR19300,hmmpanther:PTHR19300:SF35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGGCTTGG	.	5	ESCA
MIR518F	0	.	GRCh37	19	54203326	54203326	+	RNA	SNP	C	C	A	rs557837040	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.58C>A	.	.	ENST00000384973	1/1	95	79	16	145	145	0	MIR518F,non_coding_transcript_exon_variant,,ENST00000384973,;MIR525,downstream_gene_variant,,ENST00000384978,;MIR518B,upstream_gene_variant,,ENST00000385127,;MIR520B,upstream_gene_variant,,ENST00000384989,;MIR523,downstream_gene_variant,,ENST00000385281,;MIR519B,downstream_gene_variant,,ENST00000385090,;	A	ENSG00000207706	ENST00000384973	Transcript	non_coding_transcript_exon_variant	58	.	.	.	.	rs557837040	.	.	1	MIR518F	HGNC	32104	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGCGCTTC	by1000G	5	ESCA
ZSCAN5B	0	.	GRCh37	19	56701233	56701233	+	Missense_Mutation	SNP	C	C	T	rs185491243	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1451G>A	p.Arg484His	p.R484H	ENST00000586855	5/5	51	39	12	109	109	0	ZSCAN5B,missense_variant,p.Arg484His,ENST00000586855,;ZSCAN5B,missense_variant,p.Arg484His,ENST00000358992,;ZSCAN5B,downstream_gene_variant,,ENST00000587032,;GALP,downstream_gene_variant,,ENST00000440823,;GALP,downstream_gene_variant,,ENST00000357330,;ZSCAN5B,downstream_gene_variant,,ENST00000589938,;	T	ENSG00000197213	ENST00000586855	Transcript	missense_variant	1765	1451	484	R/H	cGt/cAt	rs185491243	.	.	-1	ZSCAN5B	HGNC	34246	protein_coding	YES	CCDS46203.1	ENSP00000466072	ZSA5B_HUMAN	K7ESD3_HUMAN,K7EJD1_HUMAN	UPI000059D7BA	.	tolerated(0.07)	possibly_damaging(0.685)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF163,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	T:0.0002	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGACGCTTG	byCluster|by1000G	5	ESCA
FBXL12	0	.	GRCh37	19	9929491	9929491	+	5'UTR	SNP	A	A	G	rs764094932	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2T>C	.	.	ENST00000247977	1/3	40	34	6	84	84	0	FBXL12,5_prime_UTR_variant,,ENST00000586073,;FBXL12,5_prime_UTR_variant,,ENST00000588922,;FBXL12,5_prime_UTR_variant,,ENST00000586469,;FBXL12,5_prime_UTR_variant,,ENST00000592067,;FBXL12,5_prime_UTR_variant,,ENST00000589626,;FBXL12,5_prime_UTR_variant,,ENST00000247977,;FBXL12,5_prime_UTR_variant,,ENST00000586651,;FBXL12,intron_variant,,ENST00000590277,;FBXL12,intron_variant,,ENST00000585379,;SNORA70,upstream_gene_variant,,ENST00000363367,;AC008752.1,upstream_gene_variant,,ENST00000401283,;FBXL12,5_prime_UTR_variant,,ENST00000590808,;FBXL12,upstream_gene_variant,,ENST00000592732,;FBXL12,upstream_gene_variant,,ENST00000589438,;RPL10P15,upstream_gene_variant,,ENST00000585756,;	G	ENSG00000127452	ENST00000247977	Transcript	5_prime_UTR_variant	241	.	.	.	.	rs764094932	.	.	-1	FBXL12	HGNC	13611	protein_coding	YES	CCDS12218.1	ENSP00000247977	FXL12_HUMAN	K7EPN7_HUMAN,K7ELM5_HUMAN	UPI000006EBD0	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGATCCCG	.	5	ESCA
AHCYL1	0	.	GRCh37	1	110565757	110565757	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1455C>A	.	.	ENST00000369799	17/17	29	22	6	44	44	0	AHCYL1,3_prime_UTR_variant,,ENST00000369799,;AHCYL1,downstream_gene_variant,,ENST00000393614,;AHCYL1,downstream_gene_variant,,ENST00000359172,;AHCYL1,downstream_gene_variant,,ENST00000481423,;AHCYL1,downstream_gene_variant,,ENST00000469401,;	A	ENSG00000168710	ENST00000369799	Transcript	3_prime_UTR_variant	3415	.	.	.	.	.	.	.	1	AHCYL1	HGNC	344	protein_coding	YES	CCDS818.1	ENSP00000358814	SAHH2_HUMAN	Q9BTL0_HUMAN	UPI00000022AC	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGTCATACG	.	4	ESCA
RBM15	0	.	GRCh37	1	110883406	110883406	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1379G>C	p.Gly460Ala	p.G460A	ENST00000369784	1/3	20	17	3	44	44	0	RBM15,missense_variant,p.Gly460Ala,ENST00000602849,;RBM15,missense_variant,p.Gly460Ala,ENST00000369784,;RBM15,missense_variant,p.Gly460Ala,ENST00000487146,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,;	C	ENSG00000162775	ENST00000369784	Transcript	missense_variant	2279	1379	460	G/A	gGa/gCa	.	.	.	1	RBM15	HGNC	14959	protein_coding	YES	CCDS822.1	ENSP00000358799	RBM15_HUMAN	.	UPI000013E1C5	.	deleterious(0)	probably_damaging(0.999)	1/3	.	PROSITE_profiles:PS50102,hmmpanther:PTHR23189:SF43,hmmpanther:PTHR23189,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGGGAGGCC	.	2	ESCA
CCNL2	0	.	GRCh37	1	1330816	1330816	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552C>G	p.%3D	p.L184L	ENST00000400809	4/11	45	37	8	66	65	0	CCNL2,synonymous_variant,p.%3D,ENST00000400809,;CCNL2,synonymous_variant,p.%3D,ENST00000408918,;CCNL2,5_prime_UTR_variant,,ENST00000408952,;RP4-758J18.2,upstream_gene_variant,,ENST00000444362,;RP4-758J18.2,upstream_gene_variant,,ENST00000570344,;RP4-758J18.2,upstream_gene_variant,,ENST00000448629,;CCNL2,downstream_gene_variant,,ENST00000497013,;RP4-758J18.2,upstream_gene_variant,,ENST00000576232,;CCNL2,non_coding_transcript_exon_variant,,ENST00000471930,;CCNL2,upstream_gene_variant,,ENST00000505849,;CCNL2,upstream_gene_variant,,ENST00000469113,;RP4-758J18.2,upstream_gene_variant,,ENST00000453521,;CCNL2,synonymous_variant,p.%3D,ENST00000481223,;CCNL2,synonymous_variant,p.%3D,ENST00000488340,;CCNL2,3_prime_UTR_variant,,ENST00000482621,;CCNL2,3_prime_UTR_variant,,ENST00000425598,;CCNL2,non_coding_transcript_exon_variant,,ENST00000463895,;CCNL2,non_coding_transcript_exon_variant,,ENST00000473872,;CCNL2,non_coding_transcript_exon_variant,,ENST00000496007,;RP4-758J18.2,upstream_gene_variant,,ENST00000572242,;CCNL2,upstream_gene_variant,,ENST00000480479,;RP4-758J18.2,upstream_gene_variant,,ENST00000418833,;CCNL2,upstream_gene_variant,,ENST00000418865,;CCNL2,upstream_gene_variant,,ENST00000480646,;RP4-758J18.2,upstream_gene_variant,,ENST00000447725,;CCNL2,upstream_gene_variant,,ENST00000482365,;CCNL2,upstream_gene_variant,,ENST00000492998,;	C	ENSG00000221978	ENST00000400809	Transcript	synonymous_variant	558	552	184	L	ctC/ctG	.	.	.	-1	CCNL2	HGNC	20570	protein_coding	YES	CCDS30557.1	ENSP00000383611	CCNL2_HUMAN	J3QSH2_HUMAN,B4DE38_HUMAN	UPI00000713F5	.	.	.	4/11	.	Superfamily_domains:SSF47954,SMART_domains:SM00385,PIRSF_domain:PIRSF036580,Pfam_domain:PF00134,Gene3D:1.10.472.10,hmmpanther:PTHR10026:SF45,hmmpanther:PTHR10026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTGAGAAC	.	5	ESCA
BCL9	0	.	GRCh37	1	147091533	147091533	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1572A>G	p.%3D	p.E524E	ENST00000234739	8/10	30	18	12	63	63	0	BCL9,synonymous_variant,p.%3D,ENST00000234739,;BCL9,downstream_gene_variant,,ENST00000473292,;	G	ENSG00000116128	ENST00000234739	Transcript	synonymous_variant	2312	1572	524	E	gaA/gaG	.	.	.	1	BCL9	HGNC	1008	protein_coding	YES	CCDS30833.1	ENSP00000234739	BCL9_HUMAN	.	UPI000013C9B9	.	.	.	8/10	.	hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGAAGGCTG	.	5	ESCA
S100A7	0	.	GRCh37	1	153433102	153433102	+	5'UTR	SNP	C	C	G	rs563241840	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-36G>C	.	.	ENST00000368723	1/3	26	12	13	40	40	0	S100A7,5_prime_UTR_variant,,ENST00000368723,;S100A7,upstream_gene_variant,,ENST00000368722,;	G	ENSG00000143556	ENST00000368723	Transcript	5_prime_UTR_variant	76	.	.	.	.	rs563241840	.	.	-1	S100A7	HGNC	10497	protein_coding	YES	CCDS1039.1	ENSP00000357712	S10A7_HUMAN	.	UPI000013D90F	.	.	.	1/3	.	.	T:0.0008	T:0	T:0	.	T:0	T:0	T:0.0041	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCACGAGTA	byFrequency|by1000G	5	ESCA
ARHGEF2	0	.	GRCh37	1	155920753	155920753	+	Missense_Mutation	SNP	C	C	T	rs533748068	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2570G>A	p.Arg857Gln	p.R857Q	ENST00000361247	20/22	9	6	3	20	20	0	ARHGEF2,missense_variant,p.Arg857Gln,ENST00000361247,;ARHGEF2,missense_variant,p.Arg858Gln,ENST00000368315,;ARHGEF2,missense_variant,p.Arg829Gln,ENST00000313695,;ARHGEF2,missense_variant,p.Arg829Gln,ENST00000368316,;ARHGEF2,missense_variant,p.Arg856Gln,ENST00000313667,;ARHGEF2,missense_variant,p.Arg902Gln,ENST00000462460,;ARHGEF2,missense_variant,p.Arg124Gln,ENST00000470541,;ARHGEF2,intron_variant,,ENST00000477754,;ARHGEF2,downstream_gene_variant,,ENST00000474428,;ARHGEF2,downstream_gene_variant,,ENST00000470975,;	T	ENSG00000116584	ENST00000361247	Transcript	missense_variant	2670	2570	857	R/Q	cGa/cAa	rs533748068	.	.	-1	ARHGEF2	HGNC	682	protein_coding	YES	CCDS53376.1	ENSP00000354837	ARHG2_HUMAN	.	UPI000045892C	.	tolerated(0.23)	benign(0.141)	20/22	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF14	T:0.0004	T:0	T:0	.	T:0.001	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCGAGCC	byFrequency|by1000G	2	ESCA
IGSF9	0	.	GRCh37	1	159904038	159904038	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1046A>G	p.Asn349Ser	p.N349S	ENST00000368094	9/21	34	21	12	52	52	0	IGSF9,missense_variant,p.Asn349Ser,ENST00000368094,;IGSF9,missense_variant,p.Asn333Ser,ENST00000361509,;IGSF9,non_coding_transcript_exon_variant,,ENST00000476102,;IGSF9,upstream_gene_variant,,ENST00000493195,;IGSF9,upstream_gene_variant,,ENST00000496645,;	C	ENSG00000085552	ENST00000368094	Transcript	missense_variant	1244	1046	349	N/S	aAc/aGc	.	.	.	-1	IGSF9	HGNC	18132	protein_coding	YES	CCDS44254.1	ENSP00000357073	TUTLA_HUMAN	Q6XYD8_HUMAN	UPI000004A10B	.	deleterious(0.02)	benign(0.008)	9/21	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF534,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGTTGGCA	.	5	ESCA
CDK11A	0	.	GRCh37	1	1635409	1635409	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1795-30C>A	.	.	ENST00000404249	.	92	73	19	168	168	0	CDK11A,intron_variant,,ENST00000356200,;CDK11A,intron_variant,,ENST00000404249,;CDK11A,intron_variant,,ENST00000358779,;CDK11A,intron_variant,,ENST00000378633,;CDK11A,intron_variant,,ENST00000357760,;CDK11A,intron_variant,,ENST00000378638,;CDK11A,downstream_gene_variant,,ENST00000378635,;RP1-283E3.8,non_coding_transcript_exon_variant,,ENST00000598846,;CDK11A,non_coding_transcript_exon_variant,,ENST00000495016,;CDK11A,non_coding_transcript_exon_variant,,ENST00000468397,;CDK11A,intron_variant,,ENST00000509982,;CDK11A,intron_variant,,ENST00000460465,;CDK11A,intron_variant,,ENST00000491311,;CDK11A,intron_variant,,ENST00000463652,;CDK11A,intron_variant,,ENST00000356937,;CDK11A,intron_variant,,ENST00000478901,;CDK11A,downstream_gene_variant,,ENST00000492390,;CDK11A,downstream_gene_variant,,ENST00000468800,;CDK11A,downstream_gene_variant,,ENST00000464748,;CDK11A,downstream_gene_variant,,ENST00000474916,;CDK11A,downstream_gene_variant,,ENST00000489300,;MMP23A,downstream_gene_variant,,ENST00000412810,;MMP23A,downstream_gene_variant,,ENST00000234610,;	T	ENSG00000008128	ENST00000404249	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CDK11A	HGNC	1730	protein_coding	YES	CCDS44042.1	ENSP00000384442	CD11A_HUMAN	Q5QPQ9_HUMAN,Q4VBY6_HUMAN	UPI000022B1E1	.	.	.	.	16/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGGCCAGT	.	5	ESCA
POU2F1	0	.	GRCh37	1	167343528	167343528	+	Missense_Mutation	SNP	G	G	C	rs771777271	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586G>C	p.Ala196Pro	p.A196P	ENST00000367866	6/16	23	18	5	52	52	0	POU2F1,missense_variant,p.Ala173Pro,ENST00000420254,;POU2F1,missense_variant,p.Ala81Pro,ENST00000443275,;POU2F1,missense_variant,p.Ala185Pro,ENST00000367862,;POU2F1,missense_variant,p.Ala196Pro,ENST00000367866,;POU2F1,missense_variant,p.Ala173Pro,ENST00000452019,;POU2F1,missense_variant,p.Ala173Pro,ENST00000541643,;POU2F1,intron_variant,,ENST00000429375,;RP11-52A20.2,upstream_gene_variant,,ENST00000607611,;POU2F1,non_coding_transcript_exon_variant,,ENST00000492850,;POU2F1,non_coding_transcript_exon_variant,,ENST00000470928,;POU2F1,non_coding_transcript_exon_variant,,ENST00000367865,;POU2F1,downstream_gene_variant,,ENST00000557909,;POU2F1,3_prime_UTR_variant,,ENST00000560232,;POU2F1,3_prime_UTR_variant,,ENST00000271411,;POU2F1,non_coding_transcript_exon_variant,,ENST00000557874,;POU2F1,downstream_gene_variant,,ENST00000442313,;	C	ENSG00000143190	ENST00000367866	Transcript	missense_variant	655	586	196	A/P	Gca/Cca	rs771777271	.	.	1	POU2F1	HGNC	9212	protein_coding	YES	CCDS1259.2	ENSP00000356840	.	J3KP77_HUMAN	UPI0000EE3C74	.	deleterious(0)	unknown(0)	6/16	.	hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATCGCACAG	.	5	ESCA
GPR52	0	.	GRCh37	1	174417375	174417375	+	Missense_Mutation	SNP	C	C	G	rs145259584	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126C>G	p.Phe42Leu	p.F42L	ENST00000367685	1/1	43	35	7	57	57	0	GPR52,missense_variant,p.Phe42Leu,ENST00000367685,;RABGAP1L,intron_variant,,ENST00000357444,;RABGAP1L,intron_variant,,ENST00000367689,;RABGAP1L,intron_variant,,ENST00000251507,;RABGAP1L,intron_variant,,ENST00000526253,;RABGAP1L,intron_variant,,ENST00000367690,;	G	ENSG00000203737	ENST00000367685	Transcript	missense_variant	164	126	42	F/L	ttC/ttG	rs145259584	.	.	1	GPR52	HGNC	4508	protein_coding	YES	CCDS30941.1	ENSP00000356658	GPR52_HUMAN	F2YGU0_HUMAN	UPI0000153A3C	.	tolerated(1)	benign(0)	1/1	.	hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF248,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCGAGAC	byCluster	4	ESCA
HMCN1	0	.	GRCh37	1	185902946	185902946	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1818C>G	p.%3D	p.L606L	ENST00000271588	11/107	55	44	11	104	104	0	HMCN1,synonymous_variant,p.%3D,ENST00000367492,;HMCN1,synonymous_variant,p.%3D,ENST00000271588,;	G	ENSG00000143341	ENST00000271588	Transcript	synonymous_variant	2047	1818	606	L	ctC/ctG	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	.	11/107	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCACAGT	.	5	ESCA
CAMSAP2	0	.	GRCh37	1	200817688	200817688	+	Silent	SNP	T	T	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1791T>G	p.%3D	p.G597G	ENST00000358823	11/17	31	19	11	60	60	0	CAMSAP2,synonymous_variant,p.%3D,ENST00000413307,;CAMSAP2,synonymous_variant,p.%3D,ENST00000358823,;CAMSAP2,synonymous_variant,p.%3D,ENST00000236925,;CAMSAP2,intron_variant,,ENST00000447701,;	G	ENSG00000118200	ENST00000358823	Transcript	synonymous_variant	2061	1791	597	G	ggT/ggG	.	.	.	1	CAMSAP2	HGNC	29188	protein_coding	YES	CCDS1404.1	ENSP00000351684	CAMP2_HUMAN	.	UPI000020470D	.	.	.	11/17	.	hmmpanther:PTHR21595:SF1,hmmpanther:PTHR21595	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAAGGTGCCTT	.	4	ESCA
KDM5B	0	.	GRCh37	1	202742369	202742369	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453A>G	p.%3D	p.K151K	ENST00000367265	4/27	27	16	11	54	54	0	KDM5B,synonymous_variant,p.%3D,ENST00000367264,;KDM5B,synonymous_variant,p.%3D,ENST00000367265,;KDM5B,5_prime_UTR_variant,,ENST00000235790,;KDM5B,non_coding_transcript_exon_variant,,ENST00000470573,;KDM5B,downstream_gene_variant,,ENST00000467487,;KDM5B,3_prime_UTR_variant,,ENST00000602511,;	C	ENSG00000117139	ENST00000367265	Transcript	synonymous_variant	1618	453	151	K	aaA/aaG	.	.	.	-1	KDM5B	HGNC	18039	protein_coding	YES	CCDS30974.1	ENSP00000356234	KDM5B_HUMAN	Q9UIW7_HUMAN,Q9UFD3_HUMAN,Q9UFC7_HUMAN,Q9NSZ7_HUMAN,Q6UGB8_HUMAN,B3KV94_HUMAN,B3KMS8_HUMAN,B3KMS2_HUMAN	UPI0000032AA2	.	.	.	4/27	.	Superfamily_domains:SSF46774,SMART_domains:SM01014,SMART_domains:SM00501,Gene3D:1.10.150.60,Pfam_domain:PF01388,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF3,PROSITE_profiles:PS51011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCATTTTCT	.	5	ESCA
LIN9	0	.	GRCh37	1	226475472	226475476	+	Frame_Shift_Del	DEL	TGGTG	TGGTG	-	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	TGGTG	TGGTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.335_339delCACCA	p.Thr112ArgfsTer2	p.T112Rfs*2	ENST00000328205	5/15	65	57	7	82	82	0	LIN9,frameshift_variant,p.Thr72ArgfsTer2,ENST00000460719,;LIN9,frameshift_variant,p.Thr77ArgfsTer2,ENST00000481685,;LIN9,frameshift_variant,p.Thr112ArgfsTer2,ENST00000328205,;LIN9,frameshift_variant,p.Thr44ArgfsTer2,ENST00000359525,;LIN9,frameshift_variant,p.Thr167ArgfsTer2,ENST00000366808,;LIN9,frameshift_variant,p.Thr61ArgfsTer2,ENST00000366801,;	-	ENSG00000183814	ENST00000328205	Transcript	frameshift_variant	881-885	335-339	112-113	TP/X	aCACCA/a	.	.	.	-1	LIN9	HGNC	30830	protein_coding	YES	CCDS1553.1	ENSP00000329102	LIN9_HUMAN	B1B047_HUMAN	UPI00001B2F3C	.	.	.	5/15	.	hmmpanther:PTHR21689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTTATCTGGTGTTGAC	.	2	ESCA
ITPKB	0	.	GRCh37	1	226822416	226822416	+	Missense_Mutation	SNP	C	C	T	rs554325553	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2797G>A	p.Val933Ile	p.V933I	ENST00000429204	8/8	35	31	3	50	50	0	ITPKB,missense_variant,p.Val933Ile,ENST00000272117,;ITPKB,missense_variant,p.Val933Ile,ENST00000429204,;	T	ENSG00000143772	ENST00000429204	Transcript	missense_variant	3125	2797	933	V/I	Gtc/Atc	rs554325553,COSM904743,COSM904742	.	.	-1	ITPKB	HGNC	6179	protein_coding	YES	CCDS1555.1	ENSP00000411152	IP3KB_HUMAN	.	UPI000013D92B	.	tolerated(1)	benign(0)	8/8	.	hmmpanther:PTHR12400:SF4,hmmpanther:PTHR12400,Pfam_domain:PF03770,Superfamily_domains:SSF56104	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GTCGACGAGGT	by1000G	3	ESCA
SLC9A1	0	.	GRCh37	1	27425903	27425904	+	3'UTR	INS	-	-	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*894dupC	.	.	ENST00000263980	12/12	54	46	8	100	100	0	SLC9A1,3_prime_UTR_variant,,ENST00000263980,;SLC9A1,downstream_gene_variant,,ENST00000545949,;SLC9A1,non_coding_transcript_exon_variant,,ENST00000490329,;SLC9A1,non_coding_transcript_exon_variant,,ENST00000374089,;SLC9A1,downstream_gene_variant,,ENST00000447808,;	G	ENSG00000090020	ENST00000263980	Transcript	3_prime_UTR_variant	3918-3919	.	.	.	.	.	.	.	-1	SLC9A1	HGNC	11071	protein_coding	YES	CCDS295.1	ENSP00000263980	SL9A1_HUMAN	B4DTZ6_HUMAN,B1ALD5_HUMAN	UPI000012FD1B	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGACGTGGGGG	.	3	ESCA
PRDM16	0	.	GRCh37	1	3348663	3348663	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3655G>C	p.Glu1219Gln	p.E1219Q	ENST00000270722	16/17	20	15	5	32	32	0	PRDM16,missense_variant,p.Glu1218Gln,ENST00000441472,;PRDM16,missense_variant,p.Glu1027Gln,ENST00000509860,;PRDM16,missense_variant,p.Glu1219Gln,ENST00000270722,;PRDM16,missense_variant,p.Glu1218Gln,ENST00000442529,;PRDM16,missense_variant,p.Glu1219Gln,ENST00000378398,;PRDM16,missense_variant,p.Glu1219Gln,ENST00000378391,;PRDM16,intron_variant,,ENST00000514189,;PRDM16,intron_variant,,ENST00000511072,;PRDM16,non_coding_transcript_exon_variant,,ENST00000512462,;PRDM16,intron_variant,,ENST00000378389,;	C	ENSG00000142611	ENST00000270722	Transcript	missense_variant	3704	3655	1219	E/Q	Gag/Cag	.	.	.	1	PRDM16	HGNC	14000	protein_coding	YES	CCDS41236.2	ENSP00000270722	PRD16_HUMAN	.	UPI0000458A29	.	deleterious(0.01)	benign(0.323)	16/17	.	hmmpanther:PTHR24393:SF4,hmmpanther:PTHR24393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTGAGGCT	.	5	ESCA
KNCN	0	.	GRCh37	1	47015625	47015625	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.152-686C>A	.	.	ENST00000396314	.	20	14	6	35	35	0	KNCN,missense_variant,p.Asp67Glu,ENST00000481882,;KNCN,intron_variant,,ENST00000396314,;MKNK1-AS1,intron_variant,,ENST00000602433,;KNCN,upstream_gene_variant,,ENST00000524908,;KNCN,non_coding_transcript_exon_variant,,ENST00000294445,;	T	ENSG00000162456	ENST00000396314	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KNCN	HGNC	26488	protein_coding	YES	CCDS44133.1	ENSP00000379607	KNCN_HUMAN	.	UPI00015294E6	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGGTCCAG	.	5	ESCA
LRRC7	0	.	GRCh37	1	70484450	70484450	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1255C>A	p.Gln419Lys	p.Q419K	ENST00000035383	13/25	69	59	10	113	113	0	LRRC7,missense_variant,p.Gln419Lys,ENST00000035383,;LRRC7,missense_variant,p.Gln424Lys,ENST00000310961,;LRRC7,5_prime_UTR_variant,,ENST00000415775,;RP11-181B18.1,intron_variant,,ENST00000414132,;RP11-181B18.1,downstream_gene_variant,,ENST00000425754,;	A	ENSG00000033122	ENST00000035383	Transcript	missense_variant	1285	1255	419	Q/K	Caa/Aaa	.	.	.	1	LRRC7	HGNC	18531	protein_coding	YES	CCDS645.1	ENSP00000035383	LRRC7_HUMAN	.	UPI000006F29B	.	tolerated(0.75)	probably_damaging(0.93)	13/25	.	hmmpanther:PTHR23155:SF459,hmmpanther:PTHR23155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CAAAGCAAAGA	.	3	ESCA
NEGR1	0	.	GRCh37	1	71869644	71869644	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3485G>T	.	.	ENST00000357731	7/7	75	63	11	146	146	0	NEGR1,3_prime_UTR_variant,,ENST00000306821,;NEGR1,3_prime_UTR_variant,,ENST00000357731,;NEGR1,downstream_gene_variant,,ENST00000434200,;ZRANB2-AS2,intron_variant,,ENST00000583678,;ZRANB2-AS2,intron_variant,,ENST00000594152,;ZRANB2-AS2,intron_variant,,ENST00000600103,;ZRANB2-AS2,intron_variant,,ENST00000599146,;ZRANB2-AS2,intron_variant,,ENST00000430605,;ZRANB2-AS2,intron_variant,,ENST00000608579,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585499,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587306,;ZRANB2-AS2,upstream_gene_variant,,ENST00000586006,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587066,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585415,;ZRANB2-AS2,upstream_gene_variant,,ENST00000590186,;NEGR1,downstream_gene_variant,,ENST00000474357,;	A	ENSG00000172260	ENST00000357731	Transcript	3_prime_UTR_variant	4790	.	.	.	.	.	.	.	-1	NEGR1	HGNC	17302	protein_coding	YES	CCDS661.1	ENSP00000350364	NEGR1_HUMAN	Q8N440_HUMAN,Q68DZ8_HUMAN	UPI00000477EE	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GACCTCTTTTT	.	3	ESCA
GBP1	0	.	GRCh37	1	89521730	89521730	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1337delA	p.Lys446SerfsTer20	p.K446Sfs*20	ENST00000370473	8/11	205	162	43	228	228	0	GBP1,frameshift_variant,p.Lys446SerfsTer20,ENST00000370473,;GBP1,non_coding_transcript_exon_variant,,ENST00000495131,;GBP1,non_coding_transcript_exon_variant,,ENST00000468959,;GBP1,downstream_gene_variant,,ENST00000493139,;GBP1,upstream_gene_variant,,ENST00000484970,;GBP1,upstream_gene_variant,,ENST00000479889,;GBP1,downstream_gene_variant,,ENST00000459831,;	-	ENSG00000117228	ENST00000370473	Transcript	frameshift_variant	1557	1337	446	K/X	aAg/ag	.	.	.	-1	GBP1	HGNC	4182	protein_coding	YES	CCDS718.1	ENSP00000359504	GBP1_HUMAN	.	UPI000013C9DF	.	.	.	8/11	.	hmmpanther:PTHR10751:SF21,hmmpanther:PTHR10751,Gene3D:1f5nA01,Pfam_domain:PF02841,Superfamily_domains:0037397	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAGTACTTTTTC	.	3	ESCA
KIAA1107	0	.	GRCh37	1	92643979	92643979	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1238G>A	p.Ser413Asn	p.S413N	ENST00000370378	7/9	69	42	27	92	92	0	KIAA1107,missense_variant,p.Ser413Asn,ENST00000370378,;KIAA1107,missense_variant,p.Ser468Asn,ENST00000409154,;	A	ENSG00000069712	ENST00000370378	Transcript	missense_variant	1336	1238	413	S/N	aGt/aAt	.	.	.	1	KIAA1107	HGNC	29192	protein_coding	YES	CCDS44172.1	ENSP00000359404	.	E9PEZ5_HUMAN	UPI00017C1449	.	tolerated(0.88)	benign(0.014)	7/9	.	hmmpanther:PTHR22427	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGAGTACCC	.	5	ESCA
AGRN	0	.	GRCh37	1	987191	987191	+	Nonsense_Mutation	SNP	G	G	T	rs139415524	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5647G>T	p.Glu1883Ter	p.E1883*	ENST00000379370	33/36	37	24	12	93	93	0	AGRN,stop_gained,p.Glu1883Ter,ENST00000379370,;AGRN,stop_gained,p.Glu186Ter,ENST00000419249,;RP11-54O7.14,upstream_gene_variant,,ENST00000418300,;AGRN,downstream_gene_variant,,ENST00000466223,;AGRN,downstream_gene_variant,,ENST00000478677,;AGRN,upstream_gene_variant,,ENST00000461111,;AGRN,downstream_gene_variant,,ENST00000492947,;	T	ENSG00000188157	ENST00000379370	Transcript	stop_gained	5697	5647	1883	E/*	Gag/Tag	rs139415524	.	.	1	AGRN	HGNC	329	protein_coding	YES	CCDS30551.1	ENSP00000368678	AGRIN_HUMAN	Q5XG79_HUMAN	UPI00001D7C8B	.	.	.	33/36	.	Superfamily_domains:SSF49899,Gene3D:2.60.120.200,hmmpanther:PTHR10574:SF227,hmmpanther:PTHR10574,PROSITE_profiles:PS50025	A:0.0026	A:0.0083	A:0	.	A:0.002	A:0	A:0	A:0.0041	A:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACCGAGAGG	byFrequency|byCluster|by1000G	5	ESCA
LPPR5	0	.	GRCh37	1	99358618	99358618	+	3'UTR	SNP	T	T	A	rs753562802	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10A>T	.	.	ENST00000263177	6/6	52	43	9	98	98	0	LPPR5,3_prime_UTR_variant,,ENST00000263177,;LPPR5,3_prime_UTR_variant,,ENST00000370188,;	A	ENSG00000117598	ENST00000263177	Transcript	3_prime_UTR_variant	1198	.	.	.	.	rs753562802	.	.	-1	LPPR5	Uniprot_gn	.	protein_coding	YES	CCDS30778.1	ENSP00000263177	LPPR5_HUMAN	.	UPI0000048D53	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCTGCTTC	.	5	ESCA
DZANK1	0	.	GRCh37	20	18370413	18370413	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1950G>T	p.Met650Ile	p.M650I	ENST00000262547	19/21	34	31	3	40	40	0	DZANK1,missense_variant,p.Met650Ile,ENST00000358866,;DZANK1,missense_variant,p.Met536Ile,ENST00000357236,;DZANK1,missense_variant,p.Met628Ile,ENST00000329494,;DZANK1,missense_variant,p.Met650Ile,ENST00000262547,;DZANK1,non_coding_transcript_exon_variant,,ENST00000476058,;DZANK1,non_coding_transcript_exon_variant,,ENST00000487128,;DZANK1,downstream_gene_variant,,ENST00000480488,;DZANK1,3_prime_UTR_variant,,ENST00000377630,;DZANK1,3_prime_UTR_variant,,ENST00000608192,;DZANK1,3_prime_UTR_variant,,ENST00000609267,;	A	ENSG00000089091	ENST00000262547	Transcript	missense_variant	2159	1950	650	M/I	atG/atT	.	.	.	-1	DZANK1	HGNC	15858	protein_coding	YES	CCDS46582.1	ENSP00000262547	DZAN1_HUMAN	.	UPI0000E064B4	.	tolerated(0.08)	benign(0.002)	19/21	.	PROSITE_profiles:PS50297,hmmpanther:PTHR16058:SF4,hmmpanther:PTHR16058,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TTATTCATAAC	.	2	ESCA
VSX1	0	.	GRCh37	20	25058370	25058370	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.759C>T	p.%3D	p.L253L	ENST00000376709	4/5	27	21	6	30	30	0	VSX1,synonymous_variant,p.%3D,ENST00000429762,;VSX1,synonymous_variant,p.%3D,ENST00000424574,;VSX1,synonymous_variant,p.%3D,ENST00000376709,;VSX1,intron_variant,,ENST00000444511,;VSX1,intron_variant,,ENST00000451258,;VSX1,downstream_gene_variant,,ENST00000376707,;VSX1,downstream_gene_variant,,ENST00000398332,;VSX1,synonymous_variant,p.%3D,ENST00000409285,;VSX1,non_coding_transcript_exon_variant,,ENST00000557285,;VSX1,intron_variant,,ENST00000409958,;	A	ENSG00000100987	ENST00000376709	Transcript	synonymous_variant	1023	759	253	L	ctC/ctT	.	.	.	-1	VSX1	HGNC	12723	protein_coding	YES	CCDS13168.1	ENSP00000365899	VSX1_HUMAN	.	UPI0000138E43	.	.	.	4/5	.	PROSITE_profiles:PS51496,hmmpanther:PTHR24323	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTTGAGCAC	.	5	ESCA
NOP56	0	.	GRCh37	20	2638990	2638990	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50G>A	.	.	ENST00000329276	12/12	64	49	15	73	73	0	NOP56,3_prime_UTR_variant,,ENST00000329276,;NOP56,downstream_gene_variant,,ENST00000445139,;IDH3B,downstream_gene_variant,,ENST00000380851,;IDH3B,downstream_gene_variant,,ENST00000380843,;NOP56,downstream_gene_variant,,ENST00000415272,;SNORD86,downstream_gene_variant,,ENST00000391196,;SNORD110,downstream_gene_variant,,ENST00000408189,;SNORA51,downstream_gene_variant,,ENST00000606420,;SNORD57,downstream_gene_variant,,ENST00000448188,;SNORD56,downstream_gene_variant,,ENST00000413522,;NOP56,non_coding_transcript_exon_variant,,ENST00000467857,;NOP56,non_coding_transcript_exon_variant,,ENST00000466447,;NOP56,non_coding_transcript_exon_variant,,ENST00000492135,;NOP56,non_coding_transcript_exon_variant,,ENST00000462630,;IDH3B,downstream_gene_variant,,ENST00000474315,;IDH3B,downstream_gene_variant,,ENST00000462967,;NOP56,downstream_gene_variant,,ENST00000480992,;IDH3B,downstream_gene_variant,,ENST00000491065,;IDH3B,downstream_gene_variant,,ENST00000492240,;NOP56,downstream_gene_variant,,ENST00000480447,;IDH3B,downstream_gene_variant,,ENST00000488299,;NOP56,downstream_gene_variant,,ENST00000471023,;IDH3B,downstream_gene_variant,,ENST00000466999,;NOP56,downstream_gene_variant,,ENST00000484998,;NOP56,downstream_gene_variant,,ENST00000470143,;IDH3B,downstream_gene_variant,,ENST00000477689,;NOP56,downstream_gene_variant,,ENST00000496775,;NOP56,downstream_gene_variant,,ENST00000490753,;NOP56,downstream_gene_variant,,ENST00000494697,;NOP56,downstream_gene_variant,,ENST00000460258,;IDH3B,downstream_gene_variant,,ENST00000466494,;NOP56,downstream_gene_variant,,ENST00000469588,;IDH3B,downstream_gene_variant,,ENST00000479376,;NOP56,3_prime_UTR_variant,,ENST00000467196,;	A	ENSG00000101361	ENST00000329276	Transcript	3_prime_UTR_variant	2351	.	.	.	.	.	.	.	1	NOP56	HGNC	15911	protein_coding	YES	CCDS13030.1	ENSP00000370589	NOP56_HUMAN	Q9BSN3_HUMAN	UPI000016A81D	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGTGACATT	.	5	ESCA
RASSF2	0	.	GRCh37	20	4764195	4764195	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*724A>T	.	.	ENST00000379400	12/12	22	15	6	40	40	0	RASSF2,3_prime_UTR_variant,,ENST00000379376,;RASSF2,3_prime_UTR_variant,,ENST00000379400,;RASSF2,non_coding_transcript_exon_variant,,ENST00000478553,;	A	ENSG00000101265	ENST00000379400	Transcript	3_prime_UTR_variant	1901	.	.	.	.	.	.	.	-1	RASSF2	HGNC	9883	protein_coding	YES	CCDS13083.1	ENSP00000368710	RASF2_HUMAN	.	UPI0000001C0A	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACATAGAAC	.	5	ESCA
PMEPA1	0	.	GRCh37	20	56225019	56225019	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2090C>T	.	.	ENST00000341744	4/4	26	13	13	48	48	0	PMEPA1,3_prime_UTR_variant,,ENST00000265626,;PMEPA1,3_prime_UTR_variant,,ENST00000341744,;PMEPA1,3_prime_UTR_variant,,ENST00000395816,;PMEPA1,3_prime_UTR_variant,,ENST00000347215,;PMEPA1,downstream_gene_variant,,ENST00000395814,;PMEPA1,downstream_gene_variant,,ENST00000395819,;PMEPA1,downstream_gene_variant,,ENST00000414037,;	A	ENSG00000124225	ENST00000341744	Transcript	3_prime_UTR_variant	3274	.	.	.	.	.	.	.	-1	PMEPA1	HGNC	14107	protein_coding	YES	CCDS13463.1	ENSP00000345826	PMEPA_HUMAN	.	UPI000004970A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCGGGATAA	.	5	ESCA
TUBB1	0	.	GRCh37	20	57598917	57598917	+	Silent	SNP	C	C	T	rs769442145	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435C>T	p.%3D	p.S145S	ENST00000217133	4/4	46	38	8	53	53	0	TUBB1,synonymous_variant,p.%3D,ENST00000217133,;ATP5E,downstream_gene_variant,,ENST00000395663,;ATP5E,downstream_gene_variant,,ENST00000395659,;ATP5E,downstream_gene_variant,,ENST00000243997,;	T	ENSG00000101162	ENST00000217133	Transcript	synonymous_variant	704	435	145	S	tcC/tcT	rs769442145	.	.	1	TUBB1	HGNC	16257	protein_coding	YES	CCDS13475.1	ENSP00000217133	TBB1_HUMAN	.	UPI0000071B14	.	.	.	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF74,PROSITE_patterns:PS00227,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCCGGGAT	byFrequency	5	ESCA
BMP2	0	.	GRCh37	20	6759945	6759945	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*209C>G	.	.	ENST00000378827	3/3	132	78	54	207	207	0	BMP2,3_prime_UTR_variant,,ENST00000378827,;	G	ENSG00000125845	ENST00000378827	Transcript	3_prime_UTR_variant	2619	.	.	.	.	.	.	.	1	BMP2	HGNC	1069	protein_coding	YES	CCDS13099.1	ENSP00000368104	BMP2_HUMAN	U3N491_HUMAN,C8C069_HUMAN,C8C060_HUMAN	UPI0000126A21	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAATCAGAGA	.	5	ESCA
LAMP5	0	.	GRCh37	20	9510833	9510833	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*366C>A	.	.	ENST00000246070	6/6	26	20	5	35	35	0	LAMP5,3_prime_UTR_variant,,ENST00000246070,;LAMP5,downstream_gene_variant,,ENST00000427562,;	A	ENSG00000125869	ENST00000246070	Transcript	3_prime_UTR_variant	1701	.	.	.	.	.	.	.	1	LAMP5	HGNC	16097	protein_coding	YES	CCDS13106.1	ENSP00000246070	LAMP5_HUMAN	.	UPI0000128675	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACCCCTTTA	.	5	ESCA
TPTE	0	.	GRCh37	21	10998232	10998232	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1321G>C	.	.	ENST00000415664	10/32	129	117	12	210	210	0	TPTE,non_coding_transcript_exon_variant,,ENST00000415664,;BAGE2,non_coding_transcript_exon_variant,,ENST00000496773,;	G	ENSG00000166157	ENST00000415664	Transcript	non_coding_transcript_exon_variant	1321	.	.	.	.	.	.	.	-1	TPTE	HGNC	12023	processed_transcript	.	.	.	.	.	.	.	.	.	10/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTCTCTTTTT	.	3	ESCA
GAB4	0	.	GRCh37	22	17443733	17443733	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1615G>C	p.Val539Leu	p.V539L	ENST00000400588	10/10	21	17	4	35	35	0	GAB4,missense_variant,p.Val539Leu,ENST00000400588,;GAB4,downstream_gene_variant,,ENST00000520505,;GAB4,downstream_gene_variant,,ENST00000523144,;GAB4,3_prime_UTR_variant,,ENST00000465611,;	G	ENSG00000215568	ENST00000400588	Transcript	missense_variant	1723	1615	539	V/L	Gtg/Ctg	.	.	.	-1	GAB4	HGNC	18325	protein_coding	YES	CCDS42976.1	ENSP00000383431	GAB4_HUMAN	.	UPI00002326B5	.	deleterious(0)	benign(0.011)	10/10	.	hmmpanther:PTHR12156:SF20,hmmpanther:PTHR12156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCACCTTCT	.	2	ESCA
MAPK1	0	.	GRCh37	22	22127181	22127181	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.947A>G	p.Tyr316Cys	p.Y316C	ENST00000215832	7/9	58	51	6	71	71	0	MAPK1,missense_variant,p.Tyr316Cys,ENST00000398822,;MAPK1,missense_variant,p.Tyr272Cys,ENST00000544786,;MAPK1,missense_variant,p.Tyr316Cys,ENST00000215832,;MAPK1,upstream_gene_variant,,ENST00000491588,;	C	ENSG00000100030	ENST00000215832	Transcript	missense_variant	1136	947	316	Y/C	tAt/tGt	COSM1291220	.	.	-1	MAPK1	HGNC	6871	protein_coding	YES	CCDS13795.1	ENSP00000215832	MK01_HUMAN	Q1HBJ4_HUMAN,B4DHN0_HUMAN	UPI000000104F	.	deleterious(0.01)	benign(0.237)	7/9	.	hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF161,Gene3D:1.10.510.10,Superfamily_domains:SSF56112,Prints_domain:PR01770	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTAATACTGC	.	4	ESCA
CABIN1	0	.	GRCh37	22	24466798	24466798	+	Silent	SNP	C	C	T	rs141185155	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2280C>T	p.%3D	p.S760S	ENST00000398319	17/37	34	26	7	63	63	0	CABIN1,synonymous_variant,p.%3D,ENST00000398319,;CABIN1,synonymous_variant,p.%3D,ENST00000405822,;CABIN1,synonymous_variant,p.%3D,ENST00000263119,;CABIN1,non_coding_transcript_exon_variant,,ENST00000484593,;	T	ENSG00000099991	ENST00000398319	Transcript	synonymous_variant	2665	2280	760	S	tcC/tcT	rs141185155,COSM3673235	.	.	1	CABIN1	HGNC	24187	protein_coding	YES	CCDS13823.1	ENSP00000381364	CABIN_HUMAN	.	UPI0000126D6C	.	.	.	17/37	.	hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCCGATGT	byCluster	5	ESCA
MTFP1	0	.	GRCh37	22	30824783	30824783	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*262G>T	.	.	ENST00000266263	4/4	14	9	5	24	24	0	MTFP1,3_prime_UTR_variant,,ENST00000407550,;MTFP1,3_prime_UTR_variant,,ENST00000355143,;RP4-539M6.19,3_prime_UTR_variant,,ENST00000439023,;MTFP1,3_prime_UTR_variant,,ENST00000266263,;RP4-539M6.19,3_prime_UTR_variant,,ENST00000439838,;SEC14L2,downstream_gene_variant,,ENST00000312932,;SEC14L2,downstream_gene_variant,,ENST00000403484,;RP4-539M6.19,3_prime_UTR_variant,,ENST00000454552,;SEC14L2,downstream_gene_variant,,ENST00000467218,;MTFP1,downstream_gene_variant,,ENST00000412752,;SEC14L2,downstream_gene_variant,,ENST00000478762,;MTFP1,downstream_gene_variant,,ENST00000489658,;	T	ENSG00000242114	ENST00000266263	Transcript	3_prime_UTR_variant	1113	.	.	.	.	.	.	.	1	MTFP1	HGNC	26945	protein_coding	YES	CCDS33635.1	ENSP00000266263	MTFP1_HUMAN	.	UPI000000DB3E	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	GCCCTGTCTTT	.	3	ESCA
POU3F3	0	.	GRCh37	2	105473134	105473134	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1166C>G	p.Ser389Ter	p.S389*	ENST00000361360	1/1	35	25	10	83	83	0	POU3F3,stop_gained,p.Ser389Ter,ENST00000361360,;RP11-13J10.1,intron_variant,,ENST00000598623,;LINC01158,upstream_gene_variant,,ENST00000447876,;	G	ENSG00000198914	ENST00000361360	Transcript	stop_gained	1166	1166	389	S/*	tCa/tGa	.	.	.	1	POU3F3	HGNC	9216	protein_coding	YES	CCDS33265.1	ENSP00000355001	PO3F3_HUMAN	.	UPI0000131D87	.	.	.	1/1	.	hmmpanther:PTHR11636:SF78,hmmpanther:PTHR11636,Gene3D:1.10.10.60,PIRSF_domain:PIRSF002629	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTCAAGCA	.	5	ESCA
PSD4	0	.	GRCh37	2	113940984	113940984	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951C>T	p.%3D	p.T317T	ENST00000245796	2/17	36	25	11	67	67	0	PSD4,synonymous_variant,p.%3D,ENST00000441564,;PSD4,synonymous_variant,p.%3D,ENST00000245796,;PSD4,intron_variant,,ENST00000485525,;PSD4,downstream_gene_variant,,ENST00000465917,;PSD4,non_coding_transcript_exon_variant,,ENST00000418251,;PSD4,upstream_gene_variant,,ENST00000409656,;	T	ENSG00000125637	ENST00000245796	Transcript	synonymous_variant	1146	951	317	T	acC/acT	.	.	.	1	PSD4	HGNC	19096	protein_coding	YES	CCDS33276.1	ENSP00000245796	PSD4_HUMAN	B3KN27_HUMAN	UPI00004A0748	.	.	.	2/17	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGTACCCCTCC	.	4	ESCA
CCDC74B	0	.	GRCh37	2	130900736	130900736	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295+106C>T	.	.	ENST00000310463	.	52	34	18	105	105	0	CCDC74B,missense_variant,p.Pro134Leu,ENST00000409234,;CCDC74B,5_prime_UTR_variant,,ENST00000392984,;CCDC74B,intron_variant,,ENST00000457413,;CCDC74B,intron_variant,,ENST00000409943,;CCDC74B,intron_variant,,ENST00000409128,;CCDC74B,intron_variant,,ENST00000310463,;CCDC74B,downstream_gene_variant,,ENST00000441670,;MED15P9,downstream_gene_variant,,ENST00000427638,;CCDC74B,intron_variant,,ENST00000434929,;CCDC74B,intron_variant,,ENST00000423263,;CCDC74B,upstream_gene_variant,,ENST00000498526,;CCDC74B,upstream_gene_variant,,ENST00000496704,;	A	ENSG00000152076	ENST00000310463	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CCDC74B	HGNC	25267	protein_coding	YES	CCDS2155.1	ENSP00000308873	CC74B_HUMAN	.	UPI000006D822	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGGGTTGG	.	5	ESCA
TNFAIP6	0	.	GRCh37	2	152226702	152226702	+	Missense_Mutation	SNP	G	G	A	rs375122098	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.563G>A	p.Cys188Tyr	p.C188Y	ENST00000243347	4/6	50	33	16	71	71	0	TNFAIP6,missense_variant,p.Cys188Tyr,ENST00000243347,;MIR4773-2,downstream_gene_variant,,ENST00000585225,;RN7SL124P,upstream_gene_variant,,ENST00000498656,;TNFAIP6,non_coding_transcript_exon_variant,,ENST00000460812,;	A	ENSG00000123610	ENST00000243347	Transcript	missense_variant	638	563	188	C/Y	tGc/tAc	rs375122098	.	.	1	TNFAIP6	HGNC	11898	protein_coding	YES	CCDS2193.1	ENSP00000243347	TSG6_HUMAN	.	UPI0000071080	.	deleterious(0)	probably_damaging(0.999)	4/6	.	PROSITE_profiles:PS01180,hmmpanther:PTHR24038,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTGCTTGG	.	5	ESCA
SCN2A	0	.	GRCh37	2	166231377	166231377	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4155G>C	p.Glu1385Asp	p.E1385D	ENST00000357398	22/27	29	23	6	52	52	0	SCN2A,missense_variant,p.Glu1385Asp,ENST00000283256,;SCN2A,missense_variant,p.Glu1385Asp,ENST00000375437,;SCN2A,missense_variant,p.Glu1385Asp,ENST00000375427,;SCN2A,missense_variant,p.Glu1385Asp,ENST00000357398,;SCN2A,non_coding_transcript_exon_variant,,ENST00000480032,;	C	ENSG00000136531	ENST00000357398	Transcript	missense_variant	4445	4155	1385	E/D	gaG/gaC	.	.	.	1	SCN2A	HGNC	10588	protein_coding	YES	CCDS33313.1	ENSP00000349973	SCN2A_HUMAN	F8T7W7_HUMAN	UPI000002A663	.	tolerated(1)	benign(0.001)	22/27	.	hmmpanther:PTHR10037:SF133,hmmpanther:PTHR10037,Pfam_domain:PF00520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGAGTGCAA	.	5	ESCA
ITGA6	0	.	GRCh37	2	173338951	173338951	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.944C>T	p.Ser315Leu	p.S315L	ENST00000409080	6/25	25	20	5	68	68	0	ITGA6,missense_variant,p.Ser354Leu,ENST00000264106,;ITGA6,missense_variant,p.Ser354Leu,ENST00000375221,;ITGA6,missense_variant,p.Ser310Leu,ENST00000343713,;ITGA6,missense_variant,p.Ser310Leu,ENST00000458358,;ITGA6,missense_variant,p.Ser201Leu,ENST00000412899,;ITGA6,missense_variant,p.Ser354Leu,ENST00000442250,;ITGA6,missense_variant,p.Ser315Leu,ENST00000264107,;ITGA6,missense_variant,p.Ser196Leu,ENST00000409532,;ITGA6,missense_variant,p.Ser315Leu,ENST00000409080,;ITGA6,downstream_gene_variant,,ENST00000497107,;	T	ENSG00000091409	ENST00000409080	Transcript	missense_variant	944	944	315	S/L	tCa/tTa	.	.	.	1	ITGA6	HGNC	6142	protein_coding	YES	CCDS46451.1	ENSP00000386896	ITA6_HUMAN	C9JXX7_HUMAN	UPI0000EA87E5	.	deleterious(0)	probably_damaging(0.993)	6/25	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF9,hmmpanther:PTHR23220,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318,Prints_domain:PR01185	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTTCATTTG	.	4	ESCA
ALS2	0	.	GRCh37	2	202565652	202565652	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*922C>T	.	.	ENST00000264276	34/34	10	6	4	16	16	0	ALS2,3_prime_UTR_variant,,ENST00000264276,;MPP4,upstream_gene_variant,,ENST00000315506,;MPP4,upstream_gene_variant,,ENST00000396886,;MPP4,upstream_gene_variant,,ENST00000428900,;MPP4,upstream_gene_variant,,ENST00000409474,;MPP4,upstream_gene_variant,,ENST00000359962,;MPP4,upstream_gene_variant,,ENST00000409143,;ALS2,downstream_gene_variant,,ENST00000457679,;MPP4,upstream_gene_variant,,ENST00000602867,;ALS2,downstream_gene_variant,,ENST00000439495,;MPP4,upstream_gene_variant,,ENST00000409818,;MPP4,upstream_gene_variant,,ENST00000486212,;MPP4,upstream_gene_variant,,ENST00000483841,;	A	ENSG00000003393	ENST00000264276	Transcript	3_prime_UTR_variant	6269	.	.	.	.	.	.	.	-1	ALS2	HGNC	443	protein_coding	YES	CCDS42800.1	ENSP00000264276	ALS2_HUMAN	J3KQ43_HUMAN,J3KQ33_HUMAN,A8K4R4_HUMAN	UPI0000231C77	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTTCAGTGTGA	.	3	ESCA
CCDC85A	0	.	GRCh37	2	56612244	56612244	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*754T>A	.	.	ENST00000407595	6/6	12	6	6	46	46	0	CCDC85A,3_prime_UTR_variant,,ENST00000407595,;RP11-482H16.1,non_coding_transcript_exon_variant,,ENST00000607540,;	A	ENSG00000055813	ENST00000407595	Transcript	3_prime_UTR_variant	2918	.	.	.	.	.	.	.	1	CCDC85A	HGNC	29400	protein_coding	YES	CCDS46290.1	ENSP00000384040	CC85A_HUMAN	.	UPI00001C1DC1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAACCTTCATA	.	3	ESCA
ANKRD36B	0	.	GRCh37	2	98167802	98167802	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1605C>G	.	.	ENST00000258459	18/44	142	123	19	279	279	0	ANKRD36B,non_coding_transcript_exon_variant,,ENST00000419390,;ANKRD36B,non_coding_transcript_exon_variant,,ENST00000443455,;ANKRD36B,non_coding_transcript_exon_variant,,ENST00000377003,;ANKRD36B,non_coding_transcript_exon_variant,,ENST00000258459,;ANKRD36B,non_coding_transcript_exon_variant,,ENST00000359901,;ANKRD36B,non_coding_transcript_exon_variant,,ENST00000438709,;	C	ENSG00000196912	ENST00000258459	Transcript	non_coding_transcript_exon_variant	1605	.	.	.	.	.	.	.	-1	ANKRD36B	HGNC	29333	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	18/44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAAAGAATCT	.	4	ESCA
ATP2B2	0	.	GRCh37	3	10369319	10369319	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1179G>A	.	.	ENST00000360273	23/23	26	21	5	69	69	0	ATP2B2,3_prime_UTR_variant,,ENST00000343816,;ATP2B2,3_prime_UTR_variant,,ENST00000383800,;ATP2B2,3_prime_UTR_variant,,ENST00000397077,;ATP2B2,3_prime_UTR_variant,,ENST00000352432,;ATP2B2,3_prime_UTR_variant,,ENST00000360273,;ATP2B2,downstream_gene_variant,,ENST00000452124,;MIR378B,upstream_gene_variant,,ENST00000578876,;ATP2B2,downstream_gene_variant,,ENST00000467702,;ATP2B2,downstream_gene_variant,,ENST00000468426,;ATP2B2,3_prime_UTR_variant,,ENST00000460129,;	T	ENSG00000157087	ENST00000360273	Transcript	3_prime_UTR_variant	5350	.	.	.	.	.	.	.	-1	ATP2B2	HGNC	815	protein_coding	YES	CCDS33701.1	ENSP00000353414	AT2B2_HUMAN	Q4J699_HUMAN,Q4J696_HUMAN	UPI00001261EF	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTCTTAGT	.	5	ESCA
DPPA2	0	.	GRCh37	3	109027896	109027896	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.373C>T	p.His125Tyr	p.H125Y	ENST00000478945	5/9	31	22	8	71	71	0	DPPA2,missense_variant,p.His125Tyr,ENST00000478945,;	A	ENSG00000163530	ENST00000478945	Transcript	missense_variant	620	373	125	H/Y	Cat/Tat	.	.	.	-1	DPPA2	HGNC	19197	protein_coding	YES	CCDS2956.1	ENSP00000417710	DPPA2_HUMAN	.	UPI000007143F	.	tolerated(0.12)	probably_damaging(0.932)	5/9	.	Gene3D:1.10.720.30,hmmpanther:PTHR16073:SF7,hmmpanther:PTHR16073,PROSITE_profiles:PS50800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATGCCTAT	.	5	ESCA
PVRL3	0	.	GRCh37	3	110831057	110831057	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.341A>G	p.Gln114Arg	p.Q114R	ENST00000485303	2/6	35	25	10	87	87	0	PVRL3,missense_variant,p.Gln114Arg,ENST00000485303,;PVRL3,missense_variant,p.Gln114Arg,ENST00000486596,;PVRL3,missense_variant,p.Gln114Arg,ENST00000319792,;PVRL3,missense_variant,p.Gln91Arg,ENST00000493615,;PVRL3,missense_variant,p.Gln67Arg,ENST00000461477,;PVRL3,missense_variant,p.Gln99Arg,ENST00000481766,;PVRL3,5_prime_UTR_variant,,ENST00000491525,;PVRL3,non_coding_transcript_exon_variant,,ENST00000470618,;PVRL3,non_coding_transcript_exon_variant,,ENST00000488016,;PVRL3,downstream_gene_variant,,ENST00000478327,;	G	ENSG00000177707	ENST00000485303	Transcript	missense_variant	616	341	114	Q/R	cAa/cGa	.	.	.	1	PVRL3	HGNC	17664	protein_coding	YES	CCDS2957.1	ENSP00000418070	PVRL3_HUMAN	.	UPI000004A2B6	.	tolerated(0.22)	possibly_damaging(0.721)	2/6	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF10,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCAAGGAG	.	5	ESCA
SLC12A8	0	.	GRCh37	3	124826791	124826791	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1239C>A	p.%3D	p.T413T	ENST00000393469	9/13	32	27	5	69	69	0	SLC12A8,synonymous_variant,p.%3D,ENST00000430155,;SLC12A8,synonymous_variant,p.%3D,ENST00000314584,;SLC12A8,synonymous_variant,p.%3D,ENST00000393469,;SLC12A8,synonymous_variant,p.%3D,ENST00000469902,;SLC12A8,synonymous_variant,p.%3D,ENST00000423114,;SLC12A8,downstream_gene_variant,,ENST00000479826,;SLC12A8,non_coding_transcript_exon_variant,,ENST00000465475,;SLC12A8,non_coding_transcript_exon_variant,,ENST00000465777,;SLC12A8,non_coding_transcript_exon_variant,,ENST00000479352,;SLC12A8,intron_variant,,ENST00000483944,;SLC12A8,downstream_gene_variant,,ENST00000485849,;SLC12A8,downstream_gene_variant,,ENST00000495105,;SLC12A8,upstream_gene_variant,,ENST00000461616,;SLC12A8,3_prime_UTR_variant,,ENST00000473262,;SLC12A8,non_coding_transcript_exon_variant,,ENST00000479231,;SLC12A8,non_coding_transcript_exon_variant,,ENST00000485954,;	T	ENSG00000221955	ENST00000393469	Transcript	synonymous_variant	1289	1239	413	T	acC/acA	.	.	.	-1	SLC12A8	HGNC	15595	protein_coding	YES	CCDS43143.1	ENSP00000377112	S12A8_HUMAN	C9IZN2_HUMAN	UPI000049DFB2	.	.	.	9/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCGGGGTCAG	.	4	ESCA
ZNF148	0	.	GRCh37	3	124945667	124945667	+	3'UTR	SNP	C	C	A	rs762405249	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5518G>T	.	.	ENST00000360647	9/9	14	11	3	26	26	0	ZNF148,3_prime_UTR_variant,,ENST00000360647,;SLC12A8,intron_variant,,ENST00000423114,;	A	ENSG00000163848	ENST00000360647	Transcript	3_prime_UTR_variant	8389	.	.	.	.	rs762405249	.	.	-1	ZNF148	HGNC	12933	protein_coding	YES	CCDS3031.1	ENSP00000353863	ZN148_HUMAN	C9K0U4_HUMAN,C9JRX0_HUMAN,C9J6Y6_HUMAN	UPI000013C2FF	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAGGCTGCTG	.	2	ESCA
GRIP2	0	.	GRCh37	3	14567437	14567437	+	Intron	SNP	G	G	A	rs369716360	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.108C>T	.	.	ENST00000273083	2/24	12	7	5	33	33	0	GRIP2,splice_region_variant,,ENST00000273083,;GRIP2,splice_region_variant,,ENST00000443613,;GRIP2,splice_region_variant,,ENST00000507975,;GRIP2,splice_region_variant,,ENST00000383795,;GRIP2,splice_region_variant,,ENST00000413414,;GRIP2,non_coding_transcript_exon_variant,,ENST00000422481,;	A	ENSG00000144596	ENST00000273083	Transcript	splice_region_variant	108	.	.	.	.	rs369716360	.	.	-1	GRIP2	HGNC	23841	processed_transcript	YES	.	.	.	.	.	.	.	.	2/24	.	.	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER	CCATCGTCTGC	byFrequency|byCluster	3	ESCA
DAZL	0	.	GRCh37	3	16629129	16629129	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1038G>C	.	.	ENST00000250863	11/11	94	49	45	164	164	0	DAZL,3_prime_UTR_variant,,ENST00000399444,;DAZL,3_prime_UTR_variant,,ENST00000250863,;	G	ENSG00000092345	ENST00000250863	Transcript	3_prime_UTR_variant	2274	.	.	.	.	.	.	.	-1	DAZL	HGNC	2685	protein_coding	YES	CCDS54556.1	ENSP00000250863	DAZL_HUMAN	.	UPI0000412129	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCACATTCT	.	5	ESCA
CLCN2	0	.	GRCh37	3	184075234	184075234	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814G>C	p.Val272Leu	p.V272L	ENST00000265593	8/24	97	10	86	115	115	0	CLCN2,missense_variant,p.Val228Leu,ENST00000434054,;CLCN2,missense_variant,p.Val272Leu,ENST00000344937,;CLCN2,missense_variant,p.Val272Leu,ENST00000265593,;CLCN2,missense_variant,p.Val272Leu,ENST00000457512,;CLCN2,5_prime_UTR_variant,,ENST00000423355,;EIF2B5,intron_variant,,ENST00000444495,;POLR2H,upstream_gene_variant,,ENST00000412877,;POLR2H,upstream_gene_variant,,ENST00000456318,;POLR2H,upstream_gene_variant,,ENST00000438240,;POLR2H,upstream_gene_variant,,ENST00000460083,;CLCN2,upstream_gene_variant,,ENST00000475279,;CLCN2,non_coding_transcript_exon_variant,,ENST00000485667,;CLCN2,upstream_gene_variant,,ENST00000491162,;CLCN2,upstream_gene_variant,,ENST00000430397,;CLCN2,downstream_gene_variant,,ENST00000465231,;	G	ENSG00000114859	ENST00000265593	Transcript	missense_variant	986	814	272	V/L	Gtg/Ctg	.	.	.	-1	CLCN2	HGNC	2020	protein_coding	YES	CCDS3263.1	ENSP00000265593	CLCN2_HUMAN	.	UPI000013D645	.	deleterious(0)	probably_damaging(0.997)	8/24	.	hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF64,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCACTGCAA	.	5	ESCA
TP63	0	.	GRCh37	3	189585728	189585728	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.989G>A	p.Arg330Lys	p.R330K	ENST00000264731	7/14	63	53	10	92	92	0	TP63,missense_variant,p.Arg236Lys,ENST00000392461,;TP63,missense_variant,p.Arg236Lys,ENST00000354600,;TP63,missense_variant,p.Arg236Lys,ENST00000456148,;TP63,missense_variant,p.Arg330Lys,ENST00000392460,;TP63,missense_variant,p.Arg330Lys,ENST00000320472,;TP63,missense_variant,p.Arg330Lys,ENST00000440651,;TP63,missense_variant,p.Arg151Lys,ENST00000449992,;TP63,missense_variant,p.Arg330Lys,ENST00000264731,;TP63,missense_variant,p.Arg330Lys,ENST00000418709,;TP63,missense_variant,p.Arg236Lys,ENST00000437221,;TP63,missense_variant,p.Arg245Lys,ENST00000382063,;TP63,missense_variant,p.Arg236Lys,ENST00000392463,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,;	A	ENSG00000073282	ENST00000264731	Transcript	missense_variant	1078	989	330	R/K	aGa/aAa	.	.	.	1	TP63	HGNC	15979	protein_coding	YES	CCDS3293.1	ENSP00000264731	P63_HUMAN	.	UPI0000073CF2	.	tolerated(0.34)	probably_damaging(0.989)	7/14	.	hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCAGAGAGT	.	5	ESCA
MUC4	0	.	GRCh37	3	195509844	195509844	+	Silent	SNP	G	G	A	rs750734665	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8607C>T	p.%3D	p.D2869D	ENST00000463781	2/25	133	120	12	259	258	1	MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000470451,;MUC4,synonymous_variant,p.%3D,ENST00000477086,;MUC4,synonymous_variant,p.%3D,ENST00000466475,;MUC4,synonymous_variant,p.%3D,ENST00000478156,;MUC4,synonymous_variant,p.%3D,ENST00000479406,;MUC4,synonymous_variant,p.%3D,ENST00000477756,;MUC4,synonymous_variant,p.%3D,ENST00000462323,;MUC4,synonymous_variant,p.%3D,ENST00000480843,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,;	A	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	9067	8607	2869	D	gaC/gaT	rs750734665	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGCGTCGGT	byFrequency	4	ESCA
TM4SF19	0	.	GRCh37	3	196050665	196050665	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*23G>T	.	.	ENST00000273695	5/5	51	34	17	60	60	0	TM4SF19,missense_variant,p.Ala217Ser,ENST00000446879,;TM4SF19,missense_variant,p.Ala85Ser,ENST00000440822,;TM4SF19,3_prime_UTR_variant,,ENST00000273695,;TM4SF19,3_prime_UTR_variant,,ENST00000454715,;TM4SF19-AS1,non_coding_transcript_exon_variant,,ENST00000444939,;TM4SF19-AS1,intron_variant,,ENST00000452051,;TM4SF19-AS1,downstream_gene_variant,,ENST00000420226,;TM4SF19,3_prime_UTR_variant,,ENST00000442633,;	A	ENSG00000145107	ENST00000273695	Transcript	3_prime_UTR_variant	779	.	.	.	.	.	.	.	-1	TM4SF19	HGNC	25167	protein_coding	YES	CCDS3316.1	ENSP00000273695	T4S19_HUMAN	.	UPI000013D9CC	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGCTTGCA	.	5	ESCA
CMC1	0	.	GRCh37	3	28364174	28364174	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3054T>C	.	.	ENST00000466830	4/4	42	34	7	48	48	0	CMC1,3_prime_UTR_variant,,ENST00000466830,;AZI2,3_prime_UTR_variant,,ENST00000479665,;AZI2,intron_variant,,ENST00000429369,;CMC1,downstream_gene_variant,,ENST00000423894,;CMC1,downstream_gene_variant,,ENST00000418849,;AZI2,non_coding_transcript_exon_variant,,ENST00000295748,;CMC1,downstream_gene_variant,,ENST00000495428,;CMC1,downstream_gene_variant,,ENST00000469102,;CMC1,downstream_gene_variant,,ENST00000467644,;CMC1,downstream_gene_variant,,ENST00000482499,;AZI2,downstream_gene_variant,,ENST00000476174,;CMC1,downstream_gene_variant,,ENST00000396610,;CMC1,downstream_gene_variant,,ENST00000477739,;AZI2,downstream_gene_variant,,ENST00000492044,;CMC1,downstream_gene_variant,,ENST00000334841,;AZI2,downstream_gene_variant,,ENST00000463512,;	C	ENSG00000187118	ENST00000466830	Transcript	3_prime_UTR_variant	3574	.	.	.	.	.	.	.	1	CMC1	HGNC	28783	protein_coding	YES	CCDS33722.1	ENSP00000418348	COXM1_HUMAN	.	UPI0000161ABD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGTTCATT	.	5	ESCA
IL5RA	0	.	GRCh37	3	3139822	3139822	+	Missense_Mutation	SNP	T	T	A	.	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520A>T	p.Arg174Trp	p.R174W	ENST00000446632	6/12	40	15	24	112	112	0	IL5RA,missense_variant,p.Arg174Trp,ENST00000311981,;IL5RA,missense_variant,p.Arg174Trp,ENST00000418488,;IL5RA,missense_variant,p.Arg174Trp,ENST00000430514,;IL5RA,missense_variant,p.Arg174Trp,ENST00000256452,;IL5RA,missense_variant,p.Arg174Trp,ENST00000446632,;IL5RA,missense_variant,p.Arg174Trp,ENST00000445701,;IL5RA,missense_variant,p.Arg174Trp,ENST00000456302,;IL5RA,missense_variant,p.Arg174Trp,ENST00000383846,;IL5RA,missense_variant,p.Arg174Trp,ENST00000438560,;IL5RA,intron_variant,,ENST00000445864,;IL5RA,downstream_gene_variant,,ENST00000427088,;SNORA43,upstream_gene_variant,,ENST00000517240,;	A	ENSG00000091181	ENST00000446632	Transcript	missense_variant	1095	520	174	R/W	Agg/Tgg	COSM583192	.	.	-1	IL5RA	HGNC	6017	protein_coding	YES	CCDS2559.1	ENSP00000412209	IL5RA_HUMAN	C9J6C4_HUMAN,C9J3K8_HUMAN	UPI000013C656	.	deleterious(0)	probably_damaging(0.999)	6/12	.	Superfamily_domains:SSF49265,Gene3D:2.60.40.10,Pfam_domain:PF09240,PROSITE_patterns:PS01356,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF17	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAACCTATAGT	.	5	ESCA
CNOT10	0	.	GRCh37	3	32804464	32804464	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2020+109A>G	.	.	ENST00000454516	.	9	5	4	33	33	0	CNOT10,3_prime_UTR_variant,,ENST00000538368,;CNOT10,intron_variant,,ENST00000430408,;CNOT10,intron_variant,,ENST00000328834,;CNOT10,intron_variant,,ENST00000331889,;CNOT10,intron_variant,,ENST00000454516,;CNOT10,intron_variant,,ENST00000471003,;CNOT10,intron_variant,,ENST00000416457,;CNOT10,intron_variant,,ENST00000435630,;CNOT10,upstream_gene_variant,,ENST00000481526,;CNOT10,upstream_gene_variant,,ENST00000479397,;CNOT10,upstream_gene_variant,,ENST00000468599,;	G	ENSG00000182973	ENST00000454516	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CNOT10	HGNC	23817	protein_coding	YES	CCDS58822.1	ENSP00000399862	CNO10_HUMAN	B7Z5B3_HUMAN	UPI000206533D	.	.	.	.	15/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTTAGGTTG	.	2	ESCA
CTNNB1	0	.	GRCh37	3	41266472	41266472	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.269G>T	p.Arg90Leu	p.R90L	ENST00000349496	4/15	22	18	4	48	48	0	CTNNB1,missense_variant,p.Arg90Leu,ENST00000349496,;CTNNB1,missense_variant,p.Arg90Leu,ENST00000450969,;CTNNB1,missense_variant,p.Arg90Leu,ENST00000431914,;CTNNB1,missense_variant,p.Arg90Leu,ENST00000396185,;CTNNB1,missense_variant,p.Arg90Leu,ENST00000405570,;CTNNB1,missense_variant,p.Arg83Leu,ENST00000453024,;CTNNB1,missense_variant,p.Arg90Leu,ENST00000396183,;CTNNB1,missense_variant,p.Arg90Leu,ENST00000441708,;CTNNB1,downstream_gene_variant,,ENST00000426215,;CTNNB1,downstream_gene_variant,,ENST00000433400,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000488914,;	T	ENSG00000168036	ENST00000349496	Transcript	missense_variant	549	269	90	R/L	cGa/cTa	COSM1423031	.	.	1	CTNNB1	HGNC	2514	protein_coding	YES	CCDS2694.1	ENSP00000344456	CTNB1_HUMAN	G9GAG7_HUMAN,E9PDF9_HUMAN,E7EV28_HUMAN,E7EMJ5_HUMAN,C9IZ65_HUMAN,B4DGU4_HUMAN	UPI000012862F	.	tolerated(0.07)	probably_damaging(0.966)	4/15	.	hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53,Prints_domain:PR01869	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.A5_Q143del|c.14_430del417|5,CODON|p.W25_I140del|c.73_420del348|3,CODON|p.Q28_H134del|c.82_402del321|5	RADIA|MUSE	GACTCGAGCTC	.	2	ESCA
DAPP1	0	.	GRCh37	4	100784193	100784193	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.564G>T	p.%3D	p.L188L	ENST00000512369	6/9	80	46	33	168	168	0	DAPP1,synonymous_variant,p.%3D,ENST00000512369,;DAPP1,synonymous_variant,p.%3D,ENST00000296414,;DAPP1,non_coding_transcript_exon_variant,,ENST00000507994,;DAPP1,upstream_gene_variant,,ENST00000514301,;	T	ENSG00000070190	ENST00000512369	Transcript	synonymous_variant	632	564	188	L	ctG/ctT	.	.	.	1	DAPP1	HGNC	16500	protein_coding	YES	CCDS47112.1	ENSP00000423602	DAPP1_HUMAN	.	UPI0000037612	.	.	.	6/9	.	PROSITE_profiles:PS50003,hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF30,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTGCACAG	.	5	ESCA
PPP3CA	0	.	GRCh37	4	102251465	102251465	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58+16431C>G	.	.	ENST00000394854	.	67	53	13	125	125	0	PPP3CA,intron_variant,,ENST00000512215,;PPP3CA,intron_variant,,ENST00000529324,;PPP3CA,intron_variant,,ENST00000507176,;PPP3CA,intron_variant,,ENST00000394853,;PPP3CA,intron_variant,,ENST00000323055,;PPP3CA,intron_variant,,ENST00000394854,;PPP3CA,intron_variant,,ENST00000525819,;PPP3CA,intron_variant,,ENST00000523694,;MIR1255A,non_coding_transcript_exon_variant,,ENST00000408338,;	C	ENSG00000138814	ENST00000394854	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PPP3CA	HGNC	9314	protein_coding	YES	CCDS34037.1	ENSP00000378323	PP2BA_HUMAN	Q9UMM5_HUMAN,Q9UMB2_HUMAN,E9PPC8_HUMAN,E9PK68_HUMAN,E7ETC2_HUMAN	UPI0000110660	.	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATGGATAAG	.	5	ESCA
FAT4	0	.	GRCh37	4	126336313	126336313	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6195T>C	p.%3D	p.I2065I	ENST00000394329	5/17	25	18	7	57	57	0	FAT4,synonymous_variant,p.%3D,ENST00000394329,;FAT4,synonymous_variant,p.%3D,ENST00000335110,;	C	ENSG00000196159	ENST00000394329	Transcript	synonymous_variant	6208	6195	2065	I	atT/atC	.	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	.	5/17	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTATTGATAC	.	5	ESCA
GRIA2	0	.	GRCh37	4	158281215	158281215	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2211G>A	p.%3D	p.K737K	ENST00000296526	13/16	27	21	6	73	73	0	GRIA2,synonymous_variant,p.%3D,ENST00000264426,;GRIA2,synonymous_variant,p.%3D,ENST00000507898,;GRIA2,synonymous_variant,p.%3D,ENST00000393815,;GRIA2,synonymous_variant,p.%3D,ENST00000296526,;GRIA2,synonymous_variant,p.%3D,ENST00000449365,;GRIA2,synonymous_variant,p.%3D,ENST00000510854,;AC079233.1,upstream_gene_variant,,ENST00000578227,;GRIA2,synonymous_variant,p.%3D,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,;GRIA2,upstream_gene_variant,,ENST00000503980,;	A	ENSG00000120251	ENST00000296526	Transcript	synonymous_variant	2536	2211	737	K	aaG/aaA	.	.	.	1	GRIA2	HGNC	4572	protein_coding	YES	CCDS3797.1	ENSP00000296526	GRIA2_HUMAN	D6RFM6_HUMAN,D6REK8_HUMAN,D6RDX5_HUMAN,D6RBV7_HUMAN,D6R9Z0_HUMAN,A8MT92_HUMAN	UPI000002AA8D	.	.	.	13/16	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF99,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAGCCTTG	.	5	ESCA
MARCH1	0	.	GRCh37	4	164466807	164466807	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.512G>T	p.Trp171Leu	p.W171L	ENST00000503008	7/8	23	18	4	66	66	0	MARCH1,missense_variant,p.Trp171Leu,ENST00000503008,;MARCH1,missense_variant,p.Trp154Leu,ENST00000339875,;MARCH1,missense_variant,p.Trp171Leu,ENST00000274056,;MARCH1,missense_variant,p.Trp427Leu,ENST00000514618,;MARCH1,3_prime_UTR_variant,,ENST00000510786,;	A	ENSG00000145416	ENST00000503008	Transcript	missense_variant	1489	512	171	W/L	tGg/tTg	.	.	.	-1	MARCH1	HGNC	26077	protein_coding	YES	CCDS54814.1	ENSP00000427223	MARH1_HUMAN	D6REN1_HUMAN	UPI0000037BB3	.	deleterious(0.03)	benign(0.225)	7/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23012:SF53,hmmpanther:PTHR23012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGACCAAACC	.	4	ESCA
ATP10D	0	.	GRCh37	4	47548721	47548721	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1477A>G	p.Met493Val	p.M493V	ENST00000273859	10/23	21	11	9	63	63	0	ATP10D,missense_variant,p.Met478Val,ENST00000504445,;ATP10D,missense_variant,p.Met493Val,ENST00000273859,;ATP10D,missense_variant,p.Met141Val,ENST00000503288,;	G	ENSG00000145246	ENST00000273859	Transcript	missense_variant	1746	1477	493	M/V	Atg/Gtg	COSM3780293	.	.	1	ATP10D	HGNC	13549	protein_coding	YES	CCDS3476.1	ENSP00000273859	AT10D_HUMAN	.	UPI00001AE9B7	.	tolerated(0.56)	benign(0.002)	10/23	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF61,Pfam_domain:PF12710,TIGRFAM_domain:TIGR01652	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCAATATGGCA	.	4	ESCA
AASDH	0	.	GRCh37	4	57216134	57216134	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1783C>T	p.Leu595Phe	p.L595F	ENST00000205214	11/15	55	44	11	87	87	0	AASDH,missense_variant,p.Leu110Phe,ENST00000434343,;AASDH,missense_variant,p.Leu442Phe,ENST00000602986,;AASDH,missense_variant,p.Leu595Phe,ENST00000451613,;AASDH,missense_variant,p.Leu595Phe,ENST00000205214,;AASDH,missense_variant,p.Leu595Phe,ENST00000502617,;AASDH,missense_variant,p.Leu495Phe,ENST00000513376,;AASDH,3_prime_UTR_variant,,ENST00000503808,;AASDH,3_prime_UTR_variant,,ENST00000514745,;	A	ENSG00000157426	ENST00000205214	Transcript	missense_variant	1964	1783	595	L/F	Ctc/Ttc	.	.	.	-1	AASDH	HGNC	23993	protein_coding	YES	CCDS3504.1	ENSP00000205214	ACSF4_HUMAN	G3V0G4_HUMAN	UPI000020B8EF	.	tolerated(0.42)	benign(0.116)	11/15	.	Superfamily_domains:SSF47336,Pfam_domain:PF00550,Gene3D:1.10.1200.10,hmmpanther:PTHR24095:SF43,hmmpanther:PTHR24095,PROSITE_profiles:PS50075	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GAGGAGCCGGA	.	4	ESCA
CENPC	0	.	GRCh37	4	68355801	68355801	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2554A>T	p.Lys852Ter	p.K852*	ENST00000273853	17/19	91	82	9	116	115	1	CENPC,stop_gained,p.Lys852Ter,ENST00000273853,;CENPC,3_prime_UTR_variant,,ENST00000506882,;CENPC,3_prime_UTR_variant,,ENST00000515140,;CENPC,3_prime_UTR_variant,,ENST00000513216,;CENPC,downstream_gene_variant,,ENST00000510189,;	A	ENSG00000145241	ENST00000273853	Transcript	stop_gained	2805	2554	852	K/*	Aag/Tag	.	.	.	-1	CENPC	HGNC	1854	protein_coding	YES	CCDS47063.1	ENSP00000273853	CENPC_HUMAN	.	UPI00004135A3	.	.	.	17/19	.	hmmpanther:PTHR16684,Superfamily_domains:SSF51182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGCTTAACAA	.	4	ESCA
WDFY3	0	.	GRCh37	4	85729487	85729487	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2429G>C	p.Arg810Thr	p.R810T	ENST00000295888	15/68	75	65	9	131	131	0	WDFY3,missense_variant,p.Arg810Thr,ENST00000295888,;WDFY3,missense_variant,p.Arg810Thr,ENST00000322366,;WDFY3-AS1,intron_variant,,ENST00000510449,;WDFY3,intron_variant,,ENST00000505923,;WDFY3,upstream_gene_variant,,ENST00000512267,;WDFY3,downstream_gene_variant,,ENST00000426414,;	G	ENSG00000163625	ENST00000295888	Transcript	missense_variant	2837	2429	810	R/T	aGg/aCg	.	.	.	-1	WDFY3	HGNC	20751	protein_coding	YES	CCDS3609.1	ENSP00000295888	WDFY3_HUMAN	D6RJE4_HUMAN,A7E1Z6_HUMAN	UPI000013E2C7	.	tolerated(0.3)	benign(0.306)	15/68	.	hmmpanther:PTHR13743:SF55,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTACCTTTTC	.	4	ESCA
FNIP1	0	.	GRCh37	5	130980297	130980297	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*81C>T	.	.	ENST00000510461	18/18	33	23	9	66	66	0	FNIP1,3_prime_UTR_variant,,ENST00000307968,;FNIP1,3_prime_UTR_variant,,ENST00000510461,;FNIP1,3_prime_UTR_variant,,ENST00000307954,;CTC-432M15.3,intron_variant,,ENST00000514667,;	A	ENSG00000217128	ENST00000510461	Transcript	3_prime_UTR_variant	3678	.	.	.	.	.	.	.	-1	FNIP1	HGNC	29418	protein_coding	YES	CCDS34227.1	ENSP00000421985	FNIP1_HUMAN	B3KX44_HUMAN	UPI00001AEE81	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAGAATCT	.	5	ESCA
PCDHA9	0	.	GRCh37	5	140229864	140229864	+	Missense_Mutation	SNP	G	G	A	rs140634296	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1784G>A	p.Arg595His	p.R595H	ENST00000532602	1/4	23	12	11	39	39	0	PCDHA9,missense_variant,p.Arg595His,ENST00000378122,;PCDHA9,missense_variant,p.Arg595His,ENST00000532602,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	A	ENSG00000204961	ENST00000532602	Transcript	missense_variant	2817	1784	595	R/H	cGc/cAc	rs140634296	.	.	1	PCDHA9	HGNC	8675	protein_coding	YES	CCDS54920.1	ENSP00000436042	PCDA9_HUMAN	.	UPI00001273D1	.	tolerated_low_confidence(0.07)	probably_damaging(0.981)	1/4	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGCGCGCAG	by1000G	5	ESCA
PCDHGA9	0	.	GRCh37	5	140782780	140782780	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.261G>A	p.%3D	p.A87A	ENST00000573521	1/4	34	23	10	49	49	0	PCDHGA9,synonymous_variant,p.%3D,ENST00000573521,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGB6,upstream_gene_variant,,ENST00000520790,;	A	ENSG00000261934	ENST00000573521	Transcript	synonymous_variant	261	261	87	A	gcG/gcA	.	.	.	1	PCDHGA9	HGNC	8707	protein_coding	YES	CCDS58981.1	ENSP00000460274	PCDG9_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI00000721C3	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF86,hmmpanther:PTHR24028,Pfam_domain:PF08266,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGCGGGTAG	.	5	ESCA
MAT2B	0	.	GRCh37	5	162940973	162940973	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499G>A	p.Glu167Lys	p.E167K	ENST00000321757	4/7	36	27	8	87	87	0	MAT2B,missense_variant,p.Glu167Lys,ENST00000321757,;MAT2B,missense_variant,p.Glu102Lys,ENST00000421814,;MAT2B,missense_variant,p.Glu156Lys,ENST00000280969,;MAT2B,missense_variant,p.Glu167Lys,ENST00000518095,;MAT2B,upstream_gene_variant,,ENST00000521838,;MAT2B,3_prime_UTR_variant,,ENST00000520449,;MAT2B,non_coding_transcript_exon_variant,,ENST00000523606,;MAT2B,downstream_gene_variant,,ENST00000519719,;	A	ENSG00000038274	ENST00000321757	Transcript	missense_variant	638	499	167	E/K	Gaa/Aaa	.	.	.	1	MAT2B	HGNC	6905	protein_coding	YES	CCDS4365.1	ENSP00000325425	MAT2B_HUMAN	.	UPI0000037B81	.	deleterious(0)	probably_damaging(0.99)	4/7	.	hmmpanther:PTHR10491,hmmpanther:PTHR10491:SF2,Gene3D:3.40.50.720,Pfam_domain:PF04321,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGAGAAAAG	.	5	ESCA
AGXT2	0	.	GRCh37	5	35049407	35049407	+	5'Flank	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000231420	.	59	52	7	76	76	0	PRLR,synonymous_variant,p.%3D,ENST00000348262,;PRLR,synonymous_variant,p.%3D,ENST00000397391,;PRLR,synonymous_variant,p.%3D,ENST00000231423,;PRLR,3_prime_UTR_variant,,ENST00000513753,;PRLR,intron_variant,,ENST00000542609,;AGXT2,upstream_gene_variant,,ENST00000231420,;AC010368.2,upstream_gene_variant,,ENST00000594869,;PRLR,3_prime_UTR_variant,,ENST00000509140,;PRLR,3_prime_UTR_variant,,ENST00000514088,;AGXT2,upstream_gene_variant,,ENST00000505542,;AGXT2,upstream_gene_variant,,ENST00000510428,;	T	ENSG00000113492	ENST00000231420	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1209	-1	AGXT2	HGNC	14412	protein_coding	YES	CCDS3908.1	ENSP00000231420	AGT2_HUMAN	.	UPI0000125709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGGTCAATGT	.	3	ESCA
PRKAA1	0	.	GRCh37	5	40767573	40767573	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.861T>C	p.%3D	p.D287D	ENST00000354209	7/10	52	35	17	51	51	0	PRKAA1,synonymous_variant,p.%3D,ENST00000397128,;PRKAA1,synonymous_variant,p.%3D,ENST00000354209,;PRKAA1,downstream_gene_variant,,ENST00000296800,;PRKAA1,non_coding_transcript_exon_variant,,ENST00000506652,;PRKAA1,non_coding_transcript_exon_variant,,ENST00000505783,;PRKAA1,downstream_gene_variant,,ENST00000509874,;PRKAA1,upstream_gene_variant,,ENST00000513152,;	G	ENSG00000132356	ENST00000354209	Transcript	synonymous_variant	1046	861	287	D	gaT/gaC	.	.	.	-1	PRKAA1	HGNC	9376	protein_coding	YES	CCDS3933.2	ENSP00000346148	AAPK1_HUMAN	.	UPI00003529FB	.	.	.	7/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF81,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGATATCTTT	.	5	ESCA
PIK3R1	0	.	GRCh37	5	67597262	67597262	+	3'UTR	SNP	G	G	A	rs201899089	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3833G>A	.	.	ENST00000521381	16/16	24	19	5	59	58	1	PIK3R1,3_prime_UTR_variant,,ENST00000274335,;PIK3R1,3_prime_UTR_variant,,ENST00000521381,;PIK3R1,3_prime_UTR_variant,,ENST00000396611,;PIK3R1,downstream_gene_variant,,ENST00000336483,;PIK3R1,downstream_gene_variant,,ENST00000521657,;PIK3R1,downstream_gene_variant,,ENST00000320694,;PIK3R1,downstream_gene_variant,,ENST00000523872,;PIK3R1,downstream_gene_variant,,ENST00000518813,;	A	ENSG00000145675	ENST00000521381	Transcript	3_prime_UTR_variant	6624	.	.	.	.	rs201899089	.	.	1	PIK3R1	HGNC	8979	protein_coding	YES	CCDS3993.1	ENSP00000428056	P85A_HUMAN	J7GXU7_HUMAN,J7GU64_HUMAN,E5RJY0_HUMAN,E5RHI0_HUMAN,E5RGI8_HUMAN,B3KWZ7_HUMAN	UPI000013D9FF	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TATATGTGTGT	.	2	ESCA
MAP1B	0	.	GRCh37	5	71482557	71482557	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486C>G	p.Phe162Leu	p.F162L	ENST00000296755	4/7	20	13	7	51	51	0	MAP1B,missense_variant,p.Phe162Leu,ENST00000511641,;MAP1B,missense_variant,p.Phe36Leu,ENST00000504492,;MAP1B,missense_variant,p.Phe162Leu,ENST00000296755,;MAP1B,downstream_gene_variant,,ENST00000512974,;MAP1B,3_prime_UTR_variant,,ENST00000513526,;	G	ENSG00000131711	ENST00000296755	Transcript	missense_variant	784	486	162	F/L	ttC/ttG	.	.	.	1	MAP1B	HGNC	6836	protein_coding	YES	CCDS4012.1	ENSP00000296755	MAP1B_HUMAN	D6RGJ3_HUMAN,D6RA40_HUMAN	UPI000013E382	.	.	unknown(0)	4/7	.	hmmpanther:PTHR13843,hmmpanther:PTHR13843:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTTCATAGA	.	5	ESCA
THBS4	0	.	GRCh37	5	79354543	79354543	+	Missense_Mutation	SNP	G	G	A	rs553602331	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662G>A	p.Arg221Gln	p.R221Q	ENST00000350881	5/22	32	19	13	74	74	0	THBS4,missense_variant,p.Arg221Gln,ENST00000350881,;THBS4,missense_variant,p.Arg130Gln,ENST00000511733,;CTD-2201I18.1,intron_variant,,ENST00000503007,;THBS4,downstream_gene_variant,,ENST00000510218,;THBS4,downstream_gene_variant,,ENST00000513310,;	A	ENSG00000113296	ENST00000350881	Transcript	missense_variant	852	662	221	R/Q	cGg/cAg	rs553602331,COSM173468	.	.	1	THBS4	HGNC	11788	protein_coding	YES	CCDS4049.1	ENSP00000339730	TSP4_HUMAN	E7ES19_HUMAN	UPI000013D591	.	tolerated(0.14)	possibly_damaging(0.667)	5/22	.	hmmpanther:PTHR10199:SF4,hmmpanther:PTHR10199,Pfam_domain:PF11598,Gene3D:1.20.5.10,Superfamily_domains:0053531	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAACCGGCAGT	by1000G	5	ESCA
BCLAF1	0	.	GRCh37	6	136579981	136579981	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2267G>T	.	.	ENST00000531224	13/13	37	33	4	56	56	0	BCLAF1,3_prime_UTR_variant,,ENST00000353331,;BCLAF1,3_prime_UTR_variant,,ENST00000531224,;BCLAF1,3_prime_UTR_variant,,ENST00000527536,;BCLAF1,downstream_gene_variant,,ENST00000392348,;BCLAF1,downstream_gene_variant,,ENST00000534762,;BCLAF1,downstream_gene_variant,,ENST00000530767,;BCLAF1,downstream_gene_variant,,ENST00000527759,;BCLAF1,downstream_gene_variant,,ENST00000031135,;BCLAF1,downstream_gene_variant,,ENST00000529917,;BCLAF1,3_prime_UTR_variant,,ENST00000527613,;BCLAF1,intron_variant,,ENST00000533422,;BCLAF1,downstream_gene_variant,,ENST00000534269,;BCLAF1,downstream_gene_variant,,ENST00000526228,;BCLAF1,downstream_gene_variant,,ENST00000529522,;BCLAF1,downstream_gene_variant,,ENST00000530429,;BCLAF1,downstream_gene_variant,,ENST00000532384,;	A	ENSG00000029363	ENST00000531224	Transcript	3_prime_UTR_variant	5283	.	.	.	.	.	.	.	-1	BCLAF1	HGNC	16863	protein_coding	YES	CCDS5177.1	ENSP00000435210	BCLF1_HUMAN	B0AZU3_HUMAN	UPI000006FCE7	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	ATACACACCTA	.	3	ESCA
MTHFD1L	0	.	GRCh37	6	151293122	151293122	+	Missense_Mutation	SNP	A	A	G	rs780895264	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2053A>G	p.Ile685Val	p.I685V	ENST00000367321	20/28	35	27	7	104	104	0	MTHFD1L,missense_variant,p.Ile685Val,ENST00000367321,;MTHFD1L,non_coding_transcript_exon_variant,,ENST00000478643,;	G	ENSG00000120254	ENST00000367321	Transcript	missense_variant	2327	2053	685	I/V	Att/Gtt	rs780895264	.	.	1	MTHFD1L	HGNC	21055	protein_coding	YES	CCDS5228.1	ENSP00000356290	C1TM_HUMAN	Q5JYA8_HUMAN,Q5JYA3_HUMAN,B7ZM99_HUMAN,B2RD24_HUMAN	UPI00001CE513	.	deleterious(0)	probably_damaging(1)	20/28	.	HAMAP:MF_01543,hmmpanther:PTHR10025,hmmpanther:PTHR10025:SF14,Pfam_domain:PF01268,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAACATTGCT	.	5	ESCA
GABBR1	0	.	GRCh37	6	29588992	29588992	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209C>A	p.%3D	p.I403I	ENST00000377034	11/23	43	35	8	55	55	0	GABBR1,synonymous_variant,p.%3D,ENST00000377016,;GABBR1,synonymous_variant,p.%3D,ENST00000376977,;GABBR1,synonymous_variant,p.%3D,ENST00000355973,;GABBR1,synonymous_variant,p.%3D,ENST00000377012,;GABBR1,synonymous_variant,p.%3D,ENST00000377034,;GABBR1,synonymous_variant,p.%3D,ENST00000494877,;GABBR1,3_prime_UTR_variant,,ENST00000472823,;GABBR1,3_prime_UTR_variant,,ENST00000491829,;GABBR1,non_coding_transcript_exon_variant,,ENST00000494634,;GABBR1,downstream_gene_variant,,ENST00000485508,;GABBR1,downstream_gene_variant,,ENST00000477029,;	T	ENSG00000204681	ENST00000377034	Transcript	synonymous_variant	1545	1209	403	I	atC/atA	.	.	.	-1	GABBR1	HGNC	4070	protein_coding	YES	CCDS4663.1	ENSP00000366233	GABR1_HUMAN	F8WAV2_HUMAN,F8WAS6_HUMAN,C9JZG6_HUMAN	UPI000004618A	.	.	.	11/23	.	hmmpanther:PTHR10519:SF3,hmmpanther:PTHR10519,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTAGATCTT	.	5	ESCA
CSNK2B-LY6G5B-1181	0	.	GRCh37	6	31637232	31637232	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.504C>T	p.%3D	p.F168F	ENST00000375880	6/8	19	14	4	32	32	0	CSNK2B-LY6G5B-1181,synonymous_variant,p.%3D,ENST00000375880,;CSNK2B,synonymous_variant,p.%3D,ENST00000375885,;CSNK2B,synonymous_variant,p.%3D,ENST00000375865,;CSNK2B,synonymous_variant,p.%3D,ENST00000375866,;CSNK2B,synonymous_variant,p.%3D,ENST00000375882,;CSNK2B-LY6G5B-1181,intron_variant,,ENST00000409691,;GPANK1,upstream_gene_variant,,ENST00000456540,;GPANK1,upstream_gene_variant,,ENST00000375906,;GPANK1,upstream_gene_variant,,ENST00000375900,;GPANK1,upstream_gene_variant,,ENST00000458083,;GPANK1,upstream_gene_variant,,ENST00000445768,;LY6G5B,upstream_gene_variant,,ENST00000409525,;GPANK1,upstream_gene_variant,,ENST00000375895,;GPANK1,upstream_gene_variant,,ENST00000375896,;GPANK1,upstream_gene_variant,,ENST00000375893,;LY6G5B,upstream_gene_variant,,ENST00000375864,;LY6G5B,upstream_gene_variant,,ENST00000471088,;CSNK2B,non_coding_transcript_exon_variant,,ENST00000468255,;CSNK2B,non_coding_transcript_exon_variant,,ENST00000481269,;CSNK2B,downstream_gene_variant,,ENST00000475875,;CSNK2B,downstream_gene_variant,,ENST00000465481,;	T	ENSG00000263020	ENST00000375880	Transcript	synonymous_variant	622	504	168	F	ttC/ttT	.	.	.	1	CSNK2B-LY6G5B-1181	Uniprot_gn	.	protein_coding	YES	.	ENSP00000365040	.	Q5SRQ3_HUMAN	UPI00004702F4	.	.	.	6/8	.	hmmpanther:PTHR11740,Pfam_domain:PF01214,Gene3D:2.20.25.20,SMART_domains:SM01085,Superfamily_domains:0047698,Prints_domain:PR00472	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTCATGGT	.	5	ESCA
NOTCH4	0	.	GRCh37	6	32184785	32184785	+	Missense_Mutation	SNP	C	C	T	rs11963697	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1798G>A	p.Val600Ile	p.V600I	ENST00000375023	11/30	48	40	7	76	76	0	NOTCH4,missense_variant,p.Val600Ile,ENST00000375023,;NOTCH4,upstream_gene_variant,,ENST00000465528,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,;	T	ENSG00000204301	ENST00000375023	Transcript	missense_variant	1937	1798	600	V/I	Gtt/Att	rs11963697	.	.	-1	NOTCH4	HGNC	7884	protein_coding	YES	CCDS34420.1	ENSP00000364163	NOTC4_HUMAN	.	UPI0000130571	.	tolerated(0.1)	benign(0.005)	11/30	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Superfamily_domains:SSF57196	G:0.0028	G:0.0098	G:0.0014	.	G:0	G:0	G:0	G:0.0046	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAACGGGAC	byFrequency|byCluster|byHapMap|by1000G	4	ESCA
ZNF76	0	.	GRCh37	6	35263676	35263676	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*651T>A	.	.	ENST00000373953	14/14	25	20	5	44	44	0	ZNF76,3_prime_UTR_variant,,ENST00000440666,;ZNF76,3_prime_UTR_variant,,ENST00000339411,;ZNF76,3_prime_UTR_variant,,ENST00000373953,;ZNF76,downstream_gene_variant,,ENST00000469195,;DEF6,upstream_gene_variant,,ENST00000542066,;ZNF76,downstream_gene_variant,,ENST00000498555,;DEF6,upstream_gene_variant,,ENST00000316637,;ZNF76,3_prime_UTR_variant,,ENST00000229405,;ZNF76,downstream_gene_variant,,ENST00000486891,;ZNF76,downstream_gene_variant,,ENST00000479226,;	A	ENSG00000065029	ENST00000373953	Transcript	3_prime_UTR_variant	2630	.	.	.	.	.	.	.	1	ZNF76	HGNC	13149	protein_coding	YES	CCDS4801.1	ENSP00000363064	ZNF76_HUMAN	E7EX64_HUMAN	UPI000013C41C	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTTTAATT	.	2	ESCA
LHFPL5	0	.	GRCh37	6	35787239	35787239	+	Intron	SNP	C	C	T	rs368091965	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*15C>T	.	.	ENST00000360215	3/4	49	40	9	82	82	0	LHFPL5,splice_region_variant,,ENST00000360215,;LHFPL5,downstream_gene_variant,,ENST00000373853,;LHFPL5,non_coding_transcript_exon_variant,,ENST00000496656,;	T	ENSG00000197753	ENST00000360215	Transcript	splice_region_variant	1052	.	.	.	.	rs368091965	.	.	1	LHFPL5	HGNC	21253	protein_coding	YES	CCDS4812.1	ENSP00000353346	TMHS_HUMAN	.	UPI000006E12D	.	.	.	3/4	.	.	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0.0007	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGTCGGTGA	byCluster|by1000G	4	ESCA
UFL1	0	.	GRCh37	6	97001214	97001214	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2220C>G	p.%3D	p.V740V	ENST00000369278	19/19	34	30	4	66	66	0	UFL1,synonymous_variant,p.%3D,ENST00000369278,;	G	ENSG00000014123	ENST00000369278	Transcript	synonymous_variant	2286	2220	740	V	gtC/gtG	.	.	.	1	UFL1	HGNC	23039	protein_coding	YES	CCDS5034.1	ENSP00000358283	UFL1_HUMAN	B7ZAY8_HUMAN	UPI0000072D61	.	.	.	19/19	.	hmmpanther:PTHR31057,hmmpanther:PTHR31057:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTAGTCAGTCA	.	4	ESCA
EPHB4	0	.	GRCh37	7	100419977	100419977	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724G>T	p.Asp242Tyr	p.D242Y	ENST00000358173	4/17	35	26	9	57	57	0	EPHB4,missense_variant,p.Asp242Tyr,ENST00000360620,;EPHB4,missense_variant,p.Asp242Tyr,ENST00000358173,;RN7SL750P,upstream_gene_variant,,ENST00000582814,;EPHB4,non_coding_transcript_exon_variant,,ENST00000489808,;EPHB4,non_coding_transcript_exon_variant,,ENST00000477446,;SLC12A9,upstream_gene_variant,,ENST00000461016,;EPHB4,non_coding_transcript_exon_variant,,ENST00000487222,;EPHB4,upstream_gene_variant,,ENST00000492878,;	A	ENSG00000196411	ENST00000358173	Transcript	missense_variant	1193	724	242	D/Y	Gat/Tat	.	.	.	-1	EPHB4	HGNC	3395	protein_coding	YES	CCDS5706.1	ENSP00000350896	EPHB4_HUMAN	Q541P7_HUMAN	UPI0000000DBB	.	deleterious(0)	probably_damaging(0.982)	4/17	.	hmmpanther:PTHR24416:SF296,hmmpanther:PTHR24416,PROSITE_patterns:PS00791,PIRSF_domain:PIRSF000666	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATCCTCAC	.	4	ESCA
DNAJC2	0	.	GRCh37	7	102957429	102957429	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1275G>A	p.%3D	p.E425E	ENST00000379263	13/17	29	23	6	52	52	0	DNAJC2,synonymous_variant,p.%3D,ENST00000249270,;DNAJC2,synonymous_variant,p.%3D,ENST00000379263,;PMPCB,intron_variant,,ENST00000420236,;PMPCB,downstream_gene_variant,,ENST00000428154,;PMPCB,downstream_gene_variant,,ENST00000249269,;DNAJC2,non_coding_transcript_exon_variant,,ENST00000475090,;DNAJC2,non_coding_transcript_exon_variant,,ENST00000492497,;DNAJC2,non_coding_transcript_exon_variant,,ENST00000464253,;DNAJC2,non_coding_transcript_exon_variant,,ENST00000475065,;PMPCB,intron_variant,,ENST00000444457,;PMPCB,downstream_gene_variant,,ENST00000469560,;PMPCB,downstream_gene_variant,,ENST00000453466,;PMPCB,downstream_gene_variant,,ENST00000443722,;	T	ENSG00000105821	ENST00000379263	Transcript	synonymous_variant	1526	1275	425	E	gaG/gaA	.	.	.	-1	DNAJC2	HGNC	13192	protein_coding	YES	CCDS43628.1	ENSP00000368565	DNJC2_HUMAN	Q08AR5_HUMAN,C9IZ83_HUMAN	UPI000020F858	.	.	.	13/17	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCTCTTT	.	5	ESCA
NRCAM	0	.	GRCh37	7	107872819	107872819	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378G>A	p.%3D	p.R126R	ENST00000379028	7/33	36	28	8	59	59	0	NRCAM,synonymous_variant,p.%3D,ENST00000379022,;NRCAM,synonymous_variant,p.%3D,ENST00000351718,;NRCAM,synonymous_variant,p.%3D,ENST00000417701,;NRCAM,synonymous_variant,p.%3D,ENST00000413765,;NRCAM,synonymous_variant,p.%3D,ENST00000379024,;NRCAM,synonymous_variant,p.%3D,ENST00000379028,;NRCAM,synonymous_variant,p.%3D,ENST00000425651,;NRCAM,downstream_gene_variant,,ENST00000418239,;NRCAM,downstream_gene_variant,,ENST00000419936,;NRCAM,downstream_gene_variant,,ENST00000456431,;NRCAM,downstream_gene_variant,,ENST00000442580,;	T	ENSG00000091129	ENST00000379028	Transcript	synonymous_variant	849	378	126	R	agG/agA	.	.	.	-1	NRCAM	HGNC	7994	protein_coding	YES	CCDS47686.1	ENSP00000368314	NRCAM_HUMAN	C9JUR7_HUMAN,C9JF43_HUMAN,B3KRX0_HUMAN	UPI00005E2661	.	.	.	7/33	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF554,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TCGTTCCTTGC	.	4	ESCA
KIAA1549	0	.	GRCh37	7	138522658	138522658	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5846A>G	p.His1949Arg	p.H1949R	ENST00000422774	20/20	31	27	4	51	51	0	TMEM213,missense_variant,p.Trp67Arg,ENST00000413208,;KIAA1549,missense_variant,p.His1949Arg,ENST00000422774,;KIAA1549,missense_variant,p.His1883Arg,ENST00000242365,;KIAA1549,missense_variant,p.His1933Arg,ENST00000440172,;	C	ENSG00000122778	ENST00000422774	Transcript	missense_variant	5895	5846	1949	H/R	cAc/cGc	.	.	.	-1	KIAA1549	HGNC	22219	protein_coding	YES	CCDS56513.1	ENSP00000416040	K1549_HUMAN	.	UPI0001837EBD	.	deleterious(0.03)	benign(0.055)	20/20	.	hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTGTGGAAG	.	2	ESCA
ERVW-1	0	.	GRCh37	7	92098694	92098694	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1002T>C	p.%3D	p.G334G	ENST00000493463	1/1	39	23	16	69	69	0	ERVW-1,synonymous_variant,p.%3D,ENST00000603053,;ERVW-1,synonymous_variant,p.%3D,ENST00000493463,;AC007566.10,intron_variant,,ENST00000427458,;ERVW-1,intron_variant,,ENST00000603704,;ERVW-1,intron_variant,,ENST00000604270,;	G	ENSG00000242950	ENST00000493463	Transcript	synonymous_variant	1926	1002	334	G	ggT/ggC	.	.	.	-1	ERVW-1	HGNC	13525	protein_coding	YES	CCDS5626.1	ENSP00000419945	ENW1_HUMAN	Q9UQF1_HUMAN,Q96TB5_HUMAN,D0EYG5_HUMAN	UPI00000389BB	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF41,Pfam_domain:PF00429,Superfamily_domains:SSF58069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGTACCTAG	.	5	ESCA
RIMS2	0	.	GRCh37	8	104892864	104892864	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.699-4662A>G	.	.	ENST00000406091	.	91	83	8	87	87	0	RIMS2,5_prime_UTR_variant,,ENST00000436393,;RIMS2,intron_variant,,ENST00000406091,;RIMS2,intron_variant,,ENST00000408894,;RIMS2,intron_variant,,ENST00000504942,;RIMS2,intron_variant,,ENST00000507740,;RIMS2,intron_variant,,ENST00000262231,;RIMS2,intron_variant,,ENST00000515551,;RIMS2,intron_variant,,ENST00000522174,;	G	ENSG00000176406	ENST00000406091	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RIMS2	HGNC	17283	protein_coding	YES	CCDS55269.1	ENSP00000384892	RIMS2_HUMAN	E9PFB6_HUMAN	UPI0001597063	.	.	.	.	3/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GATGTATTTTT	.	3	ESCA
ZFPM2	0	.	GRCh37	8	106815849	106815849	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*83A>T	.	.	ENST00000407775	8/8	92	80	12	85	85	0	ZFPM2,3_prime_UTR_variant,,ENST00000520492,;ZFPM2,3_prime_UTR_variant,,ENST00000407775,;ZFPM2,downstream_gene_variant,,ENST00000517361,;ZFPM2,downstream_gene_variant,,ENST00000378472,;RP11-152P17.2,intron_variant,,ENST00000524045,;RP11-152P17.2,intron_variant,,ENST00000509144,;RP11-152P17.2,intron_variant,,ENST00000521622,;RP11-152P17.2,intron_variant,,ENST00000520594,;RP11-152P17.2,intron_variant,,ENST00000520433,;RP11-152P17.2,intron_variant,,ENST00000518932,;ZFPM2,downstream_gene_variant,,ENST00000522296,;RP11-152P17.2,intron_variant,,ENST00000520078,;	T	ENSG00000169946	ENST00000407775	Transcript	3_prime_UTR_variant	3789	.	.	.	.	.	.	.	1	ZFPM2	HGNC	16700	protein_coding	YES	CCDS47908.1	ENSP00000384179	FOG2_HUMAN	Q9NPQ0_HUMAN,F5H542_HUMAN,E7ET52_HUMAN,E5RJX0_HUMAN	UPI000057A0B4	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGAATTACA	.	4	ESCA
FDFT1	0	.	GRCh37	8	11666396	11666396	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193A>G	p.Met65Val	p.M65V	ENST00000220584	2/8	21	16	4	51	51	0	FDFT1,start_lost,p.Met1?,ENST00000530664,;FDFT1,start_lost,p.Met1?,ENST00000528812,;FDFT1,missense_variant,p.Met65Val,ENST00000220584,;FDFT1,missense_variant,p.Met65Val,ENST00000530337,;FDFT1,missense_variant,p.Met65Val,ENST00000443614,;FDFT1,missense_variant,p.Met58Val,ENST00000525900,;FDFT1,5_prime_UTR_variant,,ENST00000538689,;FDFT1,upstream_gene_variant,,ENST00000528643,;FDFT1,upstream_gene_variant,,ENST00000525777,;FDFT1,intron_variant,,ENST00000446331,;FDFT1,start_lost,p.Met1?,ENST00000532266,;FDFT1,3_prime_UTR_variant,,ENST00000525607,;FDFT1,non_coding_transcript_exon_variant,,ENST00000531249,;FDFT1,non_coding_transcript_exon_variant,,ENST00000525954,;FDFT1,non_coding_transcript_exon_variant,,ENST00000531733,;FDFT1,intron_variant,,ENST00000525283,;FDFT1,intron_variant,,ENST00000529464,;	G	ENSG00000079459	ENST00000220584	Transcript	missense_variant	415	193	65	M/V	Atg/Gtg	.	.	.	1	FDFT1	HGNC	3629	protein_coding	YES	CCDS5985.1	ENSP00000220584	FDFT_HUMAN	Q6IAX1_HUMAN,E9PJG4_HUMAN,B7Z1J3_HUMAN,B4DT56_HUMAN,B3KQ95_HUMAN	UPI000012A5D5	.	tolerated(0.06)	benign(0.005)	2/8	.	Superfamily_domains:SSF48576,Pfam_domain:PF00494,TIGRFAM_domain:TIGR01559,Gene3D:1.10.600.10,hmmpanther:PTHR11626	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAAATGCGG	.	2	ESCA
TBC1D31	0	.	GRCh37	8	124094947	124094947	+	Missense_Mutation	SNP	A	A	G	rs757300043	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.230A>G	p.Asn77Ser	p.N77S	ENST00000287380	3/22	59	47	12	55	55	0	TBC1D31,missense_variant,p.Asn77Ser,ENST00000309336,;TBC1D31,missense_variant,p.Asn67Ser,ENST00000522276,;TBC1D31,missense_variant,p.Asn77Ser,ENST00000327098,;TBC1D31,missense_variant,p.Asn77Ser,ENST00000287380,;TBC1D31,5_prime_UTR_variant,,ENST00000518684,;TBC1D31,intron_variant,,ENST00000522420,;TBC1D31,intron_variant,,ENST00000378080,;TBC1D31,intron_variant,,ENST00000519418,;TBC1D31,intron_variant,,ENST00000520368,;TBC1D31,intron_variant,,ENST00000521676,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000518099,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000521980,;TBC1D31,intron_variant,,ENST00000524307,;	G	ENSG00000156787	ENST00000287380	Transcript	missense_variant	320	230	77	N/S	aAt/aGt	rs757300043	.	.	1	TBC1D31	HGNC	30888	protein_coding	YES	CCDS6338.1	ENSP00000287380	TBC31_HUMAN	E5RG45_HUMAN	UPI000013DEAB	.	tolerated(0.4)	benign(0.004)	3/22	.	hmmpanther:PTHR19853,hmmpanther:PTHR19853:SF1,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCAATCTTG	.	5	ESCA
FAM83A	0	.	GRCh37	8	124214741	124214741	+	Intron	SNP	C	C	A	rs540481735	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774-4656C>A	.	.	ENST00000518448	.	98	37	60	94	93	1	FAM83A,intron_variant,,ENST00000522648,;FAM83A,intron_variant,,ENST00000518448,;FAM83A,intron_variant,,ENST00000536633,;FAM83A,intron_variant,,ENST00000276699,;FAM83A,intron_variant,,ENST00000546351,;FAM83A,intron_variant,,ENST00000318462,;FAM83A-AS1,non_coding_transcript_exon_variant,,ENST00000517519,;FAM83A-AS1,non_coding_transcript_exon_variant,,ENST00000523330,;FAM83A-AS1,non_coding_transcript_exon_variant,,ENST00000520576,;FAM83A,downstream_gene_variant,,ENST00000521468,;	A	ENSG00000147689	ENST00000518448	Transcript	intron_variant	.	.	.	.	.	rs540481735	.	.	1	FAM83A	HGNC	28210	protein_coding	YES	CCDS6340.1	ENSP00000428876	FA83A_HUMAN	.	UPI000019275C	.	.	.	.	4/4	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TTAGCCGAGAT	by1000G	2	ESCA
PLEC	0	.	GRCh37	8	145004664	145004664	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2756C>T	p.Ser919Leu	p.S919L	ENST00000322810	20/32	43	36	7	56	56	0	PLEC,missense_variant,p.Ser919Leu,ENST00000322810,;PLEC,missense_variant,p.Ser805Leu,ENST00000527096,;PLEC,missense_variant,p.Ser782Leu,ENST00000345136,;PLEC,missense_variant,p.Ser786Leu,ENST00000357649,;PLEC,missense_variant,p.Ser750Leu,ENST00000398774,;PLEC,missense_variant,p.Ser782Leu,ENST00000354589,;PLEC,missense_variant,p.Ser768Leu,ENST00000356346,;PLEC,missense_variant,p.Ser809Leu,ENST00000436759,;PLEC,missense_variant,p.Ser760Leu,ENST00000354958,;PLEC,downstream_gene_variant,,ENST00000526416,;PLEC,upstream_gene_variant,,ENST00000527303,;PLEC,downstream_gene_variant,,ENST00000528025,;	A	ENSG00000178209	ENST00000322810	Transcript	missense_variant	2926	2756	919	S/L	tCa/tTa	.	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	unknown(0)	20/32	.	Superfamily_domains:SSF46966,SMART_domains:SM00150,Gene3D:1.20.58.60,hmmpanther:PTHR11915:SF247,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTGAGAGG	.	5	ESCA
ZNF517	0	.	GRCh37	8	146035992	146035992	+	3'Flank	SNP	A	A	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000359971	.	66	29	37	96	96	0	ZNF517,3_prime_UTR_variant,,ENST00000525105,;ZNF517,downstream_gene_variant,,ENST00000359971,;ZNF517,downstream_gene_variant,,ENST00000531720,;ZNF517,downstream_gene_variant,,ENST00000528012,;ZNF517,downstream_gene_variant,,ENST00000529429,;ZNF517,intron_variant,,ENST00000526178,;ZNF517,downstream_gene_variant,,ENST00000533965,;ZNF517,downstream_gene_variant,,ENST00000530879,;	T	ENSG00000197363	ENST00000359971	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1463	1	ZNF517	HGNC	27984	protein_coding	YES	CCDS6434.1	ENSP00000353058	ZN517_HUMAN	.	UPI000045770F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGAGCTGT	.	5	ESCA
IDO1	0	.	GRCh37	8	39785379	39785379	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.887G>C	p.Arg296Thr	p.R296T	ENST00000518237	10/10	43	35	8	61	61	0	IDO1,missense_variant,p.Arg296Thr,ENST00000522495,;IDO1,missense_variant,p.Arg296Thr,ENST00000518237,;RP11-44K6.3,intron_variant,,ENST00000517623,;IDO1,3_prime_UTR_variant,,ENST00000253513,;IDO1,non_coding_transcript_exon_variant,,ENST00000523779,;IDO1,downstream_gene_variant,,ENST00000521480,;IDO1,downstream_gene_variant,,ENST00000521636,;	C	ENSG00000131203	ENST00000518237	Transcript	missense_variant	1526	887	296	R/T	aGa/aCa	.	.	.	1	IDO1	HGNC	6059	protein_coding	YES	CCDS47847.1	ENSP00000430950	I23O1_HUMAN	E5RIX2_HUMAN,E5RH36_HUMAN,E5RGR8_HUMAN	UPI00000012AA	.	deleterious(0.01)	probably_damaging(1)	10/10	.	PROSITE_patterns:PS00877,Pfam_domain:PF01231,Superfamily_domains:SSF140959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGAGAAGAT	.	5	ESCA
TOX	0	.	GRCh37	8	59719147	59719148	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1158dupA	.	.	ENST00000361421	9/9	37	33	4	76	76	0	TOX,3_prime_UTR_variant,,ENST00000361421,;	T	ENSG00000198846	ENST00000361421	Transcript	3_prime_UTR_variant	2960-2961	.	.	.	.	.	.	.	-1	TOX	HGNC	18988	protein_coding	YES	CCDS34897.1	ENSP00000354842	TOX_HUMAN	B4DYA1_HUMAN	UPI0000070A73	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TAATAGTTTTT	.	2	ESCA
ZFHX4	0	.	GRCh37	8	77767813	77767813	+	Missense_Mutation	SNP	T	T	G	rs773766567	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8656T>G	p.Phe2886Val	p.F2886V	ENST00000521891	10/11	26	11	15	26	26	0	ZFHX4,missense_variant,p.Phe2841Val,ENST00000455469,;ZFHX4,missense_variant,p.Phe2860Val,ENST00000518282,;ZFHX4,missense_variant,p.Phe2841Val,ENST00000050961,;ZFHX4,missense_variant,p.Phe2886Val,ENST00000521891,;ZFHX4,downstream_gene_variant,,ENST00000522409,;	G	ENSG00000091656	ENST00000521891	Transcript	missense_variant	9104	8656	2886	F/V	Ttt/Gtt	rs773766567	.	.	1	ZFHX4	HGNC	30939	protein_coding	YES	CCDS47878.2	ENSP00000430497	.	Q9H7F3_HUMAN,Q86WW5_HUMAN,Q6DK57_HUMAN,G3V138_HUMAN,E5RI93_HUMAN,E5RHS1_HUMAN,E5RGK3_HUMAN,E5RG79_HUMAN	UPI0000424CC7	.	.	benign(0.061)	10/11	.	hmmpanther:PTHR24208:SF40,hmmpanther:PTHR24208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGCTTTTAC	.	5	ESCA
SET	0	.	GRCh37	9	131446208	131446208	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34C>G	p.Gln12Glu	p.Q12E	ENST00000372692	1/8	39	29	10	81	81	0	SET,missense_variant,p.Gln12Glu,ENST00000372692,;SET,missense_variant,p.Gln12Glu,ENST00000454747,;SET,upstream_gene_variant,,ENST00000409104,;	G	ENSG00000119335	ENST00000372692	Transcript	missense_variant	275	34	12	Q/E	Caa/Gaa	.	.	.	1	SET	HGNC	10760	protein_coding	YES	CCDS48037.1	ENSP00000361777	SET_HUMAN	Q5VXV3_HUMAN,B2REB7_HUMAN	UPI000006D7FF	.	deleterious_low_confidence(0.02)	unknown(0)	1/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF58	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCTCAAAAG	.	5	ESCA
SSNA1	0	.	GRCh37	9	140084285	140084285	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279C>A	p.%3D	p.L93L	ENST00000322310	3/3	49	16	33	85	85	0	SSNA1,synonymous_variant,p.%3D,ENST00000322310,;TPRN,downstream_gene_variant,,ENST00000409012,;TPRN,downstream_gene_variant,,ENST00000321773,;TPRN,downstream_gene_variant,,ENST00000333046,;ANAPC2,upstream_gene_variant,,ENST00000323927,;SSNA1,non_coding_transcript_exon_variant,,ENST00000464553,;SSNA1,non_coding_transcript_exon_variant,,ENST00000459860,;SSNA1,non_coding_transcript_exon_variant,,ENST00000463511,;ANAPC2,upstream_gene_variant,,ENST00000495611,;TPRN,downstream_gene_variant,,ENST00000541945,;TPRN,downstream_gene_variant,,ENST00000477345,;	A	ENSG00000176101	ENST00000322310	Transcript	synonymous_variant	359	279	93	L	ctC/ctA	.	.	.	1	SSNA1	HGNC	11321	protein_coding	YES	CCDS7034.1	ENSP00000313752	SSNA1_HUMAN	.	UPI0000140DC3	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCTCAGCGT	.	5	ESCA
GNAQ	0	.	GRCh37	9	80430560	80430560	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448G>A	p.Glu150Lys	p.E150K	ENST00000286548	3/7	36	25	11	84	84	0	GNAQ,missense_variant,p.Glu150Lys,ENST00000286548,;GNAQ,missense_variant,p.Glu121Lys,ENST00000411677,;GNAQ,5_prime_UTR_variant,,ENST00000397476,;	T	ENSG00000156052	ENST00000286548	Transcript	missense_variant	671	448	150	E/K	Gaa/Aaa	.	.	.	-1	GNAQ	HGNC	4390	protein_coding	YES	CCDS6658.1	ENSP00000286548	GNAQ_HUMAN	G3V1P7_HUMAN	UPI000006D0FB	.	deleterious(0.01)	possibly_damaging(0.897)	3/7	.	hmmpanther:PTHR10218:SF184,hmmpanther:PTHR10218,Gene3D:1.10.400.10,Pfam_domain:PF00503,SMART_domains:SM00275,Superfamily_domains:SSF47895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATTCTCGTC	.	5	ESCA
LRCH2	0	.	GRCh37	X	114398259	114398259	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1443G>A	p.%3D	p.L481L	ENST00000317135	11/21	55	38	16	65	65	0	LRCH2,synonymous_variant,p.%3D,ENST00000538422,;LRCH2,synonymous_variant,p.%3D,ENST00000317135,;	T	ENSG00000130224	ENST00000317135	Transcript	synonymous_variant	1474	1443	481	L	ttG/ttA	.	.	.	-1	LRCH2	HGNC	29292	protein_coding	YES	CCDS48155.1	ENSP00000325091	LRCH2_HUMAN	.	UPI000022DB30	.	.	.	11/21	.	hmmpanther:PTHR23155:SF409,hmmpanther:PTHR23155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGCAATAA	.	5	ESCA
MIR507	0	.	GRCh37	X	146312548	146312548	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.48G>C	.	.	ENST00000385234	1/1	23	16	6	37	37	0	MIR507,non_coding_transcript_exon_variant,,ENST00000385234,;MIR506,upstream_gene_variant,,ENST00000384998,;	G	ENSG00000207969	ENST00000385234	Transcript	non_coding_transcript_exon_variant	48	.	.	.	.	.	.	.	-1	MIR507	HGNC	32144	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTCTAGAC	.	5	ESCA
MAP7D2	0	.	GRCh37	X	20043083	20043083	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1398G>T	p.Lys466Asn	p.K466N	ENST00000379643	10/17	24	19	5	26	26	0	MAP7D2,missense_variant,p.Lys466Asn,ENST00000379643,;MAP7D2,missense_variant,p.Lys380Asn,ENST00000443379,;MAP7D2,missense_variant,p.Lys310Asn,ENST00000543767,;MAP7D2,missense_variant,p.Lys373Asn,ENST00000452324,;MAP7D2,missense_variant,p.Lys425Asn,ENST00000379651,;MAP7D2,non_coding_transcript_exon_variant,,ENST00000466145,;MAP7D2,intron_variant,,ENST00000485173,;	A	ENSG00000184368	ENST00000379643	Transcript	missense_variant	1436	1398	466	K/N	aaG/aaT	.	.	.	-1	MAP7D2	HGNC	25899	protein_coding	YES	CCDS55386.1	ENSP00000368964	MA7D2_HUMAN	.	UPI00015E039B	.	deleterious(0.01)	unknown(0)	10/17	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15073:SF3,hmmpanther:PTHR15073,Pfam_domain:PF05672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCCTTCTC	.	5	ESCA
DMD	0	.	GRCh37	X	32382799	32382799	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HX-01A-11D-A33E-09	TCGA-LN-A7HX-10A-01D-A33H-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5054A>G	p.Asp1685Gly	p.D1685G	ENST00000357033	36/79	29	23	6	25	25	0	DMD,missense_variant,p.Asp41Gly,ENST00000448370,;DMD,missense_variant,p.Asp1685Gly,ENST00000357033,;DMD,missense_variant,p.Asp1681Gly,ENST00000378677,;DMD,missense_variant,p.Asp101Gly,ENST00000420596,;DMD,intron_variant,,ENST00000488902,;	C	ENSG00000198947	ENST00000357033	Transcript	missense_variant	5261	5054	1685	D/G	gAc/gGc	.	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	benign(0.182)	36/79	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF261,Pfam_domain:PF00435,SMART_domains:SM00150,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGGTCAAAA	.	5	ESCA
SORCS3	0	.	GRCh37	10	106937814	106937814	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1902-10T>A	.	.	ENST00000369701	.	91	61	30	102	102	0	SORCS3,5_prime_UTR_variant,,ENST00000369699,;SORCS3,intron_variant,,ENST00000393176,;SORCS3,intron_variant,,ENST00000369701,;	A	ENSG00000156395	ENST00000369701	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SORCS3	HGNC	16699	protein_coding	YES	CCDS7558.1	ENSP00000358715	SORC3_HUMAN	B7Z891_HUMAN	UPI0000135CE1	.	.	.	.	13/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTTCCAAC	.	5	ESCA
SORCS3	0	.	GRCh37	10	106937815	106937815	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1902-9C>A	.	.	ENST00000369701	.	91	61	30	100	100	0	SORCS3,5_prime_UTR_variant,,ENST00000369699,;SORCS3,intron_variant,,ENST00000393176,;SORCS3,intron_variant,,ENST00000369701,;	A	ENSG00000156395	ENST00000369701	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SORCS3	HGNC	16699	protein_coding	YES	CCDS7558.1	ENSP00000358715	SORC3_HUMAN	B7Z891_HUMAN	UPI0000135CE1	.	.	.	.	13/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTCCAACA	.	5	ESCA
VWA2	0	.	GRCh37	10	116048824	116048824	+	Silent	SNP	C	C	T	rs199884277	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1698C>T	p.%3D	p.D566D	ENST00000603594	12/12	44	40	4	41	41	0	VWA2,synonymous_variant,p.%3D,ENST00000603594,;VWA2,synonymous_variant,p.%3D,ENST00000392982,;VWA2,non_coding_transcript_exon_variant,,ENST00000298715,;	T	ENSG00000165816	ENST00000603594	Transcript	synonymous_variant	2019	1698	566	D	gaC/gaT	rs199884277	.	.	1	VWA2	HGNC	24709	protein_coding	YES	.	ENSP00000473752	VWA2_HUMAN	.	UPI00001C0885	.	.	.	12/12	.	Superfamily_domains:SSF53300,SMART_domains:SM00327,Pfam_domain:PF00092,Gene3D:3.40.50.410,hmmpanther:PTHR22992,hmmpanther:PTHR22992:SF9,PROSITE_profiles:PS50234	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGACGTGAC	byCluster	4	ESCA
RAB11FIP2	0	.	GRCh37	10	119767619	119767619	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*890A>G	.	.	ENST00000355624	5/5	12	7	5	20	20	0	RAB11FIP2,3_prime_UTR_variant,,ENST00000355624,;RAB11FIP2,downstream_gene_variant,,ENST00000369199,;RAB11FIP2,intron_variant,,ENST00000476207,;	C	ENSG00000107560	ENST00000355624	Transcript	3_prime_UTR_variant	2869	.	.	.	.	.	.	.	-1	RAB11FIP2	HGNC	29152	protein_coding	YES	CCDS7602.1	ENSP00000347839	RFIP2_HUMAN	.	UPI0000073B4B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGCTATATTAG	.	3	ESCA
OAT	0	.	GRCh37	10	126097428	126097428	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306G>A	p.%3D	p.K102K	ENST00000368845	3/10	84	51	33	93	93	0	OAT,synonymous_variant,p.%3D,ENST00000368845,;OAT,5_prime_UTR_variant,,ENST00000539214,;OAT,non_coding_transcript_exon_variant,,ENST00000476917,;OAT,non_coding_transcript_exon_variant,,ENST00000490096,;OAT,downstream_gene_variant,,ENST00000492376,;OAT,upstream_gene_variant,,ENST00000483711,;OAT,upstream_gene_variant,,ENST00000467675,;	T	ENSG00000065154	ENST00000368845	Transcript	synonymous_variant	399	306	102	K	aaG/aaA	.	.	.	-1	OAT	HGNC	8091	protein_coding	YES	CCDS7639.1	ENSP00000357838	OAT_HUMAN	.	UPI0000000C1B	.	.	.	3/10	.	hmmpanther:PTHR11986:SF18,hmmpanther:PTHR11986,Pfam_domain:PF00202,Gene3D:3.40.640.10,TIGRFAM_domain:TIGR01885,PIRSF_domain:PIRSF000521,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTCTTCAG	.	5	ESCA
ADAM12	0	.	GRCh37	10	127708373	127708373	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2560C>G	p.Pro854Ala	p.P854A	ENST00000368679	22/23	94	75	19	95	95	0	ADAM12,missense_variant,p.Pro854Ala,ENST00000368679,;	C	ENSG00000148848	ENST00000368679	Transcript	missense_variant	2870	2560	854	P/A	Cct/Gct	.	.	.	-1	ADAM12	HGNC	190	protein_coding	YES	CCDS7653.1	ENSP00000357668	ADA12_HUMAN	.	UPI000036672C	.	deleterious(0)	probably_damaging(0.999)	22/23	.	hmmpanther:PTHR11905:SF112,hmmpanther:PTHR11905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGGGGGGT	.	5	ESCA
PRTFDC1	0	.	GRCh37	10	25138797	25138797	+	Missense_Mutation	SNP	G	G	C	rs770784719	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.654C>G	p.His218Gln	p.H218Q	ENST00000320152	9/9	38	29	9	33	33	0	PRTFDC1,missense_variant,p.His218Gln,ENST00000320152,;PRTFDC1,3_prime_UTR_variant,,ENST00000376378,;	C	ENSG00000099256	ENST00000320152	Transcript	missense_variant	683	654	218	H/Q	caC/caG	rs770784719	.	.	-1	PRTFDC1	HGNC	23333	protein_coding	YES	CCDS7145.1	ENSP00000318602	PRDC1_HUMAN	.	UPI0000073D65	.	tolerated(0.6)	benign(0.002)	9/9	.	Superfamily_domains:SSF53271,Gene3D:3.40.50.2020,hmmpanther:PTHR22573:SF35,hmmpanther:PTHR22573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACCGTGCTC	.	5	ESCA
MAP3K8	0	.	GRCh37	10	30739243	30739243	+	Silent	SNP	C	C	T	rs569267728	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.561C>T	p.%3D	p.H187H	ENST00000263056	5/9	43	33	9	54	54	0	MAP3K8,synonymous_variant,p.%3D,ENST00000263056,;MAP3K8,synonymous_variant,p.%3D,ENST00000542547,;MAP3K8,synonymous_variant,p.%3D,ENST00000415139,;MAP3K8,synonymous_variant,p.%3D,ENST00000375321,;MAP3K8,synonymous_variant,p.%3D,ENST00000413724,;MAP3K8,non_coding_transcript_exon_variant,,ENST00000430603,;	T	ENSG00000107968	ENST00000263056	Transcript	synonymous_variant	1257	561	187	H	caC/caT	rs569267728	.	.	1	MAP3K8	HGNC	6860	protein_coding	YES	CCDS7166.1	ENSP00000263056	M3K8_HUMAN	Q5T857_HUMAN,Q5T853_HUMAN	UPI000013D395	.	.	.	5/9	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF94,hmmpanther:PTHR24361,Gene3D:3.30.200.20,Pfam_domain:PF00069,PIRSF_domain:PIRSF038171,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCACGAGAA	.	5	ESCA
HERC4	0	.	GRCh37	10	69751986	69751986	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1241C>G	p.Pro414Arg	p.P414R	ENST00000395198	11/26	26	21	5	36	36	0	HERC4,missense_variant,p.Pro414Arg,ENST00000373700,;HERC4,missense_variant,p.Pro304Arg,ENST00000277817,;HERC4,missense_variant,p.Pro414Arg,ENST00000412272,;HERC4,missense_variant,p.Pro414Arg,ENST00000395198,;HERC4,3_prime_UTR_variant,,ENST00000395187,;HERC4,3_prime_UTR_variant,,ENST00000473533,;HERC4,3_prime_UTR_variant,,ENST00000427635,;HERC4,upstream_gene_variant,,ENST00000460168,;	C	ENSG00000148634	ENST00000395198	Transcript	missense_variant	1489	1241	414	P/R	cCt/cGt	.	.	.	-1	HERC4	HGNC	24521	protein_coding	YES	CCDS41533.1	ENSP00000378624	HERC4_HUMAN	D6RFK9_HUMAN	UPI00004C6F56	.	tolerated(0.5)	benign(0.018)	11/26	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGGATAG	.	5	ESCA
TET1	0	.	GRCh37	10	70451883	70451883	+	3'UTR	SNP	G	G	T	rs185755380	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*312G>T	.	.	ENST00000373644	12/12	113	94	19	123	121	1	TET1,3_prime_UTR_variant,,ENST00000373644,;	T	ENSG00000138336	ENST00000373644	Transcript	3_prime_UTR_variant	6932	.	.	.	.	rs185755380	.	.	1	TET1	HGNC	29484	protein_coding	YES	CCDS7281.1	ENSP00000362748	TET1_HUMAN	.	UPI000013D114	.	.	.	12/12	.	.	C:0.0014	C:0	C:0	.	C:0.005	C:0	C:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTATGAAACA	byFrequency|byCluster|by1000G	5	ESCA
TSPAN15	0	.	GRCh37	10	71266819	71266819	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*85G>A	.	.	ENST00000373290	8/8	54	42	11	60	60	0	TSPAN15,3_prime_UTR_variant,,ENST00000373290,;TSPAN15,intron_variant,,ENST00000452130,;TSPAN15,non_coding_transcript_exon_variant,,ENST00000486093,;TSPAN15,downstream_gene_variant,,ENST00000459981,;TSPAN15,downstream_gene_variant,,ENST00000490083,;TSPAN15,non_coding_transcript_exon_variant,,ENST00000470508,;TSPAN15,downstream_gene_variant,,ENST00000475069,;	A	ENSG00000099282	ENST00000373290	Transcript	3_prime_UTR_variant	1092	.	.	.	.	.	.	.	1	TSPAN15	HGNC	23298	protein_coding	YES	CCDS7294.1	ENSP00000362387	TSN15_HUMAN	.	UPI00001370A4	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCGGCCCCT	.	5	ESCA
TNKS2	0	.	GRCh37	10	93609336	93609336	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2679A>G	p.Ile893Met	p.I893M	ENST00000371627	20/27	48	33	15	33	33	0	TNKS2,missense_variant,p.Ile893Met,ENST00000371627,;	G	ENSG00000107854	ENST00000371627	Transcript	missense_variant	3058	2679	893	I/M	atA/atG	.	.	.	1	TNKS2	HGNC	15677	protein_coding	YES	CCDS7417.1	ENSP00000360689	TNKS2_HUMAN	.	UPI00000362BE	.	deleterious(0.03)	benign(0.309)	20/27	.	PROSITE_profiles:PS50105,hmmpanther:PTHR24180,hmmpanther:PTHR24180:SF11,Gene3D:1.10.150.50,Pfam_domain:PF07647,SMART_domains:SM00454,Superfamily_domains:SSF47769	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATATATTTGA	.	5	ESCA
FRAT1	0	.	GRCh37	10	99079857	99079857	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647C>T	p.Ala216Val	p.A216V	ENST00000371021	1/1	61	50	11	55	55	0	FRAT1,missense_variant,p.Ala216Val,ENST00000371021,;FRAT1,upstream_gene_variant,,ENST00000490980,;	T	ENSG00000165879	ENST00000371021	Transcript	missense_variant	836	647	216	A/V	gCc/gTc	.	.	.	1	FRAT1	HGNC	3944	protein_coding	YES	CCDS7455.1	ENSP00000360060	FRAT1_HUMAN	.	UPI000006D6B7	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Pfam_domain:PF05350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGGCCGTGC	.	5	ESCA
RDX	0	.	GRCh37	11	110102443	110102443	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1748+155C>T	.	.	ENST00000405097	.	46	36	9	31	31	0	RDX,3_prime_UTR_variant,,ENST00000343115,;RDX,3_prime_UTR_variant,,ENST00000544551,;RDX,intron_variant,,ENST00000528900,;RDX,intron_variant,,ENST00000528498,;RDX,intron_variant,,ENST00000530301,;RDX,intron_variant,,ENST00000405097,;RDX,downstream_gene_variant,,ENST00000530085,;RDX,3_prime_UTR_variant,,ENST00000530131,;RDX,non_coding_transcript_exon_variant,,ENST00000527537,;RDX,non_coding_transcript_exon_variant,,ENST00000532461,;RDX,non_coding_transcript_exon_variant,,ENST00000533961,;RDX,intron_variant,,ENST00000530749,;	A	ENSG00000137710	ENST00000405097	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RDX	HGNC	9944	protein_coding	YES	CCDS58174.1	ENSP00000384136	RADI_HUMAN	Q9NST9_HUMAN,E9PQ82_HUMAN,E9PNV3_HUMAN,E9PKN5_HUMAN,B0YJ88_HUMAN	UPI0000EE3914	.	.	.	.	14/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGAGCTC	.	5	ESCA
ANKK1	0	.	GRCh37	11	113270738	113270738	+	Missense_Mutation	SNP	G	G	A	rs778503691	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2047G>A	p.Ala683Thr	p.A683T	ENST00000303941	8/8	74	60	14	55	55	0	ANKK1,missense_variant,p.Ala683Thr,ENST00000303941,;ANKK1,downstream_gene_variant,,ENST00000542948,;	A	ENSG00000170209	ENST00000303941	Transcript	missense_variant	2141	2047	683	A/T	Gca/Aca	rs778503691,COSM923188	.	.	1	ANKK1	HGNC	21027	protein_coding	YES	CCDS44734.1	ENSP00000306678	ANKK1_HUMAN	.	UPI000000DCCF	.	tolerated(0.06)	benign(0.425)	8/8	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24198,hmmpanther:PTHR24198:SF5,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCACGCAAAT	byFrequency	5	ESCA
ARCN1	0	.	GRCh37	11	118472173	118472173	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*744C>G	.	.	ENST00000264028	10/10	60	28	32	70	70	0	ARCN1,3_prime_UTR_variant,,ENST00000264028,;ARCN1,3_prime_UTR_variant,,ENST00000359415,;ARCN1,intron_variant,,ENST00000534182,;PHLDB1,upstream_gene_variant,,ENST00000361417,;ARCN1,downstream_gene_variant,,ENST00000392859,;	G	ENSG00000095139	ENST00000264028	Transcript	3_prime_UTR_variant	2375	.	.	.	.	.	.	.	1	ARCN1	HGNC	649	protein_coding	YES	CCDS8400.1	ENSP00000264028	COPD_HUMAN	B0YIW5_HUMAN	UPI0000127ED7	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAATCATTCA	.	5	ESCA
PDZD3	0	.	GRCh37	11	119056655	119056655	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38T>C	p.Leu13Ser	p.L13S	ENST00000355547	2/11	86	37	48	56	56	0	PDZD3,missense_variant,p.Leu13Ser,ENST00000322712,;PDZD3,missense_variant,p.Leu13Ser,ENST00000355547,;PDZD3,5_prime_UTR_variant,,ENST00000525131,;PDZD3,5_prime_UTR_variant,,ENST00000531114,;NLRX1,downstream_gene_variant,,ENST00000292199,;NLRX1,downstream_gene_variant,,ENST00000409991,;NLRX1,downstream_gene_variant,,ENST00000409265,;CCDC153,downstream_gene_variant,,ENST00000415318,;PDZD3,upstream_gene_variant,,ENST00000392817,;NLRX1,downstream_gene_variant,,ENST00000525863,;NLRX1,downstream_gene_variant,,ENST00000409109,;CCDC153,downstream_gene_variant,,ENST00000503566,;PDZD3,missense_variant,p.Leu13Ser,ENST00000533688,;PDZD3,non_coding_transcript_exon_variant,,ENST00000526279,;PDZD3,non_coding_transcript_exon_variant,,ENST00000527308,;PDZD3,non_coding_transcript_exon_variant,,ENST00000529573,;PDZD3,non_coding_transcript_exon_variant,,ENST00000526836,;PDZD3,non_coding_transcript_exon_variant,,ENST00000529098,;PDZD3,non_coding_transcript_exon_variant,,ENST00000527028,;PDZD3,non_coding_transcript_exon_variant,,ENST00000527951,;PDZD3,non_coding_transcript_exon_variant,,ENST00000534790,;PDZD3,non_coding_transcript_exon_variant,,ENST00000528730,;CCDC153,downstream_gene_variant,,ENST00000375140,;NLRX1,downstream_gene_variant,,ENST00000481860,;	C	ENSG00000172367	ENST00000355547	Transcript	missense_variant	53	38	13	L/S	tTa/tCa	.	.	.	1	PDZD3	HGNC	19891	protein_coding	YES	CCDS53719.1	ENSP00000347742	NHRF4_HUMAN	.	UPI000007079F	.	tolerated(0.08)	benign(0.094)	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCGTTAACTC	.	5	ESCA
OR10G8	0	.	GRCh37	11	123900843	123900843	+	Missense_Mutation	SNP	T	T	C	rs753563106	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514T>C	p.Trp172Arg	p.W172R	ENST00000431524	1/1	179	169	10	92	92	0	OR10G8,missense_variant,p.Trp172Arg,ENST00000431524,;	C	ENSG00000234560	ENST00000431524	Transcript	missense_variant	547	514	172	W/R	Tgg/Cgg	rs753563106	.	.	1	OR10G8	HGNC	14845	protein_coding	YES	CCDS31704.1	ENSP00000389072	O10G8_HUMAN	.	UPI0000040A8F	.	tolerated(0.25)	benign(0)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF146,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAACTGGATC	byFrequency|byCluster	2	ESCA
OR8B4	0	.	GRCh37	11	124294378	124294378	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390C>A	p.%3D	p.L130L	ENST00000356130	1/1	72	45	27	31	31	0	OR8B4,synonymous_variant,p.%3D,ENST00000356130,;	T	ENSG00000198657	ENST00000356130	Transcript	synonymous_variant	412	390	130	L	ctC/ctA	.	.	.	-1	OR8B4	HGNC	8473	protein_coding	YES	CCDS31710.1	ENSP00000348449	OR8B4_HUMAN	.	UPI00000015B0	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF208,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTAGAGCAG	.	5	ESCA
RPUSD4	0	.	GRCh37	11	126080863	126080863	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277A>G	p.Lys93Glu	p.K93E	ENST00000298317	2/7	118	84	34	66	66	0	RPUSD4,missense_variant,p.Lys93Glu,ENST00000533628,;RPUSD4,missense_variant,p.Lys93Glu,ENST00000532674,;RPUSD4,missense_variant,p.Lys93Glu,ENST00000298317,;FAM118B,upstream_gene_variant,,ENST00000528985,;FAM118B,upstream_gene_variant,,ENST00000533050,;FAM118B,upstream_gene_variant,,ENST00000529731,;FAM118B,upstream_gene_variant,,ENST00000530043,;FAM118B,upstream_gene_variant,,ENST00000360194,;RNU4-86P,downstream_gene_variant,,ENST00000410135,;RP11-50B3.4,upstream_gene_variant,,ENST00000532866,;RPUSD4,non_coding_transcript_exon_variant,,ENST00000534393,;FAM118B,upstream_gene_variant,,ENST00000525728,;RPUSD4,upstream_gene_variant,,ENST00000530036,;RPUSD4,non_coding_transcript_exon_variant,,ENST00000525812,;RPUSD4,non_coding_transcript_exon_variant,,ENST00000532800,;RPUSD4,non_coding_transcript_exon_variant,,ENST00000526942,;RPUSD4,upstream_gene_variant,,ENST00000530903,;	C	ENSG00000165526	ENST00000298317	Transcript	missense_variant	331	277	93	K/E	Aag/Gag	.	.	.	-1	RPUSD4	HGNC	25898	protein_coding	YES	CCDS8469.1	ENSP00000298317	RUSD4_HUMAN	B4DUN4_HUMAN	UPI0000071274	.	deleterious(0)	possibly_damaging(0.688)	2/7	.	hmmpanther:PTHR10436,hmmpanther:PTHR10436:SF48,Superfamily_domains:SSF55120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTTAGCAA	.	5	ESCA
RP11-713P17.3	0	.	GRCh37	11	133902537	133902537	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.371G>A	.	.	ENST00000533922	1/3	56	38	17	36	36	0	RP11-713P17.3,non_coding_transcript_exon_variant,,ENST00000533922,;RP11-713P17.3,non_coding_transcript_exon_variant,,ENST00000532706,;RP11-713P17.3,upstream_gene_variant,,ENST00000527712,;RP11-713P17.5,downstream_gene_variant,,ENST00000532272,;RP11-713P17.3,upstream_gene_variant,,ENST00000529070,;RP11-713P17.4,downstream_gene_variant,,ENST00000526377,;RP11-713P17.3,upstream_gene_variant,,ENST00000533091,;RP11-713P17.3,upstream_gene_variant,,ENST00000531938,;	A	ENSG00000204241	ENST00000533922	Transcript	non_coding_transcript_exon_variant	371	.	.	.	.	.	.	.	1	RP11-713P17.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCAGCACAG	.	5	ESCA
RP11-713P17.3	0	.	GRCh37	11	133902538	133902538	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.372C>A	.	.	ENST00000533922	1/3	56	38	17	36	36	0	RP11-713P17.3,non_coding_transcript_exon_variant,,ENST00000533922,;RP11-713P17.3,non_coding_transcript_exon_variant,,ENST00000532706,;RP11-713P17.3,upstream_gene_variant,,ENST00000527712,;RP11-713P17.5,downstream_gene_variant,,ENST00000532272,;RP11-713P17.3,upstream_gene_variant,,ENST00000529070,;RP11-713P17.4,downstream_gene_variant,,ENST00000526377,;RP11-713P17.3,upstream_gene_variant,,ENST00000533091,;RP11-713P17.3,upstream_gene_variant,,ENST00000531938,;	A	ENSG00000204241	ENST00000533922	Transcript	non_coding_transcript_exon_variant	372	.	.	.	.	.	.	.	1	RP11-713P17.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGCACAGC	.	5	ESCA
SLC22A25	0	.	GRCh37	11	62931426	62931426	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1514C>T	p.Ala505Val	p.A505V	ENST00000306494	9/9	69	34	35	77	77	0	SLC22A25,missense_variant,p.Ala505Val,ENST00000306494,;SLC22A10,intron_variant,,ENST00000535888,;SLC22A25,downstream_gene_variant,,ENST00000403374,;SLC22A10,intron_variant,,ENST00000525620,;SLC22A25,3_prime_UTR_variant,,ENST00000527057,;SLC22A25,3_prime_UTR_variant,,ENST00000528239,;SLC22A25,3_prime_UTR_variant,,ENST00000525295,;	A	ENSG00000196600	ENST00000306494	Transcript	missense_variant	1514	1514	505	A/V	gCc/gTc	.	.	.	-1	SLC22A25	HGNC	32935	protein_coding	YES	CCDS31592.1	ENSP00000307443	S22AP_HUMAN	.	UPI00001A72A5	.	deleterious(0.01)	benign(0.064)	9/9	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF185,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGGCAAAG	.	5	ESCA
MYO7A	0	.	GRCh37	11	76883843	76883843	+	Missense_Mutation	SNP	G	G	A	rs782410686	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1847G>A	p.Arg616Gln	p.R616Q	ENST00000409709	16/49	65	52	13	44	44	0	MYO7A,missense_variant,p.Arg616Gln,ENST00000409893,;MYO7A,missense_variant,p.Arg605Gln,ENST00000409619,;MYO7A,missense_variant,p.Arg616Gln,ENST00000409709,;MYO7A,missense_variant,p.Arg616Gln,ENST00000458637,;	A	ENSG00000137474	ENST00000409709	Transcript	missense_variant	2119	1847	616	R/Q	cGg/cAg	rs782410686	.	.	1	MYO7A	HGNC	7606	protein_coding	YES	CCDS53683.1	ENSP00000386331	MYO7A_HUMAN	.	UPI00001FAFE6	.	tolerated(1)	probably_damaging(0.964)	16/49	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF258,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGCGGTCAC	byFrequency	5	ESCA
NFYB	0	.	GRCh37	12	104519955	104519955	+	Silent	SNP	A	A	G	rs762750390	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168T>C	p.%3D	p.D56D	ENST00000240055	4/8	64	39	24	57	57	0	NFYB,synonymous_variant,p.%3D,ENST00000551446,;NFYB,synonymous_variant,p.%3D,ENST00000551727,;NFYB,synonymous_variant,p.%3D,ENST00000240055,;RNA5SP370,downstream_gene_variant,,ENST00000362545,;NFYB,non_coding_transcript_exon_variant,,ENST00000550189,;NFYB,downstream_gene_variant,,ENST00000550881,;	G	ENSG00000120837	ENST00000240055	Transcript	synonymous_variant	396	168	56	D	gaT/gaC	rs762750390	.	.	-1	NFYB	HGNC	7805	protein_coding	YES	CCDS9098.1	ENSP00000240055	NFYB_HUMAN	.	UPI0000127178	.	.	.	4/8	.	hmmpanther:PTHR11064:SF24,hmmpanther:PTHR11064,Gene3D:1.10.20.10,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATATCTTG	.	5	ESCA
KIAA1033	0	.	GRCh37	12	105551051	105551051	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2863G>T	p.Glu955Ter	p.E955*	ENST00000332180	28/33	57	40	16	54	54	0	KIAA1033,stop_gained,p.Glu955Ter,ENST00000332180,;KIAA1033,stop_gained,p.Glu33Ter,ENST00000551224,;KIAA1033,stop_gained,p.Glu33Ter,ENST00000552203,;KIAA1033,non_coding_transcript_exon_variant,,ENST00000551290,;KIAA1033,3_prime_UTR_variant,,ENST00000550053,;KIAA1033,non_coding_transcript_exon_variant,,ENST00000550786,;	T	ENSG00000136051	ENST00000332180	Transcript	stop_gained	2950	2863	955	E/*	Gaa/Taa	.	.	.	1	KIAA1033	HGNC	29174	protein_coding	YES	CCDS41826.1	ENSP00000328062	WASH7_HUMAN	F8W1W1_HUMAN,F8VQX3_HUMAN,F8VNZ5_HUMAN	UPI00001C1F3B	.	.	.	28/33	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31409,hmmpanther:PTHR31409:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGAACTA	.	5	ESCA
KLRC4	0	.	GRCh37	12	10562233	10562233	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-59A>G	.	.	ENST00000309384	1/4	33	13	20	30	30	0	KLRC4,5_prime_UTR_variant,,ENST00000309384,;NKG2-E,downstream_gene_variant,,ENST00000539033,;KLRC3,downstream_gene_variant,,ENST00000381904,;KLRC3,downstream_gene_variant,,ENST00000396439,;KLRC4-KLRK1,intron_variant,,ENST00000591546,;KLRC4-KLRK1,intron_variant,,ENST00000590131,;KLRC4-KLRK1,intron_variant,,ENST00000543812,;KLRC4-KLRK1,intron_variant,,ENST00000585507,;KLRC4-KLRK1,intron_variant,,ENST00000588263,;KLRC4-KLRK1,intron_variant,,ENST00000588447,;KLRC4-KLRK1,intron_variant,,ENST00000591937,;KLRC4-KLRK1,intron_variant,,ENST00000590323,;KLRC4-KLRK1,upstream_gene_variant,,ENST00000586581,;KLRC4-KLRK1,upstream_gene_variant,,ENST00000543572,;KLRC4-KLRK1,upstream_gene_variant,,ENST00000539370,;KLRC4-KLRK1,upstream_gene_variant,,ENST00000539300,;KLRC4-KLRK1,upstream_gene_variant,,ENST00000585711,;	C	ENSG00000183542	ENST00000309384	Transcript	5_prime_UTR_variant	124	.	.	.	.	.	.	.	-1	KLRC4	HGNC	6377	protein_coding	YES	CCDS8624.1	ENSP00000310216	NKG2F_HUMAN	H3BU71_HUMAN,H3BRK7_HUMAN	UPI000013EE96	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTATAAGTG	.	5	ESCA
KSR2	0	.	GRCh37	12	117977636	117977636	+	Silent	SNP	C	C	T	rs756688718	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1575G>A	p.%3D	p.T525T	ENST00000339824	10/20	33	12	20	35	35	0	KSR2,synonymous_variant,p.%3D,ENST00000425217,;KSR2,synonymous_variant,p.%3D,ENST00000302438,;KSR2,synonymous_variant,p.%3D,ENST00000339824,;KSR2,non_coding_transcript_exon_variant,,ENST00000545002,;KSR2,non_coding_transcript_exon_variant,,ENST00000543793,;	T	ENSG00000171435	ENST00000339824	Transcript	synonymous_variant	2303	1575	525	T	acG/acA	rs756688718	.	.	-1	KSR2	HGNC	18610	protein_coding	YES	.	ENSP00000339952	KSR2_HUMAN	E9PB13_HUMAN	UPI000152636C	.	.	.	10/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23257:SF376,hmmpanther:PTHR23257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGACGTCGT	.	5	ESCA
GRIN2B	0	.	GRCh37	12	13761566	13761566	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1981G>C	p.Asp661His	p.D661H	ENST00000609686	9/13	84	39	45	88	88	0	GRIN2B,missense_variant,p.Asp661His,ENST00000609686,;	G	ENSG00000273079	ENST00000609686	Transcript	missense_variant	2191	1981	661	D/H	Gac/Cac	.	.	.	-1	GRIN2B	HGNC	4586	protein_coding	YES	CCDS8662.1	ENSP00000477455	NMDE2_HUMAN	Q59HA9_HUMAN	UPI000013026C	.	deleterious(0)	probably_damaging(0.964)	9/13	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF16,Pfam_domain:PF00497,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTCCACAT	.	5	ESCA
EPS8	0	.	GRCh37	12	15777165	15777165	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2221C>G	p.Pro741Ala	p.P741A	ENST00000281172	19/21	52	30	21	64	64	0	EPS8,missense_variant,p.Pro481Ala,ENST00000540613,;EPS8,missense_variant,p.Pro481Ala,ENST00000542903,;EPS8,missense_variant,p.Pro741Ala,ENST00000543612,;EPS8,missense_variant,p.Pro741Ala,ENST00000281172,;EPS8,missense_variant,p.Pro741Ala,ENST00000543523,;EPS8,3_prime_UTR_variant,,ENST00000543468,;EPS8,non_coding_transcript_exon_variant,,ENST00000545610,;	C	ENSG00000151491	ENST00000281172	Transcript	missense_variant	2658	2221	741	P/A	Cct/Gct	.	.	.	-1	EPS8	HGNC	3420	protein_coding	YES	CCDS31753.1	ENSP00000281172	EPS8_HUMAN	F5H3Q6_HUMAN,F5H2B8_HUMAN,F5H1B5_HUMAN,F5GYM8_HUMAN,B4DX66_HUMAN	UPI000012A0BC	.	tolerated(0.35)	possibly_damaging(0.452)	19/21	.	hmmpanther:PTHR12287,hmmpanther:PTHR12287:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAGGGTTGA	.	5	ESCA
SLC38A1	0	.	GRCh37	12	46591568	46591568	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1297C>G	p.Leu433Val	p.L433V	ENST00000398637	16/17	77	59	18	86	86	0	SLC38A1,missense_variant,p.Leu433Val,ENST00000549049,;SLC38A1,missense_variant,p.Leu433Val,ENST00000398637,;SLC38A1,missense_variant,p.Leu433Val,ENST00000546893,;SLC38A1,missense_variant,p.Leu433Val,ENST00000552197,;SLC38A1,missense_variant,p.Leu433Val,ENST00000439706,;SLC38A1,downstream_gene_variant,,ENST00000549633,;SLC38A1,non_coding_transcript_exon_variant,,ENST00000548979,;	C	ENSG00000111371	ENST00000398637	Transcript	missense_variant	1992	1297	433	L/V	Ctt/Gtt	.	.	.	-1	SLC38A1	HGNC	13447	protein_coding	YES	CCDS41774.1	ENSP00000381634	S38A1_HUMAN	Q8NCD8_HUMAN,F8VX12_HUMAN	UPI000004D33C	.	deleterious(0)	benign(0.182)	16/17	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22950:SF184,hmmpanther:PTHR22950,Pfam_domain:PF01490	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGAATGA	.	5	ESCA
DYRK4	0	.	GRCh37	12	4705422	4705422	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390G>A	p.%3D	p.V130V	ENST00000540757	5/13	18	8	9	45	45	0	DYRK4,synonymous_variant,p.%3D,ENST00000540757,;DYRK4,synonymous_variant,p.%3D,ENST00000542744,;DYRK4,synonymous_variant,p.%3D,ENST00000010132,;DYRK4,synonymous_variant,p.%3D,ENST00000543431,;DYRK4,downstream_gene_variant,,ENST00000536645,;DYRK4,non_coding_transcript_exon_variant,,ENST00000536157,;DYRK4,upstream_gene_variant,,ENST00000540644,;DYRK4,downstream_gene_variant,,ENST00000542905,;	A	ENSG00000010219	ENST00000540757	Transcript	synonymous_variant	550	390	130	V	gtG/gtA	.	.	.	1	DYRK4	HGNC	3095	protein_coding	YES	CCDS8530.1	ENSP00000441755	DYRK4_HUMAN	D3JEN3_HUMAN,D3JEN2_HUMAN,B4DQW1_HUMAN	UPI000006E05C	.	.	.	5/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,hmmpanther:PTHR24058:SF22,hmmpanther:PTHR24058,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTGGCCCT	.	5	ESCA
ZBTB39	0	.	GRCh37	12	57397269	57397269	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1433A>G	p.Lys478Arg	p.K478R	ENST00000300101	2/2	40	26	14	49	49	0	ZBTB39,missense_variant,p.Lys478Arg,ENST00000300101,;	C	ENSG00000166860	ENST00000300101	Transcript	missense_variant	1519	1433	478	K/R	aAg/aGg	.	.	.	-1	ZBTB39	HGNC	29014	protein_coding	YES	CCDS31839.1	ENSP00000300101	ZBT39_HUMAN	.	UPI0000139682	.	tolerated(0.35)	probably_damaging(0.986)	2/2	.	hmmpanther:PTHR24385,hmmpanther:PTHR24385:SF46,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCTTCAAG	.	5	ESCA
MDM2	0	.	GRCh37	12	69229656	69229656	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732G>A	p.%3D	p.Q244Q	ENST00000462284	9/11	59	50	9	59	59	0	MDM2,synonymous_variant,p.%3D,ENST00000540827,;MDM2,synonymous_variant,p.%3D,ENST00000299252,;MDM2,synonymous_variant,p.%3D,ENST00000462284,;MDM2,synonymous_variant,p.%3D,ENST00000360430,;MDM2,synonymous_variant,p.%3D,ENST00000348801,;MDM2,synonymous_variant,p.%3D,ENST00000258149,;MDM2,synonymous_variant,p.%3D,ENST00000539479,;MDM2,synonymous_variant,p.%3D,ENST00000356290,;MDM2,synonymous_variant,p.%3D,ENST00000428863,;MDM2,synonymous_variant,p.%3D,ENST00000543323,;MDM2,synonymous_variant,p.%3D,ENST00000258148,;MDM2,synonymous_variant,p.%3D,ENST00000523991,;MDM2,synonymous_variant,p.%3D,ENST00000350057,;MDM2,intron_variant,,ENST00000393415,;MDM2,intron_variant,,ENST00000393410,;MDM2,intron_variant,,ENST00000393413,;MDM2,intron_variant,,ENST00000544561,;MDM2,intron_variant,,ENST00000393412,;MDM2,intron_variant,,ENST00000545204,;MDM2,intron_variant,,ENST00000517852,;MDM2,intron_variant,,ENST00000478070,;MDM2,3_prime_UTR_variant,,ENST00000542502,;MDM2,3_prime_UTR_variant,,ENST00000311420,;MDM2,3_prime_UTR_variant,,ENST00000481186,;MDM2,3_prime_UTR_variant,,ENST00000393417,;MDM2,3_prime_UTR_variant,,ENST00000540352,;MDM2,3_prime_UTR_variant,,ENST00000536089,;MDM2,intron_variant,,ENST00000546048,;MDM2,intron_variant,,ENST00000496959,;MDM2,intron_variant,,ENST00000537182,;	A	ENSG00000135679	ENST00000462284	Transcript	synonymous_variant	1034	732	244	Q	caG/caA	.	.	.	1	MDM2	HGNC	6973	protein_coding	YES	CCDS8986.2	ENSP00000417281	MDM2_HUMAN	Q546E6_HUMAN,A8WFP2_HUMAN,A7UKY0_HUMAN	UPI00006CA35C	.	.	.	9/11	.	hmmpanther:PTHR10360,hmmpanther:PTHR10360:SF11,PIRSF_domain:PIRSF500700,PIRSF_domain:PIRSF006748,Superfamily_domains:SSF47592	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATCAGGATTC	.	4	ESCA
OTOGL	0	.	GRCh37	12	80714314	80714314	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3888G>A	p.%3D	p.R1296R	ENST00000458043	33/58	46	40	6	36	36	0	OTOGL,synonymous_variant,p.%3D,ENST00000458043,;OTOGL,synonymous_variant,p.%3D,ENST00000547103,;	A	ENSG00000165899	ENST00000458043	Transcript	synonymous_variant	3894	3888	1296	R	cgG/cgA	.	.	.	1	OTOGL	HGNC	26901	protein_coding	YES	.	ENSP00000400895	.	E2QRK2_HUMAN	UPI0001D089C5	.	.	.	33/58	.	Superfamily_domains:0050434,Gene3D:2.80.10.50,Pfam_domain:PF05270,hmmpanther:PTHR11339:SF225,hmmpanther:PTHR11339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCGGAGAGC	.	4	ESCA
PTPRQ	0	.	GRCh37	12	80982205	80982205	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4571G>T	p.Trp1524Leu	p.W1524L	ENST00000266688	31/50	32	25	6	25	25	0	PTPRQ,missense_variant,p.Trp1524Leu,ENST00000266688,;RP11-272K23.3,intron_variant,,ENST00000550634,;	T	ENSG00000139304	ENST00000266688	Transcript	missense_variant	4571	4571	1524	W/L	tGg/tTg	.	.	.	1	PTPRQ	HGNC	9679	protein_coding	YES	.	ENSP00000266688	PTPRQ_HUMAN	.	UPI00020655BB	.	deleterious(0)	probably_damaging(0.991)	31/50	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF527,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTGGATTT	.	5	ESCA
CEP290	0	.	GRCh37	12	88478393	88478393	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4674G>T	p.Lys1558Asn	p.K1558N	ENST00000552810	35/54	100	82	18	78	78	0	CEP290,missense_variant,p.Lys1558Asn,ENST00000552810,;CEP290,missense_variant,p.Lys618Asn,ENST00000397838,;CEP290,missense_variant,p.Lys1560Asn,ENST00000309041,;CEP290,missense_variant,p.Lys618Asn,ENST00000547691,;	A	ENSG00000198707	ENST00000552810	Transcript	missense_variant	5018	4674	1558	K/N	aaG/aaT	.	.	.	-1	CEP290	HGNC	29021	protein_coding	YES	CCDS55858.1	ENSP00000448012	CE290_HUMAN	.	UPI0000D60D15	.	.	probably_damaging(0.999)	35/54	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATACTTCTT	.	5	ESCA
TMPO	0	.	GRCh37	12	98927030	98927030	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.995G>C	p.Arg332Thr	p.R332T	ENST00000266732	4/4	59	46	13	48	48	0	TMPO,missense_variant,p.Arg332Thr,ENST00000266732,;TMPO,intron_variant,,ENST00000393053,;TMPO,intron_variant,,ENST00000261210,;TMPO,intron_variant,,ENST00000556029,;TMPO,intron_variant,,ENST00000343315,;TMPO,intron_variant,,ENST00000556678,;TMPO,downstream_gene_variant,,ENST00000547214,;TMPO,downstream_gene_variant,,ENST00000546828,;TMPO,downstream_gene_variant,,ENST00000549938,;TMPO,intron_variant,,ENST00000552831,;	C	ENSG00000120802	ENST00000266732	Transcript	missense_variant	1233	995	332	R/T	aGa/aCa	.	.	.	1	TMPO	HGNC	11875	protein_coding	YES	CCDS9064.1	ENSP00000266732	LAP2A_HUMAN	.	UPI000013D709	.	deleterious_low_confidence(0)	benign(0.019)	4/4	.	hmmpanther:PTHR12019,hmmpanther:PTHR12019:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGTAGAGAGA	.	5	ESCA
BIVM-ERCC5	0	.	GRCh37	13	103524642	103524642	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4049C>T	p.Pro1351Ser	p.P1351S	ENST00000602836	21/21	73	34	38	62	62	0	BIVM-ERCC5,missense_variant,p.Pro1351Ser,ENST00000602836,;ERCC5,missense_variant,p.Pro925Ser,ENST00000355739,;ERCC5,missense_variant,p.Pro158Ser,ENST00000375954,;ERCC5,upstream_gene_variant,,ENST00000472247,;ERCC5,downstream_gene_variant,,ENST00000481099,;	T	ENSG00000270181	ENST00000602836	Transcript	missense_variant	4049	4051	1351	P/S	Cct/Tct	.	.	.	1	BIVM-ERCC5	HGNC	43690	protein_coding	YES	.	ENSP00000473384	.	.	UPI0002B83330	.	tolerated(0.44)	benign(0.303)	21/21	.	hmmpanther:PTHR16171,TIGRFAM_domain:TIGR00600,Superfamily_domains:SSF47807	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCCCTGGC	.	5	ESCA
GAS6	0	.	GRCh37	13	114541138	114541138	+	Missense_Mutation	SNP	C	C	A	rs376538659	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493G>T	p.Gly165Trp	p.G165W	ENST00000327773	6/15	91	43	48	112	112	0	GAS6,missense_variant,p.Gly111Trp,ENST00000355761,;GAS6,missense_variant,p.Gly165Trp,ENST00000327773,;GAS6,missense_variant,p.Gly165Trp,ENST00000357389,;GAS6,upstream_gene_variant,,ENST00000450766,;GAS6,upstream_gene_variant,,ENST00000418959,;GAS6-AS1,non_coding_transcript_exon_variant,,ENST00000458001,;GAS6,upstream_gene_variant,,ENST00000610073,;GAS6,upstream_gene_variant,,ENST00000480426,;	A	ENSG00000183087	ENST00000327773	Transcript	missense_variant	640	493	165	G/W	Ggg/Tgg	rs376538659,COSM1171955	.	.	-1	GAS6	HGNC	4168	protein_coding	YES	CCDS45072.1	ENSP00000331831	GAS6_HUMAN	B4DZY7_HUMAN	UPI0000073CCA	.	deleterious(0)	probably_damaging(1)	6/15	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24035:SF21,hmmpanther:PTHR24035,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,Pfam_domain:PF14670,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCCGTTCT	byFrequency|byCluster	5	ESCA
SACS	0	.	GRCh37	13	23911518	23911518	+	Missense_Mutation	SNP	C	C	T	rs200888451	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6497G>A	p.Arg2166His	p.R2166H	ENST00000382298	10/10	30	13	17	26	26	0	SACS,missense_variant,p.Arg2166His,ENST00000382292,;SACS,missense_variant,p.Arg1416His,ENST00000402364,;SACS,missense_variant,p.Arg2166His,ENST00000382298,;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,;	T	ENSG00000151835	ENST00000382298	Transcript	missense_variant	7086	6497	2166	R/H	cGt/cAt	rs200888451	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	probably_damaging(0.996)	10/10	.	hmmpanther:PTHR15600:SF26,hmmpanther:PTHR15600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCACGTTCT	byCluster	5	ESCA
TRPC4	0	.	GRCh37	13	38266166	38266166	+	Missense_Mutation	SNP	C	C	A	rs755900356	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1204G>T	p.Val402Phe	p.V402F	ENST00000379681	4/11	30	12	18	45	45	0	TRPC4,missense_variant,p.Val402Phe,ENST00000379673,;TRPC4,missense_variant,p.Val229Phe,ENST00000338947,;TRPC4,missense_variant,p.Val402Phe,ENST00000379681,;TRPC4,missense_variant,p.Val402Phe,ENST00000447043,;TRPC4,missense_variant,p.Val229Phe,ENST00000379679,;TRPC4,missense_variant,p.Val402Phe,ENST00000355779,;TRPC4,missense_variant,p.Val402Phe,ENST00000358477,;TRPC4,missense_variant,p.Val402Phe,ENST00000426868,;TRPC4,missense_variant,p.Val402Phe,ENST00000379705,;TRPC4,intron_variant,,ENST00000488717,;	A	ENSG00000133107	ENST00000379681	Transcript	missense_variant	1439	1204	402	V/F	Gtc/Ttc	rs755900356	.	.	-1	TRPC4	HGNC	12336	protein_coding	YES	CCDS45037.1	ENSP00000369003	TRPC4_HUMAN	.	UPI000006E5BE	.	deleterious(0.01)	probably_damaging(0.998)	4/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25,TIGRFAM_domain:TIGR00870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTCGACGATGG	.	4	ESCA
PPP1R13B	0	.	GRCh37	14	104212750	104212750	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1110C>G	p.%3D	p.L370L	ENST00000202556	9/17	41	20	21	52	52	0	PPP1R13B,synonymous_variant,p.%3D,ENST00000202556,;PPP1R13B,5_prime_UTR_variant,,ENST00000423488,;PPP1R13B,non_coding_transcript_exon_variant,,ENST00000555183,;PPP1R13B,non_coding_transcript_exon_variant,,ENST00000555991,;PPP1R13B,intron_variant,,ENST00000556325,;PPP1R13B,upstream_gene_variant,,ENST00000555391,;PPP1R13B,downstream_gene_variant,,ENST00000555708,;PPP1R13B,synonymous_variant,p.%3D,ENST00000556597,;PPP1R13B,3_prime_UTR_variant,,ENST00000557082,;PPP1R13B,upstream_gene_variant,,ENST00000557744,;	C	ENSG00000088808	ENST00000202556	Transcript	synonymous_variant	1393	1110	370	L	ctC/ctG	.	.	.	-1	PPP1R13B	HGNC	14950	protein_coding	YES	CCDS41997.1	ENSP00000202556	ASPP1_HUMAN	G3V5J1_HUMAN	UPI000049DDC7	.	.	.	9/17	.	hmmpanther:PTHR24131,hmmpanther:PTHR24131:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTGAGAGA	.	5	ESCA
EDDM3A	0	.	GRCh37	14	21216340	21216340	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*157C>A	.	.	ENST00000326842	2/2	69	44	24	49	49	0	EDDM3A,3_prime_UTR_variant,,ENST00000326842,;	A	ENSG00000181562	ENST00000326842	Transcript	3_prime_UTR_variant	728	.	.	.	.	.	.	.	1	EDDM3A	HGNC	16978	protein_coding	YES	CCDS9556.1	ENSP00000315098	EP3A_HUMAN	.	UPI000003EE00	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATACCAAAT	.	5	ESCA
DHRS2	0	.	GRCh37	14	24114459	24114459	+	Missense_Mutation	SNP	C	C	G	rs144980250	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.851C>G	p.Ser284Cys	p.S284C	ENST00000344777	9/9	48	29	18	34	34	0	DHRS2,missense_variant,p.Ser284Cys,ENST00000344777,;DHRS2,synonymous_variant,p.%3D,ENST00000557535,;DHRS2,synonymous_variant,p.%3D,ENST00000250383,;DHRS2,3_prime_UTR_variant,,ENST00000553600,;DHRS2,downstream_gene_variant,,ENST00000432832,;DHRS2,downstream_gene_variant,,ENST00000553896,;DHRS2,non_coding_transcript_exon_variant,,ENST00000556701,;DHRS2,non_coding_transcript_exon_variant,,ENST00000556729,;DHRS2,non_coding_transcript_exon_variant,,ENST00000556550,;	G	ENSG00000100867	ENST00000344777	Transcript	missense_variant	1289	851	284	S/C	tCt/tGt	rs144980250	.	.	1	DHRS2	HGNC	18349	protein_coding	YES	CCDS41927.1	ENSP00000344674	DHRS2_HUMAN	C9JZP6_HUMAN	UPI00001A3E34	.	deleterious_low_confidence(0)	possibly_damaging(0.701)	9/9	.	PIRSF_domain:PIRSF000126	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCTCTGAGA	byCluster	5	ESCA
FOXG1	0	.	GRCh37	14	29237879	29237879	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1394C>T	p.Thr465Met	p.T465M	ENST00000382535	2/2	98	89	8	79	79	0	FOXG1,missense_variant,p.Thr465Met,ENST00000313071,;FOXG1,missense_variant,p.Thr465Met,ENST00000382535,;C14orf23,upstream_gene_variant,,ENST00000552957,;C14orf23,upstream_gene_variant,,ENST00000399387,;C14orf23,upstream_gene_variant,,ENST00000548213,;RP11-966I7.1,upstream_gene_variant,,ENST00000549487,;RP11-966I7.1,upstream_gene_variant,,ENST00000551395,;RP11-966I7.1,upstream_gene_variant,,ENST00000546560,;	T	ENSG00000176165	ENST00000382535	Transcript	missense_variant	1763	1394	465	T/M	aCg/aTg	COSM955149	.	.	1	FOXG1	HGNC	3811	protein_coding	YES	CCDS9636.1	ENSP00000371975	FOXG1_HUMAN	.	UPI00001AE46C	.	deleterious_low_confidence(0.01)	possibly_damaging(0.521)	2/2	.	hmmpanther:PTHR25042:SF8,hmmpanther:PTHR25042	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TACGACGGGAC	.	3	ESCA
COCH	0	.	GRCh37	14	31348140	31348140	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363C>A	p.Phe121Leu	p.F121L	ENST00000396618	5/12	55	32	23	47	47	0	COCH,missense_variant,p.Phe105Leu,ENST00000556908,;COCH,missense_variant,p.Phe121Leu,ENST00000216361,;COCH,missense_variant,p.Phe9Leu,ENST00000460581,;COCH,missense_variant,p.Phe121Leu,ENST00000475087,;COCH,missense_variant,p.Phe121Leu,ENST00000396618,;COCH,intron_variant,,ENST00000555881,;COCH,upstream_gene_variant,,ENST00000382493,;COCH,upstream_gene_variant,,ENST00000468826,;RP11-829H16.3,intron_variant,,ENST00000555108,;COCH,non_coding_transcript_exon_variant,,ENST00000553833,;COCH,intron_variant,,ENST00000557065,;COCH,intron_variant,,ENST00000553772,;COCH,downstream_gene_variant,,ENST00000555117,;	A	ENSG00000100473	ENST00000396618	Transcript	missense_variant	419	363	121	F/L	ttC/ttA	.	.	.	1	COCH	HGNC	2180	protein_coding	YES	CCDS9640.1	ENSP00000379862	COCH_HUMAN	G3V5G6_HUMAN,G3V4C4_HUMAN	UPI0000048EBB	.	deleterious(0.01)	benign(0.028)	5/12	.	PROSITE_profiles:PS50820,hmmpanther:PTHR22992:SF84,hmmpanther:PTHR22992,Pfam_domain:PF03815,Gene3D:1jbiA00,Superfamily_domains:0039469	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCACAGT	.	4	ESCA
DPPA3P2	0	.	GRCh37	14	36840759	36840759	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.390C>T	.	.	ENST00000557188	1/1	133	99	33	118	118	0	DPPA3P2,non_coding_transcript_exon_variant,,ENST00000557188,;DPPA3P2,non_coding_transcript_exon_variant,,ENST00000340350,;DPPA3P2,non_coding_transcript_exon_variant,,ENST00000553589,;	T	ENSG00000188831	ENST00000557188	Transcript	non_coding_transcript_exon_variant	390	.	.	.	.	.	.	.	1	DPPA3P2	HGNC	20417	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAACGCTAG	.	5	ESCA
FAM179B	0	.	GRCh37	14	45542728	45542728	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5127G>C	p.Glu1709Asp	p.E1709D	ENST00000361577	19/19	62	39	22	35	35	0	FAM179B,missense_variant,p.Glu144Asp,ENST00000556823,;FAM179B,missense_variant,p.Glu1709Asp,ENST00000361577,;FAM179B,missense_variant,p.Glu1762Asp,ENST00000361462,;FAM179B,3_prime_UTR_variant,,ENST00000382233,;FAM179B,3_prime_UTR_variant,,ENST00000557423,;	C	ENSG00000198718	ENST00000361577	Transcript	missense_variant	5341	5127	1709	E/D	gaG/gaC	.	.	.	1	FAM179B	HGNC	19959	protein_coding	YES	CCDS9681.1	ENSP00000355045	F179B_HUMAN	.	UPI00001C1F79	.	deleterious(0.02)	possibly_damaging(0.499)	19/19	.	hmmpanther:PTHR21567:SF6,hmmpanther:PTHR21567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D1713N|c.5137G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGAGGAATT	.	5	ESCA
C14orf166	0	.	GRCh37	14	52466445	52466445	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393G>A	p.%3D	p.K131K	ENST00000261700	5/8	51	31	20	46	46	0	C14orf166,synonymous_variant,p.%3D,ENST00000553362,;C14orf166,synonymous_variant,p.%3D,ENST00000261700,;C14orf166,synonymous_variant,p.%3D,ENST00000556760,;C14orf166,3_prime_UTR_variant,,ENST00000557553,;C14orf166,non_coding_transcript_exon_variant,,ENST00000555319,;C14orf166,non_coding_transcript_exon_variant,,ENST00000553707,;C14orf166,upstream_gene_variant,,ENST00000553479,;	A	ENSG00000087302	ENST00000261700	Transcript	synonymous_variant	558	393	131	K	aaG/aaA	.	.	.	1	C14orf166	HGNC	23169	protein_coding	YES	CCDS9705.1	ENSP00000261700	CN166_HUMAN	Q549M8_HUMAN	UPI000012759D	.	.	.	5/8	.	hmmpanther:PTHR15924,Pfam_domain:PF10036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAAGGCTGG	.	5	ESCA
ELMSAN1	0	.	GRCh37	14	74196531	74196531	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1907C>G	p.Ser636Cys	p.S636C	ENST00000286523	4/12	67	43	24	47	47	0	ELMSAN1,missense_variant,p.Ser636Cys,ENST00000435371,;ELMSAN1,missense_variant,p.Ser636Cys,ENST00000394071,;ELMSAN1,missense_variant,p.Ser636Cys,ENST00000286523,;ELMSAN1,missense_variant,p.Ser636Cys,ENST00000423556,;ELMSAN1,3_prime_UTR_variant,,ENST00000451078,;ELMSAN1,upstream_gene_variant,,ENST00000476562,;ELMSAN1,upstream_gene_variant,,ENST00000483269,;ELMSAN1,upstream_gene_variant,,ENST00000462716,;	C	ENSG00000156030	ENST00000286523	Transcript	missense_variant	2690	1907	636	S/C	tCt/tGt	.	.	.	-1	ELMSAN1	HGNC	19853	protein_coding	YES	CCDS9819.1	ENSP00000286523	EMSA1_HUMAN	F6RU81_HUMAN,C9JYU7_HUMAN	UPI00001FD815	.	deleterious(0)	probably_damaging(0.999)	4/12	.	hmmpanther:PTHR16089:SF24,hmmpanther:PTHR16089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGAGAGCGC	.	5	ESCA
CIPC	0	.	GRCh37	14	77572068	77572068	+	Missense_Mutation	SNP	C	C	G	rs377615689	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17C>G	p.Pro6Arg	p.P6R	ENST00000361786	2/4	49	35	14	54	54	0	CIPC,missense_variant,p.Pro6Arg,ENST00000361786,;CIPC,missense_variant,p.Pro6Arg,ENST00000554658,;CIPC,missense_variant,p.Pro6Arg,ENST00000555611,;CIPC,missense_variant,p.Pro6Arg,ENST00000557115,;CIPC,missense_variant,p.Pro6Arg,ENST00000555437,;CIPC,missense_variant,p.Pro6Arg,ENST00000554447,;CIPC,missense_variant,p.Pro6Arg,ENST00000555200,;RP11-463C8.4,missense_variant,p.Pro6Arg,ENST00000557752,;CIPC,non_coding_transcript_exon_variant,,ENST00000556863,;	G	ENSG00000198894	ENST00000361786	Transcript	missense_variant	334	17	6	P/R	cCa/cGa	rs377615689	.	.	1	CIPC	HGNC	20365	protein_coding	YES	CCDS9855.1	ENSP00000355319	K1737_HUMAN	G3V5Y7_HUMAN,G3V5J4_HUMAN,G3V405_HUMAN,G3V3Y7_HUMAN	UPI0000073FD0	.	deleterious_low_confidence(0)	possibly_damaging(0.499)	2/4	.	.	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACCCATCCA	.	5	ESCA
HERC2P3	0	.	GRCh37	15	20657659	20657659	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2300G>T	.	.	ENST00000428453	16/27	166	141	25	173	173	0	HERC2P3,non_coding_transcript_exon_variant,,ENST00000437318,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000428453,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000430598,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000440774,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000426501,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000440441,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000424611,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000429257,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000545640,;HERC2P3,downstream_gene_variant,,ENST00000544900,;	A	ENSG00000180229	ENST00000428453	Transcript	non_coding_transcript_exon_variant	2300	.	.	.	.	.	.	.	-1	HERC2P3	HGNC	4871	processed_transcript	YES	.	.	.	.	.	.	.	.	16/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GCGTGCCGGAA	.	3	ESCA
WHAMMP3	0	.	GRCh37	15	23201597	23201597	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.856G>T	.	.	ENST00000400153	3/11	46	29	17	44	44	0	WHAMMP3,non_coding_transcript_exon_variant,,ENST00000400153,;WHAMMP3,non_coding_transcript_exon_variant,,ENST00000560810,;WHAMMP3,non_coding_transcript_exon_variant,,ENST00000340286,;	A	ENSG00000187667	ENST00000400153	Transcript	non_coding_transcript_exon_variant	856	.	.	.	.	.	.	.	-1	WHAMMP3	HGNC	27892	processed_transcript	YES	.	.	.	.	.	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CAGGGCAACTA	.	3	ESCA
ATP10A	0	.	GRCh37	15	25924401	25924401	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*87A>C	.	.	ENST00000356865	21/21	105	67	37	114	112	1	ATP10A,3_prime_UTR_variant,,ENST00000356865,;ATP10A,downstream_gene_variant,,ENST00000555756,;ATP10A,3_prime_UTR_variant,,ENST00000555815,;ATP10A,downstream_gene_variant,,ENST00000555450,;	G	ENSG00000206190	ENST00000356865	Transcript	3_prime_UTR_variant	4699	.	.	.	.	.	.	.	-1	ATP10A	HGNC	13542	protein_coding	YES	CCDS32178.1	ENSP00000349325	AT10A_HUMAN	.	UPI0000124FAB	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACATCTCCC	.	5	ESCA
BUB1B	0	.	GRCh37	15	40509785	40509785	+	Missense_Mutation	SNP	G	G	T	rs760104068	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2767G>T	p.Asp923Tyr	p.D923Y	ENST00000287598	21/23	62	49	13	81	81	0	BUB1B,missense_variant,p.Asp937Tyr,ENST00000412359,;BUB1B,missense_variant,p.Asp923Tyr,ENST00000287598,;PAK6,5_prime_UTR_variant,,ENST00000453867,;PAK6,5_prime_UTR_variant,,ENST00000441369,;RP11-133K1.2,non_coding_transcript_exon_variant,,ENST00000559936,;BUB1B,non_coding_transcript_exon_variant,,ENST00000558151,;RP11-133K1.2,non_coding_transcript_exon_variant,,ENST00000558965,;RP11-133K1.2,upstream_gene_variant,,ENST00000558658,;RP11-133K1.2,upstream_gene_variant,,ENST00000559435,;	T	ENSG00000156970	ENST00000287598	Transcript	missense_variant	2962	2767	923	D/Y	Gat/Tat	rs760104068	.	.	1	BUB1B	HGNC	1149	protein_coding	YES	CCDS10053.1	ENSP00000287598	BUB1B_HUMAN	.	UPI000006E699	.	deleterious(0.01)	possibly_damaging(0.903)	21/23	.	hmmpanther:PTHR14030,hmmpanther:PTHR14030:SF1,Gene3D:1.10.510.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGGATGTT	byFrequency	5	ESCA
CYP1A1	0	.	GRCh37	15	75014841	75014841	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598G>C	p.Ala200Pro	p.A200P	ENST00000379727	2/7	49	32	17	72	72	0	CYP1A1,missense_variant,p.Ala200Pro,ENST00000567032,;CYP1A1,missense_variant,p.Ala200Pro,ENST00000379727,;CYP1A1,missense_variant,p.Ala200Pro,ENST00000395049,;CYP1A1,missense_variant,p.Ala200Pro,ENST00000395048,;CYP1A1,5_prime_UTR_variant,,ENST00000564596,;CYP1A1,5_prime_UTR_variant,,ENST00000566503,;CYP1A1,intron_variant,,ENST00000562201,;CYP1A1,intron_variant,,ENST00000569630,;	G	ENSG00000140465	ENST00000379727	Transcript	missense_variant	797	598	200	A/P	Gcc/Ccc	.	.	.	-1	CYP1A1	HGNC	2595	protein_coding	YES	CCDS10268.1	ENSP00000369050	CP1A1_HUMAN	A4F4K4_HUMAN,A4F3V8_HUMAN,A0N0X8_HUMAN	UPI0000128195	.	deleterious(0)	probably_damaging(0.99)	2/7	.	Prints_domain:PR00463,Superfamily_domains:SSF48264,Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24299:SF8,hmmpanther:PTHR24299	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGCACAGA	.	5	ESCA
PEAK1	0	.	GRCh37	15	77473641	77473641	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628A>T	p.Ile210Phe	p.I210F	ENST00000560626	4/7	36	29	7	39	39	0	PEAK1,missense_variant,p.Ile210Phe,ENST00000560626,;PEAK1,missense_variant,p.Ile210Phe,ENST00000558305,;PEAK1,missense_variant,p.Ile210Phe,ENST00000564328,;PEAK1,missense_variant,p.Ile210Phe,ENST00000312493,;PEAK1,downstream_gene_variant,,ENST00000565820,;PEAK1,downstream_gene_variant,,ENST00000567808,;PEAK1,upstream_gene_variant,,ENST00000559791,;PEAK1,upstream_gene_variant,,ENST00000560854,;	A	ENSG00000173517	ENST00000560626	Transcript	missense_variant	1104	628	210	I/F	Att/Ttt	.	.	.	-1	PEAK1	HGNC	29431	protein_coding	YES	CCDS42062.1	ENSP00000452796	PEAK1_HUMAN	H3BUZ5_HUMAN,H3BUE6_HUMAN	UPI00002378D0	.	tolerated(0.08)	benign(0.355)	4/7	.	hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CAGAATAACAT	.	4	ESCA
C16orf62	0	.	GRCh37	16	19590313	19590313	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.701-61C>T	.	.	ENST00000438132	.	41	25	15	34	34	0	C16orf62,missense_variant,p.Pro3Ser,ENST00000448695,;C16orf62,5_prime_UTR_variant,,ENST00000543152,;C16orf62,intron_variant,,ENST00000513947,;C16orf62,intron_variant,,ENST00000417362,;C16orf62,intron_variant,,ENST00000563649,;C16orf62,intron_variant,,ENST00000542263,;C16orf62,intron_variant,,ENST00000544670,;C16orf62,intron_variant,,ENST00000251143,;C16orf62,intron_variant,,ENST00000538853,;C16orf62,intron_variant,,ENST00000438132,;C16orf62,intron_variant,,ENST00000567245,;C16orf62,upstream_gene_variant,,ENST00000562446,;C16orf62,intron_variant,,ENST00000539322,;	T	ENSG00000103544	ENST00000438132	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C16orf62	HGNC	24641	protein_coding	YES	CCDS32397.2	ENSP00000400815	.	I3L1U5_HUMAN,H3BV68_HUMAN,E7EWW0_HUMAN	UPI0001E1129C	.	.	.	.	5/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCCACTG	.	5	ESCA
AC004381.6	0	.	GRCh37	16	20818390	20818390	+	Missense_Mutation	SNP	G	G	A	rs745451778	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115G>A	p.Glu39Lys	p.E39K	ENST00000261377	2/20	128	122	5	108	108	0	AC004381.6,missense_variant,p.Glu39Lys,ENST00000568046,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000568647,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000564274,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000563068,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000261377,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000568894,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000348433,;AC004381.6,intron_variant,,ENST00000566276,;AC004381.6,intron_variant,,ENST00000568501,;AC004381.6,intron_variant,,ENST00000565340,;ERI2,intron_variant,,ENST00000564349,;ERI2,upstream_gene_variant,,ENST00000563117,;ERI2,upstream_gene_variant,,ENST00000569729,;ERI2,upstream_gene_variant,,ENST00000389345,;ERI2,upstream_gene_variant,,ENST00000357967,;AC004381.6,upstream_gene_variant,,ENST00000563617,;ERI2,upstream_gene_variant,,ENST00000300005,;AC004381.6,non_coding_transcript_exon_variant,,ENST00000567297,;AC004381.6,intron_variant,,ENST00000568476,;ERI2,upstream_gene_variant,,ENST00000568251,;ERI2,upstream_gene_variant,,ENST00000563537,;ERI2,upstream_gene_variant,,ENST00000565884,;ERI2,upstream_gene_variant,,ENST00000566223,;ERI2,upstream_gene_variant,,ENST00000567562,;ERI2,upstream_gene_variant,,ENST00000562277,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000566518,;AC004381.6,missense_variant,p.Glu39Lys,ENST00000566993,;ERI2,upstream_gene_variant,,ENST00000568805,;ERI2,upstream_gene_variant,,ENST00000567859,;	A	ENSG00000005189	ENST00000261377	Transcript	missense_variant	324	115	39	E/K	Gag/Aag	rs745451778	.	.	1	AC004381.6	Clone_based_vega_gene	.	protein_coding	YES	CCDS10591.1	ENSP00000261377	REXON_HUMAN	H3BV93_HUMAN,H3BUT7_HUMAN,H3BSE4_HUMAN,H3BSC5_HUMAN,H3BR13_HUMAN,H3BQ98_HUMAN,H3BPB2_HUMAN,H3BM72_HUMAN	UPI0000073454	.	tolerated_low_confidence(0.16)	benign(0.007)	2/20	.	hmmpanther:PTHR12801:SF61,hmmpanther:PTHR12801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTCGAGGAG	.	2	ESCA
CHD9	0	.	GRCh37	16	53279712	53279712	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3404A>G	p.Asn1135Ser	p.N1135S	ENST00000566029	15/39	99	64	35	104	104	0	CHD9,missense_variant,p.Asn1135Ser,ENST00000566029,;CHD9,missense_variant,p.Asn1135Ser,ENST00000564845,;CHD9,missense_variant,p.Asn661Ser,ENST00000565803,;CHD9,missense_variant,p.Asn1135Ser,ENST00000447540,;CHD9,missense_variant,p.Asn1135Ser,ENST00000398510,;CHD9,non_coding_transcript_exon_variant,,ENST00000565119,;CHD9,non_coding_transcript_exon_variant,,ENST00000219084,;CHD9,non_coding_transcript_exon_variant,,ENST00000564255,;CHD9,non_coding_transcript_exon_variant,,ENST00000569225,;CHD9,upstream_gene_variant,,ENST00000562806,;	G	ENSG00000177200	ENST00000566029	Transcript	missense_variant	3613	3404	1135	N/S	aAt/aGt	COSM3377899	.	.	1	CHD9	HGNC	25701	protein_coding	YES	CCDS45485.1	ENSP00000457466	CHD9_HUMAN	H3BV31_HUMAN,H3BSP3_HUMAN,H3BRU9_HUMAN	UPI00001FF1A0	.	.	probably_damaging(0.999)	15/39	.	Superfamily_domains:SSF52540,Pfam_domain:PF00176,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF48	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCAATACCA	.	5	ESCA
CES1	0	.	GRCh37	16	55866958	55866958	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10C>T	p.Arg4Cys	p.R4C	ENST00000360526	1/14	259	216	42	236	236	0	CES1,missense_variant,p.Arg4Cys,ENST00000360526,;CES1,missense_variant,p.Arg4Cys,ENST00000422046,;CES1,missense_variant,p.Arg4Cys,ENST00000361503,;CES1,upstream_gene_variant,,ENST00000566555,;CES1,non_coding_transcript_exon_variant,,ENST00000565403,;CES1,non_coding_transcript_exon_variant,,ENST00000563005,;	A	ENSG00000198848	ENST00000360526	Transcript	missense_variant	113	10	4	R/C	Cgt/Tgt	.	.	.	-1	CES1	HGNC	1863	protein_coding	YES	CCDS32450.1	ENSP00000353720	EST1_HUMAN	B7Z795_HUMAN	UPI000054B390	.	tolerated(0.24)	benign(0.001)	1/14	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11559:SF179,hmmpanther:PTHR11559,Pfam_domain:PF00135	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCACGGAGCC	.	4	ESCA
CNOT1	0	.	GRCh37	16	58577401	58577401	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4434+110A>G	.	.	ENST00000317147	.	92	54	37	87	87	0	CNOT1,missense_variant,p.Asn1515Ser,ENST00000441024,;CNOT1,intron_variant,,ENST00000317147,;CNOT1,intron_variant,,ENST00000569240,;CNOT1,intron_variant,,ENST00000245138,;CNOT1,downstream_gene_variant,,ENST00000567285,;CNOT1,upstream_gene_variant,,ENST00000568917,;CNOT1,downstream_gene_variant,,ENST00000567133,;CNOT1,intron_variant,,ENST00000566240,;CNOT1,intron_variant,,ENST00000567188,;CNOT1,upstream_gene_variant,,ENST00000563283,;	C	ENSG00000125107	ENST00000317147	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CNOT1	HGNC	7877	protein_coding	YES	CCDS10799.1	ENSP00000320949	CNOT1_HUMAN	H3BUY8_HUMAN,H3BT18_HUMAN,H3BPF1_HUMAN,B7Z6X2_HUMAN,B3KS60_HUMAN	UPI00001FF2F6	.	.	.	.	31/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGATTATTA	.	5	ESCA
PDPR	0	.	GRCh37	16	70187417	70187417	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2176A>G	p.Ile726Val	p.I726V	ENST00000288050	18/19	110	91	19	104	104	0	PDPR,missense_variant,p.Ile84Val,ENST00000563930,;PDPR,missense_variant,p.Ile109Val,ENST00000569042,;PDPR,missense_variant,p.Ile71Val,ENST00000542659,;PDPR,missense_variant,p.Ile726Val,ENST00000288050,;PDPR,missense_variant,p.Ile84Val,ENST00000567896,;PDPR,missense_variant,p.Ile626Val,ENST00000398122,;PDPR,missense_variant,p.Ile84Val,ENST00000567046,;PDPR,missense_variant,p.Ile726Val,ENST00000568530,;RP11-296I10.3,downstream_gene_variant,,ENST00000566989,;PDPR,intron_variant,,ENST00000562100,;PDPR,3_prime_UTR_variant,,ENST00000564563,;PDPR,intron_variant,,ENST00000565186,;PDPR,downstream_gene_variant,,ENST00000561920,;	G	ENSG00000090857	ENST00000288050	Transcript	missense_variant	3133	2176	726	I/V	Ata/Gta	COSM704340	.	.	1	PDPR	HGNC	30264	protein_coding	YES	CCDS45520.1	ENSP00000288050	PDPR_HUMAN	H3BV59_HUMAN,H3BU60_HUMAN,B7ZAR9_HUMAN,B3KSE1_HUMAN,A8MT40_HUMAN	UPI00001FF513	.	deleterious(0.02)	benign(0.033)	18/19	.	Pfam_domain:PF01571,Superfamily_domains:SSF103025	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATATAAAT	.	5	ESCA
RFWD3	0	.	GRCh37	16	74657208	74657208	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*618G>C	.	.	ENST00000361070	13/13	29	17	11	19	19	0	RFWD3,3_prime_UTR_variant,,ENST00000361070,;RFWD3,downstream_gene_variant,,ENST00000571750,;	G	ENSG00000168411	ENST00000361070	Transcript	3_prime_UTR_variant	3041	.	.	.	.	.	.	.	-1	RFWD3	HGNC	25539	protein_coding	YES	CCDS32486.1	ENSP00000354361	RFWD3_HUMAN	I3L4I5_HUMAN,I3L2T2_HUMAN,I3L299_HUMAN,I3L284_HUMAN	UPI0000366B66	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACACAAGTG	.	5	ESCA
TERF2IP	0	.	GRCh37	16	75681753	75681753	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-28G>C	.	.	ENST00000300086	1/3	67	39	28	79	79	0	TERF2IP,5_prime_UTR_variant,,ENST00000300086,;KARS,upstream_gene_variant,,ENST00000319410,;KARS,upstream_gene_variant,,ENST00000568682,;KARS,upstream_gene_variant,,ENST00000568378,;KARS,upstream_gene_variant,,ENST00000570215,;KARS,upstream_gene_variant,,ENST00000302445,;KARS,intron_variant,,ENST00000566560,;TERF2IP,upstream_gene_variant,,ENST00000569234,;KARS,upstream_gene_variant,,ENST00000564578,;KARS,upstream_gene_variant,,ENST00000562875,;KARS,upstream_gene_variant,,ENST00000566249,;	C	ENSG00000166848	ENST00000300086	Transcript	5_prime_UTR_variant	70	.	.	.	.	.	.	.	1	TERF2IP	HGNC	19246	protein_coding	YES	CCDS32491.1	ENSP00000300086	TE2IP_HUMAN	.	UPI0000136B77	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTAGCTCTT	.	2	ESCA
MAP2K4	0	.	GRCh37	17	11985275	11985275	+	Intron	SNP	C	C	T	rs572154384	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393+428C>T	.	.	ENST00000353533	.	56	29	26	45	45	0	MAP2K4,intron_variant,,ENST00000353533,;MAP2K4,intron_variant,,ENST00000415385,;MIR744,non_coding_transcript_exon_variant,,ENST00000578242,;MAP2K4,intron_variant,,ENST00000582897,;MAP2K4,intron_variant,,ENST00000579089,;MAP2K4,intron_variant,,ENST00000581941,;MAP2K4,intron_variant,,ENST00000602375,;MAP2K4,intron_variant,,ENST00000602811,;MAP2K4,intron_variant,,ENST00000582183,;MAP2K4,intron_variant,,ENST00000538465,;MAP2K4,intron_variant,,ENST00000602537,;MAP2K4,intron_variant,,ENST00000602686,;MAP2K4,intron_variant,,ENST00000602305,;	T	ENSG00000065559	ENST00000353533	Transcript	intron_variant	.	.	.	.	.	rs572154384	.	.	1	MAP2K4	HGNC	6844	protein_coding	YES	CCDS11162.1	ENSP00000262445	MP2K4_HUMAN	J3QQR2_HUMAN,J3KTI6_HUMAN	UPI000012F48E	.	.	.	.	3/10	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCACGCACA	by1000G	5	ESCA
FAM83G	0	.	GRCh37	17	18874831	18874831	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2313C>T	p.%3D	p.T771T	ENST00000388995	6/6	118	44	74	111	111	0	FAM83G,synonymous_variant,p.%3D,ENST00000585154,;FAM83G,synonymous_variant,p.%3D,ENST00000388995,;FAM83G,synonymous_variant,p.%3D,ENST00000345041,;SLC5A10,intron_variant,,ENST00000417251,;SLC5A10,intron_variant,,ENST00000395647,;SLC5A10,intron_variant,,ENST00000395643,;SLC5A10,intron_variant,,ENST00000395642,;SLC5A10,intron_variant,,ENST00000395645,;SLC5A10,intron_variant,,ENST00000317977,;FAM83G,downstream_gene_variant,,ENST00000399096,;	A	ENSG00000188522	ENST00000388995	Transcript	synonymous_variant	2537	2313	771	T	acC/acT	.	.	.	-1	FAM83G	HGNC	32554	protein_coding	YES	CCDS42276.1	ENSP00000373647	FA83G_HUMAN	.	UPI0000E03260	.	.	.	6/6	.	hmmpanther:PTHR16181:SF5,hmmpanther:PTHR16181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCGGTCAT	.	5	ESCA
NOS2	0	.	GRCh37	17	26091136	26091136	+	Silent	SNP	G	G	T	rs768818086	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2463C>A	p.%3D	p.P821P	ENST00000313735	21/27	59	22	36	68	68	0	NOS2,synonymous_variant,p.%3D,ENST00000313735,;	T	ENSG00000007171	ENST00000313735	Transcript	synonymous_variant	2697	2463	821	P	ccC/ccA	rs768818086	.	.	-1	NOS2	HGNC	7873	protein_coding	YES	CCDS11223.1	ENSP00000327251	NOS2_HUMAN	Q9UM94_HUMAN	UPI000011D645	.	.	.	21/27	.	PROSITE_profiles:PS51384,hmmpanther:PTHR19384:SF56,hmmpanther:PTHR19384,Pfam_domain:PF00667,Gene3D:1.20.990.10,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF63380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCAGGGGGG	.	5	ESCA
NAGLU	0	.	GRCh37	17	40695161	40695161	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1137G>T	p.%3D	p.L379L	ENST00000225927	6/6	66	28	38	56	56	0	NAGLU,missense_variant,p.Gly60Cys,ENST00000592454,;NAGLU,synonymous_variant,p.%3D,ENST00000225927,;NAGLU,3_prime_UTR_variant,,ENST00000591587,;NAGLU,downstream_gene_variant,,ENST00000590358,;NAGLU,downstream_gene_variant,,ENST00000586516,;RP11-400F19.8,intron_variant,,ENST00000585572,;HSD17B1P1,upstream_gene_variant,,ENST00000590052,;	T	ENSG00000108784	ENST00000225927	Transcript	synonymous_variant	1238	1137	379	L	ctG/ctT	.	.	.	1	NAGLU	HGNC	7632	protein_coding	YES	CCDS11427.1	ENSP00000225927	ANAG_HUMAN	.	UPI000013C885	.	.	.	6/6	.	hmmpanther:PTHR12872,Pfam_domain:PF05089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTGGTTCT	.	5	ESCA
MED13	0	.	GRCh37	17	60033165	60033165	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5658G>T	p.Gln1886His	p.Q1886H	ENST00000397786	25/30	30	18	12	23	23	0	MED13,missense_variant,p.Gln1886His,ENST00000397786,;MED13,upstream_gene_variant,,ENST00000582786,;	A	ENSG00000108510	ENST00000397786	Transcript	missense_variant	5735	5658	1886	Q/H	caG/caT	.	.	.	-1	MED13	HGNC	22474	protein_coding	YES	CCDS42366.1	ENSP00000380888	MED13_HUMAN	.	UPI0000D7D6F6	.	tolerated(0.2)	probably_damaging(0.991)	25/30	.	hmmpanther:PTHR12950:SF22,hmmpanther:PTHR12950,Pfam_domain:PF06333	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGACTGCAA	.	5	ESCA
TP53	0	.	GRCh37	17	7578179	7578179	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	6/11	63	24	39	72	72	0	TP53,stop_gained,p.Glu224Ter,ENST00000413465,;TP53,stop_gained,p.Glu224Ter,ENST00000420246,;TP53,stop_gained,p.Glu224Ter,ENST00000269305,;TP53,stop_gained,p.Glu92Ter,ENST00000509690,;TP53,stop_gained,p.Glu224Ter,ENST00000359597,;TP53,stop_gained,p.Glu131Ter,ENST00000514944,;TP53,stop_gained,p.Glu224Ter,ENST00000445888,;TP53,stop_gained,p.Glu224Ter,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,splice_region_variant,,ENST00000504937,;TP53,splice_region_variant,,ENST00000504290,;TP53,splice_region_variant,,ENST00000510385,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	860	670	224	E/*	Gag/Tag	TP53_g.12739del,TP53_g.12739G>T,TP53_g.12739G>A,COSM10894,COSM44922,COSM46248	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E224*|c.670G>T|5,CODON|p.0?|c.1_1182del1182|6,CODON|p.E224D|c.672G>C|3,CODON|p.E224D|c.672G>C|8,CODON|p.E224E|c.672G>A|3,CODON|p.E224E|c.672G>A|9,CODON|p.E224E|c.672G>A|3,CODON|p.E131D|c.393G>C|3,CODON|p.E224D|c.672G>C|3,CODON|p.E224D|c.672G>T|7,CODON|p.E224E|c.672G>A|3,CODON|p.E131E|c.393G>A|3,BUFFER|p.?|c.672+2T>A|3,BUFFER|p.?|c.672+2T>A|3,BUFFER|p.?|c.672+2T>C|8,BUFFER|p.?|c.393+2T>A|3,BUFFER|p.?|c.672+2T>A|3,BUFFER|p.?|c.672+1G>A|4,BUFFER|p.?|c.393+1G>A|8,BUFFER|p.?|c.672+1G>A|8,BUFFER|p.?|c.672+1G>T|5,BUFFER|p.?|c.672+1G>A|8,BUFFER|p.?|c.672+1G>C|3,BUFFER|p.?|c.672+1G>T|3,BUFFER|p.?|c.672+1G>A|4,BUFFER|p.?|c.393+1G>T|6,BUFFER|p.?|c.672+1G>A|19,BUFFER|p.?|c.672+1G>T|16,BUFFER|p.?|c.672+1G>T|6,BUFFER|p.?|c.672+1G>T|6,BUFFER|p.E224K|c.670G>A|4,BUFFER|p.P223L|c.668C>T|3,BUFFER|p.P222P|c.666G>C|3,BUFFER|p.P222L|c.665C>T|4,BUFFER|p.P222T|c.664C>A|3,BUFFER|p.E221G|c.662A>G|3,BUFFER|p.E221fs*4|c.660_661insN|3,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E128*|c.382G>T|6,BUFFER|p.E221*|c.661G>T|10,BUFFER|p.Y220*|c.660T>G|3,BUFFER|p.Y220S|c.659A>C|4,BUFFER|p.Y220C|c.659A>G|264,BUFFER|p.Y220C|c.659A>G|63,BUFFER|p.Y127C|c.380A>G|63,BUFFER|p.Y127S|c.380A>C|4,BUFFER|p.Y220S|c.659A>C|3,BUFFER|p.Y220C|c.659A>G|25,BUFFER|p.Y220S|c.659A>C|3,BUFFER|p.Y220S|c.659A>C|4,BUFFER|p.Y220C|c.659A>G|61,BUFFER|p.Y220S|c.659A>C|13,BUFFER|p.Y220C|c.659A>G|33	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTCAGGCG	.	5	ESCA
ENDOV	0	.	GRCh37	17	78410075	78410075	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*132G>A	.	.	ENST00000518137	10/10	36	16	20	47	47	0	ENDOV,3_prime_UTR_variant,,ENST00000517795,;ENDOV,3_prime_UTR_variant,,ENST00000518907,;ENDOV,3_prime_UTR_variant,,ENST00000518901,;ENDOV,3_prime_UTR_variant,,ENST00000520367,;ENDOV,3_prime_UTR_variant,,ENST00000518137,;ENDOV,3_prime_UTR_variant,,ENST00000520284,;	A	ENSG00000173818	ENST00000518137	Transcript	3_prime_UTR_variant	1009	.	.	.	.	.	.	.	1	ENDOV	HGNC	26640	protein_coding	YES	CCDS54172.1	ENSP00000429190	ENDOV_HUMAN	I3L4V7_HUMAN,I3L1V3_HUMAN,E5RHX4_HUMAN	UPI0000072E31	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAACGCGGTG	.	5	ESCA
CYP4F35P	0	.	GRCh37	18	14337526	14337526	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.105C>A	.	.	ENST00000582957	1/4	26	10	15	35	35	0	CYP4F35P,non_coding_transcript_exon_variant,,ENST00000582957,;CYP4F35P,upstream_gene_variant,,ENST00000578285,;	A	ENSG00000265787	ENST00000582957	Transcript	non_coding_transcript_exon_variant	105	.	.	.	.	.	.	.	1	CYP4F35P	HGNC	39954	lincRNA	YES	.	.	.	.	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTACAGACC	.	5	ESCA
POTEC	0	.	GRCh37	18	14542998	14542998	+	Missense_Mutation	SNP	C	C	A	rs760410303	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148G>T	p.Asp50Tyr	p.D50Y	ENST00000358970	1/11	226	212	14	258	258	0	POTEC,missense_variant,p.Asp50Tyr,ENST00000358970,;POTEC,non_coding_transcript_exon_variant,,ENST00000389891,;POTEC,missense_variant,p.Asp50Tyr,ENST00000511306,;	A	ENSG00000183206	ENST00000358970	Transcript	missense_variant	148	148	50	D/Y	Gac/Tac	rs760410303	.	.	-1	POTEC	HGNC	33894	protein_coding	YES	CCDS45835.1	ENSP00000351856	POTEC_HUMAN	.	UPI0000197B83	.	deleterious_low_confidence(0.03)	probably_damaging(0.92)	1/11	.	hmmpanther:PTHR24118:SF38,hmmpanther:PTHR24118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCGTCGTGGT	byFrequency	2	ESCA
ANKRD30B	0	.	GRCh37	18	14850253	14850253	+	Missense_Mutation	SNP	G	G	C	rs776867847	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3079G>C	p.Asp1027His	p.D1027H	ENST00000358984	35/36	54	22	32	35	35	0	ANKRD30B,missense_variant,p.Asp1027His,ENST00000358984,;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,;	C	ENSG00000180777	ENST00000358984	Transcript	missense_variant	3259	3079	1027	D/H	Gat/Cat	rs776867847	.	.	1	ANKRD30B	HGNC	24165	protein_coding	YES	CCDS54182.1	ENSP00000351875	AN30B_HUMAN	.	UPI0000425FF7	.	tolerated(0.06)	probably_damaging(0.969)	35/36	.	hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCGATATA	byFrequency	5	ESCA
KIAA1468	0	.	GRCh37	18	59925833	59925833	+	Missense_Mutation	SNP	C	C	T	rs780897375	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2126C>T	p.Ala709Val	p.A709V	ENST00000398130	15/29	62	20	41	58	58	0	KIAA1468,missense_variant,p.Ala709Val,ENST00000256858,;KIAA1468,missense_variant,p.Ala709Val,ENST00000398130,;KIAA1468,downstream_gene_variant,,ENST00000591227,;KIAA1468,missense_variant,p.Ala709Val,ENST00000587725,;KIAA1468,upstream_gene_variant,,ENST00000588446,;	T	ENSG00000134444	ENST00000398130	Transcript	missense_variant	2358	2126	709	A/V	gCg/gTg	rs780897375	.	.	1	KIAA1468	HGNC	29289	protein_coding	YES	CCDS11979.2	ENSP00000381198	K1468_HUMAN	Q96ES0_HUMAN	UPI0000DA5AF7	.	tolerated(0.14)	benign(0.275)	15/29	.	hmmpanther:PTHR32059,hmmpanther:PTHR32059:SF0,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTGCGTGGA	byFrequency	5	ESCA
TNFRSF11A	0	.	GRCh37	18	60028959	60028959	+	Silent	SNP	G	G	A	rs138444094	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.663G>A	p.%3D	p.A221A	ENST00000586569	7/10	84	66	17	79	79	0	TNFRSF11A,synonymous_variant,p.%3D,ENST00000586569,;TNFRSF11A,intron_variant,,ENST00000269485,;TNFRSF11A,downstream_gene_variant,,ENST00000587697,;	A	ENSG00000141655	ENST00000586569	Transcript	synonymous_variant	701	663	221	A	gcG/gcA	rs138444094	.	.	1	TNFRSF11A	HGNC	11908	protein_coding	YES	CCDS11980.1	ENSP00000465500	TNR11_HUMAN	N0GVH0_HUMAN	UPI000003BC8A	.	.	.	7/10	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR23097:SF29,hmmpanther:PTHR23097	A:0.0008	A:0.003	A:0	.	A:0	A:0	A:0	A:0.0009	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCGCGTCTGT	byFrequency|byCluster|by1000G	5	ESCA
CCDC102B	0	.	GRCh37	18	66504325	66504325	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.325G>T	p.Val109Phe	p.V109F	ENST00000360242	2/8	70	22	47	60	60	0	CCDC102B,missense_variant,p.Val109Phe,ENST00000584156,;CCDC102B,missense_variant,p.Val109Phe,ENST00000319445,;CCDC102B,missense_variant,p.Val109Phe,ENST00000358653,;CCDC102B,missense_variant,p.Val109Phe,ENST00000584775,;CCDC102B,missense_variant,p.Val109Phe,ENST00000360242,;CCDC102B,missense_variant,p.Val109Phe,ENST00000582371,;CCDC102B,missense_variant,p.Val109Phe,ENST00000581520,;CCDC102B,downstream_gene_variant,,ENST00000578970,;CCDC102B,non_coding_transcript_exon_variant,,ENST00000577772,;	T	ENSG00000150636	ENST00000360242	Transcript	missense_variant	442	325	109	V/F	Gtt/Ttt	.	.	.	1	CCDC102B	HGNC	26295	protein_coding	YES	CCDS11996.2	ENSP00000353377	C102B_HUMAN	J3QLG6_HUMAN,J3QL62_HUMAN,J3KRT2_HUMAN,J3KRG3_HUMAN,A1A4H1_HUMAN	UPI0000201E87	.	deleterious(0)	probably_damaging(0.997)	2/8	.	hmmpanther:PTHR13140:SF295,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAAGTTCGA	.	5	ESCA
ZNF433	0	.	GRCh37	19	12127157	12127157	+	Silent	SNP	G	G	A	rs374806336	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.525C>T	p.%3D	p.C175C	ENST00000344980	4/4	62	45	17	64	64	0	ZNF433,synonymous_variant,p.%3D,ENST00000344980,;ZNF433,synonymous_variant,p.%3D,ENST00000550507,;ZNF433,synonymous_variant,p.%3D,ENST00000419886,;ZNF433,downstream_gene_variant,,ENST00000411841,;ZNF433,downstream_gene_variant,,ENST00000550745,;ZNF433,downstream_gene_variant,,ENST00000478765,;ZNF433,downstream_gene_variant,,ENST00000552904,;ZNF433,downstream_gene_variant,,ENST00000547560,;ZNF433,downstream_gene_variant,,ENST00000455504,;CTD-2006C1.2,intron_variant,,ENST00000406892,;CTD-2006C1.2,intron_variant,,ENST00000495324,;CTD-2006C1.2,intron_variant,,ENST00000476474,;CTD-2006C1.2,intron_variant,,ENST00000588047,;CTD-2006C1.10,downstream_gene_variant,,ENST00000547473,;ZNF433,downstream_gene_variant,,ENST00000548669,;	A	ENSG00000197647	ENST00000344980	Transcript	synonymous_variant	696	525	175	C	tgC/tgT	rs374806336	.	.	-1	ZNF433	HGNC	20811	protein_coding	YES	CCDS45983.1	ENSP00000339767	ZN433_HUMAN	F8W652_HUMAN,F8W0C9_HUMAN,F8VXJ9_HUMAN	UPI0000071556	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF00096,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24379:SF25,hmmpanther:PTHR24379,PROSITE_profiles:PS50157	A:0.0004	A:0	A:0.0029	.	A:0	A:0	A:0	A:0.0005	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCGCATTC	byFrequency|byCluster|by1000G	5	ESCA
ZNF563	0	.	GRCh37	19	12430312	12430312	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.527A>T	p.Lys176Ile	p.K176I	ENST00000293725	4/4	107	70	37	106	106	0	ZNF563,missense_variant,p.Lys176Ile,ENST00000293725,;ZNF563,missense_variant,p.Lys176Ile,ENST00000595977,;ZNF563,missense_variant,p.Lys88Ile,ENST00000594577,;ZNF563,downstream_gene_variant,,ENST00000601858,;	A	ENSG00000188868	ENST00000293725	Transcript	missense_variant	733	527	176	K/I	aAa/aTa	.	.	.	-1	ZNF563	HGNC	30498	protein_coding	YES	CCDS12270.1	ENSP00000293725	ZN563_HUMAN	M0R1Q6_HUMAN	UPI0000072E62	.	deleterious(0)	probably_damaging(0.999)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF14,hmmpanther:PTHR24379,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTTTTCCA	.	5	ESCA
PKN1	0	.	GRCh37	19	14581013	14581013	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2350A>G	p.Thr784Ala	p.T784A	ENST00000342216	19/22	52	31	20	56	56	0	PKN1,missense_variant,p.Thr778Ala,ENST00000242783,;PKN1,missense_variant,p.Thr784Ala,ENST00000342216,;PKN1,intron_variant,,ENST00000586237,;PTGER1,downstream_gene_variant,,ENST00000292513,;PKN1,upstream_gene_variant,,ENST00000592960,;PKN1,missense_variant,p.Thr182Ala,ENST00000591461,;PKN1,non_coding_transcript_exon_variant,,ENST00000585839,;PKN1,non_coding_transcript_exon_variant,,ENST00000586039,;PKN1,downstream_gene_variant,,ENST00000586900,;PKN1,downstream_gene_variant,,ENST00000587215,;	G	ENSG00000123143	ENST00000342216	Transcript	missense_variant	2381	2350	784	T/A	Acc/Gcc	COSM1390954	.	.	1	PKN1	HGNC	9405	protein_coding	YES	CCDS42514.1	ENSP00000343325	PKN1_HUMAN	.	UPI0000366D4D	.	deleterious(0)	probably_damaging(0.997)	19/22	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF69,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTGGGACCCCG	.	3	ESCA
ZNF66	0	.	GRCh37	19	20959180	20959180	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000344519	.	108	97	11	99	99	0	ZNF66,5_prime_UTR_variant,,ENST00000594534,;ZNF66,5_prime_UTR_variant,,ENST00000360204,;ZNF66,upstream_gene_variant,,ENST00000344519,;	A	ENSG00000160229	ENST00000344519	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	51	1	ZNF66	HGNC	13135	protein_coding	YES	.	ENSP00000461425	ZNF66_HUMAN	.	UPI00025A2C0A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCAGCCTCTG	.	4	ESCA
ZNF100	0	.	GRCh37	19	21909627	21909627	+	Missense_Mutation	SNP	C	C	T	rs762415292	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1487G>A	p.Arg496Gln	p.R496Q	ENST00000358296	5/5	83	77	5	59	59	0	ZNF100,missense_variant,p.Arg432Gln,ENST00000305570,;ZNF100,missense_variant,p.Arg496Gln,ENST00000358296,;ZNF100,downstream_gene_variant,,ENST00000594401,;	T	ENSG00000197020	ENST00000358296	Transcript	missense_variant	1686	1487	496	R/Q	cGa/cAa	rs762415292	.	.	-1	ZNF100	HGNC	12880	protein_coding	YES	CCDS42538.1	ENSP00000351042	ZN100_HUMAN	Q6MZN6_HUMAN	UPI00001614AC	.	tolerated(1)	benign(0.003)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF78,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGATCGGTTA	byFrequency	2	ESCA
ZNF724P	0	.	GRCh37	19	23433093	23433093	+	5'UTR	SNP	A	A	G	rs558123088	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-49T>C	.	.	ENST00000418100	1/4	111	74	37	92	92	0	ZNF724P,5_prime_UTR_variant,,ENST00000597537,;ZNF724P,5_prime_UTR_variant,,ENST00000418100,;ZNF724P,5_prime_UTR_variant,,ENST00000597037,;RP11-15H20.5,downstream_gene_variant,,ENST00000593576,;RP11-15H20.5,downstream_gene_variant,,ENST00000600039,;	G	ENSG00000196081	ENST00000418100	Transcript	5_prime_UTR_variant	70	.	.	.	.	rs558123088	.	.	-1	ZNF724P	HGNC	32460	protein_coding	YES	.	ENSP00000413411	ZN724_HUMAN	M0R3J2_HUMAN	UPI0000EE61E4	.	.	.	1/4	.	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCAATGCTT	by1000G	5	ESCA
ZNF254	0	.	GRCh37	19	24310988	24310988	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*206A>G	.	.	ENST00000357002	4/4	16	7	9	10	10	0	ZNF254,3_prime_UTR_variant,,ENST00000357002,;ZNF254,3_prime_UTR_variant,,ENST00000342944,;ZNF254,downstream_gene_variant,,ENST00000595187,;ZNF254,downstream_gene_variant,,ENST00000594886,;	G	ENSG00000213096	ENST00000357002	Transcript	3_prime_UTR_variant	2301	.	.	.	.	.	.	.	1	ZNF254	HGNC	13047	protein_coding	YES	CCDS32983.1	ENSP00000349494	ZN254_HUMAN	F5H2M4_HUMAN	UPI0000366DB6	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTAAGATAATT	.	4	ESCA
ZNF302	0	.	GRCh37	19	35175213	35175213	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271G>A	p.Glu91Lys	p.E91K	ENST00000505242	5/5	268	257	10	153	153	0	ZNF302,missense_variant,p.Glu91Lys,ENST00000505163,;ZNF302,missense_variant,p.Glu91Lys,ENST00000457781,;ZNF302,missense_variant,p.Met22Ile,ENST00000509528,;ZNF302,missense_variant,p.Glu91Lys,ENST00000423823,;ZNF302,missense_variant,p.Glu135Lys,ENST00000446502,;ZNF302,missense_variant,p.Glu91Lys,ENST00000505242,;ZNF302,3_prime_UTR_variant,,ENST00000507959,;ZNF302,3_prime_UTR_variant,,ENST00000505365,;ZNF302,downstream_gene_variant,,ENST00000506901,;ZNF302,downstream_gene_variant,,ENST00000502743,;ZNF302,non_coding_transcript_exon_variant,,ENST00000509196,;ZNF302,downstream_gene_variant,,ENST00000512455,;ZNF302,downstream_gene_variant,,ENST00000510002,;	A	ENSG00000089335	ENST00000505242	Transcript	missense_variant	765	271	91	E/K	Gaa/Aaa	.	.	.	1	ZNF302	HGNC	13848	protein_coding	YES	CCDS46042.1	ENSP00000421028	ZN302_HUMAN	Q7Z4B9_HUMAN,D6RAM0_HUMAN	UPI0000001668	.	tolerated(0.33)	possibly_damaging(0.641)	5/5	.	hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGATGAAGAT	.	2	ESCA
ZNF570	0	.	GRCh37	19	37976197	37976197	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62G>T	.	.	ENST00000330173	5/5	63	43	20	37	37	0	ZNF570,3_prime_UTR_variant,,ENST00000388801,;ZNF570,3_prime_UTR_variant,,ENST00000330173,;ZNF570,3_prime_UTR_variant,,ENST00000586475,;ZNF570,downstream_gene_variant,,ENST00000589725,;CTD-2086O20.3,upstream_gene_variant,,ENST00000591976,;ZNF570,3_prime_UTR_variant,,ENST00000588644,;ZNF570,downstream_gene_variant,,ENST00000590664,;	T	ENSG00000171827	ENST00000330173	Transcript	3_prime_UTR_variant	2202	.	.	.	.	.	.	.	1	ZNF570	HGNC	26416	protein_coding	YES	CCDS12504.1	ENSP00000331540	ZN570_HUMAN	K7EP64_HUMAN,K7ENX9_HUMAN,K7EMF5_HUMAN,B4DMP1_HUMAN	UPI000006DC96	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACCTTGGTCTG	.	4	ESCA
EEF2	0	.	GRCh37	19	3982015	3982015	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827C>T	p.Ser276Leu	p.S276L	ENST00000309311	6/15	73	56	16	75	75	0	EEF2,missense_variant,p.Ser276Leu,ENST00000309311,;EEF2,upstream_gene_variant,,ENST00000600794,;SNORD37,downstream_gene_variant,,ENST00000384048,;EEF2,downstream_gene_variant,,ENST00000600720,;EEF2,non_coding_transcript_exon_variant,,ENST00000598436,;EEF2,non_coding_transcript_exon_variant,,ENST00000598182,;EEF2,upstream_gene_variant,,ENST00000596417,;EEF2,downstream_gene_variant,,ENST00000594885,;	A	ENSG00000167658	ENST00000309311	Transcript	missense_variant	916	827	276	S/L	tCa/tTa	.	.	.	-1	EEF2	HGNC	3214	protein_coding	YES	CCDS12117.1	ENSP00000307940	EF2_HUMAN	Q8TA90_HUMAN,B4DMC6_HUMAN	UPI00001649F3	.	tolerated(0.07)	benign(0.069)	6/15	.	hmmpanther:PTHR23115:SF103,hmmpanther:PTHR23115,Gene3D:1n0uA03,Pfam_domain:PF00009,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTGACTTG	.	5	ESCA
ZNF665	0	.	GRCh37	19	53669199	53669199	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544G>A	p.Glu182Lys	p.E182K	ENST00000396424	4/4	66	49	16	51	51	0	ZNF665,missense_variant,p.Glu182Lys,ENST00000396424,;ZNF665,missense_variant,p.Glu117Lys,ENST00000600412,;CTD-2245F17.2,downstream_gene_variant,,ENST00000600257,;ZNF665,upstream_gene_variant,,ENST00000596564,;	T	ENSG00000197497	ENST00000396424	Transcript	missense_variant	634	544	182	E/K	Gaa/Aaa	.	.	.	-1	ZNF665	HGNC	25885	protein_coding	YES	CCDS46169.1	ENSP00000379702	ZN665_HUMAN	.	UPI000059D78D	.	tolerated(0.24)	benign(0.023)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF132,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTCATCAC	.	5	ESCA
KIR3DL1	0	.	GRCh37	19	55329985	55329985	+	Silent	SNP	C	C	A	rs200379896	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.286C>A	p.%3D	p.R96R	ENST00000391728	3/9	67	53	14	58	58	0	KIR3DL1,synonymous_variant,p.%3D,ENST00000541392,;KIR3DL1,synonymous_variant,p.%3D,ENST00000538269,;KIR3DL1,synonymous_variant,p.%3D,ENST00000326542,;KIR3DL1,synonymous_variant,p.%3D,ENST00000402254,;KIR3DL1,synonymous_variant,p.%3D,ENST00000391728,;KIR3DL1,intron_variant,,ENST00000358178,;KIR2DL4,downstream_gene_variant,,ENST00000396284,;KIR2DL4,downstream_gene_variant,,ENST00000357494,;KIR2DL4,downstream_gene_variant,,ENST00000396289,;KIR2DL4,downstream_gene_variant,,ENST00000345540,;KIR2DL4,downstream_gene_variant,,ENST00000346587,;KIR2DL4,downstream_gene_variant,,ENST00000396293,;KIR2DL4,downstream_gene_variant,,ENST00000359085,;KIR2DL4,downstream_gene_variant,,ENST00000463062,;KIR2DL4,downstream_gene_variant,,ENST00000486965,;	A	ENSG00000167633	ENST00000391728	Transcript	synonymous_variant	319	286	96	R	Cgg/Agg	rs200379896	.	.	1	KIR3DL1	HGNC	6338	protein_coding	YES	CCDS42621.1	ENSP00000375608	KI3L1_HUMAN	Q5UCE2_HUMAN,Q8NHL0_HUMAN	UPI000012DB24	.	.	.	3/9	.	hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF19,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726	T:0.0036	T:0.0136	T:0	.	T:0	T:0	T:0	T:0.0133	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGTCGGGGT	byFrequency|byCluster|by1000G	5	ESCA
ISOC2	0	.	GRCh37	19	55966407	55966407	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534A>G	p.%3D	p.E178E	ENST00000085068	5/6	131	78	53	145	145	0	ISOC2,synonymous_variant,p.%3D,ENST00000425675,;ISOC2,synonymous_variant,p.%3D,ENST00000438389,;ISOC2,synonymous_variant,p.%3D,ENST00000085068,;ISOC2,synonymous_variant,p.%3D,ENST00000589080,;ISOC2,synonymous_variant,p.%3D,ENST00000587226,;ISOC2,non_coding_transcript_exon_variant,,ENST00000590921,;ISOC2,downstream_gene_variant,,ENST00000589108,;ISOC2,downstream_gene_variant,,ENST00000591718,;	C	ENSG00000063241	ENST00000085068	Transcript	synonymous_variant	671	534	178	E	gaA/gaG	.	.	.	-1	ISOC2	HGNC	26278	protein_coding	YES	CCDS12925.1	ENSP00000085068	ISOC2_HUMAN	.	UPI00000719D3	.	.	.	5/6	.	hmmpanther:PTHR14119,hmmpanther:PTHR14119:SF4,Pfam_domain:PF00857,Gene3D:3.40.50.850,Superfamily_domains:SSF52499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E178K|c.532G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCTTCGCT	.	5	ESCA
ZNF814	0	.	GRCh37	19	58386173	58386173	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.585G>A	p.%3D	p.E195E	ENST00000435989	3/3	117	73	44	79	78	0	ZNF814,synonymous_variant,p.%3D,ENST00000435989,;ZNF814,intron_variant,,ENST00000600634,;ZNF814,intron_variant,,ENST00000597342,;ZNF814,intron_variant,,ENST00000595048,;ZNF814,intron_variant,,ENST00000595295,;ZNF814,intron_variant,,ENST00000596604,;ZNF814,intron_variant,,ENST00000597832,;ZNF814,downstream_gene_variant,,ENST00000597807,;ZNF814,intron_variant,,ENST00000594629,;ZNF814,intron_variant,,ENST00000597348,;ZNF814,intron_variant,,ENST00000595894,;CTD-2583A14.9,downstream_gene_variant,,ENST00000602124,;ZNF814,upstream_gene_variant,,ENST00000594159,;	T	ENSG00000204514	ENST00000435989	Transcript	synonymous_variant	820	585	195	E	gaG/gaA	.	.	.	-1	ZNF814	HGNC	33258	protein_coding	YES	CCDS46212.1	ENSP00000410545	ZN814_HUMAN	.	UPI0001662BAD	.	.	.	3/3	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCTCCCC	.	5	ESCA
ARHGEF18	0	.	GRCh37	19	7506809	7506809	+	Missense_Mutation	SNP	G	G	A	rs760864454	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.667G>A	p.Ala223Thr	p.A223T	ENST00000359920	3/20	37	33	3	38	38	0	ARHGEF18,missense_variant,p.Ala223Thr,ENST00000359920,;ARHGEF18,missense_variant,p.Ala65Thr,ENST00000319670,;CTD-2207O23.3,missense_variant,p.Ala181Thr,ENST00000593531,;ARHGEF18,missense_variant,p.Ala65Thr,ENST00000599752,;ARHGEF18,non_coding_transcript_exon_variant,,ENST00000595600,;	A	ENSG00000104880	ENST00000359920	Transcript	missense_variant	920	667	223	A/T	Gcc/Acc	rs760864454	.	.	1	ARHGEF18	HGNC	17090	protein_coding	YES	CCDS45946.1	ENSP00000352995	ARHGI_HUMAN	M0R125_HUMAN	UPI0000D6170D	.	tolerated(0.08)	benign(0.194)	3/20	.	hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACACCGCCTCG	byFrequency	2	ESCA
MYO1F	0	.	GRCh37	19	8587613	8587613	+	Silent	SNP	C	C	G	rs201007272	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2955G>C	p.%3D	p.P985P	ENST00000338257	26/28	67	47	20	49	49	0	MYO1F,synonymous_variant,p.%3D,ENST00000338257,;MYO1F,downstream_gene_variant,,ENST00000596245,;MYO1F,downstream_gene_variant,,ENST00000600885,;MYO1F,downstream_gene_variant,,ENST00000598005,;	G	ENSG00000142347	ENST00000338257	Transcript	synonymous_variant	3223	2955	985	P	ccG/ccC	rs201007272	.	.	-1	MYO1F	HGNC	7600	protein_coding	YES	CCDS42494.1	ENSP00000344871	MYO1F_HUMAN	Q14779_HUMAN,M0QXU2_HUMAN	UPI00001678F0	.	.	.	26/28	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGACGGAGG	byCluster	5	ESCA
MUC16	0	.	GRCh37	19	9045688	9045688	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35943A>G	p.%3D	p.T11981T	ENST00000397910	5/84	121	108	12	131	131	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;	C	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	36147	35943	11981	T	acA/acG	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	5/84	.	hmmpanther:PTHR14672,hmmpanther:PTHR14672:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACCTGTGGT	.	4	ESCA
AMY2B	0	.	GRCh37	1	104114305	104114305	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81T>C	p.%3D	p.S27S	ENST00000361355	3/12	162	85	77	192	192	0	AMY2B,synonymous_variant,p.%3D,ENST00000435302,;AMY2B,synonymous_variant,p.%3D,ENST00000361355,;AMY2B,synonymous_variant,p.%3D,ENST00000453959,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,synonymous_variant,p.%3D,ENST00000477657,;ACTG1P4,downstream_gene_variant,,ENST00000425123,;	C	ENSG00000240038	ENST00000361355	Transcript	synonymous_variant	697	81	27	S	tcT/tcC	.	.	.	1	AMY2B	HGNC	478	protein_coding	YES	CCDS782.1	ENSP00000354610	AMY2B_HUMAN	C9JWK7_HUMAN,C9J2Z5_HUMAN	UPI0000000CB1	.	.	.	3/12	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Gene3D:3.20.20.80,SMART_domains:SM00642,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATCTATTGT	.	5	ESCA
SLC16A1	0	.	GRCh37	1	113460201	113460201	+	Missense_Mutation	SNP	C	C	T	rs774651624	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827G>A	p.Gly276Glu	p.G276E	ENST00000538576	4/5	56	31	24	53	53	0	SLC16A1,missense_variant,p.Gly276Glu,ENST00000369626,;SLC16A1,missense_variant,p.Gly276Glu,ENST00000433570,;SLC16A1,missense_variant,p.Gly276Glu,ENST00000458229,;SLC16A1,missense_variant,p.Gly276Glu,ENST00000443580,;SLC16A1,missense_variant,p.Gly276Glu,ENST00000538576,;SLC16A1,downstream_gene_variant,,ENST00000429288,;SLC16A1,downstream_gene_variant,,ENST00000481750,;	T	ENSG00000155380	ENST00000538576	Transcript	missense_variant	1659	827	276	G/E	gGa/gAa	rs774651624	.	.	-1	SLC16A1	HGNC	10922	protein_coding	YES	CCDS858.1	ENSP00000441065	MOT1_HUMAN	Q5T8R5_HUMAN,Q5T8R4_HUMAN,Q5T8R3_HUMAN	UPI00000012F5	.	deleterious(0)	probably_damaging(0.982)	4/5	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11360:SF24,hmmpanther:PTHR11360,Pfam_domain:PF07690,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00892,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGTCCAAAA	.	5	ESCA
SYT6	0	.	GRCh37	1	114633461	114633462	+	3'UTR	INS	-	-	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1294dupA	.	.	ENST00000609117	8/8	52	46	6	45	45	0	SYT6,3_prime_UTR_variant,,ENST00000393296,;SYT6,3_prime_UTR_variant,,ENST00000609117,;SYT6,3_prime_UTR_variant,,ENST00000607941,;SYT6,3_prime_UTR_variant,,ENST00000369547,;SYT6,downstream_gene_variant,,ENST00000610222,;SYT6,3_prime_UTR_variant,,ENST00000610121,;SYT6,downstream_gene_variant,,ENST00000610096,;	T	ENSG00000134207	ENST00000609117	Transcript	3_prime_UTR_variant	2876-2877	.	.	.	.	.	.	.	-1	SYT6	HGNC	18638	protein_coding	YES	CCDS871.1	ENSP00000477344	.	I6L9C3_HUMAN,B1AMB7_HUMAN,B1AMB6_HUMAN	UPI000000DACA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAACAATTTTT	.	2	ESCA
PLOD1	0	.	GRCh37	1	12017059	12017059	+	Silent	SNP	C	C	T	rs567164584	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729C>T	p.%3D	p.N243N	ENST00000196061	7/19	63	43	20	70	69	1	PLOD1,synonymous_variant,p.%3D,ENST00000376369,;PLOD1,synonymous_variant,p.%3D,ENST00000196061,;PLOD1,intron_variant,,ENST00000429000,;PLOD1,downstream_gene_variant,,ENST00000449038,;PLOD1,non_coding_transcript_exon_variant,,ENST00000485046,;PLOD1,downstream_gene_variant,,ENST00000358133,;PLOD1,non_coding_transcript_exon_variant,,ENST00000465920,;	T	ENSG00000083444	ENST00000196061	Transcript	synonymous_variant	756	729	243	N	aaC/aaT	rs567164584	.	.	1	PLOD1	HGNC	9081	protein_coding	YES	CCDS142.1	ENSP00000196061	PLOD1_HUMAN	Q9UL44_HUMAN	UPI000013C611	.	.	.	7/19	.	hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF5	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAACGGGCC	by1000G	5	ESCA
MEX3A	0	.	GRCh37	1	156044300	156044300	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2065A>C	.	.	ENST00000532414	2/2	37	26	11	61	61	0	MEX3A,3_prime_UTR_variant,,ENST00000532414,;RAB25,downstream_gene_variant,,ENST00000361084,;AL355388.1,upstream_gene_variant,,ENST00000410679,;RAB25,downstream_gene_variant,,ENST00000473336,;MEX3A,downstream_gene_variant,,ENST00000442784,;RAB25,downstream_gene_variant,,ENST00000497968,;RAB25,downstream_gene_variant,,ENST00000487325,;	G	ENSG00000254726	ENST00000532414	Transcript	3_prime_UTR_variant	3628	.	.	.	.	.	.	.	-1	MEX3A	HGNC	33482	protein_coding	YES	CCDS53377.1	ENSP00000432845	MEX3A_HUMAN	.	UPI0000ECD9C5	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTATTCGTG	.	5	ESCA
CD1B	0	.	GRCh37	1	158299306	158299306	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740G>A	p.Gly247Asp	p.G247D	ENST00000368168	4/6	102	75	27	89	89	0	CD1B,missense_variant,p.Gly247Asp,ENST00000368168,;CD1B,intron_variant,,ENST00000451207,;	T	ENSG00000158485	ENST00000368168	Transcript	missense_variant	848	740	247	G/D	gGc/gAc	.	.	.	-1	CD1B	HGNC	1635	protein_coding	YES	CCDS1176.1	ENSP00000357150	CD1B_HUMAN	Q9UN97_HUMAN,B4E0D3_HUMAN	UPI0000127333	.	tolerated(0.11)	possibly_damaging(0.641)	4/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR16675:SF130,hmmpanther:PTHR16675,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTGCCCTGC	.	5	ESCA
IFI16	0	.	GRCh37	1	158988029	158988035	+	Frame_Shift_Del	DEL	CAGTGGC	CAGTGGC	-	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	CAGTGGC	CAGTGGC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562_568delGTGGCCA	p.Val188AsnfsTer4	p.V188Nfs*4	ENST00000368131	5/11	102	90	12	92	92	0	IFI16,frameshift_variant,p.Val30AsnfsTer4,ENST00000567661,;IFI16,frameshift_variant,p.Val188AsnfsTer4,ENST00000295809,;IFI16,frameshift_variant,p.Val188AsnfsTer4,ENST00000340979,;IFI16,frameshift_variant,p.Val136AsnfsTer4,ENST00000430894,;IFI16,frameshift_variant,p.Val188AsnfsTer4,ENST00000368132,;IFI16,frameshift_variant,p.Val188AsnfsTer4,ENST00000368131,;IFI16,frameshift_variant,p.Val30AsnfsTer4,ENST00000474473,;IFI16,frameshift_variant,p.Val188AsnfsTer4,ENST00000448393,;IFI16,frameshift_variant,p.Val132AsnfsTer4,ENST00000359709,;IFI16,downstream_gene_variant,,ENST00000566111,;IFI16,downstream_gene_variant,,ENST00000426592,;IFI16,downstream_gene_variant,,ENST00000447473,;IFI16,non_coding_transcript_exon_variant,,ENST00000493884,;IFI16,non_coding_transcript_exon_variant,,ENST00000483916,;	-	ENSG00000163565	ENST00000368131	Transcript	frameshift_variant	850-856	560-566	187-189	TVA/X	aCAGTGGCc/ac	.	.	.	1	IFI16	HGNC	5395	protein_coding	YES	CCDS1180.3	ENSP00000357113	IF16_HUMAN	H3BVE6_HUMAN,H3BR88_HUMAN,H3BR65_HUMAN,H3BM18_HUMAN	UPI00001412C9	.	.	.	5/11	.	PROSITE_profiles:PS50834,hmmpanther:PTHR12200:SF5,hmmpanther:PTHR12200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGAAAACAGTGGCCAAAT	.	3	ESCA
PLEKHM2	0	.	GRCh37	1	16059221	16059221	+	Missense_Mutation	SNP	C	C	G	rs756525436	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2920C>G	p.Gln974Glu	p.Q974E	ENST00000375799	19/20	45	33	12	53	53	0	PLEKHM2,missense_variant,p.Gln954Glu,ENST00000375793,;PLEKHM2,missense_variant,p.Gln974Glu,ENST00000375799,;SLC25A34,upstream_gene_variant,,ENST00000294454,;RP11-288I21.1,intron_variant,,ENST00000453804,;PLEKHM2,splice_region_variant,,ENST00000477849,;	G	ENSG00000116786	ENST00000375799	Transcript	missense_variant	3147	2920	974	Q/E	Cag/Gag	rs756525436	.	.	1	PLEKHM2	HGNC	29131	protein_coding	YES	CCDS44063.1	ENSP00000364956	PKHM2_HUMAN	.	UPI00001C1D9C	.	deleterious(0)	probably_damaging(0.995)	19/20	.	hmmpanther:PTHR22835:SF132,hmmpanther:PTHR22835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTATCAGGTA	.	5	ESCA
B4GALT3	0	.	GRCh37	1	161143503	161143503	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.695A>G	p.Gln232Arg	p.Q232R	ENST00000319769	6/8	105	75	29	113	113	0	B4GALT3,missense_variant,p.Gln232Arg,ENST00000319769,;B4GALT3,missense_variant,p.Gln232Arg,ENST00000367998,;PPOX,intron_variant,,ENST00000432542,;PPOX,intron_variant,,ENST00000535223,;PPOX,downstream_gene_variant,,ENST00000367999,;PPOX,downstream_gene_variant,,ENST00000352210,;PPOX,downstream_gene_variant,,ENST00000537523,;PPOX,downstream_gene_variant,,ENST00000544598,;PPOX,downstream_gene_variant,,ENST00000537829,;B4GALT3,non_coding_transcript_exon_variant,,ENST00000470882,;B4GALT3,non_coding_transcript_exon_variant,,ENST00000466504,;PPOX,intron_variant,,ENST00000497522,;PPOX,intron_variant,,ENST00000495483,;B4GALT3,downstream_gene_variant,,ENST00000496313,;B4GALT3,downstream_gene_variant,,ENST00000482288,;B4GALT3,downstream_gene_variant,,ENST00000465740,;B4GALT3,downstream_gene_variant,,ENST00000460415,;B4GALT3,downstream_gene_variant,,ENST00000493164,;PPOX,downstream_gene_variant,,ENST00000462977,;PPOX,downstream_gene_variant,,ENST00000470607,;B4GALT3,downstream_gene_variant,,ENST00000467863,;PPOX,downstream_gene_variant,,ENST00000494216,;B4GALT3,downstream_gene_variant,,ENST00000487004,;B4GALT3,upstream_gene_variant,,ENST00000486938,;PPOX,downstream_gene_variant,,ENST00000460611,;PPOX,downstream_gene_variant,,ENST00000466452,;PPOX,downstream_gene_variant,,ENST00000462866,;PPOX,downstream_gene_variant,,ENST00000539753,;PPOX,downstream_gene_variant,,ENST00000541818,;	C	ENSG00000158850	ENST00000319769	Transcript	missense_variant	918	695	232	Q/R	cAg/cGg	.	.	.	-1	B4GALT3	HGNC	926	protein_coding	YES	CCDS1222.1	ENSP00000320965	B4GT3_HUMAN	.	UPI0000070AD6	.	tolerated(0.12)	benign(0.063)	6/8	.	hmmpanther:PTHR19300:SF33,hmmpanther:PTHR19300,Gene3D:3.90.550.10,Pfam_domain:PF02709,Superfamily_domains:SSF53448,Prints_domain:PR02050	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTACTGGGGG	.	5	ESCA
EPHA2	0	.	GRCh37	1	16456798	16456798	+	Missense_Mutation	SNP	G	G	T	rs572281924	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2592C>A	p.Phe864Leu	p.F864L	ENST00000358432	15/17	50	43	7	78	78	0	EPHA2,missense_variant,p.Phe864Leu,ENST00000358432,;EPHA2,downstream_gene_variant,,ENST00000480202,;EPHA2,downstream_gene_variant,,ENST00000462805,;	T	ENSG00000142627	ENST00000358432	Transcript	missense_variant	2747	2592	864	F/L	ttC/ttA	rs572281924	.	.	-1	EPHA2	HGNC	3386	protein_coding	YES	CCDS169.1	ENSP00000351209	EPHA2_HUMAN	Q96HF4_HUMAN,Q8IZL0_HUMAN	UPI00000731AB	.	deleterious(0.01)	benign(0.144)	15/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF306,hmmpanther:PTHR24416,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF56112,Prints_domain:PR00109	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R861C|c.2581C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TCAGCGAACTT	by1000G	4	ESCA
PAPPA2	0	.	GRCh37	1	176734935	176734935	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4285C>T	p.Leu1429Phe	p.L1429F	ENST00000367662	15/23	47	43	3	59	59	0	PAPPA2,missense_variant,p.Leu1429Phe,ENST00000367662,;	T	ENSG00000116183	ENST00000367662	Transcript	missense_variant	5449	4285	1429	L/F	Ctt/Ttt	.	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	deleterious(0)	probably_damaging(0.992)	15/23	.	hmmpanther:PTHR19325:SF349,hmmpanther:PTHR19325,SMART_domains:SM00032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGCCCTTCAG	.	2	ESCA
DHX9	0	.	GRCh37	1	182850531	182850531	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2757A>G	p.%3D	p.L919L	ENST00000367549	23/28	57	40	16	41	41	0	DHX9,synonymous_variant,p.%3D,ENST00000367549,;DHX9,non_coding_transcript_exon_variant,,ENST00000473076,;DHX9,non_coding_transcript_exon_variant,,ENST00000485081,;DHX9,non_coding_transcript_exon_variant,,ENST00000474446,;DHX9,downstream_gene_variant,,ENST00000490519,;	G	ENSG00000135829	ENST00000367549	Transcript	synonymous_variant	2867	2757	919	L	ttA/ttG	.	.	.	1	DHX9	HGNC	2750	protein_coding	YES	CCDS41444.1	ENSP00000356520	DHX9_HUMAN	.	UPI00001AEF15	.	.	.	23/28	.	hmmpanther:PTHR18934:SF84,hmmpanther:PTHR18934,Pfam_domain:PF04408,SMART_domains:SM00847,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTATCAGT	.	5	ESCA
TNNT2	0	.	GRCh37	1	201336929	201336929	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.139G>A	p.Glu47Lys	p.E47K	ENST00000509001	6/16	104	91	13	66	66	0	TNNT2,missense_variant,p.Glu47Lys,ENST00000367318,;TNNT2,missense_variant,p.Glu59Lys,ENST00000458432,;TNNT2,missense_variant,p.Glu52Lys,ENST00000422165,;TNNT2,missense_variant,p.Glu47Lys,ENST00000367317,;TNNT2,missense_variant,p.Glu42Lys,ENST00000360372,;TNNT2,missense_variant,p.Glu47Lys,ENST00000367315,;TNNT2,missense_variant,p.Glu47Lys,ENST00000509001,;TNNT2,missense_variant,p.Glu47Lys,ENST00000367322,;TNNT2,missense_variant,p.Glu49Lys,ENST00000421663,;TNNT2,missense_variant,p.Glu42Lys,ENST00000438742,;TNNT2,missense_variant,p.Glu57Lys,ENST00000455702,;TNNT2,missense_variant,p.Glu46Lys,ENST00000412633,;TNNT2,missense_variant,p.Glu56Lys,ENST00000367320,;TNNT2,missense_variant,p.Glu52Lys,ENST00000236918,;TNNT2,splice_region_variant,,ENST00000475686,;TNNT2,splice_region_variant,,ENST00000466570,;TNNT2,upstream_gene_variant,,ENST00000460780,;TNNT2,upstream_gene_variant,,ENST00000476888,;TNNT2,upstream_gene_variant,,ENST00000479297,;TNNT2,non_coding_transcript_exon_variant,,ENST00000503459,;TNNT2,non_coding_transcript_exon_variant,,ENST00000491504,;TNNT2,non_coding_transcript_exon_variant,,ENST00000472177,;TNNT2,non_coding_transcript_exon_variant,,ENST00000445079,;TNNT2,non_coding_transcript_exon_variant,,ENST00000494095,;TNNT2,upstream_gene_variant,,ENST00000515042,;	T	ENSG00000118194	ENST00000509001	Transcript	missense_variant	426	139	47	E/K	Gaa/Aaa	.	.	.	-1	TNNT2	HGNC	11949	protein_coding	YES	CCDS30969.1	ENSP00000422031	TNNT2_HUMAN	Q8IZA1_HUMAN,Q15608_HUMAN,A9QLG2_HUMAN,A9QLG1_HUMAN	UPI000014A55F	.	tolerated(0.74)	unknown(0)	6/16	.	hmmpanther:PTHR11521:SF5,hmmpanther:PTHR11521,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTTCATCTT	.	4	ESCA
FCAMR	0	.	GRCh37	1	207139152	207139152	+	Missense_Mutation	SNP	T	T	C	rs767535460	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221A>G	p.Glu74Gly	p.E74G	ENST00000324852	4/8	90	28	61	102	102	0	FCAMR,missense_variant,p.Glu74Gly,ENST00000324852,;FCAMR,missense_variant,p.Glu74Gly,ENST00000450945,;FCAMR,missense_variant,p.Glu74Gly,ENST00000400962,;FCAMR,non_coding_transcript_exon_variant,,ENST00000487149,;FCAMR,non_coding_transcript_exon_variant,,ENST00000488345,;FCAMR,upstream_gene_variant,,ENST00000486178,;FCAMR,3_prime_UTR_variant,,ENST00000324863,;	C	ENSG00000162897	ENST00000324852	Transcript	missense_variant	696	221	74	E/G	gAg/gGg	rs767535460	.	.	-1	FCAMR	HGNC	24692	protein_coding	YES	CCDS53468.1	ENSP00000316491	.	.	UPI0000EE5E27	.	tolerated(0.32)	benign(0.037)	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCTCCCAC	.	5	ESCA
PLXNA2	0	.	GRCh37	1	208315682	208315682	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498G>A	p.Glu500Lys	p.E500K	ENST00000367033	4/32	59	33	26	81	81	0	PLXNA2,missense_variant,p.Glu500Lys,ENST00000367033,;	T	ENSG00000076356	ENST00000367033	Transcript	missense_variant	2256	1498	500	E/K	Gag/Aag	.	.	.	-1	PLXNA2	HGNC	9100	protein_coding	YES	CCDS31013.1	ENSP00000356000	PLXA2_HUMAN	.	UPI000022B239	.	deleterious(0.03)	benign(0.03)	4/32	.	PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625,Gene3D:2.130.10.10,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCAGACA	.	5	ESCA
FAM43B	0	.	GRCh37	1	20879570	20879570	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.104G>C	p.Ser35Thr	p.S35T	ENST00000332947	1/1	24	14	9	42	42	0	FAM43B,missense_variant,p.Ser35Thr,ENST00000332947,;	C	ENSG00000183114	ENST00000332947	Transcript	missense_variant	639	104	35	S/T	aGc/aCc	.	.	.	1	FAM43B	HGNC	31791	protein_coding	YES	CCDS209.1	ENSP00000331397	FA43B_HUMAN	.	UPI00001C0D42	.	tolerated(0.18)	benign(0.011)	1/1	.	hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTCCAGCTTCC	.	4	ESCA
SPATA17	0	.	GRCh37	1	217842377	217842377	+	Silent	SNP	A	A	T	rs747713714	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.243A>T	p.%3D	p.V81V	ENST00000366933	4/11	70	61	9	40	40	0	SPATA17,synonymous_variant,p.%3D,ENST00000366933,;SPATA17,splice_region_variant,,ENST00000470448,;	T	ENSG00000162814	ENST00000366933	Transcript	synonymous_variant	298	243	81	V	gtA/gtT	rs747713714	.	.	1	SPATA17	HGNC	25184	protein_coding	YES	CCDS1519.1	ENSP00000355900	SPT17_HUMAN	R4GN71_HUMAN	UPI00000717C2	.	.	.	4/11	.	Superfamily_domains:SSF52540,hmmpanther:PTHR22706	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGTAGCATA	byFrequency	4	ESCA
ZNF678	0	.	GRCh37	1	227843492	227843492	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1541A>C	p.Glu514Ala	p.E514A	ENST00000343776	4/4	103	80	22	91	91	0	ZNF678,missense_variant,p.Glu569Ala,ENST00000397097,;ZNF678,missense_variant,p.Glu514Ala,ENST00000343776,;ZNF678,intron_variant,,ENST00000608949,;ZNF678,downstream_gene_variant,,ENST00000440339,;ZNF678,downstream_gene_variant,,ENST00000465266,;	C	ENSG00000181450	ENST00000343776	Transcript	missense_variant	1886	1541	514	E/A	gAg/gCg	.	.	.	1	ZNF678	HGNC	28652	protein_coding	YES	.	ENSP00000344828	ZN678_HUMAN	.	UPI000019862A	.	deleterious(0)	benign(0.286)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409,Gene3D:3.30.160.60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGAGGAAC	.	5	ESCA
KIF26B	0	.	GRCh37	1	245849500	245849500	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3215G>T	p.Ser1072Ile	p.S1072I	ENST00000407071	12/15	21	9	12	12	12	0	KIF26B,missense_variant,p.Ser1072Ile,ENST00000407071,;KIF26B,missense_variant,p.Ser691Ile,ENST00000366518,;KIF26B,non_coding_transcript_exon_variant,,ENST00000483253,;	T	ENSG00000162849	ENST00000407071	Transcript	missense_variant	3655	3215	1072	S/I	aGc/aTc	.	.	.	1	KIF26B	HGNC	25484	protein_coding	YES	CCDS44342.1	ENSP00000385545	KI26B_HUMAN	B4DF75_HUMAN	UPI0000695D71	.	deleterious(0)	unknown(0)	12/15	.	hmmpanther:PTHR24115:SF363,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCAGCCTGT	.	5	ESCA
SERINC2	0	.	GRCh37	1	31901872	31901872	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855C>G	p.%3D	p.L285L	ENST00000373710	8/11	60	44	16	68	68	0	SERINC2,synonymous_variant,p.%3D,ENST00000536384,;SERINC2,synonymous_variant,p.%3D,ENST00000373710,;SERINC2,synonymous_variant,p.%3D,ENST00000536859,;SERINC2,synonymous_variant,p.%3D,ENST00000373709,;AC114494.1,downstream_gene_variant,,ENST00000596131,;SERINC2,non_coding_transcript_exon_variant,,ENST00000491976,;SERINC2,downstream_gene_variant,,ENST00000487207,;	G	ENSG00000168528	ENST00000373710	Transcript	synonymous_variant	1128	855	285	L	ctC/ctG	.	.	.	1	SERINC2	HGNC	23231	protein_coding	YES	CCDS55583.1	ENSP00000362814	SERC2_HUMAN	.	UPI000059CF90	.	.	.	8/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10383:SF22,hmmpanther:PTHR10383,Pfam_domain:PF03348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCTACAC	.	5	ESCA
COL9A2	0	.	GRCh37	1	40782797	40782797	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73A>T	p.Ile25Phe	p.I25F	ENST00000372748	1/32	146	46	100	64	64	0	COL9A2,missense_variant,p.Ile25Phe,ENST00000372736,;COL9A2,missense_variant,p.Ile25Phe,ENST00000372748,;COL9A2,upstream_gene_variant,,ENST00000417105,;COL9A2,splice_region_variant,,ENST00000495948,;COL9A2,upstream_gene_variant,,ENST00000490132,;COL9A2,splice_region_variant,,ENST00000461118,;COL9A2,intron_variant,,ENST00000482722,;COL9A2,upstream_gene_variant,,ENST00000488463,;COL9A2,upstream_gene_variant,,ENST00000496215,;	A	ENSG00000049089	ENST00000372748	Transcript	missense_variant	170	73	25	I/F	Att/Ttt	.	.	.	-1	COL9A2	HGNC	2218	protein_coding	YES	CCDS450.1	ENSP00000361834	CO9A2_HUMAN	D3DPU8_HUMAN	UPI0000126D47	.	tolerated(0.14)	unknown(0)	1/32	.	hmmpanther:PTHR24021:SF18,hmmpanther:PTHR24021	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAATCTGCG	.	5	ESCA
EDN2	0	.	GRCh37	1	41945149	41945149	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.468delC	p.Phe157LeufsTer75	p.F157Lfs*75	ENST00000372587	5/5	131	118	12	76	76	0	EDN2,frameshift_variant,p.Phe157LeufsTer75,ENST00000372587,;EDN2,non_coding_transcript_exon_variant,,ENST00000490783,;EDN2,non_coding_transcript_exon_variant,,ENST00000467046,;EDN2,non_coding_transcript_exon_variant,,ENST00000460255,;EDN2,non_coding_transcript_exon_variant,,ENST00000467872,;	-	ENSG00000127129	ENST00000372587	Transcript	frameshift_variant	538	468	156	L/X	ctC/ct	.	.	.	-1	EDN2	HGNC	3177	protein_coding	YES	CCDS462.1	ENSP00000361668	EDN2_HUMAN	.	UPI0000040AF7	.	.	.	5/5	.	hmmpanther:PTHR13874:SF8,hmmpanther:PTHR13874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGCAAAGAGGCT	.	2	ESCA
NRD1	0	.	GRCh37	1	52303157	52303157	+	Splice_Site	SNP	A	A	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.764+2T>A	.	p.X255_splice	ENST00000354831	.	70	49	20	55	55	0	NRD1,splice_donor_variant,,ENST00000354831,;NRD1,splice_donor_variant,,ENST00000539524,;NRD1,intron_variant,,ENST00000352171,;NRD1,intron_variant,,ENST00000544028,;MIR761,upstream_gene_variant,,ENST00000390787,;NRD1,non_coding_transcript_exon_variant,,ENST00000475715,;NRD1,intron_variant,,ENST00000485608,;NRD1,downstream_gene_variant,,ENST00000491410,;NRD1,upstream_gene_variant,,ENST00000473805,;	T	ENSG00000078618	ENST00000354831	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	NRD1	HGNC	7995	protein_coding	YES	CCDS559.1	ENSP00000346890	.	G3V1R5_HUMAN,B1AKJ5_HUMAN	UPI0000458A53	.	.	.	.	3/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTAACCTGC	.	5	ESCA
PODN	0	.	GRCh37	1	53542922	53542922	+	Missense_Mutation	SNP	C	C	G	rs769502354	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.786C>G	p.Asn262Lys	p.N262K	ENST00000312553	6/11	50	28	22	37	37	0	PODN,missense_variant,p.Asn262Lys,ENST00000312553,;PODN,missense_variant,p.Asn243Lys,ENST00000371500,;PODN,intron_variant,,ENST00000395871,;RP11-334A14.5,intron_variant,,ENST00000447867,;PODN,upstream_gene_variant,,ENST00000490650,;PODN,upstream_gene_variant,,ENST00000471285,;PODN,downstream_gene_variant,,ENST00000471210,;HIGD1AP11,upstream_gene_variant,,ENST00000438361,;	G	ENSG00000174348	ENST00000312553	Transcript	missense_variant	793	786	262	N/K	aaC/aaG	rs769502354,COSM910741	.	.	1	PODN	HGNC	23174	protein_coding	YES	CCDS573.1	ENSP00000308315	PODN_HUMAN	.	UPI000034ECE9	.	tolerated(0.28)	probably_damaging(0.979)	6/11	.	hmmpanther:PTHR24369:SF12,hmmpanther:PTHR24369,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAACGGCTC	byFrequency	5	ESCA
TNFRSF25	0	.	GRCh37	1	6521428	6521428	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*66A>C	.	.	ENST00000377782	10/10	16	12	4	24	24	0	TNFRSF25,3_prime_UTR_variant,,ENST00000356876,;TNFRSF25,3_prime_UTR_variant,,ENST00000351959,;ESPN,3_prime_UTR_variant,,ENST00000434576,;TNFRSF25,3_prime_UTR_variant,,ENST00000377782,;PLEKHG5,downstream_gene_variant,,ENST00000400913,;ESPN,downstream_gene_variant,,ENST00000416731,;TNFRSF25,downstream_gene_variant,,ENST00000348333,;TNFRSF25,downstream_gene_variant,,ENST00000481401,;PLEKHG5,downstream_gene_variant,,ENST00000340850,;ESPN,downstream_gene_variant,,ENST00000377828,;PLEKHG5,downstream_gene_variant,,ENST00000377748,;ESPN,downstream_gene_variant,,ENST00000461727,;TNFRSF25,downstream_gene_variant,,ENST00000351748,;ESPN,non_coding_transcript_exon_variant,,ENST00000468561,;ESPN,downstream_gene_variant,,ENST00000475228,;TNFRSF25,downstream_gene_variant,,ENST00000461703,;TNFRSF25,downstream_gene_variant,,ENST00000475730,;TNFRSF25,3_prime_UTR_variant,,ENST00000485036,;TNFRSF25,3_prime_UTR_variant,,ENST00000480393,;TNFRSF25,non_coding_transcript_exon_variant,,ENST00000513135,;TNFRSF25,non_coding_transcript_exon_variant,,ENST00000473343,;TNFRSF25,downstream_gene_variant,,ENST00000515145,;TNFRSF25,downstream_gene_variant,,ENST00000453260,;TNFRSF25,downstream_gene_variant,,ENST00000414040,;PLEKHG5,downstream_gene_variant,,ENST00000489097,;TNFRSF25,downstream_gene_variant,,ENST00000453341,;TNFRSF25,downstream_gene_variant,,ENST00000469691,;TNFRSF25,downstream_gene_variant,,ENST00000510563,;ESPN,downstream_gene_variant,,ENST00000477679,;TNFRSF25,downstream_gene_variant,,ENST00000502588,;TNFRSF25,downstream_gene_variant,,ENST00000502730,;	G	ENSG00000215788	ENST00000377782	Transcript	3_prime_UTR_variant	1415	.	.	.	.	.	.	.	-1	TNFRSF25	HGNC	11910	protein_coding	YES	CCDS72.1	ENSP00000367013	TNR25_HUMAN	B3KSV7_HUMAN	UPI000002B5CB	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGCATAAGTA	.	2	ESCA
NOC2L	0	.	GRCh37	1	880079	880079	+	Missense_Mutation	SNP	C	C	T	rs747335515	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2245G>A	p.Asp749Asn	p.D749N	ENST00000327044	19/19	20	16	4	28	28	0	NOC2L,missense_variant,p.Asp749Asn,ENST00000327044,;SAMD11,downstream_gene_variant,,ENST00000342066,;SAMD11,downstream_gene_variant,,ENST00000455979,;SAMD11,downstream_gene_variant,,ENST00000341065,;NOC2L,downstream_gene_variant,,ENST00000496938,;SAMD11,downstream_gene_variant,,ENST00000478729,;NOC2L,non_coding_transcript_exon_variant,,ENST00000483767,;NOC2L,non_coding_transcript_exon_variant,,ENST00000477976,;SAMD11,downstream_gene_variant,,ENST00000464948,;SAMD11,downstream_gene_variant,,ENST00000466827,;SAMD11,downstream_gene_variant,,ENST00000474461,;	T	ENSG00000188976	ENST00000327044	Transcript	missense_variant	2295	2245	749	D/N	Gac/Aac	rs747335515	.	.	-1	NOC2L	HGNC	24517	protein_coding	YES	CCDS3.1	ENSP00000317992	NOC2L_HUMAN	.	UPI000041820C	.	deleterious_low_confidence(0)	possibly_damaging(0.555)	19/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12687:SF4,hmmpanther:PTHR12687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAGTCGTCCT	.	4	ESCA
GBP1P1	0	.	GRCh37	1	89886764	89886764	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.428+15C>T	.	.	ENST00000394662	.	131	106	25	122	122	0	GBP1P1,non_coding_transcript_exon_variant,,ENST00000513638,;GBP1P1,intron_variant,,ENST00000394662,;	T	ENSG00000225492	ENST00000394662	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GBP1P1	HGNC	39561	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	3/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTGACCCAGAA	.	3	ESCA
CBFA2T2	0	.	GRCh37	20	32212784	32212784	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934C>G	p.Leu312Val	p.L312V	ENST00000346541	7/12	106	101	5	69	69	0	CBFA2T2,missense_variant,p.Leu312Val,ENST00000375279,;CBFA2T2,missense_variant,p.Leu312Val,ENST00000346541,;CBFA2T2,missense_variant,p.Leu303Val,ENST00000342704,;CBFA2T2,missense_variant,p.Leu283Val,ENST00000492345,;CBFA2T2,missense_variant,p.Leu283Val,ENST00000397800,;CBFA2T2,missense_variant,p.Leu322Val,ENST00000359606,;CBFA2T2,downstream_gene_variant,,ENST00000397798,;CBFA2T2,downstream_gene_variant,,ENST00000344201,;CBFA2T2,non_coding_transcript_exon_variant,,ENST00000491618,;	G	ENSG00000078699	ENST00000346541	Transcript	missense_variant	1471	934	312	L/V	Cta/Gta	.	.	.	1	CBFA2T2	HGNC	1536	protein_coding	YES	CCDS13221.1	ENSP00000262653	MTG8R_HUMAN	Q68DC6_HUMAN,D1LYX4_HUMAN,B4DFM9_HUMAN,A2A2D9_HUMAN	UPI0000073E07	.	tolerated(0.53)	benign(0.045)	7/12	.	Prints_domain:PR01877,hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATGCTAGAG	.	2	ESCA
DIDO1	0	.	GRCh37	20	61513761	61513761	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3547G>C	p.Glu1183Gln	p.E1183Q	ENST00000266070	16/16	73	41	32	62	62	0	DIDO1,missense_variant,p.Glu1183Gln,ENST00000266070,;DIDO1,missense_variant,p.Glu1183Gln,ENST00000395343,;DIDO1,downstream_gene_variant,,ENST00000395335,;DIDO1,downstream_gene_variant,,ENST00000395340,;	G	ENSG00000101191	ENST00000266070	Transcript	missense_variant	3873	3547	1183	E/Q	Gag/Cag	.	.	.	-1	DIDO1	HGNC	2680	protein_coding	YES	CCDS33506.1	ENSP00000266070	DIDO1_HUMAN	.	UPI0000206380	.	.	probably_damaging(0.939)	16/16	.	hmmpanther:PTHR14914:SF7,hmmpanther:PTHR14914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTCAAGAC	.	5	ESCA
SLC17A9	0	.	GRCh37	20	61594982	61594982	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772C>T	p.Leu258Phe	p.L258F	ENST00000370351	7/13	33	18	15	35	35	0	SLC17A9,missense_variant,p.Leu258Phe,ENST00000370351,;SLC17A9,missense_variant,p.Leu252Phe,ENST00000370349,;SLC17A9,non_coding_transcript_exon_variant,,ENST00000488738,;SLC17A9,non_coding_transcript_exon_variant,,ENST00000487303,;SLC17A9,non_coding_transcript_exon_variant,,ENST00000459704,;SLC17A9,upstream_gene_variant,,ENST00000483113,;	T	ENSG00000101194	ENST00000370351	Transcript	missense_variant	903	772	258	L/F	Ctc/Ttc	.	.	.	1	SLC17A9	HGNC	16192	protein_coding	YES	CCDS42901.1	ENSP00000359376	S17A9_HUMAN	.	UPI000014051D	.	tolerated(0.05)	possibly_damaging(0.768)	7/13	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,Pfam_domain:PF07690,Gene3D:1.20.1250.20,hmmpanther:PTHR11662:SF183,hmmpanther:PTHR11662,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATCCTCCTC	.	5	ESCA
BAGE2	0	.	GRCh37	21	11039097	11039097	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1107G>T	.	.	ENST00000470054	6/10	178	171	7	175	175	0	BAGE2,non_coding_transcript_exon_variant,,ENST00000470054,;BAGE2,non_coding_transcript_exon_variant,,ENST00000496773,;	A	ENSG00000187172	ENST00000470054	Transcript	non_coding_transcript_exon_variant	1107	.	.	.	.	.	.	.	-1	BAGE2	HGNC	15723	processed_transcript	YES	.	.	.	.	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTCCTTGTA	.	2	ESCA
BACH1	0	.	GRCh37	21	30693632	30693632	+	Missense_Mutation	SNP	T	T	C	rs763385315	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31T>C	p.Tyr11His	p.Y11H	ENST00000399921	2/5	31	23	8	36	36	0	BACH1,missense_variant,p.Tyr11His,ENST00000548467,;BACH1,missense_variant,p.Tyr11His,ENST00000286800,;BACH1,missense_variant,p.Tyr11His,ENST00000548219,;BACH1,missense_variant,p.Tyr11His,ENST00000399921,;BACH1,missense_variant,p.Tyr11His,ENST00000546469,;BACH1,missense_variant,p.Tyr11His,ENST00000550131,;BACH1,missense_variant,p.Tyr11His,ENST00000447177,;BACH1,missense_variant,p.Tyr11His,ENST00000547141,;BACH1,missense_variant,p.Tyr11His,ENST00000451655,;BACH1,missense_variant,p.Tyr11His,ENST00000435072,;	C	ENSG00000156273	ENST00000399921	Transcript	missense_variant	274	31	11	Y/H	Tat/Cat	rs763385315	.	.	1	BACH1	HGNC	935	protein_coding	YES	CCDS13585.1	ENSP00000382805	BACH1_HUMAN	Q6ICU0_HUMAN,F8VZL7_HUMAN,C9JMP6_HUMAN,C9IYR0_HUMAN,C9IYH8_HUMAN	UPI000012673F	.	deleterious(0)	probably_damaging(0.993)	2/5	.	Superfamily_domains:SSF54695,Gene3D:3.30.710.10,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCTATGAA	.	5	ESCA
KRTAP10-6	0	.	GRCh37	21	46011332	46011332	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1034G>T	p.Cys345Phe	p.C345F	ENST00000400368	1/1	93	52	41	71	71	0	KRTAP10-6,missense_variant,p.Cys345Phe,ENST00000400368,;TSPEAR,intron_variant,,ENST00000323084,;	A	ENSG00000188155	ENST00000400368	Transcript	missense_variant	1055	1034	345	C/F	tGc/tTc	COSM189121	.	.	-1	KRTAP10-6	HGNC	20523	protein_coding	YES	CCDS42959.1	ENSP00000383219	KR106_HUMAN	.	UPI0000E5A408	.	deleterious(0.01)	probably_damaging(0.997)	1/1	.	hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF18	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.M348V|c.1042A>G|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGGCAGAGG	.	5	ESCA
SLC7A4	0	.	GRCh37	22	21384088	21384088	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1535T>C	p.Leu512Pro	p.L512P	ENST00000382932	3/5	57	45	11	73	73	0	SLC7A4,missense_variant,p.Leu512Pro,ENST00000403586,;SLC7A4,missense_variant,p.Leu512Pro,ENST00000382932,;P2RX6,downstream_gene_variant,,ENST00000401443,;P2RX6,downstream_gene_variant,,ENST00000413302,;P2RX6,downstream_gene_variant,,ENST00000402329,;SLC7A4,downstream_gene_variant,,ENST00000426145,;P2RX6,downstream_gene_variant,,ENST00000336296,;P2RX6,downstream_gene_variant,,ENST00000443995,;MIR649,downstream_gene_variant,,ENST00000384843,;AC002472.11,upstream_gene_variant,,ENST00000450652,;P2RX6,downstream_gene_variant,,ENST00000442475,;P2RX6,downstream_gene_variant,,ENST00000487342,;P2RX6,downstream_gene_variant,,ENST00000432930,;P2RX6,downstream_gene_variant,,ENST00000422210,;	G	ENSG00000099960	ENST00000382932	Transcript	missense_variant	1603	1535	512	L/P	cTg/cCg	.	.	.	-1	SLC7A4	HGNC	11062	protein_coding	YES	CCDS33608.1	ENSP00000372390	CTR4_HUMAN	C9JM63_HUMAN	UPI0000169EC7	.	deleterious(0)	probably_damaging(0.986)	3/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11785:SF196,hmmpanther:PTHR11785,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCAGGATG	.	5	ESCA
EWSR1	0	.	GRCh37	22	29694864	29694864	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1574G>A	p.Gly525Glu	p.G525E	ENST00000414183	15/18	36	32	4	40	40	0	EWSR1,missense_variant,p.Gly519Glu,ENST00000406548,;EWSR1,missense_variant,p.Gly525Glu,ENST00000414183,;EWSR1,missense_variant,p.Gly447Glu,ENST00000332050,;EWSR1,missense_variant,p.Gly520Glu,ENST00000397938,;EWSR1,missense_variant,p.Gly464Glu,ENST00000332035,;EWSR1,missense_variant,p.Gly482Glu,ENST00000331029,;EWSR1,missense_variant,p.Gly176Glu,ENST00000360091,;EWSR1,non_coding_transcript_exon_variant,,ENST00000490315,;EWSR1,non_coding_transcript_exon_variant,,ENST00000483629,;EWSR1,non_coding_transcript_exon_variant,,ENST00000469669,;EWSR1,non_coding_transcript_exon_variant,,ENST00000479135,;	A	ENSG00000182944	ENST00000414183	Transcript	missense_variant	1595	1574	525	G/E	gGa/gAa	.	.	.	1	EWSR1	HGNC	3508	protein_coding	YES	CCDS13852.2	ENSP00000400142	EWS_HUMAN	.	UPI000006DE88	.	deleterious(0)	unknown(0)	15/18	.	PROSITE_profiles:PS50199,hmmpanther:PTHR23238:SF3,hmmpanther:PTHR23238,Gene3D:1n0zA00,Pfam_domain:PF00641,SMART_domains:SM00547,Superfamily_domains:SSF90209	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCTGGAGACT	.	4	ESCA
TXN2	0	.	GRCh37	22	36877656	36877656	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-46G>C	.	.	ENST00000216185	1/4	184	105	79	170	170	0	TXN2,5_prime_UTR_variant,,ENST00000416967,;TXN2,5_prime_UTR_variant,,ENST00000216185,;TXN2,upstream_gene_variant,,ENST00000403313,;TXN2,non_coding_transcript_exon_variant,,ENST00000487725,;TXN2,upstream_gene_variant,,ENST00000411915,;	G	ENSG00000100348	ENST00000216185	Transcript	5_prime_UTR_variant	422	.	.	.	.	.	.	.	-1	TXN2	HGNC	17772	protein_coding	YES	CCDS13928.1	ENSP00000216185	THIOM_HUMAN	M0QXH0_HUMAN,B4DX69_HUMAN	UPI0000001BCB	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTGCCTGTC	.	5	ESCA
PDXP	0	.	GRCh37	22	38061677	38061677	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.690C>T	p.%3D	p.P230P	ENST00000215904	2/2	56	31	24	68	68	0	SH3BP1,synonymous_variant,p.%3D,ENST00000599616,;PDXP,synonymous_variant,p.%3D,ENST00000403251,;PDXP,synonymous_variant,p.%3D,ENST00000215904,;RN7SL385P,downstream_gene_variant,,ENST00000468873,;SH3BP1,3_prime_UTR_variant,,ENST00000451997,;	T	ENSG00000241360	ENST00000215904	Transcript	synonymous_variant	746	690	230	P	ccC/ccT	.	.	.	1	PDXP	HGNC	30259	protein_coding	YES	CCDS13953.1	ENSP00000215904	PLPP_HUMAN	B1AHD3_HUMAN	UPI000006D362	.	.	.	2/2	.	hmmpanther:PTHR19288,hmmpanther:PTHR19288:SF32,TIGRFAM_domain:TIGR01452,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01460,Pfam_domain:PF13242,PIRSF_domain:PIRSF000915,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCCCGCACG	.	5	ESCA
MIEF1	0	.	GRCh37	22	39914049	39914049	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3721T>C	.	.	ENST00000325301	6/6	29	26	3	38	38	0	MIEF1,3_prime_UTR_variant,,ENST00000325301,;ATF4,upstream_gene_variant,,ENST00000337304,;MIEF1,downstream_gene_variant,,ENST00000402881,;MIEF1,downstream_gene_variant,,ENST00000404569,;ATF4,upstream_gene_variant,,ENST00000396680,;ATF4,upstream_gene_variant,,ENST00000404241,;MIEF1,downstream_gene_variant,,ENST00000428069,;MIEF1,downstream_gene_variant,,ENST00000433117,;	C	ENSG00000100335	ENST00000325301	Transcript	3_prime_UTR_variant	5537	.	.	.	.	.	.	.	1	MIEF1	HGNC	25979	protein_coding	YES	CCDS13995.1	ENSP00000327124	MID51_HUMAN	B0QY94_HUMAN	UPI000006FEB4	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTCCTTTTTC	.	2	ESCA
CACNA1I	0	.	GRCh37	22	40085211	40085211	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2801C>T	.	.	ENST00000402142	37/37	19	16	3	15	15	0	CACNA1I,3_prime_UTR_variant,,ENST00000402142,;CACNA1I,3_prime_UTR_variant,,ENST00000400164,;CACNA1I,3_prime_UTR_variant,,ENST00000336649,;CACNA1I,3_prime_UTR_variant,,ENST00000404898,;CACNA1I,downstream_gene_variant,,ENST00000401624,;CACNA1I,downstream_gene_variant,,ENST00000407673,;	T	ENSG00000100346	ENST00000402142	Transcript	3_prime_UTR_variant	9473	.	.	.	.	.	.	.	1	CACNA1I	HGNC	1396	protein_coding	YES	CCDS46710.1	ENSP00000385019	CAC1I_HUMAN	.	UPI000012727D	.	.	.	37/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GTGGGCAGGCA	.	3	ESCA
EP300	0	.	GRCh37	22	41566507	41566507	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4384C>T	p.Arg1462Ter	p.R1462*	ENST00000263253	27/31	76	61	15	97	96	1	EP300,stop_gained,p.Arg1462Ter,ENST00000263253,;RNU6-375P,downstream_gene_variant,,ENST00000517050,;RP1-85F18.6,intron_variant,,ENST00000415054,;RP1-85F18.5,downstream_gene_variant,,ENST00000420537,;	T	ENSG00000100393	ENST00000263253	Transcript	stop_gained	5603	4384	1462	R/*	Cga/Tga	.	.	.	1	EP300	HGNC	3373	protein_coding	YES	CCDS14010.1	ENSP00000263253	EP300_HUMAN	B5A250_HUMAN	UPI00001AE876	.	.	.	27/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF4,Pfam_domain:PF08214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAGCGACTG	.	5	ESCA
TCF20	0	.	GRCh37	22	42607581	42607581	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3731A>T	p.Asp1244Val	p.D1244V	ENST00000359486	1/5	45	22	22	48	48	0	TCF20,missense_variant,p.Asp1244Val,ENST00000335626,;TCF20,missense_variant,p.Asp1244Val,ENST00000359486,;TCF20,upstream_gene_variant,,ENST00000404876,;TCF20,downstream_gene_variant,,ENST00000515426,;	A	ENSG00000100207	ENST00000359486	Transcript	missense_variant	3868	3731	1244	D/V	gAt/gTt	.	.	.	-1	TCF20	HGNC	11631	protein_coding	YES	CCDS14033.1	ENSP00000352463	TCF20_HUMAN	I3L1M7_HUMAN	UPI00001A95D9	.	.	probably_damaging(0.98)	1/5	.	hmmpanther:PTHR14955,hmmpanther:PTHR14955:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGATCCTCC	.	5	ESCA
IL1F10	0	.	GRCh37	2	113831923	113831923	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50A>G	p.Gln17Arg	p.Q17R	ENST00000393197	2/4	43	27	15	47	47	0	IL1F10,missense_variant,p.Gln17Arg,ENST00000341010,;IL1F10,missense_variant,p.Gln17Arg,ENST00000393197,;IL1F10,intron_variant,,ENST00000337569,;IL1F10,upstream_gene_variant,,ENST00000496265,;	G	ENSG00000136697	ENST00000393197	Transcript	missense_variant	471	50	17	Q/R	cAg/cGg	.	.	.	1	IL1F10	HGNC	15552	protein_coding	YES	CCDS2112.1	ENSP00000376893	IL1FA_HUMAN	.	UPI000003C9C3	.	tolerated(0.08)	probably_damaging(0.986)	2/4	.	Prints_domain:PR01360,Superfamily_domains:SSF50353,SMART_domains:SM00125,Gene3D:2.80.10.50,hmmpanther:PTHR10078:SF8,hmmpanther:PTHR10078	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACCAGAAGG	.	5	ESCA
WASH2P	0	.	GRCh37	2	114354120	114354120	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1807C>T	.	.	ENST00000538033	4/7	36	30	6	28	28	0	WASH2P,non_coding_transcript_exon_variant,,ENST00000538033,;WASH2P,non_coding_transcript_exon_variant,,ENST00000326632,;WASH2P,non_coding_transcript_exon_variant,,ENST00000453662,;DDX11L2,downstream_gene_variant,,ENST00000437401,;DDX11L2,downstream_gene_variant,,ENST00000535848,;DDX11L2,downstream_gene_variant,,ENST00000457993,;	T	ENSG00000146556	ENST00000538033	Transcript	non_coding_transcript_exon_variant	1807	.	.	.	.	.	.	.	1	WASH2P	HGNC	33145	retained_intron	YES	.	.	.	.	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AACTGCCCACC	.	2	ESCA
MYO7B	0	.	GRCh37	2	128391782	128391782	+	Missense_Mutation	SNP	G	G	A	rs760243996	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5465G>A	p.Arg1822Gln	p.R1822Q	ENST00000428314	40/47	88	51	37	58	58	0	MYO7B,missense_variant,p.Arg1822Gln,ENST00000409816,;MYO7B,missense_variant,p.Arg1823Gln,ENST00000389524,;MYO7B,missense_variant,p.Arg1822Gln,ENST00000428314,;MYO7B,missense_variant,p.Arg675Gln,ENST00000409090,;LIMS2,downstream_gene_variant,,ENST00000409254,;LIMS2,downstream_gene_variant,,ENST00000410038,;LIMS2,downstream_gene_variant,,ENST00000409455,;LIMS2,downstream_gene_variant,,ENST00000355119,;LIMS2,downstream_gene_variant,,ENST00000409286,;LIMS2,downstream_gene_variant,,ENST00000426981,;LIMS2,downstream_gene_variant,,ENST00000410011,;LIMS2,downstream_gene_variant,,ENST00000324938,;LIMS2,downstream_gene_variant,,ENST00000545738,;LIMS2,downstream_gene_variant,,ENST00000409754,;LIMS2,downstream_gene_variant,,ENST00000409808,;LIMS2,downstream_gene_variant,,ENST00000494613,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;LIMS2,downstream_gene_variant,,ENST00000476932,;LIMS2,downstream_gene_variant,,ENST00000413578,;LIMS2,downstream_gene_variant,,ENST00000466410,;MYO7B,upstream_gene_variant,,ENST00000494959,;LIMS2,downstream_gene_variant,,ENST00000469300,;LIMS2,downstream_gene_variant,,ENST00000484252,;	A	ENSG00000169994	ENST00000428314	Transcript	missense_variant	5518	5465	1822	R/Q	cGg/cAg	rs760243996	.	.	1	MYO7B	HGNC	7607	protein_coding	YES	CCDS46405.1	ENSP00000415090	MYO7B_HUMAN	C9JC21_HUMAN,B9A063_HUMAN	UPI00006C04F0	.	tolerated(0.07)	benign(0.421)	40/47	.	PROSITE_profiles:PS50057,SMART_domains:SM00295,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGCGGGATG	byFrequency	5	ESCA
HS6ST1	0	.	GRCh37	2	129025972	129025972	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1000A>G	p.Ile334Val	p.I334V	ENST00000259241	2/2	106	68	38	75	75	0	HS6ST1,missense_variant,p.Ile334Val,ENST00000259241,;HS6ST1,intron_variant,,ENST00000469019,;HS6ST1,downstream_gene_variant,,ENST00000463963,;	C	ENSG00000136720	ENST00000259241	Transcript	missense_variant	1014	1000	334	I/V	Atc/Gtc	.	.	.	-1	HS6ST1	HGNC	5201	protein_coding	YES	CCDS42748.1	ENSP00000259241	H6ST1_HUMAN	B4E2L3_HUMAN	UPI0000D61231	.	tolerated(0.2)	benign(0.027)	2/2	.	hmmpanther:PTHR12812,hmmpanther:PTHR12812:SF1,Pfam_domain:PF03567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGATGGTGT	.	5	ESCA
CCDC148	0	.	GRCh37	2	159028672	159028672	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1729C>T	p.Gln577Ter	p.Q577*	ENST00000283233	14/14	46	32	14	36	36	0	CCDC148,stop_gained,p.Gln586Ter,ENST00000409187,;CCDC148,stop_gained,p.Gln577Ter,ENST00000283233,;CCDC148-AS1,intron_variant,,ENST00000412781,;CCDC148,3_prime_UTR_variant,,ENST00000448656,;CCDC148,3_prime_UTR_variant,,ENST00000454257,;	A	ENSG00000153237	ENST00000283233	Transcript	stop_gained	2043	1729	577	Q/*	Caa/Taa	COSM126599	.	.	-1	CCDC148	HGNC	25191	protein_coding	YES	CCDS33304.1	ENSP00000283233	CC148_HUMAN	.	UPI0000208F63	.	.	.	14/14	.	hmmpanther:PTHR21549:SF1,hmmpanther:PTHR21549	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTGAGGAC	.	5	ESCA
SATB2	0	.	GRCh37	2	200322723	200322723	+	5'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-721T>A	.	.	ENST00000417098	1/11	65	58	6	61	61	0	SATB2,5_prime_UTR_variant,,ENST00000443023,;SATB2,5_prime_UTR_variant,,ENST00000417098,;SATB2,intron_variant,,ENST00000260926,;SATB2,intron_variant,,ENST00000457245,;SATB2,upstream_gene_variant,,ENST00000428695,;SATB2-AS1,non_coding_transcript_exon_variant,,ENST00000441234,;SATB2-AS1,non_coding_transcript_exon_variant,,ENST00000442967,;SATB2,intron_variant,,ENST00000463386,;SATB2,upstream_gene_variant,,ENST00000440919,;	T	ENSG00000119042	ENST00000417098	Transcript	5_prime_UTR_variant	97	.	.	.	.	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGTCATCAGG	.	4	ESCA
ADAM23	0	.	GRCh37	2	207406859	207406859	+	Splice_Site	SNP	G	G	T	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.656+1G>T	.	p.X219_splice	ENST00000264377	.	79	21	57	55	55	0	ADAM23,splice_donor_variant,,ENST00000374415,;ADAM23,splice_donor_variant,,ENST00000374416,;ADAM23,splice_donor_variant,,ENST00000264377,;	T	ENSG00000114948	ENST00000264377	Transcript	splice_donor_variant	.	.	.	.	.	COSM1482689,COSM1482690	.	.	1	ADAM23	HGNC	202	protein_coding	YES	CCDS2369.1	ENSP00000264377	ADA23_HUMAN	Q53TK5_HUMAN,Q53TC0_HUMAN,Q53RX4_HUMAN	UPI0000044543	.	.	.	.	5/25	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCAGTAAGT	.	5	ESCA
ZNF512	0	.	GRCh37	2	27845339	27845339	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1011T>C	.	.	ENST00000355467	14/14	56	30	26	39	39	0	ZNF512,3_prime_UTR_variant,,ENST00000355467,;ZNF512,3_prime_UTR_variant,,ENST00000379717,;ZNF512,intron_variant,,ENST00000556601,;CCDC121,downstream_gene_variant,,ENST00000394775,;ZNF512,downstream_gene_variant,,ENST00000416005,;ZNF512,downstream_gene_variant,,ENST00000413371,;CCDC121,downstream_gene_variant,,ENST00000324364,;RP11-158I13.2,intron_variant,,ENST00000505973,;ZNF512,non_coding_transcript_exon_variant,,ENST00000488055,;	C	ENSG00000243943	ENST00000355467	Transcript	3_prime_UTR_variant	2798	.	.	.	.	.	.	.	1	ZNF512	HGNC	29380	protein_coding	YES	CCDS1758.1	ENSP00000347648	ZN512_HUMAN	Q658M0_HUMAN	UPI0000141030	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TATTGTCCTAT	.	4	ESCA
CRIM1	0	.	GRCh37	2	36691738	36691738	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.931A>C	p.Ile311Leu	p.I311L	ENST00000280527	5/17	131	105	26	96	96	0	CRIM1,missense_variant,p.Ile311Leu,ENST00000280527,;CRIM1,missense_variant,p.Ile203Leu,ENST00000426856,;	C	ENSG00000150938	ENST00000280527	Transcript	missense_variant	1298	931	311	I/L	Ata/Cta	.	.	.	1	CRIM1	HGNC	2359	protein_coding	YES	CCDS1783.1	ENSP00000280527	CRIM1_HUMAN	Q53TR0_HUMAN,Q53TH9_HUMAN,Q4ZG85_HUMAN,B4DUW0_HUMAN	UPI000004C628	.	tolerated(0.6)	possibly_damaging(0.651)	5/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGCATAGTC	.	5	ESCA
EML6	0	.	GRCh37	2	55074758	55074758	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1185C>G	p.%3D	p.V395V	ENST00000356458	8/41	62	30	32	65	65	0	EML6,synonymous_variant,p.%3D,ENST00000356458,;RNU7-81P,upstream_gene_variant,,ENST00000516698,;	G	ENSG00000214595	ENST00000356458	Transcript	synonymous_variant	1705	1185	395	V	gtC/gtG	.	.	.	1	EML6	HGNC	35412	protein_coding	YES	CCDS46286.1	ENSP00000348842	EMAL6_HUMAN	.	UPI00006C0432	.	.	.	8/41	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13720:SF8,hmmpanther:PTHR13720,Gene3D:2.130.10.10,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGTCAGGCA	.	5	ESCA
VRK2	0	.	GRCh37	2	58276079	58276079	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113G>A	p.Gly38Glu	p.G38E	ENST00000435505	5/16	116	66	50	64	64	0	VRK2,missense_variant,p.Gly43Glu,ENST00000428021,;VRK2,missense_variant,p.Gly38Glu,ENST00000340157,;VRK2,missense_variant,p.Gly15Glu,ENST00000440705,;VRK2,missense_variant,p.Gly38Glu,ENST00000417641,;VRK2,missense_variant,p.Gly38Glu,ENST00000412104,;VRK2,missense_variant,p.Gly38Glu,ENST00000435505,;VRK2,missense_variant,p.Gly38Glu,ENST00000432057,;	A	ENSG00000028116	ENST00000435505	Transcript	missense_variant	858	113	38	G/E	gGa/gAa	.	.	.	1	VRK2	HGNC	12719	protein_coding	YES	CCDS1859.1	ENSP00000408002	VRK2_HUMAN	.	UPI000013D498	.	deleterious(0)	probably_damaging(1)	5/16	.	PROSITE_profiles:PS50011,hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF100,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGGAGGAT	.	5	ESCA
SFXN5	0	.	GRCh37	2	73215478	73215478	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535-1G>C	.	p.X179_splice	ENST00000272433	.	41	34	7	30	30	0	SFXN5,splice_acceptor_variant,,ENST00000272433,;SFXN5,splice_acceptor_variant,,ENST00000411783,;SFXN5,splice_acceptor_variant,,ENST00000410065,;SFXN5,splice_acceptor_variant,,ENST00000416579,;SFXN5,splice_acceptor_variant,,ENST00000463277,;SFXN5,splice_acceptor_variant,,ENST00000482542,;SFXN5,splice_acceptor_variant,,ENST00000474528,;SFXN5,splice_acceptor_variant,,ENST00000464825,;SFXN5,intron_variant,,ENST00000461352,;SFXN5,upstream_gene_variant,,ENST00000482289,;	G	ENSG00000144040	ENST00000272433	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	SFXN5	HGNC	16073	protein_coding	YES	CCDS1922.1	ENSP00000272433	SFXN5_HUMAN	.	UPI000006D292	.	.	.	.	9/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCACCTTTGA	.	3	ESCA
LRRTM4	0	.	GRCh37	2	77749339	77749339	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-182G>T	.	.	ENST00000409093	1/4	55	42	12	43	43	0	LRRTM4,5_prime_UTR_variant,,ENST00000409088,;LRRTM4,5_prime_UTR_variant,,ENST00000409093,;LRRTM4,5_prime_UTR_variant,,ENST00000409884,;LRRTM4,5_prime_UTR_variant,,ENST00000409911,;LRRTM4,intron_variant,,ENST00000456154,;LRRTM4,upstream_gene_variant,,ENST00000409282,;	A	ENSG00000176204	ENST00000409093	Transcript	5_prime_UTR_variant	156	.	.	.	.	.	.	.	-1	LRRTM4	HGNC	19411	protein_coding	YES	CCDS46346.1	ENSP00000386357	LRRT4_HUMAN	C9JM64_HUMAN	UPI0000047808	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGACCCCAGT	.	5	ESCA
C2orf68	0	.	GRCh37	2	85839075	85839075	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33C>A	p.His11Gln	p.H11Q	ENST00000306336	1/4	14	8	5	13	13	0	C2orf68,missense_variant,p.His11Gln,ENST00000306336,;C2orf68,missense_variant,p.His11Gln,ENST00000409734,;USP39,upstream_gene_variant,,ENST00000323701,;USP39,upstream_gene_variant,,ENST00000409766,;USP39,upstream_gene_variant,,ENST00000448971,;USP39,upstream_gene_variant,,ENST00000442708,;USP39,upstream_gene_variant,,ENST00000409470,;USP39,upstream_gene_variant,,ENST00000409025,;USP39,upstream_gene_variant,,ENST00000450066,;USP39,intron_variant,,ENST00000459775,;USP39,intron_variant,,ENST00000474572,;USP39,intron_variant,,ENST00000491659,;USP39,upstream_gene_variant,,ENST00000465282,;C2orf68,upstream_gene_variant,,ENST00000478626,;USP39,upstream_gene_variant,,ENST00000455732,;C2orf68,missense_variant,p.His11Gln,ENST00000423181,;C2orf68,upstream_gene_variant,,ENST00000420686,;USP39,upstream_gene_variant,,ENST00000458268,;USP39,upstream_gene_variant,,ENST00000493829,;	T	ENSG00000168887	ENST00000306336	Transcript	missense_variant	78	33	11	H/Q	caC/caA	.	.	.	-1	C2orf68	HGNC	34353	protein_coding	YES	CCDS42704.1	ENSP00000304410	CB068_HUMAN	L7T9J5_HUMAN	UPI00002377B0	.	tolerated_low_confidence(0.22)	benign(0.001)	1/4	.	Pfam_domain:PF10573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CAGCAGTGCCC	.	4	ESCA
MAL	0	.	GRCh37	2	95691529	95691529	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-9C>A	.	.	ENST00000309988	1/4	15	5	10	15	15	0	MAL,5_prime_UTR_variant,,ENST00000309988,;MAL,upstream_gene_variant,,ENST00000354078,;MAL,upstream_gene_variant,,ENST00000349807,;MAL,upstream_gene_variant,,ENST00000353004,;AC103563.8,intron_variant,,ENST00000448734,;MAL,non_coding_transcript_exon_variant,,ENST00000489399,;	A	ENSG00000172005	ENST00000309988	Transcript	5_prime_UTR_variant	101	.	.	.	.	.	.	.	1	MAL	HGNC	6817	protein_coding	YES	CCDS2006.1	ENSP00000310880	MAL_HUMAN	.	UPI000004494A	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGCACGCC	.	5	ESCA
ATP2B2	0	.	GRCh37	3	10442741	10442741	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.677G>A	p.Gly226Asp	p.G226D	ENST00000360273	5/23	82	64	18	69	69	0	ATP2B2,missense_variant,p.Gly226Asp,ENST00000343816,;ATP2B2,missense_variant,p.Gly226Asp,ENST00000360273,;ATP2B2,missense_variant,p.Gly226Asp,ENST00000383800,;ATP2B2,missense_variant,p.Gly226Asp,ENST00000352432,;ATP2B2,missense_variant,p.Gly226Asp,ENST00000397077,;ATP2B2,missense_variant,p.Gly113Asp,ENST00000452124,;ATP2B2,missense_variant,p.Gly226Asp,ENST00000460129,;ATP2B2,non_coding_transcript_exon_variant,,ENST00000480680,;	T	ENSG00000157087	ENST00000360273	Transcript	missense_variant	1116	677	226	G/D	gGc/gAc	.	.	.	-1	ATP2B2	HGNC	815	protein_coding	YES	CCDS33701.1	ENSP00000353414	AT2B2_HUMAN	Q4J699_HUMAN,Q4J696_HUMAN	UPI00001261EF	.	deleterious(0)	probably_damaging(1)	5/23	.	hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF247,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01494,Gene3D:2.70.150.10,Superfamily_domains:0049471	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGGCCGTCG	.	5	ESCA
PTPLB	0	.	GRCh37	3	123301134	123301134	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198T>A	p.%3D	p.A66A	ENST00000383657	2/7	113	96	17	62	62	0	PTPLB,synonymous_variant,p.%3D,ENST00000383657,;PTPLB,5_prime_UTR_variant,,ENST00000469317,;MYLK-AS1,upstream_gene_variant,,ENST00000463408,;MYLK-AS1,upstream_gene_variant,,ENST00000470449,;MYLK-AS1,upstream_gene_variant,,ENST00000485162,;	T	ENSG00000206527	ENST00000383657	Transcript	synonymous_variant	356	198	66	A	gcT/gcA	.	.	.	-1	PTPLB	HGNC	9640	protein_coding	YES	CCDS46895.1	ENSP00000373153	HACD2_HUMAN	C9JWG1_HUMAN	UPI0000160B26	.	.	.	2/7	.	hmmpanther:PTHR11035:SF17,hmmpanther:PTHR11035	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTAGCCAG	.	5	ESCA
MYLK	0	.	GRCh37	3	123452795	123452795	+	Missense_Mutation	SNP	C	C	T	rs532659627	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1048G>A	p.Ala350Thr	p.A350T	ENST00000360304	10/34	68	38	30	43	43	0	MYLK,missense_variant,p.Ala350Thr,ENST00000360304,;MYLK,missense_variant,p.Ala350Thr,ENST00000346322,;MYLK,missense_variant,p.Ala350Thr,ENST00000360772,;MYLK,missense_variant,p.Ala350Thr,ENST00000475616,;MYLK,missense_variant,p.Ala350Thr,ENST00000359169,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,non_coding_transcript_exon_variant,,ENST00000514623,;MYLK,downstream_gene_variant,,ENST00000506361,;	T	ENSG00000065534	ENST00000360304	Transcript	missense_variant	1330	1048	350	A/T	Gca/Aca	rs532659627,COSM581331,COSM581330,COSM727805	.	.	-1	MYLK	HGNC	7590	protein_coding	YES	CCDS46896.1	ENSP00000353452	MYLK_HUMAN	Q06S79_HUMAN,Q05B98_HUMAN,Q05B97_HUMAN,D6R9C2_HUMAN,B4DUE3_HUMAN	UPI000020A0AE	.	tolerated(0.67)	possibly_damaging(0.636)	10/34	.	hmmpanther:PTHR22964,hmmpanther:PTHR22964:SF44	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.A350T|c.1048G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTGCGGCCT	by1000G	5	ESCA
PLXND1	0	.	GRCh37	3	129304794	129304794	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1851+1G>C	.	p.X617_splice	ENST00000324093	.	155	132	23	104	104	0	PLXND1,splice_donor_variant,,ENST00000393239,;PLXND1,splice_donor_variant,,ENST00000324093,;PLXND1,downstream_gene_variant,,ENST00000505237,;PLXND1,splice_donor_variant,,ENST00000505665,;	G	ENSG00000004399	ENST00000324093	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	PLXND1	HGNC	9107	protein_coding	YES	CCDS33854.1	ENSP00000317128	PLXD1_HUMAN	Q6P657_HUMAN	UPI00003671AD	.	.	.	.	5/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCACTGGGT	.	4	ESCA
RYK	0	.	GRCh37	3	133913932	133913932	+	Missense_Mutation	SNP	T	T	C	rs768567317	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.877A>G	p.Ile293Val	p.I293V	ENST00000296084	8/16	69	54	15	43	43	0	RYK,missense_variant,p.Ile293Val,ENST00000296084,;RYK,missense_variant,p.Ile103Val,ENST00000427044,;RYK,missense_variant,p.Ile275Val,ENST00000460933,;RYK,non_coding_transcript_exon_variant,,ENST00000480381,;RYK,upstream_gene_variant,,ENST00000486725,;	C	ENSG00000163785	ENST00000296084	Transcript	missense_variant	877	877	293	I/V	Atc/Gtc	rs768567317	.	.	-1	RYK	HGNC	10481	protein_coding	YES	.	ENSP00000296084	RYK_HUMAN	Q8WTZ8_HUMAN,F5H8L5_HUMAN	UPI00015E08D8	.	tolerated(0.85)	benign(0.002)	8/16	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF256	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGATAGGAG	.	5	ESCA
FBLN2	0	.	GRCh37	3	13670421	13670421	+	Silent	SNP	G	G	A	rs370055863	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2586G>A	p.%3D	p.T862T	ENST00000404922	12/18	75	47	27	68	68	0	FBLN2,synonymous_variant,p.%3D,ENST00000295760,;FBLN2,synonymous_variant,p.%3D,ENST00000492059,;FBLN2,synonymous_variant,p.%3D,ENST00000404922,;FBLN2,synonymous_variant,p.%3D,ENST00000535798,;FBLN2,upstream_gene_variant,,ENST00000295761,;	A	ENSG00000163520	ENST00000404922	Transcript	synonymous_variant	2705	2586	862	T	acG/acA	rs370055863	.	.	1	FBLN2	HGNC	3601	protein_coding	YES	CCDS46761.1	ENSP00000384169	FBLN2_HUMAN	Q9Y3V7_HUMAN,C9JQS6_HUMAN	UPI000042B0C1	.	.	.	12/18	.	hmmpanther:PTHR24048,hmmpanther:PTHR24048:SF72,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACGTCACT	byFrequency|byCluster	5	ESCA
FAIM	0	.	GRCh37	3	138341108	138341108	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292A>G	p.Thr98Ala	p.T98A	ENST00000338446	4/6	208	125	82	127	127	0	FAIM,missense_variant,p.Thr86Ala,ENST00000360570,;FAIM,missense_variant,p.Thr64Ala,ENST00000393035,;FAIM,missense_variant,p.Thr64Ala,ENST00000479848,;FAIM,missense_variant,p.Thr64Ala,ENST00000464668,;FAIM,missense_variant,p.Thr64Ala,ENST00000393034,;FAIM,missense_variant,p.Thr98Ala,ENST00000338446,;FAIM,non_coding_transcript_exon_variant,,ENST00000491175,;FAIM,non_coding_transcript_exon_variant,,ENST00000464912,;FAIM,non_coding_transcript_exon_variant,,ENST00000470889,;	G	ENSG00000158234	ENST00000338446	Transcript	missense_variant	975	292	98	T/A	Acc/Gcc	.	.	.	1	FAIM	HGNC	18703	protein_coding	YES	CCDS33864.1	ENSP00000342805	FAIM1_HUMAN	C9JDZ2_HUMAN	UPI00005B2E09	.	tolerated(0.21)	benign(0.011)	4/6	.	hmmpanther:PTHR13088:SF1,hmmpanther:PTHR13088,Pfam_domain:PF06905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCGACCATA	.	5	ESCA
ACPL2	0	.	GRCh37	3	141006278	141006278	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.488G>A	p.Gly163Glu	p.G163E	ENST00000286353	5/6	41	33	7	32	32	0	ACPL2,missense_variant,p.Gly163Glu,ENST00000286353,;ACPL2,missense_variant,p.Gly125Glu,ENST00000502783,;ACPL2,missense_variant,p.Gly147Glu,ENST00000393007,;ACPL2,missense_variant,p.Gly154Glu,ENST00000508812,;ACPL2,missense_variant,p.Gly125Glu,ENST00000512457,;ACPL2,missense_variant,p.Gly163Glu,ENST00000393010,;ACPL2,missense_variant,p.Gly146Glu,ENST00000504264,;ACPL2,downstream_gene_variant,,ENST00000505013,;RP11-438D8.2,intron_variant,,ENST00000507698,;ACPL2,non_coding_transcript_exon_variant,,ENST00000514263,;ACPL2,3_prime_UTR_variant,,ENST00000514880,;	A	ENSG00000155893	ENST00000286353	Transcript	missense_variant	625	488	163	G/E	gGa/gAa	.	.	.	1	ACPL2	HGNC	26303	protein_coding	YES	CCDS3116.1	ENSP00000286353	ACPL2_HUMAN	D6RGE3_HUMAN,D6RE60_HUMAN,D6RDP0_HUMAN,D6R928_HUMAN,B7Z4T2_HUMAN	UPI0000048EC7	.	deleterious(0)	probably_damaging(1)	5/6	.	hmmpanther:PTHR11567:SF110,hmmpanther:PTHR11567,Pfam_domain:PF00328,Gene3D:3.40.50.1240,Superfamily_domains:SSF53254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGGGAGAGC	.	5	ESCA
SLC9A9	0	.	GRCh37	3	143551002	143551002	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237T>G	p.%3D	p.T79T	ENST00000316549	2/16	84	75	9	44	44	0	SLC9A9,synonymous_variant,p.%3D,ENST00000316549,;SLC9A9,synonymous_variant,p.%3D,ENST00000474151,;SLC9A9,intron_variant,,ENST00000474727,;	C	ENSG00000181804	ENST00000316549	Transcript	synonymous_variant	446	237	79	T	acT/acG	.	.	.	-1	SLC9A9	HGNC	20653	protein_coding	YES	CCDS33872.1	ENSP00000320246	SL9A9_HUMAN	.	UPI0000074664	.	.	.	2/16	.	hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF61,Pfam_domain:PF00999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAGACAGTTCC	.	4	ESCA
ZIC4	0	.	GRCh37	3	147120593	147120593	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142A>G	p.Ser48Gly	p.S48G	ENST00000525172	2/5	153	144	9	73	73	0	ZIC4,missense_variant,p.Ser36Gly,ENST00000425731,;ZIC4,missense_variant,p.Ser48Gly,ENST00000525172,;ZIC4,5_prime_UTR_variant,,ENST00000484399,;ZIC4,5_prime_UTR_variant,,ENST00000473123,;ZIC4,5_prime_UTR_variant,,ENST00000383075,;ZIC4,5_prime_UTR_variant,,ENST00000463250,;ZIC4,5_prime_UTR_variant,,ENST00000491672,;ZIC4,5_prime_UTR_variant,,ENST00000462748,;ZIC4,5_prime_UTR_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000488404,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,;	C	ENSG00000174963	ENST00000525172	Transcript	missense_variant	328	142	48	S/G	Agt/Ggt	COSM1536606	.	.	-1	ZIC4	HGNC	20393	protein_coding	YES	CCDS54652.1	ENSP00000435509	ZIC4_HUMAN	C9JZU7_HUMAN,C9JD04_HUMAN,C9J6T3_HUMAN,B3KPI4_HUMAN	UPI0001914D88	.	tolerated_low_confidence(0.32)	benign(0.001)	2/5	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGACTTTGAG	.	2	ESCA
LIPH	0	.	GRCh37	3	185245348	185245348	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552C>G	p.Phe184Leu	p.F184L	ENST00000296252	4/10	104	30	74	79	79	0	LIPH,missense_variant,p.Phe184Leu,ENST00000296252,;LIPH,intron_variant,,ENST00000452897,;LIPH,intron_variant,,ENST00000424591,;	C	ENSG00000163898	ENST00000296252	Transcript	missense_variant	694	552	184	F/L	ttC/ttG	.	.	.	-1	LIPH	HGNC	18483	protein_coding	YES	CCDS3272.1	ENSP00000296252	LIPH_HUMAN	A2IBA8_HUMAN	UPI000003AEB8	.	deleterious(0)	probably_damaging(0.936)	4/10	.	hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF12,Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGTTGAATAA	.	5	ESCA
TRA2B	0	.	GRCh37	3	185634782	185634782	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*721T>A	.	.	ENST00000453386	9/9	18	14	4	33	33	0	TRA2B,3_prime_UTR_variant,,ENST00000453386,;TRA2B,downstream_gene_variant,,ENST00000259043,;TRA2B,downstream_gene_variant,,ENST00000414862,;TRA2B,downstream_gene_variant,,ENST00000382191,;TRA2B,non_coding_transcript_exon_variant,,ENST00000463328,;TRA2B,non_coding_transcript_exon_variant,,ENST00000492417,;TRA2B,downstream_gene_variant,,ENST00000487615,;TRA2B,downstream_gene_variant,,ENST00000466832,;TRA2B,downstream_gene_variant,,ENST00000456380,;	T	ENSG00000136527	ENST00000453386	Transcript	3_prime_UTR_variant	1864	.	.	.	.	.	.	.	-1	TRA2B	HGNC	10781	protein_coding	YES	CCDS33905.1	ENSP00000416959	TRA2B_HUMAN	.	UPI00000040A0	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAACTAGTTGA	.	3	ESCA
PDCD6IP	0	.	GRCh37	3	33906852	33906852	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2377C>G	p.Gln793Glu	p.Q793E	ENST00000457054	17/18	52	22	29	67	67	0	PDCD6IP,missense_variant,p.Gln793Glu,ENST00000457054,;PDCD6IP,missense_variant,p.Gln788Glu,ENST00000307296,;PDCD6IP,non_coding_transcript_exon_variant,,ENST00000473593,;PDCD6IP,downstream_gene_variant,,ENST00000465122,;PDCD6IP,downstream_gene_variant,,ENST00000489869,;	G	ENSG00000170248	ENST00000457054	Transcript	missense_variant	2532	2377	793	Q/E	Caa/Gaa	.	.	.	1	PDCD6IP	HGNC	8766	protein_coding	YES	CCDS54561.1	ENSP00000411825	PDC6I_HUMAN	.	UPI00004121D3	.	tolerated(0.4)	benign(0)	17/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23030:SF19,hmmpanther:PTHR23030	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCACAAACG	.	5	ESCA
CX3CR1	0	.	GRCh37	3	39307268	39307268	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.829A>G	p.Thr277Ala	p.T277A	ENST00000358309	2/2	33	14	19	41	41	0	CX3CR1,missense_variant,p.Thr245Ala,ENST00000542107,;CX3CR1,missense_variant,p.Thr245Ala,ENST00000399220,;CX3CR1,missense_variant,p.Thr277Ala,ENST00000358309,;CX3CR1,missense_variant,p.Thr245Ala,ENST00000541347,;CX3CR1,downstream_gene_variant,,ENST00000435290,;CX3CR1,downstream_gene_variant,,ENST00000412814,;	C	ENSG00000168329	ENST00000358309	Transcript	missense_variant	869	829	277	T/A	Aca/Gca	.	.	.	-1	CX3CR1	HGNC	2558	protein_coding	YES	CCDS54571.1	ENSP00000351059	CX3C1_HUMAN	C9JN40_HUMAN,C9JLM2_HUMAN	UPI00004570E5	.	tolerated(0.27)	possibly_damaging(0.599)	2/2	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,hmmpanther:PTHR24227:SF9,hmmpanther:PTHR24227,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTGTCCAGA	.	5	ESCA
ABHD14B	0	.	GRCh37	3	52003994	52003994	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418G>C	p.Asp140His	p.D140H	ENST00000483233	4/5	36	15	21	53	53	0	ABHD14B,missense_variant,p.Asp140His,ENST00000361143,;ABHD14B,missense_variant,p.Asp140His,ENST00000395008,;ABHD14B,missense_variant,p.Asp140His,ENST00000461108,;ABHD14B,missense_variant,p.Asp140His,ENST00000525795,;ABHD14B,missense_variant,p.Asp138His,ENST00000315877,;ABHD14B,missense_variant,p.Asp140His,ENST00000483233,;RP11-155D18.14,intron_variant,,ENST00000489595,;PCBP4,upstream_gene_variant,,ENST00000484633,;ABHD14A,upstream_gene_variant,,ENST00000494478,;PCBP4,upstream_gene_variant,,ENST00000466412,;PCBP4,upstream_gene_variant,,ENST00000483411,;PCBP4,upstream_gene_variant,,ENST00000468324,;PCBP4,upstream_gene_variant,,ENST00000461554,;PCBP4,upstream_gene_variant,,ENST00000490063,;PCBP4,upstream_gene_variant,,ENST00000461544,;PCBP4,upstream_gene_variant,,ENST00000497653,;ABHD14A,upstream_gene_variant,,ENST00000497864,;PCBP4,upstream_gene_variant,,ENST00000395013,;PCBP4,upstream_gene_variant,,ENST00000355852,;PCBP4,upstream_gene_variant,,ENST00000428823,;ABHD14B,non_coding_transcript_exon_variant,,ENST00000487005,;RP11-155D18.12,intron_variant,,ENST00000488257,;PCBP4,upstream_gene_variant,,ENST00000471308,;PCBP4,upstream_gene_variant,,ENST00000471358,;ABHD14B,downstream_gene_variant,,ENST00000473912,;	G	ENSG00000114779	ENST00000483233	Transcript	missense_variant	925	418	140	D/H	Gac/Cac	.	.	.	-1	ABHD14B	HGNC	28235	protein_coding	YES	CCDS2842.1	ENSP00000420065	ABHEB_HUMAN	.	UPI000006F0B7	.	deleterious(0.05)	possibly_damaging(0.892)	4/5	.	hmmpanther:PTHR10992:SF281,hmmpanther:PTHR10992,Pfam_domain:PF12695,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCAGTGC	.	5	ESCA
PDZRN3	0	.	GRCh37	3	73433779	73433779	+	Silent	SNP	G	G	A	rs377558165	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1938C>T	p.%3D	p.F646F	ENST00000263666	10/10	21	9	12	30	30	0	PDZRN3,synonymous_variant,p.%3D,ENST00000466780,;PDZRN3,synonymous_variant,p.%3D,ENST00000263666,;PDZRN3,synonymous_variant,p.%3D,ENST00000462146,;PDZRN3,synonymous_variant,p.%3D,ENST00000479530,;PDZRN3,synonymous_variant,p.%3D,ENST00000535920,;PDZRN3,synonymous_variant,p.%3D,ENST00000492909,;PDZRN3,intron_variant,,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000466348,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000478209,;PDZRN3,downstream_gene_variant,,ENST00000484487,;	A	ENSG00000121440	ENST00000263666	Transcript	synonymous_variant	2053	1938	646	F	ttC/ttT	rs377558165,COSM1538776	.	.	-1	PDZRN3	HGNC	17704	protein_coding	YES	CCDS33789.1	ENSP00000263666	PZRN3_HUMAN	E7ENB6_HUMAN	UPI00001C1DE6	.	.	.	10/10	.	hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCGGAAGCG	byCluster	5	ESCA
MTMR14	0	.	GRCh37	3	9739484	9739484	+	Missense_Mutation	SNP	G	G	A	rs776656035	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1703G>A	p.Arg568Gln	p.R568Q	ENST00000296003	18/19	39	27	12	46	46	0	MTMR14,missense_variant,p.Arg568Gln,ENST00000296003,;MTMR14,intron_variant,,ENST00000420925,;MTMR14,intron_variant,,ENST00000351233,;MTMR14,intron_variant,,ENST00000353332,;MTMR14,3_prime_UTR_variant,,ENST00000414996,;MTMR14,3_prime_UTR_variant,,ENST00000447144,;MTMR14,upstream_gene_variant,,ENST00000606184,;	A	ENSG00000163719	ENST00000296003	Transcript	missense_variant	1825	1703	568	R/Q	cGg/cAg	rs776656035	.	.	1	MTMR14	HGNC	26190	protein_coding	YES	CCDS43043.1	ENSP00000296003	MTMRE_HUMAN	.	UPI000007423D	.	tolerated(0.76)	possibly_damaging(0.885)	18/19	.	hmmpanther:PTHR13524	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCGGGCTG	byFrequency	5	ESCA
OR5K4	0	.	GRCh37	3	98073474	98073474	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.777T>C	p.%3D	p.I259I	ENST00000354924	1/1	41	24	16	84	84	0	OR5K4,synonymous_variant,p.%3D,ENST00000354924,;RP11-325B23.2,intron_variant,,ENST00000508616,;	C	ENSG00000196098	ENST00000354924	Transcript	synonymous_variant	777	777	259	I	atT/atC	.	.	.	1	OR5K4	HGNC	31291	protein_coding	YES	CCDS33802.1	ENSP00000347003	OR5K4_HUMAN	.	UPI000044D411	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF198,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATTGGACC	.	5	ESCA
HSP90AB2P	0	.	GRCh37	4	13335101	13335117	+	5'Flank	DEL	AAACAACATTCAGCAAG	AAACAACATTCAGCAAG	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	AAACAACATTCAGCAAG	AAACAACATTCAGCAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000507090	.	68	51	17	57	57	0	HSP90AB2P,non_coding_transcript_exon_variant,,ENST00000602906,;HSP90AB2P,upstream_gene_variant,,ENST00000507090,;HSP90AB2P,upstream_gene_variant,,ENST00000382444,;	T	ENSG00000205940	ENST00000507090	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2989	1	HSP90AB2P	HGNC	32537	transcribed_processed_pseudogene	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	TATTGCAAACAACATTCAGCAAGGACCC	.	2	ESCA
NAA15	0	.	GRCh37	4	140282928	140282928	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1590G>C	p.Met530Ile	p.M530I	ENST00000296543	14/20	85	54	31	62	62	0	NAA15,missense_variant,p.Met530Ile,ENST00000296543,;NAA15,missense_variant,p.Met530Ile,ENST00000398947,;NAA15,downstream_gene_variant,,ENST00000468029,;	C	ENSG00000164134	ENST00000296543	Transcript	missense_variant	1913	1590	530	M/I	atG/atC	.	.	.	1	NAA15	HGNC	30782	protein_coding	YES	CCDS43270.1	ENSP00000296543	NAA15_HUMAN	.	UPI000004B631	.	deleterious(0.03)	probably_damaging(0.998)	14/20	.	PIRSF_domain:PIRSF000422,Pfam_domain:PF12569,hmmpanther:PTHR22767,hmmpanther:PTHR22767:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATGAGGAA	.	5	ESCA
LRBA	0	.	GRCh37	4	151357951	151357951	+	Missense_Mutation	SNP	A	A	T	rs138518902	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6879T>A	p.Asp2293Glu	p.D2293E	ENST00000357115	46/58	64	50	13	49	49	0	LRBA,missense_variant,p.Asp2282Glu,ENST00000535741,;LRBA,missense_variant,p.Asp2282Glu,ENST00000507224,;LRBA,missense_variant,p.Asp2293Glu,ENST00000357115,;LRBA,missense_variant,p.Asp2282Glu,ENST00000510413,;LRBA,missense_variant,p.Asp935Glu,ENST00000509835,;LRBA,non_coding_transcript_exon_variant,,ENST00000503716,;	T	ENSG00000198589	ENST00000357115	Transcript	missense_variant	7123	6879	2293	D/E	gaT/gaA	rs138518902	.	.	-1	LRBA	HGNC	1742	protein_coding	YES	CCDS3773.1	ENSP00000349629	LRBA_HUMAN	Q7KZN3_HUMAN	UPI000013E35C	.	tolerated(0.08)	possibly_damaging(0.557)	46/58	.	PROSITE_profiles:PS50197,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATCATCTTC	byCluster	5	ESCA
GRIA2	0	.	GRCh37	4	158256846	158256846	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1290G>C	p.Lys430Asn	p.K430N	ENST00000296526	10/16	92	56	36	58	58	0	GRIA2,missense_variant,p.Lys383Asn,ENST00000393815,;GRIA2,missense_variant,p.Lys430Asn,ENST00000296526,;GRIA2,missense_variant,p.Lys430Asn,ENST00000264426,;GRIA2,missense_variant,p.Lys383Asn,ENST00000507898,;GRIA2,missense_variant,p.Lys383Asn,ENST00000449365,;GRIA2,missense_variant,p.Lys383Asn,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,;	C	ENSG00000120251	ENST00000296526	Transcript	missense_variant	1615	1290	430	K/N	aaG/aaC	.	.	.	1	GRIA2	HGNC	4572	protein_coding	YES	CCDS3797.1	ENSP00000296526	GRIA2_HUMAN	D6RFM6_HUMAN,D6REK8_HUMAN,D6RDX5_HUMAN,D6RBV7_HUMAN,D6R9Z0_HUMAN,A8MT92_HUMAN	UPI000002AA8D	.	deleterious(0.03)	probably_damaging(1)	10/16	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF99,Gene3D:3.40.190.10,Pfam_domain:PF10613,SMART_domains:SM00918,SMART_domains:SM00079,Superfamily_domains:SSF53850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAAGAAAAA	.	5	ESCA
RXFP1	0	.	GRCh37	4	159493861	159493861	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61G>A	p.Gly21Ser	p.G21S	ENST00000307765	2/18	97	70	26	66	66	0	RXFP1,missense_variant,p.Gly21Ser,ENST00000343542,;RXFP1,missense_variant,p.Gly21Ser,ENST00000423548,;RXFP1,missense_variant,p.Gly21Ser,ENST00000470033,;RXFP1,missense_variant,p.Gly21Ser,ENST00000307765,;RXFP1,5_prime_UTR_variant,,ENST00000448688,;RXFP1,5_prime_UTR_variant,,ENST00000460056,;RXFP1,non_coding_transcript_exon_variant,,ENST00000484785,;RXFP1,missense_variant,p.Gly21Ser,ENST00000471616,;RXFP1,missense_variant,p.Gly21Ser,ENST00000342048,;	A	ENSG00000171509	ENST00000307765	Transcript	missense_variant	312	61	21	G/S	Ggt/Agt	.	.	.	1	RXFP1	HGNC	19718	protein_coding	YES	CCDS43276.1	ENSP00000303248	RXFP1_HUMAN	Q4W5D9_HUMAN,E9PCA3_HUMAN	UPI000013EC4B	.	tolerated(1)	benign(0)	2/18	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGGGGTGGA	.	5	ESCA
ADAM29	0	.	GRCh37	4	175897785	175897785	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109G>T	p.Ser370Ile	p.S370I	ENST00000359240	5/5	58	50	8	35	35	0	ADAM29,missense_variant,p.Ser370Ile,ENST00000514159,;ADAM29,missense_variant,p.Ser370Ile,ENST00000445694,;ADAM29,missense_variant,p.Ser370Ile,ENST00000404450,;ADAM29,missense_variant,p.Ser370Ile,ENST00000359240,;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000502940,;ADAM29,downstream_gene_variant,,ENST00000505141,;RP13-577H12.2,downstream_gene_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,;	T	ENSG00000168594	ENST00000359240	Transcript	missense_variant	1779	1109	370	S/I	aGt/aTt	.	.	.	1	ADAM29	HGNC	207	protein_coding	YES	CCDS3823.1	ENSP00000352177	ADA29_HUMAN	D6RHU0_HUMAN,D6RBU0_HUMAN	UPI000013E9DE	.	deleterious(0)	probably_damaging(0.999)	5/5	.	PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF34,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTAGTTATG	.	4	ESCA
TRIML1	0	.	GRCh37	4	189063453	189063453	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552A>T	p.Lys184Asn	p.K184N	ENST00000332517	3/6	50	43	6	20	20	0	TRIML1,missense_variant,p.Lys184Asn,ENST00000332517,;RP11-366H4.3,intron_variant,,ENST00000501322,;TRIML1,upstream_gene_variant,,ENST00000512233,;TRIML1,upstream_gene_variant,,ENST00000507581,;	T	ENSG00000184108	ENST00000332517	Transcript	missense_variant	692	552	184	K/N	aaA/aaT	.	.	.	1	TRIML1	HGNC	26698	protein_coding	YES	CCDS3851.1	ENSP00000327738	TRIML_HUMAN	.	UPI000006FC8A	.	deleterious(0)	probably_damaging(0.997)	3/6	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF291,Gene3D:3.30.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGAAAATGCA	.	4	ESCA
CSN2	0	.	GRCh37	4	70823225	70823225	+	Missense_Mutation	SNP	G	G	T	rs781240580	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442C>A	p.Pro148Thr	p.P148T	ENST00000353151	5/7	68	49	18	66	66	0	CSN2,missense_variant,p.Pro148Thr,ENST00000353151,;	T	ENSG00000135222	ENST00000353151	Transcript	missense_variant	454	442	148	P/T	Ccc/Acc	rs781240580	.	.	-1	CSN2	HGNC	2447	protein_coding	YES	CCDS3532.1	ENSP00000341030	CASB_HUMAN	.	UPI0000126FDB	.	deleterious(0.04)	probably_damaging(0.975)	5/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11500:SF0,hmmpanther:PTHR11500,Pfam_domain:PF00363,PIRSF_domain:PIRSF002372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGGCTGGA	.	5	ESCA
SHROOM3	0	.	GRCh37	4	77661903	77661903	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2577C>G	p.%3D	p.S859S	ENST00000296043	5/11	51	33	18	44	44	0	SHROOM3,synonymous_variant,p.%3D,ENST00000296043,;SHROOM3,intron_variant,,ENST00000469923,;SHROOM3,downstream_gene_variant,,ENST00000473602,;SHROOM3,downstream_gene_variant,,ENST00000481002,;SHROOM3,non_coding_transcript_exon_variant,,ENST00000486758,;	G	ENSG00000138771	ENST00000296043	Transcript	synonymous_variant	3530	2577	859	S	tcC/tcG	.	.	.	1	SHROOM3	HGNC	30422	protein_coding	YES	CCDS3579.2	ENSP00000296043	SHRM3_HUMAN	.	UPI0000E5AC1C	.	.	.	5/11	.	hmmpanther:PTHR15012:SF33,hmmpanther:PTHR15012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTCCCGGCA	.	5	ESCA
CNOT6L	0	.	GRCh37	4	78638271	78638271	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3314C>G	.	.	ENST00000264903	12/12	56	40	16	37	37	0	CNOT6L,3_prime_UTR_variant,,ENST00000504123,;CNOT6L,3_prime_UTR_variant,,ENST00000264903,;CNOT6L,downstream_gene_variant,,ENST00000515506,;CNOT6L,downstream_gene_variant,,ENST00000512485,;CNOT6L,downstream_gene_variant,,ENST00000504804,;	C	ENSG00000138767	ENST00000264903	Transcript	3_prime_UTR_variant	5064	.	.	.	.	.	.	.	-1	CNOT6L	HGNC	18042	protein_coding	YES	CCDS47082.1	ENSP00000264903	CNO6L_HUMAN	D6RGK9_HUMAN	UPI0000E445DF	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGGATTCT	.	5	ESCA
PPIC	0	.	GRCh37	5	122359198	122359198	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*372T>C	.	.	ENST00000306442	5/5	35	18	17	57	57	0	PPIC,3_prime_UTR_variant,,ENST00000306442,;RN7SL689P,upstream_gene_variant,,ENST00000577215,;SNX24,intron_variant,,ENST00000502387,;SNX24,intron_variant,,ENST00000510914,;PPIC,downstream_gene_variant,,ENST00000415659,;	G	ENSG00000168938	ENST00000306442	Transcript	3_prime_UTR_variant	1127	.	.	.	.	.	.	.	-1	PPIC	HGNC	9256	protein_coding	YES	CCDS4133.1	ENSP00000303057	PPIC_HUMAN	.	UPI0000128C7E	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGATACAAAA	.	5	ESCA
DNAH5	0	.	GRCh37	5	13719067	13719067	+	Silent	SNP	T	T	C	rs756382401	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12423A>G	p.%3D	p.T4141T	ENST00000265104	72/79	80	64	15	30	30	0	DNAH5,synonymous_variant,p.%3D,ENST00000265104,;	C	ENSG00000039139	ENST00000265104	Transcript	synonymous_variant	12528	12423	4141	T	acA/acG	rs756382401	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	.	72/79	.	Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAGTGTAAT	.	5	ESCA
DNAH5	0	.	GRCh37	5	13719141	13719141	+	Missense_Mutation	SNP	T	T	A	rs145501076	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12349A>T	p.Ile4117Leu	p.I4117L	ENST00000265104	72/79	52	38	14	23	23	0	DNAH5,missense_variant,p.Ile4117Leu,ENST00000265104,;	A	ENSG00000039139	ENST00000265104	Transcript	missense_variant	12454	12349	4117	I/L	Ata/Tta	rs145501076	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.001)	72/79	.	Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	C:0.0006	C:0.0015	C:0.0014	.	C:0	C:0	C:0	C:0.0025	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTATGATTA	byFrequency|byCluster|by1000G	5	ESCA
POU4F3	0	.	GRCh37	5	145719130	145719130	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.140G>A	p.Gly47Glu	p.G47E	ENST00000230732	2/2	68	27	40	83	83	0	POU4F3,missense_variant,p.Gly47Glu,ENST00000230732,;RBM27,downstream_gene_variant,,ENST00000506502,;CTC-359M8.1,intron_variant,,ENST00000515598,;	A	ENSG00000091010	ENST00000230732	Transcript	missense_variant	229	140	47	G/E	gGa/gAa	COSM1660069	.	.	1	POU4F3	HGNC	9220	protein_coding	YES	CCDS4281.1	ENSP00000230732	PO4F3_HUMAN	.	UPI0000131D91	.	deleterious(0.02)	possibly_damaging(0.457)	2/2	.	hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF43	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTGGAAGCT	.	5	ESCA
FAM105A	0	.	GRCh37	5	14610525	14610525	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*102T>A	.	.	ENST00000274217	8/8	42	31	11	25	25	0	FAM105A,3_prime_UTR_variant,,ENST00000274217,;FAM105A,non_coding_transcript_exon_variant,,ENST00000506258,;FAM105A,downstream_gene_variant,,ENST00000513825,;	A	ENSG00000145569	ENST00000274217	Transcript	3_prime_UTR_variant	1293	.	.	.	.	.	.	.	1	FAM105A	HGNC	25629	protein_coding	YES	CCDS3884.1	ENSP00000274217	F105A_HUMAN	.	UPI000004A036	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAATTAGGA	.	5	ESCA
CDH12	0	.	GRCh37	5	21760720	21760720	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1580G>C	p.Arg527Thr	p.R527T	ENST00000382254	13/15	110	104	6	79	79	0	CDH12,missense_variant,p.Arg487Thr,ENST00000522262,;CDH12,missense_variant,p.Arg527Thr,ENST00000504376,;CDH12,missense_variant,p.Arg527Thr,ENST00000382254,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,;	G	ENSG00000154162	ENST00000382254	Transcript	missense_variant	2667	1580	527	R/T	aGa/aCa	.	.	.	-1	CDH12	HGNC	1751	protein_coding	YES	CCDS3890.1	ENSP00000371689	CAD12_HUMAN	B3KRT0_HUMAN	UPI00000622EB	.	tolerated(0.17)	benign(0.014)	13/15	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATAATCTAAAG	.	2	ESCA
CDH10	0	.	GRCh37	5	24487458	24487458	+	3'UTR	SNP	C	C	T	rs148384899	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*314G>A	.	.	ENST00000264463	12/12	41	38	3	23	23	0	CDH10,3_prime_UTR_variant,,ENST00000264463,;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,downstream_gene_variant,,ENST00000503958,;	T	ENSG00000040731	ENST00000264463	Transcript	3_prime_UTR_variant	3189	.	.	.	.	rs148384899	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	.	.	12/12	.	.	T:0.0016	T:0	T:0	.	T:0.0079	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGCGGCTT	byFrequency|byCluster|by1000G	2	ESCA
PDE4D	0	.	GRCh37	5	58289273	58289273	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941G>A	p.Arg314Gln	p.R314Q	ENST00000340635	7/15	40	31	9	61	61	0	PDE4D,missense_variant,p.Arg12Gln,ENST00000505453,;PDE4D,missense_variant,p.Arg184Gln,ENST00000503258,;PDE4D,missense_variant,p.Arg253Gln,ENST00000546160,;PDE4D,missense_variant,p.Arg178Gln,ENST00000360047,;PDE4D,missense_variant,p.Arg314Gln,ENST00000340635,;PDE4D,missense_variant,p.Arg192Gln,ENST00000405755,;PDE4D,missense_variant,p.Arg250Gln,ENST00000507116,;PDE4D,missense_variant,p.Arg12Gln,ENST00000358923,;PDE4D,missense_variant,p.Arg253Gln,ENST00000502484,;PDE4D,missense_variant,p.Arg23Gln,ENST00000317118,;PDE4D,non_coding_transcript_exon_variant,,ENST00000405053,;PDE4D,3_prime_UTR_variant,,ENST00000309641,;PDE4D,non_coding_transcript_exon_variant,,ENST00000515011,;	T	ENSG00000113448	ENST00000340635	Transcript	missense_variant	1117	941	314	R/Q	cGg/cAg	.	.	.	-1	PDE4D	HGNC	8783	protein_coding	YES	CCDS47213.1	ENSP00000345502	PDE4D_HUMAN	D6RHE0_HUMAN	UPI0000050EB1	.	deleterious_low_confidence(0.01)	possibly_damaging(0.877)	7/15	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCGATTA	.	5	ESCA
PDE4D	0	.	GRCh37	5	58511631	58511631	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619T>C	p.Ser207Pro	p.S207P	ENST00000340635	2/15	39	25	14	54	54	0	PDE4D,missense_variant,p.Ser77Pro,ENST00000503258,;PDE4D,missense_variant,p.Ser146Pro,ENST00000546160,;PDE4D,missense_variant,p.Ser71Pro,ENST00000360047,;PDE4D,missense_variant,p.Ser207Pro,ENST00000340635,;PDE4D,missense_variant,p.Ser85Pro,ENST00000405755,;PDE4D,missense_variant,p.Ser143Pro,ENST00000507116,;PDE4D,missense_variant,p.Ser143Pro,ENST00000502575,;PDE4D,missense_variant,p.Ser146Pro,ENST00000502484,;PDE4D,intron_variant,,ENST00000505453,;PDE4D,non_coding_transcript_exon_variant,,ENST00000405053,;PDE4D,non_coding_transcript_exon_variant,,ENST00000503947,;PDE4D,non_coding_transcript_exon_variant,,ENST00000515324,;PDE4D,missense_variant,p.Ser143Pro,ENST00000309641,;PDE4D,non_coding_transcript_exon_variant,,ENST00000514231,;	G	ENSG00000113448	ENST00000340635	Transcript	missense_variant	795	619	207	S/P	Tcc/Ccc	.	.	.	-1	PDE4D	HGNC	8783	protein_coding	YES	CCDS47213.1	ENSP00000345502	PDE4D_HUMAN	D6RHE0_HUMAN	UPI0000050EB1	.	deleterious_low_confidence(0)	probably_damaging(0.987)	2/15	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGGACATAG	.	5	ESCA
TAF9	0	.	GRCh37	5	68665376	68665376	+	Intron	SNP	G	G	C	rs532216259	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-111+108C>G	.	.	ENST00000328663	.	9	2	7	18	18	0	TAF9,5_prime_UTR_variant,,ENST00000217893,;RAD17,intron_variant,,ENST00000507927,;RAD17,intron_variant,,ENST00000361732,;TAF9,intron_variant,,ENST00000380818,;TAF9,intron_variant,,ENST00000328663,;RAD17,upstream_gene_variant,,ENST00000358030,;RAD17,upstream_gene_variant,,ENST00000354868,;TAF9,upstream_gene_variant,,ENST00000380822,;TAF9,upstream_gene_variant,,ENST00000509462,;TAF9,upstream_gene_variant,,ENST00000503245,;RAD17,upstream_gene_variant,,ENST00000506564,;RAD17,upstream_gene_variant,,ENST00000345306,;RAD17,upstream_gene_variant,,ENST00000305138,;TAF9,upstream_gene_variant,,ENST00000512152,;RAD17,upstream_gene_variant,,ENST00000282891,;RAD17,upstream_gene_variant,,ENST00000354312,;RAD17,upstream_gene_variant,,ENST00000509734,;RAD17,upstream_gene_variant,,ENST00000380774,;TAF9,upstream_gene_variant,,ENST00000504109,;RAD17,upstream_gene_variant,,ENST00000521422,;TAF9,upstream_gene_variant,,ENST00000506736,;RAD17,upstream_gene_variant,,ENST00000512785,;TAF9,upstream_gene_variant,,ENST00000512561,;TAF9,upstream_gene_variant,,ENST00000508954,;RAD17,intron_variant,,ENST00000514066,;RAD17,upstream_gene_variant,,ENST00000504177,;RAD17,upstream_gene_variant,,ENST00000511349,;TAF9,upstream_gene_variant,,ENST00000502819,;	C	ENSG00000085231	ENST00000328663	Transcript	intron_variant	.	.	.	.	.	rs532216259	.	.	-1	TAF9	HGNC	11542	protein_coding	YES	CCDS4002.1	ENSP00000370193	TAF9_HUMAN	D6RIY1_HUMAN,D6RIV9_HUMAN,D6RIE8_HUMAN,D6RHW1_HUMAN,D6RGK3_HUMAN	UPI000000D8A6	.	.	.	.	1/2	.	A:0.0004	A:0	A:0.0014	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAGGAGCCG	byFrequency|by1000G	2	ESCA
ASCC3	0	.	GRCh37	6	101099510	101099510	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3001C>G	p.Leu1001Val	p.L1001V	ENST00000369162	19/42	159	123	36	142	142	0	ASCC3,missense_variant,p.Leu1001Val,ENST00000369162,;ASCC3,3_prime_UTR_variant,,ENST00000324696,;	C	ENSG00000112249	ENST00000369162	Transcript	missense_variant	3346	3001	1001	L/V	Ctc/Gtc	COSM370213	.	.	-1	ASCC3	HGNC	18697	protein_coding	YES	CCDS5046.1	ENSP00000358159	ASCC3_HUMAN	E5RFZ0_HUMAN	UPI000014145A	.	tolerated(0.05)	benign(0.026)	19/42	.	hmmpanther:PTHR11752:SF8,hmmpanther:PTHR11752,Pfam_domain:PF02889,SMART_domains:SM00611,SMART_domains:SM00973	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGTTCAT	.	5	ESCA
NCOA7	0	.	GRCh37	6	126210540	126210540	+	Missense_Mutation	SNP	G	G	A	rs377026001	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1340G>A	p.Arg447Gln	p.R447Q	ENST00000368357	10/17	58	54	4	54	54	0	NCOA7,missense_variant,p.Arg447Gln,ENST00000392477,;NCOA7,missense_variant,p.Arg332Gln,ENST00000229634,;NCOA7,missense_variant,p.Arg447Gln,ENST00000368357,;NCOA7,missense_variant,p.Arg245Gln,ENST00000413085,;	A	ENSG00000111912	ENST00000368357	Transcript	missense_variant	1692	1340	447	R/Q	cGa/cAa	rs377026001	.	.	1	NCOA7	HGNC	21081	protein_coding	YES	CCDS5132.1	ENSP00000357341	NCOA7_HUMAN	Q8N3C8_HUMAN,Q5TF98_HUMAN,Q5TF97_HUMAN,Q5TF96_HUMAN,Q3ZTS4_HUMAN	UPI00001AE66D	.	tolerated_low_confidence(0.61)	benign(0.001)	10/17	.	hmmpanther:PTHR23354:SF68,hmmpanther:PTHR23354	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAACGAAAGA	byFrequency|byCluster	2	ESCA
SOGA3	0	.	GRCh37	6	127834136	127834136	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1385G>T	p.Arg462Ile	p.R462I	ENST00000556132	4/12	63	40	22	53	53	0	SOGA3,missense_variant,p.Arg462Ile,ENST00000525778,;SOGA3,missense_variant,p.Arg462Ile,ENST00000556132,;SOGA3,missense_variant,p.Arg462Ile,ENST00000465909,;SOGA3,missense_variant,p.Arg462Ile,ENST00000368268,;SOGA3,downstream_gene_variant,,ENST00000467753,;SOGA3,missense_variant,p.Arg462Ile,ENST00000481848,;	A	ENSG00000214338	ENST00000556132	Transcript	missense_variant	2250	1385	462	R/I	aGa/aTa	.	.	.	-1	SOGA3	HGNC	21494	protein_coding	YES	CCDS43505.1	ENSP00000451768	SOGA3_HUMAN	A5PLQ8_HUMAN	UPI0000419273	.	deleterious(0)	probably_damaging(0.998)	4/12	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTCTCTTT	.	5	ESCA
SHPRH	0	.	GRCh37	6	146243864	146243864	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3654A>G	p.%3D	p.P1218P	ENST00000367505	19/30	80	66	14	62	62	0	SHPRH,synonymous_variant,p.%3D,ENST00000275233,;SHPRH,synonymous_variant,p.%3D,ENST00000438092,;SHPRH,synonymous_variant,p.%3D,ENST00000367505,;SHPRH,synonymous_variant,p.%3D,ENST00000367503,;SHPRH,3_prime_UTR_variant,,ENST00000519632,;SHPRH,3_prime_UTR_variant,,ENST00000433355,;SHPRH,non_coding_transcript_exon_variant,,ENST00000523276,;	C	ENSG00000146414	ENST00000367505	Transcript	synonymous_variant	3919	3654	1218	P	ccA/ccG	.	.	.	-1	SHPRH	HGNC	19336	protein_coding	YES	CCDS43513.2	ENSP00000356475	SHPRH_HUMAN	.	UPI0000458A24	.	.	.	19/30	.	hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGATGGAGG	.	5	ESCA
QKI	0	.	GRCh37	6	163956011	163956011	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403-3T>A	.	.	ENST00000361752	.	75	62	12	74	74	0	QKI,splice_region_variant,,ENST00000544823,;QKI,splice_region_variant,,ENST00000537041,;QKI,splice_region_variant,,ENST00000424802,;QKI,splice_region_variant,,ENST00000361195,;QKI,splice_region_variant,,ENST00000453779,;QKI,splice_region_variant,,ENST00000537883,;QKI,splice_region_variant,,ENST00000275262,;QKI,splice_region_variant,,ENST00000544436,;QKI,splice_region_variant,,ENST00000392127,;QKI,splice_region_variant,,ENST00000361752,;QKI,upstream_gene_variant,,ENST00000544361,;QKI,splice_region_variant,,ENST00000545346,;QKI,splice_region_variant,,ENST00000361758,;QKI,splice_region_variant,,ENST00000545607,;QKI,non_coding_transcript_exon_variant,,ENST00000540719,;	A	ENSG00000112531	ENST00000361752	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	QKI	HGNC	21100	protein_coding	YES	CCDS5285.1	ENSP00000355094	QKI_HUMAN	F5H8C8_HUMAN,F5H5U6_HUMAN,F5GYM3_HUMAN	UPI0000029EBD	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTTAGGAG	.	4	ESCA
FRMD1	0	.	GRCh37	6	168461507	168461507	+	Missense_Mutation	SNP	C	C	T	rs775050650	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1276G>A	p.Glu426Lys	p.E426K	ENST00000283309	9/11	73	45	27	58	58	0	FRMD1,missense_variant,p.Glu197Lys,ENST00000537786,;FRMD1,missense_variant,p.Glu358Lys,ENST00000440994,;FRMD1,missense_variant,p.Glu426Lys,ENST00000283309,;FRMD1,downstream_gene_variant,,ENST00000511714,;FRMD1,non_coding_transcript_exon_variant,,ENST00000432403,;FRMD1,3_prime_UTR_variant,,ENST00000509157,;FRMD1,3_prime_UTR_variant,,ENST00000468647,;FRMD1,non_coding_transcript_exon_variant,,ENST00000336070,;FRMD1,non_coding_transcript_exon_variant,,ENST00000358587,;FRMD1,downstream_gene_variant,,ENST00000506415,;	T	ENSG00000153303	ENST00000283309	Transcript	missense_variant	1341	1276	426	E/K	Gag/Aag	rs775050650	.	.	-1	FRMD1	HGNC	21240	protein_coding	YES	CCDS5306.1	ENSP00000283309	FRMD1_HUMAN	F5GXR0_HUMAN	UPI000013F36A	.	tolerated(0.14)	benign(0.021)	9/11	.	hmmpanther:PTHR13429,hmmpanther:PTHR13429:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCATGGA	.	5	ESCA
HIST1H3C	0	.	GRCh37	6	26045940	26045940	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302T>A	p.Leu101Gln	p.L101Q	ENST00000540144	1/1	86	52	34	120	120	0	HIST1H3C,missense_variant,p.Leu101Gln,ENST00000540144,;HIST1H2BB,upstream_gene_variant,,ENST00000357905,;U91328.2,downstream_gene_variant,,ENST00000454320,;	A	ENSG00000196532	ENST00000540144	Transcript	missense_variant	302	302	101	L/Q	cTg/cAg	.	.	.	1	HIST1H3C	HGNC	4768	protein_coding	YES	CCDS4576.1	ENSP00000439493	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0.01)	probably_damaging(1)	1/1	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CTACCTGGTGG	.	2	ESCA
HIST1H2AH	0	.	GRCh37	6	27115271	27115271	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364G>C	p.Glu122Gln	p.E122Q	ENST00000377459	1/1	93	58	35	98	98	0	HIST1H2AH,missense_variant,p.Glu122Gln,ENST00000377459,;HIST1H2BK,upstream_gene_variant,,ENST00000356950,;HIST1H2BK,upstream_gene_variant,,ENST00000396891,;MIR3143,upstream_gene_variant,,ENST00000584253,;	C	ENSG00000184825	ENST00000377459	Transcript	missense_variant	411	364	122	E/Q	Gag/Cag	.	.	.	1	HIST1H2AH	HGNC	13671	protein_coding	YES	CCDS4622.1	ENSP00000366679	H2A1H_HUMAN	A3KPC7_HUMAN	UPI0000073C8A	.	tolerated_low_confidence(0.07)	benign(0.032)	1/1	.	hmmpanther:PTHR23430:SF24,hmmpanther:PTHR23430,Gene3D:1.10.20.10,SMART_domains:SM00414	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTGAGAGC	.	5	ESCA
OR2W1	0	.	GRCh37	6	29012660	29012660	+	Missense_Mutation	SNP	A	A	T	rs746849819	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.293T>A	p.Ile98Asn	p.I98N	ENST00000377175	1/1	24	10	14	29	29	0	OR2W1,missense_variant,p.Ile98Asn,ENST00000377175,;	T	ENSG00000204704	ENST00000377175	Transcript	missense_variant	358	293	98	I/N	aTc/aAc	rs746849819	.	.	-1	OR2W1	HGNC	8281	protein_coding	YES	CCDS4656.1	ENSP00000366380	OR2W1_HUMAN	.	UPI000003FF8A	.	deleterious(0)	benign(0.248)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF169,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGATACAA	byFrequency	5	ESCA
HSPA1A	0	.	GRCh37	6	31783686	31783686	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153C>T	p.%3D	p.I51I	ENST00000375651	1/1	25	9	16	34	34	0	HSPA1A,synonymous_variant,p.%3D,ENST00000375651,;HSPA1A,intron_variant,,ENST00000458062,;HSPA1A,intron_variant,,ENST00000608703,;HSPA1L,upstream_gene_variant,,ENST00000417199,;HSPA1L,upstream_gene_variant,,ENST00000375654,;	T	ENSG00000204389	ENST00000375651	Transcript	synonymous_variant	396	153	51	I	atC/atT	.	.	.	1	HSPA1A	HGNC	5232	protein_coding	YES	CCDS34414.1	ENSP00000364802	HSP71_HUMAN	A8K5I0_HUMAN	UPI0000000C40	.	.	.	1/1	.	Superfamily_domains:SSF53067,Pfam_domain:PF00012,Gene3D:3.30.420.40,hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CTCATCGGGGA	.	3	ESCA
PRICKLE4	0	.	GRCh37	6	41754765	41754771	+	Frame_Shift_Del	DEL	AGGATTT	AGGATTT	-	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	AGGATTT	AGGATTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1053_1059delAGGATTT	p.Glu351AspfsTer3	p.E351Dfs*3	ENST00000458694	8/8	77	65	12	76	76	0	PRICKLE4,frameshift_variant,p.Glu351AspfsTer3,ENST00000394263,;PRICKLE4,frameshift_variant,p.Glu311AspfsTer3,ENST00000394260,;PRICKLE4,frameshift_variant,p.Glu351AspfsTer3,ENST00000458694,;PRICKLE4,downstream_gene_variant,,ENST00000359201,;FRS3,upstream_gene_variant,,ENST00000422888,;TOMM6,upstream_gene_variant,,ENST00000398881,;PRICKLE4,downstream_gene_variant,,ENST00000394259,;USP49,downstream_gene_variant,,ENST00000394253,;TOMM6,upstream_gene_variant,,ENST00000398884,;RP11-298J23.9,upstream_gene_variant,,ENST00000594586,;PRICKLE4,downstream_gene_variant,,ENST00000463606,;PRICKLE4,frameshift_variant,p.Glu351AspfsTer3,ENST00000335515,;PRICKLE4,3_prime_UTR_variant,,ENST00000456057,;PRICKLE4,non_coding_transcript_exon_variant,,ENST00000487182,;PRICKLE4,downstream_gene_variant,,ENST00000483200,;	-	ENSG00000124593	ENST00000458694	Transcript	frameshift_variant	1301-1307	1053-1059	351-353	EGF/X	gaAGGATTT/ga	.	.	.	1	PRICKLE4	HGNC	16805	protein_coding	YES	CCDS34449.1	ENSP00000404911	PRIC4_HUMAN	.	UPI000020DCD5	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCTGAAGGATTTTTCTT	.	3	ESCA
TDRD6	0	.	GRCh37	6	46658264	46658264	+	Missense_Mutation	SNP	C	C	G	rs375428009	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2399C>G	p.Thr800Ser	p.T800S	ENST00000316081	1/4	41	28	13	41	41	0	TDRD6,missense_variant,p.Thr800Ser,ENST00000316081,;TDRD6,missense_variant,p.Thr800Ser,ENST00000544460,;TDRD6,upstream_gene_variant,,ENST00000450697,;RP11-446F17.3,upstream_gene_variant,,ENST00000422284,;RP11-446F17.3,upstream_gene_variant,,ENST00000571590,;RP11-446F17.3,upstream_gene_variant,,ENST00000434329,;	G	ENSG00000180113	ENST00000316081	Transcript	missense_variant	2399	2399	800	T/S	aCt/aGt	rs375428009	.	.	1	TDRD6	HGNC	21339	protein_coding	YES	CCDS34470.1	ENSP00000346065	TDRD6_HUMAN	.	UPI0000251E8A	.	tolerated(0.22)	benign(0.034)	1/4	.	Superfamily_domains:SSF63748,Gene3D:2.30.30.140,Pfam_domain:PF00567,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAACTCTAA	byFrequency|byCluster	5	ESCA
B3GAT2	0	.	GRCh37	6	71666093	71666093	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40C>T	p.Pro14Ser	p.P14S	ENST00000230053	1/4	69	43	26	79	79	0	B3GAT2,missense_variant,p.Pro14Ser,ENST00000230053,;	A	ENSG00000112309	ENST00000230053	Transcript	missense_variant	649	40	14	P/S	Ccc/Tcc	.	.	.	-1	B3GAT2	HGNC	922	protein_coding	YES	CCDS4974.1	ENSP00000230053	B3GA2_HUMAN	A8K1V3_HUMAN	UPI000012670C	.	deleterious(0)	probably_damaging(0.998)	1/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10896:SF8,hmmpanther:PTHR10896	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGGCAGGA	.	5	ESCA
BMP6	0	.	GRCh37	6	7880462	7880462	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1428G>A	p.%3D	p.P476P	ENST00000283147	7/7	52	48	4	69	69	0	BMP6,synonymous_variant,p.%3D,ENST00000283147,;TXNDC5,downstream_gene_variant,,ENST00000539054,;TXNDC5,downstream_gene_variant,,ENST00000379757,;TXNDC5,downstream_gene_variant,,ENST00000473453,;TXNDC5,downstream_gene_variant,,ENST00000475802,;BLOC1S5-TXNDC5,downstream_gene_variant,,ENST00000439343,;TXNDC5,downstream_gene_variant,,ENST00000460138,;	A	ENSG00000153162	ENST00000283147	Transcript	synonymous_variant	1587	1428	476	P	ccG/ccA	.	.	.	1	BMP6	HGNC	1073	protein_coding	YES	CCDS4503.1	ENSP00000283147	BMP6_HUMAN	B4DUF7_HUMAN	UPI0000126A2D	.	.	.	7/7	.	PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF137,hmmpanther:PTHR11848,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAACCGTGCTG	.	3	ESCA
FUT9	0	.	GRCh37	6	96655745	96655745	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3634G>T	.	.	ENST00000302103	3/3	113	75	37	97	97	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	T	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	5040	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTGAATTG	.	5	ESCA
RINT1	0	.	GRCh37	7	105189044	105189044	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.883T>C	p.Ser295Pro	p.S295P	ENST00000257700	7/15	50	37	13	48	48	0	RINT1,missense_variant,p.Ser295Pro,ENST00000257700,;RINT1,downstream_gene_variant,,ENST00000493041,;RINT1,3_prime_UTR_variant,,ENST00000497979,;RINT1,downstream_gene_variant,,ENST00000467392,;RINT1,upstream_gene_variant,,ENST00000474123,;RINT1,downstream_gene_variant,,ENST00000493258,;	C	ENSG00000135249	ENST00000257700	Transcript	missense_variant	1114	883	295	S/P	Tct/Cct	.	.	.	1	RINT1	HGNC	21876	protein_coding	YES	CCDS34726.1	ENSP00000257700	RINT1_HUMAN	.	UPI000020F898	.	tolerated(0.26)	benign(0.001)	7/15	.	PROSITE_profiles:PS51386,hmmpanther:PTHR13520:SF0,hmmpanther:PTHR13520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATACTCTCTT	.	5	ESCA
PHF14	0	.	GRCh37	7	11068417	11068417	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1427G>T	p.Gly476Val	p.G476V	ENST00000403050	7/17	43	28	14	59	59	0	PHF14,missense_variant,p.Gly191Val,ENST00000445996,;PHF14,missense_variant,p.Gly476Val,ENST00000403050,;PHF14,downstream_gene_variant,,ENST00000476009,;PHF14,3_prime_UTR_variant,,ENST00000521747,;PHF14,3_prime_UTR_variant,,ENST00000423760,;PHF14,non_coding_transcript_exon_variant,,ENST00000490957,;	T	ENSG00000106443	ENST00000403050	Transcript	missense_variant	1879	1427	476	G/V	gGt/gTt	COSM1447275	.	.	1	PHF14	HGNC	22203	protein_coding	YES	CCDS47542.1	ENSP00000385795	PHF14_HUMAN	.	UPI000020EB41	.	deleterious(0)	probably_damaging(1)	7/17	.	hmmpanther:PTHR13793:SF10,hmmpanther:PTHR13793,Pfam_domain:PF13832,SMART_domains:SM00249	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGGTCTGC	.	5	ESCA
DOCK4	0	.	GRCh37	7	111366639	111366639	+	3'Flank	SNP	C	C	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000437633	.	60	45	15	49	49	0	DOCK4,3_prime_UTR_variant,,ENST00000428084,;DOCK4,3_prime_UTR_variant,,ENST00000423057,;DOCK4,downstream_gene_variant,,ENST00000445943,;DOCK4,downstream_gene_variant,,ENST00000494651,;DOCK4,downstream_gene_variant,,ENST00000437633,;DOCK4,downstream_gene_variant,,ENST00000494769,;DOCK4,downstream_gene_variant,,ENST00000486186,;	G	ENSG00000128512	ENST00000437633	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1637	-1	DOCK4	HGNC	19192	protein_coding	YES	CCDS47688.1	ENSP00000404179	DOCK4_HUMAN	Q75MU6_HUMAN	UPI0000D5BB0D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCAATTA	.	5	ESCA
CNTNAP2	0	.	GRCh37	7	147092722	147092722	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1520A>C	p.Asn507Thr	p.N507T	ENST00000361727	10/24	97	74	23	59	59	0	CNTNAP2,missense_variant,p.Asn507Thr,ENST00000361727,;	C	ENSG00000174469	ENST00000361727	Transcript	missense_variant	2036	1520	507	N/T	aAc/aCc	COSM1248651,COSM3879066	.	.	1	CNTNAP2	HGNC	13830	protein_coding	YES	CCDS5889.1	ENSP00000354778	CNTP2_HUMAN	Q9UDV4_HUMAN,Q96T77_HUMAN,Q86UL9_HUMAN,Q86UL6_HUMAN,Q86UL4_HUMAN,Q86UJ1_HUMAN,Q86UI8_HUMAN,Q75MQ9_HUMAN,Q75MF8_HUMAN,Q75MF6_HUMAN,Q75MD4_HUMAN,Q75MA1_HUMAN,Q75M92_HUMAN,Q75LG9_HUMAN,O75852_HUMAN,B7Z1Y6_HUMAN	UPI00001285FA	.	tolerated(0.42)	benign(0.008)	10/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF4,hmmpanther:PTHR10127,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATAACTCAA	.	5	ESCA
GALNTL5	0	.	GRCh37	7	151711785	151711785	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1083C>A	p.%3D	p.I361I	ENST00000392800	8/9	107	80	27	54	54	0	GALNTL5,synonymous_variant,p.%3D,ENST00000431418,;GALNTL5,synonymous_variant,p.%3D,ENST00000392800,;GALNTL5,3_prime_UTR_variant,,ENST00000426341,;GALNTL5,3_prime_UTR_variant,,ENST00000416062,;GALNTL5,3_prime_UTR_variant,,ENST00000448366,;GALNTL5,3_prime_UTR_variant,,ENST00000414073,;GALNTL5,3_prime_UTR_variant,,ENST00000416269,;	A	ENSG00000106648	ENST00000392800	Transcript	synonymous_variant	1337	1083	361	I	atC/atA	.	.	.	1	GALNTL5	HGNC	21725	protein_coding	YES	CCDS5929.1	ENSP00000376548	GLTL5_HUMAN	.	UPI000013C82E	.	.	.	8/9	.	Superfamily_domains:SSF53448,Gene3D:3.90.550.10,hmmpanther:PTHR11675:SF17,hmmpanther:PTHR11675	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G359G|c.1077A>G|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATATCAGTAA	.	5	ESCA
ABCB5	0	.	GRCh37	7	20766663	20766663	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2626A>G	p.Ile876Val	p.I876V	ENST00000404938	22/28	38	26	12	40	40	0	ABCB5,missense_variant,p.Ile431Val,ENST00000258738,;ABCB5,missense_variant,p.Ile876Val,ENST00000404938,;ABCB5,missense_variant,p.Ile43Val,ENST00000441315,;	G	ENSG00000004846	ENST00000404938	Transcript	missense_variant	3278	2626	876	I/V	Ata/Gta	.	.	.	1	ABCB5	HGNC	46	protein_coding	YES	CCDS55090.1	ENSP00000384881	ABCB5_HUMAN	.	UPI000173A253	.	tolerated(0.2)	benign(0.028)	22/28	.	PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF2,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAAGATAGCA	.	5	ESCA
KLHL7	0	.	GRCh37	7	23165551	23165551	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442+760G>A	.	.	ENST00000339077	.	15	12	3	26	26	0	KLHL7,3_prime_UTR_variant,,ENST00000410047,;KLHL7,3_prime_UTR_variant,,ENST00000322275,;KLHL7,intron_variant,,ENST00000409689,;KLHL7,intron_variant,,ENST00000539124,;KLHL7,intron_variant,,ENST00000339077,;KLHL7,intron_variant,,ENST00000322231,;KLHL7,intron_variant,,ENST00000545443,;KLHL7,intron_variant,,ENST00000542558,;KLHL7,downstream_gene_variant,,ENST00000545771,;KLHL7,intron_variant,,ENST00000459661,;KLHL7,intron_variant,,ENST00000479288,;KLHL7,downstream_gene_variant,,ENST00000479700,;KLHL7,non_coding_transcript_exon_variant,,ENST00000477076,;KLHL7,intron_variant,,ENST00000521082,;KLHL7,downstream_gene_variant,,ENST00000491352,;AK3P3,upstream_gene_variant,,ENST00000431883,;	A	ENSG00000122550	ENST00000339077	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KLHL7	HGNC	15646	protein_coding	YES	CCDS34609.1	ENSP00000343273	KLHL7_HUMAN	E5RFN1_HUMAN,B7Z4N7_HUMAN,B7Z3P9_HUMAN	UPI0000037B12	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTACTGAATCC	.	2	ESCA
BRAT1	0	.	GRCh37	7	2581386	2581386	+	Missense_Mutation	SNP	C	C	T	rs774408317	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1100G>A	p.Arg367His	p.R367H	ENST00000340611	8/14	40	36	3	57	57	0	BRAT1,missense_variant,p.Arg367His,ENST00000340611,;BRAT1,upstream_gene_variant,,ENST00000473879,;BRAT1,non_coding_transcript_exon_variant,,ENST00000469750,;BRAT1,non_coding_transcript_exon_variant,,ENST00000493232,;BRAT1,non_coding_transcript_exon_variant,,ENST00000467558,;BRAT1,downstream_gene_variant,,ENST00000421712,;	T	ENSG00000106009	ENST00000340611	Transcript	missense_variant	1357	1100	367	R/H	cGc/cAc	rs774408317	.	.	-1	BRAT1	HGNC	21701	protein_coding	YES	CCDS5334.1	ENSP00000339637	BRAT1_HUMAN	F8WDN5_HUMAN	UPI00001AEB20	.	deleterious(0.05)	benign(0.007)	8/14	.	hmmpanther:PTHR21331,hmmpanther:PTHR21331:SF1,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGTGCGGCAC	byFrequency	3	ESCA
NOD1	0	.	GRCh37	7	30491759	30491759	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1274T>G	p.Phe425Cys	p.F425C	ENST00000222823	6/14	21	7	14	45	45	0	NOD1,missense_variant,p.Phe425Cys,ENST00000222823,;NOD1,3_prime_UTR_variant,,ENST00000423334,;NOD1,downstream_gene_variant,,ENST00000419601,;NOD1,downstream_gene_variant,,ENST00000413433,;NOD1,downstream_gene_variant,,ENST00000419799,;NOD1,downstream_gene_variant,,ENST00000411552,;NOD1,missense_variant,p.Phe425Cys,ENST00000434755,;NOD1,upstream_gene_variant,,ENST00000489614,;	C	ENSG00000106100	ENST00000222823	Transcript	missense_variant	1800	1274	425	F/C	tTc/tGc	.	.	.	-1	NOD1	HGNC	16390	protein_coding	YES	CCDS5427.1	ENSP00000222823	NOD1_HUMAN	Q7Z2K1_HUMAN,C9J8X8_HUMAN	UPI00000375EE	.	deleterious(0)	probably_damaging(0.998)	6/14	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF18,PROSITE_profiles:PS50837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGGAAGACA	.	5	ESCA
GHRHR	0	.	GRCh37	7	31003737	31003737	+	Silent	SNP	G	G	C	rs759152551	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54G>C	p.%3D	p.P18P	ENST00000326139	1/13	139	98	41	137	137	0	GHRHR,synonymous_variant,p.%3D,ENST00000326139,;GHRHR,intron_variant,,ENST00000466427,;	C	ENSG00000106128	ENST00000326139	Transcript	synonymous_variant	100	54	18	P	ccG/ccC	rs759152551	.	.	1	GHRHR	HGNC	4266	protein_coding	YES	CCDS5432.1	ENSP00000320180	GHRHR_HUMAN	P78471_HUMAN,P78470_HUMAN	UPI0000061EE1	.	.	.	1/13	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12011:SF209,hmmpanther:PTHR12011,Superfamily_domains:SSF111418,Prints_domain:PR01352	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACCGACCGT	.	5	ESCA
HECW1	0	.	GRCh37	7	43602253	43602253	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*728G>T	.	.	ENST00000395891	30/30	21	14	6	22	22	0	HECW1,3_prime_UTR_variant,,ENST00000395891,;HECW1,downstream_gene_variant,,ENST00000453890,;	T	ENSG00000002746	ENST00000395891	Transcript	3_prime_UTR_variant	6154	.	.	.	.	.	.	.	1	HECW1	HGNC	22195	protein_coding	YES	CCDS5469.2	ENSP00000379228	HECW1_HUMAN	A4D1V5_HUMAN	UPI0000D74C41	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGAGAAGTT	.	5	ESCA
PURB	0	.	GRCh37	7	44924094	44924094	+	Missense_Mutation	SNP	C	C	A	rs140765435	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.854G>T	p.Arg285Leu	p.R285L	ENST00000395699	1/1	81	60	21	72	72	0	PURB,missense_variant,p.Arg285Leu,ENST00000395699,;MIR4657,upstream_gene_variant,,ENST00000578157,;RP4-673M15.1,upstream_gene_variant,,ENST00000608450,;	A	ENSG00000146676	ENST00000395699	Transcript	missense_variant	867	854	285	R/L	cGa/cTa	rs140765435	.	.	-1	PURB	HGNC	9702	protein_coding	YES	CCDS5499.1	ENSP00000379051	PURB_HUMAN	.	UPI000006F6CE	.	tolerated(0.1)	possibly_damaging(0.518)	1/1	.	hmmpanther:PTHR12611,hmmpanther:PTHR12611:SF4	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTCGTTCC	.	5	ESCA
ADCY1	0	.	GRCh37	7	45754245	45754245	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*651G>A	.	.	ENST00000297323	20/20	30	27	3	34	34	0	ADCY1,3_prime_UTR_variant,,ENST00000297323,;	A	ENSG00000164742	ENST00000297323	Transcript	3_prime_UTR_variant	4033	.	.	.	.	.	.	.	1	ADCY1	HGNC	232	protein_coding	YES	CCDS34631.1	ENSP00000297323	ADCY1_HUMAN	Q8NFM5_HUMAN,D3DVL8_HUMAN	UPI0000199C4A	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCTGCTGGC	.	2	ESCA
POM121L12	0	.	GRCh37	7	53103931	53103931	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567C>A	p.Ser189Arg	p.S189R	ENST00000408890	1/1	71	60	11	63	63	0	POM121L12,missense_variant,p.Ser189Arg,ENST00000408890,;	A	ENSG00000221900	ENST00000408890	Transcript	missense_variant	583	567	189	S/R	agC/agA	COSM332492	.	.	1	POM121L12	HGNC	25369	protein_coding	YES	CCDS43584.1	ENSP00000386133	P1L12_HUMAN	.	UPI00001B6540	.	tolerated(0.89)	probably_damaging(0.933)	1/1	.	hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF25,Pfam_domain:PF15229	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGCGCTAG	.	5	ESCA
MIOS	0	.	GRCh37	7	7628156	7628156	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1846A>G	p.Arg616Gly	p.R616G	ENST00000340080	8/13	55	49	6	57	57	0	MIOS,missense_variant,p.Arg616Gly,ENST00000405785,;MIOS,missense_variant,p.Arg616Gly,ENST00000340080,;MIOS,non_coding_transcript_exon_variant,,ENST00000493227,;	G	ENSG00000164654	ENST00000340080	Transcript	missense_variant	2267	1846	616	R/G	Aga/Gga	.	.	.	1	MIOS	HGNC	21905	protein_coding	YES	CCDS43554.1	ENSP00000339881	MIO_HUMAN	C9JUE6_HUMAN,C9JTV2_HUMAN,C9JAQ1_HUMAN	UPI000020EB0B	.	deleterious(0)	probably_damaging(0.996)	8/13	.	hmmpanther:PTHR16453	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GTGACAGAGTG	.	2	ESCA
SMURF1	0	.	GRCh37	7	98649881	98649881	+	Missense_Mutation	SNP	G	G	A	rs371859465	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668C>T	p.Thr223Met	p.T223M	ENST00000361125	7/19	69	54	15	35	35	0	SMURF1,missense_variant,p.Thr223Met,ENST00000361125,;SMURF1,missense_variant,p.Thr223Met,ENST00000361368,;AC004893.11,downstream_gene_variant,,ENST00000482799,;AC004893.11,downstream_gene_variant,,ENST00000468960,;SMURF1,non_coding_transcript_exon_variant,,ENST00000480055,;SMURF1,downstream_gene_variant,,ENST00000472627,;	A	ENSG00000198742	ENST00000361125	Transcript	missense_variant	988	668	223	T/M	aCg/aTg	rs371859465	.	.	-1	SMURF1	HGNC	16807	protein_coding	YES	CCDS34690.1	ENSP00000354621	SMUF1_HUMAN	D6W5S0_HUMAN	UPI00000015C4	.	tolerated(0.11)	benign(0.078)	7/19	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF293,PIRSF_domain:PIRSF001569	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCGTCTGT	byFrequency|byCluster	5	ESCA
CSMD3	0	.	GRCh37	8	113563014	113563014	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4450G>T	p.Glu1484Ter	p.E1484*	ENST00000297405	27/71	114	80	34	72	72	0	CSMD3,stop_gained,p.Glu1484Ter,ENST00000352409,;CSMD3,stop_gained,p.Glu1380Ter,ENST00000455883,;CSMD3,stop_gained,p.Glu1484Ter,ENST00000297405,;CSMD3,stop_gained,p.Glu824Ter,ENST00000339701,;CSMD3,stop_gained,p.Glu1444Ter,ENST00000343508,;	A	ENSG00000164796	ENST00000297405	Transcript	stop_gained	4695	4450	1484	E/*	Gaa/Taa	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	.	.	27/71	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTCCTTTA	.	5	ESCA
ATAD2	0	.	GRCh37	8	124358392	124358392	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2466A>G	p.%3D	p.V822V	ENST00000287394	18/28	85	49	35	66	66	0	ATAD2,synonymous_variant,p.%3D,ENST00000287394,;ATAD2,synonymous_variant,p.%3D,ENST00000521903,;RNU6-875P,downstream_gene_variant,,ENST00000516488,;MIR548D1,upstream_gene_variant,,ENST00000384971,;ATAD2,3_prime_UTR_variant,,ENST00000517666,;ATAD2,3_prime_UTR_variant,,ENST00000519124,;ATAD2,non_coding_transcript_exon_variant,,ENST00000521496,;	C	ENSG00000156802	ENST00000287394	Transcript	synonymous_variant	2574	2466	822	V	gtA/gtG	.	.	.	-1	ATAD2	HGNC	30123	protein_coding	YES	CCDS6343.1	ENSP00000287394	ATAD2_HUMAN	.	UPI0000052A8C	.	.	.	18/28	.	hmmpanther:PTHR23069,hmmpanther:PTHR23069:SF1,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTATATACAGT	.	5	ESCA
ZNF250	0	.	GRCh37	8	146105601	146105601	+	3'UTR	SNP	C	C	A	rs571960149	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1299G>T	.	.	ENST00000292579	6/6	14	7	6	19	19	0	ZNF250,3_prime_UTR_variant,,ENST00000292579,;ZNF250,intron_variant,,ENST00000342660,;ZNF250,intron_variant,,ENST00000543949,;ZNF250,downstream_gene_variant,,ENST00000533622,;ZNF250,downstream_gene_variant,,ENST00000417550,;ZNF250,downstream_gene_variant,,ENST00000533221,;ZNF250,downstream_gene_variant,,ENST00000525694,;ZNF250,intron_variant,,ENST00000529780,;ZNF250,intron_variant,,ENST00000528258,;ZNF250,intron_variant,,ENST00000533543,;	A	ENSG00000196150	ENST00000292579	Transcript	3_prime_UTR_variant	3099	.	.	.	.	rs571960149	.	.	-1	ZNF250	HGNC	13044	protein_coding	YES	CCDS34972.1	ENSP00000292579	ZN250_HUMAN	.	UPI0000197F51	.	.	.	6/6	.	.	A:0.0014	A:0.003	A:0	.	A:0.001	A:0.001	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAACCCCTT	byFrequency|by1000G	5	ESCA
ST18	0	.	GRCh37	8	53025816	53025816	+	Missense_Mutation	SNP	G	G	A	rs533229892	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3086C>T	p.Pro1029Leu	p.P1029L	ENST00000276480	26/26	59	32	27	52	52	0	ST18,missense_variant,p.Pro1029Leu,ENST00000276480,;ST18,3_prime_UTR_variant,,ENST00000521824,;ST18,3_prime_UTR_variant,,ENST00000522251,;ST18,3_prime_UTR_variant,,ENST00000521582,;ST18,downstream_gene_variant,,ENST00000518053,;	A	ENSG00000147488	ENST00000276480	Transcript	missense_variant	3770	3086	1029	P/L	cCg/cTg	rs533229892,COSM3925371	.	.	-1	ST18	HGNC	18695	protein_coding	YES	CCDS6149.1	ENSP00000276480	ST18_HUMAN	E5RHS3_HUMAN	UPI0000046C30	.	deleterious(0)	probably_damaging(1)	26/26	.	hmmpanther:PTHR10816:SF9,hmmpanther:PTHR10816	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCCGGGGAA	by1000G	5	ESCA
TOX	0	.	GRCh37	8	59718243	59718243	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2063C>G	.	.	ENST00000361421	9/9	156	122	34	133	133	0	TOX,3_prime_UTR_variant,,ENST00000361421,;	C	ENSG00000198846	ENST00000361421	Transcript	3_prime_UTR_variant	3865	.	.	.	.	.	.	.	-1	TOX	HGNC	18988	protein_coding	YES	CCDS34897.1	ENSP00000354842	TOX_HUMAN	B4DYA1_HUMAN	UPI0000070A73	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTAGTTAAT	.	5	ESCA
MMP16	0	.	GRCh37	8	89046539	89046539	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7150G>A	.	.	ENST00000286614	10/10	69	43	25	68	68	0	MMP16,3_prime_UTR_variant,,ENST00000286614,;	T	ENSG00000156103	ENST00000286614	Transcript	3_prime_UTR_variant	9256	.	.	.	.	.	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCAATAA	.	5	ESCA
SMC2	0	.	GRCh37	9	106860801	106860801	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393C>T	p.%3D	p.F131F	ENST00000286398	4/25	51	18	33	45	45	0	SMC2,synonymous_variant,p.%3D,ENST00000303219,;SMC2,synonymous_variant,p.%3D,ENST00000374793,;SMC2,synonymous_variant,p.%3D,ENST00000286398,;SMC2,synonymous_variant,p.%3D,ENST00000374787,;SMC2,5_prime_UTR_variant,,ENST00000440179,;	T	ENSG00000136824	ENST00000286398	Transcript	synonymous_variant	681	393	131	F	ttC/ttT	.	.	.	1	SMC2	HGNC	14011	protein_coding	YES	CCDS35086.1	ENSP00000286398	SMC2_HUMAN	Q5T821_HUMAN	UPI000013DE44	.	.	.	4/25	.	hmmpanther:PTHR18937:SF9,hmmpanther:PTHR18937,Pfam_domain:PF02463,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005719,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCTGTTC	.	5	ESCA
RAD23B	0	.	GRCh37	9	110092988	110092988	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1051T>G	.	.	ENST00000358015	10/10	51	21	30	56	56	0	RAD23B,3_prime_UTR_variant,,ENST00000358015,;RAD23B,intron_variant,,ENST00000457811,;RAD23B,downstream_gene_variant,,ENST00000416373,;	G	ENSG00000119318	ENST00000358015	Transcript	3_prime_UTR_variant	2632	.	.	.	.	.	.	.	1	RAD23B	HGNC	9813	protein_coding	YES	CCDS6769.1	ENSP00000350708	RD23B_HUMAN	Q5W0S5_HUMAN	UPI0000132F6C	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCATTAAAGT	.	5	ESCA
C9orf91	0	.	GRCh37	9	117386549	117386549	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.107-81G>A	.	.	ENST00000288502	.	23	9	14	14	14	0	C9orf91,intron_variant,,ENST00000374049,;C9orf91,intron_variant,,ENST00000288502,;C9orf91,non_coding_transcript_exon_variant,,ENST00000471206,;	A	ENSG00000157693	ENST00000288502	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C9orf91	HGNC	24513	protein_coding	YES	CCDS6808.1	ENSP00000288502	CI091_HUMAN	.	UPI00001B55A1	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGTGATGCC	.	5	ESCA
FAM129B	0	.	GRCh37	9	130286098	130286098	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.449C>T	p.Pro150Leu	p.P150L	ENST00000373312	5/14	18	8	10	36	36	0	FAM129B,missense_variant,p.Pro137Leu,ENST00000373314,;FAM129B,missense_variant,p.Pro150Leu,ENST00000373312,;FAM129B,intron_variant,,ENST00000468379,;FAM129B,intron_variant,,ENST00000478917,;FAM129B,intron_variant,,ENST00000484348,;FAM129B,downstream_gene_variant,,ENST00000476091,;	A	ENSG00000136830	ENST00000373312	Transcript	missense_variant	663	449	150	P/L	cCc/cTc	.	.	.	-1	FAM129B	HGNC	25282	protein_coding	YES	CCDS35145.1	ENSP00000362409	NIBL1_HUMAN	Q9H6L6_HUMAN	UPI00001592F0	.	deleterious(0.01)	probably_damaging(0.956)	5/14	.	PROSITE_profiles:PS50003,hmmpanther:PTHR14392:SF2,hmmpanther:PTHR14392,Gene3D:2.30.29.30,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGGGGGCA	.	5	ESCA
FAM102A	0	.	GRCh37	9	130742450	130742450	+	5'UTR	SNP	G	G	A	rs770496746	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-34C>T	.	.	ENST00000373095	1/11	39	13	26	52	52	0	FAM102A,5_prime_UTR_variant,,ENST00000373095,;FAM102A,non_coding_transcript_exon_variant,,ENST00000494606,;FAM102A,upstream_gene_variant,,ENST00000493175,;	A	ENSG00000167106	ENST00000373095	Transcript	5_prime_UTR_variant	343	.	.	.	.	rs770496746	.	.	-1	FAM102A	HGNC	31419	protein_coding	YES	CCDS35150.1	ENSP00000362187	F102A_HUMAN	.	UPI00005D3C96	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCGAAAAA	.	5	ESCA
TESK1	0	.	GRCh37	9	35609251	35609251	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1393G>A	p.Glu465Lys	p.E465K	ENST00000336395	10/10	55	43	12	41	41	0	TESK1,missense_variant,p.Glu465Lys,ENST00000336395,;CD72,downstream_gene_variant,,ENST00000259633,;CD72,downstream_gene_variant,,ENST00000396757,;MIR4667,downstream_gene_variant,,ENST00000578933,;TESK1,non_coding_transcript_exon_variant,,ENST00000498522,;TESK1,downstream_gene_variant,,ENST00000480077,;CD72,downstream_gene_variant,,ENST00000490239,;TESK1,downstream_gene_variant,,ENST00000467424,;TESK1,downstream_gene_variant,,ENST00000463897,;	A	ENSG00000107140	ENST00000336395	Transcript	missense_variant	1643	1393	465	E/K	Gaa/Aaa	.	.	.	1	TESK1	HGNC	11731	protein_coding	YES	CCDS6580.1	ENSP00000338127	TESK1_HUMAN	Q8NFJ2_HUMAN,Q8NFE2_HUMAN,Q8NFE1_HUMAN,Q8N6A2_HUMAN,B4DQQ3_HUMAN	UPI0000074302	.	tolerated(0.34)	benign(0.03)	10/10	.	hmmpanther:PTHR23257:SF372,hmmpanther:PTHR23257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCTGAAGAG	.	5	ESCA
TLE1	0	.	GRCh37	9	84249102	84249102	+	Missense_Mutation	SNP	C	C	T	rs143365960	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.487G>A	p.Gly163Ser	p.G163S	ENST00000376499	7/20	55	51	3	61	61	0	TLE1,missense_variant,p.Gly163Ser,ENST00000376499,;TLE1,missense_variant,p.Gly107Ser,ENST00000376463,;TLE1,missense_variant,p.Gly173Ser,ENST00000418319,;TLE1,5_prime_UTR_variant,,ENST00000376472,;	T	ENSG00000196781	ENST00000376499	Transcript	missense_variant	1552	487	163	G/S	Ggc/Agc	rs143365960	.	.	-1	TLE1	HGNC	11837	protein_coding	YES	CCDS6661.1	ENSP00000365682	TLE1_HUMAN	.	UPI0000137034	.	tolerated(0.12)	benign(0.01)	7/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10814	.	.	.	.	.	.	.	T:0.0005	T:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGCCGGCAC	byFrequency|byCluster	2	ESCA
WNK2	0	.	GRCh37	9	95947766	95947766	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555C>T	p.%3D	p.A185A	ENST00000297954	1/30	153	55	98	146	146	0	WNK2,synonymous_variant,p.%3D,ENST00000432730,;WNK2,synonymous_variant,p.%3D,ENST00000395475,;WNK2,synonymous_variant,p.%3D,ENST00000297954,;WNK2,synonymous_variant,p.%3D,ENST00000395477,;WNK2,synonymous_variant,p.%3D,ENST00000448039,;WNK2,5_prime_UTR_variant,,ENST00000427277,;WNK2,5_prime_UTR_variant,,ENST00000349097,;WNK2,5_prime_UTR_variant,,ENST00000356055,;	T	ENSG00000165238	ENST00000297954	Transcript	synonymous_variant	555	555	185	A	gcC/gcT	.	.	.	1	WNK2	HGNC	14542	protein_coding	YES	.	ENSP00000297954	WNK2_HUMAN	.	UPI0000236D76	.	.	.	1/30	.	hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCCGTGGC	.	5	ESCA
WWC3	0	.	GRCh37	X	10104670	10104670	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2764-3C>T	.	.	ENST00000380861	.	36	15	21	28	28	0	WWC3,splice_region_variant,,ENST00000380861,;WWC3,splice_region_variant,,ENST00000454666,;	T	ENSG00000047644	ENST00000380861	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	WWC3	HGNC	29237	protein_coding	YES	CCDS14136.1	ENSP00000370242	WWC3_HUMAN	T2C6S4_HUMAN	UPI0000225CDE	.	.	.	.	19/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTGCAGCTT	.	4	ESCA
TRPC5	0	.	GRCh37	X	111155531	111155531	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.888C>T	p.%3D	p.Y296Y	ENST00000262839	3/11	20	3	17	20	20	0	TRPC5,synonymous_variant,p.%3D,ENST00000262839,;	A	ENSG00000072315	ENST00000262839	Transcript	synonymous_variant	1807	888	296	Y	taC/taT	.	.	.	-1	TRPC5	HGNC	12337	protein_coding	YES	CCDS14561.1	ENSP00000262839	TRPC5_HUMAN	.	UPI00001374B6	.	.	.	3/11	.	hmmpanther:PTHR10117:SF24,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGGTATTT	.	5	ESCA
IRAK1	0	.	GRCh37	X	153287556	153287556	+	5'Flank	SNP	C	C	T	rs782502891	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000369980	.	29	5	23	28	28	0	MECP2,3_prime_UTR_variant,,ENST00000303391,;IRAK1,upstream_gene_variant,,ENST00000369980,;IRAK1,upstream_gene_variant,,ENST00000443220,;IRAK1,upstream_gene_variant,,ENST00000429936,;IRAK1,upstream_gene_variant,,ENST00000369974,;IRAK1,upstream_gene_variant,,ENST00000444230,;IRAK1,upstream_gene_variant,,ENST00000393687,;IRAK1,upstream_gene_variant,,ENST00000393682,;MIR718,upstream_gene_variant,,ENST00000390190,;IRAK1,upstream_gene_variant,,ENST00000477274,;IRAK1,upstream_gene_variant,,ENST00000369973,;IRAK1,upstream_gene_variant,,ENST00000463031,;	T	ENSG00000184216	ENST00000369980	Transcript	upstream_gene_variant	.	.	.	.	.	rs782502891	.	2125	-1	IRAK1	HGNC	6112	protein_coding	YES	CCDS14740.1	ENSP00000358997	IRAK1_HUMAN	.	UPI000012D873	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATACGATAC	.	5	ESCA
PLXNA3	0	.	GRCh37	X	153697205	153697205	+	Missense_Mutation	SNP	A	A	T	rs782242295	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4327A>T	p.Ile1443Phe	p.I1443F	ENST00000369682	25/33	42	12	30	31	31	0	PLXNA3,missense_variant,p.Ile1443Phe,ENST00000369682,;PLXNA3,non_coding_transcript_exon_variant,,ENST00000480645,;PLXNA3,downstream_gene_variant,,ENST00000467463,;PLXNA3,upstream_gene_variant,,ENST00000493546,;PLXNA3,non_coding_transcript_exon_variant,,ENST00000491066,;PLXNA3,upstream_gene_variant,,ENST00000497802,;PLXNA3,downstream_gene_variant,,ENST00000482598,;PLXNA3,downstream_gene_variant,,ENST00000478236,;	T	ENSG00000130827	ENST00000369682	Transcript	missense_variant	4502	4327	1443	I/F	Atc/Ttc	rs782242295	.	.	1	PLXNA3	HGNC	9101	protein_coding	YES	CCDS14752.1	ENSP00000358696	PLXA3_HUMAN	.	UPI000004E900	.	deleterious(0)	probably_damaging(0.998)	25/33	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF32,Pfam_domain:PF08337,Gene3D:1.10.506.10,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCCATCAAG	.	5	ESCA
BMX	0	.	GRCh37	X	15525518	15525518	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-9-950T>A	.	.	ENST00000357607	.	27	8	19	26	26	0	BMX,5_prime_UTR_variant,,ENST00000342014,;BMX,intron_variant,,ENST00000348343,;BMX,intron_variant,,ENST00000357607,;BMX,non_coding_transcript_exon_variant,,ENST00000463891,;	A	ENSG00000102010	ENST00000357607	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	BMX	HGNC	1079	protein_coding	YES	CCDS14168.1	ENSP00000350224	BMX_HUMAN	.	UPI0000000DFF	.	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGCTCTAGC	.	5	ESCA
PGAM4	0	.	GRCh37	X	77223837	77223837	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*534G>A	.	.	ENST00000458128	1/1	60	11	49	56	56	0	PGAM4,3_prime_UTR_variant,,ENST00000458128,;ATP7A,intron_variant,,ENST00000343533,;ATP7A,intron_variant,,ENST00000350425,;ATP7A,intron_variant,,ENST00000341514,;RP5-1000K24.2,downstream_gene_variant,,ENST00000602791,;	T	ENSG00000226784	ENST00000458128	Transcript	3_prime_UTR_variant	1299	.	.	.	.	.	.	.	-1	PGAM4	HGNC	21731	protein_coding	YES	CCDS35338.1	ENSP00000412189	PGAM4_HUMAN	O00228_HUMAN	UPI0000131CD2	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAACGAAAT	.	5	ESCA
P2RY10	0	.	GRCh37	X	78216849	78216849	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HY-01A-12D-A351-09	TCGA-LN-A7HY-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>T	p.Pro278Ser	p.P278S	ENST00000171757	4/4	21	6	15	9	9	0	P2RY10,missense_variant,p.Pro278Ser,ENST00000544091,;P2RY10,missense_variant,p.Pro278Ser,ENST00000171757,;P2RY10,downstream_gene_variant,,ENST00000475374,;P2RY10,downstream_gene_variant,,ENST00000461541,;	T	ENSG00000078589	ENST00000171757	Transcript	missense_variant	1112	832	278	P/S	Ccc/Tcc	.	.	.	1	P2RY10	HGNC	19906	protein_coding	YES	CCDS14442.1	ENSP00000171757	P2Y10_HUMAN	.	UPI0000050471	.	tolerated(0.97)	benign(0.002)	4/4	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24232:SF6,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTGTCCCGTT	.	3	ESCA
VTI1A	0	.	GRCh37	10	114220329	114220329	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141A>G	p.%3D	p.E47E	ENST00000393077	2/8	84	69	14	62	62	0	VTI1A,synonymous_variant,p.%3D,ENST00000432306,;VTI1A,synonymous_variant,p.%3D,ENST00000393077,;VTI1A,non_coding_transcript_exon_variant,,ENST00000494728,;VTI1A,non_coding_transcript_exon_variant,,ENST00000480057,;VTI1A,non_coding_transcript_exon_variant,,ENST00000489357,;VTI1A,non_coding_transcript_exon_variant,,ENST00000496445,;VTI1A,non_coding_transcript_exon_variant,,ENST00000489142,;	G	ENSG00000151532	ENST00000393077	Transcript	synonymous_variant	257	141	47	E	gaA/gaG	.	.	.	1	VTI1A	HGNC	17792	protein_coding	YES	CCDS7575.2	ENSP00000376792	VTI1A_HUMAN	.	UPI0000DD7870	.	.	.	2/8	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21230,hmmpanther:PTHR21230:SF26,Gene3D:1vcsA00,Pfam_domain:PF05008,Superfamily_domains:SSF47661	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAAGCGAA	.	5	ESCA
ATRNL1	0	.	GRCh37	10	116931078	116931078	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1348+28T>C	.	.	ENST00000355044	.	41	35	6	26	26	0	ATRNL1,3_prime_UTR_variant,,ENST00000527407,;ATRNL1,intron_variant,,ENST00000355044,;ATRNL1,non_coding_transcript_exon_variant,,ENST00000529665,;ATRNL1,non_coding_transcript_exon_variant,,ENST00000485327,;ATRNL1,intron_variant,,ENST00000524503,;	C	ENSG00000107518	ENST00000355044	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ATRNL1	HGNC	29063	protein_coding	YES	CCDS7592.1	ENSP00000347152	ATRN1_HUMAN	.	UPI000021CCF8	.	.	.	.	8/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTCTTTATTG	.	4	ESCA
MBL2	0	.	GRCh37	10	54531301	54531301	+	Missense_Mutation	SNP	C	C	A	rs199957742	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.95G>T	p.Cys32Phe	p.C32F	ENST00000373968	1/4	46	29	16	34	34	0	MBL2,missense_variant,p.Cys32Phe,ENST00000373968,;	A	ENSG00000165471	ENST00000373968	Transcript	missense_variant	160	95	32	C/F	tGc/tTc	rs199957742	.	.	-1	MBL2	HGNC	6922	protein_coding	YES	CCDS7247.1	ENSP00000363079	MBL2_HUMAN	Q9HCS8_HUMAN,Q5SQS3_HUMAN,B1PN75_HUMAN	UPI0000035011	.	deleterious(0.01)	probably_damaging(1)	1/4	.	hmmpanther:PTHR24020,hmmpanther:PTHR24020:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCAGGTC	.	5	ESCA
ZWINT	0	.	GRCh37	10	58118341	58118341	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.768G>A	p.%3D	p.G256G	ENST00000373944	7/9	57	32	25	40	40	0	ZWINT,synonymous_variant,p.%3D,ENST00000395405,;ZWINT,synonymous_variant,p.%3D,ENST00000373944,;ZWINT,synonymous_variant,p.%3D,ENST00000361148,;ZWINT,synonymous_variant,p.%3D,ENST00000318387,;ZWINT,non_coding_transcript_exon_variant,,ENST00000460654,;ZWINT,non_coding_transcript_exon_variant,,ENST00000478181,;ZWINT,downstream_gene_variant,,ENST00000467523,;ZWINT,3_prime_UTR_variant,,ENST00000489649,;ZWINT,non_coding_transcript_exon_variant,,ENST00000494312,;	T	ENSG00000122952	ENST00000373944	Transcript	synonymous_variant	807	768	256	G	ggG/ggA	.	.	.	-1	ZWINT	HGNC	13195	protein_coding	YES	CCDS7249.1	ENSP00000363055	ZWINT_HUMAN	A6NH27_HUMAN	UPI000013CB09	.	.	.	7/9	.	hmmpanther:PTHR31504:SF1,hmmpanther:PTHR31504,Pfam_domain:PF15556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCCCCAT	.	5	ESCA
LRRC20	0	.	GRCh37	10	72058732	72058732	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2378C>T	.	.	ENST00000355790	5/5	48	38	10	44	44	0	LRRC20,3_prime_UTR_variant,,ENST00000358141,;LRRC20,3_prime_UTR_variant,,ENST00000395011,;LRRC20,3_prime_UTR_variant,,ENST00000357631,;LRRC20,3_prime_UTR_variant,,ENST00000355790,;LRRC20,3_prime_UTR_variant,,ENST00000373224,;LRRC20,3_prime_UTR_variant,,ENST00000395010,;LRRC20,downstream_gene_variant,,ENST00000446961,;	A	ENSG00000172731	ENST00000355790	Transcript	3_prime_UTR_variant	3411	.	.	.	.	.	.	.	-1	LRRC20	HGNC	23421	protein_coding	YES	CCDS7302.1	ENSP00000348043	LRC20_HUMAN	.	UPI000004C613	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATGAAACC	.	5	ESCA
OPN4	0	.	GRCh37	10	88415912	88415912	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.145G>A	p.Ala49Thr	p.A49T	ENST00000372071	2/11	82	47	35	73	73	0	OPN4,missense_variant,p.Ala49Thr,ENST00000241891,;OPN4,missense_variant,p.Ala49Thr,ENST00000372071,;OPN4,missense_variant,p.Ala49Thr,ENST00000443292,;	A	ENSG00000122375	ENST00000372071	Transcript	missense_variant	372	145	49	A/T	Gca/Aca	.	.	.	1	OPN4	HGNC	14449	protein_coding	YES	CCDS31237.1	ENSP00000361141	OPN4_HUMAN	.	UPI00001544ED	.	tolerated(0.08)	benign(0.023)	2/11	.	hmmpanther:PTHR24240,hmmpanther:PTHR24240:SF72	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCAGGCACCT	.	5	ESCA
NOC3L	0	.	GRCh37	10	96117718	96117718	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.350+122A>G	.	.	ENST00000371361	.	34	18	16	29	29	0	NOC3L,intron_variant,,ENST00000371361,;NOC3L,intron_variant,,ENST00000371350,;NOC3L,upstream_gene_variant,,ENST00000543788,;NOC3L,non_coding_transcript_exon_variant,,ENST00000463649,;NOC3L,downstream_gene_variant,,ENST00000461562,;	C	ENSG00000173145	ENST00000371361	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NOC3L	HGNC	24034	protein_coding	YES	CCDS7433.1	ENSP00000360412	NOC3L_HUMAN	.	UPI000006DE09	.	.	.	.	3/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AATAATACTTT	.	4	ESCA
TM9SF3	0	.	GRCh37	10	98281367	98281367	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*653C>G	.	.	ENST00000371142	15/15	106	101	5	36	36	0	TM9SF3,3_prime_UTR_variant,,ENST00000371142,;TM9SF3,downstream_gene_variant,,ENST00000485093,;	C	ENSG00000077147	ENST00000371142	Transcript	3_prime_UTR_variant	2640	.	.	.	.	.	.	.	-1	TM9SF3	HGNC	21529	protein_coding	YES	CCDS7450.1	ENSP00000360184	TM9S3_HUMAN	Q96K55_HUMAN,Q96JZ5_HUMAN,Q8WUB5_HUMAN,Q5TB53_HUMAN	UPI000013684E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTATAGTTTTA	.	2	ESCA
SOX6	0	.	GRCh37	11	16071402	16071402	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1334A>G	p.Gln445Arg	p.Q445R	ENST00000396356	11/16	76	38	37	54	54	0	SOX6,missense_variant,p.Gln407Arg,ENST00000527619,;SOX6,missense_variant,p.Gln445Arg,ENST00000528429,;SOX6,missense_variant,p.Gln404Arg,ENST00000528252,;SOX6,missense_variant,p.Gln445Arg,ENST00000352083,;SOX6,missense_variant,p.Gln445Arg,ENST00000396356,;SOX6,missense_variant,p.Gln445Arg,ENST00000316399,;SOX6,non_coding_transcript_exon_variant,,ENST00000524650,;	C	ENSG00000110693	ENST00000396356	Transcript	missense_variant	1412	1334	445	Q/R	cAg/cGg	.	.	.	-1	SOX6	HGNC	16421	protein_coding	YES	CCDS7821.1	ENSP00000379644	SOX6_HUMAN	E9PQL4_HUMAN,E9PQ67_HUMAN,E9PN02_HUMAN	UPI00001F9DE4	.	tolerated(0.33)	possibly_damaging(0.457)	11/16	.	hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF89	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTCTGGGTG	.	5	ESCA
NLRP14	0	.	GRCh37	11	7060994	7060994	+	Silent	SNP	A	A	G	.	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339A>G	p.%3D	p.Q113Q	ENST00000299481	3/12	35	19	16	45	45	0	NLRP14,synonymous_variant,p.%3D,ENST00000299481,;	G	ENSG00000158077	ENST00000299481	Transcript	synonymous_variant	685	339	113	Q	caA/caG	COSM4036358	.	.	1	NLRP14	HGNC	22939	protein_coding	YES	CCDS7776.1	ENSP00000299481	NAL14_HUMAN	.	UPI0000167F6E	.	.	.	3/12	.	hmmpanther:PTHR24106:SF82,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACAAGAAGA	.	5	ESCA
KIAA1731	0	.	GRCh37	11	93463064	93463064	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7596G>A	p.%3D	p.V2532V	ENST00000325212	28/30	82	65	17	46	46	0	KIAA1731,synonymous_variant,p.%3D,ENST00000531404,;KIAA1731,synonymous_variant,p.%3D,ENST00000344196,;KIAA1731,synonymous_variant,p.%3D,ENST00000325212,;KIAA1731,synonymous_variant,p.%3D,ENST00000411936,;KIAA1731,synonymous_variant,p.%3D,ENST00000531700,;KIAA1731,downstream_gene_variant,,ENST00000529185,;SNORA1,downstream_gene_variant,,ENST00000384107,;MIR1304,downstream_gene_variant,,ENST00000408243,;SNORD5,downstream_gene_variant,,ENST00000459342,;SNORA8,downstream_gene_variant,,ENST00000384574,;SNORA32,downstream_gene_variant,,ENST00000384072,;SNORD6,downstream_gene_variant,,ENST00000365444,;SNORA18,downstream_gene_variant,,ENST00000384416,;SNORA25,downstream_gene_variant,,ENST00000384384,;TAF1D,downstream_gene_variant,,ENST00000546088,;TAF1D,downstream_gene_variant,,ENST00000530089,;TAF1D,downstream_gene_variant,,ENST00000533794,;TAF1D,downstream_gene_variant,,ENST00000527068,;TAF1D,downstream_gene_variant,,ENST00000540232,;TAF1D,downstream_gene_variant,,ENST00000529794,;TAF1D,downstream_gene_variant,,ENST00000393259,;TAF1D,downstream_gene_variant,,ENST00000526015,;TAF1D,downstream_gene_variant,,ENST00000530769,;TAF1D,downstream_gene_variant,,ENST00000323981,;TAF1D,downstream_gene_variant,,ENST00000529435,;TAF1D,downstream_gene_variant,,ENST00000529900,;TAF1D,downstream_gene_variant,,ENST00000527169,;TAF1D,downstream_gene_variant,,ENST00000534079,;TAF1D,downstream_gene_variant,,ENST00000525928,;	A	ENSG00000166004	ENST00000325212	Transcript	synonymous_variant	7758	7596	2532	V	gtG/gtA	.	.	.	1	KIAA1731	HGNC	29366	protein_coding	YES	CCDS44708.1	ENSP00000316681	K1731_HUMAN	E9PM20_HUMAN	UPI0000251F0E	.	.	.	28/30	.	hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22,Pfam_domain:PF15309	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGTGAATAA	.	5	ESCA
ACACB	0	.	GRCh37	12	109670566	109670566	+	Missense_Mutation	SNP	G	G	A	rs748021201	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4094G>A	p.Arg1365His	p.R1365H	ENST00000338432	29/53	59	48	11	38	38	0	ACACB,missense_variant,p.Arg1295His,ENST00000377854,;ACACB,missense_variant,p.Arg31His,ENST00000543201,;ACACB,missense_variant,p.Arg1365His,ENST00000377848,;ACACB,missense_variant,p.Arg1365His,ENST00000338432,;ACACB,missense_variant,p.Arg32His,ENST00000538526,;ACACB,upstream_gene_variant,,ENST00000542524,;	A	ENSG00000076555	ENST00000338432	Transcript	missense_variant	4213	4094	1365	R/H	cGc/cAc	rs748021201	.	.	1	ACACB	HGNC	85	protein_coding	YES	CCDS31898.1	ENSP00000341044	ACACB_HUMAN	F5H5C3_HUMAN,E9PEW7_HUMAN	UPI0000DBEEFB	.	deleterious(0)	probably_damaging(1)	29/53	.	hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF84,Pfam_domain:PF08326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGCGCATGG	byFrequency	4	ESCA
TPCN1	0	.	GRCh37	12	113717958	113717958	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516A>G	p.Ile506Val	p.I506V	ENST00000550785	16/29	42	26	16	45	45	0	TPCN1,missense_variant,p.Ile506Val,ENST00000541517,;TPCN1,missense_variant,p.Ile366Val,ENST00000392569,;TPCN1,missense_variant,p.Ile434Val,ENST00000335509,;TPCN1,missense_variant,p.Ile121Val,ENST00000546781,;TPCN1,missense_variant,p.Ile506Val,ENST00000550785,;TPCN1,splice_region_variant,,ENST00000546503,;TPCN1,splice_region_variant,,ENST00000552077,;TPCN1,splice_region_variant,,ENST00000551127,;TPCN1,splice_region_variant,,ENST00000428632,;TPCN1,upstream_gene_variant,,ENST00000550543,;TPCN1,upstream_gene_variant,,ENST00000547955,;	G	ENSG00000186815	ENST00000550785	Transcript	missense_variant	1685	1516	506	I/V	Att/Gtt	.	.	.	1	TPCN1	HGNC	18182	protein_coding	YES	CCDS44985.1	ENSP00000448083	TPC1_HUMAN	F8W1L6_HUMAN,F8W1G4_HUMAN,F8VZZ6_HUMAN,F8VV93_HUMAN,F8VR74_HUMAN,B7Z3R2_HUMAN	UPI00004066FB	.	tolerated(0.19)	benign(0.045)	16/29	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF201	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TAGGTATTAAT	.	4	ESCA
ADAMTS20	0	.	GRCh37	12	43833503	43833503	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2515A>G	p.Ile839Val	p.I839V	ENST00000389420	18/39	42	25	17	27	27	0	ADAMTS20,missense_variant,p.Ile839Val,ENST00000553158,;ADAMTS20,missense_variant,p.Ile839Val,ENST00000389420,;ADAMTS20,missense_variant,p.Ile5Val,ENST00000549670,;ADAMTS20,5_prime_UTR_variant,,ENST00000395541,;	C	ENSG00000173157	ENST00000389420	Transcript	missense_variant	2515	2515	839	I/V	Atc/Gtc	.	.	.	-1	ADAMTS20	HGNC	17178	protein_coding	YES	CCDS31778.2	ENSP00000374071	ATS20_HUMAN	.	UPI00004565F4	.	tolerated(0.19)	benign(0.065)	18/39	.	hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF05986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGATATTGA	.	5	ESCA
KMT2D	0	.	GRCh37	12	49435700	49435700	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6183G>A	p.%3D	p.L2061L	ENST00000301067	29/54	49	27	22	52	52	0	KMT2D,synonymous_variant,p.%3D,ENST00000301067,;KMT2D,upstream_gene_variant,,ENST00000549799,;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000550356,;	T	ENSG00000167548	ENST00000301067	Transcript	synonymous_variant	6183	6183	2061	L	ctG/ctA	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	29/54	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324,Gene3D:1.10.30.10,SMART_domains:SM00398,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACCAGGTA	.	5	ESCA
DAZAP2	0	.	GRCh37	12	51634874	51634874	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301+51G>A	.	.	ENST00000549555	.	103	86	16	74	74	0	DAZAP2,missense_variant,p.Ala118Thr,ENST00000425012,;DAZAP2,missense_variant,p.Ala96Thr,ENST00000449723,;DAZAP2,missense_variant,p.Ala58Thr,ENST00000551313,;DAZAP2,missense_variant,p.Ala118Thr,ENST00000604900,;DAZAP2,missense_variant,p.Ala118Thr,ENST00000412716,;DAZAP2,missense_variant,p.Ala86Thr,ENST00000549732,;DAZAP2,intron_variant,,ENST00000549555,;DAZAP2,intron_variant,,ENST00000439799,;SMAGP,downstream_gene_variant,,ENST00000603864,;SMAGP,downstream_gene_variant,,ENST00000605426,;SMAGP,downstream_gene_variant,,ENST00000605627,;SMAGP,downstream_gene_variant,,ENST00000398453,;SMAGP,downstream_gene_variant,,ENST00000603798,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000551919,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000549497,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000551534,;DAZAP2,downstream_gene_variant,,ENST00000552173,;DAZAP2,3_prime_UTR_variant,,ENST00000436900,;DAZAP2,non_coding_transcript_exon_variant,,ENST00000552459,;SMAGP,downstream_gene_variant,,ENST00000380103,;DAZAP2,downstream_gene_variant,,ENST00000549041,;	A	ENSG00000183283	ENST00000549555	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	DAZAP2	HGNC	2684	protein_coding	YES	CCDS44885.1	ENSP00000448051	DAZP2_HUMAN	.	UPI000183CBDB	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGAGCTGGG	.	4	ESCA
MDM1	0	.	GRCh37	12	68720467	68720467	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.468C>A	p.%3D	p.T156T	ENST00000303145	3/14	49	33	15	36	36	0	MDM1,synonymous_variant,p.%3D,ENST00000541686,;MDM1,synonymous_variant,p.%3D,ENST00000411698,;MDM1,synonymous_variant,p.%3D,ENST00000430606,;MDM1,synonymous_variant,p.%3D,ENST00000303145,;MDM1,3_prime_UTR_variant,,ENST00000393543,;MDM1,intron_variant,,ENST00000540418,;MDM1,non_coding_transcript_exon_variant,,ENST00000545724,;MDM1,upstream_gene_variant,,ENST00000540476,;MDM1,downstream_gene_variant,,ENST00000541087,;MDM1,upstream_gene_variant,,ENST00000536997,;MDM1,upstream_gene_variant,,ENST00000538454,;	T	ENSG00000111554	ENST00000303145	Transcript	synonymous_variant	555	468	156	T	acC/acA	.	.	.	-1	MDM1	HGNC	29917	protein_coding	YES	CCDS8983.1	ENSP00000302537	MDM1_HUMAN	F5H804_HUMAN	UPI00001FC70C	.	.	.	3/14	.	Pfam_domain:PF15501,hmmpanther:PTHR32078	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGGTAGA	.	5	ESCA
INTS6	0	.	GRCh37	13	51948408	51948408	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2040delA	p.Gly681AspfsTer30	p.G681Dfs*30	ENST00000311234	15/18	41	36	5	50	50	0	INTS6,frameshift_variant,p.Gly249AspfsTer30,ENST00000425000,;INTS6,frameshift_variant,p.Gly668AspfsTer30,ENST00000398119,;INTS6,frameshift_variant,p.Gly503AspfsTer30,ENST00000497989,;INTS6,frameshift_variant,p.Gly681AspfsTer30,ENST00000311234,;INTS6,frameshift_variant,p.Gly365AspfsTer30,ENST00000490542,;INTS6,intron_variant,,ENST00000463928,;INTS6,3_prime_UTR_variant,,ENST00000469430,;INTS6,non_coding_transcript_exon_variant,,ENST00000483441,;	-	ENSG00000102786	ENST00000311234	Transcript	frameshift_variant	2513	2040	680	K/X	aaA/aa	.	.	.	-1	INTS6	HGNC	14879	protein_coding	YES	CCDS9428.1	ENSP00000310260	INT6_HUMAN	G5E9X1_HUMAN,C9K0V7_HUMAN,C9JVX2_HUMAN,C9J885_HUMAN,C9J0C6_HUMAN,B3KQH5_HUMAN	UPI0000030C84	.	.	.	15/18	.	hmmpanther:PTHR12957:SF23,hmmpanther:PTHR12957	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE*|MUTECT*|PINDEL	TGGTCCTTTTCC	.	3	ESCA
PCDH9	0	.	GRCh37	13	66877032	66877032	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1755A>C	.	.	ENST00000544246	5/5	101	60	41	87	87	0	PCDH9,3_prime_UTR_variant,,ENST00000544246,;PCDH9,3_prime_UTR_variant,,ENST00000377865,;PCDH9,downstream_gene_variant,,ENST00000328454,;PCDH9,downstream_gene_variant,,ENST00000456367,;PCDH9-AS1,upstream_gene_variant,,ENST00000430861,;	G	ENSG00000184226	ENST00000544246	Transcript	3_prime_UTR_variant	6161	.	.	.	.	.	.	.	-1	PCDH9	HGNC	8661	protein_coding	YES	CCDS9444.1	ENSP00000442186	PCDH9_HUMAN	.	UPI00001FCE90	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGTAACAA	.	5	ESCA
UBAC2	0	.	GRCh37	13	99890703	99890703	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55delC	p.Leu19PhefsTer39	p.L19Ffs*39	ENST00000403766	2/9	62	50	12	52	52	0	UBAC2,frameshift_variant,p.Leu25PhefsTer39,ENST00000457666,;UBAC2,frameshift_variant,p.Phe61SerfsTer25,ENST00000376440,;UBAC2,frameshift_variant,p.Leu19PhefsTer102,ENST00000355700,;UBAC2,frameshift_variant,p.Leu19PhefsTer39,ENST00000403766,;UBAC2,non_coding_transcript_exon_variant,,ENST00000473091,;UBAC2,non_coding_transcript_exon_variant,,ENST00000468067,;	-	ENSG00000134882	ENST00000403766	Transcript	frameshift_variant	189	54	18	S/X	agC/ag	.	.	.	1	UBAC2	HGNC	20486	protein_coding	YES	CCDS45064.1	ENSP00000383911	UBAC2_HUMAN	B3KW74_HUMAN	UPI000003B0B4	.	.	.	2/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12917:SF11,hmmpanther:PTHR12917,Superfamily_domains:SSF144091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAGAGCCTTCT	.	3	ESCA
EDDM3B	0	.	GRCh37	14	21238744	21238744	+	Silent	SNP	C	C	T	rs755986649	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435C>T	p.%3D	p.I145I	ENST00000326783	2/2	53	48	4	24	24	0	EDDM3B,synonymous_variant,p.%3D,ENST00000326783,;	T	ENSG00000181552	ENST00000326783	Transcript	synonymous_variant	533	435	145	I	atC/atT	rs755986649,COSM3419689	.	.	1	EDDM3B	HGNC	19223	protein_coding	YES	CCDS9557.1	ENSP00000314810	EP3B_HUMAN	.	UPI000003EDF8	.	.	.	2/2	.	hmmpanther:PTHR16788:SF1,hmmpanther:PTHR16788	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTATCGGCAA	byFrequency	3	ESCA
FBXO34	0	.	GRCh37	14	55819192	55819192	+	Missense_Mutation	SNP	A	A	T	rs765201566	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2084A>T	p.Asn695Ile	p.N695I	ENST00000313833	2/2	62	43	19	43	43	0	FBXO34,missense_variant,p.Asn695Ile,ENST00000440021,;FBXO34,missense_variant,p.Asn695Ile,ENST00000313833,;FBXO34,intron_variant,,ENST00000557647,;FBXO34,downstream_gene_variant,,ENST00000555087,;FBXO34,downstream_gene_variant,,ENST00000554940,;FBXO34,missense_variant,p.Asn561Ile,ENST00000555280,;	T	ENSG00000178974	ENST00000313833	Transcript	missense_variant	2329	2084	695	N/I	aAt/aTt	rs765201566	.	.	1	FBXO34	HGNC	20201	protein_coding	YES	CCDS32086.1	ENSP00000313159	FBX34_HUMAN	G3V2U9_HUMAN	UPI00001FD5AD	.	deleterious(0)	probably_damaging(0.999)	2/2	.	hmmpanther:PTHR16271:SF11,hmmpanther:PTHR16271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTAATCGGG	byFrequency	5	ESCA
SGPP1	0	.	GRCh37	14	64151387	64151387	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1436A>T	.	.	ENST00000247225	3/3	172	111	61	50	50	0	SGPP1,3_prime_UTR_variant,,ENST00000247225,;	A	ENSG00000126821	ENST00000247225	Transcript	3_prime_UTR_variant	2857	.	.	.	.	.	.	.	-1	SGPP1	HGNC	17720	protein_coding	YES	CCDS9760.1	ENSP00000247225	SGPP1_HUMAN	.	UPI000006DEB2	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCATACCTG	.	5	ESCA
DIO2	0	.	GRCh37	14	80663936	80663936	+	3'UTR	SNP	C	C	G	rs192334437	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5096G>C	.	.	ENST00000557010	4/4	116	102	13	48	48	0	DIO2,3_prime_UTR_variant,,ENST00000557010,;DIO2,3_prime_UTR_variant,,ENST00000438257,;DIO2,downstream_gene_variant,,ENST00000422005,;DIO2,downstream_gene_variant,,ENST00000556811,;	G	ENSG00000211448	ENST00000557010	Transcript	3_prime_UTR_variant	6304	.	.	.	.	rs192334437	.	.	-1	DIO2	HGNC	2884	protein_coding	.	CCDS45146.1	ENSP00000451419	IOD2_HUMAN	Q9NZL0_HUMAN,Q9C0K2_HUMAN,G3V3A8_HUMAN,A8K845_HUMAN	UPI0000161B1B	.	.	.	4/4	.	.	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACTCAGCAC	by1000G	4	ESCA
SNAP23	0	.	GRCh37	15	42825202	42825202	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1526A>G	.	.	ENST00000249647	8/8	49	34	15	27	27	0	SNAP23,3_prime_UTR_variant,,ENST00000249647,;SNAP23,3_prime_UTR_variant,,ENST00000349777,;SNAP23,intron_variant,,ENST00000563830,;SNAP23,intron_variant,,ENST00000568841,;SNAP23,intron_variant,,ENST00000563873,;SNAP23,downstream_gene_variant,,ENST00000397138,;SNAP23,downstream_gene_variant,,ENST00000564153,;SNAP23,downstream_gene_variant,,ENST00000566327,;SNAP23,downstream_gene_variant,,ENST00000561526,;SNAP23,downstream_gene_variant,,ENST00000568859,;RP11-265N6.1,upstream_gene_variant,,ENST00000564805,;SNAP23,downstream_gene_variant,,ENST00000566035,;SNAP23,downstream_gene_variant,,ENST00000563333,;SNAP23,downstream_gene_variant,,ENST00000563765,;SNAP23,downstream_gene_variant,,ENST00000568451,;SNAP23,downstream_gene_variant,,ENST00000568514,;SNAP23,downstream_gene_variant,,ENST00000568331,;	G	ENSG00000092531	ENST00000249647	Transcript	3_prime_UTR_variant	2630	.	.	.	.	.	.	.	1	SNAP23	HGNC	11131	protein_coding	YES	CCDS10087.1	ENSP00000249647	SNP23_HUMAN	H3BV99_HUMAN,H3BR18_HUMAN,H3BM38_HUMAN,A8K287_HUMAN	UPI0000000A2C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTATTGGT	.	5	ESCA
ANKDD1A	0	.	GRCh37	15	65218355	65218355	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.457G>C	p.Asp153His	p.D153H	ENST00000380230	5/15	68	50	18	60	60	0	ANKDD1A,missense_variant,p.Asp153His,ENST00000395720,;ANKDD1A,missense_variant,p.Asp153His,ENST00000380230,;ANKDD1A,missense_variant,p.Asp62His,ENST00000496660,;ANKDD1A,missense_variant,p.Asp62His,ENST00000395723,;ANKDD1A,missense_variant,p.Asp153His,ENST00000357698,;ANKDD1A,3_prime_UTR_variant,,ENST00000319580,;AC069368.3,intron_variant,,ENST00000437723,;ANKDD1A,intron_variant,,ENST00000483400,;ANKDD1A,non_coding_transcript_exon_variant,,ENST00000491145,;ANKDD1A,intron_variant,,ENST00000496480,;ANKDD1A,missense_variant,p.Asp62His,ENST00000487867,;ANKDD1A,3_prime_UTR_variant,,ENST00000513267,;AC069368.3,downstream_gene_variant,,ENST00000502574,;	C	ENSG00000166839	ENST00000380230	Transcript	missense_variant	486	457	153	D/H	Gac/Cac	.	.	.	1	ANKDD1A	HGNC	28002	protein_coding	YES	CCDS10197.2	ENSP00000369579	AKD1A_HUMAN	Q6PI29_HUMAN	UPI0000D79C72	.	deleterious(0)	probably_damaging(0.996)	5/15	.	Superfamily_domains:SSF48403,Gene3D:1.25.40.20,hmmpanther:PTHR24125,hmmpanther:PTHR24125:SF0,PROSITE_profiles:PS50297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTGGACCAC	.	5	ESCA
CYP11A1	0	.	GRCh37	15	74653949	74653949	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.269+5709C>T	.	.	ENST00000268053	.	60	57	3	37	37	0	CYP11A1,intron_variant,,ENST00000569662,;CYP11A1,intron_variant,,ENST00000358632,;CYP11A1,intron_variant,,ENST00000419019,;CYP11A1,intron_variant,,ENST00000541301,;CYP11A1,intron_variant,,ENST00000416978,;CYP11A1,intron_variant,,ENST00000268053,;CYP11A1,intron_variant,,ENST00000450547,;CYP11A1,upstream_gene_variant,,ENST00000566674,;CTD-2311M21.3,upstream_gene_variant,,ENST00000568496,;CTD-2311M21.2,non_coding_transcript_exon_variant,,ENST00000562009,;CYP11A1,non_coding_transcript_exon_variant,,ENST00000467407,;CTD-2311M21.2,non_coding_transcript_exon_variant,,ENST00000564109,;CYP11A1,intron_variant,,ENST00000466978,;CYP11A1,intron_variant,,ENST00000435365,;CTD-2311M21.2,non_coding_transcript_exon_variant,,ENST00000569235,;	A	ENSG00000140459	ENST00000268053	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CYP11A1	HGNC	2590	protein_coding	YES	CCDS32291.1	ENSP00000268053	CP11A_HUMAN	Q2HZF3_HUMAN,H3BSZ1_HUMAN,H3BS93_HUMAN,C9JPU9_HUMAN	UPI00000725F7	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GTCACGTCTCC	.	2	ESCA
RCCD1	0	.	GRCh37	15	91500556	91500556	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380G>C	p.Gly127Ala	p.G127A	ENST00000394258	3/8	9	4	5	13	13	0	RCCD1,missense_variant,p.Gly127Ala,ENST00000555155,;RCCD1,missense_variant,p.Gly127Ala,ENST00000394258,;RCCD1,missense_variant,p.Gly127Ala,ENST00000556618,;UNC45A,downstream_gene_variant,,ENST00000418476,;UNC45A,downstream_gene_variant,,ENST00000394275,;AC068831.6,upstream_gene_variant,,ENST00000553321,;RCCD1,intron_variant,,ENST00000556774,;RCCD1,non_coding_transcript_exon_variant,,ENST00000557266,;RCCD1,non_coding_transcript_exon_variant,,ENST00000555737,;RCCD1,intron_variant,,ENST00000556333,;RCCD1,upstream_gene_variant,,ENST00000557750,;UNC45A,downstream_gene_variant,,ENST00000471780,;RCCD1,downstream_gene_variant,,ENST00000554302,;UNC45A,downstream_gene_variant,,ENST00000487875,;	C	ENSG00000166965	ENST00000394258	Transcript	missense_variant	582	380	127	G/A	gGt/gCt	.	.	.	1	RCCD1	HGNC	30457	protein_coding	YES	CCDS32333.1	ENSP00000377801	RCCD1_HUMAN	.	UPI00001FEBD4	.	tolerated(0.36)	benign(0.001)	3/8	.	Gene3D:2.130.10.30,hmmpanther:PTHR22870:SF153,hmmpanther:PTHR22870,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCCGGTGAGG	.	3	ESCA
MAPK3	0	.	GRCh37	16	30129434	30129434	+	Silent	SNP	G	G	A	rs542338052	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>T	p.%3D	p.T198T	ENST00000263025	4/9	48	35	12	32	32	0	MAPK3,synonymous_variant,p.%3D,ENST00000395202,;MAPK3,synonymous_variant,p.%3D,ENST00000263025,;MAPK3,synonymous_variant,p.%3D,ENST00000484663,;MAPK3,synonymous_variant,p.%3D,ENST00000322266,;MAPK3,synonymous_variant,p.%3D,ENST00000395199,;MAPK3,synonymous_variant,p.%3D,ENST00000481230,;MAPK3,synonymous_variant,p.%3D,ENST00000403394,;MAPK3,5_prime_UTR_variant,,ENST00000478356,;MAPK3,intron_variant,,ENST00000395200,;GDPD3,upstream_gene_variant,,ENST00000406256,;MAPK3,upstream_gene_variant,,ENST00000494643,;MAPK3,synonymous_variant,p.%3D,ENST00000466521,;MAPK3,synonymous_variant,p.%3D,ENST00000490298,;MAPK3,non_coding_transcript_exon_variant,,ENST00000483869,;MAPK3,upstream_gene_variant,,ENST00000473431,;MAPK3,upstream_gene_variant,,ENST00000461737,;MAPK3,upstream_gene_variant,,ENST00000485579,;GDPD3,upstream_gene_variant,,ENST00000360688,;	A	ENSG00000102882	ENST00000263025	Transcript	synonymous_variant	679	594	198	T	acC/acT	rs542338052	.	.	-1	MAPK3	HGNC	6877	protein_coding	YES	CCDS10672.1	ENSP00000263025	MK03_HUMAN	Q9BWJ1_HUMAN,Q7Z3H5_HUMAN,L7RXH5_HUMAN,H0YEX6_HUMAN,H0YDH9_HUMAN,E9PRH7_HUMAN,B3KR49_HUMAN	UPI0000000DD7	.	.	.	4/9	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF111,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR01770	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCCGGTGTG	by1000G	5	ESCA
ZNF646	0	.	GRCh37	16	31088787	31088787	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1142G>A	p.Arg381His	p.R381H	ENST00000300850	2/3	59	21	38	46	46	0	ZNF646,missense_variant,p.Arg381His,ENST00000394979,;ZNF646,missense_variant,p.Arg381His,ENST00000300850,;ZNF668,upstream_gene_variant,,ENST00000417935,;ZNF668,upstream_gene_variant,,ENST00000414399,;ZNF668,upstream_gene_variant,,ENST00000300849,;ZNF668,upstream_gene_variant,,ENST00000538906,;ZNF668,upstream_gene_variant,,ENST00000394983,;ZNF646,downstream_gene_variant,,ENST00000428260,;ZNF646,downstream_gene_variant,,ENST00000564189,;ZNF668,upstream_gene_variant,,ENST00000564456,;	A	ENSG00000167395	ENST00000300850	Transcript	missense_variant	1431	1142	381	R/H	cGt/cAt	.	.	.	1	ZNF646	HGNC	29004	protein_coding	YES	CCDS10702.1	ENSP00000300850	ZN646_HUMAN	H3BSD0_HUMAN,C9J3L0_HUMAN	UPI00001FFF54	.	deleterious(0)	probably_damaging(0.998)	2/3	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF182,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCGTACTT	.	5	ESCA
ZNF423	0	.	GRCh37	16	49557603	49557603	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3757G>A	p.Gly1253Arg	p.G1253R	ENST00000561648	7/8	26	12	13	36	36	0	ZNF423,missense_variant,p.Gly1253Arg,ENST00000262383,;ZNF423,missense_variant,p.Gly1193Arg,ENST00000563137,;ZNF423,missense_variant,p.Gly1193Arg,ENST00000562520,;ZNF423,missense_variant,p.Gly1253Arg,ENST00000561648,;ZNF423,missense_variant,p.Gly1136Arg,ENST00000567169,;ZNF423,missense_variant,p.Gly1136Arg,ENST00000535559,;ZNF423,missense_variant,p.Gly1193Arg,ENST00000562871,;	T	ENSG00000102935	ENST00000561648	Transcript	missense_variant	3811	3757	1253	G/R	Ggg/Agg	.	.	.	-1	ZNF423	HGNC	16762	protein_coding	YES	CCDS32445.1	ENSP00000455426	ZN423_HUMAN	F5H7S1_HUMAN,B3KNG7_HUMAN	UPI0000353ABC	.	deleterious(0)	probably_damaging(0.997)	7/8	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24385:SF49,hmmpanther:PTHR24385,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCCGTGCA	.	5	ESCA
KCTD19	0	.	GRCh37	16	67324844	67324844	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2611A>G	p.Ile871Val	p.I871V	ENST00000304372	15/16	45	38	7	25	25	0	KCTD19,missense_variant,p.Ile871Val,ENST00000304372,;KCTD19,intron_variant,,ENST00000562841,;PLEKHG4,downstream_gene_variant,,ENST00000360461,;PLEKHG4,downstream_gene_variant,,ENST00000379344,;PLEKHG4,downstream_gene_variant,,ENST00000569875,;PLEKHG4,downstream_gene_variant,,ENST00000427155,;PLEKHG4,downstream_gene_variant,,ENST00000450733,;KCTD19,non_coding_transcript_exon_variant,,ENST00000570049,;KCTD19,non_coding_transcript_exon_variant,,ENST00000566392,;KCTD19,non_coding_transcript_exon_variant,,ENST00000569333,;PLEKHG4,downstream_gene_variant,,ENST00000563969,;PLEKHG4,downstream_gene_variant,,ENST00000393966,;PLEKHG4,downstream_gene_variant,,ENST00000567136,;PLEKHG4,downstream_gene_variant,,ENST00000562289,;	C	ENSG00000168676	ENST00000304372	Transcript	missense_variant	2667	2611	871	I/V	Atc/Gtc	.	.	.	-1	KCTD19	HGNC	24753	protein_coding	YES	CCDS42179.1	ENSP00000305702	KCD19_HUMAN	J3KSZ9_HUMAN,H3BVC0_HUMAN	UPI00001D7875	.	tolerated(0.21)	benign(0)	15/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTGATGGCCA	.	4	ESCA
FOXF1	0	.	GRCh37	16	86544572	86544572	+	Missense_Mutation	SNP	G	G	A	rs148498631	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397G>A	p.Glu133Lys	p.E133K	ENST00000262426	1/2	77	20	57	79	79	0	FOXF1,missense_variant,p.Glu133Lys,ENST00000262426,;FENDRR,upstream_gene_variant,,ENST00000599749,;FENDRR,upstream_gene_variant,,ENST00000593604,;FENDRR,upstream_gene_variant,,ENST00000597578,;FENDRR,upstream_gene_variant,,ENST00000595886,;	A	ENSG00000103241	ENST00000262426	Transcript	missense_variant	440	397	133	E/K	Gag/Aag	rs148498631	.	.	1	FOXF1	HGNC	3809	protein_coding	YES	CCDS10957.2	ENSP00000262426	FOXF1_HUMAN	.	UPI000059D3CC	.	deleterious(0.01)	probably_damaging(0.997)	1/2	.	PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF148,hmmpanther:PTHR11829,Gene3D:1.10.10.10,Pfam_domain:PF00250,SMART_domains:SM00339,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	C:0.0002	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTCGAGGAG	.	5	ESCA
MYH13	0	.	GRCh37	17	10267795	10267795	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53G>A	p.Arg18Gln	p.R18Q	ENST00000418404	2/41	47	15	32	38	38	0	MYH13,missense_variant,p.Arg18Gln,ENST00000418404,;MYH13,missense_variant,p.Arg18Gln,ENST00000252172,;	T	ENSG00000006788	ENST00000418404	Transcript	missense_variant	217	53	18	R/Q	cGg/cAg	.	.	.	-1	MYH13	HGNC	7571	protein_coding	YES	CCDS45613.1	ENSP00000404570	MYH13_HUMAN	.	UPI0000DB39EA	.	deleterious(0.01)	probably_damaging(0.974)	2/41	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTCCGGAGG	.	5	ESCA
MED1	0	.	GRCh37	17	37566857	37566857	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1617C>T	p.%3D	p.N539N	ENST00000300651	17/17	42	22	20	27	27	0	MED1,synonymous_variant,p.%3D,ENST00000300651,;MED1,synonymous_variant,p.%3D,ENST00000394287,;CTB-131K11.1,downstream_gene_variant,,ENST00000582842,;MED1,3_prime_UTR_variant,,ENST00000577831,;	A	ENSG00000125686	ENST00000300651	Transcript	synonymous_variant	1841	1617	539	N	aaC/aaT	.	.	.	-1	MED1	HGNC	9234	protein_coding	YES	CCDS11336.1	ENSP00000300651	MED1_HUMAN	.	UPI0000167F57	.	.	.	17/17	.	hmmpanther:PTHR12881	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCAGGTTCTT	.	5	ESCA
HDAC5	0	.	GRCh37	17	42154296	42154299	+	3'UTR	DEL	AGGC	AGGC	-	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	AGGC	AGGC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1445_*1448delGCCT	.	.	ENST00000225983	27/27	45	25	20	26	26	0	HDAC5,3_prime_UTR_variant,,ENST00000393622,;HDAC5,3_prime_UTR_variant,,ENST00000225983,;HDAC5,3_prime_UTR_variant,,ENST00000336057,;G6PC3,downstream_gene_variant,,ENST00000590253,;G6PC3,downstream_gene_variant,,ENST00000269097,;HDAC5,downstream_gene_variant,,ENST00000586802,;G6PC3,downstream_gene_variant,,ENST00000591696,;G6PC3,downstream_gene_variant,,ENST00000585962,;G6PC3,downstream_gene_variant,,ENST00000585361,;G6PC3,downstream_gene_variant,,ENST00000588558,;HDAC5,downstream_gene_variant,,ENST00000593013,;G6PC3,downstream_gene_variant,,ENST00000590639,;HDAC5,downstream_gene_variant,,ENST00000592385,;G6PC3,downstream_gene_variant,,ENST00000593115,;HDAC5,downstream_gene_variant,,ENST00000586339,;	-	ENSG00000108840	ENST00000225983	Transcript	3_prime_UTR_variant	5141-5144	.	.	.	.	.	.	.	-1	HDAC5	HGNC	14068	protein_coding	YES	CCDS32663.1	ENSP00000225983	HDAC5_HUMAN	K7EJZ7_HUMAN,K7EJL6_HUMAN	UPI0000508BBA	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAGAGAGGCCTAGT	.	3	ESCA
TRIM37	0	.	GRCh37	17	57109426	57109426	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1779C>T	p.%3D	p.S593S	ENST00000262294	18/24	73	68	5	42	42	0	TRIM37,synonymous_variant,p.%3D,ENST00000393065,;TRIM37,synonymous_variant,p.%3D,ENST00000393066,;TRIM37,synonymous_variant,p.%3D,ENST00000376149,;TRIM37,synonymous_variant,p.%3D,ENST00000262294,;TRIM37,3_prime_UTR_variant,,ENST00000577554,;	A	ENSG00000108395	ENST00000262294	Transcript	synonymous_variant	2039	1779	593	S	tcC/tcT	.	.	.	-1	TRIM37	HGNC	7523	protein_coding	YES	CCDS32694.1	ENSP00000262294	TRI37_HUMAN	B3KMU3_HUMAN,A8K0V9_HUMAN	UPI0000167B57	.	.	.	18/24	.	hmmpanther:PTHR24103:SF229,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTACTGGAACC	.	2	ESCA
TP53	0	.	GRCh37	17	7578191	7578191	+	Missense_Mutation	SNP	A	A	C	rs530941076	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	6/11	73	17	55	63	63	0	TP53,missense_variant,p.Tyr220Asp,ENST00000413465,;TP53,missense_variant,p.Tyr220Asp,ENST00000420246,;TP53,missense_variant,p.Tyr220Asp,ENST00000269305,;TP53,missense_variant,p.Tyr88Asp,ENST00000509690,;TP53,missense_variant,p.Tyr220Asp,ENST00000359597,;TP53,missense_variant,p.Tyr127Asp,ENST00000514944,;TP53,missense_variant,p.Tyr220Asp,ENST00000445888,;TP53,missense_variant,p.Tyr220Asp,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	848	658	220	Y/D	Tat/Gat	rs530941076,TP53_g.12727T>G,TP53_g.12727T>C,TP53_g.12727T>A,COSM44637,COSM11847,COSM44672,COSM1172476,COSM2744705,COSM1630416,COSM1630417,COSM1172477,COSM2744707,COSM1630419,COSM1172479,COSM2744709,COSM3773306,COSM3732688,COSM3773305,COSM3732687,COSM2744706,COSM1726886,COSM2744708,COSM1172478,COSM1630418	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	G:0.0002	G:0.0008,G:0.0008	G:0,G:0	.	G:0,G:0	G:0,G:0	G:0,G:0	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.Y220*|c.660T>G|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y220C|c.659A>G|264,CODON|p.Y220C|c.659A>G|63,CODON|p.Y127C|c.380A>G|63,CODON|p.Y127S|c.380A>C|4,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220C|c.659A>G|25,CODON|p.Y220S|c.659A>C|3,CODON|p.Y220S|c.659A>C|4,CODON|p.Y220C|c.659A>G|61,CODON|p.Y220S|c.659A>C|13,CODON|p.Y220C|c.659A>G|33,BUFFER|p.P223L|c.668C>T|3,BUFFER|p.P222P|c.666G>C|3,BUFFER|p.P222L|c.665C>T|4,BUFFER|p.P222T|c.664C>A|3,BUFFER|p.E221G|c.662A>G|3,BUFFER|p.E221fs*4|c.660_661insN|3,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E221*|c.661G>T|6,BUFFER|p.E128*|c.382G>T|6,BUFFER|p.E221*|c.661G>T|10,BUFFER|p.?|c.252+10T>A|3,BUFFER|p.Y220N|c.658T>A|16,BUFFER|p.?|c.252+10T>C|4,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220H|c.658T>C|13,BUFFER|p.Y220H|c.658T>C|4,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.Y127H|c.379T>C|4,BUFFER|p.Y127N|c.379T>A|3,BUFFER|p.Y220N|c.658T>A|3,BUFFER|p.P219P|c.657C>T|3,BUFFER|p.Y220fs*27|c.655delC|4,BUFFER|p.V218delV|c.652_654delGTG|3,BUFFER|p.P219S|c.655C>T|4,BUFFER|p.V218G|c.653T>G|6,BUFFER|p.V218A|c.653T>C|3,BUFFER|p.V218E|c.653T>A|8,BUFFER|p.V218M|c.652G>A|7,BUFFER|p.V217A|c.650T>C|5,BUFFER|p.V217G|c.650T>G|4,BUFFER|p.V217E|c.650T>A|3,BUFFER|p.V218delV|c.646_648delGTG|8,BUFFER|p.V216G|c.647T>G|5,BUFFER|p.V216A|c.647T>C|3,BUFFER|p.V216E|c.647T>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATAGGGCA	by1000G	5	ESCA
ABHD3	0	.	GRCh37	18	19231047	19231047	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*505A>G	.	.	ENST00000289119	9/9	32	25	7	16	16	0	ABHD3,3_prime_UTR_variant,,ENST00000580981,;ABHD3,3_prime_UTR_variant,,ENST00000289119,;ABHD3,downstream_gene_variant,,ENST00000580477,;ABHD3,downstream_gene_variant,,ENST00000578270,;ABHD3,downstream_gene_variant,,ENST00000577564,;	C	ENSG00000158201	ENST00000289119	Transcript	3_prime_UTR_variant	1875	.	.	.	.	.	.	.	-1	ABHD3	HGNC	18718	protein_coding	YES	CCDS32802.1	ENSP00000289119	ABHD3_HUMAN	.	UPI0000163938	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGAATACATA	.	2	ESCA
USP14	0	.	GRCh37	18	203180	203180	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1025A>G	p.Lys342Arg	p.K342R	ENST00000261601	12/16	47	23	24	53	53	0	USP14,missense_variant,p.Lys342Arg,ENST00000261601,;USP14,missense_variant,p.Lys296Arg,ENST00000383589,;USP14,missense_variant,p.Lys331Arg,ENST00000400266,;USP14,missense_variant,p.Lys307Arg,ENST00000582707,;USP14,non_coding_transcript_exon_variant,,ENST00000578786,;USP14,non_coding_transcript_exon_variant,,ENST00000578942,;	G	ENSG00000101557	ENST00000261601	Transcript	missense_variant	1116	1025	342	K/R	aAa/aGa	.	.	.	1	USP14	HGNC	12612	protein_coding	YES	CCDS32780.1	ENSP00000261601	UBP14_HUMAN	J3KS55_HUMAN,D3DUG9_HUMAN	UPI0000163941	.	deleterious(0.03)	possibly_damaging(0.77)	12/16	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF351,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAAAGTTC	.	5	ESCA
NOL4	0	.	GRCh37	18	31432214	31432214	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*592A>T	.	.	ENST00000261592	11/11	125	111	14	92	92	0	NOL4,3_prime_UTR_variant,,ENST00000261592,;NOL4,3_prime_UTR_variant,,ENST00000269185,;NOL4,downstream_gene_variant,,ENST00000589544,;NOL4,downstream_gene_variant,,ENST00000538587,;NOL4,downstream_gene_variant,,ENST00000535384,;NOL4,downstream_gene_variant,,ENST00000535475,;NOL4,downstream_gene_variant,,ENST00000590712,;NOL4,downstream_gene_variant,,ENST00000586314,;	A	ENSG00000101746	ENST00000261592	Transcript	3_prime_UTR_variant	2807	.	.	.	.	.	.	.	-1	NOL4	HGNC	7870	protein_coding	YES	CCDS11907.2	ENSP00000261592	NOL4_HUMAN	.	UPI000059D504	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAGGTACTTA	.	4	ESCA
C3P1	0	.	GRCh37	19	10157403	10157403	+	Intron	SNP	C	C	T	rs766987156	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2091-3C>T	.	.	ENST00000497718	.	42	34	7	31	31	0	C3P1,splice_region_variant,,ENST00000495140,;C3P1,splice_region_variant,,ENST00000497718,;	T	ENSG00000167798	ENST00000497718	Transcript	splice_region_variant	.	.	.	.	.	rs766987156	.	.	1	C3P1	HGNC	34414	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	15/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCCAGCGG	.	4	ESCA
ZNF440	0	.	GRCh37	19	11942659	11942659	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668C>G	p.Thr223Ser	p.T223S	ENST00000304060	4/4	138	108	30	109	109	0	ZNF440,missense_variant,p.Thr223Ser,ENST00000304060,;ZNF440,missense_variant,p.Thr226Ser,ENST00000427505,;ZNF440,downstream_gene_variant,,ENST00000457526,;ZNF440,downstream_gene_variant,,ENST00000588954,;ZNF440,downstream_gene_variant,,ENST00000414255,;	G	ENSG00000171295	ENST00000304060	Transcript	missense_variant	832	668	223	T/S	aCt/aGt	.	.	.	1	ZNF440	HGNC	20874	protein_coding	YES	CCDS42503.1	ENSP00000305373	ZN440_HUMAN	K7EJ55_HUMAN,C9JG89_HUMAN	UPI0000074249	.	tolerated(0.1)	benign(0.37)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF35,hmmpanther:PTHR24381,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACACTGGAG	.	5	ESCA
ZNF433	0	.	GRCh37	19	12146500	12146500	+	5'UTR	SNP	C	C	G	rs184413618	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-146G>C	.	.	ENST00000344980	1/4	18	15	3	26	26	0	ZNF433,5_prime_UTR_variant,,ENST00000344980,;ZNF433,5_prime_UTR_variant,,ENST00000411841,;ZNF433,5_prime_UTR_variant,,ENST00000550745,;ZNF433,5_prime_UTR_variant,,ENST00000550507,;ZNF433,5_prime_UTR_variant,,ENST00000419886,;ZNF433,upstream_gene_variant,,ENST00000552904,;ZNF433,upstream_gene_variant,,ENST00000547560,;ZNF433,upstream_gene_variant,,ENST00000455504,;CTD-2006C1.2,non_coding_transcript_exon_variant,,ENST00000591838,;CTD-2006C1.2,non_coding_transcript_exon_variant,,ENST00000476474,;CTD-2006C1.2,upstream_gene_variant,,ENST00000591898,;ZNF433,5_prime_UTR_variant,,ENST00000548669,;CTD-2006C1.2,non_coding_transcript_exon_variant,,ENST00000588047,;CTD-2006C1.10,intron_variant,,ENST00000547473,;	G	ENSG00000197647	ENST00000344980	Transcript	5_prime_UTR_variant	26	.	.	.	.	rs184413618	.	.	-1	ZNF433	HGNC	20811	protein_coding	YES	CCDS45983.1	ENSP00000339767	ZN433_HUMAN	F8W652_HUMAN,F8W0C9_HUMAN,F8VXJ9_HUMAN	UPI0000071556	.	.	.	1/4	.	.	A:0.0008	A:0.0015	A:0.0014	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGAGCAGGGC	byFrequency|by1000G	2	ESCA
CC2D1A	0	.	GRCh37	19	14034533	14034533	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1849A>C	p.Lys617Gln	p.K617Q	ENST00000318003	17/29	56	26	29	37	37	0	CC2D1A,missense_variant,p.Lys617Gln,ENST00000589606,;CC2D1A,missense_variant,p.Lys72Gln,ENST00000587508,;CC2D1A,missense_variant,p.Lys617Gln,ENST00000318003,;CC2D1A,3_prime_UTR_variant,,ENST00000586955,;CC2D1A,non_coding_transcript_exon_variant,,ENST00000588932,;CC2D1A,non_coding_transcript_exon_variant,,ENST00000589224,;CC2D1A,non_coding_transcript_exon_variant,,ENST00000589138,;CC2D1A,downstream_gene_variant,,ENST00000589679,;CC2D1A,downstream_gene_variant,,ENST00000585896,;	C	ENSG00000132024	ENST00000318003	Transcript	missense_variant	2090	1849	617	K/Q	Aag/Cag	.	.	.	1	CC2D1A	HGNC	30237	protein_coding	YES	CCDS42512.1	ENSP00000313601	C2D1A_HUMAN	.	UPI0000203524	.	deleterious(0.02)	benign(0.394)	17/29	.	hmmpanther:PTHR13076,hmmpanther:PTHR13076:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTAAGCGG	.	5	ESCA
KIAA1683	0	.	GRCh37	19	18367981	18367981	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9C>A	.	.	ENST00000392413	4/4	49	24	24	50	50	0	KIAA1683,3_prime_UTR_variant,,ENST00000600359,;KIAA1683,3_prime_UTR_variant,,ENST00000600328,;KIAA1683,3_prime_UTR_variant,,ENST00000392413,;PDE4C,upstream_gene_variant,,ENST00000355502,;PDE4C,upstream_gene_variant,,ENST00000596647,;KIAA1683,non_coding_transcript_exon_variant,,ENST00000599638,;PDE4C,upstream_gene_variant,,ENST00000600667,;	T	ENSG00000130518	ENST00000392413	Transcript	3_prime_UTR_variant	4329	.	.	.	.	.	.	.	-1	KIAA1683	HGNC	29350	protein_coding	YES	CCDS46017.1	ENSP00000376213	K1683_HUMAN	U3KQN7_HUMAN,U3KQG6_HUMAN	UPI000194EC26	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGAGCCAGG	.	5	ESCA
ZNF93	0	.	GRCh37	19	20045338	20045338	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1574T>C	p.Ile525Thr	p.I525T	ENST00000343769	4/4	61	51	10	51	51	0	ZNF93,missense_variant,p.Ile525Thr,ENST00000343769,;AC007204.1,downstream_gene_variant,,ENST00000595282,;ZNF93,downstream_gene_variant,,ENST00000588146,;ZNF93,downstream_gene_variant,,ENST00000592160,;AC007204.2,intron_variant,,ENST00000592245,;ZNF93,downstream_gene_variant,,ENST00000586021,;	C	ENSG00000184635	ENST00000343769	Transcript	missense_variant	1602	1574	525	I/T	aTt/aCt	.	.	.	1	ZNF93	HGNC	13169	protein_coding	YES	CCDS32973.1	ENSP00000342002	ZNF93_HUMAN	K7EPV7_HUMAN,B4DJ46_HUMAN	UPI00002263B9	.	tolerated(1)	benign(0.002)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF270,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTATTAAAC	.	5	ESCA
DOT1L	0	.	GRCh37	19	2213592	2213592	+	Missense_Mutation	SNP	G	G	A	rs754539898	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1612G>A	p.Ala538Thr	p.A538T	ENST00000398665	17/28	54	23	30	43	43	0	DOT1L,missense_variant,p.Ala2Thr,ENST00000586024,;DOT1L,missense_variant,p.Ala538Thr,ENST00000398665,;AC004490.1,non_coding_transcript_exon_variant,,ENST00000585593,;DOT1L,non_coding_transcript_exon_variant,,ENST00000591498,;DOT1L,upstream_gene_variant,,ENST00000608122,;DOT1L,upstream_gene_variant,,ENST00000472540,;DOT1L,upstream_gene_variant,,ENST00000482433,;	A	ENSG00000104885	ENST00000398665	Transcript	missense_variant	1648	1612	538	A/T	Gcc/Acc	rs754539898	.	.	1	DOT1L	HGNC	24948	protein_coding	YES	CCDS42460.1	ENSP00000381657	DOT1L_HUMAN	.	UPI000002A839	.	deleterious(0.04)	benign(0.028)	17/28	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21451:SF0,hmmpanther:PTHR21451,PIRSF_domain:PIRSF037123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGGCCCAG	byFrequency	5	ESCA
ZNF257	0	.	GRCh37	19	22271020	22271020	+	Silent	SNP	G	G	A	rs761079456	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.468G>A	p.%3D	p.K156K	ENST00000594947	4/4	77	73	4	60	60	0	ZNF257,synonymous_variant,p.%3D,ENST00000597927,;ZNF257,synonymous_variant,p.%3D,ENST00000594947,;ZNF257,3_prime_UTR_variant,,ENST00000600162,;ZNF257,3_prime_UTR_variant,,ENST00000435820,;	A	ENSG00000197134	ENST00000594947	Transcript	synonymous_variant	612	468	156	K	aaG/aaA	rs761079456	.	.	1	ZNF257	HGNC	13498	protein_coding	YES	CCDS46030.1	ENSP00000470209	ZN257_HUMAN	M0R0N1_HUMAN	UPI0000E045CA	.	.	.	4/4	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF109,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATAAGTTTTC	.	2	ESCA
CEBPA	0	.	GRCh37	19	33791684	33791684	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*560C>A	.	.	ENST00000498907	1/1	16	9	7	14	14	0	CEBPA,3_prime_UTR_variant,,ENST00000498907,;CTD-2540B15.9,upstream_gene_variant,,ENST00000593041,;CTD-2540B15.11,intron_variant,,ENST00000589932,;CTD-2540B15.7,upstream_gene_variant,,ENST00000587312,;CEBPA-AS1,upstream_gene_variant,,ENST00000592982,;AC008738.1,non_coding_transcript_exon_variant,,ENST00000425420,;CEBPA-AS1,upstream_gene_variant,,ENST00000320232,;	T	ENSG00000245848	ENST00000498907	Transcript	3_prime_UTR_variant	1787	.	.	.	.	.	.	.	-1	CEBPA	HGNC	1833	protein_coding	YES	CCDS54243.1	ENSP00000427514	CEBPA_HUMAN	Q6P3S4_HUMAN	UPI0000167F92	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTAGAACTA	.	5	ESCA
ARHGEF1	0	.	GRCh37	19	42411345	42411345	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*106G>T	.	.	ENST00000337665	29/29	69	37	31	85	85	0	ARHGEF1,missense_variant,p.Gly876Val,ENST00000378152,;ARHGEF1,3_prime_UTR_variant,,ENST00000599846,;ARHGEF1,3_prime_UTR_variant,,ENST00000337665,;ARHGEF1,3_prime_UTR_variant,,ENST00000347545,;ARHGEF1,3_prime_UTR_variant,,ENST00000354532,;ARHGEF1,intron_variant,,ENST00000599589,;ARHGEF1,downstream_gene_variant,,ENST00000594258,;ARHGEF1,downstream_gene_variant,,ENST00000595723,;CTD-2575K13.6,downstream_gene_variant,,ENST00000597630,;ARHGEF1,non_coding_transcript_exon_variant,,ENST00000595897,;ARHGEF1,non_coding_transcript_exon_variant,,ENST00000593609,;ARHGEF1,non_coding_transcript_exon_variant,,ENST00000600274,;ARHGEF1,downstream_gene_variant,,ENST00000598444,;ARHGEF1,downstream_gene_variant,,ENST00000600517,;ARHGEF1,downstream_gene_variant,,ENST00000594044,;ARHGEF1,downstream_gene_variant,,ENST00000598587,;CTD-2575K13.6,downstream_gene_variant,,ENST00000598387,;	T	ENSG00000076928	ENST00000337665	Transcript	3_prime_UTR_variant	2910	.	.	.	.	.	.	.	1	ARHGEF1	HGNC	681	protein_coding	YES	CCDS12590.1	ENSP00000337261	ARHG1_HUMAN	.	UPI0000231C94	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGGGCCTGA	.	5	ESCA
SLC25A41	0	.	GRCh37	19	6433618	6433618	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.87C>T	p.%3D	p.A29A	ENST00000321510	1/7	75	39	36	69	69	0	SLC25A41,synonymous_variant,p.%3D,ENST00000321510,;SLC25A23,downstream_gene_variant,,ENST00000601322,;SLC25A23,downstream_gene_variant,,ENST00000598908,;SLC25A23,downstream_gene_variant,,ENST00000595810,;SLC25A23,downstream_gene_variant,,ENST00000601760,;SLC25A41,synonymous_variant,p.%3D,ENST00000458275,;SLC25A41,synonymous_variant,p.%3D,ENST00000597558,;SLC25A23,downstream_gene_variant,,ENST00000264088,;SLC25A23,downstream_gene_variant,,ENST00000598704,;	A	ENSG00000181240	ENST00000321510	Transcript	synonymous_variant	156	87	29	A	gcC/gcT	.	.	.	-1	SLC25A41	HGNC	28533	protein_coding	YES	CCDS45937.1	ENSP00000322649	S2541_HUMAN	.	UPI00003751E5	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGGGGCTTT	.	5	ESCA
XAB2	0	.	GRCh37	19	7684915	7684915	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2313G>T	p.%3D	p.L771L	ENST00000358368	17/19	43	35	8	44	44	0	XAB2,synonymous_variant,p.%3D,ENST00000358368,;XAB2,synonymous_variant,p.%3D,ENST00000534844,;CAMSAP3,downstream_gene_variant,,ENST00000160298,;CAMSAP3,downstream_gene_variant,,ENST00000446248,;XAB2,non_coding_transcript_exon_variant,,ENST00000595288,;CAMSAP3,downstream_gene_variant,,ENST00000593434,;XAB2,downstream_gene_variant,,ENST00000600230,;CAMSAP3,downstream_gene_variant,,ENST00000595692,;XAB2,downstream_gene_variant,,ENST00000596134,;	A	ENSG00000076924	ENST00000358368	Transcript	synonymous_variant	2351	2313	771	L	ctG/ctT	.	.	.	-1	XAB2	HGNC	14089	protein_coding	YES	CCDS32892.1	ENSP00000351137	SYF1_HUMAN	Q68CN2_HUMAN,F5H315_HUMAN	UPI0000001BDE	.	.	.	17/19	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11246,hmmpanther:PTHR11246:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGCAGCTT	.	5	ESCA
TBX15	0	.	GRCh37	1	119427370	119427370	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1476C>T	p.%3D	p.S492S	ENST00000207157	8/8	44	39	5	64	64	0	TBX15,synonymous_variant,p.%3D,ENST00000369429,;TBX15,synonymous_variant,p.%3D,ENST00000207157,;TBX15,synonymous_variant,p.%3D,ENST00000449873,;	A	ENSG00000092607	ENST00000207157	Transcript	synonymous_variant	1791	1476	492	S	tcC/tcT	.	.	.	-1	TBX15	HGNC	11594	protein_coding	YES	CCDS30816.1	ENSP00000207157	TBX15_HUMAN	Q8N8P2_HUMAN	UPI000046D38E	.	.	.	8/8	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCACGGACAT	.	4	ESCA
FLG	0	.	GRCh37	1	152276849	152276849	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10513C>T	p.His3505Tyr	p.H3505Y	ENST00000368799	3/3	140	87	52	100	100	0	FLG,missense_variant,p.His3505Tyr,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	A	ENSG00000143631	ENST00000368799	Transcript	missense_variant	10549	10513	3505	H/Y	Cat/Tat	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	unknown(0)	3/3	.	Pfam_domain:PF03516	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATGCGACC	.	5	ESCA
KIAA0907	0	.	GRCh37	1	155883705	155883705	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*207A>G	.	.	ENST00000368321	14/14	24	9	15	13	13	0	KIAA0907,3_prime_UTR_variant,,ENST00000368320,;KIAA0907,3_prime_UTR_variant,,ENST00000368321,;RIT1,upstream_gene_variant,,ENST00000368323,;RIT1,upstream_gene_variant,,ENST00000609492,;RIT1,upstream_gene_variant,,ENST00000539040,;RIT1,upstream_gene_variant,,ENST00000368322,;KIAA0907,downstream_gene_variant,,ENST00000465953,;KIAA0907,downstream_gene_variant,,ENST00000466520,;KIAA0907,downstream_gene_variant,,ENST00000478002,;RIT1,upstream_gene_variant,,ENST00000461050,;RIT1,upstream_gene_variant,,ENST00000462687,;	C	ENSG00000132680	ENST00000368321	Transcript	3_prime_UTR_variant	2076	.	.	.	.	.	.	.	-1	KIAA0907	HGNC	29145	protein_coding	YES	CCDS30885.1	ENSP00000357304	K0907_HUMAN	.	UPI00001A36E0	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTAATTAAAT	.	2	ESCA
F5	0	.	GRCh37	1	169513654	169513654	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1855A>C	p.Asn619His	p.N619H	ENST00000367797	12/25	50	41	8	40	40	0	F5,missense_variant,p.Asn624His,ENST00000367796,;F5,missense_variant,p.Asn619His,ENST00000367797,;F5,downstream_gene_variant,,ENST00000546081,;	G	ENSG00000198734	ENST00000367797	Transcript	missense_variant	2057	1855	619	N/H	Aat/Cat	.	.	.	-1	F5	HGNC	3542	protein_coding	YES	CCDS1281.1	ENSP00000356771	FA5_HUMAN	Q8TD21_HUMAN,Q2HZZ1_HUMAN,Q1L610_HUMAN	UPI0000070F01	.	deleterious(0.01)	possibly_damaging(0.861)	12/25	.	hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.40.420,Superfamily_domains:SSF49503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATTCTGGG	.	5	ESCA
VAMP4	0	.	GRCh37	1	171688314	171688314	+	Missense_Mutation	SNP	T	T	C	rs145867825	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161A>G	p.Lys54Arg	p.K54R	ENST00000236192	4/8	78	23	54	60	60	0	VAMP4,missense_variant,p.Lys54Arg,ENST00000236192,;VAMP4,missense_variant,p.Lys53Arg,ENST00000367740,;VAMP4,missense_variant,p.Lys53Arg,ENST00000415773,;VAMP4,non_coding_transcript_exon_variant,,ENST00000482519,;VAMP4,missense_variant,p.Lys54Arg,ENST00000474047,;	C	ENSG00000117533	ENST00000236192	Transcript	missense_variant	548	161	54	K/R	aAg/aGg	rs145867825	.	.	-1	VAMP4	HGNC	12645	protein_coding	YES	CCDS1298.1	ENSP00000236192	VAMP4_HUMAN	Q6IAZ3_HUMAN	UPI00000015F3	.	tolerated(0.56)	benign(0.011)	4/8	.	Superfamily_domains:SSF58038,Gene3D:2kogA00,Pfam_domain:PF00957,hmmpanther:PTHR21136,hmmpanther:PTHR21136:SF83,PROSITE_profiles:PS50892	C:0.0004	C:0.0015	C:0	.	C:0	C:0	C:0	C:0.002	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGCTTAATT	byFrequency|byCluster|by1000G	5	ESCA
USH2A	0	.	GRCh37	1	215901650	215901650	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11788G>C	p.Asp3930His	p.D3930H	ENST00000307340	61/72	97	91	5	55	55	0	USH2A,missense_variant,p.Asp3930His,ENST00000366943,;USH2A,missense_variant,p.Asp3930His,ENST00000307340,;	G	ENSG00000042781	ENST00000307340	Transcript	missense_variant	12175	11788	3930	D/H	Gac/Cac	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	benign(0.365)	61/72	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGTCTCCTT	.	2	ESCA
RYR2	0	.	GRCh37	1	237617836	237617836	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1438C>T	p.Arg480Ter	p.R480*	ENST00000366574	15/105	92	17	74	47	47	0	RYR2,stop_gained,p.Arg464Ter,ENST00000542537,;RYR2,stop_gained,p.Arg480Ter,ENST00000366574,;RYR2,stop_gained,p.Arg478Ter,ENST00000360064,;	T	ENSG00000198626	ENST00000366574	Transcript	stop_gained	1755	1438	480	R/*	Cga/Tga	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	.	15/105	.	Superfamily_domains:0048280,Pfam_domain:PF01365,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTACGAGCC	.	5	ESCA
EXO1	0	.	GRCh37	1	242015637	242015637	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205C>A	p.His69Asn	p.H69N	ENST00000366548	5/16	70	52	17	30	30	0	EXO1,missense_variant,p.His69Asn,ENST00000450748,;EXO1,missense_variant,p.His69Asn,ENST00000348581,;EXO1,missense_variant,p.His69Asn,ENST00000518483,;EXO1,missense_variant,p.His69Asn,ENST00000366548,;EXO1,intron_variant,,ENST00000437497,;EXO1,intron_variant,,ENST00000423131,;EXO1,intron_variant,,ENST00000523590,;EXO1,downstream_gene_variant,,ENST00000519225,;EXO1,non_coding_transcript_exon_variant,,ENST00000469419,;EXO1,intron_variant,,ENST00000493702,;	A	ENSG00000174371	ENST00000366548	Transcript	missense_variant	798	205	69	H/N	Cat/Aat	.	.	.	1	EXO1	HGNC	3511	protein_coding	YES	CCDS1620.1	ENSP00000355506	EXO1_HUMAN	Q5T399_HUMAN	UPI000013DDA8	.	tolerated(0.25)	benign(0.016)	5/16	.	hmmpanther:PTHR11081:SF8,hmmpanther:PTHR11081,Gene3D:3.40.50.1010,Pfam_domain:PF00752,SMART_domains:SM00485,Superfamily_domains:SSF88723	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCTCATGGG	.	5	ESCA
ZNF496	0	.	GRCh37	1	247463850	247463850	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735C>T	p.Arg579Cys	p.R579C	ENST00000294753	9/9	38	31	6	34	34	0	ZNF496,missense_variant,p.Arg615Cys,ENST00000366498,;ZNF496,missense_variant,p.Arg504Cys,ENST00000461277,;ZNF496,missense_variant,p.Arg579Cys,ENST00000294753,;ZNF496,non_coding_transcript_exon_variant,,ENST00000462139,;	A	ENSG00000162714	ENST00000294753	Transcript	missense_variant	2200	1735	579	R/C	Cgt/Tgt	.	.	.	-1	ZNF496	HGNC	23713	protein_coding	YES	CCDS1631.1	ENSP00000294753	ZN496_HUMAN	.	UPI000007025B	.	deleterious(0)	benign(0.106)	9/9	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF212,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAACGGCGCT	.	5	ESCA
PABPC4	0	.	GRCh37	1	40033068	40033068	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972+355G>T	.	.	ENST00000372858	.	34	10	24	45	45	0	PABPC4,intron_variant,,ENST00000372858,;PABPC4,intron_variant,,ENST00000372862,;PABPC4,intron_variant,,ENST00000527718,;PABPC4,intron_variant,,ENST00000372857,;PABPC4,intron_variant,,ENST00000372856,;PABPC4,intron_variant,,ENST00000421687,;PABPC4,downstream_gene_variant,,ENST00000451091,;PABPC4,upstream_gene_variant,,ENST00000437136,;PABPC4,downstream_gene_variant,,ENST00000474378,;SNORA55,non_coding_transcript_exon_variant,,ENST00000364587,;RP11-69E11.8,intron_variant,,ENST00000415255,;PABPC4,downstream_gene_variant,,ENST00000529216,;PABPC4,intron_variant,,ENST00000470443,;PABPC4,intron_variant,,ENST00000513632,;PABPC4,intron_variant,,ENST00000525669,;PABPC4,upstream_gene_variant,,ENST00000468476,;PABPC4,downstream_gene_variant,,ENST00000492519,;PABPC4,upstream_gene_variant,,ENST00000492468,;PABPC4,upstream_gene_variant,,ENST00000525045,;PABPC4,upstream_gene_variant,,ENST00000461578,;PABPC4,upstream_gene_variant,,ENST00000484555,;PABPC4,upstream_gene_variant,,ENST00000483770,;PABPC4,downstream_gene_variant,,ENST00000525751,;PABPC4,upstream_gene_variant,,ENST00000477556,;	A	ENSG00000090621	ENST00000372858	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PABPC4	HGNC	8557	protein_coding	YES	CCDS44115.1	ENSP00000361949	PABP4_HUMAN	B1ANR1_HUMAN	UPI00002057C5	.	.	.	.	7/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGACAGGCC	.	5	ESCA
SGIP1	0	.	GRCh37	1	67109265	67109267	+	In_Frame_Del	DEL	GAA	GAA	-	rs773628491	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	GAA	GAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334_336delGAA	p.Glu112del	p.E112del	ENST00000371037	7/25	31	10	21	20	20	0	SGIP1,inframe_deletion,p.Glu112del,ENST00000424320,;SGIP1,inframe_deletion,p.Glu116del,ENST00000237247,;SGIP1,inframe_deletion,p.Glu88del,ENST00000371039,;SGIP1,inframe_deletion,p.Glu112del,ENST00000371037,;SGIP1,inframe_deletion,p.Glu87del,ENST00000371036,;SGIP1,inframe_deletion,p.Glu69del,ENST00000371035,;SGIP1,non_coding_transcript_exon_variant,,ENST00000483060,;SGIP1,non_coding_transcript_exon_variant,,ENST00000468286,;	-	ENSG00000118473	ENST00000371037	Transcript	inframe_deletion	399-401	322-324	108	E/-	GAA/-	rs773628491	.	.	1	SGIP1	HGNC	25412	protein_coding	YES	CCDS30744.1	ENSP00000360076	SGIP1_HUMAN	.	UPI000045891B	.	.	.	7/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23065:SF5,hmmpanther:PTHR23065	.	.	.	.	.	.	.	-:0.0007	-:0.0015	.	.	.	.	.	.	.	MODERATE	.	deletion	.	12	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAATCGGAAGAAGA	.	2	ESCA
TGM6	0	.	GRCh37	20	2378611	2378611	+	Silent	SNP	C	C	T	rs564481002	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.591C>T	p.%3D	p.S197S	ENST00000202625	5/13	80	43	37	42	42	0	TGM6,synonymous_variant,p.%3D,ENST00000381423,;TGM6,synonymous_variant,p.%3D,ENST00000202625,;TGM6,non_coding_transcript_exon_variant,,ENST00000477505,;	T	ENSG00000166948	ENST00000202625	Transcript	synonymous_variant	652	591	197	S	agC/agT	rs564481002	.	.	1	TGM6	HGNC	16255	protein_coding	YES	CCDS13025.1	ENSP00000202625	TGM3L_HUMAN	.	UPI0000367011	.	.	.	5/13	.	hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF39,Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,Superfamily_domains:SSF54001	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAAGCCCCGG	by1000G	5	ESCA
RBM12	0	.	GRCh37	20	34238183	34238183	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2263C>T	.	.	ENST00000374114	3/3	36	24	12	24	24	0	RBM12,3_prime_UTR_variant,,ENST00000374114,;RBM12,3_prime_UTR_variant,,ENST00000359646,;CPNE1,intron_variant,,ENST00000352393,;CPNE1,intron_variant,,ENST00000414711,;CPNE1,intron_variant,,ENST00000458038,;CPNE1,intron_variant,,ENST00000397443,;CPNE1,intron_variant,,ENST00000434795,;CPNE1,intron_variant,,ENST00000317677,;CPNE1,intron_variant,,ENST00000397442,;CPNE1,intron_variant,,ENST00000440240,;CPNE1,intron_variant,,ENST00000412056,;CPNE1,intron_variant,,ENST00000317619,;CPNE1,intron_variant,,ENST00000430570,;CPNE1,intron_variant,,ENST00000416778,;CPNE1,intron_variant,,ENST00000435747,;CPNE1,intron_variant,,ENST00000420363,;CPNE1,intron_variant,,ENST00000439806,;CPNE1,intron_variant,,ENST00000437340,;CPNE1,intron_variant,,ENST00000397445,;CPNE1,intron_variant,,ENST00000414664,;CPNE1,intron_variant,,ENST00000397446,;CPNE1,intron_variant,,ENST00000437100,;RBM12,downstream_gene_variant,,ENST00000435161,;RBM12,downstream_gene_variant,,ENST00000424458,;RBM12,downstream_gene_variant,,ENST00000431148,;RBM12,downstream_gene_variant,,ENST00000374104,;RNU6-759P,upstream_gene_variant,,ENST00000516740,;CPNE1,intron_variant,,ENST00000401607,;RP1-309K20.6,intron_variant,,ENST00000541176,;RP1-309K20.6,intron_variant,,ENST00000454607,;CPNE1,intron_variant,,ENST00000439669,;CPNE1,intron_variant,,ENST00000483359,;RP1-309K20.6,intron_variant,,ENST00000441563,;	A	ENSG00000244462	ENST00000374114	Transcript	3_prime_UTR_variant	5326	.	.	.	.	.	.	.	-1	RBM12	HGNC	9898	protein_coding	YES	CCDS13261.1	ENSP00000363228	RBM12_HUMAN	Q69YJ7_HUMAN,Q5JX62_HUMAN,A6PVI1_HUMAN,A6PVI0_HUMAN	UPI0000073D24	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGATGAACAA	.	5	ESCA
COL20A1	0	.	GRCh37	20	61947988	61947988	+	Missense_Mutation	SNP	G	G	T	rs376634286	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2608G>T	p.Gly870Cys	p.G870C	ENST00000358894	21/36	74	49	25	82	82	0	COL20A1,missense_variant,p.Gly870Cys,ENST00000358894,;COL20A1,missense_variant,p.Gly877Cys,ENST00000422202,;COL20A1,missense_variant,p.Gly870Cys,ENST00000326996,;COL20A1,missense_variant,p.Gly877Cys,ENST00000435874,;COL20A1,upstream_gene_variant,,ENST00000415763,;COL20A1,upstream_gene_variant,,ENST00000455906,;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,;	T	ENSG00000101203	ENST00000358894	Transcript	missense_variant	2708	2608	870	G/C	Ggt/Tgt	rs376634286	.	.	1	COL20A1	HGNC	14670	protein_coding	YES	CCDS46628.1	ENSP00000351767	COKA1_HUMAN	.	UPI000051910D	.	deleterious(0.01)	possibly_damaging(0.597)	21/36	.	Superfamily_domains:SSF49899,SMART_domains:SM00210	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCGGTGGG	byCluster	5	ESCA
DSCAM	0	.	GRCh37	21	41414321	41414321	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5663C>T	p.Ala1888Val	p.A1888V	ENST00000400454	32/33	36	13	23	35	35	0	DSCAM,missense_variant,p.Ala1640Val,ENST00000404019,;DSCAM,missense_variant,p.Ala1888Val,ENST00000400454,;	A	ENSG00000171587	ENST00000400454	Transcript	missense_variant	6141	5663	1888	A/V	gCa/gTa	.	.	.	-1	DSCAM	HGNC	3039	protein_coding	YES	CCDS42929.1	ENSP00000383303	DSCAM_HUMAN	.	UPI00000422DF	.	deleterious(0)	probably_damaging(0.999)	32/33	.	hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACTGCCATA	.	5	ESCA
HIC2	0	.	GRCh37	22	21801761	21801761	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*729C>T	.	.	ENST00000443632	2/2	17	6	11	26	26	0	HIC2,3_prime_UTR_variant,,ENST00000443632,;HIC2,3_prime_UTR_variant,,ENST00000407598,;HIC2,3_prime_UTR_variant,,ENST00000407464,;	T	ENSG00000169635	ENST00000443632	Transcript	3_prime_UTR_variant	2949	.	.	.	.	.	.	.	1	HIC2	HGNC	18595	protein_coding	YES	CCDS13789.1	ENSP00000387757	HIC2_HUMAN	.	UPI000012C71C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTCCTGCGC	.	5	ESCA
AFF3	0	.	GRCh37	2	100199307	100199307	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2821A>G	p.Lys941Glu	p.K941E	ENST00000356421	16/24	57	36	20	52	51	0	AFF3,missense_variant,p.Lys941Glu,ENST00000409579,;AFF3,missense_variant,p.Lys941Glu,ENST00000356421,;AFF3,missense_variant,p.Lys916Glu,ENST00000317233,;AFF3,missense_variant,p.Lys916Glu,ENST00000409236,;AFF3,upstream_gene_variant,,ENST00000445815,;	C	ENSG00000144218	ENST00000356421	Transcript	missense_variant	2965	2821	941	K/E	Aag/Gag	.	.	.	-1	AFF3	HGNC	6473	protein_coding	YES	CCDS33258.1	ENSP00000348793	AFF3_HUMAN	.	UPI000041098C	.	tolerated(0.09)	benign(0.007)	16/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCTTTTTGC	.	5	ESCA
LPIN1	0	.	GRCh37	2	11966193	11966193	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000449576	.	53	48	4	26	25	1	LPIN1,3_prime_UTR_variant,,ENST00000396097,;LPIN1,3_prime_UTR_variant,,ENST00000256720,;LPIN1,downstream_gene_variant,,ENST00000449576,;LPIN1,downstream_gene_variant,,ENST00000396099,;LPIN1,downstream_gene_variant,,ENST00000404113,;LPIN1,downstream_gene_variant,,ENST00000425416,;LPIN1,downstream_gene_variant,,ENST00000487576,;LPIN1,non_coding_transcript_exon_variant,,ENST00000475922,;	G	ENSG00000134324	ENST00000449576	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1180	1	LPIN1	HGNC	13345	protein_coding	YES	CCDS58699.1	ENSP00000397908	.	F5GY24_HUMAN,C9J278_HUMAN,C9IYP2_HUMAN,B4DGZ6_HUMAN	UPI0002064F62	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTGGACAGAA	.	2	ESCA
NEB	0	.	GRCh37	2	152435902	152435902	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16654G>A	p.Asp5552Asn	p.D5552N	ENST00000397345	105/182	92	75	16	77	77	0	NEB,missense_variant,p.Asp5552Asn,ENST00000603639,;NEB,missense_variant,p.Asp5552Asn,ENST00000427231,;NEB,missense_variant,p.Asp5552Asn,ENST00000397345,;NEB,missense_variant,p.Asp5552Asn,ENST00000604864,;NEB,missense_variant,p.Asp282Asn,ENST00000413693,;NEB,intron_variant,,ENST00000172853,;NEB,intron_variant,,ENST00000409198,;	T	ENSG00000183091	ENST00000397345	Transcript	missense_variant	16857	16654	5552	D/N	Gac/Aac	.	.	.	-1	NEB	HGNC	7720	protein_coding	YES	CCDS54407.1	ENSP00000380505	.	H7C2D0_HUMAN,F8WCL5_HUMAN	UPI0002065BA0	.	.	probably_damaging(0.997)	105/182	.	PROSITE_profiles:PS51216,hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTGGTCGGGAA	.	3	ESCA
NFE2L2	0	.	GRCh37	2	178098810	178098810	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	2/5	105	53	52	63	63	0	NFE2L2,missense_variant,p.Glu63Gln,ENST00000449627,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000423513,;NFE2L2,missense_variant,p.Glu79Gln,ENST00000397062,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000446151,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000588123,;NFE2L2,missense_variant,p.Glu78Gln,ENST00000586532,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000421929,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000464747,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000448782,;NFE2L2,missense_variant,p.Glu63Gln,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	G	ENSG00000116044	ENST00000397062	Transcript	missense_variant	790	235	79	E/Q	Gag/Cag	COSM132851,COSM120958,COSM1631472	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E79Q|c.235G>C|11,BUFFER|p.E82D|c.246A>C|3,BUFFER|p.E82D|c.246A>T|6,BUFFER|p.E82G|c.245A>G|7,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81D|c.242G>A|6,BUFFER|p.G81V|c.242G>T|7,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.G81S|c.241G>A|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79K|c.235G>A|10,BUFFER|p.D77V|c.230A>T|5,BUFFER|p.D77G|c.230A>G|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTCTTCAT	.	5	ESCA
TTN	0	.	GRCh37	2	179597727	179597727	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16176G>C	p.Lys5392Asn	p.K5392N	ENST00000589042	55/363	39	31	8	49	49	0	TTN,missense_variant,p.Lys4148Asn,ENST00000342992,;TTN,missense_variant,p.Lys5392Asn,ENST00000589042,;TTN,missense_variant,p.Lys5075Asn,ENST00000591111,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000582847,;TTN-AS1,intron_variant,,ENST00000585451,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	16401	16176	5392	K/N	aaG/aaC	COSM3573510,COSM3573511	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	55/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCTTAAA	.	5	ESCA
MYLK	0	.	GRCh37	3	123356985	123356985	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4894G>T	p.Val1632Leu	p.V1632L	ENST00000360304	29/34	62	35	27	66	66	0	MYLK,missense_variant,p.Val1632Leu,ENST00000360304,;MYLK,missense_variant,p.Val1632Leu,ENST00000360772,;MYLK,missense_variant,p.Val1563Leu,ENST00000346322,;MYLK,missense_variant,p.Val1632Leu,ENST00000359169,;MYLK,missense_variant,p.Val1632Leu,ENST00000475616,;MYLK,missense_variant,p.Val432Leu,ENST00000354792,;MYLK-AS1,intron_variant,,ENST00000485162,;MYLK,downstream_gene_variant,,ENST00000514895,;MYLK,3_prime_UTR_variant,,ENST00000464489,;	A	ENSG00000065534	ENST00000360304	Transcript	missense_variant	5176	4894	1632	V/L	Gtg/Ttg	.	.	.	-1	MYLK	HGNC	7590	protein_coding	YES	CCDS46896.1	ENSP00000353452	MYLK_HUMAN	Q06S79_HUMAN,Q05B98_HUMAN,Q05B97_HUMAN,D6R9C2_HUMAN,B4DUE3_HUMAN	UPI000020A0AE	.	deleterious(0)	benign(0.218)	29/34	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22964,hmmpanther:PTHR22964:SF44,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCACTTCAG	.	5	ESCA
KALRN	0	.	GRCh37	3	124393469	124393469	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2102+8C>T	.	.	ENST00000291478	.	92	59	32	68	68	0	KALRN,splice_region_variant,,ENST00000291478,;KALRN,splice_region_variant,,ENST00000354186,;KALRN,splice_region_variant,,ENST00000428018,;KALRN,splice_region_variant,,ENST00000360013,;KALRN,3_prime_UTR_variant,,ENST00000459915,;KALRN,3_prime_UTR_variant,,ENST00000393496,;KALRN,upstream_gene_variant,,ENST00000462213,;KALRN,splice_region_variant,,ENST00000484542,;	T	ENSG00000160145	ENST00000291478	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	KALRN	HGNC	4814	protein_coding	.	CCDS3028.1	ENSP00000291478	KALRN_HUMAN	.	UPI00001AEB7E	.	.	.	.	16/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTGCCTCGT	.	5	ESCA
IQSEC1	0	.	GRCh37	3	12966156	12966156	+	Missense_Mutation	SNP	C	C	T	rs771164485	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1697G>A	p.Arg566His	p.R566H	ENST00000273221	4/14	68	19	48	69	69	0	IQSEC1,missense_variant,p.Arg552His,ENST00000429247,;IQSEC1,missense_variant,p.Arg566His,ENST00000273221,;IQSEC1,missense_variant,p.Arg567His,ENST00000450726,;	T	ENSG00000144711	ENST00000273221	Transcript	missense_variant	1914	1697	566	R/H	cGc/cAc	rs771164485,COSM1669979,COSM1669980,COSM1669981	.	.	-1	IQSEC1	HGNC	29112	protein_coding	YES	CCDS33703.1	ENSP00000273221	IQEC1_HUMAN	.	UPI00003E1F36	.	deleterious(0)	probably_damaging(1)	4/14	.	Superfamily_domains:SSF48425,SMART_domains:SM00222,Gene3D:1.10.220.20,Pfam_domain:PF01369,hmmpanther:PTHR10663:SF63,hmmpanther:PTHR10663,PROSITE_profiles:PS50190	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTGCGCTGC	byFrequency	5	ESCA
DCUN1D1	0	.	GRCh37	3	182662584	182662584	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*298A>G	.	.	ENST00000292782	7/7	132	114	17	28	28	0	DCUN1D1,3_prime_UTR_variant,,ENST00000292782,;DCUN1D1,downstream_gene_variant,,ENST00000469954,;DCUN1D1,downstream_gene_variant,,ENST00000492563,;	C	ENSG00000043093	ENST00000292782	Transcript	3_prime_UTR_variant	1232	.	.	.	.	.	.	.	-1	DCUN1D1	HGNC	18184	protein_coding	YES	CCDS3240.1	ENSP00000292782	DCNL1_HUMAN	C9JVE2_HUMAN,C9JUW4_HUMAN,C9JRU6_HUMAN,C9J8R4_HUMAN,C9J0B2_HUMAN	UPI0000073D68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCATAAAGC	.	4	ESCA
TBCCD1	0	.	GRCh37	3	186287935	186287935	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-83C>G	.	.	ENST00000424280	1/8	98	71	26	43	43	0	TBCCD1,missense_variant,p.Asp3Glu,ENST00000446782,;TBCCD1,5_prime_UTR_variant,,ENST00000413695,;TBCCD1,5_prime_UTR_variant,,ENST00000424280,;DNAJB11,intron_variant,,ENST00000439351,;DNAJB11,upstream_gene_variant,,ENST00000265028,;TBCCD1,upstream_gene_variant,,ENST00000338733,;DNAJB11,upstream_gene_variant,,ENST00000464877,;	C	ENSG00000113838	ENST00000424280	Transcript	5_prime_UTR_variant	398	.	.	.	.	.	.	.	-1	TBCCD1	HGNC	25546	protein_coding	YES	CCDS3276.1	ENSP00000411253	TBCC1_HUMAN	C9J4M0_HUMAN	UPI0000073055	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTCGGTCTGT	.	3	ESCA
TGFBR2	0	.	GRCh37	3	30713885	30713885	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1285C>G	p.Leu429Val	p.L429V	ENST00000359013	5/8	20	4	16	19	19	0	TGFBR2,missense_variant,p.Leu404Val,ENST00000295754,;TGFBR2,missense_variant,p.Leu429Val,ENST00000359013,;	G	ENSG00000163513	ENST00000359013	Transcript	missense_variant	1568	1285	429	L/V	Ctg/Gtg	.	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	deleterious(0)	probably_damaging(0.98)	5/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037393,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR00653	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCGTCTGGAC	.	5	ESCA
TRIM71	0	.	GRCh37	3	32932232	32932232	+	Silent	SNP	C	C	T	rs767735062	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1536C>T	p.%3D	p.H512H	ENST00000383763	4/4	17	12	5	13	13	0	TRIM71,synonymous_variant,p.%3D,ENST00000383763,;	T	ENSG00000206557	ENST00000383763	Transcript	synonymous_variant	1599	1536	512	H	caC/caT	rs767735062	.	.	1	TRIM71	HGNC	32669	protein_coding	YES	CCDS43060.1	ENSP00000373272	LIN41_HUMAN	.	UPI000067CB89	.	.	.	4/4	.	Superfamily_domains:SSF81296,SMART_domains:SM00557,Gene3D:2.60.40.10,Pfam_domain:PF00630,hmmpanther:PTHR24103:SF281,hmmpanther:PTHR24103,PROSITE_profiles:PS50194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCACGATGG	.	5	ESCA
BHLHE40	0	.	GRCh37	3	5025110	5025110	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972C>T	p.%3D	p.P324P	ENST00000256495	5/5	54	51	3	54	54	0	BHLHE40,synonymous_variant,p.%3D,ENST00000256495,;BHLHE40-AS1,upstream_gene_variant,,ENST00000441386,;BHLHE40-AS1,upstream_gene_variant,,ENST00000434530,;BHLHE40-AS1,upstream_gene_variant,,ENST00000420832,;BHLHE40,downstream_gene_variant,,ENST00000467610,;BHLHE40,downstream_gene_variant,,ENST00000460806,;	T	ENSG00000134107	ENST00000256495	Transcript	synonymous_variant	1575	972	324	P	ccC/ccT	.	.	.	1	BHLHE40	HGNC	1046	protein_coding	YES	CCDS2565.1	ENSP00000256495	BHE40_HUMAN	Q6IB83_HUMAN	UPI0000126923	.	.	.	5/5	.	hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCCCTTCTA	.	2	ESCA
ELOVL6	0	.	GRCh37	4	110972000	110972000	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*494T>C	.	.	ENST00000394607	5/5	33	14	18	27	27	0	ELOVL6,3_prime_UTR_variant,,ENST00000394607,;ELOVL6,3_prime_UTR_variant,,ENST00000302274,;ELOVL6,downstream_gene_variant,,ENST00000506625,;ELOVL6,downstream_gene_variant,,ENST00000507451,;ELOVL6,downstream_gene_variant,,ENST00000514184,;	G	ENSG00000170522	ENST00000394607	Transcript	3_prime_UTR_variant	1456	.	.	.	.	.	.	.	-1	ELOVL6	HGNC	15829	protein_coding	YES	CCDS3690.1	ENSP00000378105	ELOV6_HUMAN	D6RHI2_HUMAN,D6RCU0_HUMAN	UPI00000343F5	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTAGATATAC	.	5	ESCA
PCDH10	0	.	GRCh37	4	134072084	134072084	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.789T>C	p.%3D	p.S263S	ENST00000264360	1/5	34	30	4	31	31	0	PCDH10,synonymous_variant,p.%3D,ENST00000264360,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;PCDH10,upstream_gene_variant,,ENST00000511112,;	C	ENSG00000138650	ENST00000264360	Transcript	synonymous_variant	1615	789	263	S	tcT/tcC	.	.	.	1	PCDH10	HGNC	13404	protein_coding	YES	CCDS34063.1	ENSP00000264360	PCD10_HUMAN	Q9NSR3_HUMAN	UPI0000161C61	.	.	.	1/5	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028:SF0,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.P264S|c.790C>T|3	RADIA|MUSE	AACTCTCCCCC	.	2	ESCA
RAPGEF2	0	.	GRCh37	4	160259537	160259537	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1727T>G	p.Leu576Trp	p.L576W	ENST00000264431	12/24	62	15	46	81	81	0	RAPGEF2,missense_variant,p.Leu576Trp,ENST00000264431,;RAPGEF2,upstream_gene_variant,,ENST00000502485,;	G	ENSG00000109756	ENST00000264431	Transcript	missense_variant	2146	1727	576	L/W	tTg/tGg	.	.	.	1	RAPGEF2	HGNC	16854	protein_coding	YES	CCDS43277.1	ENSP00000264431	RPGF2_HUMAN	Q9UFT5_HUMAN,Q4W5Q4_HUMAN,Q17RH5_HUMAN,D6REY8_HUMAN,B4DG82_HUMAN	UPI0000033783	.	deleterious(0.01)	possibly_damaging(0.827)	12/24	.	hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF202	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCATTGCCTG	.	5	ESCA
KIAA1239	0	.	GRCh37	4	37447948	37447948	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4338C>T	p.%3D	p.S1446S	ENST00000309447	7/7	37	31	5	39	39	0	KIAA1239,synonymous_variant,p.%3D,ENST00000309447,;	T	ENSG00000174145	ENST00000309447	Transcript	synonymous_variant	5186	4338	1446	S	tcC/tcT	.	.	.	1	KIAA1239	HGNC	29229	protein_coding	YES	CCDS47040.1	ENSP00000309501	K1239_HUMAN	.	UPI00006C0875	.	.	.	7/7	.	hmmpanther:PTHR19857:SF18,hmmpanther:PTHR19857,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTCCGCAAA	.	5	ESCA
ATP10D	0	.	GRCh37	4	47560156	47560156	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2300T>G	p.Leu767Arg	p.L767R	ENST00000273859	12/23	63	35	28	34	34	0	ATP10D,missense_variant,p.Leu767Arg,ENST00000273859,;AC092597.3,intron_variant,,ENST00000508081,;ATP10D,synonymous_variant,p.%3D,ENST00000503288,;	G	ENSG00000145246	ENST00000273859	Transcript	missense_variant	2569	2300	767	L/R	cTa/cGa	.	.	.	1	ATP10D	HGNC	13549	protein_coding	YES	CCDS3476.1	ENSP00000273859	AT10D_HUMAN	.	UPI00001AE9B7	.	deleterious(0)	probably_damaging(0.99)	12/23	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF61,Gene3D:3.40.1110.10,Pfam_domain:PF12710,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCTACACA	.	5	ESCA
PROL1	0	.	GRCh37	4	71275204	71275204	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159T>A	p.Tyr53Ter	p.Y53*	ENST00000399575	3/3	32	11	21	33	33	0	PROL1,stop_gained,p.Tyr53Ter,ENST00000399575,;PROL1,non_coding_transcript_exon_variant,,ENST00000514338,;PROL1,non_coding_transcript_exon_variant,,ENST00000505023,;	A	ENSG00000171199	ENST00000399575	Transcript	stop_gained	333	159	53	Y/*	taT/taA	.	.	.	1	PROL1	HGNC	17279	protein_coding	YES	CCDS43235.1	ENSP00000382485	PROL1_HUMAN	.	UPI000020BE52	.	.	.	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14179,hmmpanther:PTHR14179:SF8,Pfam_domain:PF15621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTATGACTC	.	5	ESCA
PROL1	0	.	GRCh37	4	71275205	71275205	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.160G>A	p.Asp54Asn	p.D54N	ENST00000399575	3/3	34	11	23	33	33	0	PROL1,missense_variant,p.Asp54Asn,ENST00000399575,;PROL1,non_coding_transcript_exon_variant,,ENST00000514338,;PROL1,non_coding_transcript_exon_variant,,ENST00000505023,;	A	ENSG00000171199	ENST00000399575	Transcript	missense_variant	334	160	54	D/N	Gac/Aac	.	.	.	1	PROL1	HGNC	17279	protein_coding	YES	CCDS43235.1	ENSP00000382485	PROL1_HUMAN	.	UPI000020BE52	.	tolerated_low_confidence(0.32)	benign(0.001)	3/3	.	hmmpanther:PTHR14179,hmmpanther:PTHR14179:SF8,Pfam_domain:PF15621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATGACTCA	.	5	ESCA
DCK	0	.	GRCh37	4	71895288	71895288	+	3'UTR	SNP	A	A	T	rs554346593	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*193A>T	.	.	ENST00000286648	7/7	15	5	10	17	17	0	DCK,3_prime_UTR_variant,,ENST00000286648,;DCK,3_prime_UTR_variant,,ENST00000504952,;DCK,3_prime_UTR_variant,,ENST00000504730,;DCK,3_prime_UTR_variant,,ENST00000503359,;DCK,downstream_gene_variant,,ENST00000509764,;	T	ENSG00000156136	ENST00000286648	Transcript	3_prime_UTR_variant	1373	.	.	.	.	rs554346593	.	.	1	DCK	HGNC	2704	protein_coding	YES	CCDS3548.1	ENSP00000286648	DCK_HUMAN	F5CTF3_HUMAN,B4E0A5_HUMAN	UPI0000128FC6	.	.	.	7/7	.	.	T:0.0072	T:0.0015	T:0.0043	.	T:0.001	T:0.0149	T:0.0153	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TTTTTAAAAAA	byFrequency|byCluster|by1000G	4	ESCA
TRPC7	0	.	GRCh37	5	135692820	135692820	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256G>A	p.Val86Met	p.V86M	ENST00000513104	2/12	19	6	13	22	22	0	TRPC7,missense_variant,p.Val86Met,ENST00000502753,;TRPC7,missense_variant,p.Val86Met,ENST00000378459,;TRPC7,missense_variant,p.Val86Met,ENST00000513104,;TRPC7,missense_variant,p.Val86Met,ENST00000426057,;TRPC7,missense_variant,p.Val86Met,ENST00000355180,;TRPC7,missense_variant,p.Val86Met,ENST00000352189,;TRPC7,missense_variant,p.Val86Met,ENST00000514963,;TRPC7,missense_variant,p.Val86Met,ENST00000503275,;	T	ENSG00000069018	ENST00000513104	Transcript	missense_variant	539	256	86	V/M	Gtg/Atg	COSM248009,COSM248008	.	.	-1	TRPC7	HGNC	20754	protein_coding	YES	CCDS47267.2	ENSP00000426070	TRPC7_HUMAN	.	UPI000004F27A	.	deleterious(0)	probably_damaging(0.998)	2/12	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,TIGRFAM_domain:TIGR00870,Pfam_domain:PF12796,Gene3D:1.25.40.20,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.V86M|c.256G>A|3,SITE|p.V86M|c.256G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCACGGCCA	.	5	ESCA
CTAGE9	0	.	GRCh37	6	132031717	132031717	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441C>A	p.%3D	p.L147L	ENST00000314099	1/1	117	89	27	128	128	0	CTAGE9,synonymous_variant,p.%3D,ENST00000314099,;ENPP3,intron_variant,,ENST00000358229,;ENPP3,intron_variant,,ENST00000357639,;ENPP3,intron_variant,,ENST00000414305,;	T	ENSG00000236761	ENST00000314099	Transcript	synonymous_variant	490	441	147	L	ctC/ctA	.	.	.	-1	CTAGE9	HGNC	37275	protein_coding	YES	CCDS47475.1	ENSP00000395587	CTGE9_HUMAN	.	UPI0000073347	.	.	.	1/1	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACAGAGGAT	.	5	ESCA
CTGF	0	.	GRCh37	6	132271549	132271549	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.424C>A	p.Arg142Ser	p.R142S	ENST00000367976	3/5	28	12	16	38	38	0	CTGF,missense_variant,p.Arg142Ser,ENST00000367976,;RP11-69I8.3,upstream_gene_variant,,ENST00000435287,;	T	ENSG00000118523	ENST00000367976	Transcript	missense_variant	625	424	142	R/S	Cgt/Agt	COSM740115	.	.	-1	CTGF	HGNC	2500	protein_coding	YES	CCDS5151.1	ENSP00000356954	CTGF_HUMAN	B3KWK5_HUMAN	UPI000013CA11	.	tolerated(0.69)	benign(0.34)	3/5	.	Superfamily_domains:SSF57603,SMART_domains:SM00214,PIRSF_domain:PIRSF036495,Pfam_domain:PF00093,PROSITE_patterns:PS01208,hmmpanther:PTHR11348:SF7,hmmpanther:PTHR11348,PROSITE_profiles:PS50184	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGACGAACGT	.	5	ESCA
ESR1	0	.	GRCh37	6	152424207	152424207	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4106A>G	.	.	ENST00000440973	10/10	44	30	13	44	44	0	ESR1,3_prime_UTR_variant,,ENST00000440973,;ESR1,3_prime_UTR_variant,,ENST00000443427,;ESR1,3_prime_UTR_variant,,ENST00000456483,;ESR1,3_prime_UTR_variant,,ENST00000206249,;ESR1,intron_variant,,ENST00000427531,;ESR1,downstream_gene_variant,,ENST00000338799,;ESR1,downstream_gene_variant,,ENST00000406599,;	G	ENSG00000091831	ENST00000440973	Transcript	3_prime_UTR_variant	6264	.	.	.	.	.	.	.	1	ESR1	HGNC	3467	protein_coding	YES	CCDS5234.1	ENSP00000405330	ESR1_HUMAN	Q9UE35_HUMAN,Q9UBT1_HUMAN,Q5T5H8_HUMAN,K7R989_HUMAN,K4Q331_HUMAN,K4PXX0_HUMAN,K4PX46_HUMAN,G4XH65_HUMAN,E3WH18_HUMAN,C8CJL0_HUMAN,C7FFR5_HUMAN,B6DU67_HUMAN	UPI000004A328	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAAATTGT	.	5	ESCA
FNDC1	0	.	GRCh37	6	159653096	159653096	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1555delG	p.Ala519ArgfsTer48	p.A519Rfs*48	ENST00000297267	11/23	79	46	33	51	51	0	FNDC1,frameshift_variant,p.Ala456ArgfsTer48,ENST00000340366,;FNDC1,frameshift_variant,p.Ala519ArgfsTer48,ENST00000297267,;FNDC1,frameshift_variant,p.Ala415ArgfsTer48,ENST00000329629,;	-	ENSG00000164694	ENST00000297267	Transcript	frameshift_variant	1752	1552	518	G/X	Ggg/gg	.	.	.	1	FNDC1	HGNC	21184	protein_coding	YES	CCDS47512.1	ENSP00000297267	FNDC1_HUMAN	.	UPI0000579B80	.	.	.	11/23	.	hmmpanther:PTHR23197:SF8,hmmpanther:PTHR23197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATGGTGGGGCG	.	3	ESCA
LHFPL5	0	.	GRCh37	6	35773672	35773672	+	Silent	SNP	C	C	T	rs541264130	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.225C>T	p.%3D	p.S75S	ENST00000360215	1/4	24	18	6	37	37	0	LHFPL5,synonymous_variant,p.%3D,ENST00000360215,;LHFPL5,synonymous_variant,p.%3D,ENST00000373853,;	T	ENSG00000197753	ENST00000360215	Transcript	synonymous_variant	602	225	75	S	tcC/tcT	rs541264130	.	.	1	LHFPL5	HGNC	21253	protein_coding	YES	CCDS4812.1	ENSP00000353346	TMHS_HUMAN	.	UPI000006E12D	.	.	.	1/4	.	hmmpanther:PTHR12489:SF18,hmmpanther:PTHR12489,Pfam_domain:PF10242	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCCGAGCT	by1000G	5	ESCA
FBXL4	0	.	GRCh37	6	99322298	99322298	+	Silent	SNP	C	C	G	rs373647205	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1722G>C	p.%3D	p.P574P	ENST00000369244	10/10	22	15	6	12	12	0	FBXL4,synonymous_variant,p.%3D,ENST00000229971,;FBXL4,synonymous_variant,p.%3D,ENST00000369244,;	G	ENSG00000112234	ENST00000369244	Transcript	synonymous_variant	2151	1722	574	P	ccG/ccC	rs373647205,COSM1082769	.	.	-1	FBXL4	HGNC	13601	protein_coding	YES	CCDS5041.1	ENSP00000358247	FBXL4_HUMAN	.	UPI000012ADE3	.	.	.	10/10	.	Superfamily_domains:SSF52047,SMART_domains:SM00367,Gene3D:3.80.10.10,hmmpanther:PTHR23125:SF244,hmmpanther:PTHR23125	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGCCGGACT	byFrequency|byCluster	5	ESCA
MGAM	0	.	GRCh37	7	141705417	141705417	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.87T>C	p.%3D	p.V29V	ENST00000549489	2/48	37	33	4	42	42	0	MGAM,synonymous_variant,p.%3D,ENST00000465654,;MGAM,synonymous_variant,p.%3D,ENST00000475668,;MGAM,synonymous_variant,p.%3D,ENST00000549489,;MGAM,synonymous_variant,p.%3D,ENST00000497673,;	C	ENSG00000257335	ENST00000549489	Transcript	synonymous_variant	182	87	29	V	gtT/gtC	.	.	.	1	MGAM	HGNC	7043	protein_coding	YES	CCDS47727.1	ENSP00000447378	MGA_HUMAN	Q8TE25_HUMAN,E9PEQ5_HUMAN,E7EW87_HUMAN	UPI000183CB7B	.	.	.	2/48	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ATTGTTCTAAT	.	2	ESCA
ZNF767	0	.	GRCh37	7	149250069	149250069	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.871C>T	.	.	ENST00000463567	5/8	42	27	15	39	39	0	ZNF767,non_coding_transcript_exon_variant,,ENST00000472212,;ZNF767,non_coding_transcript_exon_variant,,ENST00000463567,;ZNF767,non_coding_transcript_exon_variant,,ENST00000486492,;	A	ENSG00000133624	ENST00000463567	Transcript	non_coding_transcript_exon_variant	871	.	.	.	.	.	.	.	-1	ZNF767	HGNC	21884	processed_transcript	YES	.	.	.	.	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCAGGGCAA	.	5	ESCA
KMT2C	0	.	GRCh37	7	151947037	151947037	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1737G>A	p.%3D	p.A579A	ENST00000262189	13/59	75	55	20	60	60	0	KMT2C,synonymous_variant,p.%3D,ENST00000355193,;KMT2C,synonymous_variant,p.%3D,ENST00000262189,;KMT2C,upstream_gene_variant,,ENST00000418673,;KMT2C,synonymous_variant,p.%3D,ENST00000558084,;	T	ENSG00000055609	ENST00000262189	Transcript	synonymous_variant	1956	1737	579	A	gcG/gcA	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	.	13/59	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAACCGCTGT	.	5	ESCA
GLI3	0	.	GRCh37	7	42000951	42000951	+	3'UTR	SNP	G	G	A	rs569438500	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2977C>T	.	.	ENST00000395925	15/15	31	22	9	25	25	0	GLI3,3_prime_UTR_variant,,ENST00000395925,;GLI3,downstream_gene_variant,,ENST00000479210,;	A	ENSG00000106571	ENST00000395925	Transcript	3_prime_UTR_variant	7805	.	.	.	.	rs569438500	.	.	-1	GLI3	HGNC	4319	protein_coding	YES	CCDS5465.1	ENSP00000379258	GLI3_HUMAN	C9J9N4_HUMAN	UPI000020EE4C	.	.	.	15/15	.	.	A:0.0006	A:0	A:0.0043	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCGACTCT	byFrequency|by1000G	5	ESCA
RSPH10B2	0	.	GRCh37	7	6803577	6803577	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418G>C	p.Val140Leu	p.V140L	ENST00000403107	5/20	131	121	10	147	147	0	RSPH10B2,missense_variant,p.Val140Leu,ENST00000404077,;RSPH10B2,missense_variant,p.Val140Leu,ENST00000403107,;RSPH10B2,missense_variant,p.Val140Leu,ENST00000297186,;RSPH10B2,missense_variant,p.Val140Leu,ENST00000433859,;RSPH10B2,5_prime_UTR_variant,,ENST00000359718,;RSPH10B2,non_coding_transcript_exon_variant,,ENST00000485129,;RSPH10B2,non_coding_transcript_exon_variant,,ENST00000497737,;RSPH10B2,non_coding_transcript_exon_variant,,ENST00000463354,;RSPH10B2,non_coding_transcript_exon_variant,,ENST00000489190,;RSPH10B2,upstream_gene_variant,,ENST00000485920,;	C	ENSG00000169402	ENST00000403107	Transcript	missense_variant	805	418	140	V/L	Gtc/Ctc	.	.	.	1	RSPH10B2	HGNC	34385	protein_coding	YES	CCDS43552.1	ENSP00000384766	R10B2_HUMAN	C9JJN2_HUMAN	UPI000020EAF6	.	tolerated(0.08)	benign(0.046)	5/20	.	hmmpanther:PTHR23084,hmmpanther:PTHR23084:SF131,Gene3D:1h3iA01,Pfam_domain:PF02493,SMART_domains:SM00698,Superfamily_domains:0038399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAATGTCCCG	.	2	ESCA
POM121C	0	.	GRCh37	7	75047748	75047748	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*331C>T	.	.	ENST00000453279	15/15	16	9	7	19	19	0	POM121C,3_prime_UTR_variant,,ENST00000453279,;POM121C,3_prime_UTR_variant,,ENST00000257665,;NSUN5P1,downstream_gene_variant,,ENST00000393633,;NSUN5P1,downstream_gene_variant,,ENST00000455158,;NSUN5P1,downstream_gene_variant,,ENST00000422386,;NSUN5P1,downstream_gene_variant,,ENST00000464979,;NSUN5P1,downstream_gene_variant,,ENST00000428392,;NSUN5P1,downstream_gene_variant,,ENST00000457988,;POM121C,downstream_gene_variant,,ENST00000473168,;POM121C,non_coding_transcript_exon_variant,,ENST00000476072,;POM121C,downstream_gene_variant,,ENST00000473609,;NSUN5P1,downstream_gene_variant,,ENST00000427550,;NSUN5P1,downstream_gene_variant,,ENST00000421140,;	A	ENSG00000135213	ENST00000453279	Transcript	3_prime_UTR_variant	4160	.	.	.	.	.	.	.	-1	POM121C	HGNC	34005	protein_coding	YES	CCDS47617.1	ENSP00000414208	P121C_HUMAN	C9JFL1_HUMAN,B4DDR5_HUMAN,A8MY32_HUMAN	UPI00001C1E87	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGGTGGAA	.	5	ESCA
MAGI2	0	.	GRCh37	7	77762345	77762345	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3064G>C	p.Glu1022Gln	p.E1022Q	ENST00000354212	18/22	57	33	23	42	42	0	MAGI2,missense_variant,p.Glu1022Gln,ENST00000354212,;MAGI2,missense_variant,p.Glu1008Gln,ENST00000419488,;MAGI2,missense_variant,p.Glu1022Gln,ENST00000522391,;MAGI2,non_coding_transcript_exon_variant,,ENST00000519748,;	G	ENSG00000187391	ENST00000354212	Transcript	missense_variant	3318	3064	1022	E/Q	Gag/Cag	.	.	.	-1	MAGI2	HGNC	18957	protein_coding	YES	CCDS5594.1	ENSP00000346151	MAGI2_HUMAN	.	UPI00001615D2	.	tolerated(0.06)	probably_damaging(0.974)	18/22	.	hmmpanther:PTHR10316:SF27,hmmpanther:PTHR10316	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCTGAGC	.	5	ESCA
KIAA1324L	0	.	GRCh37	7	86509556	86509556	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*231C>G	.	.	ENST00000450689	22/22	71	53	18	53	53	0	KIAA1324L,3_prime_UTR_variant,,ENST00000416314,;KIAA1324L,3_prime_UTR_variant,,ENST00000297222,;KIAA1324L,3_prime_UTR_variant,,ENST00000444627,;KIAA1324L,3_prime_UTR_variant,,ENST00000450689,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;	C	ENSG00000164659	ENST00000450689	Transcript	3_prime_UTR_variant	3507	.	.	.	.	.	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTGAGCTT	.	5	ESCA
FOXD4	0	.	GRCh37	9	116393	116393	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*407C>G	.	.	ENST00000382500	1/1	157	105	51	126	126	0	FOXD4,3_prime_UTR_variant,,ENST00000382500,;CBWD1,downstream_gene_variant,,ENST00000377400,;CBWD1,downstream_gene_variant,,ENST00000356521,;RP11-143M1.4,upstream_gene_variant,,ENST00000416242,;CBWD1,downstream_gene_variant,,ENST00000475990,;	C	ENSG00000170122	ENST00000382500	Transcript	3_prime_UTR_variant	2025	.	.	.	.	.	.	.	-1	FOXD4	HGNC	3805	protein_coding	YES	CCDS34975.1	ENSP00000371940	FOXD4_HUMAN	.	UPI00001AFF18	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGAGAGTAG	.	5	ESCA
CDK5RAP2	0	.	GRCh37	9	123199725	123199725	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3803T>C	p.Val1268Ala	p.V1268A	ENST00000349780	25/38	141	121	20	74	74	0	CDK5RAP2,missense_variant,p.Val662Ala,ENST00000416449,;CDK5RAP2,missense_variant,p.Val1268Ala,ENST00000349780,;CDK5RAP2,missense_variant,p.Val1236Ala,ENST00000360822,;CDK5RAP2,missense_variant,p.Val278Ala,ENST00000425647,;CDK5RAP2,missense_variant,p.Val1268Ala,ENST00000360190,;CDK5RAP2,missense_variant,p.Val1227Ala,ENST00000359309,;CDK5RAP2,downstream_gene_variant,,ENST00000479584,;CDK5RAP2,downstream_gene_variant,,ENST00000468989,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000483412,;	G	ENSG00000136861	ENST00000349780	Transcript	missense_variant	3983	3803	1268	V/A	gTc/gCc	.	.	.	-1	CDK5RAP2	HGNC	18672	protein_coding	YES	CCDS6823.1	ENSP00000343818	CK5P2_HUMAN	F8WBJ0_HUMAN,C9K0C9_HUMAN	UPI0000367673	.	tolerated(0.18)	possibly_damaging(0.539)	25/38	.	hmmpanther:PTHR13895,hmmpanther:PTHR13895:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGATGACACAG	.	4	ESCA
MEGF9	0	.	GRCh37	9	123366708	123366710	+	3'UTR	DEL	ACA	ACA	-	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	ACA	ACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*758_*760delTGT	.	.	ENST00000373930	6/6	81	14	67	40	40	0	MEGF9,3_prime_UTR_variant,,ENST00000426959,;MEGF9,3_prime_UTR_variant,,ENST00000373930,;	-	ENSG00000106780	ENST00000373930	Transcript	3_prime_UTR_variant	2679-2681	.	.	.	.	.	.	.	-1	MEGF9	HGNC	3234	protein_coding	YES	CCDS48010.2	ENSP00000363040	MEGF9_HUMAN	.	UPI000045779F	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAAATACAACGTC	.	3	ESCA
RC3H2	0	.	GRCh37	9	125611809	125611809	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*97T>A	.	.	ENST00000373670	20/20	162	89	72	92	92	0	RC3H2,3_prime_UTR_variant,,ENST00000373670,;RC3H2,3_prime_UTR_variant,,ENST00000357244,;RC3H2,3_prime_UTR_variant,,ENST00000454740,;RC3H2,downstream_gene_variant,,ENST00000423239,;RC3H2,downstream_gene_variant,,ENST00000398671,;RC3H2,3_prime_UTR_variant,,ENST00000498479,;RC3H2,downstream_gene_variant,,ENST00000495727,;	T	ENSG00000056586	ENST00000373670	Transcript	3_prime_UTR_variant	4274	.	.	.	.	.	.	.	-1	RC3H2	HGNC	21461	protein_coding	YES	CCDS43874.1	ENSP00000362774	RC3H2_HUMAN	.	UPI0000048D91	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTAAAAAA	.	5	ESCA
VAV2	0	.	GRCh37	9	136627369	136627369	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1815A>T	.	.	ENST00000371850	30/30	128	121	6	46	46	0	VAV2,3_prime_UTR_variant,,ENST00000371850,;VAV2,3_prime_UTR_variant,,ENST00000406606,;VAV2,3_prime_UTR_variant,,ENST00000371851,;AL590710.1,non_coding_transcript_exon_variant,,ENST00000343203,;	A	ENSG00000160293	ENST00000371850	Transcript	3_prime_UTR_variant	4484	.	.	.	.	.	.	.	-1	VAV2	HGNC	12658	protein_coding	YES	CCDS48053.1	ENSP00000360916	VAV2_HUMAN	.	UPI000013E06E	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTTTTCTCA	.	2	ESCA
SLC1A1	0	.	GRCh37	9	4585805	4585806	+	3'UTR	DEL	TA	TA	-	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*249_*250delTA	.	.	ENST00000262352	12/12	74	39	35	27	27	0	SLC1A1,3_prime_UTR_variant,,ENST00000262352,;SLC1A1,downstream_gene_variant,,ENST00000422398,;SPATA6L,intron_variant,,ENST00000485616,;SPATA6L,downstream_gene_variant,,ENST00000486047,;SPATA6L,downstream_gene_variant,,ENST00000461761,;	-	ENSG00000106688	ENST00000262352	Transcript	3_prime_UTR_variant	2058-2059	.	.	.	.	.	.	.	1	SLC1A1	HGNC	10939	protein_coding	YES	CCDS6452.1	ENSP00000262352	EAA3_HUMAN	.	UPI0000129B16	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAATTCTATAAGA	.	3	ESCA
ZFAND5	0	.	GRCh37	9	74969292	74969292	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1577A>G	.	.	ENST00000237937	6/6	37	5	32	27	27	0	ZFAND5,3_prime_UTR_variant,,ENST00000237937,;ZFAND5,downstream_gene_variant,,ENST00000376960,;ZFAND5,downstream_gene_variant,,ENST00000376962,;ZFAND5,downstream_gene_variant,,ENST00000343431,;ZFAND5,downstream_gene_variant,,ENST00000376956,;ZFAND5,downstream_gene_variant,,ENST00000471197,;ZFAND5,downstream_gene_variant,,ENST00000488164,;	C	ENSG00000107372	ENST00000237937	Transcript	3_prime_UTR_variant	2777	.	.	.	.	.	.	.	-1	ZFAND5	HGNC	13008	protein_coding	YES	CCDS6642.1	ENSP00000237937	ZFAN5_HUMAN	.	UPI000013C322	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTATATAGC	.	5	ESCA
PSAT1	0	.	GRCh37	9	80944123	80944123	+	3'UTR	SNP	C	C	A	rs532073374	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*121C>A	.	.	ENST00000376588	9/9	11	2	9	9	9	0	PSAT1,3_prime_UTR_variant,,ENST00000376588,;PSAT1,3_prime_UTR_variant,,ENST00000347159,;	A	ENSG00000135069	ENST00000376588	Transcript	3_prime_UTR_variant	1302	.	.	.	.	rs532073374	.	.	1	PSAT1	HGNC	19129	protein_coding	YES	CCDS6660.1	ENSP00000365773	SERC_HUMAN	B4DHQ3_HUMAN,A9LS35_HUMAN	UPI0000001C03	.	.	.	9/9	.	.	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGATTCTTCTT	by1000G	2	ESCA
KIAA2022	0	.	GRCh37	X	73958682	73958682	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A7HZ-01A-31D-A351-09	TCGA-LN-A7HZ-10A-01D-A351-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*558A>G	.	.	ENST00000055682	4/4	52	47	4	24	24	0	KIAA2022,3_prime_UTR_variant,,ENST00000055682,;KIAA2022,intron_variant,,ENST00000424929,;	C	ENSG00000050030	ENST00000055682	Transcript	3_prime_UTR_variant	5721	.	.	.	.	.	.	.	-1	KIAA2022	HGNC	29433	protein_coding	YES	CCDS35337.1	ENSP00000055682	K2022_HUMAN	.	UPI00001C207B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATATATACATA	.	2	ESCA
SLK	0	.	GRCh37	10	105762241	105762241	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1305C>T	p.%3D	p.D435D	ENST00000369755	9/19	38	24	14	62	62	0	SLK,synonymous_variant,p.%3D,ENST00000369755,;SLK,synonymous_variant,p.%3D,ENST00000335753,;	T	ENSG00000065613	ENST00000369755	Transcript	synonymous_variant	1850	1305	435	D	gaC/gaT	.	.	.	1	SLK	HGNC	11088	protein_coding	YES	CCDS7553.1	ENSP00000358770	SLK_HUMAN	.	UPI000004B6D3	.	.	.	9/19	.	hmmpanther:PTHR24361:SF53,hmmpanther:PTHR24361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGACACAGA	.	5	ESCA
KIAA1598	0	.	GRCh37	10	118708448	118708448	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595G>A	p.Val199Ile	p.V199I	ENST00000355371	7/17	45	40	4	76	76	0	KIAA1598,missense_variant,p.Val199Ile,ENST00000260777,;KIAA1598,missense_variant,p.Val199Ile,ENST00000392903,;KIAA1598,missense_variant,p.Val139Ile,ENST00000392901,;KIAA1598,missense_variant,p.Val199Ile,ENST00000355371,;KIAA1598,non_coding_transcript_exon_variant,,ENST00000497044,;	T	ENSG00000187164	ENST00000355371	Transcript	missense_variant	1093	595	199	V/I	Gtc/Atc	.	.	.	-1	KIAA1598	HGNC	29319	protein_coding	YES	CCDS44482.1	ENSP00000347532	SHOT1_HUMAN	.	UPI0000404A8F	.	tolerated(0.28)	benign(0.068)	7/17	.	hmmpanther:PTHR23213:SF179,hmmpanther:PTHR23213	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAAGACTTTTC	.	3	ESCA
SLC18A2	0	.	GRCh37	10	119013563	119013563	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528T>C	p.%3D	p.F176F	ENST00000298472	5/16	34	31	3	52	52	0	SLC18A2,synonymous_variant,p.%3D,ENST00000298472,;SLC18A2,non_coding_transcript_exon_variant,,ENST00000497497,;	C	ENSG00000165646	ENST00000298472	Transcript	synonymous_variant	671	528	176	F	ttT/ttC	.	.	.	1	SLC18A2	HGNC	10935	protein_coding	YES	CCDS7599.1	ENSP00000298472	VMAT2_HUMAN	.	UPI00001389DE	.	.	.	5/16	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24004,hmmpanther:PTHR24004:SF63,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GTGTTTGCCTT	.	2	ESCA
HTRA1	0	.	GRCh37	10	124249128	124249128	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763A>G	p.Lys255Glu	p.K255E	ENST00000368984	3/9	39	24	14	90	90	0	HTRA1,missense_variant,p.Lys255Glu,ENST00000368984,;	G	ENSG00000166033	ENST00000368984	Transcript	missense_variant	891	763	255	K/E	Aaa/Gaa	.	.	.	1	HTRA1	HGNC	9476	protein_coding	YES	CCDS7630.1	ENSP00000357980	HTRA1_HUMAN	H0Y7G9_HUMAN,A8K224_HUMAN	UPI0000114888	.	deleterious(0.03)	benign(0.344)	3/9	.	hmmpanther:PTHR22939:SF13,hmmpanther:PTHR22939,Gene3D:2.40.10.10,Pfam_domain:PF13365,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATCAAAATT	.	5	ESCA
ARL5B	0	.	GRCh37	10	18966210	18966210	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2065A>G	.	.	ENST00000377275	6/6	35	30	4	73	73	0	ARL5B,3_prime_UTR_variant,,ENST00000377275,;	G	ENSG00000165997	ENST00000377275	Transcript	3_prime_UTR_variant	2838	.	.	.	.	.	.	.	1	ARL5B	HGNC	23052	protein_coding	YES	CCDS7131.1	ENSP00000366487	ARL5B_HUMAN	B0YIW9_HUMAN	UPI000006F7A5	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCACATCAGC	.	4	ESCA
PARD3	0	.	GRCh37	10	34558748	34558748	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3265A>T	p.Thr1089Ser	p.T1089S	ENST00000374789	22/25	63	56	7	112	112	0	PARD3,missense_variant,p.Thr999Ser,ENST00000545260,;PARD3,missense_variant,p.Thr1073Ser,ENST00000545693,;PARD3,missense_variant,p.Thr1086Ser,ENST00000374788,;PARD3,missense_variant,p.Thr1029Ser,ENST00000374790,;PARD3,missense_variant,p.Thr977Ser,ENST00000374794,;PARD3,missense_variant,p.Thr1043Ser,ENST00000350537,;PARD3,missense_variant,p.Thr1089Ser,ENST00000374789,;PARD3,missense_variant,p.Thr1052Ser,ENST00000346874,;PARD3,non_coding_transcript_exon_variant,,ENST00000466092,;	A	ENSG00000148498	ENST00000374789	Transcript	missense_variant	3591	3265	1089	T/S	Aca/Tca	.	.	.	-1	PARD3	HGNC	16051	protein_coding	YES	CCDS7178.1	ENSP00000363921	PARD3_HUMAN	.	UPI0000073A9F	.	tolerated(0.25)	benign(0.129)	22/25	.	hmmpanther:PTHR16484:SF10,hmmpanther:PTHR16484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATGTCCGAT	.	4	ESCA
LDB3	0	.	GRCh37	10	88469744	88469744	+	Missense_Mutation	SNP	G	G	A	rs748672176	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1183G>A	p.Ala395Thr	p.A395T	ENST00000429277	9/14	49	26	23	98	98	0	LDB3,missense_variant,p.Ala133Thr,ENST00000352360,;LDB3,missense_variant,p.Ala390Thr,ENST00000361373,;LDB3,missense_variant,p.Ala280Thr,ENST00000458213,;LDB3,missense_variant,p.Ala280Thr,ENST00000263066,;LDB3,missense_variant,p.Ala395Thr,ENST00000429277,;	A	ENSG00000122367	ENST00000429277	Transcript	missense_variant	1328	1183	395	A/T	Gcc/Acc	rs748672176	.	.	1	LDB3	HGNC	15710	protein_coding	YES	CCDS53550.1	ENSP00000401437	LDB3_HUMAN	.	UPI00017A876A	.	tolerated(0.25)	benign(0.11)	9/14	.	hmmpanther:PTHR24214:SF9,hmmpanther:PTHR24214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCCGCCCCT	byFrequency	5	ESCA
CPEB3	0	.	GRCh37	10	93809608	93809608	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2361A>G	.	.	ENST00000265997	10/10	82	59	23	120	120	0	CPEB3,3_prime_UTR_variant,,ENST00000265997,;CPEB3,3_prime_UTR_variant,,ENST00000412050,;	C	ENSG00000107864	ENST00000265997	Transcript	3_prime_UTR_variant	4631	.	.	.	.	.	.	.	-1	CPEB3	HGNC	21746	protein_coding	YES	CCDS31246.1	ENSP00000265997	CPEB3_HUMAN	.	UPI000013F7DE	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTATAGTTA	.	5	ESCA
TRIM34	0	.	GRCh37	11	5655862	5655862	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.521A>T	p.Tyr174Phe	p.Y174F	ENST00000514226	4/8	19	15	4	40	40	0	TRIM34,missense_variant,p.Tyr174Phe,ENST00000514226,;TRIM34,missense_variant,p.Tyr174Phe,ENST00000429814,;TRIM6-TRIM34,missense_variant,p.Tyr174Phe,ENST00000457787,;TRIM6-TRIM34,missense_variant,p.Tyr528Phe,ENST00000354852,;HBG2,intron_variant,,ENST00000380259,;TRIM34,upstream_gene_variant,,ENST00000495668,;TRIM34,splice_region_variant,,ENST00000491385,;	T	ENSG00000258659	ENST00000514226	Transcript	missense_variant	858	521	174	Y/F	tAt/tTt	.	.	.	1	TRIM34	HGNC	10063	protein_coding	YES	CCDS31391.1	ENSP00000422947	TRI34_HUMAN	.	UPI000006F93F	.	tolerated(0.18)	benign(0.001)	4/8	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTATCAGG	.	5	ESCA
OR52N1	0	.	GRCh37	11	5809136	5809136	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.911A>G	p.Glu304Gly	p.E304G	ENST00000317078	1/1	105	70	34	124	124	0	OR52N1,missense_variant,p.Glu304Gly,ENST00000317078,;TRIM5,intron_variant,,ENST00000412903,;TRIM5,intron_variant,,ENST00000380027,;	C	ENSG00000181001	ENST00000317078	Transcript	missense_variant	911	911	304	E/G	gAa/gGa	.	.	.	-1	OR52N1	HGNC	14853	protein_coding	YES	CCDS31398.1	ENSP00000322823	O52N1_HUMAN	.	UPI0000041BDD	.	deleterious(0.05)	benign(0.14)	1/1	.	hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF107,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTTTCTCGT	.	5	ESCA
DPP3	0	.	GRCh37	11	66276857	66276857	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*135T>C	.	.	ENST00000360510	18/18	73	53	20	59	59	0	DPP3,3_prime_UTR_variant,,ENST00000360510,;DPP3,3_prime_UTR_variant,,ENST00000532677,;DPP3,3_prime_UTR_variant,,ENST00000453114,;DPP3,3_prime_UTR_variant,,ENST00000531863,;DPP3,3_prime_UTR_variant,,ENST00000541961,;CTD-3074O7.11,intron_variant,,ENST00000419755,;BBS1,upstream_gene_variant,,ENST00000526815,;BBS1,upstream_gene_variant,,ENST00000318312,;DPP3,downstream_gene_variant,,ENST00000530165,;BBS1,upstream_gene_variant,,ENST00000455748,;BBS1,upstream_gene_variant,,ENST00000525809,;BBS1,upstream_gene_variant,,ENST00000393994,;BBS1,upstream_gene_variant,,ENST00000524705,;BBS1,upstream_gene_variant,,ENST00000537537,;DPP3,downstream_gene_variant,,ENST00000539085,;BBS1,upstream_gene_variant,,ENST00000529766,;BBS1,upstream_gene_variant,,ENST00000533557,;BBS1,upstream_gene_variant,,ENST00000524907,;BBS1,upstream_gene_variant,,ENST00000526035,;BBS1,upstream_gene_variant,,ENST00000524458,;BBS1,upstream_gene_variant,,ENST00000529955,;BBS1,upstream_gene_variant,,ENST00000532908,;BBS1,upstream_gene_variant,,ENST00000533644,;BBS1,upstream_gene_variant,,ENST00000527251,;BBS1,upstream_gene_variant,,ENST00000526760,;BBS1,upstream_gene_variant,,ENST00000534730,;	C	ENSG00000254986	ENST00000360510	Transcript	3_prime_UTR_variant	2414	.	.	.	.	.	.	.	1	DPP3	HGNC	3008	protein_coding	YES	CCDS8141.1	ENSP00000353701	DPP3_HUMAN	E9PQF2_HUMAN,E9PQ14_HUMAN,E9PPK9_HUMAN,E9PNX5_HUMAN	UPI000012983B	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGGTGACAC	.	5	ESCA
KRTAP5-9	0	.	GRCh37	11	71260187	71260187	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484C>G	p.Pro162Ala	p.P162A	ENST00000528743	1/1	104	91	12	133	133	0	KRTAP5-9,missense_variant,p.Pro162Ala,ENST00000528743,;	G	ENSG00000254997	ENST00000528743	Transcript	missense_variant	722	484	162	P/A	Cct/Gct	.	.	.	1	KRTAP5-9	HGNC	23604	protein_coding	YES	CCDS53677.1	ENSP00000431443	KRA59_HUMAN	.	UPI000012E079	.	deleterious_low_confidence(0)	unknown(0)	1/1	.	hmmpanther:PTHR23262:SF23,hmmpanther:PTHR23262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTCCCTGTG	.	4	ESCA
LAMTOR1	0	.	GRCh37	11	71810295	71810295	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50A>G	p.Glu17Gly	p.E17G	ENST00000278671	2/5	43	26	16	52	52	0	LAMTOR1,missense_variant,p.Glu17Gly,ENST00000278671,;LAMTOR1,missense_variant,p.Glu4Gly,ENST00000544594,;LAMTOR1,missense_variant,p.Glu17Gly,ENST00000545249,;LAMTOR1,missense_variant,p.Glu17Gly,ENST00000538404,;LAMTOR1,missense_variant,p.Glu17Gly,ENST00000535107,;LRTOMT,intron_variant,,ENST00000439209,;LRTOMT,intron_variant,,ENST00000435085,;LRTOMT,intron_variant,,ENST00000307198,;LRTOMT,intron_variant,,ENST00000419228,;LRTOMT,downstream_gene_variant,,ENST00000440313,;LRTOMT,downstream_gene_variant,,ENST00000539271,;LRTOMT,downstream_gene_variant,,ENST00000289488,;LRTOMT,downstream_gene_variant,,ENST00000538478,;LRTOMT,downstream_gene_variant,,ENST00000542846,;LRTOMT,downstream_gene_variant,,ENST00000541614,;LRTOMT,downstream_gene_variant,,ENST00000447974,;LRTOMT,downstream_gene_variant,,ENST00000536917,;LRTOMT,downstream_gene_variant,,ENST00000423494,;LRTOMT,downstream_gene_variant,,ENST00000324866,;LRTOMT,downstream_gene_variant,,ENST00000539587,;snoU13,upstream_gene_variant,,ENST00000459046,;LAMTOR1,non_coding_transcript_exon_variant,,ENST00000539797,;LAMTOR1,non_coding_transcript_exon_variant,,ENST00000541403,;LAMTOR1,intron_variant,,ENST00000535872,;LRTOMT,intron_variant,,ENST00000544409,;LRTOMT,intron_variant,,ENST00000427369,;LRTOMT,downstream_gene_variant,,ENST00000412777,;LRTOMT,downstream_gene_variant,,ENST00000535883,;	C	ENSG00000149357	ENST00000278671	Transcript	missense_variant	213	50	17	E/G	gAg/gGg	.	.	.	-1	LAMTOR1	HGNC	26068	protein_coding	YES	CCDS8209.1	ENSP00000278671	LTOR1_HUMAN	B4DUK2_HUMAN	UPI0000049CB7	.	deleterious(0.04)	benign(0.006)	2/5	.	Pfam_domain:PF15454,hmmpanther:PTHR13401:SF2,hmmpanther:PTHR13401	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCTCTCGG	.	5	ESCA
KLRD1	0	.	GRCh37	12	10464159	10464159	+	Missense_Mutation	SNP	A	A	T	rs769127885	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.260A>T	p.His87Leu	p.H87L	ENST00000336164	4/6	49	31	17	85	85	0	KLRD1,missense_variant,p.His87Leu,ENST00000543420,;KLRD1,missense_variant,p.His87Leu,ENST00000336164,;KLRD1,missense_variant,p.His87Leu,ENST00000381908,;KLRD1,missense_variant,p.His56Leu,ENST00000544747,;KLRD1,missense_variant,p.His56Leu,ENST00000350274,;KLRD1,missense_variant,p.His87Leu,ENST00000381907,;KLRD1,missense_variant,p.His66Leu,ENST00000543777,;KLRD1,upstream_gene_variant,,ENST00000539792,;KLRD1,non_coding_transcript_exon_variant,,ENST00000538997,;KLRD1,missense_variant,p.His87Leu,ENST00000539374,;KLRD1,non_coding_transcript_exon_variant,,ENST00000540271,;KLRD1,intron_variant,,ENST00000344825,;	T	ENSG00000134539	ENST00000336164	Transcript	missense_variant	520	260	87	H/L	cAt/cTt	rs769127885	.	.	1	KLRD1	HGNC	6378	protein_coding	YES	CCDS8621.1	ENSP00000338130	KLRD1_HUMAN	.	UPI00004565D6	.	tolerated(0.05)	benign(0.028)	4/6	.	Superfamily_domains:SSF56436,SMART_domains:SM00034,Pfam_domain:PF00059,Gene3D:3.10.100.10,hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF15,PROSITE_profiles:PS50041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGCATCTCT	.	5	ESCA
HCAR3	0	.	GRCh37	12	123200854	123200854	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431C>T	p.Ala144Val	p.A144V	ENST00000528880	1/1	58	53	5	70	70	0	HCAR3,missense_variant,p.Ala144Val,ENST00000528880,;HCAR1,intron_variant,,ENST00000356987,;RP11-324E6.6,downstream_gene_variant,,ENST00000543611,;RP11-324E6.6,downstream_gene_variant,,ENST00000545293,;	A	ENSG00000255398	ENST00000528880	Transcript	missense_variant	586	431	144	A/V	gCa/gTa	.	.	.	-1	HCAR3	HGNC	16824	protein_coding	YES	CCDS53842.1	ENSP00000436714	HCAR3_HUMAN	.	UPI00001AFD35	.	deleterious(0.04)	probably_damaging(0.999)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF0,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGCTGCTGTC	.	3	ESCA
PGAM5	0	.	GRCh37	12	133295362	133295362	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.719+656T>C	.	.	ENST00000498926	.	36	24	12	63	63	0	PGAM5,missense_variant,p.Leu245Ser,ENST00000317555,;PGAM5,intron_variant,,ENST00000498926,;PGAM5,intron_variant,,ENST00000454808,;PGAM5,intron_variant,,ENST00000543955,;PXMP2,intron_variant,,ENST00000545677,;RP13-672B3.2,downstream_gene_variant,,ENST00000537262,;PGAM5,intron_variant,,ENST00000541034,;	C	ENSG00000247077	ENST00000498926	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PGAM5	HGNC	28763	protein_coding	YES	CCDS53845.1	ENSP00000438465	PGAM5_HUMAN	F5GXG4_HUMAN	UPI0000406AB5	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGTTGTCCG	.	5	ESCA
C12orf36	0	.	GRCh37	12	13529163	13529163	+	Silent	SNP	C	C	A	rs771357158	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177G>T	p.%3D	p.L59L	ENST00000318426	2/3	71	47	24	100	100	0	C12orf36,synonymous_variant,p.%3D,ENST00000532841,;C12orf36,synonymous_variant,p.%3D,ENST00000539026,;C12orf36,synonymous_variant,p.%3D,ENST00000318426,;C12orf36,synonymous_variant,p.%3D,ENST00000527705,;C12orf36,non_coding_transcript_exon_variant,,ENST00000531049,;	A	ENSG00000180861	ENST00000318426	Transcript	synonymous_variant	395	177	59	L	ctG/ctT	rs771357158	.	.	-1	C12orf36	HGNC	26598	protein_coding	YES	.	ENSP00000443007	CL036_HUMAN	.	UPI000014030C	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCACAGCCT	.	5	ESCA
KMT2D	0	.	GRCh37	12	49432030	49432030	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9109delC	p.His3037ThrfsTer34	p.H3037Tfs*34	ENST00000301067	34/54	29	21	8	31	31	0	KMT2D,frameshift_variant,p.His3037ThrfsTer34,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000550356,;	-	ENSG00000167548	ENST00000301067	Transcript	frameshift_variant	9109	9109	3037	H/X	Cac/ac	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	34/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAAGTGGGGGT	.	3	ESCA
MAP3K12	0	.	GRCh37	12	53878119	53878119	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1170C>G	p.Phe390Leu	p.F390L	ENST00000547035	7/14	50	44	5	70	70	0	MAP3K12,missense_variant,p.Phe390Leu,ENST00000547035,;MAP3K12,missense_variant,p.Phe357Leu,ENST00000267079,;MAP3K12,missense_variant,p.Phe390Leu,ENST00000547488,;PCBP2,downstream_gene_variant,,ENST00000455667,;PCBP2,downstream_gene_variant,,ENST00000547859,;PCBP2,downstream_gene_variant,,ENST00000359282,;PCBP2,downstream_gene_variant,,ENST00000546463,;PCBP2,downstream_gene_variant,,ENST00000552819,;PCBP2,downstream_gene_variant,,ENST00000552296,;PCBP2,downstream_gene_variant,,ENST00000562264,;PCBP2,downstream_gene_variant,,ENST00000359462,;PCBP2,downstream_gene_variant,,ENST00000437231,;PCBP2,downstream_gene_variant,,ENST00000439930,;PCBP2,downstream_gene_variant,,ENST00000447282,;MAP3K12,downstream_gene_variant,,ENST00000548565,;PCBP2,downstream_gene_variant,,ENST00000548933,;PCBP2,downstream_gene_variant,,ENST00000549863,;PCBP2,downstream_gene_variant,,ENST00000603815,;MAP3K12,downstream_gene_variant,,ENST00000547151,;MAP3K12,missense_variant,p.Phe357Leu,ENST00000552365,;MAP3K12,non_coding_transcript_exon_variant,,ENST00000547020,;PCBP2,downstream_gene_variant,,ENST00000550585,;PCBP2,downstream_gene_variant,,ENST00000550733,;MAP3K12,upstream_gene_variant,,ENST00000551511,;PCBP2,downstream_gene_variant,,ENST00000547048,;MAP3K12,downstream_gene_variant,,ENST00000551895,;MAP3K12,downstream_gene_variant,,ENST00000548690,;MAP3K12,downstream_gene_variant,,ENST00000547803,;	C	ENSG00000139625	ENST00000547035	Transcript	missense_variant	1375	1170	390	F/L	ttC/ttG	.	.	.	-1	MAP3K12	HGNC	6851	protein_coding	YES	CCDS55831.1	ENSP00000448689	M3K12_HUMAN	H3BMF0_HUMAN	UPI00001407EE	.	deleterious(0)	probably_damaging(0.999)	7/14	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23257:SF397,hmmpanther:PTHR23257,Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF500741,SMART_domains:SM00220,PIRSF_domain:PIRSF038165,Superfamily_domains:SSF56112,Prints_domain:PR00109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCGGAATGA	.	4	ESCA
GPR182	0	.	GRCh37	12	57390113	57390113	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1120G>A	p.Ala374Thr	p.A374T	ENST00000300098	2/2	44	25	19	63	63	0	GPR182,missense_variant,p.Ala374Thr,ENST00000300098,;HBCBP,upstream_gene_variant,,ENST00000600202,;ZBTB39,downstream_gene_variant,,ENST00000300101,;RP11-474N8.5,non_coding_transcript_exon_variant,,ENST00000556850,;	A	ENSG00000166856	ENST00000300098	Transcript	missense_variant	1339	1120	374	A/T	Gcc/Acc	.	.	.	1	GPR182	HGNC	13708	protein_coding	YES	CCDS8927.1	ENSP00000300098	GP182_HUMAN	.	UPI0000001652	.	tolerated_low_confidence(0.35)	benign(0)	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCAGCCCCC	.	5	ESCA
RP11-556N21.1	0	.	GRCh37	13	25155856	25155856	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.469C>A	.	.	ENST00000453498	5/13	86	76	10	175	175	0	RP11-556N21.1,non_coding_transcript_exon_variant,,ENST00000453498,;TPTE2P6,upstream_gene_variant,,ENST00000440905,;TPTE2P6,non_coding_transcript_exon_variant,,ENST00000445572,;	A	ENSG00000243008	ENST00000453498	Transcript	non_coding_transcript_exon_variant	469	.	.	.	.	.	.	.	1	RP11-556N21.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	5/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTGCAGAGG	.	4	ESCA
CHD8	0	.	GRCh37	14	21864038	21864038	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5065A>T	p.Lys1689Ter	p.K1689*	ENST00000399982	27/37	38	35	3	42	42	0	CHD8,stop_gained,p.Lys1689Ter,ENST00000557364,;CHD8,stop_gained,p.Lys1410Ter,ENST00000430710,;CHD8,stop_gained,p.Lys1689Ter,ENST00000399982,;CHD8,downstream_gene_variant,,ENST00000555935,;CHD8,upstream_gene_variant,,ENST00000553870,;SNORD8,downstream_gene_variant,,ENST00000363915,;SNORD9,upstream_gene_variant,,ENST00000362566,;CHD8,non_coding_transcript_exon_variant,,ENST00000555962,;CHD8,upstream_gene_variant,,ENST00000557329,;CHD8,upstream_gene_variant,,ENST00000555301,;RP11-689J19.1,upstream_gene_variant,,ENST00000480068,;	A	ENSG00000100888	ENST00000399982	Transcript	stop_gained	5130	5065	1689	K/*	Aaa/Taa	.	.	.	-1	CHD8	HGNC	20153	protein_coding	YES	CCDS53885.1	ENSP00000382863	CHD8_HUMAN	.	UPI00002375B9	.	.	.	27/37	.	hmmpanther:PTHR10799:SF551,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTTTATCAA	.	4	ESCA
FBXO33	0	.	GRCh37	14	39868350	39868350	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*370delT	.	.	ENST00000298097	4/4	100	87	13	97	97	0	FBXO33,3_prime_UTR_variant,,ENST00000298097,;FBXO33,downstream_gene_variant,,ENST00000554190,;	-	ENSG00000165355	ENST00000298097	Transcript	3_prime_UTR_variant	2376	.	.	.	.	.	.	.	-1	FBXO33	HGNC	19833	protein_coding	YES	CCDS9677.1	ENSP00000298097	FBX33_HUMAN	B4DFK5_HUMAN	UPI00001605E2	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATATCTATATAT	.	3	ESCA
LRRC9	0	.	GRCh37	14	60494606	60494606	+	Missense_Mutation	SNP	T	T	A	rs577421017	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3708T>A	p.Asn1236Lys	p.N1236K	ENST00000445360	28/32	55	41	14	85	85	0	LRRC9,missense_variant,p.Asn1236Lys,ENST00000445360,;RP11-16B13.1,intron_variant,,ENST00000555432,;RP11-16B13.1,intron_variant,,ENST00000554123,;LRRC9,3_prime_UTR_variant,,ENST00000254271,;LRRC9,upstream_gene_variant,,ENST00000568404,;	A	ENSG00000131951	ENST00000445360	Transcript	missense_variant	3912	3708	1236	N/K	aaT/aaA	rs577421017	.	.	1	LRRC9	HGNC	19848	protein_coding	YES	.	ENSP00000454748	LRRC9_HUMAN	H3BUS4_HUMAN	UPI000173AA0B	.	deleterious(0.01)	possibly_damaging(0.907)	28/32	.	PROSITE_profiles:PS51450,Gene3D:3.80.10.10,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAATGAAAT	.	5	ESCA
SYNE2	0	.	GRCh37	14	64691245	64691245	+	Missense_Mutation	SNP	G	G	T	rs202235545	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20449G>T	p.Val6817Leu	p.V6817L	ENST00000358025	114/116	44	20	24	64	64	0	SYNE2,missense_variant,p.Val6710Leu,ENST00000554584,;SYNE2,missense_variant,p.Val3179Leu,ENST00000394768,;SYNE2,missense_variant,p.Val6794Leu,ENST00000344113,;SYNE2,missense_variant,p.Val6817Leu,ENST00000358025,;SYNE2,missense_variant,p.Val577Leu,ENST00000554805,;SYNE2,missense_variant,p.Val339Leu,ENST00000441438,;SYNE2,missense_variant,p.Val465Leu,ENST00000458046,;SYNE2,missense_variant,p.Val672Leu,ENST00000555022,;SYNE2,missense_variant,p.Val3179Leu,ENST00000357395,;SYNE2,missense_variant,p.Val3451Leu,ENST00000555002,;ESR2,intron_variant,,ENST00000556275,;ESR2,intron_variant,,ENST00000542956,;ESR2,downstream_gene_variant,,ENST00000555278,;ESR2,downstream_gene_variant,,ENST00000357782,;ESR2,downstream_gene_variant,,ENST00000553796,;ESR2,downstream_gene_variant,,ENST00000353772,;ESR2,downstream_gene_variant,,ENST00000554572,;ESR2,downstream_gene_variant,,ENST00000358599,;SYNE2,3_prime_UTR_variant,,ENST00000555612,;SYNE2,3_prime_UTR_variant,,ENST00000553289,;ESR2,downstream_gene_variant,,ENST00000344288,;SYNE2,downstream_gene_variant,,ENST00000554928,;	T	ENSG00000054654	ENST00000358025	Transcript	missense_variant	20679	20449	6817	V/L	Gtg/Ttg	rs202235545	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	benign(0.009)	114/116	.	hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCGTGCCA	byCluster|by1000G	5	ESCA
NRDE2	0	.	GRCh37	14	90764706	90764706	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1564T>C	p.Phe522Leu	p.F522L	ENST00000354366	8/14	47	43	4	37	37	0	NRDE2,missense_variant,p.Phe291Leu,ENST00000357904,;NRDE2,missense_variant,p.Phe522Leu,ENST00000354366,;NRDE2,missense_variant,p.Phe101Leu,ENST00000554464,;NRDE2,3_prime_UTR_variant,,ENST00000553409,;NRDE2,3_prime_UTR_variant,,ENST00000556189,;	G	ENSG00000119720	ENST00000354366	Transcript	missense_variant	1797	1564	522	F/L	Ttt/Ctt	COSM554018	.	.	-1	NRDE2	HGNC	20186	protein_coding	YES	CCDS9890.1	ENSP00000346335	NRDE2_HUMAN	Q658X2_HUMAN,E9PBK4_HUMAN	UPI00001FD9DB	.	deleterious(0)	probably_damaging(0.934)	8/14	.	hmmpanther:PTHR13471,Pfam_domain:PF08424,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCAAAAGGGTT	.	3	ESCA
DNAJC17	0	.	GRCh37	15	41071496	41071496	+	Missense_Mutation	SNP	T	T	G	rs377051762	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.220A>C	p.Lys74Gln	p.K74Q	ENST00000220496	4/11	32	22	10	59	59	0	DNAJC17,missense_variant,p.Lys74Gln,ENST00000220496,;DNAJC17,downstream_gene_variant,,ENST00000561044,;DNAJC17,missense_variant,p.Lys74Gln,ENST00000560065,;DNAJC17,missense_variant,p.Lys74Gln,ENST00000560645,;DNAJC17,missense_variant,p.Lys74Gln,ENST00000559310,;DNAJC17,missense_variant,p.Lys74Gln,ENST00000561018,;DNAJC17,3_prime_UTR_variant,,ENST00000559238,;DNAJC17,non_coding_transcript_exon_variant,,ENST00000560301,;DNAJC17,upstream_gene_variant,,ENST00000558769,;DNAJC17,upstream_gene_variant,,ENST00000561110,;	G	ENSG00000104129	ENST00000220496	Transcript	missense_variant	251	220	74	K/Q	Aag/Cag	rs377051762	.	.	-1	DNAJC17	HGNC	25556	protein_coding	YES	CCDS10065.1	ENSP00000220496	DJC17_HUMAN	.	UPI00000375AE	.	tolerated(0.09)	benign(0.21)	4/11	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF46565,Gene3D:1.10.287.110,hmmpanther:PTHR24078:SF153,hmmpanther:PTHR24078,PROSITE_profiles:PS50076	C:0.0006	C:0	C:0	.	C:0.003	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTTGTCAT	byFrequency|byCluster|by1000G	5	ESCA
HERC1	0	.	GRCh37	15	63966633	63966633	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7754G>A	p.Gly2585Glu	p.G2585E	ENST00000443617	38/78	56	38	18	64	64	0	HERC1,missense_variant,p.Gly2585Glu,ENST00000443617,;HERC1,downstream_gene_variant,,ENST00000559715,;RP11-317G6.1,upstream_gene_variant,,ENST00000559303,;	T	ENSG00000103657	ENST00000443617	Transcript	missense_variant	7842	7754	2585	G/E	gGa/gAa	.	.	.	-1	HERC1	HGNC	4867	protein_coding	YES	CCDS45277.1	ENSP00000390158	HERC1_HUMAN	H0YL74_HUMAN,H0YL07_HUMAN,H0YKW7_HUMAN	UPI0000212760	.	.	benign(0.357)	38/78	.	hmmpanther:PTHR22870:SF156,hmmpanther:PTHR22870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAATCCCAAT	.	5	ESCA
SLC24A1	0	.	GRCh37	15	65916671	65916671	+	Missense_Mutation	SNP	G	G	A	rs746325831	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.253G>A	p.Glu85Lys	p.E85K	ENST00000261892	2/10	71	63	8	87	87	0	SLC24A1,missense_variant,p.Glu85Lys,ENST00000546330,;SLC24A1,missense_variant,p.Glu85Lys,ENST00000399033,;SLC24A1,missense_variant,p.Glu85Lys,ENST00000544319,;SLC24A1,missense_variant,p.Glu85Lys,ENST00000339868,;SLC24A1,missense_variant,p.Glu85Lys,ENST00000537259,;SLC24A1,missense_variant,p.Glu85Lys,ENST00000261892,;SLC24A1,intron_variant,,ENST00000425561,;SLC24A1,downstream_gene_variant,,ENST00000535950,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000434116,;	A	ENSG00000074621	ENST00000261892	Transcript	missense_variant	540	253	85	E/K	Gaa/Aaa	rs746325831,COSM3816582	.	.	1	SLC24A1	HGNC	10975	protein_coding	YES	CCDS45284.1	ENSP00000261892	NCKX1_HUMAN	.	UPI000013020C	.	.	benign(0)	2/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10846,hmmpanther:PTHR10846:SF6,TIGRFAM_domain:TIGR00927	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTCCGAAATG	byFrequency	4	ESCA
GOLGA6D	0	.	GRCh37	15	75586142	75586142	+	Missense_Mutation	SNP	G	G	A	rs764138268	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1666G>A	p.Val556Ile	p.V556I	ENST00000434739	15/18	157	136	20	273	273	0	GOLGA6D,missense_variant,p.Val556Ile,ENST00000434739,;RN7SL327P,downstream_gene_variant,,ENST00000488659,;	A	ENSG00000140478	ENST00000434739	Transcript	missense_variant	1707	1666	556	V/I	Gtc/Atc	rs764138268	.	.	1	GOLGA6D	HGNC	32204	protein_coding	YES	CCDS45308.1	ENSP00000391085	GOG6D_HUMAN	.	UPI00001AEE2C	.	tolerated(1)	benign(0.001)	15/18	.	hmmpanther:PTHR10881,Pfam_domain:PF15070	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATTCGTCCAG	byFrequency	4	ESCA
TTLL13	0	.	GRCh37	15	90805255	90805255	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000339615	.	56	37	19	69	69	0	TTLL13,missense_variant,p.Ser457Leu,ENST00000438251,;TTLL13,downstream_gene_variant,,ENST00000339615,;NGRN,upstream_gene_variant,,ENST00000379095,;NGRN,upstream_gene_variant,,ENST00000331497,;RP11-697E2.6,3_prime_UTR_variant,,ENST00000561573,;	T	ENSG00000213471	ENST00000339615	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2935	1	TTLL13	HGNC	32484	protein_coding	YES	.	ENSP00000345294	TTL13_HUMAN	.	UPI00005B2F05	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGTCATCCC	.	5	ESCA
PTX4	0	.	GRCh37	16	1536208	1536208	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1154G>A	p.Arg385Lys	p.R385K	ENST00000293922	3/3	47	31	16	99	99	0	PTX4,missense_variant,p.Arg390Lys,ENST00000447419,;PTX4,missense_variant,p.Arg385Lys,ENST00000293922,;PTX4,3_prime_UTR_variant,,ENST00000440447,;	T	ENSG00000251692	ENST00000293922	Transcript	missense_variant	1154	1154	385	R/K	aGg/aAg	.	.	.	-1	PTX4	HGNC	14171	protein_coding	YES	CCDS32362.1	ENSP00000293922	PTX4_HUMAN	.	UPI000007334C	.	tolerated(0.06)	benign(0.444)	3/3	.	hmmpanther:PTHR19277:SF34,hmmpanther:PTHR19277,Gene3D:2.60.120.200,Pfam_domain:PF00354,SMART_domains:SM00159,Superfamily_domains:SSF49899,Prints_domain:PR00895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCCCTGAAG	.	5	ESCA
NOMO2	0	.	GRCh37	16	18549919	18549919	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1149C>T	p.%3D	p.H383H	ENST00000381474	11/32	91	85	5	213	213	0	NOMO2,synonymous_variant,p.%3D,ENST00000330537,;NOMO2,synonymous_variant,p.%3D,ENST00000543392,;NOMO2,synonymous_variant,p.%3D,ENST00000381474,;NOMO2,3_prime_UTR_variant,,ENST00000564991,;NOMO2,downstream_gene_variant,,ENST00000564355,;RP11-457I16.4,downstream_gene_variant,,ENST00000575091,;	A	ENSG00000185164	ENST00000381474	Transcript	synonymous_variant	1215	1149	383	H	caC/caT	.	.	.	-1	NOMO2	HGNC	22652	protein_coding	YES	CCDS32394.1	ENSP00000370883	NOMO2_HUMAN	.	UPI00001AFC79	.	.	.	11/32	.	hmmpanther:PTHR23303,Pfam_domain:PF13620,Gene3D:2.60.40.1120,Superfamily_domains:SSF49452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGAGGTGCTC	.	2	ESCA
SLC9A3R2	0	.	GRCh37	16	2088572	2088572	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*587C>A	.	.	ENST00000424542	7/7	43	28	15	102	102	0	SLC9A3R2,3_prime_UTR_variant,,ENST00000424542,;NTHL1,downstream_gene_variant,,ENST00000566380,;SLC9A3R2,downstream_gene_variant,,ENST00000563587,;NTHL1,downstream_gene_variant,,ENST00000219066,;SLC9A3R2,downstream_gene_variant,,ENST00000432365,;SLC9A3R2,downstream_gene_variant,,ENST00000561844,;SLC9A3R2,downstream_gene_variant,,ENST00000567504,;SLC9A3R2,downstream_gene_variant,,ENST00000565855,;SLC9A3R2,downstream_gene_variant,,ENST00000566198,;SLC9A3R2,downstream_gene_variant,,ENST00000565086,;NTHL1,downstream_gene_variant,,ENST00000562951,;NTHL1,downstream_gene_variant,,ENST00000562120,;NTHL1,downstream_gene_variant,,ENST00000568513,;NTHL1,downstream_gene_variant,,ENST00000561841,;NTHL1,downstream_gene_variant,,ENST00000561862,;NTHL1,downstream_gene_variant,,ENST00000565406,;SLC9A3R2,downstream_gene_variant,,ENST00000564033,;NTHL1,downstream_gene_variant,,ENST00000567727,;	A	ENSG00000065054	ENST00000424542	Transcript	3_prime_UTR_variant	1739	.	.	.	.	.	.	.	1	SLC9A3R2	HGNC	11076	protein_coding	YES	CCDS45382.1	ENSP00000408005	NHRF2_HUMAN	Q6NTG0_HUMAN,H3BQS0_HUMAN	UPI0000070578	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCAGCCTCTT	.	2	ESCA
NFATC2IP	0	.	GRCh37	16	28975131	28975131	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1207C>T	p.%3D	p.L403L	ENST00000320805	8/8	23	20	3	65	65	0	NFATC2IP,synonymous_variant,p.%3D,ENST00000320805,;NFATC2IP,synonymous_variant,p.%3D,ENST00000564978,;NFATC2IP,synonymous_variant,p.%3D,ENST00000568148,;RP11-264B17.2,intron_variant,,ENST00000569974,;NFATC2IP,downstream_gene_variant,,ENST00000562977,;	T	ENSG00000176953	ENST00000320805	Transcript	synonymous_variant	1282	1207	403	L	Ctg/Ttg	.	.	.	1	NFATC2IP	HGNC	25906	protein_coding	YES	CCDS10645.1	ENSP00000324792	NF2IP_HUMAN	.	UPI00000316E2	.	.	.	8/8	.	PROSITE_profiles:PS50053,hmmpanther:PTHR10562,hmmpanther:PTHR10562:SF9,Pfam_domain:PF11976,Gene3D:3.10.20.90,SMART_domains:SM00213,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GGGAGCTGCCA	.	3	ESCA
ZNF720	0	.	GRCh37	16	31766690	31766690	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361+1469G>A	.	.	ENST00000316491	.	50	34	16	85	85	0	ZNF720,missense_variant,p.Gly360Arg,ENST00000399681,;ZNF720,intron_variant,,ENST00000539915,;ZNF720,intron_variant,,ENST00000316491,;ZNF720,intron_variant,,ENST00000534369,;ZNF720,downstream_gene_variant,,ENST00000398696,;ZNF720,downstream_gene_variant,,ENST00000529515,;ZNF720,downstream_gene_variant,,ENST00000530881,;ZNF720,intron_variant,,ENST00000544044,;ZNF720,intron_variant,,ENST00000542684,;ZNF720,intron_variant,,ENST00000531864,;ZNF720,downstream_gene_variant,,ENST00000533488,;ZNF720,3_prime_UTR_variant,,ENST00000534277,;ZNF720,3_prime_UTR_variant,,ENST00000398707,;ZNF720,downstream_gene_variant,,ENST00000529943,;	A	ENSG00000197302	ENST00000316491	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZNF720	HGNC	26987	protein_coding	YES	CCDS45473.1	ENSP00000319222	ZN720_HUMAN	.	UPI000003603E	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACCGGAGAG	.	5	ESCA
TP53TG3D	0	.	GRCh37	16	32266327	32266327	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*103A>G	.	.	ENST00000398664	2/2	55	40	14	85	84	0	TP53TG3D,3_prime_UTR_variant,,ENST00000398664,;TP53TG3D,3_prime_UTR_variant,,ENST00000569631,;TP53TG3D,downstream_gene_variant,,ENST00000354614,;RP11-56L13.7,upstream_gene_variant,,ENST00000562604,;TP53TG3D,non_coding_transcript_exon_variant,,ENST00000564810,;TP53TG3D,3_prime_UTR_variant,,ENST00000380148,;TP53TG3D,3_prime_UTR_variant,,ENST00000568044,;TP53TG3D,non_coding_transcript_exon_variant,,ENST00000567978,;TP53TG3D,downstream_gene_variant,,ENST00000563025,;	G	ENSG00000205456	ENST00000398664	Transcript	3_prime_UTR_variant	1113	.	.	.	.	.	.	.	1	TP53TG3D	HGNC	44657	protein_coding	YES	CCDS58456.1	ENSP00000455596	T53G3_HUMAN	.	UPI000006D8DD	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGCATCAAT	.	5	ESCA
ANKS3	0	.	GRCh37	16	4749098	4749098	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1364T>A	p.Ile455Asn	p.I455N	ENST00000304283	12/18	30	26	3	58	58	0	ANKS3,missense_variant,p.Ile455Asn,ENST00000304283,;ANKS3,missense_variant,p.Ile326Asn,ENST00000446014,;ANKS3,missense_variant,p.Ile120Asn,ENST00000588513,;ANKS3,missense_variant,p.Ile382Asn,ENST00000585773,;ANKS3,downstream_gene_variant,,ENST00000586605,;ANKS3,downstream_gene_variant,,ENST00000592421,;NUDT16L1,downstream_gene_variant,,ENST00000590460,;NUDT16L1,downstream_gene_variant,,ENST00000586252,;NUDT16L1,downstream_gene_variant,,ENST00000304301,;ANKS3,downstream_gene_variant,,ENST00000450067,;ANKS3,downstream_gene_variant,,ENST00000586166,;NUDT16L1,downstream_gene_variant,,ENST00000586536,;ANKS3,downstream_gene_variant,,ENST00000592698,;NUDT16L1,downstream_gene_variant,,ENST00000405142,;ANKS3,3_prime_UTR_variant,,ENST00000592077,;ANKS3,3_prime_UTR_variant,,ENST00000590193,;ANKS3,non_coding_transcript_exon_variant,,ENST00000591653,;ANKS3,non_coding_transcript_exon_variant,,ENST00000591185,;ANKS3,non_coding_transcript_exon_variant,,ENST00000589035,;ANKS3,non_coding_transcript_exon_variant,,ENST00000588398,;ANKS3,non_coding_transcript_exon_variant,,ENST00000590803,;ANKS3,downstream_gene_variant,,ENST00000592068,;ANKS3,downstream_gene_variant,,ENST00000590730,;ANKS3,downstream_gene_variant,,ENST00000592840,;	T	ENSG00000168096	ENST00000304283	Transcript	missense_variant	1659	1364	455	I/N	aTc/aAc	.	.	.	-1	ANKS3	HGNC	29422	protein_coding	YES	CCDS10520.1	ENSP00000304586	ANKS3_HUMAN	K7ERR7_HUMAN,K7ERF3_HUMAN,K7EQE0_HUMAN,K7EKD2_HUMAN,K7EJY2_HUMAN,D3DUE4_HUMAN	UPI00001C08FE	.	deleterious(0)	probably_damaging(0.963)	12/18	.	PROSITE_profiles:PS50105,hmmpanther:PTHR24184:SF6,hmmpanther:PTHR24184,Gene3D:1.10.150.50,Pfam_domain:PF07647,SMART_domains:SM00454,Superfamily_domains:SSF47769	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GAAAGATGCGG	.	3	ESCA
CDH11	0	.	GRCh37	16	65038654	65038654	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.119A>G	p.Glu40Gly	p.E40G	ENST00000268603	3/13	29	25	4	69	69	0	CDH11,missense_variant,p.Glu40Gly,ENST00000567934,;CDH11,missense_variant,p.Glu40Gly,ENST00000394156,;CDH11,missense_variant,p.Glu40Gly,ENST00000562998,;CDH11,missense_variant,p.Glu40Gly,ENST00000268603,;CDH11,missense_variant,p.Glu40Gly,ENST00000564317,;CDH11,missense_variant,p.Glu40Gly,ENST00000562712,;CDH11,intron_variant,,ENST00000566827,;CDH11,downstream_gene_variant,,ENST00000562882,;CDH11,downstream_gene_variant,,ENST00000562325,;CDH11,non_coding_transcript_exon_variant,,ENST00000569624,;CDH11,downstream_gene_variant,,ENST00000568340,;CDH11,downstream_gene_variant,,ENST00000565210,;	C	ENSG00000140937	ENST00000268603	Transcript	missense_variant	735	119	40	E/G	gAg/gGg	.	.	.	-1	CDH11	HGNC	1750	protein_coding	YES	CCDS10803.1	ENSP00000268603	CAD11_HUMAN	H3BUU9_HUMAN,H3BSM4_HUMAN,H3BR78_HUMAN,H3BQH2_HUMAN,H3BQB5_HUMAN,H3BPQ2_HUMAN,H3BP26_HUMAN	UPI000013D7C5	.	tolerated(0.29)	benign(0.086)	3/13	.	hmmpanther:PTHR24027:SF85,hmmpanther:PTHR24027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTTCTCATGG	.	4	ESCA
CTCF	0	.	GRCh37	16	67672857	67672857	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1082T>A	.	.	ENST00000264010	12/12	51	37	14	70	70	0	CTCF,3_prime_UTR_variant,,ENST00000401394,;CTCF,3_prime_UTR_variant,,ENST00000264010,;	A	ENSG00000102974	ENST00000264010	Transcript	3_prime_UTR_variant	3710	.	.	.	.	.	.	.	1	CTCF	HGNC	13723	protein_coding	YES	CCDS10841.1	ENSP00000264010	CTCF_HUMAN	.	UPI0000000DDE	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTACTGATTT	.	5	ESCA
ZFHX3	0	.	GRCh37	16	72831852	72831852	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4729C>T	p.Leu1577Phe	p.L1577F	ENST00000268489	9/10	47	30	17	89	89	0	ZFHX3,missense_variant,p.Leu663Phe,ENST00000397992,;ZFHX3,missense_variant,p.Leu1577Phe,ENST00000268489,;	A	ENSG00000140836	ENST00000268489	Transcript	missense_variant	5402	4729	1577	L/F	Ctt/Ttt	.	.	.	-1	ZFHX3	HGNC	777	protein_coding	YES	CCDS10908.1	ENSP00000268489	ZFHX3_HUMAN	Q6TCJ2_HUMAN	UPI00001AE937	.	.	probably_damaging(0.994)	9/10	.	hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGGGCTC	.	5	ESCA
KARS	0	.	GRCh37	16	75665431	75665431	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1219G>A	p.Glu407Lys	p.E407K	ENST00000319410	10/15	26	23	3	37	37	0	KARS,missense_variant,p.Glu407Lys,ENST00000319410,;KARS,missense_variant,p.Glu379Lys,ENST00000302445,;KARS,intron_variant,,ENST00000568378,;KARS,downstream_gene_variant,,ENST00000568682,;KARS,downstream_gene_variant,,ENST00000566772,;KARS,downstream_gene_variant,,ENST00000570215,;KARS,3_prime_UTR_variant,,ENST00000564578,;KARS,upstream_gene_variant,,ENST00000569298,;KARS,downstream_gene_variant,,ENST00000566560,;KARS,downstream_gene_variant,,ENST00000562875,;KARS,downstream_gene_variant,,ENST00000566249,;	T	ENSG00000065427	ENST00000319410	Transcript	missense_variant	1341	1219	407	E/K	Gag/Aag	.	.	.	-1	KARS	HGNC	6215	protein_coding	YES	CCDS45532.1	ENSP00000325448	SYK_HUMAN	J3KRL2_HUMAN,H3BVA8_HUMAN	UPI00001405CB	.	tolerated(0.12)	benign(0.271)	10/15	.	HAMAP:MF_00252,PROSITE_profiles:PS50862,hmmpanther:PTHR22594:SF4,hmmpanther:PTHR22594,TIGRFAM_domain:TIGR00499,Gene3D:3.30.930.10,Pfam_domain:PF00152,Superfamily_domains:SSF55681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCTCTGGGC	.	2	ESCA
NCOR1	0	.	GRCh37	17	15950318	15950318	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6626A>T	p.Lys2209Met	p.K2209M	ENST00000268712	42/46	60	20	39	106	106	0	NCOR1,missense_variant,p.Lys149Met,ENST00000580554,;NCOR1,missense_variant,p.Lys793Met,ENST00000395857,;NCOR1,missense_variant,p.Lys150Met,ENST00000579606,;NCOR1,missense_variant,p.Lys2106Met,ENST00000395851,;NCOR1,missense_variant,p.Lys11Met,ENST00000579573,;NCOR1,missense_variant,p.Lys840Met,ENST00000395849,;NCOR1,missense_variant,p.Lys2209Met,ENST00000268712,;TTC19,downstream_gene_variant,,ENST00000470649,;NCOR1,non_coding_transcript_exon_variant,,ENST00000464381,;NCOR1,non_coding_transcript_exon_variant,,ENST00000470782,;NCOR1,non_coding_transcript_exon_variant,,ENST00000583234,;NCOR1,non_coding_transcript_exon_variant,,ENST00000458113,;RPLP1P11,downstream_gene_variant,,ENST00000453002,;	A	ENSG00000141027	ENST00000268712	Transcript	missense_variant	6884	6626	2209	K/M	aAg/aTg	.	.	.	-1	NCOR1	HGNC	7672	protein_coding	YES	CCDS11175.1	ENSP00000268712	NCOR1_HUMAN	Q9NSZ0_HUMAN,C9JAP0_HUMAN,B4DJ25_HUMAN	UPI000013D7D5	.	.	probably_damaging(0.998)	42/46	.	hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCTTCTTT	.	5	ESCA
KRTAP4-9	0	.	GRCh37	17	39261661	39261661	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21C>G	p.%3D	p.G7G	ENST00000391415	1/1	223	123	100	344	344	0	KRTAP4-9,synonymous_variant,p.%3D,ENST00000391415,;KRTAP4-16P,upstream_gene_variant,,ENST00000440582,;	G	ENSG00000212722	ENST00000391415	Transcript	synonymous_variant	78	21	7	G	ggC/ggG	.	.	.	1	KRTAP4-9	HGNC	18910	protein_coding	YES	CCDS54124.1	ENSP00000375234	KRA49_HUMAN	.	UPI000021D2D3	.	.	.	1/1	.	hmmpanther:PTHR23262:SF1,hmmpanther:PTHR23262,Pfam_domain:PF01500	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGGCTCCGT	.	5	ESCA
DLX4	0	.	GRCh37	17	48050491	48050491	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.338C>A	p.Pro113His	p.P113H	ENST00000240306	2/3	71	44	26	130	130	0	DLX4,missense_variant,p.Pro113His,ENST00000240306,;DLX4,missense_variant,p.Pro41His,ENST00000411890,;DLX4,downstream_gene_variant,,ENST00000505318,;DLX4,non_coding_transcript_exon_variant,,ENST00000503410,;DLX4,non_coding_transcript_exon_variant,,ENST00000503276,;	A	ENSG00000108813	ENST00000240306	Transcript	missense_variant	633	338	113	P/H	cCc/cAc	.	.	.	1	DLX4	HGNC	2917	protein_coding	YES	CCDS11555.1	ENSP00000240306	DLX4_HUMAN	.	UPI0000070F94	.	tolerated(0.11)	benign(0.168)	2/3	.	hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF30,Gene3D:1.10.10.60,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCCCGCCA	.	5	ESCA
SMURF2	0	.	GRCh37	17	62543830	62543830	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1959C>T	p.%3D	p.V653V	ENST00000262435	17/19	89	49	40	110	110	0	SMURF2,synonymous_variant,p.%3D,ENST00000262435,;SMURF2,3_prime_UTR_variant,,ENST00000578386,;SMURF2,3_prime_UTR_variant,,ENST00000582081,;	A	ENSG00000108854	ENST00000262435	Transcript	synonymous_variant	2147	1959	653	V	gtC/gtT	COSM4139753	.	.	-1	SMURF2	HGNC	16809	protein_coding	YES	CCDS32707.1	ENSP00000262435	SMUF2_HUMAN	Q96DE7_HUMAN	UPI00001361C5	.	.	.	17/19	.	PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF300,hmmpanther:PTHR11254,Pfam_domain:PF00632,SMART_domains:SM00119,PIRSF_domain:PIRSF001569,Superfamily_domains:SSF56204	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTGACAAT	.	5	ESCA
TP53	0	.	GRCh37	17	7574035	7574035	+	Splice_Site	SNP	T	T	G	.	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.994-2A>C	.	p.X332_splice	ENST00000269305	.	10	3	7	34	34	0	TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000269305,;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000359597,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000504937,;TP53,splice_acceptor_variant,,ENST00000504290,;TP53,splice_acceptor_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	G	ENSG00000141510	ENST00000269305	Transcript	splice_acceptor_variant	.	.	.	.	.	TP53_g.16883A>T,COSM43791,COSM3970338,COSM87027,COSM1610826,COSM318155,COSM3970337	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	9/10	.	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.G334V|c.1001G>T|5,BUFFER|p.G334V|c.1001G>T|8,BUFFER|p.G334W|c.1000G>T|3,BUFFER|p.?|c.994-1G>T|3,BUFFER|p.?|c.994-2A>G|3,BUFFER|p.?|c.994-2A>T|4,BUFFER|p.?|c.994-2A>T|7,BUFFER|p.?|c.994-2A>G|5	RADIA|MUTECT|MUSE	GGATCTGCAGC	.	3	ESCA
CHD3	0	.	GRCh37	17	7818793	7818793	+	3'Flank	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000380358	.	14	6	8	52	52	0	CHD3,downstream_gene_variant,,ENST00000380358,;CHD3,downstream_gene_variant,,ENST00000358181,;CHD3,downstream_gene_variant,,ENST00000439235,;CHD3,downstream_gene_variant,,ENST00000449744,;CHD3,downstream_gene_variant,,ENST00000330494,;CHD3,downstream_gene_variant,,ENST00000573936,;AC025335.1,non_coding_transcript_exon_variant,,ENST00000324348,;CHD3,downstream_gene_variant,,ENST00000470531,;CHD3,downstream_gene_variant,,ENST00000481999,;	T	ENSG00000170004	ENST00000380358	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2715	1	CHD3	HGNC	1918	protein_coding	YES	CCDS32553.2	ENSP00000369716	CHD3_HUMAN	Q2TAZ1_HUMAN	UPI00004DDA7C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCGAGGCTGC	.	5	ESCA
PIK3R5	0	.	GRCh37	17	8793372	8793372	+	Silent	SNP	G	G	A	rs200469610	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729C>T	p.%3D	p.I243I	ENST00000447110	8/19	35	15	19	92	92	0	PIK3R5,synonymous_variant,p.%3D,ENST00000584803,;PIK3R5,synonymous_variant,p.%3D,ENST00000581552,;PIK3R5,synonymous_variant,p.%3D,ENST00000447110,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578457,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000584456,;PIK3R5,intron_variant,,ENST00000583812,;PIK3R5,intron_variant,,ENST00000580959,;PIK3R5,upstream_gene_variant,,ENST00000578743,;PIK3R5,downstream_gene_variant,,ENST00000577981,;PIK3R5,missense_variant,p.Ser185Leu,ENST00000269300,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578515,;PIK3R5,upstream_gene_variant,,ENST00000583039,;PIK3R5,upstream_gene_variant,,ENST00000577214,;	A	ENSG00000141506	ENST00000447110	Transcript	synonymous_variant	854	729	243	I	atC/atT	rs200469610	.	.	-1	PIK3R5	HGNC	30035	protein_coding	YES	CCDS11147.1	ENSP00000392812	PI3R5_HUMAN	L7RT34_HUMAN,J3KT66_HUMAN,J3KRE9_HUMAN	UPI0000071DB4	.	.	.	8/19	.	Pfam_domain:PF10486,hmmpanther:PTHR15593:SF2,hmmpanther:PTHR15593	C:0.0004	C:0	C:0	.	C:0.002	C:0	C:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCGATGCC	byFrequency|byCluster|by1000G	5	ESCA
ROCK1P1	0	.	GRCh37	18	121622	121623	+	RNA	INS	-	-	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1862dupT	.	.	ENST00000608049	5/5	219	181	38	258	258	0	ROCK1P1,non_coding_transcript_exon_variant,,ENST00000608049,;ROCK1P1,downstream_gene_variant,,ENST00000576266,;ROCK1P1,downstream_gene_variant,,ENST00000573767,;	T	ENSG00000263006	ENST00000608049	Transcript	non_coding_transcript_exon_variant	1860-1861	.	.	.	.	.	.	.	1	ROCK1P1	HGNC	37832	processed_transcript	YES	.	.	.	.	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTGCATTGTC	.	3	ESCA
MIB1	0	.	GRCh37	18	19378178	19378178	+	Missense_Mutation	SNP	A	A	G	rs138693285	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1226A>G	p.Asn409Ser	p.N409S	ENST00000261537	8/21	42	33	9	74	74	0	MIB1,missense_variant,p.Asn409Ser,ENST00000261537,;RN7SL233P,downstream_gene_variant,,ENST00000469988,;MIB1,non_coding_transcript_exon_variant,,ENST00000577749,;MIB1,non_coding_transcript_exon_variant,,ENST00000578646,;	G	ENSG00000101752	ENST00000261537	Transcript	missense_variant	1490	1226	409	N/S	aAt/aGt	rs138693285	.	.	1	MIB1	HGNC	21086	protein_coding	YES	CCDS11871.1	ENSP00000261537	MIB1_HUMAN	B3KRA8_HUMAN	UPI000000D833	.	tolerated(0.31)	benign(0.004)	8/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24202,hmmpanther:PTHR24202:SF52	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCAATGCAT	byCluster|by1000G	5	ESCA
TRAPPC8	0	.	GRCh37	18	29410100	29410100	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*618A>T	.	.	ENST00000283351	29/29	131	93	38	193	193	0	TRAPPC8,3_prime_UTR_variant,,ENST00000283351,;TRAPPC8,downstream_gene_variant,,ENST00000582539,;TRAPPC8,downstream_gene_variant,,ENST00000581057,;TRAPPC8,downstream_gene_variant,,ENST00000582509,;TRAPPC8,3_prime_UTR_variant,,ENST00000580104,;TRAPPC8,downstream_gene_variant,,ENST00000584604,;	A	ENSG00000153339	ENST00000283351	Transcript	3_prime_UTR_variant	5262	.	.	.	.	.	.	.	-1	TRAPPC8	HGNC	29169	protein_coding	YES	CCDS11901.1	ENSP00000283351	TPPC8_HUMAN	J3QQJ5_HUMAN,J3QKL6_HUMAN	UPI0000052E22	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGATGAATG	.	5	ESCA
CELF4	0	.	GRCh37	18	34850767	34850767	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1063G>A	p.Glu355Lys	p.E355K	ENST00000420428	8/13	34	24	9	76	76	0	CELF4,missense_variant,p.Glu355Lys,ENST00000420428,;CELF4,missense_variant,p.Glu44Lys,ENST00000587657,;CELF4,missense_variant,p.Glu44Lys,ENST00000589386,;CELF4,missense_variant,p.Glu44Lys,ENST00000593271,;CELF4,missense_variant,p.Glu40Lys,ENST00000586009,;CELF4,missense_variant,p.Glu344Lys,ENST00000588597,;CELF4,missense_variant,p.Glu345Lys,ENST00000334919,;CELF4,missense_variant,p.Glu354Lys,ENST00000603232,;CELF4,missense_variant,p.Glu355Lys,ENST00000591282,;CELF4,missense_variant,p.Glu354Lys,ENST00000591287,;CELF4,missense_variant,p.Glu48Lys,ENST00000588591,;CELF4,missense_variant,p.Glu353Lys,ENST00000361795,;CELF4,missense_variant,p.Glu354Lys,ENST00000412753,;CELF4,missense_variant,p.Glu353Lys,ENST00000601019,;CELF4,downstream_gene_variant,,ENST00000601392,;CELF4,downstream_gene_variant,,ENST00000587924,;CELF4,downstream_gene_variant,,ENST00000587819,;CELF4,downstream_gene_variant,,ENST00000589229,;RP11-797E24.3,upstream_gene_variant,,ENST00000586610,;RP11-797E24.3,upstream_gene_variant,,ENST00000588766,;CELF4,non_coding_transcript_exon_variant,,ENST00000587074,;CELF4,3_prime_UTR_variant,,ENST00000590112,;CELF4,non_coding_transcript_exon_variant,,ENST00000591421,;	T	ENSG00000101489	ENST00000420428	Transcript	missense_variant	1459	1063	355	E/K	Gaa/Aaa	.	.	.	-1	CELF4	HGNC	14015	protein_coding	YES	CCDS32818.1	ENSP00000410584	CELF4_HUMAN	K7EJK3_HUMAN	UPI00000726FC	.	tolerated(0.13)	possibly_damaging(0.665)	8/13	.	hmmpanther:PTHR24622,hmmpanther:PTHR24622:SF181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A354V|c.1061C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCCGCAG	.	5	ESCA
SMARCA4	0	.	GRCh37	19	11100104	11100104	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1230G>A	p.%3D	p.L410L	ENST00000429416	8/36	105	98	6	154	154	0	SMARCA4,synonymous_variant,p.%3D,ENST00000450717,;SMARCA4,synonymous_variant,p.%3D,ENST00000358026,;SMARCA4,synonymous_variant,p.%3D,ENST00000413806,;SMARCA4,synonymous_variant,p.%3D,ENST00000590574,;SMARCA4,synonymous_variant,p.%3D,ENST00000444061,;SMARCA4,synonymous_variant,p.%3D,ENST00000344626,;SMARCA4,synonymous_variant,p.%3D,ENST00000541122,;SMARCA4,synonymous_variant,p.%3D,ENST00000429416,;SMARCA4,synonymous_variant,p.%3D,ENST00000589677,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;	A	ENSG00000127616	ENST00000429416	Transcript	synonymous_variant	1511	1230	410	L	ctG/ctA	.	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	.	8/36	.	hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTGCTGAACTT	.	2	ESCA
SIGLEC10	0	.	GRCh37	19	51919988	51919988	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.638T>A	p.Leu213His	p.L213H	ENST00000356298	3/12	130	122	8	220	220	0	SIGLEC10,missense_variant,p.Leu165His,ENST00000436984,;SIGLEC10,missense_variant,p.Leu213His,ENST00000525998,;SIGLEC10,missense_variant,p.Leu213His,ENST00000339313,;SIGLEC10,missense_variant,p.Leu155His,ENST00000442846,;SIGLEC10,missense_variant,p.Leu213His,ENST00000353836,;SIGLEC10,missense_variant,p.Leu213His,ENST00000356298,;SIGLEC10,missense_variant,p.Leu155His,ENST00000441969,;SIGLEC10,missense_variant,p.Leu155His,ENST00000439889,;SIGLEC10,missense_variant,p.Leu180His,ENST00000530476,;SIGLEC10,missense_variant,p.Leu27His,ENST00000529627,;SIGLEC10,intron_variant,,ENST00000432469,;CTD-2616J11.2,splice_region_variant,,ENST00000532688,;CTD-2616J11.3,downstream_gene_variant,,ENST00000532473,;CTD-2616J11.2,downstream_gene_variant,,ENST00000526996,;SIGLEC10,non_coding_transcript_exon_variant,,ENST00000357375,;SIGLEC10,downstream_gene_variant,,ENST00000524527,;	T	ENSG00000142512	ENST00000356298	Transcript	missense_variant	755	638	213	L/H	cTc/cAc	.	.	.	-1	SIGLEC10	HGNC	15620	protein_coding	YES	CCDS12832.1	ENSP00000348646	SIG10_HUMAN	.	UPI0000047E1A	.	deleterious(0)	probably_damaging(0.99)	3/12	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF13,hmmpanther:PTHR12035,Pfam_domain:PF08205,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.N152D|c.454A>G|3,BUFFER|p.N210D|c.628A>G|3	MUTECT|MUSE	AGGTGAGGTCG	.	2	ESCA
FPR1	0	.	GRCh37	19	52249357	52249357	+	Missense_Mutation	SNP	G	G	C	rs571424983	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.891C>G	p.Asn297Lys	p.N297K	ENST00000595042	3/3	39	34	5	62	62	0	FPR1,missense_variant,p.Asn297Lys,ENST00000304748,;FPR1,missense_variant,p.Asn297Lys,ENST00000595042,;FPR1,downstream_gene_variant,,ENST00000594900,;FPR1,downstream_gene_variant,,ENST00000600815,;	C	ENSG00000171051	ENST00000595042	Transcript	missense_variant	1033	891	297	N/K	aaC/aaG	rs571424983	.	.	-1	FPR1	HGNC	3826	protein_coding	YES	CCDS12839.1	ENSP00000471493	FPR1_HUMAN	M0R315_HUMAN,M0QZT0_HUMAN	UPI0000050484	.	deleterious(0)	probably_damaging(1)	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24225,hmmpanther:PTHR24225:SF15,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGGGTTGAG	.	2	ESCA
MYADM	0	.	GRCh37	19	54379566	54379566	+	3'UTR	SNP	T	T	A	rs537852293	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1814T>A	.	.	ENST00000391769	3/3	60	56	4	110	110	0	MYADM,3_prime_UTR_variant,,ENST00000391771,;MYADM,3_prime_UTR_variant,,ENST00000391769,;MYADM,3_prime_UTR_variant,,ENST00000336967,;MYADM,3_prime_UTR_variant,,ENST00000391770,;PRKCG,upstream_gene_variant,,ENST00000479081,;MYADM,downstream_gene_variant,,ENST00000414489,;MYADM,downstream_gene_variant,,ENST00000391768,;MYADM,downstream_gene_variant,,ENST00000439000,;MYADM,downstream_gene_variant,,ENST00000448420,;MYADM,downstream_gene_variant,,ENST00000421337,;AC008440.5,upstream_gene_variant,,ENST00000413496,;	A	ENSG00000179820	ENST00000391769	Transcript	3_prime_UTR_variant	3063	.	.	.	.	rs537852293	.	.	1	MYADM	HGNC	7544	protein_coding	YES	CCDS12866.1	ENSP00000375649	MYADM_HUMAN	C9JZL8_HUMAN,C9JJV6_HUMAN,C9JC07_HUMAN,C9J5M0_HUMAN	UPI0000001BEF	.	.	.	3/3	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTTAAATC	by1000G	2	ESCA
TNFSF9	0	.	GRCh37	19	6534855	6534855	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543G>C	p.Leu181Phe	p.L181F	ENST00000245817	3/3	24	18	6	33	33	0	TNFSF9,missense_variant,p.Leu181Phe,ENST00000245817,;	C	ENSG00000125657	ENST00000245817	Transcript	missense_variant	581	543	181	L/F	ttG/ttC	.	.	.	1	TNFSF9	HGNC	11939	protein_coding	YES	CCDS12169.1	ENSP00000245817	TNFL9_HUMAN	.	UPI00001370B7	.	deleterious(0.02)	probably_damaging(0.993)	3/3	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50049,hmmpanther:PTHR15153:SF0,hmmpanther:PTHR15153,Gene3D:2.60.120.40,Pfam_domain:PF00229,SMART_domains:SM00207,Superfamily_domains:SSF49842	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTGACCGT	.	5	ESCA
MUC16	0	.	GRCh37	19	9067553	9067553	+	Missense_Mutation	SNP	G	G	T	rs756936149	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19893C>A	p.Asp6631Glu	p.D6631E	ENST00000397910	3/84	31	12	19	45	45	0	MUC16,missense_variant,p.Asp6631Glu,ENST00000397910,;	T	ENSG00000181143	ENST00000397910	Transcript	missense_variant	20097	19893	6631	D/E	gaC/gaA	rs756936149	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	3/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGTGTCCCT	byFrequency	5	ESCA
ADAM30	0	.	GRCh37	1	120438560	120438560	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400C>A	p.%3D	p.R134R	ENST00000369400	1/1	47	36	11	58	58	0	ADAM30,synonymous_variant,p.%3D,ENST00000369400,;	T	ENSG00000134249	ENST00000369400	Transcript	synonymous_variant	559	400	134	R	Cga/Aga	.	.	.	-1	ADAM30	HGNC	208	protein_coding	YES	CCDS907.1	ENSP00000358407	ADA30_HUMAN	.	UPI000004C638	.	.	.	1/1	.	hmmpanther:PTHR11905:SF31,hmmpanther:PTHR11905,Pfam_domain:PF01562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTCGGAGAC	.	5	ESCA
PRAMEF2	0	.	GRCh37	1	12919952	12919952	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.692T>A	p.Met231Lys	p.M231K	ENST00000240189	3/4	166	158	8	344	344	0	PRAMEF2,missense_variant,p.Met231Lys,ENST00000240189,;	A	ENSG00000120952	ENST00000240189	Transcript	missense_variant	779	692	231	M/K	aTg/aAg	.	.	.	1	PRAMEF2	HGNC	28841	protein_coding	YES	CCDS149.1	ENSP00000240189	PRAM2_HUMAN	.	UPI0000139EF9	.	deleterious(0.01)	probably_damaging(0.974)	3/4	.	hmmpanther:PTHR14224:SF20,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGATGAAGA	.	2	ESCA
PDE4DIP	0	.	GRCh37	1	144917554	144917554	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1550A>T	p.Asp517Val	p.D517V	ENST00000369356	12/44	45	38	7	71	71	0	PDE4DIP,missense_variant,p.Asp304Val,ENST00000479408,;PDE4DIP,missense_variant,p.Asp517Val,ENST00000369354,;PDE4DIP,missense_variant,p.Asp517Val,ENST00000369349,;PDE4DIP,missense_variant,p.Asp654Val,ENST00000369359,;PDE4DIP,missense_variant,p.Asp680Val,ENST00000313431,;PDE4DIP,missense_variant,p.Asp654Val,ENST00000530740,;PDE4DIP,missense_variant,p.Asp583Val,ENST00000313382,;PDE4DIP,missense_variant,p.Asp517Val,ENST00000369356,;PDE4DIP,missense_variant,p.Asp680Val,ENST00000529945,;PDE4DIP,missense_variant,p.Asp517Val,ENST00000369351,;PDE4DIP,downstream_gene_variant,,ENST00000532801,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000467859,;PDE4DIP,upstream_gene_variant,,ENST00000533963,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000496263,;PDE4DIP,intron_variant,,ENST00000525886,;	A	ENSG00000178104	ENST00000369356	Transcript	missense_variant	1841	1550	517	D/V	gAt/gTt	.	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	MYOME_HUMAN	I1VE15_HUMAN	UPI0000458A81	.	deleterious(0)	possibly_damaging(0.907)	12/44	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13895:SF2,hmmpanther:PTHR13895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATGATCTCGC	.	4	ESCA
HRNR	0	.	GRCh37	1	152185648	152185648	+	Missense_Mutation	SNP	A	A	C	rs745608455	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8457T>G	p.His2819Gln	p.H2819Q	ENST00000368801	3/3	77	72	5	112	112	0	HRNR,missense_variant,p.His2819Gln,ENST00000368801,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	C	ENSG00000197915	ENST00000368801	Transcript	missense_variant	8533	8457	2819	H/Q	caT/caG	rs745608455	.	.	-1	HRNR	HGNC	20846	protein_coding	YES	CCDS30859.1	ENSP00000357791	HORN_HUMAN	Q5W8V9_HUMAN	UPI00001D7CAD	.	.	unknown(0)	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATCATGGTT	byFrequency	2	ESCA
FLG	0	.	GRCh37	1	152281918	152281918	+	Missense_Mutation	SNP	C	C	T	rs748785456	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5444G>A	p.Gly1815Glu	p.G1815E	ENST00000368799	3/3	132	124	8	195	195	0	FLG,missense_variant,p.Gly1815Glu,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	T	ENSG00000143631	ENST00000368799	Transcript	missense_variant	5480	5444	1815	G/E	gGa/gAa	rs748785456	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	probably_damaging(0.931)	3/3	.	hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGTCCACGA	byFrequency	2	ESCA
DAP3	0	.	GRCh37	1	155707999	155708000	+	Frame_Shift_Ins	INS	-	-	CT	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1165_1166dupTC	p.Leu390ArgfsTer32	p.L390Rfs*32	ENST00000368336	13/13	62	45	17	69	69	0	DAP3,frameshift_variant,p.Leu349ArgfsTer32,ENST00000535183,;DAP3,frameshift_variant,p.Leu132ArgfsTer32,ENST00000490249,;DAP3,frameshift_variant,p.Leu37ArgfsTer31,ENST00000491777,;DAP3,frameshift_variant,p.Leu202ArgfsTer32,ENST00000477394,;DAP3,frameshift_variant,p.Leu390ArgfsTer32,ENST00000368336,;DAP3,frameshift_variant,p.Leu349ArgfsTer32,ENST00000471642,;DAP3,frameshift_variant,p.Leu98ArgfsTer32,ENST00000463295,;DAP3,frameshift_variant,p.Leu356ArgfsTer32,ENST00000421487,;DAP3,frameshift_variant,p.Leu390ArgfsTer32,ENST00000343043,;DAP3,3_prime_UTR_variant,,ENST00000475056,;MSTO1,intron_variant,,ENST00000538143,;MSTO1,intron_variant,,ENST00000452804,;DAP3,non_coding_transcript_exon_variant,,ENST00000476444,;MSTO2P,intron_variant,,ENST00000538914,;	CT	ENSG00000132676	ENST00000368336	Transcript	frameshift_variant	1287-1288	1163-1164	388	P/PX	ccc/ccCTc	.	.	.	1	DAP3	HGNC	2673	protein_coding	YES	CCDS1120.1	ENSP00000357320	RT29_HUMAN	E2JL21_HUMAN	UPI000004ABE5	.	.	.	13/13	.	hmmpanther:PTHR12810,hmmpanther:PTHR12810:SF0,Pfam_domain:PF10236,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAACCCCTCGC	.	3	ESCA
CD1A	0	.	GRCh37	1	158225961	158225961	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493C>A	p.Leu165Ile	p.L165I	ENST00000289429	3/6	43	27	16	54	54	0	CD1A,missense_variant,p.Leu165Ile,ENST00000289429,;	A	ENSG00000158477	ENST00000289429	Transcript	missense_variant	1026	493	165	L/I	Ctc/Atc	.	.	.	1	CD1A	HGNC	1634	protein_coding	YES	CCDS1174.1	ENSP00000289429	CD1A_HUMAN	.	UPI0000161A54	.	tolerated(0.57)	benign(0.003)	3/6	.	Superfamily_domains:SSF54452,Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675:SF160,hmmpanther:PTHR16675	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTGCTCAAT	.	5	ESCA
TPR	0	.	GRCh37	1	186324664	186324664	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2049A>T	p.Lys683Asn	p.K683N	ENST00000367478	17/51	67	33	33	84	84	0	TPR,missense_variant,p.Lys683Asn,ENST00000367478,;TPR,non_coding_transcript_exon_variant,,ENST00000474852,;TPR,non_coding_transcript_exon_variant,,ENST00000491783,;TPR,upstream_gene_variant,,ENST00000469463,;	A	ENSG00000047410	ENST00000367478	Transcript	missense_variant	2346	2049	683	K/N	aaA/aaT	.	.	.	-1	TPR	HGNC	12017	protein_coding	YES	CCDS41446.1	ENSP00000356448	TPR_HUMAN	Q9UE33_HUMAN	UPI000046FCF4	.	.	benign(0.403)	17/51	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18898	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTTTTGTA	.	5	ESCA
PTGS2	0	.	GRCh37	1	186643414	186643414	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*71A>G	.	.	ENST00000367468	10/10	36	22	14	58	58	0	PTGS2,3_prime_UTR_variant,,ENST00000367468,;PTGS2,non_coding_transcript_exon_variant,,ENST00000490885,;PTGS2,downstream_gene_variant,,ENST00000466691,;PTGS2,downstream_gene_variant,,ENST00000559800,;PTGS2,downstream_gene_variant,,ENST00000559627,;	C	ENSG00000073756	ENST00000367468	Transcript	3_prime_UTR_variant	2023	.	.	.	.	.	.	.	-1	PTGS2	HGNC	9605	protein_coding	YES	CCDS1371.1	ENSP00000356438	PGH2_HUMAN	D9MWI3_HUMAN	UPI000000D926	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAATATAAA	.	5	ESCA
IGSF21	0	.	GRCh37	1	18692016	18692016	+	Silent	SNP	C	C	T	rs762318783	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.840C>T	p.%3D	p.S280S	ENST00000251296	6/10	21	11	10	35	35	0	IGSF21,synonymous_variant,p.%3D,ENST00000251296,;IGSF21,synonymous_variant,p.%3D,ENST00000412684,;IGSF21,non_coding_transcript_exon_variant,,ENST00000497331,;	T	ENSG00000117154	ENST00000251296	Transcript	synonymous_variant	1223	840	280	S	agC/agT	rs762318783	.	.	1	IGSF21	HGNC	28246	protein_coding	YES	CCDS184.1	ENSP00000251296	IGS21_HUMAN	.	UPI000006FCF2	.	.	.	6/10	.	hmmpanther:PTHR10489:SF442,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAGCGCCGA	.	5	ESCA
ZBTB41	0	.	GRCh37	1	197126993	197126993	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1496C>A	.	.	ENST00000367405	10/10	31	24	7	74	74	0	ZBTB41,3_prime_UTR_variant,,ENST00000367405,;ZBTB41,downstream_gene_variant,,ENST00000467322,;	T	ENSG00000177888	ENST00000367405	Transcript	3_prime_UTR_variant	4295	.	.	.	.	.	.	.	-1	ZBTB41	HGNC	24819	protein_coding	YES	CCDS30960.1	ENSP00000356375	ZBT41_HUMAN	Q8N9U5_HUMAN	UPI00001D7DE7	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTGTGATTTT	.	4	ESCA
USH2A	0	.	GRCh37	1	216052369	216052369	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8295C>T	p.%3D	p.H2765H	ENST00000307340	42/72	49	41	7	70	70	0	USH2A,synonymous_variant,p.%3D,ENST00000366943,;USH2A,synonymous_variant,p.%3D,ENST00000307340,;	A	ENSG00000042781	ENST00000307340	Transcript	synonymous_variant	8682	8295	2765	H	caC/caT	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	.	42/72	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGATGTGAGG	.	4	ESCA
WDR26	0	.	GRCh37	1	224574143	224574144	+	3'UTR	INS	-	-	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3393dupT	.	.	ENST00000414423	14/14	109	84	25	60	60	0	WDR26,3_prime_UTR_variant,,ENST00000414423,;WDR26,3_prime_UTR_variant,,ENST00000480676,;WDR26,3_prime_UTR_variant,,ENST00000295024,;WDR26,downstream_gene_variant,,ENST00000366852,;WDR26,downstream_gene_variant,,ENST00000486652,;	A	ENSG00000162923	ENST00000414423	Transcript	3_prime_UTR_variant	5573-5574	.	.	.	.	.	.	.	-1	WDR26	HGNC	21208	protein_coding	YES	CCDS31037.2	ENSP00000408108	WDR26_HUMAN	C9JCS7_HUMAN	UPI0000203FB7	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TATGATATATT	.	3	ESCA
GNPAT	0	.	GRCh37	1	231403505	231403505	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000366647	9/16	67	37	30	78	78	0	GNPAT,missense_variant,p.Glu318Gln,ENST00000366646,;GNPAT,missense_variant,p.Glu369Gln,ENST00000416000,;GNPAT,missense_variant,p.Glu379Gln,ENST00000366647,;GNPAT,downstream_gene_variant,,ENST00000436239,;GNPAT,non_coding_transcript_exon_variant,,ENST00000492459,;	C	ENSG00000116906	ENST00000366647	Transcript	missense_variant	1304	1135	379	E/Q	Gaa/Caa	.	.	.	1	GNPAT	HGNC	4416	protein_coding	YES	CCDS1592.1	ENSP00000355607	GNPAT_HUMAN	Q71V38_HUMAN	UPI0000000A2A	.	tolerated(0.25)	benign(0.035)	9/16	.	PIRSF_domain:PIRSF000437,PIRSF_domain:PIRSF500063,hmmpanther:PTHR12563:SF9,hmmpanther:PTHR12563	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTGAAAAC	.	5	ESCA
CSMD2	0	.	GRCh37	1	34024948	34024948	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8311+8245C>A	.	.	ENST00000241312	.	49	38	11	98	98	0	CSMD2,missense_variant,p.Gln2836Lys,ENST00000373381,;CSMD2,downstream_gene_variant,,ENST00000465819,;CSMD2,intron_variant,,ENST00000241312,;	T	ENSG00000121904	ENST00000241312	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CSMD2	HGNC	19290	nonsense_mediated_decay	YES	CCDS380.1	ENSP00000241312	CSMD2_HUMAN	.	UPI00004561AB	.	.	.	.	54/69	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTGGGACC	.	5	ESCA
TIE1	0	.	GRCh37	1	43770718	43770718	+	Silent	SNP	G	G	A	rs762895327	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255G>A	p.%3D	p.S85S	ENST00000372476	2/23	38	35	3	104	104	0	TIE1,synonymous_variant,p.%3D,ENST00000372476,;TIE1,synonymous_variant,p.%3D,ENST00000441333,;TIE1,synonymous_variant,p.%3D,ENST00000538015,;TIE1,upstream_gene_variant,,ENST00000433781,;TIE1,non_coding_transcript_exon_variant,,ENST00000485125,;TIE1,upstream_gene_variant,,ENST00000480269,;TIE1,upstream_gene_variant,,ENST00000488437,;	A	ENSG00000066056	ENST00000372476	Transcript	synonymous_variant	334	255	85	S	tcG/tcA	rs762895327,COSM12937	.	.	1	TIE1	HGNC	11809	protein_coding	YES	CCDS482.1	ENSP00000361554	TIE1_HUMAN	Q9HBS4_HUMAN,Q6LD63_HUMAN,E9PG63_HUMAN	UPI0000032E59	.	.	.	2/23	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GGTTCGCACCA	.	3	ESCA
LMO4	0	.	GRCh37	1	87810542	87810542	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63A>G	.	.	ENST00000370544	5/5	28	15	12	66	66	0	LMO4,3_prime_UTR_variant,,ENST00000370542,;LMO4,3_prime_UTR_variant,,ENST00000370544,;LMO4,non_coding_transcript_exon_variant,,ENST00000489303,;	G	ENSG00000143013	ENST00000370544	Transcript	3_prime_UTR_variant	1341	.	.	.	.	.	.	.	1	LMO4	HGNC	6644	protein_coding	YES	CCDS713.1	ENSP00000359575	LMO4_HUMAN	.	UPI0000004145	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCCATGTGT	.	5	ESCA
SIRPA	0	.	GRCh37	20	1919068	1919072	+	3'UTR	DEL	TGTTT	TGTTT	-	rs138322358	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	TGTTT	TGTTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*865_*869delGTTTT	.	.	ENST00000358771	8/8	86	60	26	135	134	0	SIRPA,3_prime_UTR_variant,,ENST00000356025,;SIRPA,3_prime_UTR_variant,,ENST00000400068,;SIRPA,3_prime_UTR_variant,,ENST00000358771,;	-	ENSG00000198053	ENST00000358771	Transcript	3_prime_UTR_variant	2521-2525	.	.	.	.	rs138322358	.	.	1	SIRPA	HGNC	9662	protein_coding	YES	CCDS13022.1	ENSP00000351621	SHPS1_HUMAN	B4DP97_HUMAN	UPI0000073ADE	.	.	.	8/8	.	.	-:0.0128	-:0.0461	-:0.0029	.	-:0.001	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	11	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTGTGGTGTTTTGTTT	byFrequency|byCluster|by1000G	2	ESCA
HM13	0	.	GRCh37	20	30154016	30154016	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.952G>A	p.Ala318Thr	p.A318T	ENST00000398174	11/13	54	35	18	83	83	0	HM13,missense_variant,p.Ala276Thr,ENST00000376127,;HM13,missense_variant,p.Ala318Thr,ENST00000398174,;HM13,missense_variant,p.Ala318Thr,ENST00000340852,;HM13,missense_variant,p.Ala318Thr,ENST00000335574,;HM13,downstream_gene_variant,,ENST00000344042,;HM13-IT1,downstream_gene_variant,,ENST00000421894,;HM13-AS1,downstream_gene_variant,,ENST00000412178,;HM13,non_coding_transcript_exon_variant,,ENST00000474466,;HM13,non_coding_transcript_exon_variant,,ENST00000472128,;HM13,non_coding_transcript_exon_variant,,ENST00000487964,;HM13,non_coding_transcript_exon_variant,,ENST00000493364,;HM13,non_coding_transcript_exon_variant,,ENST00000460389,;HM13,non_coding_transcript_exon_variant,,ENST00000469126,;HM13,non_coding_transcript_exon_variant,,ENST00000487281,;HM13,non_coding_transcript_exon_variant,,ENST00000494153,;HM13,non_coding_transcript_exon_variant,,ENST00000492709,;HM13,intron_variant,,ENST00000468559,;HM13,intron_variant,,ENST00000469097,;HM13,downstream_gene_variant,,ENST00000483310,;	A	ENSG00000101294	ENST00000398174	Transcript	missense_variant	1076	952	318	A/T	Gcc/Acc	.	.	.	1	HM13	HGNC	16435	protein_coding	YES	CCDS42861.1	ENSP00000381237	HM13_HUMAN	.	UPI000001358F	.	deleterious(0)	probably_damaging(0.987)	11/13	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF23,Pfam_domain:PF04258,SMART_domains:SM00730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTGCCCTC	.	5	ESCA
BPIFA2	0	.	GRCh37	20	31756970	31756970	+	Missense_Mutation	SNP	C	C	T	rs758880003	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19C>T	p.Leu7Phe	p.L7F	ENST00000253362	2/9	45	35	10	47	47	0	BPIFA2,missense_variant,p.Leu7Phe,ENST00000354932,;BPIFA2,missense_variant,p.Leu7Phe,ENST00000253362,;	T	ENSG00000131050	ENST00000253362	Transcript	missense_variant	165	19	7	L/F	Ctt/Ttt	rs758880003	.	.	1	BPIFA2	HGNC	16203	protein_coding	YES	CCDS13214.1	ENSP00000253362	BPIA2_HUMAN	.	UPI00000361E3	.	deleterious(0.04)	benign(0.101)	2/9	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAACTTGTT	.	5	ESCA
ELMO2	0	.	GRCh37	20	45014797	45014797	+	Missense_Mutation	SNP	T	T	C	rs113022678	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.643A>G	p.Ile215Val	p.I215V	ENST00000290246	9/22	27	17	10	43	43	0	ELMO2,missense_variant,p.Ile215Val,ENST00000439931,;ELMO2,missense_variant,p.Ile127Val,ENST00000372176,;ELMO2,missense_variant,p.Ile215Val,ENST00000396391,;ELMO2,missense_variant,p.Ile215Val,ENST00000450812,;ELMO2,missense_variant,p.Ile32Val,ENST00000445496,;ELMO2,missense_variant,p.Ile3Val,ENST00000425546,;ELMO2,missense_variant,p.Ile215Val,ENST00000290246,;ELMO2,missense_variant,p.Ile213Val,ENST00000352077,;ELMO2,non_coding_transcript_exon_variant,,ENST00000497412,;ELMO2,non_coding_transcript_exon_variant,,ENST00000469801,;ELMO2,non_coding_transcript_exon_variant,,ENST00000480042,;ELMO2,non_coding_transcript_exon_variant,,ENST00000460474,;ELMO2,non_coding_transcript_exon_variant,,ENST00000488853,;ELMO2,non_coding_transcript_exon_variant,,ENST00000462491,;ELMO2,downstream_gene_variant,,ENST00000462593,;ELMO2,downstream_gene_variant,,ENST00000487583,;	C	ENSG00000062598	ENST00000290246	Transcript	missense_variant	838	643	215	I/V	Atc/Gtc	rs113022678	.	.	-1	ELMO2	HGNC	17233	protein_coding	YES	CCDS13398.1	ENSP00000290246	ELMO2_HUMAN	Q7Z5G9_HUMAN,Q5JVZ4_HUMAN,Q5BLP5_HUMAN,F5GZP8_HUMAN	UPI000013F6C4	.	tolerated(1)	benign(0.024)	9/22	.	hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF8,Gene3D:1.25.10.10,Pfam_domain:PF11841,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGATTTCCT	.	5	ESCA
ZNFX1	0	.	GRCh37	20	47897085	47897086	+	5'Flank	DEL	AT	AT	-	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	AT	AT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000396105	.	51	39	12	46	46	0	ZNFX1,upstream_gene_variant,,ENST00000371744,;ZNFX1,upstream_gene_variant,,ENST00000371752,;ZNFX1,upstream_gene_variant,,ENST00000371754,;ZNFX1,upstream_gene_variant,,ENST00000396105,;SNORD12,upstream_gene_variant,,ENST00000391002,;SNORD12B,downstream_gene_variant,,ENST00000410433,;SNORD12C,downstream_gene_variant,,ENST00000386307,;ZFAS1,non_coding_transcript_exon_variant,,ENST00000326677,;ZFAS1,non_coding_transcript_exon_variant,,ENST00000450535,;ZFAS1,non_coding_transcript_exon_variant,,ENST00000441722,;ZFAS1,non_coding_transcript_exon_variant,,ENST00000458653,;ZFAS1,non_coding_transcript_exon_variant,,ENST00000428008,;ZFAS1,non_coding_transcript_exon_variant,,ENST00000371743,;ZFAS1,intron_variant,,ENST00000417721,;	-	ENSG00000124201	ENST00000396105	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2329	-1	ZNFX1	HGNC	29271	protein_coding	YES	CCDS13417.1	ENSP00000379412	ZNFX1_HUMAN	Q5JXR5_HUMAN	UPI000012DD83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGTAGAATATATA	.	2	ESCA
ELFN2	0	.	GRCh37	22	37769104	37769104	+	3'UTR	DEL	G	G	-	rs768670879	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8delC	.	.	ENST00000402918	3/3	42	32	9	52	52	0	ELFN2,3_prime_UTR_variant,,ENST00000402918,;RP1-63G5.5,intron_variant,,ENST00000430883,;RP1-63G5.5,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000424973,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000451509,;	-	ENSG00000166897	ENST00000402918	Transcript	3_prime_UTR_variant	3257	.	.	.	.	rs768670879	.	.	-1	ELFN2	HGNC	29396	protein_coding	YES	CCDS33642.1	ENSP00000385277	PPR29_HUMAN	.	UPI000004E87D	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGGAAGGGGGG	.	2	ESCA
CYP2D6	0	.	GRCh37	22	42522969	42522969	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1199C>T	p.Ser400Leu	p.S400L	ENST00000360608	8/9	38	29	9	84	84	0	CYP2D6,missense_variant,p.Ser400Leu,ENST00000360608,;CYP2D6,missense_variant,p.Ser349Leu,ENST00000359033,;CYP2D6,missense_variant,p.Ser400Leu,ENST00000389970,;NDUFA6-AS1,intron_variant,,ENST00000416037,;NDUFA6-AS1,intron_variant,,ENST00000439129,;NDUFA6-AS1,downstream_gene_variant,,ENST00000451451,;NDUFA6-AS1,downstream_gene_variant,,ENST00000600968,;NDUFA6-AS1,downstream_gene_variant,,ENST00000595777,;NDUFA6-AS1,downstream_gene_variant,,ENST00000434834,;NDUFA6-AS1,downstream_gene_variant,,ENST00000610250,;NDUFA6-AS1,downstream_gene_variant,,ENST00000417327,;NDUFA6-AS1,downstream_gene_variant,,ENST00000536447,;CYP2D6,3_prime_UTR_variant,,ENST00000360124,;CYP2D6,non_coding_transcript_exon_variant,,ENST00000488442,;NDUFA6-AS1,downstream_gene_variant,,ENST00000609499,;NDUFA6-AS1,downstream_gene_variant,,ENST00000608643,;NDUFA6-AS1,downstream_gene_variant,,ENST00000609833,;NDUFA6-AS1,downstream_gene_variant,,ENST00000547929,;	A	ENSG00000100197	ENST00000360608	Transcript	missense_variant	1314	1199	400	S/L	tCa/tTa	.	.	.	-1	CYP2D6	HGNC	2625	protein_coding	YES	CCDS46721.1	ENSP00000353820	.	Q6NWU0_HUMAN,Q007T9_HUMAN	UPI0000157756	.	deleterious(0)	possibly_damaging(0.778)	8/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF13,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR01686,Prints_domain:PR00463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGATGACAGG	.	4	ESCA
CPT1B	0	.	GRCh37	22	51009414	51009414	+	Missense_Mutation	SNP	C	C	T	rs767195024	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1934G>A	p.Arg645His	p.R645H	ENST00000360719	16/19	61	42	19	94	94	0	CPT1B,missense_variant,p.Arg645His,ENST00000395650,;CPT1B,missense_variant,p.Arg440His,ENST00000434492,;CPT1B,missense_variant,p.Arg611His,ENST00000457250,;CPT1B,missense_variant,p.Arg645His,ENST00000312108,;CPT1B,missense_variant,p.Arg645His,ENST00000405237,;CPT1B,missense_variant,p.Arg564His,ENST00000440709,;CPT1B,missense_variant,p.Arg645His,ENST00000360719,;CHKB-CPT1B,3_prime_UTR_variant,,ENST00000453634,;CHKB-CPT1B,non_coding_transcript_exon_variant,,ENST00000492556,;CPT1B,non_coding_transcript_exon_variant,,ENST00000497224,;CPT1B,downstream_gene_variant,,ENST00000479886,;CPT1B,downstream_gene_variant,,ENST00000423069,;CPT1B,downstream_gene_variant,,ENST00000475238,;	T	ENSG00000205560	ENST00000360719	Transcript	missense_variant	2072	1934	645	R/H	cGc/cAc	rs767195024	.	.	-1	CPT1B	HGNC	2329	protein_coding	YES	CCDS14098.1	ENSP00000353945	CPT1B_HUMAN	C9J7C3_HUMAN	UPI0000128314	.	deleterious(0.02)	benign(0.43)	16/19	.	hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF58,Pfam_domain:PF00755,Superfamily_domains:SSF52777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGCGGTAC	.	5	ESCA
CPT1B	0	.	GRCh37	22	51016363	51016363	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-19G>A	.	.	ENST00000360719	2/19	26	21	4	41	41	0	CPT1B,splice_region_variant,,ENST00000312108,;CPT1B,splice_region_variant,,ENST00000417176,;CPT1B,splice_region_variant,,ENST00000360719,;CPT1B,splice_region_variant,,ENST00000395650,;CPT1B,splice_region_variant,,ENST00000434492,;CPT1B,splice_region_variant,,ENST00000457250,;CPT1B,splice_region_variant,,ENST00000440709,;CPT1B,5_prime_UTR_variant,,ENST00000405237,;CHKB,downstream_gene_variant,,ENST00000406938,;CHKB-CPT1B,splice_region_variant,,ENST00000452668,;CHKB,downstream_gene_variant,,ENST00000464225,;CHKB,downstream_gene_variant,,ENST00000463053,;CHKB,downstream_gene_variant,,ENST00000471515,;CPT1B,splice_region_variant,,ENST00000460853,;CHKB-CPT1B,splice_region_variant,,ENST00000492556,;CHKB-CPT1B,splice_region_variant,,ENST00000453634,;CPT1B,upstream_gene_variant,,ENST00000476790,;CPT1B,upstream_gene_variant,,ENST00000479886,;CHKB,downstream_gene_variant,,ENST00000476289,;CHKB,downstream_gene_variant,,ENST00000492582,;CHKB,downstream_gene_variant,,ENST00000481673,;CHKB,downstream_gene_variant,,ENST00000484266,;CHKB,downstream_gene_variant,,ENST00000468532,;CPT1B,upstream_gene_variant,,ENST00000461117,;CHKB,downstream_gene_variant,,ENST00000479003,;CPT1B,upstream_gene_variant,,ENST00000423069,;CHKB,downstream_gene_variant,,ENST00000489453,;CPT1B,upstream_gene_variant,,ENST00000475238,;CHKB,downstream_gene_variant,,ENST00000465842,;	T	ENSG00000205560	ENST00000360719	Transcript	splice_region_variant	120	.	.	.	.	.	.	.	-1	CPT1B	HGNC	2329	protein_coding	YES	CCDS14098.1	ENSP00000353945	CPT1B_HUMAN	C9J7C3_HUMAN	UPI0000128314	.	.	.	2/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CGGCACCTAGG	.	3	ESCA
RGPD4	0	.	GRCh37	2	108488905	108488905	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4445G>A	p.Ser1482Asn	p.S1482N	ENST00000408999	20/23	22	14	8	38	38	0	RGPD4,missense_variant,p.Ser1482Asn,ENST00000408999,;RGPD4,missense_variant,p.Ser1482Asn,ENST00000354986,;	A	ENSG00000196862	ENST00000408999	Transcript	missense_variant	4522	4445	1482	S/N	aGc/aAc	.	.	.	1	RGPD4	HGNC	32417	protein_coding	YES	CCDS46381.1	ENSP00000386810	RGPD4_HUMAN	I1Z9D1_HUMAN	UPI0000418FF7	.	tolerated(0.66)	benign(0.003)	20/23	.	hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF86	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GTCAAGCACTC	.	2	ESCA
INHBB	0	.	GRCh37	2	121106886	121106886	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660C>T	p.%3D	p.D220D	ENST00000295228	2/2	50	36	14	65	65	0	INHBB,synonymous_variant,p.%3D,ENST00000295228,;	T	ENSG00000163083	ENST00000295228	Transcript	synonymous_variant	706	660	220	D	gaC/gaT	.	.	.	1	INHBB	HGNC	6067	protein_coding	YES	CCDS2132.1	ENSP00000295228	INHBB_HUMAN	.	UPI000012D427	.	.	.	2/2	.	hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF29,Pfam_domain:PF00688	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGACCTCAA	.	5	ESCA
THSD7B	0	.	GRCh37	2	137814518	137814518	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668C>A	p.Ser223Ter	p.S223*	ENST00000272643	2/28	43	19	23	64	64	0	THSD7B,stop_gained,p.Ser82Ter,ENST00000543459,;THSD7B,stop_gained,p.Ser223Ter,ENST00000409968,;THSD7B,stop_gained,p.Ser192Ter,ENST00000413152,;THSD7B,stop_gained,p.Ser223Ter,ENST00000272643,;THSD7B,downstream_gene_variant,,ENST00000472720,;	A	ENSG00000144229	ENST00000272643	Transcript	stop_gained	668	668	223	S/*	tCa/tAa	.	.	.	1	THSD7B	HGNC	29348	protein_coding	YES	.	ENSP00000272643	THS7B_HUMAN	.	UPI00015E0A18	.	.	.	2/28	.	PROSITE_profiles:PS50092,hmmpanther:PTHR11311:SF7,hmmpanther:PTHR11311,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGTCAAGAG	.	5	ESCA
MYCN	0	.	GRCh37	2	16085955	16085955	+	Silent	SNP	G	G	A	rs753698437	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1131G>A	p.%3D	p.S377S	ENST00000281043	3/3	32	29	3	31	31	0	MYCN,synonymous_variant,p.%3D,ENST00000281043,;RN7SL104P,downstream_gene_variant,,ENST00000498686,;MYCNOS,upstream_gene_variant,,ENST00000448719,;MYCNOS,upstream_gene_variant,,ENST00000439180,;MYCNOS,upstream_gene_variant,,ENST00000453400,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000420452,;	A	ENSG00000134323	ENST00000281043	Transcript	synonymous_variant	1428	1131	377	S	tcG/tcA	rs753698437	.	.	1	MYCN	HGNC	7559	protein_coding	YES	CCDS1687.1	ENSP00000281043	MYCN_HUMAN	Q9UMQ5_HUMAN,Q7Z7Q9_HUMAN,Q53XS5_HUMAN	UPI000012FAF8	.	.	.	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11514:SF3,hmmpanther:PTHR11514,PIRSF_domain:PIRSF001705,Prints_domain:PR00044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACTCGGAGGA	.	2	ESCA
NFE2L2	0	.	GRCh37	2	178098800	178098800	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	2/5	63	30	33	106	106	0	NFE2L2,missense_variant,p.Glu66Gly,ENST00000423513,;NFE2L2,missense_variant,p.Glu82Gly,ENST00000397062,;NFE2L2,missense_variant,p.Glu66Gly,ENST00000446151,;NFE2L2,missense_variant,p.Glu66Gly,ENST00000588123,;NFE2L2,missense_variant,p.Glu81Gly,ENST00000586532,;NFE2L2,missense_variant,p.Glu66Gly,ENST00000421929,;NFE2L2,missense_variant,p.Glu66Gly,ENST00000464747,;NFE2L2,missense_variant,p.Glu66Gly,ENST00000448782,;NFE2L2,missense_variant,p.Glu66Gly,ENST00000397063,;NFE2L2,splice_region_variant,,ENST00000449627,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	C	ENSG00000116044	ENST00000397062	Transcript	missense_variant	800	245	82	E/G	gAa/gGa	COSM132853,COSM1631471,COSM132962	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E82G|c.245A>G|7,CODON|p.E82D|c.246A>C|3,CODON|p.E82D|c.246A>T|6,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81D|c.242G>A|6,BUFFER|p.G81V|c.242G>T|7,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.G81S|c.241G>A|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79K|c.235G>A|10,BUFFER|p.E79Q|c.235G>C|11	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAATTCACCT	.	5	ESCA
SLC4A3	0	.	GRCh37	2	220493143	220493143	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.68A>G	p.Glu23Gly	p.E23G	ENST00000373762	3/23	33	30	3	84	84	0	SLC4A3,missense_variant,p.Glu23Gly,ENST00000373760,;SLC4A3,missense_variant,p.Glu23Gly,ENST00000273063,;SLC4A3,missense_variant,p.Glu23Gly,ENST00000317151,;SLC4A3,missense_variant,p.Glu23Gly,ENST00000358055,;SLC4A3,missense_variant,p.Glu23Gly,ENST00000373762,;SLC4A3,upstream_gene_variant,,ENST00000413743,;AC009955.8,upstream_gene_variant,,ENST00000455896,;SLC4A3,upstream_gene_variant,,ENST00000497589,;SLC4A3,missense_variant,p.Glu23Gly,ENST00000425141,;SLC4A3,upstream_gene_variant,,ENST00000416910,;SLC4A3,upstream_gene_variant,,ENST00000444906,;	G	ENSG00000114923	ENST00000373762	Transcript	missense_variant	337	68	23	E/G	gAg/gGg	.	.	.	1	SLC4A3	HGNC	11029	protein_coding	YES	CCDS2446.1	ENSP00000362867	B3A3_HUMAN	.	UPI000022BE50	.	deleterious_low_confidence(0.01)	benign(0.234)	3/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGGAGGAGC	.	2	ESCA
PREPL	0	.	GRCh37	2	44559740	44559740	+	Missense_Mutation	SNP	C	C	A	rs769885236	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1211G>T	p.Cys404Phe	p.C404F	ENST00000409936	9/15	55	32	23	87	87	0	PREPL,missense_variant,p.Cys404Phe,ENST00000409936,;PREPL,missense_variant,p.Cys315Phe,ENST00000409957,;PREPL,missense_variant,p.Cys404Phe,ENST00000260648,;PREPL,missense_variant,p.Cys315Phe,ENST00000541738,;PREPL,missense_variant,p.Cys315Phe,ENST00000409411,;PREPL,missense_variant,p.Cys404Phe,ENST00000409272,;PREPL,missense_variant,p.Cys404Phe,ENST00000410081,;PREPL,missense_variant,p.Cys342Phe,ENST00000378511,;PREPL,intron_variant,,ENST00000378520,;PREPL,missense_variant,p.Cys404Phe,ENST00000425263,;PREPL,missense_variant,p.Cys404Phe,ENST00000426481,;	A	ENSG00000138078	ENST00000409936	Transcript	missense_variant	1649	1211	404	C/F	tGc/tTc	rs769885236	.	.	-1	PREPL	HGNC	30228	protein_coding	YES	CCDS33190.1	ENSP00000386543	PPCEL_HUMAN	C9JMT4_HUMAN	UPI0000208358	.	tolerated(0.35)	benign(0.03)	9/15	.	hmmpanther:PTHR11757,hmmpanther:PTHR11757:SF3,Gene3D:3.40.50.1820,Pfam_domain:PF02897,Superfamily_domains:SSF50993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGCAGTTC	.	5	ESCA
CAMKMT	0	.	GRCh37	2	44993623	44993623	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817A>G	p.Asn273Asp	p.N273D	ENST00000378494	10/11	41	37	4	82	82	0	CAMKMT,missense_variant,p.Asn273Asp,ENST00000378494,;	G	ENSG00000143919	ENST00000378494	Transcript	missense_variant	861	817	273	N/D	Aat/Gat	.	.	.	1	CAMKMT	HGNC	26276	protein_coding	YES	CCDS1820.1	ENSP00000367755	CMKMT_HUMAN	D6W5A4_HUMAN	UPI0000070B33	.	tolerated(0.17)	benign(0.093)	10/11	.	PROSITE_profiles:PS51610,hmmpanther:PTHR13539,Pfam_domain:PF10294,Gene3D:3.40.50.150,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGCAATCTA	.	4	ESCA
ASB3	0	.	GRCh37	2	53897541	53897541	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*99G>A	.	.	ENST00000406625	10/10	131	108	23	160	160	0	ASB3,3_prime_UTR_variant,,ENST00000406625,;GPR75-ASB3,3_prime_UTR_variant,,ENST00000394717,;GPR75-ASB3,3_prime_UTR_variant,,ENST00000263634,;GPR75-ASB3,3_prime_UTR_variant,,ENST00000406687,;GPR75-ASB3,3_prime_UTR_variant,,ENST00000352846,;GPR75-ASB3,intron_variant,,ENST00000406053,;GPR75-ASB3,non_coding_transcript_exon_variant,,ENST00000482829,;GPR75-ASB3,downstream_gene_variant,,ENST00000470707,;	T	ENSG00000270898	ENST00000406625	Transcript	3_prime_UTR_variant	2002	.	.	.	.	.	.	.	-1	ASB3	Uniprot_gn	.	protein_coding	YES	.	ENSP00000385085	ASB3_HUMAN	.	UPI000066218F	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATCTTTTG	.	5	ESCA
USP34	0	.	GRCh37	2	61493302	61493302	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5434G>A	p.Glu1812Lys	p.E1812K	ENST00000398571	42/80	44	39	5	50	50	0	USP34,missense_variant,p.Glu90Lys,ENST00000453734,;USP34,missense_variant,p.Glu1812Lys,ENST00000398571,;USP34,intron_variant,,ENST00000472706,;USP34,splice_region_variant,,ENST00000484179,;USP34,upstream_gene_variant,,ENST00000492882,;	T	ENSG00000115464	ENST00000398571	Transcript	missense_variant	5511	5434	1812	E/K	Gaa/Aaa	.	.	.	-1	USP34	HGNC	20066	protein_coding	YES	CCDS42686.1	ENSP00000381577	UBP34_HUMAN	.	UPI0000410E09	.	tolerated(0.32)	benign(0.005)	42/80	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF97	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATTCCTGGG	.	4	ESCA
CYP26B1	0	.	GRCh37	2	72358868	72358868	+	3'UTR	SNP	G	G	A	rs369926358	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*488C>T	.	.	ENST00000001146	6/6	47	36	11	79	79	0	CYP26B1,3_prime_UTR_variant,,ENST00000412253,;CYP26B1,3_prime_UTR_variant,,ENST00000001146,;CYP26B1,downstream_gene_variant,,ENST00000546307,;CYP26B1,downstream_gene_variant,,ENST00000474509,;CYP26B1,downstream_gene_variant,,ENST00000461519,;	A	ENSG00000003137	ENST00000001146	Transcript	3_prime_UTR_variant	2231	.	.	.	.	rs369926358	.	.	-1	CYP26B1	HGNC	20581	protein_coding	YES	CCDS1919.1	ENSP00000001146	CP26B_HUMAN	E7ER08_HUMAN	UPI000003DC62	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCCGCCAAG	.	5	ESCA
TSGA10	0	.	GRCh37	2	99720450	99720450	+	Missense_Mutation	SNP	T	T	A	rs746429052	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.591A>T	p.Lys197Asn	p.K197N	ENST00000393483	10/21	73	68	4	107	107	0	TSGA10,missense_variant,p.Lys197Asn,ENST00000410001,;TSGA10,missense_variant,p.Lys197Asn,ENST00000542655,;TSGA10,missense_variant,p.Lys197Asn,ENST00000409564,;TSGA10,missense_variant,p.Lys197Asn,ENST00000539964,;TSGA10,missense_variant,p.Lys197Asn,ENST00000355053,;TSGA10,missense_variant,p.Lys197Asn,ENST00000393483,;TSGA10,missense_variant,p.Lys197Asn,ENST00000393482,;TSGA10,non_coding_transcript_exon_variant,,ENST00000478090,;TSGA10,non_coding_transcript_exon_variant,,ENST00000488960,;AC019097.7,downstream_gene_variant,,ENST00000424783,;	A	ENSG00000135951	ENST00000393483	Transcript	missense_variant	1436	591	197	K/N	aaA/aaT	rs746429052	.	.	-1	TSGA10	HGNC	14927	protein_coding	YES	CCDS2037.1	ENSP00000377123	TSG10_HUMAN	F8WA32_HUMAN	UPI0000072CE3	.	deleterious(0)	probably_damaging(0.939)	10/21	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159:SF9,hmmpanther:PTHR23159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGCTTTTTG	byFrequency	2	ESCA
LSAMP	0	.	GRCh37	3	115535488	115535488	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.920-6227G>T	.	.	ENST00000490035	.	91	86	4	101	101	0	LSAMP,missense_variant,p.Gly318Cys,ENST00000539563,;LSAMP,missense_variant,p.Gly305Cys,ENST00000333617,;LSAMP,intron_variant,,ENST00000490035,;LSAMP,non_coding_transcript_exon_variant,,ENST00000475403,;	A	ENSG00000185565	ENST00000490035	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	LSAMP	HGNC	6705	protein_coding	YES	CCDS2982.1	ENSP00000419000	LSAMP_HUMAN	.	UPI00000746A0	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTACCAATTT	.	2	ESCA
ATR	0	.	GRCh37	3	142266582	142266583	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3341dupT	p.Ser1115IlefsTer3	p.S1115Ifs*3	ENST00000350721	16/47	123	96	27	100	100	0	ATR,frameshift_variant,p.Ser1051IlefsTer3,ENST00000383101,;ATR,frameshift_variant,p.Ser1115IlefsTer3,ENST00000350721,;	A	ENSG00000175054	ENST00000350721	Transcript	frameshift_variant	3463-3464	3341-3342	1114	I/IX	ata/atTa	.	.	.	-1	ATR	HGNC	882	protein_coding	YES	CCDS3124.1	ENSP00000343741	ATR_HUMAN	.	UPI0000031A31	.	.	.	16/47	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF64,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTGATATGAT	.	3	ESCA
YEATS2	0	.	GRCh37	3	183530405	183530405	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2034T>A	.	.	ENST00000305135	31/31	82	42	40	69	69	0	YEATS2,3_prime_UTR_variant,,ENST00000305135,;MAP6D1,downstream_gene_variant,,ENST00000431348,;MAP6D1,downstream_gene_variant,,ENST00000318631,;YEATS2-AS1,upstream_gene_variant,,ENST00000609871,;YEATS2-AS1,upstream_gene_variant,,ENST00000609195,;YEATS2-AS1,upstream_gene_variant,,ENST00000425008,;YEATS2,non_coding_transcript_exon_variant,,ENST00000472593,;YEATS2,downstream_gene_variant,,ENST00000468850,;YEATS2,downstream_gene_variant,,ENST00000481343,;MAP6D1,downstream_gene_variant,,ENST00000445426,;	A	ENSG00000163872	ENST00000305135	Transcript	3_prime_UTR_variant	6498	.	.	.	.	.	.	.	1	YEATS2	HGNC	25489	protein_coding	YES	CCDS43175.1	ENSP00000306983	YETS2_HUMAN	.	UPI00001BB2B9	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGGTATTTG	.	5	ESCA
HTR3C	0	.	GRCh37	3	183776319	183776319	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664A>C	p.Lys222Gln	p.K222Q	ENST00000318351	6/9	108	81	26	97	97	0	HTR3C,missense_variant,p.Lys222Gln,ENST00000318351,;	C	ENSG00000178084	ENST00000318351	Transcript	missense_variant	698	664	222	K/Q	Aag/Cag	.	.	.	1	HTR3C	HGNC	24003	protein_coding	YES	CCDS3250.1	ENSP00000322617	5HT3C_HUMAN	.	UPI00001402D6	.	tolerated(0.27)	benign(0.219)	6/9	.	hmmpanther:PTHR18945:SF409,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAACAAGGCC	.	5	ESCA
XCR1	0	.	GRCh37	3	46062533	46062533	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.907C>T	p.Arg303Trp	p.R303W	ENST00000309285	2/2	42	38	4	63	63	0	XCR1,missense_variant,p.Arg303Trp,ENST00000542109,;XCR1,missense_variant,p.Arg303Trp,ENST00000309285,;XCR1,downstream_gene_variant,,ENST00000395946,;NRBF2P2,upstream_gene_variant,,ENST00000413087,;	A	ENSG00000173578	ENST00000309285	Transcript	missense_variant	1264	907	303	R/W	Cgg/Tgg	COSM1617650	.	.	-1	XCR1	HGNC	1625	protein_coding	YES	CCDS2736.1	ENSP00000310405	XCR1_HUMAN	Q689E2_HUMAN	UPI000004358D	.	deleterious(0.02)	possibly_damaging(0.54)	2/2	.	hmmpanther:PTHR24227:SF59,hmmpanther:PTHR24227,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGCCGGAGAA	.	3	ESCA
ARF4	0	.	GRCh37	3	57557527	57557527	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*412A>G	.	.	ENST00000303436	6/6	42	17	25	87	87	0	ARF4,3_prime_UTR_variant,,ENST00000303436,;ARF4,3_prime_UTR_variant,,ENST00000496292,;ARF4,3_prime_UTR_variant,,ENST00000489843,;PDE12,downstream_gene_variant,,ENST00000311180,;ARF4,downstream_gene_variant,,ENST00000463880,;ARF4,downstream_gene_variant,,ENST00000483848,;ARF4,3_prime_UTR_variant,,ENST00000486310,;	C	ENSG00000168374	ENST00000303436	Transcript	3_prime_UTR_variant	1223	.	.	.	.	.	.	.	-1	ARF4	HGNC	655	protein_coding	YES	CCDS2884.1	ENSP00000306010	ARF4_HUMAN	U3KQF2_HUMAN,C9JPM4_HUMAN,C9J6P1_HUMAN	UPI000013E89E	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAATAAATA	.	5	ESCA
ZNF518B	0	.	GRCh37	4	10442774	10442774	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1954G>T	.	.	ENST00000326756	3/3	122	112	10	217	217	0	ZNF518B,3_prime_UTR_variant,,ENST00000326756,;ZNF518B,downstream_gene_variant,,ENST00000507515,;	A	ENSG00000178163	ENST00000326756	Transcript	3_prime_UTR_variant	5618	.	.	.	.	.	.	.	-1	ZNF518B	HGNC	29365	protein_coding	YES	CCDS33960.1	ENSP00000317614	Z518B_HUMAN	D6RDM9_HUMAN	UPI0000160B97	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACTTCCAAAAT	.	3	ESCA
CTBP1	0	.	GRCh37	4	1206043	1206043	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1308C>T	p.%3D	p.A436A	ENST00000290921	9/9	11	5	6	21	21	0	CTBP1,synonymous_variant,p.%3D,ENST00000503594,;CTBP1,synonymous_variant,p.%3D,ENST00000504092,;CTBP1,synonymous_variant,p.%3D,ENST00000382952,;CTBP1,synonymous_variant,p.%3D,ENST00000290921,;SPON2,upstream_gene_variant,,ENST00000509233,;CTBP1,downstream_gene_variant,,ENST00000506180,;SPON2,upstream_gene_variant,,ENST00000511679,;CTBP1,downstream_gene_variant,,ENST00000505826,;SPON2,upstream_gene_variant,,ENST00000502657,;SPON2,upstream_gene_variant,,ENST00000504871,;SPON2,upstream_gene_variant,,ENST00000400762,;CTBP1,downstream_gene_variant,,ENST00000514669,;SPON2,upstream_gene_variant,,ENST00000510542,;SPON2,upstream_gene_variant,,ENST00000506266,;CTBP1,non_coding_transcript_exon_variant,,ENST00000514596,;CTBP1,downstream_gene_variant,,ENST00000511907,;CTBP1,downstream_gene_variant,,ENST00000382950,;CTBP1,downstream_gene_variant,,ENST00000510739,;	A	ENSG00000159692	ENST00000290921	Transcript	synonymous_variant	1490	1308	436	A	gcC/gcT	.	.	.	-1	CTBP1	HGNC	2494	protein_coding	YES	CCDS3348.1	ENSP00000290921	CTBP1_HUMAN	.	UPI0000128637	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCACTGGCGTG	.	3	ESCA
SH3D19	0	.	GRCh37	4	152147325	152147325	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-755C>A	.	.	ENST00000304527	1/21	19	10	8	47	46	0	SH3D19,5_prime_UTR_variant,,ENST00000424281,;SH3D19,5_prime_UTR_variant,,ENST00000304527,;SH3D19,5_prime_UTR_variant,,ENST00000455740,;SH3D19,5_prime_UTR_variant,,ENST00000409598,;SH3D19,intron_variant,,ENST00000514152,;SH3D19,upstream_gene_variant,,ENST00000409252,;SH3D19,non_coding_transcript_exon_variant,,ENST00000514013,;SH3D19,non_coding_transcript_exon_variant,,ENST00000474743,;SH3D19,intron_variant,,ENST00000604440,;SH3D19,intron_variant,,ENST00000604030,;	T	ENSG00000109686	ENST00000304527	Transcript	5_prime_UTR_variant	336	.	.	.	.	.	.	.	-1	SH3D19	HGNC	30418	protein_coding	YES	CCDS34077.2	ENSP00000302913	SH319_HUMAN	.	UPI0000251D9A	.	.	.	1/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CATTAGATTTC	.	4	ESCA
DHX15	0	.	GRCh37	4	24543614	24543614	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1367T>C	p.Leu456Pro	p.L456P	ENST00000336812	8/14	44	41	3	94	94	0	DHX15,missense_variant,p.Leu456Pro,ENST00000336812,;DHX15,upstream_gene_variant,,ENST00000508032,;DHX15,upstream_gene_variant,,ENST00000503562,;	G	ENSG00000109606	ENST00000336812	Transcript	missense_variant	1524	1367	456	L/P	cTt/cCt	.	.	.	-1	DHX15	HGNC	2738	protein_coding	YES	CCDS33966.1	ENSP00000336741	DHX15_HUMAN	.	UPI000012907A	.	deleterious(0)	probably_damaging(1)	8/14	.	PROSITE_profiles:PS51194,hmmpanther:PTHR18934:SF95,hmmpanther:PTHR18934,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S455F|c.1364C>T|3	MUTECT|MUSE	CCAAAAGGGAC	.	2	ESCA
PHOX2B	0	.	GRCh37	4	41749533	41749533	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.262G>T	p.Asp88Tyr	p.D88Y	ENST00000226382	2/3	26	23	3	72	72	0	PHOX2B,missense_variant,p.Asp28Tyr,ENST00000510424,;PHOX2B,missense_variant,p.Asp88Tyr,ENST00000226382,;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,;	A	ENSG00000109132	ENST00000226382	Transcript	missense_variant	622	262	88	D/Y	Gac/Tac	.	.	.	-1	PHOX2B	HGNC	9143	protein_coding	YES	CCDS3463.1	ENSP00000226382	PHX2B_HUMAN	.	UPI000000D936	.	tolerated(0.06)	benign(0.406)	2/3	.	hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GTGGTCCGTGA	.	2	ESCA
ATG12	0	.	GRCh37	5	115177406	115177406	+	5'UTR	SNP	C	C	T	rs764729853	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-157G>A	.	.	ENST00000509910	1/4	16	6	10	49	49	0	ATG12,5_prime_UTR_variant,,ENST00000509910,;AP3S1,5_prime_UTR_variant,,ENST00000316788,;ATG12,5_prime_UTR_variant,,ENST00000274459,;ATG12,upstream_gene_variant,,ENST00000500945,;AP3S1,non_coding_transcript_exon_variant,,ENST00000514118,;ATG12,upstream_gene_variant,,ENST00000509598,;ATG12,upstream_gene_variant,,ENST00000514775,;ATG12,5_prime_UTR_variant,,ENST00000379594,;ATG12,5_prime_UTR_variant,,ENST00000513322,;ATG12,upstream_gene_variant,,ENST00000511984,;ATG12,upstream_gene_variant,,ENST00000508464,;AP3S1,upstream_gene_variant,,ENST00000509055,;ATG12,upstream_gene_variant,,ENST00000505993,;AP3S1,upstream_gene_variant,,ENST00000395548,;AP3S1,upstream_gene_variant,,ENST00000515066,;AP3S1,upstream_gene_variant,,ENST00000506430,;ATG12,upstream_gene_variant,,ENST00000513167,;	T	ENSG00000145782	ENST00000509910	Transcript	5_prime_UTR_variant	150	.	.	.	.	rs764729853	.	.	-1	ATG12	HGNC	588	protein_coding	YES	CCDS4122.2	ENSP00000425107	ATG12_HUMAN	.	UPI0000125C66	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGTCGCAGA	byFrequency	5	ESCA
ANKHD1	0	.	GRCh37	5	139876620	139876620	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000297183	15/36	54	24	30	88	87	1	ANKHD1,stop_gained,p.Gln921Ter,ENST00000360839,;ANKHD1,stop_gained,p.Gln940Ter,ENST00000421134,;ANKHD1,stop_gained,p.Gln921Ter,ENST00000297183,;ANKHD1-EIF4EBP3,stop_gained,p.Gln921Ter,ENST00000532219,;ANKHD1,intron_variant,,ENST00000412116,;ANKHD1,intron_variant,,ENST00000246149,;ANKHD1,non_coding_transcript_exon_variant,,ENST00000462121,;ANKHD1,downstream_gene_variant,,ENST00000506755,;	T	ENSG00000131503	ENST00000297183	Transcript	stop_gained	2885	2761	921	Q/*	Cag/Tag	.	.	.	1	ANKHD1	HGNC	24714	protein_coding	YES	CCDS4224.1	ENSP00000297183	ANKH1_HUMAN	.	UPI0000074448	.	.	.	15/36	.	PROSITE_profiles:PS50297,hmmpanther:PTHR23206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAACAGATT	.	5	ESCA
PCDHA9	0	.	GRCh37	5	140229519	140229519	+	Missense_Mutation	SNP	G	G	A	rs562563367	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439G>A	p.Arg480Gln	p.R480Q	ENST00000532602	1/4	76	70	6	175	175	0	PCDHA9,missense_variant,p.Arg480Gln,ENST00000378122,;PCDHA9,missense_variant,p.Arg480Gln,ENST00000532602,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	A	ENSG00000204961	ENST00000532602	Transcript	missense_variant	2472	1439	480	R/Q	cGg/cAg	rs562563367	.	.	1	PCDHA9	HGNC	8675	protein_coding	YES	CCDS54920.1	ENSP00000436042	PCDA9_HUMAN	.	UPI00001273D1	.	tolerated_low_confidence(0.07)	benign(0.005)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCGCGGGACG	by1000G	3	ESCA
PCDHB4	0	.	GRCh37	5	140503073	140503073	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1493C>T	p.Pro498Leu	p.P498L	ENST00000194152	1/1	138	109	29	208	208	0	PCDHB4,missense_variant,p.Pro498Leu,ENST00000194152,;AC005754.8,downstream_gene_variant,,ENST00000606030,;	T	ENSG00000081818	ENST00000194152	Transcript	missense_variant	1493	1493	498	P/L	cCc/cTc	.	.	.	1	PCDHB4	HGNC	8689	protein_coding	YES	CCDS4246.1	ENSP00000194152	PCDB4_HUMAN	.	UPI00001273DF	.	deleterious_low_confidence(0.01)	benign(0.309)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF55,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCCCCTCG	.	5	ESCA
ANKH	0	.	GRCh37	5	14769157	14769157	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240G>C	p.Lys80Asn	p.K80N	ENST00000284268	2/12	61	49	11	65	65	0	ANKH,missense_variant,p.Lys80Asn,ENST00000284268,;ANKH,non_coding_transcript_exon_variant,,ENST00000503389,;ANKH,non_coding_transcript_exon_variant,,ENST00000513115,;	G	ENSG00000154122	ENST00000284268	Transcript	missense_variant	571	240	80	K/N	aaG/aaC	COSM1542786	.	.	-1	ANKH	HGNC	15492	protein_coding	YES	CCDS3885.1	ENSP00000284268	ANKH_HUMAN	B3KMG4_HUMAN	UPI000003F535	.	tolerated(0.1)	possibly_damaging(0.636)	2/12	.	Pfam_domain:PF07260	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCTTGCT	.	5	ESCA
MRPL22	0	.	GRCh37	5	154330416	154330416	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113C>A	p.Ser38Tyr	p.S38Y	ENST00000523037	3/7	40	16	23	95	95	0	MRPL22,missense_variant,p.Ser38Tyr,ENST00000523037,;MRPL22,missense_variant,p.Ser44Tyr,ENST00000522038,;MRPL22,missense_variant,p.Ser64Tyr,ENST00000439747,;MRPL22,intron_variant,,ENST00000265229,;MRPL22,intron_variant,,ENST00000519059,;MRPL22,upstream_gene_variant,,ENST00000520040,;	A	ENSG00000082515	ENST00000523037	Transcript	missense_variant	154	113	38	S/Y	tCt/tAt	.	.	.	1	MRPL22	HGNC	14480	protein_coding	YES	CCDS4331.1	ENSP00000431040	RM22_HUMAN	.	UPI0000046801	.	deleterious(0.02)	benign(0.005)	3/7	.	hmmpanther:PTHR13501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGCTTCTCTTG	.	4	ESCA
KCNIP1	0	.	GRCh37	5	170162928	170162928	+	3'Flank	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000411494	.	17	13	4	46	46	0	KCNIP1,3_prime_UTR_variant,,ENST00000390656,;KCNIP1,3_prime_UTR_variant,,ENST00000328939,;KCNIP1,3_prime_UTR_variant,,ENST00000377360,;KCNIP1,3_prime_UTR_variant,,ENST00000520740,;KCNIP1,downstream_gene_variant,,ENST00000411494,;KCNIP1,downstream_gene_variant,,ENST00000434108,;	A	ENSG00000182132	ENST00000411494	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	118	1	KCNIP1	HGNC	15521	protein_coding	YES	CCDS34286.1	ENSP00000395323	KCIP1_HUMAN	.	UPI000004A27F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTACACTTT	.	2	ESCA
C7	0	.	GRCh37	5	40934566	40934566	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.278C>T	p.Ser93Leu	p.S93L	ENST00000313164	4/18	88	76	11	113	113	0	C7,missense_variant,p.Ser93Leu,ENST00000313164,;C7,upstream_gene_variant,,ENST00000489457,;C7,splice_region_variant,,ENST00000508185,;	T	ENSG00000112936	ENST00000313164	Transcript	missense_variant	637	278	93	S/L	tCa/tTa	.	.	.	1	C7	HGNC	1346	protein_coding	YES	CCDS47201.1	ENSP00000322061	CO7_HUMAN	.	UPI000020CA08	.	deleterious(0)	possibly_damaging(0.654)	4/18	.	PROSITE_profiles:PS50068,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF312,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Prints_domain:PR00764	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTTCAGGTA	.	4	ESCA
MCIDAS	0	.	GRCh37	5	54516532	54516532	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820G>T	p.Gly274Trp	p.G274W	ENST00000513312	7/7	34	30	3	77	77	0	MCIDAS,missense_variant,p.Gly274Trp,ENST00000513312,;MCIDAS,downstream_gene_variant,,ENST00000515336,;MCIDAS,3_prime_UTR_variant,,ENST00000513468,;	A	ENSG00000234602	ENST00000513312	Transcript	missense_variant	997	820	274	G/W	Ggg/Tgg	.	.	.	-1	MCIDAS	HGNC	40050	protein_coding	YES	CCDS54853.1	ENSP00000426359	MCIN_HUMAN	.	UPI000020C760	.	deleterious(0.01)	probably_damaging(0.997)	7/7	.	hmmpanther:PTHR13372:SF3,hmmpanther:PTHR13372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CTGCCCCGCAG	.	2	ESCA
PPWD1	0	.	GRCh37	5	64878949	64878949	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1435A>G	p.Met479Val	p.M479V	ENST00000261308	8/11	57	24	33	117	117	0	PPWD1,missense_variant,p.Met479Val,ENST00000261308,;PPWD1,missense_variant,p.Met449Val,ENST00000535264,;PPWD1,missense_variant,p.Met323Val,ENST00000538977,;PPWD1,3_prime_UTR_variant,,ENST00000511908,;PPWD1,3_prime_UTR_variant,,ENST00000510930,;PPWD1,non_coding_transcript_exon_variant,,ENST00000515151,;PPWD1,non_coding_transcript_exon_variant,,ENST00000511334,;PPWD1,non_coding_transcript_exon_variant,,ENST00000513773,;PPWD1,downstream_gene_variant,,ENST00000514172,;	G	ENSG00000113593	ENST00000261308	Transcript	missense_variant	1507	1435	479	M/V	Atg/Gtg	.	.	.	1	PPWD1	HGNC	28954	protein_coding	YES	CCDS3985.1	ENSP00000261308	PPWD1_HUMAN	D6R9Q1_HUMAN,B4DWR9_HUMAN	UPI000004CAF3	.	tolerated(0.56)	benign(0.008)	8/11	.	Gene3D:2.40.100.10,hmmpanther:PTHR11071,hmmpanther:PTHR11071:SF213	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCATGGCA	.	5	ESCA
RASA1	0	.	GRCh37	5	86637113	86637113	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>T	p.Glu342Ter	p.E342*	ENST00000274376	6/25	153	118	34	358	357	1	RASA1,stop_gained,p.Glu175Ter,ENST00000512763,;RASA1,stop_gained,p.Glu165Ter,ENST00000456692,;RASA1,stop_gained,p.Glu342Ter,ENST00000274376,;RASA1,stop_gained,p.Glu176Ter,ENST00000506290,;RASA1,stop_gained,p.Glu342Ter,ENST00000515800,;RASA1,non_coding_transcript_exon_variant,,ENST00000509953,;	T	ENSG00000145715	ENST00000274376	Transcript	stop_gained	1588	1024	342	E/*	Gaa/Taa	.	.	.	1	RASA1	HGNC	9871	protein_coding	YES	CCDS34200.1	ENSP00000274376	RASA1_HUMAN	B4DTL8_HUMAN	UPI00001351F3	.	.	.	6/25	.	hmmpanther:PTHR10194,Gene3D:3.30.505.10,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGGGAAGAA	.	5	ESCA
CHD1	0	.	GRCh37	5	98204234	98204234	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4213G>A	p.Glu1405Lys	p.E1405K	ENST00000284049	30/35	35	27	8	77	77	0	CHD1,missense_variant,p.Glu1405Lys,ENST00000284049,;CHD1,non_coding_transcript_exon_variant,,ENST00000511067,;CHD1,missense_variant,p.Glu4Lys,ENST00000512844,;CHD1,missense_variant,p.Glu34Lys,ENST00000505657,;CHD1,non_coding_transcript_exon_variant,,ENST00000514344,;CHD1,downstream_gene_variant,,ENST00000508756,;CHD1,downstream_gene_variant,,ENST00000414220,;	T	ENSG00000153922	ENST00000284049	Transcript	missense_variant	4363	4213	1405	E/K	Gaa/Aaa	.	.	.	-1	CHD1	HGNC	1915	protein_coding	YES	CCDS34204.1	ENSP00000284049	CHD1_HUMAN	.	UPI000013DD75	.	tolerated(0.24)	benign(0.066)	30/35	.	Pfam_domain:PF13907,hmmpanther:PTHR10799:SF535,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGATTCTTCAG	.	4	ESCA
VNN1	0	.	GRCh37	6	133014172	133014172	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817A>G	p.Lys273Glu	p.K273E	ENST00000367928	4/7	35	29	5	61	61	0	VNN1,missense_variant,p.Lys273Glu,ENST00000367928,;	C	ENSG00000112299	ENST00000367928	Transcript	missense_variant	831	817	273	K/E	Aaa/Gaa	.	.	.	-1	VNN1	HGNC	12705	protein_coding	YES	CCDS5159.1	ENSP00000356905	VNN1_HUMAN	.	UPI000013C91E	.	tolerated(0.37)	benign(0.021)	4/7	.	Superfamily_domains:SSF56317,PIRSF_domain:PIRSF011861,Gene3D:3.60.110.10,hmmpanther:PTHR10609:SF4,hmmpanther:PTHR10609,PROSITE_profiles:PS50263	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTTCTTTG	.	5	ESCA
SYNJ2	0	.	GRCh37	6	158516863	158516864	+	Frame_Shift_Ins	INS	-	-	CACCACCT	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3960_3967dupACCACCTC	p.Leu1323HisfsTer81	p.L1323Hfs*81	ENST00000355585	27/27	67	52	15	115	114	0	SYNJ2,frameshift_variant,p.Leu1323HisfsTer81,ENST00000355585,;SYNJ2,frameshift_variant,p.Leu408HisfsTer81,ENST00000367112,;SYNJ2,frameshift_variant,p.Leu1278HisfsTer81,ENST00000367122,;SYNJ2,downstream_gene_variant,,ENST00000367121,;	CACCACCT	ENSG00000078269	ENST00000355585	Transcript	frameshift_variant	4033-4034	3958-3959	1320	P/PPPX	cca/cCACCACCTca	.	.	.	1	SYNJ2	HGNC	11504	protein_coding	YES	CCDS5254.1	ENSP00000347792	SYNJ2_HUMAN	B4DLC4_HUMAN	UPI000006E2F8	.	.	.	27/27	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTGTGCCACCA	.	2	ESCA
KDM1B	0	.	GRCh37	6	18188156	18188156	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.573+2115G>A	.	.	ENST00000297792	.	42	38	4	65	65	0	KDM1B,missense_variant,p.Ser236Asn,ENST00000388870,;KDM1B,missense_variant,p.Ser53Asn,ENST00000449850,;KDM1B,intron_variant,,ENST00000546309,;KDM1B,intron_variant,,ENST00000397244,;KDM1B,intron_variant,,ENST00000297792,;	A	ENSG00000165097	ENST00000297792	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KDM1B	HGNC	21577	protein_coding	YES	CCDS34343.1	ENSP00000297792	KDM1B_HUMAN	Q08EI0_HUMAN	UPI000023739E	.	.	.	.	8/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCAGCACAA	.	2	ESCA
UBR2	0	.	GRCh37	6	42652546	42652546	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4790C>A	p.Ser1597Tyr	p.S1597Y	ENST00000372899	44/47	82	76	6	157	157	0	UBR2,missense_variant,p.Ser1597Tyr,ENST00000372901,;UBR2,missense_variant,p.Ser1597Tyr,ENST00000372899,;UBR2,3_prime_UTR_variant,,ENST00000372883,;	A	ENSG00000024048	ENST00000372899	Transcript	missense_variant	5048	4790	1597	S/Y	tCt/tAt	.	.	.	1	UBR2	HGNC	21289	protein_coding	YES	CCDS4870.1	ENSP00000361990	UBR2_HUMAN	B3KXG6_HUMAN	UPI0000074466	.	deleterious(0.04)	benign(0.063)	44/47	.	hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAATCTAACA	.	2	ESCA
XPO5	0	.	GRCh37	6	43528718	43528718	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1038A>G	p.%3D	p.P346P	ENST00000265351	10/32	57	37	20	130	130	0	XPO5,synonymous_variant,p.%3D,ENST00000265351,;RP3-337H4.10,upstream_gene_variant,,ENST00000607635,;XPO5,upstream_gene_variant,,ENST00000424378,;XPO5,synonymous_variant,p.%3D,ENST00000496341,;	C	ENSG00000124571	ENST00000265351	Transcript	synonymous_variant	1249	1038	346	P	ccA/ccG	.	.	.	-1	XPO5	HGNC	17675	protein_coding	YES	CCDS47430.1	ENSP00000265351	XPO5_HUMAN	E2QRM3_HUMAN	UPI000006CC97	.	.	.	10/32	.	hmmpanther:PTHR11223,hmmpanther:PTHR11223:SF3,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGATGGTGT	.	5	ESCA
TFAP2D	0	.	GRCh37	6	50696619	50696619	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.649C>T	p.Arg217Cys	p.R217C	ENST00000008391	4/8	30	27	3	78	78	0	TFAP2D,missense_variant,p.Arg217Cys,ENST00000008391,;TFAP2D,non_coding_transcript_exon_variant,,ENST00000492804,;	T	ENSG00000008197	ENST00000008391	Transcript	missense_variant	877	649	217	R/C	Cgt/Tgt	.	.	.	1	TFAP2D	HGNC	15581	protein_coding	YES	CCDS4933.1	ENSP00000008391	AP2D_HUMAN	.	UPI00001A3A89	.	deleterious(0)	probably_damaging(0.999)	4/8	.	Pfam_domain:PF03299,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGCCGTTTG	.	2	ESCA
FAM135A	0	.	GRCh37	6	71186910	71186910	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.417G>C	p.Lys139Asn	p.K139N	ENST00000418814	8/22	44	31	13	76	76	0	FAM135A,missense_variant,p.Lys96Asn,ENST00000457062,;FAM135A,missense_variant,p.Lys139Asn,ENST00000505868,;FAM135A,missense_variant,p.Lys139Asn,ENST00000361499,;FAM135A,missense_variant,p.Lys139Asn,ENST00000505769,;FAM135A,missense_variant,p.Lys139Asn,ENST00000418814,;FAM135A,missense_variant,p.Lys96Asn,ENST00000370479,;FAM135A,missense_variant,p.Lys139Asn,ENST00000515323,;FAM135A,non_coding_transcript_exon_variant,,ENST00000393299,;FAM135A,intron_variant,,ENST00000194672,;FAM135A,upstream_gene_variant,,ENST00000425415,;	C	ENSG00000082269	ENST00000418814	Transcript	missense_variant	1031	417	139	K/N	aaG/aaC	.	.	.	1	FAM135A	HGNC	21084	protein_coding	YES	CCDS55028.1	ENSP00000410768	F135A_HUMAN	D6RFG9_HUMAN,D6REA8_HUMAN,D6RC17_HUMAN	UPI000004A0FF	.	tolerated(0.15)	probably_damaging(1)	8/22	.	Pfam_domain:PF12394,hmmpanther:PTHR12482,hmmpanther:PTHR12482:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGCTGCA	.	5	ESCA
CNR1	0	.	GRCh37	6	88854404	88854404	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590C>T	p.Thr197Met	p.T197M	ENST00000537554	2/2	17	12	5	33	33	0	CNR1,missense_variant,p.Thr197Met,ENST00000369499,;CNR1,missense_variant,p.Thr197Met,ENST00000428600,;CNR1,missense_variant,p.Thr197Met,ENST00000535130,;CNR1,missense_variant,p.Thr136Met,ENST00000549716,;CNR1,missense_variant,p.Thr197Met,ENST00000369501,;CNR1,missense_variant,p.Thr164Met,ENST00000468898,;CNR1,missense_variant,p.Thr197Met,ENST00000537554,;CNR1,missense_variant,p.Thr197Met,ENST00000549890,;CNR1,3_prime_UTR_variant,,ENST00000362094,;CNR1,downstream_gene_variant,,ENST00000551417,;	A	ENSG00000118432	ENST00000537554	Transcript	missense_variant	4153	590	197	T/M	aCg/aTg	.	.	.	-1	CNR1	HGNC	2159	protein_coding	YES	CCDS5015.1	ENSP00000441046	CNR1_HUMAN	S5TLS4_HUMAN,Q9BYY6_HUMAN,F8W187_HUMAN	UPI00000008AA	.	deleterious(0)	probably_damaging(0.986)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF10,Pfam_domain:PF00001,Gene3D:1.20.1070.10,PIRSF_domain:PIRSF037995,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGGCCGTGACC	.	4	ESCA
POT1	0	.	GRCh37	7	124532386	124532386	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>T	p.Gly20Cys	p.G20C	ENST00000357628	6/19	92	85	7	113	113	0	POT1,missense_variant,p.Gly20Cys,ENST00000446993,;POT1,missense_variant,p.Gly20Cys,ENST00000357628,;POT1,missense_variant,p.Gly20Cys,ENST00000609702,;POT1,5_prime_UTR_variant,,ENST00000393329,;POT1,non_coding_transcript_exon_variant,,ENST00000608261,;POT1,downstream_gene_variant,,ENST00000608437,;POT1,missense_variant,p.Gly20Cys,ENST00000607932,;POT1,missense_variant,p.Gly20Cys,ENST00000429326,;POT1,missense_variant,p.Gly20Cys,ENST00000609106,;POT1,missense_variant,p.Gly20Cys,ENST00000608057,;	A	ENSG00000128513	ENST00000357628	Transcript	missense_variant	657	58	20	G/C	Ggt/Tgt	.	.	.	-1	POT1	HGNC	17284	protein_coding	YES	CCDS5793.1	ENSP00000350249	POTE1_HUMAN	C9JPG9_HUMAN,A8MTK3_HUMAN	UPI0000073E3F	.	deleterious(0)	probably_damaging(0.989)	6/19	.	hmmpanther:PTHR14513:SF2,hmmpanther:PTHR14513,Pfam_domain:PF02765,Gene3D:2.40.50.140,SMART_domains:SM00976,Superfamily_domains:SSF50249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTACCACCCT	.	3	ESCA
SLC4A2	0	.	GRCh37	7	150769142	150769142	+	Silent	SNP	C	C	T	rs372791857	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2454C>T	p.%3D	p.F818F	ENST00000485713	16/23	32	28	4	61	61	0	SLC4A2,synonymous_variant,p.%3D,ENST00000310317,;SLC4A2,synonymous_variant,p.%3D,ENST00000413384,;SLC4A2,synonymous_variant,p.%3D,ENST00000461735,;SLC4A2,synonymous_variant,p.%3D,ENST00000485713,;SLC4A2,synonymous_variant,p.%3D,ENST00000392826,;FASTK,downstream_gene_variant,,ENST00000297532,;FASTK,downstream_gene_variant,,ENST00000353841,;FASTK,downstream_gene_variant,,ENST00000540185,;FASTK,downstream_gene_variant,,ENST00000482571,;RP11-148K1.12,downstream_gene_variant,,ENST00000485974,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000482697,;FASTK,downstream_gene_variant,,ENST00000489884,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000472204,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000460010,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000493040,;SLC4A2,downstream_gene_variant,,ENST00000469355,;SLC4A2,downstream_gene_variant,,ENST00000480107,;FASTK,downstream_gene_variant,,ENST00000460980,;FASTK,downstream_gene_variant,,ENST00000482806,;SLC4A2,downstream_gene_variant,,ENST00000494298,;FASTK,downstream_gene_variant,,ENST00000459800,;FASTK,downstream_gene_variant,,ENST00000469237,;SLC4A2,upstream_gene_variant,,ENST00000469467,;FASTK,downstream_gene_variant,,ENST00000466855,;FASTK,downstream_gene_variant,,ENST00000483953,;FASTK,downstream_gene_variant,,ENST00000465272,;FASTK,downstream_gene_variant,,ENST00000467237,;	T	ENSG00000164889	ENST00000485713	Transcript	synonymous_variant	3494	2454	818	F	ttC/ttT	rs372791857,COSM3431381	.	.	1	SLC4A2	HGNC	11028	protein_coding	YES	CCDS5917.1	ENSP00000419412	B3A2_HUMAN	Q59GF1_HUMAN,C9JVC2_HUMAN,C9J9M9_HUMAN,C9J722_HUMAN,C9J459_HUMAN,C9J035_HUMAN	UPI000013EFE9	.	.	.	16/23	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF14,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834,Prints_domain:PR01231	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0.0002	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCTTCGTCTC	byCluster|by1000G	4	ESCA
SP4	0	.	GRCh37	7	21554016	21554016	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3129T>A	.	.	ENST00000222584	6/6	119	106	13	133	133	0	SP4,3_prime_UTR_variant,,ENST00000222584,;SP4,3_prime_UTR_variant,,ENST00000448246,;	A	ENSG00000105866	ENST00000222584	Transcript	3_prime_UTR_variant	5702	.	.	.	.	.	.	.	1	SP4	HGNC	11209	protein_coding	YES	CCDS5373.1	ENSP00000222584	SP4_HUMAN	Q32M51_HUMAN	UPI000013C807	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAATTGATGT	.	4	ESCA
UPP1	0	.	GRCh37	7	48147845	48147845	+	Missense_Mutation	SNP	G	G	T	rs773220996	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.824G>T	p.Arg275Leu	p.R275L	ENST00000331803	10/10	78	49	29	82	82	0	UPP1,missense_variant,p.Arg138Leu,ENST00000429491,;UPP1,missense_variant,p.Arg275Leu,ENST00000331803,;UPP1,missense_variant,p.Arg275Leu,ENST00000341253,;UPP1,missense_variant,p.Arg275Leu,ENST00000395564,;UPP1,downstream_gene_variant,,ENST00000436673,;UPP1,downstream_gene_variant,,ENST00000416681,;UPP1,non_coding_transcript_exon_variant,,ENST00000482015,;UPP1,3_prime_UTR_variant,,ENST00000457596,;UPP1,3_prime_UTR_variant,,ENST00000417464,;UPP1,3_prime_UTR_variant,,ENST00000395560,;UPP1,non_coding_transcript_exon_variant,,ENST00000495446,;UPP1,downstream_gene_variant,,ENST00000444999,;UPP1,downstream_gene_variant,,ENST00000421046,;	T	ENSG00000183696	ENST00000331803	Transcript	missense_variant	1447	824	275	R/L	cGc/cTc	rs773220996	.	.	1	UPP1	HGNC	12576	protein_coding	YES	CCDS5507.1	ENSP00000330032	UPP1_HUMAN	C9K0J2_HUMAN,C9JIP2_HUMAN,C9J486_HUMAN	UPI0000137AC5	.	deleterious(0)	probably_damaging(1)	10/10	.	hmmpanther:PTHR21234,hmmpanther:PTHR21234:SF15,Gene3D:3.40.50.1580,Pfam_domain:PF01048,TIGRFAM_domain:TIGR01719,Superfamily_domains:SSF53167	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACCGCCTGG	byFrequency	5	ESCA
EIF2AK1	0	.	GRCh37	7	6066405	6066406	+	Frame_Shift_Ins	INS	-	-	AT	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1716_1717dupAT	p.Ser573TyrfsTer24	p.S573Yfs*24	ENST00000199389	14/15	81	55	26	62	62	0	EIF2AK1,frameshift_variant,p.Ser449TyrfsTer24,ENST00000536084,;EIF2AK1,frameshift_variant,p.Ser573TyrfsTer24,ENST00000199389,;EIF2AK1,upstream_gene_variant,,ENST00000422786,;ANKRD61,upstream_gene_variant,,ENST00000409061,;AIMP2,downstream_gene_variant,,ENST00000395236,;AIMP2,downstream_gene_variant,,ENST00000400479,;AIMP2,downstream_gene_variant,,ENST00000223029,;EIF2AK1,non_coding_transcript_exon_variant,,ENST00000490523,;	AT	ENSG00000086232	ENST00000199389	Transcript	frameshift_variant	1864-1865	1717-1718	573	S/YX	tct/tATct	.	.	.	-1	EIF2AK1	HGNC	24921	protein_coding	YES	CCDS5345.1	ENSP00000199389	E2AK1_HUMAN	Q75MR0_HUMAN	UPI0000161BAE	.	.	.	14/15	.	PROSITE_profiles:PS50011,hmmpanther:PTHR11042:SF88,hmmpanther:PTHR11042,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGCAGATGGT	.	3	ESCA
RABGEF1	0	.	GRCh37	7	66236988	66236988	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.102C>G	p.Phe34Leu	p.F34L	ENST00000284957	2/9	89	82	7	119	119	0	RABGEF1,missense_variant,p.Phe34Leu,ENST00000442563,;KCTD7,missense_variant,p.Phe34Leu,ENST00000380828,;RABGEF1,missense_variant,p.Phe48Leu,ENST00000437078,;RABGEF1,missense_variant,p.Phe34Leu,ENST00000284957,;KCTD7,missense_variant,p.Phe34Leu,ENST00000451741,;RABGEF1,missense_variant,p.Phe47Leu,ENST00000439720,;KCTD7,missense_variant,p.Phe34Leu,ENST00000510829,;RABGEF1,missense_variant,p.Phe34Leu,ENST00000450873,;RABGEF1,non_coding_transcript_exon_variant,,ENST00000484547,;RABGEF1,missense_variant,p.Phe34Leu,ENST00000607882,;KCTD7,missense_variant,p.Phe172Leu,ENST00000503687,;	G	ENSG00000154710	ENST00000284957	Transcript	missense_variant	179	102	34	F/L	ttC/ttG	.	.	.	1	RABGEF1	HGNC	17676	protein_coding	YES	CCDS5535.1	ENSP00000284957	RABX5_HUMAN	C9JDA2_HUMAN,B3KMF1_HUMAN	UPI00000730D5	.	tolerated(0.61)	benign(0.014)	2/9	.	PROSITE_profiles:PS51036,hmmpanther:PTHR23101,hmmpanther:PTHR23101:SF49,Pfam_domain:PF01754,SMART_domains:SM00259,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTTCTGCTC	.	2	ESCA
SEMA3D	0	.	GRCh37	7	84679974	84679974	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.861+5059C>A	.	.	ENST00000284136	.	57	34	23	71	71	0	SEMA3D,3_prime_UTR_variant,,ENST00000444867,;SEMA3D,intron_variant,,ENST00000284136,;SEMA3D,intron_variant,,ENST00000463315,;	T	ENSG00000153993	ENST00000284136	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SEMA3D	HGNC	10726	protein_coding	YES	CCDS34676.1	ENSP00000284136	SEM3D_HUMAN	.	UPI0000135A66	.	.	.	.	7/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTGTTCAA	.	5	ESCA
HEPACAM2	0	.	GRCh37	7	92818321	92818321	+	3'UTR	SNP	C	C	T	rs112556032	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*259G>A	.	.	ENST00000394468	10/10	20	16	4	14	14	0	HEPACAM2,3_prime_UTR_variant,,ENST00000394468,;HEPACAM2,3_prime_UTR_variant,,ENST00000440868,;HEPACAM2,3_prime_UTR_variant,,ENST00000453812,;HEPACAM2,3_prime_UTR_variant,,ENST00000341723,;HEPACAM2,non_coding_transcript_exon_variant,,ENST00000492616,;	T	ENSG00000188175	ENST00000394468	Transcript	3_prime_UTR_variant	1726	.	.	.	.	rs112556032	.	.	-1	HEPACAM2	HGNC	27364	protein_coding	YES	CCDS43616.1	ENSP00000377980	HECA2_HUMAN	.	UPI000013DA71	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTCTCCCCGTC	byCluster	3	ESCA
KCTD9	0	.	GRCh37	8	25285728	25285728	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1645A>G	.	.	ENST00000221200	12/12	56	51	5	77	77	0	KCTD9,3_prime_UTR_variant,,ENST00000221200,;GNRH1,upstream_gene_variant,,ENST00000276414,;GNRH1,upstream_gene_variant,,ENST00000421054,;RP11-395I14.2,upstream_gene_variant,,ENST00000523840,;KCTD9,downstream_gene_variant,,ENST00000519665,;	C	ENSG00000104756	ENST00000221200	Transcript	3_prime_UTR_variant	3036	.	.	.	.	.	.	.	-1	KCTD9	HGNC	22401	protein_coding	YES	CCDS6048.1	ENSP00000221200	KCTD9_HUMAN	K7ENB5_HUMAN	UPI00001540AF	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AATGATTTAAA	.	3	ESCA
ATP6V1H	0	.	GRCh37	8	54730058	54730058	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339C>G	p.Asp113Glu	p.D113E	ENST00000359530	5/14	56	37	18	61	61	0	ATP6V1H,missense_variant,p.Asp113Glu,ENST00000396774,;ATP6V1H,missense_variant,p.Asp113Glu,ENST00000355221,;ATP6V1H,missense_variant,p.Asp113Glu,ENST00000359530,;ATP6V1H,missense_variant,p.Asp73Glu,ENST00000520188,;ATP6V1H,upstream_gene_variant,,ENST00000521900,;ATP6V1H,missense_variant,p.Asp2Glu,ENST00000522849,;ATP6V1H,3_prime_UTR_variant,,ENST00000524164,;ATP6V1H,3_prime_UTR_variant,,ENST00000519588,;ATP6V1H,non_coding_transcript_exon_variant,,ENST00000521377,;	C	ENSG00000047249	ENST00000359530	Transcript	missense_variant	603	339	113	D/E	gaC/gaG	.	.	.	-1	ATP6V1H	HGNC	18303	protein_coding	YES	CCDS6153.1	ENSP00000352522	VATH_HUMAN	G3V126_HUMAN,E5RHH0_HUMAN,E5RG49_HUMAN	UPI0000000966	.	tolerated(0.99)	benign(0.429)	5/14	.	hmmpanther:PTHR10698,hmmpanther:PTHR10698:SF0,Pfam_domain:PF03224,Gene3D:1.25.10.10,PIRSF_domain:PIRSF032184,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATAGTCAAA	.	5	ESCA
GDAP1	0	.	GRCh37	8	75276667	75276667	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*65G>A	.	.	ENST00000220822	6/6	30	27	3	60	60	0	GDAP1,3_prime_UTR_variant,,ENST00000434412,;GDAP1,3_prime_UTR_variant,,ENST00000220822,;GDAP1,intron_variant,,ENST00000524195,;GDAP1,downstream_gene_variant,,ENST00000524366,;GDAP1,downstream_gene_variant,,ENST00000521096,;GDAP1,downstream_gene_variant,,ENST00000523640,;GDAP1,downstream_gene_variant,,ENST00000520797,;GDAP1,3_prime_UTR_variant,,ENST00000522568,;	A	ENSG00000104381	ENST00000220822	Transcript	3_prime_UTR_variant	1222	.	.	.	.	.	.	.	1	GDAP1	HGNC	15968	protein_coding	YES	CCDS34911.1	ENSP00000220822	GDAP1_HUMAN	B4DIH2_HUMAN	UPI00001AE62B	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGTGGCTCTC	.	4	ESCA
SMC2	0	.	GRCh37	9	106887320	106887321	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2391dupA	p.Leu798ThrfsTer12	p.L798Tfs*12	ENST00000286398	18/25	55	44	11	54	54	0	SMC2,frameshift_variant,p.Leu798ThrfsTer12,ENST00000303219,;SMC2,frameshift_variant,p.Leu798ThrfsTer12,ENST00000374793,;SMC2,frameshift_variant,p.Leu798ThrfsTer12,ENST00000286398,;SMC2,frameshift_variant,p.Leu798ThrfsTer12,ENST00000374787,;SMC2,upstream_gene_variant,,ENST00000493955,;	A	ENSG00000136824	ENST00000286398	Transcript	frameshift_variant	2673-2674	2385-2386	795-796	-/X	-/A	.	.	.	1	SMC2	HGNC	14011	protein_coding	YES	CCDS35086.1	ENSP00000286398	SMC2_HUMAN	Q5T821_HUMAN	UPI000013DE44	.	.	.	18/25	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937:SF9,hmmpanther:PTHR18937,PIRSF_domain:PIRSF005719	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTCAGAAAAA	.	3	ESCA
COL27A1	0	.	GRCh37	9	116931688	116931688	+	Missense_Mutation	SNP	C	C	T	rs141872540	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1853C>T	p.Thr618Met	p.T618M	ENST00000356083	3/61	35	27	7	75	75	0	COL27A1,missense_variant,p.Thr565Met,ENST00000451716,;COL27A1,missense_variant,p.Thr618Met,ENST00000356083,;COL27A1,missense_variant,p.Thr268Met,ENST00000494090,;	T	ENSG00000196739	ENST00000356083	Transcript	missense_variant	2244	1853	618	T/M	aCg/aTg	rs141872540	.	.	1	COL27A1	HGNC	22986	protein_coding	YES	CCDS6802.1	ENSP00000348385	CORA1_HUMAN	.	UPI0000062271	.	.	unknown(0)	3/61	.	hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF362	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTACGCCTT	byCluster	5	ESCA
GAPVD1	0	.	GRCh37	9	128126213	128126213	+	3'Flank	SNP	C	C	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000394105	.	43	28	14	102	100	1	GAPVD1,3_prime_UTR_variant,,ENST00000297933,;GAPVD1,3_prime_UTR_variant,,ENST00000470056,;GAPVD1,3_prime_UTR_variant,,ENST00000394104,;GAPVD1,3_prime_UTR_variant,,ENST00000265956,;GAPVD1,downstream_gene_variant,,ENST00000394105,;GAPVD1,downstream_gene_variant,,ENST00000394083,;GAPVD1,downstream_gene_variant,,ENST00000495955,;GAPVD1,downstream_gene_variant,,ENST00000312123,;GAPVD1,downstream_gene_variant,,ENST00000467707,;GAPVD1,downstream_gene_variant,,ENST00000474637,;	T	ENSG00000165219	ENST00000394105	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	605	1	GAPVD1	HGNC	23375	protein_coding	YES	CCDS35138.1	ENSP00000377665	GAPD1_HUMAN	C9IZX9_HUMAN	UPI00001D76F1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAATCAGGAA	.	5	ESCA
NUP214	0	.	GRCh37	9	134019964	134019964	+	Frame_Shift_Del	DEL	C	C	-	rs779093260	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1596delC	p.Thr533ProfsTer38	p.T533Pfs*38	ENST00000359428	12/36	48	42	6	42	42	0	NUP214,frameshift_variant,p.Thr533ProfsTer38,ENST00000451030,;NUP214,frameshift_variant,p.Thr109ProfsTer38,ENST00000530863,;NUP214,frameshift_variant,p.Thr533ProfsTer38,ENST00000359428,;NUP214,frameshift_variant,p.Thr533ProfsTer38,ENST00000411637,;RP11-544A12.4,intron_variant,,ENST00000587264,;RP11-544A12.4,intron_variant,,ENST00000586290,;RP11-544A12.4,intron_variant,,ENST00000415391,;RP11-544A12.4,intron_variant,,ENST00000588378,;RP11-544A12.4,intron_variant,,ENST00000589667,;RP11-544A12.4,intron_variant,,ENST00000587408,;RP11-544A12.4,intron_variant,,ENST00000589540,;RP11-544A12.4,intron_variant,,ENST00000590461,;NUP214,upstream_gene_variant,,ENST00000525980,;	-	ENSG00000126883	ENST00000359428	Transcript	frameshift_variant	1736	1592	531	A/X	gCc/gc	rs779093260	.	.	1	NUP214	HGNC	8064	protein_coding	YES	CCDS6940.1	ENSP00000352400	NU214_HUMAN	H0YDI2_HUMAN,E9PS86_HUMAN	UPI00001BBB2F	.	.	.	12/36	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCCTAGCCCCCA	.	2	ESCA
FBXW5	0	.	GRCh37	9	139835770	139835770	+	Missense_Mutation	SNP	G	G	A	rs371147879	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1390C>T	p.Arg464Cys	p.R464C	ENST00000325285	8/9	32	19	12	76	76	0	FBXW5,missense_variant,p.Arg464Cys,ENST00000325285,;FBXW5,downstream_gene_variant,,ENST00000443788,;FBXW5,downstream_gene_variant,,ENST00000433269,;C8G,upstream_gene_variant,,ENST00000224181,;C8G,upstream_gene_variant,,ENST00000371634,;FBXW5,downstream_gene_variant,,ENST00000428398,;RP11-229P13.25,upstream_gene_variant,,ENST00000569497,;FBXW5,non_coding_transcript_exon_variant,,ENST00000483559,;FBXW5,non_coding_transcript_exon_variant,,ENST00000487794,;FBXW5,non_coding_transcript_exon_variant,,ENST00000459905,;FBXW5,downstream_gene_variant,,ENST00000491246,;FBXW5,downstream_gene_variant,,ENST00000480818,;C8G,upstream_gene_variant,,ENST00000484376,;RP11-229P13.2,downstream_gene_variant,,ENST00000395082,;	A	ENSG00000159069	ENST00000325285	Transcript	missense_variant	1470	1390	464	R/C	Cgc/Tgc	rs371147879	.	.	-1	FBXW5	HGNC	13613	protein_coding	YES	CCDS7014.1	ENSP00000313034	FBXW5_HUMAN	.	UPI000006EC75	.	deleterious(0)	possibly_damaging(0.893)	8/9	.	hmmpanther:PTHR20995,hmmpanther:PTHR20995:SF15,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGCGGTGCG	byCluster|by1000G	5	ESCA
ACO1	0	.	GRCh37	9	32433728	32433729	+	Frame_Shift_Del	DEL	TG	TG	-	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	TG	TG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1856_1857delTG	p.Val619GlufsTer2	p.V619Efs*2	ENST00000309951	16/21	71	48	23	55	55	0	ACO1,frameshift_variant,p.Val619GlufsTer2,ENST00000379923,;ACO1,frameshift_variant,p.Val619GlufsTer2,ENST00000309951,;ACO1,frameshift_variant,p.Val520GlufsTer2,ENST00000541043,;	-	ENSG00000122729	ENST00000309951	Transcript	frameshift_variant	1992-1993	1854-1855	618-619	TV/TX	acTGtg/actg	.	.	.	1	ACO1	HGNC	117	protein_coding	YES	CCDS6525.1	ENSP00000309477	ACOC_HUMAN	Q9HBB2_HUMAN	UPI000012D87E	.	.	.	16/21	.	hmmpanther:PTHR11670:SF32,hmmpanther:PTHR11670,TIGRFAM_domain:TIGR01341,Superfamily_domains:SSF53732	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAAGACTGTGAAT	.	3	ESCA
CDC14B	0	.	GRCh37	9	99296415	99296415	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740C>A	p.Thr247Asn	p.T247N	ENST00000375241	9/14	40	12	28	53	53	0	CDC14B,missense_variant,p.Thr210Asn,ENST00000375242,;CDC14B,missense_variant,p.Thr225Asn,ENST00000452280,;CDC14B,missense_variant,p.Thr247Asn,ENST00000265659,;CDC14B,missense_variant,p.Thr247Asn,ENST00000463569,;CDC14B,missense_variant,p.Thr247Asn,ENST00000375240,;CDC14B,missense_variant,p.Thr247Asn,ENST00000375236,;CDC14B,missense_variant,p.Thr247Asn,ENST00000375241,;CDC14B,downstream_gene_variant,,ENST00000415608,;CDC14B,downstream_gene_variant,,ENST00000480920,;CDC14B,missense_variant,p.Thr242Asn,ENST00000412285,;CDC14B,missense_variant,p.Thr247Asn,ENST00000474602,;CDC14B,downstream_gene_variant,,ENST00000496750,;	T	ENSG00000081377	ENST00000375241	Transcript	missense_variant	1192	740	247	T/N	aCt/aAt	.	.	.	-1	CDC14B	HGNC	1719	protein_coding	YES	CCDS6722.1	ENSP00000364389	CC14B_HUMAN	.	UPI0000072924	.	deleterious(0)	benign(0.076)	9/14	.	Superfamily_domains:SSF52799,SMART_domains:SM00195,Gene3D:3.90.190.10,hmmpanther:PTHR23339,hmmpanther:PTHR23339:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAAGTCTCA	.	5	ESCA
ZCCHC18	0	.	GRCh37	X	103359001	103359001	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199C>A	p.Gln67Lys	p.Q67K	ENST00000537356	2/2	20	13	7	25	25	0	ZCCHC18,missense_variant,p.Gln67Lys,ENST00000537356,;SLC25A53,intron_variant,,ENST00000357421,;ZCCHC18,intron_variant,,ENST00000422784,;ZCCHC18,downstream_gene_variant,,ENST00000603049,;ZCCHC18,downstream_gene_variant,,ENST00000605784,;ZCCHC18,downstream_gene_variant,,ENST00000423478,;	A	ENSG00000166707	ENST00000537356	Transcript	missense_variant	1613	199	67	Q/K	Caa/Aaa	.	.	.	1	ZCCHC18	HGNC	32459	protein_coding	YES	CCDS65304.1	ENSP00000473824	ZCC18_HUMAN	.	UPI0000072244	.	deleterious(0.01)	possibly_damaging(0.801)	2/2	.	hmmpanther:PTHR23095:SF18,hmmpanther:PTHR23095,Pfam_domain:PF14893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATCCAAGTC	.	5	ESCA
MAP7D2	0	.	GRCh37	X	20030525	20030525	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2014G>C	p.Asp672His	p.D672H	ENST00000379643	15/17	39	36	3	52	52	0	MAP7D2,missense_variant,p.Asp672His,ENST00000379643,;MAP7D2,missense_variant,p.Asp586His,ENST00000443379,;MAP7D2,missense_variant,p.Asp516His,ENST00000543767,;MAP7D2,missense_variant,p.Asp579His,ENST00000452324,;MAP7D2,missense_variant,p.Asp631His,ENST00000379651,;MIR23C,downstream_gene_variant,,ENST00000579846,;MAP7D2,intron_variant,,ENST00000485173,;	G	ENSG00000184368	ENST00000379643	Transcript	missense_variant	2052	2014	672	D/H	Gat/Cat	COSM756570,COSM1151559	.	.	-1	MAP7D2	HGNC	25899	protein_coding	YES	CCDS55386.1	ENSP00000368964	MA7D2_HUMAN	.	UPI00015E039B	.	deleterious(0)	unknown(0)	15/17	.	hmmpanther:PTHR15073:SF3,hmmpanther:PTHR15073	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCCATCAAGGG	.	3	ESCA
PGK1	0	.	GRCh37	X	77359778	77359778	+	5'UTR	SNP	C	C	T	rs192936390	.	TCGA-LN-A8HZ-01A-11D-A36J-09	TCGA-LN-A8HZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-60C>T	.	.	ENST00000373316	1/11	20	7	13	24	24	0	PGK1,5_prime_UTR_variant,,ENST00000373316,;PGK1,5_prime_UTR_variant,,ENST00000442431,;PGK1,upstream_gene_variant,,ENST00000537456,;PGK1,intron_variant,,ENST00000491291,;PGK1,intron_variant,,ENST00000477335,;	T	ENSG00000102144	ENST00000373316	Transcript	5_prime_UTR_variant	108	.	.	.	.	rs192936390	.	.	1	PGK1	HGNC	8896	protein_coding	YES	CCDS14438.1	ENSP00000362413	PGK1_HUMAN	B7Z7A9_HUMAN,B4DHM5_HUMAN	UPI00000727EE	.	.	.	1/11	.	.	T:0.0050	T:0	T:0.0014	.	T:0.0179	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGTCGGCAG	byFrequency|byCluster|by1000G	5	ESCA
CWF19L1	0	.	GRCh37	10	102016226	102016226	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297A>G	p.%3D	p.K99K	ENST00000354105	5/14	45	30	14	58	58	0	CWF19L1,synonymous_variant,p.%3D,ENST00000354105,;RNU6-422P,upstream_gene_variant,,ENST00000384632,;CWF19L1,non_coding_transcript_exon_variant,,ENST00000473842,;CWF19L1,non_coding_transcript_exon_variant,,ENST00000496796,;CWF19L1,intron_variant,,ENST00000468709,;CWF19L1,intron_variant,,ENST00000482452,;CWF19L1,intron_variant,,ENST00000466955,;CWF19L1,upstream_gene_variant,,ENST00000478047,;	C	ENSG00000095485	ENST00000354105	Transcript	synonymous_variant	384	297	99	K	aaA/aaG	.	.	.	-1	CWF19L1	HGNC	25613	protein_coding	YES	CCDS7489.1	ENSP00000326411	C19L1_HUMAN	D3DR67_HUMAN	UPI0000070B3E	.	.	.	5/14	.	hmmpanther:PTHR12072:SF4,hmmpanther:PTHR12072,Gene3D:3.60.21.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACCTTTACG	.	5	ESCA
PCDH15	0	.	GRCh37	10	55581113	55581113	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*505C>T	.	.	ENST00000361849	34/34	22	16	6	24	24	0	PCDH15,3_prime_UTR_variant,,ENST00000395433,;PCDH15,3_prime_UTR_variant,,ENST00000320301,;PCDH15,3_prime_UTR_variant,,ENST00000395432,;PCDH15,3_prime_UTR_variant,,ENST00000373957,;PCDH15,3_prime_UTR_variant,,ENST00000361849,;PCDH15,3_prime_UTR_variant,,ENST00000395430,;PCDH15,intron_variant,,ENST00000395445,;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395438,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000373965,;PCDH15,downstream_gene_variant,,ENST00000437009,;PCDH15,non_coding_transcript_exon_variant,,ENST00000463095,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,;PCDH15,upstream_gene_variant,,ENST00000476074,;	A	ENSG00000150275	ENST00000361849	Transcript	3_prime_UTR_variant	6774	.	.	.	.	.	.	.	-1	PCDH15	HGNC	14674	protein_coding	YES	CCDS44404.1	ENSP00000354950	.	A2A3E7_HUMAN,A2A3D9_HUMAN	UPI0000EE048B	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTAGGTACA	.	5	ESCA
MYPN	0	.	GRCh37	10	69934313	69934313	+	Missense_Mutation	SNP	C	C	T	rs529221329	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2464C>T	p.Arg822Trp	p.R822W	ENST00000358913	11/20	28	22	5	33	33	0	MYPN,missense_variant,p.Arg822Trp,ENST00000358913,;MYPN,missense_variant,p.Arg822Trp,ENST00000540630,;MYPN,missense_variant,p.Arg547Trp,ENST00000354393,;	T	ENSG00000138347	ENST00000358913	Transcript	missense_variant	2952	2464	822	R/W	Cgg/Tgg	rs529221329	.	.	1	MYPN	HGNC	23246	protein_coding	YES	CCDS7275.1	ENSP00000351790	MYPN_HUMAN	A5PKT7_HUMAN	UPI00002288CF	.	tolerated(0.07)	benign(0.032)	11/20	.	hmmpanther:PTHR19897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCCGGATT	.	5	ESCA
NAV2	0	.	GRCh37	11	20067059	20067059	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3814A>G	p.Thr1272Ala	p.T1272A	ENST00000396087	15/41	29	22	7	32	32	0	NAV2,missense_variant,p.Thr1185Ala,ENST00000360655,;NAV2,missense_variant,p.Thr335Ala,ENST00000525322,;NAV2,missense_variant,p.Thr335Ala,ENST00000533917,;NAV2,missense_variant,p.Thr1201Ala,ENST00000527559,;NAV2,missense_variant,p.Thr1249Ala,ENST00000349880,;NAV2,missense_variant,p.Thr1272Ala,ENST00000396087,;NAV2,missense_variant,p.Thr1249Ala,ENST00000396085,;NAV2,missense_variant,p.Thr1203Ala,ENST00000540292,;NAV2,missense_variant,p.Thr335Ala,ENST00000311043,;NAV2,downstream_gene_variant,,ENST00000530408,;NAV2-AS2,intron_variant,,ENST00000533767,;NAV2,downstream_gene_variant,,ENST00000526675,;NAV2,downstream_gene_variant,,ENST00000534299,;	G	ENSG00000166833	ENST00000396087	Transcript	missense_variant	3913	3814	1272	T/A	Aca/Gca	.	.	.	1	NAV2	HGNC	15997	protein_coding	YES	CCDS58126.1	ENSP00000379396	NAV2_HUMAN	.	UPI00001E0580	.	deleterious(0)	probably_damaging(0.989)	15/41	.	hmmpanther:PTHR12784:SF6,hmmpanther:PTHR12784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAAACAGAC	.	5	ESCA
TSSC4	0	.	GRCh37	11	2423907	2423907	+	Missense_Mutation	SNP	G	G	A	rs778974704	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44G>A	p.Gly15Asp	p.G15D	ENST00000333256	3/3	43	22	21	75	75	0	TSSC4,missense_variant,p.Gly15Asp,ENST00000451491,;TSSC4,missense_variant,p.Gly15Asp,ENST00000496468,;TSSC4,missense_variant,p.Gly15Asp,ENST00000437110,;TSSC4,missense_variant,p.Gly15Asp,ENST00000435795,;TSSC4,missense_variant,p.Gly15Asp,ENST00000485682,;TSSC4,missense_variant,p.Gly15Asp,ENST00000333256,;TSSC4,intron_variant,,ENST00000380992,;TSSC4,intron_variant,,ENST00000440813,;TSSC4,intron_variant,,ENST00000380996,;TRPM5,downstream_gene_variant,,ENST00000533060,;TRPM5,downstream_gene_variant,,ENST00000533881,;TRPM5,downstream_gene_variant,,ENST00000528453,;TRPM5,downstream_gene_variant,,ENST00000452833,;TRPM5,downstream_gene_variant,,ENST00000155858,;AC124057.5,upstream_gene_variant,,ENST00000433035,;TSSC4,upstream_gene_variant,,ENST00000467308,;	A	ENSG00000184281	ENST00000333256	Transcript	missense_variant	487	44	15	G/D	gGc/gAc	rs778974704	.	.	1	TSSC4	HGNC	12386	protein_coding	YES	CCDS7735.1	ENSP00000331087	TSSC4_HUMAN	E9PME3_HUMAN,E9PL88_HUMAN,C9JHT9_HUMAN,C9JDU0_HUMAN	UPI0000161FA5	.	deleterious(0.01)	benign(0.107)	3/3	.	hmmpanther:PTHR13445,hmmpanther:PTHR13445:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGGCGAAC	.	5	ESCA
KBTBD4	0	.	GRCh37	11	47599482	47599482	+	Missense_Mutation	SNP	G	G	A	rs372890651	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118C>T	p.Arg40Trp	p.R40W	ENST00000430070	2/4	35	21	14	42	42	0	KBTBD4,missense_variant,p.Arg24Trp,ENST00000395288,;KBTBD4,missense_variant,p.Arg24Trp,ENST00000529499,;KBTBD4,missense_variant,p.Arg49Trp,ENST00000534239,;KBTBD4,missense_variant,p.Arg24Trp,ENST00000529946,;KBTBD4,missense_variant,p.Arg24Trp,ENST00000531067,;KBTBD4,missense_variant,p.Arg49Trp,ENST00000533290,;KBTBD4,missense_variant,p.Arg40Trp,ENST00000430070,;KBTBD4,missense_variant,p.Arg24Trp,ENST00000526005,;KBTBD4,missense_variant,p.Arg73Trp,ENST00000525720,;KBTBD4,3_prime_UTR_variant,,ENST00000450908,;NDUFS3,upstream_gene_variant,,ENST00000530295,;NDUFS3,upstream_gene_variant,,ENST00000529276,;NDUFS3,upstream_gene_variant,,ENST00000528192,;NDUFS3,upstream_gene_variant,,ENST00000534208,;NDUFS3,upstream_gene_variant,,ENST00000534716,;NDUFS3,upstream_gene_variant,,ENST00000263774,;RNU5E-10P,upstream_gene_variant,,ENST00000363506,;NDUFS3,intron_variant,,ENST00000533507,;PTPMT1,downstream_gene_variant,,ENST00000527079,;NDUFS3,upstream_gene_variant,,ENST00000527178,;NDUFS3,upstream_gene_variant,,ENST00000531351,;NDUFS3,upstream_gene_variant,,ENST00000525212,;KBTBD4,3_prime_UTR_variant,,ENST00000530668,;NDUFS3,upstream_gene_variant,,ENST00000524568,;NDUFS3,upstream_gene_variant,,ENST00000525378,;NDUFS3,upstream_gene_variant,,ENST00000533105,;	A	ENSG00000123444	ENST00000430070	Transcript	missense_variant	182	118	40	R/W	Cgg/Tgg	rs372890651	.	.	-1	KBTBD4	HGNC	23761	protein_coding	YES	CCDS44594.1	ENSP00000415106	KBTB4_HUMAN	E9PJY1_HUMAN,E9PJ66_HUMAN	UPI0000D4DDB6	.	deleterious(0.04)	probably_damaging(0.976)	2/4	.	hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF24,Gene3D:3.30.710.10	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACCGATCTT	byFrequency|byCluster	5	ESCA
OR52A4	0	.	GRCh37	11	5142488	5142488	+	RNA	SNP	G	G	A	rs770430743	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.911C>T	.	.	ENST00000498233	4/4	30	22	8	37	37	0	OR52A4,non_coding_transcript_exon_variant,,ENST00000498233,;OR52A4,non_coding_transcript_exon_variant,,ENST00000481634,;OR52A4,non_coding_transcript_exon_variant,,ENST00000472867,;OR52A4,non_coding_transcript_exon_variant,,ENST00000380369,;	A	ENSG00000205494	ENST00000498233	Transcript	non_coding_transcript_exon_variant	911	.	.	.	.	rs770430743	.	.	-1	OR52A4	HGNC	19579	processed_transcript	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATGAGCCA	.	5	ESCA
OR8H1	0	.	GRCh37	11	56058080	56058080	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459C>T	p.%3D	p.I153I	ENST00000313022	1/1	42	28	14	44	44	0	OR8H1,synonymous_variant,p.%3D,ENST00000313022,;	A	ENSG00000181693	ENST00000313022	Transcript	synonymous_variant	487	459	153	I	atC/atT	.	.	.	-1	OR8H1	HGNC	14824	protein_coding	YES	CCDS31526.1	ENSP00000323595	OR8H1_HUMAN	.	UPI0000041BC0	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTTGATAAA	.	5	ESCA
OR5R1	0	.	GRCh37	11	56185550	56185550	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159T>G	p.%3D	p.T53T	ENST00000312253	1/1	31	27	4	45	45	0	OR5R1,synonymous_variant,p.%3D,ENST00000312253,;OR5AL1,downstream_gene_variant,,ENST00000327258,;OR5AL1,downstream_gene_variant,,ENST00000440231,;	C	ENSG00000174942	ENST00000312253	Transcript	synonymous_variant	159	159	53	T	acT/acG	.	.	.	-1	OR5R1	HGNC	14841	protein_coding	YES	CCDS31530.1	ENSP00000308595	OR5R1_HUMAN	.	UPI000004B225	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF89,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTCGAGTATC	.	4	ESCA
OR52W1	0	.	GRCh37	11	6220894	6220894	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441T>C	p.%3D	p.G147G	ENST00000311352	1/1	60	45	15	84	83	0	OR52W1,synonymous_variant,p.%3D,ENST00000311352,;RP11-290F24.6,downstream_gene_variant,,ENST00000600308,;	C	ENSG00000175485	ENST00000311352	Transcript	synonymous_variant	519	441	147	G	ggT/ggC	.	.	.	1	OR52W1	HGNC	15239	protein_coding	YES	CCDS31407.1	ENSP00000309673	O52W1_HUMAN	.	UPI000004B213	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF58,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGGTTATGC	.	5	ESCA
TMEM134	0	.	GRCh37	11	67234982	67234984	+	In_Frame_Del	DEL	TGT	TGT	-	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	TGT	TGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.317_319delACA	p.Asn106del	p.N106del	ENST00000308022	3/7	45	31	14	65	65	0	TMEM134,inframe_deletion,p.Thr110del,ENST00000544903,;TMEM134,inframe_deletion,p.Asn97del,ENST00000452789,;TMEM134,inframe_deletion,p.Asn106del,ENST00000393877,;TMEM134,inframe_deletion,p.Asn106del,ENST00000308022,;TMEM134,non_coding_transcript_exon_variant,,ENST00000541059,;TMEM134,non_coding_transcript_exon_variant,,ENST00000535813,;TMEM134,inframe_deletion,p.Asn106del,ENST00000545682,;TMEM134,inframe_deletion,p.Thr101del,ENST00000536020,;TMEM134,inframe_deletion,p.Thr110del,ENST00000540133,;TMEM134,non_coding_transcript_exon_variant,,ENST00000501408,;TMEM134,non_coding_transcript_exon_variant,,ENST00000535585,;TMEM134,non_coding_transcript_exon_variant,,ENST00000537601,;TMEM134,non_coding_transcript_exon_variant,,ENST00000536773,;TMEM134,non_coding_transcript_exon_variant,,ENST00000541598,;TMEM134,downstream_gene_variant,,ENST00000538561,;TMEM134,upstream_gene_variant,,ENST00000543661,;TMEM134,upstream_gene_variant,,ENST00000535175,;	-	ENSG00000172663	ENST00000308022	Transcript	inframe_deletion	359-361	317-319	106-107	NT/T	aACAcc/acc	.	.	.	-1	TMEM134	HGNC	26142	protein_coding	YES	CCDS8167.1	ENSP00000312615	TM134_HUMAN	.	UPI0000071C39	.	.	.	3/7	.	hmmpanther:PTHR13558,Pfam_domain:PF05915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGCAGGTGTTGTAG	.	3	ESCA
STAB2	0	.	GRCh37	12	104063385	104063385	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2239C>A	p.Pro747Thr	p.P747T	ENST00000388887	21/69	42	32	10	44	44	0	STAB2,missense_variant,p.Pro747Thr,ENST00000388887,;RP11-341G23.3,upstream_gene_variant,,ENST00000550175,;	A	ENSG00000136011	ENST00000388887	Transcript	missense_variant	2443	2239	747	P/T	Cca/Aca	.	.	.	1	STAB2	HGNC	18629	protein_coding	YES	CCDS31888.1	ENSP00000373539	STAB2_HUMAN	H0YIF3_HUMAN	UPI00001ADDF4	.	deleterious(0.03)	probably_damaging(0.998)	21/69	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAATCCATGC	.	5	ESCA
ACACB	0	.	GRCh37	12	109675179	109675179	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4656C>T	p.%3D	p.I1552I	ENST00000338432	34/53	25	20	5	45	45	0	ACACB,synonymous_variant,p.%3D,ENST00000377854,;ACACB,synonymous_variant,p.%3D,ENST00000338432,;ACACB,synonymous_variant,p.%3D,ENST00000377848,;ACACB,synonymous_variant,p.%3D,ENST00000543201,;ACACB,synonymous_variant,p.%3D,ENST00000538526,;ACACB,upstream_gene_variant,,ENST00000537347,;ACACB,upstream_gene_variant,,ENST00000534852,;ACACB,downstream_gene_variant,,ENST00000542524,;	T	ENSG00000076555	ENST00000338432	Transcript	synonymous_variant	4775	4656	1552	I	atC/atT	.	.	.	1	ACACB	HGNC	85	protein_coding	YES	CCDS31898.1	ENSP00000341044	ACACB_HUMAN	F5H5C3_HUMAN,E9PEW7_HUMAN	UPI0000DBEEFB	.	.	.	34/53	.	hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF84,Pfam_domain:PF08326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGATCACAAA	.	5	ESCA
MSI1	0	.	GRCh37	12	120779721	120779721	+	3'UTR	SNP	C	C	T	rs534089226	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1209G>A	.	.	ENST00000257552	15/15	48	41	7	49	49	0	MSI1,3_prime_UTR_variant,,ENST00000257552,;MSI1,downstream_gene_variant,,ENST00000546985,;	T	ENSG00000135097	ENST00000257552	Transcript	3_prime_UTR_variant	2387	.	.	.	.	rs534089226	.	.	-1	MSI1	HGNC	7330	protein_coding	YES	CCDS9196.1	ENSP00000257552	MSI1H_HUMAN	B3KN16_HUMAN	UPI0000073DD8	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAACGCTCT	.	4	ESCA
AC024940.1	0	.	GRCh37	12	31477712	31477712	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-66G>A	.	.	ENST00000313737	1/1	28	24	4	77	77	0	AC024940.1,5_prime_UTR_variant,,ENST00000313737,;FAM60A,intron_variant,,ENST00000542983,;FAM60A,intron_variant,,ENST00000539004,;FAM60A,intron_variant,,ENST00000395766,;FAM60A,intron_variant,,ENST00000539409,;FAM60A,intron_variant,,ENST00000543615,;FAM60A,intron_variant,,ENST00000337682,;FAM60A,upstream_gene_variant,,ENST00000454658,;FAM60A,intron_variant,,ENST00000536836,;	A	ENSG00000177340	ENST00000313737	Transcript	5_prime_UTR_variant	463	.	.	.	.	.	.	.	1	AC024940.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000324000	.	.	UPI000013F617	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCGGAGCCT	.	2	ESCA
FAM155A	0	.	GRCh37	13	108518145	108518145	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.800C>G	p.Ala267Gly	p.A267G	ENST00000375915	1/3	34	24	10	52	52	0	FAM155A,missense_variant,p.Ala267Gly,ENST00000375915,;	C	ENSG00000204442	ENST00000375915	Transcript	missense_variant	939	800	267	A/G	gCt/gGt	COSM1606829	.	.	-1	FAM155A	HGNC	33877	protein_coding	YES	CCDS32006.1	ENSP00000365080	F155A_HUMAN	.	UPI000045882C	.	deleterious(0)	probably_damaging(0.941)	1/3	.	hmmpanther:PTHR15819,hmmpanther:PTHR15819:SF2	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.A267D|c.800C>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAAGCCTCG	.	5	ESCA
GPC6	0	.	GRCh37	13	94482729	94482729	+	Silent	SNP	C	C	A	rs780378622	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642C>A	p.%3D	p.A214A	ENST00000377047	3/9	76	45	31	116	116	0	GPC6,synonymous_variant,p.%3D,ENST00000377047,;GPC6-AS2,intron_variant,,ENST00000445540,;	A	ENSG00000183098	ENST00000377047	Transcript	synonymous_variant	1257	642	214	A	gcC/gcA	rs780378622	.	.	1	GPC6	HGNC	4454	protein_coding	YES	CCDS9469.1	ENSP00000366246	GPC6_HUMAN	.	UPI0000032F5B	.	.	.	3/9	.	hmmpanther:PTHR10822:SF26,hmmpanther:PTHR10822,Pfam_domain:PF01153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A214T|c.640G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGCCTTCAT	.	5	ESCA
YY1	0	.	GRCh37	14	100743822	100743822	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1130A>G	p.His377Arg	p.H377R	ENST00000262238	5/5	25	18	7	33	33	0	YY1,missense_variant,p.His153Arg,ENST00000554804,;YY1,missense_variant,p.His377Arg,ENST00000262238,;YY1,downstream_gene_variant,,ENST00000553625,;AL157871.2,downstream_gene_variant,,ENST00000553954,;YY1,non_coding_transcript_exon_variant,,ENST00000554579,;	G	ENSG00000100811	ENST00000262238	Transcript	missense_variant	1390	1130	377	H/R	cAt/cGt	.	.	.	1	YY1	HGNC	12856	protein_coding	YES	CCDS9957.1	ENSP00000262238	TYY1_HUMAN	G3V3M8_HUMAN	UPI00001378FC	.	deleterious(0)	probably_damaging(0.978)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR14003:SF10,hmmpanther:PTHR14003,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,PIRSF_domain:PIRSF037113,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCCATACCG	.	5	ESCA
MYH6	0	.	GRCh37	14	23871799	23871799	+	Missense_Mutation	SNP	C	C	T	rs760632098	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015G>A	p.Val339Met	p.V339M	ENST00000405093	12/39	25	13	12	44	44	0	MYH6,missense_variant,p.Val339Met,ENST00000405093,;MYH6,missense_variant,p.Val339Met,ENST00000356287,;MYH6,non_coding_transcript_exon_variant,,ENST00000557461,;	T	ENSG00000197616	ENST00000405093	Transcript	missense_variant	1086	1015	339	V/M	Gtg/Atg	rs760632098	.	.	-1	MYH6	HGNC	7576	protein_coding	YES	CCDS9600.1	ENSP00000386041	MYH6_HUMAN	Q9UQV1_HUMAN,A8CLL2_HUMAN	UPI0000160969	.	deleterious(0.01)	possibly_damaging(0.663)	12/39	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF260,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCACGTCAA	byFrequency	5	ESCA
MVP	0	.	GRCh37	16	29845364	29845364	+	Missense_Mutation	SNP	G	G	A	rs769471740	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554G>A	p.Arg185Gln	p.R185Q	ENST00000357402	5/15	21	15	5	27	27	0	MVP,missense_variant,p.Arg185Gln,ENST00000357402,;MVP,missense_variant,p.Arg185Gln,ENST00000395353,;MVP,missense_variant,p.Arg185Gln,ENST00000563915,;MVP,intron_variant,,ENST00000452209,;MVP,intron_variant,,ENST00000563558,;MVP,downstream_gene_variant,,ENST00000566066,;MVP,downstream_gene_variant,,ENST00000566252,;MVP,downstream_gene_variant,,ENST00000565164,;MVP,downstream_gene_variant,,ENST00000570234,;MVP,downstream_gene_variant,,ENST00000566554,;MVP,downstream_gene_variant,,ENST00000565830,;MVP,upstream_gene_variant,,ENST00000570061,;MVP,missense_variant,p.Arg47Gln,ENST00000563123,;MVP,3_prime_UTR_variant,,ENST00000562463,;MVP,non_coding_transcript_exon_variant,,ENST00000569612,;MVP,intron_variant,,ENST00000569887,;MVP,intron_variant,,ENST00000566859,;MVP,downstream_gene_variant,,ENST00000563096,;PAGR1,downstream_gene_variant,,ENST00000562285,;	A	ENSG00000013364	ENST00000357402	Transcript	missense_variant	692	554	185	R/Q	cGg/cAg	rs769471740	.	.	1	MVP	HGNC	7531	protein_coding	YES	CCDS10656.1	ENSP00000349977	MVP_HUMAN	H3BUK7_HUMAN,H3BRL2_HUMAN,H3BQK6_HUMAN,H3BP76_HUMAN,H3BNF2_HUMAN	UPI000012FA9C	.	tolerated(0.1)	probably_damaging(0.994)	5/15	.	PROSITE_profiles:PS51224,hmmpanther:PTHR14165:SF3,hmmpanther:PTHR14165,Pfam_domain:PF01505	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACCGGGACG	byFrequency	5	ESCA
NFAT5	0	.	GRCh37	16	69738348	69738348	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8094A>T	.	.	ENST00000432919	15/15	58	40	18	74	74	0	NFAT5,3_prime_UTR_variant,,ENST00000432919,;NFAT5,3_prime_UTR_variant,,ENST00000354436,;NFAT5,3_prime_UTR_variant,,ENST00000393742,;NFAT5,3_prime_UTR_variant,,ENST00000349945,;NQO1,downstream_gene_variant,,ENST00000379047,;NQO1,downstream_gene_variant,,ENST00000320623,;NQO1,downstream_gene_variant,,ENST00000561500,;snoU13,downstream_gene_variant,,ENST00000459361,;RP11-311C24.1,non_coding_transcript_exon_variant,,ENST00000561622,;NFAT5,3_prime_UTR_variant,,ENST00000426654,;	T	ENSG00000102908	ENST00000432919	Transcript	3_prime_UTR_variant	13952	.	.	.	.	.	.	.	1	NFAT5	HGNC	7774	protein_coding	YES	CCDS45518.1	ENSP00000396538	NFAT5_HUMAN	.	UPI000049DE1B	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATATGGCT	.	5	ESCA
SPNS2	0	.	GRCh37	17	4435944	4435944	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.900C>T	p.%3D	p.T300T	ENST00000329078	6/13	22	14	7	24	24	0	SPNS2,synonymous_variant,p.%3D,ENST00000329078,;SPNS2,upstream_gene_variant,,ENST00000571386,;SPNS2,upstream_gene_variant,,ENST00000570979,;SPNS2,upstream_gene_variant,,ENST00000573106,;SPNS2,upstream_gene_variant,,ENST00000571668,;SPNS2,upstream_gene_variant,,ENST00000570641,;SPNS2,upstream_gene_variant,,ENST00000576635,;SPNS2,upstream_gene_variant,,ENST00000573990,;	T	ENSG00000183018	ENST00000329078	Transcript	synonymous_variant	1110	900	300	T	acC/acT	.	.	.	1	SPNS2	HGNC	26992	protein_coding	YES	CCDS42237.1	ENSP00000333292	SPNS2_HUMAN	.	UPI00001C1FCB	.	.	.	6/13	.	PROSITE_profiles:PS50850,hmmpanther:PTHR24001,hmmpanther:PTHR24001:SF1,Pfam_domain:PF07690,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGACCTCATG	.	5	ESCA
FTSJ3	0	.	GRCh37	17	61899154	61899155	+	In_Frame_Ins	INS	-	-	CTC	rs751549614	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1522_1524dupGAG	p.Glu508dup	p.E508dup	ENST00000427159	15/21	20	13	6	29	29	0	FTSJ3,inframe_insertion,p.Glu508dup,ENST00000427159,;FTSJ3,downstream_gene_variant,,ENST00000584574,;DDX42,downstream_gene_variant,,ENST00000389924,;DDX42,downstream_gene_variant,,ENST00000578681,;FTSJ3,downstream_gene_variant,,ENST00000580272,;DDX42,downstream_gene_variant,,ENST00000359353,;DDX42,downstream_gene_variant,,ENST00000583590,;FTSJ3,downstream_gene_variant,,ENST00000581209,;DDX42,downstream_gene_variant,,ENST00000457800,;DDX42,downstream_gene_variant,,ENST00000582985,;FTSJ3,3_prime_UTR_variant,,ENST00000579831,;FTSJ3,non_coding_transcript_exon_variant,,ENST00000583202,;FTSJ3,non_coding_transcript_exon_variant,,ENST00000583901,;FTSJ3,downstream_gene_variant,,ENST00000580376,;DDX42,downstream_gene_variant,,ENST00000579539,;FTSJ3,downstream_gene_variant,,ENST00000579569,;FTSJ3,downstream_gene_variant,,ENST00000582476,;FTSJ3,downstream_gene_variant,,ENST00000577263,;FTSJ3,downstream_gene_variant,,ENST00000580129,;DDX42,downstream_gene_variant,,ENST00000578593,;FTSJ3,downstream_gene_variant,,ENST00000580290,;DDX42,downstream_gene_variant,,ENST00000584010,;FTSJ3,downstream_gene_variant,,ENST00000584193,;DDX42,downstream_gene_variant,,ENST00000581767,;	CTC	ENSG00000108592	ENST00000427159	Transcript	inframe_insertion	2170-2171	1524-1525	508-509	-/E	-/GAG	rs751549614	.	.	-1	FTSJ3	HGNC	17136	protein_coding	YES	CCDS11644.1	ENSP00000396673	SPB1_HUMAN	J3QSE2_HUMAN,J3QRS5_HUMAN,J3QKT6_HUMAN,J3KS36_HUMAN	UPI000013C87B	.	.	.	15/21	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,HAMAP:MF_03163,hmmpanther:PTHR10920,hmmpanther:PTHR10920:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGGATTCTCCT	.	2	ESCA
TP53	0	.	GRCh37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.818G>A	p.Arg273His	p.R273H	ENST00000269305	8/11	23	13	9	21	21	0	TP53,missense_variant,p.Arg273His,ENST00000420246,;TP53,missense_variant,p.Arg273His,ENST00000269305,;TP53,missense_variant,p.Arg141His,ENST00000509690,;TP53,missense_variant,p.Arg273His,ENST00000359597,;TP53,missense_variant,p.Arg273His,ENST00000445888,;TP53,missense_variant,p.Arg273His,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1008	818	273	R/H	cGt/cAt	CM920677,CM010472,rs28934576,CM004342,TP53_g.13798G>C,TP53_g.13798del,TP53_g.13798G>A,TP53_g.13798G>T,COSM10660,COSM43896,COSM44440,COSM10779,COSM318169,COSM99729,COSM165077,COSM3356963,COSM3675521,COSM1640828,COSM1645335,COSM1646808	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.13)	possibly_damaging(0.631)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	T:0.0002	T:0,T:0	T:0,T:0	.	T:0,T:0	T:0.001,T:0.001	T:0,T:0	.	.	pathogenic	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	25105660	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R273H|c.818G>A|116,SITE|p.R273H|c.818G>A|64,SITE|p.R273H|c.818G>A|588,SITE|p.R273H|c.818G>A|83,CODON|p.0?|c.1_1182del1182|6,CODON|p.R273L|c.818G>T|98,CODON|p.R273P|c.818G>C|4,CODON|p.R273L|c.818G>T|5,CODON|p.R273P|c.818G>C|29,CODON|p.R273L|c.818G>T|18,CODON|p.R273L|c.818G>T|12,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3,BUFFER|p.E271Q|c.811G>C|4,BUFFER|p.E271K|c.811G>A|35,BUFFER|p.E271*|c.811G>T|16,BUFFER|p.E271*|c.811G>T|3,BUFFER|p.E271K|c.811G>A|13,BUFFER|p.E271K|c.811G>A|4,BUFFER|p.E271K|c.811G>A|8,BUFFER|p.F270L|c.810T>G|4,BUFFER|p.F270L|c.810T>A|5,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270Y|c.809T>A|5,BUFFER|p.F270C|c.809T>G|16,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270S|c.809T>C|14,BUFFER|p.F270S|c.809T>C|6,BUFFER|p.F270L|c.808T>C|16,BUFFER|p.F270I|c.808T>A|3,BUFFER|p.F270V|c.808T>G|8,BUFFER|p.F270L|c.808T>C|3,BUFFER|p.F270I|c.808T>A|6,BUFFER|p.S269S|c.807C>T|3	MUTECT|MUSE	AAACACGCACC	byCluster|by1000G	2	ESCA
TP53	0	.	GRCh37	17	7577124	7577124	+	Missense_Mutation	SNP	C	C	T	rs121912657	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814G>A	p.Val272Met	p.V272M	ENST00000269305	8/11	22	15	6	20	20	0	TP53,missense_variant,p.Val272Met,ENST00000420246,;TP53,missense_variant,p.Val272Met,ENST00000269305,;TP53,missense_variant,p.Val140Met,ENST00000509690,;TP53,missense_variant,p.Val272Met,ENST00000359597,;TP53,missense_variant,p.Val272Met,ENST00000445888,;TP53,missense_variant,p.Val272Met,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1004	814	272	V/M	Gtg/Atg	CM920676,rs121912657,TP53_g.13794G>T,TP53_g.13794del,TP53_g.13794G>C,TP53_g.13794G>A,COSM10859,COSM10891,COSM13421,COSM45898,COSM99950,COSM212313,COSM1177737,COSM3388172,COSM3773300,COSM1645249,COSM2744536	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.997)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	uncertain_significance,pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S269S|c.807C>T|3,BUFFER|p.S269N|c.806G>A|4,BUFFER|p.S269C|c.805A>T|4,BUFFER|p.S269G|c.805A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCACCTCAA	byFrequency|byCluster	5	ESCA
FSCN2	0	.	GRCh37	17	79502107	79502107	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.856G>A	p.Glu286Lys	p.E286K	ENST00000334850	2/5	17	10	6	26	26	0	FSCN2,missense_variant,p.Glu286Lys,ENST00000417245,;FSCN2,missense_variant,p.Glu286Lys,ENST00000334850,;C17orf70,downstream_gene_variant,,ENST00000425898,;C17orf70,downstream_gene_variant,,ENST00000537152,;C17orf70,downstream_gene_variant,,ENST00000327787,;C17orf70,downstream_gene_variant,,ENST00000443656,;FSCN2,upstream_gene_variant,,ENST00000527221,;	A	ENSG00000186765	ENST00000334850	Transcript	missense_variant	856	856	286	E/K	Gaa/Aaa	.	.	.	1	FSCN2	HGNC	3960	protein_coding	YES	CCDS45810.1	ENSP00000334665	FSCN2_HUMAN	.	UPI0000E5925D	.	tolerated(0.2)	probably_damaging(0.925)	2/5	.	hmmpanther:PTHR10551:SF4,hmmpanther:PTHR10551,Pfam_domain:PF06268,Gene3D:2.80.10.50,PIRSF_domain:PIRSF005682	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATGAACTA	.	5	ESCA
DSC2	0	.	GRCh37	18	28662348	28662348	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1119C>A	p.%3D	p.I373I	ENST00000280904	9/16	92	78	14	94	94	0	DSC2,synonymous_variant,p.%3D,ENST00000251081,;DSC2,synonymous_variant,p.%3D,ENST00000280904,;	T	ENSG00000134755	ENST00000280904	Transcript	synonymous_variant	1563	1119	373	I	atC/atA	.	.	.	-1	DSC2	HGNC	3036	protein_coding	YES	CCDS11892.1	ENSP00000280904	DSC2_HUMAN	A9X9L1_HUMAN	UPI00001298F9	.	.	.	9/16	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF0,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTAAGATTTC	.	4	ESCA
L3MBTL4	0	.	GRCh37	18	6215816	6215816	+	Missense_Mutation	SNP	T	T	A	rs139480207	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.803A>T	p.Asn268Ile	p.N268I	ENST00000284898	11/20	61	52	9	73	73	0	L3MBTL4,missense_variant,p.Asn268Ile,ENST00000317931,;L3MBTL4,missense_variant,p.Asn268Ile,ENST00000284898,;L3MBTL4,missense_variant,p.Asn268Ile,ENST00000400105,;L3MBTL4,missense_variant,p.Asn268Ile,ENST00000400104,;L3MBTL4,missense_variant,p.Asn81Ile,ENST00000535782,;	A	ENSG00000154655	ENST00000284898	Transcript	missense_variant	1004	803	268	N/I	aAt/aTt	rs139480207	.	.	-1	L3MBTL4	HGNC	26677	protein_coding	YES	CCDS11839.2	ENSP00000284898	LMBL4_HUMAN	J3QLK8_HUMAN,J3KS41_HUMAN,J3KRN7_HUMAN	UPI000013DDC0	.	deleterious(0.03)	benign(0.339)	11/20	.	hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF78,Gene3D:2.30.30.160,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	A:0.0002	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAAATTTTCT	byFrequency|byCluster	4	ESCA
ZNF99	0	.	GRCh37	19	22941058	22941058	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1653C>A	p.%3D	p.T551T	ENST00000596209	4/4	50	38	12	82	82	0	ZNF99,synonymous_variant,p.%3D,ENST00000397104,;ZNF99,synonymous_variant,p.%3D,ENST00000596209,;CTC-451A6.4,upstream_gene_variant,,ENST00000442497,;	T	ENSG00000213973	ENST00000596209	Transcript	synonymous_variant	1744	1653	551	T	acC/acA	.	.	.	-1	ZNF99	HGNC	13175	protein_coding	YES	CCDS59369.1	ENSP00000472969	.	M0R335_HUMAN	UPI0000426011	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24375:SF102,hmmpanther:PTHR24375,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAAGGGTTGA	.	5	ESCA
ZNF91	0	.	GRCh37	19	23578124	23578124	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.30+3G>A	.	.	ENST00000300619	.	51	41	9	97	97	0	ZNF91,splice_region_variant,,ENST00000595533,;ZNF91,splice_region_variant,,ENST00000599743,;ZNF91,splice_region_variant,,ENST00000397082,;ZNF91,splice_region_variant,,ENST00000300619,;CTB-175P5.4,downstream_gene_variant,,ENST00000596283,;CTB-175P5.4,downstream_gene_variant,,ENST00000600643,;ZNF91,splice_region_variant,,ENST00000596989,;	T	ENSG00000167232	ENST00000300619	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	ZNF91	HGNC	13166	protein_coding	YES	CCDS42541.1	ENSP00000300619	ZNF91_HUMAN	M0R186_HUMAN	UPI00002038F9	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCTCACCAT	.	4	ESCA
PSG4	0	.	GRCh37	19	43698568	43698568	+	Missense_Mutation	SNP	A	A	T	rs143496527	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1167T>A	p.Ser389Arg	p.S389R	ENST00000405312	5/6	143	77	66	223	222	0	PSG4,missense_variant,p.Ser267Arg,ENST00000596907,;PSG4,missense_variant,p.Ser174Arg,ENST00000599391,;PSG4,missense_variant,p.Ser296Arg,ENST00000244295,;PSG4,missense_variant,p.Ser181Arg,ENST00000597374,;PSG4,missense_variant,p.Ser389Arg,ENST00000405312,;PSG4,missense_variant,p.Ser296Arg,ENST00000433626,;PSG4,downstream_gene_variant,,ENST00000451895,;PSG4,downstream_gene_variant,,ENST00000600572,;PSG4,downstream_gene_variant,,ENST00000599746,;PSG4,downstream_gene_variant,,ENST00000599371,;PSG4,3_prime_UTR_variant,,ENST00000601041,;PSG4,non_coding_transcript_exon_variant,,ENST00000597349,;PSG4,non_coding_transcript_exon_variant,,ENST00000490769,;PSG4,downstream_gene_variant,,ENST00000595949,;PSG4,downstream_gene_variant,,ENST00000495316,;PSG4,downstream_gene_variant,,ENST00000596199,;	T	ENSG00000243137	ENST00000405312	Transcript	missense_variant	1405	1167	389	S/R	agT/agA	rs143496527	.	.	-1	PSG4	HGNC	9521	protein_coding	YES	CCDS46093.1	ENSP00000384770	PSG4_HUMAN	M0QYU2_HUMAN	UPI000034ECBA	.	tolerated(0.15)	benign(0.044)	5/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF105,hmmpanther:PTHR19955,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCCACTATG	byCluster|by1000G	5	ESCA
RTN2	0	.	GRCh37	19	45997462	45997462	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.776C>T	p.Thr259Met	p.T259M	ENST00000245923	4/11	35	26	9	70	70	0	RTN2,missense_variant,p.Thr259Met,ENST00000344680,;RTN2,missense_variant,p.Thr259Met,ENST00000245923,;RTN2,5_prime_UTR_variant,,ENST00000590526,;PPM1N,intron_variant,,ENST00000401705,;PPM1N,upstream_gene_variant,,ENST00000451287,;RTN2,upstream_gene_variant,,ENST00000430715,;PPM1N,upstream_gene_variant,,ENST00000456399,;PPM1N,upstream_gene_variant,,ENST00000396737,;PPM1N,upstream_gene_variant,,ENST00000324688,;RTN2,upstream_gene_variant,,ENST00000590746,;RTN2,downstream_gene_variant,,ENST00000589384,;RTN2,upstream_gene_variant,,ENST00000588036,;RTN2,missense_variant,p.Thr259Met,ENST00000587597,;RTN2,missense_variant,p.Thr259Met,ENST00000591286,;RTN2,non_coding_transcript_exon_variant,,ENST00000592064,;PPM1N,upstream_gene_variant,,ENST00000415077,;RTN2,upstream_gene_variant,,ENST00000589628,;	A	ENSG00000125744	ENST00000245923	Transcript	missense_variant	1012	776	259	T/M	aCg/aTg	COSM4079369	.	.	-1	RTN2	HGNC	10468	protein_coding	YES	CCDS12665.1	ENSP00000245923	RTN2_HUMAN	K7EMR7_HUMAN	UPI00001352DC	.	deleterious_low_confidence(0.05)	benign(0.075)	4/11	.	hmmpanther:PTHR10994:SF66,hmmpanther:PTHR10994	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCCGTGCTA	.	5	ESCA
OPA3	0	.	GRCh37	19	46032310	46032310	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4G>T	.	.	ENST00000323060	2/2	18	8	10	18	18	0	OPA3,3_prime_UTR_variant,,ENST00000323060,;VASP,downstream_gene_variant,,ENST00000245932,;VASP,downstream_gene_variant,,ENST00000587444,;VASP,downstream_gene_variant,,ENST00000588273,;VASP,downstream_gene_variant,,ENST00000588463,;VASP,downstream_gene_variant,,ENST00000586014,;VASP,downstream_gene_variant,,ENST00000588482,;	A	ENSG00000125741	ENST00000323060	Transcript	3_prime_UTR_variant	625	.	.	.	.	.	.	.	-1	OPA3	HGNC	8142	protein_coding	YES	CCDS33052.1	ENSP00000319817	OPA3_HUMAN	.	UPI0000140FD5	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CGAGACCTCCT	.	4	ESCA
HRC	0	.	GRCh37	19	49656964	49656964	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1531C>T	p.His511Tyr	p.H511Y	ENST00000252825	1/6	25	13	11	21	21	0	HRC,missense_variant,p.His511Tyr,ENST00000595625,;HRC,missense_variant,p.His511Tyr,ENST00000252825,;TRPM4,upstream_gene_variant,,ENST00000598691,;PPFIA3,downstream_gene_variant,,ENST00000334186,;PPFIA3,downstream_gene_variant,,ENST00000602897,;TRPM4,upstream_gene_variant,,ENST00000355712,;HRC,upstream_gene_variant,,ENST00000598858,;TRPM4,upstream_gene_variant,,ENST00000427978,;PPFIA3,downstream_gene_variant,,ENST00000602351,;TRPM4,upstream_gene_variant,,ENST00000252826,;PPFIA3,downstream_gene_variant,,ENST00000602848,;PPFIA3,downstream_gene_variant,,ENST00000602783,;TRPM4,upstream_gene_variant,,ENST00000598502,;TRPM4,upstream_gene_variant,,ENST00000598697,;TRPM4,upstream_gene_variant,,ENST00000599628,;TRPM4,upstream_gene_variant,,ENST00000595519,;TRPM4,upstream_gene_variant,,ENST00000596338,;PPFIA3,downstream_gene_variant,,ENST00000602655,;PPFIA3,downstream_gene_variant,,ENST00000602905,;HRC,upstream_gene_variant,,ENST00000595167,;	A	ENSG00000130528	ENST00000252825	Transcript	missense_variant	1718	1531	511	H/Y	Cat/Tat	.	.	.	-1	HRC	HGNC	5178	protein_coding	YES	CCDS12759.1	ENSP00000252825	SRCH_HUMAN	.	UPI0000135F21	.	deleterious(0.05)	possibly_damaging(0.844)	1/6	.	hmmpanther:PTHR15054:SF2,hmmpanther:PTHR15054	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATGATGGG	.	5	ESCA
KLK11	0	.	GRCh37	19	51530744	51530744	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.30delG	p.Trp10Ter	p.W10*	ENST00000594768	1/6	57	48	9	87	87	0	KLK11,frameshift_variant,p.Trp10Ter,ENST00000594768,;KLK11,intron_variant,,ENST00000319720,;KLK11,intron_variant,,ENST00000391804,;KLK11,upstream_gene_variant,,ENST00000453757,;KLK11,upstream_gene_variant,,ENST00000600362,;KLK12,downstream_gene_variant,,ENST00000525263,;KLK11,upstream_gene_variant,,ENST00000601671,;KLK12,downstream_gene_variant,,ENST00000250352,;KLK12,downstream_gene_variant,,ENST00000529888,;KLK12,downstream_gene_variant,,ENST00000250351,;KLK11,upstream_gene_variant,,ENST00000593681,;KLK12,downstream_gene_variant,,ENST00000319590,;KLK11,upstream_gene_variant,,ENST00000598799,;CTC-518B2.9,upstream_gene_variant,,ENST00000594910,;KLK11,upstream_gene_variant,,ENST00000594458,;KLK11,frameshift_variant,p.Trp10Ter,ENST00000319756,;KLK12,downstream_gene_variant,,ENST00000530943,;KLK12,downstream_gene_variant,,ENST00000531374,;KLK12,downstream_gene_variant,,ENST00000526824,;KLK11,upstream_gene_variant,,ENST00000594827,;	-	ENSG00000167757	ENST00000594768	Transcript	frameshift_variant	216	30	10	W/X	tgG/tg	.	.	.	-1	KLK11	HGNC	6359	protein_coding	YES	CCDS12818.1	ENSP00000473047	KLK11_HUMAN	M0QZV0_HUMAN,M0QZI8_HUMAN	UPI000002ACDC	.	.	.	1/6	.	hmmpanther:PTHR24275:SF13,hmmpanther:PTHR24275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGACTTCCAGTC	.	3	ESCA
PRAMEF13	0	.	GRCh37	1	13448426	13448426	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1049C>G	p.Ser350Cys	p.S350C	ENST00000376132	4/4	20	9	11	38	38	0	PRAMEF13,missense_variant,p.Ser350Cys,ENST00000376132,;	C	ENSG00000204495	ENST00000376132	Transcript	missense_variant	1152	1049	350	S/C	tCt/tGt	.	.	.	-1	PRAMEF13	HGNC	13262	protein_coding	YES	CCDS41257.1	ENSP00000365302	PRA13_HUMAN	.	UPI00001D80B6	.	deleterious(0)	possibly_damaging(0.646)	4/4	.	hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF2,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CGAGAGAGGCA	.	3	ESCA
GJA8	0	.	GRCh37	1	147380384	147380384	+	Missense_Mutation	SNP	G	G	T	rs781949456	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302G>T	p.Arg101Leu	p.R101L	ENST00000240986	2/2	34	15	18	30	30	0	GJA8,missense_variant,p.Arg101Leu,ENST00000240986,;GJA8,missense_variant,p.Arg101Leu,ENST00000369235,;	T	ENSG00000121634	ENST00000240986	Transcript	missense_variant	355	302	101	R/L	cGc/cTc	rs781949456,COSM1253258	.	.	1	GJA8	HGNC	4281	protein_coding	YES	CCDS30834.1	ENSP00000240986	CXA8_HUMAN	.	UPI0000049BA0	.	deleterious(0.01)	probably_damaging(0.978)	2/2	.	Gene3D:2zw3A00,Pfam_domain:PF00029,hmmpanther:PTHR11984:SF19,hmmpanther:PTHR11984	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTCCGCATGG	byFrequency	5	ESCA
POGZ	0	.	GRCh37	1	151400613	151400613	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.845C>T	p.Thr282Met	p.T282M	ENST00000271715	6/19	41	24	16	63	63	0	POGZ,missense_variant,p.Thr282Met,ENST00000271715,;POGZ,missense_variant,p.Thr229Met,ENST00000392723,;POGZ,missense_variant,p.Thr282Met,ENST00000409503,;POGZ,missense_variant,p.Thr229Met,ENST00000361398,;POGZ,missense_variant,p.Thr229Met,ENST00000531094,;POGZ,missense_variant,p.Thr187Met,ENST00000368863,;POGZ,missense_variant,p.Thr229Met,ENST00000491586,;POGZ,coding_sequence_variant,p.%3D,ENST00000594456,;POGZ,intron_variant,,ENST00000540984,;POGZ,downstream_gene_variant,,ENST00000533461,;POGZ,upstream_gene_variant,,ENST00000529669,;POGZ,downstream_gene_variant,,ENST00000533351,;POGZ,downstream_gene_variant,,ENST00000450842,;POGZ,non_coding_transcript_exon_variant,,ENST00000485040,;POGZ,non_coding_transcript_exon_variant,,ENST00000358476,;POGZ,upstream_gene_variant,,ENST00000482678,;POGZ,upstream_gene_variant,,ENST00000495253,;POGZ,upstream_gene_variant,,ENST00000441516,;POGZ,downstream_gene_variant,,ENST00000467287,;	A	ENSG00000143442	ENST00000271715	Transcript	missense_variant	1160	845	282	T/M	aCg/aTg	.	.	.	-1	POGZ	HGNC	18801	protein_coding	YES	CCDS997.1	ENSP00000271715	POGZ_HUMAN	F5H8H4_HUMAN,E9PJY9_HUMAN,E9PIR8_HUMAN	UPI000035895F	.	tolerated(0.25)	benign(0.294)	6/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTCGTGGTC	.	5	ESCA
OR6K6	0	.	GRCh37	1	158725227	158725227	+	Missense_Mutation	SNP	G	G	A	rs764949730	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.622G>A	p.Asp208Asn	p.D208N	ENST00000368144	1/1	20	16	4	26	26	0	OR6K6,missense_variant,p.Asp208Asn,ENST00000368144,;	A	ENSG00000180433	ENST00000368144	Transcript	missense_variant	718	622	208	D/N	Gat/Aat	rs764949730	.	.	1	OR6K6	HGNC	15033	protein_coding	YES	CCDS30904.1	ENSP00000357126	OR6K6_HUMAN	.	UPI000015F229	.	deleterious(0.02)	probably_damaging(0.993)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF132,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGTGATTTC	.	4	ESCA
PAPPA2	0	.	GRCh37	1	176659289	176659289	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2154C>A	p.Ser718Arg	p.S718R	ENST00000367662	5/23	37	32	5	37	37	0	PAPPA2,missense_variant,p.Ser718Arg,ENST00000367661,;PAPPA2,missense_variant,p.Ser718Arg,ENST00000367662,;	A	ENSG00000116183	ENST00000367662	Transcript	missense_variant	3318	2154	718	S/R	agC/agA	.	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	deleterious(0)	benign(0.077)	5/23	.	hmmpanther:PTHR19325:SF349,hmmpanther:PTHR19325,Pfam_domain:PF05572,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAGCCCAGC	.	4	ESCA
RP11-480I12.4	0	.	GRCh37	1	202794595	202794595	+	5'UTR	SNP	C	C	A	rs768692952	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-40C>A	.	.	ENST00000330493	3/3	16	10	6	20	20	0	RP11-480I12.4,5_prime_UTR_variant,,ENST00000549576,;RP11-480I12.4,5_prime_UTR_variant,,ENST00000330493,;	A	ENSG00000184774	ENST00000330493	Transcript	5_prime_UTR_variant	1052	.	.	.	.	rs768692952	.	.	1	RP11-480I12.4	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000446921	MGT4L_HUMAN	.	UPI0000161151	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGGCGAATT	.	5	ESCA
PHACTR4	0	.	GRCh37	1	28696280	28696311	+	5'UTR	DEL	GTAGGATTTCCGGGAGAGGCTGCTGTGGAGGC	GTAGGATTTCCGGGAGAGGCTGCTGTGGAGGC	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	GTAGGATTTCCGGGAGAGGCTGCTGTGGAGGC	GTAGGATTTCCGGGAGAGGCTGCTGTGGAGGC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-95_-64delGTAGGATTTCCGGGAGAGGCTGCTGTGGAGGCinsT	.	.	ENST00000373839	1/14	97	48	49	80	80	0	PHACTR4,5_prime_UTR_variant,,ENST00000373839,;PHACTR4,non_coding_transcript_exon_variant,,ENST00000493669,;PHACTR4,non_coding_transcript_exon_variant,,ENST00000463428,;	T	ENSG00000204138	ENST00000373839	Transcript	5_prime_UTR_variant	167-198	.	.	.	.	.	.	.	1	PHACTR4	HGNC	25793	protein_coding	.	CCDS41293.1	ENSP00000362945	PHAR4_HUMAN	.	UPI000007419C	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCCAGGTAGGATTTCCGGGAGAGGCTGCTGTGGAGGCTGAGG	.	3	ESCA
ARHGEF16	0	.	GRCh37	1	3389659	3389659	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1040A>T	p.Glu347Val	p.E347V	ENST00000378378	7/15	31	10	21	37	37	0	ARHGEF16,missense_variant,p.Glu59Val,ENST00000445297,;ARHGEF16,missense_variant,p.Glu51Val,ENST00000413250,;ARHGEF16,missense_variant,p.Glu59Val,ENST00000378371,;ARHGEF16,missense_variant,p.Glu347Val,ENST00000378378,;ARHGEF16,missense_variant,p.Glu59Val,ENST00000378373,;ARHGEF16,missense_variant,p.Glu51Val,ENST00000418137,;ARHGEF16,non_coding_transcript_exon_variant,,ENST00000464620,;ARHGEF16,non_coding_transcript_exon_variant,,ENST00000485984,;	T	ENSG00000130762	ENST00000378378	Transcript	missense_variant	1445	1040	347	E/V	gAg/gTg	.	.	.	1	ARHGEF16	HGNC	15515	protein_coding	YES	CCDS46.2	ENSP00000367629	ARHGG_HUMAN	B0QZD3_HUMAN	UPI00002039A3	.	deleterious(0)	possibly_damaging(0.899)	7/15	.	PROSITE_profiles:PS50010,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF3,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGAGCAGC	.	5	ESCA
CSMD2	0	.	GRCh37	1	34025005	34025005	+	Intron	SNP	C	C	T	rs763974395	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8311+8188G>A	.	.	ENST00000241312	.	95	61	33	67	67	0	CSMD2,missense_variant,p.Asp2817Asn,ENST00000373381,;CSMD2,non_coding_transcript_exon_variant,,ENST00000465819,;CSMD2,intron_variant,,ENST00000241312,;	T	ENSG00000121904	ENST00000241312	Transcript	intron_variant	.	.	.	.	.	rs763974395	.	.	-1	CSMD2	HGNC	19290	nonsense_mediated_decay	YES	CCDS380.1	ENSP00000241312	CSMD2_HUMAN	.	UPI00004561AB	.	.	.	.	54/69	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACATCGTTGA	byFrequency	5	ESCA
DLGAP3	0	.	GRCh37	1	35370962	35370962	+	Missense_Mutation	SNP	C	C	T	rs777705397	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.23G>A	p.Arg8Gln	p.R8Q	ENST00000373347	3/12	81	69	11	64	64	0	DLGAP3,missense_variant,p.Arg8Gln,ENST00000373347,;DLGAP3,missense_variant,p.Arg8Gln,ENST00000235180,;DLGAP3,non_coding_transcript_exon_variant,,ENST00000495979,;	T	ENSG00000116544	ENST00000373347	Transcript	missense_variant	292	23	8	R/Q	cGa/cAa	rs777705397,COSM1342095	.	.	-1	DLGAP3	HGNC	30368	protein_coding	YES	CCDS30670.1	ENSP00000362444	DLGP3_HUMAN	B4DH33_HUMAN	UPI00003D4D81	.	deleterious_low_confidence(0)	probably_damaging(0.953)	3/12	.	hmmpanther:PTHR12353:SF4,hmmpanther:PTHR12353	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCTCGGTCG	.	4	ESCA
COL18A1	0	.	GRCh37	21	46893894	46893894	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1277G>T	p.Gly426Val	p.G426V	ENST00000355480	3/41	30	22	8	70	70	0	COL18A1,missense_variant,p.Gly661Val,ENST00000359759,;COL18A1,missense_variant,p.Gly426Val,ENST00000355480,;COL18A1,missense_variant,p.Gly246Val,ENST00000400337,;	T	ENSG00000182871	ENST00000355480	Transcript	missense_variant	1319	1277	426	G/V	gGg/gTg	COSM3551589,COSM3551590	.	.	1	COL18A1	HGNC	2195	protein_coding	YES	CCDS42972.1	ENSP00000347665	COIA1_HUMAN	D3DSM5_HUMAN	UPI000016A19D	.	.	unknown(0)	3/41	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF390	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGGGGTGA	.	5	ESCA
ERCC3	0	.	GRCh37	2	128036799	128036799	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1680C>A	p.%3D	p.V560V	ENST00000285398	10/15	48	31	17	97	97	0	ERCC3,synonymous_variant,p.%3D,ENST00000493187,;ERCC3,synonymous_variant,p.%3D,ENST00000285398,;ERCC3,3_prime_UTR_variant,,ENST00000426778,;ERCC3,3_prime_UTR_variant,,ENST00000445889,;	T	ENSG00000163161	ENST00000285398	Transcript	synonymous_variant	1775	1680	560	V	gtC/gtA	.	.	.	-1	ERCC3	HGNC	3435	protein_coding	YES	CCDS2144.1	ENSP00000285398	ERCC3_HUMAN	G3V1S1_HUMAN	UPI000013900E	.	.	.	10/15	.	PROSITE_profiles:PS51194,hmmpanther:PTHR11274:SF0,hmmpanther:PTHR11274,TIGRFAM_domain:TIGR00603,Gene3D:3.40.50.300,Superfamily_domains:SSF52540,Prints_domain:PR00851	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAAGACAAT	.	5	ESCA
SAP130	0	.	GRCh37	2	128699019	128699019	+	3'UTR	SNP	A	A	T	rs189128124	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*561T>A	.	.	ENST00000357702	21/21	10	3	7	18	18	0	SAP130,3_prime_UTR_variant,,ENST00000259235,;SAP130,3_prime_UTR_variant,,ENST00000259234,;SAP130,3_prime_UTR_variant,,ENST00000357702,;	T	ENSG00000136715	ENST00000357702	Transcript	3_prime_UTR_variant	3945	.	.	.	.	rs189128124	.	.	-1	SAP130	HGNC	29813	protein_coding	YES	CCDS54397.1	ENSP00000350333	SP130_HUMAN	Q96DP1_HUMAN,C9J683_HUMAN	UPI00005989D6	.	.	.	21/21	.	.	T:0.0050	T:0	T:0.0014	.	T:0.0099	T:0.003	T:0.0112	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTTTAAAAAA	byFrequency|by1000G	3	ESCA
ACMSD	0	.	GRCh37	2	135625109	135625109	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.487-40C>T	.	.	ENST00000356140	.	33	27	6	31	31	0	ACMSD,intron_variant,,ENST00000283054,;ACMSD,intron_variant,,ENST00000356140,;ACMSD,intron_variant,,ENST00000392928,;CCNT2-AS1,non_coding_transcript_exon_variant,,ENST00000413962,;CCNT2-AS1,non_coding_transcript_exon_variant,,ENST00000428857,;CCNT2-AS1,non_coding_transcript_exon_variant,,ENST00000392929,;CCNT2-AS1,non_coding_transcript_exon_variant,,ENST00000537615,;ACMSD,intron_variant,,ENST00000485893,;	T	ENSG00000153086	ENST00000356140	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ACMSD	HGNC	19288	protein_coding	YES	CCDS2173.2	ENSP00000348459	ACMSD_HUMAN	.	UPI000006FB91	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCATCAAAGT	.	2	ESCA
GTDC1	0	.	GRCh37	2	144704298	144704298	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*321A>G	.	.	ENST00000392869	11/11	38	26	12	44	44	0	GTDC1,3_prime_UTR_variant,,ENST00000344850,;GTDC1,3_prime_UTR_variant,,ENST00000409214,;GTDC1,3_prime_UTR_variant,,ENST00000241391,;GTDC1,3_prime_UTR_variant,,ENST00000409298,;GTDC1,3_prime_UTR_variant,,ENST00000392867,;GTDC1,3_prime_UTR_variant,,ENST00000542155,;GTDC1,3_prime_UTR_variant,,ENST00000392869,;GTDC1,downstream_gene_variant,,ENST00000463875,;AC016910.1,intron_variant,,ENST00000422799,;GTDC1,downstream_gene_variant,,ENST00000482961,;GTDC1,3_prime_UTR_variant,,ENST00000415569,;GTDC1,3_prime_UTR_variant,,ENST00000392871,;	C	ENSG00000121964	ENST00000392869	Transcript	3_prime_UTR_variant	1851	.	.	.	.	.	.	.	-1	GTDC1	HGNC	20887	protein_coding	YES	CCDS33300.1	ENSP00000376608	GTDC1_HUMAN	G5EA49_HUMAN,G1UFN1_HUMAN,C9JIH3_HUMAN,C9J2C5_HUMAN	UPI000022BC3B	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACATATGGG	.	5	ESCA
TBR1	0	.	GRCh37	2	162280507	162280507	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1818C>T	p.%3D	p.P606P	ENST00000389554	6/6	18	11	6	16	16	0	TBR1,synonymous_variant,p.%3D,ENST00000389554,;TBR1,synonymous_variant,p.%3D,ENST00000410035,;TBR1,downstream_gene_variant,,ENST00000411412,;AC009487.5,upstream_gene_variant,,ENST00000505579,;AC009487.4,upstream_gene_variant,,ENST00000437683,;AC009487.4,upstream_gene_variant,,ENST00000444164,;SLC4A10,upstream_gene_variant,,ENST00000605990,;TBR1,downstream_gene_variant,,ENST00000477804,;SLC4A10,upstream_gene_variant,,ENST00000606386,;SLC4A10,upstream_gene_variant,,ENST00000482861,;TBR1,downstream_gene_variant,,ENST00000489530,;TBR1,downstream_gene_variant,,ENST00000463544,;	T	ENSG00000136535	ENST00000389554	Transcript	synonymous_variant	2135	1818	606	P	ccC/ccT	.	.	.	1	TBR1	HGNC	11590	protein_coding	YES	CCDS33310.1	ENSP00000374205	TBR1_HUMAN	Q56A81_HUMAN,B0AZS4_HUMAN	UPI0000136A99	.	.	.	6/6	.	hmmpanther:PTHR11267:SF88,hmmpanther:PTHR11267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCCCAAGGA	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098804	178098804	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241G>A	p.Gly81Ser	p.G81S	ENST00000397062	2/5	78	56	22	83	83	0	NFE2L2,missense_variant,p.Ala65Thr,ENST00000449627,;NFE2L2,missense_variant,p.Gly65Ser,ENST00000423513,;NFE2L2,missense_variant,p.Gly81Ser,ENST00000397062,;NFE2L2,missense_variant,p.Gly65Ser,ENST00000446151,;NFE2L2,missense_variant,p.Gly65Ser,ENST00000588123,;NFE2L2,missense_variant,p.Gly80Ser,ENST00000586532,;NFE2L2,missense_variant,p.Gly65Ser,ENST00000421929,;NFE2L2,missense_variant,p.Gly65Ser,ENST00000464747,;NFE2L2,missense_variant,p.Gly65Ser,ENST00000448782,;NFE2L2,missense_variant,p.Gly65Ser,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	T	ENSG00000116044	ENST00000397062	Transcript	missense_variant	796	241	81	G/S	Ggt/Agt	COSM1009929,COSM717624	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G81S|c.241G>A|3,CODON|p.G81D|c.242G>A|6,CODON|p.G81V|c.242G>T|7,BUFFER|p.E82D|c.246A>C|3,BUFFER|p.E82D|c.246A>T|6,BUFFER|p.E82G|c.245A>G|7,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79K|c.235G>A|10,BUFFER|p.E79Q|c.235G>C|11,BUFFER|p.D77V|c.230A>T|5,BUFFER|p.D77G|c.230A>G|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCACCTGTCT	.	5	ESCA
ACSL3	0	.	GRCh37	2	223791822	223791822	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1380G>T	p.Gln460His	p.Q460H	ENST00000357430	12/17	36	17	18	52	52	0	ACSL3,missense_variant,p.Gln460His,ENST00000392066,;ACSL3,missense_variant,p.Gln460His,ENST00000357430,;ACSL3,intron_variant,,ENST00000407441,;ACSL3,downstream_gene_variant,,ENST00000421680,;ACSL3,upstream_gene_variant,,ENST00000474422,;	T	ENSG00000123983	ENST00000357430	Transcript	missense_variant	1911	1380	460	Q/H	caG/caT	.	.	.	1	ACSL3	HGNC	3570	protein_coding	YES	CCDS2455.1	ENSP00000350012	ACSL3_HUMAN	Q6PIM8_HUMAN,F5H062_HUMAN,F5GWH2_HUMAN,C9JC11_HUMAN,B3KMA6_HUMAN	UPI0000074742	.	tolerated(0.51)	probably_damaging(1)	12/17	.	hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF157,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCAGCGATT	.	5	ESCA
SCG2	0	.	GRCh37	2	224463668	224463668	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333G>A	p.Met111Ile	p.M111I	ENST00000305409	2/2	19	16	3	42	42	0	SCG2,missense_variant,p.Met111Ile,ENST00000305409,;SCG2,missense_variant,p.Met111Ile,ENST00000433889,;SCG2,missense_variant,p.Met111Ile,ENST00000421386,;	T	ENSG00000171951	ENST00000305409	Transcript	missense_variant	566	333	111	M/I	atG/atA	.	.	.	-1	SCG2	HGNC	10575	protein_coding	YES	CCDS2457.1	ENSP00000304133	SCG2_HUMAN	C9JQI2_HUMAN,C9JDT0_HUMAN	UPI000013EA45	.	tolerated(0.23)	benign(0.015)	2/2	.	hmmpanther:PTHR15119,hmmpanther:PTHR15119:SF0,Pfam_domain:PF01271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTCTCATCCA	.	2	ESCA
SCG2	0	.	GRCh37	2	224463671	224463671	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330G>A	p.Trp110Ter	p.W110*	ENST00000305409	2/2	19	16	3	44	44	0	SCG2,stop_gained,p.Trp110Ter,ENST00000305409,;SCG2,stop_gained,p.Trp110Ter,ENST00000433889,;SCG2,stop_gained,p.Trp110Ter,ENST00000421386,;	T	ENSG00000171951	ENST00000305409	Transcript	stop_gained	563	330	110	W/*	tgG/tgA	.	.	.	-1	SCG2	HGNC	10575	protein_coding	YES	CCDS2457.1	ENSP00000304133	SCG2_HUMAN	C9JQI2_HUMAN,C9JDT0_HUMAN	UPI000013EA45	.	.	.	2/2	.	hmmpanther:PTHR15119,hmmpanther:PTHR15119:SF0,Pfam_domain:PF01271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCATCCAGTC	.	2	ESCA
LRRTM4	0	.	GRCh37	2	77744758	77744759	+	Intron	INS	-	-	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1551+685dupT	.	.	ENST00000409093	.	36	24	11	38	38	0	LRRTM4,3_prime_UTR_variant,,ENST00000409088,;LRRTM4,3_prime_UTR_variant,,ENST00000409282,;LRRTM4,intron_variant,,ENST00000409093,;LRRTM4,intron_variant,,ENST00000409884,;LRRTM4,intron_variant,,ENST00000409911,;LRRTM4,downstream_gene_variant,,ENST00000456154,;	A	ENSG00000176204	ENST00000409093	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	LRRTM4	HGNC	19411	protein_coding	YES	CCDS46346.1	ENSP00000386357	LRRT4_HUMAN	C9JM64_HUMAN	UPI0000047808	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACAAACAAAAA	.	2	ESCA
HRH1	0	.	GRCh37	3	11304403	11304403	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2216T>G	.	.	ENST00000397056	3/3	17	8	9	42	42	0	HRH1,3_prime_UTR_variant,,ENST00000431010,;HRH1,3_prime_UTR_variant,,ENST00000397056,;HRH1,downstream_gene_variant,,ENST00000413416,;HRH1,downstream_gene_variant,,ENST00000438284,;	G	ENSG00000196639	ENST00000397056	Transcript	3_prime_UTR_variant	3871	.	.	.	.	.	.	.	1	HRH1	HGNC	5182	protein_coding	YES	CCDS2604.1	ENSP00000380247	HRH1_HUMAN	.	UPI0000050401	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAACTGATTG	.	5	ESCA
EIF2A	0	.	GRCh37	3	150289908	150289908	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.975T>C	p.%3D	p.H325H	ENST00000460851	10/14	52	40	12	93	93	0	EIF2A,synonymous_variant,p.%3D,ENST00000460851,;EIF2A,synonymous_variant,p.%3D,ENST00000383043,;EIF2A,synonymous_variant,p.%3D,ENST00000406576,;EIF2A,synonymous_variant,p.%3D,ENST00000487799,;EIF2A,synonymous_variant,p.%3D,ENST00000465535,;EIF2A,synonymous_variant,p.%3D,ENST00000273435,;SERP1,intron_variant,,ENST00000479209,;EIF2A,downstream_gene_variant,,ENST00000482093,;SERP1,intron_variant,,ENST00000484608,;SERP1,intron_variant,,ENST00000490945,;SERP1,intron_variant,,ENST00000463647,;SERP1,intron_variant,,ENST00000491195,;EIF2A,upstream_gene_variant,,ENST00000482471,;EIF2A,3_prime_UTR_variant,,ENST00000477551,;EIF2A,downstream_gene_variant,,ENST00000462221,;EIF2A,downstream_gene_variant,,ENST00000472926,;EIF2A,downstream_gene_variant,,ENST00000494558,;	C	ENSG00000144895	ENST00000460851	Transcript	synonymous_variant	1084	975	325	H	caT/caC	.	.	.	1	EIF2A	HGNC	3254	protein_coding	YES	CCDS46935.1	ENSP00000417229	EIF2A_HUMAN	.	UPI00000473DB	.	.	.	10/14	.	hmmpanther:PTHR13227,Gene3D:2.130.10.10,Pfam_domain:PF08662,PIRSF_domain:PIRSF017222,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCATGGACA	.	5	ESCA
HYAL2	0	.	GRCh37	3	50357934	50357934	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-14C>A	.	.	ENST00000447092	1/3	16	12	4	36	36	0	HYAL2,5_prime_UTR_variant,,ENST00000426286,;HYAL2,5_prime_UTR_variant,,ENST00000424190,;HYAL2,5_prime_UTR_variant,,ENST00000442581,;HYAL2,5_prime_UTR_variant,,ENST00000458018,;HYAL2,5_prime_UTR_variant,,ENST00000447092,;HYAL2,5_prime_UTR_variant,,ENST00000357750,;HYAL2,5_prime_UTR_variant,,ENST00000395139,;HYAL2,5_prime_UTR_variant,,ENST00000428028,;HYAL2,5_prime_UTR_variant,,ENST00000415028,;TUSC2,downstream_gene_variant,,ENST00000232496,;TUSC2,non_coding_transcript_exon_variant,,ENST00000462137,;HYAL2,non_coding_transcript_exon_variant,,ENST00000481597,;	T	ENSG00000068001	ENST00000447092	Transcript	5_prime_UTR_variant	2280	.	.	.	.	.	.	.	-1	HYAL2	HGNC	5321	protein_coding	YES	CCDS2818.1	ENSP00000401853	HYAL2_HUMAN	Q5ZF00_HUMAN,C9K016_HUMAN,C9JSI7_HUMAN,C9JSD1_HUMAN,C9JBF5_HUMAN,C9J700_HUMAN	UPI000013C4E6	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CTGCAGGAGGT	.	3	ESCA
MTTP	0	.	GRCh37	4	100540133	100540133	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2220A>T	p.Glu740Asp	p.E740D	ENST00000457717	17/19	59	47	11	83	83	0	MTTP,missense_variant,p.Glu740Asp,ENST00000457717,;MTTP,missense_variant,p.Glu767Asp,ENST00000511045,;MTTP,missense_variant,p.Glu740Asp,ENST00000265517,;RP11-766F14.1,intron_variant,,ENST00000508578,;	T	ENSG00000138823	ENST00000457717	Transcript	missense_variant	2476	2220	740	E/D	gaA/gaT	.	.	.	1	MTTP	HGNC	7467	protein_coding	YES	CCDS3651.1	ENSP00000400821	MTP_HUMAN	.	UPI000012F826	.	tolerated(0.5)	benign(0.001)	17/19	.	hmmpanther:PTHR13024:SF1,hmmpanther:PTHR13024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGAACTTCA	.	5	ESCA
BANK1	0	.	GRCh37	4	102942701	102942701	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1237G>C	p.Glu413Gln	p.E413Q	ENST00000322953	8/17	43	30	13	40	40	0	BANK1,missense_variant,p.Glu280Gln,ENST00000508653,;BANK1,missense_variant,p.Glu280Gln,ENST00000428908,;BANK1,missense_variant,p.Glu398Gln,ENST00000504592,;BANK1,missense_variant,p.Glu383Gln,ENST00000444316,;BANK1,missense_variant,p.Glu413Gln,ENST00000322953,;RP11-498M5.2,intron_variant,,ENST00000505091,;BANK1,non_coding_transcript_exon_variant,,ENST00000510950,;	C	ENSG00000153064	ENST00000322953	Transcript	missense_variant	1511	1237	413	E/Q	Gaa/Caa	.	.	.	1	BANK1	HGNC	18233	protein_coding	YES	CCDS34038.1	ENSP00000320509	BANK1_HUMAN	.	UPI0000D6159D	.	tolerated(0.09)	probably_damaging(0.997)	8/17	.	hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAAGAAAAT	.	5	ESCA
CLPTM1L	0	.	GRCh37	5	1341903	1341903	+	Silent	SNP	G	G	A	rs762040634	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.336C>T	p.%3D	p.H112H	ENST00000320895	3/17	40	25	15	57	57	0	CLPTM1L,synonymous_variant,p.%3D,ENST00000320927,;CLPTM1L,synonymous_variant,p.%3D,ENST00000320895,;CLPTM1L,upstream_gene_variant,,ENST00000507807,;CLPTM1L,upstream_gene_variant,,ENST00000511786,;	A	ENSG00000049656	ENST00000320895	Transcript	synonymous_variant	594	336	112	H	caC/caT	rs762040634	.	.	-1	CLPTM1L	HGNC	24308	protein_coding	YES	CCDS3862.1	ENSP00000313854	CLP1L_HUMAN	B3KY18_HUMAN	UPI00000707DF	.	.	.	3/17	.	hmmpanther:PTHR21347:SF1,hmmpanther:PTHR21347,Pfam_domain:PF05602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCGTGATG	byFrequency	5	ESCA
PSD2	0	.	GRCh37	5	139192910	139192910	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388G>T	p.Glu130Ter	p.E130*	ENST00000274710	3/15	31	14	16	99	99	0	PSD2,stop_gained,p.Glu130Ter,ENST00000274710,;	T	ENSG00000146005	ENST00000274710	Transcript	stop_gained	593	388	130	E/*	Gag/Tag	.	.	.	1	PSD2	HGNC	19092	protein_coding	YES	CCDS4216.1	ENSP00000274710	PSD2_HUMAN	.	UPI0000073C6B	.	.	.	3/15	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGGGAGCCA	.	5	ESCA
ADCY2	0	.	GRCh37	5	7828067	7828067	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1083C>T	.	.	ENST00000338316	25/25	28	14	14	44	44	0	ADCY2,3_prime_UTR_variant,,ENST00000338316,;C5orf49,downstream_gene_variant,,ENST00000509627,;C5orf49,downstream_gene_variant,,ENST00000399810,;ADCY2,downstream_gene_variant,,ENST00000537121,;ADCY2,downstream_gene_variant,,ENST00000489501,;	T	ENSG00000078295	ENST00000338316	Transcript	3_prime_UTR_variant	4448	.	.	.	.	.	.	.	1	ADCY2	HGNC	233	protein_coding	YES	CCDS3872.2	ENSP00000342952	ADCY2_HUMAN	Q7RTV6_HUMAN,Q71UM8_HUMAN,D6REB8_HUMAN	UPI000066D9F2	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAGCGTGAG	.	5	ESCA
ULBP2	0	.	GRCh37	6	150263195	150263195	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-14G>C	.	.	ENST00000367351	1/5	133	111	22	198	198	0	ULBP2,5_prime_UTR_variant,,ENST00000367351,;	C	ENSG00000131015	ENST00000367351	Transcript	5_prime_UTR_variant	60	.	.	.	.	.	.	.	1	ULBP2	HGNC	14894	protein_coding	YES	CCDS5222.1	ENSP00000356320	N2DL2_HUMAN	Q8IZX9_HUMAN,J7HHH7_HUMAN,J7HBC7_HUMAN	UPI0000048F60	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAGCGCTCTG	.	5	ESCA
NOTCH4	0	.	GRCh37	6	32183074	32183074	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1950C>G	p.%3D	p.L650L	ENST00000375023	12/30	34	23	11	70	70	0	NOTCH4,synonymous_variant,p.%3D,ENST00000375023,;NOTCH4,upstream_gene_variant,,ENST00000465528,;NOTCH4,downstream_gene_variant,,ENST00000473562,;	C	ENSG00000204301	ENST00000375023	Transcript	synonymous_variant	2089	1950	650	L	ctC/ctG	.	.	.	-1	NOTCH4	HGNC	7884	protein_coding	YES	CCDS34420.1	ENSP00000364163	NOTC4_HUMAN	.	UPI0000130571	.	.	.	12/30	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00181,PIRSF_domain:PIRSF002279	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACAGAGGCA	.	5	ESCA
MED20	0	.	GRCh37	6	41888792	41888792	+	5'UTR	SNP	A	A	G	rs778081762	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-36T>C	.	.	ENST00000265350	1/4	28	13	15	46	46	0	MED20,5_prime_UTR_variant,,ENST00000409312,;MED20,5_prime_UTR_variant,,ENST00000409060,;MED20,5_prime_UTR_variant,,ENST00000434077,;MED20,5_prime_UTR_variant,,ENST00000265350,;MED20,upstream_gene_variant,,ENST00000394251,;BYSL,upstream_gene_variant,,ENST00000230340,;Y_RNA,upstream_gene_variant,,ENST00000384641,;MED20,non_coding_transcript_exon_variant,,ENST00000482361,;MED20,upstream_gene_variant,,ENST00000467535,;BYSL,upstream_gene_variant,,ENST00000489290,;BYSL,upstream_gene_variant,,ENST00000494032,;BYSL,upstream_gene_variant,,ENST00000475702,;	G	ENSG00000124641	ENST00000265350	Transcript	5_prime_UTR_variant	46	.	.	.	.	rs778081762	.	.	-1	MED20	HGNC	16840	protein_coding	YES	CCDS4862.1	ENSP00000265350	MED20_HUMAN	B3KUJ9_HUMAN,A6PVP4_HUMAN	UPI0000073C85	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGTAGAAAC	.	5	ESCA
VEGFA	0	.	GRCh37	6	43752659	43752659	+	3'Flank	SNP	A	A	T	rs567722917	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000372055	.	56	28	28	129	129	0	VEGFA,3_prime_UTR_variant,,ENST00000230480,;VEGFA,3_prime_UTR_variant,,ENST00000372077,;VEGFA,3_prime_UTR_variant,,ENST00000520948,;VEGFA,3_prime_UTR_variant,,ENST00000372064,;VEGFA,3_prime_UTR_variant,,ENST00000425836,;VEGFA,3_prime_UTR_variant,,ENST00000372067,;VEGFA,downstream_gene_variant,,ENST00000520265,;VEGFA,downstream_gene_variant,,ENST00000523950,;VEGFA,downstream_gene_variant,,ENST00000324450,;VEGFA,downstream_gene_variant,,ENST00000372055,;VEGFA,downstream_gene_variant,,ENST00000519767,;VEGFA,downstream_gene_variant,,ENST00000413642,;VEGFA,downstream_gene_variant,,ENST00000523873,;VEGFA,downstream_gene_variant,,ENST00000457104,;VEGFA,downstream_gene_variant,,ENST00000482630,;VEGFA,downstream_gene_variant,,ENST00000518689,;VEGFA,downstream_gene_variant,,ENST00000518824,;VEGFA,downstream_gene_variant,,ENST00000523125,;VEGFA,downstream_gene_variant,,ENST00000417285,;VEGFA,non_coding_transcript_exon_variant,,ENST00000480614,;VEGFA,non_coding_transcript_exon_variant,,ENST00000497139,;VEGFA,downstream_gene_variant,,ENST00000493786,;	T	ENSG00000112715	ENST00000372055	Transcript	downstream_gene_variant	.	.	.	.	.	rs567722917	.	313	1	VEGFA	HGNC	12680	protein_coding	YES	CCDS34457.1	ENSP00000361125	.	Q9UNS8_HUMAN,J3KPA4_HUMAN	UPI0000D61463	.	.	.	.	.	.	T:0.0008	T:0	T:0.0043	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTATATAT	byFrequency|by1000G	5	ESCA
AHCYL2	0	.	GRCh37	7	129046260	129046260	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1248C>T	p.%3D	p.S416S	ENST00000325006	10/17	36	18	17	61	61	0	AHCYL2,synonymous_variant,p.%3D,ENST00000531335,;AHCYL2,synonymous_variant,p.%3D,ENST00000474594,;AHCYL2,synonymous_variant,p.%3D,ENST00000466924,;AHCYL2,synonymous_variant,p.%3D,ENST00000325006,;AHCYL2,synonymous_variant,p.%3D,ENST00000490911,;AHCYL2,synonymous_variant,p.%3D,ENST00000446544,;AHCYL2,synonymous_variant,p.%3D,ENST00000446212,;RNU7-16P,downstream_gene_variant,,ENST00000516471,;AHCYL2,downstream_gene_variant,,ENST00000492628,;RP11-305M3.2,downstream_gene_variant,,ENST00000450566,;	T	ENSG00000158467	ENST00000325006	Transcript	synonymous_variant	1302	1248	416	S	tcC/tcT	COSM3633181,COSM3633182,COSM3633183	.	.	1	AHCYL2	HGNC	22204	protein_coding	YES	CCDS5812.1	ENSP00000315931	SAHH3_HUMAN	.	UPI00001354E4	.	.	.	10/17	.	hmmpanther:PTHR23420:SF2,hmmpanther:PTHR23420,TIGRFAM_domain:TIGR00936,Pfam_domain:PF00670,Gene3D:3.40.50.720,Pfam_domain:PF05221,SMART_domains:SM00996,SMART_domains:SM00997,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCCATTGT	.	5	ESCA
FKBP9	0	.	GRCh37	7	33044838	33044838	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1588C>G	p.Pro530Ala	p.P530A	ENST00000242209	10/10	94	88	6	143	143	0	FKBP9,missense_variant,p.Pro583Ala,ENST00000538336,;FKBP9,missense_variant,p.Pro298Ala,ENST00000490776,;FKBP9,missense_variant,p.Pro392Ala,ENST00000538443,;FKBP9,missense_variant,p.Pro530Ala,ENST00000242209,;AVL9,intron_variant,,ENST00000404479,;FKBP9,downstream_gene_variant,,ENST00000418354,;RNU6-388P,upstream_gene_variant,,ENST00000517012,;FKBP9,non_coding_transcript_exon_variant,,ENST00000475220,;FKBP9,non_coding_transcript_exon_variant,,ENST00000471066,;FKBP9,downstream_gene_variant,,ENST00000468510,;	G	ENSG00000122642	ENST00000242209	Transcript	missense_variant	1757	1588	530	P/A	Cct/Gct	.	.	.	1	FKBP9	HGNC	3725	protein_coding	YES	CCDS5439.1	ENSP00000242209	FKBP9_HUMAN	B7ZAH5_HUMAN,B7Z230_HUMAN,A7YQ73_HUMAN	UPI00001B6B0A	.	deleterious(0)	probably_damaging(0.997)	10/10	.	hmmpanther:PTHR10516:SF111,hmmpanther:PTHR10516,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGCTCCTGGC	.	2	ESCA
ACTB	0	.	GRCh37	7	5568131	5568131	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583G>A	p.Glu195Lys	p.E195K	ENST00000331789	4/6	76	54	21	96	96	0	ACTB,missense_variant,p.Glu195Lys,ENST00000331789,;ACTB,downstream_gene_variant,,ENST00000443528,;ACTB,downstream_gene_variant,,ENST00000414620,;ACTB,downstream_gene_variant,,ENST00000417101,;ACTB,downstream_gene_variant,,ENST00000432588,;AC006483.1,upstream_gene_variant,,ENST00000579427,;ACTB,non_coding_transcript_exon_variant,,ENST00000473257,;ACTB,upstream_gene_variant,,ENST00000464611,;ACTB,3_prime_UTR_variant,,ENST00000425660,;ACTB,non_coding_transcript_exon_variant,,ENST00000493945,;ACTB,non_coding_transcript_exon_variant,,ENST00000477812,;ACTB,non_coding_transcript_exon_variant,,ENST00000462494,;ACTB,non_coding_transcript_exon_variant,,ENST00000484841,;ACTB,downstream_gene_variant,,ENST00000480301,;	T	ENSG00000075624	ENST00000331789	Transcript	missense_variant	775	583	195	E/K	Gag/Aag	.	.	.	-1	ACTB	HGNC	132	protein_coding	YES	CCDS5341.1	ENSP00000349960	ACTB_HUMAN	Q9UE89_HUMAN,Q96FU6_HUMAN,Q96DE1_HUMAN,Q6PJ43_HUMAN,Q562Z7_HUMAN,Q1KLZ0_HUMAN,E7EVS6_HUMAN,C9JZR7_HUMAN,C9JTX5_HUMAN,B4E335_HUMAN,B3KWQ3_HUMAN,A5GZ75_HUMAN,A4UCT3_HUMAN,A1E282_HUMAN	UPI000000082D	.	deleterious_low_confidence(0.02)	benign(0.131)	4/6	.	hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF187,Gene3D:3.90.640.10,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCTCGGTGA	.	5	ESCA
RNU6-389P	0	.	GRCh37	7	55750467	55750467	+	5'Flank	SNP	G	G	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000517048	.	40	30	9	82	82	0	RNU6-389P,upstream_gene_variant,,ENST00000517048,;FKBP9L,non_coding_transcript_exon_variant,,ENST00000455909,;FKBP9L,non_coding_transcript_exon_variant,,ENST00000441699,;FKBP9L,non_coding_transcript_exon_variant,,ENST00000324256,;RP11-310H4.6,upstream_gene_variant,,ENST00000432235,;	C	ENSG00000252857	ENST00000517048	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3203	1	RNU6-389P	HGNC	47352	snRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGGAGCGA	.	5	ESCA
POM121	0	.	GRCh37	7	72413094	72413094	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1767C>T	p.%3D	p.T589T	ENST00000395270	14/16	25	19	6	25	25	0	POM121,synonymous_variant,p.%3D,ENST00000446813,;POM121,synonymous_variant,p.%3D,ENST00000257622,;POM121,synonymous_variant,p.%3D,ENST00000434423,;POM121,synonymous_variant,p.%3D,ENST00000358357,;POM121,synonymous_variant,p.%3D,ENST00000395270,;	T	ENSG00000196313	ENST00000395270	Transcript	synonymous_variant	2808	1767	589	T	acC/acT	.	.	.	1	POM121	HGNC	19702	protein_coding	YES	CCDS59059.1	ENSP00000378687	P121A_HUMAN	A8MY32_HUMAN	UPI000013DA6B	.	.	.	14/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23193:SF5,hmmpanther:PTHR23193	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AGCACCGCCAC	.	2	ESCA
SEMA3D	0	.	GRCh37	7	84647607	84647607	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1506C>A	p.His502Gln	p.H502Q	ENST00000284136	13/17	26	21	5	61	61	0	SEMA3D,missense_variant,p.His502Gln,ENST00000284136,;SEMA3D,splice_region_variant,,ENST00000484038,;	T	ENSG00000153993	ENST00000284136	Transcript	missense_variant	1550	1506	502	H/Q	caC/caA	.	.	.	-1	SEMA3D	HGNC	10726	protein_coding	YES	CCDS34676.1	ENSP00000284136	SEM3D_HUMAN	.	UPI0000135A66	.	tolerated(0.59)	benign(0.004)	13/17	.	Superfamily_domains:SSF101912,SMART_domains:SM00630,Gene3D:2.130.10.10,Pfam_domain:PF01403,hmmpanther:PTHR11036:SF36,hmmpanther:PTHR11036,PROSITE_profiles:PS51004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGAGTGCTG	.	5	ESCA
PEG10	0	.	GRCh37	7	94296541	94296541	+	3'UTR	SNP	A	A	C	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2695A>C	.	.	ENST00000482108	2/2	45	41	4	52	52	0	PEG10,3_prime_UTR_variant,,ENST00000482108,;PEG10,downstream_gene_variant,,ENST00000488574,;PEG10,intron_variant,,ENST00000465184,;PEG10,intron_variant,,ENST00000493935,;	C	ENSG00000242265	ENST00000482108	Transcript	3_prime_UTR_variant	4152	.	.	.	.	.	.	.	1	PEG10	HGNC	14005	protein_coding	YES	CCDS55126.1	ENSP00000417587	PEG10_HUMAN	B4DSP0_HUMAN	UPI0000047FA3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGCTACTGCC	.	4	ESCA
ADAM18	0	.	GRCh37	8	39466616	39466616	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244C>A	p.His82Asn	p.H82N	ENST00000265707	4/20	22	13	9	32	32	0	ADAM18,missense_variant,p.His82Asn,ENST00000520772,;ADAM18,missense_variant,p.His82Asn,ENST00000265707,;ADAM18,missense_variant,p.His82Asn,ENST00000379866,;ADAM18,5_prime_UTR_variant,,ENST00000541111,;ADAM18,non_coding_transcript_exon_variant,,ENST00000520559,;ADAM18,missense_variant,p.His82Asn,ENST00000520087,;ADAM18,3_prime_UTR_variant,,ENST00000520001,;	A	ENSG00000168619	ENST00000265707	Transcript	missense_variant	289	244	82	H/N	Cat/Aat	.	.	.	1	ADAM18	HGNC	196	protein_coding	YES	CCDS6113.1	ENSP00000265707	ADA18_HUMAN	Q0VAI3_HUMAN,E5RK96_HUMAN	UPI00001254D7	.	tolerated(0.08)	benign(0.068)	4/20	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF28,Pfam_domain:PF01562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTTTGCATTCT	.	4	ESCA
ZFHX4	0	.	GRCh37	8	77778027	77778027	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1226C>A	.	.	ENST00000521891	11/11	38	28	9	69	69	0	ZFHX4,3_prime_UTR_variant,,ENST00000455469,;ZFHX4,3_prime_UTR_variant,,ENST00000518282,;ZFHX4,3_prime_UTR_variant,,ENST00000521891,;ZFHX4,downstream_gene_variant,,ENST00000050961,;	A	ENSG00000091656	ENST00000521891	Transcript	3_prime_UTR_variant	12525	.	.	.	.	.	.	.	1	ZFHX4	HGNC	30939	protein_coding	YES	CCDS47878.2	ENSP00000430497	.	Q9H7F3_HUMAN,Q86WW5_HUMAN,Q6DK57_HUMAN,G3V138_HUMAN,E5RI93_HUMAN,E5RHS1_HUMAN,E5RGK3_HUMAN,E5RG79_HUMAN	UPI0000424CC7	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACACTGCCA	.	5	ESCA
ACTL7A	0	.	GRCh37	9	111624726	111624726	+	Missense_Mutation	SNP	G	G	A	rs201993006	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>A	p.Val42Met	p.V42M	ENST00000333999	1/1	37	29	8	54	53	1	ACTL7A,missense_variant,p.Val42Met,ENST00000333999,;	A	ENSG00000187003	ENST00000333999	Transcript	missense_variant	124	124	42	V/M	Gtg/Atg	rs201993006	.	.	1	ACTL7A	HGNC	161	protein_coding	YES	CCDS6772.1	ENSP00000334300	ACL7A_HUMAN	.	UPI0000125052	.	tolerated_low_confidence(0.14)	benign(0.07)	1/1	.	hmmpanther:PTHR11937:SF167,hmmpanther:PTHR11937	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCGTGTGG	byCluster	5	ESCA
PTGS1	0	.	GRCh37	9	125143816	125143816	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.663G>A	p.%3D	p.K221K	ENST00000362012	6/11	70	62	8	72	72	0	PTGS1,synonymous_variant,p.%3D,ENST00000362012,;PTGS1,synonymous_variant,p.%3D,ENST00000373698,;PTGS1,synonymous_variant,p.%3D,ENST00000223423,;PTGS1,synonymous_variant,p.%3D,ENST00000426608,;PTGS1,synonymous_variant,p.%3D,ENST00000540753,;AL162424.1,downstream_gene_variant,,ENST00000600713,;	A	ENSG00000095303	ENST00000362012	Transcript	synonymous_variant	668	663	221	K	aaG/aaA	.	.	.	1	PTGS1	HGNC	9604	protein_coding	YES	CCDS6842.1	ENSP00000354612	PGH1_HUMAN	.	UPI0000161DAC	.	.	.	6/11	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11903:SF6,hmmpanther:PTHR11903,Pfam_domain:PF03098,Gene3D:1.10.640.10,Superfamily_domains:SSF48113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCAAGGCCTT	.	4	ESCA
ELAVL2	0	.	GRCh37	9	23690232	23690232	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2323T>C	.	.	ENST00000397312	7/7	35	8	26	41	41	0	ELAVL2,3_prime_UTR_variant,,ENST00000380110,;ELAVL2,3_prime_UTR_variant,,ENST00000397312,;ELAVL2,3_prime_UTR_variant,,ENST00000223951,;ELAVL2,3_prime_UTR_variant,,ENST00000544538,;ELAVL2,downstream_gene_variant,,ENST00000380117,;	G	ENSG00000107105	ENST00000397312	Transcript	3_prime_UTR_variant	3678	.	.	.	.	.	.	.	-1	ELAVL2	HGNC	3313	protein_coding	YES	CCDS6515.1	ENSP00000380479	ELAV2_HUMAN	C9JB16_HUMAN,B1AM48_HUMAN	UPI000013C83F	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTAAGTCAT	.	5	ESCA
TLN1	0	.	GRCh37	9	35707164	35707164	+	Silent	SNP	G	G	A	rs554877602	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4860C>T	p.%3D	p.L1620L	ENST00000314888	37/57	82	71	10	89	89	0	TLN1,synonymous_variant,p.%3D,ENST00000314888,;TLN1,synonymous_variant,p.%3D,ENST00000540444,;TLN1,intron_variant,,ENST00000464379,;TLN1,downstream_gene_variant,,ENST00000495712,;TLN1,upstream_gene_variant,,ENST00000466916,;TLN1,upstream_gene_variant,,ENST00000465002,;TLN1,upstream_gene_variant,,ENST00000486788,;	A	ENSG00000137076	ENST00000314888	Transcript	synonymous_variant	5214	4860	1620	L	ctC/ctT	rs554877602	.	.	-1	TLN1	HGNC	11845	protein_coding	YES	CCDS35009.1	ENSP00000316029	TLN1_HUMAN	.	UPI0000211375	.	.	.	37/57	.	Gene3D:1.20.1440.10,hmmpanther:PTHR19981:SF7,hmmpanther:PTHR19981	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGCGAGGGC	by1000G	4	ESCA
OSTF1	0	.	GRCh37	9	77742518	77742518	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115A>G	p.Ile39Val	p.I39V	ENST00000346234	3/10	96	89	7	100	100	0	OSTF1,missense_variant,p.Ile39Val,ENST00000346234,;	G	ENSG00000134996	ENST00000346234	Transcript	missense_variant	265	115	39	I/V	Atc/Gtc	.	.	.	1	OSTF1	HGNC	8510	protein_coding	YES	CCDS6651.1	ENSP00000340836	OSTF1_HUMAN	.	UPI0000210B5F	.	tolerated(0.08)	benign(0.006)	3/10	.	PROSITE_profiles:PS50002,hmmpanther:PTHR24155,hmmpanther:PTHR24155:SF10,Pfam_domain:PF00018,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00499,Prints_domain:PR00452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATATTATCTAC	.	2	ESCA
IARS	0	.	GRCh37	9	95009691	95009691	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2759G>A	p.Ser920Asn	p.S920N	ENST00000375643	26/34	20	16	4	33	33	0	IARS,missense_variant,p.Ser920Asn,ENST00000443024,;IARS,missense_variant,p.Ser920Asn,ENST00000375643,;IARS,missense_variant,p.Ser810Asn,ENST00000447699,;IARS,5_prime_UTR_variant,,ENST00000375629,;IARS,upstream_gene_variant,,ENST00000375627,;IARS,downstream_gene_variant,,ENST00000467876,;IARS,upstream_gene_variant,,ENST00000473915,;IARS,upstream_gene_variant,,ENST00000474340,;	T	ENSG00000196305	ENST00000375643	Transcript	missense_variant	3026	2759	920	S/N	aGc/aAc	.	.	.	-1	IARS	HGNC	5330	protein_coding	YES	CCDS6694.1	ENSP00000364794	SYIC_HUMAN	Q9P1N9_HUMAN,Q7L4K8_HUMAN,Q5TCD1_HUMAN,Q5TCC4_HUMAN,Q59G75_HUMAN,J3KR24_HUMAN	UPI0000141335	.	deleterious(0.04)	benign(0.003)	26/34	.	HAMAP:MF_02003,hmmpanther:PTHR11946:SF11,hmmpanther:PTHR11946	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACTGCTCAAC	.	2	ESCA
XIST	0	.	GRCh37	X	73070803	73070803	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1786G>A	.	.	ENST00000429829	1/6	20	5	15	21	21	0	XIST,non_coding_transcript_exon_variant,,ENST00000429829,;	T	ENSG00000229807	ENST00000429829	Transcript	non_coding_transcript_exon_variant	1786	.	.	.	.	.	.	.	-1	XIST	HGNC	12810	lincRNA	YES	.	.	.	.	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATACACGTG	.	5	ESCA
TSPAN6	0	.	GRCh37	X	99888429	99888429	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A8I0-01A-11D-A36J-09	TCGA-LN-A8I0-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558G>T	p.Gln186His	p.Q186H	ENST00000373020	5/8	46	26	20	90	90	0	TSPAN6,missense_variant,p.Gln186His,ENST00000373020,;TSPAN6,non_coding_transcript_exon_variant,,ENST00000496771,;TSPAN6,downstream_gene_variant,,ENST00000494424,;	A	ENSG00000000003	ENST00000373020	Transcript	missense_variant	670	558	186	Q/H	caG/caT	COSM3800798	.	.	-1	TSPAN6	HGNC	11858	protein_coding	YES	CCDS14470.1	ENSP00000362111	TSN6_HUMAN	.	UPI0000049052	.	tolerated(0.12)	benign(0.315)	5/8	.	hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF169,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Superfamily_domains:0037997	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCTGTGG	.	5	ESCA
C10orf76	0	.	GRCh37	10	103716479	103716479	+	Missense_Mutation	SNP	A	A	G	rs759389501	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1580T>C	p.Ile527Thr	p.I527T	ENST00000370033	22/26	18	13	5	25	25	0	C10orf76,missense_variant,p.Ile527Thr,ENST00000370033,;Y_RNA,upstream_gene_variant,,ENST00000410498,;	G	ENSG00000120029	ENST00000370033	Transcript	missense_variant	1700	1580	527	I/T	aTt/aCt	rs759389501	.	.	-1	C10orf76	HGNC	25788	protein_coding	YES	CCDS41563.1	ENSP00000359050	CJ076_HUMAN	.	UPI000047005B	.	deleterious(0.01)	benign(0.201)	22/26	.	hmmpanther:PTHR13608:SF3,hmmpanther:PTHR13608,Pfam_domain:PF08427,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACAATCTAA	.	5	ESCA
PPRC1	0	.	GRCh37	10	103901420	103901420	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3155C>T	p.Pro1052Leu	p.P1052L	ENST00000278070	5/14	40	33	7	52	52	0	PPRC1,missense_variant,p.Pro1052Leu,ENST00000413464,;PPRC1,missense_variant,p.Pro1052Leu,ENST00000278070,;PPRC1,missense_variant,p.Pro19Leu,ENST00000370012,;PPRC1,upstream_gene_variant,,ENST00000489648,;PPRC1,upstream_gene_variant,,ENST00000462933,;	T	ENSG00000148840	ENST00000278070	Transcript	missense_variant	3194	3155	1052	P/L	cCt/cTt	.	.	.	1	PPRC1	HGNC	30025	protein_coding	YES	CCDS7529.1	ENSP00000278070	PPRC1_HUMAN	.	UPI000013DB5C	.	tolerated_low_confidence(0.07)	benign(0.024)	5/14	.	hmmpanther:PTHR15528:SF5,hmmpanther:PTHR15528	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGCCTACCA	.	5	ESCA
CASC10	0	.	GRCh37	10	21784563	21784563	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377G>A	p.Gly126Glu	p.G126E	ENST00000377113	2/2	52	42	9	50	50	0	CASC10,missense_variant,p.Gly126Glu,ENST00000377113,;MIR1915,downstream_gene_variant,,ENST00000410139,;	T	ENSG00000204682	ENST00000377113	Transcript	missense_variant	825	377	126	G/E	gGa/gAa	.	.	.	-1	CASC10	HGNC	31448	protein_coding	YES	CCDS31163.1	ENSP00000366317	CSC10_HUMAN	.	UPI0000198ED5	.	deleterious_low_confidence(0)	probably_damaging(0.969)	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.C127R|c.379T>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCATCCGCGG	.	5	ESCA
ZNF33A	0	.	GRCh37	10	38343702	38343702	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650A>G	p.His217Arg	p.H217R	ENST00000374618	5/5	42	24	17	57	57	0	ZNF33A,missense_variant,p.His223Arg,ENST00000432900,;ZNF33A,missense_variant,p.His216Arg,ENST00000307441,;ZNF33A,missense_variant,p.His216Arg,ENST00000458705,;ZNF33A,missense_variant,p.His217Arg,ENST00000374618,;ZNF33A,intron_variant,,ENST00000469037,;ZNF33A,downstream_gene_variant,,ENST00000478556,;	G	ENSG00000189180	ENST00000374618	Transcript	missense_variant	828	650	217	H/R	cAc/cGc	.	.	.	1	ZNF33A	HGNC	13096	protein_coding	YES	CCDS44372.1	ENSP00000363747	ZN33A_HUMAN	.	UPI0000161788	.	tolerated(0.17)	benign(0.002)	5/5	.	hmmpanther:PTHR24377:SF204,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGCACAATT	.	5	ESCA
ZNF37BP	0	.	GRCh37	10	43015629	43015629	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1966C>T	.	.	ENST00000452075	8/8	32	26	5	34	34	0	ZNF37BP,non_coding_transcript_exon_variant,,ENST00000452075,;ZNF37BP,downstream_gene_variant,,ENST00000473592,;ZNF37BP,downstream_gene_variant,,ENST00000435805,;ZNF37BP,non_coding_transcript_exon_variant,,ENST00000452306,;	A	ENSG00000234420	ENST00000452075	Transcript	non_coding_transcript_exon_variant	1966	.	.	.	.	.	.	.	-1	ZNF37BP	HGNC	13103	processed_transcript	YES	.	.	.	.	.	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTAATGAGGTC	.	3	ESCA
C10orf54	0	.	GRCh37	10	73520601	73520601	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.568+24T>C	.	.	ENST00000394957	.	52	49	3	61	61	0	C10orf54,intron_variant,,ENST00000394957,;CDH23,intron_variant,,ENST00000224721,;C10orf54,upstream_gene_variant,,ENST00000470317,;C10orf54,non_coding_transcript_exon_variant,,ENST00000481568,;	G	ENSG00000107738	ENST00000394957	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	C10orf54	HGNC	30085	protein_coding	YES	CCDS31218.1	ENSP00000378409	GI24_HUMAN	.	UPI000004781D	.	.	.	.	3/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAAAAGGGGC	.	2	ESCA
ASCC1	0	.	GRCh37	10	73862091	73862091	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*35+1G>T	.	.	ENST00000342444	.	82	59	22	68	68	0	ASCC1,splice_donor_variant,,ENST00000530394,;ASCC1,splice_donor_variant,,ENST00000342444,;ASCC1,intron_variant,,ENST00000394919,;ASCC1,intron_variant,,ENST00000486689,;ASCC1,intron_variant,,ENST00000545550,;ASCC1,intron_variant,,ENST00000317126,;ASCC1,intron_variant,,ENST00000317168,;ASCC1,downstream_gene_variant,,ENST00000394915,;ASCC1,intron_variant,,ENST00000534259,;	A	ENSG00000138303	ENST00000342444	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	ASCC1	HGNC	24268	protein_coding	YES	CCDS55713.1	ENSP00000339404	ASCC1_HUMAN	E9PJM2_HUMAN	UPI000006F7E9	.	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTACCCACT	.	5	ESCA
COLCA1	0	.	GRCh37	11	111167343	111167343	+	5'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-140A>G	.	.	ENST00000532918	2/2	37	7	30	55	55	0	COLCA1,5_prime_UTR_variant,,ENST00000532918,;COLCA1,5_prime_UTR_variant,,ENST00000355430,;COLCA2,upstream_gene_variant,,ENST00000398035,;COLCA2,upstream_gene_variant,,ENST00000528846,;COLCA2,upstream_gene_variant,,ENST00000526216,;COLCA1,upstream_gene_variant,,ENST00000540738,;COLCA1,downstream_gene_variant,,ENST00000526150,;	C	ENSG00000196167	ENST00000532918	Transcript	5_prime_UTR_variant	2267	.	.	.	.	.	.	.	-1	COLCA1	HGNC	33789	protein_coding	YES	.	ENSP00000437253	COLC1_HUMAN	.	UPI00001C0E9B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAATGGAAG	.	5	ESCA
PLET1	0	.	GRCh37	11	112123114	112123114	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405C>T	p.%3D	p.I135I	ENST00000338832	3/4	27	9	18	35	35	0	PLET1,synonymous_variant,p.%3D,ENST00000338832,;PLET1,synonymous_variant,p.%3D,ENST00000527122,;PLET1,upstream_gene_variant,,ENST00000533819,;AP002884.1,downstream_gene_variant,,ENST00000401135,;PTS,intron_variant,,ENST00000531673,;	A	ENSG00000188771	ENST00000338832	Transcript	synonymous_variant	676	405	135	I	atC/atT	.	.	.	-1	PLET1	HGNC	30053	protein_coding	YES	.	ENSP00000341412	PLET1_HUMAN	.	UPI000023753A	.	.	.	3/4	.	hmmpanther:PTHR22527	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTGATCTG	.	5	ESCA
CEP164	0	.	GRCh37	11	117244544	117244544	+	Silent	SNP	C	C	A	rs769096956	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1230C>A	p.%3D	p.G410G	ENST00000278935	10/33	55	30	24	70	70	0	CEP164,synonymous_variant,p.%3D,ENST00000278935,;CEP164,non_coding_transcript_exon_variant,,ENST00000533706,;CEP164,non_coding_transcript_exon_variant,,ENST00000533675,;	A	ENSG00000110274	ENST00000278935	Transcript	synonymous_variant	1377	1230	410	G	ggC/ggA	rs769096956	.	.	1	CEP164	HGNC	29182	protein_coding	YES	CCDS31683.1	ENSP00000278935	CE164_HUMAN	E9PR73_HUMAN,E9PLS8_HUMAN,E9PIM2_HUMAN,E9PI05_HUMAN	UPI00001FA422	.	.	.	10/33	.	hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGCCTGGT	.	5	ESCA
PVRL1	0	.	GRCh37	11	119549353	119549353	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202C>T	p.Gln68Ter	p.Q68*	ENST00000264025	2/6	20	5	15	28	28	0	PVRL1,stop_gained,p.Gln68Ter,ENST00000340882,;PVRL1,stop_gained,p.Gln68Ter,ENST00000264025,;PVRL1,stop_gained,p.Gln68Ter,ENST00000341398,;PVRL1,non_coding_transcript_exon_variant,,ENST00000524510,;PVRL1,upstream_gene_variant,,ENST00000524429,;PVRL1,upstream_gene_variant,,ENST00000532197,;	A	ENSG00000110400	ENST00000264025	Transcript	stop_gained	733	202	68	Q/*	Cag/Tag	.	.	.	-1	PVRL1	HGNC	9706	protein_coding	YES	CCDS8426.1	ENSP00000264025	PVRL1_HUMAN	Q6SYC2_HUMAN	UPI000004A2BE	.	.	.	2/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23277:SF12,hmmpanther:PTHR23277,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00408,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTGCCATG	.	5	ESCA
OR8H2	0	.	GRCh37	11	55872693	55872693	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175C>G	p.Pro59Ala	p.P59A	ENST00000313503	1/1	143	89	54	84	84	0	OR8H2,missense_variant,p.Pro59Ala,ENST00000313503,;	G	ENSG00000181767	ENST00000313503	Transcript	missense_variant	175	175	59	P/A	Ccc/Gcc	.	.	.	1	OR8H2	HGNC	15308	protein_coding	YES	CCDS31518.1	ENSP00000323982	OR8H2_HUMAN	.	UPI0000041D0C	.	deleterious(0.01)	benign(0.216)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACTCCCATG	.	5	ESCA
MS4A6A	0	.	GRCh37	11	59939661	59939661	+	3'Flank	SNP	G	G	A	rs760776262	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000412309	.	46	26	19	40	40	0	MS4A6A,synonymous_variant,p.%3D,ENST00000323961,;MS4A6A,synonymous_variant,p.%3D,ENST00000530839,;MS4A6A,synonymous_variant,p.%3D,ENST00000529054,;MS4A6A,3_prime_UTR_variant,,ENST00000528851,;MS4A6A,3_prime_UTR_variant,,ENST00000420732,;MS4A6A,3_prime_UTR_variant,,ENST00000533989,;MS4A6A,3_prime_UTR_variant,,ENST00000426738,;MS4A6A,downstream_gene_variant,,ENST00000533023,;MS4A6A,downstream_gene_variant,,ENST00000412309,;MS4A6A,downstream_gene_variant,,ENST00000529906,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000531914,;MS4A6A,downstream_gene_variant,,ENST00000527254,;	A	ENSG00000110077	ENST00000412309	Transcript	downstream_gene_variant	.	.	.	.	.	rs760776262	.	309	-1	MS4A6A	HGNC	13375	protein_coding	YES	CCDS58134.1	ENSP00000403212	.	F8W9K1_HUMAN,E9PNG6_HUMAN,E9PMN8_HUMAN,E9PL03_HUMAN	UPI0001F77AB4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAGTCATG	.	5	ESCA
CTTN	0	.	GRCh37	11	70281137	70281137	+	Missense_Mutation	SNP	G	G	A	rs369658947	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1411G>A	p.Asp471Asn	p.D471N	ENST00000376561	17/19	478	428	50	44	44	0	CTTN,missense_variant,p.Asp471Asn,ENST00000376561,;CTTN,missense_variant,p.Asp508Asn,ENST00000301843,;CTTN,missense_variant,p.Asp471Asn,ENST00000346329,;CTTN,missense_variant,p.Asp165Asn,ENST00000529736,;CTTN,missense_variant,p.Asp192Asn,ENST00000538675,;CTTN,3_prime_UTR_variant,,ENST00000533931,;CTTN,3_prime_UTR_variant,,ENST00000393747,;	A	ENSG00000085733	ENST00000376561	Transcript	missense_variant	1582	1411	471	D/N	Gat/Aat	rs369658947	.	.	1	CTTN	HGNC	3338	protein_coding	YES	CCDS53676.1	ENSP00000365745	SRC8_HUMAN	E9PP90_HUMAN,E9PKG3_HUMAN,B4E358_HUMAN	UPI000006E3C2	.	deleterious(0.01)	probably_damaging(0.999)	17/19	.	PROSITE_profiles:PS50002,hmmpanther:PTHR10829:SF15,hmmpanther:PTHR10829,Pfam_domain:PF00018,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGGCGATGAT	byFrequency|byCluster	4	ESCA
MVK	0	.	GRCh37	12	110019329	110019329	+	Silent	SNP	G	G	T	rs759055539	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501G>T	p.%3D	p.P167P	ENST00000228510	5/11	61	36	25	66	66	0	MVK,synonymous_variant,p.%3D,ENST00000546277,;MVK,synonymous_variant,p.%3D,ENST00000539335,;MVK,synonymous_variant,p.%3D,ENST00000228510,;MVK,intron_variant,,ENST00000539696,;MVK,intron_variant,,ENST00000392727,;MVK,intron_variant,,ENST00000539575,;MVK,intron_variant,,ENST00000541384,;MVK,intron_variant,,ENST00000535044,;MVK,3_prime_UTR_variant,,ENST00000537237,;MVK,non_coding_transcript_exon_variant,,ENST00000545516,;MVK,intron_variant,,ENST00000545774,;MVK,intron_variant,,ENST00000447878,;	T	ENSG00000110921	ENST00000228510	Transcript	synonymous_variant	577	501	167	P	ccG/ccT	rs759055539	.	.	1	MVK	HGNC	7530	protein_coding	YES	CCDS9132.1	ENSP00000228510	KIME_HUMAN	F5H092_HUMAN,F5GXC0_HUMAN,B7Z1C2_HUMAN,B2RDU6_HUMAN	UPI000012DE5B	.	.	.	5/11	.	hmmpanther:PTHR10457:SF4,hmmpanther:PTHR10457,Pfam_domain:PF00288,Gene3D:3.30.230.10,TIGRFAM_domain:TIGR00549,Superfamily_domains:SSF54211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCCGCTGAA	.	5	ESCA
TMEM132C	0	.	GRCh37	12	129028603	129028603	+	Missense_Mutation	SNP	C	C	T	rs780140810	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076C>T	p.Thr359Met	p.T359M	ENST00000435159	3/9	132	84	48	27	27	0	TMEM132C,missense_variant,p.Thr359Met,ENST00000435159,;TMEM132C,5_prime_UTR_variant,,ENST00000315208,;	T	ENSG00000181234	ENST00000435159	Transcript	missense_variant	1076	1076	359	T/M	aCg/aTg	rs780140810,COSM1359999	.	.	1	TMEM132C	HGNC	25436	protein_coding	YES	.	ENSP00000410852	T132C_HUMAN	F5H439_HUMAN,E9PC33_HUMAN	UPI0001C0B37C	.	deleterious(0.02)	probably_damaging(0.909)	3/9	.	hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGACGGCCA	.	5	ESCA
GOLGA3	0	.	GRCh37	12	133347734	133347734	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1957T>C	.	.	ENST00000204726	24/24	124	73	50	118	118	0	GOLGA3,3_prime_UTR_variant,,ENST00000204726,;GOLGA3,3_prime_UTR_variant,,ENST00000450791,;GOLGA3,downstream_gene_variant,,ENST00000456883,;GOLGA3,downstream_gene_variant,,ENST00000541013,;	G	ENSG00000090615	ENST00000204726	Transcript	3_prime_UTR_variant	7013	.	.	.	.	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAATATTTGC	.	5	ESCA
PTPRO	0	.	GRCh37	12	15654736	15654736	+	Missense_Mutation	SNP	G	G	A	rs559417288	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844G>A	p.Gly282Ser	p.G282S	ENST00000281171	5/27	149	92	56	86	86	0	PTPRO,missense_variant,p.Gly282Ser,ENST00000348962,;PTPRO,missense_variant,p.Gly282Ser,ENST00000543886,;PTPRO,missense_variant,p.Gly282Ser,ENST00000281171,;	A	ENSG00000151490	ENST00000281171	Transcript	missense_variant	1174	844	282	G/S	Ggt/Agt	rs559417288	.	.	1	PTPRO	HGNC	9678	protein_coding	YES	CCDS8675.1	ENSP00000281171	PTPRO_HUMAN	B4DS16_HUMAN	UPI000013DC62	.	tolerated_low_confidence(0.46)	benign(0.001)	5/27	.	hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF251	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S280Y|c.839C>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCCGGTTGG	by1000G	5	ESCA
TMEM117	0	.	GRCh37	12	44605125	44605125	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.563C>T	p.Ala188Val	p.A188V	ENST00000266534	5/8	66	41	24	51	51	0	TMEM117,missense_variant,p.Ala188Val,ENST00000551577,;TMEM117,missense_variant,p.Ala44Val,ENST00000550495,;TMEM117,missense_variant,p.Ala188Val,ENST00000266534,;TMEM117,missense_variant,p.Ala84Val,ENST00000536799,;TMEM117,non_coding_transcript_exon_variant,,ENST00000550623,;TMEM117,non_coding_transcript_exon_variant,,ENST00000553253,;TMEM117,3_prime_UTR_variant,,ENST00000546868,;	T	ENSG00000139173	ENST00000266534	Transcript	missense_variant	690	563	188	A/V	gCa/gTa	.	.	.	1	TMEM117	HGNC	25308	protein_coding	YES	CCDS8745.1	ENSP00000266534	TM117_HUMAN	H0YI63_HUMAN	UPI0000037D18	.	tolerated(0.66)	benign(0.023)	5/8	.	hmmpanther:PTHR31226,Pfam_domain:PF15113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAGCAAGAG	.	5	ESCA
KMT2D	0	.	GRCh37	12	49428677	49428678	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10272dupT	p.Ala3425CysfsTer43	p.A3425Cfs*43	ENST00000301067	35/54	62	49	13	38	38	0	KMT2D,frameshift_variant,p.Ala3425CysfsTer43,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	frameshift_variant	10272-10273	10272-10273	3424-3425	-/X	-/T	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	35/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTTGCAATGG	.	3	ESCA
TSFM	0	.	GRCh37	12	58176601	58176601	+	Missense_Mutation	SNP	C	C	T	rs372337739	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17C>T	p.Ser6Leu	p.S6L	ENST00000323833	1/7	92	47	45	45	45	0	TSFM,missense_variant,p.Ser6Leu,ENST00000543727,;TSFM,missense_variant,p.Ser6Leu,ENST00000323833,;TSFM,missense_variant,p.Ser6Leu,ENST00000540550,;TSFM,missense_variant,p.Ser6Leu,ENST00000548851,;TSFM,missense_variant,p.Ser6Leu,ENST00000550559,;TSFM,missense_variant,p.Ser6Leu,ENST00000454289,;TSFM,5_prime_UTR_variant,,ENST00000457189,;TSFM,5_prime_UTR_variant,,ENST00000434359,;TSFM,5_prime_UTR_variant,,ENST00000350762,;RP11-571M6.15,intron_variant,,ENST00000546504,;METTL21B,downstream_gene_variant,,ENST00000551420,;METTL21B,downstream_gene_variant,,ENST00000300209,;METTL21B,downstream_gene_variant,,ENST00000548256,;METTL21B,downstream_gene_variant,,ENST00000333012,;RP11-571M6.15,intron_variant,,ENST00000553083,;TSFM,upstream_gene_variant,,ENST00000497617,;TSFM,missense_variant,p.Ser6Leu,ENST00000417094,;RP11-571M6.15,intron_variant,,ENST00000471530,;	T	ENSG00000123297	ENST00000323833	Transcript	missense_variant	43	17	6	S/L	tCg/tTg	rs372337739,COSM3368908,COSM3368907	.	.	1	TSFM	HGNC	12367	protein_coding	YES	CCDS53809.1	ENSP00000313877	EFTS_HUMAN	.	UPI000002A8C3	.	deleterious_low_confidence(0.01)	benign(0.176)	1/7	.	hmmpanther:PTHR11741	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCGGTCGCTGC	byCluster	4	ESCA
HMGA2	0	.	GRCh37	12	66358604	66358604	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1532C>A	.	.	ENST00000403681	5/5	111	76	35	111	111	0	HMGA2,3_prime_UTR_variant,,ENST00000403681,;HMGA2,downstream_gene_variant,,ENST00000539662,;	A	ENSG00000149948	ENST00000403681	Transcript	3_prime_UTR_variant	3002	.	.	.	.	.	.	.	1	HMGA2	HGNC	5009	protein_coding	YES	CCDS44936.1	ENSP00000384026	HMGA2_HUMAN	Q8IZX8_HUMAN,B2KX87_HUMAN	UPI0000000CE6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTCCTAGGT	.	5	ESCA
ING4	0	.	GRCh37	12	6772257	6772257	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11G>A	p.Gly4Glu	p.G4E	ENST00000396807	1/8	58	40	17	48	48	0	ING4,missense_variant,p.Gly4Glu,ENST00000444704,;ING4,missense_variant,p.Gly4Glu,ENST00000423703,;ING4,missense_variant,p.Gly4Glu,ENST00000412586,;ING4,missense_variant,p.Gly4Glu,ENST00000446105,;ING4,missense_variant,p.Gly4Glu,ENST00000396807,;ING4,missense_variant,p.Gly4Glu,ENST00000341550,;ING4,upstream_gene_variant,,ENST00000467678,;ZNF384,downstream_gene_variant,,ENST00000361959,;ZNF384,downstream_gene_variant,,ENST00000396801,;ZNF384,downstream_gene_variant,,ENST00000319770,;ZNF384,downstream_gene_variant,,ENST00000396799,;ING4,upstream_gene_variant,,ENST00000493873,;ZNF384,downstream_gene_variant,,ENST00000355772,;ZNF384,downstream_gene_variant,,ENST00000396795,;ZNF384,downstream_gene_variant,,ENST00000545946,;RP4-761J14.8,upstream_gene_variant,,ENST00000586338,;RP4-761J14.8,upstream_gene_variant,,ENST00000589924,;ING4,non_coding_transcript_exon_variant,,ENST00000437149,;ING4,missense_variant,p.Gly4Glu,ENST00000479301,;ING4,missense_variant,p.Gly4Glu,ENST00000469749,;ING4,missense_variant,p.Gly4Glu,ENST00000488381,;ING4,non_coding_transcript_exon_variant,,ENST00000493267,;ING4,non_coding_transcript_exon_variant,,ENST00000472002,;	T	ENSG00000111653	ENST00000396807	Transcript	missense_variant	50	11	4	G/E	gGg/gAg	.	.	.	-1	ING4	HGNC	19423	protein_coding	YES	CCDS44813.1	ENSP00000380024	ING4_HUMAN	R4GNG1_HUMAN,E9PNE3_HUMAN	UPI000006EFE0	.	deleterious(0)	possibly_damaging(0.638)	1/8	.	hmmpanther:PTHR10333,hmmpanther:PTHR10333:SF40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCCCCGCA	.	5	ESCA
SLC35E3	0	.	GRCh37	12	69145879	69145879	+	Missense_Mutation	SNP	T	T	C	rs778747700	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.581T>C	p.Met194Thr	p.M194T	ENST00000398004	3/5	165	94	70	71	71	0	SLC35E3,missense_variant,p.Met4Thr,ENST00000431174,;SLC35E3,missense_variant,p.Met194Thr,ENST00000398004,;SLC35E3,non_coding_transcript_exon_variant,,ENST00000319429,;SLC35E3,upstream_gene_variant,,ENST00000538043,;	C	ENSG00000175782	ENST00000398004	Transcript	missense_variant	853	581	194	M/T	aTg/aCg	rs778747700	.	.	1	SLC35E3	HGNC	20864	protein_coding	YES	CCDS41808.1	ENSP00000381089	S35E3_HUMAN	.	UPI0000048F4D	.	deleterious(0)	benign(0.071)	3/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11132:SF47,hmmpanther:PTHR11132,Pfam_domain:PF03151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCGATGTCAT	.	5	ESCA
ACSS3	0	.	GRCh37	12	81537017	81537017	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912G>A	p.%3D	p.G304G	ENST00000548058	5/16	67	35	32	43	43	0	ACSS3,synonymous_variant,p.%3D,ENST00000261206,;ACSS3,synonymous_variant,p.%3D,ENST00000548058,;ACSS3,non_coding_transcript_exon_variant,,ENST00000548387,;	A	ENSG00000111058	ENST00000548058	Transcript	synonymous_variant	1822	912	304	G	ggG/ggA	.	.	.	1	ACSS3	HGNC	24723	protein_coding	YES	CCDS9022.1	ENSP00000449535	ACSS3_HUMAN	F8VZB4_HUMAN	UPI000007060A	.	.	.	5/16	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF0,PROSITE_patterns:PS00455,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGGGGTTACC	.	5	ESCA
CEP290	0	.	GRCh37	12	88522769	88522769	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.896A>G	p.Asp299Gly	p.D299G	ENST00000552810	11/54	201	123	77	157	157	0	CEP290,missense_variant,p.Asp21Gly,ENST00000604024,;CEP290,missense_variant,p.Asp299Gly,ENST00000552810,;CEP290,missense_variant,p.Asp299Gly,ENST00000309041,;CEP290,5_prime_UTR_variant,,ENST00000397838,;CEP290,downstream_gene_variant,,ENST00000550962,;CEP290,missense_variant,p.Asp265Gly,ENST00000547926,;	C	ENSG00000198707	ENST00000552810	Transcript	missense_variant	1240	896	299	D/G	gAt/gGt	.	.	.	-1	CEP290	HGNC	29021	protein_coding	YES	CCDS55858.1	ENSP00000448012	CE290_HUMAN	.	UPI0000D60D15	.	.	probably_damaging(0.999)	11/54	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCATCTTCT	.	5	ESCA
FGF9	0	.	GRCh37	13	22275604	22275604	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*30A>G	.	.	ENST00000382353	3/3	46	26	20	39	39	0	FGF9,3_prime_UTR_variant,,ENST00000382353,;FGF9,non_coding_transcript_exon_variant,,ENST00000478546,;FGF9,downstream_gene_variant,,ENST00000461657,;	G	ENSG00000102678	ENST00000382353	Transcript	3_prime_UTR_variant	1187	.	.	.	.	.	.	.	1	FGF9	HGNC	3687	protein_coding	YES	CCDS9298.1	ENSP00000371790	FGF9_HUMAN	.	UPI00000374AF	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTAAAAAAG	.	5	ESCA
PCDH17	0	.	GRCh37	13	58299731	58299731	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*303C>A	.	.	ENST00000377918	4/4	39	28	11	33	33	0	PCDH17,3_prime_UTR_variant,,ENST00000377918,;PCDH17,downstream_gene_variant,,ENST00000484979,;	A	ENSG00000118946	ENST00000377918	Transcript	3_prime_UTR_variant	3809	.	.	.	.	.	.	.	1	PCDH17	HGNC	14267	protein_coding	YES	CCDS31986.1	ENSP00000367151	PCD17_HUMAN	.	UPI00001FCE5B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTACCTTTT	.	5	ESCA
PCDH17	0	.	GRCh37	13	58301076	58301076	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1648C>G	.	.	ENST00000377918	4/4	13	5	8	10	10	0	PCDH17,3_prime_UTR_variant,,ENST00000377918,;PCDH17,downstream_gene_variant,,ENST00000484979,;	G	ENSG00000118946	ENST00000377918	Transcript	3_prime_UTR_variant	5154	.	.	.	.	.	.	.	1	PCDH17	HGNC	14267	protein_coding	YES	CCDS31986.1	ENSP00000367151	PCD17_HUMAN	.	UPI00001FCE5B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TTTTCCTTTAT	.	4	ESCA
KLHL1	0	.	GRCh37	13	70275015	70275015	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*819T>C	.	.	ENST00000377844	11/11	15	5	10	23	23	0	KLHL1,3_prime_UTR_variant,,ENST00000377844,;KLHL1,downstream_gene_variant,,ENST00000545028,;	G	ENSG00000150361	ENST00000377844	Transcript	3_prime_UTR_variant	3826	.	.	.	.	.	.	.	-1	KLHL1	HGNC	6352	protein_coding	YES	CCDS9445.1	ENSP00000367075	KLHL1_HUMAN	Q96RF4_HUMAN	UPI000004B136	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGATATAT	.	5	ESCA
JAG2	0	.	GRCh37	14	105608099	105608099	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*933A>G	.	.	ENST00000331782	26/26	26	12	14	16	16	0	JAG2,3_prime_UTR_variant,,ENST00000347004,;JAG2,3_prime_UTR_variant,,ENST00000331782,;JAG2,non_coding_transcript_exon_variant,,ENST00000546616,;	C	ENSG00000184916	ENST00000331782	Transcript	3_prime_UTR_variant	5054	.	.	.	.	.	.	.	-1	JAG2	HGNC	6189	protein_coding	YES	CCDS9998.1	ENSP00000328169	JAG2_HUMAN	.	UPI0000167BD5	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATATACAGA	.	5	ESCA
HAUS4	0	.	GRCh37	14	23417087	23417087	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.698C>T	p.Ala233Val	p.A233V	ENST00000206474	7/10	49	30	19	27	27	0	HAUS4,missense_variant,p.Ala188Val,ENST00000555986,;HAUS4,missense_variant,p.Ala233Val,ENST00000206474,;HAUS4,missense_variant,p.Ala233Val,ENST00000555040,;HAUS4,missense_variant,p.Ala109Val,ENST00000490506,;RP11-298I3.5,missense_variant,p.Ala63Val,ENST00000555074,;HAUS4,missense_variant,p.Ala188Val,ENST00000555367,;HAUS4,missense_variant,p.Ala188Val,ENST00000342454,;HAUS4,missense_variant,p.Ala233Val,ENST00000541587,;HAUS4,intron_variant,,ENST00000397409,;HAUS4,intron_variant,,ENST00000347758,;HAUS4,intron_variant,,ENST00000556915,;HAUS4,downstream_gene_variant,,ENST00000554406,;HAUS4,downstream_gene_variant,,ENST00000557591,;HAUS4,downstream_gene_variant,,ENST00000554516,;HAUS4,downstream_gene_variant,,ENST00000553420,;RP11-298I3.1,intron_variant,,ENST00000548322,;RP11-298I3.1,intron_variant,,ENST00000548819,;HAUS4,non_coding_transcript_exon_variant,,ENST00000554349,;HAUS4,intron_variant,,ENST00000554446,;HAUS4,downstream_gene_variant,,ENST00000553794,;HAUS4,downstream_gene_variant,,ENST00000554373,;HAUS4,downstream_gene_variant,,ENST00000554651,;HAUS4,non_coding_transcript_exon_variant,,ENST00000554063,;HAUS4,non_coding_transcript_exon_variant,,ENST00000556421,;HAUS4,intron_variant,,ENST00000553859,;	A	ENSG00000092036	ENST00000206474	Transcript	missense_variant	951	698	233	A/V	gCt/gTt	.	.	.	-1	HAUS4	HGNC	20163	protein_coding	YES	CCDS9580.1	ENSP00000206474	HAUS4_HUMAN	G3V5A5_HUMAN,G3V541_HUMAN,G3V4X7_HUMAN	UPI000006F422	.	tolerated(1)	benign(0.024)	7/10	.	Prints_domain:PR02090,Pfam_domain:PF14735,hmmpanther:PTHR16219,hmmpanther:PTHR16219:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTAAGCAGCA	.	5	ESCA
NKX2-1	0	.	GRCh37	14	36985926	36985926	+	3'UTR	SNP	G	G	A	rs570771635	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*557C>T	.	.	ENST00000354822	3/3	41	26	15	32	32	0	NKX2-1,3_prime_UTR_variant,,ENST00000354822,;NKX2-1,3_prime_UTR_variant,,ENST00000518149,;NKX2-1,3_prime_UTR_variant,,ENST00000498187,;NKX2-1,downstream_gene_variant,,ENST00000546983,;NKX2-1,downstream_gene_variant,,ENST00000522719,;SFTA3,upstream_gene_variant,,ENST00000518529,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000524122,;SFTA3,upstream_gene_variant,,ENST00000418548,;	A	ENSG00000136352	ENST00000354822	Transcript	3_prime_UTR_variant	1862	.	.	.	.	rs570771635	.	.	-1	NKX2-1	HGNC	11825	protein_coding	YES	CCDS41945.1	ENSP00000346879	NKX21_HUMAN	Q13306_HUMAN	UPI000007328C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGGCGGCCAG	.	5	ESCA
FANCM	0	.	GRCh37	14	45667962	45667962	+	Missense_Mutation	SNP	G	G	C	rs201017015	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5832G>C	p.Leu1944Phe	p.L1944F	ENST00000267430	22/23	65	48	16	62	62	0	FANCM,missense_variant,p.Leu912Phe,ENST00000554809,;FANCM,missense_variant,p.Leu1918Phe,ENST00000542564,;FANCM,missense_variant,p.Leu1460Phe,ENST00000556250,;FANCM,missense_variant,p.Leu1944Phe,ENST00000267430,;FANCM,missense_variant,p.Leu70Phe,ENST00000555484,;MIS18BP1,downstream_gene_variant,,ENST00000310806,;FANCM,missense_variant,p.Cys135Ser,ENST00000557110,;FANCM,non_coding_transcript_exon_variant,,ENST00000553551,;	C	ENSG00000187790	ENST00000267430	Transcript	missense_variant	5917	5832	1944	L/F	ttG/ttC	rs201017015	.	.	1	FANCM	HGNC	23168	protein_coding	YES	CCDS32070.1	ENSP00000267430	FANCM_HUMAN	.	UPI000059F032	.	deleterious(0)	probably_damaging(1)	22/23	.	hmmpanther:PTHR14025,hmmpanther:PTHR14025:SF20,Pfam_domain:PF02732,Gene3D:1j23A00,Superfamily_domains:SSF52980	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTGCTAAA	byFrequency|byCluster	5	ESCA
SOS2	0	.	GRCh37	14	50597263	50597263	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3293C>T	p.Ser1098Leu	p.S1098L	ENST00000216373	20/23	96	45	50	72	72	0	SOS2,missense_variant,p.Ser1065Leu,ENST00000543680,;SOS2,missense_variant,p.Ser1098Leu,ENST00000216373,;	A	ENSG00000100485	ENST00000216373	Transcript	missense_variant	3568	3293	1098	S/L	tCa/tTa	.	.	.	-1	SOS2	HGNC	11188	protein_coding	YES	CCDS9697.1	ENSP00000216373	SOS2_HUMAN	B4DJ05_HUMAN	UPI000013C6E8	.	deleterious(0.01)	benign(0.313)	20/23	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTGAAGAA	.	5	ESCA
HIF1A	0	.	GRCh37	14	62200949	62200949	+	Missense_Mutation	SNP	A	A	T	rs764016802	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1046A>T	p.Tyr349Phe	p.Y349F	ENST00000539097	8/15	82	42	40	92	92	0	HIF1A,missense_variant,p.Tyr349Phe,ENST00000539097,;HIF1A,missense_variant,p.Tyr325Phe,ENST00000337138,;HIF1A,missense_variant,p.Tyr325Phe,ENST00000323441,;HIF1A,missense_variant,p.Tyr266Phe,ENST00000557538,;HIF1A,missense_variant,p.Tyr326Phe,ENST00000394997,;HIF1A-AS2,intron_variant,,ENST00000554254,;RP11-618G20.1,non_coding_transcript_exon_variant,,ENST00000555937,;HIF1A,upstream_gene_variant,,ENST00000555014,;	T	ENSG00000100644	ENST00000539097	Transcript	missense_variant	1275	1046	349	Y/F	tAt/tTt	rs764016802	.	.	1	HIF1A	HGNC	4910	protein_coding	YES	CCDS58324.1	ENSP00000437955	HIF1A_HUMAN	F8W9L0_HUMAN,B4E2U7_HUMAN	UPI0001982748	.	deleterious(0)	probably_damaging(0.984)	8/15	.	Superfamily_domains:SSF55785,SMART_domains:SM00086,TIGRFAM_domain:TIGR00229,Gene3D:3.30.450.20,Pfam_domain:PF14598,hmmpanther:PTHR23043:SF7,hmmpanther:PTHR23043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATATATAACA	.	5	ESCA
SMOC1	0	.	GRCh37	14	70477638	70477638	+	Missense_Mutation	SNP	C	C	T	rs776638586	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>T	p.Arg278Cys	p.R278C	ENST00000361956	8/12	52	29	23	57	57	0	SMOC1,missense_variant,p.Arg278Cys,ENST00000381280,;SMOC1,missense_variant,p.Arg278Cys,ENST00000361956,;SMOC1,non_coding_transcript_exon_variant,,ENST00000557483,;	T	ENSG00000198732	ENST00000361956	Transcript	missense_variant	1095	832	278	R/C	Cgc/Tgc	rs776638586,CM116129,COSM1515895	.	.	1	SMOC1	HGNC	20318	protein_coding	YES	CCDS32110.1	ENSP00000355110	SMOC1_HUMAN	.	UPI0000071CCF	.	deleterious(0)	probably_damaging(0.927)	8/12	.	PROSITE_profiles:PS51162,hmmpanther:PTHR12352:SF10,hmmpanther:PTHR12352,Pfam_domain:PF00086,Gene3D:4.10.800.10,SMART_domains:SM00211,Superfamily_domains:SSF57610	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCGCCCG	byFrequency|byCluster	5	ESCA
PAPOLA	0	.	GRCh37	14	96998989	96998989	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.836+3A>T	.	.	ENST00000216277	.	71	40	30	34	34	0	PAPOLA,missense_variant,p.Tyr280Phe,ENST00000557320,;PAPOLA,splice_region_variant,,ENST00000216277,;PAPOLA,splice_region_variant,,ENST00000553461,;PAPOLA,splice_region_variant,,ENST00000392990,;PAPOLA,splice_region_variant,,ENST00000555626,;PAPOLA,downstream_gene_variant,,ENST00000556619,;PAPOLA,downstream_gene_variant,,ENST00000557471,;PAPOLA,downstream_gene_variant,,ENST00000554130,;PAPOLA,splice_region_variant,,ENST00000553689,;PAPOLA,non_coding_transcript_exon_variant,,ENST00000555224,;PAPOLA,upstream_gene_variant,,ENST00000555021,;PAPOLA,downstream_gene_variant,,ENST00000553357,;PAPOLA,upstream_gene_variant,,ENST00000554666,;PAPOLA,downstream_gene_variant,,ENST00000557406,;PAPOLA,downstream_gene_variant,,ENST00000555912,;PAPOLA,upstream_gene_variant,,ENST00000555131,;	T	ENSG00000090060	ENST00000216277	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	PAPOLA	HGNC	14981	protein_coding	YES	CCDS9946.1	ENSP00000216277	PAPOA_HUMAN	G3V2A0_HUMAN,B7ZA53_HUMAN,B4DZL2_HUMAN	UPI0000074269	.	.	.	.	9/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGTATGTGT	.	5	ESCA
CCNK	0	.	GRCh37	14	99969323	99969323	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1011+2T>A	.	p.X337_splice	ENST00000389879	.	63	50	13	57	57	0	CCNK,splice_donor_variant,,ENST00000555049,;CCNK,splice_donor_variant,,ENST00000389879,;CCNK,downstream_gene_variant,,ENST00000557441,;CCNK,downstream_gene_variant,,ENST00000557165,;CCNK,non_coding_transcript_exon_variant,,ENST00000553865,;CCNK,downstream_gene_variant,,ENST00000556641,;	A	ENSG00000090061	ENST00000389879	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	CCNK	HGNC	1596	protein_coding	YES	CCDS45160.1	ENSP00000374529	CCNK_HUMAN	G3V2Q3_HUMAN,G3V235_HUMAN	UPI00001FDB50	.	.	.	.	8/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CGTGGTGAGTG	.	4	ESCA
CHEK2P2	0	.	GRCh37	15	20488873	20488873	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.356C>T	.	.	ENST00000555186	2/6	212	177	34	227	227	0	CHEK2P2,non_coding_transcript_exon_variant,,ENST00000566448,;CHEK2P2,non_coding_transcript_exon_variant,,ENST00000555186,;CHEK2P2,non_coding_transcript_exon_variant,,ENST00000554701,;	T	ENSG00000259156	ENST00000555186	Transcript	non_coding_transcript_exon_variant	356	.	.	.	.	.	.	.	1	CHEK2P2	HGNC	43578	processed_transcript	YES	.	.	.	.	.	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGTGCTGTGG	.	4	ESCA
NPAP1	0	.	GRCh37	15	24927502	24927502	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3017T>A	.	.	ENST00000329468	1/1	37	7	30	31	31	0	NPAP1,3_prime_UTR_variant,,ENST00000329468,;	A	ENSG00000185823	ENST00000329468	Transcript	3_prime_UTR_variant	6962	.	.	.	.	.	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTTTAAAA	.	5	ESCA
MAP2K1	0	.	GRCh37	15	66783011	66783011	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*58T>G	.	.	ENST00000307102	11/11	45	42	3	19	19	0	MAP2K1,3_prime_UTR_variant,,ENST00000307102,;SNAPC5,3_prime_UTR_variant,,ENST00000395589,;MAP2K1,3_prime_UTR_variant,,ENST00000566326,;SNAPC5,3_prime_UTR_variant,,ENST00000563480,;SNAPC5,downstream_gene_variant,,ENST00000307979,;SNAPC5,downstream_gene_variant,,ENST00000316634,;SNAPC5,downstream_gene_variant,,ENST00000566658,;CTD-3185P2.1,non_coding_transcript_exon_variant,,ENST00000565387,;CTD-3185P2.2,upstream_gene_variant,,ENST00000602360,;SNAPC5,3_prime_UTR_variant,,ENST00000562411,;SNAPC5,downstream_gene_variant,,ENST00000568875,;SNAPC5,downstream_gene_variant,,ENST00000565465,;	G	ENSG00000169032	ENST00000307102	Transcript	3_prime_UTR_variant	1771	.	.	.	.	.	.	.	1	MAP2K1	HGNC	6840	protein_coding	YES	CCDS10216.1	ENSP00000302486	MP2K1_HUMAN	A4QPA9_HUMAN	UPI000013EBC9	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCTTTTGGGCC	.	2	ESCA
ZWILCH	0	.	GRCh37	15	66811367	66811370	+	Frame_Shift_Del	DEL	AACA	AACA	-	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	AACA	AACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.476_479delACAA	p.Asn159ThrfsTer21	p.N159Tfs*21	ENST00000307897	5/19	68	61	7	63	63	0	ZWILCH,frameshift_variant,p.Asn159ThrfsTer21,ENST00000307897,;ZWILCH,frameshift_variant,p.Asn45ThrfsTer21,ENST00000565627,;ZWILCH,frameshift_variant,p.Asn45ThrfsTer21,ENST00000446801,;ZWILCH,frameshift_variant,p.Asn45ThrfsTer21,ENST00000564179,;ZWILCH,frameshift_variant,p.Asn45ThrfsTer21,ENST00000535141,;RPL4,intron_variant,,ENST00000568588,;ZWILCH,intron_variant,,ENST00000565960,;RPL4,intron_variant,,ENST00000564517,;ZWILCH,downstream_gene_variant,,ENST00000564309,;ZWILCH,non_coding_transcript_exon_variant,,ENST00000563698,;ZWILCH,non_coding_transcript_exon_variant,,ENST00000567926,;ZWILCH,upstream_gene_variant,,ENST00000561583,;ZWILCH,upstream_gene_variant,,ENST00000562645,;	-	ENSG00000174442	ENST00000307897	Transcript	frameshift_variant	851-854	471-474	157-158	TT/X	acAACA/ac	.	.	.	1	ZWILCH	HGNC	25468	protein_coding	YES	CCDS10219.1	ENSP00000311429	ZWILC_HUMAN	H3BSG1_HUMAN,H3BQ07_HUMAN,H3BPI7_HUMAN	UPI000013EC73	.	.	.	5/19	.	hmmpanther:PTHR15995,Pfam_domain:PF09817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TATCACAACAAACAA	.	3	ESCA
CACNA1H	0	.	GRCh37	16	1245968	1245968	+	Silent	SNP	G	G	A	rs749822770	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588G>A	p.%3D	p.S196S	ENST00000348261	5/35	188	108	80	118	117	0	CACNA1H,synonymous_variant,p.%3D,ENST00000565831,;CACNA1H,synonymous_variant,p.%3D,ENST00000358590,;CACNA1H,synonymous_variant,p.%3D,ENST00000348261,;CACNA1H,non_coding_transcript_exon_variant,,ENST00000564954,;	A	ENSG00000196557	ENST00000348261	Transcript	synonymous_variant	836	588	196	S	tcG/tcA	rs749822770	.	.	1	CACNA1H	HGNC	1395	protein_coding	YES	CCDS45375.1	ENSP00000334198	CAC1H_HUMAN	Q9NYY7_HUMAN,Q9NYY6_HUMAN	UPI000012727B	.	.	.	5/35	.	Superfamily_domains:SSF81324,Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCGGCTAT	byFrequency	5	ESCA
PDZD9	0	.	GRCh37	16	22007662	22007662	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31+4676C>T	.	.	ENST00000537222	.	114	96	18	56	56	0	PDZD9,synonymous_variant,p.%3D,ENST00000424898,;PDZD9,5_prime_UTR_variant,,ENST00000286143,;PDZD9,intron_variant,,ENST00000537222,;PDZD9,synonymous_variant,p.%3D,ENST00000523914,;CTD-2649C14.1,upstream_gene_variant,,ENST00000562640,;	A	ENSG00000155714	ENST00000537222	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PDZD9	HGNC	28740	protein_coding	YES	CCDS10602.2	ENSP00000441685	.	F5GWW8_HUMAN	UPI0000E24140	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGTCGTTGGC	.	4	ESCA
TNRC6A	0	.	GRCh37	16	24818001	24818001	+	Missense_Mutation	SNP	A	A	G	rs755651320	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4436A>G	p.His1479Arg	p.H1479R	ENST00000395799	17/25	106	57	49	62	62	0	TNRC6A,missense_variant,p.His1479Arg,ENST00000395799,;TNRC6A,missense_variant,p.His179Arg,ENST00000568750,;TNRC6A,missense_variant,p.His1430Arg,ENST00000315183,;TNRC6A,missense_variant,p.His423Arg,ENST00000450465,;TNRC6A,upstream_gene_variant,,ENST00000432286,;CTD-2515A14.1,intron_variant,,ENST00000568895,;TNRC6A,3_prime_UTR_variant,,ENST00000491718,;TNRC6A,non_coding_transcript_exon_variant,,ENST00000462400,;TNRC6A,non_coding_transcript_exon_variant,,ENST00000563201,;TNRC6A,non_coding_transcript_exon_variant,,ENST00000477487,;TNRC6A,downstream_gene_variant,,ENST00000561726,;TNRC6A,upstream_gene_variant,,ENST00000569376,;	G	ENSG00000090905	ENST00000395799	Transcript	missense_variant	4565	4436	1479	H/R	cAt/cGt	rs755651320	.	.	1	TNRC6A	HGNC	11969	protein_coding	YES	CCDS10624.2	ENSP00000379144	TNR6A_HUMAN	G8JLL8_HUMAN	UPI000059D33E	.	tolerated(0.05)	probably_damaging(0.994)	17/25	.	hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCATCAGC	.	5	ESCA
HYDIN	0	.	GRCh37	16	71061539	71061539	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3008A>G	p.Asp1003Gly	p.D1003G	ENST00000393567	20/86	22	18	4	27	27	0	HYDIN,missense_variant,p.Asp1003Gly,ENST00000448089,;HYDIN,missense_variant,p.Asp1003Gly,ENST00000448691,;HYDIN,missense_variant,p.Asp1003Gly,ENST00000393567,;HYDIN,missense_variant,p.Asp1003Gly,ENST00000321489,;HYDIN,downstream_gene_variant,,ENST00000541601,;HYDIN,downstream_gene_variant,,ENST00000538248,;HYDIN,missense_variant,p.Asp621Gly,ENST00000393552,;HYDIN,3_prime_UTR_variant,,ENST00000539447,;HYDIN,intron_variant,,ENST00000538568,;HYDIN,downstream_gene_variant,,ENST00000545230,;HYDIN,downstream_gene_variant,,ENST00000540892,;	C	ENSG00000157423	ENST00000393567	Transcript	missense_variant	3159	3008	1003	D/G	gAt/gGt	.	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	probably_damaging(0.981)	20/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TCACATCAATT	.	3	ESCA
RHOT2	0	.	GRCh37	16	723059	723059	+	Silent	SNP	G	G	A	rs757394296	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1659G>A	p.%3D	p.P553P	ENST00000315082	18/19	57	47	10	30	30	0	RHOT2,synonymous_variant,p.%3D,ENST00000569197,;RHOT2,synonymous_variant,p.%3D,ENST00000315082,;RHBDL1,upstream_gene_variant,,ENST00000219551,;RHOT2,downstream_gene_variant,,ENST00000563134,;RHBDL1,upstream_gene_variant,,ENST00000561556,;RHBDL1,upstream_gene_variant,,ENST00000352681,;RHOT2,downstream_gene_variant,,ENST00000561929,;RHOT2,downstream_gene_variant,,ENST00000569943,;RHOT2,non_coding_transcript_exon_variant,,ENST00000569358,;RHOT2,non_coding_transcript_exon_variant,,ENST00000568636,;RHOT2,non_coding_transcript_exon_variant,,ENST00000569675,;RHOT2,non_coding_transcript_exon_variant,,ENST00000562957,;RHOT2,non_coding_transcript_exon_variant,,ENST00000602564,;RHOT2,non_coding_transcript_exon_variant,,ENST00000564659,;RHOT2,downstream_gene_variant,,ENST00000567589,;RHOT2,downstream_gene_variant,,ENST00000566965,;RHOT2,downstream_gene_variant,,ENST00000563776,;RHOT2,downstream_gene_variant,,ENST00000561983,;RHOT2,downstream_gene_variant,,ENST00000568950,;RHOT2,downstream_gene_variant,,ENST00000566214,;RHOT2,downstream_gene_variant,,ENST00000570092,;RHOT2,downstream_gene_variant,,ENST00000563637,;RHOT2,downstream_gene_variant,,ENST00000569706,;RHBDL1,upstream_gene_variant,,ENST00000450775,;RHOT2,downstream_gene_variant,,ENST00000570280,;RHOT2,downstream_gene_variant,,ENST00000562598,;RHOT2,downstream_gene_variant,,ENST00000562333,;RHOT2,downstream_gene_variant,,ENST00000562708,;RHOT2,downstream_gene_variant,,ENST00000565004,;RHOT2,downstream_gene_variant,,ENST00000567017,;RHOT2,downstream_gene_variant,,ENST00000561711,;	A	ENSG00000140983	ENST00000315082	Transcript	synonymous_variant	1773	1659	553	P	ccG/ccA	rs757394296	.	.	1	RHOT2	HGNC	21169	protein_coding	YES	CCDS10417.1	ENSP00000321971	MIRO2_HUMAN	.	UPI000007310B	.	.	.	18/19	.	PROSITE_profiles:PS51423,Gene3D:3.40.50.300,PIRSF_domain:PIRSF037488,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGCCGTTCTC	byFrequency	4	ESCA
CENPN	0	.	GRCh37	16	81047747	81047747	+	Missense_Mutation	SNP	C	C	T	rs199499043	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.178C>T	p.Arg60Cys	p.R60C	ENST00000393335	3/11	57	49	8	38	38	0	CENPN,missense_variant,p.Arg60Cys,ENST00000428963,;CENPN,missense_variant,p.Arg60Cys,ENST00000299572,;CENPN,missense_variant,p.Arg60Cys,ENST00000564669,;CENPN,missense_variant,p.Arg60Cys,ENST00000439957,;CENPN,missense_variant,p.Arg60Cys,ENST00000393335,;CENPN,missense_variant,p.Arg60Cys,ENST00000305850,;CMC2,intron_variant,,ENST00000565914,;CENPN,upstream_gene_variant,,ENST00000562943,;RP11-303E16.3,downstream_gene_variant,,ENST00000562315,;CENPN,non_coding_transcript_exon_variant,,ENST00000569461,;CENPN,missense_variant,p.Arg60Cys,ENST00000568445,;	T	ENSG00000166451	ENST00000393335	Transcript	missense_variant	252	178	60	R/C	Cgt/Tgt	rs199499043	.	.	1	CENPN	HGNC	30873	protein_coding	YES	CCDS42199.1	ENSP00000377007	CENPN_HUMAN	H3BMC7_HUMAN	UPI000059D3C7	.	tolerated(0.23)	benign(0.009)	3/11	.	hmmpanther:PTHR32250:SF3,hmmpanther:PTHR32250,Pfam_domain:PF05238	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAAGCGTGCA	byCluster	3	ESCA
ZCCHC14	0	.	GRCh37	16	87441433	87441433	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2453C>G	.	.	ENST00000268616	13/13	29	18	10	15	15	0	ZCCHC14,3_prime_UTR_variant,,ENST00000268616,;ZCCHC14,downstream_gene_variant,,ENST00000561928,;MAP1LC3B,downstream_gene_variant,,ENST00000268607,;MAP1LC3B,downstream_gene_variant,,ENST00000534986,;ZCCHC14,3_prime_UTR_variant,,ENST00000568020,;MAP1LC3B,downstream_gene_variant,,ENST00000570189,;MAP1LC3B,downstream_gene_variant,,ENST00000564844,;	C	ENSG00000140948	ENST00000268616	Transcript	3_prime_UTR_variant	5521	.	.	.	.	.	.	.	-1	ZCCHC14	HGNC	24134	protein_coding	YES	CCDS10961.1	ENSP00000268616	ZCH14_HUMAN	.	UPI00000705C4	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGAGATGCA	.	5	ESCA
ZZEF1	0	.	GRCh37	17	3969750	3969750	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4240G>C	p.Glu1414Gln	p.E1414Q	ENST00000381638	28/55	101	65	35	55	55	0	ZZEF1,missense_variant,p.Glu1414Gln,ENST00000381638,;ZZEF1,upstream_gene_variant,,ENST00000573183,;ZZEF1,non_coding_transcript_exon_variant,,ENST00000572426,;ZZEF1,non_coding_transcript_exon_variant,,ENST00000570365,;ZZEF1,downstream_gene_variant,,ENST00000572699,;ZZEF1,upstream_gene_variant,,ENST00000571436,;	G	ENSG00000074755	ENST00000381638	Transcript	missense_variant	4365	4240	1414	E/Q	Gag/Cag	.	.	.	-1	ZZEF1	HGNC	29027	protein_coding	YES	CCDS11043.1	ENSP00000371051	ZZEF1_HUMAN	.	UPI00004569F7	.	tolerated(0.07)	benign(0.411)	28/55	.	hmmpanther:PTHR22772,hmmpanther:PTHR22772:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCAGGGT	.	5	ESCA
UBTF	0	.	GRCh37	17	42286802	42286802	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1823C>A	p.Ser608Tyr	p.S608Y	ENST00000302904	17/21	44	18	25	37	37	0	UBTF,missense_variant,p.Ser571Tyr,ENST00000393606,;UBTF,missense_variant,p.Ser608Tyr,ENST00000302904,;UBTF,missense_variant,p.Ser608Tyr,ENST00000529383,;UBTF,missense_variant,p.Ser608Tyr,ENST00000436088,;UBTF,missense_variant,p.Ser571Tyr,ENST00000533177,;UBTF,missense_variant,p.Ser571Tyr,ENST00000526094,;UBTF,missense_variant,p.Ser571Tyr,ENST00000527034,;UBTF,missense_variant,p.Ser571Tyr,ENST00000343638,;UBTF,downstream_gene_variant,,ENST00000529373,;UBTF,downstream_gene_variant,,ENST00000530828,;CTB-175E5.7,intron_variant,,ENST00000586560,;UBTF,non_coding_transcript_exon_variant,,ENST00000531368,;UBTF,downstream_gene_variant,,ENST00000529042,;UBTF,upstream_gene_variant,,ENST00000529947,;	T	ENSG00000108312	ENST00000302904	Transcript	missense_variant	2316	1823	608	S/Y	tCc/tAc	.	.	.	-1	UBTF	HGNC	12511	protein_coding	YES	CCDS11480.1	ENSP00000302640	UBF1_HUMAN	Q9BQR2_HUMAN,E9PLT2_HUMAN,B4DLB0_HUMAN	UPI000013797C	.	deleterious(0.01)	probably_damaging(0.98)	17/21	.	PROSITE_profiles:PS50118,hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF142,Gene3D:1.10.30.10,SMART_domains:SM00398,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGGGAGATG	.	5	ESCA
SLC4A1	0	.	GRCh37	17	42335486	42335486	+	Missense_Mutation	SNP	G	G	A	rs781454553	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150C>T	p.Arg384Cys	p.R384C	ENST00000262418	11/20	43	25	17	31	31	0	SLC4A1,missense_variant,p.Arg384Cys,ENST00000262418,;AC003043.1,intron_variant,,ENST00000597382,;SLC4A1,downstream_gene_variant,,ENST00000471005,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,;	A	ENSG00000004939	ENST00000262418	Transcript	missense_variant	1306	1150	384	R/C	Cgt/Tgt	rs781454553	.	.	-1	SLC4A1	HGNC	11027	protein_coding	YES	CCDS11481.1	ENSP00000262418	B3AT_HUMAN	Q6LDU9_HUMAN,P78488_HUMAN,E2RVJ0_HUMAN,E2J824_HUMAN	UPI00000375B8	.	deleterious(0)	probably_damaging(0.973)	11/20	.	hmmpanther:PTHR11453:SF12,hmmpanther:PTHR11453,PROSITE_patterns:PS00219,TIGRFAM_domain:TIGR00834,Pfam_domain:PF00955	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCACGCACCA	byFrequency	5	ESCA
NMT1	0	.	GRCh37	17	43186129	43186129	+	3'UTR	SNP	C	C	T	rs768617425	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3122C>T	.	.	ENST00000592782	13/13	11	8	3	18	18	0	NMT1,3_prime_UTR_variant,,ENST00000592782,;NMT1,3_prime_UTR_variant,,ENST00000258960,;PLCD3,downstream_gene_variant,,ENST00000539433,;PLCD3,downstream_gene_variant,,ENST00000322765,;NMT1,non_coding_transcript_exon_variant,,ENST00000587120,;PLCD3,downstream_gene_variant,,ENST00000540511,;PLCD3,downstream_gene_variant,,ENST00000543623,;NMT1,downstream_gene_variant,,ENST00000587670,;PLCD3,downstream_gene_variant,,ENST00000545702,;NMT1,downstream_gene_variant,,ENST00000591931,;PLCD3,downstream_gene_variant,,ENST00000544333,;NMT1,downstream_gene_variant,,ENST00000587014,;	T	ENSG00000136448	ENST00000592782	Transcript	3_prime_UTR_variant	4744	.	.	.	.	rs768617425	.	.	1	NMT1	HGNC	7857	protein_coding	YES	CCDS11494.1	ENSP00000468424	NMT1_HUMAN	Q9Y465_HUMAN,Q96HI4_HUMAN,K7EN82_HUMAN	UPI0000130275	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAGGCGGGCC	.	2	ESCA
TBKBP1	0	.	GRCh37	17	45773323	45773323	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-156C>T	.	.	ENST00000361722	1/9	59	38	20	60	60	0	TBKBP1,5_prime_UTR_variant,,ENST00000361722,;TBKBP1,intron_variant,,ENST00000578982,;TBKBP1,intron_variant,,ENST00000537587,;	T	ENSG00000198933	ENST00000361722	Transcript	5_prime_UTR_variant	694	.	.	.	.	.	.	.	1	TBKBP1	HGNC	30140	protein_coding	YES	CCDS45722.1	ENSP00000354777	TBKB1_HUMAN	J3KS71_HUMAN,F5H1U4_HUMAN	UPI000006E6FC	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTCGGGGC	.	5	ESCA
MED31	0	.	GRCh37	17	6547322	6547322	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*465G>A	.	.	ENST00000225728	4/4	14	6	8	17	17	0	MED31,3_prime_UTR_variant,,ENST00000225728,;TXNDC17,3_prime_UTR_variant,,ENST00000250101,;TXNDC17,downstream_gene_variant,,ENST00000570330,;TXNDC17,downstream_gene_variant,,ENST00000574838,;KIAA0753,upstream_gene_variant,,ENST00000571642,;KIAA0753,upstream_gene_variant,,ENST00000361413,;MED31,downstream_gene_variant,,ENST00000574128,;MED31,downstream_gene_variant,,ENST00000575197,;KIAA0753,upstream_gene_variant,,ENST00000572370,;TXNDC17,downstream_gene_variant,,ENST00000571029,;TXNDC17,downstream_gene_variant,,ENST00000577146,;TXNDC17,downstream_gene_variant,,ENST00000571957,;TXNDC17,downstream_gene_variant,,ENST00000573792,;TXNDC17,downstream_gene_variant,,ENST00000576020,;TXNDC17,downstream_gene_variant,,ENST00000574734,;KIAA0753,upstream_gene_variant,,ENST00000570455,;TXNDC17,downstream_gene_variant,,ENST00000574429,;	T	ENSG00000108590	ENST00000225728	Transcript	3_prime_UTR_variant	967	.	.	.	.	.	.	.	-1	MED31	HGNC	24260	protein_coding	YES	CCDS11078.1	ENSP00000225728	MED31_HUMAN	I3L2J1_HUMAN	UPI000007072F	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCCTATGA	.	5	ESCA
TP53	0	.	GRCh37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	7/11	107	21	86	39	39	0	TP53,missense_variant,p.Arg248Gln,ENST00000413465,;TP53,missense_variant,p.Arg248Gln,ENST00000420246,;TP53,missense_variant,p.Arg248Gln,ENST00000269305,;TP53,missense_variant,p.Arg116Gln,ENST00000509690,;TP53,missense_variant,p.Arg248Gln,ENST00000359597,;TP53,missense_variant,p.Arg155Gln,ENST00000514944,;TP53,missense_variant,p.Arg248Gln,ENST00000445888,;TP53,missense_variant,p.Arg248Gln,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	933	743	248	R/Q	cGg/cAg	rs11540652,CM920675,TP53_g.13380G>A,TP53_g.13380G>C,TP53_g.13380G>T,TP53_g.13380del,COSM10662,COSM11491,COSM6549,COSM46135,COSM340105,COSM99602,COSM241995,COSM99020,COSM241994,COSM340106,COSM3356964,COSM3378346,COSM1640830,COSM1646857,COSM1646858,COSM99021,COSM241996,COSM340107	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25032700,20377871,18798306,15450681,25105660,21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R248Q|c.743G>A|113,SITE|p.R248Q|c.743G>A|633,SITE|p.R248Q|c.743G>A|64,SITE|p.R248Q|c.743G>A|42,SITE|p.R155Q|c.464G>A|114,SITE|p.R248Q|c.743G>A|110,CODON|p.0?|c.1_1182del1182|6,CODON|p.R248Q|c.743_744GG>AA|5,CODON|p.R248R|c.744G>A|5,CODON|p.R248W|c.741_742CC>TT|15,CODON|p.R248L|c.743G>T|7,CODON|p.R248L|c.743G>T|12,CODON|p.R155L|c.464G>T|12,CODON|p.R155P|c.464G>C|5,CODON|p.R248P|c.743G>C|17,CODON|p.R248L|c.743G>T|12,CODON|p.R248P|c.743G>C|5,CODON|p.R248L|c.743G>T|74,CODON|p.R248P|c.743G>C|5,BUFFER|p.L252_I254delLTI|c.754_762delCTCACCATC|4,BUFFER|p.L252_I254delLTI|c.751_759delATCCTCACC|4,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252delL|c.754_756delCTC|9,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252fs*93|c.754delC|5,BUFFER|p.L252F|c.754C>T|10,BUFFER|p.I251I|c.753C>A|3,BUFFER|p.I251N|c.752T>A|9,BUFFER|p.I251T|c.752T>C|6,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251S|c.752T>G|12,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251fs*94|c.751delA|6,BUFFER|p.I251L|c.751A>C|3,BUFFER|p.I251F|c.751A>T|8,BUFFER|p.P250P|c.750C>T|4,BUFFER|p.P250F|c.748_749CC>TT|3,BUFFER|p.I251fs*94|c.748delC|4,BUFFER|p.P250L|c.749C>T|49,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250L|c.749C>T|8,BUFFER|p.P250L|c.749C>T|6,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250S|c.748C>T|12,BUFFER|p.R249fs*96|c.746delG|4,BUFFER|p.R249S|c.747G>T|31,BUFFER|p.R249S|c.747G>C|22,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|15,BUFFER|p.R249R|c.747G>A|6,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|314,BUFFER|p.R249S|c.747G>T|30,BUFFER|p.R249T|c.746G>C|3,BUFFER|p.R249M|c.746G>T|8,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249K|c.746G>A|17,BUFFER|p.R249M|c.746G>T|4,BUFFER|p.R249T|c.746G>C|20,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249M|c.746G>T|35,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87,BUFFER|p.N247N|c.741C>T|10,BUFFER|p.N247I|c.740A>T|7,BUFFER|p.N154I|c.461A>T|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247T|c.740A>C|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247S|c.740A>G|7,BUFFER|p.N247D|c.739A>G|5,BUFFER|p.N247Y|c.739A>T|3,BUFFER|p.M153I|c.459G>C|3,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>A|21,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>C|4,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246R|c.737T>G|12,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246T|c.737T>C|8,BUFFER|p.M153R|c.458T>G|3,BUFFER|p.M246K|c.737T>A|7,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246L|c.736A>T|3,BUFFER|p.M153V|c.457A>G|7,BUFFER|p.M246V|c.736A>G|3,BUFFER|p.M246V|c.736A>G|35,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246V|c.736A>G|4,BUFFER|p.G245G|c.735C>T|5,BUFFER|p.G245D|c.734G>A|10,BUFFER|p.G245V|c.734G>T|3,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245A|c.734G>C|8,BUFFER|p.G152D|c.455G>A|23,BUFFER|p.G152V|c.455G>T|15,BUFFER|p.G245V|c.734G>T|10,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245D|c.734G>A|119,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245D|c.734G>A|7,BUFFER|p.G245V|c.734G>T|69,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245R|c.733G>C|14,BUFFER|p.G245S|c.733G>A|22,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152S|c.454G>A|56,BUFFER|p.G245C|c.733G>T|4,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245S|c.733G>A|340,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245C|c.733G>T|50,BUFFER|p.G245S|c.733G>A|39,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152C|c.454G>T|6,BUFFER|p.G152R|c.454G>C|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G151G|c.453C>T|3,BUFFER|p.G244G|c.732C>T|8,BUFFER|p.G244G|c.732C>A|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCCGGTTC	byFrequency|byCluster	5	ESCA
LGALS3BP	0	.	GRCh37	17	76968463	76968480	+	In_Frame_Del	DEL	TCGCTGGGCACCGCCAGG	TCGCTGGGCACCGCCAGG	-	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	TCGCTGGGCACCGCCAGG	TCGCTGGGCACCGCCAGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936_953delCCTGGCGGTGCCCAGCGA	p.Asp312_Ser317del	p.D312_S317del	ENST00000262776	6/6	62	55	7	25	25	0	LGALS3BP,inframe_deletion,p.Asp312_Ser317del,ENST00000262776,;LGALS3BP,3_prime_UTR_variant,,ENST00000591778,;LGALS3BP,downstream_gene_variant,,ENST00000589906,;LGALS3BP,downstream_gene_variant,,ENST00000585407,;LGALS3BP,downstream_gene_variant,,ENST00000589775,;LGALS3BP,downstream_gene_variant,,ENST00000591274,;LGALS3BP,downstream_gene_variant,,ENST00000589527,;LGALS3BP,3_prime_UTR_variant,,ENST00000587311,;LGALS3BP,3_prime_UTR_variant,,ENST00000587251,;LGALS3BP,3_prime_UTR_variant,,ENST00000586720,;LGALS3BP,non_coding_transcript_exon_variant,,ENST00000588508,;LGALS3BP,downstream_gene_variant,,ENST00000588205,;LGALS3BP,downstream_gene_variant,,ENST00000586300,;LGALS3BP,downstream_gene_variant,,ENST00000588899,;LGALS3BP,downstream_gene_variant,,ENST00000592255,;LGALS3BP,downstream_gene_variant,,ENST00000588198,;LGALS3BP,downstream_gene_variant,,ENST00000587310,;LGALS3BP,downstream_gene_variant,,ENST00000588990,;LGALS3BP,downstream_gene_variant,,ENST00000588587,;	-	ENSG00000108679	ENST00000262776	Transcript	inframe_deletion	1245-1262	936-953	312-318	DLAVPSE/E	gaCCTGGCGGTGCCCAGCGAg/gag	.	.	.	-1	LGALS3BP	HGNC	6564	protein_coding	YES	CCDS11759.1	ENSP00000262776	LG3BP_HUMAN	K7ESM3_HUMAN,K7ES75_HUMAN,K7EP36_HUMAN,K7EKQ5_HUMAN,B4DVE1_HUMAN	UPI000006E64A	.	.	.	6/6	.	Pfam_domain:PF07707,SMART_domains:SM00875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCAGCTCGCTGGGCACCGCCAGGTCGCT	.	3	ESCA
CDH2	0	.	GRCh37	18	25572711	25572711	+	Missense_Mutation	SNP	C	C	A	rs200263846	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1252G>T	p.Ala418Ser	p.A418S	ENST00000269141	9/16	42	19	23	42	42	0	CDH2,missense_variant,p.Ala387Ser,ENST00000399380,;CDH2,missense_variant,p.Ala418Ser,ENST00000269141,;	A	ENSG00000170558	ENST00000269141	Transcript	missense_variant	1676	1252	418	A/S	Gca/Tca	rs200263846	.	.	-1	CDH2	HGNC	1759	protein_coding	YES	CCDS11891.1	ENSP00000269141	CADH2_HUMAN	C9JMH2_HUMAN,C9J126_HUMAN	UPI000013D7FD	.	deleterious(0)	possibly_damaging(0.855)	9/16	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF79,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGCGTTCC	byFrequency|byCluster	5	ESCA
ZNF271	0	.	GRCh37	18	32889613	32889613	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4007A>G	.	.	ENST00000399070	3/3	25	9	15	22	22	0	ZNF271,non_coding_transcript_exon_variant,,ENST00000399070,;ZNF271,downstream_gene_variant,,ENST00000465539,;ZNF271,downstream_gene_variant,,ENST00000540308,;	G	ENSG00000257267	ENST00000399070	Transcript	non_coding_transcript_exon_variant	4007	.	.	.	.	.	.	.	1	ZNF271	HGNC	13065	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGAAGCTC	.	5	ESCA
NEDD4L	0	.	GRCh37	18	55983218	55983218	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302G>C	p.Arg101Pro	p.R101P	ENST00000400345	6/31	67	44	23	81	81	0	NEDD4L,missense_variant,p.Arg93Pro,ENST00000586263,;NEDD4L,missense_variant,p.Arg93Pro,ENST00000357895,;NEDD4L,missense_variant,p.Arg101Pro,ENST00000400345,;NEDD4L,missense_variant,p.Arg101Pro,ENST00000356462,;NEDD4L,missense_variant,p.Arg101Pro,ENST00000256830,;NEDD4L,missense_variant,p.Arg101Pro,ENST00000382850,;NEDD4L,5_prime_UTR_variant,,ENST00000456173,;NEDD4L,5_prime_UTR_variant,,ENST00000256832,;NEDD4L,5_prime_UTR_variant,,ENST00000592846,;NEDD4L,5_prime_UTR_variant,,ENST00000431212,;NEDD4L,5_prime_UTR_variant,,ENST00000435432,;NEDD4L,5_prime_UTR_variant,,ENST00000456986,;NEDD4L,5_prime_UTR_variant,,ENST00000588494,;NEDD4L,5_prime_UTR_variant,,ENST00000587190,;NEDD4L,intron_variant,,ENST00000589054,;NEDD4L,intron_variant,,ENST00000586268,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000592601,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000588066,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000585323,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000587634,;	C	ENSG00000049759	ENST00000400345	Transcript	missense_variant	585	302	101	R/P	cGa/cCa	.	.	.	1	NEDD4L	HGNC	7728	protein_coding	YES	CCDS45872.1	ENSP00000383199	NED4L_HUMAN	K7ENS6_HUMAN,K7EN51_HUMAN	UPI000058E3AE	.	deleterious(0)	probably_damaging(1)	6/31	.	PROSITE_profiles:PS50004,hmmpanther:PTHR11254:SF310,hmmpanther:PTHR11254,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,PIRSF_domain:PIRSF001569,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACACGAGACG	.	5	ESCA
PTPRM	0	.	GRCh37	18	7955118	7955118	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.839-1G>C	.	p.X280_splice	ENST00000580170	.	16	7	8	14	14	0	PTPRM,splice_acceptor_variant,,ENST00000578916,;PTPRM,splice_acceptor_variant,,ENST00000332175,;PTPRM,splice_acceptor_variant,,ENST00000444013,;PTPRM,splice_acceptor_variant,,ENST00000400053,;PTPRM,splice_acceptor_variant,,ENST00000400060,;PTPRM,splice_acceptor_variant,,ENST00000580170,;	C	ENSG00000173482	ENST00000580170	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	PTPRM	HGNC	9675	protein_coding	YES	CCDS58613.1	ENSP00000463325	PTPRM_HUMAN	Q49AC9_HUMAN	UPI00015CFC03	.	.	.	.	6/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCAGAACCA	.	5	ESCA
PRKCSH	0	.	GRCh37	19	11547294	11547294	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000252455	3/18	57	39	17	29	29	0	PRKCSH,missense_variant,p.Tyr55Cys,ENST00000587509,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000591946,;PRKCSH,missense_variant,p.Tyr119Cys,ENST00000588269,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000589838,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000412601,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000593101,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000592741,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000591462,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000587327,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000589126,;PRKCSH,missense_variant,p.Tyr55Cys,ENST00000252455,;CCDC151,upstream_gene_variant,,ENST00000356392,;CCDC151,upstream_gene_variant,,ENST00000545100,;CCDC151,upstream_gene_variant,,ENST00000591179,;CCDC151,upstream_gene_variant,,ENST00000586836,;snoU13,upstream_gene_variant,,ENST00000459022,;PRKCSH,non_coding_transcript_exon_variant,,ENST00000593104,;PRKCSH,intron_variant,,ENST00000593053,;CCDC151,upstream_gene_variant,,ENST00000593281,;CCDC151,upstream_gene_variant,,ENST00000591345,;	G	ENSG00000130175	ENST00000252455	Transcript	missense_variant	500	164	55	Y/C	tAt/tGt	.	.	.	1	PRKCSH	HGNC	9411	protein_coding	YES	CCDS32911.1	ENSP00000252455	GLU2B_HUMAN	K7EPW7_HUMAN,K7EKX1_HUMAN,K7EJ70_HUMAN,K7EIP3_HUMAN	UPI000007007F	.	deleterious(0)	probably_damaging(1)	3/18	.	hmmpanther:PTHR12630,hmmpanther:PTHR12630:SF1,Pfam_domain:PF12999,Gene3D:4.10.400.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTATTGCG	.	5	ESCA
RASAL3	0	.	GRCh37	19	15571872	15571872	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.605G>A	p.Arg202Gln	p.R202Q	ENST00000343625	5/18	92	53	39	55	55	0	RASAL3,missense_variant,p.Arg202Gln,ENST00000343625,;RASAL3,upstream_gene_variant,,ENST00000599694,;RASAL3,upstream_gene_variant,,ENST00000608577,;RASAL3,upstream_gene_variant,,ENST00000595098,;RASAL3,splice_region_variant,,ENST00000602101,;RASAL3,upstream_gene_variant,,ENST00000597025,;	T	ENSG00000105122	ENST00000343625	Transcript	missense_variant	691	605	202	R/Q	cGg/cAg	.	.	.	-1	RASAL3	HGNC	26129	protein_coding	YES	CCDS46006.1	ENSP00000341905	RASL3_HUMAN	.	UPI0000197831	.	tolerated(0.1)	possibly_damaging(0.89)	5/18	.	hmmpanther:PTHR10194:SF82,hmmpanther:PTHR10194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACCCGAACG	.	5	ESCA
NFKBID	0	.	GRCh37	19	36387648	36387648	+	Missense_Mutation	SNP	T	T	C	rs774001311	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.238A>G	p.Ile80Val	p.I80V	ENST00000396901	6/12	55	37	18	50	50	0	NFKBID,missense_variant,p.Ile80Val,ENST00000606253,;NFKBID,missense_variant,p.Ile95Val,ENST00000585925,;NFKBID,missense_variant,p.Ile232Val,ENST00000352614,;NFKBID,missense_variant,p.Ile80Val,ENST00000396901,;NFKBID,downstream_gene_variant,,ENST00000585544,;NFKBID,non_coding_transcript_exon_variant,,ENST00000591730,;NFKBID,non_coding_transcript_exon_variant,,ENST00000588497,;NFKBID,non_coding_transcript_exon_variant,,ENST00000590094,;NFKBID,non_coding_transcript_exon_variant,,ENST00000586361,;NFKBID,upstream_gene_variant,,ENST00000590828,;NFKBID,downstream_gene_variant,,ENST00000588039,;	C	ENSG00000167604	ENST00000396901	Transcript	missense_variant	812	238	80	I/V	Att/Gtt	rs774001311	.	.	-1	NFKBID	HGNC	15671	protein_coding	YES	CCDS42552.1	ENSP00000380109	IKBD_HUMAN	.	UPI000006EE99	.	tolerated(0.44)	benign(0.014)	6/12	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24124:SF5,hmmpanther:PTHR24124,Pfam_domain:PF12796,Gene3D:1.25.40.20,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGAATGTCAA	byFrequency	5	ESCA
ZNF382	0	.	GRCh37	19	37117694	37117694	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895C>G	p.Pro299Ala	p.P299A	ENST00000292928	5/5	75	49	25	49	49	0	ZNF382,missense_variant,p.Pro298Ala,ENST00000435416,;ZNF382,missense_variant,p.Pro299Ala,ENST00000292928,;ZNF382,missense_variant,p.Pro298Ala,ENST00000439428,;ZNF382,missense_variant,p.Pro250Ala,ENST00000423582,;ZNF382,downstream_gene_variant,,ENST00000590785,;CTD-3234P18.2,upstream_gene_variant,,ENST00000585467,;	G	ENSG00000161298	ENST00000292928	Transcript	missense_variant	1008	895	299	P/A	Cct/Gct	.	.	.	1	ZNF382	HGNC	17409	protein_coding	YES	CCDS33004.1	ENSP00000292928	ZN382_HUMAN	K7EK67_HUMAN,C9JME7_HUMAN	UPI000013E0E2	.	tolerated(0.25)	benign(0.001)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF22,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTCCTTAC	.	5	ESCA
ZNF420	0	.	GRCh37	19	37619827	37619827	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1934G>A	p.Cys645Tyr	p.C645Y	ENST00000337995	5/5	93	67	25	84	84	0	ZNF420,missense_variant,p.Cys645Tyr,ENST00000337995,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF420,intron_variant,,ENST00000585862,;ZNF420,intron_variant,,ENST00000304239,;ZNF420,downstream_gene_variant,,ENST00000590332,;ZNF420,downstream_gene_variant,,ENST00000587029,;ZNF420,downstream_gene_variant,,ENST00000589245,;CTC-454I21.4,intron_variant,,ENST00000587645,;ZNF585A,intron_variant,,ENST00000588723,;ZNF420,intron_variant,,ENST00000586540,;ZNF585A,intron_variant,,ENST00000587817,;ZNF420,downstream_gene_variant,,ENST00000589461,;	A	ENSG00000197050	ENST00000337995	Transcript	missense_variant	2149	1934	645	C/Y	tGt/tAt	.	.	.	1	ZNF420	HGNC	20649	protein_coding	YES	CCDS12498.1	ENSP00000338770	ZN420_HUMAN	K7ERS3_HUMAN,K7EQC9_HUMAN,K7ELF6_HUMAN	UPI000007049F	.	deleterious(0.01)	possibly_damaging(0.86)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATGTAAGG	.	5	ESCA
ZNF569	0	.	GRCh37	19	37903687	37903687	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1873A>G	p.Ile625Val	p.I625V	ENST00000316950	6/6	91	61	29	56	56	0	ZNF569,missense_variant,p.Ile625Val,ENST00000316950,;ZNF569,missense_variant,p.Ile625Val,ENST00000392149,;ZNF569,missense_variant,p.Ile466Val,ENST00000392150,;ZNF569,downstream_gene_variant,,ENST00000592490,;ZNF569,downstream_gene_variant,,ENST00000448051,;	C	ENSG00000196437	ENST00000316950	Transcript	missense_variant	2431	1873	625	I/V	Ata/Gta	.	.	.	-1	ZNF569	HGNC	24737	protein_coding	YES	CCDS12503.1	ENSP00000325018	ZN569_HUMAN	Q17RR6_HUMAN	UPI0000202203	.	deleterious(0.02)	probably_damaging(0.978)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF68,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTATATGTA	.	5	ESCA
PPM1N	0	.	GRCh37	19	46001827	46001847	+	In_Frame_Del	DEL	GAGGCGGGGCGCAGGGCCCCC	GAGGCGGGGCGCAGGGCCCCC	-	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	GAGGCGGGGCGCAGGGCCCCC	GAGGCGGGGCGCAGGGCCCCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99_119delGGCGGGGCGCAGGGCCCCCGA	p.Ala34_Glu40del	p.A34_E40del	ENST00000451287	1/5	36	29	7	21	21	0	PPM1N,inframe_deletion,p.Ala34_Glu40del,ENST00000451287,;PPM1N,intron_variant,,ENST00000396737,;PPM1N,intron_variant,,ENST00000401705,;PPM1N,intron_variant,,ENST00000456399,;RTN2,upstream_gene_variant,,ENST00000590526,;PPM1N,upstream_gene_variant,,ENST00000396735,;RTN2,upstream_gene_variant,,ENST00000344680,;PPM1N,upstream_gene_variant,,ENST00000324688,;PPM1N,upstream_gene_variant,,ENST00000396736,;PPM1N,upstream_gene_variant,,ENST00000401593,;RTN2,upstream_gene_variant,,ENST00000245923,;RTN2,upstream_gene_variant,,ENST00000589384,;PPM1N,upstream_gene_variant,,ENST00000415077,;RTN2,upstream_gene_variant,,ENST00000587597,;RTN2,upstream_gene_variant,,ENST00000592064,;RTN2,upstream_gene_variant,,ENST00000591286,;	-	ENSG00000213889	ENST00000451287	Transcript	inframe_deletion	97-117	97-117	33-39	EAGRRAP/-	GAGGCGGGGCGCAGGGCCCCC/-	.	.	.	1	PPM1N	HGNC	26845	protein_coding	YES	CCDS46115.1	ENSP00000397050	PPM1N_HUMAN	.	UPI0000DD84FC	.	.	.	1/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13832:SF243,hmmpanther:PTHR13832	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAGGAGGAGGCGGGGCGCAGGGCCCCCGAAGG	.	2	ESCA
UHRF1	0	.	GRCh37	19	4954401	4954401	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2434C>T	.	.	ENST00000592666	14/17	72	45	27	48	48	0	UHRF1,non_coding_transcript_exon_variant,,ENST00000262952,;UHRF1,non_coding_transcript_exon_variant,,ENST00000592666,;UHRF1,non_coding_transcript_exon_variant,,ENST00000592200,;UHRF1,non_coding_transcript_exon_variant,,ENST00000587870,;UHRF1,non_coding_transcript_exon_variant,,ENST00000591699,;UHRF1,non_coding_transcript_exon_variant,,ENST00000587187,;UHRF1,non_coding_transcript_exon_variant,,ENST00000591733,;UHRF1,non_coding_transcript_exon_variant,,ENST00000398240,;UHRF1,non_coding_transcript_exon_variant,,ENST00000543616,;	T	ENSG00000034063	ENST00000592666	Transcript	non_coding_transcript_exon_variant	2434	.	.	.	.	.	.	.	1	UHRF1	HGNC	12556	processed_transcript	YES	.	.	.	.	.	.	.	.	14/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAGCGAGAG	.	5	ESCA
KIR2DL1	0	.	GRCh37	19	55295326	55295326	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*61G>A	.	.	ENST00000336077	8/8	42	37	4	27	27	0	KIR2DL3,3_prime_UTR_variant,,ENST00000434419,;KIR2DL1,3_prime_UTR_variant,,ENST00000336077,;KIR2DL4,intron_variant,,ENST00000396284,;KIR3DL1,intron_variant,,ENST00000541392,;KIR3DL1,intron_variant,,ENST00000538269,;KIR3DL1,intron_variant,,ENST00000402254,;KIR2DL1,downstream_gene_variant,,ENST00000291633,;CTB-61M7.1,intron_variant,,ENST00000400864,;KIR3DP1,upstream_gene_variant,,ENST00000580853,;	A	ENSG00000125498	ENST00000336077	Transcript	3_prime_UTR_variant	1148	.	.	.	.	.	.	.	1	KIR2DL1	HGNC	6329	protein_coding	YES	CCDS12904.1	ENSP00000336769	KI2L1_HUMAN	Q6H2H4_HUMAN,Q6H2H3_HUMAN,K7R1R8_HUMAN	UPI00001195F7	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AACCGGGTTGC	.	3	ESCA
UBL4B	0	.	GRCh37	1	110656110	110656110	+	3'UTR	SNP	C	C	A	rs775056139	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*429C>A	.	.	ENST00000334179	1/1	31	22	9	49	49	0	UBL4B,3_prime_UTR_variant,,ENST00000334179,;RP4-773N10.6,downstream_gene_variant,,ENST00000554808,;	A	ENSG00000186150	ENST00000334179	Transcript	3_prime_UTR_variant	1049	.	.	.	.	rs775056139	.	.	1	UBL4B	HGNC	32309	protein_coding	YES	CCDS820.1	ENSP00000334044	UBL4B_HUMAN	.	UPI0000072926	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCCCTAGG	.	5	ESCA
CLCN6	0	.	GRCh37	1	11894293	11894293	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1527C>T	p.%3D	p.S509S	ENST00000346436	16/23	37	21	15	28	28	0	CLCN6,synonymous_variant,p.%3D,ENST00000376487,;CLCN6,synonymous_variant,p.%3D,ENST00000346436,;CLCN6,synonymous_variant,p.%3D,ENST00000376496,;CLCN6,splice_region_variant,,ENST00000312413,;CLCN6,splice_region_variant,,ENST00000494028,;CLCN6,downstream_gene_variant,,ENST00000376492,;	T	ENSG00000011021	ENST00000346436	Transcript	synonymous_variant	1579	1527	509	S	agC/agT	.	.	.	1	CLCN6	HGNC	2024	protein_coding	YES	CCDS138.1	ENSP00000234488	CLCN6_HUMAN	.	UPI000013F2D3	.	.	.	16/23	.	Superfamily_domains:SSF81340,Pfam_domain:PF00654,Gene3D:1otsB00,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF69	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTAGCTACAT	.	5	ESCA
SPRR3	0	.	GRCh37	1	152976112	152976112	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*106T>C	.	.	ENST00000331860	3/3	125	95	29	45	45	0	SPRR3,3_prime_UTR_variant,,ENST00000295367,;SPRR3,3_prime_UTR_variant,,ENST00000331860,;SPRR3,downstream_gene_variant,,ENST00000542696,;SPRR3,downstream_gene_variant,,ENST00000443178,;SPRR3,downstream_gene_variant,,ENST00000495845,;	C	ENSG00000163209	ENST00000331860	Transcript	3_prime_UTR_variant	766	.	.	.	.	.	.	.	1	SPRR3	HGNC	11268	protein_coding	YES	CCDS1033.1	ENSP00000330391	SPRR3_HUMAN	B1AN48_HUMAN	UPI0000127F1F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACATTGTCA	.	5	ESCA
FCRL4	0	.	GRCh37	1	157559012	157559012	+	Missense_Mutation	SNP	G	G	A	rs138448208	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.289C>T	p.Arg97Cys	p.R97C	ENST00000271532	3/12	112	107	5	73	73	0	FCRL4,missense_variant,p.Arg97Cys,ENST00000271532,;FCRL4,non_coding_transcript_exon_variant,,ENST00000448509,;	A	ENSG00000163518	ENST00000271532	Transcript	missense_variant	425	289	97	R/C	Cgc/Tgc	rs138448208	.	.	-1	FCRL4	HGNC	18507	protein_coding	YES	CCDS1166.1	ENSP00000271532	FCRL4_HUMAN	.	UPI000006E26B	.	tolerated(0.1)	benign(0.417)	3/12	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF50,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0.0002	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L99L|c.297C>A|3,BUFFER|p.L99P|c.296T>C|6	MUTECT|MUSE	CAAGCGCACAG	byCluster	2	ESCA
TBX19	0	.	GRCh37	1	168283550	168283550	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1310A>G	.	.	ENST00000367821	8/8	104	16	88	41	41	0	TBX19,3_prime_UTR_variant,,ENST00000431969,;TBX19,3_prime_UTR_variant,,ENST00000367821,;TBX19,downstream_gene_variant,,ENST00000441464,;TBX19,non_coding_transcript_exon_variant,,ENST00000465440,;	G	ENSG00000143178	ENST00000367821	Transcript	3_prime_UTR_variant	2708	.	.	.	.	.	.	.	1	TBX19	HGNC	11596	protein_coding	YES	CCDS1272.1	ENSP00000356795	TBX19_HUMAN	.	UPI000003176C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTATTAGA	.	5	ESCA
CFH	0	.	GRCh37	1	196716457	196716457	+	3'UTR	SNP	G	G	A	rs463726	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*14G>A	.	.	ENST00000367429	22/22	68	60	8	62	62	0	CFH,3_prime_UTR_variant,,ENST00000367429,;CFH,non_coding_transcript_exon_variant,,ENST00000466229,;	A	ENSG00000000971	ENST00000367429	Transcript	3_prime_UTR_variant	3950	.	.	.	.	rs463726	.	.	1	CFH	HGNC	4883	protein_coding	YES	CCDS1385.1	ENSP00000356399	CFAH_HUMAN	.	UPI000013C4D1	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ATAAAGTGCAC	suspect|by2Hit2Allele	2	ESCA
ZBTB41	0	.	GRCh37	1	197125382	197125382	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3107G>C	.	.	ENST00000367405	10/10	65	44	21	154	154	0	ZBTB41,3_prime_UTR_variant,,ENST00000367405,;ZBTB41,downstream_gene_variant,,ENST00000467322,;	G	ENSG00000177888	ENST00000367405	Transcript	3_prime_UTR_variant	5906	.	.	.	.	.	.	.	-1	ZBTB41	HGNC	24819	protein_coding	YES	CCDS30960.1	ENSP00000356375	ZBT41_HUMAN	Q8N9U5_HUMAN	UPI00001D7DE7	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCTTTGG	.	5	ESCA
NAV1	0	.	GRCh37	1	201763801	201763801	+	Intron	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3517+96A>G	.	.	ENST00000367296	.	46	27	19	32	32	0	NAV1,intron_variant,,ENST00000367297,;NAV1,intron_variant,,ENST00000438083,;NAV1,intron_variant,,ENST00000367300,;NAV1,intron_variant,,ENST00000295624,;NAV1,intron_variant,,ENST00000430015,;NAV1,intron_variant,,ENST00000367302,;NAV1,intron_variant,,ENST00000367296,;NAV1,intron_variant,,ENST00000367295,;IPO9-AS1,intron_variant,,ENST00000413035,;NAV1,non_coding_transcript_exon_variant,,ENST00000469130,;NAV1,intron_variant,,ENST00000490213,;NAV1,intron_variant,,ENST00000477118,;	G	ENSG00000134369	ENST00000367296	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NAV1	HGNC	15989	protein_coding	YES	CCDS1414.2	ENSP00000356265	NAV1_HUMAN	.	UPI00004562D4	.	.	.	.	15/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATATCAAG	.	5	ESCA
KIF26B	0	.	GRCh37	1	245850736	245850736	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4451C>T	p.Pro1484Leu	p.P1484L	ENST00000407071	12/15	31	8	22	18	18	0	KIF26B,missense_variant,p.Pro1484Leu,ENST00000407071,;KIF26B,missense_variant,p.Pro1103Leu,ENST00000366518,;KIF26B,downstream_gene_variant,,ENST00000483253,;	T	ENSG00000162849	ENST00000407071	Transcript	missense_variant	4891	4451	1484	P/L	cCc/cTc	.	.	.	1	KIF26B	HGNC	25484	protein_coding	YES	CCDS44342.1	ENSP00000385545	KI26B_HUMAN	B4DF75_HUMAN	UPI0000695D71	.	tolerated(0.16)	unknown(0)	12/15	.	hmmpanther:PTHR24115:SF363,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGCCCAGTC	.	5	ESCA
CEP250	0	.	GRCh37	20	34089770	34089770	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3997G>A	p.Glu1333Lys	p.E1333K	ENST00000397527	29/35	131	78	52	58	58	0	CEP250,missense_variant,p.Glu1277Lys,ENST00000342580,;CEP250,missense_variant,p.Glu1333Lys,ENST00000397527,;CEP250,upstream_gene_variant,,ENST00000422671,;CEP250,3_prime_UTR_variant,,ENST00000425525,;	A	ENSG00000126001	ENST00000397527	Transcript	missense_variant	4717	3997	1333	E/K	Gag/Aag	.	.	.	1	CEP250	HGNC	1859	protein_coding	YES	CCDS13255.1	ENSP00000380661	CP250_HUMAN	Q5JWS6_HUMAN,Q5JWS5_HUMAN,G1UI40_HUMAN	UPI000006FE8F	.	.	possibly_damaging(0.874)	29/35	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCAGAGCTA	.	5	ESCA
ADNP	0	.	GRCh37	20	49509654	49509654	+	Missense_Mutation	SNP	T	T	A	rs761339004	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597A>T	p.Met533Leu	p.M533L	ENST00000396029	5/5	63	41	21	26	26	0	ADNP,missense_variant,p.Met533Leu,ENST00000396032,;ADNP,missense_variant,p.Met533Leu,ENST00000396029,;ADNP,missense_variant,p.Met533Leu,ENST00000349014,;ADNP,missense_variant,p.Met533Leu,ENST00000371602,;ADNP,downstream_gene_variant,,ENST00000534467,;	A	ENSG00000101126	ENST00000396029	Transcript	missense_variant	2165	1597	533	M/L	Atg/Ttg	rs761339004	.	.	-1	ADNP	HGNC	15766	protein_coding	YES	CCDS13433.1	ENSP00000379346	ADNP_HUMAN	E9PQK8_HUMAN	UPI00000375B9	.	tolerated(0.95)	benign(0.001)	5/5	.	SMART_domains:SM00355,PROSITE_patterns:PS00028,hmmpanther:PTHR15740:SF1,hmmpanther:PTHR15740,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCATCCGCA	byFrequency	5	ESCA
KRTAP13-3	0	.	GRCh37	21	31797973	31797973	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258C>T	p.%3D	p.H86H	ENST00000390690	1/1	58	39	19	53	53	0	KRTAP13-3,synonymous_variant,p.%3D,ENST00000390690,;KRTAP13-4,upstream_gene_variant,,ENST00000334068,;	A	ENSG00000240432	ENST00000390690	Transcript	synonymous_variant	314	258	86	H	caC/caT	.	.	.	-1	KRTAP13-3	HGNC	18925	protein_coding	YES	CCDS13591.1	ENSP00000375109	KR133_HUMAN	.	UPI000003B46C	.	.	.	1/1	.	hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF12,Pfam_domain:PF05287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATGTGAGT	.	5	ESCA
NDUFV3	0	.	GRCh37	21	44329103	44329103	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1394C>A	p.Ser465Tyr	p.S465Y	ENST00000354250	4/4	35	19	15	27	27	0	NDUFV3,missense_variant,p.Ser100Tyr,ENST00000340344,;NDUFV3,missense_variant,p.Ser465Tyr,ENST00000354250,;NDUFV3,non_coding_transcript_exon_variant,,ENST00000460259,;	A	ENSG00000160194	ENST00000354250	Transcript	missense_variant	1463	1394	465	S/Y	tCc/tAc	.	.	.	1	NDUFV3	HGNC	7719	protein_coding	YES	CCDS33572.1	ENSP00000346196	NDUV3_HUMAN	.	UPI000037848B	.	deleterious(0)	probably_damaging(1)	4/4	.	hmmpanther:PTHR17117,hmmpanther:PTHR17117:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCCTCAG	.	5	ESCA
AP001053.11	0	.	GRCh37	21	45232041	45232041	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.408G>A	.	.	ENST00000400385	1/2	57	41	16	34	34	0	AP001053.11,non_coding_transcript_exon_variant,,ENST00000400385,;AP001053.11,upstream_gene_variant,,ENST00000448247,;AP001053.11,upstream_gene_variant,,ENST00000437258,;AP001053.11,upstream_gene_variant,,ENST00000543603,;	T	ENSG00000215458	ENST00000400385	Transcript	non_coding_transcript_exon_variant	408	.	.	.	.	.	.	.	-1	AP001053.11	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCCCATGGT	.	5	ESCA
DRG1	0	.	GRCh37	22	31795658	31795658	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12G>T	.	.	ENST00000331457	1/9	83	69	14	38	38	0	DRG1,5_prime_UTR_variant,,ENST00000331457,;DRG1,non_coding_transcript_exon_variant,,ENST00000433341,;DRG1,non_coding_transcript_exon_variant,,ENST00000486584,;DRG1,5_prime_UTR_variant,,ENST00000416465,;	T	ENSG00000185721	ENST00000331457	Transcript	5_prime_UTR_variant	150	.	.	.	.	.	.	.	1	DRG1	HGNC	3029	protein_coding	YES	CCDS13897.1	ENSP00000329715	DRG1_HUMAN	Q9UFA5_HUMAN	UPI0000129879	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGGTACTC	.	5	ESCA
SREBF2	0	.	GRCh37	22	42274003	42274004	+	Frame_Shift_Del	DEL	GT	GT	-	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	GT	GT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1640_1641delTG	p.Val547AspfsTer105	p.V547Dfs*105	ENST00000361204	9/19	69	53	16	42	42	0	SREBF2,frameshift_variant,p.Val547AspfsTer105,ENST00000361204,;SREBF2,frameshift_variant,p.Val547AspfsTer54,ENST00000424354,;SREBF2,downstream_gene_variant,,ENST00000464119,;SREBF2,downstream_gene_variant,,ENST00000462539,;	-	ENSG00000198911	ENST00000361204	Transcript	frameshift_variant	1803-1804	1637-1638	546	G/X	gGT/g	.	.	.	1	SREBF2	HGNC	11290	protein_coding	YES	CCDS14023.1	ENSP00000354476	SRBP2_HUMAN	Q8NCY3_HUMAN	UPI00001678D0	.	.	.	9/19	.	hmmpanther:PTHR12565:SF6,hmmpanther:PTHR12565	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAAATGGTGTGAT	.	3	ESCA
NFE2L2	0	.	GRCh37	2	178098800	178098800	+	Missense_Mutation	SNP	T	T	G	.	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245A>C	p.Glu82Ala	p.E82A	ENST00000397062	2/5	137	41	96	72	72	0	NFE2L2,missense_variant,p.Glu66Ala,ENST00000423513,;NFE2L2,missense_variant,p.Glu82Ala,ENST00000397062,;NFE2L2,missense_variant,p.Glu66Ala,ENST00000446151,;NFE2L2,missense_variant,p.Glu66Ala,ENST00000588123,;NFE2L2,missense_variant,p.Glu81Ala,ENST00000586532,;NFE2L2,missense_variant,p.Glu66Ala,ENST00000421929,;NFE2L2,missense_variant,p.Glu66Ala,ENST00000464747,;NFE2L2,missense_variant,p.Glu66Ala,ENST00000448782,;NFE2L2,missense_variant,p.Glu66Ala,ENST00000397063,;NFE2L2,splice_region_variant,,ENST00000449627,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	G	ENSG00000116044	ENST00000397062	Transcript	missense_variant	800	245	82	E/A	gAa/gCa	COSM132853,COSM1631471,COSM132962	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(0.999)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.E82D|c.246A>C|3,CODON|p.E82D|c.246A>T|6,CODON|p.E82G|c.245A>G|7,BUFFER|p.E82Q|c.244G>C|6,BUFFER|p.G81D|c.242G>A|6,BUFFER|p.G81V|c.242G>T|7,BUFFER|p.G81C|c.241G>T|3,BUFFER|p.G81S|c.241G>A|3,BUFFER|p.T80R|c.239C>G|3,BUFFER|p.T80K|c.239C>A|5,BUFFER|p.T80P|c.238A>C|6,BUFFER|p.E79K|c.235G>A|10,BUFFER|p.E79Q|c.235G>C|11	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAATTCACCT	.	5	ESCA
ADCY3	0	.	GRCh37	2	25141367	25141367	+	Missense_Mutation	SNP	C	C	T	rs760416852	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490G>A	p.Ala164Thr	p.A164T	ENST00000260600	1/21	66	59	6	41	41	0	ADCY3,missense_variant,p.Ala164Thr,ENST00000260600,;ADCY3,missense_variant,p.Ala164Thr,ENST00000435135,;ADCY3,downstream_gene_variant,,ENST00000438445,;	T	ENSG00000138031	ENST00000260600	Transcript	missense_variant	1342	490	164	A/T	Gcg/Acg	rs760416852	.	.	-1	ADCY3	HGNC	234	protein_coding	YES	CCDS1715.1	ENSP00000260600	ADCY3_HUMAN	Q8NBM1_HUMAN,C9J969_HUMAN	UPI000013D0ED	.	tolerated(0.72)	benign(0.001)	1/21	.	hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF221	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.H163H|c.489C>T|3	RADIA|MUTECT|MUSE|VARSCANS	AGCCGCGTGGG	.	4	ESCA
MTHFD2	0	.	GRCh37	2	74442339	74442339	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*970A>G	.	.	ENST00000394053	8/8	54	22	31	32	32	0	MTHFD2,3_prime_UTR_variant,,ENST00000409601,;MTHFD2,3_prime_UTR_variant,,ENST00000409804,;MTHFD2,3_prime_UTR_variant,,ENST00000394053,;SLC4A5,downstream_gene_variant,,ENST00000359484,;SLC4A5,downstream_gene_variant,,ENST00000423644,;SLC4A5,downstream_gene_variant,,ENST00000394019,;MTHFD2,downstream_gene_variant,,ENST00000264090,;SLC4A5,downstream_gene_variant,,ENST00000346834,;MTHFD2,downstream_gene_variant,,ENST00000394050,;SLC4A5,downstream_gene_variant,,ENST00000483195,;SLC4A5,downstream_gene_variant,,ENST00000480696,;RP11-287D1.3,intron_variant,,ENST00000451608,;MTHFD2,downstream_gene_variant,,ENST00000470592,;MTHFD2,downstream_gene_variant,,ENST00000489041,;	G	ENSG00000065911	ENST00000394053	Transcript	3_prime_UTR_variant	2103	.	.	.	.	.	.	.	1	MTHFD2	HGNC	7434	protein_coding	YES	CCDS1935.2	ENSP00000377617	MTDC_HUMAN	Q7Z650_HUMAN,B4DY35_HUMAN,B2R7W0_HUMAN	UPI0000208708	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACTATTGAA	.	5	ESCA
CTNNA2	0	.	GRCh37	2	80875725	80875725	+	3'UTR	SNP	T	T	C	rs372255835	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*728T>C	.	.	ENST00000466387	22/22	22	18	3	21	21	0	CTNNA2,3_prime_UTR_variant,,ENST00000496558,;CTNNA2,3_prime_UTR_variant,,ENST00000466387,;CTNNA2,3_prime_UTR_variant,,ENST00000541047,;CTNNA2,3_prime_UTR_variant,,ENST00000343114,;CTNNA2,3_prime_UTR_variant,,ENST00000402739,;CTNNA2,downstream_gene_variant,,ENST00000540488,;CTNNA2,downstream_gene_variant,,ENST00000361291,;	C	ENSG00000066032	ENST00000466387	Transcript	3_prime_UTR_variant	4170	.	.	.	.	rs372255835	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TTTTTTCTTTT	.	2	ESCA
RNF103	0	.	GRCh37	2	86831974	86831975	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1049dupT	p.Arg352AlafsTer13	p.R352Afs*13	ENST00000237455	4/4	63	54	9	56	56	0	RNF103,frameshift_variant,p.Arg352AlafsTer13,ENST00000237455,;RNF103-CHMP3,intron_variant,,ENST00000440757,;CHMP3,intron_variant,,ENST00000439940,;RNF103-CHMP3,intron_variant,,ENST00000604011,;AC015971.2,intron_variant,,ENST00000439077,;AC015971.2,intron_variant,,ENST00000426549,;AC015971.2,intron_variant,,ENST00000597638,;AC015971.2,intron_variant,,ENST00000424788,;RNF103,non_coding_transcript_exon_variant,,ENST00000477307,;RNF103,intron_variant,,ENST00000463333,;RNF103,non_coding_transcript_exon_variant,,ENST00000472030,;	A	ENSG00000239305	ENST00000237455	Transcript	frameshift_variant	2018-2019	1049-1050	350	I/IX	ata/atTa	.	.	.	-1	RNF103	HGNC	12859	protein_coding	YES	CCDS33237.1	ENSP00000237455	RN103_HUMAN	.	UPI0000073F2A	.	.	.	4/4	.	hmmpanther:PTHR15302,hmmpanther:PTHR15302:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGCTTTATGGT	.	3	ESCA
SMYD1	0	.	GRCh37	2	88367423	88367423	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40G>A	p.Ala14Thr	p.A14T	ENST00000419482	1/10	149	127	22	94	94	0	SMYD1,missense_variant,p.Ala14Thr,ENST00000444564,;SMYD1,missense_variant,p.Ala14Thr,ENST00000438570,;SMYD1,missense_variant,p.Ala14Thr,ENST00000419482,;	A	ENSG00000115593	ENST00000419482	Transcript	missense_variant	125	40	14	A/T	Gct/Act	.	.	.	1	SMYD1	HGNC	20986	protein_coding	YES	CCDS33240.1	ENSP00000393453	SMYD1_HUMAN	Q5GJ33_HUMAN	UPI000006EB68	.	tolerated(0.2)	benign(0.012)	1/10	.	PROSITE_profiles:PS50280,hmmpanther:PTHR12197:SF16,hmmpanther:PTHR12197,Gene3D:2.170.270.10,SMART_domains:SM00317,Superfamily_domains:SSF82199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACCGCTGAG	.	4	ESCA
PLS1	0	.	GRCh37	3	142388241	142388241	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.80A>G	p.Asn27Ser	p.N27S	ENST00000337777	3/16	77	65	12	39	39	0	PLS1,missense_variant,p.Asn27Ser,ENST00000475296,;PLS1,missense_variant,p.Asn27Ser,ENST00000461644,;PLS1,missense_variant,p.Asn27Ser,ENST00000483373,;PLS1,missense_variant,p.Asn27Ser,ENST00000337777,;PLS1,missense_variant,p.Asn27Ser,ENST00000457734,;PLS1,missense_variant,p.Asn27Ser,ENST00000464320,;PLS1,missense_variant,p.Asn27Ser,ENST00000497002,;PLS1,missense_variant,p.Asn27Ser,ENST00000497199,;PLS1,missense_variant,p.Asn27Ser,ENST00000495744,;PLS1,5_prime_UTR_variant,,ENST00000476044,;RN7SKP25,upstream_gene_variant,,ENST00000362449,;PLS1,non_coding_transcript_exon_variant,,ENST00000460104,;	G	ENSG00000120756	ENST00000337777	Transcript	missense_variant	293	80	27	N/S	aAt/aGt	.	.	.	1	PLS1	HGNC	9090	protein_coding	YES	CCDS3125.1	ENSP00000336831	PLSI_HUMAN	C9JYI1_HUMAN,C9JVY2_HUMAN,C9JU08_HUMAN,C9JAM8_HUMAN,C9JAM3_HUMAN,C9J359_HUMAN,C9J0F3_HUMAN	UPI000013D59A	.	tolerated(0.29)	benign(0.021)	3/16	.	PROSITE_profiles:PS50222,hmmpanther:PTHR19961:SF27,hmmpanther:PTHR19961,PROSITE_patterns:PS00018,Pfam_domain:PF13499,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACAATAGTG	.	5	ESCA
GALNT15	0	.	GRCh37	3	16250103	16250103	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1005G>A	p.Trp335Ter	p.W335*	ENST00000339732	4/10	103	74	28	116	116	0	GALNT15,stop_gained,p.Trp335Ter,ENST00000339732,;GALNT15,stop_gained,p.Trp335Ter,ENST00000437509,;GALNT15,3_prime_UTR_variant,,ENST00000430410,;GALNT15,upstream_gene_variant,,ENST00000489467,;	A	ENSG00000131386	ENST00000339732	Transcript	stop_gained	1508	1005	335	W/*	tgG/tgA	.	.	.	1	GALNT15	HGNC	21531	protein_coding	YES	CCDS33711.1	ENSP00000344260	GLT15_HUMAN	B3KT16_HUMAN	UPI0000048F0D	.	.	.	4/10	.	hmmpanther:PTHR11675:SF36,hmmpanther:PTHR11675,Pfam_domain:PF00535,Gene3D:3.90.550.10,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTGGAAGCT	.	5	ESCA
BCHE	0	.	GRCh37	3	165503943	165503943	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1674G>A	p.%3D	p.L558L	ENST00000264381	3/4	124	94	30	51	51	0	BCHE,synonymous_variant,p.%3D,ENST00000540653,;BCHE,synonymous_variant,p.%3D,ENST00000264381,;BCHE,synonymous_variant,p.%3D,ENST00000479451,;BCHE,synonymous_variant,p.%3D,ENST00000488954,;BCHE,synonymous_variant,p.%3D,ENST00000497011,;BCHE,3_prime_UTR_variant,,ENST00000482958,;	T	ENSG00000114200	ENST00000264381	Transcript	synonymous_variant	1841	1674	558	L	ttG/ttA	.	.	.	-1	BCHE	HGNC	983	protein_coding	YES	CCDS3198.1	ENSP00000264381	CHLE_HUMAN	Q96HL2_HUMAN,F8WF14_HUMAN,D3DNN4_HUMAN	UPI0000127866	.	.	.	3/4	.	Gene3D:3.40.50.1820,hmmpanther:PTHR11559:SF154,hmmpanther:PTHR11559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTCCAAGAC	.	5	ESCA
DHX30	0	.	GRCh37	3	47889673	47889696	+	In_Frame_Del	DEL	TCCTGCCTGGAGACAGTGTGGGTA	TCCTGCCTGGAGACAGTGTGGGTA	-	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	TCCTGCCTGGAGACAGTGTGGGTA	TCCTGCCTGGAGACAGTGTGGGTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2292_2315delCTGCCTGGAGACAGTGTGGGTATC	p.Cys765_Ser772del	p.C765_S772del	ENST00000445061	15/22	49	35	14	46	46	0	DHX30,inframe_deletion,p.Cys737_Ser744del,ENST00000348968,;DHX30,inframe_deletion,p.Cys793_Ser800del,ENST00000457607,;DHX30,inframe_deletion,p.Cys726_Ser733del,ENST00000446256,;DHX30,inframe_deletion,p.Cys765_Ser772del,ENST00000445061,;MAP4,downstream_gene_variant,,ENST00000426837,;MAP4,downstream_gene_variant,,ENST00000360240,;MAP4,downstream_gene_variant,,ENST00000441748,;MAP4,downstream_gene_variant,,ENST00000264724,;MAP4,downstream_gene_variant,,ENST00000335271,;MAP4,downstream_gene_variant,,ENST00000420772,;MAP4,downstream_gene_variant,,ENST00000429422,;MAP4,downstream_gene_variant,,ENST00000395734,;MAP4,downstream_gene_variant,,ENST00000383737,;MIR1226,upstream_gene_variant,,ENST00000408658,;DHX30,downstream_gene_variant,,ENST00000461905,;DHX30,3_prime_UTR_variant,,ENST00000395745,;DHX30,non_coding_transcript_exon_variant,,ENST00000474183,;	-	ENSG00000132153	ENST00000445061	Transcript	inframe_deletion	2697-2720	2290-2313	764-771	SCLETVWV/-	TCCTGCCTGGAGACAGTGTGGGTA/-	.	.	.	1	DHX30	HGNC	16716	protein_coding	YES	CCDS2759.1	ENSP00000405620	DHX30_HUMAN	H7BXY3_HUMAN	UPI000007112B	.	.	.	15/22	.	Superfamily_domains:SSF52540,SMART_domains:SM00490,Gene3D:3.40.50.300,Pfam_domain:PF00271,hmmpanther:PTHR18934:SF109,hmmpanther:PTHR18934,PROSITE_profiles:PS51194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGTGTCCTGCCTGGAGACAGTGTGGGTATCAAG	.	3	ESCA
C3orf38	0	.	GRCh37	3	88199286	88199286	+	Silent	SNP	C	C	T	rs757438009	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84C>T	p.%3D	p.A28A	ENST00000318887	1/3	37	10	26	69	69	0	C3orf38,synonymous_variant,p.%3D,ENST00000486971,;C3orf38,synonymous_variant,p.%3D,ENST00000318887,;CGGBP1,upstream_gene_variant,,ENST00000462901,;CGGBP1,upstream_gene_variant,,ENST00000467332,;C3orf38,upstream_gene_variant,,ENST00000464919,;	T	ENSG00000179021	ENST00000318887	Transcript	synonymous_variant	394	84	28	A	gcC/gcT	rs757438009	.	.	1	C3orf38	HGNC	28384	protein_coding	YES	CCDS2921.2	ENSP00000322469	CC038_HUMAN	D3DU39_HUMAN	UPI000004D308	.	.	.	1/3	.	Pfam_domain:PF15008,hmmpanther:PTHR21084	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGCCCTATG	byFrequency	5	ESCA
CPOX	0	.	GRCh37	3	98311880	98311880	+	Missense_Mutation	SNP	G	G	C	rs148466102	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.469C>G	p.Leu157Val	p.L157V	ENST00000264193	1/7	167	143	24	62	62	0	CPOX,missense_variant,p.Leu157Val,ENST00000264193,;CPOX,missense_variant,p.Leu157Val,ENST00000513674,;CPOX,non_coding_transcript_exon_variant,,ENST00000515041,;	C	ENSG00000080819	ENST00000264193	Transcript	missense_variant	688	469	157	L/V	Ctg/Gtg	rs148466102	.	.	-1	CPOX	HGNC	2321	protein_coding	YES	CCDS2932.1	ENSP00000264193	HEM6_HUMAN	.	UPI0000073C93	.	tolerated(0.26)	benign(0.261)	1/7	.	hmmpanther:PTHR10755,hmmpanther:PTHR10755:SF0,Pfam_domain:PF01218,Gene3D:3.40.1500.10,Superfamily_domains:SSF102886	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCAGAATCA	byCluster	4	ESCA
IL15	0	.	GRCh37	4	142651093	142651093	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334G>C	p.Glu112Gln	p.E112Q	ENST00000296545	7/8	78	66	12	63	63	0	IL15,missense_variant,p.Glu85Gln,ENST00000514653,;IL15,missense_variant,p.Glu85Gln,ENST00000394159,;IL15,missense_variant,p.Glu112Gln,ENST00000529613,;IL15,missense_variant,p.Glu112Gln,ENST00000296545,;IL15,missense_variant,p.Glu85Gln,ENST00000477265,;IL15,missense_variant,p.Glu112Gln,ENST00000320650,;IL15,downstream_gene_variant,,ENST00000509249,;	C	ENSG00000164136	ENST00000296545	Transcript	missense_variant	1178	334	112	E/Q	Gaa/Caa	.	.	.	1	IL15	HGNC	5977	protein_coding	YES	CCDS3755.1	ENSP00000296545	IL15_HUMAN	.	UPI0000031AC7	.	tolerated(0.25)	benign(0.017)	7/8	.	Superfamily_domains:SSF47266,Pfam_domain:PF02372,hmmpanther:PTHR11323,hmmpanther:PTHR11323:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTAGAAAAT	.	5	ESCA
LRBA	0	.	GRCh37	4	151771892	151771892	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3988A>G	p.Ile1330Val	p.I1330V	ENST00000357115	24/58	36	28	8	36	36	0	LRBA,missense_variant,p.Ile1330Val,ENST00000535741,;LRBA,missense_variant,p.Ile1330Val,ENST00000507224,;LRBA,missense_variant,p.Ile1330Val,ENST00000357115,;LRBA,missense_variant,p.Ile1330Val,ENST00000510413,;LRBA,upstream_gene_variant,,ENST00000509835,;LRBA,upstream_gene_variant,,ENST00000502839,;	C	ENSG00000198589	ENST00000357115	Transcript	missense_variant	4232	3988	1330	I/V	Ata/Gta	.	.	.	-1	LRBA	HGNC	1742	protein_coding	YES	CCDS3773.1	ENSP00000349629	LRBA_HUMAN	Q7KZN3_HUMAN	UPI000013E35C	.	tolerated(0.75)	probably_damaging(0.946)	24/58	.	hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTATATCTG	.	5	ESCA
FSTL5	0	.	GRCh37	4	162307332	162307332	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2111A>T	p.His704Leu	p.H704L	ENST00000306100	16/16	39	20	19	30	30	0	FSTL5,missense_variant,p.His703Leu,ENST00000379164,;FSTL5,missense_variant,p.His703Leu,ENST00000536695,;FSTL5,missense_variant,p.His694Leu,ENST00000427802,;FSTL5,missense_variant,p.His704Leu,ENST00000306100,;RP11-234O6.2,non_coding_transcript_exon_variant,,ENST00000508189,;	A	ENSG00000168843	ENST00000306100	Transcript	missense_variant	2548	2111	704	H/L	cAc/cTc	.	.	.	-1	FSTL5	HGNC	21386	protein_coding	YES	CCDS3802.1	ENSP00000305334	FSTL5_HUMAN	Q4W5Q0_HUMAN,Q4W5K3_HUMAN,Q4W5F8_HUMAN	UPI000020B66B	.	deleterious(0.02)	possibly_damaging(0.777)	16/16	.	Superfamily_domains:0047643,Gene3D:2.130.10.10,hmmpanther:PTHR10913:SF44,hmmpanther:PTHR10913	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTAGTGGCCA	.	5	ESCA
GABRA2	0	.	GRCh37	4	46252353	46252353	+	Missense_Mutation	SNP	C	C	T	rs200987678	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1328G>A	p.Arg443Lys	p.R443K	ENST00000510861	10/10	49	41	8	68	68	0	GABRA2,missense_variant,p.Arg443Lys,ENST00000510861,;GABRA2,missense_variant,p.Arg443Lys,ENST00000356504,;GABRA2,missense_variant,p.Arg503Lys,ENST00000507069,;GABRA2,missense_variant,p.Arg443Lys,ENST00000381620,;GABRA2,missense_variant,p.Arg448Lys,ENST00000540012,;GABRA2,missense_variant,p.Arg443Lys,ENST00000514090,;GABRA2,3_prime_UTR_variant,,ENST00000513005,;GABRA2,3_prime_UTR_variant,,ENST00000510233,;	T	ENSG00000151834	ENST00000510861	Transcript	missense_variant	1502	1328	443	R/K	aGa/aAa	rs200987678,COSM734362	.	.	-1	GABRA2	HGNC	4076	protein_coding	YES	CCDS3471.1	ENSP00000421828	GBRA2_HUMAN	Q4W5L8_HUMAN,D6RBL7_HUMAN,D6RBK9_HUMAN,D6RB77_HUMAN	UPI000013DC88	.	tolerated(0.45)	benign(0.071)	10/10	.	hmmpanther:PTHR18945:SF218,hmmpanther:PTHR18945,Superfamily_domains:SSF90112,Prints_domain:PR01079	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTCTGTTT	.	5	ESCA
SPATA18	0	.	GRCh37	4	52943092	52943092	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.906C>T	p.%3D	p.L302L	ENST00000295213	7/13	85	64	20	47	47	0	SPATA18,synonymous_variant,p.%3D,ENST00000295213,;SPATA18,synonymous_variant,p.%3D,ENST00000419395,;SPATA18,non_coding_transcript_exon_variant,,ENST00000514670,;SPATA18,downstream_gene_variant,,ENST00000506829,;SPATA18,synonymous_variant,p.%3D,ENST00000505320,;SPATA18,non_coding_transcript_exon_variant,,ENST00000511028,;SPATA18,downstream_gene_variant,,ENST00000505038,;SPATA18,upstream_gene_variant,,ENST00000510549,;SPATA18,downstream_gene_variant,,ENST00000508915,;	T	ENSG00000163071	ENST00000295213	Transcript	synonymous_variant	1280	906	302	L	ctC/ctT	.	.	.	1	SPATA18	HGNC	29579	protein_coding	YES	CCDS3489.1	ENSP00000295213	MIEAP_HUMAN	.	UPI000006FB0D	.	.	.	7/13	.	hmmpanther:PTHR21771:SF0,hmmpanther:PTHR21771	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCTTGTC	.	5	ESCA
PCDHA13	0	.	GRCh37	5	140262071	140262071	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218A>G	p.Asp73Gly	p.D73G	ENST00000289272	1/4	164	120	43	91	91	0	PCDHA13,missense_variant,p.Asp73Gly,ENST00000289272,;PCDHA13,missense_variant,p.Asp73Gly,ENST00000409494,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;	G	ENSG00000239389	ENST00000289272	Transcript	missense_variant	218	218	73	D/G	gAc/gGc	.	.	.	1	PCDHA13	HGNC	8667	protein_coding	YES	CCDS4240.1	ENSP00000289272	PCDAD_HUMAN	.	UPI00001273D6	.	deleterious_low_confidence(0.01)	benign(0.113)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF08266,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGGACCTTC	.	5	ESCA
PCDHA13	0	.	GRCh37	5	140263363	140263363	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1510C>G	p.Leu504Val	p.L504V	ENST00000289272	1/4	149	115	33	86	86	0	PCDHA13,missense_variant,p.Leu504Val,ENST00000289272,;PCDHA13,missense_variant,p.Leu504Val,ENST00000409494,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;	G	ENSG00000239389	ENST00000289272	Transcript	missense_variant	1510	1510	504	L/V	Ctg/Gtg	COSM3696979	.	.	1	PCDHA13	HGNC	8667	protein_coding	YES	CCDS4240.1	ENSP00000289272	PCDAD_HUMAN	.	UPI00001273D6	.	deleterious_low_confidence(0.03)	benign(0.1)	1/4	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCGCTGTCG	.	5	ESCA
PCDHA13	0	.	GRCh37	5	140263450	140263450	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597T>G	p.Phe533Val	p.F533V	ENST00000289272	1/4	209	165	44	101	101	0	PCDHA13,missense_variant,p.Phe533Val,ENST00000289272,;PCDHA13,missense_variant,p.Phe533Val,ENST00000409494,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;	G	ENSG00000239389	ENST00000289272	Transcript	missense_variant	1597	1597	533	F/V	Ttc/Gtc	.	.	.	1	PCDHA13	HGNC	8667	protein_coding	YES	CCDS4240.1	ENSP00000289272	PCDAD_HUMAN	.	UPI00001273D6	.	deleterious_low_confidence(0.04)	benign(0.168)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGTTCCAG	.	5	ESCA
SLC6A3	0	.	GRCh37	5	1422077	1422077	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.706C>T	p.Pro236Ser	p.P236S	ENST00000270349	5/15	101	77	24	35	35	0	SLC6A3,missense_variant,p.Pro236Ser,ENST00000270349,;SLC6A3,missense_variant,p.Pro162Ser,ENST00000513308,;SLC6A3,missense_variant,p.Pro236Ser,ENST00000453492,;	A	ENSG00000142319	ENST00000270349	Transcript	missense_variant	834	706	236	P/S	Ccg/Tcg	COSM3611844	.	.	-1	SLC6A3	HGNC	11049	protein_coding	YES	CCDS3863.1	ENSP00000270349	SC6A3_HUMAN	Q6LC27_HUMAN,H0YBA7_HUMAN	UPI000013548F	.	deleterious(0.04)	probably_damaging(0.984)	5/15	.	Superfamily_domains:0053687,Pfam_domain:PF00209,hmmpanther:PTHR11616:SF38,hmmpanther:PTHR11616,PROSITE_profiles:PS50267	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCGGAGGCC	.	5	ESCA
CTD-2012J19.3	0	.	GRCh37	5	1602846	1602846	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.622+7484C>T	.	.	ENST00000605200	.	49	32	16	36	36	0	CTD-2012J19.3,intron_variant,,ENST00000605200,;RP11-43F13.1,non_coding_transcript_exon_variant,,ENST00000522848,;RP11-43F13.1,non_coding_transcript_exon_variant,,ENST00000507841,;RP11-43F13.1,non_coding_transcript_exon_variant,,ENST00000512335,;RP11-43F13.1,non_coding_transcript_exon_variant,,ENST00000507505,;RP11-43F13.1,non_coding_transcript_exon_variant,,ENST00000507290,;RP11-43F13.1,non_coding_transcript_exon_variant,,ENST00000502273,;CTD-2012J19.2,downstream_gene_variant,,ENST00000509920,;	T	ENSG00000271119	ENST00000605200	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CTD-2012J19.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GTCCACGTGCC	.	3	ESCA
ADAMTS2	0	.	GRCh37	5	178555035	178555035	+	Missense_Mutation	SNP	C	C	T	rs766088822	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2542G>A	p.Val848Ile	p.V848I	ENST00000251582	17/22	44	20	23	41	41	0	ADAMTS2,missense_variant,p.Val848Ile,ENST00000251582,;	T	ENSG00000087116	ENST00000251582	Transcript	missense_variant	2644	2542	848	V/I	Gtc/Atc	rs766088822	.	.	-1	ADAMTS2	HGNC	218	protein_coding	YES	CCDS4444.1	ENSP00000251582	ATS2_HUMAN	.	UPI00001AE729	.	deleterious(0.05)	benign(0.01)	17/22	.	hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.N847N|c.2541C>T|3,BUFFER|p.D844D|c.2532C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGACGTTGT	.	5	ESCA
RANBP3L	0	.	GRCh37	5	36253802	36253802	+	Nonsense_Mutation	SNP	G	G	A	rs375516541	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1189C>T	p.Arg397Ter	p.R397*	ENST00000502994	13/15	169	94	75	84	84	0	RANBP3L,stop_gained,p.Arg372Ter,ENST00000296604,;RANBP3L,stop_gained,p.Arg397Ter,ENST00000502994,;RANBP3L,downstream_gene_variant,,ENST00000515759,;	A	ENSG00000164188	ENST00000502994	Transcript	stop_gained	1673	1189	397	R/*	Cga/Tga	rs375516541	.	.	-1	RANBP3L	HGNC	26353	protein_coding	YES	CCDS54843.1	ENSP00000421853	RNB3L_HUMAN	.	UPI0001A5C4B2	.	.	.	13/15	.	PROSITE_profiles:PS50196,hmmpanther:PTHR23138:SF88,hmmpanther:PTHR23138,Pfam_domain:PF00638,Gene3D:2.30.29.30,SMART_domains:SM00160,Superfamily_domains:SSF50729	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	A:0	A:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTCGTACAT	byFrequency|byCluster|by1000G	5	ESCA
ROS1	0	.	GRCh37	6	117715336	117715336	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1153A>C	p.Met385Leu	p.M385L	ENST00000368508	10/43	71	46	25	46	46	0	ROS1,missense_variant,p.Met394Leu,ENST00000368507,;ROS1,missense_variant,p.Met385Leu,ENST00000368508,;GOPC,intron_variant,,ENST00000467125,;	G	ENSG00000047936	ENST00000368508	Transcript	missense_variant	1352	1153	385	M/L	Atg/Ctg	.	.	.	-1	ROS1	HGNC	10261	protein_coding	YES	CCDS5116.1	ENSP00000357494	ROS1_HUMAN	.	UPI000013D467	.	tolerated(0.24)	benign(0.039)	10/43	.	hmmpanther:PTHR24416:SF304,hmmpanther:PTHR24416,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCATGATGA	.	5	ESCA
CLVS2	0	.	GRCh37	6	123377007	123377007	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732C>T	p.%3D	p.I244I	ENST00000275162	5/6	59	44	15	31	31	0	CLVS2,synonymous_variant,p.%3D,ENST00000368438,;CLVS2,synonymous_variant,p.%3D,ENST00000275162,;	T	ENSG00000146352	ENST00000275162	Transcript	synonymous_variant	2067	732	244	I	atC/atT	COSM1545054,COSM1545053	.	.	1	CLVS2	HGNC	23046	protein_coding	YES	CCDS34525.1	ENSP00000275162	CLVS2_HUMAN	.	UPI000013DA49	.	.	.	5/6	.	PROSITE_profiles:PS50191,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF73,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087,Prints_domain:PR00180	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATCCTGCC	.	5	ESCA
AIG1	0	.	GRCh37	6	143382095	143382095	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33G>T	p.Met11Ile	p.M11I	ENST00000357847	1/6	43	24	19	22	22	0	AIG1,missense_variant,p.Met11Ile,ENST00000494282,;AIG1,missense_variant,p.Met11Ile,ENST00000344492,;AIG1,missense_variant,p.Met11Ile,ENST00000447498,;AIG1,missense_variant,p.Met11Ile,ENST00000275235,;AIG1,missense_variant,p.Met11Ile,ENST00000367598,;AIG1,missense_variant,p.Met7Ile,ENST00000367601,;AIG1,missense_variant,p.Met11Ile,ENST00000357847,;AIG1,missense_variant,p.Met11Ile,ENST00000367596,;	T	ENSG00000146416	ENST00000357847	Transcript	missense_variant	83	33	11	M/I	atG/atT	.	.	.	1	AIG1	HGNC	21607	protein_coding	YES	CCDS5198.1	ENSP00000350509	AIG1_HUMAN	Q5THU2_HUMAN,Q5T2H0_HUMAN	UPI000006F22E	.	tolerated(0.18)	benign(0)	1/6	.	hmmpanther:PTHR10989,hmmpanther:PTHR10989:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGATGGCAAT	.	5	ESCA
BTN2A1	0	.	GRCh37	6	26468869	26468869	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*92C>T	.	.	ENST00000312541	8/8	82	49	32	45	45	0	BTN2A1,3_prime_UTR_variant,,ENST00000429381,;BTN2A1,3_prime_UTR_variant,,ENST00000312541,;BTN2A1,intron_variant,,ENST00000480218,;BTN2A1,intron_variant,,ENST00000469185,;BTN2A1,downstream_gene_variant,,ENST00000541522,;BTN2A1,3_prime_UTR_variant,,ENST00000377600,;	T	ENSG00000112763	ENST00000312541	Transcript	3_prime_UTR_variant	1924	.	.	.	.	.	.	.	1	BTN2A1	HGNC	1136	protein_coding	YES	CCDS4613.1	ENSP00000312158	BT2A1_HUMAN	C9JNC3_HUMAN	UPI00000480E9	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCCCTC	.	5	ESCA
HSPA1B	0	.	GRCh37	6	31795600	31795600	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-128C>A	.	.	ENST00000375650	1/1	41	22	19	20	20	0	HSPA1B,5_prime_UTR_variant,,ENST00000375650,;HSPA1B,upstream_gene_variant,,ENST00000545241,;	A	ENSG00000204388	ENST00000375650	Transcript	5_prime_UTR_variant	89	.	.	.	.	.	.	.	1	HSPA1B	HGNC	5233	protein_coding	YES	CCDS34415.1	ENSP00000364801	HSP71_HUMAN	A8K5I0_HUMAN	UPI0000000C40	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGAACCTGTG	.	5	ESCA
XPO5	0	.	GRCh37	6	43538251	43538251	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609G>T	p.Lys203Asn	p.K203N	ENST00000265351	5/32	75	57	17	60	60	0	XPO5,missense_variant,p.Lys203Asn,ENST00000265351,;XPO5,downstream_gene_variant,,ENST00000398799,;	A	ENSG00000124571	ENST00000265351	Transcript	missense_variant	820	609	203	K/N	aaG/aaT	.	.	.	-1	XPO5	HGNC	17675	protein_coding	YES	CCDS47430.1	ENSP00000265351	XPO5_HUMAN	E2QRM3_HUMAN	UPI000006CC97	.	tolerated(0.31)	benign(0.03)	5/32	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11223,hmmpanther:PTHR11223:SF3,Gene3D:1.25.10.10,Pfam_domain:PF08389,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATACTTGTT	.	5	ESCA
TRAM2	0	.	GRCh37	6	52363725	52363725	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4270T>C	.	.	ENST00000182527	11/11	67	45	21	38	38	0	TRAM2,3_prime_UTR_variant,,ENST00000182527,;EFHC1,intron_variant,,ENST00000433625,;EFHC1,downstream_gene_variant,,ENST00000538167,;EFHC1,downstream_gene_variant,,ENST00000371068,;	G	ENSG00000065308	ENST00000182527	Transcript	3_prime_UTR_variant	5383	.	.	.	.	.	.	.	-1	TRAM2	HGNC	16855	protein_coding	YES	CCDS34477.1	ENSP00000182527	TRAM2_HUMAN	G1UI27_HUMAN	UPI00000012BF	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACAAAAAGTCT	.	3	ESCA
CYP2W1	0	.	GRCh37	7	1024635	1024635	+	Silent	SNP	G	G	C	rs753258511	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387G>C	p.%3D	p.T129T	ENST00000308919	3/9	80	43	37	60	60	0	CYP2W1,synonymous_variant,p.%3D,ENST00000340150,;CYP2W1,synonymous_variant,p.%3D,ENST00000308919,;CYP2W1,upstream_gene_variant,,ENST00000415893,;CYP2W1,upstream_gene_variant,,ENST00000468456,;CYP2W1,upstream_gene_variant,,ENST00000462453,;	C	ENSG00000073067	ENST00000308919	Transcript	synonymous_variant	400	387	129	T	acG/acC	rs753258511,COSM3784785	.	.	1	CYP2W1	HGNC	20243	protein_coding	YES	CCDS5319.2	ENSP00000310149	CP2W1_HUMAN	.	UPI000013C59A	.	.	.	3/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF50,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R131H|c.392G>A|3	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTCACGGTGCG	byFrequency	4	ESCA
HBP1	0	.	GRCh37	7	106836591	106836591	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1380T>A	p.Asp460Glu	p.D460E	ENST00000222574	9/11	62	47	14	44	44	0	HBP1,missense_variant,p.Asp460Glu,ENST00000468410,;HBP1,missense_variant,p.Asp100Glu,ENST00000607681,;HBP1,missense_variant,p.Asp460Glu,ENST00000222574,;HBP1,missense_variant,p.Asp460Glu,ENST00000485846,;HBP1,missense_variant,p.Asp452Glu,ENST00000498408,;CTA-363E19.2,upstream_gene_variant,,ENST00000607036,;HBP1,non_coding_transcript_exon_variant,,ENST00000461963,;HBP1,missense_variant,p.Asp55Glu,ENST00000463790,;HBP1,non_coding_transcript_exon_variant,,ENST00000463202,;HBP1,downstream_gene_variant,,ENST00000483809,;	A	ENSG00000105856	ENST00000222574	Transcript	missense_variant	1566	1380	460	D/E	gaT/gaA	.	.	.	1	HBP1	HGNC	23200	protein_coding	YES	CCDS5741.1	ENSP00000222574	HBP1_HUMAN	H7C4S2_HUMAN,C9JQU7_HUMAN,C9JPK6_HUMAN,C9JAW1_HUMAN,C9J8V6_HUMAN,C9J5U3_HUMAN,B4DJ36_HUMAN	UPI000006DC04	.	deleterious(0.01)	probably_damaging(0.999)	9/11	.	PROSITE_profiles:PS50118,hmmpanther:PTHR15499:SF2,hmmpanther:PTHR15499,Pfam_domain:PF00505,Gene3D:1.10.30.10,SMART_domains:SM00398,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAAGATAACAG	.	3	ESCA
HBP1	0	.	GRCh37	7	106836593	106836593	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1382A>G	p.Asn461Ser	p.N461S	ENST00000222574	9/11	60	45	15	44	44	0	HBP1,missense_variant,p.Asn461Ser,ENST00000468410,;HBP1,missense_variant,p.Asn101Ser,ENST00000607681,;HBP1,missense_variant,p.Asn461Ser,ENST00000222574,;HBP1,missense_variant,p.Asn461Ser,ENST00000485846,;HBP1,missense_variant,p.Asn453Ser,ENST00000498408,;CTA-363E19.2,upstream_gene_variant,,ENST00000607036,;HBP1,non_coding_transcript_exon_variant,,ENST00000461963,;HBP1,missense_variant,p.Asn56Ser,ENST00000463790,;HBP1,non_coding_transcript_exon_variant,,ENST00000463202,;HBP1,downstream_gene_variant,,ENST00000483809,;	G	ENSG00000105856	ENST00000222574	Transcript	missense_variant	1568	1382	461	N/S	aAc/aGc	.	.	.	1	HBP1	HGNC	23200	protein_coding	YES	CCDS5741.1	ENSP00000222574	HBP1_HUMAN	H7C4S2_HUMAN,C9JQU7_HUMAN,C9JPK6_HUMAN,C9JAW1_HUMAN,C9J8V6_HUMAN,C9J5U3_HUMAN,B4DJ36_HUMAN	UPI000006DC04	.	deleterious(0)	probably_damaging(0.999)	9/11	.	PROSITE_profiles:PS50118,hmmpanther:PTHR15499:SF2,hmmpanther:PTHR15499,Pfam_domain:PF00505,Gene3D:1.10.30.10,SMART_domains:SM00398,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGATAACAGGT	.	3	ESCA
PNPLA8	0	.	GRCh37	7	108119807	108119807	+	Missense_Mutation	SNP	A	A	C	rs144990439	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1895T>G	p.Leu632Arg	p.L632R	ENST00000422087	11/12	71	29	41	35	35	0	PNPLA8,missense_variant,p.Leu532Arg,ENST00000453144,;PNPLA8,missense_variant,p.Leu632Arg,ENST00000257694,;PNPLA8,missense_variant,p.Leu570Arg,ENST00000388728,;PNPLA8,missense_variant,p.Leu570Arg,ENST00000426128,;PNPLA8,missense_variant,p.Leu532Arg,ENST00000453085,;PNPLA8,missense_variant,p.Leu632Arg,ENST00000422087,;PNPLA8,missense_variant,p.Leu632Arg,ENST00000436062,;	C	ENSG00000135241	ENST00000422087	Transcript	missense_variant	2302	1895	632	L/R	cTg/cGg	rs144990439	.	.	-1	PNPLA8	HGNC	28900	protein_coding	YES	CCDS34733.1	ENSP00000410804	PLPL8_HUMAN	C9JAX4_HUMAN,C9J9W9_HUMAN	UPI0000073D34	.	deleterious(0)	possibly_damaging(0.752)	11/12	.	hmmpanther:PTHR24185,Pfam_domain:PF01734,Gene3D:3.40.1090.10,Superfamily_domains:SSF52151	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTCAGAAGC	.	5	ESCA
CNOT4	0	.	GRCh37	7	135079021	135079021	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1276C>G	p.Gln426Glu	p.Q426E	ENST00000541284	10/12	71	53	18	86	86	0	CNOT4,missense_variant,p.Gln426Glu,ENST00000541284,;CNOT4,missense_variant,p.Gln423Glu,ENST00000451834,;CNOT4,missense_variant,p.Gln426Glu,ENST00000423368,;CNOT4,missense_variant,p.Gln423Glu,ENST00000361528,;CNOT4,missense_variant,p.Gln423Glu,ENST00000428680,;CNOT4,missense_variant,p.Gln426Glu,ENST00000315544,;CNOT4,intron_variant,,ENST00000356162,;CNOT4,intron_variant,,ENST00000414802,;	C	ENSG00000080802	ENST00000541284	Transcript	missense_variant	1607	1276	426	Q/E	Caa/Gaa	.	.	.	-1	CNOT4	HGNC	7880	protein_coding	YES	CCDS55165.1	ENSP00000445508	CNOT4_HUMAN	.	UPI00004166A8	.	tolerated(0.19)	benign(0.013)	10/12	.	hmmpanther:PTHR12603,hmmpanther:PTHR12603:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTGAACGG	.	5	ESCA
BZW2	0	.	GRCh37	7	16685776	16685776	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-161C>G	.	.	ENST00000433922	1/12	140	104	36	50	50	0	BZW2,5_prime_UTR_variant,,ENST00000433922,;BZW2,5_prime_UTR_variant,,ENST00000415365,;BZW2,5_prime_UTR_variant,,ENST00000258761,;ANKMY2,upstream_gene_variant,,ENST00000306999,;BZW2,upstream_gene_variant,,ENST00000405202,;BZW2,upstream_gene_variant,,ENST00000452975,;BZW2,upstream_gene_variant,,ENST00000432311,;ANKMY2,upstream_gene_variant,,ENST00000421746,;BZW2,upstream_gene_variant,,ENST00000437745,;ANKMY2,upstream_gene_variant,,ENST00000453623,;ANKMY2,upstream_gene_variant,,ENST00000447802,;BZW2,upstream_gene_variant,,ENST00000436868,;	G	ENSG00000136261	ENST00000433922	Transcript	5_prime_UTR_variant	18	.	.	.	.	.	.	.	1	BZW2	HGNC	18808	protein_coding	YES	CCDS5362.1	ENSP00000397249	BZW2_HUMAN	Q75MG1_HUMAN,E7ETZ4_HUMAN,E7EMS9_HUMAN,C9JF98_HUMAN,B5MCH7_HUMAN,B5MCE7_HUMAN	UPI000003B445	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCCGTGTG	.	5	ESCA
FOXK1	0	.	GRCh37	7	4798961	4798961	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1431G>A	p.%3D	p.Q477Q	ENST00000328914	7/9	60	39	21	20	20	0	FOXK1,synonymous_variant,p.%3D,ENST00000446823,;FOXK1,synonymous_variant,p.%3D,ENST00000328914,;FOXK1,downstream_gene_variant,,ENST00000460979,;FOXK1,non_coding_transcript_exon_variant,,ENST00000496023,;	A	ENSG00000164916	ENST00000328914	Transcript	synonymous_variant	1431	1431	477	Q	caG/caA	.	.	.	1	FOXK1	HGNC	23480	protein_coding	YES	CCDS34591.1	ENSP00000328720	FOXK1_HUMAN	B3KV39_HUMAN	UPI00004158EB	.	.	.	7/9	.	hmmpanther:PTHR11829:SF107,hmmpanther:PTHR11829	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCAGCCAGT	.	5	ESCA
C7orf43	0	.	GRCh37	7	99754275	99754275	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058G>A	p.Ser353Asn	p.S353N	ENST00000316937	7/11	56	40	15	31	31	0	C7orf43,missense_variant,p.Ser259Asn,ENST00000456769,;C7orf43,missense_variant,p.Ser121Asn,ENST00000419841,;C7orf43,missense_variant,p.Ser84Asn,ENST00000457641,;C7orf43,missense_variant,p.Ser353Asn,ENST00000316937,;GAL3ST4,downstream_gene_variant,,ENST00000413800,;GAL3ST4,downstream_gene_variant,,ENST00000423751,;GAL3ST4,downstream_gene_variant,,ENST00000360039,;GAL3ST4,downstream_gene_variant,,ENST00000426974,;LAMTOR4,downstream_gene_variant,,ENST00000341942,;GAL3ST4,downstream_gene_variant,,ENST00000411994,;C7orf43,upstream_gene_variant,,ENST00000394035,;LAMTOR4,downstream_gene_variant,,ENST00000441173,;MIR4658,non_coding_transcript_exon_variant,,ENST00000584344,;C7orf43,non_coding_transcript_exon_variant,,ENST00000498638,;LAMTOR4,downstream_gene_variant,,ENST00000474831,;LAMTOR4,downstream_gene_variant,,ENST00000460732,;C7orf43,downstream_gene_variant,,ENST00000472061,;LAMTOR4,downstream_gene_variant,,ENST00000468582,;LAMTOR4,downstream_gene_variant,,ENST00000490633,;LAMTOR4,downstream_gene_variant,,ENST00000474141,;LAMTOR4,downstream_gene_variant,,ENST00000488241,;GAL3ST4,downstream_gene_variant,,ENST00000498000,;LAMTOR4,downstream_gene_variant,,ENST00000466498,;C7orf43,missense_variant,p.Ser87Asn,ENST00000448720,;C7orf43,3_prime_UTR_variant,,ENST00000419037,;C7orf43,upstream_gene_variant,,ENST00000470260,;GAL3ST4,downstream_gene_variant,,ENST00000495882,;LAMTOR4,downstream_gene_variant,,ENST00000473459,;LAMTOR4,downstream_gene_variant,,ENST00000488338,;	T	ENSG00000146826	ENST00000316937	Transcript	missense_variant	1244	1058	353	S/N	aGc/aAc	.	.	.	-1	C7orf43	HGNC	25604	protein_coding	YES	CCDS5687.1	ENSP00000324741	CG043_HUMAN	F8WFE0_HUMAN,C9JMZ9_HUMAN,B3KNS5_HUMAN	UPI000006ECC7	.	tolerated(0.3)	possibly_damaging(0.682)	7/11	.	hmmpanther:PTHR16096,hmmpanther:PTHR16096:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATGCTCTGA	.	5	ESCA
ARC	0	.	GRCh37	8	143694754	143694754	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.879G>T	p.Lys293Asn	p.K293N	ENST00000356613	1/3	64	44	19	57	57	0	ARC,missense_variant,p.Lys293Asn,ENST00000356613,;ARC,upstream_gene_variant,,ENST00000581404,;	A	ENSG00000198576	ENST00000356613	Transcript	missense_variant	2080	879	293	K/N	aaG/aaT	.	.	.	-1	ARC	HGNC	648	protein_coding	YES	CCDS34950.1	ENSP00000349022	ARC_HUMAN	.	UPI0000163B0F	.	deleterious(0.03)	probably_damaging(0.996)	1/3	.	hmmpanther:PTHR15962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTGCTTCTG	.	5	ESCA
NAT1	0	.	GRCh37	8	18080634	18080634	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*205A>G	.	.	ENST00000545197	5/5	18	7	11	50	50	0	NAT1,3_prime_UTR_variant,,ENST00000520546,;NAT1,3_prime_UTR_variant,,ENST00000518029,;NAT1,3_prime_UTR_variant,,ENST00000541942,;NAT1,3_prime_UTR_variant,,ENST00000535084,;NAT1,3_prime_UTR_variant,,ENST00000545197,;NAT1,3_prime_UTR_variant,,ENST00000539092,;NAT1,3_prime_UTR_variant,,ENST00000307719,;NAT1,3_prime_UTR_variant,,ENST00000517492,;NAT1,downstream_gene_variant,,ENST00000517837,;NAT1,downstream_gene_variant,,ENST00000517441,;NAT1,downstream_gene_variant,,ENST00000517574,;NAT1,downstream_gene_variant,,ENST00000519006,;	G	ENSG00000171428	ENST00000545197	Transcript	3_prime_UTR_variant	1503	.	.	.	.	.	.	.	1	NAT1	HGNC	7645	protein_coding	YES	CCDS55205.1	ENSP00000443194	.	Q6U7I7_HUMAN,Q5C8V2_HUMAN,Q400J6_HUMAN,Q400I9_HUMAN,Q09LL5_HUMAN,F5H5R8_HUMAN	UPI0000210A3F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATAATAATA	.	5	ESCA
KAT6A	0	.	GRCh37	8	41788202	41788202	+	3'UTR	SNP	G	G	A	rs552686729	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1521C>T	.	.	ENST00000396930	18/18	33	29	4	12	12	0	KAT6A,3_prime_UTR_variant,,ENST00000396930,;KAT6A,3_prime_UTR_variant,,ENST00000406337,;KAT6A,3_prime_UTR_variant,,ENST00000265713,;KAT6A,downstream_gene_variant,,ENST00000418721,;	A	ENSG00000083168	ENST00000396930	Transcript	3_prime_UTR_variant	8080	.	.	.	.	rs552686729	.	.	-1	KAT6A	HGNC	13013	protein_coding	YES	CCDS6124.1	ENSP00000380136	KAT6A_HUMAN	A5PKX7_HUMAN	UPI000013D666	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|VARSCANS	TATATGTGTGT	.	2	ESCA
MMP16	0	.	GRCh37	8	89052287	89052287	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1402T>C	.	.	ENST00000286614	10/10	38	21	17	38	38	0	MMP16,3_prime_UTR_variant,,ENST00000286614,;	G	ENSG00000156103	ENST00000286614	Transcript	3_prime_UTR_variant	3508	.	.	.	.	.	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAAAATGGCA	.	5	ESCA
ABCA1	0	.	GRCh37	9	107555517	107555517	+	Silent	SNP	G	G	A	rs371988457	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5571C>T	p.%3D	p.A1857A	ENST00000374736	41/50	43	7	35	85	85	0	ABCA1,synonymous_variant,p.%3D,ENST00000374736,;	A	ENSG00000165029	ENST00000374736	Transcript	synonymous_variant	5966	5571	1857	A	gcC/gcT	rs371988457,COSM1459099	.	.	-1	ABCA1	HGNC	29	protein_coding	YES	CCDS6762.1	ENSP00000363868	ABCA1_HUMAN	Q9NS76_HUMAN,Q9NP93_HUMAN,Q9H002_HUMAN	UPI000013E441	.	.	.	41/50	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR19229:SF34,hmmpanther:PTHR19229,Pfam_domain:PF12698	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACGGCCAT	byFrequency|byCluster	5	ESCA
BRINP1	0	.	GRCh37	9	121930291	121930291	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357G>T	p.Gly453Cys	p.G453C	ENST00000265922	8/8	25	10	14	18	18	0	BRINP1,missense_variant,p.Gly453Cys,ENST00000265922,;BRINP1,intron_variant,,ENST00000482797,;	A	ENSG00000078725	ENST00000265922	Transcript	missense_variant	1819	1357	453	G/C	Ggc/Tgc	.	.	.	-1	BRINP1	HGNC	2687	protein_coding	YES	CCDS6822.1	ENSP00000265922	BRNP1_HUMAN	B4DE75_HUMAN	UPI000013D6A7	.	deleterious(0)	probably_damaging(0.996)	8/8	.	hmmpanther:PTHR15564:SF7,hmmpanther:PTHR15564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGCCCTTGT	.	5	ESCA
NEK6	0	.	GRCh37	9	127019915	127019915	+	5'Flank	SNP	G	G	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000373600	.	52	16	35	62	62	0	NEK6,5_prime_UTR_variant,,ENST00000373603,;NEK6,5_prime_UTR_variant,,ENST00000540326,;NEK6,upstream_gene_variant,,ENST00000425237,;NEK6,upstream_gene_variant,,ENST00000373596,;NEK6,upstream_gene_variant,,ENST00000320246,;NEK6,upstream_gene_variant,,ENST00000545174,;NEK6,upstream_gene_variant,,ENST00000373600,;NEK6,upstream_gene_variant,,ENST00000444973,;NEK6,upstream_gene_variant,,ENST00000454453,;RP11-121A14.2,downstream_gene_variant,,ENST00000426157,;	A	ENSG00000119408	ENST00000373600	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	327	1	NEK6	HGNC	7749	protein_coding	YES	CCDS48015.1	ENSP00000362702	NEK6_HUMAN	Q5TBH2_HUMAN,Q5TBH1_HUMAN,Q5TBG7_HUMAN,Q5TBG4_HUMAN,Q5TBG2_HUMAN,Q5TBG1_HUMAN	UPI000013ED34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGACGCACAG	.	5	ESCA
CERCAM	0	.	GRCh37	9	131186799	131186800	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.676dupG	p.Ala226GlyfsTer39	p.A226Gfs*39	ENST00000372838	5/13	23	19	4	20	20	0	CERCAM,frameshift_variant,p.Ala148GlyfsTer39,ENST00000372842,;CERCAM,frameshift_variant,p.Ala226GlyfsTer39,ENST00000372838,;CERCAM,frameshift_variant,p.Ala148GlyfsTer39,ENST00000420512,;CERCAM,downstream_gene_variant,,ENST00000447915,;CERCAM,downstream_gene_variant,,ENST00000411852,;CERCAM,downstream_gene_variant,,ENST00000420034,;CERCAM,non_coding_transcript_exon_variant,,ENST00000483893,;CERCAM,upstream_gene_variant,,ENST00000487001,;CERCAM,downstream_gene_variant,,ENST00000493788,;CERCAM,non_coding_transcript_exon_variant,,ENST00000463535,;CERCAM,downstream_gene_variant,,ENST00000483737,;	G	ENSG00000167123	ENST00000372838	Transcript	frameshift_variant	1070-1071	672-673	224-225	-/X	-/G	.	.	.	1	CERCAM	HGNC	23723	protein_coding	YES	CCDS6901.2	ENSP00000361929	GT253_HUMAN	B7ZBT0_HUMAN,B7ZBS9_HUMAN,B7ZBS8_HUMAN	UPI000046FF85	.	.	.	5/13	.	Superfamily_domains:SSF53448,hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GCTGAAGGGGC	.	2	ESCA
FNBP1	0	.	GRCh37	9	132687355	132687355	+	Missense_Mutation	SNP	T	T	C	rs764441806	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.871A>G	p.Met291Val	p.M291V	ENST00000446176	9/17	64	25	39	57	57	0	FNBP1,missense_variant,p.Met291Val,ENST00000355681,;FNBP1,missense_variant,p.Met253Val,ENST00000449089,;FNBP1,missense_variant,p.Met291Val,ENST00000420781,;FNBP1,missense_variant,p.Met291Val,ENST00000446176,;FNBP1,non_coding_transcript_exon_variant,,ENST00000478129,;FNBP1,upstream_gene_variant,,ENST00000482107,;	C	ENSG00000187239	ENST00000446176	Transcript	missense_variant	1058	871	291	M/V	Atg/Gtg	rs764441806	.	.	-1	FNBP1	HGNC	17069	protein_coding	YES	CCDS48040.1	ENSP00000413625	FNBP1_HUMAN	B7ZL12_HUMAN	UPI000022408C	.	tolerated(0.08)	benign(0.002)	9/17	.	hmmpanther:PTHR12602:SF21,hmmpanther:PTHR12602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCATTGGCT	byFrequency	5	ESCA
TAF1L	0	.	GRCh37	9	32631847	32631847	+	Missense_Mutation	SNP	C	C	T	rs371427336	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3731G>A	p.Arg1244Gln	p.R1244Q	ENST00000242310	1/1	73	24	49	41	41	0	TAF1L,missense_variant,p.Arg1244Gln,ENST00000242310,;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,;AL589642.1,non_coding_transcript_exon_variant,,ENST00000541085,;	T	ENSG00000122728	ENST00000242310	Transcript	missense_variant	3821	3731	1244	R/Q	cGg/cAg	rs371427336,COSM487371	.	.	-1	TAF1L	HGNC	18056	protein_coding	YES	CCDS35003.1	ENSP00000418379	TAF1L_HUMAN	.	UPI000007408A	.	deleterious(0.01)	probably_damaging(0.987)	1/1	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0,PIRSF_domain:PIRSF003047	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCCGCCGT	byFrequency|byCluster	5	ESCA
KANK1	0	.	GRCh37	9	712709	712709	+	Missense_Mutation	SNP	G	G	A	rs575779520	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1943G>A	p.Arg648Gln	p.R648Q	ENST00000382303	7/16	20	5	14	21	21	0	KANK1,missense_variant,p.Arg490Gln,ENST00000382293,;KANK1,missense_variant,p.Arg648Gln,ENST00000382303,;KANK1,missense_variant,p.Arg648Gln,ENST00000382297,;KANK1,non_coding_transcript_exon_variant,,ENST00000489369,;KANK1,non_coding_transcript_exon_variant,,ENST00000354485,;	A	ENSG00000107104	ENST00000382303	Transcript	missense_variant	2595	1943	648	R/Q	cGg/cAg	rs575779520	.	.	1	KANK1	HGNC	19309	protein_coding	YES	CCDS34976.1	ENSP00000371740	KANK1_HUMAN	Q8WUM7_HUMAN,Q53U93_HUMAN	UPI00001AF26E	.	tolerated(0.42)	benign(0.009)	7/16	.	hmmpanther:PTHR24168,hmmpanther:PTHR24168:SF19	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCCCGGGGCG	byCluster|by1000G	3	ESCA
SOX3	0	.	GRCh37	X	139585308	139585308	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*577A>G	.	.	ENST00000370536	1/1	62	26	36	60	60	0	SOX3,3_prime_UTR_variant,,ENST00000370536,;	C	ENSG00000134595	ENST00000370536	Transcript	3_prime_UTR_variant	1918	.	.	.	.	.	.	.	-1	SOX3	HGNC	11199	protein_coding	YES	CCDS14669.1	ENSP00000359567	SOX3_HUMAN	.	UPI000006F00F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGATTGGAC	.	5	ESCA
MAGEC1	0	.	GRCh37	X	140994968	140994968	+	Missense_Mutation	SNP	A	A	T	rs749532234	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1778A>T	p.His593Leu	p.H593L	ENST00000285879	4/4	73	55	17	71	71	0	MAGEC1,missense_variant,p.His593Leu,ENST00000285879,;MAGEC1,intron_variant,,ENST00000406005,;	T	ENSG00000155495	ENST00000285879	Transcript	missense_variant	2064	1778	593	H/L	cAc/cTc	rs749532234	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	tolerated_low_confidence(1)	benign(0.227)	4/4	.	hmmpanther:PTHR11736:SF17,hmmpanther:PTHR11736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L590L|c.1770G>A|4	RADIA|MUTECT|MUSE	TCCTCACTACT	byFrequency	3	ESCA
MAGEC1	0	.	GRCh37	X	140994985	140994987	+	In_Frame_Del	DEL	CCT	CCT	-	.	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	CCT	CCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1799_1801delCTC	p.Pro600del	p.P600del	ENST00000285879	4/4	42	35	7	71	71	0	MAGEC1,inframe_deletion,p.Pro600del,ENST00000285879,;MAGEC1,intron_variant,,ENST00000406005,;	-	ENSG00000155495	ENST00000285879	Transcript	inframe_deletion	2081-2083	1795-1797	599	P/-	CCT/-	TMP_ESP_X_140994985_140994987	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	.	.	4/4	.	hmmpanther:PTHR11736:SF17,hmmpanther:PTHR11736	.	.	.	.	.	.	.	-:0.0008	-:0.0012	.	.	.	.	.	.	.	MODERATE	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGAGCCCTCCTCA	.	3	ESCA
MAGEC1	0	.	GRCh37	X	140995006	140995006	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1816A>C	p.Met606Leu	p.M606L	ENST00000285879	4/4	71	31	40	76	76	0	MAGEC1,missense_variant,p.Met606Leu,ENST00000285879,;MAGEC1,intron_variant,,ENST00000406005,;	C	ENSG00000155495	ENST00000285879	Transcript	missense_variant	2102	1816	606	M/L	Atg/Ctg	.	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	tolerated_low_confidence(1)	benign(0)	4/4	.	hmmpanther:PTHR11736:SF17,hmmpanther:PTHR11736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCCATGTCT	.	4	ESCA
CCDC22	0	.	GRCh37	X	49106138	49106138	+	Silent	SNP	C	C	T	rs782545318	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1722C>T	p.%3D	p.I574I	ENST00000376227	16/17	71	65	5	94	93	0	CCDC22,synonymous_variant,p.%3D,ENST00000376227,;FOXP3,downstream_gene_variant,,ENST00000557224,;FOXP3,downstream_gene_variant,,ENST00000376199,;FOXP3,downstream_gene_variant,,ENST00000376197,;FOXP3,downstream_gene_variant,,ENST00000376207,;FOXP3,downstream_gene_variant,,ENST00000518685,;FOXP3,downstream_gene_variant,,ENST00000455775,;	T	ENSG00000101997	ENST00000376227	Transcript	synonymous_variant	1892	1722	574	I	atC/atT	rs782545318	.	.	1	CCDC22	HGNC	28909	protein_coding	YES	CCDS14322.1	ENSP00000365401	CCD22_HUMAN	.	UPI000006FFC7	.	.	.	16/17	.	hmmpanther:PTHR15668,Pfam_domain:PF05667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCATCGAGGA	byFrequency	3	ESCA
TGIF2LX	0	.	GRCh37	X	89177504	89177504	+	Silent	SNP	G	G	A	rs371679488	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.420G>A	p.%3D	p.A140A	ENST00000561129	1/1	23	11	12	44	44	0	TGIF2LX,synonymous_variant,p.%3D,ENST00000283891,;TGIF2LX,synonymous_variant,p.%3D,ENST00000561129,;	A	ENSG00000153779	ENST00000561129	Transcript	synonymous_variant	550	420	140	A	gcG/gcA	rs371679488,COSM3143210,COSM1126330	.	.	1	TGIF2LX	HGNC	18570	protein_coding	YES	CCDS14459.1	ENSP00000453704	TF2LX_HUMAN	.	UPI0000074793	.	.	.	1/1	.	hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF16	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGCGTCTGT	byFrequency|byCluster	5	ESCA
PABPC5	0	.	GRCh37	X	90692396	90692396	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A8I1-01A-11D-A36J-09	TCGA-LN-A8I1-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*671T>A	.	.	ENST00000312600	2/2	38	33	5	80	80	0	PABPC5,3_prime_UTR_variant,,ENST00000312600,;PABPC5,downstream_gene_variant,,ENST00000373105,;PABPC5-AS1,upstream_gene_variant,,ENST00000456187,;	A	ENSG00000174740	ENST00000312600	Transcript	3_prime_UTR_variant	2034	.	.	.	.	.	.	.	1	PABPC5	HGNC	13629	protein_coding	YES	CCDS14460.1	ENSP00000308012	PABP5_HUMAN	Q5JQF3_HUMAN,B4DM75_HUMAN	UPI0000087790	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACTTTAGGC	.	4	ESCA
PDZD7	0	.	GRCh37	10	102778670	102778670	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1233G>A	p.%3D	p.A411A	ENST00000370215	8/10	33	26	7	43	43	0	PDZD7,synonymous_variant,p.%3D,ENST00000370215,;PDZD7,downstream_gene_variant,,ENST00000470414,;PDZD7,upstream_gene_variant,,ENST00000433616,;PDZD7,3_prime_UTR_variant,,ENST00000474125,;PDZD7,downstream_gene_variant,,ENST00000476306,;	T	ENSG00000186862	ENST00000370215	Transcript	synonymous_variant	1459	1233	411	A	gcG/gcA	.	.	.	-1	PDZD7	HGNC	26257	protein_coding	YES	CCDS31269.1	ENSP00000359234	PDZD7_HUMAN	S4R3X4_HUMAN	UPI0000072FD2	.	.	.	8/10	.	hmmpanther:PTHR23116,hmmpanther:PTHR23116:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAGCGCAGA	.	5	ESCA
TDRD1	0	.	GRCh37	10	115981169	115981169	+	Missense_Mutation	SNP	A	A	G	rs376481564	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2824A>G	p.Ile942Val	p.I942V	ENST00000251864	20/26	56	38	17	26	26	0	TDRD1,missense_variant,p.Ile942Val,ENST00000369282,;TDRD1,missense_variant,p.Ile828Val,ENST00000369281,;TDRD1,missense_variant,p.Ile942Val,ENST00000251864,;TDRD1,missense_variant,p.Ile942Val,ENST00000369280,;TDRD1,missense_variant,p.Ile546Val,ENST00000422662,;	G	ENSG00000095627	ENST00000251864	Transcript	missense_variant	2977	2824	942	I/V	Ata/Gta	rs376481564	.	.	1	TDRD1	HGNC	11712	protein_coding	YES	CCDS7588.1	ENSP00000251864	TDRD1_HUMAN	.	UPI00001F9753	.	tolerated(1)	benign(0.001)	20/26	.	Pfam_domain:PF00567,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF4	.	.	.	.	.	.	.	G:0	G:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTATACAA	byFrequency|byCluster	5	ESCA
PRLHR	0	.	GRCh37	10	120353994	120353994	+	Missense_Mutation	SNP	G	G	A	rs370835454	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763C>T	p.Arg255Cys	p.R255C	ENST00000239032	2/2	69	57	11	85	85	0	PRLHR,missense_variant,p.Arg255Cys,ENST00000369169,;PRLHR,missense_variant,p.Arg255Cys,ENST00000239032,;	A	ENSG00000119973	ENST00000239032	Transcript	missense_variant	902	763	255	R/C	Cgc/Tgc	rs370835454	.	.	-1	PRLHR	HGNC	4464	protein_coding	YES	CCDS7606.1	ENSP00000239032	PRLHR_HUMAN	.	UPI000013CA6F	.	tolerated(0.14)	possibly_damaging(0.479)	2/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF194,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01018	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGCGGTTGC	byFrequency|byCluster	5	ESCA
EBF3	0	.	GRCh37	10	131635210	131635212	+	3'UTR	DEL	TTT	TTT	-	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	TTT	TTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*981_*983delAAA	.	.	ENST00000368648	16/16	51	25	26	28	28	0	EBF3,3_prime_UTR_variant,,ENST00000355311,;EBF3,3_prime_UTR_variant,,ENST00000368648,;EBF3,downstream_gene_variant,,ENST00000440978,;	-	ENSG00000108001	ENST00000368648	Transcript	3_prime_UTR_variant	2710-2712	.	.	.	.	.	.	.	-1	EBF3	HGNC	19087	protein_coding	YES	CCDS31314.1	ENSP00000357637	COE3_HUMAN	Q658Y5_HUMAN	UPI000002A6FB	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AACTTGTTTTTCTA	.	3	ESCA
TTC40	0	.	GRCh37	10	134751079	134751079	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.637T>C	p.Tyr213His	p.Y213H	ENST00000368586	6/58	41	33	7	32	32	0	TTC40,missense_variant,p.Tyr213His,ENST00000368582,;TTC40,missense_variant,p.Tyr213His,ENST00000368585,;TTC40,missense_variant,p.Tyr213His,ENST00000368586,;TTC40,non_coding_transcript_exon_variant,,ENST00000475340,;	G	ENSG00000171811	ENST00000368586	Transcript	missense_variant	738	637	213	Y/H	Tac/Cac	.	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	deleterious(0)	probably_damaging(0.995)	6/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGTATTTCT	.	5	ESCA
C10orf11	0	.	GRCh37	10	78084168	78084168	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.442G>C	p.Glu148Gln	p.E148Q	ENST00000372499	5/6	65	62	3	75	75	0	C10orf11,missense_variant,p.Glu5Gln,ENST00000496424,;C10orf11,missense_variant,p.Glu148Gln,ENST00000372499,;C10orf11,non_coding_transcript_exon_variant,,ENST00000598708,;C10orf11,non_coding_transcript_exon_variant,,ENST00000593699,;C10orf11,non_coding_transcript_exon_variant,,ENST00000488655,;	C	ENSG00000148655	ENST00000372499	Transcript	missense_variant	657	442	148	E/Q	Gag/Cag	.	.	.	1	C10orf11	HGNC	23405	protein_coding	YES	CCDS7351.1	ENSP00000361577	CJ011_HUMAN	.	UPI000006D28F	.	tolerated(0.4)	benign(0.006)	5/6	.	hmmpanther:PTHR10552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTAGTGAGGAC	.	2	ESCA
ZNF518A	0	.	GRCh37	10	97920573	97920573	+	RNA	SNP	G	G	A	rs374825340	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.5349G>A	.	.	ENST00000534948	7/7	38	26	12	20	20	0	ZNF518A,non_coding_transcript_exon_variant,,ENST00000567632,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000534948,;ZNF518A,intron_variant,,ENST00000563195,;ZNF518A,intron_variant,,ENST00000442635,;ZNF518A,downstream_gene_variant,,ENST00000478086,;ZNF518A,downstream_gene_variant,,ENST00000488700,;ZNF518A,downstream_gene_variant,,ENST00000316045,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000371192,;	A	ENSG00000177853	ENST00000534948	Transcript	non_coding_transcript_exon_variant	5349	.	.	.	.	rs374825340	.	.	1	ZNF518A	HGNC	29009	processed_transcript	YES	.	.	.	.	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	C:0	C:0.0005	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTAGAAGAA	byFrequency|byCluster	5	ESCA
MYOD1	0	.	GRCh37	11	17741729	17741729	+	Missense_Mutation	SNP	C	C	T	rs753416237	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400C>T	p.Arg134Cys	p.R134C	ENST00000250003	1/3	31	28	3	51	51	0	MYOD1,missense_variant,p.Arg134Cys,ENST00000250003,;	T	ENSG00000129152	ENST00000250003	Transcript	missense_variant	615	400	134	R/C	Cgc/Tgc	rs753416237	.	.	1	MYOD1	HGNC	7611	protein_coding	YES	CCDS7826.1	ENSP00000250003	MYOD1_HUMAN	.	UPI000007280C	.	deleterious(0)	probably_damaging(1)	1/3	.	PROSITE_profiles:PS50888,hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF2,Pfam_domain:PF00010,Gene3D:4.10.280.10,SMART_domains:SM00353,Superfamily_domains:SSF47459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TCAAGCGCTGC	byFrequency	3	ESCA
NAP1L4	0	.	GRCh37	11	2981115	2981115	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Glu211Lys	p.E211K	ENST00000380542	9/16	72	26	46	60	60	0	NAP1L4,missense_variant,p.Glu223Lys,ENST00000448187,;NAP1L4,missense_variant,p.Glu96Lys,ENST00000532325,;NAP1L4,missense_variant,p.Glu211Lys,ENST00000380542,;NAP1L4,missense_variant,p.Glu211Lys,ENST00000526115,;NAP1L4,downstream_gene_variant,,ENST00000399614,;SNORA54,downstream_gene_variant,,ENST00000384281,;NAP1L4,missense_variant,p.Glu67Lys,ENST00000492685,;NAP1L4,non_coding_transcript_exon_variant,,ENST00000528363,;NAP1L4,non_coding_transcript_exon_variant,,ENST00000483643,;NAP1L4,upstream_gene_variant,,ENST00000528261,;NAP1L4,upstream_gene_variant,,ENST00000492594,;	T	ENSG00000205531	ENST00000380542	Transcript	missense_variant	772	631	211	E/K	Gaa/Aaa	.	.	.	-1	NAP1L4	HGNC	7640	protein_coding	YES	CCDS41599.1	ENSP00000369915	NP1L4_HUMAN	E9PS34_HUMAN,E9PNW0_HUMAN,E9PNJ7_HUMAN,E9PKI2_HUMAN,E9PJJ2_HUMAN,C9J6D1_HUMAN,A8MXH2_HUMAN	UPI00001303EA	.	tolerated(0.33)	benign(0.124)	9/16	.	hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF34,Pfam_domain:PF00956,Superfamily_domains:SSF143113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTTCAAAGT	.	5	ESCA
STIP1	0	.	GRCh37	11	63953634	63953634	+	5'UTR	SNP	G	G	A	rs530274717	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-100G>A	.	.	ENST00000305218	1/14	74	60	14	48	48	0	STIP1,5_prime_UTR_variant,,ENST00000305218,;STIP1,intron_variant,,ENST00000358794,;STIP1,upstream_gene_variant,,ENST00000543847,;STIP1,upstream_gene_variant,,ENST00000538945,;STIP1,upstream_gene_variant,,ENST00000540501,;STIP1,upstream_gene_variant,,ENST00000540736,;STIP1,upstream_gene_variant,,ENST00000536973,;	A	ENSG00000168439	ENST00000305218	Transcript	5_prime_UTR_variant	48	.	.	.	.	rs530274717	.	.	1	STIP1	HGNC	11387	protein_coding	YES	CCDS8058.1	ENSP00000305958	STIP1_HUMAN	.	UPI000012D225	.	.	.	1/14	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCCGGGGTCCC	by1000G	4	ESCA
MALAT1	0	.	GRCh37	11	65273214	65273214	+	RNA	SNP	G	G	C	rs373484523	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.7982G>C	.	.	ENST00000534336	1/1	60	53	7	29	29	0	MALAT1,non_coding_transcript_exon_variant,,ENST00000534336,;MALAT1,downstream_gene_variant,,ENST00000508832,;MALAT1,downstream_gene_variant,,ENST00000544868,;	C	ENSG00000251562	ENST00000534336	Transcript	non_coding_transcript_exon_variant	7982	.	.	.	.	rs373484523	.	.	1	MALAT1	HGNC	29665	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	C:0	C:0.0003	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAAGGGTAT	byFrequency|byCluster	4	ESCA
KDM2A	0	.	GRCh37	11	67023792	67023792	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1266C>G	.	.	ENST00000529006	21/21	55	38	17	22	22	0	KDM2A,3_prime_UTR_variant,,ENST00000398645,;KDM2A,3_prime_UTR_variant,,ENST00000308783,;KDM2A,3_prime_UTR_variant,,ENST00000530342,;KDM2A,3_prime_UTR_variant,,ENST00000529006,;KDM2A,non_coding_transcript_exon_variant,,ENST00000531696,;KDM2A,non_coding_transcript_exon_variant,,ENST00000524657,;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;	G	ENSG00000173120	ENST00000529006	Transcript	3_prime_UTR_variant	5201	.	.	.	.	.	.	.	1	KDM2A	HGNC	13606	protein_coding	YES	CCDS44657.1	ENSP00000432786	KDM2A_HUMAN	I3VM54_HUMAN,I3VM53_HUMAN	UPI00001678A9	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCTCTAG	.	5	ESCA
PDE2A	0	.	GRCh37	11	72287931	72287931	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*497G>A	.	.	ENST00000334456	31/31	15	6	9	20	20	0	PDE2A,3_prime_UTR_variant,,ENST00000334456,;PDE2A,3_prime_UTR_variant,,ENST00000376450,;PDE2A,3_prime_UTR_variant,,ENST00000444035,;PDE2A,downstream_gene_variant,,ENST00000540345,;PDE2A,downstream_gene_variant,,ENST00000418754,;PDE2A,downstream_gene_variant,,ENST00000542223,;PDE2A,downstream_gene_variant,,ENST00000420501,;PDE2A,downstream_gene_variant,,ENST00000544570,;PDE2A,downstream_gene_variant,,ENST00000441209,;RP11-169D4.1,downstream_gene_variant,,ENST00000450804,;PDE2A,intron_variant,,ENST00000539367,;PDE2A,downstream_gene_variant,,ENST00000536918,;PDE2A,downstream_gene_variant,,ENST00000544239,;	T	ENSG00000186642	ENST00000334456	Transcript	3_prime_UTR_variant	3569	.	.	.	.	.	.	.	-1	PDE2A	HGNC	8777	protein_coding	YES	CCDS8216.1	ENSP00000334910	PDE2A_HUMAN	F5GXX2_HUMAN,C9JPD5_HUMAN	UPI000003B340	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCGCCCC	.	2	ESCA
TENM4	0	.	GRCh37	11	78381002	78381002	+	Missense_Mutation	SNP	T	T	C	rs749341010	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6388A>G	p.Ile2130Val	p.I2130V	ENST00000278550	32/34	23	11	11	34	34	0	TENM4,missense_variant,p.Ile2130Val,ENST00000278550,;TENM4,missense_variant,p.Ile594Val,ENST00000530738,;	C	ENSG00000149256	ENST00000278550	Transcript	missense_variant	6851	6388	2130	I/V	Att/Gtt	rs749341010	.	.	-1	TENM4	HGNC	29945	protein_coding	YES	CCDS44688.1	ENSP00000278550	TEN4_HUMAN	G3CAT1_HUMAN	UPI0000DD8112	.	deleterious(0.02)	possibly_damaging(0.833)	32/34	.	hmmpanther:PTHR11219:SF9,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTAATGTCAT	byFrequency	5	ESCA
NAALAD2	0	.	GRCh37	11	89882266	89882266	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474C>A	p.%3D	p.G158G	ENST00000534061	4/19	126	53	73	107	107	0	NAALAD2,synonymous_variant,p.%3D,ENST00000526637,;NAALAD2,synonymous_variant,p.%3D,ENST00000375944,;NAALAD2,synonymous_variant,p.%3D,ENST00000525171,;NAALAD2,synonymous_variant,p.%3D,ENST00000534061,;NAALAD2,synonymous_variant,p.%3D,ENST00000321955,;NAALAD2,downstream_gene_variant,,ENST00000525497,;NAALAD2,synonymous_variant,p.%3D,ENST00000527493,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000524501,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000529090,;	A	ENSG00000077616	ENST00000534061	Transcript	synonymous_variant	704	474	158	G	ggC/ggA	.	.	.	1	NAALAD2	HGNC	14526	protein_coding	YES	CCDS8288.1	ENSP00000432481	NALD2_HUMAN	E9PJ53_HUMAN,E9PII2_HUMAN	UPI0000031A85	.	.	.	4/19	.	Superfamily_domains:SSF52025,Pfam_domain:PF02225,Gene3D:3.50.30.30,hmmpanther:PTHR10404:SF38,hmmpanther:PTHR10404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGCATGCC	.	5	ESCA
FAT3	0	.	GRCh37	11	92532036	92532036	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5857C>A	p.Leu1953Met	p.L1953M	ENST00000298047	9/27	21	7	13	24	24	0	FAT3,missense_variant,p.Leu1953Met,ENST00000298047,;FAT3,missense_variant,p.Leu1953Met,ENST00000409404,;FAT3,missense_variant,p.Leu1803Met,ENST00000525166,;	A	ENSG00000165323	ENST00000298047	Transcript	missense_variant	5874	5857	1953	L/M	Ctg/Atg	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	possibly_damaging(0.866)	9/27	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATGCTGATA	.	5	ESCA
ANO4	0	.	GRCh37	12	101505402	101505402	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2259C>G	p.%3D	p.V753V	ENST00000392979	23/27	61	52	9	34	34	0	ANO4,synonymous_variant,p.%3D,ENST00000550015,;ANO4,synonymous_variant,p.%3D,ENST00000299222,;ANO4,synonymous_variant,p.%3D,ENST00000392977,;ANO4,synonymous_variant,p.%3D,ENST00000392979,;	G	ENSG00000151572	ENST00000392979	Transcript	synonymous_variant	2620	2259	753	V	gtC/gtG	.	.	.	1	ANO4	HGNC	23837	protein_coding	YES	CCDS31884.1	ENSP00000376705	ANO4_HUMAN	.	UPI0000198E2E	.	.	.	23/27	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF04547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCATAGC	.	5	ESCA
UNG	0	.	GRCh37	12	109547654	109547654	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822G>A	p.%3D	p.Q274Q	ENST00000242576	7/7	115	77	37	75	75	0	UNG,synonymous_variant,p.%3D,ENST00000242576,;UNG,synonymous_variant,p.%3D,ENST00000336865,;RP11-968O1.5,upstream_gene_variant,,ENST00000541704,;UNG,3_prime_UTR_variant,,ENST00000539287,;UNG,3_prime_UTR_variant,,ENST00000446767,;	A	ENSG00000076248	ENST00000242576	Transcript	synonymous_variant	928	822	274	Q	caG/caA	.	.	.	1	UNG	HGNC	12572	protein_coding	YES	CCDS9124.1	ENSP00000242576	UNG_HUMAN	E5KTA5_HUMAN	UPI000002E951	.	.	.	7/7	.	HAMAP:MF_00148,hmmpanther:PTHR11264,hmmpanther:PTHR11264:SF0,Pfam_domain:PF03167,Gene3D:3.40.470.10,TIGRFAM_domain:TIGR00628,SMART_domains:SM00986,SMART_domains:SM00987,Superfamily_domains:SSF52141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACAGACGGC	.	5	ESCA
RP11-227B21.2	0	.	GRCh37	12	117890935	117890935	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.119C>T	.	.	ENST00000540161	1/2	28	24	4	22	22	0	KSR2,3_prime_UTR_variant,,ENST00000425217,;RP11-227B21.2,non_coding_transcript_exon_variant,,ENST00000540161,;NOS1,upstream_gene_variant,,ENST00000549189,;	T	ENSG00000255686	ENST00000540161	Transcript	non_coding_transcript_exon_variant	119	.	.	.	.	.	.	.	1	RP11-227B21.2	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAACAACAG	.	4	ESCA
CCDC65	0	.	GRCh37	12	49298842	49298842	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246G>C	p.Glu82Asp	p.E82D	ENST00000320516	2/8	49	33	16	25	25	0	CCDC65,missense_variant,p.Glu82Asp,ENST00000320516,;CCDC65,missense_variant,p.Glu82Asp,ENST00000552942,;CCDC65,missense_variant,p.Glu82Asp,ENST00000266984,;RP11-302B13.5,intron_variant,,ENST00000398092,;CCDC65,3_prime_UTR_variant,,ENST00000547861,;RP11-302B13.1,upstream_gene_variant,,ENST00000489971,;	C	ENSG00000139537	ENST00000320516	Transcript	missense_variant	434	246	82	E/D	gaG/gaC	.	.	.	1	CCDC65	HGNC	29937	protein_coding	YES	CCDS8772.1	ENSP00000312706	CCD65_HUMAN	B4DXQ7_HUMAN	UPI00001408DA	.	tolerated(0.09)	possibly_damaging(0.749)	2/8	.	hmmpanther:PTHR21625,hmmpanther:PTHR21625:SF0,Pfam_domain:PF14772	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGAGATCCT	.	5	ESCA
KRT77	0	.	GRCh37	12	53086350	53086350	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1282C>A	p.Leu428Met	p.L428M	ENST00000341809	7/9	34	20	14	33	33	0	KRT77,missense_variant,p.Leu428Met,ENST00000341809,;KRT77,missense_variant,p.Leu195Met,ENST00000537195,;RP11-641A6.3,upstream_gene_variant,,ENST00000547533,;KRT77,3_prime_UTR_variant,,ENST00000553168,;KRT77,downstream_gene_variant,,ENST00000550823,;	T	ENSG00000189182	ENST00000341809	Transcript	missense_variant	1311	1282	428	L/M	Ctg/Atg	.	.	.	-1	KRT77	HGNC	20411	protein_coding	YES	CCDS8837.1	ENSP00000342710	K2C1B_HUMAN	F5GY66_HUMAN	UPI00001D797A	.	deleterious(0.01)	possibly_damaging(0.873)	7/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF87,hmmpanther:PTHR23239,Gene3D:1.20.5.170,Pfam_domain:PF00038,Superfamily_domains:SSF64593,Prints_domain:PR01276	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGCTTCT	.	5	ESCA
PPM1H	0	.	GRCh37	12	63195713	63195713	+	Silent	SNP	G	G	A	rs201542231	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639C>T	p.%3D	p.R213R	ENST00000228705	3/10	37	29	8	27	27	0	PPM1H,synonymous_variant,p.%3D,ENST00000228705,;PPM1H,non_coding_transcript_exon_variant,,ENST00000548414,;PPM1H,downstream_gene_variant,,ENST00000547857,;	A	ENSG00000111110	ENST00000228705	Transcript	synonymous_variant	940	639	213	R	cgC/cgT	rs201542231	.	.	-1	PPM1H	HGNC	18583	protein_coding	YES	CCDS44934.1	ENSP00000228705	PPM1H_HUMAN	.	UPI00000557DD	.	.	.	3/10	.	hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF214,SMART_domains:SM00332	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCGCGCAG	byCluster|by1000G	5	ESCA
AVPR1A	0	.	GRCh37	12	63541286	63541286	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1110G>T	p.Lys370Asn	p.K370N	ENST00000299178	2/2	69	51	18	46	46	0	AVPR1A,missense_variant,p.Lys370Asn,ENST00000299178,;AVPR1A,missense_variant,p.Lys151Asn,ENST00000550940,;	A	ENSG00000166148	ENST00000299178	Transcript	missense_variant	1216	1110	370	K/N	aaG/aaT	.	.	.	-1	AVPR1A	HGNC	895	protein_coding	YES	CCDS8965.1	ENSP00000299178	V1AR_HUMAN	.	UPI0000050439	.	tolerated(0.27)	benign(0.002)	2/2	.	hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF17,Superfamily_domains:SSF81321,Prints_domain:PR00752	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCCTTCAT	.	5	ESCA
TMBIM4	0	.	GRCh37	12	66539653	66539653	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432A>G	p.%3D	p.Q144Q	ENST00000358230	5/7	103	78	25	48	48	0	TMBIM4,synonymous_variant,p.%3D,ENST00000542724,;TMBIM4,synonymous_variant,p.%3D,ENST00000358230,;TMBIM4,synonymous_variant,p.%3D,ENST00000398033,;TMBIM4,synonymous_variant,p.%3D,ENST00000556010,;TMBIM4,synonymous_variant,p.%3D,ENST00000286424,;TMBIM4,5_prime_UTR_variant,,ENST00000544599,;TMBIM4,synonymous_variant,p.%3D,ENST00000539652,;TMBIM4,3_prime_UTR_variant,,ENST00000545407,;TMBIM4,3_prime_UTR_variant,,ENST00000545504,;TMBIM4,3_prime_UTR_variant,,ENST00000534930,;	C	ENSG00000155957	ENST00000358230	Transcript	synonymous_variant	553	432	144	Q	caA/caG	.	.	.	-1	TMBIM4	HGNC	24257	protein_coding	YES	CCDS41805.1	ENSP00000350965	LFG4_HUMAN	G3V1R8_HUMAN	UPI00001FC6E2	.	.	.	5/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23291:SF34,hmmpanther:PTHR23291,Pfam_domain:PF01027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGATTGTAG	.	5	ESCA
ACSS3	0	.	GRCh37	12	81624851	81624851	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1530T>C	p.%3D	p.P510P	ENST00000548058	12/16	110	74	36	46	46	0	ACSS3,synonymous_variant,p.%3D,ENST00000261206,;ACSS3,synonymous_variant,p.%3D,ENST00000548058,;ACSS3,synonymous_variant,p.%3D,ENST00000548324,;	C	ENSG00000111058	ENST00000548058	Transcript	synonymous_variant	2440	1530	510	P	ccT/ccC	.	.	.	1	ACSS3	HGNC	24723	protein_coding	YES	CCDS9022.1	ENSP00000449535	ACSS3_HUMAN	F8VZB4_HUMAN	UPI000007060A	.	.	.	12/16	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF0,Gene3D:2.30.38.10,Pfam_domain:PF00501,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCTGGGGC	.	5	ESCA
FOXJ2	0	.	GRCh37	12	8206054	8206054	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*608A>G	.	.	ENST00000162391	11/11	62	37	24	26	26	0	FOXJ2,3_prime_UTR_variant,,ENST00000162391,;FOXJ2,downstream_gene_variant,,ENST00000428177,;C3AR1,downstream_gene_variant,,ENST00000307637,;FOXJ2,downstream_gene_variant,,ENST00000539192,;	G	ENSG00000065970	ENST00000162391	Transcript	3_prime_UTR_variant	3478	.	.	.	.	.	.	.	1	FOXJ2	HGNC	24818	protein_coding	YES	CCDS8587.1	ENSP00000162391	FOXJ2_HUMAN	.	UPI000012ADE1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTATTTCC	.	5	ESCA
APAF1	0	.	GRCh37	12	99128582	99128582	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000551964	.	38	16	22	21	21	0	APAF1,3_prime_UTR_variant,,ENST00000357310,;APAF1,3_prime_UTR_variant,,ENST00000550527,;APAF1,3_prime_UTR_variant,,ENST00000339433,;APAF1,3_prime_UTR_variant,,ENST00000333991,;ANKS1B,3_prime_UTR_variant,,ENST00000341752,;APAF1,3_prime_UTR_variant,,ENST00000359972,;ANKS1B,3_prime_UTR_variant,,ENST00000549558,;ANKS1B,downstream_gene_variant,,ENST00000547010,;APAF1,downstream_gene_variant,,ENST00000549007,;APAF1,downstream_gene_variant,,ENST00000547045,;ANKS1B,downstream_gene_variant,,ENST00000329257,;APAF1,downstream_gene_variant,,ENST00000552268,;APAF1,downstream_gene_variant,,ENST00000551964,;ANKS1B,downstream_gene_variant,,ENST00000547776,;APAF1,non_coding_transcript_exon_variant,,ENST00000547666,;APAF1,downstream_gene_variant,,ENST00000552929,;ANKS1B,downstream_gene_variant,,ENST00000551212,;ANKS1B,intron_variant,,ENST00000555119,;	G	ENSG00000120868	ENST00000551964	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1277	1	APAF1	HGNC	576	protein_coding	YES	CCDS9069.1	ENSP00000448165	APAF_HUMAN	.	UPI0000036328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAAATCATA	.	5	ESCA
TFDP1	0	.	GRCh37	13	114294708	114294708	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*126G>C	.	.	ENST00000375370	12/12	9	4	5	11	11	0	TFDP1,3_prime_UTR_variant,,ENST00000375370,;TFDP1,3_prime_UTR_variant,,ENST00000538138,;TFDP1,downstream_gene_variant,,ENST00000408980,;TFDP1,downstream_gene_variant,,ENST00000544902,;TFDP1,non_coding_transcript_exon_variant,,ENST00000494812,;	C	ENSG00000198176	ENST00000375370	Transcript	3_prime_UTR_variant	1571	.	.	.	.	.	.	.	1	TFDP1	HGNC	11749	protein_coding	YES	CCDS9538.1	ENSP00000364519	TFDP1_HUMAN	Q5JSB5_HUMAN	UPI0000000CB6	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATTTAGATATG	.	3	ESCA
MYCBP2	0	.	GRCh37	13	77641876	77641876	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12181G>C	p.Asp4061His	p.D4061H	ENST00000544440	71/83	65	20	45	46	46	0	MYCBP2,missense_variant,p.Asp4061His,ENST00000357337,;MYCBP2,missense_variant,p.Asp482His,ENST00000429715,;MYCBP2,missense_variant,p.Asp4061His,ENST00000544440,;MYCBP2,missense_variant,p.Asp4099His,ENST00000407578,;	G	ENSG00000005810	ENST00000544440	Transcript	missense_variant	12199	12181	4061	D/H	Gac/Cac	.	.	.	-1	MYCBP2	HGNC	23386	protein_coding	YES	.	ENSP00000444596	MYCB2_HUMAN	.	UPI0000212757	.	.	probably_damaging(0.997)	71/83	.	hmmpanther:PTHR12846:SF14,hmmpanther:PTHR12846	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGTCTCCTT	.	5	ESCA
SLITRK5	0	.	GRCh37	13	88327729	88327729	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86C>T	p.Ala29Val	p.A29V	ENST00000325089	2/2	33	30	3	31	31	0	SLITRK5,missense_variant,p.Ala29Val,ENST00000325089,;SLITRK5,intron_variant,,ENST00000400028,;MIR4500HG,upstream_gene_variant,,ENST00000436290,;MIR4500HG,upstream_gene_variant,,ENST00000441617,;MIR4500HG,upstream_gene_variant,,ENST00000606590,;MIR4500HG,upstream_gene_variant,,ENST00000453832,;	T	ENSG00000165300	ENST00000325089	Transcript	missense_variant	305	86	29	A/V	gCt/gTt	.	.	.	1	SLITRK5	HGNC	20295	protein_coding	YES	CCDS9465.1	ENSP00000366283	SLIK5_HUMAN	.	UPI000015F6F7	.	tolerated(0.15)	benign(0.004)	2/2	.	hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTGCTGTAA	.	4	ESCA
TECPR2	0	.	GRCh37	14	102963419	102963419	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3893A>G	p.Glu1298Gly	p.E1298G	ENST00000359520	18/20	86	45	41	73	73	0	TECPR2,missense_variant,p.Glu1298Gly,ENST00000359520,;RNU6-244P,upstream_gene_variant,,ENST00000391028,;TECPR2,non_coding_transcript_exon_variant,,ENST00000561099,;TECPR2,upstream_gene_variant,,ENST00000559124,;	G	ENSG00000196663	ENST00000359520	Transcript	missense_variant	4119	3893	1298	E/G	gAg/gGg	.	.	.	1	TECPR2	HGNC	19957	protein_coding	YES	CCDS32162.1	ENSP00000352510	TCPR2_HUMAN	.	UPI00001FDC38	.	deleterious(0)	benign(0.1)	18/20	.	Pfam_domain:PF06462,hmmpanther:PTHR23287:SF16,hmmpanther:PTHR23287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCGAGGAGA	.	5	ESCA
CTD-2311B13.7	0	.	GRCh37	14	19969402	19969402	+	RNA	DEL	T	T	-	rs543184938	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2891delA	.	.	ENST00000547399	1/4	77	57	20	23	23	0	CTD-2311B13.7,non_coding_transcript_exon_variant,,ENST00000547399,;	-	ENSG00000257931	ENST00000547399	Transcript	non_coding_transcript_exon_variant	2891	.	.	.	.	rs543184938	.	.	-1	CTD-2311B13.7	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/4	.	.	-:0.0006	-:0.0015	-:0	.	-:0.001	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTGTATTTTTT	byFrequency|by1000G	3	ESCA
SEC23A	0	.	GRCh37	14	39501264	39501264	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1179A>G	.	.	ENST00000307712	20/20	87	54	32	41	41	0	SEC23A,3_prime_UTR_variant,,ENST00000307712,;SEC23A,3_prime_UTR_variant,,ENST00000537403,;SEC23A,downstream_gene_variant,,ENST00000536508,;SEC23A,downstream_gene_variant,,ENST00000545328,;SEC23A,non_coding_transcript_exon_variant,,ENST00000554615,;SEC23A,downstream_gene_variant,,ENST00000555363,;	C	ENSG00000100934	ENST00000307712	Transcript	3_prime_UTR_variant	3995	.	.	.	.	.	.	.	-1	SEC23A	HGNC	10701	protein_coding	YES	CCDS9668.1	ENSP00000306881	SC23A_HUMAN	G3V5K1_HUMAN,G3V3G5_HUMAN,G3V2R6_HUMAN,B3KXI2_HUMAN	UPI000013EC46	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGATTGTGT	.	5	ESCA
STYX	0	.	GRCh37	14	53197004	53197004	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-189G>A	.	.	ENST00000354586	1/11	29	17	12	19	19	0	STYX,5_prime_UTR_variant,,ENST00000354586,;STYX,intron_variant,,ENST00000442123,;PSMC6,downstream_gene_variant,,ENST00000606149,;PSMC6,downstream_gene_variant,,ENST00000445930,;STYX,upstream_gene_variant,,ENST00000556861,;PSMC6,downstream_gene_variant,,ENST00000557557,;PSMC6,downstream_gene_variant,,ENST00000555175,;PSMC6,downstream_gene_variant,,ENST00000557632,;	A	ENSG00000198252	ENST00000354586	Transcript	5_prime_UTR_variant	105	.	.	.	.	.	.	.	1	STYX	HGNC	11447	protein_coding	YES	CCDS9711.1	ENSP00000346599	STYX_HUMAN	.	UPI00000434EF	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCCCTGTCTTC	.	3	ESCA
GPR135	0	.	GRCh37	14	59930820	59930820	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125G>A	p.%3D	p.L375L	ENST00000395116	1/1	77	73	4	66	66	0	GPR135,synonymous_variant,p.%3D,ENST00000395116,;L3HYPDH,intron_variant,,ENST00000466522,;GPR135,synonymous_variant,p.%3D,ENST00000481661,;	T	ENSG00000181619	ENST00000395116	Transcript	synonymous_variant	1241	1125	375	L	ctG/ctA	.	.	.	-1	GPR135	HGNC	19991	protein_coding	YES	CCDS9738.1	ENSP00000378548	GP135_HUMAN	.	UPI0000046D5B	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22752:SF3,hmmpanther:PTHR22752,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGTCAGCCA	.	2	ESCA
SIX4	0	.	GRCh37	14	61180669	61180669	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1802G>T	p.Gly601Val	p.G601V	ENST00000216513	3/3	53	34	19	41	41	0	SIX4,missense_variant,p.Gly601Val,ENST00000216513,;SIX4,3_prime_UTR_variant,,ENST00000554079,;	A	ENSG00000100625	ENST00000216513	Transcript	missense_variant	1862	1802	601	G/V	gGg/gTg	.	.	.	-1	SIX4	HGNC	10890	protein_coding	YES	CCDS9749.2	ENSP00000216513	SIX4_HUMAN	.	UPI000066D924	.	deleterious_low_confidence(0)	benign(0.322)	3/3	.	hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCCCCGAG	.	5	ESCA
ZFYVE26	0	.	GRCh37	14	68236404	68236404	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5528G>A	p.Cys1843Tyr	p.C1843Y	ENST00000347230	29/42	46	23	22	44	44	0	ZFYVE26,missense_variant,p.Cys1843Tyr,ENST00000555452,;ZFYVE26,missense_variant,p.Cys1843Tyr,ENST00000347230,;ZFYVE26,3_prime_UTR_variant,,ENST00000554557,;ZFYVE26,non_coding_transcript_exon_variant,,ENST00000394455,;ZFYVE26,non_coding_transcript_exon_variant,,ENST00000554523,;	T	ENSG00000072121	ENST00000347230	Transcript	missense_variant	5667	5528	1843	C/Y	tGc/tAc	.	.	.	-1	ZFYVE26	HGNC	20761	protein_coding	YES	CCDS9788.1	ENSP00000251119	ZFY26_HUMAN	.	UPI00001FD735	.	deleterious(0)	probably_damaging(1)	29/42	.	PROSITE_profiles:PS50178,hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF115,Gene3D:3.30.40.10,Pfam_domain:PF01363,SMART_domains:SM00064,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGCACACT	.	5	ESCA
SPATA7	0	.	GRCh37	14	88859798	88859798	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.156G>A	p.Met52Ile	p.M52I	ENST00000393545	3/12	47	39	7	51	51	0	SPATA7,missense_variant,p.Met52Ile,ENST00000045347,;SPATA7,missense_variant,p.Met52Ile,ENST00000393545,;SPATA7,intron_variant,,ENST00000555401,;SPATA7,intron_variant,,ENST00000356583,;SPATA7,intron_variant,,ENST00000553885,;SPATA7,intron_variant,,ENST00000556553,;SPATA7,non_coding_transcript_exon_variant,,ENST00000554102,;SPATA7,missense_variant,p.Met52Ile,ENST00000557248,;SPATA7,missense_variant,p.Met52Ile,ENST00000555515,;SPATA7,missense_variant,p.Met52Ile,ENST00000555534,;SPATA7,3_prime_UTR_variant,,ENST00000555715,;SPATA7,3_prime_UTR_variant,,ENST00000557724,;SPATA7,non_coding_transcript_exon_variant,,ENST00000553626,;SPATA7,non_coding_transcript_exon_variant,,ENST00000557567,;SPATA7,intron_variant,,ENST00000553908,;SPATA7,intron_variant,,ENST00000555356,;SPATA7,intron_variant,,ENST00000556870,;SPATA7,intron_variant,,ENST00000554168,;	A	ENSG00000042317	ENST00000393545	Transcript	missense_variant	445	156	52	M/I	atG/atA	.	.	.	1	SPATA7	HGNC	20423	protein_coding	YES	CCDS9883.1	ENSP00000377176	SPAT7_HUMAN	.	UPI00000712C7	.	deleterious(0.01)	probably_damaging(0.997)	3/12	.	Pfam_domain:PF15244,hmmpanther:PTHR14917	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACATGGCTGT	.	4	ESCA
SPG11	0	.	GRCh37	15	44881455	44881455	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4901C>G	p.Ser1634Cys	p.S1634C	ENST00000261866	28/40	51	35	16	34	34	0	SPG11,missense_variant,p.Ser1634Cys,ENST00000535302,;SPG11,missense_variant,p.Ser1634Cys,ENST00000558319,;SPG11,missense_variant,p.Ser1634Cys,ENST00000261866,;SPG11,missense_variant,p.Ser1634Cys,ENST00000427534,;SPG11,upstream_gene_variant,,ENST00000559511,;SPG11,non_coding_transcript_exon_variant,,ENST00000558253,;SPG11,non_coding_transcript_exon_variant,,ENST00000558790,;SPG11,missense_variant,p.Ser94Cys,ENST00000560858,;SPG11,3_prime_UTR_variant,,ENST00000558155,;SPG11,upstream_gene_variant,,ENST00000559822,;	C	ENSG00000104133	ENST00000261866	Transcript	missense_variant	4918	4901	1634	S/C	tCt/tGt	.	.	.	-1	SPG11	HGNC	11226	protein_coding	YES	CCDS10112.1	ENSP00000261866	SPTCS_HUMAN	H0YN96_HUMAN,C4B7M3_HUMAN	UPI0000456840	.	tolerated(0.12)	probably_damaging(0.987)	28/40	.	hmmpanther:PTHR13650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCAGAGAAG	.	5	ESCA
GNB5	0	.	GRCh37	15	52425597	52425597	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841G>A	p.Glu281Lys	p.E281K	ENST00000261837	9/13	53	26	27	54	54	0	GNB5,missense_variant,p.Glu239Lys,ENST00000358784,;GNB5,missense_variant,p.Glu169Lys,ENST00000396335,;GNB5,missense_variant,p.Glu281Lys,ENST00000261837,;CTD-2184D3.7,intron_variant,,ENST00000557898,;GNB5,non_coding_transcript_exon_variant,,ENST00000559348,;GNB5,missense_variant,p.Glu96Lys,ENST00000558519,;GNB5,non_coding_transcript_exon_variant,,ENST00000559541,;GNB5,downstream_gene_variant,,ENST00000561313,;GNB5,upstream_gene_variant,,ENST00000557936,;	T	ENSG00000069966	ENST00000261837	Transcript	missense_variant	907	841	281	E/K	Gaa/Aaa	.	.	.	-1	GNB5	HGNC	4401	protein_coding	YES	CCDS10149.1	ENSP00000261837	GBB5_HUMAN	H0YLU1_HUMAN	UPI000006E214	.	deleterious(0.02)	possibly_damaging(0.481)	9/13	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR19850,hmmpanther:PTHR19850:SF12,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,PIRSF_domain:PIRSF002394,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCATGTG	.	5	ESCA
ARPP19	0	.	GRCh37	15	52842237	52842237	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1894A>G	.	.	ENST00000566423	4/4	12	8	4	10	10	0	ARPP19,3_prime_UTR_variant,,ENST00000561650,;ARPP19,3_prime_UTR_variant,,ENST00000566423,;ARPP19,3_prime_UTR_variant,,ENST00000249822,;ARPP19,downstream_gene_variant,,ENST00000569281,;ARPP19,downstream_gene_variant,,ENST00000563277,;ARPP19,downstream_gene_variant,,ENST00000567830,;ARPP19,downstream_gene_variant,,ENST00000567669,;ARPP19,downstream_gene_variant,,ENST00000564163,;ARPP19,downstream_gene_variant,,ENST00000563566,;ARPP19,downstream_gene_variant,,ENST00000569723,;ARPP19,downstream_gene_variant,,ENST00000561971,;ARPP19,downstream_gene_variant,,ENST00000568196,;ARPP19,downstream_gene_variant,,ENST00000565288,;	C	ENSG00000128989	ENST00000566423	Transcript	3_prime_UTR_variant	2367	.	.	.	.	.	.	.	-1	ARPP19	HGNC	16967	protein_coding	YES	CCDS32242.1	ENSP00000455625	ARP19_HUMAN	H3BTD3_HUMAN	UPI000000030A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GGTCATAGGAG	.	2	ESCA
RFX7	0	.	GRCh37	15	56386365	56386365	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3561T>C	p.%3D	p.N1187N	ENST00000423270	9/9	28	11	17	22	21	0	RFX7,synonymous_variant,p.%3D,ENST00000423270,;RFX7,synonymous_variant,p.%3D,ENST00000559447,;RFX7,synonymous_variant,p.%3D,ENST00000317318,;RFX7,synonymous_variant,p.%3D,ENST00000422057,;RFX7,synonymous_variant,p.%3D,ENST00000559847,;	G	ENSG00000181827	ENST00000423270	Transcript	synonymous_variant	3561	3561	1187	N	aaT/aaC	.	.	.	-1	RFX7	HGNC	25777	protein_coding	YES	.	ENSP00000397644	RFX7_HUMAN	H0YMH6_HUMAN,H0YLP2_HUMAN	UPI000057809D	.	.	.	9/9	.	hmmpanther:PTHR12619:SF2,hmmpanther:PTHR12619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGATATTAGA	.	5	ESCA
TCF12	0	.	GRCh37	15	57580564	57580564	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2221G>C	.	.	ENST00000438423	21/21	35	21	13	24	24	0	TCF12,3_prime_UTR_variant,,ENST00000438423,;TCF12,3_prime_UTR_variant,,ENST00000343827,;TCF12,3_prime_UTR_variant,,ENST00000267811,;TCF12,3_prime_UTR_variant,,ENST00000333725,;TCF12,3_prime_UTR_variant,,ENST00000452095,;TCF12,intron_variant,,ENST00000560948,;TCF12,intron_variant,,ENST00000560836,;TCF12,downstream_gene_variant,,ENST00000559703,;TCF12,downstream_gene_variant,,ENST00000537840,;TCF12,downstream_gene_variant,,ENST00000557843,;TCF12,downstream_gene_variant,,ENST00000543579,;TCF12,downstream_gene_variant,,ENST00000559710,;TCF12,downstream_gene_variant,,ENST00000561454,;TCF12,downstream_gene_variant,,ENST00000560190,;TCF12,downstream_gene_variant,,ENST00000560191,;	C	ENSG00000140262	ENST00000438423	Transcript	3_prime_UTR_variant	4638	.	.	.	.	.	.	.	1	TCF12	HGNC	11623	protein_coding	YES	CCDS10160.1	ENSP00000388940	HTF4_HUMAN	Q9NQY9_HUMAN,Q9NQY7_HUMAN,Q9NQY6_HUMAN,Q9NQY5_HUMAN,Q9NQY4_HUMAN,Q9NQY3_HUMAN,Q9NQY2_HUMAN,Q9NQY1_HUMAN,H0YNQ5_HUMAN	UPI000018CEA6	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTGTATCC	.	5	ESCA
AQP9	0	.	GRCh37	15	58430744	58430744	+	5'UTR	SNP	A	A	C	rs775221036	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-21A>C	.	.	ENST00000219919	1/6	36	30	6	19	19	0	AQP9,5_prime_UTR_variant,,ENST00000536493,;AQP9,5_prime_UTR_variant,,ENST00000219919,;ALDH1A2,5_prime_UTR_variant,,ENST00000557967,;AQP9,intron_variant,,ENST00000558772,;ALDH1A2,intron_variant,,ENST00000558231,;ALDH1A2,intron_variant,,ENST00000558239,;AQP9,non_coding_transcript_exon_variant,,ENST00000559443,;ALDH1A2,non_coding_transcript_exon_variant,,ENST00000560122,;ALDH1A2,non_coding_transcript_exon_variant,,ENST00000558504,;ALDH1A2,non_coding_transcript_exon_variant,,ENST00000560863,;ALDH1A2,non_coding_transcript_exon_variant,,ENST00000559297,;ALDH1A2,intron_variant,,ENST00000558073,;	C	ENSG00000103569	ENST00000219919	Transcript	5_prime_UTR_variant	350	.	.	.	.	rs775221036	.	.	1	AQP9	HGNC	643	protein_coding	YES	CCDS10165.1	ENSP00000219919	AQP9_HUMAN	H0YK62_HUMAN	UPI000013C796	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	ACAGGAGTCCT	.	2	ESCA
RNF111	0	.	GRCh37	15	59373162	59373162	+	Missense_Mutation	SNP	A	A	G	rs746893754	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1976A>G	p.His659Arg	p.H659R	ENST00000559209	8/14	46	28	18	43	43	0	RNF111,missense_variant,p.His659Arg,ENST00000434298,;RNF111,missense_variant,p.His659Arg,ENST00000561186,;RNF111,missense_variant,p.His659Arg,ENST00000557998,;RNF111,missense_variant,p.His659Arg,ENST00000348370,;RNF111,missense_variant,p.His659Arg,ENST00000559209,;RNF111,non_coding_transcript_exon_variant,,ENST00000558977,;RNF111,upstream_gene_variant,,ENST00000559077,;RNF111,upstream_gene_variant,,ENST00000560216,;RNF111,upstream_gene_variant,,ENST00000560952,;	G	ENSG00000157450	ENST00000559209	Transcript	missense_variant	2112	1976	659	H/R	cAt/cGt	rs746893754	.	.	1	RNF111	HGNC	17384	protein_coding	YES	CCDS58365.1	ENSP00000453872	RN111_HUMAN	H0YKS2_HUMAN	UPI0000EE4EBD	.	deleterious(0)	probably_damaging(0.995)	8/14	.	hmmpanther:PTHR13644,hmmpanther:PTHR13644:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCATCATCAAG	.	4	ESCA
PTPN9	0	.	GRCh37	15	75809693	75809693	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435G>A	p.%3D	p.Q145Q	ENST00000306726	5/13	58	32	26	40	40	0	PTPN9,synonymous_variant,p.%3D,ENST00000561731,;PTPN9,synonymous_variant,p.%3D,ENST00000306726,;CTD-2323K18.2,upstream_gene_variant,,ENST00000566222,;	T	ENSG00000169410	ENST00000306726	Transcript	synonymous_variant	948	435	145	Q	caG/caA	.	.	.	-1	PTPN9	HGNC	9661	protein_coding	YES	CCDS10280.1	ENSP00000303554	PTN9_HUMAN	.	UPI0000000CAC	.	.	.	5/13	.	PROSITE_profiles:PS50191,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF194,Pfam_domain:PF00650,Gene3D:3.40.525.10,SMART_domains:SM00516,Superfamily_domains:SSF52087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTGAGT	.	5	ESCA
XYLT1	0	.	GRCh37	16	17197032	17197032	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5520C>T	.	.	ENST00000261381	12/12	69	55	14	32	32	0	XYLT1,3_prime_UTR_variant,,ENST00000261381,;	A	ENSG00000103489	ENST00000261381	Transcript	3_prime_UTR_variant	8485	.	.	.	.	.	.	.	-1	XYLT1	HGNC	15516	protein_coding	YES	CCDS10569.1	ENSP00000261381	XYLT1_HUMAN	.	UPI000000DCCE	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGAGATAAA	.	5	ESCA
C16orf93	0	.	GRCh37	16	30773082	30773082	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13G>C	.	.	ENST00000543610	1/9	65	37	27	57	57	0	C16orf93,5_prime_UTR_variant,,ENST00000545825,;C16orf93,5_prime_UTR_variant,,ENST00000541260,;RNF40,5_prime_UTR_variant,,ENST00000563909,;C16orf93,5_prime_UTR_variant,,ENST00000543610,;RNF40,upstream_gene_variant,,ENST00000566811,;RNF40,upstream_gene_variant,,ENST00000563683,;RNF40,upstream_gene_variant,,ENST00000324685,;RNF40,upstream_gene_variant,,ENST00000402121,;RNF40,upstream_gene_variant,,ENST00000565931,;PHKG2,downstream_gene_variant,,ENST00000328273,;PHKG2,downstream_gene_variant,,ENST00000424889,;C16orf93,upstream_gene_variant,,ENST00000535476,;RNF40,upstream_gene_variant,,ENST00000565995,;RNF40,upstream_gene_variant,,ENST00000357890,;PHKG2,downstream_gene_variant,,ENST00000563588,;C16orf93,upstream_gene_variant,,ENST00000544613,;C16orf93,5_prime_UTR_variant,,ENST00000545809,;C16orf93,non_coding_transcript_exon_variant,,ENST00000544487,;C16orf93,non_coding_transcript_exon_variant,,ENST00000544643,;C16orf93,non_coding_transcript_exon_variant,,ENST00000543128,;C16orf93,non_coding_transcript_exon_variant,,ENST00000546006,;PHKG2,downstream_gene_variant,,ENST00000563913,;RNF40,upstream_gene_variant,,ENST00000493683,;RNF40,upstream_gene_variant,,ENST00000566703,;C16orf93,upstream_gene_variant,,ENST00000433909,;PHKG2,downstream_gene_variant,,ENST00000564838,;C16orf93,upstream_gene_variant,,ENST00000537986,;	G	ENSG00000196118	ENST00000543610	Transcript	5_prime_UTR_variant	950	.	.	.	.	.	.	.	-1	C16orf93	HGNC	28078	protein_coding	YES	CCDS32434.2	ENSP00000437532	CP093_HUMAN	.	UPI0000EA2A74	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTCCGTGC	.	5	ESCA
ALG1	0	.	GRCh37	16	5125388	5125388	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391-1G>A	.	p.X131_splice	ENST00000262374	.	50	30	19	31	31	0	ALG1,splice_acceptor_variant,,ENST00000588623,;ALG1,splice_acceptor_variant,,ENST00000544428,;ALG1,splice_acceptor_variant,,ENST00000591783,;ALG1,splice_acceptor_variant,,ENST00000262374,;ALG1,intron_variant,,ENST00000586840,;ALG1,splice_acceptor_variant,,ENST00000591822,;ALG1,downstream_gene_variant,,ENST00000592793,;RP11-10K17.3,downstream_gene_variant,,ENST00000564330,;	A	ENSG00000033011	ENST00000262374	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ALG1	HGNC	18294	protein_coding	YES	CCDS10528.1	ENSP00000262374	ALG1_HUMAN	K7EID2_HUMAN,B4DP08_HUMAN	UPI000003B09B	.	.	.	.	3/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTAGAACCC	.	5	ESCA
OVCA2	0	.	GRCh37	17	1945944	1945944	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.230A>T	p.Glu77Val	p.E77V	ENST00000572195	2/2	39	25	13	27	27	0	OVCA2,missense_variant,p.Glu77Val,ENST00000572195,;DPH1,3_prime_UTR_variant,,ENST00000263083,;DPH1,3_prime_UTR_variant,,ENST00000570477,;DPH1,3_prime_UTR_variant,,ENST00000571710,;DPH1,3_prime_UTR_variant,,ENST00000571418,;DPH1,3_prime_UTR_variant,,ENST00000575162,;DPH1,intron_variant,,ENST00000607788,;RP11-667K14.3,downstream_gene_variant,,ENST00000572790,;RP11-667K14.4,downstream_gene_variant,,ENST00000572404,;DPH1,3_prime_UTR_variant,,ENST00000575667,;DPH1,non_coding_transcript_exon_variant,,ENST00000570867,;DPH1,non_coding_transcript_exon_variant,,ENST00000572214,;DPH1,non_coding_transcript_exon_variant,,ENST00000572684,;DPH1,non_coding_transcript_exon_variant,,ENST00000572248,;DPH1,downstream_gene_variant,,ENST00000263084,;DPH1,downstream_gene_variant,,ENST00000575998,;DPH1,downstream_gene_variant,,ENST00000570833,;	T	ENSG00000262664	ENST00000572195	Transcript	missense_variant	245	230	77	E/V	gAg/gTg	.	.	.	1	OVCA2	HGNC	24203	protein_coding	YES	CCDS11015.1	ENSP00000461388	OVCA2_HUMAN	.	UPI000000D9A0	.	tolerated(0.06)	possibly_damaging(0.588)	2/2	.	hmmpanther:PTHR22778,hmmpanther:PTHR22778:SF0,Pfam_domain:PF03959,Gene3D:3.40.50.1820	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGAGCAGG	.	5	ESCA
TMEM97	0	.	GRCh37	17	26652649	26652649	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247A>G	p.Ile83Val	p.I83V	ENST00000226230	2/3	72	64	8	56	56	0	TMEM97,missense_variant,p.Ile83Val,ENST00000226230,;TMEM97,missense_variant,p.Ile83Val,ENST00000582113,;TMEM97,5_prime_UTR_variant,,ENST00000336687,;TMEM97,5_prime_UTR_variant,,ENST00000583381,;TMEM97,intron_variant,,ENST00000582384,;IFT20,downstream_gene_variant,,ENST00000585313,;IFT20,downstream_gene_variant,,ENST00000578009,;IFT20,downstream_gene_variant,,ENST00000578985,;IFT20,downstream_gene_variant,,ENST00000579419,;IFT20,downstream_gene_variant,,ENST00000395418,;IFT20,downstream_gene_variant,,ENST00000357896,;IFT20,downstream_gene_variant,,ENST00000585089,;IFT20,downstream_gene_variant,,ENST00000577498,;IFT20,downstream_gene_variant,,ENST00000578122,;IFT20,downstream_gene_variant,,ENST00000582797,;IFT20,downstream_gene_variant,,ENST00000322326,;IFT20,downstream_gene_variant,,ENST00000583796,;	G	ENSG00000109084	ENST00000226230	Transcript	missense_variant	392	247	83	I/V	Att/Gtt	.	.	.	1	TMEM97	HGNC	28106	protein_coding	YES	CCDS11226.2	ENSP00000226230	TMM97_HUMAN	Q86XC5_HUMAN,B4DDT6_HUMAN	UPI00004EA896	.	tolerated(1)	benign(0.004)	2/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR31204,hmmpanther:PTHR31204:SF1,Pfam_domain:PF10914,PIRSF_domain:PIRSF031032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCCATTGCA	.	4	ESCA
ARL5C	0	.	GRCh37	17	37318973	37318973	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246C>T	p.%3D	p.S82S	ENST00000444555	5/8	55	33	22	55	55	0	ARL5C,synonymous_variant,p.%3D,ENST00000444555,;ARL5C,synonymous_variant,p.%3D,ENST00000269586,;ARL5C,downstream_gene_variant,,ENST00000583123,;ARL5C,synonymous_variant,p.%3D,ENST00000578912,;ARL5C,downstream_gene_variant,,ENST00000581554,;ARL5C,downstream_gene_variant,,ENST00000581255,;	A	ENSG00000141748	ENST00000444555	Transcript	synonymous_variant	586	246	82	S	tcC/tcT	.	.	.	-1	ARL5C	HGNC	31111	protein_coding	YES	CCDS45664.1	ENSP00000387615	ARL5C_HUMAN	.	UPI00001600CC	.	.	.	5/8	.	Prints_domain:PR00328,Superfamily_domains:SSF52540,SMART_domains:SM00177,SMART_domains:SM00178,Gene3D:3.40.50.300,Pfam_domain:PF00025,TIGRFAM_domain:TIGR00231,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF148,PROSITE_profiles:PS51417	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTGGAGTA	.	5	ESCA
DHX8	0	.	GRCh37	17	41582146	41582146	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000262415	12/23	51	29	22	41	41	0	DHX8,stop_gained,p.Gln561Ter,ENST00000540306,;DHX8,stop_gained,p.Gln561Ter,ENST00000262415,;DHX8,non_coding_transcript_exon_variant,,ENST00000587044,;	T	ENSG00000067596	ENST00000262415	Transcript	stop_gained	1753	1681	561	Q/*	Cag/Tag	.	.	.	1	DHX8	HGNC	2749	protein_coding	YES	CCDS11464.1	ENSP00000262415	DHX8_HUMAN	.	UPI00001290D9	.	.	.	12/23	.	hmmpanther:PTHR18934:SF85,hmmpanther:PTHR18934,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAGCAGAGG	.	5	ESCA
SP2	0	.	GRCh37	17	46005104	46005104	+	Missense_Mutation	SNP	G	G	A	rs771830248	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1756G>A	p.Glu586Lys	p.E586K	ENST00000376741	7/7	34	27	7	28	28	0	SP2,missense_variant,p.Glu586Lys,ENST00000376741,;AC003665.1,intron_variant,,ENST00000411573,;AC003665.1,intron_variant,,ENST00000433001,;AC003665.1,intron_variant,,ENST00000451140,;AC003665.1,intron_variant,,ENST00000585280,;RP11-6N17.3,downstream_gene_variant,,ENST00000584276,;	A	ENSG00000167182	ENST00000376741	Transcript	missense_variant	1893	1756	586	E/K	Gag/Aag	rs771830248	.	.	1	SP2	HGNC	11207	protein_coding	YES	CCDS11521.2	ENSP00000365931	SP2_HUMAN	.	UPI00005A7765	.	deleterious(0.01)	benign(0.166)	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF1,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTCGAGTGC	byFrequency	5	ESCA
NLRP1	0	.	GRCh37	17	5418260	5418260	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4236G>C	p.Gln1412His	p.Q1412H	ENST00000572272	17/17	38	24	14	35	35	0	NLRP1,missense_variant,p.Gln1412His,ENST00000572272,;NLRP1,missense_variant,p.Gln1368His,ENST00000345221,;NLRP1,missense_variant,p.Gln1368His,ENST00000269280,;NLRP1,missense_variant,p.Gln1382His,ENST00000354411,;NLRP1,missense_variant,p.Gln1338His,ENST00000577119,;NLRP1,intron_variant,,ENST00000262467,;RNU7-31P,upstream_gene_variant,,ENST00000517262,;NLRP1,3_prime_UTR_variant,,ENST00000571451,;NLRP1,intron_variant,,ENST00000574512,;NLRP1,intron_variant,,ENST00000544378,;	G	ENSG00000091592	ENST00000572272	Transcript	missense_variant	4236	4236	1412	Q/H	caG/caC	.	.	.	-1	NLRP1	HGNC	14374	protein_coding	YES	CCDS42246.1	ENSP00000460475	NALP1_HUMAN	I3L2G5_HUMAN,I3L0S2_HUMAN	UPI0000038309	.	deleterious(0)	probably_damaging(0.992)	17/17	.	PROSITE_profiles:PS50209,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF13,Gene3D:1.10.533.10,Pfam_domain:PF00619,Superfamily_domains:SSF47986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTACTGCTC	.	5	ESCA
LRRC37A3	0	.	GRCh37	17	62855652	62855652	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4612A>G	p.Lys1538Glu	p.K1538E	ENST00000584306	11/14	190	177	13	142	142	0	LRRC37A3,missense_variant,p.Lys1538Glu,ENST00000319651,;LRRC37A3,missense_variant,p.Lys1538Glu,ENST00000584306,;LRRC37A3,missense_variant,p.Lys576Glu,ENST00000400877,;LRRC37A3,missense_variant,p.Lys515Glu,ENST00000334962,;LRRC37A3,missense_variant,p.Lys656Glu,ENST00000339474,;LRRC37A3,missense_variant,p.Lys32Glu,ENST00000583510,;LRRC37A3,downstream_gene_variant,,ENST00000581368,;LRRC37A3,downstream_gene_variant,,ENST00000584788,;LRRC37A3,downstream_gene_variant,,ENST00000579305,;	C	ENSG00000176809	ENST00000584306	Transcript	missense_variant	5143	4612	1538	K/E	Aag/Gag	.	.	.	-1	LRRC37A3	HGNC	32427	protein_coding	YES	CCDS32708.1	ENSP00000464535	L37A3_HUMAN	F8W7X0_HUMAN,B4DSF2_HUMAN	UPI00005B2F0A	.	deleterious(0)	probably_damaging(0.926)	11/14	.	hmmpanther:PTHR23045,Pfam_domain:PF14914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATCTTGGATG	.	2	ESCA
TP53	0	.	GRCh37	17	7578239	7578239	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	6/11	56	18	37	60	60	0	TP53,stop_gained,p.Glu204Ter,ENST00000413465,;TP53,stop_gained,p.Glu204Ter,ENST00000420246,;TP53,stop_gained,p.Glu204Ter,ENST00000269305,;TP53,stop_gained,p.Glu72Ter,ENST00000509690,;TP53,stop_gained,p.Glu204Ter,ENST00000359597,;TP53,stop_gained,p.Glu111Ter,ENST00000514944,;TP53,stop_gained,p.Glu204Ter,ENST00000445888,;TP53,stop_gained,p.Glu204Ter,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	800	610	204	E/*	Gag/Tag	TP53_g.12679del,TP53_g.12679G>A,TP53_g.12679G>C,TP53_g.12679G>T,COSM10804,COSM44011,COSM45782,COSM43990,COSM165087,COSM437512,COSM437513,COSM165086,COSM165088,COSM437515,COSM3362449,COSM1679501,COSM165089,COSM437514	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E204*|c.610G>T|3,SITE|p.E72*|c.214G>T|10,SITE|p.E204*|c.610G>T|32,SITE|p.E111*|c.331G>T|9,SITE|p.E204*|c.610G>T|9,SITE|p.E204*|c.610G>T|9,SITE|p.E204*|c.610G>T|4,CODON|p.0?|c.1_1182del1182|6,CODON|p.E204fs*43|c.610delG|3,BUFFER|p.D207G|c.620A>G|4,BUFFER|p.L206fs*41|c.617delT|4,BUFFER|p.L206*|c.617T>A|9,BUFFER|p.Y73C|c.218A>G|19,BUFFER|p.Y112C|c.335A>G|18,BUFFER|p.Y112S|c.335A>C|3,BUFFER|p.Y205C|c.614A>G|17,BUFFER|p.Y205C|c.614A>G|5,BUFFER|p.Y205S|c.614A>C|3,BUFFER|p.Y205C|c.614A>G|72,BUFFER|p.Y205F|c.614A>T|7,BUFFER|p.Y205S|c.614A>C|14,BUFFER|p.Y205S|c.614A>C|3,BUFFER|p.Y205C|c.614A>G|18,BUFFER|p.Y205C|c.614A>G|8,BUFFER|p.Y73S|c.218A>C|3,BUFFER|p.Y205fs*4|c.613_614insC|4,BUFFER|p.Y112fs*4|c.334_335insC|4,BUFFER|p.Y73fs*4|c.217_218insC|4,BUFFER|p.Y205fs*4|c.613_614insC|4,BUFFER|p.Y205fs*4|c.613_614insC|4,BUFFER|p.Y205fs*4|c.613_614insC|4,BUFFER|p.Y205N|c.613T>A|5,BUFFER|p.Y205N|c.613T>A|3,BUFFER|p.Y112N|c.334T>A|3,BUFFER|p.Y205H|c.613T>C|6,BUFFER|p.Y205D|c.613T>G|14,BUFFER|p.Y73N|c.217T>A|3,BUFFER|p.V203V|c.609G>T|3,BUFFER|p.V203E|c.608T>A|6,BUFFER|p.V203L|c.607G>T|4,BUFFER|p.R202L|c.605G>T|3,BUFFER|p.R202H|c.605G>A|4,BUFFER|p.R202C|c.604C>T|4,BUFFER|p.R202S|c.604C>A|6,BUFFER|p.L201F|c.603G>T|3,BUFFER|p.L201F|c.603G>C|4,BUFFER|p.N200fs*47|c.598delA|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACTCCACAC	.	5	ESCA
ACTG1	0	.	GRCh37	17	79477613	79477613	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*103A>G	.	.	ENST00000575842	5/5	27	16	11	22	22	0	ACTG1,3_prime_UTR_variant,,ENST00000575842,;ACTG1,3_prime_UTR_variant,,ENST00000573283,;ACTG1,3_prime_UTR_variant,,ENST00000331925,;ACTG1,3_prime_UTR_variant,,ENST00000575087,;ACTG1,downstream_gene_variant,,ENST00000575994,;ACTG1,downstream_gene_variant,,ENST00000571691,;ACTG1,downstream_gene_variant,,ENST00000571721,;ACTG1,downstream_gene_variant,,ENST00000575659,;ACTG1,downstream_gene_variant,,ENST00000570382,;AC139149.1,downstream_gene_variant,,ENST00000584254,;RP13-766D20.2,upstream_gene_variant,,ENST00000430912,;ACTG1,3_prime_UTR_variant,,ENST00000576544,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576209,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576917,;ACTG1,non_coding_transcript_exon_variant,,ENST00000574671,;ACTG1,downstream_gene_variant,,ENST00000576214,;ACTG1,downstream_gene_variant,,ENST00000572105,;RP13-766D20.1,upstream_gene_variant,,ENST00000448147,;	C	ENSG00000184009	ENST00000575842	Transcript	3_prime_UTR_variant	1658	.	.	.	.	.	.	.	-1	ACTG1	HGNC	144	protein_coding	YES	CCDS11782.1	ENSP00000458162	ACTG_HUMAN	Q9UE89_HUMAN,Q96FU6_HUMAN,Q96DE1_HUMAN,Q6PJ43_HUMAN,Q562Z7_HUMAN,I3L3R2_HUMAN,I3L3I0_HUMAN,I3L1U9_HUMAN,B4E3A4_HUMAN,B3KWQ3_HUMAN,A5GZ75_HUMAN,A4UCT3_HUMAN,A1E282_HUMAN	UPI0000000C38	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTATTCCAG	.	5	ESCA
CCDC151	0	.	GRCh37	19	11537295	11537295	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811G>C	p.Glu271Gln	p.E271Q	ENST00000356392	6/13	36	29	7	35	35	0	CCDC151,missense_variant,p.Glu211Gln,ENST00000591179,;CCDC151,missense_variant,p.Glu271Gln,ENST00000356392,;CCDC151,missense_variant,p.Glu80Gln,ENST00000586836,;CCDC151,missense_variant,p.Glu217Gln,ENST00000545100,;CCDC151,3_prime_UTR_variant,,ENST00000591345,;CCDC151,downstream_gene_variant,,ENST00000593281,;	G	ENSG00000198003	ENST00000356392	Transcript	missense_variant	899	811	271	E/Q	Gag/Cag	.	.	.	-1	CCDC151	HGNC	28303	protein_coding	YES	CCDS42501.1	ENSP00000348757	CC151_HUMAN	K7EPK8_HUMAN,B7ZMB9_HUMAN	UPI000040CC83	.	deleterious(0.05)	possibly_damaging(0.644)	6/13	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21694:SF1,hmmpanther:PTHR21694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCTTGGT	.	5	ESCA
ZNF730	0	.	GRCh37	19	23328256	23328256	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.410T>C	p.Leu137Ser	p.L137S	ENST00000597761	4/4	75	53	22	39	39	0	ZNF730,missense_variant,p.Leu137Ser,ENST00000597761,;ZNF730,downstream_gene_variant,,ENST00000599195,;	C	ENSG00000183850	ENST00000597761	Transcript	missense_variant	609	410	137	L/S	tTg/tCg	.	.	.	1	ZNF730	HGNC	32470	protein_coding	YES	CCDS59371.1	ENSP00000472959	ZN730_HUMAN	.	UPI000035E7F4	.	tolerated(0.08)	benign(0.001)	4/4	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTTGACAA	.	5	ESCA
ZNF568	0	.	GRCh37	19	37416130	37416130	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.105C>T	p.%3D	p.S35S	ENST00000333987	4/7	98	61	36	53	53	0	ZNF568,synonymous_variant,p.%3D,ENST00000333987,;ZNF568,synonymous_variant,p.%3D,ENST00000444991,;ZNF568,synonymous_variant,p.%3D,ENST00000427117,;ZNF568,5_prime_UTR_variant,,ENST00000455427,;ZNF568,5_prime_UTR_variant,,ENST00000587130,;ZNF568,5_prime_UTR_variant,,ENST00000587857,;ZNF568,intron_variant,,ENST00000415168,;	T	ENSG00000198453	ENST00000333987	Transcript	synonymous_variant	611	105	35	S	tcC/tcT	.	.	.	1	ZNF568	HGNC	25392	protein_coding	YES	CCDS42558.1	ENSP00000334685	ZN568_HUMAN	A2VDJ6_HUMAN	UPI000059D700	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCCGAGGA	.	5	ESCA
SRRM5	0	.	GRCh37	19	44116308	44116308	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35T>C	p.Met12Thr	p.M12T	ENST00000607544	3/3	72	46	26	75	75	0	SRRM5,missense_variant,p.Met27Thr,ENST00000526798,;SRRM5,missense_variant,p.Met12Thr,ENST00000417606,;SRRM5,missense_variant,p.Met12Thr,ENST00000607544,;ZNF428,intron_variant,,ENST00000598676,;ZNF428,intron_variant,,ENST00000300811,;ZNF428,downstream_gene_variant,,ENST00000595304,;	C	ENSG00000226763	ENST00000607544	Transcript	missense_variant	357	35	12	M/T	aTg/aCg	.	.	.	1	SRRM5	HGNC	37248	protein_coding	YES	CCDS46095.1	ENSP00000476253	SRRM5_HUMAN	.	UPI000059D73E	.	tolerated(0.18)	benign(0)	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTATGTCTC	.	5	ESCA
ZNF223	0	.	GRCh37	19	44571272	44571272	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1291G>C	p.Glu431Gln	p.E431Q	ENST00000434772	5/5	43	26	16	18	18	0	ZNF223,missense_variant,p.Glu431Gln,ENST00000434772,;ZNF223,downstream_gene_variant,,ENST00000591850,;ZNF223,missense_variant,p.Glu541Gln,ENST00000591793,;ZNF223,downstream_gene_variant,,ENST00000593088,;	C	ENSG00000178386	ENST00000434772	Transcript	missense_variant	1546	1291	431	E/Q	Gag/Cag	.	.	.	1	ZNF223	HGNC	13016	protein_coding	YES	CCDS12635.1	ENSP00000401947	ZN223_HUMAN	K7EQ32_HUMAN	UPI00002025B5	.	deleterious(0.03)	probably_damaging(0.976)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,hmmpanther:PTHR24388,hmmpanther:PTHR24388:SF29,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGTGAGGAT	.	5	ESCA
CCDC61	0	.	GRCh37	19	46506729	46506729	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201C>T	p.%3D	p.F67F	ENST00000595358	3/14	120	114	6	61	61	0	CCDC61,synonymous_variant,p.%3D,ENST00000536603,;CCDC61,synonymous_variant,p.%3D,ENST00000594087,;CCDC61,synonymous_variant,p.%3D,ENST00000263284,;CCDC61,synonymous_variant,p.%3D,ENST00000594672,;CCDC61,synonymous_variant,p.%3D,ENST00000595358,;CCDC61,non_coding_transcript_exon_variant,,ENST00000599044,;CCDC61,non_coding_transcript_exon_variant,,ENST00000596161,;CCDC61,intron_variant,,ENST00000596687,;	T	ENSG00000104983	ENST00000595358	Transcript	synonymous_variant	250	201	67	F	ttC/ttT	.	.	.	1	CCDC61	HGNC	33629	protein_coding	YES	CCDS46120.2	ENSP00000471454	.	M0R0U9_HUMAN,M0QYL5_HUMAN,M0QY15_HUMAN	UPI000040C0FF	.	.	.	3/14	.	hmmpanther:PTHR22691:SF1,hmmpanther:PTHR22691	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTTCTGTCA	.	2	ESCA
ZC3H4	0	.	GRCh37	19	47587710	47587710	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1110C>T	p.%3D	p.D370D	ENST00000253048	9/15	50	28	22	53	53	0	ZC3H4,synonymous_variant,p.%3D,ENST00000253048,;ZC3H4,synonymous_variant,p.%3D,ENST00000601973,;ZC3H4,intron_variant,,ENST00000594019,;	A	ENSG00000130749	ENST00000253048	Transcript	synonymous_variant	1148	1110	370	D	gaC/gaT	.	.	.	-1	ZC3H4	HGNC	17808	protein_coding	YES	CCDS42582.1	ENSP00000253048	ZC3H4_HUMAN	.	UPI00001C2000	.	.	.	9/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13119:SF23,hmmpanther:PTHR13119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCGTCCTG	.	5	ESCA
LRRC4B	0	.	GRCh37	19	51021262	51021262	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1708G>A	p.Asp570Asn	p.D570N	ENST00000599957	3/3	10	6	4	9	9	0	LRRC4B,missense_variant,p.Asp570Asn,ENST00000599957,;LRRC4B,missense_variant,p.Asp570Asn,ENST00000389201,;LRRC4B,downstream_gene_variant,,ENST00000600381,;ASPDH,upstream_gene_variant,,ENST00000601207,;ASPDH,upstream_gene_variant,,ENST00000598657,;ASPDH,upstream_gene_variant,,ENST00000376916,;ASPDH,upstream_gene_variant,,ENST00000389208,;ASPDH,upstream_gene_variant,,ENST00000597030,;ASPDH,upstream_gene_variant,,ENST00000593569,;ASPDH,upstream_gene_variant,,ENST00000601287,;	T	ENSG00000131409	ENST00000599957	Transcript	missense_variant	1906	1708	570	D/N	Gac/Aac	.	.	.	-1	LRRC4B	HGNC	25042	protein_coding	YES	CCDS42595.1	ENSP00000471502	LRC4B_HUMAN	M0R2G0_HUMAN,A0PJJ4_HUMAN	UPI00000497E7	.	deleterious(0)	possibly_damaging(0.588)	3/3	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACGTCGTCCA	.	2	ESCA
PDZK1	0	.	GRCh37	1	145752451	145752451	+	Missense_Mutation	SNP	G	G	C	rs782182897	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484G>C	p.Asp162His	p.D162H	ENST00000344770	4/9	177	119	57	115	115	0	PDZK1,missense_variant,p.Asp162His,ENST00000417171,;PDZK1,missense_variant,p.Asp162His,ENST00000344770,;PDZK1,missense_variant,p.Asp162His,ENST00000443667,;PDZK1,intron_variant,,ENST00000451928,;	C	ENSG00000174827	ENST00000344770	Transcript	missense_variant	557	484	162	D/H	Gat/Cat	rs782182897	.	.	1	PDZK1	HGNC	8821	protein_coding	YES	CCDS924.1	ENSP00000342143	NHRF3_HUMAN	.	UPI000006D202	.	deleterious(0.02)	probably_damaging(0.934)	4/9	.	PROSITE_profiles:PS50106,hmmpanther:PTHR14191,hmmpanther:PTHR14191:SF6,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACTGATATT	.	5	ESCA
NME7	0	.	GRCh37	1	169292492	169292493	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.140dupT	p.Leu47PhefsTer7	p.L47Ffs*7	ENST00000367811	3/12	47	40	7	27	27	0	NME7,frameshift_variant,p.Leu47PhefsTer7,ENST00000367811,;NME7,frameshift_variant,p.Leu11PhefsTer7,ENST00000472647,;RP4-800F24.1,downstream_gene_variant,,ENST00000432081,;NME7,non_coding_transcript_exon_variant,,ENST00000469474,;NME7,non_coding_transcript_exon_variant,,ENST00000491225,;NME7,intron_variant,,ENST00000480478,;NME7,intron_variant,,ENST00000485609,;NME7,frameshift_variant,p.Leu47PhefsTer7,ENST00000528517,;NME7,frameshift_variant,p.Leu47PhefsTer7,ENST00000525440,;NME7,non_coding_transcript_exon_variant,,ENST00000527460,;NME7,non_coding_transcript_exon_variant,,ENST00000524967,;	A	ENSG00000143156	ENST00000367811	Transcript	frameshift_variant	397-398	140-141	47	L/FX	tta/ttTa	.	.	.	-1	NME7	HGNC	20461	protein_coding	YES	CCDS1277.1	ENSP00000356785	NDK7_HUMAN	.	UPI000012FE8C	.	.	.	3/12	.	PROSITE_profiles:PS51336,hmmpanther:PTHR11349,PIRSF_domain:PIRSF036503,SMART_domains:SM00676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CGCTTTAAAAA	.	2	ESCA
SUCO	0	.	GRCh37	1	172580459	172580459	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1060T>C	.	.	ENST00000263688	24/24	28	15	12	10	10	0	SUCO,3_prime_UTR_variant,,ENST00000608151,;SUCO,3_prime_UTR_variant,,ENST00000367723,;SUCO,3_prime_UTR_variant,,ENST00000263688,;SUCO,downstream_gene_variant,,ENST00000610051,;RNU6-693P,downstream_gene_variant,,ENST00000516134,;SUCO,downstream_gene_variant,,ENST00000609685,;	C	ENSG00000094975	ENST00000263688	Transcript	3_prime_UTR_variant	5044	.	.	.	.	.	.	.	1	SUCO	HGNC	1240	protein_coding	YES	CCDS1303.1	ENSP00000263688	SUCO_HUMAN	.	UPI0000070BAC	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTGTCTTTT	.	5	ESCA
SEC16B	0	.	GRCh37	1	177913774	177913774	+	Silent	SNP	A	A	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1803T>G	p.%3D	p.T601T	ENST00000308284	15/26	90	74	15	41	41	0	SEC16B,synonymous_variant,p.%3D,ENST00000308284,;SEC16B,downstream_gene_variant,,ENST00000464631,;SEC16B,downstream_gene_variant,,ENST00000527976,;SEC16B,non_coding_transcript_exon_variant,,ENST00000327037,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000354921,;SEC16B,3_prime_UTR_variant,,ENST00000528461,;SEC16B,non_coding_transcript_exon_variant,,ENST00000526773,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000466953,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000464428,;	C	ENSG00000120341	ENST00000308284	Transcript	synonymous_variant	1893	1803	601	T	acT/acG	.	.	.	-1	SEC16B	HGNC	30301	protein_coding	YES	CCDS44281.1	ENSP00000308339	SC16B_HUMAN	.	UPI0000203C4D	.	.	.	15/26	.	hmmpanther:PTHR13402:SF8,hmmpanther:PTHR13402,Pfam_domain:PF12931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCAGTTGT	.	5	ESCA
CR2	0	.	GRCh37	1	207639910	207639910	+	Missense_Mutation	SNP	G	G	A	rs368072577	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98G>A	p.Arg33Gln	p.R33Q	ENST00000367057	2/20	99	82	17	44	44	0	CR2,missense_variant,p.Arg33Gln,ENST00000458541,;CR2,missense_variant,p.Arg33Gln,ENST00000367057,;CR2,missense_variant,p.Arg33Gln,ENST00000367058,;CR2,missense_variant,p.Arg33Gln,ENST00000367059,;CR2,non_coding_transcript_exon_variant,,ENST00000479186,;CR2,upstream_gene_variant,,ENST00000485707,;CR2,upstream_gene_variant,,ENST00000475194,;	A	ENSG00000117322	ENST00000367057	Transcript	missense_variant	287	98	33	R/Q	cGg/cAg	rs368072577	.	.	1	CR2	HGNC	2336	protein_coding	YES	CCDS31007.1	ENSP00000356024	CR2_HUMAN	.	UPI0000366600	.	tolerated(0.13)	benign(0.049)	2/20	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF330,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGGATTA	byFrequency|byCluster	5	ESCA
CD34	0	.	GRCh37	1	208061047	208061047	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*36G>C	.	.	ENST00000310833	8/8	31	28	3	32	32	0	CD34,3_prime_UTR_variant,,ENST00000356522,;CD34,3_prime_UTR_variant,,ENST00000537704,;CD34,3_prime_UTR_variant,,ENST00000310833,;CD34,3_prime_UTR_variant,,ENST00000367036,;CD34,intron_variant,,ENST00000485761,;	G	ENSG00000174059	ENST00000310833	Transcript	3_prime_UTR_variant	1516	.	.	.	.	.	.	.	-1	CD34	HGNC	1662	protein_coding	YES	CCDS31011.1	ENSP00000310036	CD34_HUMAN	Q9UH97_HUMAN,Q8IUM0_HUMAN,B4DUX4_HUMAN	UPI000012734B	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCTCTCGGA	.	2	ESCA
LPGAT1	0	.	GRCh37	1	211956837	211956837	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.461C>G	p.Ser154Cys	p.S154C	ENST00000366997	5/8	43	33	10	20	20	0	LPGAT1,missense_variant,p.Ser154Cys,ENST00000366996,;LPGAT1,missense_variant,p.Ser154Cys,ENST00000366997,;LPGAT1,intron_variant,,ENST00000498690,;	C	ENSG00000123684	ENST00000366997	Transcript	missense_variant	688	461	154	S/C	tCt/tGt	.	.	.	-1	LPGAT1	HGNC	28985	protein_coding	YES	CCDS31018.1	ENSP00000355964	LGAT1_HUMAN	Q53YL2_HUMAN	UPI0000139467	.	deleterious(0.02)	possibly_damaging(0.841)	5/8	.	hmmpanther:PTHR10983:SF2,hmmpanther:PTHR10983,Pfam_domain:PF01553,SMART_domains:SM00563,Superfamily_domains:0039877	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATAAGATCTT	.	5	ESCA
MIA3	0	.	GRCh37	1	222791507	222791507	+	Silent	SNP	C	C	A	rs753091918	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55C>A	p.%3D	p.R19R	ENST00000344922	1/28	9	3	6	9	9	0	MIA3,synonymous_variant,p.%3D,ENST00000344922,;MIA3,synonymous_variant,p.%3D,ENST00000344507,;MIA3,synonymous_variant,p.%3D,ENST00000344441,;MIA3,non_coding_transcript_exon_variant,,ENST00000470521,;	A	ENSG00000154305	ENST00000344922	Transcript	synonymous_variant	80	55	19	R	Cgg/Agg	rs753091918	.	.	1	MIA3	HGNC	24008	protein_coding	YES	CCDS41470.1	ENSP00000340900	MIA3_HUMAN	.	UPI00001D75B3	.	.	.	1/28	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23158:SF37,hmmpanther:PTHR23158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGGCGGGTG	.	2	ESCA
HIST3H2BB	0	.	GRCh37	1	228646241	228646248	+	3'UTR	DEL	CTCTTTTC	CTCTTTTC	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	CTCTTTTC	CTCTTTTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*30_*37delCTCTTTTCinsG	.	.	ENST00000369160	1/1	86	72	14	68	68	0	HIST3H2BB,3_prime_UTR_variant,,ENST00000369160,;HIST3H2A,upstream_gene_variant,,ENST00000366695,;MIR4666A,upstream_gene_variant,,ENST00000580160,;	G	ENSG00000196890	ENST00000369160	Transcript	3_prime_UTR_variant	434-441	.	.	.	.	.	.	.	1	HIST3H2BB	HGNC	20514	protein_coding	YES	CCDS1574.1	ENSP00000375736	H2B3B_HUMAN	.	UPI00000214BE	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL|VARSCANS*	CAAAGGCTCTTTTCAGAGC	.	3	ESCA
ACTA1	0	.	GRCh37	1	229567918	229567918	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Val211Met	p.V211M	ENST00000366684	5/7	54	48	5	38	38	0	ACTA1,missense_variant,p.Val123Met,ENST00000366683,;ACTA1,missense_variant,p.Val211Met,ENST00000366684,;	T	ENSG00000143632	ENST00000366684	Transcript	missense_variant	734	631	211	V/M	Gtg/Atg	COSM4029314	.	.	-1	ACTA1	HGNC	129	protein_coding	YES	CCDS1578.1	ENSP00000355645	ACTS_HUMAN	.	UPI0000000860	.	deleterious_low_confidence(0.02)	probably_damaging(0.965)	5/7	.	hmmpanther:PTHR11937:SF165,hmmpanther:PTHR11937,Pfam_domain:PF00022,Gene3D:3.90.640.10,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGCACGATCT	.	4	ESCA
CNST	0	.	GRCh37	1	246811175	246811175	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1672G>C	p.Asp558His	p.D558H	ENST00000366513	9/11	25	20	5	15	15	0	CNST,missense_variant,p.Asp558His,ENST00000366513,;CNST,missense_variant,p.Asp558His,ENST00000366512,;CNST,non_coding_transcript_exon_variant,,ENST00000483271,;	C	ENSG00000162852	ENST00000366513	Transcript	missense_variant	1941	1672	558	D/H	Gat/Cat	.	.	.	1	CNST	HGNC	26486	protein_coding	YES	CCDS1628.1	ENSP00000355470	CNST_HUMAN	.	UPI000013E1DF	.	deleterious(0)	probably_damaging(0.973)	9/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAAAGATACT	.	5	ESCA
BAI2	0	.	GRCh37	1	32222184	32222184	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.254G>A	p.Arg85His	p.R85H	ENST00000373658	4/33	44	34	9	51	51	0	BAI2,missense_variant,p.Arg73His,ENST00000398538,;BAI2,missense_variant,p.Arg85His,ENST00000373658,;BAI2,missense_variant,p.Arg119His,ENST00000533175,;BAI2,missense_variant,p.Arg73His,ENST00000398547,;BAI2,missense_variant,p.Arg78His,ENST00000420125,;BAI2,missense_variant,p.Arg85His,ENST00000527361,;BAI2,missense_variant,p.Arg88His,ENST00000398556,;BAI2,missense_variant,p.Arg85His,ENST00000257070,;BAI2,missense_variant,p.Arg73His,ENST00000398542,;BAI2,missense_variant,p.Arg85His,ENST00000373655,;BAI2,downstream_gene_variant,,ENST00000436464,;MIR4254,downstream_gene_variant,,ENST00000581063,;BAI2,upstream_gene_variant,,ENST00000473952,;BAI2,upstream_gene_variant,,ENST00000530134,;	T	ENSG00000121753	ENST00000373658	Transcript	missense_variant	596	254	85	R/H	cGc/cAc	.	.	.	-1	BAI2	HGNC	944	protein_coding	YES	CCDS346.2	ENSP00000362762	BAI2_HUMAN	.	UPI0000E2A42F	.	deleterious(0.05)	benign(0.017)	4/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGCGGTTG	.	5	ESCA
RPF1	0	.	GRCh37	1	84961936	84961936	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.891C>T	p.%3D	p.F297F	ENST00000370654	8/9	38	13	25	13	13	0	RPF1,synonymous_variant,p.%3D,ENST00000370654,;GNG5,downstream_gene_variant,,ENST00000370641,;GNG5,downstream_gene_variant,,ENST00000370645,;GNG5,downstream_gene_variant,,ENST00000487806,;	T	ENSG00000117133	ENST00000370654	Transcript	synonymous_variant	906	891	297	F	ttC/ttT	.	.	.	1	RPF1	HGNC	30350	protein_coding	YES	CCDS695.1	ENSP00000359688	RPF1_HUMAN	.	UPI0000034DF7	.	.	.	8/9	.	Superfamily_domains:SSF52954,SMART_domains:SM00879,Pfam_domain:PF04427,Gene3D:1w94A00,hmmpanther:PTHR22734:SF1,hmmpanther:PTHR22734,PROSITE_profiles:PS50833,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCAGGAG	.	5	ESCA
HFM1	0	.	GRCh37	1	91727919	91727919	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4117C>T	p.%3D	p.L1373L	ENST00000370425	38/39	136	92	43	81	81	0	HFM1,synonymous_variant,p.%3D,ENST00000370424,;HFM1,synonymous_variant,p.%3D,ENST00000430465,;HFM1,synonymous_variant,p.%3D,ENST00000370425,;HFM1,3_prime_UTR_variant,,ENST00000294696,;Y_RNA,downstream_gene_variant,,ENST00000384090,;HFM1,non_coding_transcript_exon_variant,,ENST00000462405,;	A	ENSG00000162669	ENST00000370425	Transcript	synonymous_variant	4216	4117	1373	L	Ctg/Ttg	.	.	.	-1	HFM1	HGNC	20193	protein_coding	YES	CCDS30769.2	ENSP00000359454	HFM1_HUMAN	D2KTB2_HUMAN,C9JQP7_HUMAN,B7ZM00_HUMAN,A6NGI5_HUMAN	UPI0000F51F79	.	.	.	38/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACAGATTTT	.	5	ESCA
SIRPD	0	.	GRCh37	20	1515066	1515066	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5A>T	.	.	ENST00000381623	4/4	91	87	4	51	51	0	SIRPD,3_prime_UTR_variant,,ENST00000429387,;SIRPD,3_prime_UTR_variant,,ENST00000381621,;SIRPD,3_prime_UTR_variant,,ENST00000381623,;RP4-576H24.2,intron_variant,,ENST00000453770,;	A	ENSG00000125900	ENST00000381623	Transcript	3_prime_UTR_variant	1789	.	.	.	.	.	.	.	-1	SIRPD	HGNC	16248	protein_coding	YES	CCDS13018.1	ENSP00000371036	SIRPD_HUMAN	.	UPI000013CBD7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGTTTGGAT	.	2	ESCA
ZNF341	0	.	GRCh37	20	32376685	32376685	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1848A>G	p.%3D	p.K616K	ENST00000342427	13/15	60	40	20	31	31	0	ZNF341,synonymous_variant,p.%3D,ENST00000375200,;ZNF341,synonymous_variant,p.%3D,ENST00000342427,;RP4-553F4.6,intron_variant,,ENST00000439444,;RP4-553F4.6,intron_variant,,ENST00000443171,;RP4-553F4.6,intron_variant,,ENST00000423074,;ZNF341,missense_variant,p.Asn591Ser,ENST00000483118,;ZNF341,3_prime_UTR_variant,,ENST00000497876,;ZNF341,non_coding_transcript_exon_variant,,ENST00000493497,;	G	ENSG00000131061	ENST00000342427	Transcript	synonymous_variant	2213	1848	616	K	aaA/aaG	.	.	.	1	ZNF341	HGNC	15992	protein_coding	YES	CCDS13227.1	ENSP00000344308	ZN341_HUMAN	.	UPI000022B43D	.	.	.	13/15	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24388,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAAATGCTC	.	5	ESCA
SGK2	0	.	GRCh37	20	42195101	42195101	+	Missense_Mutation	SNP	C	C	T	rs369635262	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146C>T	p.Pro49Leu	p.P49L	ENST00000341458	1/12	88	77	11	51	51	0	SGK2,missense_variant,p.Pro49Leu,ENST00000341458,;SGK2,intron_variant,,ENST00000373100,;SGK2,intron_variant,,ENST00000412111,;SGK2,intron_variant,,ENST00000423407,;SGK2,intron_variant,,ENST00000373077,;SGK2,intron_variant,,ENST00000373092,;SGK2,intron_variant,,ENST00000426287,;SGK2,upstream_gene_variant,,ENST00000485914,;SGK2,intron_variant,,ENST00000496343,;	T	ENSG00000101049	ENST00000341458	Transcript	missense_variant	365	146	49	P/L	cCt/cTt	rs369635262	.	.	1	SGK2	HGNC	13900	protein_coding	YES	CCDS13320.1	ENSP00000340608	SGK2_HUMAN	.	UPI0000033528	.	tolerated_low_confidence(0.25)	benign(0)	1/12	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCCCTGTCC	byCluster	4	ESCA
ZNF831	0	.	GRCh37	20	57766387	57766387	+	Missense_Mutation	SNP	G	G	A	rs371038563	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313G>A	p.Val105Met	p.V105M	ENST00000371030	1/5	23	13	10	8	8	0	ZNF831,missense_variant,p.Val105Met,ENST00000371030,;	A	ENSG00000124203	ENST00000371030	Transcript	missense_variant	313	313	105	V/M	Gtg/Atg	rs371038563,COSM402220	.	.	1	ZNF831	HGNC	16167	protein_coding	YES	CCDS42894.1	ENSP00000360069	ZN831_HUMAN	.	UPI00001D82E4	.	tolerated(0.27)	benign(0.07)	1/5	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCAGGTGGGG	byCluster|by1000G	2	ESCA
DIP2A	0	.	GRCh37	21	47954536	47954536	+	Silent	SNP	A	A	G	rs776828905	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1578A>G	p.%3D	p.T526T	ENST00000417564	13/38	36	32	3	48	48	0	DIP2A,synonymous_variant,p.%3D,ENST00000427143,;DIP2A,synonymous_variant,p.%3D,ENST00000318711,;DIP2A,synonymous_variant,p.%3D,ENST00000435722,;DIP2A,synonymous_variant,p.%3D,ENST00000400274,;DIP2A,synonymous_variant,p.%3D,ENST00000457905,;DIP2A,synonymous_variant,p.%3D,ENST00000417564,;DIP2A,synonymous_variant,p.%3D,ENST00000466639,;Metazoa_SRP,upstream_gene_variant,,ENST00000607098,;DIP2A,non_coding_transcript_exon_variant,,ENST00000473752,;DIP2A,non_coding_transcript_exon_variant,,ENST00000494435,;DIP2A,upstream_gene_variant,,ENST00000480553,;	G	ENSG00000160305	ENST00000417564	Transcript	synonymous_variant	1599	1578	526	T	acA/acG	rs776828905	.	.	1	DIP2A	HGNC	17217	protein_coding	YES	CCDS46655.1	ENSP00000392066	DIP2A_HUMAN	Q9NSX6_HUMAN,Q96NX2_HUMAN	UPI00001B2E47	.	.	.	13/38	.	hmmpanther:PTHR22754:SF24,hmmpanther:PTHR22754,Pfam_domain:PF00501,Gene3D:3.40.50.980,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCACAGTGTC	byFrequency	4	ESCA
EIF4ENIF1	0	.	GRCh37	22	31836038	31836038	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2786C>T	p.Pro929Leu	p.P929L	ENST00000397525	19/19	45	26	19	32	32	0	EIF4ENIF1,missense_variant,p.Pro584Leu,ENST00000382180,;EIF4ENIF1,missense_variant,p.Pro755Leu,ENST00000344710,;EIF4ENIF1,missense_variant,p.Pro929Leu,ENST00000397525,;EIF4ENIF1,missense_variant,p.Pro905Leu,ENST00000397523,;EIF4ENIF1,missense_variant,p.Pro929Leu,ENST00000330125,;EIF4ENIF1,downstream_gene_variant,,ENST00000418321,;EIF4ENIF1,upstream_gene_variant,,ENST00000441289,;EIF4ENIF1,non_coding_transcript_exon_variant,,ENST00000495101,;DRG1,intron_variant,,ENST00000548143,;EIF4ENIF1,downstream_gene_variant,,ENST00000445424,;EIF4ENIF1,downstream_gene_variant,,ENST00000475437,;EIF4ENIF1,downstream_gene_variant,,ENST00000487671,;	A	ENSG00000184708	ENST00000397525	Transcript	missense_variant	3010	2786	929	P/L	cCc/cTc	.	.	.	-1	EIF4ENIF1	HGNC	16687	protein_coding	YES	CCDS13898.1	ENSP00000380659	4ET_HUMAN	B1AKL6_HUMAN,B1AKL5_HUMAN	UPI0000124F14	.	tolerated(0.44)	benign(0.057)	19/19	.	hmmpanther:PTHR12269	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGGGCACG	.	5	ESCA
SUN2	0	.	GRCh37	22	39138309	39138310	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1127dupT	p.Gln377ProfsTer186	p.Q377Pfs*186	ENST00000405018	9/18	42	22	20	24	24	0	SUN2,frameshift_variant,p.Gln377ProfsTer186,ENST00000405018,;SUN2,frameshift_variant,p.Gln356ProfsTer186,ENST00000405510,;SUN2,frameshift_variant,p.Gln356ProfsTer186,ENST00000406622,;SUN2,frameshift_variant,p.Gln356ProfsTer186,ENST00000216064,;SUN2,frameshift_variant,p.Gln345ProfsTer186,ENST00000411587,;SUN2,downstream_gene_variant,,ENST00000430185,;GTPBP1,downstream_gene_variant,,ENST00000489527,;SUN2,downstream_gene_variant,,ENST00000438058,;SUN2,upstream_gene_variant,,ENST00000455125,;GTPBP1,downstream_gene_variant,,ENST00000458073,;RP3-508I15.14,intron_variant,,ENST00000416406,;RP3-508I15.19,downstream_gene_variant,,ENST00000418803,;RP3-508I15.18,downstream_gene_variant,,ENST00000420118,;RP3-508I15.21,upstream_gene_variant,,ENST00000609212,;RP3-508I15.22,upstream_gene_variant,,ENST00000607991,;SUN2,non_coding_transcript_exon_variant,,ENST00000477262,;SUN2,non_coding_transcript_exon_variant,,ENST00000469086,;SUN2,non_coding_transcript_exon_variant,,ENST00000464202,;SUN2,upstream_gene_variant,,ENST00000470642,;	A	ENSG00000100242	ENST00000405018	Transcript	frameshift_variant	1401-1402	1127-1128	376	I/IX	atc/atTc	.	.	.	-1	SUN2	HGNC	14210	protein_coding	YES	CCDS56231.1	ENSP00000385616	SUN2_HUMAN	Q6NT72_HUMAN,B0QY68_HUMAN,B0QY66_HUMAN	UPI0001611146	.	.	.	9/18	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12911:SF17,hmmpanther:PTHR12911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCTGGATGCG	.	3	ESCA
ENTHD1	0	.	GRCh37	22	40140021	40140021	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1487A>G	p.Asn496Ser	p.N496S	ENST00000325157	7/7	70	57	13	20	20	0	ENTHD1,missense_variant,p.Asn496Ser,ENST00000325157,;	C	ENSG00000176177	ENST00000325157	Transcript	missense_variant	1738	1487	496	N/S	aAt/aGt	.	.	.	-1	ENTHD1	HGNC	26352	protein_coding	YES	CCDS13998.1	ENSP00000317431	ENTD1_HUMAN	.	UPI00000741D2	.	deleterious(0.02)	benign(0.007)	7/7	.	hmmpanther:PTHR12276,hmmpanther:PTHR12276:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTATTTGGA	.	5	ESCA
TAF1B	0	.	GRCh37	2	10073979	10073979	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633C>G	p.Leu545Val	p.L545V	ENST00000263663	15/15	62	52	9	35	35	0	TAF1B,missense_variant,p.Leu545Val,ENST00000263663,;TAF1B,missense_variant,p.Leu290Val,ENST00000396242,;RP11-95D17.1,upstream_gene_variant,,ENST00000602458,;TAF1B,3_prime_UTR_variant,,ENST00000434858,;	G	ENSG00000115750	ENST00000263663	Transcript	missense_variant	1821	1633	545	L/V	Ctc/Gtc	.	.	.	1	TAF1B	HGNC	11533	protein_coding	YES	CCDS33143.1	ENSP00000263663	TAF1B_HUMAN	.	UPI0000208E44	.	deleterious(0)	benign(0.334)	15/15	.	hmmpanther:PTHR31576,hmmpanther:PTHR31576:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATCTCTTC	.	5	ESCA
ACTR3	0	.	GRCh37	2	114715987	114715987	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*955G>C	.	.	ENST00000263238	12/12	64	37	27	19	19	0	ACTR3,3_prime_UTR_variant,,ENST00000263238,;ACTR3,downstream_gene_variant,,ENST00000536059,;ACTR3,downstream_gene_variant,,ENST00000535589,;ACTR3,non_coding_transcript_exon_variant,,ENST00000478928,;	C	ENSG00000115091	ENST00000263238	Transcript	3_prime_UTR_variant	2532	.	.	.	.	.	.	.	1	ACTR3	HGNC	170	protein_coding	YES	CCDS33277.1	ENSP00000263238	ARP3_HUMAN	B4DXW1_HUMAN,B4DTI0_HUMAN	UPI000000DA9A	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGAGTGCTT	.	5	ESCA
CXCR4	0	.	GRCh37	2	136873012	136873012	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.498C>G	p.Ile166Met	p.I166M	ENST00000409817	1/1	34	20	14	24	24	0	CXCR4,missense_variant,p.Ile162Met,ENST00000241393,;CXCR4,missense_variant,p.Ile166Met,ENST00000409817,;CXCR4,non_coding_transcript_exon_variant,,ENST00000466288,;	C	ENSG00000121966	ENST00000409817	Transcript	missense_variant	802	498	166	I/M	atC/atG	.	.	.	-1	CXCR4	HGNC	2561	protein_coding	YES	CCDS33295.1	ENSP00000386884	CXCR4_HUMAN	Q5MIL4_HUMAN	UPI000002A5E3	.	deleterious(0.03)	benign(0.228)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24227,hmmpanther:PTHR24227:SF7,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGGATCCA	.	5	ESCA
TTN	0	.	GRCh37	2	179648828	179648828	+	Missense_Mutation	SNP	C	C	T	rs376922544	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2744G>A	p.Arg915His	p.R915H	ENST00000589042	16/363	51	40	10	35	35	0	TTN,missense_variant,p.Arg915His,ENST00000360870,;TTN,missense_variant,p.Arg915His,ENST00000342992,;TTN,missense_variant,p.Arg869His,ENST00000342175,;TTN,missense_variant,p.Arg869His,ENST00000359218,;TTN,missense_variant,p.Arg915His,ENST00000589042,;TTN,missense_variant,p.Arg915His,ENST00000591111,;TTN,missense_variant,p.Arg869His,ENST00000460472,;TTN,downstream_gene_variant,,ENST00000436599,;RP11-88L24.4,downstream_gene_variant,,ENST00000582038,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	2969	2744	915	R/H	cGc/cAc	rs376922544	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	16/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGCGCTCT	.	5	ESCA
ZNF385B	0	.	GRCh37	2	180306890	180306890	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1087C>T	.	.	ENST00000410066	10/10	84	49	35	29	29	0	ZNF385B,3_prime_UTR_variant,,ENST00000409343,;ZNF385B,3_prime_UTR_variant,,ENST00000410066,;ZNF385B,3_prime_UTR_variant,,ENST00000336917,;ZNF385B,downstream_gene_variant,,ENST00000409692,;ZNF385B,downstream_gene_variant,,ENST00000457304,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000466398,;ZNF385B,downstream_gene_variant,,ENST00000469551,;ZNF385B,downstream_gene_variant,,ENST00000475539,;	A	ENSG00000144331	ENST00000410066	Transcript	3_prime_UTR_variant	3107	.	.	.	.	.	.	.	-1	ZNF385B	HGNC	26332	protein_coding	YES	CCDS33339.1	ENSP00000386845	Z385B_HUMAN	Q53S82_HUMAN,Q53R81_HUMAN,C9JPH4_HUMAN,C9JKK0_HUMAN,C9J0U3_HUMAN	UPI00004F9C24	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGGGCATGG	.	5	ESCA
FSIP2	0	.	GRCh37	2	186655921	186655921	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4325T>C	p.Leu1442Ser	p.L1442S	ENST00000343098	16/23	49	28	21	10	10	0	FSIP2,missense_variant,p.Leu1442Ser,ENST00000343098,;FSIP2,missense_variant,p.Leu1353Ser,ENST00000424728,;AC008174.3,intron_variant,,ENST00000436557,;AC008174.3,intron_variant,,ENST00000429929,;FSIP2,upstream_gene_variant,,ENST00000415915,;	C	ENSG00000188738	ENST00000343098	Transcript	missense_variant	4325	4325	1442	L/S	tTg/tCg	.	.	.	1	FSIP2	HGNC	21675	protein_coding	YES	CCDS54426.1	ENSP00000344403	.	J3QTJ6_HUMAN	UPI0001D420A1	.	.	benign(0.098)	16/23	.	hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTTGGCGA	.	5	ESCA
BOLL	0	.	GRCh37	2	198649982	198649982	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21+725C>T	.	.	ENST00000321801	.	49	37	11	35	35	0	BOLL,5_prime_UTR_variant,,ENST00000392296,;BOLL,intron_variant,,ENST00000282278,;BOLL,intron_variant,,ENST00000321801,;BOLL,upstream_gene_variant,,ENST00000430004,;BOLL,upstream_gene_variant,,ENST00000433157,;BOLL,downstream_gene_variant,,ENST00000486206,;BOLL,intron_variant,,ENST00000434976,;	A	ENSG00000152430	ENST00000321801	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	BOLL	HGNC	14273	protein_coding	YES	CCDS2324.1	ENSP00000314792	BOLL_HUMAN	.	UPI00001D69F3	.	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCCGCCAGC	.	5	ESCA
NOP58	0	.	GRCh37	2	203149089	203149089	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319A>T	p.Ile107Phe	p.I107F	ENST00000264279	5/15	87	64	22	43	43	0	NOP58,missense_variant,p.Ile107Phe,ENST00000264279,;NOP58,non_coding_transcript_exon_variant,,ENST00000472050,;NOP58,non_coding_transcript_exon_variant,,ENST00000467734,;NOP58,non_coding_transcript_exon_variant,,ENST00000492688,;NOP58,3_prime_UTR_variant,,ENST00000426814,;NOP58,non_coding_transcript_exon_variant,,ENST00000488403,;NOP58,non_coding_transcript_exon_variant,,ENST00000478941,;NOP58,upstream_gene_variant,,ENST00000433543,;	T	ENSG00000055044	ENST00000264279	Transcript	missense_variant	545	319	107	I/F	Atc/Ttc	.	.	.	1	NOP58	HGNC	29926	protein_coding	YES	CCDS2353.1	ENSP00000264279	NOP58_HUMAN	.	UPI0000130366	.	deleterious(0)	possibly_damaging(0.536)	5/15	.	hmmpanther:PTHR10894	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTATCCAT	.	5	ESCA
NBEAL1	0	.	GRCh37	2	204053201	204053201	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6625G>C	p.Glu2209Gln	p.E2209Q	ENST00000449802	44/55	82	64	18	45	45	0	NBEAL1,missense_variant,p.Glu2209Gln,ENST00000449802,;NBEAL1,missense_variant,p.Glu224Gln,ENST00000414576,;NBEAL1,non_coding_transcript_exon_variant,,ENST00000460355,;AC011737.2,upstream_gene_variant,,ENST00000431098,;AC011737.2,upstream_gene_variant,,ENST00000314394,;	C	ENSG00000144426	ENST00000449802	Transcript	missense_variant	6958	6625	2209	E/Q	Gaa/Caa	.	.	.	1	NBEAL1	HGNC	20681	protein_coding	YES	CCDS46495.1	ENSP00000399903	NBEL1_HUMAN	.	UPI000194EC27	.	deleterious(0)	probably_damaging(1)	44/55	.	PROSITE_profiles:PS50197,hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCTGAATAT	.	5	ESCA
CHPF	0	.	GRCh37	2	220404553	220404553	+	Missense_Mutation	SNP	C	C	T	rs772864126	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1880G>A	p.Arg627His	p.R627H	ENST00000243776	4/4	18	14	3	18	18	0	CHPF,missense_variant,p.Arg627His,ENST00000243776,;CHPF,missense_variant,p.Arg465His,ENST00000535926,;ASIC4,downstream_gene_variant,,ENST00000358078,;CHPF,downstream_gene_variant,,ENST00000373891,;TMEM198,upstream_gene_variant,,ENST00000373883,;TMEM198,upstream_gene_variant,,ENST00000421791,;TMEM198,upstream_gene_variant,,ENST00000344458,;TMEM198,upstream_gene_variant,,ENST00000451952,;ASIC4,downstream_gene_variant,,ENST00000347842,;ASIC4,downstream_gene_variant,,ENST00000474489,;	T	ENSG00000123989	ENST00000243776	Transcript	missense_variant	2129	1880	627	R/H	cGc/cAc	rs772864126	.	.	-1	CHPF	HGNC	24291	protein_coding	YES	CCDS2443.1	ENSP00000243776	CHSS2_HUMAN	.	UPI00001AE6D6	.	deleterious(0)	probably_damaging(0.998)	4/4	.	hmmpanther:PTHR12369:SF12,hmmpanther:PTHR12369,Pfam_domain:PF05679	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCAGCGGTTC	byFrequency	2	ESCA
STK11IP	0	.	GRCh37	2	220480764	220480764	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3151-2A>G	.	p.X1051_splice	ENST00000295641	.	19	8	10	23	23	0	STK11IP,splice_acceptor_variant,,ENST00000295641,;STK11IP,splice_acceptor_variant,,ENST00000456909,;STK11IP,downstream_gene_variant,,ENST00000447191,;STK11IP,splice_acceptor_variant,,ENST00000494777,;STK11IP,downstream_gene_variant,,ENST00000495941,;STK11IP,downstream_gene_variant,,ENST00000413891,;	G	ENSG00000144589	ENST00000295641	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	STK11IP	HGNC	19184	protein_coding	YES	CCDS46521.1	ENSP00000295641	S11IP_HUMAN	C9JQV3_HUMAN	UPI0001AE7798	.	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCAGGTGT	.	5	ESCA
NYAP2	0	.	GRCh37	2	226447460	226447460	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1327G>C	p.Gly443Arg	p.G443R	ENST00000272907	4/6	67	37	29	60	60	0	NYAP2,missense_variant,p.Gly443Arg,ENST00000272907,;NYAP2,intron_variant,,ENST00000409269,;	C	ENSG00000144460	ENST00000272907	Transcript	missense_variant	1740	1327	443	G/R	Ggg/Cgg	.	.	.	1	NYAP2	HGNC	29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	NYAP2_HUMAN	.	UPI00001C1DB6	.	deleterious(0)	possibly_damaging(0.881)	4/6	.	hmmpanther:PTHR22633	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATGGGGAGG	.	5	ESCA
EML4	0	.	GRCh37	2	42557907	42557907	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*560T>C	.	.	ENST00000318522	23/23	72	59	12	48	48	0	EML4,3_prime_UTR_variant,,ENST00000401738,;EML4,3_prime_UTR_variant,,ENST00000318522,;COX7A2L,downstream_gene_variant,,ENST00000468711,;EML4,downstream_gene_variant,,ENST00000453191,;EML4,downstream_gene_variant,,ENST00000402711,;EML4,non_coding_transcript_exon_variant,,ENST00000406175,;	C	ENSG00000143924	ENST00000318522	Transcript	3_prime_UTR_variant	3768	.	.	.	.	.	.	.	1	EML4	HGNC	1316	protein_coding	YES	CCDS1807.1	ENSP00000320663	EMAL4_HUMAN	F2Z2B5_HUMAN	UPI0000140350	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAATGCCGT	.	5	ESCA
SNRNP200	0	.	GRCh37	2	96940721	96940721	+	3'UTR	SNP	C	C	A	rs750544481	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29G>T	.	.	ENST00000323853	45/45	38	24	14	21	21	0	SNRNP200,3_prime_UTR_variant,,ENST00000323853,;SNRNP200,3_prime_UTR_variant,,ENST00000349783,;CIAO1,downstream_gene_variant,,ENST00000488633,;SNRNP200,non_coding_transcript_exon_variant,,ENST00000497539,;SNRNP200,downstream_gene_variant,,ENST00000484372,;SNRNP200,downstream_gene_variant,,ENST00000493271,;SNRNP200,downstream_gene_variant,,ENST00000480835,;CIAO1,downstream_gene_variant,,ENST00000272402,;SNRNP200,downstream_gene_variant,,ENST00000429650,;	A	ENSG00000144028	ENST00000323853	Transcript	3_prime_UTR_variant	6518	.	.	.	.	rs750544481	.	.	-1	SNRNP200	HGNC	30859	protein_coding	YES	CCDS2020.1	ENSP00000317123	U520_HUMAN	Q9P172_HUMAN,Q7L5W4_HUMAN,Q5ZF01_HUMAN,A4FU77_HUMAN,A2RRQ7_HUMAN	UPI0000207C53	.	.	.	45/45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTCCTTTA	.	5	ESCA
PLXNA1	0	.	GRCh37	3	126754840	126754840	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1980C>A	.	.	ENST00000393409	31/31	23	16	6	27	27	0	PLXNA1,3_prime_UTR_variant,,ENST00000393409,;PLXNA1,3_prime_UTR_variant,,ENST00000251772,;PLXNA1,downstream_gene_variant,,ENST00000505278,;PLXNA1,downstream_gene_variant,,ENST00000503234,;	A	ENSG00000114554	ENST00000393409	Transcript	3_prime_UTR_variant	7671	.	.	.	.	.	.	.	1	PLXNA1	HGNC	9099	protein_coding	YES	CCDS33847.2	ENSP00000377061	PLXA1_HUMAN	Q9NSM6_HUMAN,F8VSZ4_HUMAN,B4DE20_HUMAN,B3KY38_HUMAN	UPI00001A7983	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGGCTTACT	.	2	ESCA
SOX2	0	.	GRCh37	3	181431170	181431170	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*68A>G	.	.	ENST00000325404	1/1	92	57	34	56	56	0	SOX2,3_prime_UTR_variant,,ENST00000325404,;SOX2,downstream_gene_variant,,ENST00000431565,;SOX2-OT,intron_variant,,ENST00000498731,;SOX2-OT,intron_variant,,ENST00000595287,;SOX2-OT,intron_variant,,ENST00000593549,;SOX2-OT,intron_variant,,ENST00000597828,;SOX2-OT,intron_variant,,ENST00000493521,;SOX2-OT,intron_variant,,ENST00000593330,;SOX2-OT,intron_variant,,ENST00000477928,;SOX2-OT,intron_variant,,ENST00000600778,;SOX2-OT,intron_variant,,ENST00000596250,;SOX2-OT,intron_variant,,ENST00000600386,;SOX2-OT,intron_variant,,ENST00000598474,;SOX2-OT,intron_variant,,ENST00000476964,;SOX2-OT,intron_variant,,ENST00000492337,;SOX2-OT,intron_variant,,ENST00000466034,;SOX2-OT,intron_variant,,ENST00000491282,;SOX2-OT,intron_variant,,ENST00000498226,;SOX2-OT,intron_variant,,ENST00000599082,;SOX2-OT,intron_variant,,ENST00000469278,;SOX2-OT,intron_variant,,ENST00000600801,;SOX2-OT,intron_variant,,ENST00000597651,;SOX2-OT,downstream_gene_variant,,ENST00000600962,;SOX2-OT,downstream_gene_variant,,ENST00000476125,;	G	ENSG00000181449	ENST00000325404	Transcript	3_prime_UTR_variant	1449	.	.	.	.	.	.	.	1	SOX2	HGNC	11195	protein_coding	YES	CCDS3239.1	ENSP00000323588	SOX2_HUMAN	.	UPI000003F545	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCAAAAGAG	.	5	ESCA
ATP11B	0	.	GRCh37	3	182583393	182583393	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1350A>G	p.%3D	p.L450L	ENST00000323116	13/30	133	82	50	44	44	0	ATP11B,synonymous_variant,p.%3D,ENST00000323116,;ATP11B,synonymous_variant,p.%3D,ENST00000498086,;ATP11B,non_coding_transcript_exon_variant,,ENST00000490303,;	G	ENSG00000058063	ENST00000323116	Transcript	synonymous_variant	1610	1350	450	L	ttA/ttG	.	.	.	1	ATP11B	HGNC	13553	protein_coding	YES	CCDS33896.1	ENSP00000321195	AT11B_HUMAN	B4E3T1_HUMAN	UPI000004124E	.	.	.	13/30	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF57,Pfam_domain:PF00702,TIGRFAM_domain:TIGR01652	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTATCTTA	.	5	ESCA
OTUD4	0	.	GRCh37	4	146056332	146056332	+	3'UTR	SNP	A	A	G	rs773865503	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2250T>C	.	.	ENST00000454497	21/21	57	50	7	10	10	0	OTUD4,3_prime_UTR_variant,,ENST00000454497,;OTUD4,downstream_gene_variant,,ENST00000447906,;OTUD4,intron_variant,,ENST00000455611,;	G	ENSG00000164164	ENST00000454497	Transcript	3_prime_UTR_variant	5538	.	.	.	.	rs773865503	.	.	-1	OTUD4	HGNC	24949	protein_coding	YES	CCDS47139.1	ENSP00000409279	OTUD4_HUMAN	D6RA27_HUMAN	UPI0000DA6D4D	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTACCATCTGC	.	3	ESCA
FBXW7	0	.	GRCh37	4	153243410	153243410	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*623A>G	.	.	ENST00000281708	12/12	77	13	64	30	30	0	FBXW7,3_prime_UTR_variant,,ENST00000263981,;FBXW7,3_prime_UTR_variant,,ENST00000296555,;FBXW7,3_prime_UTR_variant,,ENST00000281708,;FBXW7,downstream_gene_variant,,ENST00000603548,;FBXW7,downstream_gene_variant,,ENST00000393956,;FBXW7,downstream_gene_variant,,ENST00000603841,;RP11-461L13.3,upstream_gene_variant,,ENST00000603766,;RP11-461L13.5,upstream_gene_variant,,ENST00000605407,;FBXW7,downstream_gene_variant,,ENST00000604316,;FBXW7,downstream_gene_variant,,ENST00000604069,;FBXW7,downstream_gene_variant,,ENST00000603821,;	C	ENSG00000109670	ENST00000281708	Transcript	3_prime_UTR_variant	3977	.	.	.	.	.	.	.	-1	FBXW7	HGNC	16712	protein_coding	YES	CCDS3777.1	ENSP00000281708	FBXW7_HUMAN	S4R3N3_HUMAN,H9CWI3_HUMAN,H9CWI2_HUMAN,G0Z2K0_HUMAN,A7BJS8_HUMAN	UPI000007007E	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATATGGAAG	.	5	ESCA
UBE2K	0	.	GRCh37	4	39776500	39776500	+	Missense_Mutation	SNP	C	C	G	rs751488135	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.346C>G	p.Leu116Val	p.L116V	ENST00000261427	5/7	15	3	12	15	15	0	UBE2K,missense_variant,p.Leu116Val,ENST00000261427,;UBE2K,missense_variant,p.Leu65Val,ENST00000503368,;UBE2K,missense_variant,p.Leu116Val,ENST00000445950,;UBE2K,intron_variant,,ENST00000295963,;UBE2K,intron_variant,,ENST00000510934,;UBE2K,non_coding_transcript_exon_variant,,ENST00000513231,;UBE2K,non_coding_transcript_exon_variant,,ENST00000438068,;UBE2K,missense_variant,p.Thr37Ser,ENST00000510719,;ZBTB12P1,upstream_gene_variant,,ENST00000535877,;ZBTB12P1,upstream_gene_variant,,ENST00000314232,;	G	ENSG00000078140	ENST00000261427	Transcript	missense_variant	630	346	116	L/V	Cta/Gta	rs751488135	.	.	1	UBE2K	HGNC	4914	protein_coding	YES	CCDS33976.1	ENSP00000261427	UBE2K_HUMAN	B3KSH4_HUMAN	UPI0000003FF1	.	deleterious(0.03)	benign(0.353)	5/7	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50127,hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF83,Gene3D:3.10.110.10,Pfam_domain:PF00179,SMART_domains:SM00212,Superfamily_domains:SSF54495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCACTATTG	.	5	ESCA
SEC31A	0	.	GRCh37	4	83799895	83799895	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390G>C	p.%3D	p.V130V	ENST00000395310	4/27	44	18	25	17	17	0	SEC31A,synonymous_variant,p.%3D,ENST00000514326,;SEC31A,synonymous_variant,p.%3D,ENST00000448323,;SEC31A,synonymous_variant,p.%3D,ENST00000505984,;SEC31A,synonymous_variant,p.%3D,ENST00000311785,;SEC31A,synonymous_variant,p.%3D,ENST00000500777,;SEC31A,synonymous_variant,p.%3D,ENST00000395310,;SEC31A,synonymous_variant,p.%3D,ENST00000509142,;SEC31A,synonymous_variant,p.%3D,ENST00000503058,;SEC31A,synonymous_variant,p.%3D,ENST00000508502,;SEC31A,synonymous_variant,p.%3D,ENST00000505472,;SEC31A,synonymous_variant,p.%3D,ENST00000432794,;SEC31A,synonymous_variant,p.%3D,ENST00000513323,;SEC31A,synonymous_variant,p.%3D,ENST00000513858,;SEC31A,synonymous_variant,p.%3D,ENST00000355196,;SEC31A,synonymous_variant,p.%3D,ENST00000443462,;SEC31A,synonymous_variant,p.%3D,ENST00000508479,;SEC31A,synonymous_variant,p.%3D,ENST00000326950,;SEC31A,synonymous_variant,p.%3D,ENST00000348405,;SEC31A,downstream_gene_variant,,ENST00000505434,;SEC31A,downstream_gene_variant,,ENST00000503210,;SEC31A,downstream_gene_variant,,ENST00000507051,;SEC31A,downstream_gene_variant,,ENST00000506495,;SEC31A,downstream_gene_variant,,ENST00000507676,;SEC31A,non_coding_transcript_exon_variant,,ENST00000506497,;SEC31A,non_coding_transcript_exon_variant,,ENST00000511975,;SEC31A,non_coding_transcript_exon_variant,,ENST00000436790,;SEC31A,intron_variant,,ENST00000507867,;SEC31A,downstream_gene_variant,,ENST00000510310,;SEC31A,3_prime_UTR_variant,,ENST00000507340,;SEC31A,intron_variant,,ENST00000507816,;	G	ENSG00000138674	ENST00000395310	Transcript	synonymous_variant	573	390	130	V	gtG/gtC	.	.	.	-1	SEC31A	HGNC	17052	protein_coding	YES	CCDS3596.1	ENSP00000378721	SC31A_HUMAN	U3KQC9_HUMAN,D6REC0_HUMAN,D6REA9_HUMAN,D6RE64_HUMAN,D6RCQ9_HUMAN,D6RBT0_HUMAN	UPI000003E7E1	.	.	.	4/27	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR13923:SF23,hmmpanther:PTHR13923,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTTCACATC	.	5	ESCA
FBN2	0	.	GRCh37	5	127866299	127866299	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.425G>A	p.Gly142Glu	p.G142E	ENST00000508053	9/71	44	34	9	41	41	0	FBN2,missense_variant,p.Gly142Glu,ENST00000262464,;FBN2,missense_variant,p.Gly142Glu,ENST00000508053,;FBN2,missense_variant,p.Gly142Glu,ENST00000502468,;FBN2,intron_variant,,ENST00000508989,;FBN2,non_coding_transcript_exon_variant,,ENST00000514742,;	T	ENSG00000138829	ENST00000508053	Transcript	missense_variant	1400	425	142	G/E	gGa/gAa	.	.	.	-1	FBN2	HGNC	3604	protein_coding	YES	CCDS34222.1	ENSP00000424571	FBN2_HUMAN	.	UPI0000519468	.	deleterious(0)	benign(0)	9/71	.	PIRSF_domain:PIRSF036312,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATCCACAG	.	5	ESCA
DNAH5	0	.	GRCh37	5	13810233	13810233	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7544C>T	p.Thr2515Met	p.T2515M	ENST00000265104	45/79	53	38	15	40	40	0	DNAH5,missense_variant,p.Thr2515Met,ENST00000265104,;DNAH5,non_coding_transcript_exon_variant,,ENST00000512443,;	A	ENSG00000039139	ENST00000265104	Transcript	missense_variant	7649	7544	2515	T/M	aCg/aTg	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	possibly_damaging(0.791)	45/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCGTCCCT	.	4	ESCA
PCDHA9	0	.	GRCh37	5	140230375	140230375	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2295G>A	p.%3D	p.Q765Q	ENST00000532602	1/4	78	43	34	77	77	0	PCDHA9,synonymous_variant,p.%3D,ENST00000378122,;PCDHA9,synonymous_variant,p.%3D,ENST00000532602,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	A	ENSG00000204961	ENST00000532602	Transcript	synonymous_variant	3328	2295	765	Q	caG/caA	.	.	.	1	PCDHA9	HGNC	8675	protein_coding	YES	CCDS54920.1	ENSP00000436042	PCDA9_HUMAN	.	UPI00001273D1	.	.	.	1/4	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGAAGAC	.	5	ESCA
PCDHB3	0	.	GRCh37	5	140481751	140481751	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1518C>G	p.Ile506Met	p.I506M	ENST00000231130	1/1	229	176	52	247	247	0	PCDHB3,missense_variant,p.Ile506Met,ENST00000231130,;PCDHB2,downstream_gene_variant,,ENST00000194155,;AC005754.7,non_coding_transcript_exon_variant,,ENST00000607216,;	G	ENSG00000113205	ENST00000231130	Transcript	missense_variant	1518	1518	506	I/M	atC/atG	COSM3827051	.	.	1	PCDHB3	HGNC	8688	protein_coding	YES	CCDS4245.1	ENSP00000231130	PCDB3_HUMAN	.	UPI00001273DD	.	deleterious_low_confidence(0)	possibly_damaging(0.458)	1/1	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028:SF19,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCATCAACGC	.	5	ESCA
PCDHGC5	0	.	GRCh37	5	140870755	140870755	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1948G>T	p.Asp650Tyr	p.D650Y	ENST00000252087	1/4	22	18	4	36	36	0	PCDHGC5,missense_variant,p.Asp650Tyr,ENST00000252087,;PCDHGB6,intron_variant,,ENST00000520790,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGA10,intron_variant,,ENST00000398610,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA12,intron_variant,,ENST00000252085,;PCDHGA11,intron_variant,,ENST00000398587,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGC3,intron_variant,,ENST00000308177,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA11,intron_variant,,ENST00000518882,;PCDHGC4,intron_variant,,ENST00000306593,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGB7,intron_variant,,ENST00000398594,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;	T	ENSG00000240764	ENST00000252087	Transcript	missense_variant	1948	1948	650	D/Y	Gac/Tac	.	.	.	1	PCDHGC5	HGNC	8718	protein_coding	YES	CCDS4263.1	ENSP00000252087	PCDGM_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006D689	.	deleterious(0)	probably_damaging(1)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF80,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGGGACAAT	.	4	ESCA
ARAP3	0	.	GRCh37	5	141033939	141033939	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4213G>A	p.Glu1405Lys	p.E1405K	ENST00000239440	33/33	62	49	13	41	41	0	ARAP3,missense_variant,p.Glu1236Lys,ENST00000508305,;ARAP3,missense_variant,p.Glu1405Lys,ENST00000239440,;ARAP3,missense_variant,p.Glu1054Lys,ENST00000513878,;FCHSD1,upstream_gene_variant,,ENST00000522783,;FCHSD1,upstream_gene_variant,,ENST00000435817,;FCHSD1,upstream_gene_variant,,ENST00000519800,;FCHSD1,upstream_gene_variant,,ENST00000522126,;ARAP3,non_coding_transcript_exon_variant,,ENST00000512390,;	T	ENSG00000120318	ENST00000239440	Transcript	missense_variant	4279	4213	1405	E/K	Gag/Aag	.	.	.	-1	ARAP3	HGNC	24097	protein_coding	YES	CCDS4266.1	ENSP00000239440	ARAP3_HUMAN	Q9H7C1_HUMAN,Q05CH1_HUMAN,B3KMD0_HUMAN	UPI0000049886	.	deleterious_low_confidence(0.02)	probably_damaging(0.991)	33/33	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTCCTCGT	.	5	ESCA
ADAM19	0	.	GRCh37	5	156908845	156908845	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2657G>T	p.Gly886Val	p.G886V	ENST00000257527	22/23	51	43	8	52	52	0	ADAM19,missense_variant,p.Gly888Val,ENST00000394020,;ADAM19,missense_variant,p.Gly886Val,ENST00000517905,;ADAM19,missense_variant,p.Gly886Val,ENST00000257527,;ADAM19,missense_variant,p.Gly457Val,ENST00000517374,;ADAM19,intron_variant,,ENST00000430702,;ADAM19,intron_variant,,ENST00000517951,;	A	ENSG00000135074	ENST00000257527	Transcript	missense_variant	2736	2657	886	G/V	gGt/gTt	.	.	.	-1	ADAM19	HGNC	197	protein_coding	YES	CCDS4338.1	ENSP00000257527	ADA19_HUMAN	.	UPI000013CF6A	.	tolerated(0.14)	benign(0.001)	22/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCACCAGGG	.	4	ESCA
MAT2B	0	.	GRCh37	5	162944449	162944449	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.721-118G>C	.	.	ENST00000321757	.	20	11	8	15	15	0	MAT2B,3_prime_UTR_variant,,ENST00000518095,;MAT2B,intron_variant,,ENST00000321757,;MAT2B,intron_variant,,ENST00000421814,;MAT2B,intron_variant,,ENST00000280969,;MAT2B,intron_variant,,ENST00000521838,;MAT2B,intron_variant,,ENST00000523606,;MAT2B,downstream_gene_variant,,ENST00000520449,;	C	ENSG00000038274	ENST00000321757	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MAT2B	HGNC	6905	protein_coding	YES	CCDS4365.1	ENSP00000325425	MAT2B_HUMAN	.	UPI0000037B81	.	.	.	.	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCAGAAAAA	.	5	ESCA
SNCB	0	.	GRCh37	5	176047521	176047521	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*291G>C	.	.	ENST00000310112	7/7	73	57	16	81	81	0	SNCB,3_prime_UTR_variant,,ENST00000393693,;SNCB,3_prime_UTR_variant,,ENST00000310112,;SNCB,downstream_gene_variant,,ENST00000506696,;SNCB,downstream_gene_variant,,ENST00000510387,;SNCB,downstream_gene_variant,,ENST00000508006,;	G	ENSG00000074317	ENST00000310112	Transcript	3_prime_UTR_variant	947	.	.	.	.	.	.	.	-1	SNCB	HGNC	11140	protein_coding	YES	CCDS4406.1	ENSP00000308057	SYUB_HUMAN	G4Y816_HUMAN	UPI000003173C	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAACACATA	.	5	ESCA
PRDM9	0	.	GRCh37	5	23527626	23527626	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2429G>T	p.Gly810Val	p.G810V	ENST00000296682	11/11	81	51	29	84	84	0	PRDM9,missense_variant,p.Gly810Val,ENST00000296682,;	T	ENSG00000164256	ENST00000296682	Transcript	missense_variant	2611	2429	810	G/V	gGg/gTg	.	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	deleterious(0)	probably_damaging(1)	11/11	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGGGCGGG	.	5	ESCA
HIVEP2	0	.	GRCh37	6	143081380	143081380	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6045A>G	p.%3D	p.R2015R	ENST00000367603	9/10	40	19	21	23	23	0	HIVEP2,synonymous_variant,p.%3D,ENST00000367603,;HIVEP2,synonymous_variant,p.%3D,ENST00000012134,;HIVEP2,synonymous_variant,p.%3D,ENST00000367604,;	C	ENSG00000010818	ENST00000367603	Transcript	synonymous_variant	6788	6045	2015	R	agA/agG	.	.	.	-1	HIVEP2	HGNC	4921	protein_coding	YES	CCDS43510.1	ENSP00000356575	ZEP2_HUMAN	B4DKE9_HUMAN	UPI00004708DD	.	.	.	9/10	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAATCTGTC	.	5	ESCA
ADGB	0	.	GRCh37	6	147123946	147123946	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4818+799T>C	.	.	ENST00000397944	.	149	84	64	77	77	0	ADGB,intron_variant,,ENST00000367493,;ADGB,intron_variant,,ENST00000367490,;ADGB,intron_variant,,ENST00000367489,;ADGB,intron_variant,,ENST00000397944,;ADGB,intron_variant,,ENST00000367488,;ADGB,downstream_gene_variant,,ENST00000326916,;KATNBL1P6,non_coding_transcript_exon_variant,,ENST00000562413,;ADGB,intron_variant,,ENST00000493950,;ADGB,intron_variant,,ENST00000480328,;KATNBL1P6,non_coding_transcript_exon_variant,,ENST00000453433,;	C	ENSG00000118492	ENST00000397944	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ADGB	HGNC	21212	protein_coding	YES	.	ENSP00000381036	ADGB_HUMAN	.	UPI000020E382	.	.	.	.	35/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAATAAATA	.	5	ESCA
AKAP12	0	.	GRCh37	6	151677145	151677145	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*296G>T	.	.	ENST00000402676	5/5	46	28	17	23	23	0	AKAP12,3_prime_UTR_variant,,ENST00000359755,;AKAP12,3_prime_UTR_variant,,ENST00000354675,;AKAP12,3_prime_UTR_variant,,ENST00000253332,;AKAP12,3_prime_UTR_variant,,ENST00000402676,;	T	ENSG00000131016	ENST00000402676	Transcript	3_prime_UTR_variant	5885	.	.	.	.	.	.	.	1	AKAP12	HGNC	370	protein_coding	YES	CCDS5229.1	ENSP00000384537	AKA12_HUMAN	.	UPI000013CDC7	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTGGCAATA	.	5	ESCA
RMND1	0	.	GRCh37	6	151766902	151766902	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45A>G	p.Ile15Met	p.I15M	ENST00000367303	2/12	40	33	6	19	19	0	RMND1,missense_variant,p.Ile15Met,ENST00000367303,;RMND1,intron_variant,,ENST00000444024,;RMND1,upstream_gene_variant,,ENST00000336451,;RMND1,non_coding_transcript_exon_variant,,ENST00000491268,;	C	ENSG00000155906	ENST00000367303	Transcript	missense_variant	168	45	15	I/M	atA/atG	.	.	.	-1	RMND1	HGNC	21176	protein_coding	YES	CCDS5232.1	ENSP00000356272	RMND1_HUMAN	Q5SZ82_HUMAN	UPI00001AEAE1	.	tolerated_low_confidence(0.09)	benign(0.234)	2/12	.	hmmpanther:PTHR16255:SF1,hmmpanther:PTHR16255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATAATATATG	.	5	ESCA
MYLIP	0	.	GRCh37	6	16147493	16147493	+	3'Flank	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000356840	.	62	31	30	46	46	0	MYLIP,3_prime_UTR_variant,,ENST00000349606,;MYLIP,downstream_gene_variant,,ENST00000356840,;U3,downstream_gene_variant,,ENST00000515984,;	G	ENSG00000007944	ENST00000356840	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	381	1	MYLIP	HGNC	21155	protein_coding	YES	CCDS4536.1	ENSP00000349298	MYLIP_HUMAN	Q5TIA5_HUMAN	UPI000006CDE0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTATAACT	.	5	ESCA
THBS2	0	.	GRCh37	6	169637866	169637866	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1154C>G	p.Ser385Cys	p.S385C	ENST00000366787	9/23	76	63	12	80	80	0	THBS2,missense_variant,p.Ser385Cys,ENST00000366787,;XXyac-YX65C7_A.2,intron_variant,,ENST00000444188,;THBS2,upstream_gene_variant,,ENST00000461848,;	C	ENSG00000186340	ENST00000366787	Transcript	missense_variant	1404	1154	385	S/C	tCt/tGt	.	.	.	-1	THBS2	HGNC	11786	protein_coding	YES	CCDS34574.1	ENSP00000355751	TSP2_HUMAN	Q6MZL6_HUMAN,Q5RI53_HUMAN	UPI0000231C7F	.	deleterious(0)	probably_damaging(0.991)	9/23	.	PROSITE_profiles:PS50092,hmmpanther:PTHR10199:SF10,hmmpanther:PTHR10199,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGAGACCAG	.	5	ESCA
NUP153	0	.	GRCh37	6	17706534	17706534	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85T>G	p.Tyr29Asp	p.Y29D	ENST00000262077	1/22	112	58	53	111	111	0	NUP153,missense_variant,p.Tyr29Asp,ENST00000537253,;NUP153,missense_variant,p.Tyr29Asp,ENST00000262077,;RP11-500C11.3,non_coding_transcript_exon_variant,,ENST00000606771,;	C	ENSG00000124789	ENST00000262077	Transcript	missense_variant	85	85	29	Y/D	Tac/Gac	.	.	.	-1	NUP153	HGNC	8062	protein_coding	YES	CCDS4541.1	ENSP00000262077	NU153_HUMAN	.	UPI000013D251	.	deleterious(0)	possibly_damaging(0.824)	1/22	.	hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGTAAGGCT	.	5	ESCA
HIST1H2AB	0	.	GRCh37	6	26033433	26033433	+	Missense_Mutation	SNP	C	C	T	rs745693623	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364G>A	p.Glu122Lys	p.E122K	ENST00000259791	1/1	83	79	4	63	63	0	HIST1H2AB,missense_variant,p.Glu122Lys,ENST00000259791,;HIST1H3B,upstream_gene_variant,,ENST00000244661,;	T	ENSG00000137259	ENST00000259791	Transcript	missense_variant	364	364	122	E/K	Gag/Aag	rs745693623,COSM450998	.	.	-1	HIST1H2AB	HGNC	4734	protein_coding	YES	CCDS4574.1	ENSP00000259791	H2A1B_HUMAN	Q08AJ9_HUMAN	UPI00000007AF	.	tolerated_low_confidence(0.19)	benign(0.071)	1/1	.	Superfamily_domains:SSF47113,SMART_domains:SM00414,Gene3D:1.10.20.10,hmmpanther:PTHR23430,hmmpanther:PTHR23430:SF24	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCTCAGTTT	.	2	ESCA
HIST1H1C	0	.	GRCh37	6	26056024	26056024	+	Silent	SNP	C	C	T	rs750505144	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633G>A	p.%3D	p.K211K	ENST00000343677	1/1	36	21	15	50	50	0	HIST1H1C,synonymous_variant,p.%3D,ENST00000343677,;	T	ENSG00000187837	ENST00000343677	Transcript	synonymous_variant	676	633	211	K	aaG/aaA	rs750505144	.	.	-1	HIST1H1C	HGNC	4716	protein_coding	YES	CCDS4577.1	ENSP00000339566	H12_HUMAN	.	UPI0000001BD9	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11467:SF23,hmmpanther:PTHR11467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.*214W|c.641A>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTTGGG	byFrequency	5	ESCA
OR2B2	0	.	GRCh37	6	27879749	27879749	+	Missense_Mutation	SNP	C	C	G	rs781638205	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349G>C	p.Val117Leu	p.V117L	ENST00000303324	1/1	60	44	16	39	38	0	OR2B2,missense_variant,p.Val117Leu,ENST00000303324,;	G	ENSG00000168131	ENST00000303324	Transcript	missense_variant	426	349	117	V/L	Gtc/Ctc	rs781638205,COSM3948911	.	.	-1	OR2B2	HGNC	13966	protein_coding	YES	CCDS4641.1	ENSP00000304419	OR2B2_HUMAN	Q6IFA1_HUMAN	UPI000004187A	.	deleterious(0.04)	benign(0.334)	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,PROSITE_patterns:PS00237,hmmpanther:PTHR26453:SF115,hmmpanther:PTHR26453,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CATGACGGCCA	.	4	ESCA
ZSCAN23	0	.	GRCh37	6	28402571	28402571	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.841G>A	p.Glu281Lys	p.E281K	ENST00000289788	4/4	61	32	28	48	48	0	ZSCAN23,missense_variant,p.Glu281Lys,ENST00000289788,;ZSCAN23,downstream_gene_variant,,ENST00000486481,;ZSCAN23,3_prime_UTR_variant,,ENST00000481983,;	T	ENSG00000187987	ENST00000289788	Transcript	missense_variant	987	841	281	E/K	Gag/Aag	.	.	.	-1	ZSCAN23	HGNC	21193	protein_coding	YES	CCDS47393.1	ENSP00000289788	ZSC23_HUMAN	.	UPI000019874A	.	deleterious(0.01)	possibly_damaging(0.761)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR23226:SF62,hmmpanther:PTHR23226,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACTCATCAC	.	5	ESCA
NELFE	0	.	GRCh37	6	31922591	31922591	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483T>C	p.%3D	p.G161G	ENST00000375429	7/11	33	29	4	22	22	0	NELFE,synonymous_variant,p.%3D,ENST00000436289,;NELFE,synonymous_variant,p.%3D,ENST00000375425,;NELFE,synonymous_variant,p.%3D,ENST00000375429,;NELFE,synonymous_variant,p.%3D,ENST00000441998,;NELFE,synonymous_variant,p.%3D,ENST00000454913,;NELFE,intron_variant,,ENST00000444811,;CFB,downstream_gene_variant,,ENST00000483004,;CFB,downstream_gene_variant,,ENST00000456570,;CFB,downstream_gene_variant,,ENST00000477310,;SKIV2L,upstream_gene_variant,,ENST00000544581,;CFB,downstream_gene_variant,,ENST00000498317,;CFB,downstream_gene_variant,,ENST00000556679,;SKIV2L,upstream_gene_variant,,ENST00000375394,;CFB,downstream_gene_variant,,ENST00000425368,;NELFE,downstream_gene_variant,,ENST00000426722,;MIR1236,downstream_gene_variant,,ENST00000408340,;SKIV2L,upstream_gene_variant,,ENST00000488648,;NELFE,non_coding_transcript_exon_variant,,ENST00000488426,;NELFE,non_coding_transcript_exon_variant,,ENST00000492185,;NELFE,non_coding_transcript_exon_variant,,ENST00000481121,;NELFE,intron_variant,,ENST00000492539,;SKIV2L,upstream_gene_variant,,ENST00000492900,;CFB,downstream_gene_variant,,ENST00000482312,;CFB,downstream_gene_variant,,ENST00000452035,;SKIV2L,upstream_gene_variant,,ENST00000474839,;SKIV2L,upstream_gene_variant,,ENST00000465703,;NELFE,downstream_gene_variant,,ENST00000494956,;CFB,downstream_gene_variant,,ENST00000467360,;NELFE,downstream_gene_variant,,ENST00000491139,;SKIV2L,upstream_gene_variant,,ENST00000461073,;	G	ENSG00000204356	ENST00000375429	Transcript	synonymous_variant	710	483	161	G	ggT/ggC	.	.	.	-1	NELFE	HGNC	13974	protein_coding	YES	CCDS4730.1	ENSP00000364578	NELFE_HUMAN	Q9BQJ6_HUMAN,A2ABK4_HUMAN,A2ABK2_HUMAN	UPI000000127D	.	.	.	7/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR17250:SF0,hmmpanther:PTHR17250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GGGGGACCATC	.	2	ESCA
DAXX	0	.	GRCh37	6	33286968	33286968	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1969G>C	p.Glu657Gln	p.E657Q	ENST00000374542	7/8	39	35	4	25	25	0	DAXX,missense_variant,p.Glu657Gln,ENST00000374542,;DAXX,missense_variant,p.Glu582Gln,ENST00000414083,;DAXX,missense_variant,p.Glu657Gln,ENST00000266000,;ZBTB22,upstream_gene_variant,,ENST00000431845,;TAPBP,upstream_gene_variant,,ENST00000489157,;TAPBP,upstream_gene_variant,,ENST00000456592,;DAXX,downstream_gene_variant,,ENST00000453407,;DAXX,downstream_gene_variant,,ENST00000446403,;ZBTB22,upstream_gene_variant,,ENST00000441117,;ZBTB22,upstream_gene_variant,,ENST00000418724,;TAPBP,upstream_gene_variant,,ENST00000467025,;TAPBP,upstream_gene_variant,,ENST00000426633,;TAPBP,upstream_gene_variant,,ENST00000434618,;TAPBP,upstream_gene_variant,,ENST00000475304,;DAXX,downstream_gene_variant,,ENST00000446511,;DAXX,downstream_gene_variant,,ENST00000468536,;DAXX,downstream_gene_variant,,ENST00000494082,;DAXX,downstream_gene_variant,,ENST00000477370,;DAXX,downstream_gene_variant,,ENST00000477162,;DAXX,downstream_gene_variant,,ENST00000490173,;DAXX,downstream_gene_variant,,ENST00000498030,;	G	ENSG00000204209	ENST00000374542	Transcript	missense_variant	2174	1969	657	E/Q	Gag/Cag	.	.	.	-1	DAXX	HGNC	2681	protein_coding	YES	CCDS4776.1	ENSP00000363668	DAXX_HUMAN	Q5STR5_HUMAN,Q4VX54_HUMAN,A2AB94_HUMAN	UPI0000128ED8	.	tolerated(0.36)	benign(0.135)	7/8	.	hmmpanther:PTHR12766:SF6,hmmpanther:PTHR12766,Pfam_domain:PF03344	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTCTCATGCA	.	3	ESCA
TREM1	0	.	GRCh37	6	41243905	41243905	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.663C>T	p.%3D	p.F221F	ENST00000244709	4/4	84	80	4	66	66	0	TREM1,synonymous_variant,p.%3D,ENST00000244709,;TREM1,3_prime_UTR_variant,,ENST00000334475,;TREM1,intron_variant,,ENST00000589614,;TREM1,downstream_gene_variant,,ENST00000591620,;TREM1,non_coding_transcript_exon_variant,,ENST00000589695,;TREM1,downstream_gene_variant,,ENST00000589882,;	A	ENSG00000124731	ENST00000244709	Transcript	synonymous_variant	727	663	221	F	ttC/ttT	.	.	.	-1	TREM1	HGNC	17760	protein_coding	YES	CCDS4854.1	ENSP00000244709	TREM1_HUMAN	Q38L15_HUMAN	UPI0000047FA9	.	.	.	4/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR19357:SF1,hmmpanther:PTHR19357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAGAGAAGAC	.	2	ESCA
CDHR3	0	.	GRCh37	7	105603730	105603730	+	5'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-35T>A	.	.	ENST00000317716	1/19	32	22	10	39	39	0	CDHR3,5_prime_UTR_variant,,ENST00000478080,;CDHR3,5_prime_UTR_variant,,ENST00000343407,;CDHR3,5_prime_UTR_variant,,ENST00000542731,;CDHR3,5_prime_UTR_variant,,ENST00000317716,;CDHR3,upstream_gene_variant,,ENST00000541203,;CDHR3,non_coding_transcript_exon_variant,,ENST00000461766,;CDHR3,intron_variant,,ENST00000470188,;CDHR3,intron_variant,,ENST00000488386,;CDHR3,upstream_gene_variant,,ENST00000496633,;	A	ENSG00000128536	ENST00000317716	Transcript	5_prime_UTR_variant	46	.	.	.	.	.	.	.	1	CDHR3	HGNC	26308	protein_coding	YES	CCDS47684.1	ENSP00000325954	CDHR3_HUMAN	E7EQG5_HUMAN	UPI00001C0C6E	.	.	.	1/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTAATGTGCT	.	5	ESCA
CNTNAP2	0	.	GRCh37	7	148114542	148114542	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1834T>C	.	.	ENST00000361727	24/24	52	36	16	16	16	0	CNTNAP2,3_prime_UTR_variant,,ENST00000361727,;CNTNAP2,downstream_gene_variant,,ENST00000538075,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000463592,;CNTNAP2,downstream_gene_variant,,ENST00000602734,;	C	ENSG00000174469	ENST00000361727	Transcript	3_prime_UTR_variant	6346	.	.	.	.	.	.	.	1	CNTNAP2	HGNC	13830	protein_coding	YES	CCDS5889.1	ENSP00000354778	CNTP2_HUMAN	Q9UDV4_HUMAN,Q96T77_HUMAN,Q86UL9_HUMAN,Q86UL6_HUMAN,Q86UL4_HUMAN,Q86UJ1_HUMAN,Q86UI8_HUMAN,Q75MQ9_HUMAN,Q75MF8_HUMAN,Q75MF6_HUMAN,Q75MD4_HUMAN,Q75MA1_HUMAN,Q75M92_HUMAN,Q75LG9_HUMAN,O75852_HUMAN,B7Z1Y6_HUMAN	UPI00001285FA	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGCTGGTTG	.	5	ESCA
SSPO	0	.	GRCh37	7	149486300	149486300	+	RNA	SNP	G	G	T	rs540269082	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4276G>T	.	.	ENST00000378016	30/109	47	31	16	35	35	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000262089,;SSPO,downstream_gene_variant,,ENST00000477518,;SSPO,non_coding_transcript_exon_variant,,ENST00000475488,;SSPO,downstream_gene_variant,,ENST00000493502,;	T	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	4276	.	.	.	.	rs540269082	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	30/109	.	.	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCGGCCAC	byCluster|by1000G	5	ESCA
RAPGEF5	0	.	GRCh37	7	22233043	22233043	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.687G>A	p.%3D	p.K229K	ENST00000344041	11/26	33	22	10	28	28	0	RAPGEF5,synonymous_variant,p.%3D,ENST00000420196,;RAPGEF5,synonymous_variant,p.%3D,ENST00000344041,;RAPGEF5,synonymous_variant,p.%3D,ENST00000401957,;RAPGEF5,5_prime_UTR_variant,,ENST00000458533,;RAPGEF5,3_prime_UTR_variant,,ENST00000405243,;RAPGEF5,non_coding_transcript_exon_variant,,ENST00000475788,;RAPGEF5,synonymous_variant,p.%3D,ENST00000451559,;	T	ENSG00000136237	ENST00000344041	Transcript	synonymous_variant	1000	687	229	K	aaG/aaA	.	.	.	-1	RAPGEF5	HGNC	16862	protein_coding	YES	CCDS55093.1	ENSP00000343656	.	C9JBS6_HUMAN,A8MQ07_HUMAN	UPI0000EA87E4	.	.	.	11/26	.	PROSITE_profiles:PS50212,hmmpanther:PTHR23113:SF26,hmmpanther:PTHR23113,Pfam_domain:PF00618,Gene3D:2ii0A01,SMART_domains:SM00229,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATCTTCTC	.	5	ESCA
SUMF2	0	.	GRCh37	7	56145799	56145799	+	Missense_Mutation	SNP	A	A	G	rs754025668	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.653A>G	p.Lys218Arg	p.K218R	ENST00000342190	7/8	51	32	19	41	41	0	SUMF2,missense_variant,p.Lys111Arg,ENST00000275607,;SUMF2,missense_variant,p.Lys134Arg,ENST00000395435,;SUMF2,missense_variant,p.Lys130Arg,ENST00000437307,;SUMF2,missense_variant,p.Lys221Arg,ENST00000413952,;SUMF2,missense_variant,p.Lys216Arg,ENST00000451338,;SUMF2,missense_variant,p.Lys218Arg,ENST00000342190,;SUMF2,missense_variant,p.Lys203Arg,ENST00000395436,;SUMF2,missense_variant,p.Lys199Arg,ENST00000413756,;SUMF2,missense_variant,p.Lys218Arg,ENST00000434526,;PHKG1,downstream_gene_variant,,ENST00000432123,;PHKG1,downstream_gene_variant,,ENST00000452681,;PHKG1,downstream_gene_variant,,ENST00000446428,;PHKG1,downstream_gene_variant,,ENST00000297373,;PHKG1,downstream_gene_variant,,ENST00000537360,;SUMF2,missense_variant,p.Ser167Gly,ENST00000447501,;SUMF2,missense_variant,p.Ser149Gly,ENST00000423763,;SUMF2,missense_variant,p.Ser134Gly,ENST00000438133,;SUMF2,synonymous_variant,p.%3D,ENST00000436782,;SUMF2,3_prime_UTR_variant,,ENST00000452216,;SUMF2,non_coding_transcript_exon_variant,,ENST00000531229,;SUMF2,non_coding_transcript_exon_variant,,ENST00000461912,;SUMF2,downstream_gene_variant,,ENST00000483327,;SUMF2,downstream_gene_variant,,ENST00000529457,;SUMF2,downstream_gene_variant,,ENST00000498777,;	G	ENSG00000129103	ENST00000342190	Transcript	missense_variant	653	653	218	K/R	aAg/aGg	rs754025668	.	.	1	SUMF2	HGNC	20415	protein_coding	YES	CCDS47589.1	ENSP00000341938	.	Q75LP3_HUMAN,F8WA42_HUMAN	UPI0001AE7021	.	tolerated(0.12)	benign(0.006)	7/8	.	hmmpanther:PTHR23150,Gene3D:1z70X00,Pfam_domain:PF03781,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAAGTTCC	.	5	ESCA
SRCRB4D	0	.	GRCh37	7	76024576	76024576	+	Missense_Mutation	SNP	G	G	A	rs148308343	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.940C>T	p.Pro314Ser	p.P314S	ENST00000275560	7/11	33	24	8	43	43	0	SRCRB4D,missense_variant,p.Pro314Ser,ENST00000275560,;ZP3,upstream_gene_variant,,ENST00000336517,;SRCRB4D,upstream_gene_variant,,ENST00000492979,;	A	ENSG00000146700	ENST00000275560	Transcript	missense_variant	1288	940	314	P/S	Ccg/Tcg	rs148308343	.	.	-1	SRCRB4D	HGNC	14461	protein_coding	YES	CCDS5585.1	ENSP00000275560	SRB4D_HUMAN	.	UPI000006D197	.	tolerated(0.29)	benign(0.009)	7/11	.	hmmpanther:PTHR19331:SF258,hmmpanther:PTHR19331	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	A:0.0009	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACGGATCTG	byFrequency|byCluster|by1000G	5	ESCA
POMZP3	0	.	GRCh37	7	76254993	76254993	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73C>T	p.Gln25Ter	p.Q25*	ENST00000310842	3/7	147	102	44	85	85	0	POMZP3,stop_gained,p.Gln25Ter,ENST00000275569,;POMZP3,stop_gained,p.Gln25Ter,ENST00000454397,;POMZP3,stop_gained,p.Gln25Ter,ENST00000310842,;UPK3B,intron_variant,,ENST00000419923,;UPK3B,intron_variant,,ENST00000443097,;AC004980.7,intron_variant,,ENST00000450661,;AC004980.7,intron_variant,,ENST00000418663,;AC004980.7,downstream_gene_variant,,ENST00000423084,;POMZP3,stop_gained,p.Gln25Ter,ENST00000424818,;	A	ENSG00000146707	ENST00000310842	Transcript	stop_gained	758	73	25	Q/*	Cag/Tag	.	.	.	-1	POMZP3	HGNC	9203	protein_coding	YES	CCDS43606.1	ENSP00000309233	POZP3_HUMAN	.	UPI000059D9C5	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCTGCTCTG	.	5	ESCA
DCAF13	0	.	GRCh37	8	104439377	104439377	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.977G>A	p.Cys326Tyr	p.C326Y	ENST00000297579	5/11	97	75	22	46	46	0	DCAF13,missense_variant,p.Cys134Tyr,ENST00000521971,;DCAF13,missense_variant,p.Cys326Tyr,ENST00000297579,;DCAF13,missense_variant,p.Cys170Tyr,ENST00000519682,;DCAF13,non_coding_transcript_exon_variant,,ENST00000521999,;DCAF13,non_coding_transcript_exon_variant,,ENST00000518554,;	A	ENSG00000164934	ENST00000297579	Transcript	missense_variant	1254	977	326	C/Y	tGt/tAt	.	.	.	1	DCAF13	HGNC	24535	protein_coding	YES	CCDS34934.1	ENSP00000297579	DCA13_HUMAN	.	UPI0000DBEF2A	.	deleterious(0)	probably_damaging(0.987)	5/11	.	PROSITE_profiles:PS50294,hmmpanther:PTHR22851:SF0,hmmpanther:PTHR22851,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATGTGGAC	.	5	ESCA
CSMD3	0	.	GRCh37	8	113236720	113236720	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*280G>T	.	.	ENST00000297405	71/71	66	55	10	34	34	0	CSMD3,3_prime_UTR_variant,,ENST00000352409,;CSMD3,3_prime_UTR_variant,,ENST00000455883,;CSMD3,3_prime_UTR_variant,,ENST00000297405,;CSMD3,3_prime_UTR_variant,,ENST00000339701,;CSMD3,3_prime_UTR_variant,,ENST00000343508,;CSMD3,non_coding_transcript_exon_variant,,ENST00000534172,;	A	ENSG00000164796	ENST00000297405	Transcript	3_prime_UTR_variant	11649	.	.	.	.	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	.	.	71/71	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATGCAAATA	.	5	ESCA
FAM91A1	0	.	GRCh37	8	124790938	124790938	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.475A>G	p.Ile159Val	p.I159V	ENST00000334705	6/24	146	124	22	61	61	0	FAM91A1,missense_variant,p.Ile159Val,ENST00000334705,;FAM91A1,missense_variant,p.Ile159Val,ENST00000521166,;FAM91A1,missense_variant,p.Ile159Val,ENST00000519721,;FAM91A1,upstream_gene_variant,,ENST00000517912,;FAM91A1,upstream_gene_variant,,ENST00000521704,;	G	ENSG00000176853	ENST00000334705	Transcript	missense_variant	721	475	159	I/V	Ata/Gta	.	.	.	1	FAM91A1	HGNC	26306	protein_coding	YES	CCDS6346.2	ENSP00000335082	F91A1_HUMAN	H0YC80_HUMAN	UPI0000E5AF4E	.	tolerated(0.41)	benign(0.001)	6/24	.	Pfam_domain:PF14647	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCAATAAAG	.	5	ESCA
ADCY8	0	.	GRCh37	8	132052045	132052045	+	Missense_Mutation	SNP	G	G	A	rs773742788	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535C>T	p.Arg179Cys	p.R179C	ENST00000286355	1/18	51	39	12	37	37	0	ADCY8,missense_variant,p.Arg179Cys,ENST00000286355,;ADCY8,missense_variant,p.Arg179Cys,ENST00000377928,;	A	ENSG00000155897	ENST00000286355	Transcript	missense_variant	2628	535	179	R/C	Cgc/Tgc	rs773742788,COSM1182043	.	.	-1	ADCY8	HGNC	239	protein_coding	YES	CCDS6363.1	ENSP00000286355	ADCY8_HUMAN	E5RFR2_HUMAN	UPI000012887C	.	deleterious(0)	probably_damaging(0.929)	1/18	.	hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF229	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGCGCCTTT	byFrequency	5	ESCA
PLEC	0	.	GRCh37	8	144996545	144996545	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7855G>C	p.Glu2619Gln	p.E2619Q	ENST00000322810	32/32	46	32	13	42	42	0	PLEC,missense_variant,p.Glu2619Gln,ENST00000322810,;PLEC,missense_variant,p.Glu2505Gln,ENST00000527096,;PLEC,missense_variant,p.Glu52Gln,ENST00000527303,;PLEC,missense_variant,p.Glu2482Gln,ENST00000345136,;PLEC,missense_variant,p.Glu2486Gln,ENST00000357649,;PLEC,missense_variant,p.Glu2450Gln,ENST00000398774,;PLEC,missense_variant,p.Glu2482Gln,ENST00000354589,;PLEC,missense_variant,p.Glu2468Gln,ENST00000356346,;PLEC,missense_variant,p.Glu2509Gln,ENST00000436759,;PLEC,missense_variant,p.Glu2460Gln,ENST00000354958,;	G	ENSG00000178209	ENST00000322810	Transcript	missense_variant	8025	7855	2619	E/Q	Gag/Cag	COSM136695	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	possibly_damaging(0.87)	32/32	.	hmmpanther:PTHR11915:SF247,hmmpanther:PTHR11915,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTCCTGCT	.	5	ESCA
PLEC	0	.	GRCh37	8	144996723	144996723	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7785G>C	p.Glu2595Asp	p.E2595D	ENST00000322810	31/32	87	62	24	61	61	0	PLEC,missense_variant,p.Glu2595Asp,ENST00000322810,;PLEC,missense_variant,p.Glu2481Asp,ENST00000527096,;PLEC,missense_variant,p.Glu2458Asp,ENST00000345136,;PLEC,missense_variant,p.Glu2462Asp,ENST00000357649,;PLEC,missense_variant,p.Glu2426Asp,ENST00000398774,;PLEC,missense_variant,p.Glu2458Asp,ENST00000354589,;PLEC,missense_variant,p.Glu2444Asp,ENST00000356346,;PLEC,missense_variant,p.Glu2485Asp,ENST00000436759,;PLEC,missense_variant,p.Glu2436Asp,ENST00000354958,;PLEC,intron_variant,,ENST00000527303,;	G	ENSG00000178209	ENST00000322810	Transcript	missense_variant	7955	7785	2595	E/D	gaG/gaC	COSM3779026,COSM3779029,COSM3779028,COSM3779031,COSM3779030,COSM3779027	.	.	-1	PLEC	HGNC	9069	protein_coding	YES	CCDS43772.1	ENSP00000323856	PLEC_HUMAN	Q96IE3_HUMAN,E9PQ28_HUMAN	UPI0000233FCD	.	.	probably_damaging(0.989)	31/32	.	hmmpanther:PTHR11915:SF247,hmmpanther:PTHR11915,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCTCACG	.	5	ESCA
ZNF252P	0	.	GRCh37	8	146203408	146203408	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.777G>T	.	.	ENST00000426361	3/3	164	123	40	56	56	0	ZNF252P,non_coding_transcript_exon_variant,,ENST00000426361,;ZNF252P,downstream_gene_variant,,ENST00000528392,;ZNF252P,downstream_gene_variant,,ENST00000527222,;ZNF252P,non_coding_transcript_exon_variant,,ENST00000427606,;ZNF252P,non_coding_transcript_exon_variant,,ENST00000592792,;ZNF252P,non_coding_transcript_exon_variant,,ENST00000355436,;	A	ENSG00000196922	ENST00000426361	Transcript	non_coding_transcript_exon_variant	777	.	.	.	.	.	.	.	-1	ZNF252P	HGNC	13046	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTCCACAC	.	5	ESCA
RPL23AP53	0	.	GRCh37	8	163319	163319	+	RNA	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.603G>C	.	.	ENST00000606975	3/3	60	49	11	49	49	0	RPL23AP53,non_coding_transcript_exon_variant,,ENST00000606975,;RPL23AP53,non_coding_transcript_exon_variant,,ENST00000521854,;	G	ENSG00000223508	ENST00000606975	Transcript	non_coding_transcript_exon_variant	603	.	.	.	.	.	.	.	-1	RPL23AP53	HGNC	35921	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GTTCTCTTTAT	.	4	ESCA
ZMAT4	0	.	GRCh37	8	40389215	40389215	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*527G>A	.	.	ENST00000297737	7/7	72	61	10	47	47	0	ZMAT4,3_prime_UTR_variant,,ENST00000297737,;ZMAT4,3_prime_UTR_variant,,ENST00000315769,;	T	ENSG00000165061	ENST00000297737	Transcript	3_prime_UTR_variant	1364	.	.	.	.	.	.	.	-1	ZMAT4	HGNC	25844	protein_coding	YES	CCDS34885.1	ENSP00000297737	ZMAT4_HUMAN	E5RIF5_HUMAN	UPI0000046C33	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGAACGGAGA	.	4	ESCA
GRIN3A	0	.	GRCh37	9	104499884	104499884	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378C>T	p.%3D	p.D126D	ENST00000361820	1/9	18	13	4	21	21	0	GRIN3A,synonymous_variant,p.%3D,ENST00000361820,;	A	ENSG00000198785	ENST00000361820	Transcript	synonymous_variant	979	378	126	D	gaC/gaT	.	.	.	-1	GRIN3A	HGNC	16767	protein_coding	YES	CCDS6758.1	ENSP00000355155	NMD3A_HUMAN	.	UPI0000367661	.	.	.	1/9	.	Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGGGCGTCCCG	.	4	ESCA
TTC16	0	.	GRCh37	9	130493299	130493299	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2237C>G	p.Ser746Cys	p.S746C	ENST00000373289	14/14	54	51	3	89	89	0	TTC16,missense_variant,p.Ser746Cys,ENST00000373289,;TOR2A,downstream_gene_variant,,ENST00000336067,;TOR2A,downstream_gene_variant,,ENST00000458505,;TOR2A,downstream_gene_variant,,ENST00000373281,;TTC16,downstream_gene_variant,,ENST00000393748,;TOR2A,downstream_gene_variant,,ENST00000373284,;TTC16,non_coding_transcript_exon_variant,,ENST00000488285,;TTC16,non_coding_transcript_exon_variant,,ENST00000489226,;TOR2A,downstream_gene_variant,,ENST00000463256,;TOR2A,downstream_gene_variant,,ENST00000494135,;TOR2A,downstream_gene_variant,,ENST00000496460,;TOR2A,downstream_gene_variant,,ENST00000472723,;TOR2A,downstream_gene_variant,,ENST00000493439,;TOR2A,downstream_gene_variant,,ENST00000463577,;	G	ENSG00000167094	ENST00000373289	Transcript	missense_variant	2317	2237	746	S/C	tCc/tGc	.	.	.	1	TTC16	HGNC	26536	protein_coding	YES	CCDS6875.1	ENSP00000362386	TTC16_HUMAN	.	UPI000006FE14	.	deleterious(0.02)	possibly_damaging(0.706)	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCTCCAGCG	.	2	ESCA
FIBCD1	0	.	GRCh37	9	133780706	133780706	+	Silent	SNP	G	G	A	rs202150215	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041C>T	p.%3D	p.Y347Y	ENST00000372338	6/7	46	25	20	54	54	0	FIBCD1,synonymous_variant,p.%3D,ENST00000448616,;FIBCD1,synonymous_variant,p.%3D,ENST00000372337,;FIBCD1,synonymous_variant,p.%3D,ENST00000372338,;FIBCD1,intron_variant,,ENST00000444139,;FIBCD1,intron_variant,,ENST00000253018,;	A	ENSG00000130720	ENST00000372338	Transcript	synonymous_variant	1284	1041	347	Y	taC/taT	rs202150215,COSM297506	.	.	-1	FIBCD1	HGNC	25922	protein_coding	YES	CCDS6937.1	ENSP00000361413	FBCD1_HUMAN	A7YSM1_HUMAN,A3KFJ8_HUMAN	UPI0000049DF9	.	.	.	6/7	.	PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF45,Gene3D:3.90.215.10,Pfam_domain:PF00147,SMART_domains:SM00186,Superfamily_domains:SSF56496	A:0.0004	A:0	A:0	.	A:0.001	A:0	A:0.001	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCGTAGCG	byFrequency|byCluster|by1000G	5	ESCA
UBAP2	0	.	GRCh37	9	33941666	33941666	+	Nonsense_Mutation	SNP	G	G	C	rs552066686	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1910C>G	p.Ser637Ter	p.S637*	ENST00000379238	16/29	39	20	19	21	21	0	UBAP2,stop_gained,p.Ser270Ter,ENST00000379225,;UBAP2,stop_gained,p.Ser637Ter,ENST00000379238,;UBAP2,stop_gained,p.Ser370Ter,ENST00000379239,;UBAP2,stop_gained,p.Ser584Ter,ENST00000418786,;UBAP2,stop_gained,p.Ser637Ter,ENST00000449054,;UBAP2,stop_gained,p.Ser392Ter,ENST00000539807,;UBAP2,stop_gained,p.Ser637Ter,ENST00000360802,;UBAP2,downstream_gene_variant,,ENST00000412543,;UBAP2,stop_gained,p.Ser15Ter,ENST00000488443,;	C	ENSG00000137073	ENST00000379238	Transcript	stop_gained	2028	1910	637	S/*	tCa/tGa	rs552066686	.	.	-1	UBAP2	HGNC	14185	protein_coding	YES	CCDS6547.1	ENSP00000368540	UBAP2_HUMAN	Q5JV03_HUMAN	UPI0000140784	.	.	.	16/29	.	hmmpanther:PTHR16308,hmmpanther:PTHR16308:SF17	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTGACTCT	byFrequency|by1000G	5	ESCA
RUSC2	0	.	GRCh37	9	35561273	35561273	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4445G>C	p.Gly1482Ala	p.G1482A	ENST00000455600	12/12	44	16	27	53	53	0	RUSC2,missense_variant,p.Gly1482Ala,ENST00000361226,;RUSC2,missense_variant,p.Gly1482Ala,ENST00000455600,;FAM166B,downstream_gene_variant,,ENST00000399742,;FAM166B,downstream_gene_variant,,ENST00000478246,;FAM166B,downstream_gene_variant,,ENST00000480287,;FAM166B,downstream_gene_variant,,ENST00000492890,;FAM166B,downstream_gene_variant,,ENST00000447837,;	C	ENSG00000198853	ENST00000455600	Transcript	missense_variant	5014	4445	1482	G/A	gGa/gCa	.	.	.	1	RUSC2	HGNC	23625	protein_coding	YES	CCDS35008.1	ENSP00000393922	RUSC2_HUMAN	.	UPI00001C1EB0	.	tolerated(0.91)	benign(0.036)	12/12	.	PROSITE_profiles:PS50002,hmmpanther:PTHR15591,hmmpanther:PTHR15591:SF14,Pfam_domain:PF07653,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGGAGACT	.	5	ESCA
SLITRK4	0	.	GRCh37	X	142718078	142718078	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.847G>C	p.Gly283Arg	p.G283R	ENST00000381779	2/2	80	50	30	32	32	0	SLITRK4,missense_variant,p.Gly283Arg,ENST00000381779,;SLITRK4,missense_variant,p.Gly283Arg,ENST00000338017,;SLITRK4,missense_variant,p.Gly283Arg,ENST00000356928,;	G	ENSG00000179542	ENST00000381779	Transcript	missense_variant	1073	847	283	G/R	Ggc/Cgc	.	.	.	-1	SLITRK4	HGNC	23502	protein_coding	YES	CCDS14679.1	ENSP00000371198	SLIK4_HUMAN	.	UPI000004E650	.	tolerated(0.37)	possibly_damaging(0.526)	2/2	.	hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGCCATTTT	.	5	ESCA
MAGEA3	0	.	GRCh37	X	151934867	151934867	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*355G>A	.	.	ENST00000393902	3/3	97	55	42	42	42	0	MAGEA3,3_prime_UTR_variant,,ENST00000393902,;MAGEA3,3_prime_UTR_variant,,ENST00000370278,;MAGEA3,downstream_gene_variant,,ENST00000417212,;	T	ENSG00000221867	ENST00000393902	Transcript	3_prime_UTR_variant	1868	.	.	.	.	.	.	.	-1	MAGEA3	HGNC	6801	protein_coding	YES	CCDS14715.1	ENSP00000377480	MAGA3_HUMAN	E7EMU0_HUMAN,B9A060_HUMAN	UPI0000062194	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGTCACAAT	.	5	ESCA
REPS2	0	.	GRCh37	X	17165604	17165605	+	3'UTR	INS	-	-	C	rs751015675	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7dupC	.	.	ENST00000357277	18/18	41	16	25	22	22	0	REPS2,3_prime_UTR_variant,,ENST00000380064,;REPS2,3_prime_UTR_variant,,ENST00000357277,;REPS2,3_prime_UTR_variant,,ENST00000303843,;REPS2,non_coding_transcript_exon_variant,,ENST00000469714,;REPS2,non_coding_transcript_exon_variant,,ENST00000470686,;	C	ENSG00000169891	ENST00000357277	Transcript	3_prime_UTR_variant	2154-2155	.	.	.	.	rs751015675	.	.	1	REPS2	HGNC	9963	protein_coding	YES	CCDS14180.2	ENSP00000349824	REPS2_HUMAN	.	UPI00001BBB18	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTGTGACCCCC	.	2	ESCA
KDM5C	0	.	GRCh37	X	53223826	53223826	+	Missense_Mutation	SNP	G	G	A	rs370672146	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3533C>T	p.Ser1178Leu	p.S1178L	ENST00000375401	23/26	36	16	19	38	38	0	KDM5C,missense_variant,p.Ser1111Leu,ENST00000452825,;KDM5C,missense_variant,p.Ser1137Leu,ENST00000375383,;KDM5C,missense_variant,p.Ser1178Leu,ENST00000375379,;KDM5C,missense_variant,p.Ser1178Leu,ENST00000375401,;KDM5C,missense_variant,p.Ser1177Leu,ENST00000404049,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,;	A	ENSG00000126012	ENST00000375401	Transcript	missense_variant	4066	3533	1178	S/L	tCg/tTg	rs370672146	.	.	-1	KDM5C	HGNC	11114	protein_coding	YES	CCDS14351.1	ENSP00000364550	KDM5C_HUMAN	.	UPI000013CBE3	.	tolerated(0.22)	benign(0.002)	23/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10694:SF31,hmmpanther:PTHR10694	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTCGATGAT	byCluster	5	ESCA
FAM46D	0	.	GRCh37	X	79698376	79698376	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.338C>A	p.Pro113Gln	p.P113Q	ENST00000538312	5/5	40	7	33	9	9	0	FAM46D,missense_variant,p.Pro113Gln,ENST00000308293,;FAM46D,missense_variant,p.Pro113Gln,ENST00000538312,;	A	ENSG00000174016	ENST00000538312	Transcript	missense_variant	672	338	113	P/Q	cCa/cAa	.	.	.	1	FAM46D	HGNC	28399	protein_coding	YES	CCDS14446.1	ENSP00000443410	FA46D_HUMAN	.	UPI0000073CF3	.	deleterious(0)	probably_damaging(1)	5/5	.	Pfam_domain:PF07984,hmmpanther:PTHR12974:SF30,hmmpanther:PTHR12974	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTACCAAAAG	.	3	ESCA
KLHL4	0	.	GRCh37	X	86873036	86873036	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FO-01A-11D-A387-09	TCGA-LN-A9FO-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.829A>T	p.Lys277Ter	p.K277*	ENST00000373114	4/11	59	42	17	21	21	0	KLHL4,stop_gained,p.Lys277Ter,ENST00000373114,;KLHL4,stop_gained,p.Lys277Ter,ENST00000373119,;	T	ENSG00000102271	ENST00000373114	Transcript	stop_gained	909	829	277	K/*	Aag/Tag	.	.	.	1	KLHL4	HGNC	6355	protein_coding	YES	CCDS14456.1	ENSP00000362206	KLHL4_HUMAN	.	UPI000002ACC4	.	.	.	4/11	.	Superfamily_domains:SSF54695,SMART_domains:SM00225,Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR24412:SF74,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATAAAGCAG	.	5	ESCA
SFXN3	0	.	GRCh37	10	102799314	102799314	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.950A>C	p.Glu317Ala	p.E317A	ENST00000224807	12/12	67	62	5	66	66	0	SFXN3,missense_variant,p.Glu313Ala,ENST00000393459,;SFXN3,missense_variant,p.Glu317Ala,ENST00000224807,;SFXN3,non_coding_transcript_exon_variant,,ENST00000470252,;SFXN3,non_coding_transcript_exon_variant,,ENST00000466982,;SFXN3,downstream_gene_variant,,ENST00000487721,;SFXN3,downstream_gene_variant,,ENST00000465383,;SFXN3,downstream_gene_variant,,ENST00000489434,;	C	ENSG00000107819	ENST00000224807	Transcript	missense_variant	1406	950	317	E/A	gAa/gCa	.	.	.	1	SFXN3	HGNC	16087	protein_coding	YES	CCDS7508.2	ENSP00000224807	SFXN3_HUMAN	.	UPI000006EE3D	.	tolerated(0.26)	benign(0.003)	12/12	.	hmmpanther:PTHR11153:SF20,hmmpanther:PTHR11153,Pfam_domain:PF03820,TIGRFAM_domain:TIGR00798	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTTGAAGTGG	.	2	ESCA
TTC40	0	.	GRCh37	10	134623983	134623983	+	Missense_Mutation	SNP	G	G	T	rs374013049	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7594C>A	p.Arg2532Ser	p.R2532S	ENST00000368586	57/58	81	76	5	53	53	0	TTC40,missense_variant,p.Arg693Ser,ENST00000263170,;TTC40,missense_variant,p.Arg2532Ser,ENST00000368586,;	T	ENSG00000171811	ENST00000368586	Transcript	missense_variant	7695	7594	2532	R/S	Cgt/Agt	rs374013049	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	tolerated_low_confidence(1)	benign(0.002)	57/58	.	.	A:0.0008	A:0	A:0	.	A:0	A:0	A:0.0041	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAACGGCCAA	byFrequency|byCluster|by1000G	2	ESCA
TTC40	0	.	GRCh37	10	134682826	134682826	+	Missense_Mutation	SNP	T	T	A	rs559618044	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4562A>T	p.His1521Leu	p.H1521L	ENST00000368586	33/58	35	31	3	28	28	0	TTC40,missense_variant,p.His1521Leu,ENST00000368586,;TTC40,downstream_gene_variant,,ENST00000368582,;TTC40,downstream_gene_variant,,ENST00000417862,;	A	ENSG00000171811	ENST00000368586	Transcript	missense_variant	4663	4562	1521	H/L	cAt/cTt	rs559618044	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	deleterious(0)	probably_damaging(0.999)	33/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	C:0.0004	C:0	C:0	.	C:0	C:0	C:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCATGGCGC	byFrequency|by1000G	4	ESCA
TTC40	0	.	GRCh37	10	134694436	134694436	+	Missense_Mutation	SNP	C	C	G	rs201792620	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3728G>C	p.Arg1243Pro	p.R1243P	ENST00000368586	28/58	51	47	4	45	45	0	TTC40,missense_variant,p.Arg1243Pro,ENST00000368582,;TTC40,missense_variant,p.Arg1243Pro,ENST00000368586,;TTC40,upstream_gene_variant,,ENST00000417862,;	G	ENSG00000171811	ENST00000368586	Transcript	missense_variant	3829	3728	1243	R/P	cGc/cCc	rs201792620	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	tolerated(0.06)	benign(0.376)	28/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCAGCGGAGG	byCluster|by1000G	2	ESCA
FAM171A1	0	.	GRCh37	10	15254423	15254423	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*491G>A	.	.	ENST00000378116	8/8	60	56	4	44	44	0	FAM171A1,3_prime_UTR_variant,,ENST00000378116,;FAM171A1,downstream_gene_variant,,ENST00000477161,;	T	ENSG00000148468	ENST00000378116	Transcript	3_prime_UTR_variant	3171	.	.	.	.	.	.	.	-1	FAM171A1	HGNC	23522	protein_coding	YES	CCDS31154.1	ENSP00000367356	F1711_HUMAN	.	UPI00001414CA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAATCAGACA	.	2	ESCA
CUBN	0	.	GRCh37	10	16992031	16992031	+	Missense_Mutation	SNP	C	C	A	rs141941868	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5049G>T	p.Leu1683Phe	p.L1683F	ENST00000377833	34/67	66	62	4	47	47	0	CUBN,missense_variant,p.Leu1683Phe,ENST00000377833,;	A	ENSG00000107611	ENST00000377833	Transcript	missense_variant	5115	5049	1683	L/F	ttG/ttT	rs141941868	.	.	-1	CUBN	HGNC	2548	protein_coding	YES	CCDS7113.1	ENSP00000367064	CUBN_HUMAN	B3KQA6_HUMAN	UPI00001AE8F4	.	deleterious(0.02)	possibly_damaging(0.521)	34/67	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF561,hmmpanther:PTHR10127,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	G:0.0006	G:0.0023	G:0	.	G:0	G:0	G:0	G:0.0007	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCATCCAAAAT	byFrequency|byCluster|by1000G	2	ESCA
MALRD1	0	.	GRCh37	10	19856477	19856477	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3662T>G	p.Val1221Gly	p.V1221G	ENST00000377266	20/25	96	84	12	103	103	0	MALRD1,missense_variant,p.Val193Gly,ENST00000377265,;MALRD1,missense_variant,p.Val36Gly,ENST00000455457,;MALRD1,missense_variant,p.Val1208Gly,ENST00000454679,;MALRD1,missense_variant,p.Val1221Gly,ENST00000377266,;	G	ENSG00000204740	ENST00000377266	Transcript	missense_variant	3662	3662	1221	V/G	gTg/gGg	.	.	.	1	MALRD1	HGNC	24331	protein_coding	YES	.	ENSP00000366477	.	U5GXS0_HUMAN	UPI000191551D	.	tolerated(0.17)	benign(0.039)	20/25	.	Superfamily_domains:SSF49899,SMART_domains:SM00137,Pfam_domain:PF00629,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF65,PROSITE_profiles:PS50060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAGTGATTG	.	5	ESCA
NEBL	0	.	GRCh37	10	21074209	21074209	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*467C>T	.	.	ENST00000377122	28/28	37	34	3	21	21	0	NEBL,3_prime_UTR_variant,,ENST00000377122,;NEBL,3_prime_UTR_variant,,ENST00000417816,;NEBL,downstream_gene_variant,,ENST00000377159,;	A	ENSG00000078114	ENST00000377122	Transcript	3_prime_UTR_variant	3909	.	.	.	.	.	.	.	-1	NEBL	HGNC	16932	protein_coding	YES	CCDS7134.1	ENSP00000366326	NEBL_HUMAN	B0YJ47_HUMAN	UPI000012FEE8	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTGGGCAATT	.	2	ESCA
SKIDA1	0	.	GRCh37	10	21805376	21805376	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1376T>C	p.Val459Ala	p.V459A	ENST00000449193	4/4	89	75	14	59	59	0	SKIDA1,missense_variant,p.Val380Ala,ENST00000444772,;SKIDA1,missense_variant,p.Val459Ala,ENST00000449193,;SKIDA1,downstream_gene_variant,,ENST00000487107,;	G	ENSG00000180592	ENST00000449193	Transcript	missense_variant	3629	1376	459	V/A	gTg/gCg	.	.	.	-1	SKIDA1	HGNC	32697	protein_coding	YES	CCDS44363.1	ENSP00000410041	.	E9PAX1_HUMAN	UPI00015386B3	.	deleterious_low_confidence(0.02)	unknown(0)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23187:SF2,hmmpanther:PTHR23187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACACTTGG	.	5	ESCA
CCDC7	0	.	GRCh37	10	32856778	32856778	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1378G>A	p.Gly460Ser	p.G460S	ENST00000362006	16/18	18	13	5	15	15	0	CCDC7,missense_variant,p.Gly460Ser,ENST00000277657,;CCDC7,missense_variant,p.Gly129Ser,ENST00000435402,;CCDC7,missense_variant,p.Gly460Ser,ENST00000362006,;C10ORF68,5_prime_UTR_variant,,ENST00000375028,;C10ORF68,5_prime_UTR_variant,,ENST00000375030,;C10ORF68,non_coding_transcript_exon_variant,,ENST00000572165,;C10ORF68,5_prime_UTR_variant,,ENST00000302316,;CCDC7,3_prime_UTR_variant,,ENST00000476558,;	A	ENSG00000216937	ENST00000362006	Transcript	missense_variant	1921	1378	460	G/S	Ggt/Agt	COSM1128063	.	.	1	CCDC7	HGNC	26533	protein_coding	YES	CCDS7173.1	ENSP00000355078	CCDC7_HUMAN	.	UPI00000745EB	.	tolerated(0.06)	probably_damaging(0.927)	16/18	.	hmmpanther:PTHR22035:SF4,hmmpanther:PTHR22035	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCAGGTGGA	.	5	ESCA
PARD3	0	.	GRCh37	10	34408625	34408625	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3593C>T	p.Ser1198Phe	p.S1198F	ENST00000374789	24/25	73	62	10	59	59	0	PARD3,missense_variant,p.Ser1108Phe,ENST00000545260,;PARD3,missense_variant,p.Ser1182Phe,ENST00000545693,;PARD3,missense_variant,p.Ser1195Phe,ENST00000374788,;PARD3,missense_variant,p.Ser1138Phe,ENST00000374790,;PARD3,missense_variant,p.Ser1086Phe,ENST00000374794,;PARD3,missense_variant,p.Ser1152Phe,ENST00000350537,;PARD3,missense_variant,p.Ser1198Phe,ENST00000374789,;PARD3,missense_variant,p.Ser1161Phe,ENST00000346874,;	A	ENSG00000148498	ENST00000374789	Transcript	missense_variant	3919	3593	1198	S/F	tCc/tTc	.	.	.	-1	PARD3	HGNC	16051	protein_coding	YES	CCDS7178.1	ENSP00000363921	PARD3_HUMAN	.	UPI0000073A9F	.	deleterious_low_confidence(0.01)	probably_damaging(0.997)	24/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16484:SF10,hmmpanther:PTHR16484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACGGACACC	.	4	ESCA
CCNY	0	.	GRCh37	10	35819102	35819102	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510G>T	p.Gln170His	p.Q170H	ENST00000374704	7/10	62	48	13	41	41	0	CCNY,missense_variant,p.Gln170His,ENST00000374704,;CCNY,missense_variant,p.Gln116His,ENST00000265375,;CCNY,missense_variant,p.Gln145His,ENST00000339497,;CCNY,missense_variant,p.Gln116His,ENST00000374706,;CCNY,downstream_gene_variant,,ENST00000493157,;CCNY,non_coding_transcript_exon_variant,,ENST00000492478,;CCNY,non_coding_transcript_exon_variant,,ENST00000465416,;CCNY,upstream_gene_variant,,ENST00000497692,;	T	ENSG00000108100	ENST00000374704	Transcript	missense_variant	690	510	170	Q/H	caG/caT	.	.	.	1	CCNY	HGNC	23354	protein_coding	YES	CCDS7189.1	ENSP00000363836	CCNY_HUMAN	R4GN48_HUMAN	UPI000013EFE5	.	tolerated(0.55)	benign(0.024)	7/10	.	hmmpanther:PTHR14248,Pfam_domain:PF00134,PIRSF_domain:PIRSF028934,Superfamily_domains:SSF47954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCAGATTTA	.	5	ESCA
ZNF33A	0	.	GRCh37	10	38343809	38343809	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757G>C	p.Gly253Arg	p.G253R	ENST00000374618	5/5	69	58	10	37	37	0	ZNF33A,missense_variant,p.Gly259Arg,ENST00000432900,;ZNF33A,missense_variant,p.Gly252Arg,ENST00000307441,;ZNF33A,missense_variant,p.Gly252Arg,ENST00000458705,;ZNF33A,missense_variant,p.Gly253Arg,ENST00000374618,;ZNF33A,intron_variant,,ENST00000469037,;ZNF33A,downstream_gene_variant,,ENST00000478556,;	C	ENSG00000189180	ENST00000374618	Transcript	missense_variant	935	757	253	G/R	Ggg/Cgg	.	.	.	1	ZNF33A	HGNC	13096	protein_coding	YES	CCDS44372.1	ENSP00000363747	ZN33A_HUMAN	.	UPI0000161788	.	tolerated(0.22)	benign(0.191)	5/5	.	hmmpanther:PTHR24377:SF204,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTGGGAGA	.	5	ESCA
RET	0	.	GRCh37	10	43615577	43615577	+	Silent	SNP	C	C	A	rs146838520	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2656C>A	p.%3D	p.R886R	ENST00000355710	15/20	70	61	9	61	61	0	RET,synonymous_variant,p.%3D,ENST00000340058,;RET,synonymous_variant,p.%3D,ENST00000355710,;	A	ENSG00000165731	ENST00000355710	Transcript	synonymous_variant	2888	2656	886	R	Cgg/Agg	CM061929,rs146838520	.	.	1	RET	HGNC	9967	protein_coding	YES	CCDS7200.1	ENSP00000347942	RET_HUMAN	Q9UQV8_HUMAN,Q9UM90_HUMAN,Q9UE13_HUMAN,Q8NFE8_HUMAN,Q8IZR8_HUMAN	UPI00001336E1	.	.	.	15/20	.	Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000631,SMART_domains:SM00219,Gene3D:1.10.510.10,Pfam_domain:PF07714,hmmpanther:PTHR24416:SF264,hmmpanther:PTHR24416,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	T:0.0002	T:0	uncertain_significance	.	16712668	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.A883F|c.2647_2648GC>TT|6,BUFFER|p.A883S|c.2647G>T|3	RADIA|MUTECT|MUSE|VARSCANS	AGGGGCGGAAG	byCluster	4	ESCA
ARHGAP22	0	.	GRCh37	10	49654430	49654430	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4G>T	.	.	ENST00000417912	10/10	87	78	9	76	76	0	ARHGAP22,3_prime_UTR_variant,,ENST00000435790,;ARHGAP22,3_prime_UTR_variant,,ENST00000374170,;ARHGAP22,3_prime_UTR_variant,,ENST00000249601,;ARHGAP22,3_prime_UTR_variant,,ENST00000374172,;ARHGAP22,3_prime_UTR_variant,,ENST00000477708,;ARHGAP22,3_prime_UTR_variant,,ENST00000417912,;ARHGAP22,3_prime_UTR_variant,,ENST00000417247,;ARHGAP22,downstream_gene_variant,,ENST00000460425,;	A	ENSG00000128805	ENST00000417912	Transcript	3_prime_UTR_variant	2305	.	.	.	.	.	.	.	-1	ARHGAP22	HGNC	30320	protein_coding	YES	CCDS58080.1	ENSP00000412461	RHG22_HUMAN	A6NHM7_HUMAN	UPI0000E5BE9D	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATTCCTTTT	.	4	ESCA
WDFY4	0	.	GRCh37	10	50165273	50165273	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8077C>A	p.Pro2693Thr	p.P2693T	ENST00000325239	51/61	62	54	7	57	57	0	WDFY4,missense_variant,p.Pro2693Thr,ENST00000325239,;WDFY4,missense_variant,p.Pro780Thr,ENST00000265453,;WDFY4,3_prime_UTR_variant,,ENST00000413659,;WDFY4,non_coding_transcript_exon_variant,,ENST00000465910,;	A	ENSG00000128815	ENST00000325239	Transcript	missense_variant	8104	8077	2693	P/T	Cca/Aca	.	.	.	1	WDFY4	HGNC	29323	protein_coding	YES	CCDS44385.1	ENSP00000320563	WDFY4_HUMAN	Q6PIM1_HUMAN	UPI000176ADB8	.	deleterious(0)	probably_damaging(1)	51/61	.	PROSITE_profiles:PS50197,hmmpanther:PTHR13743:SF52,hmmpanther:PTHR13743,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACCCCAGAG	.	4	ESCA
OGDHL	0	.	GRCh37	10	50953480	50953480	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1539G>T	p.Met513Ile	p.M513I	ENST00000374103	12/23	57	46	10	50	50	0	OGDHL,missense_variant,p.Met304Ile,ENST00000432695,;OGDHL,missense_variant,p.Met456Ile,ENST00000419399,;OGDHL,missense_variant,p.Met513Ile,ENST00000374103,;OGDHL,upstream_gene_variant,,ENST00000496884,;	A	ENSG00000197444	ENST00000374103	Transcript	missense_variant	1625	1539	513	M/I	atG/atT	COSM1505350	.	.	-1	OGDHL	HGNC	25590	protein_coding	YES	CCDS7234.1	ENSP00000363216	OGDHL_HUMAN	.	UPI000013D6A4	.	deleterious(0)	probably_damaging(1)	12/23	.	Superfamily_domains:SSF52518,PIRSF_domain:PIRSF000157,Gene3D:3.40.50.970,Pfam_domain:PF00676,TIGRFAM_domain:TIGR00239,hmmpanther:PTHR23152:SF5,hmmpanther:PTHR23152	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTACATGAG	.	5	ESCA
AKR1C4	0	.	GRCh37	10	5260694	5260694	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.943C>A	p.Pro315Thr	p.P315T	ENST00000380448	11/11	60	53	7	49	49	0	AKR1C4,missense_variant,p.Pro315Thr,ENST00000380448,;AKR1C4,missense_variant,p.Pro315Thr,ENST00000263126,;	A	ENSG00000198610	ENST00000380448	Transcript	missense_variant	1196	943	315	P/T	Cct/Act	.	.	.	1	AKR1C4	HGNC	387	protein_coding	YES	CCDS7064.1	ENSP00000369814	AK1C4_HUMAN	Q96SD9_HUMAN	UPI000013D3B2	.	deleterious(0.01)	benign(0.014)	11/11	.	hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF134,Gene3D:3.20.20.100,PIRSF_domain:PIRSF000097,Superfamily_domains:SSF51430	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCATCCTGAT	.	4	ESCA
CALML5	0	.	GRCh37	10	5541125	5541125	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277G>T	p.Asp93Tyr	p.D93Y	ENST00000380332	1/1	14	10	3	10	10	0	CALML5,missense_variant,p.Asp93Tyr,ENST00000380332,;	A	ENSG00000178372	ENST00000380332	Transcript	missense_variant	409	277	93	D/Y	Gat/Tat	.	.	.	-1	CALML5	HGNC	18180	protein_coding	YES	CCDS7068.1	ENSP00000369689	CALL5_HUMAN	.	UPI0000049C8F	.	deleterious(0)	probably_damaging(0.988)	1/1	.	PROSITE_profiles:PS50222,hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF18,PROSITE_patterns:PS00018,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCATCCTGGT	.	2	ESCA
LRRTM3	0	.	GRCh37	10	68857758	68857758	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*204C>G	.	.	ENST00000361320	3/3	40	32	8	36	36	0	LRRTM3,3_prime_UTR_variant,,ENST00000361320,;CTNNA3,intron_variant,,ENST00000433211,;CTNNA3,intron_variant,,ENST00000494580,;CTNNA3,intron_variant,,ENST00000373744,;LRRTM3,downstream_gene_variant,,ENST00000485868,;	G	ENSG00000198739	ENST00000361320	Transcript	3_prime_UTR_variant	2528	.	.	.	.	.	.	.	1	LRRTM3	HGNC	19410	protein_coding	YES	CCDS7270.1	ENSP00000355187	LRRT3_HUMAN	B4DFC3_HUMAN	UPI0000088C0F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTGCAGTAT	.	5	ESCA
HKDC1	0	.	GRCh37	10	71008284	71008284	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1370C>A	p.Thr457Asn	p.T457N	ENST00000354624	10/18	63	56	7	53	53	0	HKDC1,missense_variant,p.Thr457Asn,ENST00000354624,;HKDC1,missense_variant,p.Thr457Asn,ENST00000395086,;HKDC1,non_coding_transcript_exon_variant,,ENST00000488706,;	A	ENSG00000156510	ENST00000354624	Transcript	missense_variant	1503	1370	457	T/N	aCc/aAc	.	.	.	1	HKDC1	HGNC	23302	protein_coding	YES	CCDS7288.1	ENSP00000346643	HKDC1_HUMAN	.	UPI00003666D2	.	deleterious(0)	probably_damaging(0.992)	10/18	.	Superfamily_domains:SSF53067,Superfamily_domains:SSF53067,Gene3D:3.40.367.20,Pfam_domain:PF03727,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTGACCGCGG	.	4	ESCA
TBATA	0	.	GRCh37	10	72543169	72543169	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-34G>C	.	.	ENST00000299290	3/11	41	38	3	35	35	0	TBATA,5_prime_UTR_variant,,ENST00000299290,;TBATA,upstream_gene_variant,,ENST00000545575,;TBATA,upstream_gene_variant,,ENST00000456372,;	G	ENSG00000166220	ENST00000299290	Transcript	5_prime_UTR_variant	357	.	.	.	.	.	.	.	-1	TBATA	HGNC	23511	protein_coding	YES	CCDS7308.1	ENSP00000299290	TBATA_HUMAN	.	UPI000013E57C	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCACTTAAT	.	2	ESCA
CDH23	0	.	GRCh37	10	73571509	73571509	+	Silent	SNP	T	T	A	rs771040325	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2598T>A	p.%3D	p.A866A	ENST00000398788	18/23	51	46	5	54	54	0	CDH23,synonymous_variant,p.%3D,ENST00000398788,;CDH23,synonymous_variant,p.%3D,ENST00000224721,;PSAP,downstream_gene_variant,,ENST00000394934,;PSAP,downstream_gene_variant,,ENST00000394936,;CDH23,splice_region_variant,,ENST00000475158,;	A	ENSG00000107736	ENST00000398788	Transcript	synonymous_variant	2915	2598	866	A	gcT/gcA	rs771040325	.	.	1	CDH23	HGNC	13733	protein_coding	YES	CCDS53540.1	ENSP00000381768	CAD23_HUMAN	.	UPI0000496839	.	.	.	18/23	.	hmmpanther:PTHR24027:SF277,hmmpanther:PTHR24027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAGCTGGTAA	.	4	ESCA
SPOCK2	0	.	GRCh37	10	73820158	73820158	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2360C>A	.	.	ENST00000373109	11/11	37	33	4	21	21	0	SPOCK2,3_prime_UTR_variant,,ENST00000373109,;SPOCK2,3_prime_UTR_variant,,ENST00000536168,;SPOCK2,3_prime_UTR_variant,,ENST00000317376,;SPOCK2,downstream_gene_variant,,ENST00000460053,;SPOCK2,downstream_gene_variant,,ENST00000463279,;SPOCK2,downstream_gene_variant,,ENST00000469121,;	T	ENSG00000107742	ENST00000373109	Transcript	3_prime_UTR_variant	4080	.	.	.	.	.	.	.	-1	SPOCK2	HGNC	13564	protein_coding	YES	CCDS7313.1	ENSP00000362201	TICN2_HUMAN	B4DFA9_HUMAN	UPI0000136F51	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCACGTGTCC	.	2	ESCA
ASCC1	0	.	GRCh37	10	73912705	73912705	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.752G>T	p.Gly251Val	p.G251V	ENST00000342444	8/13	87	72	14	53	53	0	ASCC1,missense_variant,p.Gly251Val,ENST00000394915,;ASCC1,missense_variant,p.Gly223Val,ENST00000394919,;ASCC1,missense_variant,p.Gly21Val,ENST00000530394,;ASCC1,missense_variant,p.Gly155Val,ENST00000486689,;ASCC1,missense_variant,p.Gly245Val,ENST00000545550,;ASCC1,missense_variant,p.Gly223Val,ENST00000317126,;ASCC1,missense_variant,p.Gly251Val,ENST00000342444,;ASCC1,missense_variant,p.Gly223Val,ENST00000317168,;ASCC1,intron_variant,,ENST00000525286,;ASCC1,non_coding_transcript_exon_variant,,ENST00000526801,;	A	ENSG00000138303	ENST00000342444	Transcript	missense_variant	854	752	251	G/V	gGg/gTg	.	.	.	-1	ASCC1	HGNC	24268	protein_coding	YES	CCDS55713.1	ENSP00000339404	ASCC1_HUMAN	E9PJM2_HUMAN	UPI000006F7E9	.	deleterious(0)	probably_damaging(1)	8/13	.	Superfamily_domains:SSF55144,PIRSF_domain:PIRSF027019,Gene3D:3.90.1140.10,Pfam_domain:PF10469,hmmpanther:PTHR13360,hmmpanther:PTHR13360:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATCCCTGCC	.	5	ESCA
LDB3	0	.	GRCh37	10	88466294	88466294	+	Intron	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1101-3368T>A	.	.	ENST00000429277	.	144	137	7	90	90	0	LDB3,synonymous_variant,p.%3D,ENST00000361373,;LDB3,intron_variant,,ENST00000352360,;LDB3,intron_variant,,ENST00000458213,;LDB3,intron_variant,,ENST00000263066,;LDB3,intron_variant,,ENST00000429277,;	A	ENSG00000122367	ENST00000429277	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LDB3	HGNC	15710	protein_coding	YES	CCDS53550.1	ENSP00000401437	LDB3_HUMAN	.	UPI00017A876A	.	.	.	.	8/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACCCCTATTGA	.	2	ESCA
ATAD1	0	.	GRCh37	10	89514503	89514503	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027A>G	p.Met343Val	p.M343V	ENST00000308448	10/10	77	72	5	70	70	0	ATAD1,missense_variant,p.Met343Val,ENST00000308448,;ATAD1,missense_variant,p.Met255Val,ENST00000400215,;ATAD1,missense_variant,p.Met343Val,ENST00000328142,;	C	ENSG00000138138	ENST00000308448	Transcript	missense_variant	1406	1027	343	M/V	Atg/Gtg	.	.	.	-1	ATAD1	HGNC	25903	protein_coding	YES	CCDS7386.1	ENSP00000339017	ATAD1_HUMAN	.	UPI000000B2DE	.	tolerated(0.07)	benign(0.009)	10/10	.	Superfamily_domains:SSF52540,Gene3D:1.10.8.60,hmmpanther:PTHR23074:SF73,hmmpanther:PTHR23074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCATCTTTT	.	2	ESCA
DSCAML1	0	.	GRCh37	11	117395568	117395568	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1069A>T	p.Thr357Ser	p.T357S	ENST00000321322	5/33	76	66	10	75	75	0	DSCAML1,missense_variant,p.Thr87Ser,ENST00000527706,;DSCAML1,missense_variant,p.Thr357Ser,ENST00000321322,;	A	ENSG00000177103	ENST00000321322	Transcript	missense_variant	1071	1069	357	T/S	Acc/Tcc	.	.	.	-1	DSCAML1	HGNC	14656	protein_coding	YES	CCDS8384.1	ENSP00000315465	DSCL1_HUMAN	.	UPI00000726E2	.	tolerated(0.9)	benign(0.006)	5/33	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTGGTGACCT	.	4	ESCA
PHLDB1	0	.	GRCh37	11	118499143	118499143	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1604G>A	p.Ser535Asn	p.S535N	ENST00000361417	7/24	81	74	6	73	73	0	PHLDB1,missense_variant,p.Ser535Asn,ENST00000361417,;PHLDB1,missense_variant,p.Ser535Asn,ENST00000356063,;PHLDB1,intron_variant,,ENST00000530708,;PHLDB1,upstream_gene_variant,,ENST00000534140,;PHLDB1,downstream_gene_variant,,ENST00000526670,;PHLDB1,downstream_gene_variant,,ENST00000526374,;PHLDB1,downstream_gene_variant,,ENST00000532639,;PHLDB1,upstream_gene_variant,,ENST00000534672,;PHLDB1,downstream_gene_variant,,ENST00000527259,;PHLDB1,missense_variant,p.Ser535Asn,ENST00000530994,;PHLDB1,missense_variant,p.Ser535Asn,ENST00000528594,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000532517,;PHLDB1,upstream_gene_variant,,ENST00000525698,;PHLDB1,upstream_gene_variant,,ENST00000531862,;	A	ENSG00000019144	ENST00000361417	Transcript	missense_variant	2015	1604	535	S/N	aGt/aAt	.	.	.	1	PHLDB1	HGNC	23697	protein_coding	YES	CCDS8401.1	ENSP00000354498	PHLB1_HUMAN	.	UPI0000192101	.	tolerated(0.09)	benign(0.187)	7/24	.	hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCAGTGGCA	.	2	ESCA
OR10G4	0	.	GRCh37	11	123887127	123887127	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.846C>G	p.%3D	p.L282L	ENST00000320891	1/1	145	138	7	134	134	0	OR10G4,synonymous_variant,p.%3D,ENST00000320891,;	G	ENSG00000254737	ENST00000320891	Transcript	synonymous_variant	846	846	282	L	ctC/ctG	.	.	.	1	OR10G4	HGNC	14809	protein_coding	YES	CCDS31702.1	ENSP00000325076	O10G4_HUMAN	.	UPI0000041BAD	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF6,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCTCAACCC	.	2	ESCA
CCDC15	0	.	GRCh37	11	124845083	124845083	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608G>A	p.Arg203Lys	p.R203K	ENST00000344762	5/16	60	56	4	40	40	0	CCDC15,missense_variant,p.Arg203Lys,ENST00000344762,;CCDC15,missense_variant,p.Arg203Lys,ENST00000529051,;	A	ENSG00000149548	ENST00000344762	Transcript	missense_variant	867	608	203	R/K	aGg/aAg	.	.	.	1	CCDC15	HGNC	25798	protein_coding	YES	CCDS44756.1	ENSP00000341684	CCD15_HUMAN	.	UPI0000EE3BEA	.	tolerated(0.38)	benign(0.138)	5/16	.	hmmpanther:PTHR14817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAAGGAAAA	.	2	ESCA
MUC5B	0	.	GRCh37	11	1263506	1263506	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5396C>A	p.Pro1799Gln	p.P1799Q	ENST00000529681	31/49	29	26	3	48	48	0	MUC5B,missense_variant,p.Pro1799Gln,ENST00000529681,;MUC5B,missense_variant,p.Pro1802Gln,ENST00000447027,;RP11-532E4.2,non_coding_transcript_exon_variant,,ENST00000532061,;MUC5B,downstream_gene_variant,,ENST00000525715,;	A	ENSG00000117983	ENST00000529681	Transcript	missense_variant	5454	5396	1799	P/Q	cCa/cAa	.	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	unknown(0)	31/49	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237,Pfam_domain:PF13330	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCCCAACCT	.	2	ESCA
MUC5B	0	.	GRCh37	11	1272626	1272626	+	Missense_Mutation	SNP	C	C	A	rs375836524	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14516C>A	p.Ser4839Tyr	p.S4839Y	ENST00000529681	31/49	138	126	12	94	94	0	MUC5B,missense_variant,p.Ser4839Tyr,ENST00000529681,;MUC5B,missense_variant,p.Ser4842Tyr,ENST00000447027,;RP11-532E4.2,upstream_gene_variant,,ENST00000532061,;	A	ENSG00000117983	ENST00000529681	Transcript	missense_variant	14574	14516	4839	S/Y	tCc/tAc	rs375836524	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	unknown(0)	31/49	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTGTCCTCCA	byCluster|by1000G	3	ESCA
OPCML	0	.	GRCh37	11	132289974	132289974	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*113A>T	.	.	ENST00000331898	7/7	51	46	5	47	47	0	OPCML,3_prime_UTR_variant,,ENST00000374778,;OPCML,3_prime_UTR_variant,,ENST00000524381,;OPCML,3_prime_UTR_variant,,ENST00000331898,;OPCML,downstream_gene_variant,,ENST00000541867,;OPCML,non_coding_transcript_exon_variant,,ENST00000529038,;	A	ENSG00000183715	ENST00000331898	Transcript	3_prime_UTR_variant	1730	.	.	.	.	.	.	.	-1	OPCML	HGNC	8143	protein_coding	YES	CCDS8492.1	ENSP00000330862	OPCM_HUMAN	B7ZLQ0_HUMAN,B2CZX3_HUMAN,A8K0Y0_HUMAN	UPI0000055AE0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATCTAGAAT	.	4	ESCA
PSMA1	0	.	GRCh37	11	14632583	14632583	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-51C>A	.	.	ENST00000418988	2/11	67	62	5	56	56	0	PSMA1,5_prime_UTR_variant,,ENST00000418988,;PSMA1,non_coding_transcript_exon_variant,,ENST00000528018,;	T	ENSG00000129084	ENST00000418988	Transcript	5_prime_UTR_variant	278	.	.	.	.	.	.	.	-1	PSMA1	HGNC	9530	protein_coding	YES	CCDS31431.1	ENSP00000414359	PSA1_HUMAN	F5GX11_HUMAN	UPI000002B1AC	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTCTGGATTT	.	2	ESCA
TNNT3	0	.	GRCh37	11	1955826	1955826	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531G>A	p.%3D	p.K177K	ENST00000278317	13/16	37	34	3	38	38	0	TNNT3,synonymous_variant,p.%3D,ENST00000381548,;TNNT3,synonymous_variant,p.%3D,ENST00000381557,;TNNT3,synonymous_variant,p.%3D,ENST00000453458,;TNNT3,synonymous_variant,p.%3D,ENST00000381589,;TNNT3,synonymous_variant,p.%3D,ENST00000446240,;TNNT3,synonymous_variant,p.%3D,ENST00000381558,;TNNT3,synonymous_variant,p.%3D,ENST00000360603,;TNNT3,synonymous_variant,p.%3D,ENST00000381563,;TNNT3,synonymous_variant,p.%3D,ENST00000397304,;TNNT3,synonymous_variant,p.%3D,ENST00000381561,;TNNT3,synonymous_variant,p.%3D,ENST00000381549,;TNNT3,synonymous_variant,p.%3D,ENST00000381579,;TNNT3,synonymous_variant,p.%3D,ENST00000397301,;TNNT3,synonymous_variant,p.%3D,ENST00000344578,;TNNT3,synonymous_variant,p.%3D,ENST00000278317,;TNNT3,non_coding_transcript_exon_variant,,ENST00000492075,;TNNT3,non_coding_transcript_exon_variant,,ENST00000493234,;TNNT3,upstream_gene_variant,,ENST00000473100,;	A	ENSG00000130595	ENST00000278317	Transcript	synonymous_variant	750	531	177	K	aaG/aaA	.	.	.	1	TNNT3	HGNC	11950	protein_coding	YES	CCDS7727.1	ENSP00000278317	TNNT3_HUMAN	.	UPI000013DB6C	.	.	.	13/16	.	hmmpanther:PTHR11521,hmmpanther:PTHR11521:SF4,Pfam_domain:PF00992,Gene3D:1.20.5.350,Superfamily_domains:SSF90250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGAAGATTCT	.	2	ESCA
TRPM5	0	.	GRCh37	11	2426099	2426099	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*68C>A	.	.	ENST00000155858	24/24	60	54	6	41	41	0	TRPM5,3_prime_UTR_variant,,ENST00000533881,;TRPM5,3_prime_UTR_variant,,ENST00000452833,;TRPM5,3_prime_UTR_variant,,ENST00000155858,;TRPM5,downstream_gene_variant,,ENST00000533060,;TSSC4,downstream_gene_variant,,ENST00000451491,;TSSC4,downstream_gene_variant,,ENST00000496468,;TSSC4,downstream_gene_variant,,ENST00000437110,;TSSC4,downstream_gene_variant,,ENST00000380992,;TSSC4,downstream_gene_variant,,ENST00000435795,;TSSC4,downstream_gene_variant,,ENST00000485682,;TSSC4,downstream_gene_variant,,ENST00000440813,;TRPM5,downstream_gene_variant,,ENST00000528453,;TSSC4,downstream_gene_variant,,ENST00000380996,;TSSC4,downstream_gene_variant,,ENST00000333256,;AC124057.5,intron_variant,,ENST00000433035,;TSSC4,downstream_gene_variant,,ENST00000467308,;	T	ENSG00000070985	ENST00000155858	Transcript	3_prime_UTR_variant	3575	.	.	.	.	.	.	.	-1	TRPM5	HGNC	14323	protein_coding	YES	CCDS31340.1	ENSP00000155858	TRPM5_HUMAN	.	UPI000003B069	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GCAAAGGTCAG	.	2	ESCA
MUC15	0	.	GRCh37	11	26587248	26587248	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239C>G	p.Ala80Gly	p.A80G	ENST00000436318	2/4	115	108	6	99	99	0	MUC15,missense_variant,p.Ala53Gly,ENST00000455601,;MUC15,missense_variant,p.Ala80Gly,ENST00000281268,;MUC15,missense_variant,p.Ala80Gly,ENST00000527569,;MUC15,missense_variant,p.Ala80Gly,ENST00000436318,;MUC15,missense_variant,p.Ala80Gly,ENST00000529533,;ANO3,intron_variant,,ENST00000537978,;ANO3,intron_variant,,ENST00000531568,;ANO3,intron_variant,,ENST00000525139,;ANO3,intron_variant,,ENST00000256737,;ANO3,downstream_gene_variant,,ENST00000529242,;	C	ENSG00000169550	ENST00000436318	Transcript	missense_variant	373	239	80	A/G	gCa/gGa	.	.	.	-1	MUC15	HGNC	14956	protein_coding	YES	CCDS44557.1	ENSP00000416753	.	E9PII6_HUMAN	UPI0000D4B9CF	.	tolerated_low_confidence(0.16)	benign(0.032)	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTTTGCTTCA	.	2	ESCA
SLC22A18AS	0	.	GRCh37	11	2909808	2909808	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364G>A	p.Ala122Thr	p.A122T	ENST00000533594	4/4	47	41	5	35	35	0	SLC22A18AS,missense_variant,p.Ala122Thr,ENST00000533594,;SLC22A18AS,missense_variant,p.Ala19Thr,ENST00000526203,;SLC22A18AS,missense_variant,p.Ala19Thr,ENST00000455942,;CDKN1C,upstream_gene_variant,,ENST00000380725,;CDKN1C,upstream_gene_variant,,ENST00000440480,;CDKN1C,upstream_gene_variant,,ENST00000414822,;CDKN1C,upstream_gene_variant,,ENST00000430149,;CDKN1C,upstream_gene_variant,,ENST00000313407,;CDKN1C,upstream_gene_variant,,ENST00000471157,;	T	ENSG00000254827	ENST00000533594	Transcript	missense_variant	861	364	122	A/T	Gca/Aca	.	.	.	-1	SLC22A18AS	HGNC	10965	protein_coding	YES	CCDS7739.1	ENSP00000433282	BWR1B_HUMAN	.	UPI000013FBB8	.	deleterious_low_confidence(0.05)	benign(0.001)	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTGCAGACC	.	4	ESCA
RP11-707M1.1	0	.	GRCh37	11	49831674	49831674	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1899G>C	.	.	ENST00000527477	7/7	261	251	10	218	218	0	RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000527477,;RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000534201,;RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000530858,;	C	ENSG00000205035	ENST00000527477	Transcript	non_coding_transcript_exon_variant	1899	.	.	.	.	.	.	.	1	RP11-707M1.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTGGATTGT	.	2	ESCA
OR51I1	0	.	GRCh37	11	5462136	5462136	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609G>C	p.Leu203Phe	p.L203F	ENST00000380211	1/1	26	22	3	28	28	0	OR51I1,missense_variant,p.Leu203Phe,ENST00000380211,;HBE1,intron_variant,,ENST00000396895,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380259,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,;	G	ENSG00000167359	ENST00000380211	Transcript	missense_variant	609	609	203	L/F	ttG/ttC	.	.	.	-1	OR51I1	HGNC	15200	protein_coding	YES	CCDS31382.1	ENSP00000369559	O51I1_HUMAN	.	UPI0000041CD0	.	tolerated(1)	benign(0)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF66,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCACCAAGAG	.	4	ESCA
OR4A15	0	.	GRCh37	11	55135605	55135605	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246C>A	p.%3D	p.S82S	ENST00000314706	1/1	106	100	6	70	70	0	OR4A15,synonymous_variant,p.%3D,ENST00000314706,;	A	ENSG00000181958	ENST00000314706	Transcript	synonymous_variant	246	246	82	S	tcC/tcA	.	.	.	1	OR4A15	HGNC	15152	protein_coding	YES	CCDS31500.1	ENSP00000325065	O4A15_HUMAN	.	UPI000004618F	.	.	.	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF63,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGTCCCTGGG	.	2	ESCA
OR4C15	0	.	GRCh37	11	55322145	55322145	+	Silent	SNP	C	C	T	rs550631405	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363C>T	p.%3D	p.F121F	ENST00000314644	1/1	107	93	13	77	77	0	OR4C15,synonymous_variant,p.%3D,ENST00000314644,;	T	ENSG00000181939	ENST00000314644	Transcript	synonymous_variant	363	363	121	F	ttC/ttT	rs550631405,COSM429161	.	.	1	OR4C15	HGNC	15171	protein_coding	YES	CCDS31501.1	ENSP00000324958	OR4CF_HUMAN	.	UPI00003B288E	.	.	.	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451:SF14,hmmpanther:PTHR26451,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTTCCTGGA	byCluster|by1000G	4	ESCA
OR4C6	0	.	GRCh37	11	55432966	55432966	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.324G>C	p.%3D	p.V108V	ENST00000314259	1/1	51	45	5	43	43	0	OR4C6,synonymous_variant,p.%3D,ENST00000314259,;	C	ENSG00000181903	ENST00000314259	Transcript	synonymous_variant	353	324	108	V	gtG/gtC	.	.	.	1	OR4C6	HGNC	14743	protein_coding	YES	CCDS31506.1	ENSP00000324769	OR4C6_HUMAN	.	UPI0000041868	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF80,hmmpanther:PTHR26451,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GGTGTGGGGAT	.	3	ESCA
PGA3	0	.	GRCh37	11	60971723	60971723	+	Silent	SNP	C	C	A	rs527696591	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201C>A	p.%3D	p.P67P	ENST00000325558	2/9	164	155	8	154	154	0	PGA3,synonymous_variant,p.%3D,ENST00000325558,;PGA3,5_prime_UTR_variant,,ENST00000543349,;PGA3,upstream_gene_variant,,ENST00000543505,;PGA3,non_coding_transcript_exon_variant,,ENST00000539649,;PGA3,non_coding_transcript_exon_variant,,ENST00000535551,;PGA3,non_coding_transcript_exon_variant,,ENST00000537954,;PGA3,upstream_gene_variant,,ENST00000541699,;	A	ENSG00000229859	ENST00000325558	Transcript	synonymous_variant	386	201	67	P	ccC/ccA	rs527696591,COSM81573	.	.	1	PGA3	HGNC	8885	protein_coding	YES	CCDS31574.1	ENSP00000322192	PEPA3_HUMAN	F5H842_HUMAN,F5H7H3_HUMAN,F5H0H6_HUMAN	UPI00001FA851	.	.	.	2/9	.	hmmpanther:PTHR13683:SF239,hmmpanther:PTHR13683,Gene3D:2.40.70.10,Superfamily_domains:SSF50630	A:0.0008	A:0.003	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCCCCTGGA	byFrequency|by1000G	2	ESCA
MYRF	0	.	GRCh37	11	61554131	61554131	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*516C>A	.	.	ENST00000278836	27/27	51	43	8	39	39	0	MYRF,3_prime_UTR_variant,,ENST00000278836,;MYRF,3_prime_UTR_variant,,ENST00000265460,;TMEM258,downstream_gene_variant,,ENST00000537328,;MYRF,downstream_gene_variant,,ENST00000389602,;TMEM258,downstream_gene_variant,,ENST00000543510,;TMEM258,intron_variant,,ENST00000535042,;TMEM258,downstream_gene_variant,,ENST00000545210,;TMEM258,downstream_gene_variant,,ENST00000540434,;TMEM258,downstream_gene_variant,,ENST00000535297,;TMEM258,downstream_gene_variant,,ENST00000541893,;MYRF,downstream_gene_variant,,ENST00000539361,;MYRF,downstream_gene_variant,,ENST00000546247,;TMEM258,downstream_gene_variant,,ENST00000257262,;MYRF,downstream_gene_variant,,ENST00000537318,;	A	ENSG00000124920	ENST00000278836	Transcript	3_prime_UTR_variant	4068	.	.	.	.	.	.	.	1	MYRF	HGNC	1181	protein_coding	YES	CCDS44622.1	ENSP00000278836	MRF_HUMAN	.	UPI0000D45F7B	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTCCCTGGGG	.	4	ESCA
FADS1	0	.	GRCh37	11	61570536	61570536	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1296C>A	p.Phe432Leu	p.F432L	ENST00000350997	10/12	39	35	4	32	32	0	FADS1,missense_variant,p.Phe291Leu,ENST00000542506,;FADS1,missense_variant,p.Phe291Leu,ENST00000433932,;FADS1,missense_variant,p.Phe432Leu,ENST00000350997,;FADS1,missense_variant,p.Phe77Leu,ENST00000460649,;FADS1,missense_variant,p.Phe123Leu,ENST00000536991,;FADS2,intron_variant,,ENST00000574708,;FADS1,downstream_gene_variant,,ENST00000539999,;FADS1,non_coding_transcript_exon_variant,,ENST00000496123,;	T	ENSG00000149485	ENST00000350997	Transcript	missense_variant	1529	1296	432	F/L	ttC/ttA	.	.	.	-1	FADS1	HGNC	3574	protein_coding	YES	CCDS8011.2	ENSP00000322229	FADS1_HUMAN	I3ZNT3_HUMAN,I3ZNS6_HUMAN,I3ZNS3_HUMAN,I3ZNS1_HUMAN,I3ZNN6_HUMAN,I3ZNL9_HUMAN,I3ZNL2_HUMAN,I3ZNH3_HUMAN,I3ZNE3_HUMAN,F5H8G5_HUMAN,F5H852_HUMAN,F5H5X5_HUMAN,F5H3P6_HUMAN,F5H2H3_HUMAN,F5H1Q7_HUMAN,F5H0Y2_HUMAN,F5GYH4_HUMAN,C9JJB3_HUMAN,C9J425_HUMAN	UPI00001AF33B	.	deleterious(0.02)	benign(0.248)	10/12	.	hmmpanther:PTHR19353:SF19,hmmpanther:PTHR19353,Pfam_domain:PF00487,PIRSF_domain:PIRSF015921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACTGAACCA	.	4	ESCA
FADS3	0	.	GRCh37	11	61645986	61645986	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.745G>C	p.Glu249Gln	p.E249Q	ENST00000278829	5/12	73	66	7	62	62	0	FADS3,missense_variant,p.Glu249Gln,ENST00000540820,;FADS3,missense_variant,p.Glu249Gln,ENST00000278829,;FADS3,missense_variant,p.Glu221Gln,ENST00000525588,;FADS3,missense_variant,p.Glu24Gln,ENST00000527379,;FADS3,missense_variant,p.Glu125Gln,ENST00000531956,;FADS3,missense_variant,p.Glu125Gln,ENST00000534223,;FADS3,missense_variant,p.Glu125Gln,ENST00000527697,;FADS3,upstream_gene_variant,,ENST00000525094,;FADS3,splice_region_variant,,ENST00000526294,;FADS3,splice_region_variant,,ENST00000529404,;FADS3,splice_region_variant,,ENST00000414624,;FADS3,splice_region_variant,,ENST00000533676,;FADS3,downstream_gene_variant,,ENST00000534426,;	G	ENSG00000221968	ENST00000278829	Transcript	missense_variant	898	745	249	E/Q	Gag/Cag	COSM4034664,COSM4034665	.	.	-1	FADS3	HGNC	3576	protein_coding	YES	CCDS8013.1	ENSP00000278829	FADS3_HUMAN	E9PQC2_HUMAN,E9PPZ4_HUMAN	UPI000003405F	.	tolerated(0.08)	benign(0.329)	5/12	.	PIRSF_domain:PIRSF015921,Pfam_domain:PF00487,hmmpanther:PTHR19353:SF11,hmmpanther:PTHR19353	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CACCTCGACGG	.	3	ESCA
SLC22A8	0	.	GRCh37	11	62760702	62760702	+	3'UTR	SNP	G	G	T	rs756087897	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7C>A	.	.	ENST00000336232	11/11	91	84	7	66	66	0	SLC22A8,3_prime_UTR_variant,,ENST00000535878,;SLC22A8,3_prime_UTR_variant,,ENST00000336232,;SLC22A8,3_prime_UTR_variant,,ENST00000545207,;SLC22A8,downstream_gene_variant,,ENST00000430500,;SLC22A8,downstream_gene_variant,,ENST00000311438,;SLC22A8,downstream_gene_variant,,ENST00000542795,;SLC22A8,non_coding_transcript_exon_variant,,ENST00000539841,;SLC22A8,non_coding_transcript_exon_variant,,ENST00000451262,;SLC22A8,downstream_gene_variant,,ENST00000542904,;	T	ENSG00000149452	ENST00000336232	Transcript	3_prime_UTR_variant	1772	.	.	.	.	rs756087897	.	.	-1	SLC22A8	HGNC	10972	protein_coding	YES	CCDS8042.1	ENSP00000337335	S22A8_HUMAN	.	UPI0000036DF2	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTCCGTTGTC	byFrequency	2	ESCA
SF1	0	.	GRCh37	11	64535575	64535575	+	Intron	SNP	C	C	A	rs764458788	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1443+3G>T	.	.	ENST00000377387	.	33	28	5	35	35	0	SF1,splice_region_variant,,ENST00000227503,;SF1,splice_region_variant,,ENST00000377390,;SF1,splice_region_variant,,ENST00000486867,;SF1,splice_region_variant,,ENST00000422298,;SF1,splice_region_variant,,ENST00000377394,;SF1,splice_region_variant,,ENST00000334944,;SF1,splice_region_variant,,ENST00000377387,;SF1,splice_region_variant,,ENST00000433274,;SF1,upstream_gene_variant,,ENST00000443908,;SF1,downstream_gene_variant,,ENST00000432725,;SF1,upstream_gene_variant,,ENST00000413725,;SF1,downstream_gene_variant,,ENST00000489544,;SF1,downstream_gene_variant,,ENST00000496969,;SF1,splice_region_variant,,ENST00000448404,;SF1,upstream_gene_variant,,ENST00000477596,;SF1,downstream_gene_variant,,ENST00000486960,;SF1,downstream_gene_variant,,ENST00000482693,;SF1,downstream_gene_variant,,ENST00000413951,;	A	ENSG00000168066	ENST00000377387	Transcript	splice_region_variant	.	.	.	.	.	rs764458788	.	.	-1	SF1	HGNC	12950	protein_coding	YES	CCDS53661.1	ENSP00000366604	SF01_HUMAN	Q14821_HUMAN,C9J792_HUMAN,B4DX42_HUMAN	UPI0000074300	.	.	.	.	9/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGGCTCACCGG	.	3	ESCA
TRIM3	0	.	GRCh37	11	6477889	6477889	+	Missense_Mutation	SNP	C	C	G	rs373824947	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1067G>C	p.Arg356Pro	p.R356P	ENST00000525074	6/12	55	44	10	41	41	0	TRIM3,missense_variant,p.Arg356Pro,ENST00000345851,;TRIM3,missense_variant,p.Arg278Pro,ENST00000537602,;TRIM3,missense_variant,p.Arg356Pro,ENST00000359518,;TRIM3,missense_variant,p.Arg356Pro,ENST00000525074,;TRIM3,missense_variant,p.Arg237Pro,ENST00000536344,;TRIM3,downstream_gene_variant,,ENST00000528227,;TRIM3,downstream_gene_variant,,ENST00000529529,;TRIM3,non_coding_transcript_exon_variant,,ENST00000529058,;TRIM3,downstream_gene_variant,,ENST00000528932,;TRIM3,upstream_gene_variant,,ENST00000527237,;TRIM3,upstream_gene_variant,,ENST00000526845,;TRIM3,upstream_gene_variant,,ENST00000533309,;TRIM3,upstream_gene_variant,,ENST00000532542,;	G	ENSG00000110171	ENST00000525074	Transcript	missense_variant	1462	1067	356	R/P	cGc/cCc	rs373824947,COSM3752620	.	.	-1	TRIM3	HGNC	10064	protein_coding	YES	CCDS7764.1	ENSP00000433102	TRIM3_HUMAN	E9PMW5_HUMAN,E9PMK8_HUMAN,D3DQT3_HUMAN,B3KV53_HUMAN	UPI000013C8BA	.	deleterious(0)	possibly_damaging(0.899)	6/12	.	PROSITE_profiles:PS50194,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF1,Pfam_domain:PF00630,Gene3D:2.60.40.10,SMART_domains:SM00557,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGCGCACC	byCluster	5	ESCA
PCNXL3	0	.	GRCh37	11	65403111	65403111	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5296C>T	p.Arg1766Cys	p.R1766C	ENST00000355703	32/35	84	75	9	50	50	0	PCNXL3,missense_variant,p.Arg1766Cys,ENST00000355703,;SIPA1,upstream_gene_variant,,ENST00000533361,;SIPA1,upstream_gene_variant,,ENST00000527525,;SIPA1,upstream_gene_variant,,ENST00000394224,;SIPA1,upstream_gene_variant,,ENST00000526137,;SIPA1,upstream_gene_variant,,ENST00000534313,;MIR4690,upstream_gene_variant,,ENST00000578459,;PCNXL3,downstream_gene_variant,,ENST00000531280,;PCNXL3,non_coding_transcript_exon_variant,,ENST00000439247,;	T	ENSG00000197136	ENST00000355703	Transcript	missense_variant	5835	5296	1766	R/C	Cgc/Tgc	COSM1298425	.	.	1	PCNXL3	HGNC	18760	protein_coding	YES	CCDS44650.1	ENSP00000347931	PCX3_HUMAN	.	UPI0000405B22	.	deleterious(0)	probably_damaging(1)	32/35	.	Pfam_domain:PF05041,hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF4	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCTTCGCAAC	.	4	ESCA
CHKA	0	.	GRCh37	11	67837676	67837676	+	Silent	SNP	G	G	C	rs749489797	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.849C>G	p.%3D	p.P283P	ENST00000265689	6/12	103	94	9	78	78	0	CHKA,synonymous_variant,p.%3D,ENST00000356135,;CHKA,synonymous_variant,p.%3D,ENST00000265689,;CHKA,downstream_gene_variant,,ENST00000531341,;CHKA,non_coding_transcript_exon_variant,,ENST00000528235,;CHKA,downstream_gene_variant,,ENST00000530730,;CHKA,non_coding_transcript_exon_variant,,ENST00000533910,;CHKA,upstream_gene_variant,,ENST00000525155,;	C	ENSG00000110721	ENST00000265689	Transcript	synonymous_variant	876	849	283	P	ccC/ccG	rs749489797	.	.	-1	CHKA	HGNC	1937	protein_coding	YES	CCDS8178.1	ENSP00000265689	CHKA_HUMAN	E9PM06_HUMAN	UPI000013D662	.	.	.	6/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22603,hmmpanther:PTHR22603:SF21,Pfam_domain:PF01633,Gene3D:3.90.1200.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCAAGGGCAG	byFrequency	3	ESCA
CPT1A	0	.	GRCh37	11	68529067	68529067	+	Missense_Mutation	SNP	C	C	A	rs376959593	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1964G>T	p.Arg655Leu	p.R655L	ENST00000265641	16/19	160	153	7	84	84	0	CPT1A,missense_variant,p.Arg655Leu,ENST00000539743,;CPT1A,missense_variant,p.Arg655Leu,ENST00000540367,;CPT1A,missense_variant,p.Arg655Leu,ENST00000265641,;CPT1A,missense_variant,p.Arg655Leu,ENST00000376618,;CPT1A,downstream_gene_variant,,ENST00000537756,;	A	ENSG00000110090	ENST00000265641	Transcript	missense_variant	2119	1964	655	R/L	cGt/cTt	rs376959593	.	.	-1	CPT1A	HGNC	2328	protein_coding	YES	CCDS8185.1	ENSP00000265641	CPT1A_HUMAN	Q8WZ48_HUMAN,H3BUV7_HUMAN,H3BUJ0_HUMAN,H3BP22_HUMAN	UPI000013D658	.	deleterious(0)	probably_damaging(1)	16/19	.	hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF49,Pfam_domain:PF00755,Superfamily_domains:SSF52777	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTGACGATCG	byFrequency|byCluster	2	ESCA
OR2D3	0	.	GRCh37	11	6942744	6942744	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.512T>A	p.Val171Glu	p.V171E	ENST00000317834	1/1	47	41	6	50	50	0	OR2D3,missense_variant,p.Val171Glu,ENST00000317834,;ZNF215,upstream_gene_variant,,ENST00000278319,;ZNF215,upstream_gene_variant,,ENST00000529755,;ZNF215,upstream_gene_variant,,ENST00000527171,;	A	ENSG00000178358	ENST00000317834	Transcript	missense_variant	540	512	171	V/E	gTg/gAg	.	.	.	1	OR2D3	HGNC	15146	protein_coding	YES	CCDS31417.1	ENSP00000320560	OR2D3_HUMAN	.	UPI0000041C7D	.	tolerated(0.27)	possibly_damaging(0.821)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF136,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTAGTGTCTT	.	4	ESCA
FGF4	0	.	GRCh37	11	69588230	69588230	+	Silent	SNP	C	C	G	rs200135119	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.468G>C	p.%3D	p.T156T	ENST00000168712	3/3	190	183	7	77	77	0	FGF4,synonymous_variant,p.%3D,ENST00000168712,;AP001888.1,upstream_gene_variant,,ENST00000602104,;FGF4,non_coding_transcript_exon_variant,,ENST00000538040,;	G	ENSG00000075388	ENST00000168712	Transcript	synonymous_variant	787	468	156	T	acG/acC	rs200135119	.	.	-1	FGF4	HGNC	3682	protein_coding	YES	CCDS8194.1	ENSP00000168712	FGF4_HUMAN	.	UPI0000040662	.	.	.	3/3	.	Prints_domain:PR00262,Prints_domain:PR00263,Superfamily_domains:SSF50353,SMART_domains:SM00442,Gene3D:2.80.10.50,Pfam_domain:PF00167,PROSITE_patterns:PS00247,hmmpanther:PTHR11486:SF31,hmmpanther:PTHR11486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGAACGTGCA	.	2	ESCA
MAP6	0	.	GRCh37	11	75319308	75319308	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.965A>G	p.Gln322Arg	p.Q322R	ENST00000304771	2/4	118	107	11	90	90	0	MAP6,missense_variant,p.Gln322Arg,ENST00000434603,;MAP6,missense_variant,p.Gln322Arg,ENST00000304771,;MAP6,5_prime_UTR_variant,,ENST00000526740,;	C	ENSG00000171533	ENST00000304771	Transcript	missense_variant	1716	965	322	Q/R	cAg/cGg	.	.	.	-1	MAP6	HGNC	6868	protein_coding	YES	CCDS31641.1	ENSP00000307093	MAP6_HUMAN	Q6ZWB8_HUMAN	UPI0000251E6A	.	deleterious(0)	probably_damaging(0.977)	2/4	.	hmmpanther:PTHR14759:SF2,hmmpanther:PTHR14759	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTACTGGGGC	.	3	ESCA
TMEM135	0	.	GRCh37	11	87030375	87030375	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1200G>T	p.Leu400Phe	p.L400F	ENST00000305494	14/15	118	109	9	81	81	0	TMEM135,missense_variant,p.Leu400Phe,ENST00000305494,;TMEM135,missense_variant,p.Leu261Phe,ENST00000535167,;TMEM135,missense_variant,p.Leu271Phe,ENST00000532959,;TMEM135,missense_variant,p.Leu378Phe,ENST00000340353,;TMEM135,non_coding_transcript_exon_variant,,ENST00000528861,;TMEM135,non_coding_transcript_exon_variant,,ENST00000531643,;RP11-777F6.3,downstream_gene_variant,,ENST00000603803,;	T	ENSG00000166575	ENST00000305494	Transcript	missense_variant	1239	1200	400	L/F	ttG/ttT	.	.	.	1	TMEM135	HGNC	26167	protein_coding	YES	CCDS8280.1	ENSP00000306344	TM135_HUMAN	Q7Z760_HUMAN,F5H254_HUMAN,B4DKZ1_HUMAN	UPI00001FB0C7	.	deleterious(0)	probably_damaging(0.995)	14/15	.	hmmpanther:PTHR12459:SF4,hmmpanther:PTHR12459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTTGAGACC	.	2	ESCA
TYR	0	.	GRCh37	11	89028425	89028425	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1481G>T	p.Gly494Val	p.G494V	ENST00000263321	5/5	72	61	10	74	73	0	TYR,missense_variant,p.Gly494Val,ENST00000263321,;TYR,non_coding_transcript_exon_variant,,ENST00000528243,;CBX3P7,upstream_gene_variant,,ENST00000532876,;	T	ENSG00000077498	ENST00000263321	Transcript	missense_variant	1983	1481	494	G/V	gGg/gTg	.	.	.	1	TYR	HGNC	12442	protein_coding	YES	CCDS8284.1	ENSP00000263321	TYRO_HUMAN	Q9UMA2_HUMAN,Q9UMA1_HUMAN,L8B082_HUMAN	UPI000004441A	.	tolerated(0.63)	benign(0.068)	5/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCAGGGCTTG	.	4	ESCA
ANKRD49	0	.	GRCh37	11	94231384	94231384	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.406G>A	p.Ala136Thr	p.A136T	ENST00000544612	3/3	93	86	7	68	68	0	ANKRD49,missense_variant,p.Ala136Thr,ENST00000544612,;ANKRD49,missense_variant,p.Ala136Thr,ENST00000302755,;ANKRD49,missense_variant,p.Ala95Thr,ENST00000535502,;ANKRD49,3_prime_UTR_variant,,ENST00000544253,;MRE11A,upstream_gene_variant,,ENST00000393241,;ANKRD49,downstream_gene_variant,,ENST00000540349,;MRE11A,upstream_gene_variant,,ENST00000323977,;ANKRD49,downstream_gene_variant,,ENST00000541144,;MRE11A,upstream_gene_variant,,ENST00000540013,;MRE11A,upstream_gene_variant,,ENST00000538923,;ANKRD49,downstream_gene_variant,,ENST00000545130,;MRE11A,upstream_gene_variant,,ENST00000536754,;MRE11A,upstream_gene_variant,,ENST00000323929,;MRE11A,upstream_gene_variant,,ENST00000407439,;ANKRD49,non_coding_transcript_exon_variant,,ENST00000538535,;ANKRD49,non_coding_transcript_exon_variant,,ENST00000539883,;MRE11A,upstream_gene_variant,,ENST00000541157,;MRE11A,upstream_gene_variant,,ENST00000536144,;ANKRD49,3_prime_UTR_variant,,ENST00000534911,;ANKRD49,downstream_gene_variant,,ENST00000544514,;	A	ENSG00000168876	ENST00000544612	Transcript	missense_variant	903	406	136	A/T	Gca/Aca	.	.	.	1	ANKRD49	HGNC	25970	protein_coding	YES	CCDS8300.1	ENSP00000440396	ANR49_HUMAN	F5H227_HUMAN	UPI000004A09B	.	deleterious(0.02)	possibly_damaging(0.897)	3/3	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24144,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCATGCAGTG	.	2	ESCA
C12orf42	0	.	GRCh37	12	103872154	103872154	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51C>G	p.%3D	p.T17T	ENST00000378113	2/6	32	29	3	20	20	0	C12orf42,synonymous_variant,p.%3D,ENST00000378113,;C12orf42,synonymous_variant,p.%3D,ENST00000552578,;C12orf42,synonymous_variant,p.%3D,ENST00000315192,;C12orf42,synonymous_variant,p.%3D,ENST00000548883,;C12orf42,5_prime_UTR_variant,,ENST00000548048,;C12orf42,non_coding_transcript_exon_variant,,ENST00000546526,;C12orf42,non_coding_transcript_exon_variant,,ENST00000548789,;C12orf42,non_coding_transcript_exon_variant,,ENST00000550497,;C12orf42,non_coding_transcript_exon_variant,,ENST00000548196,;C12orf42,synonymous_variant,p.%3D,ENST00000551134,;C12orf42,synonymous_variant,p.%3D,ENST00000547347,;	C	ENSG00000179088	ENST00000378113	Transcript	synonymous_variant	277	51	17	T	acC/acG	.	.	.	-1	C12orf42	HGNC	24729	protein_coding	YES	CCDS44963.1	ENSP00000367353	CL042_HUMAN	F8W1Y6_HUMAN,F8VV63_HUMAN	UPI00001D7906	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGATGGTTAG	.	3	ESCA
IFT81	0	.	GRCh37	12	110628806	110628806	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1420G>A	p.Glu474Lys	p.E474K	ENST00000242591	13/19	97	87	9	60	60	0	IFT81,missense_variant,p.Glu474Lys,ENST00000242591,;IFT81,missense_variant,p.Glu474Lys,ENST00000552912,;IFT81,non_coding_transcript_exon_variant,,ENST00000551055,;IFT81,missense_variant,p.Glu444Lys,ENST00000550156,;	A	ENSG00000122970	ENST00000242591	Transcript	missense_variant	1926	1420	474	E/K	Gaa/Aaa	.	.	.	1	IFT81	HGNC	14313	protein_coding	YES	CCDS41831.1	ENSP00000242591	IFT81_HUMAN	.	UPI000000D78F	.	deleterious(0.03)	possibly_damaging(0.794)	13/19	.	hmmpanther:PTHR15614:SF2,hmmpanther:PTHR15614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGTGAAGTT	.	4	ESCA
ATXN2	0	.	GRCh37	12	111990213	111990213	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.922G>C	p.Ala308Pro	p.A308P	ENST00000377617	5/25	99	94	5	75	75	0	ATXN2,missense_variant,p.Ala51Pro,ENST00000548492,;ATXN2,missense_variant,p.Ala43Pro,ENST00000542287,;ATXN2,missense_variant,p.Ala19Pro,ENST00000535949,;ATXN2,missense_variant,p.Ala43Pro,ENST00000389153,;ATXN2,missense_variant,p.Ala148Pro,ENST00000608853,;ATXN2,missense_variant,p.Ala308Pro,ENST00000550104,;ATXN2,missense_variant,p.Ala308Pro,ENST00000377617,;ATXN2,intron_variant,,ENST00000549455,;ATXN2,missense_variant,p.Ala229Pro,ENST00000483311,;ATXN2,non_coding_transcript_exon_variant,,ENST00000392645,;ATXN2,non_coding_transcript_exon_variant,,ENST00000471866,;	G	ENSG00000204842	ENST00000377617	Transcript	missense_variant	1084	922	308	A/P	Gca/Cca	.	.	.	-1	ATXN2	HGNC	10555	protein_coding	YES	CCDS31902.1	ENSP00000366843	ATX2_HUMAN	D2CTA6_HUMAN,D2CTA5_HUMAN,D2CTA3_HUMAN	UPI0000DBEEFC	.	.	probably_damaging(1)	5/25	.	hmmpanther:PTHR12854,hmmpanther:PTHR12854:SF11,Pfam_domain:PF14438,Gene3D:2.30.30.100,Superfamily_domains:SSF50182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTGCGGCAT	.	2	ESCA
NAA25	0	.	GRCh37	12	112466912	112466912	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*423A>C	.	.	ENST00000261745	24/24	38	35	3	27	27	0	NAA25,3_prime_UTR_variant,,ENST00000261745,;NAA25,non_coding_transcript_exon_variant,,ENST00000552527,;NAA25,downstream_gene_variant,,ENST00000548181,;NAA25,downstream_gene_variant,,ENST00000549711,;	G	ENSG00000111300	ENST00000261745	Transcript	3_prime_UTR_variant	3591	.	.	.	.	.	.	.	-1	NAA25	HGNC	25783	protein_coding	YES	CCDS9159.1	ENSP00000261745	NAA25_HUMAN	.	UPI00001FBB50	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCTTGTGGC	.	2	ESCA
HECTD4	0	.	GRCh37	12	112673449	112673449	+	Missense_Mutation	SNP	C	C	T	rs775162021	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5146G>A	p.Val1716Ile	p.V1716I	ENST00000550722	36/76	50	46	4	52	52	0	HECTD4,missense_variant,p.Val1440Ile,ENST00000430131,;HECTD4,missense_variant,p.Val1716Ile,ENST00000550722,;HECTD4,missense_variant,p.Val1690Ile,ENST00000377560,;HECTD4,upstream_gene_variant,,ENST00000547519,;	T	ENSG00000173064	ENST00000550722	Transcript	missense_variant	5542	5146	1716	V/I	Gta/Ata	rs775162021	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	possibly_damaging(0.631)	36/76	.	hmmpanther:PTHR11254:SF286,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TTCTACGCTCA	byFrequency	2	ESCA
TBX3	0	.	GRCh37	12	115108860	115108860	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*786G>A	.	.	ENST00000257566	8/8	35	32	3	37	37	0	TBX3,3_prime_UTR_variant,,ENST00000349155,;TBX3,3_prime_UTR_variant,,ENST00000257566,;	T	ENSG00000135111	ENST00000257566	Transcript	3_prime_UTR_variant	3408	.	.	.	.	.	.	.	-1	TBX3	HGNC	11602	protein_coding	YES	CCDS9176.1	ENSP00000257566	TBX3_HUMAN	.	UPI0000136AA0	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATTCATTTT	.	2	ESCA
KSR2	0	.	GRCh37	12	117904627	117904627	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*377G>T	.	.	ENST00000339824	20/20	32	28	4	16	16	0	KSR2,3_prime_UTR_variant,,ENST00000425217,;KSR2,3_prime_UTR_variant,,ENST00000339824,;KSR2,downstream_gene_variant,,ENST00000302438,;	A	ENSG00000171435	ENST00000339824	Transcript	3_prime_UTR_variant	3958	.	.	.	.	.	.	.	-1	KSR2	HGNC	18610	protein_coding	YES	.	ENSP00000339952	KSR2_HUMAN	E9PB13_HUMAN	UPI000152636C	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	ACACACAGACA	.	2	ESCA
CIT	0	.	GRCh37	12	120128245	120128245	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5897G>T	p.Arg1966Leu	p.R1966L	ENST00000392521	47/48	138	119	19	79	79	0	CIT,missense_variant,p.Arg1537Leu,ENST00000392520,;CIT,missense_variant,p.Arg1924Leu,ENST00000261833,;CIT,missense_variant,p.Arg1966Leu,ENST00000392521,;CIT,non_coding_transcript_exon_variant,,ENST00000469414,;CIT,non_coding_transcript_exon_variant,,ENST00000537607,;CIT,non_coding_transcript_exon_variant,,ENST00000544872,;CIT,non_coding_transcript_exon_variant,,ENST00000545913,;	A	ENSG00000122966	ENST00000392521	Transcript	missense_variant	5953	5897	1966	R/L	cGa/cTa	.	.	.	-1	CIT	HGNC	1985	protein_coding	YES	CCDS55891.1	ENSP00000376306	CTRO_HUMAN	.	UPI0000683C41	.	deleterious_low_confidence(0.01)	probably_damaging(0.946)	47/48	.	PIRSF_domain:PIRSF038145,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCGCTTG	.	4	ESCA
VPS33A	0	.	GRCh37	12	122720350	122720350	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1423G>C	p.Asp475His	p.D475H	ENST00000267199	11/13	137	130	7	84	84	0	VPS33A,missense_variant,p.Asp475His,ENST00000267199,;VPS33A,non_coding_transcript_exon_variant,,ENST00000541169,;RP11-512M8.5,missense_variant,p.Asp436His,ENST00000535844,;VPS33A,3_prime_UTR_variant,,ENST00000543633,;	G	ENSG00000139719	ENST00000267199	Transcript	missense_variant	1536	1423	475	D/H	Gat/Cat	.	.	.	-1	VPS33A	HGNC	18179	protein_coding	YES	CCDS9231.1	ENSP00000267199	VP33A_HUMAN	Q9H6C4_HUMAN	UPI000000D7AA	.	deleterious(0)	probably_damaging(0.948)	11/13	.	hmmpanther:PTHR11679:SF31,hmmpanther:PTHR11679,Pfam_domain:PF00995,Superfamily_domains:SSF56815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCATCCATCC	.	2	ESCA
VPS33A	0	.	GRCh37	12	122723244	122723244	+	Missense_Mutation	SNP	C	C	T	rs186215132	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1192G>A	p.Ala398Thr	p.A398T	ENST00000267199	10/13	83	75	8	66	66	0	VPS33A,missense_variant,p.Ala398Thr,ENST00000267199,;VPS33A,downstream_gene_variant,,ENST00000536212,;VPS33A,non_coding_transcript_exon_variant,,ENST00000541169,;RP11-512M8.5,missense_variant,p.Ala359Thr,ENST00000535844,;VPS33A,3_prime_UTR_variant,,ENST00000543633,;	T	ENSG00000139719	ENST00000267199	Transcript	missense_variant	1305	1192	398	A/T	Gcc/Acc	rs186215132	.	.	-1	VPS33A	HGNC	18179	protein_coding	YES	CCDS9231.1	ENSP00000267199	VP33A_HUMAN	Q9H6C4_HUMAN	UPI000000D7AA	.	tolerated(0.07)	benign(0.029)	10/13	.	hmmpanther:PTHR11679:SF31,hmmpanther:PTHR11679,Pfam_domain:PF00995,Superfamily_domains:SSF56815	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGGCGATAC	byCluster|by1000G	4	ESCA
TMEM132C	0	.	GRCh37	12	129180377	129180377	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1658C>A	p.Pro553His	p.P553H	ENST00000435159	7/9	54	47	7	51	51	0	TMEM132C,missense_variant,p.Pro169His,ENST00000315208,;TMEM132C,missense_variant,p.Pro553His,ENST00000435159,;TMEM132C,splice_region_variant,,ENST00000537538,;	A	ENSG00000181234	ENST00000435159	Transcript	missense_variant	1658	1658	553	P/H	cCc/cAc	.	.	.	1	TMEM132C	HGNC	25436	protein_coding	YES	.	ENSP00000410852	T132C_HUMAN	F5H439_HUMAN,E9PC33_HUMAN	UPI0001C0B37C	.	deleterious(0)	possibly_damaging(0.834)	7/9	.	hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGGCCCACTC	.	4	ESCA
KIAA1467	0	.	GRCh37	12	13232915	13232915	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1835G>C	p.Arg612Thr	p.R612T	ENST00000197268	12/13	89	82	7	74	74	0	KIAA1467,missense_variant,p.Arg612Thr,ENST00000197268,;KIAA1467,intron_variant,,ENST00000537625,;GSG1,downstream_gene_variant,,ENST00000396310,;GSG1,downstream_gene_variant,,ENST00000432710,;GSG1,downstream_gene_variant,,ENST00000324458,;GSG1,downstream_gene_variant,,ENST00000351606,;GSG1,downstream_gene_variant,,ENST00000396302,;GSG1,downstream_gene_variant,,ENST00000537302,;GSG1,downstream_gene_variant,,ENST00000337630,;GSG1,downstream_gene_variant,,ENST00000457134,;KIAA1467,missense_variant,p.Arg612Thr,ENST00000416494,;KIAA1467,non_coding_transcript_exon_variant,,ENST00000541950,;	C	ENSG00000084444	ENST00000197268	Transcript	missense_variant	1955	1835	612	R/T	aGg/aCg	.	.	.	1	KIAA1467	HGNC	29288	protein_coding	YES	CCDS31750.1	ENSP00000197268	K1467_HUMAN	.	UPI00001FB6A1	.	deleterious(0)	probably_damaging(0.972)	12/13	.	hmmpanther:PTHR21419,hmmpanther:PTHR21419:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCTAGGATAA	.	3	ESCA
ATF7IP	0	.	GRCh37	12	14577456	14577456	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607G>T	p.Asp203Tyr	p.D203Y	ENST00000261168	2/15	113	101	11	92	92	0	ATF7IP,missense_variant,p.Asp203Tyr,ENST00000261168,;ATF7IP,missense_variant,p.Asp203Tyr,ENST00000540793,;ATF7IP,missense_variant,p.Asp203Tyr,ENST00000543189,;ATF7IP,missense_variant,p.Asp211Tyr,ENST00000544627,;ATF7IP,missense_variant,p.Asp203Tyr,ENST00000536444,;ATF7IP,missense_variant,p.Asp203Tyr,ENST00000396279,;ATF7IP,intron_variant,,ENST00000545723,;ATF7IP,intron_variant,,ENST00000538511,;ATF7IP,downstream_gene_variant,,ENST00000545769,;ATF7IP,downstream_gene_variant,,ENST00000542991,;ATF7IP,downstream_gene_variant,,ENST00000535132,;ATF7IP,downstream_gene_variant,,ENST00000536279,;ATF7IP,downstream_gene_variant,,ENST00000542508,;ATF7IP,downstream_gene_variant,,ENST00000542967,;ATF7IP,downstream_gene_variant,,ENST00000534828,;ATF7IP,downstream_gene_variant,,ENST00000542514,;ATF7IP,downstream_gene_variant,,ENST00000539057,;ATF7IP,downstream_gene_variant,,ENST00000541056,;ATF7IP,downstream_gene_variant,,ENST00000428217,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000541654,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000539659,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000537653,;	T	ENSG00000171681	ENST00000261168	Transcript	missense_variant	760	607	203	D/Y	Gat/Tat	.	.	.	1	ATF7IP	HGNC	20092	protein_coding	YES	CCDS8663.1	ENSP00000261168	MCAF1_HUMAN	F8WE35_HUMAN,F5H8I0_HUMAN,F5H6X8_HUMAN,F5H502_HUMAN,F5H3C4_HUMAN,F5H2W9_HUMAN,F5H2H9_HUMAN,F5H221_HUMAN,F5H1K9_HUMAN,F5GZ98_HUMAN,F5GZ10_HUMAN,F5GYR7_HUMAN,A8MV73_HUMAN	UPI00001FB6B1	.	deleterious_low_confidence(0)	probably_damaging(0.934)	2/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23210:SF20,hmmpanther:PTHR23210	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGTGATCCC	.	4	ESCA
CACNA1C	0	.	GRCh37	12	2760889	2760889	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4173G>T	p.%3D	p.G1391G	ENST00000347598	34/49	56	48	8	49	49	0	CACNA1C,synonymous_variant,p.%3D,ENST00000399644,;CACNA1C,synonymous_variant,p.%3D,ENST00000399595,;CACNA1C,synonymous_variant,p.%3D,ENST00000406454,;CACNA1C,synonymous_variant,p.%3D,ENST00000399617,;CACNA1C,synonymous_variant,p.%3D,ENST00000347598,;CACNA1C,synonymous_variant,p.%3D,ENST00000402845,;CACNA1C,synonymous_variant,p.%3D,ENST00000327702,;CACNA1C,synonymous_variant,p.%3D,ENST00000399634,;CACNA1C,synonymous_variant,p.%3D,ENST00000399641,;CACNA1C,synonymous_variant,p.%3D,ENST00000399603,;CACNA1C,synonymous_variant,p.%3D,ENST00000399629,;CACNA1C,synonymous_variant,p.%3D,ENST00000399601,;CACNA1C,synonymous_variant,p.%3D,ENST00000399597,;CACNA1C,synonymous_variant,p.%3D,ENST00000399655,;CACNA1C,synonymous_variant,p.%3D,ENST00000399606,;CACNA1C,synonymous_variant,p.%3D,ENST00000399637,;CACNA1C,synonymous_variant,p.%3D,ENST00000335762,;CACNA1C,synonymous_variant,p.%3D,ENST00000399591,;CACNA1C,synonymous_variant,p.%3D,ENST00000399621,;CACNA1C,synonymous_variant,p.%3D,ENST00000399638,;CACNA1C,synonymous_variant,p.%3D,ENST00000344100,;CACNA1C,synonymous_variant,p.%3D,ENST00000399649,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000483136,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000492150,;	T	ENSG00000151067	ENST00000347598	Transcript	synonymous_variant	4173	4173	1391	G	ggG/ggT	.	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	.	.	34/49	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Pfam_domain:PF00520,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTGGGGAGGG	.	4	ESCA
ITFG2	0	.	GRCh37	12	2921868	2921868	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-59G>A	.	.	ENST00000228799	1/12	26	21	5	20	20	0	ITFG2,5_prime_UTR_variant,,ENST00000419778,;ITFG2,5_prime_UTR_variant,,ENST00000542548,;ITFG2,5_prime_UTR_variant,,ENST00000228799,;ITFG2,upstream_gene_variant,,ENST00000535564,;RP4-816N1.6,non_coding_transcript_exon_variant,,ENST00000547834,;RP4-816N1.6,non_coding_transcript_exon_variant,,ENST00000547794,;RP4-816N1.6,upstream_gene_variant,,ENST00000552469,;ITFG2,5_prime_UTR_variant,,ENST00000537851,;ITFG2,5_prime_UTR_variant,,ENST00000540929,;ITFG2,non_coding_transcript_exon_variant,,ENST00000543029,;ITFG2,upstream_gene_variant,,ENST00000541659,;	A	ENSG00000111203	ENST00000228799	Transcript	5_prime_UTR_variant	81	.	.	.	.	.	.	.	1	ITFG2	HGNC	30879	protein_coding	YES	CCDS8513.1	ENSP00000228799	ITFG2_HUMAN	H0YFM4_HUMAN,E7EST0_HUMAN	UPI00000373A8	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCGCGACGGG	.	3	ESCA
PRMT8	0	.	GRCh37	12	3661874	3661874	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.418-943C>T	.	.	ENST00000382622	.	65	60	4	54	54	0	PRMT8,intron_variant,,ENST00000452611,;PRMT8,intron_variant,,ENST00000382622,;PRMT8,non_coding_transcript_exon_variant,,ENST00000261252,;PRMT8,non_coding_transcript_exon_variant,,ENST00000543701,;	T	ENSG00000111218	ENST00000382622	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PRMT8	HGNC	5188	protein_coding	YES	CCDS8521.2	ENSP00000372067	ANM8_HUMAN	.	UPI00005B2E00	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCCCTCACC	.	2	ESCA
AKAP3	0	.	GRCh37	12	4737521	4737521	+	Missense_Mutation	SNP	C	C	T	rs140759485	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547G>A	p.Val183Ile	p.V183I	ENST00000545990	5/6	69	61	8	63	63	0	AKAP3,missense_variant,p.Val183Ile,ENST00000545990,;AKAP3,missense_variant,p.Val183Ile,ENST00000228850,;AKAP3,downstream_gene_variant,,ENST00000540967,;AKAP3,downstream_gene_variant,,ENST00000536414,;RP11-500M8.7,intron_variant,,ENST00000536588,;	T	ENSG00000111254	ENST00000545990	Transcript	missense_variant	1072	547	183	V/I	Gtc/Atc	rs140759485,COSM3968232,COSM3968231	.	.	-1	AKAP3	HGNC	373	protein_coding	YES	CCDS8531.1	ENSP00000440994	AKAP3_HUMAN	F5H7P4_HUMAN,F5H2S4_HUMAN	UPI000013C8DF	.	deleterious(0.01)	possibly_damaging(0.593)	5/6	.	hmmpanther:PTHR10226,hmmpanther:PTHR10226:SF9,Pfam_domain:PF05716,SMART_domains:SM00807	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGACGGTCT	byCluster	4	ESCA
OR8S1	0	.	GRCh37	12	48919789	48919789	+	Silent	SNP	C	C	G	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375C>G	p.%3D	p.A125A	ENST00000310194	1/2	66	57	9	31	31	0	OR8S1,synonymous_variant,p.%3D,ENST00000310194,;OR8S1,intron_variant,,ENST00000551654,;	G	ENSG00000197376	ENST00000310194	Transcript	synonymous_variant	375	375	125	A	gcC/gcG	COSM693771	.	.	1	OR8S1	HGNC	19628	protein_coding	YES	CCDS31789.1	ENSP00000310632	OR8S1_HUMAN	.	UPI000013EFC1	.	.	.	1/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF239,hmmpanther:PTHR26451,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCCATCTG	.	5	ESCA
KMT2D	0	.	GRCh37	12	49427679	49427679	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10809G>A	p.%3D	p.Q3603Q	ENST00000301067	39/54	61	57	4	59	58	1	KMT2D,synonymous_variant,p.%3D,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,;	T	ENSG00000167548	ENST00000301067	Transcript	synonymous_variant	10809	10809	3603	Q	caG/caA	COSM940018,COSM940017	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	39/54	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTGCTGTTG	.	2	ESCA
KMT2D	0	.	GRCh37	12	49443837	49443837	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3534G>T	p.Gln1178His	p.Q1178H	ENST00000301067	11/54	66	62	4	43	43	0	KMT2D,missense_variant,p.Gln1178His,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000547610,;	A	ENSG00000167548	ENST00000301067	Transcript	missense_variant	3534	3534	1178	Q/H	caG/caT	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	benign(0.067)	11/54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCCCTGCCC	.	2	ESCA
PRPH	0	.	GRCh37	12	49689244	49689244	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.261C>G	p.Asn87Lys	p.N87K	ENST00000257860	1/9	45	41	4	25	25	0	PRPH,missense_variant,p.Asn87Lys,ENST00000257860,;PRPH,missense_variant,p.Asn6Lys,ENST00000451891,;PRPH,upstream_gene_variant,,ENST00000532332,;RP11-161H23.9,non_coding_transcript_exon_variant,,ENST00000553259,;PRPH,downstream_gene_variant,,ENST00000551194,;PRPH,upstream_gene_variant,,ENST00000533401,;PRPH,upstream_gene_variant,,ENST00000530631,;PRPH,upstream_gene_variant,,ENST00000537252,;	G	ENSG00000135406	ENST00000257860	Transcript	missense_variant	1760	261	87	N/K	aaC/aaG	.	.	.	1	PRPH	HGNC	9461	protein_coding	YES	CCDS8783.1	ENSP00000257860	PERI_HUMAN	.	UPI000013CF92	.	deleterious(0.05)	probably_damaging(0.997)	1/9	.	Pfam_domain:PF04732,hmmpanther:PTHR23239:SF29,hmmpanther:PTHR23239,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCAACCAGGA	.	3	ESCA
KCNA1	0	.	GRCh37	12	5023196	5023196	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1164G>T	.	.	ENST00000382545	2/2	24	18	6	21	21	0	KCNA1,3_prime_UTR_variant,,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	T	ENSG00000111262	ENST00000382545	Transcript	3_prime_UTR_variant	3759	.	.	.	.	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCAGTAATA	.	5	ESCA
ASIC1	0	.	GRCh37	12	50453616	50453616	+	Missense_Mutation	SNP	G	G	T	rs752727617	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437G>T	p.Ser146Ile	p.S146I	ENST00000228468	3/12	67	60	7	55	55	0	ASIC1,missense_variant,p.Ser146Ile,ENST00000228468,;ASIC1,missense_variant,p.Ser146Ile,ENST00000447966,;ASIC1,upstream_gene_variant,,ENST00000453327,;ASIC1,missense_variant,p.Ser146Ile,ENST00000550558,;	T	ENSG00000110881	ENST00000228468	Transcript	missense_variant	822	437	146	S/I	aGc/aTc	rs752727617	.	.	1	ASIC1	HGNC	100	protein_coding	YES	CCDS8796.1	ENSP00000228468	ASIC1_HUMAN	.	UPI000013C8D6	.	tolerated(0.45)	benign(0.009)	3/12	.	hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF110,Gene3D:2qtsA03,Pfam_domain:PF00858	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCAGCTTCA	.	4	ESCA
FAM186A	0	.	GRCh37	12	50744904	50744904	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5711C>G	p.Ser1904Cys	p.S1904C	ENST00000327337	4/8	80	71	8	61	61	0	FAM186A,missense_variant,p.Ser1904Cys,ENST00000327337,;FAM186A,missense_variant,p.Ser1904Cys,ENST00000543111,;FAM186A,upstream_gene_variant,,ENST00000543096,;	C	ENSG00000185958	ENST00000327337	Transcript	missense_variant	5711	5711	1904	S/C	tCt/tGt	.	.	.	-1	FAM186A	HGNC	26980	protein_coding	YES	CCDS44878.1	ENSP00000329995	F186A_HUMAN	.	UPI00001D7978	.	deleterious(0.01)	possibly_damaging(0.639)	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTAGAAGGA	.	4	ESCA
SLC4A8	0	.	GRCh37	12	51865176	51865176	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1764C>G	p.Tyr588Ter	p.Y588*	ENST00000453097	14/25	108	99	9	89	89	0	SLC4A8,stop_gained,p.Tyr535Ter,ENST00000394856,;SLC4A8,stop_gained,p.Tyr588Ter,ENST00000453097,;SLC4A8,stop_gained,p.Tyr535Ter,ENST00000535225,;SLC4A8,stop_gained,p.Tyr535Ter,ENST00000514353,;SLC4A8,stop_gained,p.Tyr615Ter,ENST00000358657,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000546663,;SLC4A8,downstream_gene_variant,,ENST00000550211,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000319957,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000551071,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000604314,;	G	ENSG00000050438	ENST00000453097	Transcript	stop_gained	1981	1764	588	Y/*	taC/taG	.	.	.	1	SLC4A8	HGNC	11034	protein_coding	YES	CCDS44890.1	ENSP00000405812	S4A8_HUMAN	.	UPI00005E6FB4	.	.	.	14/25	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF37,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834,Prints_domain:PR01231	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCTACATTAC	.	3	ESCA
ACVRL1	0	.	GRCh37	12	52306268	52306268	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10G>T	p.Gly4Cys	p.G4C	ENST00000388922	2/10	60	54	6	55	55	0	ACVRL1,missense_variant,p.Gly18Cys,ENST00000550683,;ACVRL1,missense_variant,p.Gly18Cys,ENST00000419526,;ACVRL1,missense_variant,p.Gly4Cys,ENST00000551576,;ACVRL1,missense_variant,p.Gly18Cys,ENST00000547400,;ACVRL1,missense_variant,p.Gly4Cys,ENST00000388922,;ACVRL1,upstream_gene_variant,,ENST00000552678,;ACVRL1,upstream_gene_variant,,ENST00000547632,;	T	ENSG00000139567	ENST00000388922	Transcript	missense_variant	293	10	4	G/C	Ggc/Tgc	.	.	.	1	ACVRL1	HGNC	175	protein_coding	YES	CCDS31804.1	ENSP00000373574	ACVL1_HUMAN	D9IPD9_HUMAN,B4DUF0_HUMAN	UPI000000D9F4	.	deleterious_low_confidence(0.01)	benign(0.299)	2/10	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTTGGGCTCC	.	4	ESCA
KRT6C	0	.	GRCh37	12	52867433	52867433	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.89G>C	p.Arg30Pro	p.R30P	ENST00000252250	1/9	176	167	9	167	167	0	KRT6C,missense_variant,p.Arg30Pro,ENST00000252250,;KRT6C,upstream_gene_variant,,ENST00000553087,;	G	ENSG00000170465	ENST00000252250	Transcript	missense_variant	137	89	30	R/P	cGc/cCc	.	.	.	-1	KRT6C	HGNC	20406	protein_coding	YES	CCDS8829.1	ENSP00000252250	K2C6C_HUMAN	.	UPI00001AE73F	.	deleterious(0.01)	unknown(0)	1/9	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGAGCGGCTG	.	2	ESCA
KRT76	0	.	GRCh37	12	53165004	53165004	+	Splice_Site	SNP	C	C	A	rs780721667	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1264-1G>T	.	p.X422_splice	ENST00000332411	.	70	63	7	56	56	0	KRT76,splice_acceptor_variant,,ENST00000332411,;	A	ENSG00000185069	ENST00000332411	Transcript	splice_acceptor_variant	.	.	.	.	.	rs780721667	.	.	-1	KRT76	HGNC	24430	protein_coding	YES	CCDS8838.1	ENSP00000330101	K22O_HUMAN	.	UPI000019B3C1	.	.	.	.	6/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCATTCTGAGG	.	3	ESCA
MYL6	0	.	GRCh37	12	56552187	56552187	+	Translation_Start_Site	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2T>C	p.Met1?	p.M1?	ENST00000550697	1/7	54	50	4	50	50	0	MYL6,start_lost,p.Met1?,ENST00000547649,;MYL6,start_lost,p.Met1?,ENST00000548293,;MYL6,start_lost,p.Met1?,ENST00000549566,;MYL6,start_lost,p.Met1?,ENST00000551589,;MYL6,start_lost,p.Met1?,ENST00000547408,;MYL6,start_lost,p.Met1?,ENST00000348108,;MYL6,start_lost,p.Met1?,ENST00000550697,;MYL6,start_lost,p.Met1?,ENST00000549392,;MYL6,start_lost,p.Met1?,ENST00000548580,;MYL6,start_lost,p.Met1?,ENST00000293422,;MYL6,start_lost,p.Met1?,ENST00000536128,;MYL6,start_lost,p.Met1?,ENST00000548400,;MYL6,splice_region_variant,,ENST00000549017,;MYL6B,downstream_gene_variant,,ENST00000552568,;SMARCC2,downstream_gene_variant,,ENST00000347471,;MYL6B,downstream_gene_variant,,ENST00000553066,;SMARCC2,downstream_gene_variant,,ENST00000267064,;SMARCC2,downstream_gene_variant,,ENST00000394023,;MYL6B,downstream_gene_variant,,ENST00000207437,;MYL6B,downstream_gene_variant,,ENST00000550443,;MYL6B,downstream_gene_variant,,ENST00000551834,;SMARCC2,downstream_gene_variant,,ENST00000550164,;RP11-977G19.5,downstream_gene_variant,,ENST00000553176,;RP11-603J24.14,upstream_gene_variant,,ENST00000548731,;MYL6,splice_region_variant,,ENST00000552297,;MYL6,splice_region_variant,,ENST00000550639,;MYL6B,intron_variant,,ENST00000548571,;MYL6,upstream_gene_variant,,ENST00000551954,;MYL6B,downstream_gene_variant,,ENST00000550152,;MYL6,splice_region_variant,,ENST00000547703,;MYL6,splice_region_variant,,ENST00000550184,;MYL6,splice_region_variant,,ENST00000548725,;MYL6,non_coding_transcript_exon_variant,,ENST00000546630,;SMARCC2,downstream_gene_variant,,ENST00000552674,;MYL6,upstream_gene_variant,,ENST00000546845,;MYL6B,downstream_gene_variant,,ENST00000550550,;MYL6B,downstream_gene_variant,,ENST00000549380,;MYL6B,downstream_gene_variant,,ENST00000549178,;MYL6B,downstream_gene_variant,,ENST00000405661,;MYL6B,downstream_gene_variant,,ENST00000548548,;	C	ENSG00000092841	ENST00000550697	Transcript	start_lost	243	2	1	M/T	aTg/aCg	.	.	.	1	MYL6	HGNC	7587	protein_coding	YES	CCDS8906.1	ENSP00000446955	MYL6_HUMAN	.	UPI0000000E0D	.	deleterious(0)	benign(0.033)	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAGATGGTGG	.	2	ESCA
PRIM1	0	.	GRCh37	12	57132266	57132266	+	Nonsense_Mutation	SNP	C	C	A	rs767715856	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1096G>T	p.Glu366Ter	p.E366*	ENST00000338193	11/13	51	43	8	46	46	0	PRIM1,stop_gained,p.Glu366Ter,ENST00000338193,;PRIM1,stop_gained,p.Glu147Ter,ENST00000549549,;PRIM1,downstream_gene_variant,,ENST00000550770,;PRIM1,3_prime_UTR_variant,,ENST00000552590,;	A	ENSG00000198056	ENST00000338193	Transcript	stop_gained	1133	1096	366	E/*	Gaa/Taa	rs767715856	.	.	-1	PRIM1	HGNC	9369	protein_coding	YES	CCDS44926.1	ENSP00000350491	PRI1_HUMAN	.	UPI00001321AF	.	.	.	11/13	.	Gene3D:1v33A01,hmmpanther:PTHR10536,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTTCCTCTT	byFrequency	4	ESCA
R3HDM2	0	.	GRCh37	12	57686359	57686359	+	Intron	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.810+2823G>C	.	.	ENST00000347140	.	104	97	7	91	91	0	R3HDM2,missense_variant,p.Arg301Pro,ENST00000402412,;R3HDM2,missense_variant,p.Arg52Pro,ENST00000429355,;R3HDM2,intron_variant,,ENST00000413953,;R3HDM2,intron_variant,,ENST00000547262,;R3HDM2,intron_variant,,ENST00000403821,;R3HDM2,intron_variant,,ENST00000347140,;R3HDM2,intron_variant,,ENST00000358907,;R3HDM2,non_coding_transcript_exon_variant,,ENST00000547019,;R3HDM2,intron_variant,,ENST00000393811,;RP11-123K3.4,intron_variant,,ENST00000548184,;	G	ENSG00000179912	ENST00000347140	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	R3HDM2	HGNC	29167	protein_coding	YES	CCDS8937.2	ENSP00000317903	R3HD2_HUMAN	C9J7N6_HUMAN	UPI00005A60D3	.	.	.	.	10/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCTCGGGCA	.	2	ESCA
KIF5A	0	.	GRCh37	12	57943936	57943936	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-119C>T	.	.	ENST00000455537	1/29	21	17	4	15	15	0	KIF5A,5_prime_UTR_variant,,ENST00000455537,;KIF5A,5_prime_UTR_variant,,ENST00000286452,;DCTN2,upstream_gene_variant,,ENST00000550954,;DCTN2,upstream_gene_variant,,ENST00000550750,;DCTN2,upstream_gene_variant,,ENST00000543672,;DCTN2,upstream_gene_variant,,ENST00000548249,;DCTN2,upstream_gene_variant,,ENST00000546670,;DCTN2,upstream_gene_variant,,ENST00000434715,;DCTN2,upstream_gene_variant,,ENST00000549712,;DCTN2,upstream_gene_variant,,ENST00000546559,;DCTN2,upstream_gene_variant,,ENST00000547345,;DCTN2,upstream_gene_variant,,ENST00000549394,;DCTN2,upstream_gene_variant,,ENST00000550201,;DCTN2,upstream_gene_variant,,ENST00000547480,;	T	ENSG00000155980	ENST00000455537	Transcript	5_prime_UTR_variant	156	.	.	.	.	.	.	.	1	KIF5A	HGNC	6323	protein_coding	YES	CCDS8945.1	ENSP00000408979	KIF5A_HUMAN	.	UPI000013DE4C	.	.	.	1/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAACTCTGTCC	.	2	ESCA
C12orf66	0	.	GRCh37	12	64609507	64609507	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472G>A	p.Glu158Lys	p.E158K	ENST00000398055	2/3	79	74	5	65	65	0	C12orf66,missense_variant,p.Glu105Lys,ENST00000544871,;C12orf66,missense_variant,p.Glu158Lys,ENST00000311915,;C12orf66,missense_variant,p.Glu158Lys,ENST00000398055,;	T	ENSG00000174206	ENST00000398055	Transcript	missense_variant	526	472	158	E/K	Gaa/Aaa	.	.	.	-1	C12orf66	HGNC	26517	protein_coding	YES	CCDS41803.1	ENSP00000381132	CL066_HUMAN	.	UPI000013F222	.	deleterious(0.02)	benign(0.377)	2/3	.	hmmpanther:PTHR31581,hmmpanther:PTHR31581:SF1,Pfam_domain:PF09404,Superfamily_domains:0053959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCTTCAGCAT	.	2	ESCA
TAPBPL	0	.	GRCh37	12	6571229	6571229	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1321G>A	p.Glu441Lys	p.E441K	ENST00000266556	7/7	58	52	6	54	54	0	TAPBPL,missense_variant,p.Glu441Lys,ENST00000266556,;VAMP1,downstream_gene_variant,,ENST00000396308,;VAMP1,downstream_gene_variant,,ENST00000361716,;TAPBPL,downstream_gene_variant,,ENST00000544021,;VAMP1,downstream_gene_variant,,ENST00000535180,;VAMP1,downstream_gene_variant,,ENST00000400911,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000539384,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000542160,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000543567,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000545700,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000544289,;VAMP1,downstream_gene_variant,,ENST00000539047,;VAMP1,downstream_gene_variant,,ENST00000544432,;VAMP1,downstream_gene_variant,,ENST00000535927,;VAMP1,downstream_gene_variant,,ENST00000538970,;	A	ENSG00000139192	ENST00000266556	Transcript	missense_variant	1486	1321	441	E/K	Gaa/Aaa	.	.	.	1	TAPBPL	HGNC	30683	protein_coding	YES	CCDS8546.1	ENSP00000266556	TPSNR_HUMAN	.	UPI000013D6F6	.	tolerated_low_confidence(0.08)	benign(0)	7/7	.	hmmpanther:PTHR23411:SF3,hmmpanther:PTHR23411	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTGAACGC	.	4	ESCA
USP5	0	.	GRCh37	12	6973255	6973255	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2140G>T	p.Gly714Cys	p.G714C	ENST00000229268	17/20	60	55	5	42	42	0	USP5,missense_variant,p.Gly714Cys,ENST00000229268,;USP5,missense_variant,p.Gly691Cys,ENST00000389231,;TPI1,upstream_gene_variant,,ENST00000396705,;TPI1,upstream_gene_variant,,ENST00000229270,;TPI1,upstream_gene_variant,,ENST00000535434,;TPI1,upstream_gene_variant,,ENST00000488464,;TPI1,upstream_gene_variant,,ENST00000495834,;TPI1,upstream_gene_variant,,ENST00000462761,;TPI1,upstream_gene_variant,,ENST00000493987,;USP5,downstream_gene_variant,,ENST00000542087,;USP5,downstream_gene_variant,,ENST00000541969,;USP5,non_coding_transcript_exon_variant,,ENST00000542371,;USP5,non_coding_transcript_exon_variant,,ENST00000537267,;	T	ENSG00000111667	ENST00000229268	Transcript	missense_variant	2192	2140	714	G/C	Ggc/Tgc	.	.	.	1	USP5	HGNC	12628	protein_coding	YES	CCDS41743.1	ENSP00000229268	UBP5_HUMAN	.	UPI00001379E1	.	deleterious(0)	probably_damaging(0.988)	17/20	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF381,Pfam_domain:PF00443,Gene3D:1.10.8.10,PIRSF_domain:PIRSF016308,Superfamily_domains:SSF46934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGCCGGGCTCC	.	3	ESCA
PTPRB	0	.	GRCh37	12	70986244	70986244	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1598G>A	p.Gly533Glu	p.G533E	ENST00000334414	7/34	46	42	4	27	27	0	PTPRB,missense_variant,p.Gly315Glu,ENST00000538708,;PTPRB,missense_variant,p.Gly315Glu,ENST00000261266,;PTPRB,missense_variant,p.Gly533Glu,ENST00000334414,;PTPRB,missense_variant,p.Gly533Glu,ENST00000550358,;PTPRB,missense_variant,p.Gly315Glu,ENST00000451516,;PTPRB,missense_variant,p.Gly532Glu,ENST00000551525,;PTPRB,missense_variant,p.Gly412Glu,ENST00000548122,;PTPRB,missense_variant,p.Gly315Glu,ENST00000550857,;PTPRB,non_coding_transcript_exon_variant,,ENST00000538174,;PTPRB,non_coding_transcript_exon_variant,,ENST00000552253,;	T	ENSG00000127329	ENST00000334414	Transcript	missense_variant	1643	1598	533	G/E	gGa/gAa	COSM3464887,COSM3464886,COSM3464885	.	.	-1	PTPRB	HGNC	9665	protein_coding	YES	CCDS44943.1	ENSP00000334928	PTPRB_HUMAN	.	UPI00002294FA	.	deleterious(0)	probably_damaging(0.998)	7/34	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF219,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CATTTCCAGGA	.	2	ESCA
TRHDE	0	.	GRCh37	12	72866848	72866848	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1337G>T	p.Trp446Leu	p.W446L	ENST00000261180	5/19	85	77	8	70	70	0	TRHDE,missense_variant,p.Trp446Leu,ENST00000261180,;TRHDE,intron_variant,,ENST00000547300,;TRHDE,splice_region_variant,,ENST00000548156,;	T	ENSG00000072657	ENST00000261180	Transcript	missense_variant	1433	1337	446	W/L	tGg/tTg	.	.	.	1	TRHDE	HGNC	30748	protein_coding	YES	CCDS9004.1	ENSP00000261180	TRHDE_HUMAN	.	UPI0000136D52	.	deleterious(0)	possibly_damaging(0.731)	5/19	.	Prints_domain:PR00756,Superfamily_domains:SSF55486,Pfam_domain:PF01433,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAGTGGTTTG	.	3	ESCA
PPP1R12A	0	.	GRCh37	12	80182458	80182458	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2772A>G	p.%3D	p.L924L	ENST00000450142	21/25	144	130	13	107	107	0	PPP1R12A,synonymous_variant,p.%3D,ENST00000550299,;PPP1R12A,synonymous_variant,p.%3D,ENST00000546369,;PPP1R12A,synonymous_variant,p.%3D,ENST00000261207,;PPP1R12A,synonymous_variant,p.%3D,ENST00000437004,;PPP1R12A,synonymous_variant,p.%3D,ENST00000450142,;PPP1R12A,synonymous_variant,p.%3D,ENST00000550107,;PPP1R12A,synonymous_variant,p.%3D,ENST00000546762,;PPP1R12A,3_prime_UTR_variant,,ENST00000550903,;PPP1R12A,non_coding_transcript_exon_variant,,ENST00000548908,;PPP1R12A,downstream_gene_variant,,ENST00000550369,;PPP1R12A,upstream_gene_variant,,ENST00000550351,;	C	ENSG00000058272	ENST00000450142	Transcript	synonymous_variant	3039	2772	924	L	ctA/ctG	.	.	.	-1	PPP1R12A	HGNC	7618	protein_coding	YES	CCDS44947.1	ENSP00000389168	MYPT1_HUMAN	F8VW28_HUMAN	UPI0000073E69	.	.	.	21/25	.	hmmpanther:PTHR24179:SF20,hmmpanther:PTHR24179,PIRSF_domain:PIRSF038141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTCTAGCCT	.	3	ESCA
SLC2A3	0	.	GRCh37	12	8077066	8077066	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1008G>C	p.Met336Ile	p.M336I	ENST00000075120	8/10	99	94	5	84	84	0	SLC2A3,missense_variant,p.Met336Ile,ENST00000075120,;SLC2A3,upstream_gene_variant,,ENST00000543435,;SLC2A3,non_coding_transcript_exon_variant,,ENST00000479059,;SLC2A3,non_coding_transcript_exon_variant,,ENST00000486749,;SLC2A3,downstream_gene_variant,,ENST00000490763,;SLC2A3,upstream_gene_variant,,ENST00000469295,;	G	ENSG00000059804	ENST00000075120	Transcript	missense_variant	1249	1008	336	M/I	atG/atC	.	.	.	-1	SLC2A3	HGNC	11007	protein_coding	YES	CCDS8586.1	ENSP00000075120	GTR3_HUMAN	.	UPI0000001C7D	.	deleterious(0.02)	benign(0.063)	8/10	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24063:SF322,hmmpanther:PTHR24063,PROSITE_patterns:PS00216,TIGRFAM_domain:TIGR00879,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTATCATATG	.	2	ESCA
PPFIA2	0	.	GRCh37	12	81762631	81762631	+	Missense_Mutation	SNP	C	C	A	rs756345122	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355G>T	p.Arg452Met	p.R452M	ENST00000549396	13/33	90	82	8	67	67	0	PPFIA2,missense_variant,p.Arg434Met,ENST00000333447,;PPFIA2,missense_variant,p.Arg378Met,ENST00000407050,;PPFIA2,missense_variant,p.Arg19Met,ENST00000541570,;PPFIA2,missense_variant,p.Arg353Met,ENST00000443686,;PPFIA2,missense_variant,p.Arg434Met,ENST00000549325,;PPFIA2,missense_variant,p.Arg452Met,ENST00000550584,;PPFIA2,missense_variant,p.Arg452Met,ENST00000552948,;PPFIA2,missense_variant,p.Arg299Met,ENST00000550359,;PPFIA2,missense_variant,p.Arg33Met,ENST00000553058,;PPFIA2,missense_variant,p.Arg452Met,ENST00000549396,;PPFIA2,missense_variant,p.Arg452Met,ENST00000548586,;PPFIA2,missense_variant,p.Arg19Met,ENST00000548670,;PPFIA2,5_prime_UTR_variant,,ENST00000541017,;PPFIA2,downstream_gene_variant,,ENST00000548790,;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,missense_variant,p.Arg19Met,ENST00000551461,;	A	ENSG00000139220	ENST00000549396	Transcript	missense_variant	1516	1355	452	R/M	aGg/aTg	rs756345122	.	.	-1	PPFIA2	HGNC	9246	protein_coding	YES	CCDS55857.1	ENSP00000450337	LIPA2_HUMAN	H0YHK3_HUMAN,F8W1Y8_HUMAN,F8VU88_HUMAN	UPI0000168655	.	deleterious(0.03)	possibly_damaging(0.82)	13/33	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTGCCTAGCC	.	3	ESCA
ATP2B1	0	.	GRCh37	12	89998032	89998032	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2534G>A	p.Gly845Glu	p.G845E	ENST00000428670	16/21	87	78	8	64	64	0	ATP2B1,missense_variant,p.Gly588Glu,ENST00000393164,;ATP2B1,missense_variant,p.Gly845Glu,ENST00000261173,;ATP2B1,missense_variant,p.Gly845Glu,ENST00000428670,;ATP2B1,missense_variant,p.Gly845Glu,ENST00000359142,;ATP2B1,missense_variant,p.Gly845Glu,ENST00000348959,;ATP2B1,upstream_gene_variant,,ENST00000550716,;ATP2B1,non_coding_transcript_exon_variant,,ENST00000551009,;ATP2B1,non_coding_transcript_exon_variant,,ENST00000549727,;ATP2B1,upstream_gene_variant,,ENST00000552275,;	T	ENSG00000070961	ENST00000428670	Transcript	missense_variant	2991	2534	845	G/E	gGa/gAa	.	.	.	-1	ATP2B1	HGNC	814	protein_coding	YES	CCDS9035.1	ENSP00000392043	AT2B1_HUMAN	Q3L582_HUMAN	UPI000002A436	.	deleterious(0)	probably_damaging(1)	16/21	.	hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF245,TIGRFAM_domain:TIGR01494,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,Superfamily_domains:0049473,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCGTCCCCAC	.	4	ESCA
CCER1	0	.	GRCh37	12	91348442	91348442	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78G>C	p.Trp26Cys	p.W26C	ENST00000358859	1/1	45	40	5	35	35	0	CCER1,missense_variant,p.Trp26Cys,ENST00000358859,;CCER1,intron_variant,,ENST00000548187,;CCER1,upstream_gene_variant,,ENST00000549707,;	G	ENSG00000197651	ENST00000358859	Transcript	missense_variant	512	78	26	W/C	tgG/tgC	.	.	.	-1	CCER1	HGNC	28373	protein_coding	YES	CCDS9036.1	ENSP00000351727	CCER1_HUMAN	.	UPI000006EE70	.	deleterious(0)	possibly_damaging(0.878)	1/1	.	Low_complexity_(Seg):seg,Pfam_domain:PF15482	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTGCCCAGCC	.	4	ESCA
C12orf74	0	.	GRCh37	12	93100603	93100603	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196T>A	p.Trp66Arg	p.W66R	ENST00000397833	2/3	74	67	7	37	37	0	C12orf74,missense_variant,p.Trp66Arg,ENST00000397833,;C12orf74,missense_variant,p.Trp66Arg,ENST00000544406,;	A	ENSG00000214215	ENST00000397833	Transcript	missense_variant	647	196	66	W/R	Tgg/Agg	.	.	.	1	C12orf74	HGNC	27887	protein_coding	YES	CCDS41819.1	ENSP00000380933	CL074_HUMAN	.	UPI00005DB386	.	tolerated(0.1)	benign(0.019)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ATGCCTGGCAG	.	3	ESCA
C12orf74	0	.	GRCh37	12	93100604	93100604	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.197G>T	p.Trp66Leu	p.W66L	ENST00000397833	2/3	75	68	7	38	38	0	C12orf74,missense_variant,p.Trp66Leu,ENST00000397833,;C12orf74,missense_variant,p.Trp66Leu,ENST00000544406,;	T	ENSG00000214215	ENST00000397833	Transcript	missense_variant	648	197	66	W/L	tGg/tTg	.	.	.	1	C12orf74	HGNC	27887	protein_coding	YES	CCDS41819.1	ENSP00000380933	CL074_HUMAN	.	UPI00005DB386	.	tolerated(1)	benign(0)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCTGGCAGG	.	4	ESCA
C12orf74	0	.	GRCh37	12	93100605	93100605	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198G>T	p.Trp66Cys	p.W66C	ENST00000397833	2/3	74	66	7	38	38	0	C12orf74,missense_variant,p.Trp66Cys,ENST00000397833,;C12orf74,missense_variant,p.Trp66Cys,ENST00000544406,;	T	ENSG00000214215	ENST00000397833	Transcript	missense_variant	649	198	66	W/C	tgG/tgT	.	.	.	1	C12orf74	HGNC	27887	protein_coding	YES	CCDS41819.1	ENSP00000380933	CL074_HUMAN	.	UPI00005DB386	.	deleterious(0.03)	benign(0.161)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTGGCAGGT	.	4	ESCA
UBE2N	0	.	GRCh37	12	93802955	93802955	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*860G>T	.	.	ENST00000318066	4/4	41	36	5	27	27	0	UBE2N,3_prime_UTR_variant,,ENST00000550657,;UBE2N,3_prime_UTR_variant,,ENST00000318066,;UBE2N,downstream_gene_variant,,ENST00000549833,;UBE2N,downstream_gene_variant,,ENST00000552442,;UBE2N,upstream_gene_variant,,ENST00000548946,;UBE2N,downstream_gene_variant,,ENST00000549490,;	A	ENSG00000177889	ENST00000318066	Transcript	3_prime_UTR_variant	1697	.	.	.	.	.	.	.	-1	UBE2N	HGNC	12492	protein_coding	YES	CCDS31875.1	ENSP00000316176	UBE2N_HUMAN	F8VQQ8_HUMAN	UPI0000003EA3	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTACTATCT	.	4	ESCA
WASF3	0	.	GRCh37	13	27256798	27256798	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1038G>T	p.%3D	p.P346P	ENST00000335327	9/10	112	102	10	88	88	0	WASF3,synonymous_variant,p.%3D,ENST00000361042,;WASF3,synonymous_variant,p.%3D,ENST00000335327,;	T	ENSG00000132970	ENST00000335327	Transcript	synonymous_variant	1216	1038	346	P	ccG/ccT	.	.	.	1	WASF3	HGNC	12734	protein_coding	YES	CCDS9318.1	ENSP00000335055	WASF3_HUMAN	Q5T8P4_HUMAN,B4DGR1_HUMAN	UPI000013CEA7	.	.	.	9/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12902:SF7,hmmpanther:PTHR12902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTCCGCCACC	.	3	ESCA
MTUS2	0	.	GRCh37	13	29599324	29599324	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.519G>T	p.%3D	p.L173L	ENST00000431530	1/14	42	36	5	47	47	0	MTUS2,synonymous_variant,p.%3D,ENST00000431530,;	T	ENSG00000132938	ENST00000431530	Transcript	synonymous_variant	577	519	173	L	ctG/ctT	.	.	.	1	MTUS2	HGNC	20595	protein_coding	YES	CCDS45022.1	ENSP00000392057	.	J3KQA9_HUMAN,B4DWQ4_HUMAN	UPI0000F734AC	.	.	.	1/14	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACTGGCAAA	.	4	ESCA
FRY	0	.	GRCh37	13	32812001	32812001	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6296G>T	p.Gly2099Val	p.G2099V	ENST00000380250	44/61	35	31	3	28	28	0	FRY,missense_variant,p.Gly2099Val,ENST00000380250,;	T	ENSG00000073910	ENST00000380250	Transcript	missense_variant	6792	6296	2099	G/V	gGg/gTg	.	.	.	1	FRY	HGNC	20367	protein_coding	YES	CCDS41875.1	ENSP00000369600	FRY_HUMAN	Q96KW3_HUMAN,F5H4D2_HUMAN	UPI000046FD40	.	deleterious(0)	probably_damaging(1)	44/61	.	Pfam_domain:PF14225,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CTCCGGGCTGC	.	2	ESCA
RFC3	0	.	GRCh37	13	34410426	34410426	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1065G>T	p.Met355Ile	p.M355I	ENST00000380071	9/9	74	69	5	50	50	0	RFC3,missense_variant,p.Met355Ile,ENST00000380071,;RFC3,intron_variant,,ENST00000434425,;	T	ENSG00000133119	ENST00000380071	Transcript	missense_variant	1195	1065	355	M/I	atG/atT	.	.	.	1	RFC3	HGNC	9971	protein_coding	YES	CCDS9352.1	ENSP00000369411	RFC3_HUMAN	.	UPI0000125168	.	tolerated(0.51)	benign(0.001)	9/9	.	hmmpanther:PTHR11669,hmmpanther:PTHR11669:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGATGTTCTG	.	2	ESCA
TRPC4	0	.	GRCh37	13	38357272	38357272	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199G>A	p.Asp67Asn	p.D67N	ENST00000379681	2/11	59	53	6	61	61	0	TRPC4,missense_variant,p.Asp67Asn,ENST00000379673,;TRPC4,missense_variant,p.Asp67Asn,ENST00000338947,;TRPC4,missense_variant,p.Asp67Asn,ENST00000379681,;TRPC4,missense_variant,p.Asp67Asn,ENST00000447043,;TRPC4,missense_variant,p.Asp67Asn,ENST00000379679,;TRPC4,missense_variant,p.Asp67Asn,ENST00000355779,;TRPC4,missense_variant,p.Asp67Asn,ENST00000358477,;TRPC4,missense_variant,p.Asp67Asn,ENST00000426868,;TRPC4,missense_variant,p.Asp67Asn,ENST00000379705,;TRPC4,missense_variant,p.Asp67Asn,ENST00000488717,;	T	ENSG00000133107	ENST00000379681	Transcript	missense_variant	434	199	67	D/N	Gat/Aat	.	.	.	-1	TRPC4	HGNC	12336	protein_coding	YES	CCDS45037.1	ENSP00000369003	TRPC4_HUMAN	.	UPI000006E5BE	.	deleterious(0)	probably_damaging(1)	2/11	.	hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,Pfam_domain:PF12796,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGGATCAATGC	.	3	ESCA
FREM2	0	.	GRCh37	13	39424336	39424336	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6541C>A	p.Pro2181Thr	p.P2181T	ENST00000280481	9/24	42	38	4	33	33	0	FREM2,missense_variant,p.Pro2181Thr,ENST00000280481,;FREM2,non_coding_transcript_exon_variant,,ENST00000482551,;	A	ENSG00000150893	ENST00000280481	Transcript	missense_variant	6757	6541	2181	P/T	Cca/Aca	.	.	.	1	FREM2	HGNC	25396	protein_coding	YES	CCDS31960.1	ENSP00000280481	FREM2_HUMAN	.	UPI00005520B9	.	deleterious(0.03)	probably_damaging(1)	9/24	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF19,Pfam_domain:PF03160,SMART_domains:SM00237,Superfamily_domains:SSF141072	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AACGCCCAAAC	.	3	ESCA
STOML3	0	.	GRCh37	13	39550710	39550710	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196G>T	p.Gly66Ter	p.G66*	ENST00000379631	3/7	117	96	20	100	100	0	STOML3,stop_gained,p.Gly66Ter,ENST00000379631,;STOML3,stop_gained,p.Gly57Ter,ENST00000423210,;	A	ENSG00000133115	ENST00000379631	Transcript	stop_gained	541	196	66	G/*	Gga/Tga	.	.	.	-1	STOML3	HGNC	19420	protein_coding	YES	CCDS9367.1	ENSP00000368952	STML3_HUMAN	.	UPI000003615B	.	.	.	3/7	.	hmmpanther:PTHR10264:SF75,hmmpanther:PTHR10264,Pfam_domain:PF01145,SMART_domains:SM00244,Prints_domain:PR00721	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGTCCCAGAC	.	5	ESCA
KBTBD6	0	.	GRCh37	13	41706476	41706476	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>A	p.Asp58Asn	p.D58N	ENST00000379485	1/1	90	79	11	53	53	0	KBTBD6,missense_variant,p.Asp58Asn,ENST00000379485,;KBTBD6,intron_variant,,ENST00000499385,;	T	ENSG00000165572	ENST00000379485	Transcript	missense_variant	407	172	58	D/N	Gat/Aat	.	.	.	-1	KBTBD6	HGNC	25340	protein_coding	YES	CCDS9376.1	ENSP00000368799	KBTB6_HUMAN	.	UPI00001969BB	.	deleterious(0)	probably_damaging(1)	1/1	.	hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF132,Gene3D:3.30.710.10,Pfam_domain:PF00651,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCATCGTAGA	.	4	ESCA
ZC3H13	0	.	GRCh37	13	46549674	46549674	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2212G>T	p.Glu738Ter	p.E738*	ENST00000282007	12/17	85	73	11	63	63	0	ZC3H13,stop_gained,p.Glu738Ter,ENST00000242848,;ZC3H13,stop_gained,p.Glu738Ter,ENST00000282007,;	A	ENSG00000123200	ENST00000282007	Transcript	stop_gained	2283	2212	738	E/*	Gaa/Taa	.	.	.	-1	ZC3H13	HGNC	20368	protein_coding	YES	CCDS9400.1	ENSP00000282007	ZC3HD_HUMAN	.	UPI0000366969	.	.	.	12/17	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13585:SF2,hmmpanther:PTHR13585	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTTCCCGCT	.	4	ESCA
KLF5	0	.	GRCh37	13	73651442	73651442	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1418G>A	.	.	ENST00000377687	4/4	132	125	6	72	72	0	KLF5,3_prime_UTR_variant,,ENST00000377687,;KLF5,downstream_gene_variant,,ENST00000539231,;KLF5,downstream_gene_variant,,ENST00000464404,;	A	ENSG00000102554	ENST00000377687	Transcript	3_prime_UTR_variant	3328	.	.	.	.	.	.	.	1	KLF5	HGNC	6349	protein_coding	YES	CCDS9448.1	ENSP00000366915	KLF5_HUMAN	Q5T6X2_HUMAN,B4DL96_HUMAN,A2TJX0_HUMAN	UPI0000000C89	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAACGATGTA	.	2	ESCA
MYCBP2	0	.	GRCh37	13	77619051	77619051	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*462T>A	.	.	ENST00000544440	83/83	42	37	5	48	48	0	MYCBP2,3_prime_UTR_variant,,ENST00000357337,;MYCBP2,3_prime_UTR_variant,,ENST00000429715,;MYCBP2,3_prime_UTR_variant,,ENST00000544440,;MYCBP2,3_prime_UTR_variant,,ENST00000407578,;	T	ENSG00000005810	ENST00000544440	Transcript	3_prime_UTR_variant	14403	.	.	.	.	.	.	.	-1	MYCBP2	HGNC	23386	protein_coding	YES	.	ENSP00000444596	MYCB2_HUMAN	.	UPI0000212757	.	.	.	83/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTTAAATAA	.	3	ESCA
POU4F1	0	.	GRCh37	13	79173478	79173478	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2072C>T	.	.	ENST00000377208	2/2	63	58	5	53	53	0	POU4F1,3_prime_UTR_variant,,ENST00000377208,;RP11-52L5.6,non_coding_transcript_exon_variant,,ENST00000607269,;RNF219-AS1,intron_variant,,ENST00000430549,;RNF219-AS1,intron_variant,,ENST00000560584,;RNF219-AS1,intron_variant,,ENST00000606124,;RNF219-AS1,intron_variant,,ENST00000607205,;RNF219-AS1,intron_variant,,ENST00000607220,;RNF219-AS1,intron_variant,,ENST00000606376,;RNF219-AS1,intron_variant,,ENST00000560209,;RNF219-AS1,intron_variant,,ENST00000444769,;RNF219-AS1,intron_variant,,ENST00000606429,;RNF219-AS1,intron_variant,,ENST00000607860,;	A	ENSG00000152192	ENST00000377208	Transcript	3_prime_UTR_variant	3544	.	.	.	.	.	.	.	-1	POU4F1	HGNC	9218	protein_coding	YES	CCDS31996.1	ENSP00000366413	PO4F1_HUMAN	.	UPI000013DCAA	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AATCCGTGAGA	.	3	ESCA
BEGAIN	0	.	GRCh37	14	101005081	101005081	+	Missense_Mutation	SNP	C	C	A	rs199676704	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1007G>T	p.Arg336Leu	p.R336L	ENST00000443071	6/6	19	15	4	21	21	0	BEGAIN,missense_variant,p.Arg336Leu,ENST00000355173,;BEGAIN,missense_variant,p.Arg336Leu,ENST00000443071,;BEGAIN,missense_variant,p.Arg272Leu,ENST00000556751,;BEGAIN,downstream_gene_variant,,ENST00000554140,;BEGAIN,downstream_gene_variant,,ENST00000557378,;BEGAIN,downstream_gene_variant,,ENST00000556188,;BEGAIN,downstream_gene_variant,,ENST00000554356,;BEGAIN,downstream_gene_variant,,ENST00000553553,;CTD-2062F14.3,upstream_gene_variant,,ENST00000553301,;	A	ENSG00000183092	ENST00000443071	Transcript	missense_variant	1153	1007	336	R/L	cGc/cTc	rs199676704	.	.	-1	BEGAIN	HGNC	24163	protein_coding	YES	CCDS9962.1	ENSP00000411124	BEGIN_HUMAN	G3V600_HUMAN,G3V536_HUMAN,G3V3R5_HUMAN,G3V2K4_HUMAN	UPI00000710B1	.	deleterious(0)	probably_damaging(0.922)	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTGCGGTCG	byCluster	4	ESCA
MIR409	0	.	GRCh37	14	101531639	101531639	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3G>T	.	.	ENST00000362237	1/1	98	92	6	66	66	0	MIR409,non_coding_transcript_exon_variant,,ENST00000362237,;MIR541,downstream_gene_variant,,ENST00000401360,;MIR656,upstream_gene_variant,,ENST00000385224,;MEG9,upstream_gene_variant,,ENST00000429368,;MIR412,upstream_gene_variant,,ENST00000362142,;MIR369,upstream_gene_variant,,ENST00000362155,;MIR410,upstream_gene_variant,,ENST00000362222,;MIR496,downstream_gene_variant,,ENST00000385226,;MIR377,downstream_gene_variant,,ENST00000362145,;	T	ENSG00000199107	ENST00000362237	Transcript	non_coding_transcript_exon_variant	3	.	.	.	.	.	.	.	1	MIR409	HGNC	32055	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATGGTACTC	.	2	ESCA
DIO3	0	.	GRCh37	14	102027984	102027984	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.151C>A	p.Arg51Ser	p.R51S	ENST00000510508	1/1	119	111	8	86	86	0	DIO3,missense_variant,p.Arg51Ser,ENST00000510508,;DIO3,missense_variant,p.Arg25Ser,ENST00000359323,;DIO3OS,upstream_gene_variant,,ENST00000553729,;DIO3OS,upstream_gene_variant,,ENST00000555174,;DIO3OS,upstream_gene_variant,,ENST00000554735,;DIO3OS,upstream_gene_variant,,ENST00000555882,;DIO3OS,upstream_gene_variant,,ENST00000557532,;DIO3OS,upstream_gene_variant,,ENST00000554441,;DIO3OS,upstream_gene_variant,,ENST00000557109,;DIO3OS,upstream_gene_variant,,ENST00000556266,;DIO3OS,upstream_gene_variant,,ENST00000554694,;DIO3OS,upstream_gene_variant,,ENST00000557661,;DIO3OS,upstream_gene_variant,,ENST00000408206,;	A	ENSG00000197406	ENST00000510508	Transcript	missense_variant	297	151	51	R/S	Cgc/Agc	.	.	.	1	DIO3	HGNC	2885	protein_coding	YES	CCDS41992.2	ENSP00000427336	.	Q86TU3_HUMAN	UPI0001B1A4B2	.	deleterious(0.01)	probably_damaging(0.992)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF4,Pfam_domain:PF00837,PIRSF_domain:PIRSF500144,PIRSF_domain:PIRSF001330	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCGCGCTTC	.	2	ESCA
PPP2R5C	0	.	GRCh37	14	102349849	102349849	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.672C>A	p.Phe224Leu	p.F224L	ENST00000422945	7/16	112	95	17	83	83	0	PPP2R5C,missense_variant,p.Phe162Leu,ENST00000557621,;PPP2R5C,missense_variant,p.Phe193Leu,ENST00000350249,;PPP2R5C,missense_variant,p.Phe193Leu,ENST00000445439,;PPP2R5C,missense_variant,p.Phe224Leu,ENST00000422945,;PPP2R5C,missense_variant,p.Phe248Leu,ENST00000328724,;PPP2R5C,missense_variant,p.Phe193Leu,ENST00000557095,;PPP2R5C,missense_variant,p.Phe193Leu,ENST00000334743,;PPP2R5C,missense_variant,p.Phe222Leu,ENST00000557268,;PPP2R5C,upstream_gene_variant,,ENST00000557716,;PPP2R5C,non_coding_transcript_exon_variant,,ENST00000556570,;PPP2R5C,non_coding_transcript_exon_variant,,ENST00000556218,;PPP2R5C,missense_variant,p.Phe43Leu,ENST00000557534,;PPP2R5C,intron_variant,,ENST00000554137,;PPP2R5C,downstream_gene_variant,,ENST00000556307,;PPP2R5C,downstream_gene_variant,,ENST00000553730,;	A	ENSG00000078304	ENST00000422945	Transcript	missense_variant	768	672	224	F/L	ttC/ttA	.	.	.	1	PPP2R5C	HGNC	9311	protein_coding	YES	CCDS53912.1	ENSP00000412324	2A5G_HUMAN	H0YJ75_HUMAN	UPI0001A7AE62	.	deleterious(0.03)	probably_damaging(0.993)	7/16	.	hmmpanther:PTHR10257,Pfam_domain:PF01603,Gene3D:1.25.10.10,PIRSF_domain:PIRSF028043,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATTCCTAGG	.	4	ESCA
PPP2R5C	0	.	GRCh37	14	102391625	102391625	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*16G>T	.	.	ENST00000422945	16/16	94	83	10	56	56	0	PPP2R5C,3_prime_UTR_variant,,ENST00000350249,;PPP2R5C,3_prime_UTR_variant,,ENST00000422945,;PPP2R5C,3_prime_UTR_variant,,ENST00000328724,;PPP2R5C,3_prime_UTR_variant,,ENST00000334743,;PPP2R5C,3_prime_UTR_variant,,ENST00000557268,;PPP2R5C,downstream_gene_variant,,ENST00000555237,;PPP2R5C,3_prime_UTR_variant,,ENST00000557071,;PPP2R5C,non_coding_transcript_exon_variant,,ENST00000554147,;	T	ENSG00000078304	ENST00000422945	Transcript	3_prime_UTR_variant	1780	.	.	.	.	.	.	.	1	PPP2R5C	HGNC	9311	protein_coding	YES	CCDS53912.1	ENSP00000412324	2A5G_HUMAN	H0YJ75_HUMAN	UPI0001A7AE62	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCGCGTCGGG	.	4	ESCA
CINP	0	.	GRCh37	14	102815064	102815064	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.514A>T	p.Arg172Trp	p.R172W	ENST00000536961	5/5	27	23	4	28	28	0	CINP,missense_variant,p.Arg157Trp,ENST00000216756,;CINP,missense_variant,p.Arg172Trp,ENST00000536961,;CINP,synonymous_variant,p.%3D,ENST00000541568,;CINP,downstream_gene_variant,,ENST00000561468,;CINP,upstream_gene_variant,,ENST00000560326,;CINP,missense_variant,p.Arg157Trp,ENST00000559514,;CINP,missense_variant,p.Arg158Trp,ENST00000559504,;CINP,downstream_gene_variant,,ENST00000558764,;	A	ENSG00000100865	ENST00000536961	Transcript	missense_variant	603	514	172	R/W	Agg/Tgg	.	.	.	-1	CINP	HGNC	23789	protein_coding	YES	.	ENSP00000442057	CINP_HUMAN	.	UPI0001D0C47E	.	deleterious(0.02)	benign(0.013)	5/5	.	hmmpanther:PTHR15827,Prints_domain:PR02040	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCTGTACA	.	5	ESCA
AHNAK2	0	.	GRCh37	14	105416412	105416412	+	Silent	SNP	G	G	A	rs187143773	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5376C>T	p.%3D	p.D1792D	ENST00000333244	7/7	291	272	18	236	236	0	AHNAK2,synonymous_variant,p.%3D,ENST00000333244,;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,;	A	ENSG00000185567	ENST00000333244	Transcript	synonymous_variant	5496	5376	1792	D	gaC/gaT	rs187143773	.	.	-1	AHNAK2	HGNC	20125	protein_coding	YES	CCDS45177.1	ENSP00000353114	AHNK2_HUMAN	.	UPI00015BB2CA	.	.	.	7/7	.	hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348	T:0.0004	.	.	.	.	.	.	A:0.0003	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGACGTCCAC	byFrequency|byCluster|by1000G	2	ESCA
AHNAK2	0	.	GRCh37	14	105418587	105418587	+	Silent	SNP	C	C	A	rs536223749	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3201G>T	p.%3D	p.P1067P	ENST00000333244	7/7	151	135	16	130	130	0	AHNAK2,synonymous_variant,p.%3D,ENST00000333244,;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,;	A	ENSG00000185567	ENST00000333244	Transcript	synonymous_variant	3321	3201	1067	P	ccG/ccT	rs536223749	.	.	-1	AHNAK2	HGNC	20125	protein_coding	YES	CCDS45177.1	ENSP00000353114	AHNK2_HUMAN	.	UPI00015BB2CA	.	.	.	7/7	.	hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348	T:0.0004	T:0.0008	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCTCCGGGAG	byFrequency|by1000G	4	ESCA
IGHV1-46	0	.	GRCh37	14	106967190	106967190	+	Silent	SNP	G	G	T	rs782812600	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210C>A	p.%3D	p.I70I	ENST00000390622	2/2	178	154	24	148	147	0	IGHV1-46,synonymous_variant,p.%3D,ENST00000390622,;IGHV1-45,upstream_gene_variant,,ENST00000390621,;LINC00221,intron_variant,,ENST00000433371,;IGHVII-46-1,downstream_gene_variant,,ENST00000519794,;	T	ENSG00000211962	ENST00000390622	Transcript	synonymous_variant	514	210	70	I	atC/atA	rs782812600	.	.	-1	IGHV1-46	HGNC	5554	IG_V_gene	YES	.	ENSP00000375031	.	.	UPI0000113ACE	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF73,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTTGATTAT	.	4	ESCA
IGHV3-53	0	.	GRCh37	14	107049107	107049107	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14T>A	p.Leu5Gln	p.L5Q	ENST00000390627	1/2	221	205	15	190	190	0	IGHV3-53,missense_variant,p.Leu5Gln,ENST00000390627,;	T	ENSG00000211967	ENST00000390627	Transcript	missense_variant	235	14	5	L/Q	cTg/cAg	.	.	.	-1	IGHV3-53	HGNC	5610	IG_V_gene	YES	.	ENSP00000375036	.	.	UPI000011AAC7	.	deleterious_low_confidence(0)	possibly_damaging(0.455)	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23266:SF91,hmmpanther:PTHR23266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTCAGCCAA	.	2	ESCA
TRAV20	0	.	GRCh37	14	22509256	22509256	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.194C>A	p.Pro65His	p.P65H	ENST00000390448	2/2	86	76	10	87	87	0	TRAV20,missense_variant,p.Pro65His,ENST00000390448,;	A	ENSG00000211800	ENST00000390448	Transcript	missense_variant	263	194	65	P/H	cCt/cAt	.	.	.	1	TRAV20	HGNC	12117	TR_V_gene	YES	.	ENSP00000452067	.	.	UPI000011D123	.	deleterious(0.01)	probably_damaging(0.927)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19433:SF56,hmmpanther:PTHR19433,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCCTGAAT	.	4	ESCA
TRAV26-1	0	.	GRCh37	14	22592089	22592089	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174C>A	p.%3D	p.S58S	ENST00000390455	2/2	64	51	12	44	44	0	TRAV26-1,synonymous_variant,p.%3D,ENST00000390455,;	A	ENSG00000211807	ENST00000390455	Transcript	synonymous_variant	383	174	58	S	tcC/tcA	.	.	.	1	TRAV26-1	HGNC	12123	TR_V_gene	YES	.	ENSP00000452431	.	.	UPI000011D129	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19433:SF59,hmmpanther:PTHR19433,Pfam_domain:PF07686,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTCCCAGGG	.	5	ESCA
MYH7	0	.	GRCh37	14	23896795	23896795	+	Silent	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1887G>T	p.%3D	p.A629A	ENST00000355349	16/40	79	75	4	47	47	0	MYH7,synonymous_variant,p.%3D,ENST00000355349,;	A	ENSG00000092054	ENST00000355349	Transcript	synonymous_variant	2050	1887	629	A	gcG/gcT	COSM337381,COSM1163052	.	.	-1	MYH7	HGNC	7577	protein_coding	YES	CCDS9601.1	ENSP00000347507	MYH7_HUMAN	Q59EV3_HUMAN,L0L5E6_HUMAN,A8CLN2_HUMAN,A8CLL2_HUMAN,A6N931_HUMAN,A6N930_HUMAN	UPI000014019B	.	.	.	16/40	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF279,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTACGCGCATC	.	2	ESCA
LRRC16B	0	.	GRCh37	14	24520164	24520164	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000342740	.	131	121	9	90	90	0	LRRC16B,upstream_gene_variant,,ENST00000342740,;LRRC16B,upstream_gene_variant,,ENST00000334420,;RP11-468E2.9,non_coding_transcript_exon_variant,,ENST00000558293,;RP11-468E2.9,non_coding_transcript_exon_variant,,ENST00000559270,;RP11-468E2.9,downstream_gene_variant,,ENST00000558622,;RP11-468E2.9,non_coding_transcript_exon_variant,,ENST00000606840,;RP11-468E2.9,non_coding_transcript_exon_variant,,ENST00000397065,;	A	ENSG00000186648	ENST00000342740	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1045	1	LRRC16B	HGNC	20272	protein_coding	YES	CCDS32054.1	ENSP00000340467	LR16B_HUMAN	.	UPI0000DBEF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACCCCGTCCC	.	2	ESCA
NEDD8	0	.	GRCh37	14	24686403	24686403	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.176A>T	p.Tyr59Phe	p.Y59F	ENST00000250495	4/4	74	69	5	40	40	0	NEDD8,missense_variant,p.Tyr59Phe,ENST00000250495,;NEDD8-MDP1,intron_variant,,ENST00000534348,;CHMP4A,upstream_gene_variant,,ENST00000530996,;CHMP4A,upstream_gene_variant,,ENST00000609024,;TM9SF1,upstream_gene_variant,,ENST00000530611,;MDP1,upstream_gene_variant,,ENST00000396833,;MDP1,upstream_gene_variant,,ENST00000288087,;TM9SF1,upstream_gene_variant,,ENST00000556387,;CHMP4A,upstream_gene_variant,,ENST00000347519,;NEDD8,downstream_gene_variant,,ENST00000524927,;CHMP4A,upstream_gene_variant,,ENST00000533011,;NEDD8,non_coding_transcript_exon_variant,,ENST00000526430,;NEDD8,non_coding_transcript_exon_variant,,ENST00000531430,;NEDD8,non_coding_transcript_exon_variant,,ENST00000527046,;NEDD8-MDP1,intron_variant,,ENST00000604306,;CHMP4A,upstream_gene_variant,,ENST00000531158,;CHMP4A,upstream_gene_variant,,ENST00000542700,;MDP1,upstream_gene_variant,,ENST00000532557,;MDP1,upstream_gene_variant,,ENST00000525696,;NEDD8-MDP1,missense_variant,p.Tyr59Phe,ENST00000605847,;NEDD8,3_prime_UTR_variant,,ENST00000396828,;NEDD8,non_coding_transcript_exon_variant,,ENST00000560427,;NEDD8-MDP1,intron_variant,,ENST00000530579,;CHMP4A,upstream_gene_variant,,ENST00000527154,;MDP1,upstream_gene_variant,,ENST00000533536,;MDP1,upstream_gene_variant,,ENST00000532742,;AL136419.6,upstream_gene_variant,,ENST00000528804,;MDP1,upstream_gene_variant,,ENST00000466422,;MDP1,upstream_gene_variant,,ENST00000528849,;MDP1,upstream_gene_variant,,ENST00000531553,;CHMP4A,upstream_gene_variant,,ENST00000534106,;CHMP4A,upstream_gene_variant,,ENST00000533523,;MDP1,upstream_gene_variant,,ENST00000530222,;AL136419.6,upstream_gene_variant,,ENST00000565988,;	A	ENSG00000129559	ENST00000250495	Transcript	missense_variant	363	176	59	Y/F	tAc/tTc	.	.	.	-1	NEDD8	HGNC	7732	protein_coding	YES	CCDS9621.1	ENSP00000250495	NEDD8_HUMAN	F8VSA6_HUMAN	UPI00000009A5	.	tolerated(0.05)	benign(0.22)	4/4	.	PROSITE_profiles:PS50053,hmmpanther:PTHR10666:SF97,hmmpanther:PTHR10666,Pfam_domain:PF00240,Gene3D:3.10.20.90,SMART_domains:SM00213,Superfamily_domains:SSF54236,Prints_domain:PR00348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTGTAATCA	.	2	ESCA
CTSG	0	.	GRCh37	14	25043995	25043995	+	Silent	SNP	G	G	C	rs143803246	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.225C>G	p.%3D	p.G75G	ENST00000216336	3/5	70	62	8	61	61	0	CTSG,synonymous_variant,p.%3D,ENST00000216336,;CTSG,non_coding_transcript_exon_variant,,ENST00000552252,;	C	ENSG00000100448	ENST00000216336	Transcript	synonymous_variant	262	225	75	G	ggC/ggG	rs143803246,COSM175717	.	.	-1	CTSG	HGNC	2532	protein_coding	YES	CCDS9631.1	ENSP00000216336	CATG_HUMAN	.	UPI00001270AC	.	.	.	3/5	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF13,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0.0002	T:0.0002	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGCGCCCAG	byCluster|by1000G	4	ESCA
C14orf23	0	.	GRCh37	14	29261363	29261363	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.400G>T	p.Gly134Trp	p.G134W	ENST00000399387	3/3	72	65	7	48	48	0	C14orf23,missense_variant,p.Gly134Trp,ENST00000399387,;C14orf23,intron_variant,,ENST00000548213,;C14orf23,intron_variant,,ENST00000550266,;	T	ENSG00000186960	ENST00000399387	Transcript	missense_variant	504	400	134	G/W	Ggg/Tgg	.	.	.	1	C14orf23	HGNC	19828	protein_coding	YES	.	ENSP00000382318	CN023_HUMAN	.	UPI0000160243	.	deleterious_low_confidence(0)	probably_damaging(0.984)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCCAGGGTCT	.	3	ESCA
NPAS3	0	.	GRCh37	14	34269169	34269169	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1656G>A	p.%3D	p.A552A	ENST00000356141	12/12	68	59	9	66	66	0	NPAS3,synonymous_variant,p.%3D,ENST00000548645,;NPAS3,synonymous_variant,p.%3D,ENST00000551492,;NPAS3,synonymous_variant,p.%3D,ENST00000551634,;NPAS3,synonymous_variant,p.%3D,ENST00000346562,;NPAS3,synonymous_variant,p.%3D,ENST00000357798,;NPAS3,synonymous_variant,p.%3D,ENST00000356141,;	A	ENSG00000151322	ENST00000356141	Transcript	synonymous_variant	1656	1656	552	A	gcG/gcA	.	.	.	1	NPAS3	HGNC	19311	protein_coding	YES	CCDS53891.1	ENSP00000348460	NPAS3_HUMAN	.	UPI00000743C2	.	.	.	12/12	.	hmmpanther:PTHR23043:SF21,hmmpanther:PTHR23043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCGCGATGCA	.	4	ESCA
PAX9	0	.	GRCh37	14	37131038	37131038	+	5'Flank	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000361487	.	53	48	5	25	25	0	PAX9,5_prime_UTR_variant,,ENST00000402703,;PAX9,upstream_gene_variant,,ENST00000554201,;PAX9,upstream_gene_variant,,ENST00000361487,;RP11-964E11.2,upstream_gene_variant,,ENST00000555107,;PAX9,non_coding_transcript_exon_variant,,ENST00000553267,;PAX9,intron_variant,,ENST00000555639,;PAX9,upstream_gene_variant,,ENST00000557107,;	A	ENSG00000198807	ENST00000361487	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	32	1	PAX9	HGNC	8623	protein_coding	YES	CCDS9662.1	ENSP00000355245	PAX9_HUMAN	Q7Z4A7_HUMAN,Q2L4T1_HUMAN,E9KY40_HUMAN	UPI0000131377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGTGATAGA	.	4	ESCA
CLEC14A	0	.	GRCh37	14	38725480	38725480	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-253G>T	.	.	ENST00000342213	1/1	100	88	12	63	63	0	CLEC14A,5_prime_UTR_variant,,ENST00000342213,;	A	ENSG00000176435	ENST00000342213	Transcript	5_prime_UTR_variant	95	.	.	.	.	.	.	.	-1	CLEC14A	HGNC	19832	protein_coding	YES	CCDS9667.1	ENSP00000353013	CLC14_HUMAN	.	UPI000000CBD4	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCAGCCCTGA	.	4	ESCA
C14orf28	0	.	GRCh37	14	45370114	45370114	+	Missense_Mutation	SNP	G	G	A	rs771127672	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.476G>A	p.Arg159Gln	p.R159Q	ENST00000325192	2/5	80	71	9	62	62	0	C14orf28,missense_variant,p.Arg159Gln,ENST00000557112,;C14orf28,missense_variant,p.Arg159Gln,ENST00000325192,;RP11-857B24.5,intron_variant,,ENST00000555157,;RP11-857B24.1,upstream_gene_variant,,ENST00000554389,;C14orf28,non_coding_transcript_exon_variant,,ENST00000553841,;C14orf28,non_coding_transcript_exon_variant,,ENST00000555826,;	A	ENSG00000179476	ENST00000325192	Transcript	missense_variant	751	476	159	R/Q	cGa/cAa	rs771127672,COSM309603	.	.	1	C14orf28	HGNC	19834	protein_coding	YES	CCDS32069.1	ENSP00000326846	CN028_HUMAN	.	UPI000015FBE3	.	tolerated_low_confidence(0.39)	benign(0.116)	2/5	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGCGATGCC	byFrequency	4	ESCA
OTX2	0	.	GRCh37	14	57268306	57268306	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*147G>T	.	.	ENST00000339475	5/5	76	72	4	76	76	0	OTX2,3_prime_UTR_variant,,ENST00000339475,;OTX2,downstream_gene_variant,,ENST00000554845,;OTX2,downstream_gene_variant,,ENST00000408990,;OTX2,downstream_gene_variant,,ENST00000554559,;OTX2,downstream_gene_variant,,ENST00000555006,;OTX2,downstream_gene_variant,,ENST00000555804,;OTX2,downstream_gene_variant,,ENST00000554788,;RP11-1085N6.6,upstream_gene_variant,,ENST00000602485,;	A	ENSG00000165588	ENST00000339475	Transcript	3_prime_UTR_variant	1318	.	.	.	.	.	.	.	-1	OTX2	HGNC	8522	protein_coding	YES	CCDS9728.1	ENSP00000343819	OTX2_HUMAN	G3V3P9_HUMAN,F1T0D1_HUMAN	UPI000000161B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTTCGTTTT	.	2	ESCA
RTN1	0	.	GRCh37	14	60097305	60097305	+	Intron	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1766-23095C>G	.	.	ENST00000267484	.	51	44	7	39	39	0	RTN1,5_prime_UTR_variant,,ENST00000395090,;RTN1,5_prime_UTR_variant,,ENST00000342503,;RTN1,intron_variant,,ENST00000267484,;RTN1,non_coding_transcript_exon_variant,,ENST00000557422,;RTN1,intron_variant,,ENST00000432103,;	C	ENSG00000139970	ENST00000267484	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RTN1	HGNC	10467	protein_coding	YES	CCDS9740.1	ENSP00000267484	RTN1_HUMAN	Q2NKQ5_HUMAN,Q2L7A7_HUMAN	UPI00001352DA	.	.	.	.	3/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCGGCTGGG	.	2	ESCA
LRRC9	0	.	GRCh37	14	60411431	60411431	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.851G>A	p.Arg284Gln	p.R284Q	ENST00000445360	8/32	71	65	6	57	57	0	LRRC9,missense_variant,p.Arg284Gln,ENST00000445360,;LRRC9,non_coding_transcript_exon_variant,,ENST00000454474,;LRRC9,missense_variant,p.Arg284Gln,ENST00000254271,;	A	ENSG00000131951	ENST00000445360	Transcript	missense_variant	1055	851	284	R/Q	cGa/cAa	.	.	.	1	LRRC9	HGNC	19848	protein_coding	YES	.	ENSP00000454748	LRRC9_HUMAN	H3BUS4_HUMAN	UPI000173AA0B	.	tolerated(0.1)	benign(0.009)	8/32	.	hmmpanther:PTHR10588,hmmpanther:PTHR10588:SF223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGAACGAGTAA	.	3	ESCA
MPP5	0	.	GRCh37	14	67799567	67799567	+	Missense_Mutation	SNP	C	C	A	rs774877439	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1922C>A	p.Thr641Lys	p.T641K	ENST00000261681	15/15	85	78	7	44	44	0	MPP5,missense_variant,p.Thr607Lys,ENST00000555925,;MPP5,missense_variant,p.Thr641Lys,ENST00000261681,;ATP6V1D,downstream_gene_variant,,ENST00000553408,;ATP6V1D,intron_variant,,ENST00000553974,;ATP6V1D,intron_variant,,ENST00000554087,;ATP6V1D,downstream_gene_variant,,ENST00000555625,;	A	ENSG00000072415	ENST00000261681	Transcript	missense_variant	2583	1922	641	T/K	aCg/aAg	rs774877439,COSM470141	.	.	1	MPP5	HGNC	18669	protein_coding	YES	CCDS9779.1	ENSP00000261681	MPP5_HUMAN	G3V2H1_HUMAN	UPI0000046FB9	.	tolerated(0.29)	possibly_damaging(0.591)	15/15	.	PROSITE_profiles:PS50052,hmmpanther:PTHR23122:SF32,hmmpanther:PTHR23122,Pfam_domain:PF00625,Gene3D:3.40.50.300,SMART_domains:SM00072,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.T641M|c.1922C>T|3	MUTECT|MUSE|VARSCANS	TGATACGGCAA	.	3	ESCA
DPF3	0	.	GRCh37	14	73190435	73190435	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431G>C	p.Arg144Thr	p.R144T	ENST00000541685	5/9	142	129	13	108	108	0	DPF3,missense_variant,p.Arg154Thr,ENST00000546183,;DPF3,missense_variant,p.Arg144Thr,ENST00000541685,;DPF3,missense_variant,p.Arg144Thr,ENST00000556509,;DPF3,splice_region_variant,,ENST00000553608,;DPF3,splice_region_variant,,ENST00000555781,;DPF3,splice_region_variant,,ENST00000557704,;DPF3,non_coding_transcript_exon_variant,,ENST00000556238,;DPF3,missense_variant,p.Arg199Thr,ENST00000366353,;DPF3,missense_variant,p.Arg144Thr,ENST00000381216,;	G	ENSG00000205683	ENST00000541685	Transcript	missense_variant	444	431	144	R/T	aGg/aCg	.	.	.	-1	DPF3	HGNC	17427	protein_coding	YES	CCDS45133.1	ENSP00000441640	DPF3_HUMAN	.	UPI0000246CC0	.	deleterious(0.01)	possibly_damaging(0.765)	5/9	.	hmmpanther:PTHR10615:SF12,hmmpanther:PTHR10615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	AAACCCTCTGA	.	2	ESCA
VSX2	0	.	GRCh37	14	74706337	74706337	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73G>C	p.Ala25Pro	p.A25P	ENST00000261980	1/5	66	58	7	59	59	0	VSX2,missense_variant,p.Ala25Pro,ENST00000261980,;	C	ENSG00000119614	ENST00000261980	Transcript	missense_variant	163	73	25	A/P	Gcc/Ccc	.	.	.	1	VSX2	HGNC	1975	protein_coding	YES	CCDS9827.1	ENSP00000261980	VSX2_HUMAN	.	UPI0000128755	.	tolerated(0.46)	benign(0.001)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGCGCCCCG	.	4	ESCA
ALKBH1	0	.	GRCh37	14	78142116	78142116	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.623G>T	p.Gly208Val	p.G208V	ENST00000216489	5/6	112	102	10	71	71	0	ALKBH1,missense_variant,p.Gly208Val,ENST00000216489,;ALKBH1,3_prime_UTR_variant,,ENST00000555100,;ALKBH1,3_prime_UTR_variant,,ENST00000557057,;	A	ENSG00000100601	ENST00000216489	Transcript	missense_variant	639	623	208	G/V	gGa/gTa	.	.	.	-1	ALKBH1	HGNC	17911	protein_coding	YES	CCDS32127.1	ENSP00000216489	ALKB1_HUMAN	.	UPI000012585D	.	deleterious(0)	probably_damaging(1)	5/6	.	Superfamily_domains:SSF51197,Pfam_domain:PF13532,TIGRFAM_domain:TIGR00568,Gene3D:3i3qA00,hmmpanther:PTHR16557,PROSITE_profiles:PS51471	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAATCCACAG	.	4	ESCA
PTPN21	0	.	GRCh37	14	89016908	89016908	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-147G>T	.	.	ENST00000556564	2/19	84	80	4	75	75	0	PTPN21,5_prime_UTR_variant,,ENST00000555243,;PTPN21,5_prime_UTR_variant,,ENST00000556564,;PTPN21,5_prime_UTR_variant,,ENST00000328736,;RP11-507K2.3,upstream_gene_variant,,ENST00000556328,;PTPN21,non_coding_transcript_exon_variant,,ENST00000554178,;PTPN21,non_coding_transcript_exon_variant,,ENST00000554628,;PTPN21,upstream_gene_variant,,ENST00000536337,;PTPN21,upstream_gene_variant,,ENST00000554270,;	A	ENSG00000070778	ENST00000556564	Transcript	5_prime_UTR_variant	139	.	.	.	.	.	.	.	-1	PTPN21	HGNC	9651	protein_coding	YES	CCDS9884.1	ENSP00000452414	PTN21_HUMAN	Q8WX29_HUMAN,G3V3S6_HUMAN	UPI000013D15F	.	.	.	2/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCGCCATTAA	.	2	ESCA
FOXN3	0	.	GRCh37	14	89629022	89629022	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209G>A	p.%3D	p.K403K	ENST00000345097	7/7	72	66	6	51	51	0	FOXN3,synonymous_variant,p.%3D,ENST00000345097,;FOXN3,synonymous_variant,p.%3D,ENST00000555353,;FOXN3,synonymous_variant,p.%3D,ENST00000557258,;FOXN3,synonymous_variant,p.%3D,ENST00000261302,;FOXN3,intron_variant,,ENST00000557572,;FOXN3,downstream_gene_variant,,ENST00000553840,;	T	ENSG00000053254	ENST00000345097	Transcript	synonymous_variant	1326	1209	403	K	aaG/aaA	.	.	.	-1	FOXN3	HGNC	1928	protein_coding	YES	CCDS41977.1	ENSP00000343288	FOXN3_HUMAN	G3V5C7_HUMAN,G3V4N5_HUMAN,G3V3A7_HUMAN	UPI000003B451	.	.	.	7/7	.	hmmpanther:PTHR13962:SF12,hmmpanther:PTHR13962	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGCTCCTTCTG	.	3	ESCA
TDP1	0	.	GRCh37	14	90509479	90509479	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1819C>T	p.Pro607Ser	p.P607S	ENST00000335725	17/17	73	60	12	48	48	0	TDP1,missense_variant,p.Pro607Ser,ENST00000393454,;TDP1,missense_variant,p.Pro607Ser,ENST00000335725,;TDP1,missense_variant,p.Pro368Ser,ENST00000357382,;TDP1,synonymous_variant,p.%3D,ENST00000555880,;TDP1,3_prime_UTR_variant,,ENST00000393452,;TDP1,3_prime_UTR_variant,,ENST00000545686,;TDP1,3_prime_UTR_variant,,ENST00000554976,;TDP1,3_prime_UTR_variant,,ENST00000555178,;	T	ENSG00000042088	ENST00000335725	Transcript	missense_variant	2069	1819	607	P/S	Ccc/Tcc	.	.	.	1	TDP1	HGNC	18884	protein_coding	YES	CCDS9888.1	ENSP00000337353	TYDP1_HUMAN	G3V5F9_HUMAN,G3V5B8_HUMAN,G3V554_HUMAN,G3V3Q0_HUMAN,G3V2U6_HUMAN,G3V2J6_HUMAN,B3KN41_HUMAN	UPI00000737ED	.	deleterious(0)	probably_damaging(0.999)	17/17	.	hmmpanther:PTHR12415:SF0,hmmpanther:PTHR12415,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTGCCCTCC	.	5	ESCA
TRIP11	0	.	GRCh37	14	92470434	92470434	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3886G>C	p.Gly1296Arg	p.G1296R	ENST00000267622	11/21	75	67	8	49	49	0	TRIP11,missense_variant,p.Gly1012Arg,ENST00000554357,;TRIP11,missense_variant,p.Gly1296Arg,ENST00000267622,;TRIP11,upstream_gene_variant,,ENST00000557017,;	G	ENSG00000100815	ENST00000267622	Transcript	missense_variant	4260	3886	1296	G/R	Ggg/Cgg	.	.	.	-1	TRIP11	HGNC	12305	protein_coding	YES	CCDS9899.1	ENSP00000267622	TRIPB_HUMAN	G3V4R7_HUMAN	UPI000013D767	.	deleterious(0.05)	probably_damaging(0.995)	11/21	.	hmmpanther:PTHR18921:SF2,hmmpanther:PTHR18921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCCCAATGC	.	4	ESCA
GOLGA5	0	.	GRCh37	14	93305928	93305928	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*137G>T	.	.	ENST00000163416	13/13	43	38	5	36	36	0	GOLGA5,3_prime_UTR_variant,,ENST00000355976,;GOLGA5,3_prime_UTR_variant,,ENST00000554700,;GOLGA5,3_prime_UTR_variant,,ENST00000163416,;	T	ENSG00000066455	ENST00000163416	Transcript	3_prime_UTR_variant	2589	.	.	.	.	.	.	.	1	GOLGA5	HGNC	4428	protein_coding	YES	CCDS9905.1	ENSP00000163416	GOGA5_HUMAN	.	UPI000013C5AA	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTATTGTACAA	.	4	ESCA
ASB2	0	.	GRCh37	14	94405565	94405565	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1506C>G	p.%3D	p.G502G	ENST00000555019	8/10	67	56	11	55	55	0	ASB2,synonymous_variant,p.%3D,ENST00000555507,;ASB2,synonymous_variant,p.%3D,ENST00000315988,;ASB2,synonymous_variant,p.%3D,ENST00000555019,;RP11-131H24.4,upstream_gene_variant,,ENST00000557646,;ASB2,downstream_gene_variant,,ENST00000556337,;ASB2,non_coding_transcript_exon_variant,,ENST00000553883,;	C	ENSG00000100628	ENST00000555019	Transcript	synonymous_variant	1937	1506	502	G	ggC/ggG	.	.	.	-1	ASB2	HGNC	16012	protein_coding	YES	CCDS55940.1	ENSP00000451575	ASB2_HUMAN	G3V484_HUMAN,B3KPZ6_HUMAN	UPI000013D23C	.	.	.	8/10	.	hmmpanther:PTHR24196:SF0,hmmpanther:PTHR24196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCGCCGTC	.	5	ESCA
SERPINA13P	0	.	GRCh37	14	95107765	95107765	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.370C>A	.	.	ENST00000469935	2/5	46	40	5	23	23	0	SERPINA13P,non_coding_transcript_exon_variant,,ENST00000469935,;SERPINA13P,non_coding_transcript_exon_variant,,ENST00000478994,;	A	ENSG00000187483	ENST00000469935	Transcript	non_coding_transcript_exon_variant	370	.	.	.	.	.	.	.	1	SERPINA13P	HGNC	30909	processed_transcript	YES	.	.	.	.	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGACAGCAG	.	4	ESCA
TCL6	0	.	GRCh37	14	96134723	96134723	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1822-1165C>A	.	.	ENST00000467865	.	37	32	4	25	25	0	TCL6,non_coding_transcript_exon_variant,,ENST00000352367,;TCL6,intron_variant,,ENST00000459662,;TCL6,intron_variant,,ENST00000483087,;TCL6,intron_variant,,ENST00000467865,;TCL6,upstream_gene_variant,,ENST00000495696,;RP11-1070N10.6,non_coding_transcript_exon_variant,,ENST00000495847,;RP11-1070N10.6,non_coding_transcript_exon_variant,,ENST00000461160,;RP11-1070N10.6,intron_variant,,ENST00000553913,;RP11-1070N10.6,intron_variant,,ENST00000488933,;TCL6,non_coding_transcript_exon_variant,,ENST00000486671,;TCL6,non_coding_transcript_exon_variant,,ENST00000484207,;TCL6,non_coding_transcript_exon_variant,,ENST00000497248,;TCL6,intron_variant,,ENST00000357168,;TCL6,upstream_gene_variant,,ENST00000465501,;	A	ENSG00000187621	ENST00000467865	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TCL6	HGNC	13463	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGGCCCTTCTT	.	3	ESCA
TARSL2	0	.	GRCh37	15	102215856	102215856	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735A>G	p.Thr579Ala	p.T579A	ENST00000335968	13/19	106	99	7	79	79	0	TARSL2,missense_variant,p.Thr579Ala,ENST00000335968,;TARSL2,missense_variant,p.Thr579Ala,ENST00000539112,;TARSL2,3_prime_UTR_variant,,ENST00000558533,;	C	ENSG00000185418	ENST00000335968	Transcript	missense_variant	1952	1735	579	T/A	Aca/Gca	.	.	.	-1	TARSL2	HGNC	24728	protein_coding	YES	CCDS10394.1	ENSP00000338093	SYTC2_HUMAN	.	UPI00001FE055	.	deleterious(0)	probably_damaging(0.999)	13/19	.	PROSITE_profiles:PS50862,HAMAP:MF_00184,hmmpanther:PTHR11451:SF19,hmmpanther:PTHR11451,Pfam_domain:PF00587,TIGRFAM_domain:TIGR00418,Gene3D:3.30.930.10,Superfamily_domains:SSF55681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTGTTGACA	.	2	ESCA
HERC2P3	0	.	GRCh37	15	20644851	20644851	+	RNA	SNP	C	C	A	rs749992706	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3097G>T	.	.	ENST00000428453	21/27	345	308	37	296	296	0	HERC2P3,non_coding_transcript_exon_variant,,ENST00000437318,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000428453,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000430598,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000426501,;HERC2P3,downstream_gene_variant,,ENST00000440774,;HERC2P3,downstream_gene_variant,,ENST00000440441,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000424611,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000436934,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000454045,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000429257,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000545640,;	A	ENSG00000180229	ENST00000428453	Transcript	non_coding_transcript_exon_variant	3097	.	.	.	.	rs749992706,COSM3499873	.	.	-1	HERC2P3	HGNC	4871	processed_transcript	YES	.	.	.	.	.	.	.	.	21/27	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODIFIER	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A803V|c.2408C>T|8	RADIA|MUTECT|MUSE|VARSCANS	CCTCGCCCTTT	.	4	ESCA
GABRB3	0	.	GRCh37	15	26789559	26789559	+	3'UTR	SNP	G	G	C	rs562059166	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3381C>G	.	.	ENST00000311550	9/9	31	26	5	34	34	0	GABRB3,3_prime_UTR_variant,,ENST00000541819,;GABRB3,3_prime_UTR_variant,,ENST00000311550,;GABRB3,downstream_gene_variant,,ENST00000545868,;GABRB3,downstream_gene_variant,,ENST00000299267,;GABRB3,downstream_gene_variant,,ENST00000400188,;GABRB3,downstream_gene_variant,,ENST00000555632,;	C	ENSG00000166206	ENST00000311550	Transcript	3_prime_UTR_variant	4915	.	.	.	.	rs562059166	.	.	-1	GABRB3	HGNC	4083	protein_coding	YES	CCDS10019.1	ENSP00000308725	GBRB3_HUMAN	G3V5B4_HUMAN	UPI000012AFB0	.	.	.	9/9	.	.	A:0.0006	A:0.0008	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTTCAGGGAGT	byFrequency|by1000G	2	ESCA
GABRB3	0	.	GRCh37	15	26790649	26790649	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2291A>G	.	.	ENST00000311550	9/9	67	53	13	44	43	0	GABRB3,3_prime_UTR_variant,,ENST00000541819,;GABRB3,3_prime_UTR_variant,,ENST00000311550,;GABRB3,downstream_gene_variant,,ENST00000545868,;GABRB3,downstream_gene_variant,,ENST00000299267,;GABRB3,downstream_gene_variant,,ENST00000400188,;GABRB3,downstream_gene_variant,,ENST00000555632,;	C	ENSG00000166206	ENST00000311550	Transcript	3_prime_UTR_variant	3825	.	.	.	.	.	.	.	-1	GABRB3	HGNC	4083	protein_coding	YES	CCDS10019.1	ENSP00000308725	GBRB3_HUMAN	G3V5B4_HUMAN	UPI000012AFB0	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAGTATAAA	.	5	ESCA
OCA2	0	.	GRCh37	15	28326850	28326850	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.171G>T	p.%3D	p.G57G	ENST00000354638	2/24	22	16	5	19	19	0	OCA2,synonymous_variant,p.%3D,ENST00000354638,;OCA2,synonymous_variant,p.%3D,ENST00000445578,;OCA2,synonymous_variant,p.%3D,ENST00000353809,;OCA2,synonymous_variant,p.%3D,ENST00000431101,;OCA2,synonymous_variant,p.%3D,ENST00000382996,;	A	ENSG00000104044	ENST00000354638	Transcript	synonymous_variant	327	171	57	G	ggG/ggT	.	.	.	-1	OCA2	HGNC	8101	protein_coding	YES	CCDS10020.1	ENSP00000346659	P_HUMAN	C9JDV3_HUMAN	UPI000013D158	.	.	.	2/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTGCCCGGC	.	5	ESCA
KATNBL1	0	.	GRCh37	15	34439631	34439631	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558G>T	p.Arg186Ser	p.R186S	ENST00000256544	6/10	64	59	4	40	40	0	KATNBL1,missense_variant,p.Arg186Ser,ENST00000256544,;KATNBL1,missense_variant,p.Arg90Ser,ENST00000560310,;KATNBL1,missense_variant,p.Arg40Ser,ENST00000559760,;KATNBL1,intron_variant,,ENST00000561270,;KATNBL1,downstream_gene_variant,,ENST00000557877,;KATNBL1,downstream_gene_variant,,ENST00000559462,;KATNBL1,upstream_gene_variant,,ENST00000561371,;KATNBL1,downstream_gene_variant,,ENST00000560108,;KATNBL1,splice_region_variant,,ENST00000540594,;KATNBL1,splice_region_variant,,ENST00000560247,;KATNBL1,splice_region_variant,,ENST00000560308,;KATNBL1,downstream_gene_variant,,ENST00000558473,;KATNBL1,downstream_gene_variant,,ENST00000560671,;KATNBL1,upstream_gene_variant,,ENST00000558681,;	A	ENSG00000134152	ENST00000256544	Transcript	missense_variant	701	558	186	R/S	agG/agT	.	.	.	-1	KATNBL1	HGNC	26199	protein_coding	YES	CCDS10034.1	ENSP00000256544	KTBL1_HUMAN	H0YNW3_HUMAN,H0YNH1_HUMAN,H0YNG2_HUMAN,H0YNF7_HUMAN,H0YLP4_HUMAN,H0YKW3_HUMAN,B4DNG1_HUMAN,B4DEM0_HUMAN	UPI0000037DAE	.	deleterious(0.01)	benign(0.207)	6/10	.	hmmpanther:PTHR14682,Pfam_domain:PF13925	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTATCCTGAG	.	2	ESCA
RNF111	0	.	GRCh37	15	59373269	59373269	+	Nonsense_Mutation	SNP	C	C	T	rs779592066	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000559209	8/14	117	108	9	111	111	0	RNF111,stop_gained,p.Gln695Ter,ENST00000434298,;RNF111,stop_gained,p.Gln695Ter,ENST00000561186,;RNF111,stop_gained,p.Gln695Ter,ENST00000557998,;RNF111,stop_gained,p.Gln695Ter,ENST00000348370,;RNF111,stop_gained,p.Gln695Ter,ENST00000559209,;RNF111,non_coding_transcript_exon_variant,,ENST00000558977,;RNF111,upstream_gene_variant,,ENST00000559077,;RNF111,upstream_gene_variant,,ENST00000560216,;RNF111,upstream_gene_variant,,ENST00000560952,;	T	ENSG00000157450	ENST00000559209	Transcript	stop_gained	2219	2083	695	Q/*	Caa/Taa	rs779592066	.	.	1	RNF111	HGNC	17384	protein_coding	YES	CCDS58365.1	ENSP00000453872	RN111_HUMAN	H0YKS2_HUMAN	UPI0000EE4EBD	.	.	.	8/14	.	hmmpanther:PTHR13644,hmmpanther:PTHR13644:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATTCTCAAATA	.	3	ESCA
HYKK	0	.	GRCh37	15	78805449	78805449	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19C>T	p.Gln7Ter	p.Q7*	ENST00000388988	2/5	47	43	4	39	39	0	HYKK,stop_gained,p.Gln7Ter,ENST00000388988,;HYKK,stop_gained,p.Gln7Ter,ENST00000566332,;HYKK,stop_gained,p.Gln7Ter,ENST00000569878,;HYKK,stop_gained,p.Gln7Ter,ENST00000360519,;HYKK,stop_gained,p.Gln7Ter,ENST00000408962,;HYKK,stop_gained,p.Gln7Ter,ENST00000563233,;HYKK,stop_gained,p.Gln7Ter,ENST00000566289,;	T	ENSG00000188266	ENST00000388988	Transcript	stop_gained	132	19	7	Q/*	Cag/Tag	.	.	.	1	HYKK	HGNC	34403	protein_coding	YES	CCDS42063.1	ENSP00000373640	HYKK_HUMAN	F8W6X5_HUMAN	UPI0000366A7F	.	.	.	2/5	.	hmmpanther:PTHR21064:SF1,hmmpanther:PTHR21064	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTATCAGCAG	.	2	ESCA
PSMA4	0	.	GRCh37	15	78834886	78834886	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108A>T	p.%3D	p.G36G	ENST00000044462	4/9	102	95	6	78	78	0	PSMA4,synonymous_variant,p.%3D,ENST00000044462,;PSMA4,synonymous_variant,p.%3D,ENST00000560737,;PSMA4,synonymous_variant,p.%3D,ENST00000559948,;PSMA4,synonymous_variant,p.%3D,ENST00000559365,;PSMA4,synonymous_variant,p.%3D,ENST00000558341,;PSMA4,synonymous_variant,p.%3D,ENST00000559146,;PSMA4,synonymous_variant,p.%3D,ENST00000558281,;PSMA4,synonymous_variant,p.%3D,ENST00000559082,;PSMA4,synonymous_variant,p.%3D,ENST00000559437,;PSMA4,intron_variant,,ENST00000413382,;PSMA4,intron_variant,,ENST00000560217,;AC027228.1,downstream_gene_variant,,ENST00000599596,;PSMA4,upstream_gene_variant,,ENST00000558094,;PSMA4,upstream_gene_variant,,ENST00000559154,;PSMA4,non_coding_transcript_exon_variant,,ENST00000557929,;PSMA4,upstream_gene_variant,,ENST00000559906,;PSMA4,non_coding_transcript_exon_variant,,ENST00000559934,;PSMA4,non_coding_transcript_exon_variant,,ENST00000558635,;PSMA4,non_coding_transcript_exon_variant,,ENST00000560033,;PSMA4,non_coding_transcript_exon_variant,,ENST00000558639,;PSMA4,intron_variant,,ENST00000560099,;PSMA4,downstream_gene_variant,,ENST00000560842,;	T	ENSG00000041357	ENST00000044462	Transcript	synonymous_variant	258	108	36	G	ggA/ggT	.	.	.	1	PSMA4	HGNC	9533	protein_coding	YES	CCDS10303.1	ENSP00000044462	PSA4_HUMAN	Q7Z474_HUMAN,H0YMZ1_HUMAN,H0YMA1_HUMAN,H0YL69_HUMAN,H0YKT8_HUMAN	UPI000000DC2A	.	.	.	4/9	.	PROSITE_profiles:PS51475,hmmpanther:PTHR11599:SF13,hmmpanther:PTHR11599,PROSITE_patterns:PS00854,Gene3D:3.60.20.10,Pfam_domain:PF00227,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGGAATTTT	.	2	ESCA
ADAMTSL3	0	.	GRCh37	15	84488679	84488679	+	Silent	SNP	G	G	A	rs202240392	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.480G>A	p.%3D	p.P160P	ENST00000286744	6/30	71	65	6	55	55	0	ADAMTSL3,synonymous_variant,p.%3D,ENST00000286744,;ADAMTSL3,synonymous_variant,p.%3D,ENST00000567476,;RNU6-1339P,downstream_gene_variant,,ENST00000363574,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000565653,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000561483,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000569510,;	A	ENSG00000156218	ENST00000286744	Transcript	synonymous_variant	704	480	160	P	ccG/ccA	rs202240392	.	.	1	ADAMTSL3	HGNC	14633	protein_coding	YES	CCDS10326.1	ENSP00000286744	ATL3_HUMAN	.	UPI00001615A5	.	.	.	6/30	.	hmmpanther:PTHR13723:SF169,hmmpanther:PTHR13723	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCCGTGTGC	byCluster|by1000G	2	ESCA
ADAMTSL3	0	.	GRCh37	15	84539610	84539610	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.859G>A	p.Gly287Ser	p.G287S	ENST00000286744	9/30	133	124	9	103	103	0	ADAMTSL3,missense_variant,p.Gly287Ser,ENST00000286744,;ADAMTSL3,missense_variant,p.Gly287Ser,ENST00000567476,;ADAMTSL3,upstream_gene_variant,,ENST00000567663,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000561483,;	A	ENSG00000156218	ENST00000286744	Transcript	missense_variant	1083	859	287	G/S	Ggc/Agc	.	.	.	1	ADAMTSL3	HGNC	14633	protein_coding	YES	CCDS10326.1	ENSP00000286744	ATL3_HUMAN	.	UPI00001615A5	.	deleterious(0)	probably_damaging(0.996)	9/30	.	hmmpanther:PTHR13723:SF169,hmmpanther:PTHR13723	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCCGGCGTC	.	2	ESCA
ZNF592	0	.	GRCh37	15	85326476	85326476	+	Silent	SNP	G	G	T	rs769889483	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570G>T	p.%3D	p.P190P	ENST00000299927	1/8	43	39	3	40	40	0	ZNF592,synonymous_variant,p.%3D,ENST00000299927,;ZNF592,synonymous_variant,p.%3D,ENST00000560079,;ZNF592,synonymous_variant,p.%3D,ENST00000559607,;	T	ENSG00000166716	ENST00000299927	Transcript	synonymous_variant	592	570	190	P	ccG/ccT	rs769889483	.	.	1	ZNF592	HGNC	28986	protein_coding	YES	CCDS32317.1	ENSP00000299927	ZN592_HUMAN	.	UPI000013E5FC	.	.	.	1/8	.	hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTTCCGGTTCC	byFrequency|byCluster	2	ESCA
ACAN	0	.	GRCh37	15	89400152	89400152	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4336G>C	p.Glu1446Gln	p.E1446Q	ENST00000439576	12/18	121	116	5	103	103	0	ACAN,missense_variant,p.Glu1446Gln,ENST00000559004,;ACAN,missense_variant,p.Glu1446Gln,ENST00000439576,;ACAN,missense_variant,p.Glu1446Gln,ENST00000561243,;ACAN,missense_variant,p.Glu1446Gln,ENST00000352105,;ACAN,upstream_gene_variant,,ENST00000560601,;	C	ENSG00000157766	ENST00000439576	Transcript	missense_variant	4710	4336	1446	E/Q	Gag/Cag	.	.	.	1	ACAN	HGNC	319	protein_coding	YES	CCDS53970.1	ENSP00000387356	.	Q6LE94_HUMAN,E7EX88_HUMAN	UPI0001B23381	.	tolerated(0.55)	possibly_damaging(0.824)	12/18	.	hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GAGTAGAGGAG	.	2	ESCA
ANPEP	0	.	GRCh37	15	90347795	90347795	+	Silent	SNP	G	G	T	rs776972114	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951C>A	p.%3D	p.A317A	ENST00000300060	5/21	49	44	5	42	42	0	ANPEP,synonymous_variant,p.%3D,ENST00000300060,;ANPEP,downstream_gene_variant,,ENST00000559874,;ANPEP,downstream_gene_variant,,ENST00000560137,;ANPEP,upstream_gene_variant,,ENST00000558177,;ANPEP,3_prime_UTR_variant,,ENST00000560028,;ANPEP,non_coding_transcript_exon_variant,,ENST00000559887,;ANPEP,upstream_gene_variant,,ENST00000560030,;	T	ENSG00000166825	ENST00000300060	Transcript	synonymous_variant	1265	951	317	A	gcC/gcA	rs776972114	.	.	-1	ANPEP	HGNC	500	protein_coding	YES	CCDS10356.1	ENSP00000300060	AMPN_HUMAN	Q8IVL7_HUMAN,Q71E46_HUMAN,H0YM04_HUMAN,H0YKT6_HUMAN,B4DV63_HUMAN,B4DP96_HUMAN	UPI00001AECCF	.	.	.	5/21	.	hmmpanther:PTHR11533:SF149,hmmpanther:PTHR11533,Pfam_domain:PF01433,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTCAGGGCATA	.	3	ESCA
CRTC3	0	.	GRCh37	15	91136924	91136924	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288G>C	p.Glu96Asp	p.E96D	ENST00000268184	3/15	89	85	4	82	82	0	CRTC3,missense_variant,p.Glu96Asp,ENST00000268184,;CRTC3,missense_variant,p.Glu96Asp,ENST00000420329,;CRTC3,intron_variant,,ENST00000560098,;CRTC3,upstream_gene_variant,,ENST00000558005,;CTD-3065B20.2,downstream_gene_variant,,ENST00000558389,;CRTC3,non_coding_transcript_exon_variant,,ENST00000558619,;CRTC3,intron_variant,,ENST00000561218,;CRTC3,upstream_gene_variant,,ENST00000561255,;CRTC3,upstream_gene_variant,,ENST00000558496,;CRTC3,upstream_gene_variant,,ENST00000561290,;CRTC3,non_coding_transcript_exon_variant,,ENST00000560927,;CRTC3,upstream_gene_variant,,ENST00000561119,;	C	ENSG00000140577	ENST00000268184	Transcript	missense_variant	292	288	96	E/D	gaG/gaC	.	.	.	1	CRTC3	HGNC	26148	protein_coding	YES	CCDS32331.1	ENSP00000268184	CRTC3_HUMAN	.	UPI00001FEB98	.	tolerated(0.14)	benign(0.298)	3/15	.	hmmpanther:PTHR13589,hmmpanther:PTHR13589:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGAGAGGCC	.	2	ESCA
TVP23A	0	.	GRCh37	16	10864159	10864159	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612C>G	p.%3D	p.G204G	ENST00000299866	7/8	54	44	10	38	38	0	TVP23A,synonymous_variant,p.%3D,ENST00000572102,;TVP23A,synonymous_variant,p.%3D,ENST00000572428,;TVP23A,synonymous_variant,p.%3D,ENST00000299866,;NUBP1,downstream_gene_variant,,ENST00000574691,;NUBP1,downstream_gene_variant,,ENST00000283027,;NUBP1,downstream_gene_variant,,ENST00000571175,;NUBP1,downstream_gene_variant,,ENST00000433392,;TVP23A,non_coding_transcript_exon_variant,,ENST00000573857,;TVP23A,non_coding_transcript_exon_variant,,ENST00000572980,;TVP23A,downstream_gene_variant,,ENST00000570692,;NUBP1,downstream_gene_variant,,ENST00000573663,;TVP23A,synonymous_variant,p.%3D,ENST00000575135,;TVP23A,synonymous_variant,p.%3D,ENST00000456096,;TVP23A,3_prime_UTR_variant,,ENST00000573360,;	C	ENSG00000166676	ENST00000299866	Transcript	synonymous_variant	904	612	204	G	ggC/ggG	.	.	.	-1	TVP23A	HGNC	20398	protein_coding	YES	CCDS45408.1	ENSP00000299866	TV23A_HUMAN	I3L3Y3_HUMAN	UPI00001D784C	.	.	.	7/8	.	hmmpanther:PTHR13019:SF8,hmmpanther:PTHR13019	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGAGGCCAGG	.	5	ESCA
CACNA1H	0	.	GRCh37	16	1271505	1271505	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*511C>T	.	.	ENST00000348261	35/35	10	7	3	11	11	0	CACNA1H,3_prime_UTR_variant,,ENST00000348261,;CACNA1H,3_prime_UTR_variant,,ENST00000358590,;CACNA1H,3_prime_UTR_variant,,ENST00000564927,;CACNA1H,downstream_gene_variant,,ENST00000562079,;TPSG1,downstream_gene_variant,,ENST00000234798,;CACNA1H,downstream_gene_variant,,ENST00000564231,;CACNA1H,downstream_gene_variant,,ENST00000565831,;CACNA1H,downstream_gene_variant,,ENST00000569107,;TPSG1,downstream_gene_variant,,ENST00000564684,;	T	ENSG00000196557	ENST00000348261	Transcript	3_prime_UTR_variant	7821	.	.	.	.	.	.	.	1	CACNA1H	HGNC	1395	protein_coding	YES	CCDS45375.1	ENSP00000334198	CAC1H_HUMAN	Q9NYY7_HUMAN,Q9NYY6_HUMAN	UPI000012727B	.	.	.	35/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGCTCGGGCC	.	2	ESCA
TPSAB1	0	.	GRCh37	16	1291473	1291473	+	Missense_Mutation	SNP	G	G	T	rs768234740	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272G>T	p.Arg91Leu	p.R91L	ENST00000338844	4/6	66	60	6	73	73	0	TPSAB1,missense_variant,p.Arg91Leu,ENST00000338844,;TPSAB1,missense_variant,p.Arg98Leu,ENST00000461509,;TPSAB1,missense_variant,p.Arg29Leu,ENST00000561736,;TPSAB1,non_coding_transcript_exon_variant,,ENST00000562432,;	T	ENSG00000172236	ENST00000338844	Transcript	missense_variant	305	272	91	R/L	cGg/cTg	rs768234740	.	.	1	TPSAB1	HGNC	12019	protein_coding	YES	CCDS10431.1	ENSP00000343577	TRYB2_HUMAN,TRYB1_HUMAN	.	UPI0000137302	.	deleterious(0.04)	probably_damaging(0.971)	4/6	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24268,hmmpanther:PTHR24268:SF98,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	ACTGCGGGAGC	byFrequency	2	ESCA
GPRC5B	0	.	GRCh37	16	19873269	19873269	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057G>T	p.Gly353Cys	p.G353C	ENST00000300571	3/4	31	26	4	48	48	0	GPRC5B,missense_variant,p.Gly353Cys,ENST00000300571,;GPRC5B,missense_variant,p.Gly379Cys,ENST00000537135,;GPRC5B,missense_variant,p.Gly353Cys,ENST00000569847,;GPRC5B,missense_variant,p.Gly353Cys,ENST00000569479,;GPRC5B,missense_variant,p.Gly353Cys,ENST00000535671,;IQCK,downstream_gene_variant,,ENST00000320394,;IQCK,downstream_gene_variant,,ENST00000568061,;GPRC5B,upstream_gene_variant,,ENST00000569102,;GPRC5B,non_coding_transcript_exon_variant,,ENST00000562348,;IQCK,downstream_gene_variant,,ENST00000308214,;IQCK,downstream_gene_variant,,ENST00000568300,;	A	ENSG00000167191	ENST00000300571	Transcript	missense_variant	1249	1057	353	G/C	Ggc/Tgc	COSM244781	.	.	-1	GPRC5B	HGNC	13308	protein_coding	YES	CCDS10581.1	ENSP00000300571	GPC5B_HUMAN	H3BT93_HUMAN,H3BT47_HUMAN,H3BSJ1_HUMAN,H3BQV9_HUMAN,H3BN33_HUMAN	UPI0000032747	.	deleterious(0)	probably_damaging(0.998)	3/4	.	hmmpanther:PTHR14511:SF9,hmmpanther:PTHR14511	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTGCCGTTGG	.	3	ESCA
PRKCB	0	.	GRCh37	16	24135200	24135200	+	Silent	SNP	G	G	T	rs766756709	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.963G>T	p.%3D	p.T321T	ENST00000303531	9/17	71	64	7	72	72	0	PRKCB,synonymous_variant,p.%3D,ENST00000303531,;PRKCB,synonymous_variant,p.%3D,ENST00000321728,;	T	ENSG00000166501	ENST00000303531	Transcript	synonymous_variant	1115	963	321	T	acG/acT	rs766756709	.	.	1	PRKCB	HGNC	9395	protein_coding	YES	CCDS10619.1	ENSP00000305355	KPCB_HUMAN	I3L1Z0_HUMAN	UPI000002ACF9	.	.	.	9/17	.	hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF63,PIRSF_domain:PIRSF000550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGACGACCAA	.	4	ESCA
XPO6	0	.	GRCh37	16	28146539	28146539	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1441G>T	p.Asp481Tyr	p.D481Y	ENST00000304658	10/24	74	65	9	55	55	0	XPO6,missense_variant,p.Asp481Tyr,ENST00000304658,;XPO6,missense_variant,p.Asp467Tyr,ENST00000565698,;XPO6,splice_region_variant,,ENST00000564337,;XPO6,splice_region_variant,,ENST00000563138,;XPO6,splice_region_variant,,ENST00000567842,;XPO6,splice_region_variant,,ENST00000565284,;XPO6,upstream_gene_variant,,ENST00000564905,;XPO6,upstream_gene_variant,,ENST00000562408,;	A	ENSG00000169180	ENST00000304658	Transcript	missense_variant	1942	1441	481	D/Y	Gat/Tat	.	.	.	-1	XPO6	HGNC	19733	protein_coding	YES	CCDS42135.1	ENSP00000302790	XPO6_HUMAN	H3BUP8_HUMAN,H3BR41_HUMAN,D3DWF9_HUMAN	UPI000006F228	.	deleterious(0)	probably_damaging(0.995)	10/24	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR21452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACATCGTCAT	.	4	ESCA
ZNF646	0	.	GRCh37	16	31087847	31087847	+	Missense_Mutation	SNP	C	C	T	rs748056194	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202C>T	p.Arg68Trp	p.R68W	ENST00000300850	2/3	64	59	5	45	45	0	ZNF646,missense_variant,p.Arg68Trp,ENST00000394979,;ZNF646,missense_variant,p.Arg68Trp,ENST00000428260,;ZNF646,missense_variant,p.Arg68Trp,ENST00000300850,;ZNF668,upstream_gene_variant,,ENST00000417935,;ZNF668,upstream_gene_variant,,ENST00000414399,;ZNF668,upstream_gene_variant,,ENST00000300849,;ZNF668,upstream_gene_variant,,ENST00000538906,;ZNF668,upstream_gene_variant,,ENST00000394983,;ZNF646,downstream_gene_variant,,ENST00000564189,;ZNF668,upstream_gene_variant,,ENST00000564456,;	T	ENSG00000167395	ENST00000300850	Transcript	missense_variant	491	202	68	R/W	Cgg/Tgg	rs748056194	.	.	1	ZNF646	HGNC	29004	protein_coding	YES	CCDS10702.1	ENSP00000300850	ZN646_HUMAN	H3BSD0_HUMAN,C9J3L0_HUMAN	UPI00001FFF54	.	deleterious(0)	possibly_damaging(0.855)	2/3	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATCGTCGGACC	byFrequency	3	ESCA
TP53TG3D	0	.	GRCh37	16	32266406	32266406	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*182G>T	.	.	ENST00000398664	2/2	161	153	8	137	137	0	TP53TG3D,3_prime_UTR_variant,,ENST00000398664,;TP53TG3D,3_prime_UTR_variant,,ENST00000569631,;TP53TG3D,downstream_gene_variant,,ENST00000354614,;RP11-56L13.7,upstream_gene_variant,,ENST00000562604,;TP53TG3D,non_coding_transcript_exon_variant,,ENST00000564810,;TP53TG3D,3_prime_UTR_variant,,ENST00000380148,;TP53TG3D,3_prime_UTR_variant,,ENST00000568044,;TP53TG3D,downstream_gene_variant,,ENST00000567978,;TP53TG3D,downstream_gene_variant,,ENST00000563025,;	T	ENSG00000205456	ENST00000398664	Transcript	3_prime_UTR_variant	1192	.	.	.	.	.	.	.	1	TP53TG3D	HGNC	44657	protein_coding	YES	CCDS58456.1	ENSP00000455596	T53G3_HUMAN	.	UPI000006D8DD	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTCTGGAAAG	.	2	ESCA
PDIA2	0	.	GRCh37	16	336368	336368	+	Missense_Mutation	SNP	C	C	A	rs199813441	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135C>A	p.Gln379Lys	p.Q379K	ENST00000219406	8/11	87	80	7	73	73	0	PDIA2,missense_variant,p.Gln376Lys,ENST00000404312,;PDIA2,missense_variant,p.Gln379Lys,ENST00000219406,;PDIA2,splice_region_variant,,ENST00000435833,;AXIN1,downstream_gene_variant,,ENST00000457798,;ARHGDIG,downstream_gene_variant,,ENST00000435035,;ARHGDIG,downstream_gene_variant,,ENST00000412541,;ARHGDIG,downstream_gene_variant,,ENST00000219409,;ARHGDIG,downstream_gene_variant,,ENST00000447871,;AXIN1,downstream_gene_variant,,ENST00000262320,;ARHGDIG,downstream_gene_variant,,ENST00000414650,;PDIA2,downstream_gene_variant,,ENST00000456379,;AXIN1,downstream_gene_variant,,ENST00000354866,;PDIA2,downstream_gene_variant,,ENST00000462950,;PDIA2,non_coding_transcript_exon_variant,,ENST00000482665,;PDIA2,non_coding_transcript_exon_variant,,ENST00000467212,;ARHGDIG,downstream_gene_variant,,ENST00000477621,;AXIN1,downstream_gene_variant,,ENST00000461023,;	A	ENSG00000185615	ENST00000219406	Transcript	missense_variant	1153	1135	379	Q/K	Cag/Aag	rs199813441	.	.	1	PDIA2	HGNC	14180	protein_coding	YES	CCDS42089.1	ENSP00000219406	PDIA2_HUMAN	B3KWF3_HUMAN	UPI0000131481	.	deleterious(0.02)	possibly_damaging(0.459)	8/11	.	PROSITE_profiles:PS51352,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF75,TIGRFAM_domain:TIGR01130,Superfamily_domains:SSF52833,Superfamily_domains:SSF52833	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAGCCAGGAG	byCluster|by1000G	2	ESCA
SLX4	0	.	GRCh37	16	3640930	3640930	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2709G>T	p.%3D	p.V903V	ENST00000294008	12/15	100	89	11	81	81	0	SLX4,synonymous_variant,p.%3D,ENST00000294008,;SLX4,downstream_gene_variant,,ENST00000466154,;	A	ENSG00000188827	ENST00000294008	Transcript	synonymous_variant	3350	2709	903	V	gtG/gtT	.	.	.	-1	SLX4	HGNC	23845	protein_coding	YES	CCDS10506.2	ENSP00000294008	SLX4_HUMAN	.	UPI000050D2C5	.	.	.	12/15	.	hmmpanther:PTHR21541	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTCCACCTT	.	4	ESCA
CREBBP	0	.	GRCh37	16	3778029	3778029	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7019G>A	p.Ser2340Asn	p.S2340N	ENST00000262367	31/31	115	107	7	102	102	0	CREBBP,missense_variant,p.Ser2340Asn,ENST00000262367,;CREBBP,missense_variant,p.Ser2302Asn,ENST00000382070,;CREBBP,downstream_gene_variant,,ENST00000571763,;CREBBP,downstream_gene_variant,,ENST00000576720,;	T	ENSG00000005339	ENST00000262367	Transcript	missense_variant	7829	7019	2340	S/N	aGt/aAt	.	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	unknown(0)	31/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTACTAAGG	.	2	ESCA
CNEP1R1	0	.	GRCh37	16	50069574	50069574	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*205G>T	.	.	ENST00000458059	7/7	49	44	5	39	39	0	CNEP1R1,3_prime_UTR_variant,,ENST00000565556,;CNEP1R1,3_prime_UTR_variant,,ENST00000427478,;CNEP1R1,3_prime_UTR_variant,,ENST00000562576,;CNEP1R1,3_prime_UTR_variant,,ENST00000458059,;CNEP1R1,downstream_gene_variant,,ENST00000566093,;CNEP1R1,3_prime_UTR_variant,,ENST00000568890,;CNEP1R1,3_prime_UTR_variant,,ENST00000565457,;CNEP1R1,downstream_gene_variant,,ENST00000566482,;CNEP1R1,downstream_gene_variant,,ENST00000389134,;	T	ENSG00000205423	ENST00000458059	Transcript	3_prime_UTR_variant	1540	.	.	.	.	.	.	.	1	CNEP1R1	HGNC	26759	protein_coding	YES	CCDS45480.1	ENSP00000405635	NEPR1_HUMAN	H3BUT5_HUMAN,H3BMF1_HUMAN	UPI000006FFD2	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCAGTATTA	.	4	ESCA
AMFR	0	.	GRCh37	16	56396854	56396854	+	Silent	SNP	C	C	G	rs540896367	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1899G>C	p.%3D	p.A633A	ENST00000290649	14/14	104	98	6	84	84	0	AMFR,synonymous_variant,p.%3D,ENST00000290649,;AMFR,synonymous_variant,p.%3D,ENST00000492830,;AMFR,downstream_gene_variant,,ENST00000567738,;AMFR,non_coding_transcript_exon_variant,,ENST00000568325,;AMFR,non_coding_transcript_exon_variant,,ENST00000566757,;AMFR,non_coding_transcript_exon_variant,,ENST00000563285,;AMFR,downstream_gene_variant,,ENST00000566334,;	G	ENSG00000159461	ENST00000290649	Transcript	synonymous_variant	2110	1899	633	A	gcG/gcC	rs540896367	.	.	-1	AMFR	HGNC	463	protein_coding	YES	CCDS10758.1	ENSP00000290649	AMFR_HUMAN	Q6PGR1_HUMAN,Q1RN03_HUMAN,H3BSK3_HUMAN,H3BQM3_HUMAN	UPI000013EDCA	.	.	.	14/14	.	Low_complexity_(Seg):seg	T:0.0008	T:0	T:0	.	T:0	T:0	T:0.0041	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTTCCGCGGC	byFrequency|byCluster|by1000G	2	ESCA
NOB1	0	.	GRCh37	16	69788599	69788599	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94G>T	p.Glu32Ter	p.E32*	ENST00000268802	2/9	54	49	5	37	37	0	NOB1,stop_gained,p.Glu32Ter,ENST00000268802,;NOB1,stop_gained,p.Glu32Ter,ENST00000569871,;NOB1,stop_gained,p.Glu32Ter,ENST00000564620,;NOB1,non_coding_transcript_exon_variant,,ENST00000562416,;NOB1,non_coding_transcript_exon_variant,,ENST00000563055,;NOB1,upstream_gene_variant,,ENST00000561677,;CTD-2033A16.2,downstream_gene_variant,,ENST00000566277,;	A	ENSG00000141101	ENST00000268802	Transcript	stop_gained	124	94	32	E/*	Gag/Tag	.	.	.	-1	NOB1	HGNC	29540	protein_coding	YES	CCDS10884.1	ENSP00000268802	NOB1_HUMAN	.	UPI0000034E10	.	.	.	2/9	.	hmmpanther:PTHR12814,SMART_domains:SM00670,PIRSF_domain:PIRSF037125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCTCCCGGA	.	4	ESCA
ST3GAL2	0	.	GRCh37	16	70428966	70428966	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452G>C	p.Arg151Pro	p.R151P	ENST00000393640	2/6	73	67	5	54	54	0	ST3GAL2,missense_variant,p.Arg151Pro,ENST00000342907,;ST3GAL2,missense_variant,p.Arg151Pro,ENST00000393640,;RP11-529K1.4,intron_variant,,ENST00000566960,;ST3GAL2,downstream_gene_variant,,ENST00000567586,;ST3GAL2,downstream_gene_variant,,ENST00000561708,;ST3GAL2,downstream_gene_variant,,ENST00000566097,;ST3GAL2,upstream_gene_variant,,ENST00000567822,;	G	ENSG00000157350	ENST00000393640	Transcript	missense_variant	2560	452	151	R/P	cGc/cCc	.	.	.	-1	ST3GAL2	HGNC	10863	protein_coding	YES	CCDS10890.1	ENSP00000377257	SIA4B_HUMAN	.	UPI0000001C5C	.	.	possibly_damaging(0.885)	2/6	.	hmmpanther:PTHR13713:SF36,hmmpanther:PTHR13713,Pfam_domain:PF00777,PIRSF_domain:PIRSF005557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACAGCGCCGG	.	2	ESCA
HYDIN	0	.	GRCh37	16	71101239	71101239	+	Missense_Mutation	SNP	C	C	A	rs369466741	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2029G>T	p.Val677Leu	p.V677L	ENST00000393567	15/86	101	92	9	78	78	0	HYDIN,missense_variant,p.Val694Leu,ENST00000288168,;HYDIN,missense_variant,p.Val677Leu,ENST00000448089,;HYDIN,missense_variant,p.Val692Leu,ENST00000393550,;HYDIN,missense_variant,p.Val677Leu,ENST00000448691,;HYDIN,missense_variant,p.Val677Leu,ENST00000393567,;HYDIN,missense_variant,p.Val694Leu,ENST00000541601,;HYDIN,missense_variant,p.Val79Leu,ENST00000542890,;HYDIN,missense_variant,p.Val704Leu,ENST00000538248,;HYDIN,missense_variant,p.Val677Leu,ENST00000321489,;HYDIN,downstream_gene_variant,,ENST00000543639,;HYDIN,missense_variant,p.Val480Leu,ENST00000545230,;HYDIN,missense_variant,p.Val295Leu,ENST00000393552,;HYDIN,3_prime_UTR_variant,,ENST00000539447,;HYDIN,upstream_gene_variant,,ENST00000540892,;	A	ENSG00000157423	ENST00000393567	Transcript	missense_variant	2180	2029	677	V/L	Gtg/Ttg	rs369466741	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	possibly_damaging(0.769)	15/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCCACGTCCA	byFrequency|byCluster	3	ESCA
CA5A	0	.	GRCh37	16	87970095	87970095	+	5'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39C>G	.	.	ENST00000309893	1/7	80	73	6	60	60	0	CA5A,5_prime_UTR_variant,,ENST00000309893,;CA5A,non_coding_transcript_exon_variant,,ENST00000568801,;	C	ENSG00000174990	ENST00000309893	Transcript	5_prime_UTR_variant	28	.	.	.	.	.	.	.	-1	CA5A	HGNC	1377	protein_coding	YES	CCDS10965.1	ENSP00000309649	CAH5A_HUMAN	.	UPI0000126DF3	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGGTGATGTT	.	3	ESCA
BANP	0	.	GRCh37	16	88052217	88052217	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.815G>T	p.Gly272Val	p.G272V	ENST00000393207	7/14	57	53	4	67	67	0	BANP,missense_variant,p.Gly241Val,ENST00000393208,;BANP,missense_variant,p.Gly241Val,ENST00000479780,;BANP,missense_variant,p.Gly272Val,ENST00000393207,;BANP,missense_variant,p.Gly272Val,ENST00000286122,;BANP,missense_variant,p.Gly280Val,ENST00000538234,;BANP,missense_variant,p.Gly247Val,ENST00000355163,;BANP,missense_variant,p.Gly241Val,ENST00000355022,;BANP,downstream_gene_variant,,ENST00000439677,;BANP,non_coding_transcript_exon_variant,,ENST00000497491,;	T	ENSG00000172530	ENST00000393207	Transcript	missense_variant	1036	815	272	G/V	gGg/gTg	COSM3787248,COSM3787247,COSM3787246	.	.	1	BANP	HGNC	13450	protein_coding	YES	CCDS54054.1	ENSP00000376902	BANP_HUMAN	C9JLT2_HUMAN	UPI0000E59DA3	.	deleterious(0)	probably_damaging(1)	7/14	.	SMART_domains:SM01025,Pfam_domain:PF10523,hmmpanther:PTHR16243,PROSITE_profiles:PS51457	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGGGGCAGG	.	2	ESCA
MYH13	0	.	GRCh37	17	10204930	10204930	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5758C>A	p.Gln1920Lys	p.Q1920K	ENST00000418404	39/41	103	94	9	73	73	0	MYH13,missense_variant,p.Gln1920Lys,ENST00000418404,;MYH13,missense_variant,p.Gln1920Lys,ENST00000252172,;RP11-401O9.4,intron_variant,,ENST00000609088,;	T	ENSG00000006788	ENST00000418404	Transcript	missense_variant	5922	5758	1920	Q/K	Cag/Aag	.	.	.	-1	MYH13	HGNC	7571	protein_coding	YES	CCDS45613.1	ENSP00000404570	MYH13_HUMAN	.	UPI0000DB39EA	.	deleterious(0)	benign(0.308)	39/41	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF267,Pfam_domain:PF01576,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACCTGGGACT	.	3	ESCA
MYH13	0	.	GRCh37	17	10216024	10216024	+	Missense_Mutation	SNP	G	G	T	rs757283120	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4232C>A	p.Ala1411Glu	p.A1411E	ENST00000418404	30/41	80	74	5	54	54	0	MYH13,missense_variant,p.Ala1411Glu,ENST00000418404,;MYH13,missense_variant,p.Ala1411Glu,ENST00000252172,;RP11-401O9.4,intron_variant,,ENST00000609088,;	T	ENSG00000006788	ENST00000418404	Transcript	missense_variant	4396	4232	1411	A/E	gCg/gAg	rs757283120	.	.	-1	MYH13	HGNC	7571	protein_coding	YES	CCDS45613.1	ENSP00000404570	MYH13_HUMAN	.	UPI0000DB39EA	.	deleterious(0.04)	benign(0.081)	30/41	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF267,Pfam_domain:PF01576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T1410M|c.4229C>T|3,BUFFER|p.T1410M|c.4229C>T|3	MUTECT|MUSE|VARSCANS	AGTTCGCCGTC	.	3	ESCA
MYH8	0	.	GRCh37	17	10296408	10296408	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5286C>T	p.%3D	p.I1762I	ENST00000403437	36/40	179	167	12	129	129	0	MYH8,synonymous_variant,p.%3D,ENST00000403437,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	A	ENSG00000133020	ENST00000403437	Transcript	synonymous_variant	5381	5286	1762	I	atC/atT	.	.	.	-1	MYH8	HGNC	7578	protein_coding	YES	CCDS11153.1	ENSP00000384330	MYH8_HUMAN	.	UPI000012FB7D	.	.	.	36/40	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF340,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF57997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAGTGATGGC	.	2	ESCA
MYH2	0	.	GRCh37	17	10432019	10432019	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3732C>A	p.%3D	p.V1244V	ENST00000245503	27/40	166	153	13	126	126	0	MYH2,synonymous_variant,p.%3D,ENST00000245503,;MYH2,synonymous_variant,p.%3D,ENST00000397183,;MYH2,intron_variant,,ENST00000532183,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	T	ENSG00000125414	ENST00000245503	Transcript	synonymous_variant	4117	3732	1244	V	gtC/gtA	.	.	.	-1	MYH2	HGNC	7572	protein_coding	YES	CCDS11156.1	ENSP00000245503	MYH2_HUMAN	J3QLR0_HUMAN,E7EX84_HUMAN,C9JIX4_HUMAN	UPI000012FB6C	.	.	.	27/40	.	Superfamily_domains:SSF90257,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF314	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGAGACCGT	.	2	ESCA
CCDC144A	0	.	GRCh37	17	16612402	16612402	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1031G>T	p.Cys344Phe	p.C344F	ENST00000443444	5/27	315	294	20	254	254	0	CCDC144A,missense_variant,p.Cys343Phe,ENST00000340621,;CCDC144A,missense_variant,p.Cys344Phe,ENST00000443444,;CCDC144A,missense_variant,p.Cys344Phe,ENST00000360524,;CCDC144A,missense_variant,p.Cys344Phe,ENST00000399273,;CCDC144A,intron_variant,,ENST00000456009,;CCDC144A,downstream_gene_variant,,ENST00000420937,;RN7SL620P,upstream_gene_variant,,ENST00000580704,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000428950,;CCDC144A,downstream_gene_variant,,ENST00000436374,;CCDC144A,missense_variant,p.Cys344Phe,ENST00000360495,;RP11-219A15.1,missense_variant,p.Cys344Phe,ENST00000448331,;CCDC144A,intron_variant,,ENST00000328495,;CCDC144A,downstream_gene_variant,,ENST00000399264,;	T	ENSG00000170160	ENST00000443444	Transcript	missense_variant	1171	1031	344	C/F	tGt/tTt	.	.	.	1	CCDC144A	HGNC	29072	protein_coding	YES	CCDS45621.1	ENSP00000439262	C144A_HUMAN	.	UPI0000F095D0	.	deleterious(0.04)	possibly_damaging(0.831)	5/27	.	hmmpanther:PTHR22245,hmmpanther:PTHR22245:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGTTGTGAGG	.	2	ESCA
CLUH	0	.	GRCh37	17	2599489	2599489	+	Silent	SNP	C	C	A	rs771106278	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2238G>T	p.%3D	p.A746A	ENST00000570628	13/26	187	172	15	121	121	0	CLUH,synonymous_variant,p.%3D,ENST00000435359,;CLUH,synonymous_variant,p.%3D,ENST00000575014,;CLUH,synonymous_variant,p.%3D,ENST00000574426,;CLUH,synonymous_variant,p.%3D,ENST00000538975,;CLUH,synonymous_variant,p.%3D,ENST00000570628,;CLUH,downstream_gene_variant,,ENST00000572129,;CLUH,non_coding_transcript_exon_variant,,ENST00000575624,;CLUH,upstream_gene_variant,,ENST00000574166,;CLUH,upstream_gene_variant,,ENST00000573641,;CLUH,upstream_gene_variant,,ENST00000574210,;CLUH,downstream_gene_variant,,ENST00000571539,;CLUH,upstream_gene_variant,,ENST00000572014,;	A	ENSG00000132361	ENST00000570628	Transcript	synonymous_variant	2344	2238	746	A	gcG/gcT	rs771106278,COSM976761,COSM976762	.	.	-1	CLUH	HGNC	29094	protein_coding	YES	CCDS45572.1	ENSP00000458986	CLU_HUMAN	I3L3A3_HUMAN,I3L350_HUMAN,I3L318_HUMAN	UPI00004C8042	.	.	.	13/26	.	HAMAP:MF_03013,hmmpanther:PTHR12601,hmmpanther:PTHR12601:SF10	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAGCCGCGTC	byFrequency	3	ESCA
SLC13A2	0	.	GRCh37	17	26820661	26820661	+	Silent	SNP	C	C	A	rs149127873	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1098C>A	p.%3D	p.T366T	ENST00000444914	7/12	79	69	10	43	43	0	SLC13A2,synonymous_variant,p.%3D,ENST00000537681,;SLC13A2,synonymous_variant,p.%3D,ENST00000545060,;SLC13A2,synonymous_variant,p.%3D,ENST00000314669,;SLC13A2,synonymous_variant,p.%3D,ENST00000444914,;SLC13A2,3_prime_UTR_variant,,ENST00000577903,;SLC13A2,3_prime_UTR_variant,,ENST00000459818,;SLC13A2,3_prime_UTR_variant,,ENST00000579281,;SLC13A2,non_coding_transcript_exon_variant,,ENST00000541739,;RP11-192H23.4,intron_variant,,ENST00000481916,;	A	ENSG00000007216	ENST00000444914	Transcript	synonymous_variant	1518	1098	366	T	acC/acA	rs149127873	.	.	1	SLC13A2	HGNC	10917	protein_coding	YES	CCDS54098.1	ENSP00000392411	.	.	UPI0001986446	.	.	.	7/12	.	hmmpanther:PTHR10283:SF66,hmmpanther:PTHR10283,Pfam_domain:PF00939	T:0.0014	T:0.0053	T:0	.	T:0	T:0	T:0	T:0.0005	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGACCGAGCA	byFrequency|byCluster|by1000G	5	ESCA
SPAG5	0	.	GRCh37	17	26912936	26912936	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1686A>T	p.%3D	p.A562A	ENST00000321765	7/24	65	61	4	43	43	0	SPAG5,synonymous_variant,p.%3D,ENST00000321765,;SPAG5,synonymous_variant,p.%3D,ENST00000584206,;RP11-192H23.4,intron_variant,,ENST00000531839,;SPAG5,synonymous_variant,p.%3D,ENST00000580083,;RP11-192H23.4,intron_variant,,ENST00000481916,;SPAG5,upstream_gene_variant,,ENST00000577259,;SPAG5,upstream_gene_variant,,ENST00000578230,;SPAG5,upstream_gene_variant,,ENST00000378976,;	A	ENSG00000076382	ENST00000321765	Transcript	synonymous_variant	2019	1686	562	A	gcA/gcT	.	.	.	-1	SPAG5	HGNC	13452	protein_coding	YES	CCDS32594.1	ENSP00000323300	SPAG5_HUMAN	.	UPI0000073414	.	.	.	7/24	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15347,hmmpanther:PTHR15347:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTCTGCTTT	.	2	ESCA
NF1	0	.	GRCh37	17	29702638	29702638	+	3'UTR	SNP	G	G	C	rs559972371	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1465G>C	.	.	ENST00000358273	58/58	77	70	6	61	61	0	NF1,3_prime_UTR_variant,,ENST00000358273,;NF1,3_prime_UTR_variant,,ENST00000356175,;NF1,intron_variant,,ENST00000444181,;NF1,downstream_gene_variant,,ENST00000456735,;NF1,upstream_gene_variant,,ENST00000498569,;NF1,upstream_gene_variant,,ENST00000488981,;NF1,intron_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000422121,;NF1,downstream_gene_variant,,ENST00000579081,;	C	ENSG00000196712	ENST00000358273	Transcript	3_prime_UTR_variant	10368	.	.	.	.	rs559972371	.	.	1	NF1	HGNC	7765	protein_coding	YES	CCDS42292.1	ENSP00000351015	NF1_HUMAN	Q9UMU3_HUMAN,Q4W6X4_HUMAN,K7EP94_HUMAN	UPI000012FFAE	.	.	.	58/58	.	.	-:0.0006	-:0.0015	-:0.0014	.	-:0	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATAATGGCTTT	byFrequency|by1000G	3	ESCA
ASIC2	0	.	GRCh37	17	32483062	32483062	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.490C>A	p.Leu164Met	p.L164M	ENST00000359872	1/10	41	36	5	50	50	0	ASIC2,missense_variant,p.Leu164Met,ENST00000359872,;ASIC2,downstream_gene_variant,,ENST00000583395,;	T	ENSG00000108684	ENST00000359872	Transcript	missense_variant	1252	490	164	L/M	Ctg/Atg	.	.	.	-1	ASIC2	HGNC	99	protein_coding	.	CCDS42296.1	ENSP00000352934	ASIC2_HUMAN	.	UPI00000441F0	.	tolerated(0.1)	possibly_damaging(0.491)	1/10	.	hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF128,Gene3D:2qtsA03,Pfam_domain:PF00858,TIGRFAM_domain:TIGR00859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCAGGTCAT	.	4	ESCA
CCL1	0	.	GRCh37	17	32687557	32687557	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*21G>T	.	.	ENST00000225842	3/3	116	103	12	86	86	0	CCL1,3_prime_UTR_variant,,ENST00000225842,;CCL13,downstream_gene_variant,,ENST00000577681,;CCL13,downstream_gene_variant,,ENST00000225844,;	A	ENSG00000108702	ENST00000225842	Transcript	3_prime_UTR_variant	382	.	.	.	.	.	.	.	-1	CCL1	HGNC	10609	protein_coding	YES	CCDS11282.1	ENSP00000225842	CCL1_HUMAN	Q76BR7_HUMAN	UPI00001362C4	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGCCCACAA	.	4	ESCA
SLFN11	0	.	GRCh37	17	33690498	33690498	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329G>T	p.Trp110Leu	p.W110L	ENST00000394566	4/7	55	47	8	49	49	0	SLFN11,missense_variant,p.Trp110Leu,ENST00000394566,;SLFN11,missense_variant,p.Trp110Leu,ENST00000591682,;SLFN11,missense_variant,p.Trp110Leu,ENST00000308377,;SLFN11,missense_variant,p.Trp110Leu,ENST00000441608,;SLFN11,downstream_gene_variant,,ENST00000430814,;SLFN11,downstream_gene_variant,,ENST00000589811,;SLFN11,downstream_gene_variant,,ENST00000427966,;SLFN11,downstream_gene_variant,,ENST00000592122,;SLFN11,downstream_gene_variant,,ENST00000588579,;SLFN11,downstream_gene_variant,,ENST00000498396,;SLFN11,downstream_gene_variant,,ENST00000589562,;SLFN11,upstream_gene_variant,,ENST00000586099,;	A	ENSG00000172716	ENST00000394566	Transcript	missense_variant	602	329	110	W/L	tGg/tTg	.	.	.	-1	SLFN11	HGNC	26633	protein_coding	YES	CCDS11294.1	ENSP00000378067	SLN11_HUMAN	K7ES87_HUMAN,K7ER38_HUMAN,K7EKT7_HUMAN,K7EIM3_HUMAN,C9JUT2_HUMAN,C9JDG6_HUMAN,C9J902_HUMAN	UPI0000140B0E	.	deleterious(0)	probably_damaging(0.999)	4/7	.	hmmpanther:PTHR12155:SF20,hmmpanther:PTHR12155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCTCCAAGAT	.	3	ESCA
GAS2L2	0	.	GRCh37	17	34071950	34071950	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2566C>A	p.Pro856Thr	p.P856T	ENST00000254466	6/6	91	84	6	66	66	0	GAS2L2,missense_variant,p.Pro840Thr,ENST00000587565,;GAS2L2,missense_variant,p.Pro856Thr,ENST00000254466,;RASL10B,downstream_gene_variant,,ENST00000268864,;	T	ENSG00000132139	ENST00000254466	Transcript	missense_variant	2594	2566	856	P/T	Ccc/Acc	COSM3362087	.	.	-1	GAS2L2	HGNC	24846	protein_coding	YES	CCDS11298.1	ENSP00000254466	GA2L2_HUMAN	.	UPI0000061E50	.	tolerated(0.21)	benign(0.113)	6/6	.	hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGGGGCTGC	.	2	ESCA
CCL18	0	.	GRCh37	17	34398331	34398331	+	Missense_Mutation	SNP	G	G	T	rs778538949	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200G>T	p.Arg67Leu	p.R67L	ENST00000004921	3/3	254	228	25	238	238	0	CCL18,missense_variant,p.Arg67Leu,ENST00000004921,;AC069363.1,upstream_gene_variant,,ENST00000588864,;AC069363.1,upstream_gene_variant,,ENST00000590992,;CCL18,non_coding_transcript_exon_variant,,ENST00000586857,;	T	ENSG00000006074	ENST00000004921	Transcript	missense_variant	263	200	67	R/L	cGg/cTg	rs778538949	.	.	1	CCL18	HGNC	10616	protein_coding	YES	CCDS11306.1	ENSP00000004921	CCL18_HUMAN	.	UPI00001362DA	.	deleterious(0.01)	benign(0.175)	3/3	.	hmmpanther:PTHR12015:SF24,hmmpanther:PTHR12015,PROSITE_patterns:PS00472,Gene3D:2.40.50.40,Pfam_domain:PF00048,SMART_domains:SM00199,Superfamily_domains:SSF54117,Prints_domain:PR00436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCGGCAGA	byFrequency	4	ESCA
ATP2A3	0	.	GRCh37	17	3850765	3850765	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015G>T	p.Val339Leu	p.V339L	ENST00000359983	8/23	66	59	6	63	63	0	ATP2A3,missense_variant,p.Val339Leu,ENST00000397043,;ATP2A3,missense_variant,p.Val339Leu,ENST00000359983,;ATP2A3,missense_variant,p.Val339Leu,ENST00000309890,;ATP2A3,missense_variant,p.Val339Leu,ENST00000397035,;ATP2A3,missense_variant,p.Val339Leu,ENST00000397041,;ATP2A3,missense_variant,p.Val339Leu,ENST00000352011,;ATP2A3,5_prime_UTR_variant,,ENST00000397039,;ATP2A3,upstream_gene_variant,,ENST00000572694,;	A	ENSG00000074370	ENST00000359983	Transcript	missense_variant	1015	1015	339	V/L	Gtg/Ttg	COSM3517014,COSM3517015	.	.	-1	ATP2A3	HGNC	813	protein_coding	YES	CCDS11042.1	ENSP00000353072	AT2A3_HUMAN	.	UPI0000161584	.	deleterious(0)	probably_damaging(0.995)	8/23	.	Superfamily_domains:0049473,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01116,Pfam_domain:PF00122,Gene3D:3.40.1110.10,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF280	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCCACGGACG	.	3	ESCA
KRT33B	0	.	GRCh37	17	39521128	39521128	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1000C>G	p.Arg334Gly	p.R334G	ENST00000251646	6/7	134	106	27	97	97	0	KRT33B,missense_variant,p.Arg334Gly,ENST00000251646,;	C	ENSG00000131738	ENST00000251646	Transcript	missense_variant	1050	1000	334	R/G	Cgg/Ggg	.	.	.	-1	KRT33B	HGNC	6451	protein_coding	YES	CCDS11389.1	ENSP00000251646	KT33B_HUMAN	.	UPI000012DAFE	.	deleterious(0.02)	probably_damaging(0.999)	6/7	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF64593,Pfam_domain:PF00038,Gene3D:1.20.5.170,hmmpanther:PTHR23239:SF99,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGCTCCA	.	5	ESCA
HAP1	0	.	GRCh37	17	39883692	39883692	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1276-296G>T	.	.	ENST00000347901	.	116	108	8	94	94	0	HAP1,missense_variant,p.Gly430Val,ENST00000310778,;HAP1,intron_variant,,ENST00000393939,;JUP,intron_variant,,ENST00000540235,;HAP1,intron_variant,,ENST00000347901,;HAP1,intron_variant,,ENST00000341193,;HAP1,upstream_gene_variant,,ENST00000458656,;HAP1,upstream_gene_variant,,ENST00000442364,;HAP1,upstream_gene_variant,,ENST00000455021,;RN7SL399P,downstream_gene_variant,,ENST00000471648,;	A	ENSG00000173805	ENST00000347901	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	HAP1	HGNC	4812	protein_coding	YES	CCDS11406.1	ENSP00000334002	HAP1_HUMAN	.	UPI000024700D	.	.	.	.	8/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAACCCACC	.	2	ESCA
BRCA1	0	.	GRCh37	17	41247865	41247865	+	Missense_Mutation	SNP	T	T	G	rs397509306,rs80357745	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668A>C	p.Lys223Thr	p.K223T	ENST00000471181	9/24	81	74	7	53	53	0	BRCA1,missense_variant,p.Lys223Thr,ENST00000352993,;BRCA1,missense_variant,p.Lys223Thr,ENST00000470026,;BRCA1,missense_variant,p.Lys223Thr,ENST00000494123,;BRCA1,missense_variant,p.Lys197Thr,ENST00000477152,;BRCA1,missense_variant,p.Lys176Thr,ENST00000493919,;BRCA1,missense_variant,p.Lys222Thr,ENST00000476777,;BRCA1,missense_variant,p.Lys223Thr,ENST00000346315,;BRCA1,missense_variant,p.Lys223Thr,ENST00000357654,;BRCA1,missense_variant,p.Lys223Thr,ENST00000354071,;BRCA1,missense_variant,p.Lys223Thr,ENST00000468300,;BRCA1,missense_variant,p.Lys176Thr,ENST00000493795,;BRCA1,missense_variant,p.Lys222Thr,ENST00000478531,;BRCA1,missense_variant,p.Lys223Thr,ENST00000491747,;BRCA1,missense_variant,p.Lys223Thr,ENST00000471181,;BRCA1,splice_region_variant,,ENST00000309486,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000497488,;BRCA1,intron_variant,,ENST00000473961,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,upstream_gene_variant,,ENST00000461574,;BRCA1,missense_variant,p.Lys7Thr,ENST00000412061,;BRCA1,splice_region_variant,,ENST00000467274,;BRCA1,splice_region_variant,,ENST00000461221,;BRCA1,splice_region_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000461798,;	G	ENSG00000012048	ENST00000471181	Transcript	missense_variant	900	668	223	K/T	aAg/aCg	rs397509306,rs80357745,CD057384	.	.	-1	BRCA1	HGNC	1100	protein_coding	YES	CCDS11456.2	ENSP00000418960	.	Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFC7_HUMAN,E7EWN5_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN	UPI0000E0360B	.	deleterious(0)	possibly_damaging(0.9)	9/24	.	hmmpanther:PTHR13763:SF0,hmmpanther:PTHR13763,PIRSF_domain:PIRSF001734	.	.	.	.	.	.	.	.	.	not_provided,not_provided,pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TACCCTTTTTT	.	2	ESCA
DHX8	0	.	GRCh37	17	41571102	41571102	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1060C>T	p.Leu354Phe	p.L354F	ENST00000262415	8/23	118	94	24	113	113	0	DHX8,missense_variant,p.Leu354Phe,ENST00000540306,;DHX8,missense_variant,p.Leu354Phe,ENST00000262415,;DHX8,downstream_gene_variant,,ENST00000605777,;DHX8,non_coding_transcript_exon_variant,,ENST00000587044,;DHX8,downstream_gene_variant,,ENST00000592258,;	T	ENSG00000067596	ENST00000262415	Transcript	missense_variant	1132	1060	354	L/F	Ctt/Ttt	.	.	.	1	DHX8	HGNC	2749	protein_coding	YES	CCDS11464.1	ENSP00000262415	DHX8_HUMAN	.	UPI00001290D9	.	tolerated(0.15)	benign(0.096)	8/23	.	hmmpanther:PTHR18934:SF85,hmmpanther:PTHR18934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATCTTGTC	.	5	ESCA
ITGA2B	0	.	GRCh37	17	42461461	42461461	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937G>A	p.Gly313Arg	p.G313R	ENST00000262407	10/30	67	60	7	57	57	0	ITGA2B,missense_variant,p.Gly313Arg,ENST00000262407,;ITGA2B,missense_variant,p.Gly313Arg,ENST00000353281,;ITGA2B,5_prime_UTR_variant,,ENST00000377068,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592253,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000591990,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592075,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000589645,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592226,;ITGA2B,upstream_gene_variant,,ENST00000592462,;ITGA2B,downstream_gene_variant,,ENST00000592944,;	T	ENSG00000005961	ENST00000262407	Transcript	missense_variant	969	937	313	G/R	Gga/Aga	.	.	.	-1	ITGA2B	HGNC	6138	protein_coding	YES	CCDS32665.1	ENSP00000262407	ITA2B_HUMAN	Q6LDK5_HUMAN,I6XCH0_HUMAN,F1C626_HUMAN	UPI00001868B8	.	deleterious(0)	probably_damaging(0.994)	10/30	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF73,hmmpanther:PTHR23220,Gene3D:3nigC00,Superfamily_domains:SSF69318,Prints_domain:PR01185	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTCCGCGCA	.	4	ESCA
KANSL1	0	.	GRCh37	17	44144914	44144914	+	Splice_Site	SNP	C	C	A	rs281865470	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1652+1G>T	.	p.X551_splice	ENST00000262419	.	80	67	13	45	45	0	KANSL1,splice_donor_variant,,ENST00000393476,;KANSL1,splice_donor_variant,,ENST00000432791,;KANSL1,splice_donor_variant,,ENST00000262419,;KANSL1,splice_donor_variant,,ENST00000572904,;KANSL1,splice_donor_variant,,ENST00000575318,;KANSL1,splice_donor_variant,,ENST00000574590,;KANSL1,splice_donor_variant,,ENST00000577114,;	A	ENSG00000120071	ENST00000262419	Transcript	splice_donor_variant	.	.	.	.	.	rs281865470,COSM1302929,COSM980252	.	.	-1	KANSL1	HGNC	24565	protein_coding	YES	CCDS11503.1	ENSP00000262419	KANL1_HUMAN	I3L243_HUMAN,I3L233_HUMAN	UPI0001AE66EA	.	.	.	.	5/14	.	.	.	.	.	.	.	.	.	.	pathogenic	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTACGTGTT	.	5	ESCA
ARRB2	0	.	GRCh37	17	4619267	4619267	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55-1G>C	.	p.X19_splice	ENST00000412477	.	60	55	5	54	54	0	ARRB2,splice_acceptor_variant,,ENST00000269260,;ARRB2,splice_acceptor_variant,,ENST00000575877,;ARRB2,splice_acceptor_variant,,ENST00000412477,;ARRB2,splice_acceptor_variant,,ENST00000574954,;ARRB2,splice_acceptor_variant,,ENST00000381488,;ARRB2,splice_acceptor_variant,,ENST00000346341,;ARRB2,splice_acceptor_variant,,ENST00000571428,;ARRB2,5_prime_UTR_variant,,ENST00000571206,;ARRB2,intron_variant,,ENST00000572457,;ARRB2,splice_acceptor_variant,,ENST00000570718,;ARRB2,splice_acceptor_variant,,ENST00000570739,;ARRB2,splice_acceptor_variant,,ENST00000574502,;ARRB2,splice_acceptor_variant,,ENST00000572782,;ARRB2,splice_acceptor_variant,,ENST00000575131,;ARRB2,splice_acceptor_variant,,ENST00000572497,;ARRB2,splice_acceptor_variant,,ENST00000571791,;ARRB2,splice_acceptor_variant,,ENST00000574888,;ARRB2,splice_acceptor_variant,,ENST00000576235,;ARRB2,intron_variant,,ENST00000573886,;ARRB2,upstream_gene_variant,,ENST00000577054,;	C	ENSG00000141480	ENST00000412477	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ARRB2	HGNC	712	protein_coding	YES	CCDS58504.1	ENSP00000403701	ARRB2_HUMAN	Q68DZ5_HUMAN,K7EL17_HUMAN	UPI0001AE6690	.	.	.	.	2/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTCAGCTCAC	.	3	ESCA
PRAC1	0	.	GRCh37	17	46801787	46801787	+	5'Flank	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000290294	.	95	84	11	84	84	0	PRAC1,upstream_gene_variant,,ENST00000290294,;HOXB13,downstream_gene_variant,,ENST00000290295,;MIR3185,non_coding_transcript_exon_variant,,ENST00000583892,;PRAC2,non_coding_transcript_exon_variant,,ENST00000432056,;PRAC2,non_coding_transcript_exon_variant,,ENST00000422730,;	C	ENSG00000159182	ENST00000290294	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1903	-1	PRAC1	HGNC	30591	protein_coding	YES	CCDS11535.1	ENSP00000290294	PRAC1_HUMAN	.	UPI00000503CB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCGGATGGC	.	4	ESCA
PHB	0	.	GRCh37	17	47486521	47486521	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.394-1G>T	.	p.X132_splice	ENST00000300408	.	89	83	5	50	50	0	PHB,splice_acceptor_variant,,ENST00000446735,;PHB,splice_acceptor_variant,,ENST00000512041,;PHB,splice_acceptor_variant,,ENST00000300408,;PHB,splice_acceptor_variant,,ENST00000504124,;PHB,splice_acceptor_variant,,ENST00000511832,;PHB,splice_acceptor_variant,,ENST00000419140,;RP11-81K2.1,intron_variant,,ENST00000576461,;PHB,downstream_gene_variant,,ENST00000434917,;RP11-1079K10.4,downstream_gene_variant,,ENST00000506504,;PHB,splice_acceptor_variant,,ENST00000508009,;PHB,splice_acceptor_variant,,ENST00000506273,;PHB,splice_acceptor_variant,,ENST00000393345,;PHB,downstream_gene_variant,,ENST00000507748,;PHB,upstream_gene_variant,,ENST00000511933,;PHB,downstream_gene_variant,,ENST00000513412,;	A	ENSG00000167085	ENST00000300408	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	PHB	HGNC	8912	protein_coding	YES	CCDS11548.1	ENSP00000300408	PHB_HUMAN	E9PCW0_HUMAN,E7ESE2_HUMAN,D6RBK0_HUMAN,C9JZ20_HUMAN,C9JW96_HUMAN,A8K401_HUMAN	UPI000000DCDE	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGAGCCTGGTT	.	2	ESCA
ITGA3	0	.	GRCh37	17	48151811	48151811	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1383-1G>T	.	p.X461_splice	ENST00000007722	.	26	20	5	30	30	0	ITGA3,splice_acceptor_variant,,ENST00000544892,;ITGA3,splice_acceptor_variant,,ENST00000512553,;ITGA3,splice_acceptor_variant,,ENST00000320031,;ITGA3,splice_acceptor_variant,,ENST00000007722,;ITGA3,upstream_gene_variant,,ENST00000506827,;ITGA3,splice_acceptor_variant,,ENST00000506401,;ITGA3,splice_acceptor_variant,,ENST00000510809,;ITGA3,splice_acceptor_variant,,ENST00000505306,;ITGA3,upstream_gene_variant,,ENST00000507771,;ITGA3,downstream_gene_variant,,ENST00000505552,;ITGA3,upstream_gene_variant,,ENST00000505612,;ITGA3,upstream_gene_variant,,ENST00000515147,;	T	ENSG00000005884	ENST00000007722	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ITGA3	HGNC	6139	protein_coding	YES	CCDS11557.1	ENSP00000007722	ITA3_HUMAN	Q86SW1_HUMAN	UPI0000140781	.	.	.	.	9/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGGGCCC	.	5	ESCA
MYCBPAP	0	.	GRCh37	17	48599356	48599356	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1300G>C	p.Asp434His	p.D434H	ENST00000323776	10/19	89	77	11	73	73	0	MYCBPAP,missense_variant,p.Asp397His,ENST00000436259,;MYCBPAP,missense_variant,p.Asp434His,ENST00000323776,;MYCBPAP,downstream_gene_variant,,ENST00000452039,;MYCBPAP,upstream_gene_variant,,ENST00000488432,;MYCBPAP,downstream_gene_variant,,ENST00000468821,;MYCBPAP,missense_variant,p.Asp409His,ENST00000437498,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000470609,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000459754,;MYCBPAP,upstream_gene_variant,,ENST00000485169,;MYCBPAP,downstream_gene_variant,,ENST00000458692,;	C	ENSG00000136449	ENST00000323776	Transcript	missense_variant	1462	1300	434	D/H	Gat/Cat	.	.	.	1	MYCBPAP	HGNC	19677	protein_coding	YES	CCDS32680.2	ENSP00000323184	MYBPP_HUMAN	.	UPI0000E5A00B	.	deleterious(0.05)	probably_damaging(0.963)	10/19	.	hmmpanther:PTHR12276:SF44,hmmpanther:PTHR12276,Pfam_domain:PF14646	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCTGATGTC	.	4	ESCA
ZNF594	0	.	GRCh37	17	5085724	5085724	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1828G>A	p.Asp610Asn	p.D610N	ENST00000399604	1/1	141	126	14	109	109	0	ZNF594,missense_variant,p.Asp610Asn,ENST00000575779,;ZNF594,missense_variant,p.Asp610Asn,ENST00000399604,;ZNF594,downstream_gene_variant,,ENST00000576772,;	T	ENSG00000180626	ENST00000399604	Transcript	missense_variant	1969	1828	610	D/N	Gac/Aac	.	.	.	-1	ZNF594	HGNC	29392	protein_coding	YES	CCDS42241.1	ENSP00000382513	ZN594_HUMAN	I3L508_HUMAN	UPI00001C1FDF	.	tolerated(0.68)	possibly_damaging(0.881)	1/1	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF127,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGGTCTGAGC	.	3	ESCA
YPEL2	0	.	GRCh37	17	57474689	57474689	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*138G>T	.	.	ENST00000312655	5/5	71	63	8	60	60	0	YPEL2,3_prime_UTR_variant,,ENST00000585166,;YPEL2,3_prime_UTR_variant,,ENST00000312655,;RP11-567L7.5,downstream_gene_variant,,ENST00000585190,;YPEL2,downstream_gene_variant,,ENST00000581865,;YPEL2,downstream_gene_variant,,ENST00000582813,;	T	ENSG00000175155	ENST00000312655	Transcript	3_prime_UTR_variant	816	.	.	.	.	.	.	.	1	YPEL2	HGNC	18326	protein_coding	YES	CCDS32695.1	ENSP00000312272	YPEL2_HUMAN	.	UPI00000215CF	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGACGCCATC	.	4	ESCA
C17orf64	0	.	GRCh37	17	58512743	58512743	+	3'Flank	SNP	G	G	T	rs140422815	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000269127	.	70	63	7	56	56	0	C17orf64,downstream_gene_variant,,ENST00000269127,;RPL12P38,non_coding_transcript_exon_variant,,ENST00000588627,;RPL12P38,upstream_gene_variant,,ENST00000471280,;	T	ENSG00000141371	ENST00000269127	Transcript	downstream_gene_variant	.	.	.	.	.	rs140422815	.	3961	1	C17orf64	HGNC	26990	protein_coding	YES	CCDS32698.2	ENSP00000269127	CQ064_HUMAN	K7EQ24_HUMAN	UPI0000161125	.	.	.	.	.	.	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTTCGTCCTT	byFrequency|by1000G	3	ESCA
ACE	0	.	GRCh37	17	61557763	61557763	+	Nonsense_Mutation	SNP	G	G	T	rs763411587	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.721G>T	p.Glu241Ter	p.E241*	ENST00000290866	5/25	126	110	15	75	75	0	ACE,stop_gained,p.Glu241Ter,ENST00000428043,;ACE,stop_gained,p.Glu241Ter,ENST00000290866,;ACE,stop_gained,p.Glu241Ter,ENST00000538928,;ACE,stop_gained,p.Glu241Ter,ENST00000582627,;ACE,upstream_gene_variant,,ENST00000490216,;ACE,upstream_gene_variant,,ENST00000290863,;ACE,upstream_gene_variant,,ENST00000413513,;ACE,upstream_gene_variant,,ENST00000421982,;ACE,non_coding_transcript_exon_variant,,ENST00000584529,;ACE,downstream_gene_variant,,ENST00000583336,;ACE,3_prime_UTR_variant,,ENST00000582678,;ACE,3_prime_UTR_variant,,ENST00000580318,;ACE,upstream_gene_variant,,ENST00000582005,;ACE,upstream_gene_variant,,ENST00000578839,;ACE,upstream_gene_variant,,ENST00000579314,;ACE,upstream_gene_variant,,ENST00000579204,;ACE,upstream_gene_variant,,ENST00000579726,;ACE,upstream_gene_variant,,ENST00000577647,;ACE,downstream_gene_variant,,ENST00000579462,;	T	ENSG00000159640	ENST00000290866	Transcript	stop_gained	745	721	241	E/*	Gaa/Taa	rs763411587,COSM2794899	.	.	1	ACE	HGNC	2707	protein_coding	YES	CCDS11637.1	ENSP00000290866	ACE_HUMAN	Q3KRI5_HUMAN,D3DU13_HUMAN	UPI000002B8AD	.	.	.	5/25	.	hmmpanther:PTHR10514:SF19,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTGGAACAC	.	4	ESCA
PITPNC1	0	.	GRCh37	17	65688960	65688960	+	Missense_Mutation	SNP	G	G	T	rs774288855	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.955G>T	p.Gly319Cys	p.G319C	ENST00000581322	9/9	46	39	7	43	43	0	PITPNC1,missense_variant,p.Gly319Cys,ENST00000335257,;PITPNC1,missense_variant,p.Gly319Cys,ENST00000581322,;PITPNC1,3_prime_UTR_variant,,ENST00000580974,;PITPNC1,3_prime_UTR_variant,,ENST00000299954,;PITPNC1,non_coding_transcript_exon_variant,,ENST00000578527,;	T	ENSG00000154217	ENST00000581322	Transcript	missense_variant	955	955	319	G/C	Ggc/Tgc	rs774288855	.	.	1	PITPNC1	HGNC	21045	protein_coding	YES	CCDS58588.1	ENSP00000464006	.	J3QS95_HUMAN,J3QRS7_HUMAN,J3QR20_HUMAN	UPI00001AE46B	.	deleterious_low_confidence(0.01)	possibly_damaging(0.575)	9/9	.	hmmpanther:PTHR10658	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCCGGCATG	byFrequency	5	ESCA
KPNA2	0	.	GRCh37	17	66040117	66040117	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1094G>T	p.Gly365Val	p.G365V	ENST00000537025	8/11	136	116	20	103	103	0	KPNA2,missense_variant,p.Gly365Val,ENST00000537025,;KPNA2,missense_variant,p.Gly365Val,ENST00000330459,;KPNA2,downstream_gene_variant,,ENST00000579754,;KPNA2,downstream_gene_variant,,ENST00000584026,;KPNA2,upstream_gene_variant,,ENST00000582898,;KPNA2,downstream_gene_variant,,ENST00000583392,;KPNA2,downstream_gene_variant,,ENST00000583269,;	T	ENSG00000182481	ENST00000537025	Transcript	missense_variant	1714	1094	365	G/V	gGc/gTc	.	.	.	1	KPNA2	HGNC	6395	protein_coding	YES	CCDS32713.1	ENSP00000438483	IMA1_HUMAN	J3QLL0_HUMAN,J3KS65_HUMAN	UPI000012D5F6	.	deleterious(0)	probably_damaging(0.986)	8/11	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF005673,Gene3D:1.25.10.10,hmmpanther:PTHR23316:SF12,hmmpanther:PTHR23316,PROSITE_profiles:PS50176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCGGCCGCC	.	4	ESCA
LINC00674	0	.	GRCh37	17	66110635	66110635	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.189G>A	.	.	ENST00000435469	2/3	107	93	13	89	89	0	LINC00674,non_coding_transcript_exon_variant,,ENST00000435469,;LINC00674,non_coding_transcript_exon_variant,,ENST00000590734,;	A	ENSG00000237854	ENST00000435469	Transcript	non_coding_transcript_exon_variant	189	.	.	.	.	.	.	.	1	LINC00674	HGNC	44355	processed_transcript	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGGAGAAGAA	.	4	ESCA
ALOX12	0	.	GRCh37	17	6901872	6901872	+	Silent	SNP	C	C	A	rs781254870	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382C>A	p.%3D	p.R128R	ENST00000251535	3/14	37	32	5	40	40	0	ALOX12,synonymous_variant,p.%3D,ENST00000251535,;ALOX12,synonymous_variant,p.%3D,ENST00000480801,;AC027763.2,intron_variant,,ENST00000399541,;AC027763.2,intron_variant,,ENST00000575889,;AC027763.2,downstream_gene_variant,,ENST00000574377,;AC027763.2,downstream_gene_variant,,ENST00000399540,;AC027763.2,downstream_gene_variant,,ENST00000573939,;AC027763.2,downstream_gene_variant,,ENST00000575727,;RP11-589P10.5,upstream_gene_variant,,ENST00000573222,;RP11-589P10.7,intron_variant,,ENST00000572547,;AC027763.2,intron_variant,,ENST00000572385,;AC027763.2,intron_variant,,ENST00000570562,;AC027763.2,downstream_gene_variant,,ENST00000571010,;	A	ENSG00000108839	ENST00000251535	Transcript	synonymous_variant	435	382	128	R	Cga/Aga	rs781254870	.	.	1	ALOX12	HGNC	429	protein_coding	YES	CCDS11084.1	ENSP00000251535	LOX12_HUMAN	.	UPI000013CD03	.	.	.	3/14	.	Superfamily_domains:SSF48484,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF4,PROSITE_profiles:PS51393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCATCGAGAG	.	4	ESCA
DLG4	0	.	GRCh37	17	7096810	7096810	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1814G>T	p.Cys605Phe	p.C605F	ENST00000399510	18/22	77	71	5	74	74	0	DLG4,missense_variant,p.Cys562Phe,ENST00000399506,;DLG4,missense_variant,p.Cys559Phe,ENST00000302955,;DLG4,missense_variant,p.Cys605Phe,ENST00000399510,;DLG4,missense_variant,p.Cys23Phe,ENST00000491753,;DLG4,upstream_gene_variant,,ENST00000489885,;	A	ENSG00000132535	ENST00000399510	Transcript	missense_variant	2667	1814	605	C/F	tGt/tTt	.	.	.	-1	DLG4	HGNC	2903	protein_coding	YES	CCDS45599.1	ENSP00000382428	DLG4_HUMAN	Q3ZCU5_HUMAN,K7EKU8_HUMAN,K7EKP9_HUMAN,B9EGL1_HUMAN,B7Z647_HUMAN	UPI0000048D63	.	deleterious(0)	probably_damaging(0.995)	18/22	.	PROSITE_profiles:PS50052,hmmpanther:PTHR23119:SF4,hmmpanther:PTHR23119,Gene3D:3.40.50.300,Pfam_domain:PF00625,SMART_domains:SM00072,PIRSF_domain:PIRSF001741,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAACACAGGAT	.	2	ESCA
SDK2	0	.	GRCh37	17	71437045	71437045	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>T	p.Asp211Tyr	p.D211Y	ENST00000392650	6/45	54	48	5	46	46	0	SDK2,missense_variant,p.Asp211Tyr,ENST00000388726,;SDK2,missense_variant,p.Asp211Tyr,ENST00000392650,;SDK2,upstream_gene_variant,,ENST00000479356,;	A	ENSG00000069188	ENST00000392650	Transcript	missense_variant	632	631	211	D/Y	Gac/Tac	.	.	.	-1	SDK2	HGNC	19308	protein_coding	YES	CCDS45769.1	ENSP00000376421	SDK2_HUMAN	.	UPI0000E5A088	.	deleterious(0)	possibly_damaging(0.781)	6/45	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF37,Gene3D:2.60.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGTCTGCAG	.	4	ESCA
OTOP2	0	.	GRCh37	17	72927175	72927175	+	Missense_Mutation	SNP	C	C	T	rs763644974	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1445C>T	p.Ser482Leu	p.S482L	ENST00000331427	6/7	80	69	10	52	52	0	OTOP2,missense_variant,p.Ser482Leu,ENST00000580223,;OTOP2,missense_variant,p.Ser482Leu,ENST00000331427,;OTOP3,upstream_gene_variant,,ENST00000328801,;OTOP2,downstream_gene_variant,,ENST00000584711,;OTOP3,upstream_gene_variant,,ENST00000580749,;	T	ENSG00000183034	ENST00000331427	Transcript	missense_variant	1537	1445	482	S/L	tCa/tTa	rs763644974	.	.	1	OTOP2	HGNC	19657	protein_coding	YES	CCDS11708.1	ENSP00000332528	OTOP2_HUMAN	.	UPI000018F613	.	tolerated(0.35)	benign(0.002)	6/7	.	hmmpanther:PTHR21522:SF35,hmmpanther:PTHR21522	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTCTCAACCC	byFrequency	4	ESCA
UBE2O	0	.	GRCh37	17	74392719	74392719	+	Missense_Mutation	SNP	C	C	A	rs777756089	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2299G>T	p.Val767Leu	p.V767L	ENST00000319380	14/18	47	42	5	40	40	0	UBE2O,missense_variant,p.Val767Leu,ENST00000319380,;UBE2O,missense_variant,p.Val282Leu,ENST00000587127,;UBE2O,downstream_gene_variant,,ENST00000590658,;UBE2O,downstream_gene_variant,,ENST00000587581,;UBE2O,non_coding_transcript_exon_variant,,ENST00000586409,;	A	ENSG00000175931	ENST00000319380	Transcript	missense_variant	2364	2299	767	V/L	Gtg/Ttg	rs777756089	.	.	-1	UBE2O	HGNC	29554	protein_coding	YES	CCDS32742.1	ENSP00000323687	UBE2O_HUMAN	.	UPI000020032F	.	tolerated(0.31)	benign(0.002)	14/18	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCACCGGCT	.	4	ESCA
TP53	0	.	GRCh37	17	7577058	7577058	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	8/11	71	65	5	60	60	0	TP53,stop_gained,p.Glu294Ter,ENST00000420246,;TP53,stop_gained,p.Glu294Ter,ENST00000269305,;TP53,stop_gained,p.Glu162Ter,ENST00000509690,;TP53,stop_gained,p.Glu294Ter,ENST00000359597,;TP53,stop_gained,p.Glu294Ter,ENST00000445888,;TP53,stop_gained,p.Glu294Ter,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	1070	880	294	E/*	Gag/Tag	TP53_g.13860G>C,TP53_g.13860G>T,TP53_g.13860G>A,TP53_g.13860del,COSM10856,COSM44127,COSM6621,COSM45824,COSM126981,COSM318363,COSM3388169,COSM2744501	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Gene3D:2.60.40.720	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E294*|c.880G>T|50,SITE|p.E294*|c.880G>T|5,SITE|p.E294*|c.880G>T|12,SITE|p.E294*|c.880G>T|5,CODON|p.0?|c.1_1182del1182|6,CODON|p.K291fs*48|c.871_889del19|8,CODON|p.E294E|c.882G>A|4,CODON|p.E294fs*51|c.880delG|9,BUFFER|p.H297Y|c.889C>T|3,BUFFER|p.H296L|c.887A>T|4,BUFFER|p.H296Y|c.886C>T|4,BUFFER|p.P295P|c.885T>C|3,BUFFER|p.P295L|c.884C>T|4,BUFFER|p.E294fs*12|c.879_880insN|3,BUFFER|p.E294K|c.880G>A|3,BUFFER|p.G293G|c.879G>C|3,BUFFER|p.G293G|c.879G>A|4,BUFFER|p.E294fs*51|c.877delG|3,BUFFER|p.G293R|c.877G>A|4,BUFFER|p.G293fs*13|c.876_877insN|3,BUFFER|p.K292T|c.875A>C|4,BUFFER|p.K292R|c.875A>G|5,BUFFER|p.K292*|c.874A>T|5,BUFFER|p.K292*|c.874A>T|3,BUFFER|p.K291N|c.873G>C|3,BUFFER|p.N288fs*13|c.859_872del14|17,BUFFER|p.K291R|c.872A>G|3,BUFFER|p.K291T|c.872A>C|3,BUFFER|p.K291*|c.871A>T|6,BUFFER|p.R290L|c.869G>T|4,BUFFER|p.R290H|c.869G>A|19	MUTECT|MUSE	AGGCTCCCCTT	.	2	ESCA
ENGASE	0	.	GRCh37	17	77082110	77082110	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1911G>A	p.%3D	p.E637E	ENST00000579016	14/14	97	91	6	72	72	0	ENGASE,synonymous_variant,p.%3D,ENST00000579016,;RBFOX3,downstream_gene_variant,,ENST00000415831,;ENGASE,downstream_gene_variant,,ENST00000311595,;RBFOX3,downstream_gene_variant,,ENST00000582043,;RBFOX3,downstream_gene_variant,,ENST00000583458,;RBFOX3,downstream_gene_variant,,ENST00000453134,;RBFOX3,downstream_gene_variant,,ENST00000580155,;ENGASE,downstream_gene_variant,,ENST00000539857,;ENGASE,downstream_gene_variant,,ENST00000585160,;ENGASE,downstream_gene_variant,,ENST00000584568,;ENGASE,3_prime_UTR_variant,,ENST00000300682,;ENGASE,non_coding_transcript_exon_variant,,ENST00000579809,;RBFOX3,downstream_gene_variant,,ENST00000581393,;ENGASE,downstream_gene_variant,,ENST00000583041,;ENGASE,downstream_gene_variant,,ENST00000578419,;ENGASE,downstream_gene_variant,,ENST00000577783,;RBFOX3,downstream_gene_variant,,ENST00000578998,;ENGASE,downstream_gene_variant,,ENST00000583646,;	A	ENSG00000167280	ENST00000579016	Transcript	synonymous_variant	1911	1911	637	E	gaG/gaA	.	.	.	1	ENGASE	HGNC	24622	protein_coding	YES	CCDS42394.1	ENSP00000462333	ENASE_HUMAN	.	UPI000006CF27	.	.	.	14/14	.	hmmpanther:PTHR13246:SF0,hmmpanther:PTHR13246	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGGAGGGGCC	.	2	ESCA
EIF4A3	0	.	GRCh37	17	78117984	78117984	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.229G>C	p.Asp77His	p.D77H	ENST00000269349	2/12	99	78	21	76	76	0	EIF4A3,missense_variant,p.Asp77His,ENST00000576547,;EIF4A3,missense_variant,p.Asp77His,ENST00000269349,;EIF4A3,non_coding_transcript_exon_variant,,ENST00000575957,;EIF4A3,upstream_gene_variant,,ENST00000570837,;EIF4A3,upstream_gene_variant,,ENST00000575978,;	G	ENSG00000141543	ENST00000269349	Transcript	missense_variant	451	229	77	D/H	Gat/Cat	COSM3970420	.	.	-1	EIF4A3	HGNC	18683	protein_coding	YES	CCDS11767.1	ENSP00000269349	IF4A3_HUMAN	.	UPI000012D374	.	deleterious(0)	probably_damaging(0.995)	2/12	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF57,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACATCTCTCC	.	5	ESCA
BAIAP2	0	.	GRCh37	17	79079945	79079945	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1336A>T	p.Ser446Cys	p.S446C	ENST00000321300	11/15	55	50	5	39	39	0	BAIAP2,missense_variant,p.Ser446Cys,ENST00000428708,;BAIAP2,missense_variant,p.Ser446Cys,ENST00000435091,;BAIAP2,missense_variant,p.Ser446Cys,ENST00000321300,;BAIAP2,missense_variant,p.Ser479Cys,ENST00000575245,;BAIAP2,missense_variant,p.Ser309Cys,ENST00000416299,;BAIAP2,missense_variant,p.Ser446Cys,ENST00000575712,;BAIAP2,missense_variant,p.Ser368Cys,ENST00000392411,;BAIAP2,missense_variant,p.Ser128Cys,ENST00000572498,;BAIAP2,missense_variant,p.Ser446Cys,ENST00000321280,;BAIAP2,intron_variant,,ENST00000575841,;BAIAP2,downstream_gene_variant,,ENST00000572073,;BAIAP2,downstream_gene_variant,,ENST00000576756,;BAIAP2,downstream_gene_variant,,ENST00000573677,;BAIAP2,downstream_gene_variant,,ENST00000574027,;BAIAP2,splice_region_variant,,ENST00000572329,;BAIAP2,splice_region_variant,,ENST00000576225,;BAIAP2,splice_region_variant,,ENST00000576995,;BAIAP2,downstream_gene_variant,,ENST00000574804,;BAIAP2,downstream_gene_variant,,ENST00000577097,;	T	ENSG00000175866	ENST00000321300	Transcript	missense_variant	1429	1336	446	S/C	Agc/Tgc	.	.	.	1	BAIAP2	HGNC	947	protein_coding	YES	CCDS11775.1	ENSP00000316338	BAIP2_HUMAN	I3L526_HUMAN,I3L327_HUMAN,I3L2M4_HUMAN,I3L1C8_HUMAN,I3L125_HUMAN,I3L113_HUMAN,I3L0Y9_HUMAN,I3L0M4_HUMAN	UPI000000D762	.	deleterious(0.04)	possibly_damaging(0.75)	11/15	.	hmmpanther:PTHR14206:SF3,hmmpanther:PTHR14206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACATGAGGTGA	.	3	ESCA
ENTHD2	0	.	GRCh37	17	79205458	79205458	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.735G>C	p.Gln245His	p.Q245H	ENST00000300714	9/12	47	37	10	43	43	0	ENTHD2,missense_variant,p.Gln161His,ENST00000374769,;ENTHD2,missense_variant,p.Gln245His,ENST00000300714,;ENTHD2,downstream_gene_variant,,ENST00000571094,;AC027601.1,non_coding_transcript_exon_variant,,ENST00000575922,;AC027601.1,intron_variant,,ENST00000569559,;ENTHD2,missense_variant,p.Gln7His,ENST00000571115,;ENTHD2,non_coding_transcript_exon_variant,,ENST00000576090,;ENTHD2,non_coding_transcript_exon_variant,,ENST00000573295,;ENTHD2,downstream_gene_variant,,ENST00000570854,;ENTHD2,downstream_gene_variant,,ENST00000574944,;	G	ENSG00000167302	ENST00000300714	Transcript	missense_variant	793	735	245	Q/H	caG/caC	.	.	.	-1	ENTHD2	HGNC	26458	protein_coding	YES	CCDS11779.1	ENSP00000300714	AP4AT_HUMAN	.	UPI0000071221	.	deleterious(0)	probably_damaging(0.986)	9/12	.	hmmpanther:PTHR21514:SF0,hmmpanther:PTHR21514	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTCCTGCTG	.	5	ESCA
FASN	0	.	GRCh37	17	80043514	80043514	+	Silent	SNP	G	G	A	rs765948097	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3966C>T	p.%3D	p.L1322L	ENST00000306749	23/43	94	87	7	100	100	0	FASN,synonymous_variant,p.%3D,ENST00000306749,;FASN,upstream_gene_variant,,ENST00000579758,;FASN,non_coding_transcript_exon_variant,,ENST00000579410,;FASN,upstream_gene_variant,,ENST00000578424,;FASN,upstream_gene_variant,,ENST00000580382,;	A	ENSG00000169710	ENST00000306749	Transcript	synonymous_variant	4185	3966	1322	L	ctC/ctT	rs765948097	.	.	-1	FASN	HGNC	3594	protein_coding	YES	CCDS11801.1	ENSP00000304592	FAS_HUMAN	.	UPI000013EB82	.	.	.	23/43	.	hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF227,Pfam_domain:PF08242,Gene3D:3.40.50.150,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCCGAGGGC	byFrequency	2	ESCA
ZNF750	0	.	GRCh37	17	80790122	80790122	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.209C>A	p.Ser70Ter	p.S70*	ENST00000269394	2/3	76	54	21	64	64	0	ZNF750,stop_gained,p.Ser70Ter,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	T	ENSG00000141579	ENST00000269394	Transcript	stop_gained	1043	209	70	S/*	tCa/tAa	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAGTGAGTTA	.	5	ESCA
ARHGEF15	0	.	GRCh37	17	8215691	8215691	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334C>A	p.Pro112Thr	p.P112T	ENST00000361926	2/16	126	112	14	111	111	0	ARHGEF15,missense_variant,p.Pro112Thr,ENST00000579439,;ARHGEF15,missense_variant,p.Pro112Thr,ENST00000361926,;ARHGEF15,missense_variant,p.Pro112Thr,ENST00000421050,;ARHGEF15,missense_variant,p.Pro112Thr,ENST00000583529,;ARHGEF15,non_coding_transcript_exon_variant,,ENST00000455564,;ARHGEF15,upstream_gene_variant,,ENST00000581809,;ARHGEF15,upstream_gene_variant,,ENST00000578286,;	A	ENSG00000198844	ENST00000361926	Transcript	missense_variant	444	334	112	P/T	Cct/Act	.	.	.	1	ARHGEF15	HGNC	15590	protein_coding	YES	CCDS11139.1	ENSP00000355026	ARHGF_HUMAN	J3QS60_HUMAN,J3KT46_HUMAN	UPI000013D2C0	.	tolerated_low_confidence(0.08)	benign(0.008)	2/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAACCTGCT	.	4	ESCA
ZNF519	0	.	GRCh37	18	14105606	14105606	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933G>C	p.Gln311His	p.Q311H	ENST00000590202	3/3	70	64	5	53	53	0	ZNF519,missense_variant,p.Gln311His,ENST00000590202,;ZNF519,intron_variant,,ENST00000589498,;RP11-411B10.3,downstream_gene_variant,,ENST00000592926,;ZNF519,intron_variant,,ENST00000591393,;ZNF519,intron_variant,,ENST00000592345,;ZNF519,intron_variant,,ENST00000592411,;ZNF519,intron_variant,,ENST00000589203,;ZNF519,intron_variant,,ENST00000592049,;ZNF519,downstream_gene_variant,,ENST00000588435,;ZNF519,intron_variant,,ENST00000587419,;	G	ENSG00000175322	ENST00000590202	Transcript	missense_variant	1086	933	311	Q/H	caG/caC	.	.	.	-1	ZNF519	HGNC	30574	protein_coding	YES	CCDS32797.1	ENSP00000464872	ZN519_HUMAN	.	UPI0000201A41	.	tolerated(0.07)	benign(0.059)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF97,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTCTCTGATG	.	2	ESCA
CTAGE1	0	.	GRCh37	18	19997426	19997426	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349T>A	p.Cys117Ser	p.C117S	ENST00000391403	1/1	162	151	10	141	141	0	CTAGE1,missense_variant,p.Cys117Ser,ENST00000391403,;CTAGE1,upstream_gene_variant,,ENST00000525417,;RP11-863N1.4,downstream_gene_variant,,ENST00000603437,;	T	ENSG00000212710	ENST00000391403	Transcript	missense_variant	453	349	117	C/S	Tgt/Agt	.	.	.	-1	CTAGE1	HGNC	24346	protein_coding	YES	CCDS45837.1	ENSP00000375220	CTGE2_HUMAN	Q8NEG8_HUMAN	UPI00000721F4	.	tolerated(0.45)	benign(0.004)	1/1	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGACAGAGTA	.	2	ESCA
CDH7	0	.	GRCh37	18	63489458	63489458	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767A>T	p.Asn256Ile	p.N256I	ENST00000397968	5/12	50	46	3	42	42	0	CDH7,missense_variant,p.Asn256Ile,ENST00000397968,;CDH7,missense_variant,p.Asn256Ile,ENST00000536984,;CDH7,missense_variant,p.Asn256Ile,ENST00000323011,;	T	ENSG00000081138	ENST00000397968	Transcript	missense_variant	1193	767	256	N/I	aAc/aTc	.	.	.	1	CDH7	HGNC	1766	protein_coding	YES	CCDS11993.1	ENSP00000381058	CADH7_HUMAN	.	UPI000013D269	.	deleterious(0)	probably_damaging(1)	5/12	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTCAACGATA	.	2	ESCA
LAMA1	0	.	GRCh37	18	6955526	6955526	+	Intron	SNP	C	C	A	rs555722981	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8095-62G>T	.	.	ENST00000389658	.	40	35	5	27	27	0	LAMA1,intron_variant,,ENST00000389658,;RP11-781P6.1,non_coding_transcript_exon_variant,,ENST00000584722,;LAMA1,non_coding_transcript_exon_variant,,ENST00000492048,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488089,;LAMA1,intron_variant,,ENST00000488064,;LAMA1,intron_variant,,ENST00000579014,;	A	ENSG00000101680	ENST00000389658	Transcript	intron_variant	.	.	.	.	.	rs555722981	.	.	-1	LAMA1	HGNC	6481	protein_coding	YES	CCDS32787.1	ENSP00000374309	LAMA1_HUMAN	Q7Z5W6_HUMAN,Q6P6D3_HUMAN	UPI00001C1FF9	.	.	.	.	56/62	.	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACGCGTGTT	byFrequency|by1000G	4	ESCA
TYK2	0	.	GRCh37	19	10461829	10461829	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3328G>C	p.Glu1110Gln	p.E1110Q	ENST00000525621	24/25	39	36	3	31	31	0	TYK2,missense_variant,p.Glu1110Gln,ENST00000525621,;TYK2,missense_variant,p.Glu1110Gln,ENST00000264818,;TYK2,missense_variant,p.Glu925Gln,ENST00000524462,;TYK2,intron_variant,,ENST00000530560,;TYK2,intron_variant,,ENST00000525976,;TYK2,downstream_gene_variant,,ENST00000529739,;TYK2,non_coding_transcript_exon_variant,,ENST00000529422,;TYK2,downstream_gene_variant,,ENST00000592137,;TYK2,3_prime_UTR_variant,,ENST00000527481,;TYK2,non_coding_transcript_exon_variant,,ENST00000524470,;TYK2,intron_variant,,ENST00000530220,;TYK2,downstream_gene_variant,,ENST00000529412,;TYK2,downstream_gene_variant,,ENST00000534228,;	G	ENSG00000105397	ENST00000525621	Transcript	missense_variant	3810	3328	1110	E/Q	Gag/Cag	.	.	.	-1	TYK2	HGNC	12440	protein_coding	YES	CCDS12236.1	ENSP00000431885	TYK2_HUMAN	E9PQM4_HUMAN,E9PQL2_HUMAN,E9PM19_HUMAN	UPI000013D573	.	deleterious(0.03)	possibly_damaging(0.745)	24/25	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF68,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,PIRSF_domain:PIRSF000636,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GAGCTCAAGGA	.	2	ESCA
TYK2	0	.	GRCh37	19	10463209	10463209	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3219G>C	p.%3D	p.L1073L	ENST00000525621	23/25	81	75	6	51	51	0	TYK2,synonymous_variant,p.%3D,ENST00000525621,;TYK2,synonymous_variant,p.%3D,ENST00000529739,;TYK2,synonymous_variant,p.%3D,ENST00000264818,;TYK2,synonymous_variant,p.%3D,ENST00000524462,;TYK2,intron_variant,,ENST00000530560,;TYK2,downstream_gene_variant,,ENST00000529370,;TYK2,upstream_gene_variant,,ENST00000525976,;TYK2,non_coding_transcript_exon_variant,,ENST00000592137,;TYK2,intron_variant,,ENST00000529422,;TYK2,missense_variant,p.Glu133Gln,ENST00000527481,;TYK2,intron_variant,,ENST00000530220,;TYK2,upstream_gene_variant,,ENST00000524470,;TYK2,downstream_gene_variant,,ENST00000529412,;TYK2,downstream_gene_variant,,ENST00000534228,;	G	ENSG00000105397	ENST00000525621	Transcript	synonymous_variant	3701	3219	1073	L	ctG/ctC	.	.	.	-1	TYK2	HGNC	12440	protein_coding	YES	CCDS12236.1	ENSP00000431885	TYK2_HUMAN	E9PQM4_HUMAN,E9PQL2_HUMAN,E9PM19_HUMAN	UPI000013D573	.	.	.	23/25	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF68,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,PIRSF_domain:PIRSF000636,Superfamily_domains:SSF56112,Prints_domain:PR00109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TCCTTCAGGCA	.	2	ESCA
ZNF563	0	.	GRCh37	19	12430083	12430083	+	Silent	SNP	C	C	A	rs187827621	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.756G>T	p.%3D	p.P252P	ENST00000293725	4/4	175	163	12	125	125	0	ZNF563,missense_variant,p.Arg213Leu,ENST00000595977,;ZNF563,synonymous_variant,p.%3D,ENST00000293725,;ZNF563,synonymous_variant,p.%3D,ENST00000594577,;ZNF563,downstream_gene_variant,,ENST00000601858,;	A	ENSG00000188868	ENST00000293725	Transcript	synonymous_variant	962	756	252	P	ccG/ccT	rs187827621	.	.	-1	ZNF563	HGNC	30498	protein_coding	YES	CCDS12270.1	ENSP00000293725	ZN563_HUMAN	M0R1Q6_HUMAN	UPI0000072E62	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF14,hmmpanther:PTHR24379,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCATACGGTTT	byCluster|by1000G	2	ESCA
CACNA1A	0	.	GRCh37	19	13410024	13410024	+	Missense_Mutation	SNP	G	G	T	rs748099275	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2423C>A	p.Thr808Lys	p.T808K	ENST00000360228	19/47	157	145	12	117	117	0	CACNA1A,missense_variant,p.Thr809Lys,ENST00000573710,;CACNA1A,missense_variant,p.Thr808Lys,ENST00000360228,;	T	ENSG00000141837	ENST00000360228	Transcript	missense_variant	2423	2423	808	T/K	aCg/aAg	rs748099275,COSM1129987,COSM1129986,COSM1129988	.	.	-1	CACNA1A	HGNC	1388	protein_coding	YES	CCDS45998.1	ENSP00000353362	CAC1A_HUMAN	Q9UN69_HUMAN,Q9UHM9_HUMAN	UPI0000141565	.	.	benign(0.005)	19/47	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCCGCGTGTAG	.	2	ESCA
PKN1	0	.	GRCh37	19	14578588	14578588	+	Silent	SNP	C	C	A	rs567970117	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1885C>A	p.%3D	p.R629R	ENST00000342216	14/22	87	78	8	87	87	0	PKN1,synonymous_variant,p.%3D,ENST00000242783,;PKN1,synonymous_variant,p.%3D,ENST00000342216,;PKN1,intron_variant,,ENST00000586237,;PTGER1,downstream_gene_variant,,ENST00000292513,;PKN1,upstream_gene_variant,,ENST00000592960,;PKN1,synonymous_variant,p.%3D,ENST00000591461,;PKN1,non_coding_transcript_exon_variant,,ENST00000585839,;PKN1,non_coding_transcript_exon_variant,,ENST00000587215,;PKN1,upstream_gene_variant,,ENST00000586039,;PKN1,downstream_gene_variant,,ENST00000586900,;	A	ENSG00000123143	ENST00000342216	Transcript	synonymous_variant	1916	1885	629	R	Cgg/Agg	rs567970117	.	.	1	PKN1	HGNC	9405	protein_coding	YES	CCDS42514.1	ENSP00000343325	PKN1_HUMAN	.	UPI0000366D4D	.	.	.	14/22	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF69,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGCCGGGGT	by1000G	4	ESCA
PLK5	0	.	GRCh37	19	1531846	1531846	+	Silent	SNP	G	G	C	rs755084609	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.678G>C	p.%3D	p.T226T	ENST00000334770	11/13	77	70	7	61	61	0	PLK5,synonymous_variant,p.%3D,ENST00000588430,;PLK5,synonymous_variant,p.%3D,ENST00000454744,;PLK5,synonymous_variant,p.%3D,ENST00000334770,;PLK5,downstream_gene_variant,,ENST00000588292,;	C	ENSG00000185988	ENST00000334770	Transcript	synonymous_variant	1567	678	226	T	acG/acC	rs755084609	.	.	1	PLK5	HGNC	27001	protein_coding	YES	CCDS59328.1	ENSP00000466248	PLK5_HUMAN	.	UPI000015FEF2	.	.	.	11/13	.	hmmpanther:PTHR24345,hmmpanther:PTHR24345:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCACGGGACG	.	4	ESCA
PGLYRP2	0	.	GRCh37	19	15582811	15582811	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1233C>A	p.His411Gln	p.H411Q	ENST00000340880	3/5	115	105	10	101	101	0	PGLYRP2,missense_variant,p.His411Gln,ENST00000340880,;PGLYRP2,missense_variant,p.His411Gln,ENST00000292609,;PGLYRP2,downstream_gene_variant,,ENST00000594637,;PGLYRP2,downstream_gene_variant,,ENST00000601792,;	T	ENSG00000161031	ENST00000340880	Transcript	missense_variant	1714	1233	411	H/Q	caC/caA	.	.	.	-1	PGLYRP2	HGNC	30013	protein_coding	YES	CCDS12330.2	ENSP00000345968	PGRP2_HUMAN	M0R2W8_HUMAN,M0QYW3_HUMAN	UPI000004EEA6	.	deleterious(0)	probably_damaging(0.959)	3/5	.	Superfamily_domains:SSF55846,SMART_domains:SM00701,SMART_domains:SM00644,Pfam_domain:PF01510,Gene3D:3.40.80.10,hmmpanther:PTHR11022,hmmpanther:PTHR11022:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGGTGTGATG	.	2	ESCA
NWD1	0	.	GRCh37	19	16883997	16883997	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2471C>A	p.Pro824Gln	p.P824Q	ENST00000524140	11/19	51	47	4	58	58	0	NWD1,missense_variant,p.Pro689Gln,ENST00000339803,;NWD1,missense_variant,p.Pro824Gln,ENST00000524140,;NWD1,missense_variant,p.Pro824Gln,ENST00000552788,;NWD1,missense_variant,p.Pro824Gln,ENST00000379808,;NWD1,missense_variant,p.Pro824Gln,ENST00000549814,;NWD1,missense_variant,p.Pro618Gln,ENST00000523826,;NWD1,3_prime_UTR_variant,,ENST00000438489,;NWD1,3_prime_UTR_variant,,ENST00000518676,;	A	ENSG00000188039	ENST00000524140	Transcript	missense_variant	2889	2471	824	P/Q	cCa/cAa	.	.	.	1	NWD1	HGNC	27619	protein_coding	YES	CCDS32945.2	ENSP00000428579	NWD1_HUMAN	.	UPI0000D6173E	.	deleterious(0.01)	probably_damaging(0.985)	11/19	.	hmmpanther:PTHR22847:SF273,hmmpanther:PTHR22847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATCCAGCAC	.	2	ESCA
CPAMD8	0	.	GRCh37	19	17088273	17088273	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1804C>A	p.Pro602Thr	p.P602T	ENST00000443236	15/42	47	41	6	47	47	0	CPAMD8,missense_variant,p.Pro602Thr,ENST00000443236,;CPAMD8,intron_variant,,ENST00000388925,;CPAMD8,upstream_gene_variant,,ENST00000593420,;CPAMD8,intron_variant,,ENST00000291440,;	T	ENSG00000160111	ENST00000443236	Transcript	missense_variant	1836	1804	602	P/T	Ccc/Acc	.	.	.	-1	CPAMD8	HGNC	23228	protein_coding	YES	CCDS42519.1	ENSP00000402505	CPMD8_HUMAN	.	UPI0000E8AC99	.	deleterious(0)	probably_damaging(0.962)	15/42	.	hmmpanther:PTHR11412:SF76,hmmpanther:PTHR11412,Pfam_domain:PF07703	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R605H|c.1814G>A|3	RADIA|MUTECT|MUSE|VARSCANS	AAGGGGGACCA	.	4	ESCA
NR2F6	0	.	GRCh37	19	17342983	17342983	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*178A>G	.	.	ENST00000291442	4/4	153	145	8	154	154	0	NR2F6,3_prime_UTR_variant,,ENST00000291442,;OCEL1,downstream_gene_variant,,ENST00000600826,;NR2F6,downstream_gene_variant,,ENST00000596878,;OCEL1,downstream_gene_variant,,ENST00000600232,;OCEL1,downstream_gene_variant,,ENST00000601529,;OCEL1,downstream_gene_variant,,ENST00000597836,;OCEL1,downstream_gene_variant,,ENST00000598068,;AC010646.3,downstream_gene_variant,,ENST00000594059,;OCEL1,downstream_gene_variant,,ENST00000215061,;OCEL1,downstream_gene_variant,,ENST00000595573,;OCEL1,downstream_gene_variant,,ENST00000601576,;OCEL1,downstream_gene_variant,,ENST00000602236,;OCEL1,downstream_gene_variant,,ENST00000594283,;OCEL1,downstream_gene_variant,,ENST00000599286,;OCEL1,downstream_gene_variant,,ENST00000599588,;OCEL1,downstream_gene_variant,,ENST00000598172,;OCEL1,downstream_gene_variant,,ENST00000596279,;OCEL1,downstream_gene_variant,,ENST00000595769,;	C	ENSG00000160113	ENST00000291442	Transcript	3_prime_UTR_variant	2113	.	.	.	.	.	.	.	-1	NR2F6	HGNC	7977	protein_coding	YES	CCDS12352.1	ENSP00000291442	NR2F6_HUMAN	M0R384_HUMAN,M0R175_HUMAN,F1D8R3_HUMAN	UPI0000129B28	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTTTGGTTT	.	2	ESCA
BABAM1	0	.	GRCh37	19	17379661	17379661	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.46G>T	p.Glu16Ter	p.E16*	ENST00000359435	2/9	98	88	10	85	85	0	BABAM1,stop_gained,p.Glu16Ter,ENST00000595632,;BABAM1,stop_gained,p.Glu16Ter,ENST00000599057,;BABAM1,stop_gained,p.Glu16Ter,ENST00000601043,;BABAM1,stop_gained,p.Glu45Ter,ENST00000601938,;BABAM1,stop_gained,p.Glu16Ter,ENST00000598188,;BABAM1,stop_gained,p.Glu16Ter,ENST00000596335,;BABAM1,stop_gained,p.Glu16Ter,ENST00000602066,;BABAM1,stop_gained,p.Glu16Ter,ENST00000601436,;BABAM1,stop_gained,p.Glu16Ter,ENST00000447614,;BABAM1,stop_gained,p.Glu16Ter,ENST00000599474,;BABAM1,stop_gained,p.Glu16Ter,ENST00000359435,;USHBP1,intron_variant,,ENST00000598309,;USHBP1,upstream_gene_variant,,ENST00000252597,;USHBP1,upstream_gene_variant,,ENST00000594190,;USHBP1,upstream_gene_variant,,ENST00000431146,;BABAM1,upstream_gene_variant,,ENST00000598567,;BABAM1,non_coding_transcript_exon_variant,,ENST00000448635,;USHBP1,upstream_gene_variant,,ENST00000598570,;USHBP1,upstream_gene_variant,,ENST00000595993,;BABAM1,stop_gained,p.Glu16Ter,ENST00000601171,;BABAM1,stop_gained,p.Glu16Ter,ENST00000594247,;CTD-2278I10.6,5_prime_UTR_variant,,ENST00000596542,;BABAM1,non_coding_transcript_exon_variant,,ENST00000595393,;USHBP1,upstream_gene_variant,,ENST00000324554,;USHBP1,upstream_gene_variant,,ENST00000596436,;USHBP1,upstream_gene_variant,,ENST00000600286,;USHBP1,upstream_gene_variant,,ENST00000597928,;	T	ENSG00000105393	ENST00000359435	Transcript	stop_gained	239	46	16	E/*	Gaa/Taa	.	.	.	1	BABAM1	HGNC	25008	protein_coding	YES	CCDS46012.1	ENSP00000352408	BABA1_HUMAN	M0R3F4_HUMAN,M0R2K3_HUMAN,M0R0I0_HUMAN	UPI0000034E01	.	.	.	2/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15660,hmmpanther:PTHR15660:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGAGGAAGAG	.	4	ESCA
HOMER3	0	.	GRCh37	19	19040124	19040124	+	3'UTR	SNP	C	C	A	rs778750746	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128G>T	.	.	ENST00000539827	9/9	80	74	6	78	78	0	HOMER3,3_prime_UTR_variant,,ENST00000594794,;HOMER3,3_prime_UTR_variant,,ENST00000433218,;HOMER3,3_prime_UTR_variant,,ENST00000221222,;HOMER3,3_prime_UTR_variant,,ENST00000539827,;HOMER3,3_prime_UTR_variant,,ENST00000392351,;DDX49,downstream_gene_variant,,ENST00000247003,;HOMER3,downstream_gene_variant,,ENST00000355887,;HOMER3,downstream_gene_variant,,ENST00000542541,;HOMER3,downstream_gene_variant,,ENST00000594439,;HOMER3,downstream_gene_variant,,ENST00000600077,;HOMER3,downstream_gene_variant,,ENST00000596482,;DDX49,downstream_gene_variant,,ENST00000438170,;DDX49,downstream_gene_variant,,ENST00000601772,;DDX49,downstream_gene_variant,,ENST00000599156,;AC002985.3,intron_variant,,ENST00000596918,;AC002985.3,intron_variant,,ENST00000593484,;DDX49,downstream_gene_variant,,ENST00000598277,;DDX49,downstream_gene_variant,,ENST00000596502,;DDX49,downstream_gene_variant,,ENST00000601803,;DDX49,downstream_gene_variant,,ENST00000602113,;DDX49,downstream_gene_variant,,ENST00000595858,;HOMER3,downstream_gene_variant,,ENST00000595756,;	A	ENSG00000051128	ENST00000539827	Transcript	3_prime_UTR_variant	1867	.	.	.	.	rs778750746	.	.	-1	HOMER3	HGNC	17514	protein_coding	YES	CCDS12391.1	ENSP00000439937	HOME3_HUMAN	M0R2U7_HUMAN,M0R2T8_HUMAN,M0QZN1_HUMAN	UPI0000140C32	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCCCGGCCC	byFrequency	2	ESCA
ZNF253	0	.	GRCh37	19	20002567	20002567	+	Missense_Mutation	SNP	C	C	A	rs200085854	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.511C>A	p.Leu171Ile	p.L171I	ENST00000589717	4/4	85	76	9	66	66	0	ZNF253,missense_variant,p.Leu107Ile,ENST00000592725,;ZNF253,missense_variant,p.Leu95Ile,ENST00000355650,;ZNF253,missense_variant,p.Leu171Ile,ENST00000589717,;AC011477.1,downstream_gene_variant,,ENST00000578823,;CTC-559E9.8,downstream_gene_variant,,ENST00000585571,;	A	ENSG00000256771	ENST00000589717	Transcript	missense_variant	603	511	171	L/I	Ctt/Att	rs200085854	.	.	1	ZNF253	HGNC	13497	protein_coding	YES	CCDS42532.1	ENSP00000468720	ZN253_HUMAN	K7EP55_HUMAN	UPI0000070CE8	.	tolerated(0.21)	benign(0.007)	4/4	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF106,Superfamily_domains:SSF57667	A:0.0014	A:0.0045	A:0	.	A:0	A:0.001	A:0	A:0.0022	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TAAATCTTTTC	byFrequency|byCluster|by1000G	3	ESCA
AP3D1	0	.	GRCh37	19	2116224	2116224	+	Missense_Mutation	SNP	G	G	T	rs748893543	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2055C>A	p.Ser685Arg	p.S685R	ENST00000355272	18/32	148	141	7	113	113	0	AP3D1,missense_variant,p.Ser685Arg,ENST00000345016,;AP3D1,missense_variant,p.Ser594Arg,ENST00000356926,;AP3D1,missense_variant,p.Ser516Arg,ENST00000350812,;AP3D1,missense_variant,p.Ser685Arg,ENST00000355272,;AP3D1,downstream_gene_variant,,ENST00000590683,;AP3D1,non_coding_transcript_exon_variant,,ENST00000591631,;AP3D1,downstream_gene_variant,,ENST00000586177,;AP3D1,upstream_gene_variant,,ENST00000589223,;AP3D1,upstream_gene_variant,,ENST00000585652,;AP3D1,upstream_gene_variant,,ENST00000591650,;AP3D1,upstream_gene_variant,,ENST00000592488,;	T	ENSG00000065000	ENST00000355272	Transcript	missense_variant	2262	2055	685	S/R	agC/agA	rs748893543	.	.	-1	AP3D1	HGNC	568	protein_coding	YES	CCDS58638.1	ENSP00000347416	AP3D1_HUMAN	Q9UEB0_HUMAN,Q9UEA9_HUMAN,B3KSV6_HUMAN	UPI0000202F99	.	tolerated(0.1)	possibly_damaging(0.651)	18/32	.	hmmpanther:PTHR22781,Pfam_domain:PF06375,PIRSF_domain:PIRSF037092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCGAGCTCTT	byFrequency	2	ESCA
ZNF98	0	.	GRCh37	19	22574497	22574497	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1540G>T	p.Gly514Ter	p.G514*	ENST00000357774	4/4	88	78	10	54	54	0	ZNF98,stop_gained,p.Gly514Ter,ENST00000357774,;ZNF98,downstream_gene_variant,,ENST00000593657,;	A	ENSG00000197360	ENST00000357774	Transcript	stop_gained	1662	1540	514	G/*	Gga/Tga	.	.	.	-1	ZNF98	HGNC	13174	protein_coding	YES	CCDS46031.1	ENSP00000350418	ZNF98_HUMAN	M0QZS3_HUMAN	UPI0000251DC5	.	.	.	4/4	.	PROSITE_profiles:PS50157,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTCCAGTAT	.	4	ESCA
GNA15	0	.	GRCh37	19	3157847	3157847	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.866C>T	p.Ser289Phe	p.S289F	ENST00000262958	6/7	171	162	9	117	117	0	GNA15,missense_variant,p.Ser289Phe,ENST00000262958,;AC005264.2,upstream_gene_variant,,ENST00000587587,;GNA15,downstream_gene_variant,,ENST00000586082,;	T	ENSG00000060558	ENST00000262958	Transcript	missense_variant	1124	866	289	S/F	tCc/tTc	.	.	.	1	GNA15	HGNC	4383	protein_coding	YES	CCDS12104.1	ENSP00000262958	GNA15_HUMAN	.	UPI000013D36D	.	deleterious(0.02)	probably_damaging(0.972)	6/7	.	hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF50,Pfam_domain:PF00503,Gene3D:3.40.50.300,SMART_domains:SM00275,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCTCCCACC	.	2	ESCA
ANKRD27	0	.	GRCh37	19	33119650	33119650	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315G>A	p.Asp439Asn	p.D439N	ENST00000306065	14/29	83	73	10	74	74	0	ANKRD27,missense_variant,p.Asp439Asn,ENST00000306065,;ANKRD27,missense_variant,p.Asp133Asn,ENST00000591100,;	T	ENSG00000105186	ENST00000306065	Transcript	missense_variant	1474	1315	439	D/N	Gac/Aac	.	.	.	-1	ANKRD27	HGNC	25310	protein_coding	YES	CCDS32986.1	ENSP00000304292	ANR27_HUMAN	K7EPM2_HUMAN,K7EIN0_HUMAN,K7EIH4_HUMAN	UPI000004FDE9	.	tolerated(0.59)	possibly_damaging(0.822)	14/29	.	hmmpanther:PTHR24170,hmmpanther:PTHR24170:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAGTCATCGC	.	4	ESCA
HPN	0	.	GRCh37	19	35533176	35533176	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-235C>A	.	.	ENST00000262626	2/13	49	44	5	35	35	0	HPN,5_prime_UTR_variant,,ENST00000262626,;HPN,intron_variant,,ENST00000597419,;HPN,intron_variant,,ENST00000392226,;HPN,intron_variant,,ENST00000600390,;SCN1B,downstream_gene_variant,,ENST00000262631,;SCN1B,downstream_gene_variant,,ENST00000595652,;SCN1B,downstream_gene_variant,,ENST00000596348,;HPN,intron_variant,,ENST00000599363,;SCN1B,downstream_gene_variant,,ENST00000602150,;	A	ENSG00000105707	ENST00000262626	Transcript	5_prime_UTR_variant	591	.	.	.	.	.	.	.	1	HPN	HGNC	5155	protein_coding	YES	CCDS32993.1	ENSP00000262626	HEPS_HUMAN	M0R244_HUMAN,B2ZDQ2_HUMAN	UPI000003FE67	.	.	.	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCCGCTGCTG	.	3	ESCA
GIPC3	0	.	GRCh37	19	3590979	3590979	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*791C>G	.	.	ENST00000322315	6/6	109	103	5	103	103	0	GIPC3,3_prime_UTR_variant,,ENST00000322315,;TBXA2R,downstream_gene_variant,,ENST00000589966,;TBXA2R,downstream_gene_variant,,ENST00000411851,;TBXA2R,downstream_gene_variant,,ENST00000375190,;	G	ENSG00000179855	ENST00000322315	Transcript	3_prime_UTR_variant	1775	.	.	.	.	.	.	.	1	GIPC3	HGNC	18183	protein_coding	YES	CCDS32871.1	ENSP00000319254	GIPC3_HUMAN	.	UPI000006F1A9	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AGAGTCCAGGC	.	2	ESCA
ARHGAP33	0	.	GRCh37	19	36269201	36269201	+	Missense_Mutation	SNP	G	G	T	rs780668839	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.209G>T	p.Arg70Leu	p.R70L	ENST00000314737	4/21	60	56	4	55	55	0	ARHGAP33,missense_variant,p.Arg70Leu,ENST00000007510,;ARHGAP33,missense_variant,p.Arg70Leu,ENST00000314737,;ARHGAP33,5_prime_UTR_variant,,ENST00000378944,;ARHGAP33,upstream_gene_variant,,ENST00000587447,;ARHGAP33,upstream_gene_variant,,ENST00000588248,;ARHGAP33,non_coding_transcript_exon_variant,,ENST00000221905,;ARHGAP33,non_coding_transcript_exon_variant,,ENST00000589133,;ARHGAP33,upstream_gene_variant,,ENST00000591438,;ARHGAP33,missense_variant,p.Arg70Leu,ENST00000590893,;ARHGAP33,upstream_gene_variant,,ENST00000601474,;ARHGAP33,upstream_gene_variant,,ENST00000586918,;	T	ENSG00000004777	ENST00000314737	Transcript	missense_variant	293	209	70	R/L	cGt/cTt	rs780668839	.	.	1	ARHGAP33	HGNC	23085	protein_coding	YES	CCDS12477.1	ENSP00000320038	RHG33_HUMAN	.	UPI000013F8F9	.	deleterious_low_confidence(0.03)	benign(0.433)	4/21	.	hmmpanther:PTHR15729,hmmpanther:PTHR15729:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGACCGTGAAG	.	2	ESCA
WDR62	0	.	GRCh37	19	36573985	36573985	+	Nonsense_Mutation	SNP	C	C	G	rs151063285	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1392C>G	p.Tyr464Ter	p.Y464*	ENST00000401500	11/32	41	38	3	33	33	0	WDR62,stop_gained,p.Tyr464Ter,ENST00000270301,;WDR62,stop_gained,p.Tyr464Ter,ENST00000401500,;WDR62,downstream_gene_variant,,ENST00000388999,;WDR62,3_prime_UTR_variant,,ENST00000587391,;	G	ENSG00000075702	ENST00000401500	Transcript	stop_gained	1427	1392	464	Y/*	taC/taG	rs151063285	.	.	1	WDR62	HGNC	24502	protein_coding	YES	CCDS46059.1	ENSP00000384792	WDR62_HUMAN	.	UPI000022A7E9	.	.	.	11/32	.	hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF362,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	T:0.0007	T:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGTACGTGGA	byCluster	3	ESCA
WDR87	0	.	GRCh37	19	38383272	38383272	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2954C>G	p.Ser985Cys	p.S985C	ENST00000303868	4/6	72	65	7	68	68	0	WDR87,missense_variant,p.Ser1024Cys,ENST00000447313,;WDR87,missense_variant,p.Ser985Cys,ENST00000303868,;WDR87,downstream_gene_variant,,ENST00000473328,;	C	ENSG00000171804	ENST00000303868	Transcript	missense_variant	3179	2954	985	S/C	tCt/tGt	.	.	.	-1	WDR87	HGNC	29934	protein_coding	YES	CCDS46063.1	ENSP00000368025	WDR87_HUMAN	B4DXE9_HUMAN	UPI0001662BC1	.	.	benign(0.179)	4/6	.	hmmpanther:PTHR19852,hmmpanther:PTHR19852:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCTAGAGTGG	.	3	ESCA
WDR87	0	.	GRCh37	19	38385259	38385259	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967G>T	p.Gly323Cys	p.G323C	ENST00000303868	4/6	25	22	3	34	34	0	WDR87,missense_variant,p.Gly362Cys,ENST00000447313,;WDR87,missense_variant,p.Gly323Cys,ENST00000303868,;WDR87,downstream_gene_variant,,ENST00000473328,;	A	ENSG00000171804	ENST00000303868	Transcript	missense_variant	1192	967	323	G/C	Ggc/Tgc	.	.	.	-1	WDR87	HGNC	29934	protein_coding	YES	CCDS46063.1	ENSP00000368025	WDR87_HUMAN	B4DXE9_HUMAN	UPI0001662BC1	.	.	probably_damaging(0.999)	4/6	.	hmmpanther:PTHR19852,hmmpanther:PTHR19852:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGCCACAGA	.	2	ESCA
RASGRP4	0	.	GRCh37	19	38905515	38905515	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1203C>A	p.%3D	p.A401A	ENST00000587738	9/17	82	74	8	82	82	0	RASGRP4,synonymous_variant,p.%3D,ENST00000454404,;RASGRP4,synonymous_variant,p.%3D,ENST00000586305,;RASGRP4,synonymous_variant,p.%3D,ENST00000293062,;RASGRP4,synonymous_variant,p.%3D,ENST00000587738,;RASGRP4,synonymous_variant,p.%3D,ENST00000587753,;RASGRP4,intron_variant,,ENST00000426920,;RASGRP4,intron_variant,,ENST00000433821,;RASGRP4,synonymous_variant,p.%3D,ENST00000589474,;RASGRP4,synonymous_variant,p.%3D,ENST00000589358,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588708,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588404,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000592322,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000589100,;RASGRP4,upstream_gene_variant,,ENST00000587287,;	T	ENSG00000171777	ENST00000587738	Transcript	synonymous_variant	1274	1203	401	A	gcC/gcA	.	.	.	-1	RASGRP4	HGNC	18958	protein_coding	YES	CCDS46068.1	ENSP00000465772	GRP4_HUMAN	.	UPI0000050F40	.	.	.	9/17	.	PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF157,hmmpanther:PTHR23113,Gene3D:2ii0A02,SMART_domains:SM00147,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCATTGGCGCT	.	4	ESCA
SARS2	0	.	GRCh37	19	39406737	39406737	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1293G>T	p.Gln431His	p.Q431H	ENST00000600042	15/17	230	209	21	210	210	0	SARS2,missense_variant,p.Gln431His,ENST00000600042,;SARS2,missense_variant,p.Gln429His,ENST00000448145,;SARS2,missense_variant,p.Gln429His,ENST00000221431,;CTC-360G5.8,missense_variant,p.Gln499His,ENST00000599996,;SARS2,missense_variant,p.Gln239His,ENST00000594171,;SARS2,missense_variant,p.Gln429His,ENST00000430193,;SARS2,missense_variant,p.Gln77His,ENST00000598831,;CCER2,upstream_gene_variant,,ENST00000571838,;SARS2,downstream_gene_variant,,ENST00000598563,;SARS2,downstream_gene_variant,,ENST00000455102,;SARS2,downstream_gene_variant,,ENST00000602034,;SARS2,upstream_gene_variant,,ENST00000594259,;SARS2,downstream_gene_variant,,ENST00000600448,;SARS2,downstream_gene_variant,,ENST00000597490,;	A	ENSG00000104835	ENST00000600042	Transcript	missense_variant	1318	1293	431	Q/H	caG/caT	.	.	.	-1	SARS2	HGNC	17697	protein_coding	YES	CCDS54265.1	ENSP00000472847	SYSM_HUMAN	M0R259_HUMAN	UPI00017A6C34	.	deleterious(0)	possibly_damaging(0.699)	15/17	.	PROSITE_profiles:PS50862,hmmpanther:PTHR11778:SF5,hmmpanther:PTHR11778,TIGRFAM_domain:TIGR00414,Gene3D:3.30.930.10,PIRSF_domain:PIRSF001529,Superfamily_domains:SSF55681,Prints_domain:PR00981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CGGCTCTGGAA	.	3	ESCA
FCGBP	0	.	GRCh37	19	40398279	40398279	+	Missense_Mutation	SNP	C	C	A	rs782387243	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6688G>T	p.Ala2230Ser	p.A2230S	ENST00000221347	14/36	62	55	7	43	43	0	FCGBP,missense_variant,p.Ala2230Ser,ENST00000221347,;FCGBP,intron_variant,,ENST00000601713,;	A	ENSG00000090920	ENST00000221347	Transcript	missense_variant	6696	6688	2230	A/S	Gcc/Tcc	rs782387243	.	.	-1	FCGBP	HGNC	13572	protein_coding	YES	CCDS12546.1	ENSP00000221347	FCGBP_HUMAN	.	UPI00001B0455	.	.	possibly_damaging(0.515)	14/36	.	PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF244,hmmpanther:PTHR11339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TCCGGCGGGCT	byFrequency	2	ESCA
CYP2B6	0	.	GRCh37	19	41522787	41522787	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*55C>T	.	.	ENST00000324071	9/9	24	19	5	25	25	0	CYP2B6,3_prime_UTR_variant,,ENST00000593831,;CYP2B6,3_prime_UTR_variant,,ENST00000330446,;CYP2B6,3_prime_UTR_variant,,ENST00000324071,;CYP2B6,non_coding_transcript_exon_variant,,ENST00000597612,;	T	ENSG00000197408	ENST00000324071	Transcript	3_prime_UTR_variant	1538	.	.	.	.	.	.	.	1	CYP2B6	HGNC	2615	protein_coding	YES	CCDS12570.1	ENSP00000324648	CP2B6_HUMAN	Q9UNX8_HUMAN,F2X1B0_HUMAN	UPI000012823F	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CGCCTCTGTAG	.	2	ESCA
ATP1A3	0	.	GRCh37	19	42492163	42492163	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321G>T	p.%3D	p.L107L	ENST00000545399	4/23	100	89	10	76	76	0	ATP1A3,synonymous_variant,p.%3D,ENST00000602133,;ATP1A3,synonymous_variant,p.%3D,ENST00000543770,;ATP1A3,synonymous_variant,p.%3D,ENST00000545399,;ATP1A3,synonymous_variant,p.%3D,ENST00000473086,;ATP1A3,synonymous_variant,p.%3D,ENST00000302102,;ATP1A3,downstream_gene_variant,,ENST00000468774,;ATP1A3,downstream_gene_variant,,ENST00000465007,;ATP1A3,synonymous_variant,p.%3D,ENST00000441343,;ATP1A3,upstream_gene_variant,,ENST00000485672,;	A	ENSG00000105409	ENST00000545399	Transcript	synonymous_variant	475	321	107	L	ctG/ctT	.	.	.	-1	ATP1A3	HGNC	801	protein_coding	YES	CCDS58664.1	ENSP00000444688	AT1A3_HUMAN	Q58I21_HUMAN,M0R116_HUMAN,M0QXF2_HUMAN	UPI0001914BDE	.	.	.	4/23	.	Transmembrane_helices:TMhelix,Prints_domain:PR00121,Superfamily_domains:0049473,SMART_domains:SM00831,Pfam_domain:PF00690,TIGRFAM_domain:TIGR01106,hmmpanther:PTHR24093:SF259,hmmpanther:PTHR24093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCCACAGCAG	.	4	ESCA
PSG10P	0	.	GRCh37	19	43358229	43358229	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.302T>C	.	.	ENST00000501199	2/6	305	294	10	256	256	0	PSG8,intron_variant,,ENST00000401467,;PSG10P,non_coding_transcript_exon_variant,,ENST00000597171,;PSG10P,non_coding_transcript_exon_variant,,ENST00000501199,;	G	ENSG00000248257	ENST00000501199	Transcript	non_coding_transcript_exon_variant	302	.	.	.	.	.	.	.	-1	PSG10P	HGNC	9515	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATATACTGTT	.	2	ESCA
IGSF23	0	.	GRCh37	19	45130811	45130811	+	Silent	SNP	G	G	T	rs553514790	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486G>T	p.%3D	p.G162G	ENST00000402988	3/5	45	41	4	26	26	0	IGSF23,synonymous_variant,p.%3D,ENST00000428245,;IGSF23,synonymous_variant,p.%3D,ENST00000441389,;IGSF23,synonymous_variant,p.%3D,ENST00000402988,;IGSF23,downstream_gene_variant,,ENST00000592507,;CTB-171A8.1,downstream_gene_variant,,ENST00000590796,;	T	ENSG00000216588	ENST00000402988	Transcript	synonymous_variant	502	486	162	G	ggG/ggT	rs553514790	.	.	1	IGSF23	HGNC	40040	protein_coding	YES	CCDS54277.1	ENSP00000385592	IGS23_HUMAN	.	UPI0000EE6D20	.	.	.	3/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCTGGGATCCT	by1000G	3	ESCA
BCL3	0	.	GRCh37	19	45262823	45262823	+	Missense_Mutation	SNP	G	G	A	rs373245726	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000164227	9/9	114	106	8	80	80	0	BCL3,missense_variant,p.Arg439Gln,ENST00000164227,;BCL3,downstream_gene_variant,,ENST00000444487,;BCL3,downstream_gene_variant,,ENST00000473468,;BCL3,non_coding_transcript_exon_variant,,ENST00000474300,;BCL3,downstream_gene_variant,,ENST00000464319,;BCL3,downstream_gene_variant,,ENST00000473473,;BCL3,downstream_gene_variant,,ENST00000477832,;BCL3,downstream_gene_variant,,ENST00000403534,;	A	ENSG00000069399	ENST00000164227	Transcript	missense_variant	1560	1316	439	R/Q	cGa/cAa	rs373245726,COSM1238295	.	.	1	BCL3	HGNC	998	protein_coding	YES	CCDS12642.2	ENSP00000164227	BCL3_HUMAN	.	UPI0000D4AF29	.	tolerated_low_confidence(0.12)	unknown(0)	9/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24118:SF44,hmmpanther:PTHR24118	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCCGAGGCC	byFrequency|byCluster	2	ESCA
PTGIR	0	.	GRCh37	19	47124484	47124484	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53G>C	.	.	ENST00000291294	3/3	80	76	4	66	66	0	PTGIR,3_prime_UTR_variant,,ENST00000597185,;PTGIR,3_prime_UTR_variant,,ENST00000594275,;PTGIR,3_prime_UTR_variant,,ENST00000598865,;PTGIR,3_prime_UTR_variant,,ENST00000291294,;PTGIR,downstream_gene_variant,,ENST00000596260,;PTGIR,downstream_gene_variant,,ENST00000595460,;	G	ENSG00000160013	ENST00000291294	Transcript	3_prime_UTR_variant	1348	.	.	.	.	.	.	.	-1	PTGIR	HGNC	9602	protein_coding	YES	CCDS12686.1	ENSP00000291294	PI2R_HUMAN	M0QZW0_HUMAN,M0QZI2_HUMAN,M0QXV5_HUMAN	UPI000005042B	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTTCTGGCT	.	2	ESCA
PTGIR	0	.	GRCh37	19	47124858	47124858	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.840C>T	p.%3D	p.F280F	ENST00000291294	3/3	79	75	4	54	54	0	PTGIR,synonymous_variant,p.%3D,ENST00000597185,;PTGIR,synonymous_variant,p.%3D,ENST00000594275,;PTGIR,synonymous_variant,p.%3D,ENST00000598865,;PTGIR,synonymous_variant,p.%3D,ENST00000291294,;PTGIR,downstream_gene_variant,,ENST00000596260,;PTGIR,downstream_gene_variant,,ENST00000595460,;	A	ENSG00000160013	ENST00000291294	Transcript	synonymous_variant	974	840	280	F	ttC/ttT	COSM998447	.	.	-1	PTGIR	HGNC	9602	protein_coding	YES	CCDS12686.1	ENSP00000291294	PI2R_HUMAN	M0QZW0_HUMAN,M0QZI2_HUMAN,M0QXV5_HUMAN	UPI000005042B	.	.	.	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11866,hmmpanther:PTHR11866:SF7,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGTAGAAGCG	.	2	ESCA
CABP5	0	.	GRCh37	19	48537601	48537601	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.367G>C	p.Gly123Arg	p.G123R	ENST00000293255	5/6	70	66	4	66	66	0	CABP5,missense_variant,p.Gly123Arg,ENST00000293255,;	G	ENSG00000105507	ENST00000293255	Transcript	missense_variant	498	367	123	G/R	Ggg/Cgg	.	.	.	-1	CABP5	HGNC	13714	protein_coding	YES	CCDS12709.1	ENSP00000293255	CABP5_HUMAN	.	UPI0000126D6A	.	deleterious(0)	probably_damaging(0.999)	5/6	.	PROSITE_profiles:PS50222,hmmpanther:PTHR23050:SF60,hmmpanther:PTHR23050,PROSITE_patterns:PS00018,Pfam_domain:PF13499,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCCCATCTC	.	2	ESCA
UHRF1	0	.	GRCh37	19	4961536	4961536	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3679G>T	.	.	ENST00000592666	17/17	18	15	3	8	8	0	UHRF1,non_coding_transcript_exon_variant,,ENST00000262952,;UHRF1,non_coding_transcript_exon_variant,,ENST00000592666,;UHRF1,non_coding_transcript_exon_variant,,ENST00000591733,;UHRF1,non_coding_transcript_exon_variant,,ENST00000398240,;UHRF1,downstream_gene_variant,,ENST00000592200,;UHRF1,downstream_gene_variant,,ENST00000587870,;UHRF1,downstream_gene_variant,,ENST00000591699,;UHRF1,downstream_gene_variant,,ENST00000587187,;UHRF1,downstream_gene_variant,,ENST00000543616,;	T	ENSG00000034063	ENST00000592666	Transcript	non_coding_transcript_exon_variant	3679	.	.	.	.	.	.	.	1	UHRF1	HGNC	12556	processed_transcript	YES	.	.	.	.	.	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTCCGACGAA	.	3	ESCA
MYH14	0	.	GRCh37	19	50771559	50771559	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2968G>A	p.Gly990Ser	p.G990S	ENST00000601313	24/43	142	135	7	115	115	0	MYH14,missense_variant,p.Gly990Ser,ENST00000440075,;MYH14,missense_variant,p.Gly990Ser,ENST00000601313,;MYH14,missense_variant,p.Gly982Ser,ENST00000376970,;MYH14,missense_variant,p.Gly949Ser,ENST00000596571,;MYH14,missense_variant,p.Gly957Ser,ENST00000425460,;MYH14,missense_variant,p.Gly957Ser,ENST00000599920,;MYH14,missense_variant,p.Gly957Ser,ENST00000598205,;MYH14,missense_variant,p.Gly990Ser,ENST00000262269,;	A	ENSG00000105357	ENST00000601313	Transcript	missense_variant	2998	2968	990	G/S	Ggc/Agc	.	.	.	1	MYH14	HGNC	23212	protein_coding	YES	CCDS54295.1	ENSP00000470298	MYH14_HUMAN	A1L2Z2_HUMAN	UPI0001641C2F	.	tolerated(0.08)	benign(0.003)	24/43	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF318,Gene3D:1.20.5.340,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCGTGGGCGAG	.	2	ESCA
CEACAM18	0	.	GRCh37	19	51986279	51986279	+	Missense_Mutation	SNP	G	G	C	rs772876360	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.865G>C	p.Asp289His	p.D289H	ENST00000451626	5/5	50	47	3	46	46	0	CEACAM18,missense_variant,p.Asp289His,ENST00000451626,;CEACAM18,missense_variant,p.Asp228His,ENST00000396477,;	C	ENSG00000213822	ENST00000451626	Transcript	missense_variant	865	865	289	D/H	Gac/Cac	rs772876360,COSM567320,COSM1000053,COSM567319,COSM1000052	.	.	1	CEACAM18	HGNC	31949	protein_coding	YES	.	ENSP00000402203	.	.	UPI0000DD8506	.	deleterious(0.01)	probably_damaging(0.965)	5/5	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955,hmmpanther:PTHR19955:SF6	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCCGACTAT	.	2	ESCA
BIRC8	0	.	GRCh37	19	53792962	53792962	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.666G>T	p.Met222Ile	p.M222I	ENST00000426466	1/1	45	41	4	40	40	0	BIRC8,missense_variant,p.Met222Ile,ENST00000426466,;FAM90A27P,downstream_gene_variant,,ENST00000593323,;FAM90A27P,downstream_gene_variant,,ENST00000338885,;	A	ENSG00000163098	ENST00000426466	Transcript	missense_variant	1914	666	222	M/I	atG/atT	.	.	.	-1	BIRC8	HGNC	14878	protein_coding	YES	CCDS12863.1	ENSP00000412957	BIRC8_HUMAN	.	UPI000003966A	.	tolerated(0.92)	benign(0.012)	1/1	.	PROSITE_profiles:PS50089,hmmpanther:PTHR10044:SF10,hmmpanther:PTHR10044,Pfam_domain:PF13920,SMART_domains:SM00184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGCACATGGG	.	3	ESCA
ZNF761	0	.	GRCh37	19	53959386	53959386	+	RNA	SNP	G	G	C	rs775653170	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2078G>C	.	.	ENST00000454407	5/5	143	135	7	131	131	0	ZNF761,non_coding_transcript_exon_variant,,ENST00000429310,;ZNF761,non_coding_transcript_exon_variant,,ENST00000454407,;ZNF761,non_coding_transcript_exon_variant,,ENST00000334095,;ZNF761,non_coding_transcript_exon_variant,,ENST00000432094,;	C	ENSG00000160336	ENST00000454407	Transcript	non_coding_transcript_exon_variant	2078	.	.	.	.	rs775653170,COSM712890	.	.	1	ZNF761	HGNC	23179	processed_transcript	YES	.	.	.	.	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODIFIER	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGTAGACTTC	byFrequency	2	ESCA
MIR519B	0	.	GRCh37	19	54198487	54198487	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.21G>A	.	.	ENST00000385090	1/1	170	163	7	169	169	0	MIR519B,mature_miRNA_variant,,ENST00000385090,;MIR525,upstream_gene_variant,,ENST00000384978,;MIR526B,downstream_gene_variant,,ENST00000384848,;MIR520A,downstream_gene_variant,,ENST00000384862,;MIR518F,upstream_gene_variant,,ENST00000384973,;MIR523,upstream_gene_variant,,ENST00000385281,;	A	ENSG00000207825	ENST00000385090	Transcript	mature_miRNA_variant	21	.	.	.	.	.	.	.	1	MIR519B	HGNC	32101	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGAGGGAAGC	.	2	ESCA
TARM1	0	.	GRCh37	19	54577262	54577262	+	Missense_Mutation	SNP	C	C	T	rs758383287	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.568G>A	p.Asp190Asn	p.D190N	ENST00000432826	4/5	63	57	6	67	67	0	TARM1,missense_variant,p.Asp190Asn,ENST00000432826,;TARM1,missense_variant,p.Asp198Asn,ENST00000446034,;	T	ENSG00000248385	ENST00000432826	Transcript	missense_variant	593	568	190	D/N	Gat/Aat	rs758383287	.	.	-1	TARM1	HGNC	37250	protein_coding	YES	CCDS46173.1	ENSP00000439454	TARM1_HUMAN	.	UPI00004FB5DD	.	tolerated(0.07)	possibly_damaging(0.449)	4/5	.	hmmpanther:PTHR11738:SF84,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCATCGCCGG	.	4	ESCA
LILRA6	0	.	GRCh37	19	54744789	54744789	+	Silent	SNP	C	C	A	rs761456455	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.873G>T	p.%3D	p.G291G	ENST00000396365	5/8	254	240	14	269	269	0	LILRA6,synonymous_variant,p.%3D,ENST00000245621,;LILRA6,synonymous_variant,p.%3D,ENST00000440558,;LILRA6,synonymous_variant,p.%3D,ENST00000396365,;LILRA6,synonymous_variant,p.%3D,ENST00000419410,;LILRA6,3_prime_UTR_variant,,ENST00000391735,;LILRB3,intron_variant,,ENST00000407860,;LILRA6,intron_variant,,ENST00000270464,;LILRA6,3_prime_UTR_variant,,ENST00000430421,;RPS9,intron_variant,,ENST00000448962,;LILRA6,downstream_gene_variant,,ENST00000474697,;	A	ENSG00000244482	ENST00000396365	Transcript	synonymous_variant	913	873	291	G	ggG/ggT	rs761456455	.	.	-1	LILRA6	HGNC	15495	protein_coding	YES	CCDS42610.1	ENSP00000379651	LIRA6_HUMAN	.	UPI000022A9CA	.	.	.	5/8	.	Superfamily_domains:SSF48726,PIRSF_domain:PIRSF001979,SMART_domains:SM00409,SMART_domains:SM00408,Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11738:SF99,hmmpanther:PTHR11738,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCCCCCGTG	.	2	ESCA
LAIR1	0	.	GRCh37	19	54872553	54872553	+	Missense_Mutation	SNP	G	G	T	rs754568622	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334C>A	p.Gln112Lys	p.Q112K	ENST00000391742	3/10	56	49	6	54	54	0	LAIR1,missense_variant,p.Gln111Lys,ENST00000474878,;LAIR1,missense_variant,p.Gln112Lys,ENST00000391742,;LAIR1,missense_variant,p.Gln2Lys,ENST00000444687,;LAIR1,missense_variant,p.Gln112Lys,ENST00000348231,;LAIR1,missense_variant,p.Gln111Lys,ENST00000434277,;LAIR1,missense_variant,p.Gln94Lys,ENST00000391743,;LAIR1,missense_variant,p.Gln105Lys,ENST00000313038,;LAIR1,downstream_gene_variant,,ENST00000438193,;LAIR1,non_coding_transcript_exon_variant,,ENST00000484116,;LAIR1,non_coding_transcript_exon_variant,,ENST00000468656,;LAIR1,intron_variant,,ENST00000463489,;LAIR1,downstream_gene_variant,,ENST00000480122,;LAIR1,missense_variant,p.Gln112Lys,ENST00000418556,;LAIR1,3_prime_UTR_variant,,ENST00000423853,;LAIR1,3_prime_UTR_variant,,ENST00000436513,;LAIR1,non_coding_transcript_exon_variant,,ENST00000467269,;LAIR1,intron_variant,,ENST00000391741,;LAIR1,intron_variant,,ENST00000420483,;LAIR1,intron_variant,,ENST00000440716,;LAIR1,intron_variant,,ENST00000498511,;LAIR1,downstream_gene_variant,,ENST00000427131,;LAIR1,upstream_gene_variant,,ENST00000460312,;LAIR1,upstream_gene_variant,,ENST00000475389,;	T	ENSG00000167613	ENST00000391742	Transcript	missense_variant	487	334	112	Q/K	Cag/Aag	rs754568622	.	.	-1	LAIR1	HGNC	6477	protein_coding	YES	CCDS12891.1	ENSP00000375622	LAIR1_HUMAN	.	UPI000011A058	.	tolerated(0.28)	benign(0.004)	3/10	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11738:SF12,hmmpanther:PTHR11738	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTCTGCTCAG	.	4	ESCA
LENG8	0	.	GRCh37	19	54965711	54965711	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.529C>T	p.His177Tyr	p.H177Y	ENST00000326764	6/16	124	112	12	125	125	0	LENG8,missense_variant,p.His177Tyr,ENST00000326764,;LENG8,missense_variant,p.His177Tyr,ENST00000431846,;LENG8,missense_variant,p.His177Tyr,ENST00000439657,;LENG8,missense_variant,p.His140Tyr,ENST00000376526,;LENG8,intron_variant,,ENST00000376514,;LENG8,downstream_gene_variant,,ENST00000436479,;LENG8,downstream_gene_variant,,ENST00000443957,;LENG8,upstream_gene_variant,,ENST00000421200,;LENG8,downstream_gene_variant,,ENST00000462541,;	T	ENSG00000167615	ENST00000326764	Transcript	missense_variant	1008	529	177	H/Y	Cac/Tac	.	.	.	1	LENG8	HGNC	15500	protein_coding	YES	CCDS12894.1	ENSP00000318374	LENG8_HUMAN	E7EWC7_HUMAN,C9J1N5_HUMAN,B0VJY8_HUMAN	UPI0000074196	.	tolerated_low_confidence(0.14)	benign(0.332)	6/16	.	hmmpanther:PTHR12436:SF4,hmmpanther:PTHR12436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGCTCACACG	.	3	ESCA
KIR2DS4	0	.	GRCh37	19	55349038	55349038	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78C>A	p.His26Gln	p.H26Q	ENST00000339924	3/8	98	91	7	93	93	0	KIR3DL1,intron_variant,,ENST00000402254,;KIR2DS4,missense_variant,p.His26Gln,ENST00000391729,;KIR2DS4,missense_variant,p.His26Gln,ENST00000339924,;	A	ENSG00000221957	ENST00000339924	Transcript	missense_variant	167	78	26	H/Q	caC/caA	.	.	.	1	KIR2DS4	HGNC	6336	polymorphic_pseudogene	YES	.	ENSP00000340011	.	Q8NHJ0_HUMAN,K7QX36_HUMAN	.	.	tolerated_low_confidence(0.22)	benign(0.44)	3/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCACAGAAA	.	2	ESCA
DUXA	0	.	GRCh37	19	57670600	57670600	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.227C>A	p.Pro76Gln	p.P76Q	ENST00000554048	3/6	59	51	8	54	54	0	DUXA,missense_variant,p.Pro76Gln,ENST00000554048,;	T	ENSG00000258873	ENST00000554048	Transcript	missense_variant	227	227	76	P/Q	cCa/cAa	.	.	.	-1	DUXA	HGNC	32179	protein_coding	YES	CCDS33126.1	ENSP00000452398	DUXA_HUMAN	.	UPI0000198B7E	.	deleterious(0.01)	benign(0.216)	3/6	.	SMART_domains:SM00389,Gene3D:1.10.10.60,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF312	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTTCTGGTCTT	.	3	ESCA
ZNF17	0	.	GRCh37	19	57932722	57932722	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1862A>G	p.Tyr621Cys	p.Y621C	ENST00000601808	3/3	97	90	7	72	72	0	ZNF17,missense_variant,p.Tyr623Cys,ENST00000307658,;ZNF17,missense_variant,p.Tyr621Cys,ENST00000601808,;AC004076.7,intron_variant,,ENST00000597410,;AC003002.6,downstream_gene_variant,,ENST00000596400,;AC003002.6,downstream_gene_variant,,ENST00000596617,;ZNF17,downstream_gene_variant,,ENST00000597350,;ZNF17,downstream_gene_variant,,ENST00000595206,;ZNF17,downstream_gene_variant,,ENST00000599867,;ZNF17,non_coding_transcript_exon_variant,,ENST00000602050,;ZNF17,downstream_gene_variant,,ENST00000595162,;	G	ENSG00000186272	ENST00000601808	Transcript	missense_variant	2075	1862	621	Y/C	tAc/tGc	.	.	.	1	ZNF17	HGNC	12958	protein_coding	YES	CCDS42636.1	ENSP00000471905	ZNF17_HUMAN	.	UPI00001D8198	.	tolerated(0.18)	benign(0.003)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF166,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGATACAACT	.	2	ESCA
RANBP3	0	.	GRCh37	19	5941834	5941834	+	Missense_Mutation	SNP	C	C	A	rs761605718	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295G>T	p.Gly99Cys	p.G99C	ENST00000340578	4/17	41	35	5	32	32	0	RANBP3,missense_variant,p.Gly31Cys,ENST00000591092,;RANBP3,missense_variant,p.Gly31Cys,ENST00000587159,;RANBP3,missense_variant,p.Gly31Cys,ENST00000034275,;RANBP3,missense_variant,p.Gly120Cys,ENST00000591333,;RANBP3,missense_variant,p.Gly99Cys,ENST00000439268,;RANBP3,missense_variant,p.Gly99Cys,ENST00000340578,;RANBP3,5_prime_UTR_variant,,ENST00000590623,;RANBP3,5_prime_UTR_variant,,ENST00000592621,;RANBP3,intron_variant,,ENST00000541471,;RANBP3,intron_variant,,ENST00000591736,;RANBP3,intron_variant,,ENST00000587479,;RANBP3,non_coding_transcript_exon_variant,,ENST00000588879,;RANBP3,non_coding_transcript_exon_variant,,ENST00000591881,;RANBP3,non_coding_transcript_exon_variant,,ENST00000591124,;RANBP3,non_coding_transcript_exon_variant,,ENST00000587956,;RANBP3,non_coding_transcript_exon_variant,,ENST00000589886,;RANBP3,non_coding_transcript_exon_variant,,ENST00000586117,;RANBP3,non_coding_transcript_exon_variant,,ENST00000590953,;RANBP3,missense_variant,p.Gly31Cys,ENST00000592771,;RANBP3,missense_variant,p.Gly31Cys,ENST00000588010,;RANBP3,synonymous_variant,p.%3D,ENST00000589353,;RANBP3,synonymous_variant,p.%3D,ENST00000587463,;RANBP3,3_prime_UTR_variant,,ENST00000587263,;RANBP3,3_prime_UTR_variant,,ENST00000592133,;RANBP3,3_prime_UTR_variant,,ENST00000585339,;	A	ENSG00000031823	ENST00000340578	Transcript	missense_variant	353	295	99	G/C	Ggc/Tgc	rs761605718,COSM4082497	.	.	-1	RANBP3	HGNC	9850	protein_coding	YES	CCDS42478.1	ENSP00000341483	RANB3_HUMAN	K7ESQ0_HUMAN,K7EMH9_HUMAN,K7EIJ4_HUMAN	UPI000006F919	.	tolerated_low_confidence(0.07)	probably_damaging(0.923)	4/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23138:SF91,hmmpanther:PTHR23138	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGCCGCCAG	byFrequency	4	ESCA
TUBB4A	0	.	GRCh37	19	6495115	6495115	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*60C>A	.	.	ENST00000264071	4/4	50	45	5	35	35	0	TUBB4A,3_prime_UTR_variant,,ENST00000264071,;TUBB4A,3_prime_UTR_variant,,ENST00000540257,;TUBB4A,downstream_gene_variant,,ENST00000598635,;TUBB4A,downstream_gene_variant,,ENST00000594075,;TUBB4A,downstream_gene_variant,,ENST00000596291,;TUBB4A,downstream_gene_variant,,ENST00000598006,;TUBB4A,downstream_gene_variant,,ENST00000594276,;TUBB4A,downstream_gene_variant,,ENST00000601152,;TUBB4A,downstream_gene_variant,,ENST00000596926,;TUBB4A,downstream_gene_variant,,ENST00000600216,;TUBB4A,downstream_gene_variant,,ENST00000597686,;TUBB4A,downstream_gene_variant,,ENST00000601640,;CTD-2396E7.10,downstream_gene_variant,,ENST00000596027,;CTD-2396E7.9,downstream_gene_variant,,ENST00000599292,;TUBB4A,downstream_gene_variant,,ENST00000594290,;TUBB4A,downstream_gene_variant,,ENST00000595324,;	T	ENSG00000104833	ENST00000264071	Transcript	3_prime_UTR_variant	1767	.	.	.	.	.	.	.	-1	TUBB4A	HGNC	20774	protein_coding	YES	CCDS12168.1	ENSP00000264071	TBB4A_HUMAN	M0R1I1_HUMAN,M0QY85_HUMAN	UPI000005FC27	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TGGGGGGCCTA	.	2	ESCA
EMR4P	0	.	GRCh37	19	6971215	6971215	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1206C>A	.	.	ENST00000600751	10/16	66	58	8	62	62	0	EMR4P,non_coding_transcript_exon_variant,,ENST00000600751,;EMR4P,non_coding_transcript_exon_variant,,ENST00000597372,;	T	ENSG00000268758	ENST00000600751	Transcript	non_coding_transcript_exon_variant	1206	.	.	.	.	.	.	.	-1	EMR4P	HGNC	19240	processed_transcript	YES	.	.	.	.	.	.	.	.	10/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACAGGAGGT	.	4	ESCA
EMR4P	0	.	GRCh37	19	6972268	6972268	+	RNA	SNP	C	C	A	rs760055766	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1029G>T	.	.	ENST00000600751	9/16	75	68	7	75	75	0	EMR4P,non_coding_transcript_exon_variant,,ENST00000600751,;EMR4P,non_coding_transcript_exon_variant,,ENST00000597372,;	A	ENSG00000268758	ENST00000600751	Transcript	non_coding_transcript_exon_variant	1029	.	.	.	.	rs760055766	.	.	-1	EMR4P	HGNC	19240	processed_transcript	YES	.	.	.	.	.	.	.	.	9/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGCCACGAGGA	.	3	ESCA
MCOLN1	0	.	GRCh37	19	7589895	7589895	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.80G>T	p.Gly27Val	p.G27V	ENST00000264079	2/14	161	153	8	188	187	1	MCOLN1,missense_variant,p.Gly27Val,ENST00000264079,;MCOLN1,missense_variant,p.Gly27Val,ENST00000601003,;MCOLN1,upstream_gene_variant,,ENST00000599334,;ZNF358,downstream_gene_variant,,ENST00000394341,;ZNF358,downstream_gene_variant,,ENST00000597229,;CTD-2207O23.11,upstream_gene_variant,,ENST00000602083,;MCOLN1,non_coding_transcript_exon_variant,,ENST00000394321,;MCOLN1,non_coding_transcript_exon_variant,,ENST00000596390,;MCOLN1,upstream_gene_variant,,ENST00000596008,;MCOLN1,upstream_gene_variant,,ENST00000594692,;MCOLN1,upstream_gene_variant,,ENST00000598406,;MCOLN1,upstream_gene_variant,,ENST00000595860,;	T	ENSG00000090674	ENST00000264079	Transcript	missense_variant	205	80	27	G/V	gGg/gTg	.	.	.	1	MCOLN1	HGNC	13356	protein_coding	YES	CCDS12180.1	ENSP00000264079	MCLN1_HUMAN	B4DFZ1_HUMAN	UPI00000377A2	.	deleterious(0.03)	benign(0.002)	2/14	.	hmmpanther:PTHR12127,hmmpanther:PTHR12127:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGCGGGGCCTT	.	2	ESCA
EVI5L	0	.	GRCh37	19	7928689	7928689	+	3'Flank	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000538904	.	58	55	3	47	47	0	EVI5L,3_prime_UTR_variant,,ENST00000270530,;CTD-3193O13.9,downstream_gene_variant,,ENST00000599142,;EVI5L,downstream_gene_variant,,ENST00000601766,;EVI5L,downstream_gene_variant,,ENST00000538904,;CTD-3193O13.9,downstream_gene_variant,,ENST00000539422,;CTD-3193O13.9,downstream_gene_variant,,ENST00000593356,;EVI5L,downstream_gene_variant,,ENST00000601984,;	C	ENSG00000142459	ENST00000538904	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	101	1	EVI5L	HGNC	30464	protein_coding	YES	CCDS54209.1	ENSP00000445905	EVI5L_HUMAN	.	UPI00019145BF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACGCGCCCTC	.	2	ESCA
CTD-3193O13.9	0	.	GRCh37	19	7934933	7934933	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3197C>A	p.Pro1066His	p.P1066H	ENST00000539422	5/6	26	22	4	40	40	0	CTD-3193O13.9,missense_variant,p.Pro481His,ENST00000599142,;CTD-3193O13.9,missense_variant,p.Pro1066His,ENST00000539422,;CTD-3193O13.11,upstream_gene_variant,,ENST00000597156,;CTD-3193O13.9,intron_variant,,ENST00000593356,;	T	ENSG00000183248	ENST00000539422	Transcript	missense_variant	3360	3197	1066	P/H	cCc/cAc	.	.	.	-1	CTD-3193O13.9	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000438970	.	F5H1R7_HUMAN	UPI0001DA930F	.	.	unknown(0)	5/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22427	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGAGGGAGGG	.	3	ESCA
LPPR3	0	.	GRCh37	19	815235	815235	+	Silent	SNP	G	G	T	rs754041682	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.354C>A	p.%3D	p.A118A	ENST00000359894	4/7	18	14	4	20	20	0	LPPR3,synonymous_variant,p.%3D,ENST00000520876,;LPPR3,synonymous_variant,p.%3D,ENST00000519502,;LPPR3,synonymous_variant,p.%3D,ENST00000359894,;PTBP1,downstream_gene_variant,,ENST00000349038,;PTBP1,downstream_gene_variant,,ENST00000394601,;PTBP1,downstream_gene_variant,,ENST00000356948,;PTBP1,downstream_gene_variant,,ENST00000350092,;LPPR3,upstream_gene_variant,,ENST00000517665,;MIR3187,downstream_gene_variant,,ENST00000583431,;PTBP1,downstream_gene_variant,,ENST00000586944,;PTBP1,downstream_gene_variant,,ENST00000585856,;	T	ENSG00000129951	ENST00000359894	Transcript	synonymous_variant	418	354	118	A	gcC/gcA	rs754041682	.	.	-1	LPPR3	Uniprot_gn	.	protein_coding	YES	CCDS12043.1	ENSP00000352962	.	K7ELK5_HUMAN	UPI00000730B6	.	.	.	4/7	.	hmmpanther:PTHR10165:SF14,hmmpanther:PTHR10165,Gene3D:1.20.144.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCCGGCGTT	byFrequency	5	ESCA
FBN3	0	.	GRCh37	19	8174147	8174147	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4582G>C	p.Gly1528Arg	p.G1528R	ENST00000600128	36/64	68	57	11	67	67	0	FBN3,missense_variant,p.Gly1528Arg,ENST00000600128,;FBN3,missense_variant,p.Gly1528Arg,ENST00000601739,;FBN3,missense_variant,p.Gly1528Arg,ENST00000270509,;FBN3,downstream_gene_variant,,ENST00000594331,;	G	ENSG00000142449	ENST00000600128	Transcript	missense_variant	4997	4582	1528	G/R	Ggc/Cgc	COSM3541532	.	.	-1	FBN3	HGNC	18794	protein_coding	YES	CCDS12196.1	ENSP00000470498	FBN3_HUMAN	.	UPI000013D88F	.	deleterious(0)	probably_damaging(1)	36/64	.	PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF0,Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,Superfamily_domains:SSF57581	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGCCCCAAG	.	5	ESCA
ACTL9	0	.	GRCh37	19	8808653	8808653	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.399G>T	p.%3D	p.L133L	ENST00000324436	1/1	27	22	5	33	33	0	ACTL9,synonymous_variant,p.%3D,ENST00000324436,;	A	ENSG00000181786	ENST00000324436	Transcript	synonymous_variant	520	399	133	L	ctG/ctT	.	.	.	-1	ACTL9	HGNC	28494	protein_coding	YES	CCDS12207.1	ENSP00000316674	ACTL9_HUMAN	.	UPI000014129E	.	.	.	1/1	.	Superfamily_domains:SSF53067,SMART_domains:SM00268,Pfam_domain:PF00022,Gene3D:3.30.420.40,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTCCAGCAG	.	5	ESCA
CTTNBP2NL	0	.	GRCh37	1	112998691	112998691	+	Missense_Mutation	SNP	G	G	T	rs201675639	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.577G>T	p.Ala193Ser	p.A193S	ENST00000271277	6/6	85	76	9	75	75	0	CTTNBP2NL,missense_variant,p.Ala193Ser,ENST00000271277,;CTTNBP2NL,missense_variant,p.Ala193Ser,ENST00000441739,;CTTNBP2NL,upstream_gene_variant,,ENST00000607039,;	T	ENSG00000143079	ENST00000271277	Transcript	missense_variant	802	577	193	A/S	Gca/Tca	rs201675639	.	.	1	CTTNBP2NL	HGNC	25330	protein_coding	YES	CCDS845.1	ENSP00000271277	CT2NL_HUMAN	B1AMN7_HUMAN	UPI000006ED23	.	deleterious(0.01)	possibly_damaging(0.622)	6/6	.	hmmpanther:PTHR23166,hmmpanther:PTHR23166:SF9	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	ACAAGGCAGCC	byCluster|by1000G	3	ESCA
AP4B1	0	.	GRCh37	1	114442519	114442519	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114+7G>T	.	.	ENST00000369569	.	51	44	7	41	41	0	AP4B1,missense_variant,p.Cys281Phe,ENST00000369566,;AP4B1,splice_region_variant,,ENST00000256658,;AP4B1,splice_region_variant,,ENST00000369567,;AP4B1,splice_region_variant,,ENST00000369569,;AP4B1,downstream_gene_variant,,ENST00000432415,;AP4B1,downstream_gene_variant,,ENST00000369564,;AP4B1,downstream_gene_variant,,ENST00000369571,;AP4B1-AS1,non_coding_transcript_exon_variant,,ENST00000419536,;AP4B1,splice_region_variant,,ENST00000479285,;AP4B1,splice_region_variant,,ENST00000460653,;AP4B1,intron_variant,,ENST00000484201,;AP4B1,upstream_gene_variant,,ENST00000479801,;AP4B1,downstream_gene_variant,,ENST00000489092,;AP4B1,downstream_gene_variant,,ENST00000489499,;AP4B1,downstream_gene_variant,,ENST00000472122,;AP4B1,upstream_gene_variant,,ENST00000462591,;	A	ENSG00000134262	ENST00000369569	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	AP4B1	HGNC	572	protein_coding	YES	CCDS865.1	ENSP00000358582	AP4B1_HUMAN	B1ALD2_HUMAN	UPI0000072F63	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGACACCTA	.	4	ESCA
TSPAN2	0	.	GRCh37	1	115604810	115604810	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216G>T	p.%3D	p.V72V	ENST00000369516	3/8	176	168	8	141	141	0	TSPAN2,synonymous_variant,p.%3D,ENST00000369514,;TSPAN2,synonymous_variant,p.%3D,ENST00000369515,;TSPAN2,synonymous_variant,p.%3D,ENST00000433172,;TSPAN2,synonymous_variant,p.%3D,ENST00000369516,;TSPAN2,upstream_gene_variant,,ENST00000491992,;	A	ENSG00000134198	ENST00000369516	Transcript	synonymous_variant	248	216	72	V	gtG/gtT	.	.	.	-1	TSPAN2	HGNC	20659	protein_coding	YES	CCDS881.1	ENSP00000358529	TSN2_HUMAN	.	UPI0000137765	.	.	.	3/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF155,PROSITE_patterns:PS00421,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Prints_domain:PR00259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACCCCACGGC	.	2	ESCA
PTCHD2	0	.	GRCh37	1	11576105	11576105	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1636C>A	p.His546Asn	p.H546N	ENST00000294484	6/21	60	55	5	67	67	0	PTCHD2,missense_variant,p.His546Asn,ENST00000389575,;PTCHD2,missense_variant,p.His546Asn,ENST00000294484,;	A	ENSG00000204624	ENST00000294484	Transcript	missense_variant	1774	1636	546	H/N	Cac/Aac	COSM3471767,COSM3471768	.	.	1	PTCHD2	HGNC	29251	protein_coding	YES	CCDS41247.1	ENSP00000294484	PTHD2_HUMAN	.	UPI00001C1D7A	.	deleterious(0.01)	probably_damaging(0.919)	6/21	.	Superfamily_domains:SSF82866,Pfam_domain:PF02460,Gene3D:2j8sB01,hmmpanther:PTHR10796:SF49,hmmpanther:PTHR10796,PROSITE_profiles:PS50156	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	CCACCCACCTG	.	2	ESCA
DRAXIN	0	.	GRCh37	1	11766385	11766385	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70C>A	p.Leu24Met	p.L24M	ENST00000294485	2/7	88	79	8	66	66	0	DRAXIN,missense_variant,p.Leu24Met,ENST00000294485,;	A	ENSG00000162490	ENST00000294485	Transcript	missense_variant	205	70	24	L/M	Ctg/Atg	.	.	.	1	DRAXIN	HGNC	25054	protein_coding	YES	CCDS135.1	ENSP00000294485	DRAXI_HUMAN	.	UPI000013E16C	.	tolerated(0.13)	possibly_damaging(0.839)	2/7	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGAGCCTGGCA	.	3	ESCA
DRAXIN	0	.	GRCh37	1	11766386	11766386	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71T>A	p.Leu24Gln	p.L24Q	ENST00000294485	2/7	88	79	8	66	66	0	DRAXIN,missense_variant,p.Leu24Gln,ENST00000294485,;	A	ENSG00000162490	ENST00000294485	Transcript	missense_variant	206	71	24	L/Q	cTg/cAg	.	.	.	1	DRAXIN	HGNC	25054	protein_coding	YES	CCDS135.1	ENSP00000294485	DRAXI_HUMAN	.	UPI000013E16C	.	tolerated(0.23)	possibly_damaging(0.779)	2/7	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGCCTGGCAG	.	3	ESCA
HSD3B2	0	.	GRCh37	1	119964835	119964835	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.711G>T	p.Arg237Ser	p.R237S	ENST00000543831	4/4	98	84	13	78	78	0	HSD3B2,missense_variant,p.Arg237Ser,ENST00000543831,;HSD3B2,missense_variant,p.Arg237Ser,ENST00000369416,;HSD3B2,downstream_gene_variant,,ENST00000433745,;HSD3B2,downstream_gene_variant,,ENST00000443865,;HSD3B2,downstream_gene_variant,,ENST00000448448,;HSD3B2,downstream_gene_variant,,ENST00000471656,;	T	ENSG00000203859	ENST00000543831	Transcript	missense_variant	960	711	237	R/S	agG/agT	.	.	.	1	HSD3B2	HGNC	5218	protein_coding	YES	CCDS902.1	ENSP00000445122	3BHS2_HUMAN	Q5QP01_HUMAN	UPI0000001C6C	.	deleterious(0)	probably_damaging(0.938)	4/4	.	hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF296,Pfam_domain:PF01073,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAGGGCTCT	.	4	ESCA
PRAMEF12	0	.	GRCh37	1	12835017	12835017	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7C>A	p.Leu3Ile	p.L3I	ENST00000357726	1/3	110	100	10	96	96	0	PRAMEF12,missense_variant,p.Leu3Ile,ENST00000357726,;	A	ENSG00000116726	ENST00000357726	Transcript	missense_variant	34	7	3	L/I	Ctc/Atc	.	.	.	1	PRAMEF12	HGNC	22125	protein_coding	YES	CCDS41254.1	ENSP00000350358	PRA12_HUMAN	.	UPI000013A190	.	tolerated(0.92)	benign(0.004)	1/3	.	hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30,PIRSF_domain:PIRSF038286	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGAGCCTCCAG	.	3	ESCA
PRAMEF10	0	.	GRCh37	1	12954931	12954931	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.352G>T	p.Gly118Ter	p.G118*	ENST00000235347	3/4	443	422	21	440	440	0	PRAMEF10,stop_gained,p.Gly118Ter,ENST00000235347,;	A	ENSG00000187545	ENST00000235347	Transcript	stop_gained	432	352	118	G/*	Gga/Tga	COSM674904	.	.	-1	PRAMEF10	HGNC	27997	protein_coding	YES	CCDS41255.1	ENSP00000235347	PRA10_HUMAN	.	UPI0000199949	.	.	.	3/4	.	PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224:SF16,hmmpanther:PTHR14224	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTCCAGACC	.	2	ESCA
RP11-417J8.6	0	.	GRCh37	1	142711340	142711340	+	RNA	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2767A>T	.	.	ENST00000610091	7/14	242	211	30	209	209	0	RP11-417J8.6,non_coding_transcript_exon_variant,,ENST00000369381,;RP11-417J8.6,non_coding_transcript_exon_variant,,ENST00000610091,;RP11-417J8.3,intron_variant,,ENST00000411746,;RP11-417J8.6,downstream_gene_variant,,ENST00000595144,;ANKRD20A12P,non_coding_transcript_exon_variant,,ENST00000416817,;	A	ENSG00000203849	ENST00000610091	Transcript	non_coding_transcript_exon_variant	2767	.	.	.	.	.	.	.	-1	RP11-417J8.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	7/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAGTGGAGA	.	4	ESCA
RP11-423O2.5	0	.	GRCh37	1	142803954	142803954	+	RNA	SNP	A	A	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1012T>C	.	.	ENST00000423385	3/3	38	33	4	34	34	0	RP11-423O2.5,non_coding_transcript_exon_variant,,ENST00000423385,;ANKRD20A14P,intron_variant,,ENST00000457776,;ASNSP5,downstream_gene_variant,,ENST00000433327,;	G	ENSG00000234978	ENST00000423385	Transcript	non_coding_transcript_exon_variant	1012	.	.	.	.	.	.	.	-1	RP11-423O2.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTAAATACCT	.	4	ESCA
ITGA10	0	.	GRCh37	1	145533913	145533913	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1559G>T	p.Gly520Val	p.G520V	ENST00000369304	13/30	78	70	7	74	74	0	ITGA10,missense_variant,p.Gly389Val,ENST00000538811,;ITGA10,missense_variant,p.Gly377Val,ENST00000539363,;ITGA10,missense_variant,p.Gly520Val,ENST00000369304,;ITGA10,downstream_gene_variant,,ENST00000481236,;ITGA10,downstream_gene_variant,,ENST00000468261,;	T	ENSG00000143127	ENST00000369304	Transcript	missense_variant	1734	1559	520	G/V	gGa/gTa	.	.	.	1	ITGA10	HGNC	6135	protein_coding	YES	CCDS918.1	ENSP00000358310	ITA10_HUMAN	.	UPI000013D8D1	.	deleterious(0.01)	probably_damaging(1)	13/30	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF26,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AACAGGACGTG	.	3	ESCA
HIST2H2AC	0	.	GRCh37	1	149858798	149858798	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274G>A	p.Glu92Lys	p.E92K	ENST00000331380	1/1	184	169	15	152	152	0	HIST2H2AC,missense_variant,p.Glu92Lys,ENST00000331380,;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,;HIST2H2BE,upstream_gene_variant,,ENST00000369155,;	A	ENSG00000184260	ENST00000331380	Transcript	missense_variant	274	274	92	E/K	Gag/Aag	COSM1747710	.	.	1	HIST2H2AC	HGNC	4738	protein_coding	YES	CCDS937.1	ENSP00000332194	H2A2C_HUMAN	.	UPI000007478F	.	deleterious_low_confidence(0)	probably_damaging(0.997)	1/1	.	hmmpanther:PTHR23430,hmmpanther:PTHR23430:SF24,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L94L|c.282G>A|4	MUTECT|MUSE|VARSCANS	ACGACGAGGAA	.	3	ESCA
LYSMD1	0	.	GRCh37	1	151133305	151133305	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53G>T	.	.	ENST00000368908	3/3	87	75	12	62	62	0	LYSMD1,3_prime_UTR_variant,,ENST00000440902,;LYSMD1,3_prime_UTR_variant,,ENST00000368908,;SCNM1,intron_variant,,ENST00000602841,;TNFAIP8L2,downstream_gene_variant,,ENST00000368910,;	A	ENSG00000163155	ENST00000368908	Transcript	3_prime_UTR_variant	1398	.	.	.	.	.	.	.	-1	LYSMD1	HGNC	32070	protein_coding	YES	CCDS986.1	ENSP00000357904	LYSM1_HUMAN	.	UPI000007311C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTCCCCCTG	.	4	ESCA
FLG	0	.	GRCh37	1	152281019	152281019	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6343C>T	p.Gln2115Ter	p.Q2115*	ENST00000368799	3/3	288	271	16	249	248	1	FLG,stop_gained,p.Gln2115Ter,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	A	ENSG00000143631	ENST00000368799	Transcript	stop_gained	6379	6343	2115	Q/*	Caa/Taa	COSM1284983	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTTGTCTTC	.	2	ESCA
FLG2	0	.	GRCh37	1	152326947	152326947	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3315C>A	p.His1105Gln	p.H1105Q	ENST00000388718	3/3	162	138	24	139	138	1	FLG2,missense_variant,p.His1105Gln,ENST00000388718,;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;	T	ENSG00000143520	ENST00000388718	Transcript	missense_variant	3388	3315	1105	H/Q	caC/caA	.	.	.	-1	FLG2	HGNC	33276	protein_coding	YES	CCDS30861.1	ENSP00000373370	FILA2_HUMAN	.	UPI00004E1DE5	.	.	unknown(0)	3/3	.	hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTGTGTTG	.	4	ESCA
LCE2C	0	.	GRCh37	1	152648660	152648660	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.169G>A	p.Gly57Ser	p.G57S	ENST00000368783	2/2	193	167	26	148	148	0	LCE2C,missense_variant,p.Gly57Ser,ENST00000368783,;LCE2B,intron_variant,,ENST00000417924,;	A	ENSG00000187180	ENST00000368783	Transcript	missense_variant	224	169	57	G/S	Ggt/Agt	.	.	.	1	LCE2C	HGNC	29460	protein_coding	YES	CCDS1019.1	ENSP00000357772	LCE2C_HUMAN	.	UPI00001927D6	.	tolerated_low_confidence(0.49)	unknown(0)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23263,hmmpanther:PTHR23263:SF18,Pfam_domain:PF14672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGTGGTCCC	.	4	ESCA
S100A4	0	.	GRCh37	1	153516390	153516390	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.151G>C	p.Asp51His	p.D51H	ENST00000368716	3/3	86	70	15	71	71	0	S100A4,missense_variant,p.Asp51His,ENST00000354332,;S100A4,missense_variant,p.Asp51His,ENST00000368715,;S100A4,missense_variant,p.Asp51His,ENST00000368714,;S100A4,missense_variant,p.Asp51His,ENST00000368716,;S100A5,upstream_gene_variant,,ENST00000368717,;S100A3,downstream_gene_variant,,ENST00000368713,;S100A5,upstream_gene_variant,,ENST00000368718,;S100A3,downstream_gene_variant,,ENST00000368712,;S100A5,upstream_gene_variant,,ENST00000359215,;S100A4,non_coding_transcript_exon_variant,,ENST00000481009,;S100A4,non_coding_transcript_exon_variant,,ENST00000468373,;	G	ENSG00000196154	ENST00000368716	Transcript	missense_variant	299	151	51	D/H	Gat/Cat	.	.	.	-1	S100A4	HGNC	10494	protein_coding	YES	CCDS1042.1	ENSP00000357705	S10A4_HUMAN	.	UPI000003417D	.	deleterious(0.02)	benign(0.133)	3/3	.	PROSITE_profiles:PS50222,hmmpanther:PTHR11639:SF15,hmmpanther:PTHR11639,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATCTGTCC	.	5	ESCA
S100A3	0	.	GRCh37	1	153520323	153520323	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142-1G>A	.	p.X48_splice	ENST00000368713	.	46	39	6	54	54	0	S100A3,splice_acceptor_variant,,ENST00000368713,;S100A3,splice_acceptor_variant,,ENST00000368712,;S100A4,intron_variant,,ENST00000368714,;S100A4,upstream_gene_variant,,ENST00000354332,;S100A4,upstream_gene_variant,,ENST00000368715,;S100A4,upstream_gene_variant,,ENST00000368716,;S100A4,upstream_gene_variant,,ENST00000468373,;S100A4,upstream_gene_variant,,ENST00000481009,;	T	ENSG00000188015	ENST00000368713	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	S100A3	HGNC	10493	protein_coding	YES	CCDS1043.1	ENSP00000357702	S10A3_HUMAN	.	UPI000003417C	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAGTCTGTGC	.	2	ESCA
ARHGEF2	0	.	GRCh37	1	155917017	155917017	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*716G>C	.	.	ENST00000361247	22/22	89	78	11	88	88	0	ARHGEF2,3_prime_UTR_variant,,ENST00000361247,;ARHGEF2,3_prime_UTR_variant,,ENST00000368315,;ARHGEF2,3_prime_UTR_variant,,ENST00000313695,;ARHGEF2,3_prime_UTR_variant,,ENST00000368316,;ARHGEF2,3_prime_UTR_variant,,ENST00000462460,;ARHGEF2,3_prime_UTR_variant,,ENST00000470541,;ARHGEF2,downstream_gene_variant,,ENST00000313667,;RXFP4,downstream_gene_variant,,ENST00000368318,;ARHGEF2,intron_variant,,ENST00000477754,;	G	ENSG00000116584	ENST00000361247	Transcript	3_prime_UTR_variant	3777	.	.	.	.	.	.	.	-1	ARHGEF2	HGNC	682	protein_coding	YES	CCDS53376.1	ENSP00000354837	ARHG2_HUMAN	.	UPI000045892C	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACACGTGCA	.	5	ESCA
CCT3	0	.	GRCh37	1	156279014	156279014	+	Silent	SNP	C	C	A	rs143692903	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1614G>T	p.%3D	p.G538G	ENST00000295688	14/14	73	67	6	62	62	0	CCT3,synonymous_variant,p.%3D,ENST00000472765,;CCT3,synonymous_variant,p.%3D,ENST00000295688,;CCT3,synonymous_variant,p.%3D,ENST00000368261,;CCT3,synonymous_variant,p.%3D,ENST00000368259,;CCT3,3_prime_UTR_variant,,ENST00000368262,;CCT3,3_prime_UTR_variant,,ENST00000368258,;	A	ENSG00000163468	ENST00000295688	Transcript	synonymous_variant	1895	1614	538	G	ggG/ggT	rs143692903	.	.	-1	CCT3	HGNC	1616	protein_coding	YES	CCDS1140.2	ENSP00000295688	TCPG_HUMAN	Q59H77_HUMAN,E9PQ35_HUMAN,B4DUR8_HUMAN	UPI000040EEFE	.	.	.	14/14	.	hmmpanther:PTHR11353:SF63,hmmpanther:PTHR11353	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGCCCCGCC	byCluster	2	ESCA
INSRR	0	.	GRCh37	1	156815775	156815775	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1947C>G	p.%3D	p.G649G	ENST00000368195	9/22	76	67	9	56	56	0	INSRR,synonymous_variant,p.%3D,ENST00000368195,;NTRK1,intron_variant,,ENST00000392302,;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,intron_variant,,ENST00000530298,;	C	ENSG00000027644	ENST00000368195	Transcript	synonymous_variant	2344	1947	649	G	ggC/ggG	.	.	.	-1	INSRR	HGNC	6093	protein_coding	YES	CCDS1160.1	ENSP00000357178	INSRR_HUMAN	I6U4P1_HUMAN	UPI000012D8BD	.	.	.	9/22	.	PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF107,Gene3D:2.60.40.10,SMART_domains:SM00060,PIRSF_domain:PIRSF000620,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTCGCCGTC	.	5	ESCA
HSPB7	0	.	GRCh37	1	16344400	16344400	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>T	p.Ser20Phe	p.S20F	ENST00000311890	1/3	57	52	4	47	47	0	HSPB7,missense_variant,p.Ser20Phe,ENST00000487046,;HSPB7,missense_variant,p.Ser20Phe,ENST00000311890,;HSPB7,missense_variant,p.Ser20Phe,ENST00000411503,;HSPB7,missense_variant,p.Ser20Phe,ENST00000545268,;HSPB7,missense_variant,p.Ser20Phe,ENST00000406363,;HSPB7,intron_variant,,ENST00000375718,;HSPB7,upstream_gene_variant,,ENST00000463576,;CLCNKA,upstream_gene_variant,,ENST00000331433,;CLCNKA,upstream_gene_variant,,ENST00000420078,;CLCNKA,upstream_gene_variant,,ENST00000439316,;CLCNKA,upstream_gene_variant,,ENST00000375692,;CLCNKA,upstream_gene_variant,,ENST00000464764,;CLCNKA,upstream_gene_variant,,ENST00000495784,;CLCNKA,upstream_gene_variant,,ENST00000477360,;HSPB7,non_coding_transcript_exon_variant,,ENST00000442459,;	A	ENSG00000173641	ENST00000311890	Transcript	missense_variant	886	59	20	S/F	tCt/tTt	.	.	.	-1	HSPB7	HGNC	5249	protein_coding	YES	CCDS30611.1	ENSP00000310111	HSPB7_HUMAN	.	UPI0000000C78	.	deleterious_low_confidence(0.01)	possibly_damaging(0.462)	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11527:SF21,hmmpanther:PTHR11527	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGAAGAGGAA	.	3	ESCA
CLCNKA	0	.	GRCh37	1	16357020	16357020	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1473G>T	p.%3D	p.L491L	ENST00000331433	15/20	82	77	5	94	94	0	CLCNKA,synonymous_variant,p.%3D,ENST00000331433,;CLCNKA,synonymous_variant,p.%3D,ENST00000420078,;CLCNKA,synonymous_variant,p.%3D,ENST00000439316,;CLCNKA,synonymous_variant,p.%3D,ENST00000375692,;CLCNKA,non_coding_transcript_exon_variant,,ENST00000464764,;CLCNKA,downstream_gene_variant,,ENST00000491433,;CLCNKA,downstream_gene_variant,,ENST00000495784,;RP11-5P18.10,downstream_gene_variant,,ENST00000447882,;	T	ENSG00000186510	ENST00000331433	Transcript	synonymous_variant	1492	1473	491	L	ctG/ctT	.	.	.	1	CLCNKA	HGNC	2026	protein_coding	YES	CCDS167.1	ENSP00000332771	CLCKA_HUMAN	.	UPI0000127993	.	.	.	15/20	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF78,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340,Prints_domain:PR00762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCTGACCGG	.	2	ESCA
ADCY10	0	.	GRCh37	1	167792265	167792265	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4149G>T	p.Leu1383Phe	p.L1383F	ENST00000367851	29/33	120	108	12	88	88	0	ADCY10,missense_variant,p.Leu1230Phe,ENST00000545172,;ADCY10,missense_variant,p.Leu1383Phe,ENST00000367851,;ADCY10,missense_variant,p.Leu1291Phe,ENST00000367848,;RP1-313L4.3,downstream_gene_variant,,ENST00000451545,;ADCY10,3_prime_UTR_variant,,ENST00000485964,;RP1-313L4.4,upstream_gene_variant,,ENST00000507585,;	A	ENSG00000143199	ENST00000367851	Transcript	missense_variant	4334	4149	1383	L/F	ttG/ttT	.	.	.	-1	ADCY10	HGNC	21285	protein_coding	YES	CCDS1265.1	ENSP00000356825	ADCYA_HUMAN	.	UPI0000204D00	.	tolerated(0.08)	benign(0.32)	29/33	.	hmmpanther:PTHR16305:SF23,hmmpanther:PTHR16305,PIRSF_domain:PIRSF011131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGTCCAAGCA	.	2	ESCA
TIPRL	0	.	GRCh37	1	168154083	168154083	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351G>T	p.Lys117Asn	p.K117N	ENST00000367833	3/7	77	69	8	54	54	0	TIPRL,missense_variant,p.Lys117Asn,ENST00000367833,;TIPRL,missense_variant,p.Lys117Asn,ENST00000367830,;	T	ENSG00000143155	ENST00000367833	Transcript	missense_variant	496	351	117	K/N	aaG/aaT	.	.	.	1	TIPRL	HGNC	30231	protein_coding	YES	CCDS1270.1	ENSP00000356807	TIPRL_HUMAN	.	UPI0000071605	.	deleterious(0.02)	possibly_damaging(0.544)	3/7	.	hmmpanther:PTHR21021,Pfam_domain:PF04176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATAAGGGAAC	.	4	ESCA
MROH9	0	.	GRCh37	1	170983336	170983336	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1675C>T	p.Pro559Ser	p.P559S	ENST00000367759	16/22	53	50	3	29	29	0	MROH9,missense_variant,p.Pro559Ser,ENST00000367759,;MROH9,missense_variant,p.Pro166Ser,ENST00000426136,;	T	ENSG00000117501	ENST00000367759	Transcript	missense_variant	1829	1675	559	P/S	Cct/Tct	.	.	.	1	MROH9	HGNC	26287	protein_coding	YES	CCDS53429.1	ENSP00000356733	MROH9_HUMAN	.	UPI0001B09232	.	tolerated(0.06)	possibly_damaging(0.821)	16/22	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAATCCTGTA	.	2	ESCA
METTL13	0	.	GRCh37	1	171759717	171759717	+	Missense_Mutation	SNP	G	G	C	rs768437267	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1435G>C	p.Ala479Pro	p.A479P	ENST00000361735	5/8	42	38	3	55	55	0	METTL13,missense_variant,p.Ala478Pro,ENST00000458517,;METTL13,missense_variant,p.Ala479Pro,ENST00000361735,;METTL13,missense_variant,p.Ala323Pro,ENST00000367737,;METTL13,missense_variant,p.Ala393Pro,ENST00000362019,;METTL13,non_coding_transcript_exon_variant,,ENST00000478330,;METTL13,intron_variant,,ENST00000466643,;METTL13,upstream_gene_variant,,ENST00000476386,;METTL13,downstream_gene_variant,,ENST00000485629,;	C	ENSG00000010165	ENST00000361735	Transcript	missense_variant	1701	1435	479	A/P	Gct/Cct	rs768437267	.	.	1	METTL13	HGNC	24248	protein_coding	YES	CCDS1299.1	ENSP00000354920	MET13_HUMAN	C4B4C6_HUMAN	UPI000006DE3D	.	deleterious(0.01)	possibly_damaging(0.904)	5/8	.	hmmpanther:PTHR12176:SF13,hmmpanther:PTHR12176,Gene3D:3.40.50.150,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGATCGCTGGC	byFrequency	2	ESCA
RABGAP1L	0	.	GRCh37	1	174517040	174517040	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1711-89473G>T	.	.	ENST00000251507	.	80	74	6	78	78	0	RABGAP1L,missense_variant,p.Met555Ile,ENST00000357444,;RABGAP1L,intron_variant,,ENST00000251507,;RABGAP1L,downstream_gene_variant,,ENST00000367689,;RABGAP1L,intron_variant,,ENST00000526253,;RABGAP1L,downstream_gene_variant,,ENST00000367690,;	T	ENSG00000152061	ENST00000251507	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RABGAP1L	HGNC	24663	protein_coding	YES	CCDS1314.1	ENSP00000251507	RBG1L_HUMAN	F1LJ00_HUMAN	UPI0000458A9F	.	.	.	.	13/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTATGAAGGT	.	3	ESCA
SWT1	0	.	GRCh37	1	185260267	185260267	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*332C>A	.	.	ENST00000367500	19/19	42	31	11	30	30	0	SWT1,3_prime_UTR_variant,,ENST00000367500,;SWT1,downstream_gene_variant,,ENST00000367501,;	A	ENSG00000116668	ENST00000367500	Transcript	3_prime_UTR_variant	3200	.	.	.	.	.	.	.	1	SWT1	HGNC	16785	protein_coding	YES	CCDS1367.1	ENSP00000356470	SWT1_HUMAN	Q5TC96_HUMAN,B3KSB6_HUMAN	UPI000013D4C5	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCCAGGGT	.	5	ESCA
CRB1	0	.	GRCh37	1	197316469	197316469	+	Splice_Site	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.849-1G>T	.	p.X283_splice	ENST00000367400	.	66	58	8	43	43	0	CRB1,splice_acceptor_variant,,ENST00000543483,;CRB1,splice_acceptor_variant,,ENST00000535699,;CRB1,splice_acceptor_variant,,ENST00000538660,;CRB1,splice_acceptor_variant,,ENST00000367400,;CRB1,intron_variant,,ENST00000367399,;CRB1,splice_acceptor_variant,,ENST00000484075,;CRB1,splice_acceptor_variant,,ENST00000475659,;	T	ENSG00000134376	ENST00000367400	Transcript	splice_acceptor_variant	.	.	.	.	.	COSM403605	.	.	1	CRB1	HGNC	2343	protein_coding	YES	CCDS1390.1	ENSP00000356370	CRUM1_HUMAN	B7Z824_HUMAN	UPI0000073345	.	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCAGATATA	.	4	ESCA
NR5A2	0	.	GRCh37	1	200144178	200144178	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*840G>T	.	.	ENST00000367362	8/8	90	80	10	69	69	0	NR5A2,3_prime_UTR_variant,,ENST00000236914,;NR5A2,3_prime_UTR_variant,,ENST00000367362,;NR5A2,downstream_gene_variant,,ENST00000544748,;	T	ENSG00000116833	ENST00000367362	Transcript	3_prime_UTR_variant	2712	.	.	.	.	.	.	.	1	NR5A2	HGNC	7984	protein_coding	YES	CCDS1401.1	ENSP00000356331	NR5A2_HUMAN	Q8WY08_HUMAN,B4E2P3_HUMAN	UPI0000130482	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGCTGAAATG	.	4	ESCA
PPP1R12B	0	.	GRCh37	1	202532001	202532001	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2603C>A	p.Ala868Asp	p.A868D	ENST00000608999	20/24	107	100	6	75	75	0	PPP1R12B,missense_variant,p.Ala94Asp,ENST00000391959,;PPP1R12B,missense_variant,p.Ala94Asp,ENST00000367270,;PPP1R12B,missense_variant,p.Ala868Asp,ENST00000608999,;PPP1R12B,missense_variant,p.Ala868Asp,ENST00000336894,;PPP1R12B,non_coding_transcript_exon_variant,,ENST00000491336,;PPP1R12B,non_coding_transcript_exon_variant,,ENST00000290419,;PPP1R12B,non_coding_transcript_exon_variant,,ENST00000466273,;PPP1R12B,upstream_gene_variant,,ENST00000462074,;PPP1R12B,upstream_gene_variant,,ENST00000465284,;PPP1R12B,non_coding_transcript_exon_variant,,ENST00000367269,;	A	ENSG00000077157	ENST00000608999	Transcript	missense_variant	2756	2603	868	A/D	gCc/gAc	.	.	.	1	PPP1R12B	HGNC	7619	protein_coding	YES	CCDS1426.1	ENSP00000476755	.	.	UPI0000458A57	.	deleterious(0.01)	possibly_damaging(0.716)	20/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24179,hmmpanther:PTHR24179:SF18,PIRSF_domain:PIRSF038141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTAGCCACCC	.	2	ESCA
ATP2B4	0	.	GRCh37	1	203669405	203669405	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.721G>C	p.Gly241Arg	p.G241R	ENST00000357681	5/21	68	56	12	57	57	0	ATP2B4,missense_variant,p.Gly241Arg,ENST00000341360,;ATP2B4,missense_variant,p.Gly241Arg,ENST00000367218,;ATP2B4,missense_variant,p.Gly241Arg,ENST00000391954,;ATP2B4,missense_variant,p.Gly241Arg,ENST00000367219,;ATP2B4,missense_variant,p.Gly241Arg,ENST00000357681,;	C	ENSG00000058668	ENST00000357681	Transcript	missense_variant	1844	721	241	G/R	Ggg/Cgg	.	.	.	1	ATP2B4	HGNC	817	protein_coding	YES	CCDS1440.1	ENSP00000350310	AT2B4_HUMAN	A1X4Q2_HUMAN	UPI000002A464	.	deleterious(0.02)	probably_damaging(1)	5/21	.	hmmpanther:PTHR24093:SF276,hmmpanther:PTHR24093,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01494,Gene3D:1.20.1110.10,Superfamily_domains:0049471,Prints_domain:PR00119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TGACAGGGGAA	.	4	ESCA
LAX1	0	.	GRCh37	1	203743063	203743063	+	Missense_Mutation	SNP	G	G	C	rs151128475	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451G>C	p.Ala151Pro	p.A151P	ENST00000442561	5/5	44	34	10	25	25	0	LAX1,missense_variant,p.Ala135Pro,ENST00000367217,;LAX1,missense_variant,p.Ala151Pro,ENST00000442561,;LAX1,non_coding_transcript_exon_variant,,ENST00000367215,;	C	ENSG00000122188	ENST00000442561	Transcript	missense_variant	841	451	151	A/P	Gcg/Ccg	rs151128475	.	.	1	LAX1	HGNC	26005	protein_coding	YES	CCDS1441.2	ENSP00000406970	LAX1_HUMAN	.	UPI000007446D	.	tolerated(0.14)	possibly_damaging(0.695)	5/5	.	hmmpanther:PTHR24091	A:0.0022	A:0.0076	A:0.0014	.	A:0	A:0	A:0	A:0.0086	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTACGCGGTG	byFrequency|byCluster|by1000G	4	ESCA
IL10	0	.	GRCh37	1	206945647	206945647	+	Missense_Mutation	SNP	C	C	A	rs550164520	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.134G>T	p.Arg45Leu	p.R45L	ENST00000423557	1/5	60	51	8	46	46	0	IL10,missense_variant,p.Arg45Leu,ENST00000423557,;IL10,upstream_gene_variant,,ENST00000471071,;IL10,upstream_gene_variant,,ENST00000367099,;	A	ENSG00000136634	ENST00000423557	Transcript	missense_variant	193	134	45	R/L	cGa/cTa	rs550164520	.	.	-1	IL10	HGNC	5962	protein_coding	YES	CCDS1467.1	ENSP00000412237	IL10_HUMAN	Q71UZ1_HUMAN,Q6LBF4_HUMAN,Q6FGW4_HUMAN	UPI0000034E50	.	deleterious(0)	probably_damaging(1)	1/5	.	hmmpanther:PTHR11585,hmmpanther:PTHR11585:SF1,Pfam_domain:PF00726,Gene3D:1.20.1250.10,SMART_domains:SM00188,Superfamily_domains:SSF47266,Prints_domain:PR01294	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCGGAGA	by1000G	4	ESCA
PIGR	0	.	GRCh37	1	207110474	207110474	+	Silent	SNP	C	C	T	rs148222338	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1011G>A	p.%3D	p.S337S	ENST00000356495	4/11	51	44	6	35	35	0	PIGR,synonymous_variant,p.%3D,ENST00000356495,;PIGR,downstream_gene_variant,,ENST00000491503,;	T	ENSG00000162896	ENST00000356495	Transcript	synonymous_variant	1195	1011	337	S	tcG/tcA	rs148222338	.	.	-1	PIGR	HGNC	8968	protein_coding	YES	CCDS1474.1	ENSP00000348888	PIGR_HUMAN	.	UPI000007407E	.	.	.	4/11	.	hmmpanther:PTHR11860:SF44,hmmpanther:PTHR11860,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	T:0.0005	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGGCGAGCC	byCluster	4	ESCA
C4BPA	0	.	GRCh37	1	207307755	207307755	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1091G>T	p.Cys364Phe	p.C364F	ENST00000367070	9/12	89	85	4	59	59	0	C4BPA,missense_variant,p.Cys364Phe,ENST00000367070,;	T	ENSG00000123838	ENST00000367070	Transcript	missense_variant	1285	1091	364	C/F	tGt/tTt	.	.	.	1	C4BPA	HGNC	1325	protein_coding	YES	CCDS1477.1	ENSP00000356037	C4BPA_HUMAN	Q5VVQ8_HUMAN,A6PVY5_HUMAN	UPI0000126C28	.	deleterious(0)	probably_damaging(0.989)	9/12	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF341,Gene3D:2.10.70.10,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTATGTTGCC	.	2	ESCA
CENPF	0	.	GRCh37	1	214814241	214814241	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2560G>T	p.Glu854Ter	p.E854*	ENST00000366955	12/20	39	36	3	19	19	0	CENPF,stop_gained,p.Glu854Ter,ENST00000366955,;	T	ENSG00000117724	ENST00000366955	Transcript	stop_gained	2728	2560	854	E/*	Gaa/Taa	.	.	.	1	CENPF	HGNC	1857	protein_coding	YES	CCDS31023.1	ENSP00000355922	CENPF_HUMAN	.	UPI00001AE985	.	.	.	12/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGTGAAGAG	.	2	ESCA
USH2A	0	.	GRCh37	1	216262371	216262371	+	Silent	SNP	C	C	A	rs777589035	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4869G>T	p.%3D	p.L1623L	ENST00000307340	23/72	96	91	5	69	69	0	USH2A,synonymous_variant,p.%3D,ENST00000307340,;USH2A,synonymous_variant,p.%3D,ENST00000366943,;RP11-22M7.2,downstream_gene_variant,,ENST00000442606,;RP11-22M7.2,downstream_gene_variant,,ENST00000430890,;RP11-22M7.2,downstream_gene_variant,,ENST00000446411,;RP11-22M7.2,downstream_gene_variant,,ENST00000445619,;USH2A,non_coding_transcript_exon_variant,,ENST00000481786,;USH2A,upstream_gene_variant,,ENST00000463147,;	A	ENSG00000042781	ENST00000307340	Transcript	synonymous_variant	5256	4869	1623	L	ctG/ctT	rs777589035	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	.	23/72	.	Superfamily_domains:SSF49899,SMART_domains:SM00282,Pfam_domain:PF02210,Gene3D:2.60.120.200,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATCCAGAGT	.	2	ESCA
USH2A	0	.	GRCh37	1	216595578	216595578	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.101G>A	p.Arg34Gln	p.R34Q	ENST00000307340	2/72	58	50	8	41	41	0	USH2A,missense_variant,p.Arg34Gln,ENST00000366942,;USH2A,missense_variant,p.Arg34Gln,ENST00000366943,;USH2A,missense_variant,p.Arg34Gln,ENST00000307340,;	T	ENSG00000042781	ENST00000307340	Transcript	missense_variant	488	101	34	R/Q	cGa/cAa	COSM3864505,COSM3864506,COSM3864507	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	benign(0)	2/72	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCTCGTGAC	.	4	ESCA
CAPN8	0	.	GRCh37	1	223718144	223718144	+	Silent	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1836C>A	p.%3D	p.L612L	ENST00000366872	17/20	65	56	9	47	47	0	CAPN8,synonymous_variant,p.%3D,ENST00000430824,;CAPN8,synonymous_variant,p.%3D,ENST00000366872,;CAPN8,intron_variant,,ENST00000442247,;CAPN8,non_coding_transcript_exon_variant,,ENST00000482401,;CAPN8,upstream_gene_variant,,ENST00000484873,;CAPN8,upstream_gene_variant,,ENST00000482183,;	T	ENSG00000203697	ENST00000366872	Transcript	synonymous_variant	1836	1836	612	L	ctC/ctA	COSM1473434,COSM1473435	.	.	-1	CAPN8	HGNC	1485	protein_coding	YES	.	ENSP00000355837	CAN8_HUMAN	.	UPI0001AE7978	.	.	.	17/20	.	PROSITE_profiles:PS50222,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF52,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTGAGGGC	.	4	ESCA
TP53BP2	0	.	GRCh37	1	224001971	224001971	+	Missense_Mutation	SNP	C	C	A	rs776842497	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.260G>T	p.Arg87Leu	p.R87L	ENST00000343537	3/18	63	58	5	69	69	0	TP53BP2,missense_variant,p.Arg87Leu,ENST00000343537,;TP53BP2,missense_variant,p.Arg21Leu,ENST00000494100,;TP53BP2,5_prime_UTR_variant,,ENST00000391878,;TP53BP2,non_coding_transcript_exon_variant,,ENST00000473135,;TP53BP2,non_coding_transcript_exon_variant,,ENST00000472180,;TP53BP2,non_coding_transcript_exon_variant,,ENST00000496282,;TP53BP2,missense_variant,p.Val38Phe,ENST00000465119,;	A	ENSG00000143514	ENST00000343537	Transcript	missense_variant	552	260	87	R/L	cGt/cTt	rs776842497	.	.	-1	TP53BP2	HGNC	12000	protein_coding	YES	CCDS44319.1	ENSP00000341957	ASPP2_HUMAN	B7Z2E9_HUMAN,B4DI25_HUMAN,B4DH76_HUMAN	UPI0000D4B5F2	.	deleterious(0)	probably_damaging(0.998)	3/18	.	hmmpanther:PTHR24131:SF8,hmmpanther:PTHR24131,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CATGACGAAGG	byFrequency	3	ESCA
DNAH14	0	.	GRCh37	1	225519255	225519255	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9561A>T	p.Leu3187Phe	p.L3187F	ENST00000430092	63/84	59	53	5	35	35	0	DNAH14,missense_variant,p.Leu3187Phe,ENST00000430092,;DNAH14,missense_variant,p.Leu3187Phe,ENST00000439375,;DNAH14,intron_variant,,ENST00000445597,;DNAH14,missense_variant,p.Leu985Phe,ENST00000327794,;	T	ENSG00000185842	ENST00000430092	Transcript	missense_variant	9776	9561	3187	L/F	ttA/ttT	.	.	.	1	DNAH14	HGNC	2945	protein_coding	.	.	ENSP00000414402	DYH14_HUMAN	C9JU64_HUMAN	UPI000192C36D	.	.	probably_damaging(0.999)	63/84	.	hmmpanther:PTHR10676:SF132,hmmpanther:PTHR10676,Pfam_domain:PF12777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTTACTAAC	.	4	ESCA
ZBTB40	0	.	GRCh37	1	22839481	22839481	+	Silent	SNP	G	G	T	rs200947242	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2526G>T	p.%3D	p.G842G	ENST00000404138	13/19	61	56	5	46	46	0	ZBTB40,synonymous_variant,p.%3D,ENST00000404138,;ZBTB40,synonymous_variant,p.%3D,ENST00000375647,;ZBTB40,synonymous_variant,p.%3D,ENST00000374651,;ZBTB40-IT1,upstream_gene_variant,,ENST00000438551,;	T	ENSG00000184677	ENST00000404138	Transcript	synonymous_variant	3037	2526	842	G	ggG/ggT	rs200947242	.	.	1	ZBTB40	HGNC	29045	protein_coding	YES	CCDS224.1	ENSP00000384527	ZBT40_HUMAN	B1AKC8_HUMAN	UPI0000204652	.	.	.	13/19	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24394:SF0,hmmpanther:PTHR24394,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTGGGGCGAA	.	3	ESCA
OBSCN	0	.	GRCh37	1	228495817	228495817	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15343G>T	p.Glu5115Ter	p.E5115*	ENST00000570156	58/116	57	53	4	58	58	0	OBSCN,stop_gained,p.Glu1792Ter,ENST00000366707,;OBSCN,stop_gained,p.Glu1277Ter,ENST00000366709,;OBSCN,stop_gained,p.Glu4158Ter,ENST00000284548,;OBSCN,stop_gained,p.Glu4158Ter,ENST00000422127,;OBSCN,stop_gained,p.Glu5115Ter,ENST00000570156,;OBSCN,downstream_gene_variant,,ENST00000483539,;OBSCN,downstream_gene_variant,,ENST00000359599,;OBSCN,downstream_gene_variant,,ENST00000602832,;	T	ENSG00000154358	ENST00000570156	Transcript	stop_gained	15417	15343	5115	E/*	Gag/Tag	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	.	58/116	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCTGAGGTG	.	2	ESCA
DISC1	0	.	GRCh37	1	231954771	231954771	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1981+508G>T	.	.	ENST00000366633	.	21	17	4	21	21	0	DISC1,3_prime_UTR_variant,,ENST00000539444,;DISC1,3_prime_UTR_variant,,ENST00000602873,;DISC1,3_prime_UTR_variant,,ENST00000602281,;DISC1,intron_variant,,ENST00000366637,;DISC1,intron_variant,,ENST00000439617,;DISC1,intron_variant,,ENST00000535983,;DISC1,intron_variant,,ENST00000366633,;DISC1,intron_variant,,ENST00000366636,;DISC1,intron_variant,,ENST00000537876,;DISC1,non_coding_transcript_exon_variant,,ENST00000427560,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;DISC1,3_prime_UTR_variant,,ENST00000295051,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000602822,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;DISC1,3_prime_UTR_variant,,ENST00000602700,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;DISC1,3_prime_UTR_variant,,ENST00000535944,;DISC1,intron_variant,,ENST00000366632,;DISC1,intron_variant,,ENST00000422590,;DISC1,intron_variant,,ENST00000602713,;	T	ENSG00000162946	ENST00000366633	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	DISC1	HGNC	2888	protein_coding	YES	CCDS53482.1	ENSP00000355593	DISC1_HUMAN	C4P0C8_HUMAN	UPI0001A61692	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTTGTCAGA	.	2	ESCA
TARBP1	0	.	GRCh37	1	234534271	234534271	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4100C>T	p.Ser1367Leu	p.S1367L	ENST00000040877	26/30	64	58	6	39	39	0	TARBP1,missense_variant,p.Ser1367Leu,ENST00000040877,;TARBP1,non_coding_transcript_exon_variant,,ENST00000484454,;TARBP1,non_coding_transcript_exon_variant,,ENST00000462259,;TARBP1,non_coding_transcript_exon_variant,,ENST00000468077,;TARBP1,non_coding_transcript_exon_variant,,ENST00000496673,;TARBP1,intron_variant,,ENST00000483404,;TARBP1,downstream_gene_variant,,ENST00000481183,;	A	ENSG00000059588	ENST00000040877	Transcript	missense_variant	4100	4100	1367	S/L	tCa/tTa	.	.	.	-1	TARBP1	HGNC	11568	protein_coding	YES	CCDS1601.1	ENSP00000040877	TARB1_HUMAN	.	UPI000006DB0F	.	deleterious(0)	possibly_damaging(0.548)	26/30	.	PROSITE_profiles:PS51624,hmmpanther:PTHR12029,hmmpanther:PTHR12029:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTGAAAGG	.	4	ESCA
RYR2	0	.	GRCh37	1	237666780	237666780	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2588C>A	p.Thr863Lys	p.T863K	ENST00000366574	22/105	71	67	4	42	42	0	RYR2,missense_variant,p.Thr847Lys,ENST00000542537,;RYR2,missense_variant,p.Thr863Lys,ENST00000366574,;RYR2,missense_variant,p.Thr861Lys,ENST00000360064,;	A	ENSG00000198626	ENST00000366574	Transcript	missense_variant	2905	2588	863	T/K	aCa/aAa	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	probably_damaging(0.936)	22/105	.	Pfam_domain:PF02026,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCACACCCA	.	2	ESCA
OR2L2	0	.	GRCh37	1	248201852	248201852	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283G>T	p.Gly95Ter	p.G95*	ENST00000366479	1/1	194	169	24	113	113	0	OR2L2,stop_gained,p.Gly95Ter,ENST00000366479,;OR2L13,intron_variant,,ENST00000366478,;	T	ENSG00000203663	ENST00000366479	Transcript	stop_gained	379	283	95	G/*	Gga/Tga	.	.	.	1	OR2L2	HGNC	8266	protein_coding	YES	CCDS31103.1	ENSP00000355435	OR2L2_HUMAN	.	UPI0000061EAA	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF189,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACTGGATGT	.	4	ESCA
OR2L3	0	.	GRCh37	1	248224700	248224700	+	Silent	SNP	C	C	A	rs769154814	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.717C>A	p.%3D	p.T239T	ENST00000359959	1/1	213	182	31	181	181	0	OR2L3,synonymous_variant,p.%3D,ENST00000359959,;OR2L13,intron_variant,,ENST00000366478,;	A	ENSG00000198128	ENST00000359959	Transcript	synonymous_variant	717	717	239	T	acC/acA	rs769154814	.	.	1	OR2L3	HGNC	15009	protein_coding	YES	CCDS31104.1	ENSP00000353044	OR2L3_HUMAN	.	UPI0000061EB8	.	.	.	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26453:SF104,hmmpanther:PTHR26453,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGACCTGCAG	byFrequency	4	ESCA
OR2T33	0	.	GRCh37	1	248436323	248436323	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.794C>A	p.Ser265Tyr	p.S265Y	ENST00000318021	1/1	168	159	9	142	142	0	OR2T33,missense_variant,p.Ser265Tyr,ENST00000318021,;	T	ENSG00000177212	ENST00000318021	Transcript	missense_variant	816	794	265	S/Y	tCc/tAc	COSM3487075	.	.	-1	OR2T33	HGNC	31255	protein_coding	YES	CCDS31109.1	ENSP00000324687	O2T33_HUMAN	.	UPI000004B237	.	deleterious(0)	probably_damaging(0.988)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF83,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGTGGACCTA	.	2	ESCA
OR2T4	0	.	GRCh37	1	248525025	248525025	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143G>A	p.Gly48Glu	p.G48E	ENST00000366475	1/1	98	87	11	104	104	0	OR2T4,missense_variant,p.Gly48Glu,ENST00000366475,;	A	ENSG00000196944	ENST00000366475	Transcript	missense_variant	143	143	48	G/E	gGa/gAa	COSM3966454	.	.	1	OR2T4	HGNC	15016	protein_coding	YES	CCDS31113.1	ENSP00000355431	OR2T4_HUMAN	.	UPI000004B9CC	.	deleterious(0)	probably_damaging(1)	1/1	.	hmmpanther:PTHR26453:SF200,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTGGGACTCT	.	4	ESCA
XKR8	0	.	GRCh37	1	28293102	28293102	+	Silent	SNP	G	G	A	rs769870415	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.579G>A	p.%3D	p.P193P	ENST00000373884	3/3	69	63	5	61	61	0	XKR8,synonymous_variant,p.%3D,ENST00000373884,;EYA3,downstream_gene_variant,,ENST00000436342,;EYA3,downstream_gene_variant,,ENST00000373871,;XKR8,non_coding_transcript_exon_variant,,ENST00000481387,;	A	ENSG00000158156	ENST00000373884	Transcript	synonymous_variant	1187	579	193	P	ccG/ccA	rs769870415	.	.	1	XKR8	HGNC	25508	protein_coding	YES	CCDS315.1	ENSP00000362991	XKR8_HUMAN	Q9NW55_HUMAN	UPI000006F5DC	.	.	.	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF8,Pfam_domain:PF09815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGCCGCTCCT	.	3	ESCA
TMEM234	0	.	GRCh37	1	32682383	32682383	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*71G>T	.	.	ENST00000309777	5/5	27	24	3	21	21	0	TMEM234,3_prime_UTR_variant,,ENST00000309777,;TMEM234,3_prime_UTR_variant,,ENST00000373593,;TMEM234,intron_variant,,ENST00000344461,;TMEM234,intron_variant,,ENST00000545122,;DCDC2B,downstream_gene_variant,,ENST00000409358,;TMEM234,non_coding_transcript_exon_variant,,ENST00000485689,;TMEM234,upstream_gene_variant,,ENST00000495091,;TMEM234,3_prime_UTR_variant,,ENST00000484490,;TMEM234,non_coding_transcript_exon_variant,,ENST00000487174,;TMEM234,non_coding_transcript_exon_variant,,ENST00000466796,;TMEM234,intron_variant,,ENST00000491434,;TMEM234,intron_variant,,ENST00000489170,;TMEM234,intron_variant,,ENST00000461402,;TMEM234,intron_variant,,ENST00000483001,;DCDC2B,downstream_gene_variant,,ENST00000487056,;	A	ENSG00000160055	ENST00000309777	Transcript	3_prime_UTR_variant	497	.	.	.	.	.	.	.	-1	TMEM234	HGNC	28837	protein_coding	YES	CCDS356.2	ENSP00000309792	TM234_HUMAN	.	UPI000006F2AF	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATCCGCTCA	.	4	ESCA
MEGF6	0	.	GRCh37	1	3421858	3421858	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2102G>T	p.Cys701Phe	p.C701F	ENST00000356575	17/37	86	80	6	76	76	0	MEGF6,missense_variant,p.Cys701Phe,ENST00000356575,;MEGF6,missense_variant,p.Cys596Phe,ENST00000294599,;MEGF6,missense_variant,p.Cys708Phe,ENST00000485002,;	A	ENSG00000162591	ENST00000356575	Transcript	missense_variant	2329	2102	701	C/F	tGc/tTc	.	.	.	-1	MEGF6	HGNC	3232	protein_coding	YES	CCDS41237.1	ENSP00000348982	MEGF6_HUMAN	.	UPI0000DACACB	.	deleterious(0)	probably_damaging(0.991)	17/37	.	hmmpanther:PTHR24035:SF29,hmmpanther:PTHR24035,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGGCAGGTG	.	2	ESCA
CDCA8	0	.	GRCh37	1	38166128	38166128	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.358G>T	p.Asp120Tyr	p.D120Y	ENST00000373055	5/10	75	62	13	60	60	0	CDCA8,missense_variant,p.Asp120Tyr,ENST00000327331,;CDCA8,missense_variant,p.Asp120Tyr,ENST00000373055,;	T	ENSG00000134690	ENST00000373055	Transcript	missense_variant	631	358	120	D/Y	Gat/Tat	.	.	.	1	CDCA8	HGNC	14629	protein_coding	YES	CCDS424.1	ENSP00000362146	BOREA_HUMAN	.	UPI000007033D	.	deleterious(0.01)	benign(0.44)	5/10	.	hmmpanther:PTHR16040,hmmpanther:PTHR16040:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTAGATGAA	.	5	ESCA
MACF1	0	.	GRCh37	1	39823254	39823254	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5446G>A	p.Glu1816Lys	p.E1816K	ENST00000545844	40/94	94	88	6	55	55	0	MACF1,missense_variant,p.Glu950Lys,ENST00000372925,;MACF1,missense_variant,p.Glu1816Lys,ENST00000361689,;MACF1,missense_variant,p.Glu2318Lys,ENST00000289893,;MACF1,missense_variant,p.Glu3878Lys,ENST00000564288,;MACF1,missense_variant,p.Glu1965Lys,ENST00000530262,;MACF1,missense_variant,p.Glu1816Lys,ENST00000539005,;MACF1,missense_variant,p.Glu3883Lys,ENST00000372915,;MACF1,missense_variant,p.Glu1816Lys,ENST00000317713,;MACF1,missense_variant,p.Glu3915Lys,ENST00000567887,;MACF1,missense_variant,p.Glu1816Lys,ENST00000545844,;MACF1,non_coding_transcript_exon_variant,,ENST00000476350,;	A	ENSG00000127603	ENST00000545844	Transcript	missense_variant	5554	5446	1816	E/K	Gag/Aag	.	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	probably_damaging(0.999)	40/94	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF46966,Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915:SF37,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGATGAGTTG	.	2	ESCA
OXCT2	0	.	GRCh37	1	40236196	40236196	+	Silent	SNP	C	C	T	rs374640877	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732G>A	p.%3D	p.E244E	ENST00000327582	1/1	60	52	7	36	36	0	OXCT2,synonymous_variant,p.%3D,ENST00000327582,;BMP8B,intron_variant,,ENST00000372827,;BMP8B,intron_variant,,ENST00000397360,;	T	ENSG00000198754	ENST00000327582	Transcript	synonymous_variant	825	732	244	E	gaG/gaA	rs374640877	.	.	-1	OXCT2	HGNC	18606	protein_coding	YES	CCDS445.1	ENSP00000361914	SCOT2_HUMAN	.	UPI000006DF0A	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13707:SF28,hmmpanther:PTHR13707,Pfam_domain:PF01144,Gene3D:3.40.1080.10,PIRSF_domain:PIRSF000858,SMART_domains:SM00882,Superfamily_domains:SSF100950	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCACCTCCAC	byFrequency|byCluster	4	ESCA
AKR1A1	0	.	GRCh37	1	46033797	46033797	+	Missense_Mutation	SNP	G	G	T	rs767979535	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.500G>T	p.Arg167Leu	p.R167L	ENST00000372070	6/10	64	55	9	45	45	0	AKR1A1,missense_variant,p.Arg167Leu,ENST00000372070,;AKR1A1,missense_variant,p.Arg167Leu,ENST00000351829,;AKR1A1,downstream_gene_variant,,ENST00000481885,;AKR1A1,downstream_gene_variant,,ENST00000471651,;AKR1A1,downstream_gene_variant,,ENST00000434299,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000473038,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000497973,;AKR1A1,non_coding_transcript_exon_variant,,ENST00000476957,;AKR1A1,intron_variant,,ENST00000495913,;AKR1A1,downstream_gene_variant,,ENST00000496999,;AKR1A1,upstream_gene_variant,,ENST00000475985,;AKR1A1,upstream_gene_variant,,ENST00000487654,;AKR1A1,upstream_gene_variant,,ENST00000475919,;	T	ENSG00000117448	ENST00000372070	Transcript	missense_variant	1247	500	167	R/L	cGg/cTg	rs767979535	.	.	1	AKR1A1	HGNC	380	protein_coding	YES	CCDS523.1	ENSP00000361140	AK1A1_HUMAN	Q5T621_HUMAN	UPI000013D31D	.	tolerated(0.48)	benign(0.003)	6/10	.	Superfamily_domains:SSF51430,PIRSF_domain:PIRSF000097,Pfam_domain:PF00248,Gene3D:3.20.20.100,hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTCGGCAGA	.	4	ESCA
DMBX1	0	.	GRCh37	1	46978148	46978148	+	Silent	SNP	C	C	A	rs142368793	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1116C>A	p.%3D	p.L372L	ENST00000360032	4/4	66	58	8	49	49	0	DMBX1,synonymous_variant,p.%3D,ENST00000360032,;DMBX1,synonymous_variant,p.%3D,ENST00000371956,;	A	ENSG00000197587	ENST00000360032	Transcript	synonymous_variant	1130	1116	372	L	ctC/ctA	rs142368793	.	.	1	DMBX1	HGNC	19026	protein_coding	YES	CCDS536.1	ENSP00000353132	DMBX1_HUMAN	.	UPI0000070B63	.	.	.	4/4	.	hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF308	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGACTCGATAC	byCluster	4	ESCA
SLC5A9	0	.	GRCh37	1	48694895	48694895	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.414+46C>T	.	.	ENST00000236495	.	49	43	5	41	41	0	SLC5A9,intron_variant,,ENST00000420136,;SLC5A9,intron_variant,,ENST00000533824,;SLC5A9,intron_variant,,ENST00000438567,;SLC5A9,intron_variant,,ENST00000236495,;RP5-1024N4.4,non_coding_transcript_exon_variant,,ENST00000606809,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000493837,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000527929,;SLC5A9,intron_variant,,ENST00000441260,;SLC5A9,intron_variant,,ENST00000425816,;	T	ENSG00000117834	ENST00000236495	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SLC5A9	HGNC	22146	protein_coding	YES	CCDS44136.1	ENSP00000236495	SC5A9_HUMAN	.	UPI0000251D94	.	.	.	.	4/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGCCTCTGG	.	4	ESCA
ELAVL4	0	.	GRCh37	1	50661318	50661318	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.645C>T	p.%3D	p.P215P	ENST00000357083	5/7	111	100	10	83	83	0	ELAVL4,synonymous_variant,p.%3D,ENST00000371824,;ELAVL4,synonymous_variant,p.%3D,ENST00000448907,;ELAVL4,synonymous_variant,p.%3D,ENST00000371821,;ELAVL4,synonymous_variant,p.%3D,ENST00000371819,;ELAVL4,synonymous_variant,p.%3D,ENST00000357083,;ELAVL4,synonymous_variant,p.%3D,ENST00000371827,;ELAVL4,synonymous_variant,p.%3D,ENST00000371823,;ELAVL4,non_coding_transcript_exon_variant,,ENST00000474675,;	T	ENSG00000162374	ENST00000357083	Transcript	synonymous_variant	687	645	215	P	ccC/ccT	.	.	.	1	ELAVL4	HGNC	3315	protein_coding	YES	CCDS44139.1	ENSP00000349594	ELAV4_HUMAN	B7Z5E0_HUMAN	UPI000006F633	.	.	.	5/7	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011,hmmpanther:PTHR24011:SF243,TIGRFAM_domain:TIGR01661,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928,Prints_domain:PR00961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGCCCAGCGG	.	3	ESCA
ZCCHC11	0	.	GRCh37	1	52956462	52956462	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1330G>T	p.Asp444Tyr	p.D444Y	ENST00000257177	8/30	81	73	7	66	66	0	ZCCHC11,missense_variant,p.Asp444Tyr,ENST00000257177,;ZCCHC11,missense_variant,p.Asp203Tyr,ENST00000484723,;ZCCHC11,missense_variant,p.Asp444Tyr,ENST00000528642,;ZCCHC11,missense_variant,p.Asp444Tyr,ENST00000371544,;ZCCHC11,non_coding_transcript_exon_variant,,ENST00000371541,;ZCCHC11,3_prime_UTR_variant,,ENST00000473856,;	A	ENSG00000134744	ENST00000257177	Transcript	missense_variant	1475	1330	444	D/Y	Gat/Tat	.	.	.	-1	ZCCHC11	HGNC	28981	protein_coding	YES	CCDS30715.1	ENSP00000257177	TUT4_HUMAN	H0YEY0_HUMAN,E9PQS7_HUMAN,E9PJN7_HUMAN	UPI00001D7D0C	.	deleterious(0)	probably_damaging(0.999)	8/30	.	hmmpanther:PTHR12271,hmmpanther:PTHR12271:SF49,Gene3D:3.30.460.10,Superfamily_domains:SSF81301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CACATCTACAT	.	2	ESCA
MROH7	0	.	GRCh37	1	55145629	55145629	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2292G>T	p.Gln764His	p.Q764H	ENST00000421030	13/24	66	60	6	64	64	0	MROH7,missense_variant,p.Gln282His,ENST00000454855,;MROH7,missense_variant,p.Gln332His,ENST00000409996,;MROH7,missense_variant,p.Gln764His,ENST00000395690,;MROH7,missense_variant,p.Gln764His,ENST00000421030,;MROH7,missense_variant,p.Gln332His,ENST00000545244,;MROH7,missense_variant,p.Gln764His,ENST00000339553,;MROH7-TTC4,missense_variant,p.Gln764His,ENST00000414150,;MROH7,3_prime_UTR_variant,,ENST00000440217,;MROH7,3_prime_UTR_variant,,ENST00000438846,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000425300,;MROH7,3_prime_UTR_variant,,ENST00000422659,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000606515,;MROH7,intron_variant,,ENST00000413188,;MROH7,intron_variant,,ENST00000440047,;	T	ENSG00000184313	ENST00000421030	Transcript	missense_variant	2577	2292	764	Q/H	caG/caT	.	.	.	1	MROH7	HGNC	24802	protein_coding	YES	CCDS41342.2	ENSP00000396622	MROH7_HUMAN	C9K0L2_HUMAN,B7ZBM2_HUMAN	UPI000198C4E2	.	tolerated(0.05)	benign(0.221)	13/24	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF9,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGCCAGGTGGC	.	3	ESCA
SLC44A5	0	.	GRCh37	1	75708676	75708676	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366A>G	p.%3D	p.P122P	ENST00000370855	8/24	47	44	3	39	39	0	SLC44A5,synonymous_variant,p.%3D,ENST00000370855,;SLC44A5,synonymous_variant,p.%3D,ENST00000370859,;SLC44A5,5_prime_UTR_variant,,ENST00000535611,;SLC44A5,non_coding_transcript_exon_variant,,ENST00000469525,;	C	ENSG00000137968	ENST00000370855	Transcript	synonymous_variant	480	366	122	P	ccA/ccG	.	.	.	-1	SLC44A5	HGNC	28524	protein_coding	YES	CCDS667.1	ENSP00000359892	CTL5_HUMAN	B7Z473_HUMAN	UPI000013E195	.	.	.	8/24	.	hmmpanther:PTHR12385:SF42,hmmpanther:PTHR12385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTCTGGGCA	.	2	ESCA
SLC44A5	0	.	GRCh37	1	75708677	75708677	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365C>A	p.Pro122Gln	p.P122Q	ENST00000370855	8/24	46	43	3	39	39	0	SLC44A5,missense_variant,p.Pro122Gln,ENST00000370855,;SLC44A5,missense_variant,p.Pro122Gln,ENST00000370859,;SLC44A5,5_prime_UTR_variant,,ENST00000535611,;SLC44A5,non_coding_transcript_exon_variant,,ENST00000469525,;	T	ENSG00000137968	ENST00000370855	Transcript	missense_variant	479	365	122	P/Q	cCa/cAa	.	.	.	-1	SLC44A5	HGNC	28524	protein_coding	YES	CCDS667.1	ENSP00000359892	CTL5_HUMAN	B7Z473_HUMAN	UPI000013E195	.	deleterious(0)	probably_damaging(1)	8/24	.	hmmpanther:PTHR12385:SF42,hmmpanther:PTHR12385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCTGGGCAC	.	2	ESCA
LMO4	0	.	GRCh37	1	87805312	87805312	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330T>A	p.%3D	p.L110L	ENST00000370544	3/5	61	56	4	51	51	0	LMO4,synonymous_variant,p.%3D,ENST00000370542,;LMO4,synonymous_variant,p.%3D,ENST00000370544,;LMO4,non_coding_transcript_exon_variant,,ENST00000489303,;LMO4,non_coding_transcript_exon_variant,,ENST00000495705,;	A	ENSG00000143013	ENST00000370544	Transcript	synonymous_variant	1110	330	110	L	ctT/ctA	.	.	.	1	LMO4	HGNC	6644	protein_coding	YES	CCDS713.1	ENSP00000359575	LMO4_HUMAN	.	UPI0000004145	.	.	.	3/5	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24208:SF93,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CATCTTAAGGT	.	2	ESCA
ANKEF1	0	.	GRCh37	20	10030541	10030541	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1324G>T	p.Ala442Ser	p.A442S	ENST00000378380	6/10	61	57	4	39	39	0	ANKEF1,missense_variant,p.Ala442Ser,ENST00000378380,;ANKEF1,missense_variant,p.Ala442Ser,ENST00000378392,;SNAP25-AS1,intron_variant,,ENST00000603542,;SNAP25-AS1,intron_variant,,ENST00000421143,;ANKEF1,non_coding_transcript_exon_variant,,ENST00000488991,;	T	ENSG00000132623	ENST00000378380	Transcript	missense_variant	1653	1324	442	A/S	Gcg/Tcg	.	.	.	1	ANKEF1	HGNC	15803	protein_coding	YES	CCDS13108.1	ENSP00000367631	ANKE1_HUMAN	.	UPI0000125B51	.	tolerated(0.73)	benign(0.013)	6/10	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24127,hmmpanther:PTHR24127:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTACGCGTTT	.	2	ESCA
SCP2D1	0	.	GRCh37	20	18794792	18794792	+	Silent	SNP	G	G	T	rs368734818	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.333G>T	p.%3D	p.P111P	ENST00000377428	1/1	73	67	6	51	51	0	SCP2D1,synonymous_variant,p.%3D,ENST00000377428,;C20orf78,intron_variant,,ENST00000278779,;C20orf78,upstream_gene_variant,,ENST00000463425,;	T	ENSG00000132631	ENST00000377428	Transcript	synonymous_variant	423	333	111	P	ccG/ccT	rs368734818,COSM395872,COSM182314	.	.	1	SCP2D1	HGNC	16211	protein_coding	YES	CCDS13139.1	ENSP00000366645	SCP2D_HUMAN	.	UPI00001285ED	.	.	.	1/1	.	hmmpanther:PTHR24314:SF7,hmmpanther:PTHR24314,Pfam_domain:PF02036,Gene3D:3.30.1050.10,Superfamily_domains:SSF55718	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0005	A:0	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATCCCGGAGTC	byCluster|by1000G	3	ESCA
TMC2	0	.	GRCh37	20	2605001	2605001	+	Silent	SNP	C	C	A	rs555212967	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2265C>A	p.%3D	p.L755L	ENST00000358864	17/20	98	91	7	68	68	0	TMC2,synonymous_variant,p.%3D,ENST00000358864,;	A	ENSG00000149488	ENST00000358864	Transcript	synonymous_variant	2280	2265	755	L	ctC/ctA	rs555212967	.	.	1	TMC2	HGNC	16527	protein_coding	YES	CCDS13029.2	ENSP00000351732	TMC2_HUMAN	.	UPI0000246C98	.	.	.	17/20	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCTCGCCAA	by1000G	2	ESCA
TTLL9	0	.	GRCh37	20	30497560	30497560	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339G>T	p.Met113Ile	p.M113I	ENST00000375938	6/17	46	42	4	45	45	0	TTLL9,missense_variant,p.Met113Ile,ENST00000375938,;TTLL9,missense_variant,p.Met63Ile,ENST00000375922,;TTLL9,missense_variant,p.Met95Ile,ENST00000375934,;TTLL9,missense_variant,p.Met63Ile,ENST00000375921,;TTLL9,missense_variant,p.Met63Ile,ENST00000310998,;TTLL9,missense_variant,p.Met113Ile,ENST00000535842,;	T	ENSG00000131044	ENST00000375938	Transcript	missense_variant	592	339	113	M/I	atG/atT	.	.	.	1	TTLL9	HGNC	16118	protein_coding	YES	CCDS42863.1	ENSP00000365105	TTLL9_HUMAN	.	UPI00001998D0	.	tolerated(0.06)	benign(0.097)	6/17	.	PROSITE_profiles:PS51221,hmmpanther:PTHR12241:SF39,hmmpanther:PTHR12241,Pfam_domain:PF03133	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TACATGGTGAA	.	3	ESCA
POFUT1	0	.	GRCh37	20	30818726	30818726	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.840G>T	p.Met280Ile	p.M280I	ENST00000375749	6/7	67	61	6	42	42	0	POFUT1,missense_variant,p.Met69Ile,ENST00000539210,;POFUT1,missense_variant,p.Met280Ile,ENST00000375749,;POFUT1,non_coding_transcript_exon_variant,,ENST00000465791,;POFUT1,non_coding_transcript_exon_variant,,ENST00000486717,;POFUT1,upstream_gene_variant,,ENST00000434904,;	T	ENSG00000101346	ENST00000375749	Transcript	missense_variant	902	840	280	M/I	atG/atT	.	.	.	1	POFUT1	HGNC	14988	protein_coding	YES	CCDS13198.1	ENSP00000364902	OFUT1_HUMAN	B4DUV4_HUMAN	UPI0000130C42	.	tolerated(0.4)	benign(0.021)	6/7	.	Pfam_domain:PF10250,hmmpanther:PTHR21420:SF3,hmmpanther:PTHR21420	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACGATGACTAT	.	4	ESCA
SUN5	0	.	GRCh37	20	31592147	31592147	+	5'UTR	SNP	C	C	A	rs751814566	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1G>T	.	.	ENST00000356173	1/13	64	55	9	53	53	0	SUN5,5_prime_UTR_variant,,ENST00000356173,;SUN5,5_prime_UTR_variant,,ENST00000375519,;SUN5,5_prime_UTR_variant,,ENST00000375523,;BPIFB2,upstream_gene_variant,,ENST00000170150,;SUN5,upstream_gene_variant,,ENST00000420875,;	A	ENSG00000167098	ENST00000356173	Transcript	5_prime_UTR_variant	93	.	.	.	.	rs751814566	.	.	-1	SUN5	HGNC	16252	protein_coding	YES	CCDS13209.1	ENSP00000348496	SUN5_HUMAN	.	UPI0000135D7C	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCATCGATTT	byFrequency	5	ESCA
BPIFB2	0	.	GRCh37	20	31596364	31596364	+	5'UTR	SNP	C	C	A	rs760381008	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-17C>A	.	.	ENST00000170150	2/16	46	40	6	33	33	0	BPIFB2,5_prime_UTR_variant,,ENST00000170150,;SUN5,upstream_gene_variant,,ENST00000356173,;SUN5,upstream_gene_variant,,ENST00000375519,;SUN5,upstream_gene_variant,,ENST00000375523,;SUN5,upstream_gene_variant,,ENST00000420875,;	A	ENSG00000078898	ENST00000170150	Transcript	5_prime_UTR_variant	179	.	.	.	.	rs760381008	.	.	1	BPIFB2	HGNC	16177	protein_coding	YES	CCDS13210.1	ENSP00000170150	BPIB2_HUMAN	.	UPI00000377B0	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGGCAGCGG	byFrequency	4	ESCA
BPIFB2	0	.	GRCh37	20	31606541	31606541	+	Silent	SNP	C	C	A	rs373815604	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.768C>A	p.%3D	p.T256T	ENST00000170150	9/16	37	29	8	26	26	0	BPIFB2,synonymous_variant,p.%3D,ENST00000170150,;	A	ENSG00000078898	ENST00000170150	Transcript	synonymous_variant	963	768	256	T	acC/acA	rs373815604	.	.	1	BPIFB2	HGNC	16177	protein_coding	YES	CCDS13210.1	ENSP00000170150	BPIB2_HUMAN	.	UPI00000377B0	.	.	.	9/16	.	Superfamily_domains:SSF55394,SMART_domains:SM00329,Gene3D:1ewfA02,Pfam_domain:PF02886,hmmpanther:PTHR10504:SF68,hmmpanther:PTHR10504	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACCGTGGG	byCluster	5	ESCA
BPIFA2	0	.	GRCh37	20	31767424	31767424	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660C>A	p.%3D	p.I220I	ENST00000253362	7/9	60	53	7	55	55	0	BPIFA2,synonymous_variant,p.%3D,ENST00000354932,;BPIFA2,synonymous_variant,p.%3D,ENST00000253362,;	A	ENSG00000131050	ENST00000253362	Transcript	synonymous_variant	806	660	220	I	atC/atA	.	.	.	1	BPIFA2	HGNC	16203	protein_coding	YES	CCDS13214.1	ENSP00000253362	BPIA2_HUMAN	.	UPI00000361E3	.	.	.	7/9	.	hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF6,Gene3D:1ewfA01,Pfam_domain:PF01273,Superfamily_domains:SSF55394	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGATCCGCAT	.	4	ESCA
CEP250	0	.	GRCh37	20	34055253	34055253	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724G>T	p.Glu242Ter	p.E242*	ENST00000397527	9/35	46	41	5	40	40	0	CEP250,stop_gained,p.Glu242Ter,ENST00000425934,;CEP250,stop_gained,p.Glu242Ter,ENST00000397524,;CEP250,stop_gained,p.Glu242Ter,ENST00000342580,;CEP250,stop_gained,p.Glu242Ter,ENST00000397527,;CEP250,downstream_gene_variant,,ENST00000446710,;CEP250,downstream_gene_variant,,ENST00000420564,;CEP250,downstream_gene_variant,,ENST00000465987,;CEP250,stop_gained,p.Glu242Ter,ENST00000461386,;CEP250,upstream_gene_variant,,ENST00000474829,;	T	ENSG00000126001	ENST00000397527	Transcript	stop_gained	1444	724	242	E/*	Gag/Tag	.	.	.	1	CEP250	HGNC	1859	protein_coding	YES	CCDS13255.1	ENSP00000380661	CP250_HUMAN	Q5JWS6_HUMAN,Q5JWS5_HUMAN,G1UI40_HUMAN	UPI000006FE8F	.	.	.	9/35	.	hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCGGGAGCCG	.	4	ESCA
MROH8	0	.	GRCh37	20	35749434	35749434	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2062C>T	p.Ala688Val	p.A688V	ENST00000343811	15/24	84	71	12	84	84	0	MROH8,missense_variant,p.Ala688Val,ENST00000343811,;MROH8,missense_variant,p.Ala490Val,ENST00000217333,;MROH8,missense_variant,p.Ala647Val,ENST00000441008,;MROH8,missense_variant,p.Ala661Val,ENST00000400441,;MROH8,missense_variant,p.Ala289Val,ENST00000417458,;	A	ENSG00000101353	ENST00000343811	Transcript	missense_variant	2062	2063	688	A/V	gCc/gTc	.	.	.	-1	MROH8	HGNC	16125	protein_coding	YES	.	ENSP00000339971	.	Q5JYR0_HUMAN,Q5JYQ9_HUMAN	UPI0000E5A31D	.	tolerated(0.49)	probably_damaging(0.999)	15/24	.	hmmpanther:PTHR23120:SF4,hmmpanther:PTHR23120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCATGGCAAAG	.	3	ESCA
RBPJL	0	.	GRCh37	20	43942722	43942722	+	Missense_Mutation	SNP	G	G	T	rs568551533	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805G>T	p.Val269Phe	p.V269F	ENST00000343694	8/12	63	58	5	53	53	0	RBPJL,missense_variant,p.Val269Phe,ENST00000343694,;RBPJL,missense_variant,p.Val269Phe,ENST00000372743,;RBPJL,missense_variant,p.Val269Phe,ENST00000372741,;RBPJL,non_coding_transcript_exon_variant,,ENST00000464504,;	T	ENSG00000124232	ENST00000343694	Transcript	missense_variant	877	805	269	V/F	Gtt/Ttt	rs568551533	.	.	1	RBPJL	HGNC	13761	protein_coding	YES	CCDS13349.1	ENSP00000341243	RBPJL_HUMAN	.	UPI0000047297	.	deleterious(0.02)	possibly_damaging(0.793)	8/12	.	hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2,Gene3D:2.80.10.50,Pfam_domain:PF09270,Superfamily_domains:0049692	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTACGTTCGC	by1000G	2	ESCA
CDH22	0	.	GRCh37	20	44856180	44856180	+	Missense_Mutation	SNP	C	C	A	rs753809330	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.637G>T	p.Gly213Cys	p.G213C	ENST00000372262	3/11	113	101	11	83	83	0	CDH22,missense_variant,p.Gly213Cys,ENST00000372262,;CDH22,missense_variant,p.Gly213Cys,ENST00000537909,;	A	ENSG00000149654	ENST00000372262	Transcript	missense_variant	1038	637	213	G/C	Ggc/Tgc	rs753809330	.	.	-1	CDH22	HGNC	13251	protein_coding	YES	CCDS13395.1	ENSP00000361336	CAD22_HUMAN	Q49AS4_HUMAN	UPI0000126DC0	.	deleterious(0)	probably_damaging(1)	3/11	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF88,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V210M|c.628G>A|3	RADIA|MUSE|VARSCANS	CTCGCCGTCCA	.	3	ESCA
SULF2	0	.	GRCh37	20	46313304	46313304	+	Silent	SNP	C	C	A	rs536732621	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.759G>T	p.%3D	p.A253A	ENST00000359930	6/21	84	79	5	54	54	0	SULF2,synonymous_variant,p.%3D,ENST00000359930,;SULF2,synonymous_variant,p.%3D,ENST00000361612,;SULF2,synonymous_variant,p.%3D,ENST00000467815,;SULF2,synonymous_variant,p.%3D,ENST00000484875,;CTD-2653D5.1,non_coding_transcript_exon_variant,,ENST00000526566,;SULF2,non_coding_transcript_exon_variant,,ENST00000474450,;SULF2,downstream_gene_variant,,ENST00000463221,;	A	ENSG00000196562	ENST00000359930	Transcript	synonymous_variant	1611	759	253	A	gcG/gcT	rs536732621,COSM1307488	.	.	-1	SULF2	HGNC	20392	protein_coding	YES	CCDS13408.1	ENSP00000353007	SULF2_HUMAN	Q5BKT1_HUMAN,B1AMP9_HUMAN	UPI000003FFBA	.	.	.	6/21	.	hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF67,Pfam_domain:PF00884,PIRSF_domain:PIRSF036665	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGGCGCGTA	by1000G	2	ESCA
TSHZ2	0	.	GRCh37	20	51872528	51872528	+	Missense_Mutation	SNP	G	G	T	rs778561966	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2531G>T	p.Arg844Leu	p.R844L	ENST00000371497	2/3	64	54	9	64	64	0	TSHZ2,missense_variant,p.Arg841Leu,ENST00000603338,;TSHZ2,missense_variant,p.Arg844Leu,ENST00000371497,;TSHZ2,missense_variant,p.Arg841Leu,ENST00000329613,;RP4-678D15.1,non_coding_transcript_exon_variant,,ENST00000606932,;TSHZ2,missense_variant,p.Arg4Leu,ENST00000605656,;	T	ENSG00000182463	ENST00000371497	Transcript	missense_variant	3418	2531	844	R/L	cGg/cTg	rs778561966	.	.	1	TSHZ2	HGNC	13010	protein_coding	YES	CCDS33490.1	ENSP00000360552	TSH2_HUMAN	S4R3C8_HUMAN	UPI0000206747	.	deleterious(0)	probably_damaging(0.998)	2/3	.	hmmpanther:PTHR12487:SF3,hmmpanther:PTHR12487,SMART_domains:SM00389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCCGGCAGT	.	5	ESCA
PMEPA1	0	.	GRCh37	20	56226924	56226924	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*185T>A	.	.	ENST00000341744	4/4	45	39	6	22	22	0	PMEPA1,3_prime_UTR_variant,,ENST00000265626,;PMEPA1,3_prime_UTR_variant,,ENST00000341744,;PMEPA1,3_prime_UTR_variant,,ENST00000395816,;PMEPA1,3_prime_UTR_variant,,ENST00000347215,;PMEPA1,downstream_gene_variant,,ENST00000395814,;PMEPA1,downstream_gene_variant,,ENST00000395819,;PMEPA1,downstream_gene_variant,,ENST00000414037,;	T	ENSG00000124225	ENST00000341744	Transcript	3_prime_UTR_variant	1369	.	.	.	.	.	.	.	-1	PMEPA1	HGNC	14107	protein_coding	YES	CCDS13463.1	ENSP00000345826	PMEPA_HUMAN	.	UPI000004970A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTGCAAGCTC	.	3	ESCA
CDH4	0	.	GRCh37	20	60499458	60499458	+	Silent	SNP	G	G	T	rs753916349	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1695G>T	p.%3D	p.T565T	ENST00000360469	11/16	76	70	6	46	46	0	CDH4,synonymous_variant,p.%3D,ENST00000543233,;CDH4,synonymous_variant,p.%3D,ENST00000360469,;	T	ENSG00000179242	ENST00000360469	Transcript	synonymous_variant	1783	1695	565	T	acG/acT	rs753916349	.	.	1	CDH4	HGNC	1763	protein_coding	YES	CCDS13488.1	ENSP00000353656	CADH4_HUMAN	Q8ND09_HUMAN	UPI000015FE86	.	.	.	11/16	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCACGGCGGC	.	3	ESCA
C20orf166	0	.	GRCh37	20	61167653	61167653	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>A	p.%3D	p.V41V	ENST00000370527	4/4	70	63	6	51	51	0	C20orf166,synonymous_variant,p.%3D,ENST00000370524,;C20orf166,synonymous_variant,p.%3D,ENST00000370523,;C20orf166,synonymous_variant,p.%3D,ENST00000370527,;RPL7P3,upstream_gene_variant,,ENST00000441388,;	A	ENSG00000174407	ENST00000370527	Transcript	synonymous_variant	902	123	41	V	gtC/gtA	.	.	.	1	C20orf166	HGNC	16159	protein_coding	YES	CCDS46627.1	ENSP00000359558	CT166_HUMAN	.	UPI000012861B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TAGGTCAGCCC	.	3	ESCA
NKAIN4	0	.	GRCh37	20	61879034	61879034	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.367G>C	p.Gly123Arg	p.G123R	ENST00000370316	4/7	52	48	4	55	55	0	NKAIN4,missense_variant,p.Gly61Arg,ENST00000370307,;NKAIN4,missense_variant,p.Gly53Arg,ENST00000370317,;NKAIN4,missense_variant,p.Gly61Arg,ENST00000370313,;NKAIN4,missense_variant,p.Gly123Arg,ENST00000370316,;NKAIN4,non_coding_transcript_exon_variant,,ENST00000466885,;NKAIN4,downstream_gene_variant,,ENST00000472670,;NKAIN4,upstream_gene_variant,,ENST00000470246,;NKAIN4,non_coding_transcript_exon_variant,,ENST00000461738,;NKAIN4,non_coding_transcript_exon_variant,,ENST00000486495,;	G	ENSG00000101198	ENST00000370316	Transcript	missense_variant	457	367	123	G/R	Ggc/Cgc	.	.	.	-1	NKAIN4	HGNC	16191	protein_coding	YES	CCDS13514.1	ENSP00000359340	NKAI4_HUMAN	A6NNM2_HUMAN	UPI000013C71B	.	tolerated(0.55)	benign(0.202)	4/7	.	Pfam_domain:PF05640,hmmpanther:PTHR13084:SF5,hmmpanther:PTHR13084	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGGCCCACTG	.	3	ESCA
RTEL1	0	.	GRCh37	20	62309668	62309668	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1078G>C	p.Gly360Arg	p.G360R	ENST00000508582	12/35	66	58	8	49	49	0	RTEL1,missense_variant,p.Gly336Arg,ENST00000370018,;RTEL1,missense_variant,p.Gly336Arg,ENST00000360203,;RTEL1,missense_variant,p.Gly360Arg,ENST00000508582,;RTEL1,missense_variant,p.Gly336Arg,ENST00000318100,;RTEL1,downstream_gene_variant,,ENST00000356810,;RTEL1,downstream_gene_variant,,ENST00000463361,;RTEL1-TNFRSF6B,missense_variant,p.Gly364Arg,ENST00000492259,;RTEL1-TNFRSF6B,missense_variant,p.Gly336Arg,ENST00000482936,;	C	ENSG00000258366	ENST00000508582	Transcript	missense_variant	1424	1078	360	G/R	Gga/Cga	.	.	.	1	RTEL1	HGNC	15888	protein_coding	YES	CCDS13530.3	ENSP00000424307	RTEL1_HUMAN	.	UPI00019B2219	.	tolerated(0.05)	possibly_damaging(0.859)	12/35	.	hmmpanther:PTHR11472:SF4,hmmpanther:PTHR11472	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE|VARSCANS	TGCCTGGAGAC	.	3	ESCA
NPBWR2	0	.	GRCh37	20	62737512	62737512	+	Missense_Mutation	SNP	C	C	G	rs75874947	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673G>C	p.Val225Leu	p.V225L	ENST00000369768	1/1	55	46	8	47	47	0	NPBWR2,missense_variant,p.Val225Leu,ENST00000369768,;	G	ENSG00000125522	ENST00000369768	Transcript	missense_variant	1013	673	225	V/L	Gtg/Ctg	rs75874947	.	.	-1	NPBWR2	HGNC	4530	protein_coding	YES	CCDS13557.1	ENSP00000358783	NPBW2_HUMAN	.	UPI000013CBB3	.	tolerated(0.11)	benign(0.168)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229:SF18,hmmpanther:PTHR24229,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	T:0.0058	T:0	T:0	.	T:0.0288	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	GCACACGGGCA	byFrequency|byCluster|by1000G	3	ESCA
PLCB1	0	.	GRCh37	20	8865325	8865325	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2829G>T	.	.	ENST00000338037	32/32	79	71	7	65	65	0	PLCB1,3_prime_UTR_variant,,ENST00000378641,;PLCB1,3_prime_UTR_variant,,ENST00000338037,;PLCB1,intron_variant,,ENST00000487210,;	T	ENSG00000182621	ENST00000338037	Transcript	3_prime_UTR_variant	6507	.	.	.	.	.	.	.	1	PLCB1	HGNC	15917	protein_coding	YES	CCDS13102.1	ENSP00000338185	PLCB1_HUMAN	.	UPI0000131A8F	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGACGTTGTG	.	4	ESCA
SCAF4	0	.	GRCh37	21	33060625	33060625	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2038C>G	p.Pro680Ala	p.P680A	ENST00000286835	16/20	119	111	8	119	119	0	SCAF4,missense_variant,p.Pro680Ala,ENST00000399804,;SCAF4,missense_variant,p.Pro680Ala,ENST00000286835,;SCAF4,missense_variant,p.Pro665Ala,ENST00000434667,;SCAF4,non_coding_transcript_exon_variant,,ENST00000467731,;SCAF4,downstream_gene_variant,,ENST00000472318,;	C	ENSG00000156304	ENST00000286835	Transcript	missense_variant	2421	2038	680	P/A	Cca/Gca	.	.	.	-1	SCAF4	HGNC	19304	protein_coding	YES	CCDS33537.1	ENSP00000286835	SFR15_HUMAN	Q0P607_HUMAN	UPI0000206D66	.	.	unknown(0)	16/20	.	Prints_domain:PR01217,hmmpanther:PTHR14124,hmmpanther:PTHR14124:SF2,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTGGAGGTG	.	2	ESCA
SYNJ1	0	.	GRCh37	21	34003657	34003657	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4487C>G	p.Ser1496Ter	p.S1496*	ENST00000433931	32/32	88	83	5	88	88	0	SYNJ1,stop_gained,p.Ser1410Ter,ENST00000382491,;SYNJ1,stop_gained,p.Ser1457Ter,ENST00000322229,;SYNJ1,stop_gained,p.Ser1496Ter,ENST00000433931,;SYNJ1,3_prime_UTR_variant,,ENST00000382499,;SYNJ1,3_prime_UTR_variant,,ENST00000438952,;SYNJ1,3_prime_UTR_variant,,ENST00000357345,;SYNJ1,downstream_gene_variant,,ENST00000418301,;	C	ENSG00000159082	ENST00000433931	Transcript	stop_gained	4495	4487	1496	S/*	tCa/tGa	.	.	.	-1	SYNJ1	HGNC	11503	protein_coding	YES	CCDS33539.2	ENSP00000409667	.	J3KQV8_HUMAN,C9J1Z6_HUMAN	UPI0001A47572	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAGTGAAGAT	.	2	ESCA
LCA5L	0	.	GRCh37	21	40777894	40777894	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1927C>A	p.His643Asn	p.H643N	ENST00000358268	10/10	123	116	7	117	117	0	LCA5L,missense_variant,p.His643Asn,ENST00000288350,;WRB,missense_variant,p.Trp77Leu,ENST00000415847,;LCA5L,missense_variant,p.His643Asn,ENST00000380671,;LCA5L,missense_variant,p.His643Asn,ENST00000358268,;WRB,intron_variant,,ENST00000541890,;LCA5L,downstream_gene_variant,,ENST00000495240,;WRB,upstream_gene_variant,,ENST00000478273,;	T	ENSG00000157578	ENST00000358268	Transcript	missense_variant	2456	1927	643	H/N	Cat/Aat	.	.	.	-1	LCA5L	HGNC	1255	protein_coding	YES	CCDS13665.1	ENSP00000351008	LCA5L_HUMAN	C9JYR0_HUMAN,C9JRD7_HUMAN,C9JIJ8_HUMAN,C9JFB6_HUMAN,C9J9Z3_HUMAN,C9J5D2_HUMAN,C9J293_HUMAN,C9J198_HUMAN	UPI00000015EE	.	tolerated(1)	benign(0)	10/10	.	hmmpanther:PTHR16650:SF9,hmmpanther:PTHR16650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCATGGCTGG	.	2	ESCA
IGLV3-19	0	.	GRCh37	22	23063527	23063527	+	Missense_Mutation	SNP	C	C	G	rs567862059	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234C>G	p.Asp78Glu	p.D78E	ENST00000390309	2/2	98	90	8	83	83	0	IGLV3-19,missense_variant,p.Asp78Glu,ENST00000390309,;	G	ENSG00000211663	ENST00000390309	Transcript	missense_variant	274	234	78	D/E	gaC/gaG	rs567862059	.	.	1	IGLV3-19	HGNC	5903	IG_V_gene	YES	.	ENSP00000374844	.	.	UPI000173A2CD	.	tolerated(0.6)	benign(0.026)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF51,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCAGACCGATT	by1000G	3	ESCA
DEPDC5	0	.	GRCh37	22	32293528	32293528	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4237G>T	p.Gly1413Trp	p.G1413W	ENST00000382112	39/42	63	59	4	49	49	0	DEPDC5,missense_variant,p.Gly1400Trp,ENST00000266091,;DEPDC5,missense_variant,p.Gly1391Trp,ENST00000400248,;DEPDC5,missense_variant,p.Gly1413Trp,ENST00000382112,;DEPDC5,missense_variant,p.Gly1422Trp,ENST00000400246,;DEPDC5,missense_variant,p.Gly1422Trp,ENST00000382111,;DEPDC5,missense_variant,p.Gly798Trp,ENST00000433147,;DEPDC5,missense_variant,p.Gly1322Trp,ENST00000535622,;DEPDC5,missense_variant,p.Gly239Trp,ENST00000539165,;DEPDC5,missense_variant,p.Gly1391Trp,ENST00000400249,;DEPDC5,3_prime_UTR_variant,,ENST00000382105,;DEPDC5,upstream_gene_variant,,ENST00000497340,;DEPDC5,3_prime_UTR_variant,,ENST00000448753,;	T	ENSG00000100150	ENST00000382112	Transcript	missense_variant	4307	4237	1413	G/W	Ggg/Tgg	.	.	.	1	DEPDC5	HGNC	18423	protein_coding	YES	CCDS46692.1	ENSP00000371546	DEPD5_HUMAN	C9JGS4_HUMAN,B4DGG3_HUMAN	UPI00004708D5	.	deleterious(0.03)	probably_damaging(0.927)	39/42	.	hmmpanther:PTHR13179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAGGGGCCT	.	2	ESCA
NPTXR	0	.	GRCh37	22	39222664	39222664	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.939G>T	p.%3D	p.L313L	ENST00000333039	3/5	49	43	6	31	31	0	NPTXR,synonymous_variant,p.%3D,ENST00000333039,;	A	ENSG00000221890	ENST00000333039	Transcript	synonymous_variant	1063	939	313	L	ctG/ctT	.	.	.	-1	NPTXR	HGNC	7954	protein_coding	YES	CCDS33647.1	ENSP00000327545	NPTXR_HUMAN	.	UPI00001B0258	.	.	.	3/5	.	hmmpanther:PTHR19277:SF94,hmmpanther:PTHR19277,Pfam_domain:PF00354,Gene3D:2.60.120.200,SMART_domains:SM00159,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TCGGGCAGAGC	.	2	ESCA
TAB1	0	.	GRCh37	22	39815583	39815583	+	Missense_Mutation	SNP	C	C	T	rs745450445	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724C>T	p.Arg242Trp	p.R242W	ENST00000216160	7/11	70	62	8	74	74	0	TAB1,missense_variant,p.Arg242Trp,ENST00000331454,;TAB1,missense_variant,p.Arg242Trp,ENST00000216160,;TAB1,downstream_gene_variant,,ENST00000461775,;TAB1,downstream_gene_variant,,ENST00000473613,;TAB1,upstream_gene_variant,,ENST00000473491,;TAB1,downstream_gene_variant,,ENST00000490819,;	T	ENSG00000100324	ENST00000216160	Transcript	missense_variant	786	724	242	R/W	Cgg/Tgg	rs745450445	.	.	1	TAB1	HGNC	18157	protein_coding	YES	CCDS13993.1	ENSP00000216160	TAB1_HUMAN	B7Z9N9_HUMAN,A8K6K3_HUMAN	UPI0000136861	.	deleterious(0.02)	probably_damaging(0.995)	7/11	.	hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF250,Gene3D:3.60.40.10,Pfam_domain:PF00481,SMART_domains:SM00332,Superfamily_domains:SSF81606	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCGGCGGATC	byFrequency|byCluster	4	ESCA
AFF3	0	.	GRCh37	2	100266105	100266105	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1242C>A	p.%3D	p.L414L	ENST00000356421	12/24	115	100	15	80	79	1	AFF3,synonymous_variant,p.%3D,ENST00000409579,;AFF3,synonymous_variant,p.%3D,ENST00000356421,;AFF3,synonymous_variant,p.%3D,ENST00000317233,;AFF3,synonymous_variant,p.%3D,ENST00000409236,;AFF3,synonymous_variant,p.%3D,ENST00000430789,;	T	ENSG00000144218	ENST00000356421	Transcript	synonymous_variant	1386	1242	414	L	ctC/ctA	.	.	.	-1	AFF3	HGNC	6473	protein_coding	YES	CCDS33258.1	ENSP00000348793	AFF3_HUMAN	.	UPI000041098C	.	.	.	12/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R415C|c.1243C>T|3	RADIA|MUTECT|MUSE|VARSCANS	GCGCGGAGAGC	.	4	ESCA
TMEM182	0	.	GRCh37	2	103431207	103431207	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470G>T	p.Gly157Val	p.G157V	ENST00000412401	5/5	69	61	8	48	48	0	TMEM182,missense_variant,p.Gly157Val,ENST00000412401,;TMEM182,missense_variant,p.Gly61Val,ENST00000409528,;TMEM182,missense_variant,p.Gly114Val,ENST00000409173,;TMEM182,splice_region_variant,,ENST00000488134,;TMEM182,intron_variant,,ENST00000486293,;TMEM182,splice_region_variant,,ENST00000484094,;	T	ENSG00000170417	ENST00000412401	Transcript	missense_variant	675	470	157	G/V	gGc/gTc	.	.	.	1	TMEM182	HGNC	26391	protein_coding	YES	CCDS2064.1	ENSP00000394178	TM182_HUMAN	.	UPI0000366F4E	.	deleterious(0)	probably_damaging(0.969)	5/5	.	Pfam_domain:PF13903,hmmpanther:PTHR32012,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAGGCATCC	.	4	ESCA
E2F6	0	.	GRCh37	2	11591836	11591836	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.477G>T	p.Glu159Asp	p.E159D	ENST00000381525	4/7	75	66	9	48	48	0	E2F6,missense_variant,p.Glu84Asp,ENST00000542100,;E2F6,missense_variant,p.Glu127Asp,ENST00000307236,;E2F6,missense_variant,p.Glu84Asp,ENST00000546212,;E2F6,missense_variant,p.Glu159Asp,ENST00000381525,;E2F6,intron_variant,,ENST00000362009,;E2F6,3_prime_UTR_variant,,ENST00000421117,;E2F6,3_prime_UTR_variant,,ENST00000444832,;E2F6,3_prime_UTR_variant,,ENST00000428221,;E2F6,3_prime_UTR_variant,,ENST00000437573,;E2F6,3_prime_UTR_variant,,ENST00000455198,;E2F6,non_coding_transcript_exon_variant,,ENST00000468775,;E2F6,upstream_gene_variant,,ENST00000471343,;	A	ENSG00000169016	ENST00000381525	Transcript	missense_variant	747	477	159	E/D	gaG/gaT	.	.	.	-1	E2F6	HGNC	3120	protein_coding	YES	CCDS1680.2	ENSP00000370936	E2F6_HUMAN	Q6Q9Z5_HUMAN,Q53YM3_HUMAN	UPI0000000C90	.	tolerated(0.1)	benign(0.411)	4/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF19,Superfamily_domains:SSF144074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTAACTCATC	.	4	ESCA
SMPD4	0	.	GRCh37	2	130909684	130909684	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*444G>C	.	.	ENST00000409031	20/20	134	127	6	119	119	0	SMPD4,3_prime_UTR_variant,,ENST00000439886,;SMPD4,3_prime_UTR_variant,,ENST00000453750,;SMPD4,3_prime_UTR_variant,,ENST00000351288,;SMPD4,3_prime_UTR_variant,,ENST00000409031,;SMPD4,3_prime_UTR_variant,,ENST00000443958,;SMPD4,3_prime_UTR_variant,,ENST00000431183,;SMPD4,downstream_gene_variant,,ENST00000339679,;SMPD4,downstream_gene_variant,,ENST00000430682,;SMPD4,downstream_gene_variant,,ENST00000452225,;SMPD4,downstream_gene_variant,,ENST00000449159,;SMPD4,downstream_gene_variant,,ENST00000457039,;SMPD4,downstream_gene_variant,,ENST00000451542,;SMPD4,downstream_gene_variant,,ENST00000426662,;SMPD4,downstream_gene_variant,,ENST00000455548,;SMPD4,downstream_gene_variant,,ENST00000473720,;SMPD4,3_prime_UTR_variant,,ENST00000433118,;SMPD4,3_prime_UTR_variant,,ENST00000454468,;SMPD4,3_prime_UTR_variant,,ENST00000412570,;SMPD4,non_coding_transcript_exon_variant,,ENST00000491128,;SMPD4,non_coding_transcript_exon_variant,,ENST00000482171,;SMPD4,downstream_gene_variant,,ENST00000435455,;SMPD4,downstream_gene_variant,,ENST00000461187,;SMPD4,downstream_gene_variant,,ENST00000491319,;	G	ENSG00000136699	ENST00000409031	Transcript	3_prime_UTR_variant	4194	.	.	.	.	.	.	.	-1	SMPD4	HGNC	32949	protein_coding	YES	CCDS42751.1	ENSP00000386531	.	C9J647_HUMAN,B1PBA3_HUMAN	UPI000036FC5A	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTCCTGGTC	.	2	ESCA
TUBA3D	0	.	GRCh37	2	132235781	132235781	+	Silent	SNP	C	C	T	rs767332287	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.48C>T	p.%3D	p.I16I	ENST00000321253	2/5	152	140	11	127	127	0	TUBA3D,synonymous_variant,p.%3D,ENST00000321253,;TUBA3D,upstream_gene_variant,,ENST00000409047,;MZT2A,intron_variant,,ENST00000445782,;MZT2A,intron_variant,,ENST00000427024,;	T	ENSG00000075886	ENST00000321253	Transcript	synonymous_variant	155	48	16	I	atC/atT	rs767332287	.	.	1	TUBA3D	HGNC	24071	protein_coding	YES	CCDS33290.1	ENSP00000326042	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	.	.	2/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Pfam_domain:PF00091,Gene3D:3.40.50.1440,Superfamily_domains:SSF52490,Prints_domain:PR01161	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATCGGCAA	byFrequency	2	ESCA
CCNT2	0	.	GRCh37	2	135705377	135705377	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.611G>T	p.Cys204Phe	p.C204F	ENST00000264157	7/9	89	80	9	61	61	0	CCNT2,missense_variant,p.Cys204Phe,ENST00000264157,;CCNT2,missense_variant,p.Cys204Phe,ENST00000295238,;CCNT2,missense_variant,p.Cys45Phe,ENST00000446247,;CCNT2,missense_variant,p.Cys27Phe,ENST00000452521,;CCNT2,missense_variant,p.Cys29Phe,ENST00000537343,;CCNT2,upstream_gene_variant,,ENST00000438691,;CCNT2,3_prime_UTR_variant,,ENST00000452839,;CCNT2,3_prime_UTR_variant,,ENST00000419781,;CCNT2,downstream_gene_variant,,ENST00000417175,;	T	ENSG00000082258	ENST00000264157	Transcript	missense_variant	641	611	204	C/F	tGc/tTc	.	.	.	1	CCNT2	HGNC	1600	protein_coding	YES	CCDS2174.1	ENSP00000264157	CCNT2_HUMAN	.	UPI000013E228	.	deleterious(0)	probably_damaging(0.999)	7/9	.	hmmpanther:PTHR10026:SF43,hmmpanther:PTHR10026,SMART_domains:SM00385,Superfamily_domains:SSF47954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTTGCAAAT	.	4	ESCA
R3HDM1	0	.	GRCh37	2	136482543	136482543	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*681G>A	.	.	ENST00000264160	26/26	34	31	3	22	22	0	R3HDM1,3_prime_UTR_variant,,ENST00000429703,;R3HDM1,3_prime_UTR_variant,,ENST00000409478,;R3HDM1,3_prime_UTR_variant,,ENST00000264160,;R3HDM1,3_prime_UTR_variant,,ENST00000410054,;R3HDM1,3_prime_UTR_variant,,ENST00000329971,;R3HDM1,downstream_gene_variant,,ENST00000445855,;R3HDM1,downstream_gene_variant,,ENST00000409606,;R3HDM1,downstream_gene_variant,,ENST00000483065,;	A	ENSG00000048991	ENST00000264160	Transcript	3_prime_UTR_variant	4351	.	.	.	.	.	.	.	1	R3HDM1	HGNC	9757	protein_coding	YES	CCDS2177.1	ENSP00000264160	R3HD1_HUMAN	Q53SQ1_HUMAN,Q4ZG59_HUMAN	UPI000007456C	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCAGGAAAA	.	2	ESCA
LRP1B	0	.	GRCh37	2	140990291	140990291	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*464C>G	.	.	ENST00000389484	91/91	58	52	6	35	35	0	LRP1B,3_prime_UTR_variant,,ENST00000389484,;LRP1B,3_prime_UTR_variant,,ENST00000437977,;	C	ENSG00000168702	ENST00000389484	Transcript	3_prime_UTR_variant	15236	.	.	.	.	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	91/91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTATGGGCACA	.	3	ESCA
LRP1B	0	.	GRCh37	2	141128402	141128402	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10885G>T	p.Val3629Leu	p.V3629L	ENST00000389484	71/91	95	87	8	55	55	0	LRP1B,missense_variant,p.Val3629Leu,ENST00000389484,;	A	ENSG00000168702	ENST00000389484	Transcript	missense_variant	11857	10885	3629	V/L	Gtg/Ttg	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	benign(0.097)	71/91	.	PROSITE_profiles:PS50068,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTCACACAGT	.	2	ESCA
SLC4A10	0	.	GRCh37	2	162480885	162480885	+	5'Flank	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000446997	.	91	84	7	77	77	0	SLC4A10,5_prime_UTR_variant,,ENST00000415876,;SLC4A10,5_prime_UTR_variant,,ENST00000375514,;SLC4A10,upstream_gene_variant,,ENST00000446997,;SLC4A10,upstream_gene_variant,,ENST00000421911,;SLC4A10,upstream_gene_variant,,ENST00000272716,;SLC4A10,upstream_gene_variant,,ENST00000535165,;SLC4A10,non_coding_transcript_exon_variant,,ENST00000605990,;SLC4A10,intron_variant,,ENST00000606386,;SLC4A10,intron_variant,,ENST00000482861,;SLC4A10,upstream_gene_variant,,ENST00000481721,;SLC4A10,upstream_gene_variant,,ENST00000461456,;SLC4A10,upstream_gene_variant,,ENST00000493021,;SLC4A10,upstream_gene_variant,,ENST00000446228,;	A	ENSG00000144290	ENST00000446997	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	51	1	SLC4A10	HGNC	13811	protein_coding	YES	CCDS54411.1	ENSP00000393066	S4A10_HUMAN	.	UPI00001D4707	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCATGTGACT	.	2	ESCA
SCN1A	0	.	GRCh37	2	166847874	166847874	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5911G>T	p.Glu1971Ter	p.E1971*	ENST00000303395	26/26	80	72	8	72	72	0	SCN1A,stop_gained,p.Glu1943Ter,ENST00000409050,;SCN1A,stop_gained,p.Glu1971Ter,ENST00000423058,;SCN1A,stop_gained,p.Glu1971Ter,ENST00000303395,;SCN1A,stop_gained,p.Glu1960Ter,ENST00000375405,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000597623,;SCN1A,downstream_gene_variant,,ENST00000473295,;	A	ENSG00000144285	ENST00000303395	Transcript	stop_gained	5911	5911	1971	E/*	Gaa/Taa	.	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	.	.	26/26	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF133,Prints_domain:PR01664	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTTTTCTGTAA	.	3	ESCA
SCN1A	0	.	GRCh37	2	166848261	166848261	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5524C>G	p.Pro1842Ala	p.P1842A	ENST00000303395	26/26	67	63	4	57	57	0	SCN1A,missense_variant,p.Pro1814Ala,ENST00000409050,;SCN1A,missense_variant,p.Pro1842Ala,ENST00000423058,;SCN1A,missense_variant,p.Pro1842Ala,ENST00000303395,;SCN1A,missense_variant,p.Pro1831Ala,ENST00000375405,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000597623,;SCN1A,downstream_gene_variant,,ENST00000473295,;	C	ENSG00000144285	ENST00000303395	Transcript	missense_variant	5524	5524	1842	P/A	Cca/Gca	.	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	tolerated(0.7)	benign(0.002)	26/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF133	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGTGGCAGAT	.	2	ESCA
XIRP2	0	.	GRCh37	2	168102950	168102950	+	Missense_Mutation	SNP	A	A	T	rs749762545	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5048A>T	p.Glu1683Val	p.E1683V	ENST00000409195	9/11	42	38	4	32	32	0	XIRP2,missense_variant,p.Glu1461Val,ENST00000409273,;XIRP2,missense_variant,p.Glu1683Val,ENST00000409195,;XIRP2,missense_variant,p.Glu1683Val,ENST00000295237,;XIRP2,intron_variant,,ENST00000409605,;XIRP2,intron_variant,,ENST00000420519,;XIRP2,intron_variant,,ENST00000409756,;XIRP2,intron_variant,,ENST00000409043,;XIRP2,intron_variant,,ENST00000409728,;	T	ENSG00000163092	ENST00000409195	Transcript	missense_variant	5137	5048	1683	E/V	gAa/gTa	rs749762545	.	.	1	XIRP2	HGNC	14303	protein_coding	YES	CCDS42769.1	ENSP00000386840	.	J3KNB1_HUMAN	UPI0000E9BBED	.	.	probably_damaging(1)	9/11	.	hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGATGAAAAAG	.	3	ESCA
HOXD9	0	.	GRCh37	2	176989292	176989292	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*389C>T	.	.	ENST00000249499	2/2	111	106	5	73	73	0	HOXD9,3_prime_UTR_variant,,ENST00000249499,;HOXD10,downstream_gene_variant,,ENST00000249501,;HOXD-AS2,intron_variant,,ENST00000440016,;	T	ENSG00000128709	ENST00000249499	Transcript	3_prime_UTR_variant	1857	.	.	.	.	.	.	.	1	HOXD9	HGNC	5140	protein_coding	YES	CCDS2267.2	ENSP00000249499	HXD9_HUMAN	.	UPI000004A10E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTGCCCAAAC	.	2	ESCA
TTN	0	.	GRCh37	2	179479481	179479481	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.48761-1G>C	.	p.X16254_splice	ENST00000589042	.	50	47	3	27	27	0	TTN,splice_acceptor_variant,,ENST00000359218,;TTN,splice_acceptor_variant,,ENST00000591111,;TTN,splice_acceptor_variant,,ENST00000589042,;TTN,splice_acceptor_variant,,ENST00000342992,;TTN,splice_acceptor_variant,,ENST00000342175,;TTN,splice_acceptor_variant,,ENST00000460472,;RP11-171I2.4,upstream_gene_variant,,ENST00000605334,;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000589234,;TTN-AS1,upstream_gene_variant,,ENST00000604956,;	G	ENSG00000155657	ENST00000589042	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	.	260/362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCTCTGAAT	.	2	ESCA
NT5C1B	0	.	GRCh37	2	18766134	18766134	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549C>G	p.%3D	p.P183P	ENST00000359846	5/10	197	187	9	111	111	0	NT5C1B,synonymous_variant,p.%3D,ENST00000359846,;NT5C1B,synonymous_variant,p.%3D,ENST00000304081,;NT5C1B,synonymous_variant,p.%3D,ENST00000600945,;NT5C1B-RDH14,synonymous_variant,p.%3D,ENST00000532967,;NT5C1B,synonymous_variant,p.%3D,ENST00000416783,;NT5C1B-RDH14,synonymous_variant,p.%3D,ENST00000444297,;NT5C1B,upstream_gene_variant,,ENST00000418427,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,downstream_gene_variant,,ENST00000460052,;NT5C1B,missense_variant,p.Pro101Arg,ENST00000406971,;NT5C1B,non_coding_transcript_exon_variant,,ENST00000490687,;	C	ENSG00000185013	ENST00000359846	Transcript	synonymous_variant	627	549	183	P	ccC/ccG	.	.	.	-1	NT5C1B	HGNC	17818	protein_coding	YES	CCDS33150.1	ENSP00000352904	5NT1B_HUMAN	B4DZ86_HUMAN	UPI000035B1B0	.	.	.	5/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTGGGGCGA	.	2	ESCA
RAPH1	0	.	GRCh37	2	204304271	204304271	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3642G>A	p.%3D	p.Q1214Q	ENST00000319170	14/14	75	71	4	47	47	0	RAPH1,synonymous_variant,p.%3D,ENST00000374493,;RAPH1,synonymous_variant,p.%3D,ENST00000319170,;ABI2,3_prime_UTR_variant,,ENST00000295851,;RAPH1,intron_variant,,ENST00000457812,;RAPH1,downstream_gene_variant,,ENST00000423104,;RAPH1,downstream_gene_variant,,ENST00000419464,;RAPH1,downstream_gene_variant,,ENST00000374488,;RAPH1,downstream_gene_variant,,ENST00000439222,;RAPH1,downstream_gene_variant,,ENST00000374489,;RAPH1,downstream_gene_variant,,ENST00000308091,;ABI2,downstream_gene_variant,,ENST00000464761,;	T	ENSG00000173166	ENST00000319170	Transcript	synonymous_variant	3942	3642	1214	Q	caG/caA	COSM3798539	.	.	-1	RAPH1	HGNC	14436	protein_coding	YES	CCDS2359.1	ENSP00000316543	RAPH1_HUMAN	C9JLG4_HUMAN	UPI000020940F	.	.	.	14/14	.	hmmpanther:PTHR11243,hmmpanther:PTHR11243:SF15	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCTGTTG	.	2	ESCA
APOB	0	.	GRCh37	2	21230801	21230801	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8939C>G	p.Ser2980Cys	p.S2980C	ENST00000233242	26/29	65	58	7	76	76	0	APOB,missense_variant,p.Ser2980Cys,ENST00000233242,;	C	ENSG00000084674	ENST00000233242	Transcript	missense_variant	9067	8939	2980	S/C	tCc/tGc	COSM1183244	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	benign(0.174)	26/29	.	hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.S2980F|c.8939C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TGAGGGAGCCA	.	4	ESCA
CDK5R2	0	.	GRCh37	2	219825902	219825902	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*256C>G	.	.	ENST00000302625	1/1	67	58	8	57	57	0	CDK5R2,3_prime_UTR_variant,,ENST00000302625,;AC097468.7,intron_variant,,ENST00000429343,;	G	ENSG00000171450	ENST00000302625	Transcript	3_prime_UTR_variant	1526	.	.	.	.	.	.	.	1	CDK5R2	HGNC	1776	protein_coding	YES	CCDS2427.1	ENSP00000304250	CD5R2_HUMAN	Q96G76_HUMAN	UPI000012738F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTGCGCCCC	.	4	ESCA
SERPINE2	0	.	GRCh37	2	224866556	224866556	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.98A>T	p.His33Leu	p.H33L	ENST00000447280	2/9	58	50	7	59	59	0	SERPINE2,missense_variant,p.His21Leu,ENST00000432738,;SERPINE2,missense_variant,p.His21Leu,ENST00000423446,;SERPINE2,missense_variant,p.His21Leu,ENST00000409304,;SERPINE2,missense_variant,p.His21Leu,ENST00000454956,;SERPINE2,missense_variant,p.His21Leu,ENST00000409840,;SERPINE2,missense_variant,p.His33Leu,ENST00000447280,;SERPINE2,missense_variant,p.His21Leu,ENST00000258405,;SERPINE2,non_coding_transcript_exon_variant,,ENST00000489065,;	A	ENSG00000135919	ENST00000447280	Transcript	missense_variant	399	98	33	H/L	cAc/cTc	.	.	.	-1	SERPINE2	HGNC	8951	protein_coding	YES	CCDS46525.1	ENSP00000415786	GDN_HUMAN	C9K031_HUMAN,C9JRK5_HUMAN,C9JN98_HUMAN,B4DMR3_HUMAN	UPI00017A7317	.	tolerated(0.39)	benign(0.001)	2/9	.	hmmpanther:PTHR11461:SF48,hmmpanther:PTHR11461	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAAGTGGGAG	.	4	ESCA
SPHKAP	0	.	GRCh37	2	228883671	228883671	+	Nonsense_Mutation	SNP	G	G	T	rs748165969	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1899C>A	p.Tyr633Ter	p.Y633*	ENST00000392056	7/12	46	41	5	44	44	0	SPHKAP,stop_gained,p.Tyr633Ter,ENST00000344657,;SPHKAP,stop_gained,p.Tyr633Ter,ENST00000392056,;	T	ENSG00000153820	ENST00000392056	Transcript	stop_gained	1946	1899	633	Y/*	taC/taA	rs748165969	.	.	-1	SPHKAP	HGNC	30619	protein_coding	YES	CCDS46537.1	ENSP00000375909	SPKAP_HUMAN	.	UPI0000411D7E	.	.	.	7/12	.	hmmpanther:PTHR10226,hmmpanther:PTHR10226:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CTGCTGTAGGT	.	2	ESCA
LRRFIP1	0	.	GRCh37	2	238688092	238688092	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1840G>C	p.Glu614Gln	p.E614Q	ENST00000308482	24/24	74	68	6	61	61	0	LRRFIP1,missense_variant,p.Glu614Gln,ENST00000308482,;LRRFIP1,intron_variant,,ENST00000489603,;LRRFIP1,non_coding_transcript_exon_variant,,ENST00000478958,;LRRFIP1,non_coding_transcript_exon_variant,,ENST00000474195,;LRRFIP1,non_coding_transcript_exon_variant,,ENST00000464608,;	C	ENSG00000124831	ENST00000308482	Transcript	missense_variant	1909	1840	614	E/Q	Gag/Cag	.	.	.	1	LRRFIP1	HGNC	6702	protein_coding	.	CCDS46551.1	ENSP00000310109	LRRF1_HUMAN	Q9BSL6_HUMAN	UPI000155D57C	.	deleterious(0)	possibly_damaging(0.682)	24/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19212:SF1,hmmpanther:PTHR19212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGAAGAGCTC	.	3	ESCA
HDAC4	0	.	GRCh37	2	240002840	240002840	+	Missense_Mutation	SNP	C	C	A	rs759772566	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2686G>T	p.Gly896Cys	p.G896C	ENST00000345617	22/27	111	99	11	90	90	0	HDAC4,missense_variant,p.Gly480Cys,ENST00000543185,;HDAC4,missense_variant,p.Gly896Cys,ENST00000345617,;MIR4441,downstream_gene_variant,,ENST00000582623,;AC017028.8,downstream_gene_variant,,ENST00000582701,;HDAC4,upstream_gene_variant,,ENST00000494800,;HDAC4,non_coding_transcript_exon_variant,,ENST00000487617,;	A	ENSG00000068024	ENST00000345617	Transcript	missense_variant	3478	2686	896	G/C	Ggc/Tgc	rs759772566,COSM3728097	.	.	-1	HDAC4	HGNC	14063	protein_coding	YES	CCDS2529.1	ENSP00000264606	HDAC4_HUMAN	Q53SM2_HUMAN,Q53SB4_HUMAN,F5H0B1_HUMAN,F5GX36_HUMAN,C9J0X4_HUMAN	UPI000013D541	.	deleterious(0)	probably_damaging(0.998)	22/27	.	hmmpanther:PTHR10625:SF100,hmmpanther:PTHR10625,Pfam_domain:PF00850,Gene3D:3.40.800.20,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCGCCGGTGA	byFrequency	4	ESCA
KIF1A	0	.	GRCh37	2	241656652	241656652	+	3'UTR	SNP	C	C	A	rs779232085	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*129G>T	.	.	ENST00000498729	49/50	88	82	5	78	77	1	KIF1A,3_prime_UTR_variant,,ENST00000498729,;KIF1A,3_prime_UTR_variant,,ENST00000320389,;KIF1A,non_coding_transcript_exon_variant,,ENST00000460788,;KIF1A,non_coding_transcript_exon_variant,,ENST00000492812,;KIF1A,downstream_gene_variant,,ENST00000465813,;KIF1A,downstream_gene_variant,,ENST00000488776,;	A	ENSG00000130294	ENST00000498729	Transcript	3_prime_UTR_variant	5752	.	.	.	.	rs779232085	.	.	-1	KIF1A	HGNC	888	protein_coding	YES	CCDS58757.1	ENSP00000438388	KIF1A_HUMAN	G1UI30_HUMAN,C9JBH1_HUMAN	UPI0002065B81	.	.	.	49/50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGGCGTCCC	.	2	ESCA
PPP1R7	0	.	GRCh37	2	242122273	242122273	+	3'UTR	SNP	G	G	T	rs764144527	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*35G>T	.	.	ENST00000234038	10/10	44	41	3	48	48	0	PPP1R7,3_prime_UTR_variant,,ENST00000234038,;PPP1R7,3_prime_UTR_variant,,ENST00000272983,;PPP1R7,3_prime_UTR_variant,,ENST00000407025,;PPP1R7,intron_variant,,ENST00000415769,;PPP1R7,downstream_gene_variant,,ENST00000450367,;PPP1R7,downstream_gene_variant,,ENST00000423280,;PPP1R7,downstream_gene_variant,,ENST00000491715,;	T	ENSG00000115685	ENST00000234038	Transcript	3_prime_UTR_variant	1592	.	.	.	.	rs764144527	.	.	1	PPP1R7	HGNC	9295	protein_coding	YES	CCDS2546.1	ENSP00000234038	PP1R7_HUMAN	.	UPI000006E65A	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTCGGAAGA	byFrequency	2	ESCA
HDLBP	0	.	GRCh37	2	242187659	242187659	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1617G>A	p.%3D	p.E539E	ENST00000391975	13/28	105	98	6	66	66	0	HDLBP,synonymous_variant,p.%3D,ENST00000310931,;HDLBP,synonymous_variant,p.%3D,ENST00000427183,;HDLBP,synonymous_variant,p.%3D,ENST00000373292,;HDLBP,synonymous_variant,p.%3D,ENST00000391976,;HDLBP,synonymous_variant,p.%3D,ENST00000452931,;HDLBP,synonymous_variant,p.%3D,ENST00000391975,;HDLBP,downstream_gene_variant,,ENST00000453141,;HDLBP,upstream_gene_variant,,ENST00000427487,;AC104841.1,upstream_gene_variant,,ENST00000578965,;HDLBP,upstream_gene_variant,,ENST00000471294,;HDLBP,downstream_gene_variant,,ENST00000477477,;HDLBP,downstream_gene_variant,,ENST00000476807,;HDLBP,splice_region_variant,,ENST00000487169,;HDLBP,non_coding_transcript_exon_variant,,ENST00000498595,;HDLBP,upstream_gene_variant,,ENST00000460826,;HDLBP,downstream_gene_variant,,ENST00000467435,;HDLBP,upstream_gene_variant,,ENST00000488923,;	T	ENSG00000115677	ENST00000391975	Transcript	synonymous_variant	1845	1617	539	E	gaG/gaA	.	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	.	.	13/28	.	PROSITE_profiles:PS50084,hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTACCTCTGG	.	2	ESCA
HDLBP	0	.	GRCh37	2	242195807	242195807	+	Missense_Mutation	SNP	C	C	T	rs757592730	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.665G>A	p.Arg222His	p.R222H	ENST00000391975	7/28	60	52	8	42	42	0	HDLBP,missense_variant,p.Arg222His,ENST00000310931,;HDLBP,missense_variant,p.Arg258His,ENST00000427183,;HDLBP,missense_variant,p.Arg100His,ENST00000373292,;HDLBP,missense_variant,p.Arg222His,ENST00000422933,;HDLBP,missense_variant,p.Arg222His,ENST00000391976,;HDLBP,missense_variant,p.Arg123His,ENST00000453141,;HDLBP,missense_variant,p.Arg222His,ENST00000391975,;HDLBP,downstream_gene_variant,,ENST00000452065,;HDLBP,downstream_gene_variant,,ENST00000428482,;HDLBP,downstream_gene_variant,,ENST00000442714,;HDLBP,upstream_gene_variant,,ENST00000477477,;HDLBP,non_coding_transcript_exon_variant,,ENST00000470710,;HDLBP,upstream_gene_variant,,ENST00000498595,;HDLBP,upstream_gene_variant,,ENST00000467435,;	T	ENSG00000115677	ENST00000391975	Transcript	missense_variant	893	665	222	R/H	cGt/cAt	rs757592730	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	tolerated(0.1)	possibly_damaging(0.835)	7/28	.	PROSITE_profiles:PS50084,hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCACGTTTG	byFrequency	4	ESCA
HDLBP	0	.	GRCh37	2	242196027	242196027	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.645C>T	p.%3D	p.I215I	ENST00000391975	6/28	77	73	4	82	82	0	HDLBP,synonymous_variant,p.%3D,ENST00000310931,;HDLBP,synonymous_variant,p.%3D,ENST00000427183,;HDLBP,synonymous_variant,p.%3D,ENST00000373292,;HDLBP,synonymous_variant,p.%3D,ENST00000428482,;HDLBP,synonymous_variant,p.%3D,ENST00000422933,;HDLBP,synonymous_variant,p.%3D,ENST00000391976,;HDLBP,synonymous_variant,p.%3D,ENST00000453141,;HDLBP,synonymous_variant,p.%3D,ENST00000391975,;HDLBP,downstream_gene_variant,,ENST00000452065,;HDLBP,downstream_gene_variant,,ENST00000442714,;HDLBP,upstream_gene_variant,,ENST00000477477,;HDLBP,non_coding_transcript_exon_variant,,ENST00000470710,;HDLBP,upstream_gene_variant,,ENST00000498595,;HDLBP,upstream_gene_variant,,ENST00000467435,;	A	ENSG00000115677	ENST00000391975	Transcript	synonymous_variant	873	645	215	I	atC/atT	.	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	.	.	6/28	.	hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,SMART_domains:SM00322,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGAGATGAG	.	2	ESCA
HDLBP	0	.	GRCh37	2	242196030	242196030	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642C>T	p.%3D	p.L214L	ENST00000391975	6/28	79	74	4	82	82	0	HDLBP,synonymous_variant,p.%3D,ENST00000310931,;HDLBP,synonymous_variant,p.%3D,ENST00000427183,;HDLBP,synonymous_variant,p.%3D,ENST00000373292,;HDLBP,synonymous_variant,p.%3D,ENST00000428482,;HDLBP,synonymous_variant,p.%3D,ENST00000422933,;HDLBP,synonymous_variant,p.%3D,ENST00000391976,;HDLBP,synonymous_variant,p.%3D,ENST00000453141,;HDLBP,synonymous_variant,p.%3D,ENST00000391975,;HDLBP,downstream_gene_variant,,ENST00000452065,;HDLBP,downstream_gene_variant,,ENST00000442714,;HDLBP,upstream_gene_variant,,ENST00000477477,;HDLBP,non_coding_transcript_exon_variant,,ENST00000470710,;HDLBP,upstream_gene_variant,,ENST00000498595,;HDLBP,upstream_gene_variant,,ENST00000467435,;	A	ENSG00000115677	ENST00000391975	Transcript	synonymous_variant	870	642	214	L	ctC/ctT	.	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	.	.	6/28	.	hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,SMART_domains:SM00322,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGATGAGTAA	.	2	ESCA
ASXL2	0	.	GRCh37	2	25994388	25994388	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.425C>G	p.Ser142Ter	p.S142*	ENST00000435504	6/13	117	103	14	83	83	0	ASXL2,stop_gained,p.Ser114Ter,ENST00000336112,;ASXL2,stop_gained,p.Ser142Ter,ENST00000435504,;ASXL2,5_prime_UTR_variant,,ENST00000272341,;ASXL2,5_prime_UTR_variant,,ENST00000404843,;ASXL2,non_coding_transcript_exon_variant,,ENST00000497092,;	C	ENSG00000143970	ENST00000435504	Transcript	stop_gained	719	425	142	S/*	tCa/tGa	COSM418767	.	.	-1	ASXL2	HGNC	23805	protein_coding	YES	.	ENSP00000391447	ASXL2_HUMAN	.	UPI00001DFBE8	.	.	.	6/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCTGACTGC	.	4	ESCA
CENPA	0	.	GRCh37	2	27015647	27015647	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234C>T	p.%3D	p.F78F	ENST00000335756	3/5	62	55	6	41	41	0	CENPA,synonymous_variant,p.%3D,ENST00000335756,;CENPA,intron_variant,,ENST00000233505,;CENPA,non_coding_transcript_exon_variant,,ENST00000472719,;CENPA,non_coding_transcript_exon_variant,,ENST00000460030,;CENPA,intron_variant,,ENST00000475662,;CENPA,3_prime_UTR_variant,,ENST00000419525,;	T	ENSG00000115163	ENST00000335756	Transcript	synonymous_variant	434	234	78	F	ttC/ttT	.	.	.	1	CENPA	HGNC	1851	protein_coding	YES	CCDS1729.1	ENSP00000336868	CENPA_HUMAN	.	UPI00001274F6	.	.	.	3/5	.	hmmpanther:PTHR11426:SF26,hmmpanther:PTHR11426,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATTCACTCG	.	2	ESCA
CENPA	0	.	GRCh37	2	27016185	27016185	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*38C>G	.	.	ENST00000335756	4/5	33	30	3	21	21	0	CENPA,3_prime_UTR_variant,,ENST00000335756,;CENPA,3_prime_UTR_variant,,ENST00000233505,;CENPA,non_coding_transcript_exon_variant,,ENST00000472719,;CENPA,non_coding_transcript_exon_variant,,ENST00000460030,;CENPA,non_coding_transcript_exon_variant,,ENST00000475662,;CENPA,3_prime_UTR_variant,,ENST00000419525,;	G	ENSG00000115163	ENST00000335756	Transcript	3_prime_UTR_variant	661	.	.	.	.	.	.	.	1	CENPA	HGNC	1851	protein_coding	YES	CCDS1729.1	ENSP00000336868	CENPA_HUMAN	.	UPI00001274F6	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCTCAGCCA	.	2	ESCA
PLB1	0	.	GRCh37	2	28820876	28820876	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2326G>T	p.Gly776Ter	p.G776*	ENST00000327757	34/58	93	83	10	60	60	0	PLB1,stop_gained,p.Gly765Ter,ENST00000422425,;PLB1,stop_gained,p.Gly764Ter,ENST00000404858,;PLB1,stop_gained,p.Gly776Ter,ENST00000327757,;PLB1,downstream_gene_variant,,ENST00000436544,;PLB1,downstream_gene_variant,,ENST00000329020,;PLB1,upstream_gene_variant,,ENST00000541605,;PLB1,upstream_gene_variant,,ENST00000479065,;PLB1,upstream_gene_variant,,ENST00000411743,;	T	ENSG00000163803	ENST00000327757	Transcript	stop_gained	2370	2326	776	G/*	Gga/Tga	.	.	.	1	PLB1	HGNC	30041	protein_coding	YES	CCDS33168.1	ENSP00000330442	PLB1_HUMAN	.	UPI0000D6117C	.	.	.	34/58	.	hmmpanther:PTHR21325,hmmpanther:PTHR21325:SF1,Gene3D:3.40.50.1110,Pfam_domain:PF00657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGCAGGAGGG	.	4	ESCA
TSSC1	0	.	GRCh37	2	3193279	3193279	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990G>T	p.Lys330Asn	p.K330N	ENST00000382125	9/9	48	35	13	56	56	0	TSSC1,missense_variant,p.Lys357Asn,ENST00000398659,;TSSC1,missense_variant,p.Lys330Asn,ENST00000382125,;TSSC1,downstream_gene_variant,,ENST00000441271,;TSSC1,splice_region_variant,,ENST00000478754,;TSSC1,downstream_gene_variant,,ENST00000463662,;TSSC1,splice_region_variant,,ENST00000455162,;TSSC1,splice_region_variant,,ENST00000496433,;TSSC1,downstream_gene_variant,,ENST00000482570,;TSSC1,downstream_gene_variant,,ENST00000435721,;	A	ENSG00000032389	ENST00000382125	Transcript	missense_variant	1183	990	330	K/N	aaG/aaT	.	.	.	-1	TSSC1	HGNC	12383	protein_coding	YES	CCDS1651.1	ENSP00000371559	TSSC1_HUMAN	.	UPI000006DFE1	.	tolerated(0.18)	benign(0.021)	9/9	.	Gene3D:2.130.10.10,hmmpanther:PTHR14205:SF15,hmmpanther:PTHR14205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCTCCTGCA	.	5	ESCA
LTBP1	0	.	GRCh37	2	33585729	33585729	+	Missense_Mutation	SNP	G	G	C	rs569029644	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4066G>C	p.Ala1356Pro	p.A1356P	ENST00000404816	27/34	69	59	9	50	50	0	LTBP1,missense_variant,p.Ala1030Pro,ENST00000407925,;LTBP1,missense_variant,p.Ala1357Pro,ENST00000354476,;LTBP1,missense_variant,p.Ala988Pro,ENST00000418533,;LTBP1,missense_variant,p.Ala192Pro,ENST00000422669,;LTBP1,missense_variant,p.Ala1031Pro,ENST00000390003,;LTBP1,missense_variant,p.Ala1356Pro,ENST00000404816,;LTBP1,missense_variant,p.Ala975Pro,ENST00000402934,;LTBP1,missense_variant,p.Ala254Pro,ENST00000272273,;LTBP1,missense_variant,p.Ala977Pro,ENST00000404525,;	C	ENSG00000049323	ENST00000404816	Transcript	missense_variant	4419	4066	1356	A/P	Gcc/Ccc	rs569029644	.	.	1	LTBP1	HGNC	6714	protein_coding	YES	CCDS33177.2	ENSP00000386043	LTBP1_HUMAN	H7C2H7_HUMAN	UPI000173A4A4	.	tolerated(0.09)	probably_damaging(0.963)	27/34	.	PROSITE_profiles:PS51364,hmmpanther:PTHR24034:SF39,hmmpanther:PTHR24034,Gene3D:3.90.290.10,Superfamily_domains:SSF57581	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGACGCCAGT	by1000G	5	ESCA
AC009499.1	0	.	GRCh37	2	33951234	33951234	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.68+19214C>A	.	.	ENST00000366209	.	25	22	3	22	22	0	AC009499.1,intron_variant,,ENST00000442026,;AC009499.1,intron_variant,,ENST00000366209,;MYADML,non_coding_transcript_exon_variant,,ENST00000474610,;MYADML,intron_variant,,ENST00000490394,;MYADML,downstream_gene_variant,,ENST00000491596,;MYADML,downstream_gene_variant,,ENST00000322472,;	A	ENSG00000203386	ENST00000366209	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	AC009499.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGCCACATC	.	2	ESCA
NRXN1	0	.	GRCh37	2	50148877	50148877	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*205G>T	.	.	ENST00000404971	24/24	105	98	7	62	62	0	NRXN1,3_prime_UTR_variant,,ENST00000401710,;NRXN1,3_prime_UTR_variant,,ENST00000404971,;NRXN1,3_prime_UTR_variant,,ENST00000406316,;NRXN1,3_prime_UTR_variant,,ENST00000378262,;NRXN1,3_prime_UTR_variant,,ENST00000412315,;NRXN1,3_prime_UTR_variant,,ENST00000342183,;NRXN1,downstream_gene_variant,,ENST00000405472,;NRXN1,downstream_gene_variant,,ENST00000401669,;NRXN1,downstream_gene_variant,,ENST00000406859,;NRXN1,downstream_gene_variant,,ENST00000402717,;NRXN1,non_coding_transcript_exon_variant,,ENST00000484192,;	A	ENSG00000179915	ENST00000404971	Transcript	3_prime_UTR_variant	6189	.	.	.	.	.	.	.	-1	NRXN1	HGNC	8008	protein_coding	YES	CCDS46282.1	ENSP00000385142	NRX1A_HUMAN	Q08AH0_HUMAN	UPI00015A218A	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCCCCTGTT	.	2	ESCA
NRXN1	0	.	GRCh37	2	51259288	51259290	+	5'UTR	DEL	AGG	AGG	-	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	AGG	AGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1093_-1091delCCT	.	.	ENST00000404971	1/24	17	12	5	11	11	0	NRXN1,5_prime_UTR_variant,,ENST00000404971,;NRXN1,5_prime_UTR_variant,,ENST00000406316,;NRXN1,5_prime_UTR_variant,,ENST00000401669,;NRXN1,5_prime_UTR_variant,,ENST00000405581,;NRXN1,upstream_gene_variant,,ENST00000405472,;NRXN1,upstream_gene_variant,,ENST00000406859,;NRXN1,upstream_gene_variant,,ENST00000402717,;AC007682.1,upstream_gene_variant,,ENST00000440698,;NRXN1,upstream_gene_variant,,ENST00000496792,;	-	ENSG00000179915	ENST00000404971	Transcript	5_prime_UTR_variant	248-250	.	.	.	.	.	.	.	-1	NRXN1	HGNC	8008	protein_coding	YES	CCDS46282.1	ENSP00000385142	NRX1A_HUMAN	Q08AH0_HUMAN	UPI00015A218A	.	.	.	1/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGGAGCAGGAGGAG	.	2	ESCA
SPTBN1	0	.	GRCh37	2	54880793	54880793	+	Silent	SNP	G	G	T	rs745480606	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5625G>T	p.%3D	p.A1875A	ENST00000356805	27/36	71	67	4	59	59	0	SPTBN1,synonymous_variant,p.%3D,ENST00000333896,;SPTBN1,synonymous_variant,p.%3D,ENST00000356805,;SPTBN1,non_coding_transcript_exon_variant,,ENST00000496323,;	T	ENSG00000115306	ENST00000356805	Transcript	synonymous_variant	5906	5625	1875	A	gcG/gcT	rs745480606	.	.	1	SPTBN1	HGNC	11275	protein_coding	YES	CCDS33198.1	ENSP00000349259	SPTB2_HUMAN	Q53RC4_HUMAN,F8W6C1_HUMAN,D6W5C0_HUMAN,B2ZZ89_HUMAN	UPI0000DBEE4B	.	.	.	27/36	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF46966,SMART_domains:SM00150,PIRSF_domain:PIRSF002297,Pfam_domain:PF00435,Gene3D:1.20.58.60,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATGCGGGTGA	.	2	ESCA
CCDC104	0	.	GRCh37	2	55762900	55762900	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.537+1G>A	.	p.X179_splice	ENST00000349456	.	62	58	4	42	42	0	CCDC104,splice_donor_variant,,ENST00000339012,;CCDC104,splice_donor_variant,,ENST00000349456,;CCDC104,splice_donor_variant,,ENST00000407816,;CCDC104,splice_donor_variant,,ENST00000406691,;CCDC104,missense_variant,p.Val180Met,ENST00000403007,;CCDC104,splice_donor_variant,,ENST00000490934,;	A	ENSG00000163001	ENST00000349456	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	CCDC104	HGNC	30540	protein_coding	YES	CCDS1854.2	ENSP00000295117	CC104_HUMAN	.	UPI000013E20A	.	.	.	.	6/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACAGGTGCCT	.	2	ESCA
ACTR2	0	.	GRCh37	2	65454994	65454994	+	5'UTR	SNP	G	G	C	rs368070570	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-50G>C	.	.	ENST00000377982	1/10	169	156	13	108	108	0	ACTR2,5_prime_UTR_variant,,ENST00000542850,;ACTR2,5_prime_UTR_variant,,ENST00000260641,;ACTR2,5_prime_UTR_variant,,ENST00000377982,;ACTR2,non_coding_transcript_exon_variant,,ENST00000471552,;ACTR2,non_coding_transcript_exon_variant,,ENST00000476840,;	C	ENSG00000138071	ENST00000377982	Transcript	5_prime_UTR_variant	24	.	.	.	.	rs368070570	.	.	1	ACTR2	HGNC	169	protein_coding	YES	CCDS46307.1	ENSP00000367220	ARP2_HUMAN	.	UPI0000445E06	.	.	.	1/10	.	.	A:0.0004	A:0.0008	A:0	.	A:0.001	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGGGCGGCGGT	byFrequency|byCluster|by1000G	3	ESCA
AAK1	0	.	GRCh37	2	69691701	69691701	+	3'Flank	SNP	A	A	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000409085	.	48	42	6	46	46	0	AAK1,intron_variant,,ENST00000409068,;AAK1,downstream_gene_variant,,ENST00000409085,;RP11-427H3.3,non_coding_transcript_exon_variant,,ENST00000606389,;RP11-427H3.3,intron_variant,,ENST00000339092,;	C	ENSG00000115977	ENST00000409085	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3218	-1	AAK1	HGNC	19679	protein_coding	YES	CCDS1893.2	ENSP00000386456	AAK1_HUMAN	.	UPI0001881663	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCAAAAAACG	.	4	ESCA
TET3	0	.	GRCh37	2	74275075	74275075	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1626G>T	p.%3D	p.L542L	ENST00000409262	1/9	42	38	4	35	35	0	TET3,synonymous_variant,p.%3D,ENST00000409262,;TET3,synonymous_variant,p.%3D,ENST00000305799,;TET3,non_coding_transcript_exon_variant,,ENST00000475405,;	T	ENSG00000187605	ENST00000409262	Transcript	synonymous_variant	1626	1626	542	L	ctG/ctT	.	.	.	1	TET3	HGNC	28313	protein_coding	YES	CCDS46339.1	ENSP00000386869	TET3_HUMAN	K9JJH7_HUMAN	UPI0000DD79F5	.	.	.	1/9	.	hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGCTGCCCCC	.	3	ESCA
LRRTM4	0	.	GRCh37	2	77749387	77749387	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-230C>A	.	.	ENST00000409093	1/4	44	40	4	23	23	0	LRRTM4,5_prime_UTR_variant,,ENST00000409088,;LRRTM4,5_prime_UTR_variant,,ENST00000409093,;LRRTM4,5_prime_UTR_variant,,ENST00000409884,;LRRTM4,5_prime_UTR_variant,,ENST00000409911,;LRRTM4,intron_variant,,ENST00000456154,;LRRTM4,upstream_gene_variant,,ENST00000409282,;	T	ENSG00000176204	ENST00000409093	Transcript	5_prime_UTR_variant	108	.	.	.	.	.	.	.	-1	LRRTM4	HGNC	19411	protein_coding	YES	CCDS46346.1	ENSP00000386357	LRRT4_HUMAN	C9JM64_HUMAN	UPI0000047808	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCAGGTTTAA	.	3	ESCA
SH2D6	0	.	GRCh37	2	85661959	85661959	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-120C>A	.	.	ENST00000340326	1/5	54	46	8	50	50	0	SH2D6,5_prime_UTR_variant,,ENST00000340326,;SH2D6,intron_variant,,ENST00000389938,;Y_RNA,downstream_gene_variant,,ENST00000384478,;SH2D6,intron_variant,,ENST00000477170,;SH2D6,intron_variant,,ENST00000481426,;SH2D6,downstream_gene_variant,,ENST00000488657,;SH2D6,upstream_gene_variant,,ENST00000488219,;SH2D6,intron_variant,,ENST00000481395,;	A	ENSG00000152292	ENST00000340326	Transcript	5_prime_UTR_variant	42	.	.	.	.	.	.	.	1	SH2D6	HGNC	30439	protein_coding	YES	CCDS1976.1	ENSP00000341867	SH2D6_HUMAN	.	UPI0000160B3D	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAGTCTGTGC	.	5	ESCA
GNLY	0	.	GRCh37	2	85922542	85922542	+	Missense_Mutation	SNP	C	C	A	rs141055775	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.152C>A	p.Pro51His	p.P51H	ENST00000263863	2/5	66	59	7	55	55	0	GNLY,missense_variant,p.Pro36His,ENST00000409696,;GNLY,missense_variant,p.Pro18His,ENST00000526018,;GNLY,missense_variant,p.Pro51His,ENST00000263863,;GNLY,missense_variant,p.Pro78His,ENST00000524600,;GNLY,non_coding_transcript_exon_variant,,ENST00000534351,;GNLY,non_coding_transcript_exon_variant,,ENST00000533041,;GNLY,non_coding_transcript_exon_variant,,ENST00000489214,;GNLY,non_coding_transcript_exon_variant,,ENST00000488945,;GNLY,non_coding_transcript_exon_variant,,ENST00000531685,;GNLY,non_coding_transcript_exon_variant,,ENST00000489980,;GNLY,non_coding_transcript_exon_variant,,ENST00000491234,;GNLY,non_coding_transcript_exon_variant,,ENST00000482900,;GNLY,non_coding_transcript_exon_variant,,ENST00000464298,;GNLY,non_coding_transcript_exon_variant,,ENST00000470974,;	A	ENSG00000115523	ENST00000263863	Transcript	missense_variant	280	152	51	P/H	cCc/cAc	rs141055775	.	.	1	GNLY	HGNC	4414	protein_coding	YES	CCDS1984.1	ENSP00000263863	GNLY_HUMAN	.	UPI0000001C18	.	deleterious(0)	probably_damaging(0.99)	2/5	.	hmmpanther:PTHR15541:SF2,hmmpanther:PTHR15541	.	.	.	.	.	.	.	T:0.0002	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGCCCCCAGG	byCluster	3	ESCA
EIF2AK3	0	.	GRCh37	2	88857134	88857134	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120A>T	.	.	ENST00000303236	17/17	25	20	5	20	20	0	EIF2AK3,3_prime_UTR_variant,,ENST00000419748,;EIF2AK3,3_prime_UTR_variant,,ENST00000303236,;EIF2AK3,downstream_gene_variant,,ENST00000415570,;AC104134.2,intron_variant,,ENST00000413234,;	A	ENSG00000172071	ENST00000303236	Transcript	3_prime_UTR_variant	3773	.	.	.	.	.	.	.	-1	EIF2AK3	HGNC	3255	protein_coding	YES	CCDS33241.1	ENSP00000307235	E2AK3_HUMAN	E7ER02_HUMAN	UPI000013E87D	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAGTAGTCC	.	5	ESCA
IGKV4-1	0	.	GRCh37	2	89185562	89185562	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256G>T	p.Asp86Tyr	p.D86Y	ENST00000390243	2/2	181	166	15	162	162	0	IGKV4-1,missense_variant,p.Asp86Tyr,ENST00000390243,;	T	ENSG00000211598	ENST00000390243	Transcript	missense_variant	431	256	86	D/Y	Gac/Tac	.	.	.	1	IGKV4-1	HGNC	5834	IG_V_gene	YES	.	ENSP00000374778	KV401_HUMAN	.	UPI0000113B70	.	deleterious(0)	probably_damaging(0.965)	2/2	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00406,Pfam_domain:PF07686,Gene3D:2.60.40.10,hmmpanther:PTHR23267:SF139,hmmpanther:PTHR23267,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCCTGACCGA	.	3	ESCA
IGKV1D-8	0	.	GRCh37	2	90259789	90259789	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16C>A	p.Pro6Thr	p.P6T	ENST00000471857	1/2	357	329	28	288	288	0	IGKV1D-8,missense_variant,p.Pro6Thr,ENST00000471857,;	A	ENSG00000239819	ENST00000471857	Transcript	missense_variant	197	16	6	P/T	Ccc/Acc	.	.	.	1	IGKV1D-8	HGNC	5759	IG_V_gene	YES	.	ENSP00000420285	.	.	UPI0000116192	.	deleterious(0)	probably_damaging(0.927)	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23267,hmmpanther:PTHR23267:SF122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTCCCCGCT	.	2	ESCA
KIAA1211L	0	.	GRCh37	2	99454683	99454683	+	Silent	SNP	C	C	A	rs147976810	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138G>T	p.%3D	p.P46P	ENST00000397899	3/10	105	88	17	76	76	0	KIAA1211L,synonymous_variant,p.%3D,ENST00000415261,;KIAA1211L,synonymous_variant,p.%3D,ENST00000397899,;KIAA1211L,synonymous_variant,p.%3D,ENST00000428096,;KIAA1211L,synonymous_variant,p.%3D,ENST00000423771,;RNU7-46P,downstream_gene_variant,,ENST00000459066,;KIAA1211L,non_coding_transcript_exon_variant,,ENST00000462314,;	A	ENSG00000196872	ENST00000397899	Transcript	synonymous_variant	470	138	46	P	ccG/ccT	rs147976810,COSM4096567	.	.	-1	KIAA1211L	HGNC	33454	protein_coding	YES	CCDS42720.1	ENSP00000380996	K121L_HUMAN	.	UPI0000E59245	.	.	.	3/10	.	hmmpanther:PTHR22118:SF5,hmmpanther:PTHR22118	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	T:0.0008	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGACGGCGA	byFrequency|byCluster|by1000G	5	ESCA
CD200R1L	0	.	GRCh37	3	112545840	112545840	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679G>C	p.Gly227Arg	p.G227R	ENST00000398214	4/6	64	60	4	53	53	0	CD200R1L,missense_variant,p.Gly206Arg,ENST00000488794,;CD200R1L,missense_variant,p.Gly206Arg,ENST00000448932,;CD200R1L,missense_variant,p.Gly227Arg,ENST00000398214,;CD200R1L,splice_region_variant,,ENST00000486723,;	G	ENSG00000206531	ENST00000398214	Transcript	missense_variant	905	679	227	G/R	Ggt/Cgt	.	.	.	-1	CD200R1L	HGNC	24665	protein_coding	YES	CCDS43131.1	ENSP00000381272	MO2R2_HUMAN	.	UPI000042263C	.	deleterious(0.01)	possibly_damaging(0.518)	4/6	.	hmmpanther:PTHR21462:SF3,hmmpanther:PTHR21462	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTACCTGAAT	.	2	ESCA
GRAMD1C	0	.	GRCh37	3	113627935	113627935	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.920A>G	p.Asp307Gly	p.D307G	ENST00000358160	9/18	102	96	6	53	53	0	GRAMD1C,missense_variant,p.Asp102Gly,ENST00000440446,;GRAMD1C,missense_variant,p.Asp307Gly,ENST00000358160,;GRAMD1C,missense_variant,p.Asp140Gly,ENST00000472026,;GRAMD1C,missense_variant,p.Thr7Ala,ENST00000488680,;GRAMD1C,missense_variant,p.Thr7Ala,ENST00000452134,;GRAMD1C,missense_variant,p.Asp102Gly,ENST00000462838,;GRAMD1C,non_coding_transcript_exon_variant,,ENST00000479212,;GRAMD1C,3_prime_UTR_variant,,ENST00000472384,;GRAMD1C,3_prime_UTR_variant,,ENST00000484714,;	G	ENSG00000178075	ENST00000358160	Transcript	missense_variant	1412	920	307	D/G	gAc/gGc	.	.	.	1	GRAMD1C	HGNC	25252	protein_coding	YES	CCDS33826.1	ENSP00000350881	GRM1C_HUMAN	C9J7B8_HUMAN,A8KA99_HUMAN	UPI00001AF15F	.	deleterious(0.02)	benign(0.011)	9/18	.	hmmpanther:PTHR23319:SF1,hmmpanther:PTHR23319	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGGACAAAA	.	2	ESCA
NPHP3	0	.	GRCh37	3	132441160	132441160	+	Nonsense_Mutation	SNP	C	C	A	rs761435204	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40G>T	p.Glu14Ter	p.E14*	ENST00000337331	1/27	19	16	3	18	18	0	NPHP3,stop_gained,p.Glu14Ter,ENST00000326682,;NPHP3,stop_gained,p.Glu14Ter,ENST00000337331,;NPHP3,stop_gained,p.Glu14Ter,ENST00000383282,;NPHP3,stop_gained,p.Glu14Ter,ENST00000343113,;NPHP3-AS1,non_coding_transcript_exon_variant,,ENST00000489343,;NPHP3-AS1,upstream_gene_variant,,ENST00000504440,;NPHP3,upstream_gene_variant,,ENST00000471145,;NPHP3,stop_gained,p.Glu14Ter,ENST00000465756,;NPHP3,stop_gained,p.Glu14Ter,ENST00000471702,;NPHP3,upstream_gene_variant,,ENST00000469232,;NPHP3,upstream_gene_variant,,ENST00000490993,;	A	ENSG00000113971	ENST00000337331	Transcript	stop_gained	127	40	14	E/*	Gaa/Taa	rs761435204	.	.	-1	NPHP3	HGNC	7907	protein_coding	YES	CCDS3078.1	ENSP00000338766	NPHP3_HUMAN	.	UPI00001B6B30	.	.	.	1/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CACTTCCCCGC	.	2	ESCA
CHST2	0	.	GRCh37	3	142840873	142840873	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1215G>T	p.%3D	p.T405T	ENST00000309575	2/2	50	42	8	41	41	0	CHST2,synonymous_variant,p.%3D,ENST00000309575,;RP11-80H8.4,upstream_gene_variant,,ENST00000483262,;	T	ENSG00000175040	ENST00000309575	Transcript	synonymous_variant	2599	1215	405	T	acG/acT	.	.	.	1	CHST2	HGNC	1970	protein_coding	YES	CCDS3129.1	ENSP00000307911	CHST2_HUMAN	.	UPI0000073CBC	.	.	.	2/2	.	hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF3,Pfam_domain:PF00685,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGACGCTGCA	.	5	ESCA
SIAH2	0	.	GRCh37	3	150460351	150460351	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552G>A	p.%3D	p.V184V	ENST00000312960	2/2	101	93	8	71	71	0	SIAH2,synonymous_variant,p.%3D,ENST00000312960,;SIAH2,synonymous_variant,p.%3D,ENST00000482706,;	T	ENSG00000181788	ENST00000312960	Transcript	synonymous_variant	1080	552	184	V	gtG/gtA	.	.	.	-1	SIAH2	HGNC	10858	protein_coding	YES	CCDS3152.1	ENSP00000322457	SIAH2_HUMAN	C9J9D7_HUMAN	UPI0000071280	.	.	.	2/2	.	PROSITE_profiles:PS51081,hmmpanther:PTHR10315:SF11,hmmpanther:PTHR10315,Pfam_domain:PF03145,Gene3D:1k2fA02,Superfamily_domains:SSF49599	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACATCACAGC	.	2	ESCA
MED12L	0	.	GRCh37	3	150804523	150804523	+	5'Flank	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000474524	.	40	34	6	32	32	0	MED12L,5_prime_UTR_variant,,ENST00000422248,;MED12L,5_prime_UTR_variant,,ENST00000309237,;MED12L,upstream_gene_variant,,ENST00000474524,;MED12L,upstream_gene_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000469768,;	T	ENSG00000144893	ENST00000474524	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	153	1	MED12L	HGNC	16050	protein_coding	YES	CCDS33876.1	ENSP00000417235	MD12L_HUMAN	.	UPI000020A46B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCATCAGTGC	.	4	ESCA
P2RY13	0	.	GRCh37	3	151046747	151046747	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97T>A	p.Ser33Thr	p.S33T	ENST00000325602	2/2	49	45	4	49	49	0	P2RY13,missense_variant,p.Ser33Thr,ENST00000325602,;MED12L,intron_variant,,ENST00000474524,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,;	T	ENSG00000181631	ENST00000325602	Transcript	missense_variant	117	97	33	S/T	Tct/Act	.	.	.	-1	P2RY13	HGNC	4537	protein_coding	YES	CCDS3158.2	ENSP00000320376	P2Y13_HUMAN	.	UPI000020A470	.	tolerated(0.13)	benign(0.013)	2/2	.	Prints_domain:PR01735,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCAGATCTGT	.	3	ESCA
OTOL1	0	.	GRCh37	3	161216961	161216961	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.367C>G	p.Pro123Ala	p.P123A	ENST00000327928	2/4	112	105	6	98	98	0	OTOL1,missense_variant,p.Pro123Ala,ENST00000327928,;	G	ENSG00000182447	ENST00000327928	Transcript	missense_variant	367	367	123	P/A	Cct/Gct	.	.	.	1	OTOL1	HGNC	34071	protein_coding	YES	CCDS46948.1	ENSP00000330808	OTOL1_HUMAN	.	UPI0000D61BA3	.	tolerated(0.2)	unknown(0)	2/4	.	hmmpanther:PTHR24022,hmmpanther:PTHR24022:SF25,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGGTCCTAAA	.	2	ESCA
SAMD7	0	.	GRCh37	3	169639075	169639075	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.160G>T	p.Val54Phe	p.V54F	ENST00000428432	4/9	110	89	21	72	72	0	SAMD7,missense_variant,p.Val54Phe,ENST00000335556,;SAMD7,missense_variant,p.Val54Phe,ENST00000428432,;SAMD7,missense_variant,p.Val54Phe,ENST00000487910,;	T	ENSG00000187033	ENST00000428432	Transcript	missense_variant	549	160	54	V/F	Gtt/Ttt	.	.	.	1	SAMD7	HGNC	25394	protein_coding	YES	CCDS3209.1	ENSP00000391299	SAMD7_HUMAN	.	UPI00001A9D13	.	deleterious(0.01)	benign(0.406)	4/9	.	hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTGTTCTA	.	5	ESCA
RP11-379K17.4	0	.	GRCh37	3	169663272	169663272	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4023G>T	.	.	ENST00000483289	2/2	8	4	4	10	10	0	RP11-379K17.4,non_coding_transcript_exon_variant,,ENST00000483289,;RP11-379K17.4,intron_variant,,ENST00000487580,;RP11-379K17.4,downstream_gene_variant,,ENST00000600502,;RP11-379K17.5,downstream_gene_variant,,ENST00000494834,;	A	ENSG00000239219	ENST00000483289	Transcript	non_coding_transcript_exon_variant	4023	.	.	.	.	.	.	.	-1	RP11-379K17.4	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAGCGAGTT	.	2	ESCA
PRKCI	0	.	GRCh37	3	169985788	169985788	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450G>T	p.Arg150Ser	p.R150S	ENST00000295797	5/18	107	85	21	90	89	0	PRKCI,missense_variant,p.Arg150Ser,ENST00000295797,;	T	ENSG00000163558	ENST00000295797	Transcript	missense_variant	755	450	150	R/S	agG/agT	.	.	.	1	PRKCI	HGNC	9404	protein_coding	YES	CCDS3212.2	ENSP00000295797	KPCI_HUMAN	.	UPI000020A798	.	deleterious(0.04)	benign(0.13)	5/18	.	Prints_domain:PR00008,Superfamily_domains:SSF57889,PIRSF_domain:PIRSF000554,SMART_domains:SM00109,Gene3D:3.30.60.20,Pfam_domain:PF00130,PROSITE_patterns:PS00479,hmmpanther:PTHR24357:SF60,hmmpanther:PTHR24357,PROSITE_profiles:PS50081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAGGGTAAA	.	5	ESCA
TBL1XR1	0	.	GRCh37	3	176742204	176742204	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1082G>C	.	.	ENST00000430069	16/16	116	94	22	61	61	0	TBL1XR1,3_prime_UTR_variant,,ENST00000457928,;TBL1XR1,3_prime_UTR_variant,,ENST00000430069,;TBL1XR1,non_coding_transcript_exon_variant,,ENST00000474363,;	G	ENSG00000177565	ENST00000430069	Transcript	3_prime_UTR_variant	2887	.	.	.	.	.	.	.	-1	TBL1XR1	HGNC	29529	protein_coding	YES	CCDS46961.1	ENSP00000405574	TBL1R_HUMAN	C9JY82_HUMAN,C9JTW8_HUMAN,C9JLJ1_HUMAN,C9JEC9_HUMAN,C9JCW4_HUMAN,C9JCK0_HUMAN,C9JBN1_HUMAN,C9J903_HUMAN,C9J7E1_HUMAN,C9J3H2_HUMAN,C9IYU9_HUMAN	UPI0000136A71	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTACACAGA	.	5	ESCA
HTR3C	0	.	GRCh37	3	183777335	183777335	+	Missense_Mutation	SNP	C	C	A	rs761075059	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>A	p.Arg278Ser	p.R278S	ENST00000318351	7/9	106	100	6	75	75	0	HTR3C,missense_variant,p.Arg278Ser,ENST00000318351,;	A	ENSG00000178084	ENST00000318351	Transcript	missense_variant	866	832	278	R/S	Cgt/Agt	rs761075059,COSM3590618	.	.	1	HTR3C	HGNC	24003	protein_coding	YES	CCDS3250.1	ENSP00000322617	5HT3C_HUMAN	.	UPI00001402D6	.	deleterious(0.01)	probably_damaging(0.91)	7/9	.	hmmpanther:PTHR18945:SF409,hmmpanther:PTHR18945,Gene3D:1.20.120.370,Pfam_domain:PF02932,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAATCGTGCC	byFrequency	2	ESCA
ATP13A5	0	.	GRCh37	3	193052744	193052744	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1088C>A	p.Pro363His	p.P363H	ENST00000342358	10/30	84	49	35	56	56	0	ATP13A5,missense_variant,p.Pro363His,ENST00000342358,;	T	ENSG00000187527	ENST00000342358	Transcript	missense_variant	1206	1088	363	P/H	cCt/cAt	.	.	.	-1	ATP13A5	HGNC	31789	protein_coding	YES	CCDS33914.1	ENSP00000341942	AT135_HUMAN	.	UPI000050EC1D	.	tolerated(0.28)	benign(0.25)	10/30	.	Superfamily_domains:0049471,Gene3D:2.70.150.10,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01657,hmmpanther:PTHR24093:SF237,hmmpanther:PTHR24093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACAGGCCCC	.	5	ESCA
MUC4	0	.	GRCh37	3	195517903	195517903	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.548C>A	p.Ser183Tyr	p.S183Y	ENST00000463781	2/25	93	74	19	79	79	0	MUC4,missense_variant,p.Ser183Tyr,ENST00000475231,;MUC4,missense_variant,p.Ser183Tyr,ENST00000463781,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.Ser183Tyr,ENST00000477086,;MUC4,missense_variant,p.Ser183Tyr,ENST00000466475,;MUC4,missense_variant,p.Ser183Tyr,ENST00000478156,;MUC4,missense_variant,p.Ser183Tyr,ENST00000470451,;MUC4,missense_variant,p.Ser183Tyr,ENST00000479406,;MUC4,missense_variant,p.Ser183Tyr,ENST00000477756,;MUC4,missense_variant,p.Ser183Tyr,ENST00000462323,;MUC4,missense_variant,p.Ser183Tyr,ENST00000480843,;	T	ENSG00000145113	ENST00000463781	Transcript	missense_variant	1008	548	183	S/Y	tCc/tAc	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	unknown(0)	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGGAAGTT	.	5	ESCA
CMC1	0	.	GRCh37	3	28364948	28364948	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3828C>G	.	.	ENST00000466830	4/4	223	216	7	150	150	0	CMC1,3_prime_UTR_variant,,ENST00000466830,;AZI2,3_prime_UTR_variant,,ENST00000479665,;AZI2,intron_variant,,ENST00000429369,;CMC1,downstream_gene_variant,,ENST00000423894,;CMC1,downstream_gene_variant,,ENST00000418849,;AZI2,non_coding_transcript_exon_variant,,ENST00000295748,;CMC1,downstream_gene_variant,,ENST00000495428,;CMC1,downstream_gene_variant,,ENST00000469102,;CMC1,downstream_gene_variant,,ENST00000467644,;CMC1,downstream_gene_variant,,ENST00000482499,;AZI2,downstream_gene_variant,,ENST00000476174,;CMC1,downstream_gene_variant,,ENST00000396610,;CMC1,downstream_gene_variant,,ENST00000477739,;AZI2,downstream_gene_variant,,ENST00000492044,;CMC1,downstream_gene_variant,,ENST00000334841,;AZI2,downstream_gene_variant,,ENST00000463512,;	G	ENSG00000187118	ENST00000466830	Transcript	3_prime_UTR_variant	4348	.	.	.	.	.	.	.	1	CMC1	HGNC	28783	protein_coding	YES	CCDS33722.1	ENSP00000418348	COXM1_HUMAN	.	UPI0000161ABD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAATTCTAAAA	.	2	ESCA
CACNA1D	0	.	GRCh37	3	53766862	53766862	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2554G>T	p.Glu852Ter	p.E852*	ENST00000288139	20/49	69	64	4	63	63	0	CACNA1D,stop_gained,p.Glu852Ter,ENST00000288139,;CACNA1D,stop_gained,p.Glu832Ter,ENST00000422281,;CACNA1D,stop_gained,p.Glu832Ter,ENST00000350061,;CACNA1D,stop_gained,p.Glu525Ter,ENST00000481478,;	T	ENSG00000157388	ENST00000288139	Transcript	stop_gained	2672	2554	852	E/*	Gag/Tag	.	.	.	1	CACNA1D	HGNC	1391	protein_coding	YES	CCDS2872.1	ENSP00000288139	CAC1D_HUMAN	.	UPI000005031A	.	.	.	20/49	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10037:SF139,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAAGAGGAG	.	2	ESCA
RAD18	0	.	GRCh37	3	8983397	8983397	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.358G>T	p.Val120Leu	p.V120L	ENST00000264926	5/13	61	57	4	49	49	0	RAD18,missense_variant,p.Val120Leu,ENST00000264926,;RAD18,downstream_gene_variant,,ENST00000413832,;RAD18,non_coding_transcript_exon_variant,,ENST00000495087,;RAD18,missense_variant,p.Cys112Phe,ENST00000421052,;RAD18,missense_variant,p.Val120Leu,ENST00000415439,;RAD18,3_prime_UTR_variant,,ENST00000418463,;	A	ENSG00000070950	ENST00000264926	Transcript	missense_variant	475	358	120	V/L	Gta/Tta	.	.	.	-1	RAD18	HGNC	18278	protein_coding	YES	CCDS2571.1	ENSP00000264926	RAD18_HUMAN	H7C0A5_HUMAN,C9J0Q4_HUMAN	UPI000013D592	.	tolerated(0.34)	benign(0.005)	5/13	.	hmmpanther:PTHR14134,hmmpanther:PTHR14134:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTACAGGAG	.	2	ESCA
MTMR14	0	.	GRCh37	3	9726928	9726928	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1161G>A	p.%3D	p.E387E	ENST00000296003	13/19	73	65	8	54	54	0	MTMR14,synonymous_variant,p.%3D,ENST00000420925,;MTMR14,synonymous_variant,p.%3D,ENST00000351233,;MTMR14,synonymous_variant,p.%3D,ENST00000353332,;MTMR14,synonymous_variant,p.%3D,ENST00000296003,;MTMR14,downstream_gene_variant,,ENST00000431250,;MTMR14,3_prime_UTR_variant,,ENST00000414996,;MTMR14,3_prime_UTR_variant,,ENST00000447144,;MTMR14,downstream_gene_variant,,ENST00000430020,;MTMR14,downstream_gene_variant,,ENST00000416864,;	A	ENSG00000163719	ENST00000296003	Transcript	synonymous_variant	1283	1161	387	E	gaG/gaA	.	.	.	1	MTMR14	HGNC	26190	protein_coding	YES	CCDS43043.1	ENSP00000296003	MTMRE_HUMAN	.	UPI000007423D	.	.	.	13/19	.	hmmpanther:PTHR13524,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGAGGAGGT	.	4	ESCA
OR5H1	0	.	GRCh37	3	97851625	97851625	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84C>G	p.Phe28Leu	p.F28L	ENST00000354565	1/1	182	170	12	174	174	0	OR5H1,missense_variant,p.Phe28Leu,ENST00000354565,;RP11-343D2.11,intron_variant,,ENST00000508964,;	G	ENSG00000231192	ENST00000354565	Transcript	missense_variant	84	84	28	F/L	ttC/ttG	.	.	.	1	OR5H1	HGNC	8346	protein_coding	YES	CCDS33797.1	ENSP00000346575	OR5H1_HUMAN	.	UPI0000197652	.	deleterious(0.01)	benign(0.32)	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF135	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTTCCTGGC	.	2	ESCA
ADH7	0	.	GRCh37	4	100350696	100350696	+	Missense_Mutation	SNP	C	C	A	rs148026590	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.173G>T	p.Arg58Leu	p.R58L	ENST00000476959	2/9	119	107	12	120	120	0	ADH7,missense_variant,p.Arg50Leu,ENST00000209665,;ADH7,missense_variant,p.Arg58Leu,ENST00000476959,;ADH7,missense_variant,p.Arg38Leu,ENST00000437033,;ADH7,5_prime_UTR_variant,,ENST00000482593,;ADH7,5_prime_UTR_variant,,ENST00000474027,;	A	ENSG00000196344	ENST00000476959	Transcript	missense_variant	203	173	58	R/L	cGc/cTc	rs148026590	.	.	-1	ADH7	HGNC	256	protein_coding	YES	CCDS54781.1	ENSP00000420269	ADH7_HUMAN	E9PFG0_HUMAN,C9JP14_HUMAN,B4DWS1_HUMAN	UPI00017A81B5	.	deleterious(0)	benign(0.416)	2/9	.	hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF406,Gene3D:3.90.180.10,Pfam_domain:PF08240,Superfamily_domains:SSF50129	T:0.0008	T:0.0023	T:0	.	T:0	T:0.001	T:0	T:0.0041	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TAATGCGAACT	byFrequency|byCluster|by1000G	3	ESCA
NFKB1	0	.	GRCh37	4	103518697	103518697	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516G>A	p.Ala506Thr	p.A506T	ENST00000226574	15/24	57	46	11	56	56	0	NFKB1,missense_variant,p.Ala325Thr,ENST00000600343,;NFKB1,missense_variant,p.Ala505Thr,ENST00000505458,;NFKB1,missense_variant,p.Ala505Thr,ENST00000394820,;NFKB1,missense_variant,p.Ala506Thr,ENST00000226574,;NFKB1,downstream_gene_variant,,ENST00000508584,;NFKB1,downstream_gene_variant,,ENST00000504044,;	A	ENSG00000109320	ENST00000226574	Transcript	missense_variant	1983	1516	506	A/T	Gct/Act	.	.	.	1	NFKB1	HGNC	7794	protein_coding	YES	CCDS3657.1	ENSP00000226574	NFKB1_HUMAN	D6RF93_HUMAN,D6RC45_HUMAN	UPI0000192724	.	tolerated(0.12)	possibly_damaging(0.674)	15/24	.	hmmpanther:PTHR24169:SF9,hmmpanther:PTHR24169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGGCTATG	.	5	ESCA
AIMP1	0	.	GRCh37	4	107248633	107248633	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207G>C	p.Glu69Asp	p.E69D	ENST00000394701	3/7	141	124	16	111	111	0	AIMP1,missense_variant,p.Glu45Asp,ENST00000358008,;AIMP1,missense_variant,p.Glu45Asp,ENST00000442366,;AIMP1,missense_variant,p.Glu69Asp,ENST00000394701,;AIMP1,missense_variant,p.Glu45Asp,ENST00000510207,;	C	ENSG00000164022	ENST00000394701	Transcript	missense_variant	248	207	69	E/D	gaG/gaC	.	.	.	1	AIMP1	HGNC	10648	protein_coding	YES	CCDS47121.1	ENSP00000378191	AIMP1_HUMAN	D6R937_HUMAN	UPI00005A76B9	.	deleterious(0.02)	probably_damaging(0.999)	3/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11586,hmmpanther:PTHR11586:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGAGAAGAA	.	4	ESCA
LARP7	0	.	GRCh37	4	113568845	113568845	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1019-1G>C	.	p.X340_splice	ENST00000509061	.	116	98	17	68	68	0	LARP7,splice_acceptor_variant,,ENST00000324052,;LARP7,splice_acceptor_variant,,ENST00000344442,;LARP7,splice_acceptor_variant,,ENST00000509061,;LARP7,missense_variant,p.Asp127His,ENST00000511529,;LARP7,intron_variant,,ENST00000513553,;LARP7,downstream_gene_variant,,ENST00000505034,;LARP7,downstream_gene_variant,,ENST00000507443,;LARP7,downstream_gene_variant,,ENST00000508577,;MIR367,downstream_gene_variant,,ENST00000362299,;MIR302D,downstream_gene_variant,,ENST00000362275,;MIR302C,downstream_gene_variant,,ENST00000362232,;MIR302A,downstream_gene_variant,,ENST00000385192,;MIR302B,downstream_gene_variant,,ENST00000362188,;MIR302B,intron_variant,,ENST00000510655,;MIR302B,intron_variant,,ENST00000509938,;MIR302B,intron_variant,,ENST00000505215,;LARP7,downstream_gene_variant,,ENST00000503316,;LARP7,splice_acceptor_variant,,ENST00000509622,;LARP7,downstream_gene_variant,,ENST00000505216,;LARP7,downstream_gene_variant,,ENST00000512589,;	C	ENSG00000174720	ENST00000509061	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	LARP7	HGNC	24912	protein_coding	YES	CCDS58924.1	ENSP00000422626	LARP7_HUMAN	D6RFF0_HUMAN,D6RF49_HUMAN,D6RAF3_HUMAN	UPI000020B34C	.	.	.	.	9/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAAGATATA	.	5	ESCA
SEC24D	0	.	GRCh37	4	119754883	119754883	+	5'UTR	SNP	C	C	G	rs748376001	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-32G>C	.	.	ENST00000280551	2/23	77	66	11	55	55	0	SEC24D,5_prime_UTR_variant,,ENST00000419654,;SEC24D,5_prime_UTR_variant,,ENST00000379735,;SEC24D,5_prime_UTR_variant,,ENST00000503683,;SEC24D,5_prime_UTR_variant,,ENST00000280551,;SEC24D,non_coding_transcript_exon_variant,,ENST00000505280,;SEC24D,5_prime_UTR_variant,,ENST00000514561,;SEC24D,5_prime_UTR_variant,,ENST00000509818,;SEC24D,5_prime_UTR_variant,,ENST00000506622,;	G	ENSG00000150961	ENST00000280551	Transcript	5_prime_UTR_variant	208	.	.	.	.	rs748376001	.	.	-1	SEC24D	HGNC	10706	protein_coding	YES	CCDS3710.1	ENSP00000280551	SC24D_HUMAN	E9PDM8_HUMAN,D6RGJ5_HUMAN	UPI00001AEA4F	.	.	.	2/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE|VARSCANS	TTCTACAAAAG	byFrequency	3	ESCA
BBS7	0	.	GRCh37	4	122774232	122774232	+	Missense_Mutation	SNP	C	C	A	rs727503821	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.728G>T	p.Cys243Phe	p.C243F	ENST00000264499	8/19	71	62	8	71	71	0	BBS7,missense_variant,p.Cys243Phe,ENST00000264499,;BBS7,missense_variant,p.Cys243Phe,ENST00000506636,;BBS7,downstream_gene_variant,,ENST00000508536,;	A	ENSG00000138686	ENST00000264499	Transcript	missense_variant	912	728	243	C/F	tGt/tTt	rs727503821	.	.	-1	BBS7	HGNC	18758	protein_coding	YES	CCDS3724.1	ENSP00000264499	BBS7_HUMAN	H0Y973_HUMAN	UPI00001684D7	.	deleterious(0)	probably_damaging(0.93)	8/19	.	hmmpanther:PTHR16074,hmmpanther:PTHR16074:SF4,Gene3D:2.130.10.10,PIRSF_domain:PIRSF011091,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAATACACAAA	byFrequency|byCluster	4	ESCA
ADAD1	0	.	GRCh37	4	123302179	123302179	+	Missense_Mutation	SNP	C	C	A	rs62000437	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205C>A	p.Leu69Ile	p.L69I	ENST00000296513	4/13	109	95	14	88	88	0	ADAD1,missense_variant,p.Leu69Ile,ENST00000388724,;ADAD1,missense_variant,p.Leu69Ile,ENST00000296513,;ADAD1,missense_variant,p.Leu69Ile,ENST00000439307,;ADAD1,missense_variant,p.Leu69Ile,ENST00000446706,;ADAD1,missense_variant,p.Leu51Ile,ENST00000388725,;ADAD1,non_coding_transcript_exon_variant,,ENST00000492454,;ADAD1,downstream_gene_variant,,ENST00000464160,;	A	ENSG00000164113	ENST00000296513	Transcript	missense_variant	390	205	69	L/I	Ctt/Att	rs62000437	.	.	1	ADAD1	HGNC	30713	protein_coding	YES	CCDS34058.1	ENSP00000296513	ADAD1_HUMAN	C9JGM6_HUMAN,C9JAT9_HUMAN	UPI000006DF76	.	tolerated(0.45)	benign(0.002)	4/13	.	hmmpanther:PTHR10910:SF44,hmmpanther:PTHR10910	G:0.0010	G:0.0038	G:0	.	G:0	G:0	G:0	G:0.0054	G:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAATCTTTCA	byFrequency|byCluster|by1000G	4	ESCA
UVSSA	0	.	GRCh37	4	1343540	1343540	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327G>T	p.%3D	p.L109L	ENST00000389851	3/14	54	44	10	44	44	0	UVSSA,synonymous_variant,p.%3D,ENST00000507531,;UVSSA,synonymous_variant,p.%3D,ENST00000389851,;UVSSA,synonymous_variant,p.%3D,ENST00000511216,;UVSSA,upstream_gene_variant,,ENST00000505716,;	T	ENSG00000163945	ENST00000389851	Transcript	synonymous_variant	774	327	109	L	ctG/ctT	.	.	.	1	UVSSA	HGNC	29304	protein_coding	YES	CCDS33938.1	ENSP00000374501	UVSSA_HUMAN	.	UPI00001C1E0C	.	.	.	3/14	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AGGCTGAGGCA	.	3	ESCA
UVSSA	0	.	GRCh37	4	1343542	1343542	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329G>T	p.Arg110Met	p.R110M	ENST00000389851	3/14	55	44	10	45	45	0	UVSSA,missense_variant,p.Arg110Met,ENST00000507531,;UVSSA,missense_variant,p.Arg110Met,ENST00000389851,;UVSSA,missense_variant,p.Arg110Met,ENST00000511216,;UVSSA,upstream_gene_variant,,ENST00000505716,;	T	ENSG00000163945	ENST00000389851	Transcript	missense_variant	776	329	110	R/M	aGg/aTg	.	.	.	1	UVSSA	HGNC	29304	protein_coding	YES	CCDS33938.1	ENSP00000374501	UVSSA_HUMAN	.	UPI00001C1E0C	.	deleterious(0)	probably_damaging(0.95)	3/14	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	GCTGAGGCAGG	.	3	ESCA
PCDH18	0	.	GRCh37	4	138452880	138452880	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363C>G	p.Phe121Leu	p.F121L	ENST00000344876	1/4	86	80	6	80	80	0	PCDH18,missense_variant,p.Phe121Leu,ENST00000344876,;PCDH18,missense_variant,p.Phe121Leu,ENST00000412923,;PCDH18,5_prime_UTR_variant,,ENST00000507846,;PCDH18,intron_variant,,ENST00000510305,;PCDH18,intron_variant,,ENST00000511115,;	C	ENSG00000189184	ENST00000344876	Transcript	missense_variant	750	363	121	F/L	ttC/ttG	.	.	.	-1	PCDH18	HGNC	14268	protein_coding	YES	CCDS34064.1	ENSP00000355082	PCD18_HUMAN	Q9NT87_HUMAN,B4DQ29_HUMAN	UPI0000047A88	.	tolerated(0.69)	benign(0.196)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF9,SMART_domains:SM00112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATATGGAAAAG	.	2	ESCA
ETFDH	0	.	GRCh37	4	159627792	159627792	+	Missense_Mutation	SNP	G	G	C	rs771456968	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1480G>C	p.Glu494Gln	p.E494Q	ENST00000511912	12/13	74	70	4	63	63	0	ETFDH,missense_variant,p.Glu447Gln,ENST00000307738,;ETFDH,missense_variant,p.Glu494Gln,ENST00000511912,;PPID,downstream_gene_variant,,ENST00000307720,;PPID,downstream_gene_variant,,ENST00000507213,;ETFDH,non_coding_transcript_exon_variant,,ENST00000506422,;PPID,downstream_gene_variant,,ENST00000512699,;	C	ENSG00000171503	ENST00000511912	Transcript	missense_variant	1812	1480	494	E/Q	Gaa/Caa	rs771456968	.	.	1	ETFDH	HGNC	3483	protein_coding	YES	CCDS3800.1	ENSP00000426638	ETFD_HUMAN	D6RAD5_HUMAN,B4DEQ0_HUMAN	UPI000013EC48	.	tolerated(0.24)	benign(0.005)	12/13	.	Superfamily_domains:SSF51905,Pfam_domain:PF05187,hmmpanther:PTHR10617,hmmpanther:PTHR10617:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACTTTGAACGG	byFrequency	2	ESCA
KLHL2	0	.	GRCh37	4	166149971	166149971	+	Silent	SNP	G	G	T	rs772024619	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177G>T	p.%3D	p.L59L	ENST00000514860	3/15	245	227	18	209	209	0	KLHL2,synonymous_variant,p.%3D,ENST00000514860,;KLHL2,synonymous_variant,p.%3D,ENST00000226725,;KLHL2,synonymous_variant,p.%3D,ENST00000509704,;KLHL2,synonymous_variant,p.%3D,ENST00000511305,;KLHL2,5_prime_UTR_variant,,ENST00000421009,;KLHL2,intron_variant,,ENST00000538127,;KLHL2,intron_variant,,ENST00000506824,;	T	ENSG00000109466	ENST00000514860	Transcript	synonymous_variant	427	177	59	L	ctG/ctT	rs772024619,COSM365296	.	.	1	KLHL2	HGNC	6353	protein_coding	YES	CCDS54815.1	ENSP00000424198	KLHL2_HUMAN	D6RGC3_HUMAN,B4DFZ5_HUMAN	UPI0000E20649	.	.	.	3/15	.	Superfamily_domains:SSF54695,PIRSF_domain:PIRSF037037,Pfam_domain:PF00651,Gene3D:3.30.710.10,hmmpanther:PTHR24412:SF155,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGCTGTGCGA	byFrequency	2	ESCA
CENPU	0	.	GRCh37	4	185637644	185637644	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.525G>A	p.%3D	p.E175E	ENST00000281453	6/13	77	72	5	93	93	0	CENPU,synonymous_variant,p.%3D,ENST00000541971,;CENPU,synonymous_variant,p.%3D,ENST00000514781,;CENPU,synonymous_variant,p.%3D,ENST00000281453,;CENPU,upstream_gene_variant,,ENST00000506535,;CENPU,synonymous_variant,p.%3D,ENST00000510146,;	T	ENSG00000151725	ENST00000281453	Transcript	synonymous_variant	596	525	175	E	gaG/gaA	.	.	.	-1	CENPU	HGNC	21348	protein_coding	YES	CCDS3838.1	ENSP00000281453	CENPU_HUMAN	D6R9S4_HUMAN	UPI00001BFAF6	.	.	.	6/13	.	Pfam_domain:PF13097,hmmpanther:PTHR32222:SF1,hmmpanther:PTHR32222	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTTTCTCTGA	.	2	ESCA
C4orf47	0	.	GRCh37	4	186361817	186361817	+	Missense_Mutation	SNP	G	G	C	rs541151554	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658G>C	p.Glu220Gln	p.E220Q	ENST00000378850	5/7	64	60	4	55	55	0	C4orf47,missense_variant,p.Glu220Gln,ENST00000378850,;CCDC110,downstream_gene_variant,,ENST00000307588,;CCDC110,downstream_gene_variant,,ENST00000393540,;C4orf47,downstream_gene_variant,,ENST00000511138,;C4orf47,downstream_gene_variant,,ENST00000511581,;C4orf47,3_prime_UTR_variant,,ENST00000508698,;CCDC110,downstream_gene_variant,,ENST00000508538,;C4orf47,downstream_gene_variant,,ENST00000512770,;C4orf47,downstream_gene_variant,,ENST00000501066,;	C	ENSG00000205129	ENST00000378850	Transcript	missense_variant	680	658	220	E/Q	Gaa/Caa	rs541151554	.	.	1	C4orf47	HGNC	34346	protein_coding	YES	CCDS47169.1	ENSP00000368127	CD047_HUMAN	D6RCA9_HUMAN,D6R9T4_HUMAN	UPI0000422C9D	.	tolerated(0.55)	benign(0.009)	5/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31144,hmmpanther:PTHR31144:SF1,Pfam_domain:PF15239	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAAGAAGAG	byFrequency|by1000G	2	ESCA
FRG1	0	.	GRCh37	4	190883076	190883076	+	Silent	SNP	G	G	C	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.729G>C	p.%3D	p.T243T	ENST00000226798	8/9	51	48	3	50	50	0	FRG1,synonymous_variant,p.%3D,ENST00000226798,;FRG1,downstream_gene_variant,,ENST00000531991,;FRG1,downstream_gene_variant,,ENST00000524583,;FRG1,non_coding_transcript_exon_variant,,ENST00000505327,;FRG1,downstream_gene_variant,,ENST00000514482,;FRG1,3_prime_UTR_variant,,ENST00000507103,;	C	ENSG00000109536	ENST00000226798	Transcript	synonymous_variant	951	729	243	T	acG/acC	COSM733762	.	.	1	FRG1	HGNC	3954	protein_coding	YES	CCDS34121.1	ENSP00000226798	FRG1_HUMAN	E9PRR7_HUMAN	UPI000012AC04	.	.	.	8/9	.	hmmpanther:PTHR12928,hmmpanther:PTHR12928:SF2,Pfam_domain:PF06229	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GAGACGCTTCT	.	2	ESCA
MXD4	0	.	GRCh37	4	2250936	2250936	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1335G>T	.	.	ENST00000337190	6/6	34	29	5	28	28	0	MXD4,3_prime_UTR_variant,,ENST00000337190,;MIR4800,downstream_gene_variant,,ENST00000537353,;MXD4,downstream_gene_variant,,ENST00000513372,;MXD4,downstream_gene_variant,,ENST00000513380,;	A	ENSG00000123933	ENST00000337190	Transcript	3_prime_UTR_variant	2279	.	.	.	.	.	.	.	-1	MXD4	HGNC	13906	protein_coding	YES	CCDS3361.1	ENSP00000337889	MAD4_HUMAN	D3DVQ5_HUMAN	UPI000012EB1A	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACCCTGAGC	.	4	ESCA
ZNF876P	0	.	GRCh37	4	248385	248385	+	RNA	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1209C>A	.	.	ENST00000356347	2/2	58	52	6	24	24	0	ZNF876P,non_coding_transcript_exon_variant,,ENST00000356347,;ZNF876P,non_coding_transcript_exon_variant,,ENST00000398732,;	A	ENSG00000198155	ENST00000356347	Transcript	non_coding_transcript_exon_variant	1209	.	.	.	.	.	.	.	1	ZNF876P	HGNC	32472	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACCCTACAA	.	4	ESCA
TBC1D19	0	.	GRCh37	4	26585671	26585671	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-145G>A	.	.	ENST00000264866	1/21	31	27	4	24	24	0	TBC1D19,5_prime_UTR_variant,,ENST00000264866,;TBC1D19,intron_variant,,ENST00000513455,;TBC1D19,intron_variant,,ENST00000512840,;TBC1D19,upstream_gene_variant,,ENST00000513596,;TBC1D19,upstream_gene_variant,,ENST00000505206,;TBC1D19,upstream_gene_variant,,ENST00000511789,;TBC1D19,intron_variant,,ENST00000504442,;TBC1D19,upstream_gene_variant,,ENST00000515568,;TBC1D19,upstream_gene_variant,,ENST00000502873,;	A	ENSG00000109680	ENST00000264866	Transcript	5_prime_UTR_variant	134	.	.	.	.	.	.	.	1	TBC1D19	HGNC	25624	protein_coding	YES	CCDS3439.1	ENSP00000264866	TBC19_HUMAN	.	UPI000004A0E3	.	.	.	1/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTCGGCAGT	.	2	ESCA
ATP10D	0	.	GRCh37	4	47562981	47562981	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2557G>T	p.Glu853Ter	p.E853*	ENST00000273859	14/23	97	89	8	69	69	0	ATP10D,stop_gained,p.Glu853Ter,ENST00000273859,;AC092597.3,upstream_gene_variant,,ENST00000508081,;ATP10D,3_prime_UTR_variant,,ENST00000503288,;	T	ENSG00000145246	ENST00000273859	Transcript	stop_gained	2826	2557	853	E/*	Gaa/Taa	.	.	.	1	ATP10D	HGNC	13549	protein_coding	YES	CCDS3476.1	ENSP00000273859	AT10D_HUMAN	.	UPI00001AE9B7	.	.	.	14/23	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF61,Gene3D:3.40.1110.10,Pfam_domain:PF12710,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACACTGAATAT	.	3	ESCA
FRYL	0	.	GRCh37	4	48622744	48622744	+	Missense_Mutation	SNP	G	G	A	rs371083439	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226C>T	p.Arg76Cys	p.R76C	ENST00000358350	6/64	87	80	7	69	69	0	FRYL,missense_variant,p.Arg168Cys,ENST00000505759,;FRYL,missense_variant,p.Arg76Cys,ENST00000358350,;FRYL,missense_variant,p.Arg76Cys,ENST00000503238,;FRYL,missense_variant,p.Arg76Cys,ENST00000507711,;FRYL,missense_variant,p.Arg76Cys,ENST00000537810,;FRYL,5_prime_UTR_variant,,ENST00000264319,;FRYL,non_coding_transcript_exon_variant,,ENST00000302806,;	A	ENSG00000075539	ENST00000358350	Transcript	missense_variant	831	226	76	R/C	Cgc/Tgc	rs371083439,COSM1055857	.	.	-1	FRYL	HGNC	29127	protein_coding	YES	CCDS43227.1	ENSP00000351113	FRYL_HUMAN	.	UPI0000EBC149	.	deleterious(0)	probably_damaging(0.991)	6/64	.	hmmpanther:PTHR12295:SF9,hmmpanther:PTHR12295	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTGCGAAGTA	byCluster	3	ESCA
STK32B	0	.	GRCh37	4	5448434	5448434	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.597C>G	p.%3D	p.G199G	ENST00000282908	7/12	65	56	8	75	75	0	STK32B,synonymous_variant,p.%3D,ENST00000510398,;STK32B,synonymous_variant,p.%3D,ENST00000512636,;STK32B,synonymous_variant,p.%3D,ENST00000282908,;STK32B,non_coding_transcript_exon_variant,,ENST00000508728,;STK32B,intron_variant,,ENST00000505508,;STK32B,3_prime_UTR_variant,,ENST00000512018,;STK32B,non_coding_transcript_exon_variant,,ENST00000511959,;	G	ENSG00000152953	ENST00000282908	Transcript	synonymous_variant	1019	597	199	G	ggC/ggG	.	.	.	1	STK32B	HGNC	14217	protein_coding	YES	CCDS3380.1	ENSP00000282908	ST32B_HUMAN	Q69YP0_HUMAN	UPI0000035B46	.	.	.	7/12	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24356:SF137,hmmpanther:PTHR24356,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGGCCCCGG	.	4	ESCA
KIT	0	.	GRCh37	4	55604640	55604640	+	Missense_Mutation	SNP	G	G	T	rs146374006	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2848G>T	p.Val950Leu	p.V950L	ENST00000288135	21/21	82	74	7	63	63	0	KIT,missense_variant,p.Val946Leu,ENST00000412167,;KIT,missense_variant,p.Val950Leu,ENST00000288135,;	T	ENSG00000157404	ENST00000288135	Transcript	missense_variant	2945	2848	950	V/L	Gtg/Ttg	rs146374006	.	.	1	KIT	HGNC	6342	protein_coding	YES	CCDS3496.1	ENSP00000288135	KIT_HUMAN	Q8TCG9_HUMAN	UPI000003F17D	.	tolerated(0.81)	benign(0.09)	21/21	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF46,PIRSF_domain:PIRSF000615,PIRSF_domain:PIRSF500951	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCCGTGGTA	byCluster	4	ESCA
MUC7	0	.	GRCh37	4	71347113	71347113	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652C>A	p.Pro218Thr	p.P218T	ENST00000413702	4/4	222	188	34	152	152	0	MUC7,missense_variant,p.Pro218Thr,ENST00000413702,;MUC7,missense_variant,p.Pro218Thr,ENST00000456088,;MUC7,missense_variant,p.Pro218Thr,ENST00000304887,;MUC7,downstream_gene_variant,,ENST00000505411,;MUC7,downstream_gene_variant,,ENST00000514512,;MUC7,downstream_gene_variant,,ENST00000504482,;	A	ENSG00000171195	ENST00000413702	Transcript	missense_variant	940	652	218	P/T	Cct/Act	.	.	.	1	MUC7	HGNC	7518	protein_coding	YES	CCDS3541.1	ENSP00000407422	MUC7_HUMAN	D6RHX1_HUMAN	UPI000013E9DD	.	tolerated(0.56)	unknown(0)	4/4	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACACCTCCT	.	4	ESCA
ENAM	0	.	GRCh37	4	71508513	71508513	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1370C>T	p.Pro457Leu	p.P457L	ENST00000396073	9/9	75	63	12	52	52	0	ENAM,missense_variant,p.Pro457Leu,ENST00000396073,;ENAM,intron_variant,,ENST00000472903,;ENAM,downstream_gene_variant,,ENST00000472597,;	T	ENSG00000132464	ENST00000396073	Transcript	missense_variant	1651	1370	457	P/L	cCc/cTc	COSM375794	.	.	1	ENAM	HGNC	3344	protein_coding	YES	CCDS3544.2	ENSP00000379383	ENAM_HUMAN	Q8NFB4_HUMAN	UPI000013CE60	.	tolerated(0.11)	benign(0.149)	9/9	.	Pfam_domain:PF15362,hmmpanther:PTHR16784:SF2,hmmpanther:PTHR16784	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCCCCTGGA	.	4	ESCA
SOWAHB	0	.	GRCh37	4	77816952	77816952	+	Missense_Mutation	SNP	C	C	A	rs762574027	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2051G>T	p.Gly684Val	p.G684V	ENST00000334306	1/1	46	41	5	39	39	0	SOWAHB,missense_variant,p.Gly684Val,ENST00000334306,;RP11-123J14.1,downstream_gene_variant,,ENST00000485829,;	A	ENSG00000186212	ENST00000334306	Transcript	missense_variant	2051	2051	684	G/V	gGg/gTg	rs762574027	.	.	-1	SOWAHB	HGNC	32958	protein_coding	YES	CCDS34017.1	ENSP00000334879	SWAHB_HUMAN	.	UPI000019777A	.	tolerated(0.11)	probably_damaging(0.988)	1/1	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,Gene3D:1.25.40.20,Pfam_domain:PF12796,hmmpanther:PTHR14491,hmmpanther:PTHR14491:SF3,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGACCCCCTGG	.	3	ESCA
GPR78	0	.	GRCh37	4	8583004	8583004	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295G>T	p.Ala99Ser	p.A99S	ENST00000382487	1/3	27	24	3	14	14	0	GPR78,missense_variant,p.Ala99Ser,ENST00000382487,;GPR78,intron_variant,,ENST00000509216,;GPR78,downstream_gene_variant,,ENST00000503981,;GPR78,upstream_gene_variant,,ENST00000504255,;GPR78,downstream_gene_variant,,ENST00000503448,;GPR78,missense_variant,p.Ala99Ser,ENST00000514302,;	T	ENSG00000155269	ENST00000382487	Transcript	missense_variant	712	295	99	A/S	Gcg/Tcg	.	.	.	1	GPR78	HGNC	4528	protein_coding	YES	CCDS3403.1	ENSP00000371927	GPR78_HUMAN	D6RB95_HUMAN,B2R7M4_HUMAN	UPI0000037A5F	.	deleterious(0.01)	probably_damaging(0.998)	1/3	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF5,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCGGCGCTG	.	2	ESCA
UNC5C	0	.	GRCh37	4	96123921	96123921	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2097C>G	p.Ile699Met	p.I699M	ENST00000453304	12/16	56	52	4	42	42	0	UNC5C,missense_variant,p.Ile718Met,ENST00000513796,;UNC5C,missense_variant,p.Ile699Met,ENST00000453304,;	C	ENSG00000182168	ENST00000453304	Transcript	missense_variant	2446	2097	699	I/M	atC/atG	.	.	.	-1	UNC5C	HGNC	12569	protein_coding	YES	CCDS3643.1	ENSP00000406022	UNC5C_HUMAN	Q4W5H4_HUMAN	UPI000004E6A5	.	tolerated(0.07)	possibly_damaging(0.459)	12/16	.	hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R700Q|c.2099G>A|3	MUTECT|VARSCANS	ACTCGGATGCT	.	2	ESCA
TSSK1B	0	.	GRCh37	5	112769133	112769133	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*300G>A	.	.	ENST00000390666	1/1	53	48	5	54	54	0	TSSK1B,3_prime_UTR_variant,,ENST00000390666,;MCC,intron_variant,,ENST00000408903,;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000383058,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,;	T	ENSG00000212122	ENST00000390666	Transcript	3_prime_UTR_variant	1596	.	.	.	.	.	.	.	-1	TSSK1B	HGNC	14968	protein_coding	YES	CCDS4112.1	ENSP00000375081	TSSK1_HUMAN	A0ZT98_HUMAN	UPI000003C96E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGCCGTTGC	.	4	ESCA
KLHL3	0	.	GRCh37	5	136957111	136957111	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*676C>T	.	.	ENST00000309755	15/15	19	16	3	12	12	0	KLHL3,3_prime_UTR_variant,,ENST00000506491,;KLHL3,3_prime_UTR_variant,,ENST00000309755,;KLHL3,3_prime_UTR_variant,,ENST00000508657,;KLHL3,downstream_gene_variant,,ENST00000541417,;KLHL3,downstream_gene_variant,,ENST00000506873,;KLHL3,non_coding_transcript_exon_variant,,ENST00000447439,;KLHL3,intron_variant,,ENST00000509694,;KLHL3,downstream_gene_variant,,ENST00000504208,;	A	ENSG00000146021	ENST00000309755	Transcript	3_prime_UTR_variant	2884	.	.	.	.	.	.	.	-1	KLHL3	HGNC	6354	protein_coding	YES	CCDS4192.1	ENSP00000312397	KLHL3_HUMAN	Q8N4I8_HUMAN,Q49A42_HUMAN	UPI000012DE05	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GAGCTGAGAAG	.	2	ESCA
PCDHA1	0	.	GRCh37	5	140167367	140167367	+	Silent	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1492C>A	p.%3D	p.R498R	ENST00000504120	1/4	175	167	8	164	164	0	PCDHA1,synonymous_variant,p.%3D,ENST00000504120,;PCDHA1,synonymous_variant,p.%3D,ENST00000394633,;PCDHA1,synonymous_variant,p.%3D,ENST00000378133,;	A	ENSG00000204970	ENST00000504120	Transcript	synonymous_variant	1492	1492	498	R	Cgg/Agg	COSM589748,COSM589747	.	.	1	PCDHA1	HGNC	8663	protein_coding	YES	CCDS54913.1	ENSP00000420840	PCDA1_HUMAN	.	UPI00001273C7	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF92,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACGGCGGGTG	.	2	ESCA
PCDHA5	0	.	GRCh37	5	140201574	140201574	+	Missense_Mutation	SNP	G	G	T	rs372036084	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214G>T	p.Asp72Tyr	p.D72Y	ENST00000529859	1/4	162	154	8	141	140	0	PCDHA5,missense_variant,p.Asp72Tyr,ENST00000529619,;PCDHA5,missense_variant,p.Asp72Tyr,ENST00000378126,;PCDHA5,missense_variant,p.Asp72Tyr,ENST00000529859,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA4,intron_variant,,ENST00000512229,;	T	ENSG00000204965	ENST00000529859	Transcript	missense_variant	214	214	72	D/Y	Gac/Tac	rs372036084	.	.	1	PCDHA5	HGNC	8671	protein_coding	YES	CCDS54917.1	ENSP00000436557	PCDA5_HUMAN	.	UPI00001273CD	.	deleterious_low_confidence(0)	probably_damaging(0.98)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF111,Gene3D:2.60.40.60,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGGGGACCTT	byCluster	2	ESCA
PCDHA9	0	.	GRCh37	5	140229361	140229361	+	Silent	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1281G>T	p.%3D	p.A427A	ENST00000532602	1/4	176	168	8	141	141	0	PCDHA9,synonymous_variant,p.%3D,ENST00000378122,;PCDHA9,synonymous_variant,p.%3D,ENST00000532602,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	T	ENSG00000204961	ENST00000532602	Transcript	synonymous_variant	2314	1281	427	A	gcG/gcT	COSM482098,COSM482097	.	.	1	PCDHA9	HGNC	8675	protein_coding	YES	CCDS54920.1	ENSP00000436042	PCDA9_HUMAN	.	UPI00001273D1	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCGCGCGGGA	.	2	ESCA
PCDHA12	0	.	GRCh37	5	140255196	140255196	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.139C>T	p.Arg47Cys	p.R47C	ENST00000398631	1/4	165	158	7	139	139	0	PCDHA12,missense_variant,p.Arg47Cys,ENST00000398631,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	T	ENSG00000251664	ENST00000398631	Transcript	missense_variant	139	139	47	R/C	Cgc/Tgc	COSM3610204	.	.	1	PCDHA12	HGNC	8666	protein_coding	YES	CCDS47285.1	ENSP00000381628	PCDAC_HUMAN	.	UPI00001273D5	.	deleterious_low_confidence(0.01)	possibly_damaging(0.883)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF76,hmmpanther:PTHR24028,Pfam_domain:PF08266,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGGCCGCATC	.	2	ESCA
PCDHB17	0	.	GRCh37	5	140537208	140537208	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1632C>G	p.Ser544Arg	p.S544R	ENST00000539533	1/1	286	272	14	255	255	0	PCDHB17,missense_variant,p.Ser544Arg,ENST00000539533,;PCDHB6,downstream_gene_variant,,ENST00000543635,;PCDHB6,downstream_gene_variant,,ENST00000231136,;	G	ENSG00000255622	ENST00000539533	Transcript	missense_variant	1632	1632	544	S/R	agC/agG	.	.	.	1	PCDHB17	Uniprot_gn	.	protein_coding	YES	.	ENSP00000438685	.	Q96T98_HUMAN	UPI000006CE19	.	deleterious_low_confidence(0)	possibly_damaging(0.493)	1/1	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAGCGAGGC	.	2	ESCA
PCDHB14	0	.	GRCh37	5	140603152	140603152	+	Silent	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75G>T	p.%3D	p.R25R	ENST00000239449	1/1	88	82	6	90	90	0	PCDHB14,synonymous_variant,p.%3D,ENST00000239449,;PCDHB14,intron_variant,,ENST00000515856,;	T	ENSG00000120327	ENST00000239449	Transcript	synonymous_variant	75	75	25	R	cgG/cgT	COSM1542176	.	.	1	PCDHB14	HGNC	8685	protein_coding	YES	CCDS4256.1	ENSP00000239449	PCDBE_HUMAN	B4DPE2_HUMAN	UPI00001273E7	.	.	.	1/1	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCGGGCAGG	.	2	ESCA
PCDHB18	0	.	GRCh37	5	140615746	140615746	+	RNA	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1809G>A	.	.	ENST00000526308	1/1	267	256	11	263	263	0	PCDHB18,non_coding_transcript_exon_variant,,ENST00000526308,;PCDHB18,non_coding_transcript_exon_variant,,ENST00000524813,;PCDHB19P,upstream_gene_variant,,ENST00000570871,;	A	ENSG00000146001	ENST00000526308	Transcript	non_coding_transcript_exon_variant	1809	.	.	.	.	.	.	.	1	PCDHB18	HGNC	14548	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGGCGCTGAG	.	2	ESCA
PCDHGA10	0	.	GRCh37	5	140794996	140794996	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2254G>T	p.Ala752Ser	p.A752S	ENST00000398610	1/4	149	140	8	127	126	1	PCDHGA10,missense_variant,p.Ala752Ser,ENST00000398610,;PCDHGB6,intron_variant,,ENST00000520790,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGB7,upstream_gene_variant,,ENST00000398594,;	T	ENSG00000253846	ENST00000398610	Transcript	missense_variant	2254	2254	752	A/S	Gct/Tct	.	.	.	1	PCDHGA10	HGNC	8697	protein_coding	YES	CCDS47292.1	ENSP00000381611	PCDGA_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI00000726C3	.	deleterious_low_confidence(0)	benign(0.419)	1/4	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCGGGCTTTC	.	2	ESCA
PCDH12	0	.	GRCh37	5	141331136	141331136	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2900C>A	p.Ser967Tyr	p.S967Y	ENST00000231484	2/4	72	66	6	66	66	0	PCDH12,missense_variant,p.Ser967Tyr,ENST00000231484,;AC005740.6,upstream_gene_variant,,ENST00000607378,;	T	ENSG00000113555	ENST00000231484	Transcript	missense_variant	4111	2900	967	S/Y	tCc/tAc	.	.	.	-1	PCDH12	HGNC	8657	protein_coding	YES	CCDS4269.1	ENSP00000231484	PCD12_HUMAN	E5RJD4_HUMAN	UPI00001313B4	.	deleterious(0)	probably_damaging(0.999)	2/4	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAAGGACAGC	.	3	ESCA
LARS	0	.	GRCh37	5	145543902	145543902	+	Missense_Mutation	SNP	T	T	C	rs199808937	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565A>G	p.Ile189Val	p.I189V	ENST00000394434	6/32	115	109	6	95	95	0	LARS,missense_variant,p.Ile189Val,ENST00000394434,;LARS,missense_variant,p.Ile143Val,ENST00000545646,;LARS,missense_variant,p.Ile162Val,ENST00000274562,;LARS,missense_variant,p.Ile135Val,ENST00000510191,;LARS,non_coding_transcript_exon_variant,,ENST00000511505,;LARS,downstream_gene_variant,,ENST00000505223,;LARS,downstream_gene_variant,,ENST00000503654,;	C	ENSG00000133706	ENST00000394434	Transcript	missense_variant	732	565	189	I/V	Att/Gtt	rs199808937,COSM3728147	.	.	-1	LARS	HGNC	6512	protein_coding	YES	CCDS34265.1	ENSP00000377954	SYLC_HUMAN	Q9NVC0_HUMAN,Q9NPU8_HUMAN,Q9HAM7_HUMAN,Q2TU79_HUMAN,B4DJ10_HUMAN,B3KXA9_HUMAN	UPI0000037316	.	tolerated(1)	benign(0.002)	6/32	.	hmmpanther:PTHR11946:SF51,hmmpanther:PTHR11946,Pfam_domain:PF00133,Gene3D:3.40.50.620,TIGRFAM_domain:TIGR00395,Superfamily_domains:SSF52374	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTGAATAGCCA	byFrequency|byCluster	2	ESCA
RBM27	0	.	GRCh37	5	145613110	145613110	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.948C>G	p.Phe316Leu	p.F316L	ENST00000265271	7/21	90	82	7	91	91	0	RBM27,missense_variant,p.Phe316Leu,ENST00000265271,;RBM27,missense_variant,p.Phe316Leu,ENST00000506502,;	G	ENSG00000091009	ENST00000265271	Transcript	missense_variant	1114	948	316	F/L	ttC/ttG	.	.	.	1	RBM27	HGNC	29243	protein_coding	YES	CCDS43378.1	ENSP00000265271	RBM27_HUMAN	.	UPI00001D7F03	.	deleterious(0.02)	benign(0.18)	7/21	.	hmmpanther:PTHR14398:SF1,hmmpanther:PTHR14398	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTTTCCCACC	.	3	ESCA
DPYSL3	0	.	GRCh37	5	146773361	146773361	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*237G>T	.	.	ENST00000343218	14/14	74	66	8	61	61	0	DPYSL3,3_prime_UTR_variant,,ENST00000398514,;DPYSL3,3_prime_UTR_variant,,ENST00000534907,;DPYSL3,3_prime_UTR_variant,,ENST00000343218,;DPYSL3,downstream_gene_variant,,ENST00000520473,;DPYSL3,downstream_gene_variant,,ENST00000507309,;DPYSL3,downstream_gene_variant,,ENST00000523458,;	A	ENSG00000113657	ENST00000343218	Transcript	3_prime_UTR_variant	2490	.	.	.	.	.	.	.	-1	DPYSL3	HGNC	3015	protein_coding	YES	CCDS56387.1	ENSP00000343690	DPYL3_HUMAN	F5GWI3_HUMAN	UPI000020CF0E	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GCATGCATGTA	.	3	ESCA
JAKMIP2	0	.	GRCh37	5	147040585	147040585	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553C>A	p.%3D	p.R185R	ENST00000265272	3/21	56	52	4	43	43	0	JAKMIP2,synonymous_variant,p.%3D,ENST00000265272,;JAKMIP2,synonymous_variant,p.%3D,ENST00000333010,;JAKMIP2,synonymous_variant,p.%3D,ENST00000507386,;JAKMIP2,non_coding_transcript_exon_variant,,ENST00000507343,;	T	ENSG00000176049	ENST00000265272	Transcript	synonymous_variant	1021	553	185	R	Cgg/Agg	.	.	.	-1	JAKMIP2	HGNC	29067	protein_coding	YES	CCDS4285.1	ENSP00000265272	JKIP2_HUMAN	.	UPI000000D782	.	.	.	3/21	.	hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTCCGAAGGT	.	2	ESCA
SLC6A7	0	.	GRCh37	5	149578905	149578905	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.699C>A	p.%3D	p.L233L	ENST00000230671	5/14	108	102	5	74	74	0	SLC6A7,synonymous_variant,p.%3D,ENST00000230671,;SLC6A7,synonymous_variant,p.%3D,ENST00000524041,;SLC6A7,downstream_gene_variant,,ENST00000513403,;	A	ENSG00000011083	ENST00000230671	Transcript	synonymous_variant	1070	699	233	L	ctC/ctA	.	.	.	1	SLC6A7	HGNC	11054	protein_coding	YES	CCDS4305.1	ENSP00000230671	SC6A7_HUMAN	.	UPI000013C93C	.	.	.	5/14	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF35,Pfam_domain:PF00209,Superfamily_domains:0053687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCTCAAGGG	.	2	ESCA
PDZD2	0	.	GRCh37	5	31983407	31983407	+	Missense_Mutation	SNP	G	G	A	rs149201593	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.623G>A	p.Arg208Gln	p.R208Q	ENST00000438447	3/25	89	84	5	77	77	0	PDZD2,missense_variant,p.Arg208Gln,ENST00000438447,;PDZD2,missense_variant,p.Arg208Gln,ENST00000282493,;PDZD2,non_coding_transcript_exon_variant,,ENST00000513852,;PDZD2,non_coding_transcript_exon_variant,,ENST00000502489,;	A	ENSG00000133401	ENST00000438447	Transcript	missense_variant	1011	623	208	R/Q	cGa/cAa	rs149201593	.	.	1	PDZD2	HGNC	18486	protein_coding	YES	CCDS34137.1	ENSP00000402033	PDZD2_HUMAN	B4DGS3_HUMAN	UPI000069648B	.	tolerated(0.46)	benign(0.003)	3/25	.	hmmpanther:PTHR11324:SF16,hmmpanther:PTHR11324	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	A:0.0011	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A210V|c.629C>T|3	MUTECT|MUSE	TGACCGAACTG	byFrequency|byCluster|by1000G	2	ESCA
FYB	0	.	GRCh37	5	39202128	39202128	+	Missense_Mutation	SNP	C	C	A	rs751971634	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.965G>T	p.Arg322Met	p.R322M	ENST00000540520	2/19	115	106	9	93	93	0	FYB,missense_variant,p.Arg312Met,ENST00000515010,;FYB,missense_variant,p.Arg312Met,ENST00000351578,;FYB,missense_variant,p.Arg312Met,ENST00000505428,;FYB,missense_variant,p.Arg322Met,ENST00000540520,;FYB,missense_variant,p.Arg312Met,ENST00000512982,;FYB,downstream_gene_variant,,ENST00000512138,;FYB,downstream_gene_variant,,ENST00000506557,;FYB,downstream_gene_variant,,ENST00000510188,;FYB,downstream_gene_variant,,ENST00000509072,;FYB,downstream_gene_variant,,ENST00000504542,;	A	ENSG00000082074	ENST00000540520	Transcript	missense_variant	1051	965	322	R/M	aGg/aTg	rs751971634	.	.	-1	FYB	HGNC	4036	protein_coding	YES	CCDS58945.1	ENSP00000442840	FYB_HUMAN	D6RFJ5_HUMAN,D6RER7_HUMAN,D6RC38_HUMAN,D6RAE8_HUMAN	UPI00017A75FB	.	deleterious(0.03)	benign(0.1)	2/19	.	hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGAACCTGGCA	.	3	ESCA
ACTBL2	0	.	GRCh37	5	56777851	56777851	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.684G>T	p.Met228Ile	p.M228I	ENST00000423391	1/1	55	51	4	53	52	1	ACTBL2,missense_variant,p.Met228Ile,ENST00000423391,;AC025470.1,upstream_gene_variant,,ENST00000584598,;CTD-2023N9.1,intron_variant,,ENST00000506106,;	A	ENSG00000169067	ENST00000423391	Transcript	missense_variant	786	684	228	M/I	atG/atT	.	.	.	-1	ACTBL2	HGNC	17780	protein_coding	YES	CCDS34163.1	ENSP00000416706	ACTBL_HUMAN	.	UPI000013EB83	.	tolerated_low_confidence(0.07)	benign(0.039)	1/1	.	hmmpanther:PTHR11937:SF168,hmmpanther:PTHR11937,Pfam_domain:PF00022,Gene3D:3.90.640.10,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGACCATCTC	.	2	ESCA
ANKRA2	0	.	GRCh37	5	72849262	72849262	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855G>T	p.Met285Ile	p.M285I	ENST00000296785	8/9	33	29	4	18	18	0	ANKRA2,missense_variant,p.Met285Ile,ENST00000296785,;ANKRA2,downstream_gene_variant,,ENST00000504641,;ANKRA2,non_coding_transcript_exon_variant,,ENST00000515249,;ANKRA2,non_coding_transcript_exon_variant,,ENST00000505301,;ANKRA2,downstream_gene_variant,,ENST00000506130,;ANKRA2,downstream_gene_variant,,ENST00000515804,;ANKRA2,downstream_gene_variant,,ENST00000514916,;	A	ENSG00000164331	ENST00000296785	Transcript	missense_variant	1514	855	285	M/I	atG/atT	.	.	.	-1	ANKRA2	HGNC	13208	protein_coding	YES	CCDS4020.1	ENSP00000296785	ANRA2_HUMAN	.	UPI0000125B54	.	deleterious(0.04)	possibly_damaging(0.898)	8/9	.	PROSITE_profiles:PS50297,hmmpanther:PTHR24124:SF3,hmmpanther:PTHR24124,Gene3D:1.25.40.20,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGATCCATAGA	.	4	ESCA
NBPF22P	0	.	GRCh37	5	85583508	85583508	+	RNA	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.774G>C	.	.	ENST00000590707	5/8	133	125	8	158	158	0	NBPF22P,non_coding_transcript_exon_variant,,ENST00000590707,;NBPF22P,non_coding_transcript_exon_variant,,ENST00000508988,;	C	ENSG00000205449	ENST00000590707	Transcript	non_coding_transcript_exon_variant	774	.	.	.	.	.	.	.	1	NBPF22P	HGNC	28731	processed_transcript	YES	.	.	.	.	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGCTGCCAGA	.	2	ESCA
PHACTR1	0	.	GRCh37	6	13228205	13228205	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1144G>T	p.Glu382Ter	p.E382*	ENST00000379350	8/10	70	62	8	58	58	0	PHACTR1,stop_gained,p.Glu382Ter,ENST00000379350,;PHACTR1,stop_gained,p.Glu382Ter,ENST00000332995,;PHACTR1,stop_gained,p.Glu217Ter,ENST00000415087,;PHACTR1,stop_gained,p.Glu237Ter,ENST00000457702,;PHACTR1,intron_variant,,ENST00000434977,;PHACTR1,intron_variant,,ENST00000379345,;	T	ENSG00000112137	ENST00000379350	Transcript	stop_gained	1273	1144	382	E/*	Gag/Tag	COSM1329304	.	.	1	PHACTR1	HGNC	20990	protein_coding	.	.	ENSP00000368655	PHAR1_HUMAN	.	UPI000020D534	.	.	.	8/10	.	hmmpanther:PTHR12751,hmmpanther:PTHR12751:SF6	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCATGAGTCA	.	4	ESCA
TXLNB	0	.	GRCh37	6	139564250	139564250	+	Missense_Mutation	SNP	C	C	T	rs760921583	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1468G>A	p.Ala490Thr	p.A490T	ENST00000358430	10/10	84	76	8	69	69	0	TXLNB,missense_variant,p.Ala490Thr,ENST00000358430,;RP1-225E12.2,upstream_gene_variant,,ENST00000590219,;RP1-225E12.2,upstream_gene_variant,,ENST00000585447,;RP1-225E12.2,upstream_gene_variant,,ENST00000588529,;RP1-225E12.2,upstream_gene_variant,,ENST00000586229,;RP1-225E12.2,upstream_gene_variant,,ENST00000415194,;RP1-225E12.2,upstream_gene_variant,,ENST00000587814,;RP1-225E12.2,upstream_gene_variant,,ENST00000591102,;RP1-225E12.2,upstream_gene_variant,,ENST00000592557,;RP1-225E12.2,upstream_gene_variant,,ENST00000587333,;RP1-225E12.2,upstream_gene_variant,,ENST00000586266,;RP1-225E12.2,upstream_gene_variant,,ENST00000587577,;RP1-225E12.2,upstream_gene_variant,,ENST00000588638,;RP1-225E12.2,upstream_gene_variant,,ENST00000590679,;RP1-225E12.2,upstream_gene_variant,,ENST00000589192,;RP1-225E12.3,intron_variant,,ENST00000585874,;	T	ENSG00000164440	ENST00000358430	Transcript	missense_variant	1701	1468	490	A/T	Gca/Aca	rs760921583	.	.	-1	TXLNB	HGNC	21617	protein_coding	YES	CCDS34545.1	ENSP00000351206	TXLNB_HUMAN	H0UI60_HUMAN	UPI0000072983	.	tolerated(0.3)	benign(0.025)	10/10	.	hmmpanther:PTHR16127,hmmpanther:PTHR16127:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTCTGCGTCAA	byFrequency	3	ESCA
SHPRH	0	.	GRCh37	6	146269407	146269407	+	Splice_Site	SNP	C	C	T	rs775241899	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1061+1G>A	.	p.X354_splice	ENST00000367505	.	104	97	6	92	92	0	SHPRH,splice_donor_variant,,ENST00000275233,;SHPRH,splice_donor_variant,,ENST00000438092,;SHPRH,splice_donor_variant,,ENST00000367505,;SHPRH,splice_donor_variant,,ENST00000367503,;SHPRH,splice_donor_variant,,ENST00000521977,;SHPRH,splice_donor_variant,,ENST00000519632,;SHPRH,splice_donor_variant,,ENST00000433355,;	T	ENSG00000146414	ENST00000367505	Transcript	splice_donor_variant	.	.	.	.	.	rs775241899	.	.	-1	SHPRH	HGNC	19336	protein_coding	YES	CCDS43513.2	ENSP00000356475	SHPRH_HUMAN	.	UPI0000458A24	.	.	.	.	5/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTACCAGCC	.	2	ESCA
ZC3H12D	0	.	GRCh37	6	149771832	149771832	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1571T>A	p.Leu524Gln	p.L524Q	ENST00000409806	6/6	70	63	7	44	44	0	ZC3H12D,missense_variant,p.Leu524Gln,ENST00000409806,;ZC3H12D,missense_variant,p.Leu524Gln,ENST00000389942,;ZC3H12D,3_prime_UTR_variant,,ENST00000416573,;ZC3H12D,downstream_gene_variant,,ENST00000542614,;ZC3H12D,downstream_gene_variant,,ENST00000458251,;ZC3H12D,upstream_gene_variant,,ENST00000498662,;	T	ENSG00000178199	ENST00000409806	Transcript	missense_variant	1890	1571	524	L/Q	cTg/cAg	.	.	.	-1	ZC3H12D	HGNC	21175	protein_coding	YES	.	ENSP00000386616	ZC12D_HUMAN	.	UPI00002377F7	.	deleterious_low_confidence(0.01)	benign(0.445)	6/6	.	hmmpanther:PTHR12876:SF11,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCCCAGGGGC	.	3	ESCA
TCP1	0	.	GRCh37	6	160206497	160206497	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.409A>T	p.Ile137Phe	p.I137F	ENST00000321394	5/12	54	47	6	54	54	0	TCP1,missense_variant,p.Ile115Phe,ENST00000539948,;TCP1,missense_variant,p.Ile137Phe,ENST00000321394,;TCP1,missense_variant,p.Ile17Phe,ENST00000538128,;TCP1,missense_variant,p.Ile137Phe,ENST00000420894,;TCP1,5_prime_UTR_variant,,ENST00000392168,;TCP1,intron_variant,,ENST00000544255,;TCP1,intron_variant,,ENST00000539756,;TCP1,downstream_gene_variant,,ENST00000536394,;TCP1,downstream_gene_variant,,ENST00000537390,;SNORA29,downstream_gene_variant,,ENST00000384183,;TCP1,intron_variant,,ENST00000543532,;MRPL18,upstream_gene_variant,,ENST00000476826,;MRPL18,upstream_gene_variant,,ENST00000479638,;TCP1,downstream_gene_variant,,ENST00000546023,;TCP1,3_prime_UTR_variant,,ENST00000538530,;TCP1,3_prime_UTR_variant,,ENST00000543517,;TCP1,non_coding_transcript_exon_variant,,ENST00000467544,;TCP1,non_coding_transcript_exon_variant,,ENST00000545764,;TCP1,downstream_gene_variant,,ENST00000536607,;TCP1,upstream_gene_variant,,ENST00000536807,;	A	ENSG00000120438	ENST00000321394	Transcript	missense_variant	690	409	137	I/F	Att/Ttt	.	.	.	-1	TCP1	HGNC	11655	protein_coding	YES	CCDS5269.1	ENSP00000317334	TCPA_HUMAN	F5H726_HUMAN,F5H676_HUMAN,F5H282_HUMAN,F5H136_HUMAN,E7EQR6_HUMAN	UPI0000136AEA	.	deleterious(0.01)	benign(0.135)	5/12	.	hmmpanther:PTHR11353,TIGRFAM_domain:TIGR02340,Pfam_domain:PF00118,Superfamily_domains:SSF48592	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACAATTAGGT	.	4	ESCA
MRPL18	0	.	GRCh37	6	160212043	160212043	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>A	p.Glu42Lys	p.E42K	ENST00000367034	2/4	108	98	10	79	79	0	MRPL18,missense_variant,p.Glu42Lys,ENST00000367034,;TCP1,upstream_gene_variant,,ENST00000392168,;TCP1,upstream_gene_variant,,ENST00000536394,;TCP1,upstream_gene_variant,,ENST00000544255,;TCP1,upstream_gene_variant,,ENST00000539948,;TCP1,upstream_gene_variant,,ENST00000321394,;TCP1,upstream_gene_variant,,ENST00000538128,;TCP1,upstream_gene_variant,,ENST00000537390,;TCP1,upstream_gene_variant,,ENST00000539756,;TCP1,upstream_gene_variant,,ENST00000420894,;MRPL18,non_coding_transcript_exon_variant,,ENST00000476826,;MRPL18,non_coding_transcript_exon_variant,,ENST00000479638,;MRPL18,non_coding_transcript_exon_variant,,ENST00000480842,;TCP1,upstream_gene_variant,,ENST00000543532,;TCP1,upstream_gene_variant,,ENST00000546023,;TCP1,upstream_gene_variant,,ENST00000538530,;TCP1,upstream_gene_variant,,ENST00000536607,;TCP1,upstream_gene_variant,,ENST00000545764,;TCP1,upstream_gene_variant,,ENST00000543517,;	A	ENSG00000112110	ENST00000367034	Transcript	missense_variant	246	124	42	E/K	Gaa/Aaa	.	.	.	1	MRPL18	HGNC	14477	protein_coding	YES	CCDS5270.1	ENSP00000356001	RM18_HUMAN	.	UPI0000037B54	.	deleterious(0.05)	benign(0.013)	2/4	.	hmmpanther:PTHR12899:SF3,hmmpanther:PTHR12899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAATGAAGCT	.	3	ESCA
SLC22A2	0	.	GRCh37	6	160664752	160664752	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1131C>A	p.Tyr377Ter	p.Y377*	ENST00000366953	7/11	78	63	15	49	49	0	SLC22A2,stop_gained,p.Tyr377Ter,ENST00000366953,;SLC22A2,downstream_gene_variant,,ENST00000366952,;SLC22A2,non_coding_transcript_exon_variant,,ENST00000486916,;SLC22A2,non_coding_transcript_exon_variant,,ENST00000491092,;	T	ENSG00000112499	ENST00000366953	Transcript	stop_gained	1390	1131	377	Y/*	taC/taA	.	.	.	-1	SLC22A2	HGNC	10966	protein_coding	YES	CCDS5276.1	ENSP00000355920	S22A2_HUMAN	Q5T7Q5_HUMAN	UPI000013D5BB	.	.	.	7/11	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00898,Gene3D:1.20.1250.20,Pfam_domain:PF00083,hmmpanther:PTHR24064:SF173,hmmpanther:PTHR24064,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGGTAGAT	.	5	ESCA
PLG	0	.	GRCh37	6	161139416	161139416	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.878G>A	p.Gly293Glu	p.G293E	ENST00000308192	8/19	53	48	5	58	58	0	PLG,missense_variant,p.Gly293Glu,ENST00000308192,;PLG,intron_variant,,ENST00000297289,;	A	ENSG00000122194	ENST00000308192	Transcript	missense_variant	941	878	293	G/E	gGg/gAg	.	.	.	1	PLG	HGNC	9071	protein_coding	YES	CCDS5279.1	ENSP00000308938	PLMN_HUMAN	Q9UMI2_HUMAN,Q68DS2_HUMAN,Q5TEH5_HUMAN,B4DPH4_HUMAN	UPI000000D8B8	.	deleterious(0.01)	probably_damaging(0.995)	8/19	.	PROSITE_profiles:PS50070,hmmpanther:PTHR24259,hmmpanther:PTHR24259:SF70,Pfam_domain:PF00051,Gene3D:2.40.20.10,SMART_domains:SM00130,PIRSF_domain:PIRSF001150,Superfamily_domains:SSF57440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCCGGGCACA	.	3	ESCA
PACRG	0	.	GRCh37	6	163483273	163483273	+	Missense_Mutation	SNP	G	G	T	rs370616018	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383G>T	p.Arg128Leu	p.R128L	ENST00000337019	4/7	73	69	4	57	57	0	PACRG,missense_variant,p.Arg44Leu,ENST00000534958,;PACRG,missense_variant,p.Arg128Leu,ENST00000366888,;PACRG,missense_variant,p.Arg128Leu,ENST00000337019,;PACRG,missense_variant,p.Arg128Leu,ENST00000366889,;PACRG,upstream_gene_variant,,ENST00000542936,;PACRG,non_coding_transcript_exon_variant,,ENST00000545186,;PACRG,3_prime_UTR_variant,,ENST00000541974,;	T	ENSG00000112530	ENST00000337019	Transcript	missense_variant	607	383	128	R/L	cGg/cTg	rs370616018	.	.	1	PACRG	HGNC	19152	protein_coding	YES	CCDS5284.1	ENSP00000337946	PACRG_HUMAN	.	UPI00001AE671	.	tolerated(0.29)	possibly_damaging(0.597)	4/7	.	hmmpanther:PTHR21207,Pfam_domain:PF10274	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTCGGCAAG	byFrequency|byCluster	2	ESCA
TDP2	0	.	GRCh37	6	24666976	24666976	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115G>A	p.Asp39Asn	p.D39N	ENST00000378198	1/7	30	26	4	14	14	0	TDP2,missense_variant,p.Asp69Asn,ENST00000545995,;TDP2,missense_variant,p.Asp39Asn,ENST00000378198,;ACOT13,upstream_gene_variant,,ENST00000230048,;ACOT13,upstream_gene_variant,,ENST00000537591,;TDP2,upstream_gene_variant,,ENST00000341060,;TDP2,non_coding_transcript_exon_variant,,ENST00000478507,;TDP2,non_coding_transcript_exon_variant,,ENST00000480495,;	T	ENSG00000111802	ENST00000378198	Transcript	missense_variant	286	115	39	D/N	Gat/Aat	.	.	.	-1	TDP2	HGNC	17768	protein_coding	YES	CCDS4557.1	ENSP00000367440	TYDP2_HUMAN	.	UPI0000032018	.	deleterious(0.01)	benign(0.243)	1/7	.	Superfamily_domains:SSF46934,Gene3D:1.10.8.10,Pfam_domain:PF14555,hmmpanther:PTHR15822,hmmpanther:PTHR15822:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCATCGCAGC	.	4	ESCA
ZFP57	0	.	GRCh37	6	29641135	29641135	+	Silent	SNP	G	G	C	rs768216433	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753C>G	p.%3D	p.R251R	ENST00000488757	4/4	82	67	14	61	61	0	ZFP57,synonymous_variant,p.%3D,ENST00000376883,;ZFP57,synonymous_variant,p.%3D,ENST00000488757,;ZFP57,synonymous_variant,p.%3D,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000533330,;MOG,downstream_gene_variant,,ENST00000490427,;MOG,downstream_gene_variant,,ENST00000396704,;MOG,downstream_gene_variant,,ENST00000483013,;MOG,downstream_gene_variant,,ENST00000376891,;MOG,downstream_gene_variant,,ENST00000376898,;MOG,downstream_gene_variant,,ENST00000494692,;MOG,downstream_gene_variant,,ENST00000376917,;MOG,downstream_gene_variant,,ENST00000376888,;MOG,downstream_gene_variant,,ENST00000376902,;MOG,downstream_gene_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000431798,;MOG,downstream_gene_variant,,ENST00000376894,;MOG,downstream_gene_variant,,ENST00000396701,;MOG,downstream_gene_variant,,ENST00000376889,;MOG,downstream_gene_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000485885,;	C	ENSG00000204644	ENST00000488757	Transcript	synonymous_variant	904	753	251	R	cgC/cgG	rs768216433	.	.	-1	ZFP57	HGNC	18791	protein_coding	YES	CCDS43436.2	ENSP00000418259	ZFP57_HUMAN	.	UPI0001951170	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF179,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACGCGGCG	byFrequency	5	ESCA
C6orf136	0	.	GRCh37	6	30615067	30615067	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59A>T	p.Gln20Leu	p.Q20L	ENST00000293604	1/6	89	80	8	56	56	0	C6orf136,missense_variant,p.Gln20Leu,ENST00000376473,;C6orf136,missense_variant,p.Gln20Leu,ENST00000376471,;C6orf136,missense_variant,p.Gln20Leu,ENST00000293604,;ATAT1,downstream_gene_variant,,ENST00000318999,;C6orf136,upstream_gene_variant,,ENST00000467801,;C6orf136,upstream_gene_variant,,ENST00000528347,;ATAT1,downstream_gene_variant,,ENST00000376485,;C6orf136,upstream_gene_variant,,ENST00000465699,;ATAT1,downstream_gene_variant,,ENST00000376478,;ATAT1,downstream_gene_variant,,ENST00000330083,;ATAT1,downstream_gene_variant,,ENST00000329992,;C6orf136,upstream_gene_variant,,ENST00000446773,;C6orf136,upstream_gene_variant,,ENST00000468785,;ATAT1,downstream_gene_variant,,ENST00000376483,;ATAT1,downstream_gene_variant,,ENST00000319027,;AL662800.2,upstream_gene_variant,,ENST00000583820,;C6orf136,non_coding_transcript_exon_variant,,ENST00000493705,;ATAT1,downstream_gene_variant,,ENST00000462304,;ATAT1,downstream_gene_variant,,ENST00000468713,;C6orf136,missense_variant,p.Gln20Leu,ENST00000463794,;C6orf136,missense_variant,p.Gln20Leu,ENST00000484551,;C6orf136,missense_variant,p.Gln20Leu,ENST00000488383,;ATAT1,downstream_gene_variant,,ENST00000479562,;C6orf136,upstream_gene_variant,,ENST00000487873,;ATAT1,downstream_gene_variant,,ENST00000471782,;	T	ENSG00000204564	ENST00000293604	Transcript	missense_variant	252	59	20	Q/L	cAg/cTg	.	.	.	1	C6orf136	HGNC	21301	protein_coding	YES	CCDS54979.1	ENSP00000293604	CF136_HUMAN	Q0P5T2_HUMAN,H7C5B5_HUMAN,H7C4Z6_HUMAN	UPI0001A51C32	.	deleterious_low_confidence(0)	benign(0.012)	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTACCAGGCTC	.	2	ESCA
NEU1	0	.	GRCh37	6	31827130	31827130	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*366G>T	.	.	ENST00000375631	6/6	54	48	6	38	38	0	NEU1,3_prime_UTR_variant,,ENST00000375631,;SLC44A4,downstream_gene_variant,,ENST00000544672,;SLC44A4,downstream_gene_variant,,ENST00000229729,;SLC44A4,downstream_gene_variant,,ENST00000375562,;SLC44A4,downstream_gene_variant,,ENST00000487680,;NEU1,3_prime_UTR_variant,,ENST00000491768,;NEU1,non_coding_transcript_exon_variant,,ENST00000495807,;NEU1,non_coding_transcript_exon_variant,,ENST00000480384,;	A	ENSG00000204386	ENST00000375631	Transcript	3_prime_UTR_variant	1744	.	.	.	.	.	.	.	-1	NEU1	HGNC	7758	protein_coding	YES	CCDS4723.1	ENSP00000364782	NEUR1_HUMAN	Q6Q4G8_HUMAN,Q6Q4G7_HUMAN,Q5JQI0_HUMAN	UPI000012FF46	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACACCAAAGA	.	4	ESCA
HLA-DMA	0	.	GRCh37	6	32917464	32917464	+	Silent	SNP	G	G	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.576C>T	p.%3D	p.F192F	ENST00000374843	3/5	74	67	7	36	36	0	HLA-DMA,synonymous_variant,p.%3D,ENST00000395305,;HLA-DMA,synonymous_variant,p.%3D,ENST00000422832,;HLA-DMA,synonymous_variant,p.%3D,ENST00000395303,;HLA-DMA,synonymous_variant,p.%3D,ENST00000456800,;HLA-DMA,synonymous_variant,p.%3D,ENST00000374843,;XXbac-BPG181M17.5,intron_variant,,ENST00000429234,;HLA-DMA,non_coding_transcript_exon_variant,,ENST00000464392,;HLA-DMA,non_coding_transcript_exon_variant,,ENST00000477541,;HLA-DMA,upstream_gene_variant,,ENST00000480785,;HLA-DMA,downstream_gene_variant,,ENST00000475627,;	A	ENSG00000204257	ENST00000374843	Transcript	synonymous_variant	662	576	192	F	ttC/ttT	COSM3374232,COSM3374233	.	.	-1	HLA-DMA	HGNC	4934	protein_coding	YES	CCDS4761.1	ENSP00000363976	DMA_HUMAN	Q6ICR9_HUMAN,Q31604_HUMAN,F6S093_HUMAN	UPI000006F879	.	.	.	3/5	.	Superfamily_domains:SSF48726,SMART_domains:SM00407,Pfam_domain:PF07654,Gene3D:2.60.40.10,hmmpanther:PTHR19944:SF13,hmmpanther:PTHR19944,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTGTGAAGTT	.	3	ESCA
ZBTB22	0	.	GRCh37	6	33283128	33283128	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1566C>T	p.%3D	p.F522F	ENST00000431845	2/2	55	46	9	51	51	0	ZBTB22,synonymous_variant,p.%3D,ENST00000431845,;ZBTB22,synonymous_variant,p.%3D,ENST00000418724,;TAPBP,upstream_gene_variant,,ENST00000489157,;DAXX,downstream_gene_variant,,ENST00000374542,;TAPBP,upstream_gene_variant,,ENST00000456592,;DAXX,downstream_gene_variant,,ENST00000414083,;ZBTB22,downstream_gene_variant,,ENST00000441117,;TAPBP,upstream_gene_variant,,ENST00000467025,;TAPBP,upstream_gene_variant,,ENST00000426633,;TAPBP,upstream_gene_variant,,ENST00000434618,;TAPBP,upstream_gene_variant,,ENST00000475304,;DAXX,downstream_gene_variant,,ENST00000266000,;DAXX,downstream_gene_variant,,ENST00000468536,;DAXX,downstream_gene_variant,,ENST00000477162,;TAPBP,upstream_gene_variant,,ENST00000476333,;TAPBP,upstream_gene_variant,,ENST00000437116,;TAPBP,upstream_gene_variant,,ENST00000480730,;DAXX,downstream_gene_variant,,ENST00000490173,;	A	ENSG00000236104	ENST00000431845	Transcript	synonymous_variant	1718	1566	522	F	ttC/ttT	.	.	.	-1	ZBTB22	HGNC	13085	protein_coding	YES	CCDS4775.1	ENSP00000407545	ZBT22_HUMAN	A2AB93_HUMAN	UPI000013C34E	.	.	.	2/2	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24414:SF4,hmmpanther:PTHR24414,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTTGAACTT	.	4	ESCA
ZBTB9	0	.	GRCh37	6	33424232	33424232	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355G>T	p.Cys452Phe	p.C452F	ENST00000395064	2/2	62	57	4	44	44	0	ZBTB9,missense_variant,p.Cys452Phe,ENST00000395064,;SYNGAP1,downstream_gene_variant,,ENST00000428982,;SYNGAP1,downstream_gene_variant,,ENST00000418600,;SYNGAP1,downstream_gene_variant,,ENST00000496374,;	T	ENSG00000213588	ENST00000395064	Transcript	missense_variant	1623	1355	452	C/F	tGt/tTt	.	.	.	1	ZBTB9	HGNC	28323	protein_coding	YES	CCDS4780.1	ENSP00000378503	ZBTB9_HUMAN	.	UPI000006E7DE	.	tolerated(1)	benign(0.006)	2/2	.	hmmpanther:PTHR24414:SF24,hmmpanther:PTHR24414,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCTGTTTTC	.	2	ESCA
CPNE5	0	.	GRCh37	6	36709970	36709970	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*75C>T	.	.	ENST00000244751	21/21	39	32	7	43	43	0	CPNE5,3_prime_UTR_variant,,ENST00000244751,;CPNE5,3_prime_UTR_variant,,ENST00000393189,;CPNE5,non_coding_transcript_exon_variant,,ENST00000459703,;CPNE5,downstream_gene_variant,,ENST00000493411,;RP3-431A14.4,downstream_gene_variant,,ENST00000494644,;	A	ENSG00000124772	ENST00000244751	Transcript	3_prime_UTR_variant	2482	.	.	.	.	.	.	.	-1	CPNE5	HGNC	2318	protein_coding	YES	CCDS4825.1	ENSP00000244751	CPNE5_HUMAN	Q7Z6C8_HUMAN,Q658T3_HUMAN	UPI0000127C15	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTCGGGGAG	.	2	ESCA
PGK2	0	.	GRCh37	6	49754035	49754035	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.866G>A	p.Gly289Glu	p.G289E	ENST00000304801	1/1	67	60	6	52	52	0	PGK2,missense_variant,p.Gly289Glu,ENST00000304801,;	T	ENSG00000170950	ENST00000304801	Transcript	missense_variant	1019	866	289	G/E	gGg/gAg	.	.	.	-1	PGK2	HGNC	8898	protein_coding	YES	CCDS4930.1	ENSP00000305995	PGK2_HUMAN	.	UPI0000001C72	.	deleterious(0)	possibly_damaging(0.732)	1/1	.	HAMAP:MF_00145,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF4,Gene3D:3.40.50.1270,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,Superfamily_domains:SSF53748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCCCCAGTA	.	4	ESCA
ELOVL5	0	.	GRCh37	6	53140028	53140028	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437C>G	p.Ser146Cys	p.S146C	ENST00000541407	6/9	99	89	9	66	66	0	ELOVL5,missense_variant,p.Ser146Cys,ENST00000541407,;ELOVL5,missense_variant,p.Ser109Cys,ENST00000370918,;ELOVL5,missense_variant,p.Ser119Cys,ENST00000304434,;ELOVL5,missense_variant,p.Ser119Cys,ENST00000542638,;MIR5685,upstream_gene_variant,,ENST00000579080,;ELOVL5,non_coding_transcript_exon_variant,,ENST00000485336,;ELOVL5,downstream_gene_variant,,ENST00000486973,;ELOVL5,downstream_gene_variant,,ENST00000465983,;	C	ENSG00000012660	ENST00000541407	Transcript	missense_variant	579	437	146	S/C	tCc/tGc	.	.	.	-1	ELOVL5	HGNC	21308	protein_coding	YES	CCDS56433.1	ENSP00000438095	ELOV5_HUMAN	.	UPI0001AE72A0	.	deleterious(0)	probably_damaging(1)	6/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11157:SF18,hmmpanther:PTHR11157,Pfam_domain:PF01151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTTTGGAGAAG	.	3	ESCA
KHDRBS2	0	.	GRCh37	6	62390931	62390931	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.987G>T	p.Leu329Phe	p.L329F	ENST00000281156	9/9	73	69	4	49	49	0	KHDRBS2,missense_variant,p.Leu329Phe,ENST00000281156,;RP1-240B8.3,non_coding_transcript_exon_variant,,ENST00000511849,;	A	ENSG00000112232	ENST00000281156	Transcript	missense_variant	1266	987	329	L/F	ttG/ttT	.	.	.	-1	KHDRBS2	HGNC	18114	protein_coding	YES	CCDS4963.1	ENSP00000281156	KHDR2_HUMAN	.	UPI000004D256	.	tolerated(0.25)	benign(0.362)	9/9	.	hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCAAGCT	.	2	ESCA
EYS	0	.	GRCh37	6	66205078	66205078	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226C>A	p.Gln76Lys	p.Q76K	ENST00000503581	4/43	62	54	7	37	37	0	EYS,missense_variant,p.Gln76Lys,ENST00000342421,;EYS,missense_variant,p.Gln76Lys,ENST00000393380,;EYS,missense_variant,p.Gln76Lys,ENST00000370616,;EYS,missense_variant,p.Gln76Lys,ENST00000370618,;EYS,missense_variant,p.Gln76Lys,ENST00000370621,;EYS,missense_variant,p.Gln76Lys,ENST00000503581,;EYS,5_prime_UTR_variant,,ENST00000471279,;EYS,non_coding_transcript_exon_variant,,ENST00000489873,;	T	ENSG00000188107	ENST00000503581	Transcript	missense_variant	764	226	76	Q/K	Cag/Aag	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	deleterious_low_confidence(0)	possibly_damaging(0.828)	4/43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATCTGGGGAA	.	4	ESCA
LMBRD1	0	.	GRCh37	6	70447905	70447905	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.565G>T	p.Gly189Cys	p.G189C	ENST00000370577	7/16	48	45	3	50	50	0	LMBRD1,missense_variant,p.Gly116Cys,ENST00000370570,;LMBRD1,missense_variant,p.Gly189Cys,ENST00000370577,;LMBRD1,missense_variant,p.Gly189Cys,ENST00000472827,;	A	ENSG00000168216	ENST00000370577	Transcript	missense_variant	795	565	189	G/C	Ggt/Tgt	.	.	.	-1	LMBRD1	HGNC	23038	protein_coding	YES	CCDS4969.1	ENSP00000359609	LMBD1_HUMAN	.	UPI000003ED25	.	deleterious(0.01)	probably_damaging(0.959)	7/16	.	hmmpanther:PTHR16130:SF2,hmmpanther:PTHR16130,Pfam_domain:PF04791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAACCATCTG	.	2	ESCA
COL19A1	0	.	GRCh37	6	70918602	70918602	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1624G>A	.	.	ENST00000322773	51/51	65	61	4	62	62	0	COL19A1,3_prime_UTR_variant,,ENST00000322773,;COL19A1,3_prime_UTR_variant,,ENST00000393344,;	A	ENSG00000082293	ENST00000322773	Transcript	3_prime_UTR_variant	5155	.	.	.	.	.	.	.	1	COL19A1	HGNC	2196	protein_coding	YES	CCDS4970.1	ENSP00000316030	COJA1_HUMAN	.	UPI000004F1E3	.	.	.	51/51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCTGGTCAGG	.	2	ESCA
CAGE1	0	.	GRCh37	6	7373495	7373496	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1556dupT	p.Leu519PhefsTer6	p.L519Ffs*6	ENST00000502583	5/14	65	57	8	47	47	0	CAGE1,frameshift_variant,p.Leu519PhefsTer6,ENST00000512086,;CAGE1,frameshift_variant,p.Leu519PhefsTer6,ENST00000502583,;CAGE1,frameshift_variant,p.Leu519PhefsTer6,ENST00000379918,;CAGE1,frameshift_variant,p.Leu519PhefsTer6,ENST00000338150,;CAGE1,frameshift_variant,p.Leu531PhefsTer6,ENST00000512691,;CAGE1,frameshift_variant,p.Leu383PhefsTer6,ENST00000296742,;CAGE1,downstream_gene_variant,,ENST00000509324,;CAGE1,frameshift_variant,p.Leu519PhefsTer6,ENST00000458291,;CAGE1,3_prime_UTR_variant,,ENST00000442019,;	A	ENSG00000164304	ENST00000502583	Transcript	frameshift_variant	2121-2122	1556-1557	519	L/FX	ttg/ttTg	.	.	.	-1	CAGE1	HGNC	21622	protein_coding	YES	CCDS54965.1	ENSP00000425493	CAGE1_HUMAN	.	UPI0001C0B380	.	.	.	5/14	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATTGCAAATT	.	3	ESCA
COL12A1	0	.	GRCh37	6	75843646	75843646	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5592G>A	p.Trp1864Ter	p.W1864*	ENST00000322507	33/66	82	76	6	53	53	0	COL12A1,stop_gained,p.Trp1864Ter,ENST00000416123,;COL12A1,stop_gained,p.Trp1864Ter,ENST00000322507,;COL12A1,stop_gained,p.Trp599Ter,ENST00000419671,;COL12A1,stop_gained,p.Trp1864Ter,ENST00000483888,;COL12A1,stop_gained,p.Trp700Ter,ENST00000345356,;	T	ENSG00000111799	ENST00000322507	Transcript	stop_gained	5902	5592	1864	W/*	tgG/tgA	.	.	.	-1	COL12A1	HGNC	2188	protein_coding	YES	CCDS43482.1	ENSP00000325146	COCA1_HUMAN	.	UPI000045890B	.	.	.	33/66	.	PROSITE_profiles:PS50853,hmmpanther:PTHR22992:SF23,hmmpanther:PTHR22992,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGTCCCAGCG	.	2	ESCA
ZAN	0	.	GRCh37	7	100358086	100358086	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3769G>T	p.Val1257Leu	p.V1257L	ENST00000546292	18/46	160	151	9	133	133	0	ZAN,missense_variant,p.Val1257Leu,ENST00000546292,;ZAN,missense_variant,p.Val1257Leu,ENST00000542585,;ZAN,missense_variant,p.Val1257Leu,ENST00000538115,;ZAN,5_prime_UTR_variant,,ENST00000546213,;ZAN,missense_variant,p.Val1257Leu,ENST00000421100,;ZAN,missense_variant,p.Val1257Leu,ENST00000349350,;ZAN,missense_variant,p.Val1257Leu,ENST00000427578,;ZAN,missense_variant,p.Val1257Leu,ENST00000348028,;ZAN,missense_variant,p.Val1257Leu,ENST00000449052,;ZAN,missense_variant,p.Val1257Leu,ENST00000443370,;	T	ENSG00000146839	ENST00000546292	Transcript	missense_variant	3917	3769	1257	V/L	Gtg/Ttg	.	.	.	1	ZAN	HGNC	12857	protein_coding	YES	.	ENSP00000445943	.	F5H0T8_HUMAN	UPI00004575C6	.	.	unknown(0)	18/46	.	SMART_domains:SM00216,Pfam_domain:PF00094,hmmpanther:PTHR11339:SF221,hmmpanther:PTHR11339,PROSITE_profiles:PS51233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R1255W|c.3763C>T|3,BUFFER|p.R1255W|c.3763C>T|3	MUTECT|MUSE	GGTTTGTGGAG	.	2	ESCA
MUC12	0	.	GRCh37	7	100648403	100648403	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14559C>G	p.Phe4853Leu	p.F4853L	ENST00000536621	2/12	134	125	8	103	103	0	MUC12,missense_variant,p.Phe4853Leu,ENST00000536621,;MUC12,missense_variant,p.Phe4996Leu,ENST00000379442,;	G	ENSG00000205277	ENST00000536621	Transcript	missense_variant	14559	14559	4853	F/L	ttC/ttG	.	.	.	1	MUC12	HGNC	7510	protein_coding	YES	CCDS55139.1	ENSP00000441929	.	F5GWV9_HUMAN	UPI0001B25898	.	.	benign(0.302)	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCTTCTACAG	.	2	ESCA
MUC12	0	.	GRCh37	7	100648615	100648615	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14771C>T	p.Ser4924Phe	p.S4924F	ENST00000536621	2/12	148	131	16	128	128	0	MUC12,missense_variant,p.Ser4924Phe,ENST00000536621,;MUC12,missense_variant,p.Ser5067Phe,ENST00000379442,;	T	ENSG00000205277	ENST00000536621	Transcript	missense_variant	14771	14771	4924	S/F	tCc/tTc	.	.	.	1	MUC12	HGNC	7510	protein_coding	YES	CCDS55139.1	ENSP00000441929	.	F5GWV9_HUMAN	UPI0001B25898	.	.	unknown(0)	2/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCTCCACAG	.	4	ESCA
RELN	0	.	GRCh37	7	103292142	103292142	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1858C>A	p.His620Asn	p.H620N	ENST00000428762	15/65	76	67	9	54	54	0	RELN,missense_variant,p.His620Asn,ENST00000424685,;RELN,missense_variant,p.His620Asn,ENST00000428762,;RELN,missense_variant,p.His620Asn,ENST00000343529,;	T	ENSG00000189056	ENST00000428762	Transcript	missense_variant	2018	1858	620	H/N	Cac/Aac	.	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	tolerated(0.11)	probably_damaging(0.985)	15/65	.	hmmpanther:PTHR11841,Superfamily_domains:SSF50939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGTGGGGGA	.	4	ESCA
LAMB4	0	.	GRCh37	7	107688467	107688467	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4212G>C	p.Arg1404Ser	p.R1404S	ENST00000388781	28/34	115	108	7	99	99	0	LAMB4,missense_variant,p.Arg1404Ser,ENST00000388781,;LAMB4,missense_variant,p.Arg430Ser,ENST00000422975,;LAMB4,missense_variant,p.Arg1404Ser,ENST00000388780,;LAMB4,missense_variant,p.Arg1404Ser,ENST00000205386,;LAMB4,upstream_gene_variant,,ENST00000475572,;	G	ENSG00000091128	ENST00000388781	Transcript	missense_variant	4296	4212	1404	R/S	agG/agC	.	.	.	-1	LAMB4	HGNC	6491	protein_coding	YES	CCDS34732.1	ENSP00000373433	LAMB4_HUMAN	C9JM08_HUMAN	UPI0000198CD5	.	deleterious(0.02)	benign(0)	28/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGACCCCTACA	.	2	ESCA
CFTR	0	.	GRCh37	7	117235030	117235030	+	Missense_Mutation	SNP	G	G	T	rs397508393	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2537G>T	p.Trp846Leu	p.W846L	ENST00000003084	15/27	72	64	8	56	56	0	CFTR,missense_variant,p.Trp816Leu,ENST00000426809,;CFTR,missense_variant,p.Trp785Leu,ENST00000454343,;CFTR,missense_variant,p.Trp846Leu,ENST00000003084,;	T	ENSG00000001626	ENST00000003084	Transcript	missense_variant	2669	2537	846	W/L	tGg/tTg	rs397508393,CM930121	.	.	1	CFTR	HGNC	1884	protein_coding	YES	CCDS5773.1	ENSP00000003084	CFTR_HUMAN	Q9UML7_HUMAN,Q9UJ19_HUMAN,Q99989_HUMAN,Q6KEJ7_HUMAN,Q6KEJ4_HUMAN,Q6KEJ1_HUMAN,Q6KEI8_HUMAN,Q6KEI7_HUMAN,Q6KEI2_HUMAN,Q6KEH8_HUMAN,Q6KEH6_HUMAN,Q6KEH3_HUMAN,Q6KEG9_HUMAN,Q6KEG6_HUMAN,Q6KEG3_HUMAN,Q6KEF9_HUMAN,Q6KEF5_HUMAN,Q6KEE7_HUMAN,Q6KEE3_HUMAN,Q6KED8_HUMAN,Q6KED3_HUMAN,Q6KEC8_HUMAN,Q6KEC3_HUMAN,Q6KEB8_HUMAN,Q6KEB2_HUMAN,Q6KEA5_HUMAN,Q6KEA0_HUMAN,Q6KE95_HUMAN,Q5I6N7_HUMAN,Q5I6N6_HUMAN,Q5I6N5_HUMAN,Q5I6N4_HUMAN,Q5I6F9_HUMAN,C9J6L5_HUMAN,A4L9V0_HUMAN	UPI000013C4D4	.	tolerated(0.05)	benign(0.099)	15/27	.	hmmpanther:PTHR24223:SF19,hmmpanther:PTHR24223,Pfam_domain:PF14396,TIGRFAM_domain:TIGR01271	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACATGGAACA	.	4	ESCA
CPED1	0	.	GRCh37	7	120907296	120907296	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2661C>A	p.%3D	p.I887I	ENST00000310396	21/23	49	46	3	50	50	0	CPED1,synonymous_variant,p.%3D,ENST00000310396,;	A	ENSG00000106034	ENST00000310396	Transcript	synonymous_variant	3128	2661	887	I	atC/atA	.	.	.	1	CPED1	HGNC	26159	protein_coding	YES	CCDS34739.1	ENSP00000309772	CPED1_HUMAN	Q75MM9_HUMAN,E9PCC8_HUMAN,E7ENG7_HUMAN	UPI000013C813	.	.	.	21/23	.	hmmpanther:PTHR14776,Pfam_domain:PF13839	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGATCATCAA	.	2	ESCA
TMEM106B	0	.	GRCh37	7	12263907	12263907	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337G>T	p.Val113Leu	p.V113L	ENST00000396667	5/9	111	105	6	111	111	0	TMEM106B,missense_variant,p.Val113Leu,ENST00000396667,;TMEM106B,missense_variant,p.Val113Leu,ENST00000396668,;TMEM106B,downstream_gene_variant,,ENST00000444443,;TMEM106B,3_prime_UTR_variant,,ENST00000420833,;	T	ENSG00000106460	ENST00000396667	Transcript	missense_variant	659	337	113	V/L	Gtg/Ttg	.	.	.	1	TMEM106B	HGNC	22407	protein_coding	YES	CCDS5358.1	ENSP00000379901	T106B_HUMAN	C9JZ87_HUMAN,C9J998_HUMAN	UPI000003ED3C	.	deleterious(0.02)	probably_damaging(0.994)	5/9	.	Transmembrane_helices:TMhelix,Pfam_domain:PF07092,Superfamily_domains:0051044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCTGTGTTT	.	2	ESCA
AHCYL2	0	.	GRCh37	7	129046266	129046266	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1254G>T	p.%3D	p.V418V	ENST00000325006	10/17	91	87	4	80	80	0	AHCYL2,synonymous_variant,p.%3D,ENST00000531335,;AHCYL2,synonymous_variant,p.%3D,ENST00000474594,;AHCYL2,synonymous_variant,p.%3D,ENST00000466924,;AHCYL2,synonymous_variant,p.%3D,ENST00000325006,;AHCYL2,synonymous_variant,p.%3D,ENST00000490911,;AHCYL2,synonymous_variant,p.%3D,ENST00000446544,;AHCYL2,synonymous_variant,p.%3D,ENST00000446212,;RNU7-16P,downstream_gene_variant,,ENST00000516471,;AHCYL2,downstream_gene_variant,,ENST00000492628,;RP11-305M3.2,downstream_gene_variant,,ENST00000450566,;	T	ENSG00000158467	ENST00000325006	Transcript	synonymous_variant	1308	1254	418	V	gtG/gtT	.	.	.	1	AHCYL2	HGNC	22204	protein_coding	YES	CCDS5812.1	ENSP00000315931	SAHH3_HUMAN	.	UPI00001354E4	.	.	.	10/17	.	hmmpanther:PTHR23420:SF2,hmmpanther:PTHR23420,TIGRFAM_domain:TIGR00936,Pfam_domain:PF00670,Gene3D:3.40.50.720,Pfam_domain:PF05221,SMART_domains:SM00996,SMART_domains:SM00997,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTGTGTATGT	.	2	ESCA
PLXNA4	0	.	GRCh37	7	132169579	132169579	+	Intron	SNP	G	G	T	rs776514346	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1371+4472C>A	.	.	ENST00000359827	.	91	84	7	78	78	0	PLXNA4,missense_variant,p.Ser522Tyr,ENST00000378539,;PLXNA4,intron_variant,,ENST00000321063,;PLXNA4,intron_variant,,ENST00000423507,;PLXNA4,intron_variant,,ENST00000359827,;	T	ENSG00000221866	ENST00000359827	Transcript	intron_variant	.	.	.	.	.	rs776514346	.	.	-1	PLXNA4	HGNC	9102	protein_coding	YES	CCDS43646.1	ENSP00000352882	PLXA4_HUMAN	.	UPI000004E55B	.	.	.	.	3/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTAGGAAGAA	.	2	ESCA
TRIM24	0	.	GRCh37	7	138255646	138255646	+	Silent	SNP	G	G	C	rs754183037	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1776G>C	p.%3D	p.T592T	ENST00000343526	11/19	190	174	15	145	145	0	TRIM24,synonymous_variant,p.%3D,ENST00000415680,;TRIM24,synonymous_variant,p.%3D,ENST00000343526,;TRIM24,non_coding_transcript_exon_variant,,ENST00000493595,;TRIM24,downstream_gene_variant,,ENST00000497516,;	C	ENSG00000122779	ENST00000343526	Transcript	synonymous_variant	1991	1776	592	T	acG/acC	rs754183037	.	.	1	TRIM24	HGNC	11812	protein_coding	YES	CCDS5847.1	ENSP00000340507	TIF1A_HUMAN	B4DYZ9_HUMAN	UPI00000012CB	.	.	.	11/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24103:SF136,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCACGATTAC	.	3	ESCA
MGAM	0	.	GRCh37	7	141720844	141720844	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.519C>A	p.%3D	p.L173L	ENST00000549489	5/48	164	152	11	104	104	0	MGAM,synonymous_variant,p.%3D,ENST00000465654,;MGAM,synonymous_variant,p.%3D,ENST00000475668,;MGAM,synonymous_variant,p.%3D,ENST00000549489,;MGAM,downstream_gene_variant,,ENST00000497673,;	A	ENSG00000257335	ENST00000549489	Transcript	synonymous_variant	614	519	173	L	ctC/ctA	.	.	.	1	MGAM	HGNC	7043	protein_coding	YES	CCDS47727.1	ENSP00000447378	MGA_HUMAN	Q8TE25_HUMAN,E9PEQ5_HUMAN,E7EW87_HUMAN	UPI000183CB7B	.	.	.	5/48	.	Superfamily_domains:SSF74650,hmmpanther:PTHR22762:SF63,hmmpanther:PTHR22762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCTCACAGC	.	2	ESCA
RP11-1220K2.2	0	.	GRCh37	7	141833840	141833840	+	Missense_Mutation	SNP	G	G	T	rs759278128	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.635G>T	p.Arg212Leu	p.R212L	ENST00000550469	7/13	69	63	6	79	79	0	RP11-1220K2.2,missense_variant,p.Arg212Leu,ENST00000477922,;RP11-1220K2.2,missense_variant,p.Arg212Leu,ENST00000550469,;	T	ENSG00000257743	ENST00000550469	Transcript	missense_variant	694	635	212	R/L	cGa/cTa	rs759278128	.	.	1	RP11-1220K2.2	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000447431	MGAL2_HUMAN	.	UPI00001411D7	.	tolerated(0.1)	benign(0.044)	7/13	.	hmmpanther:PTHR22762:SF55,hmmpanther:PTHR22762,Superfamily_domains:SSF74650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTCCGACTGC	byFrequency|byCluster	3	ESCA
TRBV7-4	0	.	GRCh37	7	142176768	142176768	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.23G>C	p.Trp8Ser	p.W8S	ENST00000390369	1/2	89	80	8	89	89	0	TRBV7-4,missense_variant,p.Trp8Ser,ENST00000390369,;TRBV6-5,downstream_gene_variant,,ENST00000390368,;	G	ENSG00000253409	ENST00000390369	Transcript	missense_variant	23	23	8	W/S	tGg/tCg	.	.	.	-1	TRBV7-4	HGNC	12238	TR_V_gene	YES	.	ENSP00000374892	.	.	UPI0001AE7164	.	deleterious(0.05)	benign(0.337)	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23268:SF20,hmmpanther:PTHR23268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACCCAGCAG	.	4	ESCA
DGKB	0	.	GRCh37	7	14880833	14880833	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.56A>T	p.Gln19Leu	p.Q19L	ENST00000403951	2/26	130	115	15	119	118	1	DGKB,missense_variant,p.Gln19Leu,ENST00000258767,;DGKB,missense_variant,p.Gln19Leu,ENST00000444700,;DGKB,missense_variant,p.Gln19Leu,ENST00000403951,;DGKB,missense_variant,p.Gln19Leu,ENST00000437998,;DGKB,missense_variant,p.Gln19Leu,ENST00000402815,;DGKB,missense_variant,p.Gln19Leu,ENST00000407950,;DGKB,missense_variant,p.Gln19Leu,ENST00000406247,;DGKB,missense_variant,p.Gln19Leu,ENST00000399322,;DGKB,non_coding_transcript_exon_variant,,ENST00000403963,;DGKB,non_coding_transcript_exon_variant,,ENST00000463981,;DGKB,intron_variant,,ENST00000467449,;DGKB,non_coding_transcript_exon_variant,,ENST00000477401,;	A	ENSG00000136267	ENST00000403951	Transcript	missense_variant	476	56	19	Q/L	cAg/cTg	.	.	.	-1	DGKB	HGNC	2850	protein_coding	YES	CCDS47547.1	ENSP00000385780	DGKB_HUMAN	C9JA18_HUMAN,B7Z3B3_HUMAN	UPI0000033B9B	.	deleterious(0.04)	benign(0.048)	2/26	.	hmmpanther:PTHR11255:SF32,hmmpanther:PTHR11255,Gene3D:1tuzA00,Pfam_domain:PF14513,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTTCTGAAGT	.	4	ESCA
KRBA1	0	.	GRCh37	7	149425722	149425722	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1583G>C	p.Gly528Ala	p.G528A	ENST00000255992	12/18	57	52	5	45	45	0	KRBA1,missense_variant,p.Gly528Ala,ENST00000485033,;KRBA1,missense_variant,p.Gly528Ala,ENST00000319551,;KRBA1,missense_variant,p.Gly528Ala,ENST00000255992,;KRBA1,non_coding_transcript_exon_variant,,ENST00000479560,;KRBA1,non_coding_transcript_exon_variant,,ENST00000466546,;KRBA1,missense_variant,p.Gly485Ala,ENST00000496259,;KRBA1,upstream_gene_variant,,ENST00000489951,;KRBA1,downstream_gene_variant,,ENST00000496080,;	C	ENSG00000133619	ENST00000255992	Transcript	missense_variant	1982	1583	528	G/A	gGa/gCa	.	.	.	1	KRBA1	HGNC	22228	protein_coding	YES	.	ENSP00000255992	.	C9J5U6_HUMAN,C4P1W5_HUMAN	UPI000049E0A4	.	tolerated(0.15)	probably_damaging(0.992)	12/18	.	hmmpanther:PTHR22740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGGGGACCGA	.	3	ESCA
SSPO	0	.	GRCh37	7	149500089	149500089	+	RNA	SNP	G	G	C	rs779416953	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.7715G>C	.	.	ENST00000378016	52/109	31	27	4	25	25	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000484709,;SSPO,downstream_gene_variant,,ENST00000472797,;SSPO,downstream_gene_variant,,ENST00000475488,;	C	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	7715	.	.	.	.	rs779416953	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	52/109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCGGGGGTG	byFrequency	4	ESCA
SSPO	0	.	GRCh37	7	149500813	149500813	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.8131G>T	.	.	ENST00000378016	55/109	112	104	8	94	94	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000484709,;SSPO,downstream_gene_variant,,ENST00000472797,;SSPO,downstream_gene_variant,,ENST00000475488,;	T	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	8131	.	.	.	.	.	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	55/109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGGGGCTGC	.	2	ESCA
SSPO	0	.	GRCh37	7	149511966	149511966	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.10516G>T	.	.	ENST00000378016	74/109	51	45	5	31	31	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000478854,;SSPO,downstream_gene_variant,,ENST00000481772,;SSPO,upstream_gene_variant,,ENST00000464974,;	T	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	10516	.	.	.	.	.	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	74/109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGGAGGGAGG	.	3	ESCA
TMEM176B	0	.	GRCh37	7	150490363	150490363	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.413C>G	p.Thr138Arg	p.T138R	ENST00000447204	5/7	33	29	3	31	31	0	TMEM176B,missense_variant,p.Thr138Arg,ENST00000429904,;TMEM176B,missense_variant,p.Thr138Arg,ENST00000492607,;TMEM176B,missense_variant,p.Thr101Arg,ENST00000450753,;TMEM176B,missense_variant,p.Thr138Arg,ENST00000326442,;TMEM176B,missense_variant,p.Thr138Arg,ENST00000447204,;TMEM176B,missense_variant,p.Thr138Arg,ENST00000434545,;RP5-1051J4.4,downstream_gene_variant,,ENST00000542395,;	C	ENSG00000106565	ENST00000447204	Transcript	missense_variant	786	413	138	T/R	aCa/aGa	.	.	.	-1	TMEM176B	HGNC	29596	protein_coding	YES	CCDS5908.1	ENSP00000410269	T176B_HUMAN	.	UPI000013C82B	.	deleterious(0)	probably_damaging(0.979)	5/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15756,hmmpanther:PTHR15756:SF6,Pfam_domain:PF04103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TAGCTGTAGCA	.	2	ESCA
KMT2C	0	.	GRCh37	7	151878492	151878492	+	Silent	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6453A>T	p.%3D	p.T2151T	ENST00000262189	36/59	32	28	3	34	34	0	KMT2C,synonymous_variant,p.%3D,ENST00000355193,;KMT2C,synonymous_variant,p.%3D,ENST00000262189,;KMT2C,intron_variant,,ENST00000558665,;KMT2C,upstream_gene_variant,,ENST00000360104,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;	A	ENSG00000055609	ENST00000262189	Transcript	synonymous_variant	6672	6453	2151	T	acA/acT	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	.	36/59	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTAGCTGTTCC	.	2	ESCA
HTR5A	0	.	GRCh37	7	154862603	154862603	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-7C>A	.	.	ENST00000287907	1/2	71	65	6	36	36	0	HTR5A,5_prime_UTR_variant,,ENST00000287907,;HTR5A-AS1,intron_variant,,ENST00000395731,;HTR5A-AS1,intron_variant,,ENST00000543018,;HTR5A-AS1,intron_variant,,ENST00000493904,;	A	ENSG00000157219	ENST00000287907	Transcript	5_prime_UTR_variant	570	.	.	.	.	.	.	.	1	HTR5A	HGNC	5300	protein_coding	YES	CCDS5936.1	ENSP00000287907	5HT5A_HUMAN	Q86UN1_HUMAN,Q75LH0_HUMAN,A4D2N2_HUMAN	UPI000004477E	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGACCCAGA	.	2	ESCA
GRIFIN	0	.	GRCh37	7	2515604	2515604	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.200C>A	.	.	ENST00000417742	2/3	66	60	6	46	46	0	GRIFIN,non_coding_transcript_exon_variant,,ENST00000417742,;GRIFIN,non_coding_transcript_exon_variant,,ENST00000420313,;	T	ENSG00000236734	ENST00000417742	Transcript	non_coding_transcript_exon_variant	200	.	.	.	.	.	.	.	-1	GRIFIN	HGNC	4577	processed_transcript	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCGGGGGCCAG	.	3	ESCA
TTYH3	0	.	GRCh37	7	2687177	2687177	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531G>C	p.%3D	p.T177T	ENST00000258796	4/14	46	41	5	54	54	0	TTYH3,synonymous_variant,p.%3D,ENST00000258796,;TTYH3,synonymous_variant,p.%3D,ENST00000407643,;TTYH3,upstream_gene_variant,,ENST00000403167,;TTYH3,downstream_gene_variant,,ENST00000400376,;TTYH3,upstream_gene_variant,,ENST00000477439,;	C	ENSG00000136295	ENST00000258796	Transcript	synonymous_variant	736	531	177	T	acG/acC	.	.	.	1	TTYH3	HGNC	22222	protein_coding	YES	CCDS34588.1	ENSP00000258796	TTYH3_HUMAN	.	UPI000020E9F9	.	.	.	4/14	.	hmmpanther:PTHR12424,hmmpanther:PTHR12424:SF4,Pfam_domain:PF04906	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGACGCTGCT	.	2	ESCA
GCK	0	.	GRCh37	7	44228666	44228666	+	5'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-114G>T	.	.	ENST00000403799	1/10	89	80	9	100	100	0	GCK,5_prime_UTR_variant,,ENST00000403799,;GCK,upstream_gene_variant,,ENST00000437084,;GCK,intron_variant,,ENST00000476008,;	A	ENSG00000106633	ENST00000403799	Transcript	5_prime_UTR_variant	357	.	.	.	.	.	.	.	-1	GCK	HGNC	4195	protein_coding	.	CCDS5479.1	ENSP00000384247	HXK4_HUMAN	M4PS83_HUMAN,M4PPE1_HUMAN,Q53Y25_HUMAN	UPI0000036BD4	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCCCTGGGA	.	4	ESCA
GCK	0	.	GRCh37	7	44228667	44228667	+	5'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-115A>T	.	.	ENST00000403799	1/10	90	81	9	99	99	0	GCK,5_prime_UTR_variant,,ENST00000403799,;GCK,upstream_gene_variant,,ENST00000437084,;GCK,intron_variant,,ENST00000476008,;	A	ENSG00000106633	ENST00000403799	Transcript	5_prime_UTR_variant	356	.	.	.	.	.	.	.	-1	GCK	HGNC	4195	protein_coding	.	CCDS5479.1	ENSP00000384247	HXK4_HUMAN	M4PS83_HUMAN,M4PPE1_HUMAN,Q53Y25_HUMAN	UPI0000036BD4	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCCCTGGGAG	.	4	ESCA
H2AFV	0	.	GRCh37	7	44882898	44882898	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59G>T	p.Arg20Leu	p.R20L	ENST00000308153	2/5	76	69	6	65	65	0	H2AFV,missense_variant,p.Arg20Leu,ENST00000222690,;H2AFV,missense_variant,p.Arg20Leu,ENST00000446531,;H2AFV,missense_variant,p.Arg20Leu,ENST00000308153,;H2AFV,missense_variant,p.Arg20Leu,ENST00000349299,;H2AFV,missense_variant,p.Arg20Leu,ENST00000437072,;H2AFV,missense_variant,p.Arg20Leu,ENST00000381124,;H2AFV,intron_variant,,ENST00000521529,;H2AFV,intron_variant,,ENST00000350771,;	A	ENSG00000105968	ENST00000308153	Transcript	missense_variant	151	59	20	R/L	cGc/cTc	.	.	.	-1	H2AFV	HGNC	20664	protein_coding	YES	CCDS5496.1	ENSP00000308405	H2AV_HUMAN	.	UPI00000001D4	.	deleterious(0.05)	benign(0.14)	2/5	.	hmmpanther:PTHR23430:SF34,hmmpanther:PTHR23430,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGAGCGAGAT	.	3	ESCA
AC011294.3	0	.	GRCh37	7	46728896	46728896	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*102C>A	.	.	ENST00000451905	3/3	57	52	5	41	41	0	AC011294.3,3_prime_UTR_variant,,ENST00000451905,;AC011294.3,non_coding_transcript_exon_variant,,ENST00000469937,;AC011294.3,intron_variant,,ENST00000487094,;	T	ENSG00000233539	ENST00000451905	Transcript	3_prime_UTR_variant	528	.	.	.	.	.	.	.	-1	AC011294.3	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000398500	.	C9J2X1_HUMAN	UPI00002522A1	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTCTGGGATG	.	3	ESCA
PMS2	0	.	GRCh37	7	6045569	6045569	+	Silent	SNP	T	T	C	rs34839707	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117A>G	p.%3D	p.V39V	ENST00000265849	2/15	457	422	35	392	392	0	PMS2,synonymous_variant,p.%3D,ENST00000265849,;PMS2,synonymous_variant,p.%3D,ENST00000382321,;PMS2,synonymous_variant,p.%3D,ENST00000406569,;AIMP2,upstream_gene_variant,,ENST00000400479,;PMS2,upstream_gene_variant,,ENST00000441476,;AIMP2,upstream_gene_variant,,ENST00000395236,;AIMP2,upstream_gene_variant,,ENST00000223029,;Y_RNA,upstream_gene_variant,,ENST00000365120,;PMS2,intron_variant,,ENST00000469652,;PMS2,non_coding_transcript_exon_variant,,ENST00000415839,;PMS2,non_coding_transcript_exon_variant,,ENST00000380416,;AIMP2,upstream_gene_variant,,ENST00000415999,;	C	ENSG00000122512	ENST00000265849	Transcript	synonymous_variant	223	117	39	V	gtA/gtG	rs34839707	.	.	-1	PMS2	HGNC	9122	protein_coding	YES	CCDS5343.1	ENSP00000265849	PMS2_HUMAN	.	UPI000013D696	.	.	.	2/15	.	Superfamily_domains:SSF55874,Gene3D:3.30.565.10,Pfam_domain:PF13589,TIGRFAM_domain:TIGR00585,hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTTTACCGC	suspect|byCluster	2	ESCA
ZNF138	0	.	GRCh37	7	64291962	64291962	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264G>C	p.%3D	p.V88V	ENST00000440155	3/3	101	93	8	64	64	0	ZNF138,synonymous_variant,p.%3D,ENST00000440155,;ZNF138,synonymous_variant,p.%3D,ENST00000437743,;ZNF138,synonymous_variant,p.%3D,ENST00000359735,;ZNF138,synonymous_variant,p.%3D,ENST00000397136,;ZNF138,synonymous_variant,p.%3D,ENST00000307355,;ZNF138,3_prime_UTR_variant,,ENST00000494380,;ZNF138,3_prime_UTR_variant,,ENST00000440598,;ZNF138,non_coding_transcript_exon_variant,,ENST00000430838,;RP11-797H7.1,downstream_gene_variant,,ENST00000427545,;	C	ENSG00000197008	ENST00000440155	Transcript	synonymous_variant	408	264	88	V	gtG/gtC	.	.	.	1	ZNF138	HGNC	12922	protein_coding	YES	CCDS34645.2	ENSP00000407262	ZN138_HUMAN	E7EWC5_HUMAN,A2RRP7_HUMAN	UPI000198CD4D	.	.	.	3/3	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGTGGATGA	.	2	ESCA
ZNF117	0	.	GRCh37	7	64438934	64438934	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015G>T	p.Gly339Cys	p.G339C	ENST00000282869	4/4	66	60	6	37	37	0	ZNF117,missense_variant,p.Gly339Cys,ENST00000282869,;ZNF117,downstream_gene_variant,,ENST00000487644,;	A	ENSG00000152926	ENST00000282869	Transcript	missense_variant	2300	1015	339	G/C	Ggc/Tgc	.	.	.	-1	ZNF117	HGNC	12897	protein_coding	YES	CCDS43593.1	ENSP00000282869	ZN117_HUMAN	.	UPI000049E07A	.	deleterious(0.01)	probably_damaging(0.999)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF120,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGCCACATT	.	4	ESCA
KDELR2	0	.	GRCh37	7	6505755	6505755	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.551G>C	p.Gly184Ala	p.G184A	ENST00000258739	4/5	70	66	4	76	76	0	KDELR2,missense_variant,p.Gly184Ala,ENST00000258739,;KDELR2,intron_variant,,ENST00000490996,;DAGLB,intron_variant,,ENST00000436575,;KDELR2,intron_variant,,ENST00000463747,;KDELR2,non_coding_transcript_exon_variant,,ENST00000454368,;KDELR2,downstream_gene_variant,,ENST00000382267,;	G	ENSG00000136240	ENST00000258739	Transcript	missense_variant	736	551	184	G/A	gGc/gCc	.	.	.	-1	KDELR2	HGNC	6305	protein_coding	YES	CCDS5351.1	ENSP00000258739	ERD22_HUMAN	.	UPI000012A0CC	.	deleterious(0)	probably_damaging(0.97)	4/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10585:SF6,hmmpanther:PTHR10585,Prints_domain:PR00660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTACGCCGGCC	.	2	ESCA
PRKAR1B	0	.	GRCh37	7	716865	716865	+	Splice_Site	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.440+1G>T	.	p.X147_splice	ENST00000406797	.	59	52	6	42	42	0	PRKAR1B,splice_donor_variant,,ENST00000544935,;PRKAR1B,splice_donor_variant,,ENST00000414568,;PRKAR1B,splice_donor_variant,,ENST00000403562,;PRKAR1B,splice_donor_variant,,ENST00000406797,;PRKAR1B,splice_donor_variant,,ENST00000417852,;PRKAR1B,splice_donor_variant,,ENST00000360274,;PRKAR1B,splice_donor_variant,,ENST00000430040,;PRKAR1B,splice_donor_variant,,ENST00000537384,;PRKAR1B,downstream_gene_variant,,ENST00000456696,;	A	ENSG00000188191	ENST00000406797	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	PRKAR1B	HGNC	9390	protein_coding	YES	CCDS34579.1	ENSP00000385749	KAP1_HUMAN	C9JSK5_HUMAN,C9J4C2_HUMAN,C9IZL8_HUMAN	UPI000021C478	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCCTACCTCCT	.	3	ESCA
ELN	0	.	GRCh37	7	73474214	73474214	+	Splice_Site	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1415-2A>T	.	p.X472_splice	ENST00000252034	.	109	100	9	92	92	0	ELN,splice_acceptor_variant,,ENST00000252034,;ELN,splice_acceptor_variant,,ENST00000380576,;ELN,splice_acceptor_variant,,ENST00000380575,;ELN,splice_acceptor_variant,,ENST00000320492,;ELN,splice_acceptor_variant,,ENST00000445912,;ELN,splice_acceptor_variant,,ENST00000414324,;ELN,splice_acceptor_variant,,ENST00000429192,;ELN,splice_acceptor_variant,,ENST00000380553,;ELN,splice_acceptor_variant,,ENST00000320399,;ELN,splice_acceptor_variant,,ENST00000458204,;ELN,splice_acceptor_variant,,ENST00000357036,;ELN,splice_acceptor_variant,,ENST00000380584,;ELN,synonymous_variant,p.%3D,ENST00000380562,;ELN,synonymous_variant,p.%3D,ENST00000358929,;CTB-51J22.1,non_coding_transcript_exon_variant,,ENST00000435932,;ELN,downstream_gene_variant,,ENST00000466878,;ELN,downstream_gene_variant,,ENST00000492210,;	T	ENSG00000049540	ENST00000252034	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ELN	HGNC	3327	protein_coding	YES	CCDS5562.2	ENSP00000252034	ELN_HUMAN	Q9UMK5_HUMAN	UPI0000D4A0DC	.	.	.	.	22/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTGCAGGGTT	.	3	ESCA
CLIP2	0	.	GRCh37	7	73731819	73731819	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-58G>A	.	.	ENST00000223398	2/17	74	65	9	67	67	0	CLIP2,5_prime_UTR_variant,,ENST00000361545,;CLIP2,5_prime_UTR_variant,,ENST00000223398,;CLIP2,upstream_gene_variant,,ENST00000395060,;	A	ENSG00000106665	ENST00000223398	Transcript	5_prime_UTR_variant	270	.	.	.	.	.	.	.	1	CLIP2	HGNC	2586	protein_coding	YES	CCDS5569.1	ENSP00000223398	CLIP2_HUMAN	Q7Z5B7_HUMAN	UPI000007061E	.	.	.	2/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGAAGATGGC	.	4	ESCA
CLIP2	0	.	GRCh37	7	73731997	73731997	+	Missense_Mutation	SNP	G	G	T	rs782459504	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.121G>T	p.Gly41Cys	p.G41C	ENST00000223398	2/17	146	135	11	138	138	0	CLIP2,missense_variant,p.Gly41Cys,ENST00000395060,;CLIP2,missense_variant,p.Gly41Cys,ENST00000361545,;CLIP2,missense_variant,p.Gly41Cys,ENST00000223398,;	T	ENSG00000106665	ENST00000223398	Transcript	missense_variant	448	121	41	G/C	Ggc/Tgc	rs782459504	.	.	1	CLIP2	HGNC	2586	protein_coding	YES	CCDS5569.1	ENSP00000223398	CLIP2_HUMAN	Q7Z5B7_HUMAN	UPI000007061E	.	deleterious(0)	possibly_damaging(0.866)	2/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAAGGTACG	.	2	ESCA
GTF2IRD1	0	.	GRCh37	7	73932624	73932624	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673A>T	p.Ser225Cys	p.S225C	ENST00000455841	5/27	30	27	3	21	21	0	GTF2IRD1,missense_variant,p.Ser193Cys,ENST00000476977,;GTF2IRD1,missense_variant,p.Ser225Cys,ENST00000455841,;GTF2IRD1,missense_variant,p.Ser193Cys,ENST00000265755,;GTF2IRD1,missense_variant,p.Ser193Cys,ENST00000424337,;GTF2IRD1,non_coding_transcript_exon_variant,,ENST00000489094,;	T	ENSG00000006704	ENST00000455841	Transcript	missense_variant	886	673	225	S/C	Agc/Tgc	.	.	.	1	GTF2IRD1	HGNC	4661	protein_coding	YES	CCDS56492.1	ENSP00000397566	GT2D1_HUMAN	.	UPI00003BF92B	.	deleterious(0)	possibly_damaging(0.87)	5/27	.	Superfamily_domains:0048894,PIRSF_domain:PIRSF016441,Pfam_domain:PF02946,Gene3D:1q60A00,hmmpanther:PTHR11697:SF84,hmmpanther:PTHR11697,PROSITE_profiles:PS51139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AACACAGCCAC	.	3	ESCA
MAGI2	0	.	GRCh37	7	77764503	77764503	+	Missense_Mutation	SNP	G	G	T	rs760408756	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2866C>A	p.Arg956Ser	p.R956S	ENST00000354212	17/22	75	63	11	54	54	0	MAGI2,missense_variant,p.Arg956Ser,ENST00000354212,;MAGI2,missense_variant,p.Arg942Ser,ENST00000419488,;MAGI2,missense_variant,p.Arg956Ser,ENST00000522391,;MAGI2,non_coding_transcript_exon_variant,,ENST00000519748,;	T	ENSG00000187391	ENST00000354212	Transcript	missense_variant	3120	2866	956	R/S	Cgc/Agc	rs760408756	.	.	-1	MAGI2	HGNC	18957	protein_coding	YES	CCDS5594.1	ENSP00000346151	MAGI2_HUMAN	.	UPI00001615D2	.	deleterious(0)	probably_damaging(1)	17/22	.	PROSITE_profiles:PS50106,hmmpanther:PTHR10316:SF27,hmmpanther:PTHR10316,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G955G|c.2865A>G|3	RADIA|MUTECT|MUSE|VARSCANS	GATGCGTCCGA	.	4	ESCA
KIAA1324L	0	.	GRCh37	7	86548598	86548598	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1428G>T	p.Gln476His	p.Q476H	ENST00000450689	11/22	112	101	11	79	79	0	KIAA1324L,missense_variant,p.Gln476His,ENST00000444627,;KIAA1324L,missense_variant,p.Gln437His,ENST00000423294,;KIAA1324L,missense_variant,p.Gln476His,ENST00000450689,;KIAA1324L,missense_variant,p.Gln236His,ENST00000297222,;KIAA1324L,missense_variant,p.Gln309His,ENST00000416314,;KIAA1324L,non_coding_transcript_exon_variant,,ENST00000474609,;KIAA1324L,non_coding_transcript_exon_variant,,ENST00000490995,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;	A	ENSG00000164659	ENST00000450689	Transcript	missense_variant	1614	1428	476	Q/H	caG/caT	.	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	tolerated(0.17)	benign(0.003)	11/22	.	hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCACTCTGGAT	.	3	ESCA
SAMD9	0	.	GRCh37	7	92733886	92733886	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1525G>T	p.Asp509Tyr	p.D509Y	ENST00000379958	3/3	81	74	6	54	54	0	SAMD9,missense_variant,p.Asp509Tyr,ENST00000446617,;SAMD9,missense_variant,p.Asp509Tyr,ENST00000379958,;	A	ENSG00000205413	ENST00000379958	Transcript	missense_variant	1795	1525	509	D/Y	Gat/Tat	.	.	.	-1	SAMD9	HGNC	1348	protein_coding	YES	CCDS34680.1	ENSP00000369292	SAMD9_HUMAN	C9JKF1_HUMAN	UPI0000038BC6	.	deleterious(0)	possibly_damaging(0.873)	3/3	.	hmmpanther:PTHR16155:SF17,hmmpanther:PTHR16155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGATCAAAGG	.	2	ESCA
TRRAP	0	.	GRCh37	7	98608682	98608682	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10904G>A	p.Arg3635His	p.R3635H	ENST00000359863	70/72	17	13	4	23	23	0	TRRAP,missense_variant,p.Arg3606His,ENST00000355540,;TRRAP,missense_variant,p.Arg3624His,ENST00000446306,;TRRAP,missense_variant,p.Arg3364His,ENST00000456197,;TRRAP,missense_variant,p.Arg3635His,ENST00000359863,;AC004893.11,upstream_gene_variant,,ENST00000360902,;	A	ENSG00000196367	ENST00000359863	Transcript	missense_variant	11113	10904	3635	R/H	cGc/cAc	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	probably_damaging(0.993)	70/72	.	PROSITE_profiles:PS50290,hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139,Pfam_domain:PF00454,SMART_domains:SM00146	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCCGCGACA	.	4	ESCA
STAG3	0	.	GRCh37	7	99811735	99811735	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*97C>A	.	.	ENST00000426455	34/34	48	41	6	35	35	0	STAG3,3_prime_UTR_variant,,ENST00000412190,;STAG3,3_prime_UTR_variant,,ENST00000426455,;STAG3,3_prime_UTR_variant,,ENST00000394018,;STAG3,3_prime_UTR_variant,,ENST00000317296,;GATS,intron_variant,,ENST00000436886,;STAG3,non_coding_transcript_exon_variant,,ENST00000491498,;STAG3,non_coding_transcript_exon_variant,,ENST00000440830,;GATS,intron_variant,,ENST00000454084,;GATS,intron_variant,,ENST00000435519,;GATS,intron_variant,,ENST00000445230,;GATS,intron_variant,,ENST00000543273,;GATS,intron_variant,,ENST00000414739,;GATS,intron_variant,,ENST00000437485,;GATS,intron_variant,,ENST00000328453,;GATS,intron_variant,,ENST00000440058,;GATS,upstream_gene_variant,,ENST00000414997,;PVRIG,upstream_gene_variant,,ENST00000471803,;STAG3,non_coding_transcript_exon_variant,,ENST00000496157,;STAG3,non_coding_transcript_exon_variant,,ENST00000492674,;STAG3,intron_variant,,ENST00000451963,;	A	ENSG00000066923	ENST00000426455	Transcript	3_prime_UTR_variant	4182	.	.	.	.	.	.	.	1	STAG3	HGNC	11356	protein_coding	YES	CCDS34703.1	ENSP00000400359	STAG3_HUMAN	D6W5U7_HUMAN,C9JYW5_HUMAN,C9JTG4_HUMAN,B4DYS8_HUMAN	UPI000020F6E0	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCCCAGGCT	.	4	ESCA
RIMS2	0	.	GRCh37	8	105264188	105264188	+	3'Flank	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000406091	.	78	70	8	68	68	0	RIMS2,3_prime_UTR_variant,,ENST00000507740,;RIMS2,downstream_gene_variant,,ENST00000406091,;RIMS2,downstream_gene_variant,,ENST00000408894,;RIMS2,downstream_gene_variant,,ENST00000339750,;RIMS2,downstream_gene_variant,,ENST00000262231,;RIMS2,downstream_gene_variant,,ENST00000523362,;RIMS2,downstream_gene_variant,,ENST00000436393,;	C	ENSG00000176406	ENST00000406091	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	140	1	RIMS2	HGNC	17283	protein_coding	YES	CCDS55269.1	ENSP00000384892	RIMS2_HUMAN	E9PFB6_HUMAN	UPI0001597063	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGTGTTCTC	.	4	ESCA
CSMD3	0	.	GRCh37	8	114326869	114326869	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.332C>G	p.Ala111Gly	p.A111G	ENST00000297405	2/71	68	58	10	50	50	0	CSMD3,missense_variant,p.Ala111Gly,ENST00000352409,;CSMD3,missense_variant,p.Ala111Gly,ENST00000455883,;CSMD3,missense_variant,p.Ala111Gly,ENST00000297405,;CSMD3,missense_variant,p.Ala71Gly,ENST00000343508,;CSMD3,non_coding_transcript_exon_variant,,ENST00000497026,;CSMD3,non_coding_transcript_exon_variant,,ENST00000493303,;	C	ENSG00000164796	ENST00000297405	Transcript	missense_variant	577	332	111	A/G	gCt/gGt	COSM748571,COSM1151009	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.05)	benign(0.3)	2/71	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTAGAGCAAAT	.	4	ESCA
DLC1	0	.	GRCh37	8	13072192	13072192	+	Intron	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1348+90586T>A	.	.	ENST00000276297	.	89	78	11	103	103	0	DLC1,synonymous_variant,p.%3D,ENST00000316609,;DLC1,intron_variant,,ENST00000512044,;DLC1,intron_variant,,ENST00000276297,;DLC1,intron_variant,,ENST00000503161,;DLC1,non_coding_transcript_exon_variant,,ENST00000506171,;DLC1,intron_variant,,ENST00000509922,;	T	ENSG00000164741	ENST00000276297	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DLC1	HGNC	2897	protein_coding	YES	CCDS5989.1	ENSP00000276297	RHG07_HUMAN	.	UPI0000210275	.	.	.	.	5/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTAAGGAGA	.	4	ESCA
TG	0	.	GRCh37	8	134034380	134034380	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7021G>C	p.Gly2341Arg	p.G2341R	ENST00000220616	40/48	63	55	8	57	57	0	TG,missense_variant,p.Gly2341Arg,ENST00000220616,;TG,missense_variant,p.Gly711Arg,ENST00000542445,;TG,missense_variant,p.Gly2284Arg,ENST00000377869,;TG,missense_variant,p.Gly137Arg,ENST00000518108,;TG,missense_variant,p.Gly474Arg,ENST00000519543,;TG,missense_variant,p.Gly797Arg,ENST00000519178,;TG,downstream_gene_variant,,ENST00000522523,;TG,3_prime_UTR_variant,,ENST00000523756,;	C	ENSG00000042832	ENST00000220616	Transcript	missense_variant	7061	7021	2341	G/R	Ggc/Cgc	COSM1551755	.	.	1	TG	HGNC	11764	protein_coding	YES	CCDS34944.1	ENSP00000220616	THYG_HUMAN	Q9NYM1_HUMAN,Q9NYD9_HUMAN,E5RG33_HUMAN	UPI000013C79F	.	deleterious(0)	probably_damaging(1)	40/48	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF53474,PIRSF_domain:PIRSF001831,Pfam_domain:PF00135,Gene3D:3.40.50.1820,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF142	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTCGGCTTC	.	4	ESCA
COL22A1	0	.	GRCh37	8	139815144	139815144	+	Missense_Mutation	SNP	G	G	C	rs376678600	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1528C>G	p.Pro510Ala	p.P510A	ENST00000303045	11/65	76	65	11	55	55	0	COL22A1,missense_variant,p.Pro510Ala,ENST00000303045,;COL22A1,missense_variant,p.Pro510Ala,ENST00000435777,;	C	ENSG00000169436	ENST00000303045	Transcript	missense_variant	1975	1528	510	P/A	Cct/Gct	rs376678600	.	.	-1	COL22A1	HGNC	22989	protein_coding	YES	CCDS6376.1	ENSP00000303153	COMA1_HUMAN	.	UPI00001C1EA1	.	.	unknown(0)	11/65	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF379,hmmpanther:PTHR24023	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGGAGCGC	byCluster|by1000G	5	ESCA
BAI1	0	.	GRCh37	8	143618431	143618431	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3654C>T	p.%3D	p.H1218H	ENST00000517894	26/31	189	179	10	130	130	0	BAI1,synonymous_variant,p.%3D,ENST00000323289,;BAI1,synonymous_variant,p.%3D,ENST00000517894,;BAI1,3_prime_UTR_variant,,ENST00000521208,;BAI1,non_coding_transcript_exon_variant,,ENST00000518820,;	T	ENSG00000181790	ENST00000517894	Transcript	synonymous_variant	4548	3654	1218	H	caC/caT	COSM454122	.	.	1	BAI1	HGNC	943	protein_coding	YES	CCDS64985.1	ENSP00000430945	BAI1_HUMAN	.	UPI00002109E8	.	.	.	26/31	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF39	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCACGCCCA	.	2	ESCA
MROH6	0	.	GRCh37	8	144650733	144650733	+	Missense_Mutation	SNP	C	C	T	rs781456662	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633G>A	p.Asp545Asn	p.D545N	ENST00000398882	10/14	50	43	6	47	47	0	MROH6,missense_variant,p.Asp545Asn,ENST00000398882,;MROH6,5_prime_UTR_variant,,ENST00000524906,;MROH6,5_prime_UTR_variant,,ENST00000533679,;MROH6,5_prime_UTR_variant,,ENST00000532862,;MROH6,5_prime_UTR_variant,,ENST00000534459,;MROH6,downstream_gene_variant,,ENST00000529971,;RP11-661A12.9,upstream_gene_variant,,ENST00000531730,;MROH6,non_coding_transcript_exon_variant,,ENST00000533582,;MROH6,upstream_gene_variant,,ENST00000532704,;MROH6,non_coding_transcript_exon_variant,,ENST00000533083,;MROH6,non_coding_transcript_exon_variant,,ENST00000533210,;MROH6,upstream_gene_variant,,ENST00000533120,;	T	ENSG00000204839	ENST00000398882	Transcript	missense_variant	1890	1633	545	D/N	Gac/Aac	rs781456662	.	.	-1	MROH6	HGNC	27814	protein_coding	YES	CCDS47928.1	ENSP00000381857	MROH6_HUMAN	E9PJR4_HUMAN	UPI0000DD7EFB	.	deleterious(0.03)	possibly_damaging(0.701)	10/14	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCGTCCCTGC	.	4	ESCA
GRINA	0	.	GRCh37	8	145066491	145066491	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772G>T	p.Val258Leu	p.V258L	ENST00000313269	5/7	48	40	8	34	34	0	GRINA,missense_variant,p.Arg237Leu,ENST00000534791,;GRINA,missense_variant,p.Val258Leu,ENST00000313269,;GRINA,missense_variant,p.Val81Leu,ENST00000533044,;GRINA,missense_variant,p.Val71Leu,ENST00000527194,;GRINA,missense_variant,p.Val258Leu,ENST00000529301,;GRINA,missense_variant,p.Val258Leu,ENST00000395068,;PARP10,intron_variant,,ENST00000530478,;PARP10,upstream_gene_variant,,ENST00000528914,;PARP10,upstream_gene_variant,,ENST00000525879,;PARP10,upstream_gene_variant,,ENST00000529311,;PARP10,upstream_gene_variant,,ENST00000528625,;PARP10,upstream_gene_variant,,ENST00000532311,;GRINA,downstream_gene_variant,,ENST00000530898,;PARP10,upstream_gene_variant,,ENST00000528136,;PARP10,upstream_gene_variant,,ENST00000534737,;PARP10,upstream_gene_variant,,ENST00000532660,;GRINA,non_coding_transcript_exon_variant,,ENST00000533377,;GRINA,non_coding_transcript_exon_variant,,ENST00000525513,;GRINA,downstream_gene_variant,,ENST00000531992,;	T	ENSG00000178719	ENST00000313269	Transcript	missense_variant	1050	772	258	V/L	Gtg/Ttg	.	.	.	1	GRINA	HGNC	4589	protein_coding	YES	CCDS34961.1	ENSP00000314380	LFG1_HUMAN	E9PQF8_HUMAN,E9PPG3_HUMAN	UPI000015A99B	.	tolerated(0.55)	benign(0.371)	5/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23291:SF16,hmmpanther:PTHR23291,Pfam_domain:PF01027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCCGTGGGC	.	4	ESCA
KBTBD11	0	.	GRCh37	8	1952500	1952500	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1270G>C	.	.	ENST00000320248	2/2	30	26	3	25	25	0	KBTBD11,3_prime_UTR_variant,,ENST00000320248,;	C	ENSG00000176595	ENST00000320248	Transcript	3_prime_UTR_variant	4108	.	.	.	.	.	.	.	1	KBTBD11	HGNC	29104	protein_coding	YES	CCDS34795.1	ENSP00000321544	KBTBB_HUMAN	.	UPI0000139C1D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGAGGACTTA	.	4	ESCA
PNMA2	0	.	GRCh37	8	26371930	26371930	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000522362	.	59	53	6	59	59	0	DPYSL2,5_prime_UTR_variant,,ENST00000521913,;PNMA2,upstream_gene_variant,,ENST00000522362,;PNMA2,upstream_gene_variant,,ENST00000521740,;PNMA2,upstream_gene_variant,,ENST00000522450,;PNMA2,upstream_gene_variant,,ENST00000523244,;PNMA2,upstream_gene_variant,,ENST00000522764,;PNMA2,upstream_gene_variant,,ENST00000518212,;PNMA2,upstream_gene_variant,,ENST00000521875,;PNMA2,upstream_gene_variant,,ENST00000523616,;	A	ENSG00000240694	ENST00000522362	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	322	-1	PNMA2	HGNC	9159	protein_coding	YES	CCDS34868.1	ENSP00000429344	PNMA2_HUMAN	.	UPI0000073D3F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAGCCCCGGC	.	4	ESCA
ZMAT4	0	.	GRCh37	8	40389096	40389096	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*646C>G	.	.	ENST00000297737	7/7	72	64	8	47	47	0	ZMAT4,3_prime_UTR_variant,,ENST00000297737,;ZMAT4,3_prime_UTR_variant,,ENST00000315769,;	C	ENSG00000165061	ENST00000297737	Transcript	3_prime_UTR_variant	1483	.	.	.	.	.	.	.	-1	ZMAT4	HGNC	25844	protein_coding	YES	CCDS34885.1	ENSP00000297737	ZMAT4_HUMAN	E5RIF5_HUMAN	UPI0000046C33	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACTTGGCTTA	.	4	ESCA
C8orf22	0	.	GRCh37	8	49985382	49985382	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-8G>A	.	.	ENST00000303202	2/5	94	72	22	100	100	0	C8orf22,5_prime_UTR_variant,,ENST00000303202,;C8orf22,5_prime_UTR_variant,,ENST00000399653,;C8orf22,5_prime_UTR_variant,,ENST00000517663,;C8orf22,5_prime_UTR_variant,,ENST00000522267,;	A	ENSG00000168333	ENST00000303202	Transcript	5_prime_UTR_variant	166	.	.	.	.	.	.	.	1	C8orf22	HGNC	31745	protein_coding	YES	CCDS59101.1	ENSP00000304926	PDPFL_HUMAN	.	UPI0000070316	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACGGGTAAAG	.	5	ESCA
PXDNL	0	.	GRCh37	8	52321611	52321611	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2573C>A	p.Pro858His	p.P858H	ENST00000356297	17/23	45	38	7	25	25	0	PXDNL,missense_variant,p.Pro858His,ENST00000543296,;PXDNL,missense_variant,p.Pro858His,ENST00000356297,;PXDNL,upstream_gene_variant,,ENST00000522933,;PXDNL,missense_variant,p.Pro124His,ENST00000522628,;	T	ENSG00000147485	ENST00000356297	Transcript	missense_variant	2674	2573	858	P/H	cCc/cAc	.	.	.	-1	PXDNL	HGNC	26359	protein_coding	YES	CCDS47855.1	ENSP00000348645	PXDNL_HUMAN	.	UPI0001AE6ED6	.	deleterious(0.03)	benign(0.005)	17/23	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Pfam_domain:PF03098,Superfamily_domains:SSF48113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCAGGGCGCG	.	4	ESCA
ERICH1	0	.	GRCh37	8	665954	665954	+	Missense_Mutation	SNP	C	C	G	rs746525048	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76G>C	p.Gly26Arg	p.G26R	ENST00000262109	2/6	111	98	12	118	118	0	ERICH1,missense_variant,p.Gly26Arg,ENST00000262109,;ERICH1,intron_variant,,ENST00000522706,;ERICH1,non_coding_transcript_exon_variant,,ENST00000518277,;ERICH1,upstream_gene_variant,,ENST00000524138,;	G	ENSG00000104714	ENST00000262109	Transcript	missense_variant	154	76	26	G/R	Gga/Cga	rs746525048	.	.	-1	ERICH1	HGNC	27234	protein_coding	YES	CCDS5955.1	ENSP00000262109	ERIC1_HUMAN	.	UPI000000DB6B	.	deleterious(0.01)	benign(0.413)	2/6	.	hmmpanther:PTHR22444,hmmpanther:PTHR22444:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTCCTTGGC	.	4	ESCA
MMP16	0	.	GRCh37	8	89052248	89052248	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1441G>C	.	.	ENST00000286614	10/10	29	25	4	28	28	0	MMP16,3_prime_UTR_variant,,ENST00000286614,;	G	ENSG00000156103	ENST00000286614	Transcript	3_prime_UTR_variant	3547	.	.	.	.	.	.	.	-1	MMP16	HGNC	7162	protein_coding	YES	CCDS6246.1	ENSP00000286614	MMP16_HUMAN	.	UPI000003DC73	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATTCATGCA	.	4	ESCA
RUNX1T1	0	.	GRCh37	8	92972711	92972711	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1607C>T	p.Thr536Ile	p.T536I	ENST00000436581	11/11	71	56	15	49	49	0	RUNX1T1,missense_variant,p.Thr536Ile,ENST00000436581,;RUNX1T1,missense_variant,p.Thr525Ile,ENST00000265814,;RUNX1T1,missense_variant,p.Thr498Ile,ENST00000518844,;RUNX1T1,missense_variant,p.Thr525Ile,ENST00000523629,;RUNX1T1,missense_variant,p.Thr488Ile,ENST00000360348,;RUNX1T1,missense_variant,p.Thr488Ile,ENST00000520724,;RUNX1T1,missense_variant,p.Thr498Ile,ENST00000396218,;RUNX1T1,missense_variant,p.Thr488Ile,ENST00000422361,;RUNX1T1,3_prime_UTR_variant,,ENST00000521751,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000521078,;	A	ENSG00000079102	ENST00000436581	Transcript	missense_variant	1618	1607	536	T/I	aCc/aTc	.	.	.	-1	RUNX1T1	HGNC	1535	protein_coding	YES	CCDS56544.1	ENSP00000402257	MTG8_HUMAN	Q9HBV9_HUMAN,E5RK76_HUMAN,E5RJB3_HUMAN,E5RHJ8_HUMAN,E5RH72_HUMAN,E5RH30_HUMAN,E5RG85_HUMAN	UPI0001D5F276	.	deleterious(0)	probably_damaging(0.939)	11/11	.	PROSITE_profiles:PS50865,hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF5,PROSITE_patterns:PS01360,Pfam_domain:PF01753,Superfamily_domains:SSF144232	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGGTTTCA	.	5	ESCA
RAD54B	0	.	GRCh37	8	95412652	95412652	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.984G>A	p.Met328Ile	p.M328I	ENST00000336148	7/15	75	68	7	70	70	0	RAD54B,missense_variant,p.Met328Ile,ENST00000336148,;RAD54B,3_prime_UTR_variant,,ENST00000463267,;FSBP,3_prime_UTR_variant,,ENST00000517506,;RAD54B,upstream_gene_variant,,ENST00000523192,;	T	ENSG00000197275	ENST00000336148	Transcript	missense_variant	1109	984	328	M/I	atG/atA	.	.	.	-1	RAD54B	HGNC	17228	protein_coding	YES	CCDS6262.1	ENSP00000336606	RA54B_HUMAN	E5RHN9_HUMAN	UPI0000070088	.	deleterious(0)	probably_damaging(1)	7/15	.	Superfamily_domains:SSF52540,SMART_domains:SM00487,Pfam_domain:PF00176,Gene3D:3.40.50.300,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF568,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACCCATTTC	.	4	ESCA
ALDOB	0	.	GRCh37	9	104187755	104187755	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.779C>A	p.Thr260Asn	p.T260N	ENST00000374855	7/9	94	80	13	80	80	0	ALDOB,missense_variant,p.Thr260Asn,ENST00000374855,;ALDOB,downstream_gene_variant,,ENST00000468981,;	T	ENSG00000136872	ENST00000374855	Transcript	missense_variant	904	779	260	T/N	aCt/aAt	.	.	.	-1	ALDOB	HGNC	417	protein_coding	YES	CCDS6756.1	ENSP00000363988	ALDOB_HUMAN	.	UPI000016A4A9	.	deleterious(0.01)	probably_damaging(0.989)	7/9	.	Superfamily_domains:SSF51569,Gene3D:3.20.20.70,Pfam_domain:PF00274,hmmpanther:PTHR11627,hmmpanther:PTHR11627:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACAGTACGG	.	4	ESCA
ABCA1	0	.	GRCh37	9	107581886	107581886	+	Silent	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3222G>T	p.%3D	p.L1074L	ENST00000374736	22/50	67	57	10	79	79	0	ABCA1,synonymous_variant,p.%3D,ENST00000374736,;	A	ENSG00000165029	ENST00000374736	Transcript	synonymous_variant	3617	3222	1074	L	ctG/ctT	.	.	.	-1	ABCA1	HGNC	29	protein_coding	YES	CCDS6762.1	ENSP00000363868	ABCA1_HUMAN	Q9NS76_HUMAN,Q9NP93_HUMAN,Q9H002_HUMAN	UPI000013E441	.	.	.	22/50	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229:SF34,hmmpanther:PTHR19229,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCAGCAGCTC	.	4	ESCA
SVEP1	0	.	GRCh37	9	113308490	113308490	+	Missense_Mutation	SNP	C	C	T	rs748669116	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.869G>A	p.Arg290Gln	p.R290Q	ENST00000401783	3/48	81	64	17	73	73	0	SVEP1,missense_variant,p.Arg290Gln,ENST00000401783,;SVEP1,missense_variant,p.Arg267Gln,ENST00000374469,;SVEP1,missense_variant,p.Arg290Gln,ENST00000302728,;SVEP1,missense_variant,p.Arg267Gln,ENST00000374461,;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,;	T	ENSG00000165124	ENST00000401783	Transcript	missense_variant	1206	869	290	R/Q	cGa/cAa	rs748669116	.	.	-1	SVEP1	HGNC	15985	protein_coding	YES	CCDS48004.1	ENSP00000384917	SVEP1_HUMAN	.	UPI000153DA74	.	.	benign(0.004)	3/48	.	Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATTCGGTCA	byFrequency	5	ESCA
OR2K2	0	.	GRCh37	9	114089878	114089878	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.836T>A	p.Val279Glu	p.V279E	ENST00000302681	1/1	90	79	11	75	75	0	OR2K2,missense_variant,p.Val279Glu,ENST00000302681,;OR2K2,missense_variant,p.Val308Glu,ENST00000374428,;	T	ENSG00000171133	ENST00000302681	Transcript	missense_variant	836	836	279	V/E	gTg/gAg	.	.	.	-1	OR2K2	HGNC	8264	protein_coding	YES	CCDS6778.1	ENSP00000305055	OR2K2_HUMAN	.	UPI000003FE16	.	deleterious(0)	possibly_damaging(0.735)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF198,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAGCACTCCG	.	4	ESCA
SLC2A6	0	.	GRCh37	9	136339163	136339163	+	Silent	SNP	G	G	T	rs372931255	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.975C>A	p.%3D	p.S325S	ENST00000371899	7/10	82	72	10	81	81	0	SLC2A6,synonymous_variant,p.%3D,ENST00000371899,;SLC2A6,synonymous_variant,p.%3D,ENST00000371897,;SLC2A6,downstream_gene_variant,,ENST00000414172,;CACFD1,downstream_gene_variant,,ENST00000542192,;SLC2A6,downstream_gene_variant,,ENST00000432868,;CACFD1,downstream_gene_variant,,ENST00000316948,;CACFD1,downstream_gene_variant,,ENST00000291722,;SLC2A6,non_coding_transcript_exon_variant,,ENST00000485978,;	T	ENSG00000160326	ENST00000371899	Transcript	synonymous_variant	1053	975	325	S	tcC/tcA	rs372931255	.	.	-1	SLC2A6	HGNC	11011	protein_coding	YES	CCDS6975.1	ENSP00000360966	GTR6_HUMAN	.	UPI0000001BE8	.	.	.	7/10	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24063,hmmpanther:PTHR24063:SF47,TIGRFAM_domain:TIGR00879,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCACGGACAG	byCluster	4	ESCA
UAP1L1	0	.	GRCh37	9	139975304	139975304	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1342G>T	p.Ala448Ser	p.A448S	ENST00000409858	7/9	67	59	8	61	61	0	UAP1L1,missense_variant,p.Ala448Ser,ENST00000409858,;UAP1L1,missense_variant,p.Ala325Ser,ENST00000360271,;UAP1L1,downstream_gene_variant,,ENST00000476184,;UAP1L1,non_coding_transcript_exon_variant,,ENST00000474787,;	T	ENSG00000197355	ENST00000409858	Transcript	missense_variant	1374	1342	448	A/S	Gcc/Tcc	.	.	.	1	UAP1L1	HGNC	28082	protein_coding	YES	CCDS7028.2	ENSP00000386935	UAP1L_HUMAN	.	UPI000016047B	.	tolerated(0.79)	benign(0.014)	7/9	.	Superfamily_domains:SSF53448,Pfam_domain:PF01704,hmmpanther:PTHR11952,hmmpanther:PTHR11952:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGGGGCCTGG	.	4	ESCA
TMEM215	0	.	GRCh37	9	32784186	32784186	+	Missense_Mutation	SNP	G	G	T	rs763352445	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5G>T	p.Arg2Leu	p.R2L	ENST00000342743	2/2	61	56	5	44	44	0	TMEM215,missense_variant,p.Arg2Leu,ENST00000342743,;	T	ENSG00000188133	ENST00000342743	Transcript	missense_variant	370	5	2	R/L	cGg/cTg	rs763352445	.	.	1	TMEM215	HGNC	33816	protein_coding	YES	CCDS6530.1	ENSP00000345468	TM215_HUMAN	.	UPI0000049371	.	deleterious(0)	probably_damaging(0.994)	2/2	.	hmmpanther:PTHR31922	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CATGCGGCCTG	byFrequency	2	ESCA
KDM4C	0	.	GRCh37	9	6793022	6793022	+	Missense_Mutation	SNP	C	C	T	rs752325707	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34C>T	p.Pro12Ser	p.P12S	ENST00000381309	2/22	83	78	5	78	78	0	KDM4C,missense_variant,p.Pro12Ser,ENST00000381306,;KDM4C,missense_variant,p.Pro12Ser,ENST00000381309,;KDM4C,missense_variant,p.Pro12Ser,ENST00000401787,;KDM4C,missense_variant,p.Pro34Ser,ENST00000535193,;KDM4C,missense_variant,p.Pro12Ser,ENST00000543771,;KDM4C,5_prime_UTR_variant,,ENST00000536108,;KDM4C,5_prime_UTR_variant,,ENST00000442236,;KDM4C,non_coding_transcript_exon_variant,,ENST00000489243,;KDM4C,missense_variant,p.Pro12Ser,ENST00000438023,;	T	ENSG00000107077	ENST00000381309	Transcript	missense_variant	599	34	12	P/S	Ccc/Tcc	rs752325707	.	.	1	KDM4C	HGNC	17071	protein_coding	YES	CCDS6471.1	ENSP00000370710	KDM4C_HUMAN	C9J879_HUMAN	UPI0000367602	.	tolerated(0.06)	benign(0.025)	2/22	.	hmmpanther:PTHR10694:SF32,hmmpanther:PTHR10694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAACCCCAGC	.	2	ESCA
TRPM3	0	.	GRCh37	9	73477993	73477993	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.293G>T	p.Gly98Val	p.G98V	ENST00000377110	3/25	70	55	15	49	49	0	TRPM3,missense_variant,p.Gly98Val,ENST00000377111,;TRPM3,missense_variant,p.Gly100Val,ENST00000423814,;TRPM3,missense_variant,p.Gly100Val,ENST00000357533,;TRPM3,missense_variant,p.Gly98Val,ENST00000377110,;TRPM3,5_prime_UTR_variant,,ENST00000377106,;TRPM3,5_prime_UTR_variant,,ENST00000361823,;TRPM3,5_prime_UTR_variant,,ENST00000377101,;TRPM3,5_prime_UTR_variant,,ENST00000360823,;TRPM3,5_prime_UTR_variant,,ENST00000396283,;TRPM3,5_prime_UTR_variant,,ENST00000377105,;TRPM3,upstream_gene_variant,,ENST00000377097,;TRPM3,upstream_gene_variant,,ENST00000358082,;TRPM3,upstream_gene_variant,,ENST00000396280,;TRPM3,upstream_gene_variant,,ENST00000396292,;TRPM3,upstream_gene_variant,,ENST00000408909,;TRPM3,upstream_gene_variant,,ENST00000396285,;TRPM3,non_coding_transcript_exon_variant,,ENST00000437699,;TRPM3,non_coding_transcript_exon_variant,,ENST00000354500,;	A	ENSG00000083067	ENST00000377110	Transcript	missense_variant	537	293	98	G/V	gGc/gTc	.	.	.	-1	TRPM3	HGNC	17992	protein_coding	YES	CCDS43835.1	ENSP00000366314	TRPM3_HUMAN	.	UPI0001596895	.	deleterious(0.05)	probably_damaging(0.999)	3/25	.	hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGGCCAACA	.	5	ESCA
SPATA31D1	0	.	GRCh37	9	84609130	84609130	+	Missense_Mutation	SNP	A	A	T	rs781262873	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3745A>T	p.Met1249Leu	p.M1249L	ENST00000344803	4/4	107	102	5	91	91	0	SPATA31D1,missense_variant,p.Met1249Leu,ENST00000344803,;SPATA31D1,downstream_gene_variant,,ENST00000603921,;	T	ENSG00000214929	ENST00000344803	Transcript	missense_variant	3792	3745	1249	M/L	Atg/Ttg	rs781262873	.	.	1	SPATA31D1	HGNC	37283	protein_coding	YES	CCDS47986.1	ENSP00000341988	S31D1_HUMAN	.	UPI00001C10A6	.	tolerated(0.13)	benign(0.013)	4/4	.	hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGACATGGGA	.	2	ESCA
SPATA31D1	0	.	GRCh37	9	84610013	84610013	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4628C>A	p.Pro1543Gln	p.P1543Q	ENST00000344803	4/4	65	58	7	67	67	0	SPATA31D1,missense_variant,p.Pro1543Gln,ENST00000344803,;SPATA31D1,downstream_gene_variant,,ENST00000603921,;	A	ENSG00000214929	ENST00000344803	Transcript	missense_variant	4675	4628	1543	P/Q	cCa/cAa	.	.	.	1	SPATA31D1	HGNC	37283	protein_coding	YES	CCDS47986.1	ENSP00000341988	S31D1_HUMAN	.	UPI00001C10A6	.	deleterious(0.05)	possibly_damaging(0.742)	4/4	.	hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTCCCAACCA	.	4	ESCA
FRMD3	0	.	GRCh37	9	85958132	85958132	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.445G>T	p.Ala149Ser	p.A149S	ENST00000304195	5/14	74	69	5	69	69	0	FRMD3,missense_variant,p.Ala149Ser,ENST00000304195,;FRMD3,missense_variant,p.Ala149Ser,ENST00000376438,;	A	ENSG00000172159	ENST00000304195	Transcript	missense_variant	652	445	149	A/S	Gcc/Tcc	.	.	.	-1	FRMD3	HGNC	24125	protein_coding	YES	CCDS43840.1	ENSP00000303508	FRMD3_HUMAN	.	UPI000066DA57	.	deleterious(0)	possibly_damaging(0.67)	5/14	.	PROSITE_profiles:PS50057,hmmpanther:PTHR23280:SF8,hmmpanther:PTHR23280,Pfam_domain:PF00373,Gene3D:1.20.80.10,SMART_domains:SM00295,Superfamily_domains:SSF47031,Prints_domain:PR00661,Prints_domain:PR00935	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTAGGCAGCAT	.	2	ESCA
CTSL	0	.	GRCh37	9	90343008	90343008	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193G>C	p.Glu65Gln	p.E65Q	ENST00000343150	3/8	237	208	28	228	228	0	CTSL,missense_variant,p.Glu65Gln,ENST00000342020,;CTSL,missense_variant,p.Glu65Gln,ENST00000340342,;CTSL,missense_variant,p.Glu65Gln,ENST00000343150,;CTSL,non_coding_transcript_exon_variant,,ENST00000482054,;CTSL,non_coding_transcript_exon_variant,,ENST00000375894,;CTSL,intron_variant,,ENST00000495822,;	C	ENSG00000135047	ENST00000343150	Transcript	missense_variant	1083	193	65	E/Q	Gaa/Caa	.	.	.	1	CTSL	HGNC	2537	protein_coding	YES	CCDS6675.1	ENSP00000345344	CATL1_HUMAN	Q9HBQ7_HUMAN,Q8NG13_HUMAN,Q5K630_HUMAN	UPI000004CAA2	.	deleterious(0.03)	possibly_damaging(0.721)	3/8	.	Superfamily_domains:SSF54001,SMART_domains:SM00848,Gene3D:3.90.70.10,Pfam_domain:PF08246,hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF306	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCAGGAATAC	.	4	ESCA
CDK20	0	.	GRCh37	9	90582309	90582309	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*68G>T	.	.	ENST00000325303	8/8	50	40	10	47	47	0	CDK20,3_prime_UTR_variant,,ENST00000375871,;CDK20,3_prime_UTR_variant,,ENST00000336654,;CDK20,3_prime_UTR_variant,,ENST00000325303,;CDK20,3_prime_UTR_variant,,ENST00000375883,;CDK20,3_prime_UTR_variant,,ENST00000605159,;CDK20,non_coding_transcript_exon_variant,,ENST00000486228,;CDK20,non_coding_transcript_exon_variant,,ENST00000459720,;CDK20,non_coding_transcript_exon_variant,,ENST00000603475,;CDK20,downstream_gene_variant,,ENST00000605591,;CDK20,downstream_gene_variant,,ENST00000604175,;	A	ENSG00000156345	ENST00000325303	Transcript	3_prime_UTR_variant	1415	.	.	.	.	.	.	.	-1	CDK20	HGNC	21420	protein_coding	YES	CCDS35060.1	ENSP00000322343	CDK20_HUMAN	A8K6P8_HUMAN	UPI00000740E8	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGCAGGTG	.	5	ESCA
ROR2	0	.	GRCh37	9	94486219	94486219	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2557C>A	p.Pro853Thr	p.P853T	ENST00000375708	9/9	67	56	11	44	44	0	ROR2,missense_variant,p.Pro853Thr,ENST00000375708,;ROR2,intron_variant,,ENST00000375715,;ROR2,non_coding_transcript_exon_variant,,ENST00000550066,;	T	ENSG00000169071	ENST00000375708	Transcript	missense_variant	2756	2557	853	P/T	Cct/Act	.	.	.	-1	ROR2	HGNC	10257	protein_coding	YES	CCDS6691.1	ENSP00000364860	ROR2_HUMAN	.	UPI000013E8CA	.	deleterious_low_confidence(0.02)	benign(0.031)	9/9	.	Low_complexity_(Seg):seg,PIRSF_domain:PIRSF000624,hmmpanther:PTHR24416:SF132,hmmpanther:PTHR24416	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGGAGGCA	.	5	ESCA
NOL8	0	.	GRCh37	9	95076562	95076562	+	Missense_Mutation	SNP	G	G	C	rs766780387	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2345C>G	p.Ala782Gly	p.A782G	ENST00000545558	7/17	51	47	4	36	36	0	NOL8,missense_variant,p.Ala782Gly,ENST00000545558,;NOL8,missense_variant,p.Ala714Gly,ENST00000358855,;NOL8,missense_variant,p.Ala782Gly,ENST00000442668,;NOL8,missense_variant,p.Ala782Gly,ENST00000535387,;NOL8,missense_variant,p.Ala714Gly,ENST00000542053,;NOL8,missense_variant,p.Ala782Gly,ENST00000432670,;NOL8,downstream_gene_variant,,ENST00000542613,;NOL8,downstream_gene_variant,,ENST00000433029,;NOL8,downstream_gene_variant,,ENST00000411621,;NOL8,downstream_gene_variant,,ENST00000536624,;NOL8,downstream_gene_variant,,ENST00000421075,;NOL8,downstream_gene_variant,,ENST00000535807,;NOL8,missense_variant,p.Ala782Gly,ENST00000544867,;NOL8,3_prime_UTR_variant,,ENST00000360868,;NOL8,3_prime_UTR_variant,,ENST00000536593,;NOL8,3_prime_UTR_variant,,ENST00000434228,;NOL8,intron_variant,,ENST00000545444,;NOL8,upstream_gene_variant,,ENST00000538802,;NOL8,downstream_gene_variant,,ENST00000445919,;NOL8,downstream_gene_variant,,ENST00000467230,;	C	ENSG00000198000	ENST00000545558	Transcript	missense_variant	2838	2345	782	A/G	gCt/gGt	rs766780387	.	.	-1	NOL8	HGNC	23387	protein_coding	YES	CCDS47993.1	ENSP00000441140	NOL8_HUMAN	F8WE42_HUMAN,F5H8B8_HUMAN,F5H7D5_HUMAN,F5H797_HUMAN,F5H692_HUMAN,F5H540_HUMAN,F5GWN9_HUMAN	UPI0000211A3D	.	deleterious(0)	probably_damaging(1)	7/17	.	hmmpanther:PTHR16274,hmmpanther:PTHR16274:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGAGCATTA	.	2	ESCA
PSMD10	0	.	GRCh37	X	107334759	107334759	+	5'UTR	DEL	C	C	-	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-9delG	.	.	ENST00000217958	1/5	98	89	9	97	97	0	PSMD10,5_prime_UTR_variant,,ENST00000361815,;PSMD10,5_prime_UTR_variant,,ENST00000372296,;PSMD10,5_prime_UTR_variant,,ENST00000372295,;PSMD10,5_prime_UTR_variant,,ENST00000217958,;ATG4A,upstream_gene_variant,,ENST00000372254,;PSMD10,upstream_gene_variant,,ENST00000340200,;ATG4A,upstream_gene_variant,,ENST00000372232,;ATG4A,upstream_gene_variant,,ENST00000345734,;ATG4A,upstream_gene_variant,,ENST00000545696,;ATG4A,upstream_gene_variant,,ENST00000457035,;PSMD10,non_coding_transcript_exon_variant,,ENST00000338548,;PSMD10,non_coding_transcript_exon_variant,,ENST00000553388,;ATG4A,upstream_gene_variant,,ENST00000343524,;ATG4A,upstream_gene_variant,,ENST00000372246,;	-	ENSG00000101843	ENST00000217958	Transcript	5_prime_UTR_variant	90	.	.	.	.	.	.	.	-1	PSMD10	HGNC	9555	protein_coding	YES	CCDS14536.1	ENSP00000217958	PSD10_HUMAN	.	UPI000013278F	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGCTGTCCCAGC	.	3	ESCA
AMOT	0	.	GRCh37	X	112059028	112059028	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.950G>T	p.Gly317Val	p.G317V	ENST00000371959	2/11	85	77	8	76	76	0	AMOT,missense_variant,p.Gly317Val,ENST00000371959,;AMOT,missense_variant,p.Gly85Val,ENST00000371962,;AMOT,missense_variant,p.Gly317Val,ENST00000524145,;AMOT,missense_variant,p.Gly85Val,ENST00000371958,;AMOT,5_prime_UTR_variant,,ENST00000304758,;	A	ENSG00000126016	ENST00000371959	Transcript	missense_variant	950	950	317	G/V	gGg/gTg	.	.	.	-1	AMOT	HGNC	17810	protein_coding	YES	CCDS48154.1	ENSP00000361027	AMOT_HUMAN	E7ERM3_HUMAN	UPI000050ED33	.	.	unknown(0)	2/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14826,hmmpanther:PTHR14826:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCCCCCAGAG	.	3	ESCA
DCAF12L2	0	.	GRCh37	X	125298851	125298851	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057G>T	p.Val353Leu	p.V353L	ENST00000538699	2/2	55	50	5	55	54	0	DCAF12L2,missense_variant,p.Val353Leu,ENST00000538699,;DCAF12L2,missense_variant,p.Val353Leu,ENST00000360028,;	A	ENSG00000198354	ENST00000538699	Transcript	missense_variant	1138	1057	353	V/L	Gtg/Ttg	.	.	.	-1	DCAF12L2	HGNC	32950	protein_coding	YES	CCDS43991.1	ENSP00000441489	DC122_HUMAN	.	UPI0000197594	.	deleterious(0.01)	probably_damaging(0.998)	2/2	.	hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF8,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCGCACGCCTG	.	3	ESCA
BCORL1	0	.	GRCh37	X	129190222	129190222	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*111C>A	.	.	ENST00000540052	12/12	79	72	7	63	63	0	BCORL1,3_prime_UTR_variant,,ENST00000456822,;BCORL1,3_prime_UTR_variant,,ENST00000540052,;BCORL1,3_prime_UTR_variant,,ENST00000303743,;BCORL1,3_prime_UTR_variant,,ENST00000218147,;BCORL1,3_prime_UTR_variant,,ENST00000359304,;	A	ENSG00000085185	ENST00000540052	Transcript	3_prime_UTR_variant	5291	.	.	.	.	.	.	.	1	BCORL1	HGNC	25657	protein_coding	YES	CCDS14616.1	ENSP00000437775	BCORL_HUMAN	Q9HAM3_HUMAN	UPI00001B4EFB	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGGACCAACAA	.	3	ESCA
RBMX2	0	.	GRCh37	X	129545421	129545421	+	Missense_Mutation	SNP	G	G	T	rs753720356	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403G>T	p.Gly135Cys	p.G135C	ENST00000305536	5/6	88	82	6	87	87	0	RBMX2,missense_variant,p.Gly135Cys,ENST00000305536,;RBMX2,non_coding_transcript_exon_variant,,ENST00000469953,;RBMX2,non_coding_transcript_exon_variant,,ENST00000487274,;	T	ENSG00000134597	ENST00000305536	Transcript	missense_variant	467	403	135	G/C	Ggc/Tgc	rs753720356	.	.	1	RBMX2	HGNC	24282	protein_coding	YES	CCDS43993.1	ENSP00000339090	RBMX2_HUMAN	Q5JY83_HUMAN	UPI00000704DB	.	deleterious(0.01)	possibly_damaging(0.652)	5/6	.	hmmpanther:PTHR23139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGGGCTGT	byFrequency	2	ESCA
ENOX2	0	.	GRCh37	X	129759235	129759235	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53C>T	.	.	ENST00000338144	16/16	55	51	4	34	34	0	ENOX2,3_prime_UTR_variant,,ENST00000370927,;ENOX2,3_prime_UTR_variant,,ENST00000338144,;ENOX2,3_prime_UTR_variant,,ENST00000394363,;ENOX2,3_prime_UTR_variant,,ENST00000370935,;	A	ENSG00000165675	ENST00000338144	Transcript	3_prime_UTR_variant	2304	.	.	.	.	.	.	.	-1	ENOX2	HGNC	2259	protein_coding	YES	CCDS14626.1	ENSP00000337146	ENOX2_HUMAN	B1AKF7_HUMAN	UPI00000729D5	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTATGCTTGT	.	2	ESCA
SAGE1	0	.	GRCh37	X	134994988	134994988	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2647G>C	p.Glu883Gln	p.E883Q	ENST00000535938	20/20	108	102	5	89	89	0	SAGE1,missense_variant,p.Glu883Gln,ENST00000370709,;SAGE1,missense_variant,p.Glu883Gln,ENST00000535938,;SAGE1,missense_variant,p.Glu507Gln,ENST00000537770,;SAGE1,missense_variant,p.Glu883Gln,ENST00000324447,;	C	ENSG00000181433	ENST00000535938	Transcript	missense_variant	2814	2647	883	E/Q	Gag/Cag	.	.	.	1	SAGE1	HGNC	30369	protein_coding	YES	CCDS14652.1	ENSP00000445959	SAGE1_HUMAN	.	UPI00001413AB	.	deleterious(0.04)	possibly_damaging(0.596)	20/20	.	hmmpanther:PTHR12957:SF7,hmmpanther:PTHR12957,Pfam_domain:PF15300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACTCGAGAAG	.	2	ESCA
OFD1	0	.	GRCh37	X	13779231	13779231	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2288C>A	p.Pro763His	p.P763H	ENST00000340096	17/23	136	130	6	117	117	0	OFD1,missense_variant,p.Pro623His,ENST00000380567,;OFD1,missense_variant,p.Pro763His,ENST00000340096,;OFD1,missense_variant,p.Pro723His,ENST00000380550,;OFD1,non_coding_transcript_exon_variant,,ENST00000490265,;OFD1,non_coding_transcript_exon_variant,,ENST00000464463,;	A	ENSG00000046651	ENST00000340096	Transcript	missense_variant	2615	2288	763	P/H	cCc/cAc	COSM1465936	.	.	1	OFD1	HGNC	2567	protein_coding	YES	CCDS14157.1	ENSP00000344314	OFD1_HUMAN	E9KL37_HUMAN,A8K2T9_HUMAN,A6NF31_HUMAN	UPI0000130C40	.	deleterious(0.04)	probably_damaging(0.957)	17/23	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCCCCCAGTC	.	2	ESCA
SLITRK4	0	.	GRCh37	X	142718475	142718475	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450C>A	p.%3D	p.A150A	ENST00000381779	2/2	57	50	7	61	61	0	SLITRK4,synonymous_variant,p.%3D,ENST00000381779,;SLITRK4,synonymous_variant,p.%3D,ENST00000338017,;SLITRK4,synonymous_variant,p.%3D,ENST00000356928,;	T	ENSG00000179542	ENST00000381779	Transcript	synonymous_variant	676	450	150	A	gcC/gcA	.	.	.	-1	SLITRK4	HGNC	23502	protein_coding	YES	CCDS14679.1	ENSP00000371198	SLIK4_HUMAN	.	UPI000004E650	.	.	.	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAAGGCTCC	.	4	ESCA
RPL10	0	.	GRCh37	X	153626899	153626899	+	Intron	SNP	G	G	T	rs781982364	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.23+16G>T	.	.	ENST00000424325	.	37	33	4	54	54	0	RPL10,intron_variant,,ENST00000344746,;RPL10,intron_variant,,ENST00000436473,;RPL10,intron_variant,,ENST00000369817,;RPL10,intron_variant,,ENST00000458500,;RPL10,intron_variant,,ENST00000424325,;DNASE1L1,downstream_gene_variant,,ENST00000369808,;DNASE1L1,downstream_gene_variant,,ENST00000447892,;DNASE1L1,downstream_gene_variant,,ENST00000309585,;DNASE1L1,downstream_gene_variant,,ENST00000369809,;RPL10,upstream_gene_variant,,ENST00000428169,;RPL10,upstream_gene_variant,,ENST00000406022,;RPL10,upstream_gene_variant,,ENST00000449494,;DNASE1L1,downstream_gene_variant,,ENST00000412184,;DNASE1L1,downstream_gene_variant,,ENST00000451865,;RPL10,upstream_gene_variant,,ENST00000427682,;DNASE1L1,downstream_gene_variant,,ENST00000014935,;DNASE1L1,downstream_gene_variant,,ENST00000369807,;DNASE1L1,downstream_gene_variant,,ENST00000393638,;RPL10,upstream_gene_variant,,ENST00000451365,;SNORA70,upstream_gene_variant,,ENST00000384436,;RPL10,non_coding_transcript_exon_variant,,ENST00000479366,;RPL10,intron_variant,,ENST00000482732,;RPL10,intron_variant,,ENST00000467168,;RPL10,intron_variant,,ENST00000491035,;RPL10,intron_variant,,ENST00000485196,;RPL10,intron_variant,,ENST00000474786,;RPL10,intron_variant,,ENST00000489200,;RPL10,intron_variant,,ENST00000492572,;DNASE1L1,downstream_gene_variant,,ENST00000497242,;	T	ENSG00000147403	ENST00000424325	Transcript	intron_variant	.	.	.	.	.	rs781982364	.	.	1	RPL10	HGNC	10298	protein_coding	YES	CCDS14746.1	ENSP00000413436	RL10_HUMAN	F8W7C6_HUMAN	UPI00000019F3	.	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AATCCGTGTAC	.	3	ESCA
DCAF8L1	0	.	GRCh37	X	27998866	27998866	+	Missense_Mutation	SNP	C	C	A	rs777227762	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586G>T	p.Ala196Ser	p.A196S	ENST00000441525	1/1	108	103	5	109	109	0	DCAF8L1,missense_variant,p.Ala196Ser,ENST00000441525,;	A	ENSG00000226372	ENST00000441525	Transcript	missense_variant	701	586	196	A/S	Gcc/Tcc	rs777227762	.	.	-1	DCAF8L1	HGNC	31810	protein_coding	YES	CCDS35222.1	ENSP00000405222	DC8L1_HUMAN	.	UPI000022DD1B	.	tolerated(0.76)	benign(0.012)	1/1	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR15574:SF29,hmmpanther:PTHR15574,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	A:0.0005	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACCGGCATGGC	byFrequency|byCluster|by1000G	2	ESCA
TAB3	0	.	GRCh37	X	30877771	30877771	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-66C>T	.	.	ENST00000378933	2/8	41	38	3	58	58	0	TAB3,5_prime_UTR_variant,,ENST00000378930,;TAB3,5_prime_UTR_variant,,ENST00000288422,;TAB3,5_prime_UTR_variant,,ENST00000378932,;TAB3,5_prime_UTR_variant,,ENST00000378933,;TAB3-AS2,downstream_gene_variant,,ENST00000445240,;TAB3,5_prime_UTR_variant,,ENST00000467136,;	A	ENSG00000157625	ENST00000378933	Transcript	5_prime_UTR_variant	113	.	.	.	.	.	.	.	-1	TAB3	HGNC	30681	protein_coding	YES	CCDS14226.1	ENSP00000368215	TAB3_HUMAN	.	UPI000013DF10	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTAATGATCTT	.	2	ESCA
DMD	0	.	GRCh37	X	32481653	32481653	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3335G>T	p.Gly1112Val	p.G1112V	ENST00000357033	25/79	77	73	4	68	68	0	DMD,missense_variant,p.Gly1112Val,ENST00000357033,;DMD,missense_variant,p.Gly1108Val,ENST00000378677,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000488902,;	A	ENSG00000198947	ENST00000357033	Transcript	missense_variant	3542	3335	1112	G/V	gGg/gTg	COSM1557783,COSM1557784,COSM1557785	.	.	-1	DMD	HGNC	2928	protein_coding	YES	CCDS14233.1	ENSP00000354923	.	Q9UPB5_HUMAN,Q9UPB4_HUMAN,Q9UMK8_HUMAN,Q9UMK7_HUMAN,Q9UMG1_HUMAN,Q9UME2_HUMAN,Q9UEH4_HUMAN,Q8WYF6_HUMAN,Q8WYF5_HUMAN,Q8WYF4_HUMAN,Q8WYF3_HUMAN,Q8WYF2_HUMAN,Q8WYF1_HUMAN,Q8WYF0_HUMAN,Q8WYE9_HUMAN,Q8WYE8_HUMAN,Q8WYE7_HUMAN,Q8WYE6_HUMAN,Q8WYE5_HUMAN,Q8WYE4_HUMAN,Q8WYE3_HUMAN,Q8WYE2_HUMAN,Q8WYE1_HUMAN,Q8WYD9_HUMAN,Q8WYD8_HUMAN,Q8WYD7_HUMAN,Q8WYD6_HUMAN,Q8WYD5_HUMAN,Q8WYD4_HUMAN,Q8WYD3_HUMAN,Q8WYD2_HUMAN,Q8WYD1_HUMAN,Q8WYD0_HUMAN,Q8WYC9_HUMAN,Q8WYC8_HUMAN,Q8WYC7_HUMAN,Q8WYC6_HUMAN,Q8WYC5_HUMAN,Q8WYC4_HUMAN,Q8WYC3_HUMAN,Q8WYC2_HUMAN,Q8WYC1_HUMAN,Q8WYC0_HUMAN,Q8WYB9_HUMAN,Q8WYB8_HUMAN,Q8WTQ2_HUMAN,Q7KZ40_HUMAN,Q7KYP7_HUMAN,Q548X2_HUMAN,Q14205_HUMAN,F2WSI7_HUMAN,E7EQS5_HUMAN	UPI000049E111	.	.	benign(0.254)	25/79	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF261,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGCCCACCT	.	2	ESCA
FAM47A	0	.	GRCh37	X	34148740	34148740	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1656G>A	p.%3D	p.R552R	ENST00000346193	1/1	191	181	9	134	134	0	FAM47A,synonymous_variant,p.%3D,ENST00000346193,;	T	ENSG00000185448	ENST00000346193	Transcript	synonymous_variant	1708	1656	552	R	cgG/cgA	.	.	.	-1	FAM47A	HGNC	29962	protein_coding	YES	CCDS43926.1	ENSP00000345029	FA47A_HUMAN	.	UPI000013F1F4	.	.	.	1/1	.	hmmpanther:PTHR23213:SF200,hmmpanther:PTHR23213,Pfam_domain:PF14642	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACACCCGACG	.	2	ESCA
GAGE10	0	.	GRCh37	X	49161383	49161383	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45C>G	p.%3D	p.L15L	ENST00000407599	2/5	585	535	50	507	507	0	GAGE10,synonymous_variant,p.%3D,ENST00000407599,;PPP1R3F,downstream_gene_variant,,ENST00000471261,;	G	ENSG00000215274	ENST00000407599	Transcript	synonymous_variant	138	45	15	L	ctC/ctG	.	.	.	1	GAGE10	HGNC	30968	protein_coding	YES	CCDS43938.1	ENSP00000385415	GAG10_HUMAN	.	UPI000059DB2B	.	.	.	2/5	.	hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF6,Pfam_domain:PF05831	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGACTCTATGT	.	3	ESCA
TSR2	0	.	GRCh37	X	54467182	54467182	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141G>T	p.%3D	p.G47G	ENST00000375151	2/5	202	190	12	172	172	0	TSR2,synonymous_variant,p.%3D,ENST00000375151,;FGD1,downstream_gene_variant,,ENST00000375135,;	T	ENSG00000158526	ENST00000375151	Transcript	synonymous_variant	162	141	47	G	ggG/ggT	.	.	.	1	TSR2	HGNC	25455	protein_coding	YES	CCDS14358.1	ENSP00000364293	TSR2_HUMAN	.	UPI0000039EBD	.	.	.	2/5	.	hmmpanther:PTHR21250:SF0,hmmpanther:PTHR21250,Pfam_domain:PF10273	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGGGGGTGC	.	2	ESCA
DGAT2L6	0	.	GRCh37	X	69421794	69421794	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.527C>A	p.Ser176Ter	p.S176*	ENST00000333026	5/7	71	64	7	64	64	0	DGAT2L6,stop_gained,p.Ser176Ter,ENST00000333026,;	A	ENSG00000184210	ENST00000333026	Transcript	stop_gained	627	527	176	S/*	tCa/tAa	.	.	.	1	DGAT2L6	HGNC	23250	protein_coding	YES	CCDS14397.1	ENSP00000328036	DG2L6_HUMAN	.	UPI00001C10BF	.	.	.	5/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12317:SF11,hmmpanther:PTHR12317,Pfam_domain:PF03982	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTCAGGCA	.	4	ESCA
FOXO4	0	.	GRCh37	X	70316309	70316309	+	5'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-70G>T	.	.	ENST00000374259	1/3	43	39	4	36	36	0	FOXO4,5_prime_UTR_variant,,ENST00000374259,;FOXO4,upstream_gene_variant,,ENST00000341558,;FOXO4,non_coding_transcript_exon_variant,,ENST00000466874,;FOXO4,upstream_gene_variant,,ENST00000464598,;	T	ENSG00000184481	ENST00000374259	Transcript	5_prime_UTR_variant	263	.	.	.	.	.	.	.	1	FOXO4	HGNC	7139	protein_coding	YES	CCDS43969.1	ENSP00000363377	FOXO4_HUMAN	.	UPI00002122FA	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCCTGAGGGG	.	2	ESCA
DACH2	0	.	GRCh37	X	85994826	85994826	+	Missense_Mutation	SNP	A	A	T	rs769434079	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1181A>T	p.His394Leu	p.H394L	ENST00000373125	7/12	79	71	8	57	57	0	DACH2,missense_variant,p.His175Leu,ENST00000510272,;DACH2,missense_variant,p.His394Leu,ENST00000373125,;DACH2,missense_variant,p.His49Leu,ENST00000484479,;DACH2,missense_variant,p.His381Leu,ENST00000373131,;DACH2,missense_variant,p.His227Leu,ENST00000508860,;DACH2,missense_variant,p.His394Leu,ENST00000461604,;DACH2,3_prime_UTR_variant,,ENST00000506327,;	T	ENSG00000126733	ENST00000373125	Transcript	missense_variant	1181	1181	394	H/L	cAc/cTc	rs769434079	.	.	1	DACH2	HGNC	16814	protein_coding	YES	CCDS14455.1	ENSP00000362217	DACH2_HUMAN	.	UPI00000717B4	.	tolerated(0.12)	possibly_damaging(0.621)	7/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCCACACCA	.	4	ESCA
DACH2	0	.	GRCh37	X	86071037	86071037	+	Missense_Mutation	SNP	A	A	G	rs753934786	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1685A>G	p.Asp562Gly	p.D562G	ENST00000373125	11/12	124	116	8	124	124	0	DACH2,missense_variant,p.Asp343Gly,ENST00000510272,;DACH2,missense_variant,p.Asp562Gly,ENST00000373125,;DACH2,missense_variant,p.Asp227Gly,ENST00000484479,;DACH2,missense_variant,p.Asp549Gly,ENST00000373131,;DACH2,missense_variant,p.Asp395Gly,ENST00000508860,;DACH2,splice_region_variant,,ENST00000461604,;DACH2,splice_region_variant,,ENST00000506327,;	G	ENSG00000126733	ENST00000373125	Transcript	missense_variant	1685	1685	562	D/G	gAt/gGt	rs753934786	.	.	1	DACH2	HGNC	16814	protein_coding	YES	CCDS14455.1	ENSP00000362217	DACH2_HUMAN	.	UPI00000717B4	.	deleterious(0.04)	benign(0.317)	11/12	.	hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCAGATACTG	.	2	ESCA
PCDH11X	0	.	GRCh37	X	91137981	91137981	+	Intron	DEL	T	T	-	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3033+3710delT	.	.	ENST00000373094	.	118	106	12	97	97	0	PCDH11X,3_prime_UTR_variant,,ENST00000395337,;PCDH11X,intron_variant,,ENST00000373088,;PCDH11X,intron_variant,,ENST00000298274,;PCDH11X,intron_variant,,ENST00000504220,;PCDH11X,intron_variant,,ENST00000406881,;PCDH11X,intron_variant,,ENST00000373094,;PCDH11X,intron_variant,,ENST00000373097,;PCDH11X,intron_variant,,ENST00000361655,;PCDH11X,downstream_gene_variant,,ENST00000361724,;	-	ENSG00000102290	ENST00000373094	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCCCCTTCCAA	.	3	ESCA
TBL1X	0	.	GRCh37	X	9673102	9673102	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FP-01A-31D-A387-09	TCGA-LN-A9FP-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1184A>T	p.His395Leu	p.H395L	ENST00000217964	13/18	100	95	5	93	93	0	TBL1X,missense_variant,p.His344Leu,ENST00000424279,;TBL1X,missense_variant,p.His395Leu,ENST00000217964,;TBL1X,missense_variant,p.His344Leu,ENST00000380961,;TBL1X,missense_variant,p.His395Leu,ENST00000407597,;TBL1X,missense_variant,p.His344Leu,ENST00000536365,;	T	ENSG00000101849	ENST00000217964	Transcript	missense_variant	1824	1184	395	H/L	cAt/cTt	.	.	.	1	TBL1X	HGNC	11585	protein_coding	YES	CCDS14133.1	ENSP00000217964	TBL1X_HUMAN	C9JYQ8_HUMAN,C9JP56_HUMAN,C9JCW3_HUMAN,C9J5F9_HUMAN	UPI0000161FAF	.	deleterious(0.01)	possibly_damaging(0.507)	13/18	.	PROSITE_profiles:PS50294,hmmpanther:PTHR22846,hmmpanther:PTHR22846:SF36,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATCCATGTGT	.	2	ESCA
TMEM180	0	.	GRCh37	10	104228949	104228949	+	Missense_Mutation	SNP	G	G	A	rs767309455	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163G>A	p.Gly55Arg	p.G55R	ENST00000238936	3/10	96	54	41	86	86	0	TMEM180,missense_variant,p.Gly55Arg,ENST00000369931,;TMEM180,missense_variant,p.Gly55Arg,ENST00000238936,;TMEM180,5_prime_UTR_variant,,ENST00000366277,;TMEM180,non_coding_transcript_exon_variant,,ENST00000450947,;TMEM180,downstream_gene_variant,,ENST00000428200,;TMEM180,upstream_gene_variant,,ENST00000469294,;	A	ENSG00000138111	ENST00000238936	Transcript	missense_variant	400	163	55	G/R	Gga/Aga	rs767309455	.	.	1	TMEM180	HGNC	26196	protein_coding	YES	CCDS7535.1	ENSP00000238936	TM180_HUMAN	B4DKJ1_HUMAN	UPI00002374ED	.	deleterious(0)	probably_damaging(0.999)	3/10	.	Pfam_domain:PF13347,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCGGAGAG	.	5	ESCA
EIF3A	0	.	GRCh37	10	120795774	120795774	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3926C>A	p.Ser1309Tyr	p.S1309Y	ENST00000369144	22/22	66	55	11	79	79	0	EIF3A,missense_variant,p.Ser1275Tyr,ENST00000541549,;EIF3A,missense_variant,p.Ser1309Tyr,ENST00000369144,;NANOS1,downstream_gene_variant,,ENST00000340087,;NANOS1,downstream_gene_variant,,ENST00000425699,;	T	ENSG00000107581	ENST00000369144	Transcript	missense_variant	4054	3926	1309	S/Y	tCt/tAt	.	.	.	-1	EIF3A	HGNC	3271	protein_coding	YES	CCDS7608.1	ENSP00000358140	EIF3A_HUMAN	F5H335_HUMAN	UPI000012D311	.	deleterious_low_confidence(0)	unknown(0)	22/22	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGAACTT	.	5	ESCA
PDE6C	0	.	GRCh37	10	95399868	95399868	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1524A>T	p.Glu508Asp	p.E508D	ENST00000371447	12/22	58	37	20	76	76	0	PDE6C,missense_variant,p.Glu508Asp,ENST00000371447,;	T	ENSG00000095464	ENST00000371447	Transcript	missense_variant	1662	1524	508	E/D	gaA/gaT	.	.	.	1	PDE6C	HGNC	8787	protein_coding	YES	CCDS7429.1	ENSP00000360502	PDE6C_HUMAN	.	UPI000013C84A	.	tolerated(0.15)	benign(0.211)	12/22	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF23,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACGAATTCCG	.	5	ESCA
TM9SF3	0	.	GRCh37	10	98281655	98281655	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*365G>A	.	.	ENST00000371142	15/15	35	22	12	33	33	0	TM9SF3,3_prime_UTR_variant,,ENST00000371142,;TM9SF3,downstream_gene_variant,,ENST00000485093,;	T	ENSG00000077147	ENST00000371142	Transcript	3_prime_UTR_variant	2352	.	.	.	.	.	.	.	-1	TM9SF3	HGNC	21529	protein_coding	YES	CCDS7450.1	ENSP00000360184	TM9S3_HUMAN	Q96K55_HUMAN,Q96JZ5_HUMAN,Q8WUB5_HUMAN,Q5TB53_HUMAN	UPI000013684E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCATCCAAGT	.	5	ESCA
ROBO3	0	.	GRCh37	11	124739843	124739843	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.646-1G>C	.	p.X216_splice	ENST00000397801	.	37	27	10	31	31	0	ROBO3,splice_acceptor_variant,,ENST00000538940,;ROBO3,splice_acceptor_variant,,ENST00000397801,;	C	ENSG00000154134	ENST00000397801	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ROBO3	HGNC	13433	protein_coding	YES	CCDS44755.1	ENSP00000380903	ROBO3_HUMAN	Q9H7C7_HUMAN,Q96HH0_HUMAN,F5H0K7_HUMAN	UPI000035AA82	.	.	.	.	3/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGATCCG	.	5	ESCA
GLB1L2	0	.	GRCh37	11	134201987	134201987	+	Missense_Mutation	SNP	C	C	T	rs201456055	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.32C>T	p.Ala11Val	p.A11V	ENST00000535456	1/19	123	59	64	154	153	0	GLB1L2,missense_variant,p.Ala11Val,ENST00000535456,;GLB1L2,missense_variant,p.Ala11Val,ENST00000389881,;GLB1L2,missense_variant,p.Ala11Val,ENST00000339772,;	T	ENSG00000149328	ENST00000535456	Transcript	missense_variant	220	32	11	A/V	gCc/gTc	rs201456055	.	.	1	GLB1L2	HGNC	25129	protein_coding	YES	CCDS31724.1	ENSP00000444628	GLBL2_HUMAN	Q8NCG3_HUMAN	UPI0000074534	.	tolerated(0.34)	benign(0.001)	1/19	.	Low_complexity_(Seg):seg,PIRSF_domain:PIRSF006336	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGGCCCGCA	byCluster|by1000G	5	ESCA
SIRT3	0	.	GRCh37	11	216056	216056	+	3'UTR	SNP	G	G	A	rs12226697	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*642C>T	.	.	ENST00000382743	7/7	18	4	14	8	8	0	SIRT3,3_prime_UTR_variant,,ENST00000382743,;SIRT3,downstream_gene_variant,,ENST00000529382,;RIC8A,downstream_gene_variant,,ENST00000524854,;RIC8A,downstream_gene_variant,,ENST00000325207,;SIRT3,downstream_gene_variant,,ENST00000532956,;RIC8A,downstream_gene_variant,,ENST00000527696,;RIC8A,downstream_gene_variant,,ENST00000527728,;RIC8A,downstream_gene_variant,,ENST00000526104,;SIRT3,downstream_gene_variant,,ENST00000525319,;SIRT3,downstream_gene_variant,,ENST00000524564,;RIC8A,downstream_gene_variant,,ENST00000529275,;RIC8A,downstream_gene_variant,,ENST00000531541,;SIRT3,downstream_gene_variant,,ENST00000529937,;RIC8A,downstream_gene_variant,,ENST00000526557,;RIC8A,downstream_gene_variant,,ENST00000527039,;RIC8A,downstream_gene_variant,,ENST00000530149,;RIC8A,downstream_gene_variant,,ENST00000532241,;SIRT3,downstream_gene_variant,,ENST00000532837,;	A	ENSG00000142082	ENST00000382743	Transcript	3_prime_UTR_variant	1945	.	.	.	.	rs12226697	.	.	-1	SIRT3	HGNC	14931	protein_coding	YES	CCDS7691.1	ENSP00000372191	SIR3_HUMAN	E9PNA0_HUMAN,E9PM52_HUMAN	UPI0000073D3C	.	.	.	7/7	.	.	A:0.0813	A:0.0688	A:0.0403	.	A:0.1548	A:0.0328	A:0.1012	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CAAATGCCTTC	byFrequency|byCluster|byHapMap|by1000G	2	ESCA
DCDC1	0	.	GRCh37	11	31349672	31349672	+	Silent	SNP	A	A	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.156T>C	p.%3D	p.D52D	ENST00000452803	3/9	38	30	8	53	53	0	DCDC1,synonymous_variant,p.%3D,ENST00000597505,;DCDC1,synonymous_variant,p.%3D,ENST00000452803,;DCDC1,synonymous_variant,p.%3D,ENST00000342355,;	G	ENSG00000170959	ENST00000452803	Transcript	synonymous_variant	358	156	52	D	gaT/gaC	.	.	.	-1	DCDC1	HGNC	20625	protein_coding	YES	CCDS7872.1	ENSP00000389792	DCDC1_HUMAN	.	UPI00001F9F1E	.	.	.	3/9	.	hmmpanther:PTHR14958,hmmpanther:PTHR14958:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAAATCATT	.	5	ESCA
OR51M1	0	.	GRCh37	11	5411427	5411427	+	Missense_Mutation	SNP	A	A	T	rs764811393	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.799A>T	p.Met267Leu	p.M267L	ENST00000328611	1/1	49	43	6	57	57	0	OR51M1,missense_variant,p.Met267Leu,ENST00000328611,;HBE1,intron_variant,,ENST00000396895,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380259,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,;	T	ENSG00000184698	ENST00000328611	Transcript	missense_variant	821	799	267	M/L	Atg/Ttg	rs764811393	.	.	1	OR51M1	HGNC	14847	protein_coding	YES	CCDS53596.1	ENSP00000333196	O51M1_HUMAN	.	UPI000066D8EB	.	tolerated(0.32)	benign(0.101)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF44,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCCATGATG	.	4	ESCA
OR5M3	0	.	GRCh37	11	56237898	56237898	+	Missense_Mutation	SNP	A	A	G	rs775746409	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76T>C	p.Phe26Leu	p.F26L	ENST00000312240	1/1	41	32	8	75	75	0	OR5M3,missense_variant,p.Phe26Leu,ENST00000312240,;	G	ENSG00000174937	ENST00000312240	Transcript	missense_variant	117	76	26	F/L	Ttc/Ctc	rs775746409	.	.	-1	OR5M3	HGNC	14806	protein_coding	YES	CCDS31532.1	ENSP00000312208	OR5M3_HUMAN	.	UPI0000041BAA	.	deleterious(0.01)	benign(0.144)	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26452:SF17,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGAAGAAGA	.	5	ESCA
MS4A1	0	.	GRCh37	11	60229937	60229937	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90C>T	p.%3D	p.L30L	ENST00000534668	2/7	53	46	7	37	37	0	MS4A1,synonymous_variant,p.%3D,ENST00000533306,;MS4A1,synonymous_variant,p.%3D,ENST00000345732,;MS4A1,synonymous_variant,p.%3D,ENST00000534668,;MS4A1,synonymous_variant,p.%3D,ENST00000389939,;MS4A1,synonymous_variant,p.%3D,ENST00000532073,;MS4A1,synonymous_variant,p.%3D,ENST00000528313,;MS4A1,downstream_gene_variant,,ENST00000524807,;MS4A1,downstream_gene_variant,,ENST00000532491,;MS4A1,non_coding_transcript_exon_variant,,ENST00000527101,;MS4A1,non_coding_transcript_exon_variant,,ENST00000534503,;MS4A1,upstream_gene_variant,,ENST00000532418,;MS4A1,upstream_gene_variant,,ENST00000530482,;	T	ENSG00000156738	ENST00000534668	Transcript	synonymous_variant	379	90	30	L	ctC/ctT	.	.	.	1	MS4A1	HGNC	7315	protein_coding	YES	CCDS31570.1	ENSP00000433277	CD20_HUMAN	.	UPI000012733B	.	.	.	2/7	.	hmmpanther:PTHR23320:SF6,hmmpanther:PTHR23320	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACTCTTCAG	.	4	ESCA
DPF2	0	.	GRCh37	11	65111529	65111529	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000528416	6/11	29	17	11	37	37	0	DPF2,missense_variant,p.Tyr209Cys,ENST00000252268,;DPF2,missense_variant,p.Tyr209Cys,ENST00000528416,;DPF2,intron_variant,,ENST00000415073,;DPF2,upstream_gene_variant,,ENST00000531989,;DPF2,non_coding_transcript_exon_variant,,ENST00000530993,;DPF2,non_coding_transcript_exon_variant,,ENST00000532264,;DPF2,3_prime_UTR_variant,,ENST00000532102,;DPF2,non_coding_transcript_exon_variant,,ENST00000532492,;DPF2,non_coding_transcript_exon_variant,,ENST00000530973,;DPF2,intron_variant,,ENST00000524666,;DPF2,upstream_gene_variant,,ENST00000532052,;DPF2,downstream_gene_variant,,ENST00000444314,;	G	ENSG00000133884	ENST00000528416	Transcript	missense_variant	759	626	209	Y/C	tAt/tGt	.	.	.	1	DPF2	HGNC	9964	protein_coding	YES	CCDS8100.1	ENSP00000436901	REQU_HUMAN	.	UPI000000D90F	.	deleterious(0)	possibly_damaging(0.815)	6/11	.	PROSITE_profiles:PS50157,hmmpanther:PTHR10615:SF13,hmmpanther:PTHR10615,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTATGCCT	.	5	ESCA
SLC25A45	0	.	GRCh37	11	65144438	65144438	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.449G>A	p.Cys150Tyr	p.C150Y	ENST00000398802	6/7	49	27	22	62	62	0	SLC25A45,missense_variant,p.Cys46Tyr,ENST00000377152,;SLC25A45,missense_variant,p.Cys88Tyr,ENST00000526432,;SLC25A45,missense_variant,p.Cys150Tyr,ENST00000398802,;SLC25A45,missense_variant,p.Cys126Tyr,ENST00000360662,;SLC25A45,missense_variant,p.Cys108Tyr,ENST00000417511,;SLC25A45,missense_variant,p.Cys150Tyr,ENST00000527174,;SLC25A45,missense_variant,p.Cys108Tyr,ENST00000294187,;SLC25A45,missense_variant,p.Cys126Tyr,ENST00000534028,;SLC25A45,downstream_gene_variant,,ENST00000530936,;RP11-867O8.5,downstream_gene_variant,,ENST00000533886,;SLC25A45,3_prime_UTR_variant,,ENST00000533629,;SLC25A45,3_prime_UTR_variant,,ENST00000526259,;SLC25A45,3_prime_UTR_variant,,ENST00000526898,;SLC25A45,non_coding_transcript_exon_variant,,ENST00000534338,;SLC25A45,non_coding_transcript_exon_variant,,ENST00000531791,;SLC25A45,downstream_gene_variant,,ENST00000529431,;SLC25A45,downstream_gene_variant,,ENST00000524438,;SLC25A45,downstream_gene_variant,,ENST00000529962,;SLC25A45,downstream_gene_variant,,ENST00000525944,;	T	ENSG00000162241	ENST00000398802	Transcript	missense_variant	653	449	150	C/Y	tGt/tAt	.	.	.	-1	SLC25A45	HGNC	27442	protein_coding	YES	CCDS41670.1	ENSP00000381782	S2545_HUMAN	E9PK53_HUMAN	UPI0000199B26	.	deleterious(0)	probably_damaging(0.992)	6/7	.	Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF249,PROSITE_profiles:PS50920	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCACAGTGC	.	5	ESCA
OR2D2	0	.	GRCh37	11	6913349	6913349	+	Missense_Mutation	SNP	T	T	A	rs202241668	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383A>T	p.Asn128Ile	p.N128I	ENST00000299459	1/1	30	14	16	43	43	0	OR2D2,missense_variant,p.Asn128Ile,ENST00000299459,;	A	ENSG00000166368	ENST00000299459	Transcript	missense_variant	482	383	128	N/I	aAt/aTt	rs202241668	.	.	-1	OR2D2	HGNC	8244	protein_coding	YES	CCDS31416.1	ENSP00000299459	OR2D2_HUMAN	.	UPI0000061F0B	.	tolerated(0.07)	benign(0.058)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26453:SF156,hmmpanther:PTHR26453,PROSITE_profiles:PS50262	C:0.0010	C:0	C:0	.	C:0.005	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGATTGCAG	byFrequency|byCluster|by1000G	5	ESCA
KLRC4	0	.	GRCh37	12	10562135	10562135	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40G>A	p.Ala14Thr	p.A14T	ENST00000309384	1/4	120	68	52	148	148	0	KLRC4,missense_variant,p.Ala14Thr,ENST00000309384,;NKG2-E,downstream_gene_variant,,ENST00000539033,;KLRC3,downstream_gene_variant,,ENST00000381904,;KLRC3,downstream_gene_variant,,ENST00000396439,;KLRC4-KLRK1,missense_variant,p.Ala6Thr,ENST00000586581,;KLRC4-KLRK1,missense_variant,p.Ala6Thr,ENST00000539300,;KLRC4-KLRK1,non_coding_transcript_exon_variant,,ENST00000539370,;KLRC4-KLRK1,intron_variant,,ENST00000591546,;KLRC4-KLRK1,intron_variant,,ENST00000590131,;KLRC4-KLRK1,intron_variant,,ENST00000543812,;KLRC4-KLRK1,intron_variant,,ENST00000585507,;KLRC4-KLRK1,intron_variant,,ENST00000588263,;KLRC4-KLRK1,intron_variant,,ENST00000588447,;KLRC4-KLRK1,intron_variant,,ENST00000591937,;KLRC4-KLRK1,intron_variant,,ENST00000590323,;KLRC4-KLRK1,upstream_gene_variant,,ENST00000543572,;KLRC4-KLRK1,upstream_gene_variant,,ENST00000585711,;	T	ENSG00000183542	ENST00000309384	Transcript	missense_variant	222	40	14	A/T	Gcc/Acc	.	.	.	-1	KLRC4	HGNC	6377	protein_coding	YES	CCDS8624.1	ENSP00000310216	NKG2F_HUMAN	H3BU71_HUMAN,H3BRK7_HUMAN	UPI000013EE96	.	tolerated(0.08)	possibly_damaging(0.721)	1/4	.	hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF148	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCCAGAC	.	5	ESCA
RIC8B	0	.	GRCh37	12	107208704	107208704	+	Silent	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363G>C	p.%3D	p.L121L	ENST00000392839	3/9	42	35	7	44	44	0	RIC8B,synonymous_variant,p.%3D,ENST00000355478,;RIC8B,synonymous_variant,p.%3D,ENST00000392837,;RIC8B,synonymous_variant,p.%3D,ENST00000552619,;RIC8B,synonymous_variant,p.%3D,ENST00000392839,;RIC8B,intron_variant,,ENST00000549643,;RIC8B,intron_variant,,ENST00000548914,;RIC8B,synonymous_variant,p.%3D,ENST00000462949,;RIC8B,non_coding_transcript_exon_variant,,ENST00000470628,;RIC8B,downstream_gene_variant,,ENST00000550215,;	C	ENSG00000111785	ENST00000392839	Transcript	synonymous_variant	469	363	121	L	ctG/ctC	.	.	.	1	RIC8B	HGNC	25555	protein_coding	YES	CCDS9109.2	ENSP00000376583	RIC8B_HUMAN	F8VR30_HUMAN	UPI00001FB46B	.	.	.	3/9	.	Superfamily_domains:SSF48371,Pfam_domain:PF10165,Gene3D:1.25.10.10,hmmpanther:PTHR12425,hmmpanther:PTHR12425:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTGTGTAA	.	5	ESCA
POLE	0	.	GRCh37	12	133209313	133209313	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6073G>A	p.Val2025Met	p.V2025M	ENST00000320574	44/49	17	10	6	29	29	0	POLE,missense_variant,p.Val2025Met,ENST00000320574,;POLE,missense_variant,p.Val1998Met,ENST00000535270,;POLE,non_coding_transcript_exon_variant,,ENST00000441786,;POLE,non_coding_transcript_exon_variant,,ENST00000544870,;POLE,downstream_gene_variant,,ENST00000434528,;POLE,upstream_gene_variant,,ENST00000538196,;POLE,3_prime_UTR_variant,,ENST00000537064,;POLE,non_coding_transcript_exon_variant,,ENST00000544692,;POLE,non_coding_transcript_exon_variant,,ENST00000544414,;POLE,non_coding_transcript_exon_variant,,ENST00000541213,;POLE,downstream_gene_variant,,ENST00000416953,;POLE,upstream_gene_variant,,ENST00000534922,;	T	ENSG00000177084	ENST00000320574	Transcript	missense_variant	6117	6073	2025	V/M	Gtg/Atg	.	.	.	-1	POLE	HGNC	9177	protein_coding	YES	CCDS9278.1	ENSP00000322570	DPOE1_HUMAN	Q9UNE8_HUMAN,Q96IE1_HUMAN,Q8WU23_HUMAN,F5H7H6_HUMAN,F5H5Q5_HUMAN,F5H3W5_HUMAN,F5H0H8_HUMAN,D3DXI9_HUMAN	UPI00001FBF97	.	deleterious(0.04)	benign(0.026)	44/49	.	hmmpanther:PTHR10670,hmmpanther:PTHR10670:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCACGGGGG	.	5	ESCA
LIMA1	0	.	GRCh37	12	50616162	50616162	+	Missense_Mutation	SNP	C	C	T	rs770526598	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272G>A	p.Arg91Gln	p.R91Q	ENST00000394943	4/11	29	8	21	24	24	0	LIMA1,missense_variant,p.Arg91Gln,ENST00000341247,;LIMA1,missense_variant,p.Arg91Gln,ENST00000394943,;LIMA1,missense_variant,p.Arg91Gln,ENST00000551691,;LIMA1,missense_variant,p.Arg91Gln,ENST00000550592,;LIMA1,5_prime_UTR_variant,,ENST00000552783,;LIMA1,upstream_gene_variant,,ENST00000552909,;LIMA1,upstream_gene_variant,,ENST00000552823,;RP3-405J10.4,intron_variant,,ENST00000551284,;LIMA1,non_coding_transcript_exon_variant,,ENST00000550611,;LIMA1,upstream_gene_variant,,ENST00000552008,;LIMA1,missense_variant,p.Arg91Gln,ENST00000552720,;LIMA1,upstream_gene_variant,,ENST00000551486,;RP3-405J10.2,upstream_gene_variant,,ENST00000548666,;	T	ENSG00000050405	ENST00000394943	Transcript	missense_variant	382	272	91	R/Q	cGg/cAg	rs770526598	.	.	-1	LIMA1	HGNC	24636	protein_coding	YES	CCDS44877.1	ENSP00000378400	LIMA1_HUMAN	Q59FE8_HUMAN,F8VVQ7_HUMAN,F8VTU2_HUMAN	UPI0000EE6469	.	tolerated(0.26)	benign(0.003)	4/11	.	hmmpanther:PTHR24206,hmmpanther:PTHR24206:SF27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCCGTAGA	byFrequency	5	ESCA
KRT1	0	.	GRCh37	12	53069050	53069050	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1862G>A	p.Gly621Glu	p.G621E	ENST00000252244	9/9	18	6	11	29	29	0	KRT1,missense_variant,p.Gly621Glu,ENST00000252244,;KRT1,downstream_gene_variant,,ENST00000548765,;	T	ENSG00000167768	ENST00000252244	Transcript	missense_variant	1921	1862	621	G/E	gGg/gAg	.	.	.	-1	KRT1	HGNC	6412	protein_coding	YES	CCDS8836.1	ENSP00000252244	K2C1_HUMAN	H6VRG1_HUMAN	UPI000013CD4D	.	deleterious_low_confidence(0)	unknown(0)	9/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF95,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCCCAGAG	.	5	ESCA
LRRIQ1	0	.	GRCh37	12	85518212	85518212	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3922C>T	p.Pro1308Ser	p.P1308S	ENST00000393217	17/27	24	19	5	45	45	0	LRRIQ1,missense_variant,p.Pro1308Ser,ENST00000393217,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,;	T	ENSG00000133640	ENST00000393217	Transcript	missense_variant	3983	3922	1308	P/S	Ccc/Tcc	.	.	.	1	LRRIQ1	HGNC	25708	protein_coding	YES	CCDS41816.1	ENSP00000376910	LRIQ1_HUMAN	A8MY60_HUMAN	UPI0000ED4E82	.	tolerated(0.57)	benign(0.018)	17/27	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTATTCCCACC	.	2	ESCA
SACS	0	.	GRCh37	13	23985390	23985390	+	5'UTR	SNP	C	C	T	rs759068639	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12G>A	.	.	ENST00000382298	2/10	59	45	13	74	74	0	SACS,5_prime_UTR_variant,,ENST00000382292,;SACS,5_prime_UTR_variant,,ENST00000382298,;	T	ENSG00000151835	ENST00000382298	Transcript	5_prime_UTR_variant	578	.	.	.	.	rs759068639	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	.	2/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCCTGGGA	.	5	ESCA
FOXO1	0	.	GRCh37	13	41132513	41132546	+	3'UTR	ONP	TAGAAAAGACCTGTACAAAGCTGGCATTTAATCT	TAGAAAAGACCTGTACAAAGCTGGCATTTAATCT	ATAGAAAAGACCTGTACAAAGCTGGCATTTAATC	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	TAGAAAAGACCTGTACAAAGCTGGCATTTAATCT	TAGAAAAGACCTGTACAAAGCTGGCATTTAATCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*640_*674delAGATTAAATGCCAGCTTTGTACAGGTCTTTTCTATinsGATTAAATGCCAGCTTTGTACAGGTCTTTTCTATT	.	.	ENST00000379561	3/3	27	24	3	27	27	0	FOXO1,3_prime_UTR_variant,,ENST00000379561,;FOXO1,downstream_gene_variant,,ENST00000473775,;	AATAGAAAAGACCTGTACAAAGCTGGCATTTAATC	ENSG00000150907	ENST00000379561	Transcript	3_prime_UTR_variant	2993-3027	.	.	.	.	.	.	.	-1	FOXO1	HGNC	3819	protein_coding	YES	CCDS9371.1	ENSP00000368880	FOXO1_HUMAN	.	UPI000013DC20	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	AAAAAATAGAAAAGACCTGTACAAAGCTGGCATTTAATCTTTTTT	.	2	ESCA
SIVA1	0	.	GRCh37	14	105223046	105223046	+	Missense_Mutation	SNP	G	G	A	rs746975954	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.419G>A	p.Arg140His	p.R140H	ENST00000329967	3/4	65	50	14	59	59	0	SIVA1,missense_variant,p.Arg140His,ENST00000553810,;SIVA1,missense_variant,p.Arg75His,ENST00000347067,;SIVA1,missense_variant,p.Arg158His,ENST00000556195,;SIVA1,missense_variant,p.Arg140His,ENST00000329967,;SIVA1,missense_variant,p.Arg140His,ENST00000553819,;SIVA1,non_coding_transcript_exon_variant,,ENST00000554013,;SIVA1,non_coding_transcript_exon_variant,,ENST00000535554,;SIVA1,non_coding_transcript_exon_variant,,ENST00000556431,;	A	ENSG00000184990	ENST00000329967	Transcript	missense_variant	521	419	140	R/H	cGc/cAc	rs746975954	.	.	1	SIVA1	HGNC	17712	protein_coding	YES	CCDS9992.1	ENSP00000329213	SIVA_HUMAN	.	UPI0000161BCE	.	tolerated(0.08)	benign(0.016)	3/4	.	hmmpanther:PTHR14365,Pfam_domain:PF05458,PIRSF_domain:PIRSF038096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGCGCACCT	.	5	ESCA
TGM1	0	.	GRCh37	14	24724341	24724341	+	Silent	SNP	C	C	T	rs750237191	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1764G>A	p.%3D	p.A588A	ENST00000206765	12/15	37	15	21	34	34	0	TGM1,synonymous_variant,p.%3D,ENST00000544573,;TGM1,synonymous_variant,p.%3D,ENST00000206765,;TGM1,downstream_gene_variant,,ENST00000559136,;TGM1,upstream_gene_variant,,ENST00000559669,;	T	ENSG00000092295	ENST00000206765	Transcript	synonymous_variant	1888	1764	588	A	gcG/gcA	rs750237191	.	.	-1	TGM1	HGNC	11777	protein_coding	YES	CCDS9622.1	ENSP00000206765	TGM1_HUMAN	H0YNM4_HUMAN,H0YN27_HUMAN,H0YMQ8_HUMAN,H0YLT9_HUMAN,H0YLJ6_HUMAN,H0YKI6_HUMAN,B4DWR7_HUMAN	UPI000000164D	.	.	.	12/15	.	Superfamily_domains:SSF49309,PIRSF_domain:PIRSF000459,Pfam_domain:PF00927,Gene3D:2.60.40.10,hmmpanther:PTHR11590:SF13,hmmpanther:PTHR11590	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACCGCGTC	byFrequency	5	ESCA
NPAS3	0	.	GRCh37	14	34270029	34270029	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2516C>A	p.Ala839Asp	p.A839D	ENST00000356141	12/12	35	31	4	37	37	0	NPAS3,missense_variant,p.Ala809Asp,ENST00000548645,;NPAS3,missense_variant,p.Ala844Asp,ENST00000551492,;NPAS3,missense_variant,p.Ala813Asp,ENST00000551634,;NPAS3,missense_variant,p.Ala807Asp,ENST00000346562,;NPAS3,missense_variant,p.Ala826Asp,ENST00000357798,;NPAS3,missense_variant,p.Ala839Asp,ENST00000356141,;	A	ENSG00000151322	ENST00000356141	Transcript	missense_variant	2516	2516	839	A/D	gCc/gAc	COSM3495789,COSM3495787,COSM3495788	.	.	1	NPAS3	HGNC	19311	protein_coding	YES	CCDS53891.1	ENSP00000348460	NPAS3_HUMAN	.	UPI00000743C2	.	deleterious_low_confidence(0)	probably_damaging(0.969)	12/12	.	hmmpanther:PTHR23043:SF21,hmmpanther:PTHR23043	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGGCCATGC	.	4	ESCA
PELI2	0	.	GRCh37	14	56755351	56755351	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.506G>C	p.Gly169Ala	p.G169A	ENST00000267460	4/6	50	37	13	47	47	0	PELI2,missense_variant,p.Gly69Ala,ENST00000561019,;PELI2,missense_variant,p.Gly169Ala,ENST00000267460,;PELI2,missense_variant,p.Gly69Ala,ENST00000559044,;	C	ENSG00000139946	ENST00000267460	Transcript	missense_variant	792	506	169	G/A	gGa/gCa	.	.	.	1	PELI2	HGNC	8828	protein_coding	YES	CCDS9726.1	ENSP00000267460	PELI2_HUMAN	Q659D8_HUMAN,H0YNF4_HUMAN,H0YK56_HUMAN	UPI0000062262	.	deleterious(0)	probably_damaging(0.957)	4/6	.	hmmpanther:PTHR12098:SF5,hmmpanther:PTHR12098,Pfam_domain:PF04710,PIRSF_domain:PIRSF038886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTGGAGTAA	.	5	ESCA
RP11-47I22.4	0	.	GRCh37	14	61997175	61997175	+	Silent	SNP	C	C	T	rs750561562	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.137C>T	p.%3D	p.G46G	ENST00000556347	2/4	78	39	39	77	77	0	RP11-47I22.4,synonymous_variant,p.%3D,ENST00000556347,;PRKCH,synonymous_variant,p.%3D,ENST00000332981,;PRKCH,synonymous_variant,p.%3D,ENST00000555082,;PRKCH,synonymous_variant,p.%3D,ENST00000555185,;PRKCH,non_coding_transcript_exon_variant,,ENST00000557599,;PRKCH,non_coding_transcript_exon_variant,,ENST00000536400,;PRKCH,non_coding_transcript_exon_variant,,ENST00000553846,;PRKCH,non_coding_transcript_exon_variant,,ENST00000555382,;PRKCH,non_coding_transcript_exon_variant,,ENST00000555628,;PRKCH,downstream_gene_variant,,ENST00000555110,;PRKCH,downstream_gene_variant,,ENST00000555233,;	T	ENSG00000258989	ENST00000556347	Transcript	synonymous_variant	137	138	46	G	ggC/ggT	rs750561562	.	.	1	RP11-47I22.4	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000452401	.	.	UPI00021CF17E	.	.	.	2/4	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF51,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGGCGTGTT	byFrequency	5	ESCA
MPP5	0	.	GRCh37	14	67800277	67800278	+	3'UTR	INS	-	-	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*610dupA	.	.	ENST00000261681	15/15	40	27	13	52	52	0	MPP5,3_prime_UTR_variant,,ENST00000555925,;MPP5,3_prime_UTR_variant,,ENST00000261681,;ATP6V1D,downstream_gene_variant,,ENST00000553408,;ATP6V1D,downstream_gene_variant,,ENST00000555723,;ATP6V1D,downstream_gene_variant,,ENST00000555431,;ATP6V1D,downstream_gene_variant,,ENST00000554236,;ATP6V1D,downstream_gene_variant,,ENST00000555474,;ATP6V1D,downstream_gene_variant,,ENST00000216442,;ATP6V1D,intron_variant,,ENST00000553974,;ATP6V1D,intron_variant,,ENST00000554087,;ATP6V1D,downstream_gene_variant,,ENST00000555625,;	A	ENSG00000072415	ENST00000261681	Transcript	3_prime_UTR_variant	3293-3294	.	.	.	.	.	.	.	1	MPP5	HGNC	18669	protein_coding	YES	CCDS9779.1	ENSP00000261681	MPP5_HUMAN	G3V2H1_HUMAN	UPI0000046FB9	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAAACAAAAA	.	3	ESCA
ZNF410	0	.	GRCh37	14	74376101	74376101	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1022C>A	p.Ser341Tyr	p.S341Y	ENST00000442160	9/14	67	37	29	66	66	0	ZNF410,missense_variant,p.Ser341Tyr,ENST00000442160,;ZNF410,missense_variant,p.Ser251Tyr,ENST00000540593,;ZNF410,missense_variant,p.Ser324Tyr,ENST00000324593,;ZNF410,missense_variant,p.Ser271Tyr,ENST00000334521,;ZNF410,missense_variant,p.Ser55Tyr,ENST00000554316,;ZNF410,missense_variant,p.Ser324Tyr,ENST00000555044,;RP5-1021I20.5,intron_variant,,ENST00000554009,;RP5-1021I20.6,downstream_gene_variant,,ENST00000602874,;RP5-1021I20.5,downstream_gene_variant,,ENST00000555916,;Y_RNA,upstream_gene_variant,,ENST00000362602,;ZNF410,non_coding_transcript_exon_variant,,ENST00000412490,;ZNF410,non_coding_transcript_exon_variant,,ENST00000541357,;ZNF410,downstream_gene_variant,,ENST00000555602,;ZNF410,3_prime_UTR_variant,,ENST00000556396,;RP5-1021I20.4,3_prime_UTR_variant,,ENST00000556551,;ZNF410,3_prime_UTR_variant,,ENST00000398139,;ZNF410,non_coding_transcript_exon_variant,,ENST00000555620,;ZNF410,non_coding_transcript_exon_variant,,ENST00000557679,;	A	ENSG00000119725	ENST00000442160	Transcript	missense_variant	1216	1022	341	S/Y	tCt/tAt	.	.	.	1	ZNF410	HGNC	20144	protein_coding	YES	CCDS55929.1	ENSP00000407130	ZN410_HUMAN	G3V4E6_HUMAN	UPI00017A6BE1	.	deleterious(0)	possibly_damaging(0.451)	9/14	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR11389:SF363,hmmpanther:PTHR11389,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATTCTAGCC	.	5	ESCA
YLPM1	0	.	GRCh37	14	75266005	75266005	+	Silent	SNP	G	G	A	rs773688684	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4005G>A	p.%3D	p.P1335P	ENST00000325680	5/21	30	18	12	33	33	0	YLPM1,synonymous_variant,p.%3D,ENST00000325680,;YLPM1,synonymous_variant,p.%3D,ENST00000238571,;YLPM1,intron_variant,,ENST00000552421,;YLPM1,synonymous_variant,p.%3D,ENST00000549293,;	A	ENSG00000119596	ENST00000325680	Transcript	synonymous_variant	4129	4005	1335	P	ccG/ccA	rs773688684	.	.	1	YLPM1	HGNC	17798	protein_coding	YES	CCDS45135.1	ENSP00000324463	YLPM1_HUMAN	B4DMQ9_HUMAN	UPI00006C1433	.	.	.	5/21	.	hmmpanther:PTHR13413:SF0,hmmpanther:PTHR13413,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACCGCCCCT	byFrequency	5	ESCA
GABRB3	0	.	GRCh37	15	26790767	26790767	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2173G>C	.	.	ENST00000311550	9/9	12	5	7	20	20	0	GABRB3,3_prime_UTR_variant,,ENST00000541819,;GABRB3,3_prime_UTR_variant,,ENST00000311550,;GABRB3,downstream_gene_variant,,ENST00000545868,;GABRB3,downstream_gene_variant,,ENST00000299267,;GABRB3,downstream_gene_variant,,ENST00000400188,;GABRB3,downstream_gene_variant,,ENST00000555632,;	G	ENSG00000166206	ENST00000311550	Transcript	3_prime_UTR_variant	3707	.	.	.	.	.	.	.	-1	GABRB3	HGNC	4083	protein_coding	YES	CCDS10019.1	ENSP00000308725	GBRB3_HUMAN	G3V5B4_HUMAN	UPI000012AFB0	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AGATACCTGAA	.	3	ESCA
DYX1C1	0	.	GRCh37	15	55790554	55790554	+	5'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-27G>C	.	.	ENST00000321149	2/10	58	45	13	61	61	0	DYX1C1,5_prime_UTR_variant,,ENST00000380679,;DYX1C1,5_prime_UTR_variant,,ENST00000321149,;DYX1C1,5_prime_UTR_variant,,ENST00000457155,;DYX1C1,5_prime_UTR_variant,,ENST00000348518,;DYX1C1,upstream_gene_variant,,ENST00000448430,;DYX1C1-CCPG1,non_coding_transcript_exon_variant,,ENST00000565113,;DYX1C1-CCPG1,upstream_gene_variant,,ENST00000568310,;DYX1C1,5_prime_UTR_variant,,ENST00000522437,;DYX1C1,upstream_gene_variant,,ENST00000524160,;DYX1C1,upstream_gene_variant,,ENST00000519017,;	G	ENSG00000256061	ENST00000321149	Transcript	5_prime_UTR_variant	342	.	.	.	.	.	.	.	-1	DYX1C1	HGNC	21493	protein_coding	YES	CCDS10154.1	ENSP00000323275	DYXC1_HUMAN	.	UPI000013E5B8	.	.	.	2/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGCGCGGCTG	.	5	ESCA
ISL2	0	.	GRCh37	15	76630258	76630258	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198C>T	p.%3D	p.C66C	ENST00000290759	2/6	140	96	43	172	172	0	ISL2,synonymous_variant,p.%3D,ENST00000290759,;RP11-685G9.2,downstream_gene_variant,,ENST00000559539,;ISL2,synonymous_variant,p.%3D,ENST00000558656,;ISL2,non_coding_transcript_exon_variant,,ENST00000558437,;	T	ENSG00000159556	ENST00000290759	Transcript	synonymous_variant	358	198	66	C	tgC/tgT	.	.	.	1	ISL2	HGNC	18524	protein_coding	YES	CCDS10290.1	ENSP00000290759	ISL2_HUMAN	.	UPI000012D8FC	.	.	.	2/6	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24204,hmmpanther:PTHR24204:SF2,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGTGCACGTG	.	5	ESCA
IREB2	0	.	GRCh37	15	78758632	78758632	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.430A>T	p.Asn144Tyr	p.N144Y	ENST00000258886	5/22	39	31	8	46	46	0	IREB2,missense_variant,p.Asn144Tyr,ENST00000258886,;IREB2,missense_variant,p.Asn144Tyr,ENST00000560440,;IREB2,downstream_gene_variant,,ENST00000560840,;IREB2,non_coding_transcript_exon_variant,,ENST00000559427,;IREB2,downstream_gene_variant,,ENST00000560454,;IREB2,missense_variant,p.Asn144Tyr,ENST00000558570,;IREB2,3_prime_UTR_variant,,ENST00000559215,;IREB2,3_prime_UTR_variant,,ENST00000558525,;	T	ENSG00000136381	ENST00000258886	Transcript	missense_variant	579	430	144	N/Y	Aat/Tat	.	.	.	1	IREB2	HGNC	6115	protein_coding	YES	CCDS10302.1	ENSP00000258886	IREB2_HUMAN	H0YLE0_HUMAN	UPI00001C1F8E	.	deleterious(0.01)	probably_damaging(0.942)	5/22	.	hmmpanther:PTHR11670:SF31,hmmpanther:PTHR11670	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCAAATCCT	.	5	ESCA
ANKRD34C	0	.	GRCh37	15	79587763	79587763	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*529C>A	.	.	ENST00000421388	2/2	45	32	13	64	64	0	ANKRD34C,3_prime_UTR_variant,,ENST00000421388,;ANKRD34C,downstream_gene_variant,,ENST00000558647,;	A	ENSG00000235711	ENST00000421388	Transcript	3_prime_UTR_variant	2606	.	.	.	.	.	.	.	1	ANKRD34C	HGNC	33888	protein_coding	YES	CCDS53965.1	ENSP00000401089	AN34C_HUMAN	.	UPI0000160A7F	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGACTCTGT	.	5	ESCA
SNX29	0	.	GRCh37	16	12293473	12293473	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1611C>T	p.%3D	p.L537L	ENST00000566228	14/21	57	39	17	52	52	0	SNX29,synonymous_variant,p.%3D,ENST00000564791,;SNX29,synonymous_variant,p.%3D,ENST00000566228,;SNX29,synonymous_variant,p.%3D,ENST00000323433,;SNX29,synonymous_variant,p.%3D,ENST00000306030,;	T	ENSG00000048471	ENST00000566228	Transcript	synonymous_variant	1680	1611	537	L	ctC/ctT	.	.	.	1	SNX29	HGNC	30542	protein_coding	YES	CCDS10553.2	ENSP00000456480	SNX29_HUMAN	J3KNF2_HUMAN	UPI00000382F9	.	.	.	14/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCTCAAAGT	.	5	ESCA
FAHD1	0	.	GRCh37	16	1877560	1877560	+	Silent	SNP	C	C	T	rs142676593	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330C>T	p.%3D	p.D110D	ENST00000382666	1/3	63	49	14	61	61	0	FAHD1,synonymous_variant,p.%3D,ENST00000382666,;FAHD1,synonymous_variant,p.%3D,ENST00000427358,;FAHD1,synonymous_variant,p.%3D,ENST00000382668,;HAGH,upstream_gene_variant,,ENST00000397356,;HAGH,upstream_gene_variant,,ENST00000397353,;HAGH,upstream_gene_variant,,ENST00000569339,;HAGH,upstream_gene_variant,,ENST00000455446,;HAGH,upstream_gene_variant,,ENST00000566709,;HAGH,upstream_gene_variant,,ENST00000564445,;HAGH,upstream_gene_variant,,ENST00000564518,;HAGH,upstream_gene_variant,,ENST00000567190,;HAGH,upstream_gene_variant,,ENST00000569700,;HAGH,upstream_gene_variant,,ENST00000565097,;	T	ENSG00000180185	ENST00000382666	Transcript	synonymous_variant	593	330	110	D	gaC/gaT	rs142676593	.	.	1	FAHD1	HGNC	14169	protein_coding	YES	CCDS32367.1	ENSP00000372112	FAHD1_HUMAN	.	UPI000051946E	.	.	.	1/3	.	Superfamily_domains:SSF56529,Pfam_domain:PF01557,Gene3D:3.90.850.10,hmmpanther:PTHR11820:SF7,hmmpanther:PTHR11820	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	A:0.0018	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGACGAGTG	byFrequency|byCluster|by1000G	5	ESCA
ATXN2L	0	.	GRCh37	16	28838251	28838251	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.685C>G	p.Gln229Glu	p.Q229E	ENST00000395547	6/24	53	30	23	45	45	0	ATXN2L,missense_variant,p.Gln229Glu,ENST00000395547,;ATXN2L,missense_variant,p.Gln229Glu,ENST00000336783,;ATXN2L,missense_variant,p.Gln229Glu,ENST00000382686,;ATXN2L,missense_variant,p.Gln169Glu,ENST00000568266,;ATXN2L,missense_variant,p.Gln229Glu,ENST00000325215,;ATXN2L,missense_variant,p.Gln229Glu,ENST00000570200,;ATXN2L,missense_variant,p.Gln229Glu,ENST00000564304,;ATXN2L,missense_variant,p.Gln229Glu,ENST00000340394,;ATXN2L,downstream_gene_variant,,ENST00000564656,;RP11-1348G14.5,upstream_gene_variant,,ENST00000568183,;RP11-24N18.1,downstream_gene_variant,,ENST00000563565,;ATXN2L,upstream_gene_variant,,ENST00000570284,;ATXN2L,splice_region_variant,,ENST00000565971,;ATXN2L,non_coding_transcript_exon_variant,,ENST00000563314,;ATXN2L,upstream_gene_variant,,ENST00000564284,;ATXN2L,downstream_gene_variant,,ENST00000566080,;ATXN2L,downstream_gene_variant,,ENST00000561539,;ATXN2L,downstream_gene_variant,,ENST00000562867,;	G	ENSG00000168488	ENST00000395547	Transcript	missense_variant	852	685	229	Q/E	Cag/Gag	.	.	.	1	ATXN2L	HGNC	31326	protein_coding	YES	CCDS10640.1	ENSP00000378917	ATX2L_HUMAN	H3BSQ5_HUMAN	UPI000016783F	.	tolerated(0.69)	possibly_damaging(0.679)	6/24	.	hmmpanther:PTHR12854,hmmpanther:PTHR12854:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTCAGCGC	.	5	ESCA
ZNF771	0	.	GRCh37	16	30429185	30429185	+	Missense_Mutation	SNP	C	C	T	rs778183012	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451C>T	p.His151Tyr	p.H151Y	ENST00000319296	3/3	14	10	4	17	17	0	ZNF771,missense_variant,p.His151Tyr,ENST00000434417,;ZNF771,missense_variant,p.His151Tyr,ENST00000319296,;ZNF771,intron_variant,,ENST00000566625,;ZNF771,downstream_gene_variant,,ENST00000564550,;SNORA42,downstream_gene_variant,,ENST00000362917,;	T	ENSG00000179965	ENST00000319296	Transcript	missense_variant	828	451	151	H/Y	Cac/Tac	rs778183012	.	.	1	ZNF771	HGNC	29653	protein_coding	YES	CCDS45460.1	ENSP00000323945	ZN771_HUMAN	B2R9V3_HUMAN	UPI00001FFEDE	.	deleterious(0)	benign(0.217)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF122,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCGCACTGC	.	2	ESCA
ZNF287	0	.	GRCh37	17	16456271	16456271	+	Silent	SNP	C	C	T	rs142954560	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1185G>A	p.%3D	p.S395S	ENST00000395824	6/6	31	22	8	56	56	0	ZNF287,synonymous_variant,p.%3D,ENST00000395824,;ZNF287,synonymous_variant,p.%3D,ENST00000395825,;ZNF287,downstream_gene_variant,,ENST00000498796,;	T	ENSG00000141040	ENST00000395824	Transcript	synonymous_variant	1803	1185	395	S	tcG/tcA	rs142954560	.	.	-1	ZNF287	HGNC	13502	protein_coding	YES	CCDS11179.2	ENSP00000379168	ZN287_HUMAN	C9JAV4_HUMAN	UPI0000200A57	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF201,hmmpanther:PTHR24402,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATACGATTT	byCluster	5	ESCA
RTN4RL1	0	.	GRCh37	17	1840984	1840984	+	Silent	SNP	G	G	A	rs766482775	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132C>T	p.%3D	p.N44N	ENST00000331238	2/2	49	45	4	49	49	0	RTN4RL1,synonymous_variant,p.%3D,ENST00000331238,;	A	ENSG00000185924	ENST00000331238	Transcript	synonymous_variant	612	132	44	N	aaC/aaT	rs766482775	.	.	-1	RTN4RL1	HGNC	21329	protein_coding	YES	CCDS45569.1	ENSP00000330631	R4RL1_HUMAN	.	UPI000018CD23	.	.	.	2/2	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF11,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GCAAAGTTGTG	.	2	ESCA
RAP1GAP2	0	.	GRCh37	17	2930267	2930267	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2010C>T	p.%3D	p.F670F	ENST00000254695	22/25	43	24	19	61	61	0	RAP1GAP2,synonymous_variant,p.%3D,ENST00000540393,;RAP1GAP2,synonymous_variant,p.%3D,ENST00000366401,;RAP1GAP2,synonymous_variant,p.%3D,ENST00000542807,;RAP1GAP2,synonymous_variant,p.%3D,ENST00000254695,;RAP1GAP2,downstream_gene_variant,,ENST00000575979,;	T	ENSG00000132359	ENST00000254695	Transcript	synonymous_variant	2100	2010	670	F	ttC/ttT	.	.	.	1	RAP1GAP2	HGNC	29176	protein_coding	YES	CCDS45573.1	ENSP00000254695	RPGP2_HUMAN	.	UPI0000D622A3	.	.	.	22/25	.	hmmpanther:PTHR15711:SF17,hmmpanther:PTHR15711	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCTTCAAGCA	.	3	ESCA
UBE2Z	0	.	GRCh37	17	47005701	47005702	+	3'UTR	INS	-	-	A	rs201929916	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1216dupA	.	.	ENST00000360943	7/7	15	7	8	10	10	0	UBE2Z,3_prime_UTR_variant,,ENST00000360943,;SNF8,downstream_gene_variant,,ENST00000290330,;SNF8,downstream_gene_variant,,ENST00000502492,;AC091133.1,upstream_gene_variant,,ENST00000435491,;SNF8,downstream_gene_variant,,ENST00000514089,;UBE2Z,non_coding_transcript_exon_variant,,ENST00000513342,;UBE2Z,downstream_gene_variant,,ENST00000506271,;SNF8,downstream_gene_variant,,ENST00000509989,;SNF8,downstream_gene_variant,,ENST00000514929,;SNF8,downstream_gene_variant,,ENST00000504000,;SNF8,downstream_gene_variant,,ENST00000576353,;UBE2Z,downstream_gene_variant,,ENST00000506498,;SNF8,downstream_gene_variant,,ENST00000509995,;SNF8,downstream_gene_variant,,ENST00000573795,;UBE2Z,downstream_gene_variant,,ENST00000504684,;SNF8,downstream_gene_variant,,ENST00000510558,;SNF8,downstream_gene_variant,,ENST00000507302,;SNF8,downstream_gene_variant,,ENST00000515572,;	A	ENSG00000159202	ENST00000360943	Transcript	3_prime_UTR_variant	2405-2406	.	.	.	.	rs201929916	.	.	1	UBE2Z	HGNC	25847	protein_coding	YES	CCDS11540.2	ENSP00000354201	UBE2Z_HUMAN	I3L4C5_HUMAN	UPI00005A774B	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	11	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCTCAGAAAAA	byCluster	2	ESCA
SGCA	0	.	GRCh37	17	48249043	48249043	+	Intron	SNP	C	C	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.983+1016C>A	.	.	ENST00000262018	.	109	86	23	49	49	0	SGCA,intron_variant,,ENST00000504073,;SGCA,intron_variant,,ENST00000543315,;SGCA,intron_variant,,ENST00000344627,;SGCA,intron_variant,,ENST00000262018,;SGCA,intron_variant,,ENST00000511303,;SGCA,downstream_gene_variant,,ENST00000451235,;HILS1,non_coding_transcript_exon_variant,,ENST00000504307,;SGCA,intron_variant,,ENST00000513942,;SGCA,upstream_gene_variant,,ENST00000508382,;SGCA,intron_variant,,ENST00000512526,;SGCA,intron_variant,,ENST00000513821,;SGCA,upstream_gene_variant,,ENST00000505964,;SGCA,downstream_gene_variant,,ENST00000502555,;SGCA,downstream_gene_variant,,ENST00000514934,;HILS1,non_coding_transcript_exon_variant,,ENST00000545329,;HILS1,non_coding_transcript_exon_variant,,ENST00000340499,;	A	ENSG00000108823	ENST00000262018	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SGCA	HGNC	10805	protein_coding	YES	CCDS32679.1	ENSP00000262018	SGCA_HUMAN	.	UPI0000135907	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTGCCCAGG	.	5	ESCA
TP53	0	.	GRCh37	17	7577022	7577022	+	Nonsense_Mutation	SNP	G	G	A	rs121913344	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	8/11	41	17	24	77	77	0	TP53,stop_gained,p.Arg306Ter,ENST00000420246,;TP53,stop_gained,p.Arg306Ter,ENST00000269305,;TP53,stop_gained,p.Arg174Ter,ENST00000509690,;TP53,stop_gained,p.Arg306Ter,ENST00000359597,;TP53,stop_gained,p.Arg306Ter,ENST00000445888,;TP53,stop_gained,p.Arg306Ter,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	1106	916	306	R/*	Cga/Tga	CM971506,rs121913344,TP53_g.13896del,TP53_g.13896C>T,COSM10663,COSM44631,COSM99947,COSM3388168,COSM1640820	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,0,0,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R306*|c.916C>T|16,SITE|p.R306*|c.916C>T|152,SITE|p.R306*|c.916C>T|24,SITE|p.R306*|c.916C>T|43,CODON|p.0?|c.1_1182del1182|6,BUFFER|p.?|c.919+2T>G|3,BUFFER|p.?|c.919+1G>C|4,BUFFER|p.?|c.919+1G>T|9,BUFFER|p.?|c.919+1G>A|6,BUFFER|p.?|c.919+1G>A|10,BUFFER|p.A307fs*38|c.919delG|4,BUFFER|p.K305N|c.915G>T|3,BUFFER|p.K305*|c.913A>T|16,BUFFER|p.K305*|c.913A>T|3,BUFFER|p.S303N|c.908G>A|3,BUFFER|p.S303T|c.908G>C|3,BUFFER|p.G302E|c.905G>A|3,BUFFER|p.S303fs*42|c.904delG|5	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACCTCGCTTAG	.	4	ESCA
TP53	0	.	GRCh37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	7/11	44	36	8	67	66	1	TP53,missense_variant,p.Arg248Gln,ENST00000413465,;TP53,missense_variant,p.Arg248Gln,ENST00000420246,;TP53,missense_variant,p.Arg248Gln,ENST00000269305,;TP53,missense_variant,p.Arg116Gln,ENST00000509690,;TP53,missense_variant,p.Arg248Gln,ENST00000359597,;TP53,missense_variant,p.Arg155Gln,ENST00000514944,;TP53,missense_variant,p.Arg248Gln,ENST00000445888,;TP53,missense_variant,p.Arg248Gln,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	933	743	248	R/Q	cGg/cAg	rs11540652,CM920675,TP53_g.13380G>A,TP53_g.13380G>C,TP53_g.13380G>T,TP53_g.13380del,COSM10662,COSM11491,COSM6549,COSM46135,COSM340105,COSM99602,COSM241995,COSM99020,COSM241994,COSM340106,COSM3356964,COSM3378346,COSM1640830,COSM1646857,COSM1646858,COSM99021,COSM241996,COSM340107	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,PROSITE_patterns:PS00348,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25032700,20377871,18798306,15450681,25105660,21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R248Q|c.743G>A|113,SITE|p.R248Q|c.743G>A|633,SITE|p.R248Q|c.743G>A|64,SITE|p.R248Q|c.743G>A|42,SITE|p.R155Q|c.464G>A|114,SITE|p.R248Q|c.743G>A|110,CODON|p.0?|c.1_1182del1182|6,CODON|p.R248Q|c.743_744GG>AA|5,CODON|p.R248R|c.744G>A|5,CODON|p.R248W|c.741_742CC>TT|15,CODON|p.R248L|c.743G>T|7,CODON|p.R248L|c.743G>T|12,CODON|p.R155L|c.464G>T|12,CODON|p.R155P|c.464G>C|5,CODON|p.R248P|c.743G>C|17,CODON|p.R248L|c.743G>T|12,CODON|p.R248P|c.743G>C|5,CODON|p.R248L|c.743G>T|74,CODON|p.R248P|c.743G>C|5,BUFFER|p.L252_I254delLTI|c.754_762delCTCACCATC|4,BUFFER|p.L252_I254delLTI|c.751_759delATCCTCACC|4,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252delL|c.754_756delCTC|9,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252fs*93|c.754delC|5,BUFFER|p.L252F|c.754C>T|10,BUFFER|p.I251I|c.753C>A|3,BUFFER|p.I251N|c.752T>A|9,BUFFER|p.I251T|c.752T>C|6,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251S|c.752T>G|12,BUFFER|p.I251T|c.752T>C|3,BUFFER|p.I251fs*94|c.751delA|6,BUFFER|p.I251L|c.751A>C|3,BUFFER|p.I251F|c.751A>T|8,BUFFER|p.P250P|c.750C>T|4,BUFFER|p.P250F|c.748_749CC>TT|3,BUFFER|p.I251fs*94|c.748delC|4,BUFFER|p.P250L|c.749C>T|49,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250L|c.749C>T|8,BUFFER|p.P250L|c.749C>T|6,BUFFER|p.P250L|c.749C>T|11,BUFFER|p.P250S|c.748C>T|12,BUFFER|p.R249fs*96|c.746delG|4,BUFFER|p.R249S|c.747G>T|31,BUFFER|p.R249S|c.747G>C|22,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|15,BUFFER|p.R249R|c.747G>A|6,BUFFER|p.R249S|c.747G>C|3,BUFFER|p.R249S|c.747G>T|314,BUFFER|p.R249S|c.747G>T|30,BUFFER|p.R249T|c.746G>C|3,BUFFER|p.R249M|c.746G>T|8,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249M|c.746G>T|9,BUFFER|p.R249K|c.746G>A|17,BUFFER|p.R249M|c.746G>T|4,BUFFER|p.R249T|c.746G>C|20,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249M|c.746G>T|35,BUFFER|p.R249T|c.746G>C|4,BUFFER|p.R249W|c.745A>T|36,BUFFER|p.R249W|c.745A>T|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249G|c.745A>G|7,BUFFER|p.R249W|c.745A>T|4,BUFFER|p.R249G|c.745A>G|4,BUFFER|p.R249W|c.745A>T|8,BUFFER|p.R249G|c.745A>G|30,BUFFER|p.R248W|c.742C>T|46,BUFFER|p.R248W|c.742C>T|92,BUFFER|p.R248W|c.742C>T|537,BUFFER|p.R155W|c.463C>T|92,BUFFER|p.R248G|c.742C>G|14,BUFFER|p.R248W|c.742C>T|31,BUFFER|p.R248W|c.742C>T|87,BUFFER|p.N247N|c.741C>T|10,BUFFER|p.N247I|c.740A>T|7,BUFFER|p.N154I|c.461A>T|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247T|c.740A>C|5,BUFFER|p.N247I|c.740A>T|5,BUFFER|p.N247S|c.740A>G|7,BUFFER|p.N247D|c.739A>G|5,BUFFER|p.N247Y|c.739A>T|3,BUFFER|p.M153I|c.459G>C|3,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>A|21,BUFFER|p.M246I|c.738G>C|3,BUFFER|p.M246I|c.738G>C|4,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246R|c.737T>G|12,BUFFER|p.M246R|c.737T>G|3,BUFFER|p.M246T|c.737T>C|8,BUFFER|p.M153R|c.458T>G|3,BUFFER|p.M246K|c.737T>A|7,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246L|c.736A>T|3,BUFFER|p.M153V|c.457A>G|7,BUFFER|p.M246V|c.736A>G|3,BUFFER|p.M246V|c.736A>G|35,BUFFER|p.M246V|c.736A>G|7,BUFFER|p.M246V|c.736A>G|4,BUFFER|p.G245G|c.735C>T|5,BUFFER|p.G245D|c.734G>A|10,BUFFER|p.G245V|c.734G>T|3,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245A|c.734G>C|8,BUFFER|p.G152D|c.455G>A|23,BUFFER|p.G152V|c.455G>T|15,BUFFER|p.G245V|c.734G>T|10,BUFFER|p.G245D|c.734G>A|23,BUFFER|p.G245D|c.734G>A|119,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245D|c.734G>A|7,BUFFER|p.G245V|c.734G>T|69,BUFFER|p.G245V|c.734G>T|15,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245R|c.733G>C|14,BUFFER|p.G245S|c.733G>A|22,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152S|c.454G>A|56,BUFFER|p.G245C|c.733G>T|4,BUFFER|p.G245S|c.733G>A|56,BUFFER|p.G245S|c.733G>A|340,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245C|c.733G>T|50,BUFFER|p.G245S|c.733G>A|39,BUFFER|p.G245C|c.733G>T|6,BUFFER|p.G245R|c.733G>C|3,BUFFER|p.G152C|c.454G>T|6,BUFFER|p.G152R|c.454G>C|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G244G|c.732C>T|3,BUFFER|p.G151G|c.453C>T|3,BUFFER|p.G244G|c.732C>T|8,BUFFER|p.G244G|c.732C>A|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCCGGTTC	byFrequency|byCluster	5	ESCA
TUBB6	0	.	GRCh37	18	12310963	12310963	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188C>T	p.Ala63Val	p.A63V	ENST00000317702	3/4	41	13	27	56	56	0	TUBB6,missense_variant,p.Ala63Val,ENST00000592683,;TUBB6,missense_variant,p.Ala63Val,ENST00000586653,;TUBB6,missense_variant,p.Ala63Val,ENST00000590967,;TUBB6,missense_variant,p.Ala63Val,ENST00000591208,;TUBB6,missense_variant,p.Ala63Val,ENST00000590693,;TUBB6,missense_variant,p.Ala63Val,ENST00000591909,;TUBB6,missense_variant,p.Ala63Val,ENST00000317702,;TUBB6,5_prime_UTR_variant,,ENST00000591463,;TUBB6,intron_variant,,ENST00000590103,;TUBB6,upstream_gene_variant,,ENST00000586691,;TUBB6,missense_variant,p.Ala63Val,ENST00000586810,;TUBB6,missense_variant,p.Ala63Val,ENST00000590388,;TUBB6,non_coding_transcript_exon_variant,,ENST00000417736,;TUBB6,non_coding_transcript_exon_variant,,ENST00000587204,;	T	ENSG00000176014	ENST00000317702	Transcript	missense_variant	422	188	63	A/V	gCc/gTc	.	.	.	1	TUBB6	HGNC	20776	protein_coding	YES	CCDS11858.1	ENSP00000318697	TBB6_HUMAN	K7ES63_HUMAN,K7EL29_HUMAN,B4E386_HUMAN,B3KS31_HUMAN	UPI0000072BFF	.	deleterious_low_confidence(0)	benign(0.204)	3/4	.	Prints_domain:PR01161,Superfamily_domains:SSF52490,SMART_domains:SM00864,Pfam_domain:PF00091,Gene3D:3.40.50.1440,hmmpanther:PTHR11588:SF88,hmmpanther:PTHR11588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGCCGCCC	.	5	ESCA
ALPK2	0	.	GRCh37	18	56149266	56149266	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6302A>G	p.Lys2101Arg	p.K2101R	ENST00000361673	13/13	40	32	8	65	65	0	ALPK2,missense_variant,p.Lys2101Arg,ENST00000361673,;	C	ENSG00000198796	ENST00000361673	Transcript	missense_variant	6516	6302	2101	K/R	aAg/aGg	.	.	.	-1	ALPK2	HGNC	20565	protein_coding	YES	CCDS11966.2	ENSP00000354991	ALPK2_HUMAN	.	UPI000022A768	.	deleterious(0.03)	possibly_damaging(0.887)	13/13	.	PROSITE_profiles:PS51158,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6,Pfam_domain:PF02816,SMART_domains:SM00811,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCCTTGTAC	.	5	ESCA
SERPINB5	0	.	GRCh37	18	61151655	61151655	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-7G>T	.	.	ENST00000382771	2/7	45	36	9	50	50	0	SERPINB5,splice_region_variant,,ENST00000424602,;SERPINB5,splice_region_variant,,ENST00000489441,;SERPINB5,splice_region_variant,,ENST00000382771,;RP11-635N19.3,upstream_gene_variant,,ENST00000602456,;SERPINB5,upstream_gene_variant,,ENST00000588986,;	T	ENSG00000206075	ENST00000382771	Transcript	splice_region_variant	286	.	.	.	.	.	.	.	1	SERPINB5	HGNC	8949	protein_coding	YES	CCDS32839.1	ENSP00000372221	SPB5_HUMAN	C9JLM5_HUMAN	UPI0000201E51	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAGGCCCGC	.	5	ESCA
TMX3	0	.	GRCh37	18	66382259	66382259	+	5'UTR	SNP	G	G	A	rs766185629	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-41C>T	.	.	ENST00000299608	1/16	41	18	23	73	73	0	TMX3,5_prime_UTR_variant,,ENST00000443099,;TMX3,5_prime_UTR_variant,,ENST00000544714,;TMX3,5_prime_UTR_variant,,ENST00000562706,;TMX3,5_prime_UTR_variant,,ENST00000299608,;CCDC102B,upstream_gene_variant,,ENST00000584775,;CCDC102B,upstream_gene_variant,,ENST00000578970,;CCDC102B,upstream_gene_variant,,ENST00000582371,;CCDC102B,upstream_gene_variant,,ENST00000582077,;TMX3,5_prime_UTR_variant,,ENST00000564008,;TMX3,5_prime_UTR_variant,,ENST00000569053,;TMX3,5_prime_UTR_variant,,ENST00000564631,;TMX3,5_prime_UTR_variant,,ENST00000565918,;TMX3,upstream_gene_variant,,ENST00000569982,;CCDC102B,upstream_gene_variant,,ENST00000580292,;	A	ENSG00000166479	ENST00000299608	Transcript	5_prime_UTR_variant	277	.	.	.	.	rs766185629	.	.	-1	TMX3	HGNC	24718	protein_coding	YES	CCDS32840.1	ENSP00000299608	TMX3_HUMAN	.	UPI000004A093	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGAGGGATA	.	5	ESCA
NFIX	0	.	GRCh37	19	13136057	13136057	+	Missense_Mutation	SNP	C	C	T	rs760403080	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250C>T	p.Arg84Trp	p.R84W	ENST00000397661	2/10	53	42	11	45	45	0	NFIX,missense_variant,p.Arg100Trp,ENST00000591028,;NFIX,missense_variant,p.Arg84Trp,ENST00000592199,;NFIX,missense_variant,p.Arg37Trp,ENST00000586873,;NFIX,missense_variant,p.Arg76Trp,ENST00000587760,;NFIX,missense_variant,p.Arg83Trp,ENST00000358552,;NFIX,missense_variant,p.Arg84Trp,ENST00000397661,;NFIX,missense_variant,p.Arg37Trp,ENST00000590027,;NFIX,missense_variant,p.Arg87Trp,ENST00000360105,;NFIX,missense_variant,p.Arg37Trp,ENST00000588228,;NFIX,missense_variant,p.Arg83Trp,ENST00000587260,;NFIX,missense_variant,p.Arg76Trp,ENST00000585575,;NFIX,missense_variant,p.Arg37Trp,ENST00000585382,;NFIX,3_prime_UTR_variant,,ENST00000586797,;	T	ENSG00000008441	ENST00000397661	Transcript	missense_variant	480	250	84	R/W	Cgg/Tgg	rs760403080	.	.	1	NFIX	HGNC	7788	protein_coding	YES	CCDS45996.1	ENSP00000380781	NFIX_HUMAN	K7ESG9_HUMAN,K7EKH0_HUMAN	UPI000002AF1D	.	deleterious(0)	probably_damaging(1)	2/10	.	PROSITE_profiles:PS51080,hmmpanther:PTHR11492:SF3,hmmpanther:PTHR11492,Pfam_domain:PF03165,SMART_domains:SM00523	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATCCGGCCC	.	5	ESCA
ZSWIM4	0	.	GRCh37	19	13942570	13942570	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*706T>A	.	.	ENST00000254323	13/13	11	5	6	12	12	0	ZSWIM4,3_prime_UTR_variant,,ENST00000254323,;ZSWIM4,downstream_gene_variant,,ENST00000592227,;ZSWIM4,downstream_gene_variant,,ENST00000440752,;ZSWIM4,downstream_gene_variant,,ENST00000590508,;MIR23A,downstream_gene_variant,,ENST00000385245,;MIR27A,downstream_gene_variant,,ENST00000385073,;MIR24-2,downstream_gene_variant,,ENST00000386972,;MIR24-2,downstream_gene_variant,,ENST00000587762,;	A	ENSG00000132003	ENST00000254323	Transcript	3_prime_UTR_variant	3865	.	.	.	.	.	.	.	1	ZSWIM4	HGNC	25704	protein_coding	YES	CCDS32924.1	ENSP00000254323	ZSWM4_HUMAN	Q9HA55_HUMAN	UPI00001C2005	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGGGGTTGGGG	.	3	ESCA
SUGP1	0	.	GRCh37	19	19416842	19416842	+	Silent	SNP	G	G	A	rs775970861	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.354C>T	p.%3D	p.T118T	ENST00000247001	4/14	112	61	51	92	92	0	SUGP1,synonymous_variant,p.%3D,ENST00000334782,;SUGP1,synonymous_variant,p.%3D,ENST00000247001,;SUGP1,synonymous_variant,p.%3D,ENST00000590439,;SUGP1,non_coding_transcript_exon_variant,,ENST00000587716,;SUGP1,non_coding_transcript_exon_variant,,ENST00000606725,;SUGP1,non_coding_transcript_exon_variant,,ENST00000585763,;SUGP1,missense_variant,p.Pro84Ser,ENST00000587119,;SUGP1,synonymous_variant,p.%3D,ENST00000535070,;SUGP1,synonymous_variant,p.%3D,ENST00000588731,;SUGP1,3_prime_UTR_variant,,ENST00000591350,;SUGP1,non_coding_transcript_exon_variant,,ENST00000588580,;SUGP1,upstream_gene_variant,,ENST00000586387,;SUGP1,upstream_gene_variant,,ENST00000591007,;SUGP1,upstream_gene_variant,,ENST00000589144,;SUGP1,downstream_gene_variant,,ENST00000585444,;	A	ENSG00000105705	ENST00000247001	Transcript	synonymous_variant	702	354	118	T	acC/acT	rs775970861	.	.	-1	SUGP1	HGNC	18643	protein_coding	YES	CCDS12399.1	ENSP00000247001	SUGP1_HUMAN	U3KPX0_HUMAN,K7ESM0_HUMAN,B3KS44_HUMAN	UPI00001B6B07	.	.	.	4/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23340,hmmpanther:PTHR23340:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGGGTGGG	.	5	ESCA
ZNF714	0	.	GRCh37	19	21300897	21300897	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1427G>T	p.Gly476Val	p.G476V	ENST00000596143	5/5	45	22	22	55	55	0	ZNF714,missense_variant,p.Gly476Val,ENST00000596143,;ZNF714,3_prime_UTR_variant,,ENST00000601416,;ZNF714,3_prime_UTR_variant,,ENST00000291770,;ZNF714,intron_variant,,ENST00000596053,;ZNF714,downstream_gene_variant,,ENST00000596367,;ZNF714,downstream_gene_variant,,ENST00000597424,;ZNF714,downstream_gene_variant,,ENST00000597086,;RNA5SP469,upstream_gene_variant,,ENST00000364165,;ZNF714,missense_variant,p.Gly476Val,ENST00000600435,;ZNF714,3_prime_UTR_variant,,ENST00000600770,;AC010620.1,upstream_gene_variant,,ENST00000456283,;	T	ENSG00000160352	ENST00000596143	Transcript	missense_variant	1752	1427	476	G/V	gGa/gTa	.	.	.	1	ZNF714	HGNC	27124	protein_coding	YES	CCDS54239.1	ENSP00000472368	ZN714_HUMAN	M0R2G4_HUMAN,M0QYV9_HUMAN	UPI000059D6C5	.	deleterious(0.03)	benign(0.035)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF104,hmmpanther:PTHR24384,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTGGAGAGA	.	5	ESCA
SLC7A9	0	.	GRCh37	19	33355188	33355188	+	Missense_Mutation	SNP	G	G	T	rs772994838	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292C>A	p.Pro98Thr	p.P98T	ENST00000023064	4/13	43	34	8	40	40	0	SLC7A9,missense_variant,p.Pro98Thr,ENST00000023064,;SLC7A9,missense_variant,p.Pro98Thr,ENST00000590341,;SLC7A9,missense_variant,p.Pro98Thr,ENST00000587772,;RN7SKP22,upstream_gene_variant,,ENST00000365097,;SLC7A9,3_prime_UTR_variant,,ENST00000592232,;SLC7A9,3_prime_UTR_variant,,ENST00000590465,;SLC7A9,non_coding_transcript_exon_variant,,ENST00000589659,;	T	ENSG00000021488	ENST00000023064	Transcript	missense_variant	484	292	98	P/T	Ccc/Acc	rs772994838	.	.	-1	SLC7A9	HGNC	11067	protein_coding	YES	CCDS12425.1	ENSP00000023064	BAT1_HUMAN	K7EIF5_HUMAN	UPI0000037773	.	tolerated(0.69)	benign(0.41)	4/13	.	hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF305,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGGGATACT	.	5	ESCA
ZNF568	0	.	GRCh37	19	37487497	37487497	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712C>T	p.Gln238Ter	p.Q238*	ENST00000455427	9/9	26	15	11	47	47	0	ZNF568,stop_gained,p.Gln238Ter,ENST00000455427,;ZNF568,stop_gained,p.Gln302Ter,ENST00000444991,;ZNF568,stop_gained,p.Gln170Ter,ENST00000433993,;ZNF568,downstream_gene_variant,,ENST00000455817,;ZNF568,downstream_gene_variant,,ENST00000588596,;ZNF568,non_coding_transcript_exon_variant,,ENST00000591887,;	T	ENSG00000198453	ENST00000455427	Transcript	stop_gained	1041	712	238	Q/*	Caa/Taa	.	.	.	1	ZNF568	HGNC	25392	protein_coding	.	CCDS56093.1	ENSP00000413396	ZN568_HUMAN	K7ELK8_HUMAN,K7EL97_HUMAN,C9K0F2_HUMAN,C9JXQ5_HUMAN	UPI0001AE649F	.	.	.	9/9	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF107,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATTCAACAT	.	5	ESCA
SPTBN4	0	.	GRCh37	19	41008395	41008395	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1184G>A	p.Gly395Asp	p.G395D	ENST00000352632	10/36	22	16	6	15	15	0	SPTBN4,missense_variant,p.Gly395Asp,ENST00000338932,;SPTBN4,missense_variant,p.Gly395Asp,ENST00000352632,;SPTBN4,missense_variant,p.Gly395Asp,ENST00000598249,;SPTBN4,missense_variant,p.Gly395Asp,ENST00000595535,;SPTBN4,missense_variant,p.Gly395Asp,ENST00000344104,;SPTBN4,non_coding_transcript_exon_variant,,ENST00000598775,;	A	ENSG00000160460	ENST00000352632	Transcript	missense_variant	1270	1184	395	G/D	gGc/gAc	.	.	.	1	SPTBN4	HGNC	14896	protein_coding	YES	CCDS12559.1	ENSP00000263373	SPTN4_HUMAN	.	UPI0000135DBB	.	deleterious(0.02)	possibly_damaging(0.677)	10/36	.	hmmpanther:PTHR11915:SF232,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGGCATCT	.	5	ESCA
ZNF234	0	.	GRCh37	19	44660752	44660752	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583C>G	p.Gln195Glu	p.Q195E	ENST00000426739	6/6	97	55	41	111	111	0	ZNF234,missense_variant,p.Gln195Glu,ENST00000592437,;ZNF234,missense_variant,p.Gln195Glu,ENST00000426739,;	G	ENSG00000263002	ENST00000426739	Transcript	missense_variant	841	583	195	Q/E	Caa/Gaa	.	.	.	1	ZNF234	HGNC	13027	protein_coding	YES	CCDS46101.1	ENSP00000400878	ZN234_HUMAN	Q86WM3_HUMAN,Q86WM2_HUMAN	UPI0000070C95	.	tolerated(0.06)	benign(0.28)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF195,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATCAAAGA	.	5	ESCA
RTN2	0	.	GRCh37	19	45992807	45992807	+	Silent	SNP	C	C	T	rs201151413	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1038G>A	p.%3D	p.A346A	ENST00000245923	6/11	36	32	4	32	32	0	RTN2,synonymous_variant,p.%3D,ENST00000590526,;RTN2,synonymous_variant,p.%3D,ENST00000344680,;RTN2,synonymous_variant,p.%3D,ENST00000430715,;RTN2,synonymous_variant,p.%3D,ENST00000245923,;PPM1N,intron_variant,,ENST00000401705,;RTN2,intron_variant,,ENST00000588036,;RTN2,intron_variant,,ENST00000590746,;RTN2,synonymous_variant,p.%3D,ENST00000587597,;RTN2,3_prime_UTR_variant,,ENST00000591286,;RTN2,non_coding_transcript_exon_variant,,ENST00000589628,;RTN2,upstream_gene_variant,,ENST00000593129,;RTN2,upstream_gene_variant,,ENST00000591789,;RTN2,downstream_gene_variant,,ENST00000592064,;RTN2,upstream_gene_variant,,ENST00000593187,;	T	ENSG00000125744	ENST00000245923	Transcript	synonymous_variant	1274	1038	346	A	gcG/gcA	rs201151413	.	.	-1	RTN2	HGNC	10468	protein_coding	YES	CCDS12665.1	ENSP00000245923	RTN2_HUMAN	K7EMR7_HUMAN	UPI00001352DC	.	.	.	6/11	.	PROSITE_profiles:PS50845,hmmpanther:PTHR10994:SF66,hmmpanther:PTHR10994,Pfam_domain:PF02453	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGTCCGCCAC	byCluster|by1000G	4	ESCA
EHD2	0	.	GRCh37	19	48244236	48244236	+	Silent	SNP	C	C	T	rs146746938	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1179C>T	p.%3D	p.L393L	ENST00000263277	6/6	26	19	7	23	23	0	EHD2,synonymous_variant,p.%3D,ENST00000263277,;EHD2,synonymous_variant,p.%3D,ENST00000538399,;GLTSCR2,upstream_gene_variant,,ENST00000246802,;EHD2,non_coding_transcript_exon_variant,,ENST00000540884,;GLTSCR2,upstream_gene_variant,,ENST00000598681,;GLTSCR2,upstream_gene_variant,,ENST00000599582,;GLTSCR2,upstream_gene_variant,,ENST00000599253,;EHD2,3_prime_UTR_variant,,ENST00000596225,;GLTSCR2,upstream_gene_variant,,ENST00000594525,;GLTSCR2,upstream_gene_variant,,ENST00000600410,;	T	ENSG00000024422	ENST00000263277	Transcript	synonymous_variant	1430	1179	393	L	ctC/ctT	rs146746938	.	.	1	EHD2	HGNC	3243	protein_coding	YES	CCDS12704.1	ENSP00000263277	EHD2_HUMAN	B7ZAY3_HUMAN,B4DU62_HUMAN,B4DNU6_HUMAN	UPI0000071B66	.	.	.	6/6	.	hmmpanther:PTHR11216:SF62,hmmpanther:PTHR11216	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTCATGCC	.	5	ESCA
FUT2	0	.	GRCh37	19	49208141	49208141	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*896G>A	.	.	ENST00000425340	2/2	54	40	14	62	62	0	FUT2,3_prime_UTR_variant,,ENST00000425340,;FUT2,intron_variant,,ENST00000391876,;FUT2,downstream_gene_variant,,ENST00000522966,;	A	ENSG00000176920	ENST00000425340	Transcript	3_prime_UTR_variant	2045	.	.	.	.	.	.	.	1	FUT2	HGNC	4013	protein_coding	YES	CCDS33069.1	ENSP00000387498	FUT2_HUMAN	Q7KZZ1_HUMAN,E7EW73_HUMAN,A8K2L2_HUMAN	UPI00000338F5	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACATGCAGCT	.	5	ESCA
HSD17B14	0	.	GRCh37	19	49316483	49316483	+	Silent	SNP	C	C	A	rs757982643	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.762G>T	p.%3D	p.G254G	ENST00000263278	9/9	47	19	28	37	37	0	HSD17B14,synonymous_variant,p.%3D,ENST00000263278,;HSD17B14,synonymous_variant,p.%3D,ENST00000599157,;HSD17B14,3_prime_UTR_variant,,ENST00000595764,;HSD17B14,3_prime_UTR_variant,,ENST00000596349,;BCAT2,upstream_gene_variant,,ENST00000402551,;BCAT2,upstream_gene_variant,,ENST00000597011,;BCAT2,upstream_gene_variant,,ENST00000601681,;BCAT2,upstream_gene_variant,,ENST00000599246,;BCAT2,upstream_gene_variant,,ENST00000316273,;BCAT2,upstream_gene_variant,,ENST00000598162,;BCAT2,upstream_gene_variant,,ENST00000545387,;BCAT2,upstream_gene_variant,,ENST00000601496,;BCAT2,upstream_gene_variant,,ENST00000596981,;	A	ENSG00000087076	ENST00000263278	Transcript	synonymous_variant	1029	762	254	G	ggG/ggT	rs757982643	.	.	-1	HSD17B14	HGNC	23238	protein_coding	YES	CCDS12736.1	ENSP00000263278	DHB14_HUMAN	.	UPI000004FACC	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCACCCGTA	.	5	ESCA
PRRG2	0	.	GRCh37	19	50086879	50086879	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166G>C	p.Glu56Gln	p.E56Q	ENST00000246794	3/7	45	35	9	50	50	0	PRRG2,missense_variant,p.Glu56Gln,ENST00000246794,;PRRG2,missense_variant,p.Glu56Gln,ENST00000596877,;NOSIP,intron_variant,,ENST00000599537,;NOSIP,upstream_gene_variant,,ENST00000391853,;NOSIP,upstream_gene_variant,,ENST00000596358,;NOSIP,upstream_gene_variant,,ENST00000339093,;NOSIP,upstream_gene_variant,,ENST00000598544,;PRRG2,intron_variant,,ENST00000596700,;PRRG2,3_prime_UTR_variant,,ENST00000597121,;PRRG2,non_coding_transcript_exon_variant,,ENST00000543867,;NOSIP,upstream_gene_variant,,ENST00000600019,;NOSIP,upstream_gene_variant,,ENST00000601340,;NOSIP,upstream_gene_variant,,ENST00000593345,;NOSIP,upstream_gene_variant,,ENST00000594932,;NOSIP,upstream_gene_variant,,ENST00000598820,;	C	ENSG00000126460	ENST00000246794	Transcript	missense_variant	335	166	56	E/Q	Gag/Cag	COSM1751070	.	.	1	PRRG2	HGNC	9470	protein_coding	YES	CCDS12773.1	ENSP00000246794	TMG2_HUMAN	M0QXL9_HUMAN	UPI0000137078	.	deleterious(0)	probably_damaging(1)	3/7	.	PROSITE_profiles:PS50998,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF12,Pfam_domain:PF00594,Gene3D:4.10.740.10,SMART_domains:SM00069,Superfamily_domains:SSF57630,Prints_domain:PR00001	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGGAGCTG	.	5	ESCA
VCAM1	0	.	GRCh37	1	101198095	101198095	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1647G>T	p.Gln549His	p.Q549H	ENST00000294728	7/9	28	24	4	50	50	0	VCAM1,missense_variant,p.Gln457His,ENST00000347652,;VCAM1,missense_variant,p.Gln350His,ENST00000370115,;VCAM1,missense_variant,p.Gln549His,ENST00000294728,;VCAM1,missense_variant,p.Gln487His,ENST00000370119,;VCAM1,upstream_gene_variant,,ENST00000603679,;	T	ENSG00000162692	ENST00000294728	Transcript	missense_variant	1748	1647	549	Q/H	caG/caT	.	.	.	1	VCAM1	HGNC	12663	protein_coding	YES	CCDS773.1	ENSP00000294728	VCAM1_HUMAN	Q68DC4_HUMAN,G0ZI12_HUMAN,G0ZFQ0_HUMAN,F8UV74_HUMAN,F8UU18_HUMAN,F2YYR6_HUMAN	UPI0000000E06	.	deleterious(0.03)	benign(0.049)	7/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00406,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AGGCAGCTCCC	.	2	ESCA
COL11A1	0	.	GRCh37	1	103343330	103343330	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*245C>T	.	.	ENST00000370096	67/67	31	15	15	53	53	0	COL11A1,3_prime_UTR_variant,,ENST00000353414,;COL11A1,3_prime_UTR_variant,,ENST00000370096,;COL11A1,3_prime_UTR_variant,,ENST00000358392,;COL11A1,downstream_gene_variant,,ENST00000512756,;COL11A1,non_coding_transcript_exon_variant,,ENST00000470170,;	A	ENSG00000060718	ENST00000370096	Transcript	3_prime_UTR_variant	5979	.	.	.	.	.	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	.	67/67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTTGAGAAT	.	5	ESCA
MFN2	0	.	GRCh37	1	12056272	12056272	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.371C>G	p.Ser124Cys	p.S124C	ENST00000235329	5/19	33	12	20	54	54	0	MFN2,missense_variant,p.Ser124Cys,ENST00000235329,;MFN2,missense_variant,p.Ser124Cys,ENST00000444836,;MFN2,downstream_gene_variant,,ENST00000412236,;MFN2,downstream_gene_variant,,ENST00000497302,;	G	ENSG00000116688	ENST00000235329	Transcript	missense_variant	693	371	124	S/C	tCt/tGt	.	.	.	1	MFN2	HGNC	16877	protein_coding	YES	CCDS30587.1	ENSP00000235329	MFN2_HUMAN	Q5JXC5_HUMAN	UPI0000039854	.	deleterious(0)	probably_damaging(0.999)	5/19	.	PROSITE_profiles:PS51718,hmmpanther:PTHR10465,hmmpanther:PTHR10465:SF1,Pfam_domain:PF00350,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCTGGGA	.	5	ESCA
VPS45	0	.	GRCh37	1	150082617	150082617	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1500G>A	p.%3D	p.Q500Q	ENST00000369130	14/15	88	64	24	63	63	0	VPS45,synonymous_variant,p.%3D,ENST00000369130,;VPS45,synonymous_variant,p.%3D,ENST00000369128,;VPS45,3_prime_UTR_variant,,ENST00000535106,;VPS45,non_coding_transcript_exon_variant,,ENST00000484306,;VPS45,non_coding_transcript_exon_variant,,ENST00000491789,;	A	ENSG00000136631	ENST00000369130	Transcript	synonymous_variant	2046	1500	500	Q	caG/caA	.	.	.	1	VPS45	HGNC	14579	protein_coding	YES	CCDS944.1	ENSP00000358126	VPS45_HUMAN	.	UPI00000015E6	.	.	.	14/15	.	hmmpanther:PTHR11679:SF3,hmmpanther:PTHR11679,Gene3D:3.40.50.1910,Pfam_domain:PF00995,PIRSF_domain:PIRSF005715,Superfamily_domains:SSF56815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCAGGATAT	.	5	ESCA
TCHH	0	.	GRCh37	1	152081784	152081784	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3909G>T	p.Glu1303Asp	p.E1303D	ENST00000368804	2/2	39	36	3	23	23	0	TCHH,missense_variant,p.Glu1303Asp,ENST00000368804,;	A	ENSG00000159450	ENST00000368804	Transcript	missense_variant	3909	3909	1303	E/D	gaG/gaT	.	.	.	-1	TCHH	HGNC	11791	protein_coding	YES	CCDS41396.1	ENSP00000357794	TRHY_HUMAN	Q5D861_HUMAN,A2RRS3_HUMAN	UPI0000458A5E	.	.	unknown(0)	2/2	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTTTGCTCTTC	.	3	ESCA
LOR	0	.	GRCh37	1	153233880	153233880	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455C>T	p.Ser152Leu	p.S152L	ENST00000368742	2/2	11	8	3	12	12	0	LOR,missense_variant,p.Ser152Leu,ENST00000368742,;	T	ENSG00000203782	ENST00000368742	Transcript	missense_variant	512	455	152	S/L	tCg/tTg	.	.	.	1	LOR	HGNC	6663	protein_coding	YES	CCDS30870.1	ENSP00000357731	LORI_HUMAN	Q6FHY3_HUMAN	UPI0000470BBD	.	.	unknown(0)	2/2	.	Low_complexity_(Seg):seg,Prints_domain:PR01228	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTTCTCGGGCC	.	3	ESCA
RUSC1	0	.	GRCh37	1	155295178	155295178	+	Silent	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1605C>G	p.%3D	p.L535L	ENST00000368352	5/10	21	15	6	20	20	0	RUSC1,synonymous_variant,p.%3D,ENST00000368354,;RUSC1,synonymous_variant,p.%3D,ENST00000292254,;RUSC1,synonymous_variant,p.%3D,ENST00000368352,;RUSC1,synonymous_variant,p.%3D,ENST00000368347,;RUSC1,synonymous_variant,p.%3D,ENST00000368349,;FDPS,downstream_gene_variant,,ENST00000356657,;FDPS,downstream_gene_variant,,ENST00000447866,;FDPS,downstream_gene_variant,,ENST00000368356,;RUSC1-AS1,upstream_gene_variant,,ENST00000450199,;RUSC1-AS1,upstream_gene_variant,,ENST00000443642,;RUSC1-AS1,upstream_gene_variant,,ENST00000543656,;RUSC1-AS1,upstream_gene_variant,,ENST00000446880,;RUSC1,non_coding_transcript_exon_variant,,ENST00000462780,;RUSC1,non_coding_transcript_exon_variant,,ENST00000497930,;RUSC1,non_coding_transcript_exon_variant,,ENST00000471876,;RUSC1,non_coding_transcript_exon_variant,,ENST00000479924,;RUSC1,non_coding_transcript_exon_variant,,ENST00000467820,;RUSC1,non_coding_transcript_exon_variant,,ENST00000490373,;RUSC1,non_coding_transcript_exon_variant,,ENST00000489860,;RUSC1,non_coding_transcript_exon_variant,,ENST00000473331,;RUSC1,non_coding_transcript_exon_variant,,ENST00000492536,;RUSC1,non_coding_transcript_exon_variant,,ENST00000468764,;RUSC1,non_coding_transcript_exon_variant,,ENST00000484664,;FDPS,downstream_gene_variant,,ENST00000489324,;FDPS,downstream_gene_variant,,ENST00000490140,;RUSC1,upstream_gene_variant,,ENST00000485924,;FDPS,downstream_gene_variant,,ENST00000492244,;	G	ENSG00000160753	ENST00000368352	Transcript	synonymous_variant	1756	1605	535	L	ctC/ctG	.	.	.	1	RUSC1	HGNC	17153	protein_coding	YES	CCDS41410.1	ENSP00000357336	RUSC1_HUMAN	Q68CX2_HUMAN	UPI000046FDA5	.	.	.	5/10	.	PROSITE_profiles:PS50826,hmmpanther:PTHR15591,Pfam_domain:PF02759,Superfamily_domains:0052343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCCACGC	.	5	ESCA
GON4L	0	.	GRCh37	1	155734853	155734853	+	Missense_Mutation	SNP	C	C	T	rs748290334	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4411G>A	p.Asp1471Asn	p.D1471N	ENST00000437809	21/32	100	70	30	62	61	0	GON4L,missense_variant,p.Asp1471Asn,ENST00000437809,;GON4L,missense_variant,p.Asp1471Asn,ENST00000361040,;GON4L,missense_variant,p.Asp1471Asn,ENST00000368331,;GON4L,missense_variant,p.Asp1471Asn,ENST00000271883,;GON4L,non_coding_transcript_exon_variant,,ENST00000471341,;GON4L,downstream_gene_variant,,ENST00000496021,;GON4L,downstream_gene_variant,,ENST00000490801,;GON4L,downstream_gene_variant,,ENST00000497369,;	T	ENSG00000116580	ENST00000437809	Transcript	missense_variant	4534	4411	1471	D/N	Gat/Aat	rs748290334	.	.	-1	GON4L	HGNC	25973	protein_coding	YES	CCDS44242.1	ENSP00000396117	GON4L_HUMAN	Q9NXJ9_HUMAN	UPI0000603C24	.	deleterious(0.02)	benign(0.004)	21/32	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16088,hmmpanther:PTHR16088:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCTTGGG	.	5	ESCA
DUSP27	0	.	GRCh37	1	167096345	167096345	+	Silent	SNP	G	G	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1977G>T	p.%3D	p.L659L	ENST00000361200	6/6	39	25	14	19	19	0	DUSP27,synonymous_variant,p.%3D,ENST00000361200,;DUSP27,synonymous_variant,p.%3D,ENST00000443333,;DUSP27,synonymous_variant,p.%3D,ENST00000271385,;DUSP27,intron_variant,,ENST00000485151,;	T	ENSG00000198842	ENST00000361200	Transcript	synonymous_variant	2143	1977	659	L	ctG/ctT	.	.	.	1	DUSP27	HGNC	25034	protein_coding	YES	CCDS30932.1	ENSP00000354483	DUS27_HUMAN	.	UPI000040DFF5	.	.	.	6/6	.	hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTGTCTGC	.	5	ESCA
CACNA1S	0	.	GRCh37	1	201027607	201027607	+	Missense_Mutation	SNP	C	C	T	rs775845281	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3538G>A	p.Asp1180Asn	p.D1180N	ENST00000362061	28/44	60	43	17	33	33	0	CACNA1S,missense_variant,p.Asp1180Asn,ENST00000367338,;CACNA1S,missense_variant,p.Asp1180Asn,ENST00000362061,;	T	ENSG00000081248	ENST00000362061	Transcript	missense_variant	3765	3538	1180	D/N	Gac/Aac	rs775845281	.	.	-1	CACNA1S	HGNC	1397	protein_coding	YES	CCDS1407.1	ENSP00000355192	CAC1S_HUMAN	Q13062_HUMAN,Q12966_HUMAN	UPI000020471D	.	deleterious(0)	probably_damaging(0.997)	28/44	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGTCTCCAA	byFrequency	5	ESCA
NAV1	0	.	GRCh37	1	201750186	201750186	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1412G>C	p.Ser471Thr	p.S471T	ENST00000367296	5/30	61	55	6	44	44	0	NAV1,missense_variant,p.Ser471Thr,ENST00000367297,;NAV1,missense_variant,p.Ser471Thr,ENST00000367300,;NAV1,missense_variant,p.Ser471Thr,ENST00000295624,;NAV1,missense_variant,p.Ser29Thr,ENST00000430015,;NAV1,missense_variant,p.Ser484Thr,ENST00000367302,;NAV1,missense_variant,p.Ser471Thr,ENST00000367296,;NAV1,missense_variant,p.Ser80Thr,ENST00000367295,;IPO9-AS1,intron_variant,,ENST00000413035,;NAV1,non_coding_transcript_exon_variant,,ENST00000490213,;NAV1,upstream_gene_variant,,ENST00000469130,;	C	ENSG00000134369	ENST00000367296	Transcript	missense_variant	1832	1412	471	S/T	aGc/aCc	.	.	.	1	NAV1	HGNC	15989	protein_coding	YES	CCDS1414.2	ENSP00000356265	NAV1_HUMAN	.	UPI00004562D4	.	tolerated(0.32)	benign(0.414)	5/30	.	hmmpanther:PTHR12784:SF3,hmmpanther:PTHR12784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGAGCTGGT	.	4	ESCA
LAMB3	0	.	GRCh37	1	209790831	209790831	+	Missense_Mutation	SNP	C	C	T	rs751750658	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3152G>A	p.Arg1051Gln	p.R1051Q	ENST00000391911	20/22	37	27	9	21	21	0	LAMB3,missense_variant,p.Arg1051Gln,ENST00000356082,;LAMB3,missense_variant,p.Arg120Gln,ENST00000455193,;LAMB3,missense_variant,p.Arg1051Gln,ENST00000391911,;LAMB3,missense_variant,p.Arg1051Gln,ENST00000367030,;CAMK1G,downstream_gene_variant,,ENST00000361322,;CAMK1G,downstream_gene_variant,,ENST00000009105,;	T	ENSG00000196878	ENST00000391911	Transcript	missense_variant	3542	3152	1051	R/Q	cGg/cAg	rs751750658	.	.	-1	LAMB3	HGNC	6490	protein_coding	YES	CCDS1487.1	ENSP00000375778	LAMB3_HUMAN	Q5THA1_HUMAN	UPI000012E76F	.	tolerated(0.65)	benign(0.002)	20/22	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10574:SF245,hmmpanther:PTHR10574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCCGGGCT	byFrequency	5	ESCA
TOMM20	0	.	GRCh37	1	235292048	235292048	+	5'UTR	SNP	G	G	A	rs762280693	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-18C>T	.	.	ENST00000366607	1/5	75	32	42	57	57	0	TOMM20,5_prime_UTR_variant,,ENST00000366607,;RBM34,downstream_gene_variant,,ENST00000366606,;RBM34,downstream_gene_variant,,ENST00000408888,;RBM34,downstream_gene_variant,,ENST00000447801,;SNORA14B,upstream_gene_variant,,ENST00000384452,;RBM34,downstream_gene_variant,,ENST00000495224,;ARID4B,downstream_gene_variant,,ENST00000474953,;	A	ENSG00000173726	ENST00000366607	Transcript	5_prime_UTR_variant	204	.	.	.	.	rs762280693	.	.	-1	TOMM20	HGNC	20947	protein_coding	YES	CCDS1603.1	ENSP00000355566	TOM20_HUMAN	.	UPI0000130CA3	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGAGCGTGG	byFrequency	5	ESCA
ZCCHC11	0	.	GRCh37	1	52940528	52940528	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2703T>G	p.Asp901Glu	p.D901E	ENST00000257177	13/30	14	2	11	34	34	0	ZCCHC11,missense_variant,p.Asp901Glu,ENST00000257177,;ZCCHC11,missense_variant,p.Asp660Glu,ENST00000484723,;ZCCHC11,missense_variant,p.Asp830Glu,ENST00000528642,;ZCCHC11,missense_variant,p.Asp901Glu,ENST00000371544,;ZCCHC11,non_coding_transcript_exon_variant,,ENST00000371541,;ZCCHC11,downstream_gene_variant,,ENST00000473856,;	C	ENSG00000134744	ENST00000257177	Transcript	missense_variant	2848	2703	901	D/E	gaT/gaG	.	.	.	-1	ZCCHC11	HGNC	28981	protein_coding	YES	CCDS30715.1	ENSP00000257177	TUT4_HUMAN	H0YEY0_HUMAN,E9PQS7_HUMAN,E9PJN7_HUMAN	UPI00001D7D0C	.	deleterious(0.01)	benign(0.129)	13/30	.	hmmpanther:PTHR12271,hmmpanther:PTHR12271:SF49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	AACTTATCAAA	.	4	ESCA
CDC25B	0	.	GRCh37	20	3782721	3782721	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1072G>A	p.Glu358Lys	p.E358K	ENST00000245960	10/16	88	46	41	66	66	0	CDC25B,missense_variant,p.Glu317Lys,ENST00000340833,;CDC25B,missense_variant,p.Glu344Lys,ENST00000439880,;CDC25B,missense_variant,p.Glu267Lys,ENST00000379598,;CDC25B,missense_variant,p.Glu294Lys,ENST00000344256,;CDC25B,missense_variant,p.Glu358Lys,ENST00000245960,;CDC25B,non_coding_transcript_exon_variant,,ENST00000467519,;CDC25B,non_coding_transcript_exon_variant,,ENST00000480816,;CDC25B,non_coding_transcript_exon_variant,,ENST00000468979,;CDC25B,upstream_gene_variant,,ENST00000495915,;	A	ENSG00000101224	ENST00000245960	Transcript	missense_variant	1769	1072	358	E/K	Gag/Aag	.	.	.	1	CDC25B	HGNC	1726	protein_coding	YES	CCDS13067.1	ENSP00000245960	MPIP2_HUMAN	D3DVY6_HUMAN,B3KS38_HUMAN	UPI000012F474	.	tolerated(0.15)	benign(0.392)	10/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10828:SF46,hmmpanther:PTHR10828,Pfam_domain:PF06617	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTGAGGAG	.	5	ESCA
DIDO1	0	.	GRCh37	20	61513659	61513659	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000266070	16/16	118	71	47	92	92	0	DIDO1,stop_gained,p.Arg1217Ter,ENST00000266070,;DIDO1,stop_gained,p.Arg1217Ter,ENST00000395343,;DIDO1,downstream_gene_variant,,ENST00000395335,;DIDO1,downstream_gene_variant,,ENST00000395340,;	A	ENSG00000101191	ENST00000266070	Transcript	stop_gained	3975	3649	1217	R/*	Cga/Tga	.	.	.	-1	DIDO1	HGNC	2680	protein_coding	YES	CCDS33506.1	ENSP00000266070	DIDO1_HUMAN	.	UPI0000206380	.	.	.	16/16	.	hmmpanther:PTHR14914:SF7,hmmpanther:PTHR14914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTCGGGTCC	.	5	ESCA
SON	0	.	GRCh37	21	34926719	34926719	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5182A>G	p.Ile1728Val	p.I1728V	ENST00000356577	3/12	41	15	26	69	69	0	SON,missense_variant,p.Ile1728Val,ENST00000381679,;SON,missense_variant,p.Ile1728Val,ENST00000300278,;SON,missense_variant,p.Ile1728Val,ENST00000356577,;SON,missense_variant,p.Ile723Val,ENST00000436227,;SON,missense_variant,p.Ile1728Val,ENST00000290239,;SON,intron_variant,,ENST00000381692,;SON,upstream_gene_variant,,ENST00000421541,;SON,missense_variant,p.Ile1728Val,ENST00000455528,;	G	ENSG00000159140	ENST00000356577	Transcript	missense_variant	5657	5182	1728	I/V	Att/Gtt	COSM419252	.	.	1	SON	HGNC	11183	protein_coding	YES	CCDS13629.1	ENSP00000348984	SON_HUMAN	.	UPI0000140BFD	.	.	benign(0.031)	3/12	.	hmmpanther:PTHR12813:SF26,hmmpanther:PTHR12813	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATATTAAT	.	5	ESCA
AGPAT3	0	.	GRCh37	21	45402309	45402309	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*36G>A	.	.	ENST00000398063	9/9	53	50	3	84	84	0	AGPAT3,3_prime_UTR_variant,,ENST00000398061,;AGPAT3,3_prime_UTR_variant,,ENST00000546158,;AGPAT3,3_prime_UTR_variant,,ENST00000398063,;AGPAT3,3_prime_UTR_variant,,ENST00000327505,;AGPAT3,3_prime_UTR_variant,,ENST00000398058,;AGPAT3,3_prime_UTR_variant,,ENST00000291572,;AGPAT3,non_coding_transcript_exon_variant,,ENST00000479117,;AGPAT3,downstream_gene_variant,,ENST00000484865,;AGPAT3,downstream_gene_variant,,ENST00000467358,;	A	ENSG00000160216	ENST00000398063	Transcript	3_prime_UTR_variant	1659	.	.	.	.	.	.	.	1	AGPAT3	HGNC	326	protein_coding	YES	CCDS13703.1	ENSP00000381140	PLCC_HUMAN	C9JQX8_HUMAN,C9JL26_HUMAN,C9JK35_HUMAN,C9J184_HUMAN	UPI000004616E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGACGGTGGTA	.	2	ESCA
APOL3	0	.	GRCh37	22	36537873	36537873	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.584G>C	p.Gly195Ala	p.G195A	ENST00000349314	3/3	22	13	8	21	21	0	APOL3,missense_variant,p.Gly124Ala,ENST00000397293,;APOL3,missense_variant,p.Gly195Ala,ENST00000349314,;APOL3,5_prime_UTR_variant,,ENST00000397287,;APOL3,5_prime_UTR_variant,,ENST00000424878,;APOL3,5_prime_UTR_variant,,ENST00000361710,;APOL3,non_coding_transcript_exon_variant,,ENST00000487423,;APOL3,downstream_gene_variant,,ENST00000534251,;APOL3,downstream_gene_variant,,ENST00000525184,;APOL3,downstream_gene_variant,,ENST00000485453,;APOL3,3_prime_UTR_variant,,ENST00000426939,;APOL3,3_prime_UTR_variant,,ENST00000432700,;APOL3,3_prime_UTR_variant,,ENST00000422426,;APOL3,3_prime_UTR_variant,,ENST00000397289,;APOL3,3_prime_UTR_variant,,ENST00000487355,;APOL3,downstream_gene_variant,,ENST00000531195,;APOL3,downstream_gene_variant,,ENST00000530895,;APOL3,downstream_gene_variant,,ENST00000487783,;	G	ENSG00000128284	ENST00000349314	Transcript	missense_variant	622	584	195	G/A	gGc/gCc	.	.	.	-1	APOL3	HGNC	14868	protein_coding	YES	CCDS13922.1	ENSP00000344577	APOL3_HUMAN	.	UPI0000141763	.	deleterious(0.01)	probably_damaging(0.99)	3/3	.	hmmpanther:PTHR14096,hmmpanther:PTHR14096:SF32,Pfam_domain:PF05461	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCGCCAGTG	.	5	ESCA
INSIG2	0	.	GRCh37	2	118866114	118866114	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*216T>G	.	.	ENST00000245787	6/6	140	122	18	55	55	0	INSIG2,3_prime_UTR_variant,,ENST00000245787,;INSIG2,non_coding_transcript_exon_variant,,ENST00000471186,;INSIG2,non_coding_transcript_exon_variant,,ENST00000485520,;INSIG2,downstream_gene_variant,,ENST00000479999,;INSIG2,downstream_gene_variant,,ENST00000467223,;INSIG2,downstream_gene_variant,,ENST00000488995,;INSIG2,downstream_gene_variant,,ENST00000411929,;	G	ENSG00000125629	ENST00000245787	Transcript	3_prime_UTR_variant	1100	.	.	.	.	.	.	.	1	INSIG2	HGNC	20452	protein_coding	YES	CCDS2122.1	ENSP00000245787	INSI2_HUMAN	B4DQ23_HUMAN	UPI0000073C50	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATATTTGAC	.	4	ESCA
NBAS	0	.	GRCh37	2	15644299	15644299	+	Silent	SNP	G	G	A	rs774810902	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.924C>T	p.%3D	p.V308V	ENST00000281513	11/52	79	67	11	80	80	0	NBAS,synonymous_variant,p.%3D,ENST00000441750,;NBAS,synonymous_variant,p.%3D,ENST00000281513,;NBAS,synonymous_variant,p.%3D,ENST00000427792,;	A	ENSG00000151779	ENST00000281513	Transcript	synonymous_variant	950	924	308	V	gtC/gtT	rs774810902	.	.	-1	NBAS	HGNC	15625	protein_coding	YES	CCDS1685.1	ENSP00000281513	NBAS_HUMAN	Q4ZG05_HUMAN,H7C007_HUMAN	UPI00001AEA68	.	.	.	11/52	.	Superfamily_domains:SSF50969,Gene3D:2.130.10.10,Pfam_domain:PF15492,hmmpanther:PTHR15922:SF2,hmmpanther:PTHR15922	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTTGACACT	.	4	ESCA
NFE2L2	0	.	GRCh37	2	178098953	178098953	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	2/5	54	37	16	44	43	0	NFE2L2,missense_variant,p.Gly15Glu,ENST00000449627,;NFE2L2,missense_variant,p.Gly15Glu,ENST00000423513,;NFE2L2,missense_variant,p.Gly31Glu,ENST00000397062,;NFE2L2,missense_variant,p.Gly15Glu,ENST00000446151,;NFE2L2,missense_variant,p.Gly15Glu,ENST00000588123,;NFE2L2,missense_variant,p.Gly30Glu,ENST00000586532,;NFE2L2,missense_variant,p.Gly15Glu,ENST00000421929,;NFE2L2,missense_variant,p.Gly15Glu,ENST00000464747,;NFE2L2,missense_variant,p.Gly15Glu,ENST00000448782,;NFE2L2,missense_variant,p.Gly15Glu,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	T	ENSG00000116044	ENST00000397062	Transcript	missense_variant	647	92	31	G/E	gGa/gAa	COSM132956,COSM1613738,COSM1259060	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(0.962)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.G31E|c.92G>A|5,CODON|p.G31A|c.92G>C|7,BUFFER|p.R34P|c.101G>C|3,BUFFER|p.R34Q|c.101G>A|11,BUFFER|p.R34G|c.100C>G|11,BUFFER|p.L30R|c.89T>G|7,BUFFER|p.L30F|c.88C>T|6,BUFFER|p.D29G|c.86A>G|11,BUFFER|p.D29H|c.85G>C|12,BUFFER|p.D29N|c.85G>A|3,BUFFER|p.D29Y|c.85G>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTCCAAGA	.	5	ESCA
MAP4K3	0	.	GRCh37	2	39553377	39553377	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572A>G	p.Tyr191Cys	p.Y191C	ENST00000263881	9/34	34	27	7	28	28	0	MAP4K3,missense_variant,p.Tyr128Cys,ENST00000437545,;MAP4K3,missense_variant,p.Tyr191Cys,ENST00000263881,;MAP4K3,missense_variant,p.Tyr191Cys,ENST00000341681,;MAP4K3,upstream_gene_variant,,ENST00000536018,;RP11-449G16.1,upstream_gene_variant,,ENST00000609671,;MAP4K3,missense_variant,p.Thr118Ala,ENST00000429397,;MAP4K3,upstream_gene_variant,,ENST00000414968,;	C	ENSG00000011566	ENST00000263881	Transcript	missense_variant	897	572	191	Y/C	tAc/tGc	.	.	.	-1	MAP4K3	HGNC	6865	protein_coding	YES	CCDS1803.1	ENSP00000263881	M4K3_HUMAN	Q53RV1_HUMAN,H7C1A4_HUMAN,B4DSS3_HUMAN,B3KMM5_HUMAN	UPI00000747E6	.	deleterious(0)	probably_damaging(1)	9/34	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF205,hmmpanther:PTHR24361,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,PIRSF_domain:PIRSF038172,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GATTGTAACCC	.	4	ESCA
XPO1	0	.	GRCh37	2	61705938	61705938	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*17G>T	.	.	ENST00000401558	25/25	48	35	12	52	52	0	XPO1,3_prime_UTR_variant,,ENST00000404992,;XPO1,3_prime_UTR_variant,,ENST00000401558,;XPO1,3_prime_UTR_variant,,ENST00000406957,;RP11-355B11.2,intron_variant,,ENST00000603652,;RP11-355B11.2,intron_variant,,ENST00000578974,;RP11-355B11.2,intron_variant,,ENST00000603028,;RP11-355B11.2,intron_variant,,ENST00000603199,;RP11-355B11.2,upstream_gene_variant,,ENST00000605437,;XPO1,3_prime_UTR_variant,,ENST00000428210,;XPO1,non_coding_transcript_exon_variant,,ENST00000481073,;XPO1,downstream_gene_variant,,ENST00000492182,;XPO1,downstream_gene_variant,,ENST00000461407,;	A	ENSG00000082898	ENST00000401558	Transcript	3_prime_UTR_variant	3961	.	.	.	.	.	.	.	-1	XPO1	HGNC	12825	protein_coding	YES	CCDS33205.1	ENSP00000384863	XPO1_HUMAN	C9JV99_HUMAN,C9JQ02_HUMAN,C9JKM9_HUMAN,C9JF49_HUMAN,C9J673_HUMAN,C9IZS4_HUMAN,C9IYM2_HUMAN,B7ZB16_HUMAN,B3KWD0_HUMAN	UPI0000001C23	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAACAGCAT	.	5	ESCA
XPO1	0	.	GRCh37	2	61725817	61725817	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.750G>C	p.Leu250Phe	p.L250F	ENST00000401558	9/25	51	31	20	43	43	0	XPO1,missense_variant,p.Leu250Phe,ENST00000404992,;XPO1,missense_variant,p.Leu250Phe,ENST00000401558,;XPO1,missense_variant,p.Leu250Phe,ENST00000406957,;XPO1,downstream_gene_variant,,ENST00000443240,;XPO1,downstream_gene_variant,,ENST00000451765,;XPO1,downstream_gene_variant,,ENST00000468259,;XPO1,downstream_gene_variant,,ENST00000476585,;XPO1,3_prime_UTR_variant,,ENST00000428210,;XPO1,3_prime_UTR_variant,,ENST00000437159,;XPO1,non_coding_transcript_exon_variant,,ENST00000475744,;XPO1,downstream_gene_variant,,ENST00000489954,;XPO1,upstream_gene_variant,,ENST00000460037,;XPO1,upstream_gene_variant,,ENST00000481073,;	G	ENSG00000082898	ENST00000401558	Transcript	missense_variant	1478	750	250	L/F	ttG/ttC	COSM1022122	.	.	-1	XPO1	HGNC	12825	protein_coding	YES	CCDS33205.1	ENSP00000384863	XPO1_HUMAN	C9JV99_HUMAN,C9JQ02_HUMAN,C9JKM9_HUMAN,C9JF49_HUMAN,C9J673_HUMAN,C9IZS4_HUMAN,C9IYM2_HUMAN,B7ZB16_HUMAN,B3KWD0_HUMAN	UPI0000001C23	.	deleterious(0)	probably_damaging(0.996)	9/25	.	hmmpanther:PTHR11223,Pfam_domain:PF08389,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATCAATGT	.	5	ESCA
DYSF	0	.	GRCh37	2	71795469	71795469	+	Splice_Site	SNP	G	G	A	rs199954546	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2864+1G>A	.	p.X955_splice	ENST00000410020	.	40	24	15	37	37	0	DYSF,splice_donor_variant,,ENST00000409582,;DYSF,splice_donor_variant,,ENST00000410020,;DYSF,splice_donor_variant,,ENST00000409744,;DYSF,splice_donor_variant,,ENST00000429174,;DYSF,splice_donor_variant,,ENST00000409762,;DYSF,splice_donor_variant,,ENST00000410041,;DYSF,splice_donor_variant,,ENST00000409651,;DYSF,splice_donor_variant,,ENST00000394120,;DYSF,splice_donor_variant,,ENST00000409366,;DYSF,splice_donor_variant,,ENST00000413539,;DYSF,splice_donor_variant,,ENST00000258104,;DYSF,upstream_gene_variant,,ENST00000461565,;	A	ENSG00000135636	ENST00000410020	Transcript	splice_donor_variant	.	.	.	.	.	rs199954546,CS080679,DYSF:c.2810+1G>A,DYSF:c.2810+1G>C,COSM1409294,COSM1409293	.	.	1	DYSF	HGNC	3097	protein_coding	YES	CCDS46328.1	ENSP00000386881	DYSF_HUMAN	A0FK00_HUMAN	UPI000171F710	.	.	.	.	26/55	.	A:0.0002	A:0,A:0	A:0,A:0	.	A:0,A:0	A:0.001,A:0.001	A:0,A:0	.	.	.	0,0,0,0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,0,0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGACGTGAGT	byCluster|by1000G	5	ESCA
NAT8	0	.	GRCh37	2	73868257	73868257	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499G>A	p.Asp167Asn	p.D167N	ENST00000272425	2/2	50	46	4	54	54	0	NAT8,missense_variant,p.Asp167Asn,ENST00000272425,;ALMS1P,upstream_gene_variant,,ENST00000450720,;	T	ENSG00000144035	ENST00000272425	Transcript	missense_variant	649	499	167	D/N	Gac/Aac	.	.	.	-1	NAT8	HGNC	18069	protein_coding	YES	CCDS1926.1	ENSP00000272425	NAT8_HUMAN	.	UPI00000707D4	.	tolerated(0.06)	benign(0.052)	2/2	.	PROSITE_profiles:PS51186,hmmpanther:PTHR13947:SF14,hmmpanther:PTHR13947,Pfam_domain:PF00583,Gene3D:3.40.630.30,Superfamily_domains:SSF55729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CTGGTCCCGGG	.	2	ESCA
DCTN1	0	.	GRCh37	2	74595885	74595885	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1824G>A	p.%3D	p.V608V	ENST00000361874	16/32	60	53	7	42	42	0	DCTN1,synonymous_variant,p.%3D,ENST00000394003,;DCTN1,synonymous_variant,p.%3D,ENST00000409868,;DCTN1,synonymous_variant,p.%3D,ENST00000407639,;DCTN1,synonymous_variant,p.%3D,ENST00000409240,;DCTN1,synonymous_variant,p.%3D,ENST00000361874,;DCTN1,synonymous_variant,p.%3D,ENST00000409567,;DCTN1,synonymous_variant,p.%3D,ENST00000409438,;DCTN1,downstream_gene_variant,,ENST00000458655,;DCTN1,intron_variant,,ENST00000497666,;DCTN1,upstream_gene_variant,,ENST00000495643,;DCTN1,downstream_gene_variant,,ENST00000463583,;DCTN1,synonymous_variant,p.%3D,ENST00000434055,;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110,;DCTN1,downstream_gene_variant,,ENST00000462813,;DCTN1,downstream_gene_variant,,ENST00000470351,;DCTN1,upstream_gene_variant,,ENST00000495895,;DCTN1,downstream_gene_variant,,ENST00000477966,;DCTN1,upstream_gene_variant,,ENST00000491465,;	T	ENSG00000204843	ENST00000361874	Transcript	synonymous_variant	2142	1824	608	V	gtG/gtA	.	.	.	-1	DCTN1	HGNC	2711	protein_coding	YES	CCDS1939.1	ENSP00000354791	DCTN1_HUMAN	Q6LCB2_HUMAN,E7EWF7_HUMAN,C9JZA4_HUMAN,C9JTE5_HUMAN,C9JJN7_HUMAN,C9JJD0_HUMAN,C9J1B7_HUMAN	UPI0000129A25	.	.	.	16/32	.	Pfam_domain:PF12455,hmmpanther:PTHR18916:SF29,hmmpanther:PTHR18916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACAGCACCAG	.	4	ESCA
IGSF11	0	.	GRCh37	3	118619908	118619908	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1459C>G	.	.	ENST00000393775	7/7	43	29	13	25	25	0	IGSF11,3_prime_UTR_variant,,ENST00000425327,;IGSF11,3_prime_UTR_variant,,ENST00000489689,;IGSF11,3_prime_UTR_variant,,ENST00000393775,;IGSF11,3_prime_UTR_variant,,ENST00000354673,;IGSF11,downstream_gene_variant,,ENST00000441144,;IGSF11,downstream_gene_variant,,ENST00000491903,;	C	ENSG00000144847	ENST00000393775	Transcript	3_prime_UTR_variant	3061	.	.	.	.	.	.	.	-1	IGSF11	HGNC	16669	protein_coding	YES	CCDS46891.1	ENSP00000377370	IGS11_HUMAN	C9JAD3_HUMAN,C9IZX3_HUMAN	UPI000013D9B3	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGACACT	.	5	ESCA
NDUFB4	0	.	GRCh37	3	120320222	120320222	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327+118C>T	.	.	ENST00000184266	.	35	23	12	16	16	0	NDUFB4,3_prime_UTR_variant,,ENST00000485064,;NDUFB4,intron_variant,,ENST00000492739,;NDUFB4,intron_variant,,ENST00000184266,;NDUFB4,3_prime_UTR_variant,,ENST00000461682,;NDUFB4,intron_variant,,ENST00000496588,;NDUFB4,intron_variant,,ENST00000491335,;	T	ENSG00000065518	ENST00000184266	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NDUFB4	HGNC	7699	protein_coding	YES	CCDS2999.1	ENSP00000184266	NDUB4_HUMAN	.	UPI000013C5EA	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCTCTGCCT	.	5	ESCA
CASR	0	.	GRCh37	3	121994703	121994703	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1422G>A	p.%3D	p.G474G	ENST00000498619	5/7	99	87	12	70	70	0	CASR,synonymous_variant,p.%3D,ENST00000296154,;CASR,synonymous_variant,p.%3D,ENST00000498619,;CASR,synonymous_variant,p.%3D,ENST00000490131,;	A	ENSG00000036828	ENST00000498619	Transcript	synonymous_variant	1860	1422	474	G	ggG/ggA	.	.	.	1	CASR	HGNC	1514	protein_coding	YES	CCDS54632.1	ENSP00000420194	.	Q2F3K6_HUMAN,Q2F3K5_HUMAN,Q2F3K4_HUMAN,Q2F3K3_HUMAN,Q2F3K2_HUMAN,E7ENE0_HUMAN	UPI000020A065	.	.	.	5/7	.	hmmpanther:PTHR24061:SF358,hmmpanther:PTHR24061,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGGGGGAGCA	.	4	ESCA
ALG1L	0	.	GRCh37	3	125648300	125648300	+	Silent	SNP	G	G	C	rs113713770	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459C>G	p.%3D	p.L153L	ENST00000340333	6/6	250	192	57	220	220	0	ALG1L,synonymous_variant,p.%3D,ENST00000340333,;FAM86JP,non_coding_transcript_exon_variant,,ENST00000485843,;FAM86JP,non_coding_transcript_exon_variant,,ENST00000467239,;FAM86JP,non_coding_transcript_exon_variant,,ENST00000486431,;FAM86JP,downstream_gene_variant,,ENST00000484500,;	C	ENSG00000189366	ENST00000340333	Transcript	synonymous_variant	623	459	153	L	ctC/ctG	rs113713770	.	.	-1	ALG1L	HGNC	33721	protein_coding	YES	CCDS33840.1	ENSP00000340009	ALG1L_HUMAN	.	UPI000020A11A	.	.	.	6/6	.	hmmpanther:PTHR13036:SF0,hmmpanther:PTHR13036	C:0.0006	C:0.0023	C:0	.	C:0	C:0	C:0	C:0.0011	C:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGGGAGCAC	byFrequency|byCluster|by1000G	5	ESCA
NR2C2	0	.	GRCh37	3	15045465	15045465	+	Missense_Mutation	SNP	C	C	G	rs759479104	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44C>G	p.Ser15Cys	p.S15C	ENST00000323373	2/15	31	23	8	54	54	0	NR2C2,missense_variant,p.Ser15Cys,ENST00000406272,;NR2C2,missense_variant,p.Ser15Cys,ENST00000435454,;NR2C2,missense_variant,p.Ser15Cys,ENST00000323373,;NR2C2,missense_variant,p.Ser15Cys,ENST00000393102,;NR2C2,missense_variant,p.Ser15Cys,ENST00000425241,;NR2C2,missense_variant,p.Ser15Cys,ENST00000437120,;NR2C2,missense_variant,p.Ser15Cys,ENST00000413118,;NR2C2,non_coding_transcript_exon_variant,,ENST00000475707,;	G	ENSG00000177463	ENST00000323373	Transcript	missense_variant	261	44	15	S/C	tCt/tGt	rs759479104	.	.	1	NR2C2	HGNC	7972	protein_coding	YES	CCDS2621.1	ENSP00000320447	NR2C2_HUMAN	F2YGU2_HUMAN,C9J2Y1_HUMAN	UPI00001AF3B4	.	deleterious_low_confidence(0.01)	possibly_damaging(0.784)	2/15	.	hmmpanther:PTHR24083:SF48,hmmpanther:PTHR24083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGACTCTGCTG	.	5	ESCA
TMEM14E	0	.	GRCh37	3	152058400	152058400	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.294G>A	p.%3D	p.L98L	ENST00000408960	1/1	95	61	33	51	51	0	TMEM14E,synonymous_variant,p.%3D,ENST00000408960,;MBNL1,intron_variant,,ENST00000545754,;MBNL1,intron_variant,,ENST00000282486,;MBNL1,intron_variant,,ENST00000485509,;MBNL1,intron_variant,,ENST00000324196,;MBNL1,intron_variant,,ENST00000459747,;MBNL1,intron_variant,,ENST00000498502,;MBNL1,intron_variant,,ENST00000493459,;MBNL1,intron_variant,,ENST00000460591,;MBNL1,intron_variant,,ENST00000357472,;MBNL1,intron_variant,,ENST00000463374,;MBNL1,intron_variant,,ENST00000465907,;MBNL1,intron_variant,,ENST00000495875,;MBNL1,intron_variant,,ENST00000282488,;MBNL1,intron_variant,,ENST00000492948,;MBNL1,intron_variant,,ENST00000324210,;MBNL1,intron_variant,,ENST00000355460,;MBNL1,intron_variant,,ENST00000485910,;MBNL1,intron_variant,,ENST00000464596,;	T	ENSG00000221962	ENST00000408960	Transcript	synonymous_variant	380	294	98	L	ctG/ctA	.	.	.	-1	TMEM14E	HGNC	34386	protein_coding	YES	CCDS43161.1	ENSP00000386163	TM14E_HUMAN	.	UPI00001D6969	.	.	.	1/1	.	Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTATCAGCAG	.	5	ESCA
OTOL1	0	.	GRCh37	3	161220969	161220969	+	Missense_Mutation	SNP	G	G	A	rs762554496	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673G>A	p.Ala225Thr	p.A225T	ENST00000327928	4/4	27	18	9	22	22	0	OTOL1,missense_variant,p.Ala225Thr,ENST00000327928,;	A	ENSG00000182447	ENST00000327928	Transcript	missense_variant	673	673	225	A/T	Gcc/Acc	rs762554496,COSM1040674	.	.	1	OTOL1	HGNC	34071	protein_coding	YES	CCDS46948.1	ENSP00000330808	OTOL1_HUMAN	.	UPI0000D61BA3	.	tolerated(0.42)	unknown(0)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24022,hmmpanther:PTHR24022:SF25	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGCCAAG	byFrequency	5	ESCA
MUC4	0	.	GRCh37	3	195506846	195506846	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11605C>T	p.His3869Tyr	p.H3869Y	ENST00000463781	2/25	158	113	45	115	115	0	MUC4,missense_variant,p.His3869Tyr,ENST00000463781,;MUC4,missense_variant,p.His3869Tyr,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,missense_variant,p.His3869Tyr,ENST00000470451,;MUC4,missense_variant,p.His3869Tyr,ENST00000477086,;MUC4,missense_variant,p.His3869Tyr,ENST00000466475,;MUC4,missense_variant,p.His3869Tyr,ENST00000478156,;MUC4,missense_variant,p.His3869Tyr,ENST00000479406,;MUC4,missense_variant,p.His3869Tyr,ENST00000477756,;MUC4,missense_variant,p.His3869Tyr,ENST00000462323,;MUC4,missense_variant,p.His3869Tyr,ENST00000480843,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,;	A	ENSG00000145113	ENST00000463781	Transcript	missense_variant	12065	11605	3869	H/Y	Cac/Tac	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	benign(0.158)	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGTGACCTG	.	5	ESCA
NBEAL2	0	.	GRCh37	3	47049918	47049918	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7865G>A	p.Arg2622His	p.R2622H	ENST00000450053	51/54	31	14	16	57	57	0	NBEAL2,missense_variant,p.Arg2622His,ENST00000450053,;NBEAL2,missense_variant,p.Arg2438His,ENST00000292309,;NBEAL2,missense_variant,p.Arg1910His,ENST00000416683,;NBEAL2,missense_variant,p.Arg871His,ENST00000383740,;NBEAL2,missense_variant,p.Arg961His,ENST00000443829,;NBEAL2,downstream_gene_variant,,ENST00000423436,;NBEAL2,non_coding_transcript_exon_variant,,ENST00000476095,;NBEAL2,non_coding_transcript_exon_variant,,ENST00000477412,;NBEAL2,downstream_gene_variant,,ENST00000486870,;NBEAL2,downstream_gene_variant,,ENST00000441027,;NBEAL2,downstream_gene_variant,,ENST00000469349,;NBEAL2,downstream_gene_variant,,ENST00000461036,;NRADDP,upstream_gene_variant,,ENST00000437305,;	A	ENSG00000160796	ENST00000450053	Transcript	missense_variant	8044	7865	2622	R/H	cGt/cAt	.	.	.	1	NBEAL2	HGNC	31928	protein_coding	YES	CCDS46817.1	ENSP00000415034	NBEL2_HUMAN	B4DVX0_HUMAN,B4DDY6_HUMAN	UPI000022C020	.	deleterious(0.04)	benign(0.072)	51/54	.	hmmpanther:PTHR13743:SF50,hmmpanther:PTHR13743,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAACGTCCTG	.	5	ESCA
BANK1	0	.	GRCh37	4	102984253	102984253	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2170G>C	p.Asp724His	p.D724H	ENST00000322953	13/17	30	21	9	55	55	0	BANK1,missense_variant,p.Asp591His,ENST00000508653,;BANK1,missense_variant,p.Asp591His,ENST00000428908,;BANK1,missense_variant,p.Asp709His,ENST00000504592,;BANK1,missense_variant,p.Asp694His,ENST00000444316,;BANK1,missense_variant,p.Asp724His,ENST00000322953,;BANK1,non_coding_transcript_exon_variant,,ENST00000504403,;	C	ENSG00000153064	ENST00000322953	Transcript	missense_variant	2444	2170	724	D/H	Gac/Cac	.	.	.	1	BANK1	HGNC	18233	protein_coding	YES	CCDS34038.1	ENSP00000320509	BANK1_HUMAN	.	UPI0000D6159D	.	deleterious(0.01)	probably_damaging(0.999)	13/17	.	hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACGAGACTGC	.	5	ESCA
TET2	0	.	GRCh37	4	106190855	106190855	+	Missense_Mutation	SNP	G	G	A	rs765853421	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4133G>A	p.Cys1378Tyr	p.C1378Y	ENST00000540549	9/11	17	5	12	27	27	0	TET2,missense_variant,p.Cys1378Tyr,ENST00000540549,;TET2,missense_variant,p.Cys1399Tyr,ENST00000513237,;TET2,missense_variant,p.Cys1378Tyr,ENST00000380013,;TET2,3_prime_UTR_variant,,ENST00000545826,;TET2,3_prime_UTR_variant,,ENST00000265149,;	A	ENSG00000168769	ENST00000540549	Transcript	missense_variant	4993	4133	1378	C/Y	tGt/tAt	rs765853421,COSM211731	.	.	1	TET2	HGNC	25941	protein_coding	YES	CCDS47120.1	ENSP00000442788	TET2_HUMAN	E7EPB1_HUMAN,D6RE87_HUMAN	UPI00001D75E4	.	deleterious(0)	probably_damaging(0.998)	9/11	.	hmmpanther:PTHR23358:SF3,hmmpanther:PTHR23358,Pfam_domain:PF12851	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.H1380Y|c.4138C>T|9	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTGTGCTC	.	5	ESCA
SCLT1	0	.	GRCh37	4	129864293	129864293	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1490A>T	p.Asn497Ile	p.N497I	ENST00000281142	17/21	40	16	24	67	67	0	SCLT1,missense_variant,p.Asn497Ile,ENST00000281142,;SCLT1,intron_variant,,ENST00000503215,;SCLT1,intron_variant,,ENST00000434680,;SCLT1,intron_variant,,ENST00000439369,;SCLT1,non_coding_transcript_exon_variant,,ENST00000502495,;SCLT1,non_coding_transcript_exon_variant,,ENST00000506233,;	A	ENSG00000151466	ENST00000281142	Transcript	missense_variant	1994	1490	497	N/I	aAt/aTt	.	.	.	-1	SCLT1	HGNC	26406	protein_coding	YES	CCDS3740.1	ENSP00000281142	SCLT1_HUMAN	.	UPI000013DC5F	.	deleterious(0.02)	benign(0.413)	17/21	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACATTTTGA	.	5	ESCA
MFSD10	0	.	GRCh37	4	2934143	2934143	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628T>C	p.Phe210Leu	p.F210L	ENST00000329687	5/12	30	21	9	42	42	0	MFSD10,missense_variant,p.Phe210Leu,ENST00000508221,;MFSD10,missense_variant,p.Phe210Leu,ENST00000507555,;MFSD10,missense_variant,p.Phe210Leu,ENST00000355443,;MFSD10,missense_variant,p.Phe210Leu,ENST00000514800,;MFSD10,missense_variant,p.Phe210Leu,ENST00000329687,;ADD1,downstream_gene_variant,,ENST00000398125,;ADD1,downstream_gene_variant,,ENST00000536424,;ADD1,downstream_gene_variant,,ENST00000541843,;ADD1,downstream_gene_variant,,ENST00000398123,;ADD1,downstream_gene_variant,,ENST00000446856,;ADD1,downstream_gene_variant,,ENST00000355842,;ADD1,downstream_gene_variant,,ENST00000514940,;ADD1,downstream_gene_variant,,ENST00000513328,;ADD1,downstream_gene_variant,,ENST00000398129,;ADD1,downstream_gene_variant,,ENST00000264758,;ADD1,downstream_gene_variant,,ENST00000503455,;NOP14-AS1,upstream_gene_variant,,ENST00000515194,;NOP14-AS1,upstream_gene_variant,,ENST00000503709,;NOP14-AS1,upstream_gene_variant,,ENST00000505731,;NOP14-AS1,upstream_gene_variant,,ENST00000507999,;NOP14-AS1,upstream_gene_variant,,ENST00000512712,;ADD1,downstream_gene_variant,,ENST00000538860,;MFSD10,splice_region_variant,,ENST00000503596,;MFSD10,3_prime_UTR_variant,,ENST00000507272,;MFSD10,non_coding_transcript_exon_variant,,ENST00000509676,;MFSD10,non_coding_transcript_exon_variant,,ENST00000512781,;MFSD10,upstream_gene_variant,,ENST00000514031,;MFSD10,upstream_gene_variant,,ENST00000508276,;ADD1,downstream_gene_variant,,ENST00000503062,;ADD1,downstream_gene_variant,,ENST00000513762,;	G	ENSG00000109736	ENST00000329687	Transcript	missense_variant	1163	628	210	F/L	Ttc/Ctc	.	.	.	-1	MFSD10	HGNC	16894	protein_coding	YES	CCDS3365.1	ENSP00000332646	MFS10_HUMAN	.	UPI0000073302	.	tolerated(0.73)	benign(0.023)	5/12	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Superfamily_domains:SSF103473,Gene3D:1.20.1250.20,Pfam_domain:PF07690,hmmpanther:PTHR24003,hmmpanther:PTHR24003:SF438,PROSITE_profiles:PS50850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGAAGAGCA	.	5	ESCA
APBB2	0	.	GRCh37	4	40895373	40895373	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1310C>T	p.Pro437Leu	p.P437L	ENST00000508593	11/18	74	58	16	86	86	0	APBB2,missense_variant,p.Pro415Leu,ENST00000513140,;APBB2,missense_variant,p.Pro436Leu,ENST00000295974,;APBB2,missense_variant,p.Pro415Leu,ENST00000506352,;APBB2,missense_variant,p.Pro406Leu,ENST00000513611,;APBB2,missense_variant,p.Pro437Leu,ENST00000508593,;APBB2,upstream_gene_variant,,ENST00000513493,;APBB2,upstream_gene_variant,,ENST00000512510,;APBB2,upstream_gene_variant,,ENST00000507831,;APBB2,non_coding_transcript_exon_variant,,ENST00000504484,;APBB2,non_coding_transcript_exon_variant,,ENST00000514094,;APBB2,non_coding_transcript_exon_variant,,ENST00000509475,;APBB2,downstream_gene_variant,,ENST00000511120,;	A	ENSG00000163697	ENST00000508593	Transcript	missense_variant	1854	1310	437	P/L	cCc/cTc	.	.	.	-1	APBB2	HGNC	582	protein_coding	YES	CCDS54762.1	ENSP00000427211	APBB2_HUMAN	Q5I0G1_HUMAN,D6RGD4_HUMAN,D6RDY3_HUMAN,D6RD19_HUMAN,D6RB55_HUMAN,D6RB00_HUMAN,D6RAJ4_HUMAN,D6RAE0_HUMAN,A8K1C3_HUMAN	UPI0001B8E1D4	.	deleterious(0.02)	probably_damaging(1)	11/18	.	Superfamily_domains:SSF50729,SMART_domains:SM00462,Gene3D:2.30.29.30,Pfam_domain:PF00640,hmmpanther:PTHR14058:SF11,hmmpanther:PTHR14058,PROSITE_profiles:PS01179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCGGGGGCG	.	5	ESCA
GABRB1	0	.	GRCh37	4	47427817	47427817	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1207C>T	p.Gln403Ter	p.Q403*	ENST00000295454	9/9	39	35	4	53	53	0	GABRB1,stop_gained,p.Gln333Ter,ENST00000538619,;GABRB1,stop_gained,p.Gln403Ter,ENST00000295454,;	T	ENSG00000163288	ENST00000295454	Transcript	stop_gained	1499	1207	403	Q/*	Cag/Tag	.	.	.	1	GABRB1	HGNC	4081	protein_coding	YES	CCDS3474.1	ENSP00000295454	GBRB1_HUMAN	D6REM0_HUMAN	UPI000012AFAC	.	.	.	9/9	.	hmmpanther:PTHR18945:SF198,hmmpanther:PTHR18945,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCATCCAGTAC	.	3	ESCA
SLC10A4	0	.	GRCh37	4	48490487	48490487	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.845T>C	p.Ile282Thr	p.I282T	ENST00000273861	3/3	31	22	9	54	54	0	SLC10A4,missense_variant,p.Ile282Thr,ENST00000273861,;ZAR1,upstream_gene_variant,,ENST00000327939,;	C	ENSG00000145248	ENST00000273861	Transcript	missense_variant	1064	845	282	I/T	aTa/aCa	.	.	.	1	SLC10A4	HGNC	22980	protein_coding	YES	CCDS3482.1	ENSP00000273861	NTCP4_HUMAN	.	UPI000006E8DB	.	tolerated(0.06)	benign(0.336)	3/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10361:SF20,hmmpanther:PTHR10361,Pfam_domain:PF01758	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	TTTCATAATGA	.	4	ESCA
EXOC1	0	.	GRCh37	4	56734599	56734599	+	Silent	SNP	C	C	T	rs750179198	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.513C>T	p.%3D	p.I171I	ENST00000381295	5/19	34	18	15	39	39	0	EXOC1,synonymous_variant,p.%3D,ENST00000381295,;EXOC1,synonymous_variant,p.%3D,ENST00000349598,;EXOC1,synonymous_variant,p.%3D,ENST00000346134,;EXOC1,non_coding_transcript_exon_variant,,ENST00000505501,;	T	ENSG00000090989	ENST00000381295	Transcript	synonymous_variant	861	513	171	I	atC/atT	rs750179198	.	.	1	EXOC1	HGNC	30380	protein_coding	YES	CCDS3502.1	ENSP00000370695	EXOC1_HUMAN	.	UPI000013574F	.	.	.	5/19	.	hmmpanther:PTHR16092,hmmpanther:PTHR16092:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATATCGAAAT	.	5	ESCA
ARHGAP24	0	.	GRCh37	4	86916404	86916404	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1597G>A	p.Asp533Asn	p.D533N	ENST00000395184	9/10	34	30	4	60	60	0	ARHGAP24,missense_variant,p.Asp440Asn,ENST00000264343,;ARHGAP24,missense_variant,p.Asp448Asn,ENST00000514229,;ARHGAP24,missense_variant,p.Asp533Asn,ENST00000395184,;ARHGAP24,missense_variant,p.Asp438Asn,ENST00000395183,;	A	ENSG00000138639	ENST00000395184	Transcript	missense_variant	2063	1597	533	D/N	Gat/Aat	.	.	.	1	ARHGAP24	HGNC	25361	protein_coding	YES	CCDS34025.1	ENSP00000378611	RHG24_HUMAN	D6RHH1_HUMAN,B3KUX7_HUMAN	UPI00001AF1D9	.	deleterious(0)	probably_damaging(0.99)	9/10	.	hmmpanther:PTHR13521,hmmpanther:PTHR13521:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|VARSCANS	CCTATGATAAT	.	2	ESCA
ADAMTS19	0	.	GRCh37	5	129072769	129072769	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3482C>G	p.Thr1161Ser	p.T1161S	ENST00000274487	23/23	30	11	18	51	51	0	ADAMTS19,missense_variant,p.Thr1161Ser,ENST00000274487,;CTC-575N7.1,intron_variant,,ENST00000503616,;ADAMTS19,downstream_gene_variant,,ENST00000509467,;	G	ENSG00000145808	ENST00000274487	Transcript	missense_variant	3627	3482	1161	T/S	aCt/aGt	.	.	.	1	ADAMTS19	HGNC	17111	protein_coding	YES	CCDS4146.1	ENSP00000274487	ATS19_HUMAN	.	UPI000013DA0D	.	deleterious(0.03)	possibly_damaging(0.474)	23/23	.	PROSITE_profiles:PS50900,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTGACTTTCA	.	4	ESCA
PWWP2A	0	.	GRCh37	5	159519671	159519671	+	Silent	SNP	C	C	T	.	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1986G>A	p.%3D	p.K662K	ENST00000307063	2/2	39	36	3	36	36	0	PWWP2A,synonymous_variant,p.%3D,ENST00000307063,;PWWP2A,intron_variant,,ENST00000523662,;PWWP2A,intron_variant,,ENST00000456329,;PWWP2A,intron_variant,,ENST00000524050,;PWWP2A,intron_variant,,ENST00000521424,;PWWP2A,downstream_gene_variant,,ENST00000520662,;	T	ENSG00000170234	ENST00000307063	Transcript	synonymous_variant	2021	1986	662	K	aaG/aaA	COSM1595172	.	.	-1	PWWP2A	HGNC	29406	protein_coding	YES	CCDS47332.1	ENSP00000305151	PWP2A_HUMAN	.	UPI0000EE3692	.	.	.	2/2	.	PROSITE_profiles:PS50812,hmmpanther:PTHR23068,hmmpanther:PTHR23068:SF4,Gene3D:2.30.30.160,Pfam_domain:PF00855,SMART_domains:SM00293,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATATCTTGGC	.	2	ESCA
FGFR4	0	.	GRCh37	5	176518014	176518014	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.512G>A	p.Arg171His	p.R171H	ENST00000292408	5/18	48	42	5	39	39	0	FGFR4,missense_variant,p.Arg171His,ENST00000393637,;FGFR4,missense_variant,p.Arg171His,ENST00000292410,;FGFR4,missense_variant,p.Arg171His,ENST00000502906,;FGFR4,missense_variant,p.Arg171His,ENST00000292408,;FGFR4,missense_variant,p.Arg171His,ENST00000393648,;FGFR4,missense_variant,p.Arg171His,ENST00000503708,;FGFR4,downstream_gene_variant,,ENST00000513166,;FGFR4,downstream_gene_variant,,ENST00000510911,;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,downstream_gene_variant,,ENST00000514472,;FGFR4,downstream_gene_variant,,ENST00000507708,;FGFR4,3_prime_UTR_variant,,ENST00000430285,;FGFR4,non_coding_transcript_exon_variant,,ENST00000509511,;FGFR4,non_coding_transcript_exon_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000483872,;FGFR4,upstream_gene_variant,,ENST00000508139,;	A	ENSG00000160867	ENST00000292408	Transcript	missense_variant	757	512	171	R/H	cGc/cAc	.	.	.	1	FGFR4	HGNC	3691	protein_coding	YES	CCDS4410.1	ENSP00000292408	FGFR4_HUMAN	G3JVM2_HUMAN,E7EWF4_HUMAN,D6RJD4_HUMAN,D6RG06_HUMAN,D6R9V0_HUMAN	UPI000012A72D	.	deleterious(0.01)	probably_damaging(1)	5/18	.	PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF312,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,PIRSF_domain:PIRSF000628,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTCCGCTGTC	.	4	ESCA
PDZD2	0	.	GRCh37	5	32108982	32108982	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*741G>A	.	.	ENST00000438447	25/25	26	15	11	39	39	0	PDZD2,3_prime_UTR_variant,,ENST00000438447,;PDZD2,3_prime_UTR_variant,,ENST00000282493,;CTD-2152M20.2,intron_variant,,ENST00000503441,;PDZD2,non_coding_transcript_exon_variant,,ENST00000513490,;PDZD2,downstream_gene_variant,,ENST00000510285,;PDZD2,downstream_gene_variant,,ENST00000515115,;PDZD2,downstream_gene_variant,,ENST00000397559,;	A	ENSG00000133401	ENST00000438447	Transcript	3_prime_UTR_variant	9649	.	.	.	.	.	.	.	1	PDZD2	HGNC	18486	protein_coding	YES	CCDS34137.1	ENSP00000402033	PDZD2_HUMAN	B4DGS3_HUMAN	UPI000069648B	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACAGAATAG	.	5	ESCA
GPR98	0	.	GRCh37	5	90001342	90001342	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8512C>G	p.Gln2838Glu	p.Q2838E	ENST00000405460	37/90	30	17	13	55	55	0	GPR98,missense_variant,p.Gln2838Glu,ENST00000405460,;GPR98,missense_variant,p.Gln404Glu,ENST00000509621,;	G	ENSG00000164199	ENST00000405460	Transcript	missense_variant	8608	8512	2838	Q/E	Caa/Gaa	.	.	.	1	GPR98	HGNC	17416	protein_coding	YES	CCDS47246.1	ENSP00000384582	GPR98_HUMAN	.	UPI00002127A7	.	.	possibly_damaging(0.848)	37/90	.	Superfamily_domains:SSF141072,Superfamily_domains:SSF141072,SMART_domains:SM00237,Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTACAAGAG	.	5	ESCA
L3MBTL3	0	.	GRCh37	6	130462127	130462127	+	3'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1229G>A	.	.	ENST00000529410	25/25	17	12	5	38	38	0	L3MBTL3,3_prime_UTR_variant,,ENST00000529410,;L3MBTL3,3_prime_UTR_variant,,ENST00000361794,;L3MBTL3,3_prime_UTR_variant,,ENST00000368139,;L3MBTL3,3_prime_UTR_variant,,ENST00000368136,;L3MBTL3,downstream_gene_variant,,ENST00000533560,;SAMD3,downstream_gene_variant,,ENST00000463253,;SAMD3,downstream_gene_variant,,ENST00000457563,;SAMD3,downstream_gene_variant,,ENST00000437477,;SAMD3,downstream_gene_variant,,ENST00000368134,;SAMD3,downstream_gene_variant,,ENST00000439090,;L3MBTL3,downstream_gene_variant,,ENST00000526019,;RP11-73O6.3,intron_variant,,ENST00000415964,;RP11-73O6.3,intron_variant,,ENST00000609978,;RP11-73O6.3,upstream_gene_variant,,ENST00000591297,;	A	ENSG00000198945	ENST00000529410	Transcript	3_prime_UTR_variant	4051	.	.	.	.	.	.	.	1	L3MBTL3	HGNC	23035	protein_coding	YES	CCDS34537.1	ENSP00000431962	LMBL3_HUMAN	E9PLL7_HUMAN	UPI00001C1E3E	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATGAAAAC	.	5	ESCA
LPA	0	.	GRCh37	6	160978445	160978445	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4790G>T	p.Ser1597Ile	p.S1597I	ENST00000447678	30/40	72	57	14	86	86	0	LPA,missense_variant,p.Ser1597Ile,ENST00000316300,;LPA,missense_variant,p.Ser1597Ile,ENST00000447678,;	A	ENSG00000198670	ENST00000447678	Transcript	missense_variant	4911	4790	1597	S/I	aGc/aTc	.	.	.	-1	LPA	HGNC	6667	protein_coding	YES	CCDS43523.1	ENSP00000395608	APOA_HUMAN	Q9UKJ7_HUMAN,Q9UIR8_HUMAN,Q9UIR6_HUMAN,Q9UIR5_HUMAN	UPI0000458AC9	.	deleterious(0.01)	probably_damaging(0.964)	30/40	.	hmmpanther:PTHR24261,Gene3D:2.40.20.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGCTTGGA	.	5	ESCA
HIST1H2BG	0	.	GRCh37	6	26216766	26216766	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.106G>A	p.Glu36Lys	p.E36K	ENST00000244601	1/1	84	69	14	93	93	0	HIST1H2BG,missense_variant,p.Glu36Lys,ENST00000244601,;HIST1H2AE,upstream_gene_variant,,ENST00000303910,;	T	ENSG00000187990	ENST00000244601	Transcript	missense_variant	107	106	36	E/K	Gag/Aag	.	.	.	-1	HIST1H2BG	HGNC	4746	protein_coding	YES	CCDS4594.1	ENSP00000244601	H2B1C_HUMAN	B2R4S9_HUMAN	UPI0000000C24	.	deleterious_low_confidence(0.01)	benign(0.145)	1/1	.	hmmpanther:PTHR23428,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCCTTAC	.	5	ESCA
HMGN4	0	.	GRCh37	6	26546306	26546306	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*599C>G	.	.	ENST00000377575	2/2	43	34	9	51	51	0	HMGN4,3_prime_UTR_variant,,ENST00000377575,;	G	ENSG00000182952	ENST00000377575	Transcript	3_prime_UTR_variant	1049	.	.	.	.	.	.	.	1	HMGN4	HGNC	4989	protein_coding	YES	CCDS4615.1	ENSP00000366798	HMGN4_HUMAN	.	UPI000013E3BB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTCTCTGA	.	5	ESCA
PKHD1	0	.	GRCh37	6	51523791	51523791	+	Silent	SNP	C	C	T	rs760027300	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11133G>A	p.%3D	p.G3711G	ENST00000371117	61/67	44	35	9	80	80	0	PKHD1,synonymous_variant,p.%3D,ENST00000371117,;	T	ENSG00000170927	ENST00000371117	Transcript	synonymous_variant	11409	11133	3711	G	ggG/ggA	rs760027300	.	.	-1	PKHD1	HGNC	9016	protein_coding	YES	CCDS4935.1	ENSP00000360158	PKHD1_HUMAN	.	UPI000013C4C0	.	.	.	61/67	.	hmmpanther:PTHR11915:SF230,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGCCCCGAT	.	5	ESCA
SENP6	0	.	GRCh37	6	76407199	76407199	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2254G>C	p.Glu752Gln	p.E752Q	ENST00000447266	18/24	33	27	5	57	57	0	SENP6,missense_variant,p.Glu348Gln,ENST00000541192,;SENP6,missense_variant,p.Glu745Gln,ENST00000370010,;SENP6,missense_variant,p.Glu752Gln,ENST00000370014,;SENP6,missense_variant,p.Glu752Gln,ENST00000447266,;SENP6,missense_variant,p.Glu368Gln,ENST00000503501,;SENP6,non_coding_transcript_exon_variant,,ENST00000474906,;	C	ENSG00000112701	ENST00000447266	Transcript	missense_variant	2732	2254	752	E/Q	Gag/Cag	.	.	.	1	SENP6	HGNC	20944	protein_coding	YES	CCDS47454.1	ENSP00000402527	SENP6_HUMAN	H0Y4F4_HUMAN	UPI0000141B65	.	tolerated(0.91)	probably_damaging(0.955)	18/24	.	PROSITE_profiles:PS50600,hmmpanther:PTHR12438:SF14,hmmpanther:PTHR12438,Pfam_domain:PF02902,Gene3D:1euvA02,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTGAGAAG	.	5	ESCA
FUT9	0	.	GRCh37	6	96656872	96656872	+	3'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4761C>T	.	.	ENST00000302103	3/3	61	48	13	86	86	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	T	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	6167	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATTCATATT	.	5	ESCA
CCNC	0	.	GRCh37	6	99997423	99997423	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559G>C	p.Asp187His	p.D187H	ENST00000520429	9/12	15	12	3	37	37	0	CCNC,missense_variant,p.Asp186His,ENST00000369220,;CCNC,missense_variant,p.Asp102His,ENST00000524049,;CCNC,missense_variant,p.Asp102His,ENST00000523985,;CCNC,missense_variant,p.Asp187His,ENST00000520371,;CCNC,missense_variant,p.Asp187His,ENST00000518714,;CCNC,missense_variant,p.Asp187His,ENST00000520429,;CCNC,missense_variant,p.Asp133His,ENST00000486428,;CCNC,missense_variant,p.Asp102His,ENST00000523799,;CCNC,downstream_gene_variant,,ENST00000369217,;CCNC,downstream_gene_variant,,ENST00000521017,;CCNC,missense_variant,p.Asp187His,ENST00000326298,;CCNC,3_prime_UTR_variant,,ENST00000523961,;CCNC,3_prime_UTR_variant,,ENST00000484049,;CCNC,non_coding_transcript_exon_variant,,ENST00000519617,;CCNC,downstream_gene_variant,,ENST00000523639,;	G	ENSG00000112237	ENST00000520429	Transcript	missense_variant	1005	559	187	D/H	Gat/Cat	.	.	.	-1	CCNC	HGNC	1581	protein_coding	YES	CCDS34502.1	ENSP00000428982	CCNC_HUMAN	Q7Z4L3_HUMAN,E5RIH8_HUMAN,E5RFX8_HUMAN	UPI0000169CFB	.	deleterious(0)	probably_damaging(1)	9/12	.	hmmpanther:PTHR10026,SMART_domains:SM00385,PIRSF_domain:PIRSF028758,Superfamily_domains:SSF47954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGATCCGTTC	.	2	ESCA
RNF148	0	.	GRCh37	7	122342776	122342776	+	Missense_Mutation	SNP	G	G	A	rs368198874	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29C>T	p.Thr10Met	p.T10M	ENST00000434824	1/1	31	16	14	46	46	0	RNF148,missense_variant,p.Thr10Met,ENST00000447240,;RNF148,missense_variant,p.Thr10Met,ENST00000434824,;CADPS2,intron_variant,,ENST00000334010,;CADPS2,intron_variant,,ENST00000449022,;CADPS2,intron_variant,,ENST00000313070,;CADPS2,intron_variant,,ENST00000412584,;RNF133,upstream_gene_variant,,ENST00000340112,;	A	ENSG00000235631	ENST00000434824	Transcript	missense_variant	246	29	10	T/M	aCg/aTg	rs368198874	.	.	-1	RNF148	HGNC	22411	protein_coding	YES	CCDS47692.1	ENSP00000388207	RN148_HUMAN	A4D0X4_HUMAN	UPI000006FF1E	.	tolerated(0.06)	benign(0.151)	1/1	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22765:SF31,hmmpanther:PTHR22765	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGCGTCGAA	byFrequency|byCluster	5	ESCA
CNOT4	0	.	GRCh37	7	135047165	135047165	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*472A>G	.	.	ENST00000541284	12/12	19	14	5	30	30	0	CNOT4,3_prime_UTR_variant,,ENST00000541284,;CNOT4,3_prime_UTR_variant,,ENST00000451834,;CNOT4,3_prime_UTR_variant,,ENST00000423368,;CNOT4,downstream_gene_variant,,ENST00000361528,;CNOT4,downstream_gene_variant,,ENST00000473470,;	C	ENSG00000080802	ENST00000541284	Transcript	3_prime_UTR_variant	2945	.	.	.	.	.	.	.	-1	CNOT4	HGNC	7880	protein_coding	YES	CCDS55165.1	ENSP00000445508	CNOT4_HUMAN	.	UPI00004166A8	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTGAATACAAG	.	4	ESCA
TAS2R60	0	.	GRCh37	7	143141198	143141198	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.653C>T	p.Thr218Ile	p.T218I	ENST00000332690	1/1	33	30	3	21	21	0	TAS2R60,missense_variant,p.Thr218Ile,ENST00000332690,;EPHA1-AS1,intron_variant,,ENST00000429289,;	T	ENSG00000185899	ENST00000332690	Transcript	missense_variant	653	653	218	T/I	aCa/aTa	.	.	.	1	TAS2R60	HGNC	20639	protein_coding	YES	CCDS5885.1	ENSP00000327724	T2R60_HUMAN	Q50KC8_HUMAN	UPI000000D824	.	tolerated(0.48)	benign(0.038)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF32,Pfam_domain:PF05296,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCACATCTC	.	2	ESCA
RBM33	0	.	GRCh37	7	155569733	155569733	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1998G>C	.	.	ENST00000401878	18/18	12	6	6	15	15	0	RBM33,3_prime_UTR_variant,,ENST00000401878,;RBM33,3_prime_UTR_variant,,ENST00000341148,;RBM33,downstream_gene_variant,,ENST00000392755,;	C	ENSG00000184863	ENST00000401878	Transcript	3_prime_UTR_variant	5709	.	.	.	.	.	.	.	1	RBM33	HGNC	27223	protein_coding	YES	CCDS5941.2	ENSP00000384160	RBM33_HUMAN	C9J7M3_HUMAN	UPI00015743D7	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATGAGTTTCA	.	2	ESCA
MEOX2	0	.	GRCh37	7	15725593	15725593	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435G>A	p.%3D	p.A145A	ENST00000262041	1/3	59	36	23	52	52	0	MEOX2,synonymous_variant,p.%3D,ENST00000262041,;AC005550.5,downstream_gene_variant,,ENST00000438923,;AC005550.4,upstream_gene_variant,,ENST00000442176,;AC005550.3,downstream_gene_variant,,ENST00000451240,;	T	ENSG00000106511	ENST00000262041	Transcript	synonymous_variant	845	435	145	A	gcG/gcA	.	.	.	-1	MEOX2	HGNC	7014	protein_coding	YES	CCDS34605.1	ENSP00000262041	MEOX2_HUMAN	Q6FHY5_HUMAN,A4D127_HUMAN	UPI000013D247	.	.	.	1/3	.	hmmpanther:PTHR24328:SF1,hmmpanther:PTHR24328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGGCGCGCA	.	5	ESCA
TBX20	0	.	GRCh37	7	35242238	35242238	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1148T>C	p.Ile383Thr	p.I383T	ENST00000408931	8/8	73	47	25	82	82	0	TBX20,missense_variant,p.Ile383Thr,ENST00000408931,;	G	ENSG00000164532	ENST00000408931	Transcript	missense_variant	1675	1148	383	I/T	aTc/aCc	.	.	.	-1	TBX20	HGNC	11598	protein_coding	YES	CCDS43568.1	ENSP00000386170	TBX20_HUMAN	C1INI6_HUMAN,C1INI5_HUMAN,C1INI4_HUMAN,C1INI3_HUMAN,C1INI2_HUMAN,C1INI1_HUMAN	UPI00004B23D3	.	deleterious_low_confidence(0.03)	benign(0.016)	8/8	.	hmmpanther:PTHR11267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGATGGGG	.	5	ESCA
KIAA0895	0	.	GRCh37	7	36406352	36406352	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179-9153G>A	.	.	ENST00000297063	.	54	45	9	51	51	0	KIAA0895,missense_variant,p.Glu34Lys,ENST00000415803,;KIAA0895,missense_variant,p.Glu34Lys,ENST00000338533,;KIAA0895,intron_variant,,ENST00000436884,;KIAA0895,intron_variant,,ENST00000317020,;KIAA0895,intron_variant,,ENST00000297063,;KIAA0895,intron_variant,,ENST00000429651,;KIAA0895,intron_variant,,ENST00000431396,;KIAA0895,intron_variant,,ENST00000440378,;KIAA0895,intron_variant,,ENST00000453212,;KIAA0895,intron_variant,,ENST00000480192,;KIAA0895,intron_variant,,ENST00000483360,;KIAA0895,intron_variant,,ENST00000483526,;KIAA0895,intron_variant,,ENST00000493327,;	T	ENSG00000164542	ENST00000297063	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KIAA0895	HGNC	22206	protein_coding	YES	CCDS43570.1	ENSP00000297063	K0895_HUMAN	.	UPI000013E3C0	.	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCTTCCC	.	5	ESCA
MMD2	0	.	GRCh37	7	4947197	4947197	+	Missense_Mutation	SNP	C	C	T	rs375097927	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.643G>A	p.Gly215Arg	p.G215R	ENST00000404774	7/7	42	27	15	23	23	0	MMD2,missense_variant,p.Gly191Arg,ENST00000401401,;MMD2,missense_variant,p.Gly215Arg,ENST00000404774,;MMD2,3_prime_UTR_variant,,ENST00000406755,;	T	ENSG00000136297	ENST00000404774	Transcript	missense_variant	838	643	215	G/R	Gga/Aga	rs375097927	.	.	-1	MMD2	HGNC	30133	protein_coding	YES	CCDS47529.1	ENSP00000384690	PAQRA_HUMAN	.	UPI000016199F	.	deleterious(0.01)	probably_damaging(0.99)	7/7	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR20855,hmmpanther:PTHR20855:SF21,Pfam_domain:PF03006	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCCGGTCA	byFrequency|byCluster	5	ESCA
IKZF1	0	.	GRCh37	7	50467846	50467846	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.955T>A	p.Ser319Thr	p.S319T	ENST00000439701	7/7	34	19	15	27	27	0	IKZF1,missense_variant,p.Ser361Thr,ENST00000331340,;IKZF1,missense_variant,p.Ser218Thr,ENST00000349824,;IKZF1,missense_variant,p.Ser274Thr,ENST00000343574,;IKZF1,missense_variant,p.Ser131Thr,ENST00000346667,;IKZF1,missense_variant,p.Ser274Thr,ENST00000357364,;IKZF1,missense_variant,p.Ser274Thr,ENST00000438033,;IKZF1,missense_variant,p.Ser319Thr,ENST00000359197,;IKZF1,missense_variant,p.Ser319Thr,ENST00000439701,;IKZF1,3_prime_UTR_variant,,ENST00000440768,;IKZF1,downstream_gene_variant,,ENST00000426121,;IKZF1,non_coding_transcript_exon_variant,,ENST00000471793,;	A	ENSG00000185811	ENST00000439701	Transcript	missense_variant	1154	955	319	S/T	Tcc/Acc	.	.	.	1	IKZF1	HGNC	13176	protein_coding	YES	CCDS59055.1	ENSP00000413025	IKZF1_HUMAN	.	UPI000002ABBE	.	tolerated(0.53)	benign(0.002)	7/7	.	hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.?|c.161-?_1560+?del|29	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCGCTCCAAC	.	5	ESCA
PCLO	0	.	GRCh37	7	82544283	82544283	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13019C>G	p.Thr4340Ser	p.T4340S	ENST00000333891	7/25	58	38	20	73	73	0	PCLO,missense_variant,p.Thr1060Ser,ENST00000437081,;PCLO,missense_variant,p.Thr4340Ser,ENST00000333891,;PCLO,missense_variant,p.Thr4340Ser,ENST00000423517,;	C	ENSG00000186472	ENST00000333891	Transcript	missense_variant	13357	13019	4340	T/S	aCc/aGc	COSM3641002,COSM3641003	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	7/25	.	hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTGGTCGGC	.	5	ESCA
STEAP4	0	.	GRCh37	7	87913329	87913329	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256T>G	p.Tyr86Asp	p.Y86D	ENST00000380079	2/5	90	59	30	87	87	0	STEAP4,missense_variant,p.Tyr86Asp,ENST00000301959,;STEAP4,missense_variant,p.Tyr86Asp,ENST00000380079,;STEAP4,missense_variant,p.Tyr86Asp,ENST00000414498,;AC003991.3,intron_variant,,ENST00000595121,;AC003991.3,intron_variant,,ENST00000434733,;AC003991.3,intron_variant,,ENST00000447758,;AC003991.3,intron_variant,,ENST00000600908,;	C	ENSG00000127954	ENST00000380079	Transcript	missense_variant	358	256	86	Y/D	Tat/Gat	.	.	.	-1	STEAP4	HGNC	21923	protein_coding	YES	CCDS43611.1	ENSP00000369419	STEA4_HUMAN	.	UPI000003C39A	.	deleterious(0)	probably_damaging(0.991)	2/5	.	hmmpanther:PTHR14239,hmmpanther:PTHR14239:SF5,Pfam_domain:PF03807,Gene3D:3.40.50.720,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCATAATGCT	.	5	ESCA
ASAP1	0	.	GRCh37	8	131414169	131414169	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21G>C	p.Arg7Ser	p.R7S	ENST00000357668	1/29	59	47	12	28	28	0	ASAP1,missense_variant,p.Arg7Ser,ENST00000518721,;ASAP1,missense_variant,p.Arg7Ser,ENST00000357668,;ASAP1,upstream_gene_variant,,ENST00000520625,;ASAP1,missense_variant,p.Arg7Ser,ENST00000524299,;ASAP1,missense_variant,p.Arg7Ser,ENST00000520927,;ASAP1,missense_variant,p.Arg7Ser,ENST00000521075,;	G	ENSG00000153317	ENST00000357668	Transcript	missense_variant	49	21	7	R/S	agG/agC	.	.	.	-1	ASAP1	HGNC	2720	protein_coding	YES	CCDS6362.1	ENSP00000350297	ASAP1_HUMAN	E5RFD9_HUMAN	UPI0000351D6E	.	deleterious_low_confidence(0)	unknown(0)	1/29	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAGCCTGGA	.	5	ESCA
ARFGEF1	0	.	GRCh37	8	68163627	68163627	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2757C>T	p.%3D	p.A919A	ENST00000262215	19/39	84	80	4	87	87	0	ARFGEF1,synonymous_variant,p.%3D,ENST00000262215,;ARFGEF1,synonymous_variant,p.%3D,ENST00000520381,;	A	ENSG00000066777	ENST00000262215	Transcript	synonymous_variant	3147	2757	919	A	gcC/gcT	.	.	.	-1	ARFGEF1	HGNC	15772	protein_coding	YES	CCDS6199.1	ENSP00000262215	BIG1_HUMAN	E5RJN9_HUMAN,E5RJB2_HUMAN,E5RHZ1_HUMAN,B3KMS9_HUMAN	UPI000013D275	.	.	.	19/39	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCTTGGCCAT	.	2	ESCA
ZFHX4	0	.	GRCh37	8	77775618	77775618	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9668C>T	p.Ser3223Leu	p.S3223L	ENST00000521891	11/11	49	32	17	39	39	0	ZFHX4,missense_variant,p.Ser3178Leu,ENST00000455469,;ZFHX4,missense_variant,p.Ser3197Leu,ENST00000518282,;ZFHX4,missense_variant,p.Ser3174Leu,ENST00000050961,;ZFHX4,missense_variant,p.Ser3223Leu,ENST00000521891,;	T	ENSG00000091656	ENST00000521891	Transcript	missense_variant	10116	9668	3223	S/L	tCa/tTa	.	.	.	1	ZFHX4	HGNC	30939	protein_coding	YES	CCDS47878.2	ENSP00000430497	.	Q9H7F3_HUMAN,Q86WW5_HUMAN,Q6DK57_HUMAN,G3V138_HUMAN,E5RI93_HUMAN,E5RHS1_HUMAN,E5RGK3_HUMAN,E5RG79_HUMAN	UPI0000424CC7	.	.	probably_damaging(0.974)	11/11	.	hmmpanther:PTHR24208:SF40,hmmpanther:PTHR24208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTCATCTG	.	5	ESCA
FABP5	0	.	GRCh37	8	82192800	82192800	+	5'UTR	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-31C>T	.	.	ENST00000297258	1/4	92	59	33	69	69	0	FABP5,5_prime_UTR_variant,,ENST00000297258,;FABP5,upstream_gene_variant,,ENST00000396359,;RP11-363E6.4,upstream_gene_variant,,ENST00000606235,;RP11-363E6.3,intron_variant,,ENST00000518880,;RP11-363E6.3,intron_variant,,ENST00000517670,;FABP5,upstream_gene_variant,,ENST00000486269,;FABP5,upstream_gene_variant,,ENST00000481695,;	T	ENSG00000164687	ENST00000297258	Transcript	5_prime_UTR_variant	203	.	.	.	.	.	.	.	1	FABP5	HGNC	3560	protein_coding	YES	CCDS6228.1	ENSP00000297258	FABP5_HUMAN	I6L8B7_HUMAN,E7DVW5_HUMAN	UPI000004068E	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCCCTCTCT	.	5	ESCA
WWP1	0	.	GRCh37	8	87393820	87393820	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296T>A	p.Ile99Lys	p.I99K	ENST00000517970	5/25	53	38	15	51	51	0	WWP1,missense_variant,p.Ile99Lys,ENST00000341922,;WWP1,missense_variant,p.Ile99Lys,ENST00000517970,;WWP1,missense_variant,p.Ile99Lys,ENST00000265428,;WWP1,intron_variant,,ENST00000349423,;WWP1,non_coding_transcript_exon_variant,,ENST00000523863,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,;	A	ENSG00000123124	ENST00000517970	Transcript	missense_variant	603	296	99	I/K	aTa/aAa	.	.	.	1	WWP1	HGNC	17004	protein_coding	YES	CCDS6242.1	ENSP00000427793	WWP1_HUMAN	H0YBS9_HUMAN	UPI0000035537	.	deleterious(0)	benign(0.115)	5/25	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,Gene3D:2.60.40.150,SMART_domains:SM00239,PIRSF_domain:PIRSF001569,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACGATAGATT	.	5	ESCA
ZNF618	0	.	GRCh37	9	116791119	116791119	+	Intron	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.809-3809G>A	.	.	ENST00000288466	.	106	94	12	70	70	0	ZNF618,synonymous_variant,p.%3D,ENST00000374124,;ZNF618,synonymous_variant,p.%3D,ENST00000374126,;ZNF618,intron_variant,,ENST00000452710,;ZNF618,intron_variant,,ENST00000288466,;ZNF618,non_coding_transcript_exon_variant,,ENST00000470105,;ZNF618,non_coding_transcript_exon_variant,,ENST00000481558,;	A	ENSG00000157657	ENST00000288466	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZNF618	HGNC	29416	protein_coding	YES	CCDS48008.1	ENSP00000288466	ZN618_HUMAN	.	UPI0000D4BD81	.	.	.	.	10/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CAGACGAACCA	.	3	ESCA
ADAMTS13	0	.	GRCh37	9	136307831	136307831	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2201C>G	p.Pro734Arg	p.P734R	ENST00000371929	18/29	32	15	16	41	41	0	ADAMTS13,missense_variant,p.Pro734Arg,ENST00000355699,;ADAMTS13,missense_variant,p.Pro703Arg,ENST00000356589,;ADAMTS13,missense_variant,p.Pro734Arg,ENST00000371929,;ADAMTS13,3_prime_UTR_variant,,ENST00000371916,;ADAMTS13,intron_variant,,ENST00000536611,;ADAMTS13,intron_variant,,ENST00000485925,;ADAMTS13,intron_variant,,ENST00000495234,;ADAMTS13,intron_variant,,ENST00000474918,;	G	ENSG00000160323	ENST00000371929	Transcript	missense_variant	2645	2201	734	P/R	cCa/cGa	.	.	.	1	ADAMTS13	HGNC	1366	protein_coding	YES	CCDS6970.1	ENSP00000360997	ATS13_HUMAN	Q6QNA4_HUMAN,B3KWF7_HUMAN	UPI0000000DAD	.	tolerated(0.27)	benign(0.284)	18/29	.	hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF161,SMART_domains:SM00209	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCCAGAGG	.	5	ESCA
CER1	0	.	GRCh37	9	14719960	14719960	+	3'UTR	SNP	A	A	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128T>A	.	.	ENST00000380911	2/2	19	2	17	17	17	0	CER1,3_prime_UTR_variant,,ENST00000380911,;	T	ENSG00000147869	ENST00000380911	Transcript	3_prime_UTR_variant	977	.	.	.	.	.	.	.	-1	CER1	HGNC	1862	protein_coding	YES	CCDS6476.1	ENSP00000370297	CER1_HUMAN	.	UPI0000051056	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TTCTAATTTAA	.	4	ESCA
HAUS7	0	.	GRCh37	X	152721028	152721028	+	Missense_Mutation	SNP	G	G	A	rs201262645	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932C>T	p.Thr311Met	p.T311M	ENST00000370211	8/10	44	11	33	40	40	0	HAUS7,missense_variant,p.Thr311Met,ENST00000370211,;HAUS7,missense_variant,p.Thr95Met,ENST00000435662,;HAUS7,missense_variant,p.Thr311Met,ENST00000370212,;HAUS7,missense_variant,p.Arg133Cys,ENST00000421080,;TREX2,5_prime_UTR_variant,,ENST00000330912,;TREX2,5_prime_UTR_variant,,ENST00000370232,;TREX2,5_prime_UTR_variant,,ENST00000334497,;TREX2,5_prime_UTR_variant,,ENST00000338525,;HAUS7,non_coding_transcript_exon_variant,,ENST00000490165,;HAUS7,non_coding_transcript_exon_variant,,ENST00000484394,;HAUS7,non_coding_transcript_exon_variant,,ENST00000460898,;HAUS7,non_coding_transcript_exon_variant,,ENST00000491286,;HAUS7,downstream_gene_variant,,ENST00000490453,;HAUS7,upstream_gene_variant,,ENST00000437046,;HAUS7,downstream_gene_variant,,ENST00000464993,;	A	ENSG00000213397	ENST00000370211	Transcript	missense_variant	976	932	311	T/M	aCg/aTg	rs201262645	.	.	-1	HAUS7	HGNC	32979	protein_coding	YES	CCDS35438.1	ENSP00000359230	HAUS7_HUMAN	.	UPI00000731E0	.	deleterious(0)	benign(0.347)	8/10	.	hmmpanther:PTHR14352:SF2,hmmpanther:PTHR14352	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.T311T|c.933G>A|3	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGTGCGTGGCC	byCluster	4	ESCA
CTAG2	0	.	GRCh37	X	153881746	153881746	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44C>T	p.Ala15Val	p.A15V	ENST00000247306	1/2	16	12	4	26	26	0	CTAG2,missense_variant,p.Ala15Val,ENST00000369585,;CTAG2,missense_variant,p.Ala15Val,ENST00000247306,;AF277315.13,upstream_gene_variant,,ENST00000442033,;	A	ENSG00000126890	ENST00000247306	Transcript	missense_variant	108	44	15	A/V	gCt/gTt	.	.	.	-1	CTAG2	HGNC	2492	protein_coding	YES	CCDS14759.1	ENSP00000247306	CTAG2_HUMAN	.	UPI000003337A	.	deleterious_low_confidence(0)	unknown(0)	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31283,hmmpanther:PTHR31283:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CATCAGCATCG	.	3	ESCA
FTHL17	0	.	GRCh37	X	31090038	31090038	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33G>A	p.%3D	p.Q11Q	ENST00000359202	1/1	10	4	5	13	13	0	FTHL17,synonymous_variant,p.%3D,ENST00000359202,;	T	ENSG00000132446	ENST00000359202	Transcript	synonymous_variant	133	33	11	Q	caG/caA	.	.	.	-1	FTHL17	HGNC	3987	protein_coding	YES	CCDS14227.1	ENSP00000368207	FHL17_HUMAN	.	UPI00000421FF	.	.	.	1/1	.	PROSITE_profiles:PS50905,hmmpanther:PTHR11431:SF33,hmmpanther:PTHR11431,Gene3D:1.20.1260.10,Superfamily_domains:SSF47240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACTTCTGGCG	.	3	ESCA
UBQLN2	0	.	GRCh37	X	56591895	56591895	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1589C>G	p.Ser530Cys	p.S530C	ENST00000338222	1/1	19	7	12	36	36	0	UBQLN2,missense_variant,p.Ser530Cys,ENST00000338222,;	G	ENSG00000188021	ENST00000338222	Transcript	missense_variant	1870	1589	530	S/C	tCt/tGt	.	.	.	1	UBQLN2	HGNC	12509	protein_coding	YES	CCDS14374.1	ENSP00000345195	UBQL2_HUMAN	.	UPI000004A059	.	deleterious(0.02)	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCTCTGGTG	.	5	ESCA
ZC3H12B	0	.	GRCh37	X	64709053	64709053	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FQ-01A-31D-A387-09	TCGA-LN-A9FQ-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372G>A	p.%3D	p.Q124Q	ENST00000338957	1/5	10	2	8	14	14	0	ZC3H12B,synonymous_variant,p.%3D,ENST00000423889,;ZC3H12B,synonymous_variant,p.%3D,ENST00000338957,;	A	ENSG00000102053	ENST00000338957	Transcript	synonymous_variant	439	372	124	Q	caG/caA	.	.	.	1	ZC3H12B	HGNC	17407	protein_coding	YES	CCDS48131.2	ENSP00000340839	.	E9PAJ6_HUMAN	UPI00001D7BEA	.	.	.	1/5	.	hmmpanther:PTHR12876:SF27,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAACAGATTCA	.	3	ESCA
TTC40	0	.	GRCh37	10	134690433	134690433	+	Silent	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4245A>G	p.%3D	p.E1415E	ENST00000368586	31/58	20	14	5	56	56	0	TTC40,synonymous_variant,p.%3D,ENST00000368582,;TTC40,synonymous_variant,p.%3D,ENST00000368586,;TTC40,upstream_gene_variant,,ENST00000417862,;	C	ENSG00000171811	ENST00000368586	Transcript	synonymous_variant	4346	4245	1415	E	gaA/gaG	.	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	.	.	31/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTCTTCCAG	.	5	ESCA
SNCG	0	.	GRCh37	10	88722801	88722801	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*59C>A	.	.	ENST00000372017	5/5	17	11	5	38	38	0	SNCG,3_prime_UTR_variant,,ENST00000372017,;SNCG,3_prime_UTR_variant,,ENST00000348795,;MMRN2,intron_variant,,ENST00000474994,;MMRN2,intron_variant,,ENST00000609457,;ADIRF-AS1,downstream_gene_variant,,ENST00000440490,;ADIRF-AS1,downstream_gene_variant,,ENST00000609111,;ADIRF-AS1,downstream_gene_variant,,ENST00000418273,;SNCG,non_coding_transcript_exon_variant,,ENST00000483064,;SNCG,downstream_gene_variant,,ENST00000465679,;ADIRF-AS1,downstream_gene_variant,,ENST00000609170,;	A	ENSG00000173267	ENST00000372017	Transcript	3_prime_UTR_variant	485	.	.	.	.	.	.	.	1	SNCG	HGNC	11141	protein_coding	YES	CCDS7380.1	ENSP00000361087	SYUG_HUMAN	Q6FHG5_HUMAN	UPI0000169F48	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCCCTCCT	.	5	ESCA
PLCE1	0	.	GRCh37	10	95892039	95892039	+	Missense_Mutation	SNP	G	G	T	rs201727715	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315G>T	p.Gly439Cys	p.G439C	ENST00000371380	2/32	21	15	6	46	46	0	PLCE1,missense_variant,p.Gly439Cys,ENST00000371380,;PLCE1,missense_variant,p.Gly439Cys,ENST00000260766,;PLCE1,missense_variant,p.Gly131Cys,ENST00000371375,;PLCE1,missense_variant,p.Gly131Cys,ENST00000371385,;	T	ENSG00000138193	ENST00000371380	Transcript	missense_variant	1550	1315	439	G/C	Ggt/Tgt	rs201727715,COSM1646367,COSM686044,COSM1146514	.	.	1	PLCE1	HGNC	17175	protein_coding	YES	CCDS41552.1	ENSP00000360431	PLCE1_HUMAN	B7ZM61_HUMAN	UPI00001F93EE	.	deleterious_low_confidence(0)	benign(0.013)	2/32	.	Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGTTGGTCCA	.	5	ESCA
MRGPRX4	0	.	GRCh37	11	18195433	18195433	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630G>A	p.%3D	p.P210P	ENST00000314254	1/1	67	63	4	79	79	0	MRGPRX4,synonymous_variant,p.%3D,ENST00000314254,;RP11-113D6.6,intron_variant,,ENST00000527671,;	A	ENSG00000179817	ENST00000314254	Transcript	synonymous_variant	1050	630	210	P	ccG/ccA	.	.	.	1	MRGPRX4	HGNC	17617	protein_coding	YES	CCDS7831.1	ENSP00000314042	MRGX4_HUMAN	.	UPI0000061F60	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF23,hmmpanther:PTHR11334,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCCGCTGAC	.	2	ESCA
SPTY2D1-AS1	0	.	GRCh37	11	18621528	18621528	+	RNA	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.195C>T	.	.	ENST00000501599	1/5	66	38	27	78	78	0	SPTY2D1-AS1,non_coding_transcript_exon_variant,,ENST00000511927,;SPTY2D1-AS1,non_coding_transcript_exon_variant,,ENST00000501599,;RP11-504G3.4,upstream_gene_variant,,ENST00000534919,;RP11-504G3.4,upstream_gene_variant,,ENST00000541939,;SPTY2D1-AS1,upstream_gene_variant,,ENST00000542172,;RP11-504G3.4,upstream_gene_variant,,ENST00000540985,;	T	ENSG00000247595	ENST00000501599	Transcript	non_coding_transcript_exon_variant	195	.	.	.	.	.	.	.	1	SPTY2D1-AS1	HGNC	44122	antisense	YES	.	.	.	.	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCACGTTTC	.	5	ESCA
SLC1A2	0	.	GRCh37	11	35440593	35440593	+	5'UTR	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-80C>T	.	.	ENST00000278379	1/11	36	25	11	77	77	0	SLC1A2,5_prime_UTR_variant,,ENST00000606205,;SLC1A2,5_prime_UTR_variant,,ENST00000278379,;SLC1A2,intron_variant,,ENST00000449068,;SLC1A2,intron_variant,,ENST00000395753,;SLC1A2,intron_variant,,ENST00000395750,;RP4-683L5.1,upstream_gene_variant,,ENST00000534165,;	A	ENSG00000110436	ENST00000278379	Transcript	5_prime_UTR_variant	204	.	.	.	.	.	.	.	-1	SLC1A2	HGNC	10940	protein_coding	YES	CCDS31459.1	ENSP00000278379	EAA2_HUMAN	A2A2U1_HUMAN	UPI0000129B12	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGCGAAGTG	.	5	ESCA
OR8H3	0	.	GRCh37	11	55889986	55889986	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138G>T	p.Met46Ile	p.M46I	ENST00000313472	1/1	70	53	17	108	108	0	OR8H3,missense_variant,p.Met46Ile,ENST00000313472,;	T	ENSG00000181761	ENST00000313472	Transcript	missense_variant	138	138	46	M/I	atG/atT	.	.	.	1	OR8H3	HGNC	15309	protein_coding	YES	CCDS31519.1	ENSP00000323928	OR8H3_HUMAN	.	UPI0000041D25	.	deleterious(0.05)	benign(0.125)	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452:SF280,hmmpanther:PTHR26452,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGATGCTATT	.	5	ESCA
OSBP	0	.	GRCh37	11	59376070	59376070	+	Missense_Mutation	SNP	G	G	A	rs770463074	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.709C>T	p.Arg237Cys	p.R237C	ENST00000263847	3/14	32	26	5	41	41	0	OSBP,missense_variant,p.Arg237Cys,ENST00000263847,;	A	ENSG00000110048	ENST00000263847	Transcript	missense_variant	1189	709	237	R/C	Cgt/Tgt	rs770463074	.	.	-1	OSBP	HGNC	8503	protein_coding	YES	CCDS7974.1	ENSP00000263847	OSBP1_HUMAN	B4DR25_HUMAN	UPI0000130EAF	.	deleterious(0)	possibly_damaging(0.8)	3/14	.	hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF52	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACGCTGCA	.	5	ESCA
ALDH3B1	0	.	GRCh37	11	67786319	67786319	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348G>A	p.%3D	p.P116P	ENST00000539229	5/13	24	20	3	34	34	0	ALDH3B1,synonymous_variant,p.%3D,ENST00000342456,;ALDH3B1,synonymous_variant,p.%3D,ENST00000539229,;ALDH3B1,synonymous_variant,p.%3D,ENST00000007633,;ALDH3B1,synonymous_variant,p.%3D,ENST00000316367,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000530046,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000526609,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000531459,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000433100,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000434449,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000527179,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000525518,;ALDH3B1,upstream_gene_variant,,ENST00000527514,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000529232,;	A	ENSG00000006534	ENST00000539229	Transcript	synonymous_variant	464	348	116	P	ccG/ccA	.	.	.	1	ALDH3B1	HGNC	410	protein_coding	YES	.	ENSP00000474034	AL3B1_HUMAN	S4R3R5_HUMAN	UPI000045652C	.	.	.	5/13	.	hmmpanther:PTHR11699:SF147,hmmpanther:PTHR11699,Pfam_domain:PF00171,Gene3D:3.40.605.10,PIRSF_domain:PIRSF036492,Superfamily_domains:SSF53720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TATCCGCTGAA	.	2	ESCA
MED13L	0	.	GRCh37	12	116429734	116429734	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3025G>T	p.Asp1009Tyr	p.D1009Y	ENST00000281928	17/31	21	16	5	35	35	0	MED13L,missense_variant,p.Asp1009Tyr,ENST00000281928,;	A	ENSG00000123066	ENST00000281928	Transcript	missense_variant	3232	3025	1009	D/Y	Gat/Tat	.	.	.	-1	MED13L	HGNC	22962	protein_coding	YES	CCDS9177.1	ENSP00000281928	MD13L_HUMAN	Q9H6Z7_HUMAN	UPI0000241C1E	.	deleterious(0)	unknown(0)	17/31	.	hmmpanther:PTHR12950,hmmpanther:PTHR12950:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGATCTGCTA	.	5	ESCA
HCAR3	0	.	GRCh37	12	123201265	123201265	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20A>G	p.Gln7Arg	p.Q7R	ENST00000528880	1/1	31	24	7	69	69	0	HCAR3,missense_variant,p.Gln7Arg,ENST00000528880,;HCAR1,intron_variant,,ENST00000356987,;RP11-324E6.6,downstream_gene_variant,,ENST00000543611,;RP11-324E6.6,downstream_gene_variant,,ENST00000545293,;	C	ENSG00000255398	ENST00000528880	Transcript	missense_variant	175	20	7	Q/R	cAg/cGg	.	.	.	-1	HCAR3	HGNC	16824	protein_coding	YES	CCDS53842.1	ENSP00000436714	HCAR3_HUMAN	.	UPI00001AFD35	.	deleterious_low_confidence(0.05)	benign(0.001)	1/1	.	hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCCTGCAGA	.	5	ESCA
PITPNM2	0	.	GRCh37	12	123498531	123498531	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.137G>T	p.Arg46Leu	p.R46L	ENST00000320201	3/25	17	14	3	18	18	0	PITPNM2,missense_variant,p.Arg46Leu,ENST00000546049,;PITPNM2,missense_variant,p.Arg46Leu,ENST00000542749,;PITPNM2,missense_variant,p.Arg46Leu,ENST00000280562,;PITPNM2,missense_variant,p.Arg46Leu,ENST00000392428,;PITPNM2,missense_variant,p.Arg46Leu,ENST00000320201,;PITPNM2,downstream_gene_variant,,ENST00000542210,;MIR4304,upstream_gene_variant,,ENST00000580964,;RN7SL133P,upstream_gene_variant,,ENST00000585256,;PITPNM2,non_coding_transcript_exon_variant,,ENST00000451868,;	A	ENSG00000090975	ENST00000320201	Transcript	missense_variant	276	137	46	R/L	cGg/cTg	.	.	.	-1	PITPNM2	HGNC	21044	protein_coding	YES	CCDS9242.1	ENSP00000322218	PITM2_HUMAN	Q9UF51_HUMAN,F5H664_HUMAN	UPI0000070D27	.	deleterious(0.01)	benign(0.351)	3/25	.	Superfamily_domains:SSF55961,Gene3D:3.30.530.20,Pfam_domain:PF02121,hmmpanther:PTHR10658,hmmpanther:PTHR10658:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	ACGGCCGGTTC	.	4	ESCA
PLEKHA5	0	.	GRCh37	12	19408050	19408050	+	Missense_Mutation	SNP	A	A	G	rs775722790	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383A>G	p.Tyr128Cys	p.Y128C	ENST00000429027	5/32	25	19	6	60	60	0	PLEKHA5,missense_variant,p.Tyr20Cys,ENST00000424268,;PLEKHA5,missense_variant,p.Tyr128Cys,ENST00000317589,;PLEKHA5,missense_variant,p.Tyr20Cys,ENST00000543806,;PLEKHA5,missense_variant,p.Tyr128Cys,ENST00000429027,;PLEKHA5,missense_variant,p.Tyr128Cys,ENST00000538714,;PLEKHA5,missense_variant,p.Tyr20Cys,ENST00000536974,;PLEKHA5,missense_variant,p.Tyr128Cys,ENST00000299275,;PLEKHA5,missense_variant,p.Tyr20Cys,ENST00000538305,;PLEKHA5,missense_variant,p.Tyr128Cys,ENST00000355397,;PLEKHA5,missense_variant,p.Tyr128Cys,ENST00000309364,;PLEKHA5,missense_variant,p.Tyr128Cys,ENST00000359180,;PLEKHA5,5_prime_UTR_variant,,ENST00000539256,;PLEKHA5,non_coding_transcript_exon_variant,,ENST00000538034,;PLEKHA5,downstream_gene_variant,,ENST00000534979,;PLEKHA5,upstream_gene_variant,,ENST00000510738,;	G	ENSG00000052126	ENST00000429027	Transcript	missense_variant	415	383	128	Y/C	tAt/tGt	rs775722790	.	.	1	PLEKHA5	HGNC	30036	protein_coding	YES	CCDS58213.1	ENSP00000404296	PKHA5_HUMAN	F5H1X3_HUMAN,B4DHK5_HUMAN	UPI000204ABA8	.	deleterious(0)	possibly_damaging(0.886)	5/32	.	hmmpanther:PTHR12752:SF3,hmmpanther:PTHR12752,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTATAACG	byFrequency	5	ESCA
SLC6A12	0	.	GRCh37	12	306657	306657	+	Missense_Mutation	SNP	C	C	T	rs373249721	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.961G>A	p.Ala321Thr	p.A321T	ENST00000428720	10/16	29	25	4	45	45	0	SLC6A12,missense_variant,p.Ala321Thr,ENST00000536824,;SLC6A12,missense_variant,p.Ala321Thr,ENST00000359674,;SLC6A12,missense_variant,p.Ala321Thr,ENST00000397296,;SLC6A12,missense_variant,p.Ala321Thr,ENST00000428720,;SLC6A12,missense_variant,p.Ala321Thr,ENST00000424061,;RP11-283I3.1,downstream_gene_variant,,ENST00000544067,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000535498,;SLC6A12,downstream_gene_variant,,ENST00000538272,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000542825,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000544782,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000545058,;SLC6A12,downstream_gene_variant,,ENST00000538580,;SLC6A12,downstream_gene_variant,,ENST00000540094,;	T	ENSG00000111181	ENST00000428720	Transcript	missense_variant	1705	961	321	A/T	Gcc/Acc	rs373249721	.	.	-1	SLC6A12	HGNC	11045	protein_coding	YES	CCDS8501.1	ENSP00000388184	S6A12_HUMAN	F5H2T6_HUMAN,B3KTU1_HUMAN	UPI000013C8DB	.	tolerated(0.39)	possibly_damaging(0.899)	10/16	.	PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF118,Pfam_domain:PF00209,Superfamily_domains:0053687,Prints_domain:PR00176	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGGCGATGC	byFrequency|byCluster	4	ESCA
MUC19	0	.	GRCh37	12	40917139	40917139	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5783-19225G>T	.	.	ENST00000454784	.	29	21	7	62	62	0	MUC19,intron_variant,,ENST00000454784,;MUC19,upstream_gene_variant,,ENST00000424466,;MUC19,non_coding_transcript_exon_variant,,ENST00000474954,;MUC19,intron_variant,,ENST00000398702,;	T	ENSG00000205592	ENST00000454784	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MUC19	HGNC	14362	protein_coding	YES	.	ENSP00000476404	.	C9JCE7_HUMAN	UPI0003B927DE	.	.	.	.	49/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCGGGTCCTC	.	5	ESCA
PPP1R1A	0	.	GRCh37	12	54974789	54974789	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.449A>G	p.Glu150Gly	p.E150G	ENST00000257905	6/7	40	32	8	114	114	0	PPP1R1A,missense_variant,p.Glu69Gly,ENST00000553113,;PPP1R1A,missense_variant,p.Glu150Gly,ENST00000257905,;PPP1R1A,missense_variant,p.Asn77Asp,ENST00000547431,;PDE1B,downstream_gene_variant,,ENST00000538346,;PDE1B,downstream_gene_variant,,ENST00000550620,;PDE1B,downstream_gene_variant,,ENST00000243052,;PDE1B,downstream_gene_variant,,ENST00000394277,;PDE1B,downstream_gene_variant,,ENST00000542335,;PPP1R1A,3_prime_UTR_variant,,ENST00000547826,;PDE1B,downstream_gene_variant,,ENST00000552774,;PDE1B,downstream_gene_variant,,ENST00000550285,;	C	ENSG00000135447	ENST00000257905	Transcript	missense_variant	620	449	150	E/G	gAa/gGa	.	.	.	-1	PPP1R1A	HGNC	9286	protein_coding	YES	CCDS44912.1	ENSP00000257905	PPR1A_HUMAN	.	UPI0000229454	.	tolerated_low_confidence(0.15)	benign(0.009)	6/7	.	Pfam_domain:PF05395,hmmpanther:PTHR15417,hmmpanther:PTHR15417:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTTCCTTA	.	5	ESCA
SHISA2	0	.	GRCh37	13	26620603	26620603	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*48G>C	.	.	ENST00000319420	2/2	22	11	11	60	60	0	SHISA2,3_prime_UTR_variant,,ENST00000319420,;	G	ENSG00000180730	ENST00000319420	Transcript	3_prime_UTR_variant	992	.	.	.	.	.	.	.	-1	SHISA2	HGNC	20366	protein_coding	YES	CCDS31951.1	ENSP00000313079	SHSA2_HUMAN	.	UPI000004BA7B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACCCCTGC	.	5	ESCA
KLF12	0	.	GRCh37	13	74260497	74260497	+	3'UTR	DEL	A	A	-	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9130delT	.	.	ENST00000377669	7/7	43	39	4	57	57	0	KLF12,3_prime_UTR_variant,,ENST00000377669,;	-	ENSG00000118922	ENST00000377669	Transcript	3_prime_UTR_variant	10366	.	.	.	.	.	.	.	-1	KLF12	HGNC	6346	protein_coding	YES	CCDS9449.1	ENSP00000366897	KLF12_HUMAN	.	UPI000013D144	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TAGGGCAAAAAA	.	2	ESCA
SLAIN1	0	.	GRCh37	13	78337586	78337586	+	3'Flank	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000488699	.	14	8	6	23	23	0	SLAIN1,3_prime_UTR_variant,,ENST00000466548,;SLAIN1,3_prime_UTR_variant,,ENST00000314070,;SLAIN1,3_prime_UTR_variant,,ENST00000351546,;SLAIN1,3_prime_UTR_variant,,ENST00000358679,;SLAIN1,3_prime_UTR_variant,,ENST00000267219,;SLAIN1,3_prime_UTR_variant,,ENST00000418532,;SLAIN1,downstream_gene_variant,,ENST00000441784,;SLAIN1,downstream_gene_variant,,ENST00000488699,;	T	ENSG00000139737	ENST00000488699	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	94	1	SLAIN1	HGNC	26387	protein_coding	YES	CCDS31995.2	ENSP00000418707	SLAI1_HUMAN	Q5T6P2_HUMAN,C9JUW9_HUMAN,C9JP03_HUMAN	UPI0001914D54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	ACTTAGATCTA	.	4	ESCA
RBM26	0	.	GRCh37	13	79928659	79928659	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1892A>T	p.Gln631Leu	p.Q631L	ENST00000267229	13/21	13	9	3	32	32	0	RBM26,missense_variant,p.Gln634Leu,ENST00000438737,;RBM26,missense_variant,p.Gln634Leu,ENST00000438724,;RBM26,missense_variant,p.Gln631Leu,ENST00000267229,;	A	ENSG00000139746	ENST00000267229	Transcript	missense_variant	1906	1892	631	Q/L	cAg/cTg	.	.	.	-1	RBM26	HGNC	20327	protein_coding	YES	CCDS9462.1	ENSP00000267229	RBM26_HUMAN	.	UPI00001A95DC	.	tolerated(0.28)	possibly_damaging(0.811)	13/21	.	hmmpanther:PTHR14398,hmmpanther:PTHR14398:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGACTGCTTC	.	3	ESCA
IGHV1-69	0	.	GRCh37	14	107169989	107169989	+	Missense_Mutation	SNP	G	G	T	rs377325190	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.293C>A	p.Ala98Asp	p.A98D	ENST00000390633	2/2	62	47	15	108	108	0	IGHV1-69,missense_variant,p.Ala98Asp,ENST00000390633,;	T	ENSG00000211973	ENST00000390633	Transcript	missense_variant	354	293	98	A/D	gCc/gAc	rs377325190	.	.	-1	IGHV1-69	HGNC	5558	IG_V_gene	YES	.	ENSP00000375042	.	.	UPI000011AAC2	.	deleterious(0.01)	benign(0.235)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF73,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	A:0.0006	A:0	A:0	.	A:0	A:0.003	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTAGGCTGTG	byFrequency|byCluster|by1000G	4	ESCA
FSCB	0	.	GRCh37	14	44976304	44976304	+	5'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-114A>T	.	.	ENST00000340446	1/1	31	25	5	30	30	0	FSCB,5_prime_UTR_variant,,ENST00000340446,;RP11-163M18.1,upstream_gene_variant,,ENST00000557465,;RP11-163M18.1,upstream_gene_variant,,ENST00000556228,;RP11-163M18.1,upstream_gene_variant,,ENST00000555433,;	A	ENSG00000189139	ENST00000340446	Transcript	5_prime_UTR_variant	179	.	.	.	.	.	.	.	-1	FSCB	HGNC	20494	protein_coding	YES	CCDS9679.1	ENSP00000344579	FSCB_HUMAN	.	UPI00001FD466	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATTTTCAAG	.	5	ESCA
LTBP2	0	.	GRCh37	14	74973428	74973428	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4006A>G	p.Ile1336Val	p.I1336V	ENST00000261978	27/36	20	15	5	44	44	0	LTBP2,missense_variant,p.Ile228Val,ENST00000556206,;LTBP2,missense_variant,p.Ile1336Val,ENST00000261978,;LTBP2,missense_variant,p.Ile1292Val,ENST00000556690,;LTBP2,missense_variant,p.Ile1336Val,ENST00000553939,;LTBP2,upstream_gene_variant,,ENST00000554861,;	C	ENSG00000119681	ENST00000261978	Transcript	missense_variant	4393	4006	1336	I/V	Atc/Gtc	.	.	.	-1	LTBP2	HGNC	6715	protein_coding	YES	CCDS9831.1	ENSP00000261978	LTBP2_HUMAN	G3V254_HUMAN	UPI000013D239	.	tolerated(0.34)	benign(0.004)	27/36	.	Superfamily_domains:SSF57184,SMART_domains:SM00179,SMART_domains:SM00181,Pfam_domain:PF07645,Gene3D:2.10.25.10,PROSITE_patterns:PS01186,hmmpanther:PTHR24034:SF40,hmmpanther:PTHR24034,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGATCTCGA	.	2	ESCA
AQR	0	.	GRCh37	15	35178780	35178780	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2764C>A	p.Pro922Thr	p.P922T	ENST00000156471	25/35	17	9	8	58	58	0	AQR,missense_variant,p.Pro922Thr,ENST00000156471,;AQR,3_prime_UTR_variant,,ENST00000543879,;	T	ENSG00000021776	ENST00000156471	Transcript	missense_variant	2990	2764	922	P/T	Cca/Aca	COSM2268345	.	.	-1	AQR	HGNC	29513	protein_coding	YES	CCDS42013.1	ENSP00000156471	AQR_HUMAN	.	UPI00001C1F85	.	tolerated(0.16)	benign(0.188)	25/35	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF5,Pfam_domain:PF13086,PIRSF_domain:PIRSF038901	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGGAACCC	.	5	ESCA
SPG21	0	.	GRCh37	15	65267070	65267070	+	Missense_Mutation	SNP	C	C	T	rs587777315	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.322G>A	p.Ala108Thr	p.A108T	ENST00000204566	5/9	26	15	10	47	46	1	SPG21,missense_variant,p.Ala108Thr,ENST00000557795,;SPG21,missense_variant,p.Ala108Thr,ENST00000433215,;SPG21,missense_variant,p.Ala108Thr,ENST00000204566,;SPG21,missense_variant,p.Ala108Thr,ENST00000558765,;SPG21,missense_variant,p.Ala81Thr,ENST00000416889,;SPG21,5_prime_UTR_variant,,ENST00000559199,;SPG21,downstream_gene_variant,,ENST00000559677,;SPG21,non_coding_transcript_exon_variant,,ENST00000560564,;SPG21,intron_variant,,ENST00000561078,;	T	ENSG00000090487	ENST00000204566	Transcript	missense_variant	618	322	108	A/T	Gct/Act	rs587777315	.	.	-1	SPG21	HGNC	20373	protein_coding	YES	CCDS10198.1	ENSP00000204566	SPG21_HUMAN	H3BRR0_HUMAN,H0YML6_HUMAN,H0YMB7_HUMAN,H0YLW1_HUMAN,H0YLT5_HUMAN,H0YLD7_HUMAN,H0YKB0_HUMAN	UPI0000074012	.	tolerated(0.64)	benign(0.352)	5/9	.	hmmpanther:PTHR15913:SF0,hmmpanther:PTHR15913,Gene3D:3.40.50.1820,Pfam_domain:PF12697,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGAAGCGCCAA	byFrequency|byCluster	4	ESCA
PEAK1	0	.	GRCh37	15	77472942	77472942	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1327G>A	p.Val443Ile	p.V443I	ENST00000560626	4/7	41	24	17	67	67	0	PEAK1,missense_variant,p.Val443Ile,ENST00000560626,;PEAK1,missense_variant,p.Val443Ile,ENST00000558305,;PEAK1,missense_variant,p.Val443Ile,ENST00000564328,;PEAK1,missense_variant,p.Val443Ile,ENST00000312493,;PEAK1,downstream_gene_variant,,ENST00000565820,;PEAK1,downstream_gene_variant,,ENST00000567808,;PEAK1,upstream_gene_variant,,ENST00000559791,;PEAK1,upstream_gene_variant,,ENST00000560854,;	T	ENSG00000173517	ENST00000560626	Transcript	missense_variant	1803	1327	443	V/I	Gtt/Att	.	.	.	-1	PEAK1	HGNC	29431	protein_coding	YES	CCDS42062.1	ENSP00000452796	PEAK1_HUMAN	H3BUZ5_HUMAN,H3BUE6_HUMAN	UPI00002378D0	.	tolerated(0.94)	benign(0.001)	4/7	.	hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAACATCTG	.	5	ESCA
FOPNL	0	.	GRCh37	16	15961272	15961272	+	3'UTR	SNP	G	G	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*25C>G	.	.	ENST00000255759	5/5	18	11	7	49	49	0	FOPNL,3_prime_UTR_variant,,ENST00000573968,;FOPNL,3_prime_UTR_variant,,ENST00000575744,;FOPNL,3_prime_UTR_variant,,ENST00000573396,;FOPNL,3_prime_UTR_variant,,ENST00000575073,;FOPNL,3_prime_UTR_variant,,ENST00000255759,;FOPNL,downstream_gene_variant,,ENST00000573429,;FOPNL,3_prime_UTR_variant,,ENST00000572415,;FOPNL,3_prime_UTR_variant,,ENST00000573087,;	C	ENSG00000133393	ENST00000255759	Transcript	3_prime_UTR_variant	580	.	.	.	.	.	.	.	-1	FOPNL	HGNC	26435	protein_coding	YES	CCDS10567.1	ENSP00000255759	FOPNL_HUMAN	I3L2N4_HUMAN	UPI000006F1B6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAAGACAAA	.	5	ESCA
PRSS22	0	.	GRCh37	16	2906218	2906218	+	Missense_Mutation	SNP	C	C	T	rs753423446	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146G>A	p.Arg49Gln	p.R49Q	ENST00000161006	3/6	20	14	5	54	54	0	PRSS22,missense_variant,p.Arg49Gln,ENST00000161006,;PRSS22,missense_variant,p.Arg49Gln,ENST00000571228,;LA16c-325D7.1,upstream_gene_variant,,ENST00000577140,;PRSS22,non_coding_transcript_exon_variant,,ENST00000577177,;PRSS22,non_coding_transcript_exon_variant,,ENST00000574768,;PRSS22,3_prime_UTR_variant,,ENST00000576381,;PRSS22,non_coding_transcript_exon_variant,,ENST00000570950,;PRSS22,upstream_gene_variant,,ENST00000572061,;PRSS22,upstream_gene_variant,,ENST00000575164,;	T	ENSG00000005001	ENST00000161006	Transcript	missense_variant	212	146	49	R/Q	cGg/cAg	rs753423446	.	.	-1	PRSS22	HGNC	14368	protein_coding	YES	CCDS10481.1	ENSP00000161006	BSSP4_HUMAN	.	UPI0000126AFA	.	deleterious(0)	probably_damaging(0.996)	3/6	.	hmmpanther:PTHR24253:SF6,hmmpanther:PTHR24253,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACCCGGTTC	byFrequency	5	ESCA
NFAT5	0	.	GRCh37	16	69732296	69732296	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2042A>G	.	.	ENST00000432919	15/15	33	19	13	54	54	0	NFAT5,3_prime_UTR_variant,,ENST00000432919,;NFAT5,3_prime_UTR_variant,,ENST00000354436,;NFAT5,3_prime_UTR_variant,,ENST00000393742,;NFAT5,3_prime_UTR_variant,,ENST00000349945,;NFAT5,downstream_gene_variant,,ENST00000567239,;NFAT5,downstream_gene_variant,,ENST00000565301,;NFAT5,downstream_gene_variant,,ENST00000566899,;RP11-311C24.1,upstream_gene_variant,,ENST00000561622,;NFAT5,3_prime_UTR_variant,,ENST00000426654,;	G	ENSG00000102908	ENST00000432919	Transcript	3_prime_UTR_variant	7900	.	.	.	.	.	.	.	1	NFAT5	HGNC	7774	protein_coding	YES	CCDS45518.1	ENSP00000396538	NFAT5_HUMAN	.	UPI000049DE1B	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATATATAC	.	5	ESCA
GABARAPL2	0	.	GRCh37	16	75611681	75611681	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*414A>G	.	.	ENST00000037243	4/4	31	16	15	31	31	0	GABARAPL2,3_prime_UTR_variant,,ENST00000037243,;GABARAPL2,3_prime_UTR_variant,,ENST00000563744,;GABARAPL2,downstream_gene_variant,,ENST00000568455,;GABARAPL2,non_coding_transcript_exon_variant,,ENST00000565985,;RP11-77K12.8,intron_variant,,ENST00000564489,;	G	ENSG00000034713	ENST00000037243	Transcript	3_prime_UTR_variant	904	.	.	.	.	.	.	.	1	GABARAPL2	HGNC	13291	protein_coding	YES	CCDS10921.1	ENSP00000037243	GBRL2_HUMAN	H3BQ50_HUMAN	UPI0000023921	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAGAATATGC	.	5	ESCA
COX10	0	.	GRCh37	17	14063220	14063220	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.651C>T	p.%3D	p.N217N	ENST00000261643	5/7	32	22	10	44	44	0	COX10,synonymous_variant,p.%3D,ENST00000261643,;COX10,synonymous_variant,p.%3D,ENST00000536205,;COX10,5_prime_UTR_variant,,ENST00000537334,;COX10,3_prime_UTR_variant,,ENST00000580561,;COX10,3_prime_UTR_variant,,ENST00000581931,;	T	ENSG00000006695	ENST00000261643	Transcript	synonymous_variant	728	651	217	N	aaC/aaT	.	.	.	1	COX10	HGNC	2260	protein_coding	YES	CCDS11166.1	ENSP00000261643	COX10_HUMAN	B4DFR1_HUMAN	UPI000013D1C8	.	.	.	5/7	.	HAMAP:MF_00154,hmmpanther:PTHR11048,hmmpanther:PTHR11048:SF3,PROSITE_patterns:PS00943,Pfam_domain:PF01040,TIGRFAM_domain:TIGR01473,PIRSF_domain:PIRSF001773	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAAACATGAA	.	5	ESCA
ACBD4	0	.	GRCh37	17	43216519	43216519	+	Silent	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.819C>T	p.%3D	p.P273P	ENST00000431281	11/12	66	49	16	91	91	0	ACBD4,missense_variant,p.Pro261Ser,ENST00000398322,;ACBD4,missense_variant,p.Pro261Ser,ENST00000321854,;ACBD4,synonymous_variant,p.%3D,ENST00000376955,;ACBD4,synonymous_variant,p.%3D,ENST00000591859,;ACBD4,synonymous_variant,p.%3D,ENST00000431281,;ACBD4,synonymous_variant,p.%3D,ENST00000586346,;ACBD4,intron_variant,,ENST00000592162,;ACBD4,downstream_gene_variant,,ENST00000591136,;ACBD4,downstream_gene_variant,,ENST00000587976,;ACBD4,downstream_gene_variant,,ENST00000587111,;ACBD4,downstream_gene_variant,,ENST00000586279,;ACBD4,non_coding_transcript_exon_variant,,ENST00000585553,;ACBD4,downstream_gene_variant,,ENST00000590289,;ACBD4,downstream_gene_variant,,ENST00000589798,;ACBD4,downstream_gene_variant,,ENST00000589752,;	T	ENSG00000181513	ENST00000431281	Transcript	synonymous_variant	1288	819	273	P	ccC/ccT	.	.	.	1	ACBD4	HGNC	23337	protein_coding	YES	CCDS45710.1	ENSP00000405969	ACBD4_HUMAN	.	UPI000007470F	.	.	.	11/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23310:SF53,hmmpanther:PTHR23310	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCCCTGAG	.	5	ESCA
TRIM25	0	.	GRCh37	17	54978858	54978858	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009A>T	p.Ile337Phe	p.I337F	ENST00000316881	4/9	34	24	10	55	55	0	TRIM25,missense_variant,p.Ile337Phe,ENST00000316881,;TRIM25,missense_variant,p.Ile337Phe,ENST00000537230,;TRIM25,non_coding_transcript_exon_variant,,ENST00000572550,;TRIM25,3_prime_UTR_variant,,ENST00000572021,;TRIM25,non_coding_transcript_exon_variant,,ENST00000570749,;TRIM25,non_coding_transcript_exon_variant,,ENST00000570473,;	A	ENSG00000121060	ENST00000316881	Transcript	missense_variant	1059	1009	337	I/F	Atc/Ttc	.	.	.	-1	TRIM25	HGNC	12932	protein_coding	YES	CCDS11591.1	ENSP00000323889	TRI25_HUMAN	.	UPI00001AE6B8	.	deleterious(0)	benign(0.439)	4/9	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF293	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGATGCCTT	.	5	ESCA
PITPNM3	0	.	GRCh37	17	6380423	6380423	+	Silent	SNP	C	C	T	rs772798913	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1011G>A	p.%3D	p.P337P	ENST00000262483	9/20	25	21	4	43	43	0	PITPNM3,synonymous_variant,p.%3D,ENST00000262483,;PITPNM3,synonymous_variant,p.%3D,ENST00000421306,;PITPNM3,upstream_gene_variant,,ENST00000576664,;PITPNM3,non_coding_transcript_exon_variant,,ENST00000572795,;	T	ENSG00000091622	ENST00000262483	Transcript	synonymous_variant	1099	1011	337	P	ccG/ccA	rs772798913	.	.	-1	PITPNM3	HGNC	21043	protein_coding	YES	CCDS11076.1	ENSP00000262483	PITM3_HUMAN	.	UPI000022A281	.	.	.	9/20	.	hmmpanther:PTHR10658	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCAACGGCCT	byFrequency	3	ESCA
WBP2	0	.	GRCh37	17	73851402	73851402	+	5'UTR	SNP	G	G	C	rs748668649	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-24C>G	.	.	ENST00000591399	2/9	11	8	3	40	40	0	WBP2,5_prime_UTR_variant,,ENST00000433525,;WBP2,5_prime_UTR_variant,,ENST00000591399,;WBP2,5_prime_UTR_variant,,ENST00000254806,;WBP2,5_prime_UTR_variant,,ENST00000585462,;WBP2,upstream_gene_variant,,ENST00000590221,;WBP2,upstream_gene_variant,,ENST00000589642,;WBP2,upstream_gene_variant,,ENST00000587374,;WBP2,upstream_gene_variant,,ENST00000593002,;WBP2,upstream_gene_variant,,ENST00000344296,;WBP2,upstream_gene_variant,,ENST00000590450,;WBP2,non_coding_transcript_exon_variant,,ENST00000589241,;WBP2,non_coding_transcript_exon_variant,,ENST00000592802,;WBP2,non_coding_transcript_exon_variant,,ENST00000416574,;WBP2,non_coding_transcript_exon_variant,,ENST00000589834,;WBP2,upstream_gene_variant,,ENST00000588373,;WBP2,upstream_gene_variant,,ENST00000591831,;WBP2,upstream_gene_variant,,ENST00000587642,;	C	ENSG00000132471	ENST00000591399	Transcript	5_prime_UTR_variant	402	.	.	.	.	rs748668649	.	.	-1	WBP2	HGNC	12738	protein_coding	YES	CCDS11731.1	ENSP00000467579	WBP2_HUMAN	K7ESN4_HUMAN,K7EIJ0_HUMAN,A6NG10_HUMAN	UPI0000138EBB	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCGAGACTCA	.	2	ESCA
MGAT5B	0	.	GRCh37	17	74928738	74928738	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1336G>A	p.Asp446Asn	p.D446N	ENST00000428789	10/16	25	13	11	44	44	0	MGAT5B,missense_variant,p.Asp446Asn,ENST00000428789,;MGAT5B,missense_variant,p.Asp435Asn,ENST00000569840,;MGAT5B,missense_variant,p.Asp435Asn,ENST00000301618,;MGAT5B,intron_variant,,ENST00000565043,;	A	ENSG00000167889	ENST00000428789	Transcript	missense_variant	1439	1336	446	D/N	Gac/Aac	.	.	.	1	MGAT5B	HGNC	24140	protein_coding	YES	CCDS45788.1	ENSP00000391227	MGT5B_HUMAN	.	UPI0000231C88	.	deleterious(0)	probably_damaging(1)	10/16	.	hmmpanther:PTHR15075:SF4,hmmpanther:PTHR15075,Pfam_domain:PF15024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCCGACAAC	.	5	ESCA
TP53	0	.	GRCh37	17	7577084	7577084	+	Missense_Mutation	SNP	T	T	A	rs121912667	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	8/11	24	20	4	48	48	0	TP53,missense_variant,p.Glu285Val,ENST00000420246,;TP53,missense_variant,p.Glu285Val,ENST00000269305,;TP53,missense_variant,p.Glu153Val,ENST00000509690,;TP53,missense_variant,p.Glu285Val,ENST00000359597,;TP53,missense_variant,p.Glu285Val,ENST00000445888,;TP53,missense_variant,p.Glu285Val,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1044	854	285	E/V	gAg/gTg	rs121912667,CM083790,TP53_g.13834A>C,TP53_g.13834A>T,TP53_g.13834A>G,COSM45649,COSM44227,COSM43614,COSM131474,COSM131484,COSM3958796,COSM1744596	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.978)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E285V|c.854A>T|3,SITE|p.E285V|c.854A>T|17,SITE|p.E285V|c.854A>T|4,CODON|p.0?|c.1_1182del1182|6,CODON|p.E285E|c.855G>A|3,CODON|p.E285G|c.854A>G|4,BUFFER|p.N288fs*13|c.859_872del14|17,BUFFER|p.L289F|c.865C>T|3,BUFFER|p.N288S|c.863A>G|6,BUFFER|p.N288Y|c.862A>T|3,BUFFER|p.E287E|c.861G>A|5,BUFFER|p.E287K|c.859G>A|6,BUFFER|p.E287*|c.859G>T|3,BUFFER|p.E287*|c.859G>T|12,BUFFER|p.E286E|c.858A>G|3,BUFFER|p.E286G|c.857A>G|4,BUFFER|p.E286V|c.857A>T|9,BUFFER|p.E286G|c.857A>G|18,BUFFER|p.E286*|c.856G>T|17,BUFFER|p.E286K|c.856G>A|14,BUFFER|p.E286K|c.856G>A|10,BUFFER|p.E286K|c.856G>A|23,BUFFER|p.E286K|c.856G>A|75,BUFFER|p.E286Q|c.856G>C|6,BUFFER|p.E286*|c.856G>T|3,BUFFER|p.E285K|c.853G>A|19,BUFFER|p.E285*|c.853G>T|5,BUFFER|p.E285K|c.853G>A|114,BUFFER|p.E285*|c.853G>T|9,BUFFER|p.E285Q|c.853G>C|4,BUFFER|p.E285*|c.853G>T|25,BUFFER|p.E285K|c.853G>A|5,BUFFER|p.E285K|c.853G>A|9,BUFFER|p.T284T|c.852A>T|3,BUFFER|p.T284A|c.850A>G|3,BUFFER|p.T284P|c.850A>C|8,BUFFER|p.R283fs*62|c.847delC|3,BUFFER|p.R283P|c.848G>C|4,BUFFER|p.R283H|c.848G>A|12,BUFFER|p.R283L|c.848G>T|4,BUFFER|p.R283P|c.848G>C|24,BUFFER|p.R283C|c.847C>T|19,BUFFER|p.R282R|c.846G>A|4,BUFFER|p.R282Q|c.845G>A|5,BUFFER|p.R282Q|c.845G>A|26,BUFFER|p.R282L|c.845G>T|3,BUFFER|p.R282Q|c.845G>A|3,BUFFER|p.R282P|c.845G>C|17,BUFFER|p.R282W|c.843_844CC>TT|10,BUFFER|p.R282G|c.844C>G|5,BUFFER|p.R282W|c.844C>T|49,BUFFER|p.R282G|c.844C>G|3,BUFFER|p.R282R|c.844C>A|3,BUFFER|p.R282W|c.844C>T|86,BUFFER|p.R282G|c.844C>G|29,BUFFER|p.R282W|c.844C>T|450,BUFFER|p.R282W|c.844C>T|58,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12	RADIA|MUTECT	CTTCCTCTGTG	byCluster	2	ESCA
TP53	0	.	GRCh37	17	7578290	7578290	+	Splice_Site	SNP	C	C	G	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560-1G>C	.	p.X187_splice	ENST00000269305	.	22	18	4	49	49	0	TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000269305,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000504937,;TP53,splice_acceptor_variant,,ENST00000505014,;TP53,splice_acceptor_variant,,ENST00000504290,;TP53,splice_acceptor_variant,,ENST00000510385,;	G	ENSG00000141510	ENST00000269305	Transcript	splice_acceptor_variant	.	.	.	.	.	CD043957,CS011574,CS083991,TP53_g.12628G>A,TP53_g.12628del,TP53_g.12628G>T,TP53_g.12628G>C,COSM43753,COSM43872,COSM43841,COSM45366,COSM341763,COSM127200,COSM335063,COSM341764,COSM127201,COSM335064,COSM127203,COSM341766,COSM335066,COSM4139869,COSM3717656,COSM1649389,COSM1649388,COSM127202,COSM335065,COSM341765	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	5/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.560-1G>C|6,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.A189_V197delAPPQHLIRV|c.565_591del27|4,BUFFER|p.P191delP|c.568_570delCCT|6,BUFFER|p.P190fs*57|c.569delC|4,BUFFER|p.P190L|c.569C>T|4,BUFFER|p.P97L|c.290C>T|6,BUFFER|p.P190L|c.569C>T|6,BUFFER|p.P190L|c.569C>T|30,BUFFER|p.P190R|c.569C>G|3,BUFFER|p.P190L|c.569C>T|6,BUFFER|p.P190L|c.569C>T|3,BUFFER|p.P58L|c.173C>T|6,BUFFER|p.P190T|c.568C>A|4,BUFFER|p.P190S|c.568C>T|8,BUFFER|p.A189V|c.566C>T|4,BUFFER|p.A189T|c.565G>A|3,BUFFER|p.G187G|c.561T>C|3,BUFFER|p.G187D|c.560G>A|7,BUFFER|p.G187V|c.560G>T|3,BUFFER|p.?|c.164-1G>A|7,BUFFER|p.?|c.560-1G>T|4,BUFFER|p.?|c.560-1G>A|20,BUFFER|p.?|c.164-1G>T|4,BUFFER|p.?|c.560-1G>A|7,BUFFER|p.?|c.560-1G>A|3,BUFFER|p.?|c.560-1G>T|4,BUFFER|p.?|c.281-1G>T|4,BUFFER|p.?|c.281-1G>A|7,BUFFER|p.?|c.560-1G>T|3,BUFFER|p.?|c.560-1G>A|7,BUFFER|p.?|c.560-1G>T|10,BUFFER|p.?|c.560-2A>G|4,BUFFER|p.?|c.281-2A>G|4,BUFFER|p.?|c.164-2A>G|4,BUFFER|p.?|c.560-2A>G|4,BUFFER|p.?|c.560-2A>G|4,BUFFER|p.?|c.560-2A>T|5,BUFFER|p.?|c.560-2A>G|8,BUFFER|p.?|c.560-2A>G|3,BUFFER|p.?|c.560-3T>G|3	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAGACCTAAGA	.	4	ESCA
USP43	0	.	GRCh37	17	9631606	9631606	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2671C>T	p.Pro891Ser	p.P891S	ENST00000285199	15/15	21	18	3	27	27	0	USP43,missense_variant,p.Pro678Ser,ENST00000574408,;USP43,missense_variant,p.Pro886Ser,ENST00000570475,;USP43,missense_variant,p.Pro891Ser,ENST00000285199,;USP43,missense_variant,p.Pro416Ser,ENST00000573955,;USP43,non_coding_transcript_exon_variant,,ENST00000570827,;	T	ENSG00000154914	ENST00000285199	Transcript	missense_variant	2767	2671	891	P/S	Ccc/Tcc	.	.	.	1	USP43	HGNC	20072	protein_coding	YES	CCDS45610.1	ENSP00000285199	UBP43_HUMAN	.	UPI0000047AFB	.	tolerated(0.3)	benign(0.003)	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTGCCCTGT	.	2	ESCA
ZNF443	0	.	GRCh37	19	12541473	12541473	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1513G>T	p.Glu505Ter	p.E505*	ENST00000301547	4/4	20	17	3	52	52	0	ZNF443,stop_gained,p.Glu505Ter,ENST00000301547,;CTD-3105H18.16,intron_variant,,ENST00000595562,;ZNF443,downstream_gene_variant,,ENST00000436821,;CTD-3105H18.18,downstream_gene_variant,,ENST00000598753,;	A	ENSG00000180855	ENST00000301547	Transcript	stop_gained	1711	1513	505	E/*	Gag/Tag	.	.	.	-1	ZNF443	HGNC	20878	protein_coding	YES	CCDS32918.1	ENSP00000301547	ZN443_HUMAN	F8WDY2_HUMAN	UPI000020344A	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF16,hmmpanther:PTHR24379,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACTCATATG	.	4	ESCA
SYCE2	0	.	GRCh37	19	13010103	13010103	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*52A>T	.	.	ENST00000293695	6/6	22	19	3	31	31	0	SYCE2,3_prime_UTR_variant,,ENST00000293695,;SYCE2,3_prime_UTR_variant,,ENST00000592819,;GCDH,intron_variant,,ENST00000591470,;GCDH,intron_variant,,ENST00000591050,;GCDH,intron_variant,,ENST00000222214,;GCDH,intron_variant,,ENST00000422947,;GCDH,intron_variant,,ENST00000457854,;GCDH,downstream_gene_variant,,ENST00000588905,;GCDH,downstream_gene_variant,,ENST00000590472,;GCDH,downstream_gene_variant,,ENST00000589039,;GCDH,upstream_gene_variant,,ENST00000588242,;GCDH,intron_variant,,ENST00000591043,;GCDH,intron_variant,,ENST00000590530,;GCDH,intron_variant,,ENST00000585420,;GCDH,downstream_gene_variant,,ENST00000421816,;AD000092.3,downstream_gene_variant,,ENST00000464444,;	A	ENSG00000161860	ENST00000293695	Transcript	3_prime_UTR_variant	728	.	.	.	.	.	.	.	-1	SYCE2	HGNC	27411	protein_coding	YES	CCDS42509.1	ENSP00000293695	SYCE2_HUMAN	.	UPI00000389A2	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCCTCACAG	.	2	ESCA
STX10	0	.	GRCh37	19	13255457	13255457	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607G>T	p.Asp203Tyr	p.D203Y	ENST00000587230	7/8	16	12	4	23	23	0	STX10,missense_variant,p.Trp201Cys,ENST00000242770,;STX10,missense_variant,p.Asp188Tyr,ENST00000587318,;STX10,missense_variant,p.Asp203Tyr,ENST00000587230,;STX10,missense_variant,p.Asp109Tyr,ENST00000588848,;STX10,missense_variant,p.Asp172Tyr,ENST00000593126,;STX10,missense_variant,p.Asp154Tyr,ENST00000343587,;STX10,missense_variant,p.Asp203Tyr,ENST00000589083,;STX10,missense_variant,p.Asp89Tyr,ENST00000591415,;STX10,downstream_gene_variant,,ENST00000591197,;NACC1,downstream_gene_variant,,ENST00000292431,;CTC-250I14.3,upstream_gene_variant,,ENST00000591825,;STX10,3_prime_UTR_variant,,ENST00000591843,;STX10,3_prime_UTR_variant,,ENST00000440593,;	A	ENSG00000104915	ENST00000587230	Transcript	missense_variant	672	607	203	D/Y	Gac/Tac	.	.	.	-1	STX10	HGNC	11428	protein_coding	YES	CCDS32922.1	ENSP00000466298	STX10_HUMAN	K7EPP9_HUMAN,K7EJ05_HUMAN	UPI000013616B	.	deleterious(0)	probably_damaging(0.981)	7/8	.	PROSITE_profiles:PS50192,hmmpanther:PTHR12380:SF45,hmmpanther:PTHR12380,Gene3D:1.20.5.110,Pfam_domain:PF05739,SMART_domains:SM00397,Superfamily_domains:SSF58038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGTCCATCT	.	5	ESCA
UNC13A	0	.	GRCh37	19	17759280	17759280	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1776C>A	p.His592Gln	p.H592Q	ENST00000519716	16/44	24	20	4	50	50	0	UNC13A,missense_variant,p.His592Gln,ENST00000252773,;UNC13A,missense_variant,p.His592Gln,ENST00000519716,;UNC13A,missense_variant,p.His590Gln,ENST00000550896,;UNC13A,missense_variant,p.His592Gln,ENST00000552293,;UNC13A,missense_variant,p.His592Gln,ENST00000551649,;UNC13A,missense_variant,p.His680Gln,ENST00000428389,;	T	ENSG00000130477	ENST00000519716	Transcript	missense_variant	1776	1776	592	H/Q	caC/caA	.	.	.	-1	UNC13A	HGNC	23150	protein_coding	YES	CCDS46013.2	ENSP00000429562	UN13A_HUMAN	.	UPI00006C19A7	.	deleterious(0)	probably_damaging(0.927)	16/44	.	PROSITE_profiles:PS50081,hmmpanther:PTHR10480,PROSITE_patterns:PS00479,Gene3D:3.30.60.20,Pfam_domain:PF00130,SMART_domains:SM00109,Superfamily_domains:SSF57889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCGTGGCA	.	5	ESCA
ISYNA1	0	.	GRCh37	19	18546480	18546480	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147A>T	p.Ile383Phe	p.I383F	ENST00000338128	9/11	12	9	3	32	32	0	ISYNA1,missense_variant,p.Ile383Phe,ENST00000338128,;ISYNA1,missense_variant,p.Ile52Phe,ENST00000581672,;ISYNA1,missense_variant,p.Ile329Phe,ENST00000457269,;ISYNA1,missense_variant,p.Ile255Phe,ENST00000578963,;ISYNA1,missense_variant,p.Ile181Phe,ENST00000317018,;ISYNA1,missense_variant,p.Ile233Phe,ENST00000545187,;SSBP4,downstream_gene_variant,,ENST00000348495,;ISYNA1,downstream_gene_variant,,ENST00000581800,;SSBP4,downstream_gene_variant,,ENST00000597724,;SSBP4,downstream_gene_variant,,ENST00000593641,;SSBP4,downstream_gene_variant,,ENST00000599699,;ISYNA1,downstream_gene_variant,,ENST00000578352,;ISYNA1,downstream_gene_variant,,ENST00000583534,;SSBP4,downstream_gene_variant,,ENST00000270061,;SSBP4,downstream_gene_variant,,ENST00000602088,;SSBP4,downstream_gene_variant,,ENST00000601357,;SSBP4,downstream_gene_variant,,ENST00000600628,;SSBP4,downstream_gene_variant,,ENST00000598159,;ISYNA1,splice_region_variant,,ENST00000583816,;ISYNA1,3_prime_UTR_variant,,ENST00000577820,;ISYNA1,3_prime_UTR_variant,,ENST00000582770,;ISYNA1,3_prime_UTR_variant,,ENST00000582811,;ISYNA1,non_coding_transcript_exon_variant,,ENST00000583309,;ISYNA1,non_coding_transcript_exon_variant,,ENST00000577916,;ISYNA1,non_coding_transcript_exon_variant,,ENST00000582287,;SSBP4,downstream_gene_variant,,ENST00000607020,;SSBP4,downstream_gene_variant,,ENST00000601444,;SSBP4,downstream_gene_variant,,ENST00000601614,;SSBP4,downstream_gene_variant,,ENST00000600244,;SSBP4,downstream_gene_variant,,ENST00000601919,;	A	ENSG00000105655	ENST00000338128	Transcript	missense_variant	1365	1147	383	I/F	Atc/Ttc	.	.	.	-1	ISYNA1	HGNC	29821	protein_coding	YES	CCDS12379.1	ENSP00000337746	INO1_HUMAN	U3KPZ1_HUMAN,J3QRY0_HUMAN,G3V1R9_HUMAN	UPI00000424BB	.	deleterious(0)	probably_damaging(1)	9/11	.	Superfamily_domains:SSF55347,PIRSF_domain:PIRSF015578,Gene3D:3.30.360.10,Pfam_domain:PF07994,hmmpanther:PTHR11510:SF5,Pfam_domain:PF01658,hmmpanther:PTHR11510	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTTGATGACCA	.	3	ESCA
ZNF254	0	.	GRCh37	19	24310230	24310230	+	Silent	SNP	C	C	A	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1428C>A	p.%3D	p.T476T	ENST00000357002	4/4	50	42	7	64	64	0	ZNF254,synonymous_variant,p.%3D,ENST00000357002,;ZNF254,synonymous_variant,p.%3D,ENST00000342944,;ZNF254,downstream_gene_variant,,ENST00000595187,;ZNF254,downstream_gene_variant,,ENST00000594886,;	A	ENSG00000213096	ENST00000357002	Transcript	synonymous_variant	1543	1428	476	T	acC/acA	COSM3892186	.	.	1	ZNF254	HGNC	13047	protein_coding	YES	CCDS32983.1	ENSP00000349494	ZN254_HUMAN	F5H2M4_HUMAN	UPI0000366DB6	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF153,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAACCCTAAC	.	5	ESCA
EEF2	0	.	GRCh37	19	3982335	3982335	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.700G>T	p.Ala234Ser	p.A234S	ENST00000309311	5/15	22	18	4	35	35	0	EEF2,missense_variant,p.Ala234Ser,ENST00000309311,;EEF2,upstream_gene_variant,,ENST00000600794,;SNORD37,downstream_gene_variant,,ENST00000384048,;EEF2,downstream_gene_variant,,ENST00000600720,;EEF2,non_coding_transcript_exon_variant,,ENST00000598436,;EEF2,upstream_gene_variant,,ENST00000598182,;EEF2,upstream_gene_variant,,ENST00000596417,;EEF2,downstream_gene_variant,,ENST00000594885,;	A	ENSG00000167658	ENST00000309311	Transcript	missense_variant	789	700	234	A/S	Gcc/Tcc	.	.	.	-1	EEF2	HGNC	3214	protein_coding	YES	CCDS12117.1	ENSP00000307940	EF2_HUMAN	Q8TA90_HUMAN,B4DMC6_HUMAN	UPI00001649F3	.	tolerated(0.45)	benign(0.001)	5/15	.	hmmpanther:PTHR23115:SF103,hmmpanther:PTHR23115,Gene3D:1n0uA03,Pfam_domain:PF00009,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTGGCCACAT	.	4	ESCA
CEACAM5	0	.	GRCh37	19	42221564	42221564	+	Silent	SNP	C	C	T	rs528850947	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1149C>T	p.%3D	p.V383V	ENST00000221992	5/10	67	57	10	133	133	0	CEACAM5,synonymous_variant,p.%3D,ENST00000398599,;CEACAM5,synonymous_variant,p.%3D,ENST00000221992,;CEACAM5,synonymous_variant,p.%3D,ENST00000405816,;CEA,intron_variant,,ENST00000598976,;CEA,intron_variant,,ENST00000435837,;CEACAM5,intron_variant,,ENST00000595403,;CEACAM5,downstream_gene_variant,,ENST00000595113,;CEACAM5,downstream_gene_variant,,ENST00000596606,;	T	ENSG00000105388	ENST00000221992	Transcript	synonymous_variant	1263	1149	383	V	gtC/gtT	rs528850947	.	.	1	CEACAM5	HGNC	1817	protein_coding	YES	CCDS12584.1	ENSP00000221992	CEAM5_HUMAN	Q7KZ28_HUMAN,M0QXV9_HUMAN	UPI000013C7E5	.	.	.	5/10	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF113,hmmpanther:PTHR19955,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGTCACAAG	.	5	ESCA
CD58	0	.	GRCh37	1	117061654	117061654	+	Intron	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743+199A>G	.	.	ENST00000369489	.	9	5	4	21	21	0	CD58,3_prime_UTR_variant,,ENST00000457047,;CD58,intron_variant,,ENST00000369489,;CD58,downstream_gene_variant,,ENST00000369487,;CD58,downstream_gene_variant,,ENST00000526981,;CD58,intron_variant,,ENST00000464088,;	C	ENSG00000116815	ENST00000369489	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CD58	HGNC	1688	protein_coding	YES	CCDS888.1	ENSP00000358501	LFA3_HUMAN	.	UPI000004D166	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACGATATGCA	.	2	ESCA
HIST2H3D	0	.	GRCh37	1	149785084	149785084	+	Missense_Mutation	SNP	C	C	G	rs782648332	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153G>C	p.Glu51Asp	p.E51D	ENST00000331491	1/1	58	47	11	110	110	0	HIST2H3D,missense_variant,p.Glu51Asp,ENST00000331491,;HIST2H2BF,upstream_gene_variant,,ENST00000545683,;HIST2H2BF,upstream_gene_variant,,ENST00000369167,;HIST2H2BF,upstream_gene_variant,,ENST00000427880,;RP11-196G18.21,upstream_gene_variant,,ENST00000420462,;HIST2H2BF,upstream_gene_variant,,ENST00000469483,;	G	ENSG00000183598	ENST00000331491	Transcript	missense_variant	153	153	51	E/D	gaG/gaC	rs782648332	.	.	-1	HIST2H3D	HGNC	25311	protein_coding	YES	CCDS41388.1	ENSP00000333277	H32_HUMAN	.	UPI0000000586	.	deleterious_low_confidence(0.03)	benign(0.011)	1/1	.	hmmpanther:PTHR11426,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGATCTCCCG	.	4	ESCA
FLG	0	.	GRCh37	1	152277995	152277995	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9367G>T	p.Gly3123Trp	p.G3123W	ENST00000368799	3/3	29	24	4	54	54	0	FLG,missense_variant,p.Gly3123Trp,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	A	ENSG00000143631	ENST00000368799	Transcript	missense_variant	9403	9367	3123	G/W	Ggg/Tgg	COSM1498439	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	unknown(0)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GTACCCCTGCC	.	2	ESCA
S100A8	0	.	GRCh37	1	153362902	153362902	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110T>C	p.Leu37Ser	p.L37S	ENST00000368733	2/3	20	16	4	49	49	0	S100A8,missense_variant,p.Leu37Ser,ENST00000368733,;S100A8,missense_variant,p.Leu37Ser,ENST00000368732,;S100A8,non_coding_transcript_exon_variant,,ENST00000477801,;	G	ENSG00000143546	ENST00000368733	Transcript	missense_variant	280	110	37	L/S	tTg/tCg	.	.	.	-1	S100A8	HGNC	10498	protein_coding	YES	CCDS1038.1	ENSP00000357722	S10A8_HUMAN	.	UPI000002C6C3	.	deleterious(0)	probably_damaging(0.991)	2/3	.	hmmpanther:PTHR11639:SF5,hmmpanther:PTHR11639,Gene3D:1.10.238.10,Pfam_domain:PF01023,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAGCAATTTC	.	5	ESCA
CD1C	0	.	GRCh37	1	158262114	158262114	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569T>C	p.Leu190Ser	p.L190S	ENST00000368170	3/6	28	16	12	47	47	0	CD1C,missense_variant,p.Leu190Ser,ENST00000368170,;CD1C,missense_variant,p.Leu125Ser,ENST00000443761,;	C	ENSG00000158481	ENST00000368170	Transcript	missense_variant	848	569	190	L/S	tTg/tCg	COSM897693	.	.	1	CD1C	HGNC	1636	protein_coding	YES	CCDS1175.1	ENSP00000357152	CD1C_HUMAN	B4DP91_HUMAN	UPI000013DF78	.	tolerated(0.14)	benign(0.132)	3/6	.	hmmpanther:PTHR16675:SF155,hmmpanther:PTHR16675,Gene3D:3.30.500.10,Superfamily_domains:SSF54452	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTTGGGTC	.	5	ESCA
KIF26B	0	.	GRCh37	1	245850135	245850135	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3850G>A	p.Glu1284Lys	p.E1284K	ENST00000407071	12/15	19	13	5	29	29	0	KIF26B,missense_variant,p.Glu1284Lys,ENST00000407071,;KIF26B,missense_variant,p.Glu903Lys,ENST00000366518,;KIF26B,non_coding_transcript_exon_variant,,ENST00000483253,;	A	ENSG00000162849	ENST00000407071	Transcript	missense_variant	4290	3850	1284	E/K	Gag/Aag	.	.	.	1	KIF26B	HGNC	25484	protein_coding	YES	CCDS44342.1	ENSP00000385545	KI26B_HUMAN	B4DF75_HUMAN	UPI0000695D71	.	deleterious(0)	unknown(0)	12/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24115:SF363,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGCGAGATG	.	5	ESCA
OR2W5	0	.	GRCh37	1	247655201	247655201	+	RNA	SNP	C	C	T	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.832C>T	.	.	ENST00000530852	1/1	31	21	10	47	47	0	OR2W5,non_coding_transcript_exon_variant,,ENST00000522351,;OR2W5,non_coding_transcript_exon_variant,,ENST00000530852,;OR2W5,non_coding_transcript_exon_variant,,ENST00000366492,;	T	ENSG00000203664	ENST00000530852	Transcript	non_coding_transcript_exon_variant	832	.	.	.	.	COSM1626961	.	.	1	OR2W5	HGNC	15424	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODIFIER	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R258C|c.772C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTACGTGTA	.	5	ESCA
ST6GALNAC5	0	.	GRCh37	1	77334224	77334224	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58A>G	p.Thr20Ala	p.T20A	ENST00000477717	2/5	49	19	30	156	155	0	ST6GALNAC5,missense_variant,p.Thr20Ala,ENST00000477717,;ST6GALNAC5,non_coding_transcript_exon_variant,,ENST00000480428,;ST6GALNAC5,non_coding_transcript_exon_variant,,ENST00000496845,;ST6GALNAC5,missense_variant,p.Thr20Ala,ENST00000318803,;	G	ENSG00000117069	ENST00000477717	Transcript	missense_variant	293	58	20	T/A	Acc/Gcc	.	.	.	1	ST6GALNAC5	HGNC	19342	protein_coding	YES	CCDS673.1	ENSP00000417583	SIA7E_HUMAN	B4DHB7_HUMAN	UPI0000001C9F	.	.	benign(0.16)	2/5	.	PIRSF_domain:PIRSF005557,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-TM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCACCAGC	.	5	ESCA
ZNF644	0	.	GRCh37	1	91406514	91406514	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397A>G	p.Lys133Glu	p.K133E	ENST00000370440	3/6	9	4	5	28	28	0	ZNF644,missense_variant,p.Lys133Glu,ENST00000370440,;ZNF644,missense_variant,p.Lys133Glu,ENST00000337393,;ZNF644,intron_variant,,ENST00000347275,;ZNF644,intron_variant,,ENST00000361321,;ZNF644,non_coding_transcript_exon_variant,,ENST00000498303,;ZNF644,intron_variant,,ENST00000467231,;	C	ENSG00000122482	ENST00000370440	Transcript	missense_variant	615	397	133	K/E	Aaa/Gaa	.	.	.	-1	ZNF644	HGNC	29222	protein_coding	YES	CCDS731.1	ENSP00000359469	ZN644_HUMAN	Q9NVH8_HUMAN,Q9H8J8_HUMAN,Q8NEI6_HUMAN	UPI000004A010	.	tolerated(0.23)	benign(0.005)	3/6	.	hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTTATTCA	.	2	ESCA
KIF3B	0	.	GRCh37	20	30919073	30919073	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2195C>T	p.Thr732Ile	p.T732I	ENST00000375712	9/9	33	29	3	42	42	0	KIF3B,missense_variant,p.Thr732Ile,ENST00000375712,;KIF3B,missense_variant,p.Thr358Ile,ENST00000418717,;	T	ENSG00000101350	ENST00000375712	Transcript	missense_variant	2362	2195	732	T/I	aCc/aTc	.	.	.	1	KIF3B	HGNC	6320	protein_coding	YES	CCDS13200.1	ENSP00000364864	KIF3B_HUMAN	.	UPI000012DDB1	.	tolerated(0.46)	possibly_damaging(0.507)	9/9	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AGGAACCCCTG	.	2	ESCA
LINC00029	0	.	GRCh37	20	61665826	61665826	+	RNA	SNP	C	C	T	rs539110796	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1374G>A	.	.	ENST00000370341	3/3	10	6	4	18	18	0	LINC00029,non_coding_transcript_exon_variant,,ENST00000456634,;LINC00029,non_coding_transcript_exon_variant,,ENST00000414668,;LINC00029,non_coding_transcript_exon_variant,,ENST00000370341,;RP11-305P22.9,intron_variant,,ENST00000606208,;RP11-305P22.9,intron_variant,,ENST00000607802,;LINC01056,upstream_gene_variant,,ENST00000455711,;	T	ENSG00000125514	ENST00000370341	Transcript	non_coding_transcript_exon_variant	1374	.	.	.	.	rs539110796	.	.	-1	LINC00029	HGNC	16184	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATAAACGCGCG	.	3	ESCA
MRAP	0	.	GRCh37	21	33680842	33680842	+	Intron	SNP	T	T	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.206+1792T>G	.	.	ENST00000399784	.	36	25	11	63	63	0	MRAP,intron_variant,,ENST00000399784,;MRAP,intron_variant,,ENST00000303645,;MRAP,intron_variant,,ENST00000339944,;MRAP,intron_variant,,ENST00000399786,;URB1,downstream_gene_variant,,ENST00000382751,;AP000266.7,non_coding_transcript_exon_variant,,ENST00000450936,;MRAP,intron_variant,,ENST00000497833,;	G	ENSG00000170262	ENST00000399784	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MRAP	HGNC	1304	protein_coding	YES	CCDS13613.1	ENSP00000382684	MRAP_HUMAN	.	UPI000013E8CC	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGTTAATTC	.	5	ESCA
SMTN	0	.	GRCh37	22	31489516	31489516	+	Intron	SNP	C	C	A	rs751223584	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1632+1683C>A	.	.	ENST00000358743	.	29	22	6	39	39	0	SMTN,missense_variant,p.Ala28Glu,ENST00000404574,;SMTN,intron_variant,,ENST00000455608,;SMTN,intron_variant,,ENST00000333137,;SMTN,intron_variant,,ENST00000358743,;SMTN,intron_variant,,ENST00000347557,;SMTN,downstream_gene_variant,,ENST00000416786,;SMTN,downstream_gene_variant,,ENST00000440425,;SMTN,downstream_gene_variant,,ENST00000426927,;SMTN,downstream_gene_variant,,ENST00000438223,;SMTN,downstream_gene_variant,,ENST00000431481,;SMTN,downstream_gene_variant,,ENST00000475548,;SMTN,downstream_gene_variant,,ENST00000482444,;SMTN,non_coding_transcript_exon_variant,,ENST00000493335,;SMTN,intron_variant,,ENST00000489337,;SMTN,intron_variant,,ENST00000460658,;SMTN,downstream_gene_variant,,ENST00000466272,;	A	ENSG00000183963	ENST00000358743	Transcript	intron_variant	.	.	.	.	.	rs751223584	.	.	1	SMTN	HGNC	11126	protein_coding	YES	CCDS13887.1	ENSP00000351593	SMTN_HUMAN	C9JP19_HUMAN,C9JGQ0_HUMAN	UPI00001B0272	.	.	.	.	11/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGGCGGTGG	byFrequency	5	ESCA
TMPRSS6	0	.	GRCh37	22	37470670	37470670	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1448G>A	p.Gly483Asp	p.G483D	ENST00000346753	12/18	21	18	3	29	29	0	TMPRSS6,missense_variant,p.Gly474Asp,ENST00000406725,;TMPRSS6,missense_variant,p.Gly474Asp,ENST00000406856,;TMPRSS6,missense_variant,p.Gly483Asp,ENST00000346753,;TMPRSS6,missense_variant,p.Gly474Asp,ENST00000381792,;	T	ENSG00000187045	ENST00000346753	Transcript	missense_variant	1565	1448	483	G/D	gGc/gAc	.	.	.	-1	TMPRSS6	HGNC	16517	protein_coding	YES	CCDS13941.1	ENSP00000334962	TMPS6_HUMAN	B0QYB6_HUMAN	UPI00000747C8	.	deleterious(0.02)	possibly_damaging(0.901)	12/18	.	Superfamily_domains:SSF57424,PIRSF_domain:PIRSF037135,SMART_domains:SM00192,Gene3D:4.10.400.10,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF96,PROSITE_profiles:PS50068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	CCAGGCCGTTG	.	2	ESCA
ENTHD1	0	.	GRCh37	22	40140045	40140045	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1463T>C	p.Leu488Pro	p.L488P	ENST00000325157	7/7	18	15	3	49	49	0	ENTHD1,missense_variant,p.Leu488Pro,ENST00000325157,;	G	ENSG00000176177	ENST00000325157	Transcript	missense_variant	1714	1463	488	L/P	cTc/cCc	.	.	.	-1	ENTHD1	HGNC	26352	protein_coding	YES	CCDS13998.1	ENSP00000317431	ENTD1_HUMAN	.	UPI00000741D2	.	tolerated(0.06)	benign(0.016)	7/7	.	hmmpanther:PTHR12276,hmmpanther:PTHR12276:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATTGAGGCTA	.	2	ESCA
DPP10	0	.	GRCh37	2	116548723	116548723	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1610C>T	p.Pro537Leu	p.P537L	ENST00000393147	18/26	33	28	4	43	43	0	DPP10,missense_variant,p.Pro537Leu,ENST00000393147,;DPP10,missense_variant,p.Pro483Leu,ENST00000409163,;DPP10,missense_variant,p.Pro526Leu,ENST00000310323,;DPP10,missense_variant,p.Pro533Leu,ENST00000410059,;	T	ENSG00000175497	ENST00000393147	Transcript	missense_variant	1965	1610	537	P/L	cCa/cTa	COSM3961025,COSM3961024	.	.	1	DPP10	HGNC	20823	protein_coding	YES	CCDS54388.1	ENSP00000376855	DPP10_HUMAN	J3KQK8_HUMAN,C9J4M8_HUMAN	UPI00015E0A22	.	tolerated(0.12)	benign(0.002)	18/26	.	hmmpanther:PTHR11731:SF21,hmmpanther:PTHR11731	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAGCCAGAAA	.	3	ESCA
SGOL2	0	.	GRCh37	2	201437233	201437233	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2164A>T	p.Ile722Leu	p.I722L	ENST00000357799	7/9	24	19	5	42	42	0	SGOL2,missense_variant,p.Ile722Leu,ENST00000357799,;SGOL2,downstream_gene_variant,,ENST00000409203,;	T	ENSG00000163535	ENST00000357799	Transcript	missense_variant	2262	2164	722	I/L	Ata/Tta	.	.	.	1	SGOL2	HGNC	30812	protein_coding	YES	CCDS42796.1	ENSP00000350447	SGOL2_HUMAN	C9JW92_HUMAN	UPI00001AEBF5	.	deleterious(0.04)	benign(0.105)	7/9	.	hmmpanther:PTHR21577:SF2,hmmpanther:PTHR21577	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAATAATT	.	5	ESCA
CCDC108	0	.	GRCh37	2	219890846	219890846	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2247C>T	p.%3D	p.C749C	ENST00000341552	14/35	15	11	4	29	29	0	CCDC108,synonymous_variant,p.%3D,ENST00000441968,;CCDC108,synonymous_variant,p.%3D,ENST00000453220,;CCDC108,synonymous_variant,p.%3D,ENST00000341552,;CCDC108,downstream_gene_variant,,ENST00000457968,;CCDC108,downstream_gene_variant,,ENST00000410037,;CCDC108,downstream_gene_variant,,ENST00000409865,;CCDC108,downstream_gene_variant,,ENST00000462848,;CCDC108,downstream_gene_variant,,ENST00000474601,;CCDC108,downstream_gene_variant,,ENST00000463683,;	A	ENSG00000181378	ENST00000341552	Transcript	synonymous_variant	2331	2247	749	C	tgC/tgT	.	.	.	-1	CCDC108	HGNC	25325	protein_coding	YES	CCDS2430.2	ENSP00000340776	CC108_HUMAN	C9JLP9_HUMAN,C9JIV0_HUMAN	UPI0000609097	.	.	.	14/35	.	hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGTGCAGTC	.	5	ESCA
CRIM1	0	.	GRCh37	2	36776815	36776815	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*971C>G	.	.	ENST00000280527	17/17	33	25	8	36	36	0	CRIM1,3_prime_UTR_variant,,ENST00000280527,;AC007401.2,intron_variant,,ENST00000406220,;FEZ2,downstream_gene_variant,,ENST00000305852,;FEZ2,downstream_gene_variant,,ENST00000441005,;FEZ2,downstream_gene_variant,,ENST00000379245,;FEZ2,downstream_gene_variant,,ENST00000405912,;FEZ2,downstream_gene_variant,,ENST00000487919,;FEZ2,downstream_gene_variant,,ENST00000487282,;FEZ2,downstream_gene_variant,,ENST00000432869,;FEZ2,downstream_gene_variant,,ENST00000414288,;FEZ2,downstream_gene_variant,,ENST00000451623,;FEZ2,downstream_gene_variant,,ENST00000475815,;FEZ2,downstream_gene_variant,,ENST00000413938,;	G	ENSG00000150938	ENST00000280527	Transcript	3_prime_UTR_variant	4449	.	.	.	.	.	.	.	1	CRIM1	HGNC	2359	protein_coding	YES	CCDS1783.1	ENSP00000280527	CRIM1_HUMAN	Q53TR0_HUMAN,Q53TH9_HUMAN,Q4ZG85_HUMAN,B4DUW0_HUMAN	UPI000004C628	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATACTGATT	.	5	ESCA
MEIS1	0	.	GRCh37	2	66739317	66739317	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.779C>T	p.Thr260Ile	p.T260I	ENST00000272369	8/13	28	25	3	65	65	0	MEIS1,missense_variant,p.Thr79Ile,ENST00000450027,;MEIS1,missense_variant,p.Thr195Ile,ENST00000495021,;MEIS1,missense_variant,p.Thr78Ile,ENST00000606455,;MEIS1,missense_variant,p.Thr260Ile,ENST00000488550,;MEIS1,missense_variant,p.Thr260Ile,ENST00000560281,;MEIS1,missense_variant,p.Thr260Ile,ENST00000407092,;MEIS1,missense_variant,p.Thr260Ile,ENST00000272369,;MEIS1,missense_variant,p.Thr258Ile,ENST00000398506,;MEIS1,intron_variant,,ENST00000444274,;MEIS1,intron_variant,,ENST00000409517,;MEIS1,3_prime_UTR_variant,,ENST00000542964,;MEIS1,3_prime_UTR_variant,,ENST00000475239,;MEIS1,3_prime_UTR_variant,,ENST00000409622,;MEIS1,non_coding_transcript_exon_variant,,ENST00000498705,;	T	ENSG00000143995	ENST00000272369	Transcript	missense_variant	1236	779	260	T/I	aCa/aTa	.	.	.	1	MEIS1	HGNC	7000	protein_coding	YES	CCDS46309.1	ENSP00000272369	MEIS1_HUMAN	Q8IZZ2_HUMAN,Q53RD5_HUMAN,Q53R57_HUMAN	UPI000000DA5A	.	tolerated(0.06)	possibly_damaging(0.713)	8/13	.	hmmpanther:PTHR11850:SF63,hmmpanther:PTHR11850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCACAGGTG	.	2	ESCA
MCEE	0	.	GRCh37	2	71336956	71336956	+	3'UTR	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*144A>G	.	.	ENST00000244217	3/3	42	31	11	69	69	0	MCEE,3_prime_UTR_variant,,ENST00000413592,;MCEE,3_prime_UTR_variant,,ENST00000244217,;MCEE,non_coding_transcript_exon_variant,,ENST00000462609,;	C	ENSG00000124370	ENST00000244217	Transcript	3_prime_UTR_variant	693	.	.	.	.	.	.	.	-1	MCEE	HGNC	16732	protein_coding	YES	CCDS1915.1	ENSP00000244217	MCEE_HUMAN	F5GZ54_HUMAN	UPI000003CA39	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTATATATT	.	5	ESCA
TMEM131	0	.	GRCh37	2	98418927	98418928	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2614dupT	p.Ser872PhefsTer9	p.S872Ffs*9	ENST00000186436	24/41	58	42	16	72	72	0	TMEM131,frameshift_variant,p.Ser872PhefsTer9,ENST00000186436,;	A	ENSG00000075568	ENST00000186436	Transcript	frameshift_variant	2843-2844	2614-2615	872	S/FX	tcc/tTcc	.	.	.	-1	TMEM131	HGNC	30366	protein_coding	YES	CCDS46368.1	ENSP00000186436	TM131_HUMAN	C9J6W0_HUMAN	UPI00006C0498	.	.	.	24/41	.	hmmpanther:PTHR22050,hmmpanther:PTHR22050:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTTGGAATAT	.	3	ESCA
UNC50	0	.	GRCh37	2	99234901	99234901	+	3'UTR	SNP	A	A	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*134A>G	.	.	ENST00000357765	6/6	49	34	14	41	41	0	UNC50,3_prime_UTR_variant,,ENST00000423713,;UNC50,3_prime_UTR_variant,,ENST00000409975,;UNC50,3_prime_UTR_variant,,ENST00000357765,;UNC50,3_prime_UTR_variant,,ENST00000393493,;UNC50,3_prime_UTR_variant,,ENST00000409347,;MGAT4A,downstream_gene_variant,,ENST00000414521,;MGAT4A,downstream_gene_variant,,ENST00000393487,;MGAT4A,downstream_gene_variant,,ENST00000264968,;UNC50,non_coding_transcript_exon_variant,,ENST00000466492,;	G	ENSG00000115446	ENST00000357765	Transcript	3_prime_UTR_variant	1066	.	.	.	.	.	.	.	1	UNC50	HGNC	16046	protein_coding	YES	CCDS2035.1	ENSP00000350409	UNC50_HUMAN	.	UPI0000031564	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATATATTA	.	5	ESCA
MORC1	0	.	GRCh37	3	108836849	108836849	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>A	p.Ala20Thr	p.A20T	ENST00000232603	1/28	58	43	15	129	128	0	MORC1,missense_variant,p.Ala20Thr,ENST00000483760,;MORC1,missense_variant,p.Ala20Thr,ENST00000232603,;	T	ENSG00000114487	ENST00000232603	Transcript	missense_variant	141	58	20	A/T	Gcc/Acc	.	.	.	-1	MORC1	HGNC	7198	protein_coding	YES	CCDS2955.1	ENSP00000232603	MORC1_HUMAN	.	UPI000013C964	.	tolerated(0.76)	benign(0.391)	1/28	.	hmmpanther:PTHR23337,hmmpanther:PTHR23337:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGGCGTGGA	.	5	ESCA
DBR1	0	.	GRCh37	3	137886121	137886121	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.516G>T	p.Leu172Phe	p.L172F	ENST00000260803	5/8	16	11	5	28	28	0	DBR1,missense_variant,p.Leu172Phe,ENST00000260803,;DBR1,5_prime_UTR_variant,,ENST00000505015,;DBR1,downstream_gene_variant,,ENST00000463982,;DBR1,missense_variant,p.Val117Phe,ENST00000477557,;DBR1,upstream_gene_variant,,ENST00000460271,;	A	ENSG00000138231	ENST00000260803	Transcript	missense_variant	670	516	172	L/F	ttG/ttT	.	.	.	-1	DBR1	HGNC	15594	protein_coding	YES	CCDS33863.1	ENSP00000260803	DBR1_HUMAN	F5GWV2_HUMAN	UPI000006DFC5	.	tolerated(0.05)	possibly_damaging(0.795)	5/8	.	hmmpanther:PTHR12849,Pfam_domain:PF00149,Gene3D:3.60.21.10,Superfamily_domains:SSF56300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGACAAGAA	.	5	ESCA
PFN2	0	.	GRCh37	3	149683744	149683744	+	3'UTR	SNP	T	T	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*532A>T	.	.	ENST00000239940	3/3	27	17	10	32	32	0	PFN2,3_prime_UTR_variant,,ENST00000494827,;PFN2,3_prime_UTR_variant,,ENST00000239940,;PFN2,3_prime_UTR_variant,,ENST00000452853,;PFN2,3_prime_UTR_variant,,ENST00000481767,;PFN2,intron_variant,,ENST00000423691,;PFN2,downstream_gene_variant,,ENST00000461868,;PFN2,downstream_gene_variant,,ENST00000475518,;RNF13,downstream_gene_variant,,ENST00000361785,;PFN2,downstream_gene_variant,,ENST00000497148,;RNF13,downstream_gene_variant,,ENST00000344229,;RNF13,downstream_gene_variant,,ENST00000482083,;PFN2,downstream_gene_variant,,ENST00000461930,;PFN2,downstream_gene_variant,,ENST00000498307,;RNF13,downstream_gene_variant,,ENST00000392894,;RNF13,downstream_gene_variant,,ENST00000491086,;PFN2,downstream_gene_variant,,ENST00000489155,;PFN2,downstream_gene_variant,,ENST00000490975,;RNF13,downstream_gene_variant,,ENST00000468289,;PFN2,downstream_gene_variant,,ENST00000481275,;ANKUB1,intron_variant,,ENST00000481585,;PFN2,3_prime_UTR_variant,,ENST00000460404,;PFN2,3_prime_UTR_variant,,ENST00000468323,;PFN2,downstream_gene_variant,,ENST00000497060,;PFN2,downstream_gene_variant,,ENST00000498169,;RNF13,downstream_gene_variant,,ENST00000493238,;	A	ENSG00000070087	ENST00000239940	Transcript	3_prime_UTR_variant	1208	.	.	.	.	.	.	.	-1	PFN2	HGNC	8882	protein_coding	YES	CCDS3148.1	ENSP00000239940	PROF2_HUMAN	C9J712_HUMAN	UPI000013CA98	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCATGCAAA	.	5	ESCA
MME	0	.	GRCh37	3	154889996	154889996	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2071G>T	p.Ala691Ser	p.A691S	ENST00000460393	21/23	42	24	18	66	66	0	MME,missense_variant,p.Ala691Ser,ENST00000360490,;MME,missense_variant,p.Ala691Ser,ENST00000460393,;MME,missense_variant,p.Ala691Ser,ENST00000492661,;MME,missense_variant,p.Ala691Ser,ENST00000493237,;MME,missense_variant,p.Ala691Ser,ENST00000462745,;MME-AS1,intron_variant,,ENST00000484721,;MME,non_coding_transcript_exon_variant,,ENST00000493888,;MME,downstream_gene_variant,,ENST00000495577,;	T	ENSG00000196549	ENST00000460393	Transcript	missense_variant	2191	2071	691	A/S	Gca/Tca	.	.	.	1	MME	HGNC	7154	protein_coding	YES	CCDS3172.1	ENSP00000418525	NEP_HUMAN	C9JR96_HUMAN,C9JDZ3_HUMAN,C9J9X7_HUMAN,C9IYX7_HUMAN	UPI0000033C41	.	deleterious(0.05)	probably_damaging(0.909)	21/23	.	Superfamily_domains:SSF55486,Gene3D:3.40.390.10,Pfam_domain:PF01431,hmmpanther:PTHR11733:SF114,hmmpanther:PTHR11733	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTGCACAG	.	5	ESCA
MIR720	0	.	GRCh37	3	164059164	164059164	+	RNA	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.36G>T	.	.	ENST00000408828	1/1	64	48	15	113	113	0	MIR720,mature_miRNA_variant,,ENST00000408828,;	T	ENSG00000221755	ENST00000408828	Transcript	mature_miRNA_variant	36	.	.	.	.	.	.	.	1	MIR720	HGNC	35375	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGGGGCCTC	.	5	ESCA
SI	0	.	GRCh37	3	164700808	164700808	+	Silent	SNP	T	T	C	rs547324596	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5229A>G	p.%3D	p.V1743V	ENST00000264382	46/48	33	26	7	60	60	0	SI,synonymous_variant,p.%3D,ENST00000264382,;	C	ENSG00000090402	ENST00000264382	Transcript	synonymous_variant	5292	5229	1743	V	gtA/gtG	rs547324596	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	.	.	46/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTGTACAGA	.	5	ESCA
SI	0	.	GRCh37	3	164709998	164709998	+	Silent	SNP	G	G	A	rs370336977	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4950C>T	p.%3D	p.Y1650Y	ENST00000264382	43/48	27	20	7	64	64	0	SI,synonymous_variant,p.%3D,ENST00000264382,;	A	ENSG00000090402	ENST00000264382	Transcript	synonymous_variant	5013	4950	1650	Y	taC/taT	rs370336977,COSM4114960	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	.	.	43/48	.	Superfamily_domains:SSF51011,Pfam_domain:PF01055	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGACGTAGGC	byFrequency|byCluster	5	ESCA
HYAL2	0	.	GRCh37	3	50357844	50357844	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77C>T	p.Thr26Ile	p.T26I	ENST00000447092	1/3	13	4	8	23	23	0	HYAL2,missense_variant,p.Thr26Ile,ENST00000426286,;HYAL2,missense_variant,p.Thr26Ile,ENST00000424190,;HYAL2,missense_variant,p.Thr26Ile,ENST00000442581,;HYAL2,missense_variant,p.Thr26Ile,ENST00000458018,;HYAL2,missense_variant,p.Thr26Ile,ENST00000447092,;HYAL2,missense_variant,p.Thr26Ile,ENST00000357750,;HYAL2,missense_variant,p.Thr26Ile,ENST00000395139,;HYAL2,missense_variant,p.Thr26Ile,ENST00000428028,;HYAL2,missense_variant,p.Thr26Ile,ENST00000415028,;TUSC2,downstream_gene_variant,,ENST00000232496,;TUSC2,non_coding_transcript_exon_variant,,ENST00000462137,;HYAL2,non_coding_transcript_exon_variant,,ENST00000481597,;	A	ENSG00000068001	ENST00000447092	Transcript	missense_variant	2370	77	26	T/I	aCa/aTa	.	.	.	-1	HYAL2	HGNC	5321	protein_coding	YES	CCDS2818.1	ENSP00000401853	HYAL2_HUMAN	Q5ZF00_HUMAN,C9K016_HUMAN,C9JSI7_HUMAN,C9JSD1_HUMAN,C9JBF5_HUMAN,C9J700_HUMAN	UPI000013C4E6	.	deleterious(0)	probably_damaging(0.993)	1/3	.	PIRSF_domain:PIRSF038193,hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	GTGCTGTGGGC	.	4	ESCA
UBA3	0	.	GRCh37	3	69105806	69105806	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1040A>T	p.Asp347Val	p.D347V	ENST00000361055	14/18	20	13	7	42	42	0	UBA3,missense_variant,p.Asp347Val,ENST00000361055,;UBA3,missense_variant,p.Asp170Val,ENST00000540295,;UBA3,missense_variant,p.Asp306Val,ENST00000415609,;UBA3,missense_variant,p.Asp333Val,ENST00000349511,;TMF1,upstream_gene_variant,,ENST00000398559,;TMF1,upstream_gene_variant,,ENST00000543976,;CTD-2013N24.2,downstream_gene_variant,,ENST00000595925,;UBA3,3_prime_UTR_variant,,ENST00000465627,;UBA3,3_prime_UTR_variant,,ENST00000461934,;TMF1,upstream_gene_variant,,ENST00000488010,;UBA3,downstream_gene_variant,,ENST00000461522,;	A	ENSG00000144744	ENST00000361055	Transcript	missense_variant	1095	1040	347	D/V	gAt/gTt	.	.	.	-1	UBA3	HGNC	12470	protein_coding	YES	CCDS2909.1	ENSP00000354340	UBA3_HUMAN	B7Z5F6_HUMAN	UPI00001E058C	.	deleterious(0)	probably_damaging(0.993)	14/18	.	Superfamily_domains:SSF69572,Gene3D:3.40.50.720,hmmpanther:PTHR10953	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACATCATTA	.	5	ESCA
DKK2	0	.	GRCh37	4	107844979	107844979	+	3'UTR	SNP	T	T	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*132A>C	.	.	ENST00000285311	4/4	18	12	5	39	39	0	DKK2,3_prime_UTR_variant,,ENST00000513208,;DKK2,3_prime_UTR_variant,,ENST00000285311,;DKK2,downstream_gene_variant,,ENST00000510463,;DKK2,non_coding_transcript_exon_variant,,ENST00000510534,;	G	ENSG00000155011	ENST00000285311	Transcript	3_prime_UTR_variant	1618	.	.	.	.	.	.	.	-1	DKK2	HGNC	2892	protein_coding	YES	CCDS3675.1	ENSP00000285311	DKK2_HUMAN	D6RGF1_HUMAN	UPI0000048EF2	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGTGATCA	.	5	ESCA
ARAP2	0	.	GRCh37	4	36230984	36230984	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.125A>G	p.Asn42Ser	p.N42S	ENST00000303965	2/33	15	8	7	50	50	0	ARAP2,missense_variant,p.Asn42Ser,ENST00000506189,;ARAP2,missense_variant,p.Asn42Ser,ENST00000303965,;ARAP2,non_coding_transcript_exon_variant,,ENST00000508066,;	C	ENSG00000047365	ENST00000303965	Transcript	missense_variant	615	125	42	N/S	aAt/aGt	.	.	.	-1	ARAP2	HGNC	16924	protein_coding	YES	CCDS3441.1	ENSP00000302895	ARAP2_HUMAN	D6RAD6_HUMAN	UPI000013E917	.	deleterious(0.04)	benign(0.411)	2/33	.	PROSITE_profiles:PS50105,Pfam_domain:PF00536,Gene3D:1.10.150.50,SMART_domains:SM00454,Superfamily_domains:SSF47769	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TGTCATTTATT	.	4	ESCA
KDR	0	.	GRCh37	4	55964887	55964887	+	Missense_Mutation	SNP	T	T	C	rs749701671	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2350A>G	p.Ile784Val	p.I784V	ENST00000263923	16/30	32	16	15	47	47	0	KDR,missense_variant,p.Ile784Val,ENST00000263923,;KDR,upstream_gene_variant,,ENST00000509309,;	C	ENSG00000128052	ENST00000263923	Transcript	missense_variant	2646	2350	784	I/V	Atc/Gtc	rs749701671	.	.	-1	KDR	HGNC	6307	protein_coding	YES	CCDS3497.1	ENSP00000263923	VGFR2_HUMAN	B4DEK3_HUMAN	UPI000003AE04	.	tolerated(0.07)	benign(0.012)	16/30	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGATGACAA	.	5	ESCA
TERT	0	.	GRCh37	5	1279450	1279450	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2086C>T	p.Arg696Cys	p.R696C	ENST00000310581	5/16	34	26	7	53	53	0	TERT,missense_variant,p.Arg696Cys,ENST00000296820,;TERT,missense_variant,p.Arg696Cys,ENST00000310581,;TERT,missense_variant,p.Arg696Cys,ENST00000508104,;TERT,missense_variant,p.Arg696Cys,ENST00000334602,;TERT,missense_variant,p.Arg696Cys,ENST00000460137,;TERT,non_coding_transcript_exon_variant,,ENST00000484238,;	A	ENSG00000164362	ENST00000310581	Transcript	missense_variant	2144	2086	696	R/C	Cgt/Tgt	COSM3941019,COSM3941020	.	.	-1	TERT	HGNC	11730	protein_coding	YES	CCDS3861.2	ENSP00000309572	TERT_HUMAN	Q9UNS6_HUMAN,Q9UNR4_HUMAN,Q9UBR6_HUMAN	UPI0000031309	.	deleterious(0)	probably_damaging(0.953)	5/16	.	PROSITE_profiles:PS50878,hmmpanther:PTHR12066:SF0,hmmpanther:PTHR12066,Superfamily_domains:SSF56672	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACGCAGCA	.	5	ESCA
PKD2L2	0	.	GRCh37	5	137230250	137230250	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.476C>T	p.Thr159Ile	p.T159I	ENST00000290431	4/14	30	21	9	79	79	0	PKD2L2,missense_variant,p.Thr159Ile,ENST00000508883,;PKD2L2,missense_variant,p.Thr125Ile,ENST00000350250,;PKD2L2,missense_variant,p.Thr159Ile,ENST00000290431,;PKD2L2,missense_variant,p.Thr159Ile,ENST00000502810,;PKD2L2,missense_variant,p.Thr69Ile,ENST00000503015,;PKD2L2,missense_variant,p.Thr69Ile,ENST00000511176,;PKD2L2,missense_variant,p.Thr159Ile,ENST00000508638,;PKD2L2,3_prime_UTR_variant,,ENST00000414094,;	T	ENSG00000078795	ENST00000290431	Transcript	missense_variant	499	476	159	T/I	aCt/aTt	.	.	.	1	PKD2L2	HGNC	9012	protein_coding	YES	CCDS43367.1	ENSP00000290431	PK2L2_HUMAN	D6RF71_HUMAN,D6RBX8_HUMAN	UPI000049E016	.	deleterious(0)	possibly_damaging(0.697)	4/14	.	hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF47,Pfam_domain:PF08016	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATACTTCTG	.	5	ESCA
PCDHA7	0	.	GRCh37	5	140215472	140215472	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1504C>A	p.Arg502Ser	p.R502S	ENST00000525929	1/4	62	40	21	157	157	0	PCDHA7,missense_variant,p.Arg502Ser,ENST00000378125,;PCDHA7,missense_variant,p.Arg502Ser,ENST00000525929,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	A	ENSG00000204963	ENST00000525929	Transcript	missense_variant	1504	1504	502	R/S	Cgc/Agc	.	.	.	1	PCDHA7	HGNC	8673	protein_coding	YES	CCDS54918.1	ENSP00000436426	PCDA7_HUMAN	.	UPI00001273CF	.	deleterious_low_confidence(0.01)	possibly_damaging(0.692)	1/4	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGAGCGCGCG	.	5	ESCA
LIFR	0	.	GRCh37	5	38475819	38475819	+	3'UTR	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5878C>A	.	.	ENST00000263409	20/20	65	35	30	68	68	0	LIFR,3_prime_UTR_variant,,ENST00000263409,;	T	ENSG00000113594	ENST00000263409	Transcript	3_prime_UTR_variant	9335	.	.	.	.	.	.	.	-1	LIFR	HGNC	6597	protein_coding	YES	CCDS3927.1	ENSP00000263409	LIFR_HUMAN	D6RJ94_HUMAN,D6RF33_HUMAN	UPI000004CAC2	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAAGTAAAA	.	5	ESCA
RICTOR	0	.	GRCh37	5	38942960	38942960	+	Nonsense_Mutation	SNP	A	A	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5027T>G	p.Leu1676Ter	p.L1676*	ENST00000357387	37/38	56	48	8	77	77	0	RICTOR,stop_gained,p.Leu1676Ter,ENST00000357387,;RICTOR,stop_gained,p.Leu1700Ter,ENST00000296782,;RICTOR,3_prime_UTR_variant,,ENST00000511516,;RICTOR,non_coding_transcript_exon_variant,,ENST00000505927,;OSMR,intron_variant,,ENST00000509237,;OSMR,intron_variant,,ENST00000508882,;	C	ENSG00000164327	ENST00000357387	Transcript	stop_gained	5058	5027	1676	L/*	tTa/tGa	.	.	.	-1	RICTOR	HGNC	28611	protein_coding	YES	CCDS34148.1	ENSP00000349959	RICTR_HUMAN	.	UPI00003529F3	.	.	.	37/38	.	hmmpanther:PTHR13298:SF11,hmmpanther:PTHR13298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATAATTCT	.	5	ESCA
HIST1H4H	0	.	GRCh37	6	26285573	26285573	+	Missense_Mutation	SNP	T	T	C	rs751532587	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.155A>G	p.Tyr52Cys	p.Y52C	ENST00000289352	1/2	50	32	17	60	60	0	HIST1H4H,missense_variant,p.Tyr52Cys,ENST00000289352,;HIST1H4H,missense_variant,p.Tyr52Cys,ENST00000377727,;	C	ENSG00000158406	ENST00000289352	Transcript	missense_variant	190	155	52	Y/C	tAt/tGt	rs751532587,COSM3829839	.	.	-1	HIST1H4H	HGNC	4788	protein_coding	YES	CCDS4604.1	ENSP00000289352	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	deleterious(0)	probably_damaging(0.962)	1/2	.	Prints_domain:PR00623,Superfamily_domains:SSF47113,SMART_domains:SM00803,SMART_domains:SM00417,Pfam_domain:PF00125,Gene3D:1.10.20.10,hmmpanther:PTHR10484	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCATAGATA	.	3	ESCA
TNXB	0	.	GRCh37	6	32014070	32014070	+	5'Flank	SNP	G	G	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000451343	.	38	25	13	78	78	0	TNXB,synonymous_variant,p.%3D,ENST00000375247,;TNXB,synonymous_variant,p.%3D,ENST00000375244,;CYP21A2,downstream_gene_variant,,ENST00000418967,;CYP21A2,downstream_gene_variant,,ENST00000435122,;TNXB,upstream_gene_variant,,ENST00000451343,;TNXB,non_coding_transcript_exon_variant,,ENST00000490077,;CYP21A2,downstream_gene_variant,,ENST00000479074,;CYP21A2,downstream_gene_variant,,ENST00000479730,;CYP21A2,downstream_gene_variant,,ENST00000486063,;TNXB,upstream_gene_variant,,ENST00000498094,;	C	ENSG00000168477	ENST00000451343	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	165	-1	TNXB	HGNC	11976	protein_coding	YES	CCDS4736.1	ENSP00000407685	TENX_HUMAN	B6RHJ5_HUMAN	UPI0000000E8E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCGGCCAC	.	5	ESCA
TNXB	0	.	GRCh37	6	32014071	32014071	+	5'Flank	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000451343	.	38	25	13	78	78	0	TNXB,missense_variant,p.Ala3494Asp,ENST00000375247,;TNXB,missense_variant,p.Ala3496Asp,ENST00000375244,;CYP21A2,downstream_gene_variant,,ENST00000418967,;CYP21A2,downstream_gene_variant,,ENST00000435122,;TNXB,upstream_gene_variant,,ENST00000451343,;TNXB,non_coding_transcript_exon_variant,,ENST00000490077,;CYP21A2,downstream_gene_variant,,ENST00000479074,;CYP21A2,downstream_gene_variant,,ENST00000479730,;CYP21A2,downstream_gene_variant,,ENST00000486063,;TNXB,upstream_gene_variant,,ENST00000498094,;	T	ENSG00000168477	ENST00000451343	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	166	-1	TNXB	HGNC	11976	protein_coding	YES	CCDS4736.1	ENSP00000407685	TENX_HUMAN	B6RHJ5_HUMAN	UPI0000000E8E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCGGCCACA	.	5	ESCA
GCLC	0	.	GRCh37	6	53373988	53373988	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814A>G	p.Ile272Val	p.I272V	ENST00000229416	7/16	31	24	7	41	41	0	GCLC,missense_variant,p.Ile272Val,ENST00000229416,;GCLC,upstream_gene_variant,,ENST00000514373,;GCLC,downstream_gene_variant,,ENST00000514004,;RP1-27K12.4,downstream_gene_variant,,ENST00000508884,;GCLC,3_prime_UTR_variant,,ENST00000504525,;GCLC,non_coding_transcript_exon_variant,,ENST00000509541,;GCLC,upstream_gene_variant,,ENST00000510837,;GCLC,upstream_gene_variant,,ENST00000504353,;	C	ENSG00000001084	ENST00000229416	Transcript	missense_variant	1298	814	272	I/V	Atc/Gtc	.	.	.	-1	GCLC	HGNC	4311	protein_coding	YES	CCDS4952.1	ENSP00000229416	GSH1_HUMAN	Q14TF0_HUMAN,D6R959_HUMAN,B4E2I4_HUMAN	UPI000000D970	.	tolerated(0.43)	benign(0.034)	7/16	.	hmmpanther:PTHR11164,hmmpanther:PTHR11164:SF0,Pfam_domain:PF03074,Superfamily_domains:SSF55931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGATAGTAG	.	5	ESCA
LRRN3	0	.	GRCh37	7	110763077	110763077	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.249A>T	p.Lys83Asn	p.K83N	ENST00000451085	4/4	18	10	7	45	45	0	LRRN3,missense_variant,p.Lys83Asn,ENST00000422987,;LRRN3,missense_variant,p.Lys83Asn,ENST00000421101,;LRRN3,missense_variant,p.Lys83Asn,ENST00000308478,;LRRN3,missense_variant,p.Lys83Asn,ENST00000451085,;IMMP2L,intron_variant,,ENST00000450877,;IMMP2L,intron_variant,,ENST00000437687,;IMMP2L,intron_variant,,ENST00000415362,;IMMP2L,intron_variant,,ENST00000452895,;IMMP2L,intron_variant,,ENST00000405709,;IMMP2L,intron_variant,,ENST00000447215,;IMMP2L,intron_variant,,ENST00000331762,;IMMP2L,intron_variant,,ENST00000489381,;	T	ENSG00000173114	ENST00000451085	Transcript	missense_variant	1295	249	83	K/N	aaA/aaT	.	.	.	1	LRRN3	HGNC	17200	protein_coding	YES	CCDS5754.1	ENSP00000397312	LRRN3_HUMAN	A4D0T1_HUMAN,E7EW58_HUMAN	UPI0000037517	.	tolerated(0.14)	benign(0.005)	4/4	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF7,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAAAATTGA	.	5	ESCA
PPP1R3A	0	.	GRCh37	7	113519505	113519505	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1642C>A	p.Pro548Thr	p.P548T	ENST00000284601	4/4	29	24	5	58	58	0	PPP1R3A,missense_variant,p.Pro548Thr,ENST00000284601,;PPP1R3A,downstream_gene_variant,,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,;	T	ENSG00000154415	ENST00000284601	Transcript	missense_variant	1711	1642	548	P/T	Cct/Act	.	.	.	-1	PPP1R3A	HGNC	9291	protein_coding	YES	CCDS5759.1	ENSP00000284601	PPR3A_HUMAN	C9JZB3_HUMAN	UPI000013DDAA	.	tolerated(0.44)	benign(0.164)	4/4	.	hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TTTAGGGTTAC	.	3	ESCA
BBS9	0	.	GRCh37	7	33423379	33423379	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1891G>A	p.Asp631Asn	p.D631N	ENST00000242067	18/23	58	51	7	90	90	0	BBS9,missense_variant,p.Asp631Asn,ENST00000242067,;BBS9,missense_variant,p.Asp198Asn,ENST00000434373,;BBS9,missense_variant,p.Asp591Asn,ENST00000350941,;BBS9,missense_variant,p.Asp596Asn,ENST00000396127,;BBS9,missense_variant,p.Asp626Asn,ENST00000355070,;BBS9,missense_variant,p.Asp596Asn,ENST00000354265,;BBS9,non_coding_transcript_exon_variant,,ENST00000496029,;BBS9,3_prime_UTR_variant,,ENST00000433714,;AC006195.2,downstream_gene_variant,,ENST00000423599,;	A	ENSG00000122507	ENST00000242067	Transcript	missense_variant	2412	1891	631	D/N	Gat/Aat	.	.	.	1	BBS9	HGNC	30000	protein_coding	YES	CCDS43566.1	ENSP00000242067	PTHB1_HUMAN	C9JRR5_HUMAN,C9JJ08_HUMAN	UPI000020ED57	.	tolerated(0.07)	possibly_damaging(0.885)	18/23	.	Pfam_domain:PF14728,hmmpanther:PTHR20991:SF0,hmmpanther:PTHR20991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAAAGATTTT	.	4	ESCA
AMPH	0	.	GRCh37	7	38468072	38468072	+	Intron	SNP	G	G	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182+1370C>A	.	.	ENST00000356264	.	19	11	8	55	55	0	AMPH,intron_variant,,ENST00000356264,;AMPH,intron_variant,,ENST00000428293,;AMPH,intron_variant,,ENST00000441628,;AMPH,intron_variant,,ENST00000325590,;AMPH,non_coding_transcript_exon_variant,,ENST00000471913,;AMPH,intron_variant,,ENST00000467580,;AMPH,intron_variant,,ENST00000462072,;AMPH,intron_variant,,ENST00000450124,;	T	ENSG00000078053	ENST00000356264	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AMPH	HGNC	471	protein_coding	YES	CCDS5456.1	ENSP00000348602	AMPH_HUMAN	Q9UQI5_HUMAN,Q9UQI4_HUMAN,Q9UQI3_HUMAN,Q9UQI2_HUMAN	UPI00001259EA	.	.	.	.	14/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAACAGCCTGA	.	4	ESCA
AMPH	0	.	GRCh37	7	38468073	38468073	+	Intron	SNP	C	C	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182+1369G>A	.	.	ENST00000356264	.	19	11	8	55	55	0	AMPH,intron_variant,,ENST00000356264,;AMPH,intron_variant,,ENST00000428293,;AMPH,intron_variant,,ENST00000441628,;AMPH,intron_variant,,ENST00000325590,;AMPH,non_coding_transcript_exon_variant,,ENST00000471913,;AMPH,intron_variant,,ENST00000467580,;AMPH,intron_variant,,ENST00000462072,;AMPH,intron_variant,,ENST00000450124,;	T	ENSG00000078053	ENST00000356264	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AMPH	HGNC	471	protein_coding	YES	CCDS5456.1	ENSP00000348602	AMPH_HUMAN	Q9UQI5_HUMAN,Q9UQI4_HUMAN,Q9UQI3_HUMAN,Q9UQI2_HUMAN	UPI00001259EA	.	.	.	.	14/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AACAGCCTGAT	.	4	ESCA
DDC	0	.	GRCh37	7	50547550	50547550	+	Missense_Mutation	SNP	C	C	A	rs765294373	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956G>T	p.Arg319Ile	p.R319I	ENST00000444124	10/15	29	23	5	52	52	0	DDC,missense_variant,p.Arg241Ile,ENST00000426377,;DDC,missense_variant,p.Arg319Ile,ENST00000444124,;DDC,missense_variant,p.Arg226Ile,ENST00000431062,;DDC,missense_variant,p.Arg200Ile,ENST00000430300,;DDC,missense_variant,p.Arg319Ile,ENST00000357936,;DDC,3_prime_UTR_variant,,ENST00000444733,;DDC,non_coding_transcript_exon_variant,,ENST00000494914,;	A	ENSG00000132437	ENST00000444124	Transcript	missense_variant	1157	956	319	R/I	aGa/aTa	rs765294373,COSM1451341	.	.	-1	DDC	HGNC	2719	protein_coding	YES	CCDS5511.1	ENSP00000403644	DDC_HUMAN	C9JMP0_HUMAN	UPI000013F150	.	tolerated(0.07)	benign(0.278)	10/15	.	Superfamily_domains:SSF53383,Gene3D:3.40.640.10,Pfam_domain:PF00282,hmmpanther:PTHR11999:SF69,hmmpanther:PTHR11999	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTCTCTTT	.	5	ESCA
PEG10	0	.	GRCh37	7	94297434	94297434	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3588C>A	.	.	ENST00000482108	2/2	25	17	8	39	39	0	PEG10,3_prime_UTR_variant,,ENST00000482108,;PEG10,downstream_gene_variant,,ENST00000488574,;PEG10,intron_variant,,ENST00000465184,;PEG10,intron_variant,,ENST00000493935,;	A	ENSG00000242265	ENST00000482108	Transcript	3_prime_UTR_variant	5045	.	.	.	.	.	.	.	1	PEG10	HGNC	14005	protein_coding	YES	CCDS55126.1	ENSP00000417587	PEG10_HUMAN	B4DSP0_HUMAN	UPI0000047FA3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACGACAAGAA	.	5	ESCA
ZNF3	0	.	GRCh37	7	99672873	99672873	+	Silent	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.156C>T	p.%3D	p.T52T	ENST00000303915	4/5	14	10	4	41	41	0	ZNF3,synonymous_variant,p.%3D,ENST00000415068,;ZNF3,synonymous_variant,p.%3D,ENST00000428683,;ZNF3,synonymous_variant,p.%3D,ENST00000303915,;ZNF3,synonymous_variant,p.%3D,ENST00000441298,;ZNF3,synonymous_variant,p.%3D,ENST00000412947,;ZNF3,synonymous_variant,p.%3D,ENST00000449785,;ZNF3,synonymous_variant,p.%3D,ENST00000292393,;ZNF3,synonymous_variant,p.%3D,ENST00000413658,;ZNF3,synonymous_variant,p.%3D,ENST00000424697,;ZNF3,synonymous_variant,p.%3D,ENST00000299667,;ZNF3,non_coding_transcript_exon_variant,,ENST00000487620,;ZNF3,non_coding_transcript_exon_variant,,ENST00000485892,;ZNF3,downstream_gene_variant,,ENST00000466121,;ZNF3,downstream_gene_variant,,ENST00000460331,;ZNF3,downstream_gene_variant,,ENST00000479192,;	A	ENSG00000166526	ENST00000303915	Transcript	synonymous_variant	1124	156	52	T	acC/acT	.	.	.	-1	ZNF3	HGNC	13089	protein_coding	YES	CCDS43619.1	ENSP00000306372	ZNF3_HUMAN	Q86U76_HUMAN,C9JK31_HUMAN,C9JIW8_HUMAN,C9JE35_HUMAN,C9J5S8_HUMAN	UPI000000D9B2	.	.	.	4/5	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24377,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TCAAAGGTTAC	.	4	ESCA
TRPS1	0	.	GRCh37	8	116422600	116422600	+	3'UTR	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3651G>T	.	.	ENST00000395715	7/7	34	31	3	64	64	0	TRPS1,3_prime_UTR_variant,,ENST00000395715,;TRPS1,downstream_gene_variant,,ENST00000520276,;TRPS1,downstream_gene_variant,,ENST00000220888,;TRPS1,downstream_gene_variant,,ENST00000518018,;TRPS1,downstream_gene_variant,,ENST00000519076,;	A	ENSG00000104447	ENST00000395715	Transcript	3_prime_UTR_variant	8114	.	.	.	.	.	.	.	-1	TRPS1	HGNC	12340	protein_coding	YES	CCDS6318.2	ENSP00000379065	TRPS1_HUMAN	F8W8T0_HUMAN,E7EVN4_HUMAN,C9J6L7_HUMAN	UPI00002104B8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TTTTTCCCTTC	.	2	ESCA
C8orf82	0	.	GRCh37	8	145753146	145753146	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.231C>G	p.Phe77Leu	p.F77L	ENST00000524821	3/3	72	58	14	76	76	0	C8orf82,missense_variant,p.Phe122Leu,ENST00000532827,;C8orf82,missense_variant,p.Phe77Leu,ENST00000524821,;C8orf82,3_prime_UTR_variant,,ENST00000313465,;ARHGAP39,downstream_gene_variant,,ENST00000276826,;LRRC24,upstream_gene_variant,,ENST00000529415,;LRRC24,upstream_gene_variant,,ENST00000533758,;C8orf82,downstream_gene_variant,,ENST00000527462,;ARHGAP39,downstream_gene_variant,,ENST00000540274,;LRRC14,downstream_gene_variant,,ENST00000292524,;ARHGAP39,downstream_gene_variant,,ENST00000377307,;LRRC14,downstream_gene_variant,,ENST00000528528,;LRRC14,downstream_gene_variant,,ENST00000530242,;LRRC14,downstream_gene_variant,,ENST00000529995,;C8orf82,missense_variant,p.Phe77Leu,ENST00000534680,;	C	ENSG00000213563	ENST00000524821	Transcript	missense_variant	447	231	77	F/L	ttC/ttG	.	.	.	-1	C8orf82	HGNC	33826	protein_coding	YES	CCDS34970.1	ENSP00000436621	CH082_HUMAN	.	UPI000006EE1C	.	deleterious(0.02)	probably_damaging(0.999)	3/3	.	hmmpanther:PTHR31449,hmmpanther:PTHR31449:SF1,Pfam_domain:PF14956	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGAGAAGAA	.	5	ESCA
TRIM55	0	.	GRCh37	8	67066571	67066571	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1524+2T>C	.	p.X508_splice	ENST00000315962	.	12	9	3	23	23	0	TRIM55,splice_donor_variant,,ENST00000276573,;TRIM55,splice_donor_variant,,ENST00000315962,;TRIM55,intron_variant,,ENST00000353317,;TRIM55,intron_variant,,ENST00000350034,;TRIM55,intron_variant,,ENST00000517647,;	C	ENSG00000147573	ENST00000315962	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	TRIM55	HGNC	14215	protein_coding	YES	CCDS6184.1	ENSP00000323913	TRI55_HUMAN	.	UPI00001CE3B7	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAGGTTAGTG	.	2	ESCA
HSDL2	0	.	GRCh37	9	115233028	115233028	+	3'UTR	SNP	C	C	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*204C>G	.	.	ENST00000398805	11/11	36	12	24	48	48	0	HSDL2,3_prime_UTR_variant,,ENST00000398805,;HSDL2,3_prime_UTR_variant,,ENST00000398803,;HSDL2,downstream_gene_variant,,ENST00000262542,;HSDL2,downstream_gene_variant,,ENST00000539114,;C9orf147,intron_variant,,ENST00000412934,;	G	ENSG00000119471	ENST00000398805	Transcript	3_prime_UTR_variant	1688	.	.	.	.	.	.	.	1	HSDL2	HGNC	18572	protein_coding	YES	CCDS43864.1	ENSP00000381785	HSDL2_HUMAN	B4E136_HUMAN,B4DWC7_HUMAN	UPI0000039E52	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATTCTAAGA	.	5	ESCA
HMCN2	0	.	GRCh37	9	133284204	133284204	+	5'Flank	SNP	G	G	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000428715	.	22	13	9	58	58	0	HMCN2,upstream_gene_variant,,ENST00000428715,;AL354898.1,downstream_gene_variant,,ENST00000277491,;HMCN2,non_coding_transcript_exon_variant,,ENST00000487727,;HMCN2,downstream_gene_variant,,ENST00000480829,;	A	ENSG00000148357	ENST00000428715	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1744	1	HMCN2	HGNC	21293	protein_coding	YES	.	ENSP00000387564	.	H0Y3X1_HUMAN	UPI0001881428	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTGTGGTG	.	5	ESCA
NOTCH1	0	.	GRCh37	9	139413049	139413049	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	6/34	21	12	9	65	65	0	NOTCH1,missense_variant,p.Arg365Cys,ENST00000277541,;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,;	A	ENSG00000148400	ENST00000277541	Transcript	missense_variant	1169	1093	365	R/C	Cgc/Tgc	COSM99651,COSM99652	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	deleterious(0.01)	possibly_damaging(0.901)	6/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R365C|c.1093C>T|4,SITE|p.R365C|c.1093C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCGGCCAT	.	5	ESCA
ZMYND19	0	.	GRCh37	9	140482240	140482240	+	Silent	SNP	A	A	T	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147T>A	p.%3D	p.A49A	ENST00000298585	3/6	50	34	15	89	89	0	ZMYND19,synonymous_variant,p.%3D,ENST00000298585,;ZMYND19,non_coding_transcript_exon_variant,,ENST00000471957,;	T	ENSG00000165724	ENST00000298585	Transcript	synonymous_variant	374	147	49	A	gcT/gcA	.	.	.	-1	ZMYND19	HGNC	21146	protein_coding	YES	CCDS7048.1	ENSP00000298585	ZMY19_HUMAN	.	UPI0000022A7D	.	.	.	3/6	.	hmmpanther:PTHR13244:SF5,hmmpanther:PTHR13244	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTAGCACC	.	5	ESCA
ADAMTSL1	0	.	GRCh37	9	18721596	18721596	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1939C>G	p.Leu647Val	p.L647V	ENST00000380548	15/29	23	15	8	66	66	0	ADAMTSL1,missense_variant,p.Leu647Val,ENST00000380548,;ADAMTSL1,missense_variant,p.Leu647Val,ENST00000276935,;ADAMTSL1,non_coding_transcript_exon_variant,,ENST00000380559,;RP11-503K16.2,upstream_gene_variant,,ENST00000412709,;	G	ENSG00000178031	ENST00000380548	Transcript	missense_variant	2278	1939	647	L/V	Ctg/Gtg	.	.	.	1	ADAMTSL1	HGNC	14632	protein_coding	YES	CCDS47954.1	ENSP00000369921	ATL1_HUMAN	H7BYE3_HUMAN	UPI000004FD83	.	deleterious(0.01)	possibly_damaging(0.507)	15/29	.	PROSITE_profiles:PS50092,hmmpanther:PTHR13723:SF157,hmmpanther:PTHR13723,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACCTGTGC	.	5	ESCA
IRAK1	0	.	GRCh37	X	153289416	153289416	+	5'Flank	SNP	C	C	A	novel	.	TCGA-LN-A9FR-01A-11D-A387-09	TCGA-LN-A9FR-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000369980	.	34	11	22	49	49	0	MECP2,3_prime_UTR_variant,,ENST00000303391,;IRAK1,upstream_gene_variant,,ENST00000369980,;IRAK1,upstream_gene_variant,,ENST00000429936,;IRAK1,upstream_gene_variant,,ENST00000369974,;IRAK1,upstream_gene_variant,,ENST00000444230,;IRAK1,upstream_gene_variant,,ENST00000393687,;IRAK1,upstream_gene_variant,,ENST00000393682,;MIR718,upstream_gene_variant,,ENST00000390190,;IRAK1,upstream_gene_variant,,ENST00000369973,;	A	ENSG00000184216	ENST00000369980	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3985	-1	IRAK1	HGNC	6112	protein_coding	YES	CCDS14740.1	ENSP00000358997	IRAK1_HUMAN	.	UPI000012D873	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGGCTGTTT	.	5	ESCA
ADAM12	0	.	GRCh37	10	127708322	127708322	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2611C>G	p.His871Asp	p.H871D	ENST00000368679	22/23	28	17	10	24	24	0	ADAM12,missense_variant,p.His871Asp,ENST00000368679,;	C	ENSG00000148848	ENST00000368679	Transcript	missense_variant	2921	2611	871	H/D	Cat/Gat	.	.	.	-1	ADAM12	HGNC	190	protein_coding	YES	CCDS7653.1	ENSP00000357668	ADA12_HUMAN	.	UPI000036672C	.	tolerated(0.61)	benign(0.001)	22/23	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATGAGTGA	.	5	ESCA
TTC40	0	.	GRCh37	10	134672745	134672745	+	Silent	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5205G>C	p.%3D	p.L1735L	ENST00000368586	38/58	12	6	6	23	23	0	TTC40,synonymous_variant,p.%3D,ENST00000368586,;TTC40,upstream_gene_variant,,ENST00000263170,;	G	ENSG00000171811	ENST00000368586	Transcript	synonymous_variant	5306	5205	1735	L	ctG/ctC	.	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	.	.	38/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGCTCAGGCA	.	3	ESCA
C1QL3	0	.	GRCh37	10	16562630	16562630	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435C>T	p.%3D	p.F145F	ENST00000298943	1/2	34	26	8	19	19	0	C1QL3,synonymous_variant,p.%3D,ENST00000298943,;	A	ENSG00000165985	ENST00000298943	Transcript	synonymous_variant	1375	435	145	F	ttC/ttT	.	.	.	-1	C1QL3	HGNC	19359	protein_coding	YES	CCDS31156.1	ENSP00000298943	C1QL3_HUMAN	.	UPI000013E53F	.	.	.	1/2	.	PROSITE_profiles:PS50871,hmmpanther:PTHR24022,hmmpanther:PTHR24022:SF24,Gene3D:2.60.120.40,Pfam_domain:PF00386,SMART_domains:SM00110,Superfamily_domains:SSF49842,Prints_domain:PR00007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTCGAACTT	.	5	ESCA
APBB1IP	0	.	GRCh37	10	26790197	26790197	+	Intron	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453+157C>T	.	.	ENST00000376236	.	8	5	3	12	12	0	APBB1IP,3_prime_UTR_variant,,ENST00000356785,;APBB1IP,intron_variant,,ENST00000376236,;	T	ENSG00000077420	ENST00000376236	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	APBB1IP	HGNC	17379	protein_coding	YES	CCDS31167.1	ENSP00000365411	AB1IP_HUMAN	.	UPI00001AF165	.	.	.	.	5/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAACCCTCCG	.	2	ESCA
RP11-85G18.6	0	.	GRCh37	10	27536913	27536913	+	Intron	SNP	T	T	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.256-2074T>C	.	.	ENST00000574842	.	54	35	18	43	43	0	RP11-85G18.6,intron_variant,,ENST00000574842,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000284414,;LRRC37A6P,downstream_gene_variant,,ENST00000575554,;LRRC37A6P,downstream_gene_variant,,ENST00000574795,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000448648,;	C	ENSG00000262412	ENST00000574842	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RP11-85G18.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTTGTATT	.	5	ESCA
ARMC4	0	.	GRCh37	10	28224072	28224072	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2362G>A	p.Glu788Lys	p.E788K	ENST00000305242	16/20	58	44	13	66	66	0	ARMC4,missense_variant,p.Glu313Lys,ENST00000545014,;ARMC4,missense_variant,p.Glu788Lys,ENST00000305242,;ARMC4,missense_variant,p.Glu480Lys,ENST00000537576,;	T	ENSG00000169126	ENST00000305242	Transcript	missense_variant	2455	2362	788	E/K	Gaa/Aaa	.	.	.	-1	ARMC4	HGNC	25583	protein_coding	YES	CCDS7157.1	ENSP00000306410	ARMC4_HUMAN	R4GN11_HUMAN,A8K906_HUMAN	UPI00001A95E1	.	tolerated(0.62)	possibly_damaging(0.507)	16/20	.	hmmpanther:PTHR23315:SF67,hmmpanther:PTHR23315,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTCACGTT	.	5	ESCA
KIF5B	0	.	GRCh37	10	32311947	32311947	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1743C>T	p.%3D	p.G581G	ENST00000302418	16/26	52	37	15	55	55	0	KIF5B,synonymous_variant,p.%3D,ENST00000302418,;KIF5B,upstream_gene_variant,,ENST00000493889,;	A	ENSG00000170759	ENST00000302418	Transcript	synonymous_variant	2201	1743	581	G	ggC/ggT	.	.	.	-1	KIF5B	HGNC	6324	protein_coding	YES	CCDS7171.1	ENSP00000307078	KINH_HUMAN	A8K048_HUMAN	UPI000012DE68	.	.	.	16/26	.	hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATGCCAGT	.	5	ESCA
RET	0	.	GRCh37	10	43600603	43600603	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.829G>C	p.Asp277His	p.D277H	ENST00000355710	4/20	73	41	31	44	44	0	RET,missense_variant,p.Asp277His,ENST00000340058,;RET,missense_variant,p.Asp277His,ENST00000355710,;RET,intron_variant,,ENST00000498820,;RET,non_coding_transcript_exon_variant,,ENST00000479913,;	C	ENSG00000165731	ENST00000355710	Transcript	missense_variant	1061	829	277	D/H	Gac/Cac	.	.	.	1	RET	HGNC	9967	protein_coding	YES	CCDS7200.1	ENSP00000347942	RET_HUMAN	Q9UQV8_HUMAN,Q9UM90_HUMAN,Q9UE13_HUMAN,Q8NFE8_HUMAN,Q8IZR8_HUMAN	UPI00001336E1	.	deleterious(0.02)	possibly_damaging(0.872)	4/20	.	PIRSF_domain:PIRSF000631,hmmpanther:PTHR24416:SF264,hmmpanther:PTHR24416	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGTCGACACC	.	5	ESCA
ITIH5	0	.	GRCh37	10	7601726	7601726	+	3'UTR	SNP	C	C	A	rs758088192	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3278G>T	.	.	ENST00000256861	14/14	16	7	8	12	12	0	ITIH5,3_prime_UTR_variant,,ENST00000256861,;ITIH5,downstream_gene_variant,,ENST00000397146,;ITIH5,downstream_gene_variant,,ENST00000446830,;ITIH5,downstream_gene_variant,,ENST00000298441,;	A	ENSG00000123243	ENST00000256861	Transcript	3_prime_UTR_variant	6228	.	.	.	.	rs758088192	.	.	-1	ITIH5	HGNC	21449	protein_coding	YES	.	ENSP00000256861	ITIH5_HUMAN	.	UPI00001F8AF3	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	AGGGCCGTCTT	.	4	ESCA
IFIT3	0	.	GRCh37	10	91099326	91099326	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.914A>G	p.Glu305Gly	p.E305G	ENST00000371818	2/2	23	12	11	15	15	0	IFIT3,missense_variant,p.Glu305Gly,ENST00000371811,;IFIT3,missense_variant,p.Glu305Gly,ENST00000371818,;LIPA,intron_variant,,ENST00000371837,;LIPA,intron_variant,,ENST00000282673,;LIPA,intron_variant,,ENST00000489359,;LIPA,intron_variant,,ENST00000487618,;LIPA,intron_variant,,ENST00000463623,;	G	ENSG00000119917	ENST00000371818	Transcript	missense_variant	1094	914	305	E/G	gAg/gGg	.	.	.	1	IFIT3	HGNC	5411	protein_coding	YES	CCDS7402.1	ENSP00000360883	IFIT3_HUMAN	Q5T765_HUMAN,B4DLS7_HUMAN	UPI000012D3E5	.	deleterious(0)	probably_damaging(0.932)	2/2	.	hmmpanther:PTHR10271:SF3,hmmpanther:PTHR10271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAGAGATGA	.	5	ESCA
ANKRD2	0	.	GRCh37	10	99343606	99343606	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*124C>T	.	.	ENST00000307518	9/9	20	12	7	20	20	0	ANKRD2,3_prime_UTR_variant,,ENST00000307518,;ANKRD2,3_prime_UTR_variant,,ENST00000370655,;ANKRD2,3_prime_UTR_variant,,ENST00000298808,;ANKRD2,3_prime_UTR_variant,,ENST00000455090,;PI4K2A,upstream_gene_variant,,ENST00000370649,;PI4K2A,upstream_gene_variant,,ENST00000555577,;HOGA1,upstream_gene_variant,,ENST00000370647,;HOGA1,upstream_gene_variant,,ENST00000370646,;HOGA1,upstream_gene_variant,,ENST00000465608,;	T	ENSG00000165887	ENST00000307518	Transcript	3_prime_UTR_variant	1474	.	.	.	.	.	.	.	1	ANKRD2	HGNC	495	protein_coding	YES	CCDS7466.1	ENSP00000306163	ANKR2_HUMAN	.	UPI0000231C90	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATACCACAAA	.	5	ESCA
GRIA4	0	.	GRCh37	11	105852133	105852133	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1667C>G	.	.	ENST00000282499	17/17	19	12	7	36	36	0	GRIA4,3_prime_UTR_variant,,ENST00000282499,;GRIA4,3_prime_UTR_variant,,ENST00000530497,;GRIA4,3_prime_UTR_variant,,ENST00000393127,;GRIA4,downstream_gene_variant,,ENST00000525187,;GRIA4,downstream_gene_variant,,ENST00000533094,;	G	ENSG00000152578	ENST00000282499	Transcript	3_prime_UTR_variant	4822	.	.	.	.	.	.	.	1	GRIA4	HGNC	4574	protein_coding	YES	CCDS8333.1	ENSP00000282499	GRIA4_HUMAN	E9PJZ5_HUMAN	UPI000013DCE6	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GAATGCCATTA	.	4	ESCA
ANO5	0	.	GRCh37	11	22281209	22281209	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1552G>A	p.Gly518Arg	p.G518R	ENST00000324559	15/22	69	54	15	81	81	0	ANO5,missense_variant,p.Gly518Arg,ENST00000324559,;CTD-3064C13.1,downstream_gene_variant,,ENST00000526935,;	A	ENSG00000171714	ENST00000324559	Transcript	missense_variant	1869	1552	518	G/R	Gga/Aga	.	.	.	1	ANO5	HGNC	27337	protein_coding	YES	CCDS31444.1	ENSP00000315371	ANO5_HUMAN	.	UPI000035B19B	.	deleterious(0)	probably_damaging(0.977)	15/22	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF23,Pfam_domain:PF04547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCACAGGATCA	.	4	ESCA
FIBIN	0	.	GRCh37	11	27017112	27017112	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*403C>T	.	.	ENST00000318627	1/1	63	45	17	69	69	0	FIBIN,3_prime_UTR_variant,,ENST00000318627,;	T	ENSG00000176971	ENST00000318627	Transcript	3_prime_UTR_variant	1485	.	.	.	.	.	.	.	1	FIBIN	HGNC	33747	protein_coding	YES	CCDS7861.1	ENSP00000321962	FIBIN_HUMAN	.	UPI000003B0F4	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTCAGCCT	.	5	ESCA
RCN1	0	.	GRCh37	11	32120056	32120056	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609G>A	p.Met203Ile	p.M203I	ENST00000054950	3/6	37	33	4	23	23	0	RCN1,missense_variant,p.Met37Ile,ENST00000530348,;RCN1,missense_variant,p.Met152Ile,ENST00000532942,;RCN1,missense_variant,p.Met203Ile,ENST00000054950,;RCN1,downstream_gene_variant,,ENST00000532721,;RP1-65P5.3,intron_variant,,ENST00000533009,;RCN1,upstream_gene_variant,,ENST00000532474,;RCN1,non_coding_transcript_exon_variant,,ENST00000533898,;RCN1,upstream_gene_variant,,ENST00000527337,;RCN1,upstream_gene_variant,,ENST00000531345,;	A	ENSG00000049449	ENST00000054950	Transcript	missense_variant	902	609	203	M/I	atG/atA	.	.	.	1	RCN1	HGNC	9934	protein_coding	YES	CCDS7876.1	ENSP00000054950	RCN1_HUMAN	Q5J7V8_HUMAN,H0YDA4_HUMAN,E9PP27_HUMAN,E9PLM2_HUMAN	UPI0000000CA7	.	deleterious(0)	probably_damaging(1)	3/6	.	PROSITE_profiles:PS50222,hmmpanther:PTHR10827,hmmpanther:PTHR10827:SF17,Pfam_domain:PF13499,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATATGAAGGA	.	2	ESCA
QSER1	0	.	GRCh37	11	32949549	32949549	+	5'UTR	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-24A>G	.	.	ENST00000399302	3/13	48	32	16	58	58	0	QSER1,5_prime_UTR_variant,,ENST00000527788,;QSER1,5_prime_UTR_variant,,ENST00000528155,;QSER1,5_prime_UTR_variant,,ENST00000399302,;QSER1,intron_variant,,ENST00000527250,;	G	ENSG00000060749	ENST00000399302	Transcript	5_prime_UTR_variant	312	.	.	.	.	.	.	.	1	QSER1	HGNC	26154	protein_coding	YES	CCDS41631.1	ENSP00000382241	QSER1_HUMAN	E9PQD3_HUMAN,B3KWV1_HUMAN	UPI0000E467AF	.	.	.	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCAGTAAC	.	5	ESCA
FBXO3	0	.	GRCh37	11	33770429	33770429	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.942G>A	p.Met314Ile	p.M314I	ENST00000265651	9/11	82	59	23	60	60	0	FBXO3,start_lost,p.Met1?,ENST00000532057,;FBXO3,start_lost,p.Met1?,ENST00000531080,;FBXO3,missense_variant,p.Met314Ile,ENST00000448981,;FBXO3,missense_variant,p.Met314Ile,ENST00000534136,;FBXO3,missense_variant,p.Met201Ile,ENST00000526785,;FBXO3,missense_variant,p.Met309Ile,ENST00000530401,;FBXO3,missense_variant,p.Met314Ile,ENST00000265651,;FBXO3,upstream_gene_variant,,ENST00000527772,;FBXO3,3_prime_UTR_variant,,ENST00000532927,;FBXO3,non_coding_transcript_exon_variant,,ENST00000530013,;	T	ENSG00000110429	ENST00000265651	Transcript	missense_variant	961	942	314	M/I	atG/atA	.	.	.	-1	FBXO3	HGNC	13582	protein_coding	YES	CCDS7887.1	ENSP00000265651	FBX3_HUMAN	Q49AF1_HUMAN,G3V1E0_HUMAN	UPI000000DB30	.	deleterious(0)	probably_damaging(0.985)	9/11	.	PROSITE_profiles:PS51087,hmmpanther:PTHR14289:SF15,hmmpanther:PTHR14289,Pfam_domain:PF04379,Gene3D:1xvsA00,Superfamily_domains:SSF110069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGACATTTC	.	5	ESCA
ZNF195	0	.	GRCh37	11	3380466	3380466	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1772C>G	p.Ser591Ter	p.S591*	ENST00000399602	6/6	48	32	16	50	50	0	ZNF195,stop_gained,p.Ser572Ter,ENST00000526601,;ZNF195,stop_gained,p.Ser523Ter,ENST00000429541,;ZNF195,stop_gained,p.Ser519Ter,ENST00000354599,;ZNF195,stop_gained,p.Ser591Ter,ENST00000399602,;ZNF195,stop_gained,p.Ser523Ter,ENST00000343338,;ZNF195,stop_gained,p.Ser568Ter,ENST00000005082,;ZNF195,intron_variant,,ENST00000528796,;ZNF195,downstream_gene_variant,,ENST00000528410,;ZNF195,downstream_gene_variant,,ENST00000438262,;ZNF195,downstream_gene_variant,,ENST00000529678,;ZNF195,downstream_gene_variant,,ENST00000534569,;ZNF195,downstream_gene_variant,,ENST00000533036,;ZNF195,downstream_gene_variant,,ENST00000427810,;ZNF195,downstream_gene_variant,,ENST00000528636,;ZNF195,downstream_gene_variant,,ENST00000524857,;ZNF195,downstream_gene_variant,,ENST00000330692,;ZNF195,downstream_gene_variant,,ENST00000530643,;ZNF195,downstream_gene_variant,,ENST00000526540,;ZNF195,downstream_gene_variant,,ENST00000529228,;ZNF195,downstream_gene_variant,,ENST00000526598,;ZNF195,downstream_gene_variant,,ENST00000528218,;ZNF195,downstream_gene_variant,,ENST00000529789,;ZNF195,downstream_gene_variant,,ENST00000525313,;	C	ENSG00000005801	ENST00000399602	Transcript	stop_gained	1899	1772	591	S/*	tCa/tGa	.	.	.	-1	ZNF195	HGNC	12986	protein_coding	YES	CCDS44522.1	ENSP00000382511	ZN195_HUMAN	.	UPI0000D6258D	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF87,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTTGAGGAC	.	5	ESCA
OR51Q1	0	.	GRCh37	11	5443799	5443799	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369C>A	p.Asp123Glu	p.D123E	ENST00000300778	1/1	19	15	4	31	31	0	OR51Q1,missense_variant,p.Asp123Glu,ENST00000300778,;HBE1,intron_variant,,ENST00000396895,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380259,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420726,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;	A	ENSG00000167360	ENST00000300778	Transcript	missense_variant	459	369	123	D/E	gaC/gaA	.	.	.	1	OR51Q1	HGNC	14851	protein_coding	YES	CCDS31381.1	ENSP00000300778	O51Q1_HUMAN	.	UPI0000041BDB	.	deleterious(0)	possibly_damaging(0.724)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,hmmpanther:PTHR26450:SF84,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGACTGCTA	.	5	ESCA
OR4A15	0	.	GRCh37	11	55135647	55135647	+	Silent	SNP	C	C	T	rs747544149	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288C>T	p.%3D	p.F96F	ENST00000314706	1/1	62	47	15	77	77	0	OR4A15,synonymous_variant,p.%3D,ENST00000314706,;	T	ENSG00000181958	ENST00000314706	Transcript	synonymous_variant	288	288	96	F	ttC/ttT	rs747544149,COSM3869361	.	.	1	OR4A15	HGNC	15152	protein_coding	YES	CCDS31500.1	ENSP00000325065	O4A15_HUMAN	.	UPI000004618F	.	.	.	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF63,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTCATAGA	byFrequency	5	ESCA
TRIM34	0	.	GRCh37	11	5655908	5655908	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567G>A	p.%3D	p.Q189Q	ENST00000514226	4/8	18	11	6	18	18	0	TRIM34,synonymous_variant,p.%3D,ENST00000514226,;TRIM34,synonymous_variant,p.%3D,ENST00000429814,;TRIM6-TRIM34,synonymous_variant,p.%3D,ENST00000457787,;TRIM6-TRIM34,synonymous_variant,p.%3D,ENST00000354852,;HBG2,intron_variant,,ENST00000380259,;TRIM34,upstream_gene_variant,,ENST00000495668,;TRIM34,non_coding_transcript_exon_variant,,ENST00000491385,;	A	ENSG00000258659	ENST00000514226	Transcript	synonymous_variant	904	567	189	Q	caG/caA	.	.	.	1	TRIM34	HGNC	10063	protein_coding	YES	CCDS31391.1	ENSP00000422947	TRI34_HUMAN	.	UPI000006F93F	.	.	.	4/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCAGCTTAG	.	5	ESCA
OR5B2	0	.	GRCh37	11	58190052	58190052	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683C>T	p.Ser228Leu	p.S228L	ENST00000302581	1/1	56	33	22	48	48	0	OR5B2,missense_variant,p.Ser228Leu,ENST00000302581,;	A	ENSG00000172365	ENST00000302581	Transcript	missense_variant	735	683	228	S/L	tCa/tTa	.	.	.	-1	OR5B2	HGNC	8323	protein_coding	YES	CCDS31550.1	ENSP00000303076	OR5B2_HUMAN	.	UPI000004B227	.	deleterious_low_confidence(0)	possibly_damaging(0.658)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF3,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGCTGAATGC	.	5	ESCA
ZFP91	0	.	GRCh37	11	58388401	58388401	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3222G>T	.	.	ENST00000316059	11/11	87	65	22	87	87	0	ZFP91,3_prime_UTR_variant,,ENST00000316059,;CNTF,upstream_gene_variant,,ENST00000361987,;ZFP91-CNTF,intron_variant,,ENST00000389919,;ZFP91-CNTF,intron_variant,,ENST00000422974,;	T	ENSG00000186660	ENST00000316059	Transcript	3_prime_UTR_variant	5106	.	.	.	.	.	.	.	1	ZFP91	HGNC	14983	protein_coding	YES	CCDS31553.1	ENSP00000339030	ZFP91_HUMAN	B4DIN6_HUMAN	UPI0000070D45	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAGAAATT	.	5	ESCA
OR4D6	0	.	GRCh37	11	59224784	59224784	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351G>A	p.%3D	p.V117V	ENST00000300127	1/1	36	30	5	18	18	0	OR4D6,synonymous_variant,p.%3D,ENST00000300127,;	A	ENSG00000166884	ENST00000300127	Transcript	synonymous_variant	374	351	117	V	gtG/gtA	.	.	.	1	OR4D6	HGNC	15175	protein_coding	YES	CCDS31562.1	ENSP00000300127	OR4D6_HUMAN	.	UPI0000046487	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF300,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTGTGATGGC	.	4	ESCA
TMEM216	0	.	GRCh37	11	61166217	61166217	+	3'UTR	SNP	C	C	T	rs763526089	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*469C>T	.	.	ENST00000515837	5/5	32	25	6	22	22	0	TMEM216,3_prime_UTR_variant,,ENST00000515837,;TMEM216,3_prime_UTR_variant,,ENST00000334888,;CPSF7,downstream_gene_variant,,ENST00000340437,;TMEM216,downstream_gene_variant,,ENST00000398979,;CPSF7,downstream_gene_variant,,ENST00000439958,;CPSF7,downstream_gene_variant,,ENST00000394888,;TMEM216,downstream_gene_variant,,ENST00000544795,;TMEM216,downstream_gene_variant,,ENST00000541473,;	T	ENSG00000187049	ENST00000515837	Transcript	3_prime_UTR_variant	1852	.	.	.	.	rs763526089	.	.	1	TMEM216	HGNC	25018	protein_coding	YES	CCDS53640.1	ENSP00000440638	TM216_HUMAN	J3QT25_HUMAN	UPI0001915109	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCGGAGA	.	5	ESCA
SHANK2	0	.	GRCh37	11	70316128	70316128	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2846G>A	.	.	ENST00000338508	33/33	31	17	14	21	21	0	SHANK2,3_prime_UTR_variant,,ENST00000409161,;SHANK2,3_prime_UTR_variant,,ENST00000338508,;SHANK2,3_prime_UTR_variant,,ENST00000424924,;SHANK2,3_prime_UTR_variant,,ENST00000423696,;SHANK2,3_prime_UTR_variant,,ENST00000449833,;SHANK2,downstream_gene_variant,,ENST00000294018,;SHANK2,downstream_gene_variant,,ENST00000412252,;	T	ENSG00000162105	ENST00000338508	Transcript	3_prime_UTR_variant	8399	.	.	.	.	.	.	.	-1	SHANK2	HGNC	14295	protein_coding	YES	.	ENSP00000345193	.	C9JFP8_HUMAN,A6NHU9_HUMAN	UPI00020653A9	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCAACAT	.	5	ESCA
RBMXL2	0	.	GRCh37	11	7111257	7111257	+	Silent	SNP	C	C	T	rs774916563	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.906C>T	p.%3D	p.Y302Y	ENST00000306904	1/1	32	27	4	21	21	0	RBMXL2,synonymous_variant,p.%3D,ENST00000306904,;	T	ENSG00000170748	ENST00000306904	Transcript	synonymous_variant	1093	906	302	Y	taC/taT	rs774916563	.	.	1	RBMXL2	HGNC	17886	protein_coding	YES	CCDS7777.1	ENSP00000304139	RMXL2_HUMAN	.	UPI000013EBA5	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF306	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P299P|c.897G>A|6	RADIA|MUTECT|MUSE|VARSCANS	TCTTACGGAGG	.	4	ESCA
TENM4	0	.	GRCh37	11	78565338	78565338	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1492G>C	p.Asp498His	p.D498H	ENST00000278550	12/34	16	13	3	14	14	0	TENM4,missense_variant,p.Asp498His,ENST00000278550,;	G	ENSG00000149256	ENST00000278550	Transcript	missense_variant	1955	1492	498	D/H	Gat/Cat	.	.	.	-1	TENM4	HGNC	29945	protein_coding	YES	CCDS44688.1	ENSP00000278550	TEN4_HUMAN	G3CAT1_HUMAN	UPI0000DD8112	.	deleterious(0)	probably_damaging(0.98)	12/34	.	hmmpanther:PTHR11219:SF9,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCCATCCAGCA	.	4	ESCA
CHORDC1	0	.	GRCh37	11	89935146	89935146	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*427G>A	.	.	ENST00000320585	11/11	19	9	9	16	16	0	CHORDC1,3_prime_UTR_variant,,ENST00000457199,;CHORDC1,3_prime_UTR_variant,,ENST00000529726,;CHORDC1,3_prime_UTR_variant,,ENST00000529987,;CHORDC1,3_prime_UTR_variant,,ENST00000320585,;CHORDC1,non_coding_transcript_exon_variant,,ENST00000533724,;CHORDC1,downstream_gene_variant,,ENST00000525317,;	T	ENSG00000110172	ENST00000320585	Transcript	3_prime_UTR_variant	1836	.	.	.	.	.	.	.	-1	CHORDC1	HGNC	14525	protein_coding	YES	CCDS8289.1	ENSP00000319255	CHRD1_HUMAN	E9PHZ2_HUMAN	UPI000013F1A2	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATTTTCAAGTA	.	4	ESCA
DDX51	0	.	GRCh37	12	132626103	132626103	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1044C>T	p.%3D	p.G348G	ENST00000397333	7/15	34	31	3	24	24	0	DDX51,synonymous_variant,p.%3D,ENST00000397333,;NOC4L,upstream_gene_variant,,ENST00000330579,;NOC4L,upstream_gene_variant,,ENST00000541954,;DDX51,non_coding_transcript_exon_variant,,ENST00000329073,;DDX51,non_coding_transcript_exon_variant,,ENST00000545991,;DDX51,non_coding_transcript_exon_variant,,ENST00000546058,;DDX51,upstream_gene_variant,,ENST00000462829,;DDX51,upstream_gene_variant,,ENST00000541489,;	A	ENSG00000185163	ENST00000397333	Transcript	synonymous_variant	1083	1044	348	G	ggC/ggT	.	.	.	-1	DDX51	HGNC	20082	protein_coding	YES	CCDS41865.1	ENSP00000380495	DDX51_HUMAN	.	UPI000049DD95	.	.	.	7/15	.	PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF68,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCGGCCGGG	.	4	ESCA
PXMP2	0	.	GRCh37	12	133272599	133272599	+	Silent	SNP	C	C	T	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366C>T	p.%3D	p.L122L	ENST00000317479	3/5	47	35	11	51	51	0	PXMP2,synonymous_variant,p.%3D,ENST00000317479,;PXMP2,synonymous_variant,p.%3D,ENST00000428960,;PXMP2,intron_variant,,ENST00000539093,;PXMP2,intron_variant,,ENST00000545677,;PXMP2,intron_variant,,ENST00000543589,;RP13-672B3.2,intron_variant,,ENST00000537262,;PXMP2,non_coding_transcript_exon_variant,,ENST00000454379,;	T	ENSG00000176894	ENST00000317479	Transcript	synonymous_variant	431	366	122	L	ctC/ctT	COSM692184	.	.	1	PXMP2	HGNC	9716	protein_coding	YES	CCDS9279.1	ENSP00000321271	PXMP2_HUMAN	.	UPI000016788C	.	.	.	3/5	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11266:SF7,hmmpanther:PTHR11266	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCATGTT	.	5	ESCA
C12orf36	0	.	GRCh37	12	13529360	13529360	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-20-1G>C	.	.	ENST00000318426	.	10	7	3	17	17	0	C12orf36,splice_acceptor_variant,,ENST00000532841,;C12orf36,splice_acceptor_variant,,ENST00000539026,;C12orf36,splice_acceptor_variant,,ENST00000318426,;C12orf36,5_prime_UTR_variant,,ENST00000527705,;C12orf36,splice_acceptor_variant,,ENST00000531049,;	G	ENSG00000180861	ENST00000318426	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	C12orf36	HGNC	26598	protein_coding	YES	.	ENSP00000443007	CL036_HUMAN	.	UPI000014030C	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTTCTGTAG	.	2	ESCA
EPS8	0	.	GRCh37	12	15811043	15811043	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1071G>A	p.%3D	p.L357L	ENST00000281172	12/21	35	25	10	46	46	0	EPS8,synonymous_variant,p.%3D,ENST00000540613,;EPS8,synonymous_variant,p.%3D,ENST00000543612,;EPS8,synonymous_variant,p.%3D,ENST00000281172,;EPS8,synonymous_variant,p.%3D,ENST00000543523,;EPS8,synonymous_variant,p.%3D,ENST00000542903,;EPS8,3_prime_UTR_variant,,ENST00000543468,;EPS8,3_prime_UTR_variant,,ENST00000546261,;EPS8,non_coding_transcript_exon_variant,,ENST00000535734,;EPS8,upstream_gene_variant,,ENST00000541465,;	T	ENSG00000151491	ENST00000281172	Transcript	synonymous_variant	1508	1071	357	L	ttG/ttA	.	.	.	-1	EPS8	HGNC	3420	protein_coding	YES	CCDS31753.1	ENSP00000281172	EPS8_HUMAN	F5H3Q6_HUMAN,F5H2B8_HUMAN,F5H1B5_HUMAN,F5GYM8_HUMAN,B4DX66_HUMAN	UPI000012A0BC	.	.	.	12/21	.	hmmpanther:PTHR12287,hmmpanther:PTHR12287:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACCAAATC	.	5	ESCA
LARP4	0	.	GRCh37	12	50870804	50870804	+	3'UTR	SNP	A	A	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1157A>T	.	.	ENST00000398473	16/16	16	11	5	15	15	0	LARP4,3_prime_UTR_variant,,ENST00000398473,;LARP4,3_prime_UTR_variant,,ENST00000293618,;LARP4,3_prime_UTR_variant,,ENST00000347328,;LARP4,3_prime_UTR_variant,,ENST00000429001,;LARP4,downstream_gene_variant,,ENST00000520064,;LARP4,downstream_gene_variant,,ENST00000518444,;	T	ENSG00000161813	ENST00000398473	Transcript	3_prime_UTR_variant	3444	.	.	.	.	.	.	.	1	LARP4	HGNC	24320	protein_coding	YES	CCDS41782.1	ENSP00000381490	LARP4_HUMAN	Q96J85_HUMAN,F8W1I4_HUMAN,F8VZ60_HUMAN,F8VXL0_HUMAN,F8VSA9_HUMAN,E5RJH8_HUMAN,E5RHZ8_HUMAN	UPI00002293C3	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAAATTTTT	.	2	ESCA
ATF1	0	.	GRCh37	12	51213717	51213717	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*155G>C	.	.	ENST00000262053	7/7	36	23	12	21	21	0	ATF1,3_prime_UTR_variant,,ENST00000262053,;ATF1,3_prime_UTR_variant,,ENST00000539132,;ATF1,3_prime_UTR_variant,,ENST00000551831,;	C	ENSG00000123268	ENST00000262053	Transcript	3_prime_UTR_variant	993	.	.	.	.	.	.	.	1	ATF1	HGNC	783	protein_coding	YES	CCDS8803.1	ENSP00000262053	ATF1_HUMAN	F8VYN3_HUMAN,F8VS03_HUMAN,B4DRF9_HUMAN	UPI0000126227	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAGAGGAGAAA	.	4	ESCA
ZBTB39	0	.	GRCh37	12	57398627	57398627	+	Silent	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75C>G	p.%3D	p.L25L	ENST00000300101	2/2	86	66	20	67	67	0	ZBTB39,synonymous_variant,p.%3D,ENST00000300101,;	C	ENSG00000166860	ENST00000300101	Transcript	synonymous_variant	161	75	25	L	ctC/ctG	.	.	.	-1	ZBTB39	HGNC	29014	protein_coding	YES	CCDS31839.1	ENSP00000300101	ZBT39_HUMAN	.	UPI0000139682	.	.	.	2/2	.	hmmpanther:PTHR24385,hmmpanther:PTHR24385:SF46,Gene3D:3.30.710.10,Pfam_domain:PF00651,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGAGAGCCG	.	5	ESCA
TMBIM4	0	.	GRCh37	12	66546114	66546114	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.249G>C	p.Leu83Phe	p.L83F	ENST00000358230	3/7	18	12	5	23	23	0	TMBIM4,missense_variant,p.Leu52Phe,ENST00000542724,;TMBIM4,missense_variant,p.Leu83Phe,ENST00000358230,;TMBIM4,missense_variant,p.Leu83Phe,ENST00000398033,;TMBIM4,missense_variant,p.Leu83Phe,ENST00000556010,;TMBIM4,missense_variant,p.Leu130Phe,ENST00000286424,;TMBIM4,5_prime_UTR_variant,,ENST00000544599,;TMBIM4,missense_variant,p.Leu83Phe,ENST00000539652,;TMBIM4,3_prime_UTR_variant,,ENST00000545407,;TMBIM4,3_prime_UTR_variant,,ENST00000534930,;TMBIM4,intron_variant,,ENST00000545504,;	G	ENSG00000155957	ENST00000358230	Transcript	missense_variant	370	249	83	L/F	ttG/ttC	.	.	.	-1	TMBIM4	HGNC	24257	protein_coding	YES	CCDS41805.1	ENSP00000350965	LFG4_HUMAN	G3V1R8_HUMAN	UPI00001FC6E2	.	tolerated(0.1)	benign(0.028)	3/7	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR23291:SF34,hmmpanther:PTHR23291,Pfam_domain:PF01027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCAAACC	.	5	ESCA
CD163	0	.	GRCh37	12	7637735	7637735	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2736G>C	p.Lys912Asn	p.K912N	ENST00000359156	11/17	28	17	11	23	23	0	CD163,missense_variant,p.Lys900Asn,ENST00000541972,;CD163,missense_variant,p.Lys912Asn,ENST00000359156,;CD163,missense_variant,p.Lys945Asn,ENST00000396620,;CD163,missense_variant,p.Lys912Asn,ENST00000432237,;CD163,upstream_gene_variant,,ENST00000542280,;CD163,upstream_gene_variant,,ENST00000537626,;CD163,non_coding_transcript_exon_variant,,ENST00000539632,;CD163,non_coding_transcript_exon_variant,,ENST00000538840,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,;	G	ENSG00000177575	ENST00000359156	Transcript	missense_variant	2939	2736	912	K/N	aaG/aaC	.	.	.	-1	CD163	HGNC	1631	protein_coding	YES	CCDS8578.1	ENSP00000352071	C163A_HUMAN	.	UPI00004565CC	.	tolerated(0.27)	benign(0.063)	11/17	.	PROSITE_profiles:PS50287,hmmpanther:PTHR19331:SF268,hmmpanther:PTHR19331,Pfam_domain:PF00530,Gene3D:3.10.250.10,SMART_domains:SM00202,Superfamily_domains:SSF56487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCTTCTC	.	5	ESCA
NAV3	0	.	GRCh37	12	78225209	78225209	+	5'UTR	SNP	C	C	G	rs766987938	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-33C>G	.	.	ENST00000536525	1/39	42	31	10	32	32	0	NAV3,5_prime_UTR_variant,,ENST00000536525,;NAV3,5_prime_UTR_variant,,ENST00000397909,;NAV3,5_prime_UTR_variant,,ENST00000266692,;NAV3,5_prime_UTR_variant,,ENST00000228327,;NAV3,5_prime_UTR_variant,,ENST00000549464,;	G	ENSG00000067798	ENST00000536525	Transcript	5_prime_UTR_variant	141	.	.	.	.	rs766987938	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	.	.	1/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTCTTTGG	.	5	ESCA
CLEC4C	0	.	GRCh37	12	7882268	7882268	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.566A>G	p.Glu189Gly	p.E189G	ENST00000542353	7/7	56	48	7	46	46	0	CLEC4C,missense_variant,p.Glu189Gly,ENST00000542353,;CLEC4C,missense_variant,p.Glu158Gly,ENST00000354629,;CLEC4C,missense_variant,p.Glu189Gly,ENST00000360345,;CLEC4C,missense_variant,p.Glu158Gly,ENST00000540085,;CLEC4C,3_prime_UTR_variant,,ENST00000537530,;CLEC4C,downstream_gene_variant,,ENST00000543765,;	C	ENSG00000198178	ENST00000542353	Transcript	missense_variant	1057	566	189	E/G	gAa/gGa	.	.	.	-1	CLEC4C	HGNC	13258	protein_coding	YES	CCDS8583.1	ENSP00000440428	CLC4C_HUMAN	H0YFH6_HUMAN	UPI000003C38D	.	tolerated(0.44)	benign(0.004)	7/7	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22802:SF204,hmmpanther:PTHR22802,PROSITE_patterns:PS00615,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTTCTGAA	.	5	ESCA
DUSP6	0	.	GRCh37	12	89745616	89745616	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.201G>A	p.%3D	p.Q67Q	ENST00000279488	1/3	16	10	5	9	9	0	DUSP6,synonymous_variant,p.%3D,ENST00000279488,;DUSP6,synonymous_variant,p.%3D,ENST00000308385,;DUSP6,synonymous_variant,p.%3D,ENST00000548755,;DUSP6,upstream_gene_variant,,ENST00000547291,;DUSP6,upstream_gene_variant,,ENST00000547140,;	T	ENSG00000139318	ENST00000279488	Transcript	synonymous_variant	1433	201	67	Q	caG/caA	.	.	.	-1	DUSP6	HGNC	3072	protein_coding	YES	CCDS9033.1	ENSP00000279488	DUS6_HUMAN	F8VZA4_HUMAN	UPI000013ED2F	.	.	.	1/3	.	PROSITE_profiles:PS50206,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF45,Gene3D:3.40.250.10,Pfam_domain:PF00581,PIRSF_domain:PIRSF000939,SMART_domains:SM00450,Superfamily_domains:SSF52821,Prints_domain:PR01764	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTCTGCAG	.	5	ESCA
APAF1	0	.	GRCh37	12	99065330	99065330	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1626G>A	p.%3D	p.E542E	ENST00000551964	12/27	69	58	11	81	81	0	APAF1,synonymous_variant,p.%3D,ENST00000357310,;APAF1,synonymous_variant,p.%3D,ENST00000550527,;APAF1,synonymous_variant,p.%3D,ENST00000339433,;APAF1,synonymous_variant,p.%3D,ENST00000547045,;APAF1,synonymous_variant,p.%3D,ENST00000359972,;APAF1,synonymous_variant,p.%3D,ENST00000549007,;APAF1,synonymous_variant,p.%3D,ENST00000551964,;APAF1,intron_variant,,ENST00000552268,;APAF1,intron_variant,,ENST00000333991,;APAF1,non_coding_transcript_exon_variant,,ENST00000555047,;	A	ENSG00000120868	ENST00000551964	Transcript	synonymous_variant	2362	1626	542	E	gaG/gaA	.	.	.	1	APAF1	HGNC	576	protein_coding	YES	CCDS9069.1	ENSP00000448165	APAF_HUMAN	.	UPI0000036328	.	.	.	12/27	.	hmmpanther:PTHR22845:SF1,hmmpanther:PTHR22845,PIRSF_domain:PIRSF037646	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGAGAATTT	.	5	ESCA
TM9SF2	0	.	GRCh37	13	100215132	100215132	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120C>G	.	.	ENST00000376387	17/17	9	3	6	26	26	0	TM9SF2,3_prime_UTR_variant,,ENST00000376387,;	G	ENSG00000125304	ENST00000376387	Transcript	3_prime_UTR_variant	2302	.	.	.	.	.	.	.	1	TM9SF2	HGNC	11865	protein_coding	YES	CCDS9493.1	ENSP00000365567	TM9S2_HUMAN	.	UPI000013684D	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAACACCGTAA	.	2	ESCA
F10	0	.	GRCh37	13	113803401	113803401	+	Missense_Mutation	SNP	G	G	A	rs781413602	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1037G>A	p.Arg346His	p.R346H	ENST00000375559	8/8	42	20	22	17	17	0	F10,missense_variant,p.Arg346His,ENST00000375559,;F10,3_prime_UTR_variant,,ENST00000409306,;F10,3_prime_UTR_variant,,ENST00000375551,;F10,downstream_gene_variant,,ENST00000410083,;F10,downstream_gene_variant,,ENST00000477269,;F10,downstream_gene_variant,,ENST00000498455,;	A	ENSG00000126218	ENST00000375559	Transcript	missense_variant	1075	1037	346	R/H	cGt/cAt	rs781413602,COSM3711005	.	.	1	F10	HGNC	3528	protein_coding	YES	CCDS9530.1	ENSP00000364709	FA10_HUMAN	Q5JVE7_HUMAN	UPI000000DB39	.	deleterious(0.04)	benign(0.307)	8/8	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24265:SF40,hmmpanther:PTHR24265,Pfam_domain:PF00089,Gene3D:2.40.10.10,PIRSF_domain:PIRSF001143,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGCGTGACT	byFrequency	5	ESCA
XPO4	0	.	GRCh37	13	21417979	21417979	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.503C>G	p.Ser168Ter	p.S168*	ENST00000255305	5/23	18	15	3	30	30	0	XPO4,stop_gained,p.Ser168Ter,ENST00000255305,;XPO4,stop_gained,p.Ser168Ter,ENST00000400602,;	C	ENSG00000132953	ENST00000255305	Transcript	stop_gained	575	503	168	S/*	tCa/tGa	COSM3467646,COSM3467645	.	.	-1	XPO4	HGNC	17796	protein_coding	YES	CCDS41872.1	ENSP00000255305	XPO4_HUMAN	Q8IVQ8_HUMAN,Q0VG75_HUMAN	UPI0000139018	.	.	.	5/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12596:SF1,hmmpanther:PTHR12596,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTGAAAAT	.	5	ESCA
VWA8	0	.	GRCh37	13	42439942	42439942	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355G>T	p.Gly452Val	p.G452V	ENST00000379310	12/45	34	22	12	77	77	0	VWA8,missense_variant,p.Gly452Val,ENST00000281496,;VWA8,missense_variant,p.Gly452Val,ENST00000379310,;VWA8,non_coding_transcript_exon_variant,,ENST00000379302,;	A	ENSG00000102763	ENST00000379310	Transcript	missense_variant	1424	1355	452	G/V	gGa/gTa	.	.	.	-1	VWA8	HGNC	29071	protein_coding	YES	CCDS41881.1	ENSP00000368612	VWA8_HUMAN	.	UPI00001606AC	.	deleterious(0)	probably_damaging(0.997)	12/45	.	hmmpanther:PTHR21610,hmmpanther:PTHR21610:SF9,Pfam_domain:PF07728,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCCACAA	.	5	ESCA
IGHV3-16	0	.	GRCh37	14	106622151	106622151	+	Missense_Mutation	SNP	G	G	C	rs58425668	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94C>G	p.Gln32Glu	p.Q32E	ENST00000390604	2/2	139	97	41	112	112	0	IGHV3-16,missense_variant,p.Gln32Glu,ENST00000390604,;IGHVII-15-1,upstream_gene_variant,,ENST00000517931,;	C	ENSG00000211944	ENST00000390604	Transcript	missense_variant	168	94	32	Q/E	Cag/Gag	rs58425668	.	.	-1	IGHV3-16	HGNC	5583	IG_V_gene	YES	.	ENSP00000375013	.	.	UPI000011AADA	.	deleterious_low_confidence(0.01)	benign(0.137)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266:SF80,hmmpanther:PTHR23266,Pfam_domain:PF07686,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	C:0.0006	C:0.0023	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	AGGCTGTACCA	byFrequency|by1000G	3	ESCA
IGHV3-43	0	.	GRCh37	14	106926605	106926605	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40T>G	p.Leu14Val	p.L14V	ENST00000434710	1/2	209	145	64	180	180	0	IGHV3-43,missense_variant,p.Leu14Val,ENST00000434710,;IGHVII-43-1,downstream_gene_variant,,ENST00000522649,;	C	ENSG00000232216	ENST00000434710	Transcript	missense_variant	120	40	14	L/V	Tta/Gta	.	.	.	-1	IGHV3-43	HGNC	5604	IG_V_gene	YES	.	ENSP00000399826	.	.	UPI000011AACC	.	deleterious_low_confidence(0)	benign(0.111)	1/2	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTAAAATAG	.	5	ESCA
NID2	0	.	GRCh37	14	52505686	52505686	+	Missense_Mutation	SNP	G	G	C	rs754851814	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2036C>G	p.Ser679Cys	p.S679C	ENST00000216286	9/22	36	27	9	35	35	0	NID2,missense_variant,p.Ser626Cys,ENST00000541773,;NID2,missense_variant,p.Ser679Cys,ENST00000216286,;NID2,upstream_gene_variant,,ENST00000556572,;NID2,non_coding_transcript_exon_variant,,ENST00000554284,;	C	ENSG00000087303	ENST00000216286	Transcript	missense_variant	2036	2036	679	S/C	tCt/tGt	rs754851814	.	.	-1	NID2	HGNC	13389	protein_coding	YES	CCDS9706.1	ENSP00000216286	NID2_HUMAN	.	UPI000013C6E1	.	deleterious(0)	benign(0.113)	9/22	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50993,Gene3D:2.40.155.10,Pfam_domain:PF07474,SMART_domains:SM00682,Superfamily_domains:SSF54511	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTAGAGGTC	byFrequency	5	ESCA
SYNE2	0	.	GRCh37	14	64518452	64518452	+	Missense_Mutation	SNP	G	G	T	rs759309364	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7821G>T	p.Trp2607Cys	p.W2607C	ENST00000358025	48/116	39	29	10	32	32	0	SYNE2,missense_variant,p.Trp2640Cys,ENST00000554584,;SYNE2,missense_variant,p.Trp2607Cys,ENST00000358025,;SYNE2,missense_variant,p.Trp2607Cys,ENST00000344113,;SYNE2,5_prime_UTR_variant,,ENST00000357395,;SYNE2,downstream_gene_variant,,ENST00000557005,;	T	ENSG00000054654	ENST00000358025	Transcript	missense_variant	8051	7821	2607	W/C	tgG/tgT	rs759309364	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	possibly_damaging(0.902)	48/116	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTGGGAACA	byFrequency	5	ESCA
EXD2	0	.	GRCh37	14	69707767	69707767	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1816C>G	p.Gln606Glu	p.Q606E	ENST00000409018	9/9	26	19	7	16	16	0	EXD2,missense_variant,p.Gln481Glu,ENST00000449989,;EXD2,missense_variant,p.Gln606Glu,ENST00000409018,;EXD2,missense_variant,p.Gln481Glu,ENST00000409014,;EXD2,missense_variant,p.Gln481Glu,ENST00000409949,;EXD2,missense_variant,p.Gln481Glu,ENST00000409242,;EXD2,missense_variant,p.Gln606Glu,ENST00000312994,;EXD2,missense_variant,p.Gln481Glu,ENST00000409675,;RP11-363J20.2,intron_variant,,ENST00000556316,;EXD2,non_coding_transcript_exon_variant,,ENST00000492815,;EXD2,downstream_gene_variant,,ENST00000465286,;	G	ENSG00000081177	ENST00000409018	Transcript	missense_variant	1944	1816	606	Q/E	Cag/Gag	.	.	.	1	EXD2	HGNC	20217	protein_coding	YES	CCDS53902.1	ENSP00000387331	EXD2_HUMAN	C9JLF4_HUMAN	UPI0000577ED7	.	tolerated(1)	benign(0.001)	9/9	.	hmmpanther:PTHR13620:SF0,hmmpanther:PTHR13620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCATCAGAAG	.	3	ESCA
EXD2	0	.	GRCh37	14	69707805	69707805	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1854C>G	p.Ile618Met	p.I618M	ENST00000409018	9/9	22	14	8	16	16	0	EXD2,missense_variant,p.Ile493Met,ENST00000449989,;EXD2,missense_variant,p.Ile618Met,ENST00000409018,;EXD2,missense_variant,p.Ile493Met,ENST00000409014,;EXD2,missense_variant,p.Ile493Met,ENST00000409949,;EXD2,missense_variant,p.Ile493Met,ENST00000409242,;EXD2,missense_variant,p.Ile618Met,ENST00000312994,;EXD2,missense_variant,p.Ile493Met,ENST00000409675,;RP11-363J20.2,intron_variant,,ENST00000556316,;EXD2,non_coding_transcript_exon_variant,,ENST00000492815,;EXD2,downstream_gene_variant,,ENST00000465286,;	G	ENSG00000081177	ENST00000409018	Transcript	missense_variant	1982	1854	618	I/M	atC/atG	.	.	.	1	EXD2	HGNC	20217	protein_coding	YES	CCDS53902.1	ENSP00000387331	EXD2_HUMAN	C9JLF4_HUMAN	UPI0000577ED7	.	deleterious(0.03)	benign(0.167)	9/9	.	hmmpanther:PTHR13620:SF0,hmmpanther:PTHR13620	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCATCCAGCT	.	2	ESCA
ULK4P3	0	.	GRCh37	15	30395997	30395997	+	RNA	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.63G>C	.	.	ENST00000568486	1/5	95	87	7	158	158	0	ULK4P3,non_coding_transcript_exon_variant,,ENST00000565158,;ULK4P3,non_coding_transcript_exon_variant,,ENST00000566138,;ULK4P3,non_coding_transcript_exon_variant,,ENST00000568486,;ULK4P3,non_coding_transcript_exon_variant,,ENST00000568274,;DNM1P28,upstream_gene_variant,,ENST00000565702,;	C	ENSG00000178081	ENST00000568486	Transcript	non_coding_transcript_exon_variant	63	.	.	.	.	.	.	.	1	ULK4P3	HGNC	15777	processed_transcript	YES	.	.	.	.	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGGGGAGAGG	.	2	ESCA
PLA2G4E	0	.	GRCh37	15	42285008	42285008	+	Missense_Mutation	SNP	C	C	T	rs139550977	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1397G>A	p.Arg466His	p.R466H	ENST00000399518	13/20	22	10	12	43	43	0	PLA2G4E,missense_variant,p.Arg466His,ENST00000399518,;PLA2G4E,missense_variant,p.Arg437His,ENST00000413860,;CTD-2382E5.1,intron_variant,,ENST00000499478,;PLA2G4E,non_coding_transcript_exon_variant,,ENST00000547930,;PLA2G4E,upstream_gene_variant,,ENST00000551073,;	T	ENSG00000188089	ENST00000399518	Transcript	missense_variant	1884	1397	466	R/H	cGc/cAc	rs139550977	.	.	-1	PLA2G4E	HGNC	24791	protein_coding	YES	CCDS55962.1	ENSP00000382434	.	B7WPN2_HUMAN	UPI0000E59BE5	.	deleterious(0.03)	benign(0.099)	13/20	.	PROSITE_profiles:PS51210,hmmpanther:PTHR10728,hmmpanther:PTHR10728:SF24,Gene3D:3.40.1090.10,Pfam_domain:PF01735,SMART_domains:SM00022,Superfamily_domains:SSF52151	T:0.0008	T:0	T:0.0014	.	T:0.003	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTGCGCTGC	byFrequency|byCluster|by1000G	5	ESCA
EIF3J	0	.	GRCh37	15	44843706	44843706	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280G>A	p.Glu94Lys	p.E94K	ENST00000261868	4/8	65	42	23	49	49	0	EIF3J,missense_variant,p.Glu94Lys,ENST00000535391,;EIF3J,missense_variant,p.Glu94Lys,ENST00000261868,;EIF3J,intron_variant,,ENST00000424492,;EIF3J,upstream_gene_variant,,ENST00000536248,;EIF3J,non_coding_transcript_exon_variant,,ENST00000558227,;EIF3J,non_coding_transcript_exon_variant,,ENST00000558053,;	A	ENSG00000104131	ENST00000261868	Transcript	missense_variant	418	280	94	E/K	Gaa/Aaa	.	.	.	1	EIF3J	HGNC	3270	protein_coding	YES	CCDS10111.1	ENSP00000261868	EIF3J_HUMAN	.	UPI000012D2F9	.	deleterious(0.04)	unknown(0)	4/8	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,HAMAP:MF_03009,hmmpanther:PTHR21681,Pfam_domain:PF08597	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAGAAATT	.	5	ESCA
DUOX2	0	.	GRCh37	15	45399058	45399058	+	Silent	SNP	G	G	C	rs760019432	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1803C>G	p.%3D	p.T601T	ENST00000603300	15/34	19	14	5	16	16	0	DUOX2,synonymous_variant,p.%3D,ENST00000389039,;DUOX2,synonymous_variant,p.%3D,ENST00000603300,;DUOX2,non_coding_transcript_exon_variant,,ENST00000558383,;	C	ENSG00000140279	ENST00000603300	Transcript	synonymous_variant	2006	1803	601	T	acC/acG	rs760019432	.	.	-1	DUOX2	HGNC	13273	protein_coding	YES	CCDS10117.1	ENSP00000475084	DUOX2_HUMAN	S6B490_HUMAN	UPI000013D775	.	.	.	15/34	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	ATGATGGTGAT	byFrequency	3	ESCA
SEMA6D	0	.	GRCh37	15	48053870	48053870	+	Missense_Mutation	SNP	G	G	A	rs758377829	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460G>A	p.Glu154Lys	p.E154K	ENST00000316364	7/19	44	31	12	40	40	0	SEMA6D,missense_variant,p.Glu154Lys,ENST00000389432,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000358066,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000389428,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000389425,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000559196,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000355997,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000389433,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000558014,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000537942,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000354744,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000536845,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000558816,;SEMA6D,missense_variant,p.Glu154Lys,ENST00000316364,;SEMA6D,downstream_gene_variant,,ENST00000560636,;SEMA6D,upstream_gene_variant,,ENST00000559064,;SEMA6D,upstream_gene_variant,,ENST00000560006,;SEMA6D,downstream_gene_variant,,ENST00000559184,;SEMA6D,downstream_gene_variant,,ENST00000561133,;SEMA6D,downstream_gene_variant,,ENST00000561106,;SEMA6D,upstream_gene_variant,,ENST00000558431,;	A	ENSG00000137872	ENST00000316364	Transcript	missense_variant	899	460	154	E/K	Gaa/Aaa	rs758377829	.	.	1	SEMA6D	HGNC	16770	protein_coding	YES	CCDS32225.1	ENSP00000324857	SEM6D_HUMAN	Q9HAH9_HUMAN,H0YMV0_HUMAN,H0YMA6_HUMAN,H0YL82_HUMAN	UPI000006E201	.	deleterious(0)	possibly_damaging(0.517)	7/19	.	Superfamily_domains:SSF101912,SMART_domains:SM00630,Gene3D:2.130.10.10,Pfam_domain:PF01403,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF65,PROSITE_profiles:PS51004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTAGAATAT	byFrequency	5	ESCA
RFX7	0	.	GRCh37	15	56390515	56390515	+	Missense_Mutation	SNP	G	G	C	rs377452165	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.871C>G	p.Gln291Glu	p.Q291E	ENST00000423270	8/9	40	29	11	47	47	0	RFX7,missense_variant,p.Gln291Glu,ENST00000423270,;RFX7,missense_variant,p.Gln194Glu,ENST00000559447,;RFX7,missense_variant,p.Gln291Glu,ENST00000317318,;RFX7,missense_variant,p.Gln194Glu,ENST00000422057,;RFX7,missense_variant,p.Gln194Glu,ENST00000559847,;	C	ENSG00000181827	ENST00000423270	Transcript	missense_variant	871	871	291	Q/E	Cag/Gag	rs377452165	.	.	-1	RFX7	HGNC	25777	protein_coding	YES	.	ENSP00000397644	RFX7_HUMAN	H0YMH6_HUMAN,H0YLP2_HUMAN	UPI000057809D	.	deleterious(0.03)	possibly_damaging(0.526)	8/9	.	hmmpanther:PTHR12619:SF2,hmmpanther:PTHR12619	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCTGAAAGG	byCluster	2	ESCA
RFX7	0	.	GRCh37	15	56436654	56436654	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.223G>C	p.Glu75Gln	p.E75Q	ENST00000423270	3/9	34	28	6	25	25	0	RFX7,missense_variant,p.Glu75Gln,ENST00000423270,;RFX7,missense_variant,p.Glu75Gln,ENST00000317318,;RFX7,5_prime_UTR_variant,,ENST00000560792,;RFX7,5_prime_UTR_variant,,ENST00000559447,;RFX7,5_prime_UTR_variant,,ENST00000422057,;RFX7,upstream_gene_variant,,ENST00000559847,;	G	ENSG00000181827	ENST00000423270	Transcript	missense_variant	223	223	75	E/Q	Gag/Cag	.	.	.	-1	RFX7	HGNC	25777	protein_coding	YES	.	ENSP00000397644	RFX7_HUMAN	H0YMH6_HUMAN,H0YLP2_HUMAN	UPI000057809D	.	tolerated(0.1)	benign(0.012)	3/9	.	hmmpanther:PTHR12619:SF2,hmmpanther:PTHR12619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCTAGGT	.	5	ESCA
TEX9	0	.	GRCh37	15	56720564	56720564	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1099-1G>C	.	p.X367_splice	ENST00000352903	.	30	22	7	16	15	0	TEX9,splice_acceptor_variant,,ENST00000537232,;TEX9,splice_acceptor_variant,,ENST00000352903,;TEX9,splice_acceptor_variant,,ENST00000560582,;MNS1,downstream_gene_variant,,ENST00000260453,;MNS1,intron_variant,,ENST00000566386,;	C	ENSG00000151575	ENST00000352903	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	TEX9	HGNC	29585	protein_coding	YES	CCDS10157.1	ENSP00000342169	TEX9_HUMAN	H0YKG1_HUMAN,B4DH73_HUMAN	UPI00000731FD	.	.	.	.	11/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACAGATGCA	.	5	ESCA
TEX9	0	.	GRCh37	15	56720645	56720645	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3G>C	.	.	ENST00000352903	12/13	22	15	7	20	20	0	TEX9,3_prime_UTR_variant,,ENST00000537232,;TEX9,3_prime_UTR_variant,,ENST00000352903,;TEX9,3_prime_UTR_variant,,ENST00000560582,;MNS1,downstream_gene_variant,,ENST00000260453,;MNS1,intron_variant,,ENST00000566386,;	C	ENSG00000151575	ENST00000352903	Transcript	3_prime_UTR_variant	1203	.	.	.	.	.	.	.	1	TEX9	HGNC	29585	protein_coding	YES	CCDS10157.1	ENSP00000342169	TEX9_HUMAN	H0YKG1_HUMAN,B4DH73_HUMAN	UPI00000731FD	.	.	.	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGTGATCTA	.	5	ESCA
ZNF280D	0	.	GRCh37	15	56993148	56993148	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364C>G	p.Gln122Glu	p.Q122E	ENST00000267807	6/22	61	58	3	60	60	0	ZNF280D,missense_variant,p.Gln109Glu,ENST00000559000,;ZNF280D,missense_variant,p.Gln122Glu,ENST00000267807,;ZNF280D,missense_variant,p.Gln109Glu,ENST00000559237,;ZNF280D,missense_variant,p.Gln122Glu,ENST00000558320,;ZNF280D,5_prime_UTR_variant,,ENST00000396245,;ZNF280D,downstream_gene_variant,,ENST00000559352,;ZNF280D,missense_variant,p.Gln122Glu,ENST00000560002,;ZNF280D,missense_variant,p.Gln122Glu,ENST00000558002,;	C	ENSG00000137871	ENST00000267807	Transcript	missense_variant	581	364	122	Q/E	Cag/Gag	.	.	.	-1	ZNF280D	HGNC	25953	protein_coding	YES	CCDS32245.1	ENSP00000267807	Z280D_HUMAN	H0YN90_HUMAN	UPI00003FF962	.	tolerated(0.06)	possibly_damaging(0.785)	6/22	.	hmmpanther:PTHR23228:SF114,hmmpanther:PTHR23228,Pfam_domain:PF13836	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCTGAACAA	.	2	ESCA
FAM219B	0	.	GRCh37	15	75198649	75198649	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272C>T	p.Ser91Leu	p.S91L	ENST00000357635	2/5	68	54	14	68	68	0	FAM219B,missense_variant,p.Ser5Leu,ENST00000565772,;FAM219B,missense_variant,p.Ser91Leu,ENST00000562698,;FAM219B,missense_variant,p.Ser91Leu,ENST00000563119,;FAM219B,missense_variant,p.Ser91Leu,ENST00000357635,;FAM219B,missense_variant,p.Ser91Leu,ENST00000457294,;FAM219B,upstream_gene_variant,,ENST00000563706,;FAM219B,missense_variant,p.Ser89Leu,ENST00000563671,;FAM219B,missense_variant,p.Ser91Leu,ENST00000564019,;FAM219B,missense_variant,p.Ser91Leu,ENST00000563069,;FAM219B,missense_variant,p.Ser12Leu,ENST00000567388,;FAM219B,non_coding_transcript_exon_variant,,ENST00000566894,;FAM219B,non_coding_transcript_exon_variant,,ENST00000564857,;FAM219B,intron_variant,,ENST00000563877,;FAM219B,intron_variant,,ENST00000569524,;FAM219B,intron_variant,,ENST00000570143,;FAM219B,intron_variant,,ENST00000569761,;FAM219B,intron_variant,,ENST00000566194,;FAM219B,intron_variant,,ENST00000563413,;FAM219B,upstream_gene_variant,,ENST00000566132,;	A	ENSG00000178761	ENST00000357635	Transcript	missense_variant	593	272	91	S/L	tCg/tTg	COSM3816753,COSM3816754	.	.	-1	FAM219B	HGNC	24695	protein_coding	YES	CCDS32295.1	ENSP00000350260	F219B_HUMAN	H3BPC2_HUMAN	UPI0000073A99	.	tolerated(0.24)	benign(0.002)	2/5	.	hmmpanther:PTHR31281:SF2,hmmpanther:PTHR31281,Pfam_domain:PF15260	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGCGAGGCC	.	5	ESCA
AKAP13	0	.	GRCh37	15	86122760	86122760	+	Missense_Mutation	SNP	G	G	C	rs111631396	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1461G>C	p.Met487Ile	p.M487I	ENST00000361243	7/37	17	10	6	13	13	0	AKAP13,missense_variant,p.Met487Ile,ENST00000394518,;AKAP13,missense_variant,p.Met487Ile,ENST00000559362,;AKAP13,missense_variant,p.Met487Ile,ENST00000361243,;AKAP13,downstream_gene_variant,,ENST00000558166,;AKAP13,downstream_gene_variant,,ENST00000558811,;RP11-815J21.2,non_coding_transcript_exon_variant,,ENST00000561409,;AKAP13,upstream_gene_variant,,ENST00000560340,;AKAP13,upstream_gene_variant,,ENST00000561337,;	C	ENSG00000170776	ENST00000361243	Transcript	missense_variant	1542	1461	487	M/I	atG/atC	rs111631396	.	.	1	AKAP13	HGNC	371	protein_coding	YES	CCDS32320.1	ENSP00000354718	AKP13_HUMAN	H0YMI5_HUMAN,A8MYJ1_HUMAN	UPI00001A8BEB	.	tolerated_low_confidence(0.26)	benign(0.013)	7/37	.	hmmpanther:PTHR13944:SF4,hmmpanther:PTHR13944	A:0.0008	A:0.003	A:0	.	A:0	A:0	A:0	A:0.0041	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATGAACCC	byFrequency|byCluster|by1000G	4	ESCA
NR2F2	0	.	GRCh37	15	96881960	96881960	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1109G>A	.	.	ENST00000394166	3/3	75	51	24	82	82	0	NR2F2,3_prime_UTR_variant,,ENST00000394166,;NR2F2,3_prime_UTR_variant,,ENST00000394171,;NR2F2,downstream_gene_variant,,ENST00000453270,;NR2F2,downstream_gene_variant,,ENST00000421109,;NR2F2,downstream_gene_variant,,ENST00000559679,;	A	ENSG00000185551	ENST00000394166	Transcript	3_prime_UTR_variant	3743	.	.	.	.	.	.	.	1	NR2F2	HGNC	7976	protein_coding	YES	CCDS10375.1	ENSP00000377721	COT2_HUMAN	H3BTC2_HUMAN,F1D8R0_HUMAN	UPI000000052E	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTGAACTG	.	5	ESCA
XYLT1	0	.	GRCh37	16	17353166	17353166	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.592G>C	p.Glu198Gln	p.E198Q	ENST00000261381	3/12	22	17	5	22	22	0	XYLT1,missense_variant,p.Glu198Gln,ENST00000261381,;XYLT1,upstream_gene_variant,,ENST00000575674,;	G	ENSG00000103489	ENST00000261381	Transcript	missense_variant	677	592	198	E/Q	Gaa/Caa	.	.	.	-1	XYLT1	HGNC	15516	protein_coding	YES	CCDS10569.1	ENSP00000261381	XYLT1_HUMAN	.	UPI000000DCCE	.	tolerated_low_confidence(0.2)	benign(0.011)	3/12	.	hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTTCCAGCT	.	2	ESCA
SRRM2	0	.	GRCh37	16	2814594	2814594	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4065G>C	p.Leu1355Phe	p.L1355F	ENST00000301740	11/15	40	20	19	44	44	0	SRRM2,missense_variant,p.Leu1355Phe,ENST00000301740,;SRRM2,downstream_gene_variant,,ENST00000576924,;SRRM2,downstream_gene_variant,,ENST00000571378,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,intron_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,upstream_gene_variant,,ENST00000572721,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000574593,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,upstream_gene_variant,,ENST00000572883,;SRRM2,upstream_gene_variant,,ENST00000576878,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,upstream_gene_variant,,ENST00000571041,;SRRM2,downstream_gene_variant,,ENST00000573451,;SRRM2,upstream_gene_variant,,ENST00000573311,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000572952,;SRRM2,upstream_gene_variant,,ENST00000574331,;SRRM2,upstream_gene_variant,,ENST00000570705,;	C	ENSG00000167978	ENST00000301740	Transcript	missense_variant	4614	4065	1355	L/F	ttG/ttC	.	.	.	1	SRRM2	HGNC	16639	protein_coding	YES	CCDS32373.1	ENSP00000301740	SRRM2_HUMAN	I3L4D8_HUMAN,I3L1I8_HUMAN,I3L1C0_HUMAN,I3L182_HUMAN,I3L0N7_HUMAN	UPI000049DDFC	.	.	unknown(0)	11/15	.	hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTGAATGG	.	5	ESCA
MYLK3	0	.	GRCh37	16	46782047	46782047	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>T	p.Thr20Ile	p.T20I	ENST00000394809	1/13	36	27	8	44	44	0	MYLK3,missense_variant,p.Thr20Ile,ENST00000394809,;MYLK3,intron_variant,,ENST00000536476,;MYLK3,intron_variant,,ENST00000569810,;	A	ENSG00000140795	ENST00000394809	Transcript	missense_variant	175	59	20	T/I	aCc/aTc	.	.	.	-1	MYLK3	HGNC	29826	protein_coding	YES	CCDS10723.2	ENSP00000378288	MYLK3_HUMAN	.	UPI000059D380	.	tolerated_low_confidence(0.09)	benign(0)	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGGTCTTG	.	5	ESCA
ARL2BP	0	.	GRCh37	16	57280047	57280047	+	Missense_Mutation	SNP	A	A	C	rs199762075	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94A>C	p.Ile32Leu	p.I32L	ENST00000219204	2/6	69	57	12	61	61	0	ARL2BP,missense_variant,p.Ile30Leu,ENST00000563234,;ARL2BP,missense_variant,p.Ile32Leu,ENST00000562023,;ARL2BP,missense_variant,p.Ile32Leu,ENST00000219204,;RP11-407G23.3,downstream_gene_variant,,ENST00000564376,;RP11-407G23.4,upstream_gene_variant,,ENST00000562409,;ARL2BP,non_coding_transcript_exon_variant,,ENST00000565794,;	C	ENSG00000102931	ENST00000219204	Transcript	missense_variant	364	94	32	I/L	Atc/Ctc	rs199762075	.	.	1	ARL2BP	HGNC	17146	protein_coding	YES	CCDS10776.1	ENSP00000219204	AR2BP_HUMAN	.	UPI00000372F1	.	tolerated(0.3)	possibly_damaging(0.599)	2/6	.	hmmpanther:PTHR15487,hmmpanther:PTHR15487:SF4,Gene3D:2k0sA00,Pfam_domain:PF11527	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTATCATG	byCluster	5	ESCA
CNOT1	0	.	GRCh37	16	58580291	58580291	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3940G>C	p.Glu1314Gln	p.E1314Q	ENST00000317147	29/49	26	19	6	24	24	0	CNOT1,missense_variant,p.Glu1314Gln,ENST00000317147,;CNOT1,missense_variant,p.Glu1309Gln,ENST00000569240,;CNOT1,missense_variant,p.Glu1314Gln,ENST00000441024,;CNOT1,missense_variant,p.Glu165Gln,ENST00000245138,;CNOT1,missense_variant,p.Glu21Gln,ENST00000567133,;CNOT1,downstream_gene_variant,,ENST00000567285,;SNORA46,downstream_gene_variant,,ENST00000384762,;CNOT1,missense_variant,p.Glu1309Gln,ENST00000567188,;CNOT1,upstream_gene_variant,,ENST00000566240,;	G	ENSG00000125107	ENST00000317147	Transcript	missense_variant	4273	3940	1314	E/Q	Gag/Cag	.	.	.	-1	CNOT1	HGNC	7877	protein_coding	YES	CCDS10799.1	ENSP00000320949	CNOT1_HUMAN	H3BUY8_HUMAN,H3BT18_HUMAN,H3BPF1_HUMAN,B7Z6X2_HUMAN,B3KS60_HUMAN	UPI00001FF2F6	.	tolerated(0.36)	benign(0.029)	29/49	.	hmmpanther:PTHR13162:SF8,hmmpanther:PTHR13162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCTCATCTA	.	5	ESCA
TANGO6	0	.	GRCh37	16	68893888	68893888	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196C>G	p.Gln66Glu	p.Q66E	ENST00000261778	2/18	52	37	14	53	53	0	TANGO6,missense_variant,p.Gln66Glu,ENST00000261778,;TANGO6,non_coding_transcript_exon_variant,,ENST00000564180,;TANGO6,upstream_gene_variant,,ENST00000561566,;	G	ENSG00000103047	ENST00000261778	Transcript	missense_variant	208	196	66	Q/E	Cag/Gag	.	.	.	1	TANGO6	HGNC	25749	protein_coding	YES	CCDS45516.1	ENSP00000261778	TNG6_HUMAN	B3KTB6_HUMAN	UPI00001FF4A8	.	tolerated(1)	benign(0)	2/18	.	hmmpanther:PTHR20959:SF1,hmmpanther:PTHR20959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCAGTGG	.	5	ESCA
FBXL16	0	.	GRCh37	16	746901	746901	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505G>A	p.Glu169Lys	p.E169K	ENST00000397621	2/6	24	13	10	23	23	0	FBXL16,missense_variant,p.Glu169Lys,ENST00000324361,;FBXL16,missense_variant,p.Glu169Lys,ENST00000397621,;FBXL16,upstream_gene_variant,,ENST00000562563,;LA16c-313D11.12,downstream_gene_variant,,ENST00000566927,;FBXL16,upstream_gene_variant,,ENST00000562585,;FBXL16,upstream_gene_variant,,ENST00000562648,;LA16c-313D11.12,downstream_gene_variant,,ENST00000575305,;	T	ENSG00000127585	ENST00000397621	Transcript	missense_variant	837	505	169	E/K	Gag/Aag	.	.	.	-1	FBXL16	HGNC	14150	protein_coding	YES	CCDS10421.1	ENSP00000380746	FXL16_HUMAN	Q8N4J3_HUMAN,B3KR59_HUMAN	UPI0000141371	.	tolerated(0.06)	benign(0.047)	2/6	.	hmmpanther:PTHR23125,hmmpanther:PTHR23125:SF233,Superfamily_domains:SSF81383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGAAGC	.	5	ESCA
TMEM11	0	.	GRCh37	17	21102020	21102020	+	Missense_Mutation	SNP	G	G	C	rs376181647	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196C>G	p.Arg66Gly	p.R66G	ENST00000317635	2/2	39	22	16	49	49	0	TMEM11,missense_variant,p.Arg66Gly,ENST00000317635,;TMEM11,non_coding_transcript_exon_variant,,ENST00000584432,;TMEM11,non_coding_transcript_exon_variant,,ENST00000584732,;TMEM11,non_coding_transcript_exon_variant,,ENST00000577419,;TMEM11,non_coding_transcript_exon_variant,,ENST00000583264,;TMEM11,non_coding_transcript_exon_variant,,ENST00000583929,;	C	ENSG00000178307	ENST00000317635	Transcript	missense_variant	668	196	66	R/G	Cgc/Ggc	rs376181647	.	.	-1	TMEM11	HGNC	16823	protein_coding	YES	CCDS11216.1	ENSP00000319992	TMM11_HUMAN	.	UPI0000131C88	.	deleterious(0)	benign(0.119)	2/2	.	Pfam_domain:PF14972,hmmpanther:PTHR15099:SF1,hmmpanther:PTHR15099	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGCGAGTGG	byFrequency|byCluster	5	ESCA
RUNDC3A	0	.	GRCh37	17	42392345	42392345	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.597C>G	p.Ile199Met	p.I199M	ENST00000426726	6/11	62	45	17	40	40	0	RUNDC3A,missense_variant,p.Ile199Met,ENST00000426726,;RUNDC3A,missense_variant,p.Ile199Met,ENST00000225441,;RUNDC3A,missense_variant,p.Ile194Met,ENST00000590941,;SLC25A39,downstream_gene_variant,,ENST00000590194,;SLC25A39,downstream_gene_variant,,ENST00000225308,;SLC25A39,downstream_gene_variant,,ENST00000377095,;SLC25A39,downstream_gene_variant,,ENST00000586016,;SLC25A39,downstream_gene_variant,,ENST00000537904,;AC003102.3,intron_variant,,ENST00000588097,;RUNDC3A,non_coding_transcript_exon_variant,,ENST00000590834,;RUNDC3A,non_coding_transcript_exon_variant,,ENST00000587483,;RUNDC3A,non_coding_transcript_exon_variant,,ENST00000593079,;RUNDC3A,upstream_gene_variant,,ENST00000588564,;SLC25A39,downstream_gene_variant,,ENST00000593166,;SLC25A39,downstream_gene_variant,,ENST00000591006,;SLC25A39,downstream_gene_variant,,ENST00000592372,;	G	ENSG00000108309	ENST00000426726	Transcript	missense_variant	871	597	199	I/M	atC/atG	COSM979933,COSM1588914	.	.	1	RUNDC3A	HGNC	16984	protein_coding	YES	CCDS45698.1	ENSP00000410862	RUN3A_HUMAN	.	UPI0000EE7B82	.	deleterious(0)	possibly_damaging(0.8)	6/11	.	hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF38	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATCGATTA	.	5	ESCA
HOXB3	0	.	GRCh37	17	46627456	46627456	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*240G>C	.	.	ENST00000470495	2/2	36	24	12	21	21	0	HOXB3,3_prime_UTR_variant,,ENST00000470495,;HOXB3,3_prime_UTR_variant,,ENST00000472863,;HOXB3,3_prime_UTR_variant,,ENST00000311626,;HOXB3,3_prime_UTR_variant,,ENST00000498678,;HOXB3,downstream_gene_variant,,ENST00000485909,;HOXB3,downstream_gene_variant,,ENST00000476342,;HOXB3,downstream_gene_variant,,ENST00000489475,;HOXB3,downstream_gene_variant,,ENST00000465120,;HOXB3,downstream_gene_variant,,ENST00000471459,;HOXB3,downstream_gene_variant,,ENST00000490677,;HOXB3,downstream_gene_variant,,ENST00000460160,;HOXB2,upstream_gene_variant,,ENST00000330070,;HOXB-AS1,intron_variant,,ENST00000508688,;HOXB-AS1,intron_variant,,ENST00000502764,;HOXB-AS1,intron_variant,,ENST00000435312,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS1,downstream_gene_variant,,ENST00000504972,;	G	ENSG00000120093	ENST00000470495	Transcript	3_prime_UTR_variant	2984	.	.	.	.	.	.	.	-1	HOXB3	HGNC	5114	protein_coding	YES	CCDS11528.1	ENSP00000417207	HXB3_HUMAN	C9J2I3_HUMAN,B7ZAD0_HUMAN,B7Z5N8_HUMAN	UPI00001AEFBF	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTCATCTC	.	5	ESCA
IGF2BP1	0	.	GRCh37	17	47132615	47132615	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5809C>T	.	.	ENST00000290341	15/15	19	10	9	22	22	0	IGF2BP1,3_prime_UTR_variant,,ENST00000290341,;	T	ENSG00000159217	ENST00000290341	Transcript	3_prime_UTR_variant	7877	.	.	.	.	.	.	.	1	IGF2BP1	HGNC	28866	protein_coding	YES	CCDS11543.1	ENSP00000290341	IF2B1_HUMAN	D3DTW3_HUMAN	UPI0000117170	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGTTTCACTCT	.	4	ESCA
PLD2	0	.	GRCh37	17	4721813	4721813	+	Silent	SNP	C	C	T	rs780498884	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2034C>T	p.%3D	p.Y678Y	ENST00000263088	20/25	16	13	3	21	21	0	PLD2,synonymous_variant,p.%3D,ENST00000263088,;PLD2,synonymous_variant,p.%3D,ENST00000572940,;PLD2,synonymous_variant,p.%3D,ENST00000576983,;PLD2,upstream_gene_variant,,ENST00000576864,;PLD2,non_coding_transcript_exon_variant,,ENST00000572127,;PLD2,non_coding_transcript_exon_variant,,ENST00000571273,;PLD2,downstream_gene_variant,,ENST00000573258,;PLD2,upstream_gene_variant,,ENST00000575945,;PLD2,downstream_gene_variant,,ENST00000576329,;PLD2,downstream_gene_variant,,ENST00000575246,;PLD2,downstream_gene_variant,,ENST00000572199,;PLD2,downstream_gene_variant,,ENST00000574796,;PLD2,downstream_gene_variant,,ENST00000575813,;	T	ENSG00000129219	ENST00000263088	Transcript	synonymous_variant	2165	2034	678	Y	taC/taT	rs780498884	.	.	1	PLD2	HGNC	9068	protein_coding	YES	CCDS11057.1	ENSP00000263088	PLD2_HUMAN	I3L222_HUMAN,I3L1F3_HUMAN	UPI0000131BDE	.	.	.	20/25	.	hmmpanther:PTHR18896,hmmpanther:PTHR18896:SF7,Pfam_domain:PF13091,Gene3D:3.30.870.10,PIRSF_domain:PIRSF009376,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCTACGTGCT	byFrequency	2	ESCA
MED13	0	.	GRCh37	17	60059646	60059646	+	Missense_Mutation	SNP	G	G	A	rs202062658	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3718C>T	p.Arg1240Cys	p.R1240C	ENST00000397786	16/30	38	19	19	35	35	0	MED13,missense_variant,p.Arg1240Cys,ENST00000397786,;	A	ENSG00000108510	ENST00000397786	Transcript	missense_variant	3795	3718	1240	R/C	Cgt/Tgt	rs202062658	.	.	-1	MED13	HGNC	22474	protein_coding	YES	CCDS42366.1	ENSP00000380888	MED13_HUMAN	.	UPI0000D7D6F6	.	deleterious(0.02)	probably_damaging(0.998)	16/30	.	hmmpanther:PTHR12950:SF22,hmmpanther:PTHR12950	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACGCCCAT	byCluster|by1000G	5	ESCA
TACO1	0	.	GRCh37	17	61681893	61681893	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281-1G>A	.	p.X94_splice	ENST00000258975	.	27	17	10	21	21	0	TACO1,splice_acceptor_variant,,ENST00000258975,;TACO1,splice_acceptor_variant,,ENST00000581120,;	A	ENSG00000136463	ENST00000258975	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	TACO1	HGNC	24316	protein_coding	YES	CCDS11640.1	ENSP00000258975	TACO1_HUMAN	Q8N9Q7_HUMAN	UPI0000042223	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCAGAAGGA	.	2	ESCA
TACO1	0	.	GRCh37	17	61683700	61683700	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415G>A	p.Glu139Lys	p.E139K	ENST00000258975	3/5	59	36	23	66	66	0	TACO1,missense_variant,p.Glu139Lys,ENST00000258975,;TACO1,non_coding_transcript_exon_variant,,ENST00000581120,;RP11-51F16.9,downstream_gene_variant,,ENST00000603263,;	A	ENSG00000136463	ENST00000258975	Transcript	missense_variant	627	415	139	E/K	Gag/Aag	.	.	.	1	TACO1	HGNC	24316	protein_coding	YES	CCDS11640.1	ENSP00000258975	TACO1_HUMAN	Q8N9Q7_HUMAN	UPI0000042223	.	deleterious(0.01)	probably_damaging(0.99)	3/5	.	HAMAP:MF_00693,hmmpanther:PTHR12532,hmmpanther:PTHR12532:SF1,Pfam_domain:PF01709,Gene3D:3.30.1270.10,Superfamily_domains:SSF75625	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATGAGGGT	.	5	ESCA
SEPT9	0	.	GRCh37	17	75471827	75471827	+	Intron	SNP	G	G	A	rs781371974	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.722-6399G>A	.	.	ENST00000427177	.	16	6	10	25	25	0	SEPT9,missense_variant,p.Arg76Gln,ENST00000427180,;SEPT9,intron_variant,,ENST00000427674,;SEPT9,intron_variant,,ENST00000591198,;SEPT9,intron_variant,,ENST00000592951,;SEPT9,intron_variant,,ENST00000591704,;SEPT9,intron_variant,,ENST00000590917,;SEPT9,intron_variant,,ENST00000590294,;SEPT9,intron_variant,,ENST00000585930,;SEPT9,intron_variant,,ENST00000590059,;SEPT9,intron_variant,,ENST00000449803,;SEPT9,intron_variant,,ENST00000585929,;SEPT9,intron_variant,,ENST00000586521,;SEPT9,intron_variant,,ENST00000431235,;SEPT9,intron_variant,,ENST00000329047,;SEPT9,intron_variant,,ENST00000541152,;SEPT9,intron_variant,,ENST00000591088,;SEPT9,intron_variant,,ENST00000588690,;SEPT9,intron_variant,,ENST00000586128,;SEPT9,intron_variant,,ENST00000590938,;SEPT9,intron_variant,,ENST00000588958,;SEPT9,intron_variant,,ENST00000591020,;SEPT9,intron_variant,,ENST00000586433,;SEPT9,intron_variant,,ENST00000593189,;SEPT9,intron_variant,,ENST00000427177,;SEPT9,intron_variant,,ENST00000591472,;SEPT9,intron_variant,,ENST00000423034,;SEPT9,intron_variant,,ENST00000592420,;RP11-75C10.9,upstream_gene_variant,,ENST00000591110,;RP11-75C10.7,downstream_gene_variant,,ENST00000585369,;SEPT9,intron_variant,,ENST00000592481,;SEPT9,intron_variant,,ENST00000588575,;	A	ENSG00000184640	ENST00000427177	Transcript	intron_variant	.	.	.	.	.	rs781371974,COSM3692036	.	.	1	SEPT9	HGNC	7323	protein_coding	YES	CCDS45790.1	ENSP00000391249	SEPT9_HUMAN	Q96QF2_HUMAN,K7ERG1_HUMAN,K7ER52_HUMAN,K7EQD7_HUMAN,K7ENQ5_HUMAN,K7EN52_HUMAN,K7ELJ9_HUMAN,K7EL40_HUMAN,K7EKN4_HUMAN,K7EK18_HUMAN,K7EJZ2_HUMAN,K7EIR4_HUMAN,K7EIE4_HUMAN	UPI00001AF955	.	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODIFIER	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCCGGCAGC	byFrequency	5	ESCA
NOTUM	0	.	GRCh37	17	79915689	79915689	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.688G>A	p.Gly230Arg	p.G230R	ENST00000409678	6/11	54	25	28	63	63	0	NOTUM,missense_variant,p.Gly230Arg,ENST00000425009,;NOTUM,missense_variant,p.Gly230Arg,ENST00000409678,;NOTUM,missense_variant,p.Gly88Arg,ENST00000477214,;NOTUM,downstream_gene_variant,,ENST00000489218,;	T	ENSG00000185269	ENST00000409678	Transcript	missense_variant	1072	688	230	G/R	Ggg/Agg	.	.	.	-1	NOTUM	HGNC	27106	protein_coding	YES	CCDS32771.2	ENSP00000387310	NOTUM_HUMAN	K7EIG3_HUMAN,C9JYG8_HUMAN	UPI000004EE80	.	deleterious(0)	probably_damaging(0.995)	6/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21562:SF7,hmmpanther:PTHR21562,Pfam_domain:PF03283	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCGGCCA	.	5	ESCA
LINC00324	0	.	GRCh37	17	8125983	8125983	+	RNA	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.842G>C	.	.	ENST00000315707	2/3	15	4	10	22	22	0	LINC00324,non_coding_transcript_exon_variant,,ENST00000315707,;RP11-849F2.8,downstream_gene_variant,,ENST00000602405,;CTC1,downstream_gene_variant,,ENST00000449476,;	G	ENSG00000178977	ENST00000315707	Transcript	non_coding_transcript_exon_variant	842	.	.	.	.	.	.	.	-1	LINC00324	HGNC	26628	lincRNA	YES	.	.	.	.	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	TGCCTCGTCTC	.	3	ESCA
CHMP1B	0	.	GRCh37	18	11852303	11852303	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*193G>C	.	.	ENST00000526991	1/1	30	10	20	32	32	0	CHMP1B,3_prime_UTR_variant,,ENST00000526991,;GNAL,intron_variant,,ENST00000535121,;GNAL,intron_variant,,ENST00000585642,;GNAL,intron_variant,,ENST00000334049,;GNAL,intron_variant,,ENST00000269162,;GNAL,intron_variant,,ENST00000423027,;GNAL,intron_variant,,ENST00000590228,;RP11-78A19.3,non_coding_transcript_exon_variant,,ENST00000586474,;RP11-78A19.4,downstream_gene_variant,,ENST00000609238,;CHMP1B,upstream_gene_variant,,ENST00000588284,;	C	ENSG00000255112	ENST00000526991	Transcript	3_prime_UTR_variant	909	.	.	.	.	.	.	.	1	CHMP1B	HGNC	24287	protein_coding	YES	CCDS54180.1	ENSP00000432279	CHM1B_HUMAN	B2RA72_HUMAN	UPI00000373BD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAAGTTCTG	.	5	ESCA
SMAD4	0	.	GRCh37	18	48604764	48604764	+	Nonsense_Mutation	SNP	T	T	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1586T>G	p.Leu529Ter	p.L529*	ENST00000342988	12/12	36	22	14	51	51	0	SMAD4,stop_gained,p.Leu529Ter,ENST00000342988,;SMAD4,stop_gained,p.Leu529Ter,ENST00000398417,;SMAD4,stop_gained,p.Leu433Ter,ENST00000588745,;SMAD4,downstream_gene_variant,,ENST00000593223,;SMAD4,non_coding_transcript_exon_variant,,ENST00000586253,;SMAD4,3_prime_UTR_variant,,ENST00000592186,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;SMAD4,downstream_gene_variant,,ENST00000590499,;	G	ENSG00000141646	ENST00000342988	Transcript	stop_gained	2124	1586	529	L/*	tTa/tGa	.	.	.	1	SMAD4	HGNC	6770	protein_coding	YES	CCDS11950.1	ENSP00000341551	SMAD4_HUMAN	Q9BYG6_HUMAN,K7ENG8_HUMAN,K7ENG1_HUMAN,K7EL18_HUMAN,K7EL15_HUMAN,K7EIJ2_HUMAN	UPI0000053431	.	.	.	12/12	.	PROSITE_profiles:PS51076,hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF33,Pfam_domain:PF03166,Gene3D:2.60.200.10,SMART_domains:SM00524,Superfamily_domains:SSF49879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1659del1659|28,BUFFER|p.E526*|c.1576G>T|4,BUFFER|p.R531R|c.1591C>A|5,BUFFER|p.R531W|c.1591C>T|3,BUFFER|p.R531Q|c.1592G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTTACACC	.	5	ESCA
C3P1	0	.	GRCh37	19	10157199	10157199	+	RNA	SNP	G	G	C	rs556051721	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2064G>C	.	.	ENST00000497718	15/37	46	37	9	30	30	0	C3P1,non_coding_transcript_exon_variant,,ENST00000495140,;C3P1,non_coding_transcript_exon_variant,,ENST00000497718,;	C	ENSG00000167798	ENST00000497718	Transcript	non_coding_transcript_exon_variant	2064	.	.	.	.	rs556051721	.	.	1	C3P1	HGNC	34414	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	15/37	.	.	A:0.0008	A:0	A:0.0058	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCTCGAGAGG	byFrequency|byCluster|by1000G	3	ESCA
ZNF844	0	.	GRCh37	19	12186303	12186303	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.368G>C	p.Arg123Thr	p.R123T	ENST00000439326	4/4	50	30	20	35	35	0	ZNF844,missense_variant,p.Arg123Thr,ENST00000439326,;ZNF844,3_prime_UTR_variant,,ENST00000441304,;ZNF844,5_prime_UTR_variant,,ENST00000550826,;	C	ENSG00000223547	ENST00000439326	Transcript	missense_variant	543	368	123	R/T	aGa/aCa	.	.	.	1	ZNF844	HGNC	25932	protein_coding	YES	CCDS45985.1	ENSP00000392024	ZN844_HUMAN	F8VS19_HUMAN	UPI0000185F5D	.	deleterious(0.03)	possibly_damaging(0.587)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24379,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTAGAGCTG	.	5	ESCA
KCTD15	0	.	GRCh37	19	34304803	34304803	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*950C>A	.	.	ENST00000430256	6/6	22	14	7	19	19	0	KCTD15,3_prime_UTR_variant,,ENST00000284006,;KCTD15,3_prime_UTR_variant,,ENST00000430256,;KCTD15,downstream_gene_variant,,ENST00000588881,;KCTD15,downstream_gene_variant,,ENST00000589786,;KCTD15,downstream_gene_variant,,ENST00000590385,;KCTD15,non_coding_transcript_exon_variant,,ENST00000592363,;	A	ENSG00000153885	ENST00000430256	Transcript	3_prime_UTR_variant	2210	.	.	.	.	.	.	.	1	KCTD15	HGNC	23297	protein_coding	YES	CCDS46039.1	ENSP00000394390	KCD15_HUMAN	K7EQS3_HUMAN,K7EPF0_HUMAN,K7EN63_HUMAN,K7EM48_HUMAN,K7EIF1_HUMAN	UPI000004D340	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACACTAGCC	.	5	ESCA
CEACAM6	0	.	GRCh37	19	42266010	42266010	+	Silent	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.837A>G	p.%3D	p.Q279Q	ENST00000199764	4/6	119	87	32	121	120	0	CEACAM6,synonymous_variant,p.%3D,ENST00000199764,;CEA,downstream_gene_variant,,ENST00000598976,;AC011513.4,intron_variant,,ENST00000601409,;	G	ENSG00000086548	ENST00000199764	Transcript	synonymous_variant	1055	837	279	Q	caA/caG	.	.	.	1	CEACAM6	HGNC	1818	protein_coding	YES	CCDS12585.1	ENSP00000199764	CEAM6_HUMAN	Q13985_HUMAN,M0QYD3_HUMAN	UPI000006DF42	.	.	.	4/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF121,hmmpanther:PTHR19955,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCAATCCAC	.	5	ESCA
DMPK	0	.	GRCh37	19	46273462	46273462	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*284G>C	.	.	ENST00000343373	14/14	69	46	22	82	81	1	DMPK,3_prime_UTR_variant,,ENST00000291270,;DMPK,3_prime_UTR_variant,,ENST00000458663,;DMPK,3_prime_UTR_variant,,ENST00000600757,;DMPK,3_prime_UTR_variant,,ENST00000447742,;DMPK,3_prime_UTR_variant,,ENST00000343373,;DMPK,downstream_gene_variant,,ENST00000593574,;DMPK,downstream_gene_variant,,ENST00000597660,;SIX5,upstream_gene_variant,,ENST00000560160,;SIX5,upstream_gene_variant,,ENST00000560168,;SIX5,upstream_gene_variant,,ENST00000317578,;DMPK,downstream_gene_variant,,ENST00000354227,;AC074212.6,intron_variant,,ENST00000590076,;AC074212.6,upstream_gene_variant,,ENST00000591530,;AC074212.6,upstream_gene_variant,,ENST00000586498,;AC074212.6,upstream_gene_variant,,ENST00000586251,;AC074212.5,downstream_gene_variant,,ENST00000559756,;AC074212.5,downstream_gene_variant,,ENST00000592217,;DMPK,downstream_gene_variant,,ENST00000595361,;DMPK,3_prime_UTR_variant,,ENST00000588522,;DMPK,non_coding_transcript_exon_variant,,ENST00000598272,;DMPK,non_coding_transcript_exon_variant,,ENST00000596686,;DMPK,downstream_gene_variant,,ENST00000600370,;	G	ENSG00000104936	ENST00000343373	Transcript	3_prime_UTR_variant	2748	.	.	.	.	.	.	.	-1	DMPK	HGNC	2933	protein_coding	YES	CCDS46119.1	ENSP00000345997	DMPK_HUMAN	E5KR08_HUMAN	UPI00001AF19C	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|VARSCANS	TCCCCCCAGCA	.	2	ESCA
SLC1A5	0	.	GRCh37	19	47278877	47278877	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1516C>T	p.Pro506Ser	p.P506S	ENST00000542575	8/8	43	27	15	29	29	0	SLC1A5,missense_variant,p.Pro278Ser,ENST00000412532,;SLC1A5,missense_variant,p.Pro506Ser,ENST00000542575,;SLC1A5,missense_variant,p.Pro304Ser,ENST00000434726,;SLC1A5,missense_variant,p.Pro330Ser,ENST00000594991,;SLC1A5,downstream_gene_variant,,ENST00000593713,;FKRP,intron_variant,,ENST00000600646,;	A	ENSG00000105281	ENST00000542575	Transcript	missense_variant	2145	1516	506	P/S	Ccc/Tcc	.	.	.	-1	SLC1A5	HGNC	10943	protein_coding	YES	CCDS12692.1	ENSP00000444408	AAAT_HUMAN	M0R144_HUMAN	UPI000012507D	.	tolerated(0.31)	benign(0.009)	8/8	.	hmmpanther:PTHR11958,hmmpanther:PTHR11958:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGGCAGCT	.	5	ESCA
CD37	0	.	GRCh37	19	49835424	49835424	+	5'Flank	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000323906	.	68	63	5	58	58	0	CD37,upstream_gene_variant,,ENST00000323906,;CD37,upstream_gene_variant,,ENST00000426897,;CD37,upstream_gene_variant,,ENST00000595660,;CD37,upstream_gene_variant,,ENST00000597602,;CD37,upstream_gene_variant,,ENST00000598095,;CD37,upstream_gene_variant,,ENST00000535669,;CTC-301O7.4,non_coding_transcript_exon_variant,,ENST00000358234,;CTC-301O7.4,non_coding_transcript_exon_variant,,ENST00000602554,;CD37,upstream_gene_variant,,ENST00000596426,;CD37,upstream_gene_variant,,ENST00000597033,;CD37,upstream_gene_variant,,ENST00000598134,;CD37,upstream_gene_variant,,ENST00000593512,;CD37,upstream_gene_variant,,ENST00000391859,;CD37,upstream_gene_variant,,ENST00000595725,;CD37,upstream_gene_variant,,ENST00000597852,;	G	ENSG00000104894	ENST00000323906	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3233	1	CD37	HGNC	1666	protein_coding	YES	CCDS12760.1	ENSP00000325708	CD37_HUMAN	M0R083_HUMAN	UPI0000127350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGGAGTTCC	.	2	ESCA
SCAF1	0	.	GRCh37	19	50157957	50157957	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3448C>G	p.Pro1150Ala	p.P1150A	ENST00000360565	9/11	25	22	3	37	37	0	SCAF1,missense_variant,p.Pro1150Ala,ENST00000360565,;IRF3,downstream_gene_variant,,ENST00000598808,;IRF3,downstream_gene_variant,,ENST00000377135,;IRF3,downstream_gene_variant,,ENST00000596765,;IRF3,downstream_gene_variant,,ENST00000601291,;IRF3,downstream_gene_variant,,ENST00000600022,;SCAF1,downstream_gene_variant,,ENST00000598359,;IRF3,downstream_gene_variant,,ENST00000599144,;IRF3,downstream_gene_variant,,ENST00000600911,;IRF3,downstream_gene_variant,,ENST00000599223,;IRF3,downstream_gene_variant,,ENST00000597198,;IRF3,downstream_gene_variant,,ENST00000596822,;IRF3,downstream_gene_variant,,ENST00000377139,;IRF3,downstream_gene_variant,,ENST00000593922,;IRF3,downstream_gene_variant,,ENST00000309877,;IRF3,downstream_gene_variant,,ENST00000599680,;IRF3,downstream_gene_variant,,ENST00000597636,;IRF3,downstream_gene_variant,,ENST00000596644,;	G	ENSG00000126461	ENST00000360565	Transcript	missense_variant	3572	3448	1150	P/A	Cct/Gct	.	.	.	1	SCAF1	HGNC	30403	protein_coding	YES	CCDS33074.1	ENSP00000353769	SFR19_HUMAN	M0R3G4_HUMAN,M0R2L3_HUMAN	UPI0000071891	.	.	possibly_damaging(0.728)	9/11	.	hmmpanther:PTHR15242,hmmpanther:PTHR15242:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCTCCTGTG	.	2	ESCA
ZNF702P	0	.	GRCh37	19	53472838	53472838	+	RNA	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1656T>C	.	.	ENST00000270443	4/4	33	25	8	33	33	0	ZNF702P,non_coding_transcript_exon_variant,,ENST00000270443,;CTD-2620I22.1,intron_variant,,ENST00000600068,;ZNF702P,downstream_gene_variant,,ENST00000599665,;ZNF702P,downstream_gene_variant,,ENST00000595402,;ZNF702P,downstream_gene_variant,,ENST00000598752,;ZNF702P,downstream_gene_variant,,ENST00000600425,;ZNF702P,non_coding_transcript_exon_variant,,ENST00000434269,;	G	ENSG00000242779	ENST00000270443	Transcript	non_coding_transcript_exon_variant	1656	.	.	.	.	.	.	.	-1	ZNF702P	HGNC	25775	processed_transcript	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAAACTTTG	.	5	ESCA
VN1R2	0	.	GRCh37	19	53761668	53761668	+	Missense_Mutation	SNP	C	C	G	rs189749880	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40C>G	p.Pro14Ala	p.P14A	ENST00000341702	1/1	25	18	7	20	20	0	VN1R2,missense_variant,p.Pro14Ala,ENST00000341702,;ZNF677,upstream_gene_variant,,ENST00000599012,;ZNF677,upstream_gene_variant,,ENST00000594681,;ZNF677,upstream_gene_variant,,ENST00000601413,;ZNF677,upstream_gene_variant,,ENST00000601828,;ZNF677,upstream_gene_variant,,ENST00000594517,;ZNF677,upstream_gene_variant,,ENST00000598513,;ZNF677,upstream_gene_variant,,ENST00000598806,;ZNF677,upstream_gene_variant,,ENST00000333952,;ZNF677,upstream_gene_variant,,ENST00000595293,;VN1R2,upstream_gene_variant,,ENST00000598458,;	G	ENSG00000196131	ENST00000341702	Transcript	missense_variant	124	40	14	P/A	Cca/Gca	rs189749880	.	.	1	VN1R2	HGNC	19872	protein_coding	YES	CCDS12862.1	ENSP00000351244	VN1R2_HUMAN	.	UPI0000062046	.	.	benign(0.035)	1/1	.	Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATCCAATA	by1000G	5	ESCA
LILRA4	0	.	GRCh37	19	54848413	54848413	+	Silent	SNP	T	T	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.954A>C	p.%3D	p.G318G	ENST00000291759	6/8	65	46	18	46	46	0	LILRA4,synonymous_variant,p.%3D,ENST00000291759,;AC008984.2,non_coding_transcript_exon_variant,,ENST00000507363,;LILRA4,synonymous_variant,p.%3D,ENST00000595581,;LILRA4,downstream_gene_variant,,ENST00000421056,;	G	ENSG00000239961	ENST00000291759	Transcript	synonymous_variant	1011	954	318	G	ggA/ggC	.	.	.	-1	LILRA4	HGNC	15503	protein_coding	YES	CCDS12890.1	ENSP00000291759	LIRA4_HUMAN	.	UPI0000202BCD	.	.	.	6/8	.	Superfamily_domains:SSF48726,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTGTCCTGG	.	5	ESCA
ARHGEF18	0	.	GRCh37	19	7505006	7505006	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180C>T	p.%3D	p.S60S	ENST00000359920	1/20	47	32	15	54	54	0	ARHGEF18,synonymous_variant,p.%3D,ENST00000359920,;ARHGEF18,intron_variant,,ENST00000319670,;CTD-2207O23.3,intron_variant,,ENST00000593531,;ARHGEF18,intron_variant,,ENST00000599752,;ARHGEF18,upstream_gene_variant,,ENST00000595600,;	T	ENSG00000104880	ENST00000359920	Transcript	synonymous_variant	433	180	60	S	tcC/tcT	.	.	.	1	ARHGEF18	HGNC	17090	protein_coding	YES	CCDS45946.1	ENSP00000352995	ARHGI_HUMAN	M0R125_HUMAN	UPI0000D6170D	.	.	.	1/20	.	hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCCAAAAG	.	5	ESCA
SLC35A3	0	.	GRCh37	1	100483235	100483235	+	Intron	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.754-3C>G	.	.	ENST00000370155	.	56	40	15	33	33	0	SLC35A3,splice_region_variant,,ENST00000427993,;SLC35A3,splice_region_variant,,ENST00000370153,;SLC35A3,splice_region_variant,,ENST00000370155,;SLC35A3,intron_variant,,ENST00000465289,;SLC35A3,downstream_gene_variant,,ENST00000422078,;SLC35A3,splice_region_variant,,ENST00000370156,;SLC35A3,splice_region_variant,,ENST00000533028,;	G	ENSG00000117620	ENST00000370155	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	SLC35A3	HGNC	11023	protein_coding	YES	CCDS762.1	ENSP00000359174	S35A3_HUMAN	E9PPQ9_HUMAN,C9JW63_HUMAN	UPI0000137AF2	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTTCAGGCA	.	4	ESCA
VCAM1	0	.	GRCh37	1	101196751	101196751	+	Intron	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1205-3C>T	.	.	ENST00000294728	.	33	20	13	28	28	0	VCAM1,splice_region_variant,,ENST00000347652,;VCAM1,splice_region_variant,,ENST00000294728,;VCAM1,splice_region_variant,,ENST00000370119,;VCAM1,intron_variant,,ENST00000370115,;VCAM1,upstream_gene_variant,,ENST00000603679,;	T	ENSG00000162692	ENST00000294728	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	VCAM1	HGNC	12663	protein_coding	YES	CCDS773.1	ENSP00000294728	VCAM1_HUMAN	Q68DC4_HUMAN,G0ZI12_HUMAN,G0ZFQ0_HUMAN,F8UV74_HUMAN,F8UU18_HUMAN,F2YYR6_HUMAN	UPI0000000E06	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTGCAGCAT	.	4	ESCA
SLC16A1	0	.	GRCh37	1	113460327	113460327	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.701T>C	p.Ile234Thr	p.I234T	ENST00000538576	4/5	55	36	18	60	60	0	SLC16A1,missense_variant,p.Ile234Thr,ENST00000369626,;SLC16A1,missense_variant,p.Ile234Thr,ENST00000433570,;SLC16A1,missense_variant,p.Ile234Thr,ENST00000458229,;SLC16A1,missense_variant,p.Ile234Thr,ENST00000443580,;SLC16A1,missense_variant,p.Ile234Thr,ENST00000538576,;SLC16A1,downstream_gene_variant,,ENST00000429288,;SLC16A1,downstream_gene_variant,,ENST00000481750,;	G	ENSG00000155380	ENST00000538576	Transcript	missense_variant	1533	701	234	I/T	aTt/aCt	.	.	.	-1	SLC16A1	HGNC	10922	protein_coding	YES	CCDS858.1	ENSP00000441065	MOT1_HUMAN	Q5T8R5_HUMAN,Q5T8R4_HUMAN,Q5T8R3_HUMAN	UPI00000012F5	.	tolerated(0.57)	benign(0.004)	4/5	.	PROSITE_profiles:PS50850,hmmpanther:PTHR11360:SF24,hmmpanther:PTHR11360,Pfam_domain:PF07690,TIGRFAM_domain:TIGR00892	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCAATAAGA	.	5	ESCA
MAGI3	0	.	GRCh37	1	113933837	113933837	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.182C>G	p.Ser61Trp	p.S61W	ENST00000307546	1/21	28	19	8	28	28	0	MAGI3,missense_variant,p.Ser61Trp,ENST00000369617,;MAGI3,missense_variant,p.Ser61Trp,ENST00000369615,;MAGI3,missense_variant,p.Ser61Trp,ENST00000307546,;MAGI3,missense_variant,p.Ser61Trp,ENST00000369611,;MAGI3,non_coding_transcript_exon_variant,,ENST00000486456,;MAGI3,upstream_gene_variant,,ENST00000477955,;	G	ENSG00000081026	ENST00000307546	Transcript	missense_variant	257	182	61	S/W	tCg/tGg	.	.	.	1	MAGI3	HGNC	29647	protein_coding	YES	CCDS44196.1	ENSP00000304604	MAGI3_HUMAN	.	UPI00004589AE	.	deleterious(0)	probably_damaging(0.981)	1/21	.	PROSITE_profiles:PS50106,hmmpanther:PTHR10316:SF10,hmmpanther:PTHR10316,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCTCGGGCA	.	5	ESCA
KIAA2013	0	.	GRCh37	1	11982770	11982770	+	Frame_Shift_Del	DEL	G	G	-	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1810delC	p.Leu604SerfsTer33	p.L604Sfs*33	ENST00000376572	2/3	32	22	10	21	21	0	KIAA2013,frameshift_variant,p.Leu604SerfsTer27,ENST00000376576,;KIAA2013,frameshift_variant,p.Leu604SerfsTer33,ENST00000376572,;	-	ENSG00000116685	ENST00000376572	Transcript	frameshift_variant	1996	1810	604	L/X	Ctc/tc	COSM1212321	.	.	-1	KIAA2013	HGNC	28513	protein_coding	YES	CCDS141.1	ENSP00000365756	K2013_HUMAN	.	UPI00000741FB	.	.	.	2/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR31386,Pfam_domain:PF10222	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGAAGAGGGTGA	.	3	ESCA
RP11-417J8.6	0	.	GRCh37	1	142620925	142620925	+	RNA	SNP	A	A	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.6559T>A	.	.	ENST00000610091	14/14	59	49	9	93	93	0	RP11-417J8.6,non_coding_transcript_exon_variant,,ENST00000369381,;RP11-417J8.6,non_coding_transcript_exon_variant,,ENST00000610091,;RP11-417J8.3,intron_variant,,ENST00000411746,;RP11-417J8.3,intron_variant,,ENST00000426408,;RP11-417J8.3,intron_variant,,ENST00000413650,;RP11-417J8.3,intron_variant,,ENST00000446205,;RP11-417J8.3,intron_variant,,ENST00000400755,;RP11-417J8.3,intron_variant,,ENST00000412092,;	T	ENSG00000203849	ENST00000610091	Transcript	non_coding_transcript_exon_variant	6559	.	.	.	.	.	.	.	-1	RP11-417J8.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTAGAGTGTT	.	4	ESCA
RNF115	0	.	GRCh37	1	145682022	145682022	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429-1G>A	.	p.X143_splice	ENST00000369291	.	58	42	15	62	62	0	RNF115,splice_acceptor_variant,,ENST00000369291,;RNF115,splice_acceptor_variant,,ENST00000539368,;	A	ENSG00000121848	ENST00000369291	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	RNF115	HGNC	18154	protein_coding	YES	CCDS922.1	ENSP00000358297	RN115_HUMAN	.	UPI00001B061B	.	.	.	.	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACAGAATAC	.	5	ESCA
BCL9	0	.	GRCh37	1	147097692	147097692	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*932G>C	.	.	ENST00000234739	10/10	66	47	19	43	43	0	BCL9,3_prime_UTR_variant,,ENST00000234739,;ACP6,downstream_gene_variant,,ENST00000609196,;	C	ENSG00000116128	ENST00000234739	Transcript	3_prime_UTR_variant	5953	.	.	.	.	.	.	.	1	BCL9	HGNC	1008	protein_coding	YES	CCDS30833.1	ENSP00000234739	BCL9_HUMAN	.	UPI000013C9B9	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTGAGAGG	.	5	ESCA
SPEN	0	.	GRCh37	1	16263967	16263967	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10336T>C	p.Ser3446Pro	p.S3446P	ENST00000375759	12/15	42	39	3	31	31	0	SPEN,missense_variant,p.Ser3446Pro,ENST00000375759,;ZBTB17,downstream_gene_variant,,ENST00000375733,;ZBTB17,downstream_gene_variant,,ENST00000375743,;ZBTB17,downstream_gene_variant,,ENST00000537142,;ZBTB17,downstream_gene_variant,,ENST00000440560,;ZBTB17,downstream_gene_variant,,ENST00000444358,;ZBTB17,downstream_gene_variant,,ENST00000462525,;SPEN,upstream_gene_variant,,ENST00000487496,;	C	ENSG00000065526	ENST00000375759	Transcript	missense_variant	10540	10336	3446	S/P	Tct/Cct	.	.	.	1	SPEN	HGNC	17575	protein_coding	YES	CCDS164.1	ENSP00000364912	MINT_HUMAN	.	UPI000006FF0C	.	.	benign(0)	12/15	.	hmmpanther:PTHR23189:SF9,hmmpanther:PTHR23189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGTCTCTCTT	.	2	ESCA
EMC1	0	.	GRCh37	1	19547378	19547378	+	Intron	SNP	G	G	A	rs549976625	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2588-36C>T	.	.	ENST00000477853	.	25	18	7	29	29	0	EMC1,intron_variant,,ENST00000375208,;EMC1,intron_variant,,ENST00000375199,;EMC1,intron_variant,,ENST00000486405,;EMC1,intron_variant,,ENST00000477853,;RP1-43E13.2,intron_variant,,ENST00000437898,;EMC1,non_coding_transcript_exon_variant,,ENST00000461353,;EMC1,non_coding_transcript_exon_variant,,ENST00000480380,;EMC1,intron_variant,,ENST00000496654,;EMC1,intron_variant,,ENST00000494770,;EMC1,intron_variant,,ENST00000462505,;EMC1,intron_variant,,ENST00000486238,;	A	ENSG00000127463	ENST00000477853	Transcript	intron_variant	.	.	.	.	.	rs549976625	.	.	-1	EMC1	HGNC	28957	protein_coding	YES	CCDS190.1	ENSP00000420608	EMC1_HUMAN	.	UPI0000070A23	.	.	.	.	20/22	.	C:0.0004	C:0	C:0	.	C:0.002	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCAGTGTCC	byFrequency|by1000G	2	ESCA
CFH	0	.	GRCh37	1	196683032	196683032	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1504C>T	p.Gln502Ter	p.Q502*	ENST00000367429	10/22	41	28	13	40	40	0	CFH,stop_gained,p.Gln502Ter,ENST00000367429,;CFH,non_coding_transcript_exon_variant,,ENST00000466229,;	T	ENSG00000000971	ENST00000367429	Transcript	stop_gained	1744	1504	502	Q/*	Caa/Taa	.	.	.	1	CFH	HGNC	4883	protein_coding	YES	CCDS1385.1	ENSP00000356399	CFAH_HUMAN	.	UPI000013C4D1	.	.	.	10/22	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF310,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCAACCC	.	5	ESCA
PFKFB2	0	.	GRCh37	1	207243747	207243747	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1215G>A	p.%3D	p.K405K	ENST00000367080	12/15	39	33	6	54	54	0	PFKFB2,synonymous_variant,p.%3D,ENST00000541914,;PFKFB2,synonymous_variant,p.%3D,ENST00000367079,;PFKFB2,synonymous_variant,p.%3D,ENST00000367080,;PFKFB2,synonymous_variant,p.%3D,ENST00000411990,;PFKFB2,synonymous_variant,p.%3D,ENST00000545806,;PFKFB2,intron_variant,,ENST00000473310,;PFKFB2,upstream_gene_variant,,ENST00000483688,;	A	ENSG00000123836	ENST00000367080	Transcript	synonymous_variant	1339	1215	405	K	aaG/aaA	.	.	.	1	PFKFB2	HGNC	8873	protein_coding	YES	CCDS31004.1	ENSP00000356047	F262_HUMAN	B0FLL2_HUMAN	UPI000012A3F0	.	.	.	12/15	.	hmmpanther:PTHR10606:SF13,hmmpanther:PTHR10606,Gene3D:3.40.50.1240,PIRSF_domain:PIRSF000709,Superfamily_domains:SSF53254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATAAGGGCGC	.	5	ESCA
SH2D5	0	.	GRCh37	1	21050598	21050598	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.777G>A	p.%3D	p.L259L	ENST00000444387	7/10	25	18	7	16	16	0	SH2D5,synonymous_variant,p.%3D,ENST00000375031,;SH2D5,synonymous_variant,p.%3D,ENST00000444387,;SH2D5,downstream_gene_variant,,ENST00000518294,;SH2D5,downstream_gene_variant,,ENST00000517430,;SH2D5,downstream_gene_variant,,ENST00000519434,;SH2D5,downstream_gene_variant,,ENST00000447746,;SH2D5,non_coding_transcript_exon_variant,,ENST00000460804,;	T	ENSG00000189410	ENST00000444387	Transcript	synonymous_variant	1175	777	259	L	ctG/ctA	.	.	.	-1	SH2D5	HGNC	28819	protein_coding	YES	CCDS44080.1	ENSP00000406026	SH2D5_HUMAN	E5RJW5_HUMAN,E5RGV2_HUMAN,E5RGJ3_HUMAN	UPI0000EE70C3	.	.	.	7/10	.	hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGCAGCTG	.	5	ESCA
ZNF678	0	.	GRCh37	1	227842420	227842420	+	Nonsense_Mutation	SNP	G	G	T	rs368224195	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.469G>T	p.Glu157Ter	p.E157*	ENST00000343776	4/4	19	12	7	8	8	0	ZNF678,stop_gained,p.Glu212Ter,ENST00000397097,;ZNF678,stop_gained,p.Glu157Ter,ENST00000343776,;ZNF678,stop_gained,p.Glu212Ter,ENST00000440339,;ZNF678,intron_variant,,ENST00000608949,;ZNF678,downstream_gene_variant,,ENST00000465266,;	T	ENSG00000181450	ENST00000343776	Transcript	stop_gained	814	469	157	E/*	Gaa/Taa	rs368224195	.	.	1	ZNF678	HGNC	28652	protein_coding	YES	.	ENSP00000344828	ZN678_HUMAN	.	UPI000019862A	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGACGAATGT	byFrequency|byCluster	3	ESCA
SPRTN	0	.	GRCh37	1	231489015	231489015	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1378C>G	p.Gln460Glu	p.Q460E	ENST00000295050	5/5	35	21	14	29	29	0	SPRTN,missense_variant,p.Gln460Glu,ENST00000295050,;SPRTN,downstream_gene_variant,,ENST00000008440,;SPRTN,downstream_gene_variant,,ENST00000366644,;SPRTN,downstream_gene_variant,,ENST00000391858,;SPRTN,downstream_gene_variant,,ENST00000469904,;	G	ENSG00000010072	ENST00000295050	Transcript	missense_variant	1714	1378	460	Q/E	Cag/Gag	.	.	.	1	SPRTN	HGNC	25356	protein_coding	YES	CCDS1594.1	ENSP00000295050	SPRTN_HUMAN	L8E708_HUMAN	UPI000006D601	.	tolerated(0.09)	benign(0.08)	5/5	.	hmmpanther:PTHR21220,SMART_domains:SM00734	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCAGAAT	.	5	ESCA
AHCTF1	0	.	GRCh37	1	247076573	247076573	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544G>C	p.Asp182His	p.D182H	ENST00000326225	4/36	80	54	25	86	86	0	AHCTF1,missense_variant,p.Asp173His,ENST00000391829,;AHCTF1,missense_variant,p.Asp208His,ENST00000366508,;AHCTF1,missense_variant,p.Asp182His,ENST00000326225,;AHCTF1,downstream_gene_variant,,ENST00000478568,;	G	ENSG00000153207	ENST00000326225	Transcript	missense_variant	641	544	182	D/H	Gat/Cat	.	.	.	-1	AHCTF1	HGNC	24618	protein_coding	YES	CCDS1629.2	ENSP00000355465	ELYS_HUMAN	C9J5C5_HUMAN	UPI0000204034	.	deleterious(0.01)	probably_damaging(1)	4/36	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTCATCCAAAC	.	3	ESCA
AHCTF1	0	.	GRCh37	1	247076585	247076585	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.532G>C	p.Asp178His	p.D178H	ENST00000326225	4/36	70	51	19	82	82	0	AHCTF1,missense_variant,p.Asp169His,ENST00000391829,;AHCTF1,missense_variant,p.Asp204His,ENST00000366508,;AHCTF1,missense_variant,p.Asp178His,ENST00000326225,;AHCTF1,downstream_gene_variant,,ENST00000478568,;	G	ENSG00000153207	ENST00000326225	Transcript	missense_variant	629	532	178	D/H	Gac/Cac	.	.	.	-1	AHCTF1	HGNC	24618	protein_coding	YES	CCDS1629.2	ENSP00000355465	ELYS_HUMAN	C9J5C5_HUMAN	UPI0000204034	.	deleterious(0)	probably_damaging(0.999)	4/36	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAGGTCAACAA	.	3	ESCA
OR2L13	0	.	GRCh37	1	248262873	248262873	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196T>C	p.Ser66Pro	p.S66P	ENST00000366478	3/3	61	42	18	52	52	0	OR2L13,missense_variant,p.Ser66Pro,ENST00000358120,;OR2L13,missense_variant,p.Ser66Pro,ENST00000366478,;	C	ENSG00000196071	ENST00000366478	Transcript	missense_variant	533	196	66	S/P	Tcc/Ccc	.	.	.	1	OR2L13	HGNC	19578	protein_coding	YES	CCDS1637.1	ENSP00000355434	OR2LD_HUMAN	.	UPI0000043517	.	deleterious(0)	probably_damaging(0.999)	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF102,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCTCCCTT	.	5	ESCA
CSMD2	0	.	GRCh37	1	34158555	34158555	+	Missense_Mutation	SNP	C	C	T	rs756045595	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000241312	25/70	36	21	15	38	38	0	CSMD2,missense_variant,p.Glu1343Lys,ENST00000373381,;CSMD2,missense_variant,p.Glu216Lys,ENST00000373380,;CSMD2,5_prime_UTR_variant,,ENST00000373388,;CSMD2,missense_variant,p.Glu1303Lys,ENST00000241312,;	T	ENSG00000121904	ENST00000241312	Transcript	missense_variant	3936	3907	1303	E/K	Gaa/Aaa	rs756045595	.	.	-1	CSMD2	HGNC	19290	nonsense_mediated_decay	YES	CCDS380.1	ENSP00000241312	CSMD2_HUMAN	.	UPI00004561AB	.	deleterious(0.02)	probably_damaging(0.916)	25/70	.	Superfamily_domains:SSF49854,SMART_domains:SM00042,Pfam_domain:PF00431,Gene3D:2.60.120.290,PROSITE_profiles:PS01180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCGATGG	.	5	ESCA
UROD	0	.	GRCh37	1	45479618	45479618	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.512C>G	p.Ser171Ter	p.S171*	ENST00000246337	6/10	24	17	7	23	23	0	UROD,stop_gained,p.Ser150Ter,ENST00000434478,;UROD,stop_gained,p.Ser171Ter,ENST00000246337,;UROD,intron_variant,,ENST00000428106,;HECTD3,upstream_gene_variant,,ENST00000372172,;ZSWIM5,downstream_gene_variant,,ENST00000359600,;UROD,non_coding_transcript_exon_variant,,ENST00000462688,;UROD,non_coding_transcript_exon_variant,,ENST00000491773,;UROD,non_coding_transcript_exon_variant,,ENST00000469548,;UROD,non_coding_transcript_exon_variant,,ENST00000494399,;UROD,non_coding_transcript_exon_variant,,ENST00000478467,;UROD,non_coding_transcript_exon_variant,,ENST00000486699,;UROD,non_coding_transcript_exon_variant,,ENST00000490385,;UROD,non_coding_transcript_exon_variant,,ENST00000460334,;UROD,non_coding_transcript_exon_variant,,ENST00000496439,;UROD,non_coding_transcript_exon_variant,,ENST00000491300,;UROD,non_coding_transcript_exon_variant,,ENST00000473012,;UROD,non_coding_transcript_exon_variant,,ENST00000460906,;UROD,upstream_gene_variant,,ENST00000472254,;UROD,upstream_gene_variant,,ENST00000466193,;UROD,upstream_gene_variant,,ENST00000465678,;UROD,downstream_gene_variant,,ENST00000463092,;UROD,downstream_gene_variant,,ENST00000461035,;	G	ENSG00000126088	ENST00000246337	Transcript	stop_gained	631	512	171	S/*	tCa/tGa	.	.	.	1	UROD	HGNC	12591	protein_coding	YES	CCDS518.1	ENSP00000246337	DCUP_HUMAN	Q71UD5_HUMAN,Q71UD4_HUMAN	UPI0000112E85	.	.	.	6/10	.	HAMAP:MF_00218,hmmpanther:PTHR21091,hmmpanther:PTHR21091:SF2,TIGRFAM_domain:TIGR01464,Pfam_domain:PF01208,Gene3D:3.20.20.210,Superfamily_domains:SSF51726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTCAAGCA	.	5	ESCA
RPE65	0	.	GRCh37	1	68914383	68914383	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18G>A	p.%3D	p.E6E	ENST00000262340	2/14	44	41	3	25	25	0	RPE65,synonymous_variant,p.%3D,ENST00000262340,;	T	ENSG00000116745	ENST00000262340	Transcript	synonymous_variant	72	18	6	E	gaG/gaA	.	.	.	-1	RPE65	HGNC	10294	protein_coding	YES	CCDS643.1	ENSP00000262340	RPE65_HUMAN	Q2EKB8_HUMAN,C7FEP0_HUMAN	UPI000004346C	.	.	.	2/14	.	hmmpanther:PTHR10543,hmmpanther:PTHR10543:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGATGCTCAAC	.	2	ESCA
SLC45A1	0	.	GRCh37	1	8395601	8395601	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1548C>G	p.Ile516Met	p.I516M	ENST00000471889	6/9	51	37	13	29	29	0	SLC45A1,missense_variant,p.Ile516Met,ENST00000289877,;SLC45A1,missense_variant,p.Ile550Met,ENST00000377479,;SLC45A1,missense_variant,p.Ile516Met,ENST00000471889,;SLC45A1,non_coding_transcript_exon_variant,,ENST00000481265,;SLC45A1,non_coding_transcript_exon_variant,,ENST00000497660,;	G	ENSG00000162426	ENST00000471889	Transcript	missense_variant	1933	1548	516	I/M	atC/atG	.	.	.	1	SLC45A1	HGNC	17939	protein_coding	YES	CCDS30577.1	ENSP00000418096	S45A1_HUMAN	.	UPI000040EA42	.	tolerated(0.34)	possibly_damaging(0.864)	6/9	.	hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF6,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCATCTGCAA	.	3	ESCA
STK35	0	.	GRCh37	20	2097509	2097509	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1090G>C	p.Asp364His	p.D364H	ENST00000381482	3/4	14	11	3	17	17	0	STK35,missense_variant,p.Asp364His,ENST00000381482,;STK35,missense_variant,p.Asp231His,ENST00000246032,;STK35,intron_variant,,ENST00000400064,;STK35,missense_variant,p.Asp225His,ENST00000493263,;	C	ENSG00000125834	ENST00000381482	Transcript	missense_variant	1361	1090	364	D/H	Gac/Cac	.	.	.	1	STK35	HGNC	16254	protein_coding	YES	CCDS13024.2	ENSP00000370891	STK35_HUMAN	.	UPI00003FCD67	.	deleterious(0)	probably_damaging(0.984)	3/4	.	PROSITE_profiles:PS50011,hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF59,PROSITE_patterns:PS00108,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCAGACAAC	.	2	ESCA
ITCH	0	.	GRCh37	20	33049899	33049899	+	Nonsense_Mutation	SNP	C	C	T	rs372589721	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000262650	15/26	70	63	6	61	61	0	ITCH,stop_gained,p.Gln433Ter,ENST00000374864,;ITCH,stop_gained,p.Gln323Ter,ENST00000535650,;ITCH,stop_gained,p.Gln474Ter,ENST00000262650,;MIR644A,upstream_gene_variant,,ENST00000385262,;ITCH,splice_region_variant,,ENST00000483727,;	T	ENSG00000078747	ENST00000262650	Transcript	stop_gained	1556	1420	474	Q/*	Caa/Taa	rs372589721	.	.	1	ITCH	HGNC	13890	protein_coding	YES	CCDS58768.1	ENSP00000262650	ITCH_HUMAN	.	UPI00000731C2	.	.	.	15/26	.	PIRSF_domain:PIRSF001569,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF66	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GTAGTCAATTA	byCluster	3	ESCA
ACTR5	0	.	GRCh37	20	37383788	37383788	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964G>C	p.Glu322Gln	p.E322Q	ENST00000243903	4/9	47	40	7	62	62	0	ACTR5,missense_variant,p.Glu322Gln,ENST00000243903,;	C	ENSG00000101442	ENST00000243903	Transcript	missense_variant	1001	964	322	E/Q	Gag/Cag	.	.	.	1	ACTR5	HGNC	14671	protein_coding	YES	CCDS13308.1	ENSP00000243903	ARP5_HUMAN	.	UPI000006F9EF	.	deleterious(0.05)	probably_damaging(0.957)	4/9	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11937:SF16,hmmpanther:PTHR11937,Pfam_domain:PF00022,SMART_domains:SM00268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCAGGAGCGT	.	2	ESCA
SPEF1	0	.	GRCh37	20	3758928	3758928	+	Silent	SNP	G	G	C	rs749206059	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642C>G	p.%3D	p.L214L	ENST00000379756	7/7	24	15	9	44	44	0	SPEF1,synonymous_variant,p.%3D,ENST00000379756,;SPEF1,non_coding_transcript_exon_variant,,ENST00000471499,;SPEF1,non_coding_transcript_exon_variant,,ENST00000463490,;	C	ENSG00000101222	ENST00000379756	Transcript	synonymous_variant	803	642	214	L	ctC/ctG	rs749206059	.	.	-1	SPEF1	HGNC	15874	protein_coding	YES	CCDS13063.2	ENSP00000369080	SPEF1_HUMAN	.	UPI000020694C	.	.	.	7/7	.	hmmpanther:PTHR12509,hmmpanther:PTHR12509:SF11,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGGAGCAG	.	5	ESCA
RIPK4	0	.	GRCh37	21	43165934	43165935	+	Frame_Shift_Ins	INS	-	-	G	rs746595711	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.920dupC	p.Glu308GlyfsTer21	p.E308Gfs*21	ENST00000332512	6/8	43	32	11	51	51	0	RIPK4,frameshift_variant,p.Glu356GlyfsTer21,ENST00000352483,;RIPK4,frameshift_variant,p.Glu245GlyfsTer21,ENST00000542057,;RIPK4,frameshift_variant,p.Glu245GlyfsTer21,ENST00000544709,;RIPK4,frameshift_variant,p.Glu308GlyfsTer21,ENST00000332512,;AP001615.9,downstream_gene_variant,,ENST00000423276,;	G	ENSG00000183421	ENST00000332512	Transcript	frameshift_variant	985-986	920-921	307	P/PX	ccg/ccCg	rs746595711	.	.	-1	RIPK4	HGNC	496	protein_coding	YES	CCDS13675.1	ENSP00000332454	RIPK4_HUMAN	B7ZAU7_HUMAN	UPI000002A3C9	.	.	.	6/8	.	hmmpanther:PTHR24198,hmmpanther:PTHR24198:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCTCCGGGGG	.	3	ESCA
CCT8L2	0	.	GRCh37	22	17072515	17072515	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.926A>C	p.Lys309Thr	p.K309T	ENST00000359963	1/1	68	53	15	41	41	0	CCT8L2,missense_variant,p.Lys309Thr,ENST00000359963,;FABP5P11,downstream_gene_variant,,ENST00000430910,;	G	ENSG00000198445	ENST00000359963	Transcript	missense_variant	1186	926	309	K/T	aAg/aCg	.	.	.	-1	CCT8L2	HGNC	15553	protein_coding	YES	CCDS13738.1	ENSP00000353048	TCPQM_HUMAN	.	UPI000006CF87	.	deleterious(0.01)	benign(0.339)	1/1	.	Superfamily_domains:SSF52029,Pfam_domain:PF00118,Gene3D:3.50.7.10,hmmpanther:PTHR11353:SF70,hmmpanther:PTHR11353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATACTTGTCC	.	5	ESCA
ZNF280A	0	.	GRCh37	22	22869365	22869365	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590C>G	p.Pro197Arg	p.P197R	ENST00000302097	2/2	51	46	5	38	38	0	ZNF280A,missense_variant,p.Pro197Arg,ENST00000302097,;snoU13,upstream_gene_variant,,ENST00000459485,;	C	ENSG00000169548	ENST00000302097	Transcript	missense_variant	843	590	197	P/R	cCt/cGt	.	.	.	-1	ZNF280A	HGNC	18597	protein_coding	YES	CCDS13800.1	ENSP00000302855	Z280A_HUMAN	.	UPI000013E78F	.	tolerated(0.06)	possibly_damaging(0.877)	2/2	.	hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF121,Pfam_domain:PF13836	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGAAGGGACC	.	2	ESCA
C22orf31	0	.	GRCh37	22	29455150	29455150	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453G>C	p.Glu151Asp	p.E151D	ENST00000216071	3/3	50	39	11	33	33	0	C22orf31,missense_variant,p.Glu151Asp,ENST00000216071,;ZNRF3,downstream_gene_variant,,ENST00000332811,;ZNRF3,downstream_gene_variant,,ENST00000544604,;	G	ENSG00000100249	ENST00000216071	Transcript	missense_variant	505	453	151	E/D	gaG/gaC	.	.	.	-1	C22orf31	HGNC	26931	protein_coding	YES	CCDS13848.1	ENSP00000216071	CV031_HUMAN	.	UPI0000073FE0	.	tolerated(0.07)	possibly_damaging(0.54)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15578,Pfam_domain:PF15578	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCTCCTT	.	5	ESCA
OSBP2	0	.	GRCh37	22	31218649	31218649	+	Intron	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.854-47767C>T	.	.	ENST00000332585	.	44	19	25	51	51	0	OSBP2,missense_variant,p.Ser11Phe,ENST00000437268,;OSBP2,intron_variant,,ENST00000401475,;OSBP2,intron_variant,,ENST00000332585,;OSBP2,intron_variant,,ENST00000446658,;OSBP2,intron_variant,,ENST00000407373,;OSBP2,intron_variant,,ENST00000445781,;OSBP2,intron_variant,,ENST00000382310,;OSBP2,intron_variant,,ENST00000403222,;OSBP2,intron_variant,,ENST00000424224,;OSBP2,intron_variant,,ENST00000477355,;OSBP2,intron_variant,,ENST00000496367,;OSBP2,intron_variant,,ENST00000464341,;	T	ENSG00000184792	ENST00000332585	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	OSBP2	HGNC	8504	protein_coding	YES	CCDS43002.1	ENSP00000332576	OSBP2_HUMAN	C9JS84_HUMAN,C9J7J0_HUMAN	UPI0000161E15	.	.	.	.	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCCGTGC	.	5	ESCA
MORC2	0	.	GRCh37	22	31330084	31330084	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2102G>C	p.Arg701Thr	p.R701T	ENST00000215862	21/27	90	72	18	57	57	0	MORC2,missense_variant,p.Arg701Thr,ENST00000215862,;MORC2,missense_variant,p.Arg763Thr,ENST00000397641,;MORC2,upstream_gene_variant,,ENST00000445980,;MORC2-AS1,downstream_gene_variant,,ENST00000441558,;MORC2,downstream_gene_variant,,ENST00000469915,;	G	ENSG00000133422	ENST00000215862	Transcript	missense_variant	3466	2102	701	R/T	aGa/aCa	.	.	.	-1	MORC2	HGNC	23573	protein_coding	YES	CCDS33636.1	ENSP00000215862	MORC2_HUMAN	.	UPI000012DB74	.	deleterious_low_confidence(0.01)	benign(0.064)	21/27	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23337:SF7,hmmpanther:PTHR23337	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAATCTGCCC	.	5	ESCA
RTCB	0	.	GRCh37	22	32802744	32802744	+	Missense_Mutation	SNP	G	G	C	rs756011780	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245C>G	p.Ser82Cys	p.S82C	ENST00000216038	4/12	20	15	5	19	19	0	RTCB,missense_variant,p.Ser82Cys,ENST00000216038,;RTCB,missense_variant,p.Ser82Cys,ENST00000451746,;RTCB,non_coding_transcript_exon_variant,,ENST00000476619,;RTCB,non_coding_transcript_exon_variant,,ENST00000485373,;RTCB,non_coding_transcript_exon_variant,,ENST00000487704,;RTCB,downstream_gene_variant,,ENST00000463455,;	C	ENSG00000100220	ENST00000216038	Transcript	missense_variant	344	245	82	S/C	tCt/tGt	rs756011780	.	.	-1	RTCB	HGNC	26935	protein_coding	YES	CCDS13905.1	ENSP00000216038	RTCB_HUMAN	.	UPI000006E0DE	.	deleterious(0)	probably_damaging(0.996)	4/12	.	HAMAP:MF_03144,hmmpanther:PTHR11118,PROSITE_patterns:PS01288,Pfam_domain:PF01139,Superfamily_domains:0044267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATAGATCGC	.	5	ESCA
LARGE	0	.	GRCh37	22	33673135	33673135	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1984G>C	p.Val662Leu	p.V662L	ENST00000354992	15/16	40	36	4	24	24	0	LARGE,missense_variant,p.Val461Leu,ENST00000452586,;LARGE,missense_variant,p.Val662Leu,ENST00000354992,;LARGE,missense_variant,p.Val613Leu,ENST00000437602,;LARGE,missense_variant,p.Val610Leu,ENST00000337431,;LARGE,missense_variant,p.Val610Leu,ENST00000402320,;LARGE,missense_variant,p.Val662Leu,ENST00000397394,;LARGE,intron_variant,,ENST00000609799,;LARGE,intron_variant,,ENST00000608642,;LARGE,intron_variant,,ENST00000610186,;	G	ENSG00000133424	ENST00000354992	Transcript	missense_variant	2556	1984	662	V/L	Gtt/Ctt	.	.	.	-1	LARGE	HGNC	6511	protein_coding	YES	CCDS13912.1	ENSP00000347088	LARGE_HUMAN	B0QZ02_HUMAN,B0QZ01_HUMAN,B0QZ00_HUMAN,B0QYZ9_HUMAN,B0QYZ8_HUMAN	UPI000012E200	.	tolerated(0.05)	benign(0.211)	15/16	.	hmmpanther:PTHR12270,hmmpanther:PTHR12270:SF18,Pfam_domain:PF13896	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CACAACAACAT	.	3	ESCA
ADSL	0	.	GRCh37	22	40757555	40757555	+	Missense_Mutation	SNP	G	G	A	rs749817666	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.926G>A	p.Arg309His	p.R309H	ENST00000216194	9/13	32	23	9	14	14	0	ADSL,missense_variant,p.Arg323His,ENST00000454266,;ADSL,missense_variant,p.Arg309His,ENST00000216194,;ADSL,missense_variant,p.Arg309His,ENST00000342312,;ADSL,upstream_gene_variant,,ENST00000498234,;ADSL,non_coding_transcript_exon_variant,,ENST00000480775,;ADSL,upstream_gene_variant,,ENST00000423176,;ADSL,downstream_gene_variant,,ENST00000477111,;	A	ENSG00000239900	ENST00000216194	Transcript	missense_variant	982	926	309	R/H	cGc/cAc	rs749817666	.	.	1	ADSL	HGNC	291	protein_coding	YES	CCDS14001.1	ENSP00000216194	PUR8_HUMAN	B4DUM2_HUMAN	UPI0000132AC7	.	deleterious(0)	probably_damaging(1)	9/13	.	hmmpanther:PTHR11444,hmmpanther:PTHR11444:SF2,TIGRFAM_domain:TIGR00928,Gene3D:1.20.200.10,Pfam_domain:PF00206,Superfamily_domains:SSF48557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGCCACC	.	5	ESCA
CYB5R3	0	.	GRCh37	22	43027454	43027454	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255C>T	p.%3D	p.I85I	ENST00000361740	3/9	75	57	18	38	38	0	CYB5R3,synonymous_variant,p.%3D,ENST00000407623,;CYB5R3,synonymous_variant,p.%3D,ENST00000396303,;CYB5R3,synonymous_variant,p.%3D,ENST00000361740,;CYB5R3,synonymous_variant,p.%3D,ENST00000352397,;CYB5R3,synonymous_variant,p.%3D,ENST00000402438,;CYB5R3,synonymous_variant,p.%3D,ENST00000438270,;CYB5R3,synonymous_variant,p.%3D,ENST00000407332,;CYB5R3,splice_region_variant,,ENST00000466276,;CYB5R3,non_coding_transcript_exon_variant,,ENST00000470741,;	A	ENSG00000100243	ENST00000361740	Transcript	synonymous_variant	255	255	85	I	atC/atT	.	.	.	-1	CYB5R3	HGNC	2873	protein_coding	YES	CCDS54535.1	ENSP00000354468	NB5R3_HUMAN	B1AHF3_HUMAN	UPI00019150F6	.	.	.	3/9	.	PROSITE_profiles:PS51384,hmmpanther:PTHR19370:SF80,hmmpanther:PTHR19370,Pfam_domain:PF00970,Gene3D:2.40.30.10,Superfamily_domains:SSF63380	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATGATCTG	.	5	ESCA
SCUBE1	0	.	GRCh37	22	43616536	43616536	+	Missense_Mutation	SNP	C	C	T	rs778296868	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1607G>A	p.Arg536His	p.R536H	ENST00000360835	14/22	87	61	25	64	64	0	SCUBE1,missense_variant,p.Arg536His,ENST00000360835,;	T	ENSG00000159307	ENST00000360835	Transcript	missense_variant	1734	1607	536	R/H	cGt/cAt	rs778296868,COSM479037	.	.	-1	SCUBE1	HGNC	13441	protein_coding	YES	CCDS14048.1	ENSP00000354080	SCUB1_HUMAN	.	UPI000020790F	.	tolerated(0.17)	probably_damaging(0.999)	14/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24046:SF4,hmmpanther:PTHR24046	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCACGGCGC	byFrequency	5	ESCA
AFF3	0	.	GRCh37	2	100203676	100203676	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2606G>C	p.Arg869Thr	p.R869T	ENST00000356421	15/24	113	82	31	110	110	0	AFF3,missense_variant,p.Arg869Thr,ENST00000409579,;AFF3,missense_variant,p.Arg869Thr,ENST00000356421,;AFF3,missense_variant,p.Arg844Thr,ENST00000317233,;AFF3,missense_variant,p.Arg844Thr,ENST00000409236,;	G	ENSG00000144218	ENST00000356421	Transcript	missense_variant	2750	2606	869	R/T	aGa/aCa	.	.	.	-1	AFF3	HGNC	6473	protein_coding	YES	CCDS33258.1	ENSP00000348793	AFF3_HUMAN	.	UPI000041098C	.	tolerated(0.41)	benign(0.117)	15/24	.	hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGTCTTGAA	.	5	ESCA
IL1R1	0	.	GRCh37	2	102781461	102781461	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.289G>A	p.Val97Met	p.V97M	ENST00000410023	4/12	74	51	22	78	78	0	IL1R1,missense_variant,p.Val97Met,ENST00000430171,;IL1R1,missense_variant,p.Val97Met,ENST00000409288,;IL1R1,missense_variant,p.Val97Met,ENST00000450319,;IL1R1,missense_variant,p.Val97Met,ENST00000424272,;IL1R1,missense_variant,p.Val97Met,ENST00000409329,;IL1R1,missense_variant,p.Val97Met,ENST00000409589,;IL1R1,missense_variant,p.Val97Met,ENST00000409929,;IL1R1,missense_variant,p.Val97Met,ENST00000233946,;IL1R1,missense_variant,p.Val97Met,ENST00000410023,;IL1R1,missense_variant,p.Val97Met,ENST00000442590,;IL1R1,5_prime_UTR_variant,,ENST00000428279,;IL1R1,downstream_gene_variant,,ENST00000452403,;IL1R1,missense_variant,p.Val77Met,ENST00000422532,;IL1R1,missense_variant,p.Val97Met,ENST00000413623,;	A	ENSG00000115594	ENST00000410023	Transcript	missense_variant	607	289	97	V/M	Gtg/Atg	COSM4083852	.	.	1	IL1R1	HGNC	5993	protein_coding	YES	CCDS2055.1	ENSP00000386380	IL1R1_HUMAN	C9JWB2_HUMAN,C9JW84_HUMAN,C9JQ36_HUMAN,C9J686_HUMAN,C9J3W8_HUMAN	UPI0000034759	.	deleterious(0.03)	possibly_damaging(0.884)	4/12	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11890:SF19,hmmpanther:PTHR11890,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726,Prints_domain:PR01536	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGCGTGGTA	.	5	ESCA
MYO7B	0	.	GRCh37	2	128324310	128324310	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378T>G	p.His126Gln	p.H126Q	ENST00000428314	5/47	19	11	7	21	21	0	MYO7B,missense_variant,p.His126Gln,ENST00000389524,;MYO7B,missense_variant,p.His126Gln,ENST00000409816,;MYO7B,missense_variant,p.His126Gln,ENST00000428314,;	G	ENSG00000169994	ENST00000428314	Transcript	missense_variant	431	378	126	H/Q	caT/caG	.	.	.	1	MYO7B	HGNC	7607	protein_coding	YES	CCDS46405.1	ENSP00000415090	MYO7B_HUMAN	C9JC21_HUMAN,B9A063_HUMAN	UPI00006C04F0	.	tolerated(0.13)	benign(0.027)	5/47	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF352,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCATATGGG	.	5	ESCA
EPC2	0	.	GRCh37	2	149544028	149544028	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*82G>A	.	.	ENST00000258484	14/14	32	19	13	37	37	0	EPC2,3_prime_UTR_variant,,ENST00000258484,;	A	ENSG00000135999	ENST00000258484	Transcript	3_prime_UTR_variant	2540	.	.	.	.	.	.	.	1	EPC2	HGNC	24543	protein_coding	YES	CCDS46422.1	ENSP00000258484	EPC2_HUMAN	Q53SN6_HUMAN,Q53SL1_HUMAN,E7ETK1_HUMAN,C9J1X4_HUMAN	UPI00005A7FE2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGGATCAC	.	5	ESCA
PSMD14	0	.	GRCh37	2	162268050	162268050	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*139C>T	.	.	ENST00000409682	12/12	11	6	5	17	17	0	PSMD14,3_prime_UTR_variant,,ENST00000409682,;TBR1,upstream_gene_variant,,ENST00000389554,;5S_rRNA,downstream_gene_variant,,ENST00000605921,;PSMD14,non_coding_transcript_exon_variant,,ENST00000477232,;PSMD14,non_coding_transcript_exon_variant,,ENST00000492908,;TBR1,upstream_gene_variant,,ENST00000463544,;	T	ENSG00000115233	ENST00000409682	Transcript	3_prime_UTR_variant	1776	.	.	.	.	.	.	.	1	PSMD14	HGNC	16889	protein_coding	YES	CCDS46437.1	ENSP00000386541	PSDE_HUMAN	Q96DE8_HUMAN,Q53TH1_HUMAN,Q4ZG77_HUMAN,C9JW37_HUMAN	UPI0000027819	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCTTCAGTCT	.	3	ESCA
DFNB59	0	.	GRCh37	2	179325074	179325074	+	Splice_Site	SNP	G	G	A	rs34458034	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668-1G>A	.	p.X223_splice	ENST00000409117	.	45	30	15	44	44	0	DFNB59,splice_acceptor_variant,,ENST00000442710,;DFNB59,splice_acceptor_variant,,ENST00000375129,;DFNB59,splice_acceptor_variant,,ENST00000409117,;FKBP7,downstream_gene_variant,,ENST00000424785,;FKBP7,downstream_gene_variant,,ENST00000464248,;DFNB59,downstream_gene_variant,,ENST00000605419,;DFNB59,splice_acceptor_variant,,ENST00000444615,;DFNB59,splice_acceptor_variant,,ENST00000437056,;AC009948.7,downstream_gene_variant,,ENST00000437039,;	A	ENSG00000204311	ENST00000409117	Transcript	splice_acceptor_variant	.	.	.	.	.	rs34458034	.	.	1	DFNB59	HGNC	29502	protein_coding	YES	CCDS42787.1	ENSP00000386647	PJVK_HUMAN	A0PK15_HUMAN	UPI0000DAD718	.	.	.	.	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTAGACCTT	byCluster	5	ESCA
TTN	0	.	GRCh37	2	179397665	179397665	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103677C>G	p.Ile34559Met	p.I34559M	ENST00000589042	358/363	30	21	8	36	36	0	TTN,missense_variant,p.Ile25619Met,ENST00000359218,;TTN,missense_variant,p.Ile25494Met,ENST00000460472,;TTN,missense_variant,p.Ile32918Met,ENST00000591111,;TTN,missense_variant,p.Ile34559Met,ENST00000589042,;TTN,missense_variant,p.Ile25686Met,ENST00000342175,;TTN,missense_variant,p.Ile31991Met,ENST00000342992,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589434,;TTN-AS1,intron_variant,,ENST00000588716,;TTN-AS1,intron_variant,,ENST00000589391,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000592182,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592836,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000591466,;TTN-AS1,intron_variant,,ENST00000591867,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000585358,;TTN-AS1,intron_variant,,ENST00000589842,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000590040,;TTN-AS1,intron_variant,,ENST00000450692,;TTN-AS1,intron_variant,,ENST00000442329,;TTN-AS1,intron_variant,,ENST00000431259,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000588257,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000588244,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000588804,;TTN-AS1,intron_variant,,ENST00000585487,;TTN-AS1,downstream_gene_variant,,ENST00000585625,;TTN-AS1,downstream_gene_variant,,ENST00000587568,;TTN-AS1,upstream_gene_variant,,ENST00000415561,;TTN-AS1,downstream_gene_variant,,ENST00000587944,;TTN-AS1,downstream_gene_variant,,ENST00000589355,;TTN-AS1,downstream_gene_variant,,ENST00000604571,;	C	ENSG00000155657	ENST00000589042	Transcript	missense_variant	103902	103677	34559	I/M	atC/atG	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	358/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTGATGCG	.	5	ESCA
TTN	0	.	GRCh37	2	179441051	179441051	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69808C>T	p.Leu23270Phe	p.L23270F	ENST00000589042	326/363	9	6	3	11	11	0	TTN,missense_variant,p.Leu14330Phe,ENST00000359218,;TTN,missense_variant,p.Leu21629Phe,ENST00000591111,;TTN,missense_variant,p.Leu23270Phe,ENST00000589042,;TTN,missense_variant,p.Leu14397Phe,ENST00000342175,;TTN,missense_variant,p.Leu20702Phe,ENST00000342992,;TTN,missense_variant,p.Leu14205Phe,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;RP11-171I2.2,upstream_gene_variant,,ENST00000603521,;RP11-171I2.5,upstream_gene_variant,,ENST00000604215,;	A	ENSG00000155657	ENST00000589042	Transcript	missense_variant	70033	69808	23270	L/F	Ctt/Ttt	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	326/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCAAGTCCAC	.	2	ESCA
MARCH4	0	.	GRCh37	2	217142429	217142429	+	Silent	SNP	G	G	A	rs138565372	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.831C>T	p.%3D	p.Y277Y	ENST00000273067	3/4	23	17	6	29	29	0	MARCH4,synonymous_variant,p.%3D,ENST00000273067,;	A	ENSG00000144583	ENST00000273067	Transcript	synonymous_variant	2598	831	277	Y	taC/taT	rs138565372,COSM209985	.	.	-1	MARCH4	HGNC	29269	protein_coding	YES	CCDS33376.1	ENSP00000273067	MARH4_HUMAN	.	UPI00001C1DB9	.	.	.	3/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23012:SF51,hmmpanther:PTHR23012	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCCGTAGCA	byFrequency|byCluster|by1000G	5	ESCA
SP110	0	.	GRCh37	2	231041301	231041301	+	Intron	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1590+953C>G	.	.	ENST00000258381	.	16	10	6	26	26	0	SP110,3_prime_UTR_variant,,ENST00000392048,;SP110,3_prime_UTR_variant,,ENST00000258382,;SP110,3_prime_UTR_variant,,ENST00000540870,;SP110,intron_variant,,ENST00000358662,;SP110,intron_variant,,ENST00000258381,;SP110,downstream_gene_variant,,ENST00000338556,;AC009950.2,downstream_gene_variant,,ENST00000600787,;AC009950.2,downstream_gene_variant,,ENST00000594622,;AC009950.2,downstream_gene_variant,,ENST00000454058,;AC009950.2,downstream_gene_variant,,ENST00000609120,;AC009950.2,downstream_gene_variant,,ENST00000595586,;SP110,upstream_gene_variant,,ENST00000480916,;SP110,upstream_gene_variant,,ENST00000477068,;SP110,downstream_gene_variant,,ENST00000489597,;SP110,upstream_gene_variant,,ENST00000483067,;	C	ENSG00000135899	ENST00000258381	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SP110	HGNC	5401	protein_coding	YES	CCDS2475.1	ENSP00000258381	SP110_HUMAN	Q2I9M3_HUMAN,Q2I9M2_HUMAN,Q2I9M1_HUMAN,Q2I9M0_HUMAN,Q2I9L9_HUMAN,E9PHK4_HUMAN,E7EM70_HUMAN,C9JZQ4_HUMAN	UPI000013CFC9	.	.	.	.	14/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGAGCTTGG	.	5	ESCA
HDAC4	0	.	GRCh37	2	239971224	239971224	+	3'UTR	SNP	T	T	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3569A>T	.	.	ENST00000345617	27/27	21	17	4	15	15	0	HDAC4,3_prime_UTR_variant,,ENST00000345617,;HDAC4,downstream_gene_variant,,ENST00000543185,;HDAC4,downstream_gene_variant,,ENST00000430200,;	A	ENSG00000068024	ENST00000345617	Transcript	3_prime_UTR_variant	7616	.	.	.	.	.	.	.	-1	HDAC4	HGNC	14063	protein_coding	YES	CCDS2529.1	ENSP00000264606	HDAC4_HUMAN	Q53SM2_HUMAN,Q53SB4_HUMAN,F5H0B1_HUMAN,F5GX36_HUMAN,C9J0X4_HUMAN	UPI000013D541	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAAGTCTACA	.	4	ESCA
NLRC4	0	.	GRCh37	2	32476497	32476497	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436C>A	p.His146Asn	p.H146N	ENST00000404025	5/10	31	22	9	15	15	0	NLRC4,missense_variant,p.His146Asn,ENST00000402280,;NLRC4,missense_variant,p.His146Asn,ENST00000360906,;NLRC4,missense_variant,p.His146Asn,ENST00000404025,;NLRC4,intron_variant,,ENST00000342905,;	T	ENSG00000091106	ENST00000404025	Transcript	missense_variant	925	436	146	H/N	Cat/Aat	.	.	.	-1	NLRC4	HGNC	16412	protein_coding	YES	CCDS33174.1	ENSP00000385090	NLRC4_HUMAN	.	UPI0000126FAD	.	tolerated(0.96)	benign(0.015)	5/10	.	hmmpanther:PTHR10044:SF97,hmmpanther:PTHR10044,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATGGTGTT	.	5	ESCA
BIRC6	0	.	GRCh37	2	32693623	32693623	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5899G>C	p.Asp1967His	p.D1967H	ENST00000421745	29/74	83	64	18	65	65	0	BIRC6,missense_variant,p.Asp1967His,ENST00000421745,;BIRC6,upstream_gene_variant,,ENST00000462504,;	C	ENSG00000115760	ENST00000421745	Transcript	missense_variant	6033	5899	1967	D/H	Gac/Cac	.	.	.	1	BIRC6	HGNC	13516	protein_coding	YES	CCDS33175.2	ENSP00000393596	BIRC6_HUMAN	.	UPI0001611442	.	.	probably_damaging(0.997)	29/74	.	hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGACAGT	.	5	ESCA
SOS1	0	.	GRCh37	2	39237798	39237798	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2437G>C	p.Asp813His	p.D813H	ENST00000426016	16/24	103	86	17	105	105	0	SOS1,missense_variant,p.Asp813His,ENST00000395038,;SOS1,missense_variant,p.Asp813His,ENST00000426016,;SOS1,missense_variant,p.Asp813His,ENST00000402219,;SOS1,upstream_gene_variant,,ENST00000474390,;	G	ENSG00000115904	ENST00000426016	Transcript	missense_variant	2524	2437	813	D/H	Gac/Cac	.	.	.	-1	SOS1	HGNC	11187	protein_coding	YES	CCDS1802.1	ENSP00000387784	SOS1_HUMAN	Q9UKX9_HUMAN,Q53SF8_HUMAN,C9K0N6_HUMAN	UPI0000135CF0	.	tolerated(0.06)	probably_damaging(0.997)	16/24	.	Superfamily_domains:0041591,SMART_domains:SM00147,Gene3D:2ii0A02,Pfam_domain:PF00617,hmmpanther:PTHR23113:SF168,hmmpanther:PTHR23113,PROSITE_profiles:PS50009	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTCTTCTT	.	5	ESCA
PPM1B	0	.	GRCh37	2	44396133	44396133	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-295C>T	.	.	ENST00000282412	1/6	137	98	39	115	115	0	PPM1B,5_prime_UTR_variant,,ENST00000409432,;PPM1B,5_prime_UTR_variant,,ENST00000409895,;PPM1B,5_prime_UTR_variant,,ENST00000419807,;PPM1B,5_prime_UTR_variant,,ENST00000282412,;PPM1B,5_prime_UTR_variant,,ENST00000345249,;PPM1B,5_prime_UTR_variant,,ENST00000378551,;RP11-559M23.1,upstream_gene_variant,,ENST00000609837,;PPM1B,non_coding_transcript_exon_variant,,ENST00000378540,;PPM1B,non_coding_transcript_exon_variant,,ENST00000409486,;AC019129.2,downstream_gene_variant,,ENST00000449397,;	T	ENSG00000138032	ENST00000282412	Transcript	5_prime_UTR_variant	118	.	.	.	.	.	.	.	1	PPM1B	HGNC	9276	protein_coding	YES	CCDS1817.1	ENSP00000282412	PPM1B_HUMAN	C9JIR6_HUMAN	UPI0000130FE7	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTCAGGGT	.	5	ESCA
FOXN2	0	.	GRCh37	2	48606340	48606340	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3758C>G	.	.	ENST00000340553	7/7	62	48	13	54	54	0	FOXN2,3_prime_UTR_variant,,ENST00000340553,;	G	ENSG00000170802	ENST00000340553	Transcript	3_prime_UTR_variant	5315	.	.	.	.	.	.	.	1	FOXN2	HGNC	5281	protein_coding	YES	CCDS1838.1	ENSP00000343633	FOXN2_HUMAN	Q6IS90_HUMAN,C9JTA7_HUMAN	UPI0000226321	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCTCTGATT	.	5	ESCA
ANXA4	0	.	GRCh37	2	70033541	70033541	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217G>A	p.Glu73Lys	p.E73K	ENST00000394295	5/13	48	30	17	31	31	0	ANXA4,missense_variant,p.Glu73Lys,ENST00000409920,;ANXA4,missense_variant,p.Glu73Lys,ENST00000394295,;ANXA4,5_prime_UTR_variant,,ENST00000536030,;ANXA4,non_coding_transcript_exon_variant,,ENST00000460942,;ANXA4,non_coding_transcript_exon_variant,,ENST00000460439,;ANXA4,non_coding_transcript_exon_variant,,ENST00000487351,;ANXA4,upstream_gene_variant,,ENST00000472124,;ANXA4,upstream_gene_variant,,ENST00000468815,;ANXA4,downstream_gene_variant,,ENST00000484219,;ANXA4,non_coding_transcript_exon_variant,,ENST00000477632,;	A	ENSG00000196975	ENST00000394295	Transcript	missense_variant	465	217	73	E/K	Gaa/Aaa	.	.	.	1	ANXA4	HGNC	542	protein_coding	YES	CCDS1894.1	ENSP00000377833	ANXA4_HUMAN	Q6MZI0_HUMAN,Q6LES2_HUMAN,B4DDF9_HUMAN	UPI000013D51A	.	deleterious(0.02)	probably_damaging(0.999)	5/13	.	Prints_domain:PR00196,Superfamily_domains:SSF47874,SMART_domains:SM00335,Pfam_domain:PF00191,Gene3D:1.10.220.10,PROSITE_patterns:PS00223,hmmpanther:PTHR10502,hmmpanther:PTHR10502:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCAGAACTG	.	5	ESCA
IGKV2-28	0	.	GRCh37	2	89521478	89521478	+	Missense_Mutation	SNP	C	C	T	rs547009276	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61G>A	p.Asp21Asn	p.D21N	ENST00000482769	2/2	27	18	9	31	31	0	IGKV2-28,missense_variant,p.Asp21Asn,ENST00000482769,;	T	ENSG00000244116	ENST00000482769	Transcript	missense_variant	91	61	21	D/N	Gat/Aat	rs547009276	.	.	-1	IGKV2-28	HGNC	5783	IG_V_gene	YES	.	ENSP00000419353	.	.	UPI00005FFCB1	.	deleterious(0.04)	benign(0.168)	2/2	.	Gene3D:2.60.40.10,hmmpanther:PTHR23267:SF155,hmmpanther:PTHR23267,PROSITE_profiles:PS50835	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	AATATCCCCAC	by1000G	3	ESCA
UNC50	0	.	GRCh37	2	99232694	99232694	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426G>A	p.%3D	p.V142V	ENST00000357765	4/6	129	123	6	124	124	0	UNC50,synonymous_variant,p.%3D,ENST00000423713,;UNC50,synonymous_variant,p.%3D,ENST00000409975,;UNC50,synonymous_variant,p.%3D,ENST00000357765,;UNC50,synonymous_variant,p.%3D,ENST00000393493,;UNC50,synonymous_variant,p.%3D,ENST00000409347,;MGAT4A,downstream_gene_variant,,ENST00000414521,;MGAT4A,downstream_gene_variant,,ENST00000393487,;MGAT4A,downstream_gene_variant,,ENST00000264968,;UNC50,upstream_gene_variant,,ENST00000466492,;	A	ENSG00000115446	ENST00000357765	Transcript	synonymous_variant	578	426	142	V	gtG/gtA	.	.	.	1	UNC50	HGNC	16046	protein_coding	YES	CCDS2035.1	ENSP00000350409	UNC50_HUMAN	.	UPI0000031564	.	.	.	4/6	.	hmmpanther:PTHR12841,Pfam_domain:PF05216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTAGTGAAACG	.	2	ESCA
MCM2	0	.	GRCh37	3	127325492	127325492	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933G>A	p.%3D	p.V311V	ENST00000265056	6/16	51	39	12	27	27	0	MCM2,synonymous_variant,p.%3D,ENST00000265056,;MCM2,synonymous_variant,p.%3D,ENST00000491422,;MCM2,downstream_gene_variant,,ENST00000472731,;MCM2,downstream_gene_variant,,ENST00000480910,;MCM2,downstream_gene_variant,,ENST00000468659,;MCM2,3_prime_UTR_variant,,ENST00000477668,;MCM2,3_prime_UTR_variant,,ENST00000474964,;	A	ENSG00000073111	ENST00000265056	Transcript	synonymous_variant	1177	933	311	V	gtG/gtA	.	.	.	1	MCM2	HGNC	6944	protein_coding	YES	CCDS3043.1	ENSP00000265056	MCM2_HUMAN	Q9BWF4_HUMAN,C9JZ21_HUMAN,C9J013_HUMAN	UPI00001A3E4E	.	.	.	6/16	.	Prints_domain:PR01658,Superfamily_domains:SSF50249,SMART_domains:SM00350,Gene3D:2.40.50.140,hmmpanther:PTHR11630:SF44,hmmpanther:PTHR11630	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTGGTGAC	.	5	ESCA
COL6A5	0	.	GRCh37	3	130119967	130119967	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4084C>G	p.His1362Asp	p.H1362D	ENST00000265379	11/42	50	39	10	34	34	0	COL6A5,missense_variant,p.His1362Asp,ENST00000432398,;COL6A5,missense_variant,p.His1362Asp,ENST00000265379,;COL6A5,missense_variant,p.His1362Asp,ENST00000312481,;	G	ENSG00000172752	ENST00000265379	Transcript	missense_variant	4578	4084	1362	H/D	Cat/Gat	.	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	deleterious(0.01)	benign(0.359)	11/42	.	hmmpanther:PTHR22992:SF93,hmmpanther:PTHR22992,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACTCATCTG	.	5	ESCA
ATP2C1	0	.	GRCh37	3	130694321	130694321	+	Missense_Mutation	SNP	C	C	T	rs779717457	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1661C>T	p.Ala554Val	p.A554V	ENST00000393221	17/28	28	25	3	22	22	0	ATP2C1,missense_variant,p.Ala515Val,ENST00000533801,;ATP2C1,missense_variant,p.Ala520Val,ENST00000328560,;ATP2C1,missense_variant,p.Ala520Val,ENST00000508532,;ATP2C1,missense_variant,p.Ala504Val,ENST00000505330,;ATP2C1,missense_variant,p.Ala474Val,ENST00000504612,;ATP2C1,missense_variant,p.Ala520Val,ENST00000359644,;ATP2C1,missense_variant,p.Ala504Val,ENST00000504948,;ATP2C1,missense_variant,p.Ala95Val,ENST00000508660,;ATP2C1,missense_variant,p.Ala504Val,ENST00000507488,;ATP2C1,missense_variant,p.Ala554Val,ENST00000393221,;ATP2C1,missense_variant,p.Ala520Val,ENST00000422190,;ATP2C1,missense_variant,p.Ala520Val,ENST00000428331,;ATP2C1,missense_variant,p.Ala504Val,ENST00000513801,;ATP2C1,missense_variant,p.Ala465Val,ENST00000504381,;ATP2C1,missense_variant,p.Ala520Val,ENST00000510168,;ATP2C1,missense_variant,p.Ala207Val,ENST00000504571,;ATP2C1,non_coding_transcript_exon_variant,,ENST00000514654,;	T	ENSG00000017260	ENST00000393221	Transcript	missense_variant	1876	1661	554	A/V	gCg/gTg	rs779717457,COSM3587460,COSM3587459	.	.	1	ATP2C1	HGNC	13211	protein_coding	YES	CCDS56278.1	ENSP00000376914	AT2C1_HUMAN	D6RGE9_HUMAN,D6R9U9_HUMAN	UPI0000EE224C	.	tolerated(0.28)	benign(0.058)	17/28	.	Prints_domain:PR00120,Superfamily_domains:SSF56784,Pfam_domain:PF00702,TIGRFAM_domain:TIGR01522,Gene3D:1.20.1110.10,hmmpanther:PTHR24093:SF214,hmmpanther:PTHR24093	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAGCGGGAC	byFrequency	4	ESCA
PLS1	0	.	GRCh37	3	142383112	142383112	+	Silent	SNP	G	G	A	rs768235395	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33G>A	p.%3D	p.E11E	ENST00000337777	2/16	89	76	12	48	48	0	PLS1,synonymous_variant,p.%3D,ENST00000475296,;PLS1,synonymous_variant,p.%3D,ENST00000461644,;PLS1,synonymous_variant,p.%3D,ENST00000483373,;PLS1,synonymous_variant,p.%3D,ENST00000337777,;PLS1,synonymous_variant,p.%3D,ENST00000457734,;PLS1,synonymous_variant,p.%3D,ENST00000464320,;PLS1,synonymous_variant,p.%3D,ENST00000497002,;PLS1,synonymous_variant,p.%3D,ENST00000497199,;PLS1,synonymous_variant,p.%3D,ENST00000495744,;PLS1,intron_variant,,ENST00000476044,;PLS1,non_coding_transcript_exon_variant,,ENST00000460104,;	A	ENSG00000120756	ENST00000337777	Transcript	synonymous_variant	246	33	11	E	gaG/gaA	rs768235395	.	.	1	PLS1	HGNC	9090	protein_coding	YES	CCDS3125.1	ENSP00000336831	PLSI_HUMAN	C9JYI1_HUMAN,C9JVY2_HUMAN,C9JU08_HUMAN,C9JAM8_HUMAN,C9JAM3_HUMAN,C9J359_HUMAN,C9J0F3_HUMAN	UPI000013D59A	.	.	.	2/16	.	PROSITE_profiles:PS50222,hmmpanther:PTHR19961:SF27,hmmpanther:PTHR19961,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGAGGAGCT	.	5	ESCA
SELT	0	.	GRCh37	3	150346029	150346029	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*613G>C	.	.	ENST00000471696	6/6	57	48	9	38	38	0	SELT,3_prime_UTR_variant,,ENST00000471696,;SELT,downstream_gene_variant,,ENST00000480740,;SELT,downstream_gene_variant,,ENST00000477889,;SELT,downstream_gene_variant,,ENST00000485923,;SELT,downstream_gene_variant,,ENST00000466234,;SELT,downstream_gene_variant,,ENST00000492132,;	C	ENSG00000198843	ENST00000471696	Transcript	3_prime_UTR_variant	1276	.	.	.	.	.	.	.	1	SELT	Uniprot_gn	.	protein_coding	YES	CCDS46936.1	ENSP00000418910	SELT_HUMAN	Q6IAK0_HUMAN,F8WBD0_HUMAN	UPI000034ECC3	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCAGAGAAC	.	5	ESCA
CLRN1-AS1	0	.	GRCh37	3	150784127	150784127	+	RNA	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.296C>G	.	.	ENST00000476886	4/5	144	125	18	68	68	0	CLRN1-AS1,non_coding_transcript_exon_variant,,ENST00000465576,;CLRN1-AS1,non_coding_transcript_exon_variant,,ENST00000476886,;	G	ENSG00000239265	ENST00000476886	Transcript	non_coding_transcript_exon_variant	296	.	.	.	.	.	.	.	1	CLRN1-AS1	HGNC	30895	antisense	YES	.	.	.	.	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCACTAAAT	.	4	ESCA
P2RY12	0	.	GRCh37	3	151056001	151056001	+	Silent	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.633C>G	p.%3D	p.L211L	ENST00000302632	3/3	111	59	51	69	69	0	P2RY12,synonymous_variant,p.%3D,ENST00000302632,;MED12L,intron_variant,,ENST00000474524,;MED12L,intron_variant,,ENST00000273432,;MED12L,downstream_gene_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,;P2RY12,non_coding_transcript_exon_variant,,ENST00000468596,;	C	ENSG00000169313	ENST00000302632	Transcript	synonymous_variant	933	633	211	L	ctC/ctG	.	.	.	-1	P2RY12	HGNC	18124	protein_coding	YES	CCDS3159.1	ENSP00000307259	P2Y12_HUMAN	.	UPI0000001662	.	.	.	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF0,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR01157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAATGAGTGT	.	5	ESCA
LRRC34	0	.	GRCh37	3	169526492	169526492	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181T>C	p.Cys61Arg	p.C61R	ENST00000446859	2/11	80	64	16	50	50	0	LRRC34,missense_variant,p.Cys61Arg,ENST00000522526,;LRRC34,missense_variant,p.Cys48Arg,ENST00000316515,;LRRC34,missense_variant,p.Cys61Arg,ENST00000446859,;LRRC34,5_prime_UTR_variant,,ENST00000522830,;LRRC34,intron_variant,,ENST00000524054,;LRRC34,upstream_gene_variant,,ENST00000524327,;LRRC34,non_coding_transcript_exon_variant,,ENST00000520726,;LRRC34,non_coding_transcript_exon_variant,,ENST00000522080,;LRRC34,non_coding_transcript_exon_variant,,ENST00000522596,;	G	ENSG00000171757	ENST00000446859	Transcript	missense_variant	297	181	61	C/R	Tgt/Cgt	.	.	.	-1	LRRC34	HGNC	28408	protein_coding	YES	CCDS54672.1	ENSP00000414635	LRC34_HUMAN	G3V115_HUMAN	UPI0000E5AA9B	.	deleterious(0)	probably_damaging(1)	2/11	.	hmmpanther:PTHR24111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATACACAGAT	.	5	ESCA
XXYLT1	0	.	GRCh37	3	194842910	194842910	+	Intron	SNP	C	C	T	rs576093979	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.785+34268G>A	.	.	ENST00000310380	.	49	37	12	33	33	0	XXYLT1,missense_variant,p.Met4Ile,ENST00000356740,;XXYLT1,intron_variant,,ENST00000355729,;XXYLT1,intron_variant,,ENST00000310380,;XXYLT1,intron_variant,,ENST00000437101,;XXYLT1,intron_variant,,ENST00000429994,;XXYLT1,intron_variant,,ENST00000473200,;XXYLT1,intron_variant,,ENST00000491138,;XXYLT1,intron_variant,,ENST00000418940,;	T	ENSG00000173950	ENST00000310380	Transcript	intron_variant	.	.	.	.	.	rs576093979	.	.	-1	XXYLT1	HGNC	26639	protein_coding	YES	CCDS43188.1	ENSP00000309640	XXLT1_HUMAN	.	UPI000003B10F	.	.	.	.	3/3	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTCATCCC	by1000G	5	ESCA
STT3B	0	.	GRCh37	3	31677544	31677544	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2469G>C	p.Lys823Asn	p.K823N	ENST00000295770	16/16	59	53	6	58	58	0	STT3B,missense_variant,p.Lys823Asn,ENST00000295770,;STT3B,non_coding_transcript_exon_variant,,ENST00000463044,;STT3B,downstream_gene_variant,,ENST00000488151,;	C	ENSG00000163527	ENST00000295770	Transcript	missense_variant	2678	2469	823	K/N	aaG/aaC	.	.	.	1	STT3B	HGNC	30611	protein_coding	YES	CCDS2650.1	ENSP00000295770	STT3B_HUMAN	.	UPI000006D7FB	.	deleterious_low_confidence(0.03)	benign(0.039)	16/16	.	hmmpanther:PTHR13872,hmmpanther:PTHR13872:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTAAGAAGAC	.	3	ESCA
TRIM71	0	.	GRCh37	3	32859540	32859540	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-33C>G	.	.	ENST00000383763	1/4	9	3	6	37	37	0	TRIM71,5_prime_UTR_variant,,ENST00000383763,;	G	ENSG00000206557	ENST00000383763	Transcript	5_prime_UTR_variant	31	.	.	.	.	.	.	.	1	TRIM71	HGNC	32669	protein_coding	YES	CCDS43060.1	ENSP00000373272	LIN41_HUMAN	.	UPI000067CB89	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCTCTGGTC	.	3	ESCA
SLC38A3	0	.	GRCh37	3	50255369	50255369	+	RNA	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1029C>G	.	.	ENST00000420502	11/16	15	6	8	32	32	0	SLC38A3,non_coding_transcript_exon_variant,,ENST00000541861,;SLC38A3,non_coding_transcript_exon_variant,,ENST00000445096,;SLC38A3,non_coding_transcript_exon_variant,,ENST00000420502,;SLC38A3,non_coding_transcript_exon_variant,,ENST00000414604,;SLC38A3,downstream_gene_variant,,ENST00000427428,;SLC38A3,downstream_gene_variant,,ENST00000445325,;SLC38A3,non_coding_transcript_exon_variant,,ENST00000417851,;SLC38A3,non_coding_transcript_exon_variant,,ENST00000417121,;SLC38A3,downstream_gene_variant,,ENST00000456338,;SLC38A3,downstream_gene_variant,,ENST00000439524,;	G	ENSG00000188338	ENST00000420502	Transcript	non_coding_transcript_exon_variant	1029	.	.	.	.	.	.	.	1	SLC38A3	HGNC	18044	processed_transcript	YES	.	.	.	.	.	.	.	.	11/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CCCATCATGGC	.	4	ESCA
CPOX	0	.	GRCh37	3	98298733	98298733	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*794G>A	.	.	ENST00000264193	7/7	60	42	17	47	47	0	CPOX,3_prime_UTR_variant,,ENST00000264193,;CPOX,intron_variant,,ENST00000512905,;CPOX,downstream_gene_variant,,ENST00000510489,;	T	ENSG00000080819	ENST00000264193	Transcript	3_prime_UTR_variant	2378	.	.	.	.	.	.	.	-1	CPOX	HGNC	2321	protein_coding	YES	CCDS2932.1	ENSP00000264193	HEM6_HUMAN	.	UPI0000073C93	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCAACTT	.	5	ESCA
AP1AR	0	.	GRCh37	4	113153085	113153085	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-163C>T	.	.	ENST00000274000	1/10	15	10	5	12	12	0	AP1AR,5_prime_UTR_variant,,ENST00000309703,;AP1AR,5_prime_UTR_variant,,ENST00000274000,;RP11-73K9.2,upstream_gene_variant,,ENST00000562919,;AP1AR,non_coding_transcript_exon_variant,,ENST00000502954,;AP1AR,non_coding_transcript_exon_variant,,ENST00000510527,;AP1AR,non_coding_transcript_exon_variant,,ENST00000506522,;	T	ENSG00000138660	ENST00000274000	Transcript	5_prime_UTR_variant	193	.	.	.	.	.	.	.	1	AP1AR	HGNC	28808	protein_coding	YES	CCDS3696.1	ENSP00000274000	AP1AR_HUMAN	.	UPI000013D9E5	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTCGTCTT	.	5	ESCA
FAT4	0	.	GRCh37	4	126336956	126336956	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6838C>A	p.Leu2280Ile	p.L2280I	ENST00000394329	5/17	33	24	9	25	25	0	FAT4,missense_variant,p.Leu2280Ile,ENST00000394329,;FAT4,missense_variant,p.Leu578Ile,ENST00000335110,;	A	ENSG00000196159	ENST00000394329	Transcript	missense_variant	6851	6838	2280	L/I	Ctt/Att	.	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	probably_damaging(0.983)	5/17	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAATTCTTCAG	.	2	ESCA
PGRMC2	0	.	GRCh37	4	129193573	129193573	+	Nonsense_Mutation	SNP	G	G	C	rs765349385	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590C>G	p.Ser197Ter	p.S197*	ENST00000520121	2/3	17	12	5	22	22	0	PGRMC2,stop_gained,p.Ser173Ter,ENST00000296425,;PGRMC2,stop_gained,p.Ser197Ter,ENST00000520121,;PGRMC2,stop_gained,p.Ser41Ter,ENST00000503588,;PGRMC2,5_prime_UTR_variant,,ENST00000512483,;PGRMC2,5_prime_UTR_variant,,ENST00000394276,;PGRMC2,5_prime_UTR_variant,,ENST00000503872,;PGRMC2,3_prime_UTR_variant,,ENST00000509070,;	C	ENSG00000164040	ENST00000520121	Transcript	stop_gained	1557	590	197	S/*	tCa/tGa	rs765349385	.	.	-1	PGRMC2	HGNC	16089	protein_coding	YES	CCDS3739.2	ENSP00000429301	.	D3DNX8_HUMAN	UPI00001B2483	.	.	.	2/3	.	hmmpanther:PTHR10281,hmmpanther:PTHR10281:SF24,Pfam_domain:PF00173,Gene3D:3.10.120.10,Superfamily_domains:SSF55856	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTGAGAGA	.	5	ESCA
MAML3	0	.	GRCh37	4	140811293	140811293	+	Missense_Mutation	SNP	G	G	A	rs750620797	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1297C>T	p.Arg433Trp	p.R433W	ENST00000509479	2/5	29	24	4	31	31	0	MAML3,missense_variant,p.Arg433Trp,ENST00000509479,;MAML3,missense_variant,p.Arg277Trp,ENST00000327122,;MAML3,intron_variant,,ENST00000502696,;MAML3,upstream_gene_variant,,ENST00000398940,;	A	ENSG00000196782	ENST00000509479	Transcript	missense_variant	2154	1297	433	R/W	Cgg/Tgg	rs750620797	.	.	-1	MAML3	HGNC	16272	protein_coding	YES	CCDS54805.1	ENSP00000421180	MAML3_HUMAN	Q9NPV6_HUMAN,E7EVW8_HUMAN	UPI00001C1E1E	.	.	probably_damaging(0.999)	2/5	.	hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCGAGGTG	byFrequency	4	ESCA
INPP4B	0	.	GRCh37	4	143159120	143159120	+	Missense_Mutation	SNP	C	C	T	rs767317526	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.733G>A	p.Asp245Asn	p.D245N	ENST00000513000	13/27	53	31	22	42	42	0	INPP4B,missense_variant,p.Asp60Asn,ENST00000511838,;INPP4B,missense_variant,p.Asp245Asn,ENST00000508116,;INPP4B,missense_variant,p.Asp245Asn,ENST00000509777,;INPP4B,missense_variant,p.Asp116Asn,ENST00000514525,;INPP4B,missense_variant,p.Asp245Asn,ENST00000262992,;INPP4B,missense_variant,p.Asp245Asn,ENST00000513000,;INPP4B,missense_variant,p.Asp245Asn,ENST00000308502,;INPP4B,missense_variant,p.Asp245Asn,ENST00000510812,;INPP4B,missense_variant,p.Asp245Asn,ENST00000512630,;INPP4B,3_prime_UTR_variant,,ENST00000506297,;	T	ENSG00000109452	ENST00000513000	Transcript	missense_variant	1167	733	245	D/N	Gac/Aac	rs767317526	.	.	-1	INPP4B	HGNC	6075	protein_coding	YES	CCDS3757.1	ENSP00000425487	INP4B_HUMAN	E9PCZ3_HUMAN,D6RJC3_HUMAN,D6RE59_HUMAN,D6R9J5_HUMAN	UPI000013D37A	.	tolerated(0.05)	probably_damaging(1)	13/27	.	hmmpanther:PTHR12187:SF3,hmmpanther:PTHR12187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTCAGATG	.	5	ESCA
LDB2	0	.	GRCh37	4	16900009	16900009	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100G>C	p.Glu34Gln	p.E34Q	ENST00000304523	1/8	51	42	9	55	55	0	LDB2,missense_variant,p.Glu10Gln,ENST00000506732,;LDB2,missense_variant,p.Glu34Gln,ENST00000304523,;LDB2,missense_variant,p.Glu34Gln,ENST00000515064,;LDB2,missense_variant,p.Glu34Gln,ENST00000441778,;LDB2,missense_variant,p.Glu34Gln,ENST00000502640,;LDB2,non_coding_transcript_exon_variant,,ENST00000510825,;LDB2,upstream_gene_variant,,ENST00000504189,;LDB2,missense_variant,p.Glu34Gln,ENST00000508918,;LDB2,missense_variant,p.Glu34Gln,ENST00000512345,;	G	ENSG00000169744	ENST00000304523	Transcript	missense_variant	424	100	34	E/Q	Gag/Cag	COSM420126,COSM1133720	.	.	-1	LDB2	HGNC	6533	protein_coding	YES	CCDS3420.1	ENSP00000306772	LDB2_HUMAN	Q4W5E7_HUMAN,D6RAT1_HUMAN	UPI0000073D86	.	deleterious(0.03)	possibly_damaging(0.817)	1/8	.	Pfam_domain:PF01803,hmmpanther:PTHR10378,hmmpanther:PTHR10378:SF8	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCATAGA	.	5	ESCA
FAM86EP	0	.	GRCh37	4	3949436	3949436	+	RNA	SNP	C	C	A	rs192426253	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.667G>T	.	.	ENST00000313946	3/4	80	57	23	92	92	0	FAM86EP,non_coding_transcript_exon_variant,,ENST00000502255,;FAM86EP,non_coding_transcript_exon_variant,,ENST00000313946,;FAM86EP,non_coding_transcript_exon_variant,,ENST00000506770,;FAM86EP,intron_variant,,ENST00000511488,;AC226119.5,intron_variant,,ENST00000514073,;AC226119.5,intron_variant,,ENST00000281228,;FAM86EP,intron_variant,,ENST00000507301,;FAM86EP,intron_variant,,ENST00000510565,;FAM86EP,downstream_gene_variant,,ENST00000504375,;FAM86EP,downstream_gene_variant,,ENST00000512092,;FAM86EP,intron_variant,,ENST00000510506,;	A	ENSG00000251669	ENST00000313946	Transcript	non_coding_transcript_exon_variant	667	.	.	.	.	rs192426253	.	.	-1	FAM86EP	HGNC	28017	processed_transcript	YES	.	.	.	.	.	.	.	.	3/4	.	.	T:0.0014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACACCGCCTG	byFrequency|by1000G	5	ESCA
ZNF721	0	.	GRCh37	4	438198	438198	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>A	p.Asp20Asn	p.D20N	ENST00000511833	3/3	49	32	16	39	39	0	ZNF721,missense_variant,p.Asp52Asn,ENST00000505900,;ZNF721,missense_variant,p.Asp8Asn,ENST00000338977,;ZNF721,missense_variant,p.Asp20Asn,ENST00000511833,;ZNF721,missense_variant,p.Asp52Asn,ENST00000506646,;ZNF721,intron_variant,,ENST00000507078,;ABCA11P,intron_variant,,ENST00000514396,;ABCA11P,intron_variant,,ENST00000451020,;ABCA11P,intron_variant,,ENST00000507854,;ZNF721,intron_variant,,ENST00000515578,;	T	ENSG00000182903	ENST00000511833	Transcript	missense_variant	252	58	20	D/N	Gac/Aac	.	.	.	-1	ZNF721	HGNC	29425	protein_coding	YES	CCDS46991.1	ENSP00000428878	ZN721_HUMAN	.	UPI0000E9B4A9	.	tolerated(0.05)	possibly_damaging(0.451)	3/3	.	hmmpanther:PTHR24376,hmmpanther:PTHR24376:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGTCTTGGG	.	5	ESCA
PIGG	0	.	GRCh37	4	517563	517563	+	Missense_Mutation	SNP	G	G	C	rs114931121	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1930G>C	p.Glu644Gln	p.E644Q	ENST00000453061	9/13	28	18	10	21	21	0	PIGG,missense_variant,p.Glu636Gln,ENST00000310340,;PIGG,missense_variant,p.Glu511Gln,ENST00000383028,;PIGG,missense_variant,p.Glu555Gln,ENST00000504346,;PIGG,missense_variant,p.Glu644Gln,ENST00000453061,;PIGG,3_prime_UTR_variant,,ENST00000296306,;PIGG,upstream_gene_variant,,ENST00000510235,;PIGG,downstream_gene_variant,,ENST00000536264,;PIGG,downstream_gene_variant,,ENST00000509768,;PIGG,downstream_gene_variant,,ENST00000503111,;PIGG,non_coding_transcript_exon_variant,,ENST00000508562,;PIGG,non_coding_transcript_exon_variant,,ENST00000511247,;PIGG,upstream_gene_variant,,ENST00000503261,;PIGG,downstream_gene_variant,,ENST00000507493,;PIGG,downstream_gene_variant,,ENST00000513679,;PIGG,downstream_gene_variant,,ENST00000506898,;PIGG,upstream_gene_variant,,ENST00000511666,;PIGG,upstream_gene_variant,,ENST00000508669,;PIGG,downstream_gene_variant,,ENST00000504187,;PIGG,downstream_gene_variant,,ENST00000506402,;	C	ENSG00000174227	ENST00000453061	Transcript	missense_variant	2036	1930	644	E/Q	Gaa/Caa	rs114931121	.	.	1	PIGG	HGNC	25985	protein_coding	YES	CCDS46992.1	ENSP00000415203	PIGG_HUMAN	E7EWV1_HUMAN,D6RC16_HUMAN	UPI00004C7A82	.	tolerated(0.3)	benign(0.033)	9/13	.	hmmpanther:PTHR23072:SF0,hmmpanther:PTHR23072	A:0.0044	A:0.0166	A:0	.	A:0	A:0	A:0	A:0.017	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCGAAGTG	byFrequency|byCluster|by1000G	4	ESCA
AFM	0	.	GRCh37	4	74357670	74357670	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.925G>C	p.Glu309Gln	p.E309Q	ENST00000226355	8/15	33	15	17	27	27	0	AFM,missense_variant,p.Glu309Gln,ENST00000226355,;AFM,upstream_gene_variant,,ENST00000505794,;	C	ENSG00000079557	ENST00000226355	Transcript	missense_variant	1018	925	309	E/Q	Gag/Cag	.	.	.	1	AFM	HGNC	316	protein_coding	YES	CCDS3557.1	ENSP00000226355	AFAM_HUMAN	.	UPI000012565D	.	tolerated(0.07)	possibly_damaging(0.658)	8/15	.	PROSITE_profiles:PS51438,hmmpanther:PTHR11385:SF13,hmmpanther:PTHR11385,Pfam_domain:PF00273,Gene3D:1.10.246.10,SMART_domains:SM00103,PIRSF_domain:PIRSF002520,Superfamily_domains:SSF48552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCAGAGCGC	.	5	ESCA
PF4V1	0	.	GRCh37	4	74719096	74719096	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17G>C	p.Arg6Thr	p.R6T	ENST00000226524	1/3	45	40	4	35	35	0	PF4V1,missense_variant,p.Arg6Thr,ENST00000226524,;CXCL6,downstream_gene_variant,,ENST00000503446,;PPBPP1,downstream_gene_variant,,ENST00000510807,;	C	ENSG00000109272	ENST00000226524	Transcript	missense_variant	191	17	6	R/T	aGg/aCg	.	.	.	1	PF4V1	HGNC	8862	protein_coding	YES	CCDS3561.1	ENSP00000226524	PF4V_HUMAN	.	UPI000013171A	.	tolerated_low_confidence(0.18)	unknown(0)	1/3	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10179,hmmpanther:PTHR10179:SF38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCAGGTCCC	.	4	ESCA
MRPL1	0	.	GRCh37	4	78830473	78830473	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724G>C	p.Glu242Gln	p.E242Q	ENST00000315567	7/9	30	26	3	39	39	0	MRPL1,missense_variant,p.Glu196Gln,ENST00000502384,;MRPL1,missense_variant,p.Glu36Gln,ENST00000504901,;MRPL1,missense_variant,p.Glu242Gln,ENST00000315567,;MRPL1,downstream_gene_variant,,ENST00000506674,;	C	ENSG00000169288	ENST00000315567	Transcript	missense_variant	1053	724	242	E/Q	Gaa/Caa	.	.	.	1	MRPL1	HGNC	14275	protein_coding	YES	CCDS3583.2	ENSP00000315017	RM01_HUMAN	.	UPI000020B07E	.	deleterious(0.04)	possibly_damaging(0.863)	7/9	.	hmmpanther:PTHR23105:SF30,hmmpanther:PTHR23105,Superfamily_domains:SSF56808	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACATGAAATT	.	4	ESCA
CCSER1	0	.	GRCh37	4	91701735	91701735	+	Intron	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2011-35178G>C	.	.	ENST00000509176	.	20	10	9	25	25	0	CCSER1,3_prime_UTR_variant,,ENST00000432775,;CCSER1,intron_variant,,ENST00000509176,;CCSER1,intron_variant,,ENST00000503421,;CCSER1,intron_variant,,ENST00000333691,;CCSER1,non_coding_transcript_exon_variant,,ENST00000504150,;CCSER1,intron_variant,,ENST00000505073,;CCSER1,intron_variant,,ENST00000513522,;CCSER1,intron_variant,,ENST00000509109,;CCSER1,downstream_gene_variant,,ENST00000510519,;	C	ENSG00000184305	ENST00000509176	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CCSER1	HGNC	29349	protein_coding	YES	CCDS47099.1	ENSP00000425040	CCSE1_HUMAN	.	UPI00005A6104	.	.	.	.	7/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCTAGTCTGA	.	2	ESCA
TMEM175	0	.	GRCh37	4	941566	941566	+	Silent	SNP	A	A	G	rs770620253	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39A>G	p.%3D	p.T13T	ENST00000264771	2/11	50	36	14	56	56	0	TMEM175,synonymous_variant,p.%3D,ENST00000514546,;TMEM175,synonymous_variant,p.%3D,ENST00000514453,;TMEM175,synonymous_variant,p.%3D,ENST00000264771,;TMEM175,synonymous_variant,p.%3D,ENST00000507319,;TMEM175,intron_variant,,ENST00000510493,;TMEM175,intron_variant,,ENST00000515492,;TMEM175,intron_variant,,ENST00000515740,;TMEM175,intron_variant,,ENST00000509508,;TMEM175,intron_variant,,ENST00000508204,;TMEM175,upstream_gene_variant,,ENST00000504180,;TMEM175,synonymous_variant,p.%3D,ENST00000513682,;TMEM175,synonymous_variant,p.%3D,ENST00000504744,;TMEM175,synonymous_variant,p.%3D,ENST00000513952,;TMEM175,non_coding_transcript_exon_variant,,ENST00000515876,;TMEM175,non_coding_transcript_exon_variant,,ENST00000505734,;TMEM175,non_coding_transcript_exon_variant,,ENST00000504850,;TMEM175,non_coding_transcript_exon_variant,,ENST00000438836,;TMEM175,non_coding_transcript_exon_variant,,ENST00000452360,;TMEM175,non_coding_transcript_exon_variant,,ENST00000504505,;TMEM175,upstream_gene_variant,,ENST00000506669,;TMEM175,upstream_gene_variant,,ENST00000502513,;	G	ENSG00000127419	ENST00000264771	Transcript	synonymous_variant	224	39	13	T	acA/acG	rs770620253	.	.	1	TMEM175	HGNC	28709	protein_coding	YES	CCDS3341.1	ENSP00000264771	TM175_HUMAN	E7ETE6_HUMAN,D6RIZ2_HUMAN,D6RBE5_HUMAN,D3DVN5_HUMAN	UPI000006D921	.	.	.	2/11	.	hmmpanther:PTHR31462:SF2,hmmpanther:PTHR31462	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATACACCGGG	byFrequency	5	ESCA
LRRTM2	0	.	GRCh37	5	138208713	138208713	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1537G>C	p.Glu513Gln	p.E513Q	ENST00000274711	2/2	65	40	24	81	81	0	LRRTM2,missense_variant,p.Glu513Gln,ENST00000274711,;LRRTM2,missense_variant,p.Glu74Gln,ENST00000521094,;LRRTM2,3_prime_UTR_variant,,ENST00000518785,;CTNNA1,intron_variant,,ENST00000302763,;CTNNA1,intron_variant,,ENST00000355078,;CTNNA1,intron_variant,,ENST00000518825,;CTNNA1,upstream_gene_variant,,ENST00000521640,;CTNNA1,upstream_gene_variant,,ENST00000517656,;CTNNA1,upstream_gene_variant,,ENST00000522013,;CTNNA1,upstream_gene_variant,,ENST00000520865,;CTNNA1,upstream_gene_variant,,ENST00000520260,;CTNNA1,upstream_gene_variant,,ENST00000518381,;CTNNA1,upstream_gene_variant,,ENST00000523298,;CTNNA1,upstream_gene_variant,,ENST00000523685,;CTNNA1,upstream_gene_variant,,ENST00000519634,;CTNNA1,upstream_gene_variant,,ENST00000540387,;CTNNA1,upstream_gene_variant,,ENST00000519768,;CTNNA1,upstream_gene_variant,,ENST00000519116,;CTNNA1,upstream_gene_variant,,ENST00000521683,;CTNNA1,upstream_gene_variant,,ENST00000517533,;CTNNA1,intron_variant,,ENST00000520400,;LRRTM2,downstream_gene_variant,,ENST00000523537,;CTNNA1,upstream_gene_variant,,ENST00000518263,;CTNNA1,upstream_gene_variant,,ENST00000522052,;CTNNA1,upstream_gene_variant,,ENST00000524292,;CTNNA1,intron_variant,,ENST00000521724,;CTNNA1,intron_variant,,ENST00000517534,;CTNNA1,intron_variant,,ENST00000523275,;	G	ENSG00000146006	ENST00000274711	Transcript	missense_variant	1916	1537	513	E/Q	Gaa/Caa	COSM3850480	.	.	-1	LRRTM2	HGNC	19409	protein_coding	YES	CCDS47272.1	ENSP00000274711	LRRT2_HUMAN	.	UPI0000070039	.	deleterious(0)	probably_damaging(0.999)	2/2	.	hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF20	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTCTTTGT	.	5	ESCA
PCDHA7	0	.	GRCh37	5	140215524	140215524	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1556C>T	p.Ala519Val	p.A519V	ENST00000525929	1/4	86	39	47	133	133	0	PCDHA7,missense_variant,p.Ala519Val,ENST00000378125,;PCDHA7,missense_variant,p.Ala519Val,ENST00000525929,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;	T	ENSG00000204963	ENST00000525929	Transcript	missense_variant	1556	1556	519	A/V	gCg/gTg	.	.	.	1	PCDHA7	HGNC	8673	protein_coding	YES	CCDS54918.1	ENSP00000436426	PCDA7_HUMAN	.	UPI00001273CF	.	deleterious_low_confidence(0.03)	possibly_damaging(0.645)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF67,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACGCGCTGC	.	5	ESCA
PCDHB17	0	.	GRCh37	5	140536041	140536041	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.465G>A	p.%3D	p.L155L	ENST00000539533	1/1	23	13	10	27	27	0	PCDHB17,synonymous_variant,p.%3D,ENST00000539533,;PCDHB6,downstream_gene_variant,,ENST00000543635,;PCDHB6,downstream_gene_variant,,ENST00000231136,;	A	ENSG00000255622	ENST00000539533	Transcript	synonymous_variant	465	465	155	L	ttG/ttA	.	.	.	1	PCDHB17	Uniprot_gn	.	protein_coding	YES	.	ENSP00000438685	.	Q96T98_HUMAN	UPI000006CE19	.	.	.	1/1	.	Superfamily_domains:SSF49313,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTGAAAAT	.	5	ESCA
C5orf54	0	.	GRCh37	5	159822044	159822044	+	Missense_Mutation	SNP	C	C	T	rs751193933	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454G>A	p.Glu152Lys	p.E152K	ENST00000408953	2/2	30	19	11	43	43	0	C5orf54,missense_variant,p.Glu152Lys,ENST00000408953,;C5orf54,missense_variant,p.Glu152Lys,ENST00000523213,;	T	ENSG00000221886	ENST00000408953	Transcript	missense_variant	962	454	152	E/K	Gaa/Aaa	rs751193933	.	.	-1	C5orf54	HGNC	30804	protein_coding	YES	CCDS34283.1	ENSP00000386184	ZBED8_HUMAN	.	UPI00000741A3	.	tolerated(0.1)	benign(0.061)	2/2	.	hmmpanther:PTHR11697:SF102,hmmpanther:PTHR11697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTCATCAA	.	5	ESCA
GABRA6	0	.	GRCh37	5	161117302	161117302	+	Missense_Mutation	SNP	C	C	A	rs767983249	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.769C>A	p.Leu257Ile	p.L257I	ENST00000274545	7/9	40	15	25	40	40	0	GABRA6,missense_variant,p.Leu247Ile,ENST00000523217,;GABRA6,missense_variant,p.Leu197Ile,ENST00000520000,;GABRA6,missense_variant,p.Leu257Ile,ENST00000274545,;GABRA6,missense_variant,p.Leu177Ile,ENST00000523691,;GABRA6,downstream_gene_variant,,ENST00000517823,;RP11-348M17.2,upstream_gene_variant,,ENST00000521984,;GABRA6,downstream_gene_variant,,ENST00000522269,;GABRA6,downstream_gene_variant,,ENST00000518888,;GABRA6,non_coding_transcript_exon_variant,,ENST00000521520,;GABRA6,downstream_gene_variant,,ENST00000524220,;	A	ENSG00000145863	ENST00000274545	Transcript	missense_variant	1202	769	257	L/I	Ctt/Att	rs767983249	.	.	1	GABRA6	HGNC	4080	protein_coding	YES	CCDS4356.1	ENSP00000274545	GBRA6_HUMAN	Q71UU0_HUMAN	UPI000013DA14	.	deleterious(0.02)	probably_damaging(0.997)	7/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF335,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Gene3D:1.20.58.390,Superfamily_domains:SSF90112,Prints_domain:PR00253	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTCTTTCC	.	5	ESCA
TRIM52	0	.	GRCh37	5	180687602	180687602	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.213G>A	p.%3D	p.A71A	ENST00000327767	1/2	17	9	8	21	21	0	TRIM52,synonymous_variant,p.%3D,ENST00000327767,;AC008443.1,downstream_gene_variant,,ENST00000599439,;CTC-338M12.4,intron_variant,,ENST00000511331,;CTC-338M12.4,downstream_gene_variant,,ENST00000506340,;TRIM52-AS1,upstream_gene_variant,,ENST00000433265,;TRIM52-AS1,upstream_gene_variant,,ENST00000507434,;CTC-338M12.4,downstream_gene_variant,,ENST00000505151,;TRIM52-AS1,upstream_gene_variant,,ENST00000514146,;TRIM52-AS1,upstream_gene_variant,,ENST00000509252,;CTC-338M12.4,downstream_gene_variant,,ENST00000417281,;TRIM52,non_coding_transcript_exon_variant,,ENST00000514805,;TRIM52,upstream_gene_variant,,ENST00000510796,;TRIM52,upstream_gene_variant,,ENST00000503005,;TRIM52,upstream_gene_variant,,ENST00000513146,;	T	ENSG00000183718	ENST00000327767	Transcript	synonymous_variant	518	213	71	A	gcG/gcA	.	.	.	-1	TRIM52	HGNC	19024	protein_coding	YES	CCDS4467.1	ENSP00000332152	TRI52_HUMAN	L0CQ38_HUMAN	UPI0000072D52	.	.	.	1/2	.	hmmpanther:PTHR24103:SF286,hmmpanther:PTHR24103,SMART_domains:SM00184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACCGCTTC	.	4	ESCA
MROH2B	0	.	GRCh37	5	41009477	41009477	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3325G>C	p.Glu1109Gln	p.E1109Q	ENST00000399564	32/42	63	54	9	22	22	0	MROH2B,missense_variant,p.Glu664Gln,ENST00000506092,;MROH2B,missense_variant,p.Glu1109Gln,ENST00000399564,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,;	G	ENSG00000171495	ENST00000399564	Transcript	missense_variant	3776	3325	1109	E/Q	Gaa/Caa	COSM1311154,COSM3828078	.	.	-1	MROH2B	HGNC	26857	protein_coding	YES	CCDS47202.1	ENSP00000382476	MRO2B_HUMAN	F5GZ06_HUMAN	UPI000020CA04	.	tolerated(0.34)	benign(0.018)	32/42	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF15,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTTCAGCCA	.	4	ESCA
PLCXD3	0	.	GRCh37	5	41510617	41510617	+	Silent	SNP	A	A	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12T>A	p.%3D	p.S4S	ENST00000377801	1/3	40	30	10	15	15	0	PLCXD3,synonymous_variant,p.%3D,ENST00000328457,;PLCXD3,synonymous_variant,p.%3D,ENST00000377801,;	T	ENSG00000182836	ENST00000377801	Transcript	synonymous_variant	87	12	4	S	tcT/tcA	.	.	.	-1	PLCXD3	HGNC	31822	protein_coding	YES	CCDS34150.1	ENSP00000367032	PLCX3_HUMAN	B3KXD1_HUMAN	UPI0000049DBB	.	.	.	1/3	.	hmmpanther:PTHR13593,hmmpanther:PTHR13593:SF33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTGAGACGA	.	5	ESCA
C5orf34	0	.	GRCh37	5	43492341	43492341	+	Missense_Mutation	SNP	A	A	G	rs145050535	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1556T>C	p.Ile519Thr	p.I519T	ENST00000306862	10/13	48	36	12	38	38	0	C5orf34,missense_variant,p.Ile519Thr,ENST00000306862,;RP11-159F24.3,intron_variant,,ENST00000505645,;C5orf34,non_coding_transcript_exon_variant,,ENST00000506213,;RP11-159F24.3,downstream_gene_variant,,ENST00000504469,;C5orf34,downstream_gene_variant,,ENST00000503655,;EEF1A1P19,downstream_gene_variant,,ENST00000513637,;	G	ENSG00000172244	ENST00000306862	Transcript	missense_variant	1932	1556	519	I/T	aTt/aCt	rs145050535,COSM1068431	.	.	-1	C5orf34	HGNC	24738	protein_coding	YES	CCDS3946.1	ENSP00000303490	CE034_HUMAN	E9PBC3_HUMAN,B4E0D7_HUMAN	UPI000013EB9E	.	tolerated(0.12)	benign(0.009)	10/13	.	Pfam_domain:PF15016	.	.	.	.	.	.	.	G:0	G:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCAATCTGA	byCluster	5	ESCA
LINC01020	0	.	GRCh37	5	5059708	5059708	+	RNA	SNP	A	A	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.656A>C	.	.	ENST00000508201	5/8	50	35	15	42	42	0	LINC01020,non_coding_transcript_exon_variant,,ENST00000508201,;LINC01020,non_coding_transcript_exon_variant,,ENST00000514474,;LINC01020,non_coding_transcript_exon_variant,,ENST00000509382,;LINC01020,downstream_gene_variant,,ENST00000507599,;	C	ENSG00000215231	ENST00000508201	Transcript	non_coding_transcript_exon_variant	656	.	.	.	.	.	.	.	1	LINC01020	HGNC	27968	lincRNA	YES	.	.	.	.	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCATCTTC	.	5	ESCA
GLRX	0	.	GRCh37	5	95150089	95150089	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*579C>G	.	.	ENST00000379979	3/3	23	16	7	37	37	0	GLRX,3_prime_UTR_variant,,ENST00000237858,;GLRX,3_prime_UTR_variant,,ENST00000379979,;RHOBTB3,intron_variant,,ENST00000513091,;GLRX,intron_variant,,ENST00000508780,;GLRX,downstream_gene_variant,,ENST00000512469,;GLRX,downstream_gene_variant,,ENST00000505427,;GLRX,intron_variant,,ENST00000507605,;GLRX,non_coding_transcript_exon_variant,,ENST00000507412,;	C	ENSG00000173221	ENST00000379979	Transcript	3_prime_UTR_variant	952	.	.	.	.	.	.	.	-1	GLRX	HGNC	4330	protein_coding	YES	CCDS4078.1	ENSP00000369314	GLRX1_HUMAN	.	UPI0000111F53	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTATGAGATC	.	3	ESCA
VNN3	0	.	GRCh37	6	133045810	133045810	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*222G>A	.	.	ENST00000427187	4/6	47	32	15	64	64	0	VNN3,missense_variant,p.Asp379Asn,ENST00000207771,;VNN3,3_prime_UTR_variant,,ENST00000414302,;VNN3,3_prime_UTR_variant,,ENST00000275223,;VNN3,3_prime_UTR_variant,,ENST00000427187,;VNN3,3_prime_UTR_variant,,ENST00000509351,;VNN3,3_prime_UTR_variant,,ENST00000367927,;VNN3,3_prime_UTR_variant,,ENST00000392393,;VNN3,3_prime_UTR_variant,,ENST00000519686,;VNN3,3_prime_UTR_variant,,ENST00000423615,;VNN3,3_prime_UTR_variant,,ENST00000425515,;VNN3,3_prime_UTR_variant,,ENST00000417437,;VNN3,downstream_gene_variant,,ENST00000450865,;VNN3,downstream_gene_variant,,ENST00000544102,;VNN3,downstream_gene_variant,,ENST00000580813,;	T	ENSG00000093134	ENST00000427187	Transcript	3_prime_UTR_variant	846	.	.	.	.	.	.	.	-1	VNN3	HGNC	16431	protein_coding	YES	.	ENSP00000444491	VNN3_HUMAN	A0AUL5_HUMAN	UPI0001737A7C	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCGTCTGTTC	.	5	ESCA
SYNJ2	0	.	GRCh37	6	158492679	158492679	+	Silent	SNP	G	G	A	rs374135325	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1986G>A	p.%3D	p.A662A	ENST00000355585	15/27	18	9	9	8	8	0	SYNJ2,synonymous_variant,p.%3D,ENST00000367121,;SYNJ2,synonymous_variant,p.%3D,ENST00000355585,;SYNJ2,synonymous_variant,p.%3D,ENST00000367122,;SYNJ2,downstream_gene_variant,,ENST00000449859,;	A	ENSG00000078269	ENST00000355585	Transcript	synonymous_variant	2061	1986	662	A	gcG/gcA	rs374135325	.	.	1	SYNJ2	HGNC	11504	protein_coding	YES	CCDS5254.1	ENSP00000347792	SYNJ2_HUMAN	B4DLC4_HUMAN	UPI000006E2F8	.	.	.	15/27	.	hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF98,Pfam_domain:PF03372,Gene3D:3.60.10.10,SMART_domains:SM00128,Superfamily_domains:SSF56219	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0002	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGGCGGGGAA	byCluster|by1000G	3	ESCA
LPAL2	0	.	GRCh37	6	160908400	160908400	+	RNA	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.614G>A	.	.	ENST00000454031	5/17	52	36	16	56	56	0	LPAL2,non_coding_transcript_exon_variant,,ENST00000435757,;LPAL2,non_coding_transcript_exon_variant,,ENST00000335388,;LPAL2,non_coding_transcript_exon_variant,,ENST00000454031,;	T	ENSG00000213071	ENST00000454031	Transcript	non_coding_transcript_exon_variant	614	.	.	.	.	.	.	.	-1	LPAL2	HGNC	21210	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	5/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGATCCGTTG	.	5	ESCA
WDR27	0	.	GRCh37	6	169857518	169857518	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*169C>T	.	.	ENST00000448612	26/26	11	6	5	9	9	0	WDR27,3_prime_UTR_variant,,ENST00000448612,;WDR27,3_prime_UTR_variant,,ENST00000333572,;WDR27,3_prime_UTR_variant,,ENST00000423258,;WDR27,non_coding_transcript_exon_variant,,ENST00000479310,;	A	ENSG00000184465	ENST00000448612	Transcript	3_prime_UTR_variant	2967	.	.	.	.	.	.	.	-1	WDR27	HGNC	21248	protein_coding	YES	CCDS47520.2	ENSP00000416289	WDR27_HUMAN	F8VUY7_HUMAN	UPI00015E06AF	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATGGCACAC	.	2	ESCA
OR5V1	0	.	GRCh37	6	29323469	29323469	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.504C>T	p.%3D	p.F168F	ENST00000377154	4/4	35	8	27	15	15	0	OR5V1,synonymous_variant,p.%3D,ENST00000543825,;OR5V1,synonymous_variant,p.%3D,ENST00000377154,;	A	ENSG00000243729	ENST00000377154	Transcript	synonymous_variant	804	504	168	F	ttC/ttT	.	.	.	-1	OR5V1	HGNC	13972	protein_coding	YES	CCDS4657.1	ENSP00000366359	OR5V1_HUMAN	.	UPI000004186B	.	.	.	4/4	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF0,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAGAAGGG	.	5	ESCA
ZFP57	0	.	GRCh37	6	29640996	29640996	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.892C>T	p.Pro298Ser	p.P298S	ENST00000488757	4/4	119	89	29	106	106	0	ZFP57,missense_variant,p.Pro278Ser,ENST00000376883,;ZFP57,missense_variant,p.Pro298Ser,ENST00000488757,;ZFP57,missense_variant,p.Pro278Ser,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000533330,;MOG,downstream_gene_variant,,ENST00000490427,;MOG,downstream_gene_variant,,ENST00000396704,;MOG,downstream_gene_variant,,ENST00000483013,;MOG,downstream_gene_variant,,ENST00000376891,;MOG,downstream_gene_variant,,ENST00000376898,;MOG,downstream_gene_variant,,ENST00000494692,;MOG,downstream_gene_variant,,ENST00000376917,;MOG,downstream_gene_variant,,ENST00000376888,;MOG,downstream_gene_variant,,ENST00000376902,;MOG,downstream_gene_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000431798,;MOG,downstream_gene_variant,,ENST00000376894,;MOG,downstream_gene_variant,,ENST00000396701,;MOG,downstream_gene_variant,,ENST00000376889,;MOG,downstream_gene_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000485885,;	A	ENSG00000204644	ENST00000488757	Transcript	missense_variant	1043	892	298	P/S	Cca/Tca	COSM3624096	.	.	-1	ZFP57	HGNC	18791	protein_coding	YES	CCDS43436.2	ENSP00000418259	ZFP57_HUMAN	.	UPI0001951170	.	tolerated(0.17)	possibly_damaging(0.547)	4/4	.	hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF179	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGGAATCC	.	5	ESCA
PKHD1	0	.	GRCh37	6	51483924	51483924	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12180C>T	p.%3D	p.F4060F	ENST00000371117	67/67	34	24	10	31	31	0	PKHD1,synonymous_variant,p.%3D,ENST00000371117,;RP3-335N17.2,intron_variant,,ENST00000589278,;RP3-335N17.2,intron_variant,,ENST00000454361,;RP3-335N17.2,upstream_gene_variant,,ENST00000587000,;	A	ENSG00000170927	ENST00000371117	Transcript	synonymous_variant	12456	12180	4060	F	ttC/ttT	.	.	.	-1	PKHD1	HGNC	9016	protein_coding	YES	CCDS4935.1	ENSP00000360158	PKHD1_HUMAN	.	UPI000013C4C0	.	.	.	67/67	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGAATGC	.	5	ESCA
OOEP	0	.	GRCh37	6	74079456	74079456	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.60C>T	p.%3D	p.S20S	ENST00000370359	1/3	36	33	3	33	33	0	OOEP,synonymous_variant,p.%3D,ENST00000370359,;OOEP,intron_variant,,ENST00000441145,;OOEP,intron_variant,,ENST00000370363,;OOEP-AS1,non_coding_transcript_exon_variant,,ENST00000445350,;RPL39P3,downstream_gene_variant,,ENST00000424573,;	A	ENSG00000203907	ENST00000370359	Transcript	synonymous_variant	60	60	20	S	tcC/tcT	.	.	.	-1	OOEP	HGNC	21382	protein_coding	YES	CCDS47451.1	ENSP00000359384	OOEP_HUMAN	.	UPI00001D8132	.	.	.	1/3	.	hmmpanther:PTHR19447:SF14,hmmpanther:PTHR19447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAGGGAGTG	.	4	ESCA
PHIP	0	.	GRCh37	6	79668285	79668285	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3689A>G	p.Tyr1230Cys	p.Y1230C	ENST00000275034	32/40	69	48	20	66	66	0	PHIP,missense_variant,p.Tyr1230Cys,ENST00000275034,;AL356776.1,downstream_gene_variant,,ENST00000516160,;PHIP,non_coding_transcript_exon_variant,,ENST00000479165,;	C	ENSG00000146247	ENST00000275034	Transcript	missense_variant	3857	3689	1230	Y/C	tAt/tGt	.	.	.	-1	PHIP	HGNC	15673	protein_coding	YES	CCDS4987.1	ENSP00000275034	PHIP_HUMAN	.	UPI000013DA40	.	deleterious(0.03)	probably_damaging(0.999)	32/40	.	PROSITE_profiles:PS50014,hmmpanther:PTHR16266:SF4,hmmpanther:PTHR16266,Pfam_domain:PF00439,Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATATATCGA	.	5	ESCA
KIAA1009	0	.	GRCh37	6	84925088	84925088	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415G>C	p.Glu139Gln	p.E139Q	ENST00000403245	5/27	43	32	11	35	35	0	KIAA1009,missense_variant,p.Glu139Gln,ENST00000403245,;KIAA1009,missense_variant,p.Glu63Gln,ENST00000257766,;KIAA1009,non_coding_transcript_exon_variant,,ENST00000497936,;KIAA1009,downstream_gene_variant,,ENST00000435955,;	G	ENSG00000135315	ENST00000403245	Transcript	missense_variant	530	415	139	E/Q	Gag/Cag	.	.	.	-1	KIAA1009	HGNC	21107	protein_coding	YES	CCDS34494.2	ENSP00000385215	CE162_HUMAN	B3KN48_HUMAN	UPI0001533DAA	.	deleterious(0.03)	possibly_damaging(0.621)	5/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTCTCAAGCC	.	4	ESCA
FBXL4	0	.	GRCh37	6	99347302	99347302	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1159T>A	p.Phe387Ile	p.F387I	ENST00000369244	7/10	23	17	5	21	21	0	FBXL4,missense_variant,p.Phe387Ile,ENST00000229971,;FBXL4,missense_variant,p.Phe387Ile,ENST00000369244,;	T	ENSG00000112234	ENST00000369244	Transcript	missense_variant	1588	1159	387	F/I	Ttt/Att	.	.	.	-1	FBXL4	HGNC	13601	protein_coding	YES	CCDS5041.1	ENSP00000358247	FBXL4_HUMAN	.	UPI000012ADE3	.	tolerated(0.07)	possibly_damaging(0.724)	7/10	.	Superfamily_domains:SSF52047,Gene3D:3.80.10.10,hmmpanther:PTHR23125:SF244,hmmpanther:PTHR23125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAAGTGGC	.	5	ESCA
PTN	0	.	GRCh37	7	136912218	136912218	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*549T>C	.	.	ENST00000348225	5/5	22	15	7	22	22	0	PTN,3_prime_UTR_variant,,ENST00000393083,;PTN,3_prime_UTR_variant,,ENST00000348225,;	G	ENSG00000105894	ENST00000348225	Transcript	3_prime_UTR_variant	1484	.	.	.	.	.	.	.	-1	PTN	HGNC	9630	protein_coding	YES	CCDS5844.1	ENSP00000341170	PTN_HUMAN	.	UPI000013297B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	TTAAAAAAAAA	.	2	ESCA
TRPV6	0	.	GRCh37	7	142574200	142574200	+	Silent	SNP	G	G	A	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723C>T	p.%3D	p.L241L	ENST00000359396	6/15	104	76	28	93	93	0	TRPV6,synonymous_variant,p.%3D,ENST00000359396,;TRPV6,intron_variant,,ENST00000436401,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,intron_variant,,ENST00000438839,;TRPV6,non_coding_transcript_exon_variant,,ENST00000463646,;TRPV6,non_coding_transcript_exon_variant,,ENST00000487077,;TRPV6,non_coding_transcript_exon_variant,,ENST00000474388,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,upstream_gene_variant,,ENST00000485138,;	A	ENSG00000165125	ENST00000359396	Transcript	synonymous_variant	969	723	241	L	ctC/ctT	COSM3922912	.	.	-1	TRPV6	HGNC	14006	protein_coding	YES	CCDS5874.1	ENSP00000352358	TRPV6_HUMAN	Q9NXZ3_HUMAN,Q8NBV5_HUMAN,C9J9W0_HUMAN	UPI000000D91B	.	.	.	6/15	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF21,PROSITE_profiles:PS50297	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGTGAGACC	.	5	ESCA
CTAGE6	0	.	GRCh37	7	143453971	143453971	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.781G>A	p.Asp261Asn	p.D261N	ENST00000470691	1/1	207	184	23	193	193	0	CTAGE6,missense_variant,p.Asp261Asn,ENST00000470691,;RNU6-267P,upstream_gene_variant,,ENST00000516714,;RP11-61L23.2,downstream_gene_variant,,ENST00000491047,;RP11-61L23.2,intron_variant,,ENST00000450076,;FAM115D,intron_variant,,ENST00000456362,;RP11-61L23.2,intron_variant,,ENST00000422705,;RP11-61L23.2,intron_variant,,ENST00000427403,;	T	ENSG00000271321	ENST00000470691	Transcript	missense_variant	819	781	261	D/N	Gat/Aat	.	.	.	-1	CTAGE6	HGNC	28644	protein_coding	YES	CCDS64790.1	ENSP00000474388	CTGE6_HUMAN	.	UPI0000199826	.	tolerated(0.81)	benign(0.03)	1/1	.	hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTTATCATTCA	.	3	ESCA
DPP6	0	.	GRCh37	7	154684078	154684078	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2486C>G	p.Ser829Cys	p.S829C	ENST00000377770	26/26	84	69	15	56	56	0	DPP6,missense_variant,p.Ser722Cys,ENST00000427557,;DPP6,missense_variant,p.Ser829Cys,ENST00000377770,;DPP6,missense_variant,p.Ser767Cys,ENST00000332007,;DPP6,missense_variant,p.Ser765Cys,ENST00000404039,;DPP6,downstream_gene_variant,,ENST00000480367,;	G	ENSG00000130226	ENST00000377770	Transcript	missense_variant	2627	2486	829	S/C	tCc/tGc	.	.	.	1	DPP6	HGNC	3010	protein_coding	YES	.	ENSP00000367001	DPP6_HUMAN	Q75MI8_HUMAN,Q75MI7_HUMAN,Q75MF0_HUMAN	UPI00001AE746	.	deleterious(0.02)	benign(0.335)	26/26	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00326,hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCCAGCC	.	5	ESCA
AC011294.3	0	.	GRCh37	7	46729005	46729005	+	Missense_Mutation	SNP	C	C	T	rs545168572	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311G>A	p.Arg104His	p.R104H	ENST00000451905	3/3	55	35	20	54	54	0	AC011294.3,missense_variant,p.Arg104His,ENST00000451905,;AC011294.3,non_coding_transcript_exon_variant,,ENST00000469937,;AC011294.3,intron_variant,,ENST00000487094,;	T	ENSG00000233539	ENST00000451905	Transcript	missense_variant	419	311	104	R/H	cGc/cAc	rs545168572	.	.	-1	AC011294.3	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000398500	.	C9J2X1_HUMAN	UPI00002522A1	.	.	benign(0.041)	3/3	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTGCGTGGC	by1000G	5	ESCA
PKD1L1	0	.	GRCh37	7	47933653	47933653	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2275C>G	p.Gln759Glu	p.Q759E	ENST00000289672	15/57	11	6	5	15	15	0	PKD1L1,missense_variant,p.Gln759Glu,ENST00000289672,;HUS1,intron_variant,,ENST00000436444,;	C	ENSG00000158683	ENST00000289672	Transcript	missense_variant	2326	2275	759	Q/E	Cag/Gag	.	.	.	-1	PKD1L1	HGNC	18053	protein_coding	YES	CCDS34633.1	ENSP00000289672	PK1L1_HUMAN	.	UPI0000130FA9	.	deleterious(0.01)	probably_damaging(0.977)	15/57	.	Pfam_domain:PF02010,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF32,PROSITE_profiles:PS51111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AATCTGAACCT	.	3	ESCA
CCDC146	0	.	GRCh37	7	76903894	76903894	+	Silent	SNP	A	A	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1365A>T	p.%3D	p.V455V	ENST00000285871	11/19	29	15	13	21	21	0	CCDC146,synonymous_variant,p.%3D,ENST00000285871,;CCDC146,synonymous_variant,p.%3D,ENST00000431197,;CCDC146,non_coding_transcript_exon_variant,,ENST00000415740,;	T	ENSG00000135205	ENST00000285871	Transcript	synonymous_variant	1492	1365	455	V	gtA/gtT	.	.	.	1	CCDC146	HGNC	29296	protein_coding	YES	CCDS34671.1	ENSP00000285871	CC146_HUMAN	Q7Z4Q3_HUMAN	UPI000020F44F	.	.	.	11/19	.	hmmpanther:PTHR32083:SF23,hmmpanther:PTHR32083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAGTAGTCAA	.	5	ESCA
AKAP9	0	.	GRCh37	7	91670145	91670145	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4850A>T	p.Glu1617Val	p.E1617V	ENST00000356239	18/50	31	24	6	44	44	0	AKAP9,missense_variant,p.Glu1617Val,ENST00000356239,;AKAP9,missense_variant,p.Glu1629Val,ENST00000359028,;AKAP9,missense_variant,p.Glu1629Val,ENST00000358100,;AKAP9,non_coding_transcript_exon_variant,,ENST00000484815,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,;	T	ENSG00000127914	ENST00000356239	Transcript	missense_variant	5083	4850	1617	E/V	gAg/gTg	.	.	.	1	AKAP9	HGNC	379	protein_coding	YES	CCDS5622.1	ENSP00000348573	AKAP9_HUMAN	Q8IW64_HUMAN	UPI000002A38D	.	.	probably_damaging(0.999)	18/50	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18932:SF10,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGAGAGAC	.	5	ESCA
RIMS2	0	.	GRCh37	8	104898029	104898029	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1202G>C	p.Arg401Thr	p.R401T	ENST00000406091	4/24	25	17	8	42	42	0	RIMS2,missense_variant,p.Arg401Thr,ENST00000406091,;RIMS2,missense_variant,p.Arg209Thr,ENST00000408894,;RIMS2,missense_variant,p.Arg401Thr,ENST00000504942,;RIMS2,missense_variant,p.Arg209Thr,ENST00000507740,;RIMS2,missense_variant,p.Arg209Thr,ENST00000262231,;RIMS2,missense_variant,p.Arg209Thr,ENST00000515551,;RIMS2,missense_variant,p.Arg179Thr,ENST00000436393,;RIMS2,non_coding_transcript_exon_variant,,ENST00000522174,;	C	ENSG00000176406	ENST00000406091	Transcript	missense_variant	1202	1202	401	R/T	aGa/aCa	.	.	.	1	RIMS2	HGNC	17283	protein_coding	YES	CCDS55269.1	ENSP00000384892	RIMS2_HUMAN	E9PFB6_HUMAN	UPI0001597063	.	tolerated_low_confidence(0.06)	benign(0.009)	4/24	.	hmmpanther:PTHR12157:SF15,hmmpanther:PTHR12157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGTAGAGCTG	.	2	ESCA
PKHD1L1	0	.	GRCh37	8	110410724	110410724	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.959G>C	p.Ser320Thr	p.S320T	ENST00000378402	12/78	59	44	14	49	49	0	PKHD1L1,missense_variant,p.Ser320Thr,ENST00000378402,;	C	ENSG00000205038	ENST00000378402	Transcript	missense_variant	1063	959	320	S/T	aGt/aCt	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	tolerated(0.62)	benign(0.006)	12/78	.	Pfam_domain:PF01833,Gene3D:2.60.40.10,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATAGTATAT	.	5	ESCA
GSDMC	0	.	GRCh37	8	130772830	130772830	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682C>G	p.Leu228Val	p.L228V	ENST00000276708	6/14	85	57	27	90	90	0	GSDMC,missense_variant,p.Leu228Val,ENST00000276708,;	C	ENSG00000147697	ENST00000276708	Transcript	missense_variant	1564	682	228	L/V	Ctc/Gtc	.	.	.	-1	GSDMC	HGNC	7151	protein_coding	YES	CCDS6360.1	ENSP00000276708	GSDMC_HUMAN	.	UPI0000071445	.	tolerated(0.24)	probably_damaging(0.96)	6/14	.	hmmpanther:PTHR16399,hmmpanther:PTHR16399:SF17,Pfam_domain:PF04598	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAGAATGG	.	5	ESCA
KIF13B	0	.	GRCh37	8	28997678	28997678	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2515C>T	p.Arg839Ter	p.R839*	ENST00000524189	21/40	14	8	6	23	23	0	KIF13B,stop_gained,p.Arg839Ter,ENST00000524189,;CTD-2647L4.1,non_coding_transcript_exon_variant,,ENST00000517632,;CTD-2647L4.1,intron_variant,,ENST00000523661,;RN7SL781P,upstream_gene_variant,,ENST00000582428,;	A	ENSG00000197892	ENST00000524189	Transcript	stop_gained	2554	2515	839	R/*	Cga/Tga	.	.	.	-1	KIF13B	HGNC	14405	protein_coding	YES	CCDS55217.1	ENSP00000427900	KI13B_HUMAN	.	UPI000035B257	.	.	.	21/40	.	hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCGCATCA	.	5	ESCA
KCNU1	0	.	GRCh37	8	36788577	36788577	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2845G>A	p.Asp949Asn	p.D949N	ENST00000399881	25/27	54	51	3	70	70	0	KCNU1,missense_variant,p.Asp949Asn,ENST00000399881,;KCNU1,3_prime_UTR_variant,,ENST00000518904,;KCNU1,3_prime_UTR_variant,,ENST00000522372,;	A	ENSG00000215262	ENST00000399881	Transcript	missense_variant	2882	2845	949	D/N	Gat/Aat	.	.	.	1	KCNU1	HGNC	18867	protein_coding	YES	CCDS55220.1	ENSP00000382770	KCNU1_HUMAN	.	UPI0000F079EF	.	tolerated(0.31)	benign(0.004)	25/27	.	hmmpanther:PTHR10027:SF23,hmmpanther:PTHR10027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCAGATAGC	.	2	ESCA
ADAM5	0	.	GRCh37	8	39233345	39233345	+	RNA	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1043C>T	.	.	ENST00000505455	9/16	87	63	23	64	64	0	ADAM5,non_coding_transcript_exon_variant,,ENST00000505455,;ADAM5,non_coding_transcript_exon_variant,,ENST00000433441,;ADAM5,non_coding_transcript_exon_variant,,ENST00000359790,;ADAM5,non_coding_transcript_exon_variant,,ENST00000417441,;ADAM5,non_coding_transcript_exon_variant,,ENST00000512764,;ADAM5,non_coding_transcript_exon_variant,,ENST00000399789,;	T	ENSG00000196115	ENST00000505455	Transcript	non_coding_transcript_exon_variant	1043	.	.	.	.	.	.	.	1	ADAM5	HGNC	212	processed_transcript	YES	.	.	.	.	.	.	.	.	9/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTCAAGGA	.	5	ESCA
PEX2	0	.	GRCh37	8	77895531	77895531	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.884C>G	p.Ser295Ter	p.S295*	ENST00000419564	4/4	37	28	9	49	49	0	PEX2,stop_gained,p.Ser295Ter,ENST00000419564,;PEX2,stop_gained,p.Ser295Ter,ENST00000522527,;PEX2,stop_gained,p.Ser295Ter,ENST00000520103,;PEX2,stop_gained,p.Ser295Ter,ENST00000357039,;PEX2,downstream_gene_variant,,ENST00000519956,;PEX2,downstream_gene_variant,,ENST00000518986,;PEX2,downstream_gene_variant,,ENST00000520203,;	C	ENSG00000164751	ENST00000419564	Transcript	stop_gained	1349	884	295	S/*	tCa/tGa	.	.	.	-1	PEX2	HGNC	9717	protein_coding	YES	CCDS6221.1	ENSP00000400984	PEX2_HUMAN	E5RIW9_HUMAN	UPI000013E3FB	.	.	.	4/4	.	hmmpanther:PTHR12590,hmmpanther:PTHR12590:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTGATTTC	.	5	ESCA
REXO1L1P	0	.	GRCh37	8	86573418	86573418	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*281G>T	.	.	ENST00000379010	1/1	329	311	18	275	275	0	REXO1L1P,3_prime_UTR_variant,,ENST00000379010,;REXO1L3P,upstream_gene_variant,,ENST00000608646,;	A	ENSG00000205176	ENST00000379010	Transcript	3_prime_UTR_variant	2309	.	.	.	.	.	.	.	-1	REXO1L1P	HGNC	24660	protein_coding	YES	.	ENSP00000368295	GOR_HUMAN	.	UPI000057A11F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGAACAGGCG	.	2	ESCA
OTUD6B	0	.	GRCh37	8	92086058	92086058	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.325-1G>C	.	p.X109_splice	ENST00000285420	.	29	17	11	30	30	0	OTUD6B,splice_acceptor_variant,,ENST00000404789,;OTUD6B,splice_acceptor_variant,,ENST00000285420,;GS1-251I9.4,upstream_gene_variant,,ENST00000522817,;GS1-251I9.4,upstream_gene_variant,,ENST00000524003,;OTUD6B,splice_acceptor_variant,,ENST00000524027,;OTUD6B,splice_acceptor_variant,,ENST00000522894,;	C	ENSG00000155100	ENST00000285420	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	OTUD6B	HGNC	24281	protein_coding	YES	CCDS6253.2	ENSP00000285420	OTU6B_HUMAN	.	UPI0000E5AF0F	.	.	.	.	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCAGATAGA	.	5	ESCA
IKBKAP	0	.	GRCh37	9	111659447	111659447	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2482G>C	p.Glu828Gln	p.E828Q	ENST00000374647	23/37	53	39	13	45	45	0	IKBKAP,missense_variant,p.Glu479Gln,ENST00000537196,;IKBKAP,missense_variant,p.Glu828Gln,ENST00000374647,;IKBKAP,upstream_gene_variant,,ENST00000495759,;	G	ENSG00000070061	ENST00000374647	Transcript	missense_variant	2790	2482	828	E/Q	Gag/Cag	.	.	.	-1	IKBKAP	HGNC	5959	protein_coding	YES	CCDS6773.1	ENSP00000363779	ELP1_HUMAN	Q4LE38_HUMAN,F5H2T0_HUMAN,B3KNB2_HUMAN,B3KMT0_HUMAN	UPI000013D2D0	.	tolerated(0.14)	benign(0.364)	23/37	.	hmmpanther:PTHR12747,Pfam_domain:PF04762,PIRSF_domain:PIRSF017233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.I830M|c.2490A>G|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTCCATGA	.	5	ESCA
IKBKAP	0	.	GRCh37	9	111670649	111670649	+	Missense_Mutation	SNP	C	C	G	rs751206488	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1396G>C	p.Gly466Arg	p.G466R	ENST00000374647	13/37	38	12	26	34	34	0	IKBKAP,missense_variant,p.Gly117Arg,ENST00000537196,;IKBKAP,missense_variant,p.Gly466Arg,ENST00000374647,;	G	ENSG00000070061	ENST00000374647	Transcript	missense_variant	1704	1396	466	G/R	Gga/Cga	rs751206488	.	.	-1	IKBKAP	HGNC	5959	protein_coding	YES	CCDS6773.1	ENSP00000363779	ELP1_HUMAN	Q4LE38_HUMAN,F5H2T0_HUMAN,B3KNB2_HUMAN,B3KMT0_HUMAN	UPI000013D2D0	.	deleterious(0.02)	benign(0.445)	13/37	.	hmmpanther:PTHR12747,Pfam_domain:PF04762,PIRSF_domain:PIRSF017233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTCCCAGTT	.	5	ESCA
CNTRL	0	.	GRCh37	9	123888025	123888025	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1836G>C	p.Lys612Asn	p.K612N	ENST00000373855	14/44	33	21	12	32	32	0	CNTRL,missense_variant,p.Lys60Asn,ENST00000373847,;CNTRL,missense_variant,p.Lys612Asn,ENST00000373855,;CNTRL,missense_variant,p.Lys60Asn,ENST00000373850,;CNTRL,missense_variant,p.Lys612Asn,ENST00000238341,;CNTRL,non_coding_transcript_exon_variant,,ENST00000373851,;	C	ENSG00000119397	ENST00000373855	Transcript	missense_variant	2096	1836	612	K/N	aaG/aaC	.	.	.	1	CNTRL	HGNC	1858	protein_coding	YES	CCDS35118.1	ENSP00000362962	CNTRL_HUMAN	Q5JVD3_HUMAN,Q5JVD6_HUMAN,Q5JVD1_HUMAN	UPI0000211718	.	.	benign(0.027)	14/44	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18877,hmmpanther:PTHR18877:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAGGATTT	.	5	ESCA
C9orf24	0	.	GRCh37	9	34381385	34381385	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454G>C	p.Glu152Gln	p.E152Q	ENST00000297623	4/7	14	8	6	32	32	0	C9orf24,missense_variant,p.Glu17Gln,ENST00000379126,;C9orf24,missense_variant,p.Glu17Gln,ENST00000379124,;C9orf24,missense_variant,p.Glu17Gln,ENST00000379133,;C9orf24,missense_variant,p.Glu152Gln,ENST00000297623,;C9orf24,missense_variant,p.Glu17Gln,ENST00000379127,;C9orf24,downstream_gene_variant,,ENST00000444429,;KIAA1161,upstream_gene_variant,,ENST00000297625,;C9orf24,upstream_gene_variant,,ENST00000481295,;	G	ENSG00000164972	ENST00000297623	Transcript	missense_variant	653	454	152	E/Q	Gag/Cag	.	.	.	-1	C9orf24	HGNC	19919	protein_coding	YES	CCDS6554.1	ENSP00000297623	SMRP1_HUMAN	.	UPI000006E5B3	.	tolerated(0.12)	probably_damaging(0.979)	4/7	.	Pfam_domain:PF15181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CCGCTCCGGCC	.	4	ESCA
RCL1	0	.	GRCh37	9	4793197	4793197	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.106C>T	p.Arg36Trp	p.R36W	ENST00000381750	1/9	38	23	14	66	66	0	RCL1,missense_variant,p.Arg36Trp,ENST00000381750,;RCL1,missense_variant,p.Arg36Trp,ENST00000381732,;RCL1,5_prime_UTR_variant,,ENST00000442869,;RCL1,non_coding_transcript_exon_variant,,ENST00000473230,;	T	ENSG00000120158	ENST00000381750	Transcript	missense_variant	329	106	36	R/W	Cgg/Tgg	.	.	.	1	RCL1	HGNC	17687	protein_coding	YES	CCDS6456.1	ENSP00000371169	RCL1_HUMAN	Q5VZU3_HUMAN	UPI000013CA7B	.	deleterious(0)	probably_damaging(0.992)	1/9	.	hmmpanther:PTHR11096:SF1,hmmpanther:PTHR11096,Gene3D:3kgdA01,Pfam_domain:PF01137,TIGRFAM_domain:TIGR03400,PIRSF_domain:PIRSF005378,Superfamily_domains:SSF55205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTCGGGCC	.	5	ESCA
PRKACG	0	.	GRCh37	9	71627781	71627781	+	3'UTR	SNP	C	C	T	rs749486602	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*172G>A	.	.	ENST00000377276	1/1	106	97	8	104	104	0	PRKACG,3_prime_UTR_variant,,ENST00000377276,;PIP5K1B,downstream_gene_variant,,ENST00000265382,;PIP5K1B,downstream_gene_variant,,ENST00000541509,;PIP5K1B,downstream_gene_variant,,ENST00000478500,;	T	ENSG00000165059	ENST00000377276	Transcript	3_prime_UTR_variant	1259	.	.	.	.	rs749486602	.	.	-1	PRKACG	HGNC	9382	protein_coding	YES	CCDS6625.1	ENSP00000366488	KAPCG_HUMAN	.	UPI000013E448	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTTTCTGTTC	.	3	ESCA
PTAR1	0	.	GRCh37	9	72374807	72374807	+	Silent	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.48G>C	p.%3D	p.V16V	ENST00000340434	1/8	85	61	24	79	79	0	PTAR1,synonymous_variant,p.%3D,ENST00000340434,;PTAR1,synonymous_variant,p.%3D,ENST00000472967,;PTAR1,synonymous_variant,p.%3D,ENST00000377200,;PTAR1,non_coding_transcript_exon_variant,,ENST00000474925,;	G	ENSG00000188647	ENST00000340434	Transcript	synonymous_variant	52	48	16	V	gtG/gtC	.	.	.	-1	PTAR1	HGNC	30449	protein_coding	YES	CCDS47978.1	ENSP00000344299	PTAR1_HUMAN	.	UPI00001D75C1	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCACAAC	.	5	ESCA
NUTM2F	0	.	GRCh37	9	97081163	97081163	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1855C>G	p.Pro619Ala	p.P619A	ENST00000253262	7/7	28	21	7	33	33	0	NUTM2F,missense_variant,p.Pro604Ala,ENST00000341207,;NUTM2F,missense_variant,p.Pro619Ala,ENST00000253262,;NUTM2F,intron_variant,,ENST00000335456,;	C	ENSG00000130950	ENST00000253262	Transcript	missense_variant	1876	1855	619	P/A	Cct/Gct	.	.	.	-1	NUTM2F	HGNC	23450	protein_coding	YES	CCDS47994.1	ENSP00000253262	NTM2F_HUMAN	.	UPI00001D771D	.	deleterious(0.02)	probably_damaging(1)	7/7	.	hmmpanther:PTHR22879,hmmpanther:PTHR22879:SF12,Pfam_domain:PF12882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GACAGGAGACT	.	2	ESCA
NOX1	0	.	GRCh37	X	100105308	100105308	+	Missense_Mutation	SNP	C	C	T	rs372154041	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.965G>A	p.Gly322Glu	p.G322E	ENST00000372966	9/13	41	30	11	38	38	0	NOX1,missense_variant,p.Gly7Glu,ENST00000427768,;NOX1,missense_variant,p.Gly285Glu,ENST00000372960,;NOX1,missense_variant,p.Gly322Glu,ENST00000217885,;NOX1,missense_variant,p.Gly322Glu,ENST00000372966,;NOX1,intron_variant,,ENST00000372964,;HNRNPA1P26,downstream_gene_variant,,ENST00000457695,;	T	ENSG00000007952	ENST00000372966	Transcript	missense_variant	1171	965	322	G/E	gGg/gAg	rs372154041	.	.	-1	NOX1	HGNC	7889	protein_coding	YES	CCDS14474.1	ENSP00000362057	NOX1_HUMAN	.	UPI00001303C1	.	deleterious(0)	probably_damaging(1)	9/13	.	PROSITE_profiles:PS51384,hmmpanther:PTHR11972:SF10,hmmpanther:PTHR11972,Pfam_domain:PF08022,Gene3D:2.40.30.10,Superfamily_domains:SSF63380	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGCCCCACT	byFrequency|byCluster	5	ESCA
DCX	0	.	GRCh37	X	110654101	110654101	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.102G>A	p.%3D	p.G34G	ENST00000338081	1/7	67	49	18	56	56	0	DCX,synonymous_variant,p.%3D,ENST00000338081,;DCX,synonymous_variant,p.%3D,ENST00000358070,;DCX,intron_variant,,ENST00000371993,;DCX,intron_variant,,ENST00000468911,;DCX,intron_variant,,ENST00000356220,;DCX,intron_variant,,ENST00000488120,;DCX,intron_variant,,ENST00000356915,;DCX,intron_variant,,ENST00000496551,;	T	ENSG00000077279	ENST00000338081	Transcript	synonymous_variant	274	102	34	G	ggG/ggA	.	.	.	-1	DCX	HGNC	2714	protein_coding	YES	CCDS14556.1	ENSP00000337697	DCX_HUMAN	E7EU50_HUMAN	UPI000013D33F	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTCCCCTTG	.	5	ESCA
GRIA3	0	.	GRCh37	X	122318240	122318240	+	5'UTR	SNP	G	G	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-148G>T	.	.	ENST00000264357	1/16	27	16	10	19	19	0	GRIA3,5_prime_UTR_variant,,ENST00000542149,;GRIA3,5_prime_UTR_variant,,ENST00000264357,;GRIA3,5_prime_UTR_variant,,ENST00000371264,;GRIA3,intron_variant,,ENST00000371266,;GRIA3,upstream_gene_variant,,ENST00000371256,;GRIA3,upstream_gene_variant,,ENST00000371251,;GRIA3,upstream_gene_variant,,ENST00000541091,;GRIA3,upstream_gene_variant,,ENST00000479118,;	T	ENSG00000125675	ENST00000264357	Transcript	5_prime_UTR_variant	145	.	.	.	.	.	.	.	1	GRIA3	HGNC	4573	protein_coding	YES	CCDS14604.1	ENSP00000264357	GRIA3_HUMAN	Q9UHA9_HUMAN	UPI000013D503	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAGGACTAG	.	5	ESCA
GPR112	0	.	GRCh37	X	135432293	135432293	+	Missense_Mutation	SNP	G	G	T	rs150281542	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6428G>T	p.Gly2143Val	p.G2143V	ENST00000394143	6/26	29	23	6	46	46	0	GPR112,missense_variant,p.Gly2080Val,ENST00000287534,;GPR112,missense_variant,p.Gly2143Val,ENST00000370652,;GPR112,missense_variant,p.Gly2143Val,ENST00000394143,;GPR112,missense_variant,p.Gly1938Val,ENST00000394141,;GPR112,missense_variant,p.Gly1938Val,ENST00000412101,;	T	ENSG00000156920	ENST00000394143	Transcript	missense_variant	6719	6428	2143	G/V	gGt/gTt	rs150281542,COSM3558266	.	.	1	GPR112	HGNC	18992	protein_coding	YES	CCDS35409.1	ENSP00000377699	GP112_HUMAN	.	UPI00004CEC5B	.	deleterious(0.03)	possibly_damaging(0.873)	6/26	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF225	T:0.0005	T:0.0008	T:0.0014	.	T:0	T:0	T:0	T:0.0005	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTGGTGCCA	byFrequency|byCluster|by1000G	5	ESCA
FGF13	0	.	GRCh37	X	137717719	137717719	+	Missense_Mutation	SNP	C	C	T	rs768293112	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530G>A	p.Arg177Gln	p.R177Q	ENST00000370603	5/6	88	71	16	57	57	0	FGF13,missense_variant,p.Arg148Gln,ENST00000441825,;FGF13,missense_variant,p.Arg121Gln,ENST00000541469,;FGF13,missense_variant,p.Arg177Gln,ENST00000370603,;FGF13,missense_variant,p.Arg177Gln,ENST00000436198,;FGF13,missense_variant,p.Arg183Gln,ENST00000455663,;FGF13,missense_variant,p.Arg167Gln,ENST00000315930,;FGF13,missense_variant,p.Arg114Gln,ENST00000305414,;	T	ENSG00000129682	ENST00000370603	Transcript	missense_variant	530	530	177	R/Q	cGa/cAa	rs768293112	.	.	-1	FGF13	HGNC	3670	protein_coding	YES	CCDS55513.1	ENSP00000359635	FGF13_HUMAN	Q9Y643_HUMAN,B1B1H9_HUMAN,B1AK17_HUMAN	UPI00001484B4	.	deleterious(0.01)	possibly_damaging(0.79)	5/6	.	hmmpanther:PTHR11486:SF75,hmmpanther:PTHR11486,Gene3D:2.80.10.50,Pfam_domain:PF00167,SMART_domains:SM00442,Superfamily_domains:SSF50353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCGGCCT	.	5	ESCA
MAGEC3	0	.	GRCh37	X	140985178	140985178	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1634A>T	p.Lys545Met	p.K545M	ENST00000298296	7/8	71	50	20	50	50	0	MAGEC3,missense_variant,p.Lys545Met,ENST00000298296,;MAGEC3,missense_variant,p.Lys247Met,ENST00000544766,;MAGEC3,missense_variant,p.Lys247Met,ENST00000409007,;MAGEC3,missense_variant,p.Lys167Met,ENST00000443323,;MAGEC3,missense_variant,p.Lys247Met,ENST00000536088,;MAGEC3,downstream_gene_variant,,ENST00000448920,;MAGEC3,downstream_gene_variant,,ENST00000483584,;	T	ENSG00000165509	ENST00000298296	Transcript	missense_variant	1634	1634	545	K/M	aAg/aTg	COSM1257105,COSM1257106	.	.	1	MAGEC3	HGNC	23798	protein_coding	YES	CCDS14676.1	ENSP00000298296	MAGC3_HUMAN	.	UPI000006E09B	.	deleterious(0.01)	possibly_damaging(0.869)	7/8	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF47,Pfam_domain:PF01454	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCAAGAACT	.	5	ESCA
FLNA	0	.	GRCh37	X	153581174	153581174	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6345C>T	p.%3D	p.I2115I	ENST00000369850	39/48	35	19	15	22	22	0	FLNA,synonymous_variant,p.%3D,ENST00000422373,;FLNA,synonymous_variant,p.%3D,ENST00000360319,;FLNA,synonymous_variant,p.%3D,ENST00000369856,;FLNA,synonymous_variant,p.%3D,ENST00000444578,;FLNA,synonymous_variant,p.%3D,ENST00000344736,;FLNA,synonymous_variant,p.%3D,ENST00000369850,;FLNA,downstream_gene_variant,,ENST00000438732,;FLNA,intron_variant,,ENST00000498411,;FLNA,upstream_gene_variant,,ENST00000498491,;FLNA,downstream_gene_variant,,ENST00000466319,;FLNA,3_prime_UTR_variant,,ENST00000415241,;FLNA,3_prime_UTR_variant,,ENST00000420627,;FLNA,non_coding_transcript_exon_variant,,ENST00000466325,;FLNA,non_coding_transcript_exon_variant,,ENST00000490936,;FLNA,downstream_gene_variant,,ENST00000474072,;FLNA,upstream_gene_variant,,ENST00000462590,;FLNA,upstream_gene_variant,,ENST00000474358,;	A	ENSG00000196924	ENST00000369850	Transcript	synonymous_variant	6582	6345	2115	I	atC/atT	.	.	.	-1	FLNA	HGNC	3754	protein_coding	YES	CCDS48194.1	ENSP00000358866	FLNA_HUMAN	Q96C61_HUMAN,Q86TQ3_HUMAN,Q6NXF2_HUMAN,Q60FE5_HUMAN	UPI000013C596	.	.	.	39/48	.	PROSITE_profiles:PS50194,hmmpanther:PTHR11915:SF173,hmmpanther:PTHR11915,Gene3D:2.60.40.10,Pfam_domain:PF00630,SMART_domains:SM00557,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGATGATGTA	.	5	ESCA
PLXNA3	0	.	GRCh37	X	153698330	153698330	+	Silent	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4806C>T	p.%3D	p.L1602L	ENST00000369682	29/33	18	9	9	17	17	0	PLXNA3,synonymous_variant,p.%3D,ENST00000369682,;PLXNA3,non_coding_transcript_exon_variant,,ENST00000493546,;PLXNA3,downstream_gene_variant,,ENST00000480645,;PLXNA3,downstream_gene_variant,,ENST00000467463,;PLXNA3,upstream_gene_variant,,ENST00000497802,;PLXNA3,downstream_gene_variant,,ENST00000491066,;PLXNA3,downstream_gene_variant,,ENST00000478236,;	T	ENSG00000130827	ENST00000369682	Transcript	synonymous_variant	4981	4806	1602	L	ctC/ctT	.	.	.	1	PLXNA3	HGNC	9101	protein_coding	YES	CCDS14752.1	ENSP00000358696	PLXA3_HUMAN	.	UPI000004E900	.	.	.	29/33	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF32,Pfam_domain:PF08337	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TTGCTCCGCAC	.	4	ESCA
MAP3K15	0	.	GRCh37	X	19391656	19391656	+	Silent	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2931C>G	p.%3D	p.L977L	ENST00000338883	21/29	77	46	31	59	59	0	MAP3K15,synonymous_variant,p.%3D,ENST00000469203,;MAP3K15,synonymous_variant,p.%3D,ENST00000359173,;MAP3K15,synonymous_variant,p.%3D,ENST00000338883,;Y_RNA,upstream_gene_variant,,ENST00000365274,;MAP3K15,splice_region_variant,,ENST00000518578,;MAP3K15,upstream_gene_variant,,ENST00000470101,;	C	ENSG00000180815	ENST00000338883	Transcript	synonymous_variant	2931	2931	977	L	ctC/ctG	.	.	.	-1	MAP3K15	HGNC	31689	protein_coding	YES	.	ENSP00000345629	M3K15_HUMAN	E7EWI5_HUMAN	UPI0000E444D0	.	.	.	21/29	.	hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCTGAGGAG	.	5	ESCA
MAP3K15	0	.	GRCh37	X	19418722	19418722	+	Missense_Mutation	SNP	T	T	A	rs779958714	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1904A>T	p.Glu635Val	p.E635V	ENST00000338883	14/29	75	48	26	81	81	0	MAP3K15,missense_variant,p.Glu467Val,ENST00000469203,;MAP3K15,missense_variant,p.Glu70Val,ENST00000359173,;MAP3K15,missense_variant,p.Glu635Val,ENST00000338883,;MAP3K15,non_coding_transcript_exon_variant,,ENST00000518578,;	A	ENSG00000180815	ENST00000338883	Transcript	missense_variant	1904	1904	635	E/V	gAg/gTg	rs779958714	.	.	-1	MAP3K15	HGNC	31689	protein_coding	YES	.	ENSP00000345629	M3K15_HUMAN	E7EWI5_HUMAN	UPI0000E444D0	.	deleterious(0.03)	possibly_damaging(0.835)	14/29	.	hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363	C:0.0003	C:0	C:0.0014	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCTCCAGC	byCluster|by1000G	5	ESCA
UBA1	0	.	GRCh37	X	47074032	47074032	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3037C>G	p.Gln1013Glu	p.Q1013E	ENST00000335972	25/26	39	28	11	28	28	0	UBA1,missense_variant,p.Gln461Glu,ENST00000377269,;UBA1,missense_variant,p.Gln1013Glu,ENST00000335972,;UBA1,missense_variant,p.Gln1013Glu,ENST00000377351,;CDK16,upstream_gene_variant,,ENST00000457458,;CDK16,upstream_gene_variant,,ENST00000517426,;CDK16,upstream_gene_variant,,ENST00000520893,;CDK16,upstream_gene_variant,,ENST00000519758,;CDK16,upstream_gene_variant,,ENST00000522883,;CDK16,upstream_gene_variant,,ENST00000357227,;CDK16,upstream_gene_variant,,ENST00000517479,;CDK16,upstream_gene_variant,,ENST00000517997,;CDK16,upstream_gene_variant,,ENST00000520295,;CDK16,upstream_gene_variant,,ENST00000522234,;	G	ENSG00000130985	ENST00000335972	Transcript	missense_variant	3220	3037	1013	Q/E	Cag/Gag	.	.	.	1	UBA1	HGNC	12469	protein_coding	YES	CCDS14275.1	ENSP00000338413	UBA1_HUMAN	Q712V1_HUMAN,Q5JRR9_HUMAN,B4DDE4_HUMAN	UPI0000137946	.	deleterious(0)	benign(0.102)	25/26	.	hmmpanther:PTHR10953:SF136,hmmpanther:PTHR10953,TIGRFAM_domain:TIGR01408,Pfam_domain:PF09358,SMART_domains:SM00985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGATCAGCCG	.	5	ESCA
CCDC22	0	.	GRCh37	X	49104664	49104664	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1105T>A	p.Cys369Ser	p.C369S	ENST00000376227	10/17	10	5	5	10	10	0	CCDC22,missense_variant,p.Cys369Ser,ENST00000376227,;FOXP3,downstream_gene_variant,,ENST00000376199,;FOXP3,downstream_gene_variant,,ENST00000376207,;FOXP3,downstream_gene_variant,,ENST00000455775,;FOXP3,downstream_gene_variant,,ENST00000557224,;FOXP3,downstream_gene_variant,,ENST00000376197,;FOXP3,downstream_gene_variant,,ENST00000518685,;CCDC22,downstream_gene_variant,,ENST00000490300,;CCDC22,downstream_gene_variant,,ENST00000496651,;	A	ENSG00000101997	ENST00000376227	Transcript	missense_variant	1275	1105	369	C/S	Tgc/Agc	.	.	.	1	CCDC22	HGNC	28909	protein_coding	YES	CCDS14322.1	ENSP00000365401	CCD22_HUMAN	.	UPI000006FFC7	.	tolerated(0.06)	benign(0.063)	10/17	.	hmmpanther:PTHR15668,Pfam_domain:PF05667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGAGTGCCGG	.	3	ESCA
DGKK	0	.	GRCh37	X	50133337	50133337	+	RNA	SNP	G	G	C	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1975C>G	.	.	ENST00000376025	12/28	52	36	16	46	46	0	DGKK,non_coding_transcript_exon_variant,,ENST00000376025,;DGKK,non_coding_transcript_exon_variant,,ENST00000546288,;	C	ENSG00000204466	ENST00000376025	Transcript	non_coding_transcript_exon_variant	1975	.	.	.	.	.	.	.	-1	DGKK	HGNC	32395	processed_transcript	YES	.	.	.	.	.	.	.	.	12/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTGGTACAT	.	5	ESCA
KDM5C	0	.	GRCh37	X	53246370	53246370	+	Silent	SNP	G	G	A	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612C>T	p.%3D	p.S204S	ENST00000375401	5/26	54	43	10	48	48	0	KDM5C,synonymous_variant,p.%3D,ENST00000452825,;KDM5C,synonymous_variant,p.%3D,ENST00000375379,;KDM5C,synonymous_variant,p.%3D,ENST00000404049,;KDM5C,synonymous_variant,p.%3D,ENST00000375383,;KDM5C,synonymous_variant,p.%3D,ENST00000375401,;KDM5C-IT1,upstream_gene_variant,,ENST00000412242,;KDM5C,downstream_gene_variant,,ENST00000495519,;KDM5C,downstream_gene_variant,,ENST00000467093,;KDM5C,upstream_gene_variant,,ENST00000497995,;KDM5C,downstream_gene_variant,,ENST00000428012,;KDM5C,downstream_gene_variant,,ENST00000429877,;KDM5C,downstream_gene_variant,,ENST00000349663,;	A	ENSG00000126012	ENST00000375401	Transcript	synonymous_variant	1145	612	204	S	tcC/tcT	.	.	.	-1	KDM5C	HGNC	11114	protein_coding	YES	CCDS14351.1	ENSP00000364550	KDM5C_HUMAN	.	UPI000013CBE3	.	.	.	5/26	.	hmmpanther:PTHR10694:SF31,hmmpanther:PTHR10694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTGGAAGG	.	5	ESCA
HUWE1	0	.	GRCh37	X	53575129	53575129	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10141A>G	p.Ser3381Gly	p.S3381G	ENST00000342160	67/83	29	23	6	49	49	0	HUWE1,missense_variant,p.Ser3381Gly,ENST00000342160,;HUWE1,missense_variant,p.Ser3381Gly,ENST00000262854,;HUWE1,missense_variant,p.Ser2415Gly,ENST00000427052,;HUWE1,missense_variant,p.Ser219Gly,ENST00000426907,;HUWE1,upstream_gene_variant,,ENST00000474288,;HUWE1,upstream_gene_variant,,ENST00000468322,;	C	ENSG00000086758	ENST00000342160	Transcript	missense_variant	10599	10141	3381	S/G	Agc/Ggc	COSM1729601,COSM1729600	.	.	-1	HUWE1	HGNC	30892	protein_coding	YES	CCDS35301.1	ENSP00000340648	HUWE1_HUMAN	Q5H963_HUMAN	UPI00004A0DAC	.	.	benign(0.153)	67/83	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11254:SF67,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGCTGGAGG	.	4	ESCA
FAM120C	0	.	GRCh37	X	54143073	54143073	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2217G>A	p.Met739Ile	p.M739I	ENST00000375180	10/16	50	30	19	29	29	0	FAM120C,missense_variant,p.Met739Ile,ENST00000375180,;FAM120C,missense_variant,p.Met739Ile,ENST00000328235,;	T	ENSG00000184083	ENST00000375180	Transcript	missense_variant	2274	2217	739	M/I	atG/atA	.	.	.	-1	FAM120C	HGNC	16949	protein_coding	YES	CCDS14356.1	ENSP00000364324	F120C_HUMAN	.	UPI000022DC3D	.	deleterious(0.03)	probably_damaging(0.971)	10/16	.	hmmpanther:PTHR15976,hmmpanther:PTHR15976:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCGCATCCT	.	5	ESCA
KLF8	0	.	GRCh37	X	56295889	56295889	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Q9-A6FU-01A-11D-A31U-09	TCGA-Q9-A6FU-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725C>T	p.Ser242Leu	p.S242L	ENST00000468660	4/6	66	51	15	69	69	0	KLF8,missense_variant,p.Ser242Leu,ENST00000374928,;KLF8,missense_variant,p.Ser242Leu,ENST00000468660,;KLF8,3_prime_UTR_variant,,ENST00000358094,;KLF8,non_coding_transcript_exon_variant,,ENST00000462627,;KLF8,downstream_gene_variant,,ENST00000476898,;	T	ENSG00000102349	ENST00000468660	Transcript	missense_variant	1013	725	242	S/L	tCa/tTa	.	.	.	1	KLF8	HGNC	6351	protein_coding	YES	CCDS14373.1	ENSP00000417303	KLF8_HUMAN	.	UPI000012DED7	.	tolerated(0.15)	benign(0.007)	4/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23223,hmmpanther:PTHR23223:SF150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATCCTCAGCCT	.	4	ESCA
C10orf82	0	.	GRCh37	10	118424288	118424288	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.445C>G	p.Leu149Val	p.L149V	ENST00000369210	4/5	53	42	10	36	36	0	C10orf82,missense_variant,p.Leu149Val,ENST00000369210,;C10orf82,missense_variant,p.Leu149Val,ENST00000588184,;C10orf82,non_coding_transcript_exon_variant,,ENST00000588224,;C10orf82,non_coding_transcript_exon_variant,,ENST00000467153,;	C	ENSG00000165863	ENST00000369210	Transcript	missense_variant	500	445	149	L/V	Ctg/Gtg	.	.	.	-1	C10orf82	HGNC	28500	protein_coding	YES	CCDS7596.1	ENSP00000358212	CJ082_HUMAN	.	UPI000006DC12	.	deleterious_low_confidence(0.02)	possibly_damaging(0.72)	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCAGATGTG	.	5	ESCA
RSU1	0	.	GRCh37	10	16796955	16796955	+	Silent	SNP	G	G	A	rs774706517	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315C>T	p.%3D	p.F105F	ENST00000377921	4/8	66	54	12	63	63	0	RSU1,synonymous_variant,p.%3D,ENST00000377921,;RSU1,synonymous_variant,p.%3D,ENST00000602389,;RSU1,synonymous_variant,p.%3D,ENST00000345264,;RSU1,non_coding_transcript_exon_variant,,ENST00000377911,;RSU1,non_coding_transcript_exon_variant,,ENST00000464074,;	A	ENSG00000148484	ENST00000377921	Transcript	synonymous_variant	617	315	105	F	ttC/ttT	rs774706517	.	.	-1	RSU1	HGNC	10464	protein_coding	YES	CCDS7112.1	ENSP00000367154	RSU1_HUMAN	.	UPI0000000C72	.	.	.	4/8	.	PROSITE_profiles:PS51450,hmmpanther:PTHR23155,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGAAGCC	.	5	ESCA
PLXDC2	0	.	GRCh37	10	20568869	20568869	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*121G>A	.	.	ENST00000377252	14/14	18	10	8	18	18	0	PLXDC2,3_prime_UTR_variant,,ENST00000377242,;PLXDC2,3_prime_UTR_variant,,ENST00000377252,;PLXDC2,non_coding_transcript_exon_variant,,ENST00000377238,;	A	ENSG00000120594	ENST00000377252	Transcript	3_prime_UTR_variant	2552	.	.	.	.	.	.	.	1	PLXDC2	HGNC	21013	protein_coding	YES	CCDS7132.1	ENSP00000366460	PXDC2_HUMAN	.	UPI0000048F2C	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTGAAGAA	.	5	ESCA
MAPK8	0	.	GRCh37	10	49628338	49628338	+	Silent	SNP	C	C	T	rs748354922	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.591C>T	p.%3D	p.I197I	ENST00000374189	6/12	36	33	3	29	29	0	MAPK8,synonymous_variant,p.%3D,ENST00000374182,;MAPK8,synonymous_variant,p.%3D,ENST00000360332,;MAPK8,synonymous_variant,p.%3D,ENST00000374176,;MAPK8,synonymous_variant,p.%3D,ENST00000395611,;MAPK8,synonymous_variant,p.%3D,ENST00000374179,;MAPK8,synonymous_variant,p.%3D,ENST00000374189,;MAPK8,synonymous_variant,p.%3D,ENST00000374174,;MAPK8,downstream_gene_variant,,ENST00000429041,;MAPK8,upstream_gene_variant,,ENST00000469879,;MAPK8,upstream_gene_variant,,ENST00000469110,;MAPK8,upstream_gene_variant,,ENST00000471272,;	T	ENSG00000107643	ENST00000374189	Transcript	synonymous_variant	772	591	197	I	atC/atT	rs748354922	.	.	1	MAPK8	HGNC	6881	protein_coding	YES	CCDS7224.1	ENSP00000363304	MK08_HUMAN	C9J762_HUMAN	UPI000012F17A	.	.	.	6/12	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF162,hmmpanther:PTHR24055,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCATCCTTGG	.	2	ESCA
MMS19	0	.	GRCh37	10	99218606	99218606	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3016G>A	p.Asp1006Asn	p.D1006N	ENST00000438925	30/31	38	25	12	32	32	0	MMS19,missense_variant,p.Asp1006Asn,ENST00000370782,;MMS19,missense_variant,p.Asp908Asn,ENST00000327238,;MMS19,missense_variant,p.Asp1006Asn,ENST00000438925,;MMS19,missense_variant,p.Asp963Asn,ENST00000355839,;MMS19,missense_variant,p.Asp66Asn,ENST00000444411,;MMS19,missense_variant,p.Asp574Asn,ENST00000434538,;MMS19,3_prime_UTR_variant,,ENST00000327277,;ZDHHC16,downstream_gene_variant,,ENST00000345745,;ZDHHC16,downstream_gene_variant,,ENST00000417044,;ZDHHC16,downstream_gene_variant,,ENST00000352634,;ZDHHC16,downstream_gene_variant,,ENST00000433086,;ZDHHC16,downstream_gene_variant,,ENST00000370842,;ZDHHC16,downstream_gene_variant,,ENST00000370854,;ZDHHC16,downstream_gene_variant,,ENST00000370846,;ZDHHC16,downstream_gene_variant,,ENST00000393760,;ZDHHC16,downstream_gene_variant,,ENST00000353979,;ZDHHC16,downstream_gene_variant,,ENST00000420089,;ZDHHC16,downstream_gene_variant,,ENST00000492733,;ZDHHC16,downstream_gene_variant,,ENST00000462924,;ZDHHC16,downstream_gene_variant,,ENST00000487315,;ZDHHC16,downstream_gene_variant,,ENST00000459777,;ZDHHC16,downstream_gene_variant,,ENST00000495735,;ZDHHC16,downstream_gene_variant,,ENST00000466895,;MMS19,3_prime_UTR_variant,,ENST00000415383,;MMS19,non_coding_transcript_exon_variant,,ENST00000485400,;MMS19,non_coding_transcript_exon_variant,,ENST00000495415,;MMS19,downstream_gene_variant,,ENST00000478452,;MMS19,downstream_gene_variant,,ENST00000480108,;	T	ENSG00000155229	ENST00000438925	Transcript	missense_variant	3352	3016	1006	D/N	Gac/Aac	.	.	.	-1	MMS19	HGNC	13824	protein_coding	YES	CCDS7464.1	ENSP00000412698	MMS19_HUMAN	.	UPI000013DDF7	.	deleterious(0)	probably_damaging(0.998)	30/31	.	hmmpanther:PTHR12891,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTCATCCA	.	5	ESCA
PGR	0	.	GRCh37	11	100922294	100922294	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	5/8	12	4	8	12	12	0	PGR,stop_gained,p.Arg638Ter,ENST00000263463,;PGR,stop_gained,p.Arg740Ter,ENST00000325455,;PGR,stop_gained,p.Arg146Ter,ENST00000534013,;PGR,stop_gained,p.Arg740Ter,ENST00000534780,;PGR,stop_gained,p.Arg701Ter,ENST00000528960,;PGR,stop_gained,p.Arg638Ter,ENST00000526300,;PGR,non_coding_transcript_exon_variant,,ENST00000533207,;PGR,upstream_gene_variant,,ENST00000530764,;	A	ENSG00000082175	ENST00000325455	Transcript	stop_gained	3672	2218	740	R/*	Cga/Tga	COSM1561169	.	.	-1	PGR	HGNC	8910	protein_coding	YES	CCDS8310.1	ENSP00000325120	PRGR_HUMAN	Q6TZ07_HUMAN	UPI0000046E22	.	.	.	5/8	.	hmmpanther:PTHR24084:SF7,hmmpanther:PTHR24084,Pfam_domain:PF00104,Gene3D:1.10.565.10,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00398	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R740*|c.2218C>T|3,CODON|p.R740Q|c.2219G>A|6	RADIA|MUTECT|MUSE	GTTTCGAAAAC	.	3	ESCA
GRIA4	0	.	GRCh37	11	105804513	105804513	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2112C>G	p.Phe704Leu	p.F704L	ENST00000282499	14/17	25	21	4	35	35	0	GRIA4,missense_variant,p.Phe704Leu,ENST00000282499,;GRIA4,missense_variant,p.Phe704Leu,ENST00000530497,;GRIA4,missense_variant,p.Phe704Leu,ENST00000393127,;GRIA4,missense_variant,p.Phe704Leu,ENST00000525187,;AP000673.1,upstream_gene_variant,,ENST00000583628,;GRIA4,upstream_gene_variant,,ENST00000533094,;GRIA4,upstream_gene_variant,,ENST00000525942,;	G	ENSG00000152578	ENST00000282499	Transcript	missense_variant	2558	2112	704	F/L	ttC/ttG	.	.	.	1	GRIA4	HGNC	4574	protein_coding	YES	CCDS8333.1	ENSP00000282499	GRIA4_HUMAN	E9PJZ5_HUMAN	UPI000013DCE6	.	deleterious(0.02)	possibly_damaging(0.476)	14/17	.	hmmpanther:PTHR18966:SF100,hmmpanther:PTHR18966,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTATTCACTAG	.	2	ESCA
JAM3	0	.	GRCh37	11	134014150	134014150	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271C>T	p.Arg91Cys	p.R91C	ENST00000299106	4/9	36	24	12	44	44	0	JAM3,missense_variant,p.Arg136Cys,ENST00000529443,;JAM3,missense_variant,p.Arg91Cys,ENST00000299106,;JAM3,missense_variant,p.Arg31Cys,ENST00000534549,;JAM3,intron_variant,,ENST00000441717,;JAM3,non_coding_transcript_exon_variant,,ENST00000524969,;JAM3,non_coding_transcript_exon_variant,,ENST00000532165,;JAM3,3_prime_UTR_variant,,ENST00000532252,;JAM3,non_coding_transcript_exon_variant,,ENST00000531302,;JAM3,upstream_gene_variant,,ENST00000533711,;	T	ENSG00000166086	ENST00000299106	Transcript	missense_variant	430	271	91	R/C	Cgt/Tgt	.	.	.	1	JAM3	HGNC	15532	protein_coding	YES	CCDS8494.2	ENSP00000299106	JAM3_HUMAN	.	UPI0000034063	.	deleterious(0)	probably_damaging(1)	4/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12231:SF5,hmmpanther:PTHR12231,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGTCGTGCA	.	5	ESCA
STIM1	0	.	GRCh37	11	4113083	4113083	+	3'UTR	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*55C>G	.	.	ENST00000300737	12/12	92	65	26	75	75	0	STIM1,3_prime_UTR_variant,,ENST00000533977,;STIM1,3_prime_UTR_variant,,ENST00000300737,;RRM1,upstream_gene_variant,,ENST00000423050,;STIM1,downstream_gene_variant,,ENST00000526596,;STIM1,downstream_gene_variant,,ENST00000527651,;RRM1,upstream_gene_variant,,ENST00000300738,;RRM1,upstream_gene_variant,,ENST00000526865,;RRM1,upstream_gene_variant,,ENST00000532710,;STIM1,downstream_gene_variant,,ENST00000534707,;STIM1,non_coding_transcript_exon_variant,,ENST00000526156,;RRM1,upstream_gene_variant,,ENST00000532170,;RRM1,upstream_gene_variant,,ENST00000533349,;RRM1,upstream_gene_variant,,ENST00000526350,;STIM1,downstream_gene_variant,,ENST00000531332,;	G	ENSG00000167323	ENST00000300737	Transcript	3_prime_UTR_variant	2682	.	.	.	.	.	.	.	1	STIM1	HGNC	11386	protein_coding	YES	CCDS7749.1	ENSP00000300737	STIM1_HUMAN	E9PRZ7_HUMAN,E9PRE4_HUMAN,E9PR09_HUMAN,E9PR07_HUMAN,E9PNJ4_HUMAN,E9PMB4_HUMAN,E9PJ19_HUMAN,E9PIQ8_HUMAN	UPI00000724B7	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTCTCCTT	.	5	ESCA
MMP26	0	.	GRCh37	11	5009484	5009484	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43T>G	p.Cys15Gly	p.C15G	ENST00000380390	2/7	55	29	26	49	49	0	MMP26,missense_variant,p.Cys15Gly,ENST00000300762,;MMP26,missense_variant,p.Cys15Gly,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	G	ENSG00000167346	ENST00000380390	Transcript	missense_variant	259	43	15	C/G	Tgt/Ggt	.	.	.	1	MMP26	HGNC	14249	protein_coding	YES	CCDS7752.1	ENSP00000369753	MMP26_HUMAN	.	UPI0000047AFC	.	deleterious(0.04)	possibly_damaging(0.57)	2/7	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF76	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F16F|c.48C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGTGTTTC	.	5	ESCA
HBB	0	.	GRCh37	11	5248189	5248189	+	Silent	SNP	C	C	A	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.63G>T	p.%3D	p.V21V	ENST00000335295	1/3	46	36	10	42	42	0	HBB,synonymous_variant,p.%3D,ENST00000335295,;HBB,synonymous_variant,p.%3D,ENST00000380315,;CoTC_ribozyme,upstream_gene_variant,,ENST00000408104,;HBB,non_coding_transcript_exon_variant,,ENST00000485743,;HBB,upstream_gene_variant,,ENST00000475226,;	A	ENSG00000244734	ENST00000335295	Transcript	synonymous_variant	113	63	21	V	gtG/gtT	COSM3448558	.	.	-1	HBB	HGNC	4827	protein_coding	YES	CCDS7753.1	ENSP00000333994	HBB_HUMAN	Q9H1I6_HUMAN,Q9GZL9_HUMAN,Q9BXA2_HUMAN,Q86VF0_HUMAN,Q7Z2K5_HUMAN,Q6VFQ5_HUMAN,Q14484_HUMAN,Q0Z944_HUMAN,K4EN30_HUMAN,J7LKS8_HUMAN,F8W6P5_HUMAN,E9M263_HUMAN,D9YZU5_HUMAN,D5FZW3_HUMAN,B5ANL9_HUMAN,B3VL12_HUMAN	UPI00000015C9	.	.	.	1/3	.	PROSITE_profiles:PS01033,hmmpanther:PTHR11442,hmmpanther:PTHR11442:SF30,Pfam_domain:PF00042,Gene3D:1.10.490.10,Superfamily_domains:SSF46458	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATCCACGTT	.	5	ESCA
OR4C16	0	.	GRCh37	11	55339864	55339864	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.261G>C	p.Lys87Asn	p.K87N	ENST00000314634	1/1	59	46	13	51	51	0	OR4C16,missense_variant,p.Lys87Asn,ENST00000314634,;	C	ENSG00000181935	ENST00000314634	Transcript	missense_variant	261	261	87	K/N	aaG/aaC	.	.	.	1	OR4C16	HGNC	15172	protein_coding	YES	CCDS31502.1	ENSP00000324913	OR4CG_HUMAN	.	UPI000013F8A8	.	tolerated(0.15)	benign(0.002)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF223,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGAAGACAAC	.	3	ESCA
C11orf48	0	.	GRCh37	11	62439163	62439163	+	5'Flank	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000532208	.	68	35	33	57	57	0	C11orf48,5_prime_UTR_variant,,ENST00000354588,;C11orf48,5_prime_UTR_variant,,ENST00000415855,;C11orf83,5_prime_UTR_variant,,ENST00000531323,;C11orf83,5_prime_UTR_variant,,ENST00000377953,;C11orf48,5_prime_UTR_variant,,ENST00000431002,;C11orf48,intron_variant,,ENST00000528862,;C11orf48,upstream_gene_variant,,ENST00000528115,;C11orf48,upstream_gene_variant,,ENST00000532208,;UBXN1,downstream_gene_variant,,ENST00000301935,;UBXN1,downstream_gene_variant,,ENST00000294119,;UBXN1,downstream_gene_variant,,ENST00000534176,;UBXN1,downstream_gene_variant,,ENST00000533000,;METTL12,downstream_gene_variant,,ENST00000532971,;UBXN1,downstream_gene_variant,,ENST00000529640,;C11orf48,upstream_gene_variant,,ENST00000377954,;C11orf48,upstream_gene_variant,,ENST00000526490,;METTL12,downstream_gene_variant,,ENST00000398922,;C11orf48,non_coding_transcript_exon_variant,,ENST00000524759,;UBXN1,downstream_gene_variant,,ENST00000532904,;METTL12,downstream_gene_variant,,ENST00000529868,;UBXN1,downstream_gene_variant,,ENST00000525717,;C11orf48,upstream_gene_variant,,ENST00000527679,;UBXN1,downstream_gene_variant,,ENST00000533476,;	T	ENSG00000162194	ENST00000532208	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	151	-1	C11orf48	HGNC	28351	protein_coding	YES	CCDS8028.1	ENSP00000436848	CK048_HUMAN	E9PL64_HUMAN	UPI00003520AA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAACAGCTT	.	5	ESCA
RAB1B	0	.	GRCh37	11	66039507	66039507	+	Intron	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88-121G>A	.	.	ENST00000311481	.	14	10	4	9	9	0	RAB1B,intron_variant,,ENST00000311481,;RAB1B,intron_variant,,ENST00000527397,;KLC2,downstream_gene_variant,,ENST00000316924,;KLC2,downstream_gene_variant,,ENST00000394078,;KLC2,downstream_gene_variant,,ENST00000417856,;KLC2,downstream_gene_variant,,ENST00000394066,;KLC2,downstream_gene_variant,,ENST00000394067,;KLC2,downstream_gene_variant,,ENST00000394065,;KLC2,downstream_gene_variant,,ENST00000421552,;RP11-867G23.3,non_coding_transcript_exon_variant,,ENST00000501708,;RP11-867G23.2,upstream_gene_variant,,ENST00000533287,;RP11-867G23.4,downstream_gene_variant,,ENST00000526951,;RP11-867G23.4,downstream_gene_variant,,ENST00000528650,;	A	ENSG00000174903	ENST00000311481	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RAB1B	HGNC	18370	protein_coding	YES	CCDS31613.1	ENSP00000310226	RAB1B_HUMAN	Q92927_HUMAN	UPI0000037B58	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGAGTGCTG	.	2	ESCA
TXNRD1	0	.	GRCh37	12	104682792	104682792	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388A>T	p.Ile130Leu	p.I130L	ENST00000525566	4/17	23	8	14	33	33	0	TXNRD1,missense_variant,p.Ile32Leu,ENST00000388854,;TXNRD1,missense_variant,p.Ile32Leu,ENST00000526691,;TXNRD1,missense_variant,p.Ile130Leu,ENST00000429002,;TXNRD1,missense_variant,p.Ile130Leu,ENST00000525566,;TXNRD1,missense_variant,p.Ile30Leu,ENST00000542918,;TXNRD1,missense_variant,p.Ile79Leu,ENST00000378070,;TXNRD1,5_prime_UTR_variant,,ENST00000529546,;TXNRD1,5_prime_UTR_variant,,ENST00000524698,;TXNRD1,5_prime_UTR_variant,,ENST00000526266,;TXNRD1,5_prime_UTR_variant,,ENST00000527335,;TXNRD1,5_prime_UTR_variant,,ENST00000526390,;TXNRD1,5_prime_UTR_variant,,ENST00000531691,;TXNRD1,5_prime_UTR_variant,,ENST00000528079,;TXNRD1,5_prime_UTR_variant,,ENST00000503506,;TXNRD1,5_prime_UTR_variant,,ENST00000529784,;TXNRD1,5_prime_UTR_variant,,ENST00000540716,;TXNRD1,5_prime_UTR_variant,,ENST00000531689,;TXNRD1,intron_variant,,ENST00000526580,;TXNRD1,intron_variant,,ENST00000354940,;TXNRD1,intron_variant,,ENST00000529751,;TXNRD1,upstream_gene_variant,,ENST00000397736,;TXNRD1,downstream_gene_variant,,ENST00000526006,;TXNRD1,5_prime_UTR_variant,,ENST00000527688,;TXNRD1,non_coding_transcript_exon_variant,,ENST00000526207,;	T	ENSG00000198431	ENST00000525566	Transcript	missense_variant	412	388	130	I/L	Ata/Tta	.	.	.	1	TXNRD1	HGNC	12437	protein_coding	YES	CCDS53820.1	ENSP00000434516	TRXR1_HUMAN	F5H780_HUMAN,E9PRI8_HUMAN,E9PQI3_HUMAN,E9PLT3_HUMAN,E9PKI4_HUMAN,E9PKD3_HUMAN,B7Z904_HUMAN,B2R5P6_HUMAN	UPI00015294EE	.	tolerated(0.16)	benign(0.003)	4/17	.	Superfamily_domains:SSF52833,Gene3D:3.40.30.10,hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF129,PROSITE_profiles:PS51354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGATAGGC	.	5	ESCA
SETD1B	0	.	GRCh37	12	122247572	122247572	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.721T>C	p.Ser241Pro	p.S241P	ENST00000267197	5/17	30	26	4	36	36	0	SETD1B,missense_variant,p.Ser241Pro,ENST00000604567,;SETD1B,missense_variant,p.Ser241Pro,ENST00000542440,;SETD1B,missense_variant,p.Ser241Pro,ENST00000267197,;	C	ENSG00000139718	ENST00000267197	Transcript	missense_variant	727	721	241	S/P	Tcc/Ccc	.	.	.	1	SETD1B	HGNC	29187	protein_coding	YES	CCDS53838.1	ENSP00000267197	SET1B_HUMAN	.	UPI00006C12ED	.	.	benign(0.253)	5/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22884:SF296,hmmpanther:PTHR22884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GCTCCTCCTCT	.	2	ESCA
AACS	0	.	GRCh37	12	125591780	125591780	+	Missense_Mutation	SNP	C	C	G	rs371263015	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.881C>G	p.Thr294Arg	p.T294R	ENST00000316519	8/18	33	17	16	42	42	0	AACS,missense_variant,p.Thr294Arg,ENST00000261686,;AACS,missense_variant,p.Thr75Arg,ENST00000537564,;AACS,missense_variant,p.Thr113Arg,ENST00000441247,;AACS,missense_variant,p.Thr294Arg,ENST00000316519,;AACS,5_prime_UTR_variant,,ENST00000316543,;AACS,downstream_gene_variant,,ENST00000537477,;AACS,downstream_gene_variant,,ENST00000418937,;	G	ENSG00000081760	ENST00000316519	Transcript	missense_variant	1087	881	294	T/R	aCg/aGg	rs371263015	.	.	1	AACS	HGNC	21298	protein_coding	YES	CCDS9263.1	ENSP00000324842	AACS_HUMAN	Q9H7A6_HUMAN,F5H6X9_HUMAN,F5H4V2_HUMAN,F5H3E3_HUMAN,F5GYN1_HUMAN	UPI0000049787	.	deleterious(0)	probably_damaging(0.994)	8/18	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF46,PROSITE_patterns:PS00455,Pfam_domain:PF00501,TIGRFAM_domain:TIGR01217,Gene3D:3.40.50.980,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCACGGGCG	byFrequency|byCluster	5	ESCA
EMP1	0	.	GRCh37	12	13369567	13369567	+	3'UTR	SNP	A	A	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1942A>T	.	.	ENST00000256951	5/5	103	64	39	78	78	0	EMP1,3_prime_UTR_variant,,ENST00000537612,;EMP1,3_prime_UTR_variant,,ENST00000256951,;EMP1,downstream_gene_variant,,ENST00000538364,;EMP1,downstream_gene_variant,,ENST00000544053,;EMP1,downstream_gene_variant,,ENST00000431267,;EMP1,downstream_gene_variant,,ENST00000396301,;EMP1,downstream_gene_variant,,ENST00000542289,;EMP1,downstream_gene_variant,,ENST00000541935,;EMP1,downstream_gene_variant,,ENST00000546357,;EMP1,downstream_gene_variant,,ENST00000536383,;	T	ENSG00000134531	ENST00000256951	Transcript	3_prime_UTR_variant	2615	.	.	.	.	.	.	.	1	EMP1	HGNC	3333	protein_coding	YES	CCDS8660.1	ENSP00000256951	EMP1_HUMAN	J3KQX4_HUMAN	UPI000000DBC8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGTAATTTG	.	5	ESCA
PDE3A	0	.	GRCh37	12	20523043	20523043	+	Silent	SNP	G	G	A	rs750288734	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.825G>A	p.%3D	p.L275L	ENST00000359062	1/16	22	19	3	12	12	0	PDE3A,synonymous_variant,p.%3D,ENST00000359062,;RP11-284H19.1,non_coding_transcript_exon_variant,,ENST00000535755,;PDE3A,upstream_gene_variant,,ENST00000542675,;	A	ENSG00000172572	ENST00000359062	Transcript	synonymous_variant	865	825	275	L	ctG/ctA	rs750288734,COSM415925	.	.	1	PDE3A	HGNC	8778	protein_coding	YES	CCDS31754.1	ENSP00000351957	PDE3A_HUMAN	.	UPI000014175F	.	.	.	1/16	.	hmmpanther:PTHR11347:SF104,hmmpanther:PTHR11347	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.L275L|c.825G>A|3	MUTECT|MUSE	CAGCTGATTGC	.	2	ESCA
CACNA1C	0	.	GRCh37	12	2690840	2690840	+	Silent	SNP	C	C	G	rs754356413	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1980C>G	p.%3D	p.L660L	ENST00000347598	14/49	70	43	26	64	64	0	CACNA1C,synonymous_variant,p.%3D,ENST00000399644,;CACNA1C,synonymous_variant,p.%3D,ENST00000399595,;CACNA1C,synonymous_variant,p.%3D,ENST00000406454,;CACNA1C,synonymous_variant,p.%3D,ENST00000399617,;CACNA1C,synonymous_variant,p.%3D,ENST00000347598,;CACNA1C,synonymous_variant,p.%3D,ENST00000402845,;CACNA1C,synonymous_variant,p.%3D,ENST00000327702,;CACNA1C,synonymous_variant,p.%3D,ENST00000399634,;CACNA1C,synonymous_variant,p.%3D,ENST00000399641,;CACNA1C,synonymous_variant,p.%3D,ENST00000399603,;CACNA1C,synonymous_variant,p.%3D,ENST00000399629,;CACNA1C,synonymous_variant,p.%3D,ENST00000480911,;CACNA1C,synonymous_variant,p.%3D,ENST00000399601,;CACNA1C,synonymous_variant,p.%3D,ENST00000399597,;CACNA1C,synonymous_variant,p.%3D,ENST00000399655,;CACNA1C,synonymous_variant,p.%3D,ENST00000399606,;CACNA1C,synonymous_variant,p.%3D,ENST00000399637,;CACNA1C,synonymous_variant,p.%3D,ENST00000335762,;CACNA1C,synonymous_variant,p.%3D,ENST00000399621,;CACNA1C,synonymous_variant,p.%3D,ENST00000399638,;CACNA1C,synonymous_variant,p.%3D,ENST00000399591,;CACNA1C,synonymous_variant,p.%3D,ENST00000344100,;CACNA1C,synonymous_variant,p.%3D,ENST00000399649,;CACNA1C,upstream_gene_variant,,ENST00000465278,;	G	ENSG00000151067	ENST00000347598	Transcript	synonymous_variant	1980	1980	660	L	ctC/ctG	rs754356413	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	.	.	14/49	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Pfam_domain:PF00520,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCTTCAT	byFrequency	5	ESCA
ANO6	0	.	GRCh37	12	45741883	45741883	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.481A>G	p.Met161Val	p.M161V	ENST00000423947	6/21	31	17	14	27	27	0	ANO6,missense_variant,p.Met122Val,ENST00000441606,;ANO6,missense_variant,p.Met140Val,ENST00000320560,;ANO6,missense_variant,p.Met161Val,ENST00000423947,;ANO6,missense_variant,p.Met140Val,ENST00000435642,;ANO6,missense_variant,p.Met140Val,ENST00000425752,;ANO6,non_coding_transcript_exon_variant,,ENST00000426898,;ANO6,downstream_gene_variant,,ENST00000551667,;	G	ENSG00000177119	ENST00000423947	Transcript	missense_variant	718	481	161	M/V	Atg/Gtg	.	.	.	1	ANO6	HGNC	25240	protein_coding	YES	CCDS55819.1	ENSP00000409126	ANO6_HUMAN	.	UPI000022935A	.	deleterious(0.03)	benign(0.094)	6/21	.	hmmpanther:PTHR12308:SF21,hmmpanther:PTHR12308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATAATGCAC	.	5	ESCA
AKAP3	0	.	GRCh37	12	4737281	4737281	+	Silent	SNP	G	G	T	rs199990710	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787C>A	p.%3D	p.R263R	ENST00000545990	5/6	27	18	8	37	37	0	AKAP3,synonymous_variant,p.%3D,ENST00000545990,;AKAP3,synonymous_variant,p.%3D,ENST00000228850,;AKAP3,downstream_gene_variant,,ENST00000540967,;AKAP3,downstream_gene_variant,,ENST00000536414,;RP11-500M8.7,intron_variant,,ENST00000536588,;	T	ENSG00000111254	ENST00000545990	Transcript	synonymous_variant	1312	787	263	R	Cgg/Agg	rs199990710,COSM939635,COSM1586498	.	.	-1	AKAP3	HGNC	373	protein_coding	YES	CCDS8531.1	ENSP00000440994	AKAP3_HUMAN	F5H7P4_HUMAN,F5H2S4_HUMAN	UPI000013C8DF	.	.	.	5/6	.	hmmpanther:PTHR10226,hmmpanther:PTHR10226:SF9,Pfam_domain:PF05716,SMART_domains:SM00807	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCGAGGAA	byCluster|by1000G	5	ESCA
MON2	0	.	GRCh37	12	62902072	62902072	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.796G>A	p.Glu266Lys	p.E266K	ENST00000393632	8/35	89	73	15	43	43	0	MON2,missense_variant,p.Glu266Lys,ENST00000546600,;MON2,missense_variant,p.Glu266Lys,ENST00000393630,;MON2,missense_variant,p.Glu266Lys,ENST00000280379,;MON2,missense_variant,p.Glu266Lys,ENST00000552115,;MON2,missense_variant,p.Glu266Lys,ENST00000393629,;MON2,missense_variant,p.Glu266Lys,ENST00000393632,;MON2,missense_variant,p.Glu266Lys,ENST00000552738,;MON2,non_coding_transcript_exon_variant,,ENST00000549378,;MON2,3_prime_UTR_variant,,ENST00000547095,;	A	ENSG00000061987	ENST00000393632	Transcript	missense_variant	1187	796	266	E/K	Gaa/Aaa	COSM942351,COSM4044057	.	.	1	MON2	HGNC	29177	protein_coding	YES	CCDS31849.1	ENSP00000377252	MON2_HUMAN	F8VZV1_HUMAN	UPI00001AEA4C	.	deleterious(0)	possibly_damaging(0.584)	8/35	.	hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF105,Pfam_domain:PF12783,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E266*|c.796G>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAAGAATTT	.	5	ESCA
SRGAP1	0	.	GRCh37	12	64456779	64456779	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.884G>A	p.Arg295Lys	p.R295K	ENST00000355086	7/22	74	62	11	53	53	0	SRGAP1,missense_variant,p.Arg255Lys,ENST00000543397,;SRGAP1,missense_variant,p.Arg295Lys,ENST00000357825,;SRGAP1,missense_variant,p.Arg295Lys,ENST00000355086,;RP11-196H14.2,intron_variant,,ENST00000535594,;SRGAP1,non_coding_transcript_exon_variant,,ENST00000537556,;	A	ENSG00000196935	ENST00000355086	Transcript	missense_variant	1408	884	295	R/K	aGa/aAa	.	.	.	1	SRGAP1	HGNC	17382	protein_coding	YES	CCDS8967.1	ENSP00000347198	SRGP1_HUMAN	.	UPI00001A9CB9	.	tolerated(0.47)	benign(0.004)	7/22	.	hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF15,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCAGACATG	.	5	ESCA
XPOT	0	.	GRCh37	12	64823865	64823865	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1774C>T	p.Gln592Ter	p.Q592*	ENST00000332707	17/25	128	115	12	42	42	0	XPOT,stop_gained,p.Gln592Ter,ENST00000332707,;XPOT,stop_gained,p.Gln114Ter,ENST00000538086,;XPOT,non_coding_transcript_exon_variant,,ENST00000541842,;XPOT,non_coding_transcript_exon_variant,,ENST00000542958,;	T	ENSG00000184575	ENST00000332707	Transcript	stop_gained	2303	1774	592	Q/*	Caa/Taa	.	.	.	1	XPOT	HGNC	12826	protein_coding	YES	CCDS31852.1	ENSP00000327821	XPOT_HUMAN	F8WDU6_HUMAN,F5GYW6_HUMAN	UPI0000161BA5	.	.	.	17/25	.	hmmpanther:PTHR15952,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGATCAACTT	.	4	ESCA
GRIP1	0	.	GRCh37	12	66932939	66932939	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337C>T	p.Arg113Cys	p.R113C	ENST00000398016	4/24	93	86	7	48	48	0	GRIP1,missense_variant,p.Arg139Cys,ENST00000541947,;GRIP1,missense_variant,p.Arg86Cys,ENST00000545666,;GRIP1,missense_variant,p.Arg113Cys,ENST00000538211,;GRIP1,missense_variant,p.Arg57Cys,ENST00000539540,;GRIP1,missense_variant,p.Arg57Cys,ENST00000542309,;GRIP1,missense_variant,p.Arg113Cys,ENST00000286445,;GRIP1,missense_variant,p.Arg57Cys,ENST00000536215,;GRIP1,missense_variant,p.Arg113Cys,ENST00000398016,;GRIP1,missense_variant,p.Arg113Cys,ENST00000359742,;GRIP1,missense_variant,p.Arg57Cys,ENST00000540433,;GRIP1,downstream_gene_variant,,ENST00000538373,;GRIP1,upstream_gene_variant,,ENST00000540854,;	A	ENSG00000155974	ENST00000398016	Transcript	missense_variant	406	337	113	R/C	Cgc/Tgc	COSM1476830	.	.	-1	GRIP1	HGNC	18708	protein_coding	YES	CCDS41807.1	ENSP00000381098	GRIP1_HUMAN	F5H5I0_HUMAN,F5H4P8_HUMAN,F5H424_HUMAN	UPI0000DD8148	.	deleterious(0)	probably_damaging(0.994)	4/24	.	PROSITE_profiles:PS50106,hmmpanther:PTHR10316:SF39,hmmpanther:PTHR10316,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGGCGGAATT	.	3	ESCA
NUP107	0	.	GRCh37	12	69109443	69109443	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1006G>A	p.Asp336Asn	p.D336N	ENST00000229179	12/28	280	185	94	55	55	0	NUP107,missense_variant,p.Asp336Asn,ENST00000229179,;NUP107,missense_variant,p.Asp185Asn,ENST00000378905,;NUP107,missense_variant,p.Asp307Asn,ENST00000539906,;NUP107,3_prime_UTR_variant,,ENST00000535718,;NUP107,downstream_gene_variant,,ENST00000537662,;	A	ENSG00000111581	ENST00000229179	Transcript	missense_variant	1338	1006	336	D/N	Gat/Aat	.	.	.	1	NUP107	HGNC	29914	protein_coding	YES	CCDS8985.1	ENSP00000229179	NU107_HUMAN	F5GY77_HUMAN	UPI000012FC0B	.	tolerated(0.64)	probably_damaging(0.962)	12/28	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13003,Pfam_domain:PF04121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTGATGAT	.	5	ESCA
PPFIA2	0	.	GRCh37	12	81760937	81760937	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1495C>G	p.Gln499Glu	p.Q499E	ENST00000549396	14/33	79	26	53	92	92	0	PPFIA2,missense_variant,p.Gln481Glu,ENST00000333447,;PPFIA2,missense_variant,p.Gln425Glu,ENST00000407050,;PPFIA2,missense_variant,p.Gln66Glu,ENST00000541570,;PPFIA2,missense_variant,p.Gln400Glu,ENST00000443686,;PPFIA2,missense_variant,p.Gln481Glu,ENST00000549325,;PPFIA2,missense_variant,p.Gln499Glu,ENST00000550584,;PPFIA2,missense_variant,p.Gln499Glu,ENST00000552948,;PPFIA2,missense_variant,p.Gln346Glu,ENST00000550359,;PPFIA2,missense_variant,p.Gln80Glu,ENST00000553058,;PPFIA2,missense_variant,p.Gln499Glu,ENST00000549396,;PPFIA2,missense_variant,p.Gln499Glu,ENST00000548586,;PPFIA2,missense_variant,p.Gln66Glu,ENST00000548670,;PPFIA2,5_prime_UTR_variant,,ENST00000541017,;PPFIA2,downstream_gene_variant,,ENST00000548790,;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,;	C	ENSG00000139220	ENST00000549396	Transcript	missense_variant	1656	1495	499	Q/E	Caa/Gaa	.	.	.	-1	PPFIA2	HGNC	9246	protein_coding	YES	CCDS55857.1	ENSP00000450337	LIPA2_HUMAN	H0YHK3_HUMAN,F8W1Y8_HUMAN,F8VU88_HUMAN	UPI0000168655	.	tolerated(0.3)	benign(0.205)	14/33	.	hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTGAATTA	.	5	ESCA
ATP2B1	0	.	GRCh37	12	89996880	89996880	+	Silent	SNP	G	G	A	rs770458245	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3000C>T	p.%3D	p.F1000F	ENST00000428670	18/21	22	16	5	36	36	0	ATP2B1,synonymous_variant,p.%3D,ENST00000550716,;ATP2B1,synonymous_variant,p.%3D,ENST00000393164,;ATP2B1,synonymous_variant,p.%3D,ENST00000261173,;ATP2B1,synonymous_variant,p.%3D,ENST00000428670,;ATP2B1,synonymous_variant,p.%3D,ENST00000359142,;ATP2B1,synonymous_variant,p.%3D,ENST00000348959,;ATP2B1,non_coding_transcript_exon_variant,,ENST00000552275,;ATP2B1,downstream_gene_variant,,ENST00000551009,;ATP2B1,downstream_gene_variant,,ENST00000549727,;	A	ENSG00000070961	ENST00000428670	Transcript	synonymous_variant	3457	3000	1000	F	ttC/ttT	rs770458245	.	.	-1	ATP2B1	HGNC	814	protein_coding	YES	CCDS9035.1	ENSP00000392043	AT2B1_HUMAN	Q3L582_HUMAN	UPI000002A436	.	.	.	18/21	.	hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF245,Pfam_domain:PF00689,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCGAATAC	.	5	ESCA
WBP4	0	.	GRCh37	13	41654920	41654920	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895G>A	p.Glu299Lys	p.E299K	ENST00000379487	9/10	34	31	3	39	39	0	WBP4,missense_variant,p.Glu299Lys,ENST00000379487,;WBP4,missense_variant,p.Glu278Lys,ENST00000542082,;	A	ENSG00000120688	ENST00000379487	Transcript	missense_variant	1295	895	299	E/K	Gaa/Aaa	.	.	.	1	WBP4	HGNC	12739	protein_coding	YES	CCDS9375.1	ENSP00000368801	WBP4_HUMAN	.	UPI0000072671	.	tolerated(0.27)	benign(0.019)	9/10	.	hmmpanther:PTHR13173	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCAAGAAATT	.	4	ESCA
PCDH9	0	.	GRCh37	13	66878818	66878818	+	Missense_Mutation	SNP	G	G	T	rs746411543	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3683C>A	p.Ala1228Asp	p.A1228D	ENST00000544246	5/5	29	24	5	28	28	0	PCDH9,missense_variant,p.Ala1194Asp,ENST00000328454,;PCDH9,missense_variant,p.Ala1228Asp,ENST00000544246,;PCDH9,missense_variant,p.Ala1228Asp,ENST00000377865,;PCDH9,missense_variant,p.Ala1194Asp,ENST00000456367,;PCDH9-AS1,intron_variant,,ENST00000430861,;	T	ENSG00000184226	ENST00000544246	Transcript	missense_variant	4375	3683	1228	A/D	gCt/gAt	rs746411543	.	.	-1	PCDH9	HGNC	8661	protein_coding	YES	CCDS9444.1	ENSP00000442186	PCDH9_HUMAN	.	UPI00001FCE90	.	tolerated(0.55)	benign(0.029)	5/5	.	hmmpanther:PTHR24027:SF25,hmmpanther:PTHR24027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTAGCACCT	byFrequency	5	ESCA
HSP90AA1	0	.	GRCh37	14	102552699	102552699	+	Missense_Mutation	SNP	T	T	A	rs372390355	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383A>T	p.Gln128Leu	p.Q128L	ENST00000334701	3/12	30	18	12	21	21	0	HSP90AA1,missense_variant,p.Gln128Leu,ENST00000334701,;HSP90AA1,missense_variant,p.Gln6Leu,ENST00000553585,;HSP90AA1,missense_variant,p.Gln6Leu,ENST00000216281,;HSP90AA1,upstream_gene_variant,,ENST00000441629,;HSP90AA1,stop_gained,p.Arg58Ter,ENST00000557234,;HSP90AA1,non_coding_transcript_exon_variant,,ENST00000556554,;HSP90AA1,upstream_gene_variant,,ENST00000554401,;HSP90AA1,upstream_gene_variant,,ENST00000555662,;HSP90AA1,upstream_gene_variant,,ENST00000560130,;HSP90AA1,upstream_gene_variant,,ENST00000557089,;	A	ENSG00000080824	ENST00000334701	Transcript	missense_variant	665	383	128	Q/L	cAg/cTg	rs372390355	.	.	-1	HSP90AA1	HGNC	5253	protein_coding	YES	CCDS32160.1	ENSP00000335153	HS90A_HUMAN	Q96HX7_HUMAN,Q8TBA7_HUMAN,Q86SX1_HUMAN,K9JA46_HUMAN	UPI0000408144	.	tolerated_low_confidence(0.24)	benign(0.194)	3/12	.	hmmpanther:PTHR11528	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCTGGGTT	.	5	ESCA
OR4K2	0	.	GRCh37	14	20345270	20345270	+	Silent	SNP	C	C	T	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.844C>T	p.%3D	p.L282L	ENST00000298642	1/1	35	32	3	35	35	0	OR4K2,synonymous_variant,p.%3D,ENST00000298642,;	T	ENSG00000165762	ENST00000298642	Transcript	synonymous_variant	880	844	282	L	Ctg/Ttg	COSM697702	.	.	1	OR4K2	HGNC	14728	protein_coding	YES	CCDS32023.1	ENSP00000298642	OR4K2_HUMAN	.	UPI0000041B4D	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF260,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACTCTGAAC	.	2	ESCA
SSTR1	0	.	GRCh37	14	38681377	38681377	+	3'UTR	SNP	T	T	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1607T>C	.	.	ENST00000267377	3/3	19	15	4	21	21	0	SSTR1,3_prime_UTR_variant,,ENST00000267377,;	C	ENSG00000139874	ENST00000267377	Transcript	3_prime_UTR_variant	3400	.	.	.	.	.	.	.	1	SSTR1	HGNC	11330	protein_coding	YES	CCDS9666.1	ENSP00000267377	SSR1_HUMAN	.	UPI0000001C3C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACATATATA	.	5	ESCA
PRPF39	0	.	GRCh37	14	45584672	45584672	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*556G>A	.	.	ENST00000355765	14/14	67	54	13	52	52	0	PRPF39,3_prime_UTR_variant,,ENST00000355765,;FKBP3,downstream_gene_variant,,ENST00000396062,;FKBP3,downstream_gene_variant,,ENST00000216330,;SNORD127,downstream_gene_variant,,ENST00000458892,;PRPF39,3_prime_UTR_variant,,ENST00000554439,;PRPF39,3_prime_UTR_variant,,ENST00000424478,;PRPF39,3_prime_UTR_variant,,ENST00000554429,;PRPF39,3_prime_UTR_variant,,ENST00000554081,;PRPF39,non_coding_transcript_exon_variant,,ENST00000554785,;PRPF39,non_coding_transcript_exon_variant,,ENST00000477626,;PRPF39,downstream_gene_variant,,ENST00000556718,;	A	ENSG00000185246	ENST00000355765	Transcript	3_prime_UTR_variant	2736	.	.	.	.	.	.	.	1	PRPF39	HGNC	20314	protein_coding	YES	CCDS9682.2	ENSP00000348010	PRP39_HUMAN	.	UPI00015BB2D5	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATGAAAAT	.	5	ESCA
PLEKHH1	0	.	GRCh37	14	68054480	68054480	+	3'UTR	SNP	G	G	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*528G>T	.	.	ENST00000329153	29/29	18	11	7	10	10	0	PLEKHH1,3_prime_UTR_variant,,ENST00000329153,;PIGH,intron_variant,,ENST00000561272,;PIGH,downstream_gene_variant,,ENST00000558493,;PIGH,downstream_gene_variant,,ENST00000559581,;PIGH,downstream_gene_variant,,ENST00000558987,;PLEKHH1,downstream_gene_variant,,ENST00000417684,;PIGH,downstream_gene_variant,,ENST00000560722,;PIGH,downstream_gene_variant,,ENST00000216452,;PIGH,downstream_gene_variant,,ENST00000559415,;PLEKHH1,downstream_gene_variant,,ENST00000559832,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000559981,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000558214,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000557971,;PLEKHH1,intron_variant,,ENST00000559168,;PIGH,downstream_gene_variant,,ENST00000559118,;PIGH,downstream_gene_variant,,ENST00000561303,;PLEKHH1,downstream_gene_variant,,ENST00000561057,;PIGH,downstream_gene_variant,,ENST00000558198,;PLEKHH1,downstream_gene_variant,,ENST00000558386,;PLEKHH1,downstream_gene_variant,,ENST00000561370,;PIGH,downstream_gene_variant,,ENST00000558001,;PLEKHH1,downstream_gene_variant,,ENST00000559766,;PLEKHH1,downstream_gene_variant,,ENST00000558366,;	T	ENSG00000054690	ENST00000329153	Transcript	3_prime_UTR_variant	4755	.	.	.	.	.	.	.	1	PLEKHH1	HGNC	17733	protein_coding	YES	CCDS45128.1	ENSP00000330278	PKHH1_HUMAN	B3KWD2_HUMAN	UPI00001C1F64	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTGGTCTCG	.	5	ESCA
TSHR	0	.	GRCh37	14	81609998	81609998	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1596G>A	p.%3D	p.K532K	ENST00000541158	11/11	38	26	11	28	28	0	TSHR,synonymous_variant,p.%3D,ENST00000298171,;TSHR,synonymous_variant,p.%3D,ENST00000541158,;RP11-114N19.3,intron_variant,,ENST00000557775,;	A	ENSG00000165409	ENST00000541158	Transcript	synonymous_variant	1918	1596	532	K	aaG/aaA	.	.	.	1	TSHR	HGNC	12373	protein_coding	YES	CCDS9872.1	ENSP00000441235	.	Q0VAP8_HUMAN,F5GYU5_HUMAN	UPI000013E4A2	.	.	.	11/11	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,Pfam_domain:PF00001,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF0,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGAAGATCCG	.	5	ESCA
ATG2B	0	.	GRCh37	14	96752109	96752109	+	Missense_Mutation	SNP	G	G	A	rs778399547	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6220C>T	p.Arg2074Cys	p.R2074C	ENST00000359933	42/42	25	12	12	15	15	0	ATG2B,missense_variant,p.Arg2074Cys,ENST00000359933,;ATG2B,downstream_gene_variant,,ENST00000261834,;ATG2B,downstream_gene_variant,,ENST00000555263,;ATG2B,downstream_gene_variant,,ENST00000553643,;	A	ENSG00000066739	ENST00000359933	Transcript	missense_variant	7114	6220	2074	R/C	Cgc/Tgc	rs778399547,COSM254555	.	.	-1	ATG2B	HGNC	20187	protein_coding	YES	CCDS9944.2	ENSP00000353010	ATG2B_HUMAN	.	UPI000155D51F	.	deleterious(0)	probably_damaging(0.995)	42/42	.	hmmpanther:PTHR13190:SF19,hmmpanther:PTHR13190,Pfam_domain:PF09333	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GTGGCGCCATT	.	4	ESCA
SNORD115-1	0	.	GRCh37	15	25415878	25415878	+	RNA	SNP	G	G	A	rs748518587	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.9G>A	.	.	ENST00000364961	1/1	46	38	8	51	51	0	SNORD115-1,non_coding_transcript_exon_variant,,ENST00000364961,;SNORD115-3,upstream_gene_variant,,ENST00000363100,;SNORD115-2,upstream_gene_variant,,ENST00000362842,;SNHG14,intron_variant,,ENST00000553149,;SNHG14,upstream_gene_variant,,ENST00000441592,;TMEM261P1,upstream_gene_variant,,ENST00000604899,;	A	ENSG00000201831	ENST00000364961	Transcript	non_coding_transcript_exon_variant	9	.	.	.	.	rs748518587	.	.	1	SNORD115-1	HGNC	33020	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATGATGAG	byFrequency	5	ESCA
DISP2	0	.	GRCh37	15	40662376	40662376	+	Missense_Mutation	SNP	G	G	A	rs146679685	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4063G>A	p.Ala1355Thr	p.A1355T	ENST00000267889	8/8	66	48	18	47	45	1	DISP2,missense_variant,p.Ala1355Thr,ENST00000267889,;DISP2,intron_variant,,ENST00000558623,;LINC00594,upstream_gene_variant,,ENST00000561261,;RP11-64K12.4,upstream_gene_variant,,ENST00000558421,;RP11-64K12.10,upstream_gene_variant,,ENST00000567002,;DISP2,downstream_gene_variant,,ENST00000559721,;	A	ENSG00000140323	ENST00000267889	Transcript	missense_variant	4150	4063	1355	A/T	Gct/Act	rs146679685,COSM258884	.	.	1	DISP2	HGNC	19712	protein_coding	YES	CCDS10056.1	ENSP00000267889	DISP2_HUMAN	.	UPI0000160F9B	.	tolerated_low_confidence(0.23)	benign(0.006)	8/8	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGCCCGCTTCC	byCluster	4	ESCA
MFAP1	0	.	GRCh37	15	44105232	44105233	+	Frame_Shift_Ins	INS	-	-	TTCC	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.836_839dupGGAA	p.Val281GlufsTer19	p.V281Efs*19	ENST00000267812	6/9	65	40	25	58	58	0	MFAP1,frameshift_variant,p.Val281GlufsTer19,ENST00000267812,;MFAP1,upstream_gene_variant,,ENST00000484386,;	TTCC	ENSG00000140259	ENST00000267812	Transcript	frameshift_variant	1072-1073	839-840	280	K/KEX	aaa/aaGGAAa	.	.	.	-1	MFAP1	HGNC	7032	protein_coding	YES	CCDS10105.1	ENSP00000267812	MFAP1_HUMAN	.	UPI000013D770	.	.	.	6/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15327,hmmpanther:PTHR15327:SF0,Pfam_domain:PF06991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGAACTTTCCA	.	3	ESCA
MYO5C	0	.	GRCh37	15	52513403	52513403	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3677A>C	p.Gln1226Pro	p.Q1226P	ENST00000261839	30/41	71	52	18	54	54	0	MYO5C,missense_variant,p.Gln1226Pro,ENST00000261839,;MYO5C,3_prime_UTR_variant,,ENST00000560809,;	G	ENSG00000128833	ENST00000261839	Transcript	missense_variant	3839	3677	1226	Q/P	cAa/cCa	.	.	.	-1	MYO5C	HGNC	7604	protein_coding	YES	CCDS42036.1	ENSP00000261839	MYO5C_HUMAN	Q14783_HUMAN,H0YM93_HUMAN	UPI000013D20E	.	tolerated(0.07)	benign(0.089)	30/41	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF313,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTTGCTTC	.	5	ESCA
SEMA4B	0	.	GRCh37	15	90771613	90771613	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2252G>A	p.Gly751Glu	p.G751E	ENST00000411539	14/14	35	21	14	24	24	0	SEMA4B,missense_variant,p.Gly751Glu,ENST00000332496,;SEMA4B,missense_variant,p.Gly751Glu,ENST00000411539,;SEMA4B,3_prime_UTR_variant,,ENST00000559247,;SEMA4B,intron_variant,,ENST00000379122,;SEMA4B,intron_variant,,ENST00000559074,;SEMA4B,downstream_gene_variant,,ENST00000559983,;CIB1,downstream_gene_variant,,ENST00000328649,;SEMA4B,3_prime_UTR_variant,,ENST00000560089,;SEMA4B,non_coding_transcript_exon_variant,,ENST00000558065,;SEMA4B,downstream_gene_variant,,ENST00000560993,;SEMA4B,downstream_gene_variant,,ENST00000561252,;SEMA4B,downstream_gene_variant,,ENST00000561321,;SEMA4B,downstream_gene_variant,,ENST00000558975,;	A	ENSG00000185033	ENST00000411539	Transcript	missense_variant	2512	2252	751	G/E	gGg/gAg	.	.	.	1	SEMA4B	HGNC	10730	protein_coding	YES	CCDS45347.1	ENSP00000394720	.	Q4VBY2_HUMAN,J3KNP4_HUMAN,H0YMR1_HUMAN,H0YMD6_HUMAN,H0YLN3_HUMAN	UPI0000197391	.	deleterious(0.01)	probably_damaging(0.992)	14/14	.	hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCAGGGGGAAT	.	4	ESCA
PRC1	0	.	GRCh37	15	91525181	91525181	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298G>C	p.Glu100Gln	p.E100Q	ENST00000394249	4/15	57	47	10	38	38	0	PRC1,missense_variant,p.Glu100Gln,ENST00000361188,;PRC1,missense_variant,p.Glu100Gln,ENST00000361919,;PRC1,missense_variant,p.Glu59Gln,ENST00000557905,;PRC1,missense_variant,p.Glu59Gln,ENST00000442656,;PRC1,missense_variant,p.Glu100Gln,ENST00000394249,;PRC1,downstream_gene_variant,,ENST00000559811,;PRC1,upstream_gene_variant,,ENST00000559828,;PRC1-AS1,splice_region_variant,,ENST00000554388,;Y_RNA,upstream_gene_variant,,ENST00000363272,;PRC1,non_coding_transcript_exon_variant,,ENST00000555745,;PRC1,downstream_gene_variant,,ENST00000556129,;PRC1,non_coding_transcript_exon_variant,,ENST00000417173,;PRC1,non_coding_transcript_exon_variant,,ENST00000553494,;PRC1,non_coding_transcript_exon_variant,,ENST00000555791,;PRC1,non_coding_transcript_exon_variant,,ENST00000560605,;PRC1,non_coding_transcript_exon_variant,,ENST00000557763,;PRC1,upstream_gene_variant,,ENST00000560914,;PRC1,upstream_gene_variant,,ENST00000556982,;	G	ENSG00000198901	ENST00000394249	Transcript	missense_variant	376	298	100	E/Q	Gaa/Caa	.	.	.	-1	PRC1	HGNC	9341	protein_coding	YES	CCDS32334.1	ENSP00000377793	PRC1_HUMAN	.	UPI00001A5ED8	.	deleterious(0)	probably_damaging(0.997)	4/15	.	Pfam_domain:PF03999,hmmpanther:PTHR19321:SF1,hmmpanther:PTHR19321,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTCTAGTT	.	5	ESCA
FAM169B	0	.	GRCh37	15	98981477	98981477	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1383C>T	.	.	ENST00000558256	7/7	73	55	17	64	64	0	FAM169B,3_prime_UTR_variant,,ENST00000332908,;FAM169B,3_prime_UTR_variant,,ENST00000558256,;	A	ENSG00000185087	ENST00000558256	Transcript	3_prime_UTR_variant	2212	.	.	.	.	.	.	.	-1	FAM169B	HGNC	26835	protein_coding	YES	CCDS45360.1	ENSP00000453554	F169B_HUMAN	.	UPI0000199E5A	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACAGACGAT	.	5	ESCA
MPG	0	.	GRCh37	16	135510	135510	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Asp211Asn	p.D211N	ENST00000219431	5/5	64	52	12	53	53	0	MPG,missense_variant,p.Asp194Asn,ENST00000436333,;MPG,missense_variant,p.Asp206Asn,ENST00000356432,;MPG,missense_variant,p.Asp194Asn,ENST00000397817,;MPG,missense_variant,p.Asp211Asn,ENST00000219431,;NPRL3,downstream_gene_variant,,ENST00000399953,;NPRL3,downstream_gene_variant,,ENST00000399951,;NPRL3,downstream_gene_variant,,ENST00000405960,;NPRL3,downstream_gene_variant,,ENST00000428323,;NPRL3,3_prime_UTR_variant,,ENST00000445810,;NPRL3,intron_variant,,ENST00000463178,;NPRL3,downstream_gene_variant,,ENST00000399957,;	A	ENSG00000103152	ENST00000219431	Transcript	missense_variant	862	631	211	D/N	Gac/Aac	COSM71681	.	.	1	MPG	HGNC	7211	protein_coding	YES	CCDS32346.1	ENSP00000219431	3MG_HUMAN	Q1W6H1_HUMAN,A2IDA3_HUMAN	UPI000002A2C0	.	tolerated(0.08)	probably_damaging(0.918)	5/5	.	HAMAP:MF_00527,hmmpanther:PTHR10429,hmmpanther:PTHR10429:SF0,Gene3D:1ewnA00,TIGRFAM_domain:TIGR00567,Pfam_domain:PF02245,Superfamily_domains:SSF50486	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAGGACCGC	.	5	ESCA
SLC9A3R2	0	.	GRCh37	16	2088256	2088256	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*271G>A	.	.	ENST00000424542	7/7	78	66	12	69	69	0	SLC9A3R2,3_prime_UTR_variant,,ENST00000432365,;SLC9A3R2,3_prime_UTR_variant,,ENST00000424542,;SLC9A3R2,3_prime_UTR_variant,,ENST00000566198,;NTHL1,downstream_gene_variant,,ENST00000566380,;SLC9A3R2,downstream_gene_variant,,ENST00000563587,;NTHL1,downstream_gene_variant,,ENST00000219066,;SLC9A3R2,downstream_gene_variant,,ENST00000561844,;SLC9A3R2,downstream_gene_variant,,ENST00000567504,;SLC9A3R2,downstream_gene_variant,,ENST00000565855,;SLC9A3R2,downstream_gene_variant,,ENST00000565086,;NTHL1,downstream_gene_variant,,ENST00000562951,;NTHL1,downstream_gene_variant,,ENST00000568513,;NTHL1,downstream_gene_variant,,ENST00000561841,;NTHL1,downstream_gene_variant,,ENST00000561862,;NTHL1,downstream_gene_variant,,ENST00000565406,;SLC9A3R2,downstream_gene_variant,,ENST00000564033,;NTHL1,downstream_gene_variant,,ENST00000567727,;	A	ENSG00000065054	ENST00000424542	Transcript	3_prime_UTR_variant	1423	.	.	.	.	.	.	.	1	SLC9A3R2	HGNC	11076	protein_coding	YES	CCDS45382.1	ENSP00000408005	NHRF2_HUMAN	Q6NTG0_HUMAN,H3BQS0_HUMAN	UPI0000070578	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGACAGAGAGA	.	3	ESCA
DNAH3	0	.	GRCh37	16	21139069	21139069	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000261383	8/62	46	37	8	52	52	0	DNAH3,stop_gained,p.Gln383Ter,ENST00000261383,;DNAH3,stop_gained,p.Gln383Ter,ENST00000415178,;CTC-508F8.1,intron_variant,,ENST00000575612,;DNAH3,non_coding_transcript_exon_variant,,ENST00000396036,;	A	ENSG00000158486	ENST00000261383	Transcript	stop_gained	1147	1147	383	Q/*	Cag/Tag	.	.	.	-1	DNAH3	HGNC	2949	protein_coding	YES	CCDS10594.1	ENSP00000261383	DYH3_HUMAN	.	UPI00001100F2	.	.	.	8/62	.	hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTGAGGCT	.	5	ESCA
MVP	0	.	GRCh37	16	29859260	29859260	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000357402	15/15	46	42	4	44	44	0	MVP,stop_gained,p.Gln878Ter,ENST00000395353,;MVP,stop_gained,p.Gln878Ter,ENST00000357402,;	T	ENSG00000013364	ENST00000357402	Transcript	stop_gained	2770	2632	878	Q/*	Cag/Tag	.	.	.	1	MVP	HGNC	7531	protein_coding	YES	CCDS10656.1	ENSP00000349977	MVP_HUMAN	H3BUK7_HUMAN,H3BRL2_HUMAN,H3BQK6_HUMAN,H3BP76_HUMAN,H3BNF2_HUMAN	UPI000012FA9C	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGCTCAGGCC	.	3	ESCA
CORO7	0	.	GRCh37	16	4411430	4411430	+	Missense_Mutation	SNP	G	G	A	rs200682379	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1619C>T	p.Thr540Met	p.T540M	ENST00000251166	17/28	62	58	4	28	28	0	CORO7,missense_variant,p.Thr320Met,ENST00000539968,;CORO7,missense_variant,p.Thr455Met,ENST00000574025,;CORO7-PAM16,missense_variant,p.Thr540Met,ENST00000572467,;CORO7,missense_variant,p.Thr522Met,ENST00000537233,;CORO7,missense_variant,p.Thr540Met,ENST00000251166,;CORO7,3_prime_UTR_variant,,ENST00000423908,;CORO7,upstream_gene_variant,,ENST00000570779,;CORO7,downstream_gene_variant,,ENST00000572044,;CORO7,downstream_gene_variant,,ENST00000572549,;CORO7-PAM16,upstream_gene_variant,,ENST00000572274,;CORO7,missense_variant,p.Arg102Cys,ENST00000576437,;CORO7-PAM16,3_prime_UTR_variant,,ENST00000575334,;CORO7,3_prime_UTR_variant,,ENST00000571227,;CORO7,3_prime_UTR_variant,,ENST00000574311,;CORO7,non_coding_transcript_exon_variant,,ENST00000575714,;CORO7,non_coding_transcript_exon_variant,,ENST00000572666,;CORO7,non_coding_transcript_exon_variant,,ENST00000575531,;CORO7,downstream_gene_variant,,ENST00000571756,;CORO7,upstream_gene_variant,,ENST00000574849,;CORO7,upstream_gene_variant,,ENST00000576637,;CORO7,downstream_gene_variant,,ENST00000573773,;CORO7,upstream_gene_variant,,ENST00000572125,;	A	ENSG00000262246	ENST00000251166	Transcript	missense_variant	1765	1619	540	T/M	aCg/aTg	rs200682379	.	.	-1	CORO7	HGNC	26161	protein_coding	YES	CCDS10513.1	ENSP00000251166	CORO7_HUMAN	I3L258_HUMAN,B3KSY4_HUMAN	UPI00001FF898	.	deleterious(0)	probably_damaging(1)	17/28	.	PROSITE_profiles:PS50294,hmmpanther:PTHR10856:SF20,hmmpanther:PTHR10856,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:0049172	A:0.0008	A:0.0015	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCGTGGGC	byFrequency|byCluster|by1000G	2	ESCA
SLC7A6	0	.	GRCh37	16	68332803	68332803	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1572G>A	.	.	ENST00000566454	12/12	27	19	8	17	17	0	SLC7A6,3_prime_UTR_variant,,ENST00000219343,;SLC7A6,3_prime_UTR_variant,,ENST00000566454,;SLC7A6OS,3_prime_UTR_variant,,ENST00000263997,;SLC7A6OS,downstream_gene_variant,,ENST00000561590,;SLC7A6,3_prime_UTR_variant,,ENST00000379152,;SLC7A6OS,non_coding_transcript_exon_variant,,ENST00000561933,;SLC7A6OS,intron_variant,,ENST00000568315,;SLC7A6,downstream_gene_variant,,ENST00000567325,;SLC7A6,downstream_gene_variant,,ENST00000563208,;SLC7A6,downstream_gene_variant,,ENST00000567346,;SLC7A6,downstream_gene_variant,,ENST00000562863,;SLC7A6OS,downstream_gene_variant,,ENST00000568538,;	A	ENSG00000103064	ENST00000566454	Transcript	3_prime_UTR_variant	3389	.	.	.	.	.	.	.	1	SLC7A6	HGNC	11064	protein_coding	YES	CCDS32470.1	ENSP00000455064	YLAT2_HUMAN	H3BUA4_HUMAN,H3BSV7_HUMAN,H3BSB6_HUMAN,H3BPV6_HUMAN,H3BPK5_HUMAN	UPI0000071C50	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGGAATTG	.	5	ESCA
ZNF469	0	.	GRCh37	16	88505440	88505440	+	Silent	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11478C>A	p.%3D	p.P3826P	ENST00000437464	2/2	45	37	8	23	23	0	ZNF469,synonymous_variant,p.%3D,ENST00000565624,;ZNF469,synonymous_variant,p.%3D,ENST00000437464,;	A	ENSG00000225614	ENST00000437464	Transcript	synonymous_variant	11478	11478	3826	P	ccC/ccA	.	.	.	1	ZNF469	HGNC	23216	protein_coding	YES	CCDS45544.1	ENSP00000402343	ZN469_HUMAN	.	UPI0000DD837B	.	.	.	2/2	.	hmmpanther:PTHR21465,hmmpanther:PTHR21465:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCCCAGCCG	.	5	ESCA
LYRM9	0	.	GRCh37	17	26206315	26206315	+	3'UTR	SNP	A	A	G	rs369671199	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*184T>C	.	.	ENST00000379103	5/5	12	8	4	10	10	0	LYRM9,3_prime_UTR_variant,,ENST00000460380,;LYRM9,3_prime_UTR_variant,,ENST00000379103,;LYRM9,3_prime_UTR_variant,,ENST00000508862,;RP1-66C13.4,intron_variant,,ENST00000582441,;LYRM9,downstream_gene_variant,,ENST00000379102,;LYRM9,downstream_gene_variant,,ENST00000503642,;LYRM9,downstream_gene_variant,,ENST00000508816,;RP11-138P22.1,non_coding_transcript_exon_variant,,ENST00000581901,;	G	ENSG00000232859	ENST00000379103	Transcript	3_prime_UTR_variant	710	.	.	.	.	rs369671199	.	.	-1	LYRM9	HGNC	27314	protein_coding	YES	CCDS45631.1	ENSP00000368397	LYRM9_HUMAN	J3QLB4_HUMAN	UPI00002014C2	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCAAACATAA	.	3	ESCA
SDF2	0	.	GRCh37	17	26988906	26988906	+	5'UTR	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12G>C	.	.	ENST00000247020	1/3	20	12	8	24	24	0	SDF2,5_prime_UTR_variant,,ENST00000247020,;SUPT6H,upstream_gene_variant,,ENST00000314616,;SUPT6H,upstream_gene_variant,,ENST00000347486,;SDF2,non_coding_transcript_exon_variant,,ENST00000585428,;SDF2,intron_variant,,ENST00000592250,;SDF2,intron_variant,,ENST00000585749,;SDF2,intron_variant,,ENST00000588472,;SDF2,intron_variant,,ENST00000587338,;SDF2,upstream_gene_variant,,ENST00000587629,;SDF2,upstream_gene_variant,,ENST00000591903,;	G	ENSG00000132581	ENST00000247020	Transcript	5_prime_UTR_variant	288	.	.	.	.	.	.	.	-1	SDF2	HGNC	10675	protein_coding	YES	CCDS11238.1	ENSP00000247020	SDF2_HUMAN	Q6IBU4_HUMAN	UPI000013CC0C	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTATCGCGGA	.	5	ESCA
MYO1D	0	.	GRCh37	17	30821801	30821801	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2997C>T	p.%3D	p.F999F	ENST00000318217	22/22	56	51	4	32	32	0	MYO1D,synonymous_variant,p.%3D,ENST00000394649,;MYO1D,synonymous_variant,p.%3D,ENST00000318217,;CDK5R1,downstream_gene_variant,,ENST00000313401,;RP11-466A19.1,upstream_gene_variant,,ENST00000581360,;MYO1D,non_coding_transcript_exon_variant,,ENST00000577576,;MYO1D,non_coding_transcript_exon_variant,,ENST00000577352,;	A	ENSG00000176658	ENST00000318217	Transcript	synonymous_variant	3302	2997	999	F	ttC/ttT	.	.	.	-1	MYO1D	HGNC	7598	protein_coding	YES	CCDS32615.1	ENSP00000324527	MYO1D_HUMAN	Q8N618_HUMAN,K7EIG7_HUMAN	UPI0000186004	.	.	.	22/22	.	Pfam_domain:PF06017	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGATGAAGCC	.	2	ESCA
SPOP	0	.	GRCh37	17	47676686	47676686	+	3'UTR	SNP	T	T	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1054A>T	.	.	ENST00000393331	12/12	32	29	3	23	23	0	SPOP,3_prime_UTR_variant,,ENST00000393331,;SPOP,3_prime_UTR_variant,,ENST00000393328,;SPOP,3_prime_UTR_variant,,ENST00000347630,;SPOP,downstream_gene_variant,,ENST00000503676,;SPOP,downstream_gene_variant,,ENST00000504102,;SPOP,downstream_gene_variant,,ENST00000507551,;SPOP,downstream_gene_variant,,ENST00000577134,;SPOP,downstream_gene_variant,,ENST00000572686,;	A	ENSG00000121067	ENST00000393331	Transcript	3_prime_UTR_variant	2650	.	.	.	.	.	.	.	-1	SPOP	HGNC	11254	protein_coding	YES	CCDS11551.1	ENSP00000377004	SPOP_HUMAN	D6RIS7_HUMAN,D6RGZ4_HUMAN,D6RFL7_HUMAN,D6RDV6_HUMAN,D6RDG8_HUMAN,D6RD94_HUMAN,D6RBH6_HUMAN,D6RA79_HUMAN,B4DUE7_HUMAN,B4DEE4_HUMAN	UPI0000003F5C	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAATTAACA	.	2	ESCA
CSHL1	0	.	GRCh37	17	61987321	61987321	+	Intron	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.472-53G>A	.	.	ENST00000309894	.	118	105	13	97	97	0	CSHL1,synonymous_variant,p.%3D,ENST00000561003,;CSHL1,synonymous_variant,p.%3D,ENST00000450719,;CSHL1,3_prime_UTR_variant,,ENST00000392824,;CSHL1,intron_variant,,ENST00000259003,;CSHL1,intron_variant,,ENST00000309894,;CSHL1,intron_variant,,ENST00000346606,;CSHL1,intron_variant,,ENST00000438387,;CSHL1,non_coding_transcript_exon_variant,,ENST00000558099,;CSHL1,non_coding_transcript_exon_variant,,ENST00000560999,;CSHL1,intron_variant,,ENST00000558609,;	T	ENSG00000204414	ENST00000309894	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CSHL1	HGNC	2442	protein_coding	YES	CCDS11652.1	ENSP00000309524	CSHL_HUMAN	I6L999_HUMAN	UPI00001602B9	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCTCCCTCT	.	4	ESCA
TP53	0	.	GRCh37	17	7578553	7578553	+	Missense_Mutation	SNP	T	T	G	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.377A>C	p.Tyr126Ser	p.Y126S	ENST00000269305	5/11	12	5	7	29	29	0	TP53,missense_variant,p.Tyr126Ser,ENST00000508793,;TP53,missense_variant,p.Tyr126Ser,ENST00000413465,;TP53,missense_variant,p.Tyr126Ser,ENST00000420246,;TP53,missense_variant,p.Tyr126Ser,ENST00000269305,;TP53,missense_variant,p.Tyr126Ser,ENST00000359597,;TP53,missense_variant,p.Tyr33Ser,ENST00000514944,;TP53,missense_variant,p.Tyr126Ser,ENST00000445888,;TP53,missense_variant,p.Tyr126Ser,ENST00000503591,;TP53,missense_variant,p.Tyr126Ser,ENST00000455263,;TP53,splice_region_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,splice_region_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	G	ENSG00000141510	ENST00000269305	Transcript	missense_variant	567	377	126	Y/S	tAc/tCc	CM115636,TP53_g.12365A>G,TP53_g.12365A>T,TP53_g.12365A>C,COSM11517,COSM249845,COSM44142,COSM1480081,COSM1610875,COSM1480082,COSM1610876,COSM3388228,COSM1731759,COSM1610877,COSM1480083	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Y126S|c.377A>C|3,CODON|p.0?|c.1_1182del1182|6,CODON|p.Y126_K132delYSPALNK|c.376_396del21|6,CODON|p.Y126_N131delYSPALN|c.376_393del18|3,CODON|p.Y126*|c.378C>G|3,CODON|p.Y126*|c.378C>G|4,CODON|p.Y126*|c.378C>G|3,CODON|p.Y126*|c.378C>A|4,CODON|p.Y33*|c.99C>G|3,CODON|p.Y126C|c.377A>G|6,CODON|p.Y33C|c.98A>G|6,CODON|p.Y126C|c.377A>G|3,CODON|p.Y126C|c.377A>G|6,CODON|p.Y126C|c.377A>G|9,CODON|p.Y126C|c.377A>G|5,BUFFER|p.L130F|c.388C>T|13,BUFFER|p.L130V|c.388C>G|5,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L130V|c.388C>G|3,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L37F|c.109C>T|7,BUFFER|p.L130F|c.388C>T|3,BUFFER|p.L130V|c.388C>G|5,BUFFER|p.L37V|c.109C>G|5,BUFFER|p.L130F|c.388C>T|4,BUFFER|p.L130V|c.388C>G|15,BUFFER|p.P128L|c.383C>T|3,BUFFER|p.P128fs*42|c.382delC|3,BUFFER|p.P128S|c.382C>T|7,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S127Y|c.380C>A|10,BUFFER|p.S34F|c.101C>T|11,BUFFER|p.S127F|c.380C>T|4,BUFFER|p.S127F|c.380C>T|33,BUFFER|p.S127F|c.380C>T|3,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S34P|c.100T>C|4,BUFFER|p.S34T|c.100T>A|4,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.S127P|c.379T>C|8,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127T|c.379T>A|10,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.Y126N|c.376T>A|7,BUFFER|p.Y33D|c.97T>G|7,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.Y126D|c.376T>G|10,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.?|c.97-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|10,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.97-1G>A|20,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>T|9,BUFFER|p.?|c.376-2A>G|4,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.97-2A>T|3,BUFFER|p.?|c.97-2A>G|10,BUFFER|p.?|c.376-2A>G|17,BUFFER|p.?|c.376-2A>G|10,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-2A>G|6,BUFFER|p.?|c.376-2A>C|4,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-4A>G|3	MUTECT|MUSE	GGGAGTACTGT	.	2	ESCA
CXADRP3	0	.	GRCh37	18	14478264	14478264	+	RNA	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1645C>T	.	.	ENST00000581457	4/4	62	58	4	40	40	0	CXADRP3,non_coding_transcript_exon_variant,,ENST00000581457,;	A	ENSG00000265766	ENST00000581457	Transcript	non_coding_transcript_exon_variant	1645	.	.	.	.	.	.	.	-1	CXADRP3	HGNC	33974	lincRNA	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGAGTTGGA	.	2	ESCA
ASXL3	0	.	GRCh37	18	31319196	31319196	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1828G>T	p.Glu610Ter	p.E610*	ENST00000269197	11/12	22	13	9	13	13	0	ASXL3,stop_gained,p.Glu610Ter,ENST00000269197,;ASXL3,3_prime_UTR_variant,,ENST00000592288,;	T	ENSG00000141431	ENST00000269197	Transcript	stop_gained	1828	1828	610	E/*	Gaa/Taa	.	.	.	1	ASXL3	HGNC	29357	protein_coding	YES	CCDS45847.1	ENSP00000269197	ASXL3_HUMAN	K7EQY1_HUMAN	UPI000156D0F3	.	.	.	11/12	.	hmmpanther:PTHR13578:SF18,hmmpanther:PTHR13578	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTGAAACG	.	4	ESCA
ACAA2	0	.	GRCh37	18	47311700	47311700	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.976C>A	p.Gln326Lys	p.Q326K	ENST00000285093	9/10	22	16	6	17	17	0	ACAA2,missense_variant,p.Gln326Lys,ENST00000285093,;ACAA2,missense_variant,p.Gln323Lys,ENST00000587994,;ACAA2,missense_variant,p.Gln271Lys,ENST00000589432,;ACAA2,non_coding_transcript_exon_variant,,ENST00000591171,;	T	ENSG00000167315	ENST00000285093	Transcript	missense_variant	1452	976	326	Q/K	Cag/Aag	.	.	.	-1	ACAA2	HGNC	83	protein_coding	YES	CCDS11939.1	ENSP00000285093	THIM_HUMAN	K7ER88_HUMAN,K7EME0_HUMAN,K7EJB1_HUMAN,K7EJ68_HUMAN	UPI000006FECE	.	deleterious(0)	probably_damaging(1)	9/10	.	hmmpanther:PTHR18919,hmmpanther:PTHR18919:SF67,Gene3D:3.40.47.10,Pfam_domain:PF02803,TIGRFAM_domain:TIGR01930,PIRSF_domain:PIRSF000429,Superfamily_domains:SSF53901	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACTGGGGAG	.	5	ESCA
SERPINB13	0	.	GRCh37	18	61264278	61264278	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.857C>G	p.Pro286Arg	p.P286R	ENST00000344731	8/8	49	30	19	47	47	0	SERPINB13,missense_variant,p.Pro286Arg,ENST00000344731,;SERPINB13,missense_variant,p.Pro234Arg,ENST00000269489,;SERPINB13,intron_variant,,ENST00000415733,;SERPINB13,downstream_gene_variant,,ENST00000431153,;SERPINB13,3_prime_UTR_variant,,ENST00000438844,;	G	ENSG00000197641	ENST00000344731	Transcript	missense_variant	959	857	286	P/R	cCc/cGc	.	.	.	1	SERPINB13	HGNC	8944	protein_coding	YES	CCDS11985.1	ENSP00000341584	SPB13_HUMAN	.	UPI000004EE29	.	deleterious(0)	probably_damaging(1)	8/8	.	hmmpanther:PTHR11461:SF152,hmmpanther:PTHR11461,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGCCCCGGT	.	5	ESCA
TYMS	0	.	GRCh37	18	671442	671442	+	Silent	SNP	G	G	A	rs549187782	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.795G>A	p.%3D	p.L265L	ENST00000323274	6/7	76	69	7	63	63	0	TYMS,synonymous_variant,p.%3D,ENST00000323224,;TYMS,synonymous_variant,p.%3D,ENST00000323250,;TYMS,synonymous_variant,p.%3D,ENST00000323274,;ENOSF1,downstream_gene_variant,,ENST00000251101,;ENOSF1,downstream_gene_variant,,ENST00000383578,;ENOSF1,downstream_gene_variant,,ENST00000580982,;ENOSF1,downstream_gene_variant,,ENST00000319815,;ENOSF1,downstream_gene_variant,,ENST00000340116,;TYMS,non_coding_transcript_exon_variant,,ENST00000581920,;ENOSF1,downstream_gene_variant,,ENST00000583973,;ENOSF1,downstream_gene_variant,,ENST00000581928,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000584259,;TYMS,downstream_gene_variant,,ENST00000579128,;ENOSF1,downstream_gene_variant,,ENST00000582745,;ENOSF1,downstream_gene_variant,,ENST00000581475,;ENOSF1,downstream_gene_variant,,ENST00000585128,;ENOSF1,downstream_gene_variant,,ENST00000581906,;ENOSF1,downstream_gene_variant,,ENST00000584646,;ENOSF1,downstream_gene_variant,,ENST00000584453,;	A	ENSG00000176890	ENST00000323274	Transcript	synonymous_variant	934	795	265	L	ctG/ctA	rs549187782	.	.	1	TYMS	HGNC	12441	protein_coding	YES	CCDS11821.1	ENSP00000315644	TYSY_HUMAN	Q53Y97_HUMAN	UPI0000001225	.	.	.	6/7	.	HAMAP:MF_00008,hmmpanther:PTHR11549,Gene3D:3.30.572.10,Pfam_domain:PF00303,TIGRFAM_domain:TIGR03284,Superfamily_domains:SSF55831	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCACTGAAAAT	by1000G	3	ESCA
YES1	0	.	GRCh37	18	723785	723785	+	3'UTR	SNP	T	T	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*639A>G	.	.	ENST00000584307	12/12	76	50	26	51	51	0	YES1,3_prime_UTR_variant,,ENST00000314574,;YES1,3_prime_UTR_variant,,ENST00000584307,;YES1,3_prime_UTR_variant,,ENST00000577961,;	C	ENSG00000176105	ENST00000584307	Transcript	3_prime_UTR_variant	2442	.	.	.	.	.	.	.	-1	YES1	HGNC	12841	protein_coding	YES	CCDS11824.1	ENSP00000462468	YES_HUMAN	.	UPI0000062316	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAATATTAA	.	5	ESCA
MRPL4	0	.	GRCh37	19	10370426	10370426	+	Silent	SNP	C	C	T	rs147343809	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.873C>T	p.%3D	p.S291S	ENST00000253099	9/9	43	26	16	39	39	0	MRPL4,synonymous_variant,p.%3D,ENST00000253099,;MRPL4,synonymous_variant,p.%3D,ENST00000307422,;MRPL4,synonymous_variant,p.%3D,ENST00000592514,;MRPL4,3_prime_UTR_variant,,ENST00000393733,;MRPL4,downstream_gene_variant,,ENST00000588502,;MRPL4,downstream_gene_variant,,ENST00000590702,;MRPL4,downstream_gene_variant,,ENST00000590669,;MRPL4,downstream_gene_variant,,ENST00000590150,;CTD-2369P2.4,intron_variant,,ENST00000587088,;CTD-2369P2.5,intron_variant,,ENST00000592893,;MRPL4,downstream_gene_variant,,ENST00000591054,;MRPL4,downstream_gene_variant,,ENST00000592071,;	T	ENSG00000105364	ENST00000253099	Transcript	synonymous_variant	1160	873	291	S	agC/agT	rs147343809	.	.	1	MRPL4	HGNC	14276	protein_coding	YES	CCDS12230.1	ENSP00000253099	RM04_HUMAN	K7ES61_HUMAN,K7EJ73_HUMAN	UPI0000072264	.	.	.	9/9	.	hmmpanther:PTHR10746:SF9,hmmpanther:PTHR10746	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAGCGACTT	byCluster|by1000G	5	ESCA
RGS9BP	0	.	GRCh37	19	33168099	33168099	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*222G>A	.	.	ENST00000334176	1/1	78	45	32	52	52	0	RGS9BP,3_prime_UTR_variant,,ENST00000334176,;ANKRD27,upstream_gene_variant,,ENST00000586693,;ANKRD27,upstream_gene_variant,,ENST00000306065,;ANKRD27,upstream_gene_variant,,ENST00000587352,;ANKRD27,upstream_gene_variant,,ENST00000586463,;ANKRD27,upstream_gene_variant,,ENST00000590519,;CTC-379B2.4,downstream_gene_variant,,ENST00000589127,;ANKRD27,upstream_gene_variant,,ENST00000588700,;	A	ENSG00000186326	ENST00000334176	Transcript	3_prime_UTR_variant	1787	.	.	.	.	.	.	.	1	RGS9BP	HGNC	30304	protein_coding	YES	CCDS12424.1	ENSP00000334134	R9BP_HUMAN	.	UPI0000198BA8	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAACGTCTGC	.	5	ESCA
DMKN	0	.	GRCh37	19	35994206	35994206	+	Intron	DEL	T	T	-	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135-418delA	.	.	ENST00000339686	.	142	106	36	85	85	0	DMKN,3_prime_UTR_variant,,ENST00000447113,;DMKN,3_prime_UTR_variant,,ENST00000474928,;DMKN,3_prime_UTR_variant,,ENST00000461300,;DMKN,3_prime_UTR_variant,,ENST00000488892,;DMKN,intron_variant,,ENST00000602679,;DMKN,intron_variant,,ENST00000434389,;DMKN,intron_variant,,ENST00000492341,;DMKN,intron_variant,,ENST00000602781,;DMKN,intron_variant,,ENST00000472252,;DMKN,intron_variant,,ENST00000419602,;DMKN,intron_variant,,ENST00000429837,;DMKN,intron_variant,,ENST00000467637,;DMKN,intron_variant,,ENST00000480502,;DMKN,intron_variant,,ENST00000443640,;DMKN,intron_variant,,ENST00000414866,;DMKN,intron_variant,,ENST00000402589,;DMKN,intron_variant,,ENST00000436012,;DMKN,intron_variant,,ENST00000339686,;DMKN,downstream_gene_variant,,ENST00000424570,;DMKN,downstream_gene_variant,,ENST00000418261,;DMKN,downstream_gene_variant,,ENST00000392206,;DMKN,downstream_gene_variant,,ENST00000458071,;DMKN,downstream_gene_variant,,ENST00000450261,;DMKN,upstream_gene_variant,,ENST00000601650,;DMKN,downstream_gene_variant,,ENST00000440396,;DMKN,upstream_gene_variant,,ENST00000593342,;DMKN,downstream_gene_variant,,ENST00000451297,;DMKN,upstream_gene_variant,,ENST00000408915,;DMKN,non_coding_transcript_exon_variant,,ENST00000474992,;DMKN,non_coding_transcript_exon_variant,,ENST00000476051,;DMKN,intron_variant,,ENST00000462126,;DMKN,upstream_gene_variant,,ENST00000466587,;DMKN,3_prime_UTR_variant,,ENST00000470746,;DMKN,3_prime_UTR_variant,,ENST00000480507,;DMKN,3_prime_UTR_variant,,ENST00000595571,;DMKN,3_prime_UTR_variant,,ENST00000462538,;DMKN,non_coding_transcript_exon_variant,,ENST00000489395,;DMKN,intron_variant,,ENST00000486450,;DMKN,intron_variant,,ENST00000498211,;DMKN,intron_variant,,ENST00000498269,;DMKN,intron_variant,,ENST00000460051,;DMKN,intron_variant,,ENST00000464709,;DMKN,intron_variant,,ENST00000476246,;DMKN,intron_variant,,ENST00000463292,;DMKN,intron_variant,,ENST00000462721,;DMKN,intron_variant,,ENST00000464894,;DMKN,intron_variant,,ENST00000493979,;DMKN,intron_variant,,ENST00000597212,;DMKN,intron_variant,,ENST00000465927,;DMKN,intron_variant,,ENST00000488542,;DMKN,intron_variant,,ENST00000482321,;DMKN,intron_variant,,ENST00000471786,;DMKN,intron_variant,,ENST00000490622,;DMKN,intron_variant,,ENST00000493517,;DMKN,intron_variant,,ENST00000498593,;DMKN,intron_variant,,ENST00000471017,;DMKN,intron_variant,,ENST00000467532,;DMKN,intron_variant,,ENST00000483855,;DMKN,intron_variant,,ENST00000488762,;DMKN,upstream_gene_variant,,ENST00000469960,;DMKN,upstream_gene_variant,,ENST00000478648,;DMKN,upstream_gene_variant,,ENST00000601368,;DMKN,upstream_gene_variant,,ENST00000486756,;DMKN,upstream_gene_variant,,ENST00000470964,;DMKN,upstream_gene_variant,,ENST00000460327,;DMKN,upstream_gene_variant,,ENST00000484064,;	-	ENSG00000161249	ENST00000339686	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DMKN	HGNC	25063	protein_coding	YES	CCDS12463.1	ENSP00000342012	DMKN_HUMAN	R4GMQ0_HUMAN	UPI00002020EB	.	.	.	.	9/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGAGTGTGGG	.	3	ESCA
ATCAY	0	.	GRCh37	19	3902495	3902495	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88G>C	p.Glu30Gln	p.E30Q	ENST00000450849	3/13	29	25	3	26	26	0	ATCAY,missense_variant,p.Glu36Gln,ENST00000398448,;ATCAY,missense_variant,p.Glu30Gln,ENST00000598136,;ATCAY,missense_variant,p.Glu30Gln,ENST00000600960,;ATCAY,missense_variant,p.Glu30Gln,ENST00000301260,;ATCAY,missense_variant,p.Glu30Gln,ENST00000450849,;ATCAY,missense_variant,p.Gln53His,ENST00000597739,;	C	ENSG00000167654	ENST00000450849	Transcript	missense_variant	555	88	30	E/Q	Gaa/Caa	.	.	.	1	ATCAY	HGNC	779	protein_coding	YES	CCDS45923.1	ENSP00000390941	ATCAY_HUMAN	M0R197_HUMAN	UPI000006DE3B	.	deleterious(0.02)	possibly_damaging(0.653)	3/13	.	hmmpanther:PTHR12112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TCCCAGAAGAG	.	2	ESCA
PRR12	0	.	GRCh37	19	50102744	50102744	+	Silent	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3894C>G	p.%3D	p.L1298L	ENST00000418929	5/14	74	54	20	45	45	0	PRR12,synonymous_variant,p.%3D,ENST00000418929,;	G	ENSG00000126464	ENST00000418929	Transcript	synonymous_variant	3906	3894	1298	L	ctC/ctG	.	.	.	1	PRR12	HGNC	29217	protein_coding	YES	CCDS46143.1	ENSP00000394510	PRR12_HUMAN	.	UPI0001596889	.	.	.	5/14	.	hmmpanther:PTHR14709:SF1,hmmpanther:PTHR14709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACTCTACCA	.	5	ESCA
MED25	0	.	GRCh37	19	50334095	50334095	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1052C>A	p.Ala351Asp	p.A351D	ENST00000312865	9/18	17	13	4	11	11	0	MED25,missense_variant,p.Ala138Asp,ENST00000538643,;MED25,missense_variant,p.Ala351Asp,ENST00000312865,;MED25,intron_variant,,ENST00000595185,;MED25,upstream_gene_variant,,ENST00000593767,;MED25,upstream_gene_variant,,ENST00000594998,;MED25,upstream_gene_variant,,ENST00000599722,;	A	ENSG00000104973	ENST00000312865	Transcript	missense_variant	1105	1052	351	A/D	gCc/gAc	.	.	.	1	MED25	HGNC	28845	protein_coding	YES	CCDS33075.1	ENSP00000326767	MED25_HUMAN	.	UPI00002029A3	.	deleterious(0.01)	benign(0.272)	9/18	.	hmmpanther:PTHR12433,hmmpanther:PTHR12433:SF10,Pfam_domain:PF11235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TGTGGCCCCTG	.	2	ESCA
ZNF534	0	.	GRCh37	19	52941771	52941771	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1097C>T	p.Pro366Leu	p.P366L	ENST00000332323	4/4	41	20	21	20	20	0	ZNF534,missense_variant,p.Pro366Leu,ENST00000332323,;ZNF534,missense_variant,p.Pro353Leu,ENST00000433050,;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000432303,;	T	ENSG00000198633	ENST00000332323	Transcript	missense_variant	1158	1097	366	P/L	cCa/cTa	.	.	.	1	ZNF534	HGNC	26337	protein_coding	YES	CCDS46165.1	ENSP00000327538	ZN534_HUMAN	.	UPI0000351984	.	deleterious(0.05)	unknown(0)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACCATACA	.	5	ESCA
ZNF525	0	.	GRCh37	19	53886016	53886016	+	3'UTR	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*744C>A	.	.	ENST00000474037	4/4	55	34	20	30	30	0	ZNF525,3_prime_UTR_variant,,ENST00000474037,;ZNF525,3_prime_UTR_variant,,ENST00000467003,;ZNF525,intron_variant,,ENST00000593918,;ZNF525,intron_variant,,ENST00000475179,;ZNF525,downstream_gene_variant,,ENST00000355326,;ZNF525,downstream_gene_variant,,ENST00000600148,;ZNF525,upstream_gene_variant,,ENST00000601790,;CTD-3141N22.1,upstream_gene_variant,,ENST00000459631,;	A	ENSG00000203326	ENST00000474037	Transcript	3_prime_UTR_variant	2318	.	.	.	.	.	.	.	1	ZNF525	HGNC	29423	protein_coding	YES	.	ENSP00000417696	.	J3KR62_HUMAN,J3KR51_HUMAN	UPI0000EE700C	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCAGACATCGT	.	4	ESCA
KIR2DL1	0	.	GRCh37	19	55286739	55286739	+	Missense_Mutation	SNP	G	G	A	rs373043299	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493G>A	p.Glu165Lys	p.E165K	ENST00000336077	4/8	150	121	29	102	102	0	KIR2DL1,missense_variant,p.Glu165Lys,ENST00000336077,;KIR2DL1,missense_variant,p.Glu165Lys,ENST00000291633,;KIR2DL4,intron_variant,,ENST00000396284,;KIR3DL1,intron_variant,,ENST00000541392,;KIR3DL1,intron_variant,,ENST00000538269,;KIR3DL1,intron_variant,,ENST00000402254,;KIR2DL3,intron_variant,,ENST00000434419,;CTB-61M7.1,intron_variant,,ENST00000400864,;	A	ENSG00000125498	ENST00000336077	Transcript	missense_variant	533	493	165	E/K	Gag/Aag	rs373043299,COSM3797519	.	.	1	KIR2DL1	HGNC	6329	protein_coding	YES	CCDS12904.1	ENSP00000336769	KI2L1_HUMAN	Q6H2H4_HUMAN,Q6H2H3_HUMAN,K7R1R8_HUMAN	UPI00001195F7	.	tolerated(0.21)	possibly_damaging(0.789)	4/8	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF00047,Gene3D:2.60.40.10,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF19	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0007	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGGGAGGCC	byCluster|by1000G	5	ESCA
CATSPERD	0	.	GRCh37	19	5724873	5724873	+	Silent	SNP	G	G	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126G>C	p.%3D	p.G42G	ENST00000381624	2/22	55	48	6	41	41	0	CATSPERD,synonymous_variant,p.%3D,ENST00000381624,;CATSPERD,splice_region_variant,,ENST00000381614,;LONP1,upstream_gene_variant,,ENST00000360614,;LONP1,upstream_gene_variant,,ENST00000593119,;LONP1,upstream_gene_variant,,ENST00000540670,;LONP1,upstream_gene_variant,,ENST00000585374,;LONP1,upstream_gene_variant,,ENST00000587365,;LONP1,upstream_gene_variant,,ENST00000590511,;LONP1,upstream_gene_variant,,ENST00000590728,;LONP1,upstream_gene_variant,,ENST00000590558,;LONP1,upstream_gene_variant,,ENST00000586617,;	C	ENSG00000174898	ENST00000381624	Transcript	synonymous_variant	187	126	42	G	ggG/ggC	.	.	.	1	CATSPERD	HGNC	28598	protein_coding	YES	CCDS12149.2	ENSP00000371037	CTSRD_HUMAN	.	UPI000059D641	.	.	.	2/22	.	Pfam_domain:PF15020	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAGGGGTATG	.	4	ESCA
OVGP1	0	.	GRCh37	1	111957458	111957458	+	Silent	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1665G>A	p.%3D	p.E555E	ENST00000369732	11/11	33	27	6	36	36	0	OVGP1,synonymous_variant,p.%3D,ENST00000369732,;OVGP1,downstream_gene_variant,,ENST00000540696,;OVGP1,downstream_gene_variant,,ENST00000481495,;OVGP1,downstream_gene_variant,,ENST00000494622,;	T	ENSG00000085465	ENST00000369732	Transcript	synonymous_variant	1721	1665	555	E	gaG/gaA	.	.	.	-1	OVGP1	HGNC	8524	protein_coding	YES	CCDS834.1	ENSP00000358747	OVGP1_HUMAN	Q9UJZ3_HUMAN	UPI0000130C53	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGTCTCAGT	.	5	ESCA
LCE1E	0	.	GRCh37	1	152760209	152760209	+	3'UTR	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*77C>G	.	.	ENST00000368770	2/2	37	23	14	38	38	0	LCE1E,3_prime_UTR_variant,,ENST00000368770,;LCE1E,downstream_gene_variant,,ENST00000368771,;	G	ENSG00000186226	ENST00000368770	Transcript	3_prime_UTR_variant	487	.	.	.	.	.	.	.	1	LCE1E	HGNC	29466	protein_coding	YES	CCDS1024.1	ENSP00000357759	LCE1E_HUMAN	.	UPI0000161050	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CTTGCCTGGAG	.	4	ESCA
IGSF8	0	.	GRCh37	1	160062078	160062078	+	Missense_Mutation	SNP	T	T	C	rs766393697	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1720A>G	p.Met574Val	p.M574V	ENST00000368086	5/7	32	18	13	25	25	0	IGSF8,missense_variant,p.Met574Val,ENST00000314485,;IGSF8,missense_variant,p.Met574Val,ENST00000368086,;KCNJ9,downstream_gene_variant,,ENST00000368088,;IGSF8,downstream_gene_variant,,ENST00000448417,;IGSF8,downstream_gene_variant,,ENST00000460351,;	C	ENSG00000162729	ENST00000368086	Transcript	missense_variant	1937	1720	574	M/V	Atg/Gtg	rs766393697	.	.	-1	IGSF8	HGNC	17813	protein_coding	YES	CCDS1195.1	ENSP00000357065	IGSF8_HUMAN	C9J8Z4_HUMAN	UPI0000073CBA	.	tolerated(0.06)	benign(0.003)	5/7	.	hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCATGTAGG	byFrequency	5	ESCA
ESRRG	0	.	GRCh37	1	216896593	216896593	+	5'UTR	SNP	C	C	A	rs573749790	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-65G>T	.	.	ENST00000366937	1/8	36	24	12	32	32	0	ESRRG,stop_gained,p.Glu17Ter,ENST00000408911,;ESRRG,5_prime_UTR_variant,,ENST00000481543,;ESRRG,5_prime_UTR_variant,,ENST00000459955,;ESRRG,5_prime_UTR_variant,,ENST00000469486,;ESRRG,5_prime_UTR_variant,,ENST00000391890,;ESRRG,5_prime_UTR_variant,,ENST00000475275,;ESRRG,5_prime_UTR_variant,,ENST00000366937,;ESRRG,intron_variant,,ENST00000487276,;ESRRG,intron_variant,,ENST00000366938,;ESRRG,intron_variant,,ENST00000360012,;ESRRG,intron_variant,,ENST00000366940,;ESRRG,intron_variant,,ENST00000361525,;ESRRG,intron_variant,,ENST00000359162,;ESRRG,intron_variant,,ENST00000493603,;ESRRG,intron_variant,,ENST00000493748,;ESRRG,intron_variant,,ENST00000463665,;ESRRG,intron_variant,,ENST00000361395,;ESRRG,non_coding_transcript_exon_variant,,ENST00000469913,;ESRRG,intron_variant,,ENST00000586199,;	A	ENSG00000196482	ENST00000366937	Transcript	5_prime_UTR_variant	203	.	.	.	.	rs573749790	.	.	-1	ESRRG	HGNC	3474	protein_coding	YES	CCDS58061.1	ENSP00000355904	ERR3_HUMAN	C9JNX5_HUMAN,C9J5W9_HUMAN,C9J0E3_HUMAN	UPI0000D4BFAB	.	.	.	1/8	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCGTAGT	by1000G	5	ESCA
C1orf65	0	.	GRCh37	1	223568089	223568089	+	Silent	SNP	G	G	C	rs763287610	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1272G>C	p.%3D	p.L424L	ENST00000366875	1/1	18	15	3	8	8	0	C1orf65,synonymous_variant,p.%3D,ENST00000366875,;	C	ENSG00000178395	ENST00000366875	Transcript	synonymous_variant	1375	1272	424	L	ctG/ctC	rs763287610	.	.	1	C1orf65	HGNC	26654	protein_coding	YES	CCDS1537.1	ENSP00000355840	CA065_HUMAN	.	UPI000006F948	.	.	.	1/1	.	Pfam_domain:PF15558	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AACCTGAGCTC	.	2	ESCA
PLD5	0	.	GRCh37	1	242687455	242687455	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124A>C	p.Ser42Arg	p.S42R	ENST00000536534	1/10	94	58	36	72	72	0	PLD5,missense_variant,p.Ser42Arg,ENST00000536534,;PLD5,5_prime_UTR_variant,,ENST00000442594,;PLD5,missense_variant,p.Ser42Arg,ENST00000366545,;PLD5,missense_variant,p.Ser42Arg,ENST00000467561,;	G	ENSG00000180287	ENST00000536534	Transcript	missense_variant	366	124	42	S/R	Agc/Cgc	.	.	.	-1	PLD5	HGNC	26879	protein_coding	YES	CCDS1621.2	ENSP00000440896	PLD5_HUMAN	J3KP61_HUMAN	UPI000040E1A4	.	deleterious(0.01)	possibly_damaging(0.686)	1/10	.	hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCTGTAGA	.	5	ESCA
LEPR	0	.	GRCh37	1	66067198	66067198	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118C>T	p.Ala373Val	p.A373V	ENST00000349533	9/20	39	13	26	51	51	0	LEPR,missense_variant,p.Ala373Val,ENST00000349533,;LEPR,missense_variant,p.Ala373Val,ENST00000344610,;LEPR,missense_variant,p.Ala373Val,ENST00000371060,;LEPR,missense_variant,p.Ala373Val,ENST00000371058,;LEPR,missense_variant,p.Ala373Val,ENST00000371059,;LEPR,intron_variant,,ENST00000406510,;LEPR,non_coding_transcript_exon_variant,,ENST00000462765,;	T	ENSG00000116678	ENST00000349533	Transcript	missense_variant	1303	1118	373	A/V	gCt/gTt	.	.	.	1	LEPR	HGNC	6554	protein_coding	YES	CCDS631.1	ENSP00000330393	LEPR_HUMAN	L0I9J6_HUMAN,A2RRQ4_HUMAN	UPI000014C37B	.	deleterious(0.01)	possibly_damaging(0.893)	9/20	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF11,Pfam_domain:PF06328,Gene3D:2.60.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTAGCTGAGA	.	5	ESCA
GBP1P1	0	.	GRCh37	1	89885842	89885842	+	RNA	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.283C>T	.	.	ENST00000394662	2/9	35	27	8	49	49	0	GBP1P1,non_coding_transcript_exon_variant,,ENST00000513638,;GBP1P1,non_coding_transcript_exon_variant,,ENST00000394662,;	T	ENSG00000225492	ENST00000394662	Transcript	non_coding_transcript_exon_variant	283	.	.	.	.	.	.	.	1	GBP1P1	HGNC	39561	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTTCTGCTG	.	5	ESCA
RALGAPA2	0	.	GRCh37	20	20563841	20563841	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2560G>T	p.Gly854Cys	p.G854C	ENST00000202677	20/40	42	32	10	45	45	0	RALGAPA2,missense_variant,p.Gly854Cys,ENST00000202677,;RALGAPA2,missense_variant,p.Gly671Cys,ENST00000430436,;	A	ENSG00000188559	ENST00000202677	Transcript	missense_variant	2568	2560	854	G/C	Ggc/Tgc	.	.	.	-1	RALGAPA2	HGNC	16207	protein_coding	YES	CCDS46584.1	ENSP00000202677	RGPA2_HUMAN	.	UPI000040F987	.	deleterious(0.01)	probably_damaging(0.952)	20/40	.	hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCCCAGAG	.	5	ESCA
SNAI1	0	.	GRCh37	20	48600834	48600834	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556G>A	p.Gly186Arg	p.G186R	ENST00000244050	2/3	26	22	4	30	30	0	SNAI1,missense_variant,p.Gly186Arg,ENST00000244050,;	A	ENSG00000124216	ENST00000244050	Transcript	missense_variant	617	556	186	G/R	Ggg/Agg	.	.	.	1	SNAI1	HGNC	11128	protein_coding	YES	CCDS13423.1	ENSP00000244050	SNAI1_HUMAN	.	UPI0000135B17	.	deleterious(0)	probably_damaging(1)	2/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR11389:SF430,hmmpanther:PTHR11389,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CCTGCGGGAAG	.	4	ESCA
SLC23A2	0	.	GRCh37	20	4913292	4913292	+	5'UTR	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-84G>A	.	.	ENST00000379333	3/17	12	7	4	9	9	0	SLC23A2,5_prime_UTR_variant,,ENST00000379333,;SLC23A2,5_prime_UTR_variant,,ENST00000424750,;SLC23A2,5_prime_UTR_variant,,ENST00000338244,;SLC23A2,non_coding_transcript_exon_variant,,ENST00000468355,;	T	ENSG00000089057	ENST00000379333	Transcript	5_prime_UTR_variant	310	.	.	.	.	.	.	.	-1	SLC23A2	HGNC	10973	protein_coding	YES	CCDS13085.1	ENSP00000368637	S23A2_HUMAN	Q4ZGM1_HUMAN	UPI0000136292	.	.	.	3/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCAGCCGGCTC	.	2	ESCA
KRTAP26-1	0	.	GRCh37	21	31692517	31692517	+	5'UTR	SNP	A	A	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-164T>C	.	.	ENST00000360542	1/1	27	20	7	26	26	0	KRTAP26-1,5_prime_UTR_variant,,ENST00000360542,;	G	ENSG00000197683	ENST00000360542	Transcript	5_prime_UTR_variant	91	.	.	.	.	.	.	.	-1	KRTAP26-1	HGNC	33760	protein_coding	YES	CCDS13588.1	ENSP00000353742	KR261_HUMAN	.	UPI00001CE052	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTATAGCCAA	.	5	ESCA
HMGN1	0	.	GRCh37	21	40720242	40720242	+	Silent	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.102G>A	p.%3D	p.A34A	ENST00000380749	4/6	20	7	12	30	30	0	HMGN1,synonymous_variant,p.%3D,ENST00000380748,;HMGN1,synonymous_variant,p.%3D,ENST00000380749,;HMGN1,synonymous_variant,p.%3D,ENST00000380747,;HMGN1,upstream_gene_variant,,ENST00000361263,;snoU13,upstream_gene_variant,,ENST00000459446,;Y_RNA,downstream_gene_variant,,ENST00000517106,;HMGN1,non_coding_transcript_exon_variant,,ENST00000485550,;HMGN1,non_coding_transcript_exon_variant,,ENST00000489072,;HMGN1,non_coding_transcript_exon_variant,,ENST00000482192,;HMGN1,non_coding_transcript_exon_variant,,ENST00000490032,;HMGN1,non_coding_transcript_exon_variant,,ENST00000479586,;HMGN1,non_coding_transcript_exon_variant,,ENST00000471260,;HMGN1,non_coding_transcript_exon_variant,,ENST00000491183,;HMGN1,synonymous_variant,p.%3D,ENST00000419378,;HMGN1,synonymous_variant,p.%3D,ENST00000443046,;HMGN1,synonymous_variant,p.%3D,ENST00000288344,;HMGN1,synonymous_variant,p.%3D,ENST00000436324,;HMGN1,synonymous_variant,p.%3D,ENST00000431390,;HMGN1,non_coding_transcript_exon_variant,,ENST00000492280,;HMGN1,non_coding_transcript_exon_variant,,ENST00000464078,;HMGN1,non_coding_transcript_exon_variant,,ENST00000482733,;HMGN1,non_coding_transcript_exon_variant,,ENST00000486741,;HMGN1,non_coding_transcript_exon_variant,,ENST00000463631,;	T	ENSG00000205581	ENST00000380749	Transcript	synonymous_variant	385	102	34	A	gcG/gcA	.	.	.	-1	HMGN1	HGNC	4984	protein_coding	YES	CCDS33559.1	ENSP00000370125	HMGN1_HUMAN	.	UPI0000047514	.	.	.	4/6	.	Low_complexity_(Seg):seg,Prints_domain:PR00925,SMART_domains:SM00527,Pfam_domain:PF01101,hmmpanther:PTHR23087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTCGCTTC	.	5	ESCA
Z83851.3	0	.	GRCh37	22	42670129	42670129	+	RNA	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.503C>T	.	.	ENST00000332965	2/2	36	30	6	23	23	0	TCF20,intron_variant,,ENST00000515426,;Z83851.3,non_coding_transcript_exon_variant,,ENST00000332965,;Z83851.3,intron_variant,,ENST00000415205,;Z83851.3,intron_variant,,ENST00000446578,;CTA-989H11.1,upstream_gene_variant,,ENST00000609564,;Z83851.4,upstream_gene_variant,,ENST00000420096,;	T	ENSG00000182057	ENST00000332965	Transcript	non_coding_transcript_exon_variant	503	.	.	.	.	.	.	.	1	Z83851.3	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGTCACACCAA	.	3	ESCA
EFCAB6	0	.	GRCh37	22	44178174	44178174	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25G>A	p.Asp9Asn	p.D9N	ENST00000262726	3/32	62	46	16	53	53	0	EFCAB6,missense_variant,p.Asp9Asn,ENST00000262726,;EFCAB6,5_prime_UTR_variant,,ENST00000358439,;EFCAB6,5_prime_UTR_variant,,ENST00000356087,;EFCAB6,intron_variant,,ENST00000396231,;EFCAB6,non_coding_transcript_exon_variant,,ENST00000485142,;EFCAB6,intron_variant,,ENST00000476600,;EFCAB6,non_coding_transcript_exon_variant,,ENST00000404038,;	T	ENSG00000186976	ENST00000262726	Transcript	missense_variant	279	25	9	D/N	Gac/Aac	.	.	.	-1	EFCAB6	HGNC	24204	protein_coding	YES	CCDS14049.1	ENSP00000262726	EFCB6_HUMAN	.	UPI0000225CD7	.	tolerated_low_confidence(0.31)	benign(0.015)	3/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGTCTGGTA	.	5	ESCA
KIAA0930	0	.	GRCh37	22	45592462	45592462	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*595C>T	.	.	ENST00000251993	10/10	75	61	14	42	42	0	KIAA0930,3_prime_UTR_variant,,ENST00000336156,;KIAA0930,3_prime_UTR_variant,,ENST00000251993,;KIAA0930,3_prime_UTR_variant,,ENST00000391627,;KIAA0930,3_prime_UTR_variant,,ENST00000423262,;KIAA0930,downstream_gene_variant,,ENST00000443310,;MIR1249,downstream_gene_variant,,ENST00000408671,;KIAA0930,downstream_gene_variant,,ENST00000474515,;KIAA0930,downstream_gene_variant,,ENST00000493003,;KIAA0930,non_coding_transcript_exon_variant,,ENST00000488038,;KIAA0930,downstream_gene_variant,,ENST00000498418,;KIAA0930,downstream_gene_variant,,ENST00000483374,;	A	ENSG00000100364	ENST00000251993	Transcript	3_prime_UTR_variant	1970	.	.	.	.	.	.	.	-1	KIAA0930	HGNC	1314	protein_coding	YES	CCDS33666.1	ENSP00000251993	K0930_HUMAN	B0QY18_HUMAN	UPI00001C0A16	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTGGAACTG	.	4	ESCA
GCC2	0	.	GRCh37	2	109092295	109092295	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000309863	9/23	33	28	5	30	30	0	GCC2,missense_variant,p.Glu1017Lys,ENST00000309863,;GCC2,downstream_gene_variant,,ENST00000492785,;GCC2,downstream_gene_variant,,ENST00000409896,;GCC2,downstream_gene_variant,,ENST00000462897,;GCC2,missense_variant,p.Glu55Lys,ENST00000447558,;GCC2,3_prime_UTR_variant,,ENST00000482325,;	A	ENSG00000135968	ENST00000309863	Transcript	missense_variant	3763	3049	1017	E/K	Gaa/Aaa	.	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	deleterious(0)	probably_damaging(0.985)	9/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCAGAAAGC	.	4	ESCA
GREB1	0	.	GRCh37	2	11742612	11742612	+	Silent	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2610C>T	p.%3D	p.L870L	ENST00000381486	17/33	107	88	18	80	80	0	GREB1,synonymous_variant,p.%3D,ENST00000234142,;GREB1,synonymous_variant,p.%3D,ENST00000432985,;GREB1,synonymous_variant,p.%3D,ENST00000381486,;AC011994.1,upstream_gene_variant,,ENST00000581704,;	T	ENSG00000196208	ENST00000381486	Transcript	synonymous_variant	2910	2610	870	L	ctC/ctT	.	.	.	1	GREB1	HGNC	24885	protein_coding	YES	CCDS42655.1	ENSP00000370896	GREB1_HUMAN	.	UPI0000163937	.	.	.	17/33	.	hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTCCCCTT	.	5	ESCA
WDR33	0	.	GRCh37	2	128520663	128520663	+	Missense_Mutation	SNP	G	G	A	rs756762892	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.697C>T	p.Arg233Cys	p.R233C	ENST00000322313	7/22	27	24	3	20	20	0	WDR33,missense_variant,p.Arg233Cys,ENST00000393006,;WDR33,missense_variant,p.Arg233Cys,ENST00000322313,;WDR33,missense_variant,p.Arg155Cys,ENST00000436787,;WDR33,3_prime_UTR_variant,,ENST00000409658,;	A	ENSG00000136709	ENST00000322313	Transcript	missense_variant	856	697	233	R/C	Cgt/Tgt	rs756762892,COSM3042915,COSM3566224	.	.	-1	WDR33	HGNC	25651	protein_coding	YES	CCDS2150.1	ENSP00000325377	WDR33_HUMAN	C9J8B4_HUMAN,B9A053_HUMAN	UPI000013D032	.	deleterious(0)	unknown(0)	7/22	.	PROSITE_profiles:PS50294,hmmpanther:PTHR22836,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCAACGAAGAA	byFrequency	3	ESCA
LRP2	0	.	GRCh37	2	170096091	170096091	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4240T>A	p.Ser1414Thr	p.S1414T	ENST00000263816	26/79	56	19	37	38	38	0	LRP2,missense_variant,p.Ser1414Thr,ENST00000263816,;LRP2,downstream_gene_variant,,ENST00000443831,;	T	ENSG00000081479	ENST00000263816	Transcript	missense_variant	4526	4240	1414	S/T	Tcg/Acg	.	.	.	-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	LRP2_HUMAN	Q9NP34_HUMAN,Q53TL0_HUMAN,Q4ZG84_HUMAN	UPI0000141BA5	.	.	benign(0.006)	26/79	.	PROSITE_profiles:PS50026,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF220,PROSITE_patterns:PS01186,PROSITE_patterns:PS00010,Pfam_domain:PF07645,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACGAGCACC	.	5	ESCA
HOXD10	0	.	GRCh37	2	176984358	176984358	+	3'UTR	SNP	T	T	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*399T>G	.	.	ENST00000249501	2/2	57	51	5	36	36	0	HOXD10,3_prime_UTR_variant,,ENST00000249501,;HOXD9,upstream_gene_variant,,ENST00000249499,;HOXD-AS2,downstream_gene_variant,,ENST00000440016,;HOXD10,downstream_gene_variant,,ENST00000549469,;HOXD10,downstream_gene_variant,,ENST00000490088,;	G	ENSG00000128710	ENST00000249501	Transcript	3_prime_UTR_variant	1677	.	.	.	.	.	.	.	1	HOXD10	HGNC	5133	protein_coding	YES	CCDS2266.1	ENSP00000249501	HXD10_HUMAN	.	UPI000013CC87	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTATGTGTGTG	.	4	ESCA
TTN	0	.	GRCh37	2	179399177	179399177	+	Silent	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.102165G>C	p.%3D	p.V34055V	ENST00000589042	358/363	25	18	6	17	17	0	TTN,synonymous_variant,p.%3D,ENST00000359218,;TTN,synonymous_variant,p.%3D,ENST00000460472,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000342175,;TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589434,;TTN-AS1,intron_variant,,ENST00000588716,;TTN-AS1,intron_variant,,ENST00000589391,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000592182,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592836,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000591466,;TTN-AS1,intron_variant,,ENST00000591867,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000585358,;TTN-AS1,intron_variant,,ENST00000589842,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000590040,;TTN-AS1,intron_variant,,ENST00000450692,;TTN-AS1,intron_variant,,ENST00000442329,;TTN-AS1,intron_variant,,ENST00000431259,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000588257,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000588244,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000588804,;TTN-AS1,intron_variant,,ENST00000585487,;TTN-AS1,downstream_gene_variant,,ENST00000585625,;TTN-AS1,downstream_gene_variant,,ENST00000587568,;TTN-AS1,upstream_gene_variant,,ENST00000415561,;TTN-AS1,downstream_gene_variant,,ENST00000587944,;TTN-AS1,downstream_gene_variant,,ENST00000589355,;TTN-AS1,downstream_gene_variant,,ENST00000604571,;	G	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	102390	102165	34055	V	gtG/gtC	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	358/363	.	PROSITE_profiles:PS50011,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:1.10.510.10,Pfam_domain:PF00069,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCACTAA	.	5	ESCA
TTN	0	.	GRCh37	2	179459077	179459077	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58144G>A	p.Glu19382Lys	p.E19382K	ENST00000589042	296/363	69	58	11	42	42	0	TTN,missense_variant,p.Glu10442Lys,ENST00000359218,;TTN,missense_variant,p.Glu17741Lys,ENST00000591111,;TTN,missense_variant,p.Glu19382Lys,ENST00000589042,;TTN,missense_variant,p.Glu10509Lys,ENST00000342175,;TTN,missense_variant,p.Glu16814Lys,ENST00000342992,;TTN,missense_variant,p.Glu10317Lys,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000590743,;TTN-AS1,upstream_gene_variant,,ENST00000589830,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	58369	58144	19382	E/K	Gag/Aag	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	296/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCATCCT	.	5	ESCA
ZNF804A	0	.	GRCh37	2	185803049	185803049	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2926G>T	p.Ala976Ser	p.A976S	ENST00000302277	4/4	21	17	4	21	21	0	ZNF804A,missense_variant,p.Ala976Ser,ENST00000302277,;	T	ENSG00000170396	ENST00000302277	Transcript	missense_variant	3520	2926	976	A/S	Gct/Tct	.	.	.	1	ZNF804A	HGNC	21711	protein_coding	YES	CCDS2291.1	ENSP00000303252	Z804A_HUMAN	.	UPI00001B4B18	.	deleterious(0.04)	probably_damaging(0.968)	4/4	.	hmmpanther:PTHR17614:SF13,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AACTGGCTGAG	.	3	ESCA
FSIP2	0	.	GRCh37	2	186671724	186671724	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17958G>A	p.Met5986Ile	p.M5986I	ENST00000343098	17/23	35	29	6	20	20	0	FSIP2,missense_variant,p.Met5986Ile,ENST00000343098,;FSIP2,missense_variant,p.Met5897Ile,ENST00000424728,;FSIP2,intron_variant,,ENST00000415915,;	A	ENSG00000188738	ENST00000343098	Transcript	missense_variant	17958	17958	5986	M/I	atG/atA	.	.	.	1	FSIP2	HGNC	21675	protein_coding	YES	CCDS54426.1	ENSP00000344403	.	J3QTJ6_HUMAN	UPI0001D420A1	.	.	benign(0)	17/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGATGAGAAA	.	4	ESCA
CLK1	0	.	GRCh37	2	201719347	201719347	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1338G>C	p.Gln446His	p.Q446H	ENST00000434813	11/13	51	47	3	42	42	0	CLK1,missense_variant,p.Gln404His,ENST00000321356,;CLK1,missense_variant,p.Gln446His,ENST00000434813,;CLK1,missense_variant,p.Gln227His,ENST00000409769,;CLK1,3_prime_UTR_variant,,ENST00000409403,;CLK1,3_prime_UTR_variant,,ENST00000432425,;CLK1,non_coding_transcript_exon_variant,,ENST00000496205,;CLK1,non_coding_transcript_exon_variant,,ENST00000473565,;CLK1,non_coding_transcript_exon_variant,,ENST00000461981,;CLK1,upstream_gene_variant,,ENST00000464454,;CLK1,upstream_gene_variant,,ENST00000461326,;CLK1,upstream_gene_variant,,ENST00000472679,;	G	ENSG00000013441	ENST00000434813	Transcript	missense_variant	1673	1338	446	Q/H	caG/caC	.	.	.	-1	CLK1	HGNC	2068	protein_coding	YES	CCDS54427.1	ENSP00000394734	CLK1_HUMAN	.	UPI00017A7024	.	tolerated(0.22)	benign(0.404)	11/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24058:SF2,hmmpanther:PTHR24058,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTTCTGTAT	.	2	ESCA
ZNF513	0	.	GRCh37	2	27601662	27601662	+	Silent	SNP	G	G	A	rs149911850	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471C>T	p.%3D	p.F157F	ENST00000323703	3/4	89	71	17	64	64	0	ZNF513,synonymous_variant,p.%3D,ENST00000407879,;ZNF513,synonymous_variant,p.%3D,ENST00000323703,;ZNF513,synonymous_variant,p.%3D,ENST00000436006,;PPM1G,downstream_gene_variant,,ENST00000344034,;SNX17,downstream_gene_variant,,ENST00000537606,;SNX17,downstream_gene_variant,,ENST00000542478,;SNX17,downstream_gene_variant,,ENST00000543024,;PPM1G,downstream_gene_variant,,ENST00000350803,;SNX17,downstream_gene_variant,,ENST00000233575,;ZNF513,intron_variant,,ENST00000491924,;SNX17,downstream_gene_variant,,ENST00000493711,;SNX17,downstream_gene_variant,,ENST00000453453,;SNX17,downstream_gene_variant,,ENST00000440760,;PPM1G,downstream_gene_variant,,ENST00000472077,;SNX17,downstream_gene_variant,,ENST00000494893,;SNX17,downstream_gene_variant,,ENST00000427123,;	A	ENSG00000163795	ENST00000323703	Transcript	synonymous_variant	670	471	157	F	ttC/ttT	rs149911850	.	.	-1	ZNF513	HGNC	26498	protein_coding	YES	CCDS1751.1	ENSP00000318373	ZN513_HUMAN	C9JT52_HUMAN	UPI00000437BA	.	.	.	3/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24382:SF3,hmmpanther:PTHR24382,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0.0002	A:0.0005	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACGAAGGT	byCluster|by1000G	5	ESCA
PLEKHH2	0	.	GRCh37	2	43971084	43971084	+	Missense_Mutation	SNP	C	C	T	rs766016768	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3511C>T	p.Pro1171Ser	p.P1171S	ENST00000282406	23/30	20	16	4	12	12	0	PLEKHH2,missense_variant,p.Pro1171Ser,ENST00000282406,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000493408,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405000,;PLEKHH2,downstream_gene_variant,,ENST00000480103,;PLEKHH2,downstream_gene_variant,,ENST00000405223,;PLEKHH2,upstream_gene_variant,,ENST00000490038,;	T	ENSG00000152527	ENST00000282406	Transcript	missense_variant	3621	3511	1171	P/S	Cct/Tct	rs766016768	.	.	1	PLEKHH2	HGNC	30506	protein_coding	YES	CCDS1812.1	ENSP00000282406	PKHH2_HUMAN	.	UPI000016021B	.	deleterious(0)	possibly_damaging(0.841)	23/30	.	PROSITE_profiles:PS50057,hmmpanther:PTHR22903,hmmpanther:PTHR22903:SF3,SMART_domains:SM00295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGATCCTTCT	.	2	ESCA
HK2	0	.	GRCh37	2	75115128	75115128	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2318C>T	p.Ser773Leu	p.S773L	ENST00000290573	16/18	32	18	13	31	31	0	HK2,missense_variant,p.Ser745Leu,ENST00000409174,;HK2,missense_variant,p.Ser773Leu,ENST00000290573,;	T	ENSG00000159399	ENST00000290573	Transcript	missense_variant	2918	2318	773	S/L	tCa/tTa	.	.	.	1	HK2	HGNC	4923	protein_coding	YES	CCDS1956.1	ENSP00000290573	HXK2_HUMAN	Q7Z7Q6_HUMAN,Q53SG7_HUMAN,Q53QX9_HUMAN,Q09LL6_HUMAN,E9PB90_HUMAN	UPI00000706E4	.	deleterious(0)	probably_damaging(0.999)	16/18	.	hmmpanther:PTHR19443:SF4,hmmpanther:PTHR19443,Gene3D:3.40.367.20,Pfam_domain:PF03727,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCAGAGC	.	5	ESCA
YWHAQ	0	.	GRCh37	2	9725328	9725328	+	3'UTR	SNP	T	T	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*87A>G	.	.	ENST00000381844	5/5	54	35	18	26	26	0	YWHAQ,3_prime_UTR_variant,,ENST00000238081,;YWHAQ,3_prime_UTR_variant,,ENST00000381844,;YWHAQ,downstream_gene_variant,,ENST00000446619,;YWHAQ,non_coding_transcript_exon_variant,,ENST00000474715,;	C	ENSG00000134308	ENST00000381844	Transcript	3_prime_UTR_variant	989	.	.	.	.	.	.	.	-1	YWHAQ	HGNC	12854	protein_coding	YES	CCDS1666.1	ENSP00000371267	1433T_HUMAN	Q53S41_HUMAN,Q53RR5_HUMAN,E9PG15_HUMAN,B4DY04_HUMAN	UPI0000124E01	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTCTTTGCT	.	5	ESCA
SPICE1	0	.	GRCh37	3	113187975	113187975	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.722C>A	p.Ser241Ter	p.S241*	ENST00000295872	8/18	35	25	9	48	48	0	SPICE1,stop_gained,p.Ser241Ter,ENST00000295872,;SPICE1,stop_gained,p.Ser53Ter,ENST00000467618,;SPICE1,non_coding_transcript_exon_variant,,ENST00000496105,;	T	ENSG00000163611	ENST00000295872	Transcript	stop_gained	982	722	241	S/*	tCa/tAa	.	.	.	-1	SPICE1	HGNC	25083	protein_coding	YES	CCDS2973.1	ENSP00000295872	SPICE_HUMAN	C9J5T2_HUMAN,C9J4W3_HUMAN,C9IZF0_HUMAN	UPI000007328D	.	.	.	8/18	.	hmmpanther:PTHR31167,hmmpanther:PTHR31167:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T239M|c.716C>T|3,BUFFER|p.T239M|c.716C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATGATGGC	.	5	ESCA
CHST13	0	.	GRCh37	3	126261328	126261328	+	Silent	SNP	C	C	T	rs763384644	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933C>T	p.%3D	p.I311I	ENST00000319340	3/3	43	38	5	21	21	0	CHST13,synonymous_variant,p.%3D,ENST00000319340,;C3orf22,intron_variant,,ENST00000505070,;	T	ENSG00000180767	ENST00000319340	Transcript	synonymous_variant	983	933	311	I	atC/atT	rs763384644	.	.	1	CHST13	HGNC	21755	protein_coding	YES	CCDS3039.1	ENSP00000317404	CHSTD_HUMAN	Q3ZCU8_HUMAN,Q3ZCR4_HUMAN	UPI00000492E5	.	.	.	3/3	.	hmmpanther:PTHR12137:SF31,hmmpanther:PTHR12137,Pfam_domain:PF03567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACATCAGCCC	byFrequency	3	ESCA
DNAJB8	0	.	GRCh37	3	128181534	128181534	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555C>T	p.%3D	p.S185S	ENST00000469083	2/2	64	56	8	36	36	0	DNAJB8,synonymous_variant,p.%3D,ENST00000319153,;DNAJB8,synonymous_variant,p.%3D,ENST00000469083,;DNAJB8-AS1,upstream_gene_variant,,ENST00000471626,;	A	ENSG00000179407	ENST00000469083	Transcript	synonymous_variant	3113	555	185	S	tcC/tcT	.	.	.	-1	DNAJB8	HGNC	23699	protein_coding	YES	CCDS3048.1	ENSP00000417418	DNJB8_HUMAN	.	UPI0000129437	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24077,hmmpanther:PTHR24077:SF242	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGGTGGACGA	.	4	ESCA
SI	0	.	GRCh37	3	164786915	164786915	+	Silent	SNP	G	G	A	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.324C>T	p.%3D	p.F108F	ENST00000264382	4/48	85	74	11	50	50	0	SI,synonymous_variant,p.%3D,ENST00000264382,;SI,3_prime_UTR_variant,,ENST00000476593,;	A	ENSG00000090402	ENST00000264382	Transcript	synonymous_variant	387	324	108	F	ttC/ttT	COSM3202850	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	.	.	4/48	.	Superfamily_domains:SSF74650,SMART_domains:SM00018,Pfam_domain:PF00088,Gene3D:4.10.110.10,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,PROSITE_profiles:PS51448	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAACGAAGAA	.	4	ESCA
TBL1XR1	0	.	GRCh37	3	176742661	176742661	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*625C>T	.	.	ENST00000430069	16/16	92	76	15	33	33	0	TBL1XR1,3_prime_UTR_variant,,ENST00000457928,;TBL1XR1,3_prime_UTR_variant,,ENST00000430069,;TBL1XR1,non_coding_transcript_exon_variant,,ENST00000474363,;	A	ENSG00000177565	ENST00000430069	Transcript	3_prime_UTR_variant	2430	.	.	.	.	.	.	.	-1	TBL1XR1	HGNC	29529	protein_coding	YES	CCDS46961.1	ENSP00000405574	TBL1R_HUMAN	C9JY82_HUMAN,C9JTW8_HUMAN,C9JLJ1_HUMAN,C9JEC9_HUMAN,C9JCW4_HUMAN,C9JCK0_HUMAN,C9JBN1_HUMAN,C9J903_HUMAN,C9J7E1_HUMAN,C9J3H2_HUMAN,C9IYU9_HUMAN	UPI0000136A71	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGGGAGCCA	.	5	ESCA
SCAP	0	.	GRCh37	3	47462508	47462508	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1257C>T	p.%3D	p.L419L	ENST00000265565	11/23	15	10	4	16	16	0	SCAP,synonymous_variant,p.%3D,ENST00000545718,;SCAP,synonymous_variant,p.%3D,ENST00000441517,;SCAP,synonymous_variant,p.%3D,ENST00000265565,;SCAP,non_coding_transcript_exon_variant,,ENST00000465628,;SCAP,non_coding_transcript_exon_variant,,ENST00000468965,;SCAP,missense_variant,p.Leu158Phe,ENST00000320017,;SCAP,3_prime_UTR_variant,,ENST00000416208,;SCAP,downstream_gene_variant,,ENST00000428413,;SCAP,downstream_gene_variant,,ENST00000494938,;	A	ENSG00000114650	ENST00000265565	Transcript	synonymous_variant	1670	1257	419	L	ctC/ctT	.	.	.	-1	SCAP	HGNC	30634	protein_coding	YES	CCDS2755.2	ENSP00000265565	SCAP_HUMAN	D6RA39_HUMAN,C9JQ35_HUMAN	UPI0000135624	.	.	.	11/23	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50156,hmmpanther:PTHR10796:SF53,hmmpanther:PTHR10796,Gene3D:2j8sB01,Pfam_domain:PF12349,Superfamily_domains:SSF82866	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER	GCAAAGAGACA	.	3	ESCA
CRYBG3	0	.	GRCh37	3	97593361	97593361	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3323C>G	p.Ser1108Cys	p.S1108C	ENST00000419587	4/4	58	48	10	57	57	0	CRYBG3,missense_variant,p.Ser1108Cys,ENST00000419587,;CRYBG3,upstream_gene_variant,,ENST00000182096,;	G	ENSG00000233280	ENST00000419587	Transcript	missense_variant	3490	3323	1108	S/C	tCt/tGt	.	.	.	1	CRYBG3	Uniprot_gn	34427	protein_coding	YES	.	ENSP00000391551	.	B4DLE8_HUMAN	UPI00017A74DC	.	.	.	4/4	.	hmmpanther:PTHR11818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCTTATT	.	5	ESCA
ELF2	0	.	GRCh37	4	139979834	139979834	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*303C>T	.	.	ENST00000394235	10/10	36	18	18	29	29	0	ELF2,3_prime_UTR_variant,,ENST00000379549,;ELF2,3_prime_UTR_variant,,ENST00000379550,;ELF2,3_prime_UTR_variant,,ENST00000265495,;ELF2,3_prime_UTR_variant,,ENST00000358635,;ELF2,3_prime_UTR_variant,,ENST00000394235,;ELF2,downstream_gene_variant,,ENST00000510408,;ELF2,downstream_gene_variant,,ENST00000512627,;ELF2,downstream_gene_variant,,ENST00000420916,;RNU6-531P,downstream_gene_variant,,ENST00000516694,;ELF2,intron_variant,,ENST00000515489,;ELF2,downstream_gene_variant,,ENST00000504314,;ELF2,downstream_gene_variant,,ENST00000514577,;	A	ENSG00000109381	ENST00000394235	Transcript	3_prime_UTR_variant	2552	.	.	.	.	.	.	.	-1	ELF2	HGNC	3317	protein_coding	YES	CCDS3744.1	ENSP00000377782	ELF2_HUMAN	.	UPI0000073EF0	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGTGTTCCA	.	5	ESCA
HTT	0	.	GRCh37	4	3134324	3134324	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2272G>A	p.Asp758Asn	p.D758N	ENST00000355072	17/67	23	19	4	35	35	0	HTT,missense_variant,p.Asp758Asn,ENST00000355072,;HTT,non_coding_transcript_exon_variant,,ENST00000510626,;	A	ENSG00000197386	ENST00000355072	Transcript	missense_variant	2417	2272	758	D/N	Gat/Aat	.	.	.	1	HTT	HGNC	4851	protein_coding	YES	CCDS43206.1	ENSP00000347184	HD_HUMAN	D3DVR8_HUMAN,D2CTD8_HUMAN,D2CTD7_HUMAN,D2CTD4_HUMAN,D2CTD2_HUMAN	UPI000013D567	.	.	benign(0.003)	17/67	.	hmmpanther:PTHR10170:SF10,hmmpanther:PTHR10170,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATCGATCAT	.	5	ESCA
RUFY3	0	.	GRCh37	4	71634361	71634361	+	Missense_Mutation	SNP	G	G	A	rs772895482	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679G>A	p.Glu227Lys	p.E227K	ENST00000381006	5/18	42	23	18	67	67	0	RUFY3,missense_variant,p.Glu287Lys,ENST00000417478,;RUFY3,missense_variant,p.Glu174Lys,ENST00000502653,;RUFY3,missense_variant,p.Glu163Lys,ENST00000513597,;RUFY3,missense_variant,p.Glu211Lys,ENST00000536664,;RUFY3,missense_variant,p.Glu227Lys,ENST00000226328,;RUFY3,missense_variant,p.Glu227Lys,ENST00000381006,;RUFY3,downstream_gene_variant,,ENST00000503876,;	A	ENSG00000018189	ENST00000381006	Transcript	missense_variant	1258	679	227	E/K	Gaa/Aaa	rs772895482	.	.	1	RUFY3	HGNC	30285	protein_coding	YES	CCDS34001.1	ENSP00000370394	RUFY3_HUMAN	D6REM9_HUMAN,D6RCQ1_HUMAN	UPI00005FB126	.	deleterious(0.01)	possibly_damaging(0.486)	5/18	.	PROSITE_profiles:PS50826,hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF37,Superfamily_domains:0052343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGAGAAGAC	.	5	ESCA
AC005609.1	0	.	GRCh37	5	140242307	140242307	+	3'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*90C>T	.	.	ENST00000502505	1/1	56	39	16	74	74	0	AC005609.1,3_prime_UTR_variant,,ENST00000502505,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA14,upstream_gene_variant,,ENST00000562220,;PCDHA14,non_coding_transcript_exon_variant,,ENST00000506751,;	A	ENSG00000249034	ENST00000502505	Transcript	3_prime_UTR_variant	918	.	.	.	.	.	.	.	-1	AC005609.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000424817	.	Q8NB83_HUMAN	UPI0000073A41	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGCGCTGTC	.	5	ESCA
CDH6	0	.	GRCh37	5	31323263	31323263	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2221G>A	p.Glu741Lys	p.E741K	ENST00000265071	12/12	29	20	8	32	32	0	CDH6,missense_variant,p.Glu741Lys,ENST00000265071,;CDH6,downstream_gene_variant,,ENST00000514738,;CDH6,downstream_gene_variant,,ENST00000504835,;	A	ENSG00000113361	ENST00000265071	Transcript	missense_variant	2486	2221	741	E/K	Gaa/Aaa	COSM74097	.	.	1	CDH6	HGNC	1765	protein_coding	YES	CCDS3894.1	ENSP00000265071	CADH6_HUMAN	.	UPI0000126D9B	.	deleterious(0)	probably_damaging(0.992)	12/12	.	Pfam_domain:PF01049,Gene3D:4.10.900.10,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTATGAAGGC	.	5	ESCA
BDP1	0	.	GRCh37	5	70810788	70810788	+	Missense_Mutation	SNP	G	G	T	rs200549009	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4488G>T	p.Met1496Ile	p.M1496I	ENST00000358731	20/39	27	21	6	16	16	0	BDP1,missense_variant,p.Met1496Ile,ENST00000358731,;BDP1,5_prime_UTR_variant,,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;BDP1,downstream_gene_variant,,ENST00000508157,;	T	ENSG00000145734	ENST00000358731	Transcript	missense_variant	4751	4488	1496	M/I	atG/atT	rs200549009	.	.	1	BDP1	HGNC	13652	protein_coding	YES	CCDS43328.1	ENSP00000351575	BDP1_HUMAN	.	UPI000020CA90	.	tolerated(0.06)	benign(0.011)	20/39	.	hmmpanther:PTHR22929:SF0,hmmpanther:PTHR22929	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAATGATATC	byCluster|by1000G	5	ESCA
ZFYVE16	0	.	GRCh37	5	79733702	79733702	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000338008	3/18	43	33	10	20	20	0	ZFYVE16,stop_gained,p.Gln400Ter,ENST00000338008,;ZFYVE16,stop_gained,p.Gln400Ter,ENST00000505560,;ZFYVE16,stop_gained,p.Gln400Ter,ENST00000510158,;ZFYVE16,upstream_gene_variant,,ENST00000511050,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000510995,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000512558,;ZFYVE16,downstream_gene_variant,,ENST00000509562,;	T	ENSG00000039319	ENST00000338008	Transcript	stop_gained	1378	1198	400	Q/*	Cag/Tag	.	.	.	1	ZFYVE16	HGNC	20756	protein_coding	YES	CCDS4050.1	ENSP00000337159	ZFY16_HUMAN	B3KXA7_HUMAN	UPI000013F4A0	.	.	.	3/18	.	hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF43,PIRSF_domain:PIRSF037289	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCAGCAT	.	5	ESCA
ZFYVE16	0	.	GRCh37	5	79733788	79733788	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1284C>G	p.Phe428Leu	p.F428L	ENST00000338008	3/18	42	33	9	17	17	0	ZFYVE16,missense_variant,p.Phe428Leu,ENST00000338008,;ZFYVE16,missense_variant,p.Phe428Leu,ENST00000505560,;ZFYVE16,missense_variant,p.Phe428Leu,ENST00000510158,;ZFYVE16,upstream_gene_variant,,ENST00000511050,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000510995,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000512558,;ZFYVE16,downstream_gene_variant,,ENST00000509562,;	G	ENSG00000039319	ENST00000338008	Transcript	missense_variant	1464	1284	428	F/L	ttC/ttG	.	.	.	1	ZFYVE16	HGNC	20756	protein_coding	YES	CCDS4050.1	ENSP00000337159	ZFY16_HUMAN	B3KXA7_HUMAN	UPI000013F4A0	.	tolerated(0.74)	benign(0.001)	3/18	.	hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF43,PIRSF_domain:PIRSF037289	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATTCAAAGA	.	5	ESCA
VCAN	0	.	GRCh37	5	82837230	82837230	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8408A>G	p.Asn2803Ser	p.N2803S	ENST00000265077	8/15	37	20	16	26	26	0	VCAN,missense_variant,p.Asn2803Ser,ENST00000265077,;VCAN,missense_variant,p.Asn1816Ser,ENST00000343200,;VCAN,intron_variant,,ENST00000342785,;VCAN,intron_variant,,ENST00000502527,;VCAN,intron_variant,,ENST00000512590,;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,;	G	ENSG00000038427	ENST00000265077	Transcript	missense_variant	8973	8408	2803	N/S	aAt/aGt	.	.	.	1	VCAN	HGNC	2464	protein_coding	YES	CCDS4060.1	ENSP00000265077	CSPG2_HUMAN	.	UPI000013178B	.	tolerated(0.8)	benign(0.002)	8/15	.	hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCAATCCCC	.	5	ESCA
MYB	0	.	GRCh37	6	135515008	135515008	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.795A>C	p.Leu265Phe	p.L265F	ENST00000341911	7/16	51	37	14	61	61	0	MYB,missense_variant,p.Leu265Phe,ENST00000533624,;MYB,missense_variant,p.Leu265Phe,ENST00000527615,;MYB,missense_variant,p.Leu265Phe,ENST00000525369,;MYB,missense_variant,p.Leu265Phe,ENST00000442647,;MYB,missense_variant,p.Leu265Phe,ENST00000528774,;MYB,missense_variant,p.Leu219Phe,ENST00000430686,;MYB,missense_variant,p.Leu265Phe,ENST00000534044,;MYB,missense_variant,p.Leu265Phe,ENST00000534121,;MYB,missense_variant,p.Leu265Phe,ENST00000316528,;MYB,missense_variant,p.Leu265Phe,ENST00000367814,;MYB,missense_variant,p.Leu241Phe,ENST00000420123,;MYB,missense_variant,p.Leu265Phe,ENST00000341911,;MYB-AS1,downstream_gene_variant,,ENST00000455534,;MYB,non_coding_transcript_exon_variant,,ENST00000531845,;MYB,missense_variant,p.Leu265Phe,ENST00000533384,;MYB,missense_variant,p.Leu265Phe,ENST00000526320,;MYB,missense_variant,p.Leu265Phe,ENST00000525514,;MYB,missense_variant,p.Leu265Phe,ENST00000367812,;MYB,missense_variant,p.Leu265Phe,ENST00000339290,;MYB,missense_variant,p.Leu265Phe,ENST00000526187,;MYB,missense_variant,p.Leu265Phe,ENST00000529262,;MYB,missense_variant,p.Leu265Phe,ENST00000525002,;MYB,missense_variant,p.Leu265Phe,ENST00000526565,;MYB,missense_variant,p.Leu265Phe,ENST00000528343,;MYB,missense_variant,p.Leu265Phe,ENST00000529586,;MYB,missense_variant,p.Leu265Phe,ENST00000438901,;MYB,missense_variant,p.Leu265Phe,ENST00000533837,;MYB,missense_variant,p.Leu265Phe,ENST00000463282,;MYB,missense_variant,p.Leu265Phe,ENST00000525477,;MYB,missense_variant,p.Leu265Phe,ENST00000533808,;MYB,missense_variant,p.Leu265Phe,ENST00000528140,;MYB,missense_variant,p.Leu265Phe,ENST00000525940,;MYB,missense_variant,p.Leu241Phe,ENST00000528345,;MYB,missense_variant,p.Leu265Phe,ENST00000531519,;MYB,missense_variant,p.Leu265Phe,ENST00000528015,;MYB,missense_variant,p.Leu265Phe,ENST00000526889,;MYB,missense_variant,p.Leu265Phe,ENST00000531737,;MYB,3_prime_UTR_variant,,ENST00000524588,;MYB,3_prime_UTR_variant,,ENST00000531634,;MYB,upstream_gene_variant,,ENST00000534736,;	C	ENSG00000118513	ENST00000341911	Transcript	missense_variant	994	795	265	L/F	ttA/ttC	.	.	.	1	MYB	HGNC	7545	protein_coding	YES	CCDS47481.1	ENSP00000339992	MYB_HUMAN	Q9UMI7_HUMAN	UPI000002AE9A	.	tolerated(0.48)	probably_damaging(0.994)	7/16	.	hmmpanther:PTHR10641:SF454,hmmpanther:PTHR10641	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGTTACATGT	.	5	ESCA
QKI	0	.	GRCh37	6	163836333	163836333	+	Silent	SNP	G	G	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108G>T	p.%3D	p.G36G	ENST00000361752	1/8	26	20	6	34	34	0	QKI,synonymous_variant,p.%3D,ENST00000424802,;QKI,synonymous_variant,p.%3D,ENST00000361195,;QKI,synonymous_variant,p.%3D,ENST00000453779,;QKI,synonymous_variant,p.%3D,ENST00000275262,;QKI,synonymous_variant,p.%3D,ENST00000392127,;QKI,synonymous_variant,p.%3D,ENST00000361752,;QKI,upstream_gene_variant,,ENST00000544436,;CAHM,upstream_gene_variant,,ENST00000604200,;QKI,synonymous_variant,p.%3D,ENST00000361758,;QKI,synonymous_variant,p.%3D,ENST00000545607,;	T	ENSG00000112531	ENST00000361752	Transcript	synonymous_variant	659	108	36	G	ggG/ggT	.	.	.	1	QKI	HGNC	21100	protein_coding	YES	CCDS5285.1	ENSP00000355094	QKI_HUMAN	F5H8C8_HUMAN,F5H5U6_HUMAN,F5GYM3_HUMAN	UPI0000029EBD	.	.	.	1/8	.	hmmpanther:PTHR11208:SF36,hmmpanther:PTHR11208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGGGATCTT	.	5	ESCA
HIST1H3G	0	.	GRCh37	6	26271561	26271561	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.52C>T	p.Arg18Cys	p.R18C	ENST00000305910	1/1	56	41	14	56	56	0	HIST1H3G,missense_variant,p.Arg18Cys,ENST00000305910,;HIST1H2BI,upstream_gene_variant,,ENST00000377733,;HIST1H2APS4,downstream_gene_variant,,ENST00000362070,;	A	ENSG00000256018	ENST00000305910	Transcript	missense_variant	52	52	18	R/C	Cgc/Tgc	.	.	.	-1	HIST1H3G	HGNC	4772	protein_coding	YES	CCDS4602.1	ENSP00000439660	H31_HUMAN	.	UPI00000003C7	.	deleterious_low_confidence(0)	probably_damaging(0.956)	1/1	.	hmmpanther:PTHR11426,PROSITE_patterns:PS00322,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGCGCGGCG	.	5	ESCA
VARS2	0	.	GRCh37	6	30888139	30888139	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1413G>A	p.%3D	p.K471K	ENST00000541562	14/30	18	12	6	16	16	0	VARS2,synonymous_variant,p.%3D,ENST00000321897,;VARS2,synonymous_variant,p.%3D,ENST00000542001,;VARS2,synonymous_variant,p.%3D,ENST00000541562,;VARS2,synonymous_variant,p.%3D,ENST00000416670,;VARS2,downstream_gene_variant,,ENST00000428017,;VARS2,downstream_gene_variant,,ENST00000421263,;VARS2,non_coding_transcript_exon_variant,,ENST00000476162,;VARS2,downstream_gene_variant,,ENST00000467717,;VARS2,non_coding_transcript_exon_variant,,ENST00000469358,;VARS2,non_coding_transcript_exon_variant,,ENST00000477288,;VARS2,upstream_gene_variant,,ENST00000477052,;VARS2,downstream_gene_variant,,ENST00000490699,;VARS2,upstream_gene_variant,,ENST00000473916,;	A	ENSG00000137411	ENST00000541562	Transcript	synonymous_variant	1494	1413	471	K	aaG/aaA	.	.	.	1	VARS2	HGNC	21642	protein_coding	YES	CCDS54980.1	ENSP00000441000	SYVM_HUMAN	B7ZCJ6_HUMAN,A2ABL6_HUMAN	UPI0001BDAB0F	.	.	.	14/30	.	Superfamily_domains:SSF50677,Pfam_domain:PF00133,Gene3D:3.90.740.10,TIGRFAM_domain:TIGR00422,hmmpanther:PTHR11946:SF71,hmmpanther:PTHR11946	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGATAAT	.	4	ESCA
CDC5L	0	.	GRCh37	6	44355478	44355478	+	5'UTR	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-83G>A	.	.	ENST00000371477	1/16	83	41	42	76	76	0	CDC5L,5_prime_UTR_variant,,ENST00000371477,;	A	ENSG00000096401	ENST00000371477	Transcript	5_prime_UTR_variant	217	.	.	.	.	.	.	.	1	CDC5L	HGNC	1743	protein_coding	YES	CCDS4912.1	ENSP00000360532	CDC5L_HUMAN	.	UPI000006EE42	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCGGCTTT	.	5	ESCA
CRISP1	0	.	GRCh37	6	49825077	49825077	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37G>A	p.Ala13Thr	p.A13T	ENST00000335847	2/8	34	29	5	24	24	0	CRISP1,missense_variant,p.Ala13Thr,ENST00000507853,;CRISP1,missense_variant,p.Ala13Thr,ENST00000329411,;CRISP1,missense_variant,p.Ala13Thr,ENST00000335847,;CRISP1,missense_variant,p.Ala13Thr,ENST00000536021,;CRISP1,missense_variant,p.Ala13Thr,ENST00000505118,;CRISP1,missense_variant,p.Ala13Thr,ENST00000355791,;	T	ENSG00000124812	ENST00000335847	Transcript	missense_variant	139	37	13	A/T	Gct/Act	COSM1445022	.	.	-1	CRISP1	HGNC	304	protein_coding	YES	CCDS4931.1	ENSP00000338276	CRIS1_HUMAN	.	UPI0000128482	.	tolerated(0.17)	benign(0.197)	2/8	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF68,Superfamily_domains:SSF55797	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAAGCAGCAG	.	4	ESCA
EYS	0	.	GRCh37	6	65655728	65655728	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2339G>T	p.Cys780Phe	p.C780F	ENST00000503581	15/43	55	36	19	39	38	1	EYS,missense_variant,p.Cys780Phe,ENST00000370616,;EYS,missense_variant,p.Cys780Phe,ENST00000370621,;EYS,missense_variant,p.Cys780Phe,ENST00000503581,;	A	ENSG00000188107	ENST00000503581	Transcript	missense_variant	2877	2339	780	C/F	tGc/tTc	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	deleterious(0)	probably_damaging(0.955)	15/43	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048,PROSITE_patterns:PS01187,Gene3D:2gy5A03,Pfam_domain:PF00008,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTTGCAAGGA	.	4	ESCA
COL9A1	0	.	GRCh37	6	70978510	70978510	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1284G>A	p.Met428Ile	p.M428I	ENST00000357250	17/38	28	24	3	12	12	0	COL9A1,missense_variant,p.Met185Ile,ENST00000370499,;COL9A1,missense_variant,p.Met185Ile,ENST00000320755,;COL9A1,missense_variant,p.Met428Ile,ENST00000357250,;COL9A1,non_coding_transcript_exon_variant,,ENST00000489611,;	T	ENSG00000112280	ENST00000357250	Transcript	missense_variant	1443	1284	428	M/I	atG/atA	.	.	.	-1	COL9A1	HGNC	2217	protein_coding	YES	CCDS4971.1	ENSP00000349790	CO9A1_HUMAN	.	UPI000020D14B	.	.	possibly_damaging(0.472)	17/38	.	hmmpanther:PTHR24023:SF454,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCCTCATGCC	.	4	ESCA
MDN1	0	.	GRCh37	6	90398430	90398430	+	Silent	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11121G>A	p.%3D	p.V3707V	ENST00000369393	66/102	17	11	6	19	19	0	MDN1,synonymous_variant,p.%3D,ENST00000369393,;MDN1,synonymous_variant,p.%3D,ENST00000428876,;	T	ENSG00000112159	ENST00000369393	Transcript	synonymous_variant	11237	11121	3707	V	gtG/gtA	.	.	.	-1	MDN1	HGNC	18302	protein_coding	YES	CCDS5024.1	ENSP00000358400	MDN1_HUMAN	M0QXR3_HUMAN	UPI000013C4B8	.	.	.	66/102	.	hmmpanther:PTHR22908:SF58,hmmpanther:PTHR22908,PIRSF_domain:PIRSF010340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTTCACCAT	.	5	ESCA
DPY19L2P2	0	.	GRCh37	7	102920598	102920598	+	RNA	SNP	A	A	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.260T>C	.	.	ENST00000312132	1/23	36	27	9	40	40	0	DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000411491,;DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000438364,;DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000312132,;DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000439473,;DPY19L2P2,non_coding_transcript_exon_variant,,ENST00000446373,;DPY19L2P2,upstream_gene_variant,,ENST00000435536,;	G	ENSG00000170629	ENST00000312132	Transcript	non_coding_transcript_exon_variant	260	.	.	.	.	.	.	.	-1	DPY19L2P2	HGNC	21764	processed_transcript	YES	.	.	.	.	.	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCATAATT	.	5	ESCA
FAM131B	0	.	GRCh37	7	143050700	143050700	+	3'UTR	SNP	T	T	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2943A>G	.	.	ENST00000443739	7/7	48	33	15	38	38	0	FAM131B,3_prime_UTR_variant,,ENST00000443739,;FAM131B,3_prime_UTR_variant,,ENST00000409408,;FAM131B,3_prime_UTR_variant,,ENST00000409346,;FAM131B,3_prime_UTR_variant,,ENST00000409578,;CLCN1,downstream_gene_variant,,ENST00000343257,;FAM131B,downstream_gene_variant,,ENST00000409222,;FAM131B,3_prime_UTR_variant,,ENST00000410085,;FAM131B,downstream_gene_variant,,ENST00000521347,;FAM131B,downstream_gene_variant,,ENST00000519279,;	C	ENSG00000159784	ENST00000443739	Transcript	3_prime_UTR_variant	4175	.	.	.	.	.	.	.	-1	FAM131B	HGNC	22202	protein_coding	YES	CCDS47734.1	ENSP00000410603	F131B_HUMAN	D3DXE4_HUMAN	UPI0001633639	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCTCTCTT	.	5	ESCA
CHPF2	0	.	GRCh37	7	150935679	150935679	+	Missense_Mutation	SNP	G	G	A	rs578130308	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2231G>A	p.Arg744His	p.R744H	ENST00000035307	4/4	24	21	3	23	23	0	CHPF2,missense_variant,p.Arg744His,ENST00000035307,;CHPF2,missense_variant,p.Arg736His,ENST00000495645,;CHPF2,downstream_gene_variant,,ENST00000482173,;SMARCD3,downstream_gene_variant,,ENST00000491651,;SMARCD3,downstream_gene_variant,,ENST00000262188,;SMARCD3,downstream_gene_variant,,ENST00000392811,;SMARCD3,downstream_gene_variant,,ENST00000356800,;MIR671,downstream_gene_variant,,ENST00000390183,;RP4-548D19.3,upstream_gene_variant,,ENST00000607902,;SMARCD3,downstream_gene_variant,,ENST00000489503,;SMARCD3,downstream_gene_variant,,ENST00000477169,;SMARCD3,downstream_gene_variant,,ENST00000496530,;SMARCD3,downstream_gene_variant,,ENST00000460431,;SMARCD3,downstream_gene_variant,,ENST00000470588,;SMARCD3,downstream_gene_variant,,ENST00000485592,;SMARCD3,downstream_gene_variant,,ENST00000472988,;SMARCD3,downstream_gene_variant,,ENST00000472103,;SMARCD3,downstream_gene_variant,,ENST00000469154,;SMARCD3,downstream_gene_variant,,ENST00000485610,;CHPF2,downstream_gene_variant,,ENST00000465601,;SMARCD3,downstream_gene_variant,,ENST00000472789,;	A	ENSG00000033100	ENST00000035307	Transcript	missense_variant	3744	2231	744	R/H	cGc/cAc	rs578130308	.	.	1	CHPF2	HGNC	29270	protein_coding	YES	CCDS34779.1	ENSP00000035307	CHPF2_HUMAN	.	UPI000003F537	.	deleterious(0.03)	benign(0.413)	4/4	.	hmmpanther:PTHR12369:SF14,hmmpanther:PTHR12369,Pfam_domain:PF05679	A:0.0006	A:0	A:0	.	A:0	A:0	A:0.0031	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACCGCTGCC	byFrequency|by1000G	2	ESCA
AMPH	0	.	GRCh37	7	38468255	38468255	+	Intron	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182+1187C>T	.	.	ENST00000356264	.	64	51	12	44	44	0	AMPH,intron_variant,,ENST00000356264,;AMPH,intron_variant,,ENST00000428293,;AMPH,intron_variant,,ENST00000441628,;AMPH,intron_variant,,ENST00000325590,;AMPH,non_coding_transcript_exon_variant,,ENST00000471913,;AMPH,intron_variant,,ENST00000467580,;AMPH,intron_variant,,ENST00000462072,;AMPH,intron_variant,,ENST00000450124,;	A	ENSG00000078053	ENST00000356264	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	AMPH	HGNC	471	protein_coding	YES	CCDS5456.1	ENSP00000348602	AMPH_HUMAN	Q9UQI5_HUMAN,Q9UQI4_HUMAN,Q9UQI3_HUMAN,Q9UQI2_HUMAN	UPI00001259EA	.	.	.	.	14/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTAGATACA	.	5	ESCA
INHBA	0	.	GRCh37	7	41730069	41730069	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.460G>A	p.Glu154Lys	p.E154K	ENST00000242208	3/3	21	12	8	19	19	0	INHBA,missense_variant,p.Glu154Lys,ENST00000442711,;INHBA,missense_variant,p.Glu154Lys,ENST00000242208,;AC005027.3,intron_variant,,ENST00000416150,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,;	T	ENSG00000122641	ENST00000242208	Transcript	missense_variant	707	460	154	E/K	Gaa/Aaa	.	.	.	-1	INHBA	HGNC	6066	protein_coding	YES	CCDS5464.1	ENSP00000242208	INHBA_HUMAN	A4D1W7_HUMAN	UPI000012D421	.	deleterious(0.02)	benign(0.393)	3/3	.	hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF133,Pfam_domain:PF00688	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTTCTGCAC	.	5	ESCA
FZD1	0	.	GRCh37	7	90896512	90896512	+	3'UTR	SNP	G	G	C	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*373G>C	.	.	ENST00000287934	1/1	41	34	6	31	31	0	FZD1,3_prime_UTR_variant,,ENST00000287934,;	C	ENSG00000157240	ENST00000287934	Transcript	3_prime_UTR_variant	2730	.	.	.	.	.	.	.	1	FZD1	HGNC	4038	protein_coding	YES	CCDS5620.1	ENSP00000287934	FZD1_HUMAN	.	UPI000005104D	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTGAGGCT	.	5	ESCA
TMEM249	0	.	GRCh37	8	145578374	145578374	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54C>T	p.%3D	p.F18F	ENST00000398633	1/5	34	21	12	34	34	0	TMEM249,synonymous_variant,p.%3D,ENST00000398633,;TMEM249,synonymous_variant,p.%3D,ENST00000526263,;SLC52A2,intron_variant,,ENST00000524541,;SLC52A2,upstream_gene_variant,,ENST00000532887,;SLC52A2,upstream_gene_variant,,ENST00000527078,;SLC52A2,upstream_gene_variant,,ENST00000530047,;FBXL6,downstream_gene_variant,,ENST00000331890,;SLC52A2,upstream_gene_variant,,ENST00000540505,;SLC52A2,upstream_gene_variant,,ENST00000526338,;FBXL6,downstream_gene_variant,,ENST00000455319,;SLC52A2,upstream_gene_variant,,ENST00000526752,;SLC52A2,upstream_gene_variant,,ENST00000402965,;SLC52A2,upstream_gene_variant,,ENST00000534725,;SLC52A2,upstream_gene_variant,,ENST00000329994,;SLC52A2,intron_variant,,ENST00000532815,;FBXL6,downstream_gene_variant,,ENST00000530687,;FBXL6,downstream_gene_variant,,ENST00000524909,;FBXL6,downstream_gene_variant,,ENST00000526524,;FBXL6,downstream_gene_variant,,ENST00000527000,;SLC52A2,upstream_gene_variant,,ENST00000526891,;GS1-393G12.13,3_prime_UTR_variant,,ENST00000531225,;SLC52A2,upstream_gene_variant,,ENST00000526779,;SLC52A2,upstream_gene_variant,,ENST00000533662,;FBXL6,downstream_gene_variant,,ENST00000530142,;FBXL6,downstream_gene_variant,,ENST00000529279,;FBXL6,downstream_gene_variant,,ENST00000524492,;TMEM249,upstream_gene_variant,,ENST00000526503,;	A	ENSG00000214597	ENST00000398633	Transcript	synonymous_variant	201	54	18	F	ttC/ttT	.	.	.	-1	TMEM249	HGNC	44155	protein_coding	YES	CCDS59117.1	ENSP00000381630	TM249_HUMAN	.	UPI000019984E	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGGAAGCG	.	5	ESCA
PSD3	0	.	GRCh37	8	18490287	18490287	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2246C>T	p.Ser749Leu	p.S749L	ENST00000327040	11/16	31	22	9	53	53	0	PSD3,missense_variant,p.Ser684Leu,ENST00000523619,;PSD3,missense_variant,p.Ser749Leu,ENST00000327040,;PSD3,missense_variant,p.Ser751Leu,ENST00000440756,;PSD3,missense_variant,p.Ser78Leu,ENST00000428502,;PSD3,missense_variant,p.Ser215Leu,ENST00000286485,;PSD3,intron_variant,,ENST00000521878,;PSD3,3_prime_UTR_variant,,ENST00000518315,;	A	ENSG00000156011	ENST00000327040	Transcript	missense_variant	2349	2246	749	S/L	tCa/tTa	.	.	.	-1	PSD3	HGNC	19093	protein_coding	YES	CCDS43720.1	ENSP00000324127	PSD3_HUMAN	E5RJE4_HUMAN,E5RJ29_HUMAN	UPI0000210A46	.	deleterious(0.04)	benign(0.048)	11/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTGAGGGA	.	5	ESCA
HR	0	.	GRCh37	8	21982912	21982912	+	Silent	SNP	G	G	A	rs369191252	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1662C>T	p.%3D	p.L554L	ENST00000381418	5/19	45	19	26	56	55	0	HR,synonymous_variant,p.%3D,ENST00000381418,;HR,synonymous_variant,p.%3D,ENST00000312841,;HR,upstream_gene_variant,,ENST00000517699,;HR,downstream_gene_variant,,ENST00000519619,;HR,downstream_gene_variant,,ENST00000522759,;HR,upstream_gene_variant,,ENST00000518461,;	A	ENSG00000168453	ENST00000381418	Transcript	synonymous_variant	3143	1662	554	L	ctC/ctT	rs369191252,COSM3647215	.	.	-1	HR	HGNC	5172	protein_coding	YES	CCDS6022.1	ENSP00000370826	HAIR_HUMAN	E5RK80_HUMAN	UPI000013EB0B	.	.	.	5/19	.	hmmpanther:PTHR12549:SF4,hmmpanther:PTHR12549	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGCGAGGCC	byFrequency|byCluster	5	ESCA
GNRH1	0	.	GRCh37	8	25280810	25280810	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37C>T	p.%3D	p.L13L	ENST00000276414	1/3	31	25	6	36	36	0	GNRH1,synonymous_variant,p.%3D,ENST00000276414,;GNRH1,synonymous_variant,p.%3D,ENST00000421054,;KCTD9,downstream_gene_variant,,ENST00000221200,;RP11-395I14.2,downstream_gene_variant,,ENST00000523840,;	A	ENSG00000147437	ENST00000276414	Transcript	synonymous_variant	1361	37	13	L	Cta/Tta	.	.	.	-1	GNRH1	HGNC	4419	protein_coding	YES	CCDS43725.1	ENSP00000276414	GON1_HUMAN	.	UPI000012B8EB	.	.	.	1/3	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10522,hmmpanther:PTHR10522:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTAGAATAA	.	5	ESCA
UNC5D	0	.	GRCh37	8	35651179	35651179	+	3'Flank	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000404895	.	67	54	13	49	49	0	UNC5D,3_prime_UTR_variant,,ENST00000453357,;AC012215.1,3_prime_UTR_variant,,ENST00000437887,;UNC5D,3_prime_UTR_variant,,ENST00000287272,;UNC5D,downstream_gene_variant,,ENST00000449677,;UNC5D,downstream_gene_variant,,ENST00000416672,;UNC5D,downstream_gene_variant,,ENST00000404895,;UNC5D,downstream_gene_variant,,ENST00000420357,;	A	ENSG00000156687	ENST00000404895	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3036	1	UNC5D	HGNC	18634	protein_coding	YES	CCDS6093.2	ENSP00000385143	UNC5D_HUMAN	.	UPI00001D6915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTACAACAT	.	5	ESCA
CHRNB3	0	.	GRCh37	8	42587155	42587155	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.705C>A	p.Phe235Leu	p.F235L	ENST00000289957	5/6	271	248	23	55	55	0	CHRNB3,missense_variant,p.Phe235Leu,ENST00000289957,;	A	ENSG00000147432	ENST00000289957	Transcript	missense_variant	833	705	235	F/L	ttC/ttA	.	.	.	1	CHRNB3	HGNC	1963	protein_coding	YES	CCDS6134.1	ENSP00000289957	ACHB3_HUMAN	.	UPI0000125272	.	deleterious(0)	probably_damaging(0.991)	5/6	.	Transmembrane_helices:TMhelix,Prints_domain:PR00252,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Gene3D:1.20.120.370,hmmpanther:PTHR18945:SF75,hmmpanther:PTHR18945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTATTCTATAC	.	3	ESCA
PLAG1	0	.	GRCh37	8	57079116	57079116	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1189G>C	p.Asp397His	p.D397H	ENST00000316981	5/5	40	18	21	32	32	0	PLAG1,missense_variant,p.Asp315His,ENST00000423799,;PLAG1,missense_variant,p.Asp397His,ENST00000316981,;PLAG1,missense_variant,p.Asp397His,ENST00000429357,;PLAG1,non_coding_transcript_exon_variant,,ENST00000522009,;	G	ENSG00000181690	ENST00000316981	Transcript	missense_variant	1669	1189	397	D/H	Gac/Cac	.	.	.	-1	PLAG1	HGNC	9045	protein_coding	YES	CCDS6165.1	ENSP00000325546	PLAG1_HUMAN	A7IT80_HUMAN,A7IT79_HUMAN	UPI000013FF2F	.	tolerated(0.07)	benign(0.122)	5/5	.	hmmpanther:PTHR10032:SF124,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTCTCCTG	.	5	ESCA
PENK	0	.	GRCh37	8	57358447	57358447	+	Silent	SNP	C	C	T	rs149051933	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66G>A	p.%3D	p.V22V	ENST00000314922	1/2	23	12	11	27	27	0	PENK,synonymous_variant,p.%3D,ENST00000314922,;PENK,synonymous_variant,p.%3D,ENST00000451791,;PENK,synonymous_variant,p.%3D,ENST00000518974,;PENK,synonymous_variant,p.%3D,ENST00000523051,;PENK,synonymous_variant,p.%3D,ENST00000518770,;PENK,synonymous_variant,p.%3D,ENST00000517415,;RP11-17A4.2,non_coding_transcript_exon_variant,,ENST00000518662,;PENK,upstream_gene_variant,,ENST00000523274,;PENK,downstream_gene_variant,,ENST00000521153,;	T	ENSG00000181195	ENST00000314922	Transcript	synonymous_variant	143	66	22	V	gtG/gtA	rs149051933	.	.	-1	PENK	HGNC	8831	protein_coding	YES	CCDS6168.1	ENSP00000324248	PENK_HUMAN	E5RFR1_HUMAN	UPI00001315A9	.	.	.	1/2	.	Prints_domain:PR01029,hmmpanther:PTHR11438:SF3,hmmpanther:PTHR11438	.	.	.	.	.	.	.	T:0	T:0.0005	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCGCACGGT	byFrequency|byCluster	5	ESCA
CHD7	0	.	GRCh37	8	61777889	61777889	+	Silent	SNP	C	C	G	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8391C>G	p.%3D	p.P2797P	ENST00000423902	38/38	15	10	4	18	18	0	CHD7,synonymous_variant,p.%3D,ENST00000423902,;CHD7,synonymous_variant,p.%3D,ENST00000524602,;CHD7,non_coding_transcript_exon_variant,,ENST00000528280,;CHD7,downstream_gene_variant,,ENST00000532149,;CHD7,downstream_gene_variant,,ENST00000531695,;	G	ENSG00000171316	ENST00000423902	Transcript	synonymous_variant	8870	8391	2797	P	ccC/ccG	.	.	.	1	CHD7	HGNC	20626	protein_coding	YES	CCDS47865.1	ENSP00000392028	CHD7_HUMAN	H0YDC1_HUMAN,E9PP20_HUMAN	UPI0000251DA6	.	.	.	38/38	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTGCCCCTGAT	.	4	ESCA
SLC10A5	0	.	GRCh37	8	82606673	82606673	+	Missense_Mutation	SNP	G	G	A	rs762483614	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535C>T	p.Leu179Phe	p.L179F	ENST00000518568	1/1	17	13	4	13	13	0	SLC10A5,missense_variant,p.Leu179Phe,ENST00000518568,;	A	ENSG00000253598	ENST00000518568	Transcript	missense_variant	1737	535	179	L/F	Ctt/Ttt	rs762483614	.	.	-1	SLC10A5	HGNC	22981	protein_coding	YES	CCDS34915.1	ENSP00000428612	NTCP5_HUMAN	.	UPI0000051F68	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF29,Pfam_domain:PF01758	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCCAAGAATTA	.	4	ESCA
ERP44	0	.	GRCh37	9	102744932	102744932	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1183delT	p.Tyr395IlefsTer6	p.Y395Ifs*6	ENST00000262455	12/12	46	31	15	24	24	0	ERP44,frameshift_variant,p.Tyr395IlefsTer6,ENST00000262455,;	-	ENSG00000023318	ENST00000262455	Transcript	frameshift_variant	1383	1183	395	Y/X	Tat/at	.	.	.	-1	ERP44	HGNC	18311	protein_coding	YES	CCDS35082.1	ENSP00000262455	ERP44_HUMAN	.	UPI0000072130	.	.	.	12/12	.	hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF49	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACCTATATTCAC	.	3	ESCA
MRPL50	0	.	GRCh37	9	104160850	104160850	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25A>T	p.Ile9Phe	p.I9F	ENST00000374865	1/2	41	29	12	34	34	0	MRPL50,missense_variant,p.Ile9Phe,ENST00000374865,;MRPL50,missense_variant,p.Ile9Phe,ENST00000539624,;ZNF189,upstream_gene_variant,,ENST00000339664,;ZNF189,upstream_gene_variant,,ENST00000259395,;ZNF189,upstream_gene_variant,,ENST00000374861,;	A	ENSG00000136897	ENST00000374865	Transcript	missense_variant	47	25	9	I/F	Att/Ttt	.	.	.	-1	MRPL50	HGNC	16654	protein_coding	YES	CCDS6753.1	ENSP00000363999	RM50_HUMAN	.	UPI0000073BDC	.	tolerated_low_confidence(0.24)	benign(0.001)	1/2	.	hmmpanther:PTHR31542:SF1,hmmpanther:PTHR31542	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTAATGCCCG	.	5	ESCA
ZNF462	0	.	GRCh37	9	109686919	109686919	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726C>A	p.Asn242Lys	p.N242K	ENST00000277225	3/13	43	21	22	17	17	0	ZNF462,missense_variant,p.Asn242Lys,ENST00000277225,;ZNF462,missense_variant,p.Asn242Lys,ENST00000457913,;ZNF462,intron_variant,,ENST00000472574,;RP11-508N12.4,downstream_gene_variant,,ENST00000451160,;ZNF462,upstream_gene_variant,,ENST00000441147,;ZNF462,upstream_gene_variant,,ENST00000374686,;ZNF462,upstream_gene_variant,,ENST00000480607,;	A	ENSG00000148143	ENST00000277225	Transcript	missense_variant	1015	726	242	N/K	aaC/aaA	.	.	.	1	ZNF462	HGNC	21684	protein_coding	YES	CCDS35096.1	ENSP00000277225	ZN462_HUMAN	U3KQ68_HUMAN,F5H0Z0_HUMAN	UPI0000470106	.	.	benign(0.403)	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAACTTTTG	.	5	ESCA
CAMSAP1	0	.	GRCh37	9	138703425	138703425	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4539C>T	p.%3D	p.I1513I	ENST00000389532	17/17	31	28	3	38	38	0	CAMSAP1,synonymous_variant,p.%3D,ENST00000389532,;CAMSAP1,synonymous_variant,p.%3D,ENST00000312405,;CAMSAP1,synonymous_variant,p.%3D,ENST00000409386,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000483991,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000482664,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000487868,;	A	ENSG00000130559	ENST00000389532	Transcript	synonymous_variant	4604	4539	1513	I	atC/atT	.	.	.	-1	CAMSAP1	HGNC	19946	protein_coding	YES	CCDS35176.2	ENSP00000374183	CAMP1_HUMAN	.	UPI0000EDA283	.	.	.	17/17	.	PROSITE_profiles:PS51508,hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF3,Pfam_domain:PF08683,SMART_domains:SM01051,Superfamily_domains:SSF50346	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTATGATGTA	.	2	ESCA
DDX58	0	.	GRCh37	9	32459470	32459470	+	Nonsense_Mutation	SNP	G	G	A	rs760856237	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2380C>T	p.Gln794Ter	p.Q794*	ENST00000379883	17/18	236	55	181	89	89	0	DDX58,stop_gained,p.Gln723Ter,ENST00000542096,;DDX58,stop_gained,p.Gln794Ter,ENST00000379883,;DDX58,stop_gained,p.Gln591Ter,ENST00000379868,;DDX58,stop_gained,p.Gln749Ter,ENST00000379882,;ACO1,downstream_gene_variant,,ENST00000309951,;	A	ENSG00000107201	ENST00000379883	Transcript	stop_gained	2538	2380	794	Q/*	Caa/Taa	rs760856237	.	.	-1	DDX58	HGNC	19102	protein_coding	YES	CCDS6526.1	ENSP00000369213	DDX58_HUMAN	A2A376_HUMAN	UPI000013C841	.	.	.	17/18	.	hmmpanther:PTHR14074,hmmpanther:PTHR14074:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTGACTAT	byFrequency	5	ESCA
PTPRD	0	.	GRCh37	9	8484252	8484252	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3280G>A	p.Gly1094Arg	p.G1094R	ENST00000381196	27/43	51	32	18	59	59	0	PTPRD,missense_variant,p.Gly673Arg,ENST00000397617,;PTPRD,missense_variant,p.Gly683Arg,ENST00000486161,;PTPRD,missense_variant,p.Gly1072Arg,ENST00000358503,;PTPRD,missense_variant,p.Gly1081Arg,ENST00000360074,;PTPRD,missense_variant,p.Gly1094Arg,ENST00000381196,;PTPRD,missense_variant,p.Gly673Arg,ENST00000397606,;PTPRD,missense_variant,p.Gly1094Arg,ENST00000356435,;PTPRD,missense_variant,p.Gly683Arg,ENST00000355233,;PTPRD,missense_variant,p.Gly680Arg,ENST00000397611,;PTPRD,missense_variant,p.Gly1094Arg,ENST00000540109,;PTPRD,missense_variant,p.Gly680Arg,ENST00000537002,;PTPRD,downstream_gene_variant,,ENST00000471274,;PTPRD,non_coding_transcript_exon_variant,,ENST00000477552,;	T	ENSG00000153707	ENST00000381196	Transcript	missense_variant	3824	3280	1094	G/R	Ggg/Agg	.	.	.	-1	PTPRD	HGNC	9668	protein_coding	YES	CCDS43786.1	ENSP00000370593	PTPRD_HUMAN	C9J6E4_HUMAN,B4DK48_HUMAN	UPI0000132990	.	deleterious(0.01)	probably_damaging(0.999)	27/43	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCCACCAG	.	5	ESCA
MST4	0	.	GRCh37	X	131209203	131209203	+	3'UTR	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1016C>T	.	.	ENST00000394334	12/12	20	3	17	16	16	0	MST4,3_prime_UTR_variant,,ENST00000394334,;MST4,3_prime_UTR_variant,,ENST00000394335,;MST4,3_prime_UTR_variant,,ENST00000354719,;FRMD7,downstream_gene_variant,,ENST00000464296,;FRMD7,downstream_gene_variant,,ENST00000370879,;FRMD7,downstream_gene_variant,,ENST00000298542,;MST4,downstream_gene_variant,,ENST00000496850,;MST4,downstream_gene_variant,,ENST00000481105,;	T	ENSG00000134602	ENST00000394334	Transcript	3_prime_UTR_variant	2520	.	.	.	.	.	.	.	1	MST4	Uniprot_gn	.	protein_coding	YES	CCDS14631.1	ENSP00000377867	MST4_HUMAN	Q96SR7_HUMAN	UPI0000030CB8	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TAGTTCATATG	.	4	ESCA
L1CAM	0	.	GRCh37	X	153127555	153127555	+	3'UTR	SNP	G	G	A	rs782762599	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*563C>T	.	.	ENST00000370060	29/29	20	15	4	11	11	0	L1CAM,3_prime_UTR_variant,,ENST00000538883,;L1CAM,3_prime_UTR_variant,,ENST00000370060,;L1CAM,3_prime_UTR_variant,,ENST00000370055,;L1CAM,3_prime_UTR_variant,,ENST00000361981,;L1CAM,3_prime_UTR_variant,,ENST00000543994,;L1CAM,3_prime_UTR_variant,,ENST00000370057,;L1CAM,downstream_gene_variant,,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000455590,;L1CAM,downstream_gene_variant,,ENST00000361699,;L1CAM,downstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000491983,;	A	ENSG00000198910	ENST00000370060	Transcript	3_prime_UTR_variant	4527	.	.	.	.	rs782762599	.	.	-1	L1CAM	HGNC	6470	protein_coding	YES	CCDS14733.1	ENSP00000359077	L1CAM_HUMAN	Q86SE4_HUMAN,Q7Z3Z9_HUMAN,Q7Z2J9_HUMAN,Q7Z2J8_HUMAN,Q7Z2J6_HUMAN,Q7Z2J0_HUMAN,Q7Z2I3_HUMAN,Q7Z2H2_HUMAN,Q7Z2F9_HUMAN,E9PHJ4_HUMAN,E7EPI4_HUMAN	UPI0000126E89	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCGATGCT	.	5	ESCA
MECP2	0	.	GRCh37	X	153291359	153291359	+	3'Flank	SNP	C	C	T	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000453960	.	33	21	12	30	30	0	MECP2,3_prime_UTR_variant,,ENST00000303391,;MECP2,downstream_gene_variant,,ENST00000453960,;	T	ENSG00000169057	ENST00000453960	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4326	-1	MECP2	HGNC	6990	protein_coding	YES	CCDS48193.1	ENSP00000395535	MECP2_HUMAN	.	UPI0000253F1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTCTAAAG	.	5	ESCA
MED14	0	.	GRCh37	X	40513746	40513746	+	Silent	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4161C>T	p.%3D	p.I1387I	ENST00000324817	30/31	29	21	8	18	18	0	MED14,synonymous_variant,p.%3D,ENST00000433003,;MED14,synonymous_variant,p.%3D,ENST00000324817,;MED14,synonymous_variant,p.%3D,ENST00000416199,;MED14,downstream_gene_variant,,ENST00000472736,;	A	ENSG00000180182	ENST00000324817	Transcript	synonymous_variant	4280	4161	1387	I	atC/atT	.	.	.	-1	MED14	HGNC	2370	protein_coding	YES	CCDS14254.1	ENSP00000323720	MED14_HUMAN	.	UPI00001414B1	.	.	.	30/31	.	hmmpanther:PTHR12809,hmmpanther:PTHR12809:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATGATTGG	.	5	ESCA
AKAP4	0	.	GRCh37	X	49958407	49958407	+	Silent	SNP	C	C	T	rs782332911	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.957G>A	p.%3D	p.Q319Q	ENST00000358526	5/6	27	19	8	24	23	0	AKAP4,synonymous_variant,p.%3D,ENST00000358526,;AKAP4,synonymous_variant,p.%3D,ENST00000376056,;AKAP4,synonymous_variant,p.%3D,ENST00000376064,;AKAP4,intron_variant,,ENST00000448865,;AKAP4,intron_variant,,ENST00000376058,;AKAP4,downstream_gene_variant,,ENST00000437370,;AKAP4,non_coding_transcript_exon_variant,,ENST00000481402,;AKAP4,downstream_gene_variant,,ENST00000480926,;	T	ENSG00000147081	ENST00000358526	Transcript	synonymous_variant	1081	957	319	Q	caG/caA	rs782332911	.	.	-1	AKAP4	HGNC	374	protein_coding	YES	CCDS14329.1	ENSP00000351327	AKAP4_HUMAN	.	UPI000013DA96	.	.	.	5/6	.	hmmpanther:PTHR10226:SF8,hmmpanther:PTHR10226,Pfam_domain:PF05716,SMART_domains:SM00807	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCTCTGGGA	.	5	ESCA
RBMY1A1	0	.	GRCh37	Y	23702662	23702662	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-S8-A6BW-01A-11D-A31U-09	TCGA-S8-A6BW-10A-01D-A31U-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391+1G>A	.	p.X131_splice	ENST00000382707	.	152	134	18	341	341	0	RBMY1A1,splice_donor_variant,,ENST00000439108,;RBMY1A1,splice_donor_variant,,ENST00000382707,;RBMY1A1,splice_donor_variant,,ENST00000303902,;RBMY1A1,intron_variant,,ENST00000361046,;	A	ENSG00000234414	ENST00000382707	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	RBMY1A1	HGNC	9912	protein_coding	YES	CCDS14796.1	ENSP00000372154	RBY1A_HUMAN	J3QTP2_HUMAN	UPI000011D6E5	.	.	.	.	4/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGGGTAATG	.	4	ESCA
SORCS1	0	.	GRCh37	10	108459009	108459009	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1376G>C	p.Arg459Thr	p.R459T	ENST00000344440	9/27	40	24	16	38	38	0	SORCS1,missense_variant,p.Arg459Thr,ENST00000263054,;SORCS1,missense_variant,p.Arg459Thr,ENST00000344440,;SORCS1,5_prime_UTR_variant,,ENST00000369698,;	G	ENSG00000108018	ENST00000344440	Transcript	missense_variant	1376	1376	459	R/T	aGa/aCa	.	.	.	-1	SORCS1	HGNC	16697	protein_coding	YES	CCDS31283.1	ENSP00000345964	SORC1_HUMAN	B3KVZ0_HUMAN	UPI000036671B	.	deleterious(0.01)	possibly_damaging(0.541)	9/27	.	hmmpanther:PTHR12106:SF8,hmmpanther:PTHR12106,Gene3D:2.130.10.140,SMART_domains:SM00602,Superfamily_domains:SSF110296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCTGCTG	.	5	ESCA
RAB11FIP2	0	.	GRCh37	10	119768209	119768209	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*300A>G	.	.	ENST00000355624	5/5	35	25	10	29	29	0	RAB11FIP2,3_prime_UTR_variant,,ENST00000355624,;RAB11FIP2,downstream_gene_variant,,ENST00000369199,;RAB11FIP2,intron_variant,,ENST00000476207,;	C	ENSG00000107560	ENST00000355624	Transcript	3_prime_UTR_variant	2279	.	.	.	.	.	.	.	-1	RAB11FIP2	HGNC	29152	protein_coding	YES	CCDS7602.1	ENSP00000347839	RFIP2_HUMAN	.	UPI0000073B4B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGATATTTC	.	5	ESCA
KNDC1	0	.	GRCh37	10	135011900	135011900	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1966C>A	p.Gln656Lys	p.Q656K	ENST00000304613	13/30	41	30	11	57	57	0	KNDC1,missense_variant,p.Gln591Lys,ENST00000368571,;KNDC1,missense_variant,p.Gln656Lys,ENST00000304613,;KNDC1,missense_variant,p.Gln656Lys,ENST00000368572,;	A	ENSG00000171798	ENST00000304613	Transcript	missense_variant	1987	1966	656	Q/K	Cag/Aag	.	.	.	1	KNDC1	HGNC	29374	protein_coding	YES	CCDS7674.1	ENSP00000304437	VKIND_HUMAN	B4DFN0_HUMAN	UPI00003529F7	.	tolerated(0.22)	benign(0.017)	13/30	.	hmmpanther:PTHR21560:SF0,hmmpanther:PTHR21560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGCCAGCAC	.	5	ESCA
ACBD5	0	.	GRCh37	10	27486034	27486034	+	3'UTR	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*325G>C	.	.	ENST00000396271	13/13	112	101	11	93	93	0	ACBD5,3_prime_UTR_variant,,ENST00000375905,;ACBD5,3_prime_UTR_variant,,ENST00000375897,;ACBD5,3_prime_UTR_variant,,ENST00000375901,;ACBD5,3_prime_UTR_variant,,ENST00000396271,;ACBD5,downstream_gene_variant,,ENST00000375888,;RNU2-24P,upstream_gene_variant,,ENST00000516830,;	G	ENSG00000107897	ENST00000396271	Transcript	3_prime_UTR_variant	2030	.	.	.	.	.	.	.	-1	ACBD5	HGNC	23338	protein_coding	YES	CCDS44368.1	ENSP00000379568	ACBD5_HUMAN	.	UPI000046FE2B	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTACTCTATGG	.	4	ESCA
CSGALNACT2	0	.	GRCh37	10	43650484	43650484	+	5'UTR	SNP	C	C	T	rs547127881	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-114C>T	.	.	ENST00000374466	2/8	31	16	15	56	56	0	CSGALNACT2,5_prime_UTR_variant,,ENST00000374464,;CSGALNACT2,5_prime_UTR_variant,,ENST00000374466,;	T	ENSG00000169826	ENST00000374466	Transcript	5_prime_UTR_variant	222	.	.	.	.	rs547127881	.	.	1	CSGALNACT2	HGNC	24292	protein_coding	YES	CCDS7201.1	ENSP00000363590	CGAT2_HUMAN	.	UPI000000D725	.	.	.	2/8	.	.	T:0.0008	T:0.0015	T:0	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTACGGCAG	byFrequency|by1000G	5	ESCA
CALML3	0	.	GRCh37	10	5568054	5568054	+	3'UTR	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*556C>A	.	.	ENST00000315238	1/1	29	13	16	44	44	0	CALML3,3_prime_UTR_variant,,ENST00000315238,;CALML3-AS1,intron_variant,,ENST00000542093,;CALML3-AS1,intron_variant,,ENST00000545372,;CALML3-AS1,upstream_gene_variant,,ENST00000543008,;RP11-116G8.5,upstream_gene_variant,,ENST00000442008,;	A	ENSG00000178363	ENST00000315238	Transcript	3_prime_UTR_variant	1131	.	.	.	.	.	.	.	1	CALML3	HGNC	1452	protein_coding	YES	CCDS7069.1	ENSP00000315299	CALL3_HUMAN	.	UPI00000015FC	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCCGCGCT	.	4	ESCA
GATA3	0	.	GRCh37	10	8116088	8116088	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*102T>C	.	.	ENST00000379328	6/6	59	54	5	51	51	0	GATA3,3_prime_UTR_variant,,ENST00000346208,;GATA3,3_prime_UTR_variant,,ENST00000379328,;GATA3,downstream_gene_variant,,ENST00000461472,;	C	ENSG00000107485	ENST00000379328	Transcript	3_prime_UTR_variant	2005	.	.	.	.	.	.	.	1	GATA3	HGNC	4172	protein_coding	YES	CCDS31143.1	ENSP00000368632	GATA3_HUMAN	.	UPI000002AA34	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGGATATATG	.	3	ESCA
UBASH3B	0	.	GRCh37	11	122685091	122685091	+	3'UTR	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4497A>G	.	.	ENST00000284273	14/14	42	18	23	49	49	0	UBASH3B,3_prime_UTR_variant,,ENST00000284273,;	G	ENSG00000154127	ENST00000284273	Transcript	3_prime_UTR_variant	6822	.	.	.	.	.	.	.	1	UBASH3B	HGNC	29884	protein_coding	YES	CCDS31694.1	ENSP00000284273	UBS3B_HUMAN	.	UPI0000047471	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTATGGCA	.	5	ESCA
HBE1	0	.	GRCh37	11	5290883	5290883	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116C>A	p.Thr39Asn	p.T39N	ENST00000380237	4/5	39	20	18	59	59	0	HBE1,missense_variant,p.Thr39Asn,ENST00000396895,;HBE1,missense_variant,p.Thr39Asn,ENST00000380237,;HBE1,missense_variant,p.Thr39Asn,ENST00000292896,;HBG2,intron_variant,,ENST00000380252,;HBG2,intron_variant,,ENST00000380259,;	T	ENSG00000213931	ENST00000380237	Transcript	missense_variant	461	116	39	T/N	aCc/aAc	.	.	.	-1	HBE1	HGNC	4830	protein_coding	YES	CCDS7756.1	ENSP00000369586	HBE_HUMAN	D9YZU7_HUMAN,A8MUF7_HUMAN	UPI00000004B9	.	deleterious(0)	possibly_damaging(0.739)	4/5	.	Prints_domain:PR00814,Superfamily_domains:SSF46458,Gene3D:1.10.490.10,Pfam_domain:PF00042,hmmpanther:PTHR11442,hmmpanther:PTHR11442:SF7,PROSITE_profiles:PS01033	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R41K|c.122G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGGGTCCAG	.	5	ESCA
OR9Q1	0	.	GRCh37	11	57948685	57948685	+	3'UTR	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*836A>G	.	.	ENST00000335397	3/3	32	22	9	30	30	0	OR9Q1,3_prime_UTR_variant,,ENST00000335397,;	G	ENSG00000186509	ENST00000335397	Transcript	3_prime_UTR_variant	2085	.	.	.	.	.	.	.	1	OR9Q1	HGNC	14724	protein_coding	YES	CCDS31543.1	ENSP00000334934	OR9Q1_HUMAN	.	UPI0000041B48	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACCATTCCC	.	5	ESCA
OR56A3	0	.	GRCh37	11	5968694	5968694	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.118C>A	p.Leu40Ile	p.L40I	ENST00000329564	1/1	40	32	8	35	35	0	OR56A3,missense_variant,p.Leu40Ile,ENST00000329564,;AC025016.1,downstream_gene_variant,,ENST00000528915,;	A	ENSG00000184478	ENST00000329564	Transcript	missense_variant	125	118	40	L/I	Ctc/Atc	.	.	.	1	OR56A3	HGNC	14786	protein_coding	YES	CCDS41614.1	ENSP00000331572	O56A3_HUMAN	.	UPI0000041BF7	.	tolerated(0.24)	benign(0.014)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26450:SF40,hmmpanther:PTHR26450,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCCTCTTG	.	4	ESCA
VWCE	0	.	GRCh37	11	61048524	61048524	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.971G>T	p.Arg324Leu	p.R324L	ENST00000335613	8/20	65	61	4	76	76	0	VWCE,missense_variant,p.Arg324Leu,ENST00000335613,;VWCE,3_prime_UTR_variant,,ENST00000301770,;VWCE,downstream_gene_variant,,ENST00000535599,;	A	ENSG00000167992	ENST00000335613	Transcript	missense_variant	1358	971	324	R/L	cGa/cTa	.	.	.	-1	VWCE	HGNC	26487	protein_coding	YES	CCDS8002.1	ENSP00000334186	VWCE_HUMAN	B4DY31_HUMAN	UPI000013E751	.	tolerated(0.38)	benign(0.001)	8/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTAGTCGTGGG	.	2	ESCA
EML3	0	.	GRCh37	11	62371469	62371469	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2116A>G	p.Ile706Val	p.I706V	ENST00000394773	18/22	32	24	8	27	27	0	EML3,missense_variant,p.Ile707Val,ENST00000278845,;EML3,missense_variant,p.Ile678Val,ENST00000494176,;EML3,missense_variant,p.Ile706Val,ENST00000394773,;EML3,missense_variant,p.Ile706Val,ENST00000529309,;EML3,missense_variant,p.Ile700Val,ENST00000394776,;EML3,missense_variant,p.Ile489Val,ENST00000531557,;MTA2,upstream_gene_variant,,ENST00000524902,;MTA2,upstream_gene_variant,,ENST00000527204,;MTA2,upstream_gene_variant,,ENST00000278823,;EML3,upstream_gene_variant,,ENST00000439994,;RP11-831H9.3,upstream_gene_variant,,ENST00000532626,;EML3,downstream_gene_variant,,ENST00000438258,;EML3,3_prime_UTR_variant,,ENST00000494448,;EML3,non_coding_transcript_exon_variant,,ENST00000460939,;EML3,non_coding_transcript_exon_variant,,ENST00000533165,;EML3,downstream_gene_variant,,ENST00000526116,;EML3,downstream_gene_variant,,ENST00000462626,;EML3,downstream_gene_variant,,ENST00000483199,;MTA2,upstream_gene_variant,,ENST00000532239,;EML3,downstream_gene_variant,,ENST00000524518,;MTA2,upstream_gene_variant,,ENST00000526844,;	C	ENSG00000149499	ENST00000394773	Transcript	missense_variant	2424	2116	706	I/V	Atc/Gtc	.	.	.	-1	EML3	HGNC	26666	protein_coding	YES	CCDS8023.2	ENSP00000378254	EMAL3_HUMAN	G3V195_HUMAN,E9PJV5_HUMAN,C9J6V3_HUMAN	UPI0000228E33	.	tolerated(0.25)	probably_damaging(0.996)	18/22	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF15,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGATGTAGA	.	5	ESCA
C2CD3	0	.	GRCh37	11	73744881	73744881	+	3'Flank	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000313663	.	10	6	4	23	23	0	C2CD3,synonymous_variant,p.%3D,ENST00000334126,;C2CD3,downstream_gene_variant,,ENST00000414160,;C2CD3,downstream_gene_variant,,ENST00000313663,;C2CD3,downstream_gene_variant,,ENST00000538361,;C2CD3,non_coding_transcript_exon_variant,,ENST00000538625,;C2CD3,non_coding_transcript_exon_variant,,ENST00000542452,;C2CD3,downstream_gene_variant,,ENST00000540452,;C2CD3,3_prime_UTR_variant,,ENST00000442398,;	C	ENSG00000168014	ENST00000313663	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	598	-1	C2CD3	HGNC	24564	protein_coding	YES	CCDS31636.1	ENSP00000323339	C2CD3_HUMAN	.	UPI0000D62650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGGCCTTCCCT	.	3	ESCA
FAT3	0	.	GRCh37	11	92086682	92086682	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1404C>G	p.His468Gln	p.H468Q	ENST00000298047	1/27	24	20	4	44	44	0	FAT3,missense_variant,p.His468Gln,ENST00000541502,;FAT3,missense_variant,p.His468Gln,ENST00000298047,;FAT3,missense_variant,p.His468Gln,ENST00000409404,;FAT3,missense_variant,p.His318Gln,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,;	G	ENSG00000165323	ENST00000298047	Transcript	missense_variant	1421	1404	468	H/Q	caC/caG	.	.	.	1	FAT3	HGNC	23112	protein_coding	YES	.	ENSP00000298047	FAT3_HUMAN	E9PQ73_HUMAN	UPI000050B6C6	.	.	possibly_damaging(0.63)	1/27	.	Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,PROSITE_patterns:PS00232,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF33,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCACACCCC	.	5	ESCA
TAS2R13	0	.	GRCh37	12	11061603	11061603	+	Missense_Mutation	SNP	G	G	A	rs749247763	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295C>T	p.Leu99Phe	p.L99F	ENST00000390677	1/1	116	80	36	158	158	0	TAS2R13,missense_variant,p.Leu99Phe,ENST00000390677,;PRR4,intron_variant,,ENST00000539853,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000536086,;PRR4,intron_variant,,ENST00000546317,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;	A	ENSG00000212128	ENST00000390677	Transcript	missense_variant	559	295	99	L/F	Ctt/Ttt	rs749247763	.	.	-1	TAS2R13	HGNC	14919	protein_coding	YES	CCDS8635.1	ENSP00000375095	T2R13_HUMAN	Q50KQ5_HUMAN	UPI0000038B15	.	tolerated(0.27)	benign(0.317)	1/1	.	hmmpanther:PTHR11394:SF28,hmmpanther:PTHR11394,Pfam_domain:PF05296,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAAGCCAGA	.	5	ESCA
SOX5	0	.	GRCh37	12	23685997	23685999	+	3'UTR	DEL	ATC	ATC	-	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	ATC	ATC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1154_*1156delGAT	.	.	ENST00000451604	15/15	41	23	18	63	63	0	SOX5,3_prime_UTR_variant,,ENST00000309359,;SOX5,3_prime_UTR_variant,,ENST00000381381,;SOX5,3_prime_UTR_variant,,ENST00000546136,;SOX5,3_prime_UTR_variant,,ENST00000451604,;SOX5,downstream_gene_variant,,ENST00000537393,;SOX5,downstream_gene_variant,,ENST00000541536,;SOX5,downstream_gene_variant,,ENST00000396007,;SOX5,downstream_gene_variant,,ENST00000545921,;SOX5,downstream_gene_variant,,ENST00000367206,;	-	ENSG00000134532	ENST00000451604	Transcript	3_prime_UTR_variant	3548-3550	.	.	.	.	.	.	.	-1	SOX5	HGNC	11201	protein_coding	YES	CCDS8699.1	ENSP00000398273	SOX5_HUMAN	T2CYZ2_HUMAN,F5GWL1_HUMAN	UPI000007405E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATAATAATCAGACA	.	3	ESCA
LYRM5	0	.	GRCh37	12	25362207	25362207	+	3'Flank	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000381356	.	24	13	10	33	33	0	LYRM5,3_prime_UTR_variant,,ENST00000553788,;KRAS,3_prime_UTR_variant,,ENST00000311936,;KRAS,3_prime_UTR_variant,,ENST00000557334,;LYRM5,downstream_gene_variant,,ENST00000556927,;LYRM5,downstream_gene_variant,,ENST00000557540,;LYRM5,downstream_gene_variant,,ENST00000556885,;LYRM5,downstream_gene_variant,,ENST00000381356,;KRAS,downstream_gene_variant,,ENST00000256078,;LYRM5,downstream_gene_variant,,ENST00000556402,;LYRM5,downstream_gene_variant,,ENST00000556351,;LYRM5,downstream_gene_variant,,ENST00000555711,;	G	ENSG00000205707	ENST00000381356	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4259	1	LYRM5	HGNC	27052	protein_coding	YES	CCDS53764.1	ENSP00000370761	LYRM5_HUMAN	G3V521_HUMAN	UPI000013F600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAACTTTAC	.	5	ESCA
OVCH1	0	.	GRCh37	12	29596294	29596294	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3157G>T	p.Ala1053Ser	p.A1053S	ENST00000318184	25/28	111	84	27	91	91	0	OVCH1,stop_gained,p.Gly78Ter,ENST00000537054,;OVCH1,missense_variant,p.Ala1053Ser,ENST00000318184,;OVCH1-AS1,intron_variant,,ENST00000550906,;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,;OVCH1,missense_variant,p.Ala89Ser,ENST00000539117,;	A	ENSG00000187950	ENST00000318184	Transcript	missense_variant	3157	3157	1053	A/S	Gct/Tct	.	.	.	-1	OVCH1	HGNC	23080	protein_coding	YES	.	ENSP00000326708	OVCH1_HUMAN	.	UPI000040640A	.	deleterious(0.04)	benign(0.025)	25/28	.	hmmpanther:PTHR24259,hmmpanther:PTHR24259:SF64,Gene3D:2.60.120.290,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTACCTATTA	.	5	ESCA
C12orf4	0	.	GRCh37	12	4598576	4598576	+	3'UTR	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*397C>T	.	.	ENST00000261250	14/14	38	32	6	34	34	0	C12orf4,3_prime_UTR_variant,,ENST00000261250,;C12orf4,downstream_gene_variant,,ENST00000545746,;C12orf4,downstream_gene_variant,,ENST00000544258,;	A	ENSG00000047621	ENST00000261250	Transcript	3_prime_UTR_variant	2144	.	.	.	.	.	.	.	-1	C12orf4	HGNC	1184	protein_coding	YES	CCDS8528.1	ENSP00000261250	CL004_HUMAN	F5H744_HUMAN,F5GXX6_HUMAN	UPI0000038C60	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAGGAAAAT	.	2	ESCA
NACA	0	.	GRCh37	12	57114751	57114752	+	Frame_Shift_Del	DEL	AG	AG	-	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562_563delCT	p.Leu188Ter	p.L188*	ENST00000550952	3/11	56	40	16	34	34	0	NACA,frameshift_variant,p.Leu188Ter,ENST00000550952,;NACA,frameshift_variant,p.Leu188Ter,ENST00000454682,;NACA,intron_variant,,ENST00000546862,;NACA,intron_variant,,ENST00000548563,;NACA,intron_variant,,ENST00000546392,;NACA,intron_variant,,ENST00000356769,;NACA,intron_variant,,ENST00000549259,;NACA,intron_variant,,ENST00000552540,;NACA,intron_variant,,ENST00000393891,;NACA,intron_variant,,ENST00000552055,;NACA,intron_variant,,ENST00000549855,;NACA,upstream_gene_variant,,ENST00000550920,;NACA,downstream_gene_variant,,ENST00000546917,;NACA,intron_variant,,ENST00000551775,;NACA,intron_variant,,ENST00000551793,;NACA,intron_variant,,ENST00000548084,;NACA,intron_variant,,ENST00000547914,;NACA,intron_variant,,ENST00000551520,;	-	ENSG00000196531	ENST00000550952	Transcript	frameshift_variant	601-602	562-563	188	L/X	CTt/t	.	.	.	-1	NACA	HGNC	7629	protein_coding	YES	CCDS44925.2	ENSP00000448035	.	F8W1N5_HUMAN,F8VZJ2_HUMAN	UPI000014145D	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTATTAAGATTAG	.	3	ESCA
CPSF6	0	.	GRCh37	12	69656282	69656283	+	In_Frame_Ins	INS	-	-	CGTGACCGAGAC	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1611_1622dupCCGTGACCGAGA	p.Asp537_Arg540dup	p.D537_R540dup	ENST00000435070	9/10	310	139	171	41	41	0	CPSF6,inframe_insertion,p.Asp574_Arg577dup,ENST00000266679,;CPSF6,inframe_insertion,p.Thr40_Glu43dup,ENST00000551516,;CPSF6,inframe_insertion,p.Asp537_Arg540dup,ENST00000435070,;CPSF6,inframe_insertion,p.Asp464_Arg467dup,ENST00000456847,;CPSF6,downstream_gene_variant,,ENST00000547486,;	CGTGACCGAGAC	ENSG00000111605	ENST00000435070	Transcript	inframe_insertion	1709-1710	1599-1600	533-534	-/RDRD	-/CGTGACCGAGAC	.	.	.	1	CPSF6	HGNC	13871	protein_coding	YES	CCDS8988.1	ENSP00000391774	CPSF6_HUMAN	.	UPI00001FC746	.	.	.	9/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23204,hmmpanther:PTHR23204:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	23	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CGGGATCGTGA	.	2	ESCA
ZDHHC17	0	.	GRCh37	12	77243230	77243230	+	Silent	SNP	G	G	A	rs779385993	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1740G>A	p.%3D	p.T580T	ENST00000426126	16/17	190	154	36	202	202	0	ZDHHC17,synonymous_variant,p.%3D,ENST00000426126,;ZDHHC17,synonymous_variant,p.%3D,ENST00000334822,;ZDHHC17,non_coding_transcript_exon_variant,,ENST00000553091,;ZDHHC17,downstream_gene_variant,,ENST00000550789,;ZDHHC17,non_coding_transcript_exon_variant,,ENST00000547673,;ZDHHC17,non_coding_transcript_exon_variant,,ENST00000550244,;ZDHHC17,downstream_gene_variant,,ENST00000552693,;	A	ENSG00000186908	ENST00000426126	Transcript	synonymous_variant	2389	1740	580	T	acG/acA	rs779385993	.	.	1	ZDHHC17	HGNC	18412	protein_coding	YES	CCDS44946.1	ENSP00000403397	ZDH17_HUMAN	A8KA01_HUMAN	UPI0000051F55	.	.	.	16/17	.	hmmpanther:PTHR24161,hmmpanther:PTHR24161:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAACGTCTAT	.	4	ESCA
CSRP2	0	.	GRCh37	12	77259983	77259983	+	Missense_Mutation	SNP	C	C	T	rs766825277	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>A	p.Ala20Thr	p.A20T	ENST00000311083	2/6	36	32	4	18	18	0	CSRP2,missense_variant,p.Ala20Thr,ENST00000547435,;CSRP2,missense_variant,p.Ala20Thr,ENST00000552330,;CSRP2,missense_variant,p.Ala20Thr,ENST00000311083,;CSRP2,missense_variant,p.Ala20Thr,ENST00000546966,;CSRP2,non_coding_transcript_exon_variant,,ENST00000551725,;CSRP2,non_coding_transcript_exon_variant,,ENST00000547557,;CSRP2,upstream_gene_variant,,ENST00000548783,;	T	ENSG00000175183	ENST00000311083	Transcript	missense_variant	182	58	20	A/T	Gca/Aca	rs766825277	.	.	-1	CSRP2	HGNC	2470	protein_coding	YES	CCDS9015.1	ENSP00000310901	CSRP2_HUMAN	.	UPI000014104B	.	deleterious(0.02)	possibly_damaging(0.711)	2/6	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24215:SF3,hmmpanther:PTHR24215,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTGCGTGGT	byFrequency	4	ESCA
MYF6	0	.	GRCh37	12	81101624	81101624	+	Silent	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126C>A	p.%3D	p.S42S	ENST00000228641	1/3	35	28	6	52	52	0	MYF6,synonymous_variant,p.%3D,ENST00000228641,;	A	ENSG00000111046	ENST00000228641	Transcript	synonymous_variant	348	126	42	S	tcC/tcA	.	.	.	1	MYF6	HGNC	7566	protein_coding	YES	CCDS9019.1	ENSP00000228641	MYF6_HUMAN	.	UPI0000001050	.	.	.	1/3	.	hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF4,Pfam_domain:PF01586,SMART_domains:SM00520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TTGTCCCCCTG	.	3	ESCA
ANKS1B	0	.	GRCh37	12	99201655	99201655	+	Intron	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3067-6752A>G	.	.	ENST00000547776	.	61	50	11	70	70	0	ANKS1B,synonymous_variant,p.%3D,ENST00000549797,;ANKS1B,synonymous_variant,p.%3D,ENST00000551560,;ANKS1B,synonymous_variant,p.%3D,ENST00000549493,;ANKS1B,synonymous_variant,p.%3D,ENST00000546364,;ANKS1B,synonymous_variant,p.%3D,ENST00000333732,;ANKS1B,synonymous_variant,p.%3D,ENST00000550693,;ANKS1B,synonymous_variant,p.%3D,ENST00000332712,;ANKS1B,synonymous_variant,p.%3D,ENST00000549025,;ANKS1B,5_prime_UTR_variant,,ENST00000551613,;ANKS1B,intron_variant,,ENST00000552748,;ANKS1B,intron_variant,,ENST00000550778,;ANKS1B,intron_variant,,ENST00000547446,;ANKS1B,intron_variant,,ENST00000547010,;ANKS1B,intron_variant,,ENST00000341752,;ANKS1B,intron_variant,,ENST00000546568,;ANKS1B,intron_variant,,ENST00000552407,;ANKS1B,intron_variant,,ENST00000329257,;ANKS1B,intron_variant,,ENST00000546960,;ANKS1B,intron_variant,,ENST00000549558,;ANKS1B,intron_variant,,ENST00000547776,;ANKS1B,intron_variant,,ENST00000551830,;ANKS1B,intron_variant,,ENST00000547362,;	C	ENSG00000185046	ENST00000547776	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ANKS1B	HGNC	24600	protein_coding	YES	CCDS55872.1	ENSP00000449629	ANS1B_HUMAN	R4GN73_HUMAN,R4GN70_HUMAN,R4GN07_HUMAN	UPI00003FE521	.	.	.	.	19/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAATCCTGC	.	5	ESCA
DCT	0	.	GRCh37	13	95131328	95131328	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.182G>A	p.Cys61Tyr	p.C61Y	ENST00000446125	1/10	47	35	12	31	31	0	DCT,missense_variant,p.Cys61Tyr,ENST00000377028,;DCT,missense_variant,p.Cys61Tyr,ENST00000446125,;DCT,non_coding_transcript_exon_variant,,ENST00000472871,;	T	ENSG00000080166	ENST00000446125	Transcript	missense_variant	609	182	61	C/Y	tGc/tAc	.	.	.	-1	DCT	HGNC	2709	protein_coding	YES	CCDS45060.1	ENSP00000392762	TYRP2_HUMAN	Q9NQD8_HUMAN,Q0PK43_HUMAN	UPI0000E13F02	.	deleterious(0)	probably_damaging(0.999)	1/10	.	hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGCACTGC	.	5	ESCA
STK24	0	.	GRCh37	13	99127553	99127553	+	Silent	SNP	T	T	C	rs768243797	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426A>G	p.%3D	p.K142K	ENST00000376547	4/11	99	70	28	89	89	0	STK24,synonymous_variant,p.%3D,ENST00000539966,;STK24,synonymous_variant,p.%3D,ENST00000397517,;STK24,synonymous_variant,p.%3D,ENST00000444574,;STK24,synonymous_variant,p.%3D,ENST00000376547,;STK24,non_coding_transcript_exon_variant,,ENST00000491878,;	C	ENSG00000102572	ENST00000376547	Transcript	synonymous_variant	572	426	142	K	aaA/aaG	rs768243797	.	.	-1	STK24	HGNC	11403	protein_coding	YES	CCDS9488.1	ENSP00000365730	STK24_HUMAN	Q5JV99_HUMAN	UPI000013606E	.	.	.	4/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF208,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCCTTTCAG	.	5	ESCA
CDC42BPB	0	.	GRCh37	14	103450049	103450049	+	Silent	SNP	C	C	T	rs373702358	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.735G>A	p.%3D	p.P245P	ENST00000361246	7/37	9	6	3	13	13	0	CDC42BPB,synonymous_variant,p.%3D,ENST00000361246,;CDC42BPB,downstream_gene_variant,,ENST00000561271,;CDC42BPB,downstream_gene_variant,,ENST00000558321,;	T	ENSG00000198752	ENST00000361246	Transcript	synonymous_variant	1024	735	245	P	ccG/ccA	rs373702358	.	.	-1	CDC42BPB	HGNC	1738	protein_coding	YES	CCDS9978.1	ENSP00000355237	MRCKB_HUMAN	.	UPI000013D27E	.	.	.	7/37	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF30,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTCCGGCGA	byCluster|by1000G	2	ESCA
PABPN1	0	.	GRCh37	14	23790583	23790583	+	5'UTR	SNP	G	G	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96G>T	.	.	ENST00000216727	1/7	82	29	52	78	78	0	PABPN1,5_prime_UTR_variant,,ENST00000216727,;BCL2L2-PABPN1,intron_variant,,ENST00000557008,;BCL2L2-PABPN1,intron_variant,,ENST00000553781,;PABPN1,upstream_gene_variant,,ENST00000557702,;PABPN1,upstream_gene_variant,,ENST00000555295,;PABPN1,upstream_gene_variant,,ENST00000556821,;AL049829.1,downstream_gene_variant,,ENST00000594872,;BCL2L2-PABPN1,downstream_gene_variant,,ENST00000556100,;PABPN1,upstream_gene_variant,,ENST00000397276,;PABPN1,upstream_gene_variant,,ENST00000556809,;PABPN1,upstream_gene_variant,,ENST00000554062,;PABPN1,upstream_gene_variant,,ENST00000553960,;	T	ENSG00000100836	ENST00000216727	Transcript	5_prime_UTR_variant	86	.	.	.	.	.	.	.	1	PABPN1	HGNC	8565	protein_coding	YES	CCDS9592.1	ENSP00000216727	PABP2_HUMAN	G3V4T2_HUMAN	UPI000006F6E7	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTAGCTCAT	.	5	ESCA
FANCM	0	.	GRCh37	14	45606438	45606438	+	Silent	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.675T>C	p.%3D	p.Y225Y	ENST00000267430	2/23	56	14	41	59	59	0	FANCM,synonymous_variant,p.%3D,ENST00000556036,;FANCM,synonymous_variant,p.%3D,ENST00000542564,;FANCM,synonymous_variant,p.%3D,ENST00000267430,;FKBP3,upstream_gene_variant,,ENST00000396062,;FKBP3,upstream_gene_variant,,ENST00000216330,;FANCM,non_coding_transcript_exon_variant,,ENST00000554030,;FKBP3,upstream_gene_variant,,ENST00000557324,;	C	ENSG00000187790	ENST00000267430	Transcript	synonymous_variant	760	675	225	Y	taT/taC	.	.	.	1	FANCM	HGNC	23168	protein_coding	YES	CCDS32070.1	ENSP00000267430	FANCM_HUMAN	.	UPI000059F032	.	.	.	2/23	.	PROSITE_profiles:PS51192,hmmpanther:PTHR14025,hmmpanther:PTHR14025:SF20,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTATTGCCA	.	5	ESCA
KTN1	0	.	GRCh37	14	56111086	56111086	+	Intron	SNP	A	A	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2173-2605A>T	.	.	ENST00000395314	.	89	38	51	72	72	0	KTN1,5_prime_UTR_variant,,ENST00000554890,;KTN1,5_prime_UTR_variant,,ENST00000554507,;KTN1,intron_variant,,ENST00000395308,;KTN1,intron_variant,,ENST00000438792,;KTN1,intron_variant,,ENST00000395309,;KTN1,intron_variant,,ENST00000413890,;KTN1,intron_variant,,ENST00000395311,;KTN1,intron_variant,,ENST00000395314,;KTN1,intron_variant,,ENST00000416613,;KTN1,intron_variant,,ENST00000459737,;KTN1,intron_variant,,ENST00000553360,;	T	ENSG00000126777	ENST00000395314	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KTN1	HGNC	6467	protein_coding	YES	CCDS41957.1	ENSP00000378725	KTN1_HUMAN	Q5GGW3_HUMAN,G3V5P0_HUMAN,G3V4L8_HUMAN,G3V475_HUMAN	UPI0000190F88	.	.	.	.	18/43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGTATAAAA	.	5	ESCA
VSX2	0	.	GRCh37	14	74726335	74726335	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610A>G	p.Arg204Gly	p.R204G	ENST00000261980	4/5	53	43	9	61	61	0	VSX2,missense_variant,p.Arg204Gly,ENST00000261980,;	G	ENSG00000119614	ENST00000261980	Transcript	missense_variant	700	610	204	R/G	Agg/Ggg	.	.	.	1	VSX2	HGNC	1975	protein_coding	YES	CCDS9827.1	ENSP00000261980	VSX2_HUMAN	.	UPI0000128755	.	deleterious(0)	probably_damaging(1)	4/5	.	Superfamily_domains:SSF46689,SMART_domains:SM00389,Pfam_domain:PF00046,Gene3D:1.10.10.60,PROSITE_patterns:PS00027,hmmpanther:PTHR24329:SF251,hmmpanther:PTHR24329,PROSITE_profiles:PS50071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGGAGGAAG	.	5	ESCA
NEK9	0	.	GRCh37	14	75553865	75553865	+	Silent	SNP	C	C	T	rs145167526	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2673G>A	p.%3D	p.A891A	ENST00000238616	21/22	31	23	8	41	41	0	NEK9,synonymous_variant,p.%3D,ENST00000238616,;NEK9,upstream_gene_variant,,ENST00000555763,;NEK9,non_coding_transcript_exon_variant,,ENST00000557026,;NEK9,non_coding_transcript_exon_variant,,ENST00000556170,;NEK9,non_coding_transcript_exon_variant,,ENST00000555405,;	T	ENSG00000119638	ENST00000238616	Transcript	synonymous_variant	2832	2673	891	A	gcG/gcA	rs145167526	.	.	-1	NEK9	HGNC	18591	protein_coding	YES	CCDS9839.1	ENSP00000238616	NEK9_HUMAN	G3V5V0_HUMAN,G3V2Z5_HUMAN	UPI00001FD89B	.	.	.	21/22	.	.	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	T:0.0005	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCACGCACA	byCluster|by1000G	5	ESCA
IRF2BPL	0	.	GRCh37	14	77491597	77491597	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*148A>G	.	.	ENST00000238647	1/1	74	32	42	83	83	0	IRF2BPL,3_prime_UTR_variant,,ENST00000238647,;	C	ENSG00000119669	ENST00000238647	Transcript	3_prime_UTR_variant	3438	.	.	.	.	.	.	.	-1	IRF2BPL	HGNC	14282	protein_coding	YES	CCDS9854.1	ENSP00000238647	I2BPL_HUMAN	.	UPI00000738BA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTATACATA	.	5	ESCA
NRXN3	0	.	GRCh37	14	80329058	80329058	+	3'Flank	SNP	G	G	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000554719	.	51	35	16	56	56	0	NRXN3,3_prime_UTR_variant,,ENST00000281127,;NRXN3,3_prime_UTR_variant,,ENST00000428277,;NRXN3,downstream_gene_variant,,ENST00000554719,;NRXN3,downstream_gene_variant,,ENST00000557594,;NRXN3,downstream_gene_variant,,ENST00000335750,;NRXN3,downstream_gene_variant,,ENST00000556003,;NRXN3,downstream_gene_variant,,ENST00000555387,;NRXN3,downstream_gene_variant,,ENST00000554738,;	T	ENSG00000021645	ENST00000554719	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	272	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCTGTTGTT	.	5	ESCA
DNM1P46	0	.	GRCh37	15	100341320	100341320	+	RNA	SNP	C	C	T	rs749937025	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.327G>A	.	.	ENST00000341853	3/5	152	129	23	151	151	0	DNM1P46,non_coding_transcript_exon_variant,,ENST00000561042,;DNM1P46,non_coding_transcript_exon_variant,,ENST00000341853,;DNM1P46,non_coding_transcript_exon_variant,,ENST00000559110,;DNM1P46,non_coding_transcript_exon_variant,,ENST00000425045,;DNM1P46,non_coding_transcript_exon_variant,,ENST00000415963,;	T	ENSG00000182397	ENST00000341853	Transcript	non_coding_transcript_exon_variant	327	.	.	.	.	rs749937025	.	.	-1	DNM1P46	HGNC	35199	processed_transcript	YES	.	.	.	.	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGCCGCTCC	byFrequency	4	ESCA
CLK3	0	.	GRCh37	15	74922200	74922200	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1893C>T	p.%3D	p.H631H	ENST00000395066	13/13	33	20	12	32	32	0	CLK3,synonymous_variant,p.%3D,ENST00000352989,;CLK3,synonymous_variant,p.%3D,ENST00000395066,;CLK3,synonymous_variant,p.%3D,ENST00000345005,;CLK3,3_prime_UTR_variant,,ENST00000348245,;CLK3,intron_variant,,ENST00000563418,;CLK3,downstream_gene_variant,,ENST00000566926,;CLK3,downstream_gene_variant,,ENST00000568139,;EDC3,downstream_gene_variant,,ENST00000315127,;EDC3,downstream_gene_variant,,ENST00000569606,;CLK3,downstream_gene_variant,,ENST00000566126,;CLK3,downstream_gene_variant,,ENST00000564096,;EDC3,downstream_gene_variant,,ENST00000568176,;CLK3,downstream_gene_variant,,ENST00000563842,;CLK3,downstream_gene_variant,,ENST00000563297,;EDC3,downstream_gene_variant,,ENST00000426797,;CLK3,downstream_gene_variant,,ENST00000568488,;CLK3,intron_variant,,ENST00000561673,;CLK3,downstream_gene_variant,,ENST00000567805,;CLK3,3_prime_UTR_variant,,ENST00000483723,;CLK3,3_prime_UTR_variant,,ENST00000564468,;CLK3,non_coding_transcript_exon_variant,,ENST00000562078,;CLK3,non_coding_transcript_exon_variant,,ENST00000454830,;CLK3,non_coding_transcript_exon_variant,,ENST00000569406,;CLK3,non_coding_transcript_exon_variant,,ENST00000568232,;EDC3,downstream_gene_variant,,ENST00000565602,;CLK3,downstream_gene_variant,,ENST00000562626,;CLK3,downstream_gene_variant,,ENST00000568605,;CLK3,downstream_gene_variant,,ENST00000569063,;	T	ENSG00000179335	ENST00000395066	Transcript	synonymous_variant	2354	1893	631	H	caC/caT	.	.	.	1	CLK3	HGNC	2071	protein_coding	YES	CCDS45304.1	ENSP00000378505	CLK3_HUMAN	H3BVF8_HUMAN,H3BUL5_HUMAN,H3BTW9_HUMAN,H3BRT8_HUMAN,H3BRE4_HUMAN,B3KTV2_HUMAN	UPI0001529A1B	.	.	.	13/13	.	hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCACACCAG	.	5	ESCA
PRKCB	0	.	GRCh37	16	24231142	24231142	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5005T>C	.	.	ENST00000303531	17/17	25	15	10	35	34	0	PRKCB,3_prime_UTR_variant,,ENST00000303531,;PRKCB,intron_variant,,ENST00000321728,;	C	ENSG00000166501	ENST00000303531	Transcript	3_prime_UTR_variant	7179	.	.	.	.	.	.	.	1	PRKCB	HGNC	9395	protein_coding	YES	CCDS10619.1	ENSP00000305355	KPCB_HUMAN	I3L1Z0_HUMAN	UPI000002ACF9	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGTGCAGC	.	5	ESCA
RBBP6	0	.	GRCh37	16	24581686	24581686	+	Missense_Mutation	SNP	A	A	G	rs767099633	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3675A>G	p.Ile1225Met	p.I1225M	ENST00000319715	17/18	46	37	9	56	56	0	RBBP6,missense_variant,p.Ile1225Met,ENST00000319715,;RBBP6,missense_variant,p.Ile1191Met,ENST00000348022,;RBBP6,intron_variant,,ENST00000381039,;RBBP6,downstream_gene_variant,,ENST00000564314,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,;	G	ENSG00000122257	ENST00000319715	Transcript	missense_variant	4107	3675	1225	I/M	atA/atG	rs767099633	.	.	1	RBBP6	HGNC	9889	protein_coding	YES	CCDS10621.1	ENSP00000317872	RBBP6_HUMAN	I3L3Y2_HUMAN,H3BUN0_HUMAN,H3BSK8_HUMAN	UPI00001A96B8	.	deleterious_low_confidence(0.02)	unknown(0)	17/18	.	hmmpanther:PTHR15439:SF1,hmmpanther:PTHR15439	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATATCAAA	.	5	ESCA
ZNF688	0	.	GRCh37	16	30581404	30581404	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664A>G	p.Arg222Gly	p.R222G	ENST00000223459	3/3	45	37	8	33	33	0	ZNF688,missense_variant,p.Arg208Gly,ENST00000563276,;ZNF688,missense_variant,p.Arg222Gly,ENST00000223459,;ZNF688,missense_variant,p.Arg208Gly,ENST00000395219,;ZNF688,downstream_gene_variant,,ENST00000563707,;ZNF688,downstream_gene_variant,,ENST00000567855,;ZNF688,downstream_gene_variant,,ENST00000566632,;AC002310.7,upstream_gene_variant,,ENST00000492040,;AC002310.7,upstream_gene_variant,,ENST00000486926,;ZNF688,non_coding_transcript_exon_variant,,ENST00000563665,;ZNF785,downstream_gene_variant,,ENST00000562128,;ZNF688,downstream_gene_variant,,ENST00000562455,;	C	ENSG00000229809	ENST00000223459	Transcript	missense_variant	1769	664	222	R/G	Agg/Ggg	.	.	.	-1	ZNF688	HGNC	30489	protein_coding	YES	CCDS10684.1	ENSP00000223459	ZN688_HUMAN	.	UPI0000071FFC	.	deleterious(0.01)	probably_damaging(0.999)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF101,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCCTCTTGA	.	5	ESCA
FBRS	0	.	GRCh37	16	30680881	30680881	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2858T>C	p.Leu953Pro	p.L953P	ENST00000356166	18/18	36	33	3	30	30	0	FBRS,missense_variant,p.Leu433Pro,ENST00000287468,;FBRS,missense_variant,p.Leu345Pro,ENST00000568722,;FBRS,missense_variant,p.Leu953Pro,ENST00000356166,;FBRS,intron_variant,,ENST00000395073,;FBRS,3_prime_UTR_variant,,ENST00000543786,;FBRS,non_coding_transcript_exon_variant,,ENST00000494101,;FBRS,downstream_gene_variant,,ENST00000570170,;	C	ENSG00000156860	ENST00000356166	Transcript	missense_variant	3946	2858	953	L/P	cTt/cCt	.	.	.	1	FBRS	HGNC	20442	protein_coding	YES	.	ENSP00000348489	.	J3KNZ9_HUMAN	UPI0000E59D83	.	.	unknown(0)	18/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14429:SF19,hmmpanther:PTHR14429	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGCCCTTTTGG	.	3	ESCA
SETD1A	0	.	GRCh37	16	30982838	30982838	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3156C>T	p.%3D	p.S1052S	ENST00000262519	13/19	33	28	5	33	33	0	SETD1A,synonymous_variant,p.%3D,ENST00000262519,;	T	ENSG00000099381	ENST00000262519	Transcript	synonymous_variant	3842	3156	1052	S	tcC/tcT	.	.	.	1	SETD1A	HGNC	29010	protein_coding	YES	CCDS32435.1	ENSP00000262519	SET1A_HUMAN	C9J2Z9_HUMAN	UPI00001C1FA9	.	.	.	13/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22884:SF295,hmmpanther:PTHR22884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TCCTCCTCGTC	.	2	ESCA
SETD1A	0	.	GRCh37	16	30982839	30982839	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3157T>G	p.Ser1053Ala	p.S1053A	ENST00000262519	13/19	34	29	5	34	34	0	SETD1A,missense_variant,p.Ser1053Ala,ENST00000262519,;	G	ENSG00000099381	ENST00000262519	Transcript	missense_variant	3843	3157	1053	S/A	Tcg/Gcg	.	.	.	1	SETD1A	HGNC	29010	protein_coding	YES	CCDS32435.1	ENSP00000262519	SET1A_HUMAN	C9J2Z9_HUMAN	UPI00001C1FA9	.	.	unknown(0)	13/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22884:SF295,hmmpanther:PTHR22884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCTCCTCGTCC	.	3	ESCA
SETD1A	0	.	GRCh37	16	30982840	30982840	+	Nonsense_Mutation	SNP	C	C	A	rs150754116	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3158C>A	p.Ser1053Ter	p.S1053*	ENST00000262519	13/19	31	26	5	33	33	0	SETD1A,stop_gained,p.Ser1053Ter,ENST00000262519,;	A	ENSG00000099381	ENST00000262519	Transcript	stop_gained	3844	3158	1053	S/*	tCg/tAg	rs150754116	.	.	1	SETD1A	HGNC	29010	protein_coding	YES	CCDS32435.1	ENSP00000262519	SET1A_HUMAN	C9J2Z9_HUMAN	UPI00001C1FA9	.	.	.	13/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22884:SF295,hmmpanther:PTHR22884	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTCCTCGTCCT	.	2	ESCA
ZNF720	0	.	GRCh37	16	31766875	31766875	+	Intron	SNP	A	A	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361+1654A>T	.	.	ENST00000316491	.	67	34	32	80	80	0	ZNF720,synonymous_variant,p.%3D,ENST00000399681,;ZNF720,intron_variant,,ENST00000539915,;ZNF720,intron_variant,,ENST00000316491,;ZNF720,intron_variant,,ENST00000534369,;ZNF720,downstream_gene_variant,,ENST00000398696,;ZNF720,downstream_gene_variant,,ENST00000529515,;ZNF720,downstream_gene_variant,,ENST00000530881,;ZNF720,intron_variant,,ENST00000544044,;ZNF720,intron_variant,,ENST00000542684,;ZNF720,intron_variant,,ENST00000531864,;ZNF720,downstream_gene_variant,,ENST00000533488,;ZNF720,3_prime_UTR_variant,,ENST00000534277,;ZNF720,3_prime_UTR_variant,,ENST00000398707,;ZNF720,downstream_gene_variant,,ENST00000529943,;	T	ENSG00000197302	ENST00000316491	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZNF720	HGNC	26987	protein_coding	YES	CCDS45473.1	ENSP00000319222	ZN720_HUMAN	.	UPI000003603E	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATATGTAA	.	5	ESCA
RP11-80F22.9	0	.	GRCh37	16	34712278	34712278	+	RNA	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1077G>T	.	.	ENST00000569028	2/2	36	29	7	41	41	0	RP11-80F22.9,non_coding_transcript_exon_variant,,ENST00000569028,;RP11-80F22.9,downstream_gene_variant,,ENST00000564452,;RP11-80F22.9,downstream_gene_variant,,ENST00000566967,;	A	ENSG00000261711	ENST00000569028	Transcript	non_coding_transcript_exon_variant	1077	.	.	.	.	.	.	.	-1	RP11-80F22.9	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGGCTTCTC	.	5	ESCA
FUK	0	.	GRCh37	16	70502787	70502787	+	Silent	SNP	C	C	T	rs753351332	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.699C>T	p.%3D	p.A233A	ENST00000288078	9/24	64	53	10	70	70	0	FUK,synonymous_variant,p.%3D,ENST00000288078,;FUK,synonymous_variant,p.%3D,ENST00000378912,;FUK,5_prime_UTR_variant,,ENST00000571514,;FUK,downstream_gene_variant,,ENST00000574784,;FUK,downstream_gene_variant,,ENST00000572784,;FUK,downstream_gene_variant,,ENST00000428974,;FUK,downstream_gene_variant,,ENST00000576453,;FUK,downstream_gene_variant,,ENST00000573352,;FUK,non_coding_transcript_exon_variant,,ENST00000571487,;FUK,non_coding_transcript_exon_variant,,ENST00000464499,;FUK,downstream_gene_variant,,ENST00000576107,;	T	ENSG00000157353	ENST00000288078	Transcript	synonymous_variant	931	699	233	A	gcC/gcT	rs753351332	.	.	1	FUK	HGNC	29500	protein_coding	YES	CCDS10891.2	ENSP00000288078	FUK_HUMAN	Q8N8I9_HUMAN,I3L3J1_HUMAN,I3L1X0_HUMAN,I3L171_HUMAN,I3L106_HUMAN,B2RDL5_HUMAN	UPI000013DEF1	.	.	.	9/24	.	hmmpanther:PTHR32463,hmmpanther:PTHR32463:SF0,Pfam_domain:PF07959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGCCGAGCG	byFrequency	5	ESCA
ACSF3	0	.	GRCh37	16	89167129	89167129	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40T>C	p.Cys14Arg	p.C14R	ENST00000317447	3/11	15	10	5	12	12	0	ACSF3,missense_variant,p.Cys14Arg,ENST00000537290,;ACSF3,missense_variant,p.Cys14Arg,ENST00000541755,;ACSF3,missense_variant,p.Cys14Arg,ENST00000317447,;ACSF3,missense_variant,p.Cys14Arg,ENST00000406948,;ACSF3,intron_variant,,ENST00000540697,;ACSF3,intron_variant,,ENST00000537895,;ACSF3,intron_variant,,ENST00000378345,;ACSF3,upstream_gene_variant,,ENST00000538340,;ACSF3,upstream_gene_variant,,ENST00000544543,;ACSF3,upstream_gene_variant,,ENST00000543676,;ACSF3,missense_variant,p.Cys14Arg,ENST00000542688,;	C	ENSG00000176715	ENST00000317447	Transcript	missense_variant	417	40	14	C/R	Tgc/Cgc	.	.	.	1	ACSF3	HGNC	27288	protein_coding	YES	CCDS10974.1	ENSP00000320646	ACSF3_HUMAN	H3BTS0_HUMAN,F5H755_HUMAN,F5H5A1_HUMAN,F5H3B2_HUMAN,F5H362_HUMAN,F5GX20_HUMAN	UPI00001AF19E	.	tolerated_low_confidence(0.38)	benign(0.001)	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A17A|c.51G>C|7	MUTECT|MUSE	TGGGCTGCGCC	.	2	ESCA
CDRT1	0	.	GRCh37	17	15522728	15522728	+	Silent	SNP	G	G	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99C>A	p.%3D	p.V33V	ENST00000395906	1/12	125	86	38	106	106	0	CDRT1,synonymous_variant,p.%3D,ENST00000395906,;RP11-385D13.1,intron_variant,,ENST00000455584,;CDRT1,upstream_gene_variant,,ENST00000261644,;	T	ENSG00000241322	ENST00000395906	Transcript	synonymous_variant	99	99	33	V	gtC/gtA	.	.	.	-1	CDRT1	HGNC	14379	protein_coding	YES	CCDS45619.1	ENSP00000379242	CDRT1_HUMAN	.	UPI00015D57D8	.	.	.	1/12	.	hmmpanther:PTHR19872:SF7,hmmpanther:PTHR19872	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTAAGACACG	.	5	ESCA
SMCR8	0	.	GRCh37	17	18219576	18219576	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.473delT	p.Ile158ThrfsTer26	p.I158Tfs*26	ENST00000406438	1/2	42	33	9	21	21	0	SMCR8,frameshift_variant,p.Ile158ThrfsTer26,ENST00000406438,;TOP3A,upstream_gene_variant,,ENST00000580095,;TOP3A,upstream_gene_variant,,ENST00000321105,;TOP3A,upstream_gene_variant,,ENST00000542570,;TOP3A,upstream_gene_variant,,ENST00000584887,;TOP3A,upstream_gene_variant,,ENST00000582230,;TOP3A,upstream_gene_variant,,ENST00000584669,;TOP3A,upstream_gene_variant,,ENST00000580713,;TOP3A,upstream_gene_variant,,ENST00000461127,;TOP3A,upstream_gene_variant,,ENST00000583328,;TOP3A,upstream_gene_variant,,ENST00000582981,;TOP3A,upstream_gene_variant,,ENST00000584582,;TOP3A,upstream_gene_variant,,ENST00000585031,;TOP3A,upstream_gene_variant,,ENST00000472959,;RPL21P121,downstream_gene_variant,,ENST00000439258,;RPL7AP65,downstream_gene_variant,,ENST00000418183,;	-	ENSG00000176994	ENST00000406438	Transcript	frameshift_variant	953	473	158	I/X	aTc/ac	.	.	.	1	SMCR8	HGNC	17921	protein_coding	YES	CCDS11195.2	ENSP00000385025	SMCR8_HUMAN	.	UPI0000E0322D	.	.	.	1/2	.	Pfam_domain:PF11704,hmmpanther:PTHR31334:SF1,hmmpanther:PTHR31334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTATATCTCTG	.	3	ESCA
USP32P2	0	.	GRCh37	17	18414580	18414580	+	RNA	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4325C>T	.	.	ENST00000412260	5/5	60	50	10	42	42	0	USP32P2,non_coding_transcript_exon_variant,,ENST00000412260,;CTD-2303H24.2,non_coding_transcript_exon_variant,,ENST00000425211,;CTD-2303H24.2,downstream_gene_variant,,ENST00000581595,;USP32P2,downstream_gene_variant,,ENST00000421108,;USP32P2,downstream_gene_variant,,ENST00000414432,;USP32P2,downstream_gene_variant,,ENST00000508093,;	A	ENSG00000233327	ENST00000412260	Transcript	non_coding_transcript_exon_variant	4325	.	.	.	.	.	.	.	-1	USP32P2	HGNC	30751	processed_transcript	YES	.	.	.	.	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAAAGGCATC	.	5	ESCA
FLOT2	0	.	GRCh37	17	27211278	27211278	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.187G>A	p.Glu63Lys	p.E63K	ENST00000394908	3/11	38	31	6	43	43	0	FLOT2,missense_variant,p.Glu118Lys,ENST00000394906,;FLOT2,missense_variant,p.Glu63Lys,ENST00000394908,;FLOT2,intron_variant,,ENST00000585169,;FLOT2,intron_variant,,ENST00000465427,;FLOT2,intron_variant,,ENST00000577789,;FLOT2,upstream_gene_variant,,ENST00000584569,;FLOT2,missense_variant,p.Arg93Gln,ENST00000580805,;FLOT2,non_coding_transcript_exon_variant,,ENST00000581509,;FLOT2,non_coding_transcript_exon_variant,,ENST00000580313,;FLOT2,intron_variant,,ENST00000582174,;FLOT2,intron_variant,,ENST00000593158,;FLOT2,intron_variant,,ENST00000586827,;	T	ENSG00000132589	ENST00000394908	Transcript	missense_variant	292	187	63	E/K	Gag/Aag	.	.	.	-1	FLOT2	HGNC	3758	protein_coding	YES	CCDS11245.2	ENSP00000378368	FLOT2_HUMAN	Q6FG43_HUMAN	UPI00001AE777	.	tolerated(0.34)	benign(0.065)	3/11	.	hmmpanther:PTHR13806,hmmpanther:PTHR13806:SF17,Pfam_domain:PF01145,Superfamily_domains:0050593	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCGGCCG	.	5	ESCA
SLC35G3	0	.	GRCh37	17	33520817	33520817	+	Silent	SNP	G	G	A	rs749966552	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510C>T	p.%3D	p.I170I	ENST00000297307	1/1	109	67	42	64	64	0	SLC35G3,synonymous_variant,p.%3D,ENST00000297307,;UNC45B,downstream_gene_variant,,ENST00000378449,;UNC45B,downstream_gene_variant,,ENST00000433649,;UNC45B,downstream_gene_variant,,ENST00000268876,;UNC45B,downstream_gene_variant,,ENST00000394570,;RP11-799D4.2,downstream_gene_variant,,ENST00000590144,;RP11-799D4.1,downstream_gene_variant,,ENST00000592961,;	A	ENSG00000164729	ENST00000297307	Transcript	synonymous_variant	596	510	170	I	atC/atT	rs749966552	.	.	-1	SLC35G3	HGNC	26848	protein_coding	YES	CCDS11293.1	ENSP00000297307	S35G3_HUMAN	.	UPI000006FEAB	.	.	.	1/1	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22911:SF32,hmmpanther:PTHR22911,Pfam_domain:PF00892,Superfamily_domains:0043518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATGATTAG	.	5	ESCA
CNTD1	0	.	GRCh37	17	40961790	40961790	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*237T>C	.	.	ENST00000588408	7/7	11	3	8	8	8	0	CNTD1,3_prime_UTR_variant,,ENST00000588527,;CNTD1,3_prime_UTR_variant,,ENST00000588408,;CNTD1,downstream_gene_variant,,ENST00000586652,;CNTD1,downstream_gene_variant,,ENST00000585355,;BECN1,downstream_gene_variant,,ENST00000586589,;BECN1,downstream_gene_variant,,ENST00000593205,;BECN1,downstream_gene_variant,,ENST00000589663,;BECN1,downstream_gene_variant,,ENST00000590764,;BECN1,downstream_gene_variant,,ENST00000590099,;BECN1,downstream_gene_variant,,ENST00000588276,;BECN1,downstream_gene_variant,,ENST00000586754,;BECN1,downstream_gene_variant,,ENST00000590852,;BECN1,downstream_gene_variant,,ENST00000361523,;BECN1,downstream_gene_variant,,ENST00000438274,;CNTD1,non_coding_transcript_exon_variant,,ENST00000315066,;BECN1,downstream_gene_variant,,ENST00000587880,;BECN1,downstream_gene_variant,,ENST00000589492,;BECN1,downstream_gene_variant,,ENST00000590185,;CNTD1,downstream_gene_variant,,ENST00000592166,;BECN1,downstream_gene_variant,,ENST00000543382,;	C	ENSG00000176563	ENST00000588408	Transcript	3_prime_UTR_variant	1506	.	.	.	.	.	.	.	1	CNTD1	HGNC	26847	protein_coding	YES	CCDS11440.1	ENSP00000465204	CNTD1_HUMAN	B4DXR6_HUMAN	UPI000006EFD8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCATTTTTG	.	2	ESCA
SLC25A11	0	.	GRCh37	17	4841060	4841060	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.921C>T	p.%3D	p.Y307Y	ENST00000225665	8/8	39	9	29	45	45	0	SLC25A11,synonymous_variant,p.%3D,ENST00000576951,;SLC25A11,synonymous_variant,p.%3D,ENST00000225665,;SLC25A11,synonymous_variant,p.%3D,ENST00000544061,;RNF167,upstream_gene_variant,,ENST00000575111,;RNF167,upstream_gene_variant,,ENST00000576452,;RNF167,upstream_gene_variant,,ENST00000571816,;RNF167,upstream_gene_variant,,ENST00000570328,;RNF167,upstream_gene_variant,,ENST00000576229,;RNF167,upstream_gene_variant,,ENST00000572382,;RNF167,upstream_gene_variant,,ENST00000573404,;RNF167,upstream_gene_variant,,ENST00000572430,;GP1BA,downstream_gene_variant,,ENST00000329125,;RNF167,upstream_gene_variant,,ENST00000262482,;RNF167,upstream_gene_variant,,ENST00000571365,;RNF167,upstream_gene_variant,,ENST00000570492,;SLC25A11,non_coding_transcript_exon_variant,,ENST00000574710,;RNF167,upstream_gene_variant,,ENST00000572554,;SLC25A11,downstream_gene_variant,,ENST00000570543,;RNF167,upstream_gene_variant,,ENST00000575400,;	A	ENSG00000108528	ENST00000225665	Transcript	synonymous_variant	1262	921	307	Y	taC/taT	.	.	.	-1	SLC25A11	HGNC	10981	protein_coding	YES	CCDS11059.1	ENSP00000225665	M2OM_HUMAN	Q6IBH0_HUMAN	UPI00000738E8	.	.	.	8/8	.	hmmpanther:PTHR24089:SF86,hmmpanther:PTHR24089,Pfam_domain:PF00153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTTGTAGGC	.	5	ESCA
ABCA10	0	.	GRCh37	17	67183913	67183913	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2239A>G	p.Ser747Gly	p.S747G	ENST00000269081	20/40	100	65	35	91	91	0	ABCA10,missense_variant,p.Ser747Gly,ENST00000269081,;ABCA10,3_prime_UTR_variant,,ENST00000416101,;ABCA10,missense_variant,p.Ser747Gly,ENST00000523419,;ABCA10,3_prime_UTR_variant,,ENST00000522406,;ABCA10,3_prime_UTR_variant,,ENST00000518929,;	C	ENSG00000154263	ENST00000269081	Transcript	missense_variant	3149	2239	747	S/G	Agt/Ggt	.	.	.	-1	ABCA10	HGNC	30	protein_coding	YES	CCDS11684.1	ENSP00000269081	ABCAA_HUMAN	K7ERP5_HUMAN	UPI000013D7F6	.	tolerated(0.47)	benign(0.012)	20/40	.	hmmpanther:PTHR19229:SF120,hmmpanther:PTHR19229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTACTGACAG	.	5	ESCA
TP53	0	.	GRCh37	17	7577018	7577018	+	Splice_Site	SNP	C	C	T	.	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.919+1G>A	.	p.X307_splice	ENST00000269305	.	70	24	45	52	52	0	TP53,splice_donor_variant,,ENST00000420246,;TP53,splice_donor_variant,,ENST00000269305,;TP53,splice_donor_variant,,ENST00000509690,;TP53,splice_donor_variant,,ENST00000359597,;TP53,splice_donor_variant,,ENST00000445888,;TP53,splice_donor_variant,,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,splice_donor_variant,,ENST00000504937,;TP53,splice_donor_variant,,ENST00000504290,;TP53,splice_donor_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	splice_donor_variant	.	.	.	.	.	CD920913,CS107068,TP53_g.13900G>A,TP53_g.13900G>T,TP53_g.13900G>C,COSM44143,COSM13585,COSM13584,COSM97868,COSM213111,COSM1230104,COSM2744491,COSM3378338,COSM3378337,COSM2744494,COSM2744492	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	8/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.919+1G>A|6,SITE|p.?|c.919+1G>A|10,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.?|c.919+2T>G|3,BUFFER|p.?|c.919+1G>C|4,BUFFER|p.?|c.919+1G>T|9,BUFFER|p.A307fs*38|c.919delG|4,BUFFER|p.R306*|c.916C>T|16,BUFFER|p.R306*|c.916C>T|152,BUFFER|p.R306*|c.916C>T|24,BUFFER|p.R306*|c.916C>T|43,BUFFER|p.K305N|c.915G>T|3,BUFFER|p.K305*|c.913A>T|16,BUFFER|p.K305*|c.913A>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTACCTCGC	.	5	ESCA
DNAH2	0	.	GRCh37	17	7661923	7661923	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2162G>T	p.Gly721Val	p.G721V	ENST00000572933	14/86	31	18	12	21	21	0	DNAH2,missense_variant,p.Gly721Val,ENST00000389173,;DNAH2,missense_variant,p.Gly721Val,ENST00000572933,;RPL29P2,downstream_gene_variant,,ENST00000498671,;DNAH2,upstream_gene_variant,,ENST00000574518,;RPL29P2,downstream_gene_variant,,ENST00000488409,;	T	ENSG00000183914	ENST00000572933	Transcript	missense_variant	3622	2162	721	G/V	gGg/gTg	.	.	.	1	DNAH2	HGNC	2948	protein_coding	YES	CCDS32551.1	ENSP00000458355	DYH2_HUMAN	.	UPI00005B2F0D	.	.	probably_damaging(0.987)	14/86	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGGGGGCCA	.	5	ESCA
SPIRE1	0	.	GRCh37	18	12496015	12496015	+	Silent	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1059A>G	p.%3D	p.P353P	ENST00000409402	7/17	90	79	11	70	70	0	SPIRE1,synonymous_variant,p.%3D,ENST00000409402,;SPIRE1,synonymous_variant,p.%3D,ENST00000410092,;SPIRE1,synonymous_variant,p.%3D,ENST00000383356,;SPIRE1,synonymous_variant,p.%3D,ENST00000309836,;SPIRE1,synonymous_variant,p.%3D,ENST00000453447,;SPIRE1,splice_region_variant,,ENST00000487491,;SPIRE1,upstream_gene_variant,,ENST00000464481,;SPIRE1,synonymous_variant,p.%3D,ENST00000592156,;SPIRE1,synonymous_variant,p.%3D,ENST00000440472,;	C	ENSG00000134278	ENST00000409402	Transcript	synonymous_variant	1327	1059	353	P	ccA/ccG	.	.	.	-1	SPIRE1	HGNC	30622	protein_coding	YES	CCDS45829.1	ENSP00000387266	SPIR1_HUMAN	Q96AS4_HUMAN,K7EQR2_HUMAN,C9JYR7_HUMAN	UPI00001C1FFE	.	.	.	7/17	.	hmmpanther:PTHR21345,hmmpanther:PTHR21345:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATACTGGATT	.	4	ESCA
SMAD2	0	.	GRCh37	18	45394822	45394822	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.527C>G	p.Pro176Arg	p.P176R	ENST00000402690	5/11	59	36	23	66	66	0	SMAD2,missense_variant,p.Pro176Arg,ENST00000402690,;SMAD2,missense_variant,p.Pro176Arg,ENST00000262160,;SMAD2,missense_variant,p.Pro176Arg,ENST00000586514,;SMAD2,missense_variant,p.Pro146Arg,ENST00000591214,;SMAD2,missense_variant,p.Pro146Arg,ENST00000356825,;SMAD2,missense_variant,p.Pro146Arg,ENST00000586040,;SMAD2,missense_variant,p.Pro176Arg,ENST00000587269,;SMAD2,downstream_gene_variant,,ENST00000587421,;SMAD2,downstream_gene_variant,,ENST00000585978,;SMAD2,downstream_gene_variant,,ENST00000589877,;SMAD2,non_coding_transcript_exon_variant,,ENST00000587353,;SMAD2,downstream_gene_variant,,ENST00000586487,;	C	ENSG00000175387	ENST00000402690	Transcript	missense_variant	922	527	176	P/R	cCt/cGt	.	.	.	-1	SMAD2	HGNC	6768	protein_coding	YES	CCDS11934.1	ENSP00000384449	SMAD2_HUMAN	Q53XR6_HUMAN,K7ESI8_HUMAN,K7ERC7_HUMAN,K7EL92_HUMAN,K7EJX0_HUMAN	UPI0000032EE7	.	deleterious(0.01)	possibly_damaging(0.56)	5/11	.	Gene3D:1ozjA00,hmmpanther:PTHR13703:SF25,hmmpanther:PTHR13703,PROSITE_profiles:PS51075,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAGGCAAA	.	5	ESCA
SERPINB4	0	.	GRCh37	18	61305185	61305185	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.941T>C	p.Leu314Pro	p.L314P	ENST00000341074	8/8	76	59	17	60	60	0	SERPINB4,missense_variant,p.Leu314Pro,ENST00000341074,;SERPINB4,missense_variant,p.Leu295Pro,ENST00000413673,;SERPINB4,missense_variant,p.Leu262Pro,ENST00000356424,;SERPINB4,downstream_gene_variant,,ENST00000436264,;SERPINB4,downstream_gene_variant,,ENST00000498496,;	G	ENSG00000206073	ENST00000341074	Transcript	missense_variant	1057	941	314	L/P	cTc/cCc	.	.	.	-1	SERPINB4	HGNC	10570	protein_coding	YES	CCDS11986.1	ENSP00000343445	SPB4_HUMAN	.	UPI0000038A1A	.	deleterious(0.02)	probably_damaging(0.994)	8/8	.	hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF155,Pfam_domain:PF00079,Gene3D:3.30.497.10,SMART_domains:SM00093,Superfamily_domains:SSF56574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGAGGTCT	.	5	ESCA
DOK6	0	.	GRCh37	18	67508990	67508990	+	3'UTR	SNP	G	G	A	rs778256799	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*371G>A	.	.	ENST00000382713	8/8	49	28	20	44	44	0	DOK6,3_prime_UTR_variant,,ENST00000382713,;CD226,intron_variant,,ENST00000578928,;	A	ENSG00000206052	ENST00000382713	Transcript	3_prime_UTR_variant	1557	.	.	.	.	rs778256799	.	.	1	DOK6	HGNC	28301	protein_coding	YES	CCDS32841.1	ENSP00000372160	DOK6_HUMAN	.	UPI000035EC7C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCCGCCCAT	byCluster	5	ESCA
ATP9B	0	.	GRCh37	18	76856506	76856506	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150G>A	p.%3D	p.L50L	ENST00000426216	2/30	164	141	23	103	103	0	ATP9B,synonymous_variant,p.%3D,ENST00000307671,;ATP9B,synonymous_variant,p.%3D,ENST00000426216,;ATP9B,synonymous_variant,p.%3D,ENST00000586722,;ATP9B,5_prime_UTR_variant,,ENST00000458297,;ATP9B,intron_variant,,ENST00000586672,;ATP9B,downstream_gene_variant,,ENST00000588600,;ATP9B,non_coding_transcript_exon_variant,,ENST00000591464,;ATP9B,non_coding_transcript_exon_variant,,ENST00000591395,;ATP9B,synonymous_variant,p.%3D,ENST00000586366,;ATP9B,non_coding_transcript_exon_variant,,ENST00000590271,;	A	ENSG00000166377	ENST00000426216	Transcript	synonymous_variant	167	150	50	L	ttG/ttA	.	.	.	1	ATP9B	HGNC	13541	protein_coding	YES	CCDS12014.1	ENSP00000398076	ATP9B_HUMAN	.	UPI00002371AF	.	.	.	2/30	.	hmmpanther:PTHR24092:SF50,hmmpanther:PTHR24092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTGGATGA	.	4	ESCA
ECSIT	0	.	GRCh37	19	11617015	11617015	+	Missense_Mutation	SNP	T	T	A	rs561466699	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1280A>T	p.Gln427Leu	p.Q427L	ENST00000270517	8/8	46	36	10	45	45	0	ECSIT,missense_variant,p.Gln427Leu,ENST00000270517,;ECSIT,missense_variant,p.Gln213Leu,ENST00000417981,;ECSIT,3_prime_UTR_variant,,ENST00000252440,;ECSIT,3_prime_UTR_variant,,ENST00000591104,;ECSIT,3_prime_UTR_variant,,ENST00000588998,;ZNF653,upstream_gene_variant,,ENST00000293771,;ECSIT,downstream_gene_variant,,ENST00000592312,;ECSIT,downstream_gene_variant,,ENST00000585318,;ZNF653,upstream_gene_variant,,ENST00000593191,;ECSIT,downstream_gene_variant,,ENST00000591352,;ECSIT,3_prime_UTR_variant,,ENST00000592571,;ECSIT,non_coding_transcript_exon_variant,,ENST00000585898,;ZNF653,upstream_gene_variant,,ENST00000590548,;ECSIT,downstream_gene_variant,,ENST00000593231,;ZNF653,upstream_gene_variant,,ENST00000588541,;CTC-398G3.6,upstream_gene_variant,,ENST00000585656,;	A	ENSG00000130159	ENST00000270517	Transcript	missense_variant	1416	1280	427	Q/L	cAg/cTg	rs561466699	.	.	-1	ECSIT	HGNC	29548	protein_coding	YES	CCDS12262.1	ENSP00000270517	ECSIT_HUMAN	K7EPL5_HUMAN,K7EM98_HUMAN,K7EJI1_HUMAN,J3KTF5_HUMAN	UPI0000072F31	.	deleterious_low_confidence(0.02)	benign(0.058)	8/8	.	hmmpanther:PTHR13113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCTGCTGT	byFrequency|byCluster	5	ESCA
GAMT	0	.	GRCh37	19	1398805	1398805	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.680C>T	p.Pro227Leu	p.P227L	ENST00000447102	5/5	45	22	23	47	47	0	GAMT,missense_variant,p.Pro227Leu,ENST00000447102,;GAMT,intron_variant,,ENST00000591788,;GAMT,intron_variant,,ENST00000252288,;NDUFS7,downstream_gene_variant,,ENST00000233627,;NDUFS7,downstream_gene_variant,,ENST00000313408,;NDUFS7,downstream_gene_variant,,ENST00000539480,;AC005329.7,upstream_gene_variant,,ENST00000585596,;AC005329.7,upstream_gene_variant,,ENST00000589734,;AC005329.7,upstream_gene_variant,,ENST00000501448,;NDUFS7,downstream_gene_variant,,ENST00000540530,;NDUFS7,downstream_gene_variant,,ENST00000534853,;NDUFS7,downstream_gene_variant,,ENST00000538662,;NDUFS7,downstream_gene_variant,,ENST00000535382,;NDUFS7,downstream_gene_variant,,ENST00000546172,;NDUFS7,downstream_gene_variant,,ENST00000543289,;NDUFS7,downstream_gene_variant,,ENST00000591358,;NDUFS7,downstream_gene_variant,,ENST00000545446,;	A	ENSG00000130005	ENST00000447102	Transcript	missense_variant	774	680	227	P/L	cCc/cTc	.	.	.	-1	GAMT	HGNC	4136	protein_coding	YES	CCDS45897.1	ENSP00000403536	GAMT_HUMAN	.	UPI0000161182	.	deleterious_low_confidence(0)	possibly_damaging(0.851)	5/5	.	PIRSF_domain:PIRSF009285,hmmpanther:PTHR32162,PROSITE_profiles:PS51559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGGGGGTC	.	5	ESCA
NOTCH3	0	.	GRCh37	19	15291625	15291625	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3009G>A	p.Trp1003Ter	p.W1003*	ENST00000263388	19/33	57	39	18	72	72	0	NOTCH3,stop_gained,p.Trp1003Ter,ENST00000263388,;NOTCH3,stop_gained,p.Trp950Ter,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,;	T	ENSG00000074181	ENST00000263388	Transcript	stop_gained	3085	3009	1003	W/*	tgG/tgA	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	.	.	19/33	.	Superfamily_domains:SSF57196,Superfamily_domains:SSF57196,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Gene3D:2gy5A03,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCACCAATC	.	5	ESCA
CHST8	0	.	GRCh37	19	34263698	34263698	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1005C>T	p.%3D	p.C335C	ENST00000262622	4/4	53	24	29	37	37	0	CHST8,synonymous_variant,p.%3D,ENST00000438847,;CHST8,synonymous_variant,p.%3D,ENST00000262622,;CHST8,synonymous_variant,p.%3D,ENST00000434302,;CHST8,downstream_gene_variant,,ENST00000591231,;	T	ENSG00000124302	ENST00000262622	Transcript	synonymous_variant	1763	1005	335	C	tgC/tgT	.	.	.	1	CHST8	HGNC	15993	protein_coding	YES	CCDS12433.1	ENSP00000262622	CHST8_HUMAN	K7ENM3_HUMAN	UPI000006F966	.	.	.	4/4	.	Pfam_domain:PF03567,hmmpanther:PTHR12137:SF7,hmmpanther:PTHR12137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGCAGCCC	.	5	ESCA
ZNF540	0	.	GRCh37	19	38103282	38103282	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1101T>A	p.Ser367Arg	p.S367R	ENST00000592533	5/5	65	51	13	71	71	0	ZNF540,missense_variant,p.Ser367Arg,ENST00000316433,;ZNF540,missense_variant,p.Ser367Arg,ENST00000343599,;ZNF540,missense_variant,p.Ser335Arg,ENST00000589117,;ZNF540,missense_variant,p.Ser367Arg,ENST00000586134,;ZNF540,missense_variant,p.Ser367Arg,ENST00000592533,;ZNF540,downstream_gene_variant,,ENST00000590588,;ZFP30,downstream_gene_variant,,ENST00000589018,;ZNF540,downstream_gene_variant,,ENST00000586792,;ZNF540,downstream_gene_variant,,ENST00000589857,;ZNF540,non_coding_transcript_exon_variant,,ENST00000589285,;	A	ENSG00000171817	ENST00000592533	Transcript	missense_variant	1433	1101	367	S/R	agT/agA	.	.	.	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	tolerated(0.33)	benign(0.083)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF138,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTAGTTTTTA	.	5	ESCA
WDR87	0	.	GRCh37	19	38376426	38376426	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7768A>G	p.Ser2590Gly	p.S2590G	ENST00000303868	6/6	53	35	17	46	46	0	WDR87,missense_variant,p.Ser2629Gly,ENST00000447313,;WDR87,missense_variant,p.Ser2590Gly,ENST00000303868,;	C	ENSG00000171804	ENST00000303868	Transcript	missense_variant	7993	7768	2590	S/G	Agt/Ggt	.	.	.	-1	WDR87	HGNC	29934	protein_coding	YES	CCDS46063.1	ENSP00000368025	WDR87_HUMAN	B4DXE9_HUMAN	UPI0001662BC1	.	.	unknown(0)	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTACTTGAGA	.	5	ESCA
ACTN4	0	.	GRCh37	19	39212306	39212306	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1420G>A	p.Ala474Thr	p.A474T	ENST00000252699	12/21	39	36	3	39	39	0	ACTN4,missense_variant,p.Ala474Thr,ENST00000252699,;ACTN4,missense_variant,p.Ala255Thr,ENST00000390009,;ACTN4,intron_variant,,ENST00000424234,;ACTN4,intron_variant,,ENST00000589528,;ACTN4,upstream_gene_variant,,ENST00000440400,;ACTN4,downstream_gene_variant,,ENST00000586538,;ACTN4,downstream_gene_variant,,ENST00000489451,;ACTN4,non_coding_transcript_exon_variant,,ENST00000588618,;	A	ENSG00000130402	ENST00000252699	Transcript	missense_variant	1496	1420	474	A/T	Gcc/Acc	.	.	.	1	ACTN4	HGNC	166	protein_coding	YES	CCDS12518.1	ENSP00000252699	ACTN4_HUMAN	Q96BG6_HUMAN	UPI0000125093	.	tolerated(0.07)	probably_damaging(0.988)	12/21	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF271,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|VARSCANS	AGATCGCCGCC	.	2	ESCA
C19orf54	0	.	GRCh37	19	41247641	41247642	+	3'UTR	INS	-	-	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*696dupA	.	.	ENST00000378313	6/6	69	51	18	57	57	0	C19orf54,3_prime_UTR_variant,,ENST00000470681,;C19orf54,3_prime_UTR_variant,,ENST00000378313,;C19orf54,intron_variant,,ENST00000596940,;C19orf54,intron_variant,,ENST00000598485,;ITPKC,downstream_gene_variant,,ENST00000263370,;C19orf54,downstream_gene_variant,,ENST00000598352,;C19orf54,downstream_gene_variant,,ENST00000598729,;C19orf54,downstream_gene_variant,,ENST00000600139,;C19orf54,downstream_gene_variant,,ENST00000339153,;C19orf54,upstream_gene_variant,,ENST00000594163,;C19orf54,3_prime_UTR_variant,,ENST00000469741,;C19orf54,3_prime_UTR_variant,,ENST00000596809,;C19orf54,downstream_gene_variant,,ENST00000597507,;ITPKC,downstream_gene_variant,,ENST00000597003,;	T	ENSG00000188493	ENST00000378313	Transcript	3_prime_UTR_variant	1872-1873	.	.	.	.	.	.	.	-1	C19orf54	HGNC	24758	protein_coding	YES	CCDS12564.2	ENSP00000367564	CS054_HUMAN	.	UPI00001B64AB	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCCACTTCTC	.	3	ESCA
LRRC4B	0	.	GRCh37	19	51020952	51020952	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2018A>G	p.His673Arg	p.H673R	ENST00000599957	3/3	59	41	17	61	61	0	LRRC4B,missense_variant,p.His673Arg,ENST00000599957,;LRRC4B,missense_variant,p.His673Arg,ENST00000389201,;LRRC4B,downstream_gene_variant,,ENST00000600381,;ASPDH,upstream_gene_variant,,ENST00000601207,;ASPDH,upstream_gene_variant,,ENST00000598657,;ASPDH,upstream_gene_variant,,ENST00000376916,;ASPDH,upstream_gene_variant,,ENST00000389208,;ASPDH,upstream_gene_variant,,ENST00000597030,;ASPDH,upstream_gene_variant,,ENST00000593569,;ASPDH,upstream_gene_variant,,ENST00000601287,;	C	ENSG00000131409	ENST00000599957	Transcript	missense_variant	2216	2018	673	H/R	cAc/cGc	.	.	.	-1	LRRC4B	HGNC	25042	protein_coding	YES	CCDS42595.1	ENSP00000471502	LRC4B_HUMAN	M0R2G0_HUMAN,A0PJJ4_HUMAN	UPI00000497E7	.	tolerated_low_confidence(0.16)	benign(0.076)	3/3	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAGTGCGCC	.	5	ESCA
SIGLEC7	0	.	GRCh37	19	51645657	51645658	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36dupG	p.Arg13GlufsTer10	p.R13Efs*10	ENST00000317643	1/7	55	39	16	32	32	0	SIGLEC7,frameshift_variant,p.Arg13GlufsTer10,ENST00000601682,;SIGLEC7,frameshift_variant,p.Arg13GlufsTer10,ENST00000305628,;SIGLEC7,frameshift_variant,p.Arg13GlufsTer10,ENST00000600577,;SIGLEC7,frameshift_variant,p.Arg13GlufsTer10,ENST00000317643,;SIGLEC7,frameshift_variant,p.Arg13GlufsTer10,ENST00000536156,;SIGLEC7,upstream_gene_variant,,ENST00000599250,;SIGLEC19P,upstream_gene_variant,,ENST00000600623,;CTD-3187F8.15,downstream_gene_variant,,ENST00000601996,;	G	ENSG00000168995	ENST00000317643	Transcript	frameshift_variant	100-101	31-32	11	W/WX	tgg/tGgg	.	.	.	1	SIGLEC7	HGNC	10876	protein_coding	YES	CCDS12826.1	ENSP00000323328	SIGL7_HUMAN	.	UPI000011B40B	.	.	.	1/7	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12035:SF43,hmmpanther:PTHR12035	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCTCTGGGGG	.	3	ESCA
POLRMT	0	.	GRCh37	19	629696	629696	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.666G>C	p.Gln222His	p.Q222H	ENST00000588649	3/21	41	35	6	57	57	0	POLRMT,missense_variant,p.Gln222His,ENST00000588649,;POLRMT,missense_variant,p.Gln158His,ENST00000590573,;POLRMT,upstream_gene_variant,,ENST00000588630,;POLRMT,upstream_gene_variant,,ENST00000586384,;POLRMT,downstream_gene_variant,,ENST00000592863,;POLRMT,downstream_gene_variant,,ENST00000607260,;POLRMT,upstream_gene_variant,,ENST00000590709,;	G	ENSG00000099821	ENST00000588649	Transcript	missense_variant	751	666	222	Q/H	caG/caC	.	.	.	-1	POLRMT	HGNC	9200	protein_coding	YES	CCDS12036.1	ENSP00000465759	RPOM_HUMAN	.	UPI000013C68E	.	tolerated(0.23)	benign(0.016)	3/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10102:SF0,hmmpanther:PTHR10102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCTGCTGACC	.	4	ESCA
MUC16	0	.	GRCh37	19	9076812	9076813	+	In_Frame_Ins	INS	-	-	TGG	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10631_10633dupCCA	p.Thr3544dup	p.T3544dup	ENST00000397910	3/84	101	83	18	81	81	0	MUC16,inframe_insertion,p.Thr3544dup,ENST00000397910,;	TGG	ENSG00000181143	ENST00000397910	Transcript	inframe_insertion	10837-10838	10633-10634	3545	M/TM	atg/aCCAtg	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	3/84	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTCCCATGGTG	.	2	ESCA
SPAG17	0	.	GRCh37	1	118579442	118579443	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3383dupA	p.Asn1128LysfsTer20	p.N1128Kfs*20	ENST00000336338	24/49	98	83	15	59	59	0	SPAG17,frameshift_variant,p.Asn1128LysfsTer20,ENST00000336338,;SPAG17,non_coding_transcript_exon_variant,,ENST00000486589,;SPAG17,intron_variant,,ENST00000470550,;	T	ENSG00000155761	ENST00000336338	Transcript	frameshift_variant	3449-3450	3383-3384	1128	N/KX	aat/aaAt	.	.	.	-1	SPAG17	HGNC	26620	protein_coding	YES	CCDS899.1	ENSP00000337804	SPG17_HUMAN	A7LBF9_HUMAN	UPI00001601FD	.	.	.	24/49	.	hmmpanther:PTHR21963	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATTCCATTTTC	.	3	ESCA
OTUD7B	0	.	GRCh37	1	149931714	149931714	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734C>T	p.Ser245Leu	p.S245L	ENST00000369135	7/12	45	24	21	34	34	0	OTUD7B,missense_variant,p.Ser245Leu,ENST00000417191,;OTUD7B,missense_variant,p.Ser245Leu,ENST00000369135,;OTUD7B,downstream_gene_variant,,ENST00000479905,;	A	ENSG00000163113	ENST00000369135	Transcript	missense_variant	1029	734	245	S/L	tCa/tTa	.	.	.	-1	OTUD7B	HGNC	16683	protein_coding	YES	CCDS41389.1	ENSP00000358131	OTU7B_HUMAN	Q5SZ59_HUMAN	UPI000020415D	.	deleterious(0.01)	benign(0.11)	7/12	.	PROSITE_profiles:PS50802,hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF11,Pfam_domain:PF02338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTGACTGT	.	5	ESCA
LCE2B	0	.	GRCh37	1	152659480	152659480	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.161G>C	p.Gly54Ala	p.G54A	ENST00000368780	2/2	126	85	41	106	106	0	LCE2B,missense_variant,p.Gly54Ala,ENST00000417924,;LCE2B,missense_variant,p.Gly54Ala,ENST00000368780,;	C	ENSG00000159455	ENST00000368780	Transcript	missense_variant	215	161	54	G/A	gGc/gCc	.	.	.	1	LCE2B	HGNC	16610	protein_coding	YES	CCDS1020.1	ENSP00000357769	LCE2B_HUMAN	.	UPI000006D1D2	.	tolerated_low_confidence(0.77)	unknown(0)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23263:SF18,hmmpanther:PTHR23263,Pfam_domain:PF14672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.I51S|c.152T>G|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGGGCTGCT	.	5	ESCA
HAX1	0	.	GRCh37	1	154248111	154248132	+	Frame_Shift_Del	DEL	TCCAGCCCTGGATGATGCCTTT	TCCAGCCCTGGATGATGCCTTT	-	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	TCCAGCCCTGGATGATGCCTTT	TCCAGCCCTGGATGATGCCTTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778_799delGCCCTGGATGATGCCTTTTCCA	p.Ala260SerfsTer34	p.A260Sfs*34	ENST00000328703	7/7	56	38	18	56	56	0	HAX1,frameshift_variant,p.Ala260SerfsTer34,ENST00000328703,;HAX1,frameshift_variant,p.Ala212SerfsTer34,ENST00000457918,;HAX1,frameshift_variant,p.Ala268SerfsTer34,ENST00000483970,;HAX1,frameshift_variant,p.Ala132SerfsTer34,ENST00000532105,;UBAP2L,downstream_gene_variant,,ENST00000433615,;HAX1,downstream_gene_variant,,ENST00000435087,;UBAP2L,downstream_gene_variant,,ENST00000361546,;UBAP2L,downstream_gene_variant,,ENST00000271877,;UBAP2L,downstream_gene_variant,,ENST00000428931,;UBAP2L,downstream_gene_variant,,ENST00000493867,;HAX1,3_prime_UTR_variant,,ENST00000447768,;HAX1,non_coding_transcript_exon_variant,,ENST00000531435,;HAX1,non_coding_transcript_exon_variant,,ENST00000459914,;HAX1,non_coding_transcript_exon_variant,,ENST00000492550,;HAX1,downstream_gene_variant,,ENST00000471326,;HAX1,downstream_gene_variant,,ENST00000477780,;	-	ENSG00000143575	ENST00000328703	Transcript	frameshift_variant	987-1008	774-795	258-265	PPALDDAF/X	ccTCCAGCCCTGGATGATGCCTTT/cc	.	.	.	1	HAX1	HGNC	16915	protein_coding	YES	CCDS1064.1	ENSP00000329002	HAX1_HUMAN	E9PIQ7_HUMAN	UPI000012C0B6	.	.	.	7/7	.	hmmpanther:PTHR14938,PIRSF_domain:PIRSF037634	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	AAGACCTCCAGCCCTGGATGATGCCTTTTCCAT	.	2	ESCA
PAPPA2	0	.	GRCh37	1	176525500	176525500	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42G>C	p.Leu14Phe	p.L14F	ENST00000367662	2/23	44	32	12	37	37	0	PAPPA2,missense_variant,p.Leu14Phe,ENST00000367661,;PAPPA2,missense_variant,p.Leu14Phe,ENST00000367662,;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,;	C	ENSG00000116183	ENST00000367662	Transcript	missense_variant	1206	42	14	L/F	ttG/ttC	.	.	.	1	PAPPA2	HGNC	14615	protein_coding	YES	CCDS41438.1	ENSP00000356634	PAPP2_HUMAN	.	UPI000004A835	.	tolerated_low_confidence(0.08)	probably_damaging(0.998)	2/23	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTGGCTGG	.	5	ESCA
UCHL5	0	.	GRCh37	1	192998780	192998780	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.254A>G	p.Asn85Ser	p.N85S	ENST00000367455	4/11	48	36	12	54	54	0	UCHL5,missense_variant,p.Asn85Ser,ENST00000367451,;UCHL5,missense_variant,p.Asn85Ser,ENST00000367449,;UCHL5,missense_variant,p.Asn76Ser,ENST00000421683,;UCHL5,missense_variant,p.Asn85Ser,ENST00000367448,;UCHL5,missense_variant,p.Asn85Ser,ENST00000367455,;UCHL5,missense_variant,p.Asn97Ser,ENST00000367450,;UCHL5,missense_variant,p.Asn85Ser,ENST00000367454,;UCHL5,5_prime_UTR_variant,,ENST00000367452,;UCHL5,5_prime_UTR_variant,,ENST00000530098,;UCHL5,upstream_gene_variant,,ENST00000420791,;UCHL5,upstream_gene_variant,,ENST00000443327,;	C	ENSG00000116750	ENST00000367455	Transcript	missense_variant	490	254	85	N/S	aAt/aGt	.	.	.	-1	UCHL5	HGNC	19678	protein_coding	YES	CCDS1378.1	ENSP00000356425	UCHL5_HUMAN	.	UPI000013CF2A	.	tolerated(0.11)	benign(0.027)	4/11	.	hmmpanther:PTHR10589,Gene3D:3.40.532.10,Pfam_domain:PF01088,PIRSF_domain:PIRSF038120,Superfamily_domains:SSF54001,Prints_domain:PR00707	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTATTAATT	.	5	ESCA
RYR2	0	.	GRCh37	1	237947387	237947387	+	Silent	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12375C>G	p.%3D	p.V4125V	ENST00000366574	90/105	29	18	11	27	27	0	RYR2,synonymous_variant,p.%3D,ENST00000542537,;RYR2,synonymous_variant,p.%3D,ENST00000366574,;RYR2,synonymous_variant,p.%3D,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,;	G	ENSG00000198626	ENST00000366574	Transcript	synonymous_variant	12692	12375	4125	V	gtC/gtG	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	.	90/105	.	hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V4131I|c.12391G>A|3,BUFFER|p.V4125I|c.12373G>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGTCCTGAA	.	5	ESCA
FMN2	0	.	GRCh37	1	240555817	240555817	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4865T>C	p.Ile1622Thr	p.I1622T	ENST00000319653	15/18	73	44	29	65	65	0	FMN2,missense_variant,p.Ile218Thr,ENST00000545751,;FMN2,missense_variant,p.Ile1622Thr,ENST00000319653,;	C	ENSG00000155816	ENST00000319653	Transcript	missense_variant	5095	4865	1622	I/T	aTt/aCt	COSM1252609	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	benign(0.127)	15/18	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.I1765S|c.5294T>G|3,BUFFER|p.Q1767H|c.5301A>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAAATTGACC	.	5	ESCA
SYNC	0	.	GRCh37	1	33149975	33149975	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1242G>A	p.%3D	p.L414L	ENST00000409190	3/5	13	9	4	11	11	0	SYNC,synonymous_variant,p.%3D,ENST00000409190,;SYNC,synonymous_variant,p.%3D,ENST00000373484,;RBBP4,3_prime_UTR_variant,,ENST00000373493,;RBBP4,downstream_gene_variant,,ENST00000414241,;RBBP4,downstream_gene_variant,,ENST00000482190,;RBBP4,downstream_gene_variant,,ENST00000373485,;RBBP4,downstream_gene_variant,,ENST00000458695,;RBBP4,downstream_gene_variant,,ENST00000544435,;RBBP4,downstream_gene_variant,,ENST00000463378,;RBBP4,downstream_gene_variant,,ENST00000492348,;RBBP4,downstream_gene_variant,,ENST00000460669,;	T	ENSG00000162520	ENST00000409190	Transcript	synonymous_variant	1701	1242	414	L	ctG/ctA	.	.	.	-1	SYNC	HGNC	28897	protein_coding	YES	CCDS367.2	ENSP00000386439	SYNCI_HUMAN	C9JTN4_HUMAN,C9JSS1_HUMAN	UPI0001881B1E	.	.	.	3/5	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Gene3D:1.20.5.170,hmmpanther:PTHR23239:SF100,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TCCTCCAGCTG	.	4	ESCA
MANEAL	0	.	GRCh37	1	38261479	38261479	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.621G>A	p.%3D	p.V207V	ENST00000373045	2/4	71	65	6	59	59	0	MANEAL,missense_variant,p.Cys11Tyr,ENST00000329006,;MANEAL,synonymous_variant,p.%3D,ENST00000373045,;MANEAL,synonymous_variant,p.%3D,ENST00000525897,;MANEAL,synonymous_variant,p.%3D,ENST00000397631,;MANEAL,synonymous_variant,p.%3D,ENST00000532512,;RP11-109P14.9,downstream_gene_variant,,ENST00000433474,;	A	ENSG00000185090	ENST00000373045	Transcript	synonymous_variant	1002	621	207	V	gtG/gtA	.	.	.	1	MANEAL	HGNC	26452	protein_coding	YES	CCDS44110.1	ENSP00000362136	MANEL_HUMAN	E9PMU5_HUMAN	UPI0000203F8E	.	.	.	2/4	.	hmmpanther:PTHR13572,hmmpanther:PTHR13572:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CTGGTGCCCGC	.	2	ESCA
PPT1	0	.	GRCh37	1	40544257	40544257	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.701C>G	p.Ser234Cys	p.S234C	ENST00000433473	7/9	1235	119	1116	50	50	0	PPT1,missense_variant,p.Ser234Cys,ENST00000433473,;PPT1,missense_variant,p.Ser263Cys,ENST00000372779,;PPT1,missense_variant,p.Ser15Cys,ENST00000530076,;PPT1,missense_variant,p.Ser131Cys,ENST00000449045,;PPT1,missense_variant,p.Ser129Cys,ENST00000439754,;PPT1,missense_variant,p.Ser159Cys,ENST00000527311,;PPT1,non_coding_transcript_exon_variant,,ENST00000372775,;PPT1,missense_variant,p.Ser234Cys,ENST00000529905,;PPT1,3_prime_UTR_variant,,ENST00000530704,;	C	ENSG00000131238	ENST00000433473	Transcript	missense_variant	1166	701	234	S/C	tCc/tGc	.	.	.	-1	PPT1	HGNC	9325	protein_coding	YES	CCDS447.1	ENSP00000394863	PPT1_HUMAN	E9PSE5_HUMAN,E9PP28_HUMAN	UPI0000132113	.	deleterious(0)	possibly_damaging(0.63)	7/9	.	Superfamily_domains:SSF53474,Pfam_domain:PF02089,Gene3D:3.40.50.1820,hmmpanther:PTHR11247,hmmpanther:PTHR11247:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATGGAATCA	.	5	ESCA
MPL	0	.	GRCh37	1	43814638	43814638	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1433C>G	p.Ser478Trp	p.S478W	ENST00000372470	9/12	44	41	3	39	39	0	MPL,missense_variant,p.Ser478Trp,ENST00000413998,;MPL,missense_variant,p.Ser478Trp,ENST00000372470,;	G	ENSG00000117400	ENST00000372470	Transcript	missense_variant	1475	1433	478	S/W	tCg/tGg	COSM1581266	.	.	1	MPL	HGNC	7217	protein_coding	YES	CCDS483.1	ENSP00000361548	TPOR_HUMAN	.	UPI000002DB88	.	deleterious(0)	probably_damaging(0.987)	9/12	.	Superfamily_domains:SSF49265,Gene3D:2.60.40.10,PROSITE_patterns:PS01352,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF8,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGTCGGACC	.	2	ESCA
RNF220	0	.	GRCh37	1	45115560	45115560	+	Silent	SNP	G	G	A	rs561320190	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1560G>A	p.%3D	p.S520S	ENST00000355387	14/15	61	37	24	43	43	0	RNF220,synonymous_variant,p.%3D,ENST00000440132,;RNF220,synonymous_variant,p.%3D,ENST00000361799,;RNF220,synonymous_variant,p.%3D,ENST00000443020,;RNF220,synonymous_variant,p.%3D,ENST00000355387,;RNF220,synonymous_variant,p.%3D,ENST00000372247,;TMEM53,intron_variant,,ENST00000372244,;TMEM53,intron_variant,,ENST00000372242,;TMEM53,intron_variant,,ENST00000372243,;RNF220,downstream_gene_variant,,ENST00000335497,;TMEM53,downstream_gene_variant,,ENST00000372235,;TMEM53,downstream_gene_variant,,ENST00000372237,;RNF220,non_coding_transcript_exon_variant,,ENST00000474394,;RNF220,non_coding_transcript_exon_variant,,ENST00000474956,;RNF220,non_coding_transcript_exon_variant,,ENST00000484745,;RNF220,non_coding_transcript_exon_variant,,ENST00000480686,;RNF220,non_coding_transcript_exon_variant,,ENST00000474064,;RNF220,non_coding_transcript_exon_variant,,ENST00000475378,;TMEM53,intron_variant,,ENST00000495630,;RNF220,downstream_gene_variant,,ENST00000497469,;RNF220,downstream_gene_variant,,ENST00000471494,;TMEM53,downstream_gene_variant,,ENST00000468117,;TMEM53,downstream_gene_variant,,ENST00000476724,;	A	ENSG00000187147	ENST00000355387	Transcript	synonymous_variant	2010	1560	520	S	tcG/tcA	rs561320190	.	.	1	RNF220	HGNC	25552	protein_coding	YES	CCDS510.1	ENSP00000347548	RN220_HUMAN	D3DPZ1_HUMAN	UPI000035895E	.	.	.	14/15	.	PROSITE_profiles:PS50089,hmmpanther:PTHR13459,Gene3D:3.30.40.10,Pfam_domain:PF13923,Superfamily_domains:SSF57850	A:0.0004	A:0.0008	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTCGTACTC	byFrequency|by1000G	5	ESCA
EPS15	0	.	GRCh37	1	51820470	51820470	+	3'UTR	SNP	T	T	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1902A>T	.	.	ENST00000371733	25/25	346	277	68	311	311	0	EPS15,3_prime_UTR_variant,,ENST00000371730,;EPS15,3_prime_UTR_variant,,ENST00000371733,;EPS15,downstream_gene_variant,,ENST00000396122,;	A	ENSG00000085832	ENST00000371733	Transcript	3_prime_UTR_variant	4690	.	.	.	.	.	.	.	-1	EPS15	HGNC	3419	protein_coding	YES	CCDS557.1	ENSP00000360798	EPS15_HUMAN	.	UPI0000161B29	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACATAAGAT	.	5	ESCA
SYDE2	0	.	GRCh37	1	85648545	85648546	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1779dupT	p.Leu594SerfsTer2	p.L594Sfs*2	ENST00000341460	3/7	55	46	9	51	51	0	SYDE2,frameshift_variant,p.Leu594SerfsTer2,ENST00000341460,;SYDE2,non_coding_transcript_exon_variant,,ENST00000234668,;	A	ENSG00000097096	ENST00000341460	Transcript	frameshift_variant	1829-1830	1779-1780	593-594	-/X	-/T	.	.	.	-1	SYDE2	HGNC	25841	protein_coding	YES	CCDS44169.1	ENSP00000340594	SYDE2_HUMAN	.	UPI0001553B04	.	.	.	3/7	.	hmmpanther:PTHR23178:SF24,hmmpanther:PTHR23178	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATCAAGATGGT	.	3	ESCA
CRNKL1	0	.	GRCh37	20	20021343	20021343	+	Missense_Mutation	SNP	G	G	A	rs566498711	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1775C>T	p.Ala592Val	p.A592V	ENST00000377340	11/15	41	27	14	23	23	0	CRNKL1,missense_variant,p.Ala592Val,ENST00000377340,;CRNKL1,missense_variant,p.Ala580Val,ENST00000377327,;CRNKL1,missense_variant,p.Ala431Val,ENST00000536226,;CRNKL1,upstream_gene_variant,,ENST00000521379,;CRNKL1,3_prime_UTR_variant,,ENST00000496549,;CRNKL1,3_prime_UTR_variant,,ENST00000490910,;CRNKL1,upstream_gene_variant,,ENST00000490258,;	A	ENSG00000101343	ENST00000377340	Transcript	missense_variant	1807	1775	592	A/V	gCc/gTc	rs566498711	.	.	-1	CRNKL1	HGNC	15762	protein_coding	YES	CCDS33446.1	ENSP00000366557	CRNL1_HUMAN	.	UPI00004A39A7	.	deleterious(0.02)	possibly_damaging(0.502)	11/15	.	Superfamily_domains:SSF48452,SMART_domains:SM00386,Gene3D:1.25.40.10,hmmpanther:PTHR11246,hmmpanther:PTHR11246:SF3	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGGCTAAT	by1000G	5	ESCA
NCOA5	0	.	GRCh37	20	44699150	44699150	+	Silent	SNP	G	G	T	rs780262412	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64C>A	p.%3D	p.R22R	ENST00000290231	3/8	29	20	9	23	23	0	NCOA5,synonymous_variant,p.%3D,ENST00000290231,;NCOA5,5_prime_UTR_variant,,ENST00000372291,;	T	ENSG00000124160	ENST00000290231	Transcript	synonymous_variant	229	64	22	R	Cga/Aga	rs780262412,COSM1412154	.	.	-1	NCOA5	HGNC	15909	protein_coding	YES	CCDS13392.1	ENSP00000290231	NCOA5_HUMAN	Q5JY17_HUMAN	UPI000000D7B2	.	.	.	3/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23295:SF3,hmmpanther:PTHR23295	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCGACTGT	.	5	ESCA
FOXRED2	0	.	GRCh37	22	36902124	36902124	+	Missense_Mutation	SNP	G	G	T	rs755978039	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.346C>A	p.Arg116Ser	p.R116S	ENST00000397224	2/9	39	30	9	33	33	0	FOXRED2,missense_variant,p.Arg116Ser,ENST00000397224,;FOXRED2,missense_variant,p.Arg116Ser,ENST00000397223,;FOXRED2,missense_variant,p.Arg116Ser,ENST00000216187,;EIF3D,downstream_gene_variant,,ENST00000216190,;EIF3D,downstream_gene_variant,,ENST00000541106,;EIF3D,downstream_gene_variant,,ENST00000405442,;FOXRED2,downstream_gene_variant,,ENST00000423980,;EIF3D,downstream_gene_variant,,ENST00000478547,;EIF3D,downstream_gene_variant,,ENST00000462641,;	T	ENSG00000100350	ENST00000397224	Transcript	missense_variant	440	346	116	R/S	Cgt/Agt	rs755978039	.	.	-1	FOXRED2	HGNC	26264	protein_coding	YES	CCDS13929.1	ENSP00000380401	FXRD2_HUMAN	B0QYA2_HUMAN,A8MUR8_HUMAN	UPI00000744FA	.	tolerated(0.47)	benign(0.026)	2/9	.	hmmpanther:PTHR23023,hmmpanther:PTHR23023:SF53,Pfam_domain:PF13738,Gene3D:3.50.50.60,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCACGCGAGT	.	5	ESCA
ODC1	0	.	GRCh37	2	10580959	10580959	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1277delC	p.Pro426HisfsTer4	p.P426Hfs*4	ENST00000234111	12/12	64	56	8	62	62	0	ODC1,frameshift_variant,p.Pro426HisfsTer4,ENST00000234111,;ODC1,frameshift_variant,p.Pro426HisfsTer4,ENST00000405333,;ODC1,downstream_gene_variant,,ENST00000443218,;ODC1,downstream_gene_variant,,ENST00000446285,;	-	ENSG00000115758	ENST00000234111	Transcript	frameshift_variant	1788	1277	426	P/X	cCa/ca	.	.	.	-1	ODC1	HGNC	8109	protein_coding	YES	CCDS1672.1	ENSP00000234111	DCOR_HUMAN	C9JG30_HUMAN	UPI0000001283	.	.	.	12/12	.	hmmpanther:PTHR11482:SF42,hmmpanther:PTHR11482	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCGGGTGGGAAG	.	3	ESCA
ANAPC1	0	.	GRCh37	2	112630660	112630660	+	Intron	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528+225T>C	.	.	ENST00000341068	.	10	7	3	21	21	0	ANAPC1,intron_variant,,ENST00000341068,;ANAPC1,non_coding_transcript_exon_variant,,ENST00000489177,;ANAPC1,intron_variant,,ENST00000451367,;	G	ENSG00000153107	ENST00000341068	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ANAPC1	HGNC	19988	protein_coding	YES	CCDS2093.1	ENSP00000339109	APC1_HUMAN	.	UPI000006EC6E	.	.	.	.	5/47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACAAACACAT	.	2	ESCA
PCDP1	0	.	GRCh37	2	120366079	120366079	+	Missense_Mutation	SNP	C	C	A	rs760871327	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135C>A	p.Gln379Lys	p.Q379K	ENST00000413369	12/24	181	158	22	143	143	0	PCDP1,missense_variant,p.Gln379Lys,ENST00000413369,;PCDP1,missense_variant,p.Gln93Lys,ENST00000602047,;PCDP1,upstream_gene_variant,,ENST00000599827,;PCDP1,intron_variant,,ENST00000597189,;PCDP1,splice_region_variant,,ENST00000295220,;PCDP1,splice_region_variant,,ENST00000413057,;	A	ENSG00000163075	ENST00000413369	Transcript	missense_variant	1222	1135	379	Q/K	Cag/Aag	rs760871327	.	.	1	PCDP1	Uniprot_gn	.	protein_coding	YES	CCDS33282.2	ENSP00000393222	PCDP1_HUMAN	.	UPI0001D322F9	.	deleterious(0.01)	possibly_damaging(0.721)	12/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGGCAGGTG	.	4	ESCA
POTEF	0	.	GRCh37	2	130834673	130834673	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1880T>C	p.Val627Ala	p.V627A	ENST00000357462	14/15	40	26	14	48	48	0	POTEF,missense_variant,p.Val627Ala,ENST00000357462,;POTEF,missense_variant,p.Val627Ala,ENST00000409914,;POTEF,3_prime_UTR_variant,,ENST00000361163,;POTEF,3_prime_UTR_variant,,ENST00000360967,;AC018865.11,downstream_gene_variant,,ENST00000423631,;	G	ENSG00000196604	ENST00000357462	Transcript	missense_variant	1974	1880	627	V/A	gTt/gCt	.	.	.	-1	POTEF	HGNC	33905	protein_coding	YES	CCDS46409.1	ENSP00000350052	POTEF_HUMAN	.	UPI0000418FEA	.	tolerated_low_confidence(1)	benign(0.001)	14/15	.	hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TTTCAACCACT	.	2	ESCA
SMPD4	0	.	GRCh37	2	130910744	130910744	+	Missense_Mutation	SNP	T	T	C	rs553662129	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2143A>G	p.Ile715Val	p.I715V	ENST00000409031	19/20	42	28	14	36	36	0	SMPD4,missense_variant,p.Ile573Val,ENST00000339679,;SMPD4,missense_variant,p.Ile590Val,ENST00000439886,;SMPD4,missense_variant,p.Ile464Val,ENST00000453750,;SMPD4,missense_variant,p.Ile686Val,ENST00000351288,;SMPD4,missense_variant,p.Ile456Val,ENST00000452225,;SMPD4,missense_variant,p.Ile715Val,ENST00000409031,;SMPD4,missense_variant,p.Ile379Val,ENST00000443958,;SMPD4,missense_variant,p.Ile613Val,ENST00000431183,;SMPD4,missense_variant,p.Ile351Val,ENST00000426662,;SMPD4,intron_variant,,ENST00000457039,;SMPD4,downstream_gene_variant,,ENST00000430682,;SMPD4,downstream_gene_variant,,ENST00000449159,;SMPD4,downstream_gene_variant,,ENST00000451542,;SMPD4,downstream_gene_variant,,ENST00000455548,;SMPD4,downstream_gene_variant,,ENST00000473720,;SMPD4,splice_region_variant,,ENST00000491319,;SMPD4,splice_region_variant,,ENST00000433118,;SMPD4,splice_region_variant,,ENST00000491128,;SMPD4,splice_region_variant,,ENST00000454468,;SMPD4,splice_region_variant,,ENST00000482171,;SMPD4,splice_region_variant,,ENST00000412570,;SMPD4,downstream_gene_variant,,ENST00000435455,;SMPD4,downstream_gene_variant,,ENST00000461187,;SMPD4,downstream_gene_variant,,ENST00000439029,;	C	ENSG00000136699	ENST00000409031	Transcript	missense_variant	3292	2143	715	I/V	Atc/Gtc	rs553662129	.	.	-1	SMPD4	HGNC	32949	protein_coding	YES	CCDS42751.1	ENSP00000386531	.	C9J647_HUMAN,B1PBA3_HUMAN	UPI000036FC5A	.	tolerated(0.24)	benign(0.004)	19/20	.	hmmpanther:PTHR12988,Pfam_domain:PF14724	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGATCTAGA	by1000G	5	ESCA
TTN	0	.	GRCh37	2	179445305	179445305	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66801A>C	p.Leu22267Phe	p.L22267F	ENST00000589042	317/363	43	28	15	35	35	0	TTN,missense_variant,p.Leu13327Phe,ENST00000359218,;TTN,missense_variant,p.Leu20626Phe,ENST00000591111,;TTN,missense_variant,p.Leu22267Phe,ENST00000589042,;TTN,missense_variant,p.Leu13394Phe,ENST00000342175,;TTN,missense_variant,p.Leu19699Phe,ENST00000342992,;TTN,missense_variant,p.Leu13202Phe,ENST00000460472,;RP11-171I2.2,non_coding_transcript_exon_variant,,ENST00000603521,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,upstream_gene_variant,,ENST00000590743,;RP11-171I2.5,downstream_gene_variant,,ENST00000604215,;TTN-AS1,upstream_gene_variant,,ENST00000589907,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	67026	66801	22267	L/F	ttA/ttC	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	317/363	.	hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTTAAGTC	.	5	ESCA
TTN	0	.	GRCh37	2	179641846	179641846	+	Intron	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4814+30A>G	.	.	ENST00000589042	.	104	85	19	77	77	0	TTN,intron_variant,,ENST00000360870,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342992,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000589042,;TTN,intron_variant,,ENST00000591111,;TTN,intron_variant,,ENST00000460472,;RP11-88L24.4,non_coding_transcript_exon_variant,,ENST00000582038,;TTN-AS1,downstream_gene_variant,,ENST00000610005,;TTN-AS1,downstream_gene_variant,,ENST00000585451,;TTN-AS1,downstream_gene_variant,,ENST00000584485,;	C	ENSG00000155657	ENST00000589042	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	.	27/362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATAATGAGCT	.	5	ESCA
ITGAV	0	.	GRCh37	2	187542313	187542313	+	3'UTR	SNP	A	A	G	rs555009023	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*294A>G	.	.	ENST00000261023	30/30	21	7	13	34	34	0	ITGAV,3_prime_UTR_variant,,ENST00000374907,;ITGAV,3_prime_UTR_variant,,ENST00000261023,;ITGAV,downstream_gene_variant,,ENST00000430709,;ITGAV,downstream_gene_variant,,ENST00000433736,;AC017101.10,intron_variant,,ENST00000453665,;ITGAV,downstream_gene_variant,,ENST00000496477,;	G	ENSG00000138448	ENST00000261023	Transcript	3_prime_UTR_variant	3715	.	.	.	.	rs555009023	.	.	1	ITGAV	HGNC	6150	protein_coding	YES	CCDS2292.1	ENSP00000261023	ITAV_HUMAN	L7RXH0_HUMAN	UPI000013D12E	.	.	.	30/30	.	.	G:0.0002	G:0	G:0	.	G:0	G:0	G:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATATAAAA	by1000G	5	ESCA
PUM2	0	.	GRCh37	2	20449661	20449661	+	3'UTR	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1685G>C	.	.	ENST00000338086	20/20	108	90	18	61	61	0	PUM2,3_prime_UTR_variant,,ENST00000319801,;PUM2,3_prime_UTR_variant,,ENST00000338086,;PUM2,3_prime_UTR_variant,,ENST00000440577,;PUM2,3_prime_UTR_variant,,ENST00000361078,;PUM2,downstream_gene_variant,,ENST00000403432,;PUM2,downstream_gene_variant,,ENST00000536417,;RNU7-113P,upstream_gene_variant,,ENST00000459273,;	G	ENSG00000055917	ENST00000338086	Transcript	3_prime_UTR_variant	4903	.	.	.	.	.	.	.	-1	PUM2	HGNC	14958	protein_coding	YES	CCDS1698.1	ENSP00000338173	PUM2_HUMAN	C9JW01_HUMAN,C9JE24_HUMAN,B4E2B6_HUMAN	UPI0000001665	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGTCACAAT	.	5	ESCA
IKZF2	0	.	GRCh37	2	213872143	213872143	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1522A>G	p.Ser508Gly	p.S508G	ENST00000457361	8/8	76	56	20	82	82	0	IKZF2,missense_variant,p.Ser508Gly,ENST00000457361,;IKZF2,missense_variant,p.Ser508Gly,ENST00000434687,;IKZF2,missense_variant,p.Ser363Gly,ENST00000374327,;IKZF2,missense_variant,p.Ser434Gly,ENST00000421754,;IKZF2,missense_variant,p.Ser436Gly,ENST00000451136,;IKZF2,missense_variant,p.Ser514Gly,ENST00000342002,;IKZF2,missense_variant,p.Ser482Gly,ENST00000374319,;IKZF2,3_prime_UTR_variant,,ENST00000413091,;AC079610.1,intron_variant,,ENST00000415387,;IKZF2,3_prime_UTR_variant,,ENST00000453575,;IKZF2,3_prime_UTR_variant,,ENST00000439848,;IKZF2,3_prime_UTR_variant,,ENST00000412444,;IKZF2,3_prime_UTR_variant,,ENST00000431520,;IKZF2,3_prime_UTR_variant,,ENST00000374326,;IKZF2,non_coding_transcript_exon_variant,,ENST00000484040,;	C	ENSG00000030419	ENST00000457361	Transcript	missense_variant	1691	1522	508	S/G	Agc/Ggc	.	.	.	-1	IKZF2	HGNC	13177	protein_coding	YES	CCDS2395.1	ENSP00000410447	IKZF2_HUMAN	Q53SU9_HUMAN,Q53RV5_HUMAN,Q53QP1_HUMAN,E7EPU0_HUMAN	UPI000013D4DA	.	deleterious(0)	benign(0.254)	8/8	.	hmmpanther:PTHR24404:SF31,hmmpanther:PTHR24404,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGCTTCTGT	.	5	ESCA
ZNF142	0	.	GRCh37	2	219505483	219505483	+	Missense_Mutation	SNP	G	G	A	rs367658234	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4498C>T	p.Arg1500Trp	p.R1500W	ENST00000411696	8/9	55	48	7	57	57	0	ZNF142,missense_variant,p.Arg1500Trp,ENST00000411696,;ZNF142,missense_variant,p.Arg1500Trp,ENST00000449707,;PLCD4,downstream_gene_variant,,ENST00000457773,;PLCD4,downstream_gene_variant,,ENST00000450993,;PLCD4,downstream_gene_variant,,ENST00000417849,;PLCD4,downstream_gene_variant,,ENST00000432688,;ZNF142,3_prime_UTR_variant,,ENST00000450765,;ZNF142,3_prime_UTR_variant,,ENST00000433921,;PLCD4,downstream_gene_variant,,ENST00000484718,;PLCD4,downstream_gene_variant,,ENST00000473443,;PLCD4,downstream_gene_variant,,ENST00000459791,;PLCD4,downstream_gene_variant,,ENST00000483685,;	A	ENSG00000115568	ENST00000411696	Transcript	missense_variant	5278	4498	1500	R/W	Cgg/Tgg	rs367658234	.	.	-1	ZNF142	HGNC	12927	protein_coding	YES	CCDS42817.1	ENSP00000398798	ZN142_HUMAN	C9J055_HUMAN	UPI000013D5FC	.	deleterious(0)	possibly_damaging(0.898)	8/9	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF43,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATCCGCATGT	byFrequency|byCluster	4	ESCA
IRS1	0	.	GRCh37	2	227600362	227600362	+	3'UTR	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*626C>G	.	.	ENST00000305123	2/2	97	80	16	65	65	0	IRS1,3_prime_UTR_variant,,ENST00000305123,;	C	ENSG00000169047	ENST00000305123	Transcript	3_prime_UTR_variant	5376	.	.	.	.	.	.	.	-1	IRS1	HGNC	6125	protein_coding	YES	CCDS2463.1	ENSP00000304895	IRS1_HUMAN	.	UPI000003BB52	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACAAGGATCA	.	5	ESCA
CRIPT	0	.	GRCh37	2	46844418	46844418	+	5'UTR	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4A>G	.	.	ENST00000238892	1/5	94	66	28	53	53	0	CRIPT,5_prime_UTR_variant,,ENST00000238892,;PIGF,upstream_gene_variant,,ENST00000306465,;PIGF,upstream_gene_variant,,ENST00000281382,;PIGF,upstream_gene_variant,,ENST00000474980,;CRIPT,intron_variant,,ENST00000486447,;PIGF,upstream_gene_variant,,ENST00000495933,;PIGF,upstream_gene_variant,,ENST00000412717,;	G	ENSG00000119878	ENST00000238892	Transcript	5_prime_UTR_variant	129	.	.	.	.	.	.	.	1	CRIPT	HGNC	14312	protein_coding	YES	CCDS1829.1	ENSP00000238892	CRIPT_HUMAN	.	UPI000006F4D2	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGGGAAGGAT	.	4	ESCA
MEIS1	0	.	GRCh37	2	66775122	66775122	+	Silent	SNP	G	G	T	rs778341280	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936G>T	p.%3D	p.T312T	ENST00000272369	9/13	88	48	40	64	63	1	MEIS1,synonymous_variant,p.%3D,ENST00000450027,;MEIS1,synonymous_variant,p.%3D,ENST00000495021,;MEIS1,synonymous_variant,p.%3D,ENST00000606455,;MEIS1,synonymous_variant,p.%3D,ENST00000488550,;MEIS1,synonymous_variant,p.%3D,ENST00000560281,;MEIS1,synonymous_variant,p.%3D,ENST00000407092,;MEIS1,synonymous_variant,p.%3D,ENST00000272369,;MEIS1,synonymous_variant,p.%3D,ENST00000398506,;MEIS1,3_prime_UTR_variant,,ENST00000444274,;MEIS1,non_coding_transcript_exon_variant,,ENST00000409517,;MEIS1,3_prime_UTR_variant,,ENST00000542964,;MEIS1,3_prime_UTR_variant,,ENST00000475239,;	T	ENSG00000143995	ENST00000272369	Transcript	synonymous_variant	1393	936	312	T	acG/acT	rs778341280	.	.	1	MEIS1	HGNC	7000	protein_coding	YES	CCDS46309.1	ENSP00000272369	MEIS1_HUMAN	Q8IZZ2_HUMAN,Q53RD5_HUMAN,Q53R57_HUMAN	UPI000000DA5A	.	.	.	9/13	.	PROSITE_profiles:PS50071,hmmpanther:PTHR11850:SF63,hmmpanther:PTHR11850,Pfam_domain:PF05920,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACACGGGACT	.	5	ESCA
ETAA1	0	.	GRCh37	2	67626404	67626404	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327delG	p.Asn110IlefsTer4	p.N110Ifs*4	ENST00000272342	2/6	239	174	65	119	119	0	ETAA1,frameshift_variant,p.Asn110IlefsTer4,ENST00000272342,;ETAA1,upstream_gene_variant,,ENST00000462772,;	-	ENSG00000143971	ENST00000272342	Transcript	frameshift_variant	457	327	109	Q/X	caG/ca	.	.	.	1	ETAA1	HGNC	24648	protein_coding	YES	CCDS1882.1	ENSP00000272342	ETAA1_HUMAN	.	UPI00001414BC	.	.	.	2/6	.	hmmpanther:PTHR16434:SF1,hmmpanther:PTHR16434,Pfam_domain:PF15350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGATCAGAATTC	.	3	ESCA
ZAP70	0	.	GRCh37	2	98351150	98351150	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057C>A	p.Arg353Ser	p.R353S	ENST00000264972	9/14	50	47	3	39	39	0	ZAP70,missense_variant,p.Arg227Ser,ENST00000442208,;ZAP70,missense_variant,p.Arg46Ser,ENST00000451498,;ZAP70,missense_variant,p.Arg353Ser,ENST00000264972,;ZAP70,non_coding_transcript_exon_variant,,ENST00000463643,;ZAP70,non_coding_transcript_exon_variant,,ENST00000487283,;ZAP70,downstream_gene_variant,,ENST00000498836,;ZAP70,downstream_gene_variant,,ENST00000483781,;ZAP70,upstream_gene_variant,,ENST00000495754,;ZAP70,upstream_gene_variant,,ENST00000489250,;	A	ENSG00000115085	ENST00000264972	Transcript	missense_variant	1272	1057	353	R/S	Cgc/Agc	.	.	.	1	ZAP70	HGNC	12858	protein_coding	YES	CCDS33254.1	ENSP00000264972	ZAP70_HUMAN	B4E0E2_HUMAN	UPI000013C370	.	deleterious(0.04)	possibly_damaging(0.698)	9/14	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF80,hmmpanther:PTHR24418,PROSITE_patterns:PS00107,Pfam_domain:PF07714,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000604,SMART_domains:SM00219,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGTGCGCCAG	.	2	ESCA
DZIP3	0	.	GRCh37	3	108363103	108363103	+	Missense_Mutation	SNP	T	T	C	rs201610955	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234T>C	p.Phe412Leu	p.F412L	ENST00000361582	14/33	111	93	18	34	34	0	DZIP3,missense_variant,p.Phe412Leu,ENST00000479138,;DZIP3,missense_variant,p.Phe412Leu,ENST00000463306,;DZIP3,missense_variant,p.Phe412Leu,ENST00000361582,;DZIP3,3_prime_UTR_variant,,ENST00000495008,;	C	ENSG00000198919	ENST00000361582	Transcript	missense_variant	1464	1234	412	F/L	Ttt/Ctt	rs201610955	.	.	1	DZIP3	HGNC	30938	protein_coding	YES	CCDS2952.1	ENSP00000355028	DZIP3_HUMAN	Q5MY58_HUMAN,D3DN61_HUMAN,C9JRX4_HUMAN,C9J9M8_HUMAN,C9J702_HUMAN	UPI000006E7D4	.	deleterious_low_confidence(0)	probably_damaging(0.986)	14/33	.	hmmpanther:PTHR12477:SF15,hmmpanther:PTHR12477	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	G:0.0002	G:0.0005	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATATTTGAT	byCluster|by1000G	5	ESCA
PLXNA1	0	.	GRCh37	3	126748339	126748339	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4830C>T	p.%3D	p.I1610I	ENST00000393409	26/31	105	92	12	45	45	0	PLXNA1,synonymous_variant,p.%3D,ENST00000393409,;PLXNA1,synonymous_variant,p.%3D,ENST00000251772,;PLXNA1,upstream_gene_variant,,ENST00000505278,;PLXNA1,non_coding_transcript_exon_variant,,ENST00000503234,;PLXNA1,non_coding_transcript_exon_variant,,ENST00000503363,;	T	ENSG00000114554	ENST00000393409	Transcript	synonymous_variant	4830	4830	1610	I	atC/atT	.	.	.	1	PLXNA1	HGNC	9099	protein_coding	YES	CCDS33847.2	ENSP00000377061	PLXA1_HUMAN	Q9NSM6_HUMAN,F8VSZ4_HUMAN,B4DE20_HUMAN,B3KY38_HUMAN	UPI00001A7983	.	.	.	26/31	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35,Pfam_domain:PF08337,Gene3D:3.10.20.90	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACATCTCCAA	.	4	ESCA
H1FX	0	.	GRCh37	3	129033894	129033894	+	3'UTR	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*210C>G	.	.	ENST00000333762	1/1	46	41	5	20	20	0	H1FX,3_prime_UTR_variant,,ENST00000333762,;H1FX-AS1,upstream_gene_variant,,ENST00000383461,;H1FX-AS1,upstream_gene_variant,,ENST00000511998,;H1FX-AS1,upstream_gene_variant,,ENST00000433902,;H1FX-AS1,upstream_gene_variant,,ENST00000537780,;H1FX-AS1,upstream_gene_variant,,ENST00000502789,;	C	ENSG00000184897	ENST00000333762	Transcript	3_prime_UTR_variant	1227	.	.	.	.	.	.	.	-1	H1FX	HGNC	4722	protein_coding	YES	CCDS3057.1	ENSP00000329662	H1X_HUMAN	.	UPI000012BF2F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCGCCGGGGCT	.	3	ESCA
ZIC4	0	.	GRCh37	3	147120551	147120551	+	Nonsense_Mutation	SNP	G	G	A	rs201698839	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.184C>T	p.Arg62Ter	p.R62*	ENST00000525172	2/5	212	188	23	75	75	0	ZIC4,stop_gained,p.Arg12Ter,ENST00000484399,;ZIC4,stop_gained,p.Arg50Ter,ENST00000425731,;ZIC4,stop_gained,p.Arg12Ter,ENST00000473123,;ZIC4,stop_gained,p.Arg12Ter,ENST00000383075,;ZIC4,stop_gained,p.Arg12Ter,ENST00000463250,;ZIC4,stop_gained,p.Arg12Ter,ENST00000491672,;ZIC4,stop_gained,p.Arg12Ter,ENST00000462748,;ZIC4,stop_gained,p.Arg62Ter,ENST00000525172,;ZIC4,stop_gained,p.Arg12Ter,ENST00000484586,;ZIC1,intron_variant,,ENST00000488404,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,;	A	ENSG00000174963	ENST00000525172	Transcript	stop_gained	370	184	62	R/*	Cga/Tga	rs201698839,COSM268161,COSM1752956	.	.	-1	ZIC4	HGNC	20393	protein_coding	YES	CCDS54652.1	ENSP00000435509	ZIC4_HUMAN	C9JZU7_HUMAN,C9JD04_HUMAN,C9J6T3_HUMAN,B3KPI4_HUMAN	UPI0001914D88	.	.	.	2/5	.	.	.	.	.	.	.	.	.	A:0	A:0.0002	.	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R12*|c.34C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TAATCGTTTCC	byFrequency|byCluster	4	ESCA
SMC4	0	.	GRCh37	3	160149603	160149603	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3287A>G	p.Tyr1096Cys	p.Y1096C	ENST00000357388	21/24	180	42	138	66	66	0	SMC4,missense_variant,p.Tyr1096Cys,ENST00000344722,;SMC4,missense_variant,p.Tyr1071Cys,ENST00000469762,;SMC4,missense_variant,p.Tyr1038Cys,ENST00000462787,;SMC4,missense_variant,p.Tyr1096Cys,ENST00000357388,;SMC4,missense_variant,p.Tyr1038Cys,ENST00000360111,;TRIM59,downstream_gene_variant,,ENST00000309784,;TRIM59,downstream_gene_variant,,ENST00000543469,;SMC4,non_coding_transcript_exon_variant,,ENST00000486711,;SMC4,non_coding_transcript_exon_variant,,ENST00000462668,;RP11-432B6.3,intron_variant,,ENST00000483754,;SMC4,downstream_gene_variant,,ENST00000488017,;	G	ENSG00000113810	ENST00000357388	Transcript	missense_variant	3738	3287	1096	Y/C	tAt/tGt	.	.	.	1	SMC4	HGNC	14013	protein_coding	YES	CCDS3189.1	ENSP00000349961	SMC4_HUMAN	C9JWF0_HUMAN,C9JVD8_HUMAN,C9JR83_HUMAN,C9JJ64_HUMAN,C9J9E4_HUMAN,C9J578_HUMAN,C9IYK2_HUMAN	UPI000006DA0A	.	deleterious(0)	probably_damaging(0.994)	21/24	.	hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF148,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGTATAAAA	.	5	ESCA
PHC3	0	.	GRCh37	3	169866908	169866908	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.539C>T	p.Ala180Val	p.A180V	ENST00000495893	5/15	303	95	208	115	115	0	PHC3,missense_variant,p.Ala164Val,ENST00000474275,;PHC3,missense_variant,p.Ala180Val,ENST00000495893,;PHC3,missense_variant,p.Ala168Val,ENST00000494943,;PHC3,missense_variant,p.Ala180Val,ENST00000475729,;PHC3,intron_variant,,ENST00000484931,;PHC3,intron_variant,,ENST00000467570,;PHC3,intron_variant,,ENST00000466189,;PHC3,downstream_gene_variant,,ENST00000465896,;RNU6-315P,upstream_gene_variant,,ENST00000362666,;PHC3,synonymous_variant,p.%3D,ENST00000479467,;PHC3,downstream_gene_variant,,ENST00000472330,;	A	ENSG00000173889	ENST00000495893	Transcript	missense_variant	571	539	180	A/V	gCa/gTa	.	.	.	-1	PHC3	HGNC	15682	protein_coding	YES	CCDS46952.1	ENSP00000420294	PHC3_HUMAN	C9JYH7_HUMAN	UPI00004DF1A6	.	deleterious(0)	probably_damaging(0.997)	5/15	.	hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTGCCGTT	.	5	ESCA
NAALADL2	0	.	GRCh37	3	175293940	175293940	+	Missense_Mutation	SNP	G	G	C	rs751338020	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1765G>C	p.Val589Leu	p.V589L	ENST00000454872	10/14	162	152	9	82	82	0	NAALADL2,missense_variant,p.Val589Leu,ENST00000454872,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000473253,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000489299,;	C	ENSG00000177694	ENST00000454872	Transcript	missense_variant	1893	1765	589	V/L	Gtg/Ctg	rs751338020	.	.	1	NAALADL2	HGNC	23219	protein_coding	YES	CCDS46960.1	ENSP00000404705	NADL2_HUMAN	C9JQ86_HUMAN	UPI0000161608	.	tolerated(0.54)	benign(0.042)	10/14	.	hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404,Gene3D:3.40.630.10,Pfam_domain:PF04389,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATCGTGCAG	byFrequency	2	ESCA
THPO	0	.	GRCh37	3	184093777	184093777	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40C>G	p.Leu14Val	p.L14V	ENST00000204615	3/6	153	145	8	38	38	0	THPO,missense_variant,p.Leu14Val,ENST00000445696,;THPO,missense_variant,p.Leu14Val,ENST00000204615,;THPO,missense_variant,p.Leu14Val,ENST00000421442,;EIF2B5,intron_variant,,ENST00000444495,;CHRD,upstream_gene_variant,,ENST00000450923,;CHRD,upstream_gene_variant,,ENST00000204604,;CHRD,upstream_gene_variant,,ENST00000310236,;CHRD,upstream_gene_variant,,ENST00000348986,;THPO,upstream_gene_variant,,ENST00000477594,;CHRD,upstream_gene_variant,,ENST00000459711,;CHRD,upstream_gene_variant,,ENST00000470150,;CHRD,upstream_gene_variant,,ENST00000356534,;CHRD,upstream_gene_variant,,ENST00000460627,;CHRD,upstream_gene_variant,,ENST00000496527,;CHRD,upstream_gene_variant,,ENST00000448472,;CHRD,upstream_gene_variant,,ENST00000420973,;CHRD,upstream_gene_variant,,ENST00000485883,;	C	ENSG00000090534	ENST00000204615	Transcript	missense_variant	255	40	14	L/V	Cta/Gta	.	.	.	-1	THPO	HGNC	11795	protein_coding	YES	CCDS3265.1	ENSP00000204615	TPO_HUMAN	.	UPI000004A8D1	.	tolerated(0.17)	unknown(0)	3/6	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTTAGGAGAA	.	2	ESCA
MUC4	0	.	GRCh37	3	195510099	195510099	+	Silent	SNP	A	A	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8352T>A	p.%3D	p.P2784P	ENST00000463781	2/25	104	71	33	138	138	0	MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000470451,;MUC4,synonymous_variant,p.%3D,ENST00000477086,;MUC4,synonymous_variant,p.%3D,ENST00000466475,;MUC4,synonymous_variant,p.%3D,ENST00000478156,;MUC4,synonymous_variant,p.%3D,ENST00000479406,;MUC4,synonymous_variant,p.%3D,ENST00000477756,;MUC4,synonymous_variant,p.%3D,ENST00000462323,;MUC4,synonymous_variant,p.%3D,ENST00000480843,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,;	T	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	8812	8352	2784	P	ccT/ccA	.	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.H2781H|c.8343C>T|7,BUFFER|p.D2781D|c.8343C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAGAGGGGT	.	5	ESCA
PRICKLE2	0	.	GRCh37	3	64082740	64082740	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1987A>G	.	.	ENST00000295902	8/8	61	23	38	70	70	0	PRICKLE2,3_prime_UTR_variant,,ENST00000295902,;PRICKLE2,downstream_gene_variant,,ENST00000564377,;RP11-129B22.1,non_coding_transcript_exon_variant,,ENST00000482609,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000460946,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000476308,;	C	ENSG00000163637	ENST00000295902	Transcript	3_prime_UTR_variant	5108	.	.	.	.	.	.	.	-1	PRICKLE2	HGNC	20340	protein_coding	YES	CCDS2902.1	ENSP00000295902	PRIC2_HUMAN	C9JY03_HUMAN	UPI0000160A8B	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTAATAGAGT	.	5	ESCA
TBCK	0	.	GRCh37	4	107237698	107237698	+	Intron	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-30+7C>G	.	.	ENST00000273980	.	93	82	11	76	76	0	TBCK,splice_region_variant,,ENST00000273980,;TBCK,splice_region_variant,,ENST00000432496,;AIMP1,5_prime_UTR_variant,,ENST00000394701,;AIMP1,intron_variant,,ENST00000442366,;AIMP1,intron_variant,,ENST00000358008,;AIMP1,intron_variant,,ENST00000510207,;TBCK,upstream_gene_variant,,ENST00000507696,;TBCK,upstream_gene_variant,,ENST00000394706,;TBCK,upstream_gene_variant,,ENST00000361687,;TBCK,upstream_gene_variant,,ENST00000394708,;TBCK,upstream_gene_variant,,ENST00000509532,;TBCK,upstream_gene_variant,,ENST00000467183,;	C	ENSG00000145348	ENST00000273980	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	TBCK	HGNC	28261	protein_coding	YES	CCDS54788.1	ENSP00000273980	TBCK_HUMAN	D6RDY5_HUMAN,D6RDG2_HUMAN,D6RC61_HUMAN,D6R950_HUMAN	UPI000013EF70	.	.	.	.	2/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCTGGACCTA	.	4	ESCA
FGA	0	.	GRCh37	4	155505138	155505138	+	3'UTR	SNP	A	A	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*138T>G	.	.	ENST00000302053	6/6	61	51	10	39	39	0	FGA,3_prime_UTR_variant,,ENST00000302053,;FGA,downstream_gene_variant,,ENST00000403106,;	C	ENSG00000171560	ENST00000302053	Transcript	3_prime_UTR_variant	2818	.	.	.	.	.	.	.	-1	FGA	HGNC	3661	protein_coding	YES	CCDS3787.1	ENSP00000306361	FIBA_HUMAN	Q86Z09_HUMAN	UPI000012A75A	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTAGCTAC	.	4	ESCA
FAT1	0	.	GRCh37	4	187541543	187541545	+	In_Frame_Del	DEL	ACA	ACA	-	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	ACA	ACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6195_6197delTGT	p.Val2067del	p.V2067del	ENST00000441802	10/27	38	22	16	39	39	0	FAT1,inframe_deletion,p.Val2067del,ENST00000441802,;	-	ENSG00000083857	ENST00000441802	Transcript	inframe_deletion	6405-6407	6195-6197	2065-2066	VV/V	gtTGTc/gtc	.	.	.	-1	FAT1	HGNC	3595	protein_coding	YES	CCDS47177.1	ENSP00000406229	FAT1_HUMAN	D6RCE4_HUMAN	UPI000051946B	.	.	.	10/27	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF40,hmmpanther:PTHR24026,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCACGACAACGTG	.	3	ESCA
GABRA2	0	.	GRCh37	4	46252490	46252490	+	Missense_Mutation	SNP	G	G	T	rs772937785	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1191C>A	p.Asn397Lys	p.N397K	ENST00000510861	10/10	64	54	10	81	81	0	GABRA2,missense_variant,p.Asn397Lys,ENST00000510861,;GABRA2,missense_variant,p.Asn397Lys,ENST00000356504,;GABRA2,missense_variant,p.Asn457Lys,ENST00000507069,;GABRA2,missense_variant,p.Asn397Lys,ENST00000381620,;GABRA2,missense_variant,p.Asn402Lys,ENST00000540012,;GABRA2,missense_variant,p.Asn397Lys,ENST00000514090,;GABRA2,3_prime_UTR_variant,,ENST00000513005,;GABRA2,3_prime_UTR_variant,,ENST00000510233,;	T	ENSG00000151834	ENST00000510861	Transcript	missense_variant	1365	1191	397	N/K	aaC/aaA	rs772937785	.	.	-1	GABRA2	HGNC	4076	protein_coding	YES	CCDS3471.1	ENSP00000421828	GBRA2_HUMAN	Q4W5L8_HUMAN,D6RBL7_HUMAN,D6RBK9_HUMAN,D6RB77_HUMAN	UPI000013DC88	.	tolerated(0.91)	benign(0.006)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR18945:SF218,hmmpanther:PTHR18945,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR01615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTGTTGGG	byFrequency	5	ESCA
GABRB1	0	.	GRCh37	4	47163459	47163459	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.434C>A	p.Pro145His	p.P145H	ENST00000295454	4/9	47	42	5	59	59	0	GABRB1,missense_variant,p.Pro75His,ENST00000538619,;GABRB1,missense_variant,p.Pro112His,ENST00000513567,;GABRB1,missense_variant,p.Pro145His,ENST00000295454,;GABRB1,3_prime_UTR_variant,,ENST00000510909,;	A	ENSG00000163288	ENST00000295454	Transcript	missense_variant	726	434	145	P/H	cCt/cAt	COSM3392888	.	.	1	GABRB1	HGNC	4081	protein_coding	YES	CCDS3474.1	ENSP00000295454	GBRB1_HUMAN	D6REM0_HUMAN	UPI000012AFAC	.	tolerated(0.1)	probably_damaging(0.951)	4/9	.	hmmpanther:PTHR18945:SF198,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GCATCCTGATG	.	3	ESCA
TBC1D14	0	.	GRCh37	4	7008436	7008436	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1429C>T	p.Leu477Phe	p.L477F	ENST00000409757	9/14	92	65	27	111	110	0	TBC1D14,missense_variant,p.Leu90Phe,ENST00000446947,;TBC1D14,missense_variant,p.Leu477Phe,ENST00000448507,;TBC1D14,missense_variant,p.Leu96Phe,ENST00000439515,;TBC1D14,missense_variant,p.Leu249Phe,ENST00000410031,;TBC1D14,missense_variant,p.Leu197Phe,ENST00000451522,;TBC1D14,missense_variant,p.Leu477Phe,ENST00000409757,;	T	ENSG00000132405	ENST00000409757	Transcript	missense_variant	1553	1429	477	L/F	Ctc/Ttc	.	.	.	1	TBC1D14	HGNC	29246	protein_coding	YES	CCDS3394.2	ENSP00000386921	TBC14_HUMAN	C9JP26_HUMAN,C9J541_HUMAN	UPI000020BAB6	.	deleterious(0.01)	probably_damaging(0.973)	9/14	.	PROSITE_profiles:PS50086,hmmpanther:PTHR22957:SF203,hmmpanther:PTHR22957,Pfam_domain:PF00566,Gene3D:2qq8A02,SMART_domains:SM00164,Superfamily_domains:SSF47923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAATCTCTGC	.	5	ESCA
ANKRD17	0	.	GRCh37	4	73941514	73941514	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*434A>G	.	.	ENST00000358602	34/34	92	80	12	57	57	0	ANKRD17,3_prime_UTR_variant,,ENST00000358602,;ANKRD17,3_prime_UTR_variant,,ENST00000509867,;ANKRD17,3_prime_UTR_variant,,ENST00000330838,;ANKRD17,3_prime_UTR_variant,,ENST00000558247,;ANKRD17,downstream_gene_variant,,ENST00000510127,;	C	ENSG00000132466	ENST00000358602	Transcript	3_prime_UTR_variant	8363	.	.	.	.	.	.	.	-1	ANKRD17	HGNC	23575	protein_coding	YES	CCDS34004.1	ENSP00000351416	ANR17_HUMAN	.	UPI00002263B0	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACATATTGA	.	4	ESCA
SHROOM3	0	.	GRCh37	4	77700367	77700367	+	3'UTR	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*37C>T	.	.	ENST00000296043	11/11	107	62	45	84	84	0	SHROOM3,3_prime_UTR_variant,,ENST00000296043,;RP11-359D14.3,intron_variant,,ENST00000449007,;	T	ENSG00000138771	ENST00000296043	Transcript	3_prime_UTR_variant	6981	.	.	.	.	.	.	.	1	SHROOM3	HGNC	30422	protein_coding	YES	CCDS3579.2	ENSP00000296043	SHRM3_HUMAN	.	UPI0000E5AC1C	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTCTCTCA	.	5	ESCA
ENOPH1	0	.	GRCh37	4	83351916	83351916	+	5'UTR	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-67G>C	.	.	ENST00000273920	1/6	24	17	6	32	32	0	ENOPH1,5_prime_UTR_variant,,ENST00000273920,;ENOPH1,5_prime_UTR_variant,,ENST00000509635,;HNRNPDL,upstream_gene_variant,,ENST00000502762,;HNRNPDL,upstream_gene_variant,,ENST00000349655,;HNRNPDL,upstream_gene_variant,,ENST00000602300,;HNRNPDL,upstream_gene_variant,,ENST00000295470,;HNRNPDL,upstream_gene_variant,,ENST00000514511,;ENOPH1,5_prime_UTR_variant,,ENST00000505846,;HNRNPDL,upstream_gene_variant,,ENST00000507721,;	C	ENSG00000145293	ENST00000273920	Transcript	5_prime_UTR_variant	202	.	.	.	.	.	.	.	1	ENOPH1	HGNC	24599	protein_coding	YES	CCDS3594.1	ENSP00000273920	ENOPH_HUMAN	D6RA00_HUMAN	UPI000006D6DB	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGCAGCCGCA	.	2	ESCA
CPZ	0	.	GRCh37	4	8609083	8609083	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1158G>A	p.%3D	p.V386V	ENST00000360986	7/11	44	31	12	59	58	1	CPZ,synonymous_variant,p.%3D,ENST00000360986,;CPZ,synonymous_variant,p.%3D,ENST00000315782,;CPZ,synonymous_variant,p.%3D,ENST00000382480,;CPZ,5_prime_UTR_variant,,ENST00000429646,;GPR78,3_prime_UTR_variant,,ENST00000514302,;CPZ,3_prime_UTR_variant,,ENST00000515606,;GPR78,non_coding_transcript_exon_variant,,ENST00000513120,;	A	ENSG00000109625	ENST00000360986	Transcript	synonymous_variant	1332	1158	386	V	gtG/gtA	.	.	.	1	CPZ	HGNC	2333	protein_coding	YES	CCDS33953.1	ENSP00000354255	CBPZ_HUMAN	.	UPI000020BCC5	.	.	.	7/11	.	Prints_domain:PR00765,Superfamily_domains:SSF53187,SMART_domains:SM00631,Gene3D:3.40.630.10,Pfam_domain:PF00246,PROSITE_patterns:PS00133,hmmpanther:PTHR11532:SF4,hmmpanther:PTHR11532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGTGTCCTA	.	5	ESCA
SLC12A7	0	.	GRCh37	5	1093658	1093658	+	Missense_Mutation	SNP	C	C	G	rs562501613	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.332G>C	p.Arg111Pro	p.R111P	ENST00000264930	3/24	39	32	7	31	31	0	SLC12A7,missense_variant,p.Arg111Pro,ENST00000264930,;	G	ENSG00000113504	ENST00000264930	Transcript	missense_variant	376	332	111	R/P	cGg/cCg	rs562501613	.	.	-1	SLC12A7	HGNC	10915	protein_coding	YES	CCDS34129.1	ENSP00000264930	S12A7_HUMAN	.	UPI0000141815	.	tolerated(0.15)	benign(0.33)	3/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11827:SF47,hmmpanther:PTHR11827,TIGRFAM_domain:TIGR00930	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCCCGCCGC	by1000G	5	ESCA
ADAMTS19	0	.	GRCh37	5	128956349	128956349	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1499C>T	p.Ala500Val	p.A500V	ENST00000274487	9/23	71	55	16	85	85	0	ADAMTS19,missense_variant,p.Ala500Val,ENST00000274487,;CTC-575N7.1,intron_variant,,ENST00000503616,;	T	ENSG00000145808	ENST00000274487	Transcript	missense_variant	1644	1499	500	A/V	gCt/gTt	.	.	.	1	ADAMTS19	HGNC	17111	protein_coding	YES	CCDS4146.1	ENSP00000274487	ATS19_HUMAN	.	UPI000013DA0D	.	deleterious(0)	possibly_damaging(0.705)	9/23	.	PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF151,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTGCTGATG	.	5	ESCA
PCDHB8	0	.	GRCh37	5	140559034	140559034	+	Silent	SNP	C	C	T	rs113701735	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1419C>T	p.%3D	p.S473S	ENST00000239444	1/1	100	77	23	136	136	0	PCDHB8,synonymous_variant,p.%3D,ENST00000239444,;PCDHB7,downstream_gene_variant,,ENST00000231137,;PCDHB16,upstream_gene_variant,,ENST00000361016,;	T	ENSG00000120322	ENST00000239444	Transcript	synonymous_variant	1664	1419	473	S	agC/agT	rs113701735,COSM589862	.	.	1	PCDHB8	HGNC	8693	protein_coding	YES	CCDS4250.1	ENSP00000239444	PCDB8_HUMAN	.	UPI000013CA80	.	.	.	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF89,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.V474I|c.1420G>A|3	RADIA|SOMATICSNIPER|VARSCANS	GGCAGCGTCAG	.	3	ESCA
PCDHGA3	0	.	GRCh37	5	140724052	140724052	+	Missense_Mutation	SNP	G	G	T	rs267600447	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452G>T	p.Arg151Leu	p.R151L	ENST00000253812	1/4	38	32	6	34	34	0	PCDHGA3,missense_variant,p.Arg151Leu,ENST00000253812,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA2,downstream_gene_variant,,ENST00000528330,;	T	ENSG00000254245	ENST00000253812	Transcript	missense_variant	452	452	151	R/L	cGa/cTa	rs267600447,COSM3393255,COSM3393254	.	.	1	PCDHGA3	HGNC	8701	protein_coding	YES	CCDS47290.1	ENSP00000253812	PCDG3_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI0000161C1A	.	deleterious_low_confidence(0.01)	benign(0.412)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF75,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	not_provided	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACCCGATTTC	.	4	ESCA
POU4F3	0	.	GRCh37	5	145719454	145719454	+	Missense_Mutation	SNP	T	T	C	rs766632966	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464T>C	p.Leu155Pro	p.L155P	ENST00000230732	2/2	16	13	3	18	18	0	POU4F3,missense_variant,p.Leu155Pro,ENST00000230732,;RBM27,downstream_gene_variant,,ENST00000506502,;CTC-359M8.1,intron_variant,,ENST00000515598,;	C	ENSG00000091010	ENST00000230732	Transcript	missense_variant	553	464	155	L/P	cTg/cCg	rs766632966	.	.	1	POU4F3	HGNC	9220	protein_coding	YES	CCDS4281.1	ENSP00000230732	PO4F3_HUMAN	.	UPI0000131D91	.	tolerated(0.24)	benign(0.032)	2/2	.	hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCACCTGCACC	.	2	ESCA
ZNF300	0	.	GRCh37	5	150276160	150276160	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.689A>C	p.Gln230Pro	p.Q230P	ENST00000446148	7/7	87	63	23	69	69	0	ZNF300,missense_variant,p.Gln178Pro,ENST00000418587,;ZNF300,missense_variant,p.Gln214Pro,ENST00000274599,;ZNF300,missense_variant,p.Gln214Pro,ENST00000394226,;ZNF300,missense_variant,p.Gln230Pro,ENST00000446148,;ZNF300,3_prime_UTR_variant,,ENST00000427179,;IRGM,intron_variant,,ENST00000520549,;	G	ENSG00000145908	ENST00000446148	Transcript	missense_variant	1117	689	230	Q/P	cAg/cCg	.	.	.	-1	ZNF300	HGNC	13091	protein_coding	YES	CCDS54940.1	ENSP00000397178	.	J3KQF6_HUMAN	UPI0001AE74AD	.	deleterious(0.02)	benign(0.175)	7/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF288	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTCTGATCA	.	5	ESCA
CDH9	0	.	GRCh37	5	26988213	26988213	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228G>T	p.Lys76Asn	p.K76N	ENST00000231021	2/12	48	44	4	61	61	0	CDH9,missense_variant,p.Lys76Asn,ENST00000511822,;CDH9,missense_variant,p.Lys76Asn,ENST00000231021,;CDH9,missense_variant,p.Lys76Asn,ENST00000513289,;CDH9,splice_region_variant,,ENST00000505045,;	A	ENSG00000113100	ENST00000231021	Transcript	missense_variant	401	228	76	K/N	aaG/aaT	COSM3410229	.	.	-1	CDH9	HGNC	1768	protein_coding	YES	CCDS3893.1	ENSP00000231021	CADH9_HUMAN	E7EPN0_HUMAN,D6RBT9_HUMAN	UPI000013C945	.	deleterious(0.02)	probably_damaging(0.998)	2/12	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF00028,Gene3D:2.60.40.60,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF99	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CTTACCTTGCC	.	2	ESCA
FGF10	0	.	GRCh37	5	44310622	44310622	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.336G>A	p.%3D	p.E112E	ENST00000264664	2/3	184	130	54	179	178	1	FGF10,synonymous_variant,p.%3D,ENST00000264664,;	T	ENSG00000070193	ENST00000264664	Transcript	synonymous_variant	451	336	112	E	gaG/gaA	.	.	.	-1	FGF10	HGNC	3666	protein_coding	YES	CCDS3950.1	ENSP00000264664	FGF10_HUMAN	Q8NFI9_HUMAN,D6RG33_HUMAN,C7FDY0_HUMAN	UPI000004065F	.	.	.	2/3	.	hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF21,Gene3D:2.80.10.50,Pfam_domain:PF00167,SMART_domains:SM00442,Superfamily_domains:SSF50353,Prints_domain:PR00263	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTATCTCCAG	.	5	ESCA
ISL1	0	.	GRCh37	5	50689371	50689371	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.977G>T	p.Ser326Ile	p.S326I	ENST00000230658	6/6	48	31	16	55	55	0	ISL1,missense_variant,p.Ser303Ile,ENST00000511384,;ISL1,missense_variant,p.Ser326Ile,ENST00000230658,;ISL1,downstream_gene_variant,,ENST00000505475,;	T	ENSG00000016082	ENST00000230658	Transcript	missense_variant	1562	977	326	S/I	aGt/aTt	.	.	.	1	ISL1	HGNC	6132	protein_coding	YES	CCDS43314.1	ENSP00000230658	ISL1_HUMAN	.	UPI0000023E3A	.	deleterious(0)	probably_damaging(0.966)	6/6	.	hmmpanther:PTHR24204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCAGTGAAG	.	5	ESCA
HMGCR	0	.	GRCh37	5	74639790	74639790	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277+1G>C	.	p.X93_splice	ENST00000287936	.	90	68	21	105	105	0	HMGCR,splice_donor_variant,,ENST00000507942,;HMGCR,splice_donor_variant,,ENST00000343975,;HMGCR,splice_donor_variant,,ENST00000287936,;HMGCR,splice_donor_variant,,ENST00000511206,;HMGCR,downstream_gene_variant,,ENST00000442032,;HMGCR,non_coding_transcript_exon_variant,,ENST00000509431,;	C	ENSG00000113161	ENST00000287936	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	HMGCR	HGNC	5006	protein_coding	YES	CCDS4027.1	ENSP00000287936	HMDH_HUMAN	D6RIW0_HUMAN,C9JKX7_HUMAN	UPI000012C9E2	.	.	.	.	3/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGGGTAATA	.	5	ESCA
SEC63	0	.	GRCh37	6	108232548	108232548	+	Splice_Site	SNP	A	A	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624+2T>G	.	p.X208_splice	ENST00000369002	.	62	45	17	81	81	0	SEC63,splice_donor_variant,,ENST00000429168,;SEC63,splice_donor_variant,,ENST00000369002,;SEC63,non_coding_transcript_exon_variant,,ENST00000484803,;SEC63,upstream_gene_variant,,ENST00000489455,;	C	ENSG00000025796	ENST00000369002	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	SEC63	HGNC	21082	protein_coding	YES	CCDS5061.1	ENSP00000357998	SEC63_HUMAN	A6PVC9_HUMAN	UPI000000DBBB	.	.	.	.	7/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTACCACA	.	5	ESCA
SYNE1	0	.	GRCh37	6	152443205	152443205	+	3'UTR	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*366G>A	.	.	ENST00000367255	146/146	19	14	5	26	26	0	SYNE1,3_prime_UTR_variant,,ENST00000356820,;SYNE1,3_prime_UTR_variant,,ENST00000539504,;SYNE1,3_prime_UTR_variant,,ENST00000423061,;SYNE1,3_prime_UTR_variant,,ENST00000367251,;SYNE1,3_prime_UTR_variant,,ENST00000367255,;SYNE1,3_prime_UTR_variant,,ENST00000341594,;SYNE1,3_prime_UTR_variant,,ENST00000367257,;SYNE1,3_prime_UTR_variant,,ENST00000448038,;SYNE1,3_prime_UTR_variant,,ENST00000265368,;ESR1,intron_variant,,ENST00000427531,;SYNE1,downstream_gene_variant,,ENST00000354674,;SYNE1,non_coding_transcript_exon_variant,,ENST00000460912,;SYNE1,non_coding_transcript_exon_variant,,ENST00000347037,;SYNE1,downstream_gene_variant,,ENST00000536990,;SYNE1,non_coding_transcript_exon_variant,,ENST00000478916,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,;	T	ENSG00000131018	ENST00000367255	Transcript	3_prime_UTR_variant	27362	.	.	.	.	.	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	.	146/146	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGCAGCAC	.	5	ESCA
QKI	0	.	GRCh37	6	163991873	163991873	+	3'UTR	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*131G>C	.	.	ENST00000361752	8/8	25	21	3	36	36	0	QKI,3_prime_UTR_variant,,ENST00000537883,;QKI,3_prime_UTR_variant,,ENST00000361752,;QKI,downstream_gene_variant,,ENST00000544361,;QKI,downstream_gene_variant,,ENST00000361195,;QKI,downstream_gene_variant,,ENST00000453779,;QKI,downstream_gene_variant,,ENST00000275262,;QKI,downstream_gene_variant,,ENST00000392127,;QKI,3_prime_UTR_variant,,ENST00000361758,;QKI,non_coding_transcript_exon_variant,,ENST00000541696,;QKI,downstream_gene_variant,,ENST00000545607,;	C	ENSG00000112531	ENST00000361752	Transcript	3_prime_UTR_variant	1708	.	.	.	.	.	.	.	1	QKI	HGNC	21100	protein_coding	YES	CCDS5285.1	ENSP00000355094	QKI_HUMAN	F5H8C8_HUMAN,F5H5U6_HUMAN,F5GYM3_HUMAN	UPI0000029EBD	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTTCGTCTTA	.	4	ESCA
RPS6KA2	0	.	GRCh37	6	166944794	166944794	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.248T>G	p.Leu83Arg	p.L83R	ENST00000503859	4/22	24	18	6	42	42	0	RPS6KA2,missense_variant,p.Leu100Arg,ENST00000506565,;RPS6KA2,missense_variant,p.Leu75Arg,ENST00000265678,;RPS6KA2,missense_variant,p.Leu59Arg,ENST00000507371,;RPS6KA2,missense_variant,p.Leu100Arg,ENST00000510118,;RPS6KA2,missense_variant,p.Leu83Arg,ENST00000503859,;RPS6KA2,5_prime_UTR_variant,,ENST00000512860,;RPS6KA2,5_prime_UTR_variant,,ENST00000366863,;RPS6KA2,5_prime_UTR_variant,,ENST00000405189,;RPS6KA2,5_prime_UTR_variant,,ENST00000481261,;RPS6KA2,5_prime_UTR_variant,,ENST00000507350,;RPS6KA2,5_prime_UTR_variant,,ENST00000511034,;Z98049.1,upstream_gene_variant,,ENST00000598601,;	C	ENSG00000071242	ENST00000503859	Transcript	missense_variant	629	248	83	L/R	cTg/cGg	.	.	.	-1	RPS6KA2	HGNC	10431	protein_coding	YES	CCDS34570.1	ENSP00000427015	KS6A2_HUMAN	D6RHW7_HUMAN,D6RD75_HUMAN,D6R910_HUMAN,B7Z3B5_HUMAN	UPI000020D48C	.	deleterious(0)	probably_damaging(0.997)	4/22	.	Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000606,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:3.30.200.20,PROSITE_patterns:PS00107,hmmpanther:PTHR24351,hmmpanther:PTHR24351:SF25,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCAGGAAC	.	5	ESCA
HIST1H2AH	0	.	GRCh37	6	27114921	27114921	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14G>T	p.Gly5Val	p.G5V	ENST00000377459	1/1	66	24	42	71	71	0	HIST1H2AH,missense_variant,p.Gly5Val,ENST00000377459,;HIST1H2BK,upstream_gene_variant,,ENST00000356950,;HIST1H2BK,upstream_gene_variant,,ENST00000396891,;MIR3143,upstream_gene_variant,,ENST00000584253,;	T	ENSG00000184825	ENST00000377459	Transcript	missense_variant	61	14	5	G/V	gGc/gTc	.	.	.	1	HIST1H2AH	HGNC	13671	protein_coding	YES	CCDS4622.1	ENSP00000366679	H2A1H_HUMAN	A3KPC7_HUMAN	UPI0000073C8A	.	deleterious_low_confidence(0)	unknown(0)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23430:SF24,hmmpanther:PTHR23430,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTGGCAAGC	.	5	ESCA
MAPK13	0	.	GRCh37	6	36107159	36107160	+	3'UTR	INS	-	-	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11dupT	.	.	ENST00000211287	12/12	16	2	14	17	17	0	MAPK13,3_prime_UTR_variant,,ENST00000373761,;MAPK13,3_prime_UTR_variant,,ENST00000211287,;MAPK13,3_prime_UTR_variant,,ENST00000373766,;MAPK13,downstream_gene_variant,,ENST00000373759,;Z95152.1,downstream_gene_variant,,ENST00000408816,;MAPK13,downstream_gene_variant,,ENST00000490334,;MAPK13,downstream_gene_variant,,ENST00000476951,;	T	ENSG00000156711	ENST00000211287	Transcript	3_prime_UTR_variant	1369-1370	.	.	.	.	.	.	.	1	MAPK13	HGNC	6875	protein_coding	YES	CCDS4818.1	ENSP00000211287	MK13_HUMAN	.	UPI000012F182	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTCATCTTGCA	.	2	ESCA
FRS3	0	.	GRCh37	6	41738548	41738548	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1288C>T	p.Pro430Ser	p.P430S	ENST00000373018	7/7	173	164	8	91	91	0	FRS3,missense_variant,p.Pro430Ser,ENST00000259748,;FRS3,missense_variant,p.Pro430Ser,ENST00000373018,;FRS3,downstream_gene_variant,,ENST00000422888,;FRS3,downstream_gene_variant,,ENST00000426290,;	A	ENSG00000137218	ENST00000373018	Transcript	missense_variant	1540	1288	430	P/S	Cct/Tct	.	.	.	-1	FRS3	HGNC	16970	protein_coding	YES	CCDS4860.1	ENSP00000362109	FRS3_HUMAN	A6PVU0_HUMAN	UPI0000073ACA	.	tolerated(0.84)	benign(0.001)	7/7	.	hmmpanther:PTHR21258:SF39,hmmpanther:PTHR21258	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTAGGGCGGT	.	2	ESCA
PGK2	0	.	GRCh37	6	49754995	49754995	+	5'UTR	SNP	C	C	T	rs773502373	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-95G>A	.	.	ENST00000304801	1/1	35	31	4	39	39	0	PGK2,5_prime_UTR_variant,,ENST00000304801,;	T	ENSG00000170950	ENST00000304801	Transcript	5_prime_UTR_variant	59	.	.	.	.	rs773502373	.	.	-1	PGK2	HGNC	8898	protein_coding	YES	CCDS4930.1	ENSP00000305995	PGK2_HUMAN	.	UPI0000001C72	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACGCCTTTGC	.	4	ESCA
RIMS1	0	.	GRCh37	6	72960111	72960111	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2320G>C	p.Asp774His	p.D774H	ENST00000521978	13/34	56	52	4	66	66	0	RIMS1,missense_variant,p.Asp774His,ENST00000491071,;RIMS1,missense_variant,p.Asp233His,ENST00000517827,;RIMS1,missense_variant,p.Asp167His,ENST00000453976,;RIMS1,missense_variant,p.Asp774His,ENST00000522291,;RIMS1,missense_variant,p.Asp774His,ENST00000520567,;RIMS1,missense_variant,p.Asp774His,ENST00000518273,;RIMS1,missense_variant,p.Asp774His,ENST00000517960,;RIMS1,missense_variant,p.Asp348His,ENST00000517433,;RIMS1,missense_variant,p.Asp248His,ENST00000523963,;RIMS1,missense_variant,p.Asp167His,ENST00000425662,;RIMS1,missense_variant,p.Asp774His,ENST00000264839,;RIMS1,missense_variant,p.Asp248His,ENST00000401910,;RIMS1,missense_variant,p.Asp774His,ENST00000348717,;RIMS1,missense_variant,p.Asp774His,ENST00000521978,;RIMS1,upstream_gene_variant,,ENST00000538414,;RIMS1,upstream_gene_variant,,ENST00000522211,;RIMS1,upstream_gene_variant,,ENST00000370420,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,;RIMS1,non_coding_transcript_exon_variant,,ENST00000524197,;	C	ENSG00000079841	ENST00000521978	Transcript	missense_variant	2320	2320	774	D/H	Gat/Cat	.	.	.	1	RIMS1	HGNC	17282	protein_coding	YES	CCDS47449.1	ENSP00000428417	RIMS1_HUMAN	.	UPI00001908FB	.	deleterious(0)	probably_damaging(0.994)	13/34	.	PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF19,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTAGATGGA	.	2	ESCA
AKIRIN2	0	.	GRCh37	6	88391386	88391386	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331T>G	p.Ser111Ala	p.S111A	ENST00000257787	2/5	98	71	27	90	90	0	AKIRIN2,missense_variant,p.Ser111Ala,ENST00000257787,;	C	ENSG00000135334	ENST00000257787	Transcript	missense_variant	856	331	111	S/A	Tct/Gct	.	.	.	-1	AKIRIN2	HGNC	21407	protein_coding	YES	CCDS5013.1	ENSP00000257787	AKIR2_HUMAN	Q9NW35_HUMAN	UPI000006D634	.	tolerated(0.17)	benign(0.052)	2/5	.	hmmpanther:PTHR13293,hmmpanther:PTHR13293:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAGAAGTAC	.	5	ESCA
MDN1	0	.	GRCh37	6	90463228	90463228	+	Intron	SNP	T	T	A	rs751283129	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3075+3A>T	.	.	ENST00000369393	.	27	17	10	52	52	0	MDN1,splice_region_variant,,ENST00000369393,;MDN1,splice_region_variant,,ENST00000428876,;MDN1,splice_region_variant,,ENST00000439638,;	A	ENSG00000112159	ENST00000369393	Transcript	splice_region_variant	.	.	.	.	.	rs751283129	.	.	-1	MDN1	HGNC	18302	protein_coding	YES	CCDS5024.1	ENSP00000358400	MDN1_HUMAN	M0QXR3_HUMAN	UPI000013C4B8	.	.	.	.	22/101	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACATACCTG	.	4	ESCA
MOSPD3	0	.	GRCh37	7	100210514	100210514	+	Missense_Mutation	SNP	G	G	C	rs753824294	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100G>C	p.Val34Leu	p.V34L	ENST00000393950	1/5	58	48	9	62	62	0	MOSPD3,missense_variant,p.Val34Leu,ENST00000493970,;MOSPD3,missense_variant,p.Val34Leu,ENST00000424091,;MOSPD3,missense_variant,p.Val34Leu,ENST00000379527,;MOSPD3,missense_variant,p.Val34Leu,ENST00000223054,;MOSPD3,missense_variant,p.Val34Leu,ENST00000393950,;PCOLCE,downstream_gene_variant,,ENST00000223061,;MOSPD3,missense_variant,p.Val34Leu,ENST00000462372,;MOSPD3,non_coding_transcript_exon_variant,,ENST00000490309,;MOSPD3,non_coding_transcript_exon_variant,,ENST00000497456,;PCOLCE,downstream_gene_variant,,ENST00000472348,;	C	ENSG00000106330	ENST00000393950	Transcript	missense_variant	382	100	34	V/L	Gtc/Ctc	rs753824294	.	.	1	MOSPD3	HGNC	25078	protein_coding	YES	CCDS5701.1	ENSP00000377522	MSPD3_HUMAN	F8WF07_HUMAN,C9J3M4_HUMAN	UPI000004A079	.	deleterious(0.01)	probably_damaging(0.996)	1/5	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF49354,Gene3D:2.60.40.360,Pfam_domain:PF00635,PROSITE_profiles:PS50202	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCGGTCCTG	byFrequency	5	ESCA
NAT16	0	.	GRCh37	7	100817776	100817776	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312+1G>C	.	p.X104_splice	ENST00000300303	.	122	116	6	115	115	0	NAT16,splice_donor_variant,,ENST00000444446,;NAT16,splice_donor_variant,,ENST00000455377,;NAT16,splice_donor_variant,,ENST00000300303,;NAT16,missense_variant,p.Val105Leu,ENST00000443096,;	G	ENSG00000167011	ENST00000300303	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	NAT16	HGNC	22030	protein_coding	YES	CCDS5713.1	ENSP00000300303	NAT16_HUMAN	C9JB11_HUMAN	UPI000013E649	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCACCACGC	.	2	ESCA
EFCAB10	0	.	GRCh37	7	105207488	105207488	+	Intron	SNP	T	T	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383+426A>G	.	.	ENST00000485614	.	31	21	10	27	27	0	EFCAB10,3_prime_UTR_variant,,ENST00000486180,;EFCAB10,intron_variant,,ENST00000480514,;EFCAB10,intron_variant,,ENST00000485614,;RINT1,intron_variant,,ENST00000257700,;EFCAB10,downstream_gene_variant,,ENST00000460135,;RP11-251G23.5,upstream_gene_variant,,ENST00000609827,;EFCAB10,intron_variant,,ENST00000469099,;EFCAB10,downstream_gene_variant,,ENST00000490493,;RINT1,intron_variant,,ENST00000497979,;	C	ENSG00000185055	ENST00000485614	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	EFCAB10	HGNC	34531	protein_coding	YES	.	ENSP00000417841	.	J3KR52_HUMAN	UPI000020F8A0	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTGTTTAGG	.	2	ESCA
EFCAB10	0	.	GRCh37	7	105209877	105209877	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.248T>C	p.Ile83Thr	p.I83T	ENST00000485614	2/5	72	45	27	67	67	0	EFCAB10,missense_variant,p.Ile83Thr,ENST00000480514,;EFCAB10,missense_variant,p.Ile83Thr,ENST00000485614,;EFCAB10,missense_variant,p.Ile83Thr,ENST00000486180,;EFCAB10,intron_variant,,ENST00000460135,;RINT1,downstream_gene_variant,,ENST00000257700,;RP11-251G23.5,upstream_gene_variant,,ENST00000609827,;EFCAB10,non_coding_transcript_exon_variant,,ENST00000469099,;EFCAB10,non_coding_transcript_exon_variant,,ENST00000490493,;RINT1,downstream_gene_variant,,ENST00000497979,;	G	ENSG00000185055	ENST00000485614	Transcript	missense_variant	281	248	83	I/T	aTa/aCa	.	.	.	-1	EFCAB10	HGNC	34531	protein_coding	YES	.	ENSP00000417841	.	J3KR52_HUMAN	UPI000020F8A0	.	deleterious(0)	probably_damaging(0.988)	2/5	.	PROSITE_profiles:PS50222,hmmpanther:PTHR21847:SF3,hmmpanther:PTHR21847,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATATGGTG	.	5	ESCA
SLC13A1	0	.	GRCh37	7	122774582	122774582	+	Missense_Mutation	SNP	G	G	T	rs140244991	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814C>A	p.Arg272Ser	p.R272S	ENST00000194130	8/15	50	35	15	62	62	0	SLC13A1,missense_variant,p.Arg272Ser,ENST00000194130,;SLC13A1,splice_region_variant,,ENST00000539873,;SLC13A1,splice_region_variant,,ENST00000439260,;SLC13A1,splice_region_variant,,ENST00000427975,;	T	ENSG00000081800	ENST00000194130	Transcript	missense_variant	854	814	272	R/S	Cgc/Agc	rs140244991	.	.	-1	SLC13A1	HGNC	10916	protein_coding	YES	CCDS5786.1	ENSP00000194130	S13A1_HUMAN	Q75MH3_HUMAN,Q75LT0_HUMAN,A4D0X1_HUMAN	UPI0000049F9D	.	tolerated(0.09)	probably_damaging(0.979)	8/15	.	hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF65,Pfam_domain:PF00939	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGCGTCTGT	byFrequency|byCluster	5	ESCA
SND1	0	.	GRCh37	7	127637865	127637865	+	Intron	DEL	C	C	-	rs767457793	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1779+6756delC	.	.	ENST00000354725	.	95	65	30	40	40	0	SND1,intron_variant,,ENST00000354725,;SND1,intron_variant,,ENST00000486037,;SND1,non_coding_transcript_exon_variant,,ENST00000467238,;SND1,intron_variant,,ENST00000484767,;SND1,intron_variant,,ENST00000470723,;	-	ENSG00000197157	ENST00000354725	Transcript	intron_variant	.	.	.	.	.	rs767457793	.	.	1	SND1	HGNC	30646	protein_coding	YES	CCDS34747.1	ENSP00000346762	SND1_HUMAN	B2R5U1_HUMAN	UPI00000727E5	.	.	.	.	16/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GACTTACACTTT	byFrequency	3	ESCA
SLC13A4	0	.	GRCh37	7	135366322	135366322	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870G>T	p.Asp624Tyr	p.D624Y	ENST00000354042	16/16	67	46	21	41	41	0	SLC13A4,missense_variant,p.Asp624Tyr,ENST00000354042,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000491630,;C7orf73,intron_variant,,ENST00000509448,;C7orf73,intron_variant,,ENST00000422968,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000471405,;	A	ENSG00000164707	ENST00000354042	Transcript	missense_variant	2560	1870	624	D/Y	Gat/Tat	.	.	.	-1	SLC13A4	HGNC	15827	protein_coding	YES	CCDS5840.1	ENSP00000297282	S13A4_HUMAN	.	UPI00000343D9	.	deleterious(0.01)	benign(0.11)	16/16	.	hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGATCAGTGA	.	5	ESCA
SNX13	0	.	GRCh37	7	17832482	17832482	+	3'UTR	SNP	T	T	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1187A>C	.	.	ENST00000428135	26/26	287	179	108	265	265	0	SNX13,3_prime_UTR_variant,,ENST00000428135,;SNX13,3_prime_UTR_variant,,ENST00000409389,;SNX13,downstream_gene_variant,,ENST00000496855,;SNX13,downstream_gene_variant,,ENST00000409076,;	G	ENSG00000071189	ENST00000428135	Transcript	3_prime_UTR_variant	4260	.	.	.	.	.	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATTTTATT	.	5	ESCA
PLEKHA8	0	.	GRCh37	7	30118228	30118228	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1385C>T	p.Ser462Phe	p.S462F	ENST00000449726	14/14	73	52	20	56	56	0	PLEKHA8,missense_variant,p.Ser488Phe,ENST00000440706,;PLEKHA8,missense_variant,p.Ser462Phe,ENST00000449726,;PLEKHA8,intron_variant,,ENST00000258679,;PLEKHA8,intron_variant,,ENST00000396257,;PLEKHA8,intron_variant,,ENST00000396259,;AC007285.7,upstream_gene_variant,,ENST00000433088,;	T	ENSG00000106086	ENST00000449726	Transcript	missense_variant	1735	1385	462	S/F	tCc/tTc	.	.	.	1	PLEKHA8	HGNC	30037	protein_coding	YES	CCDS56473.1	ENSP00000397947	PKHA8_HUMAN	.	UPI000020ECE0	.	deleterious(0.01)	probably_damaging(0.958)	14/14	.	hmmpanther:PTHR10219,hmmpanther:PTHR10219:SF16,Pfam_domain:PF08718,Gene3D:2i3fA00,Superfamily_domains:0043785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATCCTATG	.	5	ESCA
EEPD1	0	.	GRCh37	7	36339167	36339167	+	3'UTR	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*352C>A	.	.	ENST00000242108	8/8	20	14	5	9	9	0	EEPD1,3_prime_UTR_variant,,ENST00000242108,;EEPD1,3_prime_UTR_variant,,ENST00000444777,;EEPD1,3_prime_UTR_variant,,ENST00000534978,;EEPD1,downstream_gene_variant,,ENST00000468591,;EEPD1,downstream_gene_variant,,ENST00000487069,;	A	ENSG00000122547	ENST00000242108	Transcript	3_prime_UTR_variant	2780	.	.	.	.	.	.	.	1	EEPD1	HGNC	22223	protein_coding	YES	CCDS34619.1	ENSP00000242108	EEPD1_HUMAN	.	UPI000020ED9D	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	TCAGGCTGCGG	.	2	ESCA
POLR2J4	0	.	GRCh37	7	44027341	44027341	+	RNA	SNP	C	C	T	rs745910875	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.601G>A	.	.	ENST00000422304	5/9	98	68	30	97	97	0	POLR2J4,non_coding_transcript_exon_variant,,ENST00000422304,;POLR2J4,non_coding_transcript_exon_variant,,ENST00000427076,;RP5-1165K10.2,intron_variant,,ENST00000454572,;AC004951.5,non_coding_transcript_exon_variant,,ENST00000420754,;	T	ENSG00000214783	ENST00000422304	Transcript	non_coding_transcript_exon_variant	601	.	.	.	.	rs745910875	.	.	-1	POLR2J4	HGNC	28195	processed_transcript	YES	.	.	.	.	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTATCATTGC	byFrequency	5	ESCA
GTF2IRD1	0	.	GRCh37	7	73960105	73960105	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1794G>A	p.%3D	p.R598R	ENST00000455841	16/27	75	69	6	38	38	0	GTF2IRD1,missense_variant,p.Glu6Lys,ENST00000470715,;GTF2IRD1,synonymous_variant,p.%3D,ENST00000476977,;GTF2IRD1,synonymous_variant,p.%3D,ENST00000455841,;GTF2IRD1,synonymous_variant,p.%3D,ENST00000265755,;GTF2IRD1,synonymous_variant,p.%3D,ENST00000424337,;GTF2IRD1,non_coding_transcript_exon_variant,,ENST00000489094,;	A	ENSG00000006704	ENST00000455841	Transcript	synonymous_variant	2007	1794	598	R	cgG/cgA	.	.	.	1	GTF2IRD1	HGNC	4661	protein_coding	YES	CCDS56492.1	ENSP00000397566	GT2D1_HUMAN	.	UPI00003BF92B	.	.	.	16/27	.	Superfamily_domains:0048894,PIRSF_domain:PIRSF016441,Pfam_domain:PF02946,Gene3D:1q60A00,hmmpanther:PTHR11697:SF84,hmmpanther:PTHR11697,PROSITE_profiles:PS51139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CTGCGGAAGCA	.	2	ESCA
PCLO	0	.	GRCh37	7	82450626	82450626	+	Intron	SNP	T	T	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14791+1185A>C	.	.	ENST00000333891	.	25	22	3	21	20	1	PCLO,3_prime_UTR_variant,,ENST00000423517,;PCLO,intron_variant,,ENST00000333891,;PCLO,intron_variant,,ENST00000432078,;PCLO,downstream_gene_variant,,ENST00000426442,;	G	ENSG00000186472	ENST00000333891	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	.	.	20/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGGTGAAAT	.	2	ESCA
ATAD2	0	.	GRCh37	8	124359623	124359623	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1921T>C	p.Ser641Pro	p.S641P	ENST00000287394	16/28	28	12	16	25	25	0	ATAD2,missense_variant,p.Ser641Pro,ENST00000287394,;ATAD2,5_prime_UTR_variant,,ENST00000521903,;RNU6-875P,downstream_gene_variant,,ENST00000516488,;MIR548D1,upstream_gene_variant,,ENST00000384971,;ATAD2,3_prime_UTR_variant,,ENST00000517666,;ATAD2,3_prime_UTR_variant,,ENST00000519124,;ATAD2,non_coding_transcript_exon_variant,,ENST00000521496,;DUTP2,upstream_gene_variant,,ENST00000519164,;	G	ENSG00000156802	ENST00000287394	Transcript	missense_variant	2029	1921	641	S/P	Tca/Cca	.	.	.	-1	ATAD2	HGNC	30123	protein_coding	YES	CCDS6343.1	ENSP00000287394	ATAD2_HUMAN	.	UPI0000052A8C	.	deleterious(0)	possibly_damaging(0.84)	16/28	.	hmmpanther:PTHR23069,hmmpanther:PTHR23069:SF1,Gene3D:1.10.8.60,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTGATTTAA	.	5	ESCA
FAM135B	0	.	GRCh37	8	139180271	139180271	+	Silent	SNP	C	C	A	rs201150785	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125G>T	p.%3D	p.L375L	ENST00000395297	12/20	24	20	4	30	30	0	FAM135B,synonymous_variant,p.%3D,ENST00000395297,;FAM135B,synonymous_variant,p.%3D,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;	A	ENSG00000147724	ENST00000395297	Transcript	synonymous_variant	1296	1125	375	L	ctG/ctT	rs201150785	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	.	.	12/20	.	hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482	.	.	.	.	.	.	.	G:0	G:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AGGGACAGCTG	byCluster	2	ESCA
XPO7	0	.	GRCh37	8	21829470	21829470	+	Intron	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.492+18C>A	.	.	ENST00000252512	.	98	71	27	129	129	0	XPO7,missense_variant,p.Phe170Leu,ENST00000434536,;XPO7,missense_variant,p.Phe175Leu,ENST00000521303,;XPO7,intron_variant,,ENST00000252512,;XPO7,intron_variant,,ENST00000433566,;XPO7,intron_variant,,ENST00000518017,;XPO7,downstream_gene_variant,,ENST00000520754,;XPO7,downstream_gene_variant,,ENST00000519769,;	A	ENSG00000130227	ENST00000252512	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	XPO7	HGNC	14108	protein_coding	YES	CCDS47818.1	ENSP00000252512	XPO7_HUMAN	E5RIW1_HUMAN,B4DSP8_HUMAN	UPI0000134559	.	.	.	.	5/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCCTCAT	.	5	ESCA
CTD-2168K21.2	0	.	GRCh37	8	24809971	24809971	+	5'Flank	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000607735	.	80	59	21	90	90	0	CTD-2168K21.2,upstream_gene_variant,,ENST00000607735,;NEFL,non_coding_transcript_exon_variant,,ENST00000221169,;	G	ENSG00000272157	ENST00000607735	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4164	1	CTD-2168K21.2	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGACTATTT	.	5	ESCA
PLAG1	0	.	GRCh37	8	57077272	57077272	+	3'UTR	SNP	A	A	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1530T>G	.	.	ENST00000316981	5/5	142	80	61	171	171	0	PLAG1,3_prime_UTR_variant,,ENST00000316981,;PLAG1,downstream_gene_variant,,ENST00000423799,;PLAG1,downstream_gene_variant,,ENST00000429357,;PLAG1,downstream_gene_variant,,ENST00000522009,;	C	ENSG00000181690	ENST00000316981	Transcript	3_prime_UTR_variant	3513	.	.	.	.	.	.	.	-1	PLAG1	HGNC	9045	protein_coding	YES	CCDS6165.1	ENSP00000325546	PLAG1_HUMAN	A7IT80_HUMAN,A7IT79_HUMAN	UPI000013FF2F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTAATTAG	.	5	ESCA
HNF4G	0	.	GRCh37	8	76472647	76472647	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1162G>A	p.Gly388Arg	p.G388R	ENST00000396423	9/10	35	24	11	47	47	0	HNF4G,missense_variant,p.Gly388Arg,ENST00000396423,;HNF4G,missense_variant,p.Gly351Arg,ENST00000354370,;	A	ENSG00000164749	ENST00000396423	Transcript	missense_variant	1286	1162	388	G/R	Gga/Aga	.	.	.	1	HNF4G	HGNC	5026	protein_coding	YES	CCDS6220.2	ENSP00000379701	HNF4G_HUMAN	F1D8Q4_HUMAN	UPI0000D47E07	.	tolerated(0.16)	possibly_damaging(0.729)	9/10	.	hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTGGACAA	.	5	ESCA
TOMM5	0	.	GRCh37	9	37592617	37592617	+	5'Flank	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000544379	.	12	7	5	12	12	0	TOMM5,5_prime_UTR_variant,,ENST00000321301,;TOMM5,upstream_gene_variant,,ENST00000377773,;FBXO10,upstream_gene_variant,,ENST00000541829,;TOMM5,upstream_gene_variant,,ENST00000401811,;TOMM5,upstream_gene_variant,,ENST00000544379,;RP11-613M10.8,upstream_gene_variant,,ENST00000544475,;RP11-613M10.8,upstream_gene_variant,,ENST00000541804,;RP11-613M10.9,intron_variant,,ENST00000540557,;TOMM5,upstream_gene_variant,,ENST00000540941,;RP11-613M10.8,upstream_gene_variant,,ENST00000537239,;	A	ENSG00000175768	ENST00000544379	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	24	-1	TOMM5	HGNC	31369	protein_coding	YES	CCDS47968.1	ENSP00000438204	TOM5_HUMAN	H0YFG9_HUMAN	UPI000021141F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACTTCCTGTT	.	2	ESCA
PTCH1	0	.	GRCh37	9	98224234	98224235	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2606dupT	p.Met869IlefsTer27	p.M869Ifs*27	ENST00000331920	16/24	163	99	64	91	91	0	PTCH1,frameshift_variant,p.Met868IlefsTer27,ENST00000375274,;PTCH1,frameshift_variant,p.Met869IlefsTer27,ENST00000331920,;PTCH1,frameshift_variant,p.Met803IlefsTer27,ENST00000430669,;PTCH1,frameshift_variant,p.Met718IlefsTer27,ENST00000418258,;PTCH1,frameshift_variant,p.Met718IlefsTer27,ENST00000429896,;PTCH1,frameshift_variant,p.Met718IlefsTer27,ENST00000421141,;PTCH1,frameshift_variant,p.Met803IlefsTer27,ENST00000437951,;PTCH1,upstream_gene_variant,,ENST00000547615,;PTCH1,3_prime_UTR_variant,,ENST00000375290,;	A	ENSG00000185920	ENST00000331920	Transcript	frameshift_variant	2906-2907	2606-2607	869	M/IX	atg/atTg	.	.	.	-1	PTCH1	HGNC	9585	protein_coding	YES	CCDS6714.1	ENSP00000332353	PTC1_HUMAN	Q6TKQ0_HUMAN,F8VXL8_HUMAN,F8VQS6_HUMAN	UPI00001AFF9C	.	.	.	16/24	.	TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796:SF61,hmmpanther:PTHR10796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTGGCATGAT	.	3	ESCA
ARHGAP36	0	.	GRCh37	X	130217914	130217914	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526C>G	p.Pro176Ala	p.P176A	ENST00000276211	4/12	47	12	34	58	58	0	ARHGAP36,missense_variant,p.Pro176Ala,ENST00000276211,;ARHGAP36,missense_variant,p.Pro128Ala,ENST00000423277,;ARHGAP36,missense_variant,p.Pro164Ala,ENST00000370922,;ARHGAP36,missense_variant,p.Pro145Ala,ENST00000412432,;ARHGAP36,missense_variant,p.Pro40Ala,ENST00000370921,;	G	ENSG00000147256	ENST00000276211	Transcript	missense_variant	871	526	176	P/A	Ccc/Gcc	.	.	.	1	ARHGAP36	HGNC	26388	protein_coding	YES	CCDS14628.1	ENSP00000276211	RHG36_HUMAN	.	UPI0000041347	.	tolerated(0.08)	probably_damaging(0.984)	4/12	.	hmmpanther:PTHR12635:SF5,hmmpanther:PTHR12635	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTGCCCCGG	.	5	ESCA
MAGEC1	0	.	GRCh37	X	140994088	140994088	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.898C>A	p.Gln300Lys	p.Q300K	ENST00000285879	4/4	122	53	69	117	117	0	MAGEC1,missense_variant,p.Gln300Lys,ENST00000285879,;MAGEC1,intron_variant,,ENST00000406005,;	A	ENSG00000155495	ENST00000285879	Transcript	missense_variant	1184	898	300	Q/K	Cag/Aag	COSM3558663	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	deleterious_low_confidence(0)	unknown(0)	4/4	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P302P|c.906T>A|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCCCAGTCT	.	5	ESCA
SLITRK4	0	.	GRCh37	X	142718626	142718626	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.299G>T	p.Gly100Val	p.G100V	ENST00000381779	2/2	41	23	17	38	38	0	SLITRK4,missense_variant,p.Gly100Val,ENST00000381779,;SLITRK4,missense_variant,p.Gly100Val,ENST00000338017,;SLITRK4,missense_variant,p.Gly100Val,ENST00000356928,;	A	ENSG00000179542	ENST00000381779	Transcript	missense_variant	525	299	100	G/V	gGa/gTa	.	.	.	-1	SLITRK4	HGNC	23502	protein_coding	YES	CCDS14679.1	ENSP00000371198	SLIK4_HUMAN	.	UPI000004E650	.	tolerated(0.12)	probably_damaging(0.999)	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCCTCA	.	5	ESCA
SLITRK2	0	.	GRCh37	X	144905265	144905265	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1322C>G	p.Ser441Cys	p.S441C	ENST00000370490	1/1	39	26	13	39	39	0	SLITRK2,missense_variant,p.Ser441Cys,ENST00000370490,;SLITRK2,missense_variant,p.Ser441Cys,ENST00000434188,;SLITRK2,missense_variant,p.Ser441Cys,ENST00000428560,;SLITRK2,missense_variant,p.Ser441Cys,ENST00000413937,;SLITRK2,missense_variant,p.Ser441Cys,ENST00000447897,;SLITRK2,missense_variant,p.Ser441Cys,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,;	G	ENSG00000185985	ENST00000370490	Transcript	missense_variant	5577	1322	441	S/C	tCt/tGt	.	.	.	1	SLITRK2	HGNC	13449	protein_coding	YES	CCDS14680.1	ENSP00000359521	SLIK2_HUMAN	B3KTY4_HUMAN	UPI000004E64B	.	deleterious(0.03)	probably_damaging(0.95)	1/1	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF36,hmmpanther:PTHR24373,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTCTATGT	.	5	ESCA
PORCN	0	.	GRCh37	X	48379165	48379165	+	3'UTR	SNP	G	G	C	novel	.	TCGA-V5-A7RC-01B-11D-A403-09	TCGA-V5-A7RC-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*301G>C	.	.	ENST00000326194	14/14	132	126	6	61	61	0	PORCN,3_prime_UTR_variant,,ENST00000355961,;PORCN,3_prime_UTR_variant,,ENST00000355092,;PORCN,3_prime_UTR_variant,,ENST00000359882,;PORCN,3_prime_UTR_variant,,ENST00000367574,;PORCN,3_prime_UTR_variant,,ENST00000326194,;PORCN,downstream_gene_variant,,ENST00000361988,;EBP,upstream_gene_variant,,ENST00000446158,;EBP,upstream_gene_variant,,ENST00000414061,;EBP,upstream_gene_variant,,ENST00000495186,;PORCN,downstream_gene_variant,,ENST00000537758,;EBP,upstream_gene_variant,,ENST00000276096,;EBP,upstream_gene_variant,,ENST00000498425,;PORCN,3_prime_UTR_variant,,ENST00000485288,;PORCN,3_prime_UTR_variant,,ENST00000472520,;PORCN,non_coding_transcript_exon_variant,,ENST00000491243,;PORCN,downstream_gene_variant,,ENST00000459953,;	C	ENSG00000102312	ENST00000326194	Transcript	3_prime_UTR_variant	1730	.	.	.	.	.	.	.	1	PORCN	HGNC	17652	protein_coding	YES	CCDS14299.1	ENSP00000322304	PORCN_HUMAN	C9JWI5_HUMAN	UPI000014187F	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATTTGTTATT	.	2	ESCA
FRMD4A	0	.	GRCh37	10	13699134	13699142	+	In_Frame_Del	DEL	CGCCCCCCG	CGCCCCCCG	-	rs556055601	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CGCCCCCCG	CGCCCCCCG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2447_2455delCGGGGGGCG	p.Ala816_Gly818del	p.A816_G818del	ENST00000357447	22/25	30	19	11	21	21	0	FRMD4A,inframe_deletion,p.Ala816_Gly818del,ENST00000357447,;FRMD4A,inframe_deletion,p.Ala801_Gly803del,ENST00000358621,;FRMD4A,inframe_deletion,p.Ala816_Gly818del,ENST00000378503,;RP11-295P9.3,downstream_gene_variant,,ENST00000601460,;RP11-295P9.3,intron_variant,,ENST00000593351,;RP11-295P9.3,downstream_gene_variant,,ENST00000599639,;FRMD4A,upstream_gene_variant,,ENST00000475325,;RP11-295P9.3,downstream_gene_variant,,ENST00000600511,;RP11-295P9.3,downstream_gene_variant,,ENST00000600249,;RP11-295P9.3,downstream_gene_variant,,ENST00000593358,;FRMD4A,upstream_gene_variant,,ENST00000495956,;RP11-295P9.3,downstream_gene_variant,,ENST00000601758,;RP11-295P9.3,downstream_gene_variant,,ENST00000596499,;RP11-295P9.3,downstream_gene_variant,,ENST00000596235,;RP11-295P9.3,downstream_gene_variant,,ENST00000430721,;RP11-295P9.3,downstream_gene_variant,,ENST00000594575,;RP11-295P9.3,downstream_gene_variant,,ENST00000419851,;RP11-295P9.3,downstream_gene_variant,,ENST00000597920,;RP11-295P9.3,downstream_gene_variant,,ENST00000598625,;	-	ENSG00000151474	ENST00000357447	Transcript	inframe_deletion	2816-2824	2447-2455	816-819	AGGG/G	gCGGGGGGCGgt/ggt	rs556055601	.	.	-1	FRMD4A	HGNC	25491	protein_coding	YES	CCDS7101.1	ENSP00000350032	FRM4A_HUMAN	F8WAN4_HUMAN	UPI0000366665	.	.	.	22/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23281:SF12,hmmpanther:PTHR23281	-:0.0272	-:0.0666	-:0.0187	.	-:0	-:0.0179	-:0.0174	-:0.0831	-:0.0457	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACACACCGCCCCCCGCGCCC	byFrequency|byCluster|by1000G	2	ESCA
ZNF33A	0	.	GRCh37	10	38345624	38345624	+	3'UTR	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*136C>T	.	.	ENST00000374618	5/5	10	4	6	12	12	0	ZNF33A,3_prime_UTR_variant,,ENST00000432900,;ZNF33A,3_prime_UTR_variant,,ENST00000458705,;ZNF33A,3_prime_UTR_variant,,ENST00000374618,;ZNF33A,intron_variant,,ENST00000469037,;ZNF33A,downstream_gene_variant,,ENST00000307441,;ZNF33A,downstream_gene_variant,,ENST00000478556,;	T	ENSG00000189180	ENST00000374618	Transcript	3_prime_UTR_variant	2750	.	.	.	.	.	.	.	1	ZNF33A	HGNC	13096	protein_coding	YES	CCDS44372.1	ENSP00000363747	ZN33A_HUMAN	.	UPI0000161788	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AACACCTTACA	.	3	ESCA
ZNF33B	0	.	GRCh37	10	43087866	43087866	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*195A>G	.	.	ENST00000359467	5/5	21	8	13	11	11	0	ZNF33B,3_prime_UTR_variant,,ENST00000359467,;ZNF33B,intron_variant,,ENST00000486187,;ZNF33B,intron_variant,,ENST00000465206,;ZNF33B,intron_variant,,ENST00000462075,;	C	ENSG00000196693	ENST00000359467	Transcript	3_prime_UTR_variant	2647	.	.	.	.	.	.	.	-1	ZNF33B	HGNC	13097	protein_coding	YES	CCDS7198.1	ENSP00000352444	ZN33B_HUMAN	.	UPI000007257B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATATCACTT	.	5	ESCA
MYOF	0	.	GRCh37	10	95070368	95070368	+	Missense_Mutation	SNP	G	G	T	rs186335544	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5922C>A	p.Asn1974Lys	p.N1974K	ENST00000359263	52/54	114	62	51	91	91	0	MYOF,missense_variant,p.Asn1964Lys,ENST00000371502,;MYOF,missense_variant,p.Asn1961Lys,ENST00000358334,;MYOF,missense_variant,p.Asn1974Lys,ENST00000371501,;MYOF,missense_variant,p.Asn1974Lys,ENST00000359263,;MYOF,3_prime_UTR_variant,,ENST00000463743,;	T	ENSG00000138119	ENST00000359263	Transcript	missense_variant	5922	5922	1974	N/K	aaC/aaA	rs186335544	.	.	-1	MYOF	HGNC	3656	protein_coding	YES	CCDS41551.1	ENSP00000352208	MYOF_HUMAN	.	UPI000012FBA1	.	deleterious(0.04)	benign(0.072)	52/54	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF38	A:0.0004	A:0	A:0	.	A:0.002	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCGTTGAG	byFrequency|by1000G	5	ESCA
TMEM133	0	.	GRCh37	11	100864384	100864384	+	3'UTR	SNP	C	C	T	rs182905475	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*955C>T	.	.	ENST00000303130	1/1	60	40	19	34	34	0	TMEM133,3_prime_UTR_variant,,ENST00000303130,;ARHGAP42,downstream_gene_variant,,ENST00000524892,;ARHGAP42,downstream_gene_variant,,ENST00000298815,;ARHGAP42,downstream_gene_variant,,ENST00000529535,;	T	ENSG00000170647	ENST00000303130	Transcript	3_prime_UTR_variant	1574	.	.	.	.	rs182905475	.	.	1	TMEM133	HGNC	24033	protein_coding	YES	CCDS8309.1	ENSP00000303999	TM133_HUMAN	.	UPI0000070A3A	.	.	.	1/1	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTCGGATG	by1000G	5	ESCA
DYNC2H1	0	.	GRCh37	11	102988516	102988516	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.923G>A	p.Arg308His	p.R308H	ENST00000398093	6/90	115	75	40	83	83	0	DYNC2H1,missense_variant,p.Arg308His,ENST00000398093,;DYNC2H1,missense_variant,p.Arg308His,ENST00000334267,;DYNC2H1,missense_variant,p.Arg308His,ENST00000375735,;	A	ENSG00000187240	ENST00000398093	Transcript	missense_variant	923	923	308	R/H	cGc/cAc	.	.	.	1	DYNC2H1	HGNC	2962	protein_coding	YES	CCDS44717.1	ENSP00000381167	DYHC2_HUMAN	.	UPI0000481AC7	.	.	benign(0.002)	6/90	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF34,Pfam_domain:PF08385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCGCTATG	.	5	ESCA
C11orf1	0	.	GRCh37	11	111753212	111753212	+	Silent	SNP	C	C	A	rs782010241	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166C>A	p.%3D	p.R56R	ENST00000260276	2/4	54	42	11	54	54	0	C11orf1,synonymous_variant,p.%3D,ENST00000529270,;C11orf1,synonymous_variant,p.%3D,ENST00000260276,;C11orf1,synonymous_variant,p.%3D,ENST00000530799,;C11orf1,synonymous_variant,p.%3D,ENST00000530214,;C11orf1,synonymous_variant,p.%3D,ENST00000528125,;FDXACB1,upstream_gene_variant,,ENST00000528274,;FDXACB1,upstream_gene_variant,,ENST00000260257,;FDXACB1,upstream_gene_variant,,ENST00000542429,;ALG9,upstream_gene_variant,,ENST00000524880,;FDXACB1,upstream_gene_variant,,ENST00000531487,;	A	ENSG00000137720	ENST00000260276	Transcript	synonymous_variant	503	166	56	R	Cga/Aga	rs782010241,COSM1351249	.	.	1	C11orf1	HGNC	1163	protein_coding	YES	CCDS8350.1	ENSP00000260276	CK001_HUMAN	E9PLN1_HUMAN	UPI000004C5AE	.	.	.	2/4	.	Pfam_domain:PF06608	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGGCGATGC	byFrequency	5	ESCA
PKNOX2	0	.	GRCh37	11	125104986	125104986	+	5'UTR	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-155G>T	.	.	ENST00000298282	2/13	80	46	34	76	75	0	PKNOX2,5_prime_UTR_variant,,ENST00000531212,;PKNOX2,5_prime_UTR_variant,,ENST00000298282,;PKNOX2,5_prime_UTR_variant,,ENST00000527238,;PKNOX2,5_prime_UTR_variant,,ENST00000542175,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000561399,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000530517,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000559662,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000557814,;PKNOX2,intron_variant,,ENST00000531116,;PKNOX2,upstream_gene_variant,,ENST00000558729,;PKNOX2,upstream_gene_variant,,ENST00000561115,;PKNOX2,5_prime_UTR_variant,,ENST00000532623,;	T	ENSG00000165495	ENST00000298282	Transcript	5_prime_UTR_variant	117	.	.	.	.	.	.	.	1	PKNOX2	HGNC	16714	protein_coding	YES	CCDS41730.1	ENSP00000298282	PKNX2_HUMAN	H0YLX0_HUMAN,E9PRB6_HUMAN,E9PKL2_HUMAN,B7ZAF3_HUMAN	UPI000023271E	.	.	.	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGCTCAC	.	5	ESCA
NTM	0	.	GRCh37	11	132016295	132016295	+	Missense_Mutation	SNP	C	C	T	rs758413842	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287C>T	p.Thr96Met	p.T96M	ENST00000425719	2/8	40	30	10	59	59	0	NTM,missense_variant,p.Thr96Met,ENST00000374784,;NTM,missense_variant,p.Thr96Met,ENST00000374791,;NTM,missense_variant,p.Thr96Met,ENST00000539799,;NTM,missense_variant,p.Thr96Met,ENST00000425719,;NTM,missense_variant,p.Thr87Met,ENST00000550167,;NTM,missense_variant,p.Thr96Met,ENST00000374786,;NTM,missense_variant,p.Thr87Met,ENST00000427481,;NTM,non_coding_transcript_exon_variant,,ENST00000467255,;NTM,intron_variant,,ENST00000498764,;NTM,non_coding_transcript_exon_variant,,ENST00000479431,;	T	ENSG00000182667	ENST00000425719	Transcript	missense_variant	307	287	96	T/M	aCg/aTg	rs758413842	.	.	1	NTM	HGNC	17941	protein_coding	YES	CCDS44777.1	ENSP00000396722	NTRI_HUMAN	.	UPI00001A58B9	.	tolerated(0.1)	probably_damaging(0.947)	2/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19831:SF46,hmmpanther:PTHR19831,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAACGCAGT	byFrequency	5	ESCA
IGF2	0	.	GRCh37	11	2161780	2161780	+	Intron	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3-251C>A	.	.	ENST00000434045	.	53	35	18	44	44	0	IGF2,intron_variant,,ENST00000381389,;IGF2,intron_variant,,ENST00000434045,;IGF2,intron_variant,,ENST00000300632,;IGF2,upstream_gene_variant,,ENST00000381395,;IGF2,upstream_gene_variant,,ENST00000381406,;IGF2,upstream_gene_variant,,ENST00000416167,;IGF2,upstream_gene_variant,,ENST00000381392,;IGF2,upstream_gene_variant,,ENST00000418738,;IGF2-AS,non_coding_transcript_exon_variant,,ENST00000381361,;IGF2-AS,non_coding_transcript_exon_variant,,ENST00000445504,;IGF2-AS,upstream_gene_variant,,ENST00000381363,;INS-IGF2,intron_variant,,ENST00000356578,;	T	ENSG00000167244	ENST00000434045	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	IGF2	HGNC	5466	protein_coding	YES	CCDS44517.1	ENSP00000391826	IGF2_HUMAN	E3UN46_HUMAN	UPI0001751501	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGCGGGAGC	.	5	ESCA
BDNF	0	.	GRCh37	11	27680633	27680633	+	Intron	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226-501C>A	.	.	ENST00000438929	.	86	51	34	64	64	0	BDNF,5_prime_UTR_variant,,ENST00000439476,;BDNF,5_prime_UTR_variant,,ENST00000525528,;BDNF,intron_variant,,ENST00000533131,;BDNF,intron_variant,,ENST00000438929,;BDNF,intron_variant,,ENST00000356660,;BDNF,intron_variant,,ENST00000532997,;BDNF,intron_variant,,ENST00000395981,;BDNF,intron_variant,,ENST00000420794,;BDNF,intron_variant,,ENST00000418212,;BDNF,intron_variant,,ENST00000395983,;BDNF,intron_variant,,ENST00000395980,;BDNF,intron_variant,,ENST00000525950,;BDNF,intron_variant,,ENST00000395978,;BDNF,intron_variant,,ENST00000395986,;BDNF,intron_variant,,ENST00000530861,;BDNF,intron_variant,,ENST00000314915,;BDNF,intron_variant,,ENST00000533246,;BDNF-AS,intron_variant,,ENST00000502161,;BDNF-AS,intron_variant,,ENST00000530313,;BDNF-AS,intron_variant,,ENST00000530686,;BDNF-AS,intron_variant,,ENST00000499008,;BDNF-AS,intron_variant,,ENST00000501176,;BDNF-AS,intron_variant,,ENST00000499568,;BDNF-AS,intron_variant,,ENST00000500662,;BDNF-AS,downstream_gene_variant,,ENST00000532965,;BDNF,intron_variant,,ENST00000584049,;BDNF,intron_variant,,ENST00000530786,;	T	ENSG00000176697	ENST00000438929	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	BDNF	HGNC	1033	protein_coding	YES	CCDS44558.1	ENSP00000414303	BDNF_HUMAN	S5MI63_HUMAN,Q96TC2_HUMAN,Q969N8_HUMAN	UPI0001594492	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGATGTCTAG	.	5	ESCA
PEX16	0	.	GRCh37	11	45935479	45935479	+	Silent	SNP	G	G	A	rs769033920	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778C>T	p.%3D	p.L260L	ENST00000241041	9/11	82	54	28	75	75	0	PEX16,synonymous_variant,p.%3D,ENST00000241041,;PEX16,synonymous_variant,p.%3D,ENST00000533151,;PEX16,synonymous_variant,p.%3D,ENST00000532681,;PEX16,synonymous_variant,p.%3D,ENST00000378750,;PEX16,downstream_gene_variant,,ENST00000525192,;PEX16,downstream_gene_variant,,ENST00000532554,;PEX16,upstream_gene_variant,,ENST00000523721,;PEX16,downstream_gene_variant,,ENST00000529030,;PEX16,downstream_gene_variant,,ENST00000525229,;PEX16,downstream_gene_variant,,ENST00000527371,;PEX16,downstream_gene_variant,,ENST00000528674,;	A	ENSG00000121680	ENST00000241041	Transcript	synonymous_variant	796	778	260	L	Ctg/Ttg	rs769033920,COSM3447466,COSM3447467	.	.	-1	PEX16	HGNC	8857	protein_coding	YES	CCDS7917.1	ENSP00000241041	PEX16_HUMAN	E9PLS4_HUMAN	UPI000013CAC0	.	.	.	9/11	.	Pfam_domain:PF08610,hmmpanther:PTHR13299:SF0,hmmpanther:PTHR13299	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCAGGAGGC	.	5	ESCA
OR51E1	0	.	GRCh37	11	4674803	4674803	+	3'UTR	SNP	T	T	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*90T>A	.	.	ENST00000396952	2/2	45	32	13	39	39	0	OR51E1,3_prime_UTR_variant,,ENST00000530215,;OR51E1,3_prime_UTR_variant,,ENST00000396952,;	A	ENSG00000180785	ENST00000396952	Transcript	3_prime_UTR_variant	1697	.	.	.	.	.	.	.	1	OR51E1	HGNC	15194	protein_coding	YES	CCDS31358.2	ENSP00000380155	O51E1_HUMAN	.	UPI000003ACE2	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAATTTCCT	.	5	ESCA
OR51G2	0	.	GRCh37	11	4936308	4936308	+	Missense_Mutation	SNP	C	C	T	rs771383654	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586G>A	p.Asp196Asn	p.D196N	ENST00000322013	1/1	30	19	10	15	15	0	OR51G2,missense_variant,p.Asp196Asn,ENST00000322013,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	T	ENSG00000176893	ENST00000322013	Transcript	missense_variant	615	586	196	D/N	Gac/Aac	rs771383654,COSM1354242	.	.	-1	OR51G2	HGNC	15198	protein_coding	YES	CCDS31365.1	ENSP00000322593	O51G2_HUMAN	.	UPI0000041C2F	.	tolerated(0.1)	benign(0.027)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF133,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGTCGGCAC	byFrequency	5	ESCA
PATL1	0	.	GRCh37	11	59423080	59423080	+	Missense_Mutation	SNP	C	C	T	rs566436701	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.947G>A	p.Arg316His	p.R316H	ENST00000300146	8/19	83	48	34	85	85	0	PATL1,missense_variant,p.Arg316His,ENST00000300146,;	T	ENSG00000166889	ENST00000300146	Transcript	missense_variant	1032	947	316	R/H	cGt/cAt	rs566436701	.	.	-1	PATL1	HGNC	26721	protein_coding	YES	CCDS44613.1	ENSP00000300146	PATL1_HUMAN	B3KXN0_HUMAN	UPI00001FA7D8	.	tolerated(0.06)	benign(0.028)	8/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21551,hmmpanther:PTHR21551:SF2,Pfam_domain:PF09770	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P313Q|c.938C>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCACGGAAG	by1000G	5	ESCA
VWCE	0	.	GRCh37	11	61044094	61044094	+	Frame_Shift_Del	DEL	G	G	-	rs753714493,rs141301435	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1466delC	p.Pro489HisfsTer11	p.P489Hfs*11	ENST00000335613	11/20	133	97	36	113	113	0	VWCE,frameshift_variant,p.Pro489HisfsTer11,ENST00000335613,;VWCE,upstream_gene_variant,,ENST00000535710,;VWCE,3_prime_UTR_variant,,ENST00000301770,;VWCE,upstream_gene_variant,,ENST00000398808,;	-	ENSG00000167992	ENST00000335613	Transcript	frameshift_variant	1853	1466	489	P/X	cCa/ca	rs753714493,rs141301435	.	.	-1	VWCE	HGNC	26487	protein_coding	YES	CCDS8002.1	ENSP00000334186	VWCE_HUMAN	B4DY31_HUMAN	UPI000013E751	.	.	.	11/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF250,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTCTGTGGGGGG	byCluster	3	ESCA
SSH3	0	.	GRCh37	11	67075317	67075317	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792G>A	p.%3D	p.G264G	ENST00000308127	8/14	58	43	15	53	53	0	SSH3,synonymous_variant,p.%3D,ENST00000308127,;SSH3,synonymous_variant,p.%3D,ENST00000527821,;SSH3,synonymous_variant,p.%3D,ENST00000308298,;SSH3,synonymous_variant,p.%3D,ENST00000376757,;SSH3,splice_region_variant,,ENST00000532181,;SSH3,non_coding_transcript_exon_variant,,ENST00000529224,;SSH3,upstream_gene_variant,,ENST00000531495,;SSH3,downstream_gene_variant,,ENST00000534112,;SSH3,upstream_gene_variant,,ENST00000525913,;SSH3,splice_region_variant,,ENST00000532881,;SSH3,downstream_gene_variant,,ENST00000532600,;	A	ENSG00000172830	ENST00000308127	Transcript	synonymous_variant	970	792	264	G	ggG/ggA	.	.	.	1	SSH3	HGNC	30581	protein_coding	YES	CCDS8157.1	ENSP00000312081	SSH3_HUMAN	.	UPI0000038D01	.	.	.	8/14	.	hmmpanther:PTHR10159:SF107,hmmpanther:PTHR10159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCAGGTCCTC	.	5	ESCA
CARNS1	0	.	GRCh37	11	67191253	67191253	+	Silent	SNP	C	C	T	rs138253032	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2034C>T	p.%3D	p.F678F	ENST00000445895	9/9	32	24	8	37	37	0	CARNS1,synonymous_variant,p.%3D,ENST00000307823,;CARNS1,synonymous_variant,p.%3D,ENST00000531040,;CARNS1,synonymous_variant,p.%3D,ENST00000423745,;CARNS1,synonymous_variant,p.%3D,ENST00000445895,;RPS6KB2,upstream_gene_variant,,ENST00000524934,;PPP1CA,upstream_gene_variant,,ENST00000542876,;RPS6KB2,upstream_gene_variant,,ENST00000539188,;PPP1CA,upstream_gene_variant,,ENST00000546202,;RPS6KB2,upstream_gene_variant,,ENST00000312629,;CARNS1,non_coding_transcript_exon_variant,,ENST00000524740,;RPS6KB2,upstream_gene_variant,,ENST00000524814,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531388,;CARNS1,intron_variant,,ENST00000531958,;RPS6KB2,upstream_gene_variant,,ENST00000420069,;RPS6KB2,upstream_gene_variant,,ENST00000525088,;RPS6KB2,upstream_gene_variant,,ENST00000528964,;RPS6KB2,upstream_gene_variant,,ENST00000530623,;RPS6KB2,upstream_gene_variant,,ENST00000556575,;	T	ENSG00000172508	ENST00000445895	Transcript	synonymous_variant	2148	2034	678	F	ttC/ttT	rs138253032	.	.	1	CARNS1	HGNC	29268	protein_coding	YES	CCDS53667.1	ENSP00000389009	.	F5H427_HUMAN	UPI0001B99E02	.	.	.	9/9	.	PROSITE_profiles:PS50975,hmmpanther:PTHR10578:SF57,hmmpanther:PTHR10578,Pfam_domain:PF13535,Gene3D:3.30.470.20,Superfamily_domains:SSF56059	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTCGGGGC	by1000G	5	ESCA
INPPL1	0	.	GRCh37	11	71948432	71948433	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3149dupC	p.Pro1051SerfsTer34	p.P1051Sfs*34	ENST00000298229	26/28	108	77	31	80	80	0	INPPL1,frameshift_variant,p.Pro64SerfsTer34,ENST00000541752,;INPPL1,frameshift_variant,p.Pro809SerfsTer34,ENST00000538751,;INPPL1,frameshift_variant,p.Pro1051SerfsTer34,ENST00000298229,;INPPL1,frameshift_variant,p.Pro809SerfsTer34,ENST00000541756,;PHOX2A,downstream_gene_variant,,ENST00000298231,;INPPL1,upstream_gene_variant,,ENST00000320683,;PHOX2A,downstream_gene_variant,,ENST00000546310,;PHOX2A,downstream_gene_variant,,ENST00000544057,;INPPL1,intron_variant,,ENST00000535985,;INPPL1,downstream_gene_variant,,ENST00000537755,;INPPL1,downstream_gene_variant,,ENST00000544806,;INPPL1,downstream_gene_variant,,ENST00000541303,;INPPL1,downstream_gene_variant,,ENST00000545355,;INPPL1,downstream_gene_variant,,ENST00000542295,;	C	ENSG00000165458	ENST00000298229	Transcript	frameshift_variant	3348-3349	3144-3145	1048-1049	-/X	-/C	.	.	.	1	INPPL1	HGNC	6080	protein_coding	YES	CCDS8213.1	ENSP00000298229	SHIP2_HUMAN	H0YFZ4_HUMAN,F5H588_HUMAN,F5GYK9_HUMAN	UPI000013E4AF	.	.	.	26/28	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11200:SF15,hmmpanther:PTHR11200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACACTGCCCCC	.	3	ESCA
KCTD14	0	.	GRCh37	11	77727684	77727684	+	Silent	SNP	G	G	A	rs368467821	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723C>T	p.%3D	p.N241N	ENST00000353172	2/2	44	25	19	44	44	0	KCTD14,synonymous_variant,p.%3D,ENST00000533144,;KCTD14,synonymous_variant,p.%3D,ENST00000353172,;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000528251,;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000530054,;RP11-7I15.3,downstream_gene_variant,,ENST00000533697,;	A	ENSG00000151364	ENST00000353172	Transcript	synonymous_variant	768	723	241	N	aaC/aaT	rs368467821	.	.	-1	KCTD14	HGNC	23295	protein_coding	YES	CCDS8255.2	ENSP00000316482	KCD14_HUMAN	B2R9R8_HUMAN	UPI000003E7AB	.	.	.	2/2	.	hmmpanther:PTHR14499:SF3,hmmpanther:PTHR14499	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTCGTTTCT	byFrequency|byCluster	5	ESCA
CEND1	0	.	GRCh37	11	787402	787402	+	3'UTR	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*725C>T	.	.	ENST00000330106	2/2	27	18	9	11	11	0	CEND1,3_prime_UTR_variant,,ENST00000330106,;SLC25A22,downstream_gene_variant,,ENST00000531214,;SLC25A22,downstream_gene_variant,,ENST00000320230,;SLC25A22,downstream_gene_variant,,ENST00000481290,;AP006621.5,downstream_gene_variant,,ENST00000530083,;CEND1,downstream_gene_variant,,ENST00000524587,;AP006621.5,downstream_gene_variant,,ENST00000525941,;	A	ENSG00000184524	ENST00000330106	Transcript	3_prime_UTR_variant	1351	.	.	.	.	.	.	.	-1	CEND1	HGNC	24153	protein_coding	YES	CCDS7714.1	ENSP00000328336	CEND_HUMAN	.	UPI0000126A16	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTGCTGGG	.	5	ESCA
ANO4	0	.	GRCh37	12	101188779	101188781	+	5'UTR	DEL	CTT	CTT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-165_-163delTCT	.	.	ENST00000392979	1/27	56	36	20	73	73	0	ANO4,5_prime_UTR_variant,,ENST00000299222,;ANO4,5_prime_UTR_variant,,ENST00000546991,;ANO4,5_prime_UTR_variant,,ENST00000392977,;ANO4,5_prime_UTR_variant,,ENST00000392979,;ANO4,intron_variant,,ENST00000538618,;ANO4,non_coding_transcript_exon_variant,,ENST00000551148,;ANO4,intron_variant,,ENST00000549155,;	-	ENSG00000151572	ENST00000392979	Transcript	5_prime_UTR_variant	195-197	.	.	.	.	.	.	.	1	ANO4	HGNC	23837	protein_coding	YES	CCDS31884.1	ENSP00000376705	ANO4_HUMAN	.	UPI0000198E2E	.	.	.	1/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTCTCCTTCTGTT	.	3	ESCA
FAM222A	0	.	GRCh37	12	110208200	110208200	+	3'UTR	DEL	T	T	-	rs375990703	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1114delT	.	.	ENST00000538780	3/3	69	42	26	65	65	0	FAM222A,3_prime_UTR_variant,,ENST00000538780,;FAM222A,3_prime_UTR_variant,,ENST00000358906,;FAM222A-AS1,intron_variant,,ENST00000541460,;FAM222A-AS1,intron_variant,,ENST00000541723,;	-	ENSG00000139438	ENST00000538780	Transcript	3_prime_UTR_variant	3182	.	.	.	.	rs375990703	.	.	1	FAM222A	HGNC	25915	protein_coding	YES	CCDS9133.1	ENSP00000443292	F222A_HUMAN	.	UPI000013D712	.	.	.	3/3	.	.	-:0.0150	-:0.0552	-:0.0014	.	-:0	-:0.001	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAATGTTTTTT	byFrequency|byCluster|by1000G	2	ESCA
TAS2R20	0	.	GRCh37	12	11149514	11149514	+	3'UTR	SNP	C	C	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*31G>C	.	.	ENST00000538986	1/1	58	55	3	48	48	0	TAS2R20,3_prime_UTR_variant,,ENST00000538986,;PRR4,intron_variant,,ENST00000539853,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;TAS2R14,intron_variant,,ENST00000381852,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000536086,;PRR4,intron_variant,,ENST00000534923,;	G	ENSG00000255837	ENST00000538986	Transcript	3_prime_UTR_variant	961	.	.	.	.	.	.	.	-1	TAS2R20	HGNC	19109	protein_coding	YES	CCDS8639.1	ENSP00000441624	T2R20_HUMAN	Q50KF4_HUMAN	UPI000000D822	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTGCTAGAA	.	2	ESCA
TESC	0	.	GRCh37	12	117484586	117484586	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.407G>A	p.Arg136Gln	p.R136Q	ENST00000335209	5/8	44	29	14	58	57	0	TESC,missense_variant,p.Arg189Gln,ENST00000392545,;TESC,missense_variant,p.Arg136Gln,ENST00000335209,;TESC,missense_variant,p.Arg109Gln,ENST00000541210,;TESC,synonymous_variant,p.%3D,ENST00000549210,;TESC,non_coding_transcript_exon_variant,,ENST00000535198,;TESC,missense_variant,p.Arg136Gln,ENST00000470612,;TESC,3_prime_UTR_variant,,ENST00000462502,;TESC,downstream_gene_variant,,ENST00000482176,;	T	ENSG00000088992	ENST00000335209	Transcript	missense_variant	594	407	136	R/Q	cGa/cAa	.	.	.	-1	TESC	HGNC	26065	protein_coding	YES	CCDS9183.3	ENSP00000334785	CHP3_HUMAN	.	UPI0000136BF7	.	deleterious(0.03)	possibly_damaging(0.861)	5/8	.	Superfamily_domains:SSF47473,SMART_domains:SM00054,Gene3D:1.10.238.10,Pfam_domain:PF13405,hmmpanther:PTHR23056,hmmpanther:PTHR23056:SF2,PROSITE_profiles:PS50222	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTCGATAT	.	5	ESCA
ASB8	0	.	GRCh37	12	48543170	48543173	+	Frame_Shift_Del	DEL	TTCC	TTCC	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	TTCC	TTCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843_846delGGAA	p.Lys281AsnfsTer6	p.K281Nfs*6	ENST00000317697	4/4	30	18	12	32	32	0	ASB8,frameshift_variant,p.Lys281AsnfsTer6,ENST00000536549,;ASB8,frameshift_variant,p.Lys281AsnfsTer6,ENST00000317697,;PFKM,downstream_gene_variant,,ENST00000340802,;ASB8,downstream_gene_variant,,ENST00000540212,;PFKM,downstream_gene_variant,,ENST00000395233,;ASB8,downstream_gene_variant,,ENST00000536953,;PFKM,downstream_gene_variant,,ENST00000547587,;ASB8,downstream_gene_variant,,ENST00000539503,;ASB8,downstream_gene_variant,,ENST00000548228,;ASB8,downstream_gene_variant,,ENST00000535055,;ASB8,downstream_gene_variant,,ENST00000535988,;ASB8,downstream_gene_variant,,ENST00000540782,;PFKM,downstream_gene_variant,,ENST00000359794,;PFKM,downstream_gene_variant,,ENST00000312352,;ASB8,downstream_gene_variant,,ENST00000545791,;PFKM,downstream_gene_variant,,ENST00000551804,;PFKM,downstream_gene_variant,,ENST00000553055,;ASB8,downstream_gene_variant,,ENST00000539528,;ASB8,downstream_gene_variant,,ENST00000536071,;ASB8,downstream_gene_variant,,ENST00000537754,;ASB8,downstream_gene_variant,,ENST00000539464,;PFKM,downstream_gene_variant,,ENST00000547581,;ASB8,downstream_gene_variant,,ENST00000539865,;ASB8,downstream_gene_variant,,ENST00000540143,;PFKM,downstream_gene_variant,,ENST00000546964,;ASB8,downstream_gene_variant,,ENST00000536938,;	-	ENSG00000177981	ENST00000317697	Transcript	frameshift_variant	1013-1016	843-846	281-282	KE/X	aaGGAA/aa	.	.	.	-1	ASB8	HGNC	17183	protein_coding	YES	CCDS8761.1	ENSP00000320893	ASB8_HUMAN	F8VS92_HUMAN,F5H7B4_HUMAN,F5H6A7_HUMAN,F5GZZ3_HUMAN	UPI00001260EB	.	.	.	4/4	.	Superfamily_domains:SSF158235,SMART_domains:SM00969,Pfam_domain:PF07525,hmmpanther:PTHR24134:SF1,hmmpanther:PTHR24134,PROSITE_profiles:PS50225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGTATTCCTTCAA	.	3	ESCA
KMT2D	0	.	GRCh37	12	49431257	49431267	+	Frame_Shift_Del	DEL	GGCCTGGGCAG	GGCCTGGGCAG	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	GGCCTGGGCAG	GGCCTGGGCAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9872_9882delCTGCCCAGGCC	p.Pro3291HisfsTer6	p.P3291Hfs*6	ENST00000301067	34/54	37	28	9	36	36	0	KMT2D,frameshift_variant,p.Pro3291HisfsTer6,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,upstream_gene_variant,,ENST00000549743,;	-	ENSG00000167548	ENST00000301067	Transcript	frameshift_variant	9872-9882	9872-9882	3291-3294	PAQA/X	cCTGCCCAGGCC/c	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	34/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGACATGGCCTGGGCAGGGCCT	.	2	ESCA
ESPL1	0	.	GRCh37	12	53663026	53663027	+	Frame_Shift_Del	DEL	TC	TC	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	TC	TC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303_304delCT	p.Phe102CysfsTer39	p.F102Cfs*39	ENST00000257934	3/31	30	23	7	34	34	0	ESPL1,frameshift_variant,p.Phe102CysfsTer39,ENST00000257934,;ESPL1,frameshift_variant,p.Phe102CysfsTer39,ENST00000552462,;ESPL1,frameshift_variant,p.Phe102CysfsTer39,ENST00000553219,;ESPL1,upstream_gene_variant,,ENST00000550026,;ESPL1,3_prime_UTR_variant,,ENST00000552671,;	-	ENSG00000135476	ENST00000257934	Transcript	frameshift_variant	391-392	300-301	100-101	IL/IX	atTCtc/attc	.	.	.	1	ESPL1	HGNC	16856	protein_coding	YES	CCDS8852.1	ENSP00000257934	ESPL1_HUMAN	H3BRX7_HUMAN	UPI00003668C3	.	.	.	3/31	.	hmmpanther:PTHR12792	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACGAATTCTCTTT	.	3	ESCA
B4GALNT1	0	.	GRCh37	12	58023911	58023911	+	Intron	SNP	C	C	T	rs748435997	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.712+24G>A	.	.	ENST00000341156	.	42	28	14	60	60	0	B4GALNT1,missense_variant,p.Gly246Arg,ENST00000552350,;B4GALNT1,missense_variant,p.Gly246Arg,ENST00000550764,;B4GALNT1,intron_variant,,ENST00000341156,;B4GALNT1,intron_variant,,ENST00000449184,;B4GALNT1,intron_variant,,ENST00000418555,;B4GALNT1,downstream_gene_variant,,ENST00000548888,;SLC26A10,downstream_gene_variant,,ENST00000379218,;B4GALNT1,downstream_gene_variant,,ENST00000551220,;B4GALNT1,upstream_gene_variant,,ENST00000547741,;SLC26A10,downstream_gene_variant,,ENST00000320442,;SLC26A10,downstream_gene_variant,,ENST00000483647,;B4GALNT1,downstream_gene_variant,,ENST00000550943,;SLC26A10,downstream_gene_variant,,ENST00000490243,;B4GALNT1,intron_variant,,ENST00000552798,;B4GALNT1,intron_variant,,ENST00000553142,;B4GALNT1,intron_variant,,ENST00000549391,;SLC26A10,downstream_gene_variant,,ENST00000487816,;B4GALNT1,downstream_gene_variant,,ENST00000551925,;B4GALNT1,downstream_gene_variant,,ENST00000548487,;B4GALNT1,downstream_gene_variant,,ENST00000552219,;SLC26A10,downstream_gene_variant,,ENST00000474791,;SLC26A10,downstream_gene_variant,,ENST00000440686,;B4GALNT1,upstream_gene_variant,,ENST00000552468,;SLC26A10,downstream_gene_variant,,ENST00000474359,;	T	ENSG00000135454	ENST00000341156	Transcript	intron_variant	.	.	.	.	.	rs748435997	.	.	-1	B4GALNT1	HGNC	4117	protein_coding	YES	CCDS8950.1	ENSP00000341562	B4GN1_HUMAN	F8VW33_HUMAN,F8VU35_HUMAN,F8VR44_HUMAN,F8TDK4_HUMAN	UPI0000126DD5	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCCGTCTC	byFrequency	5	ESCA
DYRK2	0	.	GRCh37	12	68053496	68053499	+	3'UTR	DEL	GAGT	GAGT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	GAGT	GAGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1007_*1010delGAGT	.	.	ENST00000344096	3/3	68	44	24	57	57	0	DYRK2,3_prime_UTR_variant,,ENST00000344096,;DYRK2,downstream_gene_variant,,ENST00000393555,;DYRK2,downstream_gene_variant,,ENST00000319833,;DYRK2,downstream_gene_variant,,ENST00000543747,;DYRK2,downstream_gene_variant,,ENST00000542503,;RP11-335O4.3,intron_variant,,ENST00000425371,;	-	ENSG00000127334	ENST00000344096	Transcript	3_prime_UTR_variant	3222-3225	.	.	.	.	.	.	.	1	DYRK2	HGNC	3093	protein_coding	YES	CCDS8978.1	ENSP00000342105	DYRK2_HUMAN	G8JLB4_HUMAN,F5GXG1_HUMAN	UPI000006E92B	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGATTAGAGTGAGTT	.	3	ESCA
PAN3	0	.	GRCh37	13	28830500	28830502	+	In_Frame_Del	DEL	AGA	AGA	-	rs751740818	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AGA	AGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1080_1082delAAG	p.Arg360del	p.R360del	ENST00000380958	7/19	80	55	25	99	99	0	PAN3,inframe_deletion,p.Arg160del,ENST00000399613,;PAN3,inframe_deletion,p.Arg360del,ENST00000380958,;PAN3,inframe_deletion,p.Arg48del,ENST00000282391,;PAN3,non_coding_transcript_exon_variant,,ENST00000483842,;PAN3,non_coding_transcript_exon_variant,,ENST00000503791,;	-	ENSG00000152520	ENST00000380958	Transcript	inframe_deletion	1224-1226	1072-1074	358	R/-	AGA/-	rs751740818	.	.	1	PAN3	HGNC	29991	protein_coding	YES	CCDS9329.2	ENSP00000370345	PAN3_HUMAN	Q6ZMN5_HUMAN	UPI0001BE8112	.	.	.	7/19	.	hmmpanther:PTHR12272	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCTCCCAGAAGAAG	byFrequency	2	ESCA
EXOSC8	0	.	GRCh37	13	37576435	37576437	+	In_Frame_Del	DEL	AGG	AGG	-	rs771058109	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AGG	AGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45_47delGAG	p.Arg16del	p.R16del	ENST00000389704	2/11	37	28	9	23	23	0	EXOSC8,inframe_deletion,p.Arg16del,ENST00000389704,;ALG5,upstream_gene_variant,,ENST00000413537,;EXOSC8,upstream_gene_variant,,ENST00000481013,;ALG5,upstream_gene_variant,,ENST00000239891,;ALG5,upstream_gene_variant,,ENST00000443765,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000488108,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000489088,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000474661,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000464235,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000470423,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000488779,;ALG5,upstream_gene_variant,,ENST00000496689,;EXOSC8,non_coding_transcript_exon_variant,,ENST00000490537,;EXOSC8,intron_variant,,ENST00000239893,;EXOSC8,upstream_gene_variant,,ENST00000495092,;	-	ENSG00000120699	ENST00000389704	Transcript	inframe_deletion	308-310	43-45	15	R/-	AGG/-	rs771058109	.	.	1	EXOSC8	HGNC	17035	protein_coding	YES	CCDS31958.1	ENSP00000374354	EXOS8_HUMAN	.	UPI000004A07D	.	.	.	2/11	.	hmmpanther:PTHR11097:SF9,hmmpanther:PTHR11097,Gene3D:1e3hA01,Superfamily_domains:SSF54211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TATTACAGGAGATT	.	3	ESCA
CHD8	0	.	GRCh37	14	21897312	21897312	+	Silent	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1026G>T	p.%3D	p.L342L	ENST00000399982	2/37	100	65	34	70	70	0	CHD8,synonymous_variant,p.%3D,ENST00000553283,;CHD8,synonymous_variant,p.%3D,ENST00000557364,;CHD8,synonymous_variant,p.%3D,ENST00000430710,;CHD8,synonymous_variant,p.%3D,ENST00000399982,;CHD8,downstream_gene_variant,,ENST00000553622,;RN7SL650P,downstream_gene_variant,,ENST00000583681,;CHD8,intron_variant,,ENST00000555962,;CHD8,downstream_gene_variant,,ENST00000556833,;CHD8,downstream_gene_variant,,ENST00000553651,;	A	ENSG00000100888	ENST00000399982	Transcript	synonymous_variant	1091	1026	342	L	ctG/ctT	.	.	.	-1	CHD8	HGNC	20153	protein_coding	YES	CCDS53885.1	ENSP00000382863	CHD8_HUMAN	.	UPI00002375B9	.	.	.	2/37	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10799:SF551,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGCAGCTG	.	5	ESCA
TRAJ29	0	.	GRCh37	14	22982979	22982982	+	Missense_Mutation	DEL	AAGT	AAGT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AAGT	AAGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000390508	1/1	74	44	30	50	50	0	TRAJ29,coding_sequence_variant,,ENST00000390508,;TRAJ27,upstream_gene_variant,,ENST00000390510,;TRAJ31,downstream_gene_variant,,ENST00000390506,;TRAJ28,upstream_gene_variant,,ENST00000390509,;TRAJ30,downstream_gene_variant,,ENST00000390507,;TRAJ26,upstream_gene_variant,,ENST00000390511,;TRAJ25,upstream_gene_variant,,ENST00000390512,;TRAJ32,downstream_gene_variant,,ENST00000390505,;	-	ENSG00000211860	ENST00000390508	Transcript	coding_sequence_variant	59-?	60-?	20-?	.	.	.	.	.	1	TRAJ29	HGNC	12058	TR_J_gene	YES	.	ENSP00000452518	.	.	UPI00021CF145	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATTGCAAGTAAGTG	.	3	ESCA
LRRC16B	0	.	GRCh37	14	24530854	24530854	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2453C>A	p.Ala818Glu	p.A818E	ENST00000342740	27/40	40	30	10	19	19	0	LRRC16B,missense_variant,p.Ala818Glu,ENST00000342740,;LRRC16B,5_prime_UTR_variant,,ENST00000334420,;LRRC16B,non_coding_transcript_exon_variant,,ENST00000561354,;LRRC16B,non_coding_transcript_exon_variant,,ENST00000559694,;LRRC16B,upstream_gene_variant,,ENST00000560349,;	A	ENSG00000186648	ENST00000342740	Transcript	missense_variant	2607	2453	818	A/E	gCa/gAa	.	.	.	1	LRRC16B	HGNC	20272	protein_coding	YES	CCDS32054.1	ENSP00000340467	LR16B_HUMAN	.	UPI0000DBEF11	.	deleterious(0)	probably_damaging(0.937)	27/40	.	hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAGCAGGAC	.	5	ESCA
CLEC14A	0	.	GRCh37	14	38725089	38725089	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.139C>T	p.Arg47Trp	p.R47W	ENST00000342213	1/1	31	17	13	16	16	0	CLEC14A,missense_variant,p.Arg47Trp,ENST00000342213,;	A	ENSG00000176435	ENST00000342213	Transcript	missense_variant	486	139	47	R/W	Cgg/Tgg	.	.	.	-1	CLEC14A	HGNC	19832	protein_coding	YES	CCDS9667.1	ENSP00000353013	CLC14_HUMAN	.	UPI000000CBD4	.	tolerated(0.19)	probably_damaging(0.958)	1/1	.	PROSITE_profiles:PS50041,hmmpanther:PTHR24838:SF258,hmmpanther:PTHR24838,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCGCTTCA	.	5	ESCA
FANCM	0	.	GRCh37	14	45623219	45623219	+	Missense_Mutation	SNP	T	T	C	rs766761905	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147T>C	p.Tyr383His	p.Y383H	ENST00000267430	6/23	66	38	28	47	47	0	FANCM,missense_variant,p.Tyr383His,ENST00000556036,;FANCM,missense_variant,p.Tyr357His,ENST00000542564,;FANCM,missense_variant,p.Tyr383His,ENST00000267430,;FANCM,upstream_gene_variant,,ENST00000556250,;	C	ENSG00000187790	ENST00000267430	Transcript	missense_variant	1232	1147	383	Y/H	Tat/Cat	rs766761905	.	.	1	FANCM	HGNC	23168	protein_coding	YES	CCDS32070.1	ENSP00000267430	FANCM_HUMAN	.	UPI000059F032	.	deleterious(0)	benign(0.085)	6/23	.	hmmpanther:PTHR14025,hmmpanther:PTHR14025:SF20,Gene3D:1wp9B03	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTATATTTC	.	5	ESCA
MGAT2	0	.	GRCh37	14	50089335	50089336	+	3'UTR	DEL	CA	CA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7_*8delCA	.	.	ENST00000305386	1/1	107	76	31	42	42	0	MGAT2,3_prime_UTR_variant,,ENST00000305386,;DNAAF2,downstream_gene_variant,,ENST00000298292,;DNAAF2,downstream_gene_variant,,ENST00000406043,;RPL36AL,upstream_gene_variant,,ENST00000298289,;RP11-649E7.5,non_coding_transcript_exon_variant,,ENST00000555043,;	-	ENSG00000168282	ENST00000305386	Transcript	3_prime_UTR_variant	1847-1848	.	.	.	.	.	.	.	1	MGAT2	HGNC	7045	protein_coding	YES	CCDS9690.1	ENSP00000307423	MGAT2_HUMAN	B4DDK9_HUMAN	UPI000012B8CA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAAATCACAGTT	.	3	ESCA
ELMSAN1	0	.	GRCh37	14	74182470	74182473	+	3'UTR	DEL	AAGA	AAGA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AAGA	AAGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3531_*3534delTCTT	.	.	ENST00000286523	12/12	34	23	11	45	45	0	ELMSAN1,3_prime_UTR_variant,,ENST00000286523,;ELMSAN1,3_prime_UTR_variant,,ENST00000394071,;ELMSAN1,downstream_gene_variant,,ENST00000435371,;PNMA1,upstream_gene_variant,,ENST00000316836,;ELMSAN1,downstream_gene_variant,,ENST00000423556,;ELMSAN1,non_coding_transcript_exon_variant,,ENST00000476562,;ELMSAN1,downstream_gene_variant,,ENST00000451078,;ELMSAN1,downstream_gene_variant,,ENST00000478847,;	-	ENSG00000156030	ENST00000286523	Transcript	3_prime_UTR_variant	7452-7455	.	.	.	.	.	.	.	-1	ELMSAN1	HGNC	19853	protein_coding	YES	CCDS9819.1	ENSP00000286523	EMSA1_HUMAN	F6RU81_HUMAN,C9JYU7_HUMAN	UPI00001FD815	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATGAGAAGAAAGAG	.	3	ESCA
NPAP1	0	.	GRCh37	15	24928408	24928408	+	3'UTR	SNP	A	A	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3923A>C	.	.	ENST00000329468	1/1	9	6	3	12	12	0	NPAP1,3_prime_UTR_variant,,ENST00000329468,;	C	ENSG00000185823	ENST00000329468	Transcript	3_prime_UTR_variant	7868	.	.	.	.	.	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAAACCGGA	.	2	ESCA
PDIA3	0	.	GRCh37	15	44038854	44038854	+	Silent	SNP	C	C	T	rs747839953	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.117C>T	p.%3D	p.I39I	ENST00000300289	1/13	66	49	17	56	56	0	PDIA3,synonymous_variant,p.%3D,ENST00000300289,;PDIA3,5_prime_UTR_variant,,ENST00000538521,;CATSPER2P1,non_coding_transcript_exon_variant,,ENST00000429276,;PDIA3,non_coding_transcript_exon_variant,,ENST00000469684,;CATSPER2P1,upstream_gene_variant,,ENST00000381680,;CATSPER2P1,upstream_gene_variant,,ENST00000416302,;PDIA3,synonymous_variant,p.%3D,ENST00000455250,;PDIA3,synonymous_variant,p.%3D,ENST00000434494,;PDIA3,synonymous_variant,p.%3D,ENST00000446523,;CATSPER2P1,upstream_gene_variant,,ENST00000439564,;	T	ENSG00000167004	ENST00000300289	Transcript	synonymous_variant	265	117	39	I	atC/atT	rs747839953	.	.	1	PDIA3	HGNC	4606	protein_coding	YES	CCDS10101.1	ENSP00000300289	PDIA3_HUMAN	.	UPI0000052A4F	.	.	.	1/13	.	PROSITE_profiles:PS51352,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF60,TIGRFAM_domain:TIGR01130,Gene3D:3.40.30.10,Pfam_domain:PF00085,TIGRFAM_domain:TIGR01126,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCATCTCCGA	byFrequency	5	ESCA
UNC13C	0	.	GRCh37	15	54307297	54307297	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2197C>T	p.Gln733Ter	p.Q733*	ENST00000260323	1/32	25	15	10	14	14	0	UNC13C,stop_gained,p.Gln733Ter,ENST00000537900,;UNC13C,stop_gained,p.Gln733Ter,ENST00000545554,;UNC13C,stop_gained,p.Gln733Ter,ENST00000260323,;	T	ENSG00000137766	ENST00000260323	Transcript	stop_gained	2197	2197	733	Q/*	Cag/Tag	.	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	.	.	1/32	.	hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGCCAGTGG	.	5	ESCA
FEM1B	0	.	GRCh37	15	68582270	68582270	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.574C>T	p.His192Tyr	p.H192Y	ENST00000306917	2/2	26	19	7	20	20	0	FEM1B,missense_variant,p.His192Tyr,ENST00000306917,;FEM1B,missense_variant,p.His34Tyr,ENST00000566739,;FEM1B,downstream_gene_variant,,ENST00000570067,;FEM1B,upstream_gene_variant,,ENST00000566008,;	T	ENSG00000169018	ENST00000306917	Transcript	missense_variant	1189	574	192	H/Y	Cac/Tac	.	.	.	1	FEM1B	HGNC	3649	protein_coding	YES	CCDS10228.1	ENSP00000307298	FEM1B_HUMAN	H3BTV3_HUMAN	UPI00000011FB	.	tolerated(0.07)	probably_damaging(0.996)	2/2	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24173,Pfam_domain:PF00023,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01415	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGCACTTT	.	5	ESCA
PGPEP1L	0	.	GRCh37	15	99511702	99511702	+	3'UTR	SNP	C	C	T	rs777583521	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5G>A	.	.	ENST00000378919	5/5	97	68	29	95	95	0	PGPEP1L,3_prime_UTR_variant,,ENST00000378919,;PGPEP1L,3_prime_UTR_variant,,ENST00000535714,;IGF1R,downstream_gene_variant,,ENST00000558762,;IGF1R,downstream_gene_variant,,ENST00000268035,;RP11-654A16.3,intron_variant,,ENST00000559468,;	T	ENSG00000183571	ENST00000378919	Transcript	3_prime_UTR_variant	802	.	.	.	.	rs777583521	.	.	-1	PGPEP1L	HGNC	27080	protein_coding	YES	CCDS53977.1	ENSP00000368199	PGPIL_HUMAN	H0YF86_HUMAN	UPI00006C1572	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCCCCCGGT	byFrequency	5	ESCA
UNKL	0	.	GRCh37	16	1444165	1444165	+	Missense_Mutation	SNP	G	G	A	rs753588824	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895C>T	p.Arg299Cys	p.R299C	ENST00000389221	7/15	121	54	67	87	87	0	UNKL,missense_variant,p.Arg489Cys,ENST00000397462,;UNKL,missense_variant,p.Arg302Cys,ENST00000508903,;UNKL,missense_variant,p.Arg299Cys,ENST00000389221,;UNKL,downstream_gene_variant,,ENST00000301712,;UNKL,3_prime_UTR_variant,,ENST00000382757,;UNKL,downstream_gene_variant,,ENST00000502438,;UNKL,downstream_gene_variant,,ENST00000509981,;	A	ENSG00000059145	ENST00000389221	Transcript	missense_variant	895	895	299	R/C	Cgc/Tgc	rs753588824,COSM3957139,COSM3957140	.	.	-1	UNKL	HGNC	14184	protein_coding	YES	.	ENSP00000373873	UNKL_HUMAN	D6RA68_HUMAN	UPI0001AE676E	.	deleterious(0)	benign(0.292)	7/15	.	Superfamily_domains:SSF90229,SMART_domains:SM00356,Gene3D:1m9oA00,Pfam_domain:PF00642,hmmpanther:PTHR14493:SF37,hmmpanther:PTHR14493,PROSITE_profiles:PS50103	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCGCGGGC	.	5	ESCA
SULT1A1	0	.	GRCh37	16	28617217	28617217	+	Silent	SNP	C	C	T	rs202065838	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813G>A	p.%3D	p.A271A	ENST00000395609	10/10	79	59	19	55	55	0	SULT1A1,synonymous_variant,p.%3D,ENST00000569554,;SULT1A1,synonymous_variant,p.%3D,ENST00000395607,;SULT1A1,synonymous_variant,p.%3D,ENST00000566189,;SULT1A1,synonymous_variant,p.%3D,ENST00000314752,;SULT1A1,synonymous_variant,p.%3D,ENST00000395609,;SULT1A1,synonymous_variant,p.%3D,ENST00000350842,;SULT1A1,downstream_gene_variant,,ENST00000567512,;SULT1A1,3_prime_UTR_variant,,ENST00000564818,;SULT1A1,3_prime_UTR_variant,,ENST00000562058,;SULT1A1,3_prime_UTR_variant,,ENST00000563493,;SULT1A1,non_coding_transcript_exon_variant,,ENST00000567998,;	T	ENSG00000196502	ENST00000395609	Transcript	synonymous_variant	1572	813	271	A	gcG/gcA	rs202065838	.	.	-1	SULT1A1	HGNC	11453	protein_coding	YES	CCDS32420.1	ENSP00000378972	ST1A1_HUMAN	Q9UMT9_HUMAN,H3BRY5_HUMAN	UPI000013EA41	.	.	.	10/10	.	hmmpanther:PTHR11783:SF42,hmmpanther:PTHR11783,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	T:0.0002	T:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TTCTGCGCCAC	byCluster	3	ESCA
SH2B1	0	.	GRCh37	16	28877252	28877252	+	Intron	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-83-81G>A	.	.	ENST00000322610	.	48	22	26	32	32	0	SH2B1,5_prime_UTR_variant,,ENST00000337120,;SH2B1,intron_variant,,ENST00000395532,;SH2B1,intron_variant,,ENST00000545570,;SH2B1,intron_variant,,ENST00000322610,;SH2B1,intron_variant,,ENST00000538342,;SH2B1,intron_variant,,ENST00000563591,;SH2B1,intron_variant,,ENST00000567536,;SH2B1,intron_variant,,ENST00000359285,;SH2B1,intron_variant,,ENST00000566209,;SH2B1,upstream_gene_variant,,ENST00000566176,;SH2B1,upstream_gene_variant,,ENST00000561629,;RP11-22P6.2,upstream_gene_variant,,ENST00000567731,;SH2B1,intron_variant,,ENST00000563674,;SH2B1,upstream_gene_variant,,ENST00000569471,;	A	ENSG00000178188	ENST00000322610	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SH2B1	HGNC	30417	protein_coding	YES	CCDS53996.1	ENSP00000321221	SH2B1_HUMAN	H3BVF6_HUMAN,H3BTK4_HUMAN	UPI00001AF36C	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGACGTCTCT	.	5	ESCA
LINC00917	0	.	GRCh37	16	86371017	86371017	+	RNA	SNP	C	C	T	rs375346688	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1487G>A	.	.	ENST00000594203	3/6	90	37	52	39	39	0	LINC00917,non_coding_transcript_exon_variant,,ENST00000600892,;LINC00917,non_coding_transcript_exon_variant,,ENST00000601556,;LINC00917,non_coding_transcript_exon_variant,,ENST00000594203,;LINC00917,non_coding_transcript_exon_variant,,ENST00000304488,;LINC00917,downstream_gene_variant,,ENST00000598994,;LINC00917,downstream_gene_variant,,ENST00000599664,;LINC00917,downstream_gene_variant,,ENST00000595169,;LINC00917,downstream_gene_variant,,ENST00000599619,;	T	ENSG00000168367	ENST00000594203	Transcript	non_coding_transcript_exon_variant	1487	.	.	.	.	rs375346688	.	.	-1	LINC00917	HGNC	48607	lincRNA	YES	.	.	.	.	.	.	.	.	3/6	.	.	T:0.0006	T:0.0023	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGCTCCTG	byFrequency|byCluster|by1000G	5	ESCA
DHRS7B	0	.	GRCh37	17	21094331	21094333	+	In_Frame_Del	DEL	GAA	GAA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	GAA	GAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852_854delGAA	p.Lys285del	p.K285del	ENST00000395511	7/7	76	51	25	56	56	0	DHRS7B,inframe_deletion,p.Lys270del,ENST00000579303,;DHRS7B,inframe_deletion,p.Lys285del,ENST00000395511,;DHRS7B,inframe_deletion,p.Lys85del,ENST00000583388,;DHRS7B,intron_variant,,ENST00000581463,;DHRS7B,3_prime_UTR_variant,,ENST00000578426,;DHRS7B,non_coding_transcript_exon_variant,,ENST00000346603,;	-	ENSG00000109016	ENST00000395511	Transcript	inframe_deletion	1163-1165	843-845	281-282	GK/G	ggGAAg/ggg	.	.	.	1	DHRS7B	HGNC	24547	protein_coding	YES	CCDS11215.1	ENSP00000378887	DRS7B_HUMAN	J3QKT1_HUMAN	UPI00000739CB	.	.	.	7/7	.	hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF325,Gene3D:3.40.50.720,PIRSF_domain:PIRSF000126,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTGGGGAAGAAGA	.	2	ESCA
KANSL1	0	.	GRCh37	17	44248371	44248371	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1139T>A	p.Leu380Ter	p.L380*	ENST00000262419	2/15	72	27	44	59	59	0	KANSL1,stop_gained,p.Leu380Ter,ENST00000575318,;KANSL1,stop_gained,p.Leu380Ter,ENST00000574590,;KANSL1,stop_gained,p.Leu380Ter,ENST00000432791,;KANSL1,stop_gained,p.Leu380Ter,ENST00000262419,;KANSL1,stop_gained,p.Leu380Ter,ENST00000572904,;KANSL1,5_prime_UTR_variant,,ENST00000393476,;KANSL1,downstream_gene_variant,,ENST00000576739,;KANSL1,downstream_gene_variant,,ENST00000574655,;KANSL1,downstream_gene_variant,,ENST00000571698,;KANSL1,non_coding_transcript_exon_variant,,ENST00000576248,;KANSL1,upstream_gene_variant,,ENST00000577114,;	T	ENSG00000120071	ENST00000262419	Transcript	stop_gained	1610	1139	380	L/*	tTg/tAg	.	.	.	-1	KANSL1	HGNC	24565	protein_coding	YES	CCDS11503.1	ENSP00000262419	KANL1_HUMAN	I3L243_HUMAN,I3L233_HUMAN	UPI0001AE66EA	.	.	.	2/15	.	hmmpanther:PTHR22443:SF14,hmmpanther:PTHR22443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCCAATTCT	.	5	ESCA
EPX	0	.	GRCh37	17	56271184	56271186	+	In_Frame_Del	DEL	CAA	CAA	-	rs750121261	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CAA	CAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462_464delCAA	p.Asn154del	p.N154del	ENST00000225371	4/13	60	31	29	37	37	0	EPX,inframe_deletion,p.Asn154del,ENST00000225371,;	-	ENSG00000121053	ENST00000225371	Transcript	inframe_deletion	566-568	456-458	152-153	CN/C	tgCAAc/tgc	rs750121261	.	.	1	EPX	HGNC	3423	protein_coding	YES	CCDS11602.1	ENSP00000225371	PERE_HUMAN	.	UPI0000131629	.	.	.	4/13	.	PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF49,Pfam_domain:PF03098,Superfamily_domains:SSF48113	.	.	.	.	.	.	.	-:0.0014	-:0.0006	.	.	.	.	.	.	.	MODERATE	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACGGTGCAACAACA	byFrequency	3	ESCA
SOX9	0	.	GRCh37	17	70117939	70117939	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.407G>A	p.Ser136Asn	p.S136N	ENST00000245479	1/3	109	48	61	74	74	0	SOX9,missense_variant,p.Ser136Asn,ENST00000245479,;SOX9-AS1,intron_variant,,ENST00000414600,;SOX9-AS1,upstream_gene_variant,,ENST00000533179,;SOX9-AS1,upstream_gene_variant,,ENST00000529667,;SOX9-AS1,upstream_gene_variant,,ENST00000440093,;SOX9-AS1,upstream_gene_variant,,ENST00000533232,;	A	ENSG00000125398	ENST00000245479	Transcript	missense_variant	779	407	136	S/N	aGc/aAc	.	.	.	1	SOX9	HGNC	11204	protein_coding	YES	CCDS11689.1	ENSP00000245479	SOX9_HUMAN	.	UPI00000009D8	.	deleterious(0)	benign(0.423)	1/3	.	Superfamily_domains:SSF47095,SMART_domains:SM00398,Pfam_domain:PF00505,Gene3D:1.10.30.10,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF212,PROSITE_profiles:PS50118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCAGCAAGA	.	5	ESCA
SLC39A11	0	.	GRCh37	17	70643714	70643714	+	3'UTR	SNP	G	G	A	rs193153239	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9C>T	.	.	ENST00000542342	10/10	93	68	24	54	54	0	SLC39A11,3_prime_UTR_variant,,ENST00000542342,;SLC39A11,3_prime_UTR_variant,,ENST00000255559,;SLC39A11,downstream_gene_variant,,ENST00000582769,;CTD-3010D24.3,downstream_gene_variant,,ENST00000584975,;SLC39A11,non_coding_transcript_exon_variant,,ENST00000579988,;	A	ENSG00000133195	ENST00000542342	Transcript	3_prime_UTR_variant	1127	.	.	.	.	rs193153239	.	.	-1	SLC39A11	HGNC	14463	protein_coding	YES	CCDS54160.1	ENSP00000445829	S39AB_HUMAN	J3QLA9_HUMAN,J3KT59_HUMAN,J3KRI1_HUMAN	UPI000020017B	.	.	.	10/10	.	.	T:0.0006	T:0.0015	T:0.0014	.	T:0	T:0	T:0	T:0.0002	T:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGCGTCTCA	byFrequency|byCluster|by1000G	5	ESCA
MRPL38	0	.	GRCh37	17	73900305	73900306	+	Intron	DEL	AC	AC	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AC	AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247+315_247+316delGT	.	.	ENST00000309352	.	94	74	20	54	54	0	MRPL38,splice_region_variant,,ENST00000409963,;MRPL38,intron_variant,,ENST00000309352,;RP11-552F3.10,downstream_gene_variant,,ENST00000587267,;MRPL38,intron_variant,,ENST00000585475,;MRPL38,upstream_gene_variant,,ENST00000477023,;MRPL38,downstream_gene_variant,,ENST00000410030,;MRPL38,upstream_gene_variant,,ENST00000480203,;MRPL38,upstream_gene_variant,,ENST00000588620,;MRPL38,splice_donor_variant,,ENST00000461602,;MRPL38,splice_region_variant,,ENST00000464758,;RP11-552F3.12,splice_region_variant,,ENST00000590947,;RP11-552F3.12,intron_variant,,ENST00000593156,;MRPL38,intron_variant,,ENST00000493383,;MRPL38,intron_variant,,ENST00000493104,;MRPL38,intron_variant,,ENST00000494179,;MRPL38,intron_variant,,ENST00000477736,;MRPL38,upstream_gene_variant,,ENST00000486101,;RP11-552F3.12,downstream_gene_variant,,ENST00000587556,;MRPL38,upstream_gene_variant,,ENST00000471434,;MRPL38,upstream_gene_variant,,ENST00000477371,;MRPL38,upstream_gene_variant,,ENST00000483393,;MRPL38,upstream_gene_variant,,ENST00000474548,;	-	ENSG00000204316	ENST00000309352	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MRPL38	HGNC	14033	protein_coding	YES	CCDS11733.2	ENSP00000308275	RM38_HUMAN	B3KN96_HUMAN,B2R894_HUMAN	UPI0000038D66	.	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTACCTACAGAGT	.	3	ESCA
PSMG2	0	.	GRCh37	18	12725672	12725673	+	3'UTR	DEL	TT	TT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*143_*144delTT	.	.	ENST00000317615	7/7	153	123	30	102	102	0	PSMG2,3_prime_UTR_variant,,ENST00000585331,;PSMG2,3_prime_UTR_variant,,ENST00000317615,;PSMG2,downstream_gene_variant,,ENST00000590217,;PSMG2,downstream_gene_variant,,ENST00000586445,;PSMG2,non_coding_transcript_exon_variant,,ENST00000588824,;PSMG2,downstream_gene_variant,,ENST00000586587,;	-	ENSG00000128789	ENST00000317615	Transcript	3_prime_UTR_variant	1619-1620	.	.	.	.	.	.	.	1	PSMG2	HGNC	24929	protein_coding	YES	CCDS11862.1	ENSP00000325919	PSMG2_HUMAN	.	UPI0000039F04	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTCTCTTTGCCA	.	3	ESCA
B4GALT6	0	.	GRCh37	18	29264323	29264325	+	In_Frame_Del	DEL	AGA	AGA	-	rs773722182	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AGA	AGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.65_67delTCT	p.Phe22del	p.F22del	ENST00000306851	1/9	65	42	22	80	80	0	B4GALT6,inframe_deletion,p.Phe22del,ENST00000383131,;B4GALT6,inframe_deletion,p.Phe22del,ENST00000237019,;B4GALT6,inframe_deletion,p.Phe22del,ENST00000306851,;B4GALT6,intron_variant,,ENST00000579372,;RP11-549B18.1,upstream_gene_variant,,ENST00000565978,;	-	ENSG00000118276	ENST00000306851	Transcript	inframe_deletion	362-364	65-67	22-23	FS/S	tTCTcc/tcc	rs773722182,COSM1388385	.	.	-1	B4GALT6	HGNC	929	protein_coding	YES	CCDS11900.1	ENSP00000306459	B4GT6_HUMAN	Q6NT00_HUMAN,J3QQY9_HUMAN	UPI0000126721	.	.	.	1/9	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS51257,hmmpanther:PTHR19300,hmmpanther:PTHR19300:SF29	.	.	.	.	.	.	.	-:0.0002	-:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	deletion	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAGGGAGAAGAAG	.	2	ESCA
PIK3C3	0	.	GRCh37	18	39550410	39550410	+	Missense_Mutation	SNP	G	G	A	rs376188539	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.521G>A	p.Arg174His	p.R174H	ENST00000262039	4/25	36	24	12	37	37	0	PIK3C3,missense_variant,p.Arg161His,ENST00000585528,;PIK3C3,missense_variant,p.Arg174His,ENST00000262039,;PIK3C3,missense_variant,p.Arg111His,ENST00000398870,;PIK3C3,missense_variant,p.Arg174His,ENST00000586545,;PIK3C3,missense_variant,p.Arg129His,ENST00000591011,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000589550,;	A	ENSG00000078142	ENST00000262039	Transcript	missense_variant	607	521	174	R/H	cGt/cAt	rs376188539,COSM460132	.	.	1	PIK3C3	HGNC	8974	protein_coding	YES	CCDS11920.1	ENSP00000262039	PK3C3_HUMAN	M0R2C5_HUMAN,M0R0W7_HUMAN,M0R0U1_HUMAN,M0R0G8_HUMAN,M0QZG0_HUMAN	UPI00000708CE	.	deleterious(0)	possibly_damaging(0.812)	4/25	.	PIRSF_domain:PIRSF000587,Gene3D:2.60.40.150,Pfam_domain:PF00792,hmmpanther:PTHR10048,PROSITE_profiles:PS51547	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGTCTTG	byCluster|by1000G	5	ESCA
TCF4	0	.	GRCh37	18	52893749	52893749	+	3'Flank	SNP	T	T	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000398339	.	46	25	20	38	38	0	TCF4,3_prime_UTR_variant,,ENST00000354452,;TCF4,3_prime_UTR_variant,,ENST00000356073,;TCF4,downstream_gene_variant,,ENST00000570177,;TCF4,downstream_gene_variant,,ENST00000568740,;TCF4,downstream_gene_variant,,ENST00000565018,;TCF4,downstream_gene_variant,,ENST00000566279,;TCF4,downstream_gene_variant,,ENST00000568673,;TCF4,downstream_gene_variant,,ENST00000537578,;TCF4,downstream_gene_variant,,ENST00000544241,;TCF4,downstream_gene_variant,,ENST00000398339,;TCF4,downstream_gene_variant,,ENST00000564403,;TCF4,downstream_gene_variant,,ENST00000570287,;TCF4,downstream_gene_variant,,ENST00000543082,;TCF4,downstream_gene_variant,,ENST00000566286,;TCF4,downstream_gene_variant,,ENST00000567880,;TCF4,downstream_gene_variant,,ENST00000564228,;TCF4,downstream_gene_variant,,ENST00000537856,;TCF4,downstream_gene_variant,,ENST00000540999,;TCF4,downstream_gene_variant,,ENST00000561831,;TCF4,downstream_gene_variant,,ENST00000564999,;TCF4,downstream_gene_variant,,ENST00000457482,;TCF4,downstream_gene_variant,,ENST00000561992,;TCF4,downstream_gene_variant,,ENST00000562680,;	C	ENSG00000196628	ENST00000398339	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1418	-1	TCF4	HGNC	11634	protein_coding	YES	CCDS58631.1	ENSP00000381382	.	K7ERJ0_HUMAN,H3BUQ3_HUMAN,H3BTM9_HUMAN,H3BTC3_HUMAN,H3BT24_HUMAN,H3BSX3_HUMAN,H3BRF7_HUMAN,H3BPG3_HUMAN,H3BP59_HUMAN,H3BNZ2_HUMAN,H3BNI2_HUMAN,H3BME8_HUMAN,H3BMC8_HUMAN,G0LNT8_HUMAN,G0LNT7_HUMAN,G0LNT4_HUMAN,G0LNT3_HUMAN,E9PH57_HUMAN	UPI000059D58C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAAGTATAAA	.	5	ESCA
SMARCA4	0	.	GRCh37	19	11123693	11123693	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2343G>T	p.Met781Ile	p.M781I	ENST00000429416	17/36	52	40	12	41	41	0	SMARCA4,missense_variant,p.Met781Ile,ENST00000450717,;SMARCA4,missense_variant,p.Met781Ile,ENST00000358026,;SMARCA4,missense_variant,p.Met781Ile,ENST00000413806,;SMARCA4,missense_variant,p.Met781Ile,ENST00000590574,;SMARCA4,missense_variant,p.Met781Ile,ENST00000444061,;SMARCA4,missense_variant,p.Met781Ile,ENST00000344626,;SMARCA4,missense_variant,p.Met781Ile,ENST00000541122,;SMARCA4,missense_variant,p.Met781Ile,ENST00000429416,;SMARCA4,missense_variant,p.Met781Ile,ENST00000589677,;CTC-215O4.4,intron_variant,,ENST00000587831,;RN7SL192P,downstream_gene_variant,,ENST00000584303,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;	T	ENSG00000127616	ENST00000429416	Transcript	missense_variant	2624	2343	781	M/I	atG/atT	COSM4074038,COSM4074037	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	probably_damaging(0.953)	17/36	.	Superfamily_domains:SSF52540,SMART_domains:SM00487,Pfam_domain:PF00176,Gene3D:3.40.50.300,hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGATGGGCCT	.	5	ESCA
CYP4F8	0	.	GRCh37	19	15730494	15730498	+	RNA	INS	GCTTG	GCTTG	ACTTGC	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	GCTTG	GCTTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2278_2282delGCTTGinsACTTGC	.	.	ENST00000589787	2/9	250	180	70	147	147	0	CYP4F8,splice_region_variant,,ENST00000441682,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000589019,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000443973,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000592615,;CYP4F8,intron_variant,,ENST00000325723,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000589787,;CYP4F8,upstream_gene_variant,,ENST00000585349,;CYP4F8,upstream_gene_variant,,ENST00000589927,;CYP4F8,downstream_gene_variant,,ENST00000590209,;CYP4F8,upstream_gene_variant,,ENST00000587680,;	ACTTGC	ENSG00000186526	ENST00000589787	Transcript	non_coding_transcript_exon_variant	2278-2282	.	.	.	.	.	.	.	1	CYP4F8	HGNC	2648	retained_intron	YES	.	.	.	.	.	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA*|PINDEL|VARSCANS*|SOMATICSNIPER*	ACCGTCGCTTGTGACG	.	4	ESCA
PLVAP	0	.	GRCh37	19	17476376	17476376	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.898G>T	p.Glu300Ter	p.E300*	ENST00000252590	3/6	54	38	15	36	36	0	PLVAP,stop_gained,p.Glu300Ter,ENST00000252590,;PLVAP,intron_variant,,ENST00000595816,;PLVAP,intron_variant,,ENST00000599426,;CTD-2278I10.1,downstream_gene_variant,,ENST00000597592,;	A	ENSG00000130300	ENST00000252590	Transcript	stop_gained	960	898	300	E/*	Gag/Tag	.	.	.	-1	PLVAP	HGNC	13635	protein_coding	YES	CCDS32952.1	ENSP00000252590	PLVAP_HUMAN	.	UPI000003ED36	.	.	.	3/6	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21687,hmmpanther:PTHR21687:SF2,Pfam_domain:PF06637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTCGCGGG	.	5	ESCA
REXO1	0	.	GRCh37	19	1828269	1828269	+	Silent	SNP	A	A	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.519T>G	p.%3D	p.P173P	ENST00000170168	2/16	40	19	21	36	36	0	REXO1,synonymous_variant,p.%3D,ENST00000170168,;CTB-31O20.4,downstream_gene_variant,,ENST00000587741,;CTB-31O20.4,downstream_gene_variant,,ENST00000593201,;REXO1,non_coding_transcript_exon_variant,,ENST00000587524,;CTB-31O20.4,downstream_gene_variant,,ENST00000590823,;	C	ENSG00000079313	ENST00000170168	Transcript	synonymous_variant	614	519	173	P	ccT/ccG	.	.	.	-1	REXO1	HGNC	24616	protein_coding	YES	CCDS32866.1	ENSP00000170168	REXO1_HUMAN	.	UPI0000202F63	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGCAGGGGC	.	5	ESCA
COMP	0	.	GRCh37	19	18899065	18899065	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.931G>A	p.Ala311Thr	p.A311T	ENST00000222271	9/19	62	24	38	40	40	0	COMP,missense_variant,p.Ala278Thr,ENST00000542601,;COMP,missense_variant,p.Ala258Thr,ENST00000425807,;COMP,missense_variant,p.Ala311Thr,ENST00000222271,;COMP,upstream_gene_variant,,ENST00000546510,;	T	ENSG00000105664	ENST00000222271	Transcript	missense_variant	976	931	311	A/T	Gcc/Acc	.	.	.	-1	COMP	HGNC	2227	protein_coding	YES	CCDS12385.1	ENSP00000222271	COMP_HUMAN	G3XAP6_HUMAN	UPI000013C7F6	.	deleterious(0.03)	possibly_damaging(0.701)	9/19	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51234,hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF81,Pfam_domain:PF02412,Gene3D:1ux6A01,Superfamily_domains:0044556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGCGTCTC	.	5	ESCA
CILP2	0	.	GRCh37	19	19653755	19653755	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951G>A	p.%3D	p.G317G	ENST00000291495	6/8	113	77	36	79	79	0	CILP2,synonymous_variant,p.%3D,ENST00000291495,;CILP2,synonymous_variant,p.%3D,ENST00000586018,;CILP2,downstream_gene_variant,,ENST00000588333,;	A	ENSG00000160161	ENST00000291495	Transcript	synonymous_variant	1036	951	317	G	ggG/ggA	.	.	.	1	CILP2	HGNC	24213	protein_coding	YES	CCDS12405.1	ENSP00000291495	CILP2_HUMAN	.	UPI000013E04D	.	.	.	6/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR15031:SF0,hmmpanther:PTHR15031,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGGACCCC	.	5	ESCA
ZNF93	0	.	GRCh37	19	20045728	20045729	+	3'UTR	DEL	CA	CA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*103_*104delCA	.	.	ENST00000343769	4/4	32	17	15	15	15	0	ZNF93,3_prime_UTR_variant,,ENST00000343769,;AC007204.1,downstream_gene_variant,,ENST00000595282,;ZNF93,downstream_gene_variant,,ENST00000588146,;ZNF93,downstream_gene_variant,,ENST00000592160,;AC007204.2,intron_variant,,ENST00000592245,;ZNF93,downstream_gene_variant,,ENST00000586021,;	-	ENSG00000184635	ENST00000343769	Transcript	3_prime_UTR_variant	1992-1993	.	.	.	.	.	.	.	1	ZNF93	HGNC	13169	protein_coding	YES	CCDS32973.1	ENSP00000342002	ZNF93_HUMAN	K7EPV7_HUMAN,B4DJ46_HUMAN	UPI00002263B9	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CCCAGGCACAGTC	.	2	ESCA
ZNF682	0	.	GRCh37	19	20117176	20117176	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1135A>T	p.Lys379Ter	p.K379*	ENST00000397165	4/4	79	36	43	43	43	0	ZNF682,stop_gained,p.Lys347Ter,ENST00000358523,;ZNF682,stop_gained,p.Lys379Ter,ENST00000397165,;ZNF682,stop_gained,p.Lys385Ter,ENST00000597972,;ZNF682,stop_gained,p.Lys347Ter,ENST00000397162,;ZNF682,stop_gained,p.Lys303Ter,ENST00000595736,;ZNF682,intron_variant,,ENST00000596019,;ZNF682,intron_variant,,ENST00000602079,;ZNF682,intron_variant,,ENST00000594127,;ZNF682,downstream_gene_variant,,ENST00000593468,;ZNF682,downstream_gene_variant,,ENST00000601100,;ZNF682,non_coding_transcript_exon_variant,,ENST00000601365,;ZNF682,downstream_gene_variant,,ENST00000595534,;	A	ENSG00000197124	ENST00000397165	Transcript	stop_gained	1296	1135	379	K/*	Aag/Tag	.	.	.	-1	ZNF682	HGNC	28857	protein_coding	YES	CCDS42533.1	ENSP00000380351	ZN682_HUMAN	M0R067_HUMAN	UPI000007275A	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF116,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTTAAAGA	.	5	ESCA
ZNF682	0	.	GRCh37	19	20117944	20117944	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.367T>C	p.Cys123Arg	p.C123R	ENST00000397165	4/4	21	11	10	15	15	0	ZNF682,missense_variant,p.Cys91Arg,ENST00000358523,;ZNF682,missense_variant,p.Cys123Arg,ENST00000397165,;ZNF682,missense_variant,p.Cys129Arg,ENST00000597972,;ZNF682,missense_variant,p.Cys91Arg,ENST00000397162,;ZNF682,missense_variant,p.Cys91Arg,ENST00000601100,;ZNF682,missense_variant,p.Cys47Arg,ENST00000595736,;ZNF682,splice_region_variant,,ENST00000594127,;ZNF682,3_prime_UTR_variant,,ENST00000593468,;ZNF682,intron_variant,,ENST00000596019,;ZNF682,intron_variant,,ENST00000602079,;ZNF682,non_coding_transcript_exon_variant,,ENST00000601365,;ZNF682,downstream_gene_variant,,ENST00000595534,;	G	ENSG00000197124	ENST00000397165	Transcript	missense_variant	528	367	123	C/R	Tgt/Cgt	.	.	.	-1	ZNF682	HGNC	28857	protein_coding	YES	CCDS42533.1	ENSP00000380351	ZN682_HUMAN	M0R067_HUMAN	UPI000007275A	.	deleterious(0.02)	benign(0.004)	4/4	.	hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF116	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTACACTCAC	.	5	ESCA
ZNF493	0	.	GRCh37	19	21606101	21606101	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.640G>A	p.Glu214Lys	p.E214K	ENST00000392288	4/4	82	57	24	50	50	0	ZNF493,missense_variant,p.Glu86Lys,ENST00000355504,;ZNF493,missense_variant,p.Glu214Lys,ENST00000392288,;ZNF493,downstream_gene_variant,,ENST00000596302,;CTD-2561J22.3,intron_variant,,ENST00000600810,;ZNF493,downstream_gene_variant,,ENST00000598152,;	A	ENSG00000196268	ENST00000392288	Transcript	missense_variant	749	640	214	E/K	Gaa/Aaa	.	.	.	1	ZNF493	HGNC	23708	protein_coding	YES	CCDS42536.1	ENSP00000376110	ZN493_HUMAN	.	UPI000022ABBF	.	tolerated(0.06)	benign(0.365)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF247,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R83Q|c.248G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAGAATGT	.	5	ESCA
KMT2B	0	.	GRCh37	19	36214349	36214349	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3003delA	p.Tyr1002ThrfsTer7	p.Y1002Tfs*7	ENST00000222270	7/37	58	45	13	36	36	0	KMT2B,frameshift_variant,p.Tyr1002ThrfsTer7,ENST00000420124,;KMT2B,frameshift_variant,p.Tyr1002ThrfsTer7,ENST00000222270,;KMT2B,downstream_gene_variant,,ENST00000341701,;KMT2B,splice_region_variant,,ENST00000607650,;KMT2B,downstream_gene_variant,,ENST00000606995,;	-	ENSG00000272333	ENST00000222270	Transcript	frameshift_variant	3003	3003	1001	V/X	gtA/gt	.	.	.	1	KMT2B	Uniprot_gn	15840	protein_coding	YES	CCDS46055.1	ENSP00000222270	KMT2B_HUMAN	.	UPI00001376B5	.	.	.	7/37	.	PROSITE_profiles:PS51058,hmmpanther:PTHR22884:SF280,hmmpanther:PTHR22884,Pfam_domain:PF02008,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCCAGATACCG	.	3	ESCA
ADCK4	0	.	GRCh37	19	41209522	41209522	+	Silent	SNP	G	G	A	rs55973839	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723C>T	p.%3D	p.P241P	ENST00000324464	9/15	37	25	11	18	18	0	ADCK4,synonymous_variant,p.%3D,ENST00000243583,;ADCK4,synonymous_variant,p.%3D,ENST00000595254,;ADCK4,synonymous_variant,p.%3D,ENST00000450541,;ADCK4,synonymous_variant,p.%3D,ENST00000324464,;ADCK4,downstream_gene_variant,,ENST00000594084,;ADCK4,downstream_gene_variant,,ENST00000594720,;ADCK4,downstream_gene_variant,,ENST00000600080,;ADCK4,downstream_gene_variant,,ENST00000594490,;ADCK4,downstream_gene_variant,,ENST00000601967,;RNU6-195P,downstream_gene_variant,,ENST00000411352,;ADCK4,missense_variant,p.Pro114Leu,ENST00000599643,;ADCK4,non_coding_transcript_exon_variant,,ENST00000596455,;ADCK4,upstream_gene_variant,,ENST00000593724,;ADCK4,downstream_gene_variant,,ENST00000601451,;ADCK4,downstream_gene_variant,,ENST00000601304,;ADCK4,downstream_gene_variant,,ENST00000593544,;	A	ENSG00000123815	ENST00000324464	Transcript	synonymous_variant	1025	723	241	P	ccC/ccT	rs55973839	.	.	-1	ADCK4	HGNC	19041	protein_coding	YES	CCDS12562.1	ENSP00000315118	ADCK4_HUMAN	M0R3F7_HUMAN,M0R340_HUMAN,M0R307_HUMAN,M0R011_HUMAN,M0R001_HUMAN,M0QZZ2_HUMAN	UPI0000071B0F	.	.	.	9/15	.	Superfamily_domains:SSF56112,Pfam_domain:PF03109,hmmpanther:PTHR10566:SF22,hmmpanther:PTHR10566	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCCGGGGTA	byCluster|by1000G	4	ESCA
CGB	0	.	GRCh37	19	49526391	49526391	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250T>A	p.Phe84Ile	p.F84I	ENST00000357383	3/3	48	39	8	35	34	0	CGB,missense_variant,p.Phe84Ile,ENST00000357383,;CTB-60B18.6,missense_variant,p.Phe70Ile,ENST00000591656,;CTB-60B18.6,downstream_gene_variant,,ENST00000604577,;CTB-60B18.10,upstream_gene_variant,,ENST00000600007,;NTF6A,downstream_gene_variant,,ENST00000591175,;	T	ENSG00000104827	ENST00000357383	Transcript	missense_variant	612	250	84	F/I	Ttc/Atc	.	.	.	-1	CGB	HGNC	1886	protein_coding	YES	CCDS12749.1	ENSP00000349954	CGB2_HUMAN,CGHB_HUMAN	K7ELM3_HUMAN,J3KNZ1_HUMAN	UPI0000035497	.	deleterious(0.01)	probably_damaging(0.999)	3/3	.	Superfamily_domains:SSF57501,SMART_domains:SM00068,Gene3D:2.10.90.10,Pfam_domain:PF00007,hmmpanther:PTHR11515,hmmpanther:PTHR11515:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTCGAAGCGCA	.	2	ESCA
ZNF765	0	.	GRCh37	19	53912609	53912609	+	3'UTR	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*229G>A	.	.	ENST00000396408	4/4	65	21	44	40	40	0	ZNF765,3_prime_UTR_variant,,ENST00000396408,;ZNF765,intron_variant,,ENST00000594030,;ZNF765,downstream_gene_variant,,ENST00000505866,;ZNF765,intron_variant,,ENST00000504146,;ZNF765,intron_variant,,ENST00000507045,;ZNF765,intron_variant,,ENST00000504235,;RPL39P36,upstream_gene_variant,,ENST00000490784,;	A	ENSG00000196417	ENST00000396408	Transcript	3_prime_UTR_variant	1918	.	.	.	.	.	.	.	1	ZNF765	HGNC	25092	protein_coding	YES	CCDS46171.1	ENSP00000379689	ZN765_HUMAN	D6RF03_HUMAN	UPI000040C508	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAGTGGAGAG	.	5	ESCA
RFPL4A	0	.	GRCh37	19	56273251	56273251	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85G>T	p.Ala29Ser	p.A29S	ENST00000434937	2/3	29	9	19	16	16	0	RFPL4A,missense_variant,p.Ala29Ser,ENST00000434937,;	T	ENSG00000223638	ENST00000434937	Transcript	missense_variant	256	85	29	A/S	Gcc/Tcc	.	.	.	1	RFPL4A	HGNC	16449	protein_coding	YES	CCDS46201.1	ENSP00000392936	RFPLA_HUMAN	.	UPI0000D6181F	.	tolerated(0.2)	benign(0.007)	2/3	.	PROSITE_profiles:PS50089,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF202,Gene3D:3.30.40.10,Pfam_domain:PF15227,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GATATGCCTGC	.	3	ESCA
ZSCAN18	0	.	GRCh37	19	58596563	58596563	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1190C>T	p.Ala397Val	p.A397V	ENST00000600404	7/7	23	14	8	15	15	0	ZSCAN18,missense_variant,p.Ala341Val,ENST00000240727,;ZSCAN18,missense_variant,p.Ala238Val,ENST00000433686,;ZSCAN18,missense_variant,p.Ala205Val,ENST00000421612,;ZSCAN18,missense_variant,p.Ala341Val,ENST00000601144,;ZSCAN18,missense_variant,p.Ala397Val,ENST00000600404,;ZSCAN18,downstream_gene_variant,,ENST00000600897,;ZSCAN18,downstream_gene_variant,,ENST00000595721,;ZSCAN18,downstream_gene_variant,,ENST00000600845,;ZSCAN18,downstream_gene_variant,,ENST00000600522,;ZNF135,3_prime_UTR_variant,,ENST00000515535,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000596372,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000598497,;ZSCAN18,downstream_gene_variant,,ENST00000595784,;ZSCAN18,downstream_gene_variant,,ENST00000594191,;ZSCAN18,downstream_gene_variant,,ENST00000600318,;	A	ENSG00000121413	ENST00000600404	Transcript	missense_variant	1220	1190	397	A/V	gCg/gTg	COSM2153813,COSM2153812	.	.	-1	ZSCAN18	HGNC	21037	protein_coding	YES	CCDS46214.1	ENSP00000470123	ZSC18_HUMAN	Q69Z04_HUMAN,M0R1U9_HUMAN	UPI00017A6DAF	.	tolerated(0.13)	benign(0.033)	7/7	.	hmmpanther:PTHR10032:SF6,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCCGCGTCC	.	5	ESCA
ELAVL1	0	.	GRCh37	19	8028463	8028464	+	Frame_Shift_Del	DEL	AT	AT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AT	AT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.884_885delAT	p.Tyr295Ter	p.Y295*	ENST00000407627	6/6	80	59	21	46	46	0	ELAVL1,frameshift_variant,p.Tyr322Ter,ENST00000351593,;ELAVL1,frameshift_variant,p.Tyr295Ter,ENST00000407627,;ELAVL1,frameshift_variant,p.Tyr295Ter,ENST00000596459,;ELAVL1,intron_variant,,ENST00000596154,;ELAVL1,downstream_gene_variant,,ENST00000593807,;CTD-3193O13.14,downstream_gene_variant,,ENST00000595107,;	-	ENSG00000066044	ENST00000407627	Transcript	frameshift_variant	1014-1015	884-885	295	Y/X	tAT/t	.	.	.	-1	ELAVL1	HGNC	3312	protein_coding	YES	CCDS12193.1	ENSP00000385269	ELAV1_HUMAN	.	UPI0000129E74	.	.	.	6/6	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011,hmmpanther:PTHR24011:SF228,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTTCATAGTTT	.	3	ESCA
MUC16	0	.	GRCh37	19	9084082	9084082	+	Missense_Mutation	SNP	G	G	T	rs758301768	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7733C>A	p.Pro2578Gln	p.P2578Q	ENST00000397910	1/84	144	101	43	90	90	0	MUC16,missense_variant,p.Pro2578Gln,ENST00000397910,;	T	ENSG00000181143	ENST00000397910	Transcript	missense_variant	7937	7733	2578	P/Q	cCa/cAa	rs758301768	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	unknown(0)	1/84	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTTGGGGTC	byFrequency	5	ESCA
ZNF562	0	.	GRCh37	19	9764000	9764000	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.906C>T	p.%3D	p.S302S	ENST00000448622	6/6	196	136	59	126	126	0	ZNF562,synonymous_variant,p.%3D,ENST00000453792,;ZNF562,synonymous_variant,p.%3D,ENST00000293648,;ZNF562,synonymous_variant,p.%3D,ENST00000448622,;ZNF562,synonymous_variant,p.%3D,ENST00000590155,;ZNF562,synonymous_variant,p.%3D,ENST00000537617,;ZNF562,synonymous_variant,p.%3D,ENST00000541032,;ZNF562,synonymous_variant,p.%3D,ENST00000453372,;ZNF562,downstream_gene_variant,,ENST00000587392,;ZNF562,downstream_gene_variant,,ENST00000588653,;ZNF562,downstream_gene_variant,,ENST00000589542,;ZNF562,3_prime_UTR_variant,,ENST00000585688,;	A	ENSG00000171466	ENST00000448622	Transcript	synonymous_variant	1069	906	302	S	tcC/tcT	.	.	.	-1	ZNF562	HGNC	25950	protein_coding	YES	CCDS45956.1	ENSP00000411784	ZN562_HUMAN	K7ELE4_HUMAN,B4E2P7_HUMAN	UPI000067CA26	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF7,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAGGATGA	.	5	ESCA
GPSM2	0	.	GRCh37	1	109472923	109472923	+	3'UTR	SNP	T	T	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*361T>G	.	.	ENST00000406462	16/16	28	18	10	22	22	0	GPSM2,3_prime_UTR_variant,,ENST00000406462,;CLCC1,3_prime_UTR_variant,,ENST00000415331,;CLCC1,3_prime_UTR_variant,,ENST00000369969,;GPSM2,3_prime_UTR_variant,,ENST00000264126,;CLCC1,3_prime_UTR_variant,,ENST00000369971,;CLCC1,3_prime_UTR_variant,,ENST00000369968,;CLCC1,3_prime_UTR_variant,,ENST00000369976,;CLCC1,3_prime_UTR_variant,,ENST00000356970,;AKNAD1,intron_variant,,ENST00000357393,;CLCC1,downstream_gene_variant,,ENST00000302500,;CLCC1,downstream_gene_variant,,ENST00000348264,;CLCC1,downstream_gene_variant,,ENST00000369970,;CLCC1,intron_variant,,ENST00000482889,;CLCC1,intron_variant,,ENST00000473062,;	G	ENSG00000121957	ENST00000406462	Transcript	3_prime_UTR_variant	3189	.	.	.	.	.	.	.	1	GPSM2	HGNC	29501	protein_coding	YES	CCDS792.2	ENSP00000385510	GPSM2_HUMAN	Q5T1N9_HUMAN,B4DIF1_HUMAN,B0QZD0_HUMAN,B0QZC9_HUMAN	UPI000013D4C2	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	GCGTTTTTTTA	.	3	ESCA
RBM15	0	.	GRCh37	1	110884085	110884085	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2058C>T	p.%3D	p.S686S	ENST00000369784	1/3	28	17	10	18	18	0	RBM15,synonymous_variant,p.%3D,ENST00000602849,;RBM15,synonymous_variant,p.%3D,ENST00000369784,;RBM15,synonymous_variant,p.%3D,ENST00000487146,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,;	T	ENSG00000162775	ENST00000369784	Transcript	synonymous_variant	2958	2058	686	S	agC/agT	.	.	.	1	RBM15	HGNC	14959	protein_coding	YES	CCDS822.1	ENSP00000358799	RBM15_HUMAN	.	UPI000013E1C5	.	.	.	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23189:SF43,hmmpanther:PTHR23189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AACAGCGACAA	.	4	ESCA
SETDB1	0	.	GRCh37	1	150936765	150936765	+	Silent	SNP	C	C	T	rs770434872	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3801C>T	p.%3D	p.Y1267Y	ENST00000271640	22/22	97	62	35	88	88	0	SETDB1,synonymous_variant,p.%3D,ENST00000271640,;SETDB1,synonymous_variant,p.%3D,ENST00000368969,;CERS2,3_prime_UTR_variant,,ENST00000561294,;SETDB1,downstream_gene_variant,,ENST00000498193,;CERS2,downstream_gene_variant,,ENST00000361419,;CERS2,downstream_gene_variant,,ENST00000560793,;CERS2,downstream_gene_variant,,ENST00000457392,;CERS2,downstream_gene_variant,,ENST00000368954,;CERS2,downstream_gene_variant,,ENST00000368949,;CERS2,downstream_gene_variant,,ENST00000558062,;CERS2,downstream_gene_variant,,ENST00000271688,;CERS2,downstream_gene_variant,,ENST00000421609,;RP11-316M1.12,upstream_gene_variant,,ENST00000560481,;RP11-316M1.12,upstream_gene_variant,,ENST00000561111,;SETDB1,downstream_gene_variant,,ENST00000459773,;CERS2,downstream_gene_variant,,ENST00000345896,;CERS2,non_coding_transcript_exon_variant,,ENST00000482825,;SETDB1,non_coding_transcript_exon_variant,,ENST00000497314,;SETDB1,downstream_gene_variant,,ENST00000528749,;CERS2,downstream_gene_variant,,ENST00000559020,;SETDB1,downstream_gene_variant,,ENST00000533529,;CERS2,downstream_gene_variant,,ENST00000559660,;CERS2,downstream_gene_variant,,ENST00000460664,;	T	ENSG00000143379	ENST00000271640	Transcript	synonymous_variant	3991	3801	1267	Y	taC/taT	rs770434872,COSM1583422,COSM895643	.	.	1	SETDB1	HGNC	10761	protein_coding	YES	CCDS44217.1	ENSP00000271640	SETB1_HUMAN	E9PS59_HUMAN,B0QZE6_HUMAN	UPI0000135897	.	.	.	22/22	.	PROSITE_profiles:PS51573,hmmpanther:PTHR22884:SF323,hmmpanther:PTHR22884,Gene3D:2.170.270.10,SMART_domains:SM00317,Superfamily_domains:SSF82199	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTACGAGGT	.	5	ESCA
TCHH	0	.	GRCh37	1	152085342	152085342	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351A>C	p.Glu117Asp	p.E117D	ENST00000368804	2/2	50	36	14	63	63	0	TCHH,missense_variant,p.Glu117Asp,ENST00000368804,;	G	ENSG00000159450	ENST00000368804	Transcript	missense_variant	351	351	117	E/D	gaA/gaC	.	.	.	-1	TCHH	HGNC	11791	protein_coding	YES	CCDS41396.1	ENSP00000357794	TRHY_HUMAN	Q5D861_HUMAN,A2RRS3_HUMAN	UPI0000458A5E	.	.	unknown(0)	2/2	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTCTTCTTC	.	5	ESCA
FLG	0	.	GRCh37	1	152278627	152278627	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8735C>G	p.Ser2912Cys	p.S2912C	ENST00000368799	3/3	133	94	38	109	108	0	FLG,missense_variant,p.Ser2912Cys,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	C	ENSG00000143631	ENST00000368799	Transcript	missense_variant	8771	8735	2912	S/C	tCc/tGc	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	possibly_damaging(0.869)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGGAAGCA	.	5	ESCA
INTS3	0	.	GRCh37	1	153745101	153745101	+	Intron	SNP	T	T	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2822-14T>C	.	.	ENST00000318967	.	60	57	3	61	61	0	INTS3,synonymous_variant,p.%3D,ENST00000456435,;INTS3,synonymous_variant,p.%3D,ENST00000512605,;INTS3,intron_variant,,ENST00000435409,;INTS3,intron_variant,,ENST00000318967,;SLC27A3,upstream_gene_variant,,ENST00000458027,;SLC27A3,upstream_gene_variant,,ENST00000271857,;SLC27A3,upstream_gene_variant,,ENST00000368661,;INTS3,intron_variant,,ENST00000476843,;SLC27A3,upstream_gene_variant,,ENST00000484014,;INTS3,non_coding_transcript_exon_variant,,ENST00000368669,;INTS3,intron_variant,,ENST00000503133,;INTS3,intron_variant,,ENST00000368670,;INTS3,intron_variant,,ENST00000481797,;SLC27A3,upstream_gene_variant,,ENST00000461269,;SLC27A3,upstream_gene_variant,,ENST00000483574,;SLC27A3,upstream_gene_variant,,ENST00000468403,;	C	ENSG00000143624	ENST00000318967	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	INTS3	HGNC	26153	protein_coding	YES	CCDS1052.1	ENSP00000318641	INT3_HUMAN	.	UPI0000231CA8	.	.	.	.	27/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCCTTTTCT	.	2	ESCA
MEX3A	0	.	GRCh37	1	156047372	156047372	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556G>A	p.Val186Met	p.V186M	ENST00000532414	2/2	30	17	13	44	44	0	MEX3A,missense_variant,p.Val186Met,ENST00000532414,;LMNA,upstream_gene_variant,,ENST00000368301,;AL355388.1,downstream_gene_variant,,ENST00000410679,;MEX3A,non_coding_transcript_exon_variant,,ENST00000442784,;LMNA,upstream_gene_variant,,ENST00000502751,;	T	ENSG00000254726	ENST00000532414	Transcript	missense_variant	556	556	186	V/M	Gtg/Atg	.	.	.	-1	MEX3A	HGNC	33482	protein_coding	YES	CCDS53377.1	ENSP00000432845	MEX3A_HUMAN	.	UPI0000ECD9C5	.	deleterious(0)	probably_damaging(0.999)	2/2	.	PROSITE_profiles:PS50084,hmmpanther:PTHR23285:SF2,hmmpanther:PTHR23285,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCACGTCCT	.	5	ESCA
VANGL2	0	.	GRCh37	1	160388867	160388867	+	Missense_Mutation	SNP	C	C	T	rs149889263	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268C>T	p.Arg90Cys	p.R90C	ENST00000368061	4/8	23	12	10	19	19	0	VANGL2,missense_variant,p.Arg90Cys,ENST00000368061,;VANGL2,upstream_gene_variant,,ENST00000483408,;	T	ENSG00000162738	ENST00000368061	Transcript	missense_variant	742	268	90	R/C	Cgc/Tgc	rs149889263	.	.	1	VANGL2	HGNC	15511	protein_coding	YES	CCDS30915.1	ENSP00000357040	VANG2_HUMAN	.	UPI00001C1D79	.	deleterious(0.01)	probably_damaging(0.916)	4/8	.	hmmpanther:PTHR20886,hmmpanther:PTHR20886:SF10,Pfam_domain:PF06638,PIRSF_domain:PIRSF007991	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACACGCATC	byCluster	5	ESCA
RC3H1	0	.	GRCh37	1	173907731	173907731	+	3'UTR	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*128G>T	.	.	ENST00000367696	20/20	57	29	27	30	30	0	RC3H1,3_prime_UTR_variant,,ENST00000367694,;RC3H1,3_prime_UTR_variant,,ENST00000258349,;RC3H1,3_prime_UTR_variant,,ENST00000367696,;RC3H1,non_coding_transcript_exon_variant,,ENST00000479099,;	A	ENSG00000135870	ENST00000367696	Transcript	3_prime_UTR_variant	3882	.	.	.	.	.	.	.	-1	RC3H1	HGNC	29434	protein_coding	YES	CCDS30940.1	ENSP00000356669	RC3H1_HUMAN	B9EGU6_HUMAN	UPI00001D7DA8	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGCCTCTG	.	5	ESCA
TNR	0	.	GRCh37	1	175365941	175365941	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.979G>T	p.Ala327Ser	p.A327S	ENST00000367674	5/23	30	18	11	32	32	0	TNR,missense_variant,p.Ala52Ser,ENST00000422274,;TNR,missense_variant,p.Ala327Ser,ENST00000367674,;TNR,missense_variant,p.Ala327Ser,ENST00000263525,;	A	ENSG00000116147	ENST00000367674	Transcript	missense_variant	1688	979	327	A/S	Gcc/Tcc	.	.	.	-1	TNR	HGNC	11953	protein_coding	YES	CCDS1318.1	ENSP00000356646	TENR_HUMAN	A1L306_HUMAN	UPI000013D41C	.	tolerated(0.99)	benign(0.064)	5/23	.	hmmpanther:PTHR19143:SF39,hmmpanther:PTHR19143,SMART_domains:SM00060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGGCAACTA	.	5	ESCA
PIK3C2B	0	.	GRCh37	1	204438822	204438822	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.109C>G	p.Leu37Val	p.L37V	ENST00000367187	3/34	60	34	25	70	70	0	PIK3C2B,missense_variant,p.Leu37Val,ENST00000429009,;PIK3C2B,missense_variant,p.Leu37Val,ENST00000367187,;PIK3C2B,missense_variant,p.Leu37Val,ENST00000424712,;PIK3C2B,missense_variant,p.Leu37Val,ENST00000415899,;PIK3C2B,upstream_gene_variant,,ENST00000367184,;	C	ENSG00000133056	ENST00000367187	Transcript	missense_variant	666	109	37	L/V	Ctg/Gtg	.	.	.	-1	PIK3C2B	HGNC	8972	protein_coding	YES	CCDS1446.1	ENSP00000356155	P3C2B_HUMAN	Q5SW98_HUMAN,Q5SW97_HUMAN,Q4LE65_HUMAN,A2RUF7_HUMAN	UPI00002056D1	.	deleterious_low_confidence(0)	probably_damaging(0.978)	3/34	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10048:SF30,hmmpanther:PTHR10048	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACAGGGCAT	.	5	ESCA
NFASC	0	.	GRCh37	1	204945917	204945917	+	Missense_Mutation	SNP	G	G	A	rs113197466	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1825G>A	p.Val609Met	p.V609M	ENST00000339876	16/30	39	24	15	25	25	0	NFASC,missense_variant,p.Val603Met,ENST00000404076,;NFASC,missense_variant,p.Val609Met,ENST00000403080,;NFASC,missense_variant,p.Val609Met,ENST00000367170,;NFASC,missense_variant,p.Val609Met,ENST00000338515,;NFASC,missense_variant,p.Val620Met,ENST00000360049,;NFASC,missense_variant,p.Val609Met,ENST00000401399,;NFASC,missense_variant,p.Val620Met,ENST00000404907,;NFASC,missense_variant,p.Val609Met,ENST00000367171,;NFASC,missense_variant,p.Val620Met,ENST00000539706,;NFASC,missense_variant,p.Val579Met,ENST00000367173,;NFASC,missense_variant,p.Val609Met,ENST00000339876,;NFASC,missense_variant,p.Val596Met,ENST00000430393,;NFASC,missense_variant,p.Val620Met,ENST00000513543,;NFASC,missense_variant,p.Val609Met,ENST00000367169,;NFASC,missense_variant,p.Val609Met,ENST00000367172,;NFASC,missense_variant,p.Val609Met,ENST00000338586,;NFASC,non_coding_transcript_exon_variant,,ENST00000404977,;NFASC,upstream_gene_variant,,ENST00000471392,;NFASC,3_prime_UTR_variant,,ENST00000504476,;NFASC,non_coding_transcript_exon_variant,,ENST00000512826,;NFASC,downstream_gene_variant,,ENST00000514644,;	A	ENSG00000163531	ENST00000339876	Transcript	missense_variant	2153	1825	609	V/M	Gtg/Atg	rs113197466	.	.	1	NFASC	HGNC	29866	protein_coding	YES	CCDS53460.1	ENSP00000344786	NFASC_HUMAN	D6RHX4_HUMAN	UPI0000237208	.	deleterious(0)	probably_damaging(0.991)	16/30	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF07679,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCACCGTGCTA	.	3	ESCA
MTR	0	.	GRCh37	1	236959022	236959022	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19G>T	p.Asp7Tyr	p.D7Y	ENST00000366577	1/33	76	45	31	88	88	0	MTR,missense_variant,p.Lys134Asn,ENST00000418145,;MTR,missense_variant,p.Asp7Tyr,ENST00000366577,;MTR,missense_variant,p.Asp7Tyr,ENST00000535889,;MTR,non_coding_transcript_exon_variant,,ENST00000463959,;	T	ENSG00000116984	ENST00000366577	Transcript	missense_variant	413	19	7	D/Y	Gac/Tac	.	.	.	1	MTR	HGNC	7468	protein_coding	YES	CCDS1614.1	ENSP00000355536	METH_HUMAN	.	UPI0000036BC4	.	deleterious_low_confidence(0.03)	benign(0.017)	1/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGACCTG	.	4	ESCA
EPHA10	0	.	GRCh37	1	38227500	38227500	+	Missense_Mutation	SNP	G	G	T	rs45567442	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427C>A	p.Arg143Ser	p.R143S	ENST00000373048	3/17	30	18	12	34	34	0	EPHA10,missense_variant,p.Arg143Ser,ENST00000319637,;EPHA10,missense_variant,p.Arg143Ser,ENST00000427468,;EPHA10,missense_variant,p.Arg143Ser,ENST00000373048,;	T	ENSG00000183317	ENST00000373048	Transcript	missense_variant	427	427	143	R/S	Cgc/Agc	rs45567442,COSM3489255,COSM3489254	.	.	-1	EPHA10	HGNC	19987	protein_coding	YES	CCDS41305.1	ENSP00000362139	EPHAA_HUMAN	.	UPI00001A41BD	.	tolerated(0.68)	benign(0.257)	3/17	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF267,hmmpanther:PTHR24416,Pfam_domain:PF01404,Gene3D:2.60.120.260,SMART_domains:SM00615,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	A:0.0002	A:0.0006	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R139H|c.416G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGCGGGGAC	byFrequency|byCluster	5	ESCA
GPBP1L1	0	.	GRCh37	1	46093254	46093256	+	3'UTR	DEL	AAT	AAT	-	rs770573008	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AAT	AAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*672_*674delATT	.	.	ENST00000355105	13/13	155	108	47	121	121	0	GPBP1L1,3_prime_UTR_variant,,ENST00000355105,;GPBP1L1,3_prime_UTR_variant,,ENST00000290795,;CCDC17,upstream_gene_variant,,ENST00000528266,;CCDC17,upstream_gene_variant,,ENST00000343901,;CCDC17,upstream_gene_variant,,ENST00000445048,;CCDC17,upstream_gene_variant,,ENST00000421127,;GPBP1L1,non_coding_transcript_exon_variant,,ENST00000479235,;GPBP1L1,downstream_gene_variant,,ENST00000468724,;GPBP1L1,downstream_gene_variant,,ENST00000487436,;GPBP1L1,downstream_gene_variant,,ENST00000467032,;CCDC17,upstream_gene_variant,,ENST00000464739,;CCDC17,upstream_gene_variant,,ENST00000525599,;CCDC17,upstream_gene_variant,,ENST00000482416,;CCDC17,upstream_gene_variant,,ENST00000372044,;CCDC17,upstream_gene_variant,,ENST00000491755,;CCDC17,upstream_gene_variant,,ENST00000479529,;	-	ENSG00000159592	ENST00000355105	Transcript	3_prime_UTR_variant	3458-3460	.	.	.	.	rs770573008	.	.	-1	GPBP1L1	HGNC	28843	protein_coding	YES	CCDS528.1	ENSP00000347224	GPBL1_HUMAN	.	UPI0000072AA4	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTGTAAATAATGT	byCluster	3	ESCA
ROR1	0	.	GRCh37	1	64643832	64643832	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2108A>G	p.Glu703Gly	p.E703G	ENST00000371079	9/9	21	15	5	25	25	0	ROR1,missense_variant,p.Glu154Gly,ENST00000545203,;ROR1,missense_variant,p.Glu703Gly,ENST00000371079,;	G	ENSG00000185483	ENST00000371079	Transcript	missense_variant	2483	2108	703	E/G	gAg/gGg	.	.	.	1	ROR1	HGNC	10256	protein_coding	YES	CCDS626.1	ENSP00000360120	ROR1_HUMAN	.	UPI00001AF82C	.	deleterious(0)	probably_damaging(0.982)	9/9	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF132,Pfam_domain:PF07714,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000624,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTGAGATGG	.	5	ESCA
LPHN2	0	.	GRCh37	1	82434986	82434986	+	Missense_Mutation	SNP	G	G	A	rs373312947	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2597G>A	p.Arg866Gln	p.R866Q	ENST00000319517	13/20	75	42	32	69	68	0	LPHN2,missense_variant,p.Arg879Gln,ENST00000370730,;LPHN2,missense_variant,p.Arg879Gln,ENST00000335786,;LPHN2,missense_variant,p.Arg866Gln,ENST00000370713,;LPHN2,missense_variant,p.Arg879Gln,ENST00000370717,;LPHN2,missense_variant,p.Arg879Gln,ENST00000370727,;LPHN2,missense_variant,p.Arg879Gln,ENST00000370725,;LPHN2,missense_variant,p.Arg866Gln,ENST00000319517,;LPHN2,missense_variant,p.Arg879Gln,ENST00000271029,;LPHN2,missense_variant,p.Arg879Gln,ENST00000370728,;LPHN2,missense_variant,p.Arg866Gln,ENST00000359929,;LPHN2,missense_variant,p.Arg866Gln,ENST00000370715,;LPHN2,missense_variant,p.Arg866Gln,ENST00000370723,;LPHN2,missense_variant,p.Arg804Gln,ENST00000370721,;LPHN2,missense_variant,p.Arg866Gln,ENST00000394879,;LPHN2,missense_variant,p.Arg747Gln,ENST00000449420,;LPHN2,intron_variant,,ENST00000469377,;LPHN2,downstream_gene_variant,,ENST00000468283,;	A	ENSG00000117114	ENST00000319517	Transcript	missense_variant	2813	2597	866	R/Q	cGa/cAa	rs373312947,COSM133949,COSM3492811,COSM3492810,COSM133950	.	.	1	LPHN2	HGNC	18582	protein_coding	YES	CCDS689.1	ENSP00000322270	LPHN2_HUMAN	.	UPI000005046B	.	deleterious(0)	probably_damaging(0.999)	13/20	.	PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF61,hmmpanther:PTHR12011,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR01444	.	.	.	.	.	.	.	A:0.0005	A:0	.	0,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R879Q|c.2636G>A|4,SITE|p.R866Q|c.2597G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACCGAAATA	byFrequency|byCluster	5	ESCA
ZNF337	0	.	GRCh37	20	25656456	25656457	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1467dupA	p.Cys490MetfsTer11	p.C490Mfs*11	ENST00000376436	4/4	69	63	6	57	57	0	ZNF337,frameshift_variant,p.Cys490MetfsTer11,ENST00000252979,;ZNF337,frameshift_variant,p.Cys458MetfsTer11,ENST00000538750,;ZNF337,frameshift_variant,p.Cys490MetfsTer11,ENST00000376436,;ZNF337-AS1,non_coding_transcript_exon_variant,,ENST00000414393,;ZNF337-AS1,intron_variant,,ENST00000439498,;ZNF337-AS1,intron_variant,,ENST00000455791,;ZNF337-AS1,downstream_gene_variant,,ENST00000428254,;ZNF337-AS1,downstream_gene_variant,,ENST00000421829,;ZNF337,downstream_gene_variant,,ENST00000481610,;	T	ENSG00000130684	ENST00000376436	Transcript	frameshift_variant	2007-2008	1467-1468	489-490	-/X	-/A	.	.	.	-1	ZNF337	HGNC	15809	protein_coding	YES	CCDS13174.1	ENSP00000365619	ZN337_HUMAN	B3KPK8_HUMAN	UPI000013C35E	.	.	.	4/4	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF00096,hmmpanther:PTHR24381:SF22,hmmpanther:PTHR24381,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCGACATCCAT	.	2	ESCA
PLAGL2	0	.	GRCh37	20	30777004	30777004	+	3'Flank	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000246229	.	28	16	12	33	33	0	PLAGL2,downstream_gene_variant,,ENST00000246229,;TSPY26P,non_coding_transcript_exon_variant,,ENST00000565928,;TSPY26P,downstream_gene_variant,,ENST00000476365,;TSPY26P,downstream_gene_variant,,ENST00000400643,;	A	ENSG00000126003	ENST00000246229	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3302	-1	PLAGL2	HGNC	9047	protein_coding	YES	CCDS13197.1	ENSP00000246229	PLAL2_HUMAN	.	UPI0000001C1D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCACTTAGC	.	5	ESCA
ASXL1	0	.	GRCh37	20	31022592	31022592	+	Nonsense_Mutation	SNP	C	C	T	rs373221034	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	13/13	87	52	35	61	60	0	ASXL1,stop_gained,p.Arg693Ter,ENST00000375687,;ASXL1,stop_gained,p.Arg688Ter,ENST00000306058,;ASXL1,downstream_gene_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000470145,;ASXL1,downstream_gene_variant,,ENST00000555564,;	T	ENSG00000171456	ENST00000375687	Transcript	stop_gained	2501	2077	693	R/*	Cga/Tga	rs373221034,COSM51388,COSM4169684	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	.	.	13/13	.	hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.R693*|c.2077C>T|14	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAGCGAACA	byFrequency|byCluster	5	ESCA
ATRN	0	.	GRCh37	20	3564710	3564710	+	Missense_Mutation	SNP	A	A	G	rs780239295	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2930A>G	p.Tyr977Cys	p.Y977C	ENST00000262919	17/29	63	44	19	50	50	0	ATRN,missense_variant,p.Tyr977Cys,ENST00000446916,;ATRN,missense_variant,p.Tyr977Cys,ENST00000262919,;	G	ENSG00000088812	ENST00000262919	Transcript	missense_variant	2998	2930	977	Y/C	tAt/tGt	rs780239295	.	.	1	ATRN	HGNC	885	protein_coding	YES	CCDS13053.1	ENSP00000262919	ATRN_HUMAN	.	UPI000012661C	.	tolerated(0.14)	possibly_damaging(0.827)	17/29	.	hmmpanther:PTHR10574:SF223,hmmpanther:PTHR10574,SMART_domains:SM00423	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGTATACGA	.	5	ESCA
RGS19	0	.	GRCh37	20	62705859	62705859	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188G>A	p.Arg63Gln	p.R63Q	ENST00000395042	4/6	36	22	13	30	30	0	RGS19,missense_variant,p.Arg63Gln,ENST00000395042,;RGS19,missense_variant,p.Arg63Gln,ENST00000332298,;TCEA2,downstream_gene_variant,,ENST00000343484,;TCEA2,downstream_gene_variant,,ENST00000361317,;TCEA2,downstream_gene_variant,,ENST00000440819,;TCEA2,downstream_gene_variant,,ENST00000395053,;TCEA2,downstream_gene_variant,,ENST00000458442,;TCEA2,downstream_gene_variant,,ENST00000339217,;RGS19,non_coding_transcript_exon_variant,,ENST00000493165,;TCEA2,downstream_gene_variant,,ENST00000475236,;TCEA2,downstream_gene_variant,,ENST00000465433,;TCEA2,downstream_gene_variant,,ENST00000487164,;TCEA2,downstream_gene_variant,,ENST00000477783,;TCEA2,downstream_gene_variant,,ENST00000461072,;TCEA2,downstream_gene_variant,,ENST00000465111,;RGS19,downstream_gene_variant,,ENST00000479996,;TCEA2,downstream_gene_variant,,ENST00000495168,;	T	ENSG00000171700	ENST00000395042	Transcript	missense_variant	455	188	63	R/Q	cGg/cAg	.	.	.	-1	RGS19	HGNC	13735	protein_coding	YES	CCDS13555.1	ENSP00000378483	RGS19_HUMAN	Q9H2T9_HUMAN,B4DP94_HUMAN	UPI0000133838	.	tolerated(0.41)	benign(0.001)	4/6	.	hmmpanther:PTHR10845:SF145,hmmpanther:PTHR10845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCCCGGGAG	.	5	ESCA
TIAM1	0	.	GRCh37	21	32502599	32502599	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3977G>T	p.Trp1326Leu	p.W1326L	ENST00000286827	26/29	30	20	9	33	33	0	TIAM1,missense_variant,p.Trp1326Leu,ENST00000286827,;TIAM1,missense_variant,p.Trp1266Leu,ENST00000541036,;TIAM1,upstream_gene_variant,,ENST00000423206,;TIAM1,non_coding_transcript_exon_variant,,ENST00000491927,;	A	ENSG00000156299	ENST00000286827	Transcript	missense_variant	4449	3977	1326	W/L	tGg/tTg	.	.	.	-1	TIAM1	HGNC	11805	protein_coding	YES	CCDS13609.1	ENSP00000286827	TIAM1_HUMAN	C9JMB5_HUMAN	UPI000013DE6F	.	tolerated(0.29)	benign(0.001)	26/29	.	Superfamily_domains:SSF50729,SMART_domains:SM00233,Gene3D:2.30.29.30,hmmpanther:PTHR22826:SF88,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCCCAGTCC	.	5	ESCA
BID	0	.	GRCh37	22	18220885	18220887	+	In_Frame_Del	DEL	CTT	CTT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610_612delAAG	p.Lys204del	p.K204del	ENST00000317361	5/6	51	35	16	39	39	0	BID,inframe_deletion,p.Lys158del,ENST00000551952,;BID,inframe_deletion,p.Lys62del,ENST00000399767,;BID,inframe_deletion,p.Lys204del,ENST00000317361,;BID,inframe_deletion,p.Lys158del,ENST00000399774,;BID,inframe_deletion,p.Lys62del,ENST00000399765,;BID,3_prime_UTR_variant,,ENST00000342111,;BID,non_coding_transcript_exon_variant,,ENST00000473439,;BID,downstream_gene_variant,,ENST00000552886,;BID,non_coding_transcript_exon_variant,,ENST00000550946,;BID,non_coding_transcript_exon_variant,,ENST00000494097,;	-	ENSG00000015475	ENST00000317361	Transcript	inframe_deletion	937-939	610-612	204	K/-	AAG/-	.	.	.	-1	BID	HGNC	1050	protein_coding	YES	CCDS13747.1	ENSP00000318822	BID_HUMAN	B2ZP79_HUMAN,B1PL87_HUMAN,A8ASI8_HUMAN	UPI00001D69F1	.	.	.	5/6	.	Low_complexity_(Seg):seg,Pfam_domain:PF06393,Gene3D:1.10.437.10,PIRSF_domain:PIRSF038018,Superfamily_domains:SSF56854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCCACCTTCTTGG	.	3	ESCA
MED15	0	.	GRCh37	22	20941429	20941430	+	3'UTR	DEL	CA	CA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*440_*441delCA	.	.	ENST00000263205	18/18	16	10	6	9	9	0	MED15,3_prime_UTR_variant,,ENST00000263205,;MED15,3_prime_UTR_variant,,ENST00000292733,;MED15,3_prime_UTR_variant,,ENST00000406969,;MED15,3_prime_UTR_variant,,ENST00000425759,;MED15,downstream_gene_variant,,ENST00000542773,;MED15,downstream_gene_variant,,ENST00000382974,;MED15,downstream_gene_variant,,ENST00000541476,;MED15,downstream_gene_variant,,ENST00000478831,;MED15,3_prime_UTR_variant,,ENST00000433831,;MED15,non_coding_transcript_exon_variant,,ENST00000489651,;MED15,non_coding_transcript_exon_variant,,ENST00000493216,;MED15,non_coding_transcript_exon_variant,,ENST00000473244,;MED15,non_coding_transcript_exon_variant,,ENST00000492381,;MED15,downstream_gene_variant,,ENST00000461076,;MED15,downstream_gene_variant,,ENST00000436496,;MED15,downstream_gene_variant,,ENST00000476187,;AC007050.18,downstream_gene_variant,,ENST00000508880,;	-	ENSG00000099917	ENST00000263205	Transcript	3_prime_UTR_variant	2874-2875	.	.	.	.	.	.	.	1	MED15	HGNC	14248	protein_coding	YES	CCDS33602.1	ENSP00000263205	MED15_HUMAN	Q69YK5_HUMAN,C9JZV5_HUMAN,C9JM58_HUMAN,C9JGN2_HUMAN,C9J1I1_HUMAN,B4DM43_HUMAN,B3KWF1_HUMAN	UPI00001313C4	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCTGGTCACAGTT	.	2	ESCA
HMOX1	0	.	GRCh37	22	35782733	35782733	+	Missense_Mutation	SNP	G	G	A	rs753863879	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200G>A	p.Arg67His	p.R67H	ENST00000216117	3/5	36	24	11	41	40	1	HMOX1,missense_variant,p.Arg67His,ENST00000216117,;HMOX1,missense_variant,p.Arg67His,ENST00000412893,;HMOX1,non_coding_transcript_exon_variant,,ENST00000481190,;HMOX1,upstream_gene_variant,,ENST00000494998,;	A	ENSG00000100292	ENST00000216117	Transcript	missense_variant	539	200	67	R/H	cGc/cAc	rs753863879	.	.	1	HMOX1	HGNC	5013	protein_coding	YES	CCDS13914.1	ENSP00000216117	HMOX1_HUMAN	Q6FH11_HUMAN,D2K7W4_HUMAN,B1AHA8_HUMAN	UPI000012CAA8	.	tolerated(0.11)	benign(0.036)	3/5	.	hmmpanther:PTHR10720,hmmpanther:PTHR10720:SF1,Pfam_domain:PF01126,Gene3D:1.20.910.10,PIRSF_domain:PIRSF000343,Superfamily_domains:SSF48613	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGAGCGCAACA	.	4	ESCA
C22orf26	0	.	GRCh37	22	46449699	46449699	+	Missense_Mutation	SNP	C	C	G	rs768072686	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.275G>C	p.Arg92Pro	p.R92P	ENST00000396008	1/2	22	12	9	14	14	0	C22orf26,missense_variant,p.Arg92Pro,ENST00000333761,;C22orf26,missense_variant,p.Arg92Pro,ENST00000396008,;FLJ27365,upstream_gene_variant,,ENST00000381051,;RP6-109B7.2,downstream_gene_variant,,ENST00000439423,;RP6-109B7.3,non_coding_transcript_exon_variant,,ENST00000416202,;RP6-109B7.3,upstream_gene_variant,,ENST00000445441,;RP6-109B7.5,downstream_gene_variant,,ENST00000608644,;RP6-109B7.3,upstream_gene_variant,,ENST00000451166,;	G	ENSG00000182257	ENST00000396008	Transcript	missense_variant	326	275	92	R/P	cGg/cCg	rs768072686	.	.	-1	C22orf26	HGNC	25606	protein_coding	YES	CCDS14071.1	ENSP00000379329	CV026_HUMAN	.	UPI0000071D52	.	tolerated_low_confidence(0.12)	possibly_damaging(0.655)	1/2	.	hmmpanther:PTHR16253:SF1,hmmpanther:PTHR16253,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCCGCCGAGCT	.	4	ESCA
PLXNB2	0	.	GRCh37	22	50728431	50728431	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583G>T	p.Glu195Ter	p.E195*	ENST00000449103	3/37	44	29	15	45	43	2	PLXNB2,stop_gained,p.Glu195Ter,ENST00000359337,;PLXNB2,stop_gained,p.Glu195Ter,ENST00000449103,;PLXNB2,stop_gained,p.Glu195Ter,ENST00000432455,;PLXNB2,upstream_gene_variant,,ENST00000411680,;PLXNB2,upstream_gene_variant,,ENST00000434732,;PLXNB2,downstream_gene_variant,,ENST00000425954,;PLXNB2,upstream_gene_variant,,ENST00000496720,;	A	ENSG00000196576	ENST00000449103	Transcript	stop_gained	724	583	195	E/*	Gag/Tag	.	.	.	-1	PLXNB2	HGNC	9104	protein_coding	YES	CCDS43035.1	ENSP00000409171	PLXB2_HUMAN	Q2TBE4_HUMAN,E2PU09_HUMAN,A6QRH1_HUMAN	UPI000003812D	.	.	.	3/37	.	PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF9,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GGCCTCCCTGC	.	2	ESCA
PPP6R2	0	.	GRCh37	22	50882340	50882340	+	Silent	SNP	G	G	A	rs377165944	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2547G>A	p.%3D	p.A849A	ENST00000395741	22/23	42	25	17	46	46	0	PPP6R2,synonymous_variant,p.%3D,ENST00000395741,;PPP6R2,synonymous_variant,p.%3D,ENST00000359139,;PPP6R2,synonymous_variant,p.%3D,ENST00000401672,;PPP6R2,synonymous_variant,p.%3D,ENST00000427222,;PPP6R2,synonymous_variant,p.%3D,ENST00000395744,;PPP6R2,synonymous_variant,p.%3D,ENST00000216061,;SBF1,downstream_gene_variant,,ENST00000418590,;SBF1,downstream_gene_variant,,ENST00000390679,;SBF1,downstream_gene_variant,,ENST00000348911,;SBF1,downstream_gene_variant,,ENST00000380817,;PPP6R2,non_coding_transcript_exon_variant,,ENST00000470046,;PPP6R2,downstream_gene_variant,,ENST00000473283,;SBF1,downstream_gene_variant,,ENST00000473724,;SBF1,downstream_gene_variant,,ENST00000470434,;	A	ENSG00000100239	ENST00000395741	Transcript	synonymous_variant	2922	2547	849	A	gcG/gcA	rs377165944,COSM4105126,COSM4105127	.	.	1	PPP6R2	HGNC	19253	protein_coding	YES	CCDS56235.1	ENSP00000379090	PP6R2_HUMAN	.	UPI0000453B02	.	.	.	22/23	.	Low_complexity_(Seg):seg	A:0.0008	A:0	A:0	.	A:0	A:0	A:0.0041	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGCGCCAAA	byFrequency|byCluster|by1000G	5	ESCA
SYCE3	0	.	GRCh37	22	50989685	50989685	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256C>G	p.Gln86Glu	p.Q86E	ENST00000406915	3/3	52	34	17	31	31	0	SYCE3,missense_variant,p.Gln86Glu,ENST00000402753,;SYCE3,missense_variant,p.Gln86Glu,ENST00000406915,;KLHDC7B,downstream_gene_variant,,ENST00000395676,;CTA-384D8.31,downstream_gene_variant,,ENST00000434237,;	C	ENSG00000217442	ENST00000406915	Transcript	missense_variant	304	256	86	Q/E	Caa/Gaa	.	.	.	-1	SYCE3	HGNC	35245	protein_coding	YES	CCDS46733.1	ENSP00000385480	SYCE3_HUMAN	.	UPI000015D427	.	tolerated_low_confidence(0.15)	benign(0.022)	3/3	.	Pfam_domain:PF15191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTGCTTGG	.	5	ESCA
ST6GAL2	0	.	GRCh37	2	107449090	107449090	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1074C>A	p.Asp358Glu	p.D358E	ENST00000409382	4/6	112	53	59	71	71	0	ST6GAL2,missense_variant,p.Asp358Glu,ENST00000409087,;ST6GAL2,missense_variant,p.Asp358Glu,ENST00000409382,;ST6GAL2,missense_variant,p.Asp358Glu,ENST00000361686,;ST6GAL2,upstream_gene_variant,,ENST00000361803,;AC016994.2,upstream_gene_variant,,ENST00000425419,;	T	ENSG00000144057	ENST00000409382	Transcript	missense_variant	1685	1074	358	D/E	gaC/gaA	.	.	.	-1	ST6GAL2	HGNC	10861	protein_coding	YES	CCDS2073.1	ENSP00000386942	SIAT2_HUMAN	C9JIK2_HUMAN,C4N9P8_HUMAN	UPI000007477B	.	.	benign(0.072)	4/6	.	hmmpanther:PTHR13713:SF48,hmmpanther:PTHR13713,Pfam_domain:PF00777,Superfamily_domains:SSF88713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTGTCAAT	.	5	ESCA
GCG	0	.	GRCh37	2	163008700	163008700	+	5'UTR	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-42C>A	.	.	ENST00000418842	1/6	87	47	39	69	69	0	GCG,5_prime_UTR_variant,,ENST00000418842,;GCG,5_prime_UTR_variant,,ENST00000375497,;GCG,non_coding_transcript_exon_variant,,ENST00000492913,;GCG,upstream_gene_variant,,ENST00000497568,;	T	ENSG00000115263	ENST00000418842	Transcript	5_prime_UTR_variant	214	.	.	.	.	.	.	.	-1	GCG	HGNC	4191	protein_coding	YES	CCDS46439.1	ENSP00000387662	GLUC_HUMAN	.	UPI000012B832	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGTGAAGAG	.	5	ESCA
FAP	0	.	GRCh37	2	163074549	163074549	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.709T>C	p.Ser237Pro	p.S237P	ENST00000188790	9/26	62	33	29	29	29	0	FAP,missense_variant,p.Ser212Pro,ENST00000443424,;FAP,missense_variant,p.Ser237Pro,ENST00000188790,;FAP,downstream_gene_variant,,ENST00000447386,;FAP,non_coding_transcript_exon_variant,,ENST00000480838,;FAP,downstream_gene_variant,,ENST00000450031,;	G	ENSG00000078098	ENST00000188790	Transcript	missense_variant	917	709	237	S/P	Tcc/Ccc	.	.	.	-1	FAP	HGNC	3590	protein_coding	YES	CCDS33311.1	ENSP00000188790	SEPR_HUMAN	C9J131_HUMAN	UPI00000012A2	.	tolerated(0.15)	probably_damaging(0.999)	9/26	.	hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF111,Gene3D:2.140.10.30,Pfam_domain:PF00930,Superfamily_domains:SSF82171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAGGAATAGG	.	5	ESCA
UNC80	0	.	GRCh37	2	210805968	210805968	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6472G>A	p.Asp2158Asn	p.D2158N	ENST00000439458	43/64	103	44	58	72	72	0	UNC80,missense_variant,p.Asp2158Asn,ENST00000439458,;UNC80,missense_variant,p.Asp2153Asn,ENST00000272845,;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,;	A	ENSG00000144406	ENST00000439458	Transcript	missense_variant	6552	6472	2158	D/N	Gac/Aac	.	.	.	1	UNC80	HGNC	26582	protein_coding	YES	CCDS46504.1	ENSP00000391088	UNC80_HUMAN	.	UPI00017E10C9	.	.	probably_damaging(0.994)	43/64	.	hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCGACACT	.	5	ESCA
BARD1	0	.	GRCh37	2	215646207	215646208	+	Frame_Shift_Del	DEL	TT	TT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.390_391delAA	p.Ser131PhefsTer3	p.S131Ffs*3	ENST00000260947	4/11	75	46	29	25	25	0	BARD1,frameshift_variant,p.Ser131PhefsTer3,ENST00000260947,;BARD1,5_prime_UTR_variant,,ENST00000449967,;BARD1,intron_variant,,ENST00000421162,;BARD1,non_coding_transcript_exon_variant,,ENST00000471787,;BARD1,3_prime_UTR_variant,,ENST00000455743,;	-	ENSG00000138376	ENST00000260947	Transcript	frameshift_variant	525-526	390-391	130-131	KS/KX	aaAAgt/aagt	.	.	.	-1	BARD1	HGNC	952	protein_coding	YES	CCDS2397.1	ENSP00000260947	BARD1_HUMAN	.	UPI000013D11D	.	.	.	4/11	.	hmmpanther:PTHR24171:SF8,hmmpanther:PTHR24171	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAAACTTTTCCT	.	3	ESCA
ZFAND2B	0	.	GRCh37	2	220071745	220071745	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36G>A	p.%3D	p.E12E	ENST00000289528	1/9	114	67	47	104	104	0	ZFAND2B,synonymous_variant,p.%3D,ENST00000409319,;ZFAND2B,synonymous_variant,p.%3D,ENST00000436556,;ZFAND2B,synonymous_variant,p.%3D,ENST00000409206,;ZFAND2B,synonymous_variant,p.%3D,ENST00000422255,;ZFAND2B,synonymous_variant,p.%3D,ENST00000444522,;ZFAND2B,synonymous_variant,p.%3D,ENST00000409217,;ZFAND2B,synonymous_variant,p.%3D,ENST00000409594,;ZFAND2B,synonymous_variant,p.%3D,ENST00000409412,;ZFAND2B,synonymous_variant,p.%3D,ENST00000409336,;ZFAND2B,synonymous_variant,p.%3D,ENST00000409097,;ZFAND2B,synonymous_variant,p.%3D,ENST00000289528,;ABCB6,downstream_gene_variant,,ENST00000265316,;ABCB6,downstream_gene_variant,,ENST00000439002,;ZFAND2B,upstream_gene_variant,,ENST00000425849,;ABCB6,downstream_gene_variant,,ENST00000295750,;ZFAND2B,non_coding_transcript_exon_variant,,ENST00000468301,;ZFAND2B,upstream_gene_variant,,ENST00000469596,;ZFAND2B,synonymous_variant,p.%3D,ENST00000448496,;ZFAND2B,non_coding_transcript_exon_variant,,ENST00000489197,;ZFAND2B,non_coding_transcript_exon_variant,,ENST00000486734,;ZFAND2B,non_coding_transcript_exon_variant,,ENST00000476713,;ZFAND2B,upstream_gene_variant,,ENST00000475533,;ABCB6,downstream_gene_variant,,ENST00000497882,;ABCB6,downstream_gene_variant,,ENST00000485773,;ABCB6,downstream_gene_variant,,ENST00000487380,;ABCB6,downstream_gene_variant,,ENST00000443805,;ZFAND2B,upstream_gene_variant,,ENST00000464902,;ABCB6,downstream_gene_variant,,ENST00000492543,;ATG9A,downstream_gene_variant,,ENST00000446716,;	A	ENSG00000158552	ENST00000289528	Transcript	synonymous_variant	231	36	12	E	gaG/gaA	.	.	.	1	ZFAND2B	HGNC	25206	protein_coding	YES	CCDS2435.1	ENSP00000289528	ZFN2B_HUMAN	C9J1R6_HUMAN,B8ZZ56_HUMAN	UPI000004CC12	.	.	.	1/9	.	Superfamily_domains:SSF118310,SMART_domains:SM00154,Gene3D:4.10.1110.10,Pfam_domain:PF01428,hmmpanther:PTHR14677:SF13,hmmpanther:PTHR14677,PROSITE_profiles:PS51039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGGAGCCGAG	.	5	ESCA
OBSL1	0	.	GRCh37	2	220432086	220432087	+	Frame_Shift_Del	DEL	CA	CA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1745_1746delTG	p.Val582AlafsTer5	p.V582Afs*5	ENST00000404537	4/21	51	42	9	26	26	0	OBSL1,frameshift_variant,p.Val582AlafsTer5,ENST00000603926,;OBSL1,frameshift_variant,p.Val169AlafsTer5,ENST00000289656,;OBSL1,frameshift_variant,p.Val582AlafsTer5,ENST00000373876,;OBSL1,frameshift_variant,p.Val582AlafsTer5,ENST00000265318,;OBSL1,frameshift_variant,p.Val582AlafsTer5,ENST00000404537,;OBSL1,frameshift_variant,p.Val582AlafsTer5,ENST00000373873,;INHA,upstream_gene_variant,,ENST00000243786,;OBSL1,upstream_gene_variant,,ENST00000604031,;INHA,upstream_gene_variant,,ENST00000489456,;OBSL1,downstream_gene_variant,,ENST00000465589,;OBSL1,downstream_gene_variant,,ENST00000491370,;OBSL1,non_coding_transcript_exon_variant,,ENST00000465149,;OBSL1,upstream_gene_variant,,ENST00000462385,;	-	ENSG00000124006	ENST00000404537	Transcript	frameshift_variant	1802-1803	1745-1746	582	V/X	gTG/g	.	.	.	-1	OBSL1	HGNC	29092	protein_coding	YES	CCDS46520.1	ENSP00000385636	OBSL1_HUMAN	.	UPI0000E07EA0	.	.	.	4/21	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19900,hmmpanther:PTHR19900:SF1,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	GGAGGGCACACAG	.	2	ESCA
UGT1A5	0	.	GRCh37	2	234622316	234622316	+	Missense_Mutation	SNP	G	G	T	rs200994534	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679G>T	p.Val227Phe	p.V227F	ENST00000373414	1/5	179	78	100	134	134	0	UGT1A8,missense_variant,p.Val227Phe,ENST00000608381,;UGT1A5,missense_variant,p.Val227Phe,ENST00000373414,;UGT1A10,intron_variant,,ENST00000373445,;UGT1A6,intron_variant,,ENST00000305139,;UGT1A6,intron_variant,,ENST00000373424,;UGT1A7,intron_variant,,ENST00000373426,;UGT1A8,intron_variant,,ENST00000609637,;UGT1A6,intron_variant,,ENST00000406651,;UGT1A10,intron_variant,,ENST00000344644,;UGT1A8,intron_variant,,ENST00000373450,;UGT1A9,intron_variant,,ENST00000354728,;AC114812.8,upstream_gene_variant,,ENST00000439336,;UGT1A6,intron_variant,,ENST00000480628,;UGT1A6,intron_variant,,ENST00000478062,;UGT1A6,intron_variant,,ENST00000446481,;UGT1A6,intron_variant,,ENST00000484784,;	T	ENSG00000240224	ENST00000373414	Transcript	missense_variant	679	679	227	V/F	Gtt/Ttt	rs200994534	.	.	1	UGT1A5	HGNC	12537	protein_coding	YES	CCDS33404.1	ENSP00000362513	UD15_HUMAN	Q5QTE5_HUMAN,Q5DSZ9_HUMAN	UPI0000001043	.	tolerated(0.67)	benign(0.003)	1/5	.	Superfamily_domains:SSF53756,Pfam_domain:PF00201,hmmpanther:PTHR11926:SF166,hmmpanther:PTHR11926	T:0.0004	T:0	T:0	.	T:0	T:0.002	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTGTTTCT	byFrequency|byCluster|by1000G	5	ESCA
RAMP1	0	.	GRCh37	2	238785925	238785925	+	Missense_Mutation	SNP	G	G	A	rs775366491	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.112G>A	p.Glu38Lys	p.E38K	ENST00000254661	2/3	63	27	36	47	47	0	RAMP1,missense_variant,p.Glu16Lys,ENST00000404910,;RAMP1,missense_variant,p.Glu16Lys,ENST00000409726,;RAMP1,missense_variant,p.Glu16Lys,ENST00000403885,;RAMP1,missense_variant,p.Glu38Lys,ENST00000254661,;	A	ENSG00000132329	ENST00000254661	Transcript	missense_variant	244	112	38	E/K	Gag/Aag	rs775366491,COSM1531272	.	.	1	RAMP1	HGNC	9843	protein_coding	YES	CCDS2522.1	ENSP00000254661	RAMP1_HUMAN	Q53T50_HUMAN,Q53SN3_HUMAN,E9PC20_HUMAN	UPI00001342FF	.	tolerated(0.09)	benign(0.059)	2/3	.	hmmpanther:PTHR14076,hmmpanther:PTHR14076:SF3,Pfam_domain:PF04901	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGGAGCTC	.	5	ESCA
KLHL30	0	.	GRCh37	2	239049972	239049972	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.577G>A	p.Glu193Lys	p.E193K	ENST00000409223	2/8	46	12	34	21	21	0	KLHL30,missense_variant,p.Glu175Lys,ENST00000305959,;KLHL30,missense_variant,p.Glu193Lys,ENST00000409223,;	A	ENSG00000168427	ENST00000409223	Transcript	missense_variant	684	577	193	E/K	Gag/Aag	.	.	.	1	KLHL30	HGNC	24770	protein_coding	YES	CCDS46555.2	ENSP00000386389	KLH30_HUMAN	J3KND5_HUMAN	UPI00001D7DA5	.	deleterious(0)	possibly_damaging(0.861)	2/8	.	hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF9,Pfam_domain:PF07707,SMART_domains:SM00875,PIRSF_domain:PIRSF037037	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCGGAGCAA	.	5	ESCA
GTF3C2	0	.	GRCh37	2	27564940	27564940	+	Missense_Mutation	SNP	G	G	A	rs770595929	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.730C>T	p.Arg244Trp	p.R244W	ENST00000359541	4/19	100	75	24	84	84	0	GTF3C2,missense_variant,p.Arg244Trp,ENST00000359541,;GTF3C2,missense_variant,p.Arg244Trp,ENST00000264720,;GTF3C2,downstream_gene_variant,,ENST00000423998,;GTF3C2,downstream_gene_variant,,ENST00000457748,;AC109828.1,non_coding_transcript_exon_variant,,ENST00000590383,;AC109828.1,downstream_gene_variant,,ENST00000416453,;AC109828.1,downstream_gene_variant,,ENST00000589853,;AC109828.1,downstream_gene_variant,,ENST00000585645,;AC109828.1,downstream_gene_variant,,ENST00000585326,;AC109828.1,downstream_gene_variant,,ENST00000588707,;AC109828.1,downstream_gene_variant,,ENST00000590754,;AC109828.1,downstream_gene_variant,,ENST00000587586,;AC109828.1,downstream_gene_variant,,ENST00000589232,;AC109828.1,downstream_gene_variant,,ENST00000592265,;AC109828.1,downstream_gene_variant,,ENST00000608473,;GTF3C2,upstream_gene_variant,,ENST00000470115,;GTF3C2,upstream_gene_variant,,ENST00000480989,;	A	ENSG00000115207	ENST00000359541	Transcript	missense_variant	1160	730	244	R/W	Cgg/Tgg	rs770595929,COSM1195377	.	.	-1	GTF3C2	HGNC	4665	protein_coding	YES	CCDS1749.1	ENSP00000352536	TF3C2_HUMAN	Q53SY8_HUMAN,Q53QN0_HUMAN,C9JQ12_HUMAN,C9JNH7_HUMAN	UPI0000074025	.	deleterious(0)	benign(0.427)	4/19	.	hmmpanther:PTHR15052,hmmpanther:PTHR15052:SF2	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCCGTGGAG	byFrequency	5	ESCA
SIX2	0	.	GRCh37	2	45232391	45232391	+	3'UTR	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*918G>T	.	.	ENST00000303077	2/2	25	22	3	21	21	0	SIX2,3_prime_UTR_variant,,ENST00000303077,;	A	ENSG00000170577	ENST00000303077	Transcript	3_prime_UTR_variant	2114	.	.	.	.	.	.	.	-1	SIX2	HGNC	10888	protein_coding	YES	CCDS1822.1	ENSP00000304502	SIX2_HUMAN	.	UPI00001359C0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCCCGAAGA	.	2	ESCA
EFEMP1	0	.	GRCh37	2	56103786	56103786	+	Missense_Mutation	SNP	C	C	G	rs768998905	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852G>C	p.Glu284Asp	p.E284D	ENST00000394555	7/11	95	70	24	62	62	0	EFEMP1,missense_variant,p.Glu284Asp,ENST00000355426,;EFEMP1,missense_variant,p.Glu284Asp,ENST00000394554,;EFEMP1,missense_variant,p.Glu284Asp,ENST00000394555,;EFEMP1,intron_variant,,ENST00000424836,;	G	ENSG00000115380	ENST00000394555	Transcript	missense_variant	1288	852	284	E/D	gaG/gaC	rs768998905	.	.	-1	EFEMP1	HGNC	3218	protein_coding	YES	CCDS1857.1	ENSP00000378058	FBLN3_HUMAN	Q580Q6_HUMAN,Q53TA7_HUMAN,C9JUM4_HUMAN,C9JQX7_HUMAN,C9JPZ9_HUMAN,C9J8S9_HUMAN,C9J4J8_HUMAN,C9J4H7_HUMAN	UPI0000000C12	.	deleterious(0.04)	probably_damaging(0.999)	7/11	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24048:SF68,hmmpanther:PTHR24048,PROSITE_patterns:PS01186,Pfam_domain:PF12662,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTAGCTCATA	byFrequency	5	ESCA
SLC9C1	0	.	GRCh37	3	111859919	111859919	+	3'UTR	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*200T>C	.	.	ENST00000305815	29/29	8	5	3	18	18	0	SLC9C1,3_prime_UTR_variant,,ENST00000487372,;SLC9C1,3_prime_UTR_variant,,ENST00000305815,;SLC9C1,downstream_gene_variant,,ENST00000471295,;	G	ENSG00000172139	ENST00000305815	Transcript	3_prime_UTR_variant	3987	.	.	.	.	.	.	.	-1	SLC9C1	HGNC	31401	protein_coding	YES	CCDS33817.1	ENSP00000306627	SL9C1_HUMAN	C9J3M6_HUMAN	UPI00002372C5	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTTAAATCA	.	2	ESCA
SLC9C1	0	.	GRCh37	3	111859922	111859922	+	3'UTR	SNP	T	T	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*197A>T	.	.	ENST00000305815	29/29	8	5	3	19	19	0	SLC9C1,3_prime_UTR_variant,,ENST00000487372,;SLC9C1,3_prime_UTR_variant,,ENST00000305815,;SLC9C1,downstream_gene_variant,,ENST00000471295,;	A	ENSG00000172139	ENST00000305815	Transcript	3_prime_UTR_variant	3984	.	.	.	.	.	.	.	-1	SLC9C1	HGNC	31401	protein_coding	YES	CCDS33817.1	ENSP00000306627	SL9C1_HUMAN	C9J3M6_HUMAN	UPI00002372C5	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTAAATCAAGG	.	2	ESCA
CNTN6	0	.	GRCh37	3	1414531	1414531	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1678G>C	p.Gly560Arg	p.G560R	ENST00000446702	14/23	86	59	26	97	97	0	CNTN6,missense_variant,p.Gly488Arg,ENST00000539053,;CNTN6,missense_variant,p.Gly560Arg,ENST00000446702,;CNTN6,missense_variant,p.Gly560Arg,ENST00000350110,;CNTN6,3_prime_UTR_variant,,ENST00000397479,;	C	ENSG00000134115	ENST00000446702	Transcript	missense_variant	2305	1678	560	G/R	Ggg/Cgg	.	.	.	1	CNTN6	HGNC	2176	protein_coding	YES	CCDS2557.1	ENSP00000407822	CNTN6_HUMAN	F5H752_HUMAN	UPI0000072430	.	deleterious(0)	probably_damaging(1)	14/23	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF52,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTGGGGAT	.	5	ESCA
ZIC4	0	.	GRCh37	3	147121925	147121925	+	5'UTR	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-40C>T	.	.	ENST00000525172	1/5	39	20	19	46	46	0	ZIC4,5_prime_UTR_variant,,ENST00000484399,;ZIC4,5_prime_UTR_variant,,ENST00000525172,;ZIC4,intron_variant,,ENST00000425731,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000383075,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000491672,;ZIC4,intron_variant,,ENST00000462748,;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,;	A	ENSG00000174963	ENST00000525172	Transcript	5_prime_UTR_variant	147	.	.	.	.	.	.	.	-1	ZIC4	HGNC	20393	protein_coding	YES	CCDS54652.1	ENSP00000435509	ZIC4_HUMAN	C9JZU7_HUMAN,C9JD04_HUMAN,C9J6T3_HUMAN,B3KPI4_HUMAN	UPI0001914D88	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGTCTGG	.	5	ESCA
TBL1XR1	0	.	GRCh37	3	176755901	176755901	+	Missense_Mutation	SNP	G	G	T	rs755923382	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1107C>A	p.Asp369Glu	p.D369E	ENST00000430069	12/16	64	46	17	48	48	0	TBL1XR1,missense_variant,p.Asp369Glu,ENST00000457928,;TBL1XR1,missense_variant,p.Asp369Glu,ENST00000430069,;	T	ENSG00000177565	ENST00000430069	Transcript	missense_variant	1367	1107	369	D/E	gaC/gaA	rs755923382	.	.	-1	TBL1XR1	HGNC	29529	protein_coding	YES	CCDS46961.1	ENSP00000405574	TBL1R_HUMAN	C9JY82_HUMAN,C9JTW8_HUMAN,C9JLJ1_HUMAN,C9JEC9_HUMAN,C9JCW4_HUMAN,C9JCK0_HUMAN,C9JBN1_HUMAN,C9J903_HUMAN,C9J7E1_HUMAN,C9J3H2_HUMAN,C9IYU9_HUMAN	UPI0000136A71	.	deleterious(0.02)	probably_damaging(0.985)	12/16	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22846:SF37,hmmpanther:PTHR22846,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTCGTCAGA	byFrequency	5	ESCA
PIK3CA	0	.	GRCh37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	10/21	80	56	23	58	58	0	PIK3CA,missense_variant,p.Glu545Lys,ENST00000263967,;PIK3CA,upstream_gene_variant,,ENST00000462255,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	1790	1633	545	E/K	Gag/Aag	rs104886003,COSM763,COSM27133,COSM125370,COSM295672	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	deleterious(0.02)	probably_damaging(0.959)	10/21	.	PROSITE_profiles:PS51545,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Pfam_domain:PF00613,Gene3D:1.25.40.70,SMART_domains:SM00145,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	not_provided,pathogenic	0,1,1,1,1	21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E545K|c.1633G>A|227,SITE|p.E545K|c.1633G>A|1153,CODON|p.T544N|c.1631C>A|3,BUFFER|p.E542Q|c.1624G>C|8,BUFFER|p.E542K|c.1624G>A|115,BUFFER|p.E542K|c.1624G>A|758,BUFFER|p.E542G|c.1625A>G|3,BUFFER|p.E542V|c.1625A>T|14,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.E542V|c.1625A>T|5,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.I543V|c.1627A>G|3,BUFFER|p.E545Q|c.1633G>C|30,BUFFER|p.E545Q|c.1633G>C|9,BUFFER|p.E545A|c.1634A>C|130,BUFFER|p.E545V|c.1634A>T|4,BUFFER|p.E545A|c.1634A>C|11,BUFFER|p.E545G|c.1634A>G|14,BUFFER|p.E545G|c.1634A>G|90,BUFFER|p.E545D|c.1635G>T|13,BUFFER|p.E545D|c.1635G>C|11,BUFFER|p.E545D|c.1635G>T|4,BUFFER|p.Q546K|c.1636C>A|119,BUFFER|p.Q546E|c.1636C>G|15,BUFFER|p.Q546K|c.1636C>A|18,BUFFER|p.Q546R|c.1637A>G|20,BUFFER|p.Q546P|c.1637A>C|22,BUFFER|p.Q546P|c.1637A>C|7,BUFFER|p.Q546L|c.1637A>T|8,BUFFER|p.Q546R|c.1637A>G|41,BUFFER|p.Q546H|c.1638G>T|7,BUFFER|p.E547K|c.1639G>A|11,BUFFER|p.E547G|c.1640A>G|5,BUFFER|p.E547G|c.1640A>G|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTGAGCAG	byCluster	5	ESCA
CPN2	0	.	GRCh37	3	194063288	194063288	+	Silent	SNP	C	C	T	rs74820225	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144G>A	p.%3D	p.P48P	ENST00000323830	2/2	30	14	16	23	23	0	CPN2,synonymous_variant,p.%3D,ENST00000323830,;CPN2,synonymous_variant,p.%3D,ENST00000429275,;	T	ENSG00000178772	ENST00000323830	Transcript	synonymous_variant	234	144	48	P	ccG/ccA	rs74820225	.	.	-1	CPN2	HGNC	2313	protein_coding	YES	CCDS33920.1	ENSP00000319464	CPN2_HUMAN	.	UPI0001AE76B7	.	.	.	2/2	.	Gene3D:3.80.10.10,SMART_domains:SM00013	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T51T|c.153G>A|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGCGGGAT	byCluster|by1000G	5	ESCA
KIF15	0	.	GRCh37	3	44879865	44879865	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3270G>T	p.Gln1090His	p.Q1090H	ENST00000326047	27/35	39	26	12	21	21	0	KIF15,missense_variant,p.Gln725His,ENST00000425755,;KIF15,missense_variant,p.Gln1090His,ENST00000326047,;KIF15,3_prime_UTR_variant,,ENST00000438321,;KIF15,3_prime_UTR_variant,,ENST00000453693,;KIF15,upstream_gene_variant,,ENST00000422209,;	T	ENSG00000163808	ENST00000326047	Transcript	missense_variant	3419	3270	1090	Q/H	caG/caT	.	.	.	1	KIF15	HGNC	17273	protein_coding	YES	CCDS33744.1	ENSP00000324020	KIF15_HUMAN	D6RCT7_HUMAN	UPI000006DB0E	.	deleterious(0.01)	possibly_damaging(0.728)	27/35	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF87,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCAGGAAGA	.	5	ESCA
SETD2	0	.	GRCh37	3	47165518	47165519	+	Frame_Shift_Del	DEL	GA	GA	-	.	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	GA	GA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607_608delTC	p.Ser203IlefsTer33	p.S203Ifs*33	ENST00000409792	3/21	73	56	17	42	42	0	SETD2,frameshift_variant,p.Ser203IlefsTer33,ENST00000409792,;SETD2,frameshift_variant,p.Ser159IlefsTer33,ENST00000412450,;SETD2,frameshift_variant,p.Ser75IlefsTer33,ENST00000330022,;SETD2,upstream_gene_variant,,ENST00000445387,;SETD2,upstream_gene_variant,,ENST00000431180,;	-	ENSG00000181555	ENST00000409792	Transcript	frameshift_variant	650-651	607-608	203	S/X	TCa/a	COSM1161887	.	.	-1	SETD2	HGNC	18420	protein_coding	YES	CCDS2749.2	ENSP00000386759	SETD2_HUMAN	C9JG86_HUMAN	UPI00017E10FB	.	.	.	3/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF294	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTGATGAGAGTG	.	3	ESCA
PFKFB4	0	.	GRCh37	3	48561150	48561150	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1206C>A	p.Phe402Leu	p.F402L	ENST00000232375	11/14	42	27	15	39	39	0	PFKFB4,missense_variant,p.Phe367Leu,ENST00000383734,;PFKFB4,missense_variant,p.Phe391Leu,ENST00000536104,;PFKFB4,missense_variant,p.Phe395Leu,ENST00000416568,;PFKFB4,missense_variant,p.Phe368Leu,ENST00000541519,;PFKFB4,missense_variant,p.Phe402Leu,ENST00000232375,;PFKFB4,downstream_gene_variant,,ENST00000545984,;PFKFB4,non_coding_transcript_exon_variant,,ENST00000490115,;PFKFB4,3_prime_UTR_variant,,ENST00000417753,;PFKFB4,3_prime_UTR_variant,,ENST00000445633,;PFKFB4,downstream_gene_variant,,ENST00000478516,;	T	ENSG00000114268	ENST00000232375	Transcript	missense_variant	1319	1206	402	F/L	ttC/ttA	.	.	.	-1	PFKFB4	HGNC	8875	protein_coding	YES	CCDS2771.1	ENSP00000232375	F264_HUMAN	Q64EX5_HUMAN,Q5XLC3_HUMAN,C9JX77_HUMAN	UPI0000000DCB	.	.	possibly_damaging(0.612)	11/14	.	hmmpanther:PTHR10606:SF14,hmmpanther:PTHR10606,Gene3D:3.40.50.1240,PIRSF_domain:PIRSF000709,Superfamily_domains:SSF53254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGAGGAAGTA	.	5	ESCA
DAG1	0	.	GRCh37	3	49570287	49570287	+	Silent	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2343C>A	p.%3D	p.G781G	ENST00000545947	6/6	24	14	9	25	25	0	DAG1,synonymous_variant,p.%3D,ENST00000308775,;DAG1,synonymous_variant,p.%3D,ENST00000545947,;DAG1,synonymous_variant,p.%3D,ENST00000539901,;DAG1,synonymous_variant,p.%3D,ENST00000515359,;DAG1,synonymous_variant,p.%3D,ENST00000541308,;DAG1,synonymous_variant,p.%3D,ENST00000538711,;DAG1,downstream_gene_variant,,ENST00000431960,;DAG1,downstream_gene_variant,,ENST00000421560,;DAG1,downstream_gene_variant,,ENST00000461492,;DAG1,downstream_gene_variant,,ENST00000479935,;	A	ENSG00000173402	ENST00000545947	Transcript	synonymous_variant	3065	2343	781	G	ggC/ggA	.	.	.	1	DAG1	HGNC	2666	protein_coding	YES	CCDS2799.1	ENSP00000442600	DAG1_HUMAN	C9JYS1_HUMAN,C9JY76_HUMAN,C9JQL4_HUMAN,C9JEN1_HUMAN,C9JEH2_HUMAN,C9J6Z6_HUMAN,C9J196_HUMAN	UPI000013EDAE	.	.	.	6/6	.	hmmpanther:PTHR21559,Pfam_domain:PF05454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGGCAAGCT	.	5	ESCA
PTPRG	0	.	GRCh37	3	62229529	62229529	+	Silent	SNP	T	T	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2424T>C	p.%3D	p.P808P	ENST00000474889	15/30	91	56	35	83	83	0	PTPRG,synonymous_variant,p.%3D,ENST00000295874,;PTPRG,synonymous_variant,p.%3D,ENST00000474889,;PTPRG,non_coding_transcript_exon_variant,,ENST00000475012,;PTPRG,non_coding_transcript_exon_variant,,ENST00000485215,;PTPRG,non_coding_transcript_exon_variant,,ENST00000468576,;	C	ENSG00000144724	ENST00000474889	Transcript	synonymous_variant	2801	2424	808	P	ccT/ccC	.	.	.	1	PTPRG	HGNC	9671	protein_coding	YES	CCDS2895.1	ENSP00000418112	PTPRG_HUMAN	O60420_HUMAN	UPI00001AEBFB	.	.	.	15/30	.	hmmpanther:PTHR19134:SF189,hmmpanther:PTHR19134	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCTCGAGT	.	5	ESCA
SMARCA5	0	.	GRCh37	4	144449849	144449849	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1071T>A	p.Asp357Glu	p.D357E	ENST00000283131	8/24	72	18	53	84	84	0	SMARCA5,missense_variant,p.Asp357Glu,ENST00000283131,;	A	ENSG00000153147	ENST00000283131	Transcript	missense_variant	1533	1071	357	D/E	gaT/gaA	.	.	.	1	SMARCA5	HGNC	11101	protein_coding	YES	CCDS3761.1	ENSP00000283131	SMCA5_HUMAN	Q4W5H1_HUMAN,Q4W5G3_HUMAN	UPI000006E693	.	tolerated(0.13)	benign(0.119)	8/24	.	PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF575,hmmpanther:PTHR10799,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGATGTGTT	.	5	ESCA
SORBS2	0	.	GRCh37	4	186544452	186544452	+	Missense_Mutation	SNP	G	G	A	rs201392254	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2419C>T	p.Arg807Trp	p.R807W	ENST00000355634	16/24	41	21	20	40	40	0	SORBS2,missense_variant,p.Arg611Trp,ENST00000418609,;SORBS2,missense_variant,p.Arg707Trp,ENST00000431808,;SORBS2,missense_variant,p.Arg707Trp,ENST00000284776,;SORBS2,missense_variant,p.Arg807Trp,ENST00000355634,;SORBS2,intron_variant,,ENST00000319454,;SORBS2,intron_variant,,ENST00000448662,;SORBS2,intron_variant,,ENST00000449407,;SORBS2,intron_variant,,ENST00000437304,;SORBS2,intron_variant,,ENST00000451974,;SORBS2,intron_variant,,ENST00000438278,;SORBS2,intron_variant,,ENST00000393528,;SORBS2,intron_variant,,ENST00000319471,;SORBS2,downstream_gene_variant,,ENST00000445625,;SORBS2,intron_variant,,ENST00000498125,;SORBS2,downstream_gene_variant,,ENST00000487836,;SORBS2,downstream_gene_variant,,ENST00000495932,;SORBS2,downstream_gene_variant,,ENST00000487184,;	A	ENSG00000154556	ENST00000355634	Transcript	missense_variant	3133	2419	807	R/W	Cgg/Tgg	rs201392254	.	.	-1	SORBS2	HGNC	24098	protein_coding	YES	CCDS59482.1	ENSP00000347852	SRBS2_HUMAN	C9JZ60_HUMAN,C9JN77_HUMAN,C9JL62_HUMAN,C9JI79_HUMAN,C9JDX2_HUMAN,C9JBR8_HUMAN,C9JBB0_HUMAN,C9J8E3_HUMAN,C9J7Q5_HUMAN,C9J4Z9_HUMAN,C9J4K2_HUMAN,C9J3W4_HUMAN,C9J372_HUMAN,C9IZT7_HUMAN,C9IZ89_HUMAN	UPI000198C7F0	.	deleterious(0)	probably_damaging(0.999)	16/24	.	hmmpanther:PTHR10661,hmmpanther:PTHR10661:SF122	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCGGAAAG	byCluster|by1000G	5	ESCA
KIAA1239	0	.	GRCh37	4	37448106	37448106	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4496C>T	p.Ser1499Leu	p.S1499L	ENST00000309447	7/7	51	33	18	30	30	0	KIAA1239,missense_variant,p.Ser1499Leu,ENST00000309447,;	T	ENSG00000174145	ENST00000309447	Transcript	missense_variant	5344	4496	1499	S/L	tCg/tTg	.	.	.	1	KIAA1239	HGNC	29229	protein_coding	YES	CCDS47040.1	ENSP00000309501	K1239_HUMAN	.	UPI00006C0875	.	deleterious(0.01)	benign(0.137)	7/7	.	hmmpanther:PTHR19857:SF18,hmmpanther:PTHR19857,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACATCGGCCG	.	5	ESCA
PDS5A	0	.	GRCh37	4	39905716	39905716	+	Silent	SNP	G	G	A	rs766740882	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1329C>T	p.%3D	p.V443V	ENST00000303538	12/33	56	38	17	54	54	0	PDS5A,synonymous_variant,p.%3D,ENST00000503396,;PDS5A,synonymous_variant,p.%3D,ENST00000513798,;PDS5A,synonymous_variant,p.%3D,ENST00000303538,;PDS5A,3_prime_UTR_variant,,ENST00000512643,;PDS5A,non_coding_transcript_exon_variant,,ENST00000503867,;	A	ENSG00000121892	ENST00000303538	Transcript	synonymous_variant	1869	1329	443	V	gtC/gtT	rs766740882	.	.	-1	PDS5A	HGNC	29088	protein_coding	YES	CCDS47045.1	ENSP00000303427	PDS5A_HUMAN	Q96DB6_HUMAN,G1UI16_HUMAN,B3KMN2_HUMAN	UPI00006C6A7E	.	.	.	12/33	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF2,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTGACTTT	byFrequency	5	ESCA
OTOP1	0	.	GRCh37	4	4199591	4199591	+	Missense_Mutation	SNP	C	C	T	rs200213513	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.970G>A	p.Ala324Thr	p.A324T	ENST00000296358	5/6	50	29	20	29	29	0	OTOP1,missense_variant,p.Ala324Thr,ENST00000296358,;	T	ENSG00000163982	ENST00000296358	Transcript	missense_variant	995	970	324	A/T	Gcc/Acc	rs200213513,COSM1055444	.	.	-1	OTOP1	HGNC	19656	protein_coding	YES	CCDS3372.1	ENSP00000296358	OTOP1_HUMAN	.	UPI0000186945	.	tolerated(0.38)	benign(0.129)	5/6	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR21522:SF19,hmmpanther:PTHR21522,Pfam_domain:PF03189	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGCGGCCA	byCluster	5	ESCA
PRDM8	0	.	GRCh37	4	81122551	81122551	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327C>T	p.%3D	p.N109N	ENST00000339711	9/10	54	27	26	41	41	0	PRDM8,synonymous_variant,p.%3D,ENST00000339711,;PRDM8,synonymous_variant,p.%3D,ENST00000415738,;PRDM8,synonymous_variant,p.%3D,ENST00000504452,;PRDM8,synonymous_variant,p.%3D,ENST00000515013,;PRDM8,downstream_gene_variant,,ENST00000511825,;PRDM8,downstream_gene_variant,,ENST00000509375,;PRDM8,downstream_gene_variant,,ENST00000508061,;PRDM8,downstream_gene_variant,,ENST00000507025,;PRDM8,downstream_gene_variant,,ENST00000506547,;PRDM8,downstream_gene_variant,,ENST00000508965,;	T	ENSG00000152784	ENST00000339711	Transcript	synonymous_variant	1558	327	109	N	aaC/aaT	.	.	.	1	PRDM8	HGNC	13993	protein_coding	YES	CCDS43243.1	ENSP00000339764	PRDM8_HUMAN	Q05CA1_HUMAN,E9PEH0_HUMAN	UPI0000422A1D	.	.	.	9/10	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50280,hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF0,Gene3D:2.170.270.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAACGGACA	.	5	ESCA
ARHGAP24	0	.	GRCh37	4	86893364	86893364	+	Intron	DEL	T	T	-	rs768312734,rs774031609	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732+49delT	.	.	ENST00000395184	.	29	18	11	10	10	0	ARHGAP24,3_prime_UTR_variant,,ENST00000503995,;ARHGAP24,intron_variant,,ENST00000264343,;ARHGAP24,intron_variant,,ENST00000514229,;ARHGAP24,intron_variant,,ENST00000395184,;ARHGAP24,intron_variant,,ENST00000395183,;ARHGAP24,downstream_gene_variant,,ENST00000509300,;ARHGAP24,intron_variant,,ENST00000502537,;	-	ENSG00000138639	ENST00000395184	Transcript	intron_variant	.	.	.	.	.	rs768312734,rs774031609	.	.	1	ARHGAP24	HGNC	25361	protein_coding	YES	CCDS34025.1	ENSP00000378611	RHG24_HUMAN	D6RHH1_HUMAN,B3KUX7_HUMAN	UPI00001AF1D9	.	.	.	.	6/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	TTGGAATTTTTT	byFrequency	2	ESCA
AFF1	0	.	GRCh37	4	88029432	88029432	+	Missense_Mutation	SNP	G	G	A	rs763409340	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1498G>A	p.Glu500Lys	p.E500K	ENST00000395146	11/21	57	39	18	50	50	0	AFF1,missense_variant,p.Glu184Lys,ENST00000514970,;AFF1,missense_variant,p.Glu493Lys,ENST00000307808,;AFF1,missense_variant,p.Glu500Lys,ENST00000395146,;AFF1,missense_variant,p.Glu131Lys,ENST00000511722,;AFF1,missense_variant,p.Glu131Lys,ENST00000544085,;AFF1,downstream_gene_variant,,ENST00000503477,;	A	ENSG00000172493	ENST00000395146	Transcript	missense_variant	1773	1498	500	E/K	Gaa/Aaa	rs763409340,COSM3826386	.	.	1	AFF1	HGNC	7135	protein_coding	YES	CCDS54775.1	ENSP00000378578	AFF1_HUMAN	Q712L1_HUMAN,F5GXF9_HUMAN,D6RIZ5_HUMAN,D6RAU0_HUMAN	UPI000013EC52	.	deleterious(0.04)	unknown(0)	11/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10528:SF14,hmmpanther:PTHR10528,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCGAAGAA	byFrequency|byCluster	5	ESCA
REEP5	0	.	GRCh37	5	112214410	112214411	+	3'UTR	DEL	CA	CA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*72_*73delTG	.	.	ENST00000379638	5/5	94	71	23	67	67	0	REEP5,3_prime_UTR_variant,,ENST00000545426,;REEP5,3_prime_UTR_variant,,ENST00000379638,;REEP5,3_prime_UTR_variant,,ENST00000513339,;REEP5,downstream_gene_variant,,ENST00000261482,;CTC-487M23.8,intron_variant,,ENST00000512790,;CTC-487M23.8,intron_variant,,ENST00000503445,;REEP5,3_prime_UTR_variant,,ENST00000511865,;REEP5,non_coding_transcript_exon_variant,,ENST00000497856,;CTC-487M23.8,intron_variant,,ENST00000509024,;CTC-487M23.8,intron_variant,,ENST00000506997,;	-	ENSG00000129625	ENST00000379638	Transcript	3_prime_UTR_variant	991-992	.	.	.	.	.	.	.	-1	REEP5	HGNC	30077	protein_coding	YES	CCDS4109.2	ENSP00000368959	REEP5_HUMAN	.	UPI00001B24A5	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTATACCACAGTC	.	3	ESCA
LMNB1	0	.	GRCh37	5	126113552	126113554	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355_357delCTC	p.Leu119del	p.L119del	ENST00000261366	1/11	18	9	8	21	21	0	LMNB1,inframe_deletion,p.Leu119del,ENST00000261366,;LMNB1,inframe_deletion,p.Leu119del,ENST00000395354,;RP11-434D11.4,upstream_gene_variant,,ENST00000509185,;LMNB1,non_coding_transcript_exon_variant,,ENST00000460265,;LMNB1,non_coding_transcript_exon_variant,,ENST00000463908,;LMNB1,non_coding_transcript_exon_variant,,ENST00000492190,;LMNB1,intron_variant,,ENST00000472034,;LMNB1,intron_variant,,ENST00000504788,;	-	ENSG00000113368	ENST00000261366	Transcript	inframe_deletion	713-715	352-354	118	L/-	CTC/-	.	.	.	1	LMNB1	HGNC	6637	protein_coding	YES	CCDS4140.1	ENSP00000261366	LMNB1_HUMAN	E9PBF6_HUMAN	UPI000013D170	.	.	.	1/11	.	Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	CAGCTGCTCCTCAA	.	2	ESCA
SLC4A9	0	.	GRCh37	5	139745542	139745545	+	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs751158024	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CTTA	CTTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1909_1912delACTT	p.Thr637LeufsTer11	p.T637Lfs*11	ENST00000230993	13/22	35	28	7	40	40	0	SLC4A9,frameshift_variant,p.Thr637LeufsTer11,ENST00000230993,;SLC4A9,frameshift_variant,p.Thr637LeufsTer11,ENST00000507527,;SLC4A9,frameshift_variant,p.Thr613LeufsTer11,ENST00000506757,;SLC4A9,frameshift_variant,p.Thr599LeufsTer11,ENST00000432095,;SLC4A9,intron_variant,,ENST00000506545,;CTC-329D1.2,downstream_gene_variant,,ENST00000507521,;SLC4A9,non_coding_transcript_exon_variant,,ENST00000514849,;	-	ENSG00000113073	ENST00000230993	Transcript	frameshift_variant	1941-1944	1906-1909	636-637	LT/X	CTTAct/ct	rs751158024	.	.	1	SLC4A9	HGNC	11035	protein_coding	YES	CCDS58973.1	ENSP00000230993	B3A4_HUMAN	.	UPI000018336F	.	.	.	13/22	.	Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834,hmmpanther:PTHR11453:SF33,hmmpanther:PTHR11453,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCTTCCTTACTTCT	.	3	ESCA
PCDHB18	0	.	GRCh37	5	140616411	140616411	+	RNA	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2474A>G	.	.	ENST00000526308	1/1	110	70	40	92	92	0	PCDHB18,non_coding_transcript_exon_variant,,ENST00000526308,;PCDHB18,non_coding_transcript_exon_variant,,ENST00000524813,;PCDHB19P,upstream_gene_variant,,ENST00000570871,;	G	ENSG00000146001	ENST00000526308	Transcript	non_coding_transcript_exon_variant	2474	.	.	.	.	.	.	.	1	PCDHB18	HGNC	14548	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAAATGAGT	.	5	ESCA
FAM105A	0	.	GRCh37	5	14610461	14610461	+	3'UTR	SNP	G	G	A	rs773078189	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*38G>A	.	.	ENST00000274217	8/8	40	22	17	23	23	0	FAM105A,3_prime_UTR_variant,,ENST00000274217,;FAM105A,non_coding_transcript_exon_variant,,ENST00000506258,;FAM105A,downstream_gene_variant,,ENST00000513825,;	A	ENSG00000145569	ENST00000274217	Transcript	3_prime_UTR_variant	1229	.	.	.	.	rs773078189	.	.	1	FAM105A	HGNC	25629	protein_coding	YES	CCDS3884.1	ENSP00000274217	F105A_HUMAN	.	UPI000004A036	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGACGGTGGT	.	5	ESCA
GPX3	0	.	GRCh37	5	150400197	150400197	+	5'UTR	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-19A>G	.	.	ENST00000388825	1/5	39	26	12	37	37	0	GPX3,5_prime_UTR_variant,,ENST00000517973,;GPX3,5_prime_UTR_variant,,ENST00000388825,;GPX3,5_prime_UTR_variant,,ENST00000521650,;GPX3,upstream_gene_variant,,ENST00000521632,;GPX3,non_coding_transcript_exon_variant,,ENST00000521722,;GPX3,5_prime_UTR_variant,,ENST00000519214,;	G	ENSG00000211445	ENST00000388825	Transcript	5_prime_UTR_variant	74	.	.	.	.	.	.	.	1	GPX3	HGNC	4555	protein_coding	YES	CCDS43389.1	ENSP00000373477	GPX3_HUMAN	Q6NXQ3_HUMAN	UPI0000161B50	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGAGTGTG	.	5	ESCA
G3BP1	0	.	GRCh37	5	151183521	151183521	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1270C>T	p.Arg424Ter	p.R424*	ENST00000394123	12/12	42	27	14	38	38	0	G3BP1,stop_gained,p.Arg424Ter,ENST00000356245,;G3BP1,stop_gained,p.Arg242Ter,ENST00000543466,;G3BP1,stop_gained,p.Arg424Ter,ENST00000394123,;G3BP1,3_prime_UTR_variant,,ENST00000522761,;G3BP1,3_prime_UTR_variant,,ENST00000520177,;	T	ENSG00000145907	ENST00000394123	Transcript	stop_gained	1415	1270	424	R/*	Cga/Tga	.	.	.	1	G3BP1	HGNC	30292	protein_coding	YES	CCDS4319.1	ENSP00000377681	G3BP1_HUMAN	Q5U0Q1_HUMAN,F5H4D6_HUMAN,E5RIF8_HUMAN,E5RI46_HUMAN,E5RH42_HUMAN	UPI0000030309	.	.	.	12/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10693:SF21,hmmpanther:PTHR10693,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGACGAGAT	.	5	ESCA
SLU7	0	.	GRCh37	5	159840617	159840617	+	Missense_Mutation	SNP	C	C	T	rs756490598	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.416G>A	p.Arg139Gln	p.R139Q	ENST00000297151	5/16	54	32	22	37	37	0	SLU7,missense_variant,p.Arg139Gln,ENST00000521826,;SLU7,missense_variant,p.Arg139Gln,ENST00000297151,;SLU7,downstream_gene_variant,,ENST00000520664,;SLU7,downstream_gene_variant,,ENST00000519349,;SLU7,downstream_gene_variant,,ENST00000521190,;SLU7,downstream_gene_variant,,ENST00000518268,;	T	ENSG00000164609	ENST00000297151	Transcript	missense_variant	804	416	139	R/Q	cGa/cAa	rs756490598	.	.	-1	SLU7	HGNC	16939	protein_coding	YES	CCDS4352.1	ENSP00000297151	SLU7_HUMAN	E5RK41_HUMAN,E5RGM7_HUMAN	UPI000013E3CE	.	deleterious(0.04)	benign(0.079)	5/16	.	hmmpanther:PTHR12942,hmmpanther:PTHR12942:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACTCGCCTA	byFrequency	5	ESCA
TENM2	0	.	GRCh37	5	167671581	167671581	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5677G>A	p.Val1893Met	p.V1893M	ENST00000518659	26/29	25	17	8	29	28	1	TENM2,missense_variant,p.Val1892Met,ENST00000545108,;TENM2,missense_variant,p.Val1654Met,ENST00000520394,;TENM2,missense_variant,p.Val1772Met,ENST00000519204,;TENM2,missense_variant,p.Val1893Met,ENST00000518659,;TENM2,missense_variant,p.Val1717Met,ENST00000403607,;TENM2,downstream_gene_variant,,ENST00000517941,;	A	ENSG00000145934	ENST00000518659	Transcript	missense_variant	5716	5677	1893	V/M	Gtg/Atg	COSM591212,COSM591211,COSM1143781,COSM3975392	.	.	1	TENM2	HGNC	29943	protein_coding	YES	.	ENSP00000429430	TEN2_HUMAN	G8BLJ6_HUMAN,G3CAS7_HUMAN	UPI0001C48FC2	.	deleterious(0)	probably_damaging(0.954)	26/29	.	hmmpanther:PTHR11219:SF8,hmmpanther:PTHR11219	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCAACGTGTCA	.	4	ESCA
TENM2	0	.	GRCh37	5	167691134	167691137	+	3'Flank	DEL	ATAA	ATAA	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	ATAA	ATAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000518659	.	52	37	15	37	37	0	TENM2,3_prime_UTR_variant,,ENST00000519204,;TENM2,3_prime_UTR_variant,,ENST00000403607,;TENM2,downstream_gene_variant,,ENST00000545108,;TENM2,downstream_gene_variant,,ENST00000520394,;TENM2,downstream_gene_variant,,ENST00000518659,;	-	ENSG00000145934	ENST00000518659	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1133	1	TENM2	HGNC	29943	protein_coding	YES	.	ENSP00000429430	TEN2_HUMAN	G8BLJ6_HUMAN,G3CAS7_HUMAN	UPI0001C48FC2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTATACATAAATAAA	.	3	ESCA
SLIT3	0	.	GRCh37	5	168690685	168690685	+	Intron	SNP	G	G	A	rs377746827	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198-12222C>T	.	.	ENST00000519560	.	48	31	16	64	64	0	SLIT3,intron_variant,,ENST00000332966,;SLIT3,intron_variant,,ENST00000519560,;SLIT3,intron_variant,,ENST00000404867,;MIR585,non_coding_transcript_exon_variant,,ENST00000384887,;SLIT3,intron_variant,,ENST00000521130,;SLIT3,intron_variant,,ENST00000518140,;	A	ENSG00000184347	ENST00000519560	Transcript	intron_variant	.	.	.	.	.	rs377746827	.	.	-1	SLIT3	HGNC	11087	protein_coding	YES	CCDS4369.1	ENSP00000430333	SLIT3_HUMAN	.	UPI00001B0229	.	.	.	.	1/35	.	.	.	.	.	.	.	.	C:0.0003	C:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATAGCACAG	byCluster	5	ESCA
SPDL1	0	.	GRCh37	5	169025515	169025515	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1068C>T	p.%3D	p.V356V	ENST00000265295	9/12	57	40	17	51	51	0	SPDL1,synonymous_variant,p.%3D,ENST00000505977,;SPDL1,synonymous_variant,p.%3D,ENST00000265295,;SPDL1,downstream_gene_variant,,ENST00000513941,;SPDL1,downstream_gene_variant,,ENST00000523518,;SPDL1,downstream_gene_variant,,ENST00000510751,;SPDL1,3_prime_UTR_variant,,ENST00000507232,;	T	ENSG00000040275	ENST00000265295	Transcript	synonymous_variant	1347	1068	356	V	gtC/gtT	.	.	.	1	SPDL1	HGNC	26010	protein_coding	YES	CCDS4370.1	ENSP00000265295	SPDLY_HUMAN	D6RIF7_HUMAN,D6RIB8_HUMAN,D6REZ1_HUMAN,D6RC83_HUMAN,D6R936_HUMAN	UPI000013D5F0	.	.	.	9/12	.	HAMAP:MF_03041,hmmpanther:PTHR32123:SF9,hmmpanther:PTHR32123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGTCGACTC	.	5	ESCA
NSD1	0	.	GRCh37	5	176696681	176696681	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5384delC	p.Pro1795GlnfsTer26	p.P1795Qfs*26	ENST00000439151	16/23	70	43	27	70	70	0	NSD1,frameshift_variant,p.Pro1692GlnfsTer26,ENST00000361032,;NSD1,frameshift_variant,p.Pro1526GlnfsTer26,ENST00000354179,;NSD1,frameshift_variant,p.Pro9GlnfsTer26,ENST00000503056,;NSD1,frameshift_variant,p.Pro9GlnfsTer?,ENST00000508029,;NSD1,frameshift_variant,p.Pro9GlnfsTer26,ENST00000515735,;NSD1,frameshift_variant,p.Pro1795GlnfsTer26,ENST00000439151,;NSD1,frameshift_variant,p.Pro1526GlnfsTer26,ENST00000347982,;NSD1,frameshift_variant,p.Pro9GlnfsTer?,ENST00000504457,;NSD1,downstream_gene_variant,,ENST00000505395,;CTD-2301A4.3,downstream_gene_variant,,ENST00000460608,;CTD-2301A4.5,upstream_gene_variant,,ENST00000604252,;	-	ENSG00000165671	ENST00000439151	Transcript	frameshift_variant	5427	5382	1794	F/X	ttC/tt	.	.	.	1	NSD1	HGNC	14234	protein_coding	YES	CCDS4412.1	ENSP00000395929	NSD1_HUMAN	Q9H6H8_HUMAN,Q9H6B5_HUMAN,Q96MN8_HUMAN,Q96DQ7_HUMAN,Q658U6_HUMAN,D6RE14_HUMAN,D6RBP3_HUMAN,D6RA90_HUMAN	UPI000006F9C6	.	.	.	16/23	.	PROSITE_profiles:PS50812,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312,Gene3D:2.30.30.160,Pfam_domain:PF00855,SMART_domains:SM00293,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAGTTCCCAGT	.	3	ESCA
DOK3	0	.	GRCh37	5	176935396	176935396	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382A>C	p.Ile128Leu	p.I128L	ENST00000357198	3/6	15	9	6	22	22	0	DOK3,missense_variant,p.Ile72Leu,ENST00000312943,;DOK3,missense_variant,p.Ile72Leu,ENST00000502885,;DOK3,missense_variant,p.Ile72Leu,ENST00000510898,;DOK3,missense_variant,p.Ile72Leu,ENST00000510380,;DOK3,missense_variant,p.Ile72Leu,ENST00000506493,;DOK3,missense_variant,p.Ile72Leu,ENST00000501403,;DOK3,missense_variant,p.Ile128Leu,ENST00000357198,;DOK3,intron_variant,,ENST00000377112,;DDX41,downstream_gene_variant,,ENST00000330503,;DOK3,downstream_gene_variant,,ENST00000510389,;DOK3,downstream_gene_variant,,ENST00000509310,;DDX41,downstream_gene_variant,,ENST00000507955,;RP11-1334A24.6,downstream_gene_variant,,ENST00000506025,;DOK3,non_coding_transcript_exon_variant,,ENST00000500323,;DDX41,downstream_gene_variant,,ENST00000507900,;DDX41,downstream_gene_variant,,ENST00000512027,;DDX41,downstream_gene_variant,,ENST00000512334,;DDX41,downstream_gene_variant,,ENST00000505081,;DOK3,downstream_gene_variant,,ENST00000512660,;DDX41,downstream_gene_variant,,ENST00000511040,;DDX41,downstream_gene_variant,,ENST00000504807,;DDX41,downstream_gene_variant,,ENST00000503078,;DOK3,downstream_gene_variant,,ENST00000502380,;	G	ENSG00000146094	ENST00000357198	Transcript	missense_variant	387	382	128	I/L	Atc/Ctc	.	.	.	-1	DOK3	HGNC	24583	protein_coding	YES	CCDS4426.1	ENSP00000349727	DOK3_HUMAN	D6RC22_HUMAN,D6RAZ9_HUMAN,D6RAV2_HUMAN,D6RAM3_HUMAN,D6R977_HUMAN,D6R951_HUMAN	UPI000013DA2C	.	deleterious(0.01)	possibly_damaging(0.591)	3/6	.	hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF42,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GCGGATGACCC	.	4	ESCA
PRDM9	0	.	GRCh37	5	23526880	23526880	+	Silent	SNP	T	T	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1683T>C	p.%3D	p.F561F	ENST00000296682	11/11	91	59	31	104	104	0	PRDM9,synonymous_variant,p.%3D,ENST00000296682,;	C	ENSG00000164256	ENST00000296682	Transcript	synonymous_variant	1865	1683	561	F	ttT/ttC	.	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	.	.	11/11	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTTAGCTG	.	5	ESCA
UGT3A2	0	.	GRCh37	5	36066850	36066855	+	Frame_Shift_Del	DEL	GAGAAG	GAGAAG	AA	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	GAGAAG	GAGAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37_42delCTTCTCinsTT	p.Leu13PhefsTer13	p.L13Ffs*13	ENST00000282507	1/7	74	53	21	76	76	0	UGT3A2,frameshift_variant,p.Leu13PhefsTer13,ENST00000513300,;UGT3A2,frameshift_variant,p.Leu13PhefsTer13,ENST00000515131,;UGT3A2,frameshift_variant,p.Leu13PhefsTer13,ENST00000282507,;UGT3A2,5_prime_UTR_variant,,ENST00000545528,;UGT3A2,intron_variant,,ENST00000504954,;UGT3A2,frameshift_variant,p.Leu13PhefsTer13,ENST00000504685,;	AA	ENSG00000168671	ENST00000282507	Transcript	frameshift_variant	139-144	37-42	13-14	LL/X	CTTCTC/TT	.	.	.	-1	UGT3A2	HGNC	27266	protein_coding	YES	CCDS3914.1	ENSP00000282507	UD3A2_HUMAN	F5H377_HUMAN,D6RDU1_HUMAN	UPI000013DCE8	.	.	.	1/7	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*	CCCAGGGAGAAGGAAGC	.	4	ESCA
FCHO2	0	.	GRCh37	5	72354318	72354320	+	In_Frame_Del	DEL	TCT	TCT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	TCT	TCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1317_1319delTTC	p.Ser442del	p.S442del	ENST00000430046	17/26	198	113	85	113	113	0	FCHO2,inframe_deletion,p.Ser409del,ENST00000512348,;FCHO2,inframe_deletion,p.Ser442del,ENST00000341845,;FCHO2,inframe_deletion,p.Ser442del,ENST00000430046,;FCHO2,non_coding_transcript_exon_variant,,ENST00000508431,;	-	ENSG00000157107	ENST00000430046	Transcript	inframe_deletion	1428-1430	1312-1314	438	S/-	TCT/-	.	.	.	1	FCHO2	HGNC	25180	protein_coding	YES	CCDS47230.1	ENSP00000393776	FCHO2_HUMAN	B4DEU7_HUMAN	UPI000019971A	.	.	.	17/26	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATTCATCTTCTTC	.	3	ESCA
SIM1	0	.	GRCh37	6	100838305	100838305	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2233C>A	p.Leu745Met	p.L745M	ENST00000369208	12/12	93	63	30	83	83	0	SIM1,missense_variant,p.Leu745Met,ENST00000369208,;SIM1,missense_variant,p.Leu745Met,ENST00000262901,;SIM1,downstream_gene_variant,,ENST00000505753,;	T	ENSG00000112246	ENST00000369208	Transcript	missense_variant	3016	2233	745	L/M	Ctg/Atg	.	.	.	-1	SIM1	HGNC	10882	protein_coding	YES	CCDS5045.1	ENSP00000358210	SIM1_HUMAN	.	UPI000013D355	.	tolerated_low_confidence(0.18)	benign(0.022)	12/12	.	PROSITE_profiles:PS51302,hmmpanther:PTHR23043:SF22,hmmpanther:PTHR23043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCAGATGGG	.	5	ESCA
FOXC1	0	.	GRCh37	6	1610969	1610971	+	In_Frame_Del	DEL	AAG	AAG	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AAG	AAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.293_295delAGA	p.Lys98del	p.K98del	ENST00000380874	1/1	74	32	42	124	124	0	FOXC1,inframe_deletion,p.Lys98del,ENST00000380874,;	-	ENSG00000054598	ENST00000380874	Transcript	inframe_deletion	289-291	289-291	97	K/-	AAG/-	.	.	.	1	FOXC1	HGNC	3800	protein_coding	YES	CCDS4473.1	ENSP00000370256	FOXC1_HUMAN	C6KMR8_HUMAN	UPI000012ADC5	.	.	.	1/1	.	PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF69,hmmpanther:PTHR11829,Gene3D:1.10.10.10,Pfam_domain:PF00250,SMART_domains:SM00339,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCGGACAAGAAGAT	.	3	ESCA
NUP153	0	.	GRCh37	6	17616215	17616217	+	3'UTR	DEL	AAG	AAG	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AAG	AAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*111_*113delCTT	.	.	ENST00000262077	22/22	72	46	26	63	63	0	NUP153,3_prime_UTR_variant,,ENST00000262077,;NUP153,downstream_gene_variant,,ENST00000537253,;FAM8A1,downstream_gene_variant,,ENST00000259963,;RNU6-190P,upstream_gene_variant,,ENST00000384154,;	-	ENSG00000124789	ENST00000262077	Transcript	3_prime_UTR_variant	4539-4541	.	.	.	.	.	.	.	-1	NUP153	HGNC	8062	protein_coding	YES	CCDS4541.1	ENSP00000262077	NU153_HUMAN	.	UPI000013D251	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAATTAAAGAAGTC	.	3	ESCA
HIST1H1E	0	.	GRCh37	6	26156678	26156680	+	In_Frame_Del	DEL	GAA	GAA	-	rs545095988	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	GAA	GAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.67_69delAAG	p.Lys23del	p.K23del	ENST00000304218	1/1	38	21	17	50	50	0	HIST1H1E,inframe_deletion,p.Lys23del,ENST00000304218,;HIST1H2BD,upstream_gene_variant,,ENST00000289316,;HIST1H2BD,upstream_gene_variant,,ENST00000377777,;	-	ENSG00000168298	ENST00000304218	Transcript	inframe_deletion	120-122	60-62	20-21	VK/V	gtGAAg/gtg	rs545095988,COSM1442613	.	.	1	HIST1H1E	HGNC	4718	protein_coding	YES	CCDS4586.1	ENSP00000307705	H14_HUMAN	A3R0T8_HUMAN	UPI0000000DB9	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11467:SF16,hmmpanther:PTHR11467	-:0.0006	-:0	-:0.0043	.	-:0	-:0	-:0	-:0.0007	-:0	.	0,1	.	.	.	.	.	MODERATE	.	deletion	.	7	0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.K23delK|c.60_62delGAA|3	INDELOCATOR|VARSCANI	TCCCGTGAAGAAGA	byFrequency|byCluster|by1000G	2	ESCA
HIST1H2BF	0	.	GRCh37	6	26199784	26199784	+	5'UTR	SNP	A	A	T	rs768466925,rs778914522	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3A>T	.	.	ENST00000359985	1/1	96	63	32	74	74	0	HIST1H2BF,5_prime_UTR_variant,,ENST00000359985,;HIST1H3D,upstream_gene_variant,,ENST00000377831,;HIST1H2AD,upstream_gene_variant,,ENST00000341023,;HIST1H3D,upstream_gene_variant,,ENST00000356476,;HIST1H1PS1,downstream_gene_variant,,ENST00000404269,;RP1-34B20.4,upstream_gene_variant,,ENST00000405418,;	T	ENSG00000197846	ENST00000359985	Transcript	5_prime_UTR_variant	37	.	.	.	.	rs768466925,rs778914522	.	.	1	HIST1H2BF	HGNC	4752	protein_coding	YES	CCDS4592.1	ENSP00000353074	H2B1C_HUMAN	B2R4S9_HUMAN	UPI0000000C24	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTATCATG	.	4	ESCA
POLR1C	0	.	GRCh37	6	43487822	43487825	+	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AGAT	AGAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.406_409delGATA	p.Asp136LeufsTer28	p.D136Lfs*28	ENST00000372389	5/9	70	45	25	61	61	0	POLR1C,frameshift_variant,p.Asp136LeufsTer28,ENST00000372389,;POLR1C,frameshift_variant,p.Asp136LeufsTer28,ENST00000372344,;POLR1C,frameshift_variant,p.Asp136LeufsTer28,ENST00000304004,;POLR1C,frameshift_variant,p.Asp81LeufsTer28,ENST00000428025,;POLR1C,intron_variant,,ENST00000423780,;XPO5,downstream_gene_variant,,ENST00000265351,;XPO5,downstream_gene_variant,,ENST00000455285,;YIPF3,upstream_gene_variant,,ENST00000506469,;YIPF3,upstream_gene_variant,,ENST00000503972,;YIPF3,upstream_gene_variant,,ENST00000372422,;YIPF3,upstream_gene_variant,,ENST00000500090,;YIPF3,upstream_gene_variant,,ENST00000511831,;RP3-337H4.9,upstream_gene_variant,,ENST00000607571,;POLR1C,non_coding_transcript_exon_variant,,ENST00000455605,;POLR1C,non_coding_transcript_exon_variant,,ENST00000488601,;POLR1C,non_coding_transcript_exon_variant,,ENST00000481352,;YIPF3,upstream_gene_variant,,ENST00000488966,;YIPF3,upstream_gene_variant,,ENST00000460903,;YIPF3,upstream_gene_variant,,ENST00000502714,;YIPF3,upstream_gene_variant,,ENST00000490447,;YIPF3,upstream_gene_variant,,ENST00000510102,;XPO5,downstream_gene_variant,,ENST00000486936,;XPO5,downstream_gene_variant,,ENST00000488195,;POLR1C,downstream_gene_variant,,ENST00000512472,;XPO5,downstream_gene_variant,,ENST00000455854,;YIPF3,upstream_gene_variant,,ENST00000455768,;YIPF3,upstream_gene_variant,,ENST00000416380,;YIPF3,upstream_gene_variant,,ENST00000460547,;	-	ENSG00000171453	ENST00000372389	Transcript	frameshift_variant	489-492	401-404	134-135	EI/X	gAGATa/ga	.	.	.	1	POLR1C	HGNC	20194	protein_coding	YES	CCDS4901.1	ENSP00000361465	RPAC1_HUMAN	Q96HT3_HUMAN,D6RDJ3_HUMAN	UPI00001345BC	.	.	.	5/9	.	hmmpanther:PTHR11800:SF13,hmmpanther:PTHR11800,Pfam_domain:PF01000,Pfam_domain:PF01193,Gene3D:2.170.120.12,SMART_domains:SM00662,Superfamily_domains:SSF56553	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCACAGAGATAGATA	.	3	ESCA
AARS2	0	.	GRCh37	6	44272859	44272859	+	Missense_Mutation	SNP	C	C	T	rs779531267	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1511G>A	p.Arg504His	p.R504H	ENST00000244571	11/22	39	35	3	34	34	0	AARS2,missense_variant,p.Arg504His,ENST00000244571,;TMEM151B,intron_variant,,ENST00000438774,;AARS2,upstream_gene_variant,,ENST00000491573,;RP11-444E17.6,intron_variant,,ENST00000505802,;	T	ENSG00000124608	ENST00000244571	Transcript	missense_variant	1514	1511	504	R/H	cGc/cAc	rs779531267,COSM188996	.	.	-1	AARS2	HGNC	21022	protein_coding	YES	CCDS34464.1	ENSP00000244571	SYAM_HUMAN	.	UPI00001C1E5A	.	tolerated(0.15)	benign(0.007)	11/22	.	PROSITE_profiles:PS50860,HAMAP:MF_00036_B,hmmpanther:PTHR11777:SF8,hmmpanther:PTHR11777,Pfam_domain:PF01411,TIGRFAM_domain:TIGR00344	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CTTGGCGCTGC	byFrequency	2	ESCA
TFAP2B	0	.	GRCh37	6	50791203	50791203	+	Silent	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.165G>A	p.%3D	p.P55P	ENST00000393655	2/7	47	29	17	45	45	0	TFAP2B,synonymous_variant,p.%3D,ENST00000393655,;TFAP2B,synonymous_variant,p.%3D,ENST00000263046,;TFAP2B,synonymous_variant,p.%3D,ENST00000344788,;TFAP2B,non_coding_transcript_exon_variant,,ENST00000489228,;	A	ENSG00000008196	ENST00000393655	Transcript	synonymous_variant	334	165	55	P	ccG/ccA	.	.	.	1	TFAP2B	HGNC	11743	protein_coding	YES	CCDS4934.2	ENSP00000377265	AP2B_HUMAN	A8K557_HUMAN	UPI000020DE90	.	.	.	2/7	.	hmmpanther:PTHR10812:SF14,hmmpanther:PTHR10812	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGCCGCT	.	5	ESCA
PAQR8	0	.	GRCh37	6	52268714	52268714	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703T>G	p.Cys235Gly	p.C235G	ENST00000442253	2/2	33	17	16	21	21	0	PAQR8,missense_variant,p.Cys235Gly,ENST00000442253,;PAQR8,missense_variant,p.Cys235Gly,ENST00000360726,;PAQR8,downstream_gene_variant,,ENST00000512121,;	G	ENSG00000170915	ENST00000442253	Transcript	missense_variant	877	703	235	C/G	Tgt/Ggt	.	.	.	1	PAQR8	HGNC	15708	protein_coding	YES	CCDS4941.1	ENSP00000406197	MPRB_HUMAN	D6RCM7_HUMAN	UPI0000073877	.	tolerated(0.18)	possibly_damaging(0.681)	2/2	.	hmmpanther:PTHR20855:SF22,hmmpanther:PTHR20855,Pfam_domain:PF03006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTCTGTCAC	.	5	ESCA
FAM83B	0	.	GRCh37	6	54791310	54791310	+	Missense_Mutation	SNP	G	G	A	rs766860593	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.586G>A	p.Gly196Ser	p.G196S	ENST00000306858	3/5	49	35	13	56	56	0	FAM83B,missense_variant,p.Gly196Ser,ENST00000306858,;	A	ENSG00000168143	ENST00000306858	Transcript	missense_variant	702	586	196	G/S	Ggt/Agt	rs766860593	.	.	1	FAM83B	HGNC	21357	protein_coding	YES	CCDS34479.1	ENSP00000304078	FA83B_HUMAN	.	UPI00001D81EC	.	deleterious(0.04)	benign(0.12)	3/5	.	hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF4,Gene3D:3.30.870.10,Pfam_domain:PF07894,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAAGGTTGT	.	5	ESCA
PTP4A1	0	.	GRCh37	6	64290769	64290770	+	3'UTR	INS	-	-	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*696dupA	.	.	ENST00000370651	6/6	62	48	14	43	43	0	PTP4A1,3_prime_UTR_variant,,ENST00000370650,;PTP4A1,3_prime_UTR_variant,,ENST00000370651,;PTP4A1,downstream_gene_variant,,ENST00000578299,;PTP4A1,downstream_gene_variant,,ENST00000470661,;PTP4A1,downstream_gene_variant,,ENST00000473334,;	A	ENSG00000112245	ENST00000370651	Transcript	3_prime_UTR_variant	2365-2366	.	.	.	.	.	.	.	1	PTP4A1	HGNC	9634	protein_coding	YES	CCDS4965.1	ENSP00000359685	TP4A1_HUMAN	.	UPI00000227B8	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TCAGACAAAAA	.	2	ESCA
BCKDHB	0	.	GRCh37	6	80880998	80880998	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.634-1G>A	.	p.X212_splice	ENST00000320393	.	226	163	63	168	168	0	BCKDHB,splice_acceptor_variant,,ENST00000356489,;BCKDHB,splice_acceptor_variant,,ENST00000320393,;BCKDHB,splice_acceptor_variant,,ENST00000545529,;BCKDHB,downstream_gene_variant,,ENST00000369760,;	A	ENSG00000083123	ENST00000320393	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	BCKDHB	HGNC	987	protein_coding	YES	CCDS4994.1	ENSP00000318351	ODBB_HUMAN	Q6LCK9_HUMAN,B7ZB80_HUMAN	UPI0000001C97	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAGGTGGT	.	5	ESCA
AP1S1	0	.	GRCh37	7	100799965	100799965	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.94G>A	p.Val32Met	p.V32M	ENST00000337619	2/5	73	57	16	35	35	0	AP1S1,missense_variant,p.Val32Met,ENST00000337619,;AP1S1,missense_variant,p.Val74Met,ENST00000429457,;MIR4653,upstream_gene_variant,,ENST00000585107,;AP1S1,missense_variant,p.Val32Met,ENST00000443943,;	A	ENSG00000106367	ENST00000337619	Transcript	missense_variant	212	94	32	V/M	Gtg/Atg	.	.	.	1	AP1S1	HGNC	559	protein_coding	YES	CCDS47669.1	ENSP00000336666	AP1S1_HUMAN	.	UPI0000027F3C	.	tolerated(0.17)	benign(0.019)	2/5	.	hmmpanther:PTHR11753,hmmpanther:PTHR11753:SF11,Gene3D:3.30.450.60,Pfam_domain:PF01217,PIRSF_domain:PIRSF015588,Superfamily_domains:SSF64356	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGGTGCGC	.	5	ESCA
FOXP2	0	.	GRCh37	7	114329835	114329835	+	Splice_Site	SNP	A	A	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2079-2A>T	.	p.X693_splice	ENST00000408937	.	50	36	13	37	37	0	FOXP2,splice_acceptor_variant,,ENST00000393489,;FOXP2,splice_acceptor_variant,,ENST00000408937,;FOXP2,splice_acceptor_variant,,ENST00000393498,;FOXP2,splice_acceptor_variant,,ENST00000403559,;FOXP2,splice_acceptor_variant,,ENST00000393491,;FOXP2,splice_acceptor_variant,,ENST00000393494,;FOXP2,splice_acceptor_variant,,ENST00000350908,;FOXP2,splice_acceptor_variant,,ENST00000412402,;	T	ENSG00000128573	ENST00000408937	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	FOXP2	HGNC	13875	protein_coding	YES	CCDS43635.1	ENSP00000386200	FOXP2_HUMAN	.	UPI000007412B	.	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCAGACAT	.	5	ESCA
CAV1	0	.	GRCh37	7	116200802	116200803	+	3'UTR	INS	-	-	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1470dupT	.	.	ENST00000341049	3/3	47	41	6	29	29	0	CAV1,3_prime_UTR_variant,,ENST00000341049,;CAV1,3_prime_UTR_variant,,ENST00000393467,;CAV1,3_prime_UTR_variant,,ENST00000405348,;CAV1,downstream_gene_variant,,ENST00000393470,;CAV1,downstream_gene_variant,,ENST00000456473,;CAV1,downstream_gene_variant,,ENST00000393468,;AC006159.4,downstream_gene_variant,,ENST00000421965,;CAV1,downstream_gene_variant,,ENST00000451122,;	T	ENSG00000105974	ENST00000341049	Transcript	3_prime_UTR_variant	2276-2277	.	.	.	.	.	.	.	1	CAV1	HGNC	1527	protein_coding	YES	CCDS5767.1	ENSP00000339191	CAV1_HUMAN	Q2TNI1_HUMAN,C9JKI3_HUMAN	UPI00001270ED	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTATGATTTTT	.	2	ESCA
KCND2	0	.	GRCh37	7	120387853	120387853	+	Missense_Mutation	SNP	G	G	A	rs151258092	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1834G>A	p.Asp612Asn	p.D612N	ENST00000331113	6/6	57	46	10	40	40	0	KCND2,missense_variant,p.Asp612Asn,ENST00000331113,;KCND2,downstream_gene_variant,,ENST00000425288,;RP4-797C5.2,intron_variant,,ENST00000450480,;KCND2,downstream_gene_variant,,ENST00000473190,;	A	ENSG00000184408	ENST00000331113	Transcript	missense_variant	2799	1834	612	D/N	Gat/Aat	rs151258092,COSM1699260	.	.	1	KCND2	HGNC	6238	protein_coding	YES	CCDS5776.1	ENSP00000333496	KCND2_HUMAN	A4D0V9_HUMAN,Q75LS7_HUMAN	UPI0000073D37	.	tolerated_low_confidence(0.37)	benign(0.001)	6/6	.	.	.	.	.	.	.	.	.	A:0.0005	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACGATAGG	byCluster	5	ESCA
EPHB6	0	.	GRCh37	7	142561730	142561730	+	Missense_Mutation	SNP	G	G	A	rs776478976	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>A	p.Glu58Lys	p.E58K	ENST00000392957	7/20	74	64	9	36	36	0	EPHB6,missense_variant,p.Glu58Lys,ENST00000442129,;EPHB6,missense_variant,p.Glu58Lys,ENST00000392957,;EPHB6,intron_variant,,ENST00000411471,;EPHB6,downstream_gene_variant,,ENST00000497095,;EPHB6,missense_variant,p.Arg36Gln,ENST00000425995,;EPHB6,missense_variant,p.Glu58Lys,ENST00000422643,;EPHB6,non_coding_transcript_exon_variant,,ENST00000466783,;EPHB6,upstream_gene_variant,,ENST00000486511,;	A	ENSG00000106123	ENST00000392957	Transcript	missense_variant	959	172	58	E/K	Gag/Aag	rs776478976,COSM745255	.	.	1	EPHB6	HGNC	3396	protein_coding	YES	CCDS5873.2	ENSP00000376684	EPHB6_HUMAN	.	UPI00006635A8	.	deleterious(0)	probably_damaging(0.999)	7/20	.	PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF300,hmmpanther:PTHR24416,Gene3D:2.60.120.260,Pfam_domain:PF01404,SMART_domains:SM00615,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGACGAGGTG	.	4	ESCA
PIP	0	.	GRCh37	7	142832382	142832382	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.191A>G	p.Glu64Gly	p.E64G	ENST00000291009	2/4	74	38	36	46	46	0	PIP,missense_variant,p.Glu64Gly,ENST00000291009,;	G	ENSG00000159763	ENST00000291009	Transcript	missense_variant	231	191	64	E/G	gAa/gGa	.	.	.	1	PIP	HGNC	8993	protein_coding	YES	CCDS34768.1	ENSP00000291009	PIP_HUMAN	.	UPI0000131B05	.	deleterious(0)	benign(0.112)	2/4	.	hmmpanther:PTHR15096:SF1,hmmpanther:PTHR15096,Pfam_domain:PF05326,PIRSF_domain:PIRSF002572,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGAATGCA	.	5	ESCA
TMEM176B	0	.	GRCh37	7	150490688	150490688	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.316G>T	p.Val106Leu	p.V106L	ENST00000447204	4/7	39	24	15	25	25	0	TMEM176B,missense_variant,p.Val106Leu,ENST00000429904,;TMEM176B,missense_variant,p.Val106Leu,ENST00000492607,;TMEM176B,missense_variant,p.Val69Leu,ENST00000450753,;TMEM176B,missense_variant,p.Val106Leu,ENST00000326442,;TMEM176B,missense_variant,p.Val106Leu,ENST00000447204,;TMEM176B,missense_variant,p.Val106Leu,ENST00000434545,;RP5-1051J4.4,downstream_gene_variant,,ENST00000542395,;	A	ENSG00000106565	ENST00000447204	Transcript	missense_variant	689	316	106	V/L	Gtg/Ttg	.	.	.	-1	TMEM176B	HGNC	29596	protein_coding	YES	CCDS5908.1	ENSP00000410269	T176B_HUMAN	.	UPI000013C82B	.	deleterious(0)	benign(0.048)	4/7	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR15756,hmmpanther:PTHR15756:SF6,Pfam_domain:PF04103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCACCTGAA	.	5	ESCA
PAXIP1	0	.	GRCh37	7	154774989	154774989	+	Silent	SNP	T	T	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378A>T	p.%3D	p.G126G	ENST00000404141	5/21	100	79	21	90	90	0	PAXIP1,synonymous_variant,p.%3D,ENST00000404141,;PAXIP1,synonymous_variant,p.%3D,ENST00000397192,;PAXIP1,synonymous_variant,p.%3D,ENST00000419436,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000473219,;PAXIP1,3_prime_UTR_variant,,ENST00000457196,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000475066,;	A	ENSG00000157212	ENST00000404141	Transcript	synonymous_variant	533	378	126	G	ggA/ggT	.	.	.	-1	PAXIP1	HGNC	8624	protein_coding	YES	CCDS47753.1	ENSP00000384048	PAXI1_HUMAN	.	UPI00004166F9	.	.	.	5/21	.	PROSITE_profiles:PS50172,hmmpanther:PTHR23196:SF1,hmmpanther:PTHR23196,Pfam_domain:PF12738,Gene3D:3.40.50.10190,SMART_domains:SM00292,Superfamily_domains:SSF52113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATCTCCCCC	.	5	ESCA
AC005013.5	0	.	GRCh37	7	28997167	28997167	+	5'Flank	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000436594	.	124	67	57	86	86	0	AC005013.5,upstream_gene_variant,,ENST00000436594,;TRIL,non_coding_transcript_exon_variant,,ENST00000322982,;AC005013.1,non_coding_transcript_exon_variant,,ENST00000539664,;	T	ENSG00000228421	ENST00000436594	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	116	1	AC005013.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGCGTTCC	.	5	ESCA
CARD11	0	.	GRCh37	7	2956937	2956937	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2690G>T	p.Gly897Val	p.G897V	ENST00000396946	20/25	95	90	5	75	75	0	CARD11,missense_variant,p.Gly897Val,ENST00000396946,;CARD11,downstream_gene_variant,,ENST00000355508,;CARD11,non_coding_transcript_exon_variant,,ENST00000480332,;	A	ENSG00000198286	ENST00000396946	Transcript	missense_variant	3094	2690	897	G/V	gGc/gTc	.	.	.	-1	CARD11	HGNC	16393	protein_coding	YES	CCDS5336.2	ENSP00000380150	CAR11_HUMAN	Q8TES3_HUMAN,E2QRC0_HUMAN	UPI00003FED38	.	tolerated(0.08)	possibly_damaging(0.735)	20/25	.	hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGGCCAAAA	.	2	ESCA
ZNF12	0	.	GRCh37	7	6731402	6731404	+	In_Frame_Del	DEL	AGA	AGA	-	rs764820353	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AGA	AGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1169_1171delTCT	p.Phe390del	p.F390del	ENST00000405858	5/5	81	64	17	46	46	0	ZNF12,inframe_deletion,p.Phe390del,ENST00000405858,;ZNF12,inframe_deletion,p.Phe316del,ENST00000404360,;ZNF12,inframe_deletion,p.Phe352del,ENST00000342651,;AC073343.2,upstream_gene_variant,,ENST00000577401,;AC073343.13,intron_variant,,ENST00000366167,;	-	ENSG00000164631	ENST00000405858	Transcript	inframe_deletion	1711-1713	1169-1171	390-391	FS/S	tTCTcg/tcg	rs764820353	.	.	-1	ZNF12	HGNC	12902	protein_coding	YES	CCDS47538.1	ENSP00000385939	ZNF12_HUMAN	.	UPI000020EAF7	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF85,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTGCGAGAAGGTT	.	3	ESCA
PCLO	0	.	GRCh37	7	82584500	82584500	+	Silent	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5769T>C	p.%3D	p.H1923H	ENST00000333891	5/25	88	66	22	40	40	0	PCLO,synonymous_variant,p.%3D,ENST00000333891,;PCLO,synonymous_variant,p.%3D,ENST00000423517,;PCLO,upstream_gene_variant,,ENST00000437081,;	G	ENSG00000186472	ENST00000333891	Transcript	synonymous_variant	6107	5769	1923	H	caT/caC	.	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	.	5/25	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTTATGCAT	.	5	ESCA
CDK6	0	.	GRCh37	7	92244099	92244099	+	3'UTR	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*355T>C	.	.	ENST00000265734	8/8	43	31	12	32	32	0	CDK6,3_prime_UTR_variant,,ENST00000265734,;CDK6,downstream_gene_variant,,ENST00000424848,;CDK6,non_coding_transcript_exon_variant,,ENST00000467166,;	G	ENSG00000105810	ENST00000265734	Transcript	3_prime_UTR_variant	1748	.	.	.	.	.	.	.	-1	CDK6	HGNC	1777	protein_coding	YES	CCDS5628.1	ENSP00000265734	CDK6_HUMAN	A4D1G0_HUMAN	UPI00001108FA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTACATCATA	.	5	ESCA
RAD21	0	.	GRCh37	8	117858872	117858872	+	3'UTR	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*867G>A	.	.	ENST00000297338	14/14	95	70	24	62	62	0	RAD21,3_prime_UTR_variant,,ENST00000297338,;UTP23,intron_variant,,ENST00000520733,;UTP23,intron_variant,,ENST00000517820,;RAD21,downstream_gene_variant,,ENST00000517749,;RAD21,downstream_gene_variant,,ENST00000518055,;RAD21,downstream_gene_variant,,ENST00000523986,;UTP23,intron_variant,,ENST00000521703,;UTP23,intron_variant,,ENST00000524128,;	T	ENSG00000164754	ENST00000297338	Transcript	3_prime_UTR_variant	3051	.	.	.	.	.	.	.	-1	RAD21	HGNC	9811	protein_coding	YES	CCDS6321.1	ENSP00000297338	RAD21_HUMAN	E5RJW1_HUMAN,E5RJK5_HUMAN,E5RIN7_HUMAN,E5RI01_HUMAN,E5RG18_HUMAN,E5RFZ5_HUMAN,E5RFV8_HUMAN	UPI0000133018	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCCATCAG	.	5	ESCA
DLC1	0	.	GRCh37	8	13357530	13357530	+	Nonsense_Mutation	SNP	C	C	T	rs201093868	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51G>A	p.Trp17Ter	p.W17*	ENST00000276297	2/18	63	47	16	34	34	0	DLC1,stop_gained,p.Trp17Ter,ENST00000511869,;DLC1,stop_gained,p.Trp17Ter,ENST00000276297,;DLC1,stop_gained,p.Trp17Ter,ENST00000316609,;DLC1,upstream_gene_variant,,ENST00000517868,;DLC1,non_coding_transcript_exon_variant,,ENST00000517333,;	T	ENSG00000164741	ENST00000276297	Transcript	stop_gained	461	51	17	W/*	tgG/tgA	rs201093868	.	.	-1	DLC1	HGNC	2897	protein_coding	YES	CCDS5989.1	ENSP00000276297	RHG07_HUMAN	.	UPI0000210275	.	.	.	2/18	.	.	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATCCAGTG	byCluster	5	ESCA
ZC3H3	0	.	GRCh37	8	144620514	144620514	+	Silent	SNP	A	A	G	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1023T>C	p.%3D	p.S341S	ENST00000262577	2/12	102	74	28	49	49	0	ZC3H3,synonymous_variant,p.%3D,ENST00000262577,;7SK,upstream_gene_variant,,ENST00000408472,;7SK,upstream_gene_variant,,ENST00000517300,;RP11-661A12.5,downstream_gene_variant,,ENST00000530600,;	G	ENSG00000014164	ENST00000262577	Transcript	synonymous_variant	1055	1023	341	S	tcT/tcC	.	.	.	-1	ZC3H3	HGNC	28972	protein_coding	YES	CCDS6402.1	ENSP00000262577	ZC3H3_HUMAN	.	UPI0000160D96	.	.	.	2/12	.	hmmpanther:PTHR23102,hmmpanther:PTHR23102:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCAGAGGC	.	5	ESCA
PARP10	0	.	GRCh37	8	145059488	145059488	+	Nonsense_Mutation	SNP	G	G	A	rs372202325	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682C>T	p.Arg228Ter	p.R228*	ENST00000313028	5/11	52	33	19	61	61	0	PARP10,stop_gained,p.Arg228Ter,ENST00000313028,;PARP10,stop_gained,p.Arg228Ter,ENST00000524918,;PARP10,stop_gained,p.Arg143Ter,ENST00000313059,;PARP10,stop_gained,p.Arg240Ter,ENST00000525773,;PARP10,downstream_gene_variant,,ENST00000528914,;PARP10,downstream_gene_variant,,ENST00000525879,;PARP10,downstream_gene_variant,,ENST00000529842,;PARP10,downstream_gene_variant,,ENST00000529311,;PARP10,downstream_gene_variant,,ENST00000528625,;GRINA,upstream_gene_variant,,ENST00000313269,;PARP10,downstream_gene_variant,,ENST00000532311,;PARP10,downstream_gene_variant,,ENST00000531537,;PARP10,downstream_gene_variant,,ENST00000528136,;PARP10,downstream_gene_variant,,ENST00000531707,;PARP10,downstream_gene_variant,,ENST00000525486,;PARP10,downstream_gene_variant,,ENST00000530478,;GRINA,upstream_gene_variant,,ENST00000395068,;GRINA,upstream_gene_variant,,ENST00000529301,;PARP10,non_coding_transcript_exon_variant,,ENST00000533665,;PARP10,downstream_gene_variant,,ENST00000534737,;PARP10,downstream_gene_variant,,ENST00000532660,;PARP10,stop_gained,p.Arg228Ter,ENST00000527262,;PARP10,upstream_gene_variant,,ENST00000526007,;PARP10,downstream_gene_variant,,ENST00000526985,;PARP10,downstream_gene_variant,,ENST00000528580,;PARP10,upstream_gene_variant,,ENST00000528963,;	A	ENSG00000178685	ENST00000313028	Transcript	stop_gained	777	682	228	R/*	Cga/Tga	rs372202325	.	.	-1	PARP10	HGNC	25895	protein_coding	YES	CCDS34960.1	ENSP00000325618	PAR10_HUMAN	E9PSG8_HUMAN,E9PSE7_HUMAN,E9PQQ6_HUMAN,E9PPV8_HUMAN,E9PPU2_HUMAN,E9PM86_HUMAN,E9PLE8_HUMAN,E9PJI2_HUMAN,E9PIA6_HUMAN	UPI0000251FAB	.	.	.	5/11	.	hmmpanther:PTHR14453,hmmpanther:PTHR14453:SF55	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCGTTCTG	byFrequency|byCluster	5	ESCA
SCRT1	0	.	GRCh37	8	145559791	145559791	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.41C>T	p.Ala14Val	p.A14V	ENST00000332135	1/2	84	67	17	98	98	0	SCRT1,missense_variant,p.Ala14Val,ENST00000332135,;	A	ENSG00000170616	ENST00000332135	Transcript	missense_variant	153	41	14	A/V	gCg/gTg	COSM126053	.	.	-1	SCRT1	HGNC	15950	protein_coding	YES	CCDS6421.1	ENSP00000331692	SCRT1_HUMAN	.	UPI0000071337	.	tolerated(0.08)	benign(0.153)	1/2	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAACGCGTCA	.	5	ESCA
SH2D4A	0	.	GRCh37	8	19250858	19250860	+	In_Frame_Del	DEL	CTT	CTT	-	rs748097834	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CTT	CTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1083_1085delTCT	p.Leu362del	p.L362del	ENST00000265807	9/10	87	54	33	64	64	0	SH2D4A,inframe_deletion,p.Leu362del,ENST00000265807,;SH2D4A,inframe_deletion,p.Leu362del,ENST00000519207,;SH2D4A,inframe_deletion,p.Leu317del,ENST00000518040,;	-	ENSG00000104611	ENST00000265807	Transcript	inframe_deletion	1489-1491	1078-1080	360	L/-	CTT/-	rs748097834	.	.	1	SH2D4A	HGNC	26102	protein_coding	YES	CCDS6009.1	ENSP00000265807	SH24A_HUMAN	.	UPI000007372B	.	.	.	9/10	.	PROSITE_profiles:PS50001,hmmpanther:PTHR14388:SF5,hmmpanther:PTHR14388,Gene3D:3.30.505.10,Pfam_domain:PF00017,SMART_domains:SM00252,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATGAACTTCTTCT	.	3	ESCA
PTK2B	0	.	GRCh37	8	27277410	27277412	+	Splice_Site	DEL	AGG	AGG	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	AGG	AGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205_207delGAG	p.Glu69del	p.X69_splice	ENST00000397501	8/36	48	34	14	30	30	0	PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000338238,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000517339,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000420218,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000522517,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000544172,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000412793,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000397501,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000521164,;PTK2B,splice_acceptor_variant,p.Glu69del,ENST00000346049,;PTK2B,upstream_gene_variant,,ENST00000521000,;	-	ENSG00000120899	ENST00000397501	Transcript	splice_acceptor_variant	?-1013	?-205	?-69	.	.	.	.	.	1	PTK2B	HGNC	9612	protein_coding	YES	CCDS6057.1	ENSP00000380638	FAK2_HUMAN	E5RK84_HUMAN,E5RJ77_HUMAN,E5RHL2_HUMAN,C9JHV9_HUMAN	UPI000000D9EC	.	.	.	8/36	7/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCTGCAGGAGATC	.	3	ESCA
CSMD1	0	.	GRCh37	8	3224680	3224680	+	Missense_Mutation	SNP	C	C	A	rs756336147	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2989G>T	p.Ala997Ser	p.A997S	ENST00000537824	20/70	46	30	16	39	39	0	CSMD1,missense_variant,p.Ala998Ser,ENST00000400186,;CSMD1,missense_variant,p.Ala997Ser,ENST00000542608,;CSMD1,missense_variant,p.Ala998Ser,ENST00000602723,;CSMD1,missense_variant,p.Ala478Ser,ENST00000335551,;CSMD1,missense_variant,p.Ala997Ser,ENST00000537824,;CSMD1,missense_variant,p.Ala998Ser,ENST00000520002,;CSMD1,missense_variant,p.Ala997Ser,ENST00000539096,;CSMD1,missense_variant,p.Ala998Ser,ENST00000602557,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,;	A	ENSG00000183117	ENST00000537824	Transcript	missense_variant	2989	2989	997	A/S	Gcc/Tcc	rs756336147	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	possibly_damaging(0.769)	20/70	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGGCAACGG	.	5	ESCA
PRKDC	0	.	GRCh37	8	48841652	48841653	+	Frame_Shift_Del	DEL	CT	CT	-	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	CT	CT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2138_2139delAG	p.Glu713GlyfsTer4	p.E713Gfs*4	ENST00000314191	19/87	211	177	34	102	102	0	PRKDC,frameshift_variant,p.Glu713GlyfsTer4,ENST00000338368,;PRKDC,frameshift_variant,p.Glu713GlyfsTer4,ENST00000314191,;PRKDC,splice_region_variant,,ENST00000518216,;PRKDC,splice_region_variant,,ENST00000523565,;PRKDC,splice_region_variant,,ENST00000541488,;	-	ENSG00000253729	ENST00000314191	Transcript	frameshift_variant	2195-2196	2138-2139	713	E/X	gAG/g	.	.	.	-1	PRKDC	HGNC	9413	protein_coding	YES	.	ENSP00000313420	PRKDC_HUMAN	F5GX40_HUMAN	UPI000045790C	.	.	.	19/87	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATTACCTCTTTG	.	3	ESCA
PCMTD1	0	.	GRCh37	8	52730688	52730688	+	3'UTR	SNP	T	T	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2223A>G	.	.	ENST00000360540	7/7	47	33	14	31	31	0	PCMTD1,3_prime_UTR_variant,,ENST00000544451,;AC090186.1,3_prime_UTR_variant,,ENST00000415643,;PCMTD1,3_prime_UTR_variant,,ENST00000360540,;PCMTD1,downstream_gene_variant,,ENST00000522514,;PCMTD1,downstream_gene_variant,,ENST00000519559,;	C	ENSG00000168300	ENST00000360540	Transcript	3_prime_UTR_variant	3704	.	.	.	.	.	.	.	-1	PCMTD1	HGNC	30483	protein_coding	YES	CCDS6148.1	ENSP00000353739	PCMD1_HUMAN	.	UPI0000047CC0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTAATATATC	.	5	ESCA
ST18	0	.	GRCh37	8	53023562	53023562	+	3'UTR	SNP	C	C	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2196G>T	.	.	ENST00000276480	26/26	50	36	14	30	30	0	ST18,3_prime_UTR_variant,,ENST00000276480,;ST18,downstream_gene_variant,,ENST00000521824,;ST18,downstream_gene_variant,,ENST00000522251,;ST18,downstream_gene_variant,,ENST00000521582,;	A	ENSG00000147488	ENST00000276480	Transcript	3_prime_UTR_variant	6024	.	.	.	.	.	.	.	-1	ST18	HGNC	18695	protein_coding	YES	CCDS6149.1	ENSP00000276480	ST18_HUMAN	E5RHS3_HUMAN	UPI0000046C30	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGACCCAAT	.	5	ESCA
SDCBP	0	.	GRCh37	8	59484765	59484765	+	Silent	SNP	T	T	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132T>C	p.%3D	p.N44N	ENST00000260130	4/9	111	78	32	56	56	0	SDCBP,synonymous_variant,p.%3D,ENST00000413219,;SDCBP,synonymous_variant,p.%3D,ENST00000520168,;SDCBP,synonymous_variant,p.%3D,ENST00000447182,;SDCBP,synonymous_variant,p.%3D,ENST00000523483,;SDCBP,synonymous_variant,p.%3D,ENST00000260130,;SDCBP,synonymous_variant,p.%3D,ENST00000447267,;SDCBP,synonymous_variant,p.%3D,ENST00000422546,;SDCBP,synonymous_variant,p.%3D,ENST00000424270,;SDCBP,splice_region_variant,,ENST00000522243,;SDCBP,splice_region_variant,,ENST00000522843,;SDCBP,splice_region_variant,,ENST00000519115,;SDCBP,splice_region_variant,,ENST00000520228,;	C	ENSG00000137575	ENST00000260130	Transcript	synonymous_variant	282	132	44	N	aaT/aaC	.	.	.	1	SDCBP	HGNC	10662	protein_coding	YES	CCDS6172.1	ENSP00000260130	SDCB1_HUMAN	.	UPI000013570E	.	.	.	4/9	.	hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGATCTCTA	.	5	ESCA
ERICH1	0	.	GRCh37	8	618736	618736	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1120G>A	p.Asp374Asn	p.D374N	ENST00000262109	5/6	30	24	6	26	26	0	ERICH1,missense_variant,p.Asp374Asn,ENST00000262109,;ERICH1,missense_variant,p.Asp280Asn,ENST00000522706,;ERICH1,missense_variant,p.Asp143Asn,ENST00000522893,;ERICH1,downstream_gene_variant,,ENST00000518895,;ERICH1,missense_variant,p.Asp33Asn,ENST00000523415,;ERICH1,non_coding_transcript_exon_variant,,ENST00000523053,;	T	ENSG00000104714	ENST00000262109	Transcript	missense_variant	1198	1120	374	D/N	Gac/Aac	.	.	.	-1	ERICH1	HGNC	27234	protein_coding	YES	CCDS5955.1	ENSP00000262109	ERIC1_HUMAN	.	UPI000000DB6B	.	tolerated(0.39)	benign(0.002)	5/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22444,hmmpanther:PTHR22444:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGTCCAGCA	.	5	ESCA
ARFGEF1	0	.	GRCh37	8	68111035	68111035	+	3'UTR	SNP	G	G	C	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*134C>G	.	.	ENST00000262215	39/39	81	62	19	58	58	0	ARFGEF1,3_prime_UTR_variant,,ENST00000262215,;ARFGEF1,intron_variant,,ENST00000520381,;ARFGEF1,downstream_gene_variant,,ENST00000518230,;ARFGEF1,downstream_gene_variant,,ENST00000518789,;CSPP1,downstream_gene_variant,,ENST00000262210,;CSPP1,downstream_gene_variant,,ENST00000412460,;CSPP1,downstream_gene_variant,,ENST00000519668,;ARFGEF1,non_coding_transcript_exon_variant,,ENST00000517955,;ARFGEF1,intron_variant,,ENST00000522878,;CSPP1,downstream_gene_variant,,ENST00000521168,;ARFGEF1,non_coding_transcript_exon_variant,,ENST00000518290,;	C	ENSG00000066777	ENST00000262215	Transcript	3_prime_UTR_variant	6074	.	.	.	.	.	.	.	-1	ARFGEF1	HGNC	15772	protein_coding	YES	CCDS6199.1	ENSP00000262215	BIG1_HUMAN	E5RJN9_HUMAN,E5RJB2_HUMAN,E5RHZ1_HUMAN,B3KMS9_HUMAN	UPI000013D275	.	.	.	39/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAAGACTTC	.	5	ESCA
KIAA1429	0	.	GRCh37	8	95538542	95538543	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1929dupT	p.Thr644TyrfsTer8	p.T644Yfs*8	ENST00000297591	8/24	154	124	30	67	67	0	KIAA1429,frameshift_variant,p.Thr644TyrfsTer8,ENST00000297591,;KIAA1429,frameshift_variant,p.Thr644TyrfsTer8,ENST00000421249,;KIAA1429,frameshift_variant,p.Thr644TyrfsTer8,ENST00000437199,;KIAA1429,downstream_gene_variant,,ENST00000519001,;KIAA1429,upstream_gene_variant,,ENST00000522263,;	A	ENSG00000164944	ENST00000297591	Transcript	frameshift_variant	2005-2006	1929-1930	643-644	-/X	-/T	.	.	.	-1	KIAA1429	HGNC	24500	protein_coding	YES	CCDS34923.1	ENSP00000297591	VIR_HUMAN	.	UPI00001BBB23	.	.	.	8/24	.	hmmpanther:PTHR23185:SF0,hmmpanther:PTHR23185,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CATTGTATGAG	.	3	ESCA
CCDC180	0	.	GRCh37	9	100079410	100079410	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.991G>A	p.Glu331Lys	p.E331K	ENST00000375202	23/51	44	13	30	41	41	0	CCDC180,missense_variant,p.Glu470Lys,ENST00000357054,;CCDC180,missense_variant,p.Glu331Lys,ENST00000375202,;CCDC180,missense_variant,p.Glu331Lys,ENST00000529487,;CCDC180,missense_variant,p.Glu470Lys,ENST00000395220,;CCDC180,missense_variant,p.Glu328Lys,ENST00000411667,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000532526,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000375206,;CCDC180,non_coding_transcript_exon_variant,,ENST00000460482,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000534123,;RP11-23J9.4,non_coding_transcript_exon_variant,,ENST00000529787,;CCDC180,non_coding_transcript_exon_variant,,ENST00000494917,;	A	ENSG00000197816	ENST00000375202	Transcript	missense_variant	2343	991	331	E/K	Gag/Aag	.	.	.	1	CCDC180	HGNC	29303	protein_coding	YES	CCDS35077.2	ENSP00000364348	CC180_HUMAN	B7ZMG3_HUMAN	UPI00016277C6	.	tolerated(0.17)	possibly_damaging(0.863)	23/51	.	hmmpanther:PTHR21444:SF14,hmmpanther:PTHR21444,Pfam_domain:PF14643	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATGGAGTCC	.	5	ESCA
NOTCH1	0	.	GRCh37	9	139417576	139417577	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.467dupT	p.Pro157AlafsTer99	p.P157Afs*99	ENST00000277541	4/34	112	67	45	59	59	0	NOTCH1,frameshift_variant,p.Pro157AlafsTer99,ENST00000277541,;MIR4673,upstream_gene_variant,,ENST00000584777,;NOTCH1,non_coding_transcript_exon_variant,,ENST00000491649,;	A	ENSG00000148400	ENST00000277541	Transcript	frameshift_variant	543-544	467-468	156	L/LX	ctg/ctTg	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	4/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,Pfam_domain:PF00008,Gene3D:2gy5A03,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGGGCAGGCA	.	3	ESCA
TLN1	0	.	GRCh37	9	35700018	35700018	+	Missense_Mutation	SNP	G	G	A	rs750965317	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6721C>T	p.Arg2241Trp	p.R2241W	ENST00000314888	50/57	32	21	10	51	51	0	TLN1,missense_variant,p.Arg2241Trp,ENST00000314888,;TLN1,missense_variant,p.Arg2129Trp,ENST00000540444,;TLN1,downstream_gene_variant,,ENST00000464379,;TLN1,upstream_gene_variant,,ENST00000489255,;TLN1,downstream_gene_variant,,ENST00000466916,;TLN1,downstream_gene_variant,,ENST00000465002,;TLN1,downstream_gene_variant,,ENST00000486788,;	A	ENSG00000137076	ENST00000314888	Transcript	missense_variant	7075	6721	2241	R/W	Cgg/Tgg	rs750965317	.	.	-1	TLN1	HGNC	11845	protein_coding	YES	CCDS35009.1	ENSP00000316029	TLN1_HUMAN	.	UPI0000211375	.	deleterious(0)	benign(0.285)	50/57	.	hmmpanther:PTHR19981:SF7,hmmpanther:PTHR19981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCGGCCAT	.	5	ESCA
HRCT1	0	.	GRCh37	9	35906300	35906300	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16G>A	p.Gly6Arg	p.G6R	ENST00000354323	1/1	37	19	17	27	27	0	HRCT1,missense_variant,p.Gly6Arg,ENST00000354323,;LINC00961,upstream_gene_variant,,ENST00000443779,;	A	ENSG00000196196	ENST00000354323	Transcript	missense_variant	112	16	6	G/R	Ggg/Agg	.	.	.	1	HRCT1	HGNC	33872	protein_coding	YES	CCDS35012.1	ENSP00000346283	HRCT1_HUMAN	.	UPI0000048EC9	.	deleterious_low_confidence(0)	probably_damaging(0.999)	1/1	.	hmmpanther:PTHR23009	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGGGGAGC	.	5	ESCA
JAK2	0	.	GRCh37	9	5126757	5126757	+	Missense_Mutation	SNP	G	G	A	rs775495966	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3365G>A	p.Arg1122Gln	p.R1122Q	ENST00000381652	25/25	56	37	19	46	46	0	JAK2,missense_variant,p.Arg973Gln,ENST00000544510,;JAK2,missense_variant,p.Arg1122Gln,ENST00000539801,;JAK2,missense_variant,p.Arg1122Gln,ENST00000381652,;JAK2,non_coding_transcript_exon_variant,,ENST00000487310,;	A	ENSG00000096968	ENST00000381652	Transcript	missense_variant	3859	3365	1122	R/Q	cGa/cAa	rs775495966,COSM48453,COSM1462587	.	.	1	JAK2	HGNC	6192	protein_coding	YES	CCDS6457.1	ENSP00000371067	JAK2_HUMAN	Q8IXP2_HUMAN,F5H5U8_HUMAN	UPI000012DA9E	.	tolerated(1)	benign(0.049)	25/25	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF179,PIRSF_domain:PIRSF000636,SMART_domains:SM00219	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCGAGTGG	.	5	ESCA
MAGEC3	0	.	GRCh37	X	140984538	140984538	+	Intron	SNP	G	G	A	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1124-130G>A	.	.	ENST00000298296	.	18	2	16	14	14	0	MAGEC3,missense_variant,p.Glu34Lys,ENST00000544766,;MAGEC3,missense_variant,p.Glu34Lys,ENST00000409007,;MAGEC3,missense_variant,p.Glu34Lys,ENST00000536088,;MAGEC3,intron_variant,,ENST00000298296,;MAGEC3,intron_variant,,ENST00000443323,;MAGEC3,downstream_gene_variant,,ENST00000448920,;MAGEC3,non_coding_transcript_exon_variant,,ENST00000483584,;	A	ENSG00000165509	ENST00000298296	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MAGEC3	HGNC	23798	protein_coding	YES	CCDS14676.1	ENSP00000298296	MAGC3_HUMAN	.	UPI000006E09B	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGATGAGGAG	.	5	ESCA
NR0B1	0	.	GRCh37	X	30326923	30326923	+	Silent	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558G>A	p.%3D	p.A186A	ENST00000378970	1/2	9	1	7	10	10	0	NR0B1,synonymous_variant,p.%3D,ENST00000453287,;NR0B1,synonymous_variant,p.%3D,ENST00000378970,;NR0B1,upstream_gene_variant,,ENST00000378963,;	T	ENSG00000169297	ENST00000378970	Transcript	synonymous_variant	793	558	186	A	gcG/gcA	.	.	.	-1	NR0B1	HGNC	7960	protein_coding	YES	CCDS14223.1	ENSP00000368253	NR0B1_HUMAN	F1D8P4_HUMAN	UPI0000128ED4	.	.	.	1/2	.	hmmpanther:PTHR24081,hmmpanther:PTHR24081:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTAGCGCCTC	.	2	ESCA
FAM47C	0	.	GRCh37	X	37027774	37027774	+	Frame_Shift_Del	DEL	C	C	-	.	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1293delC	p.Lys432ArgfsTer393	p.K432Rfs*393	ENST00000358047	1/1	172	101	71	94	94	0	FAM47C,frameshift_variant,p.Lys432ArgfsTer393,ENST00000358047,;	-	ENSG00000198173	ENST00000358047	Transcript	frameshift_variant	1343	1291	431	P/X	Ccc/cc	COSM3561513,COSM3561512	.	.	1	FAM47C	HGNC	25301	protein_coding	YES	CCDS35227.1	ENSP00000367913	FA47C_HUMAN	.	UPI000041ABF8	.	.	.	1/1	.	hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642,Pfam_domain:PF14642	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	deletion	.	2	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R434H|c.1301G>A|3,BUFFER|p.R434H|c.1301G>A|3	INDELOCATOR*|VARSCANI*|PINDEL	GAGCCTCCCAAG	.	3	ESCA
TEX11	0	.	GRCh37	X	69898668	69898668	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-V5-AASV-01A-11D-A387-09	TCGA-V5-AASV-10A-01D-A38A-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1273G>A	p.Ala425Thr	p.A425T	ENST00000395889	16/31	106	35	71	84	84	0	TEX11,missense_variant,p.Ala100Thr,ENST00000374320,;TEX11,missense_variant,p.Ala410Thr,ENST00000374333,;TEX11,missense_variant,p.Ala425Thr,ENST00000395889,;TEX11,missense_variant,p.Ala425Thr,ENST00000344304,;	T	ENSG00000120498	ENST00000395889	Transcript	missense_variant	1429	1273	425	A/T	Gcc/Acc	.	.	.	-1	TEX11	HGNC	11733	protein_coding	YES	CCDS35323.1	ENSP00000379226	TEX11_HUMAN	.	UPI000013CA89	.	tolerated(0.09)	benign(0.053)	16/31	.	hmmpanther:PTHR22904:SF291,hmmpanther:PTHR22904,Gene3D:1.25.40.10,Pfam_domain:PF08631,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGGCAGCTT	.	5	ESCA
CHUK	0	.	GRCh37	10	101964869	101964871	+	In_Frame_Del	DEL	TCT	TCT	-	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	TCT	TCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1317_1319delAGA	p.Glu439del	p.E439del	ENST00000370397	12/21	79	54	25	76	76	0	CHUK,inframe_deletion,p.Glu439del,ENST00000370397,;	-	ENSG00000213341	ENST00000370397	Transcript	inframe_deletion	1404-1406	1317-1319	439-440	ED/D	gaAGAc/gac	.	.	.	-1	CHUK	HGNC	1974	protein_coding	YES	CCDS7488.1	ENSP00000359424	IKKA_HUMAN	.	UPI000013D6C7	.	.	.	12/21	.	hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTATAGTCTTCTTT	.	3	ESCA
PAX6	0	.	GRCh37	11	31822342	31822342	+	Silent	SNP	G	G	A	rs1800427	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.462C>T	p.%3D	p.D154D	ENST00000419022	8/14	34	27	7	55	55	0	PAX6,synonymous_variant,p.%3D,ENST00000379111,;PAX6,synonymous_variant,p.%3D,ENST00000379107,;PAX6,synonymous_variant,p.%3D,ENST00000379123,;PAX6,synonymous_variant,p.%3D,ENST00000379109,;PAX6,synonymous_variant,p.%3D,ENST00000455099,;PAX6,synonymous_variant,p.%3D,ENST00000379132,;PAX6,synonymous_variant,p.%3D,ENST00000241001,;PAX6,synonymous_variant,p.%3D,ENST00000419022,;PAX6,synonymous_variant,p.%3D,ENST00000379115,;PAX6,synonymous_variant,p.%3D,ENST00000379129,;PAX6,downstream_gene_variant,,ENST00000423822,;PAX6,downstream_gene_variant,,ENST00000524853,;PAX6,downstream_gene_variant,,ENST00000438681,;PAX6,non_coding_transcript_exon_variant,,ENST00000481563,;PAX6,non_coding_transcript_exon_variant,,ENST00000471303,;PAX6,non_coding_transcript_exon_variant,,ENST00000531910,;PAX6,downstream_gene_variant,,ENST00000533156,;PAX6,upstream_gene_variant,,ENST00000530373,;PAX6,downstream_gene_variant,,ENST00000534353,;PAX6,downstream_gene_variant,,ENST00000530714,;PAX6,non_coding_transcript_exon_variant,,ENST00000470027,;PAX6,non_coding_transcript_exon_variant,,ENST00000533333,;PAX6,non_coding_transcript_exon_variant,,ENST00000494377,;PAX6,non_coding_transcript_exon_variant,,ENST00000534390,;PAX6,intron_variant,,ENST00000464174,;	A	ENSG00000007372	ENST00000419022	Transcript	synonymous_variant	931	462	154	D	gaC/gaT	rs1800427	.	.	-1	PAX6	HGNC	8620	protein_coding	YES	CCDS31452.1	ENSP00000404100	PAX6_HUMAN	Q6VMP0_HUMAN,F1T0F8_HUMAN,E5LBD7_HUMAN,B1B1I9_HUMAN,B1B1I8_HUMAN	UPI000002B0A0	.	.	.	8/14	.	hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCCGTCTGC	byCluster	5	ESCA
ANO9	0	.	GRCh37	11	432006	432006	+	Silent	SNP	C	C	T	rs552399217	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.399G>A	p.%3D	p.S133S	ENST00000332826	5/23	51	43	7	71	71	0	ANO9,synonymous_variant,p.%3D,ENST00000332826,;ANO9,non_coding_transcript_exon_variant,,ENST00000532094,;ANO9,non_coding_transcript_exon_variant,,ENST00000528927,;ANO9,upstream_gene_variant,,ENST00000525857,;ANO9,upstream_gene_variant,,ENST00000526142,;ANO9,upstream_gene_variant,,ENST00000534161,;	T	ENSG00000185101	ENST00000332826	Transcript	synonymous_variant	484	399	133	S	tcG/tcA	rs552399217	.	.	-1	ANO9	HGNC	20679	protein_coding	YES	CCDS31326.1	ENSP00000332788	ANO9_HUMAN	.	UPI00001D782B	.	.	.	5/23	.	hmmpanther:PTHR12308:SF27,hmmpanther:PTHR12308	T:0.0004	T:0	T:0	.	T:0.001	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCCGAGGT	byFrequency|byCluster|by1000G	5	ESCA
BSCL2	0	.	GRCh37	11	62473729	62473729	+	Intron	SNP	A	A	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88-640T>A	.	.	ENST00000433053	.	13	8	5	9	9	0	BSCL2,splice_donor_variant,,ENST00000421906,;BSCL2,5_prime_UTR_variant,,ENST00000407022,;BSCL2,5_prime_UTR_variant,,ENST00000278893,;BSCL2,intron_variant,,ENST00000524862,;BSCL2,intron_variant,,ENST00000433053,;BSCL2,intron_variant,,ENST00000360796,;BSCL2,intron_variant,,ENST00000405837,;BSCL2,intron_variant,,ENST00000464544,;BSCL2,intron_variant,,ENST00000532818,;BSCL2,intron_variant,,ENST00000531524,;BSCL2,intron_variant,,ENST00000525000,;BSCL2,intron_variant,,ENST00000533982,;BSCL2,upstream_gene_variant,,ENST00000403550,;BSCL2,downstream_gene_variant,,ENST00000530009,;GNG3,upstream_gene_variant,,ENST00000294117,;BSCL2,upstream_gene_variant,,ENST00000448568,;BSCL2,downstream_gene_variant,,ENST00000528874,;BSCL2,upstream_gene_variant,,ENST00000537604,;BSCL2,upstream_gene_variant,,ENST00000530900,;BSCL2,intron_variant,,ENST00000301781,;HNRNPUL2-BSCL2,intron_variant,,ENST00000403734,;BSCL2,intron_variant,,ENST00000413908,;	T	ENSG00000168000	ENST00000433053	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	BSCL2	HGNC	15832	protein_coding	YES	CCDS44627.1	ENSP00000414002	BSCL2_HUMAN	F8W7Q8_HUMAN,E9PSB5_HUMAN,E9PRU2_HUMAN,E9PPN5_HUMAN,E9PJS9_HUMAN,E9PJK0_HUMAN,E9PIU3_HUMAN	UPI0000140040	.	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GACTCACCAGC	.	4	ESCA
IGHMBP2	0	.	GRCh37	11	68675711	68675711	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355G>A	p.Asp119Asn	p.D119N	ENST00000255078	3/15	674	587	87	73	73	0	IGHMBP2,missense_variant,p.Asp119Asn,ENST00000255078,;IGHMBP2,missense_variant,p.Asp119Asn,ENST00000539224,;MRPL21,upstream_gene_variant,,ENST00000450904,;MRPL21,upstream_gene_variant,,ENST00000362034,;MRPL21,upstream_gene_variant,,ENST00000567045,;IGHMBP2,3_prime_UTR_variant,,ENST00000544541,;MRPL21,upstream_gene_variant,,ENST00000541265,;MRPL21,upstream_gene_variant,,ENST00000544567,;IGHMBP2,downstream_gene_variant,,ENST00000545146,;MRPL21,upstream_gene_variant,,ENST00000565125,;MRPL21,upstream_gene_variant,,ENST00000536637,;MRPL21,upstream_gene_variant,,ENST00000541279,;	A	ENSG00000132740	ENST00000255078	Transcript	missense_variant	466	355	119	D/N	Gat/Aat	.	.	.	1	IGHMBP2	HGNC	5542	protein_coding	YES	CCDS8187.1	ENSP00000255078	SMBP2_HUMAN	F5H5K3_HUMAN	UPI000013CE82	.	deleterious(0)	possibly_damaging(0.881)	3/15	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF140,TIGRFAM_domain:TIGR00376	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTTTGATGAG	.	4	ESCA
HECTD4	0	.	GRCh37	12	112720968	112720968	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1042C>T	p.Leu348Phe	p.L348F	ENST00000550722	8/76	51	28	23	44	44	0	HECTD4,missense_variant,p.Leu98Phe,ENST00000430131,;HECTD4,missense_variant,p.Leu348Phe,ENST00000550722,;HECTD4,missense_variant,p.Leu348Phe,ENST00000377560,;HECTD4,intron_variant,,ENST00000550724,;	A	ENSG00000173064	ENST00000550722	Transcript	missense_variant	1438	1042	348	L/F	Ctt/Ttt	.	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	probably_damaging(0.976)	8/76	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAAGCGTTG	.	5	ESCA
C12orf49	0	.	GRCh37	12	117154487	117154487	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1128G>A	.	.	ENST00000261318	5/5	14	8	6	13	13	0	C12orf49,3_prime_UTR_variant,,ENST00000261318,;C12orf49,downstream_gene_variant,,ENST00000548356,;C12orf49,downstream_gene_variant,,ENST00000536380,;C12orf49,downstream_gene_variant,,ENST00000547606,;C12orf49,downstream_gene_variant,,ENST00000547630,;	T	ENSG00000111412	ENST00000261318	Transcript	3_prime_UTR_variant	1907	.	.	.	.	.	.	.	-1	C12orf49	HGNC	26128	protein_coding	YES	CCDS9179.1	ENSP00000261318	CL049_HUMAN	F8VVN2_HUMAN	UPI000004A078	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATCTCCCA	.	5	ESCA
PDE3A	0	.	GRCh37	12	20833600	20833600	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*395A>C	.	.	ENST00000359062	16/16	28	17	10	61	61	0	PDE3A,3_prime_UTR_variant,,ENST00000359062,;PDE3A,downstream_gene_variant,,ENST00000544307,;	C	ENSG00000172572	ENST00000359062	Transcript	3_prime_UTR_variant	3861	.	.	.	.	.	.	.	1	PDE3A	HGNC	8778	protein_coding	YES	CCDS31754.1	ENSP00000351957	PDE3A_HUMAN	.	UPI000014175F	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATATAATA	.	5	ESCA
SLCO1B3	0	.	GRCh37	12	21069005	21069005	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1933T>G	p.Phe645Val	p.F645V	ENST00000381545	16/16	53	28	25	64	64	0	SLCO1B3,missense_variant,p.Phe645Val,ENST00000261196,;SLCO1B3,missense_variant,p.Phe645Val,ENST00000381545,;SLCO1B7,intron_variant,,ENST00000554957,;SLCO1B3,intron_variant,,ENST00000553473,;LST3,intron_variant,,ENST00000540229,;LST3,intron_variant,,ENST00000381541,;	G	ENSG00000111700	ENST00000381545	Transcript	missense_variant	2152	1933	645	F/V	Ttt/Gtt	.	.	.	1	SLCO1B3	HGNC	10961	protein_coding	YES	CCDS8684.1	ENSP00000370956	SO1B3_HUMAN	F5H8K0_HUMAN	UPI000013544A	.	tolerated(0.23)	benign(0.007)	16/16	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF89,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTTTTGCT	.	5	ESCA
ABCD2	0	.	GRCh37	12	39973422	39973422	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1793-1G>A	.	p.X598_splice	ENST00000308666	.	42	31	10	37	37	0	ABCD2,splice_acceptor_variant,,ENST00000308666,;	T	ENSG00000173208	ENST00000308666	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	ABCD2	HGNC	66	protein_coding	YES	CCDS8734.1	ENSP00000310688	ABCD2_HUMAN	.	UPI000004C4C6	.	.	.	.	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCTTAAG	.	5	ESCA
CCND2	0	.	GRCh37	12	4409659	4409659	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*484G>A	.	.	ENST00000261254	5/5	43	31	11	28	28	0	CCND2,3_prime_UTR_variant,,ENST00000261254,;CCND2,downstream_gene_variant,,ENST00000536537,;	A	ENSG00000118971	ENST00000261254	Transcript	3_prime_UTR_variant	1623	.	.	.	.	.	.	.	1	CCND2	HGNC	1583	protein_coding	YES	CCDS8524.1	ENSP00000261254	CCND2_HUMAN	.	UPI00001275C5	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATGGGGAAG	.	5	ESCA
STAT6	0	.	GRCh37	12	57492339	57492339	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2108A>T	p.Tyr703Phe	p.Y703F	ENST00000300134	19/22	32	14	18	75	75	0	STAT6,missense_variant,p.Tyr703Phe,ENST00000454075,;STAT6,missense_variant,p.Tyr593Phe,ENST00000538913,;STAT6,missense_variant,p.Tyr593Phe,ENST00000537215,;STAT6,missense_variant,p.Tyr703Phe,ENST00000300134,;STAT6,missense_variant,p.Tyr703Phe,ENST00000543873,;STAT6,missense_variant,p.Tyr703Phe,ENST00000556155,;STAT6,missense_variant,p.Ile129Phe,ENST00000555318,;STAT6,downstream_gene_variant,,ENST00000555375,;STAT6,downstream_gene_variant,,ENST00000553533,;NAB2,downstream_gene_variant,,ENST00000357680,;NAB2,downstream_gene_variant,,ENST00000300131,;NAB2,downstream_gene_variant,,ENST00000342556,;STAT6,3_prime_UTR_variant,,ENST00000554764,;STAT6,non_coding_transcript_exon_variant,,ENST00000555222,;STAT6,downstream_gene_variant,,ENST00000557781,;STAT6,downstream_gene_variant,,ENST00000554202,;STAT6,upstream_gene_variant,,ENST00000557563,;	A	ENSG00000166888	ENST00000300134	Transcript	missense_variant	2434	2108	703	Y/F	tAt/tTt	.	.	.	-1	STAT6	HGNC	11368	protein_coding	YES	CCDS8931.1	ENSP00000300134	STAT6_HUMAN	Q6LCD8_HUMAN,Q5FBW6_HUMAN,G3V5K5_HUMAN,G3V568_HUMAN,G3V3E9_HUMAN,G3V370_HUMAN,G3V2X7_HUMAN,G3V2M3_HUMAN,G3V2L2_HUMAN,G3V2H4_HUMAN	UPI00000473FE	.	tolerated(0.49)	benign(0.002)	19/22	.	hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF45,Pfam_domain:PF14596	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTTGATACGGG	.	3	ESCA
STAT6	0	.	GRCh37	12	57492341	57492341	+	Silent	SNP	C	C	A	rs760639049	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2106G>T	p.%3D	p.P702P	ENST00000300134	19/22	32	13	18	76	76	0	STAT6,missense_variant,p.Arg128Leu,ENST00000555318,;STAT6,synonymous_variant,p.%3D,ENST00000454075,;STAT6,synonymous_variant,p.%3D,ENST00000538913,;STAT6,synonymous_variant,p.%3D,ENST00000537215,;STAT6,synonymous_variant,p.%3D,ENST00000300134,;STAT6,synonymous_variant,p.%3D,ENST00000543873,;STAT6,synonymous_variant,p.%3D,ENST00000556155,;STAT6,downstream_gene_variant,,ENST00000555375,;STAT6,downstream_gene_variant,,ENST00000553533,;NAB2,downstream_gene_variant,,ENST00000357680,;NAB2,downstream_gene_variant,,ENST00000300131,;NAB2,downstream_gene_variant,,ENST00000342556,;STAT6,3_prime_UTR_variant,,ENST00000554764,;STAT6,non_coding_transcript_exon_variant,,ENST00000555222,;STAT6,downstream_gene_variant,,ENST00000557781,;STAT6,downstream_gene_variant,,ENST00000554202,;STAT6,upstream_gene_variant,,ENST00000557563,;	A	ENSG00000166888	ENST00000300134	Transcript	synonymous_variant	2432	2106	702	P	ccG/ccT	rs760639049	.	.	-1	STAT6	HGNC	11368	protein_coding	YES	CCDS8931.1	ENSP00000300134	STAT6_HUMAN	Q6LCD8_HUMAN,Q5FBW6_HUMAN,G3V5K5_HUMAN,G3V568_HUMAN,G3V3E9_HUMAN,G3V370_HUMAN,G3V2X7_HUMAN,G3V2M3_HUMAN,G3V2L2_HUMAN,G3V2H4_HUMAN	UPI00000473FE	.	.	.	19/22	.	hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF45,Pfam_domain:PF14596	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGATACGGGGG	byFrequency	3	ESCA
SLC25A3	0	.	GRCh37	12	98987841	98987845	+	Frame_Shift_Del	DEL	CTCCG	CTCCG	-	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	CTCCG	CTCCG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86_90delTCCGC	p.Leu29GlnfsTer26	p.L29Qfs*26	ENST00000228318	2/8	48	28	20	78	78	0	SLC25A3,frameshift_variant,p.Leu29GlnfsTer27,ENST00000548847,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer27,ENST00000549338,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer27,ENST00000401722,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer24,ENST00000551265,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer26,ENST00000551917,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer26,ENST00000550695,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer27,ENST00000188376,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer27,ENST00000552981,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer26,ENST00000228318,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer26,ENST00000548046,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer27,ENST00000547534,;SLC25A3,frameshift_variant,p.Leu29GlnfsTer26,ENST00000551123,;SLC25A3,non_coding_transcript_exon_variant,,ENST00000546766,;SLC25A3,upstream_gene_variant,,ENST00000547444,;SLC25A3,upstream_gene_variant,,ENST00000547908,;RP11-481K9.4,upstream_gene_variant,,ENST00000420972,;RP11-481K9.4,upstream_gene_variant,,ENST00000557282,;	-	ENSG00000075415	ENST00000228318	Transcript	frameshift_variant	205-209	85-89	29-30	LR/X	CTCCGc/c	.	.	.	1	SLC25A3	HGNC	10989	protein_coding	YES	CCDS9066.1	ENSP00000228318	MPCP_HUMAN	Q6MZF9_HUMAN,F8VZL5_HUMAN,F8VWR4_HUMAN	UPI000012F45B	.	.	.	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGGGACCTCCGCAGCA	.	3	ESCA
DCLK1	0	.	GRCh37	13	36428681	36428681	+	Silent	SNP	C	C	T	rs200783749	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.990G>A	p.%3D	p.S330S	ENST00000255448	6/18	30	5	25	46	46	0	DCLK1,synonymous_variant,p.%3D,ENST00000360631,;DCLK1,synonymous_variant,p.%3D,ENST00000379893,;DCLK1,synonymous_variant,p.%3D,ENST00000255448,;DCLK1,synonymous_variant,p.%3D,ENST00000379892,;DCLK1,non_coding_transcript_exon_variant,,ENST00000460982,;	T	ENSG00000133083	ENST00000255448	Transcript	synonymous_variant	1202	990	330	S	tcG/tcA	rs200783749,COSM292139,COSM292140,COSM3399352,COSM1607040	.	.	-1	DCLK1	HGNC	2700	protein_coding	YES	CCDS9354.1	ENSP00000255448	DCLK1_HUMAN	.	UPI000002A7C2	.	.	.	6/18	.	hmmpanther:PTHR24347:SF123,hmmpanther:PTHR24347,Low_complexity_(Seg):seg	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	0,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S23S|c.69G>A|4,SITE|p.S330S|c.990G>A|5,SITE|p.S330S|c.990G>A|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGCGACTT	byCluster|by1000G	5	ESCA
C14orf28	0	.	GRCh37	14	45376048	45376048	+	3'UTR	SNP	G	G	T	rs530626244	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1295G>T	.	.	ENST00000325192	5/5	15	6	9	16	16	0	C14orf28,3_prime_UTR_variant,,ENST00000325192,;C14orf28,downstream_gene_variant,,ENST00000557112,;RP11-857B24.5,intron_variant,,ENST00000555157,;C14orf28,downstream_gene_variant,,ENST00000553841,;C14orf28,non_coding_transcript_exon_variant,,ENST00000555826,;	T	ENSG00000179476	ENST00000325192	Transcript	3_prime_UTR_variant	2503	.	.	.	.	rs530626244	.	.	1	C14orf28	HGNC	19834	protein_coding	YES	CCDS32069.1	ENSP00000326846	CN028_HUMAN	.	UPI000015FBE3	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGTGAAACA	byCluster	5	ESCA
FERMT2	0	.	GRCh37	14	53326257	53326257	+	Intron	SNP	G	G	A	rs375267385	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1890+34C>T	.	.	ENST00000343279	.	37	20	16	46	46	0	FERMT2,3_prime_UTR_variant,,ENST00000399304,;FERMT2,3_prime_UTR_variant,,ENST00000553663,;FERMT2,intron_variant,,ENST00000553373,;FERMT2,intron_variant,,ENST00000343279,;FERMT2,intron_variant,,ENST00000554152,;FERMT2,intron_variant,,ENST00000341590,;FERMT2,intron_variant,,ENST00000395631,;FERMT2,non_coding_transcript_exon_variant,,ENST00000557255,;FERMT2,downstream_gene_variant,,ENST00000553768,;FERMT2,intron_variant,,ENST00000555546,;	A	ENSG00000073712	ENST00000343279	Transcript	intron_variant	.	.	.	.	.	rs375267385	.	.	-1	FERMT2	HGNC	15767	protein_coding	YES	CCDS45107.1	ENSP00000342858	FERM2_HUMAN	G3V3J0_HUMAN,G3V281_HUMAN	UPI00015DFD70	.	.	.	.	15/15	.	.	.	.	.	.	.	.	C:0.0039	C:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGGACTA	byFrequency|byCluster	5	ESCA
HYPK	0	.	GRCh37	15	44093841	44093841	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.295-68A>G	.	.	ENST00000406925	.	23	11	12	45	45	0	HYPK,3_prime_UTR_variant,,ENST00000458412,;SERF2,intron_variant,,ENST00000594896,;HYPK,intron_variant,,ENST00000406925,;HYPK,intron_variant,,ENST00000442995,;SERF2,intron_variant,,ENST00000600633,;SERF2,downstream_gene_variant,,ENST00000430901,;SERINC4,upstream_gene_variant,,ENST00000249714,;SERINC4,upstream_gene_variant,,ENST00000299969,;SERINC4,upstream_gene_variant,,ENST00000319327,;SERF2,downstream_gene_variant,,ENST00000409646,;SERF2,downstream_gene_variant,,ENST00000409291,;MFAP1,downstream_gene_variant,,ENST00000267812,;HYPK,intron_variant,,ENST00000497142,;HYPK,downstream_gene_variant,,ENST00000498605,;SERF2,intron_variant,,ENST00000409617,;SERF2,intron_variant,,ENST00000448830,;MFAP1,downstream_gene_variant,,ENST00000484386,;SERINC4,upstream_gene_variant,,ENST00000412697,;RP11-296A16.1,upstream_gene_variant,,ENST00000417761,;SERINC4,upstream_gene_variant,,ENST00000457418,;SERINC4,upstream_gene_variant,,ENST00000476490,;SERINC4,upstream_gene_variant,,ENST00000448553,;	G	ENSG00000242028	ENST00000406925	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	HYPK	HGNC	18418	protein_coding	YES	CCDS10104.1	ENSP00000384474	HYPK_HUMAN	.	UPI000000D937	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACAAGCGGA	.	5	ESCA
MAPK6	0	.	GRCh37	15	52356854	52356854	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1823A>T	p.Asn608Ile	p.N608I	ENST00000261845	6/6	72	28	43	102	102	0	MAPK6,missense_variant,p.Asn608Ile,ENST00000261845,;CTD-2184D3.5,intron_variant,,ENST00000558607,;	T	ENSG00000069956	ENST00000261845	Transcript	missense_variant	2630	1823	608	N/I	aAt/aTt	.	.	.	1	MAPK6	HGNC	6879	protein_coding	YES	CCDS10147.1	ENSP00000261845	MK06_HUMAN	.	UPI000012F177	.	deleterious_low_confidence(0)	benign(0.024)	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAAATCAGT	.	5	ESCA
AP1G1	0	.	GRCh37	16	71842857	71842857	+	5'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-195G>A	.	.	ENST00000393512	1/24	56	45	11	32	32	0	AP1G1,5_prime_UTR_variant,,ENST00000569748,;AP1G1,5_prime_UTR_variant,,ENST00000433195,;AP1G1,5_prime_UTR_variant,,ENST00000570017,;AP1G1,5_prime_UTR_variant,,ENST00000393512,;AP1G1,5_prime_UTR_variant,,ENST00000299980,;AP1G1,5_prime_UTR_variant,,ENST00000423132,;AP1G1,upstream_gene_variant,,ENST00000569185,;AP1G1,upstream_gene_variant,,ENST00000567583,;AP1G1,upstream_gene_variant,,ENST00000563104,;AP1G1,upstream_gene_variant,,ENST00000563259,;AP1G1,upstream_gene_variant,,ENST00000565412,;AP1G1,upstream_gene_variant,,ENST00000569975,;AP1G1,non_coding_transcript_exon_variant,,ENST00000565161,;AP1G1,upstream_gene_variant,,ENST00000570297,;AP1G1,5_prime_UTR_variant,,ENST00000565009,;AP1G1,non_coding_transcript_exon_variant,,ENST00000566161,;AP1G1,upstream_gene_variant,,ENST00000568327,;AP1G1,upstream_gene_variant,,ENST00000450149,;	T	ENSG00000166747	ENST00000393512	Transcript	5_prime_UTR_variant	248	.	.	.	.	.	.	.	-1	AP1G1	HGNC	555	protein_coding	YES	CCDS45522.1	ENSP00000377148	AP1G1_HUMAN	H3BV30_HUMAN,H3BS13_HUMAN,H3BRM7_HUMAN,H3BR36_HUMAN,H3BPN9_HUMAN,H3BN75_HUMAN,H3BN71_HUMAN,B3KNW1_HUMAN	UPI000016A4AD	.	.	.	1/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTCCTGGT	.	5	ESCA
DNAAF1	0	.	GRCh37	16	84182611	84182611	+	Splice_Site	SNP	G	G	T	.	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.125-1G>T	.	p.X42_splice	ENST00000378553	.	19	9	10	36	36	0	DNAAF1,splice_acceptor_variant,,ENST00000378553,;DNAAF1,splice_acceptor_variant,,ENST00000334315,;HSDL1,upstream_gene_variant,,ENST00000434463,;HSDL1,upstream_gene_variant,,ENST00000568857,;HSDL1,upstream_gene_variant,,ENST00000564998,;HSDL1,upstream_gene_variant,,ENST00000219439,;HSDL1,upstream_gene_variant,,ENST00000562224,;DNAAF1,splice_acceptor_variant,,ENST00000563093,;DNAAF1,splice_acceptor_variant,,ENST00000567918,;DNAAF1,splice_acceptor_variant,,ENST00000570298,;HSDL1,upstream_gene_variant,,ENST00000567294,;	T	ENSG00000154099	ENST00000378553	Transcript	splice_acceptor_variant	.	.	.	.	.	COSM1380160	.	.	1	DNAAF1	HGNC	30539	protein_coding	YES	CCDS10943.2	ENSP00000367815	DAAF1_HUMAN	H3BP51_HUMAN	UPI000059D3C9	.	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACAGAAATT	.	5	ESCA
RTN4RL1	0	.	GRCh37	17	1838608	1838609	+	3'UTR	INS	-	-	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1181dupT	.	.	ENST00000331238	2/2	71	49	22	49	49	0	RTN4RL1,3_prime_UTR_variant,,ENST00000331238,;	A	ENSG00000185924	ENST00000331238	Transcript	3_prime_UTR_variant	2987-2988	.	.	.	.	.	.	.	-1	RTN4RL1	HGNC	21329	protein_coding	YES	CCDS45569.1	ENSP00000330631	R4RL1_HUMAN	.	UPI000018CD23	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCCTCATATA	.	3	ESCA
SLC16A11	0	.	GRCh37	17	6945037	6945037	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1377C>T	p.%3D	p.S459S	ENST00000308009	4/4	17	4	13	24	24	0	SLC16A11,synonymous_variant,p.%3D,ENST00000308009,;SLC16A11,synonymous_variant,p.%3D,ENST00000447225,;SLC16A11,downstream_gene_variant,,ENST00000574600,;SLC16A13,downstream_gene_variant,,ENST00000308027,;SLC16A11,non_coding_transcript_exon_variant,,ENST00000573338,;SLC16A13,downstream_gene_variant,,ENST00000575844,;	A	ENSG00000174326	ENST00000308009	Transcript	synonymous_variant	1715	1377	459	S	tcC/tcT	.	.	.	-1	SLC16A11	HGNC	23093	protein_coding	YES	CCDS11086.1	ENSP00000310490	MOT11_HUMAN	I3L431_HUMAN	UPI000006F985	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGGGACAG	.	5	ESCA
DNAI2	0	.	GRCh37	17	72305580	72305580	+	Intron	SNP	G	G	A	rs779484407	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1347+53G>A	.	.	ENST00000446837	.	24	20	4	40	40	0	DNAI2,intron_variant,,ENST00000307504,;DNAI2,intron_variant,,ENST00000446837,;DNAI2,intron_variant,,ENST00000582036,;DNAI2,intron_variant,,ENST00000579490,;DNAI2,intron_variant,,ENST00000311014,;AC103809.1,upstream_gene_variant,,ENST00000516976,;RP11-647F2.2,non_coding_transcript_exon_variant,,ENST00000585167,;DNAI2,intron_variant,,ENST00000579055,;DNAI2,upstream_gene_variant,,ENST00000579312,;	A	ENSG00000171595	ENST00000446837	Transcript	intron_variant	.	.	.	.	.	rs779484407	.	.	1	DNAI2	HGNC	18744	protein_coding	YES	CCDS11697.1	ENSP00000400252	DNAI2_HUMAN	.	UPI000013EC1D	.	.	.	.	9/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCCCGGCGTG	.	3	ESCA
TP53	0	.	GRCh37	17	7577115	7577115	+	Frame_Shift_Del	DEL	A	A	-	.	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.823delT	p.Cys275ValfsTer70	p.C275Vfs*70	ENST00000269305	8/11	23	16	7	35	35	0	TP53,frameshift_variant,p.Cys275ValfsTer76,ENST00000420246,;TP53,frameshift_variant,p.Cys275ValfsTer70,ENST00000269305,;TP53,frameshift_variant,p.Cys143ValfsTer?,ENST00000509690,;TP53,frameshift_variant,p.Cys275ValfsTer77,ENST00000359597,;TP53,frameshift_variant,p.Cys275ValfsTer70,ENST00000445888,;TP53,frameshift_variant,p.Cys275ValfsTer68,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	1013	823	275	C/X	Tgt/gt	TP53_g.13803T>A,TP53_g.13803T>G,TP53_g.13803del,TP53_g.13803T>C,COSM43902,COSM45251,COSM11501,COSM2744532,COSM3378443,COSM2744533	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,0,0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.A276P|c.826G>C|3,CODON|p.A276T|c.826G>A|7,CODON|p.A276S|c.826G>T|9,CODON|p.A276P|c.826G>C|16,CODON|p.C275C|c.825T>C|4,CODON|p.C275W|c.825T>G|8,CODON|p.C275*|c.825T>A|3,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278fs*67|c.833delC|3,BUFFER|p.P278F|c.832_833CC>TT|3,BUFFER|p.P278H|c.833C>A|15,BUFFER|p.P278R|c.833C>G|5,BUFFER|p.P278R|c.833C>G|30,BUFFER|p.P278R|c.833C>G|3,BUFFER|p.P278H|c.833C>A|3,BUFFER|p.P278L|c.833C>T|3,BUFFER|p.P278L|c.833C>T|11,BUFFER|p.P278L|c.833C>T|65,BUFFER|p.P278L|c.833C>T|8,BUFFER|p.P278fs*67|c.832delC|3,BUFFER|p.P278T|c.832C>A|29,BUFFER|p.P278A|c.832C>G|25,BUFFER|p.P278T|c.832C>A|8,BUFFER|p.P278A|c.832C>G|4,BUFFER|p.P278A|c.832C>G|10,BUFFER|p.P278S|c.832C>T|4,BUFFER|p.P278S|c.832C>T|3,BUFFER|p.P278S|c.832C>T|8,BUFFER|p.P278S|c.832C>T|55,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273L|c.818G>T|98,BUFFER|p.R273P|c.818G>C|4,BUFFER|p.R273H|c.818G>A|116,BUFFER|p.R273H|c.818G>A|64,BUFFER|p.R273H|c.818G>A|588,BUFFER|p.R273L|c.818G>T|5,BUFFER|p.R273H|c.818G>A|83,BUFFER|p.R273P|c.818G>C|29,BUFFER|p.R273L|c.818G>T|18,BUFFER|p.R273L|c.818G>T|12,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3	INDELOCATOR*|VARSCANI*|PINDEL	AGGCACAAACAC	.	3	ESCA
TP53	0	.	GRCh37	17	7578407	7578407	+	Missense_Mutation	SNP	G	G	C	rs138729528	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	5/11	21	13	8	39	39	0	TP53,missense_variant,p.Arg175Gly,ENST00000413465,;TP53,missense_variant,p.Arg175Gly,ENST00000420246,;TP53,missense_variant,p.Arg175Gly,ENST00000269305,;TP53,missense_variant,p.Arg43Gly,ENST00000509690,;TP53,missense_variant,p.Arg175Gly,ENST00000359597,;TP53,missense_variant,p.Arg82Gly,ENST00000514944,;TP53,missense_variant,p.Arg175Gly,ENST00000445888,;TP53,missense_variant,p.Arg175Gly,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	713	523	175	R/G	Cgc/Ggc	CM118880,rs138729528,CM011013,TP53_g.12511del,TP53_g.12511C>A,TP53_g.12511C>T,TP53_g.12511C>G,COSM10870,COSM43680,COSM43931,COSM45936,COSM707880,COSM179827,COSM707881,COSM179826,COSM707883,COSM179828,COSM4070040,COSM3691867,COSM1640852,COSM3691866,COSM179829,COSM707882	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.985)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	A:0.0002	A:0,A:0	A:0,A:0	.	A:0,A:0	A:0,A:0	A:0.001,A:0.001	.	.	.	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R82G|c.244C>G|5,SITE|p.R43G|c.127C>G|8,SITE|p.R175G|c.523C>G|5,SITE|p.R175G|c.523C>G|5,SITE|p.R175G|c.523C>G|16,CODON|p.0?|c.1_1182del1182|6,CODON|p.R175L|c.524G>T|20,CODON|p.R175H|c.524G>A|181,CODON|p.R175P|c.524G>C|6,CODON|p.R43H|c.128G>A|183,CODON|p.R82H|c.245G>A|183,CODON|p.R175H|c.524G>A|124,CODON|p.R175L|c.524G>T|3,CODON|p.R175L|c.524G>T|3,CODON|p.R175H|c.524G>A|180,CODON|p.R175H|c.524G>A|926,CODON|p.R175L|c.524G>T|3,CODON|p.R175H|c.524G>A|88,CODON|p.R43L|c.128G>T|3,CODON|p.R82L|c.245G>T|3,BUFFER|p.P177_C182delPHHERC|c.529_546del18|9,BUFFER|p.P177_C182delPHHERC|c.526_543del18|3,BUFFER|p.H179Y|c.534_535CC>TT|8,BUFFER|p.H178Q|c.534C>A|5,BUFFER|p.H178fs*69|c.532delC|10,BUFFER|p.H178P|c.533A>C|7,BUFFER|p.H178D|c.532C>G|5,BUFFER|p.H178N|c.532C>A|3,BUFFER|p.H178Y|c.532C>T|7,BUFFER|p.P177P|c.531C>T|7,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P177L|c.530C>T|20,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177R|c.530C>G|18,BUFFER|p.P177R|c.530C>G|3,BUFFER|p.P84L|c.251C>T|4,BUFFER|p.P45L|c.134C>T|4,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P177L|c.530C>T|3,BUFFER|p.P45R|c.134C>G|3,BUFFER|p.P177L|c.530C>T|4,BUFFER|p.P84R|c.251C>G|3,BUFFER|p.H178fs*69|c.528delC|3,BUFFER|p.P177S|c.529C>T|10,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C44*|c.132C>A|3,BUFFER|p.C176*|c.528C>A|11,BUFFER|p.C176W|c.528C>G|12,BUFFER|p.C83*|c.249C>A|3,BUFFER|p.C176*|c.528C>A|3,BUFFER|p.C176fs*71|c.526delT|7,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C44Y|c.131G>A|20,BUFFER|p.C176F|c.527G>T|133,BUFFER|p.C176Y|c.527G>A|73,BUFFER|p.C176F|c.527G>T|11,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176F|c.527G>T|33,BUFFER|p.C83Y|c.248G>A|19,BUFFER|p.C176Y|c.527G>A|19,BUFFER|p.C176S|c.527G>C|9,BUFFER|p.C83F|c.248G>T|33,BUFFER|p.C176Y|c.527G>A|11,BUFFER|p.C176Y|c.527G>A|9,BUFFER|p.C44F|c.131G>T|34,BUFFER|p.C176F|c.527G>T|17,BUFFER|p.C83S|c.247T>A|3,BUFFER|p.C44R|c.130T>C|4,BUFFER|p.C83R|c.247T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C44G|c.130T>G|4,BUFFER|p.C44S|c.130T>A|3,BUFFER|p.C176S|c.526T>A|12,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176S|c.526T>A|3,BUFFER|p.C83G|c.247T>G|4,BUFFER|p.C176G|c.526T>G|7,BUFFER|p.C176R|c.526T>C|4,BUFFER|p.C176G|c.526T>G|4,BUFFER|p.C176R|c.526T>C|13,BUFFER|p.C176fs*5|c.525_526insN|3,BUFFER|p.R175C|c.523C>T|18,BUFFER|p.R175S|c.523C>A|6,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R43C|c.127C>T|4,BUFFER|p.R82C|c.244C>T|4,BUFFER|p.R175C|c.523C>T|4,BUFFER|p.R174K|c.521G>A|5,BUFFER|p.R174W|c.520A>T|11,BUFFER|p.V173V|c.519G>A|6,BUFFER|p.V173V|c.519G>T|3,BUFFER|p.V173A|c.518T>C|14,BUFFER|p.V173G|c.518T>G|8,BUFFER|p.V173E|c.518T>A|4,BUFFER|p.V41E|c.122T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V80E|c.239T>A|3,BUFFER|p.V173E|c.518T>A|3,BUFFER|p.V173fs*1|c.517delG|4,BUFFER|p.V41L|c.121G>T|9,BUFFER|p.V80L|c.238G>T|9,BUFFER|p.V173M|c.517G>A|10,BUFFER|p.V80L|c.238G>C|5,BUFFER|p.V41M|c.121G>A|11,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|11,BUFFER|p.V173L|c.517G>C|15,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173L|c.517G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V80M|c.238G>A|11,BUFFER|p.V173L|c.517G>T|52,BUFFER|p.V173L|c.517G>T|9,BUFFER|p.V173M|c.517G>A|50,BUFFER|p.V41L|c.121G>C|5,BUFFER|p.V173M|c.517G>A|4,BUFFER|p.V172D|c.515T>A|11,BUFFER|p.V172A|c.515T>C|4,BUFFER|p.V172G|c.515T>G|4,BUFFER|p.V172fs*2|c.514delG|3,BUFFER|p.V79F|c.235G>T|5,BUFFER|p.V172F|c.514G>T|16,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.V40F|c.118G>T|6,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172F|c.514G>T|5,BUFFER|p.V172I|c.514G>A|8,BUFFER|p.V172F|c.514G>T|4,BUFFER|p.E171G|c.512A>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCGCCTCA	by1000G	5	ESCA
HGS	0	.	GRCh37	17	79662971	79662971	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1335C>T	p.%3D	p.S445S	ENST00000329138	15/22	22	11	10	33	33	0	HGS,synonymous_variant,p.%3D,ENST00000571237,;HGS,synonymous_variant,p.%3D,ENST00000329138,;HGS,upstream_gene_variant,,ENST00000575078,;HGS,upstream_gene_variant,,ENST00000573320,;HGS,downstream_gene_variant,,ENST00000572392,;HGS,non_coding_transcript_exon_variant,,ENST00000571885,;HGS,upstream_gene_variant,,ENST00000573949,;HGS,downstream_gene_variant,,ENST00000576498,;HGS,downstream_gene_variant,,ENST00000575058,;HGS,downstream_gene_variant,,ENST00000573080,;HGS,upstream_gene_variant,,ENST00000571647,;HGS,upstream_gene_variant,,ENST00000570355,;	T	ENSG00000185359	ENST00000329138	Transcript	synonymous_variant	1470	1335	445	S	tcC/tcT	.	.	.	1	HGS	HGNC	4897	protein_coding	YES	CCDS11784.1	ENSP00000331201	HGS_HUMAN	I3L2H4_HUMAN,I3L165_HUMAN	UPI000004493D	.	.	.	15/22	.	hmmpanther:PTHR13856,hmmpanther:PTHR13856:SF79,Pfam_domain:PF12210,PIRSF_domain:PIRSF036956	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTCCATCAA	.	5	ESCA
ABHD3	0	.	GRCh37	18	19231348	19231348	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*204G>A	.	.	ENST00000289119	9/9	56	34	21	175	175	0	ABHD3,3_prime_UTR_variant,,ENST00000580981,;ABHD3,3_prime_UTR_variant,,ENST00000289119,;ABHD3,3_prime_UTR_variant,,ENST00000578270,;ABHD3,downstream_gene_variant,,ENST00000580477,;ABHD3,downstream_gene_variant,,ENST00000577564,;	T	ENSG00000158201	ENST00000289119	Transcript	3_prime_UTR_variant	1574	.	.	.	.	.	.	.	-1	ABHD3	HGNC	18718	protein_coding	YES	CCDS32802.1	ENSP00000289119	ABHD3_HUMAN	.	UPI0000163938	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTACGTAAG	.	5	ESCA
GCDH	0	.	GRCh37	19	13010666	13010666	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*311C>G	.	.	ENST00000222214	12/12	15	5	10	30	30	0	GCDH,3_prime_UTR_variant,,ENST00000222214,;GCDH,3_prime_UTR_variant,,ENST00000422947,;GCDH,3_prime_UTR_variant,,ENST00000457854,;GCDH,3_prime_UTR_variant,,ENST00000591470,;SYCE2,intron_variant,,ENST00000592819,;GCDH,intron_variant,,ENST00000591050,;SYCE2,intron_variant,,ENST00000293695,;GCDH,downstream_gene_variant,,ENST00000588905,;GCDH,downstream_gene_variant,,ENST00000590472,;GCDH,downstream_gene_variant,,ENST00000589039,;GCDH,non_coding_transcript_exon_variant,,ENST00000588242,;SYCE2,downstream_gene_variant,,ENST00000591229,;GCDH,3_prime_UTR_variant,,ENST00000590530,;GCDH,downstream_gene_variant,,ENST00000421816,;GCDH,downstream_gene_variant,,ENST00000585420,;GCDH,downstream_gene_variant,,ENST00000591043,;AD000092.3,downstream_gene_variant,,ENST00000464444,;	G	ENSG00000105607	ENST00000222214	Transcript	3_prime_UTR_variant	1839	.	.	.	.	.	.	.	1	GCDH	HGNC	4189	protein_coding	YES	CCDS12286.1	ENSP00000222214	GCDH_HUMAN	.	UPI000012B292	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGCTGACC	.	5	ESCA
DCAF15	0	.	GRCh37	19	14066943	14066943	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482C>T	p.Ser161Leu	p.S161L	ENST00000254337	5/13	25	8	16	60	60	0	DCAF15,missense_variant,p.Ser161Leu,ENST00000254337,;PODNL1,upstream_gene_variant,,ENST00000538517,;DCAF15,upstream_gene_variant,,ENST00000587307,;PODNL1,upstream_gene_variant,,ENST00000585607,;DCAF15,upstream_gene_variant,,ENST00000585468,;PODNL1,upstream_gene_variant,,ENST00000538371,;PODNL1,upstream_gene_variant,,ENST00000587458,;PODNL1,upstream_gene_variant,,ENST00000588317,;DCAF15,upstream_gene_variant,,ENST00000588523,;DCAF15,upstream_gene_variant,,ENST00000591385,;DCAF15,downstream_gene_variant,,ENST00000591802,;	T	ENSG00000132017	ENST00000254337	Transcript	missense_variant	503	482	161	S/L	tCg/tTg	.	.	.	1	DCAF15	HGNC	25095	protein_coding	YES	CCDS32926.1	ENSP00000254337	DCA15_HUMAN	.	UPI0000203531	.	tolerated(0.06)	benign(0.116)	5/13	.	Pfam_domain:PF14939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCTCGGCCA	.	5	ESCA
APC2	0	.	GRCh37	19	1456085	1456085	+	Missense_Mutation	SNP	C	C	G	rs565260681	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650C>G	p.Ser217Trp	p.S217W	ENST00000535453	6/14	12	9	3	15	15	0	APC2,missense_variant,p.Ser217Trp,ENST00000233607,;APC2,missense_variant,p.Ser217Trp,ENST00000590469,;APC2,missense_variant,p.Ser217Trp,ENST00000535453,;APC2,intron_variant,,ENST00000238483,;APC2,downstream_gene_variant,,ENST00000587149,;APC2,downstream_gene_variant,,ENST00000587869,;APC2,downstream_gene_variant,,ENST00000590877,;CTB-25B13.12,downstream_gene_variant,,ENST00000588225,;APC2,non_coding_transcript_exon_variant,,ENST00000593146,;CTB-25B13.12,downstream_gene_variant,,ENST00000591252,;	G	ENSG00000115266	ENST00000535453	Transcript	missense_variant	2363	650	217	S/W	tCg/tGg	rs565260681	.	.	1	APC2	HGNC	24036	protein_coding	YES	CCDS12068.1	ENSP00000442954	APC2_HUMAN	K7ELQ3_HUMAN,K7EN62_HUMAN	UPI0000073D85	.	.	probably_damaging(0.993)	6/14	.	Superfamily_domains:0053482,Gene3D:1.10.287.450,hmmpanther:PTHR12607:SF3,hmmpanther:PTHR12607	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CGCCTCGCGCC	by1000G	2	ESCA
ANKLE1	0	.	GRCh37	19	17396582	17396582	+	Silent	SNP	C	C	T	rs370950297	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1629C>T	p.%3D	p.V543V	ENST00000394458	8/9	29	20	9	60	60	0	ANKLE1,synonymous_variant,p.%3D,ENST00000594072,;ANKLE1,synonymous_variant,p.%3D,ENST00000404085,;ANKLE1,synonymous_variant,p.%3D,ENST00000394458,;ANKLE1,3_prime_UTR_variant,,ENST00000433424,;ANKLE1,intron_variant,,ENST00000598347,;USHBP1,upstream_gene_variant,,ENST00000598309,;ANKLE1,3_prime_UTR_variant,,ENST00000404261,;ANKLE1,non_coding_transcript_exon_variant,,ENST00000596626,;BABAM1,downstream_gene_variant,,ENST00000594247,;ANKLE1,downstream_gene_variant,,ENST00000596099,;ANKLE1,downstream_gene_variant,,ENST00000596834,;ANKLE1,downstream_gene_variant,,ENST00000601401,;CTD-2278I10.6,downstream_gene_variant,,ENST00000596542,;	T	ENSG00000160117	ENST00000394458	Transcript	synonymous_variant	1905	1629	543	V	gtC/gtT	rs370950297	.	.	1	ANKLE1	HGNC	26812	protein_coding	YES	.	ENSP00000377971	ANKL1_HUMAN	.	UPI000165D67E	.	.	.	8/9	.	PROSITE_profiles:PS50164,hmmpanther:PTHR13428:SF5,hmmpanther:PTHR13428	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGTCGCTGT	byFrequency|byCluster	5	ESCA
MRPS12	0	.	GRCh37	19	39422990	39422990	+	Missense_Mutation	SNP	C	C	T	rs150096976	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.67C>T	p.Arg23Trp	p.R23W	ENST00000407800	2/2	75	42	32	96	96	0	MRPS12,missense_variant,p.Arg23Trp,ENST00000407800,;MRPS12,missense_variant,p.Arg23Trp,ENST00000308018,;MRPS12,missense_variant,p.Arg23Trp,ENST00000402029,;SARS2,intron_variant,,ENST00000448145,;CTC-360G5.8,intron_variant,,ENST00000599996,;SARS2,upstream_gene_variant,,ENST00000600042,;SARS2,upstream_gene_variant,,ENST00000221431,;SARS2,upstream_gene_variant,,ENST00000594171,;SARS2,upstream_gene_variant,,ENST00000430193,;CTC-360G5.9,downstream_gene_variant,,ENST00000599320,;SARS2,upstream_gene_variant,,ENST00000455102,;SARS2,upstream_gene_variant,,ENST00000598343,;MRPS12,downstream_gene_variant,,ENST00000598734,;SARS2,upstream_gene_variant,,ENST00000598598,;SARS2,upstream_gene_variant,,ENST00000593754,;	T	ENSG00000128626	ENST00000407800	Transcript	missense_variant	408	67	23	R/W	Cgg/Tgg	rs150096976	.	.	1	MRPS12	HGNC	10380	protein_coding	YES	CCDS12525.1	ENSP00000384952	RT12_HUMAN	.	UPI0000135267	.	tolerated(0.19)	benign(0.316)	2/2	.	hmmpanther:PTHR11652	.	.	.	.	.	.	.	T:0.0005	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCCCGGCTC	byFrequency|byCluster	5	ESCA
SIGLEC5	0	.	GRCh37	19	52132662	52132662	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.649C>T	p.Arg217Cys	p.R217C	ENST00000570106	3/9	60	32	28	66	66	0	SIGLEC5,missense_variant,p.Arg217Cys,ENST00000534261,;SIGLEC5,missense_variant,p.Arg217Cys,ENST00000599649,;SIGLEC5,missense_variant,p.Arg217Cys,ENST00000570106,;SIGLEC5,missense_variant,p.Arg217Cys,ENST00000429354,;SIGLEC5,missense_variant,p.Arg217Cys,ENST00000222107,;	A	ENSG00000105501	ENST00000570106	Transcript	missense_variant	649	649	217	R/C	Cgc/Tgc	.	.	.	-1	SIGLEC5	HGNC	10874	protein_coding	YES	CCDS33088.1	ENSP00000455510	SIGL5_HUMAN	.	UPI000011B40C	.	deleterious(0.03)	possibly_damaging(0.641)	3/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF49,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGCGTTTCA	.	5	ESCA
ZNF415	0	.	GRCh37	19	53611721	53611721	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1577G>A	p.Cys526Tyr	p.C526Y	ENST00000500065	4/4	78	59	19	182	182	0	ZNF415,missense_variant,p.Cys513Tyr,ENST00000440291,;ZNF415,missense_variant,p.Cys574Tyr,ENST00000455735,;ZNF415,missense_variant,p.Cys574Tyr,ENST00000448501,;ZNF415,missense_variant,p.Cys296Tyr,ENST00000601493,;ZNF415,missense_variant,p.Cys526Tyr,ENST00000500065,;ZNF415,missense_variant,p.Cys526Tyr,ENST00000243643,;ZNF415,missense_variant,p.Cys538Tyr,ENST00000421033,;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,;	T	ENSG00000170954	ENST00000500065	Transcript	missense_variant	1911	1577	526	C/Y	tGt/tAt	.	.	.	-1	ZNF415	HGNC	20636	protein_coding	YES	CCDS54313.1	ENSP00000439435	ZN415_HUMAN	.	UPI0000E04BC1	.	deleterious(0.03)	probably_damaging(0.981)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTACATTTG	.	5	ESCA
ZNF562	0	.	GRCh37	19	9771405	9771405	+	Missense_Mutation	SNP	T	T	C	rs372227919	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16A>G	p.Met6Val	p.M6V	ENST00000448622	2/6	36	28	8	69	69	0	ZNF562,missense_variant,p.Met6Val,ENST00000293648,;ZNF562,missense_variant,p.Met6Val,ENST00000448622,;ZNF562,missense_variant,p.Met6Val,ENST00000587392,;ZNF562,missense_variant,p.Met6Val,ENST00000590155,;ZNF562,missense_variant,p.Met6Val,ENST00000585350,;ZNF562,missense_variant,p.Met6Val,ENST00000589542,;ZNF562,missense_variant,p.Met6Val,ENST00000453372,;ZNF562,5_prime_UTR_variant,,ENST00000537617,;ZNF562,5_prime_UTR_variant,,ENST00000588653,;ZNF562,5_prime_UTR_variant,,ENST00000541032,;ZNF562,intron_variant,,ENST00000453792,;ZNF562,missense_variant,p.Met6Val,ENST00000585688,;	C	ENSG00000171466	ENST00000448622	Transcript	missense_variant	179	16	6	M/V	Atg/Gtg	rs372227919	.	.	-1	ZNF562	HGNC	25950	protein_coding	YES	CCDS45956.1	ENSP00000411784	ZN562_HUMAN	K7ELE4_HUMAN,B4E2P7_HUMAN	UPI000067CA26	.	deleterious(0.04)	benign(0.001)	2/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACATATCAA	.	5	ESCA
TNFRSF1B	0	.	GRCh37	1	12268239	12268239	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1162C>T	.	.	ENST00000376259	10/10	15	8	6	20	20	0	TNFRSF1B,3_prime_UTR_variant,,ENST00000376259,;TNFRSF1B,non_coding_transcript_exon_variant,,ENST00000492361,;	T	ENSG00000028137	ENST00000376259	Transcript	3_prime_UTR_variant	2637	.	.	.	.	.	.	.	1	TNFRSF1B	HGNC	11917	protein_coding	YES	CCDS145.1	ENSP00000365435	TNR1B_HUMAN	Q9UIH2_HUMAN,Q9UIG9_HUMAN,Q6LBF2_HUMAN	UPI000002FAE1	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TGCAGCCCCGC	.	4	ESCA
CRB1	0	.	GRCh37	1	197411469	197411470	+	Intron	DEL	TT	TT	-	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4005+50_4005+51delTT	.	.	ENST00000367400	.	40	34	6	36	36	0	CRB1,3_prime_UTR_variant,,ENST00000367397,;CRB1,intron_variant,,ENST00000448952,;CRB1,intron_variant,,ENST00000538660,;CRB1,intron_variant,,ENST00000544212,;CRB1,intron_variant,,ENST00000367399,;CRB1,intron_variant,,ENST00000535699,;CRB1,intron_variant,,ENST00000367400,;RP11-75C23.1,non_coding_transcript_exon_variant,,ENST00000422250,;CRB1,frameshift_variant,p.Phe1352SerfsTer12,ENST00000484075,;	-	ENSG00000134376	ENST00000367400	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CRB1	HGNC	2343	protein_coding	YES	CCDS1390.1	ENSP00000356370	CRUM1_HUMAN	B7Z824_HUMAN	UPI0000073345	.	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAATCTTTTTCA	.	3	ESCA
IKBKE	0	.	GRCh37	1	206653841	206653841	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1392C>T	p.%3D	p.S464S	ENST00000367120	13/22	64	16	47	52	51	0	IKBKE,synonymous_variant,p.%3D,ENST00000367120,;IKBKE,synonymous_variant,p.%3D,ENST00000537984,;IKBKE,non_coding_transcript_exon_variant,,ENST00000492570,;	T	ENSG00000143466	ENST00000367120	Transcript	synonymous_variant	1765	1392	464	S	tcC/tcT	.	.	.	1	IKBKE	HGNC	14552	protein_coding	YES	CCDS30996.1	ENSP00000356087	IKKE_HUMAN	.	UPI0000033727	.	.	.	13/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCCCTCCT	.	5	ESCA
ANGEL2	0	.	GRCh37	1	213181560	213181560	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.634G>C	p.Asp212His	p.D212H	ENST00000366962	3/9	59	17	42	39	39	0	ANGEL2,missense_variant,p.Asp43His,ENST00000360506,;ANGEL2,missense_variant,p.Asp43His,ENST00000535388,;ANGEL2,missense_variant,p.Asp43His,ENST00000544555,;ANGEL2,missense_variant,p.Asp86His,ENST00000540642,;ANGEL2,missense_variant,p.Asp212His,ENST00000366962,;ANGEL2,non_coding_transcript_exon_variant,,ENST00000476904,;ANGEL2,non_coding_transcript_exon_variant,,ENST00000460337,;ANGEL2,non_coding_transcript_exon_variant,,ENST00000481918,;	G	ENSG00000174606	ENST00000366962	Transcript	missense_variant	789	634	212	D/H	Gat/Cat	.	.	.	-1	ANGEL2	HGNC	30534	protein_coding	YES	CCDS1512.1	ENSP00000355929	ANGE2_HUMAN	.	UPI00001D3EF4	.	deleterious(0)	probably_damaging(0.973)	3/9	.	Superfamily_domains:SSF56219,Pfam_domain:PF03372,Gene3D:3.60.10.10,hmmpanther:PTHR12121:SF27,hmmpanther:PTHR12121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCATCAAAAT	.	5	ESCA
CLCA4	0	.	GRCh37	1	87040226	87040226	+	Missense_Mutation	SNP	G	G	A	rs201791111	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1471G>A	p.Glu491Lys	p.E491K	ENST00000370563	10/14	30	18	11	82	82	0	CLCA4,missense_variant,p.Glu491Lys,ENST00000370563,;CLCA4,downstream_gene_variant,,ENST00000263723,;RP4-651E10.4,intron_variant,,ENST00000456587,;CLCA4,downstream_gene_variant,,ENST00000496322,;	A	ENSG00000016602	ENST00000370563	Transcript	missense_variant	1513	1471	491	E/K	Gaa/Aaa	rs201791111,COSM1344675	.	.	1	CLCA4	HGNC	2018	protein_coding	YES	CCDS41355.1	ENSP00000359594	CLCA4_HUMAN	Q9NXP1_HUMAN	UPI00000389E8	.	deleterious(0)	probably_damaging(0.996)	10/14	.	hmmpanther:PTHR10579,hmmpanther:PTHR10579:SF2,Pfam_domain:PF09315,TIGRFAM_domain:TIGR00868	A:0.0006	A:0.0008	A:0	.	A:0	A:0.001	A:0.001	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTCGAAAGT	byFrequency|byCluster|by1000G	5	ESCA
BCL2L1	0	.	GRCh37	20	30309595	30309595	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427T>C	p.Phe143Leu	p.F143L	ENST00000307677	2/3	63	60	3	127	127	0	BCL2L1,missense_variant,p.Phe143Leu,ENST00000420488,;BCL2L1,missense_variant,p.Phe143Leu,ENST00000439267,;BCL2L1,missense_variant,p.Phe143Leu,ENST00000420653,;BCL2L1,missense_variant,p.Phe143Leu,ENST00000376062,;BCL2L1,missense_variant,p.Phe143Leu,ENST00000456404,;BCL2L1,missense_variant,p.Phe143Leu,ENST00000422920,;BCL2L1,missense_variant,p.Phe143Leu,ENST00000450273,;BCL2L1,missense_variant,p.Phe143Leu,ENST00000307677,;BCL2L1,intron_variant,,ENST00000376055,;BCL2L1,downstream_gene_variant,,ENST00000434194,;AL160175.1,downstream_gene_variant,,ENST00000597287,;RP11-243J16.7,downstream_gene_variant,,ENST00000412972,;	G	ENSG00000171552	ENST00000307677	Transcript	missense_variant	838	427	143	F/L	Ttt/Ctt	.	.	.	-1	BCL2L1	HGNC	992	protein_coding	YES	CCDS13189.1	ENSP00000302564	B2CL1_HUMAN	Q9H1R6_HUMAN,Q5TE64_HUMAN,Q5QP59_HUMAN,Q5QP56_HUMAN	UPI0000000CEC	.	tolerated(1)	probably_damaging(0.939)	2/3	.	PROSITE_profiles:PS50062,hmmpanther:PTHR11256:SF12,hmmpanther:PTHR11256,PROSITE_patterns:PS01080,Gene3D:1.10.437.10,Pfam_domain:PF00452,TIGRFAM_domain:TIGR00865,SMART_domains:SM00337,Superfamily_domains:SSF56854,Prints_domain:PR01862	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAAAGGCCA	.	2	ESCA
GGT7	0	.	GRCh37	20	33451262	33451262	+	Missense_Mutation	SNP	C	C	T	rs773925975	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259G>A	p.Glu87Lys	p.E87K	ENST00000336431	2/15	28	23	5	34	34	0	GGT7,missense_variant,p.Glu104Lys,ENST00000427420,;GGT7,missense_variant,p.Glu87Lys,ENST00000336431,;	T	ENSG00000131067	ENST00000336431	Transcript	missense_variant	304	259	87	E/K	Gag/Aag	rs773925975	.	.	-1	GGT7	HGNC	4259	protein_coding	YES	CCDS13242.2	ENSP00000338964	GGT7_HUMAN	A4FU32_HUMAN,A0PJJ9_HUMAN	UPI000004C2AB	.	deleterious(0.01)	probably_damaging(0.989)	2/15	.	hmmpanther:PTHR11686:SF18,hmmpanther:PTHR11686	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGTCTCGCGTA	.	4	ESCA
PANK2	0	.	GRCh37	20	3891428	3891428	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1186A>T	p.Ile396Phe	p.I396F	ENST00000316562	3/7	42	22	20	61	61	0	PANK2,missense_variant,p.Ile105Phe,ENST00000497424,;PANK2,missense_variant,p.Ile273Phe,ENST00000610179,;PANK2,missense_variant,p.Ile396Phe,ENST00000316562,;PANK2,5_prime_UTR_variant,,ENST00000495692,;PANK2,non_coding_transcript_exon_variant,,ENST00000464452,;PANK2,non_coding_transcript_exon_variant,,ENST00000471830,;PANK2,3_prime_UTR_variant,,ENST00000336066,;	T	ENSG00000125779	ENST00000316562	Transcript	missense_variant	1192	1186	396	I/F	Atc/Ttc	.	.	.	1	PANK2	HGNC	15894	protein_coding	YES	CCDS13071.2	ENSP00000313377	PANK2_HUMAN	Q52M85_HUMAN,D3DVZ1_HUMAN,A4FU43_HUMAN	UPI000036701A	.	deleterious(0.01)	probably_damaging(0.996)	3/7	.	hmmpanther:PTHR12280:SF25,hmmpanther:PTHR12280,TIGRFAM_domain:TIGR00555,Pfam_domain:PF03630,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGCATCTTA	.	5	ESCA
WFDC8	0	.	GRCh37	20	44184456	44184456	+	Missense_Mutation	SNP	C	C	T	rs750785099	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.329G>A	p.Arg110His	p.R110H	ENST00000357199	4/7	52	33	19	74	74	0	WFDC8,missense_variant,p.Arg110His,ENST00000357199,;WFDC8,missense_variant,p.Arg110His,ENST00000289953,;RNA5SP485,downstream_gene_variant,,ENST00000365053,;	T	ENSG00000158901	ENST00000357199	Transcript	missense_variant	408	329	110	R/H	cGc/cAc	rs750785099	.	.	-1	WFDC8	HGNC	16163	protein_coding	YES	CCDS13361.1	ENSP00000361735	WFDC8_HUMAN	.	UPI000016059B	.	tolerated(0.19)	benign(0.208)	4/7	.	PROSITE_profiles:PS50279,hmmpanther:PTHR10083:SF169,hmmpanther:PTHR10083,Pfam_domain:PF00014,Gene3D:4.10.410.10,SMART_domains:SM00131,Superfamily_domains:SSF57362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAGCGCTGT	byFrequency	5	ESCA
LAMA5	0	.	GRCh37	20	60912736	60912736	+	Missense_Mutation	SNP	G	G	A	rs777979653	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2074C>T	p.Arg692Trp	p.R692W	ENST00000252999	16/80	65	43	22	55	55	0	LAMA5,missense_variant,p.Arg692Trp,ENST00000252999,;LAMA5,downstream_gene_variant,,ENST00000370692,;LAMA5,upstream_gene_variant,,ENST00000474128,;	A	ENSG00000130702	ENST00000252999	Transcript	missense_variant	2141	2074	692	R/W	Cgg/Tgg	rs777979653	.	.	-1	LAMA5	HGNC	6485	protein_coding	YES	CCDS33502.1	ENSP00000252999	LAMA5_HUMAN	O75079_HUMAN	UPI0000161FDC	.	.	probably_damaging(0.983)	16/80	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF261,hmmpanther:PTHR10574,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196,Prints_domain:PR00011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCGGGGGT	byFrequency	5	ESCA
GMEB2	0	.	GRCh37	20	62221818	62221818	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1217C>T	p.Pro406Leu	p.P406L	ENST00000266068	9/9	21	11	9	19	19	0	GMEB2,missense_variant,p.Pro406Leu,ENST00000266068,;GMEB2,missense_variant,p.Pro355Leu,ENST00000370069,;GMEB2,missense_variant,p.Pro406Leu,ENST00000370077,;	A	ENSG00000101216	ENST00000266068	Transcript	missense_variant	1696	1217	406	P/L	cCg/cTg	.	.	.	-1	GMEB2	HGNC	4371	protein_coding	YES	CCDS13528.1	ENSP00000266068	GMEB2_HUMAN	Q659E7_HUMAN,Q5JTV1_HUMAN	UPI000012B8AD	.	deleterious(0)	benign(0.124)	9/9	.	hmmpanther:PTHR10417,hmmpanther:PTHR10417:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGACGGCAGG	.	5	ESCA
DEFB125	0	.	GRCh37	20	76735	76735	+	Missense_Mutation	SNP	A	A	G	rs769435585	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148A>G	p.Arg50Gly	p.R50G	ENST00000382410	2/2	43	30	13	58	58	0	DEFB125,missense_variant,p.Arg50Gly,ENST00000382410,;DEFB125,non_coding_transcript_exon_variant,,ENST00000608838,;	G	ENSG00000178591	ENST00000382410	Transcript	missense_variant	148	148	50	R/G	Agg/Ggg	rs769435585	.	.	1	DEFB125	HGNC	18105	protein_coding	YES	CCDS12989.2	ENSP00000371847	DB125_HUMAN	B2R4E8_HUMAN	UPI00001A36DE	.	tolerated(0.11)	benign(0.001)	2/2	.	hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF4,Pfam_domain:PF13841	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGTAGGAAC	byFrequency	5	ESCA
SLC25A18	0	.	GRCh37	22	18063897	18063897	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115C>T	p.Gln39Ter	p.Q39*	ENST00000327451	4/11	29	14	14	59	59	0	SLC25A18,stop_gained,p.Gln39Ter,ENST00000327451,;SLC25A18,stop_gained,p.Gln39Ter,ENST00000399813,;AC004019.13,intron_variant,,ENST00000443935,;SLC25A18,non_coding_transcript_exon_variant,,ENST00000497401,;SLC25A18,non_coding_transcript_exon_variant,,ENST00000467228,;	T	ENSG00000182902	ENST00000327451	Transcript	stop_gained	653	115	39	Q/*	Cag/Tag	.	.	.	1	SLC25A18	HGNC	10988	protein_coding	YES	CCDS13744.1	ENSP00000329033	GHC2_HUMAN	.	UPI00000015FA	.	.	.	4/11	.	PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF252,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACCAGCAT	.	5	ESCA
COMT	0	.	GRCh37	22	19951267	19951267	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.468T>C	p.%3D	p.A156A	ENST00000361682	4/6	28	16	12	58	58	0	COMT,synonymous_variant,p.%3D,ENST00000428707,;COMT,synonymous_variant,p.%3D,ENST00000403184,;COMT,synonymous_variant,p.%3D,ENST00000407537,;COMT,synonymous_variant,p.%3D,ENST00000361682,;COMT,synonymous_variant,p.%3D,ENST00000449653,;COMT,synonymous_variant,p.%3D,ENST00000412786,;COMT,synonymous_variant,p.%3D,ENST00000406520,;COMT,synonymous_variant,p.%3D,ENST00000403710,;MIR4761,upstream_gene_variant,,ENST00000585066,;COMT,non_coding_transcript_exon_variant,,ENST00000493893,;COMT,synonymous_variant,p.%3D,ENST00000207636,;COMT,downstream_gene_variant,,ENST00000467943,;	C	ENSG00000093010	ENST00000361682	Transcript	synonymous_variant	850	468	156	A	gcT/gcC	.	.	.	1	COMT	HGNC	2228	protein_coding	YES	CCDS13770.1	ENSP00000354511	COMT_HUMAN	Q7KZP0_HUMAN,F2WW53_HUMAN,E7EMS6_HUMAN	UPI0000000CBF	.	.	.	4/6	.	PROSITE_profiles:PS51682,hmmpanther:PTHR10509,hmmpanther:PTHR10509:SF2,Pfam_domain:PF01596,Gene3D:3.40.50.150,PIRSF_domain:PIRSF037177,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCGCTGGCGT	.	5	ESCA
PLA2G6	0	.	GRCh37	22	38519192	38519192	+	Missense_Mutation	SNP	C	C	T	rs587784332	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501G>A	p.Glu501Lys	p.E501K	ENST00000332509	11/17	24	14	9	51	51	0	PLA2G6,missense_variant,p.Glu447Lys,ENST00000335539,;PLA2G6,missense_variant,p.Glu447Lys,ENST00000402064,;PLA2G6,missense_variant,p.Glu501Lys,ENST00000332509,;PLA2G6,downstream_gene_variant,,ENST00000452794,;PLA2G6,downstream_gene_variant,,ENST00000490473,;PLA2G6,missense_variant,p.Glu50Lys,ENST00000454670,;PLA2G6,3_prime_UTR_variant,,ENST00000448094,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000491986,;PLA2G6,downstream_gene_variant,,ENST00000480154,;PLA2G6,upstream_gene_variant,,ENST00000496409,;PLA2G6,downstream_gene_variant,,ENST00000471636,;	T	ENSG00000184381	ENST00000332509	Transcript	missense_variant	1685	1501	501	E/K	Gag/Aag	rs587784332,CM063029	.	.	-1	PLA2G6	HGNC	9039	protein_coding	YES	CCDS13967.1	ENSP00000333142	PLPL9_HUMAN	M0R3D9_HUMAN,M0R1Q9_HUMAN,F8WEQ9_HUMAN	UPI00001310F3	.	deleterious(0)	possibly_damaging(0.713)	11/17	.	hmmpanther:PTHR24139:SF27,hmmpanther:PTHR24139,Pfam_domain:PF01734,Gene3D:3.40.1090.10,Superfamily_domains:SSF52151	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCGATGG	.	5	ESCA
TANC1	0	.	GRCh37	2	160027186	160027186	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1221C>T	p.%3D	p.N407N	ENST00000263635	10/27	64	34	29	91	91	0	TANC1,synonymous_variant,p.%3D,ENST00000263635,;TANC1,synonymous_variant,p.%3D,ENST00000454300,;	T	ENSG00000115183	ENST00000263635	Transcript	synonymous_variant	1458	1221	407	N	aaC/aaT	.	.	.	1	TANC1	HGNC	29364	protein_coding	YES	CCDS42766.1	ENSP00000263635	TANC1_HUMAN	.	UPI0000421D80	.	.	.	10/27	.	hmmpanther:PTHR24166:SF23,hmmpanther:PTHR24166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAACAGAGG	.	5	ESCA
LRP2	0	.	GRCh37	2	169985261	169985261	+	Missense_Mutation	SNP	G	G	A	rs191145030	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13880C>T	p.Ser4627Leu	p.S4627L	ENST00000263816	79/79	59	44	14	60	60	0	LRP2,missense_variant,p.Ser4627Leu,ENST00000263816,;LRP2,downstream_gene_variant,,ENST00000491228,;	A	ENSG00000081479	ENST00000263816	Transcript	missense_variant	14166	13880	4627	S/L	tCg/tTg	rs191145030	.	.	-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	LRP2_HUMAN	Q9NP34_HUMAN,Q53TL0_HUMAN,Q4ZG84_HUMAN	UPI0000141BA5	.	.	benign(0.001)	79/79	.	Low_complexity_(Seg):seg	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCGAAGGA	byCluster|by1000G	5	ESCA
TTN	0	.	GRCh37	2	179425882	179425882	+	Missense_Mutation	SNP	C	C	T	rs200843338	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84977G>A	p.Arg28326Gln	p.R28326Q	ENST00000589042	326/363	27	11	15	35	35	0	TTN,missense_variant,p.Arg19386Gln,ENST00000359218,;TTN,missense_variant,p.Arg26685Gln,ENST00000591111,;TTN,missense_variant,p.Arg28326Gln,ENST00000589042,;TTN,missense_variant,p.Arg19453Gln,ENST00000342175,;TTN,missense_variant,p.Arg25758Gln,ENST00000342992,;TTN,missense_variant,p.Arg19261Gln,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;	T	ENSG00000155657	ENST00000589042	Transcript	missense_variant	85202	84977	28326	R/Q	cGg/cAg	rs200843338	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	326/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	T:0	T:0.0002	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACCCGGAAT	byCluster|by1000G	5	ESCA
CALM2	0	.	GRCh37	2	47387564	47387564	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*351T>C	.	.	ENST00000272298	6/6	44	21	23	66	66	0	CALM2,3_prime_UTR_variant,,ENST00000272298,;CALM2,downstream_gene_variant,,ENST00000456319,;CALM2,downstream_gene_variant,,ENST00000409563,;CALM2,downstream_gene_variant,,ENST00000489742,;CALM2,downstream_gene_variant,,ENST00000484408,;CALM2,3_prime_UTR_variant,,ENST00000432899,;CALM2,non_coding_transcript_exon_variant,,ENST00000460218,;RP11-761B3.1,intron_variant,,ENST00000422269,;CALM2,downstream_gene_variant,,ENST00000482532,;	G	ENSG00000143933	ENST00000272298	Transcript	3_prime_UTR_variant	959	.	.	.	.	.	.	.	-1	CALM2	HGNC	1445	protein_coding	YES	CCDS1832.1	ENSP00000272298	CALM_HUMAN	Q96HY3_HUMAN,G3V361_HUMAN,B4DJ51_HUMAN	UPI00000000C1	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCACACTT	.	5	ESCA
IGKV1D-8	0	.	GRCh37	2	90260126	90260126	+	Missense_Mutation	SNP	C	C	A	rs367577669	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.229C>A	p.Gln77Lys	p.Q77K	ENST00000471857	2/2	171	127	44	234	234	0	IGKV1D-8,missense_variant,p.Gln77Lys,ENST00000471857,;	A	ENSG00000239819	ENST00000471857	Transcript	missense_variant	410	229	77	Q/K	Caa/Aaa	rs367577669	.	.	1	IGKV1D-8	HGNC	5759	IG_V_gene	YES	.	ENSP00000420285	.	.	UPI0000116192	.	tolerated(0.15)	benign(0.022)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267,hmmpanther:PTHR23267:SF122,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTGCAAAGT	byFrequency|byCluster	5	ESCA
FAIM	0	.	GRCh37	3	138329850	138329850	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51C>T	p.%3D	p.L17L	ENST00000338446	2/6	42	26	15	51	51	0	FAIM,synonymous_variant,p.%3D,ENST00000338446,;FAIM,intron_variant,,ENST00000360570,;FAIM,intron_variant,,ENST00000393035,;FAIM,intron_variant,,ENST00000393034,;FAIM,non_coding_transcript_exon_variant,,ENST00000470889,;FAIM,intron_variant,,ENST00000491175,;	T	ENSG00000158234	ENST00000338446	Transcript	synonymous_variant	734	51	17	L	ctC/ctT	.	.	.	1	FAIM	HGNC	18703	protein_coding	YES	CCDS33864.1	ENSP00000342805	FAIM1_HUMAN	C9JDZ2_HUMAN	UPI00005B2E09	.	.	.	2/6	.	hmmpanther:PTHR13088:SF1,hmmpanther:PTHR13088	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CATCTCTTGGT	.	3	ESCA
ABCF3	0	.	GRCh37	3	183910411	183910411	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1592A>G	p.Lys531Arg	p.K531R	ENST00000429586	17/21	55	41	14	43	43	0	ABCF3,missense_variant,p.Lys525Arg,ENST00000292808,;ABCF3,missense_variant,p.Lys531Arg,ENST00000429586,;EIF2B5,intron_variant,,ENST00000444495,;ABCF3,non_coding_transcript_exon_variant,,ENST00000473311,;ABCF3,non_coding_transcript_exon_variant,,ENST00000480562,;ABCF3,non_coding_transcript_exon_variant,,ENST00000468892,;ABCF3,non_coding_transcript_exon_variant,,ENST00000466742,;ABCF3,upstream_gene_variant,,ENST00000480539,;ABCF3,downstream_gene_variant,,ENST00000466416,;ABCF3,downstream_gene_variant,,ENST00000478288,;ABCF3,downstream_gene_variant,,ENST00000472608,;ABCF3,downstream_gene_variant,,ENST00000475728,;ABCF3,downstream_gene_variant,,ENST00000498136,;ABCF3,downstream_gene_variant,,ENST00000421340,;ABCF3,downstream_gene_variant,,ENST00000471226,;ABCF3,downstream_gene_variant,,ENST00000489719,;	G	ENSG00000161204	ENST00000429586	Transcript	missense_variant	1777	1592	531	K/R	aAg/aGg	.	.	.	1	ABCF3	HGNC	72	protein_coding	YES	CCDS3254.1	ENSP00000411471	ABCF3_HUMAN	.	UPI000007270D	.	deleterious(0.01)	probably_damaging(1)	17/21	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19211:SF45,hmmpanther:PTHR19211,Pfam_domain:PF00005,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGAAGTCTA	.	5	ESCA
SEC24B	0	.	GRCh37	4	110427668	110427668	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1673A>T	p.Asp558Val	p.D558V	ENST00000265175	7/24	73	20	53	57	57	0	SEC24B,missense_variant,p.Asp558Val,ENST00000265175,;SEC24B,missense_variant,p.Asp588Val,ENST00000504968,;SEC24B,missense_variant,p.Asp523Val,ENST00000399100,;	T	ENSG00000138802	ENST00000265175	Transcript	missense_variant	1728	1673	558	D/V	gAt/gTt	.	.	.	1	SEC24B	HGNC	10704	protein_coding	YES	CCDS47124.1	ENSP00000265175	SC24B_HUMAN	B4E2E1_HUMAN	UPI00004F6ED7	.	deleterious(0)	probably_damaging(0.931)	7/24	.	hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF7,Superfamily_domains:SSF81995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGAGTAGG	.	5	ESCA
C4orf21	0	.	GRCh37	4	113461239	113461239	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5952T>A	p.Asp1984Glu	p.D1984E	ENST00000505019	27/28	23	12	10	16	16	0	C4orf21,missense_variant,p.Asp1984Glu,ENST00000505019,;RP11-402J6.1,intron_variant,,ENST00000504009,;C4orf21,3_prime_UTR_variant,,ENST00000445413,;C4orf21,non_coding_transcript_exon_variant,,ENST00000506675,;	T	ENSG00000138658	ENST00000505019	Transcript	missense_variant	6078	5952	1984	D/E	gaT/gaA	.	.	.	-1	C4orf21	HGNC	25654	protein_coding	YES	CCDS3700.2	ENSP00000424737	CD021_HUMAN	I3L0G6_HUMAN,D6REN9_HUMAN	UPI0000EE2F8F	.	tolerated(0.74)	benign(0.019)	27/28	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,Pfam_domain:PF13087,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF325	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAATATCAGG	.	5	ESCA
PDLIM3	0	.	GRCh37	4	186427792	186427792	+	Missense_Mutation	SNP	G	G	A	rs747243505	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.677C>T	p.Ser226Leu	p.S226L	ENST00000284770	6/8	77	61	16	50	49	0	PDLIM3,missense_variant,p.Ser178Leu,ENST00000284771,;PDLIM3,missense_variant,p.Ser226Leu,ENST00000284770,;PDLIM3,3_prime_UTR_variant,,ENST00000284767,;PDLIM3,3_prime_UTR_variant,,ENST00000505886,;PDLIM3,non_coding_transcript_exon_variant,,ENST00000514142,;PDLIM3,non_coding_transcript_exon_variant,,ENST00000514308,;PDLIM3,downstream_gene_variant,,ENST00000512293,;	A	ENSG00000154553	ENST00000284770	Transcript	missense_variant	751	677	226	S/L	tCg/tTg	rs747243505	.	.	-1	PDLIM3	HGNC	20767	protein_coding	YES	CCDS3844.1	ENSP00000284770	PDLI3_HUMAN	.	UPI000013DDB6	.	tolerated(0.25)	benign(0.001)	6/8	.	hmmpanther:PTHR24214:SF7,hmmpanther:PTHR24214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCGAGGCT	byFrequency	5	ESCA
CABS1	0	.	GRCh37	4	71202757	71202757	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*194C>A	.	.	ENST00000273936	2/2	88	35	52	66	66	0	CABS1,3_prime_UTR_variant,,ENST00000273936,;	A	ENSG00000145309	ENST00000273936	Transcript	3_prime_UTR_variant	1456	.	.	.	.	.	.	.	1	CABS1	HGNC	30710	protein_coding	YES	CCDS3539.1	ENSP00000273936	CABS1_HUMAN	.	UPI0000071735	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTCTGGCA	.	5	ESCA
RUFY3	0	.	GRCh37	4	71672412	71672412	+	3'UTR	SNP	C	C	T	rs750110771	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*36C>T	.	.	ENST00000381006	18/18	78	74	4	90	90	0	RUFY3,3_prime_UTR_variant,,ENST00000502653,;RUFY3,3_prime_UTR_variant,,ENST00000381006,;RUFY3,non_coding_transcript_exon_variant,,ENST00000513593,;RUFY3,non_coding_transcript_exon_variant,,ENST00000512331,;RUFY3,non_coding_transcript_exon_variant,,ENST00000507333,;RUFY3,downstream_gene_variant,,ENST00000515442,;RUFY3,3_prime_UTR_variant,,ENST00000512103,;RUFY3,downstream_gene_variant,,ENST00000503025,;RUFY3,downstream_gene_variant,,ENST00000515479,;	T	ENSG00000018189	ENST00000381006	Transcript	3_prime_UTR_variant	2478	.	.	.	.	rs750110771	.	.	1	RUFY3	HGNC	30285	protein_coding	YES	CCDS34001.1	ENSP00000370394	RUFY3_HUMAN	D6REM9_HUMAN,D6RCQ1_HUMAN	UPI00005FB126	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTATGCAGGCT	byFrequency	2	ESCA
MAN1A1	0	.	GRCh37	6	119500460	119500460	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*524T>C	.	.	ENST00000368468	13/13	50	25	25	66	66	0	MAN1A1,3_prime_UTR_variant,,ENST00000368468,;	G	ENSG00000111885	ENST00000368468	Transcript	3_prime_UTR_variant	2928	.	.	.	.	.	.	.	-1	MAN1A1	HGNC	6821	protein_coding	YES	CCDS5122.1	ENSP00000357453	MA1A1_HUMAN	.	UPI000013D632	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATCAAATAA	.	5	ESCA
TBC1D32	0	.	GRCh37	6	121526252	121526252	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2539A>G	p.Asn847Asp	p.N847D	ENST00000398212	22/32	74	41	32	175	175	0	TBC1D32,missense_variant,p.Asn847Asp,ENST00000398212,;TBC1D32,missense_variant,p.Asn847Asp,ENST00000275159,;TBC1D32,intron_variant,,ENST00000398197,;TBC1D32,3_prime_UTR_variant,,ENST00000464622,;	C	ENSG00000146350	ENST00000398212	Transcript	missense_variant	2589	2539	847	N/D	Aac/Gac	.	.	.	-1	TBC1D32	HGNC	21485	protein_coding	YES	CCDS43501.1	ENSP00000381270	BROMI_HUMAN	A2A304_HUMAN	UPI0000E67203	.	deleterious(0.04)	benign(0.025)	22/32	.	hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3,Pfam_domain:PF14961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGTTGAATA	.	5	ESCA
HIST1H1A	0	.	GRCh37	6	26017877	26017877	+	Silent	SNP	A	A	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84T>A	p.%3D	p.A28A	ENST00000244573	1/1	52	35	17	59	58	0	HIST1H1A,synonymous_variant,p.%3D,ENST00000244573,;HIST1H4A,upstream_gene_variant,,ENST00000359907,;HIST1H3A,upstream_gene_variant,,ENST00000357647,;U91328.22,downstream_gene_variant,,ENST00000608919,;HIST1H1PS2,downstream_gene_variant,,ENST00000437528,;	T	ENSG00000124610	ENST00000244573	Transcript	synonymous_variant	164	84	28	A	gcT/gcA	.	.	.	-1	HIST1H1A	HGNC	4715	protein_coding	YES	CCDS4569.1	ENSP00000244573	H11_HUMAN	.	UPI0000001BD8	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11467:SF25,hmmpanther:PTHR11467,Prints_domain:PR00624	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTAGCAGG	.	5	ESCA
ZKSCAN3	0	.	GRCh37	6	28333434	28333434	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.989G>C	p.Ser330Thr	p.S330T	ENST00000377255	7/7	55	32	22	76	76	0	ZKSCAN3,missense_variant,p.Ser330Thr,ENST00000252211,;ZKSCAN3,missense_variant,p.Ser182Thr,ENST00000341464,;ZKSCAN3,missense_variant,p.Ser330Thr,ENST00000377255,;	C	ENSG00000189298	ENST00000377255	Transcript	missense_variant	1286	989	330	S/T	aGt/aCt	.	.	.	1	ZKSCAN3	HGNC	13853	protein_coding	YES	CCDS4650.1	ENSP00000366465	ZKSC3_HUMAN	.	UPI000013CD4A	.	tolerated(1)	benign(0.004)	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23226:SF55,hmmpanther:PTHR23226,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGAGTAAAC	.	5	ESCA
DNAH8	0	.	GRCh37	6	38957896	38957896	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12511C>T	p.Pro4171Ser	p.P4171S	ENST00000359357	86/91	74	43	31	85	85	0	DNAH8,missense_variant,p.Pro4171Ser,ENST00000359357,;DNAH8,missense_variant,p.Pro4376Ser,ENST00000327475,;DNAH8,missense_variant,p.Pro4135Ser,ENST00000441566,;	T	ENSG00000124721	ENST00000359357	Transcript	missense_variant	12765	12511	4171	P/S	Cca/Tca	.	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	probably_damaging(0.999)	86/91	.	Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGCCATCC	.	5	ESCA
TTK	0	.	GRCh37	6	80749463	80749463	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2181G>T	p.Met727Ile	p.M727I	ENST00000369798	19/22	35	22	12	92	92	0	TTK,missense_variant,p.Met727Ile,ENST00000369798,;TTK,missense_variant,p.Met726Ile,ENST00000509894,;TTK,missense_variant,p.Met726Ile,ENST00000230510,;TTK,non_coding_transcript_exon_variant,,ENST00000504590,;	T	ENSG00000112742	ENST00000369798	Transcript	missense_variant	2292	2181	727	M/I	atG/atT	.	.	.	1	TTK	HGNC	12401	protein_coding	YES	CCDS4993.1	ENSP00000358813	TTK_HUMAN	D6RIC6_HUMAN,D6RF82_HUMAN,D6REX1_HUMAN	UPI0000073C7B	.	deleterious(0.02)	probably_damaging(0.981)	19/22	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22974:SF21,hmmpanther:PTHR22974,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATGACTTA	.	5	ESCA
ZNF716	0	.	GRCh37	7	57529387	57529387	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1220C>A	p.Pro407His	p.P407H	ENST00000420713	4/4	51	45	6	57	57	0	ZNF716,missense_variant,p.Pro407His,ENST00000420713,;	A	ENSG00000182111	ENST00000420713	Transcript	missense_variant	1332	1220	407	P/H	cCc/cAc	.	.	.	1	ZNF716	HGNC	32458	protein_coding	YES	CCDS55112.1	ENSP00000394248	ZN716_HUMAN	.	UPI00004192FD	.	deleterious(0.01)	possibly_damaging(0.894)	4/4	.	Superfamily_domains:SSF57667,Pfam_domain:PF13465,Gene3D:3.30.160.60,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAACCCTACA	.	4	ESCA
MLXIPL	0	.	GRCh37	7	73008267	73008267	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2487G>A	p.%3D	p.L829L	ENST00000313375	17/17	13	6	7	51	51	0	MLXIPL,synonymous_variant,p.%3D,ENST00000313375,;MLXIPL,synonymous_variant,p.%3D,ENST00000395189,;MLXIPL,synonymous_variant,p.%3D,ENST00000429400,;MLXIPL,synonymous_variant,p.%3D,ENST00000354613,;MLXIPL,synonymous_variant,p.%3D,ENST00000414749,;MLXIPL,3_prime_UTR_variant,,ENST00000434326,;MLXIPL,downstream_gene_variant,,ENST00000453275,;MLXIPL,3_prime_UTR_variant,,ENST00000345114,;MLXIPL,downstream_gene_variant,,ENST00000467221,;MLXIPL,downstream_gene_variant,,ENST00000476404,;	T	ENSG00000009950	ENST00000313375	Transcript	synonymous_variant	2535	2487	829	L	ctG/ctA	.	.	.	-1	MLXIPL	HGNC	12744	protein_coding	YES	CCDS5553.1	ENSP00000320886	MLXPL_HUMAN	S5LSP3_HUMAN	UPI0000138F98	.	.	.	17/17	.	hmmpanther:PTHR15741:SF14,hmmpanther:PTHR15741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TCGGTCAGGAT	.	4	ESCA
EIF4H	0	.	GRCh37	7	73609938	73609938	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*300G>A	.	.	ENST00000265753	7/7	12	1	11	20	20	0	EIF4H,3_prime_UTR_variant,,ENST00000265753,;EIF4H,3_prime_UTR_variant,,ENST00000353999,;LAT2,upstream_gene_variant,,ENST00000465116,;MIR590,downstream_gene_variant,,ENST00000385008,;EIF4H,downstream_gene_variant,,ENST00000495187,;	A	ENSG00000106682	ENST00000265753	Transcript	3_prime_UTR_variant	1186	.	.	.	.	.	.	.	1	EIF4H	HGNC	12741	protein_coding	YES	CCDS5564.1	ENSP00000265753	IF4H_HUMAN	Q75MU2_HUMAN,Q75MU1_HUMAN,Q75MT8_HUMAN	UPI000012D373	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCGGAGGAG	.	3	ESCA
VPS13B	0	.	GRCh37	8	100533161	100533161	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4743G>C	p.Leu1581Phe	p.L1581F	ENST00000358544	30/62	45	14	30	85	85	0	VPS13B,missense_variant,p.Leu1581Phe,ENST00000358544,;VPS13B,missense_variant,p.Leu12Phe,ENST00000521559,;VPS13B,missense_variant,p.Leu1556Phe,ENST00000357162,;VPS13B,3_prime_UTR_variant,,ENST00000395996,;VPS13B,3_prime_UTR_variant,,ENST00000496144,;	C	ENSG00000132549	ENST00000358544	Transcript	missense_variant	4854	4743	1581	L/F	ttG/ttC	.	.	.	1	VPS13B	HGNC	2183	protein_coding	YES	CCDS6280.1	ENSP00000351346	VP13B_HUMAN	.	UPI00001D2D35	.	tolerated(0.13)	probably_damaging(0.969)	30/62	.	hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTGAAGAT	.	5	ESCA
MROH1	0	.	GRCh37	8	145247236	145247236	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880G>T	p.Ala294Ser	p.A294S	ENST00000528919	9/43	49	39	10	67	67	0	MROH1,missense_variant,p.Ala294Ser,ENST00000534366,;MROH1,missense_variant,p.Ala294Ser,ENST00000398656,;MROH1,missense_variant,p.Ala294Ser,ENST00000423230,;MROH1,missense_variant,p.Ala294Ser,ENST00000528919,;MROH1,missense_variant,p.Ala294Ser,ENST00000326134,;MROH1,non_coding_transcript_exon_variant,,ENST00000532255,;MROH1,non_coding_transcript_exon_variant,,ENST00000525287,;MROH1,non_coding_transcript_exon_variant,,ENST00000527552,;MROH1,non_coding_transcript_exon_variant,,ENST00000534508,;	T	ENSG00000179832	ENST00000528919	Transcript	missense_variant	1001	880	294	A/S	Gct/Tct	.	.	.	1	MROH1	HGNC	26958	protein_coding	YES	CCDS47938.1	ENSP00000435565	MROH1_HUMAN	.	UPI0001AE6FA6	.	tolerated(0.69)	benign(0.013)	9/43	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF13,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGCTGTG	.	5	ESCA
MYOM2	0	.	GRCh37	8	2040194	2040194	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1849C>T	p.Arg617Trp	p.R617W	ENST00000262113	16/37	65	56	9	77	77	0	MYOM2,missense_variant,p.Arg42Trp,ENST00000523438,;MYOM2,missense_variant,p.Arg617Trp,ENST00000262113,;MYOM2,non_coding_transcript_exon_variant,,ENST00000518803,;MYOM2,downstream_gene_variant,,ENST00000519518,;	T	ENSG00000036448	ENST00000262113	Transcript	missense_variant	1990	1849	617	R/W	Cgg/Tgg	COSM1313914	.	.	1	MYOM2	HGNC	7614	protein_coding	YES	CCDS5957.1	ENSP00000262113	MYOM2_HUMAN	E7EWH9_HUMAN	UPI000013D260	.	deleterious(0)	probably_damaging(0.988)	16/37	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19900:SF48,hmmpanther:PTHR19900,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P615P|c.1845G>A|3	RADIA|MUTECT|MUSE|VARSCANS	CGGGTCGGGTT	.	4	ESCA
GOLGA7	0	.	GRCh37	8	41367894	41367894	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*807G>T	.	.	ENST00000357743	5/5	56	24	32	78	78	0	GOLGA7,3_prime_UTR_variant,,ENST00000405786,;GOLGA7,3_prime_UTR_variant,,ENST00000520817,;GOLGA7,3_prime_UTR_variant,,ENST00000357743,;GOLGA7,downstream_gene_variant,,ENST00000518270,;GOLGA7,downstream_gene_variant,,ENST00000521417,;GOLGA7,downstream_gene_variant,,ENST00000523420,;GOLGA7,downstream_gene_variant,,ENST00000523128,;KRT18P37,upstream_gene_variant,,ENST00000520711,;	T	ENSG00000147533	ENST00000357743	Transcript	3_prime_UTR_variant	1422	.	.	.	.	.	.	.	1	GOLGA7	HGNC	24876	protein_coding	YES	CCDS34887.1	ENSP00000350378	GOGA7_HUMAN	.	UPI0000049C28	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCGCTGTGTCC	.	3	ESCA
SLC26A7	0	.	GRCh37	8	92409984	92409984	+	3'Flank	SNP	G	G	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000309536	.	42	36	6	30	30	0	SLC26A7,3_prime_UTR_variant,,ENST00000276609,;SLC26A7,downstream_gene_variant,,ENST00000309536,;SLC26A7,downstream_gene_variant,,ENST00000523719,;SLC26A7,non_coding_transcript_exon_variant,,ENST00000520249,;SLC26A7,downstream_gene_variant,,ENST00000517930,;SLC26A7,downstream_gene_variant,,ENST00000522181,;	A	ENSG00000147606	ENST00000309536	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3038	1	SLC26A7	HGNC	14467	protein_coding	YES	CCDS6255.1	ENSP00000309504	S26A7_HUMAN	E5RFH2_HUMAN	UPI0000046B1C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGAAGAAAGA	.	2	ESCA
MUM1L1	0	.	GRCh37	X	105451566	105451566	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50G>T	.	.	ENST00000337685	5/5	29	15	13	40	40	0	MUM1L1,3_prime_UTR_variant,,ENST00000357175,;MUM1L1,3_prime_UTR_variant,,ENST00000337685,;MUM1L1,3_prime_UTR_variant,,ENST00000372552,;	T	ENSG00000157502	ENST00000337685	Transcript	3_prime_UTR_variant	2926	.	.	.	.	.	.	.	1	MUM1L1	HGNC	26583	protein_coding	YES	CCDS55469.1	ENSP00000338641	MUML1_HUMAN	.	UPI0000212206	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTTGAAAAA	.	5	ESCA
SPANXC	0	.	GRCh37	X	140335650	140335650	+	Nonstop_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EO-01A-11D-A36J-09	TCGA-VR-A8EO-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.294G>T	p.Ter98TyrextTer11	p.*98Yext*11	ENST00000358993	2/2	32	13	18	56	56	0	SPANXC,stop_lost,p.Ter98TyrextTer11,ENST00000358993,;	A	ENSG00000198573	ENST00000358993	Transcript	stop_lost	333	294	98	*/Y	taG/taT	.	.	.	-1	SPANXC	HGNC	14331	protein_coding	YES	CCDS14673.1	ENSP00000351884	SPNXC_HUMAN	.	UPI000003B20F	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TCTTGCTACTT	.	3	ESCA
NPY4R	0	.	GRCh37	10	47088016	47088016	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*105G>A	.	.	ENST00000374312	3/3	141	132	9	110	110	0	NPY4R,3_prime_UTR_variant,,ENST00000395716,;NPY4R,3_prime_UTR_variant,,ENST00000374312,;LINC00842,intron_variant,,ENST00000503031,;	A	ENSG00000204174	ENST00000374312	Transcript	3_prime_UTR_variant	1652	.	.	.	.	.	.	.	1	NPY4R	HGNC	9329	protein_coding	YES	CCDS31193.1	ENSP00000363431	NPY4R_HUMAN	.	UPI0000050415	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCTGGGGTC	.	2	ESCA
ITIH5	0	.	GRCh37	10	7683899	7683899	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.290A>C	p.Asn97Thr	p.N97T	ENST00000256861	3/14	38	32	5	37	37	0	ITIH5,missense_variant,p.Asn97Thr,ENST00000397146,;ITIH5,missense_variant,p.Asn97Thr,ENST00000397145,;ITIH5,missense_variant,p.Asn97Thr,ENST00000256861,;ITIH5,5_prime_UTR_variant,,ENST00000446830,;ITIH5,upstream_gene_variant,,ENST00000434980,;	G	ENSG00000123243	ENST00000256861	Transcript	missense_variant	369	290	97	N/T	aAc/aCc	.	.	.	-1	ITIH5	HGNC	21449	protein_coding	YES	.	ENSP00000256861	ITIH5_HUMAN	.	UPI00001F8AF3	.	deleterious(0)	probably_damaging(1)	3/14	.	PROSITE_profiles:PS51468,hmmpanther:PTHR10338:SF62,hmmpanther:PTHR10338,Pfam_domain:PF08487,SMART_domains:SM00609	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAGTTGGTG	.	5	ESCA
PTEN	0	.	GRCh37	10	89720799	89720802	+	Frame_Shift_Del	DEL	TACT	TACT	-	.	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	TACT	TACT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.955_958delACTT	p.Thr319Ter	p.T319*	ENST00000371953	8/9	68	40	28	77	77	0	PTEN,frameshift_variant,p.Thr319Ter,ENST00000371953,;PTEN,non_coding_transcript_exon_variant,,ENST00000472832,;	-	ENSG00000171862	ENST00000371953	Transcript	frameshift_variant	2307-2310	950-953	317-318	VL/X	gTACTt/gt	COSM4898	.	.	1	PTEN	HGNC	9588	protein_coding	YES	CCDS31238.1	ENSP00000361021	PTEN_HUMAN	F6KD01_HUMAN,H6WA51_HUMAN,H6WA46_HUMAN	UPI00001328C5	.	.	.	8/9	.	PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Gene3D:1d5rA02,Pfam_domain:PF10409,PIRSF_domain:PIRSF038025,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	5	1	.	.	.	.	.	.	.	.	.	1	PASS	CODON|p.0?|c.1_1212del1212|28,CODON|p.T319fs*1|c.950_953delTACT|37,CODON|p.V317fs*3|c.951_954delACTT|4,CODON|p.L318fs*2|c.952_955delCTTA|11,CODON|p.L318fs*2|c.953_956delTTAC|4,BUFFER|p.L318P|c.953T>C|3,BUFFER|p.L318fs*2|c.954_957delTACT|11,BUFFER|p.T319fs*6|c.955_956insA|6,BUFFER|p.T319fs*24|c.956_959delCTTT|6,BUFFER|p.N323fs*2|c.962_963insA|3,BUFFER|p.T321fs*23|c.963delA|12,BUFFER|p.T321fs*3|c.963_964insA|8	INDELOCATOR*|VARSCANI*|PINDEL	ATCTAGTACTTACTT	.	3	ESCA
ZNF518A	0	.	GRCh37	10	97916723	97916723	+	RNA	SNP	C	C	G	rs782205904	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1501C>G	.	.	ENST00000534948	6/7	27	21	6	29	29	0	ZNF518A,non_coding_transcript_exon_variant,,ENST00000478086,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000567632,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000534948,;ZNF518A,intron_variant,,ENST00000563195,;ZNF518A,intron_variant,,ENST00000442635,;ZNF518A,intron_variant,,ENST00000316045,;ZNF518A,downstream_gene_variant,,ENST00000488700,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000371192,;	G	ENSG00000177853	ENST00000534948	Transcript	non_coding_transcript_exon_variant	1501	.	.	.	.	rs782205904	.	.	1	ZNF518A	HGNC	29009	processed_transcript	YES	.	.	.	.	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTCCACCC	.	5	ESCA
MUC5B	0	.	GRCh37	11	1253282	1253282	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735G>T	p.Val579Leu	p.V579L	ENST00000529681	15/49	24	11	12	38	38	0	MUC5B,missense_variant,p.Val579Leu,ENST00000529681,;MUC5B,missense_variant,p.Val582Leu,ENST00000447027,;MUC5B,downstream_gene_variant,,ENST00000531082,;MUC5B,non_coding_transcript_exon_variant,,ENST00000525715,;	T	ENSG00000117983	ENST00000529681	Transcript	missense_variant	1793	1735	579	V/L	Gtg/Ttg	.	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	unknown(0)	15/49	.	PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGGGTGGTG	.	5	ESCA
GLB1L2	0	.	GRCh37	11	134240260	134240260	+	Silent	SNP	G	G	A	rs773473553	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182G>A	p.%3D	p.L394L	ENST00000535456	12/19	33	20	12	25	25	0	GLB1L2,synonymous_variant,p.%3D,ENST00000525089,;GLB1L2,synonymous_variant,p.%3D,ENST00000535456,;GLB1L2,synonymous_variant,p.%3D,ENST00000389881,;GLB1L2,synonymous_variant,p.%3D,ENST00000339772,;GLB1L2,downstream_gene_variant,,ENST00000533324,;GLB1L2,non_coding_transcript_exon_variant,,ENST00000533355,;GLB1L2,non_coding_transcript_exon_variant,,ENST00000529077,;	A	ENSG00000149328	ENST00000535456	Transcript	synonymous_variant	1370	1182	394	L	ctG/ctA	rs773473553	.	.	1	GLB1L2	HGNC	25129	protein_coding	YES	CCDS31724.1	ENSP00000444628	GLBL2_HUMAN	Q8NCG3_HUMAN	UPI0000074534	.	.	.	12/19	.	PIRSF_domain:PIRSF006336,hmmpanther:PTHR23421,hmmpanther:PTHR23421:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCTGTCTCT	byFrequency	5	ESCA
SLC17A6	0	.	GRCh37	11	22399953	22399953	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*667T>C	.	.	ENST00000263160	12/12	88	75	13	67	67	0	SLC17A6,3_prime_UTR_variant,,ENST00000263160,;	C	ENSG00000091664	ENST00000263160	Transcript	3_prime_UTR_variant	2853	.	.	.	.	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTCCATCCATT	.	3	ESCA
SLC17A6	0	.	GRCh37	11	22399968	22399968	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*682G>C	.	.	ENST00000263160	12/12	90	78	12	64	64	0	SLC17A6,3_prime_UTR_variant,,ENST00000263160,;	C	ENSG00000091664	ENST00000263160	Transcript	3_prime_UTR_variant	2868	.	.	.	.	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAATAGTATGA	.	3	ESCA
OR5D13	0	.	GRCh37	11	55540951	55540951	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38C>A	p.Thr13Asn	p.T13N	ENST00000361760	1/1	36	21	15	26	26	0	OR5D13,missense_variant,p.Thr13Asn,ENST00000361760,;	A	ENSG00000198877	ENST00000361760	Transcript	missense_variant	38	38	13	T/N	aCt/aAt	.	.	.	1	OR5D13	HGNC	15280	protein_coding	YES	CCDS31507.1	ENSP00000354800	OR5DD_HUMAN	.	UPI0000041C36	.	deleterious(0.02)	benign(0.03)	1/1	.	hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF210,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCACTTTTA	.	5	ESCA
SCYL1	0	.	GRCh37	11	65300209	65300209	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1163A>T	p.Gln388Leu	p.Q388L	ENST00000270176	9/18	41	34	6	33	33	0	SCYL1,missense_variant,p.Gln388Leu,ENST00000420247,;SCYL1,missense_variant,p.Gln388Leu,ENST00000270176,;SCYL1,missense_variant,p.Gln245Leu,ENST00000527009,;SCYL1,missense_variant,p.Gln388Leu,ENST00000279270,;SCYL1,missense_variant,p.Gln388Leu,ENST00000525364,;SCYL1,missense_variant,p.Gln388Leu,ENST00000533862,;SCYL1,missense_variant,p.Gln388Leu,ENST00000524944,;SCYL1,upstream_gene_variant,,ENST00000528545,;SCYL1,non_coding_transcript_exon_variant,,ENST00000529178,;SCYL1,upstream_gene_variant,,ENST00000531601,;SCYL1,upstream_gene_variant,,ENST00000524897,;SCYL1,upstream_gene_variant,,ENST00000529981,;SCYL1,upstream_gene_variant,,ENST00000526454,;	T	ENSG00000142186	ENST00000270176	Transcript	missense_variant	1240	1163	388	Q/L	cAg/cTg	.	.	.	1	SCYL1	HGNC	14372	protein_coding	YES	CCDS41672.1	ENSP00000270176	NTKL_HUMAN	E9PPN3_HUMAN	UPI0000035B94	.	deleterious(0)	benign(0.15)	9/18	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR12984:SF3,hmmpanther:PTHR12984	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCAGATCT	.	5	ESCA
PPP6R3	0	.	GRCh37	11	68381717	68381718	+	3'UTR	INS	-	-	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1133dupT	.	.	ENST00000393801	25/25	105	91	14	85	85	0	PPP6R3,3_prime_UTR_variant,,ENST00000527403,;PPP6R3,3_prime_UTR_variant,,ENST00000265637,;PPP6R3,3_prime_UTR_variant,,ENST00000393799,;PPP6R3,3_prime_UTR_variant,,ENST00000524904,;PPP6R3,3_prime_UTR_variant,,ENST00000393800,;PPP6R3,3_prime_UTR_variant,,ENST00000265636,;PPP6R3,3_prime_UTR_variant,,ENST00000393801,;PPP6R3,intron_variant,,ENST00000529710,;PPP6R3,downstream_gene_variant,,ENST00000534534,;PPP6R3,downstream_gene_variant,,ENST00000524845,;PPP6R3,downstream_gene_variant,,ENST00000530734,;PPP6R3,downstream_gene_variant,,ENST00000534190,;CTD-2007L18.5,intron_variant,,ENST00000565199,;CTD-2007L18.5,downstream_gene_variant,,ENST00000564469,;CTD-2007L18.5,downstream_gene_variant,,ENST00000565473,;PPP6R3,non_coding_transcript_exon_variant,,ENST00000526307,;PPP6R3,downstream_gene_variant,,ENST00000525152,;PPP6R3,downstream_gene_variant,,ENST00000526593,;	T	ENSG00000110075	ENST00000393801	Transcript	3_prime_UTR_variant	3987-3988	.	.	.	.	.	.	.	1	PPP6R3	HGNC	1173	protein_coding	YES	CCDS53671.1	ENSP00000377390	PP6R3_HUMAN	E9PNN8_HUMAN,E9PKG4_HUMAN,E9PK08_HUMAN,E9PJD8_HUMAN	UPI0000688150	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TATATATATAG	.	3	ESCA
TRIM49	0	.	GRCh37	11	89537421	89537423	+	In_Frame_Del	DEL	TCT	TCT	-	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	TCT	TCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.215_217delAGA	p.Lys72del	p.K72del	ENST00000329758	3/8	153	107	46	103	103	0	TRIM49,inframe_deletion,p.Lys72del,ENST00000532501,;TRIM49,inframe_deletion,p.Lys72del,ENST00000329758,;	-	ENSG00000168930	ENST00000329758	Transcript	inframe_deletion	544-546	215-217	72-73	KM/M	aAGAtg/atg	.	.	.	-1	TRIM49	HGNC	13431	protein_coding	YES	CCDS8287.1	ENSP00000327604	TRI49_HUMAN	I1YAQ5_HUMAN	UPI000013431B	.	.	.	3/8	.	hmmpanther:PTHR24103:SF268,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGCCATCTTCTTC	.	3	ESCA
PARPBP	0	.	GRCh37	12	102558365	102558365	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.645G>A	p.%3D	p.E215E	ENST00000358383	5/11	105	73	32	76	76	0	PARPBP,synonymous_variant,p.%3D,ENST00000358383,;PARPBP,synonymous_variant,p.%3D,ENST00000543784,;PARPBP,synonymous_variant,p.%3D,ENST00000378128,;PARPBP,synonymous_variant,p.%3D,ENST00000541394,;PARPBP,synonymous_variant,p.%3D,ENST00000417507,;PARPBP,synonymous_variant,p.%3D,ENST00000327680,;PARPBP,synonymous_variant,p.%3D,ENST00000392911,;PARPBP,synonymous_variant,p.%3D,ENST00000412715,;PARPBP,intron_variant,,ENST00000535811,;PARPBP,intron_variant,,ENST00000457614,;	A	ENSG00000185480	ENST00000358383	Transcript	synonymous_variant	690	645	215	E	gaG/gaA	.	.	.	1	PARPBP	HGNC	26074	protein_coding	YES	CCDS9090.2	ENSP00000351153	PARI_HUMAN	.	UPI000004A06B	.	.	.	5/11	.	Superfamily_domains:SSF52540,Gene3D:1.10.486.10,hmmpanther:PTHR32121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGAGAAACA	.	5	ESCA
NAA25	0	.	GRCh37	12	112478314	112478314	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2509C>G	p.Leu837Val	p.L837V	ENST00000261745	21/24	89	67	22	86	86	0	NAA25,missense_variant,p.Leu837Val,ENST00000261745,;MIR3657,upstream_gene_variant,,ENST00000584818,;NAA25,3_prime_UTR_variant,,ENST00000549711,;NAA25,3_prime_UTR_variant,,ENST00000551858,;NAA25,non_coding_transcript_exon_variant,,ENST00000550701,;NAA25,non_coding_transcript_exon_variant,,ENST00000552527,;	C	ENSG00000111300	ENST00000261745	Transcript	missense_variant	2758	2509	837	L/V	Ctt/Gtt	.	.	.	-1	NAA25	HGNC	25783	protein_coding	YES	CCDS9159.1	ENSP00000261745	NAA25_HUMAN	.	UPI00001FBB50	.	tolerated(0.82)	benign(0.002)	21/24	.	hmmpanther:PTHR22767,hmmpanther:PTHR22767:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAAGAGTAG	.	5	ESCA
KNTC1	0	.	GRCh37	12	123104889	123104889	+	Intron	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6150-137C>G	.	.	ENST00000333479	.	30	24	5	13	13	0	HCAR1,3_prime_UTR_variant,,ENST00000356987,;KNTC1,5_prime_UTR_variant,,ENST00000534995,;KNTC1,intron_variant,,ENST00000436959,;KNTC1,intron_variant,,ENST00000537348,;KNTC1,intron_variant,,ENST00000333479,;KNTC1,intron_variant,,ENST00000450485,;KNTC1,downstream_gene_variant,,ENST00000546125,;KNTC1,intron_variant,,ENST00000541427,;KNTC1,downstream_gene_variant,,ENST00000539013,;	G	ENSG00000184445	ENST00000333479	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KNTC1	HGNC	17255	protein_coding	YES	CCDS45002.1	ENSP00000328236	KNTC1_HUMAN	J3KQF2_HUMAN,F5H5V0_HUMAN	UPI0000047FD6	.	.	.	.	59/63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAGCATATG	.	5	ESCA
MUC19	0	.	GRCh37	12	40919112	40919112	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5783-17252G>T	.	.	ENST00000454784	.	67	44	23	58	58	0	MUC19,intron_variant,,ENST00000454784,;MUC19,upstream_gene_variant,,ENST00000424466,;MUC19,non_coding_transcript_exon_variant,,ENST00000474954,;MUC19,downstream_gene_variant,,ENST00000398702,;	T	ENSG00000205592	ENST00000454784	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MUC19	HGNC	14362	protein_coding	YES	.	ENSP00000476404	.	C9JCE7_HUMAN	UPI0003B927DE	.	.	.	.	49/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTGGCCAC	.	5	ESCA
MUC19	0	.	GRCh37	12	40919113	40919113	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5783-17251G>T	.	.	ENST00000454784	.	68	45	23	56	56	0	MUC19,intron_variant,,ENST00000454784,;MUC19,upstream_gene_variant,,ENST00000424466,;MUC19,non_coding_transcript_exon_variant,,ENST00000474954,;MUC19,downstream_gene_variant,,ENST00000398702,;	T	ENSG00000205592	ENST00000454784	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MUC19	HGNC	14362	protein_coding	YES	.	ENSP00000476404	.	C9JCE7_HUMAN	UPI0003B927DE	.	.	.	.	49/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTGGCCACA	.	5	ESCA
SCN8A	0	.	GRCh37	12	52200368	52200368	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5098C>G	p.Gln1700Glu	p.Q1700E	ENST00000354534	27/27	50	38	12	44	44	0	SCN8A,missense_variant,p.Gln1700Glu,ENST00000354534,;SCN8A,missense_variant,p.Gln1659Glu,ENST00000545061,;SCN8A,3_prime_UTR_variant,,ENST00000355133,;AC068987.1,upstream_gene_variant,,ENST00000599343,;RP11-923I11.3,downstream_gene_variant,,ENST00000565518,;	G	ENSG00000196876	ENST00000354534	Transcript	missense_variant	5276	5098	1700	Q/E	Caa/Gaa	.	.	.	1	SCN8A	HGNC	10596	protein_coding	YES	CCDS44891.1	ENSP00000346534	SCN8A_HUMAN	Q9P2Q6_HUMAN,Q8WWN3_HUMAN	UPI000006FD85	.	deleterious(0.05)	possibly_damaging(0.721)	27/27	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF132	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTTCAAATC	.	5	ESCA
HELB	0	.	GRCh37	12	66703557	66703557	+	Silent	SNP	T	T	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.849T>G	p.%3D	p.L283L	ENST00000247815	4/13	76	51	25	49	49	0	HELB,synonymous_variant,p.%3D,ENST00000247815,;HELB,synonymous_variant,p.%3D,ENST00000440906,;HELB,synonymous_variant,p.%3D,ENST00000545134,;HELB,synonymous_variant,p.%3D,ENST00000542394,;	G	ENSG00000127311	ENST00000247815	Transcript	synonymous_variant	908	849	283	L	ctT/ctG	.	.	.	1	HELB	HGNC	17196	protein_coding	YES	CCDS8976.1	ENSP00000247815	HELB_HUMAN	.	UPI000013CC2D	.	.	.	4/13	.	hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF97	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTTCTCCA	.	5	ESCA
CAPS2	0	.	GRCh37	12	75710093	75710093	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647C>T	p.Ala216Val	p.A216V	ENST00000409445	7/18	63	47	15	62	62	0	CAPS2,missense_variant,p.Ala110Val,ENST00000436898,;CAPS2,missense_variant,p.Ala216Val,ENST00000409445,;CAPS2,missense_variant,p.Ala166Val,ENST00000409799,;CAPS2,missense_variant,p.Ala111Val,ENST00000552497,;CAPS2,splice_region_variant,,ENST00000393284,;CAPS2,splice_region_variant,,ENST00000551829,;CAPS2,5_prime_UTR_variant,,ENST00000442339,;CAPS2,non_coding_transcript_exon_variant,,ENST00000409004,;CAPS2,missense_variant,p.Ala111Val,ENST00000336815,;CAPS2,3_prime_UTR_variant,,ENST00000328705,;	A	ENSG00000180881	ENST00000409445	Transcript	missense_variant	844	647	216	A/V	gCa/gTa	.	.	.	-1	CAPS2	HGNC	16471	protein_coding	YES	CCDS9008.2	ENSP00000386959	CAYP2_HUMAN	F8VZC3_HUMAN	UPI000006D783	.	tolerated(0.08)	benign(0.333)	7/18	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10891:SF548,hmmpanther:PTHR10891	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTGCATCC	.	5	ESCA
NAV3	0	.	GRCh37	12	78513439	78513439	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3463C>G	p.His1155Asp	p.H1155D	ENST00000536525	15/39	51	41	10	39	39	0	NAV3,missense_variant,p.His1155Asp,ENST00000536525,;NAV3,missense_variant,p.His1155Asp,ENST00000397909,;NAV3,missense_variant,p.His1155Asp,ENST00000266692,;NAV3,missense_variant,p.His1155Asp,ENST00000228327,;NAV3,missense_variant,p.His227Asp,ENST00000552895,;NAV3,upstream_gene_variant,,ENST00000550788,;	G	ENSG00000067798	ENST00000536525	Transcript	missense_variant	3636	3463	1155	H/D	Cac/Gac	.	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	deleterious(0.04)	probably_damaging(0.999)	15/39	.	hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCCACAGA	.	5	ESCA
APAF1	0	.	GRCh37	12	99053025	99053025	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614G>A	p.Arg205Gln	p.R205Q	ENST00000551964	5/27	93	77	16	45	45	0	APAF1,missense_variant,p.Arg205Gln,ENST00000357310,;APAF1,missense_variant,p.Arg194Gln,ENST00000550527,;APAF1,missense_variant,p.Arg205Gln,ENST00000339433,;APAF1,missense_variant,p.Arg205Gln,ENST00000547045,;APAF1,missense_variant,p.Arg194Gln,ENST00000359972,;APAF1,missense_variant,p.Arg205Gln,ENST00000549007,;APAF1,missense_variant,p.Arg205Gln,ENST00000552268,;APAF1,missense_variant,p.Arg205Gln,ENST00000551964,;APAF1,missense_variant,p.Arg205Gln,ENST00000333991,;	A	ENSG00000120868	ENST00000551964	Transcript	missense_variant	1350	614	205	R/Q	cGg/cAg	COSM944889	.	.	1	APAF1	HGNC	576	protein_coding	YES	CCDS9069.1	ENSP00000448165	APAF_HUMAN	.	UPI0000036328	.	deleterious(0)	probably_damaging(0.996)	5/27	.	hmmpanther:PTHR22845:SF1,hmmpanther:PTHR22845,Gene3D:3.40.50.300,Pfam_domain:PF00931,PIRSF_domain:PIRSF037646,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACGGTTGG	.	5	ESCA
TUBA3C	0	.	GRCh37	13	19751582	19751582	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.541G>A	p.Val181Met	p.V181M	ENST00000400113	4/5	38	29	8	52	52	0	TUBA3C,missense_variant,p.Val181Met,ENST00000400113,;RP11-408E5.4,upstream_gene_variant,,ENST00000382988,;	T	ENSG00000198033	ENST00000400113	Transcript	missense_variant	646	541	181	V/M	Gtg/Atg	.	.	.	-1	TUBA3C	HGNC	12408	protein_coding	YES	CCDS9284.1	ENSP00000382982	TBA3C_HUMAN	Q1ZYQ1_HUMAN,F8VXZ7_HUMAN	UPI0000027DB1	.	deleterious_low_confidence(0.02)	probably_damaging(0.981)	4/5	.	hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF65,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	CACCACGGCCG	.	2	ESCA
RB1	0	.	GRCh37	13	48947603	48947603	+	Nonsense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1190C>G	p.Ser397Ter	p.S397*	ENST00000267163	12/27	45	29	16	34	34	0	RB1,stop_gained,p.Ser397Ter,ENST00000267163,;	G	ENSG00000139687	ENST00000267163	Transcript	stop_gained	1328	1190	397	S/*	tCa/tGa	CM961227,COSM1580298,COSM3793328,COSM1580297,COSM3793327	.	.	1	RB1	HGNC	9884	protein_coding	YES	CCDS31973.1	ENSP00000267163	RB_HUMAN	Q7KZ61_HUMAN,Q7KZ60_HUMAN,Q6LE82_HUMAN,Q6LE81_HUMAN,Q6LE80_HUMAN,Q6LE79_HUMAN,Q6LE77_HUMAN,Q6LE65_HUMAN,Q6DUF0_HUMAN,P78495_HUMAN,B4DRB3_HUMAN	UPI0000001C79	.	.	.	12/27	.	hmmpanther:PTHR13742,Pfam_domain:PF01858,Gene3D:1.10.472.10,Superfamily_domains:SSF47954	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Q395*|c.1183C>T|3,BUFFER|p.Q395Q|c.1185A>G|3,BUFFER|p.Q395Q|c.1185A>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCAGAAA	.	5	ESCA
AHNAK2	0	.	GRCh37	14	105420323	105420323	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1465T>G	p.Leu489Val	p.L489V	ENST00000333244	7/7	56	47	8	56	56	0	AHNAK2,missense_variant,p.Leu489Val,ENST00000333244,;AHNAK2,upstream_gene_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555544,;	C	ENSG00000185567	ENST00000333244	Transcript	missense_variant	1585	1465	489	L/V	Tta/Gta	.	.	.	-1	AHNAK2	HGNC	20125	protein_coding	YES	CCDS45177.1	ENSP00000353114	AHNK2_HUMAN	.	UPI00015BB2CA	.	.	benign(0.051)	7/7	.	hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTAAATCGT	.	5	ESCA
GPR132	0	.	GRCh37	14	105518224	105518224	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250delC	p.Leu84TrpfsTer27	p.L84Wfs*27	ENST00000329797	4/4	30	9	20	20	20	0	GPR132,frameshift_variant,p.Leu84TrpfsTer27,ENST00000329797,;GPR132,frameshift_variant,p.Leu84TrpfsTer27,ENST00000539291,;GPR132,frameshift_variant,p.Leu75TrpfsTer27,ENST00000392585,;GPR132,downstream_gene_variant,,ENST00000549990,;GPR132,non_coding_transcript_exon_variant,,ENST00000546679,;GPR132,3_prime_UTR_variant,,ENST00000551869,;	-	ENSG00000183484	ENST00000329797	Transcript	frameshift_variant	1162	250	84	L/X	Ctg/tg	.	.	.	-1	GPR132	HGNC	17482	protein_coding	YES	CCDS9997.1	ENSP00000328818	GP132_HUMAN	A8K7X7_HUMAN	UPI0000050461	.	.	.	4/4	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF2,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTGCCAGGCAGA	.	2	ESCA
BNIP3P1	0	.	GRCh37	14	28735149	28735150	+	RNA	INS	-	-	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1563dupA	.	.	ENST00000550043	1/1	34	22	12	16	16	0	BNIP3P1,non_coding_transcript_exon_variant,,ENST00000550043,;BNIP3P1,non_coding_transcript_exon_variant,,ENST00000355069,;BNIP3P1,downstream_gene_variant,,ENST00000547295,;	A	ENSG00000197358	ENST00000550043	Transcript	non_coding_transcript_exon_variant	1554-1555	.	.	.	.	.	.	.	1	BNIP3P1	HGNC	19922	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	9	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AAATGGAAAAA	.	2	ESCA
SAV1	0	.	GRCh37	14	51101561	51101561	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*340T>A	.	.	ENST00000324679	5/5	19	15	3	10	10	0	SAV1,3_prime_UTR_variant,,ENST00000553731,;SAV1,3_prime_UTR_variant,,ENST00000324679,;SAV1,intron_variant,,ENST00000555720,;ATL1,downstream_gene_variant,,ENST00000354525,;ATL1,downstream_gene_variant,,ENST00000357032,;ATL1,downstream_gene_variant,,ENST00000358385,;ATL1,downstream_gene_variant,,ENST00000441560,;SAV1,downstream_gene_variant,,ENST00000557458,;RN7SL452P,downstream_gene_variant,,ENST00000482923,;ATL1,downstream_gene_variant,,ENST00000556067,;	T	ENSG00000151748	ENST00000324679	Transcript	3_prime_UTR_variant	1856	.	.	.	.	.	.	.	-1	SAV1	HGNC	17795	protein_coding	YES	CCDS9701.1	ENSP00000324729	SAV1_HUMAN	B3KTQ1_HUMAN	UPI0000035DA2	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTAAAGAA	.	2	ESCA
GOLGA5	0	.	GRCh37	14	93299494	93299494	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1747A>T	p.Ser583Cys	p.S583C	ENST00000163416	10/13	77	37	40	54	54	0	GOLGA5,missense_variant,p.Ser583Cys,ENST00000355976,;GOLGA5,missense_variant,p.Ser9Cys,ENST00000554700,;GOLGA5,missense_variant,p.Ser583Cys,ENST00000163416,;	T	ENSG00000066455	ENST00000163416	Transcript	missense_variant	2003	1747	583	S/C	Agt/Tgt	.	.	.	1	GOLGA5	HGNC	4428	protein_coding	YES	CCDS9905.1	ENSP00000163416	GOGA5_HUMAN	.	UPI000013C5AA	.	deleterious(0)	probably_damaging(0.995)	10/13	.	Pfam_domain:PF09787,hmmpanther:PTHR13815:SF5,hmmpanther:PTHR13815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGCAGTCAG	.	5	ESCA
BUB1B	0	.	GRCh37	15	40510661	40510661	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2855A>T	p.Asp952Val	p.D952V	ENST00000287598	22/23	110	79	30	60	60	0	BUB1B,missense_variant,p.Asp966Val,ENST00000412359,;BUB1B,missense_variant,p.Asp952Val,ENST00000287598,;PAK6,intron_variant,,ENST00000453867,;PAK6,intron_variant,,ENST00000441369,;BUB1B,non_coding_transcript_exon_variant,,ENST00000558151,;RP11-133K1.2,intron_variant,,ENST00000558658,;RP11-133K1.2,intron_variant,,ENST00000559936,;RP11-133K1.2,intron_variant,,ENST00000558965,;RP11-133K1.2,upstream_gene_variant,,ENST00000559435,;	T	ENSG00000156970	ENST00000287598	Transcript	missense_variant	3050	2855	952	D/V	gAc/gTc	.	.	.	1	BUB1B	HGNC	1149	protein_coding	YES	CCDS10053.1	ENSP00000287598	BUB1B_HUMAN	.	UPI000006E699	.	deleterious(0)	probably_damaging(0.966)	22/23	.	hmmpanther:PTHR14030,hmmpanther:PTHR14030:SF1,Gene3D:1.10.510.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTAGACCTGT	.	5	ESCA
PLA2G4B	0	.	GRCh37	15	42137203	42137203	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1867T>C	p.%3D	p.L623L	ENST00000542534	18/25	21	13	7	19	19	0	PLA2G4B,synonymous_variant,p.%3D,ENST00000458483,;JMJD7-PLA2G4B,synonymous_variant,p.%3D,ENST00000342159,;PLA2G4B,synonymous_variant,p.%3D,ENST00000542534,;JMJD7-PLA2G4B,synonymous_variant,p.%3D,ENST00000382448,;PLA2G4B,synonymous_variant,p.%3D,ENST00000452633,;PLA2G4B,upstream_gene_variant,,ENST00000569354,;SPTBN5,downstream_gene_variant,,ENST00000320955,;JMJD7-PLA2G4B,downstream_gene_variant,,ENST00000476036,;JMJD7-PLA2G4B,3_prime_UTR_variant,,ENST00000487292,;JMJD7-PLA2G4B,non_coding_transcript_exon_variant,,ENST00000490848,;JMJD7-PLA2G4B,non_coding_transcript_exon_variant,,ENST00000491746,;PLA2G4B,non_coding_transcript_exon_variant,,ENST00000483748,;PLA2G4B,downstream_gene_variant,,ENST00000461382,;PLA2G4B,upstream_gene_variant,,ENST00000566076,;SPTBN5,downstream_gene_variant,,ENST00000563899,;	C	ENSG00000243708	ENST00000542534	Transcript	synonymous_variant	1907	1867	623	L	Ttg/Ctg	.	.	.	1	PLA2G4B	HGNC	9036	protein_coding	YES	CCDS32202.1	ENSP00000441905	.	C9K0I3_HUMAN	UPI0000070A0F	.	.	.	18/25	.	PROSITE_profiles:PS51210,hmmpanther:PTHR10728:SF31,hmmpanther:PTHR10728,Gene3D:3.40.1090.10,Pfam_domain:PF01735,SMART_domains:SM00022,Superfamily_domains:SSF52151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGCTTGGGC	.	5	ESCA
CDAN1	0	.	GRCh37	15	43023524	43023524	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1745A>G	p.Gln582Arg	p.Q582R	ENST00000356231	12/28	22	17	5	22	22	0	CDAN1,missense_variant,p.Gln582Arg,ENST00000356231,;CDAN1,upstream_gene_variant,,ENST00000562465,;	C	ENSG00000140326	ENST00000356231	Transcript	missense_variant	1769	1745	582	Q/R	cAg/cGg	.	.	.	-1	CDAN1	HGNC	1713	protein_coding	YES	CCDS32209.1	ENSP00000348564	CDAN1_HUMAN	H3BM60_HUMAN	UPI0000229BCB	.	tolerated(0.05)	benign(0.053)	12/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAACTGGAAG	.	4	ESCA
SERF2	0	.	GRCh37	15	44084311	44084311	+	5'Flank	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000409960	.	108	81	27	67	67	0	SERF2,5_prime_UTR_variant,,ENST00000381359,;SERF2,5_prime_UTR_variant,,ENST00000249786,;SERF2,upstream_gene_variant,,ENST00000430901,;SERF2,upstream_gene_variant,,ENST00000594896,;SERF2,upstream_gene_variant,,ENST00000409614,;HYPK,upstream_gene_variant,,ENST00000406925,;SERF2,upstream_gene_variant,,ENST00000403425,;SERF2,upstream_gene_variant,,ENST00000339624,;SERINC4,downstream_gene_variant,,ENST00000249714,;SERINC4,downstream_gene_variant,,ENST00000299969,;SERF2,upstream_gene_variant,,ENST00000409960,;SERINC4,downstream_gene_variant,,ENST00000319327,;SERF2,upstream_gene_variant,,ENST00000402131,;SERF2,upstream_gene_variant,,ENST00000409646,;SERF2,upstream_gene_variant,,ENST00000409291,;MIR1282,downstream_gene_variant,,ENST00000408865,;RP11-296A16.1,intron_variant,,ENST00000417761,;SERF2,upstream_gene_variant,,ENST00000486144,;SERINC4,downstream_gene_variant,,ENST00000412697,;SERF2,upstream_gene_variant,,ENST00000409617,;SERF2,upstream_gene_variant,,ENST00000475927,;SERF2,upstream_gene_variant,,ENST00000445816,;SERF2,upstream_gene_variant,,ENST00000448830,;SERINC4,downstream_gene_variant,,ENST00000457418,;SERINC4,downstream_gene_variant,,ENST00000476490,;SERINC4,downstream_gene_variant,,ENST00000448553,;	G	ENSG00000140264	ENST00000409960	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	217	1	SERF2	HGNC	10757	protein_coding	YES	CCDS55963.1	ENSP00000387187	SERF2_HUMAN	.	UPI0000D9B8DB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCCAGGC	.	5	ESCA
FBN1	0	.	GRCh37	15	48733973	48733973	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6108C>T	p.%3D	p.F2036F	ENST00000316623	50/66	53	35	17	33	33	0	FBN1,synonymous_variant,p.%3D,ENST00000316623,;FBN1,synonymous_variant,p.%3D,ENST00000559133,;FBN1,3_prime_UTR_variant,,ENST00000537463,;FBN1,non_coding_transcript_exon_variant,,ENST00000560820,;	A	ENSG00000166147	ENST00000316623	Transcript	synonymous_variant	6564	6108	2036	F	ttC/ttT	.	.	.	-1	FBN1	HGNC	3603	protein_coding	YES	CCDS32232.1	ENSP00000325527	FBN1_HUMAN	Q75N89_HUMAN,Q75N88_HUMAN,H0YN80_HUMAN	UPI0000163B0B	.	.	.	50/66	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,PROSITE_patterns:PS01187,PROSITE_patterns:PS00010,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,PIRSF_domain:PIRSF036312,SMART_domains:SM00181,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTGAAGCT	.	5	ESCA
GLDN	0	.	GRCh37	15	51697090	51697090	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*139C>T	.	.	ENST00000335449	10/10	14	10	4	10	10	0	GLDN,3_prime_UTR_variant,,ENST00000396399,;GLDN,3_prime_UTR_variant,,ENST00000335449,;GLDN,downstream_gene_variant,,ENST00000558426,;	T	ENSG00000186417	ENST00000335449	Transcript	3_prime_UTR_variant	1851	.	.	.	.	.	.	.	1	GLDN	HGNC	29514	protein_coding	YES	CCDS10140.2	ENSP00000335196	GLDN_HUMAN	.	UPI000015FAA3	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCCCGCTTA	.	5	ESCA
UNC13C	0	.	GRCh37	15	54825247	54825247	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5679G>T	p.Met1893Ile	p.M1893I	ENST00000260323	25/32	112	86	26	80	80	0	UNC13C,missense_variant,p.Met139Ile,ENST00000559093,;UNC13C,missense_variant,p.Met1891Ile,ENST00000537900,;UNC13C,missense_variant,p.Met1893Ile,ENST00000545554,;UNC13C,missense_variant,p.Met1893Ile,ENST00000260323,;	T	ENSG00000137766	ENST00000260323	Transcript	missense_variant	5679	5679	1893	M/I	atG/atT	.	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	deleterious_low_confidence(0)	probably_damaging(0.996)	25/32	.	PROSITE_profiles:PS51259,hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2,Pfam_domain:PF10540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTATGGATTT	.	5	ESCA
RNF111	0	.	GRCh37	15	59359099	59359099	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1503T>G	p.His501Gln	p.H501Q	ENST00000559209	6/14	30	21	9	30	30	0	RNF111,missense_variant,p.His501Gln,ENST00000434298,;RNF111,missense_variant,p.His501Gln,ENST00000561186,;RNF111,missense_variant,p.His501Gln,ENST00000557998,;RNF111,missense_variant,p.His501Gln,ENST00000348370,;RNF111,missense_variant,p.His501Gln,ENST00000559209,;	G	ENSG00000157450	ENST00000559209	Transcript	missense_variant	1639	1503	501	H/Q	caT/caG	.	.	.	1	RNF111	HGNC	17384	protein_coding	YES	CCDS58365.1	ENSP00000453872	RN111_HUMAN	H0YKS2_HUMAN	UPI0000EE4EBD	.	deleterious_low_confidence(0)	probably_damaging(0.997)	6/14	.	hmmpanther:PTHR13644,hmmpanther:PTHR13644:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCATACAAG	.	5	ESCA
GDPGP1	0	.	GRCh37	15	90784897	90784897	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757C>T	p.Pro253Ser	p.P253S	ENST00000558017	4/4	63	28	34	20	20	0	GDPGP1,missense_variant,p.Pro253Ser,ENST00000329600,;GDPGP1,missense_variant,p.Pro253Ser,ENST00000558017,;GDPGP1,downstream_gene_variant,,ENST00000558291,;GDPGP1,downstream_gene_variant,,ENST00000561433,;GDPGP1,downstream_gene_variant,,ENST00000559204,;RP11-697E2.4,upstream_gene_variant,,ENST00000565730,;	T	ENSG00000183208	ENST00000558017	Transcript	missense_variant	1177	757	253	P/S	Cct/Tct	.	.	.	1	GDPGP1	HGNC	34360	protein_coding	YES	CCDS32327.1	ENSP00000452793	GDPP1_HUMAN	H0YN11_HUMAN,H0YL31_HUMAN	UPI00002378F3	.	deleterious(0.01)	probably_damaging(1)	4/4	.	hmmpanther:PTHR20884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCCTGGC	.	5	ESCA
SYNM	0	.	GRCh37	15	99674046	99674047	+	3'UTR	INS	-	-	TTCTGTTATAGCCTAAG	rs11269259	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*788_*789insTTATAGCCTAAGTTCTG	.	.	ENST00000336292	5/5	32	19	13	12	12	0	SYNM,3_prime_UTR_variant,,ENST00000328642,;SYNM,3_prime_UTR_variant,,ENST00000560674,;SYNM,3_prime_UTR_variant,,ENST00000336292,;TTC23,downstream_gene_variant,,ENST00000262074,;TTC23,downstream_gene_variant,,ENST00000394132,;TTC23,downstream_gene_variant,,ENST00000394135,;TTC23,downstream_gene_variant,,ENST00000434594,;TTC23,downstream_gene_variant,,ENST00000558663,;TTC23,downstream_gene_variant,,ENST00000558613,;TTC23,downstream_gene_variant,,ENST00000394136,;RP11-6O2.4,upstream_gene_variant,,ENST00000566974,;SYNM,non_coding_transcript_exon_variant,,ENST00000558420,;SYNM,non_coding_transcript_exon_variant,,ENST00000561306,;SYNM,non_coding_transcript_exon_variant,,ENST00000561323,;TTC23,downstream_gene_variant,,ENST00000494567,;TTC23,downstream_gene_variant,,ENST00000490688,;TTC23,downstream_gene_variant,,ENST00000480371,;TTC23,downstream_gene_variant,,ENST00000459771,;	TTCTGTTATAGCCTAAG	ENSG00000182253	ENST00000336292	Transcript	3_prime_UTR_variant	5598-5599	.	.	.	.	rs11269259	.	.	1	SYNM	HGNC	24466	protein_coding	YES	.	ENSP00000336775	SYNEM_HUMAN	.	UPI00001B03B3	.	.	.	5/5	.	.	TTCTGTTATAGCCTAAG:0.2766	TTCTGTTATAGCCTAAG:0.5333	TTCTGTTATAGCCTAAG:0.2608	.	TTCTGTTATAGCCTAAG:0.0992	TTCTGTTATAGCCTAAG:0.2127	TTCTGTTATAGCCTAAG:0.1892	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GCCCTTTTCTG	byFrequency|byCluster|by1000G	2	ESCA
XPO6	0	.	GRCh37	16	28167693	28167693	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.799A>C	p.Thr267Pro	p.T267P	ENST00000304658	7/24	47	22	24	33	32	0	XPO6,missense_variant,p.Thr267Pro,ENST00000304658,;XPO6,missense_variant,p.Thr104Pro,ENST00000574435,;XPO6,missense_variant,p.Thr253Pro,ENST00000565698,;XPO6,non_coding_transcript_exon_variant,,ENST00000573645,;XPO6,non_coding_transcript_exon_variant,,ENST00000569973,;XPO6,upstream_gene_variant,,ENST00000564337,;XPO6,upstream_gene_variant,,ENST00000561488,;XPO6,upstream_gene_variant,,ENST00000566175,;XPO6,upstream_gene_variant,,ENST00000565284,;XPO6,upstream_gene_variant,,ENST00000570294,;	G	ENSG00000169180	ENST00000304658	Transcript	missense_variant	1300	799	267	T/P	Acc/Ccc	.	.	.	-1	XPO6	HGNC	19733	protein_coding	YES	CCDS42135.1	ENSP00000302790	XPO6_HUMAN	H3BUP8_HUMAN,H3BR41_HUMAN,D3DWF9_HUMAN	UPI000006F228	.	deleterious(0.01)	benign(0.37)	7/24	.	Superfamily_domains:SSF48371,Pfam_domain:PF08389,Gene3D:1.25.10.10,hmmpanther:PTHR21452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGGTGATGC	.	5	ESCA
ZNF423	0	.	GRCh37	16	49856581	49856581	+	Missense_Mutation	SNP	C	C	T	rs776265059	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16G>A	p.Val6Ile	p.V6I	ENST00000561648	1/8	27	10	16	20	20	0	ZNF423,missense_variant,p.Val6Ile,ENST00000262383,;ZNF423,missense_variant,p.Val6Ile,ENST00000561874,;ZNF423,missense_variant,p.Val6Ile,ENST00000561648,;ZNF423,intron_variant,,ENST00000563137,;ZNF423,intron_variant,,ENST00000562520,;	T	ENSG00000102935	ENST00000561648	Transcript	missense_variant	70	16	6	V/I	Gtt/Att	rs776265059	.	.	-1	ZNF423	HGNC	16762	protein_coding	YES	CCDS32445.1	ENSP00000455426	ZN423_HUMAN	F5H7S1_HUMAN,B3KNG7_HUMAN	UPI0000353ABC	.	deleterious_low_confidence(0)	benign(0.006)	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACCCCTCT	.	5	ESCA
CYLD	0	.	GRCh37	16	50785664	50785664	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.654T>C	p.%3D	p.G218G	ENST00000427738	3/18	44	21	22	52	52	0	CYLD,synonymous_variant,p.%3D,ENST00000568704,;CYLD,synonymous_variant,p.%3D,ENST00000564326,;CYLD,synonymous_variant,p.%3D,ENST00000566679,;CYLD,synonymous_variant,p.%3D,ENST00000569418,;CYLD,synonymous_variant,p.%3D,ENST00000566206,;CYLD,synonymous_variant,p.%3D,ENST00000427738,;CYLD,synonymous_variant,p.%3D,ENST00000540145,;CYLD,synonymous_variant,p.%3D,ENST00000398568,;CYLD,synonymous_variant,p.%3D,ENST00000311559,;CYLD,downstream_gene_variant,,ENST00000564634,;CYLD,downstream_gene_variant,,ENST00000569681,;CYLD,non_coding_transcript_exon_variant,,ENST00000563629,;CYLD,non_coding_transcript_exon_variant,,ENST00000569891,;	C	ENSG00000083799	ENST00000427738	Transcript	synonymous_variant	859	654	218	G	ggT/ggC	.	.	.	1	CYLD	HGNC	2584	protein_coding	YES	CCDS45482.1	ENSP00000392025	CYLD_HUMAN	H3BTB8_HUMAN,H3BSW9_HUMAN,H3BPZ5_HUMAN	UPI0000073A15	.	.	.	3/18	.	hmmpanther:PTHR11830:SF3,hmmpanther:PTHR11830,Superfamily_domains:SSF74924	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGGTCCTGG	.	5	ESCA
OGFOD1	0	.	GRCh37	16	56509434	56509434	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1424A>G	p.Tyr475Cys	p.Y475C	ENST00000566157	12/13	92	88	4	89	89	0	OGFOD1,missense_variant,p.Tyr475Cys,ENST00000566157,;OGFOD1,missense_variant,p.Tyr432Cys,ENST00000568397,;BBS2,intron_variant,,ENST00000564123,;BBS2,intron_variant,,ENST00000564459,;OGFOD1,3_prime_UTR_variant,,ENST00000336111,;	G	ENSG00000087263	ENST00000566157	Transcript	missense_variant	1547	1424	475	Y/C	tAt/tGt	.	.	.	1	OGFOD1	HGNC	25585	protein_coding	YES	CCDS10761.2	ENSP00000457258	OGFD1_HUMAN	H3BUA6_HUMAN,H3BP48_HUMAN	UPI0000049DA2	.	tolerated(0.07)	benign(0.021)	12/13	.	hmmpanther:PTHR12117,Pfam_domain:PF10637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T479fs*8|c.1428_1429insG|3	MUTECT|MUSE	AGAATATGGCG	.	2	ESCA
RLTPR	0	.	GRCh37	16	67690174	67690174	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3786C>G	p.Ile1262Met	p.I1262M	ENST00000334583	34/38	31	20	10	29	29	0	RLTPR,missense_variant,p.Ile1262Met,ENST00000334583,;RLTPR,missense_variant,p.Ile1226Met,ENST00000545661,;PARD6A,upstream_gene_variant,,ENST00000458121,;PARD6A,upstream_gene_variant,,ENST00000602551,;ACD,downstream_gene_variant,,ENST00000219251,;PARD6A,upstream_gene_variant,,ENST00000219255,;ACD,downstream_gene_variant,,ENST00000602850,;ACD,downstream_gene_variant,,ENST00000393919,;ACD,downstream_gene_variant,,ENST00000602320,;ACD,downstream_gene_variant,,ENST00000602382,;RLTPR,3_prime_UTR_variant,,ENST00000602368,;PARD6A,upstream_gene_variant,,ENST00000602727,;ACD,downstream_gene_variant,,ENST00000602860,;ACD,downstream_gene_variant,,ENST00000602656,;ACD,downstream_gene_variant,,ENST00000602821,;RLTPR,downstream_gene_variant,,ENST00000602924,;ACD,downstream_gene_variant,,ENST00000602423,;ACD,downstream_gene_variant,,ENST00000602945,;ACD,downstream_gene_variant,,ENST00000602780,;RLTPR,upstream_gene_variant,,ENST00000602705,;ACD,downstream_gene_variant,,ENST00000602519,;RLTPR,downstream_gene_variant,,ENST00000602321,;RLTPR,downstream_gene_variant,,ENST00000602931,;ACD,downstream_gene_variant,,ENST00000602622,;RLTPR,downstream_gene_variant,,ENST00000602633,;	G	ENSG00000159753	ENST00000334583	Transcript	missense_variant	4114	3786	1262	I/M	atC/atG	.	.	.	1	RLTPR	HGNC	27089	protein_coding	YES	CCDS45513.1	ENSP00000334958	LR16C_HUMAN	.	UPI00005194F2	.	tolerated(0.24)	benign(0.026)	34/38	.	hmmpanther:PTHR24112:SF41,hmmpanther:PTHR24112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGATCAAGTC	.	5	ESCA
CIRH1A	0	.	GRCh37	16	69200160	69200160	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1833+731T>C	.	.	ENST00000314423	.	19	10	8	13	13	0	CIRH1A,3_prime_UTR_variant,,ENST00000563094,;CIRH1A,intron_variant,,ENST00000314423,;CIRH1A,intron_variant,,ENST00000567500,;CIRH1A,intron_variant,,ENST00000352319,;CIRH1A,intron_variant,,ENST00000562237,;CIRH1A,upstream_gene_variant,,ENST00000567287,;	C	ENSG00000141076	ENST00000314423	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CIRH1A	HGNC	1983	protein_coding	YES	CCDS10872.1	ENSP00000327179	CIR1A_HUMAN	J3KTR0_HUMAN,J3KSE6_HUMAN,H3BPD7_HUMAN	UPI0000037300	.	.	.	.	15/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAGGTGGGGG	.	2	ESCA
CIRH1A	0	.	GRCh37	16	69200161	69200161	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1833+732G>T	.	.	ENST00000314423	.	18	9	9	13	13	0	CIRH1A,3_prime_UTR_variant,,ENST00000563094,;CIRH1A,intron_variant,,ENST00000314423,;CIRH1A,intron_variant,,ENST00000567500,;CIRH1A,intron_variant,,ENST00000352319,;CIRH1A,intron_variant,,ENST00000562237,;CIRH1A,upstream_gene_variant,,ENST00000567287,;	T	ENSG00000141076	ENST00000314423	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CIRH1A	HGNC	1983	protein_coding	YES	CCDS10872.1	ENSP00000327179	CIR1A_HUMAN	J3KTR0_HUMAN,J3KSE6_HUMAN,H3BPD7_HUMAN	UPI0000037300	.	.	.	.	15/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGTGGGGGT	.	2	ESCA
TAF15	0	.	GRCh37	17	34171736	34171736	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1433G>T	p.Gly478Val	p.G478V	ENST00000588240	15/16	65	43	22	72	71	1	TAF15,missense_variant,p.Gly478Val,ENST00000588240,;TAF15,missense_variant,p.Gly475Val,ENST00000311979,;TAF15,splice_region_variant,,ENST00000585577,;TAF15,intron_variant,,ENST00000592237,;TAF15,upstream_gene_variant,,ENST00000586593,;TAF15,downstream_gene_variant,,ENST00000586970,;TAF15,downstream_gene_variant,,ENST00000591763,;TAF15,downstream_gene_variant,,ENST00000590051,;	T	ENSG00000172660	ENST00000588240	Transcript	missense_variant	1548	1433	478	G/V	gGc/gTc	.	.	.	1	TAF15	HGNC	11547	protein_coding	YES	CCDS32623.1	ENSP00000466950	RBP56_HUMAN	Q86X94_HUMAN,K7EJB3_HUMAN	UPI000013317D	.	tolerated_low_confidence(0.07)	unknown(0)	15/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23238,hmmpanther:PTHR23238:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTGGCTATG	.	5	ESCA
TP53	0	.	GRCh37	17	7578526	7578526	+	Missense_Mutation	SNP	C	C	T	rs587781991	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	5/11	11	6	5	11	11	0	TP53,missense_variant,p.Cys135Tyr,ENST00000508793,;TP53,missense_variant,p.Cys135Tyr,ENST00000413465,;TP53,missense_variant,p.Cys128Tyr,ENST00000604348,;TP53,missense_variant,p.Cys135Tyr,ENST00000420246,;TP53,missense_variant,p.Cys135Tyr,ENST00000269305,;TP53,missense_variant,p.Cys3Tyr,ENST00000509690,;TP53,missense_variant,p.Cys135Tyr,ENST00000359597,;TP53,missense_variant,p.Cys42Tyr,ENST00000514944,;TP53,missense_variant,p.Cys135Tyr,ENST00000445888,;TP53,missense_variant,p.Cys135Tyr,ENST00000455263,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	594	404	135	C/Y	tGc/tAc	rs587781991,TP53_g.12392del,TP53_g.12392G>A,TP53_g.12392G>T,TP53_g.12392G>C,COSM10801,COSM10647,COSM44643,COSM300819,COSM303850,COSM99601,COSM300818,COSM99598,COSM303849,COSM303851,COSM99599,COSM300820,COSM3820723,COSM3932747,COSM3691869,COSM1750372,COSM2744946,COSM2744945,COSM99600,COSM303852,COSM300821	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	uncertain_significance	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.C135Y|c.404G>A|8,SITE|p.C135Y|c.404G>A|54,SITE|p.C135Y|c.404G>A|3,SITE|p.C42Y|c.125G>A|8,SITE|p.C135Y|c.404G>A|3,SITE|p.C135Y|c.404G>A|8,SITE|p.C3Y|c.8G>A|8,CODON|p.0?|c.1_1182del1182|6,CODON|p.C3W|c.9C>G|4,CODON|p.C42W|c.126C>G|3,CODON|p.C135W|c.405C>G|3,CODON|p.C135W|c.405C>G|3,CODON|p.C135C|c.405C>T|5,CODON|p.C135*|c.405C>A|8,CODON|p.C135W|c.405C>G|24,CODON|p.C135F|c.404G>T|6,CODON|p.C3S|c.8G>C|3,CODON|p.C135S|c.404G>C|3,CODON|p.C3F|c.8G>T|13,CODON|p.C135S|c.404G>C|3,CODON|p.C42F|c.125G>T|13,CODON|p.C42S|c.125G>C|3,CODON|p.C135F|c.404G>T|6,CODON|p.C135S|c.404G>C|9,CODON|p.C135F|c.404G>T|13,CODON|p.C135F|c.404G>T|13,CODON|p.C135F|c.404G>T|49,CODON|p.C135fs*35|c.403delT|5,BUFFER|p.K139*|c.415A>T|3,BUFFER|p.K139*|c.415A>T|5,BUFFER|p.K7*|c.19A>T|3,BUFFER|p.K139*|c.415A>T|3,BUFFER|p.K139E|c.415A>G|4,BUFFER|p.K46*|c.136A>T|3,BUFFER|p.A138fs*32|c.412delG|5,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A138V|c.413C>T|4,BUFFER|p.A6V|c.17C>T|4,BUFFER|p.A45V|c.134C>T|4,BUFFER|p.A138V|c.413C>T|21,BUFFER|p.A138P|c.412G>C|14,BUFFER|p.A138T|c.412G>A|5,BUFFER|p.A138fs*11|c.411_412insN|3,BUFFER|p.L137L|c.411G>A|3,BUFFER|p.L137P|c.410T>C|3,BUFFER|p.L137Q|c.410T>A|3,BUFFER|p.Q136H|c.408A>C|5,BUFFER|p.Q136Q|c.408A>G|4,BUFFER|p.Q136P|c.407A>C|3,BUFFER|p.Q136E|c.406C>G|9,BUFFER|p.Q136*|c.406C>T|35,BUFFER|p.Q4*|c.10C>T|5,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q43*|c.127C>T|5,BUFFER|p.Q4E|c.10C>G|6,BUFFER|p.Q136E|c.406C>G|6,BUFFER|p.Q136E|c.406C>G|4,BUFFER|p.Q136E|c.406C>G|5,BUFFER|p.Q43E|c.127C>G|6,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|5,BUFFER|p.Q136*|c.406C>T|3,BUFFER|p.C135G|c.403T>G|8,BUFFER|p.C135S|c.403T>A|4,BUFFER|p.C135R|c.403T>C|11,BUFFER|p.C135fs*35|c.400delT|6,BUFFER|p.F134S|c.401T>C|4,BUFFER|p.F134C|c.401T>G|9,BUFFER|p.F134V|c.400T>G|11,BUFFER|p.F41L|c.121T>C|4,BUFFER|p.F134L|c.400T>C|3,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F2L|c.4T>C|4,BUFFER|p.F134L|c.400T>C|4,BUFFER|p.F134L|c.400T>C|18,BUFFER|p.M133T|c.398T>C|5,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M40T|c.119T>C|3,BUFFER|p.M1T|c.2T>C|3,BUFFER|p.M1R|c.2T>G|3,BUFFER|p.M133R|c.398T>G|7,BUFFER|p.M133K|c.398T>A|12,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M40R|c.119T>G|3,BUFFER|p.Y126_K132delYSPALNK|c.376_396del21|6,BUFFER|p.K132N|c.396G>C|29,BUFFER|p.K132N|c.396G>T|3,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>C|5,BUFFER|p.K132N|c.396G>T|24,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>T|6,BUFFER|p.N131delN|c.393_395delCAA|4,BUFFER|p.K132R|c.395A>G|5,BUFFER|p.K132T|c.395A>C|7,BUFFER|p.K39T|c.116A>C|3,BUFFER|p.K132R|c.395A>G|39,BUFFER|p.K132M|c.395A>T|10,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K39R|c.116A>G|7,BUFFER|p.K132Q|c.394A>C|13,BUFFER|p.K39E|c.115A>G|3,BUFFER|p.K132*|c.394A>T|5,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|19,BUFFER|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.N131delN|c.391_393delAAC|8	RADIA|MUTECT|MUSE	GTTGGCAAAAC	.	3	ESCA
SLC38A10	0	.	GRCh37	17	79220340	79220340	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2376T>C	p.%3D	p.P792P	ENST00000374759	16/16	8	2	6	9	9	0	SLC38A10,synonymous_variant,p.%3D,ENST00000374759,;SLC38A10,synonymous_variant,p.%3D,ENST00000576151,;SLC38A10,synonymous_variant,p.%3D,ENST00000540966,;SLC38A10,downstream_gene_variant,,ENST00000288439,;SLC38A10,intron_variant,,ENST00000539643,;SLC38A10,downstream_gene_variant,,ENST00000573058,;SLC38A10,downstream_gene_variant,,ENST00000542075,;	G	ENSG00000157637	ENST00000374759	Transcript	synonymous_variant	2760	2376	792	P	ccT/ccC	.	.	.	-1	SLC38A10	HGNC	28237	protein_coding	YES	CCDS42397.1	ENSP00000363891	S38AA_HUMAN	F5H3T4_HUMAN	UPI000066DA6A	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGCAGGGCG	.	2	ESCA
GAS7	0	.	GRCh37	17	9821406	9821406	+	Missense_Mutation	SNP	C	C	A	rs749184881	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1229G>T	p.Arg410Leu	p.R410L	ENST00000432992	13/14	23	14	9	25	25	0	GAS7,missense_variant,p.Arg115Leu,ENST00000396115,;GAS7,missense_variant,p.Arg410Leu,ENST00000432992,;GAS7,missense_variant,p.Arg350Leu,ENST00000323816,;GAS7,missense_variant,p.Arg270Leu,ENST00000580865,;GAS7,missense_variant,p.Arg346Leu,ENST00000579158,;GAS7,missense_variant,p.Arg346Leu,ENST00000437099,;GAS7,missense_variant,p.Arg115Leu,ENST00000540214,;GAS7,missense_variant,p.Arg350Leu,ENST00000585266,;GAS7,missense_variant,p.Arg346Leu,ENST00000542249,;GAS7,intron_variant,,ENST00000583882,;GAS7,non_coding_transcript_exon_variant,,ENST00000581112,;GAS7,non_coding_transcript_exon_variant,,ENST00000578456,;	A	ENSG00000007237	ENST00000432992	Transcript	missense_variant	1390	1229	410	R/L	cGg/cTg	rs749184881	.	.	-1	GAS7	HGNC	4169	protein_coding	YES	CCDS11152.1	ENSP00000407552	GAS7_HUMAN	J3QS26_HUMAN,J3QLH8_HUMAN,J3KTK6_HUMAN,J3KTB1_HUMAN,J3KS47_HUMAN,B7Z1Q2_HUMAN	UPI00001B4B17	.	deleterious(0.01)	possibly_damaging(0.785)	13/14	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF103657,hmmpanther:PTHR23065:SF10,hmmpanther:PTHR23065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCCGCTCT	byFrequency	5	ESCA
ZNF521	0	.	GRCh37	18	22804854	22804854	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3028C>A	p.His1010Asn	p.H1010N	ENST00000361524	4/8	28	21	7	23	23	0	ZNF521,missense_variant,p.His1010Asn,ENST00000538137,;ZNF521,missense_variant,p.His790Asn,ENST00000584787,;ZNF521,missense_variant,p.His1010Asn,ENST00000361524,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,missense_variant,p.His1010Asn,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,;	T	ENSG00000198795	ENST00000361524	Transcript	missense_variant	3177	3028	1010	H/N	Cac/Aac	.	.	.	-1	ZNF521	HGNC	24605	protein_coding	YES	CCDS32806.1	ENSP00000354794	ZN521_HUMAN	J3QRW6_HUMAN,J3KTI4_HUMAN,J3KT07_HUMAN,J3KSZ4_HUMAN	UPI000006F982	.	deleterious(0)	probably_damaging(0.991)	4/8	.	SMART_domains:SM00355,PROSITE_patterns:PS00028,hmmpanther:PTHR24385,hmmpanther:PTHR24385:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGTGCATTT	.	5	ESCA
CCDC178	0	.	GRCh37	18	30795599	30795599	+	Frame_Shift_Del	DEL	A	A	-	.	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1993delT	p.Tyr665MetfsTer4	p.Y665Mfs*4	ENST00000383096	19/23	193	133	60	112	112	0	CCDC178,frameshift_variant,p.Tyr665MetfsTer4,ENST00000579947,;CCDC178,frameshift_variant,p.Tyr212MetfsTer4,ENST00000581524,;CCDC178,frameshift_variant,p.Tyr665MetfsTer4,ENST00000406524,;CCDC178,frameshift_variant,p.Tyr665MetfsTer4,ENST00000403303,;CCDC178,frameshift_variant,p.Tyr665MetfsTer4,ENST00000383096,;CCDC178,frameshift_variant,p.Tyr665MetfsTer4,ENST00000402325,;CCDC178,frameshift_variant,p.Tyr627MetfsTer4,ENST00000300227,;CCDC178,frameshift_variant,p.Tyr665MetfsTer4,ENST00000583930,;CCDC178,intron_variant,,ENST00000579916,;	-	ENSG00000166960	ENST00000383096	Transcript	frameshift_variant	2176	1993	665	Y/X	Tat/at	COSM1246603,COSM1246602	.	.	-1	CCDC178	HGNC	29588	protein_coding	YES	CCDS42424.1	ENSP00000372576	CC178_HUMAN	J3QKU2_HUMAN	UPI000022A700	.	.	.	19/23	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	deletion	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.M624I|c.1872G>A|3,BUFFER|p.M662I|c.1986G>A|3	INDELOCATOR*|VARSCANI*|PINDEL	TTGCATAAAAAA	.	3	ESCA
NOL4	0	.	GRCh37	18	31431159	31431159	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1647G>C	.	.	ENST00000261592	11/11	71	66	5	68	68	0	NOL4,3_prime_UTR_variant,,ENST00000261592,;NOL4,3_prime_UTR_variant,,ENST00000269185,;NOL4,downstream_gene_variant,,ENST00000589544,;NOL4,downstream_gene_variant,,ENST00000538587,;NOL4,downstream_gene_variant,,ENST00000535384,;NOL4,downstream_gene_variant,,ENST00000535475,;NOL4,downstream_gene_variant,,ENST00000590712,;NOL4,downstream_gene_variant,,ENST00000586314,;	G	ENSG00000101746	ENST00000261592	Transcript	3_prime_UTR_variant	3862	.	.	.	.	.	.	.	-1	NOL4	HGNC	7870	protein_coding	YES	CCDS11907.2	ENSP00000261592	NOL4_HUMAN	.	UPI000059D504	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAACTCTAAAT	.	2	ESCA
ZNF532	0	.	GRCh37	18	56652849	56652849	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1151C>T	.	.	ENST00000336078	11/11	28	24	4	18	18	0	ZNF532,3_prime_UTR_variant,,ENST00000589288,;ZNF532,3_prime_UTR_variant,,ENST00000336078,;ZNF532,downstream_gene_variant,,ENST00000586997,;ZNF532,downstream_gene_variant,,ENST00000591230,;ZNF532,downstream_gene_variant,,ENST00000591808,;ZNF532,downstream_gene_variant,,ENST00000591083,;ZNF532,downstream_gene_variant,,ENST00000588956,;ZNF532,downstream_gene_variant,,ENST00000592249,;ZNF532,downstream_gene_variant,,ENST00000589131,;ZNF532,non_coding_transcript_exon_variant,,ENST00000590442,;ZNF532,downstream_gene_variant,,ENST00000585662,;	T	ENSG00000074657	ENST00000336078	Transcript	3_prime_UTR_variant	5833	.	.	.	.	.	.	.	1	ZNF532	HGNC	30940	protein_coding	YES	CCDS11969.1	ENSP00000338217	ZN532_HUMAN	K7ER18_HUMAN,K7EQW7_HUMAN,K7EPI7_HUMAN,K7EP49_HUMAN,K7EMF9_HUMAN,K7ELB7_HUMAN,K7EL14_HUMAN,K7EKV7_HUMAN,K7EJM2_HUMAN,B4DQV3_HUMAN	UPI000013D30C	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TTTAACGTCGG	.	2	ESCA
PIGN	0	.	GRCh37	18	59768391	59768391	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1994A>T	p.Tyr665Phe	p.Y665F	ENST00000357637	22/31	51	31	19	40	40	0	PIGN,missense_variant,p.Tyr665Phe,ENST00000400334,;PIGN,missense_variant,p.Tyr665Phe,ENST00000357637,;PIGN,downstream_gene_variant,,ENST00000586566,;PIGN,non_coding_transcript_exon_variant,,ENST00000587942,;PIGN,downstream_gene_variant,,ENST00000590948,;	A	ENSG00000197563	ENST00000357637	Transcript	missense_variant	2410	1994	665	Y/F	tAt/tTt	.	.	.	-1	PIGN	HGNC	8967	protein_coding	YES	CCDS45879.1	ENSP00000350263	PIGN_HUMAN	K7ESH9_HUMAN,K7ERX5_HUMAN,K7EQG0_HUMAN,K7EPN0_HUMAN,K7ENC3_HUMAN,K7EMD7_HUMAN,K7EM45_HUMAN,K7ELE1_HUMAN,K7EL34_HUMAN,K7EK83_HUMAN	UPI0000070A47	.	tolerated(0.2)	benign(0.082)	22/31	.	hmmpanther:PTHR12250,Pfam_domain:PF04987	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACATACATG	.	5	ESCA
YES1	0	.	GRCh37	18	746023	746023	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499G>C	p.Asp167His	p.D167H	ENST00000584307	5/12	64	33	30	46	46	0	YES1,missense_variant,p.Asp167His,ENST00000314574,;YES1,missense_variant,p.Asp167His,ENST00000584307,;YES1,missense_variant,p.Asp172His,ENST00000577961,;	G	ENSG00000176105	ENST00000584307	Transcript	missense_variant	670	499	167	D/H	Gat/Cat	.	.	.	-1	YES1	HGNC	12841	protein_coding	YES	CCDS11824.1	ENSP00000462468	YES_HUMAN	.	UPI0000062316	.	deleterious(0)	probably_damaging(0.992)	5/12	.	PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF90,Gene3D:3.30.505.10,Pfam_domain:PF00017,SMART_domains:SM00252,Superfamily_domains:SSF55550,Superfamily_domains:SSF50044,Prints_domain:PR00401	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATCTTTTC	.	5	ESCA
ZNF439	0	.	GRCh37	19	11979010	11979010	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1126C>T	p.His376Tyr	p.H376Y	ENST00000304030	3/3	105	73	31	65	65	0	ZNF439,missense_variant,p.His376Tyr,ENST00000304030,;ZNF439,missense_variant,p.His240Tyr,ENST00000455282,;ZNF439,downstream_gene_variant,,ENST00000442091,;ZNF439,intron_variant,,ENST00000592534,;	T	ENSG00000171291	ENST00000304030	Transcript	missense_variant	1326	1126	376	H/Y	Cac/Tac	.	.	.	1	ZNF439	HGNC	20873	protein_coding	YES	CCDS12268.1	ENSP00000305077	ZN439_HUMAN	C9JMA7_HUMAN	UPI000006F768	.	deleterious(0)	probably_damaging(0.998)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF35,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTCACAGT	.	5	ESCA
CTD-3105H18.14	0	.	GRCh37	19	12494426	12494426	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.79A>G	p.Asn27Asp	p.N27D	ENST00000435033	2/4	106	79	27	68	68	0	CTD-3105H18.14,missense_variant,p.Asn27Asp,ENST00000435033,;CTD-3105H18.4,non_coding_transcript_exon_variant,,ENST00000507003,;	C	ENSG00000268744	ENST00000435033	Transcript	missense_variant	283	79	27	N/D	Aat/Gat	.	.	.	-1	CTD-3105H18.14	Clone_based_vega_gene	.	nonsense_mediated_decay	YES	.	ENSP00000394047	.	F2Z351_HUMAN	UPI00001CE054	.	tolerated_low_confidence(0.05)	benign(0.225)	2/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24379,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATTCTTCT	.	5	ESCA
DAND5	0	.	GRCh37	19	13084458	13084458	+	3'UTR	SNP	C	C	A	rs374830367	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10C>A	.	.	ENST00000317060	2/2	27	20	7	9	9	0	DAND5,3_prime_UTR_variant,,ENST00000317060,;DAND5,3_prime_UTR_variant,,ENST00000585548,;	A	ENSG00000179284	ENST00000317060	Transcript	3_prime_UTR_variant	759	.	.	.	.	rs374830367	.	.	1	DAND5	HGNC	26780	protein_coding	YES	CCDS12291.1	ENSP00000323155	DAND5_HUMAN	.	UPI000007258A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AGCATCGTGGA	byFrequency|byCluster	4	ESCA
RPL18A	0	.	GRCh37	19	17974110	17974110	+	3'UTR	SNP	C	C	G	rs778751529	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*38C>G	.	.	ENST00000222247	5/5	80	52	28	39	39	0	RPL18A,3_prime_UTR_variant,,ENST00000599870,;RPL18A,3_prime_UTR_variant,,ENST00000600147,;RPL18A,3_prime_UTR_variant,,ENST00000599898,;RPL18A,3_prime_UTR_variant,,ENST00000222247,;RPL18A,downstream_gene_variant,,ENST00000597648,;SNORA68,downstream_gene_variant,,ENST00000384437,;RPL18A,downstream_gene_variant,,ENST00000600238,;RPL18A,downstream_gene_variant,,ENST00000602216,;	G	ENSG00000105640	ENST00000222247	Transcript	3_prime_UTR_variant	650	.	.	.	.	rs778751529	.	.	1	RPL18A	HGNC	10311	protein_coding	YES	CCDS12367.1	ENSP00000222247	RL18A_HUMAN	Q76N54_HUMAN,M0R3D6_HUMAN,M0R1A7_HUMAN,B4DUV3_HUMAN	UPI0000133CD9	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTCAGGAA	byFrequency	5	ESCA
SCAMP4	0	.	GRCh37	19	1924143	1924143	+	Nonsense_Mutation	SNP	C	C	T	rs781068998	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.550C>T	p.Gln184Ter	p.Q184*	ENST00000316097	7/7	71	66	5	41	41	0	SCAMP4,stop_gained,p.Gln184Ter,ENST00000316097,;SCAMP4,stop_gained,p.Gln150Ter,ENST00000409472,;SCAMP4,non_coding_transcript_exon_variant,,ENST00000414057,;SCAMP4,downstream_gene_variant,,ENST00000585335,;SCAMP4,downstream_gene_variant,,ENST00000489554,;SCAMP4,non_coding_transcript_exon_variant,,ENST00000472442,;SCAMP4,downstream_gene_variant,,ENST00000452128,;AC012615.1,upstream_gene_variant,,ENST00000367461,;	T	ENSG00000227500	ENST00000316097	Transcript	stop_gained	817	550	184	Q/*	Cag/Tag	rs781068998	.	.	1	SCAMP4	HGNC	30385	protein_coding	YES	CCDS45903.1	ENSP00000316007	SCAM4_HUMAN	K7EJJ4_HUMAN,C9JWM2_HUMAN	UPI000006F786	.	.	.	7/7	.	hmmpanther:PTHR10687:SF11,hmmpanther:PTHR10687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTCCAGAAG	.	2	ESCA
CHST8	0	.	GRCh37	19	34264124	34264124	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*156G>C	.	.	ENST00000262622	4/4	10	7	3	8	8	0	CHST8,3_prime_UTR_variant,,ENST00000438847,;CHST8,3_prime_UTR_variant,,ENST00000262622,;CHST8,3_prime_UTR_variant,,ENST00000434302,;CHST8,downstream_gene_variant,,ENST00000591231,;	C	ENSG00000124302	ENST00000262622	Transcript	3_prime_UTR_variant	2189	.	.	.	.	.	.	.	1	CHST8	HGNC	15993	protein_coding	YES	CCDS12433.1	ENSP00000262622	CHST8_HUMAN	K7ENM3_HUMAN	UPI000006F966	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GGGCAGAGGCG	.	2	ESCA
ZNF461	0	.	GRCh37	19	37130506	37130507	+	Frame_Shift_Del	DEL	CT	CT	-	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	CT	CT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740_741delAG	p.Glu247ValfsTer2	p.E247Vfs*2	ENST00000588268	6/6	154	112	42	57	57	0	ZNF461,frameshift_variant,p.Glu224ValfsTer2,ENST00000360357,;ZNF461,frameshift_variant,p.Glu247ValfsTer2,ENST00000588268,;ZNF461,downstream_gene_variant,,ENST00000591370,;ZNF461,non_coding_transcript_exon_variant,,ENST00000540605,;ZNF461,upstream_gene_variant,,ENST00000589442,;ZNF461,3_prime_UTR_variant,,ENST00000396893,;ZNF461,non_coding_transcript_exon_variant,,ENST00000590487,;ZNF461,downstream_gene_variant,,ENST00000590361,;ZNF461,downstream_gene_variant,,ENST00000588844,;	-	ENSG00000197808	ENST00000588268	Transcript	frameshift_variant	968-969	740-741	247	E/X	gAG/g	.	.	.	-1	ZNF461	HGNC	21629	protein_coding	YES	CCDS54257.1	ENSP00000467931	ZN461_HUMAN	K7EJM1_HUMAN,K7EIW1_HUMAN	UPI00002021CA	.	.	.	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF277,hmmpanther:PTHR24377,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTACACTCATTG	.	3	ESCA
ZNF793	0	.	GRCh37	19	38028524	38028524	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964G>A	p.Glu322Lys	p.E322K	ENST00000445217	4/4	96	63	33	74	74	0	ZNF793,missense_variant,p.Glu322Lys,ENST00000587143,;ZNF793,missense_variant,p.Glu322Lys,ENST00000542455,;ZNF793,missense_variant,p.Glu322Lys,ENST00000445217,;ZNF793,3_prime_UTR_variant,,ENST00000588578,;ZNF793,intron_variant,,ENST00000589319,;ZNF793,downstream_gene_variant,,ENST00000587490,;ZNF793,downstream_gene_variant,,ENST00000586138,;ZNF793,downstream_gene_variant,,ENST00000587986,;ZNF793,intron_variant,,ENST00000586187,;	A	ENSG00000188227	ENST00000445217	Transcript	missense_variant	999	964	322	E/K	Gag/Aag	COSM711706	.	.	1	ZNF793	HGNC	33115	protein_coding	YES	CCDS46062.1	ENSP00000396402	ZN793_HUMAN	K7ERJ7_HUMAN	UPI0001536771	.	deleterious(0.04)	possibly_damaging(0.824)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF42,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGTGAGAAG	.	5	ESCA
ZNF540	0	.	GRCh37	19	38103432	38103432	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1251G>C	p.Glu417Asp	p.E417D	ENST00000592533	5/5	62	32	30	45	45	0	ZNF540,missense_variant,p.Glu417Asp,ENST00000316433,;ZNF540,missense_variant,p.Glu417Asp,ENST00000343599,;ZNF540,missense_variant,p.Glu385Asp,ENST00000589117,;ZNF540,missense_variant,p.Glu417Asp,ENST00000586134,;ZNF540,missense_variant,p.Glu417Asp,ENST00000592533,;ZNF540,downstream_gene_variant,,ENST00000590588,;ZFP30,downstream_gene_variant,,ENST00000589018,;ZNF540,downstream_gene_variant,,ENST00000586792,;ZNF540,downstream_gene_variant,,ENST00000589857,;ZNF540,non_coding_transcript_exon_variant,,ENST00000589285,;	C	ENSG00000171817	ENST00000592533	Transcript	missense_variant	1583	1251	417	E/D	gaG/gaC	.	.	.	1	ZNF540	HGNC	25331	protein_coding	YES	CCDS12506.1	ENSP00000466274	ZN540_HUMAN	K7EK80_HUMAN	UPI00000732BB	.	deleterious(0.01)	benign(0.103)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF138,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGAGAAGGC	.	5	ESCA
ZNF230	0	.	GRCh37	19	44516597	44516597	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*981T>C	.	.	ENST00000429154	5/5	35	29	6	32	32	0	ZNF230,3_prime_UTR_variant,,ENST00000429154,;ZNF230,downstream_gene_variant,,ENST00000585491,;ZNF230,downstream_gene_variant,,ENST00000585632,;ZNF230,3_prime_UTR_variant,,ENST00000585568,;	C	ENSG00000159882	ENST00000429154	Transcript	3_prime_UTR_variant	2634	.	.	.	.	.	.	.	1	ZNF230	HGNC	13024	protein_coding	YES	CCDS33044.1	ENSP00000409318	ZN230_HUMAN	K7EMK6_HUMAN	UPI000016960C	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAGTGTTTC	.	5	ESCA
BLOC1S3	0	.	GRCh37	19	45684003	45684003	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*840G>C	.	.	ENST00000433642	2/2	22	18	4	12	12	0	BLOC1S3,3_prime_UTR_variant,,ENST00000433642,;MARK4,intron_variant,,ENST00000587566,;BLOC1S3,intron_variant,,ENST00000592910,;TRAPPC6A,upstream_gene_variant,,ENST00000588062,;TRAPPC6A,upstream_gene_variant,,ENST00000592647,;TRAPPC6A,upstream_gene_variant,,ENST00000006275,;BLOC1S3,downstream_gene_variant,,ENST00000587722,;TRAPPC6A,upstream_gene_variant,,ENST00000585934,;BLOC1S3,intron_variant,,ENST00000588362,;AC005779.2,intron_variant,,ENST00000593083,;TRAPPC6A,upstream_gene_variant,,ENST00000587818,;AC005779.1,downstream_gene_variant,,ENST00000441087,;	C	ENSG00000189114	ENST00000433642	Transcript	3_prime_UTR_variant	1545	.	.	.	.	.	.	.	1	BLOC1S3	HGNC	20914	protein_coding	YES	CCDS12656.1	ENSP00000393840	BL1S3_HUMAN	K7EN58_HUMAN,K7ELZ0_HUMAN	UPI0000202628	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTAGAGACA	.	5	ESCA
GRIN2D	0	.	GRCh37	19	48922912	48922912	+	Silent	SNP	G	G	A	rs752875753	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1932G>A	p.%3D	p.S644S	ENST00000263269	9/13	55	46	9	41	41	0	GRIN2D,synonymous_variant,p.%3D,ENST00000263269,;	A	ENSG00000105464	ENST00000263269	Transcript	synonymous_variant	2020	1932	644	S	tcG/tcA	rs752875753	.	.	1	GRIN2D	HGNC	4588	protein_coding	YES	CCDS12719.1	ENSP00000263269	NMDE4_HUMAN	.	UPI000013D3DA	.	.	.	9/13	.	hmmpanther:PTHR18966:SF105,hmmpanther:PTHR18966,Pfam_domain:PF00497,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079,Prints_domain:PR00177	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTCGGTGCC	.	5	ESCA
RASIP1	0	.	GRCh37	19	49230042	49230042	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2127G>A	p.%3D	p.K709K	ENST00000222145	8/12	13	9	4	9	9	0	RASIP1,synonymous_variant,p.%3D,ENST00000222145,;RASIP1,intron_variant,,ENST00000599291,;RASIP1,downstream_gene_variant,,ENST00000594232,;RASIP1,upstream_gene_variant,,ENST00000601530,;	T	ENSG00000105538	ENST00000222145	Transcript	synonymous_variant	2332	2127	709	K	aaG/aaA	.	.	.	-1	RASIP1	HGNC	24716	protein_coding	YES	CCDS12731.1	ENSP00000222145	RAIN_HUMAN	Q9NX72_HUMAN,Q7L251_HUMAN,B3KVR5_HUMAN	UPI000020283D	.	.	.	8/12	.	PROSITE_profiles:PS51126,hmmpanther:PTHR16027:SF4,hmmpanther:PTHR16027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAACCTTGGT	.	2	ESCA
SUV420H2	0	.	GRCh37	19	55853280	55853280	+	5'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25G>C	.	.	ENST00000255613	2/9	57	48	9	36	36	0	SUV420H2,5_prime_UTR_variant,,ENST00000255613,;AC020922.1,5_prime_UTR_variant,,ENST00000539076,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000402499,;SUV420H2,upstream_gene_variant,,ENST00000460956,;SUV420H2,upstream_gene_variant,,ENST00000587442,;SUV420H2,5_prime_UTR_variant,,ENST00000592631,;SUV420H2,5_prime_UTR_variant,,ENST00000445196,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000464185,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000589338,;SUV420H2,non_coding_transcript_exon_variant,,ENST00000498738,;SUV420H2,upstream_gene_variant,,ENST00000474492,;SUV420H2,upstream_gene_variant,,ENST00000468951,;	C	ENSG00000133247	ENST00000255613	Transcript	5_prime_UTR_variant	224	.	.	.	.	.	.	.	1	SUV420H2	HGNC	28405	protein_coding	YES	CCDS12922.1	ENSP00000255613	SV422_HUMAN	.	UPI000000DABC	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCCAGAGGCA	.	4	ESCA
COL11A1	0	.	GRCh37	1	103496701	103496701	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.751G>T	p.Ala251Ser	p.A251S	ENST00000370096	5/67	21	12	8	20	20	0	COL11A1,missense_variant,p.Ala251Ser,ENST00000512756,;COL11A1,missense_variant,p.Ala251Ser,ENST00000353414,;COL11A1,missense_variant,p.Ala251Ser,ENST00000427239,;COL11A1,missense_variant,p.Ala251Ser,ENST00000370096,;COL11A1,missense_variant,p.Ala178Ser,ENST00000447608,;COL11A1,missense_variant,p.Ala251Ser,ENST00000358392,;	A	ENSG00000060718	ENST00000370096	Transcript	missense_variant	1064	751	251	A/S	Gct/Tct	.	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	benign(0.341)	5/67	.	hmmpanther:PTHR24023:SF42,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGCAGCCT	.	5	ESCA
AMY2B	0	.	GRCh37	1	104122112	104122112	+	Missense_Mutation	SNP	C	C	G	rs748747355	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1526C>G	p.Ser509Cys	p.S509C	ENST00000361355	12/12	545	532	13	412	412	0	AMY2B,missense_variant,p.Ser509Cys,ENST00000361355,;AMY2B,non_coding_transcript_exon_variant,,ENST00000481821,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,downstream_gene_variant,,ENST00000462971,;AMY2B,3_prime_UTR_variant,,ENST00000477657,;	G	ENSG00000240038	ENST00000361355	Transcript	missense_variant	2142	1526	509	S/C	tCt/tGt	rs748747355	.	.	1	AMY2B	HGNC	478	protein_coding	YES	CCDS782.1	ENSP00000354610	AMY2B_HUMAN	C9JWK7_HUMAN,C9J2Z5_HUMAN	UPI0000000CB1	.	deleterious(0)	probably_damaging(0.998)	12/12	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Gene3D:2.60.40.1180,SMART_domains:SM00632,Superfamily_domains:SSF51011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAATCTAAAT	.	2	ESCA
TMEM167B	0	.	GRCh37	1	109643003	109643003	+	3'Flank	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000338272	.	22	16	6	22	22	0	TMEM167B,downstream_gene_variant,,ENST00000338272,;SCARNA2,non_coding_transcript_exon_variant,,ENST00000458748,;SCARNA2,non_coding_transcript_exon_variant,,ENST00000602755,;RP5-1065J22.4,downstream_gene_variant,,ENST00000429752,;	C	ENSG00000215717	ENST00000338272	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3447	1	TMEM167B	HGNC	30187	protein_coding	YES	CCDS30789.1	ENSP00000342148	KISHB_HUMAN	.	UPI000006CCF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTTGATCGG	.	5	ESCA
IGSF9	0	.	GRCh37	1	159899523	159899523	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2231G>T	p.Cys744Phe	p.C744F	ENST00000368094	17/21	39	27	11	24	24	0	IGSF9,missense_variant,p.Cys744Phe,ENST00000368094,;IGSF9,missense_variant,p.Cys728Phe,ENST00000361509,;TAGLN2,upstream_gene_variant,,ENST00000397334,;TAGLN2,upstream_gene_variant,,ENST00000368097,;IGSF9,non_coding_transcript_exon_variant,,ENST00000476102,;IGSF9,non_coding_transcript_exon_variant,,ENST00000493195,;IGSF9,non_coding_transcript_exon_variant,,ENST00000496645,;TAGLN2,upstream_gene_variant,,ENST00000478033,;	A	ENSG00000085552	ENST00000368094	Transcript	missense_variant	2429	2231	744	C/F	tGc/tTc	.	.	.	-1	IGSF9	HGNC	18132	protein_coding	YES	CCDS44254.1	ENSP00000357073	TUTLA_HUMAN	Q6XYD8_HUMAN	UPI000004A10B	.	deleterious(0)	benign(0.361)	17/21	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10489:SF534,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGCAGACT	.	5	ESCA
LY9	0	.	GRCh37	1	160765947	160765947	+	5'Flank	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000263285	.	28	23	5	21	21	0	LY9,5_prime_UTR_variant,,ENST00000368041,;LY9,5_prime_UTR_variant,,ENST00000341032,;LY9,5_prime_UTR_variant,,ENST00000368040,;LY9,5_prime_UTR_variant,,ENST00000392203,;LY9,5_prime_UTR_variant,,ENST00000368037,;LY9,upstream_gene_variant,,ENST00000368039,;LY9,upstream_gene_variant,,ENST00000263285,;LY9,upstream_gene_variant,,ENST00000471816,;LY9,upstream_gene_variant,,ENST00000485624,;LY9,upstream_gene_variant,,ENST00000480837,;LY9,5_prime_UTR_variant,,ENST00000474998,;LY9,upstream_gene_variant,,ENST00000490902,;	G	ENSG00000122224	ENST00000263285	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1	1	LY9	HGNC	6730	protein_coding	YES	CCDS30916.1	ENSP00000263285	LY9_HUMAN	.	UPI00001416AF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCCTCCTTCA	.	5	ESCA
GPR161	0	.	GRCh37	1	168066315	168066315	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590T>C	p.Met197Thr	p.M197T	ENST00000537209	4/7	30	25	4	23	23	0	GPR161,missense_variant,p.Met177Thr,ENST00000367835,;GPR161,missense_variant,p.Met177Thr,ENST00000271357,;GPR161,missense_variant,p.Met99Thr,ENST00000539777,;GPR161,missense_variant,p.Met63Thr,ENST00000546300,;GPR161,missense_variant,p.Met45Thr,ENST00000367836,;GPR161,missense_variant,p.Met177Thr,ENST00000361697,;GPR161,missense_variant,p.Met177Thr,ENST00000367838,;GPR161,missense_variant,p.Met197Thr,ENST00000537209,;GPR161,non_coding_transcript_exon_variant,,ENST00000493800,;	G	ENSG00000143147	ENST00000537209	Transcript	missense_variant	839	590	197	M/T	aTg/aCg	.	.	.	-1	GPR161	HGNC	23694	protein_coding	YES	CCDS58043.1	ENSP00000441039	GP161_HUMAN	.	UPI0002065201	.	tolerated(0.92)	benign(0.006)	4/7	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF246,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACACATCCAT	.	4	ESCA
DNM3	0	.	GRCh37	1	172362646	172362646	+	Intron	SNP	C	C	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2522+4697C>A	.	.	ENST00000358155	.	26	15	11	26	26	0	DNM3,intron_variant,,ENST00000367731,;DNM3,intron_variant,,ENST00000355305,;DNM3,intron_variant,,ENST00000358155,;DNM3,intron_variant,,ENST00000485254,;PIGC,non_coding_transcript_exon_variant,,ENST00000484368,;PIGC,intron_variant,,ENST00000489002,;PIGC,intron_variant,,ENST00000475059,;DNM3,downstream_gene_variant,,ENST00000491124,;	A	ENSG00000197959	ENST00000358155	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	DNM3	HGNC	29125	protein_coding	YES	CCDS53431.1	ENSP00000350876	DYN3_HUMAN	E5RIK2_HUMAN	UPI0000251D91	.	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACACGGACA	.	5	ESCA
PTPRC	0	.	GRCh37	1	198608248	198608248	+	5'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-63T>C	.	.	ENST00000442510	1/33	22	15	7	27	27	0	PTPRC,5_prime_UTR_variant,,ENST00000598951,;PTPRC,5_prime_UTR_variant,,ENST00000348564,;PTPRC,5_prime_UTR_variant,,ENST00000352140,;PTPRC,5_prime_UTR_variant,,ENST00000442510,;PTPRC,5_prime_UTR_variant,,ENST00000367376,;PTPRC,5_prime_UTR_variant,,ENST00000413409,;PTPRC,5_prime_UTR_variant,,ENST00000594404,;PTPRC,5_prime_UTR_variant,,ENST00000530727,;PTPRC,5_prime_UTR_variant,,ENST00000367367,;PTPRC,5_prime_UTR_variant,,ENST00000367364,;PTPRC,intron_variant,,ENST00000367379,;PTPRC,upstream_gene_variant,,ENST00000418674,;PTPRC,upstream_gene_variant,,ENST00000427110,;PTPRC,upstream_gene_variant,,ENST00000391970,;PTPRC,5_prime_UTR_variant,,ENST00000529828,;PTPRC,non_coding_transcript_exon_variant,,ENST00000462363,;	C	ENSG00000081237	ENST00000442510	Transcript	5_prime_UTR_variant	79	.	.	.	.	.	.	.	1	PTPRC	HGNC	9666	protein_coding	YES	CCDS1397.2	ENSP00000411355	.	M9MML3_HUMAN,Q9H3X6_HUMAN,Q6QIR3_HUMAN,Q6QIQ5_HUMAN,Q6QIN9_HUMAN,Q6QIN1_HUMAN,Q6QIM3_HUMAN,Q6LDN6_HUMAN	UPI000046FDB4	.	.	.	1/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGTCTGATAA	.	2	ESCA
ZC3H11A	0	.	GRCh37	1	203765608	203765608	+	5'Flank	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000545588	.	67	42	25	62	62	0	ZC3H11A,5_prime_UTR_variant,,ENST00000367212,;ZBED6,5_prime_UTR_variant,,ENST00000550078,;ZC3H11A,5_prime_UTR_variant,,ENST00000367214,;ZC3H11A,5_prime_UTR_variant,,ENST00000432282,;ZC3H11A,5_prime_UTR_variant,,ENST00000332127,;ZC3H11A,intron_variant,,ENST00000453771,;ZC3H11A,upstream_gene_variant,,ENST00000545588,;ZC3H11A,non_coding_transcript_exon_variant,,ENST00000466470,;ZC3H11A,non_coding_transcript_exon_variant,,ENST00000492823,;ZC3H11A,intron_variant,,ENST00000461980,;ZC3H11A,upstream_gene_variant,,ENST00000495527,;	T	ENSG00000058673	ENST00000545588	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2855	1	ZC3H11A	HGNC	29093	protein_coding	YES	CCDS30978.1	ENSP00000438527	ZC11A_HUMAN	E9PBY7_HUMAN,C9J0L0_HUMAN,B4DLG2_HUMAN	UPI000006F3FD	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCCCTAAAC	.	5	ESCA
PLA2G5	0	.	GRCh37	1	20411357	20411357	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34G>A	p.Ala12Thr	p.A12T	ENST00000375108	2/5	53	38	15	68	68	0	PLA2G5,missense_variant,p.Ala12Thr,ENST00000375108,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000465698,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000478803,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000469069,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000486277,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000489871,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000460175,;	A	ENSG00000127472	ENST00000375108	Transcript	missense_variant	302	34	12	A/T	Gct/Act	.	.	.	1	PLA2G5	HGNC	9038	protein_coding	YES	CCDS202.1	ENSP00000364249	PA2G5_HUMAN	.	UPI00001310E7	.	tolerated(0.1)	benign(0.007)	2/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11716:SF10,hmmpanther:PTHR11716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGGCTTGT	.	5	ESCA
LYST	0	.	GRCh37	1	235860435	235860435	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10512C>G	p.Ile3504Met	p.I3504M	ENST00000389794	46/53	84	53	31	60	60	0	LYST,missense_variant,p.Ile3504Met,ENST00000389793,;LYST,missense_variant,p.Ile3504Met,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000473037,;	C	ENSG00000143669	ENST00000389794	Transcript	missense_variant	10687	10512	3504	I/M	atC/atG	.	.	.	-1	LYST	HGNC	1968	protein_coding	YES	CCDS31062.1	ENSP00000374444	LYST_HUMAN	.	UPI000020509E	.	deleterious(0)	probably_damaging(0.99)	46/53	.	hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF60	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAGATTGC	.	5	ESCA
FAM46B	0	.	GRCh37	1	27333125	27333125	+	Silent	SNP	G	G	A	rs143879440	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.588C>T	p.%3D	p.S196S	ENST00000289166	2/2	17	10	7	20	20	0	FAM46B,synonymous_variant,p.%3D,ENST00000289166,;	A	ENSG00000158246	ENST00000289166	Transcript	synonymous_variant	754	588	196	S	agC/agT	rs143879440,COSM907811	.	.	-1	FAM46B	HGNC	28273	protein_coding	YES	CCDS294.2	ENSP00000289166	FA46B_HUMAN	.	UPI0000374A6A	.	.	.	2/2	.	Pfam_domain:PF07984,hmmpanther:PTHR12974:SF33,hmmpanther:PTHR12974	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCGCTCTT	.	5	ESCA
HMGB4	0	.	GRCh37	1	34329981	34329981	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189G>C	p.%3D	p.L63L	ENST00000522796	4/4	36	23	13	45	45	0	HMGB4,synonymous_variant,p.%3D,ENST00000522796,;HMGB4,synonymous_variant,p.%3D,ENST00000519684,;CSMD2,intron_variant,,ENST00000373381,;RP5-1007G16.1,upstream_gene_variant,,ENST00000425631,;HMGB4,non_coding_transcript_exon_variant,,ENST00000425537,;HMGB4,downstream_gene_variant,,ENST00000458277,;CSMD2,intron_variant,,ENST00000241312,;	C	ENSG00000176256	ENST00000522796	Transcript	synonymous_variant	2094	189	63	L	ctG/ctC	.	.	.	1	HMGB4	HGNC	24954	protein_coding	YES	CCDS30668.1	ENSP00000430919	HMGB4_HUMAN	.	UPI000011E2F1	.	.	.	4/4	.	PROSITE_profiles:PS50118,hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF152,Gene3D:1.10.30.10,Pfam_domain:PF09011,SMART_domains:SM00398,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTGGCCAA	.	5	ESCA
CCDC163P	0	.	GRCh37	1	45962253	45962253	+	Missense_Mutation	SNP	C	C	T	rs759753197	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.305G>A	p.Arg102Gln	p.R102Q	ENST00000488405	4/4	25	21	4	21	21	0	CCDC163P,missense_variant,p.Arg102Gln,ENST00000490551,;CCDC163P,missense_variant,p.Arg102Gln,ENST00000432082,;CCDC163P,missense_variant,p.Arg102Gln,ENST00000488405,;MMACHC,upstream_gene_variant,,ENST00000401061,;CCDC163P,non_coding_transcript_exon_variant,,ENST00000486476,;CCDC163P,non_coding_transcript_exon_variant,,ENST00000502793,;CCDC163P,missense_variant,p.Arg102Gln,ENST00000415578,;CCDC163P,3_prime_UTR_variant,,ENST00000515561,;CCDC163P,3_prime_UTR_variant,,ENST00000514299,;	T	ENSG00000236624	ENST00000488405	Transcript	missense_variant	549	305	102	R/Q	cGa/cAa	rs759753197	.	.	-1	CCDC163P	HGNC	27003	protein_coding	YES	.	ENSP00000432622	.	E9PPK7_HUMAN	UPI000019722E	.	tolerated_low_confidence(0.3)	benign(0.417)	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGTCGTCCC	.	4	ESCA
ATPAF1	0	.	GRCh37	1	47098981	47098981	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2467G>A	.	.	ENST00000576409	9/9	122	96	25	115	115	0	ATPAF1,3_prime_UTR_variant,,ENST00000371937,;ATPAF1,3_prime_UTR_variant,,ENST00000574428,;ATPAF1,3_prime_UTR_variant,,ENST00000576409,;ATPAF1,downstream_gene_variant,,ENST00000534216,;ATPAF1,downstream_gene_variant,,ENST00000542495,;ATPAF1,downstream_gene_variant,,ENST00000532925,;ATPAF1,downstream_gene_variant,,ENST00000492233,;ATPAF1,downstream_gene_variant,,ENST00000329231,;ATPAF1,downstream_gene_variant,,ENST00000526821,;ATPAF1,downstream_gene_variant,,ENST00000529214,;	T	ENSG00000123472	ENST00000576409	Transcript	3_prime_UTR_variant	3586	.	.	.	.	.	.	.	-1	ATPAF1	HGNC	18803	protein_coding	YES	CCDS541.2	ENSP00000460964	.	I3L448_HUMAN	UPI000222BB4E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGCAAGGG	.	5	ESCA
PPAP2B	0	.	GRCh37	1	56962230	56962230	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.929T>C	p.Met310Thr	p.M310T	ENST00000371250	6/6	54	37	17	40	40	0	PPAP2B,missense_variant,p.Met310Thr,ENST00000371250,;PPAP2B,non_coding_transcript_exon_variant,,ENST00000472957,;PPAP2B,non_coding_transcript_exon_variant,,ENST00000459962,;	G	ENSG00000162407	ENST00000371250	Transcript	missense_variant	1481	929	310	M/T	aTg/aCg	.	.	.	-1	PPAP2B	HGNC	9229	protein_coding	YES	CCDS604.1	ENSP00000360296	LPP3_HUMAN	.	UPI000006F261	.	deleterious_low_confidence(0)	benign(0.272)	6/6	.	hmmpanther:PTHR10165:SF79,hmmpanther:PTHR10165	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCATGTTG	.	5	ESCA
CACHD1	0	.	GRCh37	1	65113504	65113504	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>C	p.Glu342Gln	p.E342Q	ENST00000290039	9/27	41	33	8	17	17	0	CACHD1,missense_variant,p.Glu342Gln,ENST00000290039,;CACHD1,missense_variant,p.Glu393Gln,ENST00000371073,;CACHD1,non_coding_transcript_exon_variant,,ENST00000495994,;CACHD1,non_coding_transcript_exon_variant,,ENST00000470527,;	C	ENSG00000158966	ENST00000290039	Transcript	missense_variant	1130	1024	342	E/Q	Gag/Cag	.	.	.	1	CACHD1	HGNC	29314	protein_coding	YES	CCDS628.2	ENSP00000290039	.	.	UPI0000458A70	.	deleterious(0.01)	probably_damaging(0.994)	9/27	.	PROSITE_profiles:PS50234,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF28,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAAGAGCTG	.	5	ESCA
SPTLC3	0	.	GRCh37	20	13029863	13029863	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303+85C>T	.	.	ENST00000399002	.	39	34	5	33	33	0	SPTLC3,intron_variant,,ENST00000450297,;SPTLC3,intron_variant,,ENST00000399002,;SPTLC3,intron_variant,,ENST00000434210,;SPTLC3,intron_variant,,ENST00000378194,;SPTLC3,non_coding_transcript_exon_variant,,ENST00000476791,;	T	ENSG00000172296	ENST00000399002	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SPTLC3	HGNC	16253	protein_coding	YES	CCDS13115.2	ENSP00000381968	SPTC3_HUMAN	Q8N2H1_HUMAN,B1AKS2_HUMAN	UPI0000D6BFB5	.	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AGATCCTAGAA	.	2	ESCA
MRPS26	0	.	GRCh37	20	3028466	3028466	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569C>T	p.Ala190Val	p.A190V	ENST00000380325	4/4	35	28	7	31	31	0	MRPS26,missense_variant,p.Ala190Val,ENST00000380325,;GNRH2,downstream_gene_variant,,ENST00000380346,;GNRH2,downstream_gene_variant,,ENST00000380347,;GNRH2,downstream_gene_variant,,ENST00000359100,;GNRH2,downstream_gene_variant,,ENST00000359987,;GNRH2,downstream_gene_variant,,ENST00000245983,;	T	ENSG00000125901	ENST00000380325	Transcript	missense_variant	693	569	190	A/V	gCc/gTc	.	.	.	1	MRPS26	HGNC	14045	protein_coding	YES	CCDS13043.1	ENSP00000369682	RT26_HUMAN	.	UPI00001352A1	.	deleterious(0.02)	benign(0.247)	4/4	.	hmmpanther:PTHR21035:SF2,hmmpanther:PTHR21035,Pfam_domain:PF14943	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGCCATCA	.	5	ESCA
CSE1L	0	.	GRCh37	20	47710714	47710714	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2485G>C	p.Glu829Gln	p.E829Q	ENST00000262982	23/25	153	94	59	94	94	0	CSE1L,missense_variant,p.Glu612Gln,ENST00000542325,;CSE1L,missense_variant,p.Glu773Gln,ENST00000396192,;CSE1L,missense_variant,p.Glu829Gln,ENST00000262982,;CSE1L,non_coding_transcript_exon_variant,,ENST00000469700,;	C	ENSG00000124207	ENST00000262982	Transcript	missense_variant	2608	2485	829	E/Q	Gaa/Caa	.	.	.	1	CSE1L	HGNC	2431	protein_coding	YES	CCDS13412.1	ENSP00000262982	XPO2_HUMAN	.	UPI000013D377	.	deleterious(0.03)	possibly_damaging(0.864)	23/25	.	hmmpanther:PTHR10997,hmmpanther:PTHR10997:SF8,Pfam_domain:PF03378,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTGAAATT	.	5	ESCA
BAGE2	0	.	GRCh37	21	11038730	11038730	+	Intron	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1474C>T	.	.	ENST00000470054	6/10	169	152	17	173	173	0	BAGE2,splice_region_variant,,ENST00000470054,;BAGE2,splice_region_variant,,ENST00000496773,;	A	ENSG00000187172	ENST00000470054	Transcript	splice_region_variant	1474	.	.	.	.	.	.	.	-1	BAGE2	HGNC	15723	processed_transcript	YES	.	.	.	.	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCTGTTTGG	.	4	ESCA
WRB	0	.	GRCh37	21	40759698	40759698	+	Intron	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103-2926G>C	.	.	ENST00000333781	.	110	84	26	88	88	0	WRB,5_prime_UTR_variant,,ENST00000380708,;WRB,intron_variant,,ENST00000333781,;WRB,intron_variant,,ENST00000398753,;WRB,intron_variant,,ENST00000442773,;WRB,intron_variant,,ENST00000380713,;WRB,intron_variant,,ENST00000541890,;WRB,upstream_gene_variant,,ENST00000415847,;WRB,upstream_gene_variant,,ENST00000466787,;WRB,intron_variant,,ENST00000471468,;WRB,intron_variant,,ENST00000487869,;	C	ENSG00000182093	ENST00000333781	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	WRB	HGNC	12790	protein_coding	YES	CCDS13664.1	ENSP00000327716	WRB_HUMAN	H7BYE5_HUMAN,C9JLV3_HUMAN	UPI0000138F94	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCAGACACC	.	5	ESCA
C2CD2	0	.	GRCh37	21	43305512	43305512	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3721A>T	.	.	ENST00000380486	14/14	22	16	6	25	25	0	C2CD2,3_prime_UTR_variant,,ENST00000449165,;C2CD2,3_prime_UTR_variant,,ENST00000329623,;C2CD2,3_prime_UTR_variant,,ENST00000380486,;SNORA3,downstream_gene_variant,,ENST00000515969,;C2CD2,downstream_gene_variant,,ENST00000482186,;C2CD2,downstream_gene_variant,,ENST00000482084,;	A	ENSG00000157617	ENST00000380486	Transcript	3_prime_UTR_variant	6054	.	.	.	.	.	.	.	-1	C2CD2	HGNC	1266	protein_coding	YES	CCDS42933.1	ENSP00000369853	CU025_HUMAN	.	UPI0000206BBE	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGAATGGTGC	.	2	ESCA
ARVCF	0	.	GRCh37	22	19974605	19974605	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210+3503A>G	.	.	ENST00000263207	.	25	17	8	24	24	0	ARVCF,synonymous_variant,p.%3D,ENST00000406522,;ARVCF,synonymous_variant,p.%3D,ENST00000344269,;ARVCF,synonymous_variant,p.%3D,ENST00000401994,;ARVCF,intron_variant,,ENST00000263207,;ARVCF,intron_variant,,ENST00000406259,;ARVCF,non_coding_transcript_exon_variant,,ENST00000487793,;ARVCF,non_coding_transcript_exon_variant,,ENST00000492625,;ARVCF,intron_variant,,ENST00000467828,;ARVCF,upstream_gene_variant,,ENST00000462319,;ARVCF,intron_variant,,ENST00000473551,;	C	ENSG00000099889	ENST00000263207	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ARVCF	HGNC	728	protein_coding	YES	CCDS13771.1	ENSP00000263207	ARVC_HUMAN	.	UPI00001260C8	.	.	.	.	3/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTGAGTTCGGC	.	3	ESCA
KB-1592A4.15	0	.	GRCh37	22	21470420	21470420	+	RNA	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3309G>C	.	.	ENST00000420508	6/6	660	639	21	357	357	0	KB-1592A4.15,non_coding_transcript_exon_variant,,ENST00000420508,;BCRP2,intron_variant,,ENST00000461808,;BCRP2,upstream_gene_variant,,ENST00000398241,;BCRP2,intron_variant,,ENST00000447763,;	G	ENSG00000197210	ENST00000420508	Transcript	non_coding_transcript_exon_variant	3309	.	.	.	.	.	.	.	-1	KB-1592A4.15	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATCTCAGAGT	.	2	ESCA
KIAA1671	0	.	GRCh37	22	25566894	25566894	+	Missense_Mutation	SNP	G	G	C	rs757902857	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4638G>C	p.Gln1546His	p.Q1546H	ENST00000358431	5/11	28	22	5	20	20	0	KIAA1671,missense_variant,p.Gln53His,ENST00000401395,;KIAA1671,missense_variant,p.Gln1546His,ENST00000406486,;KIAA1671,missense_variant,p.Gln1546His,ENST00000358431,;KIAA1671,non_coding_transcript_exon_variant,,ENST00000494730,;	C	ENSG00000197077	ENST00000358431	Transcript	missense_variant	4664	4638	1546	Q/H	caG/caC	rs757902857	.	.	1	KIAA1671	HGNC	29345	protein_coding	YES	CCDS46676.1	ENSP00000351207	K1671_HUMAN	.	UPI00002073DC	.	tolerated(0.11)	benign(0.012)	5/11	.	hmmpanther:PTHR22042:SF3,hmmpanther:PTHR22042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAGAGTGG	.	5	ESCA
CHEK2	0	.	GRCh37	22	29092950	29092950	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1163A>T	p.His388Leu	p.H388L	ENST00000382580	11/16	67	61	6	43	43	0	CHEK2,missense_variant,p.His124Leu,ENST00000544772,;CHEK2,missense_variant,p.His278Leu,ENST00000447421,;CHEK2,missense_variant,p.His345Leu,ENST00000404276,;CHEK2,missense_variant,p.His388Leu,ENST00000382580,;CHEK2,missense_variant,p.His254Leu,ENST00000382578,;CHEK2,missense_variant,p.His345Leu,ENST00000328354,;CHEK2,missense_variant,p.His89Leu,ENST00000434810,;CHEK2,missense_variant,p.His345Leu,ENST00000405598,;CHEK2,missense_variant,p.His254Leu,ENST00000403642,;CHEK2,3_prime_UTR_variant,,ENST00000382566,;CHEK2,intron_variant,,ENST00000348295,;CHEK2,intron_variant,,ENST00000456369,;CHEK2,intron_variant,,ENST00000402731,;CHEK2,intron_variant,,ENST00000382565,;CHEK2,downstream_gene_variant,,ENST00000425190,;CHEK2,non_coding_transcript_exon_variant,,ENST00000464581,;CHEK2,3_prime_UTR_variant,,ENST00000433728,;CHEK2,3_prime_UTR_variant,,ENST00000417588,;CHEK2,3_prime_UTR_variant,,ENST00000433028,;CHEK2,3_prime_UTR_variant,,ENST00000416671,;CHEK2,3_prime_UTR_variant,,ENST00000448511,;CHEK2,non_coding_transcript_exon_variant,,ENST00000491919,;CHEK2,downstream_gene_variant,,ENST00000439346,;	A	ENSG00000183765	ENST00000382580	Transcript	missense_variant	1239	1163	388	H/L	cAc/cTc	.	.	.	-1	CHEK2	HGNC	16627	protein_coding	YES	CCDS33629.1	ENSP00000372023	CHK2_HUMAN	B7ZBF2_HUMAN	UPI000034E4A3	.	deleterious(0)	probably_damaging(1)	11/16	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR24344,PROSITE_patterns:PS00108,hmmpanther:PTHR24344:SF21,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CACGGTGTATA	.	2	ESCA
BPIFC	0	.	GRCh37	22	32815372	32815372	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1237G>C	p.Glu413Gln	p.E413Q	ENST00000397452	13/16	87	61	26	59	59	0	BPIFC,missense_variant,p.Glu137Gln,ENST00000534972,;BPIFC,missense_variant,p.Glu170Gln,ENST00000432451,;BPIFC,missense_variant,p.Glu413Gln,ENST00000397452,;BPIFC,missense_variant,p.Glu413Gln,ENST00000300399,;	G	ENSG00000184459	ENST00000397452	Transcript	missense_variant	1348	1237	413	E/Q	Gag/Cag	.	.	.	-1	BPIFC	HGNC	16503	protein_coding	YES	CCDS13906.1	ENSP00000380594	BPIFC_HUMAN	F5H3G0_HUMAN	UPI0000071B53	.	tolerated(0.1)	benign(0.21)	13/16	.	hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF17,Pfam_domain:PF02886,Gene3D:1ewfA02,SMART_domains:SM00329,Superfamily_domains:SSF55394	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACTCTGGCA	.	5	ESCA
MYO7B	0	.	GRCh37	2	128341785	128341785	+	Missense_Mutation	SNP	C	C	A	rs746922996	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1432C>A	p.Arg478Ser	p.R478S	ENST00000428314	13/47	58	43	14	60	60	0	MYO7B,missense_variant,p.Arg478Ser,ENST00000389524,;MYO7B,missense_variant,p.Arg478Ser,ENST00000409816,;MYO7B,missense_variant,p.Arg478Ser,ENST00000428314,;	A	ENSG00000169994	ENST00000428314	Transcript	missense_variant	1485	1432	478	R/S	Cgc/Agc	rs746922996	.	.	1	MYO7B	HGNC	7607	protein_coding	YES	CCDS46405.1	ENSP00000415090	MYO7B_HUMAN	C9JC21_HUMAN,B9A063_HUMAN	UPI00006C04F0	.	tolerated(0.71)	benign(0.206)	13/47	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF352,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTACCGCTCG	byFrequency	5	ESCA
LRP1B	0	.	GRCh37	2	141459771	141459771	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6241G>A	p.Gly2081Arg	p.G2081R	ENST00000389484	39/91	78	74	4	55	55	0	LRP1B,missense_variant,p.Gly2081Arg,ENST00000389484,;	T	ENSG00000168702	ENST00000389484	Transcript	missense_variant	7213	6241	2081	G/R	Gga/Aga	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	probably_damaging(0.953)	39/91	.	PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTCCTGACA	.	2	ESCA
HOXD9	0	.	GRCh37	2	176989169	176989169	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*266T>C	.	.	ENST00000249499	2/2	26	22	3	21	21	0	HOXD9,3_prime_UTR_variant,,ENST00000249499,;HOXD10,downstream_gene_variant,,ENST00000249501,;HOXD-AS2,intron_variant,,ENST00000440016,;	C	ENSG00000128709	ENST00000249499	Transcript	3_prime_UTR_variant	1734	.	.	.	.	.	.	.	1	HOXD9	HGNC	5140	protein_coding	YES	CCDS2267.2	ENSP00000249499	HXD9_HUMAN	.	UPI000004A10E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTCCATTGGTT	.	3	ESCA
MYT1L	0	.	GRCh37	2	1893241	1893241	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2286C>T	p.%3D	p.D762D	ENST00000428368	16/25	22	16	5	34	34	0	MYT1L,synonymous_variant,p.%3D,ENST00000399161,;MYT1L,synonymous_variant,p.%3D,ENST00000428368,;MYT1L,3_prime_UTR_variant,,ENST00000602387,;MYT1L,non_coding_transcript_exon_variant,,ENST00000490585,;MYT1L,upstream_gene_variant,,ENST00000470954,;	A	ENSG00000186487	ENST00000428368	Transcript	synonymous_variant	2956	2286	762	D	gaC/gaT	.	.	.	-1	MYT1L	HGNC	7623	protein_coding	YES	CCDS46222.1	ENSP00000396103	MYT1L_HUMAN	.	UPI00004E55EA	.	.	.	16/25	.	hmmpanther:PTHR10816:SF11,hmmpanther:PTHR10816,Pfam_domain:PF08474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATGTCAGG	.	5	ESCA
USP40	0	.	GRCh37	2	234405457	234405457	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2770C>T	p.%3D	p.L924L	ENST00000450966	23/31	31	21	9	43	43	0	USP40,synonymous_variant,p.%3D,ENST00000251722,;USP40,synonymous_variant,p.%3D,ENST00000409945,;USP40,synonymous_variant,p.%3D,ENST00000427112,;USP40,synonymous_variant,p.%3D,ENST00000450966,;USP40,synonymous_variant,p.%3D,ENST00000430158,;USP40,non_coding_transcript_exon_variant,,ENST00000483216,;USP40,upstream_gene_variant,,ENST00000450940,;	A	ENSG00000085982	ENST00000450966	Transcript	synonymous_variant	2770	2770	924	L	Ctg/Ttg	.	.	.	-1	USP40	HGNC	20069	protein_coding	YES	CCDS46547.1	ENSP00000415434	UBP40_HUMAN	.	UPI0000232F06	.	.	.	23/31	.	hmmpanther:PTHR24006:SF423,hmmpanther:PTHR24006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCAGAAGTT	.	5	ESCA
OTOF	0	.	GRCh37	2	26717916	26717916	+	Missense_Mutation	SNP	C	C	T	rs370475628	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.791G>A	p.Arg264Gln	p.R264Q	ENST00000272371	9/47	39	36	3	37	37	0	OTOF,missense_variant,p.Arg264Gln,ENST00000403946,;OTOF,missense_variant,p.Arg264Gln,ENST00000272371,;	T	ENSG00000115155	ENST00000272371	Transcript	missense_variant	918	791	264	R/Q	cGg/cAg	rs370475628	.	.	-1	OTOF	HGNC	8515	protein_coding	YES	CCDS1725.1	ENSP00000272371	OTOF_HUMAN	.	UPI000013D94D	.	tolerated(0.17)	probably_damaging(0.999)	9/47	.	PROSITE_profiles:PS50004,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGCCGGGCC	byFrequency|byCluster	2	ESCA
EHBP1	0	.	GRCh37	2	63176060	63176060	+	Silent	SNP	C	C	T	rs143884885	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2184C>T	p.%3D	p.I728I	ENST00000263991	14/25	56	37	18	53	53	0	EHBP1,synonymous_variant,p.%3D,ENST00000263991,;EHBP1,synonymous_variant,p.%3D,ENST00000405289,;EHBP1,synonymous_variant,p.%3D,ENST00000405015,;EHBP1,synonymous_variant,p.%3D,ENST00000431489,;EHBP1,synonymous_variant,p.%3D,ENST00000354487,;EHBP1,intron_variant,,ENST00000444311,;EHBP1,upstream_gene_variant,,ENST00000454124,;EHBP1,intron_variant,,ENST00000469591,;	T	ENSG00000115504	ENST00000263991	Transcript	synonymous_variant	2666	2184	728	I	atC/atT	rs143884885,COSM1177335	.	.	1	EHBP1	HGNC	29144	protein_coding	YES	CCDS1872.1	ENSP00000263991	EHBP1_HUMAN	C9K0H9_HUMAN,C9JEP1_HUMAN,C9J268_HUMAN,B3KM32_HUMAN	UPI000013D49A	.	.	.	14/25	.	hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF124	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACATCGGTAG	byFrequency|byCluster	5	ESCA
RMND5A	0	.	GRCh37	2	87001009	87001009	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*475A>T	.	.	ENST00000283632	9/9	26	23	3	15	15	0	RMND5A,3_prime_UTR_variant,,ENST00000283632,;RMND5A,downstream_gene_variant,,ENST00000472843,;RMND5A,downstream_gene_variant,,ENST00000471113,;	T	ENSG00000153561	ENST00000283632	Transcript	3_prime_UTR_variant	2146	.	.	.	.	.	.	.	1	RMND5A	HGNC	25850	protein_coding	YES	CCDS1991.1	ENSP00000283632	RMD5A_HUMAN	B4DZV7_HUMAN	UPI000000DC2B	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGTTATGAAA	.	3	ESCA
ZNF148	0	.	GRCh37	3	124946044	124946044	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5141A>G	.	.	ENST00000360647	9/9	106	72	33	71	71	0	ZNF148,3_prime_UTR_variant,,ENST00000360647,;SLC12A8,intron_variant,,ENST00000423114,;ZNF148,downstream_gene_variant,,ENST00000544464,;ZNF148,downstream_gene_variant,,ENST00000468369,;ZNF148,downstream_gene_variant,,ENST00000492394,;ZNF148,downstream_gene_variant,,ENST00000484491,;	C	ENSG00000163848	ENST00000360647	Transcript	3_prime_UTR_variant	8012	.	.	.	.	.	.	.	-1	ZNF148	HGNC	12933	protein_coding	YES	CCDS3031.1	ENSP00000353863	ZN148_HUMAN	C9K0U4_HUMAN,C9JRX0_HUMAN,C9J6Y6_HUMAN	UPI000013C2FF	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTATACAAC	.	5	ESCA
NPHP3	0	.	GRCh37	3	132441186	132441186	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14C>G	p.Ser5Trp	p.S5W	ENST00000337331	1/27	14	8	6	8	8	0	NPHP3,missense_variant,p.Ser5Trp,ENST00000326682,;NPHP3,missense_variant,p.Ser5Trp,ENST00000337331,;NPHP3,missense_variant,p.Ser5Trp,ENST00000383282,;NPHP3,missense_variant,p.Ser5Trp,ENST00000343113,;NPHP3-AS1,non_coding_transcript_exon_variant,,ENST00000504440,;NPHP3-AS1,non_coding_transcript_exon_variant,,ENST00000489343,;NPHP3,upstream_gene_variant,,ENST00000471145,;NPHP3,missense_variant,p.Ser5Trp,ENST00000465756,;NPHP3,missense_variant,p.Ser5Trp,ENST00000471702,;NPHP3,upstream_gene_variant,,ENST00000469232,;NPHP3,upstream_gene_variant,,ENST00000490993,;	C	ENSG00000113971	ENST00000337331	Transcript	missense_variant	101	14	5	S/W	tCg/tGg	.	.	.	-1	NPHP3	HGNC	7907	protein_coding	YES	CCDS3078.1	ENSP00000338766	NPHP3_HUMAN	.	UPI00001B6B30	.	deleterious(0)	probably_damaging(0.999)	1/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGACGAGGCG	.	2	ESCA
FAIM	0	.	GRCh37	3	138340279	138340279	+	Silent	SNP	T	T	C	rs768985563	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111T>C	p.%3D	p.D37D	ENST00000338446	3/6	84	55	28	62	62	0	FAIM,synonymous_variant,p.%3D,ENST00000360570,;FAIM,synonymous_variant,p.%3D,ENST00000393035,;FAIM,synonymous_variant,p.%3D,ENST00000479848,;FAIM,synonymous_variant,p.%3D,ENST00000464668,;FAIM,synonymous_variant,p.%3D,ENST00000393034,;FAIM,synonymous_variant,p.%3D,ENST00000338446,;FAIM,non_coding_transcript_exon_variant,,ENST00000491175,;FAIM,non_coding_transcript_exon_variant,,ENST00000464912,;FAIM,non_coding_transcript_exon_variant,,ENST00000470889,;	C	ENSG00000158234	ENST00000338446	Transcript	synonymous_variant	794	111	37	D	gaT/gaC	rs768985563	.	.	1	FAIM	HGNC	18703	protein_coding	YES	CCDS33864.1	ENSP00000342805	FAIM1_HUMAN	C9JDZ2_HUMAN	UPI00005B2E09	.	.	.	3/6	.	hmmpanther:PTHR13088:SF1,hmmpanther:PTHR13088,Pfam_domain:PF06905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGATCTCGT	byFrequency	5	ESCA
ARHGEF26	0	.	GRCh37	3	153935682	153935682	+	Missense_Mutation	SNP	G	G	A	rs774329182	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870G>A	p.Ala624Thr	p.A624T	ENST00000356448	10/15	52	33	18	45	45	0	ARHGEF26,missense_variant,p.Ala624Thr,ENST00000465093,;ARHGEF26,missense_variant,p.Ala624Thr,ENST00000356448,;ARHGEF26,intron_variant,,ENST00000465817,;ARHGEF26,missense_variant,p.Ala624Thr,ENST00000496710,;	A	ENSG00000114790	ENST00000356448	Transcript	missense_variant	2154	1870	624	A/T	Gcc/Acc	rs774329182	.	.	1	ARHGEF26	HGNC	24490	protein_coding	YES	CCDS46938.1	ENSP00000348828	ARHGQ_HUMAN	.	UPI00001410D0	.	deleterious(0)	possibly_damaging(0.532)	10/15	.	hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF4,Gene3D:1.20.900.10,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGGGCGCCCGG	.	4	ESCA
OPA1	0	.	GRCh37	3	193380719	193380719	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2575G>C	p.Glu859Gln	p.E859Q	ENST00000361908	25/30	111	74	37	83	83	0	OPA1,missense_variant,p.Glu14Gln,ENST00000445863,;OPA1,missense_variant,p.Glu841Gln,ENST00000361715,;OPA1,missense_variant,p.Glu840Gln,ENST00000361828,;OPA1,missense_variant,p.Glu822Gln,ENST00000392438,;OPA1,missense_variant,p.Glu877Gln,ENST00000361510,;OPA1,missense_variant,p.Glu823Gln,ENST00000361150,;OPA1,missense_variant,p.Glu859Gln,ENST00000361908,;OPA1,upstream_gene_variant,,ENST00000429164,;OPA1,downstream_gene_variant,,ENST00000482865,;	C	ENSG00000198836	ENST00000361908	Transcript	missense_variant	2809	2575	859	E/Q	Gaa/Caa	.	.	.	1	OPA1	HGNC	8140	protein_coding	YES	CCDS33917.1	ENSP00000354681	OPA1_HUMAN	Q6PEK6_HUMAN,E5KLJ7_HUMAN,C9JY58_HUMAN	UPI0000422960	.	tolerated(0.78)	benign(0.011)	25/30	.	hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGAATCC	.	5	ESCA
IQCG	0	.	GRCh37	3	197665569	197665569	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365delT	p.Leu122Ter	p.L122*	ENST00000265239	5/12	143	115	28	67	67	0	IQCG,frameshift_variant,p.Leu103Ter,ENST00000416896,;IQCG,frameshift_variant,p.Leu122Ter,ENST00000453254,;IQCG,frameshift_variant,p.Leu122Ter,ENST00000455191,;IQCG,frameshift_variant,p.Leu122Ter,ENST00000265239,;IQCG,non_coding_transcript_exon_variant,,ENST00000480302,;IQCG,non_coding_transcript_exon_variant,,ENST00000463651,;IQCG,non_coding_transcript_exon_variant,,ENST00000490748,;	-	ENSG00000114473	ENST00000265239	Transcript	frameshift_variant	790	365	122	L/X	tTa/ta	.	.	.	-1	IQCG	HGNC	25251	protein_coding	YES	CCDS3331.1	ENSP00000265239	IQCG_HUMAN	C9JUC1_HUMAN,C9J6M9_HUMAN	UPI0000037D68	.	.	.	5/12	.	hmmpanther:PTHR14871,hmmpanther:PTHR14871:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTATTAACGGA	.	3	ESCA
FRMD4B	0	.	GRCh37	3	69230096	69230096	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2805G>C	p.%3D	p.L935L	ENST00000398540	21/23	12	7	5	9	9	0	FRMD4B,synonymous_variant,p.%3D,ENST00000398540,;FRMD4B,synonymous_variant,p.%3D,ENST00000478263,;FRMD4B,synonymous_variant,p.%3D,ENST00000542259,;	G	ENSG00000114541	ENST00000398540	Transcript	synonymous_variant	2889	2805	935	L	ctG/ctC	.	.	.	-1	FRMD4B	HGNC	24886	protein_coding	YES	CCDS46863.1	ENSP00000381549	FRM4B_HUMAN	E9PGA7_HUMAN,C9JAW0_HUMAN,C9JA15_HUMAN,C9J6Q2_HUMAN,B3KNA2_HUMAN	UPI00001C1DF1	.	.	.	21/23	.	hmmpanther:PTHR23281:SF16,hmmpanther:PTHR23281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTGCAGCCC	.	2	ESCA
CRYBG3	0	.	GRCh37	3	97617998	97617999	+	In_Frame_Ins	INS	-	-	TTT	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2018_2019insTTT	p.Gln673delinsHisLeu	p.Q673delinsHL	ENST00000182096	11/19	86	51	35	40	40	0	CRYBG3,protein_altering_variant,p.Gln673delinsHisLeu,ENST00000182096,;	TTT	ENSG00000080200	ENST00000182096	Transcript	protein_altering_variant	2082-2083	2018-2019	673	Q/HL	caa/caTTTa	.	.	.	1	CRYBG3	HGNC	34427	protein_coding	YES	.	ENSP00000182096	CRBG3_HUMAN	.	UPI00006E232D	.	.	.	11/19	.	PROSITE_profiles:PS50915,hmmpanther:PTHR11818:SF38,hmmpanther:PTHR11818,Gene3D:2.60.20.10,Pfam_domain:PF00030,SMART_domains:SM00247,Superfamily_domains:SSF49695,Prints_domain:PR01367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAGCAAAAGT	.	3	ESCA
NFKB1	0	.	GRCh37	4	103538205	103538205	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*454T>A	.	.	ENST00000226574	24/24	141	88	53	145	145	0	NFKB1,3_prime_UTR_variant,,ENST00000600343,;NFKB1,3_prime_UTR_variant,,ENST00000505458,;NFKB1,3_prime_UTR_variant,,ENST00000226574,;NFKB1,downstream_gene_variant,,ENST00000394820,;	A	ENSG00000109320	ENST00000226574	Transcript	3_prime_UTR_variant	3831	.	.	.	.	.	.	.	1	NFKB1	HGNC	7794	protein_coding	YES	CCDS3657.1	ENSP00000226574	NFKB1_HUMAN	D6RF93_HUMAN,D6RC45_HUMAN	UPI0000192724	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CATTTTAAAAA	.	3	ESCA
TLL1	0	.	GRCh37	4	166981293	166981293	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1960T>C	p.Tyr654His	p.Y654H	ENST00000061240	15/21	60	34	25	52	52	0	TLL1,missense_variant,p.Tyr654His,ENST00000061240,;TLL1,missense_variant,p.Tyr677His,ENST00000507499,;TLL1,3_prime_UTR_variant,,ENST00000509505,;	C	ENSG00000038295	ENST00000061240	Transcript	missense_variant	2607	1960	654	Y/H	Tac/Cac	.	.	.	1	TLL1	HGNC	11843	protein_coding	YES	CCDS3811.1	ENSP00000061240	TLL1_HUMAN	D6RCE0_HUMAN	UPI0000072EED	.	tolerated(0.28)	benign(0.085)	15/21	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,Pfam_domain:PF00431,Gene3D:2.60.120.290,PIRSF_domain:PIRSF001199,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGTACAGA	.	5	ESCA
C4orf27	0	.	GRCh37	4	170669922	170669922	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470A>T	p.Asn157Ile	p.N157I	ENST00000393381	4/8	119	73	46	84	84	0	C4orf27,missense_variant,p.Asn157Ile,ENST00000393381,;C4orf27,downstream_gene_variant,,ENST00000506125,;	A	ENSG00000056050	ENST00000393381	Transcript	missense_variant	546	470	157	N/I	aAt/aTt	.	.	.	-1	C4orf27	HGNC	26051	protein_coding	YES	CCDS3813.1	ENSP00000406598	CD027_HUMAN	.	UPI000013D19D	.	tolerated(0.45)	benign(0.005)	4/8	.	hmmpanther:PTHR13386,hmmpanther:PTHR13386:SF1,Pfam_domain:PF10228	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCATTTGGA	.	5	ESCA
KIAA1430	0	.	GRCh37	4	186084049	186084049	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1502G>T	p.Gly501Val	p.G501V	ENST00000458385	5/5	52	24	28	42	42	0	KIAA1430,missense_variant,p.Gly501Val,ENST00000458385,;	A	ENSG00000164323	ENST00000458385	Transcript	missense_variant	1622	1502	501	G/V	gGt/gTt	.	.	.	-1	KIAA1430	HGNC	29276	protein_coding	YES	CCDS47168.1	ENSP00000409964	K1430_HUMAN	D6RDU8_HUMAN	UPI00001971F9	.	deleterious(0.02)	probably_damaging(0.911)	5/5	.	hmmpanther:PTHR23035,hmmpanther:PTHR23035:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGACCACTC	.	5	ESCA
GIN1	0	.	GRCh37	5	102444392	102444392	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20A>G	p.Asn7Ser	p.N7S	ENST00000399004	2/8	73	44	28	77	77	0	GIN1,missense_variant,p.Asn7Ser,ENST00000508629,;GIN1,missense_variant,p.Asn7Ser,ENST00000399004,;GIN1,upstream_gene_variant,,ENST00000511400,;GIN1,missense_variant,p.Asn7Ser,ENST00000513747,;GIN1,missense_variant,p.Asn7Ser,ENST00000512248,;GIN1,non_coding_transcript_exon_variant,,ENST00000513603,;	C	ENSG00000145723	ENST00000399004	Transcript	missense_variant	115	20	7	N/S	aAt/aGt	.	.	.	-1	GIN1	HGNC	25959	protein_coding	YES	CCDS43349.1	ENSP00000381970	GIN1_HUMAN	.	UPI000020C3A9	.	tolerated_low_confidence(0.15)	benign(0.061)	2/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCATTTTTT	.	5	ESCA
ROPN1L	0	.	GRCh37	5	10448476	10448476	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236T>C	p.Leu79Pro	p.L79P	ENST00000503804	3/6	57	44	13	37	37	0	ROPN1L,missense_variant,p.Leu79Pro,ENST00000274134,;ROPN1L,missense_variant,p.Leu79Pro,ENST00000503804,;ROPN1L,non_coding_transcript_exon_variant,,ENST00000510520,;ROPN1L,non_coding_transcript_exon_variant,,ENST00000515762,;ROPN1L,non_coding_transcript_exon_variant,,ENST00000512022,;	C	ENSG00000145491	ENST00000503804	Transcript	missense_variant	757	236	79	L/P	cTg/cCg	.	.	.	1	ROPN1L	HGNC	24060	protein_coding	YES	CCDS3879.1	ENSP00000421405	ROP1L_HUMAN	.	UPI000013D9F3	.	deleterious(0)	probably_damaging(0.998)	3/6	.	hmmpanther:PTHR14952:SF2,hmmpanther:PTHR14952	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCCTGAAAG	.	5	ESCA
SPRY4	0	.	GRCh37	5	141693968	141693968	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775T>C	p.Ser259Pro	p.S259P	ENST00000344120	3/3	31	13	18	18	18	0	SPRY4,missense_variant,p.Ser259Pro,ENST00000344120,;SPRY4,missense_variant,p.Ser236Pro,ENST00000434127,;SPRY4,downstream_gene_variant,,ENST00000511815,;SPRY4,downstream_gene_variant,,ENST00000503582,;	G	ENSG00000187678	ENST00000344120	Transcript	missense_variant	962	775	259	S/P	Tcc/Ccc	.	.	.	-1	SPRY4	HGNC	15533	protein_coding	YES	CCDS4274.1	ENSP00000344967	SPY4_HUMAN	D6RB56_HUMAN	UPI0000167871	.	tolerated(0.13)	probably_damaging(0.917)	3/3	.	Pfam_domain:PF05210,hmmpanther:PTHR12365:SF6,hmmpanther:PTHR12365,PROSITE_profiles:PS51227	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGGACCAGC	.	5	ESCA
BOD1	0	.	GRCh37	5	173043252	173043252	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.188G>A	p.Gly63Asp	p.G63D	ENST00000311086	1/4	21	9	12	22	22	0	BOD1,missense_variant,p.Gly63Asp,ENST00000285908,;BOD1,missense_variant,p.Gly63Asp,ENST00000480951,;BOD1,missense_variant,p.Gly63Asp,ENST00000311086,;BOD1,missense_variant,p.Ala38Thr,ENST00000477985,;BOD1,upstream_gene_variant,,ENST00000462674,;BOD1,non_coding_transcript_exon_variant,,ENST00000471339,;	T	ENSG00000145919	ENST00000311086	Transcript	missense_variant	412	188	63	G/D	gGc/gAc	.	.	.	-1	BOD1	HGNC	25114	protein_coding	YES	CCDS4389.1	ENSP00000309644	BOD1_HUMAN	C9J8U9_HUMAN	UPI00001A92E5	.	deleterious(0)	probably_damaging(1)	1/4	.	hmmpanther:PTHR31532,Pfam_domain:PF05205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGGCCCCGG	.	5	ESCA
GHR	0	.	GRCh37	5	42719156	42719156	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1547T>C	p.Met516Thr	p.M516T	ENST00000230882	10/10	104	84	20	60	60	0	GHR,missense_variant,p.Met516Thr,ENST00000230882,;GHR,missense_variant,p.Met329Thr,ENST00000537449,;GHR,missense_variant,p.Met494Thr,ENST00000357703,;GHR,downstream_gene_variant,,ENST00000513625,;GHR,3_prime_UTR_variant,,ENST00000511135,;	C	ENSG00000112964	ENST00000230882	Transcript	missense_variant	1737	1547	516	M/T	aTg/aCg	.	.	.	1	GHR	HGNC	4263	protein_coding	YES	CCDS3940.1	ENSP00000230882	GHR_HUMAN	Q9NRZ8_HUMAN,Q9HCW9_HUMAN,F5H7X2_HUMAN	UPI000012B416	.	tolerated(0.59)	benign(0.004)	10/10	.	Pfam_domain:PF12772,hmmpanther:PTHR23036:SF74,hmmpanther:PTHR23036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACATGCACC	.	5	ESCA
IL31RA	0	.	GRCh37	5	55204090	55204090	+	Intron	SNP	C	C	A	rs375773462	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355-3C>A	.	.	ENST00000447346	.	44	23	20	55	55	0	IL31RA,splice_region_variant,,ENST00000447346,;IL31RA,splice_region_variant,,ENST00000490985,;IL31RA,splice_region_variant,,ENST00000359040,;IL31RA,splice_region_variant,,ENST00000354961,;IL31RA,splice_region_variant,,ENST00000396836,;IL31RA,splice_region_variant,,ENST00000396834,;IL31RA,splice_region_variant,,ENST00000297015,;	A	ENSG00000164509	ENST00000447346	Transcript	splice_region_variant	.	.	.	.	.	rs375773462	.	.	1	IL31RA	HGNC	18969	protein_coding	YES	CCDS3970.2	ENSP00000415900	IL31R_HUMAN	.	UPI00001A41DC	.	.	.	.	10/14	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCCAGTTC	byFrequency|byCluster	4	ESCA
IL31RA	0	.	GRCh37	5	55204634	55204634	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501+395C>T	.	.	ENST00000447346	.	15	9	6	14	14	0	IL31RA,3_prime_UTR_variant,,ENST00000396836,;IL31RA,3_prime_UTR_variant,,ENST00000297015,;IL31RA,intron_variant,,ENST00000447346,;IL31RA,intron_variant,,ENST00000490985,;IL31RA,intron_variant,,ENST00000359040,;IL31RA,intron_variant,,ENST00000354961,;IL31RA,intron_variant,,ENST00000396834,;	T	ENSG00000164509	ENST00000447346	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	IL31RA	HGNC	18969	protein_coding	YES	CCDS3970.2	ENSP00000415900	IL31R_HUMAN	.	UPI00001A41DC	.	.	.	.	11/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCAGTCC	.	5	ESCA
PIK3R1	0	.	GRCh37	5	67594192	67594192	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*763A>G	.	.	ENST00000521381	16/16	82	76	6	68	68	0	PIK3R1,3_prime_UTR_variant,,ENST00000274335,;PIK3R1,3_prime_UTR_variant,,ENST00000521381,;PIK3R1,3_prime_UTR_variant,,ENST00000336483,;PIK3R1,3_prime_UTR_variant,,ENST00000396611,;PIK3R1,3_prime_UTR_variant,,ENST00000521657,;PIK3R1,3_prime_UTR_variant,,ENST00000320694,;PIK3R1,3_prime_UTR_variant,,ENST00000523872,;PIK3R1,downstream_gene_variant,,ENST00000519025,;PIK3R1,downstream_gene_variant,,ENST00000521409,;PIK3R1,non_coding_transcript_exon_variant,,ENST00000518813,;PIK3R1,downstream_gene_variant,,ENST00000517698,;PIK3R1,downstream_gene_variant,,ENST00000520550,;PIK3R1,downstream_gene_variant,,ENST00000518292,;	G	ENSG00000145675	ENST00000521381	Transcript	3_prime_UTR_variant	3554	.	.	.	.	.	.	.	1	PIK3R1	HGNC	8979	protein_coding	YES	CCDS3993.1	ENSP00000428056	P85A_HUMAN	J7GXU7_HUMAN,J7GU64_HUMAN,E5RJY0_HUMAN,E5RHI0_HUMAN,E5RGI8_HUMAN,B3KWZ7_HUMAN	UPI000013D9FF	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACCAAATAGCT	.	2	ESCA
LIN28B	0	.	GRCh37	6	105530521	105530522	+	3'UTR	DEL	TG	TG	-	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	TG	TG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3864_*3865delGT	.	.	ENST00000345080	4/4	53	46	7	38	38	0	LIN28B,3_prime_UTR_variant,,ENST00000345080,;	-	ENSG00000187772	ENST00000345080	Transcript	3_prime_UTR_variant	4819-4820	.	.	.	.	.	.	.	1	LIN28B	HGNC	32207	protein_coding	YES	CCDS34504.1	ENSP00000344401	LN28B_HUMAN	A7E2T3_HUMAN	UPI000035E7BD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	AAACTCTGTCTTA	.	2	ESCA
NKAIN2	0	.	GRCh37	6	125146611	125146611	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2236T>C	.	.	ENST00000368417	7/7	81	74	7	59	59	0	NKAIN2,3_prime_UTR_variant,,ENST00000368417,;	C	ENSG00000188580	ENST00000368417	Transcript	3_prime_UTR_variant	2923	.	.	.	.	.	.	.	1	NKAIN2	HGNC	16443	protein_coding	YES	CCDS34526.1	ENSP00000357402	NKAI2_HUMAN	B3KNZ0_HUMAN,B0AZU5_HUMAN	UPI0000458919	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGAATGCTAT	.	3	ESCA
SAMD3	0	.	GRCh37	6	130496985	130496985	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822+1G>C	.	p.X274_splice	ENST00000368134	.	51	31	20	47	47	0	SAMD3,splice_donor_variant,,ENST00000532763,;SAMD3,splice_donor_variant,,ENST00000457563,;SAMD3,splice_donor_variant,,ENST00000437477,;SAMD3,splice_donor_variant,,ENST00000368134,;SAMD3,splice_donor_variant,,ENST00000439090,;SAMD3,non_coding_transcript_exon_variant,,ENST00000528422,;SAMD3,downstream_gene_variant,,ENST00000533296,;SAMD3,non_coding_transcript_exon_variant,,ENST00000526886,;	G	ENSG00000164483	ENST00000368134	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	SAMD3	HGNC	21574	protein_coding	YES	CCDS34539.1	ENSP00000357116	SAMD3_HUMAN	E9PS85_HUMAN	UPI000006DCE7	.	.	.	.	10/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTACTTTTA	.	5	ESCA
TMEM200A	0	.	GRCh37	6	130763018	130763018	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1451G>T	p.Arg484Met	p.R484M	ENST00000392429	2/2	42	34	8	38	38	0	TMEM200A,missense_variant,p.Arg484Met,ENST00000392429,;TMEM200A,missense_variant,p.Arg484Met,ENST00000545622,;TMEM200A,missense_variant,p.Arg484Met,ENST00000296978,;	T	ENSG00000164484	ENST00000392429	Transcript	missense_variant	3829	1451	484	R/M	aGg/aTg	.	.	.	1	TMEM200A	HGNC	21075	protein_coding	YES	CCDS5140.1	ENSP00000376224	T200A_HUMAN	B4DG12_HUMAN,A8K2A1_HUMAN	UPI000000DA85	.	deleterious_low_confidence(0)	probably_damaging(0.996)	2/2	.	hmmpanther:PTHR31815,hmmpanther:PTHR31815:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGGGGAA	.	5	ESCA
TULP4	0	.	GRCh37	6	158932126	158932126	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4400C>G	.	.	ENST00000367097	14/14	47	30	17	41	41	0	TULP4,3_prime_UTR_variant,,ENST00000367097,;TULP4,downstream_gene_variant,,ENST00000367094,;CACYBPP3,downstream_gene_variant,,ENST00000406011,;	G	ENSG00000130338	ENST00000367097	Transcript	3_prime_UTR_variant	10389	.	.	.	.	.	.	.	1	TULP4	HGNC	15530	protein_coding	YES	CCDS34561.1	ENSP00000356064	TULP4_HUMAN	.	UPI000013CD76	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTACTTTGT	.	5	ESCA
FKBP5	0	.	GRCh37	6	35588005	35588005	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297A>T	p.Lys99Asn	p.K99N	ENST00000536438	5/12	80	51	28	56	56	0	FKBP5,missense_variant,p.Lys99Asn,ENST00000536438,;FKBP5,missense_variant,p.Lys99Asn,ENST00000539068,;FKBP5,missense_variant,p.Lys99Asn,ENST00000357266,;FKBP5,missense_variant,p.Lys99Asn,ENST00000542713,;FKBP5,intron_variant,,ENST00000540787,;	A	ENSG00000096060	ENST00000536438	Transcript	missense_variant	613	297	99	K/N	aaA/aaT	.	.	.	-1	FKBP5	HGNC	3721	protein_coding	YES	CCDS4808.1	ENSP00000444810	FKBP5_HUMAN	B7Z7Z8_HUMAN	UPI000000D9EE	.	tolerated(0.13)	possibly_damaging(0.503)	5/12	.	PROSITE_profiles:PS50059,hmmpanther:PTHR10516,hmmpanther:PTHR10516:SF26,Pfam_domain:PF00254,Gene3D:3.10.50.40,Superfamily_domains:SSF54534	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCTTTCTT	.	5	ESCA
TMEM217	0	.	GRCh37	6	37180243	37180243	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*530T>C	.	.	ENST00000336655	4/4	22	17	5	13	13	0	TMEM217,3_prime_UTR_variant,,ENST00000356757,;TMEM217,3_prime_UTR_variant,,ENST00000336655,;TMEM217,non_coding_transcript_exon_variant,,ENST00000497775,;TMEM217,downstream_gene_variant,,ENST00000478262,;	G	ENSG00000172738	ENST00000336655	Transcript	3_prime_UTR_variant	1260	.	.	.	.	.	.	.	-1	TMEM217	HGNC	21238	protein_coding	YES	CCDS4831.1	ENSP00000338164	TM217_HUMAN	.	UPI0000071695	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTCACTGCA	.	5	ESCA
DNAH8	0	.	GRCh37	6	38891915	38891915	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10288T>C	p.Ser3430Pro	p.S3430P	ENST00000359357	71/91	86	79	6	72	72	0	DNAH8,missense_variant,p.Ser3430Pro,ENST00000359357,;DNAH8,missense_variant,p.Ser3635Pro,ENST00000327475,;DNAH8,missense_variant,p.Ser3394Pro,ENST00000441566,;DNAH8,missense_variant,p.Ser3647Pro,ENST00000449981,;RP1-207H1.3,intron_variant,,ENST00000418399,;RP1-207H1.3,intron_variant,,ENST00000416948,;RP1-207H1.2,upstream_gene_variant,,ENST00000407768,;	C	ENSG00000124721	ENST00000359357	Transcript	missense_variant	10542	10288	3430	S/P	Tca/Cca	.	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	benign(0.302)	71/91	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTATTTCAATG	.	2	ESCA
ENPP4	0	.	GRCh37	6	46108786	46108786	+	Intron	SNP	C	C	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.827-3C>A	.	.	ENST00000321037	.	42	23	18	33	33	0	ENPP4,splice_region_variant,,ENST00000321037,;	A	ENSG00000001561	ENST00000321037	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	ENPP4	HGNC	3359	protein_coding	YES	CCDS34468.1	ENSP00000318066	ENPP4_HUMAN	.	UPI0000048E43	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCAGATA	.	4	ESCA
TFAP2B	0	.	GRCh37	6	50803934	50803934	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.762G>C	p.Gln254His	p.Q254H	ENST00000393655	4/7	25	13	12	23	23	0	TFAP2B,missense_variant,p.Gln254His,ENST00000393655,;TFAP2B,missense_variant,p.Gln263His,ENST00000263046,;	C	ENSG00000008196	ENST00000393655	Transcript	missense_variant	931	762	254	Q/H	caG/caC	.	.	.	1	TFAP2B	HGNC	11743	protein_coding	YES	CCDS4934.2	ENSP00000377265	AP2B_HUMAN	A8K557_HUMAN	UPI000020DE90	.	deleterious(0.02)	benign(0.142)	4/7	.	hmmpanther:PTHR10812:SF14,hmmpanther:PTHR10812,Pfam_domain:PF03299	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCAGAGACG	.	5	ESCA
DST	0	.	GRCh37	6	56481466	56481466	+	Intron	SNP	T	T	A	rs770154837	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3319-2184A>T	.	.	ENST00000244364	.	44	36	8	40	40	0	DST,missense_variant,p.Ile2267Phe,ENST00000370765,;DST,intron_variant,,ENST00000439203,;DST,intron_variant,,ENST00000446842,;DST,intron_variant,,ENST00000370788,;DST,intron_variant,,ENST00000244364,;DST,intron_variant,,ENST00000520645,;DST,intron_variant,,ENST00000370754,;DST,intron_variant,,ENST00000361203,;DST,intron_variant,,ENST00000370769,;DST,intron_variant,,ENST00000312431,;DST,intron_variant,,ENST00000421834,;DST,downstream_gene_variant,,ENST00000522360,;	A	ENSG00000151914	ENST00000244364	Transcript	intron_variant	.	.	.	.	.	rs770154837	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	.	22/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAATTTCTG	.	5	ESCA
MYO6	0	.	GRCh37	6	76558106	76558106	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936T>G	p.Asp312Glu	p.D312E	ENST00000369977	11/35	104	88	15	72	72	0	MYO6,missense_variant,p.Asp312Glu,ENST00000369985,;MYO6,missense_variant,p.Asp312Glu,ENST00000369977,;MYO6,missense_variant,p.Asp312Glu,ENST00000369981,;MYO6,missense_variant,p.Asp312Glu,ENST00000369975,;	G	ENSG00000196586	ENST00000369977	Transcript	missense_variant	1075	936	312	D/E	gaT/gaG	.	.	.	1	MYO6	HGNC	7605	protein_coding	YES	CCDS34487.1	ENSP00000358994	MYO6_HUMAN	Q14784_HUMAN	UPI00000727CF	.	deleterious(0)	unknown(0)	11/35	.	Superfamily_domains:SSF52540,SMART_domains:SM00242,Pfam_domain:PF00063,hmmpanther:PTHR13140:SF346,hmmpanther:PTHR13140,PROSITE_profiles:PS51456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAGATGACCA	.	5	ESCA
RARS2	0	.	GRCh37	6	88226573	88226573	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1537T>G	p.Ser513Ala	p.S513A	ENST00000369536	18/20	59	46	13	42	42	0	RARS2,missense_variant,p.Ser513Ala,ENST00000369536,;SLC35A1,downstream_gene_variant,,ENST00000369556,;SLC35A1,downstream_gene_variant,,ENST00000369552,;RARS2,non_coding_transcript_exon_variant,,ENST00000493269,;RARS2,downstream_gene_variant,,ENST00000497828,;	C	ENSG00000146282	ENST00000369536	Transcript	missense_variant	1583	1537	513	S/A	Tct/Gct	.	.	.	-1	RARS2	HGNC	21406	protein_coding	YES	CCDS5011.1	ENSP00000358549	SYRM_HUMAN	H0UI22_HUMAN	UPI000020D2E6	.	tolerated(0.66)	benign(0.003)	18/20	.	hmmpanther:PTHR11956:SF3,hmmpanther:PTHR11956,Gene3D:1.10.730.10,Pfam_domain:PF05746,TIGRFAM_domain:TIGR00456,SMART_domains:SM00836,Superfamily_domains:SSF47323	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGATGATT	.	5	ESCA
MOGAT3	0	.	GRCh37	7	100843774	100843774	+	Silent	SNP	G	G	C	rs200949443	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132C>G	p.%3D	p.V44V	ENST00000223114	2/7	15	5	10	15	15	0	MOGAT3,synonymous_variant,p.%3D,ENST00000223114,;MOGAT3,synonymous_variant,p.%3D,ENST00000379423,;MOGAT3,synonymous_variant,p.%3D,ENST00000440203,;RP4-747G18.5,downstream_gene_variant,,ENST00000428316,;DGAT2L7P,downstream_gene_variant,,ENST00000379421,;DGAT2L7P,downstream_gene_variant,,ENST00000602462,;	C	ENSG00000106384	ENST00000223114	Transcript	synonymous_variant	299	132	44	V	gtC/gtG	rs200949443	.	.	-1	MOGAT3	HGNC	23249	protein_coding	YES	CCDS5714.1	ENSP00000223114	MOGT3_HUMAN	.	UPI00000622D1	.	.	.	2/7	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF13	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAAGACAAG	byCluster|by1000G	5	ESCA
PMPCB	0	.	GRCh37	7	102939017	102939017	+	Silent	SNP	A	A	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.102A>T	p.%3D	p.S34S	ENST00000249269	2/13	66	45	21	53	53	0	PMPCB,synonymous_variant,p.%3D,ENST00000428154,;PMPCB,synonymous_variant,p.%3D,ENST00000249269,;PMPCB,splice_region_variant,,ENST00000420236,;PMPCB,synonymous_variant,p.%3D,ENST00000456433,;PMPCB,synonymous_variant,p.%3D,ENST00000453466,;PMPCB,synonymous_variant,p.%3D,ENST00000443722,;PMPCB,splice_region_variant,,ENST00000444457,;PMPCB,splice_region_variant,,ENST00000498530,;	T	ENSG00000105819	ENST00000249269	Transcript	synonymous_variant	140	102	34	S	tcA/tcT	.	.	.	1	PMPCB	HGNC	9119	protein_coding	YES	CCDS5730.1	ENSP00000249269	MPPB_HUMAN	.	UPI00000712F7	.	.	.	2/13	.	hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTCATTATA	.	5	ESCA
PSMC2	0	.	GRCh37	7	103008599	103008599	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*98T>G	.	.	ENST00000435765	13/13	57	42	15	40	40	0	PSMC2,3_prime_UTR_variant,,ENST00000292644,;PSMC2,3_prime_UTR_variant,,ENST00000435765,;PSMC2,3_prime_UTR_variant,,ENST00000544811,;SLC26A5,intron_variant,,ENST00000339444,;SLC26A5,intron_variant,,ENST00000356767,;SLC26A5,intron_variant,,ENST00000393735,;	G	ENSG00000161057	ENST00000435765	Transcript	3_prime_UTR_variant	1811	.	.	.	.	.	.	.	1	PSMC2	HGNC	9548	protein_coding	YES	CCDS5731.1	ENSP00000391211	PRS7_HUMAN	Q75L23_HUMAN,C9JLS9_HUMAN,B7Z5E2_HUMAN	UPI000013237A	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATTGTATG	.	5	ESCA
DPP6	0	.	GRCh37	7	154679398	154679398	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2258C>T	p.Ser753Phe	p.S753F	ENST00000377770	23/26	32	21	11	22	22	0	DPP6,missense_variant,p.Ser646Phe,ENST00000427557,;DPP6,missense_variant,p.Ser753Phe,ENST00000377770,;DPP6,missense_variant,p.Ser691Phe,ENST00000332007,;DPP6,missense_variant,p.Ser689Phe,ENST00000404039,;DPP6,non_coding_transcript_exon_variant,,ENST00000480367,;	T	ENSG00000130226	ENST00000377770	Transcript	missense_variant	2399	2258	753	S/F	tCc/tTc	.	.	.	1	DPP6	HGNC	3010	protein_coding	YES	.	ENSP00000367001	DPP6_HUMAN	Q75MI8_HUMAN,Q75MI7_HUMAN,Q75MF0_HUMAN	UPI00001AE746	.	deleterious(0)	probably_damaging(0.999)	23/26	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00326,hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTCCGAGA	.	5	ESCA
MTURN	0	.	GRCh37	7	30197516	30197516	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*352A>C	.	.	ENST00000324453	3/3	61	39	22	38	38	0	MTURN,3_prime_UTR_variant,,ENST00000324453,;MTURN,3_prime_UTR_variant,,ENST00000324489,;MTURN,3_prime_UTR_variant,,ENST00000409688,;MTURN,intron_variant,,ENST00000455738,;MTURN,intron_variant,,ENST00000415604,;AC007036.5,intron_variant,,ENST00000511893,;	C	ENSG00000180354	ENST00000324453	Transcript	3_prime_UTR_variant	1075	.	.	.	.	.	.	.	1	MTURN	HGNC	25457	protein_coding	YES	CCDS5425.2	ENSP00000324204	CG041_HUMAN	B4DH90_HUMAN	UPI0000073903	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATAGGTTT	.	5	ESCA
URGCP	0	.	GRCh37	7	43918191	43918191	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.871G>A	p.Asp291Asn	p.D291N	ENST00000453200	6/6	36	27	9	28	28	0	URGCP,missense_variant,p.Asp248Asn,ENST00000447717,;URGCP,missense_variant,p.Asp291Asn,ENST00000453200,;URGCP,missense_variant,p.Asp248Asn,ENST00000336086,;URGCP,missense_variant,p.Asp248Asn,ENST00000443736,;URGCP,missense_variant,p.Asp248Asn,ENST00000223341,;URGCP,missense_variant,p.Asp282Asn,ENST00000402306,;URGCP-MRPS24,intron_variant,,ENST00000603700,;URGCP,downstream_gene_variant,,ENST00000455877,;URGCP,downstream_gene_variant,,ENST00000426198,;URGCP,downstream_gene_variant,,ENST00000446958,;URGCP,non_coding_transcript_exon_variant,,ENST00000497914,;URGCP,downstream_gene_variant,,ENST00000467410,;URGCP,downstream_gene_variant,,ENST00000439702,;URGCP,downstream_gene_variant,,ENST00000474376,;	T	ENSG00000106608	ENST00000453200	Transcript	missense_variant	1365	871	291	D/N	Gac/Aac	.	.	.	-1	URGCP	HGNC	30890	protein_coding	YES	CCDS47578.1	ENSP00000396918	URGCP_HUMAN	C9JKA8_HUMAN,C9J0W2_HUMAN	UPI000020EE9D	.	tolerated(0.19)	possibly_damaging(0.801)	6/6	.	hmmpanther:PTHR22796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGTCCCACT	.	5	ESCA
PKD1L1	0	.	GRCh37	7	47849073	47849073	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7684G>C	p.Glu2562Gln	p.E2562Q	ENST00000289672	51/57	128	122	6	81	81	0	PKD1L1,missense_variant,p.Glu153Gln,ENST00000433506,;PKD1L1,missense_variant,p.Glu2562Gln,ENST00000289672,;C7orf69,intron_variant,,ENST00000418326,;C7orf69,intron_variant,,ENST00000258776,;PKD1L1,non_coding_transcript_exon_variant,,ENST00000462350,;PKD1L1,non_coding_transcript_exon_variant,,ENST00000483616,;HUS1,intron_variant,,ENST00000436444,;	G	ENSG00000158683	ENST00000289672	Transcript	missense_variant	7735	7684	2562	E/Q	Gag/Cag	.	.	.	-1	PKD1L1	HGNC	18053	protein_coding	YES	CCDS34633.1	ENSP00000289672	PK1L1_HUMAN	.	UPI0000130FA9	.	deleterious(0)	probably_damaging(0.999)	51/57	.	Transmembrane_helices:TMhelix,Pfam_domain:PF08016,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCTCCAGCC	.	2	ESCA
VSTM2A	0	.	GRCh37	7	54617761	54617761	+	Missense_Mutation	SNP	G	G	A	rs202226834	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.532G>A	p.Ala178Thr	p.A178T	ENST00000407838	4/5	42	28	13	28	28	0	VSTM2A,missense_variant,p.Ala177Thr,ENST00000402026,;VSTM2A,missense_variant,p.Ala178Thr,ENST00000302287,;VSTM2A,missense_variant,p.Ala178Thr,ENST00000402613,;VSTM2A,missense_variant,p.Ala178Thr,ENST00000404951,;VSTM2A,missense_variant,p.Ala178Thr,ENST00000407838,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000466888,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000498834,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000469952,;VSTM2A,downstream_gene_variant,,ENST00000495904,;	A	ENSG00000170419	ENST00000407838	Transcript	missense_variant	938	532	178	A/T	Gca/Aca	rs202226834	.	.	1	VSTM2A	HGNC	28499	protein_coding	YES	CCDS5512.2	ENSP00000384967	VTM2A_HUMAN	.	UPI0000EE7EC1	.	tolerated(0.18)	benign(0.098)	4/5	.	hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF19	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCCGCAGCC	byFrequency|byCluster	5	ESCA
RSBN1L	0	.	GRCh37	7	77325780	77325780	+	5'UTR	SNP	G	G	T	rs747379549	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-7G>T	.	.	ENST00000334955	1/8	31	25	6	20	20	0	RSBN1L,5_prime_UTR_variant,,ENST00000334955,;RSBN1L,upstream_gene_variant,,ENST00000445288,;RSBN1L-AS1,upstream_gene_variant,,ENST00000440088,;RSBN1L-AS1,upstream_gene_variant,,ENST00000398043,;RSBN1L-AS1,upstream_gene_variant,,ENST00000416650,;RSBN1L-AS1,upstream_gene_variant,,ENST00000447009,;RSBN1L-AS1,upstream_gene_variant,,ENST00000430801,;	T	ENSG00000187257	ENST00000334955	Transcript	5_prime_UTR_variant	21	.	.	.	.	rs747379549	.	.	1	RSBN1L	HGNC	24765	protein_coding	YES	CCDS43607.1	ENSP00000334040	RSBNL_HUMAN	C9JM20_HUMAN	UPI000020F469	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGAGCGCAA	byFrequency	4	ESCA
ICA1	0	.	GRCh37	7	8260925	8260925	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.360C>G	p.%3D	p.L120L	ENST00000402384	5/14	45	25	20	59	59	0	ICA1,synonymous_variant,p.%3D,ENST00000447326,;ICA1,synonymous_variant,p.%3D,ENST00000317367,;ICA1,synonymous_variant,p.%3D,ENST00000430867,;ICA1,synonymous_variant,p.%3D,ENST00000422063,;ICA1,synonymous_variant,p.%3D,ENST00000396675,;ICA1,synonymous_variant,p.%3D,ENST00000407906,;ICA1,synonymous_variant,p.%3D,ENST00000265577,;ICA1,synonymous_variant,p.%3D,ENST00000406470,;ICA1,synonymous_variant,p.%3D,ENST00000402384,;ICA1,synonymous_variant,p.%3D,ENST00000401396,;ICA1,intron_variant,,ENST00000486677,;ICA1,upstream_gene_variant,,ENST00000476942,;ICA1,synonymous_variant,p.%3D,ENST00000339809,;ICA1,3_prime_UTR_variant,,ENST00000455539,;ICA1,downstream_gene_variant,,ENST00000457755,;ICA1,upstream_gene_variant,,ENST00000490041,;	C	ENSG00000003147	ENST00000402384	Transcript	synonymous_variant	627	360	120	L	ctC/ctG	.	.	.	-1	ICA1	HGNC	5343	protein_coding	YES	CCDS34602.1	ENSP00000385570	ICA69_HUMAN	Q9UDQ6_HUMAN,F8WET5_HUMAN,C9J3Y4_HUMAN	UPI000012D139	.	.	.	5/14	.	PROSITE_profiles:PS50870,hmmpanther:PTHR10164:SF3,hmmpanther:PTHR10164,Pfam_domain:PF06456,Gene3D:1.20.1270.60,SMART_domains:SM01015,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCAGAGGGC	.	5	ESCA
PON1	0	.	GRCh37	7	94953830	94953830	+	5'UTR	SNP	G	G	A	rs750262961	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-43C>T	.	.	ENST00000222381	1/9	38	27	11	33	33	0	PON1,5_prime_UTR_variant,,ENST00000222381,;PON1,intron_variant,,ENST00000542556,;PON1,upstream_gene_variant,,ENST00000433729,;	A	ENSG00000005421	ENST00000222381	Transcript	5_prime_UTR_variant	190	.	.	.	.	rs750262961	.	.	-1	PON1	HGNC	9204	protein_coding	YES	CCDS5638.1	ENSP00000222381	PON1_HUMAN	.	UPI000013C7FD	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGACGGGCTA	byFrequency	5	ESCA
SOX7	0	.	GRCh37	8	10584082	10584082	+	Silent	SNP	G	G	A	rs760872046	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.489C>T	p.%3D	p.N163N	ENST00000554914	6/6	28	19	9	32	32	0	SOX7,synonymous_variant,p.%3D,ENST00000554914,;SOX7,synonymous_variant,p.%3D,ENST00000553390,;SOX7,synonymous_variant,p.%3D,ENST00000304501,;CTD-2135J3.3,upstream_gene_variant,,ENST00000506149,;CTD-2135J3.3,upstream_gene_variant,,ENST00000519568,;	A	ENSG00000258724	ENST00000554914	Transcript	synonymous_variant	580	489	163	N	aaC/aaT	rs760872046	.	.	-1	SOX7	Uniprot_gn	18196	protein_coding	YES	.	ENSP00000451145	.	B4DKV0_HUMAN	UPI00017A7531	.	.	.	6/6	.	PROSITE_profiles:PS50118,hmmpanther:PTHR10270:SF210,hmmpanther:PTHR10270,Pfam_domain:PF00505,Gene3D:1.10.30.10,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTAGTTGGG	.	5	ESCA
ANGPT1	0	.	GRCh37	8	108296965	108296965	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150C>T	p.Arg384Ter	p.R384*	ENST00000517746	7/9	117	87	30	69	69	0	ANGPT1,stop_gained,p.Arg184Ter,ENST00000520734,;ANGPT1,stop_gained,p.Arg384Ter,ENST00000517746,;ANGPT1,stop_gained,p.Arg183Ter,ENST00000520052,;ANGPT1,stop_gained,p.Arg383Ter,ENST00000297450,;ANGPT1,intron_variant,,ENST00000518386,;ANGPT1,non_coding_transcript_exon_variant,,ENST00000522400,;ANGPT1,non_coding_transcript_exon_variant,,ENST00000521950,;	A	ENSG00000154188	ENST00000517746	Transcript	stop_gained	1602	1150	384	R/*	Cga/Tga	.	.	.	-1	ANGPT1	HGNC	484	protein_coding	YES	CCDS6306.1	ENSP00000428340	ANGP1_HUMAN	E5RFF4_HUMAN,B4E3G9_HUMAN,B4DTQ9_HUMAN	UPI0000034766	.	.	.	7/9	.	PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF156,Pfam_domain:PF00147,Gene3D:3.90.215.10,SMART_domains:SM00186,Superfamily_domains:SSF56496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCGGTTCC	.	5	ESCA
CSMD3	0	.	GRCh37	8	113316973	113316973	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8243G>C	p.Arg2748Thr	p.R2748T	ENST00000297405	52/71	94	90	4	56	56	0	CSMD3,missense_variant,p.Arg2678Thr,ENST00000352409,;CSMD3,missense_variant,p.Arg2748Thr,ENST00000297405,;CSMD3,missense_variant,p.Arg2018Thr,ENST00000339701,;CSMD3,missense_variant,p.Arg2708Thr,ENST00000343508,;CSMD3,intron_variant,,ENST00000455883,;	G	ENSG00000164796	ENST00000297405	Transcript	missense_variant	8488	8243	2748	R/T	aGa/aCa	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	tolerated(0.43)	possibly_damaging(0.777)	52/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTCTCCAA	.	2	ESCA
DOCK5	0	.	GRCh37	8	25154103	25154103	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.545C>G	p.Ala182Gly	p.A182G	ENST00000276440	7/52	28	24	3	26	26	0	DOCK5,missense_variant,p.Ala182Gly,ENST00000276440,;DOCK5,missense_variant,p.Ala182Gly,ENST00000481100,;DOCK5,upstream_gene_variant,,ENST00000444569,;DOCK5,non_coding_transcript_exon_variant,,ENST00000495236,;	G	ENSG00000147459	ENST00000276440	Transcript	missense_variant	589	545	182	A/G	gCc/gGc	.	.	.	1	DOCK5	HGNC	23476	protein_coding	YES	CCDS6047.1	ENSP00000276440	DOCK5_HUMAN	.	UPI000022D4F3	.	deleterious(0.01)	benign(0.103)	7/52	.	hmmpanther:PTHR23317:SF68,hmmpanther:PTHR23317	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CATTGCCCTCT	.	2	ESCA
ADAM18	0	.	GRCh37	8	39463837	39463837	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.144C>T	p.%3D	p.I48I	ENST00000265707	3/20	55	41	14	46	46	0	ADAM18,synonymous_variant,p.%3D,ENST00000520772,;ADAM18,synonymous_variant,p.%3D,ENST00000265707,;ADAM18,synonymous_variant,p.%3D,ENST00000379866,;ADAM18,5_prime_UTR_variant,,ENST00000541111,;ADAM18,non_coding_transcript_exon_variant,,ENST00000520559,;ADAM18,missense_variant,p.His60Tyr,ENST00000520001,;ADAM18,synonymous_variant,p.%3D,ENST00000520087,;	T	ENSG00000168619	ENST00000265707	Transcript	synonymous_variant	189	144	48	I	atC/atT	.	.	.	1	ADAM18	HGNC	196	protein_coding	YES	CCDS6113.1	ENSP00000265707	ADA18_HUMAN	Q0VAI3_HUMAN,E5RK96_HUMAN	UPI00001254D7	.	.	.	3/20	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF28,Pfam_domain:PF01562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACATCATTAC	.	5	ESCA
THAP1	0	.	GRCh37	8	42692592	42692592	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*513A>C	.	.	ENST00000254250	3/3	49	45	4	22	22	0	THAP1,3_prime_UTR_variant,,ENST00000345117,;THAP1,3_prime_UTR_variant,,ENST00000254250,;THAP1,downstream_gene_variant,,ENST00000529779,;THAP1,downstream_gene_variant,,ENST00000532093,;	G	ENSG00000131931	ENST00000254250	Transcript	3_prime_UTR_variant	1386	.	.	.	.	.	.	.	-1	THAP1	HGNC	20856	protein_coding	YES	CCDS6136.1	ENSP00000254250	THAP1_HUMAN	.	UPI000007035E	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ATAACTGATTC	.	2	ESCA
NBN	0	.	GRCh37	8	90990460	90990460	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572C>A	p.Pro191Gln	p.P191Q	ENST00000265433	5/16	66	50	16	51	51	0	NBN,missense_variant,p.Pro109Gln,ENST00000517772,;NBN,missense_variant,p.Pro191Gln,ENST00000265433,;NBN,missense_variant,p.Pro109Gln,ENST00000409330,;NBN,intron_variant,,ENST00000519426,;NBN,downstream_gene_variant,,ENST00000517337,;NBN,3_prime_UTR_variant,,ENST00000396252,;NBN,downstream_gene_variant,,ENST00000523444,;NBN,downstream_gene_variant,,ENST00000494804,;	T	ENSG00000104320	ENST00000265433	Transcript	missense_variant	727	572	191	P/Q	cCa/cAa	.	.	.	-1	NBN	HGNC	7652	protein_coding	YES	CCDS6249.1	ENSP00000265433	NBN_HUMAN	E5RGR7_HUMAN,E5RGN7_HUMAN	UPI0000073BF4	.	deleterious(0)	probably_damaging(0.99)	5/16	.	hmmpanther:PTHR12162,PIRSF_domain:PIRSF011869	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TTTGTGGAGGC	.	3	ESCA
MATN2	0	.	GRCh37	8	99019414	99019414	+	Missense_Mutation	SNP	C	C	T	rs773931953	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1409C>T	p.Ser470Leu	p.S470L	ENST00000520016	8/18	45	36	9	16	16	0	MATN2,missense_variant,p.Ser174Leu,ENST00000522270,;MATN2,missense_variant,p.Ser253Leu,ENST00000518154,;MATN2,missense_variant,p.Ser470Leu,ENST00000521689,;MATN2,missense_variant,p.Ser470Leu,ENST00000254898,;MATN2,missense_variant,p.Ser470Leu,ENST00000520016,;MATN2,missense_variant,p.Ser429Leu,ENST00000524308,;MATN2,missense_variant,p.Ser186Leu,ENST00000522025,;MATN2,downstream_gene_variant,,ENST00000521041,;MATN2,upstream_gene_variant,,ENST00000521952,;MATN2,downstream_gene_variant,,ENST00000523490,;	T	ENSG00000132561	ENST00000520016	Transcript	missense_variant	1533	1409	470	S/L	tCa/tTa	rs773931953	.	.	1	MATN2	HGNC	6908	protein_coding	YES	CCDS55264.1	ENSP00000430487	MATN2_HUMAN	E5RJM4_HUMAN	UPI000021037B	.	tolerated(0.63)	benign(0.049)	8/18	.	hmmpanther:PTHR22992:SF17,hmmpanther:PTHR22992,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTCAGAAG	.	5	ESCA
ADAMTS13	0	.	GRCh37	9	136321339	136321339	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3715+2T>C	.	p.X1239_splice	ENST00000371929	.	32	29	3	31	31	0	ADAMTS13,splice_donor_variant,,ENST00000356589,;ADAMTS13,splice_donor_variant,,ENST00000371929,;ADAMTS13,splice_donor_variant,,ENST00000371910,;ADAMTS13,splice_donor_variant,,ENST00000371916,;ADAMTS13,splice_donor_variant,,ENST00000355699,;CACFD1,upstream_gene_variant,,ENST00000540581,;CACFD1,upstream_gene_variant,,ENST00000291722,;CACFD1,upstream_gene_variant,,ENST00000542192,;CACFD1,upstream_gene_variant,,ENST00000316948,;ADAMTS13,splice_donor_variant,,ENST00000485925,;CACFD1,upstream_gene_variant,,ENST00000474734,;CACFD1,upstream_gene_variant,,ENST00000489519,;	C	ENSG00000160323	ENST00000371929	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	ADAMTS13	HGNC	1366	protein_coding	YES	CCDS6970.1	ENSP00000360997	ATS13_HUMAN	Q6QNA4_HUMAN,B3KWF7_HUMAN	UPI0000000DAD	.	.	.	.	26/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGGGTATGTC	.	2	ESCA
B4GALT1	0	.	GRCh37	9	33112930	33112930	+	3'UTR	SNP	T	T	C	rs532823850	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*522A>G	.	.	ENST00000379731	6/6	106	67	39	72	72	0	B4GALT1,3_prime_UTR_variant,,ENST00000379731,;B4GALT1,intron_variant,,ENST00000535206,;B4GALT1,downstream_gene_variant,,ENST00000541851,;	C	ENSG00000086062	ENST00000379731	Transcript	3_prime_UTR_variant	1906	.	.	.	.	rs532823850	.	.	-1	B4GALT1	HGNC	924	protein_coding	YES	CCDS6535.1	ENSP00000369055	B4GT1_HUMAN	B7ZAH9_HUMAN,B4DMM8_HUMAN	UPI000002D22E	.	.	.	6/6	.	.	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGATTGCAG	by1000G	5	ESCA
DCAF12L1	0	.	GRCh37	X	125685869	125685869	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723A>G	p.%3D	p.V241V	ENST00000371126	1/2	53	22	30	31	31	0	DCAF12L1,synonymous_variant,p.%3D,ENST00000371126,;	C	ENSG00000198889	ENST00000371126	Transcript	synonymous_variant	966	723	241	V	gtA/gtG	.	.	.	-1	DCAF12L1	HGNC	29395	protein_coding	YES	CCDS14610.1	ENSP00000360167	DC121_HUMAN	.	UPI0000160112	.	.	.	1/2	.	hmmpanther:PTHR19860:SF9,hmmpanther:PTHR19860,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATATACGGG	.	5	ESCA
CNKSR2	0	.	GRCh37	X	21670529	21670529	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2995G>C	p.Asp999His	p.D999H	ENST00000379510	22/22	44	19	25	40	40	0	CNKSR2,missense_variant,p.Asp999His,ENST00000379510,;CNKSR2,missense_variant,p.Asp969His,ENST00000425654,;KLHL34,downstream_gene_variant,,ENST00000379499,;	C	ENSG00000149970	ENST00000379510	Transcript	missense_variant	3031	2995	999	D/H	Gat/Cat	.	.	.	1	CNKSR2	HGNC	19701	protein_coding	YES	CCDS14198.1	ENSP00000368824	CNKR2_HUMAN	.	UPI0000070D72	.	deleterious(0)	possibly_damaging(0.718)	22/22	.	hmmpanther:PTHR12844,hmmpanther:PTHR12844:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTGGATATC	.	5	ESCA
CCDC22	0	.	GRCh37	X	49098512	49098512	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259C>G	p.Gln87Glu	p.Q87E	ENST00000376227	3/17	31	14	17	15	15	0	CCDC22,missense_variant,p.Gln87Glu,ENST00000376227,;CCDC22,non_coding_transcript_exon_variant,,ENST00000490300,;CCDC22,intron_variant,,ENST00000496651,;	G	ENSG00000101997	ENST00000376227	Transcript	missense_variant	429	259	87	Q/E	Cag/Gag	.	.	.	1	CCDC22	HGNC	28909	protein_coding	YES	CCDS14322.1	ENSP00000365401	CCD22_HUMAN	.	UPI000006FFC7	.	deleterious(0.01)	possibly_damaging(0.641)	3/17	.	hmmpanther:PTHR15668,Pfam_domain:PF05667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTATCAGAAC	.	5	ESCA
USP27X	0	.	GRCh37	X	49643121	49643121	+	5'Flank	SNP	A	A	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000508866	.	47	17	29	30	30	0	USP27X,upstream_gene_variant,,ENST00000508866,;USP27X-AS1,non_coding_transcript_exon_variant,,ENST00000437322,;	G	ENSG00000242013	ENST00000508866	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1349	1	USP27X	HGNC	13486	protein_coding	YES	CCDS65260.1	ENSP00000475071	UBP27_HUMAN	.	UPI0000EE7A8D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTCAGCGTC	.	5	ESCA
TSPYL2	0	.	GRCh37	X	53114916	53114916	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EP-01A-31D-A403-09	TCGA-VR-A8EP-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1342C>G	p.His448Asp	p.H448D	ENST00000375442	6/7	28	11	17	15	15	0	TSPYL2,missense_variant,p.His448Asp,ENST00000375442,;TSPYL2,missense_variant,p.His123Asp,ENST00000579390,;TSPYL2,3_prime_UTR_variant,,ENST00000578306,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000553557,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000463525,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000556808,;	G	ENSG00000184205	ENST00000375442	Transcript	missense_variant	1474	1342	448	H/D	Cat/Gat	.	.	.	1	TSPYL2	HGNC	24358	protein_coding	YES	CCDS14350.1	ENSP00000364591	TSYL2_HUMAN	.	UPI000004B6D6	.	deleterious_low_confidence(0.01)	benign(0.4)	6/7	.	hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATTCATGAC	.	5	ESCA
WDFY4	0	.	GRCh37	10	49996594	49996594	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3828A>T	p.Glu1276Asp	p.E1276D	ENST00000325239	20/61	79	58	20	85	85	0	WDFY4,missense_variant,p.Glu1276Asp,ENST00000325239,;WDFY4,intron_variant,,ENST00000413659,;	T	ENSG00000128815	ENST00000325239	Transcript	missense_variant	3855	3828	1276	E/D	gaA/gaT	.	.	.	1	WDFY4	HGNC	29323	protein_coding	YES	CCDS44385.1	ENSP00000320563	WDFY4_HUMAN	Q6PIM1_HUMAN	UPI000176ADB8	.	tolerated(0.15)	benign(0.008)	20/61	.	hmmpanther:PTHR13743:SF52,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGAAGCCAC	.	5	ESCA
ABTB2	0	.	GRCh37	11	34186322	34186322	+	Silent	SNP	G	G	A	rs770117269	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1899C>T	p.%3D	p.P633P	ENST00000435224	9/17	58	21	37	36	36	0	ABTB2,synonymous_variant,p.%3D,ENST00000435224,;ABTB2,synonymous_variant,p.%3D,ENST00000298992,;	A	ENSG00000166016	ENST00000435224	Transcript	synonymous_variant	2324	1899	633	P	ccC/ccT	rs770117269	.	.	-1	ABTB2	HGNC	23842	protein_coding	YES	CCDS7890.2	ENSP00000410157	ABTB2_HUMAN	.	UPI0001DD21BB	.	.	.	9/17	.	Pfam_domain:PF00023,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGGGGGTC	byFrequency	5	ESCA
OR4C6	0	.	GRCh37	11	55432949	55432949	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.307C>G	p.His103Asp	p.H103D	ENST00000314259	1/1	15	9	6	22	22	0	OR4C6,missense_variant,p.His103Asp,ENST00000314259,;	G	ENSG00000181903	ENST00000314259	Transcript	missense_variant	336	307	103	H/D	Cat/Gat	COSM363216	.	.	1	OR4C6	HGNC	14743	protein_coding	YES	CCDS31506.1	ENSP00000324769	OR4C6_HUMAN	.	UPI0000041868	.	deleterious_low_confidence(0)	probably_damaging(0.928)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF80,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGCATTTC	.	5	ESCA
SLC22A24	0	.	GRCh37	11	62886317	62886317	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.830+67G>A	.	.	ENST00000417740	.	38	16	22	58	58	0	SLC22A24,synonymous_variant,p.%3D,ENST00000326192,;SLC22A24,intron_variant,,ENST00000417740,;RPL29P22,upstream_gene_variant,,ENST00000498718,;	T	ENSG00000197658	ENST00000417740	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SLC22A24	HGNC	28542	protein_coding	YES	.	ENSP00000396586	.	C9JC66_HUMAN	UPI00016625C6	.	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGTCAGAAT	.	5	ESCA
ZNF140	0	.	GRCh37	12	133682650	133682650	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787C>T	p.His263Tyr	p.H263Y	ENST00000355557	5/5	35	27	8	31	31	0	ZNF140,missense_variant,p.His160Tyr,ENST00000544426,;ZNF140,missense_variant,p.His263Tyr,ENST00000355557,;ZNF140,3_prime_UTR_variant,,ENST00000440550,;ZNF140,downstream_gene_variant,,ENST00000429434,;ZNF140,downstream_gene_variant,,ENST00000356456,;ZNF140,downstream_gene_variant,,ENST00000412146,;ZNF140,downstream_gene_variant,,ENST00000319849,;ZNF140,3_prime_UTR_variant,,ENST00000536790,;ZNF140,downstream_gene_variant,,ENST00000392041,;	T	ENSG00000196387	ENST00000355557	Transcript	missense_variant	2070	787	263	H/Y	Cat/Tat	.	.	.	1	ZNF140	HGNC	12925	protein_coding	YES	CCDS9282.1	ENSP00000347755	ZN140_HUMAN	Q05CP6_HUMAN,I3L0D9_HUMAN,F5H4I1_HUMAN,B4DKI0_HUMAN	UPI0000074687	.	deleterious(0)	probably_damaging(0.997)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF36,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGACATCAA	.	5	ESCA
FKBP4	0	.	GRCh37	12	2912662	2912662	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*238T>A	.	.	ENST00000001008	10/10	38	27	11	37	37	0	FKBP4,3_prime_UTR_variant,,ENST00000001008,;FKBP4,intron_variant,,ENST00000544366,;FKBP4,downstream_gene_variant,,ENST00000539181,;RP4-816N1.6,intron_variant,,ENST00000547834,;RP4-816N1.7,intron_variant,,ENST00000547042,;RP4-816N1.6,downstream_gene_variant,,ENST00000552469,;RP4-816N1.6,downstream_gene_variant,,ENST00000547794,;FKBP4,downstream_gene_variant,,ENST00000543037,;	A	ENSG00000004478	ENST00000001008	Transcript	3_prime_UTR_variant	1805	.	.	.	.	.	.	.	1	FKBP4	HGNC	3720	protein_coding	YES	CCDS8512.1	ENSP00000001008	FKBP4_HUMAN	F5H1U3_HUMAN	UPI000013C4D0	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCATCCATA	.	5	ESCA
C12orf40	0	.	GRCh37	12	40077922	40077922	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1286+636G>T	.	.	ENST00000324616	.	30	22	8	41	41	0	C12orf40,splice_acceptor_variant,,ENST00000398716,;C12orf40,intron_variant,,ENST00000405531,;C12orf40,intron_variant,,ENST00000324616,;C12orf40,splice_acceptor_variant,,ENST00000468200,;	T	ENSG00000180116	ENST00000324616	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C12orf40	HGNC	26846	protein_coding	YES	CCDS41770.1	ENSP00000317671	CL040_HUMAN	.	UPI000069A925	.	.	.	.	9/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAGCTGGT	.	5	ESCA
KCNA1	0	.	GRCh37	12	5026110	5026110	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4078C>G	.	.	ENST00000382545	2/2	23	16	7	36	36	0	KCNA1,3_prime_UTR_variant,,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	G	ENSG00000111262	ENST00000382545	Transcript	3_prime_UTR_variant	6673	.	.	.	.	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACCTCAAA	.	5	ESCA
ESPL1	0	.	GRCh37	12	53663130	53663130	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404C>A	p.Ala135Asp	p.A135D	ENST00000257934	3/31	15	9	6	12	12	0	ESPL1,missense_variant,p.Ala135Asp,ENST00000257934,;ESPL1,missense_variant,p.Ala135Asp,ENST00000552462,;ESPL1,missense_variant,p.Ala135Asp,ENST00000553219,;ESPL1,upstream_gene_variant,,ENST00000550026,;ESPL1,3_prime_UTR_variant,,ENST00000552671,;	A	ENSG00000135476	ENST00000257934	Transcript	missense_variant	495	404	135	A/D	gCt/gAt	.	.	.	1	ESPL1	HGNC	16856	protein_coding	YES	CCDS8852.1	ENSP00000257934	ESPL1_HUMAN	H3BRX7_HUMAN	UPI00003668C3	.	tolerated(0.5)	benign(0.157)	3/31	.	hmmpanther:PTHR12792	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGGCTGCTC	.	5	ESCA
HOXC6	0	.	GRCh37	12	54424465	54424469	+	3'UTR	DEL	AAAAA	AAAAA	-	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	AAAAA	AAAAA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*721_*725delAAAAA	.	.	ENST00000243108	2/2	28	20	8	22	22	0	HOXC6,3_prime_UTR_variant,,ENST00000243108,;HOXC6,3_prime_UTR_variant,,ENST00000394331,;HOXC4,intron_variant,,ENST00000303406,;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC5,upstream_gene_variant,,ENST00000312492,;HOXC6,downstream_gene_variant,,ENST00000509328,;HOXC6,downstream_gene_variant,,ENST00000504315,;MIR615,upstream_gene_variant,,ENST00000384839,;RP11-834C11.14,intron_variant,,ENST00000512206,;	-	ENSG00000197757	ENST00000243108	Transcript	3_prime_UTR_variant	1591-1595	.	.	.	.	.	.	.	1	HOXC6	HGNC	5128	protein_coding	YES	CCDS8871.1	ENSP00000243108	HXC6_HUMAN	D6RBH4_HUMAN	UPI0000020BA4	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGAGAGAAAAAAAGTG	.	2	ESCA
CBX5	0	.	GRCh37	12	54635356	54635356	+	3'UTR	SNP	T	T	A	rs773118070	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*183A>T	.	.	ENST00000209875	5/5	49	33	16	32	32	0	CBX5,3_prime_UTR_variant,,ENST00000209875,;CBX5,3_prime_UTR_variant,,ENST00000439541,;CBX5,downstream_gene_variant,,ENST00000550411,;CBX5,downstream_gene_variant,,ENST00000547872,;	A	ENSG00000094916	ENST00000209875	Transcript	3_prime_UTR_variant	896	.	.	.	.	rs773118070	.	.	-1	CBX5	HGNC	1555	protein_coding	YES	CCDS8875.1	ENSP00000209875	CBX5_HUMAN	F8VNY3_HUMAN	UPI00001271FC	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTATCATTA	.	5	ESCA
DHRS12	0	.	GRCh37	13	52342254	52342254	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69G>C	.	.	ENST00000444610	10/10	16	8	8	20	20	0	DHRS12,3_prime_UTR_variant,,ENST00000444610,;DHRS12,3_prime_UTR_variant,,ENST00000218981,;DHRS12,downstream_gene_variant,,ENST00000280056,;DHRS12,downstream_gene_variant,,ENST00000472372,;DHRS12,downstream_gene_variant,,ENST00000461948,;DHRS12,downstream_gene_variant,,ENST00000490949,;DHRS12,downstream_gene_variant,,ENST00000489680,;DHRS12,downstream_gene_variant,,ENST00000469957,;	G	ENSG00000102796	ENST00000444610	Transcript	3_prime_UTR_variant	1037	.	.	.	.	.	.	.	-1	DHRS12	HGNC	25832	protein_coding	YES	CCDS58292.1	ENSP00000411565	DHR12_HUMAN	.	UPI000004742D	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTCACTGGTC	.	2	ESCA
CATSPERB	0	.	GRCh37	14	92074645	92074645	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2702T>A	p.Met901Lys	p.M901K	ENST00000256343	22/27	35	17	17	74	74	0	CATSPERB,missense_variant,p.Met901Lys,ENST00000256343,;CATSPERB,3_prime_UTR_variant,,ENST00000557036,;RP11-248B24.4,upstream_gene_variant,,ENST00000594073,;NANOGP7,upstream_gene_variant,,ENST00000554450,;	T	ENSG00000133962	ENST00000256343	Transcript	missense_variant	2859	2702	901	M/K	aTg/aAg	.	.	.	-1	CATSPERB	HGNC	20500	protein_coding	YES	CCDS32142.1	ENSP00000256343	CTSRB_HUMAN	G3V584_HUMAN,G3V352_HUMAN	UPI0000418DA1	.	tolerated(1)	benign(0)	22/27	.	hmmpanther:PTHR14705,Pfam_domain:PF15149	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGACATGTGA	.	5	ESCA
RYR3	0	.	GRCh37	15	34105086	34105086	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10280G>A	p.Trp3427Ter	p.W3427*	ENST00000389232	73/104	47	30	16	77	77	0	RYR3,stop_gained,p.Trp3427Ter,ENST00000389232,;RYR3,stop_gained,p.Trp3422Ter,ENST00000415757,;	A	ENSG00000198838	ENST00000389232	Transcript	stop_gained	10350	10280	3427	W/*	tGg/tAg	.	.	.	1	RYR3	HGNC	10485	protein_coding	YES	CCDS45210.1	ENSP00000373884	RYR3_HUMAN	.	UPI0000E5B01A	.	.	.	73/104	.	hmmpanther:PTHR13715:SF16,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATGGCAAC	.	5	ESCA
UBR1	0	.	GRCh37	15	43367261	43367261	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444C>T	p.%3D	p.F148F	ENST00000290650	4/47	53	32	21	27	27	0	UBR1,synonymous_variant,p.%3D,ENST00000382177,;UBR1,synonymous_variant,p.%3D,ENST00000290650,;UBR1,3_prime_UTR_variant,,ENST00000563239,;UBR1,non_coding_transcript_exon_variant,,ENST00000546274,;	A	ENSG00000159459	ENST00000290650	Transcript	synonymous_variant	523	444	148	F	ttC/ttT	.	.	.	-1	UBR1	HGNC	16808	protein_coding	YES	CCDS10091.1	ENSP00000290650	UBR1_HUMAN	.	UPI0000074467	.	.	.	4/47	.	PROSITE_profiles:PS51157,hmmpanther:PTHR21497:SF27,hmmpanther:PTHR21497,Pfam_domain:PF02207,SMART_domains:SM00396	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACAGAACCC	.	5	ESCA
SPG11	0	.	GRCh37	15	44887495	44887495	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4597A>T	p.Ser1533Cys	p.S1533C	ENST00000261866	26/40	52	41	11	38	38	0	SPG11,missense_variant,p.Ser1533Cys,ENST00000535302,;SPG11,missense_variant,p.Ser1533Cys,ENST00000558319,;SPG11,missense_variant,p.Ser1533Cys,ENST00000261866,;SPG11,missense_variant,p.Ser1533Cys,ENST00000427534,;SPG11,downstream_gene_variant,,ENST00000558988,;SPG11,upstream_gene_variant,,ENST00000558253,;SPG11,upstream_gene_variant,,ENST00000558790,;SPG11,intron_variant,,ENST00000558155,;SPG11,downstream_gene_variant,,ENST00000558093,;SPG11,downstream_gene_variant,,ENST00000561391,;SPG11,upstream_gene_variant,,ENST00000560858,;SPG11,downstream_gene_variant,,ENST00000558561,;	A	ENSG00000104133	ENST00000261866	Transcript	missense_variant	4614	4597	1533	S/C	Agc/Tgc	.	.	.	-1	SPG11	HGNC	11226	protein_coding	YES	CCDS10112.1	ENSP00000261866	SPTCS_HUMAN	H0YN96_HUMAN,C4B7M3_HUMAN	UPI0000456840	.	tolerated(0.06)	possibly_damaging(0.823)	26/40	.	hmmpanther:PTHR13650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCTCTTTT	.	5	ESCA
DUOXA1	0	.	GRCh37	15	45410283	45410283	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.992-16A>G	.	.	ENST00000267803	.	35	23	11	49	49	0	DUOXA1,3_prime_UTR_variant,,ENST00000558996,;DUOXA2,3_prime_UTR_variant,,ENST00000323030,;DUOXA1,intron_variant,,ENST00000267803,;DUOXA1,intron_variant,,ENST00000559014,;DUOXA1,intron_variant,,ENST00000430224,;DUOXA1,downstream_gene_variant,,ENST00000558326,;DUOXA1,downstream_gene_variant,,ENST00000558851,;DUOXA1,downstream_gene_variant,,ENST00000558422,;DUOX2,upstream_gene_variant,,ENST00000389039,;DUOXA1,downstream_gene_variant,,ENST00000558377,;DUOXA1,downstream_gene_variant,,ENST00000559644,;DUOXA1,downstream_gene_variant,,ENST00000560572,;DUOXA1,downstream_gene_variant,,ENST00000559226,;DUOX2,upstream_gene_variant,,ENST00000603300,;DUOXA1,downstream_gene_variant,,ENST00000559988,;DUOXA2,3_prime_UTR_variant,,ENST00000491993,;DUOX2,upstream_gene_variant,,ENST00000558383,;DUOXA2,downstream_gene_variant,,ENST00000350243,;DUOXA1,downstream_gene_variant,,ENST00000559013,;	C	ENSG00000140254	ENST00000267803	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	DUOXA1	HGNC	26507	protein_coding	YES	CCDS10119.1	ENSP00000267803	DOXA1_HUMAN	H0YMZ8_HUMAN,H0YLQ4_HUMAN,A8K9Q6_HUMAN	UPI000006D4D4	.	.	.	.	9/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTTTTTTC	.	5	ESCA
LEO1	0	.	GRCh37	15	52244058	52244058	+	Missense_Mutation	SNP	G	G	A	rs754922458	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1594C>T	p.Arg532Cys	p.R532C	ENST00000299601	9/12	44	28	15	48	48	0	LEO1,missense_variant,p.Arg472Cys,ENST00000315141,;LEO1,missense_variant,p.Arg532Cys,ENST00000299601,;TMOD3,downstream_gene_variant,,ENST00000561408,;TMOD3,downstream_gene_variant,,ENST00000559202,;MAPK6,upstream_gene_variant,,ENST00000560802,;TMOD3,downstream_gene_variant,,ENST00000558300,;TMOD3,downstream_gene_variant,,ENST00000558714,;LEO1,downstream_gene_variant,,ENST00000558949,;	A	ENSG00000166477	ENST00000299601	Transcript	missense_variant	1655	1594	532	R/C	Cgc/Tgc	rs754922458	.	.	-1	LEO1	HGNC	30401	protein_coding	YES	CCDS10146.1	ENSP00000299601	LEO1_HUMAN	.	UPI0000071CA0	.	deleterious(0.01)	benign(0.432)	9/12	.	hmmpanther:PTHR23146:SF0,hmmpanther:PTHR23146,Pfam_domain:PF04004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R532H|c.1595G>A|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGCGTTGGC	.	5	ESCA
THSD4	0	.	GRCh37	15	72050278	72050278	+	Missense_Mutation	SNP	C	C	T	rs766502435	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2453C>T	p.Ser818Leu	p.S818L	ENST00000355327	15/18	25	16	9	22	22	0	THSD4,missense_variant,p.Ser818Leu,ENST00000355327,;THSD4,missense_variant,p.Ser458Leu,ENST00000357769,;THSD4,missense_variant,p.Ser818Leu,ENST00000261862,;THSD4,non_coding_transcript_exon_variant,,ENST00000567838,;	T	ENSG00000187720	ENST00000355327	Transcript	missense_variant	2587	2453	818	S/L	tCg/tTg	rs766502435	.	.	1	THSD4	HGNC	25835	protein_coding	YES	CCDS10238.2	ENSP00000347484	THSD4_HUMAN	.	UPI00001A797D	.	deleterious(0)	benign(0.114)	15/18	.	PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF16,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCTCGGTGG	.	5	ESCA
IQGAP1	0	.	GRCh37	15	90931587	90931587	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14A>G	p.Asp5Gly	p.D5G	ENST00000268182	1/38	21	14	7	13	13	0	IQGAP1,missense_variant,p.Asp5Gly,ENST00000560738,;IQGAP1,missense_variant,p.Asp5Gly,ENST00000268182,;IQGAP1,5_prime_UTR_variant,,ENST00000560418,;IQGAP1,non_coding_transcript_exon_variant,,ENST00000559809,;NDUFA3P4,downstream_gene_variant,,ENST00000560814,;	G	ENSG00000140575	ENST00000268182	Transcript	missense_variant	138	14	5	D/G	gAc/gGc	.	.	.	1	IQGAP1	HGNC	6110	protein_coding	YES	CCDS10362.1	ENSP00000268182	IQGA1_HUMAN	H0YKA5_HUMAN	UPI000012D863	.	deleterious_low_confidence(0.03)	benign(0.003)	1/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCAGACGAGG	.	5	ESCA
ACSM5	0	.	GRCh37	16	20439186	20439186	+	Missense_Mutation	SNP	C	C	A	rs763570628	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.998C>A	p.Thr333Asn	p.T333N	ENST00000331849	7/14	30	22	7	26	26	0	ACSM5,missense_variant,p.Thr333Asn,ENST00000331849,;ACSM5,non_coding_transcript_exon_variant,,ENST00000570305,;ACSM5,non_coding_transcript_exon_variant,,ENST00000574748,;ACSM5,intron_variant,,ENST00000573920,;ACSM5,upstream_gene_variant,,ENST00000577024,;	A	ENSG00000183549	ENST00000331849	Transcript	missense_variant	1145	998	333	T/N	aCc/aAc	rs763570628	.	.	1	ACSM5	HGNC	26060	protein_coding	YES	CCDS10585.1	ENSP00000327916	ACSM5_HUMAN	.	UPI00001FEFB3	.	deleterious(0.04)	benign(0.128)	7/14	.	Superfamily_domains:SSF56801,Pfam_domain:PF00501,Gene3D:3.40.50.980,hmmpanther:PTHR24095:SF105,hmmpanther:PTHR24095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGACCAGGT	byFrequency	5	ESCA
VPS4A	0	.	GRCh37	16	69349973	69349973	+	Silent	SNP	G	G	A	rs576996707	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.84G>A	p.%3D	p.A28A	ENST00000254950	2/11	43	39	4	43	43	0	VPS4A,synonymous_variant,p.%3D,ENST00000254950,;RP11-343C2.11,synonymous_variant,p.%3D,ENST00000570054,;COG8,downstream_gene_variant,,ENST00000564419,;VPS4A,upstream_gene_variant,,ENST00000562754,;	A	ENSG00000132612	ENST00000254950	Transcript	synonymous_variant	240	84	28	A	gcG/gcA	rs576996707	.	.	1	VPS4A	HGNC	13488	protein_coding	YES	CCDS45517.1	ENSP00000254950	VPS4A_HUMAN	Q9UF30_HUMAN	UPI000000DC7F	.	.	.	2/11	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF82,Pfam_domain:PF04212,Gene3D:1.20.58.280,SMART_domains:SM00745,Superfamily_domains:SSF116846	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGCGCTGCG	by1000G	4	ESCA
DEF8	0	.	GRCh37	16	90021666	90021666	+	Missense_Mutation	SNP	C	C	T	rs779640162	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397C>T	p.Arg133Cys	p.R133C	ENST00000268676	4/13	39	24	15	56	56	0	DEF8,missense_variant,p.Arg72Cys,ENST00000561959,;DEF8,missense_variant,p.Arg72Cys,ENST00000567884,;DEF8,missense_variant,p.Arg12Cys,ENST00000567874,;DEF8,missense_variant,p.Arg72Cys,ENST00000418391,;DEF8,missense_variant,p.Arg106Cys,ENST00000561741,;DEF8,missense_variant,p.Arg72Cys,ENST00000563594,;DEF8,missense_variant,p.Arg72Cys,ENST00000569061,;DEF8,missense_variant,p.Arg72Cys,ENST00000569453,;DEF8,missense_variant,p.Arg12Cys,ENST00000562986,;DEF8,missense_variant,p.Arg133Cys,ENST00000268676,;DEF8,missense_variant,p.Arg72Cys,ENST00000566820,;DEF8,missense_variant,p.Arg66Cys,ENST00000562578,;DEF8,missense_variant,p.Arg72Cys,ENST00000570182,;DEF8,missense_variant,p.Arg72Cys,ENST00000567999,;DEF8,missense_variant,p.Arg76Cys,ENST00000566079,;DEF8,missense_variant,p.Arg72Cys,ENST00000563795,;DEF8,downstream_gene_variant,,ENST00000564836,;DEF8,non_coding_transcript_exon_variant,,ENST00000568096,;DEF8,non_coding_transcript_exon_variant,,ENST00000569803,;DEF8,non_coding_transcript_exon_variant,,ENST00000567243,;DEF8,upstream_gene_variant,,ENST00000562044,;DEF8,upstream_gene_variant,,ENST00000563848,;DEF8,missense_variant,p.Arg72Cys,ENST00000561784,;DEF8,upstream_gene_variant,,ENST00000568760,;	T	ENSG00000140995	ENST00000268676	Transcript	missense_variant	486	397	133	R/C	Cgc/Tgc	rs779640162	.	.	1	DEF8	HGNC	25969	protein_coding	YES	CCDS10989.1	ENSP00000268676	DEFI8_HUMAN	H3BT87_HUMAN,H3BRA7_HUMAN,H3BQX9_HUMAN,H3BNN0_HUMAN,H3BMP4_HUMAN	UPI0000359601	.	deleterious(0.01)	probably_damaging(0.972)	4/13	.	hmmpanther:PTHR12326	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCCCGCCCT	byFrequency	5	ESCA
GRAP	0	.	GRCh37	17	18925357	18925357	+	Missense_Mutation	SNP	C	C	T	rs755441479	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569G>A	p.Arg190His	p.R190H	ENST00000284154	5/5	41	21	20	86	86	0	GRAP,missense_variant,p.Arg161His,ENST00000395635,;GRAP,missense_variant,p.Ala134Thr,ENST00000573099,;GRAP,missense_variant,p.Arg190His,ENST00000284154,;SLC5A10,3_prime_UTR_variant,,ENST00000317977,;SLC5A10,downstream_gene_variant,,ENST00000417251,;SLC5A10,downstream_gene_variant,,ENST00000395647,;SLC5A10,downstream_gene_variant,,ENST00000395643,;SLC5A10,downstream_gene_variant,,ENST00000395642,;SLC5A10,downstream_gene_variant,,ENST00000395645,;GRAP,3_prime_UTR_variant,,ENST00000583020,;SLC5A10,downstream_gene_variant,,ENST00000584658,;	T	ENSG00000154016	ENST00000284154	Transcript	missense_variant	1280	569	190	R/H	cGc/cAc	rs755441479	.	.	-1	GRAP	HGNC	4562	protein_coding	YES	CCDS11202.1	ENSP00000284154	GRAP_HUMAN	K7EKU7_HUMAN,A8MW78_HUMAN	UPI000012BA7E	.	tolerated(0.6)	benign(0.003)	5/5	.	Prints_domain:PR00499,Superfamily_domains:SSF50044,SMART_domains:SM00326,Gene3D:2.30.30.40,Pfam_domain:PF07653,hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF26,PROSITE_profiles:PS50002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCGCTCC	byFrequency	5	ESCA
RP11-744K17.9	0	.	GRCh37	17	21911549	21911549	+	RNA	SNP	G	G	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2274G>C	.	.	ENST00000581223	2/2	21	17	4	29	29	0	RP11-744K17.9,non_coding_transcript_exon_variant,,ENST00000581223,;RP11-1109M24.7,non_coding_transcript_exon_variant,,ENST00000582156,;RP11-1109M24.8,upstream_gene_variant,,ENST00000578438,;RP11-1109M24.9,upstream_gene_variant,,ENST00000582046,;	C	ENSG00000266795	ENST00000581223	Transcript	non_coding_transcript_exon_variant	2274	.	.	.	.	.	.	.	1	RP11-744K17.9	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGGGGCAAT	.	5	ESCA
PIP4K2B	0	.	GRCh37	17	36935734	36935734	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556A>G	p.Met186Val	p.M186V	ENST00000269554	5/10	59	41	18	48	48	0	PIP4K2B,missense_variant,p.Met186Val,ENST00000269554,;PIP4K2B,downstream_gene_variant,,ENST00000581097,;PIP4K2B,non_coding_transcript_exon_variant,,ENST00000583278,;PIP4K2B,non_coding_transcript_exon_variant,,ENST00000311500,;	C	ENSG00000141720	ENST00000269554	Transcript	missense_variant	1037	556	186	M/V	Atg/Gtg	.	.	.	-1	PIP4K2B	HGNC	8998	protein_coding	YES	CCDS11329.1	ENSP00000269554	PI42B_HUMAN	J3QQP6_HUMAN	UPI0000032D92	.	deleterious(0.03)	benign(0.345)	5/10	.	PROSITE_profiles:PS51455,hmmpanther:PTHR23086:SF22,hmmpanther:PTHR23086,Pfam_domain:PF01504,Gene3D:2gk9B01,SMART_domains:SM00330,Superfamily_domains:SSF56104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACATGCCCA	.	5	ESCA
APPBP2	0	.	GRCh37	17	58524943	58524943	+	Nonstop_Mutation	SNP	C	C	A	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1757G>T	p.Ter586LeuextTer70	p.*586Lext*70	ENST00000083182	13/13	79	72	6	73	73	0	APPBP2,stop_lost,p.Ter586LeuextTer70,ENST00000083182,;APPBP2,downstream_gene_variant,,ENST00000589341,;	A	ENSG00000062725	ENST00000083182	Transcript	stop_lost	2045	1757	586	*/L	tGa/tTa	COSM561481	.	.	-1	APPBP2	HGNC	622	protein_coding	YES	CCDS32699.1	ENSP00000083182	APBP2_HUMAN	K7EIZ9_HUMAN	UPI000006D959	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCTCAGCAG	.	4	ESCA
TP53	0	.	GRCh37	17	7578223	7578223	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626G>A	p.Arg209Lys	p.R209K	ENST00000269305	6/11	44	19	24	93	93	0	TP53,missense_variant,p.Arg209Lys,ENST00000413465,;TP53,missense_variant,p.Arg209Lys,ENST00000420246,;TP53,missense_variant,p.Arg209Lys,ENST00000269305,;TP53,missense_variant,p.Arg77Lys,ENST00000509690,;TP53,missense_variant,p.Arg209Lys,ENST00000359597,;TP53,missense_variant,p.Arg116Lys,ENST00000514944,;TP53,missense_variant,p.Arg209Lys,ENST00000445888,;TP53,missense_variant,p.Arg209Lys,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	816	626	209	R/K	aGa/aAa	TP53_g.12695G>T,TP53_g.12695G>C,TP53_g.12695del,TP53_g.12695G>A,COSM45438,COSM45257,COSM46120,COSM45995,COSM308315,COSM984931,COSM308314,COSM984933,COSM308316,COSM984935,COSM308317,COSM984934	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.91)	benign(0.003)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R209K|c.626G>A|6,CODON|p.0?|c.1_1182del1182|6,CODON|p.R209fs*6|c.626_627delGA|3,CODON|p.R116fs*6|c.347_348delGA|3,CODON|p.R209fs*6|c.626_627delGA|3,CODON|p.R209fs*6|c.626_627delGA|11,CODON|p.R77fs*6|c.230_231delGA|3,CODON|p.R209fs*6|c.625_626delAG|23,CODON|p.R209T|c.626G>C|3,BUFFER|p.R213fs*34|c.637delC|3,BUFFER|p.F212fs*3|c.635_636delTT|5,BUFFER|p.R213*|c.637C>T|45,BUFFER|p.R120*|c.358C>T|84,BUFFER|p.R213*|c.637C>T|84,BUFFER|p.R213*|c.637C>T|84,BUFFER|p.R81*|c.241C>T|87,BUFFER|p.R213*|c.637C>T|267,BUFFER|p.R213*|c.637C>T|33,BUFFER|p.F212fs*3|c.634_635delTT|6,BUFFER|p.R213fs*34|c.634delT|5,BUFFER|p.T211T|c.633T>C|9,BUFFER|p.T211I|c.632C>T|3,BUFFER|p.T211I|c.632C>T|11,BUFFER|p.T211N|c.632C>A|4,BUFFER|p.T118I|c.353C>T|3,BUFFER|p.T79I|c.236C>T|3,BUFFER|p.T211I|c.632C>T|3,BUFFER|p.T211fs*36|c.631delA|4,BUFFER|p.T211A|c.631A>G|3,BUFFER|p.N210fs*37|c.628delA|3,BUFFER|p.R209*|c.625A>T|4,BUFFER|p.R116*|c.346A>T|4,BUFFER|p.R209*|c.625A>T|4,BUFFER|p.R209*|c.625A>T|14,BUFFER|p.R77*|c.229A>T|4,BUFFER|p.D208E|c.624C>G|3,BUFFER|p.D208V|c.623A>T|14,BUFFER|p.D208G|c.623A>G|5,BUFFER|p.D207G|c.620A>G|4,BUFFER|p.L206fs*41|c.617delT|4,BUFFER|p.L206*|c.617T>A|9	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTTCTGTCA	.	5	ESCA
TP53	0	.	GRCh37	17	7578265	7578265	+	Missense_Mutation	SNP	A	A	T	rs760043106	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	6/11	39	16	23	97	97	0	TP53,missense_variant,p.Ile195Asn,ENST00000413465,;TP53,missense_variant,p.Ile195Asn,ENST00000420246,;TP53,missense_variant,p.Ile195Asn,ENST00000269305,;TP53,missense_variant,p.Ile63Asn,ENST00000509690,;TP53,missense_variant,p.Ile195Asn,ENST00000359597,;TP53,missense_variant,p.Ile102Asn,ENST00000514944,;TP53,missense_variant,p.Ile195Asn,ENST00000445888,;TP53,missense_variant,p.Ile195Asn,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	774	584	195	I/N	aTc/aAc	rs760043106,CM092575,TP53_g.12653T>G,TP53_g.12653T>C,TP53_g.12653T>A,COSM44877,COSM44539,COSM11089,COSM1738250,COSM116924,COSM212745,COSM116921,COSM1738252,COSM212744,COSM1738254,COSM116922,COSM212746,COSM3421936,COSM3403267,COSM1738251,COSM1645297,COSM1738253,COSM212747,COSM116923	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.I102N|c.305T>A|10,SITE|p.I195N|c.584T>A|10,SITE|p.I195N|c.584T>A|4,SITE|p.I63N|c.188T>A|10,SITE|p.I195N|c.584T>A|10,SITE|p.I195N|c.584T>A|23,SITE|p.I195N|c.584T>A|10,CODON|p.0?|c.1_1182del1182|6,CODON|p.A189_V197delAPPQHLIRV|c.565_591del27|4,CODON|p.R196*|c.585_586CC>TT|7,CODON|p.I102T|c.305T>C|21,CODON|p.I63S|c.188T>G|3,CODON|p.I195T|c.584T>C|88,CODON|p.I195T|c.584T>C|21,CODON|p.I195T|c.584T>C|12,CODON|p.I63T|c.188T>C|21,CODON|p.I195T|c.584T>C|21,CODON|p.I195T|c.584T>C|10,CODON|p.I195S|c.584T>G|7,BUFFER|p.G199*|c.595G>T|5,BUFFER|p.G199R|c.595G>A|9,BUFFER|p.E198*|c.592G>T|5,BUFFER|p.E198K|c.592G>A|5,BUFFER|p.E198*|c.592G>T|4,BUFFER|p.E105*|c.313G>T|9,BUFFER|p.E198*|c.592G>T|27,BUFFER|p.E198*|c.592G>T|9,BUFFER|p.E66*|c.196G>T|9,BUFFER|p.E198*|c.592G>T|9,BUFFER|p.V197G|c.590T>G|15,BUFFER|p.V197E|c.590T>A|8,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.V65L|c.193G>T|3,BUFFER|p.V197M|c.589G>A|12,BUFFER|p.V197L|c.589G>T|5,BUFFER|p.V104L|c.310G>T|3,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.R196R|c.588A>G|4,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R196P|c.587G>C|18,BUFFER|p.R64P|c.191G>C|7,BUFFER|p.R196Q|c.587G>A|4,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R103P|c.308G>C|7,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R64fs*>27|c.190delC|3,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R103fs*51|c.307delC|3,BUFFER|p.R196fs*51|c.586delC|7,BUFFER|p.R64*|c.190C>T|65,BUFFER|p.R196*|c.586C>T|45,BUFFER|p.R196*|c.586C>T|33,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R103*|c.307C>T|64,BUFFER|p.R196*|c.586C>T|180,BUFFER|p.I195F|c.583A>T|6,BUFFER|p.I195F|c.583A>T|28,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.I63F|c.187A>T|9,BUFFER|p.I102F|c.304A>T|9,BUFFER|p.I195F|c.583A>T|5,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.L194L|c.582T>C|3,BUFFER|p.L62R|c.185T>G|17,BUFFER|p.L194R|c.581T>G|50,BUFFER|p.L194R|c.581T>G|11,BUFFER|p.L194H|c.581T>A|6,BUFFER|p.L194P|c.581T>C|9,BUFFER|p.L101R|c.302T>G|17,BUFFER|p.L194R|c.581T>G|9,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|19,BUFFER|p.L101F|c.301C>T|3,BUFFER|p.L62F|c.184C>T|3,BUFFER|p.H193fs*16|c.577_578insN|3,BUFFER|p.H193R|c.578A>G|8,BUFFER|p.H193L|c.578A>T|8,BUFFER|p.H193R|c.578A>G|89,BUFFER|p.H61P|c.182A>C|4,BUFFER|p.H100L|c.299A>T|8,BUFFER|p.H61R|c.182A>G|23,BUFFER|p.H193R|c.578A>G|21,BUFFER|p.H193L|c.578A>T|8,BUFFER|p.H193R|c.578A>G|22,BUFFER|p.H100R|c.299A>G|22,BUFFER|p.H100P|c.299A>C|4,BUFFER|p.H193P|c.578A>C|4,BUFFER|p.H193L|c.578A>T|3,BUFFER|p.H193L|c.578A>T|3,BUFFER|p.H193P|c.578A>C|16,BUFFER|p.H193R|c.578A>G|5,BUFFER|p.H193P|c.578A>C|3,BUFFER|p.H193L|c.578A>T|37,BUFFER|p.H61L|c.182A>T|10,BUFFER|p.H193N|c.577C>A|6,BUFFER|p.H193D|c.577C>G|8,BUFFER|p.H193Y|c.577C>T|5,BUFFER|p.H193Y|c.577C>T|40,BUFFER|p.H100Y|c.298C>T|15,BUFFER|p.H193Y|c.577C>T|15,BUFFER|p.H61Y|c.181C>T|15,BUFFER|p.H193Y|c.577C>T|15,BUFFER|p.H193Y|c.577C>T|3,BUFFER|p.Q192H|c.576G>T|3,BUFFER|p.Q192Q|c.576G>A|3,BUFFER|p.Q192R|c.575A>G|5,BUFFER|p.P191delP|c.572_574delCTC|3,BUFFER|p.P191delP|c.572_574delCTC|3,BUFFER|p.P191delP|c.572_574delCTC|5,BUFFER|p.P59delP|c.176_178delCTC|3,BUFFER|p.P98delP|c.293_295delCTC|3,BUFFER|p.Q192*|c.574C>T|6,BUFFER|p.Q99*|c.295C>T|17,BUFFER|p.Q192*|c.574C>T|10,BUFFER|p.Q192*|c.574C>T|17,BUFFER|p.Q192*|c.574C>T|86,BUFFER|p.Q192*|c.574C>T|17,BUFFER|p.Q60*|c.178C>T|17	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGGATAAGA	.	5	ESCA
ASF1B	0	.	GRCh37	19	14247408	14247408	+	5'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-140T>G	.	.	ENST00000263382	1/4	20	12	7	22	22	0	ASF1B,5_prime_UTR_variant,,ENST00000263382,;ASF1B,upstream_gene_variant,,ENST00000592798,;ASF1B,upstream_gene_variant,,ENST00000474890,;CTB-55O6.12,upstream_gene_variant,,ENST00000588658,;CTB-55O6.12,upstream_gene_variant,,ENST00000588387,;ASF1B,5_prime_UTR_variant,,ENST00000590835,;ASF1B,upstream_gene_variant,,ENST00000589468,;	C	ENSG00000105011	ENST00000263382	Transcript	5_prime_UTR_variant	361	.	.	.	.	.	.	.	-1	ASF1B	HGNC	20996	protein_coding	YES	CCDS12306.1	ENSP00000263382	ASF1B_HUMAN	B4DXU6_HUMAN	UPI00000437D4	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCTAGTCCG	.	2	ESCA
KLF16	0	.	GRCh37	19	1853853	1853853	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*605G>A	.	.	ENST00000250916	2/2	48	34	14	86	86	0	KLF16,3_prime_UTR_variant,,ENST00000250916,;CTB-31O20.6,downstream_gene_variant,,ENST00000592884,;KLF16,downstream_gene_variant,,ENST00000592313,;KLF16,intron_variant,,ENST00000541015,;	T	ENSG00000129911	ENST00000250916	Transcript	3_prime_UTR_variant	1435	.	.	.	.	.	.	.	-1	KLF16	HGNC	16857	protein_coding	YES	CCDS12075.1	ENSP00000250916	KLF16_HUMAN	.	UPI0000126B0D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCCCGAGGT	.	5	ESCA
ZNF257	0	.	GRCh37	19	22271249	22271249	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.697G>T	p.Glu233Ter	p.E233*	ENST00000594947	4/4	43	34	9	54	54	0	ZNF257,stop_gained,p.Glu233Ter,ENST00000594947,;ZNF257,downstream_gene_variant,,ENST00000597927,;ZNF257,downstream_gene_variant,,ENST00000600162,;ZNF257,3_prime_UTR_variant,,ENST00000435820,;	T	ENSG00000197134	ENST00000594947	Transcript	stop_gained	841	697	233	E/*	Gag/Tag	COSM1392120	.	.	1	ZNF257	HGNC	13498	protein_coding	YES	CCDS46030.1	ENSP00000470209	ZN257_HUMAN	M0R0N1_HUMAN	UPI0000E045CA	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF109,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAGAGTGT	.	5	ESCA
AMH	0	.	GRCh37	19	2250424	2250424	+	Silent	SNP	C	C	T	rs779588404	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501C>T	p.%3D	p.Y167Y	ENST00000221496	2/5	49	33	16	42	42	0	AMH,synonymous_variant,p.%3D,ENST00000221496,;AMH,intron_variant,,ENST00000592877,;JSRP1,downstream_gene_variant,,ENST00000300961,;SF3A2,downstream_gene_variant,,ENST00000221494,;JSRP1,downstream_gene_variant,,ENST00000593238,;SF3A2,downstream_gene_variant,,ENST00000586396,;JSRP1,downstream_gene_variant,,ENST00000586471,;MIR4321,upstream_gene_variant,,ENST00000592276,;AMH,non_coding_transcript_exon_variant,,ENST00000609455,;AMH,non_coding_transcript_exon_variant,,ENST00000589313,;SF3A2,downstream_gene_variant,,ENST00000587637,;SF3A2,downstream_gene_variant,,ENST00000592839,;SF3A2,downstream_gene_variant,,ENST00000592314,;SF3A2,downstream_gene_variant,,ENST00000591121,;	T	ENSG00000104899	ENST00000221496	Transcript	synonymous_variant	523	501	167	Y	taC/taT	rs779588404	.	.	1	AMH	HGNC	464	protein_coding	YES	CCDS12085.1	ENSP00000221496	MIS_HUMAN	.	UPI000013C7D0	.	.	.	2/5	.	hmmpanther:PTHR15009,Pfam_domain:PF04709,PIRSF_domain:PIRSF037270	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTACCCTGG	byFrequency	5	ESCA
ZNF254	0	.	GRCh37	19	24309076	24309076	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274C>G	p.Gln92Glu	p.Q92E	ENST00000357002	4/4	35	22	13	47	47	0	ZNF254,missense_variant,p.Gln92Glu,ENST00000357002,;ZNF254,missense_variant,p.Gln7Glu,ENST00000342944,;ZNF254,3_prime_UTR_variant,,ENST00000595187,;ZNF254,3_prime_UTR_variant,,ENST00000594886,;	G	ENSG00000213096	ENST00000357002	Transcript	missense_variant	389	274	92	Q/E	Caa/Gaa	.	.	.	1	ZNF254	HGNC	13047	protein_coding	YES	CCDS32983.1	ENSP00000349494	ZN254_HUMAN	F5H2M4_HUMAN	UPI0000366DB6	.	tolerated(0.17)	benign(0.049)	4/4	.	hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCTCAAGAC	.	5	ESCA
ZNF548	0	.	GRCh37	19	57910927	57910927	+	Silent	SNP	C	C	T	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1308C>T	p.%3D	p.S436S	ENST00000336128	4/4	46	33	12	62	62	0	ZNF548,synonymous_variant,p.%3D,ENST00000336128,;ZNF548,synonymous_variant,p.%3D,ENST00000366197,;AC004076.7,intron_variant,,ENST00000597410,;AC003002.6,intron_variant,,ENST00000596400,;AC003002.6,intron_variant,,ENST00000596617,;ZNF548,downstream_gene_variant,,ENST00000598895,;ZNF548,downstream_gene_variant,,ENST00000594668,;ZNF548,downstream_gene_variant,,ENST00000594693,;ZNF548,downstream_gene_variant,,ENST00000600927,;AC003002.4,downstream_gene_variant,,ENST00000597658,;ZNF548,downstream_gene_variant,,ENST00000597400,;ZNF548,downstream_gene_variant,,ENST00000596282,;AC003002.6,intron_variant,,ENST00000600421,;ZNF548,downstream_gene_variant,,ENST00000597047,;ZNF548,downstream_gene_variant,,ENST00000600442,;ZNF548,downstream_gene_variant,,ENST00000602086,;ZNF548,downstream_gene_variant,,ENST00000597576,;	T	ENSG00000188785	ENST00000336128	Transcript	synonymous_variant	1511	1308	436	S	agC/agT	COSM286917	.	.	1	ZNF548	HGNC	26561	protein_coding	YES	CCDS54324.1	ENSP00000337555	ZN548_HUMAN	M0R354_HUMAN,M0R041_HUMAN,M0QX17_HUMAN	UPI000059D7C2	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24387:SF189,hmmpanther:PTHR24387,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGCGAATG	.	5	ESCA
HIPK1	0	.	GRCh37	1	114520177	114520177	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4043G>T	.	.	ENST00000369558	16/16	10	7	3	30	30	0	HIPK1,3_prime_UTR_variant,,ENST00000361587,;HIPK1,3_prime_UTR_variant,,ENST00000369554,;HIPK1,3_prime_UTR_variant,,ENST00000406344,;HIPK1,3_prime_UTR_variant,,ENST00000369558,;HIPK1,3_prime_UTR_variant,,ENST00000340480,;OLFML3,upstream_gene_variant,,ENST00000369551,;HIPK1,downstream_gene_variant,,ENST00000369561,;HIPK1,downstream_gene_variant,,ENST00000426820,;HIPK1,downstream_gene_variant,,ENST00000369553,;OLFML3,upstream_gene_variant,,ENST00000393300,;OLFML3,upstream_gene_variant,,ENST00000320334,;HIPK1,downstream_gene_variant,,ENST00000369555,;OLFML3,upstream_gene_variant,,ENST00000491700,;	T	ENSG00000163349	ENST00000369558	Transcript	3_prime_UTR_variant	7908	.	.	.	.	.	.	.	1	HIPK1	HGNC	19006	protein_coding	YES	CCDS867.1	ENSP00000358571	HIPK1_HUMAN	D6RF28_HUMAN,D6RC95_HUMAN	UPI000000D74E	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTACTGAGCTA	.	2	ESCA
ASH1L	0	.	GRCh37	1	155319190	155319190	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7482G>T	p.Gln2494His	p.Q2494H	ENST00000392403	19/28	46	16	30	55	55	0	ASH1L,missense_variant,p.Gln2499His,ENST00000368346,;ASH1L,missense_variant,p.Gln2494His,ENST00000392403,;MIR555,upstream_gene_variant,,ENST00000384987,;ASH1L,upstream_gene_variant,,ENST00000478837,;ASH1L,upstream_gene_variant,,ENST00000492987,;ASH1L,upstream_gene_variant,,ENST00000548566,;	A	ENSG00000116539	ENST00000392403	Transcript	missense_variant	7961	7482	2494	Q/H	caG/caT	COSM3769697	.	.	-1	ASH1L	HGNC	19088	protein_coding	YES	CCDS1113.2	ENSP00000376204	ASH1L_HUMAN	.	UPI0000DACAC8	.	deleterious_low_confidence(0.02)	possibly_damaging(0.542)	19/28	.	PROSITE_profiles:PS50014,Gene3D:1.20.920.10,Pfam_domain:PF00439,SMART_domains:SM00297,Superfamily_domains:SSF47370	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATCTGCTT	.	5	ESCA
LMX1A	0	.	GRCh37	1	165218762	165218762	+	Nonsense_Mutation	SNP	G	G	A	rs771630092	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.379C>T	p.Arg127Ter	p.R127*	ENST00000342310	4/9	27	13	13	41	41	0	LMX1A,stop_gained,p.Arg127Ter,ENST00000294816,;LMX1A,stop_gained,p.Arg127Ter,ENST00000342310,;LMX1A,stop_gained,p.Arg127Ter,ENST00000367893,;	A	ENSG00000162761	ENST00000342310	Transcript	stop_gained	762	379	127	R/*	Cga/Tga	rs771630092	.	.	-1	LMX1A	HGNC	6653	protein_coding	YES	CCDS1247.1	ENSP00000340226	LMX1A_HUMAN	Q6NZ39_HUMAN	UPI000012E793	.	.	.	4/9	.	SMART_domains:SM00132,Gene3D:2.10.110.10,Pfam_domain:PF00412,PROSITE_patterns:PS00478,hmmpanther:PTHR24208:SF88,hmmpanther:PTHR24208,PROSITE_profiles:PS50023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCGCTCGC	.	5	ESCA
XPR1	0	.	GRCh37	1	180601390	180601390	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53A>C	p.Gln18Pro	p.Q18P	ENST00000367590	1/15	67	60	7	76	76	0	XPR1,missense_variant,p.Gln18Pro,ENST00000367589,;XPR1,missense_variant,p.Gln18Pro,ENST00000367590,;	C	ENSG00000143324	ENST00000367590	Transcript	missense_variant	251	53	18	Q/P	cAa/cCa	.	.	.	1	XPR1	HGNC	12827	protein_coding	YES	CCDS1340.1	ENSP00000356562	XPR1_HUMAN	.	UPI0000071111	.	deleterious(0)	probably_damaging(0.988)	1/15	.	Pfam_domain:PF03105,hmmpanther:PTHR10783:SF4,hmmpanther:PTHR10783,PROSITE_profiles:PS51382	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGCAATACA	.	4	ESCA
DESI2	0	.	GRCh37	1	244816601	244816601	+	5'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-15G>T	.	.	ENST00000302550	1/5	11	7	4	13	13	0	DESI2,5_prime_UTR_variant,,ENST00000263831,;DESI2,5_prime_UTR_variant,,ENST00000302550,;DESI2,upstream_gene_variant,,ENST00000418162,;DESI2,non_coding_transcript_exon_variant,,ENST00000484738,;	T	ENSG00000121644	ENST00000302550	Transcript	5_prime_UTR_variant	365	.	.	.	.	.	.	.	1	DESI2	HGNC	24264	protein_coding	YES	CCDS1626.1	ENSP00000306528	DESI2_HUMAN	.	UPI0000038D6C	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CGGCGGCCGCG	.	2	ESCA
MTF2	0	.	GRCh37	1	93599533	93599533	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315A>G	p.Ile439Val	p.I439V	ENST00000370298	13/15	17	9	7	34	34	0	MTF2,missense_variant,p.Ile382Val,ENST00000370303,;MTF2,missense_variant,p.Ile337Val,ENST00000540243,;MTF2,missense_variant,p.Ile337Val,ENST00000545708,;MTF2,missense_variant,p.Ile439Val,ENST00000370298,;MTF2,non_coding_transcript_exon_variant,,ENST00000467953,;MTF2,non_coding_transcript_exon_variant,,ENST00000471953,;MTF2,non_coding_transcript_exon_variant,,ENST00000487263,;MTF2,non_coding_transcript_exon_variant,,ENST00000489480,;MTF2,non_coding_transcript_exon_variant,,ENST00000476037,;MTF2,downstream_gene_variant,,ENST00000497976,;	G	ENSG00000143033	ENST00000370298	Transcript	missense_variant	1604	1315	439	I/V	Ata/Gta	.	.	.	1	MTF2	HGNC	29535	protein_coding	YES	CCDS742.1	ENSP00000359321	MTF2_HUMAN	.	UPI0000205B55	.	tolerated(0.56)	benign(0.002)	13/15	.	hmmpanther:PTHR12628:SF12,hmmpanther:PTHR12628	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTATAGGG	.	5	ESCA
SOX12	0	.	GRCh37	20	308959	308959	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1443C>T	.	.	ENST00000342665	1/1	47	25	21	34	34	0	SOX12,3_prime_UTR_variant,,ENST00000544632,;SOX12,3_prime_UTR_variant,,ENST00000342665,;RP5-1103G7.4,intron_variant,,ENST00000442637,;RP5-1103G7.4,upstream_gene_variant,,ENST00000414676,;	T	ENSG00000177732	ENST00000342665	Transcript	3_prime_UTR_variant	2721	.	.	.	.	.	.	.	1	SOX12	HGNC	11198	protein_coding	YES	CCDS12995.1	ENSP00000347646	SOX12_HUMAN	.	UPI0000167B9D	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTCACCGG	.	5	ESCA
ZNF217	0	.	GRCh37	20	52185370	52185370	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*457C>G	.	.	ENST00000371471	6/6	27	15	12	44	44	0	ZNF217,3_prime_UTR_variant,,ENST00000437222,;ZNF217,3_prime_UTR_variant,,ENST00000302342,;ZNF217,3_prime_UTR_variant,,ENST00000371471,;RP4-724E16.2,intron_variant,,ENST00000424252,;	C	ENSG00000171940	ENST00000371471	Transcript	3_prime_UTR_variant	4030	.	.	.	.	.	.	.	-1	ZNF217	HGNC	13009	protein_coding	YES	CCDS13443.1	ENSP00000360526	ZN217_HUMAN	A2A326_HUMAN	UPI000013C323	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGGAATA	.	5	ESCA
SCAF4	0	.	GRCh37	21	33063188	33063188	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1807C>T	p.Pro603Ser	p.P603S	ENST00000286835	15/20	53	30	22	46	46	0	SCAF4,missense_variant,p.Pro603Ser,ENST00000399804,;SCAF4,missense_variant,p.Pro603Ser,ENST00000286835,;SCAF4,missense_variant,p.Pro588Ser,ENST00000434667,;SCAF4,non_coding_transcript_exon_variant,,ENST00000472318,;SCAF4,non_coding_transcript_exon_variant,,ENST00000467731,;	A	ENSG00000156304	ENST00000286835	Transcript	missense_variant	2190	1807	603	P/S	Cca/Tca	.	.	.	-1	SCAF4	HGNC	19304	protein_coding	YES	CCDS33537.1	ENSP00000286835	SFR15_HUMAN	Q0P607_HUMAN	UPI0000206D66	.	.	possibly_damaging(0.901)	15/20	.	hmmpanther:PTHR14124,hmmpanther:PTHR14124:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGGAATAT	.	5	ESCA
DPP10	0	.	GRCh37	2	116548752	116548752	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1639T>A	p.Tyr547Asn	p.Y547N	ENST00000393147	18/26	27	21	6	21	21	0	DPP10,missense_variant,p.Tyr547Asn,ENST00000393147,;DPP10,missense_variant,p.Tyr493Asn,ENST00000409163,;DPP10,missense_variant,p.Tyr536Asn,ENST00000310323,;DPP10,missense_variant,p.Tyr543Asn,ENST00000410059,;	A	ENSG00000175497	ENST00000393147	Transcript	missense_variant	1994	1639	547	Y/N	Tat/Aat	.	.	.	1	DPP10	HGNC	20823	protein_coding	YES	CCDS54388.1	ENSP00000376855	DPP10_HUMAN	J3KQK8_HUMAN,C9J4M8_HUMAN	UPI00015E0A22	.	deleterious(0.05)	benign(0.426)	18/26	.	hmmpanther:PTHR11731:SF21,hmmpanther:PTHR11731,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGACTATGGT	.	5	ESCA
ARL6IP6	0	.	GRCh37	2	153616651	153616651	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*297C>A	.	.	ENST00000326446	4/4	44	29	15	69	69	0	ARL6IP6,3_prime_UTR_variant,,ENST00000326446,;ARL6IP6,non_coding_transcript_exon_variant,,ENST00000495469,;ARL6IP6,non_coding_transcript_exon_variant,,ENST00000463690,;ARL6IP6,downstream_gene_variant,,ENST00000425034,;ARL6IP6,downstream_gene_variant,,ENST00000455875,;	A	ENSG00000177917	ENST00000326446	Transcript	3_prime_UTR_variant	1689	.	.	.	.	.	.	.	1	ARL6IP6	HGNC	24048	protein_coding	YES	CCDS2197.1	ENSP00000315357	AR6P6_HUMAN	.	UPI000006EA01	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAACATTTT	.	5	ESCA
NFE2L2	0	.	GRCh37	2	178098960	178098960	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85G>C	p.Asp29His	p.D29H	ENST00000397062	2/5	59	45	13	19	19	0	NFE2L2,missense_variant,p.Asp13His,ENST00000449627,;NFE2L2,missense_variant,p.Asp13His,ENST00000423513,;NFE2L2,missense_variant,p.Asp29His,ENST00000397062,;NFE2L2,missense_variant,p.Asp13His,ENST00000446151,;NFE2L2,missense_variant,p.Asp13His,ENST00000588123,;NFE2L2,missense_variant,p.Asp28His,ENST00000586532,;NFE2L2,missense_variant,p.Asp13His,ENST00000421929,;NFE2L2,missense_variant,p.Asp13His,ENST00000464747,;NFE2L2,missense_variant,p.Asp13His,ENST00000448782,;NFE2L2,missense_variant,p.Asp13His,ENST00000397063,;NFE2L2,intron_variant,,ENST00000430047,;NFE2L2,upstream_gene_variant,,ENST00000458603,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534,;DNAJC19P5,upstream_gene_variant,,ENST00000443295,;	G	ENSG00000116044	ENST00000397062	Transcript	missense_variant	640	85	29	D/H	Gat/Cat	COSM124735,COSM124736,COSM132845	.	.	-1	NFE2L2	HGNC	7782	protein_coding	YES	CCDS42782.1	ENSP00000380252	NF2L2_HUMAN	Q9BZF8_HUMAN,K7ER33_HUMAN,C9J1A8_HUMAN,C9J0Y1_HUMAN	UPI000012FFD0	.	deleterious(0)	probably_damaging(1)	2/5	.	hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF3	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.D29H|c.85G>C|12,CODON|p.D29G|c.86A>G|11,BUFFER|p.G31E|c.92G>A|5,BUFFER|p.G31A|c.92G>C|7,BUFFER|p.L30R|c.89T>G|7,BUFFER|p.L30F|c.88C>T|6,BUFFER|p.D29N|c.85G>A|3,BUFFER|p.D29Y|c.85G>T|4,BUFFER|p.D27G|c.80A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATCTATAT	.	5	ESCA
BZW1	0	.	GRCh37	2	201688031	201688031	+	3'Flank	SNP	C	C	T	rs140367396	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000452790	.	61	45	16	35	33	2	BZW1,3_prime_UTR_variant,,ENST00000409600,;BZW1,downstream_gene_variant,,ENST00000359893,;BZW1,downstream_gene_variant,,ENST00000452790,;BZW1,downstream_gene_variant,,ENST00000409226,;BZW1,downstream_gene_variant,,ENST00000410110,;RP11-469M7.1,upstream_gene_variant,,ENST00000568571,;BZW1,downstream_gene_variant,,ENST00000463310,;BZW1,downstream_gene_variant,,ENST00000491576,;	T	ENSG00000082153	ENST00000452790	Transcript	downstream_gene_variant	.	.	.	.	.	rs140367396	.	1065	1	BZW1	HGNC	18380	protein_coding	YES	CCDS56155.1	ENSP00000394316	BZW1_HUMAN	Q3LIC9_HUMAN,D3DN77_HUMAN,C9JWF5_HUMAN,C9JFN4_HUMAN,C9J188_HUMAN,C9IZ80_HUMAN	UPI00006C0604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTTGCCGTTTT	byCluster|by1000G	2	ESCA
FAM126B	0	.	GRCh37	2	201845896	201845896	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*97C>G	.	.	ENST00000418596	12/12	30	22	8	31	31	0	FAM126B,3_prime_UTR_variant,,ENST00000418596,;AC005037.3,intron_variant,,ENST00000413848,;AC005037.3,downstream_gene_variant,,ENST00000332935,;FAM126B,3_prime_UTR_variant,,ENST00000286181,;	C	ENSG00000155744	ENST00000418596	Transcript	3_prime_UTR_variant	1878	.	.	.	.	.	.	.	-1	FAM126B	HGNC	28593	protein_coding	YES	CCDS2335.1	ENSP00000393667	F126B_HUMAN	C9JTA1_HUMAN,C9JNS4_HUMAN,B3KW57_HUMAN	UPI0000074347	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAACAGTGACC	.	5	ESCA
EPT1	0	.	GRCh37	2	26569221	26569221	+	Intron	SNP	C	C	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57+64C>G	.	.	ENST00000260585	.	16	9	6	11	11	0	GPR113,5_prime_UTR_variant,,ENST00000433584,;GPR113,5_prime_UTR_variant,,ENST00000541401,;GPR113,5_prime_UTR_variant,,ENST00000333478,;EPT1,intron_variant,,ENST00000447170,;EPT1,intron_variant,,ENST00000260585,;EPT1,intron_variant,,ENST00000442141,;EPT1,intron_variant,,ENST00000462301,;GPR113,upstream_gene_variant,,ENST00000481960,;GPR113,upstream_gene_variant,,ENST00000459892,;GPR113,upstream_gene_variant,,ENST00000487878,;GPR113,5_prime_UTR_variant,,ENST00000435303,;GPR113,5_prime_UTR_variant,,ENST00000447444,;	G	ENSG00000138018	ENST00000260585	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	EPT1	HGNC	29361	protein_coding	YES	CCDS46240.1	ENSP00000260585	EPT1_HUMAN	G1UI38_HUMAN,C9JEZ2_HUMAN,C9J9I1_HUMAN	UPI00003CE422	.	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCCGCGCG	.	5	ESCA
SLC8A1	0	.	GRCh37	2	40340833	40340833	+	3'Flank	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000403092	.	10	7	3	11	11	0	SLC8A1,3_prime_UTR_variant,,ENST00000542756,;SLC8A1,3_prime_UTR_variant,,ENST00000406785,;SLC8A1,downstream_gene_variant,,ENST00000408028,;SLC8A1,downstream_gene_variant,,ENST00000403092,;SLC8A1,downstream_gene_variant,,ENST00000405269,;SLC8A1,downstream_gene_variant,,ENST00000402441,;SLC8A1,downstream_gene_variant,,ENST00000542024,;SLC8A1,downstream_gene_variant,,ENST00000332839,;SLC8A1,downstream_gene_variant,,ENST00000406391,;SLC8A1,downstream_gene_variant,,ENST00000405901,;SLC8A1-AS1,intron_variant,,ENST00000599268,;SLC8A1-AS1,intron_variant,,ENST00000601679,;SLC8A1-AS1,intron_variant,,ENST00000599956,;SLC8A1-AS1,intron_variant,,ENST00000596532,;SLC8A1-AS1,intron_variant,,ENST00000597385,;SLC8A1-AS1,intron_variant,,ENST00000599740,;SLC8A1-AS1,intron_variant,,ENST00000597170,;SLC8A1-AS1,intron_variant,,ENST00000444629,;SLC8A1-AS1,intron_variant,,ENST00000593878,;SLC8A1-AS1,upstream_gene_variant,,ENST00000435515,;SLC8A1-AS1,upstream_gene_variant,,ENST00000598247,;SLC8A1-AS1,upstream_gene_variant,,ENST00000593848,;SLC8A1,downstream_gene_variant,,ENST00000407929,;	T	ENSG00000183023	ENST00000403092	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1338	-1	SLC8A1	HGNC	11068	protein_coding	YES	CCDS1806.1	ENSP00000384763	NAC1_HUMAN	Q6LAJ9_HUMAN,Q6LAJ8_HUMAN,Q4QQH3_HUMAN,E9PCL8_HUMAN,E9PB98_HUMAN	UPI000012FC46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTGCCAGAC	.	2	ESCA
SEMA4F	0	.	GRCh37	2	74902937	74902937	+	Missense_Mutation	SNP	G	G	A	rs778118707	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1544G>A	p.Arg515His	p.R515H	ENST00000357877	12/14	48	31	16	34	34	0	SEMA4F,missense_variant,p.Arg515His,ENST00000357877,;SEMA4F,missense_variant,p.Arg360His,ENST00000339773,;SEMA4F,downstream_gene_variant,,ENST00000453930,;SEMA4F,downstream_gene_variant,,ENST00000434486,;SEMA4F,non_coding_transcript_exon_variant,,ENST00000473350,;SEMA4F,3_prime_UTR_variant,,ENST00000420077,;SEMA4F,3_prime_UTR_variant,,ENST00000446927,;SEMA4F,downstream_gene_variant,,ENST00000458114,;	A	ENSG00000135622	ENST00000357877	Transcript	missense_variant	1693	1544	515	R/H	cGt/cAt	rs778118707,COSM1023096	.	.	1	SEMA4F	HGNC	10734	protein_coding	YES	CCDS1955.1	ENSP00000350547	SEM4F_HUMAN	.	UPI0000001BF5	.	tolerated(0.06)	probably_damaging(0.996)	12/14	.	Superfamily_domains:SSF103575,SMART_domains:SM00423,Gene3D:3.30.1680.10,Pfam_domain:PF01437,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF72	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGTCTCC	.	5	ESCA
RMND5A	0	.	GRCh37	2	86947764	86947764	+	5'UTR	SNP	G	G	A	rs530193703	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-27G>A	.	.	ENST00000283632	1/9	26	23	3	14	14	0	RMND5A,5_prime_UTR_variant,,ENST00000283632,;CHMP3,intron_variant,,ENST00000439940,;RNF103-CHMP3,intron_variant,,ENST00000604011,;	A	ENSG00000153561	ENST00000283632	Transcript	5_prime_UTR_variant	469	.	.	.	.	rs530193703	.	.	1	RMND5A	HGNC	25850	protein_coding	YES	CCDS1991.1	ENSP00000283632	RMD5A_HUMAN	B4DZV7_HUMAN	UPI000000DC2B	.	.	.	1/9	.	.	A:0.0058	A:0.0204	A:0.0029	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GCGCCGAGGAG	byFrequency|by1000G	2	ESCA
TOMM70A	0	.	GRCh37	3	100105093	100105093	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594G>A	p.%3D	p.E198E	ENST00000284320	3/12	109	85	24	56	56	0	TOMM70A,synonymous_variant,p.%3D,ENST00000284320,;TOMM70A,upstream_gene_variant,,ENST00000492171,;	T	ENSG00000154174	ENST00000284320	Transcript	synonymous_variant	1043	594	198	E	gaG/gaA	.	.	.	-1	TOMM70A	HGNC	11985	protein_coding	YES	CCDS33807.1	ENSP00000284320	TOM70_HUMAN	B4DZ87_HUMAN,B3KQK5_HUMAN,B3KQK0_HUMAN	UPI0000000C55	.	.	.	3/12	.	Superfamily_domains:SSF48452,SMART_domains:SM00028,Gene3D:1.25.40.10,hmmpanther:PTHR22904:SF178,hmmpanther:PTHR22904,PROSITE_profiles:PS50293	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTCTCATG	.	5	ESCA
ATP2B2	0	.	GRCh37	3	10377897	10377897	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3420+1963G>A	.	.	ENST00000360273	.	227	150	76	89	89	0	ATP2B2,intron_variant,,ENST00000343816,;ATP2B2,intron_variant,,ENST00000383800,;ATP2B2,intron_variant,,ENST00000397077,;ATP2B2,intron_variant,,ENST00000352432,;ATP2B2,intron_variant,,ENST00000360273,;ATP2B2,intron_variant,,ENST00000452124,;ATP2B2,non_coding_transcript_exon_variant,,ENST00000467702,;ATP2B2,upstream_gene_variant,,ENST00000468426,;ATP2B2,missense_variant,p.Val1125Ile,ENST00000460129,;	T	ENSG00000157087	ENST00000360273	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ATP2B2	HGNC	815	protein_coding	YES	CCDS33701.1	ENSP00000353414	AT2B2_HUMAN	Q4J699_HUMAN,Q4J696_HUMAN	UPI00001261EF	.	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTACATCCT	.	5	ESCA
ITGB5	0	.	GRCh37	3	124538659	124538659	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.965T>C	p.Leu322Pro	p.L322P	ENST00000296181	7/15	122	100	22	48	48	0	ITGB5,missense_variant,p.Leu119Pro,ENST00000496703,;ITGB5,missense_variant,p.Leu322Pro,ENST00000296181,;ITGB5,missense_variant,p.Leu57Pro,ENST00000481591,;ITGB5,intron_variant,,ENST00000488466,;ITGB5,non_coding_transcript_exon_variant,,ENST00000476988,;ITGB5,downstream_gene_variant,,ENST00000465464,;	G	ENSG00000082781	ENST00000296181	Transcript	missense_variant	1262	965	322	L/P	cTt/cCt	.	.	.	-1	ITGB5	HGNC	6160	protein_coding	YES	CCDS3030.1	ENSP00000296181	ITB5_HUMAN	L7RT22_HUMAN,D3DNA1_HUMAN	UPI000012DA10	.	deleterious(0)	probably_damaging(0.991)	7/15	.	hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF26,Pfam_domain:PF00362,Gene3D:3.40.50.410,PIRSF_domain:PIRSF002512,SMART_domains:SM00327,SMART_domains:SM00187,Superfamily_domains:SSF53300,Prints_domain:PR01186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCAAGCAAG	.	5	ESCA
MIR720	0	.	GRCh37	3	164059129	164059129	+	RNA	SNP	C	C	G	rs762466648	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1C>G	.	.	ENST00000408828	1/1	176	156	20	79	79	0	MIR720,non_coding_transcript_exon_variant,,ENST00000408828,;	G	ENSG00000221755	ENST00000408828	Transcript	non_coding_transcript_exon_variant	1	.	.	.	.	rs762466648	.	.	1	MIR720	HGNC	35375	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAGACCGGAT	.	4	ESCA
EIF5A2	0	.	GRCh37	3	170607524	170607524	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3625A>G	.	.	ENST00000295822	5/5	86	71	14	27	27	0	EIF5A2,3_prime_UTR_variant,,ENST00000295822,;EIF5A2,downstream_gene_variant,,ENST00000474096,;EIF5A2,downstream_gene_variant,,ENST00000474417,;EIF5A2,downstream_gene_variant,,ENST00000487522,;EIF5A2,downstream_gene_variant,,ENST00000460117,;	C	ENSG00000163577	ENST00000295822	Transcript	3_prime_UTR_variant	4273	.	.	.	.	.	.	.	-1	EIF5A2	HGNC	3301	protein_coding	YES	CCDS3214.1	ENSP00000295822	IF5A2_HUMAN	C9J4W5_HUMAN	UPI0000035FC3	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTATTATCCC	.	5	ESCA
NCEH1	0	.	GRCh37	3	172428680	172428680	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.191A>G	p.Lys64Arg	p.K64R	ENST00000538775	1/5	122	93	28	44	44	0	NCEH1,missense_variant,p.Lys64Arg,ENST00000538775,;NCEH1,missense_variant,p.Lys55Arg,ENST00000424772,;NCEH1,missense_variant,p.Lys32Arg,ENST00000475381,;NCEH1,missense_variant,p.Lys64Arg,ENST00000273512,;NCEH1,5_prime_UTR_variant,,ENST00000543711,;NCEH1,missense_variant,p.Lys64Arg,ENST00000421723,;	C	ENSG00000144959	ENST00000538775	Transcript	missense_variant	329	191	64	K/R	aAg/aGg	.	.	.	-1	NCEH1	HGNC	29260	protein_coding	YES	CCDS54682.1	ENSP00000442464	.	F5H7K4_HUMAN	UPI000199A4B7	.	tolerated(0.08)	benign(0.117)	1/5	.	PIRSF_domain:PIRSF037251,hmmpanther:PTHR23024:SF108,hmmpanther:PTHR23024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGCTTCCAG	.	5	ESCA
TTC14	0	.	GRCh37	3	180328087	180328087	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2070C>G	p.His690Gln	p.H690Q	ENST00000296015	12/12	71	57	13	43	43	0	TTC14,missense_variant,p.His690Gln,ENST00000296015,;TTC14,3_prime_UTR_variant,,ENST00000412756,;TTC14,intron_variant,,ENST00000382584,;CCDC39,intron_variant,,ENST00000489868,;CCDC39,intron_variant,,ENST00000473854,;CCDC39,downstream_gene_variant,,ENST00000273654,;CCDC39,downstream_gene_variant,,ENST00000442201,;TTC14,intron_variant,,ENST00000487397,;TTC14,downstream_gene_variant,,ENST00000465625,;TTC14,3_prime_UTR_variant,,ENST00000465065,;CCDC39,downstream_gene_variant,,ENST00000476379,;TTC14,downstream_gene_variant,,ENST00000470669,;	G	ENSG00000163728	ENST00000296015	Transcript	missense_variant	2202	2070	690	H/Q	caC/caG	.	.	.	1	TTC14	HGNC	24697	protein_coding	YES	CCDS3237.1	ENSP00000296015	TTC14_HUMAN	C9JBA2_HUMAN,C9J974_HUMAN	UPI00000720AE	.	tolerated_low_confidence(0.32)	unknown(0)	12/12	.	hmmpanther:PTHR23184:SF9,hmmpanther:PTHR23184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCACTCTGG	.	5	ESCA
LINC00693	0	.	GRCh37	3	28616545	28616545	+	RNA	SNP	C	C	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.264C>G	.	.	ENST00000432518	1/5	18	11	7	22	22	0	LINC00693,non_coding_transcript_exon_variant,,ENST00000432518,;LINC00693,upstream_gene_variant,,ENST00000443912,;LINC00693,upstream_gene_variant,,ENST00000445077,;	G	ENSG00000228214	ENST00000432518	Transcript	non_coding_transcript_exon_variant	264	.	.	.	.	.	.	.	1	LINC00693	HGNC	44526	antisense	YES	.	.	.	.	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCTATTT	.	5	ESCA
RBM5	0	.	GRCh37	3	50150892	50150892	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1532C>T	p.Ser511Phe	p.S511F	ENST00000347869	18/25	43	19	23	52	52	0	RBM5,missense_variant,p.Ser511Phe,ENST00000347869,;RP11-493K19.3,downstream_gene_variant,,ENST00000425674,;RP11-493K19.3,downstream_gene_variant,,ENST00000437204,;RBM5,non_coding_transcript_exon_variant,,ENST00000474470,;RBM5,non_coding_transcript_exon_variant,,ENST00000441812,;RBM5,non_coding_transcript_exon_variant,,ENST00000464087,;RBM5,non_coding_transcript_exon_variant,,ENST00000493993,;RBM5,non_coding_transcript_exon_variant,,ENST00000475128,;RBM5,downstream_gene_variant,,ENST00000489437,;RBM5,upstream_gene_variant,,ENST00000464988,;RBM5,downstream_gene_variant,,ENST00000494360,;RBM5,downstream_gene_variant,,ENST00000474818,;RBM5,upstream_gene_variant,,ENST00000492430,;RBM5,upstream_gene_variant,,ENST00000479275,;RBM5,upstream_gene_variant,,ENST00000461242,;RBM5,upstream_gene_variant,,ENST00000475590,;	T	ENSG00000003756	ENST00000347869	Transcript	missense_variant	1707	1532	511	S/F	tCt/tTt	.	.	.	1	RBM5	HGNC	9902	protein_coding	YES	CCDS2810.1	ENSP00000343054	RBM5_HUMAN	C9JR02_HUMAN,C9JFQ5_HUMAN,C9J9P7_HUMAN	UPI000013337C	.	deleterious(0.04)	benign(0.133)	18/25	.	hmmpanther:PTHR13948,hmmpanther:PTHR13948:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGTCTAGCT	.	5	ESCA
DCP1A	0	.	GRCh37	3	53326271	53326271	+	Missense_Mutation	SNP	T	T	C	rs375539952	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1211A>G	p.His404Arg	p.H404R	ENST00000607628	7/10	43	17	26	42	42	0	DCP1A,missense_variant,p.His366Arg,ENST00000606822,;DCP1A,missense_variant,p.His404Arg,ENST00000607628,;DCP1A,missense_variant,p.His404Arg,ENST00000294241,;RN7SL821P,downstream_gene_variant,,ENST00000579907,;Y_RNA,downstream_gene_variant,,ENST00000384175,;DCP1A,non_coding_transcript_exon_variant,,ENST00000480258,;DCP1A,non_coding_transcript_exon_variant,,ENST00000494659,;DCP1A,downstream_gene_variant,,ENST00000560624,;DCP1A,upstream_gene_variant,,ENST00000558034,;	C	ENSG00000162290	ENST00000607628	Transcript	missense_variant	1321	1211	404	H/R	cAt/cGt	rs375539952	.	.	-1	DCP1A	HGNC	18714	protein_coding	YES	.	ENSP00000475920	.	U3KQI9_HUMAN	UPI00001AEBBA	.	deleterious(0.03)	possibly_damaging(0.543)	7/10	.	hmmpanther:PTHR16290,hmmpanther:PTHR16290:SF2	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCATGCTGT	byCluster	5	ESCA
OR5H1	0	.	GRCh37	3	97851821	97851821	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280C>G	p.Leu94Val	p.L94V	ENST00000354565	1/1	124	105	19	73	73	0	OR5H1,missense_variant,p.Leu94Val,ENST00000354565,;RP11-343D2.11,intron_variant,,ENST00000508964,;	G	ENSG00000231192	ENST00000354565	Transcript	missense_variant	280	280	94	L/V	Ctc/Gtc	COSM3598242	.	.	1	OR5H1	HGNC	8346	protein_coding	YES	CCDS33797.1	ENSP00000346575	OR5H1_HUMAN	.	UPI0000197652	.	deleterious(0.02)	benign(0.027)	1/1	.	Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF135,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTCTCTCT	.	5	ESCA
FSTL5	0	.	GRCh37	4	162697208	162697208	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.428C>A	p.Thr143Asn	p.T143N	ENST00000306100	5/16	27	15	11	13	13	0	FSTL5,missense_variant,p.Thr142Asn,ENST00000379164,;FSTL5,missense_variant,p.Thr142Asn,ENST00000536695,;FSTL5,missense_variant,p.Thr142Asn,ENST00000427802,;FSTL5,missense_variant,p.Thr143Asn,ENST00000306100,;	T	ENSG00000168843	ENST00000306100	Transcript	missense_variant	865	428	143	T/N	aCt/aAt	COSM1539536	.	.	-1	FSTL5	HGNC	21386	protein_coding	YES	CCDS3802.1	ENSP00000305334	FSTL5_HUMAN	Q4W5Q0_HUMAN,Q4W5K3_HUMAN,Q4W5F8_HUMAN	UPI000020B66B	.	tolerated(0.2)	benign(0.001)	5/16	.	Gene3D:1.10.238.10,hmmpanther:PTHR10913:SF44,hmmpanther:PTHR10913	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCAGTAGTC	.	5	ESCA
FAM218A	0	.	GRCh37	4	165879138	165879138	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*490G>C	.	.	ENST00000513876	1/1	22	9	13	40	40	0	FAM218A,3_prime_UTR_variant,,ENST00000513876,;TRIM61,intron_variant,,ENST00000329314,;RP11-366M4.8,intron_variant,,ENST00000596751,;	C	ENSG00000250486	ENST00000513876	Transcript	3_prime_UTR_variant	1039	.	.	.	.	.	.	.	1	FAM218A	HGNC	26466	protein_coding	YES	CCDS3807.1	ENSP00000427428	F218A_HUMAN	.	UPI000006D0F5	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTGACTCT	.	5	ESCA
USP46	0	.	GRCh37	4	53494205	53494205	+	Silent	SNP	C	C	T	rs531415307	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.243G>A	p.%3D	p.A81A	ENST00000441222	3/9	81	58	22	67	67	0	USP46,synonymous_variant,p.%3D,ENST00000441222,;USP46,synonymous_variant,p.%3D,ENST00000508499,;USP46,synonymous_variant,p.%3D,ENST00000451218,;USP46,non_coding_transcript_exon_variant,,ENST00000506707,;USP46,downstream_gene_variant,,ENST00000504078,;USP46,3_prime_UTR_variant,,ENST00000503060,;USP46,3_prime_UTR_variant,,ENST00000514536,;USP46,non_coding_transcript_exon_variant,,ENST00000502443,;USP46,downstream_gene_variant,,ENST00000512656,;	T	ENSG00000109189	ENST00000441222	Transcript	synonymous_variant	428	243	81	A	gcG/gcA	rs531415307	.	.	-1	USP46	HGNC	20075	protein_coding	YES	CCDS47053.1	ENSP00000407818	UBP46_HUMAN	.	UPI0000006C18	.	.	.	3/9	.	Superfamily_domains:SSF54001,Pfam_domain:PF00443,hmmpanther:PTHR24619:SF120,hmmpanther:PTHR24619,PROSITE_profiles:PS50235	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTCCGCCAG	by1000G	5	ESCA
ADRB2	0	.	GRCh37	5	148207663	148207664	+	3'UTR	INS	-	-	T	rs756837704	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*27_*28insT	.	.	ENST00000305988	1/1	168	95	73	49	49	0	ADRB2,3_prime_UTR_variant,,ENST00000305988,;	T	ENSG00000169252	ENST00000305988	Transcript	3_prime_UTR_variant	1508-1509	.	.	.	.	rs756837704	.	.	1	ADRB2	HGNC	286	protein_coding	YES	CCDS4292.1	ENSP00000305372	ADRB2_HUMAN	Q9BYZ0_HUMAN	UPI000013EAD0	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	VARSCANI*|PINDEL	GACCCCCCCCC	.	2	ESCA
SYNPO	0	.	GRCh37	5	150031524	150031524	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1629C>A	.	.	ENST00000394243	3/3	17	12	5	17	17	0	SYNPO,3_prime_UTR_variant,,ENST00000519664,;SYNPO,3_prime_UTR_variant,,ENST00000394243,;SYNPO,3_prime_UTR_variant,,ENST00000522122,;SYNPO,intron_variant,,ENST00000307662,;SYNPO,downstream_gene_variant,,ENST00000518872,;	A	ENSG00000171992	ENST00000394243	Transcript	3_prime_UTR_variant	4793	.	.	.	.	.	.	.	1	SYNPO	HGNC	30672	protein_coding	YES	CCDS54937.1	ENSP00000377789	SYNPO_HUMAN	Q71HJ6_HUMAN	UPI000013F943	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCACCCACTT	.	5	ESCA
ERBB2IP	0	.	GRCh37	5	65349797	65349797	+	Missense_Mutation	SNP	A	A	G	rs747561237	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2651A>G	p.Tyr884Cys	p.Y884C	ENST00000506030	21/26	40	25	14	39	39	0	ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000380935,;ERBB2IP,missense_variant,p.Tyr880Cys,ENST00000511297,;ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000284037,;ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000508515,;ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000380943,;ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000380938,;ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000380936,;ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000506030,;ERBB2IP,missense_variant,p.Tyr884Cys,ENST00000380939,;ERBB2IP,intron_variant,,ENST00000416865,;ERBB2IP,upstream_gene_variant,,ENST00000511671,;ERBB2IP,upstream_gene_variant,,ENST00000503913,;	G	ENSG00000112851	ENST00000506030	Transcript	missense_variant	2742	2651	884	Y/C	tAt/tGt	rs747561237	.	.	1	ERBB2IP	HGNC	15842	protein_coding	YES	CCDS58952.1	ENSP00000426632	LAP2_HUMAN	.	UPI0001D3B314	.	deleterious(0.02)	benign(0.004)	21/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCTATGATA	byFrequency	5	ESCA
SLC30A5	0	.	GRCh37	5	68423939	68423939	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2107G>C	p.Glu703Gln	p.E703Q	ENST00000396591	15/16	47	37	10	62	62	0	SLC30A5,missense_variant,p.Glu703Gln,ENST00000396591,;SLC30A5,intron_variant,,ENST00000511158,;CTC-498J12.3,splice_region_variant,,ENST00000504129,;SLC30A5,downstream_gene_variant,,ENST00000513937,;SLC30A5,downstream_gene_variant,,ENST00000507354,;	C	ENSG00000145740	ENST00000396591	Transcript	missense_variant	2717	2107	703	E/Q	Gaa/Caa	.	.	.	1	SLC30A5	HGNC	19089	protein_coding	YES	CCDS3996.1	ENSP00000379836	ZNT5_HUMAN	Q9H9X0_HUMAN,Q9BY48_HUMAN,Q9BTR6_HUMAN	UPI0000073958	.	deleterious(0.03)	possibly_damaging(0.868)	15/16	.	hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF24,Pfam_domain:PF01545,TIGRFAM_domain:TIGR01297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTAGAACAA	.	5	ESCA
MAP1B	0	.	GRCh37	5	71493451	71493451	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4269A>T	p.Arg1423Ser	p.R1423S	ENST00000296755	5/7	17	12	4	42	42	0	MAP1B,missense_variant,p.Arg1423Ser,ENST00000296755,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000513526,;	T	ENSG00000131711	ENST00000296755	Transcript	missense_variant	4567	4269	1423	R/S	agA/agT	.	.	.	1	MAP1B	HGNC	6836	protein_coding	YES	CCDS4012.1	ENSP00000296755	MAP1B_HUMAN	D6RGJ3_HUMAN,D6RA40_HUMAN	UPI000013E382	.	.	possibly_damaging(0.787)	5/7	.	hmmpanther:PTHR13843,hmmpanther:PTHR13843:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GGCAGAGGTGC	.	4	ESCA
RBM24	0	.	GRCh37	6	17292224	17292224	+	Silent	SNP	C	C	T	rs745754217	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.585C>T	p.%3D	p.Y195Y	ENST00000379052	4/4	31	22	8	30	30	0	RBM24,synonymous_variant,p.%3D,ENST00000379052,;RBM24,synonymous_variant,p.%3D,ENST00000503965,;RBM24,synonymous_variant,p.%3D,ENST00000318204,;RBM24,synonymous_variant,p.%3D,ENST00000425446,;RBM24,3_prime_UTR_variant,,ENST00000509686,;RBM24,non_coding_transcript_exon_variant,,ENST00000504055,;RBM24,non_coding_transcript_exon_variant,,ENST00000508508,;RBM24,non_coding_transcript_exon_variant,,ENST00000510826,;	T	ENSG00000112183	ENST00000379052	Transcript	synonymous_variant	821	585	195	Y	taC/taT	rs745754217,COSM1131970	.	.	1	RBM24	HGNC	21539	protein_coding	YES	CCDS47378.1	ENSP00000368341	RBM24_HUMAN	A8KAI7_HUMAN	UPI000006E912	.	.	.	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24011,hmmpanther:PTHR24011:SF249	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Y150C|c.449A>G|3,BUFFER|p.Y195C|c.584A>G|3	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTACGCAGT	byFrequency|byCluster	4	ESCA
SCUBE3	0	.	GRCh37	6	35205712	35205712	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.746G>A	p.Ser249Asn	p.S249N	ENST00000274938	7/22	59	40	19	76	76	0	SCUBE3,missense_variant,p.Ser265Asn,ENST00000394681,;SCUBE3,missense_variant,p.Ser249Asn,ENST00000274938,;	A	ENSG00000146197	ENST00000274938	Transcript	missense_variant	746	746	249	S/N	aGt/aAt	COSM3873419,COSM3873420	.	.	1	SCUBE3	HGNC	13655	protein_coding	YES	CCDS4800.1	ENSP00000274938	SCUB3_HUMAN	Q7Z3I8_HUMAN	UPI0000074423	.	deleterious(0.01)	benign(0.334)	7/22	.	hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF2,Pfam_domain:PF14670,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACAGTAAGT	.	5	ESCA
GUCA1B	0	.	GRCh37	6	42153445	42153445	+	Missense_Mutation	SNP	A	A	G	rs767596914	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448T>C	p.Phe150Leu	p.F150L	ENST00000230361	3/4	25	21	4	32	32	0	GUCA1B,missense_variant,p.Phe150Leu,ENST00000230361,;	G	ENSG00000112599	ENST00000230361	Transcript	missense_variant	544	448	150	F/L	Ttc/Ctc	rs767596914	.	.	-1	GUCA1B	HGNC	4679	protein_coding	YES	CCDS4865.1	ENSP00000230361	GUC1B_HUMAN	.	UPI000013C92C	.	tolerated(0.13)	possibly_damaging(0.614)	3/4	.	PROSITE_profiles:PS50222,hmmpanther:PTHR23055:SF11,hmmpanther:PTHR23055,Pfam_domain:PF13499,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGGAAGATCC	.	3	ESCA
RUNX2	0	.	GRCh37	6	45514591	45514591	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1115A>T	p.Asp372Val	p.D372V	ENST00000371438	8/8	41	28	13	30	30	0	RUNX2,missense_variant,p.Asp358Val,ENST00000359524,;RUNX2,missense_variant,p.Asp440Val,ENST00000352853,;RUNX2,missense_variant,p.Asp418Val,ENST00000541979,;RUNX2,missense_variant,p.Asp350Val,ENST00000371436,;RUNX2,missense_variant,p.Asp372Val,ENST00000465038,;RUNX2,missense_variant,p.Asp372Val,ENST00000371438,;RUNX2,missense_variant,p.Asp336Val,ENST00000371432,;RUNX2,intron_variant,,ENST00000576263,;RUNX2,3_prime_UTR_variant,,ENST00000483377,;RUNX2,intron_variant,,ENST00000478660,;	T	ENSG00000124813	ENST00000371438	Transcript	missense_variant	1473	1115	372	D/V	gAc/gTc	.	.	.	1	RUNX2	HGNC	10472	protein_coding	YES	CCDS43467.2	ENSP00000360493	RUNX2_HUMAN	U3RG86_HUMAN	UPI000013532F	.	deleterious(0.01)	probably_damaging(0.998)	8/8	.	hmmpanther:PTHR11950:SF7,hmmpanther:PTHR11950,Gene3D:1b8xA03,PIRSF_domain:PIRSF009374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCAGACCCCA	.	5	ESCA
ENPP4	0	.	GRCh37	6	46107802	46107802	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482A>G	p.Glu161Gly	p.E161G	ENST00000321037	2/4	27	22	5	24	24	0	ENPP4,missense_variant,p.Glu161Gly,ENST00000321037,;	G	ENSG00000001561	ENST00000321037	Transcript	missense_variant	712	482	161	E/G	gAg/gGg	.	.	.	1	ENPP4	HGNC	3359	protein_coding	YES	CCDS34468.1	ENSP00000318066	ENPP4_HUMAN	.	UPI0000048E43	.	tolerated(0.07)	benign(0.014)	2/4	.	hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF16,Gene3D:3.40.720.10,Pfam_domain:PF01663,Superfamily_domains:SSF53649	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTGAGGAAA	.	5	ESCA
DST	0	.	GRCh37	6	56323408	56323408	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*395T>C	.	.	ENST00000244364	84/84	25	21	4	27	27	0	DST,3_prime_UTR_variant,,ENST00000446842,;DST,3_prime_UTR_variant,,ENST00000370788,;DST,3_prime_UTR_variant,,ENST00000244364,;DST,3_prime_UTR_variant,,ENST00000370754,;DST,3_prime_UTR_variant,,ENST00000370769,;DST,3_prime_UTR_variant,,ENST00000312431,;DST,3_prime_UTR_variant,,ENST00000523292,;DST,3_prime_UTR_variant,,ENST00000421834,;DST,downstream_gene_variant,,ENST00000361203,;DST,downstream_gene_variant,,ENST00000523597,;DST,non_coding_transcript_exon_variant,,ENST00000466429,;DST,non_coding_transcript_exon_variant,,ENST00000482156,;DST,non_coding_transcript_exon_variant,,ENST00000518464,;	G	ENSG00000151914	ENST00000244364	Transcript	3_prime_UTR_variant	16119	.	.	.	.	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	.	84/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATGTATCATT	.	2	ESCA
FUT9	0	.	GRCh37	6	96654285	96654285	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2174A>T	.	.	ENST00000302103	3/3	32	26	6	50	50	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	T	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	3580	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGCATAGAG	.	5	ESCA
SAP25	0	.	GRCh37	7	100169908	100169908	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2C>T	.	.	ENST00000538735	6/6	49	31	18	50	50	0	SAP25,3_prime_UTR_variant,,ENST00000538735,;LRCH4,downstream_gene_variant,,ENST00000310300,;LRCH4,downstream_gene_variant,,ENST00000497245,;LRCH4,downstream_gene_variant,,ENST00000485554,;AGFG2,downstream_gene_variant,,ENST00000300176,;LRCH4,non_coding_transcript_exon_variant,,ENST00000485071,;LRCH4,downstream_gene_variant,,ENST00000498539,;LRCH4,downstream_gene_variant,,ENST00000476881,;LRCH4,downstream_gene_variant,,ENST00000467201,;LRCH4,downstream_gene_variant,,ENST00000490359,;RP11-44M6.3,downstream_gene_variant,,ENST00000223076,;	A	ENSG00000205307	ENST00000538735	Transcript	3_prime_UTR_variant	780	.	.	.	.	.	.	.	-1	SAP25	HGNC	41908	protein_coding	YES	CCDS55137.1	ENSP00000442339	SAP25_HUMAN	.	UPI0000034E0E	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAAGGCTAT	.	5	ESCA
MUC17	0	.	GRCh37	7	100677696	100677696	+	Missense_Mutation	SNP	C	C	T	rs758069810	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000306151	3/13	86	77	9	98	96	2	MUC17,missense_variant,p.Ala1000Val,ENST00000306151,;MUC17,missense_variant,p.Ala1000Val,ENST00000379439,;	T	ENSG00000169876	ENST00000306151	Transcript	missense_variant	3063	2999	1000	A/V	gCt/gTt	rs758069810	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	probably_damaging(0.97)	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TGAGGCTAGCA	byFrequency	2	ESCA
FOXP2	0	.	GRCh37	7	114331013	114331013	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1032G>C	.	.	ENST00000408937	18/18	18	11	6	14	14	0	FOXP2,3_prime_UTR_variant,,ENST00000408937,;FOXP2,3_prime_UTR_variant,,ENST00000403559,;FOXP2,downstream_gene_variant,,ENST00000393489,;FOXP2,downstream_gene_variant,,ENST00000393498,;FOXP2,downstream_gene_variant,,ENST00000393491,;FOXP2,downstream_gene_variant,,ENST00000393494,;FOXP2,downstream_gene_variant,,ENST00000350908,;FOXP2,downstream_gene_variant,,ENST00000412402,;	C	ENSG00000128573	ENST00000408937	Transcript	3_prime_UTR_variant	3629	.	.	.	.	.	.	.	1	FOXP2	HGNC	13875	protein_coding	YES	CCDS43635.1	ENSP00000386200	FOXP2_HUMAN	.	UPI000007412B	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACAGAGTAA	.	5	ESCA
POLD2	0	.	GRCh37	7	44161677	44161677	+	5'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25G>A	.	.	ENST00000406581	3/12	26	19	7	33	33	0	POLD2,5_prime_UTR_variant,,ENST00000406581,;POLD2,5_prime_UTR_variant,,ENST00000223361,;POLD2,5_prime_UTR_variant,,ENST00000433715,;POLD2,5_prime_UTR_variant,,ENST00000456038,;POLD2,5_prime_UTR_variant,,ENST00000452185,;POLD2,5_prime_UTR_variant,,ENST00000418438,;POLD2,5_prime_UTR_variant,,ENST00000436844,;RNA5SP230,downstream_gene_variant,,ENST00000517039,;POLD2,downstream_gene_variant,,ENST00000481763,;POLD2,non_coding_transcript_exon_variant,,ENST00000463464,;POLD2,non_coding_transcript_exon_variant,,ENST00000496539,;POLD2,non_coding_transcript_exon_variant,,ENST00000470867,;POLD2,upstream_gene_variant,,ENST00000481104,;POLD2,upstream_gene_variant,,ENST00000467469,;POLD2,upstream_gene_variant,,ENST00000461116,;POLD2,upstream_gene_variant,,ENST00000464871,;	T	ENSG00000106628	ENST00000406581	Transcript	5_prime_UTR_variant	626	.	.	.	.	.	.	.	-1	POLD2	HGNC	9176	protein_coding	YES	CCDS5477.1	ENSP00000386105	DPOD2_HUMAN	C9JLE1_HUMAN,C9J8Z7_HUMAN,C9IZD2_HUMAN,A4D2J4_HUMAN	UPI000004D0E7	.	.	.	3/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGTCCACAC	.	5	ESCA
NXPH1	0	.	GRCh37	7	8791929	8791929	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*530A>C	.	.	ENST00000405863	3/3	20	11	8	18	18	0	NXPH1,3_prime_UTR_variant,,ENST00000405863,;NXPH1,downstream_gene_variant,,ENST00000602349,;NXPH1,downstream_gene_variant,,ENST00000429542,;NXPH1,downstream_gene_variant,,ENST00000438764,;NXPH1,downstream_gene_variant,,ENST00000497400,;	C	ENSG00000122584	ENST00000405863	Transcript	3_prime_UTR_variant	2257	.	.	.	.	.	.	.	1	NXPH1	HGNC	20693	protein_coding	YES	CCDS47540.1	ENSP00000384551	NXPH1_HUMAN	Q3LID8_HUMAN,C9JPD0_HUMAN,C9JE46_HUMAN,B4DJV1_HUMAN	UPI000000DC02	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAATGTGT	.	5	ESCA
TRRAP	0	.	GRCh37	7	98579513	98579513	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8735G>A	p.Ser2912Asn	p.S2912N	ENST00000359863	58/72	37	33	4	23	23	0	TRRAP,missense_variant,p.Ser2894Asn,ENST00000355540,;TRRAP,missense_variant,p.Ser2894Asn,ENST00000446306,;TRRAP,missense_variant,p.Ser2634Asn,ENST00000456197,;TRRAP,missense_variant,p.Ser2912Asn,ENST00000359863,;TRRAP,downstream_gene_variant,,ENST00000480695,;	A	ENSG00000196367	ENST00000359863	Transcript	missense_variant	8944	8735	2912	S/N	aGc/aAc	.	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	probably_damaging(0.975)	58/72	.	PROSITE_profiles:PS51189,hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139,Pfam_domain:PF02259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCAGCAGCC	.	4	ESCA
RGS22	0	.	GRCh37	8	101018284	101018284	+	Silent	SNP	T	T	A	rs757163591	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2415A>T	p.%3D	p.L805L	ENST00000360863	16/28	34	30	4	26	26	0	RGS22,synonymous_variant,p.%3D,ENST00000523287,;RGS22,synonymous_variant,p.%3D,ENST00000523437,;RGS22,synonymous_variant,p.%3D,ENST00000517828,;RGS22,synonymous_variant,p.%3D,ENST00000360863,;SNORD77,downstream_gene_variant,,ENST00000391112,;RGS22,non_coding_transcript_exon_variant,,ENST00000519421,;RGS22,non_coding_transcript_exon_variant,,ENST00000517769,;RGS22,downstream_gene_variant,,ENST00000519725,;	A	ENSG00000132554	ENST00000360863	Transcript	synonymous_variant	2610	2415	805	L	ctA/ctT	rs757163591	.	.	-1	RGS22	HGNC	24499	protein_coding	YES	CCDS43758.1	ENSP00000354109	RGS22_HUMAN	E5RHE4_HUMAN,E5RFV6_HUMAN	UPI0000E5AF25	.	.	.	16/28	.	hmmpanther:PTHR10845:SF132,hmmpanther:PTHR10845	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTGTAGCTT	byCluster	2	ESCA
PKHD1L1	0	.	GRCh37	8	110492355	110492355	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9314A>C	p.Tyr3105Ser	p.Y3105S	ENST00000378402	55/78	24	18	6	26	26	0	PKHD1L1,missense_variant,p.Tyr3105Ser,ENST00000378402,;PKHD1L1,upstream_gene_variant,,ENST00000526472,;	C	ENSG00000205038	ENST00000378402	Transcript	missense_variant	9418	9314	3105	Y/S	tAc/tCc	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	deleterious(0)	benign(0.428)	55/78	.	PROSITE_profiles:PS51484,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF213,Pfam_domain:PF10162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCTACATAT	.	2	ESCA
TRPS1	0	.	GRCh37	8	116616240	116616240	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1956C>T	p.%3D	p.S652S	ENST00000395715	4/7	75	38	37	48	47	1	TRPS1,synonymous_variant,p.%3D,ENST00000520276,;TRPS1,synonymous_variant,p.%3D,ENST00000220888,;TRPS1,synonymous_variant,p.%3D,ENST00000517323,;TRPS1,synonymous_variant,p.%3D,ENST00000519076,;TRPS1,synonymous_variant,p.%3D,ENST00000395715,;TRPS1,synonymous_variant,p.%3D,ENST00000519674,;	A	ENSG00000104447	ENST00000395715	Transcript	synonymous_variant	2534	1956	652	S	tcC/tcT	.	.	.	-1	TRPS1	HGNC	12340	protein_coding	YES	CCDS6318.2	ENSP00000379065	TRPS1_HUMAN	F8W8T0_HUMAN,E7EVN4_HUMAN,C9J6L7_HUMAN	UPI00002104B8	.	.	.	4/7	.	hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCTTGGGACTC	.	4	ESCA
ADAM3A	0	.	GRCh37	8	39356919	39356919	+	RNA	SNP	A	A	G	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.494T>C	.	.	ENST00000484602	6/10	118	91	26	56	55	0	ADAM3A,non_coding_transcript_exon_variant,,ENST00000490268,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000495171,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000460383,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000484602,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000497806,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000481351,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000424066,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000474764,;ADAM3A,non_coding_transcript_exon_variant,,ENST00000461344,;	G	ENSG00000197475	ENST00000484602	Transcript	non_coding_transcript_exon_variant	494	.	.	.	.	.	.	.	-1	ADAM3A	HGNC	209	processed_transcript	YES	.	.	.	.	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGTAGAATG	.	5	ESCA
RAB2A	0	.	GRCh37	8	61496838	61496838	+	Silent	SNP	C	C	T	rs759231678	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258C>T	p.%3D	p.Y86Y	ENST00000262646	4/8	63	34	29	70	70	0	RAB2A,synonymous_variant,p.%3D,ENST00000529579,;RAB2A,synonymous_variant,p.%3D,ENST00000531289,;RAB2A,synonymous_variant,p.%3D,ENST00000262646,;RAB2A,upstream_gene_variant,,ENST00000452437,;RAB2A,non_coding_transcript_exon_variant,,ENST00000530071,;RAB2A,stop_gained,p.Arg103Ter,ENST00000466595,;RAB2A,3_prime_UTR_variant,,ENST00000534260,;RAB2A,non_coding_transcript_exon_variant,,ENST00000525529,;RAB2A,non_coding_transcript_exon_variant,,ENST00000429861,;	T	ENSG00000104388	ENST00000262646	Transcript	synonymous_variant	609	258	86	Y	taC/taT	rs759231678	.	.	1	RAB2A	HGNC	9763	protein_coding	YES	CCDS6175.1	ENSP00000262646	RAB2A_HUMAN	.	UPI0000133168	.	.	.	4/8	.	Superfamily_domains:SSF52540,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00176,SMART_domains:SM00175,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF359,PROSITE_profiles:PS51419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTACGATAT	byFrequency	5	ESCA
PHYHD1	0	.	GRCh37	9	131702968	131702968	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.655T>C	p.Ser219Pro	p.S219P	ENST00000308941	10/12	65	19	46	69	69	0	PHYHD1,missense_variant,p.Leu205Pro,ENST00000421063,;PHYHD1,missense_variant,p.Ser219Pro,ENST00000308941,;PHYHD1,missense_variant,p.Leu226Pro,ENST00000372592,;PHYHD1,missense_variant,p.Leu205Pro,ENST00000353176,;PHYHD1,intron_variant,,ENST00000419872,;PHYHD1,intron_variant,,ENST00000442837,;DOLK,downstream_gene_variant,,ENST00000372586,;RP11-101E3.5,upstream_gene_variant,,ENST00000482796,;PHYHD1,downstream_gene_variant,,ENST00000426694,;PHYHD1,non_coding_transcript_exon_variant,,ENST00000487504,;PHYHD1,3_prime_UTR_variant,,ENST00000424503,;PHYHD1,3_prime_UTR_variant,,ENST00000412476,;PHYHD1,downstream_gene_variant,,ENST00000451000,;	C	ENSG00000175287	ENST00000308941	Transcript	missense_variant	1075	655	219	S/P	Tct/Cct	.	.	.	1	PHYHD1	HGNC	23396	protein_coding	YES	CCDS6914.1	ENSP00000309515	PHYD1_HUMAN	.	UPI0000140899	.	deleterious_low_confidence(0.01)	benign(0.001)	10/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCTCTTTG	.	5	ESCA
PRKACG	0	.	GRCh37	9	71629038	71629039	+	5'UTR	INS	-	-	GCGGCGGCG	rs752732570	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-31_-30insCGCCGCCGC	.	.	ENST00000377276	1/1	16	8	8	11	10	0	PRKACG,5_prime_UTR_variant,,ENST00000377276,;PIP5K1B,downstream_gene_variant,,ENST00000265382,;PIP5K1B,downstream_gene_variant,,ENST00000478500,;	GCGGCGGCG	ENSG00000165059	ENST00000377276	Transcript	5_prime_UTR_variant	1-2	.	.	.	.	rs752732570	.	.	-1	PRKACG	HGNC	9382	protein_coding	YES	CCDS6625.1	ENSP00000366488	KAPCG_HUMAN	.	UPI000013E448	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGTCTCGCGGC	byCluster	2	ESCA
SPATA31D1	0	.	GRCh37	9	84606906	84606906	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1521C>T	p.%3D	p.L507L	ENST00000344803	4/4	164	139	25	83	83	0	SPATA31D1,synonymous_variant,p.%3D,ENST00000344803,;SPATA31D1,downstream_gene_variant,,ENST00000603921,;	T	ENSG00000214929	ENST00000344803	Transcript	synonymous_variant	1568	1521	507	L	ctC/ctT	.	.	.	1	SPATA31D1	HGNC	37283	protein_coding	YES	CCDS47986.1	ENSP00000341988	S31D1_HUMAN	.	UPI00001C10A6	.	.	.	4/4	.	hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859,Pfam_domain:PF14650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCTCCCATC	.	4	ESCA
DOCK11	0	.	GRCh37	X	117819759	117819759	+	Missense_Mutation	SNP	G	G	A	rs766718965	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6211G>A	p.Ala2071Thr	p.A2071T	ENST00000276202	53/53	27	7	20	32	32	0	DOCK11,missense_variant,p.Ala2075Thr,ENST00000276204,;DOCK11,missense_variant,p.Ala2071Thr,ENST00000276202,;	A	ENSG00000147251	ENST00000276202	Transcript	missense_variant	6274	6211	2071	A/T	Gct/Act	rs766718965	.	.	1	DOCK11	HGNC	23483	protein_coding	YES	CCDS35373.1	ENSP00000276202	DOC11_HUMAN	B3KNP4_HUMAN	UPI000022DB8F	.	tolerated_low_confidence(0.11)	benign(0)	53/53	.	hmmpanther:PTHR23317:SF81,hmmpanther:PTHR23317	A:0.0003	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATACGCTGAA	byCluster|by1000G	5	ESCA
CXorf64	0	.	GRCh37	X	125954650	125954650	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29G>A	p.Gly10Glu	p.G10E	ENST00000371125	2/2	30	9	21	22	21	0	CXorf64,missense_variant,p.Gly10Glu,ENST00000371125,;	A	ENSG00000183631	ENST00000371125	Transcript	missense_variant	109	29	10	G/E	gGg/gAg	.	.	.	1	CXorf64	HGNC	34498	protein_coding	YES	CCDS48163.1	ENSP00000360166	CX064_HUMAN	.	UPI00004A3B00	.	tolerated(0.2)	benign(0.037)	2/2	.	Pfam_domain:PF15488	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAGGGCACG	.	5	ESCA
APEX2	0	.	GRCh37	X	55030234	55030234	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572A>T	p.His191Leu	p.H191L	ENST00000374987	5/6	18	4	14	23	23	0	APEX2,missense_variant,p.His191Leu,ENST00000374987,;APEX2,splice_region_variant,,ENST00000471758,;	T	ENSG00000169188	ENST00000374987	Transcript	missense_variant	638	572	191	H/L	cAt/cTt	.	.	.	1	APEX2	HGNC	17889	protein_coding	YES	CCDS14365.1	ENSP00000364126	APEX2_HUMAN	E5KN95_HUMAN,B7ZA71_HUMAN	UPI0000071F5B	.	deleterious(0)	possibly_damaging(0.886)	5/6	.	PROSITE_profiles:PS51435,hmmpanther:PTHR22748:SF4,hmmpanther:PTHR22748,Pfam_domain:PF03372,TIGRFAM_domain:TIGR00633,Gene3D:3.60.10.10,Superfamily_domains:SSF56219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCCATGTGA	.	5	ESCA
ZXDB	0	.	GRCh37	X	57620063	57620063	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8ER-01A-11D-A36J-09	TCGA-VR-A8ER-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1582C>T	p.Arg528Cys	p.R528C	ENST00000374888	1/1	27	10	16	26	26	0	ZXDB,missense_variant,p.Arg528Cys,ENST00000374888,;	T	ENSG00000198455	ENST00000374888	Transcript	missense_variant	1795	1582	528	R/C	Cgc/Tgc	.	.	.	1	ZXDB	HGNC	13199	protein_coding	YES	CCDS35313.1	ENSP00000364023	ZXDB_HUMAN	.	UPI000013C495	.	deleterious(0)	probably_damaging(0.962)	1/1	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR19818:SF72,hmmpanther:PTHR19818,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTCGCAGT	.	5	ESCA
A1CF	0	.	GRCh37	10	52595965	52595965	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.497delA	p.Lys166ArgfsTer56	p.K166Rfs*56	ENST00000373995	6/13	40	36	4	50	50	0	A1CF,frameshift_variant,p.Lys158ArgfsTer?,ENST00000414883,;A1CF,frameshift_variant,p.Lys158ArgfsTer56,ENST00000373993,;A1CF,frameshift_variant,p.Lys158ArgfsTer56,ENST00000282641,;A1CF,frameshift_variant,p.Lys158ArgfsTer50,ENST00000395495,;A1CF,frameshift_variant,p.Lys158ArgfsTer56,ENST00000374001,;A1CF,frameshift_variant,p.Lys166ArgfsTer56,ENST00000373995,;A1CF,frameshift_variant,p.Lys158ArgfsTer56,ENST00000373997,;A1CF,frameshift_variant,p.Lys151ArgfsTer56,ENST00000395489,;A1CF,non_coding_transcript_exon_variant,,ENST00000473480,;	-	ENSG00000148584	ENST00000373995	Transcript	frameshift_variant	756	497	166	K/X	aAg/ag	.	.	.	-1	A1CF	HGNC	24086	protein_coding	YES	CCDS7243.1	ENSP00000363107	A1CF_HUMAN	.	UPI000013DB32	.	.	.	6/13	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF313,TIGRFAM_domain:TIGR01648,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GTAACCTTTTTC	.	2	ESCA
MYO7A	0	.	GRCh37	11	76917248	76917248	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5742+1G>A	.	p.X1914_splice	ENST00000409709	.	29	25	3	61	61	0	MYO7A,splice_donor_variant,,ENST00000458169,;MYO7A,splice_donor_variant,,ENST00000409619,;MYO7A,splice_donor_variant,,ENST00000409709,;MYO7A,splice_donor_variant,,ENST00000458637,;MYO7A,splice_donor_variant,,ENST00000605744,;MYO7A,upstream_gene_variant,,ENST00000526863,;MYO7A,splice_donor_variant,,ENST00000481328,;	A	ENSG00000137474	ENST00000409709	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	MYO7A	HGNC	7606	protein_coding	YES	CCDS53683.1	ENSP00000386331	MYO7A_HUMAN	.	UPI00001FAFE6	.	.	.	.	41/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACGAGGTGAGG	.	3	ESCA
CCDC89	0	.	GRCh37	11	85396000	85396000	+	3'UTR	SNP	C	C	T	rs532847383	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*49G>A	.	.	ENST00000316398	1/1	38	31	6	38	38	0	CCDC89,3_prime_UTR_variant,,ENST00000316398,;CREBZF,upstream_gene_variant,,ENST00000534224,;CREBZF,upstream_gene_variant,,ENST00000531515,;	T	ENSG00000179071	ENST00000316398	Transcript	3_prime_UTR_variant	1321	.	.	.	.	rs532847383	.	.	-1	CCDC89	HGNC	26762	protein_coding	YES	CCDS8270.1	ENSP00000320649	CCD89_HUMAN	.	UPI000000DAB1	.	.	.	1/1	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGACGCAAA	by1000G	5	ESCA
SLITRK1	0	.	GRCh37	13	84453964	84453964	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1679C>T	p.Thr560Met	p.T560M	ENST00000377084	1/1	20	16	4	22	22	0	SLITRK1,missense_variant,p.Thr560Met,ENST00000377084,;	A	ENSG00000178235	ENST00000377084	Transcript	missense_variant	2565	1679	560	T/M	aCg/aTg	COSM164461	.	.	-1	SLITRK1	HGNC	20297	protein_coding	YES	CCDS9464.1	ENSP00000366288	SLIK1_HUMAN	.	UPI0000035971	.	deleterious(0.02)	benign(0.035)	1/1	.	hmmpanther:PTHR24373:SF33,hmmpanther:PTHR24373,Gene3D:3.80.10.10,SMART_domains:SM00082,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.T560M|c.1679C>T|4	RADIA|MUTECT|MUSE|VARSCANS	CCGGCGTCTCA	.	4	ESCA
ZNF609	0	.	GRCh37	15	64966761	64966761	+	Nonsense_Mutation	SNP	C	C	T	rs770815906	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1708C>T	p.Arg570Ter	p.R570*	ENST00000326648	4/9	22	19	3	23	23	0	ZNF609,stop_gained,p.Arg570Ter,ENST00000326648,;RNU6-549P,downstream_gene_variant,,ENST00000384433,;ZNF609,non_coding_transcript_exon_variant,,ENST00000559364,;ZNF609,downstream_gene_variant,,ENST00000558680,;	T	ENSG00000180357	ENST00000326648	Transcript	stop_gained	1836	1708	570	R/*	Cga/Tga	rs770815906,COSM963958	.	.	1	ZNF609	HGNC	29003	protein_coding	YES	CCDS32270.1	ENSP00000316527	ZN609_HUMAN	.	UPI00001D7783	.	.	.	4/9	.	hmmpanther:PTHR21564,hmmpanther:PTHR21564:SF3	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTTCGACTT	.	2	ESCA
IFT140	0	.	GRCh37	16	1570144	1570144	+	Silent	SNP	G	G	A	rs143899594	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3861C>T	p.%3D	p.D1287D	ENST00000426508	28/31	43	34	9	67	67	0	IFT140,synonymous_variant,p.%3D,ENST00000361339,;IFT140,synonymous_variant,p.%3D,ENST00000426508,;IFT140,upstream_gene_variant,,ENST00000568837,;IFT140,3_prime_UTR_variant,,ENST00000397417,;IFT140,non_coding_transcript_exon_variant,,ENST00000565298,;IFT140,downstream_gene_variant,,ENST00000566818,;	A	ENSG00000187535	ENST00000426508	Transcript	synonymous_variant	4225	3861	1287	D	gaC/gaT	rs143899594,COSM1376034	.	.	-1	IFT140	HGNC	29077	protein_coding	YES	CCDS10439.1	ENSP00000406012	IF140_HUMAN	Q9UG52_HUMAN,H3BTA5_HUMAN,H3BNC5_HUMAN	UPI0000073C64	.	.	.	28/31	.	hmmpanther:PTHR15722	A:0.0012	A:0.0045	A:0	.	A:0	A:0	A:0	A:0.0002	A:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGCGTCATA	byFrequency|byCluster|by1000G	5	ESCA
HSD3B7	0	.	GRCh37	16	30998318	30998318	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.689A>T	p.Tyr230Phe	p.Y230F	ENST00000297679	6/7	22	18	4	14	14	0	HSD3B7,missense_variant,p.Tyr230Phe,ENST00000297679,;HSD3B7,intron_variant,,ENST00000353250,;HSD3B7,intron_variant,,ENST00000262520,;STX1B,downstream_gene_variant,,ENST00000569638,;SETD1A,downstream_gene_variant,,ENST00000262519,;AC135048.1,upstream_gene_variant,,ENST00000602217,;HSD3B7,downstream_gene_variant,,ENST00000574447,;HSD3B7,downstream_gene_variant,,ENST00000562932,;STX1B,downstream_gene_variant,,ENST00000215095,;	T	ENSG00000099377	ENST00000297679	Transcript	missense_variant	782	689	230	Y/F	tAt/tTt	.	.	.	1	HSD3B7	HGNC	18324	protein_coding	YES	CCDS10698.1	ENSP00000297679	3BHS7_HUMAN	I3L2H6_HUMAN	UPI000007399B	.	deleterious(0)	probably_damaging(0.999)	6/7	.	hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF290,Gene3D:3.40.50.720,Pfam_domain:PF01073,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTCTATGTGG	.	2	ESCA
AC129492.6	0	.	GRCh37	17	7984752	7984752	+	3'UTR	SNP	C	C	T	rs766725890	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*938C>T	.	.	ENST00000399413	2/2	45	38	7	68	68	0	AC129492.6,3_prime_UTR_variant,,ENST00000399413,;ALOX12B,intron_variant,,ENST00000319144,;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000584116,;ALOX12B,upstream_gene_variant,,ENST00000583276,;	T	ENSG00000214999	ENST00000399413	Transcript	3_prime_UTR_variant	1673	.	.	.	.	rs766725890	.	.	1	AC129492.6	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000382345	YQ037_HUMAN	.	UPI0000D4AA7B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCCTCTAG	.	5	ESCA
NOL4	0	.	GRCh37	18	31599294	31599294	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1044A>T	p.Glu348Asp	p.E348D	ENST00000261592	6/11	23	19	4	38	38	0	NOL4,missense_variant,p.Glu348Asp,ENST00000261592,;NOL4,missense_variant,p.Glu348Asp,ENST00000589544,;NOL4,missense_variant,p.Glu234Asp,ENST00000269185,;NOL4,missense_variant,p.Glu274Asp,ENST00000538587,;NOL4,missense_variant,p.Glu63Asp,ENST00000535384,;NOL4,missense_variant,p.Glu193Asp,ENST00000535475,;NOL4,missense_variant,p.Glu97Asp,ENST00000586553,;NOL4,missense_variant,p.Glu332Asp,ENST00000590712,;NOL4,3_prime_UTR_variant,,ENST00000586314,;	A	ENSG00000101746	ENST00000261592	Transcript	missense_variant	1342	1044	348	E/D	gaA/gaT	.	.	.	-1	NOL4	HGNC	7870	protein_coding	YES	CCDS11907.2	ENSP00000261592	NOL4_HUMAN	.	UPI000059D504	.	tolerated_low_confidence(0.38)	probably_damaging(0.994)	6/11	.	hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATTTTCTCT	.	5	ESCA
RSBN1	0	.	GRCh37	1	114306576	114306576	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2026A>T	.	.	ENST00000261441	7/7	32	29	3	35	35	0	RSBN1,3_prime_UTR_variant,,ENST00000261441,;PHTF1,upstream_gene_variant,,ENST00000357783,;PHTF1,upstream_gene_variant,,ENST00000369596,;PHTF1,upstream_gene_variant,,ENST00000369600,;PHTF1,upstream_gene_variant,,ENST00000369604,;PHTF1,upstream_gene_variant,,ENST00000393357,;PHTF1,upstream_gene_variant,,ENST00000446739,;PHTF1,upstream_gene_variant,,ENST00000369598,;PHTF1,upstream_gene_variant,,ENST00000493212,;RSBN1,downstream_gene_variant,,ENST00000369581,;RSBN1,downstream_gene_variant,,ENST00000476412,;	A	ENSG00000081019	ENST00000261441	Transcript	3_prime_UTR_variant	4499	.	.	.	.	.	.	.	-1	RSBN1	HGNC	25642	protein_coding	YES	CCDS862.1	ENSP00000261441	RSBN1_HUMAN	.	UPI00002263B4	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAATTTTTG	.	2	ESCA
OR2W3	0	.	GRCh37	1	248058969	248058969	+	Silent	SNP	C	C	A	rs752073316	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81C>A	p.%3D	p.L27L	ENST00000537741	3/3	28	24	4	44	43	1	OR2W3,synonymous_variant,p.%3D,ENST00000537741,;OR2W3,synonymous_variant,p.%3D,ENST00000360358,;	A	ENSG00000238243	ENST00000537741	Transcript	synonymous_variant	338	81	27	L	ctC/ctA	rs752073316	.	.	1	OR2W3	HGNC	15021	protein_coding	YES	CCDS31099.1	ENSP00000445853	OR2W3_HUMAN	.	UPI0000061EA8	.	.	.	3/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF223,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCCTCTTTGT	.	2	ESCA
WDTC1	0	.	GRCh37	1	27609833	27609833	+	Silent	SNP	C	C	T	.	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.184C>T	p.%3D	p.L62L	ENST00000361771	5/16	28	25	3	35	35	0	WDTC1,synonymous_variant,p.%3D,ENST00000361771,;WDTC1,synonymous_variant,p.%3D,ENST00000319394,;WDTC1,synonymous_variant,p.%3D,ENST00000447062,;WDTC1,upstream_gene_variant,,ENST00000491239,;	T	ENSG00000142784	ENST00000361771	Transcript	synonymous_variant	567	184	62	L	Ctg/Ttg	COSM3741208	.	.	1	WDTC1	HGNC	29175	protein_coding	YES	CCDS296.1	ENSP00000355317	WDTC1_HUMAN	H0YEI6_HUMAN	UPI0000070734	.	.	.	5/16	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR15574:SF21,hmmpanther:PTHR15574,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTGCTGGCC	.	2	ESCA
C2orf40	0	.	GRCh37	2	106690395	106690395	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181T>G	p.Phe61Val	p.F61V	ENST00000238044	3/4	52	47	5	56	56	0	C2orf40,missense_variant,p.Phe25Val,ENST00000409944,;C2orf40,missense_variant,p.Phe61Val,ENST00000238044,;C2orf40,missense_variant,p.Phe63Val,ENST00000437659,;C2orf40,non_coding_transcript_exon_variant,,ENST00000489174,;C2orf40,downstream_gene_variant,,ENST00000493478,;C2orf40,non_coding_transcript_exon_variant,,ENST00000479337,;	G	ENSG00000119147	ENST00000238044	Transcript	missense_variant	290	181	61	F/V	Ttc/Gtc	.	.	.	1	C2orf40	HGNC	24642	protein_coding	YES	CCDS2072.1	ENSP00000238044	AUGN_HUMAN	B8ZZE5_HUMAN	UPI000004220E	.	deleterious(0)	probably_damaging(0.996)	3/4	.	hmmpanther:PTHR31613,Pfam_domain:PF15187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAATTCCTT	.	4	ESCA
TTN	0	.	GRCh37	2	179424596	179424596	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.86263G>C	p.Asp28755His	p.D28755H	ENST00000589042	326/363	24	17	7	38	38	0	TTN,missense_variant,p.Asp19815His,ENST00000359218,;TTN,missense_variant,p.Asp27114His,ENST00000591111,;TTN,missense_variant,p.Asp28755His,ENST00000589042,;TTN,missense_variant,p.Asp19882His,ENST00000342175,;TTN,missense_variant,p.Asp26187His,ENST00000342992,;TTN,missense_variant,p.Asp19690His,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	86488	86263	28755	D/H	Gat/Cat	COSM1305989,COSM1305988,COSM1305985,COSM1305987,COSM1305986	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	326/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817	.	.	.	.	.	.	.	.	.	.	1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATATCAAATA	.	5	ESCA
PROM2	0	.	GRCh37	2	95943191	95943191	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852G>A	p.%3D	p.E284E	ENST00000317620	7/24	26	23	3	28	28	0	PROM2,synonymous_variant,p.%3D,ENST00000317620,;PROM2,synonymous_variant,p.%3D,ENST00000542147,;PROM2,synonymous_variant,p.%3D,ENST00000403131,;PROM2,synonymous_variant,p.%3D,ENST00000317668,;PROM2,non_coding_transcript_exon_variant,,ENST00000463580,;PROM2,downstream_gene_variant,,ENST00000477767,;PROM2,upstream_gene_variant,,ENST00000497110,;PROM2,3_prime_UTR_variant,,ENST00000431567,;PROM2,non_coding_transcript_exon_variant,,ENST00000487138,;PROM2,upstream_gene_variant,,ENST00000478295,;	A	ENSG00000155066	ENST00000317620	Transcript	synonymous_variant	985	852	284	E	gaG/gaA	.	.	.	1	PROM2	HGNC	20685	protein_coding	YES	CCDS2012.1	ENSP00000318270	PROM2_HUMAN	.	UPI0000071157	.	.	.	7/24	.	Pfam_domain:PF05478,hmmpanther:PTHR22730:SF6,hmmpanther:PTHR22730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGAGCCAGC	.	2	ESCA
PROM2	0	.	GRCh37	2	95943192	95943192	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.853C>G	p.Pro285Ala	p.P285A	ENST00000317620	7/24	25	22	3	28	28	0	PROM2,missense_variant,p.Pro285Ala,ENST00000317620,;PROM2,missense_variant,p.Pro285Ala,ENST00000542147,;PROM2,missense_variant,p.Pro285Ala,ENST00000403131,;PROM2,missense_variant,p.Pro285Ala,ENST00000317668,;PROM2,non_coding_transcript_exon_variant,,ENST00000463580,;PROM2,downstream_gene_variant,,ENST00000477767,;PROM2,upstream_gene_variant,,ENST00000497110,;PROM2,3_prime_UTR_variant,,ENST00000431567,;PROM2,non_coding_transcript_exon_variant,,ENST00000487138,;PROM2,upstream_gene_variant,,ENST00000478295,;	G	ENSG00000155066	ENST00000317620	Transcript	missense_variant	986	853	285	P/A	Cca/Gca	.	.	.	1	PROM2	HGNC	20685	protein_coding	YES	CCDS2012.1	ENSP00000318270	PROM2_HUMAN	.	UPI0000071157	.	tolerated(0.38)	benign(0.024)	7/24	.	Pfam_domain:PF05478,hmmpanther:PTHR22730:SF6,hmmpanther:PTHR22730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAGCCAGCC	.	2	ESCA
ZBTB20	0	.	GRCh37	3	114070249	114070249	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.676G>A	p.Asp226Asn	p.D226N	ENST00000474710	4/5	18	14	4	25	25	0	ZBTB20,missense_variant,p.Asp153Asn,ENST00000481632,;ZBTB20,missense_variant,p.Asp153Asn,ENST00000462705,;ZBTB20,missense_variant,p.Asp153Asn,ENST00000471418,;ZBTB20,missense_variant,p.Asp153Asn,ENST00000357258,;ZBTB20,missense_variant,p.Asp226Asn,ENST00000474710,;ZBTB20,missense_variant,p.Asp153Asn,ENST00000464560,;ZBTB20,missense_variant,p.Asp153Asn,ENST00000393785,;ZBTB20,downstream_gene_variant,,ENST00000470311,;ZBTB20-AS1,upstream_gene_variant,,ENST00000475939,;ZBTB20-AS1,upstream_gene_variant,,ENST00000467304,;ZBTB20-AS1,upstream_gene_variant,,ENST00000496219,;ZBTB20,intron_variant,,ENST00000479879,;	T	ENSG00000181722	ENST00000474710	Transcript	missense_variant	855	676	226	D/N	Gac/Aac	.	.	.	-1	ZBTB20	HGNC	13503	protein_coding	YES	CCDS54626.1	ENSP00000419153	ZBT20_HUMAN	C9JCX0_HUMAN	UPI0000141957	.	tolerated(0.07)	possibly_damaging(0.689)	4/5	.	hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF351	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CGTGTCGCTGC	.	3	ESCA
BSN	0	.	GRCh37	3	49694019	49694019	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7030G>T	p.Gly2344Cys	p.G2344C	ENST00000296452	5/12	21	17	4	30	30	0	BSN,missense_variant,p.Gly2344Cys,ENST00000296452,;	T	ENSG00000164061	ENST00000296452	Transcript	missense_variant	7144	7030	2344	G/C	Ggt/Tgt	.	.	.	1	BSN	HGNC	1117	protein_coding	YES	CCDS2800.1	ENSP00000296452	BSN_HUMAN	.	UPI000013E33C	.	.	unknown(0)	5/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF1,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGGGGTGGC	.	4	ESCA
KIAA0922	0	.	GRCh37	4	154395024	154395024	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.223C>A	p.Pro75Thr	p.P75T	ENST00000409959	3/35	60	49	10	76	76	0	KIAA0922,missense_variant,p.Pro75Thr,ENST00000409663,;KIAA0922,missense_variant,p.Pro75Thr,ENST00000440693,;KIAA0922,missense_variant,p.Pro75Thr,ENST00000409959,;KIAA0922,intron_variant,,ENST00000445960,;	A	ENSG00000121210	ENST00000409959	Transcript	missense_variant	272	223	75	P/T	Cct/Act	.	.	.	1	KIAA0922	HGNC	29146	protein_coding	YES	CCDS47148.1	ENSP00000386787	T131L_HUMAN	D3DP10_HUMAN	UPI00017BE9AB	.	tolerated(0.57)	benign(0.03)	3/35	.	hmmpanther:PTHR22050,hmmpanther:PTHR22050:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAGCCTTCT	.	5	ESCA
DCUN1D4	0	.	GRCh37	4	52782876	52782876	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3126G>A	.	.	ENST00000334635	11/11	30	26	4	57	57	0	DCUN1D4,3_prime_UTR_variant,,ENST00000381441,;DCUN1D4,3_prime_UTR_variant,,ENST00000334635,;DCUN1D4,downstream_gene_variant,,ENST00000510808,;DCUN1D4,downstream_gene_variant,,ENST00000381437,;DCUN1D4,downstream_gene_variant,,ENST00000451288,;RP11-365H22.2,upstream_gene_variant,,ENST00000610270,;DCUN1D4,downstream_gene_variant,,ENST00000507659,;DCUN1D4,downstream_gene_variant,,ENST00000508257,;DCUN1D4,3_prime_UTR_variant,,ENST00000477560,;DCUN1D4,downstream_gene_variant,,ENST00000509376,;DCUN1D4,downstream_gene_variant,,ENST00000505634,;DCUN1D4,downstream_gene_variant,,ENST00000507741,;DCUN1D4,downstream_gene_variant,,ENST00000512199,;DCUN1D4,downstream_gene_variant,,ENST00000510518,;	A	ENSG00000109184	ENST00000334635	Transcript	3_prime_UTR_variant	4185	.	.	.	.	.	.	.	1	DCUN1D4	HGNC	28998	protein_coding	YES	CCDS33982.1	ENSP00000334625	DCNL4_HUMAN	B4DH26_HUMAN	UPI00001C1E10	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGTGACTCC	.	4	ESCA
JAKMIP2	0	.	GRCh37	5	147040519	147040519	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619C>T	p.Arg207Trp	p.R207W	ENST00000265272	3/21	33	28	5	48	48	0	JAKMIP2,missense_variant,p.Arg207Trp,ENST00000265272,;JAKMIP2,missense_variant,p.Arg165Trp,ENST00000333010,;JAKMIP2,missense_variant,p.Arg207Trp,ENST00000507386,;JAKMIP2,non_coding_transcript_exon_variant,,ENST00000507343,;	A	ENSG00000176049	ENST00000265272	Transcript	missense_variant	1087	619	207	R/W	Cgg/Tgg	.	.	.	-1	JAKMIP2	HGNC	29067	protein_coding	YES	CCDS4285.1	ENSP00000265272	JKIP2_HUMAN	.	UPI000000D782	.	deleterious(0)	probably_damaging(0.992)	3/21	.	hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCCGAATAT	.	4	ESCA
SIMC1	0	.	GRCh37	5	175772553	175772553	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*105C>G	.	.	ENST00000341199	9/9	26	20	6	33	33	0	SIMC1,3_prime_UTR_variant,,ENST00000443967,;SIMC1,3_prime_UTR_variant,,ENST00000430704,;SIMC1,3_prime_UTR_variant,,ENST00000332772,;SIMC1,3_prime_UTR_variant,,ENST00000341199,;KIAA1191,downstream_gene_variant,,ENST00000533553,;KIAA1191,downstream_gene_variant,,ENST00000393725,;KIAA1191,downstream_gene_variant,,ENST00000510164,;KIAA1191,downstream_gene_variant,,ENST00000298569,;RP11-843P14.2,upstream_gene_variant,,ENST00000508187,;KIAA1191,downstream_gene_variant,,ENST00000393728,;	G	ENSG00000170085	ENST00000341199	Transcript	3_prime_UTR_variant	1626	.	.	.	.	.	.	.	1	SIMC1	HGNC	24779	protein_coding	YES	CCDS4398.2	ENSP00000342075	SIMC1_HUMAN	.	UPI00000742BB	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAACCTGCA	.	5	ESCA
MRPS36	0	.	GRCh37	5	68522214	68522214	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92A>G	p.Asn31Ser	p.N31S	ENST00000256441	2/4	74	69	5	119	119	0	MRPS36,missense_variant,p.Asn31Ser,ENST00000256441,;MRPS36,5_prime_UTR_variant,,ENST00000602380,;MRPS36,5_prime_UTR_variant,,ENST00000512880,;MRPS36,non_coding_transcript_exon_variant,,ENST00000503793,;MRPS36,intron_variant,,ENST00000507022,;	G	ENSG00000134056	ENST00000256441	Transcript	missense_variant	162	92	31	N/S	aAt/aGt	.	.	.	1	MRPS36	HGNC	16631	protein_coding	YES	CCDS34174.1	ENSP00000256441	RT36_HUMAN	D6R941_HUMAN	UPI0000052862	.	tolerated(0.49)	benign(0.016)	2/4	.	hmmpanther:PTHR31601,hmmpanther:PTHR31601:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGACAATCCTA	.	2	ESCA
TSPYL4	0	.	GRCh37	6	116575240	116575240	+	5'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-69T>A	.	.	ENST00000420283	1/1	20	16	3	25	25	0	TSPYL4,5_prime_UTR_variant,,ENST00000420283,;NT5DC1,downstream_gene_variant,,ENST00000319550,;DSE,upstream_gene_variant,,ENST00000540275,;DSE,upstream_gene_variant,,ENST00000430252,;RP3-486I3.7,upstream_gene_variant,,ENST00000448740,;RP3-486I3.4,downstream_gene_variant,,ENST00000435100,;	T	ENSG00000187189	ENST00000420283	Transcript	5_prime_UTR_variant	22	.	.	.	.	.	.	.	-1	TSPYL4	HGNC	21559	protein_coding	YES	CCDS5106.1	ENSP00000410943	TSYL4_HUMAN	Q69YV8_HUMAN	UPI00001BBB76	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCCCGAAACGT	.	3	ESCA
BMPER	0	.	GRCh37	7	34094885	34094885	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.897A>C	p.Lys299Asn	p.K299N	ENST00000297161	10/16	52	44	7	51	51	0	BMPER,missense_variant,p.Lys299Asn,ENST00000297161,;BMPER,missense_variant,p.Lys299Asn,ENST00000426693,;BMPER,downstream_gene_variant,,ENST00000494786,;	C	ENSG00000164619	ENST00000297161	Transcript	missense_variant	1271	897	299	K/N	aaA/aaC	.	.	.	1	BMPER	HGNC	24154	protein_coding	YES	CCDS5442.1	ENSP00000297161	BMPER_HUMAN	.	UPI000006D462	.	tolerated(0.19)	benign(0.031)	10/16	.	PROSITE_profiles:PS50184,hmmpanther:PTHR11339:SF254,hmmpanther:PTHR11339,Superfamily_domains:SSF57603	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCAAAGTATG	.	4	ESCA
OCM2	0	.	GRCh37	7	97619361	97619361	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8ET-01A-11D-A403-09	TCGA-VR-A8ET-10B-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.56G>T	p.Cys19Phe	p.C19F	ENST00000257627	1/4	101	96	5	63	63	0	OCM2,missense_variant,p.Cys19Phe,ENST00000257627,;OCM2,non_coding_transcript_exon_variant,,ENST00000473987,;	A	ENSG00000135175	ENST00000257627	Transcript	missense_variant	148	56	19	C/F	tGc/tTc	.	.	.	-1	OCM2	HGNC	34396	protein_coding	YES	CCDS5653.1	ENSP00000257627	OCM2_HUMAN	.	UPI000013CF74	.	tolerated(0.31)	benign(0.424)	1/4	.	hmmpanther:PTHR11653,hmmpanther:PTHR11653:SF8,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGGCATTCC	.	2	ESCA
SUFU	0	.	GRCh37	10	104356918	104356918	+	Missense_Mutation	SNP	G	G	A	rs775245784	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778G>A	p.Glu260Lys	p.E260K	ENST00000369902	7/12	40	20	20	39	39	0	SUFU,missense_variant,p.Glu260Lys,ENST00000369899,;SUFU,missense_variant,p.Glu260Lys,ENST00000369902,;SUFU,missense_variant,p.Glu260Lys,ENST00000423559,;SUFU,non_coding_transcript_exon_variant,,ENST00000471000,;	A	ENSG00000107882	ENST00000369902	Transcript	missense_variant	944	778	260	E/K	Gag/Aag	rs775245784,COSM914241	.	.	1	SUFU	HGNC	16466	protein_coding	YES	CCDS7537.1	ENSP00000358918	SUFU_HUMAN	.	UPI0000073C79	.	tolerated(0.05)	benign(0.178)	7/12	.	hmmpanther:PTHR10928:SF2,hmmpanther:PTHR10928,Pfam_domain:PF12470,PIRSF_domain:PIRSF011844,Superfamily_domains:0040736	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATCGAGACA	.	5	ESCA
GPR123-AS1	0	.	GRCh37	10	134896022	134896022	+	3'Flank	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000444433	.	18	14	4	52	52	0	GPR123,missense_variant,p.Pro370Ser,ENST00000607359,;GPR123-AS1,downstream_gene_variant,,ENST00000444433,;AL445199.1,downstream_gene_variant,,ENST00000366099,;	T	ENSG00000256925	ENST00000444433	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2726	-1	GPR123-AS1	HGNC	49543	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	CAGAGCCTACT	.	2	ESCA
SLC39A12	0	.	GRCh37	10	18250587	18250587	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339A>T	p.Arg113Ser	p.R113S	ENST00000377369	3/13	28	18	9	35	35	0	SLC39A12,missense_variant,p.Arg113Ser,ENST00000377369,;SLC39A12,missense_variant,p.Arg113Ser,ENST00000377371,;SLC39A12,missense_variant,p.Arg113Ser,ENST00000377374,;SLC39A12,5_prime_UTR_variant,,ENST00000539911,;	T	ENSG00000148482	ENST00000377369	Transcript	missense_variant	612	339	113	R/S	agA/agT	.	.	.	1	SLC39A12	HGNC	20860	protein_coding	YES	CCDS44362.1	ENSP00000366586	S39AC_HUMAN	F5GX72_HUMAN	UPI00004044FC	.	deleterious(0)	possibly_damaging(0.855)	3/13	.	hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGAGTTTC	.	5	ESCA
ANKRD30A	0	.	GRCh37	10	37520407	37520407	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10A>C	.	.	ENST00000361713	35/36	45	33	12	84	84	0	ANKRD30A,3_prime_UTR_variant,,ENST00000374660,;ANKRD30A,3_prime_UTR_variant,,ENST00000361713,;ANKRD30A,3_prime_UTR_variant,,ENST00000602533,;	C	ENSG00000148513	ENST00000361713	Transcript	3_prime_UTR_variant	4135	.	.	.	.	.	.	.	1	ANKRD30A	HGNC	17234	protein_coding	YES	CCDS7193.1	ENSP00000354432	AN30A_HUMAN	R4GNA2_HUMAN	UPI0000458879	.	.	.	35/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAAGCAGTAAG	.	3	ESCA
ANKRD30A	0	.	GRCh37	10	37520412	37520412	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*15G>A	.	.	ENST00000361713	35/36	44	33	10	82	82	0	ANKRD30A,3_prime_UTR_variant,,ENST00000374660,;ANKRD30A,3_prime_UTR_variant,,ENST00000361713,;ANKRD30A,3_prime_UTR_variant,,ENST00000602533,;	A	ENSG00000148513	ENST00000361713	Transcript	3_prime_UTR_variant	4140	.	.	.	.	.	.	.	1	ANKRD30A	HGNC	17234	protein_coding	YES	CCDS7193.1	ENSP00000354432	AN30A_HUMAN	R4GNA2_HUMAN	UPI0000458879	.	.	.	35/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTAAGAAACT	.	3	ESCA
SIRT1	0	.	GRCh37	10	69672363	69672363	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1490A>G	p.Tyr497Cys	p.Y497C	ENST00000212015	8/9	52	42	9	79	79	0	SIRT1,missense_variant,p.Tyr202Cys,ENST00000432464,;SIRT1,missense_variant,p.Tyr194Cys,ENST00000403579,;SIRT1,missense_variant,p.Tyr497Cys,ENST00000212015,;SIRT1,missense_variant,p.Tyr194Cys,ENST00000406900,;	G	ENSG00000096717	ENST00000212015	Transcript	missense_variant	1543	1490	497	Y/C	tAt/tGt	.	.	.	1	SIRT1	HGNC	14929	protein_coding	YES	CCDS7273.1	ENSP00000212015	SIR1_HUMAN	E9PC49_HUMAN,A8K128_HUMAN	UPI0000073E1A	.	deleterious(0.01)	benign(0.03)	8/9	.	PROSITE_profiles:PS50305,hmmpanther:PTHR11085:SF15,hmmpanther:PTHR11085,Superfamily_domains:SSF52467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATATGCCA	.	5	ESCA
GLUD1	0	.	GRCh37	10	88854347	88854347	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.180C>T	p.%3D	p.R60R	ENST00000277865	1/13	22	13	8	34	34	0	GLUD1,synonymous_variant,p.%3D,ENST00000277865,;FAM35A,5_prime_UTR_variant,,ENST00000437629,;GLUD1,upstream_gene_variant,,ENST00000537649,;FAM35A,upstream_gene_variant,,ENST00000298786,;GLUD1,upstream_gene_variant,,ENST00000544149,;FAM35A,upstream_gene_variant,,ENST00000298784,;	A	ENSG00000148672	ENST00000277865	Transcript	synonymous_variant	277	180	60	R	cgC/cgT	.	.	.	-1	GLUD1	HGNC	4335	protein_coding	YES	CCDS7382.1	ENSP00000277865	DHE3_HUMAN	Q9UQV0_HUMAN,E9KL48_HUMAN,B3KV55_HUMAN	UPI0000001C96	.	.	.	1/13	.	hmmpanther:PTHR11606:SF10,hmmpanther:PTHR11606,Gene3D:3mw9A01,Superfamily_domains:SSF53223	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTCGCGGTC	.	5	ESCA
SLC17A6	0	.	GRCh37	11	22396367	22396367	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1108G>T	p.Ala370Ser	p.A370S	ENST00000263160	9/12	33	18	14	75	75	0	SLC17A6,missense_variant,p.Ala370Ser,ENST00000263160,;	T	ENSG00000091664	ENST00000263160	Transcript	missense_variant	1545	1108	370	A/S	Gca/Tca	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	deleterious(0)	possibly_damaging(0.855)	9/12	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11662:SF201,hmmpanther:PTHR11662,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATTGCAGAT	.	5	ESCA
ACCSL	0	.	GRCh37	11	44073269	44073269	+	Missense_Mutation	SNP	G	G	A	rs199907490	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772G>A	p.Glu258Lys	p.E258K	ENST00000378832	5/14	22	16	6	32	32	0	ACCSL,missense_variant,p.Glu258Lys,ENST00000378832,;ACCSL,splice_region_variant,,ENST00000527145,;	A	ENSG00000205126	ENST00000378832	Transcript	missense_variant	828	772	258	E/K	Gag/Aag	rs199907490	.	.	1	ACCSL	HGNC	34391	protein_coding	YES	CCDS41636.1	ENSP00000368109	1A1L2_HUMAN	.	UPI000023785D	.	deleterious(0.03)	benign(0.297)	5/14	.	hmmpanther:PTHR11751:SF344,hmmpanther:PTHR11751,Pfam_domain:PF00155,Gene3D:3.40.640.10,Superfamily_domains:SSF53383,Prints_domain:PR00753	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGCGGTAAG	byCluster	5	ESCA
RP11-707M1.1	0	.	GRCh37	11	49831413	49831413	+	RNA	SNP	A	A	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1638A>T	.	.	ENST00000527477	7/7	169	137	31	275	275	0	RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000527477,;RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000534201,;RP11-707M1.1,non_coding_transcript_exon_variant,,ENST00000530858,;	T	ENSG00000205035	ENST00000527477	Transcript	non_coding_transcript_exon_variant	1638	.	.	.	.	.	.	.	1	RP11-707M1.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTACAAGTTTT	.	4	ESCA
VPS37C	0	.	GRCh37	11	60898381	60898381	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*911G>A	.	.	ENST00000301765	5/5	44	30	14	63	63	0	VPS37C,3_prime_UTR_variant,,ENST00000301765,;CD5,downstream_gene_variant,,ENST00000347785,;VPS37C,downstream_gene_variant,,ENST00000538036,;VPS37C,downstream_gene_variant,,ENST00000536000,;	T	ENSG00000167987	ENST00000301765	Transcript	3_prime_UTR_variant	2212	.	.	.	.	.	.	.	-1	VPS37C	HGNC	26097	protein_coding	YES	CCDS31573.1	ENSP00000301765	VP37C_HUMAN	F5H4Q5_HUMAN	UPI00001AED12	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTGCTTGTG	.	5	ESCA
DEAF1	0	.	GRCh37	11	684948	684948	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820C>A	p.Pro274Thr	p.P274T	ENST00000382409	6/12	17	13	4	33	33	0	DEAF1,missense_variant,p.Pro274Thr,ENST00000382409,;DEAF1,missense_variant,p.Pro227His,ENST00000338675,;DEAF1,non_coding_transcript_exon_variant,,ENST00000530813,;DEAF1,downstream_gene_variant,,ENST00000529727,;DEAF1,downstream_gene_variant,,ENST00000525626,;DEAF1,upstream_gene_variant,,ENST00000525904,;DEAF1,downstream_gene_variant,,ENST00000528864,;DEAF1,downstream_gene_variant,,ENST00000524786,;DEAF1,missense_variant,p.Pro62Thr,ENST00000527170,;DEAF1,downstream_gene_variant,,ENST00000529717,;	T	ENSG00000177030	ENST00000382409	Transcript	missense_variant	1305	820	274	P/T	Cct/Act	COSM3810271	.	.	-1	DEAF1	HGNC	14677	protein_coding	YES	CCDS31327.1	ENSP00000371846	DEAF1_HUMAN	.	UPI00001290E6	.	deleterious(0.04)	probably_damaging(0.999)	6/12	.	hmmpanther:PTHR10237,Gene3D:3.10.390.10,Superfamily_domains:SSF63763	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	GTGAGGGTTTA	.	3	ESCA
NOS1	0	.	GRCh37	12	117672482	117672482	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3225C>T	p.%3D	p.F1075F	ENST00000338101	21/29	36	29	7	55	55	0	NOS1,synonymous_variant,p.%3D,ENST00000317775,;NOS1,synonymous_variant,p.%3D,ENST00000338101,;NOS1,3_prime_UTR_variant,,ENST00000344089,;	A	ENSG00000089250	ENST00000338101	Transcript	synonymous_variant	3230	3225	1075	F	ttC/ttT	.	.	.	-1	NOS1	HGNC	7872	protein_coding	YES	CCDS55890.1	ENSP00000337459	NOS1_HUMAN	A0PJJ7_HUMAN	UPI00001FBC10	.	.	.	21/29	.	Prints_domain:PR00371,Superfamily_domains:SSF63380,PIRSF_domain:PIRSF000333,Gene3D:1.20.990.10,Pfam_domain:PF00667,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63,PROSITE_profiles:PS51384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGGAAGAC	.	5	ESCA
HCAR2	0	.	GRCh37	12	123187116	123187116	+	Missense_Mutation	SNP	C	C	T	rs750950242	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715G>A	p.Val239Ile	p.V239I	ENST00000328880	1/1	36	28	7	37	37	0	HCAR2,missense_variant,p.Val239Ile,ENST00000328880,;HCAR1,intron_variant,,ENST00000356987,;RP11-324E6.6,intron_variant,,ENST00000543611,;	T	ENSG00000182782	ENST00000328880	Transcript	missense_variant	775	715	239	V/I	Gtc/Atc	rs750950242	.	.	-1	HCAR2	HGNC	24827	protein_coding	YES	CCDS9235.1	ENSP00000375066	HCAR2_HUMAN	.	UPI000003BCD5	.	tolerated(0.17)	possibly_damaging(0.832)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF0,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAGACGATGG	byFrequency	4	ESCA
ANHX	0	.	GRCh37	12	133795440	133795440	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*31G>A	.	.	ENST00000545940	8/8	25	16	9	51	51	0	ANHX,3_prime_UTR_variant,,ENST00000419717,;ANHX,3_prime_UTR_variant,,ENST00000545940,;AC226150.3,upstream_gene_variant,,ENST00000544259,;	T	ENSG00000227059	ENST00000545940	Transcript	3_prime_UTR_variant	2910	.	.	.	.	.	.	.	-1	ANHX	HGNC	40024	protein_coding	YES	CCDS53855.1	ENSP00000439513	ANHX_HUMAN	.	UPI0001AE6BD3	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTCCTCCTGGG	.	3	ESCA
PYROXD1	0	.	GRCh37	12	21614963	21614963	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.902A>G	p.Glu301Gly	p.E301G	ENST00000240651	9/12	32	28	4	32	32	0	PYROXD1,missense_variant,p.Glu301Gly,ENST00000240651,;PYROXD1,missense_variant,p.Glu230Gly,ENST00000538582,;PYROXD1,3_prime_UTR_variant,,ENST00000545178,;PYROXD1,3_prime_UTR_variant,,ENST00000543476,;PYROXD1,3_prime_UTR_variant,,ENST00000375266,;PYROXD1,3_prime_UTR_variant,,ENST00000544970,;PYROXD1,non_coding_transcript_exon_variant,,ENST00000536851,;PYROXD1,downstream_gene_variant,,ENST00000544187,;	G	ENSG00000121350	ENST00000240651	Transcript	missense_variant	956	902	301	E/G	gAa/gGa	.	.	.	1	PYROXD1	HGNC	26162	protein_coding	YES	CCDS31755.1	ENSP00000240651	PYRD1_HUMAN	B5MDP1_HUMAN,B3KWN8_HUMAN	UPI000006CE59	.	tolerated(0.07)	benign(0.048)	9/12	.	hmmpanther:PTHR22912:SF98,hmmpanther:PTHR22912,Pfam_domain:PF07992,Gene3D:3.50.50.60,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TGTGGAATTGA	.	2	ESCA
FAR2	0	.	GRCh37	12	29423409	29423409	+	Silent	SNP	C	C	G	rs760880258	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27C>G	p.%3D	p.G9G	ENST00000536681	2/12	28	22	6	36	36	0	FAR2,synonymous_variant,p.%3D,ENST00000536681,;FAR2,synonymous_variant,p.%3D,ENST00000182377,;FAR2,intron_variant,,ENST00000547116,;FAR2,intron_variant,,ENST00000551451,;FAR2,non_coding_transcript_exon_variant,,ENST00000547411,;FAR2,synonymous_variant,p.%3D,ENST00000552137,;	G	ENSG00000064763	ENST00000536681	Transcript	synonymous_variant	273	27	9	G	ggC/ggG	rs760880258,COSM547877,COSM938533	.	.	1	FAR2	HGNC	25531	protein_coding	YES	CCDS8717.1	ENSP00000443291	FACR2_HUMAN	F8VV73_HUMAN,F8VPF2_HUMAN	UPI0000041260	.	.	.	2/12	.	hmmpanther:PTHR11011:SF23,hmmpanther:PTHR11011	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGGCGGCAA	byFrequency	5	ESCA
YARS2	0	.	GRCh37	12	32908126	32908126	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.683A>G	p.Asp228Gly	p.D228G	ENST00000324868	1/5	63	37	26	59	59	0	YARS2,missense_variant,p.Asp228Gly,ENST00000324868,;YARS2,missense_variant,p.Asp202Gly,ENST00000548490,;	C	ENSG00000139131	ENST00000324868	Transcript	missense_variant	711	683	228	D/G	gAc/gGc	.	.	.	-1	YARS2	HGNC	24249	protein_coding	YES	CCDS31770.1	ENSP00000320658	SYYM_HUMAN	.	UPI0000046058	.	deleterious(0)	probably_damaging(1)	1/5	.	hmmpanther:PTHR11766:SF0,hmmpanther:PTHR11766,Gene3D:3.40.50.620,Pfam_domain:PF00579,TIGRFAM_domain:TIGR00234,Superfamily_domains:SSF52374,Prints_domain:PR01040	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGTCATAG	.	5	ESCA
SLC2A13	0	.	GRCh37	12	40153643	40153643	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*185C>T	.	.	ENST00000280871	10/10	20	15	5	36	36	0	SLC2A13,3_prime_UTR_variant,,ENST00000280871,;C12orf40,intron_variant,,ENST00000468200,;	A	ENSG00000151229	ENST00000280871	Transcript	3_prime_UTR_variant	2183	.	.	.	.	.	.	.	-1	SLC2A13	HGNC	15956	protein_coding	YES	CCDS8736.2	ENSP00000280871	MYCT_HUMAN	.	UPI000066D913	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATTGTTCCT	.	4	ESCA
KMT2D	0	.	GRCh37	12	49416552	49416552	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16159C>T	p.Gln5387Ter	p.Q5387*	ENST00000301067	51/54	29	19	9	58	58	0	KMT2D,stop_gained,p.Gln5387Ter,ENST00000301067,;KMT2D,stop_gained,p.Gln68Ter,ENST00000526209,;PRKAG1,upstream_gene_variant,,ENST00000548950,;PRKAG1,upstream_gene_variant,,ENST00000548065,;PRKAG1,upstream_gene_variant,,ENST00000548605,;PRKAG1,upstream_gene_variant,,ENST00000552212,;PRKAG1,upstream_gene_variant,,ENST00000548857,;PRKAG1,upstream_gene_variant,,ENST00000547082,;PRKAG1,upstream_gene_variant,,ENST00000547306,;PRKAG1,upstream_gene_variant,,ENST00000316299,;PRKAG1,upstream_gene_variant,,ENST00000551121,;PRKAG1,upstream_gene_variant,,ENST00000395170,;PRKAG1,upstream_gene_variant,,ENST00000552463,;PRKAG1,upstream_gene_variant,,ENST00000547125,;PRKAG1,upstream_gene_variant,,ENST00000551696,;RP11-386G11.5,downstream_gene_variant,,ENST00000547866,;RP11-386G11.5,downstream_gene_variant,,ENST00000552933,;RP11-386G11.5,downstream_gene_variant,,ENST00000547395,;RP11-386G11.5,downstream_gene_variant,,ENST00000552284,;PRKAG1,upstream_gene_variant,,ENST00000552657,;PRKAG1,upstream_gene_variant,,ENST00000549726,;PRKAG1,upstream_gene_variant,,ENST00000550125,;PRKAG1,upstream_gene_variant,,ENST00000550448,;PRKAG1,upstream_gene_variant,,ENST00000546531,;	A	ENSG00000167548	ENST00000301067	Transcript	stop_gained	16159	16159	5387	Q/*	Cag/Tag	COSM415828,COSM415827	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	51/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324,Gene3D:2.170.270.10,Superfamily_domains:SSF82199	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R5119W|c.15355C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACTGAGATG	.	5	ESCA
KCNA1	0	.	GRCh37	12	5021930	5021930	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1386T>A	p.Asn462Lys	p.N462K	ENST00000382545	2/2	18	13	5	38	38	0	KCNA1,missense_variant,p.Asn462Lys,ENST00000382545,;KCNA1,intron_variant,,ENST00000541095,;KCNA1,intron_variant,,ENST00000543874,;	A	ENSG00000111262	ENST00000382545	Transcript	missense_variant	2493	1386	462	N/K	aaT/aaA	.	.	.	1	KCNA1	HGNC	6218	protein_coding	YES	CCDS8535.1	ENSP00000371985	KCNA1_HUMAN	.	UPI000013C8E0	.	tolerated_low_confidence(0.9)	benign(0.005)	2/2	.	hmmpanther:PTHR11537:SF24,hmmpanther:PTHR11537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAATAATAG	.	5	ESCA
HNRNPA1	0	.	GRCh37	12	54676230	54676230	+	Silent	SNP	G	G	C	rs199763450	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.543G>C	p.%3D	p.L181L	ENST00000340913	5/11	28	24	4	65	65	0	HNRNPA1,synonymous_variant,p.%3D,ENST00000550482,;HNRNPA1,synonymous_variant,p.%3D,ENST00000546500,;HNRNPA1,synonymous_variant,p.%3D,ENST00000340913,;HNRNPA1,synonymous_variant,p.%3D,ENST00000330752,;HNRNPA1,synonymous_variant,p.%3D,ENST00000551702,;HNRNPA1,synonymous_variant,p.%3D,ENST00000547276,;HNRNPA1,synonymous_variant,p.%3D,ENST00000548688,;HNRNPA1,intron_variant,,ENST00000547708,;CBX5,upstream_gene_variant,,ENST00000209875,;HNRNPA1,downstream_gene_variant,,ENST00000550994,;RP11-968A15.8,intron_variant,,ENST00000553061,;RP11-968A15.2,downstream_gene_variant,,ENST00000547177,;HNRNPA1,upstream_gene_variant,,ENST00000551803,;HNRNPA1,synonymous_variant,p.%3D,ENST00000547566,;HNRNPA1,non_coding_transcript_exon_variant,,ENST00000547870,;HNRNPA1,upstream_gene_variant,,ENST00000551679,;HNRNPA1,upstream_gene_variant,,ENST00000551665,;	C	ENSG00000135486	ENST00000340913	Transcript	synonymous_variant	596	543	181	L	ctG/ctC	rs199763450	.	.	1	HNRNPA1	HGNC	5031	protein_coding	YES	CCDS44909.1	ENSP00000341826	ROA1_HUMAN	F8VYN5_HUMAN	UPI0000161BF2	.	.	.	5/11	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF309,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Superfamily_domains:SSF54928	C:0.0002	C:0	C:0.0014	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTGTCAAA	byCluster|by1000G	4	ESCA
ATP5B	0	.	GRCh37	12	57037213	57037213	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766A>T	p.Ile256Phe	p.I256F	ENST00000262030	5/10	30	22	7	44	44	0	ATP5B,missense_variant,p.Ile49Phe,ENST00000551570,;ATP5B,missense_variant,p.Ile193Phe,ENST00000552959,;ATP5B,missense_variant,p.Ile157Phe,ENST00000553007,;ATP5B,missense_variant,p.Ile256Phe,ENST00000552919,;ATP5B,missense_variant,p.Ile256Phe,ENST00000262030,;ATP5B,missense_variant,p.Ile195Phe,ENST00000551020,;ATP5B,intron_variant,,ENST00000552104,;SNORD59A,downstream_gene_variant,,ENST00000384304,;ATP5B,non_coding_transcript_exon_variant,,ENST00000547250,;ATP5B,non_coding_transcript_exon_variant,,ENST00000548647,;ATP5B,intron_variant,,ENST00000547808,;ATP5B,intron_variant,,ENST00000548474,;ATP5B,upstream_gene_variant,,ENST00000550162,;ATP5B,upstream_gene_variant,,ENST00000551182,;	A	ENSG00000110955	ENST00000262030	Transcript	missense_variant	817	766	256	I/F	Atc/Ttc	.	.	.	-1	ATP5B	HGNC	830	protein_coding	YES	CCDS8924.1	ENSP00000262030	ATPB_HUMAN	Q0QEN7_HUMAN	UPI000012644E	.	deleterious_low_confidence(0)	probably_damaging(0.95)	5/10	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Pfam_domain:PF00006,TIGRFAM_domain:TIGR01039,Gene3D:3.40.50.300,hmmpanther:PTHR15184:SF32,hmmpanther:PTHR15184,HAMAP:MF_01347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGATAACAC	.	5	ESCA
GNS	0	.	GRCh37	12	65134404	65134404	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.857A>G	p.Asp286Gly	p.D286G	ENST00000258145	7/14	40	28	12	69	69	0	GNS,missense_variant,p.Asp210Gly,ENST00000545273,;GNS,missense_variant,p.Asp318Gly,ENST00000543646,;GNS,missense_variant,p.Asp286Gly,ENST00000258145,;GNS,missense_variant,p.Asp230Gly,ENST00000418919,;GNS,missense_variant,p.Asp106Gly,ENST00000540196,;GNS,missense_variant,p.Asp266Gly,ENST00000542058,;GNS,non_coding_transcript_exon_variant,,ENST00000541781,;	C	ENSG00000135677	ENST00000258145	Transcript	missense_variant	1028	857	286	D/G	gAt/gGt	.	.	.	-1	GNS	HGNC	4422	protein_coding	YES	CCDS8970.1	ENSP00000258145	GNS_HUMAN	F5H4C6_HUMAN	UPI0000000CC8	.	deleterious(0)	probably_damaging(0.999)	7/14	.	PIRSF_domain:PIRSF036666,Pfam_domain:PF00884,hmmpanther:PTHR10342:SF212,hmmpanther:PTHR10342	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTATCTAAA	.	5	ESCA
RIMKLB	0	.	GRCh37	12	8929721	8929721	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3341T>C	.	.	ENST00000357529	7/7	35	22	13	50	50	0	RIMKLB,3_prime_UTR_variant,,ENST00000538135,;RIMKLB,3_prime_UTR_variant,,ENST00000357529,;RIMKLB,downstream_gene_variant,,ENST00000535829,;A2ML1-AS1,intron_variant,,ENST00000537288,;RIMKLB,intron_variant,,ENST00000299673,;RIMKLB,upstream_gene_variant,,ENST00000510357,;RIMKLB,upstream_gene_variant,,ENST00000504495,;RIMKLB,upstream_gene_variant,,ENST00000542232,;RIMKLB,intron_variant,,ENST00000544257,;	C	ENSG00000166532	ENST00000357529	Transcript	3_prime_UTR_variant	5764	.	.	.	.	.	.	.	1	RIMKLB	HGNC	29228	protein_coding	YES	CCDS41748.1	ENSP00000350136	RIMKB_HUMAN	F5H3V4_HUMAN,F5GZH5_HUMAN	UPI000013E5D1	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTATTTAAG	.	5	ESCA
SAP18	0	.	GRCh37	13	21721357	21721357	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.395G>A	p.Arg132Lys	p.R132K	ENST00000382533	4/4	21	16	5	56	56	0	SAP18,missense_variant,p.Arg113Lys,ENST00000607003,;SAP18,missense_variant,p.Arg110Lys,ENST00000450573,;SAP18,missense_variant,p.Arg132Lys,ENST00000382533,;SAP18,3_prime_UTR_variant,,ENST00000492245,;SAP18,3_prime_UTR_variant,,ENST00000467636,;RN7SL80P,upstream_gene_variant,,ENST00000580631,;SAP18,non_coding_transcript_exon_variant,,ENST00000471009,;	A	ENSG00000150459	ENST00000382533	Transcript	missense_variant	434	395	132	R/K	aGa/aAa	COSM3793183	.	.	1	SAP18	HGNC	10530	protein_coding	YES	CCDS9295.2	ENSP00000371973	.	U3KPY7_HUMAN	UPI000187B6C9	.	tolerated(0.16)	possibly_damaging(0.487)	4/4	.	hmmpanther:PTHR13082:SF1,hmmpanther:PTHR13082,Pfam_domain:PF06487,PIRSF_domain:PIRSF037637	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCAGAAAGG	.	5	ESCA
SACS	0	.	GRCh37	13	23911207	23911207	+	Missense_Mutation	SNP	C	C	T	rs768749854	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6808G>A	p.Gly2270Ser	p.G2270S	ENST00000382298	10/10	41	32	8	98	98	0	SACS,missense_variant,p.Gly2270Ser,ENST00000382292,;SACS,missense_variant,p.Gly1520Ser,ENST00000402364,;SACS,missense_variant,p.Gly2270Ser,ENST00000382298,;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,;	T	ENSG00000151835	ENST00000382298	Transcript	missense_variant	7397	6808	2270	G/S	Ggt/Agt	rs768749854	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	probably_damaging(0.999)	10/10	.	hmmpanther:PTHR15600:SF26,hmmpanther:PTHR15600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAACCTCTAA	.	5	ESCA
FAM124A	0	.	GRCh37	13	51825970	51825970	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.575G>C	p.Gly192Ala	p.G192A	ENST00000280057	4/5	10	6	4	51	51	0	FAM124A,missense_variant,p.Gly192Ala,ENST00000280057,;FAM124A,missense_variant,p.Gly156Ala,ENST00000322475,;	C	ENSG00000150510	ENST00000280057	Transcript	missense_variant	706	575	192	G/A	gGg/gCg	.	.	.	1	FAM124A	HGNC	26413	protein_coding	YES	CCDS9427.1	ENSP00000280057	F124A_HUMAN	.	UPI0000140E33	.	deleterious(0.01)	probably_damaging(0.987)	4/5	.	hmmpanther:PTHR14715:SF4,hmmpanther:PTHR14715,Pfam_domain:PF15067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	CCCTGGGACGC	.	2	ESCA
UTP14C	0	.	GRCh37	13	52603541	52603541	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.601C>T	p.Pro201Ser	p.P201S	ENST00000521776	2/2	17	10	7	59	59	0	UTP14C,missense_variant,p.Pro201Ser,ENST00000521776,;ALG11,3_prime_UTR_variant,,ENST00000523764,;ALG11,3_prime_UTR_variant,,ENST00000521508,;ALG11,downstream_gene_variant,,ENST00000519151,;	T	ENSG00000253797	ENST00000521776	Transcript	missense_variant	1334	601	201	P/S	Cct/Tct	.	.	.	1	UTP14C	HGNC	20321	protein_coding	YES	CCDS31978.1	ENSP00000428619	UT14C_HUMAN	.	UPI000006DB4B	.	deleterious(0)	probably_damaging(0.933)	2/2	.	Pfam_domain:PF04615,hmmpanther:PTHR14150:SF16,hmmpanther:PTHR14150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATCCTTTA	.	5	ESCA
GPC5	0	.	GRCh37	13	93518770	93518770	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*78C>A	.	.	ENST00000377067	8/8	28	21	7	33	33	0	GPC5,3_prime_UTR_variant,,ENST00000377067,;	A	ENSG00000179399	ENST00000377067	Transcript	3_prime_UTR_variant	2169	.	.	.	.	.	.	.	1	GPC5	HGNC	4453	protein_coding	YES	CCDS9468.1	ENSP00000366267	GPC5_HUMAN	.	UPI0000001C85	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATCCTTTTT	.	5	ESCA
IGHV3-38	0	.	GRCh37	14	106866605	106866605	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.149G>T	p.Ser50Ile	p.S50I	ENST00000390618	2/2	58	17	41	114	114	0	IGHV3-38,missense_variant,p.Ser50Ile,ENST00000390618,;	A	ENSG00000211958	ENST00000390618	Transcript	missense_variant	227	149	50	S/I	aGc/aTc	.	.	.	-1	IGHV3-38	HGNC	5601	IG_V_gene	YES	.	ENSP00000375027	.	.	UPI0000F30366	.	deleterious_low_confidence(0.02)	benign(0.081)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF91,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGCTACTG	.	5	ESCA
TOX4	0	.	GRCh37	14	21961063	21961063	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1288G>A	p.Ala430Thr	p.A430T	ENST00000405508	8/10	23	19	4	47	47	0	TOX4,missense_variant,p.Ala430Thr,ENST00000405508,;TOX4,missense_variant,p.Ala407Thr,ENST00000448790,;TOX4,missense_variant,p.Ala430Thr,ENST00000262709,;TOX4,downstream_gene_variant,,ENST00000457430,;TOX4,downstream_gene_variant,,ENST00000416256,;TOX4,downstream_gene_variant,,ENST00000494242,;TOX4,3_prime_UTR_variant,,ENST00000455393,;TOX4,non_coding_transcript_exon_variant,,ENST00000476180,;TOX4,downstream_gene_variant,,ENST00000463119,;TOX4,downstream_gene_variant,,ENST00000455138,;TOX4,downstream_gene_variant,,ENST00000473176,;TOX4,downstream_gene_variant,,ENST00000447695,;	A	ENSG00000092203	ENST00000405508	Transcript	missense_variant	1564	1288	430	A/T	Gct/Act	.	.	.	1	TOX4	HGNC	20161	protein_coding	YES	CCDS32043.1	ENSP00000385102	TOX4_HUMAN	.	UPI000006EA81	.	tolerated_low_confidence(0.32)	probably_damaging(0.956)	8/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF143	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.A429A|c.1287T>A|3	RADIA|MUTECT|MUSE|VARSCANS	CAGCTGCTGCT	.	4	ESCA
TRAV40	0	.	GRCh37	14	22783121	22783121	+	Silent	SNP	C	C	G	rs754720424	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.87C>G	p.%3D	p.T29T	ENST00000390467	2/2	16	11	5	16	16	0	TRAV40,synonymous_variant,p.%3D,ENST00000390467,;	G	ENSG00000211819	ENST00000390467	Transcript	synonymous_variant	87	87	29	T	acC/acG	rs754720424	.	.	1	TRAV40	HGNC	12141	TR_V_gene	YES	.	ENSP00000452585	.	.	UPI000011D134	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF119,hmmpanther:PTHR23267,Gene3D:2.60.40.10,Pfam_domain:PF07686,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAACCGTCTC	byFrequency	5	ESCA
SLC7A8	0	.	GRCh37	14	23652132	23652132	+	5'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-9C>G	.	.	ENST00000316902	1/11	29	21	8	63	63	0	SLC7A8,5_prime_UTR_variant,,ENST00000316902,;SLC7A8,5_prime_UTR_variant,,ENST00000525062,;SLC7A8,5_prime_UTR_variant,,ENST00000469263,;SLC7A8,5_prime_UTR_variant,,ENST00000524758,;C14orf164,upstream_gene_variant,,ENST00000492621,;C14orf164,upstream_gene_variant,,ENST00000399910,;C14orf164,upstream_gene_variant,,ENST00000498441,;	C	ENSG00000092068	ENST00000316902	Transcript	5_prime_UTR_variant	718	.	.	.	.	.	.	.	-1	SLC7A8	HGNC	11066	protein_coding	YES	CCDS9590.1	ENSP00000320378	LAT2_HUMAN	E9PQT4_HUMAN,E9PIC3_HUMAN,B3KSX4_HUMAN	UPI000012E235	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCAGTAGGA	.	5	ESCA
SIPA1L1	0	.	GRCh37	14	72128161	72128161	+	Silent	SNP	G	G	A	rs200430873	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2232G>A	p.%3D	p.P744P	ENST00000555818	7/22	35	24	10	81	81	0	SIPA1L1,synonymous_variant,p.%3D,ENST00000537413,;SIPA1L1,synonymous_variant,p.%3D,ENST00000358550,;SIPA1L1,synonymous_variant,p.%3D,ENST00000555066,;SIPA1L1,synonymous_variant,p.%3D,ENST00000381232,;SIPA1L1,synonymous_variant,p.%3D,ENST00000555818,;	A	ENSG00000197555	ENST00000555818	Transcript	synonymous_variant	2580	2232	744	P	ccG/ccA	rs200430873,COSM1607918	.	.	1	SIPA1L1	HGNC	20284	protein_coding	YES	CCDS9807.1	ENSP00000450832	SI1L1_HUMAN	G3V4Z3_HUMAN	UPI00000443CB	.	.	.	7/22	.	Superfamily_domains:0043732,Pfam_domain:PF02145,hmmpanther:PTHR15711:SF10,hmmpanther:PTHR15711,PROSITE_profiles:PS50085	A:0.0006	A:0	A:0	.	A:0.001	A:0	A:0.002	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P744P|c.2232G>A|3,BUFFER|p.P744S|c.2230C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCCGTGCTC	byFrequency|byCluster|by1000G	5	ESCA
SNORD116-18	0	.	GRCh37	15	25330543	25330543	+	RNA	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.12G>A	.	.	ENST00000383961	1/1	79	72	6	122	122	0	SNORD116-18,non_coding_transcript_exon_variant,,ENST00000383961,;SNORD116-15,downstream_gene_variant,,ENST00000384445,;SNORD116-19,upstream_gene_variant,,ENST00000384729,;SNORD116-16,downstream_gene_variant,,ENST00000384533,;SNHG14,upstream_gene_variant,,ENST00000384430,;SNORD116-17,downstream_gene_variant,,ENST00000383929,;SNORD116-20,upstream_gene_variant,,ENST00000567527,;SNORD116-20,upstream_gene_variant,,ENST00000384507,;SNORD116-20,upstream_gene_variant,,ENST00000384529,;SNHG14,intron_variant,,ENST00000546682,;SNHG14,intron_variant,,ENST00000553108,;SNHG14,intron_variant,,ENST00000549804,;SNHG14,downstream_gene_variant,,ENST00000383025,;	A	ENSG00000206688	ENST00000383961	Transcript	non_coding_transcript_exon_variant	12	.	.	.	.	.	.	.	1	SNORD116-18	HGNC	33084	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGATGACTTC	.	3	ESCA
FBN1	0	.	GRCh37	15	48704821	48704821	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8171C>T	p.Pro2724Leu	p.P2724L	ENST00000316623	65/66	31	26	5	62	62	0	FBN1,missense_variant,p.Pro2724Leu,ENST00000316623,;FBN1,non_coding_transcript_exon_variant,,ENST00000561429,;FBN1,3_prime_UTR_variant,,ENST00000559133,;	A	ENSG00000166147	ENST00000316623	Transcript	missense_variant	8627	8171	2724	P/L	cCc/cTc	.	.	.	-1	FBN1	HGNC	3603	protein_coding	YES	CCDS32232.1	ENSP00000325527	FBN1_HUMAN	Q75N89_HUMAN,Q75N88_HUMAN,H0YN80_HUMAN	UPI0000163B0B	.	.	possibly_damaging(0.651)	65/66	.	hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,PIRSF_domain:PIRSF036312	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTTGGGGTAG	.	5	ESCA
IDH2	0	.	GRCh37	15	90628068	90628068	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1251C>T	p.%3D	p.G417G	ENST00000330062	10/11	35	28	7	54	54	0	IDH2,synonymous_variant,p.%3D,ENST00000539790,;IDH2,synonymous_variant,p.%3D,ENST00000330062,;IDH2,synonymous_variant,p.%3D,ENST00000540499,;IDH2,intron_variant,,ENST00000559482,;ZNF710,downstream_gene_variant,,ENST00000268154,;RP11-617F23.1,upstream_gene_variant,,ENST00000558334,;ZNF710,downstream_gene_variant,,ENST00000560908,;IDH2,3_prime_UTR_variant,,ENST00000560061,;	A	ENSG00000182054	ENST00000330062	Transcript	synonymous_variant	1365	1251	417	G	ggC/ggT	.	.	.	-1	IDH2	HGNC	5383	protein_coding	YES	CCDS10359.1	ENSP00000331897	IDHP_HUMAN	H0YLL5_HUMAN,B4DSZ6_HUMAN,B4DFL2_HUMAN	UPI000012D1C3	.	.	.	10/11	.	hmmpanther:PTHR11822,Pfam_domain:PF00180,TIGRFAM_domain:TIGR00127,Gene3D:3.40.718.10,PIRSF_domain:PIRSF000108,Superfamily_domains:SSF53659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCAGCCCGC	.	5	ESCA
IDH2	0	.	GRCh37	15	90628069	90628069	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1250G>T	p.Gly417Val	p.G417V	ENST00000330062	10/11	35	28	7	57	57	0	IDH2,missense_variant,p.Gly287Val,ENST00000539790,;IDH2,missense_variant,p.Gly417Val,ENST00000330062,;IDH2,missense_variant,p.Gly365Val,ENST00000540499,;IDH2,intron_variant,,ENST00000559482,;ZNF710,downstream_gene_variant,,ENST00000268154,;RP11-617F23.1,upstream_gene_variant,,ENST00000558334,;ZNF710,downstream_gene_variant,,ENST00000560908,;IDH2,3_prime_UTR_variant,,ENST00000560061,;	A	ENSG00000182054	ENST00000330062	Transcript	missense_variant	1364	1250	417	G/V	gGc/gTc	.	.	.	-1	IDH2	HGNC	5383	protein_coding	YES	CCDS10359.1	ENSP00000331897	IDHP_HUMAN	H0YLL5_HUMAN,B4DSZ6_HUMAN,B4DFL2_HUMAN	UPI000012D1C3	.	tolerated_low_confidence(0.63)	probably_damaging(1)	10/11	.	hmmpanther:PTHR11822,Pfam_domain:PF00180,TIGRFAM_domain:TIGR00127,Gene3D:3.40.718.10,PIRSF_domain:PIRSF000108,Superfamily_domains:SSF53659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGCCCGCC	.	5	ESCA
CCP110	0	.	GRCh37	16	19547383	19547383	+	Missense_Mutation	SNP	C	C	T	rs372440972	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.392C>T	p.Thr131Met	p.T131M	ENST00000381396	4/15	46	37	8	96	96	0	CCP110,missense_variant,p.Thr131Met,ENST00000396212,;CCP110,missense_variant,p.Thr75Met,ENST00000561888,;CCP110,missense_variant,p.Thr131Met,ENST00000381396,;CCP110,missense_variant,p.Thr131Met,ENST00000396208,;CCP110,intron_variant,,ENST00000562083,;	T	ENSG00000103540	ENST00000381396	Transcript	missense_variant	639	392	131	T/M	aCg/aTg	rs372440972	.	.	1	CCP110	HGNC	24342	protein_coding	YES	CCDS55992.1	ENSP00000370803	CP110_HUMAN	.	UPI0000D619A9	.	tolerated(0.06)	benign(0.386)	4/15	.	hmmpanther:PTHR13594	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCATACGGAAC	byFrequency|byCluster	4	ESCA
ZNF668	0	.	GRCh37	16	31073108	31073108	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210A>T	p.Lys404Ter	p.K404*	ENST00000539836	4/4	35	25	10	58	58	0	ZNF668,stop_gained,p.Lys404Ter,ENST00000426488,;ZNF668,stop_gained,p.Lys381Ter,ENST00000300849,;ZNF668,stop_gained,p.Lys381Ter,ENST00000538906,;ZNF668,stop_gained,p.Lys404Ter,ENST00000539836,;ZNF668,stop_gained,p.Lys381Ter,ENST00000535577,;ZNF668,stop_gained,p.Lys381Ter,ENST00000394983,;ZNF668,missense_variant,p.Phe99Tyr,ENST00000417110,;ZNF668,downstream_gene_variant,,ENST00000417935,;ZNF668,downstream_gene_variant,,ENST00000414399,;ZNF668,downstream_gene_variant,,ENST00000442862,;AC135050.5,upstream_gene_variant,,ENST00000568708,;ZNF668,downstream_gene_variant,,ENST00000564456,;	A	ENSG00000167394	ENST00000539836	Transcript	stop_gained	1533	1210	404	K/*	Aag/Tag	.	.	.	-1	ZNF668	HGNC	25821	protein_coding	YES	CCDS54003.1	ENSP00000442573	.	C9JHH8_HUMAN,C9JG35_HUMAN,C9JCJ0_HUMAN	UPI00001FFF53	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF15,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTTCGTGA	.	5	ESCA
ZNF668	0	.	GRCh37	16	31073109	31073109	+	Missense_Mutation	SNP	C	C	A	rs144972780	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297C>A	p.Phe99Leu	p.F99L	ENST00000417110	1/1	39	28	11	57	57	0	ZNF668,missense_variant,p.Phe99Leu,ENST00000417110,;ZNF668,synonymous_variant,p.%3D,ENST00000426488,;ZNF668,synonymous_variant,p.%3D,ENST00000300849,;ZNF668,synonymous_variant,p.%3D,ENST00000538906,;ZNF668,synonymous_variant,p.%3D,ENST00000539836,;ZNF668,synonymous_variant,p.%3D,ENST00000535577,;ZNF668,synonymous_variant,p.%3D,ENST00000394983,;ZNF668,downstream_gene_variant,,ENST00000417935,;ZNF668,downstream_gene_variant,,ENST00000414399,;ZNF668,downstream_gene_variant,,ENST00000442862,;AC135050.5,upstream_gene_variant,,ENST00000568708,;ZNF668,downstream_gene_variant,,ENST00000564456,;	A	ENSG00000232748	ENST00000417110	Transcript	missense_variant	297	297	99	F/L	ttC/ttA	rs144972780,COSM557759,COSM1140955	.	.	1	ZNF668	Uniprot_gn	25821	protein_coding	YES	.	ENSP00000391989	.	Q4G0L6_HUMAN	UPI0000489588	.	.	benign(0)	1/1	.	.	T:0.0010	T:0	T:0	.	T:0	T:0.005	T:0	T:0.0005	T:0.002	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTCGTGAG	byFrequency|byCluster|by1000G	5	ESCA
PPL	0	.	GRCh37	16	4938128	4938128	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2489C>G	p.Ser830Cys	p.S830C	ENST00000345988	20/22	30	24	6	51	51	0	PPL,missense_variant,p.Ser251Cys,ENST00000592772,;PPL,missense_variant,p.Ser828Cys,ENST00000590782,;PPL,missense_variant,p.Ser830Cys,ENST00000345988,;PPL,downstream_gene_variant,,ENST00000589090,;PPL,downstream_gene_variant,,ENST00000590093,;PPL,downstream_gene_variant,,ENST00000588556,;	C	ENSG00000118898	ENST00000345988	Transcript	missense_variant	2579	2489	830	S/C	tCt/tGt	.	.	.	-1	PPL	HGNC	9273	protein_coding	YES	CCDS10526.1	ENSP00000340510	PEPL_HUMAN	.	UPI00001AE832	.	deleterious(0.02)	benign(0.12)	20/22	.	hmmpanther:PTHR23169,SMART_domains:SM00150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGAGATTGG	.	5	ESCA
GPR97	0	.	GRCh37	16	57712190	57712190	+	Missense_Mutation	SNP	G	G	T	rs149674334	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.454G>T	p.Val152Phe	p.V152F	ENST00000333493	4/12	60	49	10	85	84	1	GPR97,missense_variant,p.Val32Phe,ENST00000450388,;GPR97,missense_variant,p.Val152Phe,ENST00000333493,;GPR97,5_prime_UTR_variant,,ENST00000327655,;RP11-405F3.4,downstream_gene_variant,,ENST00000563062,;GPR97,missense_variant,p.Val152Phe,ENST00000567991,;GPR97,3_prime_UTR_variant,,ENST00000568245,;GPR97,non_coding_transcript_exon_variant,,ENST00000565579,;GPR97,non_coding_transcript_exon_variant,,ENST00000565902,;GPR97,upstream_gene_variant,,ENST00000569977,;	T	ENSG00000182885	ENST00000333493	Transcript	missense_variant	615	454	152	V/F	Gtc/Ttc	rs149674334,COSM1378584	.	.	1	GPR97	HGNC	13728	protein_coding	YES	CCDS10786.1	ENSP00000332900	GPR97_HUMAN	H3BS78_HUMAN,F8W8F7_HUMAN	UPI000003C9E1	.	deleterious(0)	benign(0.171)	4/12	.	hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF267	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGTCACC	byCluster	5	ESCA
LCAT	0	.	GRCh37	16	67976482	67976482	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.532G>A	p.Glu178Lys	p.E178K	ENST00000264005	5/6	22	12	10	30	30	0	LCAT,missense_variant,p.Glu178Lys,ENST00000264005,;LCAT,missense_variant,p.Glu106Lys,ENST00000570980,;LCAT,intron_variant,,ENST00000570369,;SLC12A4,downstream_gene_variant,,ENST00000537830,;SLC12A4,downstream_gene_variant,,ENST00000541864,;LCAT,upstream_gene_variant,,ENST00000576450,;SLC12A4,downstream_gene_variant,,ENST00000576616,;SLC12A4,downstream_gene_variant,,ENST00000572037,;SLC12A4,downstream_gene_variant,,ENST00000316341,;SLC12A4,downstream_gene_variant,,ENST00000338335,;SLC12A4,downstream_gene_variant,,ENST00000422611,;LCAT,upstream_gene_variant,,ENST00000570396,;CTC-479C5.17,downstream_gene_variant,,ENST00000590594,;LCAT,missense_variant,p.Glu59Lys,ENST00000573538,;LCAT,3_prime_UTR_variant,,ENST00000575467,;LCAT,non_coding_transcript_exon_variant,,ENST00000575277,;LCAT,non_coding_transcript_exon_variant,,ENST00000573846,;SLC12A4,downstream_gene_variant,,ENST00000573023,;SLC12A4,downstream_gene_variant,,ENST00000575857,;SLC12A4,downstream_gene_variant,,ENST00000570616,;SLC12A4,downstream_gene_variant,,ENST00000570802,;	T	ENSG00000213398	ENST00000264005	Transcript	missense_variant	562	532	178	E/K	Gag/Aag	.	.	.	-1	LCAT	HGNC	6522	protein_coding	YES	CCDS10854.1	ENSP00000264005	LCAT_HUMAN	J3QSE5_HUMAN	UPI0000000DE7	.	tolerated(0.74)	benign(0.005)	5/6	.	hmmpanther:PTHR11440,hmmpanther:PTHR11440:SF18,Gene3D:3.40.50.1820,Pfam_domain:PF02450,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCCTGCT	.	5	ESCA
VPS9D1	0	.	GRCh37	16	89779185	89779185	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432-61T>C	.	.	ENST00000389386	.	19	11	7	36	36	0	VPS9D1,intron_variant,,ENST00000389386,;VPS9D1,intron_variant,,ENST00000561976,;VPS9D1,upstream_gene_variant,,ENST00000565023,;VPS9D1-AS1,non_coding_transcript_exon_variant,,ENST00000562866,;VPS9D1-AS1,upstream_gene_variant,,ENST00000562298,;VPS9D1,upstream_gene_variant,,ENST00000565452,;VPS9D1,non_coding_transcript_exon_variant,,ENST00000567379,;VPS9D1,non_coding_transcript_exon_variant,,ENST00000568691,;VPS9D1,intron_variant,,ENST00000563798,;	G	ENSG00000075399	ENST00000389386	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	VPS9D1	HGNC	13526	protein_coding	YES	CCDS42220.1	ENSP00000374037	VP9D1_HUMAN	H3BM58_HUMAN	UPI00001FF749	.	.	.	.	4/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAGAGGAGT	.	5	ESCA
FANCA	0	.	GRCh37	16	89804679	89804679	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*330G>C	.	.	ENST00000389301	43/43	23	17	5	32	32	0	FANCA,3_prime_UTR_variant,,ENST00000389301,;ZNF276,3_prime_UTR_variant,,ENST00000568064,;ZNF276,3_prime_UTR_variant,,ENST00000443381,;ZNF276,3_prime_UTR_variant,,ENST00000446326,;ZNF276,3_prime_UTR_variant,,ENST00000289816,;FANCA,downstream_gene_variant,,ENST00000561722,;FANCA,downstream_gene_variant,,ENST00000567879,;FANCA,downstream_gene_variant,,ENST00000564475,;FANCA,downstream_gene_variant,,ENST00000568369,;FANCA,downstream_gene_variant,,ENST00000564870,;ZNF276,3_prime_UTR_variant,,ENST00000568295,;ZNF276,3_prime_UTR_variant,,ENST00000562530,;ZNF276,non_coding_transcript_exon_variant,,ENST00000563983,;ZNF276,non_coding_transcript_exon_variant,,ENST00000564004,;ZNF276,non_coding_transcript_exon_variant,,ENST00000561536,;ZNF276,non_coding_transcript_exon_variant,,ENST00000569901,;FANCA,downstream_gene_variant,,ENST00000564969,;FANCA,downstream_gene_variant,,ENST00000562424,;ZNF276,downstream_gene_variant,,ENST00000563541,;FANCA,downstream_gene_variant,,ENST00000568626,;ZNF276,downstream_gene_variant,,ENST00000569426,;FANCA,downstream_gene_variant,,ENST00000305699,;FANCA,downstream_gene_variant,,ENST00000567988,;ZNF276,downstream_gene_variant,,ENST00000569582,;	G	ENSG00000187741	ENST00000389301	Transcript	3_prime_UTR_variant	4729	.	.	.	.	.	.	.	-1	FANCA	HGNC	3582	protein_coding	YES	CCDS32515.1	ENSP00000373952	FANCA_HUMAN	H3BT53_HUMAN	UPI0000520A1A	.	.	.	43/43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCTAGCA	.	5	ESCA
MYH2	0	.	GRCh37	17	10435052	10435052	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2595T>G	p.Ile865Met	p.I865M	ENST00000245503	22/40	35	32	3	97	97	0	MYH2,missense_variant,p.Ile865Met,ENST00000245503,;MYH2,missense_variant,p.Ile865Met,ENST00000397183,;MYH2,intron_variant,,ENST00000532183,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	C	ENSG00000125414	ENST00000245503	Transcript	missense_variant	2980	2595	865	I/M	atT/atG	.	.	.	-1	MYH2	HGNC	7572	protein_coding	YES	CCDS11156.1	ENSP00000245503	MYH2_HUMAN	J3QLR0_HUMAN,E7EX84_HUMAN,C9JIX4_HUMAN	UPI000012FB6C	.	tolerated(0.21)	benign(0.03)	22/40	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF90257,Gene3D:1.20.5.340,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF314	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTTAATTTT	.	2	ESCA
ACACA	0	.	GRCh37	17	35633933	35633933	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.795C>A	p.%3D	p.A265A	ENST00000353139	7/56	34	18	16	72	72	0	ACACA,synonymous_variant,p.%3D,ENST00000360679,;ACACA,synonymous_variant,p.%3D,ENST00000353139,;ACACA,synonymous_variant,p.%3D,ENST00000394406,;ACACA,synonymous_variant,p.%3D,ENST00000335166,;ACACA,downstream_gene_variant,,ENST00000591148,;ACACA,3_prime_UTR_variant,,ENST00000456066,;ACACA,non_coding_transcript_exon_variant,,ENST00000590888,;	T	ENSG00000132142	ENST00000353139	Transcript	synonymous_variant	1277	795	265	A	gcC/gcA	.	.	.	-1	ACACA	HGNC	84	protein_coding	YES	CCDS42302.1	ENSP00000344789	ACACA_HUMAN	Q7Z5W8_HUMAN,K7EII5_HUMAN,K4DID9_HUMAN,B4DWK9_HUMAN,B4DK31_HUMAN,B4DIW1_HUMAN,B2ZZ90_HUMAN,A8MYL5_HUMAN	UPI00002263AC	.	.	.	7/56	.	PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF89,hmmpanther:PTHR18866,Gene3D:3.40.50.20,Pfam_domain:PF00289,Superfamily_domains:SSF52440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAAGGCAAT	.	5	ESCA
COL1A1	0	.	GRCh37	17	48272618	48272618	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1274G>T	p.Gly425Val	p.G425V	ENST00000225964	19/51	34	18	16	81	81	0	COL1A1,missense_variant,p.Gly425Val,ENST00000225964,;COL1A1,downstream_gene_variant,,ENST00000507689,;COL1A1,non_coding_transcript_exon_variant,,ENST00000471344,;COL1A1,upstream_gene_variant,,ENST00000494334,;COL1A1,downstream_gene_variant,,ENST00000474644,;COL1A1,upstream_gene_variant,,ENST00000476387,;COL1A1,downstream_gene_variant,,ENST00000485870,;COL1A1,upstream_gene_variant,,ENST00000504289,;COL1A1,downstream_gene_variant,,ENST00000495677,;COL1A1,upstream_gene_variant,,ENST00000463440,;	A	ENSG00000108821	ENST00000225964	Transcript	missense_variant	1393	1274	425	G/V	gGc/gTc	.	.	.	-1	COL1A1	HGNC	2197	protein_coding	YES	CCDS11561.1	ENSP00000225964	CO1A1_HUMAN	Q9UMA6_HUMAN,Q6LAN8_HUMAN	UPI000013C88B	.	.	unknown(0)	19/51	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF54,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGGCCGCCG	.	5	ESCA
ABCA6	0	.	GRCh37	17	67080613	67080613	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4220A>G	p.Asn1407Ser	p.N1407S	ENST00000284425	33/39	15	11	4	33	33	0	ABCA6,missense_variant,p.Asn1407Ser,ENST00000284425,;ABCA6,non_coding_transcript_exon_variant,,ENST00000446604,;ABCA6,downstream_gene_variant,,ENST00000589482,;	C	ENSG00000154262	ENST00000284425	Transcript	missense_variant	4395	4220	1407	N/S	aAt/aGt	.	.	.	-1	ABCA6	HGNC	36	protein_coding	YES	CCDS11683.1	ENSP00000284425	ABCA6_HUMAN	.	UPI000013DD9D	.	deleterious(0.02)	benign(0.217)	33/39	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229:SF13,hmmpanther:PTHR19229,Pfam_domain:PF00005,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACATTCAGC	.	5	ESCA
GRB2	0	.	GRCh37	17	73316406	73316406	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*43C>T	.	.	ENST00000392562	6/6	47	27	19	71	71	0	GRB2,3_prime_UTR_variant,,ENST00000316804,;GRB2,3_prime_UTR_variant,,ENST00000316615,;GRB2,3_prime_UTR_variant,,ENST00000392562,;GRB2,3_prime_UTR_variant,,ENST00000392564,;GRB2,3_prime_UTR_variant,,ENST00000392563,;GRB2,intron_variant,,ENST00000581959,;GRB2,downstream_gene_variant,,ENST00000578961,;GRB2,downstream_gene_variant,,ENST00000582582,;GRB2,downstream_gene_variant,,ENST00000462266,;AC011933.1,upstream_gene_variant,,ENST00000535682,;	A	ENSG00000177885	ENST00000392562	Transcript	3_prime_UTR_variant	1480	.	.	.	.	.	.	.	-1	GRB2	HGNC	4566	protein_coding	YES	CCDS11721.1	ENSP00000376345	GRB2_HUMAN	J3KT38_HUMAN,B0LPF3_HUMAN	UPI000004EF93	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGTGTTTTA	.	5	ESCA
MGAT5B	0	.	GRCh37	17	74898723	74898723	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.449T>C	p.Leu150Pro	p.L150P	ENST00000428789	3/16	55	44	11	86	86	0	MGAT5B,missense_variant,p.Leu150Pro,ENST00000428789,;MGAT5B,missense_variant,p.Leu139Pro,ENST00000569840,;MGAT5B,missense_variant,p.Leu139Pro,ENST00000301618,;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,missense_variant,p.Leu150Pro,ENST00000565043,;	C	ENSG00000167889	ENST00000428789	Transcript	missense_variant	552	449	150	L/P	cTg/cCg	.	.	.	1	MGAT5B	HGNC	24140	protein_coding	YES	CCDS45788.1	ENSP00000391227	MGT5B_HUMAN	.	UPI0000231C88	.	deleterious(0)	probably_damaging(1)	3/16	.	hmmpanther:PTHR15075:SF4,hmmpanther:PTHR15075	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATCCTGCGCC	.	4	ESCA
TP53	0	.	GRCh37	17	7577515	7577517	+	In_Frame_Del	DEL	TGA	TGA	-	.	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	TGA	TGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.764_766delTCA	p.Ile255del	p.I255del	ENST00000269305	7/11	32	9	23	39	39	0	TP53,inframe_deletion,p.Ile255del,ENST00000413465,;TP53,inframe_deletion,p.Ile255del,ENST00000420246,;TP53,inframe_deletion,p.Ile255del,ENST00000269305,;TP53,inframe_deletion,p.Ile123del,ENST00000509690,;TP53,inframe_deletion,p.Ile255del,ENST00000359597,;TP53,inframe_deletion,p.Ile255del,ENST00000445888,;TP53,inframe_deletion,p.Ile255del,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	-	ENSG00000141510	ENST00000269305	Transcript	inframe_deletion	954-956	764-766	255-256	IT/T	aTCAca/aca	COSM1480061,COSM1480062,COSM1480063	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	7/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	deletion	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.L257V|c.769C>G|5,CODON|p.T256T|c.768A>G|5,CODON|p.T256fs*89|c.766delA|3,CODON|p.T256fs*8|c.766_767insA|3,CODON|p.T256K|c.767C>A|4,CODON|p.T256A|c.766A>G|3,CODON|p.I255delI|c.763_765delATC|8,BUFFER|p.S260fs*85|c.778delT|3,BUFFER|p.D259E|c.777C>A|3,BUFFER|p.D259V|c.776A>T|17,BUFFER|p.D259V|c.776A>T|3,BUFFER|p.D259V|c.776A>T|3,BUFFER|p.D259G|c.776A>G|4,BUFFER|p.D259fs*86|c.775delG|3,BUFFER|p.D259N|c.775G>A|6,BUFFER|p.D259Y|c.775G>T|6,BUFFER|p.D259H|c.775G>C|3,BUFFER|p.D259Y|c.775G>T|23,BUFFER|p.D259Y|c.775G>T|4,BUFFER|p.D259Y|c.775G>T|6,BUFFER|p.E258D|c.774A>T|3,BUFFER|p.E258D|c.774A>C|3,BUFFER|p.E258D|c.774A>T|9,BUFFER|p.E258D|c.774A>T|3,BUFFER|p.E258G|c.773A>G|9,BUFFER|p.E258V|c.773A>T|10,BUFFER|p.E258A|c.773A>C|6,BUFFER|p.E258*|c.772G>T|20,BUFFER|p.E258K|c.772G>A|3,BUFFER|p.E258Q|c.772G>C|9,BUFFER|p.E258*|c.772G>T|8,BUFFER|p.E258*|c.772G>T|8,BUFFER|p.E258K|c.772G>A|43,BUFFER|p.E258K|c.772G>A|3,BUFFER|p.L257L|c.771G>A|3,BUFFER|p.L257P|c.770T>C|11,BUFFER|p.L257Q|c.770T>A|3,BUFFER|p.L257Q|c.770T>A|3,BUFFER|p.L257Q|c.770T>A|11,BUFFER|p.I255S|c.764T>G|4,BUFFER|p.I255S|c.764T>G|5,BUFFER|p.I255T|c.764T>C|7,BUFFER|p.I255N|c.764T>A|9,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255N|c.764T>A|3,BUFFER|p.I255S|c.764T>G|5,BUFFER|p.I255S|c.764T>G|10,BUFFER|p.I255delI|c.760_762delATC|3,BUFFER|p.I255fs*90|c.762delC|3,BUFFER|p.L252_I254delLTI|c.754_762delCTCACCATC|4,BUFFER|p.I255fs*9|c.762_763insN|3,BUFFER|p.I255V|c.763A>G|3,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|8,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|3,BUFFER|p.I255F|c.763A>T|25,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254S|c.761T>G|9,BUFFER|p.I254N|c.761T>A|4,BUFFER|p.I254S|c.761T>G|3,BUFFER|p.I254T|c.761T>C|3,BUFFER|p.I254F|c.760A>T|7,BUFFER|p.I254V|c.760A>G|6,BUFFER|p.L252_I254delLTI|c.751_759delATCCTCACC|4,BUFFER|p.I254fs*10|c.759_760insN|4,BUFFER|p.T253I|c.758C>T|4,BUFFER|p.T253N|c.758C>A|3,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.L252delL|c.754_756delCTC|9,BUFFER|p.L252delL|c.754_756delCTC|4,BUFFER|p.T253P|c.757A>C|3,BUFFER|p.T253S|c.757A>T|5,BUFFER|p.T253A|c.757A>G|3,BUFFER|p.L252fs*93|c.754delC|5,BUFFER|p.L252P|c.755T>C|10,BUFFER|p.L252P|c.755T>C|3,BUFFER|p.L252P|c.755T>C|3,BUFFER|p.L252F|c.754C>T|10,BUFFER|p.I251I|c.753C>A|3	INDELOCATOR*|VARSCANI*|PINDEL	CCAGTGTGATGATG	.	3	ESCA
BAIAP2	0	.	GRCh37	17	79005144	79005144	+	5'Flank	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000321300	.	52	44	8	98	98	0	BAIAP2,upstream_gene_variant,,ENST00000428708,;BAIAP2,upstream_gene_variant,,ENST00000435091,;BAIAP2,upstream_gene_variant,,ENST00000571530,;BAIAP2,upstream_gene_variant,,ENST00000321300,;BAIAP2,upstream_gene_variant,,ENST00000575245,;BAIAP2,upstream_gene_variant,,ENST00000575712,;BAIAP2,upstream_gene_variant,,ENST00000575989,;BAIAP2,upstream_gene_variant,,ENST00000392411,;BAIAP2,upstream_gene_variant,,ENST00000321280,;BAIAP2-AS1,non_coding_transcript_exon_variant,,ENST00000573167,;BAIAP2-AS1,non_coding_transcript_exon_variant,,ENST00000542745,;BAIAP2-AS1,non_coding_transcript_exon_variant,,ENST00000577066,;BAIAP2,upstream_gene_variant,,ENST00000573894,;BAIAP2,upstream_gene_variant,,ENST00000570913,;BAIAP2,upstream_gene_variant,,ENST00000575750,;BAIAP2,upstream_gene_variant,,ENST00000572329,;BAIAP2,upstream_gene_variant,,ENST00000576470,;	A	ENSG00000175866	ENST00000321300	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3818	1	BAIAP2	HGNC	947	protein_coding	YES	CCDS11775.1	ENSP00000316338	BAIP2_HUMAN	I3L526_HUMAN,I3L327_HUMAN,I3L2M4_HUMAN,I3L1C8_HUMAN,I3L125_HUMAN,I3L113_HUMAN,I3L0Y9_HUMAN,I3L0M4_HUMAN	UPI000000D762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGTGCTTTAAT	.	3	ESCA
INO80C	0	.	GRCh37	18	33077820	33077820	+	Missense_Mutation	SNP	T	T	C	rs375954359	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19A>G	p.Ile7Val	p.I7V	ENST00000441607	1/7	57	54	3	110	110	0	INO80C,missense_variant,p.Ile7Val,ENST00000334598,;RP11-322E11.6,missense_variant,p.Ile7Val,ENST00000589258,;INO80C,missense_variant,p.Ile7Val,ENST00000441607,;INO80C,missense_variant,p.Ile7Val,ENST00000592173,;INO80C,missense_variant,p.Ile7Val,ENST00000590757,;INO80C,missense_variant,p.Ile7Val,ENST00000587450,;INO80C,upstream_gene_variant,,ENST00000589273,;INO80C,upstream_gene_variant,,ENST00000586489,;INO80C,missense_variant,p.Ile7Val,ENST00000586449,;INO80C,non_coding_transcript_exon_variant,,ENST00000589053,;INO80C,non_coding_transcript_exon_variant,,ENST00000283410,;INO80C,non_coding_transcript_exon_variant,,ENST00000585971,;	C	ENSG00000153391	ENST00000441607	Transcript	missense_variant	88	19	7	I/V	Att/Gtt	rs375954359,COSM988155	.	.	-1	INO80C	HGNC	26994	protein_coding	YES	CCDS45853.1	ENSP00000391457	IN80C_HUMAN	K7EIY8_HUMAN,K7EKI6_HUMAN	UPI0000201BD0	.	deleterious_low_confidence(0.01)	benign(0.062)	1/7	.	hmmpanther:PTHR31200,hmmpanther:PTHR31200:SF1	.	.	.	.	.	.	.	C:0	C:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACAATTGGAA	byFrequency|byCluster	2	ESCA
RNF165	0	.	GRCh37	18	44037339	44037339	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*740T>G	.	.	ENST00000269439	8/8	28	21	6	63	63	0	RNF165,3_prime_UTR_variant,,ENST00000543885,;RNF165,3_prime_UTR_variant,,ENST00000269439,;RNF165,3_prime_UTR_variant,,ENST00000586604,;RNF165,downstream_gene_variant,,ENST00000592777,;	G	ENSG00000141622	ENST00000269439	Transcript	3_prime_UTR_variant	1832	.	.	.	.	.	.	.	1	RNF165	HGNC	31696	protein_coding	YES	CCDS32823.1	ENSP00000269439	RN165_HUMAN	K7EQ96_HUMAN	UPI00001C0E38	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGTTTACAG	.	5	ESCA
BOD1L2	0	.	GRCh37	18	54815059	54815059	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.516C>T	p.%3D	p.S172S	ENST00000585477	1/1	14	11	3	38	38	0	BOD1L2,synonymous_variant,p.%3D,ENST00000585477,;CTD-2526M8.3,upstream_gene_variant,,ENST00000590942,;	T	ENSG00000228075	ENST00000585477	Transcript	synonymous_variant	767	516	172	S	tcC/tcT	.	.	.	1	BOD1L2	HGNC	28505	protein_coding	YES	CCDS59322.1	ENSP00000467843	BD1L2_HUMAN	.	UPI000006F702	.	.	.	1/1	.	hmmpanther:PTHR31532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTCCTAAGA	.	2	ESCA
KIAA1468	0	.	GRCh37	18	59974033	59974033	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1266G>T	.	.	ENST00000398130	29/29	51	38	13	86	85	1	KIAA1468,3_prime_UTR_variant,,ENST00000256858,;KIAA1468,3_prime_UTR_variant,,ENST00000398130,;	T	ENSG00000134444	ENST00000398130	Transcript	3_prime_UTR_variant	5149	.	.	.	.	.	.	.	1	KIAA1468	HGNC	29289	protein_coding	YES	CCDS11979.2	ENSP00000381198	K1468_HUMAN	Q96ES0_HUMAN	UPI0000DA5AF7	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTAGCACAG	.	5	ESCA
CDH19	0	.	GRCh37	18	64235834	64235834	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.309G>T	p.Gln103His	p.Q103H	ENST00000262150	3/12	23	17	6	69	69	0	CDH19,missense_variant,p.Gln103His,ENST00000540086,;CDH19,missense_variant,p.Gln103His,ENST00000262150,;CDH19,missense_variant,p.Gln92His,ENST00000454642,;CDH19,downstream_gene_variant,,ENST00000580157,;CDH19,missense_variant,p.Gln103His,ENST00000579658,;	A	ENSG00000071991	ENST00000262150	Transcript	missense_variant	602	309	103	Q/H	caG/caT	.	.	.	-1	CDH19	HGNC	1758	protein_coding	YES	CCDS11994.1	ENSP00000262150	CAD19_HUMAN	Q96KY9_HUMAN,J3QS15_HUMAN,F8VVI9_HUMAN	UPI0000048ECF	.	deleterious(0)	probably_damaging(0.933)	3/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF255,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTCTGTAT	.	5	ESCA
KEAP1	0	.	GRCh37	19	10602767	10602767	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811G>A	p.Val271Met	p.V271M	ENST00000171111	3/6	21	17	4	28	28	0	KEAP1,missense_variant,p.Val271Met,ENST00000393623,;KEAP1,missense_variant,p.Val271Met,ENST00000592055,;KEAP1,missense_variant,p.Val271Met,ENST00000171111,;KEAP1,upstream_gene_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000591419,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,non_coding_transcript_exon_variant,,ENST00000588024,;KEAP1,3_prime_UTR_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,;KEAP1,upstream_gene_variant,,ENST00000590593,;	T	ENSG00000079999	ENST00000171111	Transcript	missense_variant	1359	811	271	V/M	Gtg/Atg	COSM1524059	.	.	-1	KEAP1	HGNC	23177	protein_coding	YES	CCDS12239.1	ENSP00000171111	KEAP1_HUMAN	K7ESE0_HUMAN,K7EJD8_HUMAN,K7EJ49_HUMAN	UPI000007139C	.	deleterious(0)	probably_damaging(0.986)	3/6	.	hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF07707,SMART_domains:SM00875,PIRSF_domain:PIRSF037037	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCACGGCCC	.	5	ESCA
MBD3	0	.	GRCh37	19	1575127	1575148	+	3'Flank	DEL	GCTGCTGGCAAGTGCCAGAAGG	GCTGCTGGCAAGTGCCAGAAGG	-	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	GCTGCTGGCAAGTGCCAGAAGG	GCTGCTGGCAAGTGCCAGAAGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000156825	.	46	34	12	119	119	0	MBD3,downstream_gene_variant,,ENST00000592012,;MBD3,downstream_gene_variant,,ENST00000156825,;MBD3,downstream_gene_variant,,ENST00000590550,;MBD3,downstream_gene_variant,,ENST00000434436,;AC005943.5,non_coding_transcript_exon_variant,,ENST00000588960,;RN7SL477P,upstream_gene_variant,,ENST00000488440,;MBD3,downstream_gene_variant,,ENST00000590830,;MBD3,downstream_gene_variant,,ENST00000589901,;UQCR11,downstream_gene_variant,,ENST00000585937,;	-	ENSG00000071655	ENST00000156825	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1530	-1	MBD3	HGNC	6918	protein_coding	YES	CCDS12072.1	ENSP00000156825	MBD3_HUMAN	K7EIE8_HUMAN,B3KMA8_HUMAN	UPI000003166B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTGCTGCTGCTGGCAAGTGCCAGAAGGGCTGC	.	3	ESCA
ZNF429	0	.	GRCh37	19	21720005	21720005	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150C>A	p.Leu384Ile	p.L384I	ENST00000358491	4/4	36	25	11	69	69	0	ZNF429,missense_variant,p.Leu384Ile,ENST00000358491,;ZNF429,intron_variant,,ENST00000597078,;ZNF429,upstream_gene_variant,,ENST00000594385,;ZNF429,downstream_gene_variant,,ENST00000594022,;	A	ENSG00000197013	ENST00000358491	Transcript	missense_variant	1358	1150	384	L/I	Ctt/Att	.	.	.	1	ZNF429	HGNC	20817	protein_coding	YES	CCDS42537.1	ENSP00000351280	ZN429_HUMAN	.	UPI000022ABC2	.	deleterious(0)	probably_damaging(0.991)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF239,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGACTTACT	.	5	ESCA
ZNF382	0	.	GRCh37	19	37117924	37117924	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125G>A	p.%3D	p.T375T	ENST00000292928	5/5	18	7	10	30	30	0	ZNF382,synonymous_variant,p.%3D,ENST00000435416,;ZNF382,synonymous_variant,p.%3D,ENST00000292928,;ZNF382,synonymous_variant,p.%3D,ENST00000439428,;ZNF382,synonymous_variant,p.%3D,ENST00000423582,;ZNF382,downstream_gene_variant,,ENST00000590785,;CTD-3234P18.2,upstream_gene_variant,,ENST00000585467,;	A	ENSG00000161298	ENST00000292928	Transcript	synonymous_variant	1238	1125	375	T	acG/acA	.	.	.	1	ZNF382	HGNC	17409	protein_coding	YES	CCDS33004.1	ENSP00000292928	ZN382_HUMAN	K7EK67_HUMAN,C9JME7_HUMAN	UPI000013E0E2	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF22,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATACGGGGGA	.	5	ESCA
ZNF226	0	.	GRCh37	19	44680327	44680327	+	Silent	SNP	A	A	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912A>C	p.%3D	p.G304G	ENST00000590089	7/7	27	21	5	49	49	0	ZNF226,synonymous_variant,p.%3D,ENST00000590089,;ZNF226,synonymous_variant,p.%3D,ENST00000337433,;ZNF226,synonymous_variant,p.%3D,ENST00000454662,;ZNF226,3_prime_UTR_variant,,ENST00000588883,;ZNF226,downstream_gene_variant,,ENST00000585560,;ZNF226,downstream_gene_variant,,ENST00000586286,;ZNF226,downstream_gene_variant,,ENST00000585678,;ZNF226,downstream_gene_variant,,ENST00000588127,;ZNF226,downstream_gene_variant,,ENST00000413984,;ZNF226,downstream_gene_variant,,ENST00000588742,;ZNF226,downstream_gene_variant,,ENST00000589160,;ZNF226,downstream_gene_variant,,ENST00000300823,;ZNF226,downstream_gene_variant,,ENST00000590524,;ZNF226,downstream_gene_variant,,ENST00000586203,;ZNF226,downstream_gene_variant,,ENST00000586914,;ZNF226,downstream_gene_variant,,ENST00000590467,;ZNF226,downstream_gene_variant,,ENST00000588795,;ZNF226,downstream_gene_variant,,ENST00000590578,;ZNF226,downstream_gene_variant,,ENST00000590759,;	C	ENSG00000167380	ENST00000590089	Transcript	synonymous_variant	1279	912	304	G	ggA/ggC	.	.	.	1	ZNF226	HGNC	13019	protein_coding	YES	CCDS46102.1	ENSP00000465121	ZN226_HUMAN	Q9NR94_HUMAN,K7ESM6_HUMAN,K7ERY1_HUMAN,K7EQC3_HUMAN,K7EPU4_HUMAN,K7ELM4_HUMAN,K7ELA3_HUMAN,K7EL77_HUMAN,K7EKQ6_HUMAN,K7EJ66_HUMAN	UPI000013C32A	.	.	.	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF177,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGGAGAAAA	.	5	ESCA
NKPD1	0	.	GRCh37	19	45656613	45656613	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1082C>G	p.Ser361Ter	p.S361*	ENST00000317951	4/4	11	7	4	9	9	0	NKPD1,stop_gained,p.Ser139Ter,ENST00000589776,;NKPD1,stop_gained,p.Ser361Ter,ENST00000317951,;NKPD1,stop_gained,p.Ser139Ter,ENST00000438936,;NKPD1,stop_gained,p.Ser139Ter,ENST00000429338,;MARK4,intron_variant,,ENST00000587566,;AC005757.7,upstream_gene_variant,,ENST00000589594,;	C	ENSG00000179846	ENST00000317951	Transcript	stop_gained	1082	1082	361	S/*	tCa/tGa	.	.	.	-1	NKPD1	HGNC	24739	protein_coding	YES	.	ENSP00000321976	.	J3KNK3_HUMAN	UPI000059D74A	.	.	.	4/4	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22674,hmmpanther:PTHR22674:SF4,Pfam_domain:PF07693	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAGTGACAAG	.	2	ESCA
CKM	0	.	GRCh37	19	45809917	45809917	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*91C>G	.	.	ENST00000221476	8/8	42	33	8	68	68	0	CKM,3_prime_UTR_variant,,ENST00000221476,;MARK4,downstream_gene_variant,,ENST00000262891,;MARK4,downstream_gene_variant,,ENST00000300843,;	C	ENSG00000104879	ENST00000221476	Transcript	3_prime_UTR_variant	1412	.	.	.	.	.	.	.	-1	CKM	HGNC	1994	protein_coding	YES	CCDS12659.1	ENSP00000221476	KCRM_HUMAN	.	UPI000012DCC3	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGGGGGCGG	.	5	ESCA
BAX	0	.	GRCh37	19	49464862	49464862	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*508C>T	.	.	ENST00000293288	5/5	12	9	3	17	17	0	BAX,missense_variant,p.Ala183Val,ENST00000345358,;BAX,missense_variant,p.Ala170Val,ENST00000415969,;BAX,missense_variant,p.Ala134Val,ENST00000354470,;BAX,missense_variant,p.Ala117Val,ENST00000506183,;BAX,3_prime_UTR_variant,,ENST00000391871,;BAX,3_prime_UTR_variant,,ENST00000539787,;BAX,3_prime_UTR_variant,,ENST00000293288,;FTL,upstream_gene_variant,,ENST00000331825,;CTD-2639E6.9,upstream_gene_variant,,ENST00000599784,;CTD-2639E6.9,upstream_gene_variant,,ENST00000594305,;BAX,3_prime_UTR_variant,,ENST00000356483,;BAX,non_coding_transcript_exon_variant,,ENST00000513545,;BAX,non_coding_transcript_exon_variant,,ENST00000502487,;BAX,downstream_gene_variant,,ENST00000503726,;BAX,downstream_gene_variant,,ENST00000513217,;	T	ENSG00000087088	ENST00000293288	Transcript	3_prime_UTR_variant	1165	.	.	.	.	.	.	.	1	BAX	HGNC	959	protein_coding	YES	CCDS12744.1	ENSP00000293288	BAX_HUMAN	Q9UEI8_HUMAN,Q8WXU1_HUMAN,Q5ZPJ1_HUMAN,I6LPK7_HUMAN	UPI000000D900	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCGCCTCAC	.	2	ESCA
PRKCG	0	.	GRCh37	19	54395792	54395792	+	Missense_Mutation	SNP	G	G	A	rs760409355	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.716G>A	p.Arg239Gln	p.R239Q	ENST00000263431	7/18	91	75	16	159	159	0	PRKCG,missense_variant,p.Arg126Gln,ENST00000542049,;PRKCG,missense_variant,p.Arg239Gln,ENST00000540413,;PRKCG,missense_variant,p.Arg239Gln,ENST00000536044,;PRKCG,missense_variant,p.Arg239Gln,ENST00000263431,;PRKCG,downstream_gene_variant,,ENST00000419486,;PRKCG,downstream_gene_variant,,ENST00000474397,;PRKCG,downstream_gene_variant,,ENST00000479081,;	A	ENSG00000126583	ENST00000263431	Transcript	missense_variant	998	716	239	R/Q	cGg/cAg	rs760409355	.	.	1	PRKCG	HGNC	9402	protein_coding	YES	CCDS12867.1	ENSP00000263431	KPCG_HUMAN	M0R0Z4_HUMAN,M0R0I9_HUMAN,H7BZ60_HUMAN	UPI000000DC69	.	deleterious(0.03)	benign(0.434)	7/18	.	Superfamily_domains:SSF49562,PIRSF_domain:PIRSF000550,SMART_domains:SM00239,Gene3D:2.60.40.150,Pfam_domain:PF00168,hmmpanther:PTHR24357,hmmpanther:PTHR24357:SF64,PROSITE_profiles:PS50004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCCGGCTCA	.	5	ESCA
SSC5D	0	.	GRCh37	19	56001756	56001756	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567G>A	p.%3D	p.T189T	ENST00000389623	5/14	22	16	6	36	36	0	SSC5D,synonymous_variant,p.%3D,ENST00000389623,;SSC5D,synonymous_variant,p.%3D,ENST00000587166,;SSC5D,downstream_gene_variant,,ENST00000594321,;NAT14,downstream_gene_variant,,ENST00000591590,;NAT14,downstream_gene_variant,,ENST00000588985,;SSC5D,upstream_gene_variant,,ENST00000589020,;NAT14,downstream_gene_variant,,ENST00000587400,;NAT14,downstream_gene_variant,,ENST00000205194,;NAT14,downstream_gene_variant,,ENST00000592719,;SSC5D,non_coding_transcript_exon_variant,,ENST00000588254,;	A	ENSG00000179954	ENST00000389623	Transcript	synonymous_variant	590	567	189	T	acG/acA	.	.	.	1	SSC5D	HGNC	26641	protein_coding	YES	CCDS46196.1	ENSP00000374274	SRCRL_HUMAN	M0QZ17_HUMAN	UPI000192952A	.	.	.	5/14	.	hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTGACGACAGG	.	4	ESCA
NBPF6	0	.	GRCh37	1	109008025	109008025	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1639G>T	p.Gly547Trp	p.G547W	ENST00000444143	13/15	26	12	14	44	44	0	NBPF6,missense_variant,p.Gly547Trp,ENST00000495380,;NBPF6,missense_variant,p.Gly547Trp,ENST00000444143,;NBPF6,missense_variant,p.Gly576Trp,ENST00000370040,;NBPF6,3_prime_UTR_variant,,ENST00000294652,;NBPF6,downstream_gene_variant,,ENST00000531446,;	T	ENSG00000186086	ENST00000444143	Transcript	missense_variant	1857	1639	547	G/W	Ggg/Tgg	.	.	.	1	NBPF6	HGNC	31988	protein_coding	YES	CCDS44184.1	ENSP00000402703	NBPF6_HUMAN	.	UPI0000160A67	.	deleterious(0)	probably_damaging(0.999)	13/15	.	hmmpanther:PTHR14199:SF13,hmmpanther:PTHR14199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	ATTCTGGGAAC	.	3	ESCA
CASQ2	0	.	GRCh37	1	116243784	116243784	+	3'UTR	SNP	T	T	G	rs201492152	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*78A>C	.	.	ENST00000261448	11/11	22	13	8	71	71	0	CASQ2,3_prime_UTR_variant,,ENST00000456138,;CASQ2,3_prime_UTR_variant,,ENST00000261448,;VANGL1,downstream_gene_variant,,ENST00000355485,;VANGL1,downstream_gene_variant,,ENST00000369510,;	G	ENSG00000118729	ENST00000261448	Transcript	3_prime_UTR_variant	1518	.	.	.	.	rs201492152	.	.	-1	CASQ2	HGNC	1513	protein_coding	YES	CCDS884.1	ENSP00000261448	CASQ2_HUMAN	.	UPI0000126F16	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAATTGCTTG	.	5	ESCA
RUSC1	0	.	GRCh37	1	155296483	155296483	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1974T>C	p.%3D	p.T658T	ENST00000368352	8/10	22	12	9	45	45	0	RUSC1,synonymous_variant,p.%3D,ENST00000292254,;RUSC1,synonymous_variant,p.%3D,ENST00000368352,;RUSC1,synonymous_variant,p.%3D,ENST00000368347,;RUSC1,synonymous_variant,p.%3D,ENST00000368349,;RUSC1,intron_variant,,ENST00000368354,;RUSC1-AS1,upstream_gene_variant,,ENST00000450199,;RUSC1-AS1,upstream_gene_variant,,ENST00000443642,;RUSC1,non_coding_transcript_exon_variant,,ENST00000462780,;RUSC1,non_coding_transcript_exon_variant,,ENST00000497930,;RUSC1,non_coding_transcript_exon_variant,,ENST00000485924,;RUSC1,non_coding_transcript_exon_variant,,ENST00000467820,;RUSC1,non_coding_transcript_exon_variant,,ENST00000490373,;RUSC1,non_coding_transcript_exon_variant,,ENST00000489860,;RUSC1,non_coding_transcript_exon_variant,,ENST00000473331,;RUSC1,non_coding_transcript_exon_variant,,ENST00000492536,;RUSC1,non_coding_transcript_exon_variant,,ENST00000468764,;RUSC1,intron_variant,,ENST00000471876,;RUSC1,intron_variant,,ENST00000479924,;RUSC1,intron_variant,,ENST00000484664,;	C	ENSG00000160753	ENST00000368352	Transcript	synonymous_variant	2125	1974	658	T	acT/acC	.	.	.	1	RUSC1	HGNC	17153	protein_coding	YES	CCDS41410.1	ENSP00000357336	RUSC1_HUMAN	Q68CX2_HUMAN	UPI000046FDA5	.	.	.	8/10	.	PROSITE_profiles:PS50826,hmmpanther:PTHR15591,Pfam_domain:PF02759,SMART_domains:SM00593,Superfamily_domains:0052343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCACTTTCCA	.	5	ESCA
C1orf61	0	.	GRCh37	1	156374385	156374386	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431dupA	p.Lys145GlufsTer19	p.K145Efs*19	ENST00000368243	7/7	29	19	10	68	68	0	C1orf61,frameshift_variant,p.Lys158GlufsTer19,ENST00000357975,;C1orf61,frameshift_variant,p.Lys145GlufsTer19,ENST00000368243,;C1orf61,frameshift_variant,p.Arg119LysfsTer14,ENST00000310027,;C1orf61,frameshift_variant,p.Arg45LysfsTer14,ENST00000400991,;C1orf61,frameshift_variant,p.Lys177GlufsTer19,ENST00000368242,;C1orf61,non_coding_transcript_exon_variant,,ENST00000492750,;C1orf61,non_coding_transcript_exon_variant,,ENST00000497824,;C1orf61,non_coding_transcript_exon_variant,,ENST00000462458,;C1orf61,non_coding_transcript_exon_variant,,ENST00000486517,;C1orf61,non_coding_transcript_exon_variant,,ENST00000464238,;C1orf61,non_coding_transcript_exon_variant,,ENST00000465270,;C1orf61,non_coding_transcript_exon_variant,,ENST00000471156,;C1orf61,non_coding_transcript_exon_variant,,ENST00000497822,;C1orf61,non_coding_transcript_exon_variant,,ENST00000498346,;C1orf61,non_coding_transcript_exon_variant,,ENST00000488498,;C1orf61,non_coding_transcript_exon_variant,,ENST00000465570,;C1orf61,downstream_gene_variant,,ENST00000489877,;C1orf61,downstream_gene_variant,,ENST00000484428,;C1orf61,downstream_gene_variant,,ENST00000482932,;C1orf61,downstream_gene_variant,,ENST00000489918,;C1orf61,non_coding_transcript_exon_variant,,ENST00000608007,;	T	ENSG00000125462	ENST00000368243	Transcript	frameshift_variant	548-549	431-432	144	K/KX	aag/aaAg	.	.	.	-1	C1orf61	HGNC	30780	protein_coding	YES	CCDS1142.1	ENSP00000357226	CROC4_HUMAN	.	UPI000006E362	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTTCTTTTT	.	3	ESCA
FCRL4	0	.	GRCh37	1	157545234	157545234	+	3'UTR	SNP	C	C	T	rs541546477	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*80G>A	.	.	ENST00000271532	12/12	18	11	7	20	20	0	FCRL4,3_prime_UTR_variant,,ENST00000271532,;FCRL4,non_coding_transcript_exon_variant,,ENST00000448509,;FCRL4,downstream_gene_variant,,ENST00000479869,;	T	ENSG00000163518	ENST00000271532	Transcript	3_prime_UTR_variant	1764	.	.	.	.	rs541546477	.	.	-1	FCRL4	HGNC	18507	protein_coding	YES	CCDS1166.1	ENSP00000271532	FCRL4_HUMAN	.	UPI000006E26B	.	.	.	12/12	.	.	T:0.0042	T:0	T:0	.	T:0	T:0	T:0.0215	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCCGCAAG	byFrequency|byCluster|by1000G	5	ESCA
C1orf111	0	.	GRCh37	1	162344173	162344173	+	Nonsense_Mutation	SNP	G	G	A	rs769916432	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451C>T	p.Arg151Ter	p.R151*	ENST00000367935	3/3	20	14	6	46	46	0	C1orf111,stop_gained,p.Arg151Ter,ENST00000367935,;RP11-565P22.6,intron_variant,,ENST00000431696,;C1orf226,intron_variant,,ENST00000420220,;NOS1AP,downstream_gene_variant,,ENST00000493151,;C1orf226,upstream_gene_variant,,ENST00000426197,;NOS1AP,downstream_gene_variant,,ENST00000361897,;NOS1AP,intron_variant,,ENST00000367932,;C1orf111,downstream_gene_variant,,ENST00000493255,;	A	ENSG00000171722	ENST00000367935	Transcript	stop_gained	531	451	151	R/*	Cga/Tga	rs769916432	.	.	-1	C1orf111	HGNC	27648	protein_coding	YES	CCDS1238.1	ENSP00000356912	CA111_HUMAN	.	UPI000013EC35	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTCGAGGGC	.	5	ESCA
PRRC2C	0	.	GRCh37	1	171560972	171560972	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8440G>C	p.Glu2814Gln	p.E2814Q	ENST00000338920	34/34	47	38	8	101	101	0	PRRC2C,missense_variant,p.Glu2814Gln,ENST00000338920,;PRRC2C,missense_variant,p.Glu2816Gln,ENST00000367742,;PRRC2C,missense_variant,p.Glu2749Gln,ENST00000426496,;PRRC2C,missense_variant,p.Glu2895Gln,ENST00000392078,;PRRC2C,missense_variant,p.Glu1297Gln,ENST00000495585,;PRRC2C,non_coding_transcript_exon_variant,,ENST00000498596,;PRRC2C,downstream_gene_variant,,ENST00000492811,;	C	ENSG00000117523	ENST00000338920	Transcript	missense_variant	8677	8440	2814	E/Q	Gaa/Caa	.	.	.	1	PRRC2C	HGNC	24903	protein_coding	YES	CCDS1296.2	ENSP00000343629	PRC2C_HUMAN	.	UPI0000E265EC	.	.	possibly_damaging(0.792)	34/34	.	hmmpanther:PTHR14038:SF6,hmmpanther:PTHR14038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGAAGAAACA	.	5	ESCA
KCNT2	0	.	GRCh37	1	196436841	196436841	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.535A>C	p.Asn179His	p.N179H	ENST00000294725	7/28	55	42	12	104	104	0	KCNT2,missense_variant,p.Asn179His,ENST00000609185,;KCNT2,missense_variant,p.Asn179His,ENST00000294725,;KCNT2,missense_variant,p.Asn179His,ENST00000367433,;KCNT2,missense_variant,p.Asn179His,ENST00000367431,;KCNT2,5_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,;KCNT2,upstream_gene_variant,,ENST00000498426,;	G	ENSG00000162687	ENST00000294725	Transcript	missense_variant	1451	535	179	N/H	Aat/Cat	.	.	.	-1	KCNT2	HGNC	18866	protein_coding	YES	CCDS1384.1	ENSP00000294725	KCNT2_HUMAN	A9LNM6_HUMAN	UPI00001E0966	.	deleterious(0)	probably_damaging(0.991)	7/28	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9,Gene3D:1.10.287.70,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATATTTTCCA	.	5	ESCA
IKBKE	0	.	GRCh37	1	206667323	206667323	+	Missense_Mutation	SNP	C	C	T	rs782670085	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2116C>T	p.Arg706Trp	p.R706W	ENST00000367120	21/22	29	21	8	64	64	0	IKBKE,missense_variant,p.Arg706Trp,ENST00000367120,;IKBKE,missense_variant,p.Arg621Trp,ENST00000537984,;C1orf147,intron_variant,,ENST00000367119,;	T	ENSG00000143466	ENST00000367120	Transcript	missense_variant	2489	2116	706	R/W	Cgg/Tgg	rs782670085	.	.	1	IKBKE	HGNC	14552	protein_coding	YES	CCDS30996.1	ENSP00000356087	IKKE_HUMAN	.	UPI0000033727	.	deleterious(0)	possibly_damaging(0.667)	21/22	.	hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGAACGGTAA	.	5	ESCA
RP4-559A3.7	0	.	GRCh37	1	226108914	226108914	+	Missense_Mutation	SNP	C	C	T	rs777147249	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.569G>A	p.Arg190Gln	p.R190Q	ENST00000432920	5/8	42	28	14	78	77	0	RP4-559A3.7,missense_variant,p.Arg190Gln,ENST00000432920,;PYCR2,missense_variant,p.Arg264Gln,ENST00000343818,;PYCR2,non_coding_transcript_exon_variant,,ENST00000478402,;PYCR2,downstream_gene_variant,,ENST00000472798,;PYCR2,downstream_gene_variant,,ENST00000467298,;PYCR2,downstream_gene_variant,,ENST00000489681,;PYCR2,downstream_gene_variant,,ENST00000466127,;PYCR2,downstream_gene_variant,,ENST00000446534,;PYCR2,downstream_gene_variant,,ENST00000366823,;	T	ENSG00000255835	ENST00000432920	Transcript	missense_variant	737	569	190	R/Q	cGa/cAa	rs777147249	.	.	-1	RP4-559A3.7	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000414068	.	J3KR12_HUMAN	UPI0001AE79EB	.	deleterious_low_confidence(0.01)	possibly_damaging(0.905)	5/8	.	Superfamily_domains:SSF48179,Gene3D:2ahrA02,Pfam_domain:PF14748,hmmpanther:PTHR11645:SF4,hmmpanther:PTHR11645	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTCGGATA	.	5	ESCA
HTR1D	0	.	GRCh37	1	23520239	23520239	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474G>A	p.Met158Ile	p.M158I	ENST00000374619	1/1	16	12	4	18	18	0	HTR1D,missense_variant,p.Met158Ile,ENST00000314113,;HTR1D,missense_variant,p.Met158Ile,ENST00000374619,;	T	ENSG00000179546	ENST00000374619	Transcript	missense_variant	984	474	158	M/I	atG/atA	.	.	.	-1	HTR1D	HGNC	5289	protein_coding	YES	CCDS231.1	ENSP00000363748	5HT1D_HUMAN	.	UPI00000503DE	.	deleterious(0.01)	probably_damaging(0.989)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF17,hmmpanther:PTHR24247,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGATCATGGT	.	5	ESCA
TCEB3	0	.	GRCh37	1	24078325	24078325	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1308C>T	p.%3D	p.Y436Y	ENST00000418390	4/11	42	37	5	55	55	0	TCEB3,synonymous_variant,p.%3D,ENST00000418390,;TCEB3,synonymous_variant,p.%3D,ENST00000609199,;TCEB3,downstream_gene_variant,,ENST00000487554,;	T	ENSG00000011007	ENST00000418390	Transcript	synonymous_variant	1579	1308	436	Y	taC/taT	.	.	.	1	TCEB3	HGNC	11620	protein_coding	YES	CCDS239.2	ENSP00000395574	ELOA1_HUMAN	.	UPI000181BA17	.	.	.	4/11	.	hmmpanther:PTHR15141:SF37,hmmpanther:PTHR15141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTACCTCAG	.	4	ESCA
OR2G2	0	.	GRCh37	1	247752160	247752160	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499C>T	p.%3D	p.L167L	ENST00000320065	1/1	28	18	10	42	42	0	OR2G2,synonymous_variant,p.%3D,ENST00000320065,;RP11-978I15.10,intron_variant,,ENST00000446347,;RP11-978I15.10,intron_variant,,ENST00000435333,;	T	ENSG00000177489	ENST00000320065	Transcript	synonymous_variant	499	499	167	L	Ctg/Ttg	.	.	.	1	OR2G2	HGNC	15007	protein_coding	YES	CCDS31092.1	ENSP00000326349	OR2G2_HUMAN	.	UPI0000061EB9	.	.	.	1/1	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF132,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACCCTGCAG	.	5	ESCA
OR2T33	0	.	GRCh37	1	248436732	248436732	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385C>T	p.Arg129Ter	p.R129*	ENST00000318021	1/1	71	62	9	157	156	0	OR2T33,stop_gained,p.Arg129Ter,ENST00000318021,;	A	ENSG00000177212	ENST00000318021	Transcript	stop_gained	407	385	129	R/*	Cga/Tga	.	.	.	-1	OR2T33	HGNC	31255	protein_coding	YES	CCDS31109.1	ENSP00000324687	O2T33_HUMAN	.	UPI000004B237	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF83,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATCGGAGTG	.	4	ESCA
ZFP69B	0	.	GRCh37	1	40929164	40929164	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1508A>G	p.Tyr503Cys	p.Y503C	ENST00000411995	6/6	36	28	8	45	45	0	ZFP69B,missense_variant,p.Tyr503Cys,ENST00000411995,;ZFP69B,missense_variant,p.Tyr401Cys,ENST00000361584,;ZFP69B,3_prime_UTR_variant,,ENST00000484445,;RP1-228H13.5,upstream_gene_variant,,ENST00000565390,;ZFP69B,non_coding_transcript_exon_variant,,ENST00000469416,;	G	ENSG00000187801	ENST00000411995	Transcript	missense_variant	1883	1508	503	Y/C	tAt/tGt	.	.	.	1	ZFP69B	HGNC	28053	protein_coding	YES	CCDS452.2	ENSP00000399664	ZF69B_HUMAN	D3DPV3_HUMAN	UPI000020582C	.	deleterious(0)	probably_damaging(0.936)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF135,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTATGATT	.	5	ESCA
NDUFAF5	0	.	GRCh37	20	13765855	13765855	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141C>T	p.%3D	p.F47F	ENST00000378106	1/11	87	81	6	138	138	0	NDUFAF5,synonymous_variant,p.%3D,ENST00000463598,;NDUFAF5,synonymous_variant,p.%3D,ENST00000378106,;ESF1,upstream_gene_variant,,ENST00000202816,;NDUFAF5,non_coding_transcript_exon_variant,,ENST00000481249,;NDUFAF5,non_coding_transcript_exon_variant,,ENST00000477732,;NDUFAF5,non_coding_transcript_exon_variant,,ENST00000485738,;NDUFAF5,non_coding_transcript_exon_variant,,ENST00000475968,;NDUFAF5,upstream_gene_variant,,ENST00000469177,;NDUFAF5,upstream_gene_variant,,ENST00000476536,;NDUFAF5,synonymous_variant,p.%3D,ENST00000378081,;	T	ENSG00000101247	ENST00000378106	Transcript	synonymous_variant	260	141	47	F	ttC/ttT	.	.	.	1	NDUFAF5	HGNC	15899	protein_coding	YES	CCDS13118.1	ENSP00000367346	NDUF5_HUMAN	.	UPI0000231C9F	.	.	.	1/11	.	hmmpanther:PTHR13090	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ATTTTCGACCG	.	2	ESCA
DOPEY2	0	.	GRCh37	21	37665662	37665662	+	Silent	SNP	G	G	A	rs777787261	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6690G>A	p.%3D	p.P2230P	ENST00000399151	37/37	13	9	4	24	23	0	DOPEY2,synonymous_variant,p.%3D,ENST00000399151,;SRSF9P1,downstream_gene_variant,,ENST00000399149,;	A	ENSG00000142197	ENST00000399151	Transcript	synonymous_variant	6775	6690	2230	P	ccG/ccA	rs777787261	.	.	1	DOPEY2	HGNC	1291	protein_coding	YES	CCDS13643.1	ENSP00000382104	DOP2_HUMAN	F8W8U9_HUMAN	UPI000013D876	.	.	.	37/37	.	hmmpanther:PTHR14042:SF23,hmmpanther:PTHR14042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	TTCCCGCTTCT	byFrequency	2	ESCA
POTEH	0	.	GRCh37	22	16287805	16287805	+	Missense_Mutation	SNP	C	C	A	rs764623372	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.81G>T	p.Trp27Cys	p.W27C	ENST00000343518	1/11	178	169	9	402	401	1	POTEH,missense_variant,p.Trp27Cys,ENST00000343518,;POTEH,upstream_gene_variant,,ENST00000452800,;	A	ENSG00000198062	ENST00000343518	Transcript	missense_variant	133	81	27	W/C	tgG/tgT	rs764623372	.	.	-1	POTEH	HGNC	133	protein_coding	YES	CCDS46658.1	ENSP00000340610	POTEH_HUMAN	.	UPI0000E5A425	.	deleterious_low_confidence(0.04)	possibly_damaging(0.838)	1/11	.	hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGCACCACTT	.	2	ESCA
MYO18B	0	.	GRCh37	22	26164791	26164791	+	Missense_Mutation	SNP	G	G	T	rs758802253	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.908G>T	p.Gly303Val	p.G303V	ENST00000335473	4/44	54	41	13	150	150	0	MYO18B,missense_variant,p.Gly303Val,ENST00000335473,;MYO18B,missense_variant,p.Gly303Val,ENST00000407587,;MYO18B,missense_variant,p.Gly303Val,ENST00000536101,;MYO18B,missense_variant,p.Gly303Val,ENST00000539302,;MYO18B,upstream_gene_variant,,ENST00000418374,;	T	ENSG00000133454	ENST00000335473	Transcript	missense_variant	1158	908	303	G/V	gGg/gTg	rs758802253,COSM3552796	.	.	1	MYO18B	HGNC	18150	protein_coding	YES	CCDS54507.1	ENSP00000334563	.	Q8N903_HUMAN	UPI0000207402	.	deleterious_low_confidence(0.05)	benign(0.04)	4/44	.	hmmpanther:PTHR13140:SF254,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTAGGGAGTG	.	5	ESCA
FLJ27365	0	.	GRCh37	22	46505687	46505687	+	Missense_Mutation	SNP	C	C	T	rs541213839	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280C>T	p.Arg94Cys	p.R94C	ENST00000360737	5/5	25	19	6	45	45	0	FLJ27365,missense_variant,p.Arg94Cys,ENST00000360737,;FLJ27365,downstream_gene_variant,,ENST00000381051,;MIR4763,upstream_gene_variant,,ENST00000581461,;MIRLET7B,upstream_gene_variant,,ENST00000385140,;MIRLET7A3,upstream_gene_variant,,ENST00000362116,;FLJ27365,3_prime_UTR_variant,,ENST00000435439,;	T	ENSG00000197182	ENST00000360737	Transcript	missense_variant	439	280	94	R/C	Cgc/Tgc	rs541213839	.	.	1	FLJ27365	Uniprot_gn	.	protein_coding	YES	.	ENSP00000353966	.	Q6ZNQ0_HUMAN,B1AKH8_HUMAN	UPI00001C11DA	.	deleterious_low_confidence(0.02)	possibly_damaging(0.835)	5/5	.	.	T:0.0006	T:0	T:0	.	T:0	T:0	T:0.0031	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGCGCTGG	byFrequency|by1000G	5	ESCA
PLXNB2	0	.	GRCh37	22	50728477	50728477	+	Silent	SNP	G	G	A	rs370273991	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.537C>T	p.%3D	p.N179N	ENST00000449103	3/37	13	5	8	48	48	0	PLXNB2,synonymous_variant,p.%3D,ENST00000359337,;PLXNB2,synonymous_variant,p.%3D,ENST00000449103,;PLXNB2,synonymous_variant,p.%3D,ENST00000432455,;PLXNB2,upstream_gene_variant,,ENST00000411680,;PLXNB2,upstream_gene_variant,,ENST00000434732,;PLXNB2,downstream_gene_variant,,ENST00000425954,;PLXNB2,upstream_gene_variant,,ENST00000496720,;	A	ENSG00000196576	ENST00000449103	Transcript	synonymous_variant	678	537	179	N	aaC/aaT	rs370273991	.	.	-1	PLXNB2	HGNC	9104	protein_coding	YES	CCDS43035.1	ENSP00000409171	PLXB2_HUMAN	Q2TBE4_HUMAN,E2PU09_HUMAN,A6QRH1_HUMAN	UPI000003812D	.	.	.	3/37	.	PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF9,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	A:0	A:0.0004	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	ATGCCGTTGTC	byFrequency|byCluster	4	ESCA
TGFBRAP1	0	.	GRCh37	2	105882187	105882187	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1653A>C	.	.	ENST00000393359	12/12	13	8	5	19	19	0	TGFBRAP1,3_prime_UTR_variant,,ENST00000393359,;AC012360.2,downstream_gene_variant,,ENST00000595531,;TGFBRAP1,downstream_gene_variant,,ENST00000258449,;	G	ENSG00000135966	ENST00000393359	Transcript	3_prime_UTR_variant	4663	.	.	.	.	.	.	.	-1	TGFBRAP1	HGNC	16836	protein_coding	YES	CCDS2067.1	ENSP00000377027	TGFA1_HUMAN	.	UPI0000072CA9	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAATTTCTTCA	.	2	ESCA
GPR39	0	.	GRCh37	2	133174826	133174826	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211C>A	p.His71Asn	p.H71N	ENST00000329321	1/2	30	25	4	75	75	0	GPR39,missense_variant,p.His71Asn,ENST00000329321,;	A	ENSG00000183840	ENST00000329321	Transcript	missense_variant	680	211	71	H/N	Cac/Aac	.	.	.	1	GPR39	HGNC	4496	protein_coding	YES	CCDS2170.1	ENSP00000327417	GPR39_HUMAN	Q53RU7_HUMAN,B3KVZ1_HUMAN,A4FVA5_HUMAN	UPI0000046406	.	deleterious(0)	probably_damaging(0.992)	1/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24243:SF106,hmmpanther:PTHR24243,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGACCACATG	.	4	ESCA
CYTIP	0	.	GRCh37	2	158272436	158272436	+	Missense_Mutation	SNP	G	G	A	rs367635230	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.833C>T	p.Thr278Met	p.T278M	ENST00000264192	8/8	14	7	6	29	29	0	CYTIP,missense_variant,p.Thr278Met,ENST00000264192,;CYTIP,missense_variant,p.Thr172Met,ENST00000540637,;CYTIP,downstream_gene_variant,,ENST00000418920,;CYTIP,downstream_gene_variant,,ENST00000457793,;	A	ENSG00000115165	ENST00000264192	Transcript	missense_variant	955	833	278	T/M	aCg/aTg	rs367635230,COSM3961330,COSM1305740	.	.	-1	CYTIP	HGNC	9506	protein_coding	YES	CCDS2204.1	ENSP00000264192	CYTIP_HUMAN	C9JSM2_HUMAN,C9JRF8_HUMAN,C9JNN8_HUMAN,B4DWH9_HUMAN	UPI0000035D67	.	deleterious(0.02)	probably_damaging(0.958)	8/8	.	hmmpanther:PTHR15963,hmmpanther:PTHR15963:SF1	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TACTCGTCTGC	byFrequency|byCluster	4	ESCA
PID1	0	.	GRCh37	2	229890706	229890706	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389C>T	p.Ala130Val	p.A130V	ENST00000392054	4/4	35	28	6	86	86	0	PID1,missense_variant,p.Ala50Val,ENST00000409462,;PID1,missense_variant,p.Ala132Val,ENST00000354069,;PID1,missense_variant,p.Ala99Val,ENST00000392055,;PID1,missense_variant,p.Ala130Val,ENST00000392054,;PID1,intron_variant,,ENST00000482518,;PID1,downstream_gene_variant,,ENST00000534952,;	A	ENSG00000153823	ENST00000392054	Transcript	missense_variant	729	389	130	A/V	gCc/gTc	.	.	.	-1	PID1	HGNC	26084	protein_coding	YES	CCDS2471.1	ENSP00000375907	PCLI1_HUMAN	Q4ZG81_HUMAN	UPI00001C0AF7	.	deleterious(0.03)	possibly_damaging(0.544)	4/4	.	hmmpanther:PTHR16265,hmmpanther:PTHR16265:SF0,Pfam_domain:PF14719,SMART_domains:SM00462,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTGGCCGGA	.	5	ESCA
OR6B2	0	.	GRCh37	2	240969562	240969562	+	Silent	SNP	G	G	A	rs368904252	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285C>T	p.%3D	p.V95V	ENST00000402971	1/1	23	19	3	47	47	0	OR6B2,synonymous_variant,p.%3D,ENST00000402971,;NDUFA10,upstream_gene_variant,,ENST00000307300,;NDUFA10,upstream_gene_variant,,ENST00000443626,;NDUFA10,upstream_gene_variant,,ENST00000407129,;NDUFA10,upstream_gene_variant,,ENST00000404554,;NDUFA10,upstream_gene_variant,,ENST00000252711,;NDUFA10,upstream_gene_variant,,ENST00000414580,;NDUFA10,upstream_gene_variant,,ENST00000497536,;NDUFA10,upstream_gene_variant,,ENST00000485344,;	A	ENSG00000182083	ENST00000402971	Transcript	synonymous_variant	345	285	95	V	gtC/gtT	rs368904252	.	.	-1	OR6B2	HGNC	15041	protein_coding	YES	CCDS46559.1	ENSP00000384563	OR6B2_HUMAN	I0EZ57_HUMAN	UPI0000061EBF	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF106,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F94F|c.282C>T|6	RADIA|MUTECT|VARSCANS	CACCCGACGAA	byFrequency|byCluster	3	ESCA
ZNF513	0	.	GRCh37	2	27600274	27600275	+	3'UTR	INS	-	-	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*137dupT	.	.	ENST00000323703	4/4	42	28	14	39	39	0	ZNF513,3_prime_UTR_variant,,ENST00000407879,;ZNF513,3_prime_UTR_variant,,ENST00000323703,;PPM1G,downstream_gene_variant,,ENST00000344034,;SNX17,downstream_gene_variant,,ENST00000537606,;SNX17,downstream_gene_variant,,ENST00000542478,;ZNF513,downstream_gene_variant,,ENST00000436006,;SNX17,downstream_gene_variant,,ENST00000543024,;PPM1G,downstream_gene_variant,,ENST00000350803,;SNX17,downstream_gene_variant,,ENST00000233575,;ZNF513,downstream_gene_variant,,ENST00000491924,;SNX17,downstream_gene_variant,,ENST00000493711,;SNX17,downstream_gene_variant,,ENST00000453453,;SNX17,downstream_gene_variant,,ENST00000464279,;SNX17,downstream_gene_variant,,ENST00000440760,;PPM1G,downstream_gene_variant,,ENST00000472077,;SNX17,downstream_gene_variant,,ENST00000494893,;SNX17,downstream_gene_variant,,ENST00000489402,;SNX17,downstream_gene_variant,,ENST00000427123,;	A	ENSG00000163795	ENST00000323703	Transcript	3_prime_UTR_variant	1962-1963	.	.	.	.	.	.	.	-1	ZNF513	HGNC	26498	protein_coding	YES	CCDS1751.1	ENSP00000318373	ZN513_HUMAN	C9JT52_HUMAN	UPI00000437BA	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGTCCATATG	.	3	ESCA
SUPT7L	0	.	GRCh37	2	27880464	27880464	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.492A>T	p.%3D	p.T164T	ENST00000337768	4/6	26	22	4	42	42	0	SUPT7L,synonymous_variant,p.%3D,ENST00000464789,;SUPT7L,synonymous_variant,p.%3D,ENST00000405491,;SUPT7L,synonymous_variant,p.%3D,ENST00000404798,;SUPT7L,synonymous_variant,p.%3D,ENST00000406540,;SUPT7L,synonymous_variant,p.%3D,ENST00000337768,;	A	ENSG00000119760	ENST00000337768	Transcript	synonymous_variant	1062	492	164	T	acA/acT	.	.	.	-1	SUPT7L	HGNC	30632	protein_coding	YES	CCDS42667.1	ENSP00000336750	ST65G_HUMAN	.	UPI000013607D	.	.	.	4/6	.	Pfam_domain:PF07524,SMART_domains:SM00576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATTGTGGC	.	4	ESCA
SOX11	0	.	GRCh37	2	5841246	5841246	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7067C>T	.	.	ENST00000322002	1/1	17	11	6	50	50	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	T	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	8448	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAACGGTGT	.	5	ESCA
EHBP1	0	.	GRCh37	2	63176138	63176138	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2262A>C	p.Lys754Asn	p.K754N	ENST00000263991	14/25	21	17	4	42	42	0	EHBP1,missense_variant,p.Lys754Asn,ENST00000263991,;EHBP1,missense_variant,p.Lys719Asn,ENST00000405289,;EHBP1,missense_variant,p.Lys719Asn,ENST00000405015,;EHBP1,missense_variant,p.Lys719Asn,ENST00000431489,;EHBP1,missense_variant,p.Lys719Asn,ENST00000354487,;EHBP1,missense_variant,p.Lys24Asn,ENST00000454124,;EHBP1,intron_variant,,ENST00000444311,;EHBP1,intron_variant,,ENST00000469591,;	C	ENSG00000115504	ENST00000263991	Transcript	missense_variant	2744	2262	754	K/N	aaA/aaC	.	.	.	1	EHBP1	HGNC	29144	protein_coding	YES	CCDS1872.1	ENSP00000263991	EHBP1_HUMAN	C9K0H9_HUMAN,C9JEP1_HUMAN,C9J268_HUMAN,B3KM32_HUMAN	UPI000013D49A	.	tolerated_low_confidence(0.19)	benign(0.002)	14/25	.	hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF124	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCAAAAAAAC	.	4	ESCA
RP11-221J22.1	0	.	GRCh37	3	101713621	101713621	+	RNA	SNP	T	T	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.485T>G	.	.	ENST00000465215	3/4	60	49	10	59	59	0	RP11-221J22.1,non_coding_transcript_exon_variant,,ENST00000465215,;RP11-221J22.2,non_coding_transcript_exon_variant,,ENST00000483840,;RP11-221J22.2,intron_variant,,ENST00000498624,;	G	ENSG00000214407	ENST00000465215	Transcript	non_coding_transcript_exon_variant	485	.	.	.	.	.	.	.	1	RP11-221J22.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAGTAATGG	.	5	ESCA
KALRN	0	.	GRCh37	3	124351417	124351417	+	Missense_Mutation	SNP	G	G	A	rs368927353	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236G>A	p.Arg79His	p.R79H	ENST00000454902	2/4	44	38	6	48	48	0	KALRN,missense_variant,p.Arg79His,ENST00000454902,;KALRN,missense_variant,p.Arg149His,ENST00000393496,;KALRN,missense_variant,p.Arg79His,ENST00000428018,;KALRN,missense_variant,p.Arg79His,ENST00000291478,;KALRN,missense_variant,p.Arg1745His,ENST00000354186,;KALRN,missense_variant,p.Arg1776His,ENST00000360013,;KALRN,upstream_gene_variant,,ENST00000459915,;KALRN,non_coding_transcript_exon_variant,,ENST00000471431,;	A	ENSG00000160145	ENST00000454902	Transcript	missense_variant	376	236	79	R/H	cGt/cAt	rs368927353,COSM1418511,COSM26590,COSM1418510	.	.	1	KALRN	HGNC	4814	protein_coding	.	.	ENSP00000400064	.	C9J1B4_HUMAN	UPI0000E5A8DD	.	deleterious(0)	probably_damaging(0.909)	2/4	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTGCGTCGGC	byFrequency|byCluster	4	ESCA
ACAD9	0	.	GRCh37	3	128616490	128616490	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570C>T	p.%3D	p.A190A	ENST00000308982	6/18	53	44	9	55	55	0	ACAD9,synonymous_variant,p.%3D,ENST00000308982,;ACAD9,downstream_gene_variant,,ENST00000514336,;ACAD9,upstream_gene_variant,,ENST00000511526,;ACAD9,3_prime_UTR_variant,,ENST00000512801,;ACAD9,3_prime_UTR_variant,,ENST00000505867,;ACAD9,3_prime_UTR_variant,,ENST00000514643,;ACAD9,3_prime_UTR_variant,,ENST00000505192,;ACAD9,3_prime_UTR_variant,,ENST00000511227,;ACAD9,downstream_gene_variant,,ENST00000515429,;ACAD9,upstream_gene_variant,,ENST00000508971,;	T	ENSG00000177646	ENST00000308982	Transcript	synonymous_variant	651	570	190	A	gcC/gcT	.	.	.	1	ACAD9	HGNC	21497	protein_coding	YES	CCDS3053.1	ENSP00000312618	ACAD9_HUMAN	Q9H9W4_HUMAN,Q9BUX5_HUMAN,H0Y8Z9_HUMAN	UPI00000498C3	.	.	.	6/18	.	hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF264,PROSITE_patterns:PS00072,Pfam_domain:PF02770,Gene3D:2.40.110.10,Superfamily_domains:SSF56645	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCCTCAAT	.	5	ESCA
ESYT3	0	.	GRCh37	3	138153550	138153550	+	5'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-91C>A	.	.	ENST00000389567	1/23	33	29	4	38	38	0	ESYT3,5_prime_UTR_variant,,ENST00000289135,;ESYT3,5_prime_UTR_variant,,ENST00000389567,;ESYT3,5_prime_UTR_variant,,ENST00000490835,;ESYT3,non_coding_transcript_exon_variant,,ENST00000486831,;	A	ENSG00000158220	ENST00000389567	Transcript	5_prime_UTR_variant	96	.	.	.	.	.	.	.	1	ESYT3	HGNC	24295	protein_coding	YES	CCDS3101.2	ENSP00000374218	ESYT3_HUMAN	.	UPI0000251E45	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCCTCGAGCT	.	4	ESCA
RP11-454C18.2	0	.	GRCh37	3	151493535	151493537	+	Intron	DEL	TGT	TGT	-	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	TGT	TGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.440-1084_440-1082delACA	.	.	ENST00000483843	.	107	33	74	131	131	0	RP11-454C18.2,intron_variant,,ENST00000475855,;RP11-454C18.2,intron_variant,,ENST00000483843,;RP11-64D22.2,non_coding_transcript_exon_variant,,ENST00000462937,;RP11-64D22.2,non_coding_transcript_exon_variant,,ENST00000483636,;RP11-64D22.2,intron_variant,,ENST00000463420,;RP11-64D22.2,intron_variant,,ENST00000496128,;RP11-64D22.2,downstream_gene_variant,,ENST00000471766,;RP11-64D22.2,non_coding_transcript_exon_variant,,ENST00000561502,;	-	ENSG00000242908	ENST00000483843	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RP11-454C18.2	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAATGCTGTTGTTG	.	3	ESCA
P2RY1	0	.	GRCh37	3	152555233	152555233	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*540G>A	.	.	ENST00000305097	1/1	44	38	6	60	60	0	P2RY1,3_prime_UTR_variant,,ENST00000305097,;RP11-38P22.2,upstream_gene_variant,,ENST00000460407,;	A	ENSG00000169860	ENST00000305097	Transcript	3_prime_UTR_variant	2498	.	.	.	.	.	.	.	1	P2RY1	HGNC	8539	protein_coding	YES	CCDS3169.1	ENSP00000304767	P2RY1_HUMAN	.	UPI0000001C06	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATAAGCATAG	.	4	ESCA
EIF4A2	0	.	GRCh37	3	186507053	186507053	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1219A>G	p.Ile407Val	p.I407V	ENST00000323963	11/11	29	20	9	39	39	0	EIF4A2,missense_variant,p.Ile407Val,ENST00000323963,;EIF4A2,missense_variant,p.Ile312Val,ENST00000356531,;EIF4A2,missense_variant,p.Ile408Val,ENST00000440191,;RFC4,downstream_gene_variant,,ENST00000418288,;RFC4,downstream_gene_variant,,ENST00000296273,;RFC4,downstream_gene_variant,,ENST00000433496,;RFC4,downstream_gene_variant,,ENST00000447345,;EIF4A2,downstream_gene_variant,,ENST00000445596,;EIF4A2,downstream_gene_variant,,ENST00000441007,;EIF4A2,downstream_gene_variant,,ENST00000498746,;RFC4,downstream_gene_variant,,ENST00000392481,;RFC4,downstream_gene_variant,,ENST00000417876,;SNORA81,downstream_gene_variant,,ENST00000408493,;SNORA63,downstream_gene_variant,,ENST00000363548,;SNORD2,downstream_gene_variant,,ENST00000459163,;SNORA4,downstream_gene_variant,,ENST00000584302,;SNORA63,downstream_gene_variant,,ENST00000363450,;EIF4A2,3_prime_UTR_variant,,ENST00000426808,;EIF4A2,3_prime_UTR_variant,,ENST00000443963,;EIF4A2,3_prime_UTR_variant,,ENST00000425053,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000496382,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000485101,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000494445,;EIF4A2,downstream_gene_variant,,ENST00000465032,;EIF4A2,downstream_gene_variant,,ENST00000465222,;EIF4A2,downstream_gene_variant,,ENST00000497177,;EIF4A2,downstream_gene_variant,,ENST00000475409,;EIF4A2,downstream_gene_variant,,ENST00000491473,;EIF4A2,downstream_gene_variant,,ENST00000495049,;EIF4A2,downstream_gene_variant,,ENST00000465267,;EIF4A2,downstream_gene_variant,,ENST00000486805,;EIF4A2,downstream_gene_variant,,ENST00000475653,;RFC4,downstream_gene_variant,,ENST00000460408,;RFC4,downstream_gene_variant,,ENST00000479307,;EIF4A2,downstream_gene_variant,,ENST00000468362,;EIF4A2,downstream_gene_variant,,ENST00000467585,;EIF4A2,downstream_gene_variant,,ENST00000465792,;EIF4A2,downstream_gene_variant,,ENST00000429589,;EIF4A2,downstream_gene_variant,,ENST00000466362,;EIF4A2,downstream_gene_variant,,ENST00000492144,;EIF4A2,downstream_gene_variant,,ENST00000461021,;RFC4,downstream_gene_variant,,ENST00000494047,;RFC4,downstream_gene_variant,,ENST00000449502,;	G	ENSG00000156976	ENST00000323963	Transcript	missense_variant	1283	1219	407	I/V	Att/Gtt	.	.	.	1	EIF4A2	HGNC	3284	protein_coding	YES	CCDS3282.1	ENSP00000326381	IF4A2_HUMAN	Q96B07_HUMAN,J3KSN7_HUMAN,E7EMV8_HUMAN,C9JUF0_HUMAN	UPI0000000DD2	.	tolerated(0.12)	benign(0.004)	11/11	.	PROSITE_profiles:PS51194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTATTTAA	.	5	ESCA
TPRG1	0	.	GRCh37	3	189040177	189040177	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1568C>T	.	.	ENST00000345063	6/6	30	27	3	40	40	0	TPRG1,3_prime_UTR_variant,,ENST00000345063,;TPRG1,downstream_gene_variant,,ENST00000433971,;TPRG1,downstream_gene_variant,,ENST00000485836,;	T	ENSG00000188001	ENST00000345063	Transcript	3_prime_UTR_variant	2563	.	.	.	.	.	.	.	1	TPRG1	HGNC	24759	protein_coding	YES	CCDS3292.1	ENSP00000341031	TPRG1_HUMAN	C9JDW1_HUMAN	UPI00001C08BF	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTTCCCTCT	.	2	ESCA
MUC4	0	.	GRCh37	3	195509475	195509475	+	Silent	SNP	A	A	C	rs748507668	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8976T>G	p.%3D	p.L2992L	ENST00000463781	2/25	156	135	21	164	163	1	MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,;MUC4,intron_variant,,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000470451,;MUC4,synonymous_variant,p.%3D,ENST00000477086,;MUC4,synonymous_variant,p.%3D,ENST00000466475,;MUC4,synonymous_variant,p.%3D,ENST00000478156,;MUC4,synonymous_variant,p.%3D,ENST00000479406,;MUC4,synonymous_variant,p.%3D,ENST00000477756,;MUC4,synonymous_variant,p.%3D,ENST00000462323,;MUC4,synonymous_variant,p.%3D,ENST00000480843,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,;	C	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	9436	8976	2992	L	ctT/ctG	rs748507668	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	2/25	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAAGAAGGGT	.	4	ESCA
PIGX	0	.	GRCh37	3	196460740	196460740	+	Silent	SNP	A	A	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.798A>T	p.%3D	p.V266V	ENST00000296333	7/7	87	49	38	67	67	0	PIGX,synonymous_variant,p.%3D,ENST00000392391,;PIGX,synonymous_variant,p.%3D,ENST00000541663,;PIGX,synonymous_variant,p.%3D,ENST00000314118,;PIGX,synonymous_variant,p.%3D,ENST00000296333,;PIGX,downstream_gene_variant,,ENST00000426755,;PIGX,3_prime_UTR_variant,,ENST00000415832,;PIGX,3_prime_UTR_variant,,ENST00000453218,;	T	ENSG00000163964	ENST00000296333	Transcript	synonymous_variant	920	798	266	V	gtA/gtT	.	.	.	1	PIGX	HGNC	26046	protein_coding	YES	CCDS54701.1	ENSP00000296333	.	H0Y2P9_HUMAN,C9JF71_HUMAN,B4DFZ9_HUMAN	UPI00015E0960	.	.	.	7/7	.	Transmembrane_helices:TMhelix,Pfam_domain:PF08320,SMART_domains:SM00780	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTAGCAGT	.	5	ESCA
PTH1R	0	.	GRCh37	3	46939390	46939390	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359T>A	p.Leu120Gln	p.L120Q	ENST00000313049	4/14	26	16	9	70	70	0	PTH1R,missense_variant,p.Leu120Gln,ENST00000430002,;PTH1R,missense_variant,p.Leu120Gln,ENST00000427125,;PTH1R,missense_variant,p.Leu120Gln,ENST00000418619,;PTH1R,missense_variant,p.Leu120Gln,ENST00000449590,;PTH1R,missense_variant,p.Leu120Gln,ENST00000313049,;PTH1R,upstream_gene_variant,,ENST00000422115,;PTH1R,non_coding_transcript_exon_variant,,ENST00000490109,;PTH1R,missense_variant,p.Leu120Gln,ENST00000428220,;	A	ENSG00000160801	ENST00000313049	Transcript	missense_variant	562	359	120	L/Q	cTg/cAg	.	.	.	1	PTH1R	HGNC	9608	protein_coding	YES	CCDS2747.1	ENSP00000321999	PTH1R_HUMAN	Q71UK6_HUMAN,E7EWE7_HUMAN	UPI000005041F	.	tolerated(0.41)	benign(0.016)	4/14	.	PROSITE_profiles:PS50227,hmmpanther:PTHR12011:SF24,hmmpanther:PTHR12011,PROSITE_patterns:PS00649,Pfam_domain:PF02793,SMART_domains:SM00008,Superfamily_domains:SSF111418	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCTGGGGG	.	5	ESCA
OR5H1	0	.	GRCh37	3	97851542	97851542	+	Translation_Start_Site	SNP	A	A	C	rs760093655	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1A>C	p.Met1?	p.M1?	ENST00000354565	1/1	73	66	7	89	89	0	OR5H1,start_lost,p.Met1?,ENST00000354565,;RP11-343D2.11,intron_variant,,ENST00000508964,;	C	ENSG00000231192	ENST00000354565	Transcript	start_lost	1	1	1	M/L	Atg/Ctg	rs760093655	.	.	1	OR5H1	HGNC	8346	protein_coding	YES	CCDS33797.1	ENSP00000346575	OR5H1_HUMAN	.	UPI0000197652	.	deleterious(0.01)	benign(0.076)	1/1	.	Superfamily_domains:SSF81321,Gene3D:1.20.1070.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGACATGGAA	byFrequency	4	ESCA
FAT4	0	.	GRCh37	4	126241918	126241918	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4352T>C	p.Ile1451Thr	p.I1451T	ENST00000394329	1/17	11	4	7	35	35	0	FAT4,missense_variant,p.Ile1451Thr,ENST00000394329,;	C	ENSG00000196159	ENST00000394329	Transcript	missense_variant	4365	4352	1451	I/T	aTt/aCt	.	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	possibly_damaging(0.908)	1/17	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	AGACATTAATG	.	3	ESCA
GUF1	0	.	GRCh37	4	44688650	44688650	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.858T>A	p.%3D	p.I286I	ENST00000281543	8/17	43	26	17	123	123	0	GUF1,synonymous_variant,p.%3D,ENST00000281543,;GNPDA2,intron_variant,,ENST00000609092,;GNPDA2,intron_variant,,ENST00000608855,;GUF1,non_coding_transcript_exon_variant,,ENST00000506793,;GUF1,3_prime_UTR_variant,,ENST00000513775,;	A	ENSG00000151806	ENST00000281543	Transcript	synonymous_variant	1052	858	286	I	atT/atA	.	.	.	1	GUF1	HGNC	25799	protein_coding	YES	CCDS3468.1	ENSP00000281543	GUF1_HUMAN	.	UPI000006FFEC	.	.	.	8/17	.	Superfamily_domains:SSF50447,Gene3D:2.40.30.10,Pfam_domain:PF03144,TIGRFAM_domain:TIGR01393,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF97,HAMAP:MF_00071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATTGTATC	.	5	ESCA
MOB1B	0	.	GRCh37	4	71848468	71848468	+	3'Flank	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000396051	.	25	18	7	37	37	0	MOB1B,3_prime_UTR_variant,,ENST00000309395,;MOB1B,downstream_gene_variant,,ENST00000396051,;MOB1B,intron_variant,,ENST00000511449,;	C	ENSG00000173542	ENST00000396051	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	509	1	MOB1B	HGNC	29801	protein_coding	YES	CCDS58903.1	ENSP00000379366	MOB1B_HUMAN	Q4W5E0_HUMAN,D6RCK3_HUMAN	UPI0000E203CF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATACTGAAAC	.	5	ESCA
HNRNPDL	0	.	GRCh37	4	83350556	83350556	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.288A>G	p.%3D	p.Q96Q	ENST00000295470	1/8	43	29	14	68	68	0	HNRNPDL,synonymous_variant,p.%3D,ENST00000502762,;HNRNPDL,synonymous_variant,p.%3D,ENST00000295470,;HNRNPDL,5_prime_UTR_variant,,ENST00000349655,;HNRNPDL,5_prime_UTR_variant,,ENST00000602300,;ENOPH1,upstream_gene_variant,,ENST00000273920,;ENOPH1,upstream_gene_variant,,ENST00000509635,;HNRNPDL,non_coding_transcript_exon_variant,,ENST00000514511,;HNRNPDL,upstream_gene_variant,,ENST00000507721,;ENOPH1,upstream_gene_variant,,ENST00000505846,;	C	ENSG00000152795	ENST00000295470	Transcript	synonymous_variant	464	288	96	Q	caA/caG	.	.	.	-1	HNRNPDL	HGNC	5037	protein_coding	YES	CCDS3593.1	ENSP00000295470	HNRDL_HUMAN	B4DGN3_HUMAN	UPI0000073377	.	.	.	1/8	.	hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCGTTGTAT	.	5	ESCA
PPM1K	0	.	GRCh37	4	89198299	89198299	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.537T>C	p.%3D	p.A179A	ENST00000608933	3/7	43	27	16	91	91	0	PPM1K,synonymous_variant,p.%3D,ENST00000514204,;PPM1K,synonymous_variant,p.%3D,ENST00000608933,;PPM1K,synonymous_variant,p.%3D,ENST00000295908,;PPM1K,synonymous_variant,p.%3D,ENST00000315194,;PPM1K,5_prime_UTR_variant,,ENST00000510548,;PPM1K,5_prime_UTR_variant,,ENST00000508256,;PPM1K,downstream_gene_variant,,ENST00000505022,;PPM1K,downstream_gene_variant,,ENST00000509340,;RNU6-112P,upstream_gene_variant,,ENST00000363599,;PPM1K,non_coding_transcript_exon_variant,,ENST00000506423,;PPM1K,non_coding_transcript_exon_variant,,ENST00000513546,;PPM1K,non_coding_transcript_exon_variant,,ENST00000511506,;	G	ENSG00000163644	ENST00000608933	Transcript	synonymous_variant	927	537	179	A	gcT/gcC	.	.	.	-1	PPM1K	HGNC	25415	protein_coding	YES	CCDS3629.1	ENSP00000477341	.	.	UPI00000473F1	.	.	.	3/7	.	hmmpanther:PTHR13832,Gene3D:3.60.40.10,Pfam_domain:PF00481,SMART_domains:SM00332,SMART_domains:SM00331,Superfamily_domains:SSF81606	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.R176C|c.526C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCAGCAGA	.	5	ESCA
BMPR1B	0	.	GRCh37	4	96051071	96051071	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734A>C	p.Tyr245Ser	p.Y245S	ENST00000440890	7/11	33	17	15	57	57	0	BMPR1B,missense_variant,p.Tyr245Ser,ENST00000440890,;BMPR1B,missense_variant,p.Tyr215Ser,ENST00000264568,;BMPR1B,missense_variant,p.Tyr215Ser,ENST00000509540,;BMPR1B,missense_variant,p.Tyr215Ser,ENST00000512312,;BMPR1B,missense_variant,p.Tyr215Ser,ENST00000394931,;BMPR1B,missense_variant,p.Tyr215Ser,ENST00000515059,;	C	ENSG00000138696	ENST00000440890	Transcript	missense_variant	755	734	245	Y/S	tAt/tCt	.	.	.	1	BMPR1B	HGNC	1077	protein_coding	YES	CCDS58919.1	ENSP00000401907	BMR1B_HUMAN	D6RGW8_HUMAN	UPI00017A7CB9	.	deleterious(0)	probably_damaging(0.999)	7/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255:SF62,hmmpanther:PTHR23255,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCGCTATGGGG	.	4	ESCA
PCDHA1	0	.	GRCh37	5	140166704	140166706	+	In_Frame_Del	DEL	GTC	GTC	-	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	GTC	GTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832_834delGTC	p.Val278del	p.V278del	ENST00000504120	1/4	30	26	4	50	50	0	PCDHA1,inframe_deletion,p.Val278del,ENST00000504120,;PCDHA1,inframe_deletion,p.Val278del,ENST00000394633,;PCDHA1,inframe_deletion,p.Val278del,ENST00000378133,;	-	ENSG00000204970	ENST00000504120	Transcript	inframe_deletion	829-831	829-831	277	V/-	GTC/-	.	.	.	1	PCDHA1	HGNC	8663	protein_coding	YES	CCDS54913.1	ENSP00000420840	PCDA1_HUMAN	.	UPI00001273C7	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF92,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	GGTGAAGTCGTCTT	.	2	ESCA
PCDHAC1	0	.	GRCh37	5	140306538	140306538	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61C>A	p.Gln21Lys	p.Q21K	ENST00000253807	1/4	23	17	6	38	38	0	PCDHAC1,missense_variant,p.Gln21Lys,ENST00000253807,;PCDHAC1,missense_variant,p.Gln21Lys,ENST00000409700,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA10,intron_variant,,ENST00000506939,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA11,intron_variant,,ENST00000398640,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA12,intron_variant,,ENST00000398631,;PCDHA13,intron_variant,,ENST00000289272,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA10,intron_variant,,ENST00000307360,;PCDHA9,intron_variant,,ENST00000532602,;PCDHA13,intron_variant,,ENST00000409494,;	A	ENSG00000248383	ENST00000253807	Transcript	missense_variant	61	61	21	Q/K	Cag/Aag	.	.	.	1	PCDHAC1	HGNC	8676	protein_coding	YES	CCDS4241.1	ENSP00000253807	PCDC1_HUMAN	.	UPI000013CDF7	.	deleterious(0.02)	possibly_damaging(0.799)	1/4	.	Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF112,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGACAGCTC	.	5	ESCA
PCDHB13	0	.	GRCh37	5	140595516	140595516	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1821C>G	p.%3D	p.L607L	ENST00000341948	1/1	46	30	16	85	85	0	PCDHB13,synonymous_variant,p.%3D,ENST00000341948,;PCDHB12,downstream_gene_variant,,ENST00000541609,;PCDHB12,downstream_gene_variant,,ENST00000239450,;	G	ENSG00000187372	ENST00000341948	Transcript	synonymous_variant	2008	1821	607	L	ctC/ctG	.	.	.	1	PCDHB13	HGNC	8684	protein_coding	YES	CCDS4255.1	ENSP00000345491	PCDBD_HUMAN	.	UPI0000047816	.	.	.	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCAAGGC	.	5	ESCA
RICTOR	0	.	GRCh37	5	38940856	38940856	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1550C>G	.	.	ENST00000357387	38/38	12	8	4	24	24	0	RICTOR,3_prime_UTR_variant,,ENST00000357387,;RICTOR,3_prime_UTR_variant,,ENST00000296782,;RICTOR,3_prime_UTR_variant,,ENST00000511516,;OSMR,intron_variant,,ENST00000509237,;OSMR,intron_variant,,ENST00000508882,;RICTOR,downstream_gene_variant,,ENST00000505927,;	C	ENSG00000164327	ENST00000357387	Transcript	3_prime_UTR_variant	6708	.	.	.	.	.	.	.	-1	RICTOR	HGNC	28611	protein_coding	YES	CCDS34148.1	ENSP00000349959	RICTR_HUMAN	.	UPI00003529F3	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TTTCAGTTCCA	.	2	ESCA
GPR98	0	.	GRCh37	5	89990388	89990388	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7815G>C	p.Leu2605Phe	p.L2605F	ENST00000405460	33/90	25	21	4	55	54	0	GPR98,missense_variant,p.Leu2605Phe,ENST00000405460,;GPR98,missense_variant,p.Leu171Phe,ENST00000509621,;	C	ENSG00000164199	ENST00000405460	Transcript	missense_variant	7911	7815	2605	L/F	ttG/ttC	.	.	.	1	GPR98	HGNC	17416	protein_coding	YES	CCDS47246.1	ENSP00000384582	GPR98_HUMAN	.	UPI00002127A7	.	.	benign(0.291)	33/90	.	Superfamily_domains:SSF141072,SMART_domains:SM00237,Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTTGGTGGA	.	4	ESCA
LNPEP	0	.	GRCh37	5	96315139	96315139	+	Missense_Mutation	SNP	C	C	T	rs778817575	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.317C>T	p.Pro106Leu	p.P106L	ENST00000231368	2/18	20	12	8	37	37	0	LNPEP,missense_variant,p.Pro92Leu,ENST00000395770,;LNPEP,missense_variant,p.Pro106Leu,ENST00000231368,;	T	ENSG00000113441	ENST00000231368	Transcript	missense_variant	1009	317	106	P/L	cCc/cTc	rs778817575	.	.	1	LNPEP	HGNC	6656	protein_coding	YES	CCDS4087.1	ENSP00000231368	LCAP_HUMAN	.	UPI000013C94B	.	tolerated(0.08)	benign(0.048)	2/18	.	hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTACCCTCTG	.	5	ESCA
SGK1	0	.	GRCh37	6	134490576	134490576	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*830C>G	.	.	ENST00000367858	14/14	51	33	18	116	116	0	SGK1,3_prime_UTR_variant,,ENST00000237305,;SGK1,3_prime_UTR_variant,,ENST00000367858,;SGK1,3_prime_UTR_variant,,ENST00000413996,;SGK1,3_prime_UTR_variant,,ENST00000367857,;SGK1,downstream_gene_variant,,ENST00000528577,;SGK1,downstream_gene_variant,,ENST00000475719,;SGK1,downstream_gene_variant,,ENST00000461976,;SGK1,downstream_gene_variant,,ENST00000524387,;SGK1,downstream_gene_variant,,ENST00000489458,;SGK1,downstream_gene_variant,,ENST00000531575,;SGK1,non_coding_transcript_exon_variant,,ENST00000474427,;SGK1,non_coding_transcript_exon_variant,,ENST00000477460,;SGK1,non_coding_transcript_exon_variant,,ENST00000367855,;SGK1,downstream_gene_variant,,ENST00000534658,;SGK1,downstream_gene_variant,,ENST00000524764,;SGK1,downstream_gene_variant,,ENST00000531782,;SGK1,downstream_gene_variant,,ENST00000530421,;SGK1,downstream_gene_variant,,ENST00000532021,;SGK1,downstream_gene_variant,,ENST00000473704,;SGK1,downstream_gene_variant,,ENST00000472859,;SGK1,downstream_gene_variant,,ENST00000532856,;SGK1,downstream_gene_variant,,ENST00000525877,;SGK1,downstream_gene_variant,,ENST00000475882,;SGK1,downstream_gene_variant,,ENST00000490149,;SGK1,downstream_gene_variant,,ENST00000525700,;	C	ENSG00000118515	ENST00000367858	Transcript	3_prime_UTR_variant	3009	.	.	.	.	.	.	.	-1	SGK1	HGNC	10810	protein_coding	YES	CCDS47476.1	ENSP00000356832	SGK1_HUMAN	E9PP33_HUMAN,E9PJN2_HUMAN,B7Z1G1_HUMAN	UPI000013CA0E	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACAGACGTT	.	5	ESCA
RNF182	0	.	GRCh37	6	13979008	13979008	+	3'UTR	SNP	A	A	G	rs367678081	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*914A>G	.	.	ENST00000488300	3/3	27	12	14	52	52	0	RNF182,3_prime_UTR_variant,,ENST00000537663,;RNF182,3_prime_UTR_variant,,ENST00000544682,;RNF182,3_prime_UTR_variant,,ENST00000488300,;RNF182,3_prime_UTR_variant,,ENST00000537388,;RNF182,downstream_gene_variant,,ENST00000471906,;RNF182,downstream_gene_variant,,ENST00000420478,;RNF182,downstream_gene_variant,,ENST00000423553,;RNF182,downstream_gene_variant,,ENST00000488763,;	G	ENSG00000180537	ENST00000488300	Transcript	3_prime_UTR_variant	2181	.	.	.	.	rs367678081	.	.	1	RNF182	HGNC	28522	protein_coding	YES	CCDS4531.1	ENSP00000420465	RN182_HUMAN	C9JVS8_HUMAN,C9JAK6_HUMAN,C9IZ30_HUMAN	UPI000006E1CA	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTATTATA	byCluster	5	ESCA
THBS2	0	.	GRCh37	6	169622427	169622427	+	Silent	SNP	C	C	T	rs750861595	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3138G>A	p.%3D	p.T1046T	ENST00000366787	20/23	38	21	16	59	59	0	THBS2,synonymous_variant,p.%3D,ENST00000366787,;XXyac-YX65C7_A.2,intron_variant,,ENST00000444188,;THBS2,non_coding_transcript_exon_variant,,ENST00000488355,;	T	ENSG00000186340	ENST00000366787	Transcript	synonymous_variant	3388	3138	1046	T	acG/acA	rs750861595	.	.	-1	THBS2	HGNC	11786	protein_coding	YES	CCDS34574.1	ENSP00000355751	TSP2_HUMAN	Q6MZL6_HUMAN,Q5RI53_HUMAN	UPI0000231C7F	.	.	.	20/23	.	PROSITE_profiles:PS51236,hmmpanther:PTHR10199:SF10,hmmpanther:PTHR10199,Pfam_domain:PF05735,Gene3D:2.60.120.200,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGCGTCAC	byFrequency	5	ESCA
RPS18	0	.	GRCh37	6	33239849	33239849	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-48G>A	.	.	ENST00000439602	1/6	15	9	6	36	36	0	RPS18,5_prime_UTR_variant,,ENST00000439602,;VPS52,upstream_gene_variant,,ENST00000436044,;VPS52,upstream_gene_variant,,ENST00000482399,;RPS18,upstream_gene_variant,,ENST00000474973,;VPS52,upstream_gene_variant,,ENST00000445902,;VPS52,upstream_gene_variant,,ENST00000464425,;RPS18,upstream_gene_variant,,ENST00000476222,;VPS52,upstream_gene_variant,,ENST00000463486,;VPS52,upstream_gene_variant,,ENST00000478934,;RPS18,upstream_gene_variant,,ENST00000472218,;RPS18,upstream_gene_variant,,ENST00000496813,;RPS18,upstream_gene_variant,,ENST00000490191,;RPS18,upstream_gene_variant,,ENST00000479802,;VPS52,upstream_gene_variant,,ENST00000493379,;RPS18,upstream_gene_variant,,ENST00000474626,;VPS52,upstream_gene_variant,,ENST00000495755,;	A	ENSG00000231500	ENST00000439602	Transcript	5_prime_UTR_variant	63	.	.	.	.	.	.	.	1	RPS18	HGNC	10401	protein_coding	YES	CCDS4771.1	ENSP00000393241	RS18_HUMAN	Q5GGW2_HUMAN,J3JS69_HUMAN	UPI00000040B5	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE	CTTCCGCTCTC	.	3	ESCA
RPS18	0	.	GRCh37	6	33239850	33239850	+	5'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-47C>A	.	.	ENST00000439602	1/6	15	8	6	33	33	0	RPS18,5_prime_UTR_variant,,ENST00000439602,;VPS52,upstream_gene_variant,,ENST00000436044,;VPS52,upstream_gene_variant,,ENST00000482399,;RPS18,upstream_gene_variant,,ENST00000474973,;VPS52,upstream_gene_variant,,ENST00000445902,;VPS52,upstream_gene_variant,,ENST00000464425,;RPS18,upstream_gene_variant,,ENST00000476222,;VPS52,upstream_gene_variant,,ENST00000463486,;VPS52,upstream_gene_variant,,ENST00000478934,;RPS18,upstream_gene_variant,,ENST00000472218,;RPS18,upstream_gene_variant,,ENST00000496813,;RPS18,upstream_gene_variant,,ENST00000490191,;RPS18,upstream_gene_variant,,ENST00000479802,;VPS52,upstream_gene_variant,,ENST00000493379,;RPS18,upstream_gene_variant,,ENST00000474626,;VPS52,upstream_gene_variant,,ENST00000495755,;	A	ENSG00000231500	ENST00000439602	Transcript	5_prime_UTR_variant	64	.	.	.	.	.	.	.	1	RPS18	HGNC	10401	protein_coding	YES	CCDS4771.1	ENSP00000393241	RS18_HUMAN	Q5GGW2_HUMAN,J3JS69_HUMAN	UPI00000040B5	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TTCCGCTCTCT	.	4	ESCA
HCRTR2	0	.	GRCh37	6	55142277	55142277	+	Missense_Mutation	SNP	G	G	A	rs769781293	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.862G>A	p.Ala288Thr	p.A288T	ENST00000370862	5/7	41	35	6	81	81	0	HCRTR2,missense_variant,p.Ala288Thr,ENST00000370862,;	A	ENSG00000137252	ENST00000370862	Transcript	missense_variant	1198	862	288	A/T	Gct/Act	rs769781293,COSM3874860	.	.	1	HCRTR2	HGNC	4849	protein_coding	YES	CCDS4956.1	ENSP00000359899	OX2R_HUMAN	S4X0W3_HUMAN,A6N9G8_HUMAN	UPI000013D07A	.	tolerated(0.53)	benign(0.023)	5/7	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF56,hmmpanther:PTHR24241,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR01064	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAGCGCTGTG	byFrequency	4	ESCA
COL19A1	0	.	GRCh37	6	70866605	70866605	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2282A>T	p.Lys761Ile	p.K761I	ENST00000322773	34/51	36	30	6	81	81	0	COL19A1,missense_variant,p.Lys761Ile,ENST00000322773,;COL19A1,missense_variant,p.Lys383Ile,ENST00000393344,;	T	ENSG00000082293	ENST00000322773	Transcript	missense_variant	2384	2282	761	K/I	aAa/aTa	.	.	.	1	COL19A1	HGNC	2196	protein_coding	YES	CCDS4970.1	ENSP00000316030	COJA1_HUMAN	.	UPI000004F1E3	.	deleterious(0.03)	probably_damaging(0.994)	34/51	.	Pfam_domain:PF01391,Pfam_domain:PF01391,hmmpanther:PTHR24022:SF80,hmmpanther:PTHR24022	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGAAAGGCG	.	4	ESCA
COL9A1	0	.	GRCh37	6	70925775	70925775	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*825G>T	.	.	ENST00000357250	38/38	11	8	3	32	32	0	COL9A1,3_prime_UTR_variant,,ENST00000370499,;COL9A1,3_prime_UTR_variant,,ENST00000320755,;COL9A1,3_prime_UTR_variant,,ENST00000357250,;COL9A1,downstream_gene_variant,,ENST00000489611,;COL9A1,downstream_gene_variant,,ENST00000486080,;	A	ENSG00000112280	ENST00000357250	Transcript	3_prime_UTR_variant	3750	.	.	.	.	.	.	.	-1	COL9A1	HGNC	2217	protein_coding	YES	CCDS4971.1	ENSP00000349790	CO9A1_HUMAN	.	UPI000020D14B	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATAAGCTCAGT	.	2	ESCA
MANEA	0	.	GRCh37	6	96034899	96034899	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544+40A>G	.	.	ENST00000358812	.	34	24	10	91	91	0	MANEA,missense_variant,p.Tyr195Cys,ENST00000369293,;MANEA,intron_variant,,ENST00000358812,;MANEA,upstream_gene_variant,,ENST00000474553,;	G	ENSG00000172469	ENST00000358812	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MANEA	HGNC	21072	protein_coding	YES	CCDS5032.1	ENSP00000351669	MANEA_HUMAN	.	UPI000020DF99	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTGTATATAT	.	4	ESCA
SAP25	0	.	GRCh37	7	100170802	100170802	+	5'UTR	SNP	G	G	A	rs568173547	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11C>T	.	.	ENST00000538735	3/6	34	27	6	30	30	0	SAP25,5_prime_UTR_variant,,ENST00000538735,;LRCH4,downstream_gene_variant,,ENST00000310300,;LRCH4,downstream_gene_variant,,ENST00000497245,;LRCH4,downstream_gene_variant,,ENST00000485554,;AGFG2,downstream_gene_variant,,ENST00000300176,;LRCH4,non_coding_transcript_exon_variant,,ENST00000485071,;LRCH4,downstream_gene_variant,,ENST00000498539,;LRCH4,downstream_gene_variant,,ENST00000487697,;LRCH4,downstream_gene_variant,,ENST00000476881,;LRCH4,downstream_gene_variant,,ENST00000467201,;LRCH4,downstream_gene_variant,,ENST00000490359,;RP11-44M6.3,downstream_gene_variant,,ENST00000223076,;	A	ENSG00000205307	ENST00000538735	Transcript	5_prime_UTR_variant	168	.	.	.	.	rs568173547	.	.	-1	SAP25	HGNC	41908	protein_coding	YES	CCDS55137.1	ENSP00000442339	SAP25_HUMAN	.	UPI0000034E0E	.	.	.	3/6	.	.	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGGGGGCCACC	by1000G	4	ESCA
MUC17	0	.	GRCh37	7	100685536	100685536	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10839C>A	p.Ser3613Arg	p.S3613R	ENST00000306151	3/13	78	33	45	57	57	0	MUC17,missense_variant,p.Ser3613Arg,ENST00000306151,;MUC17,missense_variant,p.Ser3613Arg,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,;	A	ENSG00000169876	ENST00000306151	Transcript	missense_variant	10903	10839	3613	S/R	agC/agA	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	benign(0.002)	3/13	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAGCAATTC	.	5	ESCA
ARMC10	0	.	GRCh37	7	102716296	102716296	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212G>T	p.Trp71Leu	p.W71L	ENST00000323716	2/7	44	17	27	32	32	0	ARMC10,missense_variant,p.Trp71Leu,ENST00000323716,;ARMC10,missense_variant,p.Trp71Leu,ENST00000434153,;ARMC10,missense_variant,p.Trp71Leu,ENST00000428183,;ARMC10,intron_variant,,ENST00000454559,;ARMC10,intron_variant,,ENST00000541300,;ARMC10,intron_variant,,ENST00000441711,;ARMC10,intron_variant,,ENST00000425331,;FBXL13,upstream_gene_variant,,ENST00000379306,;FBXL13,upstream_gene_variant,,ENST00000456695,;FBXL13,upstream_gene_variant,,ENST00000455112,;FBXL13,upstream_gene_variant,,ENST00000440067,;FBXL13,upstream_gene_variant,,ENST00000379305,;FBXL13,upstream_gene_variant,,ENST00000379308,;FBXL13,upstream_gene_variant,,ENST00000393772,;FBXL13,upstream_gene_variant,,ENST00000313221,;FBXL13,upstream_gene_variant,,ENST00000471074,;ARMC10,missense_variant,p.Trp71Leu,ENST00000323735,;ARMC10,intron_variant,,ENST00000306450,;FBXL13,upstream_gene_variant,,ENST00000448002,;	T	ENSG00000170632	ENST00000323716	Transcript	missense_variant	604	212	71	W/L	tGg/tTg	.	.	.	1	ARMC10	HGNC	21706	protein_coding	YES	CCDS5728.1	ENSP00000319412	ARM10_HUMAN	.	UPI0000039E55	.	tolerated(0.5)	benign(0)	2/7	.	hmmpanther:PTHR15712:SF19,hmmpanther:PTHR15712	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACCTGGGAGT	.	3	ESCA
ARMC10	0	.	GRCh37	7	102716313	102716313	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.229A>T	p.Lys77Ter	p.K77*	ENST00000323716	2/7	51	19	32	35	35	0	ARMC10,stop_gained,p.Lys77Ter,ENST00000323716,;ARMC10,stop_gained,p.Lys77Ter,ENST00000434153,;ARMC10,stop_gained,p.Lys77Ter,ENST00000428183,;ARMC10,intron_variant,,ENST00000454559,;ARMC10,intron_variant,,ENST00000541300,;ARMC10,intron_variant,,ENST00000441711,;ARMC10,intron_variant,,ENST00000425331,;FBXL13,upstream_gene_variant,,ENST00000379306,;FBXL13,upstream_gene_variant,,ENST00000456695,;FBXL13,upstream_gene_variant,,ENST00000455112,;FBXL13,upstream_gene_variant,,ENST00000440067,;FBXL13,upstream_gene_variant,,ENST00000379305,;FBXL13,upstream_gene_variant,,ENST00000379308,;FBXL13,upstream_gene_variant,,ENST00000393772,;FBXL13,upstream_gene_variant,,ENST00000313221,;FBXL13,upstream_gene_variant,,ENST00000471074,;ARMC10,stop_gained,p.Lys77Ter,ENST00000323735,;ARMC10,intron_variant,,ENST00000306450,;FBXL13,upstream_gene_variant,,ENST00000448002,;	T	ENSG00000170632	ENST00000323716	Transcript	stop_gained	621	229	77	K/*	Aag/Tag	.	.	.	1	ARMC10	HGNC	21706	protein_coding	YES	CCDS5728.1	ENSP00000319412	ARM10_HUMAN	.	UPI0000039E55	.	.	.	2/7	.	hmmpanther:PTHR15712:SF19,hmmpanther:PTHR15712	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGTCCAAGACC	.	3	ESCA
FLNC	0	.	GRCh37	7	128487788	128487788	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4326C>A	p.Asp1442Glu	p.D1442E	ENST00000325888	25/48	30	23	6	93	93	0	FLNC,missense_variant,p.Asp1442Glu,ENST00000325888,;FLNC,missense_variant,p.Asp1442Glu,ENST00000346177,;RP11-309L24.2,downstream_gene_variant,,ENST00000469965,;FLNC,downstream_gene_variant,,ENST00000388853,;	A	ENSG00000128591	ENST00000325888	Transcript	missense_variant	4587	4326	1442	D/E	gaC/gaA	.	.	.	1	FLNC	HGNC	3756	protein_coding	YES	CCDS43644.1	ENSP00000327145	FLNC_HUMAN	Q59H94_HUMAN,B3KM41_HUMAN	UPI000006DE6D	.	deleterious(0)	probably_damaging(0.999)	25/48	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF81296,SMART_domains:SM00557,Pfam_domain:PF00630,Gene3D:2.60.40.10,hmmpanther:PTHR11915:SF173,hmmpanther:PTHR11915,PROSITE_profiles:PS50194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGACCCTGG	.	5	ESCA
PAXIP1	0	.	GRCh37	7	154753307	154753307	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2179A>G	p.Met727Val	p.M727V	ENST00000404141	11/21	28	18	10	63	63	0	PAXIP1,missense_variant,p.Met727Val,ENST00000404141,;PAXIP1,missense_variant,p.Met727Val,ENST00000397192,;RP11-5C23.2,downstream_gene_variant,,ENST00000609134,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000473219,;PAXIP1,3_prime_UTR_variant,,ENST00000457196,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000485730,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000464717,;	C	ENSG00000157212	ENST00000404141	Transcript	missense_variant	2334	2179	727	M/V	Atg/Gtg	.	.	.	-1	PAXIP1	HGNC	8624	protein_coding	YES	CCDS47753.1	ENSP00000384048	PAXI1_HUMAN	.	UPI00004166F9	.	deleterious(0.02)	unknown(0)	11/21	.	PROSITE_profiles:PS50172,hmmpanther:PTHR23196:SF1,hmmpanther:PTHR23196,Pfam_domain:PF12738,Gene3D:3.40.50.10190,SMART_domains:SM00292,Superfamily_domains:SSF52113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCATTAATT	.	5	ESCA
ITGB8	0	.	GRCh37	7	20453254	20453254	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3634G>C	.	.	ENST00000222573	14/14	13	10	3	8	8	0	ITGB8,3_prime_UTR_variant,,ENST00000222573,;ITGB8,downstream_gene_variant,,ENST00000537992,;	C	ENSG00000105855	ENST00000222573	Transcript	3_prime_UTR_variant	6628	.	.	.	.	.	.	.	1	ITGB8	HGNC	6163	protein_coding	YES	CCDS5370.1	ENSP00000222573	ITB8_HUMAN	B4DHD4_HUMAN	UPI000012DA14	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGAAGTTCTT	.	2	ESCA
SP4	0	.	GRCh37	7	21551132	21551132	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*245T>C	.	.	ENST00000222584	6/6	19	13	6	47	47	0	SP4,3_prime_UTR_variant,,ENST00000222584,;SP4,3_prime_UTR_variant,,ENST00000448246,;	C	ENSG00000105866	ENST00000222584	Transcript	3_prime_UTR_variant	2818	.	.	.	.	.	.	.	1	SP4	HGNC	11209	protein_coding	YES	CCDS5373.1	ENSP00000222584	SP4_HUMAN	Q32M51_HUMAN	UPI000013C807	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAATATATC	.	5	ESCA
DNAH11	0	.	GRCh37	7	21584746	21584746	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474T>A	p.His158Gln	p.H158Q	ENST00000328843	2/83	45	36	8	65	65	0	DNAH11,missense_variant,p.His158Gln,ENST00000328843,;DNAH11,missense_variant,p.His158Gln,ENST00000409508,;DNAH11,non_coding_transcript_exon_variant,,ENST00000607050,;	A	ENSG00000105877	ENST00000328843	Transcript	missense_variant	505	474	158	H/Q	caT/caA	.	.	.	1	DNAH11	HGNC	2942	protein_coding	YES	.	ENSP00000330671	DYH11_HUMAN	Q75MY1_HUMAN,Q75KM7_HUMAN,O95705_HUMAN,O43352_HUMAN,O15433_HUMAN	UPI000041AC4D	.	.	benign(0.023)	2/83	.	hmmpanther:PTHR10676:SF227,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACATGTATC	.	5	ESCA
ABCA13	0	.	GRCh37	7	48654945	48654945	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14809C>A	p.Leu4937Ile	p.L4937I	ENST00000435803	59/62	48	37	10	69	69	0	ABCA13,missense_variant,p.Leu4937Ile,ENST00000435803,;ABCA13,missense_variant,p.Leu667Ile,ENST00000544596,;ABCA13,missense_variant,p.Leu710Ile,ENST00000411975,;ABCA13,3_prime_UTR_variant,,ENST00000453246,;	A	ENSG00000179869	ENST00000435803	Transcript	missense_variant	14833	14809	4937	L/I	Ctt/Att	.	.	.	1	ABCA13	HGNC	14638	protein_coding	YES	CCDS47584.1	ENSP00000411096	ABCAD_HUMAN	.	UPI00001A95EA	.	.	possibly_damaging(0.499)	59/62	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,PROSITE_profiles:PS50893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGTCTTGGT	.	5	ESCA
NXPH1	0	.	GRCh37	7	8473968	8473968	+	5'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-528A>T	.	.	ENST00000405863	1/3	27	17	9	44	44	0	NXPH1,5_prime_UTR_variant,,ENST00000405863,;NXPH1,upstream_gene_variant,,ENST00000602349,;NXPH1,upstream_gene_variant,,ENST00000429542,;NXPH1,upstream_gene_variant,,ENST00000438764,;	T	ENSG00000122584	ENST00000405863	Transcript	5_prime_UTR_variant	384	.	.	.	.	.	.	.	1	NXPH1	HGNC	20693	protein_coding	YES	CCDS47540.1	ENSP00000384551	NXPH1_HUMAN	Q3LID8_HUMAN,C9JPD0_HUMAN,C9JE46_HUMAN,B4DJV1_HUMAN	UPI000000DC02	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGGAAGCCG	.	5	ESCA
PEG10	0	.	GRCh37	7	94297698	94297698	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3852A>C	.	.	ENST00000482108	2/2	47	28	18	67	67	0	PEG10,3_prime_UTR_variant,,ENST00000482108,;PEG10,downstream_gene_variant,,ENST00000488574,;PEG10,intron_variant,,ENST00000465184,;PEG10,intron_variant,,ENST00000493935,;	C	ENSG00000242265	ENST00000482108	Transcript	3_prime_UTR_variant	5309	.	.	.	.	.	.	.	1	PEG10	HGNC	14005	protein_coding	YES	CCDS55126.1	ENSP00000417587	PEG10_HUMAN	B4DSP0_HUMAN	UPI0000047FA3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTAAATTT	.	5	ESCA
PON1	0	.	GRCh37	7	94935642	94935642	+	Missense_Mutation	SNP	A	A	C	rs761997517	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.735T>G	p.Ile245Met	p.I245M	ENST00000222381	7/9	50	44	6	67	67	0	PON1,missense_variant,p.Ile245Met,ENST00000542556,;PON1,missense_variant,p.Ile245Met,ENST00000222381,;PON1,3_prime_UTR_variant,,ENST00000433729,;PON1,upstream_gene_variant,,ENST00000462594,;	C	ENSG00000005421	ENST00000222381	Transcript	missense_variant	967	735	245	I/M	atT/atG	rs761997517	.	.	-1	PON1	HGNC	9204	protein_coding	YES	CCDS5638.1	ENSP00000222381	PON1_HUMAN	.	UPI000013C7FD	.	deleterious(0)	probably_damaging(1)	7/9	.	hmmpanther:PTHR11799,hmmpanther:PTHR11799:SF3,Gene3D:2.120.10.30,Pfam_domain:PF01731,Superfamily_domains:SSF63829,Prints_domain:PR01785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATGAATCTT	byFrequency	4	ESCA
TRPS1	0	.	GRCh37	8	116423294	116423294	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2957G>A	.	.	ENST00000395715	7/7	15	8	7	22	22	0	TRPS1,3_prime_UTR_variant,,ENST00000395715,;TRPS1,downstream_gene_variant,,ENST00000520276,;TRPS1,downstream_gene_variant,,ENST00000220888,;TRPS1,downstream_gene_variant,,ENST00000518018,;TRPS1,downstream_gene_variant,,ENST00000519076,;	T	ENSG00000104447	ENST00000395715	Transcript	3_prime_UTR_variant	7420	.	.	.	.	.	.	.	-1	TRPS1	HGNC	12340	protein_coding	YES	CCDS6318.2	ENSP00000379065	TRPS1_HUMAN	F8W8T0_HUMAN,E7EVN4_HUMAN,C9J6L7_HUMAN	UPI00002104B8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTCTTTCA	.	5	ESCA
KLHL38	0	.	GRCh37	8	124664837	124664837	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.330C>T	p.%3D	p.A110A	ENST00000325995	1/3	20	11	8	29	29	0	KLHL38,synonymous_variant,p.%3D,ENST00000325995,;CTD-2552K11.2,intron_variant,,ENST00000524355,;	A	ENSG00000175946	ENST00000325995	Transcript	synonymous_variant	354	330	110	A	gcC/gcT	.	.	.	-1	KLHL38	HGNC	34435	protein_coding	YES	CCDS43766.1	ENSP00000321475	KLH38_HUMAN	.	UPI00001D82D1	.	.	.	1/3	.	Superfamily_domains:SSF54695,PIRSF_domain:PIRSF037037,SMART_domains:SM00225,Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR24412:SF8,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCGGCCTC	.	5	ESCA
SPATC1	0	.	GRCh37	8	145095047	145095047	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.449C>A	p.Thr150Lys	p.T150K	ENST00000377470	2/5	23	20	3	38	38	0	SPATC1,missense_variant,p.Thr150Lys,ENST00000447830,;SPATC1,missense_variant,p.Thr150Lys,ENST00000377470,;	A	ENSG00000186583	ENST00000377470	Transcript	missense_variant	551	449	150	T/K	aCa/aAa	.	.	.	1	SPATC1	HGNC	30510	protein_coding	YES	CCDS6413.2	ENSP00000366690	SPERI_HUMAN	.	UPI00001D8243	.	tolerated(0.08)	benign(0.032)	2/5	.	hmmpanther:PTHR22192,hmmpanther:PTHR22192:SF16,Pfam_domain:PF15058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTAACAGGCA	.	2	ESCA
SLC52A2	0	.	GRCh37	8	145584808	145584808	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*133C>A	.	.	ENST00000532887	5/5	20	10	9	31	31	0	SLC52A2,3_prime_UTR_variant,,ENST00000532887,;SLC52A2,3_prime_UTR_variant,,ENST00000530047,;SLC52A2,3_prime_UTR_variant,,ENST00000540505,;SLC52A2,3_prime_UTR_variant,,ENST00000526752,;SLC52A2,3_prime_UTR_variant,,ENST00000402965,;SLC52A2,3_prime_UTR_variant,,ENST00000329994,;SLC52A2,downstream_gene_variant,,ENST00000527078,;FBXL6,upstream_gene_variant,,ENST00000331890,;SLC52A2,downstream_gene_variant,,ENST00000526338,;FBXL6,upstream_gene_variant,,ENST00000455319,;SLC52A2,downstream_gene_variant,,ENST00000524541,;SLC52A2,downstream_gene_variant,,ENST00000534725,;SLC52A2,downstream_gene_variant,,ENST00000532815,;FBXL6,upstream_gene_variant,,ENST00000530687,;FBXL6,upstream_gene_variant,,ENST00000524909,;FBXL6,upstream_gene_variant,,ENST00000526524,;FBXL6,upstream_gene_variant,,ENST00000527000,;SLC52A2,downstream_gene_variant,,ENST00000526891,;SLC52A2,downstream_gene_variant,,ENST00000526779,;SLC52A2,downstream_gene_variant,,ENST00000533662,;FBXL6,upstream_gene_variant,,ENST00000530142,;FBXL6,upstream_gene_variant,,ENST00000529279,;FBXL6,upstream_gene_variant,,ENST00000524492,;	A	ENSG00000185803	ENST00000532887	Transcript	3_prime_UTR_variant	2054	.	.	.	.	.	.	.	1	SLC52A2	HGNC	30224	protein_coding	YES	CCDS6423.1	ENSP00000436768	S52A2_HUMAN	F5GXA8_HUMAN,E9PRC3_HUMAN,E9PIX2_HUMAN	UPI000004470A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGATCCTGGC	.	5	ESCA
DLGAP2	0	.	GRCh37	8	1645353	1645353	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2597C>T	p.Ala866Val	p.A866V	ENST00000421627	11/12	27	23	4	70	70	0	DLGAP2,missense_variant,p.Ala869Val,ENST00000520901,;DLGAP2,missense_variant,p.Ala866Val,ENST00000421627,;	T	ENSG00000198010	ENST00000421627	Transcript	missense_variant	2731	2597	866	A/V	gCc/gTc	COSM3646836,COSM3646837	.	.	1	DLGAP2	HGNC	2906	protein_coding	YES	CCDS47760.1	ENSP00000400258	DLGP2_HUMAN	.	UPI000021BFBC	.	deleterious(0)	probably_damaging(0.999)	11/12	.	hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3,Pfam_domain:PF03359	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGGCCGGCT	.	4	ESCA
CSMD1	0	.	GRCh37	8	2823409	2823409	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9168C>A	p.Asn3056Lys	p.N3056K	ENST00000537824	59/70	37	25	12	111	110	1	CSMD1,missense_variant,p.Asn2474Lys,ENST00000335551,;CSMD1,missense_variant,p.Asn3056Lys,ENST00000537824,;CSMD1,missense_variant,p.Asn3057Lys,ENST00000602557,;CSMD1,missense_variant,p.Asn3057Lys,ENST00000520002,;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000542608,;CSMD1,intron_variant,,ENST00000602723,;	T	ENSG00000183117	ENST00000537824	Transcript	missense_variant	9168	9168	3056	N/K	aaC/aaA	.	.	.	-1	CSMD1	HGNC	14026	protein_coding	YES	CCDS55189.1	ENSP00000441462	.	F5GZ18_HUMAN	UPI0001B723C6	.	.	probably_damaging(0.999)	59/70	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF323,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTGTTGAA	.	5	ESCA
SLC20A2	0	.	GRCh37	8	42297137	42297137	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.765A>T	p.%3D	p.V255V	ENST00000342228	7/11	21	17	4	38	38	0	SLC20A2,synonymous_variant,p.%3D,ENST00000342228,;SLC20A2,synonymous_variant,p.%3D,ENST00000520262,;SLC20A2,synonymous_variant,p.%3D,ENST00000520179,;SLC20A2,non_coding_transcript_exon_variant,,ENST00000518660,;SLC20A2,non_coding_transcript_exon_variant,,ENST00000522401,;	A	ENSG00000168575	ENST00000342228	Transcript	synonymous_variant	1135	765	255	V	gtA/gtT	.	.	.	-1	SLC20A2	HGNC	10947	protein_coding	YES	CCDS6132.1	ENSP00000340465	S20A2_HUMAN	E5RJW9_HUMAN,E5RIX1_HUMAN,E5RGJ6_HUMAN,E5RGG8_HUMAN	UPI000006DC58	.	.	.	7/11	.	hmmpanther:PTHR11101,hmmpanther:PTHR11101:SF15,Pfam_domain:PF01384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAGATACTCG	.	4	ESCA
ZFHX4	0	.	GRCh37	8	77776814	77776814	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13G>T	.	.	ENST00000521891	11/11	59	43	16	84	83	1	ZFHX4,3_prime_UTR_variant,,ENST00000455469,;ZFHX4,3_prime_UTR_variant,,ENST00000518282,;ZFHX4,3_prime_UTR_variant,,ENST00000521891,;ZFHX4,downstream_gene_variant,,ENST00000050961,;	T	ENSG00000091656	ENST00000521891	Transcript	3_prime_UTR_variant	11312	.	.	.	.	.	.	.	1	ZFHX4	HGNC	30939	protein_coding	YES	CCDS47878.2	ENSP00000430497	.	Q9H7F3_HUMAN,Q86WW5_HUMAN,Q6DK57_HUMAN,G3V138_HUMAN,E5RI93_HUMAN,E5RHS1_HUMAN,E5RGK3_HUMAN,E5RG79_HUMAN	UPI0000424CC7	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACAGGATCCC	.	5	ESCA
ABCA1	0	.	GRCh37	9	107554264	107554264	+	Missense_Mutation	SNP	G	G	A	rs568280586	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5773C>T	p.Arg1925Trp	p.R1925W	ENST00000374736	43/50	21	4	17	23	23	0	ABCA1,missense_variant,p.Arg1925Trp,ENST00000374736,;	A	ENSG00000165029	ENST00000374736	Transcript	missense_variant	6168	5773	1925	R/W	Cgg/Tgg	rs568280586,COSM3779504	.	.	-1	ABCA1	HGNC	29	protein_coding	YES	CCDS6762.1	ENSP00000363868	ABCA1_HUMAN	Q9NS76_HUMAN,Q9NP93_HUMAN,Q9H002_HUMAN	UPI000013E441	.	deleterious(0)	possibly_damaging(0.676)	43/50	.	PROSITE_profiles:PS50893,hmmpanther:PTHR19229:SF34,hmmpanther:PTHR19229,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCGCTTCC	by1000G	5	ESCA
BRINP1	0	.	GRCh37	9	121929725	121929725	+	Silent	SNP	C	C	T	rs749359538	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1923G>A	p.%3D	p.S641S	ENST00000265922	8/8	23	19	4	32	32	0	BRINP1,synonymous_variant,p.%3D,ENST00000265922,;BRINP1,intron_variant,,ENST00000482797,;	T	ENSG00000078725	ENST00000265922	Transcript	synonymous_variant	2385	1923	641	S	tcG/tcA	rs749359538	.	.	-1	BRINP1	HGNC	2687	protein_coding	YES	CCDS6822.1	ENSP00000265922	BRNP1_HUMAN	B4DE75_HUMAN	UPI000013D6A7	.	.	.	8/8	.	hmmpanther:PTHR15564:SF7,hmmpanther:PTHR15564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGATCCGACAG	byFrequency	5	ESCA
OLFM1	0	.	GRCh37	9	137982066	137982066	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.122G>T	p.Ser41Ile	p.S41I	ENST00000252854	2/6	30	14	16	55	55	0	OLFM1,missense_variant,p.Ser32Ile,ENST00000371796,;OLFM1,missense_variant,p.Ser59Ile,ENST00000371793,;OLFM1,missense_variant,p.Ser48Ile,ENST00000339720,;OLFM1,missense_variant,p.Ser59Ile,ENST00000392991,;OLFM1,missense_variant,p.Ser41Ile,ENST00000277415,;OLFM1,missense_variant,p.Ser41Ile,ENST00000252854,;OLFM1,5_prime_UTR_variant,,ENST00000539529,;OLFM1,upstream_gene_variant,,ENST00000539877,;	T	ENSG00000130558	ENST00000252854	Transcript	missense_variant	309	122	41	S/I	aGc/aTc	.	.	.	1	OLFM1	HGNC	17187	protein_coding	YES	CCDS6986.1	ENSP00000252854	NOE1_HUMAN	Q6IMJ8_HUMAN,Q96BL8_HUMAN,F5H810_HUMAN,F5GZQ2_HUMAN,B3KR22_HUMAN	UPI000013CD8C	.	deleterious(0)	possibly_damaging(0.727)	2/6	.	hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF34,Pfam_domain:PF12308,Superfamily_domains:SSF50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGAGCTGGC	.	5	ESCA
OLFM1	0	.	GRCh37	9	137982067	137982067	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>T	p.%3D	p.S41S	ENST00000252854	2/6	29	13	16	55	55	0	OLFM1,synonymous_variant,p.%3D,ENST00000371796,;OLFM1,synonymous_variant,p.%3D,ENST00000371793,;OLFM1,synonymous_variant,p.%3D,ENST00000339720,;OLFM1,synonymous_variant,p.%3D,ENST00000392991,;OLFM1,synonymous_variant,p.%3D,ENST00000277415,;OLFM1,synonymous_variant,p.%3D,ENST00000252854,;OLFM1,5_prime_UTR_variant,,ENST00000539529,;OLFM1,upstream_gene_variant,,ENST00000539877,;	T	ENSG00000130558	ENST00000252854	Transcript	synonymous_variant	310	123	41	S	agC/agT	.	.	.	1	OLFM1	HGNC	17187	protein_coding	YES	CCDS6986.1	ENSP00000252854	NOE1_HUMAN	Q6IMJ8_HUMAN,Q96BL8_HUMAN,F5H810_HUMAN,F5GZQ2_HUMAN,B3KR22_HUMAN	UPI000013CD8C	.	.	.	2/6	.	hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF34,Pfam_domain:PF12308,Superfamily_domains:SSF50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGCTGGCA	.	5	ESCA
FREM1	0	.	GRCh37	9	14748440	14748440	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5755C>A	p.Leu1919Ile	p.L1919I	ENST00000422223	32/38	16	12	3	50	50	0	FREM1,missense_variant,p.Leu1920Ile,ENST00000380881,;FREM1,missense_variant,p.Leu1919Ile,ENST00000380880,;FREM1,missense_variant,p.Leu1919Ile,ENST00000422223,;FREM1,missense_variant,p.Leu455Ile,ENST00000380894,;FREM1,downstream_gene_variant,,ENST00000486223,;FREM1,3_prime_UTR_variant,,ENST00000380875,;FREM1,intron_variant,,ENST00000427623,;	T	ENSG00000164946	ENST00000422223	Transcript	missense_variant	6571	5755	1919	L/I	Ctt/Att	.	.	.	-1	FREM1	HGNC	23399	protein_coding	YES	CCDS47952.1	ENSP00000412940	FREM1_HUMAN	.	UPI000057A218	.	tolerated(0.27)	benign(0.003)	32/38	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAAGATCTG	.	5	ESCA
CNTNAP3	0	.	GRCh37	9	39176040	39176040	+	Missense_Mutation	SNP	C	C	T	rs764086285	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.977G>A	p.Arg326His	p.R326H	ENST00000297668	7/24	55	40	15	144	144	0	CNTNAP3,missense_variant,p.Arg326His,ENST00000377656,;CNTNAP3,missense_variant,p.Arg326His,ENST00000377659,;CNTNAP3,missense_variant,p.Arg238His,ENST00000358144,;CNTNAP3,missense_variant,p.Arg326His,ENST00000297668,;CNTNAP3,missense_variant,p.Arg326His,ENST00000323947,;CNTNAP3,non_coding_transcript_exon_variant,,ENST00000377653,;CNTNAP3,missense_variant,p.Arg326His,ENST00000443583,;RP11-290L7.3,upstream_gene_variant,,ENST00000425044,;	T	ENSG00000106714	ENST00000297668	Transcript	missense_variant	1051	977	326	R/H	cGt/cAt	rs764086285,COSM3413659,COSM3413660,COSM3413661	.	.	-1	CNTNAP3	HGNC	13834	protein_coding	YES	CCDS6616.1	ENSP00000297668	CNTP3_HUMAN	.	UPI000013E43B	.	tolerated(0.39)	benign(0.004)	7/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF612,hmmpanther:PTHR10127,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTACGTCTG	.	5	ESCA
PTCH1	0	.	GRCh37	9	98218581	98218581	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000331920	19/24	24	13	10	51	51	0	PTCH1,stop_gained,p.Glu1094Ter,ENST00000375274,;PTCH1,stop_gained,p.Glu1095Ter,ENST00000331920,;PTCH1,stop_gained,p.Glu1029Ter,ENST00000430669,;PTCH1,stop_gained,p.Glu944Ter,ENST00000418258,;PTCH1,stop_gained,p.Glu944Ter,ENST00000429896,;PTCH1,stop_gained,p.Glu944Ter,ENST00000421141,;PTCH1,stop_gained,p.Glu1029Ter,ENST00000437951,;PTCH1,downstream_gene_variant,,ENST00000547615,;PTCH1,3_prime_UTR_variant,,ENST00000375290,;	A	ENSG00000185920	ENST00000331920	Transcript	stop_gained	3583	3283	1095	E/*	Gag/Tag	.	.	.	-1	PTCH1	HGNC	9585	protein_coding	YES	CCDS6714.1	ENSP00000332353	PTC1_HUMAN	Q6TKQ0_HUMAN,F8VXL8_HUMAN,F8VQS6_HUMAN	UPI00001AFF9C	.	.	.	19/24	.	Superfamily_domains:SSF82866,Pfam_domain:PF02460,TIGRFAM_domain:TIGR00918,Gene3D:2j8sB01,hmmpanther:PTHR10796:SF61,hmmpanther:PTHR10796,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTCCACTC	.	5	ESCA
NXF5	0	.	GRCh37	X	101098169	101098169	+	5'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-179T>G	.	.	ENST00000537026	2/16	38	6	32	35	35	0	NXF5,5_prime_UTR_variant,,ENST00000473265,;NXF5,5_prime_UTR_variant,,ENST00000361708,;NXF5,5_prime_UTR_variant,,ENST00000537026,;NXF5,5_prime_UTR_variant,,ENST00000332614,;NXF5,5_prime_UTR_variant,,ENST00000361330,;NXF5,5_prime_UTR_variant,,ENST00000493509,;NXF5,5_prime_UTR_variant,,ENST00000372803,;NXF5,5_prime_UTR_variant,,ENST00000263032,;	C	ENSG00000126952	ENST00000537026	Transcript	5_prime_UTR_variant	182	.	.	.	.	.	.	.	-1	NXF5	HGNC	8075	protein_coding	YES	CCDS14491.2	ENSP00000442401	NXF5_HUMAN	.	UPI0000F059DC	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGAAGTTCA	.	5	ESCA
CCDC160	0	.	GRCh37	X	133379619	133379619	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.789G>T	p.Met263Ile	p.M263I	ENST00000517294	3/3	34	21	12	55	55	0	CCDC160,missense_variant,p.Met263Ile,ENST00000370809,;CCDC160,missense_variant,p.Met263Ile,ENST00000517294,;	T	ENSG00000203952	ENST00000517294	Transcript	missense_variant	1172	789	263	M/I	atG/atT	.	.	.	1	CCDC160	HGNC	37286	protein_coding	YES	CCDS48171.1	ENSP00000427951	CC160_HUMAN	.	UPI00001993FD	.	tolerated(0.16)	benign(0.043)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATGAAATC	.	5	ESCA
MXRA5	0	.	GRCh37	X	3235731	3235731	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5991C>T	p.%3D	p.P1997P	ENST00000217939	6/7	22	13	9	61	61	0	MXRA5,synonymous_variant,p.%3D,ENST00000217939,;	A	ENSG00000101825	ENST00000217939	Transcript	synonymous_variant	6146	5991	1997	P	ccC/ccT	.	.	.	-1	MXRA5	HGNC	7539	protein_coding	YES	CCDS14124.1	ENSP00000217939	MXRA5_HUMAN	.	UPI000013C73B	.	.	.	6/7	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF582,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCACGGGGGA	.	5	ESCA
KDM6A	0	.	GRCh37	X	44949998	44949998	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3767A>T	p.Tyr1256Phe	p.Y1256F	ENST00000377967	26/29	18	11	6	52	52	0	KDM6A,missense_variant,p.Tyr899Phe,ENST00000433797,;KDM6A,missense_variant,p.Tyr854Phe,ENST00000414389,;KDM6A,missense_variant,p.Tyr1177Phe,ENST00000543216,;KDM6A,missense_variant,p.Tyr1256Phe,ENST00000377967,;KDM6A,missense_variant,p.Tyr1263Phe,ENST00000382899,;KDM6A,missense_variant,p.Tyr1211Phe,ENST00000536777,;KDM6A,upstream_gene_variant,,ENST00000431196,;KDM6A,downstream_gene_variant,,ENST00000484732,;	T	ENSG00000147050	ENST00000377967	Transcript	missense_variant	3808	3767	1256	Y/F	tAc/tTc	.	.	.	1	KDM6A	HGNC	12637	protein_coding	YES	CCDS14265.1	ENSP00000367203	KDM6A_HUMAN	Q68D33_HUMAN,Q59HG3_HUMAN,Q590H7_HUMAN	UPI000013DA92	.	tolerated(0.08)	benign(0.144)	26/29	.	PROSITE_profiles:PS51184,hmmpanther:PTHR14017:SF9,hmmpanther:PTHR14017,SMART_domains:SM00558,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_4206del4206|5,BUFFER|p.R1255W|c.3763C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGTACGAAT	.	5	ESCA
PCDH11X	0	.	GRCh37	X	91874630	91874630	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EU-01A-11D-A36J-09	TCGA-VR-A8EU-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*691T>C	.	.	ENST00000373094	7/7	50	13	37	76	76	0	PCDH11X,3_prime_UTR_variant,,ENST00000373097,;PCDH11X,3_prime_UTR_variant,,ENST00000373094,;PCDH11X,downstream_gene_variant,,ENST00000406881,;PCDH11X,downstream_gene_variant,,ENST00000373088,;PCDH11X,downstream_gene_variant,,ENST00000361655,;PCDH11X,downstream_gene_variant,,ENST00000298274,;PCDH11X,downstream_gene_variant,,ENST00000504220,;	C	ENSG00000102290	ENST00000373094	Transcript	3_prime_UTR_variant	5580	.	.	.	.	.	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTACTCTTTA	.	5	ESCA
ITPRIP	0	.	GRCh37	10	106074980	106074980	+	Missense_Mutation	SNP	G	G	A	rs746792406	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.830C>T	p.Ala277Val	p.A277V	ENST00000278071	3/3	34	18	16	25	25	0	ITPRIP,missense_variant,p.Ala277Val,ENST00000337478,;ITPRIP,missense_variant,p.Ala277Val,ENST00000358187,;ITPRIP,missense_variant,p.Ala277Val,ENST00000278071,;ITPRIP,downstream_gene_variant,,ENST00000458723,;RP11-127L20.5,downstream_gene_variant,,ENST00000472915,;	A	ENSG00000148841	ENST00000278071	Transcript	missense_variant	1283	830	277	A/V	gCg/gTg	rs746792406	.	.	-1	ITPRIP	HGNC	29370	protein_coding	YES	CCDS7557.1	ENSP00000278071	IPRI_HUMAN	.	UPI0000074521	.	tolerated(0.35)	benign(0.001)	3/3	.	hmmpanther:PTHR10656:SF8,hmmpanther:PTHR10656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGCGCCATG	.	5	ESCA
AFAP1L2	0	.	GRCh37	10	116073779	116073779	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.643C>T	p.Gln215Ter	p.Q215*	ENST00000304129	7/19	54	41	13	73	73	0	AFAP1L2,stop_gained,p.Gln233Ter,ENST00000419268,;AFAP1L2,stop_gained,p.Gln215Ter,ENST00000304129,;AFAP1L2,stop_gained,p.Gln268Ter,ENST00000545353,;AFAP1L2,stop_gained,p.Gln215Ter,ENST00000369271,;	A	ENSG00000169129	ENST00000304129	Transcript	stop_gained	673	643	215	Q/*	Cag/Tag	.	.	.	-1	AFAP1L2	HGNC	25901	protein_coding	YES	CCDS31286.1	ENSP00000303042	AF1L2_HUMAN	.	UPI0000071FAF	.	.	.	7/19	.	PROSITE_profiles:PS50003,hmmpanther:PTHR14338:SF4,hmmpanther:PTHR14338,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGAGGGC	.	5	ESCA
MLLT10	0	.	GRCh37	10	21971160	21971160	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1673C>T	p.Ser558Leu	p.S558L	ENST00000307729	13/23	74	64	10	78	78	0	MLLT10,missense_variant,p.Ser558Leu,ENST00000446906,;MLLT10,missense_variant,p.Ser201Leu,ENST00000438473,;MLLT10,missense_variant,p.Ser558Leu,ENST00000377059,;MLLT10,missense_variant,p.Ser558Leu,ENST00000307729,;MLLT10,missense_variant,p.Ser558Leu,ENST00000377072,;MLLT10,intron_variant,,ENST00000420525,;	T	ENSG00000078403	ENST00000307729	Transcript	missense_variant	1851	1673	558	S/L	tCa/tTa	COSM465532,COSM1135003	.	.	1	MLLT10	HGNC	16063	protein_coding	YES	CCDS55708.1	ENSP00000307411	AF10_HUMAN	Q71UR7_HUMAN,B4DVS6_HUMAN	UPI00001F8FF7	.	tolerated(0.22)	benign(0.039)	13/23	.	hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF86	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTCTCAGAGT	.	4	ESCA
C10orf53	0	.	GRCh37	10	50916719	50916719	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*56G>C	.	.	ENST00000374112	3/3	58	29	28	50	50	0	C10orf53,3_prime_UTR_variant,,ENST00000374112,;C10orf53,3_prime_UTR_variant,,ENST00000535836,;	C	ENSG00000178645	ENST00000374112	Transcript	3_prime_UTR_variant	542	.	.	.	.	.	.	.	1	C10orf53	HGNC	27421	protein_coding	YES	CCDS31202.1	ENSP00000363226	CJ053_HUMAN	.	UPI00001406B3	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGGGTCTGT	.	5	ESCA
PCDH15	0	.	GRCh37	10	55582697	55582697	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4795C>T	p.%3D	p.L1599L	ENST00000361849	34/34	58	53	5	51	51	0	PCDH15,synonymous_variant,p.%3D,ENST00000437009,;PCDH15,synonymous_variant,p.%3D,ENST00000395433,;PCDH15,synonymous_variant,p.%3D,ENST00000320301,;PCDH15,synonymous_variant,p.%3D,ENST00000395432,;PCDH15,synonymous_variant,p.%3D,ENST00000361849,;PCDH15,synonymous_variant,p.%3D,ENST00000395430,;PCDH15,intron_variant,,ENST00000395445,;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000373957,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395438,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000373965,;PCDH15,non_coding_transcript_exon_variant,,ENST00000463095,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,;PCDH15,upstream_gene_variant,,ENST00000476074,;	A	ENSG00000150275	ENST00000361849	Transcript	synonymous_variant	5190	4795	1599	L	Ctg/Ttg	.	.	.	-1	PCDH15	HGNC	14674	protein_coding	YES	CCDS44404.1	ENSP00000354950	.	A2A3E7_HUMAN,A2A3D9_HUMAN	UPI0000EE048B	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTGCAGATCTA	.	2	ESCA
PRF1	0	.	GRCh37	10	72358262	72358262	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1215G>T	p.Gln405His	p.Q405H	ENST00000441259	3/3	34	26	8	43	43	0	PRF1,missense_variant,p.Gln405His,ENST00000373209,;PRF1,missense_variant,p.Gln405His,ENST00000441259,;	A	ENSG00000180644	ENST00000441259	Transcript	missense_variant	1376	1215	405	Q/H	caG/caT	.	.	.	-1	PRF1	HGNC	9360	protein_coding	YES	CCDS7305.1	ENSP00000398568	PERF_HUMAN	S5S2F2_HUMAN,S5RDP5_HUMAN	UPI000013162B	.	tolerated(0.15)	benign(0.001)	3/3	.	hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF3,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTCCTGGGT	.	5	ESCA
MMRN2	0	.	GRCh37	10	88702246	88702246	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2295C>T	p.%3D	p.N765N	ENST00000372027	6/7	31	18	13	33	33	0	MMRN2,synonymous_variant,p.%3D,ENST00000372027,;MMRN2,downstream_gene_variant,,ENST00000609457,;MMRN2,downstream_gene_variant,,ENST00000474994,;MMRN2,downstream_gene_variant,,ENST00000610081,;MMRN2,downstream_gene_variant,,ENST00000488950,;MMRN2,downstream_gene_variant,,ENST00000608090,;MMRN2,downstream_gene_variant,,ENST00000608753,;	A	ENSG00000173269	ENST00000372027	Transcript	synonymous_variant	2617	2295	765	N	aaC/aaT	.	.	.	-1	MMRN2	HGNC	19888	protein_coding	YES	CCDS7379.1	ENSP00000361097	MMRN2_HUMAN	R4GMY6_HUMAN	UPI000013F046	.	.	.	6/7	.	hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACGTTGGC	.	5	ESCA
CYP2C8	0	.	GRCh37	10	96824695	96824695	+	Silent	SNP	G	G	A	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.504C>T	p.%3D	p.F168F	ENST00000371270	4/9	83	79	4	101	101	0	CYP2C8,synonymous_variant,p.%3D,ENST00000539050,;CYP2C8,synonymous_variant,p.%3D,ENST00000371270,;CYP2C8,synonymous_variant,p.%3D,ENST00000535898,;CYP2C8,synonymous_variant,p.%3D,ENST00000527420,;CYP2C8,3_prime_UTR_variant,,ENST00000525991,;CYP2C8,3_prime_UTR_variant,,ENST00000490994,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000527953,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000533320,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000479946,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000526814,;	A	ENSG00000138115	ENST00000371270	Transcript	synonymous_variant	599	504	168	F	ttC/ttT	COSM3442073,COSM3442074,COSM3442075	.	.	-1	CYP2C8	HGNC	2622	protein_coding	YES	CCDS7438.1	ENSP00000360317	CP2C8_HUMAN	B7Z1F5_HUMAN	UPI0000128256	.	.	.	4/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF141,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.P166S|c.496C>T|3,BUFFER|p.P64S|c.190C>T|3	MUTECT|MUSE	AGGATGAAAGT	.	2	ESCA
GUCY1A2	0	.	GRCh37	11	106856796	106856796	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365G>C	p.Gly122Ala	p.G122A	ENST00000282249	2/9	49	45	4	74	74	0	GUCY1A2,missense_variant,p.Gly122Ala,ENST00000282249,;GUCY1A2,missense_variant,p.Gly122Ala,ENST00000526355,;GUCY1A2,missense_variant,p.Gly122Ala,ENST00000347596,;	G	ENSG00000152402	ENST00000282249	Transcript	missense_variant	755	365	122	G/A	gGt/gCt	COSM371712	.	.	-1	GUCY1A2	HGNC	4684	protein_coding	YES	CCDS58170.1	ENSP00000282249	GCYA2_HUMAN	.	UPI000002A79C	.	tolerated(0.68)	benign(0.009)	2/9	.	hmmpanther:PTHR11920:SF276,hmmpanther:PTHR11920	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTACCCAATA	.	3	ESCA
MED19	0	.	GRCh37	11	57472550	57472550	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369T>C	p.%3D	p.D123D	ENST00000337672	2/4	78	66	12	84	84	0	MED19,synonymous_variant,p.%3D,ENST00000337672,;MED19,synonymous_variant,p.%3D,ENST00000431606,;ZDHHC5,downstream_gene_variant,,ENST00000287169,;ZDHHC5,downstream_gene_variant,,ENST00000527985,;MED19,non_coding_transcript_exon_variant,,ENST00000534677,;MED19,non_coding_transcript_exon_variant,,ENST00000528205,;ZDHHC5,downstream_gene_variant,,ENST00000529480,;	G	ENSG00000156603	ENST00000337672	Transcript	synonymous_variant	391	369	123	D	gaT/gaC	.	.	.	-1	MED19	HGNC	29600	protein_coding	YES	CCDS7966.1	ENSP00000337340	MED19_HUMAN	.	UPI00000746CC	.	.	.	2/4	.	hmmpanther:PTHR22536,Pfam_domain:PF10278	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTATCATG	.	5	ESCA
SHANK2	0	.	GRCh37	11	70319282	70319282	+	Missense_Mutation	SNP	G	G	A	rs370834280	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5245C>T	p.Pro1749Ser	p.P1749S	ENST00000338508	33/33	687	660	27	113	113	0	SHANK2,missense_variant,p.Pro1152Ser,ENST00000409161,;SHANK2,missense_variant,p.Pro1027Ser,ENST00000424924,;SHANK2,missense_variant,p.Pro1369Ser,ENST00000423696,;SHANK2,missense_variant,p.Pro1372Ser,ENST00000294018,;SHANK2,missense_variant,p.Pro1749Ser,ENST00000338508,;SHANK2,missense_variant,p.Pro1153Ser,ENST00000449833,;SHANK2,3_prime_UTR_variant,,ENST00000412252,;AP001271.3,downstream_gene_variant,,ENST00000445532,;	A	ENSG00000162105	ENST00000338508	Transcript	missense_variant	5245	5245	1749	P/S	Cct/Tct	rs370834280,COSM1666305,COSM1666306	.	.	-1	SHANK2	HGNC	14295	protein_coding	YES	.	ENSP00000345193	.	C9JFP8_HUMAN,A6NHU9_HUMAN	UPI00020653A9	.	tolerated(0.37)	possibly_damaging(0.641)	33/33	.	hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGGGGGCT	byFrequency|byCluster	2	ESCA
NAALAD2	0	.	GRCh37	11	89896165	89896165	+	Silent	SNP	C	C	T	rs769202397	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1038C>T	p.%3D	p.Y346Y	ENST00000534061	9/19	119	69	50	205	205	0	NAALAD2,synonymous_variant,p.%3D,ENST00000534061,;NAALAD2,synonymous_variant,p.%3D,ENST00000321955,;NAALAD2,intron_variant,,ENST00000375944,;NAALAD2,intron_variant,,ENST00000525171,;NAALAD2,3_prime_UTR_variant,,ENST00000527493,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000524501,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000532691,;NAALAD2,downstream_gene_variant,,ENST00000529090,;	T	ENSG00000077616	ENST00000534061	Transcript	synonymous_variant	1268	1038	346	Y	taC/taT	rs769202397	.	.	1	NAALAD2	HGNC	14526	protein_coding	YES	CCDS8288.1	ENSP00000432481	NALD2_HUMAN	E9PJ53_HUMAN,E9PII2_HUMAN	UPI0000031A85	.	.	.	9/19	.	Superfamily_domains:SSF53187,Superfamily_domains:SSF52025,Gene3D:3.40.630.10,hmmpanther:PTHR10404:SF38,hmmpanther:PTHR10404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTACAATGT	byFrequency	5	ESCA
CLEC2A	0	.	GRCh37	12	10084889	10084889	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40T>A	p.Phe14Ile	p.F14I	ENST00000455827	1/5	32	17	14	51	51	0	CLEC2A,missense_variant,p.Phe14Ile,ENST00000455827,;CLEC2A,missense_variant,p.Phe14Ile,ENST00000339766,;AC091814.2,downstream_gene_variant,,ENST00000412084,;	T	ENSG00000188393	ENST00000455827	Transcript	missense_variant	92	40	14	F/I	Ttc/Atc	.	.	.	-1	CLEC2A	HGNC	24191	protein_coding	YES	CCDS44829.1	ENSP00000396163	CLC2A_HUMAN	.	UPI000156577E	.	tolerated(0.4)	benign(0.001)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGAAGCCAT	.	5	ESCA
NOS1	0	.	GRCh37	12	117718598	117718598	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1456C>T	p.Arg486Cys	p.R486C	ENST00000338101	7/29	107	95	12	130	130	0	NOS1,missense_variant,p.Arg486Cys,ENST00000317775,;NOS1,missense_variant,p.Arg486Cys,ENST00000338101,;NOS1,3_prime_UTR_variant,,ENST00000344089,;	A	ENSG00000089250	ENST00000338101	Transcript	missense_variant	1461	1456	486	R/C	Cgc/Tgc	.	.	.	-1	NOS1	HGNC	7872	protein_coding	YES	CCDS55890.1	ENSP00000337459	NOS1_HUMAN	A0PJJ7_HUMAN	UPI00001FBC10	.	deleterious(0)	probably_damaging(0.991)	7/29	.	Superfamily_domains:SSF56512,PIRSF_domain:PIRSF000333,Gene3D:3.90.340.10,Pfam_domain:PF02898,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAGCGGATGA	.	4	ESCA
PRMT8	0	.	GRCh37	12	3702562	3702562	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*214G>A	.	.	ENST00000382622	10/10	14	9	5	13	13	0	PRMT8,3_prime_UTR_variant,,ENST00000382622,;PRMT8,downstream_gene_variant,,ENST00000452611,;PRMT8,non_coding_transcript_exon_variant,,ENST00000261252,;PRMT8,non_coding_transcript_exon_variant,,ENST00000543701,;	A	ENSG00000111218	ENST00000382622	Transcript	3_prime_UTR_variant	1789	.	.	.	.	.	.	.	1	PRMT8	HGNC	5188	protein_coding	YES	CCDS8521.2	ENSP00000372067	ANM8_HUMAN	.	UPI00005B2E00	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCACGAAGGC	.	5	ESCA
OTOGL	0	.	GRCh37	12	80771648	80771648	+	Silent	SNP	C	C	T	rs751285103	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6855C>T	p.%3D	p.D2285D	ENST00000458043	58/58	78	58	20	67	67	0	OTOGL,synonymous_variant,p.%3D,ENST00000546620,;OTOGL,synonymous_variant,p.%3D,ENST00000458043,;OTOGL,synonymous_variant,p.%3D,ENST00000298820,;OTOGL,synonymous_variant,p.%3D,ENST00000547103,;OTOGL,3_prime_UTR_variant,,ENST00000551340,;	T	ENSG00000165899	ENST00000458043	Transcript	synonymous_variant	6861	6855	2285	D	gaC/gaT	rs751285103	.	.	1	OTOGL	HGNC	26901	protein_coding	YES	.	ENSP00000400895	.	E2QRK2_HUMAN	UPI0001D089C5	.	.	.	58/58	.	SMART_domains:SM00041,hmmpanther:PTHR11339:SF225,hmmpanther:PTHR11339,PROSITE_profiles:PS01225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGACGGCAA	byFrequency	5	ESCA
MRP63	0	.	GRCh37	13	21752663	21752663	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1299A>G	.	.	ENST00000309594	2/2	34	27	7	37	37	0	MRP63,3_prime_UTR_variant,,ENST00000309594,;SKA3,upstream_gene_variant,,ENST00000314759,;SKA3,upstream_gene_variant,,ENST00000400018,;SKA3,upstream_gene_variant,,ENST00000475251,;SKA3,upstream_gene_variant,,ENST00000465471,;SKA3,upstream_gene_variant,,ENST00000462482,;SKA3,upstream_gene_variant,,ENST00000298260,;	G	ENSG00000173141	ENST00000309594	Transcript	3_prime_UTR_variant	1686	.	.	.	.	.	.	.	1	MRP63	HGNC	14514	protein_coding	YES	CCDS9296.1	ENSP00000310726	RT63_HUMAN	.	UPI000004C5AC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTCAAAGTT	.	5	ESCA
GPALPP1	0	.	GRCh37	13	45602138	45602138	+	Silent	SNP	A	A	G	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1023A>G	p.%3D	p.%3D	ENST00000361121	8/12	126	115	11	139	139	0	GPALPP1,stop_retained_variant,p.%3D,ENST00000379151,;GPALPP1,stop_retained_variant,p.%3D,ENST00000357537,;GPALPP1,stop_retained_variant,p.%3D,ENST00000361121,;RP11-321C24.1,intron_variant,,ENST00000437748,;GPALPP1,upstream_gene_variant,,ENST00000473119,;GPALPP1,stop_retained_variant,p.%3D,ENST00000497558,;	G	ENSG00000133114	ENST00000361121	Transcript	stop_retained_variant	1058	1023	341	*	taA/taG	COSM1607106	.	.	1	GPALPP1	HGNC	20298	protein_coding	YES	CCDS9394.1	ENSP00000355211	GPAM1_HUMAN	.	UPI000007435F	.	.	.	8/12	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTATAAGTAAG	.	2	ESCA
GPALPP1	0	.	GRCh37	13	45602196	45602196	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*58A>G	.	.	ENST00000361121	.	73	65	8	74	73	1	GPALPP1,3_prime_UTR_variant,,ENST00000379151,;GPALPP1,intron_variant,,ENST00000357537,;GPALPP1,intron_variant,,ENST00000361121,;RP11-321C24.1,intron_variant,,ENST00000437748,;GPALPP1,upstream_gene_variant,,ENST00000473119,;GPALPP1,intron_variant,,ENST00000497558,;	G	ENSG00000133114	ENST00000361121	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GPALPP1	HGNC	20298	protein_coding	YES	CCDS9394.1	ENSP00000355211	GPAM1_HUMAN	.	UPI000007435F	.	.	.	.	8/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAATACTCTA	.	2	ESCA
ATP7B	0	.	GRCh37	13	52549268	52549268	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88G>A	p.Glu30Lys	p.E30K	ENST00000242839	2/21	51	45	6	67	67	0	ATP7B,missense_variant,p.Glu30Lys,ENST00000400370,;ATP7B,missense_variant,p.Glu30Lys,ENST00000400366,;ATP7B,missense_variant,p.Glu30Lys,ENST00000242839,;ATP7B,missense_variant,p.Glu30Lys,ENST00000418097,;ATP7B,missense_variant,p.Glu30Lys,ENST00000448424,;ATP7B,missense_variant,p.Glu30Lys,ENST00000344297,;ATP7B,5_prime_UTR_variant,,ENST00000542656,;ATP7B,upstream_gene_variant,,ENST00000482841,;ATP7B,upstream_gene_variant,,ENST00000483772,;	T	ENSG00000123191	ENST00000242839	Transcript	missense_variant	245	88	30	E/K	Gaa/Aaa	.	.	.	-1	ATP7B	HGNC	870	protein_coding	YES	CCDS41892.1	ENSP00000242839	ATP7B_HUMAN	G1FFF2_HUMAN,D3KCZ0_HUMAN,C8BMD5_HUMAN,A6YQZ1_HUMAN	UPI00001FCE15	.	tolerated_low_confidence(0.11)	benign(0.008)	2/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTCCCAGG	.	4	ESCA
PCDH17	0	.	GRCh37	13	58302459	58302459	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3031T>G	.	.	ENST00000377918	4/4	18	8	9	24	24	0	PCDH17,3_prime_UTR_variant,,ENST00000377918,;PCDH17,downstream_gene_variant,,ENST00000484979,;	G	ENSG00000118946	ENST00000377918	Transcript	3_prime_UTR_variant	6537	.	.	.	.	.	.	.	1	PCDH17	HGNC	14267	protein_coding	YES	CCDS31986.1	ENSP00000367151	PCD17_HUMAN	.	UPI00001FCE5B	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGAATGTGAA	.	5	ESCA
WDR20	0	.	GRCh37	14	102676536	102676536	+	3'Flank	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000454394	.	72	34	37	69	69	0	WDR20,3_prime_UTR_variant,,ENST00000545563,;WDR20,3_prime_UTR_variant,,ENST00000499851,;WDR20,3_prime_UTR_variant,,ENST00000299135,;WDR20,3_prime_UTR_variant,,ENST00000556511,;WDR20,3_prime_UTR_variant,,ENST00000342702,;WDR20,3_prime_UTR_variant,,ENST00000424963,;WDR20,intron_variant,,ENST00000322340,;WDR20,intron_variant,,ENST00000335263,;WDR20,intron_variant,,ENST00000559478,;WDR20,intron_variant,,ENST00000556807,;WDR20,downstream_gene_variant,,ENST00000558854,;WDR20,downstream_gene_variant,,ENST00000454394,;WDR20,downstream_gene_variant,,ENST00000559708,;WDR20,downstream_gene_variant,,ENST00000558448,;WDR20,downstream_gene_variant,,ENST00000555973,;WDR20,downstream_gene_variant,,ENST00000558135,;WDR20,downstream_gene_variant,,ENST00000557485,;WDR20,3_prime_UTR_variant,,ENST00000555879,;WDR20,intron_variant,,ENST00000556094,;	T	ENSG00000140153	ENST00000454394	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	65	1	WDR20	HGNC	19667	protein_coding	YES	CCDS55943.1	ENSP00000406084	WDR20_HUMAN	H0YNU0_HUMAN,F5H8E6_HUMAN,B3KPG5_HUMAN	UPI0000E23AC1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATGACTTT	.	5	ESCA
IGHG1	0	.	GRCh37	14	106208445	106208445	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455A>G	p.Glu152Gly	p.E152G	ENST00000390548	3/6	121	109	12	143	143	0	IGHG1,missense_variant,p.Glu152Gly,ENST00000390542,;IGHG1,missense_variant,p.Glu152Gly,ENST00000390549,;IGHG1,missense_variant,p.Glu152Gly,ENST00000390548,;	C	ENSG00000211896	ENST00000390548	Transcript	missense_variant	455	455	152	E/G	gAa/gGa	.	.	.	-1	IGHG1	HGNC	5525	IG_C_gene	YES	.	ENSP00000374990	.	.	UPI000173A69D	.	deleterious(0.01)	possibly_damaging(0.641)	3/6	.	Superfamily_domains:SSF48726,SMART_domains:SM00407,Gene3D:2.60.40.10,Pfam_domain:PF07654,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF72,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCTTCGTGG	.	4	ESCA
CHD8	0	.	GRCh37	14	21859177	21859177	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7111A>G	p.Asn2371Asp	p.N2371D	ENST00000399982	36/37	57	54	3	46	46	0	CHD8,missense_variant,p.Asn2371Asp,ENST00000557364,;CHD8,missense_variant,p.Asn148Asp,ENST00000553870,;CHD8,missense_variant,p.Asn2092Asp,ENST00000430710,;CHD8,missense_variant,p.Asn2371Asp,ENST00000399982,;SNORD9,downstream_gene_variant,,ENST00000362566,;CHD8,downstream_gene_variant,,ENST00000555962,;CHD8,downstream_gene_variant,,ENST00000557329,;CHD8,downstream_gene_variant,,ENST00000555301,;CHD8,upstream_gene_variant,,ENST00000557727,;	C	ENSG00000100888	ENST00000399982	Transcript	missense_variant	7176	7111	2371	N/D	Aat/Gat	.	.	.	-1	CHD8	HGNC	20153	protein_coding	YES	CCDS53885.1	ENSP00000382863	CHD8_HUMAN	.	UPI00002375B9	.	deleterious(0.03)	benign(0.007)	36/37	.	Superfamily_domains:SSF160481	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTATTTTTTT	.	2	ESCA
NFATC4	0	.	GRCh37	14	24845836	24845836	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2582C>T	p.Ser861Phe	p.S861F	ENST00000413692	10/10	79	68	11	74	74	0	NFATC4,missense_variant,p.Ser786Phe,ENST00000422617,;NFATC4,missense_variant,p.Ser798Phe,ENST00000250373,;NFATC4,missense_variant,p.Ser811Phe,ENST00000555590,;NFATC4,missense_variant,p.Ser830Phe,ENST00000539237,;NFATC4,missense_variant,p.Ser333Phe,ENST00000555167,;NFATC4,missense_variant,p.Ser786Phe,ENST00000555453,;NFATC4,missense_variant,p.Ser798Phe,ENST00000553708,;NFATC4,missense_variant,p.Ser728Phe,ENST00000557451,;NFATC4,missense_variant,p.Ser861Phe,ENST00000413692,;NFATC4,missense_variant,p.Ser830Phe,ENST00000556279,;NFATC4,missense_variant,p.Ser728Phe,ENST00000553879,;NFATC4,missense_variant,p.Ser811Phe,ENST00000424781,;NFATC4,missense_variant,p.Ser333Phe,ENST00000556759,;NFATC4,missense_variant,p.Ser86Phe,ENST00000555802,;NFATC4,missense_variant,p.Ser86Phe,ENST00000555393,;NFATC4,missense_variant,p.Ser728Phe,ENST00000554344,;NFATC4,intron_variant,,ENST00000554050,;NFATC4,intron_variant,,ENST00000554473,;NFATC4,intron_variant,,ENST00000556169,;NFATC4,intron_variant,,ENST00000553469,;NFATC4,intron_variant,,ENST00000554661,;NFATC4,intron_variant,,ENST00000557767,;NFATC4,intron_variant,,ENST00000554591,;NFATC4,intron_variant,,ENST00000554966,;NFATC4,downstream_gene_variant,,ENST00000554779,;NFATC4,intron_variant,,ENST00000555821,;NFATC4,downstream_gene_variant,,ENST00000440487,;NFATC4,non_coding_transcript_exon_variant,,ENST00000554655,;NFATC4,downstream_gene_variant,,ENST00000557028,;NFATC4,downstream_gene_variant,,ENST00000556957,;NFATC4,downstream_gene_variant,,ENST00000556302,;	T	ENSG00000100968	ENST00000413692	Transcript	missense_variant	2726	2582	861	S/F	tCt/tTt	COSM1188789,COSM1188788	.	.	1	NFATC4	HGNC	7778	protein_coding	YES	CCDS45089.1	ENSP00000388910	NFAC4_HUMAN	G3V4K1_HUMAN	UPI00017BD050	.	deleterious_low_confidence(0.01)	benign(0.122)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12533,hmmpanther:PTHR12533:SF9	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R795W|c.2383C>T|3,BUFFER|p.R858W|c.2572C>T|3	RADIA|MUTECT|MUSE|VARSCANS	CTCCTCTTTCT	.	4	ESCA
AKAP6	0	.	GRCh37	14	33243079	33243081	+	In_Frame_Del	DEL	AAG	AAG	-	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	AAG	AAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3572_3574delAGA	p.Lys1191del	p.K1191del	ENST00000280979	12/14	39	35	4	28	28	0	AKAP6,inframe_deletion,p.Lys78del,ENST00000554740,;AKAP6,inframe_deletion,p.Lys1191del,ENST00000280979,;AKAP6,inframe_deletion,p.Lys1191del,ENST00000557272,;AKAP6,downstream_gene_variant,,ENST00000556540,;AKAP6,downstream_gene_variant,,ENST00000555207,;	-	ENSG00000151320	ENST00000280979	Transcript	inframe_deletion	3738-3740	3568-3570	1190	K/-	AAG/-	.	.	.	1	AKAP6	HGNC	376	protein_coding	YES	CCDS9644.1	ENSP00000280979	AKAP6_HUMAN	G3V569_HUMAN,G3V3H6_HUMAN,G3V3H2_HUMAN,G3V3B5_HUMAN,D3DS91_HUMAN	UPI000013DC48	.	.	.	12/14	.	hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.M1192I|c.3576G>T|3	VARSCANI*|PINDEL	CTACAAAAGAAGAT	.	2	ESCA
PSMA6	0	.	GRCh37	14	35783624	35783624	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.646G>A	p.Glu216Lys	p.E216K	ENST00000261479	6/7	64	56	8	61	61	0	PSMA6,missense_variant,p.Glu197Lys,ENST00000540871,;PSMA6,missense_variant,p.Glu137Lys,ENST00000555764,;PSMA6,missense_variant,p.Glu222Lys,ENST00000553809,;PSMA6,missense_variant,p.Glu55Lys,ENST00000556221,;PSMA6,missense_variant,p.Glu216Lys,ENST00000261479,;PSMA6,intron_variant,,ENST00000556506,;PSMA6,3_prime_UTR_variant,,ENST00000554541,;KIAA0391,3_prime_UTR_variant,,ENST00000557565,;PSMA6,3_prime_UTR_variant,,ENST00000554961,;PSMA6,non_coding_transcript_exon_variant,,ENST00000554457,;PSMA6,downstream_gene_variant,,ENST00000554620,;PSMA6,downstream_gene_variant,,ENST00000555050,;PSMA6,downstream_gene_variant,,ENST00000554843,;PSMA6,downstream_gene_variant,,ENST00000553688,;	A	ENSG00000100902	ENST00000261479	Transcript	missense_variant	766	646	216	E/K	Gaa/Aaa	.	.	.	1	PSMA6	HGNC	9535	protein_coding	YES	CCDS9655.1	ENSP00000261479	PSA6_HUMAN	Q9BZ93_HUMAN,B4DQR4_HUMAN	UPI0000001C1E	.	deleterious(0)	probably_damaging(0.998)	6/7	.	PROSITE_profiles:PS51475,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF11,Pfam_domain:PF00227,Gene3D:3.60.20.10,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATAGAAGTT	.	4	ESCA
TRIM9	0	.	GRCh37	14	51561511	51561511	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.147C>A	p.Ser49Arg	p.S49R	ENST00000298355	1/10	156	59	96	178	178	0	TRIM9,missense_variant,p.Ser49Arg,ENST00000298355,;TRIM9,missense_variant,p.Ser49Arg,ENST00000360392,;TRIM9,missense_variant,p.Ser49Arg,ENST00000338969,;RP11-1140I5.1,downstream_gene_variant,,ENST00000554475,;	T	ENSG00000100505	ENST00000298355	Transcript	missense_variant	1269	147	49	S/R	agC/agA	.	.	.	-1	TRIM9	HGNC	16288	protein_coding	YES	CCDS9703.1	ENSP00000298355	TRIM9_HUMAN	.	UPI000006D630	.	tolerated(0.05)	benign(0.139)	1/10	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF289,SMART_domains:SM00184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGATGGCTCTG	.	5	ESCA
KTN1	0	.	GRCh37	14	56078803	56078803	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37A>G	p.Ile13Val	p.I13V	ENST00000395314	2/44	69	65	4	84	84	0	KTN1,missense_variant,p.Ile13Val,ENST00000395308,;KTN1,missense_variant,p.Ile13Val,ENST00000438792,;KTN1,missense_variant,p.Ile13Val,ENST00000395309,;KTN1,missense_variant,p.Ile13Val,ENST00000413890,;KTN1,missense_variant,p.Ile13Val,ENST00000395311,;KTN1,missense_variant,p.Ile13Val,ENST00000395314,;KTN1,missense_variant,p.Ile13Val,ENST00000416613,;KTN1,missense_variant,p.Ile13Val,ENST00000555498,;KTN1,missense_variant,p.Ile13Val,ENST00000557267,;KTN1,intron_variant,,ENST00000554567,;KTN1,missense_variant,p.Ile13Val,ENST00000459737,;	G	ENSG00000126777	ENST00000395314	Transcript	missense_variant	105	37	13	I/V	Att/Gtt	.	.	.	1	KTN1	HGNC	6467	protein_coding	YES	CCDS41957.1	ENSP00000378725	KTN1_HUMAN	Q5GGW3_HUMAN,G3V5P0_HUMAN,G3V4L8_HUMAN,G3V475_HUMAN	UPI0000190F88	.	tolerated(0.45)	benign(0.075)	2/44	.	hmmpanther:PTHR18864,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTCTTATTCCT	.	2	ESCA
SYNE2	0	.	GRCh37	14	64678706	64678706	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18751G>C	p.Glu6251Gln	p.E6251Q	ENST00000358025	104/116	96	88	7	113	113	0	SYNE2,missense_variant,p.Glu6210Gln,ENST00000554584,;SYNE2,missense_variant,p.Glu2636Gln,ENST00000394768,;SYNE2,missense_variant,p.Glu6251Gln,ENST00000344113,;SYNE2,missense_variant,p.Glu6251Gln,ENST00000358025,;SYNE2,missense_variant,p.Glu34Gln,ENST00000554805,;SYNE2,missense_variant,p.Glu129Gln,ENST00000555022,;SYNE2,missense_variant,p.Glu2636Gln,ENST00000357395,;SYNE2,missense_variant,p.Glu2885Gln,ENST00000555002,;ESR2,intron_variant,,ENST00000556275,;ESR2,intron_variant,,ENST00000542956,;SYNE2,upstream_gene_variant,,ENST00000441438,;SYNE2,upstream_gene_variant,,ENST00000458046,;SYNE2,downstream_gene_variant,,ENST00000556906,;SYNE2,downstream_gene_variant,,ENST00000553801,;SYNE2,downstream_gene_variant,,ENST00000555241,;SYNE2,3_prime_UTR_variant,,ENST00000555612,;SYNE2,3_prime_UTR_variant,,ENST00000553289,;SYNE2,non_coding_transcript_exon_variant,,ENST00000553806,;SYNE2,non_coding_transcript_exon_variant,,ENST00000554997,;SYNE2,upstream_gene_variant,,ENST00000557307,;SYNE2,upstream_gene_variant,,ENST00000557084,;	C	ENSG00000054654	ENST00000358025	Transcript	missense_variant	18981	18751	6251	E/Q	Gag/Cag	.	.	.	1	SYNE2	HGNC	17084	protein_coding	YES	CCDS9761.2	ENSP00000350719	SYNE2_HUMAN	Q6MZP0_HUMAN,G3V5D3_HUMAN,G3V403_HUMAN	UPI00003677E5	.	.	probably_damaging(0.999)	104/116	.	hmmpanther:PTHR11915:SF264,hmmpanther:PTHR11915,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATTTGAGGGC	.	2	ESCA
ATP10A	0	.	GRCh37	15	25961902	25961902	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1751C>T	p.Thr584Met	p.T584M	ENST00000356865	9/21	59	50	9	87	87	0	ATP10A,missense_variant,p.Thr584Met,ENST00000356865,;ATP10A,missense_variant,p.Thr584Met,ENST00000555815,;	A	ENSG00000206190	ENST00000356865	Transcript	missense_variant	1863	1751	584	T/M	aCg/aTg	.	.	.	-1	ATP10A	HGNC	13542	protein_coding	YES	CCDS32178.1	ENSP00000349325	AT10A_HUMAN	.	UPI0000124FAB	.	deleterious(0)	probably_damaging(0.93)	9/21	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF43,Pfam_domain:PF12710,TIGRFAM_domain:TIGR01652,Gene3D:3.40.1110.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGACGTGACG	.	5	ESCA
NOP10	0	.	GRCh37	15	34634302	34634302	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.62A>T	p.Asp21Val	p.D21V	ENST00000328848	2/2	93	81	11	140	140	0	NOP10,missense_variant,p.Asp21Val,ENST00000328848,;NOP10,intron_variant,,ENST00000557912,;NUTM1,upstream_gene_variant,,ENST00000537011,;SLC12A6,upstream_gene_variant,,ENST00000561120,;SLC12A6,upstream_gene_variant,,ENST00000558589,;NUTM1,upstream_gene_variant,,ENST00000438749,;SLC12A6,upstream_gene_variant,,ENST00000397702,;SLC12A6,upstream_gene_variant,,ENST00000354181,;SLC12A6,upstream_gene_variant,,ENST00000458406,;NUTM1,upstream_gene_variant,,ENST00000333756,;SLC12A6,upstream_gene_variant,,ENST00000559236,;SLC12A6,upstream_gene_variant,,ENST00000559484,;SLC12A6,upstream_gene_variant,,ENST00000558667,;SLC12A6,upstream_gene_variant,,ENST00000559664,;SLC12A6,upstream_gene_variant,,ENST00000561080,;SLC12A6,upstream_gene_variant,,ENST00000559523,;	A	ENSG00000182117	ENST00000328848	Transcript	missense_variant	166	62	21	D/V	gAc/gTc	.	.	.	-1	NOP10	HGNC	14378	protein_coding	YES	CCDS10037.1	ENSP00000332198	NOP10_HUMAN	.	UPI0000022AEE	.	tolerated(0.09)	possibly_damaging(0.529)	2/2	.	hmmpanther:PTHR13305,hmmpanther:PTHR13305:SF0,Pfam_domain:PF04135,Gene3D:2apoB00,Superfamily_domains:SSF144210	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGGGTCAAAT	.	4	ESCA
NOP10	0	.	GRCh37	15	34634303	34634303	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61G>T	p.Asp21Tyr	p.D21Y	ENST00000328848	2/2	92	80	11	138	138	0	NOP10,missense_variant,p.Asp21Tyr,ENST00000328848,;NOP10,intron_variant,,ENST00000557912,;NUTM1,upstream_gene_variant,,ENST00000537011,;SLC12A6,upstream_gene_variant,,ENST00000561120,;SLC12A6,upstream_gene_variant,,ENST00000558589,;NUTM1,upstream_gene_variant,,ENST00000438749,;SLC12A6,upstream_gene_variant,,ENST00000397702,;SLC12A6,upstream_gene_variant,,ENST00000354181,;SLC12A6,upstream_gene_variant,,ENST00000458406,;NUTM1,upstream_gene_variant,,ENST00000333756,;SLC12A6,upstream_gene_variant,,ENST00000559236,;SLC12A6,upstream_gene_variant,,ENST00000559484,;SLC12A6,upstream_gene_variant,,ENST00000558667,;SLC12A6,upstream_gene_variant,,ENST00000559664,;SLC12A6,upstream_gene_variant,,ENST00000561080,;SLC12A6,upstream_gene_variant,,ENST00000559523,;	A	ENSG00000182117	ENST00000328848	Transcript	missense_variant	165	61	21	D/Y	Gac/Tac	.	.	.	-1	NOP10	HGNC	14378	protein_coding	YES	CCDS10037.1	ENSP00000332198	NOP10_HUMAN	.	UPI0000022AEE	.	deleterious(0.03)	probably_damaging(0.917)	2/2	.	hmmpanther:PTHR13305,hmmpanther:PTHR13305:SF0,Pfam_domain:PF04135,Gene3D:2apoB00,Superfamily_domains:SSF144210	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGGTCAAATT	.	4	ESCA
RASGRP1	0	.	GRCh37	15	38852065	38852065	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177A>T	p.%3D	p.G59G	ENST00000310803	2/17	56	36	20	71	71	0	RASGRP1,synonymous_variant,p.%3D,ENST00000450598,;RASGRP1,synonymous_variant,p.%3D,ENST00000558432,;RASGRP1,synonymous_variant,p.%3D,ENST00000310803,;RASGRP1,synonymous_variant,p.%3D,ENST00000560929,;RASGRP1,synonymous_variant,p.%3D,ENST00000561180,;RASGRP1,synonymous_variant,p.%3D,ENST00000561117,;RASGRP1,synonymous_variant,p.%3D,ENST00000558164,;RASGRP1,synonymous_variant,p.%3D,ENST00000539159,;RASGRP1,synonymous_variant,p.%3D,ENST00000558418,;RASGRP1,synonymous_variant,p.%3D,ENST00000559830,;RASGRP1,synonymous_variant,p.%3D,ENST00000414708,;	A	ENSG00000172575	ENST00000310803	Transcript	synonymous_variant	355	177	59	G	ggA/ggT	.	.	.	-1	RASGRP1	HGNC	9878	protein_coding	YES	CCDS45222.1	ENSP00000310244	GRP1_HUMAN	H0YNG8_HUMAN,H0YN83_HUMAN,H0YKP8_HUMAN,F5H514_HUMAN	UPI000006FE1C	.	.	.	2/17	.	PROSITE_profiles:PS50212,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF174,Pfam_domain:PF00618,Gene3D:2ii0A01,SMART_domains:SM00229,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGCTCCTTT	.	5	ESCA
MGA	0	.	GRCh37	15	42058816	42058816	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8536G>A	p.Glu2846Lys	p.E2846K	ENST00000219905	24/24	41	35	6	49	49	0	MGA,missense_variant,p.Glu2846Lys,ENST00000219905,;MGA,missense_variant,p.Glu2846Lys,ENST00000570161,;MGA,missense_variant,p.Glu2807Lys,ENST00000389936,;MGA,missense_variant,p.Glu2637Lys,ENST00000545763,;MGA,missense_variant,p.Glu2637Lys,ENST00000566586,;MGA,downstream_gene_variant,,ENST00000564190,;RP11-107F6.3,downstream_gene_variant,,ENST00000562063,;RP11-107F6.3,downstream_gene_variant,,ENST00000607504,;MGA,downstream_gene_variant,,ENST00000568255,;	A	ENSG00000174197	ENST00000219905	Transcript	missense_variant	8717	8536	2846	E/K	Gaa/Aaa	COSM1188973	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	deleterious(0)	possibly_damaging(0.899)	24/24	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCTGAACTA	.	4	ESCA
AP4E1	0	.	GRCh37	15	51260514	51260514	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1906G>C	p.Gly636Arg	p.G636R	ENST00000261842	15/21	123	84	39	133	133	0	AP4E1,missense_variant,p.Gly636Arg,ENST00000261842,;AP4E1,missense_variant,p.Gly561Arg,ENST00000560508,;AP4E1,3_prime_UTR_variant,,ENST00000558439,;AP4E1,3_prime_UTR_variant,,ENST00000561393,;	C	ENSG00000081014	ENST00000261842	Transcript	missense_variant	2012	1906	636	G/R	Ggt/Cgt	.	.	.	1	AP4E1	HGNC	573	protein_coding	YES	CCDS32240.1	ENSP00000261842	AP4E1_HUMAN	.	UPI00001D89D8	.	deleterious(0)	probably_damaging(0.999)	15/21	.	hmmpanther:PTHR22780:SF13,hmmpanther:PTHR22780,PIRSF_domain:PIRSF037097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAGGGTGCA	.	5	ESCA
HERC1	0	.	GRCh37	15	64010784	64010784	+	Missense_Mutation	SNP	G	G	A	rs377537305	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3967C>T	p.Arg1323Trp	p.R1323W	ENST00000443617	21/78	56	46	10	74	74	0	HERC1,missense_variant,p.Arg1323Trp,ENST00000443617,;HERC1,intron_variant,,ENST00000561400,;RP11-317G6.1,downstream_gene_variant,,ENST00000559303,;HERC1,non_coding_transcript_exon_variant,,ENST00000560983,;	A	ENSG00000103657	ENST00000443617	Transcript	missense_variant	4055	3967	1323	R/W	Cgg/Tgg	rs377537305	.	.	-1	HERC1	HGNC	4867	protein_coding	YES	CCDS45277.1	ENSP00000390158	HERC1_HUMAN	H0YL74_HUMAN,H0YL07_HUMAN,H0YKW7_HUMAN	UPI0000212760	.	.	possibly_damaging(0.8)	21/78	.	hmmpanther:PTHR22870:SF156,hmmpanther:PTHR22870	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTCCCGTGATG	byCluster	4	ESCA
IREB2	0	.	GRCh37	15	78730581	78730582	+	5'UTR	INS	-	-	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-97dupT	.	.	ENST00000258886	1/22	171	119	52	121	121	0	IREB2,5_prime_UTR_variant,,ENST00000258886,;IREB2,intron_variant,,ENST00000560840,;IREB2,upstream_gene_variant,,ENST00000560440,;IREB2,upstream_gene_variant,,ENST00000560454,;IREB2,5_prime_UTR_variant,,ENST00000559215,;IREB2,5_prime_UTR_variant,,ENST00000558525,;IREB2,upstream_gene_variant,,ENST00000558570,;	T	ENSG00000136381	ENST00000258886	Transcript	5_prime_UTR_variant	51-52	.	.	.	.	.	.	.	1	IREB2	HGNC	6115	protein_coding	YES	CCDS10302.1	ENSP00000258886	IREB2_HUMAN	H0YLE0_HUMAN	UPI00001C1F8E	.	.	.	1/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCTCCCTTGCC	.	2	ESCA
UNC45A	0	.	GRCh37	15	91489925	91489925	+	Silent	SNP	C	C	T	rs754556176	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1281C>T	p.%3D	p.D427D	ENST00000418476	10/20	31	17	13	32	32	0	UNC45A,synonymous_variant,p.%3D,ENST00000418476,;UNC45A,synonymous_variant,p.%3D,ENST00000394275,;UNC45A,downstream_gene_variant,,ENST00000553671,;UNC45A,non_coding_transcript_exon_variant,,ENST00000554481,;UNC45A,intron_variant,,ENST00000556704,;UNC45A,upstream_gene_variant,,ENST00000471780,;UNC45A,downstream_gene_variant,,ENST00000557212,;UNC45A,upstream_gene_variant,,ENST00000487875,;	T	ENSG00000140553	ENST00000418476	Transcript	synonymous_variant	1321	1281	427	D	gaC/gaT	rs754556176	.	.	1	UNC45A	HGNC	30594	protein_coding	YES	CCDS10367.1	ENSP00000407487	UN45A_HUMAN	.	UPI000000D953	.	.	.	10/20	.	hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF275,Pfam_domain:PF11701,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGACGCTGG	.	5	ESCA
CRAMP1L	0	.	GRCh37	16	1716165	1716165	+	Silent	SNP	G	G	A	rs753839016	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2844G>A	p.%3D	p.T948T	ENST00000397412	15/21	156	132	23	128	128	0	CRAMP1L,synonymous_variant,p.%3D,ENST00000436138,;CRAMP1L,synonymous_variant,p.%3D,ENST00000293925,;CRAMP1L,synonymous_variant,p.%3D,ENST00000397412,;CRAMP1L,synonymous_variant,p.%3D,ENST00000262317,;CRAMP1L,intron_variant,,ENST00000415022,;LA16c-431H6.6,3_prime_UTR_variant,,ENST00000454337,;CRAMP1L,non_coding_transcript_exon_variant,,ENST00000466562,;CRAMP1L,non_coding_transcript_exon_variant,,ENST00000467286,;CRAMP1L,non_coding_transcript_exon_variant,,ENST00000498594,;CRAMP1L,intron_variant,,ENST00000492778,;CRAMP1L,upstream_gene_variant,,ENST00000468839,;	A	ENSG00000007545	ENST00000397412	Transcript	synonymous_variant	2943	2844	948	T	acG/acA	rs753839016	.	.	1	CRAMP1L	HGNC	14122	protein_coding	YES	CCDS10440.2	ENSP00000380559	CRML_HUMAN	B2RNX8_HUMAN	UPI000066D946	.	.	.	15/21	.	hmmpanther:PTHR21677	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCACGAGTCA	.	4	ESCA
RPL3L	0	.	GRCh37	16	1994875	1994875	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1187T>C	p.Leu396Pro	p.L396P	ENST00000268661	10/10	50	47	3	58	58	0	RPL3L,missense_variant,p.Leu396Pro,ENST00000268661,;MSRB1,upstream_gene_variant,,ENST00000564908,;MSRB1,upstream_gene_variant,,ENST00000473663,;MSRB1,upstream_gene_variant,,ENST00000399753,;MSRB1,upstream_gene_variant,,ENST00000361871,;MSRB1,upstream_gene_variant,,ENST00000489198,;	G	ENSG00000140986	ENST00000268661	Transcript	missense_variant	1282	1187	396	L/P	cTg/cCg	.	.	.	-1	RPL3L	HGNC	10351	protein_coding	YES	CCDS10450.1	ENSP00000268661	RL3L_HUMAN	H3BQN3_HUMAN	UPI0000161C28	.	deleterious(0.04)	benign(0.049)	10/10	.	hmmpanther:PTHR11363:SF3,hmmpanther:PTHR11363	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCCAGATGC	.	2	ESCA
PSMD11	0	.	GRCh37	17	30771555	30771555	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14C>T	p.Ala5Val	p.A5V	ENST00000261712	1/14	68	62	6	73	72	1	PSMD11,missense_variant,p.Ala5Val,ENST00000457654,;PSMD11,missense_variant,p.Ala5Val,ENST00000261712,;PSMD11,missense_variant,p.Ala5Val,ENST00000579451,;PSMD11,intron_variant,,ENST00000578213,;PSMD11,upstream_gene_variant,,ENST00000580904,;PSMD11,non_coding_transcript_exon_variant,,ENST00000481992,;PSMD11,non_coding_transcript_exon_variant,,ENST00000578397,;	T	ENSG00000108671	ENST00000261712	Transcript	missense_variant	277	14	5	A/V	gCg/gTg	COSM3988913	.	.	1	PSMD11	HGNC	9556	protein_coding	YES	CCDS11272.1	ENSP00000261712	PSD11_HUMAN	J3KSW3_HUMAN	UPI0000132791	.	tolerated(0.24)	benign(0.087)	1/14	.	hmmpanther:PTHR10678:SF4,hmmpanther:PTHR10678	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCGGCGGTGG	.	3	ESCA
MYO1D	0	.	GRCh37	17	31087624	31087624	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057delT	p.Cys353ValfsTer64	p.C353Vfs*64	ENST00000318217	9/22	37	33	4	35	35	0	MYO1D,frameshift_variant,p.Cys265ValfsTer64,ENST00000394649,;MYO1D,frameshift_variant,p.Cys353ValfsTer64,ENST00000318217,;MYO1D,frameshift_variant,p.Cys353ValfsTer64,ENST00000583621,;MYO1D,frameshift_variant,p.Cys353ValfsTer64,ENST00000579584,;MYO1D,upstream_gene_variant,,ENST00000584232,;MYO1D,upstream_gene_variant,,ENST00000582751,;MYO1D,upstream_gene_variant,,ENST00000580538,;	-	ENSG00000176658	ENST00000318217	Transcript	frameshift_variant	1362	1057	353	C/X	Tgt/gt	.	.	.	-1	MYO1D	HGNC	7598	protein_coding	YES	CCDS32615.1	ENSP00000324527	MYO1D_HUMAN	Q8N618_HUMAN,K7EIG7_HUMAN	UPI0000186004	.	.	.	9/22	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF333,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TCCAACAAAAAA	.	2	ESCA
KRT33B	0	.	GRCh37	17	39521427	39521427	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.876G>T	p.%3D	p.L292L	ENST00000251646	5/7	100	67	33	99	99	0	KRT33B,synonymous_variant,p.%3D,ENST00000251646,;	A	ENSG00000131738	ENST00000251646	Transcript	synonymous_variant	926	876	292	L	ctG/ctT	.	.	.	-1	KRT33B	HGNC	6451	protein_coding	YES	CCDS11389.1	ENSP00000251646	KT33B_HUMAN	.	UPI000012DAFE	.	.	.	5/7	.	Coiled-coils_(Ncoils):Coil,Prints_domain:PR01248,Pfam_domain:PF00038,Gene3D:1.20.5.170,hmmpanther:PTHR23239:SF99,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACACCAGGTT	.	5	ESCA
LRRC37A2	0	.	GRCh37	17	44632542	44632542	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4884G>A	p.Trp1628Ter	p.W1628*	ENST00000576629	13/15	21	15	6	30	30	0	LRRC37A2,stop_gained,p.Trp1628Ter,ENST00000576629,;LRRC37A2,stop_gained,p.Trp1628Ter,ENST00000333412,;ARL17A,3_prime_UTR_variant,,ENST00000336125,;ARL17A,intron_variant,,ENST00000337845,;ARL17A,intron_variant,,ENST00000573185,;ARL17A,intron_variant,,ENST00000445552,;ARL17A,intron_variant,,ENST00000329240,;ARL17A,intron_variant,,ENST00000570550,;FAM215B,downstream_gene_variant,,ENST00000458392,;LRRC37A2,non_coding_transcript_exon_variant,,ENST00000572638,;	A	ENSG00000238083	ENST00000576629	Transcript	stop_gained	5379	4884	1628	W/*	tgG/tgA	.	.	.	1	LRRC37A2	HGNC	32404	protein_coding	YES	CCDS42353.1	ENSP00000459551	L37A2_HUMAN	.	UPI0000E59258	.	.	.	13/15	.	hmmpanther:PTHR23045	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.W1628R|c.4882T>C|3	RADIA|VARSCANS	CCATGGAGGGG	.	2	ESCA
PNPO	0	.	GRCh37	17	46019112	46019112	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71A>G	p.His24Arg	p.H24R	ENST00000225573	1/7	30	13	16	20	20	0	PNPO,missense_variant,p.His24Arg,ENST00000434554,;PNPO,missense_variant,p.His24Arg,ENST00000225573,;PNPO,missense_variant,p.His24Arg,ENST00000544840,;PNPO,5_prime_UTR_variant,,ENST00000534893,;PNPO,intron_variant,,ENST00000583599,;AC003665.1,upstream_gene_variant,,ENST00000451140,;AC003665.1,upstream_gene_variant,,ENST00000411573,;AC003665.1,upstream_gene_variant,,ENST00000585280,;AC003665.1,upstream_gene_variant,,ENST00000433001,;RP11-6N17.9,upstream_gene_variant,,ENST00000582262,;PNPO,missense_variant,p.His24Arg,ENST00000585320,;PNPO,missense_variant,p.His24Arg,ENST00000582171,;PNPO,missense_variant,p.His24Arg,ENST00000583245,;PNPO,missense_variant,p.His24Arg,ENST00000584061,;PNPO,upstream_gene_variant,,ENST00000584806,;	G	ENSG00000108439	ENST00000225573	Transcript	missense_variant	176	71	24	H/R	cAc/cGc	.	.	.	1	PNPO	HGNC	30260	protein_coding	YES	CCDS11522.1	ENSP00000225573	PNPO_HUMAN	J3QQZ9_HUMAN,J3QQV6_HUMAN,B4E0V0_HUMAN	UPI000004A13F	.	tolerated_low_confidence(0.33)	benign(0)	1/7	.	hmmpanther:PTHR10851,hmmpanther:PTHR10851:SF1,PIRSF_domain:PIRSF000190	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTCACCTGT	.	5	ESCA
LUC7L3	0	.	GRCh37	17	48829423	48829424	+	3'UTR	INS	-	-	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1403dupT	.	.	ENST00000505658	10/10	71	53	18	54	54	0	LUC7L3,3_prime_UTR_variant,,ENST00000505658,;LUC7L3,intron_variant,,ENST00000503728,;LUC7L3,intron_variant,,ENST00000240304,;LUC7L3,intron_variant,,ENST00000513969,;LUC7L3,downstream_gene_variant,,ENST00000544170,;LUC7L3,downstream_gene_variant,,ENST00000511974,;LUC7L3,downstream_gene_variant,,ENST00000393227,;LUC7L3,intron_variant,,ENST00000503798,;LUC7L3,downstream_gene_variant,,ENST00000512549,;LUC7L3,downstream_gene_variant,,ENST00000508482,;LUC7L3,downstream_gene_variant,,ENST00000509487,;LUC7L3,downstream_gene_variant,,ENST00000504065,;	T	ENSG00000108848	ENST00000505658	Transcript	3_prime_UTR_variant	2889-2890	.	.	.	.	.	.	.	1	LUC7L3	HGNC	24309	protein_coding	YES	CCDS11573.1	ENSP00000425092	LC7L3_HUMAN	U3KQT3_HUMAN,D6RHH0_HUMAN	UPI00000736F2	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GATGCCTTGAT	.	3	ESCA
TOM1L1	0	.	GRCh37	17	53038554	53038554	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2-42A>G	.	.	ENST00000575882	.	23	19	4	18	18	0	TOM1L1,intron_variant,,ENST00000445275,;TOM1L1,intron_variant,,ENST00000540336,;TOM1L1,intron_variant,,ENST00000536554,;TOM1L1,intron_variant,,ENST00000572158,;TOM1L1,intron_variant,,ENST00000348161,;TOM1L1,intron_variant,,ENST00000575882,;TOM1L1,downstream_gene_variant,,ENST00000574318,;COX11,downstream_gene_variant,,ENST00000571584,;COX11,downstream_gene_variant,,ENST00000299335,;COX11,non_coding_transcript_exon_variant,,ENST00000573912,;COX11,upstream_gene_variant,,ENST00000574989,;COX11,3_prime_UTR_variant,,ENST00000574821,;COX11,3_prime_UTR_variant,,ENST00000576370,;COX11,3_prime_UTR_variant,,ENST00000572558,;TOM1L1,intron_variant,,ENST00000574653,;TOM1L1,intron_variant,,ENST00000571319,;	G	ENSG00000141198	ENST00000575882	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TOM1L1	HGNC	11983	protein_coding	YES	CCDS11582.1	ENSP00000460823	TM1L1_HUMAN	I3L4N3_HUMAN,I3L1Q1_HUMAN,B7Z9E2_HUMAN	UPI000003E7E0	.	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGAAGGACA	.	4	ESCA
ACE	0	.	GRCh37	17	61564065	61564065	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2206G>A	p.Glu736Lys	p.E736K	ENST00000290866	14/25	38	21	16	37	37	0	ACE,missense_variant,p.Glu162Lys,ENST00000490216,;ACE,missense_variant,p.Glu736Lys,ENST00000428043,;ACE,missense_variant,p.Glu736Lys,ENST00000290866,;ACE,missense_variant,p.Glu162Lys,ENST00000290863,;ACE,missense_variant,p.Glu162Lys,ENST00000413513,;ACE,missense_variant,p.Glu46Lys,ENST00000421982,;ACE,upstream_gene_variant,,ENST00000582761,;ACE,downstream_gene_variant,,ENST00000538928,;ACE,upstream_gene_variant,,ENST00000577418,;ACE,downstream_gene_variant,,ENST00000584529,;ACE,missense_variant,p.Glu162Lys,ENST00000579314,;ACE,missense_variant,p.Glu162Lys,ENST00000577647,;ACE,3_prime_UTR_variant,,ENST00000582005,;ACE,3_prime_UTR_variant,,ENST00000578839,;ACE,3_prime_UTR_variant,,ENST00000579204,;ACE,3_prime_UTR_variant,,ENST00000579726,;ACE,upstream_gene_variant,,ENST00000584865,;ACE,downstream_gene_variant,,ENST00000582678,;ACE,upstream_gene_variant,,ENST00000583645,;	A	ENSG00000159640	ENST00000290866	Transcript	missense_variant	2230	2206	736	E/K	Gag/Aag	.	.	.	1	ACE	HGNC	2707	protein_coding	YES	CCDS11637.1	ENSP00000290866	ACE_HUMAN	Q3KRI5_HUMAN,D3DU13_HUMAN	UPI000002B8AD	.	tolerated(0.5)	possibly_damaging(0.594)	14/25	.	hmmpanther:PTHR10514:SF19,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCAGGAGCTG	.	3	ESCA
PRKCA	0	.	GRCh37	17	64800691	64800691	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*536G>A	.	.	ENST00000413366	17/17	19	16	3	20	20	0	PRKCA,3_prime_UTR_variant,,ENST00000413366,;	A	ENSG00000154229	ENST00000413366	Transcript	3_prime_UTR_variant	2581	.	.	.	.	.	.	.	1	PRKCA	HGNC	9393	protein_coding	YES	CCDS11664.1	ENSP00000408695	KPCA_HUMAN	L7RSM7_HUMAN	UPI000013DD98	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCTGAAAGG	.	2	ESCA
TP53	0	.	GRCh37	17	7578556	7578556	+	Splice_Site	SNP	T	T	C	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376-2A>G	.	p.X126_splice	ENST00000269305	.	8	3	5	26	26	0	TP53,splice_acceptor_variant,,ENST00000508793,;TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000269305,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000503591,;TP53,splice_acceptor_variant,,ENST00000455263,;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	splice_acceptor_variant	.	.	.	.	.	CS114003,TP53_g.12362A>G,TP53_g.12362A>T,TP53_g.12362del,TP53_g.12362A>C,COSM45672,COSM46049,COSM45658,COSM21585,COSM562615,COSM318167,COSM3675526,COSM318166,COSM562616,COSM3675529,COSM3675528,COSM3388230,COSM3717681,COSM1649367,COSM1646843,COSM3675527,COSM318168,COSM3675530,COSM562617	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.376-2A>G|4,SITE|p.?|c.376-2A>G|10,SITE|p.?|c.97-2A>G|10,SITE|p.?|c.376-2A>G|17,SITE|p.?|c.376-2A>G|10,SITE|p.?|c.376-2A>G|6,BUFFER|p.0?|c.1_1182del1182|6,BUFFER|p.Y126_K132delYSPALNK|c.376_396del21|6,BUFFER|p.Y126_N131delYSPALN|c.376_393del18|3,BUFFER|p.P128L|c.383C>T|3,BUFFER|p.P128fs*42|c.382delC|3,BUFFER|p.P128S|c.382C>T|7,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S127Y|c.380C>A|10,BUFFER|p.S34F|c.101C>T|11,BUFFER|p.S127F|c.380C>T|4,BUFFER|p.S127F|c.380C>T|33,BUFFER|p.S127F|c.380C>T|3,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S34P|c.100T>C|4,BUFFER|p.S34T|c.100T>A|4,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.S127P|c.379T>C|8,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127T|c.379T>A|10,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>G|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>A|4,BUFFER|p.Y33*|c.99C>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y33C|c.98A>G|6,BUFFER|p.Y126C|c.377A>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y126C|c.377A>G|9,BUFFER|p.Y126S|c.377A>C|3,BUFFER|p.Y126C|c.377A>G|5,BUFFER|p.Y126N|c.376T>A|7,BUFFER|p.Y33D|c.97T>G|7,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.Y126D|c.376T>G|10,BUFFER|p.Y126D|c.376T>G|7,BUFFER|p.?|c.97-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|10,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>A|11,BUFFER|p.?|c.97-1G>A|20,BUFFER|p.?|c.376-1G>T|3,BUFFER|p.?|c.376-1G>A|19,BUFFER|p.?|c.376-1G>T|9,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.97-2A>T|3,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-2A>C|4,BUFFER|p.?|c.376-2A>T|3,BUFFER|p.?|c.376-4A>G|3	MUTECT|MUSE	AGTACTGTAGG	.	2	ESCA
KDM6B	0	.	GRCh37	17	7748330	7748382	+	Splice_Site	DEL	GGAGGCCGGGTAAGCGGCCGCTGCGTTTTGGGTCGGCCCAGTGGCTCCGGACT	GGAGGCCGGGTAAGCGGCCGCTGCGTTTTGGGTCGGCCCAGTGGCTCCGGACT	-	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	GGAGGCCGGGTAAGCGGCCGCTGCGTTTTGGGTCGGCCCAGTGGCTCCGGACT	GGAGGCCGGGTAAGCGGCCGCTGCGTTTTGGGTCGGCCCAGTGGCTCCGGACT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-154_-149+47delGGCCGGGTAAGCGGCCGCTGCGTTTTGGGTCGGCCCAGTGGCTCCGGACTGGA	.	.	ENST00000254846	2/22	47	41	6	65	65	0	KDM6B,splice_donor_variant,,ENST00000448097,;KDM6B,splice_donor_variant,,ENST00000570632,;KDM6B,splice_donor_variant,,ENST00000254846,;KDM6B,splice_donor_variant,,ENST00000571047,;KDM6B,downstream_gene_variant,,ENST00000575521,;KDM6B,downstream_gene_variant,,ENST00000572030,;	-	ENSG00000132510	ENST00000254846	Transcript	splice_donor_variant	233-?	.	.	.	.	.	.	.	1	KDM6B	HGNC	29012	protein_coding	YES	CCDS32552.1	ENSP00000254846	KDM6B_HUMAN	D3DTQ7_HUMAN	UPI00006C175B	.	.	.	2/22	2/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	PINDEL|VARSCANS*	TCCCACGGAGGCCGGGTAAGCGGCCGCTGCGTTTTGGGTCGGCCCAGTGGCTCCGGACTGGAAG	.	2	ESCA
PIEZO2	0	.	GRCh37	18	10760966	10760966	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3318A>G	p.%3D	p.G1106G	ENST00000503781	22/52	101	91	10	125	125	0	PIEZO2,synonymous_variant,p.%3D,ENST00000580640,;PIEZO2,synonymous_variant,p.%3D,ENST00000503781,;PIEZO2,synonymous_variant,p.%3D,ENST00000302079,;PIEZO2,synonymous_variant,p.%3D,ENST00000383408,;PIEZO2,synonymous_variant,p.%3D,ENST00000582913,;	C	ENSG00000154864	ENST00000503781	Transcript	synonymous_variant	3318	3318	1106	G	ggA/ggG	.	.	.	-1	PIEZO2	HGNC	26270	protein_coding	YES	.	ENSP00000421377	PIEZ2_HUMAN	J3KSM7_HUMAN	UPI0001B3CB29	.	.	.	22/52	.	hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAAGTCCATC	.	4	ESCA
PTPN2	0	.	GRCh37	18	12802116	12802116	+	Missense_Mutation	SNP	G	G	C	rs764406914	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.893C>G	p.Ser298Cys	p.S298C	ENST00000309660	8/9	54	48	5	53	53	0	PTPN2,missense_variant,p.Ser298Cys,ENST00000309660,;PTPN2,missense_variant,p.Ser13Cys,ENST00000591901,;PTPN2,missense_variant,p.Ser57Cys,ENST00000587703,;PTPN2,missense_variant,p.Ser47Cys,ENST00000585666,;PTPN2,missense_variant,p.Ser321Cys,ENST00000591115,;PTPN2,missense_variant,p.Ser298Cys,ENST00000353319,;PTPN2,missense_variant,p.Ser298Cys,ENST00000327283,;PTPN2,missense_variant,p.Ser269Cys,ENST00000591497,;PTPN2,3_prime_UTR_variant,,ENST00000591305,;	C	ENSG00000175354	ENST00000309660	Transcript	missense_variant	987	893	298	S/C	tCt/tGt	rs764406914,COSM1387813	.	.	-1	PTPN2	HGNC	9650	protein_coding	YES	CCDS11865.1	ENSP00000311857	PTN2_HUMAN	K7ER87_HUMAN,D3DUJ3_HUMAN	UPI000017284E	.	tolerated(0.14)	benign(0)	8/9	.	PIRSF_domain:PIRSF000926,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF200	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGAGATAAG	byFrequency	4	ESCA
ATP8B1	0	.	GRCh37	18	55371857	55371857	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.323T>C	p.Ile108Thr	p.I108T	ENST00000536015	4/28	42	37	5	64	64	0	ATP8B1,missense_variant,p.Ile108Thr,ENST00000283684,;ATP8B1,missense_variant,p.Ile108Thr,ENST00000536015,;RP11-35G9.3,intron_variant,,ENST00000599199,;RP11-35G9.5,intron_variant,,ENST00000588925,;ATP8B1,non_coding_transcript_exon_variant,,ENST00000589147,;ATP8B1,3_prime_UTR_variant,,ENST00000591728,;	G	ENSG00000081923	ENST00000536015	Transcript	missense_variant	443	323	108	I/T	aTa/aCa	.	.	.	-1	ATP8B1	HGNC	3706	protein_coding	YES	CCDS11965.1	ENSP00000445359	AT8B1_HUMAN	K7ERI0_HUMAN,K7EQC4_HUMAN	UPI000013DD54	.	deleterious(0)	benign(0.07)	4/28	.	hmmpanther:PTHR24092:SF48,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGTATAAAG	.	4	ESCA
ZNF440	0	.	GRCh37	19	11943541	11943541	+	Missense_Mutation	SNP	C	C	T	rs201343885	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1550C>T	p.Ala517Val	p.A517V	ENST00000304060	4/4	73	68	5	71	71	0	ZNF440,missense_variant,p.Ala517Val,ENST00000304060,;ZNF440,downstream_gene_variant,,ENST00000457526,;ZNF440,downstream_gene_variant,,ENST00000588954,;ZNF440,downstream_gene_variant,,ENST00000414255,;ZNF440,downstream_gene_variant,,ENST00000427505,;	T	ENSG00000171295	ENST00000304060	Transcript	missense_variant	1714	1550	517	A/V	gCg/gTg	rs201343885	.	.	1	ZNF440	HGNC	20874	protein_coding	YES	CCDS42503.1	ENSP00000305373	ZN440_HUMAN	K7EJ55_HUMAN,C9JG89_HUMAN	UPI0000074249	.	tolerated(0.23)	benign(0.001)	4/4	.	.	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATGCGAGCA	byCluster	2	ESCA
ASNA1	0	.	GRCh37	19	12856259	12856259	+	Silent	SNP	C	C	T	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.378C>T	p.%3D	p.S126S	ENST00000591090	4/8	56	35	20	46	46	0	ASNA1,synonymous_variant,p.%3D,ENST00000591090,;ASNA1,synonymous_variant,p.%3D,ENST00000357332,;ASNA1,synonymous_variant,p.%3D,ENST00000586561,;ASNA1,non_coding_transcript_exon_variant,,ENST00000590633,;	T	ENSG00000198356	ENST00000591090	Transcript	synonymous_variant	480	378	126	S	agC/agT	COSM991428	.	.	1	ASNA1	HGNC	752	protein_coding	YES	CCDS32920.1	ENSP00000466379	ASNA_HUMAN	K7ERW9_HUMAN	UPI0000126095	.	.	.	4/8	.	Superfamily_domains:SSF52540,Pfam_domain:PF02374,TIGRFAM_domain:TIGR00345,Gene3D:3.40.50.300,hmmpanther:PTHR10803,hmmpanther:PTHR10803:SF3,HAMAP:MF_03112	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGCATGGG	.	5	ESCA
ZNF737	0	.	GRCh37	19	20728081	20728081	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.928G>C	p.Glu310Gln	p.E310Q	ENST00000427401	4/4	50	41	9	68	68	0	ZNF737,missense_variant,p.Glu310Gln,ENST00000427401,;ZNF737,downstream_gene_variant,,ENST00000594419,;ZNF737,upstream_gene_variant,,ENST00000596530,;ZNF737,downstream_gene_variant,,ENST00000597940,;	G	ENSG00000237440	ENST00000427401	Transcript	missense_variant	1023	928	310	E/Q	Gag/Cag	.	.	.	-1	ZNF737	HGNC	32468	protein_coding	YES	CCDS54238.1	ENSP00000395733	ZN737_HUMAN	M0R1D1_HUMAN	UPI0000198506	.	deleterious(0.01)	possibly_damaging(0.874)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF93,hmmpanther:PTHR24384,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCTCTCCGC	.	4	ESCA
TBXA2R	0	.	GRCh37	19	3595700	3595700	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.983+35T>C	.	.	ENST00000411851	.	59	31	28	49	49	0	TBXA2R,missense_variant,p.Leu210Pro,ENST00000589966,;TBXA2R,missense_variant,p.Ser340Pro,ENST00000375190,;TBXA2R,intron_variant,,ENST00000411851,;GIPC3,downstream_gene_variant,,ENST00000322315,;TBXA2R,downstream_gene_variant,,ENST00000587717,;	G	ENSG00000006638	ENST00000411851	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TBXA2R	HGNC	11608	protein_coding	YES	CCDS54198.1	ENSP00000393333	TA2R_HUMAN	Q05C92_HUMAN	UPI00000711C4	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGGAGCGCT	.	5	ESCA
MEGF8	0	.	GRCh37	19	42880227	42880227	+	Missense_Mutation	SNP	A	A	T	rs766724451	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7637A>T	p.Tyr2546Phe	p.Y2546F	ENST00000334370	41/41	21	17	4	23	23	0	MEGF8,missense_variant,p.Tyr207Phe,ENST00000378073,;MEGF8,missense_variant,p.Tyr2546Phe,ENST00000334370,;MEGF8,missense_variant,p.Tyr2613Phe,ENST00000251268,;MEGF8,3_prime_UTR_variant,,ENST00000593647,;MEGF8,intron_variant,,ENST00000598762,;MEGF8,downstream_gene_variant,,ENST00000599787,;	T	ENSG00000105429	ENST00000334370	Transcript	missense_variant	8272	7637	2546	Y/F	tAc/tTc	rs766724451	.	.	1	MEGF8	HGNC	3233	protein_coding	YES	CCDS12604.2	ENSP00000334219	MEGF8_HUMAN	.	UPI00003CF1A7	.	tolerated(0.08)	possibly_damaging(0.789)	41/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTACCTGC	.	5	ESCA
PSG4	0	.	GRCh37	19	43697453	43697453	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*71A>G	.	.	ENST00000405312	6/6	167	138	28	193	193	0	PSG4,3_prime_UTR_variant,,ENST00000244295,;PSG4,3_prime_UTR_variant,,ENST00000405312,;PSG4,3_prime_UTR_variant,,ENST00000433626,;PSG4,downstream_gene_variant,,ENST00000451895,;PSG4,downstream_gene_variant,,ENST00000596907,;PSG4,downstream_gene_variant,,ENST00000599391,;PSG4,downstream_gene_variant,,ENST00000600572,;PSG4,downstream_gene_variant,,ENST00000597374,;PSG4,downstream_gene_variant,,ENST00000599746,;PSG4,downstream_gene_variant,,ENST00000599371,;PSG4,non_coding_transcript_exon_variant,,ENST00000490769,;PSG4,downstream_gene_variant,,ENST00000595949,;PSG4,downstream_gene_variant,,ENST00000597349,;PSG4,downstream_gene_variant,,ENST00000495316,;PSG4,downstream_gene_variant,,ENST00000596199,;PSG4,downstream_gene_variant,,ENST00000601041,;	C	ENSG00000243137	ENST00000405312	Transcript	3_prime_UTR_variant	1569	.	.	.	.	.	.	.	-1	PSG4	HGNC	9521	protein_coding	YES	CCDS46093.1	ENSP00000384770	PSG4_HUMAN	M0QYU2_HUMAN	UPI000034ECBA	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGCTTCTGG	.	4	ESCA
PGLYRP1	0	.	GRCh37	19	46522790	46522790	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403T>C	p.Tyr135His	p.Y135H	ENST00000008938	2/3	74	47	26	98	98	0	PGLYRP1,missense_variant,p.Tyr135His,ENST00000008938,;CCDC61,downstream_gene_variant,,ENST00000536603,;CCDC61,downstream_gene_variant,,ENST00000594087,;CCDC61,downstream_gene_variant,,ENST00000263284,;CCDC61,downstream_gene_variant,,ENST00000595358,;MIR769,downstream_gene_variant,,ENST00000390225,;CCDC61,intron_variant,,ENST00000601763,;CCDC61,downstream_gene_variant,,ENST00000596687,;CCDC61,downstream_gene_variant,,ENST00000599044,;	G	ENSG00000008438	ENST00000008938	Transcript	missense_variant	447	403	135	Y/H	Tac/Cac	.	.	.	-1	PGLYRP1	HGNC	8904	protein_coding	YES	CCDS12680.1	ENSP00000008938	PGRP1_HUMAN	.	UPI0000131870	.	deleterious(0)	probably_damaging(0.995)	2/3	.	Superfamily_domains:SSF55846,SMART_domains:SM00701,PIRSF_domain:PIRSF037945,SMART_domains:SM00644,Pfam_domain:PF01510,Gene3D:3.40.80.10,hmmpanther:PTHR11022:SF32,hmmpanther:PTHR11022	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGTAGTTGC	.	5	ESCA
PLEKHA4	0	.	GRCh37	19	49340484	49340484	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62T>G	.	.	ENST00000263265	20/20	41	23	18	48	48	0	PLEKHA4,3_prime_UTR_variant,,ENST00000355496,;PLEKHA4,3_prime_UTR_variant,,ENST00000263265,;PLEKHA4,3_prime_UTR_variant,,ENST00000597129,;HSD17B14,upstream_gene_variant,,ENST00000595764,;HSD17B14,upstream_gene_variant,,ENST00000263278,;HSD17B14,upstream_gene_variant,,ENST00000599157,;PLEKHA4,non_coding_transcript_exon_variant,,ENST00000601146,;	C	ENSG00000105559	ENST00000263265	Transcript	3_prime_UTR_variant	2958	.	.	.	.	.	.	.	-1	PLEKHA4	HGNC	14339	protein_coding	YES	CCDS12737.1	ENSP00000263265	PKHA4_HUMAN	M0R2K5_HUMAN,M0QXJ3_HUMAN	UPI00000721A6	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGATCTCC	.	5	ESCA
SPACA6P-AS	0	.	GRCh37	19	52195962	52195962	+	RNA	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.748G>A	.	.	ENST00000602324	1/2	166	98	68	220	220	0	SPACA6P-AS,non_coding_transcript_exon_variant,,ENST00000602324,;MIRLET7E,upstream_gene_variant,,ENST00000362102,;SPACA6P,upstream_gene_variant,,ENST00000576093,;SPACA6P,upstream_gene_variant,,ENST00000573266,;MIR99B,downstream_gene_variant,,ENST00000384819,;MIR125A,upstream_gene_variant,,ENST00000385273,;SPACA6P,upstream_gene_variant,,ENST00000574072,;SPACA6P,upstream_gene_variant,,ENST00000576494,;SPACA6P,upstream_gene_variant,,ENST00000571328,;AC018755.2,upstream_gene_variant,,ENST00000331594,;	T	ENSG00000269959	ENST00000602324	Transcript	non_coding_transcript_exon_variant	748	.	.	.	.	.	.	.	-1	SPACA6P-AS	HGNC	49383	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCCCCGG	.	5	ESCA
CLEC4M	0	.	GRCh37	19	7830858	7830858	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.549G>T	p.Gln183His	p.Q183H	ENST00000327325	4/7	94	65	28	127	127	0	CLEC4M,missense_variant,p.Gln132His,ENST00000334806,;CLEC4M,missense_variant,p.Gln155His,ENST00000595751,;CLEC4M,missense_variant,p.Gln183His,ENST00000327325,;CLEC4M,missense_variant,p.Gln171His,ENST00000394122,;CLEC4M,missense_variant,p.Gln161His,ENST00000248228,;CLEC4M,missense_variant,p.Gln139His,ENST00000359059,;CLEC4M,missense_variant,p.Gln183His,ENST00000357361,;CLEC4M,missense_variant,p.Gln162His,ENST00000596707,;CLEC4M,missense_variant,p.Gln155His,ENST00000596363,;CLEC4M,intron_variant,,ENST00000595496,;CLEC4M,intron_variant,,ENST00000597522,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000601089,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000598879,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000599333,;CLEC4M,upstream_gene_variant,,ENST00000602143,;	T	ENSG00000104938	ENST00000327325	Transcript	missense_variant	667	549	183	Q/H	caG/caT	.	.	.	1	CLEC4M	HGNC	13523	protein_coding	YES	CCDS12187.1	ENSP00000316228	CLC4M_HUMAN	.	UPI0000073C48	.	tolerated(0.12)	unknown(0)	4/7	.	hmmpanther:PTHR22802:SF200,hmmpanther:PTHR22802	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCAGGAGCT	.	5	ESCA
NBPF9	0	.	GRCh37	1	144816640	144816640	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.769C>G	p.Ser257Cys	p.S257C	ENST00000375552	5/15	321	294	26	407	406	0	NBPF9,missense_variant,p.Ser257Cys,ENST00000375552,;NBPF9,missense_variant,p.Ser258Cys,ENST00000338347,;NBPF9,missense_variant,p.Ser258Cys,ENST00000440491,;NBPF9,5_prime_UTR_variant,,ENST00000281815,;NBPF9,non_coding_transcript_exon_variant,,ENST00000496755,;NBPF9,non_coding_transcript_exon_variant,,ENST00000491652,;NBPF9,non_coding_transcript_exon_variant,,ENST00000468645,;NBPF9,non_coding_transcript_exon_variant,,ENST00000484811,;NBPF9,non_coding_transcript_exon_variant,,ENST00000471873,;NBPF9,non_coding_transcript_exon_variant,,ENST00000472811,;NBPF9,downstream_gene_variant,,ENST00000465793,;NBPF9,upstream_gene_variant,,ENST00000488888,;NBPF9,downstream_gene_variant,,ENST00000483630,;	G	ENSG00000168614	ENST00000375552	Transcript	missense_variant	769	770	257	S/C	tCt/tGt	.	.	.	1	NBPF9	HGNC	31991	protein_coding	YES	.	ENSP00000364702	.	Q5TB04_HUMAN,I1VE14_HUMAN	UPI000059D038	.	deleterious(0.01)	probably_damaging(0.992)	5/15	.	PROSITE_profiles:PS51316,hmmpanther:PTHR14199	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATCCTCTCATG	.	3	ESCA
ARHGAP30	0	.	GRCh37	1	161024465	161024465	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376C>T	p.Arg126Cys	p.R126C	ENST00000368013	4/12	60	50	10	49	49	0	ARHGAP30,missense_variant,p.Arg126Cys,ENST00000368013,;ARHGAP30,missense_variant,p.Arg126Cys,ENST00000368016,;ARHGAP30,intron_variant,,ENST00000368015,;ARHGAP30,3_prime_UTR_variant,,ENST00000490279,;ARHGAP30,3_prime_UTR_variant,,ENST00000471492,;ARHGAP30,3_prime_UTR_variant,,ENST00000368018,;ARHGAP30,non_coding_transcript_exon_variant,,ENST00000461003,;	A	ENSG00000186517	ENST00000368013	Transcript	missense_variant	697	376	126	R/C	Cgc/Tgc	.	.	.	-1	ARHGAP30	HGNC	27414	protein_coding	YES	CCDS30918.1	ENSP00000356992	RHG30_HUMAN	.	UPI0000160677	.	deleterious(0)	probably_damaging(1)	4/12	.	PROSITE_profiles:PS50238,hmmpanther:PTHR15729,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAGCGCTCAG	.	4	ESCA
FCGR3A	0	.	GRCh37	1	161518363	161518363	+	Missense_Mutation	SNP	T	T	G	rs758304652	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.275A>C	p.Asn92Thr	p.N92T	ENST00000367969	3/5	152	139	12	175	175	0	FCGR3A,missense_variant,p.Asn56Thr,ENST00000540048,;FCGR3A,missense_variant,p.Asn73Thr,ENST00000426740,;FCGR3A,missense_variant,p.Asn56Thr,ENST00000436743,;FCGR3A,missense_variant,p.Asn55Thr,ENST00000442336,;FCGR3A,missense_variant,p.Asn92Thr,ENST00000367969,;FCGR3A,missense_variant,p.Asn56Thr,ENST00000367967,;FCGR3A,missense_variant,p.Asn91Thr,ENST00000443193,;FCGR3A,non_coding_transcript_exon_variant,,ENST00000476031,;RP11-25K21.6,intron_variant,,ENST00000537821,;	G	ENSG00000203747	ENST00000367969	Transcript	missense_variant	459	275	92	N/T	aAt/aCt	rs758304652	.	.	-1	FCGR3A	HGNC	3619	protein_coding	YES	CCDS1232.1	ENSP00000356946	.	M9MML0_HUMAN,Q9UN20_HUMAN	UPI000013E1BC	.	tolerated(0.08)	benign(0.06)	3/5	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF14,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGAATTGTCC	.	3	ESCA
FCGR3B	0	.	GRCh37	1	161595991	161595991	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.629G>C	p.Gly210Ala	p.G210A	ENST00000531221	4/5	174	160	14	167	167	0	FCGR3B,missense_variant,p.Gly195Ala,ENST00000421702,;FCGR3B,missense_variant,p.Gly210Ala,ENST00000531221,;FCGR3B,missense_variant,p.Gly174Ala,ENST00000367964,;FCGR3B,missense_variant,p.Gly174Ala,ENST00000294800,;FCGR2B,intron_variant,,ENST00000403078,;FCGR2B,intron_variant,,ENST00000367960,;FCGR2B,intron_variant,,ENST00000428605,;FCGR2B,intron_variant,,ENST00000367962,;FCGR3A,intron_variant,,ENST00000540048,;FCGR3B,downstream_gene_variant,,ENST00000534776,;FCGR3B,downstream_gene_variant,,ENST00000533780,;FCGR3B,downstream_gene_variant,,ENST00000534489,;	G	ENSG00000162747	ENST00000531221	Transcript	missense_variant	633	629	210	G/A	gGg/gCg	COSM3477298	.	.	-1	FCGR3B	HGNC	3620	protein_coding	YES	CCDS58040.1	ENSP00000433642	.	M9MML6_HUMAN,E9PNY5_HUMAN	UPI000066D8C5	.	tolerated(0.1)	possibly_damaging(0.903)	4/5	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF14	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAAGCCCCCTG	.	3	ESCA
FMO9P	0	.	GRCh37	1	166592888	166592888	+	RNA	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.912G>T	.	.	ENST00000477875	6/7	70	47	22	94	94	0	FMO9P,non_coding_transcript_exon_variant,,ENST00000477875,;FMO9P,non_coding_transcript_exon_variant,,ENST00000488458,;	T	ENSG00000215834	ENST00000477875	Transcript	non_coding_transcript_exon_variant	912	.	.	.	.	.	.	.	1	FMO9P	HGNC	32210	processed_transcript	YES	.	.	.	.	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGAGAAATT	.	5	ESCA
RABGAP1L	0	.	GRCh37	1	174606588	174606588	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1786G>T	p.Gly596Ter	p.G596*	ENST00000251507	14/21	76	53	23	97	97	0	RABGAP1L,stop_gained,p.Gly596Ter,ENST00000251507,;RABGAP1L,non_coding_transcript_exon_variant,,ENST00000526253,;RABGAP1L,non_coding_transcript_exon_variant,,ENST00000474375,;	T	ENSG00000152061	ENST00000251507	Transcript	stop_gained	1960	1786	596	G/*	Gga/Tga	.	.	.	1	RABGAP1L	HGNC	24663	protein_coding	YES	CCDS1314.1	ENSP00000251507	RBG1L_HUMAN	F1LJ00_HUMAN	UPI0000458A9F	.	.	.	14/21	.	Superfamily_domains:SSF47923,SMART_domains:SM00164,Gene3D:2qq8A02,Pfam_domain:PF00566,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF205,PROSITE_profiles:PS50086	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTGGAGGA	.	5	ESCA
RABGAP1L	0	.	GRCh37	1	174606589	174606589	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1787G>T	p.Gly596Val	p.G596V	ENST00000251507	14/21	78	55	23	98	98	0	RABGAP1L,missense_variant,p.Gly596Val,ENST00000251507,;RABGAP1L,non_coding_transcript_exon_variant,,ENST00000526253,;RABGAP1L,non_coding_transcript_exon_variant,,ENST00000474375,;	T	ENSG00000152061	ENST00000251507	Transcript	missense_variant	1961	1787	596	G/V	gGa/gTa	.	.	.	1	RABGAP1L	HGNC	24663	protein_coding	YES	CCDS1314.1	ENSP00000251507	RBG1L_HUMAN	F1LJ00_HUMAN	UPI0000458A9F	.	deleterious(0)	probably_damaging(0.984)	14/21	.	Superfamily_domains:SSF47923,SMART_domains:SM00164,Gene3D:2qq8A02,Pfam_domain:PF00566,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF205,PROSITE_profiles:PS50086	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTGGAGGAG	.	5	ESCA
RALGPS2	0	.	GRCh37	1	178780524	178780524	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372T>C	p.%3D	p.Y124Y	ENST00000367635	6/20	180	147	32	172	172	0	RALGPS2,synonymous_variant,p.%3D,ENST00000324778,;RALGPS2,synonymous_variant,p.%3D,ENST00000367635,;RALGPS2,synonymous_variant,p.%3D,ENST00000367634,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000495034,;	C	ENSG00000116191	ENST00000367635	Transcript	synonymous_variant	710	372	124	Y	taT/taC	.	.	.	1	RALGPS2	HGNC	30279	protein_coding	YES	CCDS1325.1	ENSP00000356607	RGPS2_HUMAN	.	UPI000000DBE1	.	.	.	6/20	.	PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF180,hmmpanther:PTHR23113,Pfam_domain:PF00617,Gene3D:2ii0A02,SMART_domains:SM00147,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTATATTAA	.	5	ESCA
RALGPS2	0	.	GRCh37	1	178848093	178848093	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.802G>C	p.Glu268Gln	p.E268Q	ENST00000367635	10/20	91	84	7	84	84	0	RALGPS2,missense_variant,p.Glu233Gln,ENST00000324778,;RALGPS2,missense_variant,p.Glu6Gln,ENST00000415888,;RALGPS2,missense_variant,p.Glu268Gln,ENST00000367635,;RALGPS2,missense_variant,p.Glu268Gln,ENST00000367634,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000477383,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000495034,;	C	ENSG00000116191	ENST00000367635	Transcript	missense_variant	1140	802	268	E/Q	Gaa/Caa	COSM3789152	.	.	1	RALGPS2	HGNC	30279	protein_coding	YES	CCDS1325.1	ENSP00000356607	RGPS2_HUMAN	.	UPI000000DBE1	.	deleterious(0.03)	benign(0.308)	10/20	.	PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF180,hmmpanther:PTHR23113,Gene3D:2ii0A02,SMART_domains:SM00147,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGAAGAACTA	.	2	ESCA
RALGPS2	0	.	GRCh37	1	178848102	178848102	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811A>C	p.Lys271Gln	p.K271Q	ENST00000367635	10/20	90	83	6	87	87	0	RALGPS2,missense_variant,p.Lys236Gln,ENST00000324778,;RALGPS2,missense_variant,p.Lys9Gln,ENST00000415888,;RALGPS2,missense_variant,p.Lys271Gln,ENST00000367635,;RALGPS2,missense_variant,p.Lys271Gln,ENST00000367634,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000477383,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000495034,;	C	ENSG00000116191	ENST00000367635	Transcript	missense_variant	1149	811	271	K/Q	Aaa/Caa	.	.	.	1	RALGPS2	HGNC	30279	protein_coding	YES	CCDS1325.1	ENSP00000356607	RGPS2_HUMAN	.	UPI000000DBE1	.	deleterious(0)	benign(0.034)	10/20	.	PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF180,hmmpanther:PTHR23113,SMART_domains:SM00147,Superfamily_domains:0041591	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACAAAAATTT	.	2	ESCA
UBR4	0	.	GRCh37	1	19478158	19478158	+	Missense_Mutation	SNP	C	C	T	rs55848569	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7192G>A	p.Asp2398Asn	p.D2398N	ENST00000375254	48/106	32	28	4	42	42	0	UBR4,missense_variant,p.Asp13Asn,ENST00000425413,;UBR4,missense_variant,p.Asp2398Asn,ENST00000375267,;UBR4,missense_variant,p.Asp1108Asn,ENST00000417040,;UBR4,missense_variant,p.Asp2398Asn,ENST00000375254,;UBR4,missense_variant,p.Asp2398Asn,ENST00000375217,;UBR4,missense_variant,p.Asp2398Asn,ENST00000375226,;UBR4,downstream_gene_variant,,ENST00000497018,;UBR4,non_coding_transcript_exon_variant,,ENST00000419533,;	T	ENSG00000127481	ENST00000375254	Transcript	missense_variant	7220	7192	2398	D/N	Gat/Aat	rs55848569	.	.	-1	UBR4	HGNC	30313	protein_coding	YES	CCDS189.1	ENSP00000364403	UBR4_HUMAN	Q96HY5_HUMAN	UPI000021276F	.	.	probably_damaging(0.94)	48/106	.	hmmpanther:PTHR21725	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTTATCAGCCT	by1000G	3	ESCA
C1orf74	0	.	GRCh37	1	209956409	209956409	+	Missense_Mutation	SNP	C	C	T	rs748935585	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.571G>A	p.Asp191Asn	p.D191N	ENST00000294811	2/2	75	58	16	81	81	0	C1orf74,missense_variant,p.Asp191Asn,ENST00000294811,;TRAF3IP3,downstream_gene_variant,,ENST00000367024,;TRAF3IP3,downstream_gene_variant,,ENST00000367023,;TRAF3IP3,downstream_gene_variant,,ENST00000367025,;TRAF3IP3,downstream_gene_variant,,ENST00000400959,;TRAF3IP3,downstream_gene_variant,,ENST00000477431,;TRAF3IP3,downstream_gene_variant,,ENST00000010338,;IRF6,downstream_gene_variant,,ENST00000367021,;TRAF3IP3,downstream_gene_variant,,ENST00000367026,;RP3-434O14.8,downstream_gene_variant,,ENST00000430751,;TRAF3IP3,downstream_gene_variant,,ENST00000488702,;TRAF3IP3,downstream_gene_variant,,ENST00000467830,;TRAF3IP3,downstream_gene_variant,,ENST00000480569,;TRAF3IP3,downstream_gene_variant,,ENST00000460314,;TRAF3IP3,downstream_gene_variant,,ENST00000476050,;TRAF3IP3,downstream_gene_variant,,ENST00000471368,;TRAF3IP3,downstream_gene_variant,,ENST00000478359,;	T	ENSG00000162757	ENST00000294811	Transcript	missense_variant	828	571	191	D/N	Gat/Aat	rs748935585	.	.	-1	C1orf74	HGNC	26319	protein_coding	YES	CCDS1491.1	ENSP00000294811	CA074_HUMAN	.	UPI0000073C4E	.	tolerated(0.64)	benign(0.004)	2/2	.	hmmpanther:PTHR31366,Pfam_domain:PF14953	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCATCTCCCT	byFrequency	5	ESCA
USH2A	0	.	GRCh37	1	216595333	216595333	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.346C>T	p.%3D	p.L116L	ENST00000307340	2/72	71	58	13	66	66	0	USH2A,synonymous_variant,p.%3D,ENST00000366942,;USH2A,synonymous_variant,p.%3D,ENST00000366943,;USH2A,synonymous_variant,p.%3D,ENST00000307340,;	A	ENSG00000042781	ENST00000307340	Transcript	synonymous_variant	733	346	116	L	Ctg/Ttg	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	.	2/72	.	hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCAGATCAT	.	5	ESCA
MORN1	0	.	GRCh37	1	2290084	2290084	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.816C>A	p.%3D	p.V272V	ENST00000378531	9/14	31	15	16	48	48	0	MORN1,synonymous_variant,p.%3D,ENST00000378531,;MORN1,synonymous_variant,p.%3D,ENST00000378529,;RP4-740C4.7,downstream_gene_variant,,ENST00000607858,;MORN1,non_coding_transcript_exon_variant,,ENST00000607342,;MORN1,non_coding_transcript_exon_variant,,ENST00000606372,;	T	ENSG00000116151	ENST00000378531	Transcript	synonymous_variant	990	816	272	V	gtC/gtA	.	.	.	-1	MORN1	HGNC	25852	protein_coding	YES	CCDS40.1	ENSP00000367792	MORN1_HUMAN	.	UPI000007293C	.	.	.	9/14	.	hmmpanther:PTHR23084,hmmpanther:PTHR23084:SF123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTGACCTC	.	5	ESCA
GALNT2	0	.	GRCh37	1	230417319	230417319	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2115C>T	.	.	ENST00000366672	16/16	10	3	7	9	9	0	GALNT2,3_prime_UTR_variant,,ENST00000366672,;GALNT2,downstream_gene_variant,,ENST00000543760,;RP5-956O18.3,non_coding_transcript_exon_variant,,ENST00000414640,;GALNT2,non_coding_transcript_exon_variant,,ENST00000485438,;	T	ENSG00000143641	ENST00000366672	Transcript	3_prime_UTR_variant	3903	.	.	.	.	.	.	.	1	GALNT2	HGNC	4124	protein_coding	YES	CCDS1582.1	ENSP00000355632	GALT2_HUMAN	.	UPI0000074053	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCCCTTCAC	.	2	ESCA
RER1	0	.	GRCh37	1	2330933	2330933	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.266C>T	p.Pro89Leu	p.P89L	ENST00000605895	4/7	79	70	9	78	78	0	RER1,missense_variant,p.Pro89Leu,ENST00000488353,;RER1,missense_variant,p.Pro89Leu,ENST00000605895,;RER1,missense_variant,p.Pro89Leu,ENST00000306256,;RER1,missense_variant,p.Pro89Leu,ENST00000378512,;RER1,missense_variant,p.Pro89Leu,ENST00000443438,;RER1,intron_variant,,ENST00000378513,;RER1,intron_variant,,ENST00000378518,;RER1,upstream_gene_variant,,ENST00000462129,;RER1,downstream_gene_variant,,ENST00000493207,;	T	ENSG00000157916	ENST00000605895	Transcript	missense_variant	399	266	89	P/L	cCt/cTt	COSM1223542	.	.	1	RER1	HGNC	30309	protein_coding	YES	CCDS41232.1	ENSP00000475168	RER1_HUMAN	Q5T094_HUMAN,Q5T092_HUMAN	UPI0000000C69	.	deleterious(0.02)	probably_damaging(1)	4/7	.	hmmpanther:PTHR10743,Pfam_domain:PF03248,PIRSF_domain:PIRSF016013	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATCCTTCCT	.	4	ESCA
OR2L8	0	.	GRCh37	1	248112321	248112321	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.162C>A	p.%3D	p.L54L	ENST00000357191	1/1	154	138	15	146	146	0	OR2L8,synonymous_variant,p.%3D,ENST00000357191,;OR2L13,intron_variant,,ENST00000366478,;	A	ENSG00000196936	ENST00000357191	Transcript	synonymous_variant	162	162	54	L	ctC/ctA	.	.	.	1	OR2L8	HGNC	15014	protein_coding	YES	CCDS31101.1	ENSP00000349719	OR2L8_HUMAN	.	UPI0000061E5D	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF104,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CATCTCCACAC	.	3	ESCA
COL16A1	0	.	GRCh37	1	32154674	32154674	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633A>T	p.Ile545Phe	p.I545F	ENST00000373672	24/71	22	18	4	24	24	0	COL16A1,missense_variant,p.Ile545Phe,ENST00000373672,;COL16A1,missense_variant,p.Ile264Phe,ENST00000373667,;COL16A1,missense_variant,p.Ile545Phe,ENST00000373668,;COL16A1,missense_variant,p.Ile545Phe,ENST00000271069,;COL16A1,non_coding_transcript_exon_variant,,ENST00000482478,;COL16A1,non_coding_transcript_exon_variant,,ENST00000529928,;COL16A1,non_coding_transcript_exon_variant,,ENST00000474000,;	A	ENSG00000084636	ENST00000373672	Transcript	missense_variant	2150	1633	545	I/F	Atc/Ttc	.	.	.	-1	COL16A1	HGNC	2193	protein_coding	YES	CCDS41297.1	ENSP00000362776	COGA1_HUMAN	.	UPI0000203DD1	.	.	unknown(0)	24/71	.	hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGGATGCCAG	.	4	ESCA
TRAPPC3	0	.	GRCh37	1	36602741	36602741	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63C>T	.	.	ENST00000373166	5/5	45	38	7	48	48	0	TRAPPC3,3_prime_UTR_variant,,ENST00000373163,;TRAPPC3,3_prime_UTR_variant,,ENST00000373166,;TRAPPC3,3_prime_UTR_variant,,ENST00000373162,;TRAPPC3,downstream_gene_variant,,ENST00000373159,;TRAPPC3,non_coding_transcript_exon_variant,,ENST00000462715,;TRAPPC3,downstream_gene_variant,,ENST00000469757,;TRAPPC3,downstream_gene_variant,,ENST00000497251,;	A	ENSG00000054116	ENST00000373166	Transcript	3_prime_UTR_variant	697	.	.	.	.	.	.	.	-1	TRAPPC3	HGNC	19942	protein_coding	YES	CCDS404.1	ENSP00000362261	TPPC3_HUMAN	.	UPI0000052E1F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGGGAGCAC	.	4	ESCA
ZFYVE9	0	.	GRCh37	1	52798576	52798576	+	Missense_Mutation	SNP	A	A	C	rs200871651	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3575A>C	p.Asn1192Thr	p.N1192T	ENST00000287727	14/19	37	31	5	56	56	0	ZFYVE9,missense_variant,p.Asn1192Thr,ENST00000371591,;ZFYVE9,missense_variant,p.Asn1133Thr,ENST00000357206,;ZFYVE9,missense_variant,p.Asn1192Thr,ENST00000287727,;ZFYVE9,non_coding_transcript_exon_variant,,ENST00000469134,;	C	ENSG00000157077	ENST00000287727	Transcript	missense_variant	3747	3575	1192	N/T	aAt/aCt	rs200871651	.	.	1	ZFYVE9	HGNC	6775	protein_coding	YES	CCDS563.1	ENSP00000287727	ZFYV9_HUMAN	.	UPI0000001620	.	deleterious(0.04)	benign(0.392)	14/19	.	Pfam_domain:PF11979,PIRSF_domain:PIRSF037289	.	.	.	.	.	.	.	G:0.0002	G:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAATCAGC	byFrequency|byCluster	5	ESCA
LPPR4	0	.	GRCh37	1	99774081	99774081	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1515C>A	.	.	ENST00000370185	7/7	38	33	4	59	59	0	LPPR4,3_prime_UTR_variant,,ENST00000370185,;LPPR4,3_prime_UTR_variant,,ENST00000457765,;LPPR4,3_prime_UTR_variant,,ENST00000370184,;	A	ENSG00000117600	ENST00000370185	Transcript	3_prime_UTR_variant	4304	.	.	.	.	.	.	.	1	LPPR4	Uniprot_gn	.	protein_coding	YES	CCDS757.1	ENSP00000359204	LPPR4_HUMAN	.	UPI0000161229	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTCATAAG	.	4	ESCA
JAG1	0	.	GRCh37	20	10619018	10619018	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1128A>G	.	.	ENST00000254958	26/26	87	75	12	85	85	0	JAG1,3_prime_UTR_variant,,ENST00000254958,;JAG1,intron_variant,,ENST00000423891,;SLX4IP,downstream_gene_variant,,ENST00000488816,;	C	ENSG00000101384	ENST00000254958	Transcript	3_prime_UTR_variant	5301	.	.	.	.	.	.	.	-1	JAG1	HGNC	6188	protein_coding	YES	CCDS13112.1	ENSP00000254958	JAG1_HUMAN	B7U6M8_HUMAN,B4DYR1_HUMAN	UPI00000498B5	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAGATTGGTG	.	4	ESCA
ZNF343	0	.	GRCh37	20	2465211	2465211	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396C>T	p.%3D	p.F132F	ENST00000278772	6/6	54	49	5	44	44	0	ZNF343,synonymous_variant,p.%3D,ENST00000278772,;ZNF343,synonymous_variant,p.%3D,ENST00000445484,;ZNF343,non_coding_transcript_exon_variant,,ENST00000465019,;RP4-734P14.4,intron_variant,,ENST00000461548,;	A	ENSG00000088876	ENST00000278772	Transcript	synonymous_variant	884	396	132	F	ttC/ttT	.	.	.	-1	ZNF343	HGNC	16017	protein_coding	YES	CCDS13028.1	ENSP00000278772	ZN343_HUMAN	.	UPI000013DB8F	.	.	.	6/6	.	hmmpanther:PTHR24381:SF97,hmmpanther:PTHR24381,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCAGGAAGAT	.	2	ESCA
RPN2	0	.	GRCh37	20	35864999	35864999	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1770G>T	p.Met590Ile	p.M590I	ENST00000237530	16/17	59	40	19	35	35	0	RPN2,missense_variant,p.Met590Ile,ENST00000237530,;RPN2,missense_variant,p.Met97Ile,ENST00000437329,;RPN2,missense_variant,p.Met558Ile,ENST00000373622,;RPN2,intron_variant,,ENST00000456400,;RPN2,non_coding_transcript_exon_variant,,ENST00000470352,;	T	ENSG00000118705	ENST00000237530	Transcript	missense_variant	2081	1770	590	M/I	atG/atT	.	.	.	1	RPN2	HGNC	10382	protein_coding	YES	CCDS13291.1	ENSP00000237530	RPN2_HUMAN	.	UPI0000000C52	.	tolerated(0.08)	possibly_damaging(0.588)	16/17	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12640:SF0,hmmpanther:PTHR12640,Pfam_domain:PF05817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATGTATGT	.	5	ESCA
PTPRT	0	.	GRCh37	20	41100980	41100980	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000373187	8/31	56	32	23	75	75	0	PTPRT,missense_variant,p.Arg459Gln,ENST00000373201,;PTPRT,missense_variant,p.Arg459Gln,ENST00000356100,;PTPRT,missense_variant,p.Arg459Gln,ENST00000373198,;PTPRT,missense_variant,p.Arg459Gln,ENST00000373193,;PTPRT,missense_variant,p.Arg459Gln,ENST00000373184,;PTPRT,missense_variant,p.Arg459Gln,ENST00000373190,;PTPRT,missense_variant,p.Arg459Gln,ENST00000373187,;	T	ENSG00000196090	ENST00000373187	Transcript	missense_variant	1376	1376	459	R/Q	cGg/cAg	.	.	.	-1	PTPRT	HGNC	9682	protein_coding	YES	CCDS42874.1	ENSP00000362283	PTPRT_HUMAN	.	UPI0000246C03	.	tolerated(0.32)	benign(0.002)	8/31	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCCGGATG	.	5	ESCA
SPO11	0	.	GRCh37	20	55904959	55904959	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.36C>T	p.%3D	p.F12F	ENST00000371263	1/13	168	150	18	160	160	0	SPO11,synonymous_variant,p.%3D,ENST00000371260,;SPO11,synonymous_variant,p.%3D,ENST00000345868,;SPO11,synonymous_variant,p.%3D,ENST00000371263,;SPO11,upstream_gene_variant,,ENST00000418127,;SPO11,upstream_gene_variant,,ENST00000494972,;RP3-481F12.1,downstream_gene_variant,,ENST00000455840,;	T	ENSG00000054796	ENST00000371263	Transcript	synonymous_variant	145	36	12	F	ttC/ttT	.	.	.	1	SPO11	HGNC	11250	protein_coding	YES	CCDS13456.1	ENSP00000360310	SPO11_HUMAN	.	UPI0000135E5E	.	.	.	1/13	.	hmmpanther:PTHR10848,Pfam_domain:PF03533,Prints_domain:PR01551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGTTCTTCGA	.	4	ESCA
KRTAP6-1	0	.	GRCh37	21	31986206	31986206	+	Silent	SNP	G	G	A	rs143074400	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18C>T	p.%3D	p.Y6Y	ENST00000329122	1/1	98	80	18	128	128	0	KRTAP6-1,synonymous_variant,p.%3D,ENST00000329122,;KRTAP20-1,upstream_gene_variant,,ENST00000334664,;	A	ENSG00000184724	ENST00000329122	Transcript	synonymous_variant	44	18	6	Y	taC/taT	rs143074400	.	.	-1	KRTAP6-1	HGNC	18931	protein_coding	YES	CCDS13602.1	ENSP00000332690	KRA61_HUMAN	.	UPI00001A9E58	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31678:SF2,hmmpanther:PTHR31678	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCGTAGTA	byCluster|by1000G	5	ESCA
SLC5A3	0	.	GRCh37	21	35477900	35477900	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8246G>T	.	.	ENST00000608209	2/2	56	42	14	68	68	0	SLC5A3,3_prime_UTR_variant,,ENST00000608209,;SLC5A3,3_prime_UTR_variant,,ENST00000381151,;MRPS6,intron_variant,,ENST00000399312,;MRPS6,intron_variant,,ENST00000477091,;MRPS6,intron_variant,,ENST00000488492,;AP000320.7,intron_variant,,ENST00000362077,;	T	ENSG00000272962	ENST00000608209	Transcript	3_prime_UTR_variant	10915	.	.	.	.	.	.	.	1	SLC5A3	Uniprot_gn	11038	protein_coding	YES	CCDS33549.1	ENSP00000477068	.	.	UPI00001359F3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGGGTGTAT	.	5	ESCA
HPS4	0	.	GRCh37	22	26866727	26866727	+	Missense_Mutation	SNP	C	C	T	rs111522254	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554G>A	p.Arg185His	p.R185H	ENST00000398145	7/14	50	45	4	68	68	0	HPS4,missense_variant,p.Arg185His,ENST00000422379,;HPS4,missense_variant,p.Arg185His,ENST00000336873,;HPS4,missense_variant,p.Arg180His,ENST00000398141,;HPS4,missense_variant,p.Arg180His,ENST00000402105,;HPS4,missense_variant,p.Arg185His,ENST00000398145,;HPS4,non_coding_transcript_exon_variant,,ENST00000459918,;HPS4,3_prime_UTR_variant,,ENST00000439453,;HPS4,3_prime_UTR_variant,,ENST00000429411,;HPS4,3_prime_UTR_variant,,ENST00000464362,;HPS4,non_coding_transcript_exon_variant,,ENST00000496385,;HPS4,non_coding_transcript_exon_variant,,ENST00000466781,;HPS4,non_coding_transcript_exon_variant,,ENST00000485842,;HPS4,downstream_gene_variant,,ENST00000481910,;	T	ENSG00000100099	ENST00000398145	Transcript	missense_variant	1171	554	185	R/H	cGc/cAc	rs111522254	.	.	-1	HPS4	HGNC	15844	protein_coding	YES	CCDS13835.1	ENSP00000381213	HPS4_HUMAN	.	UPI000012CB6F	.	tolerated(0.05)	possibly_damaging(0.809)	7/14	.	hmmpanther:PTHR14407:SF9,hmmpanther:PTHR14407	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GCGAGCGCTGG	byCluster|by1000G	2	ESCA
UGGT1	0	.	GRCh37	2	128900707	128900707	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1759G>A	p.Glu587Lys	p.E587K	ENST00000259253	17/41	131	100	30	129	129	0	UGGT1,missense_variant,p.Glu587Lys,ENST00000259253,;UGGT1,missense_variant,p.Glu563Lys,ENST00000375990,;UGGT1,3_prime_UTR_variant,,ENST00000376723,;UGGT1,3_prime_UTR_variant,,ENST00000438277,;UGGT1,upstream_gene_variant,,ENST00000488439,;AC108059.4,upstream_gene_variant,,ENST00000411629,;	A	ENSG00000136731	ENST00000259253	Transcript	missense_variant	1806	1759	587	E/K	Gaa/Aaa	.	.	.	1	UGGT1	HGNC	15663	protein_coding	YES	CCDS2154.1	ENSP00000259253	UGGG1_HUMAN	.	UPI00000707D8	.	tolerated(0.17)	benign(0.003)	17/41	.	hmmpanther:PTHR11226:SF3,hmmpanther:PTHR11226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTGAACAT	.	5	ESCA
WDSUB1	0	.	GRCh37	2	160114319	160114320	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.901dupA	p.Met301AsnfsTer11	p.M301Nfs*11	ENST00000409990	8/11	74	47	27	62	62	0	WDSUB1,frameshift_variant,p.Met301AsnfsTer11,ENST00000392796,;WDSUB1,frameshift_variant,p.Met301AsnfsTer11,ENST00000409124,;WDSUB1,frameshift_variant,p.Met301AsnfsTer11,ENST00000409990,;WDSUB1,frameshift_variant,p.Met301AsnfsTer11,ENST00000359774,;WDSUB1,intron_variant,,ENST00000358147,;	T	ENSG00000196151	ENST00000409990	Transcript	frameshift_variant	1158-1159	901-902	301	M/NX	atg/aAtg	.	.	.	-1	WDSUB1	HGNC	26697	protein_coding	YES	CCDS2208.1	ENSP00000387078	WSDU1_HUMAN	.	UPI0000141898	.	.	.	8/11	.	PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22849,hmmpanther:PTHR22849:SF0,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998,Prints_domain:PR00320	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTCCATTGAA	.	3	ESCA
SLC38A11	0	.	GRCh37	2	165811955	165811955	+	5'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-251T>A	.	.	ENST00000409149	1/11	13	9	4	21	21	0	SLC38A11,5_prime_UTR_variant,,ENST00000409149,;SLC38A11,5_prime_UTR_variant,,ENST00000409058,;SLC38A11,5_prime_UTR_variant,,ENST00000303735,;SLC38A11,upstream_gene_variant,,ENST00000409662,;SLC38A11,upstream_gene_variant,,ENST00000492134,;	T	ENSG00000169507	ENST00000409149	Transcript	5_prime_UTR_variant	42	.	.	.	.	.	.	.	-1	SLC38A11	HGNC	26836	protein_coding	YES	CCDS56142.1	ENSP00000386272	S38AB_HUMAN	.	UPI0000E44805	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGCAGCCTG	.	2	ESCA
DNAH7	0	.	GRCh37	2	196799411	196799411	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3375A>G	p.%3D	p.V1125V	ENST00000312428	21/65	96	78	18	64	64	0	DNAH7,synonymous_variant,p.%3D,ENST00000312428,;	C	ENSG00000118997	ENST00000312428	Transcript	synonymous_variant	3476	3375	1125	V	gtA/gtG	.	.	.	-1	DNAH7	HGNC	18661	protein_coding	YES	CCDS42794.1	ENSP00000311273	DYH7_HUMAN	C9JUY3_HUMAN	UPI0000141B95	.	.	.	21/65	.	hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Pfam_domain:PF08393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTCTACAAC	.	5	ESCA
PUM2	0	.	GRCh37	2	20450658	20450658	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*688A>T	.	.	ENST00000338086	20/20	98	70	28	100	100	0	PUM2,3_prime_UTR_variant,,ENST00000319801,;PUM2,3_prime_UTR_variant,,ENST00000338086,;PUM2,3_prime_UTR_variant,,ENST00000440577,;PUM2,3_prime_UTR_variant,,ENST00000361078,;PUM2,downstream_gene_variant,,ENST00000403432,;PUM2,downstream_gene_variant,,ENST00000536417,;RNU7-113P,upstream_gene_variant,,ENST00000459273,;	A	ENSG00000055917	ENST00000338086	Transcript	3_prime_UTR_variant	3906	.	.	.	.	.	.	.	-1	PUM2	HGNC	14958	protein_coding	YES	CCDS1698.1	ENSP00000338173	PUM2_HUMAN	C9JW01_HUMAN,C9JE24_HUMAN,B4E2B6_HUMAN	UPI0000001665	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTATATACAAT	.	5	ESCA
MARCH4	0	.	GRCh37	2	217123346	217123346	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*689C>A	.	.	ENST00000273067	4/4	145	107	38	173	173	0	MARCH4,3_prime_UTR_variant,,ENST00000273067,;AC012513.6,upstream_gene_variant,,ENST00000417481,;	T	ENSG00000144583	ENST00000273067	Transcript	3_prime_UTR_variant	3689	.	.	.	.	.	.	.	-1	MARCH4	HGNC	29269	protein_coding	YES	CCDS33376.1	ENSP00000273067	MARH4_HUMAN	.	UPI00001C1DB9	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTAAGCCCTC	.	5	ESCA
DOCK10	0	.	GRCh37	2	225710304	225710304	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2291T>C	p.Phe764Ser	p.F764S	ENST00000258390	20/56	40	37	3	42	42	0	DOCK10,missense_variant,p.Phe764Ser,ENST00000258390,;DOCK10,missense_variant,p.Phe758Ser,ENST00000409592,;	G	ENSG00000135905	ENST00000258390	Transcript	missense_variant	2359	2291	764	F/S	tTt/tCt	.	.	.	-1	DOCK10	HGNC	23479	protein_coding	YES	CCDS46528.1	ENSP00000258390	DOC10_HUMAN	Q4ZG60_HUMAN,Q3LIC8_HUMAN	UPI000021D2A7	.	deleterious(0)	probably_damaging(0.925)	20/56	.	PROSITE_profiles:PS51650,hmmpanther:PTHR23317:SF71,hmmpanther:PTHR23317,Pfam_domain:PF14429	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAAAAAGAA	.	2	ESCA
SP140L	0	.	GRCh37	2	231266421	231266421	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1543G>C	p.Asp515His	p.D515H	ENST00000415673	18/19	110	98	12	110	110	0	SP140L,missense_variant,p.Asp515His,ENST00000415673,;SP140L,3_prime_UTR_variant,,ENST00000396563,;SP140L,3_prime_UTR_variant,,ENST00000243810,;SP140L,downstream_gene_variant,,ENST00000444636,;SP140L,non_coding_transcript_exon_variant,,ENST00000483728,;SP140L,non_coding_transcript_exon_variant,,ENST00000497212,;SP140L,downstream_gene_variant,,ENST00000496870,;SP140L,downstream_gene_variant,,ENST00000466656,;	C	ENSG00000185404	ENST00000415673	Transcript	missense_variant	1629	1543	515	D/H	Gat/Cat	.	.	.	1	SP140L	HGNC	25105	protein_coding	YES	CCDS46538.1	ENSP00000397911	SP14L_HUMAN	.	UPI000020974D	.	deleterious(0)	probably_damaging(0.991)	18/19	.	PROSITE_profiles:PS50014,hmmpanther:PTHR13711:SF156,hmmpanther:PTHR13711,Pfam_domain:PF00439,Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GGTTGGATAAA	.	2	ESCA
COL6A3	0	.	GRCh37	2	238242105	238242105	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9316C>T	p.Leu3106Phe	p.L3106F	ENST00000295550	42/44	59	52	7	81	81	0	COL6A3,missense_variant,p.Leu2499Phe,ENST00000472056,;COL6A3,missense_variant,p.Leu2900Phe,ENST00000409809,;COL6A3,missense_variant,p.Leu3106Phe,ENST00000295550,;COL6A3,missense_variant,p.Leu2905Phe,ENST00000347401,;COL6A3,missense_variant,p.Leu2906Phe,ENST00000346358,;COL6A3,missense_variant,p.Leu2900Phe,ENST00000353578,;COL6A3,non_coding_transcript_exon_variant,,ENST00000493608,;COL6A3,upstream_gene_variant,,ENST00000473258,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;	A	ENSG00000163359	ENST00000295550	Transcript	missense_variant	9769	9316	3106	L/F	Ctc/Ttc	.	.	.	-1	COL6A3	HGNC	2213	protein_coding	YES	CCDS33412.1	ENSP00000295550	CO6A3_HUMAN	Q8N4Z1_HUMAN,D9ZGF2_HUMAN	UPI0000456F39	.	.	unknown(0)	42/44	.	Superfamily_domains:SSF57362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTGAGAGCCA	.	4	ESCA
CTNNA2	0	.	GRCh37	2	80808922	80808922	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1985T>A	p.Leu662His	p.L662H	ENST00000466387	18/22	63	55	8	75	75	0	CTNNA2,missense_variant,p.Leu662His,ENST00000496558,;CTNNA2,missense_variant,p.Leu696His,ENST00000361291,;CTNNA2,missense_variant,p.Leu662His,ENST00000541047,;CTNNA2,missense_variant,p.Leu341His,ENST00000343114,;CTNNA2,missense_variant,p.Leu662His,ENST00000540488,;CTNNA2,missense_variant,p.Leu662His,ENST00000466387,;CTNNA2,missense_variant,p.Leu662His,ENST00000402739,;AC008067.2,intron_variant,,ENST00000609950,;AC008067.2,intron_variant,,ENST00000430876,;AC008067.2,intron_variant,,ENST00000596887,;AC008067.2,downstream_gene_variant,,ENST00000595478,;	A	ENSG00000066032	ENST00000466387	Transcript	missense_variant	2709	1985	662	L/H	cTc/cAc	.	.	.	1	CTNNA2	HGNC	2510	protein_coding	YES	CCDS42703.2	ENSP00000418191	CTNA2_HUMAN	F6KRI5_HUMAN,C9J144_HUMAN,C9IZ88_HUMAN	UPI00001A3E86	.	tolerated(0.06)	probably_damaging(0.914)	18/22	.	hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Pfam_domain:PF01044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGCTCATTG	.	4	ESCA
SH2D6	0	.	GRCh37	2	85661489	85661489	+	5'Flank	SNP	G	G	A	rs72936697	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000340326	.	163	143	20	140	139	0	SH2D6,missense_variant,p.Arg23Gln,ENST00000389938,;SH2D6,upstream_gene_variant,,ENST00000340326,;Y_RNA,upstream_gene_variant,,ENST00000384478,;SH2D6,non_coding_transcript_exon_variant,,ENST00000477170,;SH2D6,non_coding_transcript_exon_variant,,ENST00000481426,;SH2D6,downstream_gene_variant,,ENST00000488657,;SH2D6,upstream_gene_variant,,ENST00000488219,;SH2D6,intron_variant,,ENST00000481395,;	A	ENSG00000152292	ENST00000340326	Transcript	upstream_gene_variant	.	.	.	.	.	rs72936697	.	429	1	SH2D6	HGNC	30439	protein_coding	YES	CCDS1976.1	ENSP00000341867	SH2D6_HUMAN	.	UPI0000160B3D	.	.	.	.	.	.	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTCGGAATG	byFrequency|byCluster|by1000G	4	ESCA
TRMT10C	0	.	GRCh37	3	101283942	101283942	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.317G>C	p.Arg106Thr	p.R106T	ENST00000309922	2/2	83	79	4	42	42	0	TRMT10C,missense_variant,p.Arg106Thr,ENST00000495642,;TRMT10C,missense_variant,p.Arg106Thr,ENST00000309922,;	C	ENSG00000174173	ENST00000309922	Transcript	missense_variant	471	317	106	R/T	aGa/aCa	COSM1308327	.	.	1	TRMT10C	HGNC	26022	protein_coding	YES	CCDS43122.1	ENSP00000312356	MRRP1_HUMAN	C9JVB6_HUMAN	UPI0000034E2A	.	deleterious(0)	benign(0.119)	2/2	.	hmmpanther:PTHR13563,hmmpanther:PTHR13563:SF5	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCAGAGAAG	.	2	ESCA
CBLB	0	.	GRCh37	3	105421182	105421182	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1715G>C	p.Ser572Thr	p.S572T	ENST00000264122	12/19	54	51	3	67	67	0	CBLB,missense_variant,p.Ser572Thr,ENST00000405772,;CBLB,missense_variant,p.Ser572Thr,ENST00000403724,;CBLB,missense_variant,p.Ser594Thr,ENST00000394027,;CBLB,missense_variant,p.Ser572Thr,ENST00000264122,;CBLB,upstream_gene_variant,,ENST00000394030,;	G	ENSG00000114423	ENST00000264122	Transcript	missense_variant	2037	1715	572	S/T	aGt/aCt	.	.	.	-1	CBLB	HGNC	1542	protein_coding	YES	CCDS2948.1	ENSP00000264122	CBLB_HUMAN	C9JU85_HUMAN,B5MC15_HUMAN	UPI00001AE89F	.	tolerated_low_confidence(0.19)	benign(0.011)	12/19	.	hmmpanther:PTHR23007,hmmpanther:PTHR23007:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCTACTCAGT	.	2	ESCA
STXBP5L	0	.	GRCh37	3	121100248	121100248	+	Missense_Mutation	SNP	G	G	A	rs745826307	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2528G>A	p.Arg843Gln	p.R843Q	ENST00000273666	23/28	178	124	54	115	115	0	STXBP5L,missense_variant,p.Arg786Gln,ENST00000471262,;STXBP5L,missense_variant,p.Arg819Gln,ENST00000472879,;STXBP5L,missense_variant,p.Arg843Gln,ENST00000273666,;STXBP5L,missense_variant,p.Arg819Gln,ENST00000471454,;STXBP5L,missense_variant,p.Arg843Gln,ENST00000492541,;STXBP5L,missense_variant,p.Arg817Gln,ENST00000497029,;	A	ENSG00000145087	ENST00000273666	Transcript	missense_variant	2799	2528	843	R/Q	cGg/cAg	rs745826307	.	.	1	STXBP5L	HGNC	30757	protein_coding	YES	CCDS43137.1	ENSP00000273666	STB5L_HUMAN	C9JUZ7_HUMAN	UPI00001C1DEA	.	deleterious(0.01)	probably_damaging(0.981)	23/28	.	hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Pfam_domain:PF08596,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACGGAAAA	byFrequency	5	ESCA
IFT122	0	.	GRCh37	3	129218827	129218827	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2444C>A	p.Pro815His	p.P815H	ENST00000296266	20/31	177	132	45	83	83	0	IFT122,missense_variant,p.Pro653His,ENST00000349441,;IFT122,missense_variant,p.Pro640His,ENST00000504021,;IFT122,missense_variant,p.Pro756His,ENST00000507564,;IFT122,missense_variant,p.Pro705His,ENST00000347300,;IFT122,missense_variant,p.Pro126His,ENST00000507221,;IFT122,missense_variant,p.Pro261His,ENST00000509522,;IFT122,missense_variant,p.Pro555His,ENST00000440957,;IFT122,missense_variant,p.Pro815His,ENST00000296266,;IFT122,missense_variant,p.Pro614His,ENST00000431818,;IFT122,missense_variant,p.Pro764His,ENST00000348417,;IFT122,non_coding_transcript_exon_variant,,ENST00000513932,;IFT122,3_prime_UTR_variant,,ENST00000512220,;IFT122,non_coding_transcript_exon_variant,,ENST00000506507,;IFT122,non_coding_transcript_exon_variant,,ENST00000511425,;IFT122,downstream_gene_variant,,ENST00000512814,;	A	ENSG00000163913	ENST00000296266	Transcript	missense_variant	2636	2444	815	P/H	cCc/cAc	.	.	.	1	IFT122	HGNC	13556	protein_coding	YES	CCDS3060.1	ENSP00000296266	IF122_HUMAN	H7C3C0_HUMAN	UPI0000141042	.	tolerated(0.11)	possibly_damaging(0.723)	20/31	.	hmmpanther:PTHR12764:SF4,hmmpanther:PTHR12764,Gene3D:1.25.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCCCAAAG	.	5	ESCA
CLRN1-AS1	0	.	GRCh37	3	150780576	150780576	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.124-137G>T	.	.	ENST00000476886	.	41	31	10	19	19	0	CLRN1-AS1,non_coding_transcript_exon_variant,,ENST00000465576,;CLRN1-AS1,intron_variant,,ENST00000476886,;	T	ENSG00000239265	ENST00000476886	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CLRN1-AS1	HGNC	30895	antisense	YES	.	.	.	.	.	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGGATCCA	.	5	ESCA
MBNL1	0	.	GRCh37	3	152181215	152181215	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1060A>G	.	.	ENST00000282486	10/10	128	100	28	69	69	0	MBNL1,3_prime_UTR_variant,,ENST00000545754,;MBNL1,3_prime_UTR_variant,,ENST00000282486,;MBNL1,3_prime_UTR_variant,,ENST00000324196,;MBNL1,3_prime_UTR_variant,,ENST00000498502,;MBNL1,3_prime_UTR_variant,,ENST00000493459,;MBNL1,3_prime_UTR_variant,,ENST00000357472,;MBNL1,3_prime_UTR_variant,,ENST00000463374,;MBNL1,3_prime_UTR_variant,,ENST00000282488,;MBNL1,3_prime_UTR_variant,,ENST00000324210,;MBNL1,3_prime_UTR_variant,,ENST00000355460,;MBNL1,3_prime_UTR_variant,,ENST00000485910,;MBNL1,downstream_gene_variant,,ENST00000478535,;MBNL1,downstream_gene_variant,,ENST00000485509,;MBNL1,downstream_gene_variant,,ENST00000465907,;MBNL1,downstream_gene_variant,,ENST00000492948,;MBNL1,downstream_gene_variant,,ENST00000464596,;RP11-362A9.3,intron_variant,,ENST00000463255,;MBNL1,non_coding_transcript_exon_variant,,ENST00000497971,;	G	ENSG00000152601	ENST00000282486	Transcript	3_prime_UTR_variant	4069	.	.	.	.	.	.	.	1	MBNL1	HGNC	6923	protein_coding	YES	CCDS3165.1	ENSP00000282486	MBNL1_HUMAN	C9JCX1_HUMAN,C9J7P7_HUMAN	UPI000003B440	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCAAAAGAC	.	5	ESCA
PIK3CA	0	.	GRCh37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	10/21	191	158	33	100	100	0	PIK3CA,missense_variant,p.Glu545Lys,ENST00000263967,;PIK3CA,upstream_gene_variant,,ENST00000462255,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	1790	1633	545	E/K	Gag/Aag	rs104886003,COSM763,COSM27133,COSM125370,COSM295672	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	deleterious(0.02)	probably_damaging(0.959)	10/21	.	PROSITE_profiles:PS51545,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Pfam_domain:PF00613,Gene3D:1.25.40.70,SMART_domains:SM00145,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	not_provided,pathogenic	0,1,1,1,1	21264207	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E545K|c.1633G>A|227,SITE|p.E545K|c.1633G>A|1153,CODON|p.T544N|c.1631C>A|3,BUFFER|p.E542Q|c.1624G>C|8,BUFFER|p.E542K|c.1624G>A|115,BUFFER|p.E542K|c.1624G>A|758,BUFFER|p.E542G|c.1625A>G|3,BUFFER|p.E542V|c.1625A>T|14,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.E542V|c.1625A>T|5,BUFFER|p.E542A|c.1625A>C|3,BUFFER|p.I543V|c.1627A>G|3,BUFFER|p.E545Q|c.1633G>C|30,BUFFER|p.E545Q|c.1633G>C|9,BUFFER|p.E545A|c.1634A>C|130,BUFFER|p.E545V|c.1634A>T|4,BUFFER|p.E545A|c.1634A>C|11,BUFFER|p.E545G|c.1634A>G|14,BUFFER|p.E545G|c.1634A>G|90,BUFFER|p.E545D|c.1635G>T|13,BUFFER|p.E545D|c.1635G>C|11,BUFFER|p.E545D|c.1635G>T|4,BUFFER|p.Q546K|c.1636C>A|119,BUFFER|p.Q546E|c.1636C>G|15,BUFFER|p.Q546K|c.1636C>A|18,BUFFER|p.Q546R|c.1637A>G|20,BUFFER|p.Q546P|c.1637A>C|22,BUFFER|p.Q546P|c.1637A>C|7,BUFFER|p.Q546L|c.1637A>T|8,BUFFER|p.Q546R|c.1637A>G|41,BUFFER|p.Q546H|c.1638G>T|7,BUFFER|p.E547K|c.1639G>A|11,BUFFER|p.E547G|c.1640A>G|5,BUFFER|p.E547G|c.1640A>G|5	RADIA|MUTECT|MUSE|VARSCANS	TCACTGAGCAG	byCluster	4	ESCA
ZNF639	0	.	GRCh37	3	179052373	179052373	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*163A>G	.	.	ENST00000326361	7/7	45	36	9	11	11	0	ZNF639,3_prime_UTR_variant,,ENST00000496856,;ZNF639,3_prime_UTR_variant,,ENST00000484866,;ZNF639,3_prime_UTR_variant,,ENST00000326361,;ZNF639,downstream_gene_variant,,ENST00000481587,;ZNF639,downstream_gene_variant,,ENST00000491818,;ZNF639,downstream_gene_variant,,ENST00000466264,;ZNF639,downstream_gene_variant,,ENST00000494234,;RP11-255C15.4,upstream_gene_variant,,ENST00000610130,;ZNF639,downstream_gene_variant,,ENST00000466663,;ZNF639,downstream_gene_variant,,ENST00000483460,;	G	ENSG00000121864	ENST00000326361	Transcript	3_prime_UTR_variant	2066	.	.	.	.	.	.	.	1	ZNF639	HGNC	30950	protein_coding	YES	CCDS3227.1	ENSP00000325634	ZN639_HUMAN	J3KR68_HUMAN,J3KR59_HUMAN,C9J3R1_HUMAN,C9IZP0_HUMAN	UPI000003EA4C	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATATAAAT	.	5	ESCA
TTC14	0	.	GRCh37	3	180320003	180320003	+	5'UTR	SNP	C	C	A	rs751432916	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-47C>A	.	.	ENST00000296015	1/12	226	213	13	146	146	0	TTC14,5_prime_UTR_variant,,ENST00000491380,;TTC14,5_prime_UTR_variant,,ENST00000382584,;TTC14,5_prime_UTR_variant,,ENST00000296015,;TTC14,5_prime_UTR_variant,,ENST00000412756,;TTC14,upstream_gene_variant,,ENST00000492617,;CCDC39,downstream_gene_variant,,ENST00000473854,;TTC14,upstream_gene_variant,,ENST00000495660,;RP11-496B10.3,upstream_gene_variant,,ENST00000472596,;TTC14,5_prime_UTR_variant,,ENST00000465065,;TTC14,5_prime_UTR_variant,,ENST00000470669,;TTC14,upstream_gene_variant,,ENST00000462895,;	A	ENSG00000163728	ENST00000296015	Transcript	5_prime_UTR_variant	86	.	.	.	.	rs751432916	.	.	1	TTC14	HGNC	24697	protein_coding	YES	CCDS3237.1	ENSP00000296015	TTC14_HUMAN	C9JBA2_HUMAN,C9J974_HUMAN	UPI00000720AE	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGAACAGGGA	.	2	ESCA
UTS2B	0	.	GRCh37	3	190999931	190999931	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.48G>C	p.Leu16Phe	p.L16F	ENST00000340524	5/9	164	155	9	94	94	0	UTS2B,missense_variant,p.Leu16Phe,ENST00000427544,;UTS2B,missense_variant,p.Leu16Phe,ENST00000432514,;UTS2B,missense_variant,p.Leu16Phe,ENST00000340524,;UTS2B,non_coding_transcript_exon_variant,,ENST00000463450,;UTS2B,missense_variant,p.Leu16Phe,ENST00000425357,;UTS2B,missense_variant,p.Leu16Phe,ENST00000440476,;UTS2B,missense_variant,p.Leu16Phe,ENST00000446788,;	G	ENSG00000188958	ENST00000340524	Transcript	missense_variant	835	48	16	L/F	ttG/ttC	.	.	.	-1	UTS2B	HGNC	30894	protein_coding	YES	CCDS3300.1	ENSP00000340526	UTS2B_HUMAN	C9JU87_HUMAN	UPI000013FF7F	.	tolerated(0.13)	benign(0.151)	5/9	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAACAAAGT	.	2	ESCA
LMLN	0	.	GRCh37	3	197765629	197765629	+	3'UTR	SNP	G	G	A	rs369637343	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*91G>A	.	.	ENST00000420910	17/17	48	29	19	24	24	0	LMLN,3_prime_UTR_variant,,ENST00000330198,;LMLN,3_prime_UTR_variant,,ENST00000420910,;LMLN,downstream_gene_variant,,ENST00000332636,;LMLN,downstream_gene_variant,,ENST00000482695,;LMLN-AS1,non_coding_transcript_exon_variant,,ENST00000423460,;LMLN,non_coding_transcript_exon_variant,,ENST00000451139,;	A	ENSG00000185621	ENST00000420910	Transcript	3_prime_UTR_variant	2170	.	.	.	.	rs369637343	.	.	1	LMLN	HGNC	15991	protein_coding	YES	CCDS46988.1	ENSP00000410926	LMLN_HUMAN	B4DR62_HUMAN	UPI000192C367	.	.	.	17/17	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATGGTAGA	byCluster|by1000G	5	ESCA
HTR1F	0	.	GRCh37	3	88039924	88039924	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25C>A	p.Gln9Lys	p.Q9K	ENST00000319595	1/1	42	34	7	72	71	1	HTR1F,missense_variant,p.Gln9Lys,ENST00000319595,;	A	ENSG00000179097	ENST00000319595	Transcript	missense_variant	79	25	9	Q/K	Caa/Aaa	.	.	.	1	HTR1F	HGNC	5292	protein_coding	YES	CCDS2920.1	ENSP00000322924	5HT1F_HUMAN	Q9P2Q4_HUMAN	UPI00000503DF	.	tolerated(0.91)	benign(0.001)	1/1	.	hmmpanther:PTHR24247:SF34,hmmpanther:PTHR24247,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00515	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATCAAAAC	.	5	ESCA
SLC39A8	0	.	GRCh37	4	103236927	103236927	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.280A>G	p.Ser94Gly	p.S94G	ENST00000394833	2/8	87	40	47	134	134	0	SLC39A8,missense_variant,p.Ser94Gly,ENST00000356736,;SLC39A8,missense_variant,p.Ser94Gly,ENST00000394833,;SLC39A8,missense_variant,p.Ser94Gly,ENST00000424970,;SLC39A8,non_coding_transcript_exon_variant,,ENST00000512657,;SLC39A8,non_coding_transcript_exon_variant,,ENST00000502903,;SLC39A8,non_coding_transcript_exon_variant,,ENST00000514000,;SLC39A8,non_coding_transcript_exon_variant,,ENST00000510255,;	C	ENSG00000138821	ENST00000394833	Transcript	missense_variant	757	280	94	S/G	Agc/Ggc	.	.	.	-1	SLC39A8	HGNC	20862	protein_coding	YES	CCDS3656.1	ENSP00000378310	S39A8_HUMAN	.	UPI0000046C4E	.	tolerated(0.56)	benign(0.002)	2/8	.	hmmpanther:PTHR12191:SF2,hmmpanther:PTHR12191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCTGGTTA	.	5	ESCA
NDNF	0	.	GRCh37	4	121966862	121966862	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.131C>A	p.Ser44Ter	p.S44*	ENST00000379692	2/4	80	41	39	105	103	1	NDNF,stop_gained,p.Ser44Ter,ENST00000515757,;NDNF,stop_gained,p.Ser44Ter,ENST00000511408,;NDNF,stop_gained,p.Ser44Ter,ENST00000379692,;	T	ENSG00000173376	ENST00000379692	Transcript	stop_gained	658	131	44	S/*	tCa/tAa	.	.	.	-1	NDNF	HGNC	26256	protein_coding	YES	CCDS3717.2	ENSP00000369014	NDNF_HUMAN	D6RF18_HUMAN,D6R972_HUMAN	UPI00001D6985	.	.	.	2/4	.	hmmpanther:PTHR14619,hmmpanther:PTHR14619:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTACTGACGAA	.	5	ESCA
CPEB2	0	.	GRCh37	4	15068289	15068289	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*285G>C	.	.	ENST00000538197	12/12	40	33	7	90	90	0	CPEB2,3_prime_UTR_variant,,ENST00000541112,;CPEB2,3_prime_UTR_variant,,ENST00000382395,;CPEB2,3_prime_UTR_variant,,ENST00000259997,;CPEB2,3_prime_UTR_variant,,ENST00000382401,;CPEB2,3_prime_UTR_variant,,ENST00000538197,;CPEB2,3_prime_UTR_variant,,ENST00000442003,;CPEB2,downstream_gene_variant,,ENST00000507071,;CPEB2,downstream_gene_variant,,ENST00000345451,;CPEB2,downstream_gene_variant,,ENST00000509684,;RP11-665G4.1,intron_variant,,ENST00000502344,;RP11-665G4.1,intron_variant,,ENST00000513384,;	C	ENSG00000137449	ENST00000538197	Transcript	3_prime_UTR_variant	3390	.	.	.	.	.	.	.	1	CPEB2	HGNC	21745	protein_coding	YES	CCDS56325.1	ENSP00000443985	.	J3KN18_HUMAN,H0Y9D9_HUMAN,F5H160_HUMAN	UPI0001D0434B	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATATGAGAAT	.	5	ESCA
TRIM2	0	.	GRCh37	4	154260058	154260058	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3940C>T	.	.	ENST00000338700	12/12	70	60	10	31	31	0	TRIM2,3_prime_UTR_variant,,ENST00000338700,;TRIM2,downstream_gene_variant,,ENST00000437508,;	T	ENSG00000109654	ENST00000338700	Transcript	3_prime_UTR_variant	6321	.	.	.	.	.	.	.	1	TRIM2	HGNC	15974	protein_coding	YES	CCDS3781.2	ENSP00000339659	TRIM2_HUMAN	C9JVI3_HUMAN,C9J084_HUMAN	UPI00005A60C0	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATATCGTTCT	.	4	ESCA
FAM218A	0	.	GRCh37	4	165879878	165879878	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1230C>G	.	.	ENST00000513876	1/1	73	68	5	66	66	0	FAM218A,3_prime_UTR_variant,,ENST00000513876,;TRIM61,intron_variant,,ENST00000329314,;RP11-366M4.8,intron_variant,,ENST00000596751,;	G	ENSG00000250486	ENST00000513876	Transcript	3_prime_UTR_variant	1779	.	.	.	.	.	.	.	1	FAM218A	HGNC	26466	protein_coding	YES	CCDS3807.1	ENSP00000427428	F218A_HUMAN	.	UPI000006D0F5	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTATCAAAAT	.	2	ESCA
MFAP3L	0	.	GRCh37	4	170912904	170912904	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855G>C	p.Glu285Asp	p.E285D	ENST00000361618	3/3	34	30	4	31	31	0	MFAP3L,missense_variant,p.Glu182Asp,ENST00000393704,;MFAP3L,missense_variant,p.Glu285Asp,ENST00000361618,;MFAP3L,downstream_gene_variant,,ENST00000507601,;MFAP3L,downstream_gene_variant,,ENST00000512698,;MFAP3L,downstream_gene_variant,,ENST00000502832,;RP11-6E9.4,intron_variant,,ENST00000508955,;	G	ENSG00000198948	ENST00000361618	Transcript	missense_variant	1163	855	285	E/D	gaG/gaC	.	.	.	-1	MFAP3L	HGNC	29083	protein_coding	YES	CCDS34103.1	ENSP00000354583	MFA3L_HUMAN	D6RGZ8_HUMAN,D6RDM6_HUMAN,D6RCF0_HUMAN,D6RCC0_HUMAN,D6RAB5_HUMAN,D6R9L7_HUMAN	UPI0000073AA1	.	tolerated(0.48)	benign(0.005)	3/3	.	hmmpanther:PTHR14340,hmmpanther:PTHR14340:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGACCTCATC	.	2	ESCA
FAM184B	0	.	GRCh37	4	17634044	17634044	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*111T>C	.	.	ENST00000265018	18/18	36	19	16	66	66	0	FAM184B,3_prime_UTR_variant,,ENST00000265018,;MED28,3_prime_UTR_variant,,ENST00000237380,;MED28,non_coding_transcript_exon_variant,,ENST00000499786,;MED28,downstream_gene_variant,,ENST00000503945,;	G	ENSG00000047662	ENST00000265018	Transcript	3_prime_UTR_variant	3507	.	.	.	.	.	.	.	-1	FAM184B	HGNC	29235	protein_coding	YES	CCDS47033.1	ENSP00000265018	F184B_HUMAN	.	UPI000020BD7C	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATATATAAAT	.	5	ESCA
DCTD	0	.	GRCh37	4	183815663	183815663	+	Missense_Mutation	SNP	C	C	T	rs764782245	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.373G>A	p.Ala125Thr	p.A125T	ENST00000357067	4/6	78	63	15	101	101	0	DCTD,missense_variant,p.Ala114Thr,ENST00000503182,;DCTD,missense_variant,p.Ala114Thr,ENST00000438320,;DCTD,missense_variant,p.Ala125Thr,ENST00000357067,;DCTD,missense_variant,p.Ala114Thr,ENST00000510370,;DCTD,missense_variant,p.Ala114Thr,ENST00000510307,;DCTD,missense_variant,p.Ala114Thr,ENST00000512766,;DCTD,downstream_gene_variant,,ENST00000514754,;DCTD,3_prime_UTR_variant,,ENST00000507631,;DCTD,3_prime_UTR_variant,,ENST00000500813,;DCTD,3_prime_UTR_variant,,ENST00000507543,;	T	ENSG00000129187	ENST00000357067	Transcript	missense_variant	439	373	125	A/T	Gct/Act	rs764782245,COSM1053582	.	.	-1	DCTD	HGNC	2710	protein_coding	YES	CCDS34108.1	ENSP00000349576	DCTD_HUMAN	D6RJA9_HUMAN,D6RC36_HUMAN,D6RBN2_HUMAN,D6RBJ9_HUMAN,D6RAR9_HUMAN,D6RAD7_HUMAN,D6R9S0_HUMAN	UPI00004EC28E	.	tolerated(0.15)	possibly_damaging(0.64)	4/6	.	hmmpanther:PTHR11086,PROSITE_patterns:PS00903,Gene3D:3.40.140.10,Pfam_domain:PF00383,PIRSF_domain:PIRSF006019,Superfamily_domains:SSF53927	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTAGCGCATT	byFrequency	5	ESCA
SPATA18	0	.	GRCh37	4	52917943	52917943	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73C>T	p.%3D	p.L25L	ENST00000295213	1/13	76	55	21	147	147	0	SPATA18,synonymous_variant,p.%3D,ENST00000295213,;SPATA18,synonymous_variant,p.%3D,ENST00000419395,;RP11-535C7.1,downstream_gene_variant,,ENST00000511875,;SPATA18,non_coding_transcript_exon_variant,,ENST00000514670,;SPATA18,non_coding_transcript_exon_variant,,ENST00000506829,;SPATA18,synonymous_variant,p.%3D,ENST00000505038,;SPATA18,synonymous_variant,p.%3D,ENST00000505320,;SPATA18,synonymous_variant,p.%3D,ENST00000503055,;SPATA18,synonymous_variant,p.%3D,ENST00000508915,;SPATA18,non_coding_transcript_exon_variant,,ENST00000511028,;	T	ENSG00000163071	ENST00000295213	Transcript	synonymous_variant	447	73	25	L	Ctg/Ttg	.	.	.	1	SPATA18	HGNC	29579	protein_coding	YES	CCDS3489.1	ENSP00000295213	MIEAP_HUMAN	.	UPI000006FB0D	.	.	.	1/13	.	hmmpanther:PTHR21771:SF0,hmmpanther:PTHR21771	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGGCTGAAG	.	5	ESCA
UTP3	0	.	GRCh37	4	71554831	71554831	+	Missense_Mutation	SNP	G	G	A	rs780006978	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437G>A	p.Arg146Gln	p.R146Q	ENST00000254803	1/1	54	41	13	41	41	0	UTP3,missense_variant,p.Arg146Gln,ENST00000254803,;ENAM,downstream_gene_variant,,ENST00000472903,;	A	ENSG00000132467	ENST00000254803	Transcript	missense_variant	636	437	146	R/Q	cGa/cAa	rs780006978	.	.	1	UTP3	HGNC	24477	protein_coding	YES	CCDS3546.1	ENSP00000254803	SAS10_HUMAN	.	UPI0000073D63	.	tolerated(0.27)	benign(0.098)	1/1	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13237,hmmpanther:PTHR13237:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCGAGGCC	.	5	ESCA
UTP3	0	.	GRCh37	4	71554832	71554832	+	Silent	SNP	A	A	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438A>T	p.%3D	p.R146R	ENST00000254803	1/1	54	40	13	41	41	0	UTP3,synonymous_variant,p.%3D,ENST00000254803,;ENAM,downstream_gene_variant,,ENST00000472903,;	T	ENSG00000132467	ENST00000254803	Transcript	synonymous_variant	637	438	146	R	cgA/cgT	.	.	.	1	UTP3	HGNC	24477	protein_coding	YES	CCDS3546.1	ENSP00000254803	SAS10_HUMAN	.	UPI0000073D63	.	.	.	1/1	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13237,hmmpanther:PTHR13237:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCGAGGCCG	.	5	ESCA
AFF1	0	.	GRCh37	4	88029349	88029349	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1415A>G	p.His472Arg	p.H472R	ENST00000395146	11/21	76	30	45	58	58	0	AFF1,missense_variant,p.His156Arg,ENST00000514970,;AFF1,missense_variant,p.His465Arg,ENST00000307808,;AFF1,missense_variant,p.His472Arg,ENST00000395146,;AFF1,missense_variant,p.His103Arg,ENST00000511722,;AFF1,missense_variant,p.His103Arg,ENST00000544085,;AFF1,downstream_gene_variant,,ENST00000503477,;	G	ENSG00000172493	ENST00000395146	Transcript	missense_variant	1690	1415	472	H/R	cAt/cGt	.	.	.	1	AFF1	HGNC	7135	protein_coding	YES	CCDS54775.1	ENSP00000378578	AFF1_HUMAN	Q712L1_HUMAN,F5GXF9_HUMAN,D6RIZ5_HUMAN,D6RAU0_HUMAN	UPI000013EC52	.	deleterious(0.01)	unknown(0)	11/21	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10528:SF14,hmmpanther:PTHR10528,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCACATTCCA	.	5	ESCA
GRID2	0	.	GRCh37	4	94128579	94128579	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.760T>C	p.Phe254Leu	p.F254L	ENST00000282020	5/16	86	77	8	115	115	0	GRID2,missense_variant,p.Phe254Leu,ENST00000282020,;GRID2,missense_variant,p.Phe159Leu,ENST00000510992,;GRID2,5_prime_UTR_variant,,ENST00000512631,;GRID2,non_coding_transcript_exon_variant,,ENST00000505687,;	C	ENSG00000152208	ENST00000282020	Transcript	missense_variant	1018	760	254	F/L	Ttt/Ctt	.	.	.	1	GRID2	HGNC	4576	protein_coding	YES	CCDS3637.1	ENSP00000282020	GRID2_HUMAN	Q4W5S4_HUMAN,Q4W5L9_HUMAN,Q4W5F4_HUMAN,Q4W5B7_HUMAN,D6R976_HUMAN	UPI00001AEA78	.	tolerated(0.6)	benign(0.365)	5/16	.	hmmpanther:PTHR18966:SF109,hmmpanther:PTHR18966,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGCTTTTGAC	.	4	ESCA
PDHA2	0	.	GRCh37	4	96762268	96762268	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967G>T	p.Val323Leu	p.V323L	ENST00000295266	1/1	57	43	14	72	72	0	PDHA2,missense_variant,p.Val323Leu,ENST00000295266,;	T	ENSG00000163114	ENST00000295266	Transcript	missense_variant	1030	967	323	V/L	Gta/Tta	.	.	.	1	PDHA2	HGNC	8807	protein_coding	YES	CCDS3644.1	ENSP00000295266	ODPAT_HUMAN	.	UPI0000130C31	.	tolerated(1)	benign(0.008)	1/1	.	hmmpanther:PTHR11516,hmmpanther:PTHR11516:SF27,Pfam_domain:PF00676,Gene3D:3.40.50.970,TIGRFAM_domain:TIGR03182,Superfamily_domains:SSF52518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATGGTAAAC	.	5	ESCA
SLC35A4	0	.	GRCh37	5	139946715	139946715	+	5'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-40A>G	.	.	ENST00000514199	2/2	15	10	5	31	31	0	SLC35A4,5_prime_UTR_variant,,ENST00000323146,;SLC35A4,5_prime_UTR_variant,,ENST00000514199,;APBB3,upstream_gene_variant,,ENST00000511201,;APBB3,upstream_gene_variant,,ENST00000412920,;APBB3,upstream_gene_variant,,ENST00000508496,;APBB3,upstream_gene_variant,,ENST00000354402,;APBB3,upstream_gene_variant,,ENST00000356738,;APBB3,upstream_gene_variant,,ENST00000358580,;APBB3,upstream_gene_variant,,ENST00000357560,;SLC35A4,non_coding_transcript_exon_variant,,ENST00000508770,;APBB3,intron_variant,,ENST00000507279,;APBB3,intron_variant,,ENST00000513766,;APBB3,upstream_gene_variant,,ENST00000505617,;SLC35A4,non_coding_transcript_exon_variant,,ENST00000514137,;APBB3,upstream_gene_variant,,ENST00000467078,;APBB3,upstream_gene_variant,,ENST00000515056,;APBB3,upstream_gene_variant,,ENST00000506165,;APBB3,upstream_gene_variant,,ENST00000511463,;APBB3,upstream_gene_variant,,ENST00000503850,;APBB3,upstream_gene_variant,,ENST00000511459,;APBB3,upstream_gene_variant,,ENST00000503979,;APBB3,upstream_gene_variant,,ENST00000510241,;APBB3,upstream_gene_variant,,ENST00000509914,;APBB3,upstream_gene_variant,,ENST00000506289,;APBB3,upstream_gene_variant,,ENST00000513507,;APBB3,upstream_gene_variant,,ENST00000504872,;APBB3,upstream_gene_variant,,ENST00000506958,;APBB3,upstream_gene_variant,,ENST00000511896,;	G	ENSG00000176087	ENST00000514199	Transcript	5_prime_UTR_variant	1647	.	.	.	.	.	.	.	1	SLC35A4	HGNC	20753	protein_coding	YES	CCDS4231.1	ENSP00000424566	S35A4_HUMAN	.	UPI0000036D2F	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT	TTGCAATCCCT	.	3	ESCA
PCDHA8	0	.	GRCh37	5	140223323	140223323	+	Intron	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2394+23C>A	.	.	ENST00000531613	.	67	40	27	96	96	0	PCDHA8,missense_variant,p.Thr806Asn,ENST00000378123,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA8,intron_variant,,ENST00000531613,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA9,upstream_gene_variant,,ENST00000378122,;PCDHA9,upstream_gene_variant,,ENST00000532602,;	A	ENSG00000204962	ENST00000531613	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	PCDHA8	HGNC	8674	protein_coding	YES	CCDS54919.1	ENSP00000434655	PCDA8_HUMAN	.	UPI00001273D0	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGAACTCATA	.	5	ESCA
GABRG2	0	.	GRCh37	5	161582271	161582271	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1897T>C	.	.	ENST00000414552	11/11	34	16	18	45	45	0	GABRG2,3_prime_UTR_variant,,ENST00000356592,;GABRG2,3_prime_UTR_variant,,ENST00000414552,;GABRG2,downstream_gene_variant,,ENST00000393933,;GABRG2,downstream_gene_variant,,ENST00000361925,;GABRG2,downstream_gene_variant,,ENST00000522990,;GABRG2,downstream_gene_variant,,ENST00000523372,;	C	ENSG00000113327	ENST00000414552	Transcript	3_prime_UTR_variant	3670	.	.	.	.	.	.	.	1	GABRG2	HGNC	4087	protein_coding	YES	CCDS47333.1	ENSP00000410732	GBRG2_HUMAN	.	UPI00017503BD	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATTAAATG	.	5	ESCA
CPEB4	0	.	GRCh37	5	173384140	173384142	+	3'UTR	DEL	AAC	AAC	-	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	AAC	AAC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1007_*1009delACA	.	.	ENST00000265085	10/10	58	47	10	106	106	0	CPEB4,3_prime_UTR_variant,,ENST00000334035,;CPEB4,3_prime_UTR_variant,,ENST00000265085,;CPEB4,downstream_gene_variant,,ENST00000522336,;CPEB4,downstream_gene_variant,,ENST00000519835,;CPEB4,downstream_gene_variant,,ENST00000517880,;CPEB4,downstream_gene_variant,,ENST00000520867,;CPEB4,downstream_gene_variant,,ENST00000519467,;	-	ENSG00000113742	ENST00000265085	Transcript	3_prime_UTR_variant	4644-4646	.	.	.	.	.	.	.	1	CPEB4	HGNC	21747	protein_coding	YES	CCDS4390.1	ENSP00000265085	CPEB4_HUMAN	.	UPI000020C179	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTAAAAAACAACAA	.	2	ESCA
MAP3K1	0	.	GRCh37	5	56152526	56152526	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.582G>A	p.Met194Ile	p.M194I	ENST00000399503	2/20	61	45	16	79	79	0	MAP3K1,missense_variant,p.Met194Ile,ENST00000399503,;snoU13,upstream_gene_variant,,ENST00000459264,;AC008937.2,intron_variant,,ENST00000415589,;	A	ENSG00000095015	ENST00000399503	Transcript	missense_variant	582	582	194	M/I	atG/atA	.	.	.	1	MAP3K1	HGNC	6848	protein_coding	YES	CCDS43318.1	ENSP00000382423	M3K1_HUMAN	.	UPI000015153B	.	deleterious_low_confidence(0)	probably_damaging(0.914)	2/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATGCCAGC	.	5	ESCA
ARID1B	0	.	GRCh37	6	157405821	157405821	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2063T>C	p.Leu688Pro	p.L688P	ENST00000346085	6/20	48	44	3	43	43	0	ARID1B,missense_variant,p.Leu97Pro,ENST00000319584,;ARID1B,missense_variant,p.Leu675Pro,ENST00000367148,;ARID1B,missense_variant,p.Leu688Pro,ENST00000346085,;ARID1B,missense_variant,p.Leu675Pro,ENST00000350026,;ARID1B,missense_variant,p.Leu174Pro,ENST00000414678,;ARID1B,missense_variant,p.Leu617Pro,ENST00000275248,;ARID1B,non_coding_transcript_exon_variant,,ENST00000452544,;ARID1B,upstream_gene_variant,,ENST00000493658,;	C	ENSG00000049618	ENST00000346085	Transcript	missense_variant	2064	2063	688	L/P	cTc/cCc	.	.	.	1	ARID1B	HGNC	18040	protein_coding	YES	CCDS55072.1	ENSP00000344546	ARI1B_HUMAN	.	UPI000058E4B2	.	.	probably_damaging(1)	6/20	.	hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGACCTCCCCA	.	2	ESCA
MTCH1	0	.	GRCh37	6	36936736	36936736	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1062A>T	p.%3D	p.R354R	ENST00000373616	12/12	64	52	12	79	79	0	MTCH1,synonymous_variant,p.%3D,ENST00000418541,;MTCH1,synonymous_variant,p.%3D,ENST00000373627,;MTCH1,synonymous_variant,p.%3D,ENST00000373616,;PI16,downstream_gene_variant,,ENST00000373674,;MTCH1,downstream_gene_variant,,ENST00000538808,;MTCH1,downstream_gene_variant,,ENST00000460219,;MTCH1,non_coding_transcript_exon_variant,,ENST00000471737,;MTCH1,downstream_gene_variant,,ENST00000492754,;PI16,downstream_gene_variant,,ENST00000491324,;	A	ENSG00000137409	ENST00000373616	Transcript	synonymous_variant	1187	1062	354	R	cgA/cgT	.	.	.	-1	MTCH1	HGNC	17586	protein_coding	YES	CCDS4828.1	ENSP00000362718	MTCH1_HUMAN	A8YXX5_HUMAN	UPI000006FD55	.	.	.	12/12	.	hmmpanther:PTHR10780,hmmpanther:PTHR10780:SF3,Gene3D:1okcA00,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGCCTCGGAA	.	4	ESCA
TREML2	0	.	GRCh37	6	41168696	41168696	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51C>T	p.%3D	p.V17V	ENST00000483722	1/5	63	54	8	91	91	0	TREML2,synonymous_variant,p.%3D,ENST00000483722,;	A	ENSG00000112195	ENST00000483722	Transcript	synonymous_variant	237	51	17	V	gtC/gtT	.	.	.	-1	TREML2	HGNC	21092	protein_coding	YES	CCDS4853.2	ENSP00000418767	TRML2_HUMAN	.	UPI0000074452	.	.	.	1/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR16423,hmmpanther:PTHR16423:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGAGACGCA	.	4	ESCA
TTBK1	0	.	GRCh37	6	43230870	43230870	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1768G>C	p.Glu590Gln	p.E590Q	ENST00000259750	13/15	15	11	4	19	19	0	TTBK1,missense_variant,p.Glu539Gln,ENST00000304139,;TTBK1,missense_variant,p.Glu590Gln,ENST00000259750,;	C	ENSG00000146216	ENST00000259750	Transcript	missense_variant	1851	1768	590	E/Q	Gag/Cag	.	.	.	1	TTBK1	HGNC	19140	protein_coding	YES	CCDS34455.1	ENSP00000259750	TTBK1_HUMAN	.	UPI000041512B	.	.	possibly_damaging(0.696)	13/15	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCAGAGCCC	.	5	ESCA
C6orf57	0	.	GRCh37	6	71289168	71289168	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.116G>A	p.Gly39Glu	p.G39E	ENST00000370474	2/3	99	64	34	116	116	0	C6orf57,missense_variant,p.Gly39Glu,ENST00000370474,;	A	ENSG00000154079	ENST00000370474	Transcript	missense_variant	140	116	39	G/E	gGa/gAa	.	.	.	1	C6orf57	HGNC	20957	protein_coding	YES	CCDS4972.1	ENSP00000359505	CF057_HUMAN	.	UPI000013DD88	.	tolerated(0.53)	benign(0.006)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAGGAAAGT	.	5	ESCA
LAMB1	0	.	GRCh37	7	107638866	107638866	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285C>T	p.%3D	p.L95L	ENST00000222399	4/34	119	67	52	103	103	0	LAMB1,synonymous_variant,p.%3D,ENST00000393561,;LAMB1,synonymous_variant,p.%3D,ENST00000439976,;LAMB1,synonymous_variant,p.%3D,ENST00000393560,;LAMB1,synonymous_variant,p.%3D,ENST00000222399,;LAMB1,downstream_gene_variant,,ENST00000393559,;U3,downstream_gene_variant,,ENST00000458938,;	A	ENSG00000091136	ENST00000222399	Transcript	synonymous_variant	516	285	95	L	ctC/ctT	.	.	.	-1	LAMB1	HGNC	6486	protein_coding	YES	CCDS5750.1	ENSP00000222399	LAMB1_HUMAN	Q75MC8_HUMAN,E9PCS6_HUMAN	UPI00001AE63F	.	.	.	4/34	.	PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF233,hmmpanther:PTHR10574,Pfam_domain:PF00055,SMART_domains:SM00136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATGAGATG	.	5	ESCA
TMEM229A	0	.	GRCh37	7	123671981	123671981	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1077C>A	p.Phe359Leu	p.F359L	ENST00000455783	1/1	83	50	33	96	96	0	TMEM229A,missense_variant,p.Phe359Leu,ENST00000455783,;RP5-921G16.1,upstream_gene_variant,,ENST00000484322,;RP4-630C24.3,downstream_gene_variant,,ENST00000472838,;	T	ENSG00000234224	ENST00000455783	Transcript	missense_variant	1543	1077	359	F/L	ttC/ttA	.	.	.	-1	TMEM229A	HGNC	37279	protein_coding	YES	CCDS47694.1	ENSP00000395244	T229A_HUMAN	.	UPI0001823FDC	.	tolerated(0.28)	probably_damaging(0.979)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR31746,hmmpanther:PTHR31746:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAGGAATAT	.	5	ESCA
INTS1	0	.	GRCh37	7	1520578	1520578	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3851-9G>A	.	.	ENST00000404767	.	28	20	8	24	24	0	INTS1,missense_variant,p.Arg1480Gln,ENST00000389470,;INTS1,intron_variant,,ENST00000404767,;INTS1,upstream_gene_variant,,ENST00000482994,;INTS1,downstream_gene_variant,,ENST00000468115,;	T	ENSG00000164880	ENST00000404767	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	INTS1	HGNC	24555	protein_coding	YES	CCDS47526.1	ENSP00000385722	INT1_HUMAN	.	UPI0000D7211C	.	.	.	.	28/47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAACCGTAGC	.	5	ESCA
HDAC9	0	.	GRCh37	7	18688191	18688191	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1352G>A	p.Arg451Gln	p.R451Q	ENST00000441542	10/25	75	65	10	77	77	0	HDAC9,missense_variant,p.Arg407Gln,ENST00000401921,;HDAC9,missense_variant,p.Arg448Gln,ENST00000405010,;HDAC9,missense_variant,p.Arg404Gln,ENST00000428307,;HDAC9,missense_variant,p.Arg451Gln,ENST00000441542,;HDAC9,missense_variant,p.Arg446Gln,ENST00000417496,;HDAC9,missense_variant,p.Arg435Gln,ENST00000406072,;HDAC9,missense_variant,p.Arg448Gln,ENST00000406451,;HDAC9,missense_variant,p.Arg420Gln,ENST00000456174,;HDAC9,missense_variant,p.Arg448Gln,ENST00000432645,;HDAC9,missense_variant,p.Arg371Gln,ENST00000524023,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;	A	ENSG00000048052	ENST00000441542	Transcript	missense_variant	1352	1352	451	R/Q	cGa/cAa	COSM1088167,COSM1088164,COSM1088165,COSM1088166	.	.	1	HDAC9	HGNC	14065	protein_coding	YES	CCDS47553.1	ENSP00000408617	HDAC9_HUMAN	Q8N926_HUMAN,Q75N15_HUMAN,Q75N14_HUMAN,Q75N10_HUMAN,C9JLX1_HUMAN,C9J835_HUMAN,C9J1W4_HUMAN,C9IZS0_HUMAN	UPI000019AB75	.	deleterious(0)	probably_damaging(0.991)	10/25	.	hmmpanther:PTHR10625:SF116,hmmpanther:PTHR10625,PIRSF_domain:PIRSF037911	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACCGAACCC	.	5	ESCA
NCF1	0	.	GRCh37	7	74193766	74193766	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393C>A	p.Asn131Lys	p.N131K	ENST00000289473	4/11	130	91	38	97	97	0	NCF1,missense_variant,p.Asn138Lys,ENST00000442021,;NCF1,missense_variant,p.Asn131Lys,ENST00000289473,;NCF1,missense_variant,p.Asn131Lys,ENST00000433458,;NCF1,splice_region_variant,,ENST00000443956,;NCF1,splice_region_variant,,ENST00000438106,;NCF1,upstream_gene_variant,,ENST00000486097,;NCF1,splice_region_variant,,ENST00000449343,;NCF1,splice_region_variant,,ENST00000398421,;NCF1,splice_region_variant,,ENST00000464878,;NCF1,intron_variant,,ENST00000455062,;NCF1,upstream_gene_variant,,ENST00000488197,;STAG3L2,intron_variant,,ENST00000380775,;	A	ENSG00000158517	ENST00000289473	Transcript	missense_variant	463	393	131	N/K	aaC/aaA	.	.	.	1	NCF1	HGNC	7660	protein_coding	YES	CCDS34657.1	ENSP00000289473	NCF1_HUMAN	.	UPI000013DF7E	.	tolerated(0.45)	benign(0.037)	4/11	.	Superfamily_domains:SSF64268,Gene3D:3.30.1520.10,hmmpanther:PTHR15706	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACAACCAGTG	.	5	ESCA
YWHAG	0	.	GRCh37	7	75959019	75959019	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619G>A	p.Glu207Lys	p.E207K	ENST00000307630	2/2	39	35	4	37	37	0	YWHAG,missense_variant,p.Glu207Lys,ENST00000307630,;	T	ENSG00000170027	ENST00000307630	Transcript	missense_variant	842	619	207	E/K	Gag/Aag	COSM1091817	.	.	-1	YWHAG	HGNC	12852	protein_coding	YES	CCDS5584.1	ENSP00000306330	1433G_HUMAN	B4DHC4_HUMAN	UPI000000106B	.	deleterious_low_confidence(0.02)	possibly_damaging(0.817)	2/2	.	hmmpanther:PTHR18860,hmmpanther:PTHR18860:SF2,Gene3D:3iquA00,Pfam_domain:PF00244,SMART_domains:SM00101,PIRSF_domain:PIRSF000868,Superfamily_domains:SSF48445,Prints_domain:PR00305	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCTCGGCGA	.	4	ESCA
SEMA3A	0	.	GRCh37	7	83640589	83640589	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835C>G	p.Leu279Val	p.L279V	ENST00000265362	8/17	81	73	8	87	87	0	SEMA3A,missense_variant,p.Leu279Val,ENST00000265362,;SEMA3A,missense_variant,p.Leu279Val,ENST00000436949,;	C	ENSG00000075213	ENST00000265362	Transcript	missense_variant	1150	835	279	L/V	Ctg/Gtg	.	.	.	-1	SEMA3A	HGNC	10723	protein_coding	YES	CCDS5599.1	ENSP00000265362	SEM3A_HUMAN	Q86UJ2_HUMAN,Q75MQ2_HUMAN,C9JD25_HUMAN,C9J9C4_HUMAN	UPI0000135A60	.	deleterious(0.01)	probably_damaging(0.923)	8/17	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF23,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CACCAGACTTC	.	3	ESCA
BAIAP2L1	0	.	GRCh37	7	97939821	97939821	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.891G>T	p.Leu297Phe	p.L297F	ENST00000005260	9/14	136	128	8	90	90	0	BAIAP2L1,missense_variant,p.Leu297Phe,ENST00000005260,;RP4-607J23.2,downstream_gene_variant,,ENST00000608882,;RP4-607J23.2,downstream_gene_variant,,ENST00000609873,;BAIAP2L1,non_coding_transcript_exon_variant,,ENST00000462558,;BRI3,downstream_gene_variant,,ENST00000485422,;BAIAP2L1,upstream_gene_variant,,ENST00000480580,;BRI3,downstream_gene_variant,,ENST00000491463,;	A	ENSG00000006453	ENST00000005260	Transcript	missense_variant	1107	891	297	L/F	ttG/ttT	.	.	.	-1	BAIAP2L1	HGNC	21649	protein_coding	YES	CCDS34687.1	ENSP00000005260	BI2L1_HUMAN	.	UPI0000035DA9	.	deleterious(0.01)	probably_damaging(0.999)	9/14	.	hmmpanther:PTHR14206,hmmpanther:PTHR14206:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGATCAAGGG	.	2	ESCA
SPAG1	0	.	GRCh37	8	101196196	101196196	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501G>C	p.Glu167Asp	p.E167D	ENST00000388798	6/19	159	145	13	138	138	0	SPAG1,missense_variant,p.Glu167Asp,ENST00000520508,;SPAG1,missense_variant,p.Glu167Asp,ENST00000388798,;SPAG1,missense_variant,p.Glu167Asp,ENST00000251809,;SPAG1,missense_variant,p.Glu167Asp,ENST00000520643,;Y_RNA,upstream_gene_variant,,ENST00000362797,;	C	ENSG00000104450	ENST00000388798	Transcript	missense_variant	692	501	167	E/D	gaG/gaC	.	.	.	1	SPAG1	HGNC	11212	protein_coding	YES	CCDS34930.1	ENSP00000373450	SPAG1_HUMAN	.	UPI000016783D	.	deleterious(0.03)	probably_damaging(0.948)	6/19	.	hmmpanther:PTHR22904:SF310,hmmpanther:PTHR22904	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGGAGAAGGA	.	3	ESCA
KLF10	0	.	GRCh37	8	103663830	103663830	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.730C>T	p.Gln244Ter	p.Q244*	ENST00000285407	3/4	68	39	29	63	63	0	KLF10,stop_gained,p.Gln233Ter,ENST00000395884,;KLF10,stop_gained,p.Gln244Ter,ENST00000285407,;	A	ENSG00000155090	ENST00000285407	Transcript	stop_gained	1031	730	244	Q/*	Cag/Tag	.	.	.	-1	KLF10	HGNC	11810	protein_coding	YES	CCDS6294.1	ENSP00000285407	KLF10_HUMAN	.	UPI000012DED8	.	.	.	3/4	.	hmmpanther:PTHR23223,hmmpanther:PTHR23223:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTGAGACC	.	5	ESCA
RIMS2	0	.	GRCh37	8	105261014	105261014	+	Missense_Mutation	SNP	C	C	T	rs763285258	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3562C>T	p.Arg1188Cys	p.R1188C	ENST00000406091	21/24	50	42	7	62	62	0	RIMS2,missense_variant,p.Arg1188Cys,ENST00000406091,;RIMS2,missense_variant,p.Arg1195Cys,ENST00000408894,;RIMS2,missense_variant,p.Arg124Cys,ENST00000339750,;RIMS2,missense_variant,p.Arg1002Cys,ENST00000507740,;RIMS2,missense_variant,p.Arg1027Cys,ENST00000262231,;RIMS2,missense_variant,p.Arg124Cys,ENST00000523362,;RIMS2,missense_variant,p.Arg1206Cys,ENST00000436393,;	T	ENSG00000176406	ENST00000406091	Transcript	missense_variant	3562	3562	1188	R/C	Cgc/Tgc	rs763285258,COSM1453911,COSM3374726,COSM1453908,COSM1453910,COSM1453909	.	.	1	RIMS2	HGNC	17283	protein_coding	YES	CCDS55269.1	ENSP00000384892	RIMS2_HUMAN	E9PFB6_HUMAN	UPI0001597063	.	deleterious_low_confidence(0)	probably_damaging(0.997)	21/24	.	hmmpanther:PTHR12157:SF15,hmmpanther:PTHR12157	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGACGCCAG	byFrequency	5	ESCA
PNOC	0	.	GRCh37	8	28196744	28196744	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.314T>G	p.Phe105Cys	p.F105C	ENST00000301908	3/4	33	27	5	40	40	0	PNOC,missense_variant,p.Phe105Cys,ENST00000301908,;PNOC,missense_variant,p.Phe105Cys,ENST00000518479,;PNOC,missense_variant,p.Phe41Cys,ENST00000522209,;RP11-380I10.4,non_coding_transcript_exon_variant,,ENST00000521731,;PNOC,non_coding_transcript_exon_variant,,ENST00000519592,;	G	ENSG00000168081	ENST00000301908	Transcript	missense_variant	522	314	105	F/C	tTc/tGc	.	.	.	1	PNOC	HGNC	9163	protein_coding	YES	CCDS6066.1	ENSP00000301908	PNOC_HUMAN	Q9BYY3_HUMAN,E7EVP0_HUMAN,B7Z749_HUMAN	UPI0000131D53	.	deleterious(0.05)	possibly_damaging(0.659)	3/4	.	hmmpanther:PTHR11438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGTTCCAGG	.	5	ESCA
YTHDF3	0	.	GRCh37	8	64100283	64100285	+	In_Frame_Del	DEL	GAG	GAG	-	rs753684267	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	GAG	GAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1716_1718delGGA	p.Glu573del	p.E573del	ENST00000539294	4/5	35	18	17	32	32	0	YTHDF3,inframe_deletion,p.Glu384del,ENST00000542911,;YTHDF3,inframe_deletion,p.Glu573del,ENST00000539294,;YTHDF3,inframe_deletion,p.Glu68del,ENST00000518373,;YTHDF3,intron_variant,,ENST00000517371,;YTHDF3,non_coding_transcript_exon_variant,,ENST00000520640,;YTHDF3,non_coding_transcript_exon_variant,,ENST00000521674,;YTHDF3,non_coding_transcript_exon_variant,,ENST00000517303,;YTHDF3,downstream_gene_variant,,ENST00000523056,;YTHDF3,downstream_gene_variant,,ENST00000523455,;YTHDF3,downstream_gene_variant,,ENST00000518438,;YTHDF3,downstream_gene_variant,,ENST00000518763,;YTHDF3,downstream_gene_variant,,ENST00000517375,;YTHDF3,downstream_gene_variant,,ENST00000521547,;YTHDF3,3_prime_UTR_variant,,ENST00000524135,;	-	ENSG00000185728	ENST00000539294	Transcript	inframe_deletion	2027-2029	1711-1713	571	E/-	GAG/-	rs753684267	.	.	1	YTHDF3	HGNC	26465	protein_coding	YES	.	ENSP00000473496	.	R4GN55_HUMAN,R4GMX0_HUMAN	UPI0002C8850B	.	.	.	4/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12357:SF9,hmmpanther:PTHR12357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAAGAAGAGGAGGA	.	3	ESCA
SULF1	0	.	GRCh37	8	70571279	70571279	+	3'UTR	SNP	G	G	C	rs187437769	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*509G>C	.	.	ENST00000260128	23/23	73	48	25	85	85	0	SULF1,3_prime_UTR_variant,,ENST00000419716,;SULF1,3_prime_UTR_variant,,ENST00000402687,;SULF1,3_prime_UTR_variant,,ENST00000260128,;SULF1,3_prime_UTR_variant,,ENST00000458141,;SULF1,non_coding_transcript_exon_variant,,ENST00000521946,;SULF1,3_prime_UTR_variant,,ENST00000531512,;SULF1,non_coding_transcript_exon_variant,,ENST00000530674,;SULF1,downstream_gene_variant,,ENST00000532015,;	C	ENSG00000137573	ENST00000260128	Transcript	3_prime_UTR_variant	3842	.	.	.	.	rs187437769	.	.	1	SULF1	HGNC	20391	protein_coding	YES	CCDS6204.1	ENSP00000260128	SULF1_HUMAN	Q96E28_HUMAN,E9PS14_HUMAN,E9PPQ3_HUMAN,E9PLS5_HUMAN,E9PJL8_HUMAN,E9PI06_HUMAN	UPI000003FD82	.	.	.	23/23	.	.	C:0.0004	C:0	C:0	.	C:0	C:0.002	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTAGAGCTC	byFrequency|by1000G	5	ESCA
ZFHX4	0	.	GRCh37	8	77767878	77767878	+	Silent	SNP	G	G	A	rs773478219	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8721G>A	p.%3D	p.P2907P	ENST00000521891	10/11	45	27	18	40	39	0	ZFHX4,synonymous_variant,p.%3D,ENST00000455469,;ZFHX4,synonymous_variant,p.%3D,ENST00000518282,;ZFHX4,synonymous_variant,p.%3D,ENST00000050961,;ZFHX4,synonymous_variant,p.%3D,ENST00000521891,;ZFHX4,downstream_gene_variant,,ENST00000522409,;	A	ENSG00000091656	ENST00000521891	Transcript	synonymous_variant	9169	8721	2907	P	ccG/ccA	rs773478219	.	.	1	ZFHX4	HGNC	30939	protein_coding	YES	CCDS47878.2	ENSP00000430497	.	Q9H7F3_HUMAN,Q86WW5_HUMAN,Q6DK57_HUMAN,G3V138_HUMAN,E5RI93_HUMAN,E5RHS1_HUMAN,E5RGK3_HUMAN,E5RG79_HUMAN	UPI0000424CC7	.	.	.	10/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24208:SF40,hmmpanther:PTHR24208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCCGAGCTC	.	5	ESCA
CA1	0	.	GRCh37	8	86244762	86244762	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470A>T	p.Lys157Met	p.K157M	ENST00000523953	7/9	73	61	11	64	64	0	CA1,missense_variant,p.Lys157Met,ENST00000523953,;CA1,missense_variant,p.Lys157Met,ENST00000432364,;CA1,missense_variant,p.Lys44Met,ENST00000520663,;CA1,missense_variant,p.Lys157Met,ENST00000517618,;CA1,missense_variant,p.Lys91Met,ENST00000524324,;CA1,missense_variant,p.Lys157Met,ENST00000256119,;CA1,missense_variant,p.Lys157Met,ENST00000523022,;CA1,missense_variant,p.Lys157Met,ENST00000431316,;CA1,missense_variant,p.Lys157Met,ENST00000517590,;CA1,missense_variant,p.Lys157Met,ENST00000542576,;CA1,missense_variant,p.Lys44Met,ENST00000519991,;CA1,missense_variant,p.Lys94Met,ENST00000521679,;CA1,intron_variant,,ENST00000522389,;CA1,downstream_gene_variant,,ENST00000522579,;CA1,downstream_gene_variant,,ENST00000522662,;CA1,downstream_gene_variant,,ENST00000523858,;CA1,downstream_gene_variant,,ENST00000522814,;CA1,downstream_gene_variant,,ENST00000521846,;CA1,downstream_gene_variant,,ENST00000518341,;CA1,3_prime_UTR_variant,,ENST00000517429,;CA1,non_coding_transcript_exon_variant,,ENST00000518233,;CA1,non_coding_transcript_exon_variant,,ENST00000523712,;	A	ENSG00000133742	ENST00000523953	Transcript	missense_variant	1517	470	157	K/M	aAg/aTg	.	.	.	-1	CA1	HGNC	1368	protein_coding	YES	CCDS6237.1	ENSP00000430656	CAH1_HUMAN	E5RIF9_HUMAN,E5RHS7_HUMAN,E5RHP7_HUMAN,E5RH81_HUMAN,E5RGU8_HUMAN,E5RG43_HUMAN,E5RFL2_HUMAN	UPI000013CEEF	.	tolerated(0.07)	benign(0.404)	7/9	.	PROSITE_profiles:PS51144,hmmpanther:PTHR18952:SF82,hmmpanther:PTHR18952,Gene3D:3.10.200.10,Pfam_domain:PF00194,SMART_domains:SM01057,Superfamily_domains:SSF51069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGCTTTGGG	.	5	ESCA
TLR4	0	.	GRCh37	9	120476760	120476760	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2354T>G	p.Leu785Arg	p.L785R	ENST00000355622	3/3	27	21	6	33	33	0	TLR4,missense_variant,p.Leu785Arg,ENST00000355622,;TLR4,missense_variant,p.Leu745Arg,ENST00000394487,;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;	G	ENSG00000136869	ENST00000355622	Transcript	missense_variant	2455	2354	785	L/R	cTg/cGg	.	.	.	1	TLR4	HGNC	11850	protein_coding	YES	CCDS6818.1	ENSP00000363089	TLR4_HUMAN	K9MSZ3_HUMAN,D0EWT7_HUMAN	UPI0000137057	.	deleterious(0)	probably_damaging(1)	3/3	.	PROSITE_profiles:PS50104,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.40.50.10140,Pfam_domain:PF01582,SMART_domains:SM00255,PIRSF_domain:PIRSF037595,Superfamily_domains:SSF52200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCTGTACC	.	5	ESCA
PDCL	0	.	GRCh37	9	125582106	125582106	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*258A>T	.	.	ENST00000259467	4/4	38	32	5	75	75	0	PDCL,3_prime_UTR_variant,,ENST00000259467,;PDCL,intron_variant,,ENST00000436632,;PDCL,downstream_gene_variant,,ENST00000394285,;	A	ENSG00000136940	ENST00000259467	Transcript	3_prime_UTR_variant	1330	.	.	.	.	.	.	.	-1	PDCL	HGNC	8770	protein_coding	YES	CCDS6845.1	ENSP00000259467	PHLP_HUMAN	Q9UNX2_HUMAN,Q9UNX1_HUMAN	UPI0000131988	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACAATAACAG	.	4	ESCA
ALDH1B1	0	.	GRCh37	9	38396393	38396393	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.648C>G	p.%3D	p.L216L	ENST00000377698	2/2	25	20	5	52	52	0	ALDH1B1,synonymous_variant,p.%3D,ENST00000377698,;	G	ENSG00000137124	ENST00000377698	Transcript	synonymous_variant	801	648	216	L	ctC/ctG	.	.	.	1	ALDH1B1	HGNC	407	protein_coding	YES	CCDS6615.1	ENSP00000366927	AL1B1_HUMAN	B4DLJ0_HUMAN	UPI0000073000	.	.	.	2/2	.	Superfamily_domains:SSF53720,Gene3D:3.40.605.10,Pfam_domain:PF00171,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A218S|c.652G>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCTCTGC	.	5	ESCA
KIAA2026	0	.	GRCh37	9	5968230	5968248	+	Frame_Shift_Del	DEL	CTGCTCTAATAGAATATCC	CTGCTCTAATAGAATATCC	-	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	CTGCTCTAATAGAATATCC	CTGCTCTAATAGAATATCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1983_2001delGGATATTCTATTAGAGCAG	p.Arg661SerfsTer11	p.R661Sfs*11	ENST00000399933	3/8	26	18	8	21	21	0	KIAA2026,frameshift_variant,p.Arg594SerfsTer11,ENST00000513355,;KIAA2026,frameshift_variant,p.Arg661SerfsTer11,ENST00000381461,;KIAA2026,frameshift_variant,p.Arg661SerfsTer11,ENST00000399933,;KIAA2026,upstream_gene_variant,,ENST00000540714,;	-	ENSG00000183354	ENST00000399933	Transcript	frameshift_variant	1983-2001	1983-2001	661-667	RDILLEQ/X	agGGATATTCTATTAGAGCAG/ag	.	.	.	-1	KIAA2026	HGNC	23378	protein_coding	YES	.	ENSP00000382815	K2026_HUMAN	.	UPI0001533DB0	.	.	.	3/8	.	hmmpanther:PTHR31095:SF2,hmmpanther:PTHR31095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TAGTGACTGCTCTAATAGAATATCCCTTAC	.	2	ESCA
C9orf57	0	.	GRCh37	9	74667123	74667123	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*89G>T	.	.	ENST00000377024	5/5	38	24	14	31	31	0	C9orf57,3_prime_UTR_variant,,ENST00000377024,;C9orf57,3_prime_UTR_variant,,ENST00000424431,;	A	ENSG00000204669	ENST00000377024	Transcript	3_prime_UTR_variant	671	.	.	.	.	.	.	.	-1	C9orf57	HGNC	27037	protein_coding	YES	CCDS47980.1	ENSP00000366223	CI057_HUMAN	.	UPI0000160595	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGGCTAATT	.	5	ESCA
SPATA31D1	0	.	GRCh37	9	84607398	84607398	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2013C>A	p.%3D	p.S671S	ENST00000344803	4/4	133	117	15	183	183	0	SPATA31D1,synonymous_variant,p.%3D,ENST00000344803,;SPATA31D1,downstream_gene_variant,,ENST00000603921,;	A	ENSG00000214929	ENST00000344803	Transcript	synonymous_variant	2060	2013	671	S	tcC/tcA	.	.	.	1	SPATA31D1	HGNC	37283	protein_coding	YES	CCDS47986.1	ENSP00000341988	S31D1_HUMAN	.	UPI00001C10A6	.	.	.	4/4	.	hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859,Pfam_domain:PF14650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTCCATCAT	.	4	ESCA
PTCH1	0	.	GRCh37	9	98239986	98239986	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1348-2A>T	.	p.X450_splice	ENST00000331920	.	42	5	36	74	74	0	PTCH1,splice_acceptor_variant,,ENST00000331920,;PTCH1,splice_acceptor_variant,,ENST00000430669,;PTCH1,splice_acceptor_variant,,ENST00000418258,;PTCH1,splice_acceptor_variant,,ENST00000421141,;PTCH1,splice_acceptor_variant,,ENST00000375274,;PTCH1,splice_acceptor_variant,,ENST00000429896,;PTCH1,splice_acceptor_variant,,ENST00000437951,;PTCH1,intron_variant,,ENST00000375271,;PTCH1,downstream_gene_variant,,ENST00000547672,;PTCH1,downstream_gene_variant,,ENST00000551630,;PTCH1,downstream_gene_variant,,ENST00000553011,;PTCH1,downstream_gene_variant,,ENST00000468211,;PTCH1,downstream_gene_variant,,ENST00000551845,;PTCH1,downstream_gene_variant,,ENST00000546820,;PTCH1,downstream_gene_variant,,ENST00000548420,;PTCH1,downstream_gene_variant,,ENST00000548379,;PTCH1,downstream_gene_variant,,ENST00000553256,;PTCH1,downstream_gene_variant,,ENST00000548945,;PTCH1,splice_acceptor_variant,,ENST00000375290,;PTCH1,downstream_gene_variant,,ENST00000488809,;PTCH1,downstream_gene_variant,,ENST00000550914,;PTCH1,downstream_gene_variant,,ENST00000550136,;PTCH1,downstream_gene_variant,,ENST00000551623,;	A	ENSG00000185920	ENST00000331920	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	PTCH1	HGNC	9585	protein_coding	YES	CCDS6714.1	ENSP00000332353	PTC1_HUMAN	Q6TKQ0_HUMAN,F8VXL8_HUMAN,F8VQS6_HUMAN	UPI00001AFF9C	.	.	.	.	9/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGCTGCAAG	.	5	ESCA
GPRASP1	0	.	GRCh37	X	101912226	101912226	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3385C>G	p.Leu1129Val	p.L1129V	ENST00000537097	6/6	63	8	54	45	45	0	GPRASP1,missense_variant,p.Leu1129Val,ENST00000415986,;GPRASP1,missense_variant,p.Leu1129Val,ENST00000361600,;GPRASP1,missense_variant,p.Leu1129Val,ENST00000537097,;GPRASP1,missense_variant,p.Leu1129Val,ENST00000444152,;RP4-769N13.7,intron_variant,,ENST00000602441,;RP4-769N13.6,intron_variant,,ENST00000486740,;RP4-769N13.6,intron_variant,,ENST00000602463,;RP4-769N13.6,intron_variant,,ENST00000602366,;GPRASP1,downstream_gene_variant,,ENST00000466098,;	G	ENSG00000198932	ENST00000537097	Transcript	missense_variant	4198	3385	1129	L/V	Ctt/Gtt	.	.	.	1	GPRASP1	HGNC	24834	protein_coding	YES	CCDS35352.1	ENSP00000445683	GASP1_HUMAN	.	UPI0000073B80	.	deleterious(0)	probably_damaging(0.999)	6/6	.	hmmpanther:PTHR15712:SF22,hmmpanther:PTHR15712	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATCTTAGG	.	5	ESCA
IRS4	0	.	GRCh37	X	107976076	107976076	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3499G>T	p.Ala1167Ser	p.A1167S	ENST00000372129	1/1	39	9	30	47	47	0	IRS4,missense_variant,p.Ala1167Ser,ENST00000372129,;RP6-24A23.6,upstream_gene_variant,,ENST00000563887,;RP6-24A23.3,upstream_gene_variant,,ENST00000608811,;RP6-24A23.3,upstream_gene_variant,,ENST00000436013,;	A	ENSG00000133124	ENST00000372129	Transcript	missense_variant	3576	3499	1167	A/S	Gct/Tct	.	.	.	-1	IRS4	HGNC	6128	protein_coding	YES	CCDS14544.1	ENSP00000361202	IRS4_HUMAN	.	UPI0000073FE7	.	deleterious_low_confidence(0.01)	unknown(0)	1/1	.	hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTAGCAACAG	.	5	ESCA
WASH6P	0	.	GRCh37	X	155252079	155252079	+	RNA	SNP	T	T	G	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1087T>G	.	.	ENST00000461007	1/2	82	63	18	125	125	0	WASH6P,non_coding_transcript_exon_variant,,ENST00000340131,;WASH6P,non_coding_transcript_exon_variant,,ENST00000476066,;WASH6P,non_coding_transcript_exon_variant,,ENST00000475594,;AJ271736.10,non_coding_transcript_exon_variant,,ENST00000285718,;WASH6P,non_coding_transcript_exon_variant,,ENST00000482170,;WASH6P,non_coding_transcript_exon_variant,,ENST00000484415,;WASH6P,non_coding_transcript_exon_variant,,ENST00000479401,;WASH6P,non_coding_transcript_exon_variant,,ENST00000492963,;WASH6P,non_coding_transcript_exon_variant,,ENST00000496011,;WASH6P,non_coding_transcript_exon_variant,,ENST00000461007,;WASH6P,non_coding_transcript_exon_variant,,ENST00000460206,;WASH6P,intron_variant,,ENST00000469624,;WASH6P,upstream_gene_variant,,ENST00000464205,;WASH6P,upstream_gene_variant,,ENST00000483079,;WASH6P,upstream_gene_variant,,ENST00000483286,;WASH6P,upstream_gene_variant,,ENST00000496301,;AJ271736.10,downstream_gene_variant,,ENST00000483543,;WASH6P,non_coding_transcript_exon_variant,,ENST00000359512,;DDX11L16,downstream_gene_variant,,ENST00000445777,;DDX11L16,downstream_gene_variant,,ENST00000507418,;	G	ENSG00000182484	ENST00000461007	Transcript	non_coding_transcript_exon_variant	1087	.	.	.	.	.	.	.	1	WASH6P	HGNC	31685	processed_transcript	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACATCAGCT	.	4	ESCA
TMEM47	0	.	GRCh37	X	34648476	34648476	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.500C>T	p.Ala167Val	p.A167V	ENST00000275954	3/3	41	13	27	69	69	0	TMEM47,missense_variant,p.Ala167Val,ENST00000275954,;	A	ENSG00000147027	ENST00000275954	Transcript	missense_variant	759	500	167	A/V	gCc/gTc	.	.	.	-1	TMEM47	HGNC	18515	protein_coding	YES	CCDS14235.1	ENSP00000275954	TMM47_HUMAN	.	UPI0000073CBB	.	deleterious(0.01)	probably_damaging(0.992)	3/3	.	Transmembrane_helices:TMhelix,Pfam_domain:PF13903,hmmpanther:PTHR14399,hmmpanther:PTHR14399:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGGCACCC	.	5	ESCA
CLCN5	0	.	GRCh37	X	49689825	49689825	+	5'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-84C>A	.	.	ENST00000376088	3/15	53	49	4	87	87	0	CLCN5,5_prime_UTR_variant,,ENST00000482218,;CLCN5,5_prime_UTR_variant,,ENST00000376091,;CLCN5,5_prime_UTR_variant,,ENST00000376088,;	A	ENSG00000171365	ENST00000376088	Transcript	5_prime_UTR_variant	558	.	.	.	.	.	.	.	1	CLCN5	HGNC	2023	protein_coding	YES	CCDS48115.1	ENSP00000365256	CLCN5_HUMAN	.	UPI0000212052	.	.	.	3/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCTGCCTTTC	.	3	ESCA
PHF8	0	.	GRCh37	X	54040940	54040940	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EW-01A-11D-A36J-09	TCGA-VR-A8EW-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.761A>G	p.Asn254Ser	p.N254S	ENST00000357988	7/22	54	46	8	44	44	0	PHF8,missense_variant,p.Asn218Ser,ENST00000338154,;PHF8,missense_variant,p.Asn218Ser,ENST00000338946,;PHF8,missense_variant,p.Asn122Ser,ENST00000396282,;PHF8,missense_variant,p.Asn254Ser,ENST00000357988,;PHF8,missense_variant,p.Asn218Ser,ENST00000322659,;PHF8,downstream_gene_variant,,ENST00000453905,;PHF8,downstream_gene_variant,,ENST00000437224,;PHF8,upstream_gene_variant,,ENST00000443302,;PHF8,downstream_gene_variant,,ENST00000415025,;PHF8,downstream_gene_variant,,ENST00000425862,;PHF8,upstream_gene_variant,,ENST00000413386,;PHF8,upstream_gene_variant,,ENST00000490635,;	C	ENSG00000172943	ENST00000357988	Transcript	missense_variant	1120	761	254	N/S	aAc/aGc	.	.	.	-1	PHF8	HGNC	20672	protein_coding	YES	CCDS55420.1	ENSP00000350676	PHF8_HUMAN	Q5JPR8_HUMAN,B3KMV4_HUMAN,B0QZZ4_HUMAN,B0QZZ3_HUMAN,B0QZZ2_HUMAN,B0QZE1_HUMAN	UPI00001C2071	.	deleterious(0)	possibly_damaging(0.688)	7/22	.	PROSITE_profiles:PS51184,hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF11,Gene3D:1vrbA01,SMART_domains:SM00558,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAGTTTTCG	.	5	ESCA
SORCS1	0	.	GRCh37	10	108335566	108335566	+	3'Flank	SNP	A	A	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000344440	.	63	53	9	100	100	0	SORCS1,3_prime_UTR_variant,,ENST00000263054,;SORCS1,downstream_gene_variant,,ENST00000369698,;SORCS1,downstream_gene_variant,,ENST00000452214,;SORCS1,downstream_gene_variant,,ENST00000344440,;SORCS1,downstream_gene_variant,,ENST00000473866,;	T	ENSG00000108018	ENST00000344440	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1398	-1	SORCS1	HGNC	16697	protein_coding	YES	CCDS31283.1	ENSP00000345964	SORC1_HUMAN	B3KVZ0_HUMAN	UPI000036671B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTAAACACAA	.	4	ESCA
SLC18A2	0	.	GRCh37	10	119013947	119013947	+	Missense_Mutation	SNP	T	T	A	rs147489556	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639T>A	p.Asp213Glu	p.D213E	ENST00000298472	6/16	32	24	7	26	26	0	SLC18A2,missense_variant,p.Asp213Glu,ENST00000298472,;SLC18A2,non_coding_transcript_exon_variant,,ENST00000497497,;	A	ENSG00000165646	ENST00000298472	Transcript	missense_variant	782	639	213	D/E	gaT/gaA	rs147489556	.	.	1	SLC18A2	HGNC	10935	protein_coding	YES	CCDS7599.1	ENSP00000298472	VMAT2_HUMAN	.	UPI00001389DE	.	tolerated(0.07)	benign(0.297)	6/16	.	PROSITE_profiles:PS50850,hmmpanther:PTHR24004,hmmpanther:PTHR24004:SF63,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGATGATGA	byFrequency|byCluster	5	ESCA
RP11-85G18.6	0	.	GRCh37	10	27537518	27537518	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.256-1469C>T	.	.	ENST00000574842	.	256	217	38	274	274	0	RP11-85G18.6,intron_variant,,ENST00000574842,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000284414,;LRRC37A6P,downstream_gene_variant,,ENST00000575554,;LRRC37A6P,downstream_gene_variant,,ENST00000574795,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000448648,;	T	ENSG00000262412	ENST00000574842	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RP11-85G18.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATGCCAGGC	.	4	ESCA
ZEB1	0	.	GRCh37	10	31809133	31809133	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.873G>C	p.Lys291Asn	p.K291N	ENST00000361642	7/9	37	34	3	49	49	0	ZEB1,missense_variant,p.Lys270Asn,ENST00000560721,;ZEB1,missense_variant,p.Lys274Asn,ENST00000446923,;ZEB1,missense_variant,p.Lys216Asn,ENST00000558440,;ZEB1,missense_variant,p.Lys291Asn,ENST00000361642,;ZEB1,missense_variant,p.Lys274Asn,ENST00000559476,;ZEB1,missense_variant,p.Lys290Asn,ENST00000320985,;ZEB1,missense_variant,p.Lys298Asn,ENST00000561212,;ZEB1,missense_variant,p.Lys223Asn,ENST00000542815,;ZEB1,downstream_gene_variant,,ENST00000424869,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558863,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558655,;	C	ENSG00000148516	ENST00000361642	Transcript	missense_variant	936	873	291	K/N	aaG/aaC	.	.	.	1	ZEB1	HGNC	11642	protein_coding	YES	CCDS53505.1	ENSP00000354487	ZEB1_HUMAN	F6TDF5_HUMAN	UPI000068F51D	.	deleterious(0)	probably_damaging(0.998)	7/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AGTAAGAAATG	.	2	ESCA
FAM21B	0	.	GRCh37	10	47946902	47946902	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3538G>C	p.Asp1180His	p.D1180H	ENST00000358474	28/29	35	27	8	44	44	0	FAM21B,missense_variant,p.Asp1150His,ENST00000355876,;FAM21B,missense_variant,p.Asp1180His,ENST00000358474,;	C	ENSG00000152726	ENST00000358474	Transcript	missense_variant	3538	3538	1180	D/H	Gat/Cat	.	.	.	1	FAM21B	HGNC	23417	protein_coding	YES	CCDS44379.1	ENSP00000351259	FA21B_HUMAN	Q6P0Q7_HUMAN,Q5SNT8_HUMAN	UPI00001D80AD	.	deleterious(0)	probably_damaging(0.979)	28/29	.	hmmpanther:PTHR21669:SF4,hmmpanther:PTHR21669	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ACATTGATATC	.	2	ESCA
SLC16A9	0	.	GRCh37	10	61413642	61413642	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1142T>C	p.Ile381Thr	p.I381T	ENST00000395348	5/6	43	38	5	73	73	0	SLC16A9,missense_variant,p.Ile381Thr,ENST00000395347,;SLC16A9,missense_variant,p.Ile381Thr,ENST00000395348,;	G	ENSG00000165449	ENST00000395348	Transcript	missense_variant	1779	1142	381	I/T	aTc/aCc	.	.	.	-1	SLC16A9	HGNC	23520	protein_coding	YES	CCDS7256.1	ENSP00000378757	MOT9_HUMAN	.	UPI000004D33D	.	tolerated(1)	benign(0.001)	5/6	.	Superfamily_domains:SSF103473,Pfam_domain:PF07690,Gene3D:1.20.1250.20,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF16,PROSITE_profiles:PS50850,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.I380I|c.1140C>T|3	RADIA|MUTECT|MUSE|VARSCANS	CCATGATGATT	.	4	ESCA
TNKS2	0	.	GRCh37	10	93624433	93624433	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1677T>G	.	.	ENST00000371627	27/27	59	52	7	107	107	0	TNKS2,3_prime_UTR_variant,,ENST00000371627,;	G	ENSG00000107854	ENST00000371627	Transcript	3_prime_UTR_variant	5557	.	.	.	.	.	.	.	1	TNKS2	HGNC	15677	protein_coding	YES	CCDS7417.1	ENSP00000360689	TNKS2_HUMAN	.	UPI00000362BE	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATCTTGAAGT	.	4	ESCA
NOC3L	0	.	GRCh37	10	96109877	96109877	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1121C>G	p.Ser374Ter	p.S374*	ENST00000371361	9/21	57	50	7	53	53	0	NOC3L,stop_gained,p.Ser112Ter,ENST00000543788,;NOC3L,stop_gained,p.Ser374Ter,ENST00000371361,;NOC3L,stop_gained,p.Ser374Ter,ENST00000371350,;NOC3L,non_coding_transcript_exon_variant,,ENST00000463649,;	C	ENSG00000173145	ENST00000371361	Transcript	stop_gained	1222	1121	374	S/*	tCa/tGa	.	.	.	-1	NOC3L	HGNC	24034	protein_coding	YES	CCDS7433.1	ENSP00000360412	NOC3L_HUMAN	.	UPI000006DE09	.	.	.	9/21	.	Superfamily_domains:SSF48371,PIRSF_domain:PIRSF028977,hmmpanther:PTHR14428:SF5,hmmpanther:PTHR14428	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTTTGACATG	.	4	ESCA
ACAT1	0	.	GRCh37	11	108005929	108005930	+	Frame_Shift_Ins	INS	-	-	CT	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396_397insTC	p.Ile133SerfsTer3	p.I133Sfs*3	ENST00000265838	5/12	50	39	11	65	65	0	ACAT1,frameshift_variant,p.Ile133SerfsTer3,ENST00000265838,;ACAT1,frameshift_variant,p.Ile69SerfsTer3,ENST00000528370,;ACAT1,frameshift_variant,p.Ile133SerfsTer3,ENST00000299355,;ACAT1,frameshift_variant,p.Ile43SerfsTer3,ENST00000527942,;ACAT1,downstream_gene_variant,,ENST00000526119,;ACAT1,downstream_gene_variant,,ENST00000531853,;ACAT1,intron_variant,,ENST00000531813,;ACAT1,upstream_gene_variant,,ENST00000534773,;ACAT1,upstream_gene_variant,,ENST00000533610,;ACAT1,downstream_gene_variant,,ENST00000524833,;ACAT1,upstream_gene_variant,,ENST00000532792,;	CT	ENSG00000075239	ENST00000265838	Transcript	frameshift_variant	486-487	395-396	132	A/AX	gcc/gcCTc	.	.	.	1	ACAT1	HGNC	93	protein_coding	YES	CCDS8339.1	ENSP00000265838	THIL_HUMAN	E9PKF3_HUMAN	UPI0000136E41	.	.	.	5/12	.	Superfamily_domains:SSF53901,PIRSF_domain:PIRSF000429,TIGRFAM_domain:TIGR01930,Pfam_domain:PF00108,Gene3D:3.40.47.10,PROSITE_patterns:PS00098,hmmpanther:PTHR18919:SF79,hmmpanther:PTHR18919	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAAGCCATCA	.	3	ESCA
NPAT	0	.	GRCh37	11	108032507	108032507	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3306T>C	p.%3D	p.N1102N	ENST00000278612	17/18	39	35	4	42	42	0	NPAT,synonymous_variant,p.%3D,ENST00000278612,;NPAT,synonymous_variant,p.%3D,ENST00000527296,;NPAT,non_coding_transcript_exon_variant,,ENST00000530859,;NPAT,upstream_gene_variant,,ENST00000530926,;	G	ENSG00000149308	ENST00000278612	Transcript	synonymous_variant	3412	3306	1102	N	aaT/aaC	.	.	.	-1	NPAT	HGNC	7896	protein_coding	YES	CCDS41710.1	ENSP00000278612	NPAT_HUMAN	.	UPI00001FA306	.	.	.	17/18	.	hmmpanther:PTHR15087:SF5,hmmpanther:PTHR15087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACACATTGGG	.	4	ESCA
GALNT18	0	.	GRCh37	11	11398890	11398890	+	Silent	SNP	C	C	T	rs755784655	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.816G>A	p.%3D	p.R272R	ENST00000227756	5/11	46	40	5	49	49	0	GALNT18,synonymous_variant,p.%3D,ENST00000227756,;	T	ENSG00000110328	ENST00000227756	Transcript	synonymous_variant	1228	816	272	R	cgG/cgA	rs755784655	.	.	-1	GALNT18	HGNC	30488	protein_coding	YES	CCDS7807.1	ENSP00000227756	GLT18_HUMAN	Q58A54_HUMAN	UPI000004B63C	.	.	.	5/11	.	Superfamily_domains:SSF53448,Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCTTCCGGTT	.	4	ESCA
MICAL2	0	.	GRCh37	11	12257748	12257748	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2020G>A	p.Asp674Asn	p.D674N	ENST00000256194	16/28	74	64	9	101	101	0	MICAL2,missense_variant,p.Asp674Asn,ENST00000379612,;MICAL2,missense_variant,p.Asp674Asn,ENST00000256194,;MICAL2,missense_variant,p.Asp674Asn,ENST00000527546,;MICAL2,missense_variant,p.Asp674Asn,ENST00000342902,;MICAL2,missense_variant,p.Asp674Asn,ENST00000537344,;MICAL2,non_coding_transcript_exon_variant,,ENST00000526475,;MICAL2,non_coding_transcript_exon_variant,,ENST00000530691,;MICAL2,non_coding_transcript_exon_variant,,ENST00000528931,;MICAL2,upstream_gene_variant,,ENST00000525075,;	A	ENSG00000133816	ENST00000256194	Transcript	missense_variant	2308	2020	674	D/N	Gac/Aac	.	.	.	1	MICAL2	HGNC	24693	protein_coding	YES	CCDS7809.1	ENSP00000256194	MICA2_HUMAN	E9PRE0_HUMAN,E9PNC3_HUMAN,E9PL42_HUMAN,E9PKI3_HUMAN,E9PJB0_HUMAN	UPI000000DA92	.	tolerated(0.05)	benign(0.24)	16/28	.	hmmpanther:PTHR11915:SF239,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAATGACATG	.	4	ESCA
DCDC1	0	.	GRCh37	11	30902833	30902833	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5096G>C	p.Arg1699Pro	p.R1699P	ENST00000597505	35/36	67	57	9	61	61	0	DCDC1,missense_variant,p.Arg1699Pro,ENST00000597505,;DCDC1,downstream_gene_variant,,ENST00000406071,;DCDC1,missense_variant,p.Arg734Pro,ENST00000444572,;DCDC1,3_prime_UTR_variant,,ENST00000303697,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,;	G	ENSG00000170959	ENST00000597505	Transcript	missense_variant	5096	5096	1699	R/P	cGt/cCt	.	.	.	-1	DCDC1	HGNC	20625	protein_coding	.	.	ENSP00000472625	.	M0R2J8_HUMAN	UPI0002A47319	.	deleterious(0)	possibly_damaging(0.655)	35/36	.	Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGACGAGAG	.	5	ESCA
CAPRIN1	0	.	GRCh37	11	34107731	34107731	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1087A>G	p.Met363Val	p.M363V	ENST00000341394	10/19	19	13	6	37	37	0	CAPRIN1,missense_variant,p.Met363Val,ENST00000341394,;CAPRIN1,missense_variant,p.Met363Val,ENST00000532820,;CAPRIN1,missense_variant,p.Met363Val,ENST00000389645,;CAPRIN1,missense_variant,p.Met282Val,ENST00000529307,;CAPRIN1,missense_variant,p.Met363Val,ENST00000530820,;CAPRIN1,intron_variant,,ENST00000528856,;CAPRIN1,upstream_gene_variant,,ENST00000533657,;	G	ENSG00000135387	ENST00000341394	Transcript	missense_variant	1276	1087	363	M/V	Atg/Gtg	.	.	.	1	CAPRIN1	HGNC	6743	protein_coding	YES	CCDS31453.1	ENSP00000340329	CAPR1_HUMAN	G3V153_HUMAN,E9PLA9_HUMAN	UPI0000251DB5	.	deleterious(0)	benign(0.113)	10/19	.	hmmpanther:PTHR22922,hmmpanther:PTHR22922:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTATGGCA	.	5	ESCA
ATL3	0	.	GRCh37	11	63439335	63439335	+	5'Flank	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000398868	.	41	38	3	38	38	0	ATL3,5_prime_UTR_variant,,ENST00000540699,;ATL3,5_prime_UTR_variant,,ENST00000538786,;ATL3,upstream_gene_variant,,ENST00000398868,;ATL3,upstream_gene_variant,,ENST00000332645,;ATL3,upstream_gene_variant,,ENST00000535789,;	A	ENSG00000184743	ENST00000398868	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	251	-1	ATL3	HGNC	24526	protein_coding	YES	CCDS41663.1	ENSP00000381844	ATLA3_HUMAN	F5H6I7_HUMAN	UPI0000071A21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCCGAGGCT	.	2	ESCA
NAALADL1	0	.	GRCh37	11	64825853	64825853	+	Silent	SNP	G	G	A	rs372762648	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.141C>T	p.%3D	p.T47T	ENST00000358658	1/18	99	91	8	103	103	0	NAALADL1,synonymous_variant,p.%3D,ENST00000356632,;NAALADL1,synonymous_variant,p.%3D,ENST00000339885,;NAALADL1,synonymous_variant,p.%3D,ENST00000355369,;NAALADL1,synonymous_variant,p.%3D,ENST00000358658,;NAALADL1,synonymous_variant,p.%3D,ENST00000355721,;NAALADL1,synonymous_variant,p.%3D,ENST00000340252,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000528977,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000529274,;	A	ENSG00000168060	ENST00000358658	Transcript	synonymous_variant	169	141	47	T	acC/acT	rs372762648	.	.	-1	NAALADL1	HGNC	23536	protein_coding	YES	CCDS31604.1	ENSP00000351484	NALDL_HUMAN	E9PRC7_HUMAN,E9PLR8_HUMAN,E9PKW7_HUMAN,E9PKG8_HUMAN,E9PJQ1_HUMAN,E9PIU1_HUMAN,E9PII9_HUMAN	UPI000013E761	.	.	.	1/18	.	hmmpanther:PTHR10404:SF40,hmmpanther:PTHR10404,Gene3D:3.40.630.10	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGACGGTCTC	byFrequency|byCluster	3	ESCA
NAALAD2	0	.	GRCh37	11	89882218	89882218	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426G>C	p.Glu142Asp	p.E142D	ENST00000534061	4/19	149	136	13	200	200	0	NAALAD2,missense_variant,p.Glu88Asp,ENST00000526637,;NAALAD2,missense_variant,p.Glu142Asp,ENST00000375944,;NAALAD2,missense_variant,p.Glu142Asp,ENST00000525171,;NAALAD2,missense_variant,p.Glu142Asp,ENST00000534061,;NAALAD2,missense_variant,p.Glu142Asp,ENST00000321955,;NAALAD2,downstream_gene_variant,,ENST00000525497,;NAALAD2,missense_variant,p.Glu142Asp,ENST00000527493,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000524501,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000529090,;	C	ENSG00000077616	ENST00000534061	Transcript	missense_variant	656	426	142	E/D	gaG/gaC	.	.	.	1	NAALAD2	HGNC	14526	protein_coding	YES	CCDS8288.1	ENSP00000432481	NALD2_HUMAN	E9PJ53_HUMAN,E9PII2_HUMAN	UPI0000031A85	.	tolerated(0.11)	benign(0.189)	4/19	.	Superfamily_domains:SSF52025,Gene3D:3.50.30.30,hmmpanther:PTHR10404:SF38,hmmpanther:PTHR10404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TATGAGAATGT	.	3	ESCA
FAM71C	0	.	GRCh37	12	100042091	100042091	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.139G>C	p.Glu47Gln	p.E47Q	ENST00000324341	1/2	53	48	5	49	49	0	FAM71C,missense_variant,p.Glu47Gln,ENST00000324341,;ANKS1B,intron_variant,,ENST00000329257,;ANKS1B,intron_variant,,ENST00000549866,;ANKS1B,intron_variant,,ENST00000547010,;ANKS1B,intron_variant,,ENST00000547776,;ANKS1B,intron_variant,,ENST00000552232,;	C	ENSG00000180219	ENST00000324341	Transcript	missense_variant	561	139	47	E/Q	Gag/Cag	COSM1365106	.	.	1	FAM71C	HGNC	28594	protein_coding	YES	CCDS9072.1	ENSP00000315247	FA71C_HUMAN	.	UPI0000073857	.	deleterious(0)	probably_damaging(0.996)	1/2	.	hmmpanther:PTHR22574:SF11,hmmpanther:PTHR22574	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTTTGAGAGC	.	4	ESCA
PPTC7	0	.	GRCh37	12	110973069	110973069	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1773C>T	.	.	ENST00000354300	6/6	76	64	12	105	105	0	PPTC7,3_prime_UTR_variant,,ENST00000354300,;RAD9B,downstream_gene_variant,,ENST00000409246,;RAD9B,downstream_gene_variant,,ENST00000409778,;RAD9B,downstream_gene_variant,,ENST00000392672,;RAD9B,downstream_gene_variant,,ENST00000409300,;RAD9B,downstream_gene_variant,,ENST00000409425,;RAD9B,downstream_gene_variant,,ENST00000358071,;PPTC7,downstream_gene_variant,,ENST00000548721,;	A	ENSG00000196850	ENST00000354300	Transcript	3_prime_UTR_variant	2977	.	.	.	.	.	.	.	-1	PPTC7	HGNC	30695	protein_coding	YES	CCDS9149.1	ENSP00000346255	PPTC7_HUMAN	.	UPI000003F57A	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTGACATG	.	5	ESCA
HNF1A	0	.	GRCh37	12	121435420	121435420	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1453A>G	p.Thr485Ala	p.T485A	ENST00000257555	7/10	36	29	7	25	25	0	HNF1A,missense_variant,p.Thr485Ala,ENST00000400024,;HNF1A,missense_variant,p.Thr485Ala,ENST00000544413,;HNF1A,missense_variant,p.Thr485Ala,ENST00000541395,;HNF1A,missense_variant,p.Thr67Ala,ENST00000538626,;HNF1A,missense_variant,p.Thr57Ala,ENST00000535955,;HNF1A,missense_variant,p.Thr485Ala,ENST00000257555,;HNF1A,3_prime_UTR_variant,,ENST00000402929,;C12orf43,downstream_gene_variant,,ENST00000445832,;HNF1A,downstream_gene_variant,,ENST00000543427,;RP11-216P16.2,downstream_gene_variant,,ENST00000606238,;HNF1A,3_prime_UTR_variant,,ENST00000544574,;HNF1A,3_prime_UTR_variant,,ENST00000541924,;HNF1A,3_prime_UTR_variant,,ENST00000560968,;HNF1A,3_prime_UTR_variant,,ENST00000538646,;HNF1A,3_prime_UTR_variant,,ENST00000540108,;HNF1A,non_coding_transcript_exon_variant,,ENST00000543255,;	G	ENSG00000135100	ENST00000257555	Transcript	missense_variant	1679	1453	485	T/A	Acc/Gcc	.	.	.	1	HNF1A	HGNC	11621	protein_coding	YES	CCDS9209.1	ENSP00000257555	.	E0YMJ2_HUMAN,E0YMJ1_HUMAN,B8YNW1_HUMAN,B8YNU9_HUMAN	UPI000013CF6C	.	tolerated(1)	benign(0)	7/10	.	hmmpanther:PTHR11568:SF4,hmmpanther:PTHR11568,Pfam_domain:PF04812	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTGACCCAG	.	5	ESCA
CACNA1C	0	.	GRCh37	12	2721273	2721273	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3888+94G>T	.	.	ENST00000347598	.	33	29	4	27	27	0	CACNA1C,3_prime_UTR_variant,,ENST00000480911,;CACNA1C,intron_variant,,ENST00000399644,;CACNA1C,intron_variant,,ENST00000399595,;CACNA1C,intron_variant,,ENST00000406454,;CACNA1C,intron_variant,,ENST00000399617,;CACNA1C,intron_variant,,ENST00000347598,;CACNA1C,intron_variant,,ENST00000402845,;CACNA1C,intron_variant,,ENST00000327702,;CACNA1C,intron_variant,,ENST00000399634,;CACNA1C,intron_variant,,ENST00000399641,;CACNA1C,intron_variant,,ENST00000399603,;CACNA1C,intron_variant,,ENST00000399629,;CACNA1C,intron_variant,,ENST00000399601,;CACNA1C,intron_variant,,ENST00000399597,;CACNA1C,intron_variant,,ENST00000399655,;CACNA1C,intron_variant,,ENST00000399606,;CACNA1C,intron_variant,,ENST00000399637,;CACNA1C,intron_variant,,ENST00000335762,;CACNA1C,intron_variant,,ENST00000399621,;CACNA1C,intron_variant,,ENST00000399638,;CACNA1C,intron_variant,,ENST00000399591,;CACNA1C,intron_variant,,ENST00000344100,;CACNA1C,intron_variant,,ENST00000399649,;CACNA1C-AS3,upstream_gene_variant,,ENST00000543559,;CACNA1C,downstream_gene_variant,,ENST00000496818,;	T	ENSG00000151067	ENST00000347598	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	.	.	.	30/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAAGAGGGA	.	2	ESCA
KIAA1551	0	.	GRCh37	12	32145344	32145344	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5119T>A	p.Phe1707Ile	p.F1707I	ENST00000312561	6/6	56	52	4	56	56	0	KIAA1551,missense_variant,p.Phe1707Ile,ENST00000312561,;KIAA1551,non_coding_transcript_exon_variant,,ENST00000535596,;KIAA1551,non_coding_transcript_exon_variant,,ENST00000541981,;KIAA1551,non_coding_transcript_exon_variant,,ENST00000397578,;KIAA1551,non_coding_transcript_exon_variant,,ENST00000543763,;	A	ENSG00000174718	ENST00000312561	Transcript	missense_variant	5533	5119	1707	F/I	Ttc/Atc	.	.	.	1	KIAA1551	HGNC	25559	protein_coding	YES	CCDS8725.2	ENSP00000310338	K1551_HUMAN	J3KPI3_HUMAN,F5H488_HUMAN	UPI0000577B2F	.	tolerated(0.22)	benign(0.11)	6/6	.	hmmpanther:PTHR21604,Pfam_domain:PF15395	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAGCTTCAGT	.	2	ESCA
OR6C68	0	.	GRCh37	12	55886973	55886973	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.812G>A	p.Gly271Asp	p.G271D	ENST00000548615	1/1	71	58	13	67	67	0	OR6C68,missense_variant,p.Gly271Asp,ENST00000548615,;OR6C68,missense_variant,p.Gly276Asp,ENST00000379662,;RP11-110A12.2,intron_variant,,ENST00000556750,;RP11-110A12.2,intron_variant,,ENST00000555138,;RP11-110A12.2,upstream_gene_variant,,ENST00000554049,;	A	ENSG00000205327	ENST00000548615	Transcript	missense_variant	812	812	271	G/D	gGt/gAt	.	.	.	1	OR6C68	HGNC	31297	protein_coding	YES	CCDS31826.2	ENSP00000448811	O6C68_HUMAN	.	UPI00015E1642	.	tolerated_low_confidence(0.05)	benign(0.344)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26454:SF19,hmmpanther:PTHR26454,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAGGTGTGT	.	5	ESCA
TBC1D30	0	.	GRCh37	12	65224154	65224154	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283-3T>C	.	.	ENST00000539867	.	37	31	6	65	65	0	TBC1D30,splice_region_variant,,ENST00000539867,;TBC1D30,splice_region_variant,,ENST00000539120,;TBC1D30,splice_region_variant,,ENST00000229088,;TBC1D30,splice_region_variant,,ENST00000544190,;TBC1D30,splice_region_variant,,ENST00000542120,;TBC1D30,intron_variant,,ENST00000544457,;	C	ENSG00000111490	ENST00000539867	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	TBC1D30	HGNC	29164	protein_coding	YES	CCDS53813.1	ENSP00000440207	TBC30_HUMAN	F8VZ81_HUMAN,F5H7L7_HUMAN	UPI000013F308	.	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTTAGGTT	.	4	ESCA
IFNG	0	.	GRCh37	12	68553407	68553407	+	5'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12C>A	.	.	ENST00000229135	1/4	44	35	9	44	44	0	IFNG,5_prime_UTR_variant,,ENST00000229135,;IFNG-AS1,intron_variant,,ENST00000536914,;	T	ENSG00000111537	ENST00000229135	Transcript	5_prime_UTR_variant	121	.	.	.	.	.	.	.	-1	IFNG	HGNC	5438	protein_coding	YES	CCDS8980.1	ENSP00000229135	IFNG_HUMAN	A1Z2M2_HUMAN	UPI000002C7C8	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGAGAATTA	.	5	ESCA
WNK1	0	.	GRCh37	12	922899	922899	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.851A>G	p.Tyr284Cys	p.Y284C	ENST00000315939	2/28	43	40	3	42	42	0	WNK1,missense_variant,p.Tyr284Cys,ENST00000315939,;WNK1,missense_variant,p.Tyr284Cys,ENST00000535572,;WNK1,missense_variant,p.Tyr284Cys,ENST00000447667,;WNK1,missense_variant,p.Tyr284Cys,ENST00000530271,;WNK1,missense_variant,p.Tyr284Cys,ENST00000537687,;	G	ENSG00000060237	ENST00000315939	Transcript	missense_variant	1494	851	284	Y/C	tAt/tGt	.	.	.	1	WNK1	HGNC	14540	protein_coding	YES	CCDS8506.1	ENSP00000313059	WNK1_HUMAN	Q96CZ6_HUMAN	UPI000013CD65	.	deleterious(0)	unknown(0)	2/28	.	PROSITE_profiles:PS50011,hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF46,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTTATGATT	.	2	ESCA
AMDHD1	0	.	GRCh37	12	96350673	96350673	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520G>C	p.Glu174Gln	p.E174Q	ENST00000266736	4/9	59	51	8	50	50	0	AMDHD1,missense_variant,p.Glu174Gln,ENST00000266736,;AMDHD1,downstream_gene_variant,,ENST00000553023,;AMDHD1,stop_lost,p.Ter112SerextTer22,ENST00000548310,;AMDHD1,non_coding_transcript_exon_variant,,ENST00000549171,;	C	ENSG00000139344	ENST00000266736	Transcript	missense_variant	626	520	174	E/Q	Gag/Cag	.	.	.	1	AMDHD1	HGNC	28577	protein_coding	YES	CCDS9057.1	ENSP00000266736	HUTI_HUMAN	.	UPI000013D70B	.	tolerated(0.07)	benign(0.056)	4/9	.	hmmpanther:PTHR22642,hmmpanther:PTHR22642:SF1,Gene3D:3.20.20.140,Pfam_domain:PF13147,TIGRFAM_domain:TIGR01224,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R175R|c.525C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TGATTGAGCGC	.	4	ESCA
MYO16	0	.	GRCh37	13	109562480	109562480	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1841A>C	p.Asn614Thr	p.N614T	ENST00000356711	16/35	47	44	3	58	58	0	MYO16,missense_variant,p.Asn126Thr,ENST00000457511,;MYO16,missense_variant,p.Asn614Thr,ENST00000251041,;MYO16,missense_variant,p.Asn614Thr,ENST00000356711,;MYO16,missense_variant,p.Asn614Thr,ENST00000357550,;MYO16,non_coding_transcript_exon_variant,,ENST00000375857,;	C	ENSG00000041515	ENST00000356711	Transcript	missense_variant	1967	1841	614	N/T	aAt/aCt	.	.	.	1	MYO16	HGNC	29822	protein_coding	YES	CCDS32008.1	ENSP00000349145	MYO16_HUMAN	.	UPI0000160FF2	.	tolerated(0.09)	benign(0.41)	16/35	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF345,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTAATAATT	.	2	ESCA
SAP18	0	.	GRCh37	13	21721403	21721403	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441G>C	p.Gln147His	p.Q147H	ENST00000382533	4/4	40	28	11	53	53	0	SAP18,missense_variant,p.Gln128His,ENST00000607003,;SAP18,missense_variant,p.Gln125His,ENST00000450573,;SAP18,missense_variant,p.Gln147His,ENST00000382533,;SAP18,3_prime_UTR_variant,,ENST00000492245,;SAP18,3_prime_UTR_variant,,ENST00000467636,;RN7SL80P,upstream_gene_variant,,ENST00000580631,;SAP18,non_coding_transcript_exon_variant,,ENST00000471009,;	C	ENSG00000150459	ENST00000382533	Transcript	missense_variant	480	441	147	Q/H	caG/caC	.	.	.	1	SAP18	HGNC	10530	protein_coding	YES	CCDS9295.2	ENSP00000371973	.	U3KPY7_HUMAN	UPI000187B6C9	.	deleterious(0.03)	probably_damaging(0.977)	4/4	.	hmmpanther:PTHR13082:SF1,hmmpanther:PTHR13082,Pfam_domain:PF06487,PIRSF_domain:PIRSF037637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCAGATAGG	.	5	ESCA
KBTBD7	0	.	GRCh37	13	41766370	41766370	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2024G>A	p.Arg675Gln	p.R675Q	ENST00000379483	1/1	42	37	4	64	64	0	KBTBD7,missense_variant,p.Arg675Gln,ENST00000379483,;	T	ENSG00000120696	ENST00000379483	Transcript	missense_variant	2333	2024	675	R/Q	cGa/cAa	.	.	.	-1	KBTBD7	HGNC	25266	protein_coding	YES	CCDS9377.1	ENSP00000368797	KBTB7_HUMAN	B4DS80_HUMAN	UPI0000071F8F	.	tolerated_low_confidence(0.56)	benign(0.001)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTCGCTGA	.	4	ESCA
BTBD6	0	.	GRCh37	14	105716550	105716550	+	Silent	SNP	C	C	T	rs371770383	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.999C>T	p.%3D	p.L333L	ENST00000392554	4/4	25	15	9	24	24	0	BTBD6,synonymous_variant,p.%3D,ENST00000536364,;BTBD6,synonymous_variant,p.%3D,ENST00000392554,;BTBD6,synonymous_variant,p.%3D,ENST00000537513,;BTBD6,synonymous_variant,p.%3D,ENST00000327471,;BTBD6,synonymous_variant,p.%3D,ENST00000463376,;BRF1,intron_variant,,ENST00000379937,;BRF1,intron_variant,,ENST00000546417,;BRF1,intron_variant,,ENST00000546474,;BRF1,intron_variant,,ENST00000327359,;BRF1,intron_variant,,ENST00000440513,;BRF1,upstream_gene_variant,,ENST00000550208,;BRF1,upstream_gene_variant,,ENST00000550375,;BRF1,downstream_gene_variant,,ENST00000550692,;BRF1,upstream_gene_variant,,ENST00000552127,;BRF1,upstream_gene_variant,,ENST00000392557,;BRF1,upstream_gene_variant,,ENST00000446501,;BRF1,upstream_gene_variant,,ENST00000551787,;BRF1,upstream_gene_variant,,ENST00000379932,;BTBD6,non_coding_transcript_exon_variant,,ENST00000392553,;	T	ENSG00000184887	ENST00000392554	Transcript	synonymous_variant	1296	999	333	L	ctC/ctT	rs371770383	.	.	1	BTBD6	HGNC	19897	protein_coding	YES	CCDS10002.2	ENSP00000376337	BTBD6_HUMAN	F8VPC8_HUMAN	UPI00001FDD27	.	.	.	4/4	.	hmmpanther:PTHR24413:SF4,hmmpanther:PTHR24413	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCGCCCC	byFrequency|byCluster	5	ESCA
NRL	0	.	GRCh37	14	24583968	24583968	+	5'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-65G>C	.	.	ENST00000561028	1/3	51	48	3	59	59	0	NRL,5_prime_UTR_variant,,ENST00000561028,;DCAF11,5_prime_UTR_variant,,ENST00000559115,;NRL,5_prime_UTR_variant,,ENST00000558280,;DCAF11,5_prime_UTR_variant,,ENST00000559017,;DCAF11,upstream_gene_variant,,ENST00000396936,;DCAF11,upstream_gene_variant,,ENST00000559354,;DCAF11,upstream_gene_variant,,ENST00000560713,;DCAF11,upstream_gene_variant,,ENST00000559593,;DCAF11,upstream_gene_variant,,ENST00000558215,;DCAF11,upstream_gene_variant,,ENST00000560901,;DCAF11,upstream_gene_variant,,ENST00000559144,;DCAF11,upstream_gene_variant,,ENST00000561001,;DCAF11,upstream_gene_variant,,ENST00000560459,;DCAF11,upstream_gene_variant,,ENST00000559796,;DCAF11,upstream_gene_variant,,ENST00000396941,;DCAF11,upstream_gene_variant,,ENST00000561375,;DCAF11,upstream_gene_variant,,ENST00000561041,;DCAF11,upstream_gene_variant,,ENST00000558638,;PCK2,downstream_gene_variant,,ENST00000559171,;DCAF11,upstream_gene_variant,,ENST00000446197,;DCAF11,upstream_gene_variant,,ENST00000559288,;DCAF11,upstream_gene_variant,,ENST00000559382,;DCAF11,upstream_gene_variant,,ENST00000558408,;DCAF11,upstream_gene_variant,,ENST00000559396,;DCAF11,upstream_gene_variant,,ENST00000557810,;DCAF11,non_coding_transcript_exon_variant,,ENST00000561056,;DCAF11,upstream_gene_variant,,ENST00000557809,;DCAF11,upstream_gene_variant,,ENST00000560171,;DCAF11,upstream_gene_variant,,ENST00000561016,;DCAF11,upstream_gene_variant,,ENST00000557952,;DCAF11,upstream_gene_variant,,ENST00000558624,;DCAF11,upstream_gene_variant,,ENST00000558706,;DCAF11,upstream_gene_variant,,ENST00000560046,;DCAF11,upstream_gene_variant,,ENST00000326009,;DCAF11,upstream_gene_variant,,ENST00000559451,;DCAF11,upstream_gene_variant,,ENST00000560457,;DCAF11,upstream_gene_variant,,ENST00000557888,;DCAF11,upstream_gene_variant,,ENST00000558914,;DCAF11,upstream_gene_variant,,ENST00000560614,;DCAF11,upstream_gene_variant,,ENST00000557802,;	G	ENSG00000129535	ENST00000561028	Transcript	5_prime_UTR_variant	256	.	.	.	.	.	.	.	-1	NRL	HGNC	8002	protein_coding	YES	CCDS9608.1	ENSP00000454062	NRL_HUMAN	H0YNW2_HUMAN,A8MX14_HUMAN	UPI000000CC15	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGCCAAGGG	.	2	ESCA
NIN	0	.	GRCh37	14	51192707	51192707	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6156G>T	p.Arg2052Ser	p.R2052S	ENST00000382041	30/30	77	57	19	91	91	0	NIN,missense_variant,p.Arg2052Ser,ENST00000245441,;NIN,missense_variant,p.Arg2052Ser,ENST00000382041,;NIN,missense_variant,p.Arg1543Ser,ENST00000389869,;NIN,missense_variant,p.Arg1339Ser,ENST00000382043,;NIN,missense_variant,p.Arg2052Ser,ENST00000530997,;NIN,3_prime_UTR_variant,,ENST00000389868,;NIN,3_prime_UTR_variant,,ENST00000324330,;NIN,downstream_gene_variant,,ENST00000530853,;NIN,downstream_gene_variant,,ENST00000453196,;RP11-248J18.3,upstream_gene_variant,,ENST00000602615,;NIN,3_prime_UTR_variant,,ENST00000476352,;NIN,non_coding_transcript_exon_variant,,ENST00000555984,;NIN,downstream_gene_variant,,ENST00000485005,;	A	ENSG00000100503	ENST00000382041	Transcript	missense_variant	6347	6156	2052	R/S	agG/agT	.	.	.	-1	NIN	HGNC	14906	protein_coding	YES	CCDS32079.1	ENSP00000371472	NIN_HUMAN	H7C162_HUMAN,E9PJH9_HUMAN	UPI0000DBEF14	.	deleterious(0.04)	benign(0.008)	30/30	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAGCCTTTT	.	5	ESCA
LRRC9	0	.	GRCh37	14	60483421	60483421	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3230G>C	p.Arg1077Thr	p.R1077T	ENST00000445360	24/32	78	67	11	84	84	0	LRRC9,missense_variant,p.Arg1077Thr,ENST00000445360,;RP11-16B13.1,intron_variant,,ENST00000555432,;RP11-16B13.1,intron_variant,,ENST00000554123,;LRRC9,missense_variant,p.Arg1077Thr,ENST00000254271,;	C	ENSG00000131951	ENST00000445360	Transcript	missense_variant	3434	3230	1077	R/T	aGa/aCa	.	.	.	1	LRRC9	HGNC	19848	protein_coding	YES	.	ENSP00000454748	LRRC9_HUMAN	H3BUS4_HUMAN	UPI000173AA0B	.	deleterious(0)	benign(0.219)	24/32	.	Pfam_domain:PF14580	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTAGACTTA	.	4	ESCA
PPM1A	0	.	GRCh37	14	60712739	60712739	+	Missense_Mutation	SNP	G	G	A	rs756484147	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174G>A	p.Met58Ile	p.M58I	ENST00000325642	1/6	50	42	7	46	46	0	PPM1A,missense_variant,p.Met58Ile,ENST00000325642,;PPM1A,5_prime_UTR_variant,,ENST00000529574,;PPM1A,upstream_gene_variant,,ENST00000525399,;PPM1A,upstream_gene_variant,,ENST00000395076,;PPM1A,upstream_gene_variant,,ENST00000325658,;PPM1A,upstream_gene_variant,,ENST00000528241,;CTD-2184C24.2,intron_variant,,ENST00000529171,;CTD-2184C24.2,upstream_gene_variant,,ENST00000553269,;CTD-2184C24.2,upstream_gene_variant,,ENST00000553775,;CTD-2184C24.2,upstream_gene_variant,,ENST00000532515,;PPM1A,missense_variant,p.Met58Ile,ENST00000531143,;PPM1A,missense_variant,p.Met58Ile,ENST00000532036,;	A	ENSG00000100614	ENST00000325642	Transcript	missense_variant	270	174	58	M/I	atG/atA	rs756484147	.	.	1	PPM1A	HGNC	9275	protein_coding	YES	CCDS45120.1	ENSP00000327255	PPM1A_HUMAN	E9PL75_HUMAN,E9PKB5_HUMAN,E9PJN3_HUMAN	UPI0000E01530	.	deleterious_low_confidence(0.02)	benign(0)	1/6	.	hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATGTGTGA	byFrequency	4	ESCA
LINC00238	0	.	GRCh37	14	66954918	66954918	+	RNA	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.356G>A	.	.	ENST00000411796	3/11	35	27	8	46	46	0	LINC00238,non_coding_transcript_exon_variant,,ENST00000411796,;LINC00238,non_coding_transcript_exon_variant,,ENST00000432289,;LINC00238,non_coding_transcript_exon_variant,,ENST00000389594,;LINC00238,non_coding_transcript_exon_variant,,ENST00000450299,;LINC00238,non_coding_transcript_exon_variant,,ENST00000359454,;RP11-72M17.1,intron_variant,,ENST00000556361,;RP11-72M17.1,intron_variant,,ENST00000556874,;	A	ENSG00000196553	ENST00000411796	Transcript	non_coding_transcript_exon_variant	356	.	.	.	.	.	.	.	1	LINC00238	HGNC	20100	lincRNA	YES	.	.	.	.	.	.	.	.	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGTGAGGAA	.	5	ESCA
ADAM20	0	.	GRCh37	14	70989758	70989759	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1866dupT	p.Pro623SerfsTer16	p.P623Sfs*16	ENST00000256389	2/2	31	18	13	20	20	0	ADAM20,frameshift_variant,p.Pro623SerfsTer16,ENST00000256389,;RP11-486O13.4,intron_variant,,ENST00000556646,;	A	ENSG00000134007	ENST00000256389	Transcript	frameshift_variant	2111-2112	1866-1867	622-623	-/X	-/T	.	.	.	-1	ADAM20	HGNC	199	protein_coding	YES	CCDS32111.1	ENSP00000256389	ADA20_HUMAN	.	UPI0000183495	.	.	.	2/2	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF133,Pfam_domain:PF08516,SMART_domains:SM00608	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTGGGAATTA	.	2	ESCA
MAP3K9	0	.	GRCh37	14	71196964	71196964	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*133T>C	.	.	ENST00000555993	13/13	36	27	8	28	28	0	MAP3K9,3_prime_UTR_variant,,ENST00000553414,;MAP3K9,3_prime_UTR_variant,,ENST00000554146,;MAP3K9,3_prime_UTR_variant,,ENST00000381250,;MAP3K9,3_prime_UTR_variant,,ENST00000555993,;MAP3K9,3_prime_UTR_variant,,ENST00000554752,;	G	ENSG00000006432	ENST00000555993	Transcript	3_prime_UTR_variant	3853	.	.	.	.	.	.	.	-1	MAP3K9	HGNC	6861	protein_coding	YES	CCDS32112.1	ENSP00000451263	M3K9_HUMAN	Q8NEB1_HUMAN,B4DSG3_HUMAN,B4DGF4_HUMAN,B3KRI5_HUMAN	UPI00001D7B5C	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCCATCTTC	.	5	ESCA
PSMC1	0	.	GRCh37	14	90725515	90725515	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15G>C	p.Gln5His	p.Q5H	ENST00000261303	2/11	62	57	4	55	55	0	PSMC1,missense_variant,p.Gln5His,ENST00000261303,;PSMC1,5_prime_UTR_variant,,ENST00000543772,;PSMC1,intron_variant,,ENST00000553835,;PSMC1,non_coding_transcript_exon_variant,,ENST00000555679,;PSMC1,non_coding_transcript_exon_variant,,ENST00000554624,;PSMC1,non_coding_transcript_exon_variant,,ENST00000557357,;	C	ENSG00000100764	ENST00000261303	Transcript	missense_variant	118	15	5	Q/H	caG/caC	.	.	.	1	PSMC1	HGNC	9547	protein_coding	YES	CCDS32139.1	ENSP00000261303	PRS4_HUMAN	Q53XL8_HUMAN,G3V4X1_HUMAN,B4DR63_HUMAN	UPI00000041A5	.	tolerated_low_confidence(0.2)	possibly_damaging(0.781)	2/11	.	hmmpanther:PTHR23073:SF9,hmmpanther:PTHR23073	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTCAGAGTGG	.	2	ESCA
MAP1A	0	.	GRCh37	15	43819502	43819502	+	Missense_Mutation	SNP	C	C	A	rs772633603	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5831C>A	p.Thr1944Lys	p.T1944K	ENST00000300231	4/6	36	32	4	50	50	0	MAP1A,missense_variant,p.Thr1944Lys,ENST00000399453,;MAP1A,missense_variant,p.Thr1944Lys,ENST00000300231,;MAP1A,missense_variant,p.Thr2182Lys,ENST00000382031,;	A	ENSG00000166963	ENST00000300231	Transcript	missense_variant	6281	5831	1944	T/K	aCg/aAg	rs772633603	.	.	1	MAP1A	HGNC	6835	protein_coding	YES	CCDS42031.1	ENSP00000300231	MAP1A_HUMAN	.	UPI000013E63C	.	.	benign(0)	4/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13843:SF6,hmmpanther:PTHR13843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CACCACGGAGC	.	3	ESCA
PAQR5	0	.	GRCh37	15	69677148	69677148	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312C>T	p.%3D	p.F104F	ENST00000340965	5/9	64	55	8	36	36	0	PAQR5,synonymous_variant,p.%3D,ENST00000340965,;PAQR5,synonymous_variant,p.%3D,ENST00000558684,;PAQR5,synonymous_variant,p.%3D,ENST00000561153,;PAQR5,synonymous_variant,p.%3D,ENST00000395407,;PAQR5,non_coding_transcript_exon_variant,,ENST00000561027,;PAQR5,downstream_gene_variant,,ENST00000561250,;	T	ENSG00000137819	ENST00000340965	Transcript	synonymous_variant	980	312	104	F	ttC/ttT	.	.	.	1	PAQR5	HGNC	29645	protein_coding	YES	CCDS10232.1	ENSP00000343877	MPRG_HUMAN	H0YL06_HUMAN	UPI000013D0D0	.	.	.	5/9	.	hmmpanther:PTHR20855:SF38,hmmpanther:PTHR20855,Pfam_domain:PF03006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTTCAGCTC	.	4	ESCA
CSK	0	.	GRCh37	15	75090969	75090969	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29C>A	p.Ser10Tyr	p.S10Y	ENST00000220003	3/13	63	55	8	90	90	0	CSK,missense_variant,p.Ser10Tyr,ENST00000439220,;CSK,missense_variant,p.Ser10Tyr,ENST00000220003,;CSK,missense_variant,p.Ser10Tyr,ENST00000569915,;CSK,missense_variant,p.Ser10Tyr,ENST00000567571,;CSK,missense_variant,p.Ser10Tyr,ENST00000309470,;CSK,missense_variant,p.Ser10Tyr,ENST00000569462,;CSK,5_prime_UTR_variant,,ENST00000567123,;CSK,non_coding_transcript_exon_variant,,ENST00000562066,;CSK,non_coding_transcript_exon_variant,,ENST00000563894,;CSK,upstream_gene_variant,,ENST00000567135,;CSK,upstream_gene_variant,,ENST00000568329,;CSK,upstream_gene_variant,,ENST00000566464,;CSK,upstream_gene_variant,,ENST00000569321,;CSK,upstream_gene_variant,,ENST00000564216,;CSK,upstream_gene_variant,,ENST00000563010,;	A	ENSG00000103653	ENST00000220003	Transcript	missense_variant	758	29	10	S/Y	tCc/tAc	.	.	.	1	CSK	HGNC	2444	protein_coding	YES	CCDS10269.1	ENSP00000220003	CSK_HUMAN	Q53EL3_HUMAN,H3BUM9_HUMAN,H3BU69_HUMAN,H3BN15_HUMAN,B4DMZ0_HUMAN,B2R6Q4_HUMAN	UPI0000128541	.	deleterious(0)	possibly_damaging(0.483)	3/13	.	Gene3D:2.30.30.40,hmmpanther:PTHR24418:SF52,hmmpanther:PTHR24418,PROSITE_profiles:PS50002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCATCCGGTA	.	4	ESCA
RCN2	0	.	GRCh37	15	77242113	77242113	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*550G>C	.	.	ENST00000394885	7/7	118	111	7	147	147	0	RCN2,3_prime_UTR_variant,,ENST00000320963,;RCN2,3_prime_UTR_variant,,ENST00000394885,;RCN2,3_prime_UTR_variant,,ENST00000394883,;RCN2,downstream_gene_variant,,ENST00000557805,;RCN2,downstream_gene_variant,,ENST00000558598,;RCN2,downstream_gene_variant,,ENST00000560833,;	C	ENSG00000117906	ENST00000394885	Transcript	3_prime_UTR_variant	1727	.	.	.	.	.	.	.	1	RCN2	HGNC	9935	protein_coding	YES	CCDS10291.1	ENSP00000378349	RCN2_HUMAN	.	UPI0000000C65	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATAGAACTT	.	2	ESCA
RCN2	0	.	GRCh37	15	77242231	77242231	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*668G>A	.	.	ENST00000394885	7/7	42	38	4	73	73	0	RCN2,3_prime_UTR_variant,,ENST00000394885,;RCN2,downstream_gene_variant,,ENST00000320963,;RCN2,downstream_gene_variant,,ENST00000394883,;RCN2,downstream_gene_variant,,ENST00000557805,;RCN2,downstream_gene_variant,,ENST00000558598,;RCN2,downstream_gene_variant,,ENST00000560833,;	A	ENSG00000117906	ENST00000394885	Transcript	3_prime_UTR_variant	1845	.	.	.	.	.	.	.	1	RCN2	HGNC	9935	protein_coding	YES	CCDS10291.1	ENSP00000378349	RCN2_HUMAN	.	UPI0000000C65	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AAAATGAAATG	.	2	ESCA
FANCI	0	.	GRCh37	15	89859688	89859688	+	Nonstop_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3985T>C	p.Ter1329GlnextTer6	p.*1329Qext*6	ENST00000310775	38/38	42	34	7	52	52	0	FANCI,stop_lost,p.Ter1329GlnextTer6,ENST00000310775,;FANCI,stop_lost,p.Ter1269GlnextTer6,ENST00000300027,;POLG,3_prime_UTR_variant,,ENST00000268124,;POLG,3_prime_UTR_variant,,ENST00000442287,;FANCI,downstream_gene_variant,,ENST00000561894,;FANCI,downstream_gene_variant,,ENST00000566615,;FANCI,downstream_gene_variant,,ENST00000565522,;FANCI,3_prime_UTR_variant,,ENST00000447611,;POLG,3_prime_UTR_variant,,ENST00000530292,;FANCI,non_coding_transcript_exon_variant,,ENST00000566895,;POLG,downstream_gene_variant,,ENST00000526671,;POLG,downstream_gene_variant,,ENST00000528881,;POLG,downstream_gene_variant,,ENST00000530715,;	C	ENSG00000140525	ENST00000310775	Transcript	stop_lost	4071	3985	1329	*/Q	Taa/Caa	.	.	.	1	FANCI	HGNC	25568	protein_coding	YES	CCDS45346.1	ENSP00000310842	FANCI_HUMAN	H3BT54_HUMAN,H3BS60_HUMAN,H3BQE2_HUMAN	UPI00001FEB1D	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAATAAATG	.	5	ESCA
NDUFAB1	0	.	GRCh37	16	23592379	23592380	+	3'Flank	INS	-	-	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000570319	.	81	72	9	79	79	0	NDUFAB1,3_prime_UTR_variant,,ENST00000007516,;NDUFAB1,3_prime_UTR_variant,,ENST00000562133,;NDUFAB1,downstream_gene_variant,,ENST00000570319,;NDUFAB1,downstream_gene_variant,,ENST00000567761,;NDUFAB1,3_prime_UTR_variant,,ENST00000484769,;	A	ENSG00000004779	ENST00000570319	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	812	-1	NDUFAB1	HGNC	7694	protein_coding	YES	CCDS10614.1	ENSP00000458770	ACPM_HUMAN	I3L505_HUMAN,A4UCS3_HUMAN,A4UCS2_HUMAN	UPI0000125321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAATTTAAATA	.	3	ESCA
DOC2A	0	.	GRCh37	16	30017262	30017262	+	3'UTR	SNP	C	C	T	rs746025351	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*245G>A	.	.	ENST00000350119	11/11	39	25	14	42	42	0	DOC2A,3_prime_UTR_variant,,ENST00000564979,;DOC2A,3_prime_UTR_variant,,ENST00000350119,;DOC2A,3_prime_UTR_variant,,ENST00000564944,;DOC2A,3_prime_UTR_variant,,ENST00000564357,;DOC2A,downstream_gene_variant,,ENST00000563125,;INO80E,downstream_gene_variant,,ENST00000562291,;INO80E,downstream_gene_variant,,ENST00000563197,;INO80E,downstream_gene_variant,,ENST00000567254,;INO80E,downstream_gene_variant,,ENST00000304516,;INO80E,downstream_gene_variant,,ENST00000567705,;DOC2A,downstream_gene_variant,,ENST00000565273,;DOC2A,downstream_gene_variant,,ENST00000563378,;DOC2A,downstream_gene_variant,,ENST00000567332,;DOC2A,downstream_gene_variant,,ENST00000574405,;DOC2A,downstream_gene_variant,,ENST00000570194,;DOC2A,non_coding_transcript_exon_variant,,ENST00000564233,;DOC2A,downstream_gene_variant,,ENST00000566456,;INO80E,downstream_gene_variant,,ENST00000567987,;DOC2A,downstream_gene_variant,,ENST00000561671,;INO80E,downstream_gene_variant,,ENST00000569957,;INO80E,downstream_gene_variant,,ENST00000540562,;INO80E,downstream_gene_variant,,ENST00000567065,;INO80E,downstream_gene_variant,,ENST00000562441,;DOC2A,downstream_gene_variant,,ENST00000566310,;	T	ENSG00000149927	ENST00000350119	Transcript	3_prime_UTR_variant	1639	.	.	.	.	rs746025351	.	.	-1	DOC2A	HGNC	2985	protein_coding	YES	CCDS10666.1	ENSP00000340017	DOC2A_HUMAN	H3BU41_HUMAN,H3BSH4_HUMAN,H3BNF7_HUMAN	UPI000013DBC8	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCCGGGTG	.	5	ESCA
UBN1	0	.	GRCh37	16	4921228	4921228	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1632T>A	p.%3D	p.A544A	ENST00000396658	11/17	75	68	7	60	60	0	UBN1,synonymous_variant,p.%3D,ENST00000590769,;UBN1,synonymous_variant,p.%3D,ENST00000545171,;UBN1,synonymous_variant,p.%3D,ENST00000396658,;UBN1,synonymous_variant,p.%3D,ENST00000262376,;UBN1,intron_variant,,ENST00000586716,;UBN1,downstream_gene_variant,,ENST00000585857,;UBN1,upstream_gene_variant,,ENST00000589191,;UBN1,downstream_gene_variant,,ENST00000587027,;	A	ENSG00000118900	ENST00000396658	Transcript	synonymous_variant	2335	1632	544	A	gcT/gcA	.	.	.	1	UBN1	HGNC	12506	protein_coding	YES	CCDS10525.1	ENSP00000379894	UBN1_HUMAN	K7EQR1_HUMAN	UPI0000071469	.	.	.	11/17	.	hmmpanther:PTHR16426:SF14,hmmpanther:PTHR16426,Pfam_domain:PF14075	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGGCTTGGGA	.	3	ESCA
UBN1	0	.	GRCh37	16	4924401	4924401	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1990G>C	p.Asp664His	p.D664H	ENST00000396658	14/17	53	48	5	75	75	0	UBN1,missense_variant,p.Asp664His,ENST00000590769,;UBN1,missense_variant,p.Asp124His,ENST00000586716,;UBN1,missense_variant,p.Asp664His,ENST00000545171,;UBN1,missense_variant,p.Asp664His,ENST00000396658,;UBN1,missense_variant,p.Asp664His,ENST00000262376,;UBN1,downstream_gene_variant,,ENST00000585857,;UBN1,upstream_gene_variant,,ENST00000589191,;UBN1,upstream_gene_variant,,ENST00000586152,;	C	ENSG00000118900	ENST00000396658	Transcript	missense_variant	2693	1990	664	D/H	Gac/Cac	COSM3794878	.	.	1	UBN1	HGNC	12506	protein_coding	YES	CCDS10525.1	ENSP00000379894	UBN1_HUMAN	K7EQR1_HUMAN	UPI0000071469	.	deleterious(0)	possibly_damaging(0.866)	14/17	.	hmmpanther:PTHR16426:SF14,hmmpanther:PTHR16426	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGAAGACTTG	.	3	ESCA
VPS4A	0	.	GRCh37	16	69352763	69352763	+	Silent	SNP	C	C	T	rs759037249	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381C>T	p.%3D	p.N127N	ENST00000254950	5/11	56	44	11	57	57	0	VPS4A,synonymous_variant,p.%3D,ENST00000254950,;RP11-343C2.11,synonymous_variant,p.%3D,ENST00000570054,;COG8,downstream_gene_variant,,ENST00000562595,;VPS4A,upstream_gene_variant,,ENST00000564399,;COG8,downstream_gene_variant,,ENST00000564419,;VPS4A,upstream_gene_variant,,ENST00000562754,;VPS4A,upstream_gene_variant,,ENST00000566354,;	T	ENSG00000132612	ENST00000254950	Transcript	synonymous_variant	537	381	127	N	aaC/aaT	rs759037249	.	.	1	VPS4A	HGNC	13488	protein_coding	YES	CCDS45517.1	ENSP00000254950	VPS4A_HUMAN	Q9UF30_HUMAN	UPI000000DC7F	.	.	.	5/11	.	hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF82,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAACGACGT	byFrequency	5	ESCA
ATXN1L	0	.	GRCh37	16	71888328	71888328	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2615A>G	.	.	ENST00000427980	3/3	26	22	4	52	52	0	ATXN1L,3_prime_UTR_variant,,ENST00000427980,;IST1,intron_variant,,ENST00000568581,;ATXN1L,intron_variant,,ENST00000569119,;	G	ENSG00000224470	ENST00000427980	Transcript	3_prime_UTR_variant	4978	.	.	.	.	.	.	.	1	ATXN1L	HGNC	33279	protein_coding	YES	CCDS45523.1	ENSP00000415822	ATX1L_HUMAN	G1UI23_HUMAN	UPI0000198982	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATGCATATAT	.	4	ESCA
PRPF8	0	.	GRCh37	17	1554764	1554764	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6594G>T	p.Lys2198Asn	p.K2198N	ENST00000572621	40/42	55	45	10	57	57	0	PRPF8,missense_variant,p.Lys2198Asn,ENST00000572621,;PRPF8,missense_variant,p.Lys2198Asn,ENST00000304992,;RILP,upstream_gene_variant,,ENST00000301336,;PRPF8,upstream_gene_variant,,ENST00000571958,;RILP,upstream_gene_variant,,ENST00000574810,;PRPF8,downstream_gene_variant,,ENST00000575116,;PRPF8,non_coding_transcript_exon_variant,,ENST00000572723,;RILP,upstream_gene_variant,,ENST00000570858,;RILP,upstream_gene_variant,,ENST00000573398,;PRPF8,downstream_gene_variant,,ENST00000576585,;	A	ENSG00000174231	ENST00000572621	Transcript	missense_variant	6860	6594	2198	K/N	aaG/aaT	.	.	.	-1	PRPF8	HGNC	17340	protein_coding	YES	CCDS11010.1	ENSP00000460348	PRP8_HUMAN	.	UPI000006F2DD	.	tolerated(0.08)	benign(0.016)	40/42	.	hmmpanther:PTHR11140:SF0,hmmpanther:PTHR11140,Pfam_domain:PF01398,SMART_domains:SM00232	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATCTTGGC	.	5	ESCA
NOS2	0	.	GRCh37	17	26087701	26087701	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2958C>G	p.Ile986Met	p.I986M	ENST00000313735	24/27	164	141	23	195	195	0	NOS2,missense_variant,p.Ile986Met,ENST00000313735,;	C	ENSG00000007171	ENST00000313735	Transcript	missense_variant	3192	2958	986	I/M	atC/atG	.	.	.	-1	NOS2	HGNC	7873	protein_coding	YES	CCDS11223.1	ENSP00000327251	NOS2_HUMAN	Q9UM94_HUMAN	UPI000011D645	.	deleterious(0)	probably_damaging(1)	24/27	.	hmmpanther:PTHR19384:SF56,hmmpanther:PTHR19384,Gene3D:3.40.50.80,Pfam_domain:PF00175,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF52343,Prints_domain:PR00371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCGCGATGCC	.	4	ESCA
TLCD1	0	.	GRCh37	17	27051820	27051820	+	Missense_Mutation	SNP	A	A	T	rs772481817	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452T>A	p.Leu151His	p.L151H	ENST00000292090	4/4	37	26	11	56	56	0	TLCD1,missense_variant,p.Leu104His,ENST00000394933,;TLCD1,missense_variant,p.Leu17His,ENST00000581236,;TLCD1,missense_variant,p.Leu151His,ENST00000292090,;TLCD1,missense_variant,p.Leu80His,ENST00000580518,;RPL23A,downstream_gene_variant,,ENST00000472628,;RPL23A,downstream_gene_variant,,ENST00000394938,;NEK8,upstream_gene_variant,,ENST00000268766,;NEK8,upstream_gene_variant,,ENST00000579060,;RPL23A,downstream_gene_variant,,ENST00000394935,;RPL23A,downstream_gene_variant,,ENST00000422514,;RPL23A,downstream_gene_variant,,ENST00000578181,;RPL23A,downstream_gene_variant,,ENST00000355731,;NEK8,upstream_gene_variant,,ENST00000579671,;RPL23A,downstream_gene_variant,,ENST00000496182,;SNORD42A,downstream_gene_variant,,ENST00000459584,;SNORD4B,downstream_gene_variant,,ENST00000459083,;SNORD4A,downstream_gene_variant,,ENST00000459174,;SNORD42B,downstream_gene_variant,,ENST00000458893,;AC010761.14,upstream_gene_variant,,ENST00000587898,;AC010761.8,upstream_gene_variant,,ENST00000582718,;NEK8,upstream_gene_variant,,ENST00000593261,;RPL23A,downstream_gene_variant,,ENST00000582736,;NEK8,upstream_gene_variant,,ENST00000581000,;RPL23A,downstream_gene_variant,,ENST00000580755,;NEK8,upstream_gene_variant,,ENST00000543014,;NEK8,upstream_gene_variant,,ENST00000584342,;	T	ENSG00000160606	ENST00000292090	Transcript	missense_variant	563	452	151	L/H	cTc/cAc	rs772481817	.	.	-1	TLCD1	HGNC	25177	protein_coding	YES	CCDS11242.1	ENSP00000292090	TLCD1_HUMAN	K7ELX5_HUMAN	UPI000006DF3D	.	deleterious(0)	probably_damaging(1)	4/4	.	SMART_domains:SM00724,Pfam_domain:PF03798,hmmpanther:PTHR13439:SF5,hmmpanther:PTHR13439,PROSITE_profiles:PS50922,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGAGGAAG	.	5	ESCA
CCL5	0	.	GRCh37	17	34199418	34199418	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239G>A	p.Trp80Ter	p.W80*	ENST00000293272	3/3	123	110	13	112	112	0	CCL5,stop_gained,p.Trp80Ter,ENST00000366113,;CCL5,stop_gained,p.Trp80Ter,ENST00000293272,;CCL5,missense_variant,p.Met103Ile,ENST00000463941,;C17orf66,upstream_gene_variant,,ENST00000311880,;C17orf66,upstream_gene_variant,,ENST00000587626,;C17orf66,upstream_gene_variant,,ENST00000592980,;AC015849.2,intron_variant,,ENST00000413928,;C17orf66,upstream_gene_variant,,ENST00000587585,;C17orf66,upstream_gene_variant,,ENST00000589015,;C17orf66,upstream_gene_variant,,ENST00000587573,;C17orf66,upstream_gene_variant,,ENST00000462028,;C17orf66,upstream_gene_variant,,ENST00000585840,;	T	ENSG00000161570	ENST00000293272	Transcript	stop_gained	442	239	80	W/*	tGg/tAg	.	.	.	-1	CCL5	HGNC	10632	protein_coding	YES	CCDS11300.1	ENSP00000293272	CCL5_HUMAN	D0EI67_HUMAN	UPI000004A187	.	.	.	3/3	.	hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF82,Gene3D:2.40.50.40,Pfam_domain:PF00048,SMART_domains:SM00199,Superfamily_domains:SSF54117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACCCATTTC	.	4	ESCA
CNP	0	.	GRCh37	17	40127302	40127303	+	3'UTR	DEL	CT	CT	-	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	CT	CT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1362_*1363delCT	.	.	ENST00000393892	4/4	29	25	4	28	28	0	CNP,3_prime_UTR_variant,,ENST00000393892,;CNP,downstream_gene_variant,,ENST00000393888,;CNP,downstream_gene_variant,,ENST00000472031,;DNAJC7,downstream_gene_variant,,ENST00000457167,;CNP,downstream_gene_variant,,ENST00000591072,;DNAJC7,downstream_gene_variant,,ENST00000587727,;DNAJC7,downstream_gene_variant,,ENST00000316603,;DNAJC7,downstream_gene_variant,,ENST00000426588,;CNP,downstream_gene_variant,,ENST00000592105,;CNP,downstream_gene_variant,,ENST00000486438,;DNAJC7,downstream_gene_variant,,ENST00000588814,;CNP,downstream_gene_variant,,ENST00000592861,;	-	ENSG00000173786	ENST00000393892	Transcript	3_prime_UTR_variant	2770-2771	.	.	.	.	.	.	.	1	CNP	HGNC	2158	protein_coding	YES	CCDS11414.2	ENSP00000377470	CN37_HUMAN	K7ERZ0_HUMAN,K7EN66_HUMAN,C9K0L8_HUMAN,B4DFN6_HUMAN	UPI0000127BEE	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TCTCCCCTCTGCT	.	2	ESCA
HDAC5	0	.	GRCh37	17	42160016	42160016	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2547A>T	p.%3D	p.V849V	ENST00000225983	20/27	62	32	29	51	51	0	HDAC5,synonymous_variant,p.%3D,ENST00000393622,;HDAC5,synonymous_variant,p.%3D,ENST00000225983,;HDAC5,synonymous_variant,p.%3D,ENST00000586802,;HDAC5,synonymous_variant,p.%3D,ENST00000336057,;HDAC5,non_coding_transcript_exon_variant,,ENST00000588419,;HDAC5,non_coding_transcript_exon_variant,,ENST00000593013,;HDAC5,non_coding_transcript_exon_variant,,ENST00000592385,;HDAC5,upstream_gene_variant,,ENST00000586339,;	A	ENSG00000108840	ENST00000225983	Transcript	synonymous_variant	2871	2547	849	V	gtA/gtT	.	.	.	-1	HDAC5	HGNC	14068	protein_coding	YES	CCDS32663.1	ENSP00000225983	HDAC5_HUMAN	K7EJZ7_HUMAN,K7EJL6_HUMAN	UPI0000508BBA	.	.	.	20/27	.	hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF57,Gene3D:3.40.800.20,Pfam_domain:PF00850,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768,Prints_domain:PR01270	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGCTACAGA	.	5	ESCA
ABCA6	0	.	GRCh37	17	67092434	67092434	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3355A>G	p.Ile1119Val	p.I1119V	ENST00000284425	25/39	131	75	55	172	172	0	ABCA6,missense_variant,p.Ile1119Val,ENST00000284425,;MIR4524B,upstream_gene_variant,,ENST00000581569,;ABCA6,non_coding_transcript_exon_variant,,ENST00000446604,;LOC100421166,upstream_gene_variant,,ENST00000586611,;	C	ENSG00000154262	ENST00000284425	Transcript	missense_variant	3530	3355	1119	I/V	Att/Gtt	.	.	.	-1	ABCA6	HGNC	36	protein_coding	YES	CCDS11683.1	ENSP00000284425	ABCA6_HUMAN	.	UPI000013DD9D	.	tolerated(0.23)	benign(0.026)	25/39	.	hmmpanther:PTHR19229:SF13,hmmpanther:PTHR19229,Pfam_domain:PF12698	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAATAAATG	.	5	ESCA
UNC13D	0	.	GRCh37	17	73824077	73824077	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3242C>T	p.Ala1081Val	p.A1081V	ENST00000207549	32/32	79	72	7	102	101	1	UNC13D,splice_donor_variant,,ENST00000412096,;UNC13D,missense_variant,p.Ala137Val,ENST00000589670,;UNC13D,missense_variant,p.Ala1081Val,ENST00000207549,;UNK,downstream_gene_variant,,ENST00000589666,;UNK,downstream_gene_variant,,ENST00000587258,;UNK,downstream_gene_variant,,ENST00000293218,;UNC13D,downstream_gene_variant,,ENST00000586930,;UNC13D,3_prime_UTR_variant,,ENST00000586519,;UNC13D,downstream_gene_variant,,ENST00000590856,;UNC13D,downstream_gene_variant,,ENST00000591563,;	A	ENSG00000092929	ENST00000207549	Transcript	missense_variant	3622	3242	1081	A/V	gCc/gTc	.	.	.	-1	UNC13D	HGNC	23147	protein_coding	YES	CCDS11730.1	ENSP00000207549	UN13D_HUMAN	K7EIH3_HUMAN	UPI000015FC91	.	deleterious_low_confidence(0.01)	possibly_damaging(0.83)	32/32	.	hmmpanther:PTHR15015:SF20,hmmpanther:PTHR15015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGAGGCCTGC	.	2	ESCA
WBP2	0	.	GRCh37	17	73841877	73841877	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*938G>T	.	.	ENST00000591399	9/9	56	39	17	59	59	0	WBP2,3_prime_UTR_variant,,ENST00000590221,;WBP2,3_prime_UTR_variant,,ENST00000591399,;WBP2,3_prime_UTR_variant,,ENST00000254806,;WBP2,3_prime_UTR_variant,,ENST00000585462,;WBP2,downstream_gene_variant,,ENST00000433525,;UNC13D,upstream_gene_variant,,ENST00000590762,;WBP2,downstream_gene_variant,,ENST00000589642,;UNC13D,upstream_gene_variant,,ENST00000412096,;WBP2,downstream_gene_variant,,ENST00000586257,;WBP2,downstream_gene_variant,,ENST00000587374,;UNC13D,upstream_gene_variant,,ENST00000592386,;UNC13D,upstream_gene_variant,,ENST00000586147,;UNC13D,upstream_gene_variant,,ENST00000586108,;WBP2,downstream_gene_variant,,ENST00000593002,;WBP2,downstream_gene_variant,,ENST00000344296,;UNC13D,upstream_gene_variant,,ENST00000207549,;UNC13D,upstream_gene_variant,,ENST00000585574,;UNC13D,upstream_gene_variant,,ENST00000587504,;WBP2,downstream_gene_variant,,ENST00000590450,;WBP2,3_prime_UTR_variant,,ENST00000591831,;WBP2,non_coding_transcript_exon_variant,,ENST00000587642,;WBP2,downstream_gene_variant,,ENST00000589241,;WBP2,downstream_gene_variant,,ENST00000589236,;WBP2,downstream_gene_variant,,ENST00000588373,;UNC13D,upstream_gene_variant,,ENST00000587495,;UNC13D,upstream_gene_variant,,ENST00000588774,;WBP2,downstream_gene_variant,,ENST00000589834,;WBP2,downstream_gene_variant,,ENST00000416574,;UNC13D,upstream_gene_variant,,ENST00000591563,;	A	ENSG00000132471	ENST00000591399	Transcript	3_prime_UTR_variant	2149	.	.	.	.	.	.	.	-1	WBP2	HGNC	12738	protein_coding	YES	CCDS11731.1	ENSP00000467579	WBP2_HUMAN	K7ESN4_HUMAN,K7EIJ0_HUMAN,A6NG10_HUMAN	UPI0000138EBB	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGTCAAATA	.	5	ESCA
TP53	0	.	GRCh37	17	7574000	7574000	+	Nonsense_Mutation	SNP	C	C	A	rs375573770	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	10/11	34	18	16	27	27	0	TP53,stop_gained,p.Glu343Ter,ENST00000269305,;TP53,stop_gained,p.Glu343Ter,ENST00000445888,;TP53,3_prime_UTR_variant,,ENST00000420246,;TP53,3_prime_UTR_variant,,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000359597,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	1217	1027	343	E/*	Gag/Tag	rs375573770,CM103214,TP53_g.16918G>T,COSM11078,COSM308326	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	10/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF07710,Gene3D:1olgA00,Superfamily_domains:SSF47719,Prints_domain:PR00386	.	.	.	.	.	.	.	G:0.0002	G:0	.	0,0,0,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E343*|c.1027G>T|8,SITE|p.E343*|c.1027G>T|5,CODON|p.0?|c.1_1182del1182|6,BUFFER|p.E346*|c.1036G>T|3,BUFFER|p.R342P|c.1025G>C|4,BUFFER|p.R342P|c.1025G>C|7,BUFFER|p.R342fs*3|c.1024delC|3,BUFFER|p.R342fs*3|c.1024delC|3,BUFFER|p.R342fs*3|c.1023delC|3,BUFFER|p.R342*|c.1024C>T|49,BUFFER|p.R342*|c.1024C>T|97	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCTCGGA	.	5	ESCA
ZNF750	0	.	GRCh37	17	80789439	80789439	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.892delT	p.Ser298LeufsTer68	p.S298Lfs*68	ENST00000269394	2/3	93	73	20	75	75	0	ZNF750,frameshift_variant,p.Ser298LeufsTer68,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	-	ENSG00000141579	ENST00000269394	Transcript	frameshift_variant	1726	892	298	S/X	Tct/ct	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTGGAGATGGAG	.	3	ESCA
MEP1B	0	.	GRCh37	18	29797884	29797884	+	Missense_Mutation	SNP	C	C	G	rs184031989	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2047C>G	p.Arg683Gly	p.R683G	ENST00000269202	14/15	55	51	4	70	70	0	MEP1B,missense_variant,p.Arg683Gly,ENST00000269202,;MEP1B,missense_variant,p.Arg683Gly,ENST00000581447,;GAREM,intron_variant,,ENST00000583696,;	G	ENSG00000141434	ENST00000269202	Transcript	missense_variant	2094	2047	683	R/G	Cgt/Ggt	rs184031989	.	.	1	MEP1B	HGNC	7020	protein_coding	YES	CCDS45846.1	ENSP00000269202	MEP1B_HUMAN	J3KRK1_HUMAN	UPI0000201B8B	.	deleterious(0.01)	benign(0.01)	14/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATATCGTGAA	byFrequency|by1000G	2	ESCA
SEC11C	0	.	GRCh37	18	56819910	56819910	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340C>T	p.His114Tyr	p.H114Y	ENST00000587834	3/6	68	64	4	73	73	0	SEC11C,missense_variant,p.His114Tyr,ENST00000587834,;SEC11C,missense_variant,p.His114Tyr,ENST00000588875,;SEC11C,downstream_gene_variant,,ENST00000592774,;SEC11C,downstream_gene_variant,,ENST00000593132,;SEC11C,non_coding_transcript_exon_variant,,ENST00000585864,;SEC11C,non_coding_transcript_exon_variant,,ENST00000509791,;SEC11C,intron_variant,,ENST00000299714,;SEC11C,upstream_gene_variant,,ENST00000591406,;	T	ENSG00000166562	ENST00000587834	Transcript	missense_variant	812	340	114	H/Y	Cat/Tat	COSM3526821	.	.	1	SEC11C	HGNC	23400	protein_coding	YES	CCDS11970.1	ENSP00000468633	SC11C_HUMAN	B4DI03_HUMAN	UPI0000000DC8	.	deleterious(0.04)	benign(0.33)	3/6	.	hmmpanther:PTHR10806,hmmpanther:PTHR10806:SF3,Pfam_domain:PF00717,Gene3D:2.10.109.10,TIGRFAM_domain:TIGR02228,Superfamily_domains:SSF51306	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTTCATGAA	.	2	ESCA
DSEL	0	.	GRCh37	18	65180960	65180960	+	Missense_Mutation	SNP	G	G	A	rs778536579	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916C>T	p.Arg306Cys	p.R306C	ENST00000310045	2/2	78	59	18	60	60	0	DSEL,missense_variant,p.Arg306Cys,ENST00000310045,;RP11-638L3.1,upstream_gene_variant,,ENST00000583687,;CTD-2541J13.2,non_coding_transcript_exon_variant,,ENST00000583493,;CTD-2541J13.2,downstream_gene_variant,,ENST00000581951,;	A	ENSG00000171451	ENST00000310045	Transcript	missense_variant	2390	916	306	R/C	Cgc/Tgc	rs778536579,COSM1389560	.	.	-1	DSEL	HGNC	18144	protein_coding	YES	CCDS11995.1	ENSP00000310565	DSEL_HUMAN	.	UPI00000740A1	.	deleterious(0)	probably_damaging(0.999)	2/2	.	hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF2	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGCGCTGGG	.	5	ESCA
ZNF799	0	.	GRCh37	19	12501412	12501412	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1800C>G	p.%3D	p.L600L	ENST00000430385	4/4	106	100	6	108	108	0	ZNF799,synonymous_variant,p.%3D,ENST00000419318,;ZNF799,synonymous_variant,p.%3D,ENST00000430385,;CTD-3105H18.16,downstream_gene_variant,,ENST00000595562,;ZNF799,downstream_gene_variant,,ENST00000595766,;ZNF799,non_coding_transcript_exon_variant,,ENST00000460935,;CTD-3105H18.14,intron_variant,,ENST00000435033,;	C	ENSG00000196466	ENST00000430385	Transcript	synonymous_variant	2001	1800	600	L	ctC/ctG	.	.	.	-1	ZNF799	HGNC	28071	protein_coding	YES	CCDS45989.1	ENSP00000411084	ZN799_HUMAN	M0R135_HUMAN,D3YTF2_HUMAN	UPI000016184E	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24379:SF16,hmmpanther:PTHR24379,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAACTGAGAGA	.	2	ESCA
ZNF791	0	.	GRCh37	19	12738587	12738587	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244G>T	p.Glu82Ter	p.E82*	ENST00000343325	4/4	100	88	12	78	78	0	ZNF791,stop_gained,p.Glu82Ter,ENST00000343325,;ZNF791,stop_gained,p.Glu50Ter,ENST00000458122,;ZNF791,missense_variant,p.Gln61His,ENST00000446165,;ZNF791,5_prime_UTR_variant,,ENST00000600752,;ZNF791,5_prime_UTR_variant,,ENST00000540038,;AC010422.1,upstream_gene_variant,,ENST00000408416,;ZNF490,intron_variant,,ENST00000465656,;ZNF791,3_prime_UTR_variant,,ENST00000597691,;ZNF791,3_prime_UTR_variant,,ENST00000598225,;	T	ENSG00000173875	ENST00000343325	Transcript	stop_gained	406	244	82	E/*	Gaa/Taa	.	.	.	1	ZNF791	HGNC	26895	protein_coding	YES	CCDS12273.1	ENSP00000342974	ZN791_HUMAN	M0R0E8_HUMAN,F5GXD7_HUMAN,B7Z586_HUMAN	UPI0000203455	.	.	.	4/4	.	hmmpanther:PTHR24379,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGCAGAAAAC	.	4	ESCA
CASP14	0	.	GRCh37	19	15164553	15164553	+	Missense_Mutation	SNP	G	G	C	rs575021361	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.187G>C	p.Glu63Gln	p.E63Q	ENST00000427043	4/7	64	44	20	60	60	0	CASP14,missense_variant,p.Glu63Gln,ENST00000427043,;CASP14,missense_variant,p.Glu63Gln,ENST00000221740,;AC004699.1,downstream_gene_variant,,ENST00000411269,;CASP14,upstream_gene_variant,,ENST00000598738,;	C	ENSG00000105141	ENST00000427043	Transcript	missense_variant	495	187	63	E/Q	Gaa/Caa	rs575021361	.	.	1	CASP14	HGNC	1502	protein_coding	YES	CCDS12323.1	ENSP00000393417	CASPE_HUMAN	B2CIS9_HUMAN	UPI0000044176	.	deleterious(0.01)	probably_damaging(0.938)	4/7	.	Low_complexity_(Seg):seg,Superfamily_domains:SSF52129,SMART_domains:SM00115,Gene3D:3.40.50.1460,Pfam_domain:PF00656,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF131,PROSITE_profiles:PS50208	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGGAAGAG	by1000G	5	ESCA
ZNF737	0	.	GRCh37	19	20728406	20728406	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.603C>G	p.Phe201Leu	p.F201L	ENST00000427401	4/4	64	59	5	80	80	0	ZNF737,missense_variant,p.Phe137Leu,ENST00000594419,;ZNF737,missense_variant,p.Phe201Leu,ENST00000427401,;ZNF737,upstream_gene_variant,,ENST00000596530,;ZNF737,downstream_gene_variant,,ENST00000597940,;	C	ENSG00000237440	ENST00000427401	Transcript	missense_variant	698	603	201	F/L	ttC/ttG	.	.	.	-1	ZNF737	HGNC	32468	protein_coding	YES	CCDS54238.1	ENSP00000395733	ZN737_HUMAN	M0R1D1_HUMAN	UPI0000198506	.	deleterious(0)	benign(0.156)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF93,hmmpanther:PTHR24384,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTTGAAGGG	.	2	ESCA
ZNF556	0	.	GRCh37	19	2878078	2878078	+	Silent	SNP	G	G	A	rs371373885	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1122G>A	p.%3D	p.T374T	ENST00000307635	4/4	58	53	5	62	62	0	ZNF556,synonymous_variant,p.%3D,ENST00000586426,;ZNF556,synonymous_variant,p.%3D,ENST00000307635,;ZNF556,downstream_gene_variant,,ENST00000586470,;AC006130.4,upstream_gene_variant,,ENST00000586202,;	A	ENSG00000172000	ENST00000307635	Transcript	synonymous_variant	1209	1122	374	T	acG/acA	rs371373885,COSM994321	.	.	1	ZNF556	HGNC	25669	protein_coding	YES	CCDS12097.1	ENSP00000302603	ZN556_HUMAN	.	UPI000006DA0F	.	.	.	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF142,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAAACGTGTGG	byFrequency|byCluster	3	ESCA
NPHS1	0	.	GRCh37	19	36333075	36333075	+	Missense_Mutation	SNP	C	C	T	rs769019215	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2614G>A	p.Val872Ile	p.V872I	ENST00000378910	19/29	38	27	10	51	51	0	NPHS1,missense_variant,p.Val872Ile,ENST00000378910,;NPHS1,missense_variant,p.Val872Ile,ENST00000353632,;NPHS1,downstream_gene_variant,,ENST00000585400,;	T	ENSG00000161270	ENST00000378910	Transcript	missense_variant	2614	2614	872	V/I	Gtt/Att	CD024189,rs769019215	.	.	-1	NPHS1	HGNC	7908	protein_coding	YES	CCDS32996.1	ENSP00000368190	NPHN_HUMAN	.	UPI000004EF61	.	tolerated(0.29)	benign(0.014)	19/29	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11640:SF31,hmmpanther:PTHR11640,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAACGATGT	.	5	ESCA
ZNF850	0	.	GRCh37	19	37241026	37241026	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916G>A	p.Glu306Lys	p.E306K	ENST00000591344	5/5	105	76	29	109	109	0	ZNF850,missense_variant,p.Glu306Lys,ENST00000591344,;ZNF850,intron_variant,,ENST00000589390,;	T	ENSG00000267041	ENST00000591344	Transcript	missense_variant	1075	916	306	E/K	Gag/Aag	.	.	.	-1	ZNF850	HGNC	27994	protein_coding	YES	CCDS59379.1	ENSP00000464976	ZN850_HUMAN	.	UPI00001D815D	.	deleterious(0.05)	benign(0.21)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24409:SF10,hmmpanther:PTHR24409,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCACCAG	.	5	ESCA
RYR1	0	.	GRCh37	19	39075637	39075637	+	Missense_Mutation	SNP	G	G	A	rs764602570	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14701G>A	p.Glu4901Lys	p.E4901K	ENST00000359596	102/106	85	77	7	65	65	0	RYR1,missense_variant,p.Glu4896Lys,ENST00000355481,;RYR1,missense_variant,p.Glu4901Lys,ENST00000359596,;RYR1,missense_variant,p.Glu4896Lys,ENST00000360985,;MAP4K1,downstream_gene_variant,,ENST00000396857,;MAP4K1,downstream_gene_variant,,ENST00000589130,;MAP4K1,downstream_gene_variant,,ENST00000591517,;MAP4K1,downstream_gene_variant,,ENST00000586296,;MAP4K1,downstream_gene_variant,,ENST00000591921,;MAP4K1,downstream_gene_variant,,ENST00000593196,;MAP4K1,downstream_gene_variant,,ENST00000591210,;	A	ENSG00000196218	ENST00000359596	Transcript	missense_variant	14701	14701	4901	E/K	Gag/Aag	rs764602570	.	.	1	RYR1	HGNC	10483	protein_coding	YES	CCDS33011.1	ENSP00000352608	RYR1_HUMAN	O75591_HUMAN,B4DET7_HUMAN	UPI0000D7E62F	.	.	unknown(0)	102/106	.	hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF00520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGACGAGATC	byFrequency	3	ESCA
LHB	0	.	GRCh37	19	49519433	49519433	+	Silent	SNP	G	G	C	rs770539036	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318C>G	p.%3D	p.L106L	ENST00000221421	3/3	96	88	7	108	108	0	LHB,synonymous_variant,p.%3D,ENST00000221421,;RUVBL2,downstream_gene_variant,,ENST00000595090,;RUVBL2,downstream_gene_variant,,ENST00000413176,;RUVBL2,downstream_gene_variant,,ENST00000601968,;CTB-60B18.10,downstream_gene_variant,,ENST00000600007,;RUVBL2,downstream_gene_variant,,ENST00000595002,;RUVBL2,downstream_gene_variant,,ENST00000596247,;RUVBL2,downstream_gene_variant,,ENST00000221413,;RUVBL2,downstream_gene_variant,,ENST00000594338,;	C	ENSG00000104826	ENST00000221421	Transcript	synonymous_variant	318	318	106	L	ctC/ctG	rs770539036	.	.	-1	LHB	HGNC	6584	protein_coding	YES	CCDS12748.1	ENSP00000221421	LSHB_HUMAN	Q8WXL0_HUMAN	UPI00000378AB	.	.	.	3/3	.	hmmpanther:PTHR11515,hmmpanther:PTHR11515:SF12,PROSITE_patterns:PS00689,Gene3D:2.10.90.10,Pfam_domain:PF00007,SMART_domains:SM00068,Superfamily_domains:SSF57501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAGCTGAGAGC	.	2	ESCA
MIR515-2	0	.	GRCh37	19	54188332	54188332	+	RNA	SNP	G	G	A	rs372763623	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.70G>A	.	.	ENST00000384883	1/1	75	61	14	83	83	0	MIR515-2,non_coding_transcript_exon_variant,,ENST00000384883,;MIR519C,upstream_gene_variant,,ENST00000385053,;MIR1283-1,upstream_gene_variant,,ENST00000408494,;MIR520F,downstream_gene_variant,,ENST00000384824,;	A	ENSG00000207615	ENST00000384883	Transcript	non_coding_transcript_exon_variant	70	.	.	.	.	rs372763623	.	.	1	MIR515-2	HGNC	32097	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCGTTACT	byFrequency|byCluster	5	ESCA
ZIK1	0	.	GRCh37	19	58099931	58099931	+	Missense_Mutation	SNP	G	G	A	rs767832787	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>A	p.Ala33Thr	p.A33T	ENST00000597850	3/4	91	63	27	102	102	0	ZIK1,missense_variant,p.Ala14Thr,ENST00000597219,;ZIK1,missense_variant,p.Ala20Thr,ENST00000536878,;ZIK1,missense_variant,p.Ala33Thr,ENST00000597850,;ZIK1,missense_variant,p.Ala14Thr,ENST00000600053,;ZIK1,5_prime_UTR_variant,,ENST00000599456,;ZIK1,intron_variant,,ENST00000598689,;ZIK1,intron_variant,,ENST00000307468,;ZIK1,non_coding_transcript_exon_variant,,ENST00000598726,;	A	ENSG00000171649	ENST00000597850	Transcript	missense_variant	312	97	33	A/T	Gcc/Acc	rs767832787,COSM1002341	.	.	1	ZIK1	HGNC	33104	protein_coding	YES	CCDS33135.1	ENSP00000472867	ZIK1_HUMAN	M0R1S7_HUMAN,M0QYQ8_HUMAN	UPI00001609B2	.	deleterious(0)	benign(0.158)	3/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24387:SF194,hmmpanther:PTHR24387,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCGCCATT	byFrequency	5	ESCA
MISP	0	.	GRCh37	19	757214	757214	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268G>A	p.Glu90Lys	p.E90K	ENST00000215582	2/5	107	97	10	92	92	0	MISP,missense_variant,p.Glu90Lys,ENST00000215582,;	A	ENSG00000099812	ENST00000215582	Transcript	missense_variant	371	268	90	E/K	Gag/Aag	.	.	.	1	MISP	HGNC	27000	protein_coding	YES	CCDS12042.1	ENSP00000215582	MISP_HUMAN	.	UPI00000745CD	.	tolerated(0.15)	possibly_damaging(0.801)	2/5	.	hmmpanther:PTHR18839:SF2,hmmpanther:PTHR18839	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGGATGAGGGT	.	3	ESCA
MUC16	0	.	GRCh37	19	9064268	9064268	+	Silent	SNP	C	C	T	rs762167753	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.23178G>A	p.%3D	p.A7726A	ENST00000397910	3/84	41	35	6	29	29	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;	T	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	23382	23178	7726	A	gcG/gcA	rs762167753	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	3/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTGTCGCCGG	byFrequency	4	ESCA
VCAM1	0	.	GRCh37	1	101186144	101186144	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177G>C	p.Trp59Cys	p.W59C	ENST00000294728	2/9	36	32	3	48	48	0	VCAM1,missense_variant,p.Trp59Cys,ENST00000347652,;VCAM1,missense_variant,p.Trp59Cys,ENST00000370115,;VCAM1,missense_variant,p.Trp59Cys,ENST00000294728,;VCAM1,intron_variant,,ENST00000370119,;	C	ENSG00000162692	ENST00000294728	Transcript	missense_variant	278	177	59	W/C	tgG/tgC	.	.	.	1	VCAM1	HGNC	12663	protein_coding	YES	CCDS773.1	ENSP00000294728	VCAM1_HUMAN	Q68DC4_HUMAN,G0ZI12_HUMAN,G0ZFQ0_HUMAN,F8UV74_HUMAN,F8UU18_HUMAN,F2YYR6_HUMAN	UPI0000000E06	.	deleterious(0)	probably_damaging(1)	2/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTGGAGAAC	.	4	ESCA
MOV10	0	.	GRCh37	1	113235484	113235484	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000413052	7/21	32	25	6	31	31	0	MOV10,missense_variant,p.Tyr302Cys,ENST00000369644,;MOV10,missense_variant,p.Tyr358Cys,ENST00000357443,;MOV10,missense_variant,p.Tyr358Cys,ENST00000369645,;MOV10,missense_variant,p.Tyr358Cys,ENST00000413052,;RP11-426L16.3,downstream_gene_variant,,ENST00000421943,;MOV10,non_coding_transcript_exon_variant,,ENST00000468624,;MOV10,non_coding_transcript_exon_variant,,ENST00000496577,;MOV10,downstream_gene_variant,,ENST00000475429,;MOV10,upstream_gene_variant,,ENST00000479858,;MOV10,downstream_gene_variant,,ENST00000465579,;MOV10,upstream_gene_variant,,ENST00000471160,;MOV10,upstream_gene_variant,,ENST00000482545,;MOV10,upstream_gene_variant,,ENST00000488160,;	G	ENSG00000155363	ENST00000413052	Transcript	missense_variant	1463	1073	358	Y/C	tAt/tGt	.	.	.	1	MOV10	HGNC	7200	protein_coding	YES	CCDS853.1	ENSP00000399797	MOV10_HUMAN	Q5JR04_HUMAN,B3KQ43_HUMAN	UPI000012FA84	.	deleterious(0.01)	probably_damaging(0.938)	7/21	.	hmmpanther:PTHR10887:SF326,hmmpanther:PTHR10887	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACTATGACC	.	5	ESCA
HRNR	0	.	GRCh37	1	152191248	152191248	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2857C>A	p.His953Asn	p.H953N	ENST00000368801	3/3	111	85	26	135	135	0	HRNR,missense_variant,p.His953Asn,ENST00000368801,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	T	ENSG00000197915	ENST00000368801	Transcript	missense_variant	2933	2857	953	H/N	Cac/Aac	.	.	.	-1	HRNR	HGNC	20846	protein_coding	YES	CCDS30859.1	ENSP00000357791	HORN_HUMAN	Q5W8V9_HUMAN	UPI00001D7CAD	.	.	unknown(0)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF23,hmmpanther:PTHR22571	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTGACCTG	.	5	ESCA
FLG	0	.	GRCh37	1	152280935	152280935	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6427G>A	p.Gly2143Arg	p.G2143R	ENST00000368799	3/3	136	117	18	160	160	0	FLG,missense_variant,p.Gly2143Arg,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,;	T	ENSG00000143631	ENST00000368799	Transcript	missense_variant	6463	6427	2143	G/R	Ggg/Agg	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	probably_damaging(0.953)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCCCCGGGT	.	4	ESCA
OR10K1	0	.	GRCh37	1	158435698	158435698	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347C>A	p.Ala116Glu	p.A116E	ENST00000289451	1/1	36	31	5	37	37	0	OR10K1,missense_variant,p.Ala116Glu,ENST00000289451,;	A	ENSG00000173285	ENST00000289451	Transcript	missense_variant	427	347	116	A/E	gCa/gAa	.	.	.	1	OR10K1	HGNC	14693	protein_coding	YES	CCDS30897.1	ENSP00000289451	O10K1_HUMAN	.	UPI0000041B19	.	deleterious(0)	probably_damaging(0.934)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26451:SF112,hmmpanther:PTHR26451,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGGCAGCCA	.	4	ESCA
OR6N1	0	.	GRCh37	1	158736112	158736112	+	Missense_Mutation	SNP	C	C	T	rs145448358	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361G>A	p.Asp121Asn	p.D121N	ENST00000335094	1/1	64	47	17	37	37	0	OR6N1,missense_variant,p.Asp121Asn,ENST00000335094,;	T	ENSG00000197403	ENST00000335094	Transcript	missense_variant	381	361	121	D/N	Gat/Aat	rs145448358,COSM230885	.	.	-1	OR6N1	HGNC	15034	protein_coding	YES	CCDS30905.1	ENSP00000335535	OR6N1_HUMAN	.	UPI000003FE15	.	deleterious(0)	probably_damaging(1)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,PROSITE_patterns:PS00237,hmmpanther:PTHR26453:SF123,hmmpanther:PTHR26453,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.D121N|c.361G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATCGTAGG	byCluster	5	ESCA
FCGR3A	0	.	GRCh37	1	161512778	161512778	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*24G>C	.	.	ENST00000367969	5/5	50	36	13	49	49	0	FCGR3A,3_prime_UTR_variant,,ENST00000426740,;FCGR3A,3_prime_UTR_variant,,ENST00000367969,;FCGR3A,3_prime_UTR_variant,,ENST00000443193,;FCGR3A,3_prime_UTR_variant,,ENST00000540048,;FCGR3A,3_prime_UTR_variant,,ENST00000436743,;FCGR3A,3_prime_UTR_variant,,ENST00000367967,;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR3A,downstream_gene_variant,,ENST00000476031,;RPS23P10,upstream_gene_variant,,ENST00000416185,;	G	ENSG00000203747	ENST00000367969	Transcript	3_prime_UTR_variant	1081	.	.	.	.	.	.	.	-1	FCGR3A	HGNC	3619	protein_coding	YES	CCDS1232.1	ENSP00000356946	.	M9MML0_HUMAN,Q9UN20_HUMAN	UPI000013E1BC	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCTTATT	.	5	ESCA
NADK	0	.	GRCh37	1	1687745	1687745	+	Missense_Mutation	SNP	G	G	C	rs780742778	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972C>G	p.Ile324Met	p.I324M	ENST00000344463	8/14	38	33	5	62	62	0	NADK,missense_variant,p.Ile324Met,ENST00000378625,;NADK,missense_variant,p.Ile324Met,ENST00000344463,;NADK,missense_variant,p.Ile147Met,ENST00000400922,;NADK,missense_variant,p.Ile179Met,ENST00000341991,;NADK,missense_variant,p.Ile147Met,ENST00000342348,;NADK,missense_variant,p.Ile179Met,ENST00000341426,;NADK,3_prime_UTR_variant,,ENST00000469045,;NADK,downstream_gene_variant,,ENST00000492768,;NADK,missense_variant,p.Ile48Met,ENST00000489538,;NADK,3_prime_UTR_variant,,ENST00000497186,;NADK,non_coding_transcript_exon_variant,,ENST00000477235,;NADK,non_coding_transcript_exon_variant,,ENST00000480499,;NADK,non_coding_transcript_exon_variant,,ENST00000492845,;NADK,downstream_gene_variant,,ENST00000460602,;NADK,upstream_gene_variant,,ENST00000498806,;NADK,upstream_gene_variant,,ENST00000497615,;NADK,upstream_gene_variant,,ENST00000497747,;	C	ENSG00000008130	ENST00000344463	Transcript	missense_variant	1194	972	324	I/M	atC/atG	rs780742778,COSM352852	.	.	-1	NADK	HGNC	29831	protein_coding	YES	CCDS55562.1	ENSP00000340925	NADK_HUMAN	.	UPI000013CBEB	.	deleterious(0)	probably_damaging(0.998)	8/14	.	HAMAP:MF_00361,hmmpanther:PTHR20275:SF8,hmmpanther:PTHR20275,Gene3D:3.40.50.10330,Pfam_domain:PF01513,Superfamily_domains:SSF111331	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGGCAGATGAT	.	3	ESCA
FASLG	0	.	GRCh37	1	172634774	172634774	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464C>G	p.Ser155Ter	p.S155*	ENST00000367721	4/4	36	30	6	37	37	0	FASLG,stop_gained,p.Ser155Ter,ENST00000367721,;FASLG,3_prime_UTR_variant,,ENST00000340030,;	G	ENSG00000117560	ENST00000367721	Transcript	stop_gained	648	464	155	S/*	tCa/tGa	.	.	.	1	FASLG	HGNC	11936	protein_coding	YES	CCDS1304.1	ENSP00000356694	TNFL6_HUMAN	Q53ZZ1_HUMAN	UPI000000D91A	.	.	.	4/4	.	PROSITE_profiles:PS50049,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF30,Gene3D:2.60.120.40,SMART_domains:SM00207,Superfamily_domains:SSF49842,Prints_domain:PR01681	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACTCAAGGT	.	4	ESCA
RALGPS2	0	.	GRCh37	1	178855196	178855196	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1133C>T	p.Pro378Leu	p.P378L	ENST00000367635	13/20	60	44	16	58	58	0	RALGPS2,missense_variant,p.Pro378Leu,ENST00000367635,;RALGPS2,missense_variant,p.Pro378Leu,ENST00000367634,;RALGPS2,downstream_gene_variant,,ENST00000324778,;RALGPS2,downstream_gene_variant,,ENST00000415888,;RALGPS2,upstream_gene_variant,,ENST00000367632,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000477383,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000480743,;	T	ENSG00000116191	ENST00000367635	Transcript	missense_variant	1471	1133	378	P/L	cCc/cTc	.	.	.	1	RALGPS2	HGNC	30279	protein_coding	YES	CCDS1325.1	ENSP00000356607	RGPS2_HUMAN	.	UPI000000DBE1	.	tolerated(0.16)	benign(0.045)	13/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGCCCCATG	.	5	ESCA
HMCN1	0	.	GRCh37	1	186099708	186099708	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13109A>C	p.Asn4370Thr	p.N4370T	ENST00000271588	85/107	52	48	4	66	66	0	HMCN1,missense_variant,p.Asn4370Thr,ENST00000367492,;HMCN1,missense_variant,p.Asn4370Thr,ENST00000271588,;	C	ENSG00000143341	ENST00000271588	Transcript	missense_variant	13338	13109	4370	N/T	aAt/aCt	.	.	.	1	HMCN1	HGNC	19194	protein_coding	YES	CCDS30956.1	ENSP00000271588	HMCN1_HUMAN	.	UPI0000458C0E	.	.	possibly_damaging(0.817)	85/107	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19897:SF158,hmmpanther:PTHR19897,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCTGAATTGTG	.	3	ESCA
RGS18	0	.	GRCh37	1	192129548	192129548	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.262G>A	p.Asp88Asn	p.D88N	ENST00000367460	3/5	106	94	12	126	126	0	RGS18,missense_variant,p.Asp88Asn,ENST00000367460,;RGS18,non_coding_transcript_exon_variant,,ENST00000492967,;RGS18,non_coding_transcript_exon_variant,,ENST00000481707,;RGS18,non_coding_transcript_exon_variant,,ENST00000491030,;	A	ENSG00000150681	ENST00000367460	Transcript	missense_variant	443	262	88	D/N	Gac/Aac	.	.	.	1	RGS18	HGNC	14261	protein_coding	YES	CCDS1374.1	ENSP00000356430	RGS18_HUMAN	.	UPI0000044571	.	tolerated(0.08)	possibly_damaging(0.596)	3/5	.	PROSITE_profiles:PS50132,hmmpanther:PTHR10845:SF153,hmmpanther:PTHR10845,Pfam_domain:PF00615,Gene3D:1.10.196.10,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTGACAAA	.	4	ESCA
NFASC	0	.	GRCh37	1	204987007	204987007	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1340C>T	.	.	ENST00000339876	30/30	29	25	3	36	36	0	NFASC,3_prime_UTR_variant,,ENST00000404076,;NFASC,3_prime_UTR_variant,,ENST00000367170,;NFASC,3_prime_UTR_variant,,ENST00000447819,;NFASC,3_prime_UTR_variant,,ENST00000338515,;NFASC,3_prime_UTR_variant,,ENST00000360049,;NFASC,3_prime_UTR_variant,,ENST00000425360,;NFASC,3_prime_UTR_variant,,ENST00000401399,;NFASC,3_prime_UTR_variant,,ENST00000404907,;NFASC,3_prime_UTR_variant,,ENST00000367171,;NFASC,3_prime_UTR_variant,,ENST00000539706,;NFASC,3_prime_UTR_variant,,ENST00000367173,;NFASC,3_prime_UTR_variant,,ENST00000339876,;NFASC,3_prime_UTR_variant,,ENST00000430393,;NFASC,3_prime_UTR_variant,,ENST00000367169,;NFASC,3_prime_UTR_variant,,ENST00000367172,;NFASC,3_prime_UTR_variant,,ENST00000338586,;NFASC,downstream_gene_variant,,ENST00000413225,;NFASC,downstream_gene_variant,,ENST00000513543,;NFASC,non_coding_transcript_exon_variant,,ENST00000495396,;NFASC,non_coding_transcript_exon_variant,,ENST00000503221,;NFASC,downstream_gene_variant,,ENST00000504476,;	T	ENSG00000163531	ENST00000339876	Transcript	3_prime_UTR_variant	5391	.	.	.	.	.	.	.	1	NFASC	HGNC	29866	protein_coding	YES	CCDS53460.1	ENSP00000344786	NFASC_HUMAN	D6RHX4_HUMAN	UPI0000237208	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TTATGCAGCGC	.	2	ESCA
CD55	0	.	GRCh37	1	207527382	207527382	+	Intron	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1200-5509G>C	.	.	ENST00000314754	.	52	39	13	63	63	0	CD55,missense_variant,p.Gly371Ala,ENST00000391920,;CD55,intron_variant,,ENST00000367067,;CD55,intron_variant,,ENST00000367064,;CD55,intron_variant,,ENST00000391921,;CD55,intron_variant,,ENST00000367062,;CD55,intron_variant,,ENST00000314754,;CD55,intron_variant,,ENST00000367065,;CD55,intron_variant,,ENST00000465534,;CD55,intron_variant,,ENST00000482390,;CD55,intron_variant,,ENST00000476590,;	C	ENSG00000196352	ENST00000314754	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CD55	HGNC	2665	protein_coding	YES	CCDS44307.1	ENSP00000316333	DAF_HUMAN	Q76N74_HUMAN	UPI000002EA80	.	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTGGGTCAT	.	5	ESCA
KIF26B	0	.	GRCh37	1	245772708	245772708	+	Missense_Mutation	SNP	G	G	A	rs770867836	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1792G>A	p.Val598Met	p.V598M	ENST00000407071	8/15	72	66	5	78	78	0	KIF26B,missense_variant,p.Val598Met,ENST00000407071,;KIF26B,missense_variant,p.Val217Met,ENST00000366518,;	A	ENSG00000162849	ENST00000407071	Transcript	missense_variant	2232	1792	598	V/M	Gtg/Atg	rs770867836	.	.	1	KIF26B	HGNC	25484	protein_coding	YES	CCDS44342.1	ENSP00000385545	KI26B_HUMAN	B4DF75_HUMAN	UPI0000695D71	.	deleterious(0)	unknown(0)	8/15	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF363,hmmpanther:PTHR24115,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCGCCGTGGAA	byFrequency	2	ESCA
OR2G3	0	.	GRCh37	1	247769531	247769531	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.644C>G	p.Ser215Cys	p.S215C	ENST00000320002	1/1	42	37	5	36	36	0	OR2G3,missense_variant,p.Ser215Cys,ENST00000320002,;RNU6-691P,downstream_gene_variant,,ENST00000516585,;RP11-978I15.10,intron_variant,,ENST00000446347,;RP11-978I15.10,intron_variant,,ENST00000435333,;	G	ENSG00000177476	ENST00000320002	Transcript	missense_variant	676	644	215	S/C	tCc/tGc	.	.	.	1	OR2G3	HGNC	15008	protein_coding	YES	CCDS31093.1	ENSP00000326301	OR2G3_HUMAN	.	UPI0000041CD9	.	deleterious(0)	benign(0.041)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF110,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCCATCT	.	4	ESCA
OR2L8	0	.	GRCh37	1	248112840	248112840	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681G>A	p.Met227Ile	p.M227I	ENST00000357191	1/1	90	82	8	110	110	0	OR2L8,missense_variant,p.Met227Ile,ENST00000357191,;OR2L13,intron_variant,,ENST00000366478,;	A	ENSG00000196936	ENST00000357191	Transcript	missense_variant	681	681	227	M/I	atG/atA	COSM680544	.	.	1	OR2L8	HGNC	15014	protein_coding	YES	CCDS31101.1	ENSP00000349719	OR2L8_HUMAN	.	UPI0000061E5D	.	deleterious(0.05)	benign(0.289)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF104,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CACATGAAATC	.	3	ESCA
GUCA2B	0	.	GRCh37	1	42620505	42620505	+	Missense_Mutation	SNP	C	C	T	rs747856024	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.245C>T	p.Ser82Leu	p.S82L	ENST00000372581	2/3	14	10	3	12	12	0	GUCA2B,missense_variant,p.Ser82Leu,ENST00000372581,;	T	ENSG00000044012	ENST00000372581	Transcript	missense_variant	275	245	82	S/L	tCg/tTg	rs747856024,COSM3489707	.	.	1	GUCA2B	HGNC	4683	protein_coding	YES	CCDS464.1	ENSP00000361662	GUC2B_HUMAN	.	UPI000002E39E	.	deleterious(0.04)	benign(0.232)	2/3	.	hmmpanther:PTHR11318:SF1,hmmpanther:PTHR11318,Gene3D:1o8rA00,Pfam_domain:PF02058,PIRSF_domain:PIRSF001849,Superfamily_domains:0041741,Prints_domain:PR00774	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CGCCTCGCAGG	byFrequency	4	ESCA
SPATA6	0	.	GRCh37	1	48878823	48878823	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239A>G	p.Tyr80Cys	p.Y80C	ENST00000371847	4/13	111	104	6	121	121	0	SPATA6,missense_variant,p.Tyr80Cys,ENST00000371843,;SPATA6,missense_variant,p.Tyr80Cys,ENST00000371847,;SPATA6,intron_variant,,ENST00000396199,;SPATA6,splice_region_variant,,ENST00000463938,;SPATA6,splice_region_variant,,ENST00000471975,;SPATA6,splice_region_variant,,ENST00000465990,;SPATA6,intron_variant,,ENST00000487543,;	C	ENSG00000132122	ENST00000371847	Transcript	missense_variant	404	239	80	Y/C	tAt/tGt	.	.	.	-1	SPATA6	HGNC	18309	protein_coding	YES	CCDS551.1	ENSP00000360913	SPAT6_HUMAN	.	UPI0000049C41	.	tolerated(0.13)	benign(0.001)	4/13	.	hmmpanther:PTHR16435:SF3,hmmpanther:PTHR16435,Pfam_domain:PF14909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATCATCTAAA	.	2	ESCA
PODN	0	.	GRCh37	1	53544114	53544114	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1076T>A	p.Leu359Gln	p.L359Q	ENST00000312553	8/11	63	56	7	56	56	0	PODN,missense_variant,p.Leu359Gln,ENST00000312553,;PODN,missense_variant,p.Leu340Gln,ENST00000371500,;PODN,missense_variant,p.Leu217Gln,ENST00000395871,;RP11-334A14.5,intron_variant,,ENST00000447867,;PODN,upstream_gene_variant,,ENST00000490650,;PODN,upstream_gene_variant,,ENST00000471285,;PODN,downstream_gene_variant,,ENST00000471210,;	A	ENSG00000174348	ENST00000312553	Transcript	missense_variant	1083	1076	359	L/Q	cTg/cAg	.	.	.	1	PODN	HGNC	23174	protein_coding	YES	CCDS573.1	ENSP00000308315	PODN_HUMAN	.	UPI000034ECE9	.	deleterious(0)	probably_damaging(0.987)	8/11	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24369:SF12,hmmpanther:PTHR24369,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00368,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCCTGGTGC	.	4	ESCA
TNFRSF25	0	.	GRCh37	1	6521693	6521693	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1082G>A	p.Arg361His	p.R361H	ENST00000377782	10/10	19	14	5	20	20	0	TNFRSF25,missense_variant,p.Arg352His,ENST00000356876,;TNFRSF25,missense_variant,p.Arg307His,ENST00000348333,;TNFRSF25,missense_variant,p.Arg315His,ENST00000351959,;TNFRSF25,missense_variant,p.Arg361His,ENST00000377782,;TNFRSF25,missense_variant,p.Arg169His,ENST00000351748,;PLEKHG5,downstream_gene_variant,,ENST00000400913,;ESPN,downstream_gene_variant,,ENST00000416731,;TNFRSF25,downstream_gene_variant,,ENST00000481401,;PLEKHG5,downstream_gene_variant,,ENST00000340850,;ESPN,downstream_gene_variant,,ENST00000377828,;PLEKHG5,downstream_gene_variant,,ENST00000377748,;ESPN,downstream_gene_variant,,ENST00000461727,;ESPN,downstream_gene_variant,,ENST00000434576,;ESPN,downstream_gene_variant,,ENST00000475228,;TNFRSF25,downstream_gene_variant,,ENST00000461703,;ESPN,downstream_gene_variant,,ENST00000468561,;TNFRSF25,downstream_gene_variant,,ENST00000475730,;TNFRSF25,3_prime_UTR_variant,,ENST00000414040,;TNFRSF25,3_prime_UTR_variant,,ENST00000510563,;TNFRSF25,3_prime_UTR_variant,,ENST00000485036,;TNFRSF25,3_prime_UTR_variant,,ENST00000480393,;TNFRSF25,3_prime_UTR_variant,,ENST00000502588,;TNFRSF25,3_prime_UTR_variant,,ENST00000502730,;TNFRSF25,non_coding_transcript_exon_variant,,ENST00000453260,;TNFRSF25,non_coding_transcript_exon_variant,,ENST00000513135,;TNFRSF25,non_coding_transcript_exon_variant,,ENST00000473343,;TNFRSF25,downstream_gene_variant,,ENST00000515145,;PLEKHG5,downstream_gene_variant,,ENST00000489097,;TNFRSF25,downstream_gene_variant,,ENST00000453341,;TNFRSF25,downstream_gene_variant,,ENST00000469691,;ESPN,downstream_gene_variant,,ENST00000477679,;	T	ENSG00000215788	ENST00000377782	Transcript	missense_variant	1150	1082	361	R/H	cGc/cAc	COSM2239029	.	.	-1	TNFRSF25	HGNC	11910	protein_coding	YES	CCDS72.1	ENSP00000367013	TNR25_HUMAN	B3KSV7_HUMAN	UPI000002B5CB	.	deleterious(0)	probably_damaging(0.999)	10/10	.	Superfamily_domains:SSF47986,SMART_domains:SM00005,Pfam_domain:PF00531,Gene3D:1.10.533.10,hmmpanther:PTHR23097:SF104,hmmpanther:PTHR23097,PROSITE_profiles:PS50017	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GCGTGCGCACG	.	4	ESCA
LRRC7	0	.	GRCh37	1	70225961	70225961	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.74C>A	p.Ser25Ter	p.S25*	ENST00000035383	1/25	43	32	10	48	48	0	LRRC7,stop_gained,p.Ser63Ter,ENST00000370958,;LRRC7,stop_gained,p.Ser25Ter,ENST00000035383,;LRRC7,stop_gained,p.Ser30Ter,ENST00000310961,;LRRC7,5_prime_UTR_variant,,ENST00000415775,;	A	ENSG00000033122	ENST00000035383	Transcript	stop_gained	104	74	25	S/*	tCa/tAa	COSM3712195,COSM3712196	.	.	1	LRRC7	HGNC	18531	protein_coding	YES	CCDS645.1	ENSP00000035383	LRRC7_HUMAN	.	UPI000006F29B	.	.	.	1/25	.	hmmpanther:PTHR23155:SF459,hmmpanther:PTHR23155,Gene3D:3.80.10.10	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCAGTTT	.	5	ESCA
RERE	0	.	GRCh37	1	8555218	8555218	+	Missense_Mutation	SNP	T	T	A	rs749407468	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009A>T	p.Met337Leu	p.M337L	ENST00000337907	11/24	38	32	6	38	38	0	RERE,missense_variant,p.Met19Leu,ENST00000464972,;RERE,missense_variant,p.Met337Leu,ENST00000400908,;RERE,missense_variant,p.Met69Leu,ENST00000377464,;RERE,missense_variant,p.Met337Leu,ENST00000337907,;RERE,missense_variant,p.Met337Leu,ENST00000400907,;RERE,non_coding_transcript_exon_variant,,ENST00000507012,;RERE,non_coding_transcript_exon_variant,,ENST00000480342,;	A	ENSG00000142599	ENST00000337907	Transcript	missense_variant	1644	1009	337	M/L	Atg/Ttg	rs749407468	.	.	-1	RERE	HGNC	9965	protein_coding	YES	CCDS95.1	ENSP00000338629	RERE_HUMAN	K7EJQ1_HUMAN,K7EIQ4_HUMAN,K7EIE3_HUMAN	UPI00001419CC	.	.	possibly_damaging(0.67)	11/24	.	PROSITE_profiles:PS51156,hmmpanther:PTHR13859,hmmpanther:PTHR13859:SF12,Pfam_domain:PF01448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCATGCTCC	.	5	ESCA
C1orf52	0	.	GRCh37	1	85725158	85725158	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.159G>A	p.%3D	p.E53E	ENST00000471115	1/3	139	119	20	126	126	0	C1orf52,synonymous_variant,p.%3D,ENST00000344356,;C1orf52,synonymous_variant,p.%3D,ENST00000471115,;Y_RNA,upstream_gene_variant,,ENST00000411322,;C1orf52,non_coding_transcript_exon_variant,,ENST00000294661,;C1orf52,non_coding_transcript_exon_variant,,ENST00000493514,;	T	ENSG00000162642	ENST00000471115	Transcript	synonymous_variant	168	159	53	E	gaG/gaA	.	.	.	-1	C1orf52	HGNC	24871	protein_coding	YES	CCDS703.1	ENSP00000419417	CA052_HUMAN	.	UPI0000072AC0	.	.	.	1/3	.	hmmpanther:PTHR31833:SF2,hmmpanther:PTHR31833,Pfam_domain:PF15559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCTTCTCCGC	.	4	ESCA
C20orf202	0	.	GRCh37	20	1187643	1187643	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.266G>C	p.Arg89Thr	p.R89T	ENST00000400633	2/2	45	40	5	71	71	0	C20orf202,missense_variant,p.Arg89Thr,ENST00000400633,;	C	ENSG00000215595	ENST00000400633	Transcript	missense_variant	329	266	89	R/T	aGa/aCa	.	.	.	1	C20orf202	HGNC	37254	protein_coding	YES	CCDS46567.1	ENSP00000383474	CT202_HUMAN	.	UPI0000141828	.	deleterious(0)	probably_damaging(0.997)	2/2	.	hmmpanther:PTHR32289:SF5,hmmpanther:PTHR32289	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCAGAGCTC	.	4	ESCA
CD93	0	.	GRCh37	20	23066586	23066586	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244C>T	p.Arg82Trp	p.R82W	ENST00000246006	1/2	88	67	21	102	102	0	CD93,missense_variant,p.Arg82Trp,ENST00000246006,;	A	ENSG00000125810	ENST00000246006	Transcript	missense_variant	392	244	82	R/W	Cgg/Tgg	COSM248875	.	.	-1	CD93	HGNC	15855	protein_coding	YES	CCDS13149.1	ENSP00000246006	C1QR1_HUMAN	.	UPI00001273BC	.	deleterious(0.02)	possibly_damaging(0.72)	1/2	.	PROSITE_profiles:PS50041,hmmpanther:PTHR24838,hmmpanther:PTHR24838:SF261,Gene3D:3.10.100.10,Pfam_domain:PF00059,PIRSF_domain:PIRSF001775,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCGCCTCA	.	5	ESCA
MMP24	0	.	GRCh37	20	33862200	33862200	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1726C>A	p.%3D	p.R576R	ENST00000246186	9/9	49	37	11	54	54	0	MMP24,synonymous_variant,p.%3D,ENST00000246186,;EDEM2,intron_variant,,ENST00000540582,;EIF6,downstream_gene_variant,,ENST00000374450,;EIF6,downstream_gene_variant,,ENST00000374436,;EIF6,downstream_gene_variant,,ENST00000374443,;RP4-614O4.11,intron_variant,,ENST00000444717,;MMP24-AS1,intron_variant,,ENST00000438751,;MMP24-AS1,intron_variant,,ENST00000456350,;MMP24-AS1,intron_variant,,ENST00000455178,;MMP24-AS1,intron_variant,,ENST00000566203,;MMP24-AS1,intron_variant,,ENST00000454184,;MMP24-AS1,intron_variant,,ENST00000433764,;MMP24-AS1,downstream_gene_variant,,ENST00000456790,;MMP24-AS1,downstream_gene_variant,,ENST00000435366,;MMP24-AS1,downstream_gene_variant,,ENST00000424358,;MMP24-AS1,upstream_gene_variant,,ENST00000453892,;EIF6,downstream_gene_variant,,ENST00000447927,;EIF6,downstream_gene_variant,,ENST00000440766,;	A	ENSG00000125966	ENST00000246186	Transcript	synonymous_variant	1811	1726	576	R	Cgg/Agg	.	.	.	1	MMP24	HGNC	7172	protein_coding	YES	CCDS46593.1	ENSP00000246186	MMP24_HUMAN	Q86VV6_HUMAN	UPI000012F259	.	.	.	9/9	.	hmmpanther:PTHR10201:SF138,hmmpanther:PTHR10201,Pfam_domain:PF11857	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGCGGCGG	.	5	ESCA
EIF6	0	.	GRCh37	20	33868521	33868521	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.305C>T	p.Ser102Leu	p.S102L	ENST00000374450	4/7	56	50	6	62	62	0	EIF6,missense_variant,p.Ser102Leu,ENST00000456600,;EIF6,missense_variant,p.Ser102Leu,ENST00000374450,;EIF6,missense_variant,p.Ser102Leu,ENST00000374436,;EIF6,intron_variant,,ENST00000374443,;MMP24,downstream_gene_variant,,ENST00000246186,;EDEM2,upstream_gene_variant,,ENST00000540582,;RP4-614O4.11,upstream_gene_variant,,ENST00000444717,;MMP24-AS1,upstream_gene_variant,,ENST00000456790,;MMP24-AS1,upstream_gene_variant,,ENST00000435366,;MMP24-AS1,upstream_gene_variant,,ENST00000424358,;FAM83C-AS1,upstream_gene_variant,,ENST00000429167,;MMP24-AS1,upstream_gene_variant,,ENST00000438751,;MMP24-AS1,upstream_gene_variant,,ENST00000456350,;MMP24-AS1,upstream_gene_variant,,ENST00000455178,;MMP24-AS1,upstream_gene_variant,,ENST00000566203,;MMP24-AS1,upstream_gene_variant,,ENST00000454184,;MMP24-AS1,upstream_gene_variant,,ENST00000433764,;EIF6,intron_variant,,ENST00000462894,;EIF6,stop_gained,p.Gln142Ter,ENST00000415116,;EIF6,intron_variant,,ENST00000447927,;EIF6,intron_variant,,ENST00000440766,;	A	ENSG00000242372	ENST00000374450	Transcript	missense_variant	570	305	102	S/L	tCa/tTa	.	.	.	-1	EIF6	HGNC	6159	protein_coding	YES	CCDS13249.1	ENSP00000363574	IF6_HUMAN	B7ZBH1_HUMAN	UPI0000001224	.	deleterious(0)	probably_damaging(0.992)	4/7	.	Superfamily_domains:SSF55909,PIRSF_domain:PIRSF006413,SMART_domains:SM00654,TIGRFAM_domain:TIGR00323,Gene3D:3.75.10.10,Pfam_domain:PF01912,hmmpanther:PTHR10784,hmmpanther:PTHR10784:SF0,HAMAP:MF_00032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTGAGAGC	.	4	ESCA
RALGAPB	0	.	GRCh37	20	37146211	37146211	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000262879	8/30	56	52	4	76	76	0	RALGAPB,stop_gained,p.Gln150Ter,ENST00000397038,;RALGAPB,stop_gained,p.Gln372Ter,ENST00000397040,;RALGAPB,stop_gained,p.Gln372Ter,ENST00000397042,;RALGAPB,stop_gained,p.Gln372Ter,ENST00000262879,;RALGAPB,stop_gained,p.Gln200Ter,ENST00000438490,;RALGAPB,stop_gained,p.Gln372Ter,ENST00000537204,;MIR548O2,downstream_gene_variant,,ENST00000583129,;RALGAPB,non_coding_transcript_exon_variant,,ENST00000461423,;	T	ENSG00000170471	ENST00000262879	Transcript	stop_gained	1398	1114	372	Q/*	Caa/Taa	COSM3363239	.	.	1	RALGAPB	HGNC	29221	protein_coding	YES	CCDS13305.1	ENSP00000262879	RLGPB_HUMAN	Q6MZJ2_HUMAN	UPI000000DBFD	.	.	.	8/30	.	hmmpanther:PTHR21344	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCCTCAAAGT	.	2	ESCA
FITM2	0	.	GRCh37	20	42935620	42935620	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.434G>A	p.Gly145Asp	p.G145D	ENST00000396825	2/2	32	29	3	28	28	0	FITM2,missense_variant,p.Gly145Asp,ENST00000396825,;	T	ENSG00000197296	ENST00000396825	Transcript	missense_variant	455	434	145	G/D	gGc/gAc	.	.	.	-1	FITM2	HGNC	16135	protein_coding	YES	CCDS33473.1	ENSP00000380037	FITM2_HUMAN	.	UPI0000128612	.	tolerated(0.08)	probably_damaging(0.995)	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23129,hmmpanther:PTHR23129:SF1,Pfam_domain:PF10261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AAAAGCCCCCT	.	2	ESCA
ELMO2	0	.	GRCh37	20	44994974	44994974	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1025T>A	.	.	ENST00000290246	22/22	69	50	18	69	69	0	ELMO2,3_prime_UTR_variant,,ENST00000372176,;ELMO2,3_prime_UTR_variant,,ENST00000396391,;ELMO2,3_prime_UTR_variant,,ENST00000452857,;ELMO2,3_prime_UTR_variant,,ENST00000290246,;SLC35C2,upstream_gene_variant,,ENST00000543605,;SLC35C2,upstream_gene_variant,,ENST00000372229,;SLC35C2,upstream_gene_variant,,ENST00000243896,;ELMO2,downstream_gene_variant,,ENST00000454865,;ELMO2,downstream_gene_variant,,ENST00000439931,;SLC35C2,upstream_gene_variant,,ENST00000372230,;SLC35C2,upstream_gene_variant,,ENST00000317734,;ELMO2,downstream_gene_variant,,ENST00000445496,;SLC35C2,upstream_gene_variant,,ENST00000372227,;ELMO2,downstream_gene_variant,,ENST00000352077,;SLC35C2,upstream_gene_variant,,ENST00000484188,;ELMO2,downstream_gene_variant,,ENST00000464448,;SLC35C2,upstream_gene_variant,,ENST00000484318,;SLC35C2,upstream_gene_variant,,ENST00000481809,;ELMO2,3_prime_UTR_variant,,ENST00000467800,;	T	ENSG00000062598	ENST00000290246	Transcript	3_prime_UTR_variant	3383	.	.	.	.	.	.	.	-1	ELMO2	HGNC	17233	protein_coding	YES	CCDS13398.1	ENSP00000290246	ELMO2_HUMAN	Q7Z5G9_HUMAN,Q5JVZ4_HUMAN,Q5BLP5_HUMAN,F5GZP8_HUMAN	UPI000013F6C4	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACGTATGTCC	.	5	ESCA
MOCS3	0	.	GRCh37	20	49576280	49576280	+	Missense_Mutation	SNP	G	G	T	rs760591680,rs777426907	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.901G>T	p.Gly301Trp	p.G301W	ENST00000244051	1/1	22	18	4	40	40	0	MOCS3,missense_variant,p.Gly301Trp,ENST00000244051,;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000371582,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000371588,;DPM1,upstream_gene_variant,,ENST00000371583,;DPM1,upstream_gene_variant,,ENST00000466152,;	T	ENSG00000124217	ENST00000244051	Transcript	missense_variant	918	901	301	G/W	Ggg/Tgg	rs760591680,rs777426907	.	.	1	MOCS3	HGNC	15765	protein_coding	YES	CCDS13435.1	ENSP00000244051	MOCS3_HUMAN	.	UPI000012F369	.	deleterious(0)	probably_damaging(1)	1/1	.	HAMAP:MF_03049,hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF102,Gene3D:3.40.50.720,Pfam_domain:PF05237,Superfamily_domains:SSF69572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCGGGGAA	.	5	ESCA
PI4KAP2	0	.	GRCh37	22	21834224	21834224	+	RNA	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3045G>T	.	.	ENST00000480319	7/11	104	79	24	102	102	0	PI4KAP2,non_coding_transcript_exon_variant,,ENST00000450651,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000494740,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000486209,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000463608,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000480319,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000462560,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000479693,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000467443,;PI4KAP2,upstream_gene_variant,,ENST00000470274,;PI4KAP2,upstream_gene_variant,,ENST00000477296,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000546263,;PI4KAP2,non_coding_transcript_exon_variant,,ENST00000360806,;	A	ENSG00000183506	ENST00000480319	Transcript	non_coding_transcript_exon_variant	3045	.	.	.	.	.	.	.	-1	PI4KAP2	HGNC	33577	retained_intron	YES	.	.	.	.	.	.	.	.	7/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGCATCGG	.	5	ESCA
GGA1	0	.	GRCh37	22	38020994	38020994	+	Missense_Mutation	SNP	A	A	G	rs756451398	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.851A>G	p.Asn284Ser	p.N284S	ENST00000343632	10/17	51	38	12	70	70	0	GGA1,missense_variant,p.Asn301Ser,ENST00000381756,;GGA1,missense_variant,p.Asn211Ser,ENST00000406772,;GGA1,missense_variant,p.Asn284Ser,ENST00000343632,;GGA1,missense_variant,p.Asn251Ser,ENST00000337437,;GGA1,intron_variant,,ENST00000325180,;GGA1,downstream_gene_variant,,ENST00000423024,;GGA1,downstream_gene_variant,,ENST00000439161,;GGA1,downstream_gene_variant,,ENST00000449944,;GGA1,downstream_gene_variant,,ENST00000326597,;GGA1,downstream_gene_variant,,ENST00000429218,;GGA1,downstream_gene_variant,,ENST00000411501,;GGA1,downstream_gene_variant,,ENST00000405147,;GGA1,downstream_gene_variant,,ENST00000413251,;GGA1,downstream_gene_variant,,ENST00000453208,;GGA1,non_coding_transcript_exon_variant,,ENST00000475445,;GGA1,downstream_gene_variant,,ENST00000481613,;GGA1,upstream_gene_variant,,ENST00000463672,;GGA1,downstream_gene_variant,,ENST00000491295,;	G	ENSG00000100083	ENST00000343632	Transcript	missense_variant	1237	851	284	N/S	aAt/aGt	rs756451398,COSM1327234	.	.	1	GGA1	HGNC	17842	protein_coding	YES	CCDS13951.1	ENSP00000341344	GGA1_HUMAN	B0QYS5_HUMAN,B0QYS4_HUMAN,B0QYS3_HUMAN,B0QYS2_HUMAN,B0QYS1_HUMAN,B0QYS0_HUMAN,B0QYR9_HUMAN,B0QYR8_HUMAN	UPI0000001BEE	.	tolerated(0.32)	probably_damaging(0.983)	10/17	.	PROSITE_profiles:PS50909,hmmpanther:PTHR13856:SF82,hmmpanther:PTHR13856,Gene3D:1.20.58.160,Pfam_domain:PF03127,Superfamily_domains:SSF89009	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGCCAATGACA	.	4	ESCA
REV1	0	.	GRCh37	2	100019466	100019466	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3270G>C	p.Leu1090Phe	p.L1090F	ENST00000258428	20/23	36	32	4	40	40	0	REV1,missense_variant,p.Leu1090Phe,ENST00000258428,;REV1,missense_variant,p.Leu1089Phe,ENST00000393445,;EIF5B,downstream_gene_variant,,ENST00000289371,;RP11-527J8.1,upstream_gene_variant,,ENST00000608144,;REV1,intron_variant,,ENST00000482595,;REV1,downstream_gene_variant,,ENST00000465835,;REV1,3_prime_UTR_variant,,ENST00000413697,;REV1,non_coding_transcript_exon_variant,,ENST00000465086,;REV1,downstream_gene_variant,,ENST00000472000,;REV1,downstream_gene_variant,,ENST00000485487,;EIF5B,downstream_gene_variant,,ENST00000470023,;REV1,downstream_gene_variant,,ENST00000477121,;REV1,downstream_gene_variant,,ENST00000438366,;EIF5B,downstream_gene_variant,,ENST00000494190,;	G	ENSG00000135945	ENST00000258428	Transcript	missense_variant	3499	3270	1090	L/F	ttG/ttC	.	.	.	-1	REV1	HGNC	14060	protein_coding	YES	CCDS2045.1	ENSP00000258428	REV1_HUMAN	.	UPI0000073A14	.	tolerated(0.05)	benign(0.033)	20/23	.	PIRSF_domain:PIRSF036573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTATTCAAAGG	.	4	ESCA
WDR33	0	.	GRCh37	2	128477915	128477915	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1684G>C	p.Glu562Gln	p.E562Q	ENST00000322313	16/22	27	23	4	25	25	0	WDR33,missense_variant,p.Glu562Gln,ENST00000322313,;	G	ENSG00000136709	ENST00000322313	Transcript	missense_variant	1843	1684	562	E/Q	Gaa/Caa	.	.	.	-1	WDR33	HGNC	25651	protein_coding	YES	CCDS2150.1	ENSP00000325377	WDR33_HUMAN	C9J8B4_HUMAN,B9A053_HUMAN	UPI000013D032	.	deleterious_low_confidence(0)	unknown(0)	16/22	.	hmmpanther:PTHR22836	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTTTCAATTT	.	2	ESCA
ZRANB3	0	.	GRCh37	2	135957809	135957809	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*103G>C	.	.	ENST00000264159	21/21	32	28	4	50	50	0	ZRANB3,3_prime_UTR_variant,,ENST00000401392,;ZRANB3,3_prime_UTR_variant,,ENST00000536680,;ZRANB3,3_prime_UTR_variant,,ENST00000264159,;ZRANB3,intron_variant,,ENST00000412849,;ZRANB3,3_prime_UTR_variant,,ENST00000403017,;ZRANB3,downstream_gene_variant,,ENST00000474919,;	G	ENSG00000121988	ENST00000264159	Transcript	3_prime_UTR_variant	3460	.	.	.	.	.	.	.	-1	ZRANB3	HGNC	25249	protein_coding	YES	CCDS46419.1	ENSP00000264159	ZRAB3_HUMAN	.	UPI0000509F0C	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TTGTTCTGAAA	.	3	ESCA
ACVR2A	0	.	GRCh37	2	148685804	148685805	+	3'UTR	INS	-	-	GGG	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*962_*963insGGG	.	.	ENST00000241416	11/11	23	15	8	42	42	0	ACVR2A,3_prime_UTR_variant,,ENST00000241416,;ACVR2A,downstream_gene_variant,,ENST00000404590,;ACVR2A,downstream_gene_variant,,ENST00000535787,;ORC4,downstream_gene_variant,,ENST00000392857,;ACVR2A,downstream_gene_variant,,ENST00000495775,;	GGG	ENSG00000121989	ENST00000241416	Transcript	3_prime_UTR_variant	3139-3140	.	.	.	.	.	.	.	1	ACVR2A	HGNC	173	protein_coding	YES	CCDS33301.1	ENSP00000241416	AVR2A_HUMAN	B4DWQ2_HUMAN	UPI0000126673	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	AAGTGAGCTGT	.	2	ESCA
SCN1A	0	.	GRCh37	2	166897845	166897845	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2311G>A	p.Asp771Asn	p.D771N	ENST00000303395	13/26	84	72	11	74	74	0	SCN1A,missense_variant,p.Asp771Asn,ENST00000303395,;SCN1A,missense_variant,p.Asp760Asn,ENST00000375405,;SCN1A,missense_variant,p.Asp771Asn,ENST00000423058,;SCN1A,missense_variant,p.Asp743Asn,ENST00000409050,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000595268,;AC010127.3,downstream_gene_variant,,ENST00000597623,;	T	ENSG00000144285	ENST00000303395	Transcript	missense_variant	2311	2311	771	D/N	Gac/Aac	.	.	.	-1	SCN1A	HGNC	10585	protein_coding	YES	CCDS54413.1	ENSP00000303540	SCN1A_HUMAN	F8T7W7_HUMAN	UPI000003C71D	.	deleterious(0)	probably_damaging(0.999)	13/26	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF133,Gene3D:1.20.120.350,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGTCAACAA	.	4	ESCA
ADAM23	0	.	GRCh37	2	207452097	207452097	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1786C>T	p.Gln596Ter	p.Q596*	ENST00000264377	19/26	148	138	9	200	200	0	ADAM23,stop_gained,p.Gln596Ter,ENST00000374415,;ADAM23,stop_gained,p.Gln596Ter,ENST00000374416,;ADAM23,stop_gained,p.Gln596Ter,ENST00000264377,;	T	ENSG00000114948	ENST00000264377	Transcript	stop_gained	2114	1786	596	Q/*	Cag/Tag	.	.	.	1	ADAM23	HGNC	202	protein_coding	YES	CCDS2369.1	ENSP00000264377	ADA23_HUMAN	Q53TK5_HUMAN,Q53TC0_HUMAN,Q53RX4_HUMAN	UPI0000044543	.	.	.	19/26	.	SMART_domains:SM00608,Pfam_domain:PF08516,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAATCAGGTA	.	2	ESCA
TNS1	0	.	GRCh37	2	218667583	218667583	+	3'UTR	SNP	T	T	C	rs577390598	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1599A>G	.	.	ENST00000171887	33/33	61	55	6	118	118	0	TNS1,3_prime_UTR_variant,,ENST00000171887,;TNS1,3_prime_UTR_variant,,ENST00000446688,;TNS1,downstream_gene_variant,,ENST00000430930,;TNS1,downstream_gene_variant,,ENST00000419504,;TNS1,downstream_gene_variant,,ENST00000490566,;AC009469.1,upstream_gene_variant,,ENST00000546295,;	C	ENSG00000079308	ENST00000171887	Transcript	3_prime_UTR_variant	7260	.	.	.	.	rs577390598	.	.	-1	TNS1	HGNC	11973	protein_coding	YES	CCDS2407.1	ENSP00000171887	TENS1_HUMAN	Q9UFN8_HUMAN,Q9H757_HUMAN,C9JZT0_HUMAN,C9JI43_HUMAN,C9JFT7_HUMAN	UPI0000456EEB	.	.	.	33/33	.	.	C:0.0002	C:0	C:0	.	C:0.001	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	ATTTATATATC	by1000G	2	ESCA
DOCK10	0	.	GRCh37	2	225751206	225751206	+	Silent	SNP	C	C	T	rs561976782	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459G>A	p.%3D	p.E153E	ENST00000258390	5/56	24	17	6	44	44	0	DOCK10,synonymous_variant,p.%3D,ENST00000258390,;DOCK10,synonymous_variant,p.%3D,ENST00000409592,;DOCK10,non_coding_transcript_exon_variant,,ENST00000471810,;DOCK10,non_coding_transcript_exon_variant,,ENST00000492369,;DOCK10,upstream_gene_variant,,ENST00000543715,;	T	ENSG00000135905	ENST00000258390	Transcript	synonymous_variant	527	459	153	E	gaG/gaA	rs561976782	.	.	-1	DOCK10	HGNC	23479	protein_coding	YES	CCDS46528.1	ENSP00000258390	DOC10_HUMAN	Q4ZG60_HUMAN,Q3LIC8_HUMAN	UPI000021D2A7	.	.	.	5/56	.	hmmpanther:PTHR23317:SF71,hmmpanther:PTHR23317,Pfam_domain:PF11878,Superfamily_domains:SSF50729	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATCTCAAA	by1000G	5	ESCA
COL4A3	0	.	GRCh37	2	228125795	228125795	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1115-3C>T	.	.	ENST00000396578	.	50	44	6	83	83	0	COL4A3,splice_region_variant,,ENST00000396578,;AC097662.2,intron_variant,,ENST00000437673,;AC097662.2,intron_variant,,ENST00000396588,;AC097662.2,intron_variant,,ENST00000439598,;AC097662.2,upstream_gene_variant,,ENST00000606119,;	T	ENSG00000169031	ENST00000396578	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	COL4A3	HGNC	2204	protein_coding	YES	CCDS42829.1	ENSP00000379823	CO4A3_HUMAN	Q548X1_HUMAN,A9QVI3_HUMAN	UPI000013E9F3	.	.	.	.	19/51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ATTCCCAGGTC	.	2	ESCA
TMEM214	0	.	GRCh37	2	27255943	27255943	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.60T>A	p.%3D	p.P20P	ENST00000238788	1/17	77	73	4	81	81	0	TMEM214,synonymous_variant,p.%3D,ENST00000404032,;TMEM214,synonymous_variant,p.%3D,ENST00000238788,;TMEM214,upstream_gene_variant,,ENST00000425720,;TMEM214,upstream_gene_variant,,ENST00000444135,;TMEM214,synonymous_variant,p.%3D,ENST00000321326,;TMEM214,non_coding_transcript_exon_variant,,ENST00000495312,;TMEM214,upstream_gene_variant,,ENST00000460904,;TMEM214,upstream_gene_variant,,ENST00000435172,;TMEM214,upstream_gene_variant,,ENST00000478980,;TMEM214,upstream_gene_variant,,ENST00000475258,;	A	ENSG00000119777	ENST00000238788	Transcript	synonymous_variant	122	60	20	P	ccT/ccA	.	.	.	1	TMEM214	HGNC	25983	protein_coding	YES	CCDS42664.1	ENSP00000238788	TM214_HUMAN	B2RD07_HUMAN	UPI00003FF926	.	.	.	1/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGCCTGGGGT	.	2	ESCA
ATRAID	0	.	GRCh37	2	27439826	27439826	+	3'UTR	SNP	G	G	A	rs754675453	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10G>A	.	.	ENST00000380171	7/7	27	21	6	16	16	0	ATRAID,3_prime_UTR_variant,,ENST00000606999,;ATRAID,3_prime_UTR_variant,,ENST00000405489,;ATRAID,3_prime_UTR_variant,,ENST00000380171,;SLC5A6,upstream_gene_variant,,ENST00000432106,;SLC5A6,upstream_gene_variant,,ENST00000412471,;CAD,upstream_gene_variant,,ENST00000403525,;ATRAID,downstream_gene_variant,,ENST00000419744,;SLC5A6,upstream_gene_variant,,ENST00000430186,;SLC5A6,upstream_gene_variant,,ENST00000442731,;SLC5A6,upstream_gene_variant,,ENST00000310574,;SLC5A6,upstream_gene_variant,,ENST00000414408,;CAD,upstream_gene_variant,,ENST00000264705,;SLC5A6,upstream_gene_variant,,ENST00000428518,;ATRAID,non_coding_transcript_exon_variant,,ENST00000472515,;ATRAID,downstream_gene_variant,,ENST00000484646,;ATRAID,downstream_gene_variant,,ENST00000491220,;SLC5A6,upstream_gene_variant,,ENST00000488743,;	A	ENSG00000138085	ENST00000380171	Transcript	3_prime_UTR_variant	1042	.	.	.	.	rs754675453	.	.	1	ATRAID	HGNC	24090	protein_coding	YES	CCDS1741.1	ENSP00000369518	ARAID_HUMAN	C9JA62_HUMAN	UPI0000456D96	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAGGTCTTA	byFrequency	5	ESCA
SRD5A2	0	.	GRCh37	2	31805773	31805773	+	RNA	SNP	C	C	A	rs760689799	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.364G>T	.	.	ENST00000405650	1/5	56	50	6	52	51	0	SRD5A2,non_coding_transcript_exon_variant,,ENST00000233139,;SRD5A2,non_coding_transcript_exon_variant,,ENST00000405650,;	A	ENSG00000049319	ENST00000405650	Transcript	non_coding_transcript_exon_variant	364	.	.	.	.	rs760689799	.	.	-1	SRD5A2	HGNC	11285	processed_transcript	YES	.	.	.	.	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATCCCCGC	.	4	ESCA
TRABD2A	0	.	GRCh37	2	85051238	85051238	+	Silent	SNP	G	G	A	rs748011854	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1026C>T	p.%3D	p.A342A	ENST00000335459	5/6	70	47	22	66	66	0	TRABD2A,synonymous_variant,p.%3D,ENST00000335459,;TRABD2A,synonymous_variant,p.%3D,ENST00000409520,;DNAH6,downstream_gene_variant,,ENST00000237449,;DNAH6,downstream_gene_variant,,ENST00000389394,;TRABD2A,non_coding_transcript_exon_variant,,ENST00000496500,;TRABD2A,non_coding_transcript_exon_variant,,ENST00000479944,;	A	ENSG00000186854	ENST00000335459	Transcript	synonymous_variant	1232	1026	342	A	gcC/gcT	rs748011854	.	.	-1	TRABD2A	HGNC	27013	protein_coding	YES	CCDS46349.1	ENSP00000335004	TIKI1_HUMAN	.	UPI000058F1DB	.	.	.	5/6	.	hmmpanther:PTHR31120,hmmpanther:PTHR31120:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATACGGCTTC	.	5	ESCA
IGKV2D-28	0	.	GRCh37	2	89999560	89999560	+	3'Flank	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000453166	.	88	75	12	115	115	0	IGKV2D-28,missense_variant,p.Pro101Leu,ENST00000558026,;IGKV2D-28,downstream_gene_variant,,ENST00000453166,;	T	ENSG00000242534	ENST00000453166	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2	1	IGKV2D-28	HGNC	5799	IG_V_gene	YES	.	ENSP00000393492	.	.	UPI00005FFCB1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTCCCACAG	.	4	ESCA
KANSL3	0	.	GRCh37	2	97271233	97271233	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1757A>T	p.Glu586Val	p.E586V	ENST00000431828	15/21	37	32	4	55	55	0	KANSL3,missense_variant,p.Glu499Val,ENST00000441706,;KANSL3,missense_variant,p.Glu499Val,ENST00000599854,;KANSL3,missense_variant,p.Glu586Val,ENST00000431828,;KANSL3,missense_variant,p.Glu406Val,ENST00000440133,;KANSL3,non_coding_transcript_exon_variant,,ENST00000487070,;KANSL3,missense_variant,p.Glu612Val,ENST00000420155,;KANSL3,3_prime_UTR_variant,,ENST00000597150,;KANSL3,3_prime_UTR_variant,,ENST00000354204,;KANSL3,3_prime_UTR_variant,,ENST00000447759,;KANSL3,3_prime_UTR_variant,,ENST00000444759,;KANSL3,non_coding_transcript_exon_variant,,ENST00000476534,;KANSL3,upstream_gene_variant,,ENST00000484020,;KANSL3,downstream_gene_variant,,ENST00000488907,;	A	ENSG00000114982	ENST00000431828	Transcript	missense_variant	1834	1757	586	E/V	gAa/gTa	.	.	.	-1	KANSL3	HGNC	25473	protein_coding	YES	CCDS46361.1	ENSP00000396749	KANL3_HUMAN	F8WEN2_HUMAN,B4E1W4_HUMAN	UPI0000207C82	.	deleterious_low_confidence(0.02)	possibly_damaging(0.529)	15/21	.	hmmpanther:PTHR13136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGTTCTGAT	.	4	ESCA
PCNP	0	.	GRCh37	3	101312722	101312722	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1125C>G	.	.	ENST00000265260	5/5	66	50	16	59	59	0	PCNP,3_prime_UTR_variant,,ENST00000296024,;PCNP,3_prime_UTR_variant,,ENST00000265260,;PCNP,3_prime_UTR_variant,,ENST00000469941,;PCNP,downstream_gene_variant,,ENST00000470490,;PCNP,downstream_gene_variant,,ENST00000486406,;PCNP,3_prime_UTR_variant,,ENST00000460231,;PCNP,downstream_gene_variant,,ENST00000498274,;PCNP,downstream_gene_variant,,ENST00000465366,;	G	ENSG00000081154	ENST00000265260	Transcript	3_prime_UTR_variant	1783	.	.	.	.	.	.	.	1	PCNP	HGNC	30023	protein_coding	YES	CCDS2942.1	ENSP00000265260	PCNP_HUMAN	.	UPI0000070241	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAATCTCACC	.	5	ESCA
TATDN2	0	.	GRCh37	3	10312013	10312013	+	Missense_Mutation	SNP	G	G	A	rs760026472	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147G>A	p.Ala383Thr	p.A383T	ENST00000287652	4/8	35	20	15	40	39	1	TATDN2,missense_variant,p.Ala383Thr,ENST00000448281,;TATDN2,missense_variant,p.Ala383Thr,ENST00000287652,;TATDN2,upstream_gene_variant,,ENST00000426850,;RP11-438J1.1,missense_variant,p.Ala326Thr,ENST00000437082,;RP11-438J1.1,3_prime_UTR_variant,,ENST00000450534,;	A	ENSG00000157014	ENST00000287652	Transcript	missense_variant	2198	1147	383	A/T	Gcc/Acc	rs760026472	.	.	1	TATDN2	HGNC	28988	protein_coding	YES	CCDS33698.1	ENSP00000287652	TATD2_HUMAN	H7BZJ2_HUMAN	UPI000013DEC1	.	tolerated(0.42)	benign(0.014)	4/8	.	hmmpanther:PTHR10060,hmmpanther:PTHR10060:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACTACGCCAGC	byFrequency	4	ESCA
DPPA4	0	.	GRCh37	3	109049625	109049625	+	Missense_Mutation	SNP	C	C	T	rs201133846	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.425G>A	p.Arg142Gln	p.R142Q	ENST00000335658	5/7	71	55	16	84	84	0	DPPA4,missense_variant,p.Arg142Gln,ENST00000335658,;DPPA4,downstream_gene_variant,,ENST00000477303,;DPPA4,non_coding_transcript_exon_variant,,ENST00000478791,;DPPA4,intron_variant,,ENST00000463966,;DPPA4,3_prime_UTR_variant,,ENST00000495679,;DPPA4,non_coding_transcript_exon_variant,,ENST00000487299,;DPPA4,downstream_gene_variant,,ENST00000489281,;DPPA4,upstream_gene_variant,,ENST00000475135,;	T	ENSG00000121570	ENST00000335658	Transcript	missense_variant	480	425	142	R/Q	cGg/cAg	rs201133846	.	.	-1	DPPA4	HGNC	19200	protein_coding	YES	CCDS33814.1	ENSP00000335306	DPPA4_HUMAN	C9J7A7_HUMAN	UPI000022C153	.	tolerated(0.36)	benign(0.002)	5/7	.	hmmpanther:PTHR16073,hmmpanther:PTHR16073:SF8	T:0.0006	T:0.0023	T:0	.	T:0	T:0	T:0	T:0.0018	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTCCGGATT	byFrequency|byCluster|by1000G	5	ESCA
NAA50	0	.	GRCh37	3	113440608	113440608	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.509G>A	p.%3D	p.%3D	ENST00000240922	5/5	81	70	11	89	89	0	NAA50,stop_retained_variant,p.%3D,ENST00000240922,;NAA50,stop_retained_variant,p.%3D,ENST00000493454,;NAA50,stop_retained_variant,p.%3D,ENST00000493900,;NAA50,stop_retained_variant,p.%3D,ENST00000477813,;NAA50,stop_retained_variant,p.%3D,ENST00000497525,;NAA50,stop_retained_variant,p.%3D,ENST00000497255,;NAA50,downstream_gene_variant,,ENST00000478020,;NAA50,downstream_gene_variant,,ENST00000467022,;NAA50,3_prime_UTR_variant,,ENST00000481432,;	T	ENSG00000121579	ENST00000240922	Transcript	stop_retained_variant	834	509	170	*	tGa/tAa	.	.	.	-1	NAA50	HGNC	29533	protein_coding	YES	CCDS2975.1	ENSP00000240922	NAA50_HUMAN	B0AZT5_HUMAN	UPI000003B017	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTTCAGTTG	.	4	ESCA
UROC1	0	.	GRCh37	3	126224599	126224599	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758G>A	p.Ser253Asn	p.S253N	ENST00000383579	8/21	91	83	8	105	105	0	UROC1,missense_variant,p.Ser253Asn,ENST00000383579,;UROC1,missense_variant,p.Ser253Asn,ENST00000290868,;	T	ENSG00000159650	ENST00000383579	Transcript	missense_variant	792	758	253	S/N	aGt/aAt	COSM3944793,COSM3944792	.	.	-1	UROC1	HGNC	26444	protein_coding	YES	CCDS54636.1	ENSP00000373073	HUTU_HUMAN	.	UPI0000480109	.	deleterious(0)	probably_damaging(0.982)	8/21	.	HAMAP:MF_00577,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Pfam_domain:PF01175,Superfamily_domains:SSF111326	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCCACTCATT	.	3	ESCA
CLSTN2	0	.	GRCh37	3	140265422	140265422	+	Missense_Mutation	SNP	C	C	T	rs776997183	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1573C>T	p.Arg525Cys	p.R525C	ENST00000458420	10/17	52	43	9	65	65	0	CLSTN2,missense_variant,p.Arg525Cys,ENST00000458420,;CLSTN2,non_coding_transcript_exon_variant,,ENST00000511524,;	T	ENSG00000158258	ENST00000458420	Transcript	missense_variant	1763	1573	525	R/C	Cgc/Tgc	rs776997183	.	.	1	CLSTN2	HGNC	17448	protein_coding	YES	CCDS3112.1	ENSP00000402460	CSTN2_HUMAN	B3KUA5_HUMAN,B3KU27_HUMAN	UPI00001B0051	.	deleterious(0)	probably_damaging(0.985)	10/17	.	hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF3,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCCGCCCT	byFrequency	5	ESCA
ARHGEF26	0	.	GRCh37	3	153935706	153935706	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1894A>T	p.Met632Leu	p.M632L	ENST00000356448	10/15	96	89	6	85	85	0	ARHGEF26,missense_variant,p.Met632Leu,ENST00000465093,;ARHGEF26,missense_variant,p.Met632Leu,ENST00000356448,;ARHGEF26,intron_variant,,ENST00000465817,;ARHGEF26,missense_variant,p.Met632Leu,ENST00000496710,;	T	ENSG00000114790	ENST00000356448	Transcript	missense_variant	2178	1894	632	M/L	Atg/Ttg	.	.	.	1	ARHGEF26	HGNC	24490	protein_coding	YES	CCDS46938.1	ENSP00000348828	ARHGQ_HUMAN	.	UPI00001410D0	.	tolerated(0.15)	benign(0.032)	10/15	.	hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF4,Gene3D:1.20.900.10,Superfamily_domains:SSF48065,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGAGATGATG	.	2	ESCA
YEATS2	0	.	GRCh37	3	183439839	183439839	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452C>G	p.Ser151Cys	p.S151C	ENST00000305135	5/31	69	57	12	48	48	0	YEATS2,missense_variant,p.Ser151Cys,ENST00000305135,;	G	ENSG00000163872	ENST00000305135	Transcript	missense_variant	647	452	151	S/C	tCt/tGt	.	.	.	1	YEATS2	HGNC	25489	protein_coding	YES	CCDS43175.1	ENSP00000306983	YETS2_HUMAN	.	UPI00001BB2B9	.	deleterious(0.04)	possibly_damaging(0.571)	5/31	.	hmmpanther:PTHR23195,hmmpanther:PTHR23195:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTATCTGACA	.	5	ESCA
CNTN4	0	.	GRCh37	3	3081620	3081620	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2164-101G>T	.	.	ENST00000397461	.	17	9	7	19	19	0	CNTN4,intron_variant,,ENST00000397459,;CNTN4,intron_variant,,ENST00000397461,;CNTN4,intron_variant,,ENST00000448906,;CNTN4,intron_variant,,ENST00000418658,;CNTN4,intron_variant,,ENST00000358480,;CNTN4,intron_variant,,ENST00000427331,;CNTN4-AS1,non_coding_transcript_exon_variant,,ENST00000442749,;CNTN4,non_coding_transcript_exon_variant,,ENST00000484686,;CNTN4,intron_variant,,ENST00000427741,;CNTN4,downstream_gene_variant,,ENST00000430505,;	T	ENSG00000144619	ENST00000397461	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CNTN4	HGNC	2174	protein_coding	YES	CCDS43041.1	ENSP00000380602	CNTN4_HUMAN	G3XAD4_HUMAN,C9JMQ2_HUMAN,C9JGK9_HUMAN	UPI000007446C	.	.	.	.	18/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTGGAGAAG	.	5	ESCA
MAP4	0	.	GRCh37	3	47958058	47958058	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1259A>G	p.Gln420Arg	p.Q420R	ENST00000360240	7/19	33	30	3	34	34	0	MAP4,missense_variant,p.Gln437Arg,ENST00000426837,;MAP4,missense_variant,p.Gln420Arg,ENST00000360240,;MAP4,missense_variant,p.Gln420Arg,ENST00000395734,;MAP4,intron_variant,,ENST00000383737,;MAP4,downstream_gene_variant,,ENST00000423088,;MAP4,intron_variant,,ENST00000482752,;	C	ENSG00000047849	ENST00000360240	Transcript	missense_variant	1778	1259	420	Q/R	cAg/cGg	.	.	.	-1	MAP4	HGNC	6862	protein_coding	YES	CCDS33750.1	ENSP00000353375	MAP4_HUMAN	.	UPI000020A6A4	.	deleterious(0)	benign(0.157)	7/19	.	hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGCCTGTGCC	.	2	ESCA
LRTM1	0	.	GRCh37	3	54958911	54958911	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339G>A	p.%3D	p.L113L	ENST00000273286	2/3	26	18	7	39	39	0	LRTM1,synonymous_variant,p.%3D,ENST00000273286,;LRTM1,synonymous_variant,p.%3D,ENST00000493075,;CACNA2D3,intron_variant,,ENST00000474759,;CACNA2D3,intron_variant,,ENST00000415676,;CACNA2D3,intron_variant,,ENST00000490478,;CACNA2D3,intron_variant,,ENST00000288197,;CACNA2D3,intron_variant,,ENST00000471363,;	T	ENSG00000144771	ENST00000273286	Transcript	synonymous_variant	502	339	113	L	ctG/ctA	.	.	.	-1	LRTM1	HGNC	25023	protein_coding	YES	CCDS2876.1	ENSP00000273286	LRTM1_HUMAN	.	UPI000006CEEC	.	.	.	2/3	.	Superfamily_domains:SSF52058,SMART_domains:SM00369,Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24369:SF18,hmmpanther:PTHR24369,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTCCAGGGA	.	5	ESCA
ARF4	0	.	GRCh37	3	57557144	57557144	+	3'UTR	SNP	G	G	A	rs201857922	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*795C>T	.	.	ENST00000303436	6/6	18	14	4	36	36	0	ARF4,3_prime_UTR_variant,,ENST00000303436,;ARF4,3_prime_UTR_variant,,ENST00000496292,;ARF4,3_prime_UTR_variant,,ENST00000489843,;PDE12,downstream_gene_variant,,ENST00000311180,;ARF4,downstream_gene_variant,,ENST00000463880,;ARF4,downstream_gene_variant,,ENST00000483848,;ARF4,3_prime_UTR_variant,,ENST00000486310,;	A	ENSG00000168374	ENST00000303436	Transcript	3_prime_UTR_variant	1606	.	.	.	.	rs201857922	.	.	-1	ARF4	HGNC	655	protein_coding	YES	CCDS2884.1	ENSP00000306010	ARF4_HUMAN	U3KQF2_HUMAN,C9JPM4_HUMAN,C9J6P1_HUMAN	UPI000013E89E	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AAAATGTATTC	.	2	ESCA
ZNF518B	0	.	GRCh37	4	10445192	10445192	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2761A>T	p.Arg921Trp	p.R921W	ENST00000326756	3/3	33	21	12	29	29	0	ZNF518B,missense_variant,p.Arg921Trp,ENST00000326756,;ZNF518B,downstream_gene_variant,,ENST00000507515,;	A	ENSG00000178163	ENST00000326756	Transcript	missense_variant	3200	2761	921	R/W	Agg/Tgg	.	.	.	-1	ZNF518B	HGNC	29365	protein_coding	YES	CCDS33960.1	ENSP00000317614	Z518B_HUMAN	D6RDM9_HUMAN	UPI0000160B97	.	deleterious(0)	probably_damaging(0.999)	3/3	.	hmmpanther:PTHR10032:SF188,hmmpanther:PTHR10032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCTTGCAA	.	5	ESCA
TET2	0	.	GRCh37	4	106159255	106159255	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3409+747A>G	.	.	ENST00000540549	.	49	34	14	52	52	0	TET2,3_prime_UTR_variant,,ENST00000305737,;TET2,3_prime_UTR_variant,,ENST00000394764,;TET2,intron_variant,,ENST00000413648,;TET2,intron_variant,,ENST00000540549,;TET2,intron_variant,,ENST00000380013,;TET2,intron_variant,,ENST00000545826,;TET2,intron_variant,,ENST00000513237,;TET2,downstream_gene_variant,,ENST00000514870,;TET2,intron_variant,,ENST00000265149,;	G	ENSG00000168769	ENST00000540549	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TET2	HGNC	25941	protein_coding	YES	CCDS47120.1	ENSP00000442788	TET2_HUMAN	E7EPB1_HUMAN,D6RE87_HUMAN	UPI00001D75E4	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTATACTG	.	5	ESCA
CCDC109B	0	.	GRCh37	4	110605697	110605697	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.711G>A	p.Trp237Ter	p.W237*	ENST00000394650	6/8	36	33	3	48	48	0	CCDC109B,stop_gained,p.Trp237Ter,ENST00000394650,;CASP6,downstream_gene_variant,,ENST00000265164,;CASP6,downstream_gene_variant,,ENST00000352981,;CCDC109B,downstream_gene_variant,,ENST00000452915,;CASP6,downstream_gene_variant,,ENST00000510324,;CCDC109B,non_coding_transcript_exon_variant,,ENST00000494604,;CASP6,downstream_gene_variant,,ENST00000505117,;CCDC109B,downstream_gene_variant,,ENST00000472310,;CASP6,downstream_gene_variant,,ENST00000507550,;	A	ENSG00000005059	ENST00000394650	Transcript	stop_gained	844	711	237	W/*	tgG/tgA	.	.	.	1	CCDC109B	HGNC	26076	protein_coding	YES	CCDS3683.2	ENSP00000378145	MCUB_HUMAN	.	UPI000037446B	.	.	.	6/8	.	Transmembrane_helices:TMhelix,Pfam_domain:PF04678,hmmpanther:PTHR13462:SF6,hmmpanther:PTHR13462	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GCCTGGCTCAC	.	2	ESCA
JADE1	0	.	GRCh37	4	129792508	129792508	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1622-2A>G	.	p.X541_splice	ENST00000226319	.	20	17	3	43	43	0	JADE1,splice_acceptor_variant,,ENST00000452328,;JADE1,splice_acceptor_variant,,ENST00000512960,;JADE1,splice_acceptor_variant,,ENST00000226319,;SCLT1,intron_variant,,ENST00000503565,;	G	ENSG00000077684	ENST00000226319	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	JADE1	HGNC	30027	protein_coding	YES	CCDS34062.1	ENSP00000226319	JADE1_HUMAN	D6RGE7_HUMAN,D6RFK0_HUMAN,D6RCS1_HUMAN,D6RC05_HUMAN,D6RBB3_HUMAN	UPI000020B45B	.	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTATAGGTGT	.	2	ESCA
DCHS2	0	.	GRCh37	4	155180876	155180876	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5245G>C	p.Asp1749His	p.D1749H	ENST00000357232	20/25	56	51	5	55	55	0	DCHS2,missense_variant,p.Asp1749His,ENST00000357232,;	G	ENSG00000197410	ENST00000357232	Transcript	missense_variant	5245	5245	1749	D/H	Gat/Cat	.	.	.	-1	DCHS2	HGNC	23111	protein_coding	YES	CCDS3785.1	ENSP00000349768	PCD23_HUMAN	B3KT73_HUMAN	UPI000035B018	.	deleterious(0)	probably_damaging(1)	20/25	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF257,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAATCAAGAA	.	2	ESCA
RBPJ	0	.	GRCh37	4	26364087	26364087	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.60-23888A>G	.	.	ENST00000342295	.	16	12	4	21	21	0	RBPJ,5_prime_UTR_variant,,ENST00000514730,;RBPJ,5_prime_UTR_variant,,ENST00000506956,;RBPJ,5_prime_UTR_variant,,ENST00000512351,;RBPJ,5_prime_UTR_variant,,ENST00000355476,;RBPJ,5_prime_UTR_variant,,ENST00000511546,;RBPJ,5_prime_UTR_variant,,ENST00000505958,;RBPJ,5_prime_UTR_variant,,ENST00000514675,;RBPJ,5_prime_UTR_variant,,ENST00000504907,;RBPJ,5_prime_UTR_variant,,ENST00000509158,;RBPJ,5_prime_UTR_variant,,ENST00000342320,;RBPJ,5_prime_UTR_variant,,ENST00000514807,;RBPJ,intron_variant,,ENST00000345843,;RBPJ,intron_variant,,ENST00000342295,;RBPJ,intron_variant,,ENST00000361572,;RBPJ,intron_variant,,ENST00000515573,;RBPJ,intron_variant,,ENST00000507561,;RBPJ,intron_variant,,ENST00000507574,;RBPJ,intron_variant,,ENST00000510778,;RBPJ,intron_variant,,ENST00000348160,;RBPJ,intron_variant,,ENST00000512671,;RBPJ,upstream_gene_variant,,ENST00000504938,;RBPJ,non_coding_transcript_exon_variant,,ENST00000511401,;RBPJ,non_coding_transcript_exon_variant,,ENST00000514656,;RBPJ,intron_variant,,ENST00000515023,;RBPJ,intron_variant,,ENST00000514380,;RBPJ,intron_variant,,ENST00000513182,;RBPJ,upstream_gene_variant,,ENST00000511451,;	G	ENSG00000168214	ENST00000342295	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RBPJ	HGNC	5724	protein_coding	YES	CCDS3437.1	ENSP00000345206	SUH_HUMAN	D6RBQ8_HUMAN,D6RB37_HUMAN,D6RA45_HUMAN,D6R946_HUMAN	UPI000020BDF1	.	.	.	.	2/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AGACTATCATT	.	2	ESCA
PCDH7	0	.	GRCh37	4	30723525	30723525	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.481C>G	p.Leu161Val	p.L161V	ENST00000543491	1/3	30	26	4	23	23	0	PCDH7,missense_variant,p.Leu161Val,ENST00000543491,;PCDH7,missense_variant,p.Leu161Val,ENST00000361762,;PCDH7,upstream_gene_variant,,ENST00000511884,;PCDH7,upstream_gene_variant,,ENST00000507864,;	G	ENSG00000169851	ENST00000543491	Transcript	missense_variant	481	481	161	L/V	Ctt/Gtt	.	.	.	1	PCDH7	HGNC	8659	protein_coding	YES	CCDS54753.1	ENSP00000441802	.	F5GWJ1_HUMAN	UPI0001CB27C3	.	tolerated(0.09)	benign(0.302)	1/3	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF14,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACACTTTAC	.	4	ESCA
HTT	0	.	GRCh37	4	3136265	3136265	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2631C>T	p.%3D	p.F877F	ENST00000355072	19/67	37	33	3	49	49	0	HTT,synonymous_variant,p.%3D,ENST00000355072,;HTT,splice_region_variant,,ENST00000510626,;	T	ENSG00000197386	ENST00000355072	Transcript	synonymous_variant	2776	2631	877	F	ttC/ttT	.	.	.	1	HTT	HGNC	4851	protein_coding	YES	CCDS43206.1	ENSP00000347184	HD_HUMAN	D3DVR8_HUMAN,D2CTD8_HUMAN,D2CTD7_HUMAN,D2CTD4_HUMAN,D2CTD2_HUMAN	UPI000013D567	.	.	.	19/67	.	hmmpanther:PTHR10170:SF10,hmmpanther:PTHR10170,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUSE|VARSCANS	GACTTCAGGTA	.	3	ESCA
DCAF4L1	0	.	GRCh37	4	41987000	41987000	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2000G>T	.	.	ENST00000333141	1/1	103	90	13	126	126	0	DCAF4L1,3_prime_UTR_variant,,ENST00000333141,;RP11-814H16.2,downstream_gene_variant,,ENST00000608029,;	T	ENSG00000182308	ENST00000333141	Transcript	3_prime_UTR_variant	3288	.	.	.	.	.	.	.	1	DCAF4L1	HGNC	27723	protein_coding	YES	CCDS33978.1	ENSP00000327796	DC4L1_HUMAN	.	UPI0000160C25	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGTAGATACA	.	4	ESCA
GNPDA2	0	.	GRCh37	4	44704415	44704415	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*683A>G	.	.	ENST00000295448	7/7	72	60	12	122	122	0	GNPDA2,3_prime_UTR_variant,,ENST00000295448,;GNPDA2,3_prime_UTR_variant,,ENST00000507917,;GNPDA2,intron_variant,,ENST00000608855,;GNPDA2,intron_variant,,ENST00000609092,;GNPDA2,downstream_gene_variant,,ENST00000509756,;GUF1,downstream_gene_variant,,ENST00000281543,;GNPDA2,downstream_gene_variant,,ENST00000507534,;RP11-700J17.2,upstream_gene_variant,,ENST00000610267,;GUF1,downstream_gene_variant,,ENST00000511493,;GNPDA2,downstream_gene_variant,,ENST00000511187,;GUF1,downstream_gene_variant,,ENST00000506793,;	C	ENSG00000163281	ENST00000295448	Transcript	3_prime_UTR_variant	1671	.	.	.	.	.	.	.	-1	GNPDA2	HGNC	21526	protein_coding	YES	CCDS3469.1	ENSP00000295448	GNPI2_HUMAN	.	UPI000004D013	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TATATTAGGGA	.	2	ESCA
FGF5	0	.	GRCh37	4	81188301	81188301	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.323A>C	p.Lys108Thr	p.K108T	ENST00000312465	1/3	99	92	7	94	94	0	FGF5,missense_variant,p.Lys108Thr,ENST00000456523,;FGF5,missense_variant,p.Lys108Thr,ENST00000312465,;FGF5,non_coding_transcript_exon_variant,,ENST00000380628,;FGF5,upstream_gene_variant,,ENST00000503413,;FGF5,missense_variant,p.Lys69Thr,ENST00000507780,;	C	ENSG00000138675	ENST00000312465	Transcript	missense_variant	549	323	108	K/T	aAa/aCa	.	.	.	1	FGF5	HGNC	3683	protein_coding	YES	CCDS34021.1	ENSP00000311697	FGF5_HUMAN	Q8NF90_HUMAN,Q8NBG6_HUMAN	UPI0000039721	.	tolerated(0.25)	benign(0.446)	1/3	.	hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF23,Gene3D:2.80.10.50,Pfam_domain:PF00167,SMART_domains:SM00442,Superfamily_domains:SSF50353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TGGCAAAGTCA	.	2	ESCA
SLC12A7	0	.	GRCh37	5	1079589	1079589	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1320G>C	p.%3D	p.R440R	ENST00000264930	10/24	36	32	4	37	37	0	SLC12A7,synonymous_variant,p.%3D,ENST00000264930,;SLC12A7,upstream_gene_variant,,ENST00000513223,;SLC12A7,non_coding_transcript_exon_variant,,ENST00000510943,;SLC12A7,upstream_gene_variant,,ENST00000504576,;	G	ENSG00000113504	ENST00000264930	Transcript	synonymous_variant	1364	1320	440	R	cgG/cgC	.	.	.	-1	SLC12A7	HGNC	10915	protein_coding	YES	CCDS34129.1	ENSP00000264930	S12A7_HUMAN	.	UPI0000141815	.	.	.	10/24	.	hmmpanther:PTHR11827:SF47,hmmpanther:PTHR11827,Pfam_domain:PF00324,TIGRFAM_domain:TIGR00930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCGGACCGGTT	.	3	ESCA
IL13	0	.	GRCh37	5	131993940	131993940	+	Missense_Mutation	SNP	C	C	T	rs78181870	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.62C>T	p.Thr21Met	p.T21M	ENST00000304506	1/4	54	45	9	57	57	0	IL13,missense_variant,p.Thr21Met,ENST00000304506,;AC004041.2,intron_variant,,ENST00000435042,;AC004041.2,upstream_gene_variant,,ENST00000417516,;AC004041.2,upstream_gene_variant,,ENST00000458509,;IL13,intron_variant,,ENST00000468334,;IL13,intron_variant,,ENST00000487267,;IL13,intron_variant,,ENST00000459878,;IL13,non_coding_transcript_exon_variant,,ENST00000462480,;	T	ENSG00000169194	ENST00000304506	Transcript	missense_variant	76	62	21	T/M	aCg/aTg	rs78181870	.	.	1	IL13	HGNC	5973	protein_coding	YES	CCDS4157.1	ENSP00000304915	IL13_HUMAN	Q4VB53_HUMAN	UPI0000167822	.	tolerated(0.2)	benign(0.003)	1/4	.	Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11322,hmmpanther:PTHR11322:SF0,Pfam_domain:PF03487,SMART_domains:SM00190	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCACGGTCA	byCluster|by1000G	5	ESCA
MZB1	0	.	GRCh37	5	138725440	138725440	+	Missense_Mutation	SNP	C	C	G	rs747771086	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.106G>C	p.Asp36His	p.D36H	ENST00000302125	1/4	40	37	3	56	56	0	MZB1,missense_variant,p.Asp36His,ENST00000302125,;MZB1,missense_variant,p.Asp36His,ENST00000457570,;MZB1,5_prime_UTR_variant,,ENST00000412103,;PROB1,downstream_gene_variant,,ENST00000434752,;MZB1,missense_variant,p.Asp34His,ENST00000503351,;MZB1,missense_variant,p.Asp36His,ENST00000513389,;MZB1,missense_variant,p.Asp36His,ENST00000417694,;MZB1,missense_variant,p.Asp36His,ENST00000503481,;MZB1,non_coding_transcript_exon_variant,,ENST00000509591,;MZB1,non_coding_transcript_exon_variant,,ENST00000503120,;MZB1,upstream_gene_variant,,ENST00000511979,;	G	ENSG00000170476	ENST00000302125	Transcript	missense_variant	164	106	36	D/H	Gat/Cat	rs747771086	.	.	-1	MZB1	HGNC	30125	protein_coding	YES	CCDS47273.1	ENSP00000303920	MZB1_HUMAN	B3KQ72_HUMAN	UPI0000035F67	.	deleterious(0.01)	probably_damaging(0.91)	1/4	.	hmmpanther:PTHR15881:SF1,hmmpanther:PTHR15881	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCATCATCCA	.	2	ESCA
DPYSL3	0	.	GRCh37	5	146773349	146773349	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*249A>G	.	.	ENST00000343218	14/14	46	42	4	62	62	0	DPYSL3,3_prime_UTR_variant,,ENST00000398514,;DPYSL3,3_prime_UTR_variant,,ENST00000534907,;DPYSL3,3_prime_UTR_variant,,ENST00000343218,;DPYSL3,downstream_gene_variant,,ENST00000520473,;DPYSL3,downstream_gene_variant,,ENST00000507309,;DPYSL3,downstream_gene_variant,,ENST00000523458,;	C	ENSG00000113657	ENST00000343218	Transcript	3_prime_UTR_variant	2502	.	.	.	.	.	.	.	-1	DPYSL3	HGNC	3015	protein_coding	YES	CCDS56387.1	ENSP00000343690	DPYL3_HUMAN	F5GWI3_HUMAN	UPI000020CF0E	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTGTCTGAT	.	4	ESCA
PROP1	0	.	GRCh37	5	177420005	177420005	+	Missense_Mutation	SNP	C	C	T	rs766326238	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.386G>A	p.Arg129His	p.R129H	ENST00000308304	3/3	36	33	3	43	43	0	PROP1,missense_variant,p.Arg129His,ENST00000308304,;	T	ENSG00000175325	ENST00000308304	Transcript	missense_variant	695	386	129	R/H	cGc/cAc	rs766326238	.	.	-1	PROP1	HGNC	9455	protein_coding	YES	CCDS4430.1	ENSP00000311290	PROP1_HUMAN	.	UPI00001AEEA4	.	deleterious(0)	probably_damaging(0.997)	3/3	.	hmmpanther:PTHR24329:SF283,hmmpanther:PTHR24329,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|VARSCANS	GTGAGCGCTCT	byFrequency	2	ESCA
EGFLAM	0	.	GRCh37	5	38338853	38338853	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.261C>T	p.%3D	p.S87S	ENST00000354891	3/23	46	32	14	55	55	0	EGFLAM,synonymous_variant,p.%3D,ENST00000354891,;EGFLAM,synonymous_variant,p.%3D,ENST00000322350,;EGFLAM,3_prime_UTR_variant,,ENST00000504709,;	T	ENSG00000164318	ENST00000354891	Transcript	synonymous_variant	607	261	87	S	agC/agT	.	.	.	1	EGFLAM	HGNC	26810	protein_coding	YES	CCDS56363.1	ENSP00000346964	EGFLA_HUMAN	D6RJD2_HUMAN	UPI000022C806	.	.	.	3/23	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10574:SF202,hmmpanther:PTHR10574,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAGCGTGCC	.	5	ESCA
BHMT2	0	.	GRCh37	5	78376682	78376682	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431T>C	p.Val144Ala	p.V144A	ENST00000255192	4/8	56	44	11	60	60	0	BHMT2,missense_variant,p.Val144Ala,ENST00000255192,;BHMT2,intron_variant,,ENST00000521567,;BHMT2,downstream_gene_variant,,ENST00000518666,;DMGDH,intron_variant,,ENST00000520388,;BHMT2,3_prime_UTR_variant,,ENST00000519743,;BHMT2,non_coding_transcript_exon_variant,,ENST00000518758,;BHMT2,downstream_gene_variant,,ENST00000523472,;BHMT2,upstream_gene_variant,,ENST00000523046,;	C	ENSG00000132840	ENST00000255192	Transcript	missense_variant	497	431	144	V/A	gTg/gCg	.	.	.	1	BHMT2	HGNC	1048	protein_coding	YES	CCDS4045.1	ENSP00000255192	BHMT2_HUMAN	E5RH96_HUMAN	UPI00000701B9	.	tolerated(0.25)	possibly_damaging(0.89)	4/8	.	PROSITE_profiles:PS50970,hmmpanther:PTHR21091,hmmpanther:PTHR21091:SF94,Gene3D:3.20.20.330,Pfam_domain:PF02574,PIRSF_domain:PIRSF037505,Superfamily_domains:SSF82282	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATGTGGACT	.	5	ESCA
CMYA5	0	.	GRCh37	5	79030185	79030185	+	Nonsense_Mutation	SNP	C	C	G	rs754682869	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5597C>G	p.Ser1866Ter	p.S1866*	ENST00000446378	2/13	48	44	4	56	56	0	CMYA5,stop_gained,p.Ser1866Ter,ENST00000446378,;CMYA5,upstream_gene_variant,,ENST00000506603,;	G	ENSG00000164309	ENST00000446378	Transcript	stop_gained	5628	5597	1866	S/*	tCa/tGa	rs754682869	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	.	2/13	.	hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACAATCAAAAT	byFrequency	3	ESCA
CMYA5	0	.	GRCh37	5	79031154	79031154	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6566C>G	p.Ser2189Trp	p.S2189W	ENST00000446378	2/13	56	45	11	42	42	0	CMYA5,missense_variant,p.Ser2189Trp,ENST00000446378,;CMYA5,upstream_gene_variant,,ENST00000506603,;	G	ENSG00000164309	ENST00000446378	Transcript	missense_variant	6597	6566	2189	S/W	tCg/tGg	.	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	probably_damaging(0.992)	2/13	.	hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATCGAGCA	.	5	ESCA
TBC1D32	0	.	GRCh37	6	121655463	121655463	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114G>T	p.Glu38Asp	p.E38D	ENST00000398212	1/32	44	40	4	65	65	0	TBC1D32,missense_variant,p.Glu38Asp,ENST00000422369,;TBC1D32,missense_variant,p.Glu38Asp,ENST00000398212,;TBC1D32,missense_variant,p.Glu38Asp,ENST00000275159,;TBC1D32,missense_variant,p.Glu38Asp,ENST00000464622,;	A	ENSG00000146350	ENST00000398212	Transcript	missense_variant	164	114	38	E/D	gaG/gaT	COSM1072785	.	.	-1	TBC1D32	HGNC	21485	protein_coding	YES	CCDS43501.1	ENSP00000381270	BROMI_HUMAN	A2A304_HUMAN	UPI0000E67203	.	tolerated(0.19)	possibly_damaging(0.73)	1/32	.	hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3,Pfam_domain:PF14961	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAATCTCTTC	.	4	ESCA
BTN3A1	0	.	GRCh37	6	26412804	26412804	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1019-593C>T	.	.	ENST00000289361	.	38	26	11	46	46	0	BTN3A1,3_prime_UTR_variant,,ENST00000425234,;BTN3A1,intron_variant,,ENST00000414912,;BTN3A1,intron_variant,,ENST00000289361,;BTN3A1,intron_variant,,ENST00000476549,;BTN3A1,non_coding_transcript_exon_variant,,ENST00000502361,;BTN3A1,intron_variant,,ENST00000513047,;BTN3A1,intron_variant,,ENST00000082468,;	T	ENSG00000026950	ENST00000289361	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	BTN3A1	HGNC	1138	protein_coding	YES	CCDS4608.1	ENSP00000289361	BT3A1_HUMAN	E9PFB8_HUMAN,E7EPR2_HUMAN,B4DQ62_HUMAN,A6PVC0_HUMAN	UPI000013C904	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCCCAGCAC	.	5	ESCA
HIST1H2AM	0	.	GRCh37	6	27860562	27860562	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366G>A	p.%3D	p.E122E	ENST00000359611	1/1	104	88	15	128	128	0	HIST1H2AM,synonymous_variant,p.%3D,ENST00000359611,;HIST1H2BO,upstream_gene_variant,,ENST00000303806,;HIST1H3J,upstream_gene_variant,,ENST00000359303,;RNU7-26P,downstream_gene_variant,,ENST00000458980,;HIST1H3J,non_coding_transcript_exon_variant,,ENST00000479986,;	T	ENSG00000233224	ENST00000359611	Transcript	synonymous_variant	402	366	122	E	gaG/gaA	.	.	.	-1	HIST1H2AM	HGNC	4735	protein_coding	YES	CCDS4639.1	ENSP00000352627	H2A1_HUMAN	A4FTV9_HUMAN,A3KPC7_HUMAN	UPI0000000E01	.	.	.	1/1	.	hmmpanther:PTHR23430:SF24,hmmpanther:PTHR23430,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGCTCTCAGT	.	4	ESCA
NRM	0	.	GRCh37	6	30656474	30656474	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753C>A	p.His251Gln	p.H251Q	ENST00000259953	5/5	45	35	10	59	59	0	NRM,missense_variant,p.His192Gln,ENST00000376420,;NRM,missense_variant,p.His251Gln,ENST00000376421,;NRM,missense_variant,p.His251Gln,ENST00000444096,;NRM,missense_variant,p.His251Gln,ENST00000259953,;PPP1R18,upstream_gene_variant,,ENST00000399199,;PPP1R18,upstream_gene_variant,,ENST00000274853,;NRM,non_coding_transcript_exon_variant,,ENST00000462857,;NRM,non_coding_transcript_exon_variant,,ENST00000482141,;NRM,non_coding_transcript_exon_variant,,ENST00000474864,;NRM,non_coding_transcript_exon_variant,,ENST00000470733,;NRM,non_coding_transcript_exon_variant,,ENST00000495946,;PPP1R18,upstream_gene_variant,,ENST00000467662,;PPP1R18,upstream_gene_variant,,ENST00000488324,;	T	ENSG00000137404	ENST00000259953	Transcript	missense_variant	1105	753	251	H/Q	caC/caA	.	.	.	-1	NRM	HGNC	8003	protein_coding	YES	CCDS4686.1	ENSP00000259953	NRM_HUMAN	B4DP16_HUMAN	UPI0000049DF1	.	tolerated(0.8)	benign(0.004)	5/5	.	hmmpanther:PTHR31040	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AGCAGGTGGAG	.	4	ESCA
BRD2	0	.	GRCh37	6	32940401	32940402	+	5'UTR	DEL	AG	AG	-	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-273_-272delAG	.	.	ENST00000395289	2/14	106	74	32	66	66	0	BRD2,5_prime_UTR_variant,,ENST00000395289,;BRD2,5_prime_UTR_variant,,ENST00000374825,;BRD2,5_prime_UTR_variant,,ENST00000607833,;BRD2,5_prime_UTR_variant,,ENST00000374831,;BRD2,5_prime_UTR_variant,,ENST00000443797,;BRD2,intron_variant,,ENST00000456339,;BRD2,upstream_gene_variant,,ENST00000449025,;BRD2,upstream_gene_variant,,ENST00000449085,;HLA-DMA,upstream_gene_variant,,ENST00000422832,;BRD2,downstream_gene_variant,,ENST00000496118,;BRD2,upstream_gene_variant,,ENST00000606059,;BRD2,upstream_gene_variant,,ENST00000395287,;XXbac-BPG181M17.6,non_coding_transcript_exon_variant,,ENST00000580587,;BRD2-IT1,downstream_gene_variant,,ENST00000415875,;BRD2,downstream_gene_variant,,ENST00000580234,;HLA-DMA,upstream_gene_variant,,ENST00000464392,;BRD2,downstream_gene_variant,,ENST00000584808,;BRD2,downstream_gene_variant,,ENST00000581002,;BRD2,5_prime_UTR_variant,,ENST00000482914,;BRD2,5_prime_UTR_variant,,ENST00000495733,;BRD2,upstream_gene_variant,,ENST00000481259,;BRD2,upstream_gene_variant,,ENST00000464592,;BRD2,upstream_gene_variant,,ENST00000463639,;	-	ENSG00000204256	ENST00000395289	Transcript	5_prime_UTR_variant	1327-1328	.	.	.	.	.	.	.	1	BRD2	HGNC	1103	protein_coding	YES	CCDS56420.1	ENSP00000378704	BRD2_HUMAN	U3KQA6_HUMAN	UPI0000227E6A	.	.	.	2/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTTTGAAGAGTCA	.	3	ESCA
MDN1	0	.	GRCh37	6	90438848	90438848	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5151A>T	p.%3D	p.L1717L	ENST00000369393	36/102	23	19	4	33	33	0	MDN1,synonymous_variant,p.%3D,ENST00000369393,;MDN1,synonymous_variant,p.%3D,ENST00000428876,;	A	ENSG00000112159	ENST00000369393	Transcript	synonymous_variant	5267	5151	1717	L	ctA/ctT	.	.	.	-1	MDN1	HGNC	18302	protein_coding	YES	CCDS5024.1	ENSP00000358400	MDN1_HUMAN	M0QXR3_HUMAN	UPI000013C4B8	.	.	.	36/102	.	hmmpanther:PTHR22908:SF58,hmmpanther:PTHR22908,PIRSF_domain:PIRSF010340	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTGTAGGAC	.	2	ESCA
CASP8AP2	0	.	GRCh37	6	90573976	90573976	+	RNA	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.3985C>G	.	.	ENST00000551025	7/9	49	32	16	88	88	0	CASP8AP2,non_coding_transcript_exon_variant,,ENST00000551025,;CASP8AP2,non_coding_transcript_exon_variant,,ENST00000237177,;CASP8AP2,intron_variant,,ENST00000548224,;CASP8AP2,downstream_gene_variant,,ENST00000444163,;CASP8AP2,downstream_gene_variant,,ENST00000419040,;CASP8AP2,downstream_gene_variant,,ENST00000552401,;	G	ENSG00000118412	ENST00000551025	Transcript	non_coding_transcript_exon_variant	3985	.	.	.	.	.	.	.	1	CASP8AP2	HGNC	1510	processed_transcript	YES	.	.	.	.	.	.	.	.	7/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACCTGAGA	.	5	ESCA
PHF14	0	.	GRCh37	7	11022380	11022380	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.494C>T	p.Ser165Phe	p.S165F	ENST00000403050	3/17	54	48	5	50	50	0	PHF14,missense_variant,p.Ser165Phe,ENST00000403050,;PHF14,intron_variant,,ENST00000445996,;PHF14,intron_variant,,ENST00000476009,;PHF14,non_coding_transcript_exon_variant,,ENST00000490957,;PHF14,intron_variant,,ENST00000521747,;PHF14,intron_variant,,ENST00000423760,;	T	ENSG00000106443	ENST00000403050	Transcript	missense_variant	946	494	165	S/F	tCt/tTt	.	.	.	1	PHF14	HGNC	22203	protein_coding	YES	CCDS47542.1	ENSP00000385795	PHF14_HUMAN	.	UPI000020EB41	.	deleterious_low_confidence(0.03)	unknown(0)	3/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13793:SF10,hmmpanther:PTHR13793	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCTTCTGTTC	.	3	ESCA
SLC13A1	0	.	GRCh37	7	122774551	122774551	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.845G>C	p.Gly282Ala	p.G282A	ENST00000194130	8/15	100	78	21	98	98	0	SLC13A1,missense_variant,p.Gly282Ala,ENST00000194130,;SLC13A1,3_prime_UTR_variant,,ENST00000539873,;SLC13A1,3_prime_UTR_variant,,ENST00000439260,;SLC13A1,3_prime_UTR_variant,,ENST00000427975,;	G	ENSG00000081800	ENST00000194130	Transcript	missense_variant	885	845	282	G/A	gGa/gCa	COSM3632627	.	.	-1	SLC13A1	HGNC	10916	protein_coding	YES	CCDS5786.1	ENSP00000194130	S13A1_HUMAN	Q75MH3_HUMAN,Q75LT0_HUMAN,A4D0X1_HUMAN	UPI0000049F9D	.	tolerated(1)	probably_damaging(0.999)	8/15	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF65,Pfam_domain:PF00939	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATCCAAAG	.	5	ESCA
CNTNAP2	0	.	GRCh37	7	147183046	147183046	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1690G>A	p.Glu564Lys	p.E564K	ENST00000361727	11/24	61	54	7	69	69	0	CNTNAP2,missense_variant,p.Glu564Lys,ENST00000361727,;	A	ENSG00000174469	ENST00000361727	Transcript	missense_variant	2206	1690	564	E/K	Gag/Aag	COSM3950140	.	.	1	CNTNAP2	HGNC	13830	protein_coding	YES	CCDS5889.1	ENSP00000354778	CNTP2_HUMAN	Q9UDV4_HUMAN,Q96T77_HUMAN,Q86UL9_HUMAN,Q86UL6_HUMAN,Q86UL4_HUMAN,Q86UJ1_HUMAN,Q86UI8_HUMAN,Q75MQ9_HUMAN,Q75MF8_HUMAN,Q75MF6_HUMAN,Q75MD4_HUMAN,Q75MA1_HUMAN,Q75M92_HUMAN,Q75LG9_HUMAN,O75852_HUMAN,B7Z1Y6_HUMAN	UPI00001285FA	.	deleterious(0)	probably_damaging(0.976)	11/24	.	PROSITE_profiles:PS50026,hmmpanther:PTHR10127:SF4,hmmpanther:PTHR10127,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGTGAGCAT	.	4	ESCA
TWISTNB	0	.	GRCh37	7	19745033	19745033	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255-490A>G	.	.	ENST00000222567	.	36	30	5	27	27	0	TWISTNB,intron_variant,,ENST00000222567,;MIR3146,non_coding_transcript_exon_variant,,ENST00000580367,;	C	ENSG00000105849	ENST00000222567	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TWISTNB	HGNC	18027	protein_coding	YES	CCDS34606.1	ENSP00000222567	RPA43_HUMAN	.	UPI000006CEF4	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTATACTAG	.	5	ESCA
STK31	0	.	GRCh37	7	23768795	23768795	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.410C>G	p.Ser137Cys	p.S137C	ENST00000355870	6/24	97	91	5	115	115	0	STK31,missense_variant,p.Ser114Cys,ENST00000456014,;STK31,missense_variant,p.Ser137Cys,ENST00000355870,;STK31,missense_variant,p.Ser114Cys,ENST00000428484,;STK31,missense_variant,p.Ser114Cys,ENST00000354639,;STK31,missense_variant,p.Ser93Cys,ENST00000422637,;STK31,missense_variant,p.Ser137Cys,ENST00000433467,;STK31,downstream_gene_variant,,ENST00000444333,;STK31,non_coding_transcript_exon_variant,,ENST00000529549,;STK31,non_coding_transcript_exon_variant,,ENST00000528479,;STK31,non_coding_transcript_exon_variant,,ENST00000405627,;STK31,non_coding_transcript_exon_variant,,ENST00000476399,;STK31,downstream_gene_variant,,ENST00000461866,;	G	ENSG00000196335	ENST00000355870	Transcript	missense_variant	529	410	137	S/C	tCt/tGt	.	.	.	1	STK31	HGNC	11407	protein_coding	YES	CCDS5386.1	ENSP00000348132	STK31_HUMAN	Q75MZ9_HUMAN,F8W6E7_HUMAN,E9PRQ0_HUMAN,C9JQW5_HUMAN,B3KY91_HUMAN	UPI0000167B73	.	deleterious(0)	probably_damaging(0.926)	6/24	.	PROSITE_profiles:PS50304,hmmpanther:PTHR12302:SF0,hmmpanther:PTHR12302,Pfam_domain:PF00567,Gene3D:2.40.50.90,Superfamily_domains:SSF63748,Superfamily_domains:0047647	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTTTTCTAGTG	.	2	ESCA
CREB5	0	.	GRCh37	7	28859157	28859157	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*261A>G	.	.	ENST00000357727	11/11	35	30	4	72	72	0	CREB5,3_prime_UTR_variant,,ENST00000409603,;CREB5,3_prime_UTR_variant,,ENST00000396298,;CREB5,3_prime_UTR_variant,,ENST00000357727,;CREB5,3_prime_UTR_variant,,ENST00000498316,;CREB5,3_prime_UTR_variant,,ENST00000396299,;CREB5,3_prime_UTR_variant,,ENST00000396300,;	G	ENSG00000146592	ENST00000357727	Transcript	3_prime_UTR_variant	2178	.	.	.	.	.	.	.	1	CREB5	HGNC	16844	protein_coding	YES	CCDS5417.1	ENSP00000350359	CREB5_HUMAN	H9KVC5_HUMAN,C9JN33_HUMAN	UPI0000457534	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTTTATAAAC	.	4	ESCA
FIGNL1	0	.	GRCh37	7	50513641	50513641	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1345C>G	p.Leu449Val	p.L449V	ENST00000419119	2/2	48	42	6	63	63	0	FIGNL1,missense_variant,p.Leu449Val,ENST00000433017,;FIGNL1,missense_variant,p.Leu449Val,ENST00000419119,;FIGNL1,missense_variant,p.Leu449Val,ENST00000356889,;FIGNL1,missense_variant,p.Leu449Val,ENST00000395556,;FIGNL1,downstream_gene_variant,,ENST00000422854,;FIGNL1,downstream_gene_variant,,ENST00000420829,;FIGNL1,downstream_gene_variant,,ENST00000448788,;FIGNL1,downstream_gene_variant,,ENST00000440350,;FIGNL1,downstream_gene_variant,,ENST00000436590,;FIGNL1,downstream_gene_variant,,ENST00000435566,;	C	ENSG00000132436	ENST00000419119	Transcript	missense_variant	2899	1345	449	L/V	Cta/Gta	COSM128005	.	.	-1	FIGNL1	HGNC	13286	protein_coding	YES	CCDS5510.1	ENSP00000410811	FIGL1_HUMAN	C9JTG6_HUMAN,C9JTB2_HUMAN,C9JP37_HUMAN,C9JKI6_HUMAN,C9JHJ4_HUMAN	UPI000013CE5D	.	deleterious(0)	probably_damaging(0.977)	2/2	.	hmmpanther:PTHR23074:SF75,hmmpanther:PTHR23074,Pfam_domain:PF00004,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AATTAGAGTTT	.	3	ESCA
ZNF117	0	.	GRCh37	7	64437400	64437400	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1097C>T	.	.	ENST00000282869	4/4	45	37	7	65	65	0	ZNF117,3_prime_UTR_variant,,ENST00000282869,;ZNF117,downstream_gene_variant,,ENST00000487644,;	A	ENSG00000152926	ENST00000282869	Transcript	3_prime_UTR_variant	3834	.	.	.	.	.	.	.	-1	ZNF117	HGNC	12897	protein_coding	YES	CCDS43593.1	ENSP00000282869	ZN117_HUMAN	.	UPI000049E07A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTTGAGGAT	.	5	ESCA
GRM3	0	.	GRCh37	7	86468286	86468286	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1456T>C	p.Trp486Arg	p.W486R	ENST00000361669	4/6	88	73	15	103	103	0	GRM3,missense_variant,p.Trp358Arg,ENST00000536043,;GRM3,missense_variant,p.Trp486Arg,ENST00000361669,;GRM3,missense_variant,p.Trp78Arg,ENST00000546348,;GRM3,intron_variant,,ENST00000439827,;GRM3,intron_variant,,ENST00000394720,;	C	ENSG00000198822	ENST00000361669	Transcript	missense_variant	2555	1456	486	W/R	Tgg/Cgg	.	.	.	1	GRM3	HGNC	4595	protein_coding	YES	CCDS5600.1	ENSP00000355316	GRM3_HUMAN	C9JUH9_HUMAN,C9JIT1_HUMAN,A4D1D0_HUMAN	UPI0000153EFC	.	deleterious(0)	probably_damaging(0.998)	4/6	.	hmmpanther:PTHR24060,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCACTGGGCA	.	5	ESCA
TRRAP	0	.	GRCh37	7	98565243	98565243	+	Silent	SNP	C	C	T	rs771243011	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7413C>T	p.%3D	p.Y2471Y	ENST00000359863	50/72	40	34	6	35	35	0	TRRAP,synonymous_variant,p.%3D,ENST00000355540,;TRRAP,synonymous_variant,p.%3D,ENST00000446306,;TRRAP,synonymous_variant,p.%3D,ENST00000456197,;TRRAP,synonymous_variant,p.%3D,ENST00000359863,;	T	ENSG00000196367	ENST00000359863	Transcript	synonymous_variant	7622	7413	2471	Y	taC/taT	rs771243011	.	.	1	TRRAP	HGNC	12347	protein_coding	YES	CCDS59066.1	ENSP00000352925	TRRAP_HUMAN	C9K0N1_HUMAN	UPI00004575B4	.	.	.	50/72	.	hmmpanther:PTHR11139:SF1,hmmpanther:PTHR11139	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTACGAGCG	.	4	ESCA
FAM200A	0	.	GRCh37	7	99145817	99145817	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214G>C	p.Ala72Pro	p.A72P	ENST00000449309	2/2	42	35	7	44	44	0	FAM200A,missense_variant,p.Ala72Pro,ENST00000408938,;FAM200A,missense_variant,p.Ala72Pro,ENST00000449309,;	G	ENSG00000221909	ENST00000449309	Transcript	missense_variant	594	214	72	A/P	Gca/Cca	.	.	.	-1	FAM200A	HGNC	25401	protein_coding	YES	CCDS5668.1	ENSP00000411372	F200A_HUMAN	J3QT35_HUMAN	UPI0000037C3E	.	deleterious(0.01)	probably_damaging(0.963)	2/2	.	hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF99	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGCCACTC	.	5	ESCA
TRIM4	0	.	GRCh37	7	99489970	99489970	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1319A>T	p.Glu440Val	p.E440V	ENST00000355947	7/7	27	19	8	42	42	0	TRIM4,missense_variant,p.Glu414Val,ENST00000349062,;TRIM4,missense_variant,p.Glu440Val,ENST00000355947,;TRIM4,intron_variant,,ENST00000447480,;	A	ENSG00000146833	ENST00000355947	Transcript	missense_variant	1449	1319	440	E/V	gAg/gTg	.	.	.	-1	TRIM4	HGNC	16275	protein_coding	YES	CCDS5679.1	ENSP00000348216	TRIM4_HUMAN	B4DEC5_HUMAN	UPI000013DA79	.	deleterious(0.01)	probably_damaging(0.999)	7/7	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF91,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCTCTTGC	.	4	ESCA
PKHD1L1	0	.	GRCh37	8	110456047	110456047	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4707C>A	p.Ser1569Arg	p.S1569R	ENST00000378402	37/78	76	66	9	95	95	0	PKHD1L1,missense_variant,p.Ser1569Arg,ENST00000378402,;	A	ENSG00000205038	ENST00000378402	Transcript	missense_variant	4811	4707	1569	S/R	agC/agA	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	tolerated(0.18)	benign(0.424)	37/78	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF213,Pfam_domain:PF01833,Gene3D:2.60.40.10,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAAGCAACAT	.	4	ESCA
FBXL6	0	.	GRCh37	8	145580145	145580145	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1040G>A	p.Arg347Gln	p.R347Q	ENST00000331890	7/9	66	59	7	62	62	0	FBXL6,missense_variant,p.Arg347Gln,ENST00000331890,;FBXL6,missense_variant,p.Arg341Gln,ENST00000455319,;SLC52A2,intron_variant,,ENST00000524541,;SLC52A2,upstream_gene_variant,,ENST00000532887,;TMEM249,upstream_gene_variant,,ENST00000398633,;SLC52A2,upstream_gene_variant,,ENST00000527078,;SLC52A2,upstream_gene_variant,,ENST00000530047,;SLC52A2,upstream_gene_variant,,ENST00000540505,;SLC52A2,upstream_gene_variant,,ENST00000526338,;SLC52A2,upstream_gene_variant,,ENST00000526752,;SLC52A2,upstream_gene_variant,,ENST00000402965,;TMEM249,upstream_gene_variant,,ENST00000526263,;SLC52A2,upstream_gene_variant,,ENST00000534725,;SLC52A2,upstream_gene_variant,,ENST00000329994,;FBXL6,non_coding_transcript_exon_variant,,ENST00000524909,;FBXL6,non_coding_transcript_exon_variant,,ENST00000526524,;FBXL6,non_coding_transcript_exon_variant,,ENST00000527000,;SLC52A2,intron_variant,,ENST00000532815,;FBXL6,downstream_gene_variant,,ENST00000530687,;SLC52A2,upstream_gene_variant,,ENST00000526891,;FBXL6,non_coding_transcript_exon_variant,,ENST00000530142,;FBXL6,non_coding_transcript_exon_variant,,ENST00000524492,;GS1-393G12.13,upstream_gene_variant,,ENST00000531225,;SLC52A2,upstream_gene_variant,,ENST00000526779,;SLC52A2,upstream_gene_variant,,ENST00000533662,;FBXL6,downstream_gene_variant,,ENST00000529279,;TMEM249,upstream_gene_variant,,ENST00000526503,;	T	ENSG00000182325	ENST00000331890	Transcript	missense_variant	1105	1040	347	R/Q	cGa/cAa	.	.	.	-1	FBXL6	HGNC	13603	protein_coding	YES	CCDS6422.1	ENSP00000330098	FBXL6_HUMAN	Q71RB6_HUMAN	UPI000006E3A5	.	deleterious(0.04)	benign(0.027)	7/9	.	Superfamily_domains:SSF52047,Gene3D:3.80.10.10,hmmpanther:PTHR23125,hmmpanther:PTHR23125:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCCTCGTCCC	.	4	ESCA
FSD1L	0	.	GRCh37	9	108308773	108308773	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*9C>T	.	.	ENST00000481272	14/14	46	41	4	74	74	0	FSD1L,3_prime_UTR_variant,,ENST00000539376,;FSD1L,3_prime_UTR_variant,,ENST00000484973,;FSD1L,3_prime_UTR_variant,,ENST00000374710,;FSD1L,3_prime_UTR_variant,,ENST00000374707,;FSD1L,3_prime_UTR_variant,,ENST00000481272,;FSD1L,3_prime_UTR_variant,,ENST00000394926,;	T	ENSG00000106701	ENST00000481272	Transcript	3_prime_UTR_variant	1721	.	.	.	.	.	.	.	1	FSD1L	HGNC	13753	protein_coding	YES	CCDS47999.1	ENSP00000417492	FSD1L_HUMAN	Q8N450_HUMAN	UPI0001931361	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTACTCAGAAT	.	3	ESCA
SVEP1	0	.	GRCh37	9	113170469	113170469	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7411G>A	p.Glu2471Lys	p.E2471K	ENST00000401783	38/48	33	30	3	23	23	0	SVEP1,missense_variant,p.Glu2471Lys,ENST00000401783,;SVEP1,missense_variant,p.Glu2448Lys,ENST00000374469,;SVEP1,missense_variant,p.Glu397Lys,ENST00000297826,;	T	ENSG00000165124	ENST00000401783	Transcript	missense_variant	7748	7411	2471	E/K	Gaa/Aaa	.	.	.	-1	SVEP1	HGNC	15985	protein_coding	YES	CCDS48004.1	ENSP00000384917	SVEP1_HUMAN	.	UPI000153DA74	.	.	probably_damaging(0.999)	38/48	.	Superfamily_domains:SSF57535,SMART_domains:SM00032,Gene3D:2.10.70.10,Pfam_domain:PF00084,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,PROSITE_profiles:PS50923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAATTCAAAGC	.	2	ESCA
CIZ1	0	.	GRCh37	9	130941328	130941328	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1158G>A	p.%3D	p.Q386Q	ENST00000393608	8/17	47	40	7	69	69	0	CIZ1,synonymous_variant,p.%3D,ENST00000325721,;CIZ1,synonymous_variant,p.%3D,ENST00000357558,;CIZ1,synonymous_variant,p.%3D,ENST00000415526,;CIZ1,synonymous_variant,p.%3D,ENST00000538431,;CIZ1,synonymous_variant,p.%3D,ENST00000372938,;CIZ1,synonymous_variant,p.%3D,ENST00000277465,;CIZ1,synonymous_variant,p.%3D,ENST00000541172,;CIZ1,synonymous_variant,p.%3D,ENST00000393608,;CIZ1,intron_variant,,ENST00000372948,;CIZ1,intron_variant,,ENST00000372954,;CIZ1,downstream_gene_variant,,ENST00000324544,;CIZ1,intron_variant,,ENST00000476239,;CIZ1,intron_variant,,ENST00000476727,;CIZ1,downstream_gene_variant,,ENST00000498156,;CIZ1,upstream_gene_variant,,ENST00000475471,;CIZ1,downstream_gene_variant,,ENST00000474442,;CIZ1,downstream_gene_variant,,ENST00000467178,;CIZ1,downstream_gene_variant,,ENST00000491954,;CIZ1,downstream_gene_variant,,ENST00000488559,;CIZ1,upstream_gene_variant,,ENST00000471839,;	T	ENSG00000148337	ENST00000393608	Transcript	synonymous_variant	1361	1158	386	Q	caG/caA	.	.	.	-1	CIZ1	HGNC	16744	protein_coding	YES	CCDS6894.1	ENSP00000377232	CIZ1_HUMAN	Q9Y3F8_HUMAN,F6WSM2_HUMAN,F6VD24_HUMAN,B0EXJ7_HUMAN	UPI0000141722	.	.	.	8/17	.	hmmpanther:PTHR15491:SF9,hmmpanther:PTHR15491	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCCTGTGA	.	5	ESCA
CRAT	0	.	GRCh37	9	131857575	131857575	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*101C>G	.	.	ENST00000318080	14/14	79	67	11	113	113	0	CRAT,3_prime_UTR_variant,,ENST00000455396,;CRAT,3_prime_UTR_variant,,ENST00000318080,;DOLPP1,downstream_gene_variant,,ENST00000406974,;DOLPP1,downstream_gene_variant,,ENST00000540102,;DOLPP1,downstream_gene_variant,,ENST00000372546,;RP11-247A12.1,upstream_gene_variant,,ENST00000434250,;CRAT,downstream_gene_variant,,ENST00000467343,;DOLPP1,downstream_gene_variant,,ENST00000327812,;CRAT,downstream_gene_variant,,ENST00000458362,;	C	ENSG00000095321	ENST00000318080	Transcript	3_prime_UTR_variant	2277	.	.	.	.	.	.	.	-1	CRAT	HGNC	2342	protein_coding	YES	CCDS6919.1	ENSP00000315013	CACP_HUMAN	.	UPI000014021A	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAAGAGGGA	.	5	ESCA
ABL1	0	.	GRCh37	9	133750256	133750256	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1144G>C	p.Asp382His	p.D382H	ENST00000372348	7/11	61	52	9	76	76	0	ABL1,missense_variant,p.Asp363His,ENST00000318560,;ABL1,missense_variant,p.Asp382His,ENST00000372348,;	C	ENSG00000097007	ENST00000372348	Transcript	missense_variant	1518	1144	382	D/H	Gat/Cat	.	.	.	1	ABL1	HGNC	76	protein_coding	YES	CCDS35165.1	ENSP00000361423	ABL1_HUMAN	Q59FK4_HUMAN	UPI000013E4DE	.	deleterious(0)	probably_damaging(0.99)	7/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF87,PROSITE_patterns:PS00109,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGAGATCTT	.	5	ESCA
GLIS3	0	.	GRCh37	9	4118563	4118563	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.915G>T	p.Leu305Phe	p.L305F	ENST00000381971	4/11	41	29	11	70	70	0	GLIS3,missense_variant,p.Leu150Phe,ENST00000324333,;GLIS3,missense_variant,p.Leu305Phe,ENST00000381971,;GLIS3,downstream_gene_variant,,ENST00000478315,;GLIS3,downstream_gene_variant,,ENST00000478844,;GLIS3,downstream_gene_variant,,ENST00000477901,;GLIS3,downstream_gene_variant,,ENST00000481827,;GLIS3,downstream_gene_variant,,ENST00000462164,;GLIS3,non_coding_transcript_exon_variant,,ENST00000490709,;GLIS3,downstream_gene_variant,,ENST00000473846,;GLIS3,downstream_gene_variant,,ENST00000491889,;GLIS3,upstream_gene_variant,,ENST00000467497,;	A	ENSG00000107249	ENST00000381971	Transcript	missense_variant	1509	915	305	L/F	ttG/ttT	.	.	.	-1	GLIS3	HGNC	28510	protein_coding	YES	CCDS43784.1	ENSP00000371398	GLIS3_HUMAN	Q1PHK4_HUMAN,Q1PHJ8_HUMAN,Q1PHJ7_HUMAN,Q1PHJ2_HUMAN,Q1PHI3_HUMAN	UPI0000DA4C5E	.	deleterious(0)	probably_damaging(0.997)	4/11	.	hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF71	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGACAAGGA	.	5	ESCA
PTPRD	0	.	GRCh37	9	8317510	8317510	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*364G>A	.	.	ENST00000381196	43/43	37	30	7	43	43	0	PTPRD,3_prime_UTR_variant,,ENST00000397617,;PTPRD,3_prime_UTR_variant,,ENST00000486161,;PTPRD,3_prime_UTR_variant,,ENST00000358503,;PTPRD,3_prime_UTR_variant,,ENST00000360074,;PTPRD,3_prime_UTR_variant,,ENST00000381196,;PTPRD,3_prime_UTR_variant,,ENST00000397606,;PTPRD,3_prime_UTR_variant,,ENST00000356435,;PTPRD,3_prime_UTR_variant,,ENST00000355233,;PTPRD,3_prime_UTR_variant,,ENST00000397611,;PTPRD,3_prime_UTR_variant,,ENST00000537002,;PTPRD,intron_variant,,ENST00000540109,;	T	ENSG00000153707	ENST00000381196	Transcript	3_prime_UTR_variant	6647	.	.	.	.	.	.	.	-1	PTPRD	HGNC	9668	protein_coding	YES	CCDS43786.1	ENSP00000370593	PTPRD_HUMAN	C9J6E4_HUMAN,B4DK48_HUMAN	UPI0000132990	.	.	.	43/43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTGCTGAAC	.	5	ESCA
KIF27	0	.	GRCh37	9	86504111	86504111	+	Nonsense_Mutation	SNP	G	G	A	rs748394033	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1867C>T	p.Arg623Ter	p.R623*	ENST00000297814	7/18	90	60	30	96	96	0	KIF27,stop_gained,p.Arg623Ter,ENST00000413982,;KIF27,stop_gained,p.Arg14Ter,ENST00000376347,;KIF27,stop_gained,p.Arg623Ter,ENST00000334204,;KIF27,stop_gained,p.Arg623Ter,ENST00000297814,;	A	ENSG00000165115	ENST00000297814	Transcript	stop_gained	2011	1867	623	R/*	Cga/Tga	rs748394033	.	.	-1	KIF27	HGNC	18632	protein_coding	YES	CCDS6665.1	ENSP00000297814	KIF27_HUMAN	B4DMY5_HUMAN	UPI000018F32F	.	.	.	7/18	.	hmmpanther:PTHR24115:SF404,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R623Q|c.1868G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTCGTGTTC	byFrequency	5	ESCA
DCAF12L2	0	.	GRCh37	X	125298882	125298882	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1026G>T	p.%3D	p.R342R	ENST00000538699	2/2	40	33	7	32	32	0	DCAF12L2,synonymous_variant,p.%3D,ENST00000538699,;DCAF12L2,synonymous_variant,p.%3D,ENST00000360028,;	A	ENSG00000198354	ENST00000538699	Transcript	synonymous_variant	1107	1026	342	R	cgG/cgT	.	.	.	-1	DCAF12L2	HGNC	32950	protein_coding	YES	CCDS43991.1	ENSP00000441489	DC122_HUMAN	.	UPI0000197594	.	.	.	2/2	.	hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF8,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGCCGGAT	.	5	ESCA
SPANXC	0	.	GRCh37	X	140335751	140335751	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.193G>C	p.Glu65Gln	p.E65Q	ENST00000358993	2/2	294	267	27	246	246	0	SPANXC,missense_variant,p.Glu65Gln,ENST00000358993,;	G	ENSG00000198573	ENST00000358993	Transcript	missense_variant	232	193	65	E/Q	Gag/Cag	.	.	.	-1	SPANXC	HGNC	14331	protein_coding	YES	CCDS14673.1	ENSP00000351884	SPNXC_HUMAN	.	UPI000003B20F	.	tolerated(0.2)	benign(0.006)	2/2	.	hmmpanther:PTHR23425:SF1,hmmpanther:PTHR23425,Pfam_domain:PF07458	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTGGAG	.	4	ESCA
GAB3	0	.	GRCh37	X	153944371	153944371	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306G>A	p.%3D	p.E102E	ENST00000424127	2/10	23	6	16	38	38	0	GAB3,synonymous_variant,p.%3D,ENST00000424127,;GAB3,synonymous_variant,p.%3D,ENST00000369575,;GAB3,synonymous_variant,p.%3D,ENST00000369568,;GAB3,non_coding_transcript_exon_variant,,ENST00000496390,;	T	ENSG00000160219	ENST00000424127	Transcript	synonymous_variant	358	306	102	E	gaG/gaA	.	.	.	-1	GAB3	HGNC	17515	protein_coding	YES	CCDS48198.1	ENSP00000399588	GAB3_HUMAN	.	UPI0000F23D6F	.	.	.	2/10	.	Superfamily_domains:SSF50729,SMART_domains:SM00233,Gene3D:2.30.29.30,Pfam_domain:PF00169,hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF2,PROSITE_profiles:PS50003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTGCTCAGT	.	5	ESCA
ELK1	0	.	GRCh37	X	47495781	47495781	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EX-01A-11D-A36J-09	TCGA-VR-A8EX-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*447C>T	.	.	ENST00000247161	6/6	104	94	10	104	104	0	ELK1,3_prime_UTR_variant,,ENST00000247161,;ELK1,3_prime_UTR_variant,,ENST00000592066,;ELK1,3_prime_UTR_variant,,ENST00000376983,;ELK1,downstream_gene_variant,,ENST00000343894,;ELK1,downstream_gene_variant,,ENST00000480157,;	A	ENSG00000126767	ENST00000247161	Transcript	3_prime_UTR_variant	1834	.	.	.	.	.	.	.	-1	ELK1	HGNC	3321	protein_coding	YES	CCDS14283.1	ENSP00000247161	ELK1_HUMAN	Q8N9S0_HUMAN,Q86SR6_HUMAN,K7ENR1_HUMAN	UPI0000129E66	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAACGCAGAC	.	3	ESCA
C10orf2	0	.	GRCh37	10	102753223	102753224	+	Frame_Shift_Ins	INS	-	-	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2016dupC	p.Thr673HisfsTer23	p.T673Hfs*23	ENST00000311916	5/5	44	36	8	38	38	0	C10orf2,frameshift_variant,p.Thr673HisfsTer23,ENST00000311916,;C10orf2,3_prime_UTR_variant,,ENST00000370228,;LZTS2,upstream_gene_variant,,ENST00000370223,;LZTS2,upstream_gene_variant,,ENST00000429732,;LZTS2,upstream_gene_variant,,ENST00000426584,;C10orf2,non_coding_transcript_exon_variant,,ENST00000473656,;C10orf2,downstream_gene_variant,,ENST00000476766,;C10orf2,downstream_gene_variant,,ENST00000459764,;LZTS2,upstream_gene_variant,,ENST00000489526,;	C	ENSG00000107815	ENST00000311916	Transcript	frameshift_variant	2196-2197	2011-2012	671	A/AX	gcc/gCcc	.	.	.	1	C10orf2	HGNC	1160	protein_coding	YES	CCDS7506.1	ENSP00000309595	PEO1_HUMAN	E5KSY5_HUMAN,Q9H6V3_HUMAN	UPI000006D9D6	.	.	.	5/5	.	hmmpanther:PTHR12873	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCAGGCCCCC	.	3	ESCA
SEC61A2	0	.	GRCh37	10	12206507	12206507	+	3'UTR	SNP	G	G	T	rs182102192	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*54G>T	.	.	ENST00000298428	12/12	125	70	55	99	99	0	SEC61A2,3_prime_UTR_variant,,ENST00000298428,;SEC61A2,3_prime_UTR_variant,,ENST00000379033,;SEC61A2,3_prime_UTR_variant,,ENST00000419021,;SEC61A2,3_prime_UTR_variant,,ENST00000379020,;SEC61A2,intron_variant,,ENST00000304267,;NUDT5,downstream_gene_variant,,ENST00000491614,;NUDT5,downstream_gene_variant,,ENST00000378937,;NUDT5,downstream_gene_variant,,ENST00000537776,;SEC61A2,intron_variant,,ENST00000495368,;NUDT5,downstream_gene_variant,,ENST00000378952,;SEC61A2,intron_variant,,ENST00000475268,;NUDT5,downstream_gene_variant,,ENST00000476462,;	T	ENSG00000065665	ENST00000298428	Transcript	3_prime_UTR_variant	1574	.	.	.	.	rs182102192	.	.	1	SEC61A2	HGNC	17702	protein_coding	YES	CCDS7088.1	ENSP00000298428	S61A2_HUMAN	Q9NVQ7_HUMAN	UPI0000000B0A	.	.	.	12/12	.	.	A:0.0016	A:0.0061	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATCGTTTTT	byFrequency|by1000G	5	ESCA
GPR123-AS1	0	.	GRCh37	10	134895346	134895346	+	3'Flank	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000444433	.	50	29	20	45	45	0	GPR123,missense_variant,p.Thr330Asn,ENST00000607359,;GPR123-AS1,downstream_gene_variant,,ENST00000444433,;AL445199.1,downstream_gene_variant,,ENST00000366099,;	A	ENSG00000256925	ENST00000444433	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3402	-1	GPR123-AS1	HGNC	49543	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGACCCCCT	.	5	ESCA
GPR123	0	.	GRCh37	10	134942261	134942261	+	Missense_Mutation	SNP	G	G	A	rs776693044	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.929G>A	p.Arg310His	p.R310H	ENST00000392607	7/7	14	7	7	22	22	0	GPR123,missense_variant,p.Arg1029His,ENST00000607359,;GPR123,missense_variant,p.Arg213His,ENST00000392606,;GPR123,missense_variant,p.Arg310His,ENST00000392607,;	A	ENSG00000197177	ENST00000392607	Transcript	missense_variant	1365	929	310	R/H	cGt/cAt	rs776693044,COSM4012854,COSM4012855	.	.	1	GPR123	HGNC	13838	protein_coding	YES	CCDS41580.1	ENSP00000376384	GP123_HUMAN	.	UPI00003D41AD	.	deleterious(0)	probably_damaging(0.999)	7/7	.	PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF261,PROSITE_patterns:PS00650	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGCGTGAGG	.	5	ESCA
FRMPD2	0	.	GRCh37	10	49395321	49395321	+	Missense_Mutation	SNP	C	C	A	rs142488456	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2180G>T	p.Arg727Leu	p.R727L	ENST00000374201	17/29	48	30	18	30	30	0	FRMPD2,missense_variant,p.Arg727Leu,ENST00000374201,;FRMPD2,missense_variant,p.Arg695Leu,ENST00000407470,;FRMPD2,missense_variant,p.Arg702Leu,ENST00000305531,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000494505,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000486151,;	A	ENSG00000170324	ENST00000374201	Transcript	missense_variant	2483	2180	727	R/L	cGg/cTg	rs142488456,COSM1347943	.	.	-1	FRMPD2	HGNC	28572	protein_coding	YES	CCDS31195.1	ENSP00000363317	FRPD2_HUMAN	.	UPI0000D60F5F	.	tolerated(0.54)	benign(0.001)	17/29	.	hmmpanther:PTHR19964:SF42,hmmpanther:PTHR19964	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCCGGCCA	byCluster	5	ESCA
ASAH2	0	.	GRCh37	10	51974561	51974561	+	Missense_Mutation	SNP	C	C	T	rs549196716	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1082G>A	p.Arg361His	p.R361H	ENST00000395526	8/20	125	81	43	104	104	0	ASAH2,missense_variant,p.Arg342His,ENST00000329428,;ASAH2,missense_variant,p.Arg203His,ENST00000443575,;ASAH2,missense_variant,p.Arg361His,ENST00000447815,;ASAH2,missense_variant,p.Arg361His,ENST00000395526,;	T	ENSG00000188611	ENST00000395526	Transcript	missense_variant	1082	1082	361	R/H	cGt/cAt	rs549196716,COSM415008,COSM415007	.	.	-1	ASAH2	HGNC	18860	protein_coding	YES	CCDS7239.2	ENSP00000378897	ASAH2_HUMAN	.	UPI00004042A7	.	tolerated(1)	benign(0.001)	8/20	.	hmmpanther:PTHR12670,Pfam_domain:PF04734	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAACGTGGT	by1000G	5	ESCA
NDST2	0	.	GRCh37	10	75566417	75566417	+	Missense_Mutation	SNP	G	G	C	rs534521520	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1246C>G	p.Leu416Val	p.L416V	ENST00000309979	5/15	28	17	10	34	34	0	NDST2,missense_variant,p.Leu293Val,ENST00000299641,;NDST2,missense_variant,p.Leu416Val,ENST00000309979,;ZSWIM8,downstream_gene_variant,,ENST00000603187,;ZSWIM8,downstream_gene_variant,,ENST00000604729,;ZSWIM8,downstream_gene_variant,,ENST00000604524,;ZSWIM8,downstream_gene_variant,,ENST00000603114,;ZSWIM8,downstream_gene_variant,,ENST00000412198,;NDST2,upstream_gene_variant,,ENST00000429742,;ZSWIM8,downstream_gene_variant,,ENST00000466354,;ZSWIM8,downstream_gene_variant,,ENST00000605216,;ZSWIM8,downstream_gene_variant,,ENST00000398706,;NDST2,downstream_gene_variant,,ENST00000465929,;NDST2,downstream_gene_variant,,ENST00000398701,;NDST2,downstream_gene_variant,,ENST00000463410,;RP11-574K11.31,missense_variant,p.Leu416Val,ENST00000603027,;ZSWIM8,downstream_gene_variant,,ENST00000492395,;RP11-574K11.31,upstream_gene_variant,,ENST00000603706,;	C	ENSG00000166507	ENST00000309979	Transcript	missense_variant	1803	1246	416	L/V	Ctg/Gtg	rs534521520	.	.	-1	NDST2	HGNC	7681	protein_coding	YES	CCDS7335.1	ENSP00000310657	NDST2_HUMAN	J3KNC8_HUMAN,B4DVV6_HUMAN,B4DU70_HUMAN,B4DE98_HUMAN	UPI0000001C41	.	tolerated(0.58)	benign(0.004)	5/15	.	hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF36,Pfam_domain:PF12062	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCAGAGCAA	by1000G	5	ESCA
ENTPD1	0	.	GRCh37	10	97604276	97604276	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493G>T	p.Glu165Ter	p.E165*	ENST00000371207	5/10	96	68	27	69	69	0	ENTPD1,stop_gained,p.Glu160Ter,ENST00000453258,;ENTPD1,stop_gained,p.Glu153Ter,ENST00000371205,;ENTPD1,stop_gained,p.Glu15Ter,ENST00000539125,;ENTPD1,stop_gained,p.Glu45Ter,ENST00000543964,;ENTPD1,stop_gained,p.Glu15Ter,ENST00000371203,;ENTPD1,stop_gained,p.Glu165Ter,ENST00000371207,;ENTPD1-AS1,intron_variant,,ENST00000416301,;RP11-429G19.3,intron_variant,,ENST00000433113,;ENTPD1,non_coding_transcript_exon_variant,,ENST00000490659,;ENTPD1,non_coding_transcript_exon_variant,,ENST00000494070,;ENTPD1,intron_variant,,ENST00000483213,;ENTPD1,downstream_gene_variant,,ENST00000461927,;ENTPD1,upstream_gene_variant,,ENST00000422161,;ENTPD1,non_coding_transcript_exon_variant,,ENST00000371206,;	T	ENSG00000138185	ENST00000371207	Transcript	stop_gained	556	493	165	E/*	Gag/Tag	.	.	.	1	ENTPD1	HGNC	3363	protein_coding	YES	CCDS53556.1	ENSP00000360250	ENTP1_HUMAN	.	UPI0000EE3B3A	.	.	.	5/10	.	hmmpanther:PTHR11782:SF32,hmmpanther:PTHR11782,Pfam_domain:PF01150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGGAGAGG	.	5	ESCA
OPCML	0	.	GRCh37	11	132286834	132286834	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3253G>T	.	.	ENST00000331898	7/7	113	80	33	60	60	0	OPCML,3_prime_UTR_variant,,ENST00000524381,;OPCML,3_prime_UTR_variant,,ENST00000331898,;OPCML,downstream_gene_variant,,ENST00000374778,;OPCML,downstream_gene_variant,,ENST00000541867,;OPCML,downstream_gene_variant,,ENST00000529038,;	A	ENSG00000183715	ENST00000331898	Transcript	3_prime_UTR_variant	4870	.	.	.	.	.	.	.	-1	OPCML	HGNC	8143	protein_coding	YES	CCDS8492.1	ENSP00000330862	OPCM_HUMAN	B7ZLQ0_HUMAN,B2CZX3_HUMAN,A8K0Y0_HUMAN	UPI0000055AE0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGGCATTAC	.	5	ESCA
OTOG	0	.	GRCh37	11	17650754	17650754	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6639G>A	p.Met2213Ile	p.M2213I	ENST00000399391	39/55	34	18	16	35	35	0	OTOG,missense_variant,p.Met2140Ile,ENST00000399397,;OTOG,missense_variant,p.Met1219Ile,ENST00000342528,;OTOG,missense_variant,p.Met2213Ile,ENST00000399391,;	A	ENSG00000188162	ENST00000399391	Transcript	missense_variant	6639	6639	2213	M/I	atG/atA	.	.	.	1	OTOG	HGNC	8516	protein_coding	YES	CCDS59225.1	ENSP00000382323	OTOG_HUMAN	H9KVB3_HUMAN	UPI0001662628	.	.	benign(0.135)	39/55	.	PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF228,hmmpanther:PTHR11339,Pfam_domain:PF00094,SMART_domains:SM00216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATGTACAT	.	5	ESCA
MRGPRX3	0	.	GRCh37	11	18159894	18159894	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*176T>G	.	.	ENST00000396275	3/3	44	34	9	15	15	0	MRGPRX3,3_prime_UTR_variant,,ENST00000396275,;RP11-113D6.6,downstream_gene_variant,,ENST00000527671,;MRGPRX3,downstream_gene_variant,,ENST00000531264,;	G	ENSG00000179826	ENST00000396275	Transcript	3_prime_UTR_variant	1506	.	.	.	.	.	.	.	1	MRGPRX3	HGNC	17980	protein_coding	YES	CCDS7830.1	ENSP00000379571	MRGX3_HUMAN	E9PPY5_HUMAN	UPI0000061FCF	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAGCATTAGTC	.	4	ESCA
SLC17A6	0	.	GRCh37	11	22363299	22363299	+	Silent	SNP	C	C	T	.	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312C>T	p.%3D	p.I104I	ENST00000263160	2/12	157	100	56	130	130	0	SLC17A6,synonymous_variant,p.%3D,ENST00000263160,;CTD-2140G10.2,upstream_gene_variant,,ENST00000530569,;CTD-2140G10.2,upstream_gene_variant,,ENST00000531304,;CTD-2140G10.2,upstream_gene_variant,,ENST00000528009,;SLC17A6,upstream_gene_variant,,ENST00000534115,;	T	ENSG00000091664	ENST00000263160	Transcript	synonymous_variant	749	312	104	I	atC/atT	COSM925993	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	2/12	.	PROSITE_profiles:PS50850,hmmpanther:PTHR11662:SF201,hmmpanther:PTHR11662,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATCCACCG	.	5	ESCA
FRMD8	0	.	GRCh37	11	65172410	65172410	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1147A>G	p.Ser383Gly	p.S383G	ENST00000317568	10/11	176	132	44	57	57	0	FRMD8,missense_variant,p.Ser327Gly,ENST00000355991,;FRMD8,missense_variant,p.Ser383Gly,ENST00000317568,;FRMD8,missense_variant,p.Ser349Gly,ENST00000416776,;	G	ENSG00000126391	ENST00000317568	Transcript	missense_variant	1310	1147	383	S/G	Agt/Ggt	.	.	.	1	FRMD8	HGNC	25462	protein_coding	YES	CCDS8102.1	ENSP00000319726	FRMD8_HUMAN	Q96MK6_HUMAN,E9PRA3_HUMAN	UPI000000DAAC	.	tolerated(0.29)	benign(0.003)	10/11	.	hmmpanther:PTHR13283	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGACAGTGCG	.	5	ESCA
PACS1	0	.	GRCh37	11	66010644	66010644	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2785G>A	p.Asp929Asn	p.D929N	ENST00000320580	24/24	63	34	29	38	38	0	PACS1,missense_variant,p.Asp73Asn,ENST00000529677,;PACS1,missense_variant,p.Asp465Asn,ENST00000529757,;PACS1,missense_variant,p.Asp57Asn,ENST00000531597,;PACS1,missense_variant,p.Asp57Asn,ENST00000524815,;PACS1,missense_variant,p.Asp929Asn,ENST00000320580,;RP11-755F10.1,downstream_gene_variant,,ENST00000531086,;PACS1,downstream_gene_variant,,ENST00000525798,;	A	ENSG00000175115	ENST00000320580	Transcript	missense_variant	2818	2785	929	D/N	Gat/Aat	.	.	.	1	PACS1	HGNC	30032	protein_coding	YES	CCDS8129.1	ENSP00000316454	PACS1_HUMAN	Q9NTH2_HUMAN,E9PSG7_HUMAN,E9PSE1_HUMAN,E9PNZ9_HUMAN,B4DF77_HUMAN	UPI0000190973	.	deleterious(0)	probably_damaging(0.955)	24/24	.	hmmpanther:PTHR13280:SF16,hmmpanther:PTHR13280,Pfam_domain:PF10254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCGATGGG	.	5	ESCA
RIN1	0	.	GRCh37	11	66103925	66103925	+	5'UTR	SNP	C	C	A	rs576729986	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-52G>T	.	.	ENST00000311320	1/10	83	57	26	32	32	0	RIN1,5_prime_UTR_variant,,ENST00000311320,;RIN1,intron_variant,,ENST00000530056,;BRMS1,downstream_gene_variant,,ENST00000425825,;RIN1,upstream_gene_variant,,ENST00000424433,;BRMS1,downstream_gene_variant,,ENST00000359957,;BRMS1,downstream_gene_variant,,ENST00000524699,;BRMS1,downstream_gene_variant,,ENST00000530756,;RP11-867G23.12,non_coding_transcript_exon_variant,,ENST00000526655,;RIN1,upstream_gene_variant,,ENST00000524804,;RIN1,upstream_gene_variant,,ENST00000534824,;RIN1,upstream_gene_variant,,ENST00000526246,;BRMS1,downstream_gene_variant,,ENST00000534617,;RIN1,upstream_gene_variant,,ENST00000530745,;RIN1,upstream_gene_variant,,ENST00000528006,;BRMS1,downstream_gene_variant,,ENST00000527375,;BRMS1,downstream_gene_variant,,ENST00000525127,;BRMS1,downstream_gene_variant,,ENST00000530238,;	A	ENSG00000174791	ENST00000311320	Transcript	5_prime_UTR_variant	76	.	.	.	.	rs576729986	.	.	-1	RIN1	HGNC	18749	protein_coding	YES	CCDS31614.1	ENSP00000310406	RIN1_HUMAN	.	UPI000013F14D	.	.	.	1/10	.	.	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCACGCACA	by1000G	5	ESCA
NPAS4	0	.	GRCh37	11	66190167	66190167	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453C>T	p.%3D	p.F151F	ENST00000311034	4/8	84	45	39	21	21	0	NPAS4,synonymous_variant,p.%3D,ENST00000311034,;NPAS4,synonymous_variant,p.%3D,ENST00000525148,;NPAS4,upstream_gene_variant,,ENST00000524617,;	T	ENSG00000174576	ENST00000311034	Transcript	synonymous_variant	629	453	151	F	ttC/ttT	.	.	.	1	NPAS4	HGNC	18983	protein_coding	YES	CCDS8138.1	ENSP00000311196	NPAS4_HUMAN	.	UPI0000074744	.	.	.	4/8	.	Superfamily_domains:SSF55785,Gene3D:3.30.450.20,hmmpanther:PTHR23043:SF13,hmmpanther:PTHR23043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTTCAACAC	.	5	ESCA
GDPD4	0	.	GRCh37	11	76979559	76979559	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.650C>A	p.Ser217Tyr	p.S217Y	ENST00000315938	9/16	159	62	97	45	45	0	GDPD4,missense_variant,p.Ser217Tyr,ENST00000376217,;GDPD4,missense_variant,p.Ser217Tyr,ENST00000315938,;GDPD4,downstream_gene_variant,,ENST00000527489,;GDPD4,downstream_gene_variant,,ENST00000532155,;	T	ENSG00000178795	ENST00000315938	Transcript	missense_variant	901	650	217	S/Y	tCc/tAc	.	.	.	-1	GDPD4	HGNC	24849	protein_coding	YES	CCDS8249.1	ENSP00000320815	GDPD4_HUMAN	.	UPI00001B3DB6	.	deleterious(0)	probably_damaging(0.99)	9/16	.	PROSITE_profiles:PS51704,hmmpanther:PTHR23344:SF13,hmmpanther:PTHR23344,Pfam_domain:PF03009,Gene3D:3.20.20.190,Superfamily_domains:SSF51695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAAGGACATC	.	5	ESCA
CUX2	0	.	GRCh37	12	111785396	111785396	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3728G>A	p.Gly1243Asp	p.G1243D	ENST00000261726	22/22	51	35	16	41	41	0	CUX2,missense_variant,p.Gly1243Asp,ENST00000261726,;	A	ENSG00000111249	ENST00000261726	Transcript	missense_variant	3882	3728	1243	G/D	gGt/gAt	.	.	.	1	CUX2	HGNC	19347	protein_coding	YES	CCDS41837.1	ENSP00000261726	CUX2_HUMAN	Q9BZX3_HUMAN,Q9BZV4_HUMAN	UPI00001FBB07	.	tolerated(0.14)	benign(0.009)	22/22	.	hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGGGTCCTG	.	5	ESCA
GOLGA3	0	.	GRCh37	12	133384931	133384931	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724A>G	p.Lys242Glu	p.K242E	ENST00000204726	5/24	59	38	21	41	41	0	GOLGA3,missense_variant,p.Lys242Glu,ENST00000204726,;GOLGA3,missense_variant,p.Lys242Glu,ENST00000537452,;GOLGA3,missense_variant,p.Lys242Glu,ENST00000450791,;GOLGA3,missense_variant,p.Lys242Glu,ENST00000456883,;GOLGA3,missense_variant,p.Lys242Glu,ENST00000545875,;	C	ENSG00000090615	ENST00000204726	Transcript	missense_variant	1283	724	242	K/E	Aaa/Gaa	.	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	deleterious_low_confidence(0)	possibly_damaging(0.547)	5/24	.	hmmpanther:PTHR18902:SF20,hmmpanther:PTHR18902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTTGCTTG	.	5	ESCA
ST8SIA1	0	.	GRCh37	12	22354310	22354310	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*176A>G	.	.	ENST00000396037	5/5	16	11	5	16	16	0	ST8SIA1,3_prime_UTR_variant,,ENST00000396037,;ST8SIA1,3_prime_UTR_variant,,ENST00000539510,;ST8SIA1,downstream_gene_variant,,ENST00000540824,;ST8SIA1,intron_variant,,ENST00000545524,;ST8SIA1,intron_variant,,ENST00000544732,;ST8SIA1,downstream_gene_variant,,ENST00000508924,;ST8SIA1,downstream_gene_variant,,ENST00000545494,;ST8SIA1,3_prime_UTR_variant,,ENST00000261197,;	C	ENSG00000111728	ENST00000396037	Transcript	3_prime_UTR_variant	1729	.	.	.	.	.	.	.	-1	ST8SIA1	HGNC	10869	protein_coding	YES	CCDS8697.1	ENSP00000379353	SIA8A_HUMAN	H0YFU1_HUMAN	UPI000013596F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTTATTTG	.	5	ESCA
NUDT4	0	.	GRCh37	12	93795826	93795826	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2671G>A	.	.	ENST00000337179	5/5	25	21	4	11	11	0	NUDT4,3_prime_UTR_variant,,ENST00000549992,;NUDT4,3_prime_UTR_variant,,ENST00000337179,;NUDT4,3_prime_UTR_variant,,ENST00000415493,;NUDT4,downstream_gene_variant,,ENST00000546925,;NUDT4,downstream_gene_variant,,ENST00000548662,;NUDT4,downstream_gene_variant,,ENST00000550056,;NUDT4,downstream_gene_variant,,ENST00000547014,;UBE2N,downstream_gene_variant,,ENST00000548946,;	A	ENSG00000173598	ENST00000337179	Transcript	3_prime_UTR_variant	3657	.	.	.	.	.	.	.	1	NUDT4	HGNC	8051	protein_coding	YES	CCDS9044.1	ENSP00000338352	NUDT4_HUMAN	.	UPI00000730C3	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	AAGTAGAAACT	.	2	ESCA
FAM155A	0	.	GRCh37	13	108183540	108183540	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.916-320437C>A	.	.	ENST00000375915	.	202	151	51	86	86	0	FAM155A,intron_variant,,ENST00000375915,;MIR1267,non_coding_transcript_exon_variant,,ENST00000408723,;	T	ENSG00000204442	ENST00000375915	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	FAM155A	HGNC	33877	protein_coding	YES	CCDS32006.1	ENSP00000365080	F155A_HUMAN	.	UPI000045882C	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTTGAAATG	.	5	ESCA
MYO16	0	.	GRCh37	13	109793189	109793189	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4563C>T	p.%3D	p.V1521V	ENST00000356711	32/35	21	10	10	19	19	0	MYO16,synonymous_variant,p.%3D,ENST00000356711,;MYO16,synonymous_variant,p.%3D,ENST00000357550,;	T	ENSG00000041515	ENST00000356711	Transcript	synonymous_variant	4689	4563	1521	V	gtC/gtT	.	.	.	1	MYO16	HGNC	29822	protein_coding	YES	CCDS32008.1	ENSP00000349145	MYO16_HUMAN	.	UPI0000160FF2	.	.	.	32/35	.	Pfam_domain:PF15439	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTCCTGGA	.	5	ESCA
LRCH1	0	.	GRCh37	13	47266728	47266728	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1072G>C	p.Glu358Gln	p.E358Q	ENST00000389797	8/20	57	42	14	28	28	0	LRCH1,missense_variant,p.Glu358Gln,ENST00000389797,;LRCH1,missense_variant,p.Glu358Gln,ENST00000311191,;LRCH1,missense_variant,p.Glu358Gln,ENST00000389798,;LRCH1,downstream_gene_variant,,ENST00000478412,;LRCH1,downstream_gene_variant,,ENST00000463929,;LRCH1,non_coding_transcript_exon_variant,,ENST00000443945,;	C	ENSG00000136141	ENST00000389797	Transcript	missense_variant	1209	1072	358	E/Q	Gaa/Caa	.	.	.	1	LRCH1	HGNC	20309	protein_coding	YES	CCDS53865.1	ENSP00000374447	LRCH1_HUMAN	C9JWE0_HUMAN,C9J5B8_HUMAN	UPI00015DFE06	.	tolerated(0.64)	possibly_damaging(0.579)	8/20	.	hmmpanther:PTHR23155:SF434,hmmpanther:PTHR23155	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAGAACAG	.	5	ESCA
RTL1	0	.	GRCh37	14	101347177	101347177	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3949G>A	p.Ala1317Thr	p.A1317T	ENST00000534062	1/1	132	88	43	79	79	0	RTL1,missense_variant,p.Ala1317Thr,ENST00000534062,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,upstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,;MIR127,upstream_gene_variant,,ENST00000384876,;MIR431,upstream_gene_variant,,ENST00000385266,;	T	ENSG00000254656	ENST00000534062	Transcript	missense_variant	4008	3949	1317	A/T	Gcc/Acc	.	.	.	-1	RTL1	HGNC	14665	protein_coding	YES	CCDS53910.1	ENSP00000435342	RTL1_HUMAN	.	UPI00001D7B9E	.	tolerated_low_confidence(0.75)	benign(0.007)	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCCCTGG	.	5	ESCA
RCOR1	0	.	GRCh37	14	103193618	103193619	+	3'UTR	INS	-	-	C	rs11410469	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*783dupC	.	.	ENST00000262241	12/12	58	43	15	22	22	0	RCOR1,3_prime_UTR_variant,,ENST00000262241,;RCOR1,3_prime_UTR_variant,,ENST00000570597,;RCOR1,downstream_gene_variant,,ENST00000560472,;	C	ENSG00000089902	ENST00000262241	Transcript	3_prime_UTR_variant	2459-2460	.	.	.	.	rs11410469	.	.	1	RCOR1	HGNC	17441	protein_coding	YES	CCDS9974.2	ENSP00000262241	.	J3KN32_HUMAN	UPI0000D6A053	.	.	.	12/12	.	.	C:0.0938	C:0.1989	C:0.0879	.	C:0.006	C:0.0974	C:0.0429	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	8	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TCCTGACCCCC	byFrequency|byCluster|by1000G	2	ESCA
SALL2	0	.	GRCh37	14	21991676	21991676	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2186G>T	p.Gly729Val	p.G729V	ENST00000327430	2/2	21	13	7	17	17	0	SALL2,missense_variant,p.Gly592Val,ENST00000450879,;SALL2,missense_variant,p.Gly729Val,ENST00000327430,;SALL2,missense_variant,p.Gly588Val,ENST00000546363,;SALL2,intron_variant,,ENST00000538754,;SALL2,intron_variant,,ENST00000317492,;SALL2,downstream_gene_variant,,ENST00000537235,;SALL2,downstream_gene_variant,,ENST00000541965,;AE000658.22,downstream_gene_variant,,ENST00000535893,;	A	ENSG00000165821	ENST00000327430	Transcript	missense_variant	2481	2186	729	G/V	gGa/gTa	.	.	.	-1	SALL2	HGNC	10526	protein_coding	YES	CCDS32045.1	ENSP00000333537	SALL2_HUMAN	F5H1G6_HUMAN	UPI00001AF54D	.	tolerated(0.47)	possibly_damaging(0.826)	2/2	.	hmmpanther:PTHR23233:SF15,hmmpanther:PTHR23233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCACCT	.	5	ESCA
G2E3	0	.	GRCh37	14	31085591	31085591	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1972G>T	p.Val658Leu	p.V658L	ENST00000206595	15/15	145	83	61	86	86	0	G2E3,missense_variant,p.Val688Leu,ENST00000553504,;G2E3,missense_variant,p.Val658Leu,ENST00000206595,;G2E3,missense_variant,p.Val612Leu,ENST00000438909,;G2E3,non_coding_transcript_exon_variant,,ENST00000549159,;G2E3,downstream_gene_variant,,ENST00000548934,;	T	ENSG00000092140	ENST00000206595	Transcript	missense_variant	2126	1972	658	V/L	Gtg/Ttg	.	.	.	1	G2E3	HGNC	20338	protein_coding	YES	CCDS9638.1	ENSP00000206595	G2E3_HUMAN	G3V5B6_HUMAN,G3V3B6_HUMAN,F8W0F5_HUMAN,F8VY49_HUMAN,F5GX24_HUMAN	UPI000013F3A8	.	tolerated(0.68)	benign(0.004)	15/15	.	Superfamily_domains:SSF56204,SMART_domains:SM00119,Pfam_domain:PF00632,hmmpanther:PTHR12420,hmmpanther:PTHR12420:SF13,PROSITE_profiles:PS50237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCATGTGGAT	.	5	ESCA
SIX6	0	.	GRCh37	14	60976547	60976547	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.431G>A	p.Arg144His	p.R144H	ENST00000327720	1/2	50	33	17	53	53	0	SIX6,missense_variant,p.Arg144His,ENST00000327720,;C14orf39,intron_variant,,ENST00000556799,;	A	ENSG00000184302	ENST00000327720	Transcript	missense_variant	879	431	144	R/H	cGc/cAc	.	.	.	1	SIX6	HGNC	10892	protein_coding	YES	CCDS9747.1	ENSP00000328596	SIX6_HUMAN	Q6P051_HUMAN,Q5M8S8_HUMAN	UPI000013E4DB	.	deleterious(0)	probably_damaging(0.993)	1/2	.	PROSITE_profiles:PS50071,hmmpanther:PTHR10390:SF12,hmmpanther:PTHR10390,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTACGCGAGT	.	5	ESCA
PCSK6	0	.	GRCh37	15	101910603	101910603	+	Missense_Mutation	SNP	C	C	T	rs759298704	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000348070	13/23	57	36	21	40	40	0	PCSK6,missense_variant,p.Arg552Gln,ENST00000358417,;PCSK6,missense_variant,p.Arg387Gln,ENST00000331826,;PCSK6,missense_variant,p.Arg552Gln,ENST00000348070,;PCSK6,missense_variant,p.Arg552Gln,ENST00000398181,;PCSK6,missense_variant,p.Arg552Gln,ENST00000344273,;PCSK6,missense_variant,p.Arg381Gln,ENST00000398185,;PCSK6,synonymous_variant,p.%3D,ENST00000559605,;PCSK6,upstream_gene_variant,,ENST00000558951,;PCSK6,non_coding_transcript_exon_variant,,ENST00000560902,;PCSK6,non_coding_transcript_exon_variant,,ENST00000560921,;PCSK6,non_coding_transcript_exon_variant,,ENST00000561109,;PCSK6,non_coding_transcript_exon_variant,,ENST00000558716,;PCSK6,non_coding_transcript_exon_variant,,ENST00000560271,;PCSK6,non_coding_transcript_exon_variant,,ENST00000561177,;PCSK6,non_coding_transcript_exon_variant,,ENST00000559678,;PCSK6,non_coding_transcript_exon_variant,,ENST00000561444,;PCSK6,intron_variant,,ENST00000557794,;PCSK6,non_coding_transcript_exon_variant,,ENST00000558154,;	T	ENSG00000140479	ENST00000348070	Transcript	missense_variant	1655	1655	552	R/Q	cGa/cAa	rs759298704	.	.	-1	PCSK6	HGNC	8569	protein_coding	YES	.	ENSP00000305056	PCSK6_HUMAN	A2RQD9_HUMAN	UPI00001AE92B	.	deleterious(0)	probably_damaging(0.999)	13/23	.	hmmpanther:PTHR10795:SF345,hmmpanther:PTHR10795,Pfam_domain:PF01483,Gene3D:2.60.120.260,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCGGCGT	byFrequency	5	ESCA
BCL2A1	0	.	GRCh37	15	80263190	80263190	+	Missense_Mutation	SNP	G	G	C	rs775618108	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272C>G	p.Thr91Ser	p.T91S	ENST00000267953	1/2	63	45	18	47	47	0	BCL2A1,missense_variant,p.Thr91Ser,ENST00000267953,;BCL2A1,missense_variant,p.Thr91Ser,ENST00000335661,;	C	ENSG00000140379	ENST00000267953	Transcript	missense_variant	599	272	91	T/S	aCc/aGc	rs775618108	.	.	-1	BCL2A1	HGNC	991	protein_coding	YES	CCDS10312.1	ENSP00000267953	B2LA1_HUMAN	.	UPI00001268AE	.	deleterious(0.01)	probably_damaging(0.997)	1/2	.	PROSITE_profiles:PS50062,hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF10,PROSITE_patterns:PS01080,Pfam_domain:PF00452,Gene3D:1.10.437.10,SMART_domains:SM00337,Superfamily_domains:SSF56854,Prints_domain:PR01862,Prints_domain:PR01867	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATATGGTTACA	.	4	ESCA
GPR139	0	.	GRCh37	16	20043281	20043281	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838A>G	p.Ile280Val	p.I280V	ENST00000570682	2/2	66	39	27	49	49	0	GPR139,missense_variant,p.Ile280Val,ENST00000570682,;GPR139,3_prime_UTR_variant,,ENST00000326571,;	C	ENSG00000180269	ENST00000570682	Transcript	missense_variant	1139	838	280	I/V	Atc/Gtc	.	.	.	-1	GPR139	HGNC	19995	protein_coding	YES	CCDS32398.1	ENSP00000458791	GP139_HUMAN	.	UPI000004C566	.	tolerated(1)	benign(0.012)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22751:SF49,hmmpanther:PTHR22751,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGATGGCTG	.	5	ESCA
UBN1	0	.	GRCh37	16	4927081	4927081	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3234C>G	p.%3D	p.A1078A	ENST00000396658	15/17	42	19	22	30	30	0	UBN1,synonymous_variant,p.%3D,ENST00000590769,;UBN1,synonymous_variant,p.%3D,ENST00000545171,;UBN1,synonymous_variant,p.%3D,ENST00000396658,;UBN1,synonymous_variant,p.%3D,ENST00000262376,;UBN1,downstream_gene_variant,,ENST00000586716,;UBN1,3_prime_UTR_variant,,ENST00000589191,;UBN1,non_coding_transcript_exon_variant,,ENST00000586152,;	G	ENSG00000118900	ENST00000396658	Transcript	synonymous_variant	3937	3234	1078	A	gcC/gcG	.	.	.	1	UBN1	HGNC	12506	protein_coding	YES	CCDS10525.1	ENSP00000379894	UBN1_HUMAN	K7EQR1_HUMAN	UPI0000071469	.	.	.	15/17	.	hmmpanther:PTHR16426:SF14,hmmpanther:PTHR16426	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCCCCCGG	.	5	ESCA
FLJ00104	0	.	GRCh37	16	87738888	87738888	+	5'UTR	SNP	G	G	T	rs12447897	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2768C>A	.	.	ENST00000446344	1/2	38	18	19	10	10	0	FLJ00104,5_prime_UTR_variant,,ENST00000446344,;KLHDC4,downstream_gene_variant,,ENST00000353170,;KLHDC4,downstream_gene_variant,,ENST00000270583,;KLHDC4,downstream_gene_variant,,ENST00000562261,;KLHDC4,downstream_gene_variant,,ENST00000347925,;KLHDC4,intron_variant,,ENST00000568499,;KLHDC4,downstream_gene_variant,,ENST00000316853,;KLHDC4,upstream_gene_variant,,ENST00000568346,;KLHDC4,downstream_gene_variant,,ENST00000566349,;KLHDC4,intron_variant,,ENST00000567298,;KLHDC4,downstream_gene_variant,,ENST00000562155,;KLHDC4,downstream_gene_variant,,ENST00000569487,;KLHDC4,downstream_gene_variant,,ENST00000566661,;	T	ENSG00000205047	ENST00000446344	Transcript	5_prime_UTR_variant	403	.	.	.	.	rs12447897	.	.	-1	FLJ00104	Uniprot_gn	.	protein_coding	YES	.	ENSP00000392909	.	Q9H7I4_HUMAN,Q86VH3_HUMAN	UPI000018F332	.	.	.	1/2	.	.	T:0.0994	T:0.0371	T:0.2176	.	T:0.0883	T:0.0805	T:0.1309	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGGGCCCCG	byFrequency|byCluster|byHapMap|by1000G	4	ESCA
LMF1	0	.	GRCh37	16	920752	920752	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1209C>T	p.%3D	p.V403V	ENST00000262301	8/11	49	28	21	46	46	0	LMF1,synonymous_variant,p.%3D,ENST00000543238,;LMF1,synonymous_variant,p.%3D,ENST00000399843,;LMF1,synonymous_variant,p.%3D,ENST00000568897,;LMF1,synonymous_variant,p.%3D,ENST00000262301,;LMF1,downstream_gene_variant,,ENST00000570014,;LMF1,downstream_gene_variant,,ENST00000566627,;LMF1,upstream_gene_variant,,ENST00000570168,;LMF1,downstream_gene_variant,,ENST00000568268,;LMF1,3_prime_UTR_variant,,ENST00000545827,;LMF1,non_coding_transcript_exon_variant,,ENST00000569516,;LMF1,upstream_gene_variant,,ENST00000565276,;LMF1,downstream_gene_variant,,ENST00000565198,;	A	ENSG00000103227	ENST00000262301	Transcript	synonymous_variant	1228	1209	403	V	gtC/gtT	.	.	.	-1	LMF1	HGNC	14154	protein_coding	YES	CCDS45373.1	ENSP00000262301	LMF1_HUMAN	H3BVI4_HUMAN,H3BN37_HUMAN,B3KS80_HUMAN	UPI000006E366	.	.	.	8/11	.	hmmpanther:PTHR14463,Pfam_domain:PF06762	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTGACGAT	.	5	ESCA
MYH1	0	.	GRCh37	17	10401141	10401141	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4275C>G	p.%3D	p.L1425L	ENST00000226207	31/40	130	96	34	55	55	0	MYH1,synonymous_variant,p.%3D,ENST00000226207,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	C	ENSG00000109061	ENST00000226207	Transcript	synonymous_variant	4370	4275	1425	L	ctC/ctG	.	.	.	-1	MYH1	HGNC	7567	protein_coding	YES	CCDS11155.1	ENSP00000226207	MYH1_HUMAN	.	UPI000013C891	.	.	.	31/40	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF264,Pfam_domain:PF01576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGGAGCCT	.	5	ESCA
MYH2	0	.	GRCh37	17	10428870	10428870	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4435G>T	p.Glu1479Ter	p.E1479*	ENST00000245503	32/40	97	70	26	44	44	0	MYH2,stop_gained,p.Glu1479Ter,ENST00000245503,;MYH2,stop_gained,p.Glu1479Ter,ENST00000397183,;MYH2,intron_variant,,ENST00000532183,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	A	ENSG00000125414	ENST00000245503	Transcript	stop_gained	4820	4435	1479	E/*	Gag/Tag	COSM3513923	.	.	-1	MYH2	HGNC	7572	protein_coding	YES	CCDS11156.1	ENSP00000245503	MYH2_HUMAN	J3QLR0_HUMAN,E7EX84_HUMAN,C9JIX4_HUMAN	UPI000012FB6C	.	.	.	32/40	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF90257,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF314	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCCTTCT	.	5	ESCA
DNAH9	0	.	GRCh37	17	11648203	11648203	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6201C>T	p.%3D	p.D2067D	ENST00000262442	31/69	47	36	11	38	38	0	DNAH9,synonymous_variant,p.%3D,ENST00000454412,;DNAH9,synonymous_variant,p.%3D,ENST00000262442,;AC005701.1,upstream_gene_variant,,ENST00000584990,;	T	ENSG00000007174	ENST00000262442	Transcript	synonymous_variant	6269	6201	2067	D	gaC/gaT	.	.	.	1	DNAH9	HGNC	2953	protein_coding	YES	CCDS11160.1	ENSP00000262442	DYH9_HUMAN	Q92865_HUMAN	UPI0000141BA2	.	.	.	31/69	.	hmmpanther:PTHR10676:SF36,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGACCAGGT	.	5	ESCA
KCNJ12	0	.	GRCh37	17	21319092	21319092	+	Silent	SNP	C	C	T	rs782723700	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438C>T	p.%3D	p.Y146Y	ENST00000583088	3/3	74	68	5	65	65	0	KCNJ12,synonymous_variant,p.%3D,ENST00000331718,;KCNJ12,synonymous_variant,p.%3D,ENST00000583088,;	T	ENSG00000184185	ENST00000583088	Transcript	synonymous_variant	1333	438	146	Y	taC/taT	rs782723700	.	.	1	KCNJ12	HGNC	6258	protein_coding	YES	CCDS11219.1	ENSP00000463778	IRK12_HUMAN	.	UPI00000725C7	.	.	.	3/3	.	Transmembrane_helices:TMhelix,Prints_domain:PR01320,Superfamily_domains:SSF81324,Gene3D:1.10.287.70,PIRSF_domain:PIRSF005465,Pfam_domain:PF01007,hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTACGGGCT	byFrequency	2	ESCA
CASC3	0	.	GRCh37	17	38324562	38324562	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1857T>C	p.%3D	p.P619P	ENST00000264645	11/14	87	29	58	50	50	0	CASC3,synonymous_variant,p.%3D,ENST00000264645,;CASC3,non_coding_transcript_exon_variant,,ENST00000583902,;CASC3,downstream_gene_variant,,ENST00000474190,;CASC3,upstream_gene_variant,,ENST00000394114,;CASC3,downstream_gene_variant,,ENST00000577605,;CASC3,downstream_gene_variant,,ENST00000418132,;CASC3,downstream_gene_variant,,ENST00000579238,;	C	ENSG00000108349	ENST00000264645	Transcript	synonymous_variant	2083	1857	619	P	ccT/ccC	.	.	.	1	CASC3	HGNC	17040	protein_coding	YES	CCDS11362.1	ENSP00000264645	CASC3_HUMAN	.	UPI000000DAAA	.	.	.	11/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCCTACTTA	.	5	ESCA
USP32	0	.	GRCh37	17	58275786	58275786	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3269T>A	p.Phe1090Tyr	p.F1090Y	ENST00000300896	27/34	105	74	31	54	54	0	USP32,missense_variant,p.Phe760Tyr,ENST00000592339,;USP32,missense_variant,p.Phe1090Tyr,ENST00000300896,;	T	ENSG00000170832	ENST00000300896	Transcript	missense_variant	3464	3269	1090	F/Y	tTc/tAc	.	.	.	-1	USP32	HGNC	19143	protein_coding	YES	CCDS32697.1	ENSP00000300896	UBP32_HUMAN	Q86WP5_HUMAN,Q6IRT0_HUMAN,Q4VC15_HUMAN,K7EQL6_HUMAN	UPI0000047AF8	.	deleterious(0.05)	probably_damaging(0.977)	27/34	.	Pfam_domain:PF00443,hmmpanther:PTHR24006:SF392,hmmpanther:PTHR24006,PROSITE_profiles:PS50235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGAAATAC	.	5	ESCA
SLC13A5	0	.	GRCh37	17	6616733	6616733	+	5'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-81G>C	.	.	ENST00000433363	1/12	43	30	12	35	35	0	SLC13A5,5_prime_UTR_variant,,ENST00000433363,;SLC13A5,upstream_gene_variant,,ENST00000293800,;SLC13A5,upstream_gene_variant,,ENST00000572352,;SLC13A5,upstream_gene_variant,,ENST00000576323,;SLC13A5,upstream_gene_variant,,ENST00000573648,;SLC13A5,upstream_gene_variant,,ENST00000381074,;SLC13A5,upstream_gene_variant,,ENST00000575230,;SLC13A5,upstream_gene_variant,,ENST00000572094,;	G	ENSG00000141485	ENST00000433363	Transcript	5_prime_UTR_variant	154	.	.	.	.	.	.	.	-1	SLC13A5	HGNC	23089	protein_coding	YES	CCDS11079.1	ENSP00000406220	S13A5_HUMAN	Q6ZMG6_HUMAN,Q68D44_HUMAN,I3L4V4_HUMAN	UPI000000D834	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCCGGGGA	.	5	ESCA
SLC2A4	0	.	GRCh37	17	7190439	7190439	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*491T>C	.	.	ENST00000317370	11/11	38	23	14	22	21	1	SLC2A4,3_prime_UTR_variant,,ENST00000317370,;YBX2,downstream_gene_variant,,ENST00000571464,;YBX2,downstream_gene_variant,,ENST00000007699,;SLC2A4,downstream_gene_variant,,ENST00000424875,;SLC2A4,downstream_gene_variant,,ENST00000571308,;RP1-4G17.2,upstream_gene_variant,,ENST00000576271,;YBX2,downstream_gene_variant,,ENST00000570627,;SLC2A4,3_prime_UTR_variant,,ENST00000572485,;YBX2,downstream_gene_variant,,ENST00000571485,;YBX2,downstream_gene_variant,,ENST00000570720,;SLC2A4,downstream_gene_variant,,ENST00000570783,;YBX2,downstream_gene_variant,,ENST00000571834,;	C	ENSG00000181856	ENST00000317370	Transcript	3_prime_UTR_variant	2289	.	.	.	.	.	.	.	1	SLC2A4	HGNC	11009	protein_coding	YES	CCDS11097.1	ENSP00000320935	GTR4_HUMAN	.	UPI000004F0B3	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTTTTTTTTTT	.	2	ESCA
UNK	0	.	GRCh37	17	73820554	73820555	+	3'UTR	DEL	TA	TA	-	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69_*70delAT	.	.	ENST00000589666	16/16	68	61	7	13	13	0	UNK,3_prime_UTR_variant,,ENST00000589666,;UNK,3_prime_UTR_variant,,ENST00000293218,;UNK,downstream_gene_variant,,ENST00000587258,;UNC13D,downstream_gene_variant,,ENST00000589670,;UNC13D,downstream_gene_variant,,ENST00000207549,;UNC13D,downstream_gene_variant,,ENST00000412096,;RP11-552F3.4,upstream_gene_variant,,ENST00000586808,;UNC13D,downstream_gene_variant,,ENST00000586519,;	-	ENSG00000132478	ENST00000589666	Transcript	3_prime_UTR_variant	2599-2600	.	.	.	.	.	.	.	1	UNK	HGNC	29369	protein_coding	YES	CCDS45778.2	ENSP00000464893	UNK_HUMAN	.	UPI00001C1FC3	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	13	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTAAAGTATATAT	.	2	ESCA
TP53	0	.	GRCh37	17	7579563	7579563	+	Frame_Shift_Del	DEL	C	C	-	rs756847009	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124delG	p.Asp42IlefsTer2	p.D42Ifs*2	ENST00000269305	4/11	121	66	55	32	32	0	TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000508793,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000413465,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000604348,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000420246,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000269305,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000359597,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000445888,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000503591,;TP53,frameshift_variant,p.Asp42IlefsTer2,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	314	124	42	D/X	Gat/at	rs756847009,TP53_g.11355G>T,COSM46409	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6	INDELOCATOR*|VARSCANI*|PINDEL	TCAAATCATCCA	.	3	ESCA
PGS1	0	.	GRCh37	17	76392413	76392413	+	Missense_Mutation	SNP	C	C	T	rs752050948	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.358C>T	p.Arg120Trp	p.R120W	ENST00000262764	3/10	81	54	27	55	55	0	PGS1,missense_variant,p.Arg104Trp,ENST00000587356,;PGS1,missense_variant,p.Arg119Trp,ENST00000592043,;PGS1,missense_variant,p.Arg120Trp,ENST00000262764,;PGS1,intron_variant,,ENST00000329897,;PGS1,intron_variant,,ENST00000589689,;SNORA30,upstream_gene_variant,,ENST00000363193,;PGS1,non_coding_transcript_exon_variant,,ENST00000586325,;PGS1,non_coding_transcript_exon_variant,,ENST00000585521,;PGS1,upstream_gene_variant,,ENST00000588281,;PGS1,3_prime_UTR_variant,,ENST00000589425,;PGS1,3_prime_UTR_variant,,ENST00000586510,;PGS1,intron_variant,,ENST00000588169,;PGS1,intron_variant,,ENST00000589426,;PGS1,upstream_gene_variant,,ENST00000591996,;	T	ENSG00000087157	ENST00000262764	Transcript	missense_variant	384	358	120	R/W	Cgg/Tgg	rs752050948	.	.	1	PGS1	HGNC	30029	protein_coding	YES	CCDS42391.1	ENSP00000262764	PGPS1_HUMAN	.	UPI00000435E5	.	deleterious(0)	probably_damaging(1)	3/10	.	hmmpanther:PTHR12586:SF1,hmmpanther:PTHR12586,Pfam_domain:PF13091,Gene3D:3.30.870.10,PIRSF_domain:PIRSF000850,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGGCGGGTC	.	5	ESCA
ALOX15B	0	.	GRCh37	17	7942529	7942529	+	Missense_Mutation	SNP	G	G	C	rs777404728	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.56G>C	p.Trp19Ser	p.W19S	ENST00000380183	1/14	105	73	31	97	97	0	ALOX15B,missense_variant,p.Trp19Ser,ENST00000380183,;ALOX15B,missense_variant,p.Trp19Ser,ENST00000573359,;ALOX15B,missense_variant,p.Trp19Ser,ENST00000572022,;ALOX15B,missense_variant,p.Trp19Ser,ENST00000380173,;snoU13,upstream_gene_variant,,ENST00000459145,;ALOX15B,non_coding_transcript_exon_variant,,ENST00000571240,;	C	ENSG00000179593	ENST00000380183	Transcript	missense_variant	195	56	19	W/S	tGg/tCg	rs777404728	.	.	1	ALOX15B	HGNC	434	protein_coding	YES	CCDS11128.1	ENSP00000369530	LX15B_HUMAN	.	UPI0000140991	.	tolerated(0.16)	probably_damaging(0.999)	1/14	.	PROSITE_profiles:PS50095,hmmpanther:PTHR11771:SF46,hmmpanther:PTHR11771,Gene3D:2.60.60.20,Pfam_domain:PF01477,SMART_domains:SM00308,Superfamily_domains:SSF49723,Prints_domain:PR00467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATGGGACA	.	5	ESCA
ATP8B1	0	.	GRCh37	18	55314727	55314727	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*993C>T	.	.	ENST00000536015	28/28	16	10	6	19	19	0	ATP8B1,3_prime_UTR_variant,,ENST00000283684,;ATP8B1,3_prime_UTR_variant,,ENST00000536015,;RP11-35G9.3,intron_variant,,ENST00000599199,;RP11-35G9.5,intron_variant,,ENST00000588925,;RP11-35G9.3,intron_variant,,ENST00000591854,;RP11-35G9.3,intron_variant,,ENST00000592201,;	A	ENSG00000081923	ENST00000536015	Transcript	3_prime_UTR_variant	4869	.	.	.	.	.	.	.	-1	ATP8B1	HGNC	3706	protein_coding	YES	CCDS11965.1	ENSP00000445359	AT8B1_HUMAN	K7ERI0_HUMAN,K7EQC4_HUMAN	UPI000013DD54	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATAAGTCATT	.	2	ESCA
LINC00668	0	.	GRCh37	18	6927413	6927413	+	RNA	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.407G>A	.	.	ENST00000580197	3/3	24	20	4	17	17	0	LINC00668,non_coding_transcript_exon_variant,,ENST00000583316,;LINC00668,non_coding_transcript_exon_variant,,ENST00000581571,;LINC00668,non_coding_transcript_exon_variant,,ENST00000580197,;LINC00668,non_coding_transcript_exon_variant,,ENST00000578497,;LINC00668,intron_variant,,ENST00000581725,;LINC00668,downstream_gene_variant,,ENST00000579012,;LINC00668,downstream_gene_variant,,ENST00000583840,;LINC00668,upstream_gene_variant,,ENST00000578278,;SCML2P1,non_coding_transcript_exon_variant,,ENST00000584511,;	T	ENSG00000265933	ENST00000580197	Transcript	non_coding_transcript_exon_variant	407	.	.	.	.	.	.	.	-1	LINC00668	HGNC	44328	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTCCGCAAC	.	5	ESCA
ZNF430	0	.	GRCh37	19	21240141	21240141	+	Nonsense_Mutation	SNP	A	A	T	rs764937867	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027A>T	p.Lys343Ter	p.K343*	ENST00000261560	5/5	47	35	12	49	49	0	ZNF430,stop_gained,p.Lys343Ter,ENST00000261560,;ZNF430,downstream_gene_variant,,ENST00000599548,;ZNF430,upstream_gene_variant,,ENST00000597922,;AC012627.1,downstream_gene_variant,,ENST00000578233,;	T	ENSG00000118620	ENST00000261560	Transcript	stop_gained	1208	1027	343	K/*	Aaa/Taa	rs764937867	.	.	1	ZNF430	HGNC	20808	protein_coding	YES	CCDS32978.1	ENSP00000261560	ZN430_HUMAN	Q69YQ2_HUMAN,Q2NKJ9_HUMAN	UPI000020389E	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF41,hmmpanther:PTHR24384,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGAAACCC	.	5	ESCA
ANKRD24	0	.	GRCh37	19	4217366	4217366	+	Missense_Mutation	SNP	C	C	T	rs778596061	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2209C>T	p.Arg737Trp	p.R737W	ENST00000600132	18/22	88	52	36	47	47	0	ANKRD24,missense_variant,p.Arg827Trp,ENST00000262970,;ANKRD24,missense_variant,p.Arg737Trp,ENST00000600132,;ANKRD24,missense_variant,p.Arg708Trp,ENST00000597689,;ANKRD24,missense_variant,p.Arg737Trp,ENST00000318934,;ANKRD24,downstream_gene_variant,,ENST00000595096,;	T	ENSG00000089847	ENST00000600132	Transcript	missense_variant	2485	2209	737	R/W	Cgg/Tgg	rs778596061	.	.	1	ANKRD24	HGNC	29424	protein_coding	YES	CCDS45925.1	ENSP00000471252	ANR24_HUMAN	.	UPI000041F5A9	.	tolerated_low_confidence(0.13)	benign(0.001)	18/22	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24137,hmmpanther:PTHR24137:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCCGGCAG	byFrequency	5	ESCA
TOMM40	0	.	GRCh37	19	45406379	45406379	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1039C>T	p.His347Tyr	p.H347Y	ENST00000426677	9/9	159	103	56	153	153	0	TOMM40,missense_variant,p.His347Tyr,ENST00000252487,;TOMM40,missense_variant,p.His347Tyr,ENST00000426677,;TOMM40,missense_variant,p.His347Tyr,ENST00000405636,;TOMM40,3_prime_UTR_variant,,ENST00000592434,;APOE,upstream_gene_variant,,ENST00000252486,;APOE,upstream_gene_variant,,ENST00000446996,;APOE,upstream_gene_variant,,ENST00000425718,;APOE,upstream_gene_variant,,ENST00000434152,;TOMM40,3_prime_UTR_variant,,ENST00000592041,;APOE,upstream_gene_variant,,ENST00000485628,;	T	ENSG00000130204	ENST00000426677	Transcript	missense_variant	1219	1039	347	H/Y	Cac/Tac	.	.	.	1	TOMM40	HGNC	18001	protein_coding	YES	CCDS12646.1	ENSP00000410339	TOM40_HUMAN	K7EKG6_HUMAN,K7EJ57_HUMAN	UPI0000130CBB	.	deleterious(0.01)	probably_damaging(0.995)	9/9	.	hmmpanther:PTHR10802,hmmpanther:PTHR10802:SF1,Pfam_domain:PF01459,Gene3D:2.40.160.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAATCACCGC	.	5	ESCA
KDELR1	0	.	GRCh37	19	48887553	48887553	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538G>A	p.Ala180Thr	p.A180T	ENST00000330720	4/5	33	30	3	50	50	0	KDELR1,missense_variant,p.Ala118Thr,ENST00000597017,;KDELR1,missense_variant,p.Ala180Thr,ENST00000330720,;KDELR1,missense_variant,p.Arg202His,ENST00000600980,;	T	ENSG00000105438	ENST00000330720	Transcript	missense_variant	733	538	180	A/T	Gcc/Acc	COSM191502	.	.	-1	KDELR1	HGNC	6304	protein_coding	YES	CCDS12718.1	ENSP00000329471	ERD21_HUMAN	Q8NBW7_HUMAN	UPI000012A0CA	.	tolerated(0.07)	possibly_damaging(0.531)	4/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10585:SF7,hmmpanther:PTHR10585	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATGGCGATGA	.	2	ESCA
NLRP12	0	.	GRCh37	19	54312981	54312981	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1932G>T	p.Lys644Asn	p.K644N	ENST00000324134	3/10	25	6	18	30	30	0	NLRP12,missense_variant,p.Lys644Asn,ENST00000535162,;NLRP12,missense_variant,p.Lys644Asn,ENST00000391775,;NLRP12,missense_variant,p.Lys644Asn,ENST00000354278,;NLRP12,missense_variant,p.Lys644Asn,ENST00000391773,;NLRP12,missense_variant,p.Lys644Asn,ENST00000324134,;NLRP12,missense_variant,p.Lys644Asn,ENST00000391772,;NLRP12,missense_variant,p.Lys644Asn,ENST00000345770,;NLRP12,missense_variant,p.Lys644Asn,ENST00000351894,;NLRP12,upstream_gene_variant,,ENST00000492915,;	A	ENSG00000142405	ENST00000324134	Transcript	missense_variant	2101	1932	644	K/N	aaG/aaT	.	.	.	-1	NLRP12	HGNC	22938	protein_coding	YES	CCDS12864.1	ENSP00000319377	NAL12_HUMAN	.	UPI00001412CE	.	tolerated(0.07)	benign(0.014)	3/10	.	hmmpanther:PTHR24106:SF6,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATCTTGGA	.	5	ESCA
LILRA1	0	.	GRCh37	19	55107747	55107747	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1052C>T	p.Pro351Leu	p.P351L	ENST00000251372	7/10	58	22	36	87	87	0	LILRA1,missense_variant,p.Pro351Leu,ENST00000251372,;LILRA1,intron_variant,,ENST00000453777,;LILRB1,intron_variant,,ENST00000418536,;LILRB1,intron_variant,,ENST00000448689,;LILRB1,intron_variant,,ENST00000396321,;LILRA1,non_coding_transcript_exon_variant,,ENST00000473156,;LILRA1,non_coding_transcript_exon_variant,,ENST00000495417,;LILRA1,non_coding_transcript_exon_variant,,ENST00000477255,;	T	ENSG00000104974	ENST00000251372	Transcript	missense_variant	1234	1052	351	P/L	cCg/cTg	.	.	.	1	LILRA1	HGNC	6602	protein_coding	YES	CCDS12901.1	ENSP00000251372	LIRA1_HUMAN	.	UPI0000034C00	.	tolerated(0.88)	benign(0.049)	7/10	.	hmmpanther:PTHR11738:SF89,hmmpanther:PTHR11738,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,PIRSF_domain:PIRSF001979,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCCGTTCC	.	5	ESCA
LONP1	0	.	GRCh37	19	5719848	5719848	+	Frame_Shift_Del	DEL	C	C	-	rs747867148	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296delG	p.Gly99AlafsTer11	p.G99Afs*11	ENST00000360614	1/18	35	21	14	14	14	0	LONP1,frameshift_variant,p.Gly99AlafsTer11,ENST00000360614,;LONP1,frameshift_variant,p.Gly99AlafsTer11,ENST00000587365,;LONP1,splice_region_variant,,ENST00000585374,;LONP1,5_prime_UTR_variant,,ENST00000590729,;LONP1,intron_variant,,ENST00000593119,;LONP1,intron_variant,,ENST00000540670,;CATSPERD,upstream_gene_variant,,ENST00000381614,;CATSPERD,upstream_gene_variant,,ENST00000381624,;LONP1,non_coding_transcript_exon_variant,,ENST00000590511,;LONP1,non_coding_transcript_exon_variant,,ENST00000590728,;LONP1,frameshift_variant,p.Gly12AlafsTer11,ENST00000590558,;LONP1,intron_variant,,ENST00000586617,;LONP1,upstream_gene_variant,,ENST00000587552,;	-	ENSG00000196365	ENST00000360614	Transcript	frameshift_variant	454	296	99	G/X	gGc/gc	rs747867148	.	.	-1	LONP1	HGNC	9479	protein_coding	YES	CCDS12148.1	ENSP00000353826	LONM_HUMAN	K7EKE6_HUMAN,F5GZ27_HUMAN	UPI000012E7EF	.	.	.	1/18	.	Low_complexity_(Seg):seg,HAMAP:MF_03120,PIRSF_domain:PIRSF001174	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	GCGCTGCCCCCC	.	2	ESCA
C3	0	.	GRCh37	19	6719280	6719280	+	Missense_Mutation	SNP	G	G	A	rs753544234	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.209C>T	p.Ser70Phe	p.S70F	ENST00000245907	2/41	117	104	13	62	62	0	C3,missense_variant,p.Ser29Phe,ENST00000600744,;C3,missense_variant,p.Ser70Phe,ENST00000245907,;C3,non_coding_transcript_exon_variant,,ENST00000594936,;C3,upstream_gene_variant,,ENST00000595577,;	A	ENSG00000125730	ENST00000245907	Transcript	missense_variant	302	209	70	S/F	tCc/tTc	rs753544234	.	.	-1	C3	HGNC	1318	protein_coding	YES	CCDS32883.1	ENSP00000245907	CO3_HUMAN	Q6LDJ0_HUMAN,M0R1Q1_HUMAN	UPI000013EC9B	.	tolerated(0.7)	benign(0.001)	2/41	.	hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF81	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACTGGACAGC	.	4	ESCA
CCL25	0	.	GRCh37	19	8117952	8117952	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19G>T	p.Ala7Ser	p.A7S	ENST00000390669	1/5	249	161	87	154	154	0	CCL25,missense_variant,p.Ala7Ser,ENST00000315626,;CCL25,missense_variant,p.Ala7Ser,ENST00000253451,;CCL25,missense_variant,p.Ala7Ser,ENST00000390669,;CCL25,missense_variant,p.Ala7Ser,ENST00000458625,;	T	ENSG00000131142	ENST00000390669	Transcript	missense_variant	69	19	7	A/S	Gcc/Tcc	.	.	.	1	CCL25	HGNC	10624	protein_coding	YES	CCDS12194.1	ENSP00000375086	CCL25_HUMAN	.	UPI000013CDD5	.	tolerated(0.05)	benign(0.122)	1/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF70	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGGCCTGC	.	5	ESCA
RP11-782C8.1	0	.	GRCh37	1	143119076	143119076	+	RNA	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.16C>T	.	.	ENST00000438000	1/4	79	62	17	82	82	0	RP11-782C8.1,non_coding_transcript_exon_variant,,ENST00000454861,;RP11-782C8.2,non_coding_transcript_exon_variant,,ENST00000412204,;RP11-782C8.1,non_coding_transcript_exon_variant,,ENST00000428930,;RP11-782C8.2,non_coding_transcript_exon_variant,,ENST00000422129,;RP11-782C8.1,non_coding_transcript_exon_variant,,ENST00000447407,;RP11-782C8.1,non_coding_transcript_exon_variant,,ENST00000438000,;	T	ENSG00000230850	ENST00000438000	Transcript	non_coding_transcript_exon_variant	16	.	.	.	.	.	.	.	1	RP11-782C8.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGTCCTCTG	.	4	ESCA
NTRK1	0	.	GRCh37	1	156843511	156843511	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937C>G	p.Leu313Val	p.L313V	ENST00000524377	8/17	46	28	18	28	28	0	NTRK1,missense_variant,p.Leu283Val,ENST00000392302,;NTRK1,missense_variant,p.Leu313Val,ENST00000524377,;NTRK1,missense_variant,p.Leu313Val,ENST00000358660,;NTRK1,missense_variant,p.Leu313Val,ENST00000368196,;NTRK1,non_coding_transcript_exon_variant,,ENST00000489021,;NTRK1,synonymous_variant,p.%3D,ENST00000497019,;NTRK1,non_coding_transcript_exon_variant,,ENST00000530298,;NTRK1,upstream_gene_variant,,ENST00000534682,;	G	ENSG00000198400	ENST00000524377	Transcript	missense_variant	978	937	313	L/V	Ctg/Gtg	.	.	.	1	NTRK1	HGNC	8031	protein_coding	YES	CCDS1161.1	ENSP00000431418	NTRK1_HUMAN	.	UPI000013D5D3	.	deleterious(0.03)	benign(0.2)	8/17	.	hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF133,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCTCTGCGC	.	5	ESCA
CDK11B	0	.	GRCh37	1	1572523	1572523	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621A>G	p.Lys541Glu	p.K541E	ENST00000407249	16/21	84	76	8	59	59	0	CDK11B,missense_variant,p.Lys539Glu,ENST00000317673,;CDK11B,missense_variant,p.Lys541Glu,ENST00000407249,;CDK11B,missense_variant,p.Lys494Glu,ENST00000341832,;CDK11B,missense_variant,p.Lys528Glu,ENST00000340677,;CDK11B,missense_variant,p.Lys374Glu,ENST00000513088,;MMP23B,downstream_gene_variant,,ENST00000378675,;MMP23B,downstream_gene_variant,,ENST00000356026,;MMP23B,downstream_gene_variant,,ENST00000503792,;MMP23B,downstream_gene_variant,,ENST00000435358,;MMP23B,downstream_gene_variant,,ENST00000479814,;MMP23B,downstream_gene_variant,,ENST00000472264,;MMP23B,downstream_gene_variant,,ENST00000489782,;MMP23B,downstream_gene_variant,,ENST00000486400,;MMP23B,downstream_gene_variant,,ENST00000490017,;MMP23B,downstream_gene_variant,,ENST00000512731,;	C	ENSG00000248333	ENST00000407249	Transcript	missense_variant	1621	1621	541	K/E	Aaa/Gaa	.	.	.	-1	CDK11B	HGNC	1729	protein_coding	YES	.	ENSP00000464036	.	Q6P5Y5_HUMAN,Q5QPQ9_HUMAN,J3QR44_HUMAN,A4VCI5_HUMAN	UPI0000D61E1A	.	.	unknown(0)	16/21	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF107,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGTTTCACCC	.	2	ESCA
FCRL2	0	.	GRCh37	1	157746838	157746838	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26T>C	p.Ile9Thr	p.I9T	ENST00000361516	1/12	73	46	26	49	49	0	FCRL2,missense_variant,p.Ile9Thr,ENST00000361516,;FCRL2,missense_variant,p.Ile9Thr,ENST00000392274,;FCRL2,missense_variant,p.Ile9Thr,ENST00000368181,;FCRL2,non_coding_transcript_exon_variant,,ENST00000462774,;	G	ENSG00000132704	ENST00000361516	Transcript	missense_variant	75	26	9	I/T	aTc/aCc	.	.	.	-1	FCRL2	HGNC	14875	protein_coding	YES	CCDS1168.1	ENSP00000355157	FCRL2_HUMAN	.	UPI000006E1F3	.	deleterious_low_confidence(0)	benign(0.084)	1/12	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGATGACC	.	5	ESCA
CDK11A	0	.	GRCh37	1	1635742	1635742	+	Missense_Mutation	SNP	T	T	C	rs754154891	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1606A>G	p.Lys536Glu	p.K536E	ENST00000404249	15/20	50	32	18	47	47	0	CDK11A,missense_variant,p.Lys502Glu,ENST00000356200,;CDK11A,missense_variant,p.Lys536Glu,ENST00000404249,;CDK11A,missense_variant,p.Lys526Glu,ENST00000358779,;CDK11A,missense_variant,p.Lys539Glu,ENST00000378633,;CDK11A,missense_variant,p.Lys535Glu,ENST00000357760,;CDK11A,missense_variant,p.Lys502Glu,ENST00000378638,;CDK11A,downstream_gene_variant,,ENST00000378635,;RP1-283E3.8,non_coding_transcript_exon_variant,,ENST00000598846,;CDK11A,non_coding_transcript_exon_variant,,ENST00000495016,;CDK11A,3_prime_UTR_variant,,ENST00000509982,;CDK11A,3_prime_UTR_variant,,ENST00000460465,;CDK11A,non_coding_transcript_exon_variant,,ENST00000468800,;CDK11A,non_coding_transcript_exon_variant,,ENST00000464748,;CDK11A,non_coding_transcript_exon_variant,,ENST00000491311,;CDK11A,non_coding_transcript_exon_variant,,ENST00000468397,;CDK11A,non_coding_transcript_exon_variant,,ENST00000356937,;CDK11A,non_coding_transcript_exon_variant,,ENST00000489300,;CDK11A,downstream_gene_variant,,ENST00000492390,;CDK11A,upstream_gene_variant,,ENST00000463652,;CDK11A,upstream_gene_variant,,ENST00000478901,;CDK11A,downstream_gene_variant,,ENST00000474916,;MMP23A,downstream_gene_variant,,ENST00000412810,;MMP23A,downstream_gene_variant,,ENST00000234610,;	C	ENSG00000008128	ENST00000404249	Transcript	missense_variant	1686	1606	536	K/E	Aaa/Gaa	rs754154891	.	.	-1	CDK11A	HGNC	1730	protein_coding	YES	CCDS44042.1	ENSP00000384442	CD11A_HUMAN	Q5QPQ9_HUMAN,Q4VBY6_HUMAN	UPI000022B1E1	.	tolerated(0.11)	unknown(0)	15/20	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24056:SF107,hmmpanther:PTHR24056,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R532R|c.1596G>T|3	RADIA|MUTECT|MUSE	GTGTTTCACCC	byFrequency	3	ESCA
MROH9	0	.	GRCh37	1	170967362	170967362	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1543G>T	p.Glu515Ter	p.E515*	ENST00000367759	15/22	74	56	18	68	68	0	MROH9,stop_gained,p.Glu515Ter,ENST00000367759,;MROH9,stop_gained,p.Glu122Ter,ENST00000426136,;MROH9,stop_gained,p.Glu515Ter,ENST00000367758,;	T	ENSG00000117501	ENST00000367759	Transcript	stop_gained	1697	1543	515	E/*	Gaa/Taa	.	.	.	1	MROH9	HGNC	26287	protein_coding	YES	CCDS53429.1	ENSP00000356733	MROH9_HUMAN	.	UPI0001B09232	.	.	.	15/22	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTAGAAGGT	.	5	ESCA
ZBTB41	0	.	GRCh37	1	197126797	197126797	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1692T>G	.	.	ENST00000367405	10/10	64	44	20	71	71	0	ZBTB41,3_prime_UTR_variant,,ENST00000367405,;ZBTB41,downstream_gene_variant,,ENST00000467322,;	C	ENSG00000177888	ENST00000367405	Transcript	3_prime_UTR_variant	4491	.	.	.	.	.	.	.	-1	ZBTB41	HGNC	24819	protein_coding	YES	CCDS30960.1	ENSP00000356375	ZBT41_HUMAN	Q8N9U5_HUMAN	UPI00001D7DE7	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTAAACTCA	.	5	ESCA
IPO9	0	.	GRCh37	1	201847577	201847577	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2395C>G	.	.	ENST00000361565	24/24	58	33	25	56	56	0	IPO9,3_prime_UTR_variant,,ENST00000361565,;IPO9,downstream_gene_variant,,ENST00000456707,;	G	ENSG00000198700	ENST00000361565	Transcript	3_prime_UTR_variant	5590	.	.	.	.	.	.	.	1	IPO9	HGNC	19425	protein_coding	YES	CCDS1415.1	ENSP00000354742	IPO9_HUMAN	.	UPI000007304B	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAGACAAACA	.	5	ESCA
LEFTY2	0	.	GRCh37	1	226128687	226128687	+	Missense_Mutation	SNP	C	C	T	rs202147285	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154G>A	p.Val52Ile	p.V52I	ENST00000366820	1/4	262	158	104	151	151	0	LEFTY2,missense_variant,p.Val52Ile,ENST00000366820,;LEFTY2,missense_variant,p.Val52Ile,ENST00000420304,;RP4-559A3.6,upstream_gene_variant,,ENST00000513672,;LEFTY2,upstream_gene_variant,,ENST00000474493,;	T	ENSG00000143768	ENST00000366820	Transcript	missense_variant	503	154	52	V/I	Gtc/Atc	rs202147285	.	.	-1	LEFTY2	HGNC	3122	protein_coding	YES	CCDS1549.1	ENSP00000355785	LFTY2_HUMAN	.	UPI0000136CBB	.	tolerated(0.07)	benign(0.036)	1/4	.	hmmpanther:PTHR11848:SF7,hmmpanther:PTHR11848,Pfam_domain:PF00688,PIRSF_domain:PIRSF037402,Prints_domain:PR01427	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGACCAGCT	byCluster	5	ESCA
FMN2	0	.	GRCh37	1	240255243	240255258	+	5'UTR	DEL	CAGATGCGAGCGGGGC	CAGATGCGAGCGGGGC	-	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	CAGATGCGAGCGGGGC	CAGATGCGAGCGGGGC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-164_-149delATGCGAGCGGGGCCAG	.	.	ENST00000319653	1/18	33	26	7	15	15	0	FMN2,5_prime_UTR_variant,,ENST00000319653,;FMN2,intron_variant,,ENST00000447095,;	-	ENSG00000155816	ENST00000319653	Transcript	5_prime_UTR_variant	64-79	.	.	.	.	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CGGCGGCAGATGCGAGCGGGGCCAGCC	.	2	ESCA
RGS7	0	.	GRCh37	1	240938884	240938884	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*579G>C	.	.	ENST00000366565	18/18	21	12	9	14	14	0	RGS7,3_prime_UTR_variant,,ENST00000440928,;RGS7,3_prime_UTR_variant,,ENST00000366564,;RGS7,3_prime_UTR_variant,,ENST00000366565,;RGS7,3_prime_UTR_variant,,ENST00000366563,;RGS7,3_prime_UTR_variant,,ENST00000348120,;RGS7,intron_variant,,ENST00000331110,;RGS7,downstream_gene_variant,,ENST00000446183,;RGS7,downstream_gene_variant,,ENST00000366562,;PRKRIRP8,upstream_gene_variant,,ENST00000447914,;	G	ENSG00000182901	ENST00000366565	Transcript	3_prime_UTR_variant	2425	.	.	.	.	.	.	.	-1	RGS7	HGNC	10003	protein_coding	YES	CCDS31071.1	ENSP00000355523	RGS7_HUMAN	.	UPI000040E182	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGGATCAACTT	.	4	ESCA
PLD5	0	.	GRCh37	1	242264075	242264075	+	Missense_Mutation	SNP	C	C	G	rs746309934	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1249G>C	p.Asp417His	p.D417H	ENST00000536534	9/10	92	62	30	51	51	0	PLD5,missense_variant,p.Asp417His,ENST00000536534,;PLD5,missense_variant,p.Asp355His,ENST00000427495,;PLD5,missense_variant,p.Asp325His,ENST00000442594,;PLD5,3_prime_UTR_variant,,ENST00000366545,;PLD5,3_prime_UTR_variant,,ENST00000314833,;	G	ENSG00000180287	ENST00000536534	Transcript	missense_variant	1491	1249	417	D/H	Gat/Cat	rs746309934	.	.	-1	PLD5	HGNC	26879	protein_coding	YES	CCDS1621.2	ENSP00000440896	PLD5_HUMAN	J3KP61_HUMAN	UPI000040E1A4	.	tolerated(0.44)	probably_damaging(0.972)	9/10	.	hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185,Pfam_domain:PF13918,Gene3D:3.30.870.10,Superfamily_domains:SSF56024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATCAAAAA	byFrequency	5	ESCA
OR2M3	0	.	GRCh37	1	248367307	248367307	+	Nonstop_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.938G>C	p.Ter313SerextTer3	p.*313Sext*3	ENST00000456743	1/1	112	57	55	44	44	0	OR2M3,stop_lost,p.Ter313SerextTer3,ENST00000456743,;	C	ENSG00000228198	ENST00000456743	Transcript	stop_lost	976	938	313	*/S	tGa/tCa	.	.	.	1	OR2M3	HGNC	8269	protein_coding	YES	CCDS31107.1	ENSP00000389625	OR2M3_HUMAN	.	UPI000004B234	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGTGAGTTA	.	5	ESCA
FPGT	0	.	GRCh37	1	74671545	74671545	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29T>C	.	.	ENST00000609362	4/4	52	41	11	17	17	0	FPGT,3_prime_UTR_variant,,ENST00000370898,;FPGT,3_prime_UTR_variant,,ENST00000534056,;FPGT,3_prime_UTR_variant,,ENST00000609362,;FPGT,3_prime_UTR_variant,,ENST00000370894,;FPGT-TNNI3K,intron_variant,,ENST00000370895,;FPGT-TNNI3K,intron_variant,,ENST00000370893,;FPGT-TNNI3K,intron_variant,,ENST00000534632,;FPGT-TNNI3K,intron_variant,,ENST00000370899,;TNNI3K,intron_variant,,ENST00000370891,;FPGT-TNNI3K,intron_variant,,ENST00000557284,;FPGT,downstream_gene_variant,,ENST00000482102,;FPGT,downstream_gene_variant,,ENST00000467578,;FPGT,downstream_gene_variant,,ENST00000472069,;FPGT,intron_variant,,ENST00000524915,;FPGT-TNNI3K,intron_variant,,ENST00000533006,;FPGT,downstream_gene_variant,,ENST00000529485,;	C	ENSG00000254685	ENST00000609362	Transcript	3_prime_UTR_variant	1851	.	.	.	.	.	.	.	1	FPGT	HGNC	3825	protein_coding	YES	.	ENSP00000476680	.	.	UPI000013D402	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCTTTTTG	.	5	ESCA
SNTA1	0	.	GRCh37	20	32026730	32026733	+	Frame_Shift_Del	DEL	ACAG	ACAG	-	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	ACAG	ACAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.410_413delCTGT	p.Ser137Ter	p.S137*	ENST00000217381	2/8	82	17	65	66	66	0	SNTA1,frameshift_variant,p.Ser137Ter,ENST00000217381,;	-	ENSG00000101400	ENST00000217381	Transcript	frameshift_variant	682-685	410-413	137-138	SV/X	tCTGTg/tg	.	.	.	-1	SNTA1	HGNC	11167	protein_coding	YES	CCDS13220.1	ENSP00000217381	SNTA1_HUMAN	B3KTR0_HUMAN	UPI0000135B08	.	.	.	2/8	.	PROSITE_profiles:PS50106,PROSITE_profiles:PS50003,hmmpanther:PTHR10554:SF6,hmmpanther:PTHR10554,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,SMART_domains:SM00233,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCATTCACAGACAGG	.	3	ESCA
SALL4	0	.	GRCh37	20	50405596	50405596	+	Missense_Mutation	SNP	G	G	A	rs747787961	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2546C>T	p.Ser849Leu	p.S849L	ENST00000217086	3/4	32	18	14	37	37	0	SALL4,missense_variant,p.Ser849Leu,ENST00000217086,;SALL4,missense_variant,p.Ser412Leu,ENST00000395997,;SALL4,missense_variant,p.Ser72Leu,ENST00000371539,;SALL4,downstream_gene_variant,,ENST00000481363,;SALL4,downstream_gene_variant,,ENST00000483130,;	A	ENSG00000101115	ENST00000217086	Transcript	missense_variant	2658	2546	849	S/L	tCg/tTg	rs747787961,COSM4099441	.	.	-1	SALL4	HGNC	15924	protein_coding	YES	CCDS13438.1	ENSP00000217086	SALL4_HUMAN	.	UPI0000135527	.	tolerated(0.18)	benign(0.069)	3/4	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF19	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCGAGGGT	byFrequency	5	ESCA
TPTE	0	.	GRCh37	21	10910363	10910363	+	Missense_Mutation	SNP	C	C	T	rs746975259	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1393G>A	p.Asp465Asn	p.D465N	ENST00000361285	22/24	215	196	19	115	115	0	TPTE,missense_variant,p.Asp465Asn,ENST00000361285,;TPTE,missense_variant,p.Asp427Asn,ENST00000342420,;TPTE,missense_variant,p.Asp447Asn,ENST00000298232,;TPTE,non_coding_transcript_exon_variant,,ENST00000415664,;TPTE,non_coding_transcript_exon_variant,,ENST00000447568,;	T	ENSG00000166157	ENST00000361285	Transcript	missense_variant	1723	1393	465	D/N	Gat/Aat	rs746975259	.	.	-1	TPTE	HGNC	12023	protein_coding	YES	CCDS13560.2	ENSP00000355208	TPTE_HUMAN	.	UPI000016A18A	.	tolerated(0.95)	benign(0.004)	22/24	.	PROSITE_profiles:PS51182,hmmpanther:PTHR12305,Pfam_domain:PF10409,Gene3D:1d5rA02,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TACATCAATTA	byFrequency	3	ESCA
USP25	0	.	GRCh37	21	17191133	17191133	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1048C>G	p.His350Asp	p.H350D	ENST00000285679	10/24	80	50	30	61	61	0	USP25,missense_variant,p.His350Asp,ENST00000400183,;USP25,missense_variant,p.His350Asp,ENST00000285679,;USP25,missense_variant,p.His350Asp,ENST00000285681,;USP25,intron_variant,,ENST00000351097,;USP25,downstream_gene_variant,,ENST00000549362,;USP25,downstream_gene_variant,,ENST00000547201,;	G	ENSG00000155313	ENST00000285679	Transcript	missense_variant	1417	1048	350	H/D	Cat/Gat	.	.	.	1	USP25	HGNC	12624	protein_coding	YES	CCDS33515.1	ENSP00000285679	UBP25_HUMAN	Q9HA22_HUMAN	UPI000002B680	.	tolerated(0.26)	benign(0.21)	10/24	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF111,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTACATTCA	.	5	ESCA
CECR2	0	.	GRCh37	22	17978486	17978486	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.327C>T	p.%3D	p.D109D	ENST00000262608	3/18	43	24	18	37	37	0	CECR2,synonymous_variant,p.%3D,ENST00000400573,;CECR2,synonymous_variant,p.%3D,ENST00000342247,;CECR2,synonymous_variant,p.%3D,ENST00000262608,;CECR2,5_prime_UTR_variant,,ENST00000400585,;CECR2,non_coding_transcript_exon_variant,,ENST00000497534,;	T	ENSG00000099954	ENST00000262608	Transcript	synonymous_variant	327	327	109	D	gaC/gaT	.	.	.	1	CECR2	HGNC	1840	protein_coding	YES	.	ENSP00000262608	CECR2_HUMAN	.	UPI0001AE62C8	.	.	.	3/18	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGACAATTC	.	5	ESCA
GNAZ	0	.	GRCh37	22	23437787	23437787	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96G>A	.	.	ENST00000248996	2/3	36	26	9	20	20	0	GNAZ,5_prime_UTR_variant,,ENST00000248996,;RTDR1,intron_variant,,ENST00000216036,;GNAZ,non_coding_transcript_exon_variant,,ENST00000492538,;	A	ENSG00000128266	ENST00000248996	Transcript	5_prime_UTR_variant	571	.	.	.	.	.	.	.	1	GNAZ	HGNC	4395	protein_coding	YES	CCDS13804.1	ENSP00000248996	GNAZ_HUMAN	.	UPI0000001249	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCAGCTGGG	.	5	ESCA
RTCB	0	.	GRCh37	22	32808177	32808177	+	5'UTR	SNP	C	C	G	rs770671346	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-34G>C	.	.	ENST00000216038	1/12	35	19	15	14	14	0	RTCB,5_prime_UTR_variant,,ENST00000216038,;RTCB,5_prime_UTR_variant,,ENST00000451746,;BPIFC,downstream_gene_variant,,ENST00000534972,;BPIFC,downstream_gene_variant,,ENST00000397452,;BPIFC,downstream_gene_variant,,ENST00000300399,;BPIFC,downstream_gene_variant,,ENST00000432451,;RTCB,upstream_gene_variant,,ENST00000476619,;RTCB,upstream_gene_variant,,ENST00000485373,;RTCB,non_coding_transcript_exon_variant,,ENST00000463455,;RTCB,non_coding_transcript_exon_variant,,ENST00000487704,;	G	ENSG00000100220	ENST00000216038	Transcript	5_prime_UTR_variant	66	.	.	.	.	rs770671346	.	.	-1	RTCB	HGNC	26935	protein_coding	YES	CCDS13905.1	ENSP00000216038	RTCB_HUMAN	.	UPI000006E0DE	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCCGCTTT	.	5	ESCA
SOX10	0	.	GRCh37	22	38368452	38368452	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1050G>A	.	.	ENST00000396884	4/4	24	14	10	10	10	0	SOX10,3_prime_UTR_variant,,ENST00000360880,;SOX10,3_prime_UTR_variant,,ENST00000396884,;POLR2F,intron_variant,,ENST00000407936,;SOX10,intron_variant,,ENST00000446929,;POLR2F,intron_variant,,ENST00000405557,;POLR2F,downstream_gene_variant,,ENST00000606538,;POLR2F,downstream_gene_variant,,ENST00000442738,;POLR2F,downstream_gene_variant,,ENST00000492213,;POLR2F,downstream_gene_variant,,ENST00000470701,;POLR2F,downstream_gene_variant,,ENST00000484894,;POLR2F,intron_variant,,ENST00000443002,;POLR2F,downstream_gene_variant,,ENST00000483713,;	T	ENSG00000100146	ENST00000396884	Transcript	3_prime_UTR_variant	2734	.	.	.	.	.	.	.	-1	SOX10	HGNC	11190	protein_coding	YES	CCDS13964.1	ENSP00000380093	SOX10_HUMAN	A6PVD3_HUMAN	UPI00001362AA	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTGCAGAAC	.	2	ESCA
CNTNAP5	0	.	GRCh37	2	125262121	125262121	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1312G>A	p.Glu438Lys	p.E438K	ENST00000431078	8/24	254	240	13	49	49	0	CNTNAP5,missense_variant,p.Glu438Lys,ENST00000431078,;	A	ENSG00000155052	ENST00000431078	Transcript	missense_variant	1676	1312	438	E/K	Gaa/Aaa	.	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	deleterious(0.04)	possibly_damaging(0.889)	8/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R435C|c.1303C>T|3	MUTECT|MUSE	TAGCTGAAATC	.	2	ESCA
ZEB2	0	.	GRCh37	2	145157783	145157783	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.971C>T	p.Ser324Phe	p.S324F	ENST00000558170	8/10	29	10	19	58	58	0	ZEB2,missense_variant,p.Ser324Phe,ENST00000427902,;ZEB2,missense_variant,p.Ser324Phe,ENST00000392861,;ZEB2,missense_variant,p.Ser300Phe,ENST00000539609,;ZEB2,missense_variant,p.Ser324Phe,ENST00000409487,;ZEB2,missense_variant,p.Ser324Phe,ENST00000303660,;ZEB2,missense_variant,p.Ser324Phe,ENST00000558170,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000440875,;ZEB2,downstream_gene_variant,,ENST00000497268,;	A	ENSG00000169554	ENST00000558170	Transcript	missense_variant	2156	971	324	S/F	tCc/tTc	COSM3567348	.	.	-1	ZEB2	HGNC	14881	protein_coding	YES	CCDS2186.1	ENSP00000454157	ZEB2_HUMAN	U3KPV5_HUMAN,Q53TG0_HUMAN,Q53TD9_HUMAN,E7EUW9_HUMAN,E7ESP8_HUMAN,C9JUQ1_HUMAN,C9JU62_HUMAN,A0JP08_HUMAN	UPI00001359A2	.	deleterious(0)	probably_damaging(0.994)	8/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF2,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTAGGAACCA	.	5	ESCA
HOXD8	0	.	GRCh37	2	176996750	176996750	+	3'UTR	DEL	A	A	-	rs201637028	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*417delA	.	.	ENST00000313173	2/2	26	14	12	32	32	0	HOXD8,3_prime_UTR_variant,,ENST00000544999,;HOXD8,3_prime_UTR_variant,,ENST00000429017,;HOXD8,3_prime_UTR_variant,,ENST00000313173,;HOXD8,downstream_gene_variant,,ENST00000548663,;HOXD3,upstream_gene_variant,,ENST00000432796,;HOXD8,downstream_gene_variant,,ENST00000450510,;HOXD-AS2,intron_variant,,ENST00000440016,;HOXD-AS2,downstream_gene_variant,,ENST00000426965,;HOXD3,upstream_gene_variant,,ENST00000459979,;	-	ENSG00000175879	ENST00000313173	Transcript	3_prime_UTR_variant	1910	.	.	.	.	rs201637028	.	.	1	HOXD8	HGNC	5139	protein_coding	YES	CCDS2268.1	ENSP00000315949	HXD8_HUMAN	.	UPI000012CF8B	.	.	.	2/2	.	.	-:0.0060	-:0.0159	-:0.0029	.	-:0.001	-:0.004	-:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	7	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTAATTAAAAAA	byFrequency|byCluster|by1000G	2	ESCA
APOB	0	.	GRCh37	2	21228972	21228972	+	Missense_Mutation	SNP	C	C	G	rs747606537	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10768G>C	p.Glu3590Gln	p.E3590Q	ENST00000233242	26/29	88	63	24	42	42	0	APOB,missense_variant,p.Glu3590Gln,ENST00000233242,;	G	ENSG00000084674	ENST00000233242	Transcript	missense_variant	10896	10768	3590	E/Q	Gaa/Caa	rs747606537	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	benign(0.028)	26/29	.	hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTCCAGGG	.	5	ESCA
USP37	0	.	GRCh37	2	219346828	219346828	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1800A>G	p.%3D	p.P600P	ENST00000258399	17/26	43	16	27	44	44	0	USP37,synonymous_variant,p.%3D,ENST00000258399,;USP37,synonymous_variant,p.%3D,ENST00000418019,;USP37,synonymous_variant,p.%3D,ENST00000415516,;USP37,synonymous_variant,p.%3D,ENST00000454775,;USP37,non_coding_transcript_exon_variant,,ENST00000475553,;USP37,upstream_gene_variant,,ENST00000473554,;	C	ENSG00000135913	ENST00000258399	Transcript	synonymous_variant	2213	1800	600	P	ccA/ccG	.	.	.	-1	USP37	HGNC	20063	protein_coding	YES	CCDS2418.1	ENSP00000258399	UBP37_HUMAN	.	UPI0000160023	.	.	.	17/26	.	PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF125,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGGTGGTTT	.	5	ESCA
ASIC4	0	.	GRCh37	2	220399921	220399921	+	Silent	SNP	G	G	A	rs111598906	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1428G>A	p.%3D	p.P476P	ENST00000347842	5/9	42	26	15	35	35	0	ASIC4,synonymous_variant,p.%3D,ENST00000358078,;ASIC4,synonymous_variant,p.%3D,ENST00000347842,;CHPF,downstream_gene_variant,,ENST00000243776,;CHPF,downstream_gene_variant,,ENST00000535926,;ASIC4,downstream_gene_variant,,ENST00000473709,;ASIC4,non_coding_transcript_exon_variant,,ENST00000474489,;ASIC4,downstream_gene_variant,,ENST00000461395,;	A	ENSG00000072182	ENST00000347842	Transcript	synonymous_variant	1442	1428	476	P	ccG/ccA	rs111598906	.	.	1	ASIC4	HGNC	21263	protein_coding	YES	CCDS2442.1	ENSP00000326627	ASIC4_HUMAN	.	UPI0000456EFC	.	.	.	5/9	.	hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF13,Pfam_domain:PF00858	A:0.0012	A:0.0038	A:0.0014	.	A:0	A:0	A:0	A:0.0011	A:0.0005	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGCCCGTGCTT	byFrequency|byCluster|by1000G	4	ESCA
SOX11	0	.	GRCh37	2	5840084	5840084	+	3'UTR	DEL	C	C	-	rs550037015	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5905delC	.	.	ENST00000322002	1/1	67	54	13	41	41	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	-	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	7286	.	.	.	.	rs550037015	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAACGGCTTACA	by1000G	3	ESCA
ADD2	0	.	GRCh37	2	70910897	70910897	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951G>A	p.%3D	p.V317V	ENST00000264436	10/16	33	24	8	16	16	0	ADD2,synonymous_variant,p.%3D,ENST00000413157,;ADD2,synonymous_variant,p.%3D,ENST00000264436,;ADD2,synonymous_variant,p.%3D,ENST00000430656,;ADD2,synonymous_variant,p.%3D,ENST00000407644,;ADD2,synonymous_variant,p.%3D,ENST00000355733,;ADD2,intron_variant,,ENST00000456320,;ADD2,intron_variant,,ENST00000522886,;AC007395.3,upstream_gene_variant,,ENST00000457851,;ADD2,synonymous_variant,p.%3D,ENST00000403045,;	T	ENSG00000075340	ENST00000264436	Transcript	synonymous_variant	1396	951	317	V	gtG/gtA	.	.	.	-1	ADD2	HGNC	244	protein_coding	YES	CCDS1906.1	ENSP00000264436	ADDB_HUMAN	Q96HD4_HUMAN,C9J299_HUMAN,C9J080_HUMAN	UPI0000125503	.	.	.	10/16	.	hmmpanther:PTHR10672:SF6,hmmpanther:PTHR10672,Gene3D:3.40.225.10,Pfam_domain:PF00596,SMART_domains:SM01007,Superfamily_domains:SSF53639	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGACACCTG	.	5	ESCA
ALMS1P	0	.	GRCh37	2	73901066	73901066	+	RNA	SNP	G	G	A	rs765988088	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.864G>A	.	.	ENST00000450720	5/7	70	54	16	45	45	0	ALMS1P,non_coding_transcript_exon_variant,,ENST00000450720,;ALMS1P,non_coding_transcript_exon_variant,,ENST00000428767,;	A	ENSG00000163016	ENST00000450720	Transcript	non_coding_transcript_exon_variant	864	.	.	.	.	rs765988088,COSM4164579	.	.	1	ALMS1P	HGNC	29586	processed_transcript	YES	.	.	.	.	.	.	.	.	5/7	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODIFIER	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTCGACATT	byFrequency	5	ESCA
IGKV2D-30	0	.	GRCh37	2	89976335	89976335	+	Missense_Mutation	SNP	C	C	T	rs375913148	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.206C>T	p.Pro69Leu	p.P69L	ENST00000474213	2/2	168	129	39	101	101	0	IGKV2D-30,missense_variant,p.Pro69Leu,ENST00000474213,;	T	ENSG00000239571	ENST00000474213	Transcript	missense_variant	241	206	69	P/L	cCa/cTa	rs375913148	.	.	1	IGKV2D-30	HGNC	5801	IG_V_gene	YES	.	ENSP00000418948	.	.	UPI0000176997	.	deleterious(0.02)	probably_damaging(0.986)	2/2	.	Superfamily_domains:SSF48726,SMART_domains:SM00406,Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR23267,hmmpanther:PTHR23267:SF134,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCCAAGGC	byFrequency|byCluster	5	ESCA
ARID5A	0	.	GRCh37	2	97217709	97217709	+	Missense_Mutation	SNP	G	G	A	rs150071690	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1444G>A	p.Gly482Ser	p.G482S	ENST00000357485	7/7	103	93	10	31	31	0	ARID5A,missense_variant,p.Gly482Ser,ENST00000357485,;ARID5A,missense_variant,p.Gly414Ser,ENST00000454558,;ARID5A,3_prime_UTR_variant,,ENST00000412735,;ARID5A,non_coding_transcript_exon_variant,,ENST00000497920,;ARID5A,downstream_gene_variant,,ENST00000467498,;ARID5A,downstream_gene_variant,,ENST00000470579,;	A	ENSG00000196843	ENST00000357485	Transcript	missense_variant	1522	1444	482	G/S	Ggc/Agc	rs150071690	.	.	1	ARID5A	HGNC	17361	protein_coding	YES	CCDS33251.1	ENSP00000350078	ARI5A_HUMAN	C9J1Q0_HUMAN	UPI00001C1DBB	.	tolerated(0.1)	benign(0.067)	7/7	.	hmmpanther:PTHR13964:SF19,hmmpanther:PTHR13964	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTCCGGCCTG	byCluster	3	ESCA
SI	0	.	GRCh37	3	164709256	164709256	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4993A>G	p.Ile1665Val	p.I1665V	ENST00000264382	44/48	98	67	31	59	59	0	SI,missense_variant,p.Ile1665Val,ENST00000264382,;	C	ENSG00000090402	ENST00000264382	Transcript	missense_variant	5056	4993	1665	I/V	Att/Gtt	.	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	tolerated(0.49)	possibly_damaging(0.779)	44/48	.	Superfamily_domains:SSF51011,Pfam_domain:PF01055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAATATCTT	.	5	ESCA
WDR49	0	.	GRCh37	3	167293772	167293772	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.420C>A	p.%3D	p.A140A	ENST00000308378	4/15	139	112	27	67	67	0	WDR49,synonymous_variant,p.%3D,ENST00000472600,;WDR49,synonymous_variant,p.%3D,ENST00000453925,;WDR49,synonymous_variant,p.%3D,ENST00000308378,;WDR49,synonymous_variant,p.%3D,ENST00000479765,;WDR49,intron_variant,,ENST00000466760,;WDR49,upstream_gene_variant,,ENST00000476376,;WDR49,3_prime_UTR_variant,,ENST00000460448,;	T	ENSG00000174776	ENST00000308378	Transcript	synonymous_variant	726	420	140	A	gcC/gcA	.	.	.	-1	WDR49	HGNC	26587	protein_coding	YES	CCDS3201.1	ENSP00000311343	WDR49_HUMAN	.	UPI00000746AD	.	.	.	4/15	.	SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR22844:SF132,hmmpanther:PTHR22844,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCTGGCTTC	.	5	ESCA
SEMA3F	0	.	GRCh37	3	50225441	50225441	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2251C>T	p.Arg751Cys	p.R751C	ENST00000002829	19/19	11	3	7	15	15	0	SEMA3F,missense_variant,p.Arg652Cys,ENST00000413852,;SEMA3F,missense_variant,p.Arg751Cys,ENST00000002829,;SEMA3F,missense_variant,p.Arg720Cys,ENST00000434342,;GNAT1,upstream_gene_variant,,ENST00000433068,;GNAT1,upstream_gene_variant,,ENST00000440836,;SEMA3F,downstream_gene_variant,,ENST00000450338,;GNAT1,upstream_gene_variant,,ENST00000232461,;SEMA3F,downstream_gene_variant,,ENST00000470737,;GNAT1,upstream_gene_variant,,ENST00000467787,;SEMA3F,downstream_gene_variant,,ENST00000493743,;	T	ENSG00000001617	ENST00000002829	Transcript	missense_variant	2735	2251	751	R/C	Cgc/Tgc	.	.	.	1	SEMA3F	HGNC	10728	protein_coding	YES	CCDS2811.1	ENSP00000002829	SEM3F_HUMAN	.	UPI0000135A69	.	tolerated(0.08)	possibly_damaging(0.836)	19/19	.	hmmpanther:PTHR11036:SF27,hmmpanther:PTHR11036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACTGGCGCCAT	.	3	ESCA
FOXP1	0	.	GRCh37	3	71247378	71247378	+	Missense_Mutation	SNP	G	G	A	rs757649540	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.155C>T	p.Ala52Val	p.A52V	ENST00000318779	6/7	64	60	4	81	81	0	FOXP1,missense_variant,p.Ala52Val,ENST00000318779,;FOXP1,missense_variant,p.Ala52Val,ENST00000498215,;FOXP1,missense_variant,p.Ala52Val,ENST00000318789,;FOXP1,missense_variant,p.Ala52Val,ENST00000475937,;FOXP1,missense_variant,p.Ala52Val,ENST00000468577,;FOXP1,missense_variant,p.Ala52Val,ENST00000493089,;FOXP1,missense_variant,p.Ala52Val,ENST00000484350,;FOXP1,missense_variant,p.Ala52Val,ENST00000327590,;	A	ENSG00000114861	ENST00000318779	Transcript	missense_variant	631	155	52	A/V	gCc/gTc	rs757649540	.	.	-1	FOXP1	HGNC	3823	protein_coding	.	CCDS33785.1	ENSP00000318721	FOXP1_HUMAN	.	UPI000006E23C	.	tolerated_low_confidence(0.74)	benign(0.269)	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGTGGGCGAGG	byFrequency	2	ESCA
CNTN3	0	.	GRCh37	3	74313560	74313560	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3079C>A	p.Leu1027Met	p.L1027M	ENST00000263665	22/22	35	16	18	69	69	0	CNTN3,missense_variant,p.Leu1027Met,ENST00000263665,;CNTN3,non_coding_transcript_exon_variant,,ENST00000477856,;	T	ENSG00000113805	ENST00000263665	Transcript	missense_variant	3107	3079	1027	L/M	Ctg/Atg	.	.	.	-1	CNTN3	HGNC	2173	protein_coding	YES	CCDS33790.1	ENSP00000263665	CNTN3_HUMAN	.	UPI00001A7974	.	deleterious(0.02)	possibly_damaging(0.839)	22/22	.	hmmpanther:PTHR10489:SF54,hmmpanther:PTHR10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAGGACAT	.	5	ESCA
COL25A1	0	.	GRCh37	4	109745237	109745237	+	Intron	SNP	G	G	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1845+93C>G	.	.	ENST00000399132	.	64	40	24	44	44	0	COL25A1,3_prime_UTR_variant,,ENST00000399127,;COL25A1,3_prime_UTR_variant,,ENST00000399126,;COL25A1,intron_variant,,ENST00000512961,;COL25A1,intron_variant,,ENST00000399132,;COL25A1,intron_variant,,ENST00000494183,;COL25A1,downstream_gene_variant,,ENST00000505377,;	C	ENSG00000188517	ENST00000399132	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	COL25A1	HGNC	18603	protein_coding	YES	CCDS43258.1	ENSP00000382083	COPA1_HUMAN	D6R8Y2_HUMAN	UPI0000225CD2	.	.	.	.	35/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAAGATTAA	.	5	ESCA
ADAM29	0	.	GRCh37	4	175897001	175897002	+	Frame_Shift_Del	DEL	GA	GA	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	GA	GA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.325_326delGAinsT	p.Asp109SerfsTer21	p.D109Sfs*21	ENST00000359240	5/5	87	60	27	59	59	0	ADAM29,frameshift_variant,p.Asp109SerfsTer21,ENST00000514159,;ADAM29,frameshift_variant,p.Asp109SerfsTer21,ENST00000445694,;ADAM29,frameshift_variant,p.Asp109SerfsTer21,ENST00000404450,;ADAM29,frameshift_variant,p.Asp109SerfsTer21,ENST00000359240,;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000502940,;ADAM29,downstream_gene_variant,,ENST00000505141,;RP13-577H12.2,downstream_gene_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,;	T	ENSG00000168594	ENST00000359240	Transcript	frameshift_variant	995-996	325-326	109	D/X	GAc/Tc	.	.	.	1	ADAM29	HGNC	207	protein_coding	YES	CCDS3823.1	ENSP00000352177	ADA29_HUMAN	D6RHU0_HUMAN,D6RBU0_HUMAN	UPI000013E9DE	.	.	.	5/5	.	hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF34,Pfam_domain:PF01562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL|VARSCANS*|SOMATICSNIPER*	GAAGGGGACCCAG	.	5	ESCA
UFSP2	0	.	GRCh37	4	186324742	186324742	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1229G>A	p.Gly410Glu	p.G410E	ENST00000264689	11/12	58	33	24	52	52	0	UFSP2,missense_variant,p.Gly410Glu,ENST00000264689,;UFSP2,missense_variant,p.Gly309Glu,ENST00000511485,;UFSP2,missense_variant,p.Gly139Glu,ENST00000509180,;ANKRD37,downstream_gene_variant,,ENST00000335174,;ANKRD37,downstream_gene_variant,,ENST00000507479,;UFSP2,3_prime_UTR_variant,,ENST00000514247,;UFSP2,3_prime_UTR_variant,,ENST00000510755,;UFSP2,non_coding_transcript_exon_variant,,ENST00000510206,;ANKRD37,downstream_gene_variant,,ENST00000511393,;ANKRD37,downstream_gene_variant,,ENST00000506424,;	T	ENSG00000109775	ENST00000264689	Transcript	missense_variant	1346	1229	410	G/E	gGa/gAa	.	.	.	-1	UFSP2	HGNC	25640	protein_coding	YES	CCDS3842.1	ENSP00000264689	UFSP2_HUMAN	D6RA67_HUMAN	UPI000020B7C0	.	deleterious(0)	probably_damaging(1)	11/12	.	hmmpanther:PTHR13226:SF9,hmmpanther:PTHR13226,Pfam_domain:PF07910	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCCTAGT	.	5	ESCA
LIMCH1	0	.	GRCh37	4	41633188	41633188	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936-7761G>T	.	.	ENST00000313860	.	57	41	15	36	36	0	LIMCH1,missense_variant,p.Cys432Phe,ENST00000503057,;LIMCH1,intron_variant,,ENST00000512632,;LIMCH1,intron_variant,,ENST00000512820,;LIMCH1,intron_variant,,ENST00000508501,;LIMCH1,intron_variant,,ENST00000313860,;LIMCH1,intron_variant,,ENST00000513024,;LIMCH1,intron_variant,,ENST00000396595,;LIMCH1,intron_variant,,ENST00000514096,;LIMCH1,intron_variant,,ENST00000509277,;LIMCH1,intron_variant,,ENST00000508466,;LIMCH1,intron_variant,,ENST00000511496,;LIMCH1,intron_variant,,ENST00000381753,;LIMCH1,intron_variant,,ENST00000512946,;	T	ENSG00000064042	ENST00000313860	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LIMCH1	HGNC	29191	protein_coding	YES	CCDS33977.1	ENSP00000316891	LIMC1_HUMAN	D6RJ93_HUMAN,D6RGH8_HUMAN,D6R8Y0_HUMAN	UPI0000D61554	.	.	.	.	8/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTGTGCTT	.	5	ESCA
GABRG1	0	.	GRCh37	4	46042955	46042955	+	3'UTR	SNP	T	T	G	rs780640412	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50A>C	.	.	ENST00000295452	9/9	32	21	11	33	33	0	GABRG1,3_prime_UTR_variant,,ENST00000295452,;	G	ENSG00000163285	ENST00000295452	Transcript	3_prime_UTR_variant	1616	.	.	.	.	rs780640412	.	.	-1	GABRG1	HGNC	4086	protein_coding	YES	CCDS3470.1	ENSP00000295452	GBRG1_HUMAN	.	UPI0000047AE2	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATTCTACT	.	5	ESCA
NUDT12	0	.	GRCh37	5	102895755	102895755	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.195delG	p.Glu67ArgfsTer28	p.E67Rfs*28	ENST00000230792	2/7	163	105	58	58	58	0	NUDT12,frameshift_variant,p.Glu67ArgfsTer28,ENST00000230792,;NUDT12,intron_variant,,ENST00000507423,;NUDT12,upstream_gene_variant,,ENST00000515407,;NUDT12,non_coding_transcript_exon_variant,,ENST00000508889,;	-	ENSG00000112874	ENST00000230792	Transcript	frameshift_variant	292	195	65	L/X	ctG/ct	.	.	.	-1	NUDT12	HGNC	18826	protein_coding	YES	CCDS4096.1	ENSP00000230792	NUD12_HUMAN	.	UPI0000073C53	.	.	.	2/7	.	PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCAAGCAGAAA	.	3	ESCA
TMED7	0	.	GRCh37	5	114951349	114951349	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*557G>C	.	.	ENST00000456936	3/3	52	29	22	44	44	0	TMED7,3_prime_UTR_variant,,ENST00000456936,;TMED7-TICAM2,intron_variant,,ENST00000282382,;TICAM2,intron_variant,,ENST00000408996,;TMED7-TICAM2,intron_variant,,ENST00000333314,;TMED7,downstream_gene_variant,,ENST00000508420,;AC010226.4,intron_variant,,ENST00000515570,;AC010226.4,intron_variant,,ENST00000508517,;TMED7,downstream_gene_variant,,ENST00000503010,;TMED7-TICAM2,intron_variant,,ENST00000514548,;	G	ENSG00000134970	ENST00000456936	Transcript	3_prime_UTR_variant	1613	.	.	.	.	.	.	.	-1	TMED7	HGNC	24253	protein_coding	YES	CCDS4120.1	ENSP00000405926	TMED7_HUMAN	G3V2Y2_HUMAN,B4E2C1_HUMAN	UPI000007008A	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGTCTGACA	.	5	ESCA
FBN2	0	.	GRCh37	5	127611766	127611766	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7558G>A	p.Gly2520Arg	p.G2520R	ENST00000508053	65/71	71	45	25	57	57	0	FBN2,missense_variant,p.Gly2520Arg,ENST00000262464,;FBN2,missense_variant,p.Gly2520Arg,ENST00000508053,;	T	ENSG00000138829	ENST00000508053	Transcript	missense_variant	8533	7558	2520	G/R	Ggg/Agg	COSM3918562,COSM3918561	.	.	-1	FBN2	HGNC	3604	protein_coding	YES	CCDS34222.1	ENSP00000424571	FBN2_HUMAN	.	UPI0000519468	.	deleterious(0)	probably_damaging(1)	65/71	.	Superfamily_domains:SSF57184,SMART_domains:SM00179,PIRSF_domain:PIRSF036312,SMART_domains:SM00181,Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01186,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF19,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACCCCCTCG	.	5	ESCA
FGF18	0	.	GRCh37	5	170883890	170883890	+	3'UTR	SNP	G	G	T	rs747043243	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*81G>T	.	.	ENST00000274625	5/5	89	61	27	27	27	0	FGF18,3_prime_UTR_variant,,ENST00000274625,;	T	ENSG00000156427	ENST00000274625	Transcript	3_prime_UTR_variant	1249	.	.	.	.	rs747043243	.	.	1	FGF18	HGNC	3674	protein_coding	YES	CCDS4378.1	ENSP00000274625	FGF18_HUMAN	.	UPI000003C116	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACATGAAAAA	.	5	ESCA
CDH6	0	.	GRCh37	5	31305356	31305356	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1075C>G	p.Leu359Val	p.L359V	ENST00000265071	7/12	220	205	15	79	79	0	CDH6,missense_variant,p.Leu304Val,ENST00000514738,;CDH6,missense_variant,p.Leu359Val,ENST00000265071,;CDH6,downstream_gene_variant,,ENST00000508132,;	G	ENSG00000113361	ENST00000265071	Transcript	missense_variant	1340	1075	359	L/V	Ctc/Gtc	.	.	.	1	CDH6	HGNC	1765	protein_coding	YES	CCDS3894.1	ENSP00000265071	CADH6_HUMAN	.	UPI0000126D9B	.	tolerated(0.17)	benign(0.301)	7/12	.	Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATTTCTCTAC	.	2	ESCA
ADAMTS12	0	.	GRCh37	5	33561131	33561131	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4125+1G>A	.	p.X1375_splice	ENST00000504830	.	229	86	143	110	110	0	ADAMTS12,splice_donor_variant,,ENST00000504830,;ADAMTS12,splice_donor_variant,,ENST00000352040,;	T	ENSG00000151388	ENST00000504830	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	ADAMTS12	HGNC	14605	protein_coding	YES	CCDS34140.1	ENSP00000422554	ATS12_HUMAN	.	UPI000013DC51	.	.	.	.	20/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTACCTTGC	.	5	ESCA
KIAA0947	0	.	GRCh37	5	5447558	5447558	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.443C>T	p.Thr148Ile	p.T148I	ENST00000296564	8/19	153	120	32	67	67	0	KIAA0947,missense_variant,p.Thr148Ile,ENST00000296564,;KIAA0947,non_coding_transcript_exon_variant,,ENST00000512608,;	T	ENSG00000164151	ENST00000296564	Transcript	missense_variant	665	443	148	T/I	aCt/aTt	.	.	.	1	KIAA0947	HGNC	29154	protein_coding	YES	CCDS47187.1	ENSP00000296564	K0947_HUMAN	.	UPI00015542F9	.	tolerated(0.24)	benign(0.264)	8/19	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11852,hmmpanther:PTHR11852:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAACTCAGG	.	5	ESCA
TNPO1	0	.	GRCh37	5	72201229	72201229	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2689G>T	p.Gly897Cys	p.G897C	ENST00000337273	24/25	90	55	35	94	94	0	TNPO1,missense_variant,p.Gly847Cys,ENST00000523768,;TNPO1,missense_variant,p.Gly889Cys,ENST00000506351,;TNPO1,missense_variant,p.Gly897Cys,ENST00000337273,;TNPO1,missense_variant,p.Gly847Cys,ENST00000454282,;TNPO1,missense_variant,p.Gly192Cys,ENST00000605210,;TNPO1,non_coding_transcript_exon_variant,,ENST00000503084,;	T	ENSG00000083312	ENST00000337273	Transcript	missense_variant	3115	2689	897	G/C	Ggt/Tgt	.	.	.	1	TNPO1	HGNC	6401	protein_coding	YES	CCDS43329.1	ENSP00000336712	TNPO1_HUMAN	S4R398_HUMAN	UPI000020CAB6	.	deleterious(0)	possibly_damaging(0.891)	24/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATGGTGTT	.	5	ESCA
GPR98	0	.	GRCh37	5	89924433	89924433	+	Silent	SNP	G	G	A	rs773901506	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1293G>A	p.%3D	p.A431A	ENST00000405460	8/90	87	62	25	85	85	0	GPR98,synonymous_variant,p.%3D,ENST00000405460,;GPR98,synonymous_variant,p.%3D,ENST00000504142,;	A	ENSG00000164199	ENST00000405460	Transcript	synonymous_variant	1389	1293	431	A	gcG/gcA	rs773901506,COSM3140515	.	.	1	GPR98	HGNC	17416	protein_coding	YES	CCDS47246.1	ENSP00000384582	GPR98_HUMAN	.	UPI00002127A7	.	.	.	8/90	.	Superfamily_domains:SSF141072,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.A431A|c.1293G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGCGAATTG	.	5	ESCA
SYNE1	0	.	GRCh37	6	152545638	152545638	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21513C>G	p.Asp7171Glu	p.D7171E	ENST00000367255	117/146	71	50	20	60	60	0	SYNE1,missense_variant,p.Asp1695Glu,ENST00000356820,;SYNE1,missense_variant,p.Asp7100Glu,ENST00000448038,;SYNE1,missense_variant,p.Asp7171Glu,ENST00000367255,;SYNE1,missense_variant,p.Asp7100Glu,ENST00000423061,;SYNE1,missense_variant,p.Asp6783Glu,ENST00000341594,;SYNE1,missense_variant,p.Asp7171Glu,ENST00000265368,;SYNE1,missense_variant,p.Asp93Glu,ENST00000367251,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,;	C	ENSG00000131018	ENST00000367255	Transcript	missense_variant	22115	21513	7171	D/E	gaC/gaG	.	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	benign(0.008)	117/146	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF46966,SMART_domains:SM00150,Pfam_domain:PF00435,Gene3D:1.20.58.60,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTGTCCAC	.	5	ESCA
TRIM27	0	.	GRCh37	6	28876806	28876806	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.830T>G	p.Ile277Ser	p.I277S	ENST00000377199	5/8	77	51	26	52	52	0	TRIM27,missense_variant,p.Ile277Ser,ENST00000377199,;TRIM27,missense_variant,p.Ile277Ser,ENST00000377194,;TRIM27,upstream_gene_variant,,ENST00000414543,;TRIM27,downstream_gene_variant,,ENST00000498117,;TRIM27,upstream_gene_variant,,ENST00000467742,;TRIM27,non_coding_transcript_exon_variant,,ENST00000481474,;	C	ENSG00000204713	ENST00000377199	Transcript	missense_variant	1187	830	277	I/S	aTc/aGc	.	.	.	-1	TRIM27	HGNC	9975	protein_coding	YES	CCDS4654.1	ENSP00000366404	TRI27_HUMAN	Q9NZT8_HUMAN	UPI0000000DCE	.	tolerated(0.06)	benign(0)	5/8	.	hmmpanther:PTHR24103:SF271,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGGATTTTC	.	5	ESCA
ATAT1	0	.	GRCh37	6	30612374	30612375	+	Intron	DEL	CA	CA	-	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	CA	CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933-1298_933-1297delCA	.	.	ENST00000330083	.	100	75	25	42	42	0	ATAT1,3_prime_UTR_variant,,ENST00000318999,;ATAT1,3_prime_UTR_variant,,ENST00000329992,;ATAT1,3_prime_UTR_variant,,ENST00000376483,;ATAT1,3_prime_UTR_variant,,ENST00000319027,;ATAT1,intron_variant,,ENST00000376485,;ATAT1,intron_variant,,ENST00000376478,;ATAT1,intron_variant,,ENST00000330083,;C6orf136,upstream_gene_variant,,ENST00000376473,;C6orf136,upstream_gene_variant,,ENST00000376471,;C6orf136,upstream_gene_variant,,ENST00000293604,;C6orf136,upstream_gene_variant,,ENST00000446773,;AL662800.2,upstream_gene_variant,,ENST00000583820,;ATAT1,intron_variant,,ENST00000462304,;ATAT1,intron_variant,,ENST00000468713,;C6orf136,upstream_gene_variant,,ENST00000493705,;ATAT1,intron_variant,,ENST00000479562,;ATAT1,intron_variant,,ENST00000471782,;C6orf136,upstream_gene_variant,,ENST00000463794,;C6orf136,upstream_gene_variant,,ENST00000484551,;C6orf136,upstream_gene_variant,,ENST00000488383,;ATAT1,downstream_gene_variant,,ENST00000493388,;	-	ENSG00000137343	ENST00000330083	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ATAT1	HGNC	21186	protein_coding	YES	CCDS54978.1	ENSP00000327832	ATAT_HUMAN	.	UPI000000DBC9	.	.	.	.	10/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTCTCAGTGTT	.	3	ESCA
ABHD16A	0	.	GRCh37	6	31664812	31664812	+	Splice_Site	SNP	T	T	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.344-2A>C	.	p.X115_splice	ENST00000395952	.	115	64	50	73	73	0	ABHD16A,splice_acceptor_variant,,ENST00000395952,;ABHD16A,splice_acceptor_variant,,ENST00000440843,;XXbac-BPG32J3.20,splice_acceptor_variant,,ENST00000461287,;ABHD16A,splice_acceptor_variant,,ENST00000375842,;ABHD16A,splice_acceptor_variant,,ENST00000538874,;MIR4646,downstream_gene_variant,,ENST00000580775,;ABHD16A,splice_acceptor_variant,,ENST00000498420,;ABHD16A,splice_acceptor_variant,,ENST00000482224,;ABHD16A,splice_acceptor_variant,,ENST00000468037,;ABHD16A,splice_acceptor_variant,,ENST00000492084,;ABHD16A,splice_acceptor_variant,,ENST00000495769,;ABHD16A,intron_variant,,ENST00000477462,;ABHD16A,upstream_gene_variant,,ENST00000492899,;ABHD16A,upstream_gene_variant,,ENST00000496579,;	G	ENSG00000204427	ENST00000395952	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	ABHD16A	HGNC	13921	protein_coding	YES	CCDS4713.1	ENSP00000379282	ABHGA_HUMAN	B3KNX9_HUMAN	UPI00001267A2	.	.	.	.	4/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCCTGGTAG	.	5	ESCA
RIMS1	0	.	GRCh37	6	73110497	73110497	+	3'Flank	SNP	A	A	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000521978	.	29	16	12	28	28	0	RIMS1,3_prime_UTR_variant,,ENST00000414192,;RIMS1,3_prime_UTR_variant,,ENST00000491071,;RIMS1,3_prime_UTR_variant,,ENST00000517827,;RIMS1,3_prime_UTR_variant,,ENST00000538414,;RIMS1,3_prime_UTR_variant,,ENST00000522211,;RIMS1,3_prime_UTR_variant,,ENST00000520567,;RIMS1,3_prime_UTR_variant,,ENST00000517433,;RIMS1,3_prime_UTR_variant,,ENST00000523963,;RIMS1,3_prime_UTR_variant,,ENST00000425662,;RIMS1,3_prime_UTR_variant,,ENST00000264839,;RIMS1,3_prime_UTR_variant,,ENST00000401910,;RIMS1,3_prime_UTR_variant,,ENST00000348717,;RIMS1,downstream_gene_variant,,ENST00000453976,;RIMS1,downstream_gene_variant,,ENST00000522291,;RIMS1,downstream_gene_variant,,ENST00000518273,;RIMS1,downstream_gene_variant,,ENST00000517960,;RIMS1,downstream_gene_variant,,ENST00000521978,;RIMS1,downstream_gene_variant,,ENST00000370420,;RIMS1,non_coding_transcript_exon_variant,,ENST00000431478,;RIMS1,non_coding_transcript_exon_variant,,ENST00000463023,;	G	ENSG00000079841	ENST00000521978	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	81	1	RIMS1	HGNC	17282	protein_coding	YES	CCDS47449.1	ENSP00000428417	RIMS1_HUMAN	.	UPI00001908FB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGCATTGTT	.	5	ESCA
EPHA7	0	.	GRCh37	6	93956675	93956675	+	Missense_Mutation	SNP	C	C	T	rs776802108	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2561G>A	p.Arg854His	p.R854H	ENST00000369303	15/17	45	32	13	55	55	0	EPHA7,missense_variant,p.Arg854His,ENST00000369303,;	T	ENSG00000135333	ENST00000369303	Transcript	missense_variant	2746	2561	854	R/H	cGt/cAt	rs776802108,COSM3876200,COSM3876199	.	.	-1	EPHA7	HGNC	3390	protein_coding	YES	CCDS5031.1	ENSP00000358309	EPHA7_HUMAN	.	UPI0000044771	.	deleterious(0.01)	probably_damaging(0.994)	15/17	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF266,hmmpanther:PTHR24416,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,PIRSF_domain:PIRSF000666,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAACGATAA	byFrequency	5	ESCA
ANKRD7	0	.	GRCh37	7	117864739	117864739	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-146G>A	.	.	ENST00000265224	1/7	70	46	24	27	27	0	ANKRD7,5_prime_UTR_variant,,ENST00000357099,;ANKRD7,5_prime_UTR_variant,,ENST00000265224,;ANKRD7,upstream_gene_variant,,ENST00000433239,;ANKRD7,upstream_gene_variant,,ENST00000486422,;ANKRD7,upstream_gene_variant,,ENST00000417525,;ANKRD7,intron_variant,,ENST00000477532,;	A	ENSG00000106013	ENST00000265224	Transcript	5_prime_UTR_variant	10	.	.	.	.	.	.	.	1	ANKRD7	HGNC	18588	protein_coding	YES	CCDS43638.1	ENSP00000265224	ANKR7_HUMAN	Q9UPM1_HUMAN	UPI0000E826A8	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCGGCTGC	.	5	ESCA
PRRT4	0	.	GRCh37	7	127999980	127999980	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66C>T	p.%3D	p.G22G	ENST00000446477	3/6	169	131	38	91	91	0	PRRT4,synonymous_variant,p.%3D,ENST00000489517,;PRRT4,synonymous_variant,p.%3D,ENST00000489835,;PRRT4,synonymous_variant,p.%3D,ENST00000535159,;PRRT4,synonymous_variant,p.%3D,ENST00000446477,;PRRT4,synonymous_variant,p.%3D,ENST00000495931,;PRRT4,synonymous_variant,p.%3D,ENST00000435512,;PRRT4,synonymous_variant,p.%3D,ENST00000464607,;PRRT4,upstream_gene_variant,,ENST00000480290,;	A	ENSG00000224940	ENST00000446477	Transcript	synonymous_variant	380	66	22	G	ggC/ggT	.	.	.	-1	PRRT4	HGNC	37280	protein_coding	YES	CCDS55160.1	ENSP00000415026	PRRT4_HUMAN	C9JWH6_HUMAN,C9JVX5_HUMAN,C9JQT1_HUMAN	UPI0000DD7E1D	.	.	.	3/6	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGGGGCCCAC	.	5	ESCA
ARHGEF5	0	.	GRCh37	7	144071936	144071936	+	Missense_Mutation	SNP	C	C	T	rs771323721	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4252C>T	p.His1418Tyr	p.H1418Y	ENST00000056217	11/15	23	18	5	12	12	0	ARHGEF5,missense_variant,p.His1418Tyr,ENST00000056217,;ARHGEF5,missense_variant,p.His340Tyr,ENST00000471847,;ARHGEF5,missense_variant,p.His672Tyr,ENST00000474817,;	T	ENSG00000050327	ENST00000056217	Transcript	missense_variant	4426	4252	1418	H/Y	Cac/Tac	rs771323721	.	.	1	ARHGEF5	HGNC	13209	protein_coding	YES	CCDS34771.1	ENSP00000056217	ARHG5_HUMAN	H9XFB6_HUMAN	UPI00004028DC	.	tolerated(0.53)	benign(0.07)	11/15	.	PROSITE_profiles:PS50003,hmmpanther:PTHR12845:SF2,hmmpanther:PTHR12845,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CAGTCCACCTG	byFrequency	2	ESCA
NCAPG2	0	.	GRCh37	7	158448144	158448144	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2392G>T	p.Asp798Tyr	p.D798Y	ENST00000409423	21/29	198	124	74	31	31	0	NCAPG2,missense_variant,p.Asp590Tyr,ENST00000275830,;NCAPG2,missense_variant,p.Asp798Tyr,ENST00000409423,;NCAPG2,missense_variant,p.Asp600Tyr,ENST00000441982,;NCAPG2,missense_variant,p.Asp798Tyr,ENST00000449727,;NCAPG2,missense_variant,p.Asp798Tyr,ENST00000356309,;NCAPG2,missense_variant,p.Asp798Tyr,ENST00000409339,;NCAPG2,missense_variant,p.Asp299Tyr,ENST00000541468,;NCAPG2,downstream_gene_variant,,ENST00000475918,;NCAPG2,downstream_gene_variant,,ENST00000474940,;NCAPG2,3_prime_UTR_variant,,ENST00000432615,;NCAPG2,non_coding_transcript_exon_variant,,ENST00000467785,;	A	ENSG00000146918	ENST00000409423	Transcript	missense_variant	2565	2392	798	D/Y	Gat/Tat	.	.	.	-1	NCAPG2	HGNC	21904	protein_coding	YES	CCDS43686.1	ENSP00000386569	CNDG2_HUMAN	.	UPI000000DA46	.	tolerated(1)	benign(0.076)	21/29	.	Coiled-coils_(Ncoils):Coil,Pfam_domain:PF12422,hmmpanther:PTHR16199,hmmpanther:PTHR16199:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATCTGCCT	.	5	ESCA
NPVF	0	.	GRCh37	7	25266610	25266610	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174T>G	p.Asn58Lys	p.N58K	ENST00000222674	2/3	58	30	27	51	51	0	NPVF,missense_variant,p.Asn58Lys,ENST00000222674,;	C	ENSG00000105954	ENST00000222674	Transcript	missense_variant	221	174	58	N/K	aaT/aaG	.	.	.	-1	NPVF	HGNC	13782	protein_coding	YES	CCDS5395.1	ENSP00000222674	NPVF_HUMAN	.	UPI000004CB0B	.	deleterious(0.01)	benign(0.242)	2/3	.	hmmpanther:PTHR14403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAAAATTGAG	.	5	ESCA
GGCT	0	.	GRCh37	7	30540160	30540160	+	Silent	SNP	A	A	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279T>G	p.%3D	p.S93S	ENST00000275428	2/4	85	54	31	29	29	0	GGCT,synonymous_variant,p.%3D,ENST00000409436,;GGCT,synonymous_variant,p.%3D,ENST00000005374,;GGCT,synonymous_variant,p.%3D,ENST00000409390,;GGCT,synonymous_variant,p.%3D,ENST00000598361,;GGCT,synonymous_variant,p.%3D,ENST00000275428,;GGCT,intron_variant,,ENST00000409144,;GGCT,synonymous_variant,p.%3D,ENST00000426081,;GGCT,intron_variant,,ENST00000440082,;GGCT,intron_variant,,ENST00000447901,;	C	ENSG00000006625	ENST00000275428	Transcript	synonymous_variant	414	279	93	S	tcT/tcG	.	.	.	-1	GGCT	HGNC	21705	protein_coding	YES	CCDS5428.1	ENSP00000275428	GGCT_HUMAN	M0QZK8_HUMAN	UPI00000473DC	.	.	.	2/4	.	Superfamily_domains:SSF110857,Gene3D:3.10.490.10,Pfam_domain:PF13772,hmmpanther:PTHR12935	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCAGAGAATT	.	5	ESCA
C7orf25	0	.	GRCh37	7	42948996	42948996	+	3'Flank	SNP	T	T	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000431882	.	20	14	6	28	28	0	C7orf25,3_prime_UTR_variant,,ENST00000350427,;C7orf25,3_prime_UTR_variant,,ENST00000447342,;C7orf25,downstream_gene_variant,,ENST00000425683,;C7orf25,downstream_gene_variant,,ENST00000431882,;C7orf25,downstream_gene_variant,,ENST00000438029,;C7orf25,downstream_gene_variant,,ENST00000432637,;PSMA2,3_prime_UTR_variant,,ENST00000442788,;PSMA2,downstream_gene_variant,,ENST00000433579,;	G	ENSG00000136197	ENST00000431882	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	56	-1	C7orf25	HGNC	21703	protein_coding	YES	CCDS47576.1	ENSP00000416290	CG025_HUMAN	C9K0L6_HUMAN,C9JF90_HUMAN	UPI000159689A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATATAGACG	.	5	ESCA
PAPOLB	0	.	GRCh37	7	4899602	4899602	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1837G>C	p.Val613Leu	p.V613L	ENST00000404991	1/1	102	93	9	70	70	0	PAPOLB,missense_variant,p.Val613Leu,ENST00000404991,;RADIL,intron_variant,,ENST00000399583,;RADIL,intron_variant,,ENST00000536091,;RADIL,intron_variant,,ENST00000445392,;	G	ENSG00000218823	ENST00000404991	Transcript	missense_variant	2024	1837	613	V/L	Gtt/Ctt	.	.	.	-1	PAPOLB	HGNC	15970	protein_coding	YES	.	ENSP00000384700	PAPOB_HUMAN	A4D1Z6_HUMAN	UPI0000131304	.	tolerated_low_confidence(0.13)	benign(0.008)	1/1	.	hmmpanther:PTHR10682,hmmpanther:PTHR10682:SF19,PIRSF_domain:PIRSF018425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACAACTCTGG	.	2	ESCA
AC006455.1	0	.	GRCh37	7	62809792	62809792	+	5'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-218C>A	.	.	ENST00000456890	1/1	55	46	9	69	69	0	AC006455.1,5_prime_UTR_variant,,ENST00000456890,;RP5-905H7.9,intron_variant,,ENST00000426550,;RP5-905H7.10,non_coding_transcript_exon_variant,,ENST00000429931,;RP5-905H7.7,upstream_gene_variant,,ENST00000454641,;RP5-905H7.6,downstream_gene_variant,,ENST00000426192,;	A	ENSG00000230000	ENST00000456890	Transcript	5_prime_UTR_variant	554	.	.	.	.	.	.	.	1	AC006455.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000407928	.	.	UPI000019793E	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GGCTCCGAAGA	.	2	ESCA
PCLO	0	.	GRCh37	7	82474678	82474678	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13955C>T	p.Ser4652Leu	p.S4652L	ENST00000333891	13/25	77	73	4	76	76	0	PCLO,missense_variant,p.Ser4652Leu,ENST00000333891,;PCLO,missense_variant,p.Ser4652Leu,ENST00000423517,;PCLO,non_coding_transcript_exon_variant,,ENST00000426442,;PCLO,3_prime_UTR_variant,,ENST00000413807,;PCLO,downstream_gene_variant,,ENST00000456006,;	A	ENSG00000186472	ENST00000333891	Transcript	missense_variant	14293	13955	4652	S/L	tCa/tTa	.	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	13/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTGAATGA	.	2	ESCA
PCLO	0	.	GRCh37	7	82544508	82544508	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12794G>C	p.Gly4265Ala	p.G4265A	ENST00000333891	7/25	72	57	15	41	41	0	PCLO,missense_variant,p.Gly985Ala,ENST00000437081,;PCLO,missense_variant,p.Gly4265Ala,ENST00000333891,;PCLO,missense_variant,p.Gly4265Ala,ENST00000423517,;	G	ENSG00000186472	ENST00000333891	Transcript	missense_variant	13132	12794	4265	G/A	gGc/gCc	.	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	7/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGCCCAGT	.	5	ESCA
PCLO	0	.	GRCh37	7	82585180	82585180	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5089C>G	p.Pro1697Ala	p.P1697A	ENST00000333891	5/25	55	39	16	37	37	0	PCLO,missense_variant,p.Pro1697Ala,ENST00000333891,;PCLO,missense_variant,p.Pro1697Ala,ENST00000423517,;	C	ENSG00000186472	ENST00000333891	Transcript	missense_variant	5427	5089	1697	P/A	Cca/Gca	.	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	5/25	.	hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGGCTCTT	.	5	ESCA
COL1A2	0	.	GRCh37	7	94056317	94056317	+	Intron	SNP	A	A	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3106-3A>C	.	.	ENST00000297268	.	86	58	28	44	44	0	COL1A2,splice_region_variant,,ENST00000297268,;COL1A2,splice_region_variant,,ENST00000488121,;COL1A2,non_coding_transcript_exon_variant,,ENST00000481570,;COL1A2,non_coding_transcript_exon_variant,,ENST00000492110,;COL1A2,downstream_gene_variant,,ENST00000469732,;COL1A2,downstream_gene_variant,,ENST00000473573,;COL1A2,downstream_gene_variant,,ENST00000478215,;COL1A2,downstream_gene_variant,,ENST00000497316,;COL1A2,upstream_gene_variant,,ENST00000464916,;	C	ENSG00000164692	ENST00000297268	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	COL1A2	HGNC	2198	protein_coding	YES	CCDS34682.1	ENSP00000297268	CO1A2_HUMAN	Q75N18_HUMAN,A2TIK1_HUMAN	UPI00003B0CFC	.	.	.	.	46/51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTAAAGGGT	.	4	ESCA
ZNF789	0	.	GRCh37	7	99074101	99074101	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22A>G	p.Lys8Glu	p.K8E	ENST00000331410	2/5	49	45	3	26	26	0	ZNF789,missense_variant,p.Lys8Glu,ENST00000331410,;ZNF789,missense_variant,p.Lys8Glu,ENST00000379724,;ZNF789,splice_region_variant,,ENST00000493485,;ZNF789,splice_region_variant,,ENST00000483089,;ZNF789,splice_region_variant,,ENST00000448667,;ZNF789,intron_variant,,ENST00000481472,;ZNF789,splice_region_variant,,ENST00000488485,;ZNF789,splice_region_variant,,ENST00000468705,;ZNF789,splice_region_variant,,ENST00000447047,;ZNF789,splice_region_variant,,ENST00000465438,;	G	ENSG00000198556	ENST00000331410	Transcript	missense_variant	292	22	8	K/E	Aag/Gag	.	.	.	1	ZNF789	HGNC	27801	protein_coding	YES	CCDS34693.1	ENSP00000331927	ZN789_HUMAN	.	UPI00001D74C1	.	deleterious(0.02)	benign(0.006)	2/5	.	Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGGAAGGTG	.	2	ESCA
CSMD3	0	.	GRCh37	8	113392631	113392631	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6086T>G	p.Phe2029Cys	p.F2029C	ENST00000297405	38/71	98	74	24	58	58	0	CSMD3,missense_variant,p.Phe1959Cys,ENST00000352409,;CSMD3,missense_variant,p.Phe1925Cys,ENST00000455883,;CSMD3,missense_variant,p.Phe2029Cys,ENST00000297405,;CSMD3,missense_variant,p.Phe1299Cys,ENST00000339701,;CSMD3,missense_variant,p.Phe1989Cys,ENST00000343508,;	C	ENSG00000164796	ENST00000297405	Transcript	missense_variant	6331	6086	2029	F/C	tTt/tGt	.	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	deleterious(0)	probably_damaging(0.997)	38/71	.	PROSITE_profiles:PS01180,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGAAAATTT	.	5	ESCA
ZNF707	0	.	GRCh37	8	144776548	144776548	+	Missense_Mutation	SNP	G	G	A	rs782359327	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.964G>A	p.Gly322Ser	p.G322S	ENST00000532205	8/8	202	174	28	90	90	0	ZNF707,missense_variant,p.Gly322Ser,ENST00000358656,;ZNF707,missense_variant,p.Gly322Ser,ENST00000532205,;ZNF707,missense_variant,p.Gly322Ser,ENST00000532158,;ZNF707,missense_variant,p.Gly322Ser,ENST00000418203,;ZNF707,missense_variant,p.Gly322Ser,ENST00000454097,;ZNF707,downstream_gene_variant,,ENST00000534303,;ZNF707,downstream_gene_variant,,ENST00000442058,;ZNF707,downstream_gene_variant,,ENST00000530574,;ZNF707,downstream_gene_variant,,ENST00000526315,;ZNF707,downstream_gene_variant,,ENST00000529833,;ZNF707,downstream_gene_variant,,ENST00000526970,;RP11-429J17.2,upstream_gene_variant,,ENST00000531565,;ZNF707,non_coding_transcript_exon_variant,,ENST00000527561,;ZNF707,downstream_gene_variant,,ENST00000532571,;ZNF707,downstream_gene_variant,,ENST00000530341,;ZNF707,downstream_gene_variant,,ENST00000531811,;ZNF707,3_prime_UTR_variant,,ENST00000533031,;ZNF707,non_coding_transcript_exon_variant,,ENST00000532486,;ZNF707,downstream_gene_variant,,ENST00000525862,;ZNF707,downstream_gene_variant,,ENST00000532003,;ZNF707,downstream_gene_variant,,ENST00000527293,;ZNF707,downstream_gene_variant,,ENST00000533254,;ZNF707,downstream_gene_variant,,ENST00000534589,;ZNF707,downstream_gene_variant,,ENST00000528134,;ZNF707,downstream_gene_variant,,ENST00000528456,;ZNF707,downstream_gene_variant,,ENST00000525538,;ZNF707,downstream_gene_variant,,ENST00000531254,;ZNF707,downstream_gene_variant,,ENST00000525619,;ZNF707,downstream_gene_variant,,ENST00000531985,;ZNF707,downstream_gene_variant,,ENST00000525185,;	A	ENSG00000181135	ENST00000532205	Transcript	missense_variant	1863	964	322	G/S	Ggc/Agc	rs782359327	.	.	1	ZNF707	HGNC	27815	protein_coding	YES	CCDS47932.1	ENSP00000436212	ZN707_HUMAN	E9PS67_HUMAN,E9PQ20_HUMAN,E9PNV7_HUMAN,E9PHZ0_HUMAN	UPI0000160D8F	.	deleterious(0.01)	probably_damaging(0.999)	8/8	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24402:SF169,hmmpanther:PTHR24402,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTGCGGCAAG	byFrequency	4	ESCA
INTS10	0	.	GRCh37	8	19677964	19677964	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376T>A	p.Leu126Ile	p.L126I	ENST00000397977	4/17	87	79	8	53	53	0	INTS10,missense_variant,p.Leu126Ile,ENST00000397977,;INTS10,upstream_gene_variant,,ENST00000523846,;INTS10,intron_variant,,ENST00000521758,;INTS10,upstream_gene_variant,,ENST00000522806,;INTS10,3_prime_UTR_variant,,ENST00000522114,;INTS10,3_prime_UTR_variant,,ENST00000523869,;INTS10,upstream_gene_variant,,ENST00000521357,;INTS10,downstream_gene_variant,,ENST00000520985,;INTS10,upstream_gene_variant,,ENST00000522081,;INTS10,upstream_gene_variant,,ENST00000523143,;INTS10,downstream_gene_variant,,ENST00000518424,;	A	ENSG00000104613	ENST00000397977	Transcript	missense_variant	774	376	126	L/I	Tta/Ata	.	.	.	1	INTS10	HGNC	25548	protein_coding	YES	CCDS6011.2	ENSP00000381064	INT10_HUMAN	E5RJN5_HUMAN	UPI0000210A61	.	deleterious(0.03)	possibly_damaging(0.741)	4/17	.	hmmpanther:PTHR16055,Prints_domain:PR02106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACACGTTAGAA	.	3	ESCA
EFCAB1	0	.	GRCh37	8	49647767	49647767	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-57C>T	.	.	ENST00000262103	1/6	74	47	27	14	14	0	EFCAB1,5_prime_UTR_variant,,ENST00000262103,;EFCAB1,5_prime_UTR_variant,,ENST00000523092,;EFCAB1,5_prime_UTR_variant,,ENST00000433756,;EFCAB1,upstream_gene_variant,,ENST00000522254,;EFCAB1,non_coding_transcript_exon_variant,,ENST00000521721,;EFCAB1,non_coding_transcript_exon_variant,,ENST00000521002,;EFCAB1,5_prime_UTR_variant,,ENST00000521701,;	A	ENSG00000034239	ENST00000262103	Transcript	5_prime_UTR_variant	25	.	.	.	.	.	.	.	-1	EFCAB1	HGNC	25678	protein_coding	YES	CCDS6145.1	ENSP00000262103	EFCB1_HUMAN	.	UPI000006E520	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGAGACCCT	.	5	ESCA
CA8	0	.	GRCh37	8	61135295	61135295	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.651G>T	p.%3D	p.V217V	ENST00000317995	7/9	67	54	13	34	34	0	CA8,synonymous_variant,p.%3D,ENST00000317995,;CA8,non_coding_transcript_exon_variant,,ENST00000528666,;CA8,non_coding_transcript_exon_variant,,ENST00000524872,;	A	ENSG00000178538	ENST00000317995	Transcript	synonymous_variant	916	651	217	V	gtG/gtT	.	.	.	-1	CA8	HGNC	1382	protein_coding	YES	CCDS6174.1	ENSP00000314407	CAH8_HUMAN	B4DFA0_HUMAN	UPI000000D816	.	.	.	7/9	.	PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF99,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATACACCCA	.	5	ESCA
PI15	0	.	GRCh37	8	75765903	75765903	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4415T>C	.	.	ENST00000260113	6/6	125	97	27	58	58	0	PI15,3_prime_UTR_variant,,ENST00000260113,;PI15,downstream_gene_variant,,ENST00000523773,;RP11-758M4.4,intron_variant,,ENST00000522914,;RP11-758M4.4,intron_variant,,ENST00000518128,;RP11-758M4.4,intron_variant,,ENST00000523860,;	C	ENSG00000137558	ENST00000260113	Transcript	3_prime_UTR_variant	5371	.	.	.	.	.	.	.	1	PI15	HGNC	8946	protein_coding	YES	CCDS6218.1	ENSP00000260113	PI15_HUMAN	.	UPI00000422F7	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTTGTTGT	.	5	ESCA
COL15A1	0	.	GRCh37	9	101749650	101749650	+	Silent	SNP	G	G	A	rs199838728	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723G>A	p.%3D	p.S241S	ENST00000375001	4/42	75	15	59	57	57	0	COL15A1,synonymous_variant,p.%3D,ENST00000375001,;COL15A1,downstream_gene_variant,,ENST00000471477,;	A	ENSG00000204291	ENST00000375001	Transcript	synonymous_variant	1146	723	241	S	tcG/tcA	rs199838728	.	.	1	COL15A1	HGNC	2192	protein_coding	YES	CCDS35081.1	ENSP00000364140	COFA1_HUMAN	.	UPI0000211506	.	.	.	4/42	.	hmmpanther:PTHR24023:SF398,hmmpanther:PTHR24023	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTCGGTGAG	byCluster|by1000G	5	ESCA
ZFP37	0	.	GRCh37	9	115806537	115806537	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361G>T	p.Asp121Tyr	p.D121Y	ENST00000374227	4/4	48	32	16	25	25	0	ZFP37,missense_variant,p.Asp136Tyr,ENST00000553380,;ZFP37,missense_variant,p.Asp122Tyr,ENST00000555206,;ZFP37,missense_variant,p.Asp121Tyr,ENST00000374227,;	A	ENSG00000136866	ENST00000374227	Transcript	missense_variant	389	361	121	D/Y	Gat/Tat	.	.	.	-1	ZFP37	HGNC	12863	protein_coding	YES	CCDS6787.1	ENSP00000363344	ZFP37_HUMAN	.	UPI000013D04B	.	tolerated(0.12)	benign(0.413)	4/4	.	hmmpanther:PTHR24381:SF139,hmmpanther:PTHR24381	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATCTTTCT	.	5	ESCA
COL5A1	0	.	GRCh37	9	137658326	137658326	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2115G>A	p.%3D	p.P705P	ENST00000371817	22/66	99	93	6	50	50	0	COL5A1,synonymous_variant,p.%3D,ENST00000371817,;	A	ENSG00000130635	ENST00000371817	Transcript	synonymous_variant	2529	2115	705	P	ccG/ccA	.	.	.	1	COL5A1	HGNC	2209	protein_coding	YES	CCDS6982.1	ENSP00000360882	CO5A1_HUMAN	Q9UML4_HUMAN,Q96HC0_HUMAN,Q59EE7_HUMAN	UPI0000210EE3	.	.	.	22/66	.	hmmpanther:PTHR24023:SF387,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCCGGGGCC	.	2	ESCA
NOTCH1	0	.	GRCh37	9	139413042	139413042	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1099+1G>A	.	p.X367_splice	ENST00000277541	.	120	21	99	48	48	0	NOTCH1,splice_donor_variant,,ENST00000277541,;MIR4673,downstream_gene_variant,,ENST00000584777,;NOTCH1,downstream_gene_variant,,ENST00000491649,;	T	ENSG00000148400	ENST00000277541	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	.	.	.	6/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R365C|c.1093C>T|4,BUFFER|p.R365C|c.1093C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCACCTGTG	.	5	ESCA
C9orf24	0	.	GRCh37	9	34381092	34381092	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510G>A	p.%3D	p.S170S	ENST00000297623	5/7	44	24	19	13	13	0	C9orf24,synonymous_variant,p.%3D,ENST00000379126,;C9orf24,synonymous_variant,p.%3D,ENST00000379124,;C9orf24,synonymous_variant,p.%3D,ENST00000379133,;C9orf24,synonymous_variant,p.%3D,ENST00000297623,;C9orf24,synonymous_variant,p.%3D,ENST00000379127,;C9orf24,downstream_gene_variant,,ENST00000444429,;KIAA1161,upstream_gene_variant,,ENST00000297625,;C9orf24,upstream_gene_variant,,ENST00000481295,;	T	ENSG00000164972	ENST00000297623	Transcript	synonymous_variant	709	510	170	S	tcG/tcA	.	.	.	-1	C9orf24	HGNC	19919	protein_coding	YES	CCDS6554.1	ENSP00000297623	SMRP1_HUMAN	.	UPI000006E5B3	.	.	.	5/7	.	Pfam_domain:PF15181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCGCGACAG	.	5	ESCA
PTPRD	0	.	GRCh37	9	8517873	8517873	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1518C>A	p.Asp506Glu	p.D506E	ENST00000381196	18/43	70	42	28	52	51	1	PTPRD,missense_variant,p.Asp496Glu,ENST00000397617,;PTPRD,missense_variant,p.Asp506Glu,ENST00000486161,;PTPRD,missense_variant,p.Asp493Glu,ENST00000358503,;PTPRD,missense_variant,p.Asp493Glu,ENST00000360074,;PTPRD,missense_variant,p.Asp506Glu,ENST00000381196,;PTPRD,missense_variant,p.Asp496Glu,ENST00000397606,;PTPRD,missense_variant,p.Asp506Glu,ENST00000356435,;PTPRD,missense_variant,p.Asp506Glu,ENST00000355233,;PTPRD,missense_variant,p.Asp503Glu,ENST00000397611,;PTPRD,missense_variant,p.Asp506Glu,ENST00000540109,;PTPRD,missense_variant,p.Asp503Glu,ENST00000537002,;	T	ENSG00000153707	ENST00000381196	Transcript	missense_variant	2062	1518	506	D/E	gaC/gaA	.	.	.	-1	PTPRD	HGNC	9668	protein_coding	YES	CCDS43786.1	ENSP00000370593	PTPRD_HUMAN	C9J6E4_HUMAN,B4DK48_HUMAN	UPI0000132990	.	tolerated(0.37)	benign(0.02)	18/43	.	Superfamily_domains:SSF49265,Gene3D:2.60.40.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF204,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATGTCACT	.	5	ESCA
SPTLC1	0	.	GRCh37	9	94842356	94842356	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369A>G	p.%3D	p.A123A	ENST00000262554	5/15	34	20	14	28	28	0	SPTLC1,synonymous_variant,p.%3D,ENST00000262554,;SPTLC1,synonymous_variant,p.%3D,ENST00000337841,;SPTLC1,non_coding_transcript_exon_variant,,ENST00000477888,;SPTLC1,non_coding_transcript_exon_variant,,ENST00000482632,;	C	ENSG00000090054	ENST00000262554	Transcript	synonymous_variant	375	369	123	A	gcA/gcG	.	.	.	-1	SPTLC1	HGNC	11277	protein_coding	YES	CCDS6692.1	ENSP00000262554	SPTC1_HUMAN	B4DR90_HUMAN	UPI000012E27B	.	.	.	5/15	.	hmmpanther:PTHR13693,hmmpanther:PTHR13693:SF2,Pfam_domain:PF00155,Gene3D:3.40.640.10,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGATGCTAA	.	5	ESCA
NXF5	0	.	GRCh37	X	101095814	101095814	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534T>C	p.%3D	p.S178S	ENST00000537026	9/16	256	158	98	201	201	0	NXF5,synonymous_variant,p.%3D,ENST00000473265,;NXF5,synonymous_variant,p.%3D,ENST00000361708,;NXF5,synonymous_variant,p.%3D,ENST00000537026,;NXF5,synonymous_variant,p.%3D,ENST00000332614,;NXF5,synonymous_variant,p.%3D,ENST00000361330,;NXF5,synonymous_variant,p.%3D,ENST00000372803,;NXF5,synonymous_variant,p.%3D,ENST00000263032,;NXF5,intron_variant,,ENST00000493509,;	G	ENSG00000126952	ENST00000537026	Transcript	synonymous_variant	894	534	178	S	tcT/tcC	.	.	.	-1	NXF5	HGNC	8075	protein_coding	YES	CCDS14491.2	ENSP00000442401	NXF5_HUMAN	.	UPI0000F059DC	.	.	.	9/16	.	Superfamily_domains:SSF52058,Gene3D:3.80.10.10,hmmpanther:PTHR10662,hmmpanther:PTHR10662:SF26,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCAGAAAG	.	5	ESCA
TCEAL2	0	.	GRCh37	X	101381791	101381791	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-12G>A	.	.	ENST00000372780	3/3	89	59	30	76	76	0	TCEAL2,5_prime_UTR_variant,,ENST00000329035,;TCEAL2,5_prime_UTR_variant,,ENST00000372780,;TCEAL2,non_coding_transcript_exon_variant,,ENST00000476749,;	A	ENSG00000184905	ENST00000372780	Transcript	5_prime_UTR_variant	208	.	.	.	.	.	.	.	1	TCEAL2	HGNC	29818	protein_coding	YES	CCDS14496.1	ENSP00000361866	TCAL2_HUMAN	.	UPI00000709E1	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGGGAAAT	.	5	ESCA
MORC4	0	.	GRCh37	X	106224144	106224144	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.913G>C	p.Asp305His	p.D305H	ENST00000355610	7/17	82	45	36	82	82	0	MORC4,missense_variant,p.Asp53His,ENST00000535534,;MORC4,missense_variant,p.Asp305His,ENST00000255495,;MORC4,missense_variant,p.Asp305His,ENST00000355610,;MORC4,intron_variant,,ENST00000604604,;	G	ENSG00000133131	ENST00000355610	Transcript	missense_variant	1188	913	305	D/H	Gat/Cat	.	.	.	-1	MORC4	HGNC	23485	protein_coding	YES	CCDS14525.2	ENSP00000347821	MORC4_HUMAN	.	UPI00003E75D3	.	deleterious(0)	possibly_damaging(0.874)	7/17	.	hmmpanther:PTHR23336,hmmpanther:PTHR23336:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATCATATT	.	5	ESCA
ZCCHC16	0	.	GRCh37	X	111700252	111700252	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1363C>G	.	.	ENST00000340433	1/1	67	46	20	93	93	0	ZCCHC16,3_prime_UTR_variant,,ENST00000340433,;	G	ENSG00000187823	ENST00000340433	Transcript	3_prime_UTR_variant	2526	.	.	.	.	.	.	.	1	ZCCHC16	HGNC	25214	protein_coding	YES	CCDS35369.1	ENSP00000340590	ZCH16_HUMAN	.	UPI00001975B5	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTCCCTGC	.	5	ESCA
NKAP	0	.	GRCh37	X	119066177	119066177	+	Missense_Mutation	SNP	T	T	C	rs768575536	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740A>G	p.Lys247Arg	p.K247R	ENST00000371410	6/9	73	50	23	21	21	0	NKAP,missense_variant,p.Lys247Arg,ENST00000371410,;NKAP,splice_region_variant,,ENST00000477789,;NKAP,non_coding_transcript_exon_variant,,ENST00000482407,;	C	ENSG00000101882	ENST00000371410	Transcript	missense_variant	907	740	247	K/R	aAg/aGg	rs768575536	.	.	-1	NKAP	HGNC	29873	protein_coding	YES	CCDS14592.1	ENSP00000360464	NKAP_HUMAN	.	UPI000004A07B	.	tolerated(0.1)	unknown(0)	6/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13087,hmmpanther:PTHR13087:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTCTTCCTA	.	5	ESCA
SMARCA1	0	.	GRCh37	X	128580984	128580984	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*302C>A	.	.	ENST00000371122	25/25	54	32	22	50	50	0	SMARCA1,3_prime_UTR_variant,,ENST00000371122,;SMARCA1,3_prime_UTR_variant,,ENST00000371121,;SMARCA1,3_prime_UTR_variant,,ENST00000371123,;	T	ENSG00000102038	ENST00000371122	Transcript	3_prime_UTR_variant	3597	.	.	.	.	.	.	.	-1	SMARCA1	HGNC	11097	protein_coding	YES	CCDS14612.1	ENSP00000360163	SMCA1_HUMAN	F6TQG2_HUMAN	UPI0000161FA6	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCAGGTAGA	.	5	ESCA
RP1-171K16.5	0	.	GRCh37	X	140714645	140714645	+	RNA	SNP	A	A	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.463A>T	.	.	ENST00000412163	2/2	69	48	21	72	72	0	RP1-171K16.5,non_coding_transcript_exon_variant,,ENST00000412163,;SPANXA2-OT1,intron_variant,,ENST00000421554,;	T	ENSG00000223438	ENST00000412163	Transcript	non_coding_transcript_exon_variant	463	.	.	.	.	.	.	.	1	RP1-171K16.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTAATTTTT	.	5	ESCA
MAGEC1	0	.	GRCh37	X	140993814	140993814	+	Silent	SNP	C	C	G	rs766166929	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.624C>G	p.%3D	p.S208S	ENST00000285879	4/4	333	276	57	301	301	0	MAGEC1,synonymous_variant,p.%3D,ENST00000285879,;MAGEC1,intron_variant,,ENST00000406005,;	G	ENSG00000155495	ENST00000285879	Transcript	synonymous_variant	910	624	208	S	tcC/tcG	rs766166929	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTCCACTTT	.	4	ESCA
MAGEA1	0	.	GRCh37	X	152482520	152482520	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.491C>T	p.Pro164Leu	p.P164L	ENST00000356661	3/3	126	121	5	143	143	0	MAGEA1,missense_variant,p.Pro164Leu,ENST00000356661,;	A	ENSG00000198681	ENST00000356661	Transcript	missense_variant	710	491	164	P/L	cCc/cTc	.	.	.	-1	MAGEA1	HGNC	6796	protein_coding	YES	CCDS14720.1	ENSP00000349085	MAGA1_HUMAN	A8IF97_HUMAN	UPI0000035FCB	.	deleterious(0.03)	possibly_damaging(0.861)	3/3	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF49,hmmpanther:PTHR11736,Pfam_domain:PF01454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGTGGGGTCT	.	2	ESCA
FIGF	0	.	GRCh37	X	15364202	15364202	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53C>T	.	.	ENST00000297904	7/7	126	74	51	86	86	0	FIGF,3_prime_UTR_variant,,ENST00000297904,;FIGF,non_coding_transcript_exon_variant,,ENST00000488351,;	A	ENSG00000165197	ENST00000297904	Transcript	3_prime_UTR_variant	1548	.	.	.	.	.	.	.	-1	FIGF	HGNC	3708	protein_coding	YES	CCDS14166.1	ENSP00000297904	VEGFD_HUMAN	.	UPI00000012B2	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTGGCAAAG	.	5	ESCA
P2RY8	0	.	GRCh37	X	1584361	1584362	+	3'UTR	INS	-	-	C	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10dupG	.	.	ENST00000381297	2/2	75	57	18	28	28	0	P2RY8,3_prime_UTR_variant,,ENST00000381297,;P2RY8,downstream_gene_variant,,ENST00000460672,;	C	ENSG00000182162	ENST00000381297	Transcript	3_prime_UTR_variant	1301-1302	.	.	.	.	.	.	.	-1	P2RY8	HGNC	15524	protein_coding	YES	CCDS14115.1	ENSP00000370697	P2RY8_HUMAN	.	UPI000000DA6D	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCTGCGCCCCC	.	3	ESCA
RS1	0	.	GRCh37	X	18658899	18658899	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1225C>A	.	.	ENST00000379984	6/6	57	31	25	34	34	0	RS1,3_prime_UTR_variant,,ENST00000379984,;CDKL5,intron_variant,,ENST00000379989,;CDKL5,intron_variant,,ENST00000379996,;RS1,downstream_gene_variant,,ENST00000476595,;	T	ENSG00000102104	ENST00000379984	Transcript	3_prime_UTR_variant	1941	.	.	.	.	.	.	.	-1	RS1	HGNC	10457	protein_coding	YES	CCDS14187.1	ENSP00000369320	XLRS1_HUMAN	Q0QD39_HUMAN	UPI0000139001	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTGATTCC	.	5	ESCA
PHEX	0	.	GRCh37	X	22117197	22117197	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1007C>T	p.Ser336Phe	p.S336F	ENST00000379374	9/22	131	93	38	87	87	0	PHEX,missense_variant,p.Ser336Phe,ENST00000379374,;PHEX,missense_variant,p.Ser239Phe,ENST00000535894,;PHEX,missense_variant,p.Ser39Phe,ENST00000418858,;PHEX,missense_variant,p.Ser336Phe,ENST00000537599,;PHEX,non_coding_transcript_exon_variant,,ENST00000475778,;	T	ENSG00000102174	ENST00000379374	Transcript	missense_variant	1572	1007	336	S/F	tCc/tTc	COSM3560414	.	.	1	PHEX	HGNC	8918	protein_coding	YES	CCDS14204.1	ENSP00000368682	PHEX_HUMAN	D1LZJ7_HUMAN,B4DWG8_HUMAN	UPI0000033C42	.	deleterious(0.01)	probably_damaging(0.999)	9/22	.	Superfamily_domains:SSF55486,Pfam_domain:PF05649,hmmpanther:PTHR11733:SF117,hmmpanther:PTHR11733	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCCGAGA	.	5	ESCA
ZC3H12B	0	.	GRCh37	X	64721861	64721861	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1283A>G	p.Lys428Arg	p.K428R	ENST00000338957	5/5	44	30	13	48	48	0	ZC3H12B,missense_variant,p.Lys417Arg,ENST00000423889,;ZC3H12B,missense_variant,p.Lys428Arg,ENST00000338957,;	G	ENSG00000102053	ENST00000338957	Transcript	missense_variant	1350	1283	428	K/R	aAa/aGa	.	.	.	1	ZC3H12B	HGNC	17407	protein_coding	YES	CCDS48131.2	ENSP00000340839	.	E9PAJ6_HUMAN	UPI00001D7BEA	.	tolerated(0.07)	benign(0.183)	5/5	.	hmmpanther:PTHR12876:SF27,hmmpanther:PTHR12876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCAAACGTG	.	5	ESCA
ZMYM3	0	.	GRCh37	X	70460112	70460112	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EY-01A-11D-A36J-09	TCGA-VR-A8EY-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*654T>A	.	.	ENST00000353904	25/25	16	9	7	11	11	0	ZMYM3,3_prime_UTR_variant,,ENST00000373988,;ZMYM3,3_prime_UTR_variant,,ENST00000373984,;ZMYM3,3_prime_UTR_variant,,ENST00000314425,;ZMYM3,3_prime_UTR_variant,,ENST00000353904,;ZMYM3,3_prime_UTR_variant,,ENST00000373998,;ZMYM3,non_coding_transcript_exon_variant,,ENST00000489332,;ZMYM3,downstream_gene_variant,,ENST00000470832,;	T	ENSG00000147130	ENST00000353904	Transcript	3_prime_UTR_variant	4955	.	.	.	.	.	.	.	-1	ZMYM3	HGNC	13054	protein_coding	YES	CCDS14409.1	ENSP00000343909	ZMYM3_HUMAN	.	UPI000013C339	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCATTTGG	.	5	ESCA
SH3PXD2A	0	.	GRCh37	10	105356821	105356821	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4752G>C	.	.	ENST00000355946	14/14	31	19	11	21	21	0	SH3PXD2A,3_prime_UTR_variant,,ENST00000369774,;SH3PXD2A,3_prime_UTR_variant,,ENST00000355946,;SH3PXD2A,intron_variant,,ENST00000427662,;SH3PXD2A,downstream_gene_variant,,ENST00000540321,;SH3PXD2A,downstream_gene_variant,,ENST00000538130,;SH3PXD2A,downstream_gene_variant,,ENST00000420222,;NEURL1,downstream_gene_variant,,ENST00000369777,;NEURL1,downstream_gene_variant,,ENST00000369780,;SH3PXD2A,downstream_gene_variant,,ENST00000315994,;	G	ENSG00000107957	ENST00000355946	Transcript	3_prime_UTR_variant	8210	.	.	.	.	.	.	.	-1	SH3PXD2A	HGNC	23664	protein_coding	YES	CCDS31278.1	ENSP00000348215	SPD2A_HUMAN	.	UPI000041B175	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGTCTGCAG	.	5	ESCA
DMBT1	0	.	GRCh37	10	124352022	124352022	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2411G>C	p.Gly804Ala	p.G804A	ENST00000368909	20/53	175	154	21	157	157	0	DMBT1,missense_variant,p.Gly794Ala,ENST00000344338,;DMBT1,missense_variant,p.Gly794Ala,ENST00000368955,;DMBT1,missense_variant,p.Gly804Ala,ENST00000368909,;DMBT1,missense_variant,p.Gly804Ala,ENST00000338354,;DMBT1,intron_variant,,ENST00000368956,;DMBT1,intron_variant,,ENST00000359586,;DMBT1,intron_variant,,ENST00000330163,;	C	ENSG00000187908	ENST00000368909	Transcript	missense_variant	2517	2411	804	G/A	gGa/gCa	.	.	.	1	DMBT1	HGNC	2926	protein_coding	YES	CCDS44490.1	ENSP00000357905	DMBT1_HUMAN	B6V682_HUMAN	UPI000047021C	.	deleterious(0.01)	unknown(0)	20/53	.	Superfamily_domains:SSF56487,SMART_domains:SM00202,Gene3D:3.10.250.10,Pfam_domain:PF00530,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF250,PROSITE_profiles:PS50287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAGGACACG	.	4	ESCA
CAMK1D	0	.	GRCh37	10	12811688	12811688	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455A>C	p.Tyr152Ser	p.Y152S	ENST00000378847	5/11	54	29	25	64	64	0	CAMK1D,missense_variant,p.Tyr152Ser,ENST00000378845,;CAMK1D,missense_variant,p.Tyr152Ser,ENST00000378847,;	C	ENSG00000183049	ENST00000378847	Transcript	missense_variant	792	455	152	Y/S	tAc/tCc	.	.	.	1	CAMK1D	HGNC	19341	protein_coding	YES	CCDS7091.1	ENSP00000368124	KCC1D_HUMAN	.	UPI000003CA33	.	deleterious(0)	possibly_damaging(0.688)	5/11	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF116,hmmpanther:PTHR24347,PROSITE_patterns:PS00108,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGTACTACA	.	5	ESCA
ITGA8	0	.	GRCh37	10	15719594	15719594	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673C>A	p.Gln225Lys	p.Q225K	ENST00000378076	6/30	63	43	20	103	103	0	ITGA8,missense_variant,p.Gln225Lys,ENST00000378076,;	T	ENSG00000077943	ENST00000378076	Transcript	missense_variant	1027	673	225	Q/K	Caa/Aaa	.	.	.	-1	ITGA8	HGNC	6144	protein_coding	YES	CCDS31155.1	ENSP00000367316	ITA8_HUMAN	.	UPI00001D80A0	.	deleterious(0.01)	probably_damaging(0.996)	6/30	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTGCCAGT	.	5	ESCA
MRC1L1	0	.	GRCh37	10	17865242	17865242	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.231G>T	p.%3D	p.V77V	ENST00000331429	2/30	121	98	22	170	170	0	MRC1L1,synonymous_variant,p.%3D,ENST00000331429,;MRC1L1,synonymous_variant,p.%3D,ENST00000457317,;	T	ENSG00000183748	ENST00000331429	Transcript	synonymous_variant	334	231	77	V	gtG/gtT	.	.	.	1	MRC1L1	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000332124	.	B4DLK9_HUMAN	UPI00001AFE88	.	.	.	2/30	.	PROSITE_profiles:PS50231,hmmpanther:PTHR22803:SF55,hmmpanther:PTHR22803,Pfam_domain:PF00652,Gene3D:2.80.10.50,SMART_domains:SM00458,Superfamily_domains:SSF50370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGTGCCATC	.	4	ESCA
ZNF438	0	.	GRCh37	10	31138755	31138755	+	Silent	SNP	C	C	T	rs568845590	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.579G>A	p.%3D	p.A193A	ENST00000436087	7/8	38	27	11	37	37	0	ZNF438,synonymous_variant,p.%3D,ENST00000452305,;ZNF438,synonymous_variant,p.%3D,ENST00000413025,;ZNF438,synonymous_variant,p.%3D,ENST00000361310,;ZNF438,synonymous_variant,p.%3D,ENST00000538351,;ZNF438,synonymous_variant,p.%3D,ENST00000442986,;ZNF438,synonymous_variant,p.%3D,ENST00000444692,;ZNF438,synonymous_variant,p.%3D,ENST00000436087,;ZNF438,synonymous_variant,p.%3D,ENST00000331737,;ZNF438,intron_variant,,ENST00000375311,;ZNF438,intron_variant,,ENST00000609683,;	T	ENSG00000183621	ENST00000436087	Transcript	synonymous_variant	1062	579	193	A	gcG/gcA	rs568845590	.	.	-1	ZNF438	HGNC	21029	protein_coding	YES	CCDS7168.1	ENSP00000406934	ZN438_HUMAN	Q5T427_HUMAN	UPI00001B3D8F	.	.	.	7/8	.	hmmpanther:PTHR24397:SF2,hmmpanther:PTHR24397	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCAGCGCAGC	byFrequency|byCluster	5	ESCA
C10orf10	0	.	GRCh37	10	45472671	45472671	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*169C>T	.	.	ENST00000298295	2/2	15	11	4	17	17	0	C10orf10,3_prime_UTR_variant,,ENST00000298295,;RASSF4,intron_variant,,ENST00000427758,;RASSF4,intron_variant,,ENST00000428466,;RASSF4,intron_variant,,ENST00000334940,;RASSF4,intron_variant,,ENST00000374417,;RASSF4,intron_variant,,ENST00000340258,;C10orf10,downstream_gene_variant,,ENST00000448778,;RASSF4,intron_variant,,ENST00000462822,;C10orf10,intron_variant,,ENST00000496638,;RASSF4,intron_variant,,ENST00000472561,;RASSF4,intron_variant,,ENST00000483709,;RASSF4,intron_variant,,ENST00000489171,;RASSF4,upstream_gene_variant,,ENST00000465735,;	A	ENSG00000165507	ENST00000298295	Transcript	3_prime_UTR_variant	1026	.	.	.	.	.	.	.	-1	C10orf10	HGNC	23355	protein_coding	YES	CCDS7210.1	ENSP00000298295	DEPP_HUMAN	.	UPI000006E55C	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTGTTATC	.	4	ESCA
FRMPD2	0	.	GRCh37	10	49444551	49444551	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.967A>G	p.Thr323Ala	p.T323A	ENST00000374201	9/29	62	44	17	64	64	0	FRMPD2,missense_variant,p.Thr323Ala,ENST00000374201,;FRMPD2,missense_variant,p.Thr292Ala,ENST00000407470,;FRMPD2,missense_variant,p.Thr299Ala,ENST00000305531,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000486151,;	C	ENSG00000170324	ENST00000374201	Transcript	missense_variant	1270	967	323	T/A	Aca/Gca	.	.	.	-1	FRMPD2	HGNC	28572	protein_coding	YES	CCDS31195.1	ENSP00000363317	FRPD2_HUMAN	.	UPI0000D60F5F	.	tolerated(0.14)	benign(0.141)	9/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGTGTCATCG	.	5	ESCA
OGDHL	0	.	GRCh37	10	50946061	50946061	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2449A>T	p.Asn817Tyr	p.N817Y	ENST00000374103	19/23	31	25	6	46	46	0	OGDHL,missense_variant,p.Asn608Tyr,ENST00000432695,;OGDHL,missense_variant,p.Asn760Tyr,ENST00000419399,;OGDHL,missense_variant,p.Asn817Tyr,ENST00000374103,;OGDHL,non_coding_transcript_exon_variant,,ENST00000490844,;	A	ENSG00000197444	ENST00000374103	Transcript	missense_variant	2535	2449	817	N/Y	Aac/Tac	.	.	.	-1	OGDHL	HGNC	25590	protein_coding	YES	CCDS7234.1	ENSP00000363216	OGDHL_HUMAN	.	UPI000013D6A4	.	tolerated(0.63)	probably_damaging(0.954)	19/23	.	Superfamily_domains:SSF52518,PIRSF_domain:PIRSF000157,SMART_domains:SM00861,Gene3D:3.40.50.970,Pfam_domain:PF02779,TIGRFAM_domain:TIGR00239,hmmpanther:PTHR23152:SF5,hmmpanther:PTHR23152	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTTGACCA	.	5	ESCA
LRRTM3	0	.	GRCh37	10	68687865	68687865	+	Silent	SNP	G	G	A	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1191G>A	p.%3D	p.P397P	ENST00000361320	2/3	29	24	5	35	35	0	LRRTM3,synonymous_variant,p.%3D,ENST00000361320,;CTNNA3,intron_variant,,ENST00000433211,;CTNNA3,intron_variant,,ENST00000494580,;CTNNA3,intron_variant,,ENST00000373744,;	A	ENSG00000198739	ENST00000361320	Transcript	synonymous_variant	1769	1191	397	P	ccG/ccA	COSM3666763,COSM3666764	.	.	1	LRRTM3	HGNC	19410	protein_coding	YES	CCDS7270.1	ENSP00000355187	LRRT3_HUMAN	B4DFC3_HUMAN	UPI0000088C0F	.	.	.	2/3	.	hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF54	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCCGACGGT	.	5	ESCA
ADIRF	0	.	GRCh37	10	88728258	88728258	+	5'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-44G>C	.	.	ENST00000372013	1/3	50	22	27	42	42	0	ADIRF,5_prime_UTR_variant,,ENST00000372013,;ADIRF,5_prime_UTR_variant,,ENST00000416348,;MMRN2,intron_variant,,ENST00000474994,;MMRN2,intron_variant,,ENST00000609457,;ADIRF-AS1,non_coding_transcript_exon_variant,,ENST00000609111,;ADIRF-AS1,intron_variant,,ENST00000440490,;ADIRF-AS1,intron_variant,,ENST00000418273,;RP11-96C23.15,downstream_gene_variant,,ENST00000609363,;RP11-96C23.5,upstream_gene_variant,,ENST00000433214,;ADIRF,5_prime_UTR_variant,,ENST00000561504,;ADIRF-AS1,upstream_gene_variant,,ENST00000609170,;	C	ENSG00000148671	ENST00000372013	Transcript	5_prime_UTR_variant	310	.	.	.	.	.	.	.	1	ADIRF	HGNC	24043	protein_coding	YES	CCDS7381.1	ENSP00000361083	ADIRF_HUMAN	Q5TBU5_HUMAN	UPI0000000C61	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAACGTCGCT	.	5	ESCA
EIF4G2	0	.	GRCh37	11	10830442	10830442	+	5'Flank	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000526148	.	100	71	28	169	169	0	EIF4G2,5_prime_UTR_variant,,ENST00000527419,;EIF4G2,5_prime_UTR_variant,,ENST00000339995,;EIF4G2,5_prime_UTR_variant,,ENST00000530702,;EIF4G2,5_prime_UTR_variant,,ENST00000524932,;EIF4G2,5_prime_UTR_variant,,ENST00000530211,;EIF4G2,5_prime_UTR_variant,,ENST00000532570,;EIF4G2,upstream_gene_variant,,ENST00000396525,;EIF4G2,upstream_gene_variant,,ENST00000532082,;EIF4G2,upstream_gene_variant,,ENST00000527526,;EIF4G2,upstream_gene_variant,,ENST00000531416,;EIF4G2,upstream_gene_variant,,ENST00000525681,;EIF4G2,upstream_gene_variant,,ENST00000526148,;RP11-685M7.3,upstream_gene_variant,,ENST00000499765,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000531507,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000525972,;EIF4G2,upstream_gene_variant,,ENST00000525995,;ZBED5,downstream_gene_variant,,ENST00000533903,;ZBED5,downstream_gene_variant,,ENST00000525350,;EIF4G2,5_prime_UTR_variant,,ENST00000528562,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000534246,;EIF4G2,upstream_gene_variant,,ENST00000527015,;EIF4G2,upstream_gene_variant,,ENST00000532349,;EIF4G2,upstream_gene_variant,,ENST00000534605,;EIF4G2,upstream_gene_variant,,ENST00000533485,;EIF4G2,upstream_gene_variant,,ENST00000531647,;EIF4G2,upstream_gene_variant,,ENST00000532152,;EIF4G2,upstream_gene_variant,,ENST00000532383,;	A	ENSG00000110321	ENST00000526148	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	922	-1	EIF4G2	HGNC	3297	protein_coding	YES	CCDS31428.1	ENSP00000433664	.	Q59G42_HUMAN,Q2TU89_HUMAN,H0YEN8_HUMAN,H0YEC5_HUMAN,H0YDC0_HUMAN,H0YD99_HUMAN,H0YD77_HUMAN,H0YCF8_HUMAN,D3DQV9_HUMAN,B4DZF2_HUMAN	UPI000013C8BE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTGCCACCT	.	5	ESCA
SRPR	0	.	GRCh37	11	126137598	126137598	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211C>G	p.Gln71Glu	p.Q71E	ENST00000332118	3/14	19	15	4	32	32	0	SRPR,missense_variant,p.Gln43Glu,ENST00000532259,;SRPR,missense_variant,p.Gln71Glu,ENST00000332118,;FAM118B,downstream_gene_variant,,ENST00000533050,;FOXRED1,upstream_gene_variant,,ENST00000532125,;FOXRED1,upstream_gene_variant,,ENST00000442061,;FOXRED1,upstream_gene_variant,,ENST00000263578,;SRPR,non_coding_transcript_exon_variant,,ENST00000530680,;FOXRED1,upstream_gene_variant,,ENST00000533839,;FOXRED1,upstream_gene_variant,,ENST00000534011,;FOXRED1,upstream_gene_variant,,ENST00000526366,;SRPR,non_coding_transcript_exon_variant,,ENST00000528744,;FOXRED1,upstream_gene_variant,,ENST00000526525,;FAM118B,downstream_gene_variant,,ENST00000531935,;SRPR,upstream_gene_variant,,ENST00000531104,;FOXRED1,upstream_gene_variant,,ENST00000527004,;SRPR,upstream_gene_variant,,ENST00000527817,;FOXRED1,upstream_gene_variant,,ENST00000525770,;SRPR,upstream_gene_variant,,ENST00000532268,;FOXRED1,upstream_gene_variant,,ENST00000532101,;FOXRED1,upstream_gene_variant,,ENST00000525083,;FOXRED1,upstream_gene_variant,,ENST00000529802,;FOXRED1,upstream_gene_variant,,ENST00000534315,;FOXRED1,upstream_gene_variant,,ENST00000524751,;	C	ENSG00000182934	ENST00000332118	Transcript	missense_variant	366	211	71	Q/E	Cag/Gag	.	.	.	-1	SRPR	HGNC	11307	protein_coding	YES	CCDS31717.1	ENSP00000328023	SRPR_HUMAN	.	UPI0000135F5A	.	deleterious(0)	probably_damaging(0.998)	3/14	.	Superfamily_domains:SSF64356,Pfam_domain:PF04086,hmmpanther:PTHR11564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCTGAAAAC	.	2	ESCA
KIRREL3	0	.	GRCh37	11	126294541	126294541	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2271C>A	p.%3D	p.S757S	ENST00000525144	17/17	33	20	12	50	50	0	KIRREL3,synonymous_variant,p.%3D,ENST00000529097,;KIRREL3,synonymous_variant,p.%3D,ENST00000525144,;KIRREL3,synonymous_variant,p.%3D,ENST00000416561,;ST3GAL4,intron_variant,,ENST00000524834,;KIRREL3,downstream_gene_variant,,ENST00000526519,;KIRREL3,downstream_gene_variant,,ENST00000532647,;	T	ENSG00000149571	ENST00000525144	Transcript	synonymous_variant	2521	2271	757	S	tcC/tcA	.	.	.	-1	KIRREL3	HGNC	23204	protein_coding	YES	CCDS53723.1	ENSP00000435466	KIRR3_HUMAN	B4DT91_HUMAN	UPI00000740A0	.	.	.	17/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11640:SF49,hmmpanther:PTHR11640	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGGGAGTG	.	5	ESCA
SLC17A6	0	.	GRCh37	11	22400216	22400216	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*930C>A	.	.	ENST00000263160	12/12	31	23	7	62	62	0	SLC17A6,3_prime_UTR_variant,,ENST00000263160,;	A	ENSG00000091664	ENST00000263160	Transcript	3_prime_UTR_variant	3116	.	.	.	.	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATATCTTTCT	.	5	ESCA
LIN7C	0	.	GRCh37	11	27523450	27523450	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55G>C	p.Glu19Gln	p.E19Q	ENST00000278193	2/5	115	107	8	72	72	0	LIN7C,missense_variant,p.Glu19Gln,ENST00000524596,;LIN7C,missense_variant,p.Glu19Gln,ENST00000278193,;BDNF-AS,upstream_gene_variant,,ENST00000502161,;BDNF-AS,upstream_gene_variant,,ENST00000501176,;BDNF-AS,upstream_gene_variant,,ENST00000530686,;BDNF-AS,upstream_gene_variant,,ENST00000499568,;BDNF-AS,upstream_gene_variant,,ENST00000532965,;BDNF-AS,upstream_gene_variant,,ENST00000499008,;BDNF-AS,upstream_gene_variant,,ENST00000500662,;	G	ENSG00000148943	ENST00000278193	Transcript	missense_variant	76	55	19	E/Q	Gaa/Caa	.	.	.	-1	LIN7C	HGNC	17789	protein_coding	YES	CCDS7864.1	ENSP00000278193	LIN7C_HUMAN	.	UPI000000BB45	.	tolerated_low_confidence(0.08)	possibly_damaging(0.601)	2/5	.	PROSITE_profiles:PS51022,hmmpanther:PTHR14063,Pfam_domain:PF02828,SMART_domains:SM00569,Superfamily_domains:SSF101288,PIRSF_domain:PIRSF038039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAATTCAATTG	.	2	ESCA
MPPED2	0	.	GRCh37	11	30431949	30431949	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1066G>C	.	.	ENST00000358117	6/6	52	43	9	52	52	0	MPPED2,3_prime_UTR_variant,,ENST00000358117,;MPPED2,intron_variant,,ENST00000448418,;MPPED2,downstream_gene_variant,,ENST00000529220,;MPPED2,downstream_gene_variant,,ENST00000524667,;MPPED2,downstream_gene_variant,,ENST00000526437,;	G	ENSG00000066382	ENST00000358117	Transcript	3_prime_UTR_variant	2074	.	.	.	.	.	.	.	-1	MPPED2	HGNC	1180	protein_coding	YES	CCDS7870.1	ENSP00000350833	MPPD2_HUMAN	F2Z346_HUMAN	UPI0000124E87	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTGCTAGCG	.	5	ESCA
CHRM4	0	.	GRCh37	11	46407570	46407570	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538G>T	p.Val180Leu	p.V180L	ENST00000433765	1/1	21	15	5	43	43	0	CHRM4,missense_variant,p.Val180Leu,ENST00000433765,;MDK,downstream_gene_variant,,ENST00000395565,;MDK,downstream_gene_variant,,ENST00000407067,;MDK,downstream_gene_variant,,ENST00000359803,;MDK,downstream_gene_variant,,ENST00000405308,;MDK,downstream_gene_variant,,ENST00000533952,;MDK,downstream_gene_variant,,ENST00000441869,;MDK,downstream_gene_variant,,ENST00000395566,;MDK,downstream_gene_variant,,ENST00000395569,;MDK,downstream_gene_variant,,ENST00000533283,;MDK,downstream_gene_variant,,ENST00000481047,;MDK,downstream_gene_variant,,ENST00000489525,;MDK,downstream_gene_variant,,ENST00000490240,;	A	ENSG00000180720	ENST00000433765	Transcript	missense_variant	538	538	180	V/L	Gtg/Ttg	COSM3383487	.	.	-1	CHRM4	HGNC	1953	protein_coding	YES	CCDS44581.1	ENSP00000409378	ACM4_HUMAN	.	UPI00001252BB	.	deleterious(0)	probably_damaging(0.914)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF60,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCACCGTCC	.	5	ESCA
OR5L2	0	.	GRCh37	11	55594893	55594893	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199T>C	p.Ser67Pro	p.S67P	ENST00000378397	1/1	69	49	20	71	71	0	OR5L2,missense_variant,p.Ser67Pro,ENST00000378397,;	C	ENSG00000205030	ENST00000378397	Transcript	missense_variant	199	199	67	S/P	Tcc/Ccc	.	.	.	1	OR5L2	HGNC	8351	protein_coding	YES	CCDS31511.1	ENSP00000367650	OR5L2_HUMAN	.	UPI0000041C49	.	deleterious(0.01)	benign(0.055)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF154,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F68S|c.203T>C|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTGTCCTTT	.	5	ESCA
OR5M3	0	.	GRCh37	11	56237538	56237538	+	Missense_Mutation	SNP	G	G	T	rs537773767	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436C>A	p.Pro146Thr	p.P146T	ENST00000312240	1/1	49	39	10	53	53	0	OR5M3,missense_variant,p.Pro146Thr,ENST00000312240,;	T	ENSG00000174937	ENST00000312240	Transcript	missense_variant	477	436	146	P/T	Cct/Act	rs537773767	.	.	-1	OR5M3	HGNC	14806	protein_coding	YES	CCDS31532.1	ENSP00000312208	OR5M3_HUMAN	.	UPI0000041BAA	.	tolerated(0.16)	benign(0.261)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF17,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	C:0.0002	C:0	C:0.0014	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAAGGGAAAG	by1000G	5	ESCA
GLYATL2	0	.	GRCh37	11	58607019	58607019	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.67G>T	p.Glu23Ter	p.E23*	ENST00000287275	2/6	60	52	8	38	38	0	GLYATL2,stop_gained,p.Glu23Ter,ENST00000532258,;GLYATL2,stop_gained,p.Glu23Ter,ENST00000287275,;GLYATL2,intron_variant,,ENST00000533636,;	A	ENSG00000156689	ENST00000287275	Transcript	stop_gained	458	67	23	E/*	Gaa/Taa	.	.	.	-1	GLYATL2	HGNC	24178	protein_coding	YES	CCDS41649.1	ENSP00000287275	GLYL2_HUMAN	.	UPI000003FFB7	.	.	.	2/6	.	hmmpanther:PTHR15298:SF4,hmmpanther:PTHR15298,Pfam_domain:PF06021	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGATTCAGGGA	.	4	ESCA
FADS3	0	.	GRCh37	11	61645046	61645046	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822G>A	p.%3D	p.L274L	ENST00000278829	7/12	24	20	3	27	27	0	FADS3,synonymous_variant,p.%3D,ENST00000540820,;FADS3,synonymous_variant,p.%3D,ENST00000278829,;FADS3,synonymous_variant,p.%3D,ENST00000525588,;FADS3,synonymous_variant,p.%3D,ENST00000527379,;FADS3,synonymous_variant,p.%3D,ENST00000531956,;FADS3,synonymous_variant,p.%3D,ENST00000534223,;FADS3,synonymous_variant,p.%3D,ENST00000527697,;FADS3,upstream_gene_variant,,ENST00000525094,;FADS3,non_coding_transcript_exon_variant,,ENST00000526294,;FADS3,non_coding_transcript_exon_variant,,ENST00000529404,;FADS3,non_coding_transcript_exon_variant,,ENST00000533676,;FADS3,downstream_gene_variant,,ENST00000534426,;FADS3,downstream_gene_variant,,ENST00000414624,;	T	ENSG00000221968	ENST00000278829	Transcript	synonymous_variant	975	822	274	L	ctG/ctA	.	.	.	-1	FADS3	HGNC	3576	protein_coding	YES	CCDS8013.1	ENSP00000278829	FADS3_HUMAN	E9PQC2_HUMAN,E9PPZ4_HUMAN	UPI000003405F	.	.	.	7/12	.	Transmembrane_helices:TMhelix,PIRSF_domain:PIRSF015921,Pfam_domain:PF00487,hmmpanther:PTHR19353:SF11,hmmpanther:PTHR19353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GTGAGCAGCGG	.	3	ESCA
ATG2A	0	.	GRCh37	11	64664919	64664919	+	Silent	SNP	G	G	C	rs745463710	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5115C>G	p.%3D	p.S1705S	ENST00000377264	37/41	92	67	25	109	109	0	ATG2A,synonymous_variant,p.%3D,ENST00000418259,;ATG2A,synonymous_variant,p.%3D,ENST00000377264,;ATG2A,synonymous_variant,p.%3D,ENST00000421419,;MIR194-2,upstream_gene_variant,,ENST00000413053,;ATG2A,non_coding_transcript_exon_variant,,ENST00000472525,;	C	ENSG00000110046	ENST00000377264	Transcript	synonymous_variant	5228	5115	1705	S	tcC/tcG	rs745463710	.	.	-1	ATG2A	HGNC	29028	protein_coding	YES	CCDS31602.1	ENSP00000366475	ATG2A_HUMAN	B4DV45_HUMAN	UPI00001C1F21	.	.	.	37/41	.	hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTCGGAGCA	.	5	ESCA
TBX10	0	.	GRCh37	11	67399058	67399058	+	3'UTR	SNP	C	C	A	rs774829938	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*18G>T	.	.	ENST00000335385	8/8	40	30	10	43	43	0	TBX10,3_prime_UTR_variant,,ENST00000335385,;NUDT8,upstream_gene_variant,,ENST00000301490,;NUDT8,upstream_gene_variant,,ENST00000376693,;RP11-655M14.13,upstream_gene_variant,,ENST00000533311,;NUDT8,upstream_gene_variant,,ENST00000534054,;	A	ENSG00000167800	ENST00000335385	Transcript	3_prime_UTR_variant	1264	.	.	.	.	rs774829938	.	.	-1	TBX10	HGNC	11593	protein_coding	YES	CCDS31621.1	ENSP00000335191	TBX10_HUMAN	.	UPI000017DA69	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTCCCCCCA	.	5	ESCA
PDE2A	0	.	GRCh37	11	72316222	72316222	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283G>T	p.Glu95Ter	p.E95*	ENST00000334456	4/31	68	59	8	69	69	0	PDE2A,stop_gained,p.Glu86Ter,ENST00000540345,;PDE2A,stop_gained,p.Glu95Ter,ENST00000334456,;PDE2A,stop_gained,p.Glu74Ter,ENST00000542969,;PDE2A,stop_gained,p.Glu88Ter,ENST00000376450,;PDE2A,stop_gained,p.Glu88Ter,ENST00000544570,;PDE2A,stop_gained,p.Glu74Ter,ENST00000538749,;PDE2A,stop_gained,p.Glu86Ter,ENST00000444035,;PDE2A,intron_variant,,ENST00000418754,;PDE2A,non_coding_transcript_exon_variant,,ENST00000485058,;PDE2A,non_coding_transcript_exon_variant,,ENST00000540380,;PDE2A,stop_gained,p.Glu88Ter,ENST00000536308,;PDE2A,3_prime_UTR_variant,,ENST00000537631,;PDE2A,3_prime_UTR_variant,,ENST00000539367,;PDE2A,3_prime_UTR_variant,,ENST00000535701,;PDE2A,3_prime_UTR_variant,,ENST00000541998,;PDE2A,3_prime_UTR_variant,,ENST00000543575,;PDE2A,intron_variant,,ENST00000543750,;	A	ENSG00000186642	ENST00000334456	Transcript	stop_gained	529	283	95	E/*	Gag/Tag	.	.	.	-1	PDE2A	HGNC	8777	protein_coding	YES	CCDS8216.1	ENSP00000334910	PDE2A_HUMAN	F5GXX2_HUMAN,C9JPD5_HUMAN	UPI000003B340	.	.	.	4/31	.	hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF102,Superfamily_domains:SSF55781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCCTCACACA	.	4	ESCA
NEU3	0	.	GRCh37	11	74705730	74705730	+	Silent	SNP	C	C	T	rs368435848	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271C>T	p.%3D	p.L91L	ENST00000294064	2/3	46	43	3	30	30	0	NEU3,synonymous_variant,p.%3D,ENST00000531619,;NEU3,synonymous_variant,p.%3D,ENST00000531509,;NEU3,synonymous_variant,p.%3D,ENST00000534628,;NEU3,synonymous_variant,p.%3D,ENST00000544263,;NEU3,synonymous_variant,p.%3D,ENST00000294064,;NEU3,intron_variant,,ENST00000529024,;NEU3,intron_variant,,ENST00000545272,;NEU3,intron_variant,,ENST00000532963,;NEU3,downstream_gene_variant,,ENST00000526068,;	T	ENSG00000162139	ENST00000294064	Transcript	synonymous_variant	1198	271	91	L	Ctg/Ttg	rs368435848	.	.	1	NEU3	HGNC	7760	protein_coding	YES	CCDS44682.1	ENSP00000294064	.	B4E0V4_HUMAN,A8K327_HUMAN	UPI000015F481	.	.	.	2/3	.	hmmpanther:PTHR10628,hmmpanther:PTHR10628:SF7,Gene3D:2.120.10.10,Pfam_domain:PF13088,Superfamily_domains:SSF50939	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGTGCTGAGG	byFrequency|byCluster	2	ESCA
DLG2	0	.	GRCh37	11	83167151	83167151	+	3'Flank	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000376104	.	54	47	7	47	47	0	DLG2,3_prime_UTR_variant,,ENST00000426717,;DLG2,3_prime_UTR_variant,,ENST00000398309,;DLG2,downstream_gene_variant,,ENST00000524982,;DLG2,downstream_gene_variant,,ENST00000280241,;DLG2,downstream_gene_variant,,ENST00000330014,;DLG2,downstream_gene_variant,,ENST00000376104,;DLG2,downstream_gene_variant,,ENST00000532653,;DLG2,downstream_gene_variant,,ENST00000537455,;DLG2,downstream_gene_variant,,ENST00000376106,;DLG2,downstream_gene_variant,,ENST00000543673,;DLG2,downstream_gene_variant,,ENST00000418306,;DLG2,downstream_gene_variant,,ENST00000404783,;DLG2,downstream_gene_variant,,ENST00000529159,;AP003026.1,downstream_gene_variant,,ENST00000420284,;	G	ENSG00000150672	ENST00000376104	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1811	-1	DLG2	HGNC	2901	protein_coding	YES	CCDS44690.1	ENSP00000365272	DLG2_HUMAN	F8W750_HUMAN,E9PQT9_HUMAN	UPI0000E59399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATGAGGAGG	.	5	ESCA
CTSC	0	.	GRCh37	11	88070930	88070931	+	5'UTR	INS	-	-	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-91dupT	.	.	ENST00000227266	1/7	49	35	14	31	31	0	CTSC,5_prime_UTR_variant,,ENST00000227266,;CTSC,upstream_gene_variant,,ENST00000524463,;CTSC,upstream_gene_variant,,ENST00000527018,;CTSC,upstream_gene_variant,,ENST00000529974,;CTSC,upstream_gene_variant,,ENST00000393301,;CTSC,upstream_gene_variant,,ENST00000533865,;CTSC,upstream_gene_variant,,ENST00000534131,;	A	ENSG00000109861	ENST00000227266	Transcript	5_prime_UTR_variant	25-26	.	.	.	.	.	.	.	-1	CTSC	HGNC	2528	protein_coding	YES	CCDS8282.1	ENSP00000227266	CATC_HUMAN	I3V9T0_HUMAN	UPI000006D22D	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCTTGAAATA	.	3	ESCA
PPP1CC	0	.	GRCh37	12	111180517	111180517	+	5'UTR	SNP	T	T	C	rs752042430	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-5A>G	.	.	ENST00000340766	1/8	25	13	12	21	21	0	PPP1CC,5_prime_UTR_variant,,ENST00000551676,;PPP1CC,5_prime_UTR_variant,,ENST00000550991,;PPP1CC,5_prime_UTR_variant,,ENST00000335007,;PPP1CC,5_prime_UTR_variant,,ENST00000340766,;PPP1CC,non_coding_transcript_exon_variant,,ENST00000551690,;	C	ENSG00000186298	ENST00000340766	Transcript	5_prime_UTR_variant	228	.	.	.	.	rs752042430	.	.	-1	PPP1CC	HGNC	9283	protein_coding	YES	CCDS58279.1	ENSP00000341779	PP1G_HUMAN	Q9UPN1_HUMAN,C4TNW6_HUMAN,C4TNW5_HUMAN	UPI000002B16F	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCCTTCCCA	.	5	ESCA
HECTD4	0	.	GRCh37	12	112622969	112622969	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9363G>A	p.%3D	p.V3121V	ENST00000550722	61/76	63	49	14	45	45	0	HECTD4,synonymous_variant,p.%3D,ENST00000430131,;HECTD4,synonymous_variant,p.%3D,ENST00000550722,;HECTD4,synonymous_variant,p.%3D,ENST00000377560,;	T	ENSG00000173064	ENST00000550722	Transcript	synonymous_variant	9759	9363	3121	V	gtG/gtA	.	.	.	-1	HECTD4	HGNC	26611	protein_coding	YES	.	ENSP00000449784	.	F8VWT9_HUMAN,F8VU57_HUMAN	UPI00020CE513	.	.	.	61/76	.	hmmpanther:PTHR11254:SF286,hmmpanther:PTHR11254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGTCACTTC	.	5	ESCA
SPPL3	0	.	GRCh37	12	121202639	121202639	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*163A>C	.	.	ENST00000353487	11/11	29	25	4	38	38	0	SPPL3,3_prime_UTR_variant,,ENST00000353487,;SPPL3,downstream_gene_variant,,ENST00000543608,;SPPL3,downstream_gene_variant,,ENST00000536996,;SPPL3,downstream_gene_variant,,ENST00000543854,;RP11-173P15.7,upstream_gene_variant,,ENST00000542620,;SPPL3,non_coding_transcript_exon_variant,,ENST00000392495,;SPPL3,downstream_gene_variant,,ENST00000545209,;	G	ENSG00000157837	ENST00000353487	Transcript	3_prime_UTR_variant	1822	.	.	.	.	.	.	.	-1	SPPL3	HGNC	30424	protein_coding	YES	CCDS9208.1	ENSP00000288680	SPPL3_HUMAN	F5H7J2_HUMAN,F5H6I1_HUMAN,F5H4Y6_HUMAN,F5H4L1_HUMAN,F5H2A2_HUMAN	UPI0000013590	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCACCTCTCTC	.	4	ESCA
CAMKK2	0	.	GRCh37	12	121676556	121676556	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1946C>T	.	.	ENST00000324774	17/17	90	69	20	77	77	0	CAMKK2,3_prime_UTR_variant,,ENST00000324774,;CAMKK2,3_prime_UTR_variant,,ENST00000347034,;CAMKK2,3_prime_UTR_variant,,ENST00000545538,;CAMKK2,3_prime_UTR_variant,,ENST00000538733,;CAMKK2,3_prime_UTR_variant,,ENST00000337174,;CAMKK2,3_prime_UTR_variant,,ENST00000392474,;CAMKK2,downstream_gene_variant,,ENST00000412367,;CAMKK2,downstream_gene_variant,,ENST00000404169,;P2RX4,downstream_gene_variant,,ENST00000337233,;P2RX4,downstream_gene_variant,,ENST00000359949,;CAMKK2,downstream_gene_variant,,ENST00000392473,;CAMKK2,downstream_gene_variant,,ENST00000402834,;P2RX4,downstream_gene_variant,,ENST00000543171,;CAMKK2,downstream_gene_variant,,ENST00000446440,;P2RX4,downstream_gene_variant,,ENST00000499638,;P2RX4,downstream_gene_variant,,ENST00000543984,;	A	ENSG00000110931	ENST00000324774	Transcript	3_prime_UTR_variant	4542	.	.	.	.	.	.	.	-1	CAMKK2	HGNC	1470	protein_coding	YES	CCDS9216.1	ENSP00000312741	KKCC2_HUMAN	Q8IZW1_HUMAN,F5H4I7_HUMAN,F5H360_HUMAN	UPI000013D208	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGGGCCAG	.	5	ESCA
PDE3A	0	.	GRCh37	12	20807137	20807137	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3182C>T	p.Pro1061Leu	p.P1061L	ENST00000359062	15/16	34	18	16	54	54	0	PDE3A,missense_variant,p.Pro1061Leu,ENST00000359062,;PDE3A,splice_region_variant,,ENST00000544307,;	T	ENSG00000172572	ENST00000359062	Transcript	missense_variant	3222	3182	1061	P/L	cCa/cTa	.	.	.	1	PDE3A	HGNC	8778	protein_coding	YES	CCDS31754.1	ENSP00000351957	PDE3A_HUMAN	.	UPI000014175F	.	tolerated(0.17)	benign(0.065)	15/16	.	hmmpanther:PTHR11347:SF104,hmmpanther:PTHR11347,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTCCAAGTA	.	5	ESCA
YARS2	0	.	GRCh37	12	32908804	32908804	+	Missense_Mutation	SNP	G	G	T	rs761092249	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5C>A	p.Ala2Glu	p.A2E	ENST00000324868	1/5	11	3	7	45	45	0	YARS2,missense_variant,p.Ala2Glu,ENST00000324868,;YARS2,upstream_gene_variant,,ENST00000548490,;	T	ENSG00000139131	ENST00000324868	Transcript	missense_variant	33	5	2	A/E	gCg/gAg	rs761092249	.	.	-1	YARS2	HGNC	24249	protein_coding	YES	CCDS31770.1	ENSP00000320658	SYYM_HUMAN	.	UPI0000046058	.	deleterious_low_confidence(0)	probably_damaging(0.967)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCGCCGCCATC	byFrequency	3	ESCA
KMT2D	0	.	GRCh37	12	49413108	49413108	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2455C>T	.	.	ENST00000301067	54/54	52	8	44	58	58	0	KMT2D,3_prime_UTR_variant,,ENST00000301067,;PRKAG1,upstream_gene_variant,,ENST00000548950,;PRKAG1,upstream_gene_variant,,ENST00000548065,;PRKAG1,upstream_gene_variant,,ENST00000548605,;PRKAG1,upstream_gene_variant,,ENST00000552212,;PRKAG1,upstream_gene_variant,,ENST00000548857,;PRKAG1,upstream_gene_variant,,ENST00000547082,;PRKAG1,upstream_gene_variant,,ENST00000547306,;PRKAG1,upstream_gene_variant,,ENST00000316299,;PRKAG1,upstream_gene_variant,,ENST00000551121,;PRKAG1,upstream_gene_variant,,ENST00000395170,;PRKAG1,upstream_gene_variant,,ENST00000552463,;PRKAG1,upstream_gene_variant,,ENST00000547125,;KMT2D,downstream_gene_variant,,ENST00000526209,;PRKAG1,upstream_gene_variant,,ENST00000551696,;RP11-386G11.5,downstream_gene_variant,,ENST00000547866,;RP11-386G11.5,downstream_gene_variant,,ENST00000552933,;RP11-386G11.5,downstream_gene_variant,,ENST00000547395,;RP11-386G11.5,downstream_gene_variant,,ENST00000552284,;PRKAG1,upstream_gene_variant,,ENST00000552657,;PRKAG1,upstream_gene_variant,,ENST00000549726,;PRKAG1,upstream_gene_variant,,ENST00000550125,;PRKAG1,upstream_gene_variant,,ENST00000550448,;PRKAG1,upstream_gene_variant,,ENST00000546531,;	A	ENSG00000167548	ENST00000301067	Transcript	3_prime_UTR_variant	19069	.	.	.	.	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	54/54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACTGAGTATGT	.	3	ESCA
KMT2D	0	.	GRCh37	12	49413111	49413111	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2452A>T	.	.	ENST00000301067	54/54	51	7	44	60	60	0	KMT2D,3_prime_UTR_variant,,ENST00000301067,;PRKAG1,upstream_gene_variant,,ENST00000548950,;PRKAG1,upstream_gene_variant,,ENST00000548065,;PRKAG1,upstream_gene_variant,,ENST00000548605,;PRKAG1,upstream_gene_variant,,ENST00000552212,;PRKAG1,upstream_gene_variant,,ENST00000548857,;PRKAG1,upstream_gene_variant,,ENST00000547082,;PRKAG1,upstream_gene_variant,,ENST00000547306,;PRKAG1,upstream_gene_variant,,ENST00000316299,;PRKAG1,upstream_gene_variant,,ENST00000551121,;PRKAG1,upstream_gene_variant,,ENST00000395170,;PRKAG1,upstream_gene_variant,,ENST00000552463,;PRKAG1,upstream_gene_variant,,ENST00000547125,;KMT2D,downstream_gene_variant,,ENST00000526209,;PRKAG1,upstream_gene_variant,,ENST00000551696,;RP11-386G11.5,downstream_gene_variant,,ENST00000547866,;RP11-386G11.5,downstream_gene_variant,,ENST00000552933,;RP11-386G11.5,downstream_gene_variant,,ENST00000547395,;RP11-386G11.5,downstream_gene_variant,,ENST00000552284,;PRKAG1,upstream_gene_variant,,ENST00000552657,;PRKAG1,upstream_gene_variant,,ENST00000549726,;PRKAG1,upstream_gene_variant,,ENST00000550125,;PRKAG1,upstream_gene_variant,,ENST00000550448,;PRKAG1,upstream_gene_variant,,ENST00000546531,;	A	ENSG00000167548	ENST00000301067	Transcript	3_prime_UTR_variant	19066	.	.	.	.	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	54/54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAGTATGTGCG	.	3	ESCA
FAM186A	0	.	GRCh37	12	50749945	50749945	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670A>T	p.Ile224Phe	p.I224F	ENST00000327337	4/8	71	58	13	58	58	0	FAM186A,missense_variant,p.Ile224Phe,ENST00000327337,;FAM186A,missense_variant,p.Ile224Phe,ENST00000543111,;	A	ENSG00000185958	ENST00000327337	Transcript	missense_variant	670	670	224	I/F	Att/Ttt	.	.	.	-1	FAM186A	HGNC	26980	protein_coding	YES	CCDS44878.1	ENSP00000329995	F186A_HUMAN	.	UPI00001D7978	.	deleterious(0)	probably_damaging(0.975)	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTAATCATCT	.	5	ESCA
INHBE	0	.	GRCh37	12	57850342	57850342	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.764A>T	p.Asp255Val	p.D255V	ENST00000266646	2/2	71	7	63	62	62	0	INHBE,missense_variant,p.Asp255Val,ENST00000266646,;INHBE,missense_variant,p.Asp200Val,ENST00000547970,;GLI1,upstream_gene_variant,,ENST00000228682,;GLI1,upstream_gene_variant,,ENST00000546141,;GLI1,upstream_gene_variant,,ENST00000528432,;GLI1,upstream_gene_variant,,ENST00000532291,;GLI1,upstream_gene_variant,,ENST00000543426,;INHBE,non_coding_transcript_exon_variant,,ENST00000551553,;INHBE,non_coding_transcript_exon_variant,,ENST00000553033,;GLI1,upstream_gene_variant,,ENST00000530789,;	T	ENSG00000139269	ENST00000266646	Transcript	missense_variant	980	764	255	D/V	gAc/gTc	.	.	.	1	INHBE	HGNC	24029	protein_coding	YES	CCDS8939.1	ENSP00000266646	INHBE_HUMAN	.	UPI000012D42C	.	deleterious(0)	probably_damaging(0.976)	2/2	.	PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF6,hmmpanther:PTHR11848,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTAGACTTCC	.	5	ESCA
NCAPD2	0	.	GRCh37	12	6623482	6623482	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639C>A	p.His213Gln	p.H213Q	ENST00000315579	7/32	77	61	16	40	40	0	NCAPD2,missense_variant,p.His168Gln,ENST00000545962,;NCAPD2,missense_variant,p.His213Gln,ENST00000315579,;NCAPD2,missense_variant,p.His85Gln,ENST00000382457,;NCAPD2,downstream_gene_variant,,ENST00000539714,;SCARNA10,downstream_gene_variant,,ENST00000459255,;SCARNA10,downstream_gene_variant,,ENST00000541782,;NCAPD2,upstream_gene_variant,,ENST00000542472,;NCAPD2,upstream_gene_variant,,ENST00000536090,;NCAPD2,downstream_gene_variant,,ENST00000541399,;NCAPD2,3_prime_UTR_variant,,ENST00000539084,;NCAPD2,non_coding_transcript_exon_variant,,ENST00000545732,;	A	ENSG00000010292	ENST00000315579	Transcript	missense_variant	1438	639	213	H/Q	caC/caA	.	.	.	1	NCAPD2	HGNC	24305	protein_coding	YES	CCDS8548.1	ENSP00000325017	CND1_HUMAN	F5GZK7_HUMAN	UPI000013C8CA	.	tolerated(0.26)	possibly_damaging(0.723)	7/32	.	hmmpanther:PTHR14222,hmmpanther:PTHR14222:SF2,Pfam_domain:PF12922,PIRSF_domain:PIRSF017127	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCACCAGAA	.	5	ESCA
GDF3	0	.	GRCh37	12	7842479	7842479	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1090G>T	p.Gly364Trp	p.G364W	ENST00000329913	2/2	30	5	25	42	42	0	GDF3,missense_variant,p.Gly364Trp,ENST00000329913,;	A	ENSG00000184344	ENST00000329913	Transcript	missense_variant	1138	1090	364	G/W	Ggg/Tgg	.	.	.	-1	GDF3	HGNC	4218	protein_coding	YES	CCDS8581.1	ENSP00000331745	GDF3_HUMAN	.	UPI0000049E0E	.	deleterious_low_confidence(0)	probably_damaging(0.999)	2/2	.	PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF38,hmmpanther:PTHR11848,SMART_domains:SM00204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACCCACACC	.	5	ESCA
ENOX1	0	.	GRCh37	13	43986988	43986988	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.63G>C	p.Met21Ile	p.M21I	ENST00000261488	4/17	41	31	10	69	69	0	ENOX1,missense_variant,p.Met21Ile,ENST00000412891,;ENOX1,missense_variant,p.Met21Ile,ENST00000261488,;	G	ENSG00000120658	ENST00000261488	Transcript	missense_variant	641	63	21	M/I	atG/atC	.	.	.	-1	ENOX1	HGNC	25474	protein_coding	YES	CCDS9389.1	ENSP00000261488	ENOX1_HUMAN	.	UPI0000071D6F	.	tolerated_low_confidence(0.71)	benign(0)	4/17	.	hmmpanther:PTHR16001:SF6,hmmpanther:PTHR16001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCCATCAT	.	5	ESCA
KLHL1	0	.	GRCh37	13	70274735	70274735	+	3'UTR	DEL	T	T	-	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1099delA	.	.	ENST00000377844	11/11	89	74	15	164	164	0	KLHL1,3_prime_UTR_variant,,ENST00000377844,;KLHL1,downstream_gene_variant,,ENST00000545028,;	-	ENSG00000150361	ENST00000377844	Transcript	3_prime_UTR_variant	4106	.	.	.	.	.	.	.	-1	KLHL1	HGNC	6352	protein_coding	YES	CCDS9445.1	ENSP00000367075	KLHL1_HUMAN	Q96RF4_HUMAN	UPI000004B136	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGCAAATTTTTT	.	3	ESCA
FBXL3	0	.	GRCh37	13	77579711	77579711	+	3'UTR	SNP	G	G	A	rs750622908	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1569C>T	.	.	ENST00000355619	5/5	13	5	8	24	24	0	FBXL3,3_prime_UTR_variant,,ENST00000355619,;CLN5,downstream_gene_variant,,ENST00000377453,;FBXL3,downstream_gene_variant,,ENST00000417323,;FBXL3,intron_variant,,ENST00000477982,;FBXL3,intron_variant,,ENST00000485797,;	A	ENSG00000005812	ENST00000355619	Transcript	3_prime_UTR_variant	3181	.	.	.	.	rs750622908	.	.	-1	FBXL3	HGNC	13599	protein_coding	YES	CCDS9457.1	ENSP00000347834	FBXL3_HUMAN	.	UPI0000035C8B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTTCGAATCT	.	3	ESCA
SCEL	0	.	GRCh37	13	78211301	78211301	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1810A>G	p.Ile604Val	p.I604V	ENST00000349847	30/33	28	11	17	56	56	0	SCEL,missense_variant,p.Ile584Val,ENST00000377246,;SCEL,missense_variant,p.Ile604Val,ENST00000349847,;SCEL,missense_variant,p.Ile562Val,ENST00000535157,;	G	ENSG00000136155	ENST00000349847	Transcript	missense_variant	1894	1810	604	I/V	Ata/Gta	.	.	.	1	SCEL	HGNC	10573	protein_coding	YES	CCDS9459.1	ENSP00000302579	SCEL_HUMAN	.	UPI000013CFF1	.	deleterious(0.03)	probably_damaging(0.998)	30/33	.	hmmpanther:PTHR15468:SF6,hmmpanther:PTHR15468	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATACATACAA	.	5	ESCA
CYP46A1	0	.	GRCh37	14	100172827	100172827	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444-157C>T	.	.	ENST00000261835	.	20	16	4	13	13	0	CYP46A1,5_prime_UTR_variant,,ENST00000554176,;CYP46A1,intron_variant,,ENST00000380228,;CYP46A1,intron_variant,,ENST00000423126,;CYP46A1,intron_variant,,ENST00000261835,;CYP46A1,intron_variant,,ENST00000554611,;	T	ENSG00000036530	ENST00000261835	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CYP46A1	HGNC	2641	protein_coding	YES	CCDS9954.1	ENSP00000261835	CP46A_HUMAN	B4DHP8_HUMAN	UPI00001281DC	.	.	.	.	5/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACTCCAACCT	.	4	ESCA
BEGAIN	0	.	GRCh37	14	101012872	101012872	+	Missense_Mutation	SNP	C	C	T	rs780841110	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.142G>A	p.Glu48Lys	p.E48K	ENST00000443071	2/6	48	35	12	50	50	0	BEGAIN,missense_variant,p.Glu67Lys,ENST00000554140,;BEGAIN,missense_variant,p.Glu48Lys,ENST00000557378,;BEGAIN,missense_variant,p.Glu48Lys,ENST00000556188,;BEGAIN,missense_variant,p.Glu48Lys,ENST00000355173,;BEGAIN,missense_variant,p.Glu60Lys,ENST00000553553,;BEGAIN,missense_variant,p.Glu48Lys,ENST00000443071,;BEGAIN,5_prime_UTR_variant,,ENST00000554356,;BEGAIN,5_prime_UTR_variant,,ENST00000556751,;BEGAIN,non_coding_transcript_exon_variant,,ENST00000554747,;BEGAIN,upstream_gene_variant,,ENST00000554274,;	T	ENSG00000183092	ENST00000443071	Transcript	missense_variant	288	142	48	E/K	Gag/Aag	rs780841110	.	.	-1	BEGAIN	HGNC	24163	protein_coding	YES	CCDS9962.1	ENSP00000411124	BEGIN_HUMAN	G3V600_HUMAN,G3V536_HUMAN,G3V3R5_HUMAN,G3V2K4_HUMAN	UPI00000710B1	.	deleterious(0)	probably_damaging(0.996)	2/6	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCCTGCG	.	5	ESCA
MIR410	0	.	GRCh37	14	101532274	101532274	+	RNA	SNP	A	A	G	rs771017364	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.26A>G	.	.	ENST00000362222	1/1	44	36	7	54	54	0	MIR410,non_coding_transcript_exon_variant,,ENST00000362222,;MIR541,downstream_gene_variant,,ENST00000401360,;MIR656,upstream_gene_variant,,ENST00000385224,;MEG9,upstream_gene_variant,,ENST00000554016,;MEG9,upstream_gene_variant,,ENST00000429368,;MIR409,downstream_gene_variant,,ENST00000362237,;MIR412,downstream_gene_variant,,ENST00000362142,;MIR369,downstream_gene_variant,,ENST00000362155,;MIR377,downstream_gene_variant,,ENST00000362145,;	G	ENSG00000199092	ENST00000362222	Transcript	non_coding_transcript_exon_variant	26	.	.	.	.	rs771017364	.	.	1	MIR410	HGNC	32065	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGATGAGT	byFrequency	5	ESCA
LINC00221	0	.	GRCh37	14	106950237	106950237	+	RNA	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.432C>T	.	.	ENST00000334298	3/3	62	52	10	56	56	0	LINC00221,non_coding_transcript_exon_variant,,ENST00000334298,;LINC00221,intron_variant,,ENST00000433371,;LINC00221,downstream_gene_variant,,ENST00000449670,;IGHVII-44-2,non_coding_transcript_exon_variant,,ENST00000517728,;IGHVIV-44-1,upstream_gene_variant,,ENST00000519334,;	T	ENSG00000187156	ENST00000334298	Transcript	non_coding_transcript_exon_variant	432	.	.	.	.	.	.	.	1	LINC00221	HGNC	20169	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCTCTGG	.	5	ESCA
TRMT5	0	.	GRCh37	14	61446377	61446377	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239G>T	p.Arg80Leu	p.R80L	ENST00000261249	2/5	34	27	7	23	23	0	TRMT5,missense_variant,p.Arg80Leu,ENST00000261249,;TRMT5,missense_variant,p.Arg107Leu,ENST00000555420,;TRMT5,missense_variant,p.Arg108Leu,ENST00000553903,;SLC38A6,upstream_gene_variant,,ENST00000451406,;SLC38A6,upstream_gene_variant,,ENST00000456840,;SLC38A6,upstream_gene_variant,,ENST00000267488,;SLC38A6,upstream_gene_variant,,ENST00000526105,;SLC38A6,upstream_gene_variant,,ENST00000354886,;SLC38A6,upstream_gene_variant,,ENST00000533744,;RP11-193F5.1,intron_variant,,ENST00000553946,;SLC38A6,upstream_gene_variant,,ENST00000532148,;SLC38A6,upstream_gene_variant,,ENST00000554304,;SLC38A6,upstream_gene_variant,,ENST00000491344,;SLC38A6,upstream_gene_variant,,ENST00000525723,;SLC38A6,upstream_gene_variant,,ENST00000528350,;SLC38A6,upstream_gene_variant,,ENST00000529345,;SLC38A6,upstream_gene_variant,,ENST00000525585,;SLC38A6,upstream_gene_variant,,ENST00000527591,;SLC38A6,upstream_gene_variant,,ENST00000524402,;	A	ENSG00000126814	ENST00000261249	Transcript	missense_variant	624	239	80	R/L	cGa/cTa	.	.	.	-1	TRMT5	HGNC	23141	protein_coding	YES	CCDS32092.1	ENSP00000261249	TRM5_HUMAN	.	UPI000016003D	.	deleterious(0)	possibly_damaging(0.856)	2/5	.	hmmpanther:PTHR23245:SF25,hmmpanther:PTHR23245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCTCGGACA	.	5	ESCA
MPP5	0	.	GRCh37	14	67787942	67787942	+	Missense_Mutation	SNP	C	C	G	rs764579763	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1706C>G	p.Ser569Cys	p.S569C	ENST00000261681	13/15	85	46	39	65	65	0	MPP5,missense_variant,p.Ser535Cys,ENST00000555925,;MPP5,missense_variant,p.Ser569Cys,ENST00000261681,;ATP6V1D,intron_variant,,ENST00000553974,;ATP6V1D,intron_variant,,ENST00000554087,;	G	ENSG00000072415	ENST00000261681	Transcript	missense_variant	2367	1706	569	S/C	tCt/tGt	rs764579763	.	.	1	MPP5	HGNC	18669	protein_coding	YES	CCDS9779.1	ENSP00000261681	MPP5_HUMAN	G3V2H1_HUMAN	UPI0000046FB9	.	deleterious(0)	probably_damaging(0.956)	13/15	.	PROSITE_profiles:PS50052,hmmpanther:PTHR23122:SF32,hmmpanther:PTHR23122,Pfam_domain:PF00625,Gene3D:3.30.63.10,SMART_domains:SM00072,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACTCTGGCA	.	5	ESCA
SYNJ2BP	0	.	GRCh37	14	70839645	70839645	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*63A>G	.	.	ENST00000256366	4/4	28	18	9	50	50	0	SYNJ2BP,3_prime_UTR_variant,,ENST00000256366,;SYNJ2BP,non_coding_transcript_exon_variant,,ENST00000554216,;SYNJ2BP-COX16,intron_variant,,ENST00000555276,;	C	ENSG00000213463	ENST00000256366	Transcript	3_prime_UTR_variant	583	.	.	.	.	.	.	.	-1	SYNJ2BP	HGNC	18955	protein_coding	YES	CCDS9803.1	ENSP00000256366	SYJ2B_HUMAN	.	UPI00000373B1	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGAATAGCAG	.	5	ESCA
CPSF2	0	.	GRCh37	14	92588341	92588341	+	5'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-225G>T	.	.	ENST00000298875	1/16	13	6	6	13	13	0	CPSF2,5_prime_UTR_variant,,ENST00000553427,;CPSF2,5_prime_UTR_variant,,ENST00000298875,;NDUFB1,upstream_gene_variant,,ENST00000605997,;NDUFB1,upstream_gene_variant,,ENST00000555441,;NDUFB1,upstream_gene_variant,,ENST00000329559,;NDUFB1,upstream_gene_variant,,ENST00000553514,;NDUFB1,upstream_gene_variant,,ENST00000556555,;CPSF2,5_prime_UTR_variant,,ENST00000554290,;NDUFB1,upstream_gene_variant,,ENST00000553666,;	T	ENSG00000165934	ENST00000298875	Transcript	5_prime_UTR_variant	61	.	.	.	.	.	.	.	1	CPSF2	HGNC	2325	protein_coding	YES	CCDS9902.1	ENSP00000298875	CPSF2_HUMAN	G3V3T7_HUMAN,B3KN45_HUMAN	UPI0000185F22	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CGGCTGCCACT	.	4	ESCA
GABRB3	0	.	GRCh37	15	26792519	26792519	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*421A>G	.	.	ENST00000311550	9/9	16	12	4	26	26	0	GABRB3,3_prime_UTR_variant,,ENST00000541819,;GABRB3,3_prime_UTR_variant,,ENST00000311550,;GABRB3,3_prime_UTR_variant,,ENST00000299267,;GABRB3,3_prime_UTR_variant,,ENST00000400188,;GABRB3,downstream_gene_variant,,ENST00000545868,;GABRB3,3_prime_UTR_variant,,ENST00000555632,;	C	ENSG00000166206	ENST00000311550	Transcript	3_prime_UTR_variant	1955	.	.	.	.	.	.	.	-1	GABRB3	HGNC	4083	protein_coding	YES	CCDS10019.1	ENSP00000308725	GBRB3_HUMAN	G3V5B4_HUMAN	UPI000012AFB0	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	ACATCTAACTT	.	4	ESCA
IGDCC4	0	.	GRCh37	15	65689261	65689261	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.908A>G	p.Gln303Arg	p.Q303R	ENST00000352385	6/20	98	54	44	59	59	0	IGDCC4,missense_variant,p.Gln303Arg,ENST00000352385,;IGDCC4,upstream_gene_variant,,ENST00000559327,;	C	ENSG00000103742	ENST00000352385	Transcript	missense_variant	1118	908	303	Q/R	cAg/cGg	.	.	.	-1	IGDCC4	HGNC	13770	protein_coding	YES	CCDS10206.1	ENSP00000319623	IGDC4_HUMAN	.	UPI000006F31C	.	tolerated(0.4)	benign(0.034)	6/20	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCTGCGCG	.	5	ESCA
CALML4	0	.	GRCh37	15	68483936	68483936	+	3'Flank	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000467889	.	46	28	17	46	46	0	CALML4,3_prime_UTR_variant,,ENST00000395465,;PIAS1,downstream_gene_variant,,ENST00000545237,;CALML4,downstream_gene_variant,,ENST00000448060,;RP11-315D16.2,downstream_gene_variant,,ENST00000562767,;CALML4,downstream_gene_variant,,ENST00000540479,;PIAS1,downstream_gene_variant,,ENST00000249636,;CALML4,downstream_gene_variant,,ENST00000467889,;CALML4,3_prime_UTR_variant,,ENST00000478113,;CALML4,downstream_gene_variant,,ENST00000467188,;PIAS1,downstream_gene_variant,,ENST00000563996,;CALML4,downstream_gene_variant,,ENST00000395463,;	C	ENSG00000129007	ENST00000467889	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2206	-1	CALML4	HGNC	18445	protein_coding	YES	CCDS10226.2	ENSP00000419081	CALL4_HUMAN	H3BS46_HUMAN	UPI0000251E74	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCTTGCAG	.	5	ESCA
PAQR5	0	.	GRCh37	15	69652327	69652327	+	5'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-93G>C	.	.	ENST00000340965	3/9	18	13	5	23	23	0	PAQR5,5_prime_UTR_variant,,ENST00000340965,;PAQR5,5_prime_UTR_variant,,ENST00000561153,;PAQR5,5_prime_UTR_variant,,ENST00000395407,;PAQR5,intron_variant,,ENST00000558684,;PAQR5,non_coding_transcript_exon_variant,,ENST00000561027,;PAQR5,upstream_gene_variant,,ENST00000561250,;	C	ENSG00000137819	ENST00000340965	Transcript	5_prime_UTR_variant	576	.	.	.	.	.	.	.	1	PAQR5	HGNC	29645	protein_coding	YES	CCDS10232.1	ENSP00000343877	MPRG_HUMAN	H0YL06_HUMAN	UPI000013D0D0	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTAGGCAGA	.	2	ESCA
CSPG4	0	.	GRCh37	15	75985560	75985560	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103G>A	p.Glu35Lys	p.E35K	ENST00000308508	2/10	232	117	115	271	271	0	CSPG4,missense_variant,p.Glu35Lys,ENST00000308508,;	T	ENSG00000173546	ENST00000308508	Transcript	missense_variant	196	103	35	E/K	Gag/Aag	.	.	.	-1	CSPG4	HGNC	2466	protein_coding	YES	CCDS10284.1	ENSP00000312506	CSPG4_HUMAN	.	UPI00001AEEB6	.	deleterious(0.02)	benign(0.199)	2/10	.	Superfamily_domains:SSF49899,Gene3D:2.60.120.200,hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF11,PROSITE_profiles:PS50025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTCACCGA	.	5	ESCA
BLM	0	.	GRCh37	15	91295023	91295023	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806G>C	p.Ser269Thr	p.S269T	ENST00000355112	4/22	43	33	9	43	43	0	BLM,missense_variant,p.Ser269Thr,ENST00000560509,;BLM,missense_variant,p.Ser269Thr,ENST00000355112,;SNORD18,downstream_gene_variant,,ENST00000363807,;BLM,non_coding_transcript_exon_variant,,ENST00000558599,;BLM,downstream_gene_variant,,ENST00000559282,;BLM,missense_variant,p.Ser269Thr,ENST00000559724,;	C	ENSG00000197299	ENST00000355112	Transcript	missense_variant	924	806	269	S/T	aGc/aCc	.	.	.	1	BLM	HGNC	1058	protein_coding	YES	CCDS10363.1	ENSP00000347232	BLM_HUMAN	.	UPI00001269FA	.	tolerated(0.2)	benign(0.021)	4/22	.	Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TAATAGCGAAA	.	4	ESCA
ZC3H7A	0	.	GRCh37	16	11852417	11852417	+	Intron	SNP	T	T	C	rs766819537	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2320-22A>G	.	.	ENST00000396516	.	38	19	19	38	38	0	ZC3H7A,5_prime_UTR_variant,,ENST00000575984,;ZC3H7A,intron_variant,,ENST00000571198,;ZC3H7A,intron_variant,,ENST00000355758,;ZC3H7A,intron_variant,,ENST00000396516,;ZC3H7A,intron_variant,,ENST00000571405,;ZC3H7A,intron_variant,,ENST00000570862,;ZC3H7A,downstream_gene_variant,,ENST00000572938,;	C	ENSG00000122299	ENST00000396516	Transcript	intron_variant	.	.	.	.	.	rs766819537	.	.	-1	ZC3H7A	HGNC	30959	protein_coding	YES	CCDS10550.1	ENSP00000379773	Z3H7A_HUMAN	I3L3S2_HUMAN,I3L3F9_HUMAN,I3L382_HUMAN,I3L1Y3_HUMAN	UPI000000DB79	.	.	.	.	18/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATATGATTA	byFrequency	5	ESCA
ABCA3	0	.	GRCh37	16	2326068	2326068	+	3'UTR	SNP	G	G	C	rs749749806	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*607C>G	.	.	ENST00000301732	33/33	25	19	6	25	25	0	ABCA3,3_prime_UTR_variant,,ENST00000301732,;ABCA3,3_prime_UTR_variant,,ENST00000382381,;MIR4717,downstream_gene_variant,,ENST00000584656,;MIR940,downstream_gene_variant,,ENST00000567888,;MIR940,downstream_gene_variant,,ENST00000401276,;MIR940,downstream_gene_variant,,ENST00000563734,;MIR940,downstream_gene_variant,,ENST00000562838,;ABCA3,downstream_gene_variant,,ENST00000566200,;	C	ENSG00000167972	ENST00000301732	Transcript	3_prime_UTR_variant	6423	.	.	.	.	rs749749806	.	.	-1	ABCA3	HGNC	33	protein_coding	YES	CCDS10466.1	ENSP00000301732	ABCA3_HUMAN	.	UPI0000001232	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGAGATGCT	.	5	ESCA
COG7	0	.	GRCh37	16	23400171	23400171	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*70C>G	.	.	ENST00000307149	17/17	27	21	5	37	37	0	COG7,3_prime_UTR_variant,,ENST00000307149,;COG7,downstream_gene_variant,,ENST00000563164,;COG7,downstream_gene_variant,,ENST00000569635,;COG7,3_prime_UTR_variant,,ENST00000561854,;COG7,non_coding_transcript_exon_variant,,ENST00000566364,;	C	ENSG00000168434	ENST00000307149	Transcript	3_prime_UTR_variant	2569	.	.	.	.	.	.	.	-1	COG7	HGNC	18622	protein_coding	YES	CCDS10610.1	ENSP00000305442	COG7_HUMAN	.	UPI0000127E42	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTGAGCAA	.	5	ESCA
IL27	0	.	GRCh37	16	28511194	28511194	+	Silent	SNP	C	C	T	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510G>A	p.%3D	p.E170E	ENST00000356897	5/5	20	17	3	31	31	0	IL27,synonymous_variant,p.%3D,ENST00000356897,;APOBR,downstream_gene_variant,,ENST00000328423,;APOBR,downstream_gene_variant,,ENST00000431282,;APOBR,downstream_gene_variant,,ENST00000564831,;IL27,downstream_gene_variant,,ENST00000568075,;CLN3,upstream_gene_variant,,ENST00000569430,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000567160,;	T	ENSG00000197272	ENST00000356897	Transcript	synonymous_variant	533	510	170	E	gaG/gaA	COSM3817696	.	.	-1	IL27	HGNC	19157	protein_coding	YES	CCDS10633.1	ENSP00000349365	IL27A_HUMAN	H3BQY2_HUMAN	UPI0000141330	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR20879:SF0,hmmpanther:PTHR20879	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTCCTCTTC	.	2	ESCA
IL27	0	.	GRCh37	16	28511197	28511197	+	Silent	SNP	T	T	C	rs751249936	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507A>G	p.%3D	p.E169E	ENST00000356897	5/5	19	16	3	30	30	0	IL27,synonymous_variant,p.%3D,ENST00000356897,;APOBR,downstream_gene_variant,,ENST00000328423,;APOBR,downstream_gene_variant,,ENST00000431282,;APOBR,downstream_gene_variant,,ENST00000564831,;IL27,downstream_gene_variant,,ENST00000568075,;CLN3,upstream_gene_variant,,ENST00000569430,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000567160,;	C	ENSG00000197272	ENST00000356897	Transcript	synonymous_variant	530	507	169	E	gaA/gaG	rs751249936	.	.	-1	IL27	HGNC	19157	protein_coding	YES	CCDS10633.1	ENSP00000349365	IL27A_HUMAN	H3BQY2_HUMAN	UPI0000141330	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR20879:SF0,hmmpanther:PTHR20879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E166D|c.498G>C|3	MUTECT|MUSE	TCCTCTTCCTC	.	2	ESCA
SULT1A1	0	.	GRCh37	16	28620562	28620562	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4-382A>G	.	.	ENST00000395609	.	99	66	32	101	101	0	SULT1A1,5_prime_UTR_variant,,ENST00000395607,;SULT1A1,intron_variant,,ENST00000566189,;SULT1A1,intron_variant,,ENST00000567512,;SULT1A1,intron_variant,,ENST00000314752,;SULT1A1,intron_variant,,ENST00000395609,;SULT1A1,intron_variant,,ENST00000350842,;SULT1A1,upstream_gene_variant,,ENST00000569554,;SULT1A1,non_coding_transcript_exon_variant,,ENST00000567998,;SULT1A1,intron_variant,,ENST00000564818,;SULT1A1,intron_variant,,ENST00000562058,;SULT1A1,intron_variant,,ENST00000563493,;	C	ENSG00000196502	ENST00000395609	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SULT1A1	HGNC	11453	protein_coding	YES	CCDS32420.1	ENSP00000378972	ST1A1_HUMAN	Q9UMT9_HUMAN,H3BRY5_HUMAN	UPI000013EA41	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTTGTCTC	.	5	ESCA
VKORC1	0	.	GRCh37	16	31105918	31105918	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.133G>C	p.Val45Leu	p.V45L	ENST00000394975	1/3	31	27	4	23	23	0	VKORC1,missense_variant,p.Val45Leu,ENST00000394975,;RP11-196G11.1,missense_variant,p.Val45Leu,ENST00000532364,;VKORC1,missense_variant,p.Val45Leu,ENST00000319788,;RP11-196G11.1,missense_variant,p.Val45Leu,ENST00000529564,;VKORC1,missense_variant,p.Val45Leu,ENST00000354895,;VKORC1,missense_variant,p.Val45Leu,ENST00000300851,;VKORC1,intron_variant,,ENST00000420057,;VKORC1,intron_variant,,ENST00000498155,;VKORC1,upstream_gene_variant,,ENST00000394971,;VKORC1,upstream_gene_variant,,ENST00000472468,;RP11-196G11.1,missense_variant,p.Val3Leu,ENST00000533518,;PRSS53,upstream_gene_variant,,ENST00000486499,;	G	ENSG00000167397	ENST00000394975	Transcript	missense_variant	361	133	45	V/L	Gtg/Ctg	.	.	.	-1	VKORC1	HGNC	23663	protein_coding	YES	CCDS10703.1	ENSP00000378426	VKOR1_HUMAN	I3L1P9_HUMAN	UPI000006DDEE	.	tolerated(1)	benign(0.165)	1/3	.	SMART_domains:SM00756,Pfam_domain:PF07884,hmmpanther:PTHR14519	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCACGTCGC	.	4	ESCA
ITGAD	0	.	GRCh37	16	31424553	31424553	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1982C>G	p.Ser661Ter	p.S661*	ENST00000389202	16/30	27	18	9	36	36	0	ITGAD,stop_gained,p.Ser661Ter,ENST00000389202,;ITGAD,downstream_gene_variant,,ENST00000444228,;	G	ENSG00000156886	ENST00000389202	Transcript	stop_gained	2031	1982	661	S/*	tCa/tGa	.	.	.	1	ITGAD	HGNC	6146	protein_coding	YES	CCDS32438.1	ENSP00000373854	ITAD_HUMAN	Q59H14_HUMAN	UPI000004B27A	.	.	.	16/30	.	Superfamily_domains:SSF69179,Pfam_domain:PF08441,Gene3D:1jv2A02,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTCACTGG	.	5	ESCA
MSLNL	0	.	GRCh37	16	830591	830591	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.410C>T	p.Ala137Val	p.A137V	ENST00000293892	3/16	79	56	23	90	90	0	MSLNL,missense_variant,p.Ala137Val,ENST00000293892,;MSLNL,intron_variant,,ENST00000442466,;MSLNL,intron_variant,,ENST00000543963,;RPUSD1,downstream_gene_variant,,ENST00000007264,;RPUSD1,downstream_gene_variant,,ENST00000561734,;RPUSD1,downstream_gene_variant,,ENST00000565809,;RPUSD1,downstream_gene_variant,,ENST00000567114,;MSLNL,upstream_gene_variant,,ENST00000537221,;	A	ENSG00000162006	ENST00000293892	Transcript	missense_variant	410	410	137	A/V	gCa/gTa	.	.	.	-1	MSLNL	HGNC	14170	protein_coding	YES	.	ENSP00000293892	MSLNL_HUMAN	.	UPI0000072242	.	.	benign(0.024)	3/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATGCGTGC	.	5	ESCA
CDH13	0	.	GRCh37	16	83065787	83065787	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471G>T	p.%3D	p.V157V	ENST00000268613	4/15	39	31	7	62	62	0	CDH13,synonymous_variant,p.%3D,ENST00000446376,;CDH13,synonymous_variant,p.%3D,ENST00000565636,;CDH13,synonymous_variant,p.%3D,ENST00000566620,;CDH13,synonymous_variant,p.%3D,ENST00000428848,;CDH13,synonymous_variant,p.%3D,ENST00000268613,;CDH13,synonymous_variant,p.%3D,ENST00000431540,;CDH13,non_coding_transcript_exon_variant,,ENST00000569454,;CDH13,non_coding_transcript_exon_variant,,ENST00000566333,;CDH13,intron_variant,,ENST00000539548,;CDH13,downstream_gene_variant,,ENST00000562601,;CDH13,downstream_gene_variant,,ENST00000568770,;CDH13,downstream_gene_variant,,ENST00000569144,;	T	ENSG00000140945	ENST00000268613	Transcript	synonymous_variant	564	471	157	V	gtG/gtT	.	.	.	1	CDH13	HGNC	1753	protein_coding	YES	CCDS58485.1	ENSP00000268613	CAD13_HUMAN	.	UPI00020E71A6	.	.	.	4/15	.	hmmpanther:PTHR24027:SF80,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM01055,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGTGATTGT	.	5	ESCA
ZNF276	0	.	GRCh37	16	89807142	89807142	+	3'Flank	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000443381	.	26	7	19	32	32	0	ZNF276,3_prime_UTR_variant,,ENST00000289816,;FANCA,intron_variant,,ENST00000389301,;FANCA,intron_variant,,ENST00000567879,;FANCA,intron_variant,,ENST00000564475,;FANCA,intron_variant,,ENST00000568369,;FANCA,intron_variant,,ENST00000564870,;FANCA,upstream_gene_variant,,ENST00000561722,;ZNF276,downstream_gene_variant,,ENST00000568064,;ZNF276,downstream_gene_variant,,ENST00000443381,;ZNF276,downstream_gene_variant,,ENST00000446326,;FANCA,intron_variant,,ENST00000564969,;FANCA,intron_variant,,ENST00000568626,;FANCA,intron_variant,,ENST00000305699,;ZNF276,downstream_gene_variant,,ENST00000563983,;FANCA,downstream_gene_variant,,ENST00000568983,;ZNF276,downstream_gene_variant,,ENST00000564004,;FANCA,upstream_gene_variant,,ENST00000562424,;ZNF276,downstream_gene_variant,,ENST00000568295,;ZNF276,downstream_gene_variant,,ENST00000561536,;ZNF276,downstream_gene_variant,,ENST00000569901,;FANCA,downstream_gene_variant,,ENST00000561660,;FANCA,downstream_gene_variant,,ENST00000567988,;ZNF276,downstream_gene_variant,,ENST00000569582,;ZNF276,downstream_gene_variant,,ENST00000562530,;	T	ENSG00000158805	ENST00000443381	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2163	1	ZNF276	HGNC	23330	protein_coding	YES	CCDS45554.1	ENSP00000415836	ZN276_HUMAN	.	UPI0000EE7D9C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGAAGCTGGC	.	5	ESCA
PROCA1	0	.	GRCh37	17	27031456	27031456	+	Intron	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.228-3C>T	.	.	ENST00000301039	.	30	17	12	28	28	0	PROCA1,splice_region_variant,,ENST00000301039,;PROCA1,splice_region_variant,,ENST00000439862,;PROCA1,splice_region_variant,,ENST00000415329,;PROCA1,intron_variant,,ENST00000581289,;SUPT6H,downstream_gene_variant,,ENST00000314616,;SUPT6H,downstream_gene_variant,,ENST00000347486,;PROCA1,splice_region_variant,,ENST00000422880,;PROCA1,splice_region_variant,,ENST00000584073,;PROCA1,non_coding_transcript_exon_variant,,ENST00000579650,;PROCA1,downstream_gene_variant,,ENST00000578097,;PROCA1,splice_region_variant,,ENST00000495203,;PROCA1,3_prime_UTR_variant,,ENST00000473751,;SUPT6H,downstream_gene_variant,,ENST00000583340,;SUPT6H,downstream_gene_variant,,ENST00000581510,;	A	ENSG00000167525	ENST00000301039	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	PROCA1	HGNC	28600	protein_coding	YES	CCDS11239.1	ENSP00000301039	PRCA1_HUMAN	K7ESJ9_HUMAN	UPI000006D0EE	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTGCCACA	.	5	ESCA
SUZ12	0	.	GRCh37	17	30327334	30327334	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1312A>T	.	.	ENST00000322652	16/16	11	7	4	10	10	0	SUZ12,3_prime_UTR_variant,,ENST00000580398,;SUZ12,3_prime_UTR_variant,,ENST00000322652,;RP11-640N20.1,downstream_gene_variant,,ENST00000583346,;SUZ12,downstream_gene_variant,,ENST00000578106,;RP11-640N20.1,downstream_gene_variant,,ENST00000582184,;	T	ENSG00000178691	ENST00000322652	Transcript	3_prime_UTR_variant	3761	.	.	.	.	.	.	.	1	SUZ12	HGNC	17101	protein_coding	YES	CCDS11270.1	ENSP00000316578	SUZ12_HUMAN	.	UPI000006F727	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGATATATAA	.	2	ESCA
ZPBP2	0	.	GRCh37	17	38027810	38027810	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.338A>G	p.Tyr113Cys	p.Y113C	ENST00000348931	4/8	49	39	10	66	66	0	ZPBP2,missense_variant,p.Tyr113Cys,ENST00000348931,;ZPBP2,missense_variant,p.Tyr113Cys,ENST00000584588,;ZPBP2,missense_variant,p.Tyr91Cys,ENST00000377940,;ZPBP2,intron_variant,,ENST00000583811,;	G	ENSG00000186075	ENST00000348931	Transcript	missense_variant	529	338	113	Y/C	tAt/tGt	.	.	.	1	ZPBP2	HGNC	20678	protein_coding	YES	CCDS11352.1	ENSP00000335384	ZPBP2_HUMAN	.	UPI00001D79E4	.	deleterious(0)	probably_damaging(0.992)	4/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR15443:SF4,hmmpanther:PTHR15443,Gene3D:2.60.40.10,Pfam_domain:PF07354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTATAAGA	.	5	ESCA
MED24	0	.	GRCh37	17	38178915	38178915	+	Silent	SNP	C	C	T	rs761413512	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2415G>A	p.%3D	p.P805P	ENST00000394128	21/26	29	20	9	21	21	0	MED24,synonymous_variant,p.%3D,ENST00000422942,;MED24,synonymous_variant,p.%3D,ENST00000535071,;MED24,synonymous_variant,p.%3D,ENST00000501516,;MED24,synonymous_variant,p.%3D,ENST00000356271,;MED24,synonymous_variant,p.%3D,ENST00000394128,;MED24,synonymous_variant,p.%3D,ENST00000394126,;MED24,synonymous_variant,p.%3D,ENST00000394127,;CSF3,downstream_gene_variant,,ENST00000225474,;CSF3,downstream_gene_variant,,ENST00000331769,;MED24,downstream_gene_variant,,ENST00000580885,;CSF3,downstream_gene_variant,,ENST00000394149,;SNORD124,downstream_gene_variant,,ENST00000459577,;MED24,upstream_gene_variant,,ENST00000470126,;MED24,3_prime_UTR_variant,,ENST00000535508,;MED24,non_coding_transcript_exon_variant,,ENST00000492176,;MED24,upstream_gene_variant,,ENST00000579364,;MED24,downstream_gene_variant,,ENST00000580921,;MED24,downstream_gene_variant,,ENST00000578901,;MED24,downstream_gene_variant,,ENST00000580720,;MED24,downstream_gene_variant,,ENST00000584782,;MED24,downstream_gene_variant,,ENST00000581058,;MED24,downstream_gene_variant,,ENST00000495586,;CSF3,downstream_gene_variant,,ENST00000579852,;MED24,upstream_gene_variant,,ENST00000491466,;	T	ENSG00000008838	ENST00000394128	Transcript	synonymous_variant	2497	2415	805	P	ccG/ccA	rs761413512	.	.	-1	MED24	HGNC	22963	protein_coding	YES	CCDS11359.1	ENSP00000377686	MED24_HUMAN	J3QRH9_HUMAN,J3KSU0_HUMAN,F5H5K2_HUMAN	UPI000013677A	.	.	.	21/26	.	hmmpanther:PTHR12898,hmmpanther:PTHR12898:SF1,Pfam_domain:PF11277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCCGGGGG	byFrequency	5	ESCA
KRT12	0	.	GRCh37	17	39023236	39023236	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.203G>A	p.Gly68Asp	p.G68D	ENST00000251643	1/8	53	39	14	68	68	0	KRT12,missense_variant,p.Gly68Asp,ENST00000251643,;RP5-1110E20.1,downstream_gene_variant,,ENST00000579136,;	T	ENSG00000187242	ENST00000251643	Transcript	missense_variant	227	203	68	G/D	gGc/gAc	.	.	.	-1	KRT12	HGNC	6414	protein_coding	YES	CCDS11378.1	ENSP00000251643	K1C12_HUMAN	.	UPI000012DAE4	.	deleterious(0.02)	unknown(0)	1/8	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF115,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGCCGGAA	.	5	ESCA
PTRF	0	.	GRCh37	17	40557038	40557038	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.840C>T	p.%3D	p.R280R	ENST00000357037	2/2	49	38	11	42	42	0	PTRF,synonymous_variant,p.%3D,ENST00000357037,;	A	ENSG00000177469	ENST00000357037	Transcript	synonymous_variant	1260	840	280	R	cgC/cgT	.	.	.	-1	PTRF	HGNC	9688	protein_coding	YES	CCDS11425.1	ENSP00000349541	PTRF_HUMAN	.	UPI00001AF3C2	.	.	.	2/2	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15240:SF3,hmmpanther:PTHR15240,Pfam_domain:PF15237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAGGCGCGT	.	5	ESCA
UBTF	0	.	GRCh37	17	42293021	42293021	+	Splice_Site	DEL	C	C	-	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.474+1delG	.	p.X158_splice	ENST00000302904	.	88	79	9	36	36	0	UBTF,splice_donor_variant,,ENST00000393606,;UBTF,splice_donor_variant,,ENST00000302904,;UBTF,splice_donor_variant,,ENST00000529383,;UBTF,splice_donor_variant,,ENST00000436088,;UBTF,splice_donor_variant,,ENST00000533177,;UBTF,splice_donor_variant,,ENST00000526094,;UBTF,splice_donor_variant,,ENST00000530828,;UBTF,splice_donor_variant,,ENST00000527034,;UBTF,splice_donor_variant,,ENST00000343638,;UBTF,upstream_gene_variant,,ENST00000529373,;CTB-175E5.7,intron_variant,,ENST00000586560,;UBTF,non_coding_transcript_exon_variant,,ENST00000537550,;UBTF,upstream_gene_variant,,ENST00000529042,;	-	ENSG00000108312	ENST00000302904	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	UBTF	HGNC	12511	protein_coding	YES	CCDS11480.1	ENSP00000302640	UBF1_HUMAN	Q9BQR2_HUMAN,E9PLT2_HUMAN,B4DLB0_HUMAN	UPI000013797C	.	.	.	.	5/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCCCACCTTCT	.	3	ESCA
CDC27	0	.	GRCh37	17	45199823	45199823	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2397A>G	p.%3D	p.Q799Q	ENST00000531206	18/19	50	40	10	36	36	0	CDC27,synonymous_variant,p.%3D,ENST00000066544,;CDC27,synonymous_variant,p.%3D,ENST00000527547,;CDC27,synonymous_variant,p.%3D,ENST00000531206,;CDC27,synonymous_variant,p.%3D,ENST00000446365,;CDC27,3_prime_UTR_variant,,ENST00000571643,;AC002558.1,downstream_gene_variant,,ENST00000408089,;CDC27,3_prime_UTR_variant,,ENST00000533415,;CDC27,3_prime_UTR_variant,,ENST00000570740,;CDC27,downstream_gene_variant,,ENST00000526866,;	C	ENSG00000004897	ENST00000531206	Transcript	synonymous_variant	2401	2397	799	Q	caA/caG	.	.	.	-1	CDC27	HGNC	1728	protein_coding	YES	CCDS45720.1	ENSP00000434614	CDC27_HUMAN	I0EZ72_HUMAN,I0EZ68_HUMAN	UPI0000E59FE6	.	.	.	18/19	.	hmmpanther:PTHR12558,hmmpanther:PTHR12558:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCTTGGGT	.	5	ESCA
HOXB3	0	.	GRCh37	17	46627744	46627744	+	Silent	SNP	A	A	G	rs766930995	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1248T>C	p.%3D	p.P416P	ENST00000470495	2/2	56	46	9	29	29	0	HOXB3,synonymous_variant,p.%3D,ENST00000485909,;HOXB3,synonymous_variant,p.%3D,ENST00000470495,;HOXB3,synonymous_variant,p.%3D,ENST00000476342,;HOXB3,synonymous_variant,p.%3D,ENST00000472863,;HOXB3,synonymous_variant,p.%3D,ENST00000489475,;HOXB3,synonymous_variant,p.%3D,ENST00000490677,;HOXB3,synonymous_variant,p.%3D,ENST00000460160,;HOXB3,synonymous_variant,p.%3D,ENST00000311626,;HOXB3,synonymous_variant,p.%3D,ENST00000498678,;HOXB3,downstream_gene_variant,,ENST00000465120,;HOXB3,downstream_gene_variant,,ENST00000471459,;HOXB2,upstream_gene_variant,,ENST00000330070,;HOXB-AS1,non_coding_transcript_exon_variant,,ENST00000508688,;HOXB-AS1,non_coding_transcript_exon_variant,,ENST00000502764,;HOXB-AS1,non_coding_transcript_exon_variant,,ENST00000435312,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS1,downstream_gene_variant,,ENST00000504972,;	G	ENSG00000120093	ENST00000470495	Transcript	synonymous_variant	2696	1248	416	P	ccT/ccC	rs766930995	.	.	-1	HOXB3	HGNC	5114	protein_coding	YES	CCDS11528.1	ENSP00000417207	HXB3_HUMAN	C9J2I3_HUMAN,B7ZAD0_HUMAN,B7Z5N8_HUMAN	UPI00001AEFBF	.	.	.	2/2	.	Pfam_domain:PF13293,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGAGGCGC	byFrequency	5	ESCA
CA10	0	.	GRCh37	17	50235351	50235351	+	5'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-205T>C	.	.	ENST00000451037	1/9	34	30	4	29	29	0	CA10,5_prime_UTR_variant,,ENST00000285273,;CA10,5_prime_UTR_variant,,ENST00000575181,;CA10,5_prime_UTR_variant,,ENST00000340813,;CA10,5_prime_UTR_variant,,ENST00000451037,;CA10,5_prime_UTR_variant,,ENST00000442502,;CA10,intron_variant,,ENST00000570565,;CA10,non_coding_transcript_exon_variant,,ENST00000573294,;CA10,5_prime_UTR_variant,,ENST00000571371,;	G	ENSG00000154975	ENST00000451037	Transcript	5_prime_UTR_variant	737	.	.	.	.	.	.	.	-1	CA10	HGNC	1369	protein_coding	YES	CCDS32684.1	ENSP00000405388	CAH10_HUMAN	I3L375_HUMAN,B4DGL6_HUMAN	UPI000000167C	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTCGACGGAT	.	4	ESCA
HSF5	0	.	GRCh37	17	56544249	56544249	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1017C>A	p.Phe339Leu	p.F339L	ENST00000323777	3/6	49	28	20	62	62	0	HSF5,missense_variant,p.Phe339Leu,ENST00000323777,;	T	ENSG00000176160	ENST00000323777	Transcript	missense_variant	1127	1017	339	F/L	ttC/ttA	.	.	.	-1	HSF5	HGNC	26862	protein_coding	YES	CCDS32690.1	ENSP00000313243	HSF5_HUMAN	.	UPI0000161929	.	tolerated(0.06)	possibly_damaging(0.472)	3/6	.	hmmpanther:PTHR10015,hmmpanther:PTHR10015:SF138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGGAAGTA	.	5	ESCA
SEPT4	0	.	GRCh37	17	56604047	56604047	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398C>G	p.Ser133Cys	p.S133C	ENST00000457347	3/13	31	27	3	57	57	0	SEPT4,missense_variant,p.Ser99Cys,ENST00000426861,;SEPT4,missense_variant,p.Ser123Cys,ENST00000583291,;SEPT4,missense_variant,p.Ser133Cys,ENST00000457347,;SEPT4,missense_variant,p.Ser99Cys,ENST00000317256,;SEPT4,missense_variant,p.Ser110Cys,ENST00000412945,;SEPT4,missense_variant,p.Ser99Cys,ENST00000393086,;SEPT4,missense_variant,p.Ser118Cys,ENST00000317268,;SEPT4,5_prime_UTR_variant,,ENST00000583114,;SEPT4,intron_variant,,ENST00000579371,;SEPT4,intron_variant,,ENST00000580809,;SEPT4,intron_variant,,ENST00000577729,;SEPT4,intron_variant,,ENST00000580844,;SEPT4,downstream_gene_variant,,ENST00000581607,;RP11-112H10.4,intron_variant,,ENST00000580589,;RP11-112H10.4,intron_variant,,ENST00000580769,;RP11-112H10.4,intron_variant,,ENST00000578022,;SEPT4,non_coding_transcript_exon_variant,,ENST00000584528,;SEPT4,non_coding_transcript_exon_variant,,ENST00000580740,;SEPT4,non_coding_transcript_exon_variant,,ENST00000580791,;SEPT4,intron_variant,,ENST00000581921,;SEPT4,non_coding_transcript_exon_variant,,ENST00000580796,;SEPT4,non_coding_transcript_exon_variant,,ENST00000582248,;SEPT4,non_coding_transcript_exon_variant,,ENST00000583273,;SEPT4,non_coding_transcript_exon_variant,,ENST00000584789,;SEPT4,non_coding_transcript_exon_variant,,ENST00000584488,;SEPT4,non_coding_transcript_exon_variant,,ENST00000577440,;SEPT4,non_coding_transcript_exon_variant,,ENST00000585170,;SEPT4,non_coding_transcript_exon_variant,,ENST00000578747,;SEPT4,intron_variant,,ENST00000581615,;SEPT4,intron_variant,,ENST00000582270,;SEPT4,intron_variant,,ENST00000578131,;SEPT4,downstream_gene_variant,,ENST00000582976,;	C	ENSG00000108387	ENST00000457347	Transcript	missense_variant	543	398	133	S/C	tCt/tGt	.	.	.	-1	SEPT4	HGNC	9165	protein_coding	YES	CCDS58582.1	ENSP00000402000	SEPT4_HUMAN	.	UPI00017A809C	.	deleterious(0)	benign(0.019)	3/13	.	hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTCAGAGGAA	.	3	ESCA
BRIP1	0	.	GRCh37	17	59878759	59878759	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.995G>C	p.Cys332Ser	p.C332S	ENST00000259008	8/20	67	55	11	67	67	0	BRIP1,missense_variant,p.Cys332Ser,ENST00000259008,;BRIP1,missense_variant,p.Cys332Ser,ENST00000577598,;	G	ENSG00000136492	ENST00000259008	Transcript	missense_variant	1263	995	332	C/S	tGc/tCc	.	.	.	-1	BRIP1	HGNC	20473	protein_coding	YES	CCDS11631.1	ENSP00000259008	FANCJ_HUMAN	J3KS24_HUMAN	UPI000013D01F	.	tolerated(0.58)	benign(0.008)	8/20	.	PROSITE_profiles:PS51193,hmmpanther:PTHR11472:SF6,hmmpanther:PTHR11472,Pfam_domain:PF06733,TIGRFAM_domain:TIGR00604,SMART_domains:SM00487,SMART_domains:SM00488	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGCACATC	.	5	ESCA
MED13	0	.	GRCh37	17	60059673	60059673	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3691G>A	p.Asp1231Asn	p.D1231N	ENST00000397786	16/30	73	60	13	56	56	0	MED13,missense_variant,p.Asp1231Asn,ENST00000397786,;	T	ENSG00000108510	ENST00000397786	Transcript	missense_variant	3768	3691	1231	D/N	Gac/Aac	.	.	.	-1	MED13	HGNC	22474	protein_coding	YES	CCDS42366.1	ENSP00000380888	MED13_HUMAN	.	UPI0000D7D6F6	.	deleterious(0.02)	probably_damaging(0.998)	16/30	.	hmmpanther:PTHR12950:SF22,hmmpanther:PTHR12950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTCATTGC	.	5	ESCA
GNA13	0	.	GRCh37	17	63010777	63010777	+	Silent	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732T>A	p.%3D	p.L244L	ENST00000439174	4/4	109	70	38	113	113	0	GNA13,synonymous_variant,p.%3D,ENST00000541118,;GNA13,synonymous_variant,p.%3D,ENST00000439174,;	T	ENSG00000120063	ENST00000439174	Transcript	synonymous_variant	978	732	244	L	ctT/ctA	.	.	.	-1	GNA13	HGNC	4381	protein_coding	YES	CCDS11661.1	ENSP00000400717	GNA13_HUMAN	F5H1G8_HUMAN	UPI0000073EBA	.	.	.	4/4	.	hmmpanther:PTHR10218:SF85,hmmpanther:PTHR10218,Gene3D:3.40.50.300,Pfam_domain:PF00503,SMART_domains:SM00275,Superfamily_domains:SSF52540,Prints_domain:PR00318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAAAGTAT	.	5	ESCA
ST6GALNAC1	0	.	GRCh37	17	74621943	74621943	+	Silent	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1563T>A	p.%3D	p.T521T	ENST00000156626	8/9	58	53	5	40	40	0	ST6GALNAC1,synonymous_variant,p.%3D,ENST00000156626,;ST6GALNAC1,synonymous_variant,p.%3D,ENST00000590784,;ST6GALNAC1,downstream_gene_variant,,ENST00000590878,;ST6GALNAC1,downstream_gene_variant,,ENST00000589004,;ST6GALNAC1,3_prime_UTR_variant,,ENST00000585633,;ST6GALNAC1,3_prime_UTR_variant,,ENST00000359088,;ST6GALNAC1,3_prime_UTR_variant,,ENST00000592042,;ST6GALNAC1,non_coding_transcript_exon_variant,,ENST00000588375,;ST6GALNAC1,downstream_gene_variant,,ENST00000589813,;	T	ENSG00000070526	ENST00000156626	Transcript	synonymous_variant	1763	1563	521	T	acT/acA	.	.	.	-1	ST6GALNAC1	HGNC	23614	protein_coding	YES	CCDS11748.1	ENSP00000156626	SIA7A_HUMAN	.	UPI0000001C00	.	.	.	8/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13713:SF1,hmmpanther:PTHR13713,Pfam_domain:PF00777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCCCAGTGGT	.	3	ESCA
FXR2	0	.	GRCh37	17	7507177	7507177	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.347T>G	p.Ile116Ser	p.I116S	ENST00000250113	5/17	55	52	3	104	104	0	FXR2,missense_variant,p.Ile116Ser,ENST00000250113,;FXR2,missense_variant,p.Ile73Ser,ENST00000571597,;FXR2,non_coding_transcript_exon_variant,,ENST00000576693,;FXR2,upstream_gene_variant,,ENST00000573957,;	C	ENSG00000129245	ENST00000250113	Transcript	missense_variant	682	347	116	I/S	aTt/aGt	.	.	.	-1	FXR2	HGNC	4024	protein_coding	YES	CCDS45604.1	ENSP00000250113	FXR2_HUMAN	.	UPI0000072727	.	deleterious(0)	probably_damaging(0.999)	5/17	.	PROSITE_profiles:PS51641,hmmpanther:PTHR10603,hmmpanther:PTHR10603:SF3,Pfam_domain:PF05641	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACAATTTCA	.	2	ESCA
TP53	0	.	GRCh37	17	7578542	7578542	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	5/11	24	10	14	34	34	0	TP53,missense_variant,p.Leu130Val,ENST00000508793,;TP53,missense_variant,p.Leu130Val,ENST00000413465,;TP53,missense_variant,p.Leu130Val,ENST00000420246,;TP53,missense_variant,p.Leu130Val,ENST00000269305,;TP53,missense_variant,p.Leu130Val,ENST00000359597,;TP53,missense_variant,p.Leu37Val,ENST00000514944,;TP53,missense_variant,p.Leu130Val,ENST00000445888,;TP53,missense_variant,p.Leu130Val,ENST00000455263,;TP53,5_prime_UTR_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	578	388	130	L/V	Ctc/Gtc	CM016206,TP53_g.12376del,TP53_g.12376C>T,TP53_g.12376C>A,TP53_g.12376C>G,COSM11462,COSM11449,COSM45499,COSM437616,COSM247951,COSM1167680,COSM247950,COSM437617,COSM1167681,COSM3403293,COSM3970380,COSM1649369,COSM1728015,COSM1167682,COSM247952,COSM437618	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.997)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.L130V|c.388C>G|5,SITE|p.L130V|c.388C>G|3,SITE|p.L130V|c.388C>G|5,SITE|p.L37V|c.109C>G|5,SITE|p.L130V|c.388C>G|15,CODON|p.0?|c.1_1182del1182|6,CODON|p.Y126_K132delYSPALNK|c.376_396del21|6,CODON|p.Y126_N131delYSPALN|c.376_393del18|3,CODON|p.L130L|c.390C>T|4,CODON|p.L130H|c.389T>A|5,CODON|p.L130P|c.389T>C|5,CODON|p.L130R|c.389T>G|8,BUFFER|p.M133T|c.398T>C|5,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M133T|c.398T>C|3,BUFFER|p.M40T|c.119T>C|3,BUFFER|p.M1T|c.2T>C|3,BUFFER|p.M1R|c.2T>G|3,BUFFER|p.M133R|c.398T>G|7,BUFFER|p.M133K|c.398T>A|12,BUFFER|p.M133R|c.398T>G|3,BUFFER|p.M40R|c.119T>G|3,BUFFER|p.K132N|c.396G>C|29,BUFFER|p.K132N|c.396G>T|3,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>C|5,BUFFER|p.K132N|c.396G>T|24,BUFFER|p.K132N|c.396G>C|5,BUFFER|p.K132N|c.396G>T|6,BUFFER|p.K39N|c.117G>T|6,BUFFER|p.N131delN|c.393_395delCAA|4,BUFFER|p.K132R|c.395A>G|5,BUFFER|p.K132T|c.395A>C|7,BUFFER|p.K39T|c.116A>C|3,BUFFER|p.K132R|c.395A>G|39,BUFFER|p.K132M|c.395A>T|10,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K132T|c.395A>C|3,BUFFER|p.K132R|c.395A>G|7,BUFFER|p.K39R|c.116A>G|7,BUFFER|p.K132Q|c.394A>C|13,BUFFER|p.K39E|c.115A>G|3,BUFFER|p.K132*|c.394A>T|5,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|3,BUFFER|p.K132E|c.394A>G|19,BUFFER|p.N131delN|c.391_393delAAC|8,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131I|c.392A>T|7,BUFFER|p.N131I|c.392A>T|3,BUFFER|p.N131S|c.392A>G|5,BUFFER|p.N38I|c.113A>T|3,BUFFER|p.N131Y|c.391A>T|8,BUFFER|p.L130F|c.388C>T|13,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L130F|c.388C>T|7,BUFFER|p.L37F|c.109C>T|7,BUFFER|p.L130F|c.388C>T|3,BUFFER|p.L130F|c.388C>T|4,BUFFER|p.P128L|c.383C>T|3,BUFFER|p.P128fs*42|c.382delC|3,BUFFER|p.P128S|c.382C>T|7,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S127Y|c.380C>A|10,BUFFER|p.S34F|c.101C>T|11,BUFFER|p.S127F|c.380C>T|4,BUFFER|p.S127F|c.380C>T|33,BUFFER|p.S127F|c.380C>T|3,BUFFER|p.S127F|c.380C>T|11,BUFFER|p.S34P|c.100T>C|4,BUFFER|p.S34T|c.100T>A|4,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.S127P|c.379T>C|8,BUFFER|p.S127T|c.379T>A|4,BUFFER|p.S127T|c.379T>A|10,BUFFER|p.S127T|c.379T>A|3,BUFFER|p.S127P|c.379T>C|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>G|4,BUFFER|p.Y126*|c.378C>G|3,BUFFER|p.Y126*|c.378C>A|4,BUFFER|p.Y33*|c.99C>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y33C|c.98A>G|6,BUFFER|p.Y126C|c.377A>G|3,BUFFER|p.Y126C|c.377A>G|6,BUFFER|p.Y126C|c.377A>G|9,BUFFER|p.Y126S|c.377A>C|3,BUFFER|p.Y126C|c.377A>G|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGAGGGCAG	.	5	ESCA
CEP192	0	.	GRCh37	18	13056017	13056017	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3428A>T	p.Lys1143Ile	p.K1143I	ENST00000506447	19/45	26	18	8	50	50	0	CEP192,missense_variant,p.Lys547Ile,ENST00000325971,;CEP192,missense_variant,p.Lys884Ile,ENST00000589596,;CEP192,missense_variant,p.Lys1143Ile,ENST00000506447,;CEP192,missense_variant,p.Lys668Ile,ENST00000430049,;CEP192,missense_variant,p.Lys682Ile,ENST00000511820,;CEP192,missense_variant,p.Lys743Ile,ENST00000510237,;CEP192,3_prime_UTR_variant,,ENST00000513432,;CEP192,upstream_gene_variant,,ENST00000585938,;CEP192,upstream_gene_variant,,ENST00000589993,;	T	ENSG00000101639	ENST00000506447	Transcript	missense_variant	3508	3428	1143	K/I	aAa/aTa	.	.	.	1	CEP192	HGNC	25515	protein_coding	YES	CCDS32792.2	ENSP00000427550	.	E9PF99_HUMAN	UPI0001B09235	.	deleterious(0.01)	possibly_damaging(0.483)	19/45	.	hmmpanther:PTHR16029:SF10,hmmpanther:PTHR16029	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CTCCAAAAGTG	.	4	ESCA
MYOM1	0	.	GRCh37	18	3084019	3084019	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4346A>T	p.Lys1449Met	p.K1449M	ENST00000356443	32/38	66	42	24	44	44	0	MYOM1,missense_variant,p.Lys1449Met,ENST00000356443,;MYOM1,missense_variant,p.Lys1449Met,ENST00000400569,;MYOM1,missense_variant,p.Lys1353Met,ENST00000261606,;MYOM1,missense_variant,p.Arg120Trp,ENST00000581075,;	A	ENSG00000101605	ENST00000356443	Transcript	missense_variant	4680	4346	1449	K/M	aAg/aTg	.	.	.	-1	MYOM1	HGNC	7613	protein_coding	YES	CCDS45824.1	ENSP00000348821	MYOM1_HUMAN	.	UPI000022A657	.	deleterious(0.02)	benign(0.023)	32/38	.	hmmpanther:PTHR19900:SF36,hmmpanther:PTHR19900	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCCTTAAAG	.	5	ESCA
PIGN	0	.	GRCh37	18	59780447	59780447	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1354G>T	p.Val452Leu	p.V452L	ENST00000357637	16/31	36	27	9	66	66	0	PIGN,missense_variant,p.Val452Leu,ENST00000400334,;PIGN,missense_variant,p.Val452Leu,ENST00000357637,;PIGN,intron_variant,,ENST00000586566,;PIGN,upstream_gene_variant,,ENST00000587942,;PIGN,upstream_gene_variant,,ENST00000590948,;	A	ENSG00000197563	ENST00000357637	Transcript	missense_variant	1770	1354	452	V/L	Gtg/Ttg	.	.	.	-1	PIGN	HGNC	8967	protein_coding	YES	CCDS45879.1	ENSP00000350263	PIGN_HUMAN	K7ESH9_HUMAN,K7ERX5_HUMAN,K7EQG0_HUMAN,K7EPN0_HUMAN,K7ENC3_HUMAN,K7EMD7_HUMAN,K7EM45_HUMAN,K7ELE1_HUMAN,K7EL34_HUMAN,K7EK83_HUMAN	UPI0000070A47	.	tolerated(0.25)	benign(0.026)	16/31	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12250,Pfam_domain:PF04987	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCACAAAAC	.	5	ESCA
CDH19	0	.	GRCh37	18	64176315	64176315	+	Missense_Mutation	SNP	C	C	A	rs748560534	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1745G>T	p.Cys582Phe	p.C582F	ENST00000262150	11/12	39	33	6	79	79	0	CDH19,missense_variant,p.Cys582Phe,ENST00000262150,;CDH19,intron_variant,,ENST00000540086,;CDH19,3_prime_UTR_variant,,ENST00000579658,;	A	ENSG00000071991	ENST00000262150	Transcript	missense_variant	2038	1745	582	C/F	tGc/tTc	rs748560534	.	.	-1	CDH19	HGNC	1758	protein_coding	YES	CCDS11994.1	ENSP00000262150	CAD19_HUMAN	Q96KY9_HUMAN,J3QS15_HUMAN,F8VVI9_HUMAN	UPI0000048ECF	.	deleterious(0)	probably_damaging(0.998)	11/12	.	hmmpanther:PTHR24027:SF255,hmmpanther:PTHR24027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T581P|c.1741A>C|3	RADIA|MUTECT|MUSE|VARSCANS	ACTGGCAGGTC	.	4	ESCA
GADD45GIP1	0	.	GRCh37	19	13065136	13065136	+	Silent	SNP	C	C	T	rs746106552	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555G>A	p.%3D	p.K185K	ENST00000316939	2/2	59	36	23	22	22	0	GADD45GIP1,synonymous_variant,p.%3D,ENST00000316939,;RAD23A,downstream_gene_variant,,ENST00000541222,;RAD23A,downstream_gene_variant,,ENST00000316856,;RAD23A,downstream_gene_variant,,ENST00000592268,;RAD23A,downstream_gene_variant,,ENST00000586534,;RAD23A,downstream_gene_variant,,ENST00000590881,;AC092069.1,upstream_gene_variant,,ENST00000410560,;RAD23A,downstream_gene_variant,,ENST00000588826,;RAD23A,downstream_gene_variant,,ENST00000593114,;RAD23A,downstream_gene_variant,,ENST00000591467,;RAD23A,downstream_gene_variant,,ENST00000591499,;RAD23A,downstream_gene_variant,,ENST00000586375,;	T	ENSG00000179271	ENST00000316939	Transcript	synonymous_variant	579	555	185	K	aaG/aaA	rs746106552	.	.	-1	GADD45GIP1	HGNC	29996	protein_coding	YES	CCDS12290.1	ENSP00000323065	G45IP_HUMAN	Q7LAX7_HUMAN	UPI000006E725	.	.	.	2/2	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31761:SF1,hmmpanther:PTHR31761,Pfam_domain:PF10147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTCCTTCTT	.	5	ESCA
CACNA1A	0	.	GRCh37	19	13470461	13470461	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937C>T	p.Gln313Ter	p.Q313*	ENST00000360228	6/47	93	85	8	66	66	0	CACNA1A,stop_gained,p.Gln313Ter,ENST00000573710,;CACNA1A,stop_gained,p.Gln313Ter,ENST00000360228,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000593160,;	A	ENSG00000141837	ENST00000360228	Transcript	stop_gained	937	937	313	Q/*	Cag/Tag	.	.	.	-1	CACNA1A	HGNC	1388	protein_coding	YES	CCDS45998.1	ENSP00000353362	CAC1A_HUMAN	Q9UN69_HUMAN,Q9UHM9_HUMAN	UPI0000141565	.	.	.	6/47	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF00520,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GCACTGGAAAA	.	3	ESCA
CD97	0	.	GRCh37	19	14515276	14515276	+	Missense_Mutation	SNP	G	G	A	rs748373111	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1531G>A	p.Glu511Lys	p.E511K	ENST00000242786	13/20	37	21	16	33	33	0	CD97,missense_variant,p.Glu511Lys,ENST00000242786,;CD97,missense_variant,p.Glu462Lys,ENST00000357355,;CD97,missense_variant,p.Glu418Lys,ENST00000358600,;DDX39A,downstream_gene_variant,,ENST00000242776,;CTC-548K16.5,intron_variant,,ENST00000590626,;CD97,non_coding_transcript_exon_variant,,ENST00000591565,;DDX39A,downstream_gene_variant,,ENST00000589318,;CD97,downstream_gene_variant,,ENST00000586849,;DDX39A,downstream_gene_variant,,ENST00000587730,;DDX39A,downstream_gene_variant,,ENST00000324340,;DDX39A,downstream_gene_variant,,ENST00000588692,;	A	ENSG00000123146	ENST00000242786	Transcript	missense_variant	1611	1531	511	E/K	Gag/Aag	rs748373111,COSM991864	.	.	1	CD97	HGNC	1711	protein_coding	YES	CCDS32929.1	ENSP00000242786	CD97_HUMAN	.	UPI0000161C9A	.	tolerated(0.44)	benign(0.041)	13/20	.	PROSITE_profiles:PS50221,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF253,Pfam_domain:PF01825,SMART_domains:SM00303	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCGAGGGC	byFrequency	5	ESCA
SSBP4	0	.	GRCh37	19	18541720	18541720	+	Missense_Mutation	SNP	A	A	G	rs151097251	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349A>G	p.Met117Val	p.M117V	ENST00000270061	5/18	161	79	81	146	146	0	SSBP4,missense_variant,p.Met117Val,ENST00000348495,;SSBP4,missense_variant,p.Met139Val,ENST00000597724,;SSBP4,missense_variant,p.Met117Val,ENST00000270061,;SSBP4,missense_variant,p.Met15Val,ENST00000602088,;SSBP4,missense_variant,p.Met15Val,ENST00000601357,;ISYNA1,downstream_gene_variant,,ENST00000338128,;SSBP4,upstream_gene_variant,,ENST00000593641,;SSBP4,upstream_gene_variant,,ENST00000599699,;ISYNA1,downstream_gene_variant,,ENST00000581672,;ISYNA1,downstream_gene_variant,,ENST00000457269,;ISYNA1,downstream_gene_variant,,ENST00000578963,;ISYNA1,downstream_gene_variant,,ENST00000317018,;ISYNA1,downstream_gene_variant,,ENST00000545187,;SSBP4,non_coding_transcript_exon_variant,,ENST00000600628,;SSBP4,non_coding_transcript_exon_variant,,ENST00000598159,;SSBP4,3_prime_UTR_variant,,ENST00000607020,;SSBP4,3_prime_UTR_variant,,ENST00000601614,;SSBP4,upstream_gene_variant,,ENST00000601444,;ISYNA1,downstream_gene_variant,,ENST00000583309,;ISYNA1,downstream_gene_variant,,ENST00000577820,;SSBP4,upstream_gene_variant,,ENST00000600244,;ISYNA1,downstream_gene_variant,,ENST00000582770,;ISYNA1,downstream_gene_variant,,ENST00000582811,;SSBP4,upstream_gene_variant,,ENST00000601919,;ISYNA1,downstream_gene_variant,,ENST00000583816,;ISYNA1,downstream_gene_variant,,ENST00000577916,;ISYNA1,downstream_gene_variant,,ENST00000582287,;	G	ENSG00000130511	ENST00000270061	Transcript	missense_variant	643	349	117	M/V	Atg/Gtg	rs151097251	.	.	1	SSBP4	HGNC	15676	protein_coding	YES	CCDS12378.1	ENSP00000270061	SSBP4_HUMAN	.	UPI0000135F98	.	tolerated(0.37)	benign(0.02)	5/18	.	Pfam_domain:PF04503,hmmpanther:PTHR12610:SF7,hmmpanther:PTHR12610	.	.	.	.	.	.	.	G:0	G:0.0003	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCATGGCG	byFrequency|byCluster	5	ESCA
ZNF556	0	.	GRCh37	19	2877636	2877636	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.680G>C	p.Gly227Ala	p.G227A	ENST00000307635	4/4	45	15	30	44	44	0	ZNF556,missense_variant,p.Gly226Ala,ENST00000586426,;ZNF556,missense_variant,p.Gly227Ala,ENST00000307635,;ZNF556,downstream_gene_variant,,ENST00000586470,;AC006130.4,upstream_gene_variant,,ENST00000586202,;	C	ENSG00000172000	ENST00000307635	Transcript	missense_variant	767	680	227	G/A	gGa/gCa	.	.	.	1	ZNF556	HGNC	25669	protein_coding	YES	CCDS12097.1	ENSP00000302603	ZN556_HUMAN	.	UPI000006DA0F	.	tolerated(0.12)	probably_damaging(0.93)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF142,hmmpanther:PTHR24381,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGGAGAGA	.	5	ESCA
FZR1	0	.	GRCh37	19	3532004	3532004	+	Missense_Mutation	SNP	C	C	T	rs758199150	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.919C>T	p.Arg307Trp	p.R307W	ENST00000395095	9/13	12	10	2	11	11	0	FZR1,missense_variant,p.Arg218Trp,ENST00000313639,;FZR1,missense_variant,p.Arg307Trp,ENST00000395095,;FZR1,missense_variant,p.Arg307Trp,ENST00000441788,;FZR1,missense_variant,p.Arg307Trp,ENST00000591290,;FZR1,upstream_gene_variant,,ENST00000588084,;FZR1,downstream_gene_variant,,ENST00000588327,;FZR1,upstream_gene_variant,,ENST00000586212,;FZR1,downstream_gene_variant,,ENST00000592214,;	T	ENSG00000105325	ENST00000395095	Transcript	missense_variant	919	919	307	R/W	Cgg/Tgg	rs758199150	.	.	1	FZR1	HGNC	24824	protein_coding	YES	CCDS45916.1	ENSP00000378529	FZR_HUMAN	.	UPI00001D6A23	.	deleterious(0)	probably_damaging(0.971)	9/13	.	PROSITE_profiles:PS50294,hmmpanther:PTHR19918:SF6,hmmpanther:PTHR19918,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGAGCGGCGG	.	2	ESCA
UPK1A	0	.	GRCh37	19	36159309	36159309	+	Intron	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85-47G>C	.	.	ENST00000222275	.	23	18	4	33	33	0	UPK1A,intron_variant,,ENST00000222275,;UPK1A,intron_variant,,ENST00000379013,;UPK1A-AS1,non_coding_transcript_exon_variant,,ENST00000443196,;RN7SL765P,downstream_gene_variant,,ENST00000580260,;	C	ENSG00000105668	ENST00000222275	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	UPK1A	HGNC	12577	protein_coding	YES	CCDS12470.1	ENSP00000222275	UPK1A_HUMAN	.	UPI0000137CD9	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCAGGGCTG	.	5	ESCA
ZNF234	0	.	GRCh37	19	44661674	44661674	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1505A>T	p.His502Leu	p.H502L	ENST00000426739	6/6	44	36	8	64	64	0	ZNF234,missense_variant,p.His502Leu,ENST00000592437,;ZNF234,missense_variant,p.His502Leu,ENST00000426739,;	T	ENSG00000263002	ENST00000426739	Transcript	missense_variant	1763	1505	502	H/L	cAt/cTt	.	.	.	1	ZNF234	HGNC	13027	protein_coding	YES	CCDS46101.1	ENSP00000400878	ZN234_HUMAN	Q86WM3_HUMAN,Q86WM2_HUMAN	UPI0000070C95	.	deleterious(0)	probably_damaging(1)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF195,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTCATTGTA	.	5	ESCA
FOXA3	0	.	GRCh37	19	46376187	46376187	+	Missense_Mutation	SNP	C	C	G	rs764381945	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.924C>G	p.Asn308Lys	p.N308K	ENST00000302177	2/2	54	46	8	93	93	0	FOXA3,missense_variant,p.Asn308Lys,ENST00000302177,;FOXA3,downstream_gene_variant,,ENST00000594297,;	G	ENSG00000170608	ENST00000302177	Transcript	missense_variant	1121	924	308	N/K	aaC/aaG	rs764381945	.	.	1	FOXA3	HGNC	5023	protein_coding	YES	CCDS12677.1	ENSP00000304004	FOXA3_HUMAN	M0QZW5_HUMAN	UPI0000000DF9	.	deleterious(0)	probably_damaging(0.913)	2/2	.	hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF55,Pfam_domain:PF09354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAACCTAAT	.	5	ESCA
CD37	0	.	GRCh37	19	49843497	49843497	+	Intron	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.769-11T>A	.	.	ENST00000323906	.	35	31	3	44	44	0	CD37,intron_variant,,ENST00000323906,;CD37,intron_variant,,ENST00000426897,;TEAD2,downstream_gene_variant,,ENST00000311227,;TEAD2,downstream_gene_variant,,ENST00000598810,;TEAD2,downstream_gene_variant,,ENST00000377214,;TEAD2,downstream_gene_variant,,ENST00000593945,;CD37,downstream_gene_variant,,ENST00000597602,;CD37,downstream_gene_variant,,ENST00000535669,;CD37,downstream_gene_variant,,ENST00000594743,;TEAD2,downstream_gene_variant,,ENST00000539846,;CD37,downstream_gene_variant,,ENST00000595660,;CD37,downstream_gene_variant,,ENST00000598095,;TEAD2,downstream_gene_variant,,ENST00000601519,;CTC-301O7.4,non_coding_transcript_exon_variant,,ENST00000358234,;CTC-301O7.4,non_coding_transcript_exon_variant,,ENST00000602554,;CTC-301O7.4,downstream_gene_variant,,ENST00000602721,;CD37,downstream_gene_variant,,ENST00000597033,;CD37,upstream_gene_variant,,ENST00000600121,;CD37,downstream_gene_variant,,ENST00000596426,;CD37,non_coding_transcript_exon_variant,,ENST00000597852,;CD37,intron_variant,,ENST00000391859,;CD37,intron_variant,,ENST00000595725,;CD37,downstream_gene_variant,,ENST00000593512,;CD37,downstream_gene_variant,,ENST00000598134,;	A	ENSG00000104894	ENST00000323906	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CD37	HGNC	1666	protein_coding	YES	CCDS12760.1	ENSP00000325708	CD37_HUMAN	M0R083_HUMAN	UPI0000127350	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCTCCTTTCTC	.	3	ESCA
ZNF841	0	.	GRCh37	19	52568311	52568311	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*49C>G	.	.	ENST00000389534	7/7	15	3	12	27	27	0	ZNF841,3_prime_UTR_variant,,ENST00000601738,;ZNF841,3_prime_UTR_variant,,ENST00000389534,;ZNF841,3_prime_UTR_variant,,ENST00000426391,;ZNF841,3_prime_UTR_variant,,ENST00000594295,;ZNF841,downstream_gene_variant,,ENST00000359973,;ZNF432,upstream_gene_variant,,ENST00000600368,;CTC-471J1.2,upstream_gene_variant,,ENST00000569091,;ZNF432,intron_variant,,ENST00000598446,;ZNF841,downstream_gene_variant,,ENST00000595599,;	C	ENSG00000197608	ENST00000389534	Transcript	3_prime_UTR_variant	3284	.	.	.	.	.	.	.	-1	ZNF841	HGNC	27611	protein_coding	YES	CCDS46161.1	ENSP00000374185	ZN841_HUMAN	M0QYV6_HUMAN	UPI00001D818B	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CATGAGACTTC	.	4	ESCA
PTPRH	0	.	GRCh37	19	55716838	55716838	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000376350	4/20	103	84	18	149	149	0	PTPRH,missense_variant,p.Asp159Tyr,ENST00000376350,;PTPRH,intron_variant,,ENST00000263434,;PTPRH,non_coding_transcript_exon_variant,,ENST00000586310,;PTPRH,non_coding_transcript_exon_variant,,ENST00000588559,;PTPRH,non_coding_transcript_exon_variant,,ENST00000588370,;PTPRH,non_coding_transcript_exon_variant,,ENST00000586852,;PTPRH,downstream_gene_variant,,ENST00000587662,;	A	ENSG00000080031	ENST00000376350	Transcript	missense_variant	498	475	159	D/Y	Gat/Tat	.	.	.	-1	PTPRH	HGNC	9672	protein_coding	YES	CCDS33110.1	ENSP00000365528	PTPRH_HUMAN	.	UPI000006EDE6	.	.	unknown(0)	4/20	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF254,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCATCTCCAG	.	4	ESCA
NLRP9	0	.	GRCh37	19	56243981	56243981	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1216T>A	p.Tyr406Asn	p.Y406N	ENST00000332836	2/9	13	6	7	37	37	0	NLRP9,missense_variant,p.Tyr406Asn,ENST00000332836,;NLRP9,missense_variant,p.Tyr406Asn,ENST00000590200,;RN7SKP109,upstream_gene_variant,,ENST00000410592,;	T	ENSG00000185792	ENST00000332836	Transcript	missense_variant	1244	1216	406	Y/N	Tat/Aat	.	.	.	-1	NLRP9	HGNC	22941	protein_coding	YES	CCDS12934.1	ENSP00000331857	NALP9_HUMAN	.	UPI00001B6B39	.	tolerated(0.27)	benign(0.035)	2/9	.	hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TGTATATGTCC	.	4	ESCA
NLRP8	0	.	GRCh37	19	56467027	56467027	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1603C>G	p.His535Asp	p.H535D	ENST00000291971	3/10	49	45	4	58	58	0	NLRP8,missense_variant,p.His535Asp,ENST00000590542,;NLRP8,missense_variant,p.His535Asp,ENST00000291971,;	G	ENSG00000179709	ENST00000291971	Transcript	missense_variant	1674	1603	535	H/D	Cac/Gac	.	.	.	1	NLRP8	HGNC	22940	protein_coding	YES	CCDS12937.1	ENSP00000291971	NALP8_HUMAN	.	UPI00001BB3C9	.	tolerated(0.2)	benign(0.077)	3/10	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGAGCCACGTG	.	3	ESCA
ACSBG2	0	.	GRCh37	19	6190785	6190785	+	Intron	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*35+82G>C	.	.	ENST00000586696	.	12	7	5	11	11	0	ACSBG2,intron_variant,,ENST00000586696,;ACSBG2,intron_variant,,ENST00000591403,;ACSBG2,intron_variant,,ENST00000588485,;ACSBG2,intron_variant,,ENST00000252669,;ACSBG2,intron_variant,,ENST00000588304,;RFX2,intron_variant,,ENST00000592883,;RFX2,non_coding_transcript_exon_variant,,ENST00000587700,;RFX2,intron_variant,,ENST00000585324,;RFX2,intron_variant,,ENST00000589712,;ACSBG2,intron_variant,,ENST00000591741,;RFX2,downstream_gene_variant,,ENST00000589641,;RFX2,downstream_gene_variant,,ENST00000589523,;ACSBG2,intron_variant,,ENST00000590132,;	C	ENSG00000130377	ENST00000586696	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ACSBG2	HGNC	24174	protein_coding	YES	CCDS12159.1	ENSP00000465589	ACBG2_HUMAN	K7ESC8_HUMAN,K7ERT0_HUMAN,K7EL11_HUMAN	UPI00001414E6	.	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCTGTGACTGG	.	3	ESCA
ZNF559	0	.	GRCh37	19	9448582	9448582	+	Intron	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-57+48T>A	.	.	ENST00000393883	.	18	12	6	38	38	0	ZNF559,5_prime_UTR_variant,,ENST00000592896,;ZNF559,5_prime_UTR_variant,,ENST00000586255,;ZNF559,5_prime_UTR_variant,,ENST00000585377,;ZNF559,5_prime_UTR_variant,,ENST00000588124,;ZNF559,intron_variant,,ENST00000589208,;ZNF559,intron_variant,,ENST00000538743,;ZNF559,intron_variant,,ENST00000393883,;ZNF177,intron_variant,,ENST00000602856,;ZNF559,intron_variant,,ENST00000603380,;ZNF559,intron_variant,,ENST00000587557,;ZNF559-ZNF177,intron_variant,,ENST00000603656,;ZNF177,intron_variant,,ENST00000602738,;ZNF559,intron_variant,,ENST00000605750,;ZNF559,intron_variant,,ENST00000592504,;ZNF559,intron_variant,,ENST00000317221,;ZNF559-ZNF177,intron_variant,,ENST00000446085,;ZNF559,intron_variant,,ENST00000592298,;ZNF559-ZNF177,intron_variant,,ENST00000541595,;ZNF559,intron_variant,,ENST00000585352,;ZNF559,upstream_gene_variant,,ENST00000591652,;ZNF559-ZNF177,non_coding_transcript_exon_variant,,ENST00000605301,;ZNF559-ZNF177,intron_variant,,ENST00000605522,;ZNF559-ZNF177,intron_variant,,ENST00000605471,;ZNF559-ZNF177,intron_variant,,ENST00000603099,;ZNF559-ZNF177,intron_variant,,ENST00000605775,;ZNF559-ZNF177,intron_variant,,ENST00000603974,;ZNF559-ZNF177,intron_variant,,ENST00000604886,;ZNF559-ZNF177,intron_variant,,ENST00000605093,;ZNF559-ZNF177,intron_variant,,ENST00000593242,;ZNF559-ZNF177,intron_variant,,ENST00000604543,;ZNF559-ZNF177,intron_variant,,ENST00000605071,;ZNF559-ZNF177,intron_variant,,ENST00000603024,;ZNF559-ZNF177,intron_variant,,ENST00000605006,;	A	ENSG00000188321	ENST00000393883	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZNF559	HGNC	28197	protein_coding	YES	CCDS12211.1	ENSP00000377461	ZN559_HUMAN	S4R3F2_HUMAN,K7ERK9_HUMAN,B4DP29_HUMAN	UPI00000733B2	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGATTGACTT	.	2	ESCA
C1orf159	0	.	GRCh37	1	1026335	1026335	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72+517A>G	.	.	ENST00000421241	.	48	38	10	64	64	0	C1orf159,missense_variant,p.Asn34Ser,ENST00000379339,;C1orf159,missense_variant,p.Asn34Ser,ENST00000448924,;C1orf159,intron_variant,,ENST00000294576,;C1orf159,intron_variant,,ENST00000427787,;C1orf159,intron_variant,,ENST00000379319,;C1orf159,intron_variant,,ENST00000442117,;C1orf159,intron_variant,,ENST00000379320,;C1orf159,intron_variant,,ENST00000475119,;C1orf159,intron_variant,,ENST00000462097,;C1orf159,intron_variant,,ENST00000421241,;C1orf159,intron_variant,,ENST00000434641,;C1orf159,intron_variant,,ENST00000437760,;C1orf159,downstream_gene_variant,,ENST00000480643,;C1orf159,intron_variant,,ENST00000482816,;C1orf159,3_prime_UTR_variant,,ENST00000477196,;C1orf159,intron_variant,,ENST00000467751,;C1orf159,intron_variant,,ENST00000473600,;C1orf159,intron_variant,,ENST00000465822,;C1orf159,intron_variant,,ENST00000379325,;C1orf159,downstream_gene_variant,,ENST00000472741,;C1orf159,upstream_gene_variant,,ENST00000487177,;	C	ENSG00000131591	ENST00000421241	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	C1orf159	HGNC	26062	protein_coding	YES	CCDS7.2	ENSP00000400736	CA159_HUMAN	J3QRL0_HUMAN,J3KSJ6_HUMAN,B2REC4_HUMAN	UPI0000049DAC	.	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGTTGATC	.	5	ESCA
AMY2B	0	.	GRCh37	1	104114789	104114789	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226A>G	p.Arg76Gly	p.R76G	ENST00000361355	4/12	257	124	132	401	401	0	AMY2B,missense_variant,p.Arg76Gly,ENST00000435302,;AMY2B,missense_variant,p.Arg76Gly,ENST00000361355,;AMY2B,missense_variant,p.Arg76Gly,ENST00000453959,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,missense_variant,p.Arg76Gly,ENST00000477657,;ACTG1P4,downstream_gene_variant,,ENST00000425123,;	G	ENSG00000240038	ENST00000361355	Transcript	missense_variant	842	226	76	R/G	Aga/Gga	.	.	.	1	AMY2B	HGNC	478	protein_coding	YES	CCDS782.1	ENSP00000354610	AMY2B_HUMAN	C9JWK7_HUMAN,C9J2Z5_HUMAN	UPI0000000CB1	.	deleterious(0.01)	probably_damaging(0.999)	4/12	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Gene3D:3.20.20.80,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445,Prints_domain:PR00110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAAGATAC	.	5	ESCA
CHIAP2	0	.	GRCh37	1	111827665	111827665	+	RNA	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1764T>C	.	.	ENST00000369743	9/9	61	32	29	70	70	0	CHIAP2,non_coding_transcript_exon_variant,,ENST00000449687,;CHIAP2,non_coding_transcript_exon_variant,,ENST00000369743,;CHIAP2,downstream_gene_variant,,ENST00000456752,;CHIAP2,non_coding_transcript_exon_variant,,ENST00000532686,;	C	ENSG00000203878	ENST00000369743	Transcript	non_coding_transcript_exon_variant	1764	.	.	.	.	.	.	.	1	CHIAP2	HGNC	44463	processed_transcript	YES	.	.	.	.	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGATTTCAC	.	5	ESCA
HIPK1	0	.	GRCh37	1	114483016	114483016	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11A>T	p.Gln4Leu	p.Q4L	ENST00000369558	2/16	46	31	14	47	47	0	HIPK1,missense_variant,p.Gln4Leu,ENST00000503968,;HIPK1,missense_variant,p.Gln4Leu,ENST00000369559,;HIPK1,missense_variant,p.Gln4Leu,ENST00000514621,;HIPK1,missense_variant,p.Gln4Leu,ENST00000369561,;HIPK1,missense_variant,p.Gln4Leu,ENST00000369558,;HIPK1,missense_variant,p.Gln4Leu,ENST00000369554,;HIPK1,missense_variant,p.Gln4Leu,ENST00000369555,;HIPK1,missense_variant,p.Gln4Leu,ENST00000426820,;	T	ENSG00000163349	ENST00000369558	Transcript	missense_variant	243	11	4	Q/L	cAg/cTg	.	.	.	1	HIPK1	HGNC	19006	protein_coding	YES	CCDS867.1	ENSP00000358571	HIPK1_HUMAN	D6RF28_HUMAN,D6RC95_HUMAN	UPI000000D74E	.	deleterious(0)	unknown(0)	2/16	.	hmmpanther:PTHR24058:SF43,hmmpanther:PTHR24058,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACAGCTGC	.	5	ESCA
HMGCS2	0	.	GRCh37	1	120298175	120298175	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1062A>C	p.Lys354Asn	p.K354N	ENST00000369406	6/10	67	54	13	68	68	0	HMGCS2,missense_variant,p.Lys312Asn,ENST00000544913,;HMGCS2,missense_variant,p.Lys354Asn,ENST00000369406,;HMGCS2,non_coding_transcript_exon_variant,,ENST00000476640,;HMGCS2,non_coding_transcript_exon_variant,,ENST00000472375,;	G	ENSG00000134240	ENST00000369406	Transcript	missense_variant	1112	1062	354	K/N	aaA/aaC	.	.	.	-1	HMGCS2	HGNC	5008	protein_coding	YES	CCDS905.1	ENSP00000358414	HMCS2_HUMAN	.	UPI000000DA7A	.	deleterious(0.01)	possibly_damaging(0.805)	6/10	.	hmmpanther:PTHR11877,hmmpanther:PTHR11877:SF16,Pfam_domain:PF08540,TIGRFAM_domain:TIGR01833,Superfamily_domains:SSF53901	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCTTTATC	.	5	ESCA
ATAD3C	0	.	GRCh37	1	1396169	1396169	+	Silent	SNP	C	C	T	rs746646562	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852C>T	p.%3D	p.F284F	ENST00000378785	10/12	78	51	26	69	69	0	ATAD3C,synonymous_variant,p.%3D,ENST00000378785,;ATAD3C,downstream_gene_variant,,ENST00000475091,;ATAD3C,upstream_gene_variant,,ENST00000484537,;	T	ENSG00000215915	ENST00000378785	Transcript	synonymous_variant	1847	852	284	F	ttC/ttT	rs746646562	.	.	1	ATAD3C	HGNC	32151	protein_coding	YES	CCDS44039.1	ENSP00000368062	ATD3C_HUMAN	.	UPI00001619C0	.	.	.	10/12	.	hmmpanther:PTHR23075,hmmpanther:PTHR23075:SF5,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCGACTG	byFrequency	5	ESCA
SEC22B	0	.	GRCh37	1	145116546	145116546	+	RNA	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1632T>A	.	.	ENST00000453618	5/5	142	130	11	125	125	0	SEC22B,non_coding_transcript_exon_variant,,ENST00000453618,;	A	ENSG00000223380	ENST00000453618	Transcript	non_coding_transcript_exon_variant	1632	.	.	.	.	.	.	.	1	SEC22B	HGNC	10700	processed_transcript	YES	.	.	.	.	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TATATTAAGAT	.	3	ESCA
TMEM240	0	.	GRCh37	1	1470689	1470689	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50A>T	.	.	ENST00000378733	4/4	12	8	4	8	8	0	TMEM240,3_prime_UTR_variant,,ENST00000378733,;TMEM240,3_prime_UTR_variant,,ENST00000425828,;ATAD3A,downstream_gene_variant,,ENST00000536055,;ATAD3A,downstream_gene_variant,,ENST00000378756,;ATAD3A,downstream_gene_variant,,ENST00000339113,;ATAD3A,downstream_gene_variant,,ENST00000378755,;	A	ENSG00000205090	ENST00000378733	Transcript	3_prime_UTR_variant	583	.	.	.	.	.	.	.	-1	TMEM240	HGNC	25186	protein_coding	YES	CCDS44040.1	ENSP00000368007	TM240_HUMAN	.	UPI0000418FB6	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTACATCTGTA	.	2	ESCA
TRIM46	0	.	GRCh37	1	155147392	155147392	+	Intron	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64-470T>A	.	.	ENST00000334634	.	13	10	3	28	28	0	TRIM46,intron_variant,,ENST00000368382,;TRIM46,intron_variant,,ENST00000392451,;TRIM46,intron_variant,,ENST00000334634,;TRIM46,intron_variant,,ENST00000543729,;TRIM46,intron_variant,,ENST00000368383,;TRIM46,intron_variant,,ENST00000545012,;TRIM46,intron_variant,,ENST00000368385,;RP11-201K10.3,intron_variant,,ENST00000473363,;KRTCAP2,upstream_gene_variant,,ENST00000295682,;TRIM46,non_coding_transcript_exon_variant,,ENST00000468878,;TRIM46,intron_variant,,ENST00000474430,;TRIM46,intron_variant,,ENST00000464760,;KRTCAP2,upstream_gene_variant,,ENST00000492892,;KRTCAP2,upstream_gene_variant,,ENST00000463527,;KRTCAP2,upstream_gene_variant,,ENST00000461136,;KRTCAP2,upstream_gene_variant,,ENST00000487350,;KRTCAP2,upstream_gene_variant,,ENST00000491084,;KRTCAP2,upstream_gene_variant,,ENST00000490672,;KRTCAP2,upstream_gene_variant,,ENST00000471891,;KRTCAP2,upstream_gene_variant,,ENST00000482246,;KRTCAP2,upstream_gene_variant,,ENST00000497317,;	A	ENSG00000163462	ENST00000334634	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TRIM46	HGNC	19019	protein_coding	YES	CCDS1097.1	ENSP00000334657	TRI46_HUMAN	F5GYK0_HUMAN	UPI000022B316	.	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACGTATGGAGC	.	2	ESCA
FCRL5	0	.	GRCh37	1	157512730	157512730	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1042G>A	p.Glu348Lys	p.E348K	ENST00000361835	6/17	38	30	7	40	40	0	FCRL5,missense_variant,p.Glu348Lys,ENST00000361835,;FCRL5,missense_variant,p.Glu348Lys,ENST00000368190,;FCRL5,missense_variant,p.Glu348Lys,ENST00000368189,;FCRL5,missense_variant,p.Glu348Lys,ENST00000356953,;FCRL5,missense_variant,p.Glu263Lys,ENST00000368191,;FCRL5,downstream_gene_variant,,ENST00000368188,;FCRL5,non_coding_transcript_exon_variant,,ENST00000481082,;	T	ENSG00000143297	ENST00000361835	Transcript	missense_variant	1200	1042	348	E/K	Gag/Aag	.	.	.	-1	FCRL5	HGNC	18508	protein_coding	YES	CCDS1165.1	ENSP00000354691	FCRL5_HUMAN	.	UPI0000458907	.	tolerated(0.48)	possibly_damaging(0.526)	6/17	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00408,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF49,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCTCTGTAG	.	5	ESCA
OR10R2	0	.	GRCh37	1	158449905	158449905	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.238T>C	p.Tyr80His	p.Y80H	ENST00000368152	1/1	38	29	9	40	40	0	OR10R2,missense_variant,p.Tyr80His,ENST00000368152,;RP11-144L1.4,non_coding_transcript_exon_variant,,ENST00000419738,;RP11-144L1.4,intron_variant,,ENST00000426251,;	C	ENSG00000198965	ENST00000368152	Transcript	missense_variant	238	238	80	Y/H	Tac/Cac	.	.	.	1	OR10R2	HGNC	14820	protein_coding	YES	CCDS30898.1	ENSP00000357134	O10R2_HUMAN	.	UPI000004CA1C	.	deleterious(0)	probably_damaging(1)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF42,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F82F|c.246C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAATGTACTTC	.	5	ESCA
FCGR3A	0	.	GRCh37	1	161519707	161519707	+	5'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-73G>A	.	.	ENST00000367969	1/5	62	43	19	75	75	0	FCGR3A,5_prime_UTR_variant,,ENST00000367969,;FCGR3A,5_prime_UTR_variant,,ENST00000443193,;FCGR3A,intron_variant,,ENST00000540048,;FCGR3A,intron_variant,,ENST00000436743,;FCGR3A,intron_variant,,ENST00000442336,;FCGR3A,intron_variant,,ENST00000367967,;FCGR3A,upstream_gene_variant,,ENST00000426740,;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR3A,upstream_gene_variant,,ENST00000476031,;	T	ENSG00000203747	ENST00000367969	Transcript	5_prime_UTR_variant	112	.	.	.	.	.	.	.	-1	FCGR3A	HGNC	3619	protein_coding	YES	CCDS1232.1	ENSP00000356946	.	M9MML0_HUMAN,Q9UN20_HUMAN	UPI000013E1BC	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCCCACCA	.	5	ESCA
PRRC2C	0	.	GRCh37	1	171535752	171535752	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6322G>C	p.Glu2108Gln	p.E2108Q	ENST00000338920	22/34	23	17	6	44	44	0	PRRC2C,missense_variant,p.Glu2108Gln,ENST00000338920,;PRRC2C,missense_variant,p.Glu2110Gln,ENST00000367742,;PRRC2C,missense_variant,p.Glu2108Gln,ENST00000426496,;PRRC2C,missense_variant,p.Glu2110Gln,ENST00000392078,;PRRC2C,missense_variant,p.Glu656Gln,ENST00000495585,;	C	ENSG00000117523	ENST00000338920	Transcript	missense_variant	6559	6322	2108	E/Q	Gaa/Caa	.	.	.	1	PRRC2C	HGNC	24903	protein_coding	YES	CCDS1296.2	ENSP00000343629	PRC2C_HUMAN	.	UPI0000E265EC	.	.	probably_damaging(0.97)	22/34	.	hmmpanther:PTHR14038:SF6,hmmpanther:PTHR14038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CAGTAGAAAAC	.	4	ESCA
ASTN1	0	.	GRCh37	1	176832564	176832564	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*856G>C	.	.	ENST00000361833	23/23	27	19	8	24	24	0	ASTN1,3_prime_UTR_variant,,ENST00000367654,;ASTN1,3_prime_UTR_variant,,ENST00000361833,;ASTN1,intron_variant,,ENST00000367657,;	G	ENSG00000152092	ENST00000361833	Transcript	3_prime_UTR_variant	4755	.	.	.	.	.	.	.	-1	ASTN1	HGNC	773	protein_coding	YES	CCDS1319.1	ENSP00000354536	ASTN1_HUMAN	Q96BL7_HUMAN	UPI0000160388	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGTCTATCC	.	5	ESCA
FAM20B	0	.	GRCh37	1	179013235	179013235	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.253G>A	p.Gly85Arg	p.G85R	ENST00000263733	2/8	35	22	12	43	43	0	FAM20B,missense_variant,p.Gly85Arg,ENST00000440702,;FAM20B,missense_variant,p.Gly85Arg,ENST00000263733,;	A	ENSG00000116199	ENST00000263733	Transcript	missense_variant	589	253	85	G/R	Ggg/Agg	.	.	.	1	FAM20B	HGNC	23017	protein_coding	YES	CCDS1328.1	ENSP00000263733	XYLK_HUMAN	.	UPI000000DB7F	.	deleterious(0.01)	benign(0.285)	2/8	.	hmmpanther:PTHR12450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V87A|c.260T>C|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGGGGGCA	.	5	ESCA
ERVMER61-1	0	.	GRCh37	1	187611070	187611070	+	RNA	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.471C>A	.	.	ENST00000429725	3/3	28	22	6	31	31	0	ERVMER61-1,non_coding_transcript_exon_variant,,ENST00000429725,;	A	ENSG00000230426	ENST00000429725	Transcript	non_coding_transcript_exon_variant	471	.	.	.	.	.	.	.	1	ERVMER61-1	HGNC	27919	lincRNA	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATCCCTGTGT	.	5	ESCA
IGFN1	0	.	GRCh37	1	201187713	201187713	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9825C>A	p.%3D	p.V3275V	ENST00000335211	18/24	43	35	8	48	48	0	IGFN1,synonymous_variant,p.%3D,ENST00000295591,;IGFN1,synonymous_variant,p.%3D,ENST00000412892,;IGFN1,synonymous_variant,p.%3D,ENST00000335211,;IGFN1,downstream_gene_variant,,ENST00000451870,;RP11-567E21.3,downstream_gene_variant,,ENST00000453155,;IGFN1,3_prime_UTR_variant,,ENST00000437879,;IGFN1,non_coding_transcript_exon_variant,,ENST00000473483,;	A	ENSG00000163395	ENST00000335211	Transcript	synonymous_variant	9955	9825	3275	V	gtC/gtA	.	.	.	1	IGFN1	HGNC	24607	protein_coding	YES	CCDS53455.1	ENSP00000334714	IGFN1_HUMAN	.	UPI0001B300F4	.	.	.	18/24	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,Pfam_domain:PF00041,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF145,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGTCACAGC	.	5	ESCA
EIF4G3	0	.	GRCh37	1	21503254	21503254	+	5'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-495G>T	.	.	ENST00000602326	1/35	37	14	23	45	45	0	EIF4G3,5_prime_UTR_variant,,ENST00000400422,;EIF4G3,5_prime_UTR_variant,,ENST00000438975,;EIF4G3,5_prime_UTR_variant,,ENST00000602326,;EIF4G3,5_prime_UTR_variant,,ENST00000411888,;EIF4G3,upstream_gene_variant,,ENST00000356916,;AL031005.1,upstream_gene_variant,,ENST00000584440,;	A	ENSG00000075151	ENST00000602326	Transcript	5_prime_UTR_variant	90	.	.	.	.	.	.	.	-1	EIF4G3	HGNC	3298	protein_coding	YES	CCDS55580.1	ENSP00000473510	IF4G3_HUMAN	Q59GJ0_HUMAN,F5H564_HUMAN	UPI0001639589	.	.	.	1/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGGATCTTTAT	.	4	ESCA
KCNK2	0	.	GRCh37	1	215259722	215259722	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>A	p.Asp20Asn	p.D20N	ENST00000444842	2/7	95	78	16	67	67	0	KCNK2,missense_variant,p.Asp20Asn,ENST00000444842,;KCNK2,missense_variant,p.Asp16Asn,ENST00000391895,;KCNK2,missense_variant,p.Asp5Asn,ENST00000391894,;KCNK2,5_prime_UTR_variant,,ENST00000478774,;KCNK2,5_prime_UTR_variant,,ENST00000457122,;KCNK2,missense_variant,p.Asp16Asn,ENST00000486921,;KCNK2,missense_variant,p.Asp20Asn,ENST00000470177,;KCNK2,missense_variant,p.Asp5Asn,ENST00000474771,;KCNK2,missense_variant,p.Asp16Asn,ENST00000467031,;	A	ENSG00000082482	ENST00000444842	Transcript	missense_variant	208	58	20	D/N	Gac/Aac	.	.	.	1	KCNK2	HGNC	6277	protein_coding	YES	CCDS41467.1	ENSP00000394033	KCNK2_HUMAN	C9JXY2_HUMAN,C9JDK1_HUMAN	UPI000013D4B8	.	tolerated_low_confidence(0.07)	probably_damaging(0.998)	2/7	.	hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF21,Prints_domain:PR01499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTGACTTG	.	5	ESCA
USH2A	0	.	GRCh37	1	216062375	216062375	+	Missense_Mutation	SNP	G	G	A	rs147333637	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7616C>T	p.Pro2539Leu	p.P2539L	ENST00000307340	41/72	33	25	8	32	32	0	USH2A,missense_variant,p.Pro2539Leu,ENST00000366943,;USH2A,missense_variant,p.Pro2539Leu,ENST00000307340,;RP5-1111A8.3,intron_variant,,ENST00000414995,;	A	ENSG00000042781	ENST00000307340	Transcript	missense_variant	8003	7616	2539	P/L	cCg/cTg	rs147333637	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	probably_damaging(0.998)	41/72	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Gene3D:2.60.40.10,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50853	A:0.0012	A:0.0008	A:0	.	A:0.003	A:0.002	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCGGAGGA	byFrequency|byCluster|by1000G	5	ESCA
DNAH14	0	.	GRCh37	1	225268267	225268267	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.187G>A	p.Val63Met	p.V63M	ENST00000328556	1/20	47	23	23	27	27	0	DNAH14,missense_variant,p.Val63Met,ENST00000328556,;DNAH14,missense_variant,p.Val919Met,ENST00000445597,;DNAH14,missense_variant,p.Val985Met,ENST00000430092,;DNAH14,missense_variant,p.Val985Met,ENST00000439375,;	A	ENSG00000185842	ENST00000328556	Transcript	missense_variant	187	187	63	V/M	Gtg/Atg	.	.	.	1	DNAH14	HGNC	2945	protein_coding	.	.	ENSP00000332424	.	H9KV43_HUMAN	UPI000198C4F6	.	tolerated(0.08)	benign(0.246)	1/20	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF132	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTGTGCTT	.	5	ESCA
MAP10	0	.	GRCh37	1	232946075	232946075	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2162G>C	.	.	ENST00000418460	1/1	30	20	9	31	31	0	MAP10,3_prime_UTR_variant,,ENST00000418460,;	C	ENSG00000212916	ENST00000418460	Transcript	3_prime_UTR_variant	5433	.	.	.	.	.	.	.	1	MAP10	HGNC	29265	protein_coding	YES	CCDS44334.1	ENSP00000403208	MAP10_HUMAN	.	UPI0000418F25	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AACATGAAATA	.	4	ESCA
CEP85	0	.	GRCh37	1	26604553	26604553	+	3'UTR	SNP	C	C	A	rs550448673	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*769C>A	.	.	ENST00000252992	14/14	13	5	8	13	13	0	CEP85,3_prime_UTR_variant,,ENST00000252992,;CEP85,3_prime_UTR_variant,,ENST00000453146,;UBXN11,downstream_gene_variant,,ENST00000374217,;UBXN11,downstream_gene_variant,,ENST00000374222,;UBXN11,downstream_gene_variant,,ENST00000357089,;UBXN11,downstream_gene_variant,,ENST00000314675,;CEP85,downstream_gene_variant,,ENST00000451429,;SH3BGRL3,upstream_gene_variant,,ENST00000319041,;UBXN11,downstream_gene_variant,,ENST00000374221,;SH3BGRL3,upstream_gene_variant,,ENST00000270792,;UBXN11,downstream_gene_variant,,ENST00000374223,;CEP85,non_coding_transcript_exon_variant,,ENST00000469609,;CEP85,downstream_gene_variant,,ENST00000491670,;CEP85,3_prime_UTR_variant,,ENST00000476272,;UBXN11,downstream_gene_variant,,ENST00000496466,;UBXN11,downstream_gene_variant,,ENST00000475591,;UBXN11,downstream_gene_variant,,ENST00000494942,;UBXN11,downstream_gene_variant,,ENST00000472155,;	A	ENSG00000130695	ENST00000252992	Transcript	3_prime_UTR_variant	3189	.	.	.	.	rs550448673	.	.	1	CEP85	HGNC	25309	protein_coding	YES	CCDS277.1	ENSP00000252992	CEP85_HUMAN	.	UPI0000231C37	.	.	.	14/14	.	.	G:0.0004	G:0.0015	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CTCTTCTCTGT	byFrequency|by1000G	4	ESCA
LRRC7	0	.	GRCh37	1	70397207	70397207	+	Missense_Mutation	SNP	C	C	G	rs755151095	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.551C>G	p.Ala184Gly	p.A184G	ENST00000035383	6/25	78	62	16	71	71	0	LRRC7,missense_variant,p.Ala184Gly,ENST00000035383,;LRRC7,missense_variant,p.Ala189Gly,ENST00000310961,;LRRC7,5_prime_UTR_variant,,ENST00000415775,;	G	ENSG00000033122	ENST00000035383	Transcript	missense_variant	581	551	184	A/G	gCc/gGc	rs755151095,COSM1503350	.	.	1	LRRC7	HGNC	18531	protein_coding	YES	CCDS645.1	ENSP00000035383	LRRC7_HUMAN	.	UPI000006F29B	.	deleterious(0.01)	benign(0.007)	6/25	.	hmmpanther:PTHR23155:SF459,hmmpanther:PTHR23155,Pfam_domain:PF12799,Gene3D:3.80.10.10,SMART_domains:SM00365,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGGCCCAGT	.	5	ESCA
ANKRD13C	0	.	GRCh37	1	70727271	70727271	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1129C>A	.	.	ENST00000370944	13/13	9	7	2	11	11	0	ANKRD13C,3_prime_UTR_variant,,ENST00000370944,;ANKRD13C,3_prime_UTR_variant,,ENST00000262346,;ANKRD13C,downstream_gene_variant,,ENST00000464236,;	T	ENSG00000118454	ENST00000370944	Transcript	3_prime_UTR_variant	3069	.	.	.	.	.	.	.	-1	ANKRD13C	HGNC	25374	protein_coding	YES	CCDS648.2	ENSP00000359982	AN13C_HUMAN	.	UPI0000140CE0	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGGAGACAAT	.	2	ESCA
PKN2	0	.	GRCh37	1	89289999	89289999	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2349G>C	p.Leu783Phe	p.L783F	ENST00000370521	18/22	66	41	24	94	94	0	PKN2,missense_variant,p.Leu735Phe,ENST00000370513,;PKN2,missense_variant,p.Leu626Phe,ENST00000370505,;PKN2,missense_variant,p.Leu783Phe,ENST00000370521,;PKN2,missense_variant,p.Leu457Phe,ENST00000544045,;PKN2,upstream_gene_variant,,ENST00000449189,;TCEB1P19,upstream_gene_variant,,ENST00000411919,;	C	ENSG00000065243	ENST00000370521	Transcript	missense_variant	2708	2349	783	L/F	ttG/ttC	.	.	.	1	PKN2	HGNC	9406	protein_coding	YES	CCDS714.1	ENSP00000359552	PKN2_HUMAN	Q6P5W9_HUMAN	UPI000004D291	.	deleterious(0.01)	probably_damaging(0.997)	18/22	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24357:SF76,hmmpanther:PTHR24357,PROSITE_patterns:PS00108,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTTGAAATT	.	5	ESCA
SNX7	0	.	GRCh37	1	99150484	99150484	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224C>A	p.Pro75Gln	p.P75Q	ENST00000306121	2/9	48	32	16	55	55	0	SNX7,missense_variant,p.Pro11Gln,ENST00000370189,;SNX7,missense_variant,p.Pro75Gln,ENST00000306121,;SNX7,missense_variant,p.Pro75Gln,ENST00000529992,;SNX7,missense_variant,p.Pro11Gln,ENST00000454199,;SNX7,3_prime_UTR_variant,,ENST00000528824,;	A	ENSG00000162627	ENST00000306121	Transcript	missense_variant	233	224	75	P/Q	cCa/cAa	.	.	.	1	SNX7	HGNC	14971	protein_coding	YES	CCDS755.2	ENSP00000304429	SNX7_HUMAN	B7ZC83_HUMAN	UPI0000205396	.	deleterious(0.04)	possibly_damaging(0.477)	2/9	.	hmmpanther:PTHR10555:SF21,hmmpanther:PTHR10555	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGCCAACAT	.	5	ESCA
MYH7B	0	.	GRCh37	20	33577641	33577641	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1812G>T	p.Lys604Asn	p.K604N	ENST00000262873	18/43	75	57	18	80	80	0	MYH7B,missense_variant,p.Lys604Asn,ENST00000262873,;MIR499A,upstream_gene_variant,,ENST00000384903,;	T	ENSG00000078814	ENST00000262873	Transcript	missense_variant	1904	1812	604	K/N	aaG/aaT	.	.	.	1	MYH7B	HGNC	15906	protein_coding	YES	CCDS42869.1	ENSP00000262873	MYH7B_HUMAN	.	UPI0000253BD4	.	.	probably_damaging(0.999)	18/43	.	PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF310,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGGAAGTCACC	.	4	ESCA
RIMS4	0	.	GRCh37	20	43386383	43386383	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382A>C	p.Asn128His	p.N128H	ENST00000541604	4/6	37	22	14	33	33	0	RIMS4,missense_variant,p.Asn128His,ENST00000541604,;RIMS4,missense_variant,p.Asn127His,ENST00000372851,;	G	ENSG00000101098	ENST00000541604	Transcript	missense_variant	382	382	128	N/H	Aac/Cac	.	.	.	-1	RIMS4	HGNC	16183	protein_coding	YES	CCDS56191.1	ENSP00000439287	RIMS4_HUMAN	.	UPI0000367043	.	deleterious_low_confidence(0)	possibly_damaging(0.548)	4/6	.	Superfamily_domains:SSF49562,Gene3D:2.60.40.150,hmmpanther:PTHR12157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGTTCCGCT	.	5	ESCA
DNTTIP1	0	.	GRCh37	20	44439840	44439840	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6G>C	.	.	ENST00000372622	13/13	38	32	5	42	42	0	DNTTIP1,3_prime_UTR_variant,,ENST00000372622,;DNTTIP1,3_prime_UTR_variant,,ENST00000435014,;DNTTIP1,3_prime_UTR_variant,,ENST00000456939,;UBE2C,upstream_gene_variant,,ENST00000352551,;UBE2C,upstream_gene_variant,,ENST00000372568,;UBE2C,upstream_gene_variant,,ENST00000243893,;UBE2C,upstream_gene_variant,,ENST00000356455,;UBE2C,upstream_gene_variant,,ENST00000405520,;UBE2C,upstream_gene_variant,,ENST00000335046,;UBE2C,upstream_gene_variant,,ENST00000496085,;	C	ENSG00000101457	ENST00000372622	Transcript	3_prime_UTR_variant	1064	.	.	.	.	.	.	.	1	DNTTIP1	HGNC	16160	protein_coding	YES	CCDS13369.1	ENSP00000361705	TDIF1_HUMAN	F2Z2A4_HUMAN	UPI0000136B4E	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCGGGTCCC	.	5	ESCA
ZSWIM1	0	.	GRCh37	20	44513275	44513275	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*586A>G	.	.	ENST00000372523	2/2	120	82	38	61	61	0	ZSWIM1,3_prime_UTR_variant,,ENST00000372523,;ZSWIM1,intron_variant,,ENST00000372520,;NEURL2,downstream_gene_variant,,ENST00000372518,;NEURL2,downstream_gene_variant,,ENST00000545238,;SPATA25,downstream_gene_variant,,ENST00000372519,;	G	ENSG00000168612	ENST00000372523	Transcript	3_prime_UTR_variant	2139	.	.	.	.	.	.	.	1	ZSWIM1	HGNC	16155	protein_coding	YES	CCDS13382.2	ENSP00000361601	ZSWM1_HUMAN	A8K5I9_HUMAN	UPI0000470896	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	GGATTACAGGC	.	2	ESCA
ZSWIM1	0	.	GRCh37	20	44513394	44513394	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*705A>G	.	.	ENST00000372523	2/2	79	58	21	57	57	0	ZSWIM1,3_prime_UTR_variant,,ENST00000372523,;ZSWIM1,intron_variant,,ENST00000372520,;NEURL2,downstream_gene_variant,,ENST00000372518,;NEURL2,downstream_gene_variant,,ENST00000545238,;SPATA25,downstream_gene_variant,,ENST00000372519,;	G	ENSG00000168612	ENST00000372523	Transcript	3_prime_UTR_variant	2258	.	.	.	.	.	.	.	1	ZSWIM1	HGNC	16155	protein_coding	YES	CCDS13382.2	ENSP00000361601	ZSWM1_HUMAN	A8K5I9_HUMAN	UPI0000470896	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCTGTAATCCC	.	3	ESCA
ZSWIM1	0	.	GRCh37	20	44513395	44513395	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*706A>G	.	.	ENST00000372523	2/2	81	59	21	59	59	0	ZSWIM1,3_prime_UTR_variant,,ENST00000372523,;ZSWIM1,intron_variant,,ENST00000372520,;NEURL2,downstream_gene_variant,,ENST00000372518,;NEURL2,downstream_gene_variant,,ENST00000545238,;SPATA25,downstream_gene_variant,,ENST00000372519,;	G	ENSG00000168612	ENST00000372523	Transcript	3_prime_UTR_variant	2259	.	.	.	.	.	.	.	1	ZSWIM1	HGNC	16155	protein_coding	YES	CCDS13382.2	ENSP00000361601	ZSWM1_HUMAN	A8K5I9_HUMAN	UPI0000470896	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTAATCCCA	.	4	ESCA
TAF4	0	.	GRCh37	20	60581599	60581599	+	Silent	SNP	G	G	A	rs145691580	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2190C>T	p.%3D	p.V730V	ENST00000252996	7/15	102	84	17	58	58	0	TAF4,synonymous_variant,p.%3D,ENST00000252996,;TAF4,splice_region_variant,,ENST00000488539,;TAF4,downstream_gene_variant,,ENST00000609045,;TAF4,non_coding_transcript_exon_variant,,ENST00000609041,;TAF4,non_coding_transcript_exon_variant,,ENST00000436129,;TAF4,downstream_gene_variant,,ENST00000486599,;	A	ENSG00000130699	ENST00000252996	Transcript	synonymous_variant	2190	2190	730	V	gtC/gtT	rs145691580	.	.	-1	TAF4	HGNC	11537	protein_coding	YES	CCDS33500.1	ENSP00000252996	TAF4_HUMAN	.	UPI000020630A	.	.	.	7/15	.	hmmpanther:PTHR15138,hmmpanther:PTHR15138:SF13	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCCGACCTG	byCluster	5	ESCA
HELZ2	0	.	GRCh37	20	62194076	62194076	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6099G>A	p.%3D	p.L2033L	ENST00000467148	8/19	92	61	30	69	69	0	HELZ2,synonymous_variant,p.%3D,ENST00000467148,;HELZ2,synonymous_variant,p.%3D,ENST00000427522,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,upstream_gene_variant,,ENST00000478861,;	T	ENSG00000130589	ENST00000467148	Transcript	synonymous_variant	6169	6099	2033	L	ctG/ctA	.	.	.	-1	HELZ2	HGNC	30021	protein_coding	YES	CCDS33508.1	ENSP00000417401	HELZ2_HUMAN	Q3C1U4_HUMAN	UPI0000246BF7	.	.	.	8/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF332	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTCAGGCC	.	5	ESCA
KCNE2	0	.	GRCh37	21	35743430	35743430	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*281C>A	.	.	ENST00000290310	2/2	29	18	11	45	45	0	KCNE2,3_prime_UTR_variant,,ENST00000290310,;SMIM11,upstream_gene_variant,,ENST00000399292,;SMIM11,upstream_gene_variant,,ENST00000399295,;SMIM11,upstream_gene_variant,,ENST00000399299,;AP000320.6,non_coding_transcript_exon_variant,,ENST00000440403,;SMIM11,upstream_gene_variant,,ENST00000495363,;SMIM11,upstream_gene_variant,,ENST00000481710,;SMIM11,upstream_gene_variant,,ENST00000489469,;SMIM11,upstream_gene_variant,,ENST00000474455,;	A	ENSG00000159197	ENST00000290310	Transcript	3_prime_UTR_variant	793	.	.	.	.	.	.	.	1	KCNE2	HGNC	6242	protein_coding	YES	CCDS13635.1	ENSP00000290310	KCNE2_HUMAN	Q2N1I3_HUMAN	UPI000004A1D8	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGCCAAATT	.	5	ESCA
DOPEY2	0	.	GRCh37	21	37605164	37605164	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2413A>G	p.Thr805Ala	p.T805A	ENST00000399151	15/37	33	11	22	45	45	0	DOPEY2,missense_variant,p.Thr805Ala,ENST00000399151,;	G	ENSG00000142197	ENST00000399151	Transcript	missense_variant	2498	2413	805	T/A	Act/Gct	.	.	.	1	DOPEY2	HGNC	1291	protein_coding	YES	CCDS13643.1	ENSP00000382104	DOP2_HUMAN	F8W8U9_HUMAN	UPI000013D876	.	tolerated(0.3)	benign(0.001)	15/37	.	hmmpanther:PTHR14042:SF23,hmmpanther:PTHR14042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGACTGAC	.	5	ESCA
ELFN2	0	.	GRCh37	22	37770857	37770857	+	Missense_Mutation	SNP	C	C	T	rs762167710	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.718G>A	p.Val240Ile	p.V240I	ENST00000402918	3/3	119	65	53	129	129	0	ELFN2,missense_variant,p.Val240Ile,ENST00000402918,;RP1-63G5.5,intron_variant,,ENST00000430883,;RP1-63G5.5,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000424973,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000451509,;	T	ENSG00000166897	ENST00000402918	Transcript	missense_variant	1504	718	240	V/I	Gta/Ata	rs762167710	.	.	-1	ELFN2	HGNC	29396	protein_coding	YES	CCDS33642.1	ENSP00000385277	PPR29_HUMAN	.	UPI000004E87D	.	tolerated(1)	benign(0.002)	3/3	.	hmmpanther:PTHR24367:SF248,hmmpanther:PTHR24367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTACGGTGA	byFrequency	5	ESCA
CBX7	0	.	GRCh37	22	39527194	39527194	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2702G>A	.	.	ENST00000216133	6/6	48	36	12	70	70	0	CBX7,3_prime_UTR_variant,,ENST00000216133,;CBX7,downstream_gene_variant,,ENST00000401405,;CBX7,downstream_gene_variant,,ENST00000434260,;CBX7,intron_variant,,ENST00000475962,;CBX7,downstream_gene_variant,,ENST00000490741,;	T	ENSG00000100307	ENST00000216133	Transcript	3_prime_UTR_variant	3664	.	.	.	.	.	.	.	-1	CBX7	HGNC	1557	protein_coding	YES	CCDS13986.1	ENSP00000216133	CBX7_HUMAN	.	UPI00001271FE	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGCATTCC	.	5	ESCA
MIEF1	0	.	GRCh37	22	39909952	39909952	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1016T>C	p.Leu339Pro	p.L339P	ENST00000325301	6/6	44	32	12	62	62	0	MIEF1,missense_variant,p.Leu339Pro,ENST00000402881,;MIEF1,missense_variant,p.Leu339Pro,ENST00000404569,;MIEF1,missense_variant,p.Leu339Pro,ENST00000325301,;MIEF1,downstream_gene_variant,,ENST00000434364,;MIEF1,3_prime_UTR_variant,,ENST00000433117,;MIEF1,downstream_gene_variant,,ENST00000428069,;	C	ENSG00000100335	ENST00000325301	Transcript	missense_variant	1440	1016	339	L/P	cTg/cCg	.	.	.	1	MIEF1	HGNC	25979	protein_coding	YES	CCDS13995.1	ENSP00000327124	MID51_HUMAN	B0QY94_HUMAN	UPI000006FEB4	.	deleterious(0.01)	possibly_damaging(0.773)	6/6	.	hmmpanther:PTHR16451:SF2,hmmpanther:PTHR16451,Pfam_domain:PF03281	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGCTGAGCC	.	5	ESCA
AFF3	0	.	GRCh37	2	100623662	100623662	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510T>C	p.%3D	p.T170T	ENST00000356421	5/24	33	18	15	52	52	0	AFF3,synonymous_variant,p.%3D,ENST00000409579,;AFF3,synonymous_variant,p.%3D,ENST00000356421,;AFF3,synonymous_variant,p.%3D,ENST00000317233,;AFF3,synonymous_variant,p.%3D,ENST00000423966,;AFF3,synonymous_variant,p.%3D,ENST00000409236,;AFF3,synonymous_variant,p.%3D,ENST00000432037,;AFF3,downstream_gene_variant,,ENST00000416492,;AFF3,downstream_gene_variant,,ENST00000441400,;AFF3,downstream_gene_variant,,ENST00000415384,;AFF3,downstream_gene_variant,,ENST00000440445,;AFF3,downstream_gene_variant,,ENST00000424600,;AFF3,non_coding_transcript_exon_variant,,ENST00000498090,;AFF3,upstream_gene_variant,,ENST00000430789,;	G	ENSG00000144218	ENST00000356421	Transcript	synonymous_variant	654	510	170	T	acT/acC	.	.	.	-1	AFF3	HGNC	6473	protein_coding	YES	CCDS33258.1	ENSP00000348793	AFF3_HUMAN	.	UPI000041098C	.	.	.	5/24	.	hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUSE|VARSCANS	CCCATAGTGCC	.	3	ESCA
NCK2	0	.	GRCh37	2	106498469	106498469	+	Silent	SNP	G	G	A	rs375512251	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912G>A	p.%3D	p.V304V	ENST00000233154	4/5	56	38	17	34	34	0	NCK2,synonymous_variant,p.%3D,ENST00000233154,;NCK2,synonymous_variant,p.%3D,ENST00000393349,;NCK2,intron_variant,,ENST00000522586,;NCK2,intron_variant,,ENST00000451463,;NCK2,downstream_gene_variant,,ENST00000425756,;NCK2,downstream_gene_variant,,ENST00000393348,;	A	ENSG00000071051	ENST00000233154	Transcript	synonymous_variant	1354	912	304	V	gtG/gtA	rs375512251	.	.	1	NCK2	HGNC	7665	protein_coding	YES	CCDS33266.1	ENSP00000233154	NCK2_HUMAN	Q53TG4_HUMAN,Q53T91_HUMAN,E9PEE2_HUMAN,E7EPF5_HUMAN	UPI000012FE3F	.	.	.	4/5	.	PROSITE_profiles:PS50001,hmmpanther:PTHR22820,hmmpanther:PTHR22820:SF29,Gene3D:3.30.505.10,Pfam_domain:PF00017,SMART_domains:SM00252,PIRSF_domain:PIRSF037874,Superfamily_domains:SSF55550	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGTGGAGGG	byCluster	5	ESCA
RANBP2	0	.	GRCh37	2	109380774	109380774	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3779C>T	p.Ser1260Leu	p.S1260L	ENST00000283195	20/29	40	37	3	49	49	0	RANBP2,missense_variant,p.Ser1260Leu,ENST00000283195,;	T	ENSG00000153201	ENST00000283195	Transcript	missense_variant	3905	3779	1260	S/L	tCa/tTa	.	.	.	1	RANBP2	HGNC	9848	protein_coding	YES	CCDS2079.1	ENSP00000283195	RBP2_HUMAN	I1Z9D1_HUMAN	UPI0000207FB9	.	deleterious(0)	possibly_damaging(0.448)	20/29	.	PROSITE_profiles:PS50196,hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF8,Pfam_domain:PF00638,Gene3D:2.30.29.30,SMART_domains:SM00160,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGATCAGACA	.	2	ESCA
LRP1B	0	.	GRCh37	2	141294187	141294187	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7605C>G	p.His2535Gln	p.H2535Q	ENST00000389484	46/91	56	51	5	86	86	0	LRP1B,missense_variant,p.His2535Gln,ENST00000389484,;	C	ENSG00000168702	ENST00000389484	Transcript	missense_variant	8577	7605	2535	H/Q	caC/caG	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	possibly_damaging(0.537)	46/91	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,PROSITE_patterns:PS01209,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D2538N|c.7612G>A|3	MUTECT|MUSE|VARSCANS	TTACAGTGAGG	.	3	ESCA
SLC38A11	0	.	GRCh37	2	165811955	165811955	+	5'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-251T>A	.	.	ENST00000409149	1/11	12	8	4	23	23	0	SLC38A11,5_prime_UTR_variant,,ENST00000409149,;SLC38A11,5_prime_UTR_variant,,ENST00000409058,;SLC38A11,5_prime_UTR_variant,,ENST00000303735,;SLC38A11,upstream_gene_variant,,ENST00000409662,;SLC38A11,upstream_gene_variant,,ENST00000492134,;	T	ENSG00000169507	ENST00000409149	Transcript	5_prime_UTR_variant	42	.	.	.	.	.	.	.	-1	SLC38A11	HGNC	26836	protein_coding	YES	CCDS56142.1	ENSP00000386272	S38AB_HUMAN	.	UPI0000E44805	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGCAGCCTG	.	2	ESCA
GALNT3	0	.	GRCh37	2	166615871	166615871	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1048A>G	p.Arg350Gly	p.R350G	ENST00000392701	5/11	43	30	13	36	36	0	GALNT3,missense_variant,p.Arg88Gly,ENST00000409882,;GALNT3,missense_variant,p.Arg350Gly,ENST00000412248,;GALNT3,missense_variant,p.Arg350Gly,ENST00000392701,;GALNT3,3_prime_UTR_variant,,ENST00000437849,;GALNT3,non_coding_transcript_exon_variant,,ENST00000463254,;	C	ENSG00000115339	ENST00000392701	Transcript	missense_variant	1824	1048	350	R/G	Agg/Ggg	.	.	.	-1	GALNT3	HGNC	4125	protein_coding	YES	CCDS2226.1	ENSP00000376465	GALT3_HUMAN	C9JXX2_HUMAN,C9JW45_HUMAN,C9J388_HUMAN,C9J2C3_HUMAN	UPI000013C989	.	deleterious(0)	probably_damaging(0.999)	5/11	.	hmmpanther:PTHR11675:SF33,hmmpanther:PTHR11675,Gene3D:3.90.550.10,Pfam_domain:PF00535,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCTTCTTT	.	5	ESCA
CHRNA1	0	.	GRCh37	2	175614679	175614679	+	Missense_Mutation	SNP	G	G	A	rs374391312	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1072C>T	p.Arg358Trp	p.R358W	ENST00000261007	8/10	22	17	5	25	25	0	CHRNA1,missense_variant,p.Arg251Trp,ENST00000409542,;CHRNA1,missense_variant,p.Arg333Trp,ENST00000409219,;CHRNA1,missense_variant,p.Arg333Trp,ENST00000348749,;CHRNA1,missense_variant,p.Arg358Trp,ENST00000261007,;CHRNA1,downstream_gene_variant,,ENST00000409323,;AC018890.6,intron_variant,,ENST00000442996,;CHRNA1,3_prime_UTR_variant,,ENST00000435083,;	A	ENSG00000138435	ENST00000261007	Transcript	missense_variant	1139	1072	358	R/W	Cgg/Tgg	CM086805,rs374391312	.	.	-1	CHRNA1	HGNC	1955	protein_coding	YES	CCDS33331.1	ENSP00000261007	ACHA_HUMAN	A9X444_HUMAN	UPI000012524E	.	deleterious(0)	probably_damaging(0.998)	8/10	.	hmmpanther:PTHR18945:SF74,hmmpanther:PTHR18945,Pfam_domain:PF02932,Gene3D:1.20.120.370,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCGCACCC	byFrequency|byCluster	5	ESCA
CHRNA1	0	.	GRCh37	2	175614871	175614871	+	Missense_Mutation	SNP	C	C	G	rs137852803	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880G>C	p.Val294Leu	p.V294L	ENST00000261007	8/10	50	39	10	63	63	0	CHRNA1,missense_variant,p.Val187Leu,ENST00000409542,;CHRNA1,missense_variant,p.Val269Leu,ENST00000409219,;CHRNA1,missense_variant,p.Val269Leu,ENST00000348749,;CHRNA1,missense_variant,p.Val294Leu,ENST00000261007,;CHRNA1,downstream_gene_variant,,ENST00000409323,;AC018890.6,intron_variant,,ENST00000442996,;CHRNA1,3_prime_UTR_variant,,ENST00000435083,;	G	ENSG00000138435	ENST00000261007	Transcript	missense_variant	947	880	294	V/L	Gtc/Ctc	CM973279,rs137852803	.	.	-1	CHRNA1	HGNC	1955	protein_coding	YES	CCDS33331.1	ENSP00000261007	ACHA_HUMAN	A9X444_HUMAN	UPI000012524E	.	deleterious(0.05)	benign(0.405)	8/10	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF74,hmmpanther:PTHR18945,Pfam_domain:PF02932,Gene3D:1.20.120.370,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGACAGAGA	byCluster	5	ESCA
OSBPL6	0	.	GRCh37	2	179247885	179247885	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1831G>T	p.Val611Phe	p.V611F	ENST00000392505	18/26	32	18	13	26	26	0	OSBPL6,missense_variant,p.Val550Phe,ENST00000409631,;OSBPL6,missense_variant,p.Val555Phe,ENST00000409045,;OSBPL6,missense_variant,p.Val590Phe,ENST00000315022,;OSBPL6,missense_variant,p.Val550Phe,ENST00000359685,;OSBPL6,missense_variant,p.Val611Phe,ENST00000392505,;OSBPL6,missense_variant,p.Val586Phe,ENST00000190611,;OSBPL6,downstream_gene_variant,,ENST00000357080,;	T	ENSG00000079156	ENST00000392505	Transcript	missense_variant	2375	1831	611	V/F	Gtc/Ttc	.	.	.	1	OSBPL6	HGNC	16388	protein_coding	YES	CCDS56150.1	ENSP00000376293	OSBL6_HUMAN	.	UPI0000E5A29F	.	deleterious(0)	probably_damaging(0.999)	18/26	.	Superfamily_domains:0051579,Pfam_domain:PF01237,hmmpanther:PTHR10972:SF76,hmmpanther:PTHR10972	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAAAGTCTCT	.	5	ESCA
TTN	0	.	GRCh37	2	179414518	179414533	+	Frame_Shift_Del	DEL	GGGGCATCCCACCACA	GGGGCATCCCACCACA	-	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	GGGGCATCCCACCACA	GGGGCATCCCACCACA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.91916_91931delTGTGGTGGGATGCCCC	p.Leu30639HisfsTer9	p.L30639Hfs*9	ENST00000589042	338/363	69	60	9	68	68	0	TTN,frameshift_variant,p.Leu21699HisfsTer9,ENST00000359218,;TTN,frameshift_variant,p.Leu28998HisfsTer9,ENST00000591111,;TTN,frameshift_variant,p.Leu30639HisfsTer9,ENST00000589042,;TTN,frameshift_variant,p.Leu21766HisfsTer9,ENST00000342175,;TTN,frameshift_variant,p.Leu28071HisfsTer9,ENST00000342992,;TTN,frameshift_variant,p.Leu21574HisfsTer9,ENST00000460472,;RP11-65L3.2,non_coding_transcript_exon_variant,,ENST00000603415,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;	-	ENSG00000155657	ENST00000589042	Transcript	frameshift_variant	92141-92156	91916-91931	30639-30644	LWWDAP/X	cTGTGGTGGGATGCCCCa/ca	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	338/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TTGAGTGGGGCATCCCACCACAGAGTC	.	2	ESCA
STAT1	0	.	GRCh37	2	191873731	191873731	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.231C>A	p.Phe77Leu	p.F77L	ENST00000361099	4/25	43	14	29	43	43	0	STAT1,missense_variant,p.Phe77Leu,ENST00000540176,;STAT1,missense_variant,p.Phe79Leu,ENST00000392323,;STAT1,missense_variant,p.Phe77Leu,ENST00000454414,;STAT1,missense_variant,p.Phe77Leu,ENST00000392322,;STAT1,missense_variant,p.Phe77Leu,ENST00000361099,;STAT1,missense_variant,p.Phe77Leu,ENST00000424722,;STAT1,missense_variant,p.Phe77Leu,ENST00000409465,;STAT1,downstream_gene_variant,,ENST00000432058,;STAT1,missense_variant,p.Phe77Leu,ENST00000452281,;	T	ENSG00000115415	ENST00000361099	Transcript	missense_variant	619	231	77	F/L	ttC/ttA	COSM3425882	.	.	-1	STAT1	HGNC	11362	protein_coding	YES	CCDS2309.1	ENSP00000354394	STAT1_HUMAN	Q67C41_HUMAN,E9PH66_HUMAN,E7EPD2_HUMAN,E7ENM1_HUMAN	UPI00000473FB	.	tolerated(0.19)	benign(0.113)	4/25	.	Superfamily_domains:0035539,SMART_domains:SM00964,Pfam_domain:PF02865,Gene3D:1bgfA00,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF18	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAAGAAGTT	.	5	ESCA
APOB	0	.	GRCh37	2	21257724	21257724	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.868G>A	p.Asp290Asn	p.D290N	ENST00000233242	8/29	100	78	22	71	71	0	APOB,missense_variant,p.Asp290Asn,ENST00000233242,;APOB,missense_variant,p.Asp290Asn,ENST00000399256,;	T	ENSG00000084674	ENST00000233242	Transcript	missense_variant	996	868	290	D/N	Gac/Aac	.	.	.	-1	APOB	HGNC	603	protein_coding	YES	CCDS1703.1	ENSP00000233242	APOB_HUMAN	S5FVK9_HUMAN,Q9UE53_HUMAN,Q9UE52_HUMAN,Q13828_HUMAN	UPI0000141B94	.	.	possibly_damaging(0.741)	8/29	.	PROSITE_profiles:PS51211,hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1,Pfam_domain:PF01347,Gene3D:1lshA01,SMART_domains:SM00638,Superfamily_domains:SSF56968	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGTCTTCAA	.	5	ESCA
BARD1	0	.	GRCh37	2	215646173	215646173	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.425C>A	p.Ser142Ter	p.S142*	ENST00000260947	4/11	39	9	29	50	50	0	BARD1,stop_gained,p.Ser142Ter,ENST00000260947,;BARD1,5_prime_UTR_variant,,ENST00000449967,;BARD1,intron_variant,,ENST00000421162,;BARD1,non_coding_transcript_exon_variant,,ENST00000471787,;BARD1,3_prime_UTR_variant,,ENST00000455743,;	T	ENSG00000138376	ENST00000260947	Transcript	stop_gained	560	425	142	S/*	tCa/tAa	COSM1016077,COSM1591867	.	.	-1	BARD1	HGNC	952	protein_coding	YES	CCDS2397.1	ENSP00000260947	BARD1_HUMAN	.	UPI000013D11D	.	.	.	4/11	.	hmmpanther:PTHR24171:SF8,hmmpanther:PTHR24171	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAATTGAATTC	.	5	ESCA
CUL3	0	.	GRCh37	2	225367752	225367752	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1415G>A	p.Gly472Glu	p.G472E	ENST00000264414	10/16	51	13	37	61	61	0	CUL3,missense_variant,p.Gly406Glu,ENST00000344951,;CUL3,missense_variant,p.Gly472Glu,ENST00000264414,;CUL3,missense_variant,p.Gly448Glu,ENST00000409777,;CUL3,missense_variant,p.Gly448Glu,ENST00000409096,;CUL3,non_coding_transcript_exon_variant,,ENST00000481135,;CUL3,downstream_gene_variant,,ENST00000484081,;CUL3,upstream_gene_variant,,ENST00000487558,;AC073052.1,upstream_gene_variant,,ENST00000440417,;	T	ENSG00000036257	ENST00000264414	Transcript	missense_variant	1754	1415	472	G/E	gGa/gAa	.	.	.	-1	CUL3	HGNC	2553	protein_coding	YES	CCDS2462.1	ENSP00000264414	CUL3_HUMAN	Q53S54_HUMAN,Q53RD1_HUMAN	UPI0000001C83	.	deleterious(0.03)	probably_damaging(0.997)	10/16	.	PROSITE_profiles:PS50069,hmmpanther:PTHR11932,Pfam_domain:PF00888,Gene3D:1.20.1310.10,SMART_domains:SM00182,Superfamily_domains:SSF75632	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTCCTTCC	.	5	ESCA
COL4A4	0	.	GRCh37	2	227973326	227973326	+	Missense_Mutation	SNP	C	C	T	rs762358388	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.706G>A	p.Val236Met	p.V236M	ENST00000396625	12/48	50	14	36	87	87	0	COL4A4,missense_variant,p.Val236Met,ENST00000329662,;COL4A4,missense_variant,p.Val236Met,ENST00000396625,;	T	ENSG00000081052	ENST00000396625	Transcript	missense_variant	914	706	236	V/M	Gtg/Atg	rs762358388	.	.	-1	COL4A4	HGNC	2206	protein_coding	YES	CCDS42828.1	ENSP00000379866	CO4A4_HUMAN	.	UPI000013D987	.	.	possibly_damaging(0.664)	12/48	.	hmmpanther:PTHR24021:SF5,hmmpanther:PTHR24021	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCACACCGG	.	5	ESCA
PRKCE	0	.	GRCh37	2	46372357	46372357	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1718A>G	p.Tyr573Cys	p.Y573C	ENST00000306156	12/15	46	36	10	74	74	0	PRKCE,missense_variant,p.Tyr573Cys,ENST00000306156,;PRKCE,non_coding_transcript_exon_variant,,ENST00000469753,;PRKCE,non_coding_transcript_exon_variant,,ENST00000480633,;	G	ENSG00000171132	ENST00000306156	Transcript	missense_variant	2045	1718	573	Y/C	tAc/tGc	.	.	.	1	PRKCE	HGNC	9401	protein_coding	YES	CCDS1824.1	ENSP00000306124	KPCE_HUMAN	Q53RT0_HUMAN,L7RTI5_HUMAN,C9JR22_HUMAN	UPI000012DF6B	.	deleterious(0)	probably_damaging(1)	12/15	.	Superfamily_domains:SSF56112,PIRSF_domain:PIRSF501106,PIRSF_domain:PIRSF000551,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24357:SF52,hmmpanther:PTHR24357,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACTACATAG	.	5	ESCA
CCDC88A	0	.	GRCh37	2	55529026	55529026	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4651C>T	p.Gln1551Ter	p.Q1551*	ENST00000336838	27/33	40	34	6	42	42	0	CCDC88A,stop_gained,p.Gln1551Ter,ENST00000413716,;CCDC88A,stop_gained,p.Gln569Ter,ENST00000412148,;CCDC88A,stop_gained,p.Gln1552Ter,ENST00000436346,;CCDC88A,stop_gained,p.Gln505Ter,ENST00000456975,;CCDC88A,stop_gained,p.Gln1524Ter,ENST00000263630,;CCDC88A,stop_gained,p.Gln1551Ter,ENST00000336838,;CCDC88A,stop_gained,p.Gln727Ter,ENST00000426576,;CCDC88A,intron_variant,,ENST00000444458,;CCDC88A,intron_variant,,ENST00000422883,;	A	ENSG00000115355	ENST00000336838	Transcript	stop_gained	5185	4651	1551	Q/*	Cag/Tag	.	.	.	-1	CCDC88A	HGNC	25523	protein_coding	YES	CCDS46288.1	ENSP00000338728	GRDN_HUMAN	C9J225_HUMAN,B4DSN0_HUMAN	UPI00005B7220	.	.	.	27/33	.	hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACTGCTTGG	.	4	ESCA
MRPL19	0	.	GRCh37	2	75882271	75882271	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.739C>G	p.Leu247Val	p.L247V	ENST00000393909	6/6	77	69	8	144	144	0	MRPL19,missense_variant,p.Leu34Val,ENST00000453233,;MRPL19,missense_variant,p.Leu247Val,ENST00000393909,;MRPL19,missense_variant,p.Leu247Val,ENST00000409374,;MRPL19,intron_variant,,ENST00000492255,;MRPL19,intron_variant,,ENST00000358788,;MRPL19,downstream_gene_variant,,ENST00000476622,;GCFC2,intron_variant,,ENST00000470285,;AC005034.3,upstream_gene_variant,,ENST00000423067,;	G	ENSG00000115364	ENST00000393909	Transcript	missense_variant	764	739	247	L/V	Ctt/Gtt	.	.	.	1	MRPL19	HGNC	14052	protein_coding	YES	CCDS1960.2	ENSP00000377486	RM19_HUMAN	S4R3W9_HUMAN,H7C2J0_HUMAN,B4DIG4_HUMAN,A8K5D5_HUMAN	UPI00002087A4	.	tolerated(0.13)	benign(0.346)	6/6	.	hmmpanther:PTHR15680,hmmpanther:PTHR15680:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGATCTTTGT	.	4	ESCA
CD47	0	.	GRCh37	3	107764071	107764071	+	3'Flank	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000361309	.	21	11	9	61	61	0	CD47,3_prime_UTR_variant,,ENST00000355354,;CD47,downstream_gene_variant,,ENST00000398258,;CD47,downstream_gene_variant,,ENST00000517766,;CD47,downstream_gene_variant,,ENST00000361309,;CD47,non_coding_transcript_exon_variant,,ENST00000471694,;	C	ENSG00000196776	ENST00000361309	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1857	-1	CD47	HGNC	1682	protein_coding	YES	CCDS43126.1	ENSP00000355361	CD47_HUMAN	.	UPI0000049C6C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGAGAGTTT	.	5	ESCA
SLC35A5	0	.	GRCh37	3	112282359	112282359	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.109G>C	p.Val37Leu	p.V37L	ENST00000492406	2/7	19	10	9	53	53	0	SLC35A5,missense_variant,p.Val37Leu,ENST00000484995,;SLC35A5,missense_variant,p.Val37Leu,ENST00000468642,;SLC35A5,missense_variant,p.Val37Leu,ENST00000492406,;ATG3,upstream_gene_variant,,ENST00000492886,;ATG3,upstream_gene_variant,,ENST00000402314,;ATG3,upstream_gene_variant,,ENST00000283290,;SLC35A5,non_coding_transcript_exon_variant,,ENST00000460713,;ATG3,upstream_gene_variant,,ENST00000495756,;SLC35A5,missense_variant,p.Val37Leu,ENST00000261034,;ATG3,upstream_gene_variant,,ENST00000488910,;ATG3,upstream_gene_variant,,ENST00000465980,;SLC35A5,upstream_gene_variant,,ENST00000494706,;ATG3,upstream_gene_variant,,ENST00000496423,;	C	ENSG00000138459	ENST00000492406	Transcript	missense_variant	392	109	37	V/L	Gtg/Ctg	.	.	.	1	SLC35A5	HGNC	20792	protein_coding	YES	CCDS2967.1	ENSP00000417654	S35A5_HUMAN	C9JXZ8_HUMAN,C9J7U8_HUMAN,B4DMD4_HUMAN	UPI0000048EAD	.	tolerated(0.53)	benign(0.002)	2/7	.	hmmpanther:PTHR10231,hmmpanther:PTHR10231:SF40,PIRSF_domain:PIRSF005799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTAGTGAAG	.	5	ESCA
LEKR1	0	.	GRCh37	3	156746172	156746172	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1649T>A	p.Phe550Tyr	p.F550Y	ENST00000356539	12/13	24	17	6	40	40	0	LEKR1,missense_variant,p.Phe550Tyr,ENST00000356539,;LEKR1,missense_variant,p.Phe246Tyr,ENST00000470811,;	A	ENSG00000197980	ENST00000356539	Transcript	missense_variant	1763	1649	550	F/Y	tTt/tAt	.	.	.	1	LEKR1	HGNC	33765	protein_coding	.	.	ENSP00000348936	.	J3KP02_HUMAN	UPI0001BB2D45	.	deleterious(0.01)	benign(0.294)	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAATTTAACC	.	5	ESCA
OPA1	0	.	GRCh37	3	193409884	193409884	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2962G>A	p.Ala988Thr	p.A988T	ENST00000361908	29/30	119	94	24	87	87	0	OPA1,missense_variant,p.Ala952Thr,ENST00000361150,;OPA1,missense_variant,p.Ala970Thr,ENST00000361715,;OPA1,missense_variant,p.Ala988Thr,ENST00000361908,;OPA1,missense_variant,p.Ala969Thr,ENST00000361828,;OPA1,missense_variant,p.Ala951Thr,ENST00000392438,;OPA1,missense_variant,p.Ala1006Thr,ENST00000361510,;OPA1,non_coding_transcript_exon_variant,,ENST00000495261,;	A	ENSG00000198836	ENST00000361908	Transcript	missense_variant	3196	2962	988	A/T	Gct/Act	.	.	.	1	OPA1	HGNC	8140	protein_coding	YES	CCDS33917.1	ENSP00000354681	OPA1_HUMAN	Q6PEK6_HUMAN,E5KLJ7_HUMAN,C9JY58_HUMAN	UPI0000422960	.	deleterious(0.02)	benign(0.119)	29/30	.	hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATGCTTTC	.	5	ESCA
ZDHHC19	0	.	GRCh37	3	195937566	195937566	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189T>C	p.%3D	p.V63V	ENST00000296326	2/8	40	35	4	48	48	0	ZDHHC19,synonymous_variant,p.%3D,ENST00000296326,;SLC51A,upstream_gene_variant,,ENST00000416660,;PCYT1A,downstream_gene_variant,,ENST00000441879,;ZDHHC19,non_coding_transcript_exon_variant,,ENST00000488508,;ZDHHC19,synonymous_variant,p.%3D,ENST00000438232,;ZDHHC19,synonymous_variant,p.%3D,ENST00000397544,;ZDHHC19,intron_variant,,ENST00000465519,;	G	ENSG00000163958	ENST00000296326	Transcript	synonymous_variant	269	189	63	V	gtT/gtC	.	.	.	-1	ZDHHC19	HGNC	20713	protein_coding	YES	CCDS43190.1	ENSP00000296326	ZDH19_HUMAN	B3KVI1_HUMAN	UPI00006BFF56	.	.	.	2/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22883:SF7,hmmpanther:PTHR22883	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTGATAACAGG	.	3	ESCA
POMGNT2	0	.	GRCh37	3	43122845	43122845	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.79G>A	p.Glu27Lys	p.E27K	ENST00000344697	2/2	19	14	4	39	39	0	POMGNT2,missense_variant,p.Glu27Lys,ENST00000441964,;POMGNT2,missense_variant,p.Glu27Lys,ENST00000344697,;	T	ENSG00000144647	ENST00000344697	Transcript	missense_variant	425	79	27	E/K	Gag/Aag	.	.	.	-1	POMGNT2	HGNC	25902	protein_coding	YES	CCDS2709.1	ENSP00000344125	PMGT2_HUMAN	.	UPI0000037921	.	deleterious_low_confidence(0.01)	benign(0.339)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR20961:SF0,hmmpanther:PTHR20961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCTCACGCA	.	5	ESCA
DALRD3	0	.	GRCh37	3	49053422	49053422	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1427C>T	p.Ala476Val	p.A476V	ENST00000341949	10/12	16	2	14	26	26	0	DALRD3,missense_variant,p.Ala309Val,ENST00000313778,;DALRD3,missense_variant,p.Ala123Val,ENST00000438585,;DALRD3,missense_variant,p.Ala476Val,ENST00000341949,;DALRD3,missense_variant,p.Ala309Val,ENST00000395462,;DALRD3,missense_variant,p.Ala309Val,ENST00000440857,;DALRD3,synonymous_variant,p.%3D,ENST00000441576,;WDR6,downstream_gene_variant,,ENST00000419837,;WDR6,downstream_gene_variant,,ENST00000395474,;WDR6,downstream_gene_variant,,ENST00000448293,;WDR6,downstream_gene_variant,,ENST00000415265,;NDUFAF3,upstream_gene_variant,,ENST00000326912,;WDR6,downstream_gene_variant,,ENST00000489427,;DALRD3,downstream_gene_variant,,ENST00000420952,;WDR6,downstream_gene_variant,,ENST00000491365,;WDR6,downstream_gene_variant,,ENST00000608424,;WDR6,downstream_gene_variant,,ENST00000429900,;WDR6,downstream_gene_variant,,ENST00000438660,;MIR191,downstream_gene_variant,,ENST00000384873,;MIR425,downstream_gene_variant,,ENST00000362162,;DALRD3,downstream_gene_variant,,ENST00000492585,;DALRD3,downstream_gene_variant,,ENST00000496568,;WDR6,downstream_gene_variant,,ENST00000489684,;WDR6,downstream_gene_variant,,ENST00000461687,;WDR6,downstream_gene_variant,,ENST00000472878,;DALRD3,non_coding_transcript_exon_variant,,ENST00000498794,;DALRD3,non_coding_transcript_exon_variant,,ENST00000481001,;DALRD3,non_coding_transcript_exon_variant,,ENST00000467457,;DALRD3,non_coding_transcript_exon_variant,,ENST00000484831,;DALRD3,non_coding_transcript_exon_variant,,ENST00000472331,;DALRD3,non_coding_transcript_exon_variant,,ENST00000498498,;DALRD3,non_coding_transcript_exon_variant,,ENST00000460505,;WDR6,downstream_gene_variant,,ENST00000452875,;WDR6,downstream_gene_variant,,ENST00000498023,;WDR6,downstream_gene_variant,,ENST00000488572,;WDR6,downstream_gene_variant,,ENST00000471162,;WDR6,downstream_gene_variant,,ENST00000462064,;WDR6,downstream_gene_variant,,ENST00000473238,;WDR6,downstream_gene_variant,,ENST00000492780,;WDR6,downstream_gene_variant,,ENST00000420783,;	A	ENSG00000178149	ENST00000341949	Transcript	missense_variant	1434	1427	476	A/V	gCt/gTt	.	.	.	-1	DALRD3	HGNC	25536	protein_coding	YES	CCDS33754.1	ENSP00000344989	DALD3_HUMAN	.	UPI00000622F0	.	deleterious(0.01)	benign(0.039)	10/12	.	hmmpanther:PTHR16043,hmmpanther:PTHR16043:SF0,Pfam_domain:PF05746,Gene3D:1.10.730.10,SMART_domains:SM00836,Superfamily_domains:SSF47323	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACAGCAATG	.	5	ESCA
KBTBD8	0	.	GRCh37	3	67058470	67058470	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1467C>T	p.%3D	p.T489T	ENST00000417314	4/4	67	64	3	98	98	0	KBTBD8,synonymous_variant,p.%3D,ENST00000417314,;KBTBD8,synonymous_variant,p.%3D,ENST00000460576,;KBTBD8,synonymous_variant,p.%3D,ENST00000295568,;KBTBD8,downstream_gene_variant,,ENST00000460784,;KBTBD8,downstream_gene_variant,,ENST00000484414,;KBTBD8,downstream_gene_variant,,ENST00000469661,;	T	ENSG00000163376	ENST00000417314	Transcript	synonymous_variant	1516	1467	489	T	acC/acT	.	.	.	1	KBTBD8	HGNC	30691	protein_coding	YES	CCDS2906.2	ENSP00000401878	KBTB8_HUMAN	C9JAA6_HUMAN,C9J331_HUMAN	UPI0000209974	.	.	.	4/4	.	hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF24,Pfam_domain:PF01344,Gene3D:1zgkA00,SMART_domains:SM00612,PIRSF_domain:PIRSF037037,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAACCTGTGG	.	2	ESCA
ADH1C	0	.	GRCh37	4	100266027	100266027	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559G>T	p.Val187Phe	p.V187F	ENST00000515683	5/9	41	28	13	62	62	0	ADH1C,non_coding_transcript_exon_variant,,ENST00000511397,;ADH1C,non_coding_transcript_exon_variant,,ENST00000510055,;ADH1C,downstream_gene_variant,,ENST00000505942,;ADH1C,missense_variant,p.Val187Phe,ENST00000515683,;	A	ENSG00000248144	ENST00000515683	Transcript	missense_variant	911	559	187	V/F	Gtt/Ttt	.	.	.	-1	ADH1C	HGNC	251	polymorphic_pseudogene	YES	.	ENSP00000426083	.	.	.	.	.	benign(0.198)	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAACTTTGA	.	5	ESCA
BOD1L1	0	.	GRCh37	4	13604639	13604639	+	Silent	SNP	C	C	T	rs182239378	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3885G>A	p.%3D	p.S1295S	ENST00000040738	10/26	30	27	3	42	42	0	BOD1L1,synonymous_variant,p.%3D,ENST00000040738,;	T	ENSG00000038219	ENST00000040738	Transcript	synonymous_variant	4021	3885	1295	S	tcG/tcA	rs182239378,COSM243217	.	.	-1	BOD1L1	HGNC	31792	protein_coding	YES	CCDS3411.2	ENSP00000040738	BD1L1_HUMAN	.	UPI000066D9E3	.	.	.	10/26	.	hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3	T:0.0004	T:0	T:0	.	T:0.002	T:0	T:0	T:0	T:0.0002	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCATACGATTC	byFrequency|byCluster|by1000G	2	ESCA
SLC10A7	0	.	GRCh37	4	147363928	147363928	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435+7A>G	.	.	ENST00000335472	.	55	49	6	88	88	0	SLC10A7,missense_variant,p.Lys148Glu,ENST00000394059,;SLC10A7,splice_region_variant,,ENST00000264986,;SLC10A7,splice_region_variant,,ENST00000507030,;SLC10A7,splice_region_variant,,ENST00000335472,;SLC10A7,splice_region_variant,,ENST00000394062,;SLC10A7,3_prime_UTR_variant,,ENST00000511374,;SLC10A7,intron_variant,,ENST00000432059,;SLC10A7,splice_region_variant,,ENST00000507560,;SLC10A7,non_coding_transcript_exon_variant,,ENST00000511315,;	C	ENSG00000120519	ENST00000335472	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	SLC10A7	HGNC	23088	protein_coding	YES	CCDS34073.1	ENSP00000334594	NTCP7_HUMAN	B3KWW2_HUMAN	UPI000020B547	.	.	.	.	5/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGTTTACTTA	.	4	ESCA
LRBA	0	.	GRCh37	4	151682999	151682999	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5581G>C	p.Glu1861Gln	p.E1861Q	ENST00000357115	35/58	69	19	49	78	78	0	LRBA,missense_variant,p.Glu1861Gln,ENST00000535741,;LRBA,missense_variant,p.Glu1861Gln,ENST00000507224,;LRBA,missense_variant,p.Glu1861Gln,ENST00000357115,;LRBA,missense_variant,p.Glu1861Gln,ENST00000510413,;LRBA,missense_variant,p.Glu514Gln,ENST00000509835,;	G	ENSG00000198589	ENST00000357115	Transcript	missense_variant	5825	5581	1861	E/Q	Gag/Cag	.	.	.	-1	LRBA	HGNC	1742	protein_coding	YES	CCDS3773.1	ENSP00000349629	LRBA_HUMAN	Q7KZN3_HUMAN	UPI000013E35C	.	deleterious(0)	possibly_damaging(0.904)	35/58	.	hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CCACTCCTATA	.	3	ESCA
SLIT2	0	.	GRCh37	4	20493433	20493433	+	Silent	SNP	C	C	T	rs557268494	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.825C>T	p.%3D	p.A275A	ENST00000504154	9/37	70	50	20	51	51	0	SLIT2,synonymous_variant,p.%3D,ENST00000273739,;SLIT2,synonymous_variant,p.%3D,ENST00000504154,;SLIT2,synonymous_variant,p.%3D,ENST00000503823,;SLIT2,synonymous_variant,p.%3D,ENST00000503837,;	T	ENSG00000145147	ENST00000504154	Transcript	synonymous_variant	1077	825	275	A	gcC/gcT	rs557268494	.	.	1	SLIT2	HGNC	11086	protein_coding	YES	CCDS3426.1	ENSP00000422591	SLIT2_HUMAN	Q4W5N0_HUMAN,Q4W5K2_HUMAN,B3KNE2_HUMAN	UPI00000747E4	.	.	.	9/37	.	hmmpanther:PTHR24373:SF107,hmmpanther:PTHR24373,Pfam_domain:PF01462,SMART_domains:SM00013	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCCGCCTG	byFrequency|byCluster	5	ESCA
N4BP2	0	.	GRCh37	4	40098975	40098975	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15G>T	p.Arg5Ser	p.R5S	ENST00000261435	3/18	30	25	5	72	72	0	N4BP2,missense_variant,p.Arg5Ser,ENST00000261435,;N4BP2,intron_variant,,ENST00000515550,;N4BP2,missense_variant,p.Arg5Ser,ENST00000511480,;	T	ENSG00000078177	ENST00000261435	Transcript	missense_variant	431	15	5	R/S	agG/agT	.	.	.	1	N4BP2	HGNC	29851	protein_coding	YES	CCDS3457.1	ENSP00000261435	N4BP2_HUMAN	D6R9J2_HUMAN	UPI00001A962C	.	deleterious(0)	possibly_damaging(0.662)	3/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAGGAAAAA	.	2	ESCA
GABRG1	0	.	GRCh37	4	46086016	46086016	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.308A>G	p.Asp103Gly	p.D103G	ENST00000295452	3/9	33	22	11	66	66	0	GABRG1,missense_variant,p.Asp103Gly,ENST00000295452,;	C	ENSG00000163285	ENST00000295452	Transcript	missense_variant	476	308	103	D/G	gAt/gGt	.	.	.	-1	GABRG1	HGNC	4086	protein_coding	YES	CCDS3470.1	ENSP00000295452	GBRG1_HUMAN	.	UPI0000047AE2	.	deleterious(0.04)	possibly_damaging(0.528)	3/9	.	hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF93,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGATCAACT	.	5	ESCA
KDR	0	.	GRCh37	4	55991617	55991617	+	5'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-157C>A	.	.	ENST00000263923	1/30	14	12	2	14	14	0	KDR,5_prime_UTR_variant,,ENST00000263923,;KDR,upstream_gene_variant,,ENST00000512566,;	T	ENSG00000128052	ENST00000263923	Transcript	5_prime_UTR_variant	140	.	.	.	.	.	.	.	-1	KDR	HGNC	6307	protein_coding	YES	CCDS3497.1	ENSP00000263923	VGFR2_HUMAN	B4DEK3_HUMAN	UPI000003AE04	.	.	.	1/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCGCGGCTGCA	.	2	ESCA
GC	0	.	GRCh37	4	72669648	72669648	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16A>G	p.Ser6Gly	p.S6G	ENST00000504199	1/14	33	23	10	57	57	0	GC,missense_variant,p.Ser6Gly,ENST00000504199,;	C	ENSG00000145321	ENST00000504199	Transcript	missense_variant	111	16	6	S/G	Agt/Ggt	.	.	.	-1	GC	HGNC	4187	protein_coding	YES	CCDS56332.1	ENSP00000421725	VTDB_HUMAN	D6RF20_HUMAN	UPI0001D3B4EE	.	tolerated_low_confidence(0.23)	benign(0.012)	1/14	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCACTCCAAG	.	5	ESCA
IBSP	0	.	GRCh37	4	88723869	88723869	+	Missense_Mutation	SNP	C	C	G	rs779343614	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.169C>G	p.Arg57Gly	p.R57G	ENST00000226284	4/7	46	38	7	47	47	0	IBSP,missense_variant,p.Arg57Gly,ENST00000226284,;	G	ENSG00000029559	ENST00000226284	Transcript	missense_variant	236	169	57	R/G	Cga/Gga	rs779343614	.	.	1	IBSP	HGNC	5341	protein_coding	YES	CCDS3624.1	ENSP00000226284	SIAL_HUMAN	.	UPI000013C899	.	deleterious(0)	probably_damaging(0.976)	4/7	.	hmmpanther:PTHR10345:SF0,hmmpanther:PTHR10345,Pfam_domain:PF05432	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAAACGATTT	byFrequency	5	ESCA
C5orf30	0	.	GRCh37	5	102614021	102614021	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1780C>G	.	.	ENST00000319933	3/3	27	11	15	66	66	0	C5orf30,3_prime_UTR_variant,,ENST00000510890,;C5orf30,3_prime_UTR_variant,,ENST00000319933,;C5orf30,downstream_gene_variant,,ENST00000515669,;	G	ENSG00000181751	ENST00000319933	Transcript	3_prime_UTR_variant	2709	.	.	.	.	.	.	.	1	C5orf30	HGNC	25052	protein_coding	YES	CCDS4095.1	ENSP00000326110	CE030_HUMAN	.	UPI0000070E95	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTACCCTGTG	.	5	ESCA
TRIM36	0	.	GRCh37	5	114462496	114462496	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1891C>A	p.Gln631Lys	p.Q631K	ENST00000282369	10/10	13	8	4	31	31	0	TRIM36,missense_variant,p.Gln476Lys,ENST00000514154,;TRIM36,missense_variant,p.Gln631Lys,ENST00000282369,;TRIM36,missense_variant,p.Gln619Lys,ENST00000513154,;	T	ENSG00000152503	ENST00000282369	Transcript	missense_variant	2013	1891	631	Q/K	Caa/Aaa	.	.	.	-1	TRIM36	HGNC	16280	protein_coding	YES	CCDS4115.1	ENSP00000282369	TRI36_HUMAN	E9PBG3_HUMAN	UPI000013DCD9	.	tolerated(0.33)	probably_damaging(0.955)	10/10	.	PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF29,Pfam_domain:PF00622,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TGGTTGTGAAG	.	4	ESCA
PKD2L2	0	.	GRCh37	5	137260764	137260764	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1587G>A	p.%3D	p.K529K	ENST00000290431	11/14	49	43	6	84	84	0	PKD2L2,synonymous_variant,p.%3D,ENST00000508883,;PKD2L2,synonymous_variant,p.%3D,ENST00000350250,;PKD2L2,synonymous_variant,p.%3D,ENST00000290431,;PKD2L2,synonymous_variant,p.%3D,ENST00000502810,;PKD2L2,synonymous_variant,p.%3D,ENST00000508638,;	A	ENSG00000078795	ENST00000290431	Transcript	synonymous_variant	1610	1587	529	K	aaG/aaA	.	.	.	1	PKD2L2	HGNC	9012	protein_coding	YES	CCDS43367.1	ENSP00000290431	PK2L2_HUMAN	D6RF71_HUMAN,D6RBX8_HUMAN	UPI000049E016	.	.	.	11/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF47,Prints_domain:PR01433	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGAAGAAAGC	.	4	ESCA
TNIP1	0	.	GRCh37	5	150409930	150409930	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*344C>T	.	.	ENST00000389378	18/18	51	42	9	76	76	0	TNIP1,3_prime_UTR_variant,,ENST00000520931,;TNIP1,3_prime_UTR_variant,,ENST00000389378,;TNIP1,3_prime_UTR_variant,,ENST00000523338,;TNIP1,3_prime_UTR_variant,,ENST00000315050,;TNIP1,intron_variant,,ENST00000517504,;GPX3,downstream_gene_variant,,ENST00000517973,;GPX3,downstream_gene_variant,,ENST00000520059,;TNIP1,downstream_gene_variant,,ENST00000521591,;TNIP1,downstream_gene_variant,,ENST00000518977,;TNIP1,downstream_gene_variant,,ENST00000523200,;GPX3,downstream_gene_variant,,ENST00000521632,;TNIP1,downstream_gene_variant,,ENST00000524280,;GPX3,downstream_gene_variant,,ENST00000388825,;TNIP1,downstream_gene_variant,,ENST00000522226,;GPX3,downstream_gene_variant,,ENST00000521650,;GPX3,downstream_gene_variant,,ENST00000521722,;TNIP1,downstream_gene_variant,,ENST00000521423,;GPX3,downstream_gene_variant,,ENST00000520597,;GPX3,downstream_gene_variant,,ENST00000519214,;TNIP1,downstream_gene_variant,,ENST00000519339,;TNIP1,downstream_gene_variant,,ENST00000522574,;TNIP1,downstream_gene_variant,,ENST00000517329,;	A	ENSG00000145901	ENST00000389378	Transcript	3_prime_UTR_variant	2844	.	.	.	.	.	.	.	-1	TNIP1	HGNC	16903	protein_coding	YES	CCDS34280.1	ENSP00000374029	TNIP1_HUMAN	E7EWG2_HUMAN,E7EW68_HUMAN,E7EW15_HUMAN,B7Z5B0_HUMAN,A4F1X2_HUMAN,A4F1W8_HUMAN	UPI000000DCDC	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGAAGGAAGG	.	5	ESCA
ADAM19	0	.	GRCh37	5	156908789	156908789	+	Intron	SNP	G	G	C	rs766815187	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2703+10C>G	.	.	ENST00000257527	.	57	36	21	38	38	0	ADAM19,missense_variant,p.Arg905Gly,ENST00000517905,;ADAM19,intron_variant,,ENST00000430702,;ADAM19,intron_variant,,ENST00000394020,;ADAM19,intron_variant,,ENST00000257527,;ADAM19,intron_variant,,ENST00000517374,;ADAM19,intron_variant,,ENST00000517951,;	C	ENSG00000135074	ENST00000257527	Transcript	intron_variant	.	.	.	.	.	rs766815187	.	.	-1	ADAM19	HGNC	197	protein_coding	YES	CCDS4338.1	ENSP00000257527	ADA19_HUMAN	.	UPI000013CF6A	.	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCCGTGGAC	.	5	ESCA
CDHR2	0	.	GRCh37	5	176011726	176011726	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2444G>T	p.Gly815Val	p.G815V	ENST00000510636	19/32	48	39	8	69	69	0	CDHR2,missense_variant,p.Gly815Val,ENST00000261944,;CDHR2,missense_variant,p.Gly815Val,ENST00000506348,;CDHR2,missense_variant,p.Gly815Val,ENST00000510636,;CDHR2,upstream_gene_variant,,ENST00000513031,;CDHR2,upstream_gene_variant,,ENST00000508085,;	T	ENSG00000074276	ENST00000510636	Transcript	missense_variant	2718	2444	815	G/V	gGc/gTc	.	.	.	1	CDHR2	HGNC	18231	protein_coding	YES	CCDS34297.1	ENSP00000424565	CDHR2_HUMAN	.	UPI0000DBEE8C	.	deleterious(0.02)	benign(0.197)	19/32	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF286,Gene3D:2.60.40.60,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGGGCATCC	.	5	ESCA
RP11-1277A3.2	0	.	GRCh37	5	177099159	177099159	+	5'Flank	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000500444	.	33	29	3	25	25	0	RP11-1277A3.2,non_coding_transcript_exon_variant,,ENST00000515045,;RP11-1277A3.2,upstream_gene_variant,,ENST00000500444,;	C	ENSG00000246596	ENST00000500444	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	9	-1	RP11-1277A3.2	Clone_based_vega_gene	.	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCGGGCCCCG	.	3	ESCA
RP11-1277A3.2	0	.	GRCh37	5	177099160	177099160	+	5'Flank	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000500444	.	33	29	3	25	25	0	RP11-1277A3.2,non_coding_transcript_exon_variant,,ENST00000515045,;RP11-1277A3.2,upstream_gene_variant,,ENST00000500444,;	A	ENSG00000246596	ENST00000500444	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	10	-1	RP11-1277A3.2	Clone_based_vega_gene	.	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCGGGCCCCGA	.	3	ESCA
TBC1D9B	0	.	GRCh37	5	179289817	179289817	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*631A>G	.	.	ENST00000356834	22/22	47	25	22	42	42	0	TBC1D9B,3_prime_UTR_variant,,ENST00000355235,;TBC1D9B,3_prime_UTR_variant,,ENST00000519746,;TBC1D9B,3_prime_UTR_variant,,ENST00000356834,;TBC1D9B,3_prime_UTR_variant,,ENST00000444477,;TBC1D9B,intron_variant,,ENST00000522472,;C5orf45,upstream_gene_variant,,ENST00000520698,;C5orf45,upstream_gene_variant,,ENST00000376931,;C5orf45,upstream_gene_variant,,ENST00000523084,;CTC-241N9.1,downstream_gene_variant,,ENST00000499601,;TBC1D9B,downstream_gene_variant,,ENST00000524222,;C5orf45,upstream_gene_variant,,ENST00000292586,;C5orf45,upstream_gene_variant,,ENST00000518219,;C5orf45,upstream_gene_variant,,ENST00000521333,;C5orf45,upstream_gene_variant,,ENST00000403396,;C5orf45,upstream_gene_variant,,ENST00000518235,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000518085,;C5orf45,upstream_gene_variant,,ENST00000517338,;TBC1D9B,downstream_gene_variant,,ENST00000522180,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000520794,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000521469,;C5orf45,upstream_gene_variant,,ENST00000519398,;C5orf45,upstream_gene_variant,,ENST00000519318,;C5orf45,upstream_gene_variant,,ENST00000520995,;TBC1D9B,downstream_gene_variant,,ENST00000522921,;C5orf45,upstream_gene_variant,,ENST00000520150,;TBC1D9B,downstream_gene_variant,,ENST00000519757,;C5orf45,upstream_gene_variant,,ENST00000523835,;C5orf45,upstream_gene_variant,,ENST00000521299,;C5orf45,upstream_gene_variant,,ENST00000522663,;C5orf45,upstream_gene_variant,,ENST00000519213,;C5orf45,upstream_gene_variant,,ENST00000524068,;C5orf45,upstream_gene_variant,,ENST00000523737,;C5orf45,upstream_gene_variant,,ENST00000522157,;C5orf45,upstream_gene_variant,,ENST00000519208,;	C	ENSG00000197226	ENST00000356834	Transcript	3_prime_UTR_variant	4422	.	.	.	.	.	.	.	-1	TBC1D9B	HGNC	29097	protein_coding	YES	CCDS43408.1	ENSP00000349291	TBC9B_HUMAN	.	UPI000034ECFF	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAATATATCAG	.	5	ESCA
CDH10	0	.	GRCh37	5	24491686	24491686	+	Silent	SNP	C	C	G	rs184571175	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1875G>C	p.%3D	p.L625L	ENST00000264463	11/12	29	22	6	44	44	0	CDH10,synonymous_variant,p.%3D,ENST00000264463,;CDH10,splice_region_variant,,ENST00000502921,;CDH10,splice_region_variant,,ENST00000510477,;CDH10,splice_region_variant,,ENST00000503958,;	G	ENSG00000040731	ENST00000264463	Transcript	synonymous_variant	2383	1875	625	L	ctG/ctC	rs184571175,COSM591851	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	.	.	11/12	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACCCAGTAG	byFrequency|byCluster|by1000G	5	ESCA
RICTOR	0	.	GRCh37	5	38991089	38991089	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.545G>T	p.Arg182Ile	p.R182I	ENST00000357387	7/38	64	32	32	81	81	0	RICTOR,missense_variant,p.Arg166Ile,ENST00000514735,;RICTOR,missense_variant,p.Arg182Ile,ENST00000357387,;RICTOR,missense_variant,p.Arg182Ile,ENST00000296782,;RICTOR,missense_variant,p.Arg182Ile,ENST00000511516,;RICTOR,non_coding_transcript_exon_variant,,ENST00000513566,;RICTOR,non_coding_transcript_exon_variant,,ENST00000510711,;	A	ENSG00000164327	ENST00000357387	Transcript	missense_variant	576	545	182	R/I	aGa/aTa	.	.	.	-1	RICTOR	HGNC	28611	protein_coding	YES	CCDS34148.1	ENSP00000349959	RICTR_HUMAN	.	UPI00003529F3	.	deleterious(0)	probably_damaging(0.999)	7/38	.	Superfamily_domains:SSF48371,Pfam_domain:PF14664,hmmpanther:PTHR13298:SF11,hmmpanther:PTHR13298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATTCTGTCT	.	5	ESCA
CARD6	0	.	GRCh37	5	40853632	40853632	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2198T>A	p.Leu733His	p.L733H	ENST00000254691	3/3	30	24	6	45	45	0	CARD6,missense_variant,p.Leu733His,ENST00000254691,;CARD6,intron_variant,,ENST00000381677,;	A	ENSG00000132357	ENST00000254691	Transcript	missense_variant	2397	2198	733	L/H	cTc/cAc	.	.	.	1	CARD6	HGNC	16394	protein_coding	YES	CCDS3935.1	ENSP00000254691	CARD6_HUMAN	.	UPI000013CE50	.	deleterious(0)	benign(0.213)	3/3	.	hmmpanther:PTHR22797:SF26,hmmpanther:PTHR22797	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGCTCTTTC	.	2	ESCA
C6	0	.	GRCh37	5	41186174	41186174	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.724G>C	p.Glu242Gln	p.E242Q	ENST00000263413	6/18	39	32	6	50	50	0	C6,missense_variant,p.Glu242Gln,ENST00000263413,;C6,missense_variant,p.Glu242Gln,ENST00000337836,;C6,intron_variant,,ENST00000475349,;	G	ENSG00000039537	ENST00000263413	Transcript	missense_variant	989	724	242	E/Q	Gag/Cag	COSM592893	.	.	-1	C6	HGNC	1339	protein_coding	YES	CCDS3936.1	ENSP00000263413	CO6_HUMAN	C9JX36_HUMAN,C9JC72_HUMAN	UPI000013D401	.	tolerated(0.82)	benign(0.026)	6/18	.	hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,PROSITE_profiles:PS51412	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCTCAAAGC	.	5	ESCA
MAP3K1	0	.	GRCh37	5	56179413	56179413	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3726A>G	p.%3D	p.E1242E	ENST00000399503	15/20	56	29	27	109	109	0	MAP3K1,synonymous_variant,p.%3D,ENST00000399503,;MAP3K1,upstream_gene_variant,,ENST00000469188,;	G	ENSG00000095015	ENST00000399503	Transcript	synonymous_variant	3726	3726	1242	E	gaA/gaG	.	.	.	1	MAP3K1	HGNC	6848	protein_coding	YES	CCDS43318.1	ENSP00000382423	M3K1_HUMAN	.	UPI000015153B	.	.	.	15/20	.	hmmpanther:PTHR24361:SF255,hmmpanther:PTHR24361,Gene3D:3.30.200.20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGAATGGCT	.	5	ESCA
RAB3C	0	.	GRCh37	5	58147162	58147162	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668C>A	p.Pro223His	p.P223H	ENST00000282878	5/5	49	33	15	63	63	0	RAB3C,missense_variant,p.Pro223His,ENST00000282878,;CTD-2176I21.2,intron_variant,,ENST00000510198,;RAB3C,non_coding_transcript_exon_variant,,ENST00000381158,;	A	ENSG00000152932	ENST00000282878	Transcript	missense_variant	837	668	223	P/H	cCc/cAc	.	.	.	1	RAB3C	HGNC	30269	protein_coding	YES	CCDS3976.1	ENSP00000282878	RAB3C_HUMAN	.	UPI0000133178	.	tolerated(0.1)	benign(0.011)	5/5	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF445,Gene3D:3.40.50.300,SMART_domains:SM00176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGCCCAACT	.	5	ESCA
SEMA5A	0	.	GRCh37	5	9066719	9066719	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2113A>T	p.Lys705Ter	p.K705*	ENST00000382496	17/23	52	21	30	38	38	0	SEMA5A,stop_gained,p.Lys705Ter,ENST00000382496,;	A	ENSG00000112902	ENST00000382496	Transcript	stop_gained	2779	2113	705	K/*	Aag/Tag	.	.	.	-1	SEMA5A	HGNC	10736	protein_coding	YES	CCDS3875.1	ENSP00000371936	SEM5A_HUMAN	D6RAF4_HUMAN,B4DE33_HUMAN	UPI000004F25D	.	.	.	17/23	.	hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTTCAGCT	.	5	ESCA
PRDM1	0	.	GRCh37	6	106536292	106536292	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259C>A	p.Leu87Met	p.L87M	ENST00000369096	2/7	78	57	20	103	103	0	PRDM1,missense_variant,p.Leu51Met,ENST00000424894,;PRDM1,missense_variant,p.Leu87Met,ENST00000369096,;PRDM1,missense_variant,p.Leu51Met,ENST00000369091,;PRDM1,non_coding_transcript_exon_variant,,ENST00000489365,;	A	ENSG00000057657	ENST00000369096	Transcript	missense_variant	493	259	87	L/M	Ctg/Atg	.	.	.	1	PRDM1	HGNC	9346	protein_coding	YES	CCDS5054.2	ENSP00000358092	PRDM1_HUMAN	Q5T4E8_HUMAN,B2REA5_HUMAN	UPI0000D49069	.	deleterious(0)	probably_damaging(1)	2/7	.	PROSITE_profiles:PS50280,hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF339,Gene3D:2.170.270.10,SMART_domains:SM00317,PIRSF_domain:PIRSF013212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATCTGCTT	.	5	ESCA
AIM1	0	.	GRCh37	6	106967402	106967402	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1095G>A	p.%3D	p.E365E	ENST00000369066	2/20	25	16	9	29	29	0	AIM1,synonymous_variant,p.%3D,ENST00000369066,;	A	ENSG00000112297	ENST00000369066	Transcript	synonymous_variant	1582	1095	365	E	gaG/gaA	.	.	.	1	AIM1	HGNC	356	protein_coding	YES	CCDS34506.1	ENSP00000358062	AIM1_HUMAN	B3KPT0_HUMAN	UPI000013C91D	.	.	.	2/20	.	hmmpanther:PTHR11818:SF2,hmmpanther:PTHR11818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGAGAATCA	.	5	ESCA
AK9	0	.	GRCh37	6	109980576	109980576	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.485G>C	p.Arg162Thr	p.R162T	ENST00000424296	7/41	67	40	27	32	32	0	AK9,missense_variant,p.Arg162Thr,ENST00000424296,;AK9,missense_variant,p.Arg162Thr,ENST00000368948,;AK9,missense_variant,p.Arg50Thr,ENST00000524674,;AK9,missense_variant,p.Arg162Thr,ENST00000285397,;AK9,missense_variant,p.Arg85Thr,ENST00000448084,;AK9,missense_variant,p.Arg162Thr,ENST00000532976,;AK9,5_prime_UTR_variant,,ENST00000341338,;AK9,upstream_gene_variant,,ENST00000605986,;	G	ENSG00000155085	ENST00000424296	Transcript	missense_variant	562	485	162	R/T	aGa/aCa	.	.	.	-1	AK9	HGNC	33814	protein_coding	YES	CCDS55048.1	ENSP00000410186	KAD9_HUMAN	E9PPU7_HUMAN,E9PPM3_HUMAN	UPI0001A48FC8	.	deleterious(0)	probably_damaging(0.997)	7/41	.	hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF61,Pfam_domain:PF00406,Gene3D:3.40.50.300,SMART_domains:SM00382	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGTCTTTGC	.	5	ESCA
FIG4	0	.	GRCh37	6	110083318	110083318	+	Silent	SNP	A	A	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1296A>C	p.%3D	p.R432R	ENST00000230124	12/23	123	104	18	60	60	0	FIG4,synonymous_variant,p.%3D,ENST00000441478,;FIG4,synonymous_variant,p.%3D,ENST00000230124,;FIG4,upstream_gene_variant,,ENST00000415980,;	C	ENSG00000112367	ENST00000230124	Transcript	synonymous_variant	1420	1296	432	R	cgA/cgC	.	.	.	1	FIG4	HGNC	16873	protein_coding	YES	CCDS5078.1	ENSP00000230124	FIG4_HUMAN	Q5TCS4_HUMAN,Q5JRV4_HUMAN	UPI000000D9A3	.	.	.	12/23	.	PROSITE_profiles:PS50275,hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCGACTAAA	.	5	ESCA
PTPRK	0	.	GRCh37	6	128540204	128540204	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.731A>T	p.Lys244Met	p.K244M	ENST00000368213	6/31	166	89	76	105	105	0	PTPRK,missense_variant,p.Lys244Met,ENST00000532331,;PTPRK,missense_variant,p.Lys244Met,ENST00000368226,;PTPRK,missense_variant,p.Lys244Met,ENST00000368215,;PTPRK,missense_variant,p.Lys244Met,ENST00000368207,;PTPRK,missense_variant,p.Lys244Met,ENST00000368210,;PTPRK,missense_variant,p.Lys244Met,ENST00000368227,;PTPRK,missense_variant,p.Lys244Met,ENST00000368213,;PTPRK,missense_variant,p.Lys61Met,ENST00000490332,;PTPRK,non_coding_transcript_exon_variant,,ENST00000524534,;PTPRK,non_coding_transcript_exon_variant,,ENST00000498284,;PTPRK,non_coding_transcript_exon_variant,,ENST00000368205,;PTPRK,non_coding_transcript_exon_variant,,ENST00000524481,;PTPRK,downstream_gene_variant,,ENST00000495748,;PTPRK,3_prime_UTR_variant,,ENST00000531050,;	A	ENSG00000152894	ENST00000368213	Transcript	missense_variant	956	731	244	K/M	aAg/aTg	.	.	.	-1	PTPRK	HGNC	9674	protein_coding	YES	CCDS47473.1	ENSP00000357196	PTPRK_HUMAN	.	UPI0001747A04	.	deleterious(0)	possibly_damaging(0.755)	6/31	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR19134:SF209,hmmpanther:PTHR19134,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTCTTAGTC	.	5	ESCA
ENPP1	0	.	GRCh37	6	132172330	132172330	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479C>A	p.Thr160Asn	p.T160N	ENST00000360971	4/25	68	48	20	59	59	0	ENPP1,missense_variant,p.Thr160Asn,ENST00000360971,;ENPP1,missense_variant,p.Thr160Asn,ENST00000513998,;ENPP1,non_coding_transcript_exon_variant,,ENST00000486853,;	A	ENSG00000197594	ENST00000360971	Transcript	missense_variant	499	479	160	T/N	aCc/aAc	.	.	.	1	ENPP1	HGNC	3356	protein_coding	YES	CCDS5150.2	ENSP00000354238	ENPP1_HUMAN	Q9NS95_HUMAN	UPI00001303F0	.	tolerated(0.26)	benign(0.102)	4/25	.	Superfamily_domains:0049461,SMART_domains:SM00201,Pfam_domain:PF01033,hmmpanther:PTHR10151:SF64,hmmpanther:PTHR10151,PROSITE_profiles:PS50958	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGACCAGAA	.	5	ESCA
NHSL1	0	.	GRCh37	6	138756407	138756407	+	Intron	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.677-1590C>G	.	.	ENST00000427025	.	79	67	11	58	58	0	NHSL1,intron_variant,,ENST00000343505,;NHSL1,intron_variant,,ENST00000427025,;NHSL1,intron_variant,,ENST00000342260,;MIR3145,mature_miRNA_variant,,ENST00000580727,;	C	ENSG00000135540	ENST00000427025	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NHSL1	HGNC	21021	protein_coding	YES	CCDS55063.1	ENSP00000394546	NHSL1_HUMAN	B4DS58_HUMAN	UPI0001750345	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTGAGTGT	.	4	ESCA
HECA	0	.	GRCh37	6	139498225	139498225	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1615G>A	p.Val539Ile	p.V539I	ENST00000367658	4/4	94	44	50	58	58	0	HECA,missense_variant,p.Val539Ile,ENST00000367658,;RP1-225E12.2,intron_variant,,ENST00000590219,;RP1-225E12.2,intron_variant,,ENST00000585447,;RP1-225E12.2,intron_variant,,ENST00000588529,;RP1-225E12.2,intron_variant,,ENST00000586229,;RP1-225E12.2,intron_variant,,ENST00000415194,;RP1-225E12.2,intron_variant,,ENST00000586266,;RP1-225E12.2,intron_variant,,ENST00000588638,;RP1-225E12.2,intron_variant,,ENST00000587577,;RP1-225E12.2,intron_variant,,ENST00000591102,;RP1-225E12.2,intron_variant,,ENST00000590679,;RP1-225E12.2,intron_variant,,ENST00000589192,;RP1-225E12.3,intron_variant,,ENST00000585874,;	A	ENSG00000112406	ENST00000367658	Transcript	missense_variant	1900	1615	539	V/I	Gtt/Att	.	.	.	1	HECA	HGNC	21041	protein_coding	YES	CCDS5194.1	ENSP00000356630	HDC_HUMAN	.	UPI000006D0F2	.	deleterious(0.02)	probably_damaging(0.987)	4/4	.	hmmpanther:PTHR13425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAAGTTCTC	.	5	ESCA
SYNE1	0	.	GRCh37	6	152702455	152702455	+	Nonsense_Mutation	SNP	T	T	A	rs119103243	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8695A>T	p.Arg2899Ter	p.R2899*	ENST00000367255	56/146	27	16	11	24	24	0	SYNE1,stop_gained,p.Arg16Ter,ENST00000454018,;SYNE1,stop_gained,p.Arg2906Ter,ENST00000423061,;SYNE1,stop_gained,p.Arg2906Ter,ENST00000448038,;SYNE1,stop_gained,p.Arg2899Ter,ENST00000367255,;SYNE1,stop_gained,p.Arg2938Ter,ENST00000341594,;SYNE1,stop_gained,p.Arg2899Ter,ENST00000265368,;SYNE1-AS1,non_coding_transcript_exon_variant,,ENST00000412161,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,;SYNE1,upstream_gene_variant,,ENST00000471834,;	A	ENSG00000131018	ENST00000367255	Transcript	stop_gained	9297	8695	2899	R/*	Aga/Tga	CM070290,rs119103243,SYNE1:c.8695A>T	.	.	-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	SYNE1_HUMAN	.	UPI000204AF58	.	.	.	56/146	.	Superfamily_domains:SSF46966,SMART_domains:SM00150,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTCTGCTGA	byFrequency|byCluster	5	ESCA
OR12D2	0	.	GRCh37	6	29364590	29364590	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114T>A	p.%3D	p.T38T	ENST00000383555	1/1	54	15	38	63	63	0	OR12D2,synonymous_variant,p.%3D,ENST00000383555,;OR5V1,intron_variant,,ENST00000377154,;	A	ENSG00000168787	ENST00000383555	Transcript	synonymous_variant	175	114	38	T	acT/acA	.	.	.	1	OR12D2	HGNC	8178	protein_coding	YES	CCDS4659.1	ENSP00000373047	O12D2_HUMAN	.	UPI00001406A8	.	.	.	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26451:SF52,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGACTGGGAA	.	5	ESCA
TRIM10	0	.	GRCh37	6	30128472	30128472	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.164C>T	p.Pro55Leu	p.P55L	ENST00000449742	1/7	37	25	11	77	77	0	TRIM10,missense_variant,p.Pro55Leu,ENST00000376704,;TRIM10,missense_variant,p.Pro55Leu,ENST00000449742,;TRIM15,upstream_gene_variant,,ENST00000376688,;TRIM15,upstream_gene_variant,,ENST00000376694,;	A	ENSG00000204613	ENST00000449742	Transcript	missense_variant	240	164	55	P/L	cCt/cTt	.	.	.	-1	TRIM10	HGNC	10072	protein_coding	YES	CCDS34375.1	ENSP00000397073	TRI10_HUMAN	.	UPI000000D736	.	tolerated(0.93)	benign(0.014)	1/7	.	PROSITE_profiles:PS50089,hmmpanther:PTHR24103:SF44,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Pfam_domain:PF15227,SMART_domains:SM00184,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTAGGGGAC	.	5	ESCA
PRRC2A	0	.	GRCh37	6	31592989	31592989	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505G>A	p.Glu169Lys	p.E169K	ENST00000376033	6/31	31	19	11	29	29	0	PRRC2A,missense_variant,p.Glu169Lys,ENST00000376033,;PRRC2A,missense_variant,p.Glu169Lys,ENST00000376007,;SNORA38,downstream_gene_variant,,ENST00000363946,;PRRC2A,non_coding_transcript_exon_variant,,ENST00000469577,;PRRC2A,non_coding_transcript_exon_variant,,ENST00000464079,;PRRC2A,upstream_gene_variant,,ENST00000483470,;PRRC2A,upstream_gene_variant,,ENST00000464890,;	A	ENSG00000204469	ENST00000376033	Transcript	missense_variant	739	505	169	E/K	Gaa/Aaa	.	.	.	1	PRRC2A	HGNC	13918	protein_coding	YES	CCDS4708.1	ENSP00000365201	PRC2A_HUMAN	.	UPI000020E56F	.	.	unknown(0)	6/31	.	hmmpanther:PTHR14038,Pfam_domain:PF07001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GAGAGGAATTT	.	4	ESCA
GRM4	0	.	GRCh37	6	33990592	33990592	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6C>A	.	.	ENST00000538487	11/11	53	16	37	59	59	0	GRM4,3_prime_UTR_variant,,ENST00000544773,;GRM4,3_prime_UTR_variant,,ENST00000374181,;GRM4,3_prime_UTR_variant,,ENST00000609222,;GRM4,3_prime_UTR_variant,,ENST00000455714,;GRM4,3_prime_UTR_variant,,ENST00000535756,;GRM4,3_prime_UTR_variant,,ENST00000374177,;GRM4,3_prime_UTR_variant,,ENST00000538487,;GRM4,non_coding_transcript_exon_variant,,ENST00000545715,;GRM4,non_coding_transcript_exon_variant,,ENST00000609860,;GRM4,downstream_gene_variant,,ENST00000609278,;	T	ENSG00000124493	ENST00000538487	Transcript	3_prime_UTR_variant	3189	.	.	.	.	.	.	.	-1	GRM4	HGNC	4596	protein_coding	YES	CCDS4787.1	ENSP00000440556	GRM4_HUMAN	A8K0J8_HUMAN,A1L4F9_HUMAN	UPI000004A7DE	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGGACTCG	.	5	ESCA
ADCY10P1	0	.	GRCh37	6	41078986	41078986	+	RNA	SNP	G	G	T	rs146079468	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1475G>T	.	.	ENST00000567255	6/23	51	36	15	38	38	0	ADCY10P1,non_coding_transcript_exon_variant,,ENST00000567255,;ADCY10P1,non_coding_transcript_exon_variant,,ENST00000457653,;	T	ENSG00000161912	ENST00000567255	Transcript	non_coding_transcript_exon_variant	1475	.	.	.	.	rs146079468	.	.	1	ADCY10P1	HGNC	44143	processed_transcript	YES	.	.	.	.	.	.	.	.	6/23	.	.	A:0.0022	A:0.0076	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTCGGCCTT	byFrequency|by1000G	5	ESCA
SRF	0	.	GRCh37	6	43148477	43148477	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1549C>T	.	.	ENST00000265354	7/7	10	8	2	25	24	1	SRF,3_prime_UTR_variant,,ENST00000265354,;CUL9,upstream_gene_variant,,ENST00000354495,;SRF,downstream_gene_variant,,ENST00000457278,;CUL9,upstream_gene_variant,,ENST00000372647,;CUL9,upstream_gene_variant,,ENST00000252050,;CUL9,upstream_gene_variant,,ENST00000451399,;CUL9,upstream_gene_variant,,ENST00000515773,;	T	ENSG00000112658	ENST00000265354	Transcript	3_prime_UTR_variant	3434	.	.	.	.	.	.	.	1	SRF	HGNC	11291	protein_coding	YES	CCDS4889.1	ENSP00000265354	SRF_HUMAN	F5H6V4_HUMAN	UPI0000135F3B	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCAGCAGTGG	.	2	ESCA
TNFRSF21	0	.	GRCh37	6	47251781	47251781	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1136A>G	p.Lys379Arg	p.K379R	ENST00000296861	3/6	55	52	3	75	75	0	TNFRSF21,missense_variant,p.Lys379Arg,ENST00000296861,;	C	ENSG00000146072	ENST00000296861	Transcript	missense_variant	1530	1136	379	K/R	aAg/aGg	COSM1546726	.	.	-1	TNFRSF21	HGNC	13469	protein_coding	YES	CCDS4921.1	ENSP00000296861	TNR21_HUMAN	.	UPI000004680F	.	deleterious(0.02)	possibly_damaging(0.452)	3/6	.	hmmpanther:PTHR23097:SF99,hmmpanther:PTHR23097	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCCTTTTTC	.	2	ESCA
EYS	0	.	GRCh37	6	64499116	64499116	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7413G>T	p.%3D	p.G2471G	ENST00000503581	38/43	41	34	6	37	37	0	EYS,synonymous_variant,p.%3D,ENST00000370616,;EYS,synonymous_variant,p.%3D,ENST00000398580,;EYS,synonymous_variant,p.%3D,ENST00000370621,;EYS,synonymous_variant,p.%3D,ENST00000503581,;EYS,splice_region_variant,,ENST00000486069,;	A	ENSG00000188107	ENST00000503581	Transcript	synonymous_variant	7951	7413	2471	G	ggG/ggT	.	.	.	-1	EYS	HGNC	21555	protein_coding	YES	CCDS47445.1	ENSP00000424243	EYS_HUMAN	.	UPI000188F466	.	.	.	38/43	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24048:SF65,hmmpanther:PTHR24048,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCAACCCTGG	.	4	ESCA
RIMS1	0	.	GRCh37	6	72922726	72922726	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1679-20750C>T	.	.	ENST00000521978	.	37	29	7	27	27	0	RIMS1,5_prime_UTR_variant,,ENST00000523963,;RIMS1,5_prime_UTR_variant,,ENST00000401910,;RIMS1,intron_variant,,ENST00000491071,;RIMS1,intron_variant,,ENST00000522291,;RIMS1,intron_variant,,ENST00000520567,;RIMS1,intron_variant,,ENST00000518273,;RIMS1,intron_variant,,ENST00000517960,;RIMS1,intron_variant,,ENST00000517433,;RIMS1,intron_variant,,ENST00000264839,;RIMS1,intron_variant,,ENST00000348717,;RIMS1,intron_variant,,ENST00000521978,;RIMS1,upstream_gene_variant,,ENST00000517827,;RIMS1,upstream_gene_variant,,ENST00000453976,;RIMS1,upstream_gene_variant,,ENST00000425662,;RIMS1,intron_variant,,ENST00000370419,;RIMS1,upstream_gene_variant,,ENST00000524197,;	T	ENSG00000079841	ENST00000521978	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RIMS1	HGNC	17282	protein_coding	YES	CCDS47449.1	ENSP00000428417	RIMS1_HUMAN	.	UPI00001908FB	.	.	.	.	6/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGCGCTTC	.	5	ESCA
MUC12	0	.	GRCh37	7	100652377	100652377	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.15188T>C	p.Met5063Thr	p.M5063T	ENST00000536621	5/12	35	31	4	40	40	0	MUC12,missense_variant,p.Met5063Thr,ENST00000536621,;MUC12,missense_variant,p.Met5206Thr,ENST00000379442,;MUC12,upstream_gene_variant,,ENST00000305119,;	C	ENSG00000205277	ENST00000536621	Transcript	missense_variant	15188	15188	5063	M/T	aTg/aCg	.	.	.	1	MUC12	HGNC	7510	protein_coding	YES	CCDS55139.1	ENSP00000441929	.	F5GWV9_HUMAN	UPI0001B25898	.	.	benign(0.095)	5/12	.	Superfamily_domains:0047452,Pfam_domain:PF01390,PROSITE_profiles:PS50024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCAGATGGATG	.	4	ESCA
LAMB1	0	.	GRCh37	7	107600921	107600921	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2283C>G	p.Ser761Arg	p.S761R	ENST00000222399	18/34	44	40	4	39	39	0	LAMB1,missense_variant,p.Ser785Arg,ENST00000393561,;LAMB1,missense_variant,p.Ser761Arg,ENST00000393560,;LAMB1,missense_variant,p.Ser761Arg,ENST00000222399,;	C	ENSG00000091136	ENST00000222399	Transcript	missense_variant	2514	2283	761	S/R	agC/agG	.	.	.	-1	LAMB1	HGNC	6486	protein_coding	YES	CCDS5750.1	ENSP00000222399	LAMB1_HUMAN	Q75MC8_HUMAN,E9PCS6_HUMAN	UPI00001AE63F	.	deleterious(0.01)	benign(0.167)	18/34	.	PROSITE_profiles:PS51116,hmmpanther:PTHR10574:SF233,hmmpanther:PTHR10574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GAAATGCTAAA	.	2	ESCA
DOCK4	0	.	GRCh37	7	111503550	111503550	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2351C>G	p.Ala784Gly	p.A784G	ENST00000437633	23/52	41	20	21	44	44	0	DOCK4,missense_variant,p.Ala772Gly,ENST00000445943,;DOCK4,missense_variant,p.Ala784Gly,ENST00000428084,;DOCK4,missense_variant,p.Ala236Gly,ENST00000423057,;DOCK4,missense_variant,p.Ala784Gly,ENST00000437633,;DOCK4,non_coding_transcript_exon_variant,,ENST00000476846,;	C	ENSG00000128512	ENST00000437633	Transcript	missense_variant	2608	2351	784	A/G	gCc/gGc	.	.	.	-1	DOCK4	HGNC	19192	protein_coding	YES	CCDS47688.1	ENSP00000404179	DOCK4_HUMAN	Q75MU6_HUMAN	UPI0000D5BB0D	.	tolerated(0.09)	probably_damaging(0.991)	23/52	.	hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTGGCTACT	.	5	ESCA
AGAP3	0	.	GRCh37	7	150840668	150840668	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2514G>C	p.%3D	p.T838T	ENST00000397238	17/18	22	18	4	28	28	0	AGAP3,synonymous_variant,p.%3D,ENST00000463381,;AGAP3,synonymous_variant,p.%3D,ENST00000461065,;AGAP3,synonymous_variant,p.%3D,ENST00000397238,;AGAP3,non_coding_transcript_exon_variant,,ENST00000473633,;	C	ENSG00000133612	ENST00000397238	Transcript	synonymous_variant	2514	2514	838	T	acG/acC	.	.	.	1	AGAP3	HGNC	16923	protein_coding	YES	CCDS43681.1	ENSP00000380413	AGAP3_HUMAN	Q96T14_HUMAN,D3DX07_HUMAN	UPI0000DAC777	.	.	.	17/18	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR23180:SF198,hmmpanther:PTHR23180,Pfam_domain:PF12796,Gene3D:1.25.40.20,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V835I|c.2503G>A|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCACGCAGCT	.	5	ESCA
WDR60	0	.	GRCh37	7	158727131	158727131	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2669G>T	p.Arg890Ile	p.R890I	ENST00000407559	23/25	58	29	29	64	64	0	WDR60,missense_variant,p.Arg890Ile,ENST00000407559,;WDR60,missense_variant,p.Arg20Ile,ENST00000454771,;WDR60,3_prime_UTR_variant,,ENST00000444851,;WDR60,non_coding_transcript_exon_variant,,ENST00000467220,;	T	ENSG00000126870	ENST00000407559	Transcript	missense_variant	2827	2669	890	R/I	aGa/aTa	.	.	.	1	WDR60	HGNC	21862	protein_coding	YES	CCDS47757.1	ENSP00000384290	WDR60_HUMAN	H7C1E8_HUMAN,A4D230_HUMAN	UPI000020E761	.	deleterious(0)	possibly_damaging(0.766)	23/25	.	hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF30,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACAAGACAAG	.	5	ESCA
EVX1	0	.	GRCh37	7	27282614	27282614	+	5'UTR	SNP	T	T	G	rs369569472	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-36T>G	.	.	ENST00000496902	1/3	31	12	19	50	50	0	EVX1,5_prime_UTR_variant,,ENST00000496902,;EVX1,5_prime_UTR_variant,,ENST00000222761,;EVX1,upstream_gene_variant,,ENST00000580535,;EVX1,upstream_gene_variant,,ENST00000535619,;RP1-170O19.17,upstream_gene_variant,,ENST00000523608,;EVX1-AS,intron_variant,,ENST00000517726,;EVX1-AS,intron_variant,,ENST00000519218,;EVX1-AS,upstream_gene_variant,,ENST00000519050,;EVX1,upstream_gene_variant,,ENST00000518886,;	G	ENSG00000106038	ENST00000496902	Transcript	5_prime_UTR_variant	451	.	.	.	.	rs369569472	.	.	1	EVX1	HGNC	3506	protein_coding	YES	CCDS5413.1	ENSP00000419266	EVX1_HUMAN	B4DQJ0_HUMAN	UPI000012A2AD	.	.	.	1/3	.	.	C:0.0004	C:0	C:0	.	C:0.001	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCACTTGGGG	byFrequency|byCluster|by1000G	5	ESCA
URGCP	0	.	GRCh37	7	43918839	43918839	+	Nonsense_Mutation	SNP	C	C	A	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.223G>T	p.Glu75Ter	p.E75*	ENST00000453200	6/6	76	63	12	55	55	0	URGCP,stop_gained,p.Glu32Ter,ENST00000447717,;URGCP,stop_gained,p.Glu75Ter,ENST00000453200,;URGCP,stop_gained,p.Glu32Ter,ENST00000336086,;URGCP,stop_gained,p.Glu32Ter,ENST00000455877,;URGCP,stop_gained,p.Glu32Ter,ENST00000443736,;URGCP,stop_gained,p.Glu32Ter,ENST00000223341,;URGCP,stop_gained,p.Glu32Ter,ENST00000426198,;URGCP,stop_gained,p.Glu66Ter,ENST00000402306,;URGCP-MRPS24,intron_variant,,ENST00000603700,;URGCP,downstream_gene_variant,,ENST00000446958,;URGCP,non_coding_transcript_exon_variant,,ENST00000497914,;URGCP,3_prime_UTR_variant,,ENST00000439702,;URGCP,non_coding_transcript_exon_variant,,ENST00000467410,;URGCP,non_coding_transcript_exon_variant,,ENST00000474376,;	A	ENSG00000106608	ENST00000453200	Transcript	stop_gained	717	223	75	E/*	Gaa/Taa	COSM673964	.	.	-1	URGCP	HGNC	30890	protein_coding	YES	CCDS47578.1	ENSP00000396918	URGCP_HUMAN	C9JKA8_HUMAN,C9J0W2_HUMAN	UPI000020EE9D	.	.	.	6/6	.	hmmpanther:PTHR22796	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTCTTGAA	.	4	ESCA
ZNF890P	0	.	GRCh37	7	5161474	5161474	+	RNA	SNP	T	T	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1081A>C	.	.	ENST00000422060	6/6	33	26	7	51	51	0	ZNF890P,non_coding_transcript_exon_variant,,ENST00000422060,;ZNF890P,non_coding_transcript_exon_variant,,ENST00000530367,;OR10AH1P,downstream_gene_variant,,ENST00000608262,;	G	ENSG00000159904	ENST00000422060	Transcript	non_coding_transcript_exon_variant	1081	.	.	.	.	.	.	.	-1	ZNF890P	HGNC	38691	processed_transcript	YES	.	.	.	.	.	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCCTGAGCT	.	5	ESCA
TNRC18	0	.	GRCh37	7	5348561	5348561	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8645G>T	p.Ser2882Ile	p.S2882I	ENST00000430969	29/30	73	61	12	31	31	0	TNRC18,missense_variant,p.Ser2882Ile,ENST00000430969,;TNRC18,missense_variant,p.Ser2882Ile,ENST00000399537,;SLC29A4,downstream_gene_variant,,ENST00000297195,;TNRC18,downstream_gene_variant,,ENST00000328270,;SLC29A4,downstream_gene_variant,,ENST00000396872,;SLC29A4,downstream_gene_variant,,ENST00000406453,;	A	ENSG00000182095	ENST00000430969	Transcript	missense_variant	8994	8645	2882	S/I	aGc/aTc	.	.	.	-1	TNRC18	HGNC	11962	protein_coding	YES	CCDS47534.1	ENSP00000395538	TNC18_HUMAN	H7C3U5_HUMAN,C9J9K1_HUMAN	UPI00016632FD	.	.	unknown(0)	29/30	.	SMART_domains:SM00439,Pfam_domain:PF01426,hmmpanther:PTHR12505:SF21,hmmpanther:PTHR12505,PROSITE_profiles:PS51038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCGGCTGGAC	.	5	ESCA
GUSB	0	.	GRCh37	7	65444472	65444472	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.638G>C	p.Gly213Ala	p.G213A	ENST00000304895	4/12	87	74	13	70	70	0	GUSB,missense_variant,p.Gly213Ala,ENST00000345660,;GUSB,missense_variant,p.Gly213Ala,ENST00000304895,;GUSB,intron_variant,,ENST00000421103,;GUSB,non_coding_transcript_exon_variant,,ENST00000476486,;GUSB,non_coding_transcript_exon_variant,,ENST00000465785,;GUSB,non_coding_transcript_exon_variant,,ENST00000478118,;GUSB,intron_variant,,ENST00000475316,;GUSB,intron_variant,,ENST00000479038,;GUSB,3_prime_UTR_variant,,ENST00000446111,;GUSB,3_prime_UTR_variant,,ENST00000447929,;GUSB,intron_variant,,ENST00000430730,;GUSB,upstream_gene_variant,,ENST00000462371,;GUSB,upstream_gene_variant,,ENST00000489482,;GUSB,upstream_gene_variant,,ENST00000466883,;	G	ENSG00000169919	ENST00000304895	Transcript	missense_variant	769	638	213	G/A	gGa/gCa	.	.	.	-1	GUSB	HGNC	4696	protein_coding	YES	CCDS5530.1	ENSP00000302728	BGLR_HUMAN	.	UPI000013E9E0	.	deleterious(0.01)	possibly_damaging(0.817)	4/12	.	hmmpanther:PTHR10066:SF51,hmmpanther:PTHR10066,Pfam_domain:PF02837,Gene3D:2.60.120.260,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTCCAGCG	.	5	ESCA
ELN	0	.	GRCh37	7	73456951	73456951	+	Silent	SNP	C	C	G	rs138649857	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.240C>G	p.%3D	p.G80G	ENST00000252034	6/33	90	50	40	64	64	0	ELN,synonymous_variant,p.%3D,ENST00000380562,;ELN,synonymous_variant,p.%3D,ENST00000442310,;ELN,synonymous_variant,p.%3D,ENST00000252034,;ELN,synonymous_variant,p.%3D,ENST00000380576,;ELN,synonymous_variant,p.%3D,ENST00000380575,;ELN,synonymous_variant,p.%3D,ENST00000431562,;ELN,synonymous_variant,p.%3D,ENST00000320492,;ELN,synonymous_variant,p.%3D,ENST00000445912,;ELN,synonymous_variant,p.%3D,ENST00000414324,;ELN,synonymous_variant,p.%3D,ENST00000429192,;ELN,synonymous_variant,p.%3D,ENST00000358929,;ELN,synonymous_variant,p.%3D,ENST00000320399,;ELN,synonymous_variant,p.%3D,ENST00000458204,;ELN,synonymous_variant,p.%3D,ENST00000417091,;ELN,synonymous_variant,p.%3D,ENST00000357036,;ELN,synonymous_variant,p.%3D,ENST00000380584,;ELN,synonymous_variant,p.%3D,ENST00000428787,;ELN,synonymous_variant,p.%3D,ENST00000438906,;ELN,intron_variant,,ENST00000438880,;ELN,intron_variant,,ENST00000380553,;ELN,3_prime_UTR_variant,,ENST00000416107,;ELN,non_coding_transcript_exon_variant,,ENST00000479432,;ELN,non_coding_transcript_exon_variant,,ENST00000492003,;ELN,non_coding_transcript_exon_variant,,ENST00000473323,;ELN,non_coding_transcript_exon_variant,,ENST00000468517,;ELN,non_coding_transcript_exon_variant,,ENST00000480728,;ELN,non_coding_transcript_exon_variant,,ENST00000462506,;ELN,downstream_gene_variant,,ENST00000494160,;ELN,upstream_gene_variant,,ENST00000493839,;ELN,upstream_gene_variant,,ENST00000419398,;ELN,upstream_gene_variant,,ENST00000477397,;	G	ENSG00000049540	ENST00000252034	Transcript	synonymous_variant	639	240	80	G	ggC/ggG	rs138649857,COSM1251133	.	.	1	ELN	HGNC	3327	protein_coding	YES	CCDS5562.2	ENSP00000252034	ELN_HUMAN	Q9UMK5_HUMAN	UPI0000D4A0DC	.	.	.	6/33	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24018:SF2,hmmpanther:PTHR24018	.	.	.	.	.	.	.	T:0.0005	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGGCGCCTT	byCluster	5	ESCA
COL28A1	0	.	GRCh37	7	7491958	7491958	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1501G>T	p.Gly501Cys	p.G501C	ENST00000399429	18/35	46	33	13	65	65	0	COL28A1,missense_variant,p.Gly501Cys,ENST00000399429,;COL28A1,3_prime_UTR_variant,,ENST00000444268,;	A	ENSG00000215018	ENST00000399429	Transcript	missense_variant	1642	1501	501	G/C	Ggt/Tgt	.	.	.	-1	COL28A1	HGNC	22442	protein_coding	YES	CCDS43553.1	ENSP00000382356	COSA1_HUMAN	H7C3P2_HUMAN,H7BZU0_HUMAN	UPI000155D64E	.	deleterious(0.01)	probably_damaging(1)	18/35	.	hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF375,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACCTTGTA	.	5	ESCA
MAGI2	0	.	GRCh37	7	77649090	77649090	+	Missense_Mutation	SNP	C	C	G	rs760239278	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3910G>C	p.Gly1304Arg	p.G1304R	ENST00000354212	22/22	21	15	6	13	13	0	MAGI2,missense_variant,p.Gly1304Arg,ENST00000354212,;MAGI2,missense_variant,p.Gly1290Arg,ENST00000419488,;MAGI2,3_prime_UTR_variant,,ENST00000522391,;	G	ENSG00000187391	ENST00000354212	Transcript	missense_variant	4164	3910	1304	G/R	Ggc/Cgc	rs760239278	.	.	-1	MAGI2	HGNC	18957	protein_coding	YES	CCDS5594.1	ENSP00000346151	MAGI2_HUMAN	.	UPI00001615D2	.	deleterious(0.03)	possibly_damaging(0.618)	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGGCCGCAGG	byFrequency	2	ESCA
SEMA3D	0	.	GRCh37	7	84685162	84685162	+	Silent	SNP	A	A	T	rs556375076	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732T>A	p.%3D	p.I244I	ENST00000284136	7/17	82	64	18	108	108	0	SEMA3D,synonymous_variant,p.%3D,ENST00000284136,;SEMA3D,synonymous_variant,p.%3D,ENST00000444867,;SEMA3D,upstream_gene_variant,,ENST00000463315,;	T	ENSG00000153993	ENST00000284136	Transcript	synonymous_variant	776	732	244	I	atT/atA	rs556375076	.	.	-1	SEMA3D	HGNC	10726	protein_coding	YES	CCDS34676.1	ENSP00000284136	SEM3D_HUMAN	.	UPI0000135A66	.	.	.	7/17	.	Superfamily_domains:SSF101912,SMART_domains:SM00630,Gene3D:2.130.10.10,Pfam_domain:PF01403,hmmpanther:PTHR11036:SF36,hmmpanther:PTHR11036,PROSITE_profiles:PS51004	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTCCAATAAA	by1000G	4	ESCA
DLX6	0	.	GRCh37	7	96639848	96639848	+	3'UTR	SNP	C	C	T	rs554371394	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*489C>T	.	.	ENST00000518156	3/3	11	9	2	13	13	0	DLX6,3_prime_UTR_variant,,ENST00000007660,;DLX6,3_prime_UTR_variant,,ENST00000518156,;DLX6,downstream_gene_variant,,ENST00000555308,;DLX6-AS1,intron_variant,,ENST00000458352,;DLX6-AS1,intron_variant,,ENST00000430404,;DLX6-AS1,intron_variant,,ENST00000430027,;DLX6-AS1,intron_variant,,ENST00000605417,;DLX6-AS1,intron_variant,,ENST00000452769,;DLX6-AS1,intron_variant,,ENST00000437331,;DLX6-AS1,intron_variant,,ENST00000437541,;DLX6-AS2,upstream_gene_variant,,ENST00000606174,;DLX6,downstream_gene_variant,,ENST00000493273,;	T	ENSG00000006377	ENST00000518156	Transcript	3_prime_UTR_variant	1801	.	.	.	.	rs554371394	.	.	1	DLX6	HGNC	2919	protein_coding	YES	CCDS47647.2	ENSP00000428480	DLX6_HUMAN	.	UPI0000EE57E0	.	.	.	3/3	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTGCACAAA	by1000G	2	ESCA
LONRF1	0	.	GRCh37	8	12592793	12592793	+	Splice_Site	SNP	A	A	G	.	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1566+2T>C	.	p.X522_splice	ENST00000398246	.	42	28	13	93	93	0	LONRF1,splice_donor_variant,,ENST00000533751,;LONRF1,splice_donor_variant,,ENST00000398246,;LONRF1,splice_donor_variant,,ENST00000524526,;LONRF1,downstream_gene_variant,,ENST00000530693,;LONRF1,splice_donor_variant,,ENST00000526610,;LONRF1,splice_donor_variant,,ENST00000526680,;LONRF1,downstream_gene_variant,,ENST00000534446,;	G	ENSG00000154359	ENST00000398246	Transcript	splice_donor_variant	.	.	.	.	.	COSM1095920	.	.	-1	LONRF1	HGNC	26302	protein_coding	YES	CCDS5987.2	ENSP00000381298	LONF1_HUMAN	E9PQH4_HUMAN	UPI0000696489	.	.	.	.	7/11	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTACCTCT	.	5	ESCA
CPSF1	0	.	GRCh37	8	145626338	145626338	+	Silent	SNP	G	G	A	rs782746758	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.519C>T	p.%3D	p.H173H	ENST00000349769	6/38	65	46	19	33	33	0	CPSF1,synonymous_variant,p.%3D,ENST00000349769,;CPSF1,synonymous_variant,p.%3D,ENST00000531042,;MIR1234,upstream_gene_variant,,ENST00000408875,;CPSF1,non_coding_transcript_exon_variant,,ENST00000532560,;CPSF1,non_coding_transcript_exon_variant,,ENST00000531683,;CPSF1,upstream_gene_variant,,ENST00000533492,;CPSF1,upstream_gene_variant,,ENST00000527916,;CPSF1,upstream_gene_variant,,ENST00000527827,;	A	ENSG00000071894	ENST00000349769	Transcript	synonymous_variant	614	519	173	H	caC/caT	rs782746758	.	.	-1	CPSF1	HGNC	2324	protein_coding	YES	CCDS34966.1	ENSP00000339353	CPSF1_HUMAN	Q9C0J6_HUMAN,E9PIM1_HUMAN,D3DWL9_HUMAN	UPI00001282EE	.	.	.	6/38	.	hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF2,Pfam_domain:PF10433	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCGTGCTC	byFrequency	5	ESCA
BNIP3L	0	.	GRCh37	8	26265848	26265848	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567C>A	p.Phe189Leu	p.F189L	ENST00000380629	5/6	103	77	25	56	56	0	BNIP3L,missense_variant,p.Phe189Leu,ENST00000380629,;BNIP3L,missense_variant,p.Phe167Leu,ENST00000523949,;BNIP3L,missense_variant,p.Phe149Leu,ENST00000518611,;BNIP3L,missense_variant,p.Phe149Leu,ENST00000520409,;BNIP3L,missense_variant,p.Phe149Leu,ENST00000523515,;BNIP3L,non_coding_transcript_exon_variant,,ENST00000521254,;BNIP3L,3_prime_UTR_variant,,ENST00000520077,;	A	ENSG00000104765	ENST00000380629	Transcript	missense_variant	800	567	189	F/L	ttC/ttA	.	.	.	1	BNIP3L	HGNC	1085	protein_coding	YES	CCDS6050.1	ENSP00000370003	BNI3L_HUMAN	Q6IBV1_HUMAN,B4DTN1_HUMAN,B0AZS9_HUMAN	UPI000004CF4D	.	tolerated(0.12)	benign(0.137)	5/6	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR15186:SF3,hmmpanther:PTHR15186,Pfam_domain:PF06553	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTCATTCC	.	5	ESCA
LEPROTL1	0	.	GRCh37	8	29964500	29964500	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.279+2498G>T	.	.	ENST00000523116	.	14	12	2	8	8	0	LEPROTL1,3_prime_UTR_variant,,ENST00000321250,;LEPROTL1,intron_variant,,ENST00000523116,;LEPROTL1,intron_variant,,ENST00000520682,;LEPROTL1,intron_variant,,ENST00000442880,;LEPROTL1,downstream_gene_variant,,ENST00000519466,;LEPROTL1,downstream_gene_variant,,ENST00000518001,;LEPROTL1,downstream_gene_variant,,ENST00000518192,;LEPROTL1,intron_variant,,ENST00000520739,;	T	ENSG00000104660	ENST00000523116	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LEPROTL1	HGNC	6555	protein_coding	YES	CCDS47834.1	ENSP00000428281	LERL1_HUMAN	.	UPI000020FF8F	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACAAGTAACT	.	2	ESCA
TEX15	0	.	GRCh37	8	30701460	30701460	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5074G>C	p.Glu1692Gln	p.E1692Q	ENST00000256246	1/4	64	48	15	45	45	0	TEX15,missense_variant,p.Glu1692Gln,ENST00000256246,;TEX15,downstream_gene_variant,,ENST00000523186,;	G	ENSG00000133863	ENST00000256246	Transcript	missense_variant	5149	5074	1692	E/Q	Gaa/Caa	.	.	.	-1	TEX15	HGNC	11738	protein_coding	YES	CCDS6080.1	ENSP00000256246	TEX15_HUMAN	D3DSV6_HUMAN	UPI000013CEF9	.	deleterious(0)	probably_damaging(0.998)	1/4	.	Pfam_domain:PF15326,hmmpanther:PTHR22380,hmmpanther:PTHR22380:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTTCTACCA	.	5	ESCA
UNC5D	0	.	GRCh37	8	35583947	35583947	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1581G>T	p.Met527Ile	p.M527I	ENST00000404895	10/17	59	39	19	102	102	0	UNC5D,missense_variant,p.Met103Ile,ENST00000449677,;UNC5D,missense_variant,p.Met522Ile,ENST00000453357,;UNC5D,missense_variant,p.Met532Ile,ENST00000416672,;UNC5D,missense_variant,p.Met527Ile,ENST00000404895,;UNC5D,missense_variant,p.Met458Ile,ENST00000287272,;UNC5D,missense_variant,p.Met460Ile,ENST00000420357,;UNC5D,non_coding_transcript_exon_variant,,ENST00000474634,;	T	ENSG00000156687	ENST00000404895	Transcript	missense_variant	1909	1581	527	M/I	atG/atT	.	.	.	1	UNC5D	HGNC	18634	protein_coding	YES	CCDS6093.2	ENSP00000385143	UNC5D_HUMAN	.	UPI00001D6915	.	tolerated(0.19)	benign(0.001)	10/17	.	hmmpanther:PTHR12582:SF5,hmmpanther:PTHR12582	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATGCCCTA	.	5	ESCA
EYA1	0	.	GRCh37	8	72110754	72110754	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*821G>C	.	.	ENST00000340726	18/18	43	32	11	37	37	0	EYA1,3_prime_UTR_variant,,ENST00000388741,;EYA1,3_prime_UTR_variant,,ENST00000388742,;EYA1,3_prime_UTR_variant,,ENST00000340726,;EYA1,3_prime_UTR_variant,,ENST00000388740,;EYA1,3_prime_UTR_variant,,ENST00000303824,;EYA1,downstream_gene_variant,,ENST00000419131,;EYA1,downstream_gene_variant,,ENST00000388743,;RP11-326E22.1,intron_variant,,ENST00000521685,;EYA1,3_prime_UTR_variant,,ENST00000465115,;EYA1,downstream_gene_variant,,ENST00000496494,;	G	ENSG00000104313	ENST00000340726	Transcript	3_prime_UTR_variant	3240	.	.	.	.	.	.	.	-1	EYA1	HGNC	3519	protein_coding	YES	CCDS34906.1	ENSP00000342626	EYA1_HUMAN	Q4A4D0_HUMAN	UPI000012A3B3	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCCTCATG	.	5	ESCA
RPL30	0	.	GRCh37	8	99054886	99054886	+	Frame_Shift_Del	DEL	A	A	-	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285delT	p.Ile96SerfsTer33	p.I96Sfs*33	ENST00000521291	3/4	33	26	7	36	36	0	RPL30,frameshift_variant,p.Ile96SerfsTer33,ENST00000521291,;RPL30,frameshift_variant,p.Ile96SerfsTer33,ENST00000287038,;RPL30,frameshift_variant,p.Ile96SerfsTer?,ENST00000521726,;RPL30,frameshift_variant,p.Ile32SerfsTer?,ENST00000523172,;RPL30,frameshift_variant,p.Ile77SerfsTer33,ENST00000396070,;SNORA72,upstream_gene_variant,,ENST00000384339,;KB-1208A12.3,non_coding_transcript_exon_variant,,ENST00000501016,;RPL30,intron_variant,,ENST00000518164,;RPL30,downstream_gene_variant,,ENST00000522156,;RPL30,downstream_gene_variant,,ENST00000517805,;RPL30,3_prime_UTR_variant,,ENST00000518850,;RPL30,non_coding_transcript_exon_variant,,ENST00000517489,;RPL30,non_coding_transcript_exon_variant,,ENST00000521534,;RPL30,downstream_gene_variant,,ENST00000521112,;RPL30,downstream_gene_variant,,ENST00000520998,;	-	ENSG00000156482	ENST00000521291	Transcript	frameshift_variant	432	285	95	A/X	gcT/gc	.	.	.	-1	RPL30	HGNC	10333	protein_coding	YES	CCDS34928.1	ENSP00000428085	RL30_HUMAN	E5RJH3_HUMAN,E5RI99_HUMAN	UPI0000001623	.	.	.	3/4	.	Superfamily_domains:SSF55315,Pfam_domain:PF01248,Gene3D:3.30.1330.30,PROSITE_patterns:PS00993,hmmpanther:PTHR11449,hmmpanther:PTHR11449:SF1,HAMAP:MF_00481	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATGATAGCCAG	.	3	ESCA
POP1	0	.	GRCh37	8	99153104	99153104	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1582G>C	p.Glu528Gln	p.E528Q	ENST00000401707	11/16	99	95	4	96	96	0	POP1,missense_variant,p.Glu528Gln,ENST00000401707,;POP1,missense_variant,p.Glu528Gln,ENST00000349693,;	C	ENSG00000104356	ENST00000401707	Transcript	missense_variant	1663	1582	528	E/Q	Gaa/Caa	.	.	.	1	POP1	HGNC	30129	protein_coding	YES	CCDS6277.1	ENSP00000385787	POP1_HUMAN	E5RK39_HUMAN	UPI0000131F33	.	tolerated(0.11)	benign(0.025)	11/16	.	hmmpanther:PTHR22731:SF3,hmmpanther:PTHR22731	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ATCCAGAAAAA	.	2	ESCA
NR4A3	0	.	GRCh37	9	102628028	102628028	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1879G>C	.	.	ENST00000330847	7/7	33	28	5	59	59	0	NR4A3,3_prime_UTR_variant,,ENST00000330847,;NR4A3,downstream_gene_variant,,ENST00000395097,;	C	ENSG00000119508	ENST00000330847	Transcript	3_prime_UTR_variant	3837	.	.	.	.	.	.	.	1	NR4A3	HGNC	7982	protein_coding	YES	CCDS6742.1	ENSP00000333122	NR4A3_HUMAN	.	UPI0000160FE4	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCCAGATAGG	.	4	ESCA
PAPPA	0	.	GRCh37	9	118949454	118949455	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438dupT	p.Ile147TyrfsTer4	p.I147Yfs*4	ENST00000328252	2/22	49	28	21	35	35	0	PAPPA,frameshift_variant,p.Ile147TyrfsTer4,ENST00000328252,;PAPPA,upstream_gene_variant,,ENST00000534838,;	T	ENSG00000182752	ENST00000328252	Transcript	frameshift_variant	806-807	437-438	146	Y/YX	tat/taTt	.	.	.	1	PAPPA	HGNC	8602	protein_coding	YES	CCDS6813.1	ENSP00000330658	PAPP1_HUMAN	Q5QFB7_HUMAN,F5GZ19_HUMAN	UPI00001E0589	.	.	.	2/22	.	hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347,Gene3D:2.60.120.200,Pfam_domain:PF13385,SMART_domains:SM00560,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTTATATCT	.	3	ESCA
NEK6	0	.	GRCh37	9	127113426	127113426	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*200T>C	.	.	ENST00000373600	11/11	51	48	3	47	47	0	NEK6,3_prime_UTR_variant,,ENST00000546191,;NEK6,3_prime_UTR_variant,,ENST00000373603,;NEK6,3_prime_UTR_variant,,ENST00000540326,;NEK6,3_prime_UTR_variant,,ENST00000394199,;NEK6,3_prime_UTR_variant,,ENST00000320246,;NEK6,3_prime_UTR_variant,,ENST00000539416,;NEK6,3_prime_UTR_variant,,ENST00000545174,;NEK6,3_prime_UTR_variant,,ENST00000373600,;PSMB7,downstream_gene_variant,,ENST00000259457,;NEK6,downstream_gene_variant,,ENST00000454453,;AL137846.1,upstream_gene_variant,,ENST00000583657,;PSMB7,downstream_gene_variant,,ENST00000498485,;	C	ENSG00000119408	ENST00000373600	Transcript	3_prime_UTR_variant	1459	.	.	.	.	.	.	.	1	NEK6	HGNC	7749	protein_coding	YES	CCDS48015.1	ENSP00000362702	NEK6_HUMAN	Q5TBH2_HUMAN,Q5TBH1_HUMAN,Q5TBG7_HUMAN,Q5TBG4_HUMAN,Q5TBG2_HUMAN,Q5TBG1_HUMAN	UPI000013ED34	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGGTCAGAT	.	2	ESCA
NOTCH1	0	.	GRCh37	9	139409151	139409151	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2018G>C	p.Ser673Thr	p.S673T	ENST00000277541	13/34	127	96	30	95	95	0	NOTCH1,missense_variant,p.Ser673Thr,ENST00000277541,;MIR4673,downstream_gene_variant,,ENST00000584777,;	G	ENSG00000148400	ENST00000277541	Transcript	missense_variant	2094	2018	673	S/T	aGc/aCc	.	.	.	-1	NOTCH1	HGNC	7881	protein_coding	YES	CCDS43905.1	ENSP00000277541	NOTC1_HUMAN	H9CXX2_HUMAN	UPI0000210F68	.	tolerated(0.4)	benign(0.023)	13/34	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF37,hmmpanther:PTHR24033,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002279,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATGCTCCCT	.	5	ESCA
ABCA2	0	.	GRCh37	9	139915182	139915182	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1229G>A	p.Trp410Ter	p.W410*	ENST00000341511	9/49	81	67	13	52	52	0	ABCA2,stop_gained,p.Trp409Ter,ENST00000371605,;ABCA2,stop_gained,p.Trp410Ter,ENST00000341511,;ABCA2,stop_gained,p.Trp410Ter,ENST00000265662,;ABCA2,synonymous_variant,p.%3D,ENST00000470535,;ABCA2,non_coding_transcript_exon_variant,,ENST00000492260,;ABCA2,upstream_gene_variant,,ENST00000466707,;ABCA2,downstream_gene_variant,,ENST00000398207,;ABCA2,upstream_gene_variant,,ENST00000467624,;ABCA2,stop_gained,p.Trp439Ter,ENST00000459850,;ABCA2,stop_gained,p.Trp439Ter,ENST00000487109,;ABCA2,3_prime_UTR_variant,,ENST00000464876,;ABCA2,non_coding_transcript_exon_variant,,ENST00000494046,;ABCA2,downstream_gene_variant,,ENST00000476211,;ABCA2,upstream_gene_variant,,ENST00000479446,;ABCA2,upstream_gene_variant,,ENST00000488535,;ABCA2,downstream_gene_variant,,ENST00000425423,;	T	ENSG00000107331	ENST00000341511	Transcript	stop_gained	1279	1229	410	W/*	tGg/tAg	.	.	.	-1	ABCA2	HGNC	32	protein_coding	YES	CCDS43909.1	ENSP00000344155	ABCA2_HUMAN	Q9UPU0_HUMAN,B4DI99_HUMAN	UPI00015E02DC	.	.	.	9/49	.	hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF116	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGCCCAGAGC	.	5	ESCA
PLAA	0	.	GRCh37	9	26947000	26947000	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44G>A	p.Arg15Gln	p.R15Q	ENST00000397292	1/14	57	54	3	58	58	0	PLAA,missense_variant,p.Arg15Gln,ENST00000520884,;PLAA,missense_variant,p.Arg15Gln,ENST00000397292,;IFT74,upstream_gene_variant,,ENST00000517444,;IFT74,upstream_gene_variant,,ENST00000443698,;PLAA,upstream_gene_variant,,ENST00000523212,;IFT74,upstream_gene_variant,,ENST00000519968,;IFT74,upstream_gene_variant,,ENST00000433700,;	T	ENSG00000137055	ENST00000397292	Transcript	missense_variant	462	44	15	R/Q	cGg/cAg	.	.	.	-1	PLAA	HGNC	9043	protein_coding	YES	CCDS35000.1	ENSP00000380460	PLAP_HUMAN	.	UPI00000372D6	.	tolerated(0.54)	benign(0.002)	1/14	.	PROSITE_profiles:PS50294,hmmpanther:PTHR19849:SF0,hmmpanther:PTHR19849,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCCCGGAGC	.	2	ESCA
FAM74A3	0	.	GRCh37	9	40715957	40715957	+	RNA	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.296A>G	.	.	ENST00000604146	1/2	326	277	49	536	536	0	FAM74A3,non_coding_transcript_exon_variant,,ENST00000355345,;FAM74A3,non_coding_transcript_exon_variant,,ENST00000604146,;RP11-395E19.5,upstream_gene_variant,,ENST00000432614,;RP11-395E19.2,upstream_gene_variant,,ENST00000433824,;	G	ENSG00000204844	ENST00000604146	Transcript	non_coding_transcript_exon_variant	296	.	.	.	.	.	.	.	1	FAM74A3	HGNC	32031	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CGTGGAGAGCT	.	2	ESCA
KANK1	0	.	GRCh37	9	712040	712040	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1274C>T	p.Ala425Val	p.A425V	ENST00000382303	7/16	32	29	3	48	48	0	KANK1,missense_variant,p.Ala267Val,ENST00000382293,;KANK1,missense_variant,p.Ala425Val,ENST00000382303,;KANK1,missense_variant,p.Ala425Val,ENST00000382297,;KANK1,non_coding_transcript_exon_variant,,ENST00000489369,;KANK1,non_coding_transcript_exon_variant,,ENST00000354485,;	T	ENSG00000107104	ENST00000382303	Transcript	missense_variant	1926	1274	425	A/V	gCa/gTa	.	.	.	1	KANK1	HGNC	19309	protein_coding	YES	CCDS34976.1	ENSP00000371740	KANK1_HUMAN	Q8WUM7_HUMAN,Q53U93_HUMAN	UPI00001AF26E	.	tolerated(0.78)	benign(0.005)	7/16	.	hmmpanther:PTHR24168,hmmpanther:PTHR24168:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GGATGCAGCTG	.	3	ESCA
KLF9	0	.	GRCh37	9	73002625	73002625	+	3'UTR	SNP	G	G	A	rs536409284	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67C>T	.	.	ENST00000377126	2/2	16	8	8	33	33	0	KLF9,3_prime_UTR_variant,,ENST00000377126,;	A	ENSG00000119138	ENST00000377126	Transcript	3_prime_UTR_variant	2063	.	.	.	.	rs536409284	.	.	-1	KLF9	HGNC	1123	protein_coding	YES	CCDS6633.1	ENSP00000366330	KLF9_HUMAN	.	UPI0000126B0A	.	.	.	2/2	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CACGCGTCTGT	by1000G	4	ESCA
PRPS2	0	.	GRCh37	X	12828231	12828231	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505A>G	p.Ile169Val	p.I169V	ENST00000398491	4/7	13	7	6	22	22	0	PRPS2,missense_variant,p.Ile166Val,ENST00000489404,;PRPS2,missense_variant,p.Ile166Val,ENST00000380668,;PRPS2,missense_variant,p.Ile169Val,ENST00000398491,;PRPS2,missense_variant,p.Tyr145Cys,ENST00000380663,;PRPS2,missense_variant,p.Ile79Val,ENST00000461630,;	G	ENSG00000101911	ENST00000398491	Transcript	missense_variant	597	505	169	I/V	Atc/Gtc	.	.	.	1	PRPS2	HGNC	9465	protein_coding	YES	CCDS43918.1	ENSP00000381504	PRPS2_HUMAN	.	UPI000004A051	.	tolerated(1)	benign(0.002)	4/7	.	HAMAP:MF_00583_B,hmmpanther:PTHR10210,hmmpanther:PTHR10210:SF30,Gene3D:3.40.50.2020,TIGRFAM_domain:TIGR01251,Superfamily_domains:SSF53271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	ACTGTATCATT	.	4	ESCA
ZNF449	0	.	GRCh37	X	134481196	134481196	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153C>G	p.%3D	p.L51L	ENST00000339249	2/5	18	12	6	18	18	0	ZNF449,synonymous_variant,p.%3D,ENST00000370760,;ZNF449,synonymous_variant,p.%3D,ENST00000339249,;ZNF449,synonymous_variant,p.%3D,ENST00000370761,;ZNF75D,upstream_gene_variant,,ENST00000370766,;ZNF75D,upstream_gene_variant,,ENST00000494295,;	G	ENSG00000173275	ENST00000339249	Transcript	synonymous_variant	293	153	51	L	ctC/ctG	.	.	.	1	ZNF449	HGNC	21039	protein_coding	YES	CCDS14649.1	ENSP00000339585	ZN449_HUMAN	Q7Z3P1_HUMAN	UPI000013F1DE	.	.	.	2/5	.	Superfamily_domains:SSF47353,SMART_domains:SM00431,Pfam_domain:PF02023,hmmpanther:PTHR23226:SF4,hmmpanther:PTHR23226,PROSITE_profiles:PS50804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTCTGGGA	.	5	ESCA
MOSPD2	0	.	GRCh37	X	14891657	14891657	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7G>T	p.Glu3Ter	p.E3*	ENST00000380492	1/15	27	10	17	61	61	0	MOSPD2,stop_gained,p.Glu3Ter,ENST00000482354,;MOSPD2,stop_gained,p.Glu3Ter,ENST00000497603,;MOSPD2,stop_gained,p.Glu3Ter,ENST00000380492,;FANCB,upstream_gene_variant,,ENST00000324138,;FANCB,upstream_gene_variant,,ENST00000398334,;FANCB,upstream_gene_variant,,ENST00000452869,;MOSPD2,splice_region_variant,,ENST00000461777,;FANCB,upstream_gene_variant,,ENST00000489126,;	T	ENSG00000130150	ENST00000380492	Transcript	stop_gained	95	7	3	E/*	Gag/Tag	.	.	.	1	MOSPD2	HGNC	28381	protein_coding	YES	CCDS14162.1	ENSP00000369860	MSPD2_HUMAN	.	UPI00000735BA	.	.	.	1/15	.	hmmpanther:PTHR19993,hmmpanther:PTHR19993:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCAGAGGTG	.	5	ESCA
NAA10	0	.	GRCh37	X	153197547	153197547	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.363C>G	p.%3D	p.L121L	ENST00000464845	6/8	52	26	25	36	36	0	NAA10,synonymous_variant,p.%3D,ENST00000432089,;NAA10,synonymous_variant,p.%3D,ENST00000370015,;NAA10,synonymous_variant,p.%3D,ENST00000393712,;NAA10,synonymous_variant,p.%3D,ENST00000464845,;NAA10,intron_variant,,ENST00000370009,;NAA10,intron_variant,,ENST00000370011,;RENBP,downstream_gene_variant,,ENST00000412763,;RENBP,downstream_gene_variant,,ENST00000393700,;ARHGAP4,upstream_gene_variant,,ENST00000442262,;RENBP,downstream_gene_variant,,ENST00000451114,;RENBP,downstream_gene_variant,,ENST00000369997,;NAA10,non_coding_transcript_exon_variant,,ENST00000393710,;ARHGAP4,upstream_gene_variant,,ENST00000470979,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000494813,;NAA10,non_coding_transcript_exon_variant,,ENST00000477750,;NAA10,non_coding_transcript_exon_variant,,ENST00000484950,;NAA10,non_coding_transcript_exon_variant,,ENST00000477882,;NAA10,non_coding_transcript_exon_variant,,ENST00000460996,;NAA10,non_coding_transcript_exon_variant,,ENST00000467451,;NAA10,non_coding_transcript_exon_variant,,ENST00000466877,;RENBP,downstream_gene_variant,,ENST00000457282,;NAA10,downstream_gene_variant,,ENST00000488481,;RENBP,downstream_gene_variant,,ENST00000442361,;NAA10,upstream_gene_variant,,ENST00000482485,;RENBP,downstream_gene_variant,,ENST00000423624,;NAA10,downstream_gene_variant,,ENST00000478177,;	C	ENSG00000102030	ENST00000464845	Transcript	synonymous_variant	682	363	121	L	ctC/ctG	.	.	.	-1	NAA10	HGNC	18704	protein_coding	YES	CCDS14737.1	ENSP00000417763	NAA10_HUMAN	.	UPI0000125DBA	.	.	.	6/8	.	PROSITE_profiles:PS51186,hmmpanther:PTHR23091:SF201,hmmpanther:PTHR23091,Pfam_domain:PF00583,Gene3D:3.40.630.30,Superfamily_domains:SSF55729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATAGAGGTG	.	5	ESCA
MIR221	0	.	GRCh37	X	45605608	45605608	+	RNA	SNP	G	G	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.87C>G	.	.	ENST00000385135	1/1	37	28	9	32	32	0	MIR221,non_coding_transcript_exon_variant,,ENST00000385135,;RP6-99M1.2,intron_variant,,ENST00000602461,;MIR222,downstream_gene_variant,,ENST00000384992,;	C	ENSG00000207870	ENST00000385135	Transcript	non_coding_transcript_exon_variant	87	.	.	.	.	.	.	.	-1	MIR221	HGNC	31601	miRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTGAAACC	.	5	ESCA
UBQLN2	0	.	GRCh37	X	56591114	56591114	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.808C>T	p.Arg270Cys	p.R270C	ENST00000338222	1/1	20	3	16	27	27	0	UBQLN2,missense_variant,p.Arg270Cys,ENST00000338222,;	T	ENSG00000188021	ENST00000338222	Transcript	missense_variant	1089	808	270	R/C	Cgc/Tgc	.	.	.	1	UBQLN2	HGNC	12509	protein_coding	YES	CCDS14374.1	ENSP00000345195	UBQL2_HUMAN	.	UPI000004A059	.	deleterious(0)	benign(0.348)	1/1	.	hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACGGCGCATG	.	5	ESCA
RGAG4	0	.	GRCh37	X	71350086	71350086	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1305A>G	p.%3D	p.E435E	ENST00000545866	1/2	45	4	41	24	24	0	RGAG4,synonymous_variant,p.%3D,ENST00000609883,;RGAG4,synonymous_variant,p.%3D,ENST00000545866,;NHSL2,intron_variant,,ENST00000540800,;NHSL2,upstream_gene_variant,,ENST00000373677,;NHSL2,upstream_gene_variant,,ENST00000510661,;NHSL2,upstream_gene_variant,,ENST00000535692,;RGAG4,synonymous_variant,p.%3D,ENST00000479991,;RP11-262D11.1,upstream_gene_variant,,ENST00000513469,;	C	ENSG00000242732	ENST00000545866	Transcript	synonymous_variant	1673	1305	435	E	gaA/gaG	.	.	.	-1	RGAG4	HGNC	29430	protein_coding	YES	CCDS55446.1	ENSP00000441366	RGAG4_HUMAN	.	UPI00001C2079	.	.	.	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15503:SF2,hmmpanther:PTHR15503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCCTTCTGG	.	5	ESCA
KIAA2022	0	.	GRCh37	X	73962184	73962184	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8EZ-01A-11D-A36J-09	TCGA-VR-A8EZ-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2208T>C	p.%3D	p.A736A	ENST00000055682	3/4	35	17	18	58	58	0	KIAA2022,synonymous_variant,p.%3D,ENST00000055682,;KIAA2022,upstream_gene_variant,,ENST00000424929,;	G	ENSG00000050030	ENST00000055682	Transcript	synonymous_variant	2820	2208	736	A	gcT/gcC	.	.	.	-1	KIAA2022	HGNC	29433	protein_coding	YES	CCDS35337.1	ENSP00000055682	K2022_HUMAN	.	UPI00001C207B	.	.	.	3/4	.	hmmpanther:PTHR10322:SF2,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCCAGCAGC	.	5	ESCA
CELF2	0	.	GRCh37	10	11371790	11371790	+	Intron	SNP	T	T	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45-629T>A	.	.	ENST00000450189	.	16	13	3	16	16	0	CELF2,3_prime_UTR_variant,,ENST00000379261,;CELF2,3_prime_UTR_variant,,ENST00000354440,;CELF2,intron_variant,,ENST00000427450,;CELF2,intron_variant,,ENST00000608830,;CELF2,intron_variant,,ENST00000399850,;CELF2,intron_variant,,ENST00000416382,;CELF2,intron_variant,,ENST00000609692,;CELF2,intron_variant,,ENST00000417956,;CELF2,intron_variant,,ENST00000542579,;CELF2,intron_variant,,ENST00000450189,;CELF2,intron_variant,,ENST00000315874,;CELF2,downstream_gene_variant,,ENST00000354897,;CELF2,downstream_gene_variant,,ENST00000537122,;CELF2,downstream_gene_variant,,ENST00000609870,;	A	ENSG00000048740	ENST00000450189	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CELF2	HGNC	2550	protein_coding	YES	CCDS44355.1	ENSP00000389951	.	E9PC62_HUMAN,B4DIB6_HUMAN	UPI0000F58F21	.	.	.	.	13/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAATTTAATA	.	2	ESCA
EBF3	0	.	GRCh37	10	131635637	131635637	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*556G>A	.	.	ENST00000368648	16/16	45	42	3	37	37	0	EBF3,3_prime_UTR_variant,,ENST00000355311,;EBF3,3_prime_UTR_variant,,ENST00000368648,;EBF3,downstream_gene_variant,,ENST00000440978,;	T	ENSG00000108001	ENST00000368648	Transcript	3_prime_UTR_variant	2285	.	.	.	.	.	.	.	-1	EBF3	HGNC	19087	protein_coding	YES	CCDS31314.1	ENSP00000357637	COE3_HUMAN	Q658Y5_HUMAN	UPI000002A6FB	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCCCTCCCT	.	2	ESCA
KNDC1	0	.	GRCh37	10	135015007	135015007	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2992A>G	p.Lys998Glu	p.K998E	ENST00000304613	17/30	58	54	4	48	48	0	KNDC1,missense_variant,p.Lys933Glu,ENST00000368571,;KNDC1,missense_variant,p.Lys998Glu,ENST00000304613,;KNDC1,missense_variant,p.Lys1000Glu,ENST00000368572,;	G	ENSG00000171798	ENST00000304613	Transcript	missense_variant	3013	2992	998	K/E	Aaa/Gaa	.	.	.	1	KNDC1	HGNC	29374	protein_coding	YES	CCDS7674.1	ENSP00000304437	VKIND_HUMAN	B4DFN0_HUMAN	UPI00003529F7	.	tolerated(0.29)	benign(0.082)	17/30	.	hmmpanther:PTHR21560:SF0,hmmpanther:PTHR21560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGAAAAGAG	.	2	ESCA
CCNYL2	0	.	GRCh37	10	42965691	42965691	+	RNA	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.462A>G	.	.	ENST00000483242	2/9	50	42	8	48	48	0	CCNYL2,non_coding_transcript_exon_variant,,ENST00000483242,;	C	ENSG00000182632	ENST00000483242	Transcript	non_coding_transcript_exon_variant	462	.	.	.	.	.	.	.	-1	CCNYL2	HGNC	23495	processed_transcript	YES	.	.	.	.	.	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAGATCTTGC	.	4	ESCA
ADO	0	.	GRCh37	10	64567946	64567946	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2314A>G	.	.	ENST00000373783	1/1	64	53	11	36	36	0	ADO,3_prime_UTR_variant,,ENST00000373783,;EGR2,downstream_gene_variant,,ENST00000439032,;EGR2,downstream_gene_variant,,ENST00000242480,;EGR2,downstream_gene_variant,,ENST00000411732,;RP11-436D10.3,upstream_gene_variant,,ENST00000425290,;	G	ENSG00000181915	ENST00000373783	Transcript	3_prime_UTR_variant	3431	.	.	.	.	.	.	.	1	ADO	HGNC	23506	protein_coding	YES	CCDS7266.2	ENSP00000362888	AEDO_HUMAN	.	UPI00001F8D78	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTAAATTAGT	.	4	ESCA
ANXA11	0	.	GRCh37	10	81918943	81918943	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1189G>T	p.Glu397Ter	p.E397*	ENST00000438331	14/17	27	23	3	24	24	0	ANXA11,stop_gained,p.Glu364Ter,ENST00000537102,;ANXA11,stop_gained,p.Glu397Ter,ENST00000438331,;ANXA11,stop_gained,p.Glu397Ter,ENST00000535999,;ANXA11,stop_gained,p.Glu397Ter,ENST00000265447,;ANXA11,stop_gained,p.Glu397Ter,ENST00000360615,;ANXA11,stop_gained,p.Glu397Ter,ENST00000422982,;ANXA11,stop_gained,p.Glu397Ter,ENST00000372231,;ANXA11,stop_gained,p.Glu30Ter,ENST00000447489,;ANXA11,upstream_gene_variant,,ENST00000463340,;	A	ENSG00000122359	ENST00000438331	Transcript	stop_gained	1672	1189	397	E/*	Gag/Tag	.	.	.	-1	ANXA11	HGNC	535	protein_coding	YES	CCDS7364.1	ENSP00000398610	ANX11_HUMAN	Q5T0G9_HUMAN,Q5T0G8_HUMAN,Q5T0G7_HUMAN,B4DVE7_HUMAN	UPI0000125B8D	.	.	.	14/17	.	Superfamily_domains:SSF47874,SMART_domains:SM00335,Pfam_domain:PF00191,Gene3D:1.10.220.10,PROSITE_patterns:PS00223,hmmpanther:PTHR10502,hmmpanther:PTHR10502:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTACTCATTGA	.	3	ESCA
HTR7	0	.	GRCh37	10	92502148	92502148	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*91T>C	.	.	ENST00000336152	4/4	51	46	5	46	46	0	HTR7,3_prime_UTR_variant,,ENST00000371719,;HTR7,3_prime_UTR_variant,,ENST00000371721,;HTR7,3_prime_UTR_variant,,ENST00000277874,;HTR7,3_prime_UTR_variant,,ENST00000336152,;	G	ENSG00000148680	ENST00000336152	Transcript	3_prime_UTR_variant	1558	.	.	.	.	.	.	.	-1	HTR7	HGNC	5302	protein_coding	YES	CCDS7408.1	ENSP00000337949	5HT7R_HUMAN	.	UPI0000049B68	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACAGAAGCTGC	.	4	ESCA
PPP1R3C	0	.	GRCh37	10	93388602	93388602	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1082C>G	.	.	ENST00000238994	2/2	24	21	3	25	25	0	PPP1R3C,3_prime_UTR_variant,,ENST00000238994,;	C	ENSG00000119938	ENST00000238994	Transcript	3_prime_UTR_variant	2121	.	.	.	.	.	.	.	-1	PPP1R3C	HGNC	9293	protein_coding	YES	CCDS7416.1	ENSP00000238994	PPR3C_HUMAN	B4DRR5_HUMAN	UPI000006EFF1	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCATTGAGAAT	.	2	ESCA
CADM1	0	.	GRCh37	11	115049492	115049492	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1082C>T	p.Ser361Phe	p.S361F	ENST00000452722	9/10	33	28	5	37	37	0	CADM1,missense_variant,p.Ser361Phe,ENST00000452722,;CADM1,missense_variant,p.Ser390Phe,ENST00000331581,;CADM1,missense_variant,p.Ser362Phe,ENST00000536727,;CADM1,missense_variant,p.Ser332Phe,ENST00000545380,;CADM1,missense_variant,p.Ser333Phe,ENST00000542447,;CADM1,missense_variant,p.Ser372Phe,ENST00000537058,;CADM1,non_coding_transcript_exon_variant,,ENST00000543375,;CADM1,non_coding_transcript_exon_variant,,ENST00000545960,;CADM1,non_coding_transcript_exon_variant,,ENST00000537140,;CADM1,non_coding_transcript_exon_variant,,ENST00000546000,;CADM1,non_coding_transcript_exon_variant,,ENST00000540852,;	A	ENSG00000182985	ENST00000452722	Transcript	missense_variant	1103	1082	361	S/F	tCc/tTc	.	.	.	-1	CADM1	HGNC	5951	protein_coding	YES	CCDS8373.1	ENSP00000395359	CADM1_HUMAN	Q6MZK6_HUMAN,F5H8J9_HUMAN,F5H0H5_HUMAN	UPI0000049C25	.	deleterious(0)	possibly_damaging(0.781)	9/10	.	hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCGGGAATCT	.	4	ESCA
TBCEL	0	.	GRCh37	11	120930683	120930683	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.845C>G	p.Pro282Arg	p.P282R	ENST00000422003	7/8	82	63	18	70	70	0	TBCEL,missense_variant,p.Pro282Arg,ENST00000422003,;TBCEL,missense_variant,p.Pro49Arg,ENST00000533134,;TBCEL,missense_variant,p.Pro282Arg,ENST00000529397,;TBCEL,downstream_gene_variant,,ENST00000524726,;TBCEL,3_prime_UTR_variant,,ENST00000284259,;TBCEL,3_prime_UTR_variant,,ENST00000531148,;TBCEL,3_prime_UTR_variant,,ENST00000533712,;TBCEL,non_coding_transcript_exon_variant,,ENST00000533169,;	G	ENSG00000154114	ENST00000422003	Transcript	missense_variant	1033	845	282	P/R	cCa/cGa	.	.	.	1	TBCEL	HGNC	28115	protein_coding	YES	CCDS31692.1	ENSP00000403925	TBCEL_HUMAN	E9PNS0_HUMAN,E9PJJ0_HUMAN	UPI0000D62697	.	deleterious(0)	probably_damaging(0.992)	7/8	.	hmmpanther:PTHR15140,hmmpanther:PTHR15140:SF10,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGCCATCAG	.	5	ESCA
OR8G5	0	.	GRCh37	11	124135465	124135465	+	Missense_Mutation	SNP	C	C	T	rs773370353	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.743C>T	p.Thr248Ile	p.T248I	ENST00000524943	1/1	124	92	32	94	94	0	OR8G5,missense_variant,p.Thr248Ile,ENST00000524943,;OR8G1,intron_variant,,ENST00000341493,;	T	ENSG00000255298	ENST00000524943	Transcript	missense_variant	743	743	248	T/I	aCc/aTc	rs773370353	.	.	1	OR8G5	HGNC	19622	protein_coding	YES	CCDS66256.1	ENSP00000477014	OR8G5_HUMAN	B2RND3_HUMAN	UPI00003B286B	.	tolerated(0.09)	benign(0.163)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26452:SF73,hmmpanther:PTHR26452,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGACCATCC	byFrequency	5	ESCA
NELL1	0	.	GRCh37	11	21306014	21306014	+	Intron	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1549+55014G>A	.	.	ENST00000357134	.	34	24	10	41	40	1	NELL1,intron_variant,,ENST00000325319,;NELL1,intron_variant,,ENST00000357134,;NELL1,intron_variant,,ENST00000298925,;NELL1,intron_variant,,ENST00000532434,;NELL1,non_coding_transcript_exon_variant,,ENST00000534263,;NELL1,non_coding_transcript_exon_variant,,ENST00000529218,;CTD-2302A16.2,non_coding_transcript_exon_variant,,ENST00000525269,;CTD-2302A16.2,non_coding_transcript_exon_variant,,ENST00000444420,;	A	ENSG00000165973	ENST00000357134	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	NELL1	HGNC	7750	protein_coding	YES	CCDS7855.1	ENSP00000349654	NELL1_HUMAN	K9UUD5_HUMAN	UPI000013E53D	.	.	.	.	14/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AACTGGGAGAT	.	4	ESCA
DGKZ	0	.	GRCh37	11	46402059	46402059	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*562T>A	.	.	ENST00000454345	32/32	84	46	38	57	57	0	DGKZ,3_prime_UTR_variant,,ENST00000456247,;DGKZ,3_prime_UTR_variant,,ENST00000543978,;DGKZ,3_prime_UTR_variant,,ENST00000343674,;DGKZ,3_prime_UTR_variant,,ENST00000454345,;DGKZ,3_prime_UTR_variant,,ENST00000395574,;MDK,upstream_gene_variant,,ENST00000395565,;MDK,upstream_gene_variant,,ENST00000359803,;DGKZ,downstream_gene_variant,,ENST00000421244,;DGKZ,downstream_gene_variant,,ENST00000524869,;DGKZ,downstream_gene_variant,,ENST00000527911,;MDK,upstream_gene_variant,,ENST00000533952,;MDK,upstream_gene_variant,,ENST00000441869,;MDK,upstream_gene_variant,,ENST00000395566,;MDK,upstream_gene_variant,,ENST00000395569,;CHRM4,downstream_gene_variant,,ENST00000433765,;MDK,upstream_gene_variant,,ENST00000407067,;DGKZ,downstream_gene_variant,,ENST00000318201,;MDK,upstream_gene_variant,,ENST00000405308,;DGKZ,downstream_gene_variant,,ENST00000528615,;DGKZ,downstream_gene_variant,,ENST00000532868,;MIR4688,downstream_gene_variant,,ENST00000577966,;DGKZ,downstream_gene_variant,,ENST00000529660,;MDK,upstream_gene_variant,,ENST00000533283,;DGKZ,3_prime_UTR_variant,,ENST00000524984,;DGKZ,non_coding_transcript_exon_variant,,ENST00000534802,;DGKZ,non_coding_transcript_exon_variant,,ENST00000528173,;DGKZ,non_coding_transcript_exon_variant,,ENST00000527211,;DGKZ,downstream_gene_variant,,ENST00000532941,;MDK,upstream_gene_variant,,ENST00000481047,;DGKZ,downstream_gene_variant,,ENST00000531879,;DGKZ,downstream_gene_variant,,ENST00000529698,;MDK,upstream_gene_variant,,ENST00000489525,;MDK,upstream_gene_variant,,ENST00000490240,;	A	ENSG00000149091	ENST00000454345	Transcript	3_prime_UTR_variant	4041	.	.	.	.	.	.	.	1	DGKZ	HGNC	2857	protein_coding	YES	CCDS41640.1	ENSP00000412178	DGKZ_HUMAN	Q7Z5X8_HUMAN,E9PNL8_HUMAN	UPI000013DB71	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACATGTTTA	.	5	ESCA
MYBPC3	0	.	GRCh37	11	47362785	47362785	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1801C>T	p.%3D	p.L601L	ENST00000545968	19/35	32	24	8	35	35	0	MYBPC3,synonymous_variant,p.%3D,ENST00000545968,;MYBPC3,synonymous_variant,p.%3D,ENST00000256993,;MYBPC3,synonymous_variant,p.%3D,ENST00000399249,;MYBPC3,synonymous_variant,p.%3D,ENST00000544791,;	A	ENSG00000134571	ENST00000545968	Transcript	synonymous_variant	1856	1801	601	L	Ctg/Ttg	.	.	.	-1	MYBPC3	HGNC	7551	protein_coding	YES	CCDS53621.1	ENSP00000442795	MYPC3_HUMAN	B6D426_HUMAN	UPI000006EEAA	.	.	.	19/35	.	hmmpanther:PTHR19900,hmmpanther:PTHR19900:SF52,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCAGTTTGT	.	5	ESCA
OR5AR1	0	.	GRCh37	11	56431333	56431333	+	Missense_Mutation	SNP	C	C	T	rs749905249	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172C>T	p.Pro58Ser	p.P58S	ENST00000302969	1/1	67	52	15	64	64	0	OR5AR1,missense_variant,p.Pro58Ser,ENST00000302969,;	T	ENSG00000172459	ENST00000302969	Transcript	missense_variant	196	172	58	P/S	Ccc/Tcc	rs749905249	.	.	1	OR5AR1	HGNC	15260	protein_coding	YES	CCDS31535.1	ENSP00000302639	O5AR1_HUMAN	B9EIN0_HUMAN	UPI0000041C93	.	deleterious(0.02)	possibly_damaging(0.788)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF54,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACACCCATG	.	5	ESCA
MALAT1	0	.	GRCh37	11	65271488	65271488	+	RNA	SNP	G	G	C	rs766252481	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.6256G>C	.	.	ENST00000534336	1/1	26	15	11	30	30	0	MALAT1,non_coding_transcript_exon_variant,,ENST00000534336,;MALAT1,downstream_gene_variant,,ENST00000508832,;MALAT1,downstream_gene_variant,,ENST00000544868,;	C	ENSG00000251562	ENST00000534336	Transcript	non_coding_transcript_exon_variant	6256	.	.	.	.	rs766252481	.	.	1	MALAT1	HGNC	29665	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTGCATGT	byFrequency	5	ESCA
ILK	0	.	GRCh37	11	6631755	6631755	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1272C>T	p.%3D	p.L424L	ENST00000396751	12/12	62	47	14	44	44	0	ILK,synonymous_variant,p.%3D,ENST00000528995,;ILK,synonymous_variant,p.%3D,ENST00000420936,;ILK,synonymous_variant,p.%3D,ENST00000396751,;ILK,synonymous_variant,p.%3D,ENST00000537806,;ILK,synonymous_variant,p.%3D,ENST00000299421,;TAF10,downstream_gene_variant,,ENST00000299424,;TPP1,downstream_gene_variant,,ENST00000533371,;TPP1,downstream_gene_variant,,ENST00000299427,;RP11-732A19.2,upstream_gene_variant,,ENST00000527398,;ILK,intron_variant,,ENST00000526318,;ILK,downstream_gene_variant,,ENST00000534706,;ILK,downstream_gene_variant,,ENST00000526711,;ILK,downstream_gene_variant,,ENST00000528784,;TPP1,downstream_gene_variant,,ENST00000524924,;TAF10,downstream_gene_variant,,ENST00000531760,;TPP1,downstream_gene_variant,,ENST00000524611,;ILK,downstream_gene_variant,,ENST00000524735,;TPP1,downstream_gene_variant,,ENST00000532191,;ILK,downstream_gene_variant,,ENST00000530016,;TAF10,downstream_gene_variant,,ENST00000527248,;ILK,3_prime_UTR_variant,,ENST00000527394,;ILK,3_prime_UTR_variant,,ENST00000527327,;ILK,3_prime_UTR_variant,,ENST00000532063,;TAF10,non_coding_transcript_exon_variant,,ENST00000526743,;ILK,downstream_gene_variant,,ENST00000526114,;TAF10,downstream_gene_variant,,ENST00000532344,;ILK,downstream_gene_variant,,ENST00000527121,;	T	ENSG00000166333	ENST00000396751	Transcript	synonymous_variant	1728	1272	424	L	ctC/ctT	.	.	.	1	ILK	HGNC	6040	protein_coding	YES	CCDS7768.1	ENSP00000379975	ILK_HUMAN	B7Z1I0_HUMAN	UPI0000000DC2	.	.	.	12/12	.	Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000654,Pfam_domain:PF07714,Gene3D:1.10.510.10,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF30,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AAGCTCATGAA	.	4	ESCA
CTD-3074O7.2	0	.	GRCh37	11	66325358	66325358	+	3'Flank	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000504911	.	44	38	5	44	44	0	CTD-3074O7.2,downstream_gene_variant,,ENST00000504911,;ACTN3,downstream_gene_variant,,ENST00000511191,;ACTN3,synonymous_variant,p.%3D,ENST00000513398,;ACTN3,synonymous_variant,p.%3D,ENST00000502692,;	T	ENSG00000250105	ENST00000504911	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	979	-1	CTD-3074O7.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCAGCCACCG	.	4	ESCA
WNT11	0	.	GRCh37	11	75897448	75897448	+	3'UTR	SNP	C	C	T	rs757308593	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*661G>A	.	.	ENST00000322563	5/5	57	43	14	47	47	0	WNT11,3_prime_UTR_variant,,ENST00000322563,;RP11-619A14.2,upstream_gene_variant,,ENST00000527314,;	T	ENSG00000085741	ENST00000322563	Transcript	3_prime_UTR_variant	1851	.	.	.	.	rs757308593	.	.	-1	WNT11	HGNC	12776	protein_coding	YES	CCDS8242.1	ENSP00000325526	WNT11_HUMAN	.	UPI000003148D	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGGCGGGCT	.	4	ESCA
KIAA1731	0	.	GRCh37	11	93416746	93416746	+	Missense_Mutation	SNP	G	G	C	rs749676590	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.787G>C	p.Glu263Gln	p.E263Q	ENST00000325212	8/30	41	32	8	31	31	0	KIAA1731,missense_variant,p.Glu263Gln,ENST00000325212,;KIAA1731,missense_variant,p.Glu263Gln,ENST00000411936,;KIAA1731,5_prime_UTR_variant,,ENST00000344196,;	C	ENSG00000166004	ENST00000325212	Transcript	missense_variant	949	787	263	E/Q	Gaa/Caa	rs749676590	.	.	1	KIAA1731	HGNC	29366	protein_coding	YES	CCDS44708.1	ENSP00000316681	K1731_HUMAN	E9PM20_HUMAN	UPI0000251F0E	.	deleterious(0)	probably_damaging(0.997)	8/30	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAAGAACTC	.	5	ESCA
SETD1B	0	.	GRCh37	12	122257764	122257764	+	Silent	SNP	G	G	C	rs774331353	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3744G>C	p.%3D	p.V1248V	ENST00000267197	11/17	76	45	30	76	76	0	SETD1B,synonymous_variant,p.%3D,ENST00000604567,;SETD1B,synonymous_variant,p.%3D,ENST00000542440,;SETD1B,synonymous_variant,p.%3D,ENST00000267197,;	C	ENSG00000139718	ENST00000267197	Transcript	synonymous_variant	3750	3744	1248	V	gtG/gtC	rs774331353	.	.	1	SETD1B	HGNC	29187	protein_coding	YES	CCDS53838.1	ENSP00000267197	SET1B_HUMAN	.	UPI00006C12ED	.	.	.	11/17	.	hmmpanther:PTHR22884:SF296,hmmpanther:PTHR22884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGTGGAGGC	.	5	ESCA
SLCO1A2	0	.	GRCh37	12	21447016	21447016	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1300G>C	p.Asp434His	p.D434H	ENST00000307378	12/16	34	16	17	45	45	0	SLCO1A2,missense_variant,p.Asp432His,ENST00000390670,;SLCO1A2,missense_variant,p.Asp434His,ENST00000307378,;SLCO1A2,missense_variant,p.Asp302His,ENST00000537524,;SLCO1A2,missense_variant,p.Asp434His,ENST00000452078,;SLCO1A2,missense_variant,p.Asp302His,ENST00000458504,;SLCO1A2,3_prime_UTR_variant,,ENST00000544020,;SLCO1A2,3_prime_UTR_variant,,ENST00000544290,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000480394,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000463718,;	G	ENSG00000084453	ENST00000307378	Transcript	missense_variant	2021	1300	434	D/H	Gac/Cac	.	.	.	-1	SLCO1A2	HGNC	10956	protein_coding	YES	CCDS8686.1	ENSP00000305974	SO1A2_HUMAN	C9K059_HUMAN,C9JUW6_HUMAN,C9JTF6_HUMAN,C9JHU9_HUMAN,C9JGK7_HUMAN,C9JG34_HUMAN,C9JCA7_HUMAN,B4DJE6_HUMAN	UPI0000037575	.	tolerated(0.08)	benign(0.003)	12/16	.	Superfamily_domains:SSF100895,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,hmmpanther:PTHR11388:SF16,hmmpanther:PTHR11388,PROSITE_profiles:PS50850,PROSITE_profiles:PS51465	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGTCATTTT	.	5	ESCA
MUC19	0	.	GRCh37	12	40919410	40919410	+	Intron	SNP	C	C	T	rs760979199	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5783-16954C>T	.	.	ENST00000454784	.	98	56	42	81	81	0	MUC19,intron_variant,,ENST00000454784,;MUC19,upstream_gene_variant,,ENST00000424466,;MUC19,non_coding_transcript_exon_variant,,ENST00000474954,;MUC19,downstream_gene_variant,,ENST00000398702,;	T	ENSG00000205592	ENST00000454784	Transcript	intron_variant	.	.	.	.	.	rs760979199	.	.	1	MUC19	HGNC	14362	protein_coding	YES	.	ENSP00000476404	.	C9JCE7_HUMAN	UPI0003B927DE	.	.	.	.	49/83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGCCGAAGT	.	5	ESCA
CNOT2	0	.	GRCh37	12	70738008	70738008	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1391T>C	p.Leu464Pro	p.L464P	ENST00000229195	14/16	61	54	7	44	44	0	CNOT2,missense_variant,p.Leu464Pro,ENST00000551043,;CNOT2,missense_variant,p.Leu464Pro,ENST00000229195,;CNOT2,missense_variant,p.Leu115Pro,ENST00000551483,;CNOT2,missense_variant,p.Leu464Pro,ENST00000418359,;CNOT2,missense_variant,p.Leu175Pro,ENST00000552599,;CNOT2,missense_variant,p.Leu455Pro,ENST00000548159,;CNOT2,missense_variant,p.Leu91Pro,ENST00000548338,;CNOT2,missense_variant,p.Leu47Pro,ENST00000551710,;CNOT2,downstream_gene_variant,,ENST00000550160,;CNOT2,upstream_gene_variant,,ENST00000549705,;CNOT2,downstream_gene_variant,,ENST00000548686,;CNOT2,missense_variant,p.Leu154Pro,ENST00000546673,;CNOT2,splice_region_variant,,ENST00000549709,;CNOT2,splice_region_variant,,ENST00000551434,;CNOT2,splice_region_variant,,ENST00000550705,;CNOT2,downstream_gene_variant,,ENST00000548939,;	C	ENSG00000111596	ENST00000229195	Transcript	missense_variant	1970	1391	464	L/P	cTt/cCt	.	.	.	1	CNOT2	HGNC	7878	protein_coding	YES	CCDS31857.1	ENSP00000229195	CNOT2_HUMAN	F8VWH8_HUMAN,F8VVY1_HUMAN,F8VUB4_HUMAN,F8VRS2_HUMAN,F8VQD8_HUMAN,F8VPX5_HUMAN,F8VP97_HUMAN	UPI0000052E12	.	deleterious(0)	probably_damaging(1)	14/16	.	hmmpanther:PTHR23326,Pfam_domain:PF04153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGCTGTATG	.	4	ESCA
ZDHHC17	0	.	GRCh37	12	77247116	77247116	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2351G>C	.	.	ENST00000426126	17/17	66	61	5	61	61	0	ZDHHC17,3_prime_UTR_variant,,ENST00000426126,;ZDHHC17,3_prime_UTR_variant,,ENST00000334822,;ZDHHC17,downstream_gene_variant,,ENST00000553091,;ZDHHC17,downstream_gene_variant,,ENST00000550789,;ZDHHC17,downstream_gene_variant,,ENST00000547673,;ZDHHC17,downstream_gene_variant,,ENST00000550244,;ZDHHC17,downstream_gene_variant,,ENST00000552693,;	C	ENSG00000186908	ENST00000426126	Transcript	3_prime_UTR_variant	4899	.	.	.	.	.	.	.	1	ZDHHC17	HGNC	18412	protein_coding	YES	CCDS44946.1	ENSP00000403397	ZDH17_HUMAN	A8KA01_HUMAN	UPI0000051F55	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTATGATGGT	.	2	ESCA
NAV3	0	.	GRCh37	12	78392116	78392116	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.741-1G>T	.	p.X247_splice	ENST00000536525	.	29	16	12	25	25	0	NAV3,splice_acceptor_variant,,ENST00000536525,;NAV3,splice_acceptor_variant,,ENST00000397909,;NAV3,splice_acceptor_variant,,ENST00000266692,;NAV3,splice_acceptor_variant,,ENST00000550503,;NAV3,splice_acceptor_variant,,ENST00000228327,;NAV3,splice_acceptor_variant,,ENST00000549464,;NAV3,splice_acceptor_variant,,ENST00000547725,;	T	ENSG00000067798	ENST00000536525	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	NAV3	HGNC	15998	protein_coding	YES	CCDS41815.1	ENSP00000446132	NAV3_HUMAN	F8VZV4_HUMAN	UPI00001FB1E8	.	.	.	.	6/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCAGGCTTC	.	5	ESCA
CLEC4A	0	.	GRCh37	12	8276480	8276480	+	Silent	SNP	T	T	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6T>G	p.%3D	p.T2T	ENST00000229332	1/6	41	17	24	35	35	0	CLEC4A,synonymous_variant,p.%3D,ENST00000345999,;CLEC4A,synonymous_variant,p.%3D,ENST00000352620,;CLEC4A,synonymous_variant,p.%3D,ENST00000360500,;CLEC4A,synonymous_variant,p.%3D,ENST00000229332,;CLEC4A,upstream_gene_variant,,ENST00000546339,;	G	ENSG00000111729	ENST00000229332	Transcript	synonymous_variant	253	6	2	T	acT/acG	.	.	.	1	CLEC4A	HGNC	13257	protein_coding	YES	CCDS8590.1	ENSP00000229332	CLC4A_HUMAN	.	UPI000003C38E	.	.	.	1/6	.	hmmpanther:PTHR22802:SF203,hmmpanther:PTHR22802	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACTTCGGA	.	5	ESCA
LRRIQ1	0	.	GRCh37	12	85492759	85492759	+	Missense_Mutation	SNP	A	A	T	rs768644704	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3196A>T	p.Ile1066Phe	p.I1066F	ENST00000393217	13/27	58	52	6	33	33	0	LRRIQ1,missense_variant,p.Ile1066Phe,ENST00000393217,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,;	T	ENSG00000133640	ENST00000393217	Transcript	missense_variant	3257	3196	1066	I/F	Atc/Ttc	rs768644704	.	.	1	LRRIQ1	HGNC	25708	protein_coding	YES	CCDS41816.1	ENSP00000376910	LRIQ1_HUMAN	A8MY60_HUMAN	UPI0000ED4E82	.	deleterious(0)	benign(0.398)	13/27	.	Superfamily_domains:SSF52058,Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF66,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTACTATCTCT	byFrequency	4	ESCA
LINC00612	0	.	GRCh37	12	9208308	9208308	+	RNA	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2087T>C	.	.	ENST00000538094	3/3	56	30	26	53	53	0	LINC00612,non_coding_transcript_exon_variant,,ENST00000538094,;	G	ENSG00000214851	ENST00000538094	Transcript	non_coding_transcript_exon_variant	2087	.	.	.	.	.	.	.	-1	LINC00612	HGNC	28621	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACAAGCCTC	.	5	ESCA
COL4A2	0	.	GRCh37	13	111077333	111077333	+	Missense_Mutation	SNP	G	G	A	rs374976511	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349G>A	p.Asp117Asn	p.D117N	ENST00000360467	6/48	57	53	4	68	68	0	COL4A2,missense_variant,p.Asp117Asn,ENST00000360467,;COL4A2,downstream_gene_variant,,ENST00000400163,;	A	ENSG00000134871	ENST00000360467	Transcript	missense_variant	655	349	117	D/N	Gat/Aat	rs374976511,COSM416438	.	.	1	COL4A2	HGNC	2203	protein_coding	YES	CCDS41907.1	ENSP00000353654	CO4A2_HUMAN	A2A352_HUMAN	UPI000041C713	.	.	possibly_damaging(0.586)	6/48	.	Low_complexity_(Seg):seg,Pfam_domain:PF01391,hmmpanther:PTHR24023:SF366,hmmpanther:PTHR24023	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCCGATGGA	byFrequency|byCluster	2	ESCA
SACS	0	.	GRCh37	13	23915230	23915230	+	Missense_Mutation	SNP	G	G	A	rs373613604	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2785C>T	p.Arg929Cys	p.R929C	ENST00000382298	10/10	43	32	11	38	38	0	SACS,missense_variant,p.Arg929Cys,ENST00000382292,;SACS,missense_variant,p.Arg179Cys,ENST00000402364,;SACS,missense_variant,p.Arg929Cys,ENST00000382298,;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,;	A	ENSG00000151835	ENST00000382298	Transcript	missense_variant	3374	2785	929	R/C	Cgc/Tgc	rs373613604	.	.	-1	SACS	HGNC	10519	protein_coding	YES	CCDS9300.2	ENSP00000371735	SACS_HUMAN	.	UPI000047039D	.	.	possibly_damaging(0.53)	10/10	.	hmmpanther:PTHR15600:SF26,hmmpanther:PTHR15600	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGCGCTTGA	byFrequency|byCluster	5	ESCA
PARP4	0	.	GRCh37	13	25016071	25016072	+	Frame_Shift_Del	DEL	TT	TT	-	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	TT	TT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3578_3579delAA	p.Lys1193SerfsTer3	p.K1193Sfs*3	ENST00000381989	30/34	36	31	5	41	41	0	PARP4,frameshift_variant,p.Lys1193SerfsTer3,ENST00000381989,;TPTE2P6,intron_variant,,ENST00000445572,;	-	ENSG00000102699	ENST00000381989	Transcript	frameshift_variant	3684-3685	3578-3579	1193	K/X	aAA/a	.	.	.	-1	PARP4	HGNC	271	protein_coding	YES	CCDS9307.1	ENSP00000371419	PARP4_HUMAN	.	UPI000013C76E	.	.	.	30/34	.	hmmpanther:PTHR10338:SF7,hmmpanther:PTHR10338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	AGAAACTTTTGGA	.	2	ESCA
EPSTI1	0	.	GRCh37	13	43537397	43537397	+	Silent	SNP	T	T	C	rs150771459	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483A>G	p.%3D	p.R161R	ENST00000313640	5/13	71	62	8	79	79	0	EPSTI1,synonymous_variant,p.%3D,ENST00000398762,;EPSTI1,synonymous_variant,p.%3D,ENST00000313640,;EPSTI1,synonymous_variant,p.%3D,ENST00000537828,;EPSTI1,synonymous_variant,p.%3D,ENST00000313624,;EPSTI1,non_coding_transcript_exon_variant,,ENST00000476830,;EPSTI1,non_coding_transcript_exon_variant,,ENST00000535677,;EPSTI1,downstream_gene_variant,,ENST00000542706,;EPSTI1,3_prime_UTR_variant,,ENST00000538562,;EPSTI1,non_coding_transcript_exon_variant,,ENST00000540470,;	C	ENSG00000133106	ENST00000313640	Transcript	synonymous_variant	548	483	161	R	agA/agG	rs150771459	.	.	-1	EPSTI1	HGNC	16465	protein_coding	YES	CCDS31964.1	ENSP00000318982	ESIP1_HUMAN	F5H799_HUMAN	UPI0000074657	.	.	.	5/13	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22529:SF1,hmmpanther:PTHR22529	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTCTCTCTG	byCluster	4	ESCA
FARP1	0	.	GRCh37	13	99083388	99083388	+	Missense_Mutation	SNP	G	G	C	rs767461691	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1997G>C	p.Arg666Thr	p.R666T	ENST00000319562	18/27	27	16	11	34	34	0	FARP1,missense_variant,p.Arg666Thr,ENST00000319562,;FARP1,missense_variant,p.Arg666Thr,ENST00000376586,;FARP1,missense_variant,p.Arg31Thr,ENST00000423063,;FARP1,missense_variant,p.Arg666Thr,ENST00000595437,;FARP1,missense_variant,p.Arg19Thr,ENST00000596256,;FARP1-AS1,downstream_gene_variant,,ENST00000432229,;FARP1,upstream_gene_variant,,ENST00000597777,;	C	ENSG00000152767	ENST00000319562	Transcript	missense_variant	2262	1997	666	R/T	aGa/aCa	rs767461691	.	.	1	FARP1	HGNC	3591	protein_coding	YES	CCDS9487.1	ENSP00000322926	FARP1_HUMAN	M0QYB0_HUMAN	UPI000007052C	.	deleterious(0)	probably_damaging(0.967)	18/27	.	PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF105,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGAGACT	.	5	ESCA
EVL	0	.	GRCh37	14	100599115	100599115	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.899T>C	p.Met300Thr	p.M300T	ENST00000392920	8/14	43	25	17	58	58	0	EVL,missense_variant,p.Met300Thr,ENST00000392920,;EVL,missense_variant,p.Met304Thr,ENST00000544450,;EVL,missense_variant,p.Met115Thr,ENST00000554695,;EVL,missense_variant,p.Met298Thr,ENST00000402714,;EVL,missense_variant,p.Met194Thr,ENST00000557384,;EVL,downstream_gene_variant,,ENST00000557153,;EVL,downstream_gene_variant,,ENST00000553910,;EVL,upstream_gene_variant,,ENST00000553799,;EVL,missense_variant,p.Met104Thr,ENST00000554031,;EVL,splice_region_variant,,ENST00000554045,;EVL,upstream_gene_variant,,ENST00000553694,;EVL,upstream_gene_variant,,ENST00000554518,;EVL,downstream_gene_variant,,ENST00000553875,;	C	ENSG00000196405	ENST00000392920	Transcript	missense_variant	1122	899	300	M/T	aTg/aCg	.	.	.	1	EVL	HGNC	20234	protein_coding	YES	CCDS9955.1	ENSP00000376652	EVL_HUMAN	Q499Z9_HUMAN,G3V5F7_HUMAN,G3V314_HUMAN,G3V2K5_HUMAN	UPI000002A92F	.	tolerated(0.87)	benign(0)	8/14	.	hmmpanther:PTHR11202,hmmpanther:PTHR11202:SF4,PIRSF_domain:PIRSF038010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAATGGTGA	.	5	ESCA
IGHV1-3	0	.	GRCh37	14	106471256	106471256	+	Missense_Mutation	SNP	T	T	G	rs544941582	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.341A>C	p.Tyr114Ser	p.Y114S	ENST00000390595	2/2	89	73	16	97	97	0	IGHV1-3,missense_variant,p.Tyr114Ser,ENST00000390595,;IGHVIII-2-1,upstream_gene_variant,,ENST00000518843,;	G	ENSG00000211935	ENST00000390595	Transcript	missense_variant	383	341	114	Y/S	tAc/tCc	rs544941582	.	.	-1	IGHV1-3	HGNC	5552	IG_V_gene	YES	.	ENSP00000375004	.	.	UPI0000115FEB	.	deleterious(0)	probably_damaging(0.972)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266:SF73,hmmpanther:PTHR23266,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	G:0.0004	G:0.0015	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACAGTAATAC	byFrequency|by1000G	5	ESCA
NRXN3	0	.	GRCh37	14	80158529	80158529	+	Intron	SNP	T	T	C	rs748740814	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2498-5444T>C	.	.	ENST00000554719	.	21	10	10	36	36	0	NRXN3,synonymous_variant,p.%3D,ENST00000428277,;NRXN3,intron_variant,,ENST00000554719,;NRXN3,intron_variant,,ENST00000281127,;NRXN3,intron_variant,,ENST00000557594,;NRXN3,intron_variant,,ENST00000335750,;RP11-242P2.1,intron_variant,,ENST00000553322,;NRXN3,intron_variant,,ENST00000556003,;NRXN3,synonymous_variant,p.%3D,ENST00000555387,;NRXN3,synonymous_variant,p.%3D,ENST00000554738,;	C	ENSG00000021645	ENST00000554719	Transcript	intron_variant	.	.	.	.	.	rs748740814	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	.	14/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATAATGAACG	.	5	ESCA
FOXN3	0	.	GRCh37	14	89623682	89623682	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5076T>G	.	.	ENST00000345097	7/7	22	15	6	28	28	0	FOXN3,3_prime_UTR_variant,,ENST00000345097,;FOXN3,3_prime_UTR_variant,,ENST00000261302,;FOXN3,intron_variant,,ENST00000557572,;FOXN3,downstream_gene_variant,,ENST00000557258,;	C	ENSG00000053254	ENST00000345097	Transcript	3_prime_UTR_variant	6666	.	.	.	.	.	.	.	-1	FOXN3	HGNC	1928	protein_coding	YES	CCDS41977.1	ENSP00000343288	FOXN3_HUMAN	G3V5C7_HUMAN,G3V4N5_HUMAN,G3V3A7_HUMAN	UPI000003B451	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGAACTGC	.	5	ESCA
SIN3A	0	.	GRCh37	15	75714814	75714814	+	Intron	SNP	A	A	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366+174T>G	.	.	ENST00000394947	.	26	20	6	20	20	0	SIN3A,3_prime_UTR_variant,,ENST00000567289,;SIN3A,intron_variant,,ENST00000394949,;SIN3A,intron_variant,,ENST00000568431,;SIN3A,intron_variant,,ENST00000394947,;SIN3A,intron_variant,,ENST00000564778,;SIN3A,intron_variant,,ENST00000360439,;SIN3A,intron_variant,,ENST00000562776,;SIN3A,downstream_gene_variant,,ENST00000568309,;SIN3A,downstream_gene_variant,,ENST00000568190,;SIN3A,downstream_gene_variant,,ENST00000570115,;	C	ENSG00000169375	ENST00000394947	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SIN3A	HGNC	19353	protein_coding	YES	CCDS10279.1	ENSP00000378402	SIN3A_HUMAN	H3BT34_HUMAN,H3BQ88_HUMAN,H3BQ76_HUMAN,H3BP90_HUMAN,H3BNZ3_HUMAN,H3BNA0_HUMAN	UPI000013EAD4	.	.	.	.	3/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGGCACTGAT	.	2	ESCA
NUPR1	0	.	GRCh37	16	28549406	28549406	+	Silent	SNP	C	C	T	rs773166279	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237G>A	p.%3D	p.G79G	ENST00000395641	2/3	34	30	4	29	29	0	NUPR1,synonymous_variant,p.%3D,ENST00000324873,;NUPR1,synonymous_variant,p.%3D,ENST00000395641,;NUPR1,3_prime_UTR_variant,,ENST00000567646,;	T	ENSG00000176046	ENST00000395641	Transcript	synonymous_variant	338	237	79	G	ggG/ggA	rs773166279	.	.	-1	NUPR1	HGNC	29990	protein_coding	YES	CCDS42137.1	ENSP00000379003	NUPR1_HUMAN	.	UPI000016955C	.	.	.	2/3	.	hmmpanther:PTHR17149,hmmpanther:PTHR17149:SF2,Pfam_domain:PF10195	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGTGCCCGCC	.	4	ESCA
NETO2	0	.	GRCh37	16	47115515	47115515	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1617A>C	.	.	ENST00000562435	9/9	182	103	78	111	111	0	NETO2,3_prime_UTR_variant,,ENST00000562435,;NETO2,downstream_gene_variant,,ENST00000303155,;NETO2,downstream_gene_variant,,ENST00000564667,;NETO2,downstream_gene_variant,,ENST00000563078,;NETO2,downstream_gene_variant,,ENST00000562559,;	G	ENSG00000171208	ENST00000562435	Transcript	3_prime_UTR_variant	3580	.	.	.	.	.	.	.	-1	NETO2	HGNC	14644	protein_coding	YES	CCDS10727.1	ENSP00000455169	NETO2_HUMAN	.	UPI000003C718	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATTTAAAA	.	5	ESCA
FTO	0	.	GRCh37	16	53967949	53967949	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1292G>C	p.Arg431Thr	p.R431T	ENST00000471389	8/9	58	28	30	78	78	0	FTO,missense_variant,p.Arg32Thr,ENST00000431610,;FTO,missense_variant,p.Arg3Thr,ENST00000268349,;FTO,missense_variant,p.Arg53Thr,ENST00000463855,;FTO,missense_variant,p.Arg431Thr,ENST00000471389,;FTO,missense_variant,p.Arg32Thr,ENST00000460382,;FTO,missense_variant,p.Arg135Thr,ENST00000394647,;FTO,3_prime_UTR_variant,,ENST00000464071,;	C	ENSG00000140718	ENST00000471389	Transcript	missense_variant	1514	1292	431	R/T	aGg/aCg	.	.	.	1	FTO	HGNC	24678	protein_coding	YES	CCDS32448.1	ENSP00000418823	FTO_HUMAN	B4DHN4_HUMAN	UPI000013D7B3	.	deleterious(0.01)	benign(0.243)	8/9	.	hmmpanther:PTHR31291,hmmpanther:PTHR31291:SF2,Pfam_domain:PF12934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAAGGAATG	.	5	ESCA
CTCF	0	.	GRCh37	16	67671824	67671824	+	3'UTR	SNP	G	G	A	rs548584766	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*49G>A	.	.	ENST00000264010	12/12	51	46	5	25	25	0	CTCF,3_prime_UTR_variant,,ENST00000401394,;CTCF,3_prime_UTR_variant,,ENST00000264010,;	A	ENSG00000102974	ENST00000264010	Transcript	3_prime_UTR_variant	2677	.	.	.	.	rs548584766	.	.	1	CTCF	HGNC	13723	protein_coding	YES	CCDS10841.1	ENSP00000264010	CTCF_HUMAN	.	UPI0000000DDE	.	.	.	12/12	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAACGGCCCG	by1000G	4	ESCA
PKD1L2	0	.	GRCh37	16	81219257	81219257	+	5'Flank	SNP	G	G	A	rs199529211	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000527937	.	85	45	40	69	69	0	PKD1L2,missense_variant,p.Arg141Cys,ENST00000526632,;PKD1L2,missense_variant,p.Arg613Cys,ENST00000337114,;PKD1L2,upstream_gene_variant,,ENST00000531391,;PKD1L2,upstream_gene_variant,,ENST00000527937,;PKD1L2,upstream_gene_variant,,ENST00000529791,;PKD1L2,non_coding_transcript_exon_variant,,ENST00000299598,;PKD1L2,missense_variant,p.Arg613Cys,ENST00000525539,;PKD1L2,upstream_gene_variant,,ENST00000533478,;	A	ENSG00000166473	ENST00000527937	Transcript	upstream_gene_variant	.	.	.	.	.	rs199529211	.	4325	-1	PKD1L2	HGNC	21715	protein_coding	YES	.	ENSP00000432818	PK1L2_HUMAN	.	UPI00001C0DE3	.	.	.	.	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.003	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCGAAGCA	byCluster|by1000G	5	ESCA
LLGL1	0	.	GRCh37	17	18137986	18137986	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874A>G	p.Asn292Asp	p.N292D	ENST00000316843	8/23	80	57	23	69	69	0	LLGL1,missense_variant,p.Asn292Asp,ENST00000316843,;LLGL1,non_coding_transcript_exon_variant,,ENST00000479155,;	G	ENSG00000131899	ENST00000316843	Transcript	missense_variant	970	874	292	N/D	Aac/Gac	.	.	.	1	LLGL1	HGNC	6628	protein_coding	YES	CCDS32586.1	ENSP00000321537	L2GL1_HUMAN	A0PJG1_HUMAN	UPI000049DE38	.	deleterious(0.01)	benign(0.297)	8/23	.	hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF21,Pfam_domain:PF08366,Gene3D:2.130.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTAACAAG	.	5	ESCA
TMEM132E	0	.	GRCh37	17	32908041	32908041	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-55G>A	.	.	ENST00000321639	1/10	101	52	49	142	142	0	TMEM132E,5_prime_UTR_variant,,ENST00000321639,;C17orf102,upstream_gene_variant,,ENST00000357754,;	A	ENSG00000181291	ENST00000321639	Transcript	5_prime_UTR_variant	274	.	.	.	.	.	.	.	1	TMEM132E	HGNC	26991	protein_coding	YES	CCDS11283.1	ENSP00000316532	T132E_HUMAN	.	UPI000035960F	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGGCCAAG	.	5	ESCA
TMEM132E	0	.	GRCh37	17	32953491	32953491	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.413C>T	p.Ser138Leu	p.S138L	ENST00000321639	2/10	62	31	30	77	77	0	TMEM132E,missense_variant,p.Ser138Leu,ENST00000321639,;	T	ENSG00000181291	ENST00000321639	Transcript	missense_variant	741	413	138	S/L	tCg/tTg	COSM472574	.	.	1	TMEM132E	HGNC	26991	protein_coding	YES	CCDS11283.1	ENSP00000316532	T132E_HUMAN	.	UPI000035960F	.	deleterious(0)	possibly_damaging(0.453)	2/10	.	hmmpanther:PTHR13388:SF7,hmmpanther:PTHR13388	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTCGCAGC	.	5	ESCA
DHX8	0	.	GRCh37	17	41601024	41601024	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3472A>G	p.Thr1158Ala	p.T1158A	ENST00000262415	23/23	75	62	13	57	57	0	DHX8,missense_variant,p.Thr1158Ala,ENST00000262415,;DHX8,intron_variant,,ENST00000540306,;DHX8,intron_variant,,ENST00000589898,;DHX8,intron_variant,,ENST00000587574,;ETV4,downstream_gene_variant,,ENST00000591713,;ETV4,downstream_gene_variant,,ENST00000586826,;ETV4,downstream_gene_variant,,ENST00000319349,;ETV4,downstream_gene_variant,,ENST00000545954,;ETV4,downstream_gene_variant,,ENST00000393664,;ETV4,downstream_gene_variant,,ENST00000545089,;ETV4,downstream_gene_variant,,ENST00000538265,;DHX8,intron_variant,,ENST00000587044,;	G	ENSG00000067596	ENST00000262415	Transcript	missense_variant	3544	3472	1158	T/A	Acc/Gcc	.	.	.	1	DHX8	HGNC	2749	protein_coding	YES	CCDS11464.1	ENSP00000262415	DHX8_HUMAN	.	UPI00001290D9	.	deleterious(0.03)	benign(0.112)	23/23	.	hmmpanther:PTHR18934:SF85,hmmpanther:PTHR18934,Pfam_domain:PF07717,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACCACCAAG	.	4	ESCA
ABCA9	0	.	GRCh37	17	66992115	66992115	+	Missense_Mutation	SNP	T	T	G	rs533072475	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3476A>C	p.Tyr1159Ser	p.Y1159S	ENST00000340001	26/39	55	48	7	59	59	0	ABCA9,missense_variant,p.Tyr1159Ser,ENST00000370732,;ABCA9,missense_variant,p.Tyr1121Ser,ENST00000453985,;ABCA9,missense_variant,p.Tyr1159Ser,ENST00000340001,;ABCA9,upstream_gene_variant,,ENST00000460872,;	G	ENSG00000154258	ENST00000340001	Transcript	missense_variant	3688	3476	1159	Y/S	tAt/tCt	rs533072475	.	.	-1	ABCA9	HGNC	39	protein_coding	YES	CCDS11681.1	ENSP00000342216	ABCA9_HUMAN	K7EJJ0_HUMAN	UPI00000747B1	.	tolerated(0.33)	benign(0.004)	26/39	.	Pfam_domain:PF12698,hmmpanther:PTHR19229:SF11,hmmpanther:PTHR19229	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCCATATTCA	by1000G	4	ESCA
ITGB4	0	.	GRCh37	17	73726332	73726332	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.749G>C	p.Gly250Ala	p.G250A	ENST00000200181	8/40	84	73	10	57	57	0	ITGB4,missense_variant,p.Gly250Ala,ENST00000579662,;ITGB4,missense_variant,p.Gly250Ala,ENST00000450894,;ITGB4,missense_variant,p.Gly250Ala,ENST00000339591,;ITGB4,missense_variant,p.Gly250Ala,ENST00000449880,;ITGB4,missense_variant,p.Gly250Ala,ENST00000200181,;ITGB4,intron_variant,,ENST00000582629,;ITGB4,non_coding_transcript_exon_variant,,ENST00000584558,;ITGB4,upstream_gene_variant,,ENST00000584374,;ITGB4,non_coding_transcript_exon_variant,,ENST00000580542,;	C	ENSG00000132470	ENST00000200181	Transcript	missense_variant	936	749	250	G/A	gGc/gCc	.	.	.	1	ITGB4	HGNC	6158	protein_coding	YES	CCDS11727.1	ENSP00000200181	ITB4_HUMAN	.	UPI00001AE5C0	.	deleterious(0.03)	probably_damaging(0.912)	8/40	.	hmmpanther:PTHR10082:SF6,hmmpanther:PTHR10082,Gene3D:3.40.50.410,Pfam_domain:PF00362,PIRSF_domain:PIRSF002513,SMART_domains:SM00187,Superfamily_domains:SSF53300,Prints_domain:PR01186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTGGCTGGC	.	4	ESCA
FOXJ1	0	.	GRCh37	17	74134094	74134094	+	Silent	SNP	C	C	T	rs768447827	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606G>A	p.%3D	p.A202A	ENST00000322957	3/3	53	45	7	62	62	0	FOXJ1,synonymous_variant,p.%3D,ENST00000322957,;RNF157,downstream_gene_variant,,ENST00000269391,;RNF157-AS1,upstream_gene_variant,,ENST00000585542,;RNF157-AS1,upstream_gene_variant,,ENST00000590137,;RNF157-AS1,upstream_gene_variant,,ENST00000586627,;RNF157,downstream_gene_variant,,ENST00000589912,;	T	ENSG00000129654	ENST00000322957	Transcript	synonymous_variant	961	606	202	A	gcG/gcA	rs768447827	.	.	-1	FOXJ1	HGNC	3816	protein_coding	YES	CCDS32739.1	ENSP00000323880	FOXJ1_HUMAN	.	UPI000000DB81	.	.	.	3/3	.	Superfamily_domains:SSF46785,SMART_domains:SM00339,Gene3D:1.10.10.10,Pfam_domain:PF00250,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF119,PROSITE_profiles:PS50039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCTCCGCGTA	byCluster	4	ESCA
TP53	0	.	GRCh37	17	7577106	7577106	+	Missense_Mutation	SNP	G	G	C	rs17849781	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	8/11	39	18	21	30	30	0	TP53,missense_variant,p.Pro278Ala,ENST00000420246,;TP53,missense_variant,p.Pro278Ala,ENST00000269305,;TP53,missense_variant,p.Pro146Ala,ENST00000509690,;TP53,missense_variant,p.Pro278Ala,ENST00000359597,;TP53,missense_variant,p.Pro278Ala,ENST00000445888,;TP53,missense_variant,p.Pro278Ala,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1022	832	278	P/A	Cct/Gct	CM052927,CX0910928,rs17849781,CM011015,TP53_g.13812C>G,TP53_g.13812C>A,TP53_g.13812del,TP53_g.13812C>T,COSM43697,COSM10939,COSM10814,COSM45178,COSM368635,COSM139044,COSM99725,COSM3421932,COSM3773297,COSM3717626,COSM1646810,COSM1646809,COSM3421931	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.01)	probably_damaging(1)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P278A|c.832C>G|25,SITE|p.P278A|c.832C>G|4,SITE|p.P278A|c.832C>G|10,CODON|p.0?|c.1_1182del1182|6,CODON|p.P278fs*67|c.833delC|3,CODON|p.P278F|c.832_833CC>TT|3,CODON|p.P278H|c.833C>A|15,CODON|p.P278R|c.833C>G|5,CODON|p.P278R|c.833C>G|30,CODON|p.P278R|c.833C>G|3,CODON|p.P278H|c.833C>A|3,CODON|p.P278L|c.833C>T|3,CODON|p.P278L|c.833C>T|11,CODON|p.P278L|c.833C>T|65,CODON|p.P278L|c.833C>T|8,CODON|p.P278fs*67|c.832delC|3,BUFFER|p.R282W|c.843_844CC>TT|10,BUFFER|p.D281D|c.843C>T|5,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>G|20,BUFFER|p.D281E|c.843C>A|3,BUFFER|p.D281E|c.843C>A|12,BUFFER|p.D281V|c.842A>T|5,BUFFER|p.D281G|c.842A>G|10,BUFFER|p.D281H|c.841G>C|6,BUFFER|p.D281H|c.841G>C|28,BUFFER|p.D281H|c.841G>C|3,BUFFER|p.D281H|c.841G>C|4,BUFFER|p.D281Y|c.841G>T|7,BUFFER|p.D281N|c.841G>A|7,BUFFER|p.D281N|c.841G>A|3,BUFFER|p.D281Y|c.841G>T|13,BUFFER|p.D281Y|c.841G>T|4,BUFFER|p.D281N|c.841G>A|27,BUFFER|p.R280R|c.840A>G|3,BUFFER|p.R280S|c.840A>T|11,BUFFER|p.R280S|c.840A>C|6,BUFFER|p.R280T|c.839G>C|63,BUFFER|p.R280T|c.839G>C|4,BUFFER|p.R280I|c.839G>T|17,BUFFER|p.R280K|c.839G>A|17,BUFFER|p.R280K|c.839G>A|6,BUFFER|p.R280I|c.839G>T|4,BUFFER|p.R280K|c.839G>A|57,BUFFER|p.R280I|c.839G>T|3,BUFFER|p.R280T|c.839G>C|10,BUFFER|p.R280K|c.839G>A|11,BUFFER|p.R280*|c.838A>T|12,BUFFER|p.R280G|c.838A>G|6,BUFFER|p.R280G|c.838A>G|3,BUFFER|p.R280G|c.838A>G|23,BUFFER|p.R280fs*65|c.835delG|5,BUFFER|p.G279E|c.836G>A|4,BUFFER|p.G279E|c.836G>A|34,BUFFER|p.G279V|c.836G>T|3,BUFFER|p.G279R|c.835G>A|7,BUFFER|p.G279W|c.835G>T|3,BUFFER|p.P278T|c.832C>A|29,BUFFER|p.P278T|c.832C>A|8,BUFFER|p.P278S|c.832C>T|4,BUFFER|p.P278S|c.832C>T|3,BUFFER|p.P278S|c.832C>T|8,BUFFER|p.P278S|c.832C>T|55,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCAGGACAGG	.	5	ESCA
CCDC137	0	.	GRCh37	17	79633892	79633892	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96G>T	p.%3D	p.L32L	ENST00000329214	1/6	13	9	4	16	16	0	CCDC137,synonymous_variant,p.%3D,ENST00000574107,;CCDC137,synonymous_variant,p.%3D,ENST00000329214,;OXLD1,upstream_gene_variant,,ENST00000374741,;OXLD1,upstream_gene_variant,,ENST00000571503,;PDE6G,upstream_gene_variant,,ENST00000571224,;PDE6G,upstream_gene_variant,,ENST00000574777,;OXLD1,upstream_gene_variant,,ENST00000573786,;CCDC137,synonymous_variant,p.%3D,ENST00000575223,;CCDC137,synonymous_variant,p.%3D,ENST00000574200,;CCDC137,upstream_gene_variant,,ENST00000571916,;CCDC137,upstream_gene_variant,,ENST00000572531,;OXLD1,upstream_gene_variant,,ENST00000571092,;OXLD1,upstream_gene_variant,,ENST00000571757,;OXLD1,upstream_gene_variant,,ENST00000575992,;OXLD1,upstream_gene_variant,,ENST00000575963,;	T	ENSG00000185298	ENST00000329214	Transcript	synonymous_variant	499	96	32	L	ctG/ctT	.	.	.	1	CCDC137	HGNC	33451	protein_coding	YES	CCDS42400.1	ENSP00000329360	CC137_HUMAN	H6QX63_HUMAN	UPI00001983C7	.	.	.	1/6	.	hmmpanther:PTHR21838	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	CCGCTGGGGAA	.	3	ESCA
ABHD3	0	.	GRCh37	18	19284763	19284763	+	5'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-137G>T	.	.	ENST00000289119	1/9	19	7	12	13	13	0	ABHD3,5_prime_UTR_variant,,ENST00000289119,;ABHD3,upstream_gene_variant,,ENST00000580981,;ABHD3,upstream_gene_variant,,ENST00000584464,;ABHD3,upstream_gene_variant,,ENST00000578270,;ABHD3,upstream_gene_variant,,ENST00000579875,;MIB1,upstream_gene_variant,,ENST00000578646,;ABHD3,upstream_gene_variant,,ENST00000577928,;ABHD3,upstream_gene_variant,,ENST00000577891,;ABHD3,upstream_gene_variant,,ENST00000579982,;	A	ENSG00000158201	ENST00000289119	Transcript	5_prime_UTR_variant	4	.	.	.	.	.	.	.	-1	ABHD3	HGNC	18718	protein_coding	YES	CCDS32802.1	ENSP00000289119	ABHD3_HUMAN	.	UPI0000163938	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCTTCCGACAA	.	4	ESCA
TMEM200C	0	.	GRCh37	18	5892004	5892004	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>G	p.Pro20Arg	p.P20R	ENST00000581347	3/3	54	48	6	42	42	0	TMEM200C,missense_variant,p.Pro20Arg,ENST00000383490,;TMEM200C,missense_variant,p.Pro20Arg,ENST00000581347,;RP11-945C19.4,intron_variant,,ENST00000577694,;RP11-945C19.4,downstream_gene_variant,,ENST00000580845,;RP11-945C19.4,downstream_gene_variant,,ENST00000582939,;	C	ENSG00000206432	ENST00000581347	Transcript	missense_variant	705	59	20	P/R	cCc/cGc	.	.	.	-1	TMEM200C	HGNC	37208	protein_coding	YES	CCDS45825.1	ENSP00000463375	T200C_HUMAN	.	UPI000020198E	.	deleterious(0)	probably_damaging(0.997)	3/3	.	hmmpanther:PTHR31815,hmmpanther:PTHR31815:SF2,Pfam_domain:PF10177	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R19C|c.55C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TTGGGGGGCGG	.	4	ESCA
SERPINB11	0	.	GRCh37	18	61377452	61377452	+	Missense_Mutation	SNP	G	G	A	rs769803949	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.25G>A	p.Val9Ile	p.V9I	ENST00000544088	2/8	75	68	7	57	57	0	SERPINB11,missense_variant,p.Val9Ile,ENST00000538847,;SERPINB11,missense_variant,p.Val9Ile,ENST00000544088,;SERPINB11,5_prime_UTR_variant,,ENST00000536691,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000489748,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000467649,;SERPINB11,missense_variant,p.Val9Ile,ENST00000382749,;	A	ENSG00000206072	ENST00000544088	Transcript	missense_variant	87	25	9	V/I	Gtt/Att	rs769803949	.	.	1	SERPINB11	HGNC	14221	protein_coding	YES	.	ENSP00000441497	.	F5GYW9_HUMAN,F5GWT8_HUMAN	UPI00015AAB67	.	tolerated(0.33)	benign(0.013)	2/8	.	hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF137,Gene3D:3.30.497.10,Pfam_domain:PF00079,Superfamily_domains:SSF56574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTAACGTTGAA	byFrequency	3	ESCA
ARHGAP28	0	.	GRCh37	18	6912058	6912058	+	Splice_Site	SNP	G	G	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1619-1G>T	.	p.X540_splice	ENST00000419673	.	27	22	4	18	18	0	ARHGAP28,splice_acceptor_variant,,ENST00000383472,;ARHGAP28,splice_acceptor_variant,,ENST00000531294,;ARHGAP28,splice_acceptor_variant,,ENST00000314319,;ARHGAP28,splice_acceptor_variant,,ENST00000419673,;	T	ENSG00000088756	ENST00000419673	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	ARHGAP28	HGNC	25509	protein_coding	YES	CCDS32785.1	ENSP00000392660	RHG28_HUMAN	J3KTC0_HUMAN	UPI00004CEC5C	.	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTAGGAGAG	.	2	ESCA
SMARCA4	0	.	GRCh37	19	11152145	11152145	+	Missense_Mutation	SNP	C	C	T	rs775399739	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4333C>T	p.Arg1445Trp	p.R1445W	ENST00000429416	31/36	127	35	91	67	67	0	SMARCA4,missense_variant,p.Arg1415Trp,ENST00000450717,;SMARCA4,missense_variant,p.Arg1477Trp,ENST00000358026,;SMARCA4,missense_variant,p.Arg1415Trp,ENST00000413806,;SMARCA4,missense_variant,p.Arg1412Trp,ENST00000590574,;SMARCA4,missense_variant,p.Arg1412Trp,ENST00000444061,;SMARCA4,missense_variant,p.Arg1445Trp,ENST00000344626,;SMARCA4,missense_variant,p.Arg1415Trp,ENST00000541122,;SMARCA4,missense_variant,p.Arg1445Trp,ENST00000429416,;SMARCA4,missense_variant,p.Arg1415Trp,ENST00000589677,;SMARCA4,downstream_gene_variant,,ENST00000592158,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000538456,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;	T	ENSG00000127616	ENST00000429416	Transcript	missense_variant	4614	4333	1445	R/W	Cgg/Tgg	rs775399739	.	.	1	SMARCA4	HGNC	11100	protein_coding	YES	CCDS12253.1	ENSP00000395654	SMCA4_HUMAN	B4DSI8_HUMAN,A7E2E1_HUMAN	UPI000006F973	.	.	probably_damaging(0.978)	31/36	.	Superfamily_domains:SSF47370,hmmpanther:PTHR10799:SF76,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGGCGGCCG	.	5	ESCA
ZNF536	0	.	GRCh37	19	30936428	30936428	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1959C>T	p.%3D	p.H653H	ENST00000355537	2/5	79	51	28	98	98	0	ZNF536,synonymous_variant,p.%3D,ENST00000585628,;ZNF536,synonymous_variant,p.%3D,ENST00000355537,;ZNF536,downstream_gene_variant,,ENST00000591488,;	T	ENSG00000198597	ENST00000355537	Transcript	synonymous_variant	2106	1959	653	H	caC/caT	.	.	.	1	ZNF536	HGNC	29025	protein_coding	YES	CCDS32984.1	ENSP00000347730	ZN536_HUMAN	K7EKT4_HUMAN,K7EJP8_HUMAN	UPI000006ED3E	.	.	.	2/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R657H|c.1970G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCACAAGCG	.	5	ESCA
ZFP14	0	.	GRCh37	19	36831606	36831606	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1122G>A	p.%3D	p.G374G	ENST00000270001	5/5	45	41	4	54	54	0	ZFP14,synonymous_variant,p.%3D,ENST00000270001,;	T	ENSG00000142065	ENST00000270001	Transcript	synonymous_variant	1238	1122	374	G	ggG/ggA	.	.	.	-1	ZFP14	HGNC	29312	protein_coding	YES	CCDS33002.1	ENSP00000270001	ZFP14_HUMAN	.	UPI000013AD55	.	.	.	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24377:SF253,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCTTCCCACA	.	3	ESCA
ZBTB7A	0	.	GRCh37	19	4048040	4048040	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1465G>A	p.Gly489Ser	p.G489S	ENST00000322357	3/3	22	19	3	28	28	0	ZBTB7A,missense_variant,p.Gly489Ser,ENST00000322357,;ZBTB7A,missense_variant,p.Gly489Ser,ENST00000601588,;AC016586.1,upstream_gene_variant,,ENST00000535853,;	T	ENSG00000178951	ENST00000322357	Transcript	missense_variant	1744	1465	489	G/S	Ggc/Agc	.	.	.	-1	ZBTB7A	HGNC	18078	protein_coding	YES	CCDS12119.1	ENSP00000323670	ZBT7A_HUMAN	.	UPI000006E9D9	.	tolerated(0.61)	possibly_damaging(0.77)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23229,hmmpanther:PTHR23229:SF69	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCCGTCTT	.	2	ESCA
CIC	0	.	GRCh37	19	42791176	42791177	+	Frame_Shift_Ins	INS	-	-	TGTT	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.237_240dupTGTT	p.Ala81CysfsTer4	p.A81Cfs*4	ENST00000575354	3/20	70	39	31	77	77	0	CIC,frameshift_variant,p.Ala81CysfsTer4,ENST00000575354,;CIC,frameshift_variant,p.Ala990CysfsTer4,ENST00000572681,;CIC,frameshift_variant,p.Ala81CysfsTer4,ENST00000160740,;CIC,downstream_gene_variant,,ENST00000575839,;	TGTT	ENSG00000079432	ENST00000575354	Transcript	frameshift_variant	276-277	236-237	79	A/AVX	gct/gcTGTTt	.	.	.	1	CIC	HGNC	14214	protein_coding	YES	CCDS12601.1	ENSP00000458663	CIC_HUMAN	.	UPI000013C5A0	.	.	.	3/20	.	hmmpanther:PTHR13059:SF11,hmmpanther:PTHR13059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGCAGCTGTTG	.	3	ESCA
SEMA6B	0	.	GRCh37	19	4543276	4543276	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*337G>T	.	.	ENST00000586582	17/17	85	63	21	126	126	0	SEMA6B,3_prime_UTR_variant,,ENST00000301293,;SEMA6B,3_prime_UTR_variant,,ENST00000586582,;SEMA6B,intron_variant,,ENST00000586965,;LRG1,upstream_gene_variant,,ENST00000306390,;RN7SL121P,upstream_gene_variant,,ENST00000584223,;LRG1,upstream_gene_variant,,ENST00000586883,;SEMA6B,downstream_gene_variant,,ENST00000589889,;CTB-50L17.14,upstream_gene_variant,,ENST00000586020,;	A	ENSG00000167680	ENST00000586582	Transcript	3_prime_UTR_variant	3315	.	.	.	.	.	.	.	-1	SEMA6B	HGNC	10739	protein_coding	YES	CCDS12131.1	ENSP00000467290	SEM6B_HUMAN	.	UPI000004BA6B	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCACCCCGAG	.	5	ESCA
SEMA6B	0	.	GRCh37	19	4543277	4543277	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*336G>C	.	.	ENST00000586582	17/17	86	65	21	126	125	0	SEMA6B,3_prime_UTR_variant,,ENST00000301293,;SEMA6B,3_prime_UTR_variant,,ENST00000586582,;SEMA6B,intron_variant,,ENST00000586965,;LRG1,upstream_gene_variant,,ENST00000306390,;RN7SL121P,upstream_gene_variant,,ENST00000584223,;LRG1,upstream_gene_variant,,ENST00000586883,;SEMA6B,downstream_gene_variant,,ENST00000589889,;CTB-50L17.14,upstream_gene_variant,,ENST00000586020,;	G	ENSG00000167680	ENST00000586582	Transcript	3_prime_UTR_variant	3314	.	.	.	.	.	.	.	-1	SEMA6B	HGNC	10739	protein_coding	YES	CCDS12131.1	ENSP00000467290	SEM6B_HUMAN	.	UPI000004BA6B	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCCCGAGA	.	5	ESCA
SLC8A2	0	.	GRCh37	19	47960551	47960551	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.976C>T	p.His326Tyr	p.H326Y	ENST00000236877	3/10	14	5	9	13	13	0	SLC8A2,missense_variant,p.His82Tyr,ENST00000542837,;SLC8A2,missense_variant,p.His326Tyr,ENST00000236877,;SLC8A2,intron_variant,,ENST00000539381,;SLC8A2,downstream_gene_variant,,ENST00000594353,;	A	ENSG00000118160	ENST00000236877	Transcript	missense_variant	1372	976	326	H/Y	Cac/Tac	.	.	.	-1	SLC8A2	HGNC	11069	protein_coding	YES	CCDS33065.1	ENSP00000236877	NAC2_HUMAN	M0R211_HUMAN,M0R1Z4_HUMAN,F5H6L7_HUMAN,F5GYS4_HUMAN	UPI000012FC49	.	tolerated(0.34)	benign(0.006)	3/10	.	Coiled-coils_(Ncoils):Coil,TIGRFAM_domain:TIGR00845,hmmpanther:PTHR11878	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGTGCTTCT	.	5	ESCA
POLD1	0	.	GRCh37	19	50905960	50905960	+	Missense_Mutation	SNP	G	G	C	rs777944185	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932G>C	p.Arg311Pro	p.R311P	ENST00000440232	8/27	42	36	6	37	37	0	POLD1,missense_variant,p.Arg311Pro,ENST00000595904,;POLD1,missense_variant,p.Arg311Pro,ENST00000440232,;POLD1,missense_variant,p.Arg311Pro,ENST00000599857,;POLD1,downstream_gene_variant,,ENST00000593887,;POLD1,downstream_gene_variant,,ENST00000601098,;POLD1,upstream_gene_variant,,ENST00000596425,;POLD1,missense_variant,p.Arg311Pro,ENST00000600859,;POLD1,downstream_gene_variant,,ENST00000600746,;	C	ENSG00000062822	ENST00000440232	Transcript	missense_variant	985	932	311	R/P	cGc/cCc	rs777944185	.	.	1	POLD1	HGNC	9175	protein_coding	YES	CCDS12795.1	ENSP00000406046	DPOD1_HUMAN	M0R2J2_HUMAN	UPI000007288E	.	deleterious(0)	probably_damaging(0.997)	8/27	.	Superfamily_domains:SSF53098,SMART_domains:SM00486,Pfam_domain:PF03104,Gene3D:3.30.420.10,hmmpanther:PTHR10322,hmmpanther:PTHR10322:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCGCGTGC	byFrequency	5	ESCA
ZIM2	0	.	GRCh37	19	57286355	57286355	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1285C>A	p.Gln429Lys	p.Q429K	ENST00000391708	12/12	24	18	6	35	34	1	ZIM2,missense_variant,p.Gln429Lys,ENST00000221722,;ZIM2,missense_variant,p.Gln429Lys,ENST00000601070,;ZIM2,missense_variant,p.Gln429Lys,ENST00000593711,;ZIM2,missense_variant,p.Gln429Lys,ENST00000599935,;ZIM2,missense_variant,p.Gln429Lys,ENST00000391708,;AC006115.3,intron_variant,,ENST00000597946,;AC006115.3,intron_variant,,ENST00000595954,;AC006115.3,intron_variant,,ENST00000594400,;ZIM2,3_prime_UTR_variant,,ENST00000597281,;ZIM2,3_prime_UTR_variant,,ENST00000595671,;ZIM2,downstream_gene_variant,,ENST00000596270,;	T	ENSG00000269699	ENST00000391708	Transcript	missense_variant	1828	1285	429	Q/K	Caa/Aaa	.	.	.	-1	ZIM2	HGNC	12875	protein_coding	YES	CCDS33123.1	ENSP00000375589	ZIM2_HUMAN	.	UPI000013C3DF	.	tolerated(0.05)	benign(0.326)	12/12	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF110,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|VARSCANS	ATGTTGAAGAA	.	3	ESCA
DUS3L	0	.	GRCh37	19	5788046	5788046	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1084T>C	p.Phe362Leu	p.F362L	ENST00000309061	5/13	56	27	29	53	53	0	DUS3L,missense_variant,p.Phe362Leu,ENST00000309061,;DUS3L,missense_variant,p.Phe120Leu,ENST00000320699,;PRR22,upstream_gene_variant,,ENST00000419421,;CTB-54O9.9,upstream_gene_variant,,ENST00000586012,;DUS3L,upstream_gene_variant,,ENST00000590343,;DUS3L,downstream_gene_variant,,ENST00000592491,;PRR22,upstream_gene_variant,,ENST00000390672,;DUS3L,downstream_gene_variant,,ENST00000590681,;DUS3L,missense_variant,p.Phe48Leu,ENST00000591560,;DUS3L,3_prime_UTR_variant,,ENST00000590110,;DUS3L,non_coding_transcript_exon_variant,,ENST00000593229,;DUS3L,non_coding_transcript_exon_variant,,ENST00000590087,;DUS3L,non_coding_transcript_exon_variant,,ENST00000589085,;DUS3L,upstream_gene_variant,,ENST00000592468,;DUS3L,downstream_gene_variant,,ENST00000589854,;DUS3L,downstream_gene_variant,,ENST00000585587,;DUS3L,upstream_gene_variant,,ENST00000589841,;DUS3L,upstream_gene_variant,,ENST00000592673,;	G	ENSG00000141994	ENST00000309061	Transcript	missense_variant	1181	1084	362	F/L	Ttt/Ctt	.	.	.	-1	DUS3L	HGNC	26920	protein_coding	YES	CCDS32880.1	ENSP00000311977	DUS3L_HUMAN	D6W636_HUMAN	UPI0000140953	.	deleterious(0)	probably_damaging(0.999)	5/13	.	hmmpanther:PTHR11082,hmmpanther:PTHR11082:SF8,Pfam_domain:PF01207,Gene3D:3.20.20.70,Superfamily_domains:SSF51395	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAAAGATGT	.	5	ESCA
S1PR1	0	.	GRCh37	1	101704654	101704654	+	Silent	SNP	C	C	T	rs777562427	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.114C>T	p.%3D	p.S38S	ENST00000305352	2/2	41	28	12	58	58	0	S1PR1,synonymous_variant,p.%3D,ENST00000305352,;RP4-575N6.5,upstream_gene_variant,,ENST00000561748,;RP4-575N6.4,upstream_gene_variant,,ENST00000432195,;S1PR1,non_coding_transcript_exon_variant,,ENST00000475821,;S1PR1,non_coding_transcript_exon_variant,,ENST00000475289,;	T	ENSG00000170989	ENST00000305352	Transcript	synonymous_variant	489	114	38	S	agC/agT	rs777562427	.	.	1	S1PR1	HGNC	3165	protein_coding	YES	CCDS777.1	ENSP00000305416	S1PR1_HUMAN	Q7L853_HUMAN	UPI0000050421	.	.	.	2/2	.	hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF16,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00642	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAGCGCGGA	.	5	ESCA
AMPD2	0	.	GRCh37	1	110172511	110172511	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2118delC	p.Asn706LysfsTer71	p.N706Kfs*71	ENST00000256578	15/18	134	108	26	85	85	0	AMPD2,frameshift_variant,p.Asn588LysfsTer71,ENST00000528454,;AMPD2,frameshift_variant,p.Asn631LysfsTer71,ENST00000358729,;AMPD2,frameshift_variant,p.Asn706LysfsTer71,ENST00000256578,;AMPD2,frameshift_variant,p.Asn706LysfsTer71,ENST00000528667,;AMPD2,frameshift_variant,p.Asn625LysfsTer71,ENST00000342115,;AMPD2,frameshift_variant,p.Asn677LysfsTer82,ENST00000369840,;AMPD2,frameshift_variant,p.Asn95LysfsTer69,ENST00000476688,;AMPD2,frameshift_variant,p.Asn587LysfsTer71,ENST00000393688,;AMPD2,downstream_gene_variant,,ENST00000527846,;AMPD2,downstream_gene_variant,,ENST00000474459,;AMPD2,downstream_gene_variant,,ENST00000531203,;AMPD2,downstream_gene_variant,,ENST00000531734,;RP5-1160K1.6,intron_variant,,ENST00000369843,;AMPD2,non_coding_transcript_exon_variant,,ENST00000526301,;AMPD2,downstream_gene_variant,,ENST00000459643,;AMPD2,intron_variant,,ENST00000479919,;AMPD2,downstream_gene_variant,,ENST00000529299,;AMPD2,downstream_gene_variant,,ENST00000486282,;AMPD2,downstream_gene_variant,,ENST00000534144,;AMPD2,downstream_gene_variant,,ENST00000532851,;AMPD2,downstream_gene_variant,,ENST00000533132,;AMPD2,downstream_gene_variant,,ENST00000467071,;AMPD2,downstream_gene_variant,,ENST00000525415,;AMPD2,downstream_gene_variant,,ENST00000528270,;AMPD2,upstream_gene_variant,,ENST00000528958,;AMPD2,downstream_gene_variant,,ENST00000524975,;	-	ENSG00000116337	ENST00000256578	Transcript	frameshift_variant	2478	2118	706	N/X	aaC/aa	.	.	.	1	AMPD2	HGNC	469	protein_coding	YES	CCDS805.1	ENSP00000256578	AMPD2_HUMAN	E9PIJ1_HUMAN	UPI0000125956	.	.	.	15/18	.	hmmpanther:PTHR11359:SF3,hmmpanther:PTHR11359,Gene3D:3.20.20.140,Pfam_domain:PF00962,TIGRFAM_domain:TIGR01429,PIRSF_domain:PIRSF001251,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGAGAACATTTC	.	3	ESCA
PRAMEF6	0	.	GRCh37	1	13001384	13001384	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.299T>G	p.Leu100Arg	p.L100R	ENST00000376189	3/4	178	163	14	316	316	0	PRAMEF6,missense_variant,p.Leu100Arg,ENST00000415464,;PRAMEF6,missense_variant,p.Leu100Arg,ENST00000355096,;PRAMEF6,missense_variant,p.Leu100Arg,ENST00000376189,;PRAMEF6,intron_variant,,ENST00000376192,;	C	ENSG00000232423	ENST00000376189	Transcript	missense_variant	399	299	100	L/R	cTt/cGt	.	.	.	-1	PRAMEF6	HGNC	30583	protein_coding	YES	CCDS30594.1	ENSP00000365360	PRAM6_HUMAN	.	UPI0000418E57	.	deleterious(0)	probably_damaging(0.96)	3/4	.	hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CTTGAAGTTTC	.	2	ESCA
PRAMEF5	0	.	GRCh37	1	13365855	13365855	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.299T>G	p.Leu100Arg	p.L100R	ENST00000376168	3/4	71	64	7	150	150	0	PRAMEF5,missense_variant,p.Leu100Arg,ENST00000376168,;	G	ENSG00000204502	ENST00000376168	Transcript	missense_variant	399	299	100	L/R	cTt/cGt	.	.	.	1	PRAMEF5	HGNC	27995	protein_coding	YES	CCDS30596.1	ENSP00000365338	PRAM5_HUMAN	.	UPI0000418F6D	.	deleterious(0)	probably_damaging(0.96)	3/4	.	hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R97R|c.291G>A|3	RADIA|MUTECT|VARSCANS	GAAACTTCAAG	.	3	ESCA
MTX1	0	.	GRCh37	1	155185406	155185406	+	3'Flank	SNP	A	A	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000368376	.	69	62	7	60	60	0	MTX1,downstream_gene_variant,,ENST00000368376,;MTX1,downstream_gene_variant,,ENST00000609421,;MTX1,downstream_gene_variant,,ENST00000316721,;RP11-263K19.6,upstream_gene_variant,,ENST00000455788,;GBAP1,non_coding_transcript_exon_variant,,ENST00000368374,;GBAP1,non_coding_transcript_exon_variant,,ENST00000486869,;MTX1,downstream_gene_variant,,ENST00000495589,;GBAP1,downstream_gene_variant,,ENST00000462587,;GBAP1,non_coding_transcript_exon_variant,,ENST00000486197,;GBAP1,non_coding_transcript_exon_variant,,ENST00000473223,;GBAP1,non_coding_transcript_exon_variant,,ENST00000459805,;MTX1,downstream_gene_variant,,ENST00000481771,;MTX1,downstream_gene_variant,,ENST00000424959,;GBAP1,downstream_gene_variant,,ENST00000463838,;MTX1,downstream_gene_variant,,ENST00000495492,;GBAP1,non_coding_transcript_exon_variant,,ENST00000313929,;GBAP1,non_coding_transcript_exon_variant,,ENST00000566701,;	T	ENSG00000173171	ENST00000368376	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1792	1	MTX1	HGNC	7504	protein_coding	YES	CCDS1100.1	ENSP00000357360	MTX1_HUMAN	.	UPI0000225CC9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCGCACACTC	.	3	ESCA
KIRREL	0	.	GRCh37	1	158063493	158063493	+	Missense_Mutation	SNP	C	C	T	rs778661101	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1660C>T	p.Arg554Trp	p.R554W	ENST00000359209	13/15	35	29	6	33	33	0	KIRREL,missense_variant,p.Arg390Trp,ENST00000360089,;KIRREL,missense_variant,p.Arg570Trp,ENST00000368173,;KIRREL,missense_variant,p.Arg368Trp,ENST00000368172,;KIRREL,missense_variant,p.Arg454Trp,ENST00000416935,;KIRREL,missense_variant,p.Arg554Trp,ENST00000359209,;KIRREL,missense_variant,p.Arg451Trp,ENST00000392272,;	T	ENSG00000183853	ENST00000359209	Transcript	missense_variant	1727	1660	554	R/W	Cgg/Tgg	rs778661101,COSM897647,COSM1151870,COSM897648	.	.	1	KIRREL	HGNC	15734	protein_coding	YES	CCDS1172.2	ENSP00000352138	KIRR1_HUMAN	.	UPI0000443FBD	.	deleterious(0)	possibly_damaging(0.791)	13/15	.	hmmpanther:PTHR11640:SF14,hmmpanther:PTHR11640	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACCGGGAG	.	5	ESCA
FMO3	0	.	GRCh37	1	171086361	171086361	+	Missense_Mutation	SNP	G	G	A	rs761653296	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1378G>A	p.Glu460Lys	p.E460K	ENST00000367755	9/9	44	30	13	36	36	0	FMO3,missense_variant,p.Glu460Lys,ENST00000367755,;FMO3,missense_variant,p.Glu397Lys,ENST00000538429,;FMO3,missense_variant,p.Glu440Lys,ENST00000542847,;FMO3,missense_variant,p.Glu460Lys,ENST00000392085,;	A	ENSG00000007933	ENST00000367755	Transcript	missense_variant	1489	1378	460	E/K	Gaa/Aaa	rs761653296	.	.	1	FMO3	HGNC	3771	protein_coding	YES	CCDS1292.1	ENSP00000356729	FMO3_HUMAN	.	UPI000016A103	.	tolerated(0.29)	benign(0.12)	9/9	.	hmmpanther:PTHR23023:SF44,hmmpanther:PTHR23023,Pfam_domain:PF00743,Gene3D:3.50.50.60,PIRSF_domain:PIRSF000332,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCATGGAAGTT	.	4	ESCA
RGSL1	0	.	GRCh37	1	182443066	182443066	+	Missense_Mutation	SNP	G	G	T	rs531534371	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820G>T	p.Ala274Ser	p.A274S	ENST00000294854	6/22	35	23	12	27	27	0	RGSL1,missense_variant,p.Ala274Ser,ENST00000294854,;RGSL1,missense_variant,p.Ala309Ser,ENST00000542961,;RGSL1,downstream_gene_variant,,ENST00000437548,;RGSL1,downstream_gene_variant,,ENST00000447374,;RGSL1,downstream_gene_variant,,ENST00000426890,;RGSL1,missense_variant,p.Ala309Ser,ENST00000443996,;RGSL1,non_coding_transcript_exon_variant,,ENST00000367561,;RGSL1,intron_variant,,ENST00000422241,;RGSL1,intron_variant,,ENST00000416676,;RGSL1,upstream_gene_variant,,ENST00000415960,;RGSL1,downstream_gene_variant,,ENST00000444367,;	T	ENSG00000121446	ENST00000294854	Transcript	missense_variant	840	820	274	A/S	Gct/Tct	rs531534371	.	.	1	RGSL1	HGNC	18636	protein_coding	YES	CCDS58049.1	ENSP00000457748	RGSL_HUMAN	H3BNQ0_HUMAN	UPI000156571A	.	tolerated(0.87)	benign(0.002)	6/22	.	hmmpanther:PTHR10845:SF137,hmmpanther:PTHR10845	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGATGCTATT	by1000G	5	ESCA
DNAH14	0	.	GRCh37	1	225237932	225237932	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1846C>A	p.Gln616Lys	p.Q616K	ENST00000445597	12/61	118	54	63	59	59	0	DNAH14,missense_variant,p.Gln616Lys,ENST00000445597,;DNAH14,missense_variant,p.Gln645Lys,ENST00000430092,;DNAH14,missense_variant,p.Gln645Lys,ENST00000439375,;	A	ENSG00000185842	ENST00000445597	Transcript	missense_variant	1846	1846	616	Q/K	Caa/Aaa	.	.	.	1	DNAH14	HGNC	2945	protein_coding	.	.	ENSP00000409472	DYH14_HUMAN	C9JU64_HUMAN	UPI0001642868	.	tolerated(0.18)	benign(0)	12/61	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGCCAAGAT	.	5	ESCA
ACTA1	0	.	GRCh37	1	229567270	229567270	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1110C>A	p.%3D	p.S370S	ENST00000366684	7/7	57	36	20	41	41	0	ACTA1,synonymous_variant,p.%3D,ENST00000366683,;ACTA1,synonymous_variant,p.%3D,ENST00000366684,;	T	ENSG00000143632	ENST00000366684	Transcript	synonymous_variant	1213	1110	370	S	tcC/tcA	.	.	.	-1	ACTA1	HGNC	129	protein_coding	YES	CCDS1578.1	ENSP00000355645	ACTS_HUMAN	.	UPI0000000860	.	.	.	7/7	.	hmmpanther:PTHR11937:SF165,hmmpanther:PTHR11937,Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGATGGAAGG	.	5	ESCA
HNRNPR	0	.	GRCh37	1	23636857	23636857	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*90T>A	.	.	ENST00000374616	11/11	37	23	14	35	35	0	HNRNPR,3_prime_UTR_variant,,ENST00000374616,;HNRNPR,3_prime_UTR_variant,,ENST00000478691,;HNRNPR,3_prime_UTR_variant,,ENST00000302271,;HNRNPR,3_prime_UTR_variant,,ENST00000427764,;HNRNPR,3_prime_UTR_variant,,ENST00000606561,;HNRNPR,3_prime_UTR_variant,,ENST00000374612,;HNRNPR,downstream_gene_variant,,ENST00000426846,;HNRNPR,non_coding_transcript_exon_variant,,ENST00000476660,;HNRNPR,downstream_gene_variant,,ENST00000463552,;HNRNPR,upstream_gene_variant,,ENST00000464516,;HNRNPR,downstream_gene_variant,,ENST00000470941,;	T	ENSG00000125944	ENST00000374616	Transcript	3_prime_UTR_variant	2110	.	.	.	.	.	.	.	-1	HNRNPR	HGNC	5047	protein_coding	YES	CCDS44085.1	ENSP00000363745	HNRPR_HUMAN	S4R3J4_HUMAN,Q7Z334_HUMAN	UPI000006F30B	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAGATGAAA	.	5	ESCA
IL22RA1	0	.	GRCh37	1	24460793	24460793	+	Missense_Mutation	SNP	G	G	A	rs777028986	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.439C>T	p.Arg147Cys	p.R147C	ENST00000270800	4/7	56	35	20	47	47	0	IL22RA1,missense_variant,p.Arg147Cys,ENST00000270800,;	A	ENSG00000142677	ENST00000270800	Transcript	missense_variant	478	439	147	R/C	Cgt/Tgt	rs777028986,COSM1687214	.	.	-1	IL22RA1	HGNC	13700	protein_coding	YES	CCDS247.1	ENSP00000270800	I22R1_HUMAN	.	UPI0000071143	.	tolerated(0.07)	benign(0.014)	4/7	.	hmmpanther:PTHR20859:SF20,hmmpanther:PTHR20859,Gene3D:2.60.40.10	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCACGGATTG	byFrequency	5	ESCA
EMILIN3	0	.	GRCh37	20	39990470	39990470	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1739T>C	p.Leu580Pro	p.L580P	ENST00000332312	4/4	40	36	4	32	32	0	EMILIN3,missense_variant,p.Leu580Pro,ENST00000332312,;LPIN3,downstream_gene_variant,,ENST00000373257,;LPIN3,downstream_gene_variant,,ENST00000445975,;LPIN3,downstream_gene_variant,,ENST00000491528,;LPIN3,downstream_gene_variant,,ENST00000496565,;	G	ENSG00000183798	ENST00000332312	Transcript	missense_variant	1932	1739	580	L/P	cTt/cCt	.	.	.	-1	EMILIN3	HGNC	16123	protein_coding	YES	CCDS13316.1	ENSP00000332806	EMIL3_HUMAN	Q495S5_HUMAN	UPI00001D82E8	.	deleterious(0)	probably_damaging(0.982)	4/4	.	hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGAAGTGAG	.	2	ESCA
MYT1	0	.	GRCh37	20	62871250	62871250	+	Silent	SNP	G	G	A	rs149774713	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3231G>A	p.%3D	p.P1077P	ENST00000328439	22/23	55	49	5	65	65	0	MYT1,synonymous_variant,p.%3D,ENST00000536311,;MYT1,synonymous_variant,p.%3D,ENST00000328439,;	A	ENSG00000196132	ENST00000328439	Transcript	synonymous_variant	3595	3231	1077	P	ccG/ccA	rs149774713,COSM387265,COSM2933407,COSM2933408	.	.	1	MYT1	HGNC	7622	protein_coding	YES	CCDS13558.1	ENSP00000327465	MYT1_HUMAN	.	UPI000012FBFA	.	.	.	22/23	.	hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF10	.	.	.	.	.	.	.	A:0.0002	A:0	.	0,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCCGCACAT	byCluster	4	ESCA
CRYZL1	0	.	GRCh37	21	34974620	34974641	+	Frame_Shift_Del	DEL	TGTGCTAACTGAATAGCTATTG	TGTGCTAACTGAATAGCTATTG	-	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	TGTGCTAACTGAATAGCTATTG	TGTGCTAACTGAATAGCTATTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.476_497delCAATAGCTATTCAGTTAGCACA	p.Thr159IlefsTer7	p.T159Ifs*7	ENST00000381554	8/13	56	32	24	56	56	0	CRYZL1,frameshift_variant,p.Thr159IlefsTer7,ENST00000431177,;CRYZL1,frameshift_variant,p.Thr121IlefsTer7,ENST00000445393,;CRYZL1,frameshift_variant,p.Thr183IlefsTer7,ENST00000361534,;CRYZL1,frameshift_variant,p.Thr103IlefsTer7,ENST00000440526,;CRYZL1,frameshift_variant,p.Thr159IlefsTer7,ENST00000381554,;CRYZL1,frameshift_variant,p.Thr159IlefsTer7,ENST00000381540,;CRYZL1,frameshift_variant,p.Thr144IlefsTer7,ENST00000290244,;CRYZL1,frameshift_variant,p.Thr107IlefsTer7,ENST00000426935,;CRYZL1,frameshift_variant,p.Thr19IlefsTer7,ENST00000414079,;CRYZL1,coding_sequence_variant,,ENST00000417979,;AP000304.12,intron_variant,,ENST00000429238,;CRYZL1,upstream_gene_variant,,ENST00000441940,;CRYZL1,upstream_gene_variant,,ENST00000480893,;CRYZL1,upstream_gene_variant,,ENST00000479964,;CRYZL1,frameshift_variant,p.Thr159IlefsTer7,ENST00000420072,;CRYZL1,frameshift_variant,p.Thr144IlefsTer7,ENST00000429827,;CRYZL1,frameshift_variant,p.Thr57IlefsTer7,ENST00000452420,;CRYZL1,non_coding_transcript_exon_variant,,ENST00000488167,;CRYZL1,upstream_gene_variant,,ENST00000437996,;CRYZL1,downstream_gene_variant,,ENST00000490714,;	-	ENSG00000205758	ENST00000381554	Transcript	frameshift_variant	562-583	476-497	159-166	TIAIQLAH/X	aCAATAGCTATTCAGTTAGCACAt/at	.	.	.	-1	CRYZL1	HGNC	2420	protein_coding	YES	CCDS13633.2	ENSP00000370966	QORL1_HUMAN	C9K0F7_HUMAN,C9JQD0_HUMAN,C9JAL0_HUMAN	UPI0000038C61	.	.	.	8/13	.	hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF10,Gene3D:3.40.50.720,Pfam_domain:PF00107,SMART_domains:SM00829,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTATGATGTGCTAACTGAATAGCTATTGTACCA	.	3	ESCA
RANBP1	0	.	GRCh37	22	20109826	20109826	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.192C>G	p.%3D	p.L64L	ENST00000331821	3/6	33	22	10	26	26	0	RANBP1,synonymous_variant,p.%3D,ENST00000432879,;RANBP1,synonymous_variant,p.%3D,ENST00000411892,;RANBP1,synonymous_variant,p.%3D,ENST00000331821,;RANBP1,synonymous_variant,p.%3D,ENST00000402752,;RANBP1,synonymous_variant,p.%3D,ENST00000423859,;RANBP1,synonymous_variant,p.%3D,ENST00000421656,;RANBP1,synonymous_variant,p.%3D,ENST00000418705,;RANBP1,synonymous_variant,p.%3D,ENST00000416427,;RANBP1,5_prime_UTR_variant,,ENST00000430524,;TRMT2A,upstream_gene_variant,,ENST00000403707,;RANBP1,upstream_gene_variant,,ENST00000448394,;SNORA77,upstream_gene_variant,,ENST00000578179,;RANBP1,downstream_gene_variant,,ENST00000467920,;RANBP1,3_prime_UTR_variant,,ENST00000435265,;RANBP1,non_coding_transcript_exon_variant,,ENST00000488484,;RANBP1,upstream_gene_variant,,ENST00000486575,;	G	ENSG00000099901	ENST00000331821	Transcript	synonymous_variant	294	192	64	L	ctC/ctG	.	.	.	1	RANBP1	HGNC	9847	protein_coding	YES	CCDS13775.1	ENSP00000327583	RANG_HUMAN	D3DX26_HUMAN,C9JIC6_HUMAN	UPI00001132A0	.	.	.	3/6	.	PROSITE_profiles:PS50196,hmmpanther:PTHR23138,Gene3D:2.30.29.30,Pfam_domain:PF00638,SMART_domains:SM00160,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GATCTCCCAGA	.	4	ESCA
H1F0	0	.	GRCh37	22	38201158	38201158	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-394G>A	.	.	ENST00000340857	1/1	18	12	6	9	9	0	H1F0,5_prime_UTR_variant,,ENST00000340857,;GCAT,upstream_gene_variant,,ENST00000451984,;GCAT,upstream_gene_variant,,ENST00000445195,;GCAT,upstream_gene_variant,,ENST00000248924,;GCAT,upstream_gene_variant,,ENST00000323205,;GCAT,upstream_gene_variant,,ENST00000415371,;GCAT,upstream_gene_variant,,ENST00000426858,;GCAT,upstream_gene_variant,,ENST00000478203,;	A	ENSG00000189060	ENST00000340857	Transcript	5_prime_UTR_variant	45	.	.	.	.	.	.	.	1	H1F0	HGNC	4714	protein_coding	YES	CCDS13956.1	ENSP00000344504	H10_HUMAN	.	UPI0000161F7B	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCCGGGAGCAG	.	4	ESCA
TMEM185B	0	.	GRCh37	2	120980160	120980160	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393C>G	p.%3D	p.V131V	ENST00000426077	1/1	33	24	9	32	32	0	TMEM185B,synonymous_variant,p.%3D,ENST00000426077,;	C	ENSG00000226479	ENST00000426077	Transcript	synonymous_variant	825	393	131	V	gtC/gtG	.	.	.	-1	TMEM185B	HGNC	18896	protein_coding	YES	CCDS58722.1	ENSP00000453399	T185B_HUMAN	.	UPI0000074167	.	.	.	1/1	.	Pfam_domain:PF10269,hmmpanther:PTHR13568,hmmpanther:PTHR13568:SF5,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCAGACGCA	.	5	ESCA
ARL6IP6	0	.	GRCh37	2	153577006	153577006	+	Intron	SNP	T	T	C	rs574413561	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.401-41T>C	.	.	ENST00000326446	.	65	49	16	46	46	0	ARL6IP6,intron_variant,,ENST00000326446,;PRPF40A,upstream_gene_variant,,ENST00000410080,;PRPF40A,upstream_gene_variant,,ENST00000493468,;PRPF40A,upstream_gene_variant,,ENST00000545856,;PRPF40A,upstream_gene_variant,,ENST00000448428,;ARL6IP6,non_coding_transcript_exon_variant,,ENST00000463690,;ARL6IP6,intron_variant,,ENST00000495469,;PRPF40A,upstream_gene_variant,,ENST00000486100,;ARL6IP6,intron_variant,,ENST00000425034,;ARL6IP6,intron_variant,,ENST00000455875,;PRPF40A,upstream_gene_variant,,ENST00000450303,;PRPF40A,upstream_gene_variant,,ENST00000489741,;PRPF40A,upstream_gene_variant,,ENST00000354363,;	C	ENSG00000177917	ENST00000326446	Transcript	intron_variant	.	.	.	.	.	rs574413561	.	.	1	ARL6IP6	HGNC	24048	protein_coding	YES	CCDS2197.1	ENSP00000315357	AR6P6_HUMAN	.	UPI000006EA01	.	.	.	.	1/3	.	C:0.0002	C:0	C:0	.	C:0	C:0	C:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTATAGTAT	by1000G	5	ESCA
DCAF17	0	.	GRCh37	2	172305296	172305296	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427A>T	p.Lys143Ter	p.K143*	ENST00000375255	4/14	63	55	7	79	79	0	DCAF17,stop_gained,p.Lys143Ter,ENST00000375255,;DCAF17,stop_gained,p.Lys143Ter,ENST00000539783,;DCAF17,upstream_gene_variant,,ENST00000339506,;DCAF17,non_coding_transcript_exon_variant,,ENST00000495925,;DCAF17,non_coding_transcript_exon_variant,,ENST00000490217,;DCAF17,non_coding_transcript_exon_variant,,ENST00000468592,;DCAF17,3_prime_UTR_variant,,ENST00000436317,;DCAF17,non_coding_transcript_exon_variant,,ENST00000480855,;	T	ENSG00000115827	ENST00000375255	Transcript	stop_gained	754	427	143	K/*	Aaa/Taa	.	.	.	1	DCAF17	HGNC	25784	protein_coding	YES	CCDS2243.2	ENSP00000364404	DCA17_HUMAN	.	UPI00004C429A	.	.	.	4/14	.	hmmpanther:PTHR14815,hmmpanther:PTHR14815:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAGAAAATA	.	4	ESCA
TTN	0	.	GRCh37	2	179428350	179428350	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.82509C>A	p.%3D	p.G27503G	ENST00000589042	326/363	78	56	22	71	71	0	TTN,synonymous_variant,p.%3D,ENST00000359218,;TTN,synonymous_variant,p.%3D,ENST00000591111,;TTN,synonymous_variant,p.%3D,ENST00000589042,;TTN,synonymous_variant,p.%3D,ENST00000342175,;TTN,synonymous_variant,p.%3D,ENST00000342992,;TTN,synonymous_variant,p.%3D,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000438095,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;	T	ENSG00000155657	ENST00000589042	Transcript	synonymous_variant	82734	82509	27503	G	ggC/ggA	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	326/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E18435K|c.55303G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTAGCCCTC	.	5	ESCA
FSIP2	0	.	GRCh37	2	186620970	186620970	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1310C>G	p.Pro437Arg	p.P437R	ENST00000343098	9/23	55	46	9	47	47	0	FSIP2,missense_variant,p.Pro437Arg,ENST00000343098,;FSIP2,missense_variant,p.Pro348Arg,ENST00000424728,;FSIP2,intron_variant,,ENST00000546113,;FSIP2,intron_variant,,ENST00000429412,;	G	ENSG00000188738	ENST00000343098	Transcript	missense_variant	1310	1310	437	P/R	cCt/cGt	.	.	.	1	FSIP2	HGNC	21675	protein_coding	YES	CCDS54426.1	ENSP00000344403	.	J3QTJ6_HUMAN	UPI0001D420A1	.	.	benign(0.022)	9/23	.	hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATCCTGCTG	.	5	ESCA
PIKFYVE	0	.	GRCh37	2	209150489	209150489	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.653T>C	p.Leu218Ser	p.L218S	ENST00000264380	6/42	62	50	11	39	39	0	PIKFYVE,missense_variant,p.Leu218Ser,ENST00000452564,;PIKFYVE,missense_variant,p.Leu218Ser,ENST00000407449,;PIKFYVE,missense_variant,p.Leu230Ser,ENST00000422495,;PIKFYVE,missense_variant,p.Leu218Ser,ENST00000264380,;PIKFYVE,missense_variant,p.Leu132Ser,ENST00000308862,;PIKFYVE,missense_variant,p.Leu121Ser,ENST00000392202,;PIKFYVE,3_prime_UTR_variant,,ENST00000443896,;	C	ENSG00000115020	ENST00000264380	Transcript	missense_variant	811	653	218	L/S	tTa/tCa	.	.	.	1	PIKFYVE	HGNC	23785	protein_coding	YES	CCDS2382.1	ENSP00000264380	FYV1_HUMAN	.	UPI0000366FD6	.	deleterious(0)	probably_damaging(0.998)	6/42	.	Superfamily_domains:SSF57903,SMART_domains:SM00064,Gene3D:3.30.40.10,hmmpanther:PTHR11353:SF57,hmmpanther:PTHR11353,PROSITE_profiles:PS50178	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTTAAGTT	.	5	ESCA
AGAP1	0	.	GRCh37	2	237032618	237032618	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2426C>T	p.Ala809Val	p.A809V	ENST00000304032	18/18	134	96	37	127	127	0	AGAP1,missense_variant,p.Ala809Val,ENST00000304032,;AGAP1,missense_variant,p.Ala211Val,ENST00000453371,;AGAP1,missense_variant,p.Ala756Val,ENST00000336665,;AGAP1,missense_variant,p.Ala648Val,ENST00000428334,;AGAP1,missense_variant,p.Ala1021Val,ENST00000409538,;AGAP1,downstream_gene_variant,,ENST00000418654,;AGAP1,downstream_gene_variant,,ENST00000466575,;	T	ENSG00000157985	ENST00000304032	Transcript	missense_variant	3006	2426	809	A/V	gCc/gTc	.	.	.	1	AGAP1	HGNC	16922	protein_coding	YES	CCDS33408.1	ENSP00000307634	AGAP1_HUMAN	Q53S93_HUMAN,Q4ZG54_HUMAN,Q4ZG22_HUMAN,F5GXM9_HUMAN	UPI00005E1AE1	.	deleterious(0.01)	probably_damaging(0.963)	18/18	.	PROSITE_profiles:PS50297,hmmpanther:PTHR23180:SF226,hmmpanther:PTHR23180,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACGCCCGGC	.	5	ESCA
OR6B2	0	.	GRCh37	2	240968939	240968939	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.908A>G	p.Lys303Arg	p.K303R	ENST00000402971	1/1	57	53	3	58	58	0	OR6B2,missense_variant,p.Lys303Arg,ENST00000402971,;NDUFA10,upstream_gene_variant,,ENST00000307300,;NDUFA10,upstream_gene_variant,,ENST00000443626,;NDUFA10,upstream_gene_variant,,ENST00000407129,;NDUFA10,upstream_gene_variant,,ENST00000404554,;NDUFA10,upstream_gene_variant,,ENST00000252711,;NDUFA10,upstream_gene_variant,,ENST00000414580,;NDUFA10,upstream_gene_variant,,ENST00000497536,;NDUFA10,upstream_gene_variant,,ENST00000485344,;	C	ENSG00000182083	ENST00000402971	Transcript	missense_variant	968	908	303	K/R	aAg/aGg	.	.	.	-1	OR6B2	HGNC	15041	protein_coding	YES	CCDS46559.1	ENSP00000384563	OR6B2_HUMAN	I0EZ57_HUMAN	UPI0000061EBF	.	tolerated(0.34)	benign(0.007)	1/1	.	hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF106,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCCTTTTTC	.	2	ESCA
SNED1	0	.	GRCh37	2	241979571	241979571	+	Silent	SNP	C	C	T	.	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1125C>T	p.%3D	p.C375C	ENST00000310397	7/32	52	46	6	55	54	1	SNED1,synonymous_variant,p.%3D,ENST00000420591,;SNED1,synonymous_variant,p.%3D,ENST00000401644,;SNED1,synonymous_variant,p.%3D,ENST00000342631,;SNED1,synonymous_variant,p.%3D,ENST00000401884,;SNED1,synonymous_variant,p.%3D,ENST00000405547,;SNED1,synonymous_variant,p.%3D,ENST00000310397,;SNED1,synonymous_variant,p.%3D,ENST00000431690,;AC005237.4,intron_variant,,ENST00000458377,;SNED1,non_coding_transcript_exon_variant,,ENST00000493358,;	T	ENSG00000162804	ENST00000310397	Transcript	synonymous_variant	1125	1125	375	C	tgC/tgT	COSM1018795	.	.	1	SNED1	HGNC	24696	protein_coding	YES	CCDS46562.1	ENSP00000308893	SNED1_HUMAN	.	UPI0000DD7AB0	.	.	.	7/32	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF28,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2gy5A03,Pfam_domain:PF12661,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGTGCCAGGC	.	2	ESCA
AGBL5	0	.	GRCh37	2	27275949	27275949	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>A	p.%3D	p.A41A	ENST00000360131	2/15	44	30	14	51	51	0	AGBL5,synonymous_variant,p.%3D,ENST00000421915,;AGBL5,synonymous_variant,p.%3D,ENST00000360131,;AGBL5,synonymous_variant,p.%3D,ENST00000453161,;AGBL5,synonymous_variant,p.%3D,ENST00000451003,;AGBL5,synonymous_variant,p.%3D,ENST00000323064,;AGBL5,downstream_gene_variant,,ENST00000437006,;AGBL5-AS1,upstream_gene_variant,,ENST00000444217,;RP11-503P10.1,downstream_gene_variant,,ENST00000607407,;AGBL5,synonymous_variant,p.%3D,ENST00000487078,;AGBL5,non_coding_transcript_exon_variant,,ENST00000477136,;AGBL5,non_coding_transcript_exon_variant,,ENST00000489683,;	A	ENSG00000084693	ENST00000360131	Transcript	synonymous_variant	282	123	41	A	gcC/gcA	.	.	.	1	AGBL5	HGNC	26147	protein_coding	YES	CCDS1732.3	ENSP00000353249	CBPC5_HUMAN	C9JTY1_HUMAN,C9JQG9_HUMAN,C9JHM6_HUMAN,C9JCE1_HUMAN	UPI000006FE54	.	.	.	2/15	.	hmmpanther:PTHR12756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGCCCTGAC	.	5	ESCA
BIRC6	0	.	GRCh37	2	32661251	32661251	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3630A>T	p.Lys1210Asn	p.K1210N	ENST00000421745	15/74	96	85	10	73	73	0	BIRC6,missense_variant,p.Lys96Asn,ENST00000444173,;BIRC6,missense_variant,p.Lys1210Asn,ENST00000421745,;BIRC6,missense_variant,p.Lys37Asn,ENST00000431454,;	T	ENSG00000115760	ENST00000421745	Transcript	missense_variant	3764	3630	1210	K/N	aaA/aaT	.	.	.	1	BIRC6	HGNC	13516	protein_coding	YES	CCDS33175.2	ENSP00000393596	BIRC6_HUMAN	.	UPI0001611442	.	.	benign(0.068)	15/74	.	hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTAAAGGTGA	.	4	ESCA
LTBP1	0	.	GRCh37	2	33413734	33413734	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1517C>A	p.Pro506Gln	p.P506Q	ENST00000404816	7/34	48	29	18	42	42	0	LTBP1,missense_variant,p.Pro180Gln,ENST00000407925,;LTBP1,missense_variant,p.Pro99Gln,ENST00000432635,;LTBP1,missense_variant,p.Pro506Gln,ENST00000354476,;LTBP1,missense_variant,p.Pro180Gln,ENST00000418533,;LTBP1,missense_variant,p.Pro180Gln,ENST00000390003,;LTBP1,missense_variant,p.Pro506Gln,ENST00000404816,;LTBP1,missense_variant,p.Pro180Gln,ENST00000402934,;LTBP1,missense_variant,p.Pro180Gln,ENST00000404525,;	A	ENSG00000049323	ENST00000404816	Transcript	missense_variant	1870	1517	506	P/Q	cCa/cAa	.	.	.	1	LTBP1	HGNC	6714	protein_coding	YES	CCDS33177.2	ENSP00000386043	LTBP1_HUMAN	H7C2H7_HUMAN	UPI000173A4A4	.	tolerated(0.08)	benign(0.018)	7/34	.	hmmpanther:PTHR24034:SF39,hmmpanther:PTHR24034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCCAACAG	.	5	ESCA
CEBPZ	0	.	GRCh37	2	37428939	37428939	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3133A>G	p.Thr1045Ala	p.T1045A	ENST00000234170	16/16	68	47	21	44	44	0	CEBPZ,missense_variant,p.Thr1045Ala,ENST00000234170,;CEBPZ-AS1,intron_variant,,ENST00000397064,;CEBPZ-AS1,intron_variant,,ENST00000392061,;CEBPZ-AS1,intron_variant,,ENST00000402297,;CEBPZ-AS1,intron_variant,,ENST00000406711,;CEBPZ-AS1,intron_variant,,ENST00000397226,;CEBPZ,non_coding_transcript_exon_variant,,ENST00000489306,;CEBPZ-AS1,downstream_gene_variant,,ENST00000470216,;	C	ENSG00000115816	ENST00000234170	Transcript	missense_variant	3279	3133	1045	T/A	Acc/Gcc	.	.	.	-1	CEBPZ	HGNC	24218	protein_coding	YES	CCDS1787.1	ENSP00000234170	CEBPZ_HUMAN	.	UPI0000072AAB	.	tolerated(0.79)	unknown(0)	16/16	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.K1048delK|c.3140_3142delAAA|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGGTTTTAA	.	5	ESCA
SPRED2	0	.	GRCh37	2	65538410	65538410	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2225A>T	.	.	ENST00000356388	6/6	77	53	24	80	80	0	SPRED2,3_prime_UTR_variant,,ENST00000356388,;SPRED2,downstream_gene_variant,,ENST00000452315,;SPRED2,downstream_gene_variant,,ENST00000421087,;SPRED2,downstream_gene_variant,,ENST00000443619,;	A	ENSG00000198369	ENST00000356388	Transcript	3_prime_UTR_variant	3672	.	.	.	.	.	.	.	-1	SPRED2	HGNC	17722	protein_coding	YES	CCDS33211.1	ENSP00000348753	SPRE2_HUMAN	C9J623_HUMAN	UPI000013E7B4	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAAATGTCCC	.	5	ESCA
GCFC2	0	.	GRCh37	2	75921495	75921495	+	Missense_Mutation	SNP	G	G	C	rs533618591	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.892C>G	p.Gln298Glu	p.Q298E	ENST00000321027	6/17	89	79	10	66	66	0	GCFC2,missense_variant,p.Gln298Glu,ENST00000321027,;GCFC2,missense_variant,p.Gln260Glu,ENST00000409857,;GCFC2,3_prime_UTR_variant,,ENST00000541687,;MRPL19,downstream_gene_variant,,ENST00000453233,;GCFC2,downstream_gene_variant,,ENST00000442309,;MRPL19,downstream_gene_variant,,ENST00000358788,;RP11-342K6.3,upstream_gene_variant,,ENST00000604464,;GCFC2,3_prime_UTR_variant,,ENST00000472230,;GCFC2,non_coding_transcript_exon_variant,,ENST00000470197,;GCFC2,non_coding_transcript_exon_variant,,ENST00000486016,;	C	ENSG00000005436	ENST00000321027	Transcript	missense_variant	1026	892	298	Q/E	Caa/Gaa	rs533618591	.	.	-1	GCFC2	HGNC	1317	protein_coding	YES	CCDS1961.1	ENSP00000318690	GCFC2_HUMAN	B3KUM5_HUMAN,A4UHR0_HUMAN	UPI000013C96B	.	tolerated(0.61)	benign(0.01)	6/17	.	hmmpanther:PTHR12214:SF1,hmmpanther:PTHR12214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTTGTACGT	.	4	ESCA
GNLY	0	.	GRCh37	2	85921438	85921438	+	5'UTR	SNP	C	C	T	rs537250218	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-104C>T	.	.	ENST00000263863	1/5	31	22	9	30	30	0	GNLY,5_prime_UTR_variant,,ENST00000263863,;GNLY,upstream_gene_variant,,ENST00000409696,;GNLY,upstream_gene_variant,,ENST00000526018,;GNLY,upstream_gene_variant,,ENST00000524600,;GNLY,upstream_gene_variant,,ENST00000534351,;GNLY,upstream_gene_variant,,ENST00000533041,;GNLY,non_coding_transcript_exon_variant,,ENST00000489214,;GNLY,non_coding_transcript_exon_variant,,ENST00000482900,;GNLY,intron_variant,,ENST00000488945,;GNLY,upstream_gene_variant,,ENST00000531685,;GNLY,upstream_gene_variant,,ENST00000489980,;GNLY,upstream_gene_variant,,ENST00000491234,;GNLY,upstream_gene_variant,,ENST00000464298,;GNLY,upstream_gene_variant,,ENST00000470974,;	T	ENSG00000115523	ENST00000263863	Transcript	5_prime_UTR_variant	25	.	.	.	.	rs537250218	.	.	1	GNLY	HGNC	4414	protein_coding	YES	CCDS1984.1	ENSP00000263863	GNLY_HUMAN	.	UPI0000001C18	.	.	.	1/5	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACACGGGGG	by1000G	5	ESCA
CNNM4	0	.	GRCh37	2	97427122	97427122	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.386C>A	p.Ser129Tyr	p.S129Y	ENST00000377075	1/7	24	18	6	24	24	0	CNNM4,missense_variant,p.Ser129Tyr,ENST00000377075,;	A	ENSG00000158158	ENST00000377075	Transcript	missense_variant	484	386	129	S/Y	tCc/tAc	.	.	.	1	CNNM4	HGNC	105	protein_coding	YES	CCDS2024.2	ENSP00000366275	CNNM4_HUMAN	.	UPI0000207C95	.	deleterious(0)	possibly_damaging(0.73)	1/7	.	hmmpanther:PTHR12064:SF26,hmmpanther:PTHR12064	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CACGTCCGGCG	.	4	ESCA
ANKRD23	0	.	GRCh37	2	97508119	97508119	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.157G>A	p.Glu53Lys	p.E53K	ENST00000318357	2/9	94	58	36	85	85	0	ANKRD23,missense_variant,p.Glu53Lys,ENST00000331001,;ANKRD23,missense_variant,p.Glu53Lys,ENST00000318357,;ANKRD23,missense_variant,p.Glu53Lys,ENST00000418232,;ANKRD23,non_coding_transcript_exon_variant,,ENST00000462692,;ANKRD23,upstream_gene_variant,,ENST00000476975,;ANKRD39,3_prime_UTR_variant,,ENST00000443120,;ANKRD23,upstream_gene_variant,,ENST00000482175,;	T	ENSG00000163126	ENST00000318357	Transcript	missense_variant	199	157	53	E/K	Gaa/Aaa	.	.	.	-1	ANKRD23	HGNC	24470	protein_coding	YES	CCDS2027.1	ENSP00000321679	ANR23_HUMAN	.	UPI000000D7C6	.	tolerated(0.11)	possibly_damaging(0.459)	2/9	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24154	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCTTCCA	.	5	ESCA
BBX	0	.	GRCh37	3	107435527	107435527	+	Missense_Mutation	SNP	G	G	A	rs76764171	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.236G>A	p.Arg79Gln	p.R79Q	ENST00000325805	5/18	62	50	11	42	41	1	BBX,missense_variant,p.Arg79Gln,ENST00000416476,;BBX,missense_variant,p.Arg79Gln,ENST00000413213,;BBX,missense_variant,p.Arg79Gln,ENST00000402543,;BBX,missense_variant,p.Arg79Gln,ENST00000402163,;BBX,missense_variant,p.Arg79Gln,ENST00000457496,;BBX,missense_variant,p.Arg79Gln,ENST00000406780,;BBX,missense_variant,p.Arg79Gln,ENST00000456419,;BBX,missense_variant,p.Arg79Gln,ENST00000458458,;BBX,missense_variant,p.Arg109Gln,ENST00000431630,;BBX,missense_variant,p.Arg79Gln,ENST00000415149,;BBX,missense_variant,p.Arg79Gln,ENST00000449335,;BBX,missense_variant,p.Arg79Gln,ENST00000449271,;BBX,missense_variant,p.Arg79Gln,ENST00000429270,;BBX,missense_variant,p.Arg79Gln,ENST00000427402,;BBX,missense_variant,p.Arg79Gln,ENST00000449213,;BBX,missense_variant,p.Arg79Gln,ENST00000325805,;BBX,downstream_gene_variant,,ENST00000456817,;BBX,intron_variant,,ENST00000472032,;BBX,intron_variant,,ENST00000485939,;BBX,non_coding_transcript_exon_variant,,ENST00000497629,;	A	ENSG00000114439	ENST00000325805	Transcript	missense_variant	523	236	79	R/Q	cGa/cAa	rs76764171,COSM1327133,COSM1327132	.	.	1	BBX	HGNC	14422	protein_coding	YES	CCDS46881.1	ENSP00000319974	BBX_HUMAN	Q9H6A7_HUMAN,C9K0D1_HUMAN,C9JZA0_HUMAN,C9JYU6_HUMAN,C9JSH4_HUMAN,C9JNU3_HUMAN,C9JIZ2_HUMAN,C9JE62_HUMAN,C9JC04_HUMAN,C9J8D0_HUMAN,C9J0J4_HUMAN,C9J067_HUMAN,C9IYS9_HUMAN	UPI000007315E	.	deleterious(0)	probably_damaging(0.99)	5/18	.	SMART_domains:SM00398,hmmpanther:PTHR13059	A:0.0004	A:0	A:0	.	A:0	A:0.002	A:0	A:0	A:0.0003	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCAGCGAGCCC	byFrequency|byCluster|by1000G	4	ESCA
HGD	0	.	GRCh37	3	120365861	120365861	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.508G>A	p.Gly170Ser	p.G170S	ENST00000283871	8/14	69	52	17	34	34	0	HGD,missense_variant,p.Gly129Ser,ENST00000476082,;HGD,missense_variant,p.Gly14Ser,ENST00000475447,;HGD,missense_variant,p.Gly170Ser,ENST00000283871,;HGD,upstream_gene_variant,,ENST00000494453,;HGD,downstream_gene_variant,,ENST00000485313,;HGD,missense_variant,p.Gly47Ser,ENST00000492108,;	T	ENSG00000113924	ENST00000283871	Transcript	missense_variant	968	508	170	G/S	Ggc/Agc	.	.	.	-1	HGD	HGNC	4892	protein_coding	YES	CCDS3000.1	ENSP00000283871	HGD_HUMAN	B3KW64_HUMAN	UPI000020A025	.	deleterious(0.01)	probably_damaging(0.992)	8/14	.	hmmpanther:PTHR11056,TIGRFAM_domain:TIGR01015,Pfam_domain:PF04209,Superfamily_domains:SSF51182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCCAAACT	.	5	ESCA
CHCHD6	0	.	GRCh37	3	126423151	126423151	+	5'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-5T>C	.	.	ENST00000290913	1/8	42	38	4	37	37	0	CHCHD6,5_prime_UTR_variant,,ENST00000508789,;CHCHD6,5_prime_UTR_variant,,ENST00000290913,;CHCHD6,non_coding_transcript_exon_variant,,ENST00000514908,;CHCHD6,5_prime_UTR_variant,,ENST00000503119,;	C	ENSG00000159685	ENST00000290913	Transcript	5_prime_UTR_variant	89	.	.	.	.	.	.	.	1	CHCHD6	HGNC	28184	protein_coding	YES	CCDS3041.1	ENSP00000290913	CHCH6_HUMAN	.	UPI0000034DFB	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	GCATCTCGCCA	.	3	ESCA
MBD4	0	.	GRCh37	3	129151262	129151262	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1665+84G>A	.	.	ENST00000249910	.	42	28	13	31	31	0	MBD4,3_prime_UTR_variant,,ENST00000507208,;MBD4,intron_variant,,ENST00000393278,;MBD4,intron_variant,,ENST00000503197,;MBD4,intron_variant,,ENST00000249910,;MBD4,intron_variant,,ENST00000429544,;EFCAB12,upstream_gene_variant,,ENST00000503957,;EFCAB12,upstream_gene_variant,,ENST00000505956,;EFCAB12,upstream_gene_variant,,ENST00000326085,;MBD4,downstream_gene_variant,,ENST00000509587,;MBD4,downstream_gene_variant,,ENST00000505883,;MBD4,intron_variant,,ENST00000509828,;MBD4,downstream_gene_variant,,ENST00000515266,;MBD4,downstream_gene_variant,,ENST00000511009,;	T	ENSG00000129071	ENST00000249910	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MBD4	HGNC	6919	protein_coding	YES	CCDS3058.1	ENSP00000249910	MBD4_HUMAN	.	UPI0000073E6A	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATCCAATAA	.	5	ESCA
TRPC1	0	.	GRCh37	3	142511809	142511809	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1581G>A	p.%3D	p.Q527Q	ENST00000476941	9/13	70	40	30	38	38	0	TRPC1,synonymous_variant,p.%3D,ENST00000273482,;TRPC1,synonymous_variant,p.%3D,ENST00000476941,;	A	ENSG00000144935	ENST00000476941	Transcript	synonymous_variant	2067	1581	527	Q	caG/caA	.	.	.	1	TRPC1	HGNC	12333	protein_coding	YES	CCDS58856.1	ENSP00000419313	TRPC1_HUMAN	.	UPI00001374A4	.	.	.	9/13	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF3,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTACAGGTAAA	.	4	ESCA
WWTR1	0	.	GRCh37	3	149238505	149238505	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*87G>T	.	.	ENST00000465804	8/8	37	26	11	26	26	0	WWTR1,3_prime_UTR_variant,,ENST00000360632,;WWTR1,3_prime_UTR_variant,,ENST00000465804,;WWTR1,3_prime_UTR_variant,,ENST00000467467,;WWTR1,downstream_gene_variant,,ENST00000472417,;RNU6-1098P,upstream_gene_variant,,ENST00000516772,;WWTR1,3_prime_UTR_variant,,ENST00000471586,;WWTR1,downstream_gene_variant,,ENST00000494754,;	A	ENSG00000018408	ENST00000465804	Transcript	3_prime_UTR_variant	1547	.	.	.	.	.	.	.	-1	WWTR1	HGNC	24042	protein_coding	YES	CCDS3144.1	ENSP00000419465	WWTR1_HUMAN	C9JR84_HUMAN,C9JQS8_HUMAN,C9J588_HUMAN,C9J038_HUMAN	UPI000006D122	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCACCTGCA	.	2	ESCA
MASP1	0	.	GRCh37	3	186953887	186953887	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1772C>A	p.Ala591Asp	p.A591D	ENST00000296280	11/11	29	22	7	20	20	0	MASP1,missense_variant,p.Ala478Asp,ENST00000392472,;MASP1,missense_variant,p.Ala591Asp,ENST00000296280,;MASP1,intron_variant,,ENST00000337774,;MASP1,non_coding_transcript_exon_variant,,ENST00000495249,;MASP1,intron_variant,,ENST00000468121,;MASP1,non_coding_transcript_exon_variant,,ENST00000480349,;	T	ENSG00000127241	ENST00000296280	Transcript	missense_variant	1998	1772	591	A/D	gCc/gAc	.	.	.	-1	MASP1	HGNC	6901	protein_coding	YES	CCDS33908.1	ENSP00000296280	MASP1_HUMAN	Q9NSY8_HUMAN,C9JLU5_HUMAN	UPI000007256E	.	deleterious(0)	possibly_damaging(0.861)	11/11	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,PIRSF_domain:PIRSF001155,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCGGCCACC	.	5	ESCA
TOP2B	0	.	GRCh37	3	25672379	25672379	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1303G>A	p.Ala435Thr	p.A435T	ENST00000435706	11/36	48	22	25	40	40	0	TOP2B,missense_variant,p.Ala440Thr,ENST00000264331,;TOP2B,missense_variant,p.Ala435Thr,ENST00000435706,;TOP2B,missense_variant,p.Ala435Thr,ENST00000424225,;TOP2B,upstream_gene_variant,,ENST00000491510,;	T	ENSG00000077097	ENST00000435706	Transcript	missense_variant	1505	1303	435	A/T	Gct/Act	.	.	.	-1	TOP2B	HGNC	11990	protein_coding	YES	CCDS46776.1	ENSP00000396704	TOP2B_HUMAN	Q8WTY5_HUMAN,Q6LC06_HUMAN,E9PCY5_HUMAN,B4DLV2_HUMAN	UPI000002B59A	.	deleterious(0.02)	benign(0.047)	11/36	.	hmmpanther:PTHR10169,hmmpanther:PTHR10169:SF36,Pfam_domain:PF00204,SMART_domains:SM00433	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAGCCTTAA	.	5	ESCA
CRTAP	0	.	GRCh37	3	33188551	33188551	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4611C>T	.	.	ENST00000320954	7/7	58	35	22	82	82	0	CRTAP,3_prime_UTR_variant,,ENST00000320954,;CRTAP,downstream_gene_variant,,ENST00000449224,;SUSD5,downstream_gene_variant,,ENST00000309558,;RP11-627J17.1,intron_variant,,ENST00000607832,;	T	ENSG00000170275	ENST00000320954	Transcript	3_prime_UTR_variant	5916	.	.	.	.	.	.	.	1	CRTAP	HGNC	2379	protein_coding	YES	CCDS2657.1	ENSP00000323696	CRTAP_HUMAN	Q8NB01_HUMAN,B4DPA3_HUMAN	UPI000012700A	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCATCTGCCA	.	5	ESCA
RYBP	0	.	GRCh37	3	72426588	72426588	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*948A>G	.	.	ENST00000477973	4/4	20	13	7	20	20	0	RYBP,3_prime_UTR_variant,,ENST00000477973,;	C	ENSG00000163602	ENST00000477973	Transcript	3_prime_UTR_variant	1900	.	.	.	.	.	.	.	-1	RYBP	HGNC	10480	protein_coding	YES	.	ENSP00000419494	RYBP_HUMAN	.	UPI0001B794AD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAATGGATG	.	5	ESCA
SRGAP3	0	.	GRCh37	3	9100060	9100060	+	Missense_Mutation	SNP	C	C	A	rs777078285	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.898G>T	p.Asp300Tyr	p.D300Y	ENST00000383836	7/22	66	41	25	60	60	0	SRGAP3,missense_variant,p.Asp300Tyr,ENST00000360413,;SRGAP3,missense_variant,p.Asp300Tyr,ENST00000383836,;SRGAP3,non_coding_transcript_exon_variant,,ENST00000433332,;SRGAP3,downstream_gene_variant,,ENST00000480750,;SRGAP3,non_coding_transcript_exon_variant,,ENST00000485983,;SRGAP3,downstream_gene_variant,,ENST00000470951,;	A	ENSG00000196220	ENST00000383836	Transcript	missense_variant	1326	898	300	D/Y	Gat/Tat	rs777078285	.	.	-1	SRGAP3	HGNC	19744	protein_coding	YES	CCDS2572.1	ENSP00000373347	SRGP3_HUMAN	.	UPI0000074099	.	deleterious(0)	probably_damaging(0.999)	7/22	.	hmmpanther:PTHR14166:SF8,hmmpanther:PTHR14166,Superfamily_domains:SSF103657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACATCCAGCC	.	5	ESCA
PROS1	0	.	GRCh37	3	93593094	93593094	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2026T>A	p.Ser676Thr	p.S676T	ENST00000394236	15/15	122	101	20	76	76	0	PROS1,missense_variant,p.Ser676Thr,ENST00000394236,;PROS1,missense_variant,p.Ser545Thr,ENST00000407433,;	T	ENSG00000184500	ENST00000394236	Transcript	missense_variant	2343	2026	676	S/T	Tct/Act	.	.	.	-1	PROS1	HGNC	9456	protein_coding	YES	CCDS2923.1	ENSP00000377783	PROS_HUMAN	Q8IXD5_HUMAN,Q8IXD4_HUMAN,Q8IXD2_HUMAN,Q6J1N0_HUMAN,Q06F35_HUMAN,G5E9F8_HUMAN,C9K0R0_HUMAN,B4E1L6_HUMAN	UPI00001323E8	.	tolerated_low_confidence(0.13)	benign(0.012)	15/15	.	hmmpanther:PTHR24040,hmmpanther:PTHR24040:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTAAGAATTCT	.	4	ESCA
NPY2R	0	.	GRCh37	4	156136360	156136360	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*123T>C	.	.	ENST00000329476	2/2	30	24	6	22	22	0	NPY2R,3_prime_UTR_variant,,ENST00000506608,;NPY2R,3_prime_UTR_variant,,ENST00000329476,;	C	ENSG00000185149	ENST00000329476	Transcript	3_prime_UTR_variant	1758	.	.	.	.	.	.	.	1	NPY2R	HGNC	7957	protein_coding	YES	CCDS3791.1	ENSP00000332591	NPY2R_HUMAN	.	UPI000003B342	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCATCTGCT	.	5	ESCA
GRIA2	0	.	GRCh37	4	158254480	158254480	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1130A>C	p.Glu377Ala	p.E377A	ENST00000296526	8/16	71	44	26	94	94	0	GRIA2,missense_variant,p.Glu330Ala,ENST00000393815,;GRIA2,missense_variant,p.Glu377Ala,ENST00000296526,;GRIA2,missense_variant,p.Glu377Ala,ENST00000264426,;GRIA2,missense_variant,p.Glu330Ala,ENST00000507898,;GRIA2,missense_variant,p.Glu330Ala,ENST00000449365,;GRIA2,missense_variant,p.Glu330Ala,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,;	C	ENSG00000120251	ENST00000296526	Transcript	missense_variant	1455	1130	377	E/A	gAg/gCg	COSM115858	.	.	1	GRIA2	HGNC	4572	protein_coding	YES	CCDS3797.1	ENSP00000296526	GRIA2_HUMAN	D6RFM6_HUMAN,D6REK8_HUMAN,D6RDX5_HUMAN,D6RBV7_HUMAN,D6R9Z0_HUMAN,A8MT92_HUMAN	UPI000002AA8D	.	deleterious(0)	probably_damaging(1)	8/16	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF99,Gene3D:3.40.190.10,Pfam_domain:PF01094,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGAGCTCA	.	5	ESCA
CCDC110	0	.	GRCh37	4	186380437	186380437	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1304T>A	p.Leu435Gln	p.L435Q	ENST00000307588	6/7	33	30	3	28	28	0	CCDC110,missense_variant,p.Leu435Gln,ENST00000510617,;CCDC110,missense_variant,p.Leu435Gln,ENST00000307588,;CCDC110,missense_variant,p.Leu398Gln,ENST00000393540,;CCDC110,downstream_gene_variant,,ENST00000506876,;CCDC110,downstream_gene_variant,,ENST00000506962,;CCDC110,downstream_gene_variant,,ENST00000507501,;CCDC110,downstream_gene_variant,,ENST00000510481,;CCDC110,upstream_gene_variant,,ENST00000508538,;CCDC110,downstream_gene_variant,,ENST00000504020,;	T	ENSG00000168491	ENST00000307588	Transcript	missense_variant	1380	1304	435	L/Q	cTa/cAa	.	.	.	-1	CCDC110	HGNC	28504	protein_coding	YES	CCDS3843.1	ENSP00000306776	CC110_HUMAN	.	UPI0000070BFC	.	deleterious(0)	probably_damaging(1)	6/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTTAGGTAA	.	2	ESCA
ZNF876P	0	.	GRCh37	4	206477	206477	+	RNA	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.79T>C	.	.	ENST00000356347	1/2	61	40	21	89	89	0	ZNF876P,non_coding_transcript_exon_variant,,ENST00000356347,;	C	ENSG00000198155	ENST00000356347	Transcript	non_coding_transcript_exon_variant	79	.	.	.	.	.	.	.	1	ZNF876P	HGNC	32472	processed_transcript	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGATTCGGC	.	5	ESCA
DTHD1	0	.	GRCh37	4	36345331	36345331	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2231delT	p.Leu744ArgfsTer35	p.L744Rfs*35	ENST00000456874	9/9	21	15	6	25	25	0	DTHD1,frameshift_variant,p.Leu744ArgfsTer35,ENST00000456874,;DTHD1,frameshift_variant,p.Leu784ArgfsTer35,ENST00000507598,;DTHD1,frameshift_variant,p.Leu579ArgfsTer35,ENST00000357504,;RP11-431M7.2,intron_variant,,ENST00000504344,;DTHD1,non_coding_transcript_exon_variant,,ENST00000503528,;	-	ENSG00000197057	ENST00000456874	Transcript	frameshift_variant	2289	2231	744	L/X	cTg/cg	.	.	.	1	DTHD1	HGNC	37261	protein_coding	YES	CCDS54754.1	ENSP00000401597	DTHD1_HUMAN	.	UPI00006C079E	.	.	.	9/9	.	PROSITE_profiles:PS50017,hmmpanther:PTHR24199:SF7,hmmpanther:PTHR24199,Pfam_domain:PF00531,Gene3D:1.10.533.10,Superfamily_domains:SSF47986	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCCTCCTGGCTC	.	3	ESCA
FRAS1	0	.	GRCh37	4	79460559	79460559	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11410G>A	p.Asp3804Asn	p.D3804N	ENST00000264895	73/74	22	11	11	32	32	0	FRAS1,missense_variant,p.Asp2033Asn,ENST00000512123,;FRAS1,missense_variant,p.Asp3804Asn,ENST00000264895,;	A	ENSG00000138759	ENST00000264895	Transcript	missense_variant	11850	11410	3804	D/N	Gat/Aat	.	.	.	1	FRAS1	HGNC	19185	protein_coding	YES	CCDS54771.1	ENSP00000264895	FRAS1_HUMAN	Q69YV4_HUMAN,Q4W596_HUMAN	UPI000021D4C2	.	.	probably_damaging(1)	73/74	.	hmmpanther:PTHR11878:SF29,hmmpanther:PTHR11878	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTGGATGGA	.	5	ESCA
CTNND2	0	.	GRCh37	5	10973545	10973545	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*20C>T	.	.	ENST00000304623	22/22	101	87	14	52	52	0	CTNND2,3_prime_UTR_variant,,ENST00000304623,;CTNND2,3_prime_UTR_variant,,ENST00000359640,;CTNND2,3_prime_UTR_variant,,ENST00000503622,;CTNND2,3_prime_UTR_variant,,ENST00000511377,;CTNND2,3_prime_UTR_variant,,ENST00000458100,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,downstream_gene_variant,,ENST00000506324,;CTNND2,3_prime_UTR_variant,,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,;	A	ENSG00000169862	ENST00000304623	Transcript	3_prime_UTR_variant	3888	.	.	.	.	.	.	.	-1	CTNND2	HGNC	2516	protein_coding	YES	CCDS3881.1	ENSP00000307134	CTND2_HUMAN	E7EPC8_HUMAN,D6RF55_HUMAN,D6RBA8_HUMAN,D6R9A8_HUMAN	UPI000013E9AB	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCCGGAGCGC	.	4	ESCA
DNAH5	0	.	GRCh37	5	13870950	13870950	+	Missense_Mutation	SNP	G	G	C	rs749162833	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3760C>G	p.Arg1254Gly	p.R1254G	ENST00000265104	24/79	137	108	29	70	70	0	DNAH5,missense_variant,p.Arg1254Gly,ENST00000265104,;CTB-51A17.1,intron_variant,,ENST00000503244,;	C	ENSG00000039139	ENST00000265104	Transcript	missense_variant	3865	3760	1254	R/G	Cgg/Ggg	rs749162833	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.111)	24/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCCGAATAT	byFrequency	5	ESCA
PCDHGB1	0	.	GRCh37	5	140729955	140729955	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128C>T	p.Ser43Leu	p.S43L	ENST00000523390	1/4	46	31	14	74	74	0	PCDHGB1,missense_variant,p.Ser43Leu,ENST00000523390,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA4,upstream_gene_variant,,ENST00000571252,;	T	ENSG00000254221	ENST00000523390	Transcript	missense_variant	128	128	43	S/L	tCa/tTa	.	.	.	1	PCDHGB1	HGNC	8708	protein_coding	YES	CCDS54923.1	ENSP00000429273	PCDGD_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI0000073588	.	deleterious(0.01)	benign(0.133)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF106,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF08266,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCTCACGGG	.	5	ESCA
TIGD6	0	.	GRCh37	5	149375184	149375187	+	Frame_Shift_Del	DEL	GAAT	GAAT	-	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	GAAT	GAAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.725_728delATTC	p.His242ProfsTer14	p.H242Pfs*14	ENST00000296736	2/2	62	45	17	46	46	0	TIGD6,frameshift_variant,p.His242ProfsTer14,ENST00000296736,;TIGD6,frameshift_variant,p.His242ProfsTer14,ENST00000515406,;SLC26A2,downstream_gene_variant,,ENST00000503336,;HMGXB3,upstream_gene_variant,,ENST00000503427,;TIGD6,downstream_gene_variant,,ENST00000532987,;	-	ENSG00000164296	ENST00000296736	Transcript	frameshift_variant	1500-1503	725-728	242-243	HS/X	cATTCc/cc	.	.	.	-1	TIGD6	HGNC	18332	protein_coding	YES	CCDS4301.1	ENSP00000296736	TIGD6_HUMAN	.	UPI000006D946	.	.	.	2/2	.	Pfam_domain:PF03184,hmmpanther:PTHR19303:SF179,hmmpanther:PTHR19303	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGGAGGGAATGAATG	.	3	ESCA
NDST1	0	.	GRCh37	5	149900924	149900924	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108C>T	p.%3D	p.Y36Y	ENST00000261797	2/15	53	37	16	50	50	0	NDST1,synonymous_variant,p.%3D,ENST00000261797,;NDST1,synonymous_variant,p.%3D,ENST00000519157,;NDST1,synonymous_variant,p.%3D,ENST00000522491,;NDST1,synonymous_variant,p.%3D,ENST00000523767,;NDST1,downstream_gene_variant,,ENST00000518299,;NDST1,downstream_gene_variant,,ENST00000518346,;NDST1,downstream_gene_variant,,ENST00000524161,;	T	ENSG00000070614	ENST00000261797	Transcript	synonymous_variant	610	108	36	Y	taC/taT	.	.	.	1	NDST1	HGNC	7680	protein_coding	YES	CCDS34277.1	ENSP00000261797	NDST1_HUMAN	E5RGN9_HUMAN,E5RG58_HUMAN,E5RG24_HUMAN	UPI000012CDA5	.	.	.	2/15	.	Transmembrane_helices:TMhelix,Pfam_domain:PF12062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTACTACCT	.	5	ESCA
ATP10B	0	.	GRCh37	5	160049468	160049468	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1745A>T	p.Asp582Val	p.D582V	ENST00000327245	14/26	36	18	17	45	45	0	ATP10B,missense_variant,p.Asp582Val,ENST00000327245,;ATP10B,missense_variant,p.Asp190Val,ENST00000520108,;CTC-348L5.1,intron_variant,,ENST00000523598,;	A	ENSG00000118322	ENST00000327245	Transcript	missense_variant	2592	1745	582	D/V	gAt/gTt	.	.	.	-1	ATP10B	HGNC	13543	protein_coding	YES	CCDS43394.1	ENSP00000313600	AT10B_HUMAN	.	UPI0000191DAE	.	deleterious(0)	probably_damaging(1)	14/26	.	Pfam_domain:PF12710,TIGRFAM_domain:TIGR01652,Gene3D:3.40.1110.10,hmmpanther:PTHR24092:SF42,hmmpanther:PTHR24092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAATCAGCA	.	5	ESCA
NPM1	0	.	GRCh37	5	170817096	170817096	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.100G>C	p.Asp34His	p.D34H	ENST00000296930	2/11	48	39	9	76	76	0	NPM1,missense_variant,p.Asp34His,ENST00000351986,;NPM1,missense_variant,p.Asp26His,ENST00000523622,;NPM1,missense_variant,p.Asp34His,ENST00000517671,;NPM1,missense_variant,p.Asp34His,ENST00000393820,;NPM1,missense_variant,p.Asp34His,ENST00000296930,;NPM1,intron_variant,,ENST00000521672,;MIR3912,upstream_gene_variant,,ENST00000577566,;NPM1,non_coding_transcript_exon_variant,,ENST00000518587,;NPM1,non_coding_transcript_exon_variant,,ENST00000523339,;NPM1,upstream_gene_variant,,ENST00000521710,;NPM1,upstream_gene_variant,,ENST00000521260,;	C	ENSG00000181163	ENST00000296930	Transcript	missense_variant	401	100	34	D/H	Gat/Cat	.	.	.	1	NPM1	HGNC	7910	protein_coding	YES	CCDS4376.1	ENSP00000296930	NPM_HUMAN	Q9BTI9_HUMAN,E5RI98_HUMAN	UPI00001303ED	.	deleterious(0.01)	probably_damaging(0.929)	2/11	.	hmmpanther:PTHR22747,hmmpanther:PTHR22747:SF16,Pfam_domain:PF03066,Gene3D:2.60.120.340,Superfamily_domains:SSF69203	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGGTGGATAAT	.	4	ESCA
CTD-2139B15.2	0	.	GRCh37	5	17354553	17354553	+	RNA	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.412G>A	.	.	ENST00000511821	2/2	72	49	22	57	57	0	CTD-2139B15.2,non_coding_transcript_exon_variant,,ENST00000511821,;FTH1P10,non_coding_transcript_exon_variant,,ENST00000401830,;FTH1P10,upstream_gene_variant,,ENST00000430907,;	A	ENSG00000248223	ENST00000511821	Transcript	non_coding_transcript_exon_variant	412	.	.	.	.	.	.	.	1	CTD-2139B15.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGCGGCTGC	.	5	ESCA
HK3	0	.	GRCh37	5	176308099	176308099	+	Missense_Mutation	SNP	C	C	T	rs750375133	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2747G>A	p.Arg916His	p.R916H	ENST00000292432	19/19	48	20	27	46	46	0	HK3,missense_variant,p.Arg916His,ENST00000292432,;UNC5A,downstream_gene_variant,,ENST00000329542,;UNC5A,downstream_gene_variant,,ENST00000261961,;HK3,downstream_gene_variant,,ENST00000514058,;HK3,non_coding_transcript_exon_variant,,ENST00000506834,;HK3,downstream_gene_variant,,ENST00000514666,;	T	ENSG00000160883	ENST00000292432	Transcript	missense_variant	2839	2747	916	R/H	cGc/cAc	rs750375133	.	.	-1	HK3	HGNC	4925	protein_coding	YES	CCDS4407.1	ENSP00000292432	HXK3_HUMAN	.	UPI000006E237	.	deleterious(0)	probably_damaging(1)	19/19	.	hmmpanther:PTHR19443:SF1,hmmpanther:PTHR19443,Pfam_domain:PF03727,Gene3D:3.40.367.20,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGGCGGCAG	.	5	ESCA
DROSHA	0	.	GRCh37	5	31424578	31424578	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3217G>C	p.Asp1073His	p.D1073H	ENST00000511367	27/35	93	85	8	44	44	0	DROSHA,missense_variant,p.Asp1036His,ENST00000442743,;DROSHA,missense_variant,p.Asp1073His,ENST00000511367,;DROSHA,missense_variant,p.Asp1036His,ENST00000513349,;DROSHA,missense_variant,p.Asp1073His,ENST00000344624,;DROSHA,splice_region_variant,,ENST00000510178,;DROSHA,splice_region_variant,,ENST00000504133,;DROSHA,upstream_gene_variant,,ENST00000511778,;	G	ENSG00000113360	ENST00000511367	Transcript	missense_variant	3462	3217	1073	D/H	Gac/Cac	.	.	.	-1	DROSHA	HGNC	17904	protein_coding	YES	CCDS47195.1	ENSP00000425979	RNC_HUMAN	E5RHD1_HUMAN	UPI0000134351	.	deleterious(0.01)	possibly_damaging(0.497)	27/35	.	Superfamily_domains:SSF69065,SMART_domains:SM00535,hmmpanther:PTHR11207	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGGTCCTGGA	.	3	ESCA
LIFR	0	.	GRCh37	5	38490352	38490352	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2107G>T	p.Gly703Ter	p.G703*	ENST00000263409	15/20	152	137	15	81	81	0	LIFR,stop_gained,p.Gly703Ter,ENST00000263409,;LIFR,stop_gained,p.Gly703Ter,ENST00000453190,;LIFR,downstream_gene_variant,,ENST00000503088,;LIFR,3_prime_UTR_variant,,ENST00000506003,;LIFR,upstream_gene_variant,,ENST00000508477,;	A	ENSG00000113594	ENST00000263409	Transcript	stop_gained	2270	2107	703	G/*	Gga/Tga	.	.	.	-1	LIFR	HGNC	6597	protein_coding	YES	CCDS3927.1	ENSP00000263409	LIFR_HUMAN	D6RJ94_HUMAN,D6RF33_HUMAN	UPI000004CAC2	.	.	.	15/20	.	Superfamily_domains:SSF49265,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCATCCATACA	.	4	ESCA
CMYA5	0	.	GRCh37	5	79030465	79030465	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5877A>G	p.%3D	p.Q1959Q	ENST00000446378	2/13	27	17	10	21	21	0	CMYA5,synonymous_variant,p.%3D,ENST00000446378,;CMYA5,upstream_gene_variant,,ENST00000506603,;	G	ENSG00000164309	ENST00000446378	Transcript	synonymous_variant	5908	5877	1959	Q	caA/caG	.	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	.	2/13	.	hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAAGAAGC	.	5	ESCA
PLN	0	.	GRCh37	6	118881345	118881345	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1102C>T	.	.	ENST00000357525	2/2	51	40	11	33	33	0	PLN,3_prime_UTR_variant,,ENST00000357525,;CEP85L,intron_variant,,ENST00000360290,;CEP85L,intron_variant,,ENST00000419517,;CEP85L,intron_variant,,ENST00000368488,;CEP85L,intron_variant,,ENST00000434604,;CEP85L,intron_variant,,ENST00000392500,;CEP85L,intron_variant,,ENST00000368491,;CEP85L,downstream_gene_variant,,ENST00000483035,;	T	ENSG00000198523	ENST00000357525	Transcript	3_prime_UTR_variant	1453	.	.	.	.	.	.	.	1	PLN	HGNC	9080	protein_coding	YES	CCDS5120.1	ENSP00000350132	PPLA_HUMAN	Q5R352_HUMAN	UPI0000113623	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CTGACCCTTGA	.	3	ESCA
KIAA0319	0	.	GRCh37	6	24588968	24588968	+	Missense_Mutation	SNP	T	T	C	rs749197241	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.847A>G	p.Ser283Gly	p.S283G	ENST00000378214	4/21	72	44	27	39	39	0	KIAA0319,missense_variant,p.Ser283Gly,ENST00000543707,;KIAA0319,missense_variant,p.Ser238Gly,ENST00000430948,;KIAA0319,missense_variant,p.Ser283Gly,ENST00000378214,;KIAA0319,missense_variant,p.Ser274Gly,ENST00000535378,;KIAA0319,missense_variant,p.Ser283Gly,ENST00000537886,;	C	ENSG00000137261	ENST00000378214	Transcript	missense_variant	1372	847	283	S/G	Agc/Ggc	rs749197241	.	.	-1	KIAA0319	HGNC	21580	protein_coding	YES	CCDS34348.1	ENSP00000367459	K0319_HUMAN	.	UPI000020D61A	.	tolerated(0.09)	benign(0.024)	4/21	.	hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGCTGAGCT	.	5	ESCA
TFAP2B	0	.	GRCh37	6	50815237	50815237	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4132A>C	.	.	ENST00000393655	7/7	47	32	15	48	48	0	TFAP2B,3_prime_UTR_variant,,ENST00000393655,;TFAP2B,3_prime_UTR_variant,,ENST00000263046,;	C	ENSG00000008196	ENST00000393655	Transcript	3_prime_UTR_variant	5684	.	.	.	.	.	.	.	1	TFAP2B	HGNC	11743	protein_coding	YES	CCDS4934.2	ENSP00000377265	AP2B_HUMAN	A8K557_HUMAN	UPI000020DE90	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCTTTATAAAC	.	4	ESCA
CPED1	0	.	GRCh37	7	120782104	120782104	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1964A>G	p.Glu655Gly	p.E655G	ENST00000310396	16/23	86	79	7	67	67	0	CPED1,missense_variant,p.Glu435Gly,ENST00000423795,;CPED1,missense_variant,p.Glu655Gly,ENST00000450913,;CPED1,missense_variant,p.Glu655Gly,ENST00000310396,;	G	ENSG00000106034	ENST00000310396	Transcript	missense_variant	2431	1964	655	E/G	gAg/gGg	.	.	.	1	CPED1	HGNC	26159	protein_coding	YES	CCDS34739.1	ENSP00000309772	CPED1_HUMAN	Q75MM9_HUMAN,E9PCC8_HUMAN,E7ENG7_HUMAN	UPI000013C813	.	tolerated(0.13)	benign(0.355)	16/23	.	hmmpanther:PTHR14776,Pfam_domain:PF12733	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGGTGAGACTC	.	3	ESCA
UNCX	0	.	GRCh37	7	1273157	1273157	+	Missense_Mutation	SNP	C	C	A	rs767399902	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.276C>A	p.Asp92Glu	p.D92E	ENST00000316333	2/3	123	113	10	93	93	0	UNCX,missense_variant,p.Asp92Glu,ENST00000316333,;	A	ENSG00000164853	ENST00000316333	Transcript	missense_variant	387	276	92	D/E	gaC/gaA	rs767399902	.	.	1	UNCX	HGNC	33194	protein_coding	YES	CCDS34583.1	ENSP00000314480	UNC4_HUMAN	.	UPI0000D61BE6	.	deleterious(0.04)	benign(0.168)	2/3	.	Superfamily_domains:SSF46689,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCAGACTCGGG	.	3	ESCA
DGKB	0	.	GRCh37	7	14652969	14652969	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357G>A	p.Glu453Lys	p.E453K	ENST00000403951	16/26	122	106	16	77	77	0	DGKB,missense_variant,p.Glu453Lys,ENST00000258767,;DGKB,missense_variant,p.Glu434Lys,ENST00000444700,;DGKB,missense_variant,p.Glu453Lys,ENST00000403951,;DGKB,missense_variant,p.Glu452Lys,ENST00000402815,;DGKB,missense_variant,p.Glu445Lys,ENST00000407950,;DGKB,missense_variant,p.Glu453Lys,ENST00000406247,;DGKB,missense_variant,p.Glu453Lys,ENST00000399322,;DGKB,non_coding_transcript_exon_variant,,ENST00000403963,;DGKB,non_coding_transcript_exon_variant,,ENST00000471732,;	T	ENSG00000136267	ENST00000403951	Transcript	missense_variant	1777	1357	453	E/K	Gaa/Aaa	.	.	.	-1	DGKB	HGNC	2850	protein_coding	YES	CCDS47547.1	ENSP00000385780	DGKB_HUMAN	C9JA18_HUMAN,B7Z3B3_HUMAN	UPI0000033B9B	.	tolerated(0.11)	benign(0.292)	16/26	.	PROSITE_profiles:PS50146,hmmpanther:PTHR11255:SF32,hmmpanther:PTHR11255,Pfam_domain:PF00781,SMART_domains:SM00046,Superfamily_domains:SSF111331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGTTCTCCTT	.	4	ESCA
RSPH10B	0	.	GRCh37	7	6000459	6000459	+	Missense_Mutation	SNP	C	C	T	rs749914563	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436G>A	p.Val146Met	p.V146M	ENST00000405415	5/20	100	66	33	64	64	0	RSPH10B,missense_variant,p.Val146Met,ENST00000441023,;RSPH10B,missense_variant,p.Val146Met,ENST00000337579,;RSPH10B,missense_variant,p.Val146Met,ENST00000404406,;RSPH10B,missense_variant,p.Val146Met,ENST00000405415,;RSPH10B,upstream_gene_variant,,ENST00000539903,;RSPH10B,non_coding_transcript_exon_variant,,ENST00000541997,;RSPH10B,non_coding_transcript_exon_variant,,ENST00000539630,;RSPH10B,non_coding_transcript_exon_variant,,ENST00000535104,;	T	ENSG00000155026	ENST00000405415	Transcript	missense_variant	823	436	146	V/M	Gtg/Atg	rs749914563	.	.	-1	RSPH10B	HGNC	27362	protein_coding	YES	CCDS34598.1	ENSP00000385443	R10B1_HUMAN	C9JJN2_HUMAN	UPI000020EAA5	.	tolerated(0.32)	benign(0.103)	5/20	.	hmmpanther:PTHR23084,hmmpanther:PTHR23084:SF131,Pfam_domain:PF02493,Gene3D:1h3iA01,SMART_domains:SM00698,Superfamily_domains:0038399	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACACGCCGT	byFrequency	4	ESCA
AC010091.1	0	.	GRCh37	7	81218218	81218218	+	RNA	SNP	A	A	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.695T>G	.	.	ENST00000413944	6/10	52	43	8	36	36	0	AC010091.1,non_coding_transcript_exon_variant,,ENST00000413944,;AC010091.1,intron_variant,,ENST00000455420,;	C	ENSG00000233491	ENST00000413944	Transcript	non_coding_transcript_exon_variant	695	.	.	.	.	.	.	.	-1	AC010091.1	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACAACATCA	.	5	ESCA
ZFPM2	0	.	GRCh37	8	106816113	106816113	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*347A>T	.	.	ENST00000407775	8/8	121	98	23	95	95	0	ZFPM2,3_prime_UTR_variant,,ENST00000407775,;ZFPM2,downstream_gene_variant,,ENST00000517361,;ZFPM2,downstream_gene_variant,,ENST00000378472,;ZFPM2,downstream_gene_variant,,ENST00000520492,;RP11-152P17.2,intron_variant,,ENST00000524045,;RP11-152P17.2,intron_variant,,ENST00000509144,;RP11-152P17.2,intron_variant,,ENST00000521622,;RP11-152P17.2,intron_variant,,ENST00000520594,;RP11-152P17.2,intron_variant,,ENST00000520433,;RP11-152P17.2,intron_variant,,ENST00000518932,;ZFPM2,downstream_gene_variant,,ENST00000522296,;RP11-152P17.2,intron_variant,,ENST00000520078,;	T	ENSG00000169946	ENST00000407775	Transcript	3_prime_UTR_variant	4053	.	.	.	.	.	.	.	1	ZFPM2	HGNC	16700	protein_coding	YES	CCDS47908.1	ENSP00000384179	FOG2_HUMAN	Q9NPQ0_HUMAN,F5H542_HUMAN,E7ET52_HUMAN,E5RJX0_HUMAN	UPI000057A0B4	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAATACAG	.	5	ESCA
TRAPPC9	0	.	GRCh37	8	141461322	141461322	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.445C>T	p.Arg149Ter	p.R149*	ENST00000389328	2/23	47	26	21	22	22	0	TRAPPC9,stop_gained,p.Arg51Ter,ENST00000389327,;TRAPPC9,stop_gained,p.Arg149Ter,ENST00000389328,;TRAPPC9,stop_gained,p.Arg51Ter,ENST00000438773,;TRAPPC9,upstream_gene_variant,,ENST00000520857,;	A	ENSG00000167632	ENST00000389328	Transcript	stop_gained	460	445	149	R/*	Cga/Tga	.	.	.	-1	TRAPPC9	HGNC	30832	protein_coding	YES	CCDS34946.1	ENSP00000373979	TPPC9_HUMAN	.	UPI0000DBEF2B	.	.	.	2/23	.	Pfam_domain:PF08626,hmmpanther:PTHR21512,hmmpanther:PTHR21512:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTCGCTGGG	.	5	ESCA
ZC3H3	0	.	GRCh37	8	144519895	144519895	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*331G>T	.	.	ENST00000262577	12/12	88	66	22	80	80	0	ZC3H3,3_prime_UTR_variant,,ENST00000262577,;	A	ENSG00000014164	ENST00000262577	Transcript	3_prime_UTR_variant	3210	.	.	.	.	.	.	.	-1	ZC3H3	HGNC	28972	protein_coding	YES	CCDS6402.1	ENSP00000262577	ZC3H3_HUMAN	.	UPI0000160D96	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCACTGG	.	5	ESCA
XKR4	0	.	GRCh37	8	56436193	56436193	+	Missense_Mutation	SNP	C	C	T	rs372636201	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360C>T	p.Arg454Cys	p.R454C	ENST00000327381	3/3	71	51	20	56	56	0	XKR4,missense_variant,p.Arg454Cys,ENST00000327381,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,;	T	ENSG00000206579	ENST00000327381	Transcript	missense_variant	1460	1360	454	R/C	Cgc/Tgc	rs372636201,COSM1166414	.	.	1	XKR4	HGNC	29394	protein_coding	YES	CCDS34893.1	ENSP00000328326	XKR4_HUMAN	.	UPI000016098C	.	deleterious(0.01)	probably_damaging(0.991)	3/3	.	Pfam_domain:PF09815,hmmpanther:PTHR32129:SF14,hmmpanther:PTHR32129	.	.	.	.	.	.	.	G:0	G:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACACGCTGC	byFrequency|byCluster	5	ESCA
AGPAT5	0	.	GRCh37	8	6615051	6615051	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*142C>G	.	.	ENST00000285518	8/8	32	24	7	48	48	0	AGPAT5,3_prime_UTR_variant,,ENST00000518327,;AGPAT5,3_prime_UTR_variant,,ENST00000285518,;AGPAT5,downstream_gene_variant,,ENST00000533159,;AGPAT5,downstream_gene_variant,,ENST00000530716,;AGPAT5,3_prime_UTR_variant,,ENST00000523234,;	G	ENSG00000155189	ENST00000285518	Transcript	3_prime_UTR_variant	1549	.	.	.	.	.	.	.	1	AGPAT5	HGNC	20886	protein_coding	YES	CCDS34796.1	ENSP00000285518	PLCE_HUMAN	Q6NUM7_HUMAN	UPI000003B4CB	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGACGAAAG	.	5	ESCA
PMP2	0	.	GRCh37	8	82354544	82354544	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1089G>T	.	.	ENST00000256103	4/4	81	65	15	70	70	0	PMP2,3_prime_UTR_variant,,ENST00000256103,;PMP2,downstream_gene_variant,,ENST00000519260,;RP11-157I4.4,intron_variant,,ENST00000524085,;	A	ENSG00000147588	ENST00000256103	Transcript	3_prime_UTR_variant	1625	.	.	.	.	.	.	.	-1	PMP2	HGNC	9117	protein_coding	YES	CCDS6229.1	ENSP00000256103	MYP2_HUMAN	.	UPI000013CEEB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCACAATGC	.	5	ESCA
CCDC180	0	.	GRCh37	9	100085112	100085112	+	Intron	SNP	G	G	A	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1292-3G>A	.	.	ENST00000375202	.	50	29	21	38	38	0	CCDC180,splice_region_variant,,ENST00000357054,;CCDC180,splice_region_variant,,ENST00000375202,;CCDC180,splice_region_variant,,ENST00000529487,;CCDC180,splice_region_variant,,ENST00000395220,;CCDC180,splice_region_variant,,ENST00000411667,;RP11-23J9.4,splice_region_variant,,ENST00000532526,;RP11-23J9.4,splice_region_variant,,ENST00000375206,;CCDC180,splice_region_variant,,ENST00000460482,;RP11-23J9.4,splice_region_variant,,ENST00000534123,;RP11-23J9.4,splice_region_variant,,ENST00000529787,;CCDC180,splice_region_variant,,ENST00000494917,;	A	ENSG00000197816	ENST00000375202	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	CCDC180	HGNC	29303	protein_coding	YES	CCDS35077.2	ENSP00000364348	CC180_HUMAN	B7ZMG3_HUMAN	UPI00016277C6	.	.	.	.	25/50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGGAGACA	.	4	ESCA
C9orf24	0	.	GRCh37	9	34397641	34397641	+	5'UTR	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-10A>G	.	.	ENST00000297623	1/7	46	29	16	50	50	0	C9orf24,5_prime_UTR_variant,,ENST00000297623,;FAM219A,downstream_gene_variant,,ENST00000379087,;FAM219A,downstream_gene_variant,,ENST00000379078,;FAM219A,downstream_gene_variant,,ENST00000297620,;FAM219A,downstream_gene_variant,,ENST00000445726,;C9orf24,upstream_gene_variant,,ENST00000444429,;FAM219A,downstream_gene_variant,,ENST00000379080,;FAM219A,downstream_gene_variant,,ENST00000422409,;FAM219A,downstream_gene_variant,,ENST00000379081,;FAM219A,downstream_gene_variant,,ENST00000379089,;FAM219A,downstream_gene_variant,,ENST00000379084,;	C	ENSG00000164972	ENST00000297623	Transcript	5_prime_UTR_variant	190	.	.	.	.	.	.	.	-1	C9orf24	HGNC	19919	protein_coding	YES	CCDS6554.1	ENSP00000297623	SMRP1_HUMAN	.	UPI000006E5B3	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTCTTGGAG	.	5	ESCA
AGTR2	0	.	GRCh37	X	115304321	115304321	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.788T>C	p.Leu263Pro	p.L263P	ENST00000371906	3/3	29	21	8	22	22	0	AGTR2,missense_variant,p.Leu263Pro,ENST00000371906,;	C	ENSG00000180772	ENST00000371906	Transcript	missense_variant	978	788	263	L/P	cTg/cCg	.	.	.	1	AGTR2	HGNC	338	protein_coding	YES	CCDS14569.1	ENSP00000360973	AGTR2_HUMAN	Q6UVH2_HUMAN	UPI0000125687	.	deleterious(0.01)	probably_damaging(0.99)	3/3	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228:SF8,hmmpanther:PTHR24228,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTCTGGCCT	.	5	ESCA
FRMPD4	0	.	GRCh37	X	12734448	12734448	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870A>G	p.Ser624Gly	p.S624G	ENST00000380682	15/17	11	4	7	14	14	0	FRMPD4,missense_variant,p.Ser624Gly,ENST00000380682,;	G	ENSG00000169933	ENST00000380682	Transcript	missense_variant	2376	1870	624	S/G	Agt/Ggt	.	.	.	1	FRMPD4	HGNC	29007	protein_coding	YES	CCDS35201.1	ENSP00000370057	FRPD4_HUMAN	.	UPI00001C2066	.	tolerated_low_confidence(0.26)	benign(0)	15/17	.	hmmpanther:PTHR13436,hmmpanther:PTHR13436:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACAGAAGTCTA	.	2	ESCA
SLC10A3	0	.	GRCh37	X	153715758	153715758	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*88T>G	.	.	ENST00000263512	2/2	50	34	16	57	57	0	SLC10A3,3_prime_UTR_variant,,ENST00000393587,;SLC10A3,3_prime_UTR_variant,,ENST00000263512,;SLC10A3,3_prime_UTR_variant,,ENST00000369649,;SLC10A3,3_prime_UTR_variant,,ENST00000393586,;UBL4A,upstream_gene_variant,,ENST00000369660,;UBL4A,upstream_gene_variant,,ENST00000369653,;SLC10A3,downstream_gene_variant,,ENST00000453912,;UBL4A,upstream_gene_variant,,ENST00000477777,;UBL4A,upstream_gene_variant,,ENST00000481237,;UBL4A,upstream_gene_variant,,ENST00000421431,;UBL4A,upstream_gene_variant,,ENST00000417913,;	C	ENSG00000126903	ENST00000263512	Transcript	3_prime_UTR_variant	2021	.	.	.	.	.	.	.	-1	SLC10A3	HGNC	22979	protein_coding	YES	CCDS14755.1	ENSP00000263512	P3_HUMAN	Q5HY78_HUMAN	UPI0000131021	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAATAAGC	.	5	ESCA
PHKA2	0	.	GRCh37	X	18954191	18954191	+	Nonsense_Mutation	SNP	G	G	C	rs754223529	.	TCGA-VR-A8Q7-01A-11D-A37C-09	TCGA-VR-A8Q7-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1119C>G	p.Tyr373Ter	p.Y373*	ENST00000379942	11/33	12	6	6	18	18	0	PHKA2,stop_gained,p.Tyr373Ter,ENST00000379942,;	C	ENSG00000044446	ENST00000379942	Transcript	stop_gained	1785	1119	373	Y/*	taC/taG	rs754223529	.	.	-1	PHKA2	HGNC	8926	protein_coding	YES	CCDS14190.1	ENSP00000369274	KPB2_HUMAN	.	UPI000012DF4B	.	.	.	11/33	.	hmmpanther:PTHR10749,hmmpanther:PTHR10749:SF5,Pfam_domain:PF00723,Superfamily_domains:SSF48208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	ACAGCGTAGAG	byFrequency	4	ESCA
TTC40	0	.	GRCh37	10	134752203	134752203	+	Silent	SNP	C	C	T	rs148231376	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.426G>A	p.%3D	p.P142P	ENST00000368586	5/58	27	18	9	22	22	0	TTC40,synonymous_variant,p.%3D,ENST00000368582,;TTC40,synonymous_variant,p.%3D,ENST00000368585,;TTC40,synonymous_variant,p.%3D,ENST00000368586,;TTC40,non_coding_transcript_exon_variant,,ENST00000475340,;	T	ENSG00000171811	ENST00000368586	Transcript	synonymous_variant	527	426	142	P	ccG/ccA	rs148231376	.	.	-1	TTC40	HGNC	25247	protein_coding	YES	CCDS58101.1	ENSP00000357575	TTC40_HUMAN	.	UPI0001B79116	.	.	.	5/58	.	hmmpanther:PTHR15977:SF13,hmmpanther:PTHR15977	T:0.0004	T:0.0015	T:0	.	T:0	T:0	T:0	T:0.0007	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGGAACGGCCT	byFrequency|byCluster|by1000G	4	ESCA
KIAA1217	0	.	GRCh37	10	24835385	24835385	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*132A>G	.	.	ENST00000376454	21/21	15	8	7	16	16	0	KIAA1217,3_prime_UTR_variant,,ENST00000376454,;KIAA1217,3_prime_UTR_variant,,ENST00000396445,;KIAA1217,3_prime_UTR_variant,,ENST00000376451,;KIAA1217,3_prime_UTR_variant,,ENST00000376452,;KIAA1217,3_prime_UTR_variant,,ENST00000376462,;KIAA1217,3_prime_UTR_variant,,ENST00000458595,;KIAA1217,downstream_gene_variant,,ENST00000307544,;KIAA1217,downstream_gene_variant,,ENST00000396446,;KIAA1217,downstream_gene_variant,,ENST00000492009,;	G	ENSG00000120549	ENST00000376454	Transcript	3_prime_UTR_variant	5994	.	.	.	.	.	.	.	1	KIAA1217	HGNC	25428	protein_coding	YES	CCDS31165.1	ENSP00000365637	SKT_HUMAN	.	UPI000013EC2A	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAATACTGGA	.	5	ESCA
RBM17	0	.	GRCh37	10	6139040	6139040	+	Silent	SNP	C	C	T	rs369487973	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12C>T	p.%3D	p.Y4Y	ENST00000446108	2/12	47	28	19	61	60	0	RBM17,synonymous_variant,p.%3D,ENST00000379888,;RBM17,synonymous_variant,p.%3D,ENST00000418631,;RBM17,synonymous_variant,p.%3D,ENST00000446108,;RBM17,synonymous_variant,p.%3D,ENST00000432931,;RBM17,intron_variant,,ENST00000437845,;	T	ENSG00000134453	ENST00000446108	Transcript	synonymous_variant	656	12	4	Y	taC/taT	rs369487973,COSM1348479	.	.	1	RBM17	HGNC	16944	protein_coding	YES	CCDS7077.1	ENSP00000388638	SPF45_HUMAN	Q5W011_HUMAN,Q5W009_HUMAN	UPI000000D96A	.	.	.	2/12	.	PIRSF_domain:PIRSF031066,hmmpanther:PTHR13288,hmmpanther:PTHR13288:SF8	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTACGATGA	byFrequency|byCluster	5	ESCA
ZNF365	0	.	GRCh37	10	64219517	64219517	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.942C>T	p.%3D	p.G314G	ENST00000410046	4/8	23	19	4	44	44	0	ZNF365,synonymous_variant,p.%3D,ENST00000410046,;ZNF365,synonymous_variant,p.%3D,ENST00000395255,;	T	ENSG00000138311	ENST00000410046	Transcript	synonymous_variant	1222	942	314	G	ggC/ggT	.	.	.	1	ZNF365	HGNC	18194	protein_coding	YES	CCDS7264.1	ENSP00000387091	ZN365_HUMAN	C9J1G1_HUMAN	UPI00002323B9	.	.	.	4/8	.	hmmpanther:PTHR15739	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGGCGAAGC	.	4	ESCA
BTAF1	0	.	GRCh37	10	93719887	93719887	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1239A>G	p.Ile413Met	p.I413M	ENST00000265990	11/38	35	21	13	40	40	0	BTAF1,missense_variant,p.Ile413Met,ENST00000265990,;BTAF1,non_coding_transcript_exon_variant,,ENST00000471217,;	G	ENSG00000095564	ENST00000265990	Transcript	missense_variant	1547	1239	413	I/M	atA/atG	.	.	.	1	BTAF1	HGNC	17307	protein_coding	YES	CCDS7419.1	ENSP00000265990	BTAF1_HUMAN	Q8N6J1_HUMAN,Q2M1V9_HUMAN,B4E0W6_HUMAN	UPI0000136782	.	tolerated(0.06)	possibly_damaging(0.872)	11/38	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR10799:SF225,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAATAAAATA	.	5	ESCA
SDHD	0	.	GRCh37	11	111965683	111965683	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.469T>C	p.Trp157Arg	p.W157R	ENST00000375549	4/4	140	127	12	183	183	0	SDHD,missense_variant,p.Trp157Arg,ENST00000375549,;SDHD,missense_variant,p.Trp118Arg,ENST00000525291,;SDHD,3_prime_UTR_variant,,ENST00000528182,;SDHD,3_prime_UTR_variant,,ENST00000526592,;SDHD,3_prime_UTR_variant,,ENST00000528048,;SDHD,intron_variant,,ENST00000528021,;SDHD,3_prime_UTR_variant,,ENST00000530923,;SDHD,intron_variant,,ENST00000532699,;SDHD,intron_variant,,ENST00000525987,;SDHD,intron_variant,,ENST00000534010,;SDHD,intron_variant,,ENST00000531744,;	C	ENSG00000204370	ENST00000375549	Transcript	missense_variant	604	469	157	W/R	Tgg/Cgg	.	.	.	1	SDHD	HGNC	10683	protein_coding	YES	CCDS31678.1	ENSP00000364699	DHSD_HUMAN	G3V173_HUMAN	UPI0000129396	.	deleterious(0)	probably_damaging(0.994)	4/4	.	hmmpanther:PTHR13337:SF2,hmmpanther:PTHR13337,Pfam_domain:PF05328,Gene3D:1.20.1300.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGCTGTGGAAG	.	3	ESCA
OR5AP2	0	.	GRCh37	11	56409727	56409727	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189C>G	p.%3D	p.T63T	ENST00000302981	1/1	26	21	5	20	20	0	OR5AP2,synonymous_variant,p.%3D,ENST00000302981,;OR5AP2,synonymous_variant,p.%3D,ENST00000544374,;AP002517.1,downstream_gene_variant,,ENST00000584225,;	C	ENSG00000172464	ENST00000302981	Transcript	synonymous_variant	189	189	63	T	acC/acG	.	.	.	-1	OR5AP2	HGNC	15258	protein_coding	YES	CCDS31534.1	ENSP00000303111	O5AP2_HUMAN	.	UPI0000061EE6	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF151,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ATGGGGGTGTG	.	3	ESCA
DDB1	0	.	GRCh37	11	61091537	61091537	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835C>T	p.Arg279Trp	p.R279W	ENST00000301764	7/27	35	27	8	28	28	0	DDB1,missense_variant,p.Arg94Trp,ENST00000541513,;DDB1,missense_variant,p.Arg62Trp,ENST00000535174,;DDB1,missense_variant,p.Arg279Trp,ENST00000301764,;DDB1,intron_variant,,ENST00000450997,;DDB1,intron_variant,,ENST00000543658,;DDB1,downstream_gene_variant,,ENST00000539426,;DDB1,upstream_gene_variant,,ENST00000539739,;DDB1,upstream_gene_variant,,ENST00000537877,;DDB1,upstream_gene_variant,,ENST00000535967,;DDB1,non_coding_transcript_exon_variant,,ENST00000545930,;DDB1,downstream_gene_variant,,ENST00000543162,;DDB1,missense_variant,p.Arg279Trp,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000537120,;DDB1,non_coding_transcript_exon_variant,,ENST00000540784,;DDB1,non_coding_transcript_exon_variant,,ENST00000539712,;	A	ENSG00000167986	ENST00000301764	Transcript	missense_variant	1233	835	279	R/W	Cgg/Tgg	.	.	.	-1	DDB1	HGNC	2717	protein_coding	YES	CCDS31576.1	ENSP00000301764	DDB1_HUMAN	F8WF81_HUMAN,F5H775_HUMAN,F5H6C5_HUMAN,F5H581_HUMAN,F5H2L3_HUMAN,F5H0Y5_HUMAN,F5GZY8_HUMAN,F5GZ34_HUMAN,F5GYG8_HUMAN	UPI0000000CB7	.	tolerated(0.06)	probably_damaging(0.995)	7/27	.	hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF3,Pfam_domain:PF10433	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCCGGCCTT	.	5	ESCA
GCN1L1	0	.	GRCh37	12	120584968	120584968	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4835C>T	p.Ser1612Phe	p.S1612F	ENST00000300648	38/58	47	34	13	45	44	1	GCN1L1,missense_variant,p.Ser1612Phe,ENST00000300648,;	A	ENSG00000089154	ENST00000300648	Transcript	missense_variant	4848	4835	1612	S/F	tCc/tTc	COSM3457001	.	.	-1	GCN1L1	HGNC	4199	protein_coding	YES	CCDS41847.1	ENSP00000300648	GCN1L_HUMAN	B4DM32_HUMAN	UPI00001FBC69	.	.	probably_damaging(0.998)	38/58	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCAGGGATGGG	.	4	ESCA
DENR	0	.	GRCh37	12	123254440	123254440	+	3'UTR	SNP	A	A	T	rs765528370	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*815A>T	.	.	ENST00000280557	8/8	14	9	5	14	14	0	DENR,3_prime_UTR_variant,,ENST00000280557,;DENR,3_prime_UTR_variant,,ENST00000455982,;CCDC62,upstream_gene_variant,,ENST00000392441,;CCDC62,upstream_gene_variant,,ENST00000539171,;CCDC62,upstream_gene_variant,,ENST00000253079,;Y_RNA,downstream_gene_variant,,ENST00000384187,;CCDC62,upstream_gene_variant,,ENST00000341952,;	T	ENSG00000139726	ENST00000280557	Transcript	3_prime_UTR_variant	1598	.	.	.	.	rs765528370	.	.	1	DENR	HGNC	2769	protein_coding	YES	CCDS45003.1	ENSP00000280557	DENR_HUMAN	.	UPI000012918D	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACTGATCTAA	.	5	ESCA
ALG10	0	.	GRCh37	12	34175557	34175558	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26dupT	p.Ser10LeufsTer41	p.S10Lfs*41	ENST00000266483	1/3	105	84	21	98	98	0	ALG10,frameshift_variant,p.Ser10LeufsTer41,ENST00000266483,;ALG10,frameshift_variant,p.Ser10LeufsTer41,ENST00000538927,;AC046130.1,downstream_gene_variant,,ENST00000401300,;RP11-847H18.2,non_coding_transcript_exon_variant,,ENST00000501954,;ALG10,frameshift_variant,p.Ser10LeufsTer44,ENST00000541875,;ALG10,non_coding_transcript_exon_variant,,ENST00000541178,;	T	ENSG00000139133	ENST00000266483	Transcript	frameshift_variant	342-343	23-24	8	Y/YX	tat/taTt	.	.	.	1	ALG10	HGNC	23162	protein_coding	YES	CCDS41769.1	ENSP00000266483	AG10A_HUMAN	.	UPI000004E870	.	.	.	1/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12989,hmmpanther:PTHR12989:SF11,PIRSF_domain:PIRSF028810	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTACTATTTCT	.	3	ESCA
ITGA5	0	.	GRCh37	12	54795803	54795803	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2208C>T	p.%3D	p.P736P	ENST00000293379	21/30	45	36	9	35	35	0	ITGA5,synonymous_variant,p.%3D,ENST00000293379,;ITGA5,upstream_gene_variant,,ENST00000547197,;RP11-753H16.5,intron_variant,,ENST00000552785,;RP11-753H16.3,intron_variant,,ENST00000550474,;ITGA5,non_coding_transcript_exon_variant,,ENST00000552564,;ITGA5,non_coding_transcript_exon_variant,,ENST00000552583,;ITGA5,downstream_gene_variant,,ENST00000550141,;ITGA5,upstream_gene_variant,,ENST00000552431,;ITGA5,upstream_gene_variant,,ENST00000552387,;ITGA5,downstream_gene_variant,,ENST00000551861,;ITGA5,downstream_gene_variant,,ENST00000551564,;ITGA5,downstream_gene_variant,,ENST00000435631,;ITGA5,upstream_gene_variant,,ENST00000549601,;ITGA5,downstream_gene_variant,,ENST00000553071,;	A	ENSG00000161638	ENST00000293379	Transcript	synonymous_variant	2470	2208	736	P	ccC/ccT	.	.	.	-1	ITGA5	HGNC	6141	protein_coding	YES	CCDS8880.1	ENSP00000293379	ITA5_HUMAN	.	UPI000012D9F3	.	.	.	21/30	.	hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF3,Gene3D:2.60.40.1510,Pfam_domain:PF08441,Superfamily_domains:SSF69179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATGGGGTT	.	5	ESCA
OSBPL8	0	.	GRCh37	12	76746994	76746994	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2675A>T	.	.	ENST00000261183	24/24	49	33	16	55	55	0	OSBPL8,3_prime_UTR_variant,,ENST00000261183,;OSBPL8,3_prime_UTR_variant,,ENST00000393249,;BBS10,upstream_gene_variant,,ENST00000393262,;OSBPL8,downstream_gene_variant,,ENST00000393250,;	A	ENSG00000091039	ENST00000261183	Transcript	3_prime_UTR_variant	5825	.	.	.	.	.	.	.	-1	OSBPL8	HGNC	16396	protein_coding	YES	CCDS31862.1	ENSP00000261183	OSBL8_HUMAN	Q96E43_HUMAN,Q6ZME5_HUMAN,F8VZB8_HUMAN,F8VVE7_HUMAN,F8VVD3_HUMAN,F8VQX7_HUMAN	UPI000006ECD1	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGTGATATAAA	.	4	ESCA
DACH1	0	.	GRCh37	13	72013129	72013129	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1658C>A	.	.	ENST00000305425	11/11	58	27	30	66	66	0	DACH1,3_prime_UTR_variant,,ENST00000305425,;DACH1,3_prime_UTR_variant,,ENST00000313174,;DACH1,3_prime_UTR_variant,,ENST00000354591,;DACH1,downstream_gene_variant,,ENST00000359684,;	T	ENSG00000165659	ENST00000305425	Transcript	3_prime_UTR_variant	4208	.	.	.	.	.	.	.	-1	DACH1	HGNC	2663	protein_coding	YES	CCDS41899.1	ENSP00000304994	DACH1_HUMAN	.	UPI00001FCE9E	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTATGTTCCA	.	5	ESCA
DMXL2	0	.	GRCh37	15	51773127	51773127	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6176C>A	p.Ala2059Asp	p.A2059D	ENST00000543779	24/43	36	23	12	41	41	0	DMXL2,missense_variant,p.Ala1423Asp,ENST00000449909,;DMXL2,missense_variant,p.Ala2059Asp,ENST00000543779,;DMXL2,missense_variant,p.Ala184Asp,ENST00000560891,;DMXL2,missense_variant,p.Ala2059Asp,ENST00000251076,;RP11-707P17.1,intron_variant,,ENST00000561007,;	T	ENSG00000104093	ENST00000543779	Transcript	missense_variant	6266	6176	2059	A/D	gCt/gAt	.	.	.	-1	DMXL2	HGNC	2938	protein_coding	YES	CCDS53946.1	ENSP00000441858	DMXL2_HUMAN	.	UPI00001FE4C2	.	deleterious(0)	probably_damaging(1)	24/43	.	hmmpanther:PTHR13950:SF11,hmmpanther:PTHR13950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTAGCCAAT	.	5	ESCA
CCNB2	0	.	GRCh37	15	59397386	59397386	+	5'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-82G>C	.	.	ENST00000288207	1/9	38	33	5	38	38	0	CCNB2,5_prime_UTR_variant,,ENST00000559622,;CCNB2,5_prime_UTR_variant,,ENST00000288207,;CCNB2,non_coding_transcript_exon_variant,,ENST00000561077,;	C	ENSG00000157456	ENST00000288207	Transcript	5_prime_UTR_variant	110	.	.	.	.	.	.	.	1	CCNB2	HGNC	1580	protein_coding	YES	CCDS10170.1	ENSP00000288207	CCNB2_HUMAN	.	UPI00001275B3	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TAACGGCGCCT	.	3	ESCA
TMC5	0	.	GRCh37	16	19451843	19451843	+	Silent	SNP	G	G	A	rs771364798	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483G>A	p.%3D	p.P161P	ENST00000396229	3/22	21	15	6	30	30	0	TMC5,synonymous_variant,p.%3D,ENST00000381414,;TMC5,synonymous_variant,p.%3D,ENST00000542583,;TMC5,synonymous_variant,p.%3D,ENST00000541464,;TMC5,synonymous_variant,p.%3D,ENST00000396229,;	A	ENSG00000103534	ENST00000396229	Transcript	synonymous_variant	1232	483	161	P	ccG/ccA	rs771364798,COSM4058848	.	.	1	TMC5	HGNC	22999	protein_coding	YES	CCDS45431.1	ENSP00000379531	TMC5_HUMAN	.	UPI00001FEF87	.	.	.	3/22	.	hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF5	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACCGGACTA	byFrequency	5	ESCA
IL4R	0	.	GRCh37	16	27373610	27373610	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937T>G	p.Phe313Val	p.F313V	ENST00000395762	11/11	66	43	23	54	54	0	IL4R,missense_variant,p.Phe313Val,ENST00000395762,;IL4R,missense_variant,p.Phe298Val,ENST00000380922,;IL4R,missense_variant,p.Phe313Val,ENST00000543915,;IL4R,missense_variant,p.Phe313Val,ENST00000170630,;IL4R,missense_variant,p.Phe166Val,ENST00000565179,;IL4R,intron_variant,,ENST00000565352,;IL4R,non_coding_transcript_exon_variant,,ENST00000565915,;IL4R,3_prime_UTR_variant,,ENST00000568746,;IL4R,non_coding_transcript_exon_variant,,ENST00000563886,;	G	ENSG00000077238	ENST00000395762	Transcript	missense_variant	1196	937	313	F/V	Ttt/Gtt	.	.	.	1	IL4R	HGNC	6015	protein_coding	YES	CCDS10629.1	ENSP00000379111	IL4RA_HUMAN	J9JII2_HUMAN,H3BTD9_HUMAN,A1Z2K8_HUMAN	UPI0000044371	.	deleterious(0.01)	benign(0.114)	11/11	.	hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGTTTTCTG	.	5	ESCA
SHCBP1	0	.	GRCh37	16	46650016	46650016	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438A>G	p.%3D	p.E146E	ENST00000303383	4/13	44	36	8	37	37	0	SHCBP1,synonymous_variant,p.%3D,ENST00000303383,;SHCBP1,upstream_gene_variant,,ENST00000569702,;SHCBP1,downstream_gene_variant,,ENST00000564272,;SHCBP1,non_coding_transcript_exon_variant,,ENST00000566016,;SHCBP1,upstream_gene_variant,,ENST00000565887,;	C	ENSG00000171241	ENST00000303383	Transcript	synonymous_variant	705	438	146	E	gaA/gaG	.	.	.	-1	SHCBP1	HGNC	29547	protein_coding	YES	CCDS10720.1	ENSP00000306473	SHCBP_HUMAN	.	UPI000013E898	.	.	.	4/13	.	hmmpanther:PTHR14695,hmmpanther:PTHR14695:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGTTCAGC	.	5	ESCA
HP	0	.	GRCh37	16	72094632	72094632	+	Missense_Mutation	SNP	C	C	T	rs367968695	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1064C>T	p.Ala355Val	p.A355V	ENST00000355906	7/7	77	59	18	75	75	0	HP,missense_variant,p.Ala353Val,ENST00000567185,;HP,missense_variant,p.Ala296Val,ENST00000398131,;HP,missense_variant,p.Ala355Val,ENST00000355906,;HP,missense_variant,p.Ala391Val,ENST00000357763,;HP,missense_variant,p.Ala296Val,ENST00000570083,;HP,missense_variant,p.Ala296Val,ENST00000565574,;HP,missense_variant,p.Ala314Val,ENST00000567612,;HP,3_prime_UTR_variant,,ENST00000562526,;HPR,intron_variant,,ENST00000356967,;TXNL4B,intron_variant,,ENST00000562153,;HP,downstream_gene_variant,,ENST00000569639,;HP,downstream_gene_variant,,ENST00000564499,;HPR,upstream_gene_variant,,ENST00000540303,;HP,downstream_gene_variant,,ENST00000568417,;HPR,upstream_gene_variant,,ENST00000561690,;HP,downstream_gene_variant,,ENST00000576168,;HP,non_coding_transcript_exon_variant,,ENST00000566821,;HP,downstream_gene_variant,,ENST00000561927,;HP,downstream_gene_variant,,ENST00000565807,;HP,downstream_gene_variant,,ENST00000562488,;HPR,upstream_gene_variant,,ENST00000566168,;	T	ENSG00000257017	ENST00000355906	Transcript	missense_variant	1122	1064	355	A/V	gCg/gTg	rs367968695	.	.	1	HP	HGNC	5141	protein_coding	YES	CCDS45524.1	ENSP00000348170	HPT_HUMAN	Q6PEJ8_HUMAN	UPI000012CB71	.	deleterious(0)	probably_damaging(0.997)	7/7	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24265,hmmpanther:PTHR24265:SF25,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGATGCGGGCA	byFrequency|byCluster	5	ESCA
JMJD8	0	.	GRCh37	16	733202	733202	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.607G>A	p.Gly203Arg	p.G203R	ENST00000412368	7/9	52	42	10	55	55	0	JMJD8,missense_variant,p.Gly182Arg,ENST00000562111,;JMJD8,missense_variant,p.Gly152Arg,ENST00000562824,;JMJD8,missense_variant,p.Gly182Arg,ENST00000609261,;JMJD8,missense_variant,p.Gly222Arg,ENST00000454700,;JMJD8,missense_variant,p.Gly252Arg,ENST00000293882,;JMJD8,missense_variant,p.Gly203Arg,ENST00000412368,;STUB1,downstream_gene_variant,,ENST00000565677,;STUB1,downstream_gene_variant,,ENST00000567173,;RHBDL1,downstream_gene_variant,,ENST00000352681,;WDR24,downstream_gene_variant,,ENST00000293883,;RHBDL1,downstream_gene_variant,,ENST00000219551,;STUB1,downstream_gene_variant,,ENST00000219548,;STUB1,downstream_gene_variant,,ENST00000564316,;WDR24,downstream_gene_variant,,ENST00000248142,;STUB1,downstream_gene_variant,,ENST00000564370,;STUB1,downstream_gene_variant,,ENST00000566408,;LA16c-313D11.9,upstream_gene_variant,,ENST00000571933,;LA16c-313D11.9,upstream_gene_variant,,ENST00000567091,;STUB1,downstream_gene_variant,,ENST00000566181,;JMJD8,missense_variant,p.Met75Ile,ENST00000565258,;JMJD8,non_coding_transcript_exon_variant,,ENST00000565302,;JMJD8,non_coding_transcript_exon_variant,,ENST00000568689,;JMJD8,non_coding_transcript_exon_variant,,ENST00000569396,;JMJD8,non_coding_transcript_exon_variant,,ENST00000563088,;JMJD8,non_coding_transcript_exon_variant,,ENST00000567120,;JMJD8,non_coding_transcript_exon_variant,,ENST00000570037,;JMJD8,non_coding_transcript_exon_variant,,ENST00000569441,;JMJD8,non_coding_transcript_exon_variant,,ENST00000564436,;STUB1,downstream_gene_variant,,ENST00000569248,;STUB1,downstream_gene_variant,,ENST00000565813,;RHBDL1,downstream_gene_variant,,ENST00000450775,;JMJD8,downstream_gene_variant,,ENST00000566199,;STUB1,downstream_gene_variant,,ENST00000563505,;JMJD8,upstream_gene_variant,,ENST00000568313,;WDR24,downstream_gene_variant,,ENST00000567014,;STUB1,downstream_gene_variant,,ENST00000567790,;JMJD8,downstream_gene_variant,,ENST00000567901,;	T	ENSG00000161999	ENST00000412368	Transcript	missense_variant	664	607	203	G/R	Gga/Aga	.	.	.	-1	JMJD8	HGNC	14148	protein_coding	YES	CCDS45369.1	ENSP00000399475	JMJD8_HUMAN	.	UPI0000471011	.	deleterious(0)	probably_damaging(0.999)	7/9	.	PROSITE_profiles:PS51184,hmmpanther:PTHR12480,hmmpanther:PTHR12480:SF12,Pfam_domain:PF13621,Gene3D:1vrbA01,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTCCATGCC	.	5	ESCA
SLC5A10	0	.	GRCh37	17	18862953	18862953	+	Missense_Mutation	SNP	G	G	T	rs746981215	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.325G>T	p.Val109Leu	p.V109L	ENST00000395647	4/15	21	17	4	37	37	0	SLC5A10,missense_variant,p.Val109Leu,ENST00000395645,;SLC5A10,missense_variant,p.Val109Leu,ENST00000417251,;SLC5A10,missense_variant,p.Val53Leu,ENST00000317977,;SLC5A10,missense_variant,p.Val109Leu,ENST00000395647,;SLC5A10,missense_variant,p.Val109Leu,ENST00000395643,;SLC5A10,missense_variant,p.Val53Leu,ENST00000395642,;	T	ENSG00000154025	ENST00000395647	Transcript	missense_variant	366	325	109	V/L	Gtg/Ttg	rs746981215	.	.	1	SLC5A10	HGNC	23155	protein_coding	YES	CCDS11201.2	ENSP00000379008	SC5AA_HUMAN	.	UPI00001401D2	.	tolerated(0.28)	benign(0.082)	4/15	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50283,hmmpanther:PTHR11819:SF57,hmmpanther:PTHR11819,Pfam_domain:PF00474,TIGRFAM_domain:TIGR00813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	TGTTCGTGCCC	byFrequency	2	ESCA
SUPT6H	0	.	GRCh37	17	27020751	27020751	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3671A>T	p.Gln1224Leu	p.Q1224L	ENST00000314616	28/37	45	38	6	51	51	0	SUPT6H,missense_variant,p.Gln1224Leu,ENST00000314616,;SUPT6H,missense_variant,p.Gln1224Leu,ENST00000347486,;SUPT6H,upstream_gene_variant,,ENST00000581510,;SUPT6H,upstream_gene_variant,,ENST00000580471,;SUPT6H,downstream_gene_variant,,ENST00000581908,;SUPT6H,downstream_gene_variant,,ENST00000583972,;	T	ENSG00000109111	ENST00000314616	Transcript	missense_variant	3954	3671	1224	Q/L	cAg/cTg	.	.	.	1	SUPT6H	HGNC	11470	protein_coding	YES	CCDS32596.1	ENSP00000319104	SPT6H_HUMAN	J3QS64_HUMAN	UPI000015FFA7	.	deleterious(0)	possibly_damaging(0.644)	28/37	.	PIRSF_domain:PIRSF036947,SMART_domains:SM00316,hmmpanther:PTHR10145:SF6,hmmpanther:PTHR10145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCAGGCCA	.	4	ESCA
IKZF3	0	.	GRCh37	17	37922218	37922218	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355A>G	p.Tyr452Cys	p.Y452C	ENST00000346872	8/8	49	30	19	34	34	0	IKZF3,missense_variant,p.Tyr413Cys,ENST00000351680,;IKZF3,missense_variant,p.Tyr379Cys,ENST00000439167,;IKZF3,missense_variant,p.Tyr418Cys,ENST00000535189,;IKZF3,missense_variant,p.Tyr309Cys,ENST00000377944,;IKZF3,missense_variant,p.Tyr365Cys,ENST00000377958,;IKZF3,missense_variant,p.Tyr452Cys,ENST00000346872,;IKZF3,missense_variant,p.Tyr396Cys,ENST00000467757,;IKZF3,missense_variant,p.Tyr205Cys,ENST00000583368,;IKZF3,missense_variant,p.Tyr318Cys,ENST00000377945,;IKZF3,missense_variant,p.Tyr374Cys,ENST00000346243,;IKZF3,missense_variant,p.Tyr231Cys,ENST00000377952,;IKZF3,missense_variant,p.Tyr357Cys,ENST00000439016,;IKZF3,missense_variant,p.Tyr270Cys,ENST00000394189,;IKZF3,missense_variant,p.Tyr413Cys,ENST00000350532,;RP11-94L15.2,upstream_gene_variant,,ENST00000488188,;IKZF3,3_prime_UTR_variant,,ENST00000348427,;IKZF3,3_prime_UTR_variant,,ENST00000293068,;	C	ENSG00000161405	ENST00000346872	Transcript	missense_variant	1417	1355	452	Y/C	tAt/tGt	.	.	.	-1	IKZF3	HGNC	13178	protein_coding	YES	CCDS11346.1	ENSP00000344544	IKZF3_HUMAN	B4DVV5_HUMAN	UPI000006E6CC	.	deleterious(0)	possibly_damaging(0.823)	8/8	.	hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF29,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCGATACACA	.	5	ESCA
TP53	0	.	GRCh37	17	7578469	7578469	+	Frame_Shift_Del	DEL	C	C	-	rs762846821	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.461delG	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	5/11	26	18	8	31	31	0	TP53,frameshift_variant,p.Gly154AlafsTer?,ENST00000508793,;TP53,frameshift_variant,p.Gly154AlafsTer16,ENST00000413465,;TP53,frameshift_variant,p.Gly154AlafsTer16,ENST00000420246,;TP53,frameshift_variant,p.Gly154AlafsTer16,ENST00000269305,;TP53,frameshift_variant,p.Gly22AlafsTer16,ENST00000509690,;TP53,frameshift_variant,p.Gly154AlafsTer16,ENST00000359597,;TP53,frameshift_variant,p.Gly61AlafsTer16,ENST00000514944,;TP53,frameshift_variant,p.Gly154AlafsTer16,ENST00000445888,;TP53,frameshift_variant,p.Gly154AlafsTer16,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	651	461	154	G/X	gGc/gc	rs762846821,CM951223,TP53_g.12449G>C,TP53_g.12449G>T,TP53_g.12449G>A,COSM6815,COSM45622,COSM46378,COSM342243,COSM342244,COSM342246,COSM1649372,COSM342245	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,1,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.P152fs*14|c.454_466del13|5,CODON|p.T62P|c.184A>C|3,CODON|p.T155P|c.463A>C|16,CODON|p.T155P|c.463A>C|3,CODON|p.T23P|c.67A>C|4,CODON|p.T155P|c.463A>C|3,CODON|p.T155A|c.463A>G|8,CODON|p.G154I|c.460_461GG>AT|3,CODON|p.G154G|c.462C>T|9,BUFFER|p.R158fs*11|c.472_475delCGCG|3,BUFFER|p.R158L|c.473G>T|14,BUFFER|p.R158H|c.473G>A|24,BUFFER|p.R158H|c.473G>A|24,BUFFER|p.R158H|c.473G>A|78,BUFFER|p.R158H|c.473G>A|7,BUFFER|p.R158L|c.473G>T|63,BUFFER|p.R158H|c.473G>A|11,BUFFER|p.R158P|c.473G>C|10,BUFFER|p.R158L|c.473G>T|5,BUFFER|p.R158L|c.473G>T|14,BUFFER|p.R65H|c.194G>A|24,BUFFER|p.R26L|c.77G>T|19,BUFFER|p.R26H|c.77G>A|25,BUFFER|p.R65L|c.194G>T|14,BUFFER|p.R158C|c.471_472CC>TT|6,BUFFER|p.R158fs*12|c.472delC|6,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R158C|c.472C>T|17,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R26C|c.76C>T|7,BUFFER|p.R65C|c.193C>T|7,BUFFER|p.R158G|c.472C>G|12,BUFFER|p.R158C|c.472C>T|7,BUFFER|p.R65G|c.193C>G|3,BUFFER|p.R158G|c.472C>G|3,BUFFER|p.R26G|c.76C>G|4,BUFFER|p.V157V|c.471C>A|3,BUFFER|p.V157G|c.470T>G|9,BUFFER|p.V157D|c.470T>A|8,BUFFER|p.V157F|c.469G>T|7,BUFFER|p.V157F|c.469G>T|8,BUFFER|p.V157L|c.469G>C|6,BUFFER|p.V157F|c.469G>T|22,BUFFER|p.V157F|c.469G>T|162,BUFFER|p.V157I|c.469G>A|10,BUFFER|p.V157F|c.469G>T|22,BUFFER|p.V25F|c.73G>T|25,BUFFER|p.V64F|c.190G>T|22,BUFFER|p.V157fs*13|c.468delC|3,BUFFER|p.R156P|c.467G>C|26,BUFFER|p.R63P|c.188G>C|4,BUFFER|p.R156H|c.467G>A|11,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R156P|c.467G>C|4,BUFFER|p.R24P|c.71G>C|4,BUFFER|p.R156L|c.467G>T|3,BUFFER|p.R156fs*14|c.466delC|9,BUFFER|p.R156S|c.466C>A|3,BUFFER|p.R156G|c.466C>G|3,BUFFER|p.R156C|c.466C>T|4,BUFFER|p.T155T|c.465C>T|4,BUFFER|p.T155N|c.464C>A|4,BUFFER|p.T155N|c.464C>A|5,BUFFER|p.T62N|c.185C>A|6,BUFFER|p.T155N|c.464C>A|25,BUFFER|p.T155I|c.464C>T|15,BUFFER|p.T23N|c.68C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.T155N|c.464C>A|6,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G61V|c.182G>T|3,BUFFER|p.G22V|c.65G>T|4,BUFFER|p.G154D|c.461G>A|6,BUFFER|p.G154V|c.461G>T|38,BUFFER|p.T150fs*16|c.448_460del13|4,BUFFER|p.G154S|c.460G>A|9,BUFFER|p.P153P|c.459C>T|6,BUFFER|p.P153L|c.458C>T|6,BUFFER|p.P153T|c.457C>A|3,BUFFER|p.P153S|c.457C>T|8,BUFFER|p.P153fs*28|c.456_457insN|4,BUFFER|p.P153fs*28|c.455_456insN|3,BUFFER|p.P152fs*18|c.455delC|6,BUFFER|p.P152P|c.456G>A|4,BUFFER|p.P152Q|c.455C>A|5,BUFFER|p.P152L|c.455C>T|70,BUFFER|p.P20L|c.59C>T|10,BUFFER|p.P152L|c.455C>T|10,BUFFER|p.P152R|c.455C>G|6,BUFFER|p.P59L|c.176C>T|10,BUFFER|p.P152L|c.455C>T|10,BUFFER|p.P152L|c.455C>T|4,BUFFER|p.P152L|c.455C>T|3,BUFFER|p.P152fs*18|c.454delC|3,BUFFER|p.P152fs*29|c.453_454insN|5,BUFFER|p.P152T|c.454C>A|7,BUFFER|p.P152S|c.454C>T|24,BUFFER|p.P151P|c.453C>T|8,BUFFER|p.P151P|c.453C>G|4,BUFFER|p.P152fs*18|c.451delC|9,BUFFER|p.P58H|c.173C>A|6,BUFFER|p.P151R|c.452C>G|8,BUFFER|p.P151H|c.452C>A|29,BUFFER|p.P151H|c.452C>A|6,BUFFER|p.P19R|c.56C>G|3,BUFFER|p.P151L|c.452C>T|7,BUFFER|p.P151H|c.452C>A|6,BUFFER|p.P19H|c.56C>A|6,BUFFER|p.P151T|c.451C>A|3,BUFFER|p.P19T|c.55C>A|3,BUFFER|p.P58S|c.172C>T|6,BUFFER|p.P151T|c.451C>A|16,BUFFER|p.P151A|c.451C>G|14,BUFFER|p.P151A|c.451C>G|3,BUFFER|p.P151S|c.451C>T|68,BUFFER|p.P151S|c.451C>T|6,BUFFER|p.P58T|c.172C>A|3,BUFFER|p.P151S|c.451C>T|3,BUFFER|p.P151A|c.451C>G|7,BUFFER|p.P151A|c.451C>G|7,BUFFER|p.P151S|c.451C>T|4,BUFFER|p.P151T|c.451C>A|3,BUFFER|p.P19A|c.55C>G|7,BUFFER|p.P58A|c.172C>G|7,BUFFER|p.P19S|c.55C>T|6,BUFFER|p.P151A|c.451C>G|3,BUFFER|p.P151fs*30|c.450_451insN|5	INDELOCATOR*|VARSCANI*|PINDEL	CGGGTGCCGGGC	.	3	ESCA
TP53	0	.	GRCh37	17	7579406	7579406	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	4/11	82	67	15	90	90	0	TP53,stop_gained,p.Ser94Ter,ENST00000508793,;TP53,stop_gained,p.Ser94Ter,ENST00000413465,;TP53,stop_gained,p.Ser94Ter,ENST00000604348,;TP53,stop_gained,p.Ser94Ter,ENST00000420246,;TP53,stop_gained,p.Ser94Ter,ENST00000269305,;TP53,stop_gained,p.Ser94Ter,ENST00000359597,;TP53,stop_gained,p.Ser94Ter,ENST00000445888,;TP53,stop_gained,p.Ser94Ter,ENST00000503591,;TP53,stop_gained,p.Ser94Ter,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	stop_gained	471	281	94	S/*	tCa/tAa	TP53_g.11512C>G,TP53_g.11512C>T,TP53_g.11512C>A,COSM45653,COSM45500,COSM2745056,COSM1386891,COSM2745058,COSM1386892,COSM3733628,COSM3970391,COSM2745057,COSM3733627	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Gene3D:2.60.40.720	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S94*|c.281C>A|4,CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,CODON|p.S94*|c.281C>G|4,BUFFER|p.P98S|c.292C>T|4,BUFFER|p.S96F|c.287C>T|3,BUFFER|p.S96P|c.286T>C|3,BUFFER|p.S95F|c.284C>T|3,BUFFER|p.S95P|c.283T>C|3,BUFFER|p.S95P|c.283T>C|3,BUFFER|p.S95P|c.283T>C|3,BUFFER|p.W91*|c.273G>A|5,BUFFER|p.W91*|c.273G>A|3,BUFFER|p.W91*|c.273G>A|9,BUFFER|p.W91*|c.273G>A|9,BUFFER|p.W91*|c.273G>A|17,BUFFER|p.W91*|c.272G>A|3,BUFFER|p.W91*|c.272G>A|3,BUFFER|p.W91*|c.272G>A|7,BUFFER|p.A76_S90del15|c.226_270del45|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATGACAGG	.	5	ESCA
ROCK1	0	.	GRCh37	18	18547850	18547850	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3055A>G	p.Arg1019Gly	p.R1019G	ENST00000399799	26/33	57	40	16	47	47	0	ROCK1,missense_variant,p.Arg1019Gly,ENST00000399799,;ROCK1,downstream_gene_variant,,ENST00000584875,;ROCK1,downstream_gene_variant,,ENST00000583556,;	C	ENSG00000067900	ENST00000399799	Transcript	missense_variant	3996	3055	1019	R/G	Aga/Gga	.	.	.	-1	ROCK1	HGNC	10251	protein_coding	YES	CCDS11870.2	ENSP00000382697	ROCK1_HUMAN	.	UPI000006F0A4	.	tolerated(0.54)	benign(0.003)	26/33	.	hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF28,PIRSF_domain:PIRSF037568	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTCTATCAA	.	5	ESCA
ZCCHC2	0	.	GRCh37	18	60242142	60242142	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2828C>T	p.Pro943Leu	p.P943L	ENST00000269499	13/14	16	13	3	39	39	0	ZCCHC2,missense_variant,p.Pro622Leu,ENST00000586834,;ZCCHC2,missense_variant,p.Pro943Leu,ENST00000269499,;ZCCHC2,intron_variant,,ENST00000587612,;ZCCHC2,missense_variant,p.Pro863Leu,ENST00000585873,;ZCCHC2,non_coding_transcript_exon_variant,,ENST00000585949,;ZCCHC2,upstream_gene_variant,,ENST00000591145,;	T	ENSG00000141664	ENST00000269499	Transcript	missense_variant	3246	2828	943	P/L	cCc/cTc	.	.	.	1	ZCCHC2	HGNC	22916	protein_coding	YES	CCDS45880.1	ENSP00000269499	ZCHC2_HUMAN	K7ERQ9_HUMAN,B2RPG6_HUMAN	UPI00016D385A	.	deleterious(0.01)	benign(0)	13/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16195,hmmpanther:PTHR16195:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TTCTCCCCAGC	.	4	ESCA
ZNF536	0	.	GRCh37	19	31048152	31048152	+	3'UTR	SNP	G	G	C	rs374051474	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*81G>C	.	.	ENST00000355537	5/5	58	54	4	66	66	0	ZNF536,3_prime_UTR_variant,,ENST00000355537,;ZNF536,intron_variant,,ENST00000592773,;	C	ENSG00000198597	ENST00000355537	Transcript	3_prime_UTR_variant	4131	.	.	.	.	rs374051474	.	.	1	ZNF536	HGNC	29025	protein_coding	YES	CCDS32984.1	ENSP00000347730	ZN536_HUMAN	K7EKT4_HUMAN,K7EJP8_HUMAN	UPI000006ED3E	.	.	.	5/5	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAATCGTGTAA	byCluster|by1000G	2	ESCA
GAPDHS	0	.	GRCh37	19	36033823	36033823	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.660-24C>T	.	.	ENST00000222286	.	31	25	6	40	40	0	GAPDHS,intron_variant,,ENST00000585510,;GAPDHS,intron_variant,,ENST00000222286,;TMEM147,upstream_gene_variant,,ENST00000392205,;TMEM147,upstream_gene_variant,,ENST00000392204,;TMEM147,upstream_gene_variant,,ENST00000222284,;AD000090.2,non_coding_transcript_exon_variant,,ENST00000444728,;AD000090.2,non_coding_transcript_exon_variant,,ENST00000588286,;AD000090.2,non_coding_transcript_exon_variant,,ENST00000590717,;AD000090.2,non_coding_transcript_exon_variant,,ENST00000589137,;AD000090.2,non_coding_transcript_exon_variant,,ENST00000590125,;GAPDHS,intron_variant,,ENST00000586334,;TMEM147,upstream_gene_variant,,ENST00000596232,;TMEM147,upstream_gene_variant,,ENST00000593027,;TMEM147,upstream_gene_variant,,ENST00000599895,;TMEM147,upstream_gene_variant,,ENST00000477168,;TMEM147,upstream_gene_variant,,ENST00000595467,;TMEM147,upstream_gene_variant,,ENST00000595180,;	T	ENSG00000105679	ENST00000222286	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GAPDHS	HGNC	24864	protein_coding	YES	CCDS12465.1	ENSP00000222286	G3PT_HUMAN	K7EP73_HUMAN	UPI000012AE83	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGTCCGTGC	.	2	ESCA
SERTAD3	0	.	GRCh37	19	40947446	40947446	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542G>C	p.Trp181Ser	p.W181S	ENST00000322354	2/2	29	22	6	38	38	0	SERTAD3,missense_variant,p.Trp181Ser,ENST00000392028,;SERTAD3,missense_variant,p.Trp181Ser,ENST00000322354,;SERTAD3,downstream_gene_variant,,ENST00000599706,;SERTAD3,downstream_gene_variant,,ENST00000596456,;CTC-492K19.4,upstream_gene_variant,,ENST00000599050,;SERTAD3,upstream_gene_variant,,ENST00000601217,;	G	ENSG00000167565	ENST00000322354	Transcript	missense_variant	1039	542	181	W/S	tGg/tCg	.	.	.	-1	SERTAD3	HGNC	17931	protein_coding	YES	CCDS12558.1	ENSP00000325414	SRTD3_HUMAN	M0R352_HUMAN,M0QXL4_HUMAN	UPI0000072807	.	tolerated(0.09)	probably_damaging(0.991)	2/2	.	hmmpanther:PTHR15530,hmmpanther:PTHR15530:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCCCAAGAA	.	5	ESCA
KCNA7	0	.	GRCh37	19	49573965	49573965	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.726G>A	p.Met242Ile	p.M242I	ENST00000221444	2/2	62	46	16	51	51	0	KCNA7,missense_variant,p.Met242Ile,ENST00000221444,;	T	ENSG00000104848	ENST00000221444	Transcript	missense_variant	1082	726	242	M/I	atG/atA	.	.	.	-1	KCNA7	HGNC	6226	protein_coding	YES	CCDS12755.1	ENSP00000221444	KCNA7_HUMAN	.	UPI000004F638	.	deleterious(0.04)	probably_damaging(0.987)	2/2	.	hmmpanther:PTHR11537:SF19,hmmpanther:PTHR11537,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324,Prints_domain:PR00169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTCATCAC	.	5	ESCA
BSG	0	.	GRCh37	19	581392	581392	+	Silent	SNP	G	G	C	rs147227117	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.870G>C	p.%3D	p.L290L	ENST00000333511	6/9	61	57	4	72	72	0	BSG,synonymous_variant,p.%3D,ENST00000353555,;BSG,synonymous_variant,p.%3D,ENST00000573784,;BSG,synonymous_variant,p.%3D,ENST00000545507,;BSG,synonymous_variant,p.%3D,ENST00000333511,;BSG,synonymous_variant,p.%3D,ENST00000346916,;BSG,downstream_gene_variant,,ENST00000576984,;BSG,downstream_gene_variant,,ENST00000573216,;BSG,downstream_gene_variant,,ENST00000574970,;BSG,non_coding_transcript_exon_variant,,ENST00000571735,;BSG,downstream_gene_variant,,ENST00000572899,;BSG,downstream_gene_variant,,ENST00000590218,;BSG,downstream_gene_variant,,ENST00000576925,;	C	ENSG00000172270	ENST00000333511	Transcript	synonymous_variant	940	870	290	L	ctG/ctC	rs147227117	.	.	1	BSG	HGNC	1116	protein_coding	YES	CCDS12033.1	ENSP00000333769	BASI_HUMAN	R4GN83_HUMAN,R4GMX5_HUMAN	UPI0000051E38	.	.	.	6/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10075,hmmpanther:PTHR10075:SF12,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AACCTGAACAT	byCluster	2	ESCA
MUC16	0	.	GRCh37	19	9018487	9018487	+	Missense_Mutation	SNP	G	G	A	rs780625713	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37687C>T	p.Arg12563Cys	p.R12563C	ENST00000397910	24/84	82	76	6	121	121	0	MUC16,missense_variant,p.Arg12563Cys,ENST00000397910,;	A	ENSG00000181143	ENST00000397910	Transcript	missense_variant	37891	37687	12563	R/C	Cgc/Tgc	rs780625713	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	probably_damaging(0.923)	24/84	.	Superfamily_domains:0047452,Pfam_domain:PF01390,Gene3D:1ivzA00,hmmpanther:PTHR14672,hmmpanther:PTHR14672:SF0,PROSITE_profiles:PS50024	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGCGATGCA	byFrequency	2	ESCA
ZNF559	0	.	GRCh37	19	9434927	9434927	+	5'Flank	SNP	C	C	T	rs529399270	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000393883	.	52	39	12	53	53	0	ZNF559,5_prime_UTR_variant,,ENST00000589208,;ZNF559,5_prime_UTR_variant,,ENST00000585377,;ZNF559,5_prime_UTR_variant,,ENST00000592298,;ZNF559,intron_variant,,ENST00000592896,;ZNF559,intron_variant,,ENST00000538743,;ZNF559,intron_variant,,ENST00000603380,;ZNF559,intron_variant,,ENST00000586255,;ZNF559,intron_variant,,ENST00000587557,;ZNF559,intron_variant,,ENST00000605750,;ZNF559,intron_variant,,ENST00000592504,;ZNF559,intron_variant,,ENST00000317221,;ZNF559-ZNF177,intron_variant,,ENST00000446085,;ZNF559,intron_variant,,ENST00000585352,;ZNF559,upstream_gene_variant,,ENST00000393883,;ZNF177,upstream_gene_variant,,ENST00000602856,;ZNF559-ZNF177,upstream_gene_variant,,ENST00000603656,;ZNF177,upstream_gene_variant,,ENST00000602738,;ZNF559-ZNF177,upstream_gene_variant,,ENST00000541595,;ZNF559,upstream_gene_variant,,ENST00000588124,;ZNF559-ZNF177,intron_variant,,ENST00000605301,;ZNF559-ZNF177,intron_variant,,ENST00000605522,;ZNF559-ZNF177,intron_variant,,ENST00000603099,;ZNF559-ZNF177,upstream_gene_variant,,ENST00000605471,;ZNF559-ZNF177,intron_variant,,ENST00000605775,;ZNF559-ZNF177,intron_variant,,ENST00000604886,;ZNF559-ZNF177,intron_variant,,ENST00000605093,;ZNF559-ZNF177,intron_variant,,ENST00000593242,;ZNF559-ZNF177,intron_variant,,ENST00000604543,;ZNF559-ZNF177,intron_variant,,ENST00000603024,;ZNF559-ZNF177,intron_variant,,ENST00000605006,;ZNF559-ZNF177,upstream_gene_variant,,ENST00000603974,;ZNF559-ZNF177,upstream_gene_variant,,ENST00000605071,;	T	ENSG00000188321	ENST00000393883	Transcript	upstream_gene_variant	.	.	.	.	.	rs529399270	.	1	1	ZNF559	HGNC	28197	protein_coding	YES	CCDS12211.1	ENSP00000377461	ZN559_HUMAN	S4R3F2_HUMAN,K7ERK9_HUMAN,B4DP29_HUMAN	UPI00000733B2	.	.	.	.	.	.	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGGCGTTCG	by1000G	5	ESCA
NOTCH2	0	.	GRCh37	1	120454894	120454894	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3035A>G	.	.	ENST00000256646	34/34	32	26	6	34	34	0	NOTCH2,3_prime_UTR_variant,,ENST00000256646,;RP5-1042I8.7,upstream_gene_variant,,ENST00000566949,;	C	ENSG00000134250	ENST00000256646	Transcript	3_prime_UTR_variant	10671	.	.	.	.	.	.	.	-1	NOTCH2	HGNC	7882	protein_coding	YES	CCDS908.1	ENSP00000256646	NOTC2_HUMAN	Q9UFD5_HUMAN,Q13560_HUMAN	UPI000013CF1D	.	.	.	34/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCATAGTAC	.	5	ESCA
SPTA1	0	.	GRCh37	1	158651381	158651381	+	Missense_Mutation	SNP	C	C	T	rs764818739	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.467G>A	p.Arg156Gln	p.R156Q	ENST00000368147	4/52	59	45	13	60	60	0	SPTA1,missense_variant,p.Arg156Gln,ENST00000368147,;SPTA1,intron_variant,,ENST00000467387,;	T	ENSG00000163554	ENST00000368147	Transcript	missense_variant	648	467	156	R/Q	cGg/cAg	rs764818739,COSM1499097	.	.	-1	SPTA1	HGNC	11272	protein_coding	YES	CCDS41423.1	ENSP00000357129	SPTA1_HUMAN	O60686_HUMAN	UPI0000458906	.	tolerated(1)	benign(0.006)	4/52	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF240,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCCGCAGC	.	5	ESCA
RASAL2	0	.	GRCh37	1	178414791	178414791	+	Missense_Mutation	SNP	G	G	A	rs757727946	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621G>A	p.Ala541Thr	p.A541T	ENST00000367649	9/18	44	31	13	54	53	1	RASAL2,missense_variant,p.Ala393Thr,ENST00000462775,;RASAL2,missense_variant,p.Ala541Thr,ENST00000367649,;RASAL2,missense_variant,p.Ala523Thr,ENST00000448150,;	A	ENSG00000075391	ENST00000367649	Transcript	missense_variant	1973	1621	541	A/T	Gca/Aca	rs757727946	.	.	1	RASAL2	HGNC	9874	protein_coding	YES	CCDS1321.2	ENSP00000356621	NGAP_HUMAN	Q8IW42_HUMAN,Q6P4F9_HUMAN	UPI00019B254F	.	tolerated(0.33)	probably_damaging(0.999)	9/18	.	PROSITE_profiles:PS50018,hmmpanther:PTHR10194:SF52,hmmpanther:PTHR10194,Pfam_domain:PF00616,Gene3D:1.10.506.10,SMART_domains:SM00323,Superfamily_domains:SSF48350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ATGACGCACTG	.	4	ESCA
SKI	0	.	GRCh37	1	2237626	2237626	+	Silent	SNP	G	G	A	rs751933078	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1935G>A	p.%3D	p.R645R	ENST00000378536	6/7	41	37	4	46	46	0	SKI,synonymous_variant,p.%3D,ENST00000378536,;SKI,downstream_gene_variant,,ENST00000478223,;SKI,downstream_gene_variant,,ENST00000508416,;SKI,downstream_gene_variant,,ENST00000507179,;	A	ENSG00000157933	ENST00000378536	Transcript	synonymous_variant	2007	1935	645	R	cgG/cgA	rs751933078	.	.	1	SKI	HGNC	10896	protein_coding	YES	CCDS39.1	ENSP00000367797	SKI_HUMAN	Q7Z462_HUMAN,Q7Z461_HUMAN,Q7Z459_HUMAN	UPI00001359DE	.	.	.	6/7	.	hmmpanther:PTHR10005:SF15,hmmpanther:PTHR10005,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCGGCAGGC	.	2	ESCA
OBSCN	0	.	GRCh37	1	228527712	228527712	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.20196G>T	p.Gln6732His	p.Q6732H	ENST00000570156	81/116	25	18	7	16	16	0	OBSCN,missense_variant,p.Gln3409His,ENST00000366707,;OBSCN,missense_variant,p.Gln2894His,ENST00000366709,;OBSCN,missense_variant,p.Gln5775His,ENST00000284548,;OBSCN,missense_variant,p.Gln392His,ENST00000441106,;OBSCN,missense_variant,p.Gln5775His,ENST00000422127,;OBSCN,missense_variant,p.Gln6732His,ENST00000570156,;	T	ENSG00000154358	ENST00000570156	Transcript	missense_variant	20270	20196	6732	Q/H	caG/caT	.	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	probably_damaging(0.953)	81/116	.	PROSITE_profiles:PS50010,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCAGGCGGC	.	5	ESCA
CDC20	0	.	GRCh37	1	43825769	43825770	+	Splice_Site	INS	-	-	T	rs755204301	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556+2dupT	.	p.X186_splice	ENST00000372462	.	34	27	7	34	34	0	CDC20,splice_donor_variant,,ENST00000310955,;CDC20,splice_donor_variant,,ENST00000372462,;ELOVL1,downstream_gene_variant,,ENST00000413844,;ELOVL1,downstream_gene_variant,,ENST00000372458,;RP1-92O14.3,upstream_gene_variant,,ENST00000424948,;CDC20,splice_donor_variant,,ENST00000478882,;CDC20,upstream_gene_variant,,ENST00000482046,;ELOVL1,downstream_gene_variant,,ENST00000468865,;ELOVL1,downstream_gene_variant,,ENST00000482302,;ELOVL1,downstream_gene_variant,,ENST00000465321,;ELOVL1,downstream_gene_variant,,ENST00000478481,;ELOVL1,downstream_gene_variant,,ENST00000496932,;ELOVL1,downstream_gene_variant,,ENST00000497050,;ELOVL1,downstream_gene_variant,,ENST00000487209,;ELOVL1,downstream_gene_variant,,ENST00000470769,;ELOVL1,downstream_gene_variant,,ENST00000479439,;ELOVL1,downstream_gene_variant,,ENST00000470968,;ELOVL1,downstream_gene_variant,,ENST00000479686,;ELOVL1,downstream_gene_variant,,ENST00000464204,;ELOVL1,downstream_gene_variant,,ENST00000497569,;	T	ENSG00000117399	ENST00000372462	Transcript	splice_donor_variant	.	.	.	.	.	rs755204301	.	.	1	CDC20	HGNC	1723	protein_coding	YES	CCDS484.1	ENSP00000361540	CDC20_HUMAN	.	UPI0000072C04	.	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTATTGTAAGT	.	3	ESCA
KLF17	0	.	GRCh37	1	44596234	44596234	+	Missense_Mutation	SNP	C	C	T	rs745641456	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.976C>T	p.Arg326Cys	p.R326C	ENST00000372299	3/4	49	38	11	53	53	0	KLF17,missense_variant,p.Arg326Cys,ENST00000372299,;KLF17,non_coding_transcript_exon_variant,,ENST00000476802,;	T	ENSG00000171872	ENST00000372299	Transcript	missense_variant	1034	976	326	R/C	Cgt/Tgt	rs745641456,COSM3419260,COSM3419259	.	.	1	KLF17	HGNC	18830	protein_coding	YES	CCDS508.1	ENSP00000361373	KLF17_HUMAN	.	UPI000013E95E	.	deleterious(0.03)	benign(0.247)	3/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR23223,hmmpanther:PTHR23223:SF5,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTCCGTTCT	byFrequency	5	ESCA
ASB17	0	.	GRCh37	1	76397722	76397722	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255T>C	p.%3D	p.F85F	ENST00000284142	1/3	53	36	17	52	52	0	ASB17,synonymous_variant,p.%3D,ENST00000284142,;	G	ENSG00000154007	ENST00000284142	Transcript	synonymous_variant	395	255	85	F	ttT/ttC	.	.	.	-1	ASB17	HGNC	19769	protein_coding	YES	CCDS671.1	ENSP00000284142	ASB17_HUMAN	.	UPI0000073CD7	.	.	.	1/3	.	hmmpanther:PTHR20966,hmmpanther:PTHR20966:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTAAAACT	.	5	ESCA
C20orf26	0	.	GRCh37	20	20258012	20258012	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2706C>A	p.%3D	p.I902I	ENST00000245957	22/27	41	28	13	37	37	0	C20orf26,synonymous_variant,p.%3D,ENST00000377309,;C20orf26,synonymous_variant,p.%3D,ENST00000245957,;C20orf26,intron_variant,,ENST00000488640,;C20orf26,synonymous_variant,p.%3D,ENST00000377308,;	A	ENSG00000089101	ENST00000245957	Transcript	synonymous_variant	2782	2706	902	I	atC/atA	.	.	.	1	C20orf26	HGNC	15872	protein_coding	YES	CCDS33447.1	ENSP00000245957	CT026_HUMAN	C9JMV0_HUMAN,C9JHE8_HUMAN,C9J610_HUMAN	UPI0000206AE4	.	.	.	22/27	.	hmmpanther:PTHR21178:SF8,hmmpanther:PTHR21178	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGATCCTGGC	.	5	ESCA
MIR663A	0	.	GRCh37	20	26188852	26188852	+	Intron	SNP	C	C	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.111+907G>T	.	.	ENST00000427348	.	16	11	5	11	11	0	MIR663A,non_coding_transcript_exon_variant,,ENST00000596223,;MIR663A,non_coding_transcript_exon_variant,,ENST00000596111,;MIR663A,non_coding_transcript_exon_variant,,ENST00000597267,;MIR663A,non_coding_transcript_exon_variant,,ENST00000385250,;MIR663A,intron_variant,,ENST00000597979,;MIR663A,intron_variant,,ENST00000601901,;MIR663A,intron_variant,,ENST00000600263,;MIR663A,intron_variant,,ENST00000601119,;MIR663A,intron_variant,,ENST00000601079,;MIR663A,intron_variant,,ENST00000609044,;MIR663A,intron_variant,,ENST00000597361,;MIR663A,intron_variant,,ENST00000427348,;MIR663A,intron_variant,,ENST00000608521,;MIR663A,intron_variant,,ENST00000598451,;MIR663A,intron_variant,,ENST00000609914,;MIR663A,intron_variant,,ENST00000609248,;MIR663A,intron_variant,,ENST00000594130,;MIR663A,intron_variant,,ENST00000596767,;MIR663A,intron_variant,,ENST00000596058,;MIR663A,intron_variant,,ENST00000610014,;MIR663A,intron_variant,,ENST00000598150,;MIR663A,intron_variant,,ENST00000609687,;MIR663A,intron_variant,,ENST00000608487,;MIR663A,intron_variant,,ENST00000609012,;MIR663A,intron_variant,,ENST00000600225,;MIR663A,intron_variant,,ENST00000432499,;MIR663A,intron_variant,,ENST00000594135,;MIR663A,intron_variant,,ENST00000594150,;MIR663A,intron_variant,,ENST00000608084,;MIR663A,upstream_gene_variant,,ENST00000609202,;MIR663A,upstream_gene_variant,,ENST00000600222,;MIR663A,upstream_gene_variant,,ENST00000598448,;MIR663A,upstream_gene_variant,,ENST00000596537,;	A	ENSG00000227195	ENST00000427348	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MIR663A	HGNC	32919	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER	GGCCGCGGGAT	.	2	ESCA
VPS16	0	.	GRCh37	20	2844831	2844831	+	Missense_Mutation	SNP	G	G	A	rs762665854	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1618G>A	p.Glu540Lys	p.E540K	ENST00000380445	17/24	80	58	21	93	93	0	VPS16,missense_variant,p.Glu226Lys,ENST00000380443,;VPS16,missense_variant,p.Glu396Lys,ENST00000380469,;VPS16,missense_variant,p.Glu540Lys,ENST00000380445,;PTPRA,5_prime_UTR_variant,,ENST00000380393,;VPS16,downstream_gene_variant,,ENST00000417508,;VPS16,downstream_gene_variant,,ENST00000453689,;VPS16,non_coding_transcript_exon_variant,,ENST00000481812,;VPS16,non_coding_transcript_exon_variant,,ENST00000487461,;VPS16,upstream_gene_variant,,ENST00000466415,;	A	ENSG00000215305	ENST00000380445	Transcript	missense_variant	1690	1618	540	E/K	Gag/Aag	rs762665854	.	.	1	VPS16	HGNC	14584	protein_coding	YES	CCDS13036.1	ENSP00000369810	VPS16_HUMAN	A1A4H0_HUMAN	UPI0000138B87	.	deleterious(0.01)	possibly_damaging(0.798)	17/24	.	hmmpanther:PTHR12811,hmmpanther:PTHR12811:SF0,Pfam_domain:PF04840,PIRSF_domain:PIRSF007949	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTGGAGTAT	.	5	ESCA
PMEPA1	0	.	GRCh37	20	56284579	56284579	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.60C>T	p.%3D	p.V20V	ENST00000341744	1/4	61	45	15	66	66	0	PMEPA1,synonymous_variant,p.%3D,ENST00000341744,;PMEPA1,synonymous_variant,p.%3D,ENST00000395819,;PMEPA1,intron_variant,,ENST00000265626,;PMEPA1,intron_variant,,ENST00000395816,;PMEPA1,intron_variant,,ENST00000347215,;PMEPA1,intron_variant,,ENST00000472841,;	A	ENSG00000124225	ENST00000341744	Transcript	synonymous_variant	380	60	20	V	gtC/gtT	.	.	.	-1	PMEPA1	HGNC	14107	protein_coding	YES	CCDS13463.1	ENSP00000345826	PMEPA_HUMAN	.	UPI000004970A	.	.	.	1/4	.	hmmpanther:PTHR16514,hmmpanther:PTHR16514:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGAGACATT	.	5	ESCA
CHODL	0	.	GRCh37	21	19635169	19635169	+	Silent	SNP	G	G	A	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.696G>A	p.%3D	p.L232L	ENST00000299295	5/6	60	48	12	64	64	0	CHODL,synonymous_variant,p.%3D,ENST00000299295,;CHODL,synonymous_variant,p.%3D,ENST00000543733,;CHODL,synonymous_variant,p.%3D,ENST00000400127,;CHODL,synonymous_variant,p.%3D,ENST00000400128,;CHODL,intron_variant,,ENST00000338326,;CHODL,intron_variant,,ENST00000400131,;CHODL,intron_variant,,ENST00000400135,;	A	ENSG00000154645	ENST00000299295	Transcript	synonymous_variant	1087	696	232	L	ctG/ctA	COSM725475	.	.	1	CHODL	HGNC	17807	protein_coding	YES	CCDS13570.1	ENSP00000299295	CHODL_HUMAN	.	UPI0000037746	.	.	.	5/6	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR14789	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACTGGTTGC	.	5	ESCA
NCAM2	0	.	GRCh37	21	22838967	22838967	+	Silent	SNP	T	T	C	rs190741777	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1695T>C	p.%3D	p.Y565Y	ENST00000400546	13/18	30	19	11	33	33	0	NCAM2,synonymous_variant,p.%3D,ENST00000400546,;NCAM2,synonymous_variant,p.%3D,ENST00000284894,;NCAM2,non_coding_transcript_exon_variant,,ENST00000484983,;	C	ENSG00000154654	ENST00000400546	Transcript	synonymous_variant	1944	1695	565	Y	taT/taC	rs190741777	.	.	1	NCAM2	HGNC	7657	protein_coding	YES	CCDS42910.1	ENSP00000383392	NCAM2_HUMAN	D3DSC5_HUMAN	UPI00001A3703	.	.	.	13/18	.	PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF35,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	C:0.0017	C:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTATGAAAT	byCluster|by1000G	5	ESCA
TMEM50B	0	.	GRCh37	21	34822035	34822035	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1090G>A	.	.	ENST00000542230	7/7	14	9	5	11	11	0	TMEM50B,3_prime_UTR_variant,,ENST00000542230,;IFNGR2,intron_variant,,ENST00000421802,;TMEM50B,upstream_gene_variant,,ENST00000484377,;TMEM50B,upstream_gene_variant,,ENST00000470682,;TMEM50B,upstream_gene_variant,,ENST00000468874,;TMEM50B,3_prime_UTR_variant,,ENST00000420455,;TMEM50B,downstream_gene_variant,,ENST00000441128,;TMEM50B,downstream_gene_variant,,ENST00000442441,;	T	ENSG00000142188	ENST00000542230	Transcript	3_prime_UTR_variant	1782	.	.	.	.	.	.	.	-1	TMEM50B	HGNC	1280	protein_coding	YES	CCDS13625.1	ENSP00000439768	TM50B_HUMAN	C9K0I4_HUMAN	UPI0000048EAC	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATTCCACTT	.	5	ESCA
SEC14L2	0	.	GRCh37	22	30811777	30811777	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.694A>G	p.Ile232Val	p.I232V	ENST00000312932	9/12	11	6	5	28	28	0	SEC14L2,missense_variant,p.Ile232Val,ENST00000405717,;SEC14L2,missense_variant,p.Ile232Val,ENST00000312932,;SEC14L2,missense_variant,p.Ile149Val,ENST00000402592,;RP4-539M6.19,missense_variant,p.Ile66Val,ENST00000439838,;SEC14L2,missense_variant,p.Ile158Val,ENST00000403484,;SEC14L2,missense_variant,p.Ile178Val,ENST00000428195,;RP4-539M6.19,intron_variant,,ENST00000439023,;RNF215,intron_variant,,ENST00000431544,;KIAA1658,downstream_gene_variant,,ENST00000598426,;RP4-539M6.20,upstream_gene_variant,,ENST00000608677,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000467218,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000483116,;RP4-539M6.19,intron_variant,,ENST00000454552,;SEC14L2,intron_variant,,ENST00000478762,;SEC14L2,intron_variant,,ENST00000464335,;	G	ENSG00000100003	ENST00000312932	Transcript	missense_variant	954	694	232	I/V	Atc/Gtc	.	.	.	1	SEC14L2	HGNC	10699	protein_coding	YES	CCDS13876.1	ENSP00000316203	S14L2_HUMAN	C9JZI9_HUMAN,B7Z3Z8_HUMAN	UPI0000135433	.	tolerated(0.08)	benign(0.003)	9/12	.	PROSITE_profiles:PS50191,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF64,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AACATATCAGC	.	3	ESCA
SLC9A4	0	.	GRCh37	2	103095550	103095550	+	Frame_Shift_Del	DEL	C	C	-	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.510delC	p.Leu171TrpfsTer13	p.L171Wfs*13	ENST00000295269	2/12	35	30	5	47	47	0	SLC9A4,frameshift_variant,p.Leu171TrpfsTer13,ENST00000295269,;	-	ENSG00000180251	ENST00000295269	Transcript	frameshift_variant	966	509	170	A/X	gCc/gc	COSM359489	.	.	1	SLC9A4	HGNC	11077	protein_coding	YES	CCDS33264.1	ENSP00000295269	SL9A4_HUMAN	.	UPI000047F996	.	.	.	2/12	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10110:SF103,hmmpanther:PTHR10110,Pfam_domain:PF00999,TIGRFAM_domain:TIGR00840	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	deletion	.	1	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TCAACGCCTTGG	.	2	ESCA
PLEKHA3	0	.	GRCh37	2	179355543	179355543	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313+2T>C	.	p.X105_splice	ENST00000234453	.	33	25	8	31	31	0	PLEKHA3,splice_donor_variant,,ENST00000234453,;PLEKHA3,upstream_gene_variant,,ENST00000421187,;PLEKHA3,splice_donor_variant,,ENST00000461474,;PLEKHA3,splice_donor_variant,,ENST00000453653,;	C	ENSG00000116095	ENST00000234453	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	PLEKHA3	HGNC	14338	protein_coding	YES	CCDS33336.1	ENSP00000234453	PKHA3_HUMAN	.	UPI000000DA8A	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGGTAACTA	.	5	ESCA
CWC22	0	.	GRCh37	2	180843003	180843003	+	Silent	SNP	T	T	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495A>T	p.%3D	p.S165S	ENST00000410053	6/20	108	88	19	116	116	0	CWC22,synonymous_variant,p.%3D,ENST00000404136,;CWC22,synonymous_variant,p.%3D,ENST00000410053,;CWC22,synonymous_variant,p.%3D,ENST00000295749,;	A	ENSG00000163510	ENST00000410053	Transcript	synonymous_variant	795	495	165	S	tcA/tcT	.	.	.	-1	CWC22	HGNC	29322	protein_coding	YES	CCDS46465.1	ENSP00000387006	CWC22_HUMAN	B7WP74_HUMAN	UPI00001C1DAE	.	.	.	6/20	.	hmmpanther:PTHR18034:SF3,hmmpanther:PTHR18034,Pfam_domain:PF02854,Gene3D:1.25.40.180,SMART_domains:SM00543,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATTGACTT	.	5	ESCA
RPL37A	0	.	GRCh37	2	217364062	217364062	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73A>T	p.Met25Leu	p.M25L	ENST00000491306	2/4	30	24	6	29	29	0	RPL37A,start_lost,p.Met1?,ENST00000427280,;RPL37A,start_lost,p.Met1?,ENST00000598925,;RPL37A,start_lost,p.Met1?,ENST00000456586,;RPL37A,start_lost,p.Met1?,ENST00000441179,;RPL37A,missense_variant,p.Met25Leu,ENST00000600880,;RPL37A,missense_variant,p.Met25Leu,ENST00000446558,;RPL37A,missense_variant,p.Met25Leu,ENST00000491306,;AC098820.3,upstream_gene_variant,,ENST00000453157,;AC098820.3,upstream_gene_variant,,ENST00000438978,;RPL37A,missense_variant,p.Met25Leu,ENST00000420712,;RPL37A,non_coding_transcript_exon_variant,,ENST00000359681,;RPL37A,non_coding_transcript_exon_variant,,ENST00000487233,;RPL37A,non_coding_transcript_exon_variant,,ENST00000478153,;RPL37A,non_coding_transcript_exon_variant,,ENST00000490649,;AC098820.3,upstream_gene_variant,,ENST00000431856,;	T	ENSG00000197756	ENST00000491306	Transcript	missense_variant	759	73	25	M/L	Atg/Ttg	.	.	.	1	RPL37A	HGNC	10348	protein_coding	YES	CCDS2404.1	ENSP00000418082	RL37A_HUMAN	C9J4Z3_HUMAN	UPI0000003E77	.	tolerated(0.06)	benign(0.012)	2/4	.	HAMAP:MF_00327,hmmpanther:PTHR11517,TIGRFAM_domain:TIGR00280,Pfam_domain:PF01780,Gene3D:2.20.25.30,Superfamily_domains:SSF57829	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAAATGGTG	.	5	ESCA
COL4A4	0	.	GRCh37	2	227871082	227871082	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*959C>T	.	.	ENST00000396625	48/48	21	14	6	17	17	0	COL4A4,3_prime_UTR_variant,,ENST00000396625,;COL4A4,downstream_gene_variant,,ENST00000329662,;	A	ENSG00000081052	ENST00000396625	Transcript	3_prime_UTR_variant	6240	.	.	.	.	.	.	.	-1	COL4A4	HGNC	2206	protein_coding	YES	CCDS42828.1	ENSP00000379866	CO4A4_HUMAN	.	UPI000013D987	.	.	.	48/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	AGCGCGTGCCT	.	3	ESCA
COL6A3	0	.	GRCh37	2	238259828	238259828	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6761G>A	p.Gly2254Glu	p.G2254E	ENST00000295550	27/44	40	24	16	44	44	0	COL6A3,missense_variant,p.Gly2054Glu,ENST00000346358,;COL6A3,missense_variant,p.Gly2053Glu,ENST00000347401,;COL6A3,missense_variant,p.Gly1647Glu,ENST00000472056,;COL6A3,missense_variant,p.Gly2048Glu,ENST00000353578,;COL6A3,missense_variant,p.Gly2048Glu,ENST00000409809,;COL6A3,missense_variant,p.Gly2254Glu,ENST00000295550,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;	T	ENSG00000163359	ENST00000295550	Transcript	missense_variant	7214	6761	2254	G/E	gGa/gAa	COSM210532	.	.	-1	COL6A3	HGNC	2213	protein_coding	YES	CCDS33412.1	ENSP00000295550	CO6A3_HUMAN	Q8N4Z1_HUMAN,D9ZGF2_HUMAN	UPI0000456F39	.	.	unknown(0)	27/44	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22992,hmmpanther:PTHR22992:SF83	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCCGCTT	.	5	ESCA
AGBL5	0	.	GRCh37	2	27276797	27276797	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.421C>A	p.His141Asn	p.H141N	ENST00000360131	4/15	58	40	18	55	55	0	AGBL5,missense_variant,p.His141Asn,ENST00000360131,;AGBL5,missense_variant,p.His141Asn,ENST00000453161,;AGBL5,missense_variant,p.His141Asn,ENST00000323064,;AGBL5,downstream_gene_variant,,ENST00000421915,;AGBL5,downstream_gene_variant,,ENST00000451003,;AGBL5,downstream_gene_variant,,ENST00000437006,;RP11-503P10.1,non_coding_transcript_exon_variant,,ENST00000607407,;AGBL5-AS1,upstream_gene_variant,,ENST00000444217,;AGBL5,missense_variant,p.His141Asn,ENST00000487078,;AGBL5,non_coding_transcript_exon_variant,,ENST00000477136,;AGBL5,non_coding_transcript_exon_variant,,ENST00000489683,;	A	ENSG00000084693	ENST00000360131	Transcript	missense_variant	580	421	141	H/N	Cat/Aat	COSM720672,COSM1647298	.	.	1	AGBL5	HGNC	26147	protein_coding	YES	CCDS1732.3	ENSP00000353249	CBPC5_HUMAN	C9JTY1_HUMAN,C9JQG9_HUMAN,C9JHM6_HUMAN,C9JCE1_HUMAN	UPI000006FE54	.	deleterious(0.01)	benign(0.152)	4/15	.	hmmpanther:PTHR12756	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTTCATCGT	.	5	ESCA
NRXN1	0	.	GRCh37	2	50148604	50148604	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*478C>G	.	.	ENST00000404971	24/24	53	40	13	58	58	0	NRXN1,3_prime_UTR_variant,,ENST00000401710,;NRXN1,3_prime_UTR_variant,,ENST00000404971,;NRXN1,3_prime_UTR_variant,,ENST00000406316,;NRXN1,3_prime_UTR_variant,,ENST00000378262,;NRXN1,3_prime_UTR_variant,,ENST00000412315,;NRXN1,3_prime_UTR_variant,,ENST00000342183,;NRXN1,downstream_gene_variant,,ENST00000405472,;NRXN1,downstream_gene_variant,,ENST00000401669,;NRXN1,downstream_gene_variant,,ENST00000406859,;NRXN1,downstream_gene_variant,,ENST00000402717,;NRXN1,non_coding_transcript_exon_variant,,ENST00000484192,;	C	ENSG00000179915	ENST00000404971	Transcript	3_prime_UTR_variant	6462	.	.	.	.	.	.	.	-1	NRXN1	HGNC	8008	protein_coding	YES	CCDS46282.1	ENSP00000385142	NRX1A_HUMAN	Q08AH0_HUMAN	UPI00015A218A	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAGGTTTG	.	5	ESCA
ALMS1	0	.	GRCh37	2	73718079	73718079	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8990A>C	p.Asn2997Thr	p.N2997T	ENST00000264448	10/23	32	24	7	34	34	0	ALMS1,missense_variant,p.Asn2955Thr,ENST00000409009,;ALMS1,missense_variant,p.Asn2997Thr,ENST00000264448,;AC096546.1,upstream_gene_variant,,ENST00000408160,;ALMS1,non_coding_transcript_exon_variant,,ENST00000484298,;ALMS1,intron_variant,,ENST00000423048,;	C	ENSG00000116127	ENST00000264448	Transcript	missense_variant	9101	8990	2997	N/T	aAt/aCt	.	.	.	1	ALMS1	HGNC	428	protein_coding	YES	CCDS42697.1	ENSP00000264448	ALMS1_HUMAN	A6NMY3_HUMAN	UPI0000212786	.	.	benign(0.069)	10/23	.	hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGAATAATC	.	5	ESCA
IAH1	0	.	GRCh37	2	9628294	9628294	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.583T>A	p.Ser195Thr	p.S195T	ENST00000497473	6/6	62	40	21	56	56	0	IAH1,missense_variant,p.Ser82Thr,ENST00000470914,;IAH1,missense_variant,p.Ser195Thr,ENST00000497473,;IAH1,missense_variant,p.Ser82Thr,ENST00000482918,;IAH1,missense_variant,p.Ser175Thr,ENST00000481367,;IAH1,missense_variant,p.Ser82Thr,ENST00000545602,;IAH1,3_prime_UTR_variant,,ENST00000481688,;IAH1,downstream_gene_variant,,ENST00000496603,;IAH1,downstream_gene_variant,,ENST00000495797,;ADAM17,downstream_gene_variant,,ENST00000310823,;IAH1,non_coding_transcript_exon_variant,,ENST00000489468,;IAH1,non_coding_transcript_exon_variant,,ENST00000490621,;IAH1,non_coding_transcript_exon_variant,,ENST00000487850,;IAH1,downstream_gene_variant,,ENST00000495494,;IAH1,3_prime_UTR_variant,,ENST00000351760,;IAH1,3_prime_UTR_variant,,ENST00000492223,;IAH1,non_coding_transcript_exon_variant,,ENST00000484826,;IAH1,downstream_gene_variant,,ENST00000495050,;	A	ENSG00000134330	ENST00000497473	Transcript	missense_variant	620	583	195	S/T	Tca/Aca	.	.	.	1	IAH1	HGNC	27696	protein_coding	YES	CCDS42651.1	ENSP00000417580	IAH1_HUMAN	C9JDY4_HUMAN,C9J5J2_HUMAN,B4DMV3_HUMAN	UPI00000382E7	.	deleterious(0.04)	possibly_damaging(0.612)	6/6	.	hmmpanther:PTHR14209,Pfam_domain:PF00657,Gene3D:3.40.50.1110,Superfamily_domains:SSF52266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTATCAGAT	.	5	ESCA
TRIM42	0	.	GRCh37	3	140397293	140397293	+	Silent	SNP	C	C	T	rs757444882	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.222C>T	p.%3D	p.P74P	ENST00000286349	1/5	41	34	6	31	31	0	TRIM42,synonymous_variant,p.%3D,ENST00000286349,;	T	ENSG00000155890	ENST00000286349	Transcript	synonymous_variant	413	222	74	P	ccC/ccT	rs757444882	.	.	1	TRIM42	HGNC	19014	protein_coding	YES	CCDS3113.1	ENSP00000286349	TRI42_HUMAN	.	UPI00001AEAE0	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATCCCAACTG	.	4	ESCA
AGTR1	0	.	GRCh37	3	148460393	148460393	+	3'UTR	SNP	T	T	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*491T>G	.	.	ENST00000542281	4/4	36	28	8	25	25	0	AGTR1,3_prime_UTR_variant,,ENST00000404754,;AGTR1,3_prime_UTR_variant,,ENST00000542281,;AGTR1,3_prime_UTR_variant,,ENST00000418473,;AGTR1,3_prime_UTR_variant,,ENST00000402260,;AGTR1,3_prime_UTR_variant,,ENST00000497524,;AGTR1,3_prime_UTR_variant,,ENST00000349243,;AGTR1,downstream_gene_variant,,ENST00000461609,;AGTR1,downstream_gene_variant,,ENST00000474935,;AGTR1,downstream_gene_variant,,ENST00000475347,;	G	ENSG00000144891	ENST00000542281	Transcript	3_prime_UTR_variant	2017	.	.	.	.	.	.	.	1	AGTR1	HGNC	336	protein_coding	YES	CCDS3137.1	ENSP00000443186	AGTR1_HUMAN	Q53YY0_HUMAN,D3DNG8_HUMAN	UPI0000039D66	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGTACAAA	.	5	ESCA
FXR1	0	.	GRCh37	3	180652996	180652996	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.175A>G	p.Ile59Val	p.I59V	ENST00000357559	3/17	109	65	43	87	87	0	FXR1,missense_variant,p.Ile59Val,ENST00000357559,;FXR1,missense_variant,p.Ile59Val,ENST00000445140,;FXR1,missense_variant,p.Ile63Val,ENST00000484042,;FXR1,missense_variant,p.Ile46Val,ENST00000480918,;FXR1,5_prime_UTR_variant,,ENST00000305586,;FXR1,5_prime_UTR_variant,,ENST00000468861,;FXR1,5_prime_UTR_variant,,ENST00000484790,;FXR1,5_prime_UTR_variant,,ENST00000465551,;FXR1,intron_variant,,ENST00000491062,;FXR1,intron_variant,,ENST00000484958,;FXR1,intron_variant,,ENST00000469882,;FXR1,non_coding_transcript_exon_variant,,ENST00000479176,;FXR1,non_coding_transcript_exon_variant,,ENST00000472339,;FXR1,intron_variant,,ENST00000475315,;FXR1,downstream_gene_variant,,ENST00000461801,;	G	ENSG00000114416	ENST00000357559	Transcript	missense_variant	559	175	59	I/V	Att/Gtt	.	.	.	1	FXR1	HGNC	4023	protein_coding	YES	CCDS3238.1	ENSP00000350170	FXR1_HUMAN	C9JZE0_HUMAN,C9JY20_HUMAN,C9J5B4_HUMAN,C9IZ22_HUMAN	UPI000013EA6E	.	tolerated(0.08)	benign(0.342)	3/17	.	hmmpanther:PTHR10603,hmmpanther:PTHR10603:SF6,Pfam_domain:PF05641	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAAATTAGT	.	5	ESCA
TP63	0	.	GRCh37	3	189614087	189614087	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1796C>G	.	.	ENST00000264731	14/14	51	46	5	33	33	0	TP63,3_prime_UTR_variant,,ENST00000354600,;TP63,3_prime_UTR_variant,,ENST00000264731,;TP63,3_prime_UTR_variant,,ENST00000382063,;TP63,downstream_gene_variant,,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000456148,;TP63,downstream_gene_variant,,ENST00000392460,;TP63,downstream_gene_variant,,ENST00000320472,;TP63,downstream_gene_variant,,ENST00000440651,;TP63,downstream_gene_variant,,ENST00000449992,;TP63,downstream_gene_variant,,ENST00000392463,;	G	ENSG00000073282	ENST00000264731	Transcript	3_prime_UTR_variant	3928	.	.	.	.	.	.	.	1	TP63	HGNC	15979	protein_coding	YES	CCDS3293.1	ENSP00000264731	P63_HUMAN	.	UPI0000073CF2	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTTCTTCTT	.	3	ESCA
PPP1R2	0	.	GRCh37	3	195251628	195251628	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.297C>G	p.Ile99Met	p.I99M	ENST00000328432	3/6	61	30	31	47	47	0	PPP1R2,missense_variant,p.Ile99Met,ENST00000328432,;PPP1R2,intron_variant,,ENST00000438848,;RNU6ATAC24P,upstream_gene_variant,,ENST00000516811,;PPP1R2,missense_variant,p.Ile45Met,ENST00000418939,;PPP1R2,3_prime_UTR_variant,,ENST00000413183,;PPP1R2,downstream_gene_variant,,ENST00000462906,;	C	ENSG00000184203	ENST00000328432	Transcript	missense_variant	658	297	99	I/M	atC/atG	COSM3774827	.	.	-1	PPP1R2	HGNC	9288	protein_coding	YES	CCDS3309.1	ENSP00000328178	IPP2_HUMAN	.	UPI0000049C96	.	tolerated(0.25)	benign(0.016)	3/6	.	Pfam_domain:PF04979,hmmpanther:PTHR12398,hmmpanther:PTHR12398:SF22	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTAAGATGTC	.	5	ESCA
MUC20	0	.	GRCh37	3	195456532	195456532	+	Silent	SNP	T	T	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1983T>G	p.%3D	p.G661G	ENST00000447234	3/4	105	89	15	77	77	0	MUC20,synonymous_variant,p.%3D,ENST00000447234,;MUC20,synonymous_variant,p.%3D,ENST00000320736,;MUC20,synonymous_variant,p.%3D,ENST00000445522,;MUC20,synonymous_variant,p.%3D,ENST00000423938,;MUC20,synonymous_variant,p.%3D,ENST00000436408,;LINC00969,non_coding_transcript_exon_variant,,ENST00000594446,;LINC00969,non_coding_transcript_exon_variant,,ENST00000595086,;LINC00969,intron_variant,,ENST00000600197,;LINC00969,downstream_gene_variant,,ENST00000600288,;LINC00969,downstream_gene_variant,,ENST00000599566,;LINC00969,downstream_gene_variant,,ENST00000597662,;LINC00969,downstream_gene_variant,,ENST00000455807,;MUC20,downstream_gene_variant,,ENST00000485430,;MUC20,downstream_gene_variant,,ENST00000480350,;MUC20,non_coding_transcript_exon_variant,,ENST00000498018,;	G	ENSG00000176945	ENST00000447234	Transcript	synonymous_variant	2109	1983	661	G	ggT/ggG	.	.	.	1	MUC20	HGNC	23282	protein_coding	YES	CCDS63877.1	ENSP00000414350	MUC20_HUMAN	I0EZ60_HUMAN,I0EZ59_HUMAN,I0CMK3_HUMAN,I0CMJ9_HUMAN	UPI000198CC5A	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAGGTTTCCT	.	4	ESCA
TGFBR2	0	.	GRCh37	3	30691784	30691784	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361A>G	p.Thr121Ala	p.T121A	ENST00000359013	4/8	22	13	9	39	39	0	TGFBR2,missense_variant,p.Thr96Ala,ENST00000295754,;TGFBR2,missense_variant,p.Thr121Ala,ENST00000359013,;	G	ENSG00000163513	ENST00000359013	Transcript	missense_variant	644	361	121	T/A	Aca/Gca	.	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	tolerated(0.07)	possibly_damaging(0.512)	4/8	.	hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:2.10.60.10,Pfam_domain:PF08917,PIRSF_domain:PIRSF037393,Superfamily_domains:SSF57302	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATAACACTA	.	5	ESCA
CTNNB1	0	.	GRCh37	3	41278166	41278166	+	Missense_Mutation	SNP	C	C	T	rs772401455	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2042C>T	p.Ser681Phe	p.S681F	ENST00000349496	13/15	31	22	9	37	37	0	CTNNB1,missense_variant,p.Ser681Phe,ENST00000349496,;CTNNB1,missense_variant,p.Ser681Phe,ENST00000396185,;CTNNB1,missense_variant,p.Ser681Phe,ENST00000405570,;CTNNB1,missense_variant,p.Ser674Phe,ENST00000453024,;CTNNB1,missense_variant,p.Ser681Phe,ENST00000396183,;CTNNB1,upstream_gene_variant,,ENST00000471014,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000465552,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000485265,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000482042,;	T	ENSG00000168036	ENST00000349496	Transcript	missense_variant	2322	2042	681	S/F	tCt/tTt	rs772401455	.	.	1	CTNNB1	HGNC	2514	protein_coding	YES	CCDS2694.1	ENSP00000344456	CTNB1_HUMAN	G9GAG7_HUMAN,E9PDF9_HUMAN,E7EV28_HUMAN,E7EMJ5_HUMAN,C9IZ65_HUMAN,B4DGU4_HUMAN	UPI000012862F	.	deleterious(0)	possibly_damaging(0.709)	13/15	.	hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCTCTCT	.	5	ESCA
EPHA6	0	.	GRCh37	3	97356914	97356914	+	Silent	SNP	T	T	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2772T>G	p.%3D	p.A924A	ENST00000389672	14/18	37	26	11	42	42	0	EPHA6,synonymous_variant,p.%3D,ENST00000389672,;EPHA6,synonymous_variant,p.%3D,ENST00000502694,;EPHA6,synonymous_variant,p.%3D,ENST00000514100,;EPHA6,downstream_gene_variant,,ENST00000442602,;EPHA6,synonymous_variant,p.%3D,ENST00000477384,;EPHA6,downstream_gene_variant,,ENST00000508345,;	G	ENSG00000080224	ENST00000389672	Transcript	synonymous_variant	2810	2772	924	A	gcT/gcG	.	.	.	1	EPHA6	HGNC	19296	protein_coding	YES	CCDS46876.1	ENSP00000374323	.	H0Y8K5_HUMAN	UPI000004BB12	.	.	.	14/18	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF24,hmmpanther:PTHR24416,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCTTATAC	.	5	ESCA
TRIM2	0	.	GRCh37	4	154258074	154258074	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1956A>T	.	.	ENST00000338700	12/12	16	9	7	16	16	0	TRIM2,3_prime_UTR_variant,,ENST00000338700,;TRIM2,downstream_gene_variant,,ENST00000437508,;	T	ENSG00000109654	ENST00000338700	Transcript	3_prime_UTR_variant	4337	.	.	.	.	.	.	.	1	TRIM2	HGNC	15974	protein_coding	YES	CCDS3781.2	ENSP00000339659	TRIM2_HUMAN	C9JVI3_HUMAN,C9J084_HUMAN	UPI00005A60C0	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGAAGACAC	.	5	ESCA
MSANTD1	0	.	GRCh37	4	3257920	3257920	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*228G>T	.	.	ENST00000438480	3/3	22	14	8	49	49	0	MSANTD1,3_prime_UTR_variant,,ENST00000507492,;MSANTD1,3_prime_UTR_variant,,ENST00000438480,;MSANTD1,intron_variant,,ENST00000510580,;MSANTD1,intron_variant,,ENST00000505599,;	T	ENSG00000188981	ENST00000438480	Transcript	3_prime_UTR_variant	2812	.	.	.	.	.	.	.	1	MSANTD1	HGNC	33741	protein_coding	YES	CCDS47003.1	ENSP00000411584	MSD1_HUMAN	.	UPI000036721F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACACAGGCCAG	.	4	ESCA
EVC	0	.	GRCh37	4	5800490	5800490	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2275A>T	p.Ser759Cys	p.S759C	ENST00000382674	15/24	36	22	13	59	59	0	EVC,missense_variant,p.Ser759Cys,ENST00000382674,;EVC,missense_variant,p.Ser759Cys,ENST00000264956,;EVC,non_coding_transcript_exon_variant,,ENST00000515113,;CRMP1,intron_variant,,ENST00000506216,;EVC,downstream_gene_variant,,ENST00000506240,;	T	ENSG00000072840	ENST00000382674	Transcript	missense_variant	2459	2275	759	S/C	Agc/Tgc	.	.	.	1	EVC	HGNC	3497	protein_coding	YES	CCDS3383.1	ENSP00000372120	EVC_HUMAN	Q4W5F2_HUMAN,Q4W5A3_HUMAN	UPI000012A2A5	.	deleterious(0.01)	probably_damaging(0.976)	15/24	.	hmmpanther:PTHR16795:SF12,hmmpanther:PTHR16795	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAGAGCCGG	.	5	ESCA
SGCD	0	.	GRCh37	5	156191205	156191205	+	3'Flank	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000337851	.	15	10	5	18	18	0	SGCD,3_prime_UTR_variant,,ENST00000435422,;SGCD,downstream_gene_variant,,ENST00000337851,;	G	ENSG00000170624	ENST00000337851	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4590	1	SGCD	HGNC	10807	protein_coding	YES	CCDS47325.1	ENSP00000338343	SGCD_HUMAN	.	UPI00001678CF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATAAAATG	.	5	ESCA
GRK6	0	.	GRCh37	5	176869147	176869147	+	3'UTR	SNP	G	G	A	rs369806590	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*319G>A	.	.	ENST00000528793	16/16	19	15	4	25	25	0	GRK6,3_prime_UTR_variant,,ENST00000355472,;GRK6,3_prime_UTR_variant,,ENST00000528793,;GRK6,3_prime_UTR_variant,,ENST00000393576,;PRR7,upstream_gene_variant,,ENST00000323249,;GRK6,downstream_gene_variant,,ENST00000355958,;PRR7,upstream_gene_variant,,ENST00000502922,;PRR7,upstream_gene_variant,,ENST00000507881,;PRR7-AS1,intron_variant,,ENST00000425316,;PRR7-AS1,downstream_gene_variant,,ENST00000506465,;PRR7-AS1,downstream_gene_variant,,ENST00000511565,;PRR7-AS1,downstream_gene_variant,,ENST00000514846,;GRK6,downstream_gene_variant,,ENST00000515666,;	A	ENSG00000198055	ENST00000528793	Transcript	3_prime_UTR_variant	2092	.	.	.	.	rs369806590	.	.	1	GRK6	HGNC	4545	protein_coding	YES	CCDS47348.1	ENSP00000433511	GRK6_HUMAN	D6RHC7_HUMAN,D6RDA3_HUMAN,D6R9V4_HUMAN	UPI000002AAC9	.	.	.	16/16	.	.	A:0.0032	A:0	A:0.0086	.	A:0.0099	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGCGGGAGC	byFrequency|byCluster|by1000G	5	ESCA
SREK1	0	.	GRCh37	5	65476614	65476614	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1918A>G	.	.	ENST00000334121	12/12	22	9	13	23	23	0	SREK1,3_prime_UTR_variant,,ENST00000334121,;SREK1,downstream_gene_variant,,ENST00000380918,;SREK1,non_coding_transcript_exon_variant,,ENST00000284041,;SREK1,non_coding_transcript_exon_variant,,ENST00000519259,;SREK1,downstream_gene_variant,,ENST00000522214,;SREK1,downstream_gene_variant,,ENST00000520953,;SREK1,downstream_gene_variant,,ENST00000522912,;SREK1,downstream_gene_variant,,ENST00000519205,;	G	ENSG00000153914	ENST00000334121	Transcript	3_prime_UTR_variant	3952	.	.	.	.	.	.	.	1	SREK1	HGNC	17882	protein_coding	YES	CCDS43323.1	ENSP00000334538	SREK1_HUMAN	Q69YM5_HUMAN,E5RJ76_HUMAN	UPI00000467F2	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCAACAGCT	.	5	ESCA
CLVS2	0	.	GRCh37	6	123376961	123376961	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686A>C	p.His229Pro	p.H229P	ENST00000275162	5/6	23	17	5	35	35	0	CLVS2,missense_variant,p.His83Pro,ENST00000368438,;CLVS2,missense_variant,p.His229Pro,ENST00000275162,;	C	ENSG00000146352	ENST00000275162	Transcript	missense_variant	2021	686	229	H/P	cAt/cCt	.	.	.	1	CLVS2	HGNC	23046	protein_coding	YES	CCDS34525.1	ENSP00000275162	CLVS2_HUMAN	.	UPI000013DA49	.	deleterious(0)	probably_damaging(0.988)	5/6	.	PROSITE_profiles:PS50191,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF73,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087,Prints_domain:PR00180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGCATGGTA	.	5	ESCA
EPB41L2	0	.	GRCh37	6	131186736	131186736	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2769G>C	p.%3D	p.L923L	ENST00000337057	17/20	75	49	25	66	66	0	EPB41L2,synonymous_variant,p.%3D,ENST00000525193,;EPB41L2,synonymous_variant,p.%3D,ENST00000527659,;EPB41L2,synonymous_variant,p.%3D,ENST00000524581,;EPB41L2,synonymous_variant,p.%3D,ENST00000445890,;EPB41L2,synonymous_variant,p.%3D,ENST00000528282,;EPB41L2,synonymous_variant,p.%3D,ENST00000530481,;EPB41L2,synonymous_variant,p.%3D,ENST00000337057,;EPB41L2,synonymous_variant,p.%3D,ENST00000531410,;EPB41L2,synonymous_variant,p.%3D,ENST00000527017,;EPB41L2,synonymous_variant,p.%3D,ENST00000368128,;EPB41L2,synonymous_variant,p.%3D,ENST00000529208,;EPB41L2,synonymous_variant,p.%3D,ENST00000527411,;EPB41L2,intron_variant,,ENST00000392427,;EPB41L2,intron_variant,,ENST00000530757,;EPB41L2,intron_variant,,ENST00000525271,;EPB41L2,downstream_gene_variant,,ENST00000527423,;EPB41L2,downstream_gene_variant,,ENST00000456097,;EPB41L2,downstream_gene_variant,,ENST00000525198,;EPB41L2,downstream_gene_variant,,ENST00000533912,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000368126,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000452150,;EPB41L2,downstream_gene_variant,,ENST00000534166,;	G	ENSG00000079819	ENST00000337057	Transcript	synonymous_variant	2951	2769	923	L	ctG/ctC	.	.	.	-1	EPB41L2	HGNC	3379	protein_coding	YES	CCDS5141.1	ENSP00000338481	E41L2_HUMAN	E9PRG1_HUMAN,E9PQN0_HUMAN,E9PQD2_HUMAN,E9PJP4_HUMAN,E9PIG0_HUMAN	UPI0000129AF9	.	.	.	17/20	.	hmmpanther:PTHR23280:SF17,hmmpanther:PTHR23280,Pfam_domain:PF05902,PIRSF_domain:PIRSF002304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGTCAGTAA	.	5	ESCA
TPMT	0	.	GRCh37	6	18130964	18130964	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673G>C	p.Glu225Gln	p.E225Q	ENST00000309983	9/9	45	38	6	66	66	0	TPMT,missense_variant,p.Glu225Gln,ENST00000309983,;	G	ENSG00000137364	ENST00000309983	Transcript	missense_variant	759	673	225	E/Q	Gaa/Caa	.	.	.	-1	TPMT	HGNC	12014	protein_coding	YES	CCDS4543.1	ENSP00000312304	TPMT_HUMAN	.	UPI0000137261	.	tolerated(0.11)	benign(0.014)	9/9	.	PROSITE_profiles:PS51585,HAMAP:MF_00812,hmmpanther:PTHR10259,Gene3D:3.40.50.150,Pfam_domain:PF05724,PIRSF_domain:PIRSF023956,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGTTCTTCAA	.	5	ESCA
COL11A2	0	.	GRCh37	6	33147260	33147260	+	Missense_Mutation	SNP	G	G	A	rs143965711	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1193C>T	p.Ala398Val	p.A398V	ENST00000374708	12/64	70	55	14	70	70	0	COL11A2,missense_variant,p.Ala424Val,ENST00000395197,;COL11A2,missense_variant,p.Ala437Val,ENST00000374713,;COL11A2,missense_variant,p.Ala377Val,ENST00000361917,;COL11A2,missense_variant,p.Ala403Val,ENST00000374712,;COL11A2,missense_variant,p.Ala463Val,ENST00000357486,;COL11A2,missense_variant,p.Ala398Val,ENST00000374708,;COL11A2,missense_variant,p.Ala484Val,ENST00000457788,;COL11A2,missense_variant,p.Ala484Val,ENST00000341947,;COL11A2,missense_variant,p.Ala458Val,ENST00000374714,;COL11A2,upstream_gene_variant,,ENST00000477772,;	A	ENSG00000204248	ENST00000374708	Transcript	missense_variant	1452	1193	398	A/V	gCg/gTg	rs143965711	.	.	-1	COL11A2	HGNC	2187	protein_coding	YES	CCDS43452.1	ENSP00000363840	.	Q6LCP7_HUMAN,Q4VXY6_HUMAN	UPI000013E9A5	.	.	possibly_damaging(0.695)	12/64	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF509	.	.	.	.	.	.	.	A:0.0003	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGCGCCAGC	byCluster	5	ESCA
TCP11	0	.	GRCh37	6	35087129	35087129	+	Silent	SNP	A	A	G	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1194T>C	p.%3D	p.S398S	ENST00000311875	9/10	71	51	20	61	61	0	TCP11,synonymous_variant,p.%3D,ENST00000244645,;TCP11,synonymous_variant,p.%3D,ENST00000311875,;TCP11,synonymous_variant,p.%3D,ENST00000512012,;TCP11,synonymous_variant,p.%3D,ENST00000412155,;TCP11,synonymous_variant,p.%3D,ENST00000502480,;TCP11,synonymous_variant,p.%3D,ENST00000418521,;TCP11,synonymous_variant,p.%3D,ENST00000373974,;TCP11,synonymous_variant,p.%3D,ENST00000373979,;TCP11,synonymous_variant,p.%3D,ENST00000444780,;TCP11,downstream_gene_variant,,ENST00000486638,;TCP11,downstream_gene_variant,,ENST00000507706,;TCP11,downstream_gene_variant,,ENST00000492680,;TCP11,downstream_gene_variant,,ENST00000505400,;TCP11,3_prime_UTR_variant,,ENST00000505911,;TCP11,3_prime_UTR_variant,,ENST00000455706,;TCP11,3_prime_UTR_variant,,ENST00000504758,;TCP11,3_prime_UTR_variant,,ENST00000427376,;TCP11,downstream_gene_variant,,ENST00000509988,;TCP11,downstream_gene_variant,,ENST00000469514,;TCP11,downstream_gene_variant,,ENST00000479418,;TCP11,downstream_gene_variant,,ENST00000505335,;	G	ENSG00000124678	ENST00000311875	Transcript	synonymous_variant	1612	1194	398	S	tcT/tcC	COSM376308,COSM376307	.	.	-1	TCP11	HGNC	11658	protein_coding	YES	CCDS47413.1	ENSP00000308708	TCP11_HUMAN	D6RGY5_HUMAN,D6RGC0_HUMAN,D6RG02_HUMAN,D6R9R9_HUMAN,D6R989_HUMAN,B7Z7Q2_HUMAN	UPI0000EE4D7F	.	.	.	9/10	.	hmmpanther:PTHR12832:SF16,hmmpanther:PTHR12832,Pfam_domain:PF05794	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGAGATAC	.	5	ESCA
KIF6	0	.	GRCh37	6	39693181	39693181	+	5'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-95G>A	.	.	ENST00000287152	1/23	20	17	3	27	27	0	KIF6,5_prime_UTR_variant,,ENST00000287152,;KIF6,5_prime_UTR_variant,,ENST00000373216,;KIF6,upstream_gene_variant,,ENST00000373215,;KIF6,upstream_gene_variant,,ENST00000538893,;KIF6,non_coding_transcript_exon_variant,,ENST00000482238,;	T	ENSG00000164627	ENST00000287152	Transcript	5_prime_UTR_variant	1	.	.	.	.	.	.	.	-1	KIF6	HGNC	21202	protein_coding	YES	CCDS4844.1	ENSP00000287152	KIF6_HUMAN	.	UPI0000457436	.	.	.	1/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCAACAGTAG	.	4	ESCA
DST	0	.	GRCh37	6	56489969	56489969	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3205C>G	p.Leu1069Val	p.L1069V	ENST00000244364	21/84	85	69	15	92	92	0	DST,missense_variant,p.Leu67Val,ENST00000522360,;DST,missense_variant,p.Leu1069Val,ENST00000439203,;DST,missense_variant,p.Leu1069Val,ENST00000446842,;DST,missense_variant,p.Leu1395Val,ENST00000370788,;DST,missense_variant,p.Leu1069Val,ENST00000244364,;DST,missense_variant,p.Leu1435Val,ENST00000520645,;DST,missense_variant,p.Leu1069Val,ENST00000370765,;DST,missense_variant,p.Leu1573Val,ENST00000370754,;DST,missense_variant,p.Leu1395Val,ENST00000361203,;DST,missense_variant,p.Leu1395Val,ENST00000370769,;DST,missense_variant,p.Leu1395Val,ENST00000312431,;DST,missense_variant,p.Leu1395Val,ENST00000421834,;DST,missense_variant,p.Leu1069Val,ENST00000518935,;	C	ENSG00000151914	ENST00000244364	Transcript	missense_variant	3413	3205	1069	L/V	Ctc/Gtc	COSM1697465,COSM1697464,COSM1697466,COSM1697467	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	benign(0.001)	21/84	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF38,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGAGATCTG	.	5	ESCA
LSMEM1	0	.	GRCh37	7	112126404	112126404	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128-574C>T	.	.	ENST00000312849	.	64	54	10	48	48	0	LSMEM1,splice_region_variant,,ENST00000429049,;LSMEM1,intron_variant,,ENST00000312849,;LSMEM1,intron_variant,,ENST00000439068,;LSMEM1,non_coding_transcript_exon_variant,,ENST00000486022,;LSMEM1,upstream_gene_variant,,ENST00000471030,;LSMEM1,splice_region_variant,,ENST00000455302,;	T	ENSG00000181016	ENST00000312849	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LSMEM1	HGNC	22036	protein_coding	YES	CCDS5756.1	ENSP00000323304	LSME1_HUMAN	.	UPI000006F884	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TATTTCAGTGT	.	3	ESCA
NOD1	0	.	GRCh37	7	30477261	30477261	+	Missense_Mutation	SNP	T	T	A	rs55924701	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2465A>T	p.Asn822Ile	p.N822I	ENST00000222823	10/14	39	27	12	57	57	0	NOD1,missense_variant,p.Asn822Ile,ENST00000222823,;NOD1,3_prime_UTR_variant,,ENST00000434755,;NOD1,intron_variant,,ENST00000489614,;NOD1,upstream_gene_variant,,ENST00000467706,;	A	ENSG00000106100	ENST00000222823	Transcript	missense_variant	2991	2465	822	N/I	aAt/aTt	rs55924701	.	.	-1	NOD1	HGNC	16390	protein_coding	YES	CCDS5427.1	ENSP00000222823	NOD1_HUMAN	Q7Z2K1_HUMAN,C9J8X8_HUMAN	UPI00000375EE	.	deleterious(0)	probably_damaging(1)	10/14	.	Superfamily_domains:SSF52047,SMART_domains:SM00368,Pfam_domain:PF13516,Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTGATTGCCC	byCluster	5	ESCA
FAM220A	0	.	GRCh37	7	6370735	6370735	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51G>T	p.Gln17His	p.Q17H	ENST00000313324	2/2	30	23	7	51	51	0	FAM220A,missense_variant,p.Gln17His,ENST00000524898,;FAM220A,missense_variant,p.Gln17His,ENST00000313324,;FAM220A,missense_variant,p.Gln17His,ENST00000530143,;FAM220A,downstream_gene_variant,,ENST00000578372,;FAM220A,downstream_gene_variant,,ENST00000533877,;	A	ENSG00000178397	ENST00000313324	Transcript	missense_variant	519	51	17	Q/H	caG/caT	.	.	.	-1	FAM220A	HGNC	22422	protein_coding	YES	CCDS34599.1	ENSP00000317289	F220A_HUMAN	E9PQY0_HUMAN,E9PQC6_HUMAN	UPI000013F4F0	.	tolerated(0.14)	benign(0.089)	2/2	.	hmmpanther:PTHR31980,Pfam_domain:PF15487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGCCTGCTG	.	5	ESCA
ZNF107	0	.	GRCh37	7	64168548	64168548	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1866C>A	p.Asn622Lys	p.N622K	ENST00000395391	4/4	54	40	13	62	62	0	ZNF107,missense_variant,p.Asn622Lys,ENST00000344930,;ZNF107,missense_variant,p.Asn622Lys,ENST00000395391,;ZNF107,missense_variant,p.Asn622Lys,ENST00000423627,;ZNF107,downstream_gene_variant,,ENST00000360117,;	A	ENSG00000196247	ENST00000395391	Transcript	missense_variant	3241	1866	622	N/K	aaC/aaA	.	.	.	1	ZNF107	HGNC	12887	protein_coding	YES	CCDS5527.1	ENSP00000378789	ZN107_HUMAN	Q9H3U2_HUMAN,C9JSF9_HUMAN	UPI000000DBC2	.	tolerated(0.39)	benign(0.101)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF121,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAAACCTAAC	.	5	ESCA
PCLO	0	.	GRCh37	7	82583352	82583352	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6917A>G	p.Lys2306Arg	p.K2306R	ENST00000333891	5/25	58	47	11	65	65	0	PCLO,missense_variant,p.Lys2306Arg,ENST00000333891,;PCLO,missense_variant,p.Lys2306Arg,ENST00000423517,;PCLO,upstream_gene_variant,,ENST00000437081,;	C	ENSG00000186472	ENST00000333891	Transcript	missense_variant	7255	6917	2306	K/R	aAg/aGg	.	.	.	-1	PCLO	HGNC	13406	protein_coding	YES	CCDS47630.1	ENSP00000334319	PCLO_HUMAN	.	UPI0001573469	.	.	unknown(0)	5/25	.	hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCCTTCTTG	.	5	ESCA
YWHAZ	0	.	GRCh37	8	101931859	101931859	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1062A>G	.	.	ENST00000395957	7/7	19	14	5	19	19	0	YWHAZ,3_prime_UTR_variant,,ENST00000395957,;YWHAZ,3_prime_UTR_variant,,ENST00000395958,;YWHAZ,3_prime_UTR_variant,,ENST00000395956,;YWHAZ,3_prime_UTR_variant,,ENST00000457309,;YWHAZ,3_prime_UTR_variant,,ENST00000353245,;YWHAZ,downstream_gene_variant,,ENST00000419477,;YWHAZ,downstream_gene_variant,,ENST00000522819,;YWHAZ,downstream_gene_variant,,ENST00000521309,;YWHAZ,downstream_gene_variant,,ENST00000395951,;YWHAZ,downstream_gene_variant,,ENST00000521607,;YWHAZ,downstream_gene_variant,,ENST00000395953,;YWHAZ,downstream_gene_variant,,ENST00000395948,;YWHAZ,downstream_gene_variant,,ENST00000522542,;YWHAZ,intron_variant,,ENST00000523848,;YWHAZ,downstream_gene_variant,,ENST00000518736,;YWHAZ,downstream_gene_variant,,ENST00000517727,;YWHAZ,downstream_gene_variant,,ENST00000480304,;	C	ENSG00000164924	ENST00000395957	Transcript	3_prime_UTR_variant	2142	.	.	.	.	.	.	.	-1	YWHAZ	HGNC	12855	protein_coding	YES	CCDS6290.1	ENSP00000379287	1433Z_HUMAN	Q6LD62_HUMAN,Q2F831_HUMAN,H0YB80_HUMAN,E9PD24_HUMAN,E7EVZ2_HUMAN,E7ESK7_HUMAN,E5RIR4_HUMAN,E5RGE1_HUMAN,D0PNI1_HUMAN,B7Z2E6_HUMAN,B0AZS6_HUMAN	UPI000003300D	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAATTTCCT	.	5	ESCA
RP1	0	.	GRCh37	8	55542624	55542624	+	Missense_Mutation	SNP	T	T	C	rs539588544	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6182T>C	p.Ile2061Thr	p.I2061T	ENST00000220676	4/4	39	28	11	41	41	0	RP1,missense_variant,p.Ile2061Thr,ENST00000220676,;	C	ENSG00000104237	ENST00000220676	Transcript	missense_variant	6330	6182	2061	I/T	aTc/aCc	rs539588544	.	.	1	RP1	HGNC	10263	protein_coding	YES	CCDS6160.1	ENSP00000220676	RP1_HUMAN	A0FDN2_HUMAN	UPI000013455B	.	deleterious(0.01)	benign(0.231)	4/4	.	hmmpanther:PTHR23005:SF4,hmmpanther:PTHR23005	C:0.0002	C:0	C:0	.	C:0.001	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAATCTTTA	by1000G	5	ESCA
RRS1	0	.	GRCh37	8	67342902	67342902	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*438A>G	.	.	ENST00000320270	1/1	40	31	8	34	34	0	RRS1,3_prime_UTR_variant,,ENST00000320270,;ADHFE1,intron_variant,,ENST00000523113,;ADHFE1,upstream_gene_variant,,ENST00000415254,;ADHFE1,upstream_gene_variant,,ENST00000396623,;ADHFE1,upstream_gene_variant,,ENST00000379385,;RP11-346I3.4,upstream_gene_variant,,ENST00000499642,;ADHFE1,upstream_gene_variant,,ENST00000496501,;ADHFE1,upstream_gene_variant,,ENST00000422166,;ADHFE1,upstream_gene_variant,,ENST00000449512,;ADHFE1,upstream_gene_variant,,ENST00000424777,;ADHFE1,upstream_gene_variant,,ENST00000466920,;ADHFE1,upstream_gene_variant,,ENST00000443372,;ADHFE1,upstream_gene_variant,,ENST00000419955,;ADHFE1,upstream_gene_variant,,ENST00000426810,;ADHFE1,upstream_gene_variant,,ENST00000276576,;ADHFE1,upstream_gene_variant,,ENST00000431959,;ADHFE1,upstream_gene_variant,,ENST00000463261,;ADHFE1,upstream_gene_variant,,ENST00000396621,;	G	ENSG00000179041	ENST00000320270	Transcript	3_prime_UTR_variant	1640	.	.	.	.	.	.	.	1	RRS1	HGNC	17083	protein_coding	YES	CCDS6189.1	ENSP00000322396	RRS1_HUMAN	.	UPI0000134B8A	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGAATTGAA	.	5	ESCA
HEMGN	0	.	GRCh37	9	100692787	100692787	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.890T>C	p.Leu297Pro	p.L297P	ENST00000259456	4/5	56	53	3	35	35	0	HEMGN,missense_variant,p.Leu297Pro,ENST00000259456,;	G	ENSG00000136929	ENST00000259456	Transcript	missense_variant	1034	890	297	L/P	cTt/cCt	.	.	.	-1	HEMGN	HGNC	17509	protein_coding	YES	CCDS6731.1	ENSP00000259456	HEMGN_HUMAN	.	UPI000004D311	.	deleterious(0.05)	benign(0.013)	4/5	.	hmmpanther:PTHR15993:SF6,hmmpanther:PTHR15993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAAAGGCCT	.	2	ESCA
CDK5RAP2	0	.	GRCh37	9	123173662	123173662	+	Missense_Mutation	SNP	T	T	C	rs748523387	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4388A>G	p.Asn1463Ser	p.N1463S	ENST00000349780	29/38	38	11	27	41	41	0	CDK5RAP2,missense_variant,p.Asn857Ser,ENST00000416449,;CDK5RAP2,missense_variant,p.Asn1463Ser,ENST00000349780,;CDK5RAP2,missense_variant,p.Asn1431Ser,ENST00000360822,;CDK5RAP2,missense_variant,p.Asn473Ser,ENST00000425647,;CDK5RAP2,missense_variant,p.Asn1463Ser,ENST00000360190,;CDK5RAP2,missense_variant,p.Asn1422Ser,ENST00000359309,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000483412,;	C	ENSG00000136861	ENST00000349780	Transcript	missense_variant	4568	4388	1463	N/S	aAt/aGt	rs748523387	.	.	-1	CDK5RAP2	HGNC	18672	protein_coding	YES	CCDS6823.1	ENSP00000343818	CK5P2_HUMAN	F8WBJ0_HUMAN,C9K0C9_HUMAN	UPI0000367673	.	tolerated(0.11)	possibly_damaging(0.899)	29/38	.	hmmpanther:PTHR13895,hmmpanther:PTHR13895:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCATTGAGG	byFrequency	5	ESCA
PSMD5	0	.	GRCh37	9	123580063	123580070	+	3'UTR	DEL	TCTGACAT	TCTGACAT	-	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	TCTGACAT	TCTGACAT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*114_*121delATGTCAGA	.	.	ENST00000210313	10/10	20	9	11	15	15	0	PSMD5,3_prime_UTR_variant,,ENST00000210313,;PSMD5,intron_variant,,ENST00000604848,;PSMD5,intron_variant,,ENST00000373920,;PSMD5,downstream_gene_variant,,ENST00000373904,;RP11-27I1.6,upstream_gene_variant,,ENST00000603920,;	-	ENSG00000095261	ENST00000210313	Transcript	3_prime_UTR_variant	1704-1711	.	.	.	.	.	.	.	-1	PSMD5	HGNC	9563	protein_coding	YES	CCDS6824.1	ENSP00000210313	PSMD5_HUMAN	.	UPI0000132785	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTAACATCTGACATTCCAT	.	2	ESCA
TOPORS	0	.	GRCh37	9	32543771	32543771	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.752A>T	p.Gln251Leu	p.Q251L	ENST00000360538	3/3	20	8	11	32	32	0	TOPORS,missense_variant,p.Gln251Leu,ENST00000360538,;TOPORS,missense_variant,p.Gln186Leu,ENST00000379858,;AL353671.2,upstream_gene_variant,,ENST00000359975,;AL353671.1,downstream_gene_variant,,ENST00000366355,;	A	ENSG00000197579	ENST00000360538	Transcript	missense_variant	869	752	251	Q/L	cAa/cTa	.	.	.	-1	TOPORS	HGNC	21653	protein_coding	YES	CCDS6527.1	ENSP00000353735	TOPRS_HUMAN	.	UPI000006F223	.	deleterious(0.02)	possibly_damaging(0.776)	3/3	.	hmmpanther:PTHR12456:SF12,hmmpanther:PTHR12456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCTTGAATT	.	5	ESCA
FAM214B	0	.	GRCh37	9	35106621	35106621	+	Missense_Mutation	SNP	G	G	A	rs373199885	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.973C>T	p.Arg325Trp	p.R325W	ENST00000378561	4/8	66	36	29	81	81	0	FAM214B,missense_variant,p.Arg325Trp,ENST00000378554,;FAM214B,missense_variant,p.Arg20Trp,ENST00000378566,;FAM214B,missense_variant,p.Arg325Trp,ENST00000603301,;FAM214B,missense_variant,p.Arg325Trp,ENST00000322813,;FAM214B,missense_variant,p.Arg325Trp,ENST00000605244,;FAM214B,missense_variant,p.Arg325Trp,ENST00000488109,;FAM214B,missense_variant,p.Arg325Trp,ENST00000378557,;FAM214B,missense_variant,p.Arg325Trp,ENST00000378561,;STOML2,upstream_gene_variant,,ENST00000452248,;STOML2,upstream_gene_variant,,ENST00000356493,;FAM214B,downstream_gene_variant,,ENST00000605104,;STOML2,upstream_gene_variant,,ENST00000487490,;FAM214B,downstream_gene_variant,,ENST00000605392,;	A	ENSG00000005238	ENST00000378561	Transcript	missense_variant	4029	973	325	R/W	Cgg/Tgg	rs373199885	.	.	-1	FAM214B	HGNC	25666	protein_coding	YES	CCDS6578.1	ENSP00000367823	F214B_HUMAN	.	UPI0000169E3E	.	tolerated(0.11)	benign(0)	4/8	.	hmmpanther:PTHR13199:SF12,hmmpanther:PTHR13199,Low_complexity_(Seg):seg	A:0.0010	A:0.0038	A:0	.	A:0	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCGGAGGC	byFrequency|byCluster|by1000G	5	ESCA
IDH3G	0	.	GRCh37	X	153052328	153052328	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852C>T	p.%3D	p.C284C	ENST00000217901	10/13	72	53	19	101	101	0	IDH3G,synonymous_variant,p.%3D,ENST00000454076,;IDH3G,synonymous_variant,p.%3D,ENST00000444450,;IDH3G,synonymous_variant,p.%3D,ENST00000427365,;IDH3G,synonymous_variant,p.%3D,ENST00000370093,;IDH3G,synonymous_variant,p.%3D,ENST00000217901,;IDH3G,synonymous_variant,p.%3D,ENST00000370092,;SRPK3,downstream_gene_variant,,ENST00000370108,;SRPK3,downstream_gene_variant,,ENST00000370100,;SRPK3,downstream_gene_variant,,ENST00000489426,;SRPK3,downstream_gene_variant,,ENST00000430541,;SRPK3,downstream_gene_variant,,ENST00000393786,;SRPK3,downstream_gene_variant,,ENST00000458681,;SRPK3,downstream_gene_variant,,ENST00000370104,;SRPK3,downstream_gene_variant,,ENST00000370101,;IDH3G,downstream_gene_variant,,ENST00000444338,;IDH3G,downstream_gene_variant,,ENST00000497043,;IDH3G,downstream_gene_variant,,ENST00000491235,;IDH3G,downstream_gene_variant,,ENST00000495356,;IDH3G,downstream_gene_variant,,ENST00000461215,;	A	ENSG00000067829	ENST00000217901	Transcript	synonymous_variant	1049	852	284	C	tgC/tgT	.	.	.	-1	IDH3G	HGNC	5386	protein_coding	YES	CCDS14730.1	ENSP00000217901	IDH3G_HUMAN	Q2Q9S4_HUMAN,E7EQB8_HUMAN,D3DWV9_HUMAN	UPI0000000DBC	.	.	.	10/13	.	hmmpanther:PTHR11835:SF42,hmmpanther:PTHR11835,PROSITE_patterns:PS00470,TIGRFAM_domain:TIGR00175,Pfam_domain:PF00180,Gene3D:3.40.718.10,Superfamily_domains:SSF53659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGCGCAGAC	.	5	ESCA
CD99	0	.	GRCh37	X	2656238	2656238	+	Intron	SNP	C	C	A	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.476-3C>A	.	.	ENST00000381192	.	105	71	34	149	149	0	CD99,splice_region_variant,,ENST00000381192,;CD99,splice_region_variant,,ENST00000381187,;CD99,downstream_gene_variant,,ENST00000381184,;CD99,downstream_gene_variant,,ENST00000482405,;CD99,3_prime_UTR_variant,,ENST00000381177,;	A	ENSG00000002586	ENST00000381192	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	CD99	HGNC	7082	protein_coding	YES	CCDS14119.1	ENSP00000370588	CD99_HUMAN	.	UPI0000000C42	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTTCAGCAG	.	4	ESCA
SHROOM4	0	.	GRCh37	X	50381301	50381301	+	Missense_Mutation	SNP	C	C	T	rs145605338	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277G>A	p.Ala93Thr	p.A93T	ENST00000376020	3/9	38	34	4	61	61	0	SHROOM4,missense_variant,p.Ala93Thr,ENST00000376020,;SHROOM4,missense_variant,p.Ala93Thr,ENST00000289292,;SHROOM4,5_prime_UTR_variant,,ENST00000460112,;	T	ENSG00000158352	ENST00000376020	Transcript	missense_variant	303	277	93	A/T	Gcc/Acc	rs145605338	.	.	-1	SHROOM4	HGNC	29215	protein_coding	YES	CCDS35277.1	ENSP00000365188	SHRM4_HUMAN	.	UPI00001C2068	.	tolerated(0.52)	benign(0.004)	3/9	.	hmmpanther:PTHR15012:SF31,hmmpanther:PTHR15012,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	T:0.0013	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGGCGTTCC	byFrequency|byCluster	4	ESCA
MAGED1	0	.	GRCh37	X	51636761	51636761	+	5'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-127C>T	.	.	ENST00000375695	1/14	78	74	4	82	82	0	MAGED1,5_prime_UTR_variant,,ENST00000326587,;MAGED1,5_prime_UTR_variant,,ENST00000375722,;MAGED1,5_prime_UTR_variant,,ENST00000375695,;MAGED1,intron_variant,,ENST00000375772,;MAGED1,non_coding_transcript_exon_variant,,ENST00000494718,;MAGED1,non_coding_transcript_exon_variant,,ENST00000485420,;MAGED1,non_coding_transcript_exon_variant,,ENST00000470461,;MAGED1,upstream_gene_variant,,ENST00000482188,;MAGED1,upstream_gene_variant,,ENST00000473931,;MAGED1,upstream_gene_variant,,ENST00000482599,;	T	ENSG00000179222	ENST00000375695	Transcript	5_prime_UTR_variant	27	.	.	.	.	.	.	.	1	MAGED1	HGNC	6813	protein_coding	YES	CCDS35279.1	ENSP00000364847	MAGD1_HUMAN	.	UPI0000074161	.	.	.	1/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGTGCGGCTG	.	2	ESCA
TSPYL2	0	.	GRCh37	X	53114892	53114892	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1318A>G	p.Ile440Val	p.I440V	ENST00000375442	6/7	41	26	14	33	33	0	TSPYL2,missense_variant,p.Ile440Val,ENST00000375442,;TSPYL2,missense_variant,p.Ile115Val,ENST00000579390,;TSPYL2,3_prime_UTR_variant,,ENST00000578306,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000553557,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000463525,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000556808,;	G	ENSG00000184205	ENST00000375442	Transcript	missense_variant	1450	1318	440	I/V	Atc/Gtc	.	.	.	1	TSPYL2	HGNC	24358	protein_coding	YES	CCDS14350.1	ENSP00000364591	TSYL2_HUMAN	.	UPI000004B6D6	.	deleterious_low_confidence(0.03)	benign(0.122)	6/7	.	hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGAGATCTCA	.	5	ESCA
PCDH11X	0	.	GRCh37	X	91873845	91873845	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA4G-01A-11D-A37C-09	TCGA-VR-AA4G-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3950C>T	p.Ser1317Leu	p.S1317L	ENST00000373094	7/7	74	50	24	85	85	0	PCDH11X,missense_variant,p.Ser1309Leu,ENST00000406881,;PCDH11X,missense_variant,p.Ser1307Leu,ENST00000373097,;PCDH11X,missense_variant,p.Ser1317Leu,ENST00000373094,;PCDH11X,missense_variant,p.Ser1280Leu,ENST00000373088,;PCDH11X,missense_variant,p.Ser1299Leu,ENST00000361655,;PCDH11X,missense_variant,p.Ser1280Leu,ENST00000298274,;PCDH11X,3_prime_UTR_variant,,ENST00000504220,;	T	ENSG00000102290	ENST00000373094	Transcript	missense_variant	4795	3950	1317	S/L	tCa/tTa	COSM462165	.	.	1	PCDH11X	HGNC	8656	protein_coding	YES	CCDS14461.1	ENSP00000362186	PC11X_HUMAN	Q70LT5_HUMAN,Q70LT4_HUMAN	UPI0000070BD8	.	deleterious_low_confidence(0)	probably_damaging(0.989)	7/7	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF15	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTCAATTA	.	5	ESCA
WBP1L	0	.	GRCh37	10	104574488	104574488	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1400G>C	.	.	ENST00000448841	4/4	40	25	15	60	60	0	WBP1L,3_prime_UTR_variant,,ENST00000448841,;WBP1L,3_prime_UTR_variant,,ENST00000369889,;	C	ENSG00000166272	ENST00000448841	Transcript	3_prime_UTR_variant	2576	.	.	.	.	.	.	.	1	WBP1L	HGNC	23510	protein_coding	YES	CCDS44473.1	ENSP00000414721	WBP1L_HUMAN	Q1EG69_HUMAN	UPI0000EE3B72	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCGATAGG	.	5	ESCA
USP6NL	0	.	GRCh37	10	11505038	11505038	+	Missense_Mutation	SNP	G	G	A	rs753637873	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1940C>T	p.Pro647Leu	p.P647L	ENST00000277575	14/14	70	53	17	100	100	0	USP6NL,missense_variant,p.Pro630Leu,ENST00000609104,;USP6NL,missense_variant,p.Pro653Leu,ENST00000379237,;USP6NL,missense_variant,p.Pro647Leu,ENST00000277575,;	A	ENSG00000148429	ENST00000277575	Transcript	missense_variant	1983	1940	647	P/L	cCc/cTc	rs753637873	.	.	-1	USP6NL	HGNC	16858	protein_coding	YES	CCDS44357.1	ENSP00000277575	US6NL_HUMAN	.	UPI0000251ED1	.	deleterious_low_confidence(0.04)	probably_damaging(1)	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAGGGGGGA	.	5	ESCA
RAB11FIP2	0	.	GRCh37	10	119764789	119764789	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3720C>G	.	.	ENST00000355624	5/5	51	39	11	53	53	0	RAB11FIP2,3_prime_UTR_variant,,ENST00000355624,;RAB11FIP2,downstream_gene_variant,,ENST00000369199,;RAB11FIP2,downstream_gene_variant,,ENST00000476207,;	C	ENSG00000107560	ENST00000355624	Transcript	3_prime_UTR_variant	5699	.	.	.	.	.	.	.	-1	RAB11FIP2	HGNC	29152	protein_coding	YES	CCDS7602.1	ENSP00000347839	RFIP2_HUMAN	.	UPI0000073B4B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTGATGGA	.	5	ESCA
BAG3	0	.	GRCh37	10	121436865	121436865	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*71G>C	.	.	ENST00000369085	4/4	12	8	4	20	20	0	BAG3,3_prime_UTR_variant,,ENST00000369085,;BAG3,downstream_gene_variant,,ENST00000450186,;	C	ENSG00000151929	ENST00000369085	Transcript	3_prime_UTR_variant	2105	.	.	.	.	.	.	.	1	BAG3	HGNC	939	protein_coding	YES	CCDS7615.1	ENSP00000358081	BAG3_HUMAN	.	UPI0000000C7A	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TTTCAGAGACT	.	3	ESCA
CUBN	0	.	GRCh37	10	16878337	16878337	+	Silent	SNP	C	C	T	rs147563157	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10077G>A	p.%3D	p.S3359S	ENST00000377833	63/67	52	49	3	91	91	0	CUBN,synonymous_variant,p.%3D,ENST00000377833,;	T	ENSG00000107611	ENST00000377833	Transcript	synonymous_variant	10143	10077	3359	S	tcG/tcA	rs147563157	.	.	-1	CUBN	HGNC	2548	protein_coding	YES	CCDS7113.1	ENSP00000367064	CUBN_HUMAN	B3KQA6_HUMAN	UPI00001AE8F4	.	.	.	63/67	.	PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	G:0.0002	G:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACAGCCGAAGC	byCluster|by1000G	2	ESCA
MLLT10	0	.	GRCh37	10	22015215	22015215	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1921C>T	p.His641Tyr	p.H641Y	ENST00000307729	15/23	26	21	5	53	53	0	MLLT10,missense_variant,p.His641Tyr,ENST00000446906,;MLLT10,missense_variant,p.His300Tyr,ENST00000438473,;MLLT10,missense_variant,p.His641Tyr,ENST00000377059,;MLLT10,missense_variant,p.His641Tyr,ENST00000307729,;MLLT10,missense_variant,p.His657Tyr,ENST00000377072,;	T	ENSG00000078403	ENST00000307729	Transcript	missense_variant	2099	1921	641	H/Y	Cat/Tat	.	.	.	1	MLLT10	HGNC	16063	protein_coding	YES	CCDS55708.1	ENSP00000307411	AF10_HUMAN	Q71UR7_HUMAN,B4DVS6_HUMAN	UPI00001F8FF7	.	deleterious(0)	benign(0.114)	15/23	.	hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF86	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCATATG	.	5	ESCA
WAC	0	.	GRCh37	10	28821727	28821727	+	5'Flank	SNP	C	C	G	rs541145912	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000354911	.	35	25	9	78	78	0	WAC,5_prime_UTR_variant,,ENST00000375646,;WAC,5_prime_UTR_variant,,ENST00000526722,;WAC,5_prime_UTR_variant,,ENST00000375664,;WAC,upstream_gene_variant,,ENST00000442148,;WAC,upstream_gene_variant,,ENST00000420266,;WAC,upstream_gene_variant,,ENST00000414108,;WAC,upstream_gene_variant,,ENST00000428935,;WAC,upstream_gene_variant,,ENST00000354911,;WAC,upstream_gene_variant,,ENST00000448193,;WAC,upstream_gene_variant,,ENST00000347934,;WAC-AS1,upstream_gene_variant,,ENST00000528337,;WAC-AS1,upstream_gene_variant,,ENST00000527986,;WAC,non_coding_transcript_exon_variant,,ENST00000528491,;WAC,non_coding_transcript_exon_variant,,ENST00000532233,;WAC,upstream_gene_variant,,ENST00000530865,;WAC,upstream_gene_variant,,ENST00000345541,;WAC,upstream_gene_variant,,ENST00000439676,;WAC,upstream_gene_variant,,ENST00000424454,;	G	ENSG00000095787	ENST00000354911	Transcript	upstream_gene_variant	.	.	.	.	.	rs541145912	.	621	1	WAC	HGNC	17327	protein_coding	YES	CCDS7159.1	ENSP00000346986	WAC_HUMAN	J3QTA0_HUMAN,E9PMZ7_HUMAN,C9JVK6_HUMAN,C9JMU2_HUMAN,C9JD58_HUMAN	UPI000013D398	.	.	.	.	.	.	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTCGCGCC	by1000G	5	ESCA
ITIH2	0	.	GRCh37	10	7786241	7786241	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2406G>C	p.Gln802His	p.Q802H	ENST00000358415	18/21	25	16	9	35	35	0	ITIH2,missense_variant,p.Gln791His,ENST00000379587,;ITIH2,missense_variant,p.Gln802His,ENST00000358415,;	C	ENSG00000151655	ENST00000358415	Transcript	missense_variant	2572	2406	802	Q/H	caG/caC	.	.	.	1	ITIH2	HGNC	6167	protein_coding	YES	CCDS31141.1	ENSP00000351190	ITIH2_HUMAN	.	UPI000036665E	.	deleterious(0.01)	benign(0.013)	18/21	.	hmmpanther:PTHR10338:SF14,hmmpanther:PTHR10338,Pfam_domain:PF06668	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCAGAGGCA	.	5	ESCA
TM9SF3	0	.	GRCh37	10	98281716	98281716	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*304G>A	.	.	ENST00000371142	15/15	65	44	20	90	90	0	TM9SF3,3_prime_UTR_variant,,ENST00000371142,;TM9SF3,downstream_gene_variant,,ENST00000485093,;	T	ENSG00000077147	ENST00000371142	Transcript	3_prime_UTR_variant	2291	.	.	.	.	.	.	.	-1	TM9SF3	HGNC	21529	protein_coding	YES	CCDS7450.1	ENSP00000360184	TM9S3_HUMAN	Q96K55_HUMAN,Q96JZ5_HUMAN,Q8WUB5_HUMAN,Q5TB53_HUMAN	UPI000013684E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCACTGA	.	5	ESCA
ZNF259	0	.	GRCh37	11	116652907	116652907	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1146G>C	p.Glu382Asp	p.E382D	ENST00000227322	12/14	43	29	14	59	59	0	ZNF259,missense_variant,p.Glu309Asp,ENST00000429220,;ZNF259,missense_variant,p.Glu382Asp,ENST00000227322,;ZNF259,intron_variant,,ENST00000444935,;ZNF259,3_prime_UTR_variant,,ENST00000449430,;ZNF259,downstream_gene_variant,,ENST00000425791,;ZNF259,downstream_gene_variant,,ENST00000487030,;ZNF259,downstream_gene_variant,,ENST00000498065,;ZNF259,downstream_gene_variant,,ENST00000431973,;	G	ENSG00000109917	ENST00000227322	Transcript	missense_variant	1206	1146	382	E/D	gaG/gaC	.	.	.	-1	ZNF259	HGNC	13051	protein_coding	YES	CCDS8375.1	ENSP00000227322	ZPR1_HUMAN	B4DVT8_HUMAN	UPI000013C471	.	tolerated(0.23)	benign(0.005)	12/14	.	SMART_domains:SM00709,Pfam_domain:PF03367,TIGRFAM_domain:TIGR00310,hmmpanther:PTHR10876,hmmpanther:PTHR10876:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCTCCGT	.	5	ESCA
CBL	0	.	GRCh37	11	119170428	119170428	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2658G>C	p.Glu886Asp	p.E886D	ENST00000264033	16/16	16	13	3	53	53	0	CBL,missense_variant,p.Glu886Asp,ENST00000264033,;	C	ENSG00000110395	ENST00000264033	Transcript	missense_variant	3034	2658	886	E/D	gaG/gaC	.	.	.	1	CBL	HGNC	1541	protein_coding	YES	CCDS8418.1	ENSP00000264033	CBL_HUMAN	.	UPI000013D4A7	.	tolerated_low_confidence(0.34)	benign(0.057)	16/16	.	Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50030,hmmpanther:PTHR23007:SF5,hmmpanther:PTHR23007,Pfam_domain:PF00627,SMART_domains:SM00165,Superfamily_domains:SSF46934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCGAGATGGC	.	2	ESCA
GLB1L3	0	.	GRCh37	11	134153679	134153679	+	Silent	SNP	C	C	T	rs200592634	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.576C>T	p.%3D	p.S192S	ENST00000431683	6/20	39	27	11	46	46	0	GLB1L3,synonymous_variant,p.%3D,ENST00000389887,;GLB1L3,synonymous_variant,p.%3D,ENST00000431683,;GLB1L3,upstream_gene_variant,,ENST00000486034,;GLB1L3,upstream_gene_variant,,ENST00000498012,;GLB1L3,upstream_gene_variant,,ENST00000532985,;	T	ENSG00000166105	ENST00000431683	Transcript	synonymous_variant	576	576	192	S	agC/agT	rs200592634	.	.	1	GLB1L3	HGNC	25147	protein_coding	YES	CCDS44780.1	ENSP00000396615	GLBL3_HUMAN	.	UPI0001633637	.	.	.	6/20	.	hmmpanther:PTHR23421,hmmpanther:PTHR23421:SF59,Gene3D:3.20.20.80,Pfam_domain:PF01301,PIRSF_domain:PIRSF006336,Superfamily_domains:SSF51445	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAGCTTCAT	byCluster|by1000G	5	ESCA
USH1C	0	.	GRCh37	11	17565937	17565937	+	5'Flank	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000005226	.	67	53	14	76	76	0	USH1C,5_prime_UTR_variant,,ENST00000318024,;USH1C,5_prime_UTR_variant,,ENST00000527020,;OTOG,upstream_gene_variant,,ENST00000399397,;USH1C,upstream_gene_variant,,ENST00000005226,;OTOG,upstream_gene_variant,,ENST00000428619,;OTOG,upstream_gene_variant,,ENST00000399391,;USH1C,5_prime_UTR_variant,,ENST00000526313,;OTOG,upstream_gene_variant,,ENST00000498332,;	C	ENSG00000006611	ENST00000005226	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	83	-1	USH1C	HGNC	12597	protein_coding	YES	CCDS7825.1	ENSP00000005226	USH1C_HUMAN	.	UPI00001D965A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CGACCGCGACC	.	4	ESCA
SIGIRR	0	.	GRCh37	11	406070	406070	+	Intron	SNP	G	G	C	rs201999242	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1070-11C>G	.	.	ENST00000431843	.	28	17	11	33	33	0	SIGIRR,missense_variant,p.Pro450Ala,ENST00000382520,;SIGIRR,missense_variant,p.Pro450Ala,ENST00000531205,;SIGIRR,intron_variant,,ENST00000526395,;SIGIRR,intron_variant,,ENST00000397632,;SIGIRR,intron_variant,,ENST00000431843,;SIGIRR,intron_variant,,ENST00000528845,;SIGIRR,intron_variant,,ENST00000332725,;SIGIRR,downstream_gene_variant,,ENST00000528058,;PKP3,downstream_gene_variant,,ENST00000525642,;SIGIRR,downstream_gene_variant,,ENST00000528209,;PKP3,downstream_gene_variant,,ENST00000331563,;SIGIRR,downstream_gene_variant,,ENST00000530494,;SIGIRR,downstream_gene_variant,,ENST00000530683,;SIGIRR,downstream_gene_variant,,ENST00000527136,;SIGIRR,downstream_gene_variant,,ENST00000528116,;SIGIRR,downstream_gene_variant,,ENST00000529486,;SIGIRR,downstream_gene_variant,,ENST00000525299,;SIGIRR,downstream_gene_variant,,ENST00000534217,;SIGIRR,downstream_gene_variant,,ENST00000528698,;SIGIRR,downstream_gene_variant,,ENST00000526788,;SIGIRR,intron_variant,,ENST00000527987,;SIGIRR,intron_variant,,ENST00000527295,;SIGIRR,downstream_gene_variant,,ENST00000528536,;SIGIRR,downstream_gene_variant,,ENST00000525070,;SIGIRR,downstream_gene_variant,,ENST00000534145,;	C	ENSG00000185187	ENST00000431843	Transcript	intron_variant	.	.	.	.	.	rs201999242	.	.	-1	SIGIRR	HGNC	30575	protein_coding	YES	CCDS31325.1	ENSP00000403104	SIGIR_HUMAN	.	UPI000049DD22	.	.	.	.	9/9	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGGGAGACC	byCluster|by1000G	5	ESCA
ACCS	0	.	GRCh37	11	44089204	44089204	+	Silent	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27C>T	p.%3D	p.F9F	ENST00000263776	2/15	48	35	12	71	71	0	ACCS,synonymous_variant,p.%3D,ENST00000524990,;ACCS,synonymous_variant,p.%3D,ENST00000432284,;ACCS,synonymous_variant,p.%3D,ENST00000533404,;ACCS,synonymous_variant,p.%3D,ENST00000263776,;CTD-2609K8.3,upstream_gene_variant,,ENST00000531268,;ACCS,non_coding_transcript_exon_variant,,ENST00000533208,;ACCS,non_coding_transcript_exon_variant,,ENST00000526577,;ACCS,non_coding_transcript_exon_variant,,ENST00000527603,;	T	ENSG00000110455	ENST00000263776	Transcript	synonymous_variant	461	27	9	F	ttC/ttT	COSM3791486	.	.	1	ACCS	HGNC	23989	protein_coding	YES	CCDS7907.1	ENSP00000263776	1A1L1_HUMAN	E9PS61_HUMAN,E9PRT9_HUMAN	UPI000006D45A	.	.	.	2/15	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCAGGGC	.	5	ESCA
OR5D16	0	.	GRCh37	11	55606363	55606363	+	Missense_Mutation	SNP	G	G	T	rs779730613	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136G>T	p.Gly46Trp	p.G46W	ENST00000378396	1/1	63	42	20	86	86	0	OR5D16,missense_variant,p.Gly46Trp,ENST00000378396,;	T	ENSG00000205029	ENST00000378396	Transcript	missense_variant	136	136	46	G/W	Ggg/Tgg	rs779730613	.	.	1	OR5D16	HGNC	15283	protein_coding	YES	CCDS31512.1	ENSP00000367649	OR5DG_HUMAN	.	UPI0000046198	.	deleterious(0)	probably_damaging(0.999)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF243,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTGGGATG	byFrequency	5	ESCA
OR52N1	0	.	GRCh37	11	5809409	5809409	+	Missense_Mutation	SNP	A	A	G	rs773631047	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.638T>C	p.Ile213Thr	p.I213T	ENST00000317078	1/1	22	15	7	31	31	0	OR52N1,missense_variant,p.Ile213Thr,ENST00000317078,;TRIM5,intron_variant,,ENST00000412903,;TRIM5,intron_variant,,ENST00000380027,;	G	ENSG00000181001	ENST00000317078	Transcript	missense_variant	638	638	213	I/T	aTc/aCc	rs773631047	.	.	-1	OR52N1	HGNC	14853	protein_coding	YES	CCDS31398.1	ENSP00000322823	O52N1_HUMAN	.	UPI0000041BDD	.	deleterious(0.01)	benign(0.364)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF107,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGATATCA	byFrequency	5	ESCA
OR5B21	0	.	GRCh37	11	58275221	58275221	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.358C>T	p.Arg120Cys	p.R120C	ENST00000360374	1/1	16	12	4	18	18	0	OR5B21,missense_variant,p.Arg120Cys,ENST00000360374,;RP11-655C2.3,upstream_gene_variant,,ENST00000531715,;RP11-655C2.3,upstream_gene_variant,,ENST00000527054,;RP11-655C2.3,upstream_gene_variant,,ENST00000528978,;	A	ENSG00000198283	ENST00000360374	Transcript	missense_variant	358	358	120	R/C	Cgc/Tgc	.	.	.	-1	OR5B21	HGNC	19616	protein_coding	YES	CCDS31552.1	ENSP00000353537	OR5BL_HUMAN	.	UPI000015FCAA	.	deleterious_low_confidence(0.03)	possibly_damaging(0.549)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF288,hmmpanther:PTHR26452,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGCGATCAT	.	5	ESCA
ZFP91	0	.	GRCh37	11	58384873	58384873	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1407C>T	p.%3D	p.L469L	ENST00000316059	11/11	29	18	11	15	15	0	ZFP91,synonymous_variant,p.%3D,ENST00000316059,;ZFP91-CNTF,synonymous_variant,p.%3D,ENST00000389919,;ZFP91-CNTF,synonymous_variant,p.%3D,ENST00000422974,;	T	ENSG00000186660	ENST00000316059	Transcript	synonymous_variant	1578	1407	469	L	ctC/ctT	.	.	.	1	ZFP91	HGNC	14983	protein_coding	YES	CCDS31553.1	ENSP00000339030	ZFP91_HUMAN	B4DIN6_HUMAN	UPI0000070D45	.	.	.	11/11	.	hmmpanther:PTHR11389:SF437,hmmpanther:PTHR11389,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCATCAC	.	5	ESCA
GLYAT	0	.	GRCh37	11	58478152	58478152	+	Silent	SNP	G	G	C	rs772285364	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.399C>G	p.%3D	p.L133L	ENST00000344743	5/6	50	25	24	64	64	0	GLYAT,synonymous_variant,p.%3D,ENST00000278400,;GLYAT,synonymous_variant,p.%3D,ENST00000529732,;GLYAT,synonymous_variant,p.%3D,ENST00000344743,;GLYAT,intron_variant,,ENST00000586098,;	C	ENSG00000149124	ENST00000344743	Transcript	synonymous_variant	541	399	133	L	ctC/ctG	rs772285364	.	.	-1	GLYAT	HGNC	13734	protein_coding	YES	CCDS7970.1	ENSP00000340200	GLYAT_HUMAN	.	UPI00003667C7	.	.	.	5/6	.	hmmpanther:PTHR15298,hmmpanther:PTHR15298:SF5,Pfam_domain:PF06021,Superfamily_domains:SSF55729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATAGAGAAT	.	5	ESCA
OR52E6	0	.	GRCh37	11	5862196	5862196	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.932C>A	p.Thr311Lys	p.T311K	ENST00000329322	1/1	26	11	15	53	53	0	OR52E6,missense_variant,p.Thr315Lys,ENST00000379946,;OR52E6,missense_variant,p.Thr311Lys,ENST00000329322,;TRIM5,intron_variant,,ENST00000412903,;TRIM5,intron_variant,,ENST00000380027,;	T	ENSG00000205409	ENST00000329322	Transcript	missense_variant	932	932	311	T/K	aCa/aAa	.	.	.	-1	OR52E6	HGNC	15215	protein_coding	YES	CCDS53597.1	ENSP00000328878	O52E6_HUMAN	.	UPI00000015AE	.	tolerated_low_confidence(1)	benign(0)	1/1	.	hmmpanther:PTHR26450:SF45,hmmpanther:PTHR26450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTGTCTTG	.	5	ESCA
MALAT1	0	.	GRCh37	11	65266460	65266460	+	RNA	SNP	T	T	A	rs754397792	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1228T>A	.	.	ENST00000534336	1/1	77	66	11	70	70	0	MALAT1,non_coding_transcript_exon_variant,,ENST00000534336,;AP000769.7,upstream_gene_variant,,ENST00000602344,;MALAT1,upstream_gene_variant,,ENST00000508832,;MALAT1,upstream_gene_variant,,ENST00000544868,;	A	ENSG00000251562	ENST00000534336	Transcript	non_coding_transcript_exon_variant	1228	.	.	.	.	rs754397792	.	.	1	MALAT1	HGNC	29665	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAATTCCGGT	.	4	ESCA
CARNS1	0	.	GRCh37	11	67186432	67186432	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570A>G	p.%3D	p.A190A	ENST00000445895	4/9	35	27	8	36	36	0	CARNS1,synonymous_variant,p.%3D,ENST00000423745,;CARNS1,synonymous_variant,p.%3D,ENST00000307823,;CARNS1,synonymous_variant,p.%3D,ENST00000445895,;CARNS1,synonymous_variant,p.%3D,ENST00000531040,;PPP1CA,intron_variant,,ENST00000546202,;PPP1CA,intron_variant,,ENST00000542876,;CARNS1,upstream_gene_variant,,ENST00000524740,;CARNS1,downstream_gene_variant,,ENST00000529925,;CARNS1,downstream_gene_variant,,ENST00000525907,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531958,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531388,;	G	ENSG00000172508	ENST00000445895	Transcript	synonymous_variant	684	570	190	A	gcA/gcG	.	.	.	1	CARNS1	HGNC	29268	protein_coding	YES	CCDS53667.1	ENSP00000389009	.	F5H427_HUMAN	UPI0001B99E02	.	.	.	4/9	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCAGCAGAACT	.	3	ESCA
CARNS1	0	.	GRCh37	11	67186451	67186451	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.589A>C	p.Thr197Pro	p.T197P	ENST00000445895	4/9	33	24	9	33	33	0	CARNS1,missense_variant,p.Thr74Pro,ENST00000423745,;CARNS1,missense_variant,p.Thr74Pro,ENST00000307823,;CARNS1,missense_variant,p.Thr197Pro,ENST00000445895,;CARNS1,missense_variant,p.Thr197Pro,ENST00000531040,;PPP1CA,intron_variant,,ENST00000546202,;PPP1CA,intron_variant,,ENST00000542876,;CARNS1,upstream_gene_variant,,ENST00000524740,;CARNS1,downstream_gene_variant,,ENST00000529925,;CARNS1,downstream_gene_variant,,ENST00000525907,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531958,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531388,;	C	ENSG00000172508	ENST00000445895	Transcript	missense_variant	703	589	197	T/P	Acc/Ccc	.	.	.	1	CARNS1	HGNC	29268	protein_coding	YES	CCDS53667.1	ENSP00000389009	.	F5H427_HUMAN	UPI0001B99E02	.	tolerated(0.14)	benign(0.192)	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCTGACCTGC	.	3	ESCA
SUV420H1	0	.	GRCh37	11	67957421	67957421	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123G>C	p.Lys41Asn	p.K41N	ENST00000304363	2/11	158	76	82	66	66	0	SUV420H1,missense_variant,p.Lys41Asn,ENST00000434573,;SUV420H1,missense_variant,p.Lys41Asn,ENST00000402789,;SUV420H1,missense_variant,p.Lys41Asn,ENST00000405515,;SUV420H1,missense_variant,p.Lys41Asn,ENST00000304363,;SUV420H1,missense_variant,p.Lys41Asn,ENST00000402185,;SUV420H1,missense_variant,p.Lys41Asn,ENST00000401547,;SUV420H1,intron_variant,,ENST00000458496,;SUV420H1,intron_variant,,ENST00000453170,;SUV420H1,missense_variant,p.Lys41Asn,ENST00000427752,;SUV420H1,missense_variant,p.Lys41Asn,ENST00000441488,;SUV420H1,non_coding_transcript_exon_variant,,ENST00000466295,;	G	ENSG00000110066	ENST00000304363	Transcript	missense_variant	477	123	41	K/N	aaG/aaC	.	.	.	-1	SUV420H1	HGNC	24283	protein_coding	YES	CCDS31623.1	ENSP00000305899	SV421_HUMAN	E9PKD9_HUMAN,C9JP58_HUMAN,C9JFG1_HUMAN,C9J6S5_HUMAN	UPI00001FADE7	.	deleterious(0)	possibly_damaging(0.756)	2/11	.	PROSITE_profiles:PS51570,hmmpanther:PTHR12977,hmmpanther:PTHR12977:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCCTTCAG	.	5	ESCA
OR10A2	0	.	GRCh37	11	6891244	6891244	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.259C>T	p.Gln87Ter	p.Q87*	ENST00000307322	1/1	39	28	10	42	42	0	OR10A2,stop_gained,p.Gln87Ter,ENST00000307322,;	T	ENSG00000170790	ENST00000307322	Transcript	stop_gained	321	259	87	Q/*	Cag/Tag	.	.	.	1	OR10A2	HGNC	8161	protein_coding	YES	CCDS31415.1	ENSP00000303862	O10A2_HUMAN	.	UPI000015F21C	.	.	.	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00245,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF90,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTCAGATG	.	5	ESCA
NOX4	0	.	GRCh37	11	89222092	89222092	+	Intron	SNP	A	A	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153+1534T>G	.	.	ENST00000263317	.	195	100	94	117	117	0	NOX4,3_prime_UTR_variant,,ENST00000393282,;NOX4,intron_variant,,ENST00000375979,;NOX4,intron_variant,,ENST00000535633,;NOX4,intron_variant,,ENST00000527956,;NOX4,intron_variant,,ENST00000542487,;NOX4,intron_variant,,ENST00000343727,;NOX4,intron_variant,,ENST00000413594,;NOX4,intron_variant,,ENST00000532825,;NOX4,intron_variant,,ENST00000531342,;NOX4,intron_variant,,ENST00000527626,;NOX4,intron_variant,,ENST00000534731,;NOX4,intron_variant,,ENST00000263317,;NOX4,intron_variant,,ENST00000525196,;NOX4,intron_variant,,ENST00000528341,;NOX4,intron_variant,,ENST00000424319,;NOX4,intron_variant,,ENST00000525278,;NOX4,intron_variant,,ENST00000529343,;	C	ENSG00000086991	ENST00000263317	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NOX4	HGNC	7891	protein_coding	YES	CCDS8285.1	ENSP00000263317	NOX4_HUMAN	E7EMD7_HUMAN	UPI000045655B	.	.	.	.	2/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGCAACTTG	.	5	ESCA
TAF1D	0	.	GRCh37	11	93469859	93469859	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693+1G>C	.	p.X231_splice	ENST00000448108	.	69	64	5	38	38	0	TAF1D,splice_donor_variant,,ENST00000448108,;TAF1D,downstream_gene_variant,,ENST00000532455,;C11orf54,upstream_gene_variant,,ENST00000530620,;C11orf54,upstream_gene_variant,,ENST00000528099,;C11orf54,upstream_gene_variant,,ENST00000533585,;C11orf54,upstream_gene_variant,,ENST00000530279,;C11orf54,upstream_gene_variant,,ENST00000331239,;TAF1D,downstream_gene_variant,,ENST00000527690,;C11orf54,upstream_gene_variant,,ENST00000527003,;C11orf54,upstream_gene_variant,,ENST00000531650,;C11orf54,upstream_gene_variant,,ENST00000540113,;C11orf54,upstream_gene_variant,,ENST00000528288,;C11orf54,upstream_gene_variant,,ENST00000354421,;SNORA1,upstream_gene_variant,,ENST00000384107,;SNORD5,upstream_gene_variant,,ENST00000459342,;SNORA8,upstream_gene_variant,,ENST00000384574,;SNORA40,upstream_gene_variant,,ENST00000388090,;SNORA18,upstream_gene_variant,,ENST00000384416,;MIR1304,upstream_gene_variant,,ENST00000408243,;TAF1D,upstream_gene_variant,,ENST00000530089,;TAF1D,upstream_gene_variant,,ENST00000546088,;C11orf54,upstream_gene_variant,,ENST00000531516,;TAF1D,downstream_gene_variant,,ENST00000532235,;TAF1D,splice_donor_variant,,ENST00000528734,;TAF1D,splice_donor_variant,,ENST00000527068,;TAF1D,splice_donor_variant,,ENST00000323981,;TAF1D,splice_donor_variant,,ENST00000393259,;TAF1D,splice_donor_variant,,ENST00000526015,;TAF1D,non_coding_transcript_exon_variant,,ENST00000529794,;TAF1D,intron_variant,,ENST00000527169,;TAF1D,upstream_gene_variant,,ENST00000533794,;TAF1D,upstream_gene_variant,,ENST00000540232,;TAF1D,upstream_gene_variant,,ENST00000529435,;TAF1D,downstream_gene_variant,,ENST00000529508,;TAF1D,downstream_gene_variant,,ENST00000534770,;TAF1D,upstream_gene_variant,,ENST00000530769,;TAF1D,upstream_gene_variant,,ENST00000529900,;TAF1D,upstream_gene_variant,,ENST00000534079,;TAF1D,upstream_gene_variant,,ENST00000525928,;	G	ENSG00000166012	ENST00000448108	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	TAF1D	HGNC	28759	protein_coding	YES	CCDS8293.1	ENSP00000410409	TAF1D_HUMAN	H0YG36_HUMAN	UPI000006D0AF	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTACTGCCA	.	2	ESCA
WSCD2	0	.	GRCh37	12	108618549	108618549	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.716G>A	p.Arg239Lys	p.R239K	ENST00000332082	6/10	15	10	5	14	14	0	WSCD2,missense_variant,p.Arg86Lys,ENST00000551638,;WSCD2,missense_variant,p.Arg239Lys,ENST00000549903,;WSCD2,missense_variant,p.Arg239Lys,ENST00000332082,;WSCD2,missense_variant,p.Arg239Lys,ENST00000547525,;WSCD2,missense_variant,p.Arg239Lys,ENST00000261400,;WSCD2,upstream_gene_variant,,ENST00000546629,;	A	ENSG00000075035	ENST00000332082	Transcript	missense_variant	1534	716	239	R/K	aGg/aAg	.	.	.	1	WSCD2	HGNC	29117	protein_coding	YES	CCDS41828.1	ENSP00000331933	WSCD2_HUMAN	F8W030_HUMAN	UPI00001C1F3A	.	tolerated(0.68)	benign(0.094)	6/10	.	SMART_domains:SM00321,Pfam_domain:PF01822,hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF5,PROSITE_profiles:PS51212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGCAGGCCCG	.	5	ESCA
TAS2R30	0	.	GRCh37	12	11286602	11286602	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.242G>A	p.Arg81Lys	p.R81K	ENST00000539585	1/1	82	61	20	93	93	0	TAS2R30,missense_variant,p.Arg81Lys,ENST00000539585,;TAS2R14,intron_variant,,ENST00000381852,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000546265,;PRR4,intron_variant,,ENST00000541175,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;	T	ENSG00000256188	ENST00000539585	Transcript	missense_variant	642	242	81	R/K	aGa/aAa	COSM3416502	.	.	-1	TAS2R30	HGNC	19112	protein_coding	YES	CCDS53750.1	ENSP00000444736	.	Q50KG7_HUMAN	UPI000006202F	.	tolerated(0.1)	benign(0.16)	1/1	.	hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF48,Pfam_domain:PF05296,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATTCTTACT	.	5	ESCA
PRB2	0	.	GRCh37	12	11546642	11546642	+	Nonsense_Mutation	SNP	G	G	A	rs774225297	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370C>T	p.Gln124Ter	p.Q124*	ENST00000389362	3/4	151	139	12	245	245	0	PRB2,stop_gained,p.Gln124Ter,ENST00000389362,;PRB1,intron_variant,,ENST00000546254,;PRB2,downstream_gene_variant,,ENST00000565533,;PRB2,downstream_gene_variant,,ENST00000545829,;	A	ENSG00000121335	ENST00000389362	Transcript	stop_gained	406	370	124	Q/*	Caa/Taa	rs774225297	.	.	-1	PRB2	HGNC	9338	protein_coding	YES	CCDS41757.2	ENSP00000374013	PRB2_HUMAN	.	UPI0000EE5993	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23203,hmmpanther:PTHR23203:SF2,Pfam_domain:PF15240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTTGTGGGG	.	2	ESCA
NOS1	0	.	GRCh37	12	117655876	117655876	+	Missense_Mutation	SNP	C	C	T	rs201476356	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4366G>A	p.Glu1456Lys	p.E1456K	ENST00000338101	28/29	23	18	5	36	36	0	NOS1,missense_variant,p.Glu1422Lys,ENST00000317775,;NOS1,missense_variant,p.Glu1456Lys,ENST00000338101,;NOS1,3_prime_UTR_variant,,ENST00000344089,;	T	ENSG00000089250	ENST00000338101	Transcript	missense_variant	4371	4366	1456	E/K	Gaa/Aaa	rs201476356,COSM935606	.	.	-1	NOS1	HGNC	7872	protein_coding	YES	CCDS55890.1	ENSP00000337459	NOS1_HUMAN	A0PJJ7_HUMAN	UPI00001FBC10	.	deleterious(0.02)	possibly_damaging(0.698)	28/29	.	PIRSF_domain:PIRSF000333	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	G:0.0023	G:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCAATGA	byCluster|by1000G	5	ESCA
CCDC60	0	.	GRCh37	12	119954500	119954500	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956G>C	p.Arg319Thr	p.R319T	ENST00000327554	8/14	30	26	4	49	49	0	CCDC60,missense_variant,p.Arg319Thr,ENST00000327554,;RP11-768F21.1,intron_variant,,ENST00000535511,;RP11-768F21.1,intron_variant,,ENST00000537366,;RP11-768F21.1,intron_variant,,ENST00000509470,;	C	ENSG00000183273	ENST00000327554	Transcript	missense_variant	1421	956	319	R/T	aGa/aCa	COSM3456894	.	.	1	CCDC60	HGNC	28610	protein_coding	YES	CCDS9190.1	ENSP00000333374	CCD60_HUMAN	F5H5H4_HUMAN	UPI000019906E	.	tolerated(0.1)	benign(0.015)	8/14	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAAAGAAAAG	.	4	ESCA
MPHOSPH9	0	.	GRCh37	12	123661309	123661309	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1926C>T	p.%3D	p.V642V	ENST00000392425	12/20	59	43	15	67	67	0	MPHOSPH9,synonymous_variant,p.%3D,ENST00000302349,;MPHOSPH9,synonymous_variant,p.%3D,ENST00000541076,;MPHOSPH9,synonymous_variant,p.%3D,ENST00000606320,;MPHOSPH9,synonymous_variant,p.%3D,ENST00000392425,;MPHOSPH9,upstream_gene_variant,,ENST00000606321,;MPHOSPH9,synonymous_variant,p.%3D,ENST00000302373,;MPHOSPH9,synonymous_variant,p.%3D,ENST00000539024,;MPHOSPH9,3_prime_UTR_variant,,ENST00000545556,;MPHOSPH9,non_coding_transcript_exon_variant,,ENST00000541823,;	A	ENSG00000051825	ENST00000392425	Transcript	synonymous_variant	2033	1926	642	V	gtC/gtT	.	.	.	-1	MPHOSPH9	HGNC	7215	protein_coding	YES	.	ENSP00000376220	MPP9_HUMAN	.	UPI00001D62B9	.	.	.	12/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14926:SF1,hmmpanther:PTHR14926	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTGACCTG	.	5	ESCA
GLT1D1	0	.	GRCh37	12	129431943	129431943	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.480G>A	p.%3D	p.K160K	ENST00000281703	6/8	22	15	7	38	38	0	GLT1D1,synonymous_variant,p.%3D,ENST00000281703,;GLT1D1,synonymous_variant,p.%3D,ENST00000442111,;GLT1D1,synonymous_variant,p.%3D,ENST00000542193,;GLT1D1,synonymous_variant,p.%3D,ENST00000537468,;GLT1D1,3_prime_UTR_variant,,ENST00000413816,;GLT1D1,3_prime_UTR_variant,,ENST00000441390,;RP11-753B7.2,upstream_gene_variant,,ENST00000539058,;	A	ENSG00000151948	ENST00000281703	Transcript	synonymous_variant	526	480	160	K	aaG/aaA	.	.	.	1	GLT1D1	HGNC	26483	protein_coding	YES	CCDS9265.1	ENSP00000281703	GL1D1_HUMAN	.	UPI0000070E33	.	.	.	6/8	.	Superfamily_domains:SSF53756,Gene3D:3.40.50.2000,Pfam_domain:PF00534,hmmpanther:PTHR12526,hmmpanther:PTHR12526:SF331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAGAATTG	.	5	ESCA
DERA	0	.	GRCh37	12	16109917	16109917	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.79A>T	p.Arg27Trp	p.R27W	ENST00000428559	2/9	41	32	8	57	57	0	DERA,missense_variant,p.Arg48Trp,ENST00000531803,;DERA,missense_variant,p.Arg27Trp,ENST00000428559,;DERA,missense_variant,p.Arg27Trp,ENST00000532964,;DERA,5_prime_UTR_variant,,ENST00000524480,;DERA,5_prime_UTR_variant,,ENST00000526530,;DERA,5_prime_UTR_variant,,ENST00000533447,;DERA,missense_variant,p.Arg27Trp,ENST00000528821,;DERA,missense_variant,p.Arg27Trp,ENST00000526521,;	T	ENSG00000023697	ENST00000428559	Transcript	missense_variant	291	79	27	R/W	Agg/Tgg	.	.	.	1	DERA	HGNC	24269	protein_coding	YES	CCDS44838.1	ENSP00000416583	DEOC_HUMAN	G3V158_HUMAN,E9PPK3_HUMAN	UPI00001291A2	.	deleterious(0)	possibly_damaging(0.838)	2/9	.	hmmpanther:PTHR10889:SF5,hmmpanther:PTHR10889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGAGGCGT	.	5	ESCA
IQSEC3	0	.	GRCh37	12	247635	247635	+	Missense_Mutation	SNP	C	C	T	rs370321433	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1106C>T	p.Ala369Val	p.A369V	ENST00000538872	4/14	10	5	5	11	11	0	IQSEC3,missense_variant,p.Ala369Val,ENST00000538872,;IQSEC3,missense_variant,p.Ala66Val,ENST00000382841,;IQSEC3,missense_variant,p.Ala369Val,ENST00000326261,;RP11-598F7.4,intron_variant,,ENST00000505893,;RP11-598F7.4,downstream_gene_variant,,ENST00000508953,;	T	ENSG00000120645	ENST00000538872	Transcript	missense_variant	1224	1106	369	A/V	gCg/gTg	rs370321433	.	.	1	IQSEC3	HGNC	29193	protein_coding	YES	CCDS53728.1	ENSP00000437554	IQEC3_HUMAN	.	UPI0000DBEEF0	.	deleterious(0.03)	probably_damaging(0.965)	4/14	.	hmmpanther:PTHR10663:SF62,hmmpanther:PTHR10663	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAAAGCGCTCA	byCluster	3	ESCA
FGD4	0	.	GRCh37	12	32772733	32772733	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1440G>A	p.%3D	p.E480E	ENST00000427716	11/17	47	38	9	59	59	0	FGD4,synonymous_variant,p.%3D,ENST00000381025,;FGD4,synonymous_variant,p.%3D,ENST00000546442,;FGD4,synonymous_variant,p.%3D,ENST00000531134,;FGD4,synonymous_variant,p.%3D,ENST00000427716,;FGD4,synonymous_variant,p.%3D,ENST00000525053,;FGD4,synonymous_variant,p.%3D,ENST00000266482,;FGD4,synonymous_variant,p.%3D,ENST00000534526,;FGD4,3_prime_UTR_variant,,ENST00000494977,;FGD4,3_prime_UTR_variant,,ENST00000395740,;FGD4,3_prime_UTR_variant,,ENST00000493087,;FGD4,3_prime_UTR_variant,,ENST00000551984,;	A	ENSG00000139132	ENST00000427716	Transcript	synonymous_variant	1864	1440	480	E	gaG/gaA	.	.	.	1	FGD4	HGNC	19125	protein_coding	YES	CCDS8727.1	ENSP00000394487	FGD4_HUMAN	J3KSS3_HUMAN,F8W1R0_HUMAN	UPI000004CCA6	.	.	.	11/17	.	PROSITE_profiles:PS50003,hmmpanther:PTHR12673:SF98,hmmpanther:PTHR12673,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGAGACTCA	.	5	ESCA
KIF21A	0	.	GRCh37	12	39703442	39703442	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4223C>G	p.Ser1408Cys	p.S1408C	ENST00000361418	33/38	38	18	20	51	51	0	KIF21A,missense_variant,p.Ser709Cys,ENST00000552961,;KIF21A,missense_variant,p.Ser1408Cys,ENST00000361418,;KIF21A,missense_variant,p.Ser389Cys,ENST00000551264,;KIF21A,missense_variant,p.Ser1371Cys,ENST00000544797,;KIF21A,missense_variant,p.Ser1409Cys,ENST00000395670,;KIF21A,missense_variant,p.Ser1355Cys,ENST00000541463,;KIF21A,missense_variant,p.Ser1395Cys,ENST00000361961,;KIF21A,downstream_gene_variant,,ENST00000547745,;KIF21A,non_coding_transcript_exon_variant,,ENST00000547733,;	C	ENSG00000139116	ENST00000361418	Transcript	missense_variant	4239	4223	1408	S/C	tCt/tGt	.	.	.	-1	KIF21A	HGNC	19349	protein_coding	YES	CCDS53776.1	ENSP00000354878	KI21A_HUMAN	.	UPI0000212ED9	.	deleterious(0)	probably_damaging(0.928)	33/38	.	PROSITE_profiles:PS50294,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF398,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAAGATGTT	.	5	ESCA
KIF21A	0	.	GRCh37	12	39760156	39760156	+	Missense_Mutation	SNP	C	C	A	rs767553587	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.899G>T	p.Gly300Val	p.G300V	ENST00000361418	6/38	49	31	17	54	54	0	KIF21A,missense_variant,p.Gly300Val,ENST00000541463,;KIF21A,missense_variant,p.Gly123Val,ENST00000552908,;KIF21A,missense_variant,p.Gly300Val,ENST00000361961,;KIF21A,missense_variant,p.Gly300Val,ENST00000361418,;KIF21A,missense_variant,p.Gly300Val,ENST00000544797,;KIF21A,missense_variant,p.Gly300Val,ENST00000395670,;	A	ENSG00000139116	ENST00000361418	Transcript	missense_variant	915	899	300	G/V	gGa/gTa	rs767553587	.	.	-1	KIF21A	HGNC	19349	protein_coding	YES	CCDS53776.1	ENSP00000354878	KI21A_HUMAN	.	UPI0000212ED9	.	deleterious(0)	probably_damaging(1)	6/38	.	PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF398,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGTCCACAG	byFrequency	5	ESCA
LRRK2	0	.	GRCh37	12	40689290	40689290	+	Silent	SNP	G	G	A	rs201042000	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2940G>A	p.%3D	p.E980E	ENST00000298910	23/51	31	15	16	58	58	0	LRRK2,synonymous_variant,p.%3D,ENST00000343742,;LRRK2,synonymous_variant,p.%3D,ENST00000298910,;LRRK2,upstream_gene_variant,,ENST00000479187,;LRRK2,upstream_gene_variant,,ENST00000430804,;	A	ENSG00000188906	ENST00000298910	Transcript	synonymous_variant	2998	2940	980	E	gaG/gaA	rs201042000	.	.	1	LRRK2	HGNC	18618	protein_coding	YES	CCDS31774.1	ENSP00000298910	LRRK2_HUMAN	.	UPI00006C128E	.	.	.	23/51	.	hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF417,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGAGAGAGA	byCluster	5	ESCA
KCNH3	0	.	GRCh37	12	49935472	49935472	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.370G>A	p.Ala124Thr	p.A124T	ENST00000257981	3/15	39	36	3	44	44	0	KCNH3,missense_variant,p.Ala124Thr,ENST00000257981,;KCNH3,non_coding_transcript_exon_variant,,ENST00000550434,;KCNH3,upstream_gene_variant,,ENST00000551415,;	A	ENSG00000135519	ENST00000257981	Transcript	missense_variant	630	370	124	A/T	Gct/Act	.	.	.	1	KCNH3	HGNC	6252	protein_coding	YES	CCDS8786.1	ENSP00000257981	KCNH3_HUMAN	Q8N500_HUMAN	UPI000012DCA6	.	deleterious(0)	possibly_damaging(0.739)	3/15	.	Superfamily_domains:SSF55785,SMART_domains:SM00086,TIGRFAM_domain:TIGR00229,Pfam_domain:PF13426,Gene3D:3.30.450.20,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF481,PROSITE_profiles:PS50113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTGGCTCTC	.	2	ESCA
EIF4B	0	.	GRCh37	12	53434012	53434013	+	3'UTR	INS	-	-	TA	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6_*7dupTA	.	.	ENST00000262056	15/15	41	32	9	36	36	0	EIF4B,3_prime_UTR_variant,,ENST00000416762,;EIF4B,3_prime_UTR_variant,,ENST00000420463,;EIF4B,3_prime_UTR_variant,,ENST00000262056,;RP11-983P16.4,non_coding_transcript_exon_variant,,ENST00000550601,;RP11-983P16.4,non_coding_transcript_exon_variant,,ENST00000546566,;RP11-983P16.4,intron_variant,,ENST00000552905,;RP11-983P16.4,downstream_gene_variant,,ENST00000607643,;RP11-983P16.4,downstream_gene_variant,,ENST00000546793,;RP11-983P16.4,downstream_gene_variant,,ENST00000546767,;EIF4B,non_coding_transcript_exon_variant,,ENST00000549592,;EIF4B,downstream_gene_variant,,ENST00000553209,;EIF4B,downstream_gene_variant,,ENST00000550704,;	TA	ENSG00000063046	ENST00000262056	Transcript	3_prime_UTR_variant	2167-2168	.	.	.	.	.	.	.	1	EIF4B	HGNC	3285	protein_coding	YES	CCDS41788.1	ENSP00000262056	IF4B_HUMAN	.	UPI000006F988	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GACCTCTACAT	.	3	ESCA
METAP2	0	.	GRCh37	12	95906601	95906601	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1093A>G	p.Thr365Ala	p.T365A	ENST00000323666	10/11	40	16	24	72	72	0	METAP2,missense_variant,p.Thr342Ala,ENST00000261220,;METAP2,missense_variant,p.Thr365Ala,ENST00000323666,;METAP2,missense_variant,p.Thr364Ala,ENST00000551840,;METAP2,missense_variant,p.Thr329Ala,ENST00000550777,;METAP2,missense_variant,p.Thr342Ala,ENST00000546753,;USP44,downstream_gene_variant,,ENST00000258499,;USP44,downstream_gene_variant,,ENST00000393091,;METAP2,3_prime_UTR_variant,,ENST00000535095,;	G	ENSG00000111142	ENST00000323666	Transcript	missense_variant	1322	1093	365	T/A	Acc/Gcc	.	.	.	1	METAP2	HGNC	16672	protein_coding	YES	CCDS9052.1	ENSP00000325312	MAP2_HUMAN	.	UPI000004493E	.	deleterious(0.01)	probably_damaging(0.999)	10/11	.	HAMAP:MF_03175,hmmpanther:PTHR10804:SF95,hmmpanther:PTHR10804,TIGRFAM_domain:TIGR00501,Gene3D:3.90.230.10,Pfam_domain:PF00557,Superfamily_domains:SSF55920,Prints_domain:PR00599	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAACCTTT	.	5	ESCA
XPO4	0	.	GRCh37	13	21353718	21353718	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4143G>A	.	.	ENST00000255305	23/23	11	8	3	18	18	0	XPO4,3_prime_UTR_variant,,ENST00000255305,;XPO4,3_prime_UTR_variant,,ENST00000400602,;	T	ENSG00000132953	ENST00000255305	Transcript	3_prime_UTR_variant	7671	.	.	.	.	.	.	.	-1	XPO4	HGNC	17796	protein_coding	YES	CCDS41872.1	ENSP00000255305	XPO4_HUMAN	Q8IVQ8_HUMAN,Q0VG75_HUMAN	UPI0000139018	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTTCAAGCG	.	2	ESCA
FLT3	0	.	GRCh37	13	28622425	28622425	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1192G>A	p.Asp398Asn	p.D398N	ENST00000241453	9/24	86	71	15	90	90	0	FLT3,missense_variant,p.Asp398Asn,ENST00000241453,;FLT3,missense_variant,p.Asp398Asn,ENST00000537084,;FLT3,missense_variant,p.Asp398Asn,ENST00000380982,;FLT3,missense_variant,p.Asp398Asn,ENST00000380987,;	T	ENSG00000122025	ENST00000241453	Transcript	missense_variant	1274	1192	398	D/N	Gat/Aat	COSM3468064	.	.	-1	FLT3	HGNC	3765	protein_coding	YES	CCDS31953.1	ENSP00000241453	FLT3_HUMAN	.	UPI00001FC90B	.	tolerated(0.49)	benign(0)	9/24	.	PIRSF_domain:PIRSF000615,hmmpanther:PTHR24416:SF278,hmmpanther:PTHR24416	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTATCAAGAC	.	5	ESCA
COG6	0	.	GRCh37	13	40239254	40239254	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391G>A	p.Asp131Asn	p.D131N	ENST00000455146	4/19	177	114	62	212	212	0	COG6,missense_variant,p.Asp131Asn,ENST00000455146,;COG6,missense_variant,p.Asp131Asn,ENST00000422759,;COG6,missense_variant,p.Asp131Asn,ENST00000416691,;MIR4305,upstream_gene_variant,,ENST00000583252,;COG6,missense_variant,p.Asp70Asn,ENST00000536488,;COG6,3_prime_UTR_variant,,ENST00000543804,;COG6,3_prime_UTR_variant,,ENST00000356576,;	A	ENSG00000133103	ENST00000455146	Transcript	missense_variant	441	391	131	D/N	Gat/Aat	COSM3782803,COSM3782804	.	.	1	COG6	HGNC	18621	protein_coding	YES	CCDS9370.1	ENSP00000397441	COG6_HUMAN	B4DG73_HUMAN	UPI000019271E	.	tolerated(0.06)	possibly_damaging(0.805)	4/19	.	hmmpanther:PTHR21506,Pfam_domain:PF06419,SMART_domains:SM01087	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCAAGATTTA	.	5	ESCA
FOXO1	0	.	GRCh37	13	41134632	41134632	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.996G>A	p.Met332Ile	p.M332I	ENST00000379561	2/3	25	21	4	36	36	0	FOXO1,missense_variant,p.Met332Ile,ENST00000379561,;FOXO1,downstream_gene_variant,,ENST00000473775,;	T	ENSG00000150907	ENST00000379561	Transcript	missense_variant	1381	996	332	M/I	atG/atA	COSM459285,COSM459286	.	.	-1	FOXO1	HGNC	3819	protein_coding	YES	CCDS9371.1	ENSP00000368880	FOXO1_HUMAN	.	UPI000013DC20	.	tolerated(0.31)	benign(0.039)	2/3	.	hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF159	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCGGTCATAAT	.	3	ESCA
ZC3H13	0	.	GRCh37	13	46538007	46538010	+	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	TTTC	TTTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4642_4645delGAAA	p.Glu1548HisfsTer6	p.E1548Hfs*6	ENST00000282007	17/17	78	61	17	96	96	0	ZC3H13,frameshift_variant,p.Glu1547HisfsTer6,ENST00000242848,;ZC3H13,frameshift_variant,p.Glu1548HisfsTer6,ENST00000282007,;ZC3H13,frameshift_variant,p.Glu503HisfsTer6,ENST00000378921,;	-	ENSG00000123200	ENST00000282007	Transcript	frameshift_variant	4713-4716	4642-4645	1548-1549	ET/X	GAAAca/ca	.	.	.	-1	ZC3H13	HGNC	20368	protein_coding	YES	CCDS9400.1	ENSP00000282007	ZC3HD_HUMAN	.	UPI0000366969	.	.	.	17/17	.	hmmpanther:PTHR13585:SF2,hmmpanther:PTHR13585	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GACATGTTTCTTTGA	.	3	ESCA
SLAIN1	0	.	GRCh37	13	78338105	78338105	+	3'Flank	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000488699	.	34	23	11	52	52	0	SLAIN1,3_prime_UTR_variant,,ENST00000466548,;SLAIN1,3_prime_UTR_variant,,ENST00000351546,;SLAIN1,3_prime_UTR_variant,,ENST00000358679,;SLAIN1,3_prime_UTR_variant,,ENST00000267219,;SLAIN1,3_prime_UTR_variant,,ENST00000418532,;SLAIN1,downstream_gene_variant,,ENST00000441784,;SLAIN1,downstream_gene_variant,,ENST00000314070,;SLAIN1,downstream_gene_variant,,ENST00000488699,;	T	ENSG00000139737	ENST00000488699	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	613	1	SLAIN1	HGNC	26387	protein_coding	YES	CCDS31995.2	ENSP00000418707	SLAI1_HUMAN	Q5T6P2_HUMAN,C9JUW9_HUMAN,C9JP03_HUMAN	UPI0001914D54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTCATTGC	.	5	ESCA
IGHV5-51	0	.	GRCh37	14	107034864	107034864	+	Silent	SNP	A	A	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.216T>A	p.%3D	p.P72P	ENST00000390626	2/2	46	37	9	65	65	0	IGHV5-51,synonymous_variant,p.%3D,ENST00000390626,;IGHVIII-51-1,downstream_gene_variant,,ENST00000519403,;	T	ENSG00000211966	ENST00000390626	Transcript	synonymous_variant	275	216	72	P	ccT/ccA	.	.	.	-1	IGHV5-51	HGNC	5659	IG_V_gene	YES	.	ENSP00000375035	.	.	UPI000011AAC8	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACCAGGATA	.	5	ESCA
BMS1P18	0	.	GRCh37	14	19904313	19904313	+	RNA	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.206C>G	.	.	ENST00000549877	2/2	99	86	13	108	108	0	BMS1P18,non_coding_transcript_exon_variant,,ENST00000549877,;BMS1P18,non_coding_transcript_exon_variant,,ENST00000551545,;BMS1P18,non_coding_transcript_exon_variant,,ENST00000551908,;CTD-2314B22.3,intron_variant,,ENST00000400192,;CTD-2314B22.3,intron_variant,,ENST00000547648,;CTD-2314B22.3,intron_variant,,ENST00000549813,;CTD-2314B22.3,intron_variant,,ENST00000548875,;CTD-2314B22.3,intron_variant,,ENST00000548903,;CTD-2314B22.3,intron_variant,,ENST00000551334,;CTD-2314B22.3,intron_variant,,ENST00000553153,;CTD-2314B22.3,intron_variant,,ENST00000546382,;CTD-2314B22.3,intron_variant,,ENST00000552602,;CTD-2314B22.3,intron_variant,,ENST00000547285,;CTD-2314B22.3,intron_variant,,ENST00000455088,;	G	ENSG00000215394	ENST00000549877	Transcript	non_coding_transcript_exon_variant	206	.	.	.	.	.	.	.	1	BMS1P18	HGNC	19436	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TAACCCAGTAA	.	2	ESCA
JPH4	0	.	GRCh37	14	24041061	24041061	+	Missense_Mutation	SNP	C	C	T	rs201428906	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1220G>A	p.Arg407Gln	p.R407Q	ENST00000397118	5/7	21	15	6	36	36	0	JPH4,missense_variant,p.Arg72Gln,ENST00000544177,;JPH4,missense_variant,p.Arg407Gln,ENST00000356300,;JPH4,missense_variant,p.Arg407Gln,ENST00000397118,;AP1G2,upstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000397120,;AP1G2,upstream_gene_variant,,ENST00000308724,;AP1G2,upstream_gene_variant,,ENST00000556843,;RP11-66N24.3,downstream_gene_variant,,ENST00000555968,;AP1G2,upstream_gene_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000557619,;AP1G2,upstream_gene_variant,,ENST00000556943,;AP1G2,upstream_gene_variant,,ENST00000554069,;AP1G2,upstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000556743,;AP1G2,upstream_gene_variant,,ENST00000535852,;AP1G2,upstream_gene_variant,,ENST00000460049,;JPH4,downstream_gene_variant,,ENST00000553505,;AP1G2,upstream_gene_variant,,ENST00000554816,;AP1G2,upstream_gene_variant,,ENST00000555896,;AP1G2,upstream_gene_variant,,ENST00000553756,;AP1G2,upstream_gene_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000465445,;	T	ENSG00000092051	ENST00000397118	Transcript	missense_variant	2123	1220	407	R/Q	cGa/cAa	rs201428906,COSM4050111	.	.	-1	JPH4	HGNC	20156	protein_coding	YES	CCDS9603.1	ENSP00000380307	JPH4_HUMAN	.	UPI00001C1F68	.	tolerated(0.11)	benign(0.001)	5/7	.	PIRSF_domain:PIRSF037387,hmmpanther:PTHR23085:SF14,hmmpanther:PTHR23085	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATTCGAGCT	byCluster|by1000G	5	ESCA
CTAGE5	0	.	GRCh37	14	39763208	39763208	+	Missense_Mutation	SNP	C	C	T	rs139644527	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.515C>T	p.Ala172Val	p.A172V	ENST00000396158	7/24	105	71	34	102	102	0	CTAGE5,missense_variant,p.Ala138Val,ENST00000396165,;CTAGE5,missense_variant,p.Ala172Val,ENST00000396158,;CTAGE5,missense_variant,p.Ala129Val,ENST00000555716,;RP11-407N17.3,missense_variant,p.Ala702Val,ENST00000553728,;CTAGE5,missense_variant,p.Ala167Val,ENST00000341502,;CTAGE5,missense_variant,p.Ala138Val,ENST00000553352,;CTAGE5,missense_variant,p.Ala167Val,ENST00000280083,;CTAGE5,missense_variant,p.Ala92Val,ENST00000556148,;CTAGE5,missense_variant,p.Ala155Val,ENST00000341749,;CTAGE5,missense_variant,p.Ala167Val,ENST00000348007,;RP11-407N17.3,missense_variant,p.Ala138Val,ENST00000603904,;CTAGE5,missense_variant,p.Ala87Val,ENST00000557038,;CTAGE5,downstream_gene_variant,,ENST00000554392,;CTAGE5,non_coding_transcript_exon_variant,,ENST00000556990,;	T	ENSG00000150527	ENST00000396158	Transcript	missense_variant	851	515	172	A/V	gCg/gTg	rs139644527	.	.	1	CTAGE5	HGNC	7057	protein_coding	YES	CCDS58316.1	ENSP00000379462	CTGE5_HUMAN	.	UPI0001AE69C9	.	tolerated(0.29)	benign(0.027)	7/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.0011	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGGCGGATA	byCluster|by1000G	5	ESCA
AKAP5	0	.	GRCh37	14	64935503	64935503	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391A>G	p.Lys131Glu	p.K131E	ENST00000394718	2/2	77	65	11	77	77	0	AKAP5,missense_variant,p.Lys131Glu,ENST00000394718,;AKAP5,missense_variant,p.Lys131Glu,ENST00000320636,;ZBTB25,intron_variant,,ENST00000555424,;ZBTB25,intron_variant,,ENST00000555220,;	G	ENSG00000179841	ENST00000394718	Transcript	missense_variant	769	391	131	K/E	Aaa/Gaa	.	.	.	1	AKAP5	HGNC	375	protein_coding	YES	CCDS9764.1	ENSP00000378207	AKAP5_HUMAN	.	UPI0000140927	.	deleterious(0.01)	benign(0.339)	2/2	.	hmmpanther:PTHR15182:SF0,hmmpanther:PTHR15182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATAAAATTC	.	5	ESCA
ACOT6	0	.	GRCh37	14	74083610	74083610	+	5'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-269C>T	.	.	ENST00000381139	1/2	21	14	7	15	15	0	ACOT6,5_prime_UTR_variant,,ENST00000381139,;ACOT6,intron_variant,,ENST00000554229,;RP3-414A15.10,non_coding_transcript_exon_variant,,ENST00000555011,;RP3-414A15.10,downstream_gene_variant,,ENST00000555500,;	T	ENSG00000205669	ENST00000381139	Transcript	5_prime_UTR_variant	63	.	.	.	.	.	.	.	1	ACOT6	HGNC	33159	protein_coding	YES	CCDS32118.1	ENSP00000370531	ACOT6_HUMAN	G3V3W6_HUMAN	UPI00005BB7DB	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTACCCCCAA	.	5	ESCA
SYNDIG1L	0	.	GRCh37	14	74876117	74876117	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331G>T	p.Ala111Ser	p.A111S	ENST00000331628	2/4	44	35	8	42	42	0	SYNDIG1L,missense_variant,p.Ala111Ser,ENST00000554823,;SYNDIG1L,missense_variant,p.Ala111Ser,ENST00000331628,;SYNDIG1L,downstream_gene_variant,,ENST00000554953,;	A	ENSG00000183379	ENST00000331628	Transcript	missense_variant	579	331	111	A/S	Gct/Tct	.	.	.	-1	SYNDIG1L	HGNC	32388	protein_coding	YES	CCDS41970.1	ENSP00000331474	SYN1L_HUMAN	G3V402_HUMAN	UPI0000D6242F	.	tolerated(0.96)	benign(0.03)	2/4	.	hmmpanther:PTHR14768:SF4,hmmpanther:PTHR14768	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGCTTGGC	.	5	ESCA
NRDE2	0	.	GRCh37	14	90756756	90756756	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2038T>A	p.Phe680Ile	p.F680I	ENST00000354366	10/14	70	57	13	50	50	0	NRDE2,missense_variant,p.Phe449Ile,ENST00000357904,;NRDE2,missense_variant,p.Phe680Ile,ENST00000354366,;NRDE2,downstream_gene_variant,,ENST00000554464,;NRDE2,3_prime_UTR_variant,,ENST00000553409,;NRDE2,3_prime_UTR_variant,,ENST00000556189,;NRDE2,upstream_gene_variant,,ENST00000555903,;	T	ENSG00000119720	ENST00000354366	Transcript	missense_variant	2271	2038	680	F/I	Ttc/Atc	.	.	.	-1	NRDE2	HGNC	20186	protein_coding	YES	CCDS9890.1	ENSP00000346335	NRDE2_HUMAN	Q658X2_HUMAN,E9PBK4_HUMAN	UPI00001FD9DB	.	tolerated(0.42)	benign(0.002)	10/14	.	hmmpanther:PTHR13471,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGAAAAAAG	.	5	ESCA
RPS6KA5	0	.	GRCh37	14	91338321	91338321	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*97C>G	.	.	ENST00000261991	17/17	60	44	16	63	63	0	RPS6KA5,3_prime_UTR_variant,,ENST00000261991,;RPS6KA5,3_prime_UTR_variant,,ENST00000536315,;RPS6KA5,downstream_gene_variant,,ENST00000556178,;	C	ENSG00000100784	ENST00000261991	Transcript	3_prime_UTR_variant	2680	.	.	.	.	.	.	.	-1	RPS6KA5	HGNC	10434	protein_coding	YES	CCDS9893.1	ENSP00000261991	KS6A5_HUMAN	Q9UG98_HUMAN,B7Z2Y5_HUMAN	UPI0000031C30	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGAGACCAA	.	5	ESCA
SETD3	0	.	GRCh37	14	99870582	99870582	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000331768	11/13	50	38	12	57	57	0	SETD3,missense_variant,p.Arg386Gln,ENST00000331768,;SETD3,3_prime_UTR_variant,,ENST00000446066,;SETD3,intron_variant,,ENST00000489770,;SETD3,downstream_gene_variant,,ENST00000453764,;	T	ENSG00000183576	ENST00000331768	Transcript	missense_variant	1317	1157	386	R/Q	cGa/cAa	.	.	.	-1	SETD3	HGNC	20493	protein_coding	YES	CCDS9951.1	ENSP00000327436	SETD3_HUMAN	.	UPI000000CC6D	.	deleterious(0.01)	possibly_damaging(0.581)	11/13	.	PROSITE_profiles:PS51565,hmmpanther:PTHR13271,hmmpanther:PTHR13271:SF8,Pfam_domain:PF09273,Gene3D:2h21A02,Superfamily_domains:0040997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTCGGAGA	.	5	ESCA
ASB7	0	.	GRCh37	15	101170231	101170231	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801C>T	p.%3D	p.F267F	ENST00000332783	5/6	127	100	26	118	118	0	ASB7,synonymous_variant,p.%3D,ENST00000332783,;ASB7,synonymous_variant,p.%3D,ENST00000343276,;ASB7,intron_variant,,ENST00000558747,;	T	ENSG00000183475	ENST00000332783	Transcript	synonymous_variant	1586	801	267	F	ttC/ttT	.	.	.	1	ASB7	HGNC	17182	protein_coding	YES	CCDS10387.1	ENSP00000328327	ASB7_HUMAN	.	UPI00001B3F4D	.	.	.	5/6	.	hmmpanther:PTHR24123:SF13,hmmpanther:PTHR24123,Gene3D:1.25.40.20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCTTACA	.	5	ESCA
SNORD115-41	0	.	GRCh37	15	25490689	25490689	+	RNA	SNP	A	A	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.65A>C	.	.	ENST00000363608	1/1	34	21	12	63	63	0	SNORD115-41,non_coding_transcript_exon_variant,,ENST00000363608,;SNORD115-40,downstream_gene_variant,,ENST00000606510,;SNORD115-43,upstream_gene_variant,,ENST00000365503,;SNORD115-42,upstream_gene_variant,,ENST00000364273,;SNORD115-39,downstream_gene_variant,,ENST00000363694,;SNHG14,intron_variant,,ENST00000453082,;	C	ENSG00000200478	ENST00000363608	Transcript	non_coding_transcript_exon_variant	65	.	.	.	.	.	.	.	1	SNORD115-41	HGNC	33060	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAATAGGATT	.	5	ESCA
STARD9	0	.	GRCh37	15	42985567	42985567	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11791C>T	p.His3931Tyr	p.H3931Y	ENST00000290607	23/33	32	25	6	40	40	0	STARD9,missense_variant,p.His3931Tyr,ENST00000290607,;STARD9,missense_variant,p.His1259Tyr,ENST00000562619,;	T	ENSG00000159433	ENST00000290607	Transcript	missense_variant	11848	11791	3931	H/Y	Cac/Tac	.	.	.	1	STARD9	HGNC	19162	protein_coding	YES	CCDS53935.1	ENSP00000290607	STAR9_HUMAN	B4DMS6_HUMAN	UPI0001BE8155	.	.	benign(0.386)	23/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCCACCAG	.	5	ESCA
CTDSPL2	0	.	GRCh37	15	44818183	44818183	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1811A>C	.	.	ENST00000260327	13/13	145	117	27	163	163	0	CTDSPL2,3_prime_UTR_variant,,ENST00000558373,;CTDSPL2,3_prime_UTR_variant,,ENST00000260327,;CTDSPL2,3_prime_UTR_variant,,ENST00000396780,;CTDSPL2,downstream_gene_variant,,ENST00000558966,;EIF3J-AS1,downstream_gene_variant,,ENST00000560750,;CTDSPL2,downstream_gene_variant,,ENST00000559738,;CTDSPL2,downstream_gene_variant,,ENST00000559175,;CTDSPL2,downstream_gene_variant,,ENST00000560620,;	C	ENSG00000137770	ENST00000260327	Transcript	3_prime_UTR_variant	3775	.	.	.	.	.	.	.	1	CTDSPL2	HGNC	26936	protein_coding	YES	CCDS10110.1	ENSP00000260327	CTSL2_HUMAN	H0YNW9_HUMAN,H0YNU2_HUMAN,H0YMH7_HUMAN	UPI000004A0B3	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAAAACAAAA	.	5	ESCA
DMXL2	0	.	GRCh37	15	51857295	51857295	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.354G>C	p.Trp118Cys	p.W118C	ENST00000543779	4/43	143	115	28	143	143	0	DMXL2,missense_variant,p.Trp118Cys,ENST00000449909,;DMXL2,missense_variant,p.Trp118Cys,ENST00000543779,;DMXL2,missense_variant,p.Trp118Cys,ENST00000251076,;DMXL2,non_coding_transcript_exon_variant,,ENST00000560421,;DMXL2,downstream_gene_variant,,ENST00000558507,;	G	ENSG00000104093	ENST00000543779	Transcript	missense_variant	444	354	118	W/C	tgG/tgC	.	.	.	-1	DMXL2	HGNC	2938	protein_coding	YES	CCDS53946.1	ENSP00000441858	DMXL2_HUMAN	.	UPI00001FE4C2	.	deleterious(0)	probably_damaging(0.999)	4/43	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR13950:SF11,hmmpanther:PTHR13950	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATCCCATGC	.	5	ESCA
UNC13C	0	.	GRCh37	15	54307496	54307496	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2396C>G	p.Ser799Cys	p.S799C	ENST00000260323	1/32	26	17	8	38	38	0	UNC13C,missense_variant,p.Ser799Cys,ENST00000537900,;UNC13C,missense_variant,p.Ser799Cys,ENST00000545554,;UNC13C,missense_variant,p.Ser799Cys,ENST00000260323,;	G	ENSG00000137766	ENST00000260323	Transcript	missense_variant	2396	2396	799	S/C	tCt/tGt	.	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	deleterious_low_confidence(0)	probably_damaging(0.935)	1/32	.	hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATCTACAC	.	5	ESCA
UNC13C	0	.	GRCh37	15	54542505	54542505	+	Missense_Mutation	SNP	C	C	T	rs563857639	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3311C>T	p.Thr1104Met	p.T1104M	ENST00000260323	7/32	24	20	4	33	33	0	UNC13C,missense_variant,p.Thr1102Met,ENST00000537900,;UNC13C,missense_variant,p.Thr1104Met,ENST00000545554,;UNC13C,missense_variant,p.Thr1104Met,ENST00000260323,;	T	ENSG00000137766	ENST00000260323	Transcript	missense_variant	3311	3311	1104	T/M	aCg/aTg	rs563857639	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	deleterious_low_confidence(0.01)	probably_damaging(0.97)	7/32	.	PROSITE_profiles:PS50081,hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2,PROSITE_patterns:PS00479,Pfam_domain:PF00130,Gene3D:3.30.60.20,SMART_domains:SM00109,Superfamily_domains:SSF57889	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGACGGCTA	by1000G	4	ESCA
UNC13C	0	.	GRCh37	15	54614270	54614270	+	Missense_Mutation	SNP	C	C	G	rs769553822	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4402C>G	p.Arg1468Gly	p.R1468G	ENST00000260323	13/32	49	42	7	68	68	0	UNC13C,missense_variant,p.Arg1466Gly,ENST00000537900,;UNC13C,missense_variant,p.Arg1468Gly,ENST00000545554,;UNC13C,missense_variant,p.Arg1468Gly,ENST00000260323,;UNC13C,non_coding_transcript_exon_variant,,ENST00000561210,;HNRNPA1P74,upstream_gene_variant,,ENST00000560782,;	G	ENSG00000137766	ENST00000260323	Transcript	missense_variant	4402	4402	1468	R/G	Cga/Gga	rs769553822	.	.	1	UNC13C	HGNC	23149	protein_coding	YES	CCDS45264.1	ENSP00000260323	UN13C_HUMAN	H3BRP8_HUMAN	UPI0000DD82AB	.	deleterious_low_confidence(0)	probably_damaging(0.998)	13/32	.	hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGATCGATTT	byFrequency	5	ESCA
PTPLAD1	0	.	GRCh37	15	65855215	65855215	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.525G>C	p.Leu175Phe	p.L175F	ENST00000261875	6/11	93	71	21	114	114	0	PTPLAD1,missense_variant,p.Leu58Phe,ENST00000569894,;PTPLAD1,missense_variant,p.Leu175Phe,ENST00000261875,;PTPLAD1,missense_variant,p.Leu150Phe,ENST00000568793,;PTPLAD1,missense_variant,p.Leu58Phe,ENST00000566074,;PTPLAD1,missense_variant,p.Leu58Phe,ENST00000562901,;PTPLAD1,missense_variant,p.Leu120Phe,ENST00000442729,;PTPLAD1,missense_variant,p.Leu58Phe,ENST00000562832,;PTPLAD1,missense_variant,p.Leu213Phe,ENST00000565299,;PTPLAD1,missense_variant,p.Leu58Phe,ENST00000566511,;	C	ENSG00000074696	ENST00000261875	Transcript	missense_variant	691	525	175	L/F	ttG/ttC	.	.	.	1	PTPLAD1	HGNC	24175	protein_coding	YES	CCDS45282.1	ENSP00000261875	HACD3_HUMAN	H3BRL8_HUMAN,H3BMZ1_HUMAN	UPI00001D6EF0	.	tolerated(0.18)	benign(0.076)	6/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11035,hmmpanther:PTHR11035:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTGGGAAA	.	5	ESCA
PTPLAD1	0	.	GRCh37	15	65856552	65856552	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.533-1G>C	.	p.X178_splice	ENST00000261875	.	30	25	4	44	44	0	PTPLAD1,splice_acceptor_variant,,ENST00000569894,;PTPLAD1,splice_acceptor_variant,,ENST00000261875,;PTPLAD1,splice_acceptor_variant,,ENST00000568793,;PTPLAD1,splice_acceptor_variant,,ENST00000566074,;PTPLAD1,splice_acceptor_variant,,ENST00000562901,;PTPLAD1,splice_acceptor_variant,,ENST00000442729,;PTPLAD1,splice_acceptor_variant,,ENST00000562832,;PTPLAD1,splice_acceptor_variant,,ENST00000565299,;PTPLAD1,splice_acceptor_variant,,ENST00000566511,;	C	ENSG00000074696	ENST00000261875	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	PTPLAD1	HGNC	24175	protein_coding	YES	CCDS45282.1	ENSP00000261875	HACD3_HUMAN	H3BRL8_HUMAN,H3BMZ1_HUMAN	UPI00001D6EF0	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CTATAGAGTCC	.	4	ESCA
TMED3	0	.	GRCh37	15	79614407	79614407	+	Missense_Mutation	SNP	C	C	T	rs754708207	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505C>T	p.Arg169Trp	p.R169W	ENST00000299705	3/3	37	27	10	53	53	0	TMED3,missense_variant,p.Arg169Trp,ENST00000299705,;TMED3,intron_variant,,ENST00000536821,;TMED3,intron_variant,,ENST00000424155,;TMED3,non_coding_transcript_exon_variant,,ENST00000558562,;TMED3,3_prime_UTR_variant,,ENST00000543455,;	T	ENSG00000166557	ENST00000299705	Transcript	missense_variant	693	505	169	R/W	Cgg/Tgg	rs754708207	.	.	1	TMED3	HGNC	28889	protein_coding	YES	CCDS10310.1	ENSP00000299705	TMED3_HUMAN	Q9UMB6_HUMAN	UPI0000048ED6	.	deleterious(0)	probably_damaging(0.997)	3/3	.	hmmpanther:PTHR22811,hmmpanther:PTHR22811:SF60,Pfam_domain:PF01105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGACCGGGCC	byFrequency	5	ESCA
ADAMTSL3	0	.	GRCh37	15	84708145	84708145	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1587G>T	.	.	ENST00000286744	30/30	34	19	14	53	53	0	ADAMTSL3,3_prime_UTR_variant,,ENST00000286744,;ADAMTSL3,3_prime_UTR_variant,,ENST00000567476,;	T	ENSG00000156218	ENST00000286744	Transcript	3_prime_UTR_variant	6887	.	.	.	.	.	.	.	1	ADAMTSL3	HGNC	14633	protein_coding	YES	CCDS10326.1	ENSP00000286744	ATL3_HUMAN	.	UPI00001615A5	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTTGAGCAC	.	5	ESCA
LITAF	0	.	GRCh37	16	11643500	11643500	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479G>A	p.Arg160His	p.R160H	ENST00000571688	4/4	28	16	12	37	37	0	LITAF,missense_variant,p.Arg160His,ENST00000339430,;LITAF,missense_variant,p.Arg160His,ENST00000574763,;LITAF,missense_variant,p.Arg160His,ENST00000571688,;LITAF,missense_variant,p.Arg160His,ENST00000570904,;LITAF,missense_variant,p.Arg160His,ENST00000576036,;LITAF,missense_variant,p.Arg67His,ENST00000572255,;LITAF,synonymous_variant,p.%3D,ENST00000381810,;LITAF,3_prime_UTR_variant,,ENST00000413364,;LITAF,3_prime_UTR_variant,,ENST00000571459,;LITAF,downstream_gene_variant,,ENST00000570798,;LITAF,downstream_gene_variant,,ENST00000574701,;LITAF,downstream_gene_variant,,ENST00000571976,;LITAF,downstream_gene_variant,,ENST00000571627,;LITAF,3_prime_UTR_variant,,ENST00000575426,;LITAF,3_prime_UTR_variant,,ENST00000573332,;	T	ENSG00000189067	ENST00000571688	Transcript	missense_variant	710	479	160	R/H	cGt/cAt	.	.	.	-1	LITAF	HGNC	16841	protein_coding	YES	CCDS32386.1	ENSP00000459533	LITAF_HUMAN	I3L3U8_HUMAN,I3L329_HUMAN,I3L1R0_HUMAN,I3L1I9_HUMAN,I3L1H3_HUMAN	UPI000007094D	.	deleterious(0)	probably_damaging(0.984)	4/4	.	hmmpanther:PTHR23292,hmmpanther:PTHR23292:SF2,Pfam_domain:PF10601,SMART_domains:SM00714	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAACGCTTG	.	5	ESCA
HS3ST6	0	.	GRCh37	16	1961956	1961956	+	Missense_Mutation	SNP	C	C	T	rs752407140	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.571G>A	p.Ala191Thr	p.A191T	ENST00000443547	2/2	54	41	13	81	81	0	HS3ST6,missense_variant,p.Ala222Thr,ENST00000293937,;HS3ST6,missense_variant,p.Ala191Thr,ENST00000443547,;HS3ST6,missense_variant,p.Ala239Thr,ENST00000454677,;	T	ENSG00000162040	ENST00000443547	Transcript	missense_variant	571	571	191	A/T	Gcc/Acc	rs752407140	.	.	-1	HS3ST6	HGNC	14178	protein_coding	YES	CCDS45381.1	ENSP00000390354	.	C9JH64_HUMAN	UPI0000E02544	.	deleterious(0.01)	probably_damaging(0.99)	2/2	.	hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF7,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGGCGCTCC	byFrequency	5	ESCA
SLC9A3R2	0	.	GRCh37	16	2086465	2086465	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555C>T	p.%3D	p.A185A	ENST00000424542	3/7	54	28	25	60	60	0	SLC9A3R2,synonymous_variant,p.%3D,ENST00000563587,;SLC9A3R2,synonymous_variant,p.%3D,ENST00000432365,;SLC9A3R2,synonymous_variant,p.%3D,ENST00000561844,;SLC9A3R2,synonymous_variant,p.%3D,ENST00000565855,;SLC9A3R2,synonymous_variant,p.%3D,ENST00000424542,;SLC9A3R2,synonymous_variant,p.%3D,ENST00000566198,;NTHL1,downstream_gene_variant,,ENST00000566380,;NTHL1,downstream_gene_variant,,ENST00000219066,;SLC9A3R2,downstream_gene_variant,,ENST00000567504,;SLC9A3R2,non_coding_transcript_exon_variant,,ENST00000565086,;NTHL1,downstream_gene_variant,,ENST00000562951,;SLC9A3R2,non_coding_transcript_exon_variant,,ENST00000564033,;NTHL1,downstream_gene_variant,,ENST00000568513,;NTHL1,downstream_gene_variant,,ENST00000561841,;NTHL1,downstream_gene_variant,,ENST00000561862,;NTHL1,downstream_gene_variant,,ENST00000565406,;NTHL1,downstream_gene_variant,,ENST00000567727,;	T	ENSG00000065054	ENST00000424542	Transcript	synonymous_variant	693	555	185	A	gcC/gcT	.	.	.	1	SLC9A3R2	HGNC	11076	protein_coding	YES	CCDS45382.1	ENSP00000408005	NHRF2_HUMAN	Q6NTG0_HUMAN,H3BQS0_HUMAN	UPI0000070578	.	.	.	3/7	.	PROSITE_profiles:PS50106,hmmpanther:PTHR14191:SF4,hmmpanther:PTHR14191,Pfam_domain:PF00595,Gene3D:2.30.42.10,PIRSF_domain:PIRSF037866,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCCGCCCG	.	5	ESCA
DCUN1D3	0	.	GRCh37	16	20869628	20869628	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1580C>T	.	.	ENST00000324344	3/3	68	54	13	105	105	0	DCUN1D3,3_prime_UTR_variant,,ENST00000324344,;ERI2,intron_variant,,ENST00000564349,;DCUN1D3,downstream_gene_variant,,ENST00000563934,;	A	ENSG00000188215	ENST00000324344	Transcript	3_prime_UTR_variant	2781	.	.	.	.	.	.	.	-1	DCUN1D3	HGNC	28734	protein_coding	YES	CCDS10592.1	ENSP00000319482	DCNL3_HUMAN	.	UPI000005032C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGCGTGGAG	.	5	ESCA
SLC9A3R2	0	.	GRCh37	16	2088287	2088287	+	3'UTR	SNP	G	G	A	rs537532339	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*302G>A	.	.	ENST00000424542	7/7	131	75	56	195	194	1	SLC9A3R2,3_prime_UTR_variant,,ENST00000432365,;SLC9A3R2,3_prime_UTR_variant,,ENST00000424542,;SLC9A3R2,3_prime_UTR_variant,,ENST00000566198,;NTHL1,downstream_gene_variant,,ENST00000566380,;SLC9A3R2,downstream_gene_variant,,ENST00000563587,;NTHL1,downstream_gene_variant,,ENST00000219066,;SLC9A3R2,downstream_gene_variant,,ENST00000561844,;SLC9A3R2,downstream_gene_variant,,ENST00000567504,;SLC9A3R2,downstream_gene_variant,,ENST00000565855,;SLC9A3R2,downstream_gene_variant,,ENST00000565086,;NTHL1,downstream_gene_variant,,ENST00000562951,;NTHL1,downstream_gene_variant,,ENST00000568513,;NTHL1,downstream_gene_variant,,ENST00000561841,;NTHL1,downstream_gene_variant,,ENST00000561862,;NTHL1,downstream_gene_variant,,ENST00000565406,;SLC9A3R2,downstream_gene_variant,,ENST00000564033,;NTHL1,downstream_gene_variant,,ENST00000567727,;	A	ENSG00000065054	ENST00000424542	Transcript	3_prime_UTR_variant	1454	.	.	.	.	rs537532339	.	.	1	SLC9A3R2	HGNC	11076	protein_coding	YES	CCDS45382.1	ENSP00000408005	NHRF2_HUMAN	Q6NTG0_HUMAN,H3BQS0_HUMAN	UPI0000070578	.	.	.	7/7	.	.	A:0.0006	A:0	A:0	.	A:0.003	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGCGGGGCG	byFrequency|by1000G	5	ESCA
RBBP6	0	.	GRCh37	16	24581206	24581206	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3195G>A	p.%3D	p.E1065E	ENST00000319715	17/18	58	33	25	63	63	0	RBBP6,synonymous_variant,p.%3D,ENST00000319715,;RBBP6,synonymous_variant,p.%3D,ENST00000348022,;RBBP6,synonymous_variant,p.%3D,ENST00000564314,;RBBP6,intron_variant,,ENST00000381039,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,;	A	ENSG00000122257	ENST00000319715	Transcript	synonymous_variant	3627	3195	1065	E	gaG/gaA	.	.	.	1	RBBP6	HGNC	9889	protein_coding	YES	CCDS10621.1	ENSP00000317872	RBBP6_HUMAN	I3L3Y2_HUMAN,H3BUN0_HUMAN,H3BSK8_HUMAN	UPI00001A96B8	.	.	.	17/18	.	hmmpanther:PTHR15439:SF1,hmmpanther:PTHR15439	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGAGACTCC	.	5	ESCA
SRCAP	0	.	GRCh37	16	30749318	30749318	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7957G>T	p.Glu2653Ter	p.E2653*	ENST00000262518	34/34	13	6	7	11	11	0	SRCAP,stop_gained,p.Glu2653Ter,ENST00000262518,;SRCAP,stop_gained,p.Glu2495Ter,ENST00000344771,;SRCAP,stop_gained,p.Glu2591Ter,ENST00000395059,;RP11-2C24.4,upstream_gene_variant,,ENST00000483578,;SRCAP,stop_gained,p.Glu2476Ter,ENST00000380361,;SRCAP,downstream_gene_variant,,ENST00000474008,;	T	ENSG00000080603	ENST00000262518	Transcript	stop_gained	8342	7957	2653	E/*	Gag/Tag	.	.	.	1	SRCAP	HGNC	16974	protein_coding	YES	CCDS10689.2	ENSP00000262518	SRCAP_HUMAN	G1UI29_HUMAN,C9J4U4_HUMAN	UPI000059D368	.	.	.	34/34	.	hmmpanther:PTHR10799:SF581,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTGGAGCTC	.	2	ESCA
PRSS36	0	.	GRCh37	16	31151696	31151696	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2208C>G	p.Ile736Met	p.I736M	ENST00000268281	14/15	50	35	14	74	74	0	PRSS36,missense_variant,p.Ile736Met,ENST00000268281,;PRSS36,missense_variant,p.Ile731Met,ENST00000569305,;PRSS36,intron_variant,,ENST00000418068,;PRSS8,upstream_gene_variant,,ENST00000568261,;PRSS8,upstream_gene_variant,,ENST00000567797,;PRSS8,upstream_gene_variant,,ENST00000317508,;PRSS8,upstream_gene_variant,,ENST00000567531,;PRSS36,3_prime_UTR_variant,,ENST00000571878,;PRSS36,non_coding_transcript_exon_variant,,ENST00000562368,;PRSS36,downstream_gene_variant,,ENST00000563693,;PRSS8,upstream_gene_variant,,ENST00000567833,;PRSS8,upstream_gene_variant,,ENST00000564025,;	C	ENSG00000178226	ENST00000268281	Transcript	missense_variant	2267	2208	736	I/M	atC/atG	.	.	.	-1	PRSS36	HGNC	26906	protein_coding	YES	CCDS32436.1	ENSP00000268281	POLS2_HUMAN	B4DNP1_HUMAN	UPI00001FFF6A	.	tolerated(0.05)	benign(0.116)	14/15	.	Superfamily_domains:SSF50494,PIRSF_domain:PIRSF037933,SMART_domains:SM00020,Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAGATTCG	.	5	ESCA
SEPT12	0	.	GRCh37	16	4838399	4838399	+	5'UTR	SNP	C	C	A	rs550303536	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-141G>T	.	.	ENST00000268231	1/10	17	11	5	19	19	0	SEPT12,5_prime_UTR_variant,,ENST00000268231,;SMIM22,5_prime_UTR_variant,,ENST00000589721,;SMIM22,upstream_gene_variant,,ENST00000589327,;SEPT12,upstream_gene_variant,,ENST00000396693,;SEPT12,upstream_gene_variant,,ENST00000591624,;SEPT12,non_coding_transcript_exon_variant,,ENST00000591861,;SEPT12,upstream_gene_variant,,ENST00000590303,;SEPT12,upstream_gene_variant,,ENST00000590741,;SEPT12,upstream_gene_variant,,ENST00000587603,;SMIM22,upstream_gene_variant,,ENST00000591004,;SEPT12,upstream_gene_variant,,ENST00000588241,;	A	ENSG00000140623	ENST00000268231	Transcript	5_prime_UTR_variant	124	.	.	.	.	rs550303536	.	.	-1	SEPT12	HGNC	26348	protein_coding	YES	CCDS10522.1	ENSP00000268231	SEP12_HUMAN	K7EP92_HUMAN	UPI000007422A	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTGCACTTG	byCluster	5	ESCA
RBL2	0	.	GRCh37	16	53499461	53499461	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1810C>T	p.Pro604Ser	p.P604S	ENST00000262133	13/22	163	102	61	175	175	0	RBL2,missense_variant,p.Pro388Ser,ENST00000544545,;RBL2,missense_variant,p.Pro604Ser,ENST00000262133,;RBL2,missense_variant,p.Pro530Ser,ENST00000544405,;RBL2,non_coding_transcript_exon_variant,,ENST00000379935,;RBL2,non_coding_transcript_exon_variant,,ENST00000562850,;RBL2,downstream_gene_variant,,ENST00000561512,;RBL2,upstream_gene_variant,,ENST00000562837,;	T	ENSG00000103479	ENST00000262133	Transcript	missense_variant	1947	1810	604	P/S	Cca/Tca	.	.	.	1	RBL2	HGNC	9894	protein_coding	YES	CCDS10748.1	ENSP00000262133	RBL2_HUMAN	J3KSF7_HUMAN	UPI000013D264	.	deleterious(0.01)	benign(0.41)	13/22	.	hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF8,Pfam_domain:PF01858,Superfamily_domains:SSF47954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCCACTC	.	5	ESCA
DDX19A	0	.	GRCh37	16	70404231	70404231	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1126G>T	p.Glu376Ter	p.E376*	ENST00000302243	10/12	44	28	15	53	53	0	DDX19A,stop_gained,p.Glu286Ter,ENST00000443119,;DDX19A,stop_gained,p.Glu294Ter,ENST00000575878,;DDX19A,stop_gained,p.Glu376Ter,ENST00000302243,;DDX19A,stop_gained,p.Glu345Ter,ENST00000417604,;RP11-529K1.3,downstream_gene_variant,,ENST00000567706,;DDX19A,3_prime_UTR_variant,,ENST00000569319,;DDX19A,3_prime_UTR_variant,,ENST00000569771,;DDX19A,non_coding_transcript_exon_variant,,ENST00000566574,;DDX19A,non_coding_transcript_exon_variant,,ENST00000562140,;DDX19A,downstream_gene_variant,,ENST00000568779,;RP11-529K1.3,downstream_gene_variant,,ENST00000565116,;DDX19A,downstream_gene_variant,,ENST00000567012,;	T	ENSG00000168872	ENST00000302243	Transcript	stop_gained	1289	1126	376	E/*	Gag/Tag	.	.	.	1	DDX19A	HGNC	25628	protein_coding	YES	CCDS10889.1	ENSP00000306117	DD19A_HUMAN	Q69YM2_HUMAN,Q68DY7_HUMAN,H3BTB3_HUMAN	UPI000007100E	.	.	.	10/12	.	PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF194,hmmpanther:PTHR24031,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTGAGCGC	.	5	ESCA
HYDIN	0	.	GRCh37	16	71019134	71019134	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4286C>G	p.Ser1429Cys	p.S1429C	ENST00000393567	28/86	46	30	16	67	67	0	HYDIN,missense_variant,p.Ser1429Cys,ENST00000393567,;HYDIN,3_prime_UTR_variant,,ENST00000393552,;	C	ENSG00000157423	ENST00000393567	Transcript	missense_variant	4437	4286	1429	S/C	tCt/tGt	.	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	probably_damaging(0.987)	28/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGAAGAC	.	5	ESCA
PHLPP2	0	.	GRCh37	16	71679091	71679091	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3702C>T	.	.	ENST00000568954	19/19	51	39	12	46	46	0	PHLPP2,3_prime_UTR_variant,,ENST00000356272,;PHLPP2,3_prime_UTR_variant,,ENST00000568954,;PHLPP2,3_prime_UTR_variant,,ENST00000393524,;PHLPP2,intron_variant,,ENST00000360429,;PHLPP2,intron_variant,,ENST00000540628,;MARVELD3,downstream_gene_variant,,ENST00000299952,;MARVELD3,downstream_gene_variant,,ENST00000565261,;PHLPP2,downstream_gene_variant,,ENST00000567016,;MARVELD3,downstream_gene_variant,,ENST00000561682,;PHLPP2,intron_variant,,ENST00000568004,;PHLPP2,intron_variant,,ENST00000564884,;	A	ENSG00000040199	ENST00000568954	Transcript	3_prime_UTR_variant	8053	.	.	.	.	.	.	.	-1	PHLPP2	HGNC	29149	protein_coding	YES	CCDS32479.1	ENSP00000457991	PHLP2_HUMAN	.	UPI0000229F5A	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTGGGAGAA	.	5	ESCA
TERF2IP	0	.	GRCh37	16	75690378	75690378	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1069G>C	p.Asp357His	p.D357H	ENST00000300086	3/3	44	27	16	42	42	0	TERF2IP,missense_variant,p.Asp357His,ENST00000300086,;TERF2IP,intron_variant,,ENST00000564671,;TERF2IP,downstream_gene_variant,,ENST00000569234,;	C	ENSG00000166848	ENST00000300086	Transcript	missense_variant	1166	1069	357	D/H	Gat/Cat	.	.	.	1	TERF2IP	HGNC	19246	protein_coding	YES	CCDS32491.1	ENSP00000300086	TE2IP_HUMAN	.	UPI0000136B77	.	deleterious(0)	probably_damaging(1)	3/3	.	hmmpanther:PTHR16466:SF6,hmmpanther:PTHR16466,Pfam_domain:PF11626	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGCTGATGGA	.	5	ESCA
ANKRD11	0	.	GRCh37	16	89349603	89349603	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3347C>T	p.Ala1116Val	p.A1116V	ENST00000301030	9/13	34	30	3	38	38	0	ANKRD11,missense_variant,p.Ala1116Val,ENST00000378330,;ANKRD11,missense_variant,p.Ala1116Val,ENST00000301030,;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;ANKRD11,downstream_gene_variant,,ENST00000562275,;ANKRD11,downstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000378332,;	A	ENSG00000167522	ENST00000301030	Transcript	missense_variant	3808	3347	1116	A/V	gCa/gTa	.	.	.	-1	ANKRD11	HGNC	21316	protein_coding	YES	CCDS32513.1	ENSP00000301030	ANR11_HUMAN	.	UPI00004569E1	.	.	possibly_damaging(0.601)	9/13	.	hmmpanther:PTHR24145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTCTGCGATG	.	4	ESCA
AFG3L1P	0	.	GRCh37	16	90057396	90057396	+	RNA	SNP	C	C	T	rs377595175	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.954C>T	.	.	ENST00000437774	8/11	17	10	7	21	21	0	AFG3L1P,non_coding_transcript_exon_variant,,ENST00000437774,;AFG3L1P,non_coding_transcript_exon_variant,,ENST00000418696,;AFG3L1P,non_coding_transcript_exon_variant,,ENST00000457926,;AFG3L1P,non_coding_transcript_exon_variant,,ENST00000436447,;AFG3L1P,non_coding_transcript_exon_variant,,ENST00000388970,;AFG3L1P,intron_variant,,ENST00000458301,;AFG3L1P,non_coding_transcript_exon_variant,,ENST00000427658,;AFG3L1P,non_coding_transcript_exon_variant,,ENST00000355531,;AFG3L1P,non_coding_transcript_exon_variant,,ENST00000557444,;	T	ENSG00000223959	ENST00000437774	Transcript	non_coding_transcript_exon_variant	954	.	.	.	.	rs377595175	.	.	1	AFG3L1P	HGNC	314	processed_transcript	.	.	.	.	.	.	.	.	.	8/11	.	.	.	.	.	.	.	.	.	T:0.0007	T:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGGCGTTGG	.	5	ESCA
MYO15A	0	.	GRCh37	17	18023073	18023073	+	Missense_Mutation	SNP	C	C	T	rs200056157	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.959C>T	p.Ser320Leu	p.S320L	ENST00000205890	2/66	88	67	21	147	147	0	MYO15A,missense_variant,p.Ser320Leu,ENST00000205890,;MYO15A,non_coding_transcript_exon_variant,,ENST00000583079,;	T	ENSG00000091536	ENST00000205890	Transcript	missense_variant	1297	959	320	S/L	tCg/tTg	rs200056157	.	.	1	MYO15A	HGNC	7594	protein_coding	YES	CCDS42271.1	ENSP00000205890	MYO15_HUMAN	K7EQV1_HUMAN,G3V4G3_HUMAN	UPI0000E59E6E	.	.	benign(0.177)	2/66	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	G:0	G:0.0004	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGTCGGGGT	byFrequency|byCluster	5	ESCA
ITGA2B	0	.	GRCh37	17	42462407	42462407	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.708G>C	p.%3D	p.S236S	ENST00000262407	7/30	53	42	11	71	71	0	ITGA2B,synonymous_variant,p.%3D,ENST00000262407,;ITGA2B,synonymous_variant,p.%3D,ENST00000353281,;ITGA2B,intron_variant,,ENST00000377068,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592253,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000591990,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592944,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592075,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000589645,;ITGA2B,intron_variant,,ENST00000592226,;ITGA2B,upstream_gene_variant,,ENST00000592462,;	G	ENSG00000005961	ENST00000262407	Transcript	synonymous_variant	740	708	236	S	tcG/tcC	.	.	.	-1	ITGA2B	HGNC	6138	protein_coding	YES	CCDS32665.1	ENSP00000262407	ITA2B_HUMAN	Q6LDK5_HUMAN,I6XCH0_HUMAN,F1C626_HUMAN	UPI00001868B8	.	.	.	7/30	.	PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF73,hmmpanther:PTHR23220,Gene3D:3nigC00,Superfamily_domains:SSF69318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTCGAGAA	.	5	ESCA
EFTUD2	0	.	GRCh37	17	42931671	42931671	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2313G>C	p.Gln771His	p.Q771H	ENST00000426333	23/28	48	43	5	41	41	0	EFTUD2,missense_variant,p.Gln736His,ENST00000402521,;EFTUD2,missense_variant,p.Gln771His,ENST00000591382,;EFTUD2,missense_variant,p.Gln771His,ENST00000426333,;EFTUD2,missense_variant,p.Gln761His,ENST00000592576,;EFTUD2,missense_variant,p.Gln105His,ENST00000590124,;HIGD1B,downstream_gene_variant,,ENST00000587021,;HIGD1B,downstream_gene_variant,,ENST00000591513,;HIGD1B,downstream_gene_variant,,ENST00000253410,;EFTUD2,missense_variant,p.Gln54His,ENST00000589769,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000590367,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000586276,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000590977,;EFTUD2,downstream_gene_variant,,ENST00000588340,;HIGD1B,downstream_gene_variant,,ENST00000586911,;	G	ENSG00000108883	ENST00000426333	Transcript	missense_variant	2611	2313	771	Q/H	caG/caC	.	.	.	-1	EFTUD2	HGNC	30858	protein_coding	YES	CCDS11489.1	ENSP00000392094	U5S1_HUMAN	K7EIV5_HUMAN,K7EIT3_HUMAN,B3KX19_HUMAN	UPI0000137931	.	deleterious(0)	probably_damaging(0.986)	23/28	.	hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF5,Gene3D:3.30.230.10,Pfam_domain:PF03764,SMART_domains:SM00889,Superfamily_domains:SSF54211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCCACTGGAA	.	4	ESCA
PRKCA	0	.	GRCh37	17	64801322	64801322	+	3'UTR	SNP	C	C	T	rs536546490	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1167C>T	.	.	ENST00000413366	17/17	41	29	12	39	39	0	PRKCA,3_prime_UTR_variant,,ENST00000413366,;	T	ENSG00000154229	ENST00000413366	Transcript	3_prime_UTR_variant	3212	.	.	.	.	rs536546490	.	.	1	PRKCA	HGNC	9393	protein_coding	YES	CCDS11664.1	ENSP00000408695	KPCA_HUMAN	L7RSM7_HUMAN	UPI000013DD98	.	.	.	17/17	.	.	-:0.0006	-:0	-:0	.	-:0.003	-:0	-:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAAACCCGGA	byFrequency|by1000G	2	ESCA
GALK1	0	.	GRCh37	17	73759429	73759429	+	Silent	SNP	C	C	T	rs765744088	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.447G>A	p.%3D	p.T149T	ENST00000588479	3/8	57	31	25	48	48	0	GALK1,synonymous_variant,p.%3D,ENST00000437911,;GALK1,synonymous_variant,p.%3D,ENST00000225614,;GALK1,synonymous_variant,p.%3D,ENST00000588479,;GALK1,upstream_gene_variant,,ENST00000592997,;GALK1,synonymous_variant,p.%3D,ENST00000587707,;GALK1,3_prime_UTR_variant,,ENST00000586244,;GALK1,non_coding_transcript_exon_variant,,ENST00000592494,;GALK1,downstream_gene_variant,,ENST00000589030,;GALK1,upstream_gene_variant,,ENST00000586733,;GALK1,upstream_gene_variant,,ENST00000589643,;	T	ENSG00000108479	ENST00000588479	Transcript	synonymous_variant	1022	447	149	T	acG/acA	rs765744088	.	.	-1	GALK1	HGNC	4118	protein_coding	YES	CCDS11728.1	ENSP00000465930	GALK1_HUMAN	Q71UH7_HUMAN,C8CHJ6_HUMAN	UPI000012B056	.	.	.	3/8	.	hmmpanther:PTHR10457:SF6,hmmpanther:PTHR10457,TIGRFAM_domain:TIGR00131,Gene3D:3.30.230.10,Pfam_domain:PF00288,PIRSF_domain:PIRSF000530,Superfamily_domains:SSF54211,Prints_domain:PR00959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTACGTGGC	byFrequency	5	ESCA
TP53	0	.	GRCh37	17	7576652	7576652	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.993+201G>A	.	.	ENST00000269305	.	41	28	12	53	53	0	TP53,synonymous_variant,p.%3D,ENST00000420246,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000269305,;TP53,intron_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000445888,;TP53,intron_variant,,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,intron_variant,,ENST00000504937,;TP53,intron_variant,,ENST00000504290,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	.	9/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTCTGGTC	.	5	ESCA
TP53	0	.	GRCh37	17	7578442	7578442	+	Missense_Mutation	SNP	T	T	C	rs148924904	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	5/11	24	12	12	18	18	0	TP53,missense_variant,p.Tyr163Cys,ENST00000508793,;TP53,missense_variant,p.Tyr163Cys,ENST00000413465,;TP53,missense_variant,p.Tyr163Cys,ENST00000420246,;TP53,missense_variant,p.Tyr163Cys,ENST00000269305,;TP53,missense_variant,p.Tyr31Cys,ENST00000509690,;TP53,missense_variant,p.Tyr163Cys,ENST00000359597,;TP53,missense_variant,p.Tyr70Cys,ENST00000514944,;TP53,missense_variant,p.Tyr163Cys,ENST00000445888,;TP53,missense_variant,p.Tyr163Cys,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	678	488	163	Y/C	tAc/tGc	CM942135,rs148924904,TP53_g.12476A>C,TP53_g.12476A>G,TP53_g.12476del,TP53_g.12476A>T,COSM10808,COSM45025,COSM129852,COSM308332,COSM308331,COSM129853,COSM129855,COSM308333,COSM3388214,COSM1649381,COSM129854,COSM308334	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(0.999)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	25404506	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Y163C|c.488A>G|126,SITE|p.Y70C|c.209A>G|30,SITE|p.Y31C|c.92A>G|33,SITE|p.Y163C|c.488A>G|9,SITE|p.Y163C|c.488A>G|13,SITE|p.Y163C|c.488A>G|30,SITE|p.Y163C|c.488A>G|30,CODON|p.0?|c.1_1182del1182|6,CODON|p.Y163*|c.489C>G|5,CODON|p.Y163Y|c.489C>T|3,CODON|p.Y163*|c.489C>A|3,CODON|p.Y163S|c.488A>C|5,BUFFER|p.Q167fs*13|c.499_500delCA|3,BUFFER|p.Q167*|c.499C>T|5,BUFFER|p.Q167*|c.499C>T|5,BUFFER|p.Q167*|c.499C>T|26,BUFFER|p.Q35*|c.103C>T|5,BUFFER|p.Q74*|c.220C>T|5,BUFFER|p.Q167fs*14|c.497_498insC|3,BUFFER|p.S166*|c.497C>A|8,BUFFER|p.S166L|c.497C>T|5,BUFFER|p.S166*|c.497C>G|11,BUFFER|p.S166P|c.496T>C|6,BUFFER|p.Q165L|c.494A>T|3,BUFFER|p.Q72*|c.214C>T|6,BUFFER|p.Q33*|c.97C>T|6,BUFFER|p.Q165*|c.493C>T|30,BUFFER|p.Q165*|c.493C>T|6,BUFFER|p.Q165*|c.493C>T|4,BUFFER|p.Q165*|c.493C>T|6,BUFFER|p.Q165*|c.493C>T|4,BUFFER|p.K164N|c.492G>T|6,BUFFER|p.K164M|c.491A>T|4,BUFFER|p.K164E|c.490A>G|3,BUFFER|p.K164E|c.490A>G|3,BUFFER|p.K164E|c.490A>G|13,BUFFER|p.K164*|c.490A>T|11,BUFFER|p.K71E|c.211A>G|3,BUFFER|p.K32E|c.94A>G|4,BUFFER|p.Y163H|c.487T>C|19,BUFFER|p.Y70D|c.208T>G|3,BUFFER|p.Y163N|c.487T>A|5,BUFFER|p.Y163N|c.487T>A|5,BUFFER|p.Y163D|c.487T>G|3,BUFFER|p.Y70N|c.208T>A|5,BUFFER|p.Y163N|c.487T>A|22,BUFFER|p.Y163D|c.487T>G|3,BUFFER|p.Y31D|c.91T>G|3,BUFFER|p.Y31N|c.91T>A|5,BUFFER|p.Y163D|c.487T>G|6,BUFFER|p.I162M|c.486C>G|3,BUFFER|p.I162N|c.485T>A|6,BUFFER|p.I162N|c.485T>A|9,BUFFER|p.I162S|c.485T>G|5,BUFFER|p.I69N|c.206T>A|6,BUFFER|p.I162N|c.485T>A|6,BUFFER|p.I30N|c.89T>A|6,BUFFER|p.I162V|c.484A>G|5,BUFFER|p.I162F|c.484A>T|11,BUFFER|p.A161A|c.483C>T|5,BUFFER|p.A161fs*9|c.481delG|3,BUFFER|p.A161V|c.482C>T|9,BUFFER|p.A161D|c.482C>A|9,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|3,BUFFER|p.A161T|c.481G>A|10,BUFFER|p.A29T|c.85G>A|10,BUFFER|p.A161T|c.481G>A|52,BUFFER|p.A68T|c.202G>A|10,BUFFER|p.A161S|c.481G>T|3,BUFFER|p.M160I|c.480G>T|4,BUFFER|p.M160I|c.480G>A|3,BUFFER|p.M160K|c.479T>A|4,BUFFER|p.M160L|c.478A>C|3,BUFFER|p.M160V|c.478A>G|5,BUFFER|p.A159A|c.477C>T|8	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTGTAGATG	byCluster	5	ESCA
MC2R	0	.	GRCh37	18	13884645	13884645	+	Silent	SNP	G	G	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.873C>A	p.%3D	p.I291I	ENST00000327606	2/2	22	16	5	33	33	0	MC2R,synonymous_variant,p.%3D,ENST00000327606,;MC2R,downstream_gene_variant,,ENST00000399821,;	T	ENSG00000185231	ENST00000327606	Transcript	synonymous_variant	1054	873	291	I	atC/atA	COSM289724	.	.	-1	MC2R	HGNC	6930	protein_coding	YES	CCDS11869.1	ENSP00000333821	ACTHR_HUMAN	R4GMM0_HUMAN	UPI00000503E5	.	.	.	2/2	.	hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF3,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00520,Prints_domain:PR00534	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGATCAT	.	5	ESCA
ANKRD30B	0	.	GRCh37	18	14779985	14779985	+	Nonsense_Mutation	SNP	C	C	T	rs767362328	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1447C>T	p.Arg483Ter	p.R483*	ENST00000358984	11/36	137	88	49	123	122	1	ANKRD30B,stop_gained,p.Arg483Ter,ENST00000447268,;ANKRD30B,stop_gained,p.Arg483Ter,ENST00000358984,;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,stop_gained,p.Arg483Ter,ENST00000580206,;	T	ENSG00000180777	ENST00000358984	Transcript	stop_gained	1627	1447	483	R/*	Cga/Tga	rs767362328	.	.	1	ANKRD30B	HGNC	24165	protein_coding	YES	CCDS54182.1	ENSP00000351875	AN30B_HUMAN	.	UPI0000425FF7	.	.	.	11/36	.	hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R483Q|c.1448G>A|5,BUFFER|p.R483Q|c.1448G>A|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAACGAGAG	byFrequency	5	ESCA
GREB1L	0	.	GRCh37	18	19080511	19080511	+	Missense_Mutation	SNP	C	C	T	rs375805199	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3980C>T	p.Thr1327Met	p.T1327M	ENST00000580732	23/33	55	44	11	45	45	0	GREB1L,missense_variant,p.Thr1218Met,ENST00000269218,;GREB1L,missense_variant,p.Thr1327Met,ENST00000424526,;GREB1L,missense_variant,p.Thr1327Met,ENST00000580732,;GREB1L,3_prime_UTR_variant,,ENST00000400483,;GREB1L,non_coding_transcript_exon_variant,,ENST00000578955,;	T	ENSG00000141449	ENST00000580732	Transcript	missense_variant	4361	3980	1327	T/M	aCg/aTg	rs375805199,COSM986922	.	.	1	GREB1L	HGNC	31042	protein_coding	YES	CCDS45836.1	ENSP00000464162	GRB1L_HUMAN	.	UPI0001642876	.	deleterious(0)	probably_damaging(1)	23/33	.	hmmpanther:PTHR15720:SF12,hmmpanther:PTHR15720	.	.	.	.	.	.	.	T:0	T:0.0003	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGACGGGCT	.	5	ESCA
ABHD3	0	.	GRCh37	18	19284501	19284501	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126C>T	p.%3D	p.V42V	ENST00000289119	1/9	109	94	15	113	113	0	ABHD3,synonymous_variant,p.%3D,ENST00000580981,;ABHD3,synonymous_variant,p.%3D,ENST00000289119,;ABHD3,upstream_gene_variant,,ENST00000584464,;ABHD3,upstream_gene_variant,,ENST00000578270,;ABHD3,non_coding_transcript_exon_variant,,ENST00000579875,;MIB1,upstream_gene_variant,,ENST00000578646,;ABHD3,synonymous_variant,p.%3D,ENST00000577891,;ABHD3,non_coding_transcript_exon_variant,,ENST00000577928,;ABHD3,non_coding_transcript_exon_variant,,ENST00000579982,;	A	ENSG00000158201	ENST00000289119	Transcript	synonymous_variant	266	126	42	V	gtC/gtT	.	.	.	-1	ABHD3	HGNC	18718	protein_coding	YES	CCDS32802.1	ENSP00000289119	ABHD3_HUMAN	.	UPI0000163938	.	.	.	1/9	.	PIRSF_domain:PIRSF005211,hmmpanther:PTHR10794:SF24,hmmpanther:PTHR10794,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAAGCGACGCT	.	4	ESCA
SYT4	0	.	GRCh37	18	40850370	40850370	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1214G>A	p.Trp405Ter	p.W405*	ENST00000255224	4/4	26	22	4	30	30	0	SYT4,stop_gained,p.Trp405Ter,ENST00000255224,;SYT4,stop_gained,p.Trp387Ter,ENST00000590752,;SYT4,downstream_gene_variant,,ENST00000596867,;SYT4,downstream_gene_variant,,ENST00000593720,;SYT4,non_coding_transcript_exon_variant,,ENST00000586678,;SYT4,non_coding_transcript_exon_variant,,ENST00000585604,;SYT4,downstream_gene_variant,,ENST00000591820,;SYT4,downstream_gene_variant,,ENST00000589479,;	T	ENSG00000132872	ENST00000255224	Transcript	stop_gained	1583	1214	405	W/*	tGg/tAg	.	.	.	-1	SYT4	HGNC	11512	protein_coding	YES	CCDS11922.1	ENSP00000255224	SYT4_HUMAN	M0QZF3_HUMAN,B4DMA9_HUMAN	UPI000013669E	.	.	.	4/4	.	hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF114,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTCCAGTGC	.	4	ESCA
KATNAL2	0	.	GRCh37	18	44584698	44584698	+	Missense_Mutation	SNP	C	C	T	rs750377654	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.209C>T	p.Ser70Leu	p.S70L	ENST00000245121	4/15	44	38	5	67	67	0	KATNAL2,missense_variant,p.Ser32Leu,ENST00000588433,;KATNAL2,missense_variant,p.Ser70Leu,ENST00000245121,;KATNAL2,missense_variant,p.Ser142Leu,ENST00000356157,;KATNAL2,missense_variant,p.Ser122Leu,ENST00000585469,;KATNAL2,intron_variant,,ENST00000592005,;KATNAL2,downstream_gene_variant,,ENST00000585383,;	T	ENSG00000167216	ENST00000245121	Transcript	missense_variant	403	209	70	S/L	tCg/tTg	rs750377654,COSM1211358	.	.	1	KATNAL2	HGNC	25387	protein_coding	YES	CCDS32828.1	ENSP00000245121	KATL2_HUMAN	K7EM02_HUMAN	UPI0000456B8E	.	tolerated(0.17)	benign(0.001)	4/15	.	hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF78,HAMAP:MF_03025	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAATCGCTCA	byFrequency	4	ESCA
TCF4	0	.	GRCh37	18	52896218	52896218	+	Missense_Mutation	SNP	C	C	T	rs121909121	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000398339	19/21	38	25	13	34	34	0	TCF4,missense_variant,p.Arg446Gln,ENST00000570177,;TCF4,missense_variant,p.Arg551Gln,ENST00000568740,;TCF4,missense_variant,p.Arg580Gln,ENST00000565018,;TCF4,missense_variant,p.Arg520Gln,ENST00000566279,;TCF4,missense_variant,p.Arg556Gln,ENST00000568673,;TCF4,missense_variant,p.Arg556Gln,ENST00000537578,;TCF4,missense_variant,p.Arg509Gln,ENST00000544241,;TCF4,missense_variant,p.Arg682Gln,ENST00000398339,;TCF4,missense_variant,p.Arg586Gln,ENST00000564403,;TCF4,missense_variant,p.Arg416Gln,ENST00000570287,;TCF4,missense_variant,p.Arg534Gln,ENST00000543082,;TCF4,missense_variant,p.Arg573Gln,ENST00000566286,;TCF4,missense_variant,p.Arg516Gln,ENST00000567880,;TCF4,missense_variant,p.Arg505Gln,ENST00000564228,;TCF4,missense_variant,p.Arg446Gln,ENST00000537856,;TCF4,missense_variant,p.Arg580Gln,ENST00000354452,;TCF4,missense_variant,p.Arg552Gln,ENST00000540999,;TCF4,missense_variant,p.Arg416Gln,ENST00000561831,;TCF4,missense_variant,p.Arg576Gln,ENST00000564999,;TCF4,missense_variant,p.Arg420Gln,ENST00000457482,;TCF4,missense_variant,p.Arg576Gln,ENST00000356073,;TCF4,missense_variant,p.Arg446Gln,ENST00000561992,;TCF4,non_coding_transcript_exon_variant,,ENST00000562680,;	T	ENSG00000196628	ENST00000398339	Transcript	missense_variant	2102	2045	682	R/Q	cGg/cAg	CM072075,rs121909121	.	.	-1	TCF4	HGNC	11634	protein_coding	YES	CCDS58631.1	ENSP00000381382	.	K7ERJ0_HUMAN,H3BUQ3_HUMAN,H3BTM9_HUMAN,H3BTC3_HUMAN,H3BT24_HUMAN,H3BSX3_HUMAN,H3BRF7_HUMAN,H3BPG3_HUMAN,H3BP59_HUMAN,H3BNZ2_HUMAN,H3BNI2_HUMAN,H3BME8_HUMAN,H3BMC8_HUMAN,G0LNT8_HUMAN,G0LNT7_HUMAN,G0LNT4_HUMAN,G0LNT3_HUMAN,E9PH57_HUMAN	UPI000059D58C	.	deleterious(0)	probably_damaging(1)	19/21	.	Superfamily_domains:SSF47459,SMART_domains:SM00353,Gene3D:4.10.280.10,Pfam_domain:PF00010,hmmpanther:PTHR11793,hmmpanther:PTHR11793:SF10,PROSITE_profiles:PS50888	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACCCGCAGA	.	5	ESCA
MC4R	0	.	GRCh37	18	58039811	58039811	+	5'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-229G>A	.	.	ENST00000299766	1/1	47	30	16	48	48	0	MC4R,5_prime_UTR_variant,,ENST00000299766,;	T	ENSG00000166603	ENST00000299766	Transcript	5_prime_UTR_variant	191	.	.	.	.	.	.	.	-1	MC4R	HGNC	6932	protein_coding	YES	CCDS11976.1	ENSP00000299766	MC4R_HUMAN	K4N7A9_HUMAN,A0N0W8_HUMAN	UPI000013E5E3	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCATTCT	.	5	ESCA
TXNL4A	0	.	GRCh37	18	77733717	77733717	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397C>T	p.Pro133Ser	p.P133S	ENST00000269601	3/3	43	29	14	45	45	0	TXNL4A,missense_variant,p.Pro133Ser,ENST00000269601,;TXNL4A,missense_variant,p.Pro62Ser,ENST00000592957,;TXNL4A,missense_variant,p.Pro62Ser,ENST00000592837,;TXNL4A,missense_variant,p.Pro62Ser,ENST00000585474,;TXNL4A,3_prime_UTR_variant,,ENST00000588162,;HSBP1L1,downstream_gene_variant,,ENST00000451882,;TXNL4A,downstream_gene_variant,,ENST00000591711,;TXNL4A,non_coding_transcript_exon_variant,,ENST00000586612,;TXNL4A,3_prime_UTR_variant,,ENST00000585769,;TXNL4A,3_prime_UTR_variant,,ENST00000355491,;HSBP1L1,downstream_gene_variant,,ENST00000587347,;TXNL4A,downstream_gene_variant,,ENST00000586295,;HSBP1L1,downstream_gene_variant,,ENST00000589516,;HSBP1L1,downstream_gene_variant,,ENST00000590571,;TXNL4A,downstream_gene_variant,,ENST00000586825,;	A	ENSG00000141759	ENST00000269601	Transcript	missense_variant	598	397	133	P/S	Ccc/Tcc	.	.	.	-1	TXNL4A	HGNC	30551	protein_coding	YES	CCDS32852.1	ENSP00000269601	TXN4A_HUMAN	K7ESL1_HUMAN	UPI00000223B3	.	deleterious(0.01)	probably_damaging(0.947)	3/3	.	hmmpanther:PTHR12052,Pfam_domain:PF02966,Gene3D:3.40.30.10,PIRSF_domain:PIRSF017199,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGGGGACA	.	5	ESCA
JAK3	0	.	GRCh37	19	17937609	17937609	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3318G>C	p.Glu1106Asp	p.E1106D	ENST00000458235	24/24	38	31	7	40	40	0	JAK3,missense_variant,p.Glu1106Asp,ENST00000458235,;JAK3,missense_variant,p.Glu1106Asp,ENST00000527670,;JAK3,downstream_gene_variant,,ENST00000534444,;JAK3,intron_variant,,ENST00000527031,;	G	ENSG00000105639	ENST00000458235	Transcript	missense_variant	3418	3318	1106	E/D	gaG/gaC	.	.	.	-1	JAK3	HGNC	6193	protein_coding	YES	CCDS12366.1	ENSP00000391676	JAK3_HUMAN	Q9UMU1_HUMAN,Q6LD09_HUMAN	UPI0000071146	.	tolerated_low_confidence(0.24)	benign(0.001)	24/24	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGTCTCACA	.	5	ESCA
PDE4C	0	.	GRCh37	19	18322638	18322638	+	Silent	SNP	G	G	A	rs765811198	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1722C>T	p.%3D	p.R574R	ENST00000355502	18/19	21	16	5	24	24	0	PDE4C,synonymous_variant,p.%3D,ENST00000597297,;PDE4C,synonymous_variant,p.%3D,ENST00000594465,;PDE4C,synonymous_variant,p.%3D,ENST00000594617,;PDE4C,synonymous_variant,p.%3D,ENST00000262805,;PDE4C,synonymous_variant,p.%3D,ENST00000447275,;PDE4C,synonymous_variant,p.%3D,ENST00000598111,;PDE4C,synonymous_variant,p.%3D,ENST00000355502,;PDE4C,synonymous_variant,p.%3D,ENST00000539010,;AC068499.10,non_coding_transcript_exon_variant,,ENST00000594805,;AC068499.10,downstream_gene_variant,,ENST00000599416,;PDE4C,3_prime_UTR_variant,,ENST00000599188,;PDE4C,non_coding_transcript_exon_variant,,ENST00000597360,;	A	ENSG00000105650	ENST00000355502	Transcript	synonymous_variant	2594	1722	574	R	cgC/cgT	rs765811198	.	.	-1	PDE4C	HGNC	8782	protein_coding	YES	CCDS12373.1	ENSP00000347689	PDE4C_HUMAN	Q9UPJ5_HUMAN,Q9P1U3_HUMAN,Q32MM7_HUMAN,O76105_HUMAN,M0R1P5_HUMAN,B7Z2S3_HUMAN	UPI0000127BF8	.	.	.	18/19	.	hmmpanther:PTHR11347:SF94,hmmpanther:PTHR11347,Pfam_domain:PF00233,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604,Prints_domain:PR00387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTCGCGGTC	byFrequency	5	ESCA
ZNF91	0	.	GRCh37	19	23544910	23544910	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.871G>A	p.Glu291Lys	p.E291K	ENST00000300619	4/4	79	68	11	91	91	0	ZNF91,missense_variant,p.Glu259Lys,ENST00000397082,;ZNF91,missense_variant,p.Glu291Lys,ENST00000300619,;ZNF91,intron_variant,,ENST00000599743,;ZNF91,downstream_gene_variant,,ENST00000595533,;ZNF91,intron_variant,,ENST00000596989,;ZNF91,upstream_gene_variant,,ENST00000593341,;ZNF91,upstream_gene_variant,,ENST00000599281,;ZNF91,upstream_gene_variant,,ENST00000596528,;	T	ENSG00000167232	ENST00000300619	Transcript	missense_variant	1077	871	291	E/K	Gag/Aag	.	.	.	-1	ZNF91	HGNC	13166	protein_coding	YES	CCDS42541.1	ENSP00000300619	ZNF91_HUMAN	M0R186_HUMAN	UPI00002038F9	.	deleterious(0.05)	possibly_damaging(0.57)	4/4	.	Superfamily_domains:SSF57667,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF100,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCTCTCCAG	.	4	ESCA
APLP1	0	.	GRCh37	19	36370269	36370269	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1882G>A	p.Glu628Lys	p.E628K	ENST00000221891	17/17	74	60	13	75	75	0	APLP1,missense_variant,p.Glu266Lys,ENST00000587274,;APLP1,missense_variant,p.Glu628Lys,ENST00000221891,;APLP1,missense_variant,p.Glu621Lys,ENST00000586861,;APLP1,missense_variant,p.Glu588Lys,ENST00000537454,;APLP1,downstream_gene_variant,,ENST00000592316,;APLP1,downstream_gene_variant,,ENST00000588808,;RN7SL402P,upstream_gene_variant,,ENST00000465059,;APLP1,non_coding_transcript_exon_variant,,ENST00000591165,;APLP1,downstream_gene_variant,,ENST00000589298,;APLP1,3_prime_UTR_variant,,ENST00000590561,;APLP1,downstream_gene_variant,,ENST00000590926,;	A	ENSG00000105290	ENST00000221891	Transcript	missense_variant	2074	1882	628	E/K	Gag/Aag	.	.	.	1	APLP1	HGNC	597	protein_coding	YES	CCDS32997.1	ENSP00000221891	APLP1_HUMAN	K7EQJ4_HUMAN,K7ELK0_HUMAN,A4UCT6_HUMAN	UPI000020215E	.	deleterious(0)	probably_damaging(0.996)	17/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23103:SF13,hmmpanther:PTHR23103,Pfam_domain:PF10515,Prints_domain:PR00203	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAGGAGCAG	.	5	ESCA
ZNF180	0	.	GRCh37	19	44981054	44981054	+	Silent	SNP	C	C	T	rs781643414	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1644G>A	p.%3D	p.P548P	ENST00000221327	5/5	57	43	14	77	76	1	ZNF180,synonymous_variant,p.%3D,ENST00000592529,;ZNF180,synonymous_variant,p.%3D,ENST00000391956,;ZNF180,synonymous_variant,p.%3D,ENST00000221327,;ZNF180,downstream_gene_variant,,ENST00000587047,;ZNF180,downstream_gene_variant,,ENST00000586637,;ZNF180,downstream_gene_variant,,ENST00000591064,;AC069278.4,upstream_gene_variant,,ENST00000591684,;ZNF180,downstream_gene_variant,,ENST00000585514,;ZNF180,3_prime_UTR_variant,,ENST00000592095,;ZNF180,3_prime_UTR_variant,,ENST00000590088,;ZNF285B,downstream_gene_variant,,ENST00000561698,;ZNF285B,downstream_gene_variant,,ENST00000318605,;	T	ENSG00000167384	ENST00000221327	Transcript	synonymous_variant	1926	1644	548	P	ccG/ccA	rs781643414	.	.	-1	ZNF180	HGNC	12970	protein_coding	YES	CCDS12639.1	ENSP00000221327	ZN180_HUMAN	K7EQX9_HUMAN,K7EQP0_HUMAN	UPI000013C7BD	.	.	.	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF27,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATACGGTTT	byFrequency	5	ESCA
CKM	0	.	GRCh37	19	45821144	45821144	+	Missense_Mutation	SNP	C	C	A	rs780576836	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287G>T	p.Arg96Leu	p.R96L	ENST00000221476	3/8	54	45	9	70	70	0	CKM,missense_variant,p.Arg96Leu,ENST00000221476,;	A	ENSG00000104879	ENST00000221476	Transcript	missense_variant	462	287	96	R/L	cGc/cTc	rs780576836,COSM2157082	.	.	-1	CKM	HGNC	1994	protein_coding	YES	CCDS12659.1	ENSP00000221476	KCRM_HUMAN	.	UPI000012DCC3	.	tolerated(0.07)	possibly_damaging(0.558)	3/8	.	PROSITE_profiles:PS51509,hmmpanther:PTHR11547,Gene3D:1.10.135.10,Pfam_domain:PF02807,Superfamily_domains:SSF48034	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTGGCGATCC	.	5	ESCA
ACPT	0	.	GRCh37	19	51294951	51294951	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342G>A	p.%3D	p.E114E	ENST00000270593	4/11	46	38	8	62	62	0	ACPT,synonymous_variant,p.%3D,ENST00000270593,;ACPT,intron_variant,,ENST00000270594,;CTD-2568A17.8,downstream_gene_variant,,ENST00000594114,;	A	ENSG00000142513	ENST00000270593	Transcript	synonymous_variant	342	342	114	E	gaG/gaA	.	.	.	1	ACPT	HGNC	14376	protein_coding	YES	CCDS12802.1	ENSP00000270593	PPAT_HUMAN	.	UPI0000048D54	.	.	.	4/11	.	hmmpanther:PTHR11567:SF117,hmmpanther:PTHR11567,Pfam_domain:PF00328,Gene3D:3.40.50.1240,Superfamily_domains:SSF53254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTGGAGAGTGC	.	3	ESCA
NLRP12	0	.	GRCh37	19	54308650	54308650	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2298C>T	p.%3D	p.L766L	ENST00000324134	5/10	23	13	9	32	32	0	NLRP12,synonymous_variant,p.%3D,ENST00000535162,;NLRP12,synonymous_variant,p.%3D,ENST00000391775,;NLRP12,synonymous_variant,p.%3D,ENST00000354278,;NLRP12,synonymous_variant,p.%3D,ENST00000391773,;NLRP12,synonymous_variant,p.%3D,ENST00000324134,;NLRP12,synonymous_variant,p.%3D,ENST00000391772,;NLRP12,synonymous_variant,p.%3D,ENST00000345770,;NLRP12,synonymous_variant,p.%3D,ENST00000351894,;NLRP12,non_coding_transcript_exon_variant,,ENST00000492915,;	A	ENSG00000142405	ENST00000324134	Transcript	synonymous_variant	2467	2298	766	L	ctC/ctT	.	.	.	-1	NLRP12	HGNC	22938	protein_coding	YES	CCDS12864.1	ENSP00000319377	NAL12_HUMAN	.	UPI00001412CE	.	.	.	5/10	.	hmmpanther:PTHR24106:SF6,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTATGAGAGC	.	5	ESCA
NLRP7	0	.	GRCh37	19	55450647	55450647	+	Missense_Mutation	SNP	C	C	T	rs758296123	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1540G>A	p.Asp514Asn	p.D514N	ENST00000588756	6/13	20	15	5	36	36	0	NLRP7,missense_variant,p.Asp514Asn,ENST00000590030,;NLRP7,missense_variant,p.Asp542Asn,ENST00000446217,;NLRP7,missense_variant,p.Asp514Asn,ENST00000588756,;NLRP7,missense_variant,p.Asp514Asn,ENST00000448121,;NLRP7,missense_variant,p.Asp514Asn,ENST00000328092,;NLRP7,missense_variant,p.Asp514Asn,ENST00000592784,;NLRP7,missense_variant,p.Asp514Asn,ENST00000340844,;NLRP7,downstream_gene_variant,,ENST00000590659,;NLRP7,downstream_gene_variant,,ENST00000587103,;NLRP7,downstream_gene_variant,,ENST00000587844,;NLRP7,missense_variant,p.Asp514Asn,ENST00000586379,;	T	ENSG00000167634	ENST00000588756	Transcript	missense_variant	2027	1540	514	D/N	Gac/Aac	rs758296123,COSM4081413,COSM4081412,COSM4081414	.	.	-1	NLRP7	HGNC	22947	protein_coding	YES	CCDS46183.1	ENSP00000467123	NALP7_HUMAN	K7ER92_HUMAN,K7EPY3_HUMAN,K7EP54_HUMAN	UPI000174C6C4	.	tolerated(0.89)	benign(0.03)	6/13	.	hmmpanther:PTHR24106:SF87,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGTCGGGGT	.	5	ESCA
MUC16	0	.	GRCh37	19	9003588	9003588	+	Missense_Mutation	SNP	G	G	A	rs369380417	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.40052C>T	p.Thr13351Met	p.T13351M	ENST00000397910	49/84	56	48	7	77	77	0	MUC16,missense_variant,p.Thr13351Met,ENST00000397910,;MUC16,missense_variant,p.Thr191Met,ENST00000599436,;MUC16,upstream_gene_variant,,ENST00000380951,;MUC16,missense_variant,p.Thr191Met,ENST00000601404,;MUC16,upstream_gene_variant,,ENST00000596768,;	A	ENSG00000181143	ENST00000397910	Transcript	missense_variant	40256	40052	13351	T/M	aCg/aTg	rs369380417,COSM1397846,COSM1397845	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	probably_damaging(0.992)	49/84	.	Superfamily_domains:0047452,Pfam_domain:PF01390,Gene3D:1ivzA00,hmmpanther:PTHR14672,PROSITE_profiles:PS50024,hmmpanther:PTHR14672:SF0	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0.0002	A:0	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTCCGTGGTG	byCluster|by1000G	4	ESCA
GPR88	0	.	GRCh37	1	101007106	101007106	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1429C>G	.	.	ENST00000315033	2/2	26	10	16	65	64	0	GPR88,3_prime_UTR_variant,,ENST00000315033,;	G	ENSG00000181656	ENST00000315033	Transcript	3_prime_UTR_variant	3023	.	.	.	.	.	.	.	1	GPR88	HGNC	4539	protein_coding	YES	CCDS772.1	ENSP00000314223	GPR88_HUMAN	.	UPI00001403B3	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTTCAAATG	.	5	ESCA
IGSF3	0	.	GRCh37	1	117146501	117146501	+	Missense_Mutation	SNP	G	G	A	rs761064394	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1429C>T	p.Arg477Cys	p.R477C	ENST00000369483	7/12	27	21	6	49	49	0	IGSF3,missense_variant,p.Arg477Cys,ENST00000318837,;IGSF3,missense_variant,p.Arg457Cys,ENST00000369486,;IGSF3,missense_variant,p.Arg477Cys,ENST00000369483,;	A	ENSG00000143061	ENST00000369483	Transcript	missense_variant	2134	1429	477	R/C	Cgc/Tgc	rs761064394	.	.	-1	IGSF3	HGNC	5950	protein_coding	YES	CCDS30814.1	ENSP00000358495	IGSF3_HUMAN	.	UPI0000140437	.	deleterious(0.02)	possibly_damaging(0.832)	7/12	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF21,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R456C|c.1366C>T|3,BUFFER|p.R476C|c.1426C>T|3	MUTECT|MUSE	GCTGCGGCGGT	.	2	ESCA
VPS13D	0	.	GRCh37	1	12378163	12378163	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7183C>A	p.Leu2395Ile	p.L2395I	ENST00000358136	31/70	44	33	11	49	49	0	VPS13D,missense_variant,p.Leu2395Ile,ENST00000358136,;VPS13D,missense_variant,p.Leu1218Ile,ENST00000011700,;VPS13D,missense_variant,p.Leu2395Ile,ENST00000356315,;VPS13D,non_coding_transcript_exon_variant,,ENST00000460333,;VPS13D,non_coding_transcript_exon_variant,,ENST00000487188,;	A	ENSG00000048707	ENST00000358136	Transcript	missense_variant	7313	7183	2395	L/I	Ctc/Atc	.	.	.	1	VPS13D	HGNC	23595	protein_coding	YES	CCDS30588.1	ENSP00000350854	.	M0QXS2_HUMAN,J3KP14_HUMAN	UPI0000451CA9	.	.	possibly_damaging(0.694)	31/70	.	hmmpanther:PTHR16166:SF93,hmmpanther:PTHR16166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTTCTCAAC	.	5	ESCA
SNX27	0	.	GRCh37	1	151671278	151671278	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5201C>T	.	.	ENST00000368843	12/12	63	28	34	79	79	0	SNX27,3_prime_UTR_variant,,ENST00000368843,;SNX27,3_prime_UTR_variant,,ENST00000458013,;CELF3,downstream_gene_variant,,ENST00000290585,;CELF3,downstream_gene_variant,,ENST00000290583,;CELF3,downstream_gene_variant,,ENST00000392706,;CELF3,downstream_gene_variant,,ENST00000420342,;RP11-98D18.1,upstream_gene_variant,,ENST00000457548,;CELF3,downstream_gene_variant,,ENST00000470688,;SNX27,3_prime_UTR_variant,,ENST00000368841,;	T	ENSG00000143376	ENST00000368843	Transcript	3_prime_UTR_variant	6908	.	.	.	.	.	.	.	1	SNX27	HGNC	20073	protein_coding	YES	CCDS1001.1	ENSP00000357836	SNX27_HUMAN	.	UPI00001A962E	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGACCCCCT	.	5	ESCA
UBAP2L	0	.	GRCh37	1	154215741	154215741	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805C>G	p.Leu269Val	p.L269V	ENST00000428931	10/27	63	32	30	79	79	0	UBAP2L,missense_variant,p.Leu262Val,ENST00000437652,;UBAP2L,missense_variant,p.Leu280Val,ENST00000368504,;UBAP2L,missense_variant,p.Leu269Val,ENST00000343815,;UBAP2L,missense_variant,p.Leu269Val,ENST00000361546,;UBAP2L,missense_variant,p.Leu269Val,ENST00000412596,;UBAP2L,missense_variant,p.Leu280Val,ENST00000271877,;UBAP2L,missense_variant,p.Leu269Val,ENST00000428931,;UBAP2L,non_coding_transcript_exon_variant,,ENST00000466173,;	G	ENSG00000143569	ENST00000428931	Transcript	missense_variant	972	805	269	L/V	Ctg/Gtg	.	.	.	1	UBAP2L	HGNC	29877	protein_coding	YES	CCDS1063.1	ENSP00000389445	UBP2L_HUMAN	Q5VU81_HUMAN,Q5VU80_HUMAN,Q5VU78_HUMAN	UPI000013E257	.	tolerated(0.13)	unknown(0)	10/27	.	hmmpanther:PTHR16308:SF18,hmmpanther:PTHR16308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCTGCCT	.	5	ESCA
FCRL5	0	.	GRCh37	1	157512737	157512737	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1035G>A	p.%3D	p.L345L	ENST00000361835	6/17	27	23	4	38	38	0	FCRL5,synonymous_variant,p.%3D,ENST00000361835,;FCRL5,synonymous_variant,p.%3D,ENST00000368190,;FCRL5,synonymous_variant,p.%3D,ENST00000368189,;FCRL5,synonymous_variant,p.%3D,ENST00000356953,;FCRL5,synonymous_variant,p.%3D,ENST00000368191,;FCRL5,downstream_gene_variant,,ENST00000368188,;FCRL5,non_coding_transcript_exon_variant,,ENST00000481082,;	T	ENSG00000143297	ENST00000361835	Transcript	synonymous_variant	1193	1035	345	L	ctG/ctA	.	.	.	-1	FCRL5	HGNC	18508	protein_coding	YES	CCDS1165.1	ENSP00000354691	FCRL5_HUMAN	.	UPI0000458907	.	.	.	6/17	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00408,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF49,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTAGTCAGTGA	.	4	ESCA
CLCNKA	0	.	GRCh37	1	16349185	16349185	+	Missense_Mutation	SNP	C	C	T	rs77127348	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.71C>T	p.Pro24Leu	p.P24L	ENST00000331433	2/20	42	18	23	61	61	0	CLCNKA,missense_variant,p.Pro24Leu,ENST00000331433,;CLCNKA,missense_variant,p.Pro24Leu,ENST00000420078,;CLCNKA,missense_variant,p.Pro24Leu,ENST00000375692,;CLCNKA,missense_variant,p.Pro24Leu,ENST00000439316,;HSPB7,upstream_gene_variant,,ENST00000487046,;HSPB7,upstream_gene_variant,,ENST00000375718,;HSPB7,upstream_gene_variant,,ENST00000545268,;HSPB7,upstream_gene_variant,,ENST00000406363,;HSPB7,upstream_gene_variant,,ENST00000311890,;HSPB7,upstream_gene_variant,,ENST00000463576,;HSPB7,upstream_gene_variant,,ENST00000411503,;CLCNKA,non_coding_transcript_exon_variant,,ENST00000495784,;CLCNKA,non_coding_transcript_exon_variant,,ENST00000464764,;CLCNKA,upstream_gene_variant,,ENST00000491433,;CLCNKA,downstream_gene_variant,,ENST00000477360,;HSPB7,upstream_gene_variant,,ENST00000442459,;	T	ENSG00000186510	ENST00000331433	Transcript	missense_variant	90	71	24	P/L	cCc/cTc	rs77127348	.	.	1	CLCNKA	HGNC	2026	protein_coding	YES	CCDS167.1	ENSP00000332771	CLCKA_HUMAN	.	UPI0000127993	.	deleterious(0)	possibly_damaging(0.901)	2/20	.	hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF78,Prints_domain:PR01119	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCCCTGTC	byCluster|by1000G	5	ESCA
GPR52	0	.	GRCh37	1	174417614	174417614	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.365C>G	p.Ser122Ter	p.S122*	ENST00000367685	1/1	27	15	11	51	51	0	GPR52,stop_gained,p.Ser122Ter,ENST00000367685,;RABGAP1L,intron_variant,,ENST00000357444,;RABGAP1L,intron_variant,,ENST00000367689,;RABGAP1L,intron_variant,,ENST00000251507,;RABGAP1L,intron_variant,,ENST00000526253,;RABGAP1L,intron_variant,,ENST00000367690,;	G	ENSG00000203737	ENST00000367685	Transcript	stop_gained	403	365	122	S/*	tCa/tGa	.	.	.	1	GPR52	HGNC	4508	protein_coding	YES	CCDS30941.1	ENSP00000356658	GPR52_HUMAN	F2YGU0_HUMAN	UPI0000153A3C	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF248,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCAGTTC	.	5	ESCA
CRB1	0	.	GRCh37	1	197404164	197404164	+	Silent	SNP	C	C	T	rs62636284	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3171C>T	p.%3D	p.N1057N	ENST00000367400	9/12	40	32	8	50	50	0	CRB1,synonymous_variant,p.%3D,ENST00000544212,;CRB1,synonymous_variant,p.%3D,ENST00000367399,;CRB1,synonymous_variant,p.%3D,ENST00000535699,;CRB1,synonymous_variant,p.%3D,ENST00000367397,;CRB1,synonymous_variant,p.%3D,ENST00000367400,;CRB1,intron_variant,,ENST00000538660,;RP11-75C23.1,downstream_gene_variant,,ENST00000422250,;CRB1,synonymous_variant,p.%3D,ENST00000484075,;	T	ENSG00000134376	ENST00000367400	Transcript	synonymous_variant	3306	3171	1057	N	aaC/aaT	rs62636284,RISN_CRB1:c.3171C>T	.	.	1	CRB1	HGNC	2343	protein_coding	YES	CCDS1390.1	ENSP00000356370	CRUM1_HUMAN	B7Z824_HUMAN	UPI0000073345	.	.	.	9/12	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24049,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899	T:0.0002	T:0,T:0	T:0,T:0	.	T:0,T:0	T:0,T:0	T:0.001,T:0.001	G:0.0002	G:0	not_provided	.	.	.	.	.	.	LOW	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.E1058K|c.3172G>A|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACAACGAAAC	byCluster|by1000G	5	ESCA
KCTD3	0	.	GRCh37	1	215793774	215793774	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2262G>A	p.%3D	p.R754R	ENST00000259154	18/18	81	62	19	95	95	0	KCTD3,synonymous_variant,p.%3D,ENST00000259154,;USH2A,downstream_gene_variant,,ENST00000366943,;KCTD3,downstream_gene_variant,,ENST00000452413,;USH2A,downstream_gene_variant,,ENST00000307340,;KCTD3,non_coding_transcript_exon_variant,,ENST00000495537,;KCTD3,downstream_gene_variant,,ENST00000465650,;	A	ENSG00000136636	ENST00000259154	Transcript	synonymous_variant	2556	2262	754	R	agG/agA	.	.	.	1	KCTD3	HGNC	21305	protein_coding	YES	CCDS1515.1	ENSP00000259154	KCTD3_HUMAN	B4DJX2_HUMAN	UPI0000071A2E	.	.	.	18/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15859,hmmpanther:PTHR15859:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTAGGAAGAA	.	3	ESCA
SIPA1L2	0	.	GRCh37	1	232650439	232650439	+	Missense_Mutation	SNP	C	C	T	rs780265795	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.647G>A	p.Arg216Gln	p.R216Q	ENST00000366630	2/22	21	16	5	39	39	0	SIPA1L2,missense_variant,p.Arg216Gln,ENST00000366630,;SIPA1L2,missense_variant,p.Arg216Gln,ENST00000262861,;	T	ENSG00000116991	ENST00000366630	Transcript	missense_variant	1006	647	216	R/Q	cGa/cAa	rs780265795	.	.	-1	SIPA1L2	HGNC	23800	protein_coding	YES	CCDS41474.1	ENSP00000355589	SI1L2_HUMAN	.	UPI00001D7D6A	.	tolerated(0.4)	probably_damaging(0.99)	2/22	.	hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACTCGGTAC	.	5	ESCA
FMN2	0	.	GRCh37	1	240370862	240370862	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2750G>A	p.Gly917Glu	p.G917E	ENST00000319653	5/18	54	36	17	81	81	0	FMN2,missense_variant,p.Gly917Glu,ENST00000319653,;FMN2,downstream_gene_variant,,ENST00000447095,;	A	ENSG00000155816	ENST00000319653	Transcript	missense_variant	2980	2750	917	G/E	gGa/gAa	COSM679786,COSM370376	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	unknown(0)	5/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,Pfam_domain:PF06346,SMART_domains:SM00498,Prints_domain:PR01217	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCGGAGCGG	.	5	ESCA
FMN2	0	.	GRCh37	1	240637787	240637787	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*333G>C	.	.	ENST00000319653	18/18	37	32	5	35	35	0	FMN2,3_prime_UTR_variant,,ENST00000545751,;FMN2,3_prime_UTR_variant,,ENST00000319653,;AL646016.1,intron_variant,,ENST00000596886,;FMN2,downstream_gene_variant,,ENST00000543681,;FMN2,non_coding_transcript_exon_variant,,ENST00000496950,;	C	ENSG00000155816	ENST00000319653	Transcript	3_prime_UTR_variant	5732	.	.	.	.	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TGTGAGAATAT	.	3	ESCA
RGS7	0	.	GRCh37	1	240939036	240939036	+	3'UTR	SNP	C	C	T	rs765719469	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*427G>A	.	.	ENST00000366565	18/18	44	34	10	66	66	0	RGS7,3_prime_UTR_variant,,ENST00000440928,;RGS7,3_prime_UTR_variant,,ENST00000446183,;RGS7,3_prime_UTR_variant,,ENST00000366564,;RGS7,3_prime_UTR_variant,,ENST00000366565,;RGS7,3_prime_UTR_variant,,ENST00000366563,;RGS7,3_prime_UTR_variant,,ENST00000348120,;RGS7,intron_variant,,ENST00000331110,;RGS7,downstream_gene_variant,,ENST00000366562,;PRKRIRP8,upstream_gene_variant,,ENST00000447914,;	T	ENSG00000182901	ENST00000366565	Transcript	3_prime_UTR_variant	2273	.	.	.	.	rs765719469	.	.	-1	RGS7	HGNC	10003	protein_coding	YES	CCDS31071.1	ENSP00000355523	RGS7_HUMAN	.	UPI000040E182	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGCGGAAT	.	5	ESCA
NR0B2	0	.	GRCh37	1	27240299	27240299	+	Missense_Mutation	SNP	G	G	A	rs374067965	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.133C>T	p.Arg45Trp	p.R45W	ENST00000254227	1/2	36	17	18	45	45	0	NR0B2,missense_variant,p.Arg45Trp,ENST00000254227,;NUDC,intron_variant,,ENST00000435827,;	A	ENSG00000131910	ENST00000254227	Transcript	missense_variant	159	133	45	R/W	Cgg/Tgg	rs374067965	.	.	-1	NR0B2	HGNC	7961	protein_coding	YES	CCDS291.1	ENSP00000254227	NR0B2_HUMAN	.	UPI0000135956	.	deleterious(0.01)	benign(0.236)	1/2	.	hmmpanther:PTHR24081,hmmpanther:PTHR24081:SF0,Gene3D:1.10.565.10,Superfamily_domains:SSF48508	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCCGGTGCT	byFrequency|byCluster	5	ESCA
SNRNP40	0	.	GRCh37	1	31742271	31742271	+	Intron	SNP	T	T	A	rs534806922	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.776-184A>T	.	.	ENST00000263694	.	23	8	15	19	19	0	SNRNP40,5_prime_UTR_variant,,ENST00000373720,;SNRNP40,intron_variant,,ENST00000446633,;SNRNP40,intron_variant,,ENST00000263694,;SNRNP40,intron_variant,,ENST00000489853,;SNRNP40,downstream_gene_variant,,ENST00000474025,;	A	ENSG00000060688	ENST00000263694	Transcript	intron_variant	.	.	.	.	.	rs534806922	.	.	-1	SNRNP40	HGNC	30857	protein_coding	YES	CCDS340.1	ENSP00000263694	SNR40_HUMAN	A0MNP2_HUMAN	UPI000006FD38	.	.	.	.	6/9	.	C:0.0002	C:0	C:0	.	C:0	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACACATCTAAA	by1000G	2	ESCA
KHDRBS1	0	.	GRCh37	1	32508359	32508359	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*134C>G	.	.	ENST00000327300	9/9	55	23	32	57	57	0	KHDRBS1,3_prime_UTR_variant,,ENST00000327300,;KHDRBS1,downstream_gene_variant,,ENST00000492989,;KHDRBS1,non_coding_transcript_exon_variant,,ENST00000307714,;KHDRBS1,intron_variant,,ENST00000484270,;	G	ENSG00000121774	ENST00000327300	Transcript	3_prime_UTR_variant	1633	.	.	.	.	.	.	.	1	KHDRBS1	HGNC	18116	protein_coding	YES	CCDS350.1	ENSP00000313829	KHDR1_HUMAN	B4E043_HUMAN	UPI0000073DA7	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCTCCCC	.	5	ESCA
KHDRBS1	0	.	GRCh37	1	32508568	32508568	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*343C>G	.	.	ENST00000327300	9/9	46	23	23	63	63	0	KHDRBS1,3_prime_UTR_variant,,ENST00000327300,;KHDRBS1,downstream_gene_variant,,ENST00000492989,;KHDRBS1,non_coding_transcript_exon_variant,,ENST00000307714,;KHDRBS1,intron_variant,,ENST00000484270,;	G	ENSG00000121774	ENST00000327300	Transcript	3_prime_UTR_variant	1842	.	.	.	.	.	.	.	1	KHDRBS1	HGNC	18116	protein_coding	YES	CCDS350.1	ENSP00000313829	KHDR1_HUMAN	B4E043_HUMAN	UPI0000073DA7	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTTCAAAAA	.	5	ESCA
SH3D21	0	.	GRCh37	1	36785719	36785719	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1455C>T	p.%3D	p.V485V	ENST00000453908	14/16	47	36	11	68	68	0	SH3D21,synonymous_variant,p.%3D,ENST00000505871,;SH3D21,synonymous_variant,p.%3D,ENST00000426732,;SH3D21,synonymous_variant,p.%3D,ENST00000312808,;SH3D21,synonymous_variant,p.%3D,ENST00000453908,;RP11-268J15.5,upstream_gene_variant,,ENST00000373137,;SH3D21,downstream_gene_variant,,ENST00000373139,;EVA1B,downstream_gene_variant,,ENST00000270824,;SH3D21,non_coding_transcript_exon_variant,,ENST00000474766,;SH3D21,non_coding_transcript_exon_variant,,ENST00000508854,;EVA1B,downstream_gene_variant,,ENST00000490466,;SH3D21,3_prime_UTR_variant,,ENST00000480549,;	T	ENSG00000214193	ENST00000453908	Transcript	synonymous_variant	1483	1455	485	V	gtC/gtT	.	.	.	1	SH3D21	HGNC	26236	protein_coding	YES	CCDS53298.1	ENSP00000403476	SH321_HUMAN	B5MDU9_HUMAN	UPI0000EE3027	.	.	.	14/16	.	hmmpanther:PTHR14167,hmmpanther:PTHR14167:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGTCTTGAC	.	5	ESCA
MACF1	0	.	GRCh37	1	39835766	39835766	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6817C>T	p.Gln2273Ter	p.Q2273*	ENST00000545844	46/94	84	77	6	70	70	0	MACF1,stop_gained,p.Gln1407Ter,ENST00000372925,;MACF1,stop_gained,p.Gln2273Ter,ENST00000361689,;MACF1,stop_gained,p.Gln2775Ter,ENST00000289893,;MACF1,stop_gained,p.Gln4335Ter,ENST00000564288,;MACF1,stop_gained,p.Gln2273Ter,ENST00000539005,;MACF1,stop_gained,p.Gln4340Ter,ENST00000372915,;MACF1,stop_gained,p.Gln2273Ter,ENST00000317713,;MACF1,stop_gained,p.Gln4372Ter,ENST00000567887,;MACF1,stop_gained,p.Gln2273Ter,ENST00000545844,;MACF1,non_coding_transcript_exon_variant,,ENST00000476350,;	T	ENSG00000127603	ENST00000545844	Transcript	stop_gained	6925	6817	2273	Q/*	Cag/Tag	.	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	.	46/94	.	Superfamily_domains:SSF46966,SMART_domains:SM00150,Gene3D:1.20.58.60,hmmpanther:PTHR11915:SF37,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTCCAGAAA	.	2	ESCA
PTCH2	0	.	GRCh37	1	45292420	45292420	+	Missense_Mutation	SNP	C	C	G	rs751579508	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2716G>C	p.Glu906Gln	p.E906Q	ENST00000372192	18/22	24	7	16	25	25	0	PTCH2,missense_variant,p.Glu906Gln,ENST00000447098,;PTCH2,missense_variant,p.Glu906Gln,ENST00000372192,;PTCH2,upstream_gene_variant,,ENST00000438067,;	G	ENSG00000117425	ENST00000372192	Transcript	missense_variant	2847	2716	906	E/Q	Gag/Cag	rs751579508	.	.	-1	PTCH2	HGNC	9586	protein_coding	YES	CCDS516.1	ENSP00000361266	PTC2_HUMAN	.	UPI00001328B8	.	tolerated(0.13)	possibly_damaging(0.739)	18/22	.	TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF62	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTCCAAGG	.	5	ESCA
PRPF38A	0	.	GRCh37	1	52871486	52871486	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.265G>C	p.Glu89Gln	p.E89Q	ENST00000257181	2/10	83	67	16	60	60	0	PRPF38A,missense_variant,p.Glu89Gln,ENST00000257181,;ZCCHC11,downstream_gene_variant,,ENST00000528457,;ORC1,upstream_gene_variant,,ENST00000371566,;ORC1,upstream_gene_variant,,ENST00000371568,;PRPF38A,non_coding_transcript_exon_variant,,ENST00000487160,;PRPF38A,intron_variant,,ENST00000474048,;ZCCHC11,downstream_gene_variant,,ENST00000527941,;	C	ENSG00000134748	ENST00000257181	Transcript	missense_variant	451	265	89	E/Q	Gag/Cag	.	.	.	1	PRPF38A	HGNC	25930	protein_coding	YES	CCDS567.1	ENSP00000257181	PR38A_HUMAN	.	UPI000006D9C2	.	deleterious(0)	probably_damaging(0.993)	2/10	.	hmmpanther:PTHR23142,Pfam_domain:PF03371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTAGAGTTT	.	5	ESCA
ACADM	0	.	GRCh37	1	76228539	76228539	+	3'Flank	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000420607	.	213	179	34	196	196	0	ACADM,3_prime_UTR_variant,,ENST00000370841,;ACADM,3_prime_UTR_variant,,ENST00000541113,;ACADM,3_prime_UTR_variant,,ENST00000370834,;ACADM,3_prime_UTR_variant,,ENST00000543667,;ACADM,downstream_gene_variant,,ENST00000420607,;ACADM,intron_variant,,ENST00000481374,;ACADM,3_prime_UTR_variant,,ENST00000526196,;ACADM,3_prime_UTR_variant,,ENST00000525808,;ACADM,non_coding_transcript_exon_variant,,ENST00000529059,;ACADM,intron_variant,,ENST00000528016,;ACADM,downstream_gene_variant,,ENST00000534334,;ACADM,downstream_gene_variant,,ENST00000526129,;ACADM,downstream_gene_variant,,ENST00000532207,;	G	ENSG00000117054	ENST00000420607	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	45	1	ACADM	HGNC	89	protein_coding	YES	CCDS44165.1	ENSP00000409612	ACADM_HUMAN	B4DVB1_HUMAN,B4DJE7_HUMAN	UPI0000EE3287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTGAAAACA	.	4	ESCA
ST6GALNAC3	0	.	GRCh37	1	77094397	77094397	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.824G>A	p.Gly275Glu	p.G275E	ENST00000328299	5/5	53	25	28	58	58	0	ST6GALNAC3,missense_variant,p.Gly275Glu,ENST00000328299,;	A	ENSG00000184005	ENST00000328299	Transcript	missense_variant	972	824	275	G/E	gGg/gAg	.	.	.	1	ST6GALNAC3	HGNC	19343	protein_coding	YES	CCDS672.1	ENSP00000329214	SIA7C_HUMAN	.	UPI000006F75A	.	.	probably_damaging(1)	5/5	.	hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF49,Pfam_domain:PF00777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATGGGGGTC	.	5	ESCA
GTF2B	0	.	GRCh37	1	89318712	89318712	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*184T>G	.	.	ENST00000370500	7/7	65	17	48	96	96	0	GTF2B,3_prime_UTR_variant,,ENST00000370500,;GTF2B,downstream_gene_variant,,ENST00000418217,;GTF2B,downstream_gene_variant,,ENST00000448623,;GTF2B,downstream_gene_variant,,ENST00000494819,;	C	ENSG00000137947	ENST00000370500	Transcript	3_prime_UTR_variant	1254	.	.	.	.	.	.	.	-1	GTF2B	HGNC	4648	protein_coding	YES	CCDS715.1	ENSP00000359531	TF2B_HUMAN	.	UPI0000136C21	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAAATTTAA	.	5	ESCA
C20orf112	0	.	GRCh37	20	31041537	31041537	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415G>A	p.Asp139Asn	p.D139N	ENST00000359676	4/8	36	32	4	40	40	0	C20orf112,missense_variant,p.Asp139Asn,ENST00000359676,;RP5-1184F4.5,downstream_gene_variant,,ENST00000442179,;C20orf112,non_coding_transcript_exon_variant,,ENST00000475781,;	T	ENSG00000197183	ENST00000359676	Transcript	missense_variant	558	415	139	D/N	Gat/Aat	.	.	.	-1	C20orf112	HGNC	16106	protein_coding	YES	CCDS13202.1	ENSP00000352704	CT112_HUMAN	.	UPI0000128600	.	deleterious(0.02)	probably_damaging(0.995)	4/8	.	hmmpanther:PTHR12449:SF16,hmmpanther:PTHR12449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAATCGTAGC	.	4	ESCA
PLCG1	0	.	GRCh37	20	39795158	39795158	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2043G>T	p.Met681Ile	p.M681I	ENST00000373272	18/32	17	11	6	16	16	0	PLCG1,missense_variant,p.Met681Ile,ENST00000373272,;PLCG1,missense_variant,p.Met681Ile,ENST00000244007,;PLCG1,missense_variant,p.Met681Ile,ENST00000373271,;PLCG1,non_coding_transcript_exon_variant,,ENST00000465571,;PLCG1,downstream_gene_variant,,ENST00000473632,;PLCG1,downstream_gene_variant,,ENST00000483646,;PLCG1,upstream_gene_variant,,ENST00000599785,;PLCG1,downstream_gene_variant,,ENST00000470528,;PLCG1,upstream_gene_variant,,ENST00000483175,;PLCG1,upstream_gene_variant,,ENST00000477870,;PLCG1,downstream_gene_variant,,ENST00000492148,;	T	ENSG00000124181	ENST00000373272	Transcript	missense_variant	2448	2043	681	M/I	atG/atT	.	.	.	1	PLCG1	HGNC	9065	protein_coding	YES	CCDS13313.1	ENSP00000362369	PLCG1_HUMAN	.	UPI00001B94DD	.	tolerated(0.17)	probably_damaging(0.995)	18/32	.	PROSITE_profiles:PS50001,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF52,Pfam_domain:PF00017,Gene3D:3.30.505.10,PIRSF_domain:PIRSF000952,SMART_domains:SM00252,Superfamily_domains:SSF55550,Prints_domain:PR00401	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATGCTAAT	.	5	ESCA
PRNP	0	.	GRCh37	20	4681389	4681389	+	3'UTR	DEL	T	T	-	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*764delT	.	.	ENST00000379440	2/2	124	88	36	90	90	0	PRNP,3_prime_UTR_variant,,ENST00000430350,;PRNP,3_prime_UTR_variant,,ENST00000379440,;PRNP,downstream_gene_variant,,ENST00000424424,;PRNP,downstream_gene_variant,,ENST00000457586,;	-	ENSG00000171867	ENST00000379440	Transcript	3_prime_UTR_variant	1810	.	.	.	.	.	.	.	1	PRNP	HGNC	9449	protein_coding	YES	CCDS13080.1	ENSP00000368752	PRIO_HUMAN	Q86XR1_HUMAN,Q6SES1_HUMAN,Q53YK7_HUMAN,O75942_HUMAN,A2A2V1_HUMAN	UPI0000033C27	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTCCCATTTTAG	.	3	ESCA
CDH26	0	.	GRCh37	20	58533735	58533735	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-47G>A	.	.	ENST00000348616	1/18	28	24	4	30	30	0	CDH26,5_prime_UTR_variant,,ENST00000244047,;CDH26,5_prime_UTR_variant,,ENST00000348616,;	A	ENSG00000124215	ENST00000348616	Transcript	5_prime_UTR_variant	254	.	.	.	.	.	.	.	1	CDH26	HGNC	15902	protein_coding	YES	CCDS13485.1	ENSP00000339390	CAD26_HUMAN	.	UPI000013CB55	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGAGGACTGG	.	4	ESCA
ANGPT4	0	.	GRCh37	20	858914	858914	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1110C>T	p.%3D	p.L370L	ENST00000381922	7/9	26	20	6	20	20	0	ANGPT4,synonymous_variant,p.%3D,ENST00000546022,;ANGPT4,synonymous_variant,p.%3D,ENST00000381922,;	A	ENSG00000101280	ENST00000381922	Transcript	synonymous_variant	1213	1110	370	L	ctC/ctT	.	.	.	-1	ANGPT4	HGNC	487	protein_coding	YES	CCDS13009.1	ENSP00000371347	ANGP4_HUMAN	.	UPI0000062232	.	.	.	7/9	.	PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF31,hmmpanther:PTHR19143,Pfam_domain:PF00147,Gene3D:3.90.215.10,SMART_domains:SM00186,Superfamily_domains:SSF56496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGTGAGCTG	.	5	ESCA
BACH1	0	.	GRCh37	21	30716607	30716607	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1453C>T	.	.	ENST00000399921	5/5	26	22	4	23	23	0	BACH1,3_prime_UTR_variant,,ENST00000286800,;BACH1,3_prime_UTR_variant,,ENST00000399921,;BACH1,intron_variant,,ENST00000468059,;BACH1,intron_variant,,ENST00000422809,;	T	ENSG00000156273	ENST00000399921	Transcript	3_prime_UTR_variant	3907	.	.	.	.	.	.	.	1	BACH1	HGNC	935	protein_coding	YES	CCDS13585.1	ENSP00000382805	BACH1_HUMAN	Q6ICU0_HUMAN,F8VZL7_HUMAN,C9JMP6_HUMAN,C9IYR0_HUMAN,C9IYH8_HUMAN	UPI000012673F	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACTTCTATAG	.	4	ESCA
EVA1C	0	.	GRCh37	21	33887546	33887546	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*46G>A	.	.	ENST00000300255	8/8	102	88	14	45	45	0	EVA1C,3_prime_UTR_variant,,ENST00000401402,;EVA1C,3_prime_UTR_variant,,ENST00000300255,;EVA1C,3_prime_UTR_variant,,ENST00000382699,;EVA1C,non_coding_transcript_exon_variant,,ENST00000485488,;EVA1C,downstream_gene_variant,,ENST00000496615,;EVA1C,3_prime_UTR_variant,,ENST00000435323,;EVA1C,3_prime_UTR_variant,,ENST00000457807,;EVA1C,3_prime_UTR_variant,,ENST00000437338,;EVA1C,non_coding_transcript_exon_variant,,ENST00000464037,;	A	ENSG00000166979	ENST00000300255	Transcript	3_prime_UTR_variant	1845	.	.	.	.	.	.	.	1	EVA1C	HGNC	13239	protein_coding	YES	CCDS13614.1	ENSP00000300255	EVA1C_HUMAN	C9JS02_HUMAN,B3KWG0_HUMAN	UPI00000373F4	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAAGGATCCC	.	4	ESCA
ZNF280B	0	.	GRCh37	22	22840888	22840888	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1204C>G	.	.	ENST00000360412	4/4	14	6	8	21	21	0	ZNF280B,3_prime_UTR_variant,,ENST00000360412,;ZNF280B,intron_variant,,ENST00000406426,;	C	ENSG00000198477	ENST00000360412	Transcript	3_prime_UTR_variant	3612	.	.	.	.	.	.	.	-1	ZNF280B	HGNC	23022	protein_coding	YES	CCDS13799.1	ENSP00000353586	Z280B_HUMAN	.	UPI000013FF86	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCAGAAGGG	.	5	ESCA
UPB1	0	.	GRCh37	22	24896222	24896222	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.252C>A	p.%3D	p.P84P	ENST00000326010	2/10	20	10	10	19	19	0	UPB1,synonymous_variant,p.%3D,ENST00000382760,;UPB1,synonymous_variant,p.%3D,ENST00000326010,;UPB1,intron_variant,,ENST00000413389,;UPB1,intron_variant,,ENST00000415388,;	A	ENSG00000100024	ENST00000326010	Transcript	synonymous_variant	596	252	84	P	ccC/ccA	.	.	.	1	UPB1	HGNC	16297	protein_coding	YES	CCDS13827.1	ENSP00000324343	BUP1_HUMAN	A4QPH4_HUMAN	UPI0000126B4C	.	.	.	2/10	.	Superfamily_domains:SSF56317,Gene3D:3.60.110.10,hmmpanther:PTHR23088:SF9,hmmpanther:PTHR23088,PROSITE_profiles:PS50263	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CTCCCCGCAAA	.	4	ESCA
SGSM1	0	.	GRCh37	22	25280128	25280128	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1769C>A	p.Thr590Lys	p.T590K	ENST00000400359	16/26	35	27	7	35	35	0	SGSM1,missense_variant,p.Thr590Lys,ENST00000400359,;SGSM1,missense_variant,p.Thr535Lys,ENST00000400358,;SGSM1,non_coding_transcript_exon_variant,,ENST00000480523,;SGSM1,non_coding_transcript_exon_variant,,ENST00000473458,;	A	ENSG00000167037	ENST00000400359	Transcript	missense_variant	1776	1769	590	T/K	aCa/aAa	.	.	.	1	SGSM1	HGNC	29410	protein_coding	YES	CCDS46674.1	ENSP00000383212	SGSM1_HUMAN	.	UPI00006EB130	.	deleterious(0)	possibly_damaging(0.774)	16/26	.	hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGACAGCCA	.	5	ESCA
LRP5L	0	.	GRCh37	22	25750717	25750717	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501C>A	p.Phe167Leu	p.F167L	ENST00000402859	5/6	62	33	28	63	63	0	LRP5L,missense_variant,p.Phe167Leu,ENST00000402859,;LRP5L,missense_variant,p.Phe167Leu,ENST00000444995,;LRP5L,missense_variant,p.Phe167Leu,ENST00000402785,;LRP5L,3_prime_UTR_variant,,ENST00000474163,;LRP5L,non_coding_transcript_exon_variant,,ENST00000467672,;LRP5L,downstream_gene_variant,,ENST00000484509,;CTA-246H3.11,upstream_gene_variant,,ENST00000434827,;	T	ENSG00000100068	ENST00000402859	Transcript	missense_variant	1025	501	167	F/L	ttC/ttA	.	.	.	-1	LRP5L	HGNC	25323	protein_coding	YES	CCDS33626.1	ENSP00000384291	LRP5L_HUMAN	.	UPI000006DF62	.	deleterious(0)	probably_damaging(0.983)	5/6	.	PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF202,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTGAAAAT	.	5	ESCA
ZNRF3	0	.	GRCh37	22	29446744	29446744	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2575C>T	p.Arg859Ter	p.R859*	ENST00000544604	8/9	65	36	29	70	70	0	ZNRF3,stop_gained,p.Arg759Ter,ENST00000406323,;ZNRF3,stop_gained,p.Arg759Ter,ENST00000332811,;ZNRF3,stop_gained,p.Arg759Ter,ENST00000402174,;ZNRF3,stop_gained,p.Arg859Ter,ENST00000544604,;	T	ENSG00000183579	ENST00000544604	Transcript	stop_gained	2750	2575	859	R/*	Cga/Tga	COSM1415461,COSM4103266	.	.	1	ZNRF3	HGNC	18126	protein_coding	YES	CCDS56225.1	ENSP00000443824	ZNRF3_HUMAN	.	UPI0000EE5944	.	.	.	8/9	.	hmmpanther:PTHR16200:SF3,hmmpanther:PTHR16200	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACGCGAGGC	.	5	ESCA
KREMEN1	0	.	GRCh37	22	29542154	29542154	+	Intron	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1416+4066G>A	.	.	ENST00000327813	.	113	92	21	94	94	0	KREMEN1,3_prime_UTR_variant,,ENST00000400335,;KREMEN1,3_prime_UTR_variant,,ENST00000400338,;KREMEN1,intron_variant,,ENST00000327813,;KREMEN1,downstream_gene_variant,,ENST00000407188,;KREMEN1,intron_variant,,ENST00000479755,;	A	ENSG00000183762	ENST00000327813	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	KREMEN1	HGNC	17550	protein_coding	YES	CCDS13849.1	ENSP00000331242	KREM1_HUMAN	.	UPI000002AD01	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTCGGCTTT	.	5	ESCA
TCN2	0	.	GRCh37	22	31019043	31019043	+	Nonsense_Mutation	SNP	C	C	T	rs769817524	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1195C>T	p.Arg399Ter	p.R399*	ENST00000215838	8/9	50	44	6	62	62	0	TCN2,stop_gained,p.Arg372Ter,ENST00000407817,;TCN2,stop_gained,p.Arg395Ter,ENST00000405742,;TCN2,stop_gained,p.Arg399Ter,ENST00000215838,;TCN2,3_prime_UTR_variant,,ENST00000450638,;TCN2,non_coding_transcript_exon_variant,,ENST00000493542,;	T	ENSG00000185339	ENST00000215838	Transcript	stop_gained	1689	1195	399	R/*	Cga/Tga	rs769817524,CM087884,TCN2base_D0088:g.72338C>T	.	.	1	TCN2	HGNC	11653	protein_coding	YES	CCDS13881.1	ENSP00000215838	TCO2_HUMAN	.	UPI0000167BDB	.	.	.	8/9	.	hmmpanther:PTHR10559,hmmpanther:PTHR10559:SF14,Pfam_domain:PF14478	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	0,1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCTCCGAGAC	.	4	ESCA
PRR14L	0	.	GRCh37	22	32112599	32112599	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1226G>C	p.Arg409Thr	p.R409T	ENST00000327423	4/9	89	73	16	69	69	0	PRR14L,missense_variant,p.Arg409Thr,ENST00000434485,;PRR14L,missense_variant,p.Arg409Thr,ENST00000397493,;PRR14L,missense_variant,p.Arg409Thr,ENST00000327423,;PRR14L,upstream_gene_variant,,ENST00000330495,;PRR14L,downstream_gene_variant,,ENST00000461722,;PRR14L,upstream_gene_variant,,ENST00000492705,;PRR14L,upstream_gene_variant,,ENST00000431684,;	G	ENSG00000183530	ENST00000327423	Transcript	missense_variant	1416	1226	409	R/T	aGa/aCa	.	.	.	-1	PRR14L	HGNC	28738	protein_coding	YES	CCDS13900.2	ENSP00000331845	PR14L_HUMAN	C9J9V0_HUMAN	UPI0000207582	.	deleterious(0.03)	benign(0.124)	4/9	.	hmmpanther:PTHR14522,hmmpanther:PTHR14522:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTCTTTCA	.	5	ESCA
RFPL2	0	.	GRCh37	22	32587270	32587270	+	Missense_Mutation	SNP	C	C	T	rs770071733	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626G>A	p.Arg209Gln	p.R209Q	ENST00000400237	5/5	86	36	49	70	70	0	RFPL2,missense_variant,p.Arg209Gln,ENST00000400237,;RFPL2,missense_variant,p.Arg119Gln,ENST00000248983,;RFPL2,missense_variant,p.Arg148Gln,ENST00000248980,;RFPL2,missense_variant,p.Arg119Gln,ENST00000400236,;RFPL2,non_coding_transcript_exon_variant,,ENST00000489846,;	T	ENSG00000128253	ENST00000400237	Transcript	missense_variant	1562	626	209	R/Q	cGa/cAa	rs770071733	.	.	-1	RFPL2	HGNC	9979	protein_coding	YES	CCDS43009.2	ENSP00000383096	RFPL2_HUMAN	.	UPI000013CC66	.	tolerated(0.42)	benign(0.004)	5/5	.	PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF211,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCGGACG	.	5	ESCA
ELFN2	0	.	GRCh37	22	37769180	37769180	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2395G>A	p.Ala799Thr	p.A799T	ENST00000402918	3/3	47	36	10	49	49	0	ELFN2,missense_variant,p.Ala799Thr,ENST00000402918,;RP1-63G5.5,intron_variant,,ENST00000430883,;RP1-63G5.5,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000424973,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000451509,;	T	ENSG00000166897	ENST00000402918	Transcript	missense_variant	3181	2395	799	A/T	Gcc/Acc	.	.	.	-1	ELFN2	HGNC	29396	protein_coding	YES	CCDS33642.1	ENSP00000385277	PPR29_HUMAN	.	UPI000004E87D	.	deleterious(0)	probably_damaging(1)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D801D|c.2403C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGCGAACT	.	5	ESCA
TMEM163	0	.	GRCh37	2	135215728	135215728	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.684G>C	p.%3D	p.V228V	ENST00000281924	7/8	14	7	7	24	24	0	TMEM163,synonymous_variant,p.%3D,ENST00000281924,;MGAT5,downstream_gene_variant,,ENST00000409645,;TMEM163,non_coding_transcript_exon_variant,,ENST00000476823,;TMEM163,non_coding_transcript_exon_variant,,ENST00000467316,;AC013718.1,upstream_gene_variant,,ENST00000538722,;	G	ENSG00000152128	ENST00000281924	Transcript	synonymous_variant	749	684	228	V	gtG/gtC	.	.	.	-1	TMEM163	HGNC	25380	protein_coding	YES	CCDS2172.1	ENSP00000281924	TM163_HUMAN	.	UPI000007217C	.	.	.	7/8	.	Transmembrane_helices:TMhelix,Superfamily_domains:0054606,Gene3D:3h90A01,hmmpanther:PTHR31937:SF2,hmmpanther:PTHR31937	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CCACCCACGAG	.	4	ESCA
MLTK	0	.	GRCh37	2	174074471	174074471	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.759C>G	p.Phe253Leu	p.F253L	ENST00000375213	10/20	16	7	8	29	29	0	MLTK,missense_variant,p.Phe253Leu,ENST00000409176,;MLTK,missense_variant,p.Phe152Leu,ENST00000431503,;MLTK,missense_variant,p.Phe253Leu,ENST00000375213,;MLTK,missense_variant,p.Phe253Leu,ENST00000338983,;MLTK,missense_variant,p.Phe253Leu,ENST00000539448,;MLK7-AS1,non_coding_transcript_exon_variant,,ENST00000423106,;MLK7-AS1,intron_variant,,ENST00000422703,;MLK7-AS1,upstream_gene_variant,,ENST00000419609,;MLTK,non_coding_transcript_exon_variant,,ENST00000476618,;	G	ENSG00000091436	ENST00000375213	Transcript	missense_variant	837	759	253	F/L	ttC/ttG	.	.	.	1	MLTK	Uniprot_gn	.	protein_coding	YES	CCDS42777.1	ENSP00000364361	MLTK_HUMAN	C9J3F7_HUMAN	UPI0000073F69	.	deleterious(0.02)	probably_damaging(0.998)	10/20	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23257,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR00109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTCAAGCA	.	5	ESCA
MFSD6	0	.	GRCh37	2	191366244	191366244	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1300G>A	.	.	ENST00000392328	8/8	10	5	5	13	13	0	MFSD6,3_prime_UTR_variant,,ENST00000434582,;MFSD6,3_prime_UTR_variant,,ENST00000392328,;MFSD6,3_prime_UTR_variant,,ENST00000281416,;TMEM194B,downstream_gene_variant,,ENST00000409150,;MFSD6,downstream_gene_variant,,ENST00000535751,;MFSD6,downstream_gene_variant,,ENST00000444317,;MFSD6,intron_variant,,ENST00000412482,;MFSD6,downstream_gene_variant,,ENST00000486123,;	A	ENSG00000151690	ENST00000392328	Transcript	3_prime_UTR_variant	4000	.	.	.	.	.	.	.	1	MFSD6	HGNC	24711	protein_coding	YES	CCDS2306.1	ENSP00000376141	MFSD6_HUMAN	C9JJH2_HUMAN,C9JAZ7_HUMAN,C9J134_HUMAN,C9IYL1_HUMAN,B7Z810_HUMAN,B7Z7Y2_HUMAN	UPI000022BD91	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAGCTGAATAA	.	3	ESCA
MFSD6	0	.	GRCh37	2	191366293	191366293	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1349G>A	.	.	ENST00000392328	8/8	22	12	10	30	30	0	MFSD6,3_prime_UTR_variant,,ENST00000434582,;MFSD6,3_prime_UTR_variant,,ENST00000392328,;MFSD6,3_prime_UTR_variant,,ENST00000281416,;TMEM194B,downstream_gene_variant,,ENST00000409150,;MFSD6,downstream_gene_variant,,ENST00000535751,;MFSD6,downstream_gene_variant,,ENST00000444317,;MFSD6,intron_variant,,ENST00000412482,;MFSD6,downstream_gene_variant,,ENST00000486123,;	A	ENSG00000151690	ENST00000392328	Transcript	3_prime_UTR_variant	4049	.	.	.	.	.	.	.	1	MFSD6	HGNC	24711	protein_coding	YES	CCDS2306.1	ENSP00000376141	MFSD6_HUMAN	C9JJH2_HUMAN,C9JAZ7_HUMAN,C9J134_HUMAN,C9IYL1_HUMAN,B7Z810_HUMAN,B7Z7Y2_HUMAN	UPI000022BD91	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGAGAGAGA	.	5	ESCA
HECW2	0	.	GRCh37	2	197066110	197066110	+	Missense_Mutation	SNP	G	G	A	rs560792476	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4610C>T	p.Ala1537Val	p.A1537V	ENST00000260983	29/29	30	19	10	53	53	0	HECW2,missense_variant,p.Ala1537Val,ENST00000260983,;HECW2,missense_variant,p.Ala1181Val,ENST00000409111,;	A	ENSG00000138411	ENST00000260983	Transcript	missense_variant	4793	4610	1537	A/V	gCg/gTg	rs560792476	.	.	-1	HECW2	HGNC	29853	protein_coding	YES	CCDS33354.1	ENSP00000260983	HECW2_HUMAN	C9JPI9_HUMAN,C9JHL2_HUMAN	UPI00001A75E8	.	deleterious(0)	probably_damaging(0.991)	29/29	.	PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF127,hmmpanther:PTHR11254,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGCGCTCTG	byCluster|by1000G	5	ESCA
ZDBF2	0	.	GRCh37	2	207172018	207172018	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2766C>A	p.%3D	p.I922I	ENST00000374423	5/5	47	36	11	61	61	0	ZDBF2,synonymous_variant,p.%3D,ENST00000374423,;	A	ENSG00000204186	ENST00000374423	Transcript	synonymous_variant	3152	2766	922	I	atC/atA	.	.	.	1	ZDBF2	HGNC	29313	protein_coding	YES	CCDS46501.1	ENSP00000363545	ZDBF2_HUMAN	N0DVB2_HUMAN	UPI000022BDE3	.	.	.	5/5	.	hmmpanther:PTHR21639:SF2,hmmpanther:PTHR21639	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATATCATTTT	.	5	ESCA
ZDBF2	0	.	GRCh37	2	207174923	207174923	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5671C>G	p.Gln1891Glu	p.Q1891E	ENST00000374423	5/5	26	22	3	40	40	0	ZDBF2,missense_variant,p.Gln1891Glu,ENST00000374423,;	G	ENSG00000204186	ENST00000374423	Transcript	missense_variant	6057	5671	1891	Q/E	Caa/Gaa	.	.	.	1	ZDBF2	HGNC	29313	protein_coding	YES	CCDS46501.1	ENSP00000363545	ZDBF2_HUMAN	N0DVB2_HUMAN	UPI000022BDE3	.	tolerated(0.19)	benign(0.042)	5/5	.	hmmpanther:PTHR21639:SF2,hmmpanther:PTHR21639	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAACTCAAGCT	.	4	ESCA
MAP2	0	.	GRCh37	2	210595823	210595823	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*702G>C	.	.	ENST00000360351	15/15	45	13	32	40	40	0	MAP2,3_prime_UTR_variant,,ENST00000360351,;MAP2,3_prime_UTR_variant,,ENST00000392194,;MAP2,downstream_gene_variant,,ENST00000447185,;MAP2,downstream_gene_variant,,ENST00000199940,;MAP2,downstream_gene_variant,,ENST00000361559,;MAP2,downstream_gene_variant,,ENST00000475600,;	C	ENSG00000078018	ENST00000360351	Transcript	3_prime_UTR_variant	6692	.	.	.	.	.	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTTGATCAG	.	5	ESCA
PID1	0	.	GRCh37	2	229889476	229889476	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*872C>T	.	.	ENST00000392054	4/4	15	8	7	28	28	0	PID1,3_prime_UTR_variant,,ENST00000409462,;PID1,3_prime_UTR_variant,,ENST00000392055,;PID1,3_prime_UTR_variant,,ENST00000392054,;PID1,downstream_gene_variant,,ENST00000354069,;PID1,intron_variant,,ENST00000482518,;PID1,downstream_gene_variant,,ENST00000534952,;	A	ENSG00000153823	ENST00000392054	Transcript	3_prime_UTR_variant	1959	.	.	.	.	.	.	.	-1	PID1	HGNC	26084	protein_coding	YES	CCDS2471.1	ENSP00000375907	PCLI1_HUMAN	Q4ZG81_HUMAN	UPI00001C0AF7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCTGATCAC	.	5	ESCA
PLB1	0	.	GRCh37	2	28789701	28789717	+	Splice_Site	DEL	TGGCGAGTGAGTACGCG	TGGCGAGTGAGTACGCG	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	TGGCGAGTGAGTACGCG	TGGCGAGTGAGTACGCG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1319_1324+11delTGGCGAGTGAGTACGCGinsA	.	p.X440_splice	ENST00000327757	20/58	88	61	27	97	97	0	PLB1,splice_donor_variant,,ENST00000327757,;PLB1,splice_donor_variant,,ENST00000422425,;PLB1,splice_donor_variant,,ENST00000436544,;PLB1,splice_donor_variant,,ENST00000329020,;PLB1,splice_donor_variant,,ENST00000404858,;PLB1,splice_donor_variant,,ENST00000485642,;	A	ENSG00000163803	ENST00000327757	Transcript	splice_donor_variant	1363-?	1319-?	440-?	.	.	.	.	.	1	PLB1	HGNC	30041	protein_coding	YES	CCDS33168.1	ENSP00000330442	PLB1_HUMAN	.	UPI0000D6117C	.	.	.	20/58	20/57	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	CCACCCTGGCGAGTGAGTACGCGGCGGC	.	2	ESCA
SOX11	0	.	GRCh37	2	5837384	5837384	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3205C>A	.	.	ENST00000322002	1/1	51	8	43	33	33	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,intron_variant,,ENST00000455579,;	A	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	4586	.	.	.	.	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTCACTGC	.	5	ESCA
MAT2A	0	.	GRCh37	2	85771763	85771763	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*868G>A	.	.	ENST00000306434	9/9	25	19	6	35	34	1	MAT2A,3_prime_UTR_variant,,ENST00000306434,;GGCX,downstream_gene_variant,,ENST00000233838,;MAT2A,downstream_gene_variant,,ENST00000409017,;GGCX,downstream_gene_variant,,ENST00000465637,;MAT2A,downstream_gene_variant,,ENST00000490878,;MAT2A,downstream_gene_variant,,ENST00000481412,;MAT2A,downstream_gene_variant,,ENST00000465151,;MAT2A,downstream_gene_variant,,ENST00000469221,;	A	ENSG00000168906	ENST00000306434	Transcript	3_prime_UTR_variant	2179	.	.	.	.	.	.	.	1	MAT2A	HGNC	6904	protein_coding	YES	CCDS1977.1	ENSP00000303147	METK2_HUMAN	B4DN45_HUMAN,B4DEX8_HUMAN	UPI0000000C32	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTTGCACAC	.	2	ESCA
MYH15	0	.	GRCh37	3	108163547	108163547	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2655G>A	p.%3D	p.L885L	ENST00000273353	23/42	82	69	12	56	56	0	MYH15,synonymous_variant,p.%3D,ENST00000273353,;MYH15,non_coding_transcript_exon_variant,,ENST00000478998,;	T	ENSG00000144821	ENST00000273353	Transcript	synonymous_variant	2712	2655	885	L	ctG/ctA	.	.	.	-1	MYH15	HGNC	31073	protein_coding	YES	CCDS43127.1	ENSP00000273353	MYH15_HUMAN	H9XFA0_HUMAN	UPI0000253B6F	.	.	.	23/42	.	Superfamily_domains:SSF90257,Gene3D:1.20.5.340,hmmpanther:PTHR13140:SF263,hmmpanther:PTHR13140,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTCAGTTC	.	5	ESCA
KIAA2018	0	.	GRCh37	3	113367480	113367480	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6311C>G	.	.	ENST00000316407	7/7	131	115	16	101	101	0	KIAA2018,3_prime_UTR_variant,,ENST00000491165,;KIAA2018,3_prime_UTR_variant,,ENST00000316407,;KIAA2018,downstream_gene_variant,,ENST00000478658,;KIAA2018,downstream_gene_variant,,ENST00000496826,;	C	ENSG00000176542	ENST00000316407	Transcript	3_prime_UTR_variant	13460	.	.	.	.	.	.	.	-1	KIAA2018	HGNC	30494	protein_coding	YES	CCDS43133.1	ENSP00000320794	K2018_HUMAN	.	UPI00004800D8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCTGGATTCC	.	4	ESCA
POGLUT1	0	.	GRCh37	3	119204210	119204210	+	Missense_Mutation	SNP	C	C	G	rs746467283	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614C>G	p.Ser205Cys	p.S205C	ENST00000295588	6/11	173	155	18	117	117	0	POGLUT1,missense_variant,p.Ser205Cys,ENST00000295588,;POGLUT1,downstream_gene_variant,,ENST00000476573,;POGLUT1,3_prime_UTR_variant,,ENST00000486607,;POGLUT1,3_prime_UTR_variant,,ENST00000497447,;POGLUT1,upstream_gene_variant,,ENST00000473648,;	G	ENSG00000163389	ENST00000295588	Transcript	missense_variant	698	614	205	S/C	tCt/tGt	rs746467283	.	.	1	POGLUT1	HGNC	22954	protein_coding	YES	CCDS2988.1	ENSP00000295588	PGLT1_HUMAN	B4DJ97_HUMAN	UPI000003B0C3	.	deleterious(0.01)	probably_damaging(0.95)	6/11	.	hmmpanther:PTHR12203,Pfam_domain:PF05686,SMART_domains:SM00672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAACTCTACAG	.	4	ESCA
POLQ	0	.	GRCh37	3	121230769	121230769	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1576G>A	p.Glu526Lys	p.E526K	ENST00000264233	10/30	102	83	19	83	83	0	POLQ,missense_variant,p.Glu526Lys,ENST00000264233,;	T	ENSG00000051341	ENST00000264233	Transcript	missense_variant	1705	1576	526	E/K	Gaa/Aaa	.	.	.	-1	POLQ	HGNC	9186	protein_coding	YES	CCDS33833.1	ENSP00000264233	DPOLQ_HUMAN	.	UPI0000D61B5F	.	tolerated(0.11)	possibly_damaging(0.49)	10/30	.	PROSITE_profiles:PS51194,hmmpanther:PTHR11752,hmmpanther:PTHR11752:SF48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTTCTTCTC	.	5	ESCA
PLXND1	0	.	GRCh37	3	129279267	129279267	+	Missense_Mutation	SNP	G	G	A	rs569800532	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5039C>T	p.Thr1680Met	p.T1680M	ENST00000324093	31/36	50	38	11	40	40	0	PLXND1,missense_variant,p.Thr1680Met,ENST00000324093,;PLXND1,missense_variant,p.Thr1680Met,ENST00000393239,;PLXND1,missense_variant,p.Thr24Met,ENST00000506979,;PLXND1,upstream_gene_variant,,ENST00000504689,;PLXND1,missense_variant,p.Thr275Met,ENST00000512744,;PLXND1,non_coding_transcript_exon_variant,,ENST00000508630,;PLXND1,upstream_gene_variant,,ENST00000501038,;PLXND1,downstream_gene_variant,,ENST00000503166,;PLXND1,upstream_gene_variant,,ENST00000512807,;PLXND1,upstream_gene_variant,,ENST00000504524,;PLXND1,downstream_gene_variant,,ENST00000504979,;	A	ENSG00000004399	ENST00000324093	Transcript	missense_variant	5218	5039	1680	T/M	aCg/aTg	rs569800532,COSM296192	.	.	-1	PLXND1	HGNC	9107	protein_coding	YES	CCDS33854.1	ENSP00000317128	PLXD1_HUMAN	Q6P657_HUMAN	UPI00003671AD	.	deleterious(0.01)	probably_damaging(0.982)	31/36	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF7,Pfam_domain:PF08337	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGTCCGTAGGC	byCluster	5	ESCA
ATP2C1	0	.	GRCh37	3	130659491	130659491	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.480A>G	p.%3D	p.K160K	ENST00000393221	6/28	268	204	63	219	219	0	ATP2C1,synonymous_variant,p.%3D,ENST00000533801,;ATP2C1,synonymous_variant,p.%3D,ENST00000328560,;ATP2C1,synonymous_variant,p.%3D,ENST00000508532,;ATP2C1,synonymous_variant,p.%3D,ENST00000505330,;ATP2C1,synonymous_variant,p.%3D,ENST00000504612,;ATP2C1,synonymous_variant,p.%3D,ENST00000359644,;ATP2C1,synonymous_variant,p.%3D,ENST00000504948,;ATP2C1,synonymous_variant,p.%3D,ENST00000507488,;ATP2C1,synonymous_variant,p.%3D,ENST00000393221,;ATP2C1,synonymous_variant,p.%3D,ENST00000422190,;ATP2C1,synonymous_variant,p.%3D,ENST00000428331,;ATP2C1,synonymous_variant,p.%3D,ENST00000513801,;ATP2C1,synonymous_variant,p.%3D,ENST00000504381,;ATP2C1,synonymous_variant,p.%3D,ENST00000510168,;ATP2C1,downstream_gene_variant,,ENST00000505072,;	G	ENSG00000017260	ENST00000393221	Transcript	synonymous_variant	695	480	160	K	aaA/aaG	.	.	.	1	ATP2C1	HGNC	13211	protein_coding	YES	CCDS56278.1	ENSP00000376914	AT2C1_HUMAN	D6RGE9_HUMAN,D6R9U9_HUMAN	UPI0000EE224C	.	.	.	6/28	.	Superfamily_domains:0049473,TIGRFAM_domain:TIGR01494,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01522,Gene3D:1.20.1110.10,hmmpanther:PTHR24093:SF214,hmmpanther:PTHR24093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAAATCTCT	.	5	ESCA
ATP2C1	0	.	GRCh37	3	130720678	130720678	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2826+520C>T	.	.	ENST00000393221	.	90	64	26	81	81	0	ATP2C1,3_prime_UTR_variant,,ENST00000508532,;ATP2C1,3_prime_UTR_variant,,ENST00000505330,;ATP2C1,3_prime_UTR_variant,,ENST00000504948,;ATP2C1,3_prime_UTR_variant,,ENST00000428331,;ATP2C1,3_prime_UTR_variant,,ENST00000510168,;ATP2C1,intron_variant,,ENST00000533801,;ATP2C1,intron_variant,,ENST00000328560,;ATP2C1,intron_variant,,ENST00000504612,;ATP2C1,intron_variant,,ENST00000359644,;ATP2C1,intron_variant,,ENST00000507488,;ATP2C1,intron_variant,,ENST00000393221,;ATP2C1,intron_variant,,ENST00000422190,;ATP2C1,intron_variant,,ENST00000513801,;ATP2C1,intron_variant,,ENST00000504381,;ATP2C1,downstream_gene_variant,,ENST00000508660,;ATP2C1,non_coding_transcript_exon_variant,,ENST00000514654,;ATP2C1,downstream_gene_variant,,ENST00000507194,;	T	ENSG00000017260	ENST00000393221	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ATP2C1	HGNC	13211	protein_coding	YES	CCDS56278.1	ENSP00000376914	AT2C1_HUMAN	D6RGE9_HUMAN,D6R9U9_HUMAN	UPI0000EE224C	.	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTTCCTTTT	.	5	ESCA
SLITRK3	0	.	GRCh37	3	164907208	164907208	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1411C>T	p.%3D	p.L471L	ENST00000475390	2/2	102	93	8	47	47	0	SLITRK3,synonymous_variant,p.%3D,ENST00000475390,;SLITRK3,synonymous_variant,p.%3D,ENST00000241274,;SLITRK3,downstream_gene_variant,,ENST00000497724,;	A	ENSG00000121871	ENST00000475390	Transcript	synonymous_variant	1855	1411	471	L	Ctg/Ttg	.	.	.	-1	SLITRK3	HGNC	23501	protein_coding	YES	CCDS3197.1	ENSP00000420091	SLIK3_HUMAN	C9K0R4_HUMAN	UPI000004F259	.	.	.	2/2	.	hmmpanther:PTHR24373:SF14,hmmpanther:PTHR24373,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGTCAGCTTCT	.	3	ESCA
LRRIQ4	0	.	GRCh37	3	169539752	169539752	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43C>G	p.His15Asp	p.H15D	ENST00000340806	1/5	137	121	15	58	58	0	LRRIQ4,missense_variant,p.His15Asp,ENST00000340806,;	G	ENSG00000188306	ENST00000340806	Transcript	missense_variant	43	43	15	H/D	Cat/Gat	.	.	.	1	LRRIQ4	HGNC	34298	protein_coding	YES	CCDS46951.1	ENSP00000342188	LRIQ4_HUMAN	.	UPI0000197671	.	tolerated_low_confidence(0.21)	benign(0.015)	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATTCATCAG	.	4	ESCA
MCF2L2	0	.	GRCh37	3	182933848	182933848	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2405C>G	p.Ser802Ter	p.S802*	ENST00000328913	22/30	80	64	16	66	66	0	MCF2L2,stop_gained,p.Ser802Ter,ENST00000473233,;MCF2L2,stop_gained,p.Ser802Ter,ENST00000328913,;MCF2L2,non_coding_transcript_exon_variant,,ENST00000488149,;	C	ENSG00000053524	ENST00000328913	Transcript	stop_gained	2703	2405	802	S/*	tCa/tGa	.	.	.	-1	MCF2L2	HGNC	30319	protein_coding	YES	CCDS3243.1	ENSP00000328118	MF2L2_HUMAN	C9J326_HUMAN	UPI00001A962F	.	.	.	22/30	.	PROSITE_profiles:PS50010,hmmpanther:PTHR22826:SF89,hmmpanther:PTHR22826,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTTGAGAAT	.	5	ESCA
THPO	0	.	GRCh37	3	184091254	184091254	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.345T>C	p.%3D	p.S115S	ENST00000204615	5/6	54	45	8	52	52	0	THPO,synonymous_variant,p.%3D,ENST00000204615,;THPO,synonymous_variant,p.%3D,ENST00000445696,;THPO,synonymous_variant,p.%3D,ENST00000421442,;EIF2B5,intron_variant,,ENST00000444495,;POLR2H,downstream_gene_variant,,ENST00000430783,;POLR2H,downstream_gene_variant,,ENST00000429568,;POLR2H,downstream_gene_variant,,ENST00000296223,;POLR2H,downstream_gene_variant,,ENST00000456318,;POLR2H,downstream_gene_variant,,ENST00000438240,;POLR2H,downstream_gene_variant,,ENST00000443489,;POLR2H,downstream_gene_variant,,ENST00000452961,;THPO,upstream_gene_variant,,ENST00000477594,;POLR2H,downstream_gene_variant,,ENST00000476003,;	G	ENSG00000090534	ENST00000204615	Transcript	synonymous_variant	560	345	115	S	tcT/tcC	.	.	.	-1	THPO	HGNC	11795	protein_coding	YES	CCDS3265.1	ENSP00000204615	TPO_HUMAN	.	UPI000004A8D1	.	.	.	5/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10560,Pfam_domain:PF00758,Gene3D:1.20.1250.10,Superfamily_domains:SSF47266,Prints_domain:PR01485	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCCAGAAAG	.	5	ESCA
IQCG	0	.	GRCh37	3	197639584	197639584	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.925C>G	p.His309Asp	p.H309D	ENST00000265239	9/12	101	72	29	81	81	0	IQCG,missense_variant,p.His309Asp,ENST00000455191,;IQCG,missense_variant,p.His309Asp,ENST00000265239,;IQCG,downstream_gene_variant,,ENST00000453254,;IQCG,non_coding_transcript_exon_variant,,ENST00000485787,;IQCG,non_coding_transcript_exon_variant,,ENST00000469822,;IQCG,downstream_gene_variant,,ENST00000473225,;IQCG,non_coding_transcript_exon_variant,,ENST00000478903,;IQCG,non_coding_transcript_exon_variant,,ENST00000490748,;	C	ENSG00000114473	ENST00000265239	Transcript	missense_variant	1350	925	309	H/D	Cat/Gat	.	.	.	-1	IQCG	HGNC	25251	protein_coding	YES	CCDS3331.1	ENSP00000265239	IQCG_HUMAN	C9JUC1_HUMAN,C9J6M9_HUMAN	UPI0000037D68	.	deleterious(0)	probably_damaging(0.993)	9/12	.	hmmpanther:PTHR14871,hmmpanther:PTHR14871:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTATGAGTCC	.	5	ESCA
DLEC1	0	.	GRCh37	3	38163174	38163174	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4922G>T	p.Trp1641Leu	p.W1641L	ENST00000308059	35/37	23	4	19	35	35	0	DLEC1,missense_variant,p.Trp1641Leu,ENST00000308059,;DLEC1,missense_variant,p.Trp1641Leu,ENST00000346219,;DLEC1,missense_variant,p.Trp1644Leu,ENST00000452631,;ACAA1,downstream_gene_variant,,ENST00000452171,;ACAA1,downstream_gene_variant,,ENST00000333167,;ACAA1,downstream_gene_variant,,ENST00000421218,;ACAA1,downstream_gene_variant,,ENST00000444607,;ACAA1,downstream_gene_variant,,ENST00000544624,;ACAA1,downstream_gene_variant,,ENST00000450296,;ACAA1,downstream_gene_variant,,ENST00000301810,;Y_RNA,downstream_gene_variant,,ENST00000365095,;ACAA1,intron_variant,,ENST00000451419,;ACAA1,downstream_gene_variant,,ENST00000480865,;DLEC1,non_coding_transcript_exon_variant,,ENST00000478428,;ACAA1,downstream_gene_variant,,ENST00000411549,;ACAA1,downstream_gene_variant,,ENST00000469600,;ACAA1,downstream_gene_variant,,ENST00000423611,;ACAA1,downstream_gene_variant,,ENST00000440176,;ACAA1,downstream_gene_variant,,ENST00000447223,;ACAA1,downstream_gene_variant,,ENST00000469559,;	T	ENSG00000008226	ENST00000308059	Transcript	missense_variant	4943	4922	1641	W/L	tGg/tTg	.	.	.	1	DLEC1	HGNC	2899	protein_coding	YES	CCDS2672.2	ENSP00000308597	DLEC1_HUMAN	.	UPI00006EB134	.	tolerated(0.09)	benign(0.138)	35/37	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGGGTGG	.	5	ESCA
FAM208A	0	.	GRCh37	3	56662638	56662638	+	Missense_Mutation	SNP	T	T	C	rs377606389	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3752A>G	p.Tyr1251Cys	p.Y1251C	ENST00000493960	19/24	55	42	13	88	88	0	FAM208A,missense_variant,p.Tyr1190Cys,ENST00000355628,;FAM208A,missense_variant,p.Tyr1251Cys,ENST00000493960,;FAM208A,missense_variant,p.Tyr814Cys,ENST00000431842,;FAM208A,upstream_gene_variant,,ENST00000485156,;FAM208A,non_coding_transcript_exon_variant,,ENST00000487036,;FAM208A,non_coding_transcript_exon_variant,,ENST00000461863,;FAM208A,non_coding_transcript_exon_variant,,ENST00000459993,;	C	ENSG00000163946	ENST00000493960	Transcript	missense_variant	3763	3752	1251	Y/C	tAt/tGt	rs377606389	.	.	-1	FAM208A	HGNC	30314	protein_coding	YES	CCDS46853.1	ENSP00000417509	F208A_HUMAN	.	UPI0000422561	.	deleterious(0)	probably_damaging(1)	19/24	.	hmmpanther:PTHR16207:SF1,hmmpanther:PTHR16207	.	.	.	.	.	.	.	G:0	G:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGATATTCC	.	5	ESCA
EGF	0	.	GRCh37	4	110915911	110915911	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2880C>T	p.%3D	p.L960L	ENST00000265171	20/24	33	26	7	45	45	0	EGF,synonymous_variant,p.%3D,ENST00000503392,;EGF,synonymous_variant,p.%3D,ENST00000265171,;EGF,synonymous_variant,p.%3D,ENST00000509793,;RNU6-35P,downstream_gene_variant,,ENST00000384530,;EGF,non_coding_transcript_exon_variant,,ENST00000509996,;	T	ENSG00000138798	ENST00000265171	Transcript	synonymous_variant	3325	2880	960	L	ctC/ctT	.	.	.	1	EGF	HGNC	3229	protein_coding	YES	CCDS3689.1	ENSP00000265171	EGF_HUMAN	Q6QBS2_HUMAN	UPI000013D5C8	.	.	.	20/24	.	PIRSF_domain:PIRSF001778	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCTCAGGGA	.	5	ESCA
FAT4	0	.	GRCh37	4	126372870	126372870	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10699A>G	p.Ser3567Gly	p.S3567G	ENST00000394329	9/17	15	10	5	24	24	0	FAT4,missense_variant,p.Ser3567Gly,ENST00000394329,;FAT4,missense_variant,p.Ser1865Gly,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,;	G	ENSG00000196159	ENST00000394329	Transcript	missense_variant	10712	10699	3567	S/G	Agc/Ggc	.	.	.	1	FAT4	HGNC	23109	protein_coding	YES	CCDS3732.3	ENSP00000377862	FAT4_HUMAN	B3KRB4_HUMAN	UPI000155D6E3	.	.	possibly_damaging(0.578)	9/17	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF41,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TTCTGAGCACA	.	4	ESCA
RAPGEF2	0	.	GRCh37	4	160268112	160268112	+	Missense_Mutation	SNP	C	C	T	rs774381651	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3191C>T	p.Ser1064Leu	p.S1064L	ENST00000264431	19/24	44	36	8	71	71	0	RAPGEF2,missense_variant,p.Ser1064Leu,ENST00000264431,;RAPGEF2,missense_variant,p.Ser170Leu,ENST00000502485,;RAPGEF2,missense_variant,p.Ser96Leu,ENST00000510253,;RAPGEF2,upstream_gene_variant,,ENST00000505026,;	T	ENSG00000109756	ENST00000264431	Transcript	missense_variant	3610	3191	1064	S/L	tCa/tTa	rs774381651	.	.	1	RAPGEF2	HGNC	16854	protein_coding	YES	CCDS43277.1	ENSP00000264431	RPGF2_HUMAN	Q9UFT5_HUMAN,Q4W5Q4_HUMAN,Q17RH5_HUMAN,D6REY8_HUMAN,B4DG82_HUMAN	UPI0000033783	.	tolerated(0.7)	benign(0.003)	19/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTCACGGA	.	5	ESCA
SPOCK3	0	.	GRCh37	4	167655806	167655806	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*266T>G	.	.	ENST00000357154	12/12	23	15	8	39	39	0	SPOCK3,3_prime_UTR_variant,,ENST00000357154,;SPOCK3,3_prime_UTR_variant,,ENST00000511531,;SPOCK3,3_prime_UTR_variant,,ENST00000357545,;SPOCK3,3_prime_UTR_variant,,ENST00000506886,;SPOCK3,3_prime_UTR_variant,,ENST00000511269,;SPOCK3,3_prime_UTR_variant,,ENST00000421836,;SPOCK3,3_prime_UTR_variant,,ENST00000510741,;SPOCK3,3_prime_UTR_variant,,ENST00000535728,;SPOCK3,3_prime_UTR_variant,,ENST00000541354,;SPOCK3,3_prime_UTR_variant,,ENST00000512681,;SPOCK3,3_prime_UTR_variant,,ENST00000502330,;SPOCK3,3_prime_UTR_variant,,ENST00000504953,;SPOCK3,downstream_gene_variant,,ENST00000541637,;SPOCK3,downstream_gene_variant,,ENST00000534949,;SPOCK3,non_coding_transcript_exon_variant,,ENST00000507137,;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,;	C	ENSG00000196104	ENST00000357154	Transcript	3_prime_UTR_variant	1715	.	.	.	.	.	.	.	-1	SPOCK3	HGNC	13565	protein_coding	YES	CCDS54817.1	ENSP00000349677	TICN3_HUMAN	Q4W5S3_HUMAN,Q4W5E2_HUMAN,E7EMP8_HUMAN	UPI000004BA60	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACTTATTATA	.	2	ESCA
AADAT	0	.	GRCh37	4	170983068	170983068	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1211C>T	p.Ser404Leu	p.S404L	ENST00000337664	12/13	20	14	6	31	31	0	AADAT,missense_variant,p.Ser404Leu,ENST00000337664,;AADAT,missense_variant,p.Ser404Leu,ENST00000353187,;AADAT,missense_variant,p.Ser408Leu,ENST00000509167,;AADAT,missense_variant,p.Ser404Leu,ENST00000515480,;	A	ENSG00000109576	ENST00000337664	Transcript	missense_variant	1488	1211	404	S/L	tCa/tTa	.	.	.	-1	AADAT	HGNC	17929	protein_coding	YES	CCDS3814.1	ENSP00000336808	AADAT_HUMAN	Q4W5N8_HUMAN,D6RFY7_HUMAN,D6RC56_HUMAN	UPI00000711E6	.	tolerated(1)	benign(0.001)	12/13	.	hmmpanther:PTHR11751:SF294,hmmpanther:PTHR11751,Gene3D:3.90.1150.10,Pfam_domain:PF00155,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCTGAAGAG	.	5	ESCA
NEIL3	0	.	GRCh37	4	178231034	178231034	+	5'UTR	SNP	C	C	T	rs550033836	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-74C>T	.	.	ENST00000264596	1/10	30	25	5	51	51	0	NEIL3,5_prime_UTR_variant,,ENST00000264596,;NEIL3,upstream_gene_variant,,ENST00000513321,;	T	ENSG00000109674	ENST00000264596	Transcript	5_prime_UTR_variant	45	.	.	.	.	rs550033836	.	.	1	NEIL3	HGNC	24573	protein_coding	YES	CCDS3828.1	ENSP00000264596	NEIL3_HUMAN	.	UPI000013D53D	.	.	.	1/10	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGCCCGCGCA	by1000G	2	ESCA
BEND4	0	.	GRCh37	4	42145544	42145544	+	Missense_Mutation	SNP	C	C	T	rs552724030	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.955G>A	p.Glu319Lys	p.E319K	ENST00000502486	3/6	25	17	8	41	41	0	BEND4,missense_variant,p.Glu315Lys,ENST00000504360,;BEND4,missense_variant,p.Glu319Lys,ENST00000502486,;	T	ENSG00000188848	ENST00000502486	Transcript	missense_variant	1535	955	319	E/K	Gag/Aag	rs552724030	.	.	-1	BEND4	HGNC	23815	protein_coding	YES	CCDS47048.1	ENSP00000421169	BEND4_HUMAN	.	UPI00015386AF	.	deleterious_low_confidence(0)	possibly_damaging(0.905)	3/6	.	Low_complexity_(Seg):seg	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCGTCCT	by1000G	5	ESCA
FRYL	0	.	GRCh37	4	48782141	48782141	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-430C>T	.	.	ENST00000358350	1/64	21	15	6	19	19	0	FRYL,5_prime_UTR_variant,,ENST00000358350,;FRYL,5_prime_UTR_variant,,ENST00000507711,;FRYL,5_prime_UTR_variant,,ENST00000264319,;FRYL,5_prime_UTR_variant,,ENST00000537810,;FRYL,non_coding_transcript_exon_variant,,ENST00000502520,;FRYL,non_coding_transcript_exon_variant,,ENST00000509886,;FRYL,non_coding_transcript_exon_variant,,ENST00000514783,;FRYL,non_coding_transcript_exon_variant,,ENST00000515684,;FRYL,non_coding_transcript_exon_variant,,ENST00000505437,;	A	ENSG00000075539	ENST00000358350	Transcript	5_prime_UTR_variant	176	.	.	.	.	.	.	.	-1	FRYL	HGNC	29127	protein_coding	YES	CCDS43227.1	ENSP00000351113	FRYL_HUMAN	.	UPI0000EBC149	.	.	.	1/64	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCCGGTCCCC	.	2	ESCA
SCFD2	0	.	GRCh37	4	54231952	54231952	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.157G>C	p.Asp53His	p.D53H	ENST00000401642	1/9	44	34	10	37	37	0	SCFD2,missense_variant,p.Asp53His,ENST00000388940,;SCFD2,missense_variant,p.Asp53His,ENST00000401642,;SCFD2,intron_variant,,ENST00000503450,;	G	ENSG00000184178	ENST00000401642	Transcript	missense_variant	291	157	53	D/H	Gac/Cac	.	.	.	-1	SCFD2	HGNC	30676	protein_coding	YES	CCDS33984.1	ENSP00000384182	SCFD2_HUMAN	D6RCK6_HUMAN	UPI000006FB05	.	tolerated(0.15)	benign(0.235)	1/9	.	hmmpanther:PTHR11679:SF29,hmmpanther:PTHR11679	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGTCAGGAC	.	5	ESCA
SDAD1	0	.	GRCh37	4	76890468	76890468	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.968G>C	p.Arg323Thr	p.R323T	ENST00000356260	11/22	161	154	7	63	63	0	SDAD1,missense_variant,p.Arg286Thr,ENST00000395711,;SDAD1,missense_variant,p.Arg323Thr,ENST00000356260,;SDAD1,non_coding_transcript_exon_variant,,ENST00000507396,;SDAD1,non_coding_transcript_exon_variant,,ENST00000513089,;SDAD1,downstream_gene_variant,,ENST00000515836,;SDAD1,3_prime_UTR_variant,,ENST00000395710,;SDAD1,downstream_gene_variant,,ENST00000503411,;	G	ENSG00000198301	ENST00000356260	Transcript	missense_variant	1087	968	323	R/T	aGa/aCa	.	.	.	-1	SDAD1	HGNC	25537	protein_coding	YES	CCDS3573.2	ENSP00000348596	SDA1_HUMAN	.	UPI000020B02A	.	deleterious(0)	probably_damaging(0.996)	11/22	.	hmmpanther:PTHR12730,hmmpanther:PTHR12730:SF0,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCAATCTGGAG	.	2	ESCA
SDAD1	0	.	GRCh37	4	76890482	76890482	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.954G>A	p.Met318Ile	p.M318I	ENST00000356260	11/22	162	154	8	61	61	0	SDAD1,missense_variant,p.Met281Ile,ENST00000395711,;SDAD1,missense_variant,p.Met318Ile,ENST00000356260,;SDAD1,non_coding_transcript_exon_variant,,ENST00000507396,;SDAD1,non_coding_transcript_exon_variant,,ENST00000513089,;SDAD1,downstream_gene_variant,,ENST00000515836,;SDAD1,3_prime_UTR_variant,,ENST00000395710,;SDAD1,downstream_gene_variant,,ENST00000503411,;	T	ENSG00000198301	ENST00000356260	Transcript	missense_variant	1073	954	318	M/I	atG/atA	.	.	.	-1	SDAD1	HGNC	25537	protein_coding	YES	CCDS3573.2	ENSP00000348596	SDA1_HUMAN	.	UPI000020B02A	.	tolerated(0.12)	benign(0.034)	11/22	.	hmmpanther:PTHR12730,hmmpanther:PTHR12730:SF0,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGTTCATGAG	.	2	ESCA
PCDHGA6	0	.	GRCh37	5	140755585	140755585	+	Silent	SNP	C	C	T	rs761668305	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1935C>T	p.%3D	p.A645A	ENST00000517434	1/4	81	46	35	92	92	0	PCDHGA6,synonymous_variant,p.%3D,ENST00000517434,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB2,intron_variant,,ENST00000522605,;	T	ENSG00000253731	ENST00000517434	Transcript	synonymous_variant	1935	1935	645	A	gcC/gcT	rs761668305	.	.	1	PCDHGA6	HGNC	8704	protein_coding	YES	CCDS54926.1	ENSP00000429601	PCDG6_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI00000715C8	.	.	.	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF107,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCCGTCCA	byFrequency	5	ESCA
PCDHGA6	0	.	GRCh37	5	140755848	140755848	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2198C>T	p.Ala733Val	p.A733V	ENST00000517434	1/4	67	42	25	96	96	0	PCDHGA6,missense_variant,p.Ala733Val,ENST00000517434,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB2,intron_variant,,ENST00000522605,;	T	ENSG00000253731	ENST00000517434	Transcript	missense_variant	2198	2198	733	A/V	gCg/gTg	.	.	.	1	PCDHGA6	HGNC	8704	protein_coding	YES	CCDS54926.1	ENSP00000429601	PCDG6_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI00000715C8	.	tolerated_low_confidence(0.24)	benign(0.004)	1/4	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF107	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAGCGAGCA	.	5	ESCA
PCDH1	0	.	GRCh37	5	141243774	141243774	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2122G>A	p.Glu708Lys	p.E708K	ENST00000287008	3/5	20	10	9	18	18	0	PCDH1,missense_variant,p.Glu686Lys,ENST00000536585,;PCDH1,missense_variant,p.Glu696Lys,ENST00000456271,;PCDH1,missense_variant,p.Glu708Lys,ENST00000287008,;PCDH1,missense_variant,p.Glu708Lys,ENST00000394536,;PCDH1,missense_variant,p.Glu719Lys,ENST00000357517,;PCDH1,intron_variant,,ENST00000503492,;PCDH1,downstream_gene_variant,,ENST00000514773,;PCDH1,non_coding_transcript_exon_variant,,ENST00000511044,;PCDH1,3_prime_UTR_variant,,ENST00000515351,;PCDH1,downstream_gene_variant,,ENST00000505937,;	T	ENSG00000156453	ENST00000287008	Transcript	missense_variant	2270	2122	708	E/K	Gag/Aag	COSM3765172,COSM3765173	.	.	-1	PCDH1	HGNC	8655	protein_coding	YES	CCDS4267.1	ENSP00000287008	PCDH1_HUMAN	D6RBG2_HUMAN	UPI000016158F	.	deleterious(0.04)	probably_damaging(0.998)	3/5	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,PROSITE_patterns:PS00232,hmmpanther:PTHR24027:SF30,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTCGTCCA	.	5	ESCA
FAT2	0	.	GRCh37	5	150901029	150901029	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11125G>A	p.Glu3709Lys	p.E3709K	ENST00000261800	18/23	39	24	14	41	41	0	FAT2,missense_variant,p.Glu3709Lys,ENST00000261800,;FAT2,missense_variant,p.Glu568Lys,ENST00000520200,;	T	ENSG00000086570	ENST00000261800	Transcript	missense_variant	11138	11125	3709	E/K	Gag/Aag	.	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	probably_damaging(0.968)	18/23	.	hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCCTTGG	.	5	ESCA
FAT2	0	.	GRCh37	5	150929062	150929062	+	Missense_Mutation	SNP	C	C	T	rs756688058	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4583G>A	p.Arg1528Gln	p.R1528Q	ENST00000261800	8/23	31	17	13	25	25	0	FAT2,missense_variant,p.Arg1528Gln,ENST00000261800,;	T	ENSG00000086570	ENST00000261800	Transcript	missense_variant	4596	4583	1528	R/Q	cGa/cAa	rs756688058	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	probably_damaging(1)	8/23	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTCTCGGACC	.	5	ESCA
FAT2	0	.	GRCh37	5	150948297	150948297	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196C>T	p.Gln66Ter	p.Q66*	ENST00000261800	1/23	39	22	17	45	45	0	FAT2,stop_gained,p.Gln66Ter,ENST00000261800,;	A	ENSG00000086570	ENST00000261800	Transcript	stop_gained	209	196	66	Q/*	Cag/Tag	.	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	.	1/23	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTGTGGCT	.	5	ESCA
FAM114A2	0	.	GRCh37	5	153381887	153381887	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1180C>T	p.His394Tyr	p.H394Y	ENST00000351797	11/14	38	31	7	52	52	0	FAM114A2,missense_variant,p.His394Tyr,ENST00000520667,;FAM114A2,missense_variant,p.His394Tyr,ENST00000351797,;FAM114A2,missense_variant,p.His394Tyr,ENST00000522858,;FAM114A2,missense_variant,p.His324Tyr,ENST00000520313,;FAM114A2,upstream_gene_variant,,ENST00000518914,;	A	ENSG00000055147	ENST00000351797	Transcript	missense_variant	1257	1180	394	H/Y	Cac/Tac	.	.	.	-1	FAM114A2	HGNC	1333	protein_coding	YES	CCDS4323.1	ENSP00000341597	F1142_HUMAN	E5RK42_HUMAN,E5RHP2_HUMAN,E5RHI8_HUMAN,E5RH43_HUMAN,E5RGF9_HUMAN,E5RFK2_HUMAN	UPI000013D5DA	.	deleterious(0)	probably_damaging(0.999)	11/14	.	hmmpanther:PTHR12842,hmmpanther:PTHR12842:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTGTGGAATA	.	5	ESCA
LMAN2	0	.	GRCh37	5	176758913	176758913	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*174G>A	.	.	ENST00000303127	8/8	78	64	13	86	86	0	LMAN2,3_prime_UTR_variant,,ENST00000303127,;LMAN2,downstream_gene_variant,,ENST00000514458,;LMAN2,downstream_gene_variant,,ENST00000502560,;LMAN2,downstream_gene_variant,,ENST00000515209,;LMAN2,downstream_gene_variant,,ENST00000502721,;LMAN2,downstream_gene_variant,,ENST00000504071,;	T	ENSG00000169223	ENST00000303127	Transcript	3_prime_UTR_variant	1450	.	.	.	.	.	.	.	-1	LMAN2	HGNC	16986	protein_coding	YES	CCDS4417.1	ENSP00000303366	LMAN2_HUMAN	D6RIU4_HUMAN,B4DWN1_HUMAN	UPI0000037B35	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCGGCTC	.	5	ESCA
SLC1A3	0	.	GRCh37	5	36686602	36686602	+	3'UTR	SNP	G	G	A	rs180855098	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*231G>A	.	.	ENST00000265113	10/10	35	31	4	30	30	0	SLC1A3,3_prime_UTR_variant,,ENST00000265113,;SLC1A3,3_prime_UTR_variant,,ENST00000381918,;CTD-2353F22.1,intron_variant,,ENST00000510740,;SLC1A3,downstream_gene_variant,,ENST00000506178,;	A	ENSG00000079215	ENST00000265113	Transcript	3_prime_UTR_variant	2336	.	.	.	.	rs180855098	.	.	1	SLC1A3	HGNC	10941	protein_coding	YES	CCDS3919.1	ENSP00000265113	EAA1_HUMAN	E7EUV6_HUMAN,E7EUS7_HUMAN	UPI0000129B0F	.	.	.	10/10	.	.	A:0.0008	A:0.0008	A:0	.	A:0	A:0.003	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|VARSCANS	TTACCGAATAA	byFrequency|byCluster|by1000G	2	ESCA
ATG5	0	.	GRCh37	6	106756264	106756264	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.211G>C	p.Glu71Gln	p.E71Q	ENST00000369076	3/8	67	57	10	72	72	0	ATG5,missense_variant,p.Glu71Gln,ENST00000343245,;ATG5,missense_variant,p.Glu71Gln,ENST00000369076,;ATG5,intron_variant,,ENST00000360666,;ATG5,intron_variant,,ENST00000369070,;RNU6-344P,downstream_gene_variant,,ENST00000516635,;	G	ENSG00000057663	ENST00000369076	Transcript	missense_variant	535	211	71	E/Q	Gaa/Caa	.	.	.	-1	ATG5	HGNC	589	protein_coding	YES	CCDS5055.1	ENSP00000358072	ATG5_HUMAN	A9UGY9_HUMAN	UPI0000125C62	.	deleterious(0.02)	possibly_damaging(0.791)	3/8	.	hmmpanther:PTHR13040:SF2,hmmpanther:PTHR13040	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCAAACC	.	5	ESCA
LAMA4	0	.	GRCh37	6	112466087	112466087	+	Missense_Mutation	SNP	G	G	A	rs782325644	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2402C>T	p.Thr801Met	p.T801M	ENST00000230538	19/39	44	40	4	43	43	0	LAMA4,missense_variant,p.Thr801Met,ENST00000230538,;LAMA4,missense_variant,p.Thr794Met,ENST00000424408,;LAMA4,missense_variant,p.Thr794Met,ENST00000522006,;LAMA4,missense_variant,p.Thr794Met,ENST00000389463,;LAMA4,3_prime_UTR_variant,,ENST00000523765,;	A	ENSG00000112769	ENST00000230538	Transcript	missense_variant	2800	2402	801	T/M	aCg/aTg	rs782325644,COSM1213008	.	.	-1	LAMA4	HGNC	6484	protein_coding	YES	CCDS43491.1	ENSP00000230538	LAMA4_HUMAN	E5RK79_HUMAN,E5RHF3_HUMAN,E5RFQ2_HUMAN,E5RFD7_HUMAN	UPI000013C937	.	tolerated(0.18)	benign(0.228)	19/39	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF174,Pfam_domain:PF06009	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAACCGTACGA	byFrequency	3	ESCA
TSPYL4	0	.	GRCh37	6	116579735	116579735	+	5'Flank	SNP	T	T	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000420283	.	15	6	8	17	17	0	DSE,synonymous_variant,p.%3D,ENST00000540275,;DSE,5_prime_UTR_variant,,ENST00000430252,;TSPYL4,upstream_gene_variant,,ENST00000420283,;RP3-486I3.7,downstream_gene_variant,,ENST00000448740,;RP3-486I3.4,non_coding_transcript_exon_variant,,ENST00000435100,;	A	ENSG00000187189	ENST00000420283	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4474	-1	TSPYL4	HGNC	21559	protein_coding	YES	CCDS5106.1	ENSP00000410943	TSYL4_HUMAN	Q69YV8_HUMAN	UPI00001BBB76	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GCCCTTGGCAG	.	4	ESCA
SLC18B1	0	.	GRCh37	6	133091405	133091405	+	3'UTR	SNP	C	C	T	rs759534156	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4G>A	.	.	ENST00000275227	14/14	57	35	22	43	43	0	SLC18B1,3_prime_UTR_variant,,ENST00000275227,;SLC18B1,downstream_gene_variant,,ENST00000367918,;SLC18B1,downstream_gene_variant,,ENST00000538764,;RP1-55C23.8,downstream_gene_variant,,ENST00000604951,;	T	ENSG00000146409	ENST00000275227	Transcript	3_prime_UTR_variant	1472	.	.	.	.	rs759534156	.	.	-1	SLC18B1	HGNC	21573	protein_coding	YES	CCDS5163.1	ENSP00000275227	S18B1_HUMAN	.	UPI000013DA50	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATCGGACT	byFrequency	5	ESCA
GPR116	0	.	GRCh37	6	46826698	46826698	+	Frame_Shift_Del	DEL	T	T	-	rs755080517	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2942delA	p.Asp981AlafsTer10	p.D981Afs*10	ENST00000283296	17/21	40	27	13	52	52	0	GPR116,frameshift_variant,p.Asp410AlafsTer10,ENST00000545669,;GPR116,frameshift_variant,p.Asp981AlafsTer10,ENST00000265417,;GPR116,frameshift_variant,p.Asp839AlafsTer10,ENST00000456426,;GPR116,frameshift_variant,p.Asp981AlafsTer10,ENST00000283296,;GPR116,frameshift_variant,p.Asp981AlafsTer10,ENST00000362015,;GPR116,downstream_gene_variant,,ENST00000498632,;	-	ENSG00000069122	ENST00000283296	Transcript	frameshift_variant	3231	2942	981	D/X	gAc/gc	rs755080517	.	.	-1	GPR116	HGNC	19030	protein_coding	YES	CCDS4919.1	ENSP00000283296	GP116_HUMAN	.	UPI000007075A	.	.	.	17/21	.	PROSITE_profiles:PS50221,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF272,Pfam_domain:PF01825,SMART_domains:SM00303	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACATTGTCCCCA	.	3	ESCA
MCM3	0	.	GRCh37	6	52142452	52142470	+	Frame_Shift_Del	DEL	GGGGCCAATGACTTGGCCA	GGGGCCAATGACTTGGCCA	-	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	GGGGCCAATGACTTGGCCA	GGGGCCAATGACTTGGCCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1031_1049delTGGCCAAGTCATTGGCCCC	p.Leu344GlnfsTer25	p.L344Qfs*25	ENST00000596288	7/17	60	48	12	58	58	0	MCM3,frameshift_variant,p.Leu253GlnfsTer25,ENST00000419835,;MCM3,frameshift_variant,p.Leu299GlnfsTer25,ENST00000229854,;MCM3,frameshift_variant,p.Leu344GlnfsTer25,ENST00000596288,;MCM3,upstream_gene_variant,,ENST00000421471,;MCM3,non_coding_transcript_exon_variant,,ENST00000476448,;MCM3,downstream_gene_variant,,ENST00000596983,;	-	ENSG00000112118	ENST00000596288	Transcript	frameshift_variant	1059-1077	1031-1049	344-350	LAKSLAP/X	cTGGCCAAGTCATTGGCCCCa/ca	.	.	.	-1	MCM3	HGNC	6945	protein_coding	YES	CCDS4940.2	ENSP00000472940	.	Q8NHX6_HUMAN,B4DWW4_HUMAN	UPI0000EE4F08	.	.	.	7/17	.	Superfamily_domains:SSF52540,SMART_domains:SM00350,Gene3D:3.40.50.300,Pfam_domain:PF00493,hmmpanther:PTHR11630,hmmpanther:PTHR11630:SF72,PROSITE_profiles:PS50051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	ATACTTGGGGCCAATGACTTGGCCAGCTGG	.	2	ESCA
COL19A1	0	.	GRCh37	6	70850865	70850865	+	Missense_Mutation	SNP	G	G	A	rs751938810	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1466G>A	p.Gly489Glu	p.G489E	ENST00000322773	20/51	101	78	22	134	134	0	COL19A1,missense_variant,p.Gly489Glu,ENST00000322773,;COL19A1,missense_variant,p.Gly111Glu,ENST00000393344,;	A	ENSG00000082293	ENST00000322773	Transcript	missense_variant	1568	1466	489	G/E	gGa/gAa	rs751938810	.	.	1	COL19A1	HGNC	2196	protein_coding	YES	CCDS4970.1	ENSP00000316030	COJA1_HUMAN	.	UPI000004F1E3	.	deleterious(0)	probably_damaging(1)	20/51	.	Pfam_domain:PF01391,hmmpanther:PTHR24022:SF80,hmmpanther:PTHR24022	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAGGAGAAA	.	5	ESCA
DSP	0	.	GRCh37	6	7580047	7580048	+	Frame_Shift_Ins	INS	-	-	AAGT	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3626_3629dupAGTA	p.Tyr1210Ter	p.Y1210*	ENST00000379802	23/24	19	7	11	39	39	0	DSP,frameshift_variant,p.Tyr1210Ter,ENST00000379802,;DSP,intron_variant,,ENST00000418664,;	AAGT	ENSG00000096696	ENST00000379802	Transcript	frameshift_variant	3965-3966	3624-3625	1208-1209	-/KX	-/AAGT	.	.	.	1	DSP	HGNC	3052	protein_coding	YES	CCDS4501.1	ENSP00000369129	DESP_HUMAN	G1UI31_HUMAN,B4DKX6_HUMAN	UPI000013C67F	.	.	.	23/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF234,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	5	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	AGGAACAAGTA	.	2	ESCA
SENP6	0	.	GRCh37	6	76407192	76407215	+	In_Frame_Del	DEL	TATTTTTGAGAAGGATTTTATTTT	TATTTTTGAGAAGGATTTTATTTT	-	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	TATTTTTGAGAAGGATTTTATTTT	TATTTTTGAGAAGGATTTTATTTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2248_2271delATTTTTGAGAAGGATTTTATTTTT	p.Ile750_Phe757del	p.I750_F757del	ENST00000447266	18/24	61	44	17	109	109	0	SENP6,inframe_deletion,p.Ile346_Phe353del,ENST00000541192,;SENP6,inframe_deletion,p.Ile743_Phe750del,ENST00000370010,;SENP6,inframe_deletion,p.Ile750_Phe757del,ENST00000370014,;SENP6,inframe_deletion,p.Ile750_Phe757del,ENST00000447266,;SENP6,inframe_deletion,p.Ile366_Phe373del,ENST00000503501,;SENP6,non_coding_transcript_exon_variant,,ENST00000474906,;	-	ENSG00000112701	ENST00000447266	Transcript	inframe_deletion	2725-2748	2247-2270	749-757	DIFEKDFIF/D	gaTATTTTTGAGAAGGATTTTATTTTt/gat	.	.	.	1	SENP6	HGNC	20944	protein_coding	YES	CCDS47454.1	ENSP00000402527	SENP6_HUMAN	H0Y4F4_HUMAN	UPI0000141B65	.	.	.	18/24	.	PROSITE_profiles:PS50600,hmmpanther:PTHR12438:SF14,hmmpanther:PTHR12438,Pfam_domain:PF02902,Gene3D:1euvA02,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CGTAGATATTTTTGAGAAGGATTTTATTTTTGTAC	.	3	ESCA
ZNF292	0	.	GRCh37	6	87965877	87965877	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2530C>A	p.Gln844Lys	p.Q844K	ENST00000369577	8/8	21	14	7	39	39	0	ZNF292,missense_variant,p.Gln844Lys,ENST00000369577,;ZNF292,missense_variant,p.Gln839Lys,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,downstream_gene_variant,,ENST00000466062,;	A	ENSG00000188994	ENST00000369577	Transcript	missense_variant	2573	2530	844	Q/K	Caa/Aaa	.	.	.	1	ZNF292	HGNC	18410	protein_coding	YES	CCDS47457.1	ENSP00000358590	ZN292_HUMAN	Q6ZS01_HUMAN,Q6P495_HUMAN,Q3MN16_HUMAN	UPI000020D2CC	.	tolerated(0.24)	benign(0.017)	8/8	.	hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCCCAACTT	.	5	ESCA
MANEA	0	.	GRCh37	6	96053781	96053781	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.889G>T	p.Gly297Ter	p.G297*	ENST00000358812	5/5	52	43	9	50	50	0	MANEA,stop_gained,p.Gly297Ter,ENST00000358812,;MANEA,non_coding_transcript_exon_variant,,ENST00000474553,;	T	ENSG00000172469	ENST00000358812	Transcript	stop_gained	1023	889	297	G/*	Gga/Tga	.	.	.	1	MANEA	HGNC	21072	protein_coding	YES	CCDS5032.1	ENSP00000351669	MANEA_HUMAN	.	UPI000020DF99	.	.	.	5/5	.	hmmpanther:PTHR13572:SF1,hmmpanther:PTHR13572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ATGATGGACTG	.	3	ESCA
MANEA	0	.	GRCh37	6	96053793	96053797	+	Frame_Shift_Del	DEL	GCCCT	GCCCT	CCCC	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	GCCCT	GCCCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.901_905delGCCCTinsCCCC	p.Ala301ProfsTer4	p.A301Pfs*4	ENST00000358812	5/5	47	38	9	48	48	0	MANEA,frameshift_variant,p.Ala301ProfsTer4,ENST00000358812,;MANEA,non_coding_transcript_exon_variant,,ENST00000474553,;	CCCC	ENSG00000172469	ENST00000358812	Transcript	frameshift_variant	1035-1039	901-905	301-302	AL/PX	GCCCTt/CCCCt	.	.	.	1	MANEA	HGNC	21072	protein_coding	YES	CCDS5032.1	ENSP00000351669	MANEA_HUMAN	.	UPI000020DF99	.	.	.	5/5	.	hmmpanther:PTHR13572:SF1,hmmpanther:PTHR13572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	TTTATTGCCCTTCTGG	.	2	ESCA
TES	0	.	GRCh37	7	115898649	115898649	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1113G>C	.	.	ENST00000358204	7/7	100	79	21	51	51	0	TES,3_prime_UTR_variant,,ENST00000393481,;TES,3_prime_UTR_variant,,ENST00000358204,;TES,downstream_gene_variant,,ENST00000537767,;AC002066.1,intron_variant,,ENST00000446355,;AC073130.3,intron_variant,,ENST00000444244,;TES,downstream_gene_variant,,ENST00000492891,;TES,downstream_gene_variant,,ENST00000496912,;	C	ENSG00000135269	ENST00000358204	Transcript	3_prime_UTR_variant	2594	.	.	.	.	.	.	.	1	TES	HGNC	14620	protein_coding	YES	CCDS5763.1	ENSP00000350937	TES_HUMAN	A4D0U5_HUMAN,Q9Y423_HUMAN,F8W7T0_HUMAN,B7Z6L5_HUMAN	UPI0000136BF9	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATGGATCCT	.	5	ESCA
POT1	0	.	GRCh37	7	124481087	124481087	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1309C>G	p.His437Asp	p.H437D	ENST00000357628	14/19	41	30	10	42	42	0	POT1,missense_variant,p.His306Asp,ENST00000393329,;POT1,missense_variant,p.His58Asp,ENST00000608200,;POT1,missense_variant,p.His437Asp,ENST00000357628,;POT1,missense_variant,p.His437Asp,ENST00000607932,;POT1,missense_variant,p.His437Asp,ENST00000609106,;POT1,3_prime_UTR_variant,,ENST00000608057,;POT1,non_coding_transcript_exon_variant,,ENST00000466483,;	C	ENSG00000128513	ENST00000357628	Transcript	missense_variant	1908	1309	437	H/D	Cat/Gat	.	.	.	-1	POT1	HGNC	17284	protein_coding	YES	CCDS5793.1	ENSP00000350249	POTE1_HUMAN	C9JPG9_HUMAN,A8MTK3_HUMAN	UPI0000073E3F	.	deleterious(0.01)	probably_damaging(0.972)	14/19	.	hmmpanther:PTHR14513:SF2,hmmpanther:PTHR14513	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATGAACTG	.	5	ESCA
CUL1	0	.	GRCh37	7	148497645	148497645	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2302G>A	p.Glu768Lys	p.E768K	ENST00000325222	22/22	54	24	29	75	75	0	CUL1,missense_variant,p.Glu768Lys,ENST00000602748,;CUL1,missense_variant,p.Glu768Lys,ENST00000325222,;CUL1,missense_variant,p.Glu768Lys,ENST00000409469,;	A	ENSG00000055130	ENST00000325222	Transcript	missense_variant	2581	2302	768	E/K	Gaa/Aaa	.	.	.	1	CUL1	HGNC	2551	protein_coding	YES	CCDS34772.1	ENSP00000326804	CUL1_HUMAN	Q75MQ1_HUMAN,B3KU45_HUMAN,B3KTW0_HUMAN	UPI00001286E6	.	tolerated(0.11)	benign(0.061)	22/22	.	hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF19,PROSITE_patterns:PS01256,Pfam_domain:PF10557,Gene3D:1.10.10.10,SMART_domains:SM00884,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGTGAAAAG	.	5	ESCA
FASTK	0	.	GRCh37	7	150776949	150776949	+	Missense_Mutation	SNP	C	C	T	rs756789798	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143G>A	p.Arg48Gln	p.R48Q	ENST00000297532	2/10	16	6	10	20	20	0	FASTK,missense_variant,p.Arg14Gln,ENST00000540185,;FASTK,missense_variant,p.Arg48Gln,ENST00000297532,;FASTK,missense_variant,p.Arg48Gln,ENST00000482571,;FASTK,intron_variant,,ENST00000353841,;SLC4A2,downstream_gene_variant,,ENST00000413384,;TMUB1,downstream_gene_variant,,ENST00000392818,;SLC4A2,downstream_gene_variant,,ENST00000485713,;SLC4A2,downstream_gene_variant,,ENST00000392826,;TMUB1,downstream_gene_variant,,ENST00000492838,;TMUB1,downstream_gene_variant,,ENST00000488752,;TMUB1,downstream_gene_variant,,ENST00000297533,;SLC4A2,downstream_gene_variant,,ENST00000310317,;SLC4A2,downstream_gene_variant,,ENST00000461735,;TMUB1,downstream_gene_variant,,ENST00000482202,;TMUB1,downstream_gene_variant,,ENST00000462940,;TMUB1,downstream_gene_variant,,ENST00000476627,;RP11-148K1.12,upstream_gene_variant,,ENST00000485974,;FASTK,non_coding_transcript_exon_variant,,ENST00000496663,;FASTK,non_coding_transcript_exon_variant,,ENST00000478477,;FASTK,intron_variant,,ENST00000489884,;FASTK,intron_variant,,ENST00000461979,;FASTK,non_coding_transcript_exon_variant,,ENST00000482806,;FASTK,non_coding_transcript_exon_variant,,ENST00000467237,;FASTK,intron_variant,,ENST00000460980,;SLC4A2,downstream_gene_variant,,ENST00000472204,;FASTK,upstream_gene_variant,,ENST00000466855,;FASTK,upstream_gene_variant,,ENST00000483953,;FASTK,upstream_gene_variant,,ENST00000478883,;FASTK,upstream_gene_variant,,ENST00000469237,;FASTK,upstream_gene_variant,,ENST00000459800,;SLC4A2,downstream_gene_variant,,ENST00000469467,;FASTK,upstream_gene_variant,,ENST00000465272,;	T	ENSG00000164896	ENST00000297532	Transcript	missense_variant	221	143	48	R/Q	cGg/cAg	rs756789798,COSM1187467	.	.	-1	FASTK	HGNC	24676	protein_coding	YES	CCDS5918.1	ENSP00000297532	FASTK_HUMAN	.	UPI0000000CBA	.	tolerated_low_confidence(0.05)	benign(0.007)	2/10	.	hmmpanther:PTHR21228,hmmpanther:PTHR21228:SF4	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCCGAGCA	byFrequency	5	ESCA
HOXA7	0	.	GRCh37	7	27192368	27192368	+	3'Flank	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000242159	.	68	58	10	89	89	0	HOXA7,downstream_gene_variant,,ENST00000242159,;HOXA7,downstream_gene_variant,,ENST00000519842,;HOXA6,upstream_gene_variant,,ENST00000222728,;HOXA-AS3,non_coding_transcript_exon_variant,,ENST00000518947,;HOXA-AS3,downstream_gene_variant,,ENST00000521197,;HOXA-AS3,downstream_gene_variant,,ENST00000524304,;HOXA-AS3,downstream_gene_variant,,ENST00000521231,;HOXA-AS3,downstream_gene_variant,,ENST00000518848,;HOXA7,downstream_gene_variant,,ENST00000523796,;HOXA6,upstream_gene_variant,,ENST00000521478,;HOXA3,upstream_gene_variant,,ENST00000518451,;RP1-170O19.23,upstream_gene_variant,,ENST00000498652,;RP1-170O19.22,upstream_gene_variant,,ENST00000467897,;	C	ENSG00000122592	ENST00000242159	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	967	-1	HOXA7	HGNC	5108	protein_coding	YES	CCDS5408.1	ENSP00000242159	HXA7_HUMAN	E5RHM9_HUMAN	UPI000013CAF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACTGAGAGGAG	.	4	ESCA
HOXA10	0	.	GRCh37	7	27210354	27210354	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1164C>T	.	.	ENST00000283921	2/2	139	115	23	146	146	0	HOXA10,3_prime_UTR_variant,,ENST00000283921,;RP1-170O19.20,intron_variant,,ENST00000470747,;HOXA10,downstream_gene_variant,,ENST00000396344,;MIR196B,upstream_gene_variant,,ENST00000384852,;HOXA10-AS,intron_variant,,ENST00000519694,;HOXA10-AS,intron_variant,,ENST00000523790,;HOXA10-AS,intron_variant,,ENST00000519935,;RP1-170O19.20,intron_variant,,ENST00000465941,;HOXA10,downstream_gene_variant,,ENST00000519593,;HOXA10,downstream_gene_variant,,ENST00000521421,;HOXA9,upstream_gene_variant,,ENST00000489695,;HOXA10,downstream_gene_variant,,ENST00000524368,;HOXA9,upstream_gene_variant,,ENST00000497089,;HOXA9,upstream_gene_variant,,ENST00000487384,;	A	ENSG00000253293	ENST00000283921	Transcript	3_prime_UTR_variant	2397	.	.	.	.	.	.	.	-1	HOXA10	HGNC	5100	protein_coding	YES	CCDS5410.2	ENSP00000283921	HXA10_HUMAN	.	UPI0000EE42DA	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAACGATAGA	.	5	ESCA
DAGLB	0	.	GRCh37	7	6456205	6456205	+	Intron	SNP	G	G	C	rs778575026	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1427+53C>G	.	.	ENST00000297056	.	54	44	9	73	73	0	DAGLB,3_prime_UTR_variant,,ENST00000421761,;DAGLB,intron_variant,,ENST00000428902,;DAGLB,intron_variant,,ENST00000425398,;DAGLB,intron_variant,,ENST00000297056,;DAGLB,intron_variant,,ENST00000436575,;DAGLB,3_prime_UTR_variant,,ENST00000454738,;DAGLB,intron_variant,,ENST00000497308,;DAGLB,intron_variant,,ENST00000482149,;DAGLB,intron_variant,,ENST00000462934,;	C	ENSG00000164535	ENST00000297056	Transcript	intron_variant	.	.	.	.	.	rs778575026	.	.	-1	DAGLB	HGNC	28923	protein_coding	YES	CCDS5350.1	ENSP00000297056	DGLB_HUMAN	E7ET49_HUMAN,B3KR38_HUMAN	UPI000006E01F	.	.	.	.	11/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTGACCAC	byFrequency	5	ESCA
CALN1	0	.	GRCh37	7	71252137	71252137	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*623G>C	.	.	ENST00000395275	7/7	35	20	15	45	45	0	CALN1,3_prime_UTR_variant,,ENST00000395276,;CALN1,3_prime_UTR_variant,,ENST00000395275,;CALN1,3_prime_UTR_variant,,ENST00000329008,;CALN1,downstream_gene_variant,,ENST00000431984,;CALN1,downstream_gene_variant,,ENST00000405452,;CALN1,downstream_gene_variant,,ENST00000412588,;	G	ENSG00000183166	ENST00000395275	Transcript	3_prime_UTR_variant	1798	.	.	.	.	.	.	.	-1	CALN1	HGNC	13248	protein_coding	YES	CCDS47603.1	ENSP00000378690	CABP8_HUMAN	Q86UM7_HUMAN,Q86UL5_HUMAN,Q75MW5_HUMAN,Q75MP5_HUMAN,Q75MI2_HUMAN,E9PFU3_HUMAN,A4D1Z1_HUMAN	UPI0000D4B903	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTCTAGAA	.	5	ESCA
DBF4	0	.	GRCh37	7	87537005	87537005	+	Missense_Mutation	SNP	C	C	G	rs748704015	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1552C>G	p.Leu518Val	p.L518V	ENST00000265728	12/12	69	44	25	57	57	0	DBF4,missense_variant,p.Leu518Val,ENST00000265728,;DBF4,3_prime_UTR_variant,,ENST00000431138,;DBF4,3_prime_UTR_variant,,ENST00000413643,;DBF4,downstream_gene_variant,,ENST00000430279,;DBF4,downstream_gene_variant,,ENST00000498144,;	G	ENSG00000006634	ENST00000265728	Transcript	missense_variant	2056	1552	518	L/V	Ctc/Gtc	rs748704015	.	.	1	DBF4	HGNC	17364	protein_coding	YES	CCDS5611.1	ENSP00000265728	DBF4A_HUMAN	B7Z8C6_HUMAN,B3KMY2_HUMAN	UPI000000DC33	.	tolerated(0.07)	benign(0.008)	12/12	.	hmmpanther:PTHR15375,hmmpanther:PTHR15375:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATCTCAAG	byFrequency	5	ESCA
ZNF804B	0	.	GRCh37	7	88847592	88847592	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.232G>C	p.Asp78His	p.D78H	ENST00000333190	2/4	52	41	10	52	52	0	ZNF804B,missense_variant,p.Asp78His,ENST00000333190,;	C	ENSG00000182348	ENST00000333190	Transcript	missense_variant	841	232	78	D/H	Gac/Cac	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	deleterious(0)	probably_damaging(0.994)	2/4	.	Superfamily_domains:SSF57667,Pfam_domain:PF12171,PROSITE_patterns:PS00028,hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTATGACCAT	.	5	ESCA
PKHD1L1	0	.	GRCh37	8	110408292	110408292	+	Missense_Mutation	SNP	G	G	A	rs199719733	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.848G>A	p.Arg283Gln	p.R283Q	ENST00000378402	11/78	71	59	11	75	75	0	PKHD1L1,missense_variant,p.Arg283Gln,ENST00000378402,;	A	ENSG00000205038	ENST00000378402	Transcript	missense_variant	952	848	283	R/Q	cGa/cAa	rs199719733	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	tolerated(0.89)	benign(0.003)	11/78	.	Pfam_domain:PF01833,Gene3D:2.60.40.10,SMART_domains:SM00429,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R285*|c.853C>T|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTCGAGGTG	byCluster	5	ESCA
PKHD1L1	0	.	GRCh37	8	110471942	110471942	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7123G>C	p.Asp2375His	p.D2375H	ENST00000378402	47/78	140	128	12	107	107	0	PKHD1L1,missense_variant,p.Asp2375His,ENST00000378402,;	C	ENSG00000205038	ENST00000378402	Transcript	missense_variant	7227	7123	2375	D/H	Gat/Cat	.	.	.	1	PKHD1L1	HGNC	20313	protein_coding	YES	CCDS47911.1	ENSP00000367655	PKHL1_HUMAN	.	UPI0000E5B020	.	deleterious(0)	probably_damaging(0.99)	47/78	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF213	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G2378E|c.7133G>A|3	MUTECT|MUSE|VARSCANS	TCCCTGATGGA	.	3	ESCA
ZHX1	0	.	GRCh37	8	124265591	124265591	+	Missense_Mutation	SNP	G	G	A	rs745749076	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2596C>T	p.Arg866Trp	p.R866W	ENST00000395571	3/4	102	94	8	64	64	0	ZHX1,missense_variant,p.Arg866Trp,ENST00000395571,;ZHX1,missense_variant,p.Arg866Trp,ENST00000522655,;ZHX1,missense_variant,p.Arg32Trp,ENST00000602651,;ZHX1,missense_variant,p.Arg866Trp,ENST00000297857,;ZHX1-C8ORF76,intron_variant,,ENST00000357082,;ZHX1,intron_variant,,ENST00000517516,;ZHX1,downstream_gene_variant,,ENST00000522595,;ZHX1,downstream_gene_variant,,ENST00000480132,;ZHX1,downstream_gene_variant,,ENST00000524267,;	A	ENSG00000165156	ENST00000395571	Transcript	missense_variant	3214	2596	866	R/W	Cgg/Tgg	rs745749076	.	.	-1	ZHX1	HGNC	12871	protein_coding	YES	CCDS6342.1	ENSP00000378938	ZHX1_HUMAN	.	UPI000007404F	.	deleterious_low_confidence(0)	probably_damaging(0.974)	3/4	.	hmmpanther:PTHR15467:SF4,hmmpanther:PTHR15467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTTCCGTTTCA	byCluster	3	ESCA
ATAD2	0	.	GRCh37	8	124368675	124368675	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1600G>C	p.Asp534His	p.D534H	ENST00000287394	13/28	99	87	11	54	54	0	ATAD2,missense_variant,p.Asp534His,ENST00000287394,;ATAD2,5_prime_UTR_variant,,ENST00000521903,;ATAD2,downstream_gene_variant,,ENST00000534257,;ATAD2,3_prime_UTR_variant,,ENST00000517666,;ATAD2,3_prime_UTR_variant,,ENST00000519124,;ATAD2,non_coding_transcript_exon_variant,,ENST00000550993,;ATAD2,non_coding_transcript_exon_variant,,ENST00000521496,;DUTP2,downstream_gene_variant,,ENST00000519164,;	G	ENSG00000156802	ENST00000287394	Transcript	missense_variant	1708	1600	534	D/H	Gat/Cat	.	.	.	-1	ATAD2	HGNC	30123	protein_coding	YES	CCDS6343.1	ENSP00000287394	ATAD2_HUMAN	.	UPI0000052A8C	.	deleterious(0)	probably_damaging(1)	13/28	.	hmmpanther:PTHR23069,hmmpanther:PTHR23069:SF1,Pfam_domain:PF00004,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCATCAATTT	.	4	ESCA
FAM135B	0	.	GRCh37	8	139144362	139144362	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*474G>T	.	.	ENST00000395297	20/20	42	36	6	59	59	0	FAM135B,3_prime_UTR_variant,,ENST00000395297,;FAM135B,downstream_gene_variant,,ENST00000276737,;FAM135B,downstream_gene_variant,,ENST00000482951,;	A	ENSG00000147724	ENST00000395297	Transcript	3_prime_UTR_variant	4866	.	.	.	.	.	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGAATCTATTG	.	4	ESCA
FAM135B	0	.	GRCh37	8	139144977	139144977	+	Silent	SNP	A	A	C	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4080T>G	p.%3D	p.T1360T	ENST00000395297	20/20	54	42	12	42	42	0	FAM135B,synonymous_variant,p.%3D,ENST00000395297,;FAM135B,3_prime_UTR_variant,,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;	C	ENSG00000147724	ENST00000395297	Transcript	synonymous_variant	4251	4080	1360	T	acT/acG	COSM3645403,COSM3645404	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	.	.	20/20	.	hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTAAAGTGCA	.	5	ESCA
FAM135B	0	.	GRCh37	8	139255189	139255189	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.665C>G	p.Ser222Ter	p.S222*	ENST00000395297	7/20	56	50	6	60	60	0	FAM135B,stop_gained,p.Ser222Ter,ENST00000395297,;FAM135B,stop_gained,p.Ser222Ter,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;	C	ENSG00000147724	ENST00000395297	Transcript	stop_gained	836	665	222	S/*	tCa/tGa	COSM749110,COSM749111	.	.	-1	FAM135B	HGNC	28029	protein_coding	YES	CCDS6375.2	ENSP00000378710	F135B_HUMAN	J3QSR3_HUMAN	UPI000057A0DB	.	.	.	7/20	.	hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S221F|c.662C>T|3,BUFFER|p.S221F|c.662C>T|3	RADIA|MUTECT|MUSE|VARSCANS	CCTCTGAGGAA	.	4	ESCA
SLC7A2	0	.	GRCh37	8	17412489	17412489	+	Intron	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1315+281C>T	.	.	ENST00000004531	.	27	17	10	67	67	0	SLC7A2,synonymous_variant,p.%3D,ENST00000470360,;SLC7A2,synonymous_variant,p.%3D,ENST00000398090,;SLC7A2,intron_variant,,ENST00000522656,;SLC7A2,intron_variant,,ENST00000494857,;SLC7A2,intron_variant,,ENST00000004531,;	T	ENSG00000003989	ENST00000004531	Transcript	intron_variant	.	.	.	.	.	COSM1226570	.	.	1	SLC7A2	HGNC	11060	protein_coding	YES	CCDS55203.1	ENSP00000004531	CTR2_HUMAN	.	UPI0001A336A4	.	.	.	.	7/11	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODIFIER	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTCTGTTT	.	5	ESCA
PRKDC	0	.	GRCh37	8	48866215	48866215	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.686C>G	p.Ser229Ter	p.S229*	ENST00000314191	7/87	46	37	9	33	33	0	PRKDC,stop_gained,p.Ser229Ter,ENST00000338368,;PRKDC,stop_gained,p.Ser229Ter,ENST00000314191,;PRKDC,downstream_gene_variant,,ENST00000540819,;PRKDC,non_coding_transcript_exon_variant,,ENST00000518216,;PRKDC,non_coding_transcript_exon_variant,,ENST00000523565,;	C	ENSG00000253729	ENST00000314191	Transcript	stop_gained	743	686	229	S/*	tCa/tGa	.	.	.	-1	PRKDC	HGNC	9413	protein_coding	YES	.	ENSP00000313420	PRKDC_HUMAN	F5GX40_HUMAN	UPI000045790C	.	.	.	7/87	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF54,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGTGAGGAC	.	5	ESCA
NCOA2	0	.	GRCh37	8	71050559	71050559	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3037G>C	p.Glu1013Gln	p.E1013Q	ENST00000452400	15/23	180	160	19	159	159	0	NCOA2,missense_variant,p.Glu101Gln,ENST00000267974,;NCOA2,missense_variant,p.Glu1013Gln,ENST00000452400,;NCOA2,missense_variant,p.Glu139Gln,ENST00000518363,;NCOA2,synonymous_variant,p.%3D,ENST00000518287,;NCOA2,non_coding_transcript_exon_variant,,ENST00000522054,;	G	ENSG00000140396	ENST00000452400	Transcript	missense_variant	3219	3037	1013	E/Q	Gaa/Caa	COSM750808	.	.	-1	NCOA2	HGNC	7669	protein_coding	YES	CCDS47872.1	ENSP00000399968	NCOA2_HUMAN	.	UPI000012FE42	.	deleterious(0.01)	possibly_damaging(0.563)	15/23	.	hmmpanther:PTHR10684:SF2,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAATTCAGATG	.	4	ESCA
TMEM70	0	.	GRCh37	8	74893683	74893683	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.610G>C	p.Asp204His	p.D204H	ENST00000312184	3/3	62	49	13	44	44	0	TMEM70,missense_variant,p.Asp204His,ENST00000312184,;TMEM70,downstream_gene_variant,,ENST00000517439,;Y_RNA,upstream_gene_variant,,ENST00000365350,;TMEM70,downstream_gene_variant,,ENST00000520167,;TMEM70,downstream_gene_variant,,ENST00000523794,;TMEM70,3_prime_UTR_variant,,ENST00000416961,;TMEM70,non_coding_transcript_exon_variant,,ENST00000519551,;TMEM70,downstream_gene_variant,,ENST00000517614,;RP11-367E12.4,upstream_gene_variant,,ENST00000517767,;RPS20P21,upstream_gene_variant,,ENST00000466859,;	C	ENSG00000175606	ENST00000312184	Transcript	missense_variant	683	610	204	D/H	Gat/Cat	.	.	.	1	TMEM70	HGNC	26050	protein_coding	YES	CCDS6215.1	ENSP00000312599	TMM70_HUMAN	L0R5D5_HUMAN	UPI00001BBFAB	.	deleterious(0.01)	possibly_damaging(0.878)	3/3	.	Pfam_domain:PF06979,hmmpanther:PTHR13281,hmmpanther:PTHR13281:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCAGATGCT	.	5	ESCA
LRRCC1	0	.	GRCh37	8	86027421	86027421	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.631G>A	p.Glu211Lys	p.E211K	ENST00000360375	5/19	120	112	7	75	75	0	LRRCC1,missense_variant,p.Glu211Lys,ENST00000360375,;LRRCC1,missense_variant,p.Glu191Lys,ENST00000414626,;LRRCC1,3_prime_UTR_variant,,ENST00000522770,;LRRCC1,3_prime_UTR_variant,,ENST00000517875,;LRRCC1,intron_variant,,ENST00000523669,;LRRCC1,intron_variant,,ENST00000522567,;	A	ENSG00000133739	ENST00000360375	Transcript	missense_variant	780	631	211	E/K	Gaa/Aaa	.	.	.	1	LRRCC1	HGNC	29373	protein_coding	YES	CCDS43750.1	ENSP00000353538	LRCC1_HUMAN	.	UPI000021002F	.	tolerated(0.07)	benign(0.009)	5/19	.	hmmpanther:PTHR10588:SF31,hmmpanther:PTHR10588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGACAGAAATA	.	2	ESCA
CYLC2	0	.	GRCh37	9	105767853	105767853	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.940G>C	p.Asp314His	p.D314H	ENST00000374798	5/8	63	23	40	120	120	0	CYLC2,missense_variant,p.Asp314His,ENST00000374798,;CYLC2,missense_variant,p.Asp314His,ENST00000487798,;	C	ENSG00000155833	ENST00000374798	Transcript	missense_variant	1010	940	314	D/H	Gat/Cat	.	.	.	1	CYLC2	HGNC	2583	protein_coding	YES	CCDS35085.1	ENSP00000420256	CYLC2_HUMAN	.	UPI0000128C36	.	tolerated_low_confidence(0.11)	unknown(0)	5/8	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16742	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTGATTCA	.	5	ESCA
CDC26	0	.	GRCh37	9	116029647	116029647	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154A>G	p.Ser52Gly	p.S52G	ENST00000374206	4/4	44	20	23	68	68	0	CDC26,missense_variant,p.Ser52Gly,ENST00000374206,;SLC31A1,downstream_gene_variant,,ENST00000374212,;SLC31A1,downstream_gene_variant,,ENST00000374210,;CDC26,intron_variant,,ENST00000490408,;	C	ENSG00000176386	ENST00000374206	Transcript	missense_variant	513	154	52	S/G	Agt/Ggt	.	.	.	-1	CDC26	HGNC	17839	protein_coding	YES	CCDS6790.1	ENSP00000363322	CDC26_HUMAN	.	UPI0000073C4F	.	tolerated(0.35)	benign(0.001)	4/4	.	Pfam_domain:PF10471	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCACTGCTAA	.	4	ESCA
ZNF79	0	.	GRCh37	9	130206956	130206956	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.977C>T	p.Thr326Ile	p.T326I	ENST00000342483	5/5	32	28	4	60	60	0	ZNF79,missense_variant,p.Thr326Ile,ENST00000342483,;ZNF79,missense_variant,p.Thr302Ile,ENST00000543471,;RPL12,downstream_gene_variant,,ENST00000536368,;RPL12,downstream_gene_variant,,ENST00000361436,;SNORA65,downstream_gene_variant,,ENST00000364432,;RPL12,downstream_gene_variant,,ENST00000483598,;RPL12,downstream_gene_variant,,ENST00000497825,;RPL12,downstream_gene_variant,,ENST00000497322,;	T	ENSG00000196152	ENST00000342483	Transcript	missense_variant	1383	977	326	T/I	aCt/aTt	.	.	.	1	ZNF79	HGNC	13153	protein_coding	YES	CCDS6871.1	ENSP00000362446	ZNF79_HUMAN	F5H032_HUMAN	UPI0000367683	.	tolerated(1)	benign(0.193)	5/5	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24387:SF197,hmmpanther:PTHR24387,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGACTCACA	.	4	ESCA
POMT1	0	.	GRCh37	9	134379603	134379614	+	Missense_Mutation	DEL	AAGATGTGGGGA	AAGATGTGGGGA	-	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	AAGATGTGGGGA	AAGATGTGGGGA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-3_9delAAGATGTGGGGA	.	.	ENST00000372228	2/20	52	36	16	83	83	0	POMT1,coding_sequence_variant,,ENST00000372228,;POMT1,coding_sequence_variant,,ENST00000354713,;POMT1,coding_sequence_variant,,ENST00000418774,;POMT1,coding_sequence_variant,,ENST00000402686,;POMT1,coding_sequence_variant,,ENST00000423007,;POMT1,5_prime_UTR_variant,,ENST00000415075,;POMT1,intron_variant,,ENST00000419118,;POMT1,intron_variant,,ENST00000541219,;POMT1,intron_variant,,ENST00000441334,;POMT1,intron_variant,,ENST00000404875,;POMT1,intron_variant,,ENST00000448212,;POMT1,intron_variant,,ENST00000341012,;POMT1,intron_variant,,ENST00000430619,;PRRC2B,downstream_gene_variant,,ENST00000320547,;PRRC2B,downstream_gene_variant,,ENST00000357304,;PRRC2B,downstream_gene_variant,,ENST00000405995,;POMT1,intron_variant,,ENST00000483472,;POMT1,upstream_gene_variant,,ENST00000462375,;PRRC2B,downstream_gene_variant,,ENST00000465931,;AL358781.1,upstream_gene_variant,,ENST00000321081,;	-	ENSG00000130714	ENST00000372228	Transcript	coding_sequence_variant	177-188	?-9	?-3	.	.	.	.	.	1	POMT1	HGNC	9202	protein_coding	YES	CCDS6943.1	ENSP00000361302	POMT1_HUMAN	Q5JT07_HUMAN,Q5JT03_HUMAN,Q5JSZ6_HUMAN	UPI000013CDA7	.	.	.	2/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCTACAAGATGTGGGGATTTTT	.	3	ESCA
UBAP2	0	.	GRCh37	9	33953307	33953307	+	Silent	SNP	G	G	A	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032C>T	p.%3D	p.V344V	ENST00000379238	12/29	26	9	17	59	59	0	UBAP2,synonymous_variant,p.%3D,ENST00000379238,;UBAP2,synonymous_variant,p.%3D,ENST00000379239,;UBAP2,synonymous_variant,p.%3D,ENST00000418786,;UBAP2,synonymous_variant,p.%3D,ENST00000421278,;UBAP2,synonymous_variant,p.%3D,ENST00000449054,;UBAP2,synonymous_variant,p.%3D,ENST00000412543,;UBAP2,synonymous_variant,p.%3D,ENST00000539807,;UBAP2,synonymous_variant,p.%3D,ENST00000360802,;UBAP2,upstream_gene_variant,,ENST00000379225,;SNORD121A,upstream_gene_variant,,ENST00000459386,;UBAP2,non_coding_transcript_exon_variant,,ENST00000462799,;	A	ENSG00000137073	ENST00000379238	Transcript	synonymous_variant	1150	1032	344	V	gtC/gtT	COSM1462104	.	.	-1	UBAP2	HGNC	14185	protein_coding	YES	CCDS6547.1	ENSP00000368540	UBAP2_HUMAN	Q5JV03_HUMAN	UPI0000140784	.	.	.	12/29	.	hmmpanther:PTHR16308,hmmpanther:PTHR16308:SF17	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTTGACGGC	.	5	ESCA
PRUNE2	0	.	GRCh37	9	79322566	79322566	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4624C>A	p.His1542Asn	p.H1542N	ENST00000376718	8/19	17	7	10	38	38	0	PRUNE2,missense_variant,p.His864Asn,ENST00000426088,;PRUNE2,missense_variant,p.His1542Asn,ENST00000376718,;PRUNE2,missense_variant,p.His1183Asn,ENST00000428286,;PRUNE2,upstream_gene_variant,,ENST00000480674,;	T	ENSG00000106772	ENST00000376718	Transcript	missense_variant	4748	4624	1542	H/N	Cat/Aat	.	.	.	-1	PRUNE2	HGNC	25209	protein_coding	YES	CCDS47982.1	ENSP00000365908	PRUN2_HUMAN	.	UPI0001612CC0	.	deleterious(0.04)	possibly_damaging(0.776)	8/19	.	hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGAATGAGTAT	.	4	ESCA
ARMCX6	0	.	GRCh37	X	100871258	100871258	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.353G>A	p.Cys118Tyr	p.C118Y	ENST00000539247	4/4	89	72	17	154	154	0	ARMCX6,missense_variant,p.Cys118Tyr,ENST00000538627,;ARMCX6,missense_variant,p.Cys118Tyr,ENST00000361910,;ARMCX6,missense_variant,p.Cys118Tyr,ENST00000539247,;ARMCX6,non_coding_transcript_exon_variant,,ENST00000467089,;ARMCX6,intron_variant,,ENST00000497931,;ARMCX6,intron_variant,,ENST00000462302,;ARMCX6,downstream_gene_variant,,ENST00000494624,;ARMCX6,downstream_gene_variant,,ENST00000495964,;	T	ENSG00000198960	ENST00000539247	Transcript	missense_variant	786	353	118	C/Y	tGt/tAt	.	.	.	-1	ARMCX6	HGNC	26094	protein_coding	YES	CCDS14488.1	ENSP00000444537	ARMX6_HUMAN	.	UPI00001BBFA2	.	tolerated(0.12)	benign(0.003)	4/4	.	hmmpanther:PTHR15712:SF6,hmmpanther:PTHR15712,Pfam_domain:PF04826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTACAATTT	.	5	ESCA
PAK3	0	.	GRCh37	X	110406853	110406853	+	Missense_Mutation	SNP	C	C	T	rs754649748	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772C>T	p.Pro258Ser	p.P258S	ENST00000360648	8/16	38	29	9	76	76	0	PAK3,missense_variant,p.Pro237Ser,ENST00000372010,;PAK3,missense_variant,p.Pro258Ser,ENST00000360648,;PAK3,missense_variant,p.Pro222Ser,ENST00000446737,;PAK3,missense_variant,p.Pro222Ser,ENST00000425146,;PAK3,missense_variant,p.Pro243Ser,ENST00000417227,;PAK3,missense_variant,p.Pro258Ser,ENST00000518291,;PAK3,missense_variant,p.Pro237Ser,ENST00000262836,;PAK3,missense_variant,p.Pro222Ser,ENST00000372007,;PAK3,missense_variant,p.Pro243Ser,ENST00000519681,;	T	ENSG00000077264	ENST00000360648	Transcript	missense_variant	799	772	258	P/S	Cca/Tca	rs754649748	.	.	1	PAK3	HGNC	8592	protein_coding	YES	CCDS48151.1	ENSP00000353864	PAK3_HUMAN	B1AKS5_HUMAN	UPI0000D61DBC	.	tolerated(0.28)	benign(0.005)	8/16	.	hmmpanther:PTHR24361:SF250,hmmpanther:PTHR24361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACACCACCC	.	5	ESCA
KIAA1210	0	.	GRCh37	X	118221021	118221021	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4172G>A	p.Ser1391Asn	p.S1391N	ENST00000402510	11/14	20	16	4	50	50	0	KIAA1210,missense_variant,p.Ser1391Asn,ENST00000402510,;	T	ENSG00000250423	ENST00000402510	Transcript	missense_variant	4172	4172	1391	S/N	aGc/aAc	COSM1497187,COSM1497188	.	.	-1	KIAA1210	HGNC	29218	protein_coding	YES	CCDS48156.1	ENSP00000384670	K1210_HUMAN	.	UPI0001596C4C	.	tolerated(0.25)	benign(0.009)	11/14	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATTGCTCTCA	.	4	ESCA
ZBTB33	0	.	GRCh37	X	119390487	119390487	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1198A>G	.	.	ENST00000326624	2/2	107	85	22	174	174	0	ZBTB33,3_prime_UTR_variant,,ENST00000326624,;TMEM255A,downstream_gene_variant,,ENST00000371369,;TMEM255A,downstream_gene_variant,,ENST00000440464,;TMEM255A,downstream_gene_variant,,ENST00000371352,;TMEM255A,downstream_gene_variant,,ENST00000309720,;ZBTB33,downstream_gene_variant,,ENST00000557385,;	G	ENSG00000177485	ENST00000326624	Transcript	3_prime_UTR_variant	3445	.	.	.	.	.	.	.	1	ZBTB33	HGNC	16682	protein_coding	YES	CCDS14596.1	ENSP00000314153	KAISO_HUMAN	.	UPI0000072F87	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAAATACCACT	.	3	ESCA
DCAF12L2	0	.	GRCh37	X	125299586	125299586	+	Missense_Mutation	SNP	C	C	T	rs377444816	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.322G>A	p.Ala108Thr	p.A108T	ENST00000538699	2/2	18	14	4	46	46	0	DCAF12L2,missense_variant,p.Ala108Thr,ENST00000538699,;DCAF12L2,missense_variant,p.Ala108Thr,ENST00000360028,;	T	ENSG00000198354	ENST00000538699	Transcript	missense_variant	403	322	108	A/T	Gcc/Acc	rs377444816	.	.	-1	DCAF12L2	HGNC	32950	protein_coding	YES	CCDS43991.1	ENSP00000441489	DC122_HUMAN	.	UPI0000197594	.	tolerated(0.5)	benign(0.003)	2/2	.	hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF8,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	A:0.001	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGCGTTCA	byFrequency|byCluster	5	ESCA
DCAF12L1	0	.	GRCh37	X	125685531	125685531	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000371126	1/2	18	10	8	56	56	0	DCAF12L1,missense_variant,p.Arg354Gln,ENST00000371126,;	T	ENSG00000198889	ENST00000371126	Transcript	missense_variant	1304	1061	354	R/Q	cGg/cAg	.	.	.	-1	DCAF12L1	HGNC	29395	protein_coding	YES	CCDS14610.1	ENSP00000360167	DC121_HUMAN	.	UPI0000160112	.	deleterious(0.02)	possibly_damaging(0.653)	1/2	.	hmmpanther:PTHR19860:SF9,hmmpanther:PTHR19860,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGACCGCACG	.	5	ESCA
ARHGAP36	0	.	GRCh37	X	130217775	130217775	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387G>A	p.%3D	p.K129K	ENST00000276211	4/12	37	23	14	111	111	0	ARHGAP36,synonymous_variant,p.%3D,ENST00000276211,;ARHGAP36,synonymous_variant,p.%3D,ENST00000423277,;ARHGAP36,synonymous_variant,p.%3D,ENST00000370922,;ARHGAP36,synonymous_variant,p.%3D,ENST00000412432,;ARHGAP36,5_prime_UTR_variant,,ENST00000370921,;	A	ENSG00000147256	ENST00000276211	Transcript	synonymous_variant	732	387	129	K	aaG/aaA	.	.	.	1	ARHGAP36	HGNC	26388	protein_coding	YES	CCDS14628.1	ENSP00000276211	RHG36_HUMAN	.	UPI0000041347	.	.	.	4/12	.	hmmpanther:PTHR12635:SF5,hmmpanther:PTHR12635,Gene3D:1.10.555.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCAAGCATCT	.	5	ESCA
ARHGEF6	0	.	GRCh37	X	135747832	135747832	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2356T>C	.	.	ENST00000250617	22/22	115	60	55	199	199	0	ARHGEF6,3_prime_UTR_variant,,ENST00000370620,;ARHGEF6,3_prime_UTR_variant,,ENST00000250617,;ARHGEF6,3_prime_UTR_variant,,ENST00000370622,;ARHGEF6,downstream_gene_variant,,ENST00000535227,;	G	ENSG00000129675	ENST00000250617	Transcript	3_prime_UTR_variant	5893	.	.	.	.	.	.	.	-1	ARHGEF6	HGNC	685	protein_coding	YES	CCDS14660.1	ENSP00000250617	ARHG6_HUMAN	.	UPI0000001C8E	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAAGGCCT	.	5	ESCA
CDR1	0	.	GRCh37	X	139866523	139866523	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>T	p.Trp3Cys	p.W3C	ENST00000370532	1/1	62	57	5	153	153	0	CDR1,missense_variant,p.Trp3Cys,ENST00000370532,;	A	ENSG00000184258	ENST00000370532	Transcript	missense_variant	201	9	3	W/C	tgG/tgT	COSM3964786	.	.	-1	CDR1	HGNC	1798	protein_coding	YES	CCDS14670.1	ENSP00000359563	CDR1_HUMAN	.	UPI000034ECCD	.	deleterious(0.02)	benign(0.143)	1/1	.	hmmpanther:PTHR15194	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAACCAAGC	.	2	ESCA
SPANXC	0	.	GRCh37	X	140336535	140336535	+	Missense_Mutation	SNP	T	T	A	rs782307254	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.56A>T	p.Asn19Ile	p.N19I	ENST00000358993	1/2	211	168	43	358	358	0	SPANXC,missense_variant,p.Asn19Ile,ENST00000358993,;	A	ENSG00000198573	ENST00000358993	Transcript	missense_variant	95	56	19	N/I	aAc/aTc	rs782307254	.	.	-1	SPANXC	HGNC	14331	protein_coding	YES	CCDS14673.1	ENSP00000351884	SPNXC_HUMAN	.	UPI000003B20F	.	deleterious(0)	probably_damaging(0.998)	1/2	.	hmmpanther:PTHR23425:SF1,hmmpanther:PTHR23425,Pfam_domain:PF07458	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCGTTGGAT	byFrequency	4	ESCA
FANCB	0	.	GRCh37	X	14863281	14863281	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1624C>G	p.Pro542Ala	p.P542A	ENST00000398334	8/10	80	74	6	74	74	0	FANCB,missense_variant,p.Pro542Ala,ENST00000324138,;FANCB,missense_variant,p.Pro542Ala,ENST00000398334,;FANCB,missense_variant,p.Pro542Ala,ENST00000452869,;	C	ENSG00000181544	ENST00000398334	Transcript	missense_variant	1892	1624	542	P/A	Cca/Gca	COSM160980	.	.	-1	FANCB	HGNC	3583	protein_coding	YES	CCDS14161.1	ENSP00000381378	FANCB_HUMAN	C9J5X9_HUMAN	UPI000006E70A	.	tolerated(0.07)	benign(0.081)	8/10	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACATGGCATCA	.	2	ESCA
MOSPD2	0	.	GRCh37	X	14921105	14921105	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556G>C	p.Asp186His	p.D186H	ENST00000380492	7/15	184	161	23	159	158	0	MOSPD2,missense_variant,p.Asp186His,ENST00000482354,;MOSPD2,missense_variant,p.Asp186His,ENST00000380492,;MOSPD2,non_coding_transcript_exon_variant,,ENST00000495110,;	C	ENSG00000130150	ENST00000380492	Transcript	missense_variant	644	556	186	D/H	Gat/Cat	.	.	.	1	MOSPD2	HGNC	28381	protein_coding	YES	CCDS14162.1	ENSP00000369860	MSPD2_HUMAN	.	UPI00000735BA	.	deleterious(0)	probably_damaging(0.964)	7/15	.	PROSITE_profiles:PS50191,hmmpanther:PTHR19993,hmmpanther:PTHR19993:SF1,Pfam_domain:PF00650,Gene3D:3.40.525.10,SMART_domains:SM00516,Superfamily_domains:SSF52087	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTTGATATG	.	4	ESCA
MAGEA4	0	.	GRCh37	X	151093195	151093195	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*105C>T	.	.	ENST00000360243	3/3	57	32	24	79	79	0	MAGEA4,3_prime_UTR_variant,,ENST00000370335,;MAGEA4,3_prime_UTR_variant,,ENST00000276344,;MAGEA4,3_prime_UTR_variant,,ENST00000393921,;MAGEA4,3_prime_UTR_variant,,ENST00000370337,;MAGEA4,3_prime_UTR_variant,,ENST00000393920,;MAGEA4,3_prime_UTR_variant,,ENST00000370340,;MAGEA4,3_prime_UTR_variant,,ENST00000360243,;MAGEA4,downstream_gene_variant,,ENST00000416020,;MAGEA4,downstream_gene_variant,,ENST00000448295,;MAGEA4,downstream_gene_variant,,ENST00000431971,;MAGEA4,downstream_gene_variant,,ENST00000425182,;MAGEA4,downstream_gene_variant,,ENST00000431963,;MAGEA4,downstream_gene_variant,,ENST00000441865,;MAGEA4,downstream_gene_variant,,ENST00000430273,;MAGEA4,downstream_gene_variant,,ENST00000457310,;	T	ENSG00000147381	ENST00000360243	Transcript	3_prime_UTR_variant	1326	.	.	.	.	.	.	.	1	MAGEA4	HGNC	6802	protein_coding	YES	CCDS14702.1	ENSP00000353379	MAGA4_HUMAN	C9JZJ5_HUMAN,C9JK50_HUMAN,C9JIR1_HUMAN,C9J9C2_HUMAN,B4DTE6_HUMAN	UPI000013EA1F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTCTTCAC	.	5	ESCA
IDH3G	0	.	GRCh37	X	153052328	153052328	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.852C>T	p.%3D	p.C284C	ENST00000217901	10/13	34	11	22	61	61	0	IDH3G,synonymous_variant,p.%3D,ENST00000454076,;IDH3G,synonymous_variant,p.%3D,ENST00000444450,;IDH3G,synonymous_variant,p.%3D,ENST00000427365,;IDH3G,synonymous_variant,p.%3D,ENST00000370093,;IDH3G,synonymous_variant,p.%3D,ENST00000217901,;IDH3G,synonymous_variant,p.%3D,ENST00000370092,;SRPK3,downstream_gene_variant,,ENST00000370108,;SRPK3,downstream_gene_variant,,ENST00000370100,;SRPK3,downstream_gene_variant,,ENST00000489426,;SRPK3,downstream_gene_variant,,ENST00000430541,;SRPK3,downstream_gene_variant,,ENST00000393786,;SRPK3,downstream_gene_variant,,ENST00000458681,;SRPK3,downstream_gene_variant,,ENST00000370104,;SRPK3,downstream_gene_variant,,ENST00000370101,;IDH3G,downstream_gene_variant,,ENST00000444338,;IDH3G,downstream_gene_variant,,ENST00000497043,;IDH3G,downstream_gene_variant,,ENST00000491235,;IDH3G,downstream_gene_variant,,ENST00000495356,;IDH3G,downstream_gene_variant,,ENST00000461215,;	A	ENSG00000067829	ENST00000217901	Transcript	synonymous_variant	1049	852	284	C	tgC/tgT	.	.	.	-1	IDH3G	HGNC	5386	protein_coding	YES	CCDS14730.1	ENSP00000217901	IDH3G_HUMAN	Q2Q9S4_HUMAN,E7EQB8_HUMAN,D3DWV9_HUMAN	UPI0000000DBC	.	.	.	10/13	.	hmmpanther:PTHR11835:SF42,hmmpanther:PTHR11835,PROSITE_patterns:PS00470,TIGRFAM_domain:TIGR00175,Pfam_domain:PF00180,Gene3D:3.40.718.10,Superfamily_domains:SSF53659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCGCGCAGAC	.	5	ESCA
ACE2	0	.	GRCh37	X	15618926	15618926	+	Missense_Mutation	SNP	C	C	T	rs146676783	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.109G>A	p.Glu37Lys	p.E37K	ENST00000427411	2/19	125	103	22	83	83	0	ACE2,missense_variant,p.Glu37Lys,ENST00000427411,;ACE2,missense_variant,p.Glu37Lys,ENST00000252519,;GS1-594A7.3,upstream_gene_variant,,ENST00000421585,;ACE2,non_coding_transcript_exon_variant,,ENST00000484756,;	T	ENSG00000130234	ENST00000427411	Transcript	missense_variant	326	109	37	E/K	Gaa/Aaa	rs146676783	.	.	-1	ACE2	HGNC	13557	protein_coding	YES	CCDS14169.1	ENSP00000389326	ACE2_HUMAN	.	UPI000000D907	.	deleterious(0.04)	probably_damaging(0.928)	2/19	.	hmmpanther:PTHR10514:SF24,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	T:0.0008	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCGGCTT	byFrequency|byCluster	5	ESCA
CXorf23	0	.	GRCh37	X	19934770	19934770	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*653C>G	.	.	ENST00000379687	11/11	272	82	190	186	186	0	CXorf23,3_prime_UTR_variant,,ENST00000379687,;CXorf23,3_prime_UTR_variant,,ENST00000379682,;CXorf23,upstream_gene_variant,,ENST00000456553,;CXorf23,downstream_gene_variant,,ENST00000471203,;CXorf23,downstream_gene_variant,,ENST00000466702,;CXorf23,upstream_gene_variant,,ENST00000451208,;CXorf23,3_prime_UTR_variant,,ENST00000472158,;	C	ENSG00000173681	ENST00000379687	Transcript	3_prime_UTR_variant	2736	.	.	.	.	.	.	.	-1	CXorf23	HGNC	27413	protein_coding	YES	CCDS14194.2	ENSP00000369009	CX023_HUMAN	.	UPI0000458B03	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTGAAATT	.	5	ESCA
GNL3L	0	.	GRCh37	X	54584945	54584945	+	Missense_Mutation	SNP	G	G	T	rs549795452	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1523G>T	p.Arg508Leu	p.R508L	ENST00000336470	15/16	38	32	6	44	44	0	GNL3L,missense_variant,p.Arg508Leu,ENST00000360845,;GNL3L,missense_variant,p.Arg508Leu,ENST00000336470,;	T	ENSG00000130119	ENST00000336470	Transcript	missense_variant	1662	1523	508	R/L	cGc/cTc	rs549795452,COSM1123464	.	.	1	GNL3L	HGNC	25553	protein_coding	YES	CCDS14360.1	ENSP00000338573	GNL3L_HUMAN	.	UPI000006CF81	.	tolerated(0.68)	benign(0)	15/16	.	hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF27	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACCGCCCTA	.	4	ESCA
TAF1	0	.	GRCh37	X	70612510	70612510	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2933C>T	p.Thr978Met	p.T978M	ENST00000276072	19/38	36	26	9	67	67	0	TAF1,missense_variant,p.Thr957Met,ENST00000373790,;TAF1,missense_variant,p.Thr957Met,ENST00000449580,;TAF1,missense_variant,p.Thr978Met,ENST00000276072,;TAF1,missense_variant,p.Thr978Met,ENST00000423759,;TAF1,upstream_gene_variant,,ENST00000483985,;TAF1,downstream_gene_variant,,ENST00000478305,;TAF1,downstream_gene_variant,,ENST00000474917,;TAF1,downstream_gene_variant,,ENST00000472567,;	T	ENSG00000147133	ENST00000276072	Transcript	missense_variant	2943	2933	978	T/M	aCg/aTg	.	.	.	1	TAF1	HGNC	11535	protein_coding	YES	CCDS14412.1	ENSP00000276072	TAF1_HUMAN	.	UPI000013DA9F	.	deleterious(0)	probably_damaging(0.998)	19/38	.	hmmpanther:PTHR13900:SF0,hmmpanther:PTHR13900,Pfam_domain:PF12157,PIRSF_domain:PIRSF003047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCACGGGGT	.	5	ESCA
XIST	0	.	GRCh37	X	73070744	73070744	+	RNA	SNP	G	G	A	novel	.	TCGA-VR-AA7B-01A-31D-A403-09	TCGA-VR-AA7B-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1845C>T	.	.	ENST00000429829	1/6	28	16	11	47	47	0	XIST,non_coding_transcript_exon_variant,,ENST00000429829,;	A	ENSG00000229807	ENST00000429829	Transcript	non_coding_transcript_exon_variant	1845	.	.	.	.	.	.	.	-1	XIST	HGNC	12810	lincRNA	YES	.	.	.	.	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGGCTAAA	.	5	ESCA
FAM175B	0	.	GRCh37	10	126523903	126523904	+	3'UTR	INS	-	-	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*364dupA	.	.	ENST00000298492	9/9	139	108	31	84	84	0	FAM175B,3_prime_UTR_variant,,ENST00000298492,;	A	ENSG00000165660	ENST00000298492	Transcript	3_prime_UTR_variant	1656-1657	.	.	.	.	.	.	.	1	FAM175B	HGNC	28975	protein_coding	YES	CCDS31308.2	ENSP00000298492	F175B_HUMAN	.	UPI0000403FD8	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAACTTACCTC	.	3	ESCA
RP11-85G18.6	0	.	GRCh37	10	27538198	27538198	+	Intron	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.256-789C>G	.	.	ENST00000574842	.	130	92	38	106	106	0	RP11-85G18.6,intron_variant,,ENST00000574842,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000284414,;LRRC37A6P,downstream_gene_variant,,ENST00000575554,;LRRC37A6P,downstream_gene_variant,,ENST00000574795,;LRRC37A6P,non_coding_transcript_exon_variant,,ENST00000448648,;	G	ENSG00000262412	ENST00000574842	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RP11-85G18.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTCTGTAG	.	5	ESCA
AGAP4	0	.	GRCh37	10	46321476	46321476	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1879G>T	p.Val627Phe	p.V627F	ENST00000448048	7/7	59	39	19	47	47	0	AGAP4,missense_variant,p.Val627Phe,ENST00000448048,;AGAP4,downstream_gene_variant,,ENST00000430779,;	A	ENSG00000188234	ENST00000448048	Transcript	missense_variant	2005	1879	627	V/F	Gtc/Ttc	COSM73609	.	.	-1	AGAP4	HGNC	23459	protein_coding	YES	CCDS7215.1	ENSP00000392513	AGAP4_HUMAN	.	UPI000013ED67	.	deleterious(0.02)	possibly_damaging(0.644)	7/7	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,Pfam_domain:PF12796,Gene3D:1.25.40.20,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.V627A|c.1880T>C|3	RADIA|VARSCANS	CATGACGTCCA	.	2	ESCA
ANK3	0	.	GRCh37	10	61830487	61830487	+	Silent	SNP	C	C	T	rs778769380	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10152G>A	p.%3D	p.Q3384Q	ENST00000280772	37/44	56	52	4	34	34	0	ANK3,synonymous_variant,p.%3D,ENST00000280772,;ANK3,intron_variant,,ENST00000373827,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000355288,;ANK3,intron_variant,,ENST00000511043,;ANK3,intron_variant,,ENST00000503366,;	T	ENSG00000151150	ENST00000280772	Transcript	synonymous_variant	10344	10152	3384	Q	caG/caA	rs778769380,COSM414994	.	.	-1	ANK3	HGNC	494	protein_coding	YES	CCDS7258.1	ENSP00000280772	ANK3_HUMAN	D6RFK6_HUMAN,D6RBY7_HUMAN,B1AQT1_HUMAN	UPI0000141BA9	.	.	.	37/44	.	hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF15	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCATTCTGGGC	byFrequency	2	ESCA
COL13A1	0	.	GRCh37	10	71678829	71678829	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041G>A	p.%3D	p.G347G	ENST00000398978	20/40	28	23	5	26	26	0	COL13A1,synonymous_variant,p.%3D,ENST00000517713,;COL13A1,synonymous_variant,p.%3D,ENST00000354547,;COL13A1,synonymous_variant,p.%3D,ENST00000398978,;COL13A1,synonymous_variant,p.%3D,ENST00000398964,;COL13A1,synonymous_variant,p.%3D,ENST00000398971,;COL13A1,synonymous_variant,p.%3D,ENST00000398966,;COL13A1,synonymous_variant,p.%3D,ENST00000398969,;COL13A1,synonymous_variant,p.%3D,ENST00000398973,;COL13A1,synonymous_variant,p.%3D,ENST00000520133,;COL13A1,synonymous_variant,p.%3D,ENST00000520267,;COL13A1,synonymous_variant,p.%3D,ENST00000522165,;COL13A1,synonymous_variant,p.%3D,ENST00000398968,;COL13A1,synonymous_variant,p.%3D,ENST00000398974,;COL13A1,synonymous_variant,p.%3D,ENST00000356340,;COL13A1,synonymous_variant,p.%3D,ENST00000398972,;COL13A1,synonymous_variant,p.%3D,ENST00000357811,;COL13A1,synonymous_variant,p.%3D,ENST00000479733,;	A	ENSG00000197467	ENST00000398978	Transcript	synonymous_variant	1533	1041	347	G	ggG/ggA	.	.	.	1	COL13A1	HGNC	2190	protein_coding	YES	CCDS44419.1	ENSP00000381949	CODA1_HUMAN	Q9UP45_HUMAN	UPI000046FD72	.	.	.	20/40	.	hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGGATCCC	.	5	ESCA
ZCCHC24	0	.	GRCh37	10	81192403	81192403	+	Missense_Mutation	SNP	C	C	T	rs141500674	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.358G>A	p.Glu120Lys	p.E120K	ENST00000372336	2/4	48	31	17	26	26	0	ZCCHC24,missense_variant,p.Arg60Gln,ENST00000372333,;ZCCHC24,missense_variant,p.Glu120Lys,ENST00000372336,;	T	ENSG00000165424	ENST00000372336	Transcript	missense_variant	545	358	120	E/K	Gag/Aag	rs141500674	.	.	-1	ZCCHC24	HGNC	26911	protein_coding	YES	CCDS7359.1	ENSP00000361411	ZCH24_HUMAN	.	UPI000006F100	.	deleterious_low_confidence(0.04)	possibly_damaging(0.769)	2/4	.	hmmpanther:PTHR15439,hmmpanther:PTHR15439:SF2	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCTCGGAGG	byCluster	5	ESCA
CCNJ	0	.	GRCh37	10	97819214	97819214	+	3'UTR	DEL	A	A	-	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1216delA	.	.	ENST00000465148	6/6	33	20	13	9	9	0	CCNJ,3_prime_UTR_variant,,ENST00000265992,;CCNJ,3_prime_UTR_variant,,ENST00000465148,;CCNJ,3_prime_UTR_variant,,ENST00000534974,;CCNJ,3_prime_UTR_variant,,ENST00000403870,;MIR3157,downstream_gene_variant,,ENST00000578688,;ENTPD1-AS1,intron_variant,,ENST00000416301,;ENTPD1-AS1,intron_variant,,ENST00000454638,;ENTPD1-AS1,intron_variant,,ENST00000451364,;ENTPD1-AS1,intron_variant,,ENST00000458228,;ENTPD1-AS1,intron_variant,,ENST00000452728,;ENTPD1-AS1,intron_variant,,ENST00000427846,;	-	ENSG00000107443	ENST00000465148	Transcript	3_prime_UTR_variant	2546	.	.	.	.	.	.	.	1	CCNJ	HGNC	23434	protein_coding	YES	CCDS44462.1	ENSP00000435373	CCNJ_HUMAN	B7Z894_HUMAN	UPI00001F9448	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACCAGTATTAAC	.	2	ESCA
NXPE2	0	.	GRCh37	11	114577254	114577254	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1282G>A	p.Glu428Lys	p.E428K	ENST00000389586	6/6	58	31	26	83	83	0	NXPE2,missense_variant,p.Glu428Lys,ENST00000389586,;NXPE2,intron_variant,,ENST00000375475,;	A	ENSG00000204361	ENST00000389586	Transcript	missense_variant	1472	1282	428	E/K	Gaa/Aaa	.	.	.	1	NXPE2	HGNC	26331	protein_coding	YES	CCDS44738.1	ENSP00000374237	NXPE2_HUMAN	.	UPI0001662547	.	tolerated(0.54)	benign(0.062)	6/6	.	hmmpanther:PTHR16165:SF6,hmmpanther:PTHR16165	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATGAAAAC	.	5	ESCA
KMT2A	0	.	GRCh37	11	118392772	118392772	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11804G>A	p.Arg3935His	p.R3935H	ENST00000534358	36/36	36	18	18	49	49	0	KMT2A,missense_variant,p.Arg3894His,ENST00000354520,;KMT2A,missense_variant,p.Arg3935His,ENST00000534358,;KMT2A,missense_variant,p.Arg3932His,ENST00000389506,;RP11-770J1.3,intron_variant,,ENST00000528578,;RP11-770J1.3,intron_variant,,ENST00000556583,;RP11-770J1.3,intron_variant,,ENST00000554407,;RP11-770J1.3,intron_variant,,ENST00000532597,;RP11-770J1.3,intron_variant,,ENST00000525992,;KMT2A,non_coding_transcript_exon_variant,,ENST00000527839,;KMT2A,non_coding_transcript_exon_variant,,ENST00000525408,;	A	ENSG00000118058	ENST00000534358	Transcript	missense_variant	11827	11804	3935	R/H	cGt/cAt	COSM1676476,COSM1676475	.	.	1	KMT2A	HGNC	7132	protein_coding	YES	CCDS55791.1	ENSP00000436786	KMT2A_HUMAN	Q9UPD0_HUMAN,Q9UM91_HUMAN,Q9HBJ4_HUMAN,B4DIJ7_HUMAN	UPI0001E5E732	.	.	probably_damaging(0.998)	36/36	.	PROSITE_profiles:PS50280,hmmpanther:PTHR22884:SF302,hmmpanther:PTHR22884,Pfam_domain:PF00856,Gene3D:2.170.270.10,PIRSF_domain:PIRSF010354,SMART_domains:SM00317,Superfamily_domains:SSF82199	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGCGTAAGA	.	5	ESCA
SLC17A6	0	.	GRCh37	11	22360130	22360130	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51G>C	p.Lys17Asn	p.K17N	ENST00000263160	1/12	70	51	19	81	81	0	SLC17A6,missense_variant,p.Lys17Asn,ENST00000263160,;CTD-2140G10.2,upstream_gene_variant,,ENST00000530569,;CTD-2140G10.2,upstream_gene_variant,,ENST00000531304,;CTD-2140G10.2,upstream_gene_variant,,ENST00000528009,;SLC17A6,upstream_gene_variant,,ENST00000534115,;	C	ENSG00000091664	ENST00000263160	Transcript	missense_variant	488	51	17	K/N	aaG/aaC	.	.	.	1	SLC17A6	HGNC	16703	protein_coding	YES	CCDS7856.1	ENSP00000263160	VGLU2_HUMAN	.	UPI0000073F14	.	deleterious(0.01)	possibly_damaging(0.517)	1/12	.	hmmpanther:PTHR11662:SF201,hmmpanther:PTHR11662	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAAGAATTT	.	5	ESCA
RAPSN	0	.	GRCh37	11	47460440	47460440	+	Missense_Mutation	SNP	G	G	T	rs549232026	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009C>A	p.Arg337Ser	p.R337S	ENST00000298854	7/8	50	27	23	42	42	0	RAPSN,missense_variant,p.Arg278Ser,ENST00000352508,;RAPSN,missense_variant,p.Arg337Ser,ENST00000298854,;RAPSN,missense_variant,p.Arg278Ser,ENST00000529341,;RAPSN,missense_variant,p.Pro286Gln,ENST00000524487,;RNU6-1302P,downstream_gene_variant,,ENST00000516518,;RAPSN,intron_variant,,ENST00000528356,;	T	ENSG00000165917	ENST00000298854	Transcript	missense_variant	1223	1009	337	R/S	Cgc/Agc	rs549232026	.	.	-1	RAPSN	HGNC	9863	protein_coding	YES	CCDS7936.1	ENSP00000298854	RAPSN_HUMAN	.	UPI0000071D46	.	tolerated(0.21)	benign(0.116)	7/8	.	hmmpanther:PTHR10098:SF107,hmmpanther:PTHR10098	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGCGGTAAA	by1000G	5	ESCA
OR4S2	0	.	GRCh37	11	55418727	55418727	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349delG	p.Ala117ProfsTer15	p.A117Pfs*15	ENST00000312422	1/1	53	26	27	31	31	0	OR4S2,frameshift_variant,p.Ala117ProfsTer15,ENST00000312422,;	-	ENSG00000174982	ENST00000312422	Transcript	frameshift_variant	348	348	116	M/X	atG/at	.	.	.	1	OR4S2	HGNC	15183	protein_coding	YES	CCDS31505.1	ENSP00000310337	OR4S2_HUMAN	.	UPI00001D77D2	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF110,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R120C|c.358C>T|5	INDELOCATOR*|VARSCANI*|PINDEL	TGTAATGGCCTA	.	3	ESCA
OR5T1	0	.	GRCh37	11	56043399	56043399	+	Silent	SNP	C	C	A	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.285C>A	p.%3D	p.V95V	ENST00000313033	1/1	72	47	25	58	58	0	OR5T1,synonymous_variant,p.%3D,ENST00000313033,;	A	ENSG00000181698	ENST00000313033	Transcript	synonymous_variant	371	285	95	V	gtC/gtA	COSM688611	.	.	1	OR5T1	HGNC	14821	protein_coding	YES	CCDS31525.1	ENSP00000323612	OR5T1_HUMAN	.	UPI000004B22E	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24248:SF33,hmmpanther:PTHR24248,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGTCAATTT	.	5	ESCA
ESRRA	0	.	GRCh37	11	64083538	64083538	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*100C>G	.	.	ENST00000405666	7/7	175	142	33	110	110	0	ESRRA,3_prime_UTR_variant,,ENST00000405666,;ESRRA,3_prime_UTR_variant,,ENST00000000442,;ESRRA,3_prime_UTR_variant,,ENST00000406310,;TRMT112,downstream_gene_variant,,ENST00000544844,;PRDX5,upstream_gene_variant,,ENST00000265462,;ESRRA,downstream_gene_variant,,ENST00000545035,;TRMT112,downstream_gene_variant,,ENST00000535750,;TRMT112,downstream_gene_variant,,ENST00000308774,;PRDX5,upstream_gene_variant,,ENST00000352435,;PRDX5,upstream_gene_variant,,ENST00000347941,;TRMT112,downstream_gene_variant,,ENST00000539854,;ESRRA,downstream_gene_variant,,ENST00000539594,;TRMT112,downstream_gene_variant,,ENST00000535126,;TRMT112,downstream_gene_variant,,ENST00000537918,;ESRRA,downstream_gene_variant,,ENST00000467987,;	G	ENSG00000173153	ENST00000405666	Transcript	3_prime_UTR_variant	1606	.	.	.	.	.	.	.	1	ESRRA	HGNC	3471	protein_coding	YES	CCDS41667.1	ENSP00000384851	ERR1_HUMAN	Q96I02_HUMAN,Q96F89_HUMAN,Q569H8_HUMAN,F5H0E9_HUMAN,F5GWT5_HUMAN	UPI0000167B87	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCCTGCTG	.	5	ESCA
MRGPRF	0	.	GRCh37	11	68773294	68773294	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.484G>A	p.Val162Met	p.V162M	ENST00000309099	3/3	196	181	15	41	41	0	MRGPRF,missense_variant,p.Val162Met,ENST00000441623,;MRGPRF,missense_variant,p.Val162Met,ENST00000309099,;MRGPRF,downstream_gene_variant,,ENST00000320913,;RP11-554A11.5,downstream_gene_variant,,ENST00000562506,;RP11-554A11.4,upstream_gene_variant,,ENST00000562276,;	T	ENSG00000172935	ENST00000309099	Transcript	missense_variant	867	484	162	V/M	Gtg/Atg	.	.	.	-1	MRGPRF	HGNC	24828	protein_coding	YES	CCDS8188.1	ENSP00000309782	MRGRF_HUMAN	Q8N7J6_HUMAN	UPI000012F566	.	deleterious(0.01)	possibly_damaging(0.78)	3/3	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF3,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR02108,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCACGGCCG	.	2	ESCA
UTP20	0	.	GRCh37	12	101728221	101728221	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3580G>C	p.Glu1194Gln	p.E1194Q	ENST00000261637	29/62	38	33	5	26	26	0	UTP20,missense_variant,p.Glu1194Gln,ENST00000261637,;	C	ENSG00000120800	ENST00000261637	Transcript	missense_variant	3754	3580	1194	E/Q	Gag/Cag	COSM545773	.	.	1	UTP20	HGNC	17897	protein_coding	YES	CCDS9081.1	ENSP00000261637	UTP20_HUMAN	.	UPI00001FB38B	.	deleterious(0)	possibly_damaging(0.878)	29/62	.	hmmpanther:PTHR17695:SF11,hmmpanther:PTHR17695	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTGAGAGT	.	5	ESCA
KIAA1467	0	.	GRCh37	12	13211414	13211414	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.463G>A	p.Asp155Asn	p.D155N	ENST00000197268	3/13	89	65	24	88	88	0	KIAA1467,missense_variant,p.Asp155Asn,ENST00000197268,;KIAA1467,upstream_gene_variant,,ENST00000537625,;KIAA1467,upstream_gene_variant,,ENST00000535974,;KIAA1467,missense_variant,p.Asp155Asn,ENST00000416494,;KIAA1467,upstream_gene_variant,,ENST00000541950,;	A	ENSG00000084444	ENST00000197268	Transcript	missense_variant	583	463	155	D/N	Gat/Aat	.	.	.	1	KIAA1467	HGNC	29288	protein_coding	YES	CCDS31750.1	ENSP00000197268	K1467_HUMAN	.	UPI00001FB6A1	.	deleterious(0)	probably_damaging(0.996)	3/13	.	hmmpanther:PTHR21419,hmmpanther:PTHR21419:SF25,Gene3D:2.140.10.10,Superfamily_domains:SSF50998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTGATGTG	.	5	ESCA
OVCH1	0	.	GRCh37	12	29626014	29626014	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1623A>G	p.%3D	p.P541P	ENST00000318184	15/28	44	31	13	39	39	0	OVCH1,synonymous_variant,p.%3D,ENST00000318184,;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,;	C	ENSG00000187950	ENST00000318184	Transcript	synonymous_variant	1623	1623	541	P	ccA/ccG	.	.	.	-1	OVCH1	HGNC	23080	protein_coding	YES	.	ENSP00000326708	OVCH1_HUMAN	.	UPI000040640A	.	.	.	15/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTTTGGTTC	.	5	ESCA
PKP2	0	.	GRCh37	12	32977060	32977060	+	Silent	SNP	C	C	T	rs760093803	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1725G>A	p.%3D	p.A575A	ENST00000070846	8/14	69	59	9	52	52	0	PKP2,synonymous_variant,p.%3D,ENST00000340811,;PKP2,synonymous_variant,p.%3D,ENST00000070846,;PKP2,non_coding_transcript_exon_variant,,ENST00000546498,;PKP2,non_coding_transcript_exon_variant,,ENST00000552612,;PKP2,upstream_gene_variant,,ENST00000549461,;	T	ENSG00000057294	ENST00000070846	Transcript	synonymous_variant	1750	1725	575	A	gcG/gcA	rs760093803,COSM3811891	.	.	-1	PKP2	HGNC	9024	protein_coding	YES	CCDS8731.1	ENSP00000070846	PKP2_HUMAN	.	UPI000013C576	.	.	.	8/14	.	hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCATCGCTTT	byFrequency	4	ESCA
PPHLN1	0	.	GRCh37	12	42778782	42778782	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.552A>G	p.%3D	p.E184E	ENST00000395568	6/13	93	70	22	75	75	0	PPHLN1,synonymous_variant,p.%3D,ENST00000358314,;PPHLN1,synonymous_variant,p.%3D,ENST00000337898,;PPHLN1,synonymous_variant,p.%3D,ENST00000549190,;PPHLN1,synonymous_variant,p.%3D,ENST00000552761,;PPHLN1,synonymous_variant,p.%3D,ENST00000395580,;PPHLN1,synonymous_variant,p.%3D,ENST00000395568,;PPHLN1,synonymous_variant,p.%3D,ENST00000432191,;PPHLN1,intron_variant,,ENST00000449194,;PPHLN1,intron_variant,,ENST00000256678,;PPHLN1,intron_variant,,ENST00000317560,;PPHLN1,intron_variant,,ENST00000552794,;PPHLN1,non_coding_transcript_exon_variant,,ENST00000552202,;PPHLN1,intron_variant,,ENST00000551723,;PPHLN1,upstream_gene_variant,,ENST00000547440,;PPHLN1,upstream_gene_variant,,ENST00000547696,;	G	ENSG00000134283	ENST00000395568	Transcript	synonymous_variant	636	552	184	E	gaA/gaG	.	.	.	1	PPHLN1	HGNC	19369	protein_coding	YES	CCDS31777.1	ENSP00000378935	PPHLN_HUMAN	F8VWU8_HUMAN	UPI0000351A1E	.	.	.	6/13	.	hmmpanther:PTHR15836,hmmpanther:PTHR15836:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGAAGGAAA	.	5	ESCA
KRT6A	0	.	GRCh37	12	52881551	52881551	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1648A>C	p.Lys550Gln	p.K550Q	ENST00000330722	9/9	61	57	4	43	43	0	KRT6A,missense_variant,p.Lys550Gln,ENST00000330722,;KRT6A,downstream_gene_variant,,ENST00000549600,;KRT6A,downstream_gene_variant,,ENST00000548735,;KRT6A,downstream_gene_variant,,ENST00000549898,;KRT6A,downstream_gene_variant,,ENST00000549754,;	G	ENSG00000205420	ENST00000330722	Transcript	missense_variant	1717	1648	550	K/Q	Aag/Cag	.	.	.	-1	KRT6A	HGNC	6443	protein_coding	YES	CCDS41786.1	ENSP00000369317	K2C6A_HUMAN	.	UPI000013CD4C	.	deleterious(0.04)	unknown(0)	9/9	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTACTTGATGG	.	2	ESCA
SOAT2	0	.	GRCh37	12	53497990	53497990	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.138G>A	p.%3D	p.E46E	ENST00000301466	2/15	38	24	14	25	25	0	SOAT2,synonymous_variant,p.%3D,ENST00000301466,;SOAT2,synonymous_variant,p.%3D,ENST00000551896,;IGFBP6,downstream_gene_variant,,ENST00000301464,;IGFBP6,downstream_gene_variant,,ENST00000548547,;IGFBP6,downstream_gene_variant,,ENST00000549628,;SOAT2,synonymous_variant,p.%3D,ENST00000542365,;IGFBP6,downstream_gene_variant,,ENST00000548176,;	A	ENSG00000167780	ENST00000301466	Transcript	synonymous_variant	198	138	46	E	gaG/gaA	.	.	.	1	SOAT2	HGNC	11178	protein_coding	YES	CCDS8847.1	ENSP00000301466	SOAT2_HUMAN	.	UPI0000135B61	.	.	.	2/15	.	hmmpanther:PTHR10408,hmmpanther:PTHR10408:SF10,PIRSF_domain:PIRSF000439,PIRSF_domain:PIRSF500230	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGAGGTGAG	.	5	ESCA
NUDT4	0	.	GRCh37	12	93795568	93795568	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2413C>A	.	.	ENST00000337179	5/5	15	11	4	12	12	0	NUDT4,3_prime_UTR_variant,,ENST00000549992,;NUDT4,3_prime_UTR_variant,,ENST00000337179,;NUDT4,3_prime_UTR_variant,,ENST00000415493,;NUDT4,downstream_gene_variant,,ENST00000546925,;NUDT4,downstream_gene_variant,,ENST00000548662,;NUDT4,downstream_gene_variant,,ENST00000550056,;NUDT4,downstream_gene_variant,,ENST00000547014,;UBE2N,downstream_gene_variant,,ENST00000548946,;	A	ENSG00000173598	ENST00000337179	Transcript	3_prime_UTR_variant	3399	.	.	.	.	.	.	.	1	NUDT4	HGNC	8051	protein_coding	YES	CCDS9044.1	ENSP00000338352	NUDT4_HUMAN	.	UPI00000730C3	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CCAGTCTAGCA	.	2	ESCA
TUBGCP3	0	.	GRCh37	13	113201973	113201973	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129C>T	p.Arg377Ter	p.R377*	ENST00000261965	10/22	36	33	3	25	25	0	TUBGCP3,stop_gained,p.Arg377Ter,ENST00000261965,;TUBGCP3,stop_gained,p.Arg377Ter,ENST00000375669,;TUBGCP3,upstream_gene_variant,,ENST00000462580,;TUBGCP3,non_coding_transcript_exon_variant,,ENST00000464139,;	A	ENSG00000126216	ENST00000261965	Transcript	stop_gained	1316	1129	377	R/*	Cga/Tga	.	.	.	-1	TUBGCP3	HGNC	18598	protein_coding	YES	CCDS9525.1	ENSP00000261965	GCP3_HUMAN	.	UPI000000DB88	.	.	.	10/22	.	Pfam_domain:PF04130,hmmpanther:PTHR19302:SF14,hmmpanther:PTHR19302	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGTCGTATTT	.	2	ESCA
MRP63	0	.	GRCh37	13	21751269	21751269	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.214G>C	p.Glu72Gln	p.E72Q	ENST00000309594	2/2	51	34	16	40	40	0	MRP63,missense_variant,p.Glu72Gln,ENST00000309594,;SKA3,upstream_gene_variant,,ENST00000314759,;SKA3,upstream_gene_variant,,ENST00000400018,;SKA3,upstream_gene_variant,,ENST00000475251,;SKA3,upstream_gene_variant,,ENST00000298260,;SKA3,upstream_gene_variant,,ENST00000536239,;SKA3,upstream_gene_variant,,ENST00000465471,;SKA3,upstream_gene_variant,,ENST00000462482,;	C	ENSG00000173141	ENST00000309594	Transcript	missense_variant	292	214	72	E/Q	Gag/Cag	COSM416416	.	.	1	MRP63	HGNC	14514	protein_coding	YES	CCDS9296.1	ENSP00000310726	RT63_HUMAN	.	UPI000004C5AC	.	tolerated(0.39)	benign(0.03)	2/2	.	hmmpanther:PTHR14520,Pfam_domain:PF14978,PIRSF_domain:PIRSF011124	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCGAGGCC	.	5	ESCA
PDS5B	0	.	GRCh37	13	33309450	33309450	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2389C>T	p.Leu797Phe	p.L797F	ENST00000315596	21/35	48	28	19	60	60	0	PDS5B,missense_variant,p.Leu797Phe,ENST00000315596,;PDS5B,missense_variant,p.Leu797Phe,ENST00000450460,;	T	ENSG00000083642	ENST00000315596	Transcript	missense_variant	2575	2389	797	L/F	Ctt/Ttt	.	.	.	1	PDS5B	HGNC	20418	protein_coding	YES	CCDS41878.1	ENSP00000313851	PDS5B_HUMAN	.	UPI000006D4A9	.	deleterious(0.04)	possibly_damaging(0.48)	21/35	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATCTTCTC	.	5	ESCA
FREM2	0	.	GRCh37	13	39263873	39263873	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2392C>G	p.Arg798Gly	p.R798G	ENST00000280481	1/24	53	37	16	53	53	0	FREM2,missense_variant,p.Arg798Gly,ENST00000280481,;	G	ENSG00000150893	ENST00000280481	Transcript	missense_variant	2608	2392	798	R/G	Cga/Gga	.	.	.	1	FREM2	HGNC	25396	protein_coding	YES	CCDS31960.1	ENSP00000280481	FREM2_HUMAN	.	UPI00005520B9	.	deleterious(0.01)	possibly_damaging(0.666)	1/24	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACTCGAGTG	.	5	ESCA
NDFIP2	0	.	GRCh37	13	80127108	80127108	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*460G>A	.	.	ENST00000218652	8/8	79	51	28	56	56	0	NDFIP2,3_prime_UTR_variant,,ENST00000218652,;NDFIP2,3_prime_UTR_variant,,ENST00000487865,;NDFIP2,downstream_gene_variant,,ENST00000465762,;	A	ENSG00000102471	ENST00000218652	Transcript	3_prime_UTR_variant	1523	.	.	.	.	.	.	.	1	NDFIP2	HGNC	18537	protein_coding	YES	CCDS31998.1	ENSP00000218652	NFIP2_HUMAN	.	UPI000015F962	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATGAAACA	.	5	ESCA
HS6ST3	0	.	GRCh37	13	97485218	97485218	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1182C>T	p.%3D	p.R394R	ENST00000376705	2/2	35	24	11	31	31	0	HS6ST3,synonymous_variant,p.%3D,ENST00000376705,;	T	ENSG00000185352	ENST00000376705	Transcript	synonymous_variant	1206	1182	394	R	cgC/cgT	.	.	.	1	HS6ST3	HGNC	19134	protein_coding	YES	CCDS9481.1	ENSP00000365895	H6ST3_HUMAN	B3KX95_HUMAN	UPI00001AF933	.	.	.	2/2	.	hmmpanther:PTHR12812,hmmpanther:PTHR12812:SF3,Pfam_domain:PF03567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCGCCAACG	.	5	ESCA
EIF5	0	.	GRCh37	14	103808992	103808992	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1603G>A	.	.	ENST00000216554	12/12	35	22	13	29	29	0	EIF5,3_prime_UTR_variant,,ENST00000216554,;EIF5,3_prime_UTR_variant,,ENST00000558506,;EIF5,downstream_gene_variant,,ENST00000558265,;EIF5,downstream_gene_variant,,ENST00000392715,;SNORA28,downstream_gene_variant,,ENST00000606769,;EIF5,downstream_gene_variant,,ENST00000561406,;EIF5,downstream_gene_variant,,ENST00000558800,;EIF5,downstream_gene_variant,,ENST00000561023,;EIF5,downstream_gene_variant,,ENST00000559923,;EIF5,downstream_gene_variant,,ENST00000561439,;EIF5,downstream_gene_variant,,ENST00000559011,;EIF5,downstream_gene_variant,,ENST00000561380,;	A	ENSG00000100664	ENST00000216554	Transcript	3_prime_UTR_variant	3575	.	.	.	.	.	.	.	1	EIF5	HGNC	3299	protein_coding	YES	CCDS9980.1	ENSP00000216554	IF5_HUMAN	H0YN40_HUMAN,H0YMJ8_HUMAN,H0YM54_HUMAN,H0YLZ1_HUMAN,H0YK29_HUMAN,H0YK11_HUMAN	UPI000012D3A5	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTGAAACC	.	5	ESCA
OR6S1	0	.	GRCh37	14	21109503	21109503	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.348G>A	p.%3D	p.L116L	ENST00000320704	1/1	42	36	6	41	41	0	OR6S1,synonymous_variant,p.%3D,ENST00000320704,;	T	ENSG00000181803	ENST00000320704	Transcript	synonymous_variant	348	348	116	L	ctG/ctA	.	.	.	-1	OR6S1	HGNC	15363	protein_coding	YES	CCDS32038.1	ENSP00000313110	OR6S1_HUMAN	.	UPI000003FE0D	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF7,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	GCCAACAGTAA	.	3	ESCA
CHD8	0	.	GRCh37	14	21868426	21868426	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4611delA	p.Val1538Ter	p.V1538*	ENST00000399982	23/37	150	104	46	37	37	0	CHD8,frameshift_variant,p.Val772Ter,ENST00000555935,;CHD8,frameshift_variant,p.Val1538Ter,ENST00000557364,;CHD8,frameshift_variant,p.Val1259Ter,ENST00000430710,;CHD8,frameshift_variant,p.Val1538Ter,ENST00000399982,;SNORD8,upstream_gene_variant,,ENST00000363915,;CHD8,non_coding_transcript_exon_variant,,ENST00000555962,;RP11-689J19.1,downstream_gene_variant,,ENST00000480068,;	-	ENSG00000100888	ENST00000399982	Transcript	frameshift_variant	4676	4611	1537	K/X	aaA/aa	.	.	.	-1	CHD8	HGNC	20153	protein_coding	YES	CCDS53885.1	ENSP00000382863	CHD8_HUMAN	.	UPI00002375B9	.	.	.	23/37	.	hmmpanther:PTHR10799:SF551,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTTACTTTTTT	.	3	ESCA
KLHDC2	0	.	GRCh37	14	50244592	50244592	+	Silent	SNP	G	G	A	rs773736420	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387G>A	p.%3D	p.V129V	ENST00000298307	4/13	47	30	17	42	42	0	KLHDC2,synonymous_variant,p.%3D,ENST00000298307,;KLHDC2,synonymous_variant,p.%3D,ENST00000554589,;KLHDC2,synonymous_variant,p.%3D,ENST00000557247,;KLHDC2,non_coding_transcript_exon_variant,,ENST00000553538,;KLHDC2,synonymous_variant,p.%3D,ENST00000555443,;KLHDC2,synonymous_variant,p.%3D,ENST00000555739,;KLHDC2,non_coding_transcript_exon_variant,,ENST00000556559,;KLHDC2,non_coding_transcript_exon_variant,,ENST00000557063,;KLHDC2,upstream_gene_variant,,ENST00000553579,;KLHDC2,upstream_gene_variant,,ENST00000554115,;KLHDC2,downstream_gene_variant,,ENST00000553703,;	A	ENSG00000165516	ENST00000298307	Transcript	synonymous_variant	1248	387	129	V	gtG/gtA	rs773736420	.	.	1	KLHDC2	HGNC	20231	protein_coding	YES	CCDS9693.1	ENSP00000298307	KLDC2_HUMAN	.	UPI00000372DF	.	.	.	4/13	.	hmmpanther:PTHR23244:SF261,hmmpanther:PTHR23244,Gene3D:1zgkA00,Superfamily_domains:0052715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGTGTTACA	.	5	ESCA
PLEKHG3	0	.	GRCh37	14	65197822	65197822	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.616A>C	p.Met206Leu	p.M206L	ENST00000247226	5/15	50	30	19	34	34	0	PLEKHG3,missense_variant,p.Met206Leu,ENST00000247226,;PLEKHG3,missense_variant,p.Met262Leu,ENST00000394691,;PLEKHG3,downstream_gene_variant,,ENST00000554499,;PLEKHG3,downstream_gene_variant,,ENST00000554088,;PLEKHG3,downstream_gene_variant,,ENST00000555982,;PLEKHG3,downstream_gene_variant,,ENST00000556801,;PLEKHG3,non_coding_transcript_exon_variant,,ENST00000490180,;	C	ENSG00000126822	ENST00000247226	Transcript	missense_variant	924	616	206	M/L	Atg/Ctg	.	.	.	1	PLEKHG3	HGNC	20364	protein_coding	YES	CCDS32098.1	ENSP00000247226	PKHG3_HUMAN	G3V311_HUMAN	UPI0000407D62	.	tolerated(0.07)	possibly_damaging(0.881)	5/15	.	PROSITE_profiles:PS50010,hmmpanther:PTHR22143:SF4,hmmpanther:PTHR22143,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACACCATGACC	.	5	ESCA
PIGB	0	.	GRCh37	15	55621954	55621954	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555G>T	p.Trp185Cys	p.W185C	ENST00000164305	5/12	112	95	17	55	55	0	PIGB,missense_variant,p.Trp176Cys,ENST00000566999,;PIGB,missense_variant,p.Trp185Cys,ENST00000164305,;PIGB,5_prime_UTR_variant,,ENST00000539642,;PIGB,downstream_gene_variant,,ENST00000566072,;PIGB,missense_variant,p.Val66Leu,ENST00000565367,;PIGB,3_prime_UTR_variant,,ENST00000570059,;	T	ENSG00000069943	ENST00000164305	Transcript	missense_variant	846	555	185	W/C	tgG/tgT	.	.	.	1	PIGB	HGNC	8959	protein_coding	YES	CCDS61641.1	ENSP00000164305	PIGB_HUMAN	F5H1S1_HUMAN	UPI0000072A05	.	tolerated(0.1)	benign(0.383)	5/12	.	Pfam_domain:PF03901,hmmpanther:PTHR22760:SF4,hmmpanther:PTHR22760	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATGGTATTG	.	4	ESCA
VPS13C	0	.	GRCh37	15	62207860	62207860	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8417A>T	p.Lys2806Met	p.K2806M	ENST00000261517	61/85	105	69	35	60	60	0	VPS13C,missense_variant,p.Lys2806Met,ENST00000261517,;VPS13C,missense_variant,p.Lys2806Met,ENST00000395896,;VPS13C,missense_variant,p.Lys2763Met,ENST00000249837,;VPS13C,missense_variant,p.Lys2763Met,ENST00000395898,;RN7SL613P,downstream_gene_variant,,ENST00000584412,;VPS13C,non_coding_transcript_exon_variant,,ENST00000558338,;	A	ENSG00000129003	ENST00000261517	Transcript	missense_variant	8491	8417	2806	K/M	aAg/aTg	.	.	.	-1	VPS13C	HGNC	23594	protein_coding	YES	CCDS32257.1	ENSP00000261517	VP13C_HUMAN	B4E2S9_HUMAN,B3KW10_HUMAN	UPI000023B7D3	.	deleterious(0)	probably_damaging(0.998)	61/85	.	hmmpanther:PTHR16166:SF69,hmmpanther:PTHR16166,Pfam_domain:PF06650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTCTTGAAA	.	5	ESCA
HERC1	0	.	GRCh37	15	64026961	64026961	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2608C>T	p.Gln870Ter	p.Q870*	ENST00000443617	13/78	109	88	21	63	63	0	HERC1,stop_gained,p.Gln870Ter,ENST00000443617,;HERC1,intron_variant,,ENST00000561400,;HERC1,non_coding_transcript_exon_variant,,ENST00000560519,;	A	ENSG00000103657	ENST00000443617	Transcript	stop_gained	2696	2608	870	Q/*	Caa/Taa	.	.	.	-1	HERC1	HGNC	4867	protein_coding	YES	CCDS45277.1	ENSP00000390158	HERC1_HUMAN	H0YL74_HUMAN,H0YL07_HUMAN,H0YKW7_HUMAN	UPI0000212760	.	.	.	13/78	.	hmmpanther:PTHR22870:SF156,hmmpanther:PTHR22870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTTGAGGTA	.	5	ESCA
TRIP4	0	.	GRCh37	15	64692982	64692982	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659C>G	p.Ser220Ter	p.S220*	ENST00000261884	5/13	164	101	63	63	63	0	TRIP4,stop_gained,p.Ser220Ter,ENST00000261884,;RN7SL595P,upstream_gene_variant,,ENST00000582065,;TRIP4,non_coding_transcript_exon_variant,,ENST00000559565,;TRIP4,downstream_gene_variant,,ENST00000557834,;TRIP4,downstream_gene_variant,,ENST00000559833,;TRIP4,stop_gained,p.Ser220Ter,ENST00000560567,;TRIP4,3_prime_UTR_variant,,ENST00000560920,;TRIP4,3_prime_UTR_variant,,ENST00000558820,;TRIP4,non_coding_transcript_exon_variant,,ENST00000561265,;	G	ENSG00000103671	ENST00000261884	Transcript	stop_gained	719	659	220	S/*	tCa/tGa	.	.	.	1	TRIP4	HGNC	12310	protein_coding	YES	CCDS10194.1	ENSP00000261884	TRIP4_HUMAN	.	UPI0000035D96	.	.	.	5/13	.	hmmpanther:PTHR12963:SF0,hmmpanther:PTHR12963	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACTCAAACA	.	5	ESCA
ISG20	0	.	GRCh37	15	89195433	89195433	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321C>G	p.Ile107Met	p.I107M	ENST00000306072	3/4	73	61	11	38	38	0	ISG20,missense_variant,p.Ile87Met,ENST00000559876,;ISG20,missense_variant,p.Ile107Met,ENST00000560741,;ISG20,missense_variant,p.Ile107Met,ENST00000306072,;ISG20,downstream_gene_variant,,ENST00000379224,;ISG20,non_coding_transcript_exon_variant,,ENST00000560746,;ISG20,downstream_gene_variant,,ENST00000558236,;ISG20,non_coding_transcript_exon_variant,,ENST00000557824,;ISG20,non_coding_transcript_exon_variant,,ENST00000560573,;ISG20,non_coding_transcript_exon_variant,,ENST00000558942,;ISG20,non_coding_transcript_exon_variant,,ENST00000546338,;	G	ENSG00000172183	ENST00000306072	Transcript	missense_variant	679	321	107	I/M	atC/atG	.	.	.	1	ISG20	HGNC	6130	protein_coding	YES	CCDS10345.1	ENSP00000306565	ISG20_HUMAN	.	UPI000006FE4D	.	deleterious(0.02)	benign(0.177)	3/4	.	Superfamily_domains:SSF53098,SMART_domains:SM00479,Gene3D:3.30.420.10,Pfam_domain:PF00929,hmmpanther:PTHR12801	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATCTACGA	.	5	ESCA
RP11-161M6.5	0	.	GRCh37	16	1116262	1116262	+	RNA	SNP	G	G	A	rs537743255	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.639G>A	.	.	ENST00000564390	2/2	35	20	15	29	29	0	RP11-161M6.5,non_coding_transcript_exon_variant,,ENST00000564390,;SSTR5-AS1,non_coding_transcript_exon_variant,,ENST00000565992,;SSTR5-AS1,non_coding_transcript_exon_variant,,ENST00000569832,;SSTR5-AS1,downstream_gene_variant,,ENST00000566499,;SSTR5-AS1,downstream_gene_variant,,ENST00000569734,;AC009041.1,non_coding_transcript_exon_variant,,ENST00000314015,;	A	ENSG00000261720	ENST00000564390	Transcript	non_coding_transcript_exon_variant	639	.	.	.	.	rs537743255	.	.	1	RP11-161M6.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	A:0.0012	A:0	A:0	.	A:0	A:0	A:0.0061	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACGGGTGG	byFrequency|byCluster|by1000G	5	ESCA
SOCS1	0	.	GRCh37	16	11348728	11348728	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.608A>C	p.Tyr203Ser	p.Y203S	ENST00000332029	2/2	68	46	22	47	47	0	SOCS1,missense_variant,p.Tyr203Ser,ENST00000332029,;RMI2,intron_variant,,ENST00000572173,;RMI2,intron_variant,,ENST00000573910,;	G	ENSG00000185338	ENST00000332029	Transcript	missense_variant	759	608	203	Y/S	tAc/tCc	.	.	.	-1	SOCS1	HGNC	19383	protein_coding	YES	CCDS10546.1	ENSP00000329418	SOCS1_HUMAN	Q4JHT5_HUMAN	UPI0000033166	.	deleterious(0)	possibly_damaging(0.829)	2/2	.	Superfamily_domains:SSF158235,SMART_domains:SM00253,SMART_domains:SM00969,Pfam_domain:PF07525,hmmpanther:PTHR10385:SF5,hmmpanther:PTHR10385,PROSITE_profiles:PS50225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCAGGTAGTCG	.	4	ESCA
TMC5	0	.	GRCh37	16	19475199	19475199	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1338C>T	p.%3D	p.V446V	ENST00000396229	8/22	36	22	14	47	47	0	TMC5,synonymous_variant,p.%3D,ENST00000219821,;TMC5,synonymous_variant,p.%3D,ENST00000381414,;TMC5,synonymous_variant,p.%3D,ENST00000561503,;TMC5,synonymous_variant,p.%3D,ENST00000541464,;TMC5,synonymous_variant,p.%3D,ENST00000396229,;TMC5,synonymous_variant,p.%3D,ENST00000564959,;TMC5,synonymous_variant,p.%3D,ENST00000542583,;TMC5,non_coding_transcript_exon_variant,,ENST00000567478,;	T	ENSG00000103534	ENST00000396229	Transcript	synonymous_variant	2087	1338	446	V	gtC/gtT	.	.	.	1	TMC5	HGNC	22999	protein_coding	YES	CCDS45431.1	ENSP00000379531	TMC5_HUMAN	.	UPI00001FEF87	.	.	.	8/22	.	hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V446I|c.1336G>A|3,BUFFER|p.V200I|c.598G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGTCCTCTC	.	5	ESCA
DOC2A	0	.	GRCh37	16	30020351	30020351	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.493A>T	p.Ile165Phe	p.I165F	ENST00000350119	5/11	46	32	14	43	43	0	DOC2A,missense_variant,p.Ile47Phe,ENST00000563125,;DOC2A,missense_variant,p.Ile165Phe,ENST00000565273,;DOC2A,missense_variant,p.Ile165Phe,ENST00000563378,;DOC2A,missense_variant,p.Ile165Phe,ENST00000564979,;DOC2A,missense_variant,p.Ile47Phe,ENST00000567332,;DOC2A,missense_variant,p.Ile165Phe,ENST00000350119,;DOC2A,missense_variant,p.Ile165Phe,ENST00000564944,;INO80E,downstream_gene_variant,,ENST00000562291,;INO80E,downstream_gene_variant,,ENST00000563197,;INO80E,downstream_gene_variant,,ENST00000304516,;INO80E,downstream_gene_variant,,ENST00000567705,;DOC2A,downstream_gene_variant,,ENST00000574405,;DOC2A,upstream_gene_variant,,ENST00000564357,;DOC2A,downstream_gene_variant,,ENST00000567824,;DOC2A,downstream_gene_variant,,ENST00000570194,;DOC2A,missense_variant,p.Ile47Phe,ENST00000561671,;DOC2A,missense_variant,p.Ile47Phe,ENST00000566310,;DOC2A,non_coding_transcript_exon_variant,,ENST00000564233,;DOC2A,downstream_gene_variant,,ENST00000566456,;INO80E,downstream_gene_variant,,ENST00000567987,;INO80E,downstream_gene_variant,,ENST00000569957,;INO80E,downstream_gene_variant,,ENST00000540562,;INO80E,downstream_gene_variant,,ENST00000567065,;INO80E,downstream_gene_variant,,ENST00000562441,;	A	ENSG00000149927	ENST00000350119	Transcript	missense_variant	684	493	165	I/F	Atc/Ttc	.	.	.	-1	DOC2A	HGNC	2985	protein_coding	YES	CCDS10666.1	ENSP00000340017	DOC2A_HUMAN	H3BU41_HUMAN,H3BSH4_HUMAN,H3BNF7_HUMAN	UPI000013DBC8	.	tolerated(0.29)	probably_damaging(0.973)	5/11	.	Superfamily_domains:SSF49562,PIRSF_domain:PIRSF036931,SMART_domains:SM00239,Pfam_domain:PF00168,Gene3D:2.60.40.150,hmmpanther:PTHR10024:SF204,hmmpanther:PTHR10024,PROSITE_profiles:PS50004	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGATCCCGC	.	5	ESCA
CLDN6	0	.	GRCh37	16	3065618	3065618	+	Silent	SNP	G	G	A	rs144316528	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405C>T	p.%3D	p.P135P	ENST00000396925	3/3	73	67	6	68	68	0	CLDN6,synonymous_variant,p.%3D,ENST00000396925,;CLDN6,synonymous_variant,p.%3D,ENST00000328796,;CLDN6,intron_variant,,ENST00000572154,;TNFRSF12A,upstream_gene_variant,,ENST00000341627,;TNFRSF12A,upstream_gene_variant,,ENST00000326577,;TNFRSF12A,upstream_gene_variant,,ENST00000575124,;TNFRSF12A,upstream_gene_variant,,ENST00000573001,;CLDN9,downstream_gene_variant,,ENST00000445369,;TNFRSF12A,upstream_gene_variant,,ENST00000575836,;TNFRSF12A,upstream_gene_variant,,ENST00000574699,;TNFRSF12A,upstream_gene_variant,,ENST00000571351,;	A	ENSG00000184697	ENST00000396925	Transcript	synonymous_variant	834	405	135	P	ccC/ccT	rs144316528	.	.	-1	CLDN6	HGNC	2048	protein_coding	YES	CCDS10488.1	ENSP00000380131	CLD6_HUMAN	.	UPI00000359F8	.	.	.	3/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF41,Pfam_domain:PF00822,Prints_domain:PR01077	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	A:0.0007	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CACACGGGGAT	byFrequency|byCluster|by1000G	3	ESCA
CREBBP	0	.	GRCh37	16	3788617	3788617	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4337G>T	p.Arg1446Leu	p.R1446L	ENST00000262367	26/31	126	83	42	81	81	0	CREBBP,missense_variant,p.Arg1408Leu,ENST00000382070,;CREBBP,missense_variant,p.Arg1446Leu,ENST00000262367,;CREBBP,downstream_gene_variant,,ENST00000573517,;CREBBP,downstream_gene_variant,,ENST00000570939,;CREBBP,intron_variant,,ENST00000576720,;CREBBP,intron_variant,,ENST00000574740,;CREBBP,upstream_gene_variant,,ENST00000571763,;CREBBP,downstream_gene_variant,,ENST00000572569,;	A	ENSG00000005339	ENST00000262367	Transcript	missense_variant	5147	4337	1446	R/L	cGc/cTc	COSM88738,COSM88748	.	.	-1	CREBBP	HGNC	2348	protein_coding	YES	CCDS10509.1	ENSP00000262367	CBP_HUMAN	Q75MY6_HUMAN,I3L3I5_HUMAN,B5A253_HUMAN,B5A252_HUMAN,B5A250_HUMAN,B5A246_HUMAN,B5A244_HUMAN,B5A243_HUMAN,B5A242_HUMAN,B5A240_HUMAN,B5A239_HUMAN,B5A235_HUMAN,B5A231_HUMAN,B5A227_HUMAN,B5A226_HUMAN,B5A222_HUMAN,B5A221_HUMAN,B5A219_HUMAN,B5A218_HUMAN,B5A216_HUMAN,B5A215_HUMAN,B5A214_HUMAN,B5A212_HUMAN	UPI0000000620	.	.	unknown(0)	26/31	.	hmmpanther:PTHR13808,hmmpanther:PTHR13808:SF5,Pfam_domain:PF08214	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R1446L|c.4337G>T|4,CODON|p.R1446H|c.4337G>A|8,BUFFER|p.R1446C|c.4336C>T|16,BUFFER|p.R1446G|c.4336C>G|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTGCGGAGG	.	5	ESCA
SEPT12	0	.	GRCh37	16	4827874	4827874	+	Missense_Mutation	SNP	G	G	A	rs758246500	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1001C>T	p.Ser334Phe	p.S334F	ENST00000268231	10/10	56	35	20	50	50	0	SEPT12,missense_variant,p.Ser334Phe,ENST00000268231,;SEPT12,missense_variant,p.Ser288Phe,ENST00000396693,;SEPT12,3_prime_UTR_variant,,ENST00000587603,;SEPT12,3_prime_UTR_variant,,ENST00000588241,;	A	ENSG00000140623	ENST00000268231	Transcript	missense_variant	1265	1001	334	S/F	tCc/tTc	rs758246500	.	.	-1	SEPT12	HGNC	26348	protein_coding	YES	CCDS10522.1	ENSP00000268231	SEP12_HUMAN	K7EP92_HUMAN	UPI000007422A	.	deleterious(0.01)	benign(0.169)	10/10	.	PIRSF_domain:PIRSF006698,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF66	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGGGAGGCC	.	5	ESCA
RPGRIP1L	0	.	GRCh37	16	53720465	53720465	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.656G>C	p.Arg219Thr	p.R219T	ENST00000379925	6/27	84	53	31	63	63	0	RPGRIP1L,missense_variant,p.Arg219Thr,ENST00000562230,;RPGRIP1L,missense_variant,p.Arg219Thr,ENST00000563746,;RPGRIP1L,missense_variant,p.Arg219Thr,ENST00000564374,;RPGRIP1L,missense_variant,p.Arg219Thr,ENST00000262135,;RPGRIP1L,missense_variant,p.Arg219Thr,ENST00000379925,;	G	ENSG00000103494	ENST00000379925	Transcript	missense_variant	707	656	219	R/T	aGa/aCa	.	.	.	-1	RPGRIP1L	HGNC	29168	protein_coding	YES	CCDS32447.1	ENSP00000369257	FTM_HUMAN	J3QLR9_HUMAN,I3L2P2_HUMAN,H3BPF5_HUMAN	UPI000047DAF2	.	deleterious(0)	benign(0.091)	6/27	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14240,hmmpanther:PTHR14240:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCTTTGT	.	5	ESCA
RAP1GAP2	0	.	GRCh37	17	2901588	2901588	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118C>A	p.Pro373Gln	p.P373Q	ENST00000254695	14/25	48	35	12	42	42	0	RAP1GAP2,missense_variant,p.Pro354Gln,ENST00000540393,;RAP1GAP2,missense_variant,p.Pro358Gln,ENST00000366401,;RAP1GAP2,missense_variant,p.Pro373Gln,ENST00000542807,;RAP1GAP2,missense_variant,p.Pro373Gln,ENST00000254695,;RAP1GAP2,non_coding_transcript_exon_variant,,ENST00000574515,;	A	ENSG00000132359	ENST00000254695	Transcript	missense_variant	1208	1118	373	P/Q	cCa/cAa	COSM3515752,COSM3515753	.	.	1	RAP1GAP2	HGNC	29176	protein_coding	YES	CCDS45573.1	ENSP00000254695	RPGP2_HUMAN	.	UPI0000D622A3	.	deleterious(0)	probably_damaging(1)	14/25	.	PROSITE_profiles:PS50085,hmmpanther:PTHR15711:SF17,hmmpanther:PTHR15711,Pfam_domain:PF02145,Superfamily_domains:0043732	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCCCAGACA	.	5	ESCA
ZNF207	0	.	GRCh37	17	30697191	30697191	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*413G>A	.	.	ENST00000394670	12/12	57	32	24	51	51	0	ZNF207,3_prime_UTR_variant,,ENST00000341711,;ZNF207,3_prime_UTR_variant,,ENST00000394670,;ZNF207,3_prime_UTR_variant,,ENST00000321233,;ZNF207,3_prime_UTR_variant,,ENST00000394673,;ZNF207,intron_variant,,ENST00000577908,;ZNF207,downstream_gene_variant,,ENST00000394679,;ZNF207,downstream_gene_variant,,ENST00000342555,;ZNF207,upstream_gene_variant,,ENST00000584416,;ZNF207,intron_variant,,ENST00000579810,;ZNF207,intron_variant,,ENST00000581531,;ZNF207,downstream_gene_variant,,ENST00000579416,;ZNF207,downstream_gene_variant,,ENST00000582705,;ZNF207,downstream_gene_variant,,ENST00000584696,;	A	ENSG00000010244	ENST00000394670	Transcript	3_prime_UTR_variant	2067	.	.	.	.	.	.	.	1	ZNF207	HGNC	12998	protein_coding	YES	CCDS42294.1	ENSP00000378165	ZN207_HUMAN	Q8N395_HUMAN,J3QS27_HUMAN,J3KTL1_HUMAN,J3KRW6_HUMAN,J3KRB6_HUMAN,H0Y3M2_HUMAN	UPI000020164D	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTGGTGAG	.	5	ESCA
NPEPPS	0	.	GRCh37	17	45668212	45668212	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1225G>A	p.Glu409Lys	p.E409K	ENST00000322157	10/23	210	185	25	183	183	0	NPEPPS,missense_variant,p.Glu106Lys,ENST00000527360,;NPEPPS,missense_variant,p.Glu405Lys,ENST00000530173,;NPEPPS,missense_variant,p.Glu92Lys,ENST00000527964,;NPEPPS,missense_variant,p.Glu409Lys,ENST00000322157,;NPEPPS,missense_variant,p.Glu329Lys,ENST00000544660,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000525037,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000534814,;NPEPPS,missense_variant,p.Glu92Lys,ENST00000530514,;NPEPPS,3_prime_UTR_variant,,ENST00000527298,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000602788,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000525021,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000533538,;NPEPPS,downstream_gene_variant,,ENST00000527824,;NPEPPS,downstream_gene_variant,,ENST00000525401,;NPEPPS,upstream_gene_variant,,ENST00000529602,;NPEPPS,downstream_gene_variant,,ENST00000534727,;	A	ENSG00000141279	ENST00000322157	Transcript	missense_variant	1462	1225	409	E/K	Gag/Aag	.	.	.	1	NPEPPS	HGNC	7900	protein_coding	YES	CCDS45721.1	ENSP00000320324	PSA_HUMAN	E9PJ74_HUMAN,B7Z1H4_HUMAN	UPI0000140D51	.	tolerated(0.17)	benign(0.259)	10/23	.	hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF163,Gene3D:1.10.390.10,Pfam_domain:PF01433,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCAGGAGCTT	.	4	ESCA
SPOP	0	.	GRCh37	17	47676787	47676787	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*953G>C	.	.	ENST00000393331	12/12	68	51	17	45	45	0	SPOP,3_prime_UTR_variant,,ENST00000393331,;SPOP,3_prime_UTR_variant,,ENST00000393328,;SPOP,3_prime_UTR_variant,,ENST00000347630,;SPOP,downstream_gene_variant,,ENST00000503676,;SPOP,downstream_gene_variant,,ENST00000504102,;SPOP,downstream_gene_variant,,ENST00000507551,;SPOP,downstream_gene_variant,,ENST00000577134,;SPOP,downstream_gene_variant,,ENST00000572686,;	G	ENSG00000121067	ENST00000393331	Transcript	3_prime_UTR_variant	2549	.	.	.	.	.	.	.	-1	SPOP	HGNC	11254	protein_coding	YES	CCDS11551.1	ENSP00000377004	SPOP_HUMAN	D6RIS7_HUMAN,D6RGZ4_HUMAN,D6RFL7_HUMAN,D6RDV6_HUMAN,D6RDG8_HUMAN,D6RD94_HUMAN,D6RBH6_HUMAN,D6RA79_HUMAN,B4DUE7_HUMAN,B4DEE4_HUMAN	UPI0000003F5C	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAATCTGGGC	.	5	ESCA
hsa-mir-6080	0	.	GRCh37	17	62777687	62777687	+	RNA	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.187G>T	.	.	ENST00000400873	2/13	28	11	16	12	12	0	hsa-mir-6080,non_coding_transcript_exon_variant,,ENST00000579125,;hsa-mir-6080,non_coding_transcript_exon_variant,,ENST00000578492,;PLEKHM1P,non_coding_transcript_exon_variant,,ENST00000578036,;hsa-mir-6080,non_coding_transcript_exon_variant,,ENST00000400873,;PLEKHM1P,downstream_gene_variant,,ENST00000582986,;RP11-927P21.4,upstream_gene_variant,,ENST00000583567,;PLEKHM1P,downstream_gene_variant,,ENST00000582201,;	A	ENSG00000215769	ENST00000400873	Transcript	non_coding_transcript_exon_variant	187	.	.	.	.	.	.	.	-1	hsa-mir-6080	miRBase	.	processed_transcript	YES	.	.	.	.	.	.	.	.	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAGGCACCGG	.	5	ESCA
GNA13	0	.	GRCh37	17	63007616	63007616	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2759G>A	.	.	ENST00000439174	4/4	92	64	28	65	65	0	GNA13,3_prime_UTR_variant,,ENST00000439174,;GNA13,downstream_gene_variant,,ENST00000541118,;	T	ENSG00000120063	ENST00000439174	Transcript	3_prime_UTR_variant	4139	.	.	.	.	.	.	.	-1	GNA13	HGNC	4381	protein_coding	YES	CCDS11661.1	ENSP00000400717	GNA13_HUMAN	F5H1G8_HUMAN	UPI0000073EBA	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTACTCAGA	.	5	ESCA
SLC16A6	0	.	GRCh37	17	66265162	66265162	+	3'UTR	SNP	G	G	A	rs7225936	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*75C>T	.	.	ENST00000327268	7/7	26	14	11	25	24	1	SLC16A6,3_prime_UTR_variant,,ENST00000580666,;SLC16A6,3_prime_UTR_variant,,ENST00000327268,;ARSG,intron_variant,,ENST00000448504,;SLC16A6,downstream_gene_variant,,ENST00000583477,;ARSG,intron_variant,,ENST00000578726,;	A	ENSG00000108932	ENST00000327268	Transcript	3_prime_UTR_variant	1812	.	.	.	.	rs7225936	.	.	-1	SLC16A6	HGNC	10927	protein_coding	YES	CCDS11675.1	ENSP00000319991	MOT7_HUMAN	J3KS02_HUMAN,A1L174_HUMAN	UPI00001AA3B9	.	.	.	7/7	.	.	A:0.0264	A:0.0393	A:0.0562	.	A:0.0228	A:0.004	A:0.0143	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	CCTCTGCCTCC	byFrequency|byCluster|by2Hit2Allele|by1000G	2	ESCA
COG1	0	.	GRCh37	17	71189190	71189190	+	5'UTR	SNP	G	G	A	rs566018587	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-19G>A	.	.	ENST00000299886	1/14	20	9	11	16	16	0	COG1,5_prime_UTR_variant,,ENST00000299886,;COG1,upstream_gene_variant,,ENST00000438720,;RP11-143K11.5,intron_variant,,ENST00000580671,;COG1,upstream_gene_variant,,ENST00000582587,;	A	ENSG00000166685	ENST00000299886	Transcript	5_prime_UTR_variant	62	.	.	.	.	rs566018587	.	.	1	COG1	HGNC	6545	protein_coding	YES	CCDS11692.1	ENSP00000299886	COG1_HUMAN	J3KSY3_HUMAN	UPI0000127E34	.	.	.	1/14	.	.	C:0.0016	C:0	C:0	.	C:0	C:0	C:0.0082	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCGCCGGGGGC	byFrequency|byCluster|by1000G	4	ESCA
TP53	0	.	GRCh37	17	7578479	7578479	+	Missense_Mutation	SNP	G	G	A	rs28934874	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	5/11	34	5	29	15	15	0	TP53,missense_variant,p.Pro151Ser,ENST00000508793,;TP53,missense_variant,p.Pro151Ser,ENST00000413465,;TP53,missense_variant,p.Pro151Ser,ENST00000420246,;TP53,missense_variant,p.Pro151Ser,ENST00000269305,;TP53,missense_variant,p.Pro19Ser,ENST00000509690,;TP53,missense_variant,p.Pro151Ser,ENST00000359597,;TP53,missense_variant,p.Pro58Ser,ENST00000514944,;TP53,missense_variant,p.Pro151Ser,ENST00000445888,;TP53,missense_variant,p.Pro151Ser,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	missense_variant	641	451	151	P/S	Ccc/Tcc	CM012662,rs28934874,CM941326,TP53_g.12439C>T,TP53_g.12439del,TP53_g.12439C>A,TP53_g.12439C>G,COSM44944,COSM10905,COSM43911,COSM43969,COSM121046,COSM984959,COSM99682,COSM984961,COSM99679,COSM121047,COSM984963,COSM99680,COSM121049,COSM3717669,COSM4070056,COSM3378358,COSM3717668,COSM1640859,COSM4070055,COSM121048,COSM984962,COSM99681	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.01)	possibly_damaging(0.876)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	likely_pathogenic,pathogenic	0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	25105660	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P58S|c.172C>T|6,SITE|p.P151S|c.451C>T|68,SITE|p.P151S|c.451C>T|6,SITE|p.P151S|c.451C>T|3,SITE|p.P151S|c.451C>T|4,SITE|p.P19S|c.55C>T|6,CODON|p.0?|c.1_1182del1182|6,CODON|p.T150fs*16|c.448_460del13|4,CODON|p.P151P|c.453C>T|8,CODON|p.P151P|c.453C>G|4,CODON|p.P152fs*18|c.451delC|9,CODON|p.P58H|c.173C>A|6,CODON|p.P151R|c.452C>G|8,CODON|p.P151H|c.452C>A|29,CODON|p.P151H|c.452C>A|6,CODON|p.P19R|c.56C>G|3,CODON|p.P151L|c.452C>T|7,CODON|p.P151H|c.452C>A|6,CODON|p.P19H|c.56C>A|6,BUFFER|p.P152fs*14|c.454_466del13|5,BUFFER|p.G154I|c.460_461GG>AT|3,BUFFER|p.G154G|c.462C>T|9,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G61V|c.182G>T|3,BUFFER|p.G22V|c.65G>T|4,BUFFER|p.G154D|c.461G>A|6,BUFFER|p.G154V|c.461G>T|38,BUFFER|p.G154S|c.460G>A|9,BUFFER|p.P153P|c.459C>T|6,BUFFER|p.P153L|c.458C>T|6,BUFFER|p.P153T|c.457C>A|3,BUFFER|p.P153S|c.457C>T|8,BUFFER|p.P153fs*28|c.456_457insN|4,BUFFER|p.P153fs*28|c.455_456insN|3,BUFFER|p.P152fs*18|c.455delC|6,BUFFER|p.P152P|c.456G>A|4,BUFFER|p.P152Q|c.455C>A|5,BUFFER|p.P152L|c.455C>T|70,BUFFER|p.P20L|c.59C>T|10,BUFFER|p.P152L|c.455C>T|10,BUFFER|p.P152R|c.455C>G|6,BUFFER|p.P59L|c.176C>T|10,BUFFER|p.P152L|c.455C>T|10,BUFFER|p.P152L|c.455C>T|4,BUFFER|p.P152L|c.455C>T|3,BUFFER|p.P152fs*18|c.454delC|3,BUFFER|p.P152fs*29|c.453_454insN|5,BUFFER|p.P152T|c.454C>A|7,BUFFER|p.P152S|c.454C>T|24,BUFFER|p.P151T|c.451C>A|3,BUFFER|p.P19T|c.55C>A|3,BUFFER|p.P151T|c.451C>A|16,BUFFER|p.P151A|c.451C>G|14,BUFFER|p.P151A|c.451C>G|3,BUFFER|p.P58T|c.172C>A|3,BUFFER|p.P151A|c.451C>G|7,BUFFER|p.P151A|c.451C>G|7,BUFFER|p.P151T|c.451C>A|3,BUFFER|p.P19A|c.55C>G|7,BUFFER|p.P58A|c.172C>G|7,BUFFER|p.P151A|c.451C>G|3,BUFFER|p.P151fs*30|c.450_451insN|5,BUFFER|p.T150I|c.449C>T|4,BUFFER|p.S149S|c.447C>T|6,BUFFER|p.S149F|c.446C>T|5,BUFFER|p.S149fs*32|c.444_445insN|5,BUFFER|p.S149P|c.445T>C|4,BUFFER|p.D148N|c.442G>A|5,BUFFER|p.V147V|c.441T>G|3,BUFFER|p.V147G|c.440T>G|8,BUFFER|p.V147D|c.440T>A|3,BUFFER|p.V147fs*23|c.439delG|7	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGGGTGTGG	byCluster	5	ESCA
HGS	0	.	GRCh37	17	79660958	79660958	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.899C>T	p.Ser300Leu	p.S300L	ENST00000329138	11/22	39	29	10	28	28	0	HGS,missense_variant,p.Ser20Leu,ENST00000571237,;HGS,missense_variant,p.Ser300Leu,ENST00000329138,;HGS,downstream_gene_variant,,ENST00000572392,;HGS,non_coding_transcript_exon_variant,,ENST00000575058,;HGS,upstream_gene_variant,,ENST00000573949,;HGS,downstream_gene_variant,,ENST00000576498,;HGS,upstream_gene_variant,,ENST00000571885,;HGS,downstream_gene_variant,,ENST00000573080,;HGS,downstream_gene_variant,,ENST00000576087,;HGS,downstream_gene_variant,,ENST00000576393,;HGS,upstream_gene_variant,,ENST00000571647,;HGS,upstream_gene_variant,,ENST00000570355,;	T	ENSG00000185359	ENST00000329138	Transcript	missense_variant	1034	899	300	S/L	tCa/tTa	.	.	.	1	HGS	HGNC	4897	protein_coding	YES	CCDS11784.1	ENSP00000331201	HGS_HUMAN	I3L2H4_HUMAN,I3L165_HUMAN	UPI000004493D	.	deleterious(0)	probably_damaging(0.916)	11/22	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13856,hmmpanther:PTHR13856:SF79,PIRSF_domain:PIRSF036956	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAGCGC	.	5	ESCA
NARF	0	.	GRCh37	17	80445912	80445912	+	Missense_Mutation	SNP	A	A	T	rs768232297	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1250A>T	p.His417Leu	p.H417L	ENST00000309794	11/11	29	24	5	23	23	0	NARF,missense_variant,p.His463Leu,ENST00000457415,;NARF,missense_variant,p.His358Leu,ENST00000390006,;NARF,missense_variant,p.His417Leu,ENST00000309794,;NARF,missense_variant,p.His369Leu,ENST00000345415,;NARF,missense_variant,p.His159Leu,ENST00000584513,;NARF,downstream_gene_variant,,ENST00000412079,;NARF,downstream_gene_variant,,ENST00000577432,;NARF-IT1,downstream_gene_variant,,ENST00000584012,;NARF,3_prime_UTR_variant,,ENST00000374611,;NARF,3_prime_UTR_variant,,ENST00000582907,;NARF,non_coding_transcript_exon_variant,,ENST00000578820,;NARF,non_coding_transcript_exon_variant,,ENST00000577812,;NARF,non_coding_transcript_exon_variant,,ENST00000584445,;NARF,intron_variant,,ENST00000584965,;NARF,intron_variant,,ENST00000583908,;NARF,downstream_gene_variant,,ENST00000581202,;NARF,downstream_gene_variant,,ENST00000581795,;	T	ENSG00000141562	ENST00000309794	Transcript	missense_variant	1448	1250	417	H/L	cAc/cTc	rs768232297	.	.	1	NARF	HGNC	29916	protein_coding	YES	CCDS32777.1	ENSP00000309899	NARF_HUMAN	J3QSD9_HUMAN,J3QRB0_HUMAN,J3QL28_HUMAN,J3KS03_HUMAN,B5KGZ1_HUMAN	UPI0000073D0C	.	tolerated(0.69)	benign(0.155)	11/11	.	Superfamily_domains:SSF53920,SMART_domains:SM00902,Gene3D:1hfeS00,Pfam_domain:PF02256,hmmpanther:PTHR11615:SF124,hmmpanther:PTHR11615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACACGTGC	.	5	ESCA
TUBB6	0	.	GRCh37	18	12325138	12325138	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.350T>G	p.Leu117Arg	p.L117R	ENST00000317702	4/4	50	39	11	37	37	0	TUBB6,missense_variant,p.Leu45Arg,ENST00000591463,;TUBB6,missense_variant,p.Leu80Arg,ENST00000590103,;TUBB6,missense_variant,p.Leu117Arg,ENST00000590693,;TUBB6,missense_variant,p.Leu117Arg,ENST00000317702,;TUBB6,3_prime_UTR_variant,,ENST00000586653,;TUBB6,intron_variant,,ENST00000590967,;TUBB6,intron_variant,,ENST00000591208,;TUBB6,intron_variant,,ENST00000591909,;TUBB6,intron_variant,,ENST00000586691,;TUBB6,downstream_gene_variant,,ENST00000592683,;AFG3L2,downstream_gene_variant,,ENST00000269143,;TUBB6,3_prime_UTR_variant,,ENST00000586810,;TUBB6,3_prime_UTR_variant,,ENST00000590388,;TUBB6,non_coding_transcript_exon_variant,,ENST00000417736,;	G	ENSG00000176014	ENST00000317702	Transcript	missense_variant	584	350	117	L/R	cTg/cGg	.	.	.	1	TUBB6	HGNC	20776	protein_coding	YES	CCDS11858.1	ENSP00000318697	TBB6_HUMAN	K7ES63_HUMAN,K7EL29_HUMAN,B4E386_HUMAN,B3KS31_HUMAN	UPI0000072BFF	.	deleterious_low_confidence(0)	probably_damaging(1)	4/4	.	Prints_domain:PR01161,Prints_domain:PR01163,Superfamily_domains:SSF52490,SMART_domains:SM00864,Pfam_domain:PF00091,Gene3D:3.40.50.1440,hmmpanther:PTHR11588:SF88,hmmpanther:PTHR11588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGCTGGACG	.	5	ESCA
TUBB6	0	.	GRCh37	18	12325139	12325139	+	Silent	SNP	G	G	T	rs759576039	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351G>T	p.%3D	p.L117L	ENST00000317702	4/4	49	38	11	36	36	0	TUBB6,synonymous_variant,p.%3D,ENST00000591463,;TUBB6,synonymous_variant,p.%3D,ENST00000590103,;TUBB6,synonymous_variant,p.%3D,ENST00000590693,;TUBB6,synonymous_variant,p.%3D,ENST00000317702,;TUBB6,3_prime_UTR_variant,,ENST00000586653,;TUBB6,intron_variant,,ENST00000590967,;TUBB6,intron_variant,,ENST00000591208,;TUBB6,intron_variant,,ENST00000591909,;TUBB6,intron_variant,,ENST00000586691,;TUBB6,downstream_gene_variant,,ENST00000592683,;AFG3L2,downstream_gene_variant,,ENST00000269143,;TUBB6,3_prime_UTR_variant,,ENST00000586810,;TUBB6,3_prime_UTR_variant,,ENST00000590388,;TUBB6,non_coding_transcript_exon_variant,,ENST00000417736,;	T	ENSG00000176014	ENST00000317702	Transcript	synonymous_variant	585	351	117	L	ctG/ctT	rs759576039	.	.	1	TUBB6	HGNC	20776	protein_coding	YES	CCDS11858.1	ENSP00000318697	TBB6_HUMAN	K7ES63_HUMAN,K7EL29_HUMAN,B4E386_HUMAN,B3KS31_HUMAN	UPI0000072BFF	.	.	.	4/4	.	Prints_domain:PR01161,Prints_domain:PR01163,Superfamily_domains:SSF52490,SMART_domains:SM00864,Pfam_domain:PF00091,Gene3D:3.40.50.1440,hmmpanther:PTHR11588:SF88,hmmpanther:PTHR11588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTGGACGT	.	5	ESCA
SMAD4	0	.	GRCh37	18	48603032	48603032	+	Nonsense_Mutation	SNP	C	C	T	rs377767360	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	11/12	63	29	33	69	69	0	SMAD4,stop_gained,p.Arg445Ter,ENST00000342988,;SMAD4,stop_gained,p.Arg445Ter,ENST00000398417,;SMAD4,stop_gained,p.Arg34Ter,ENST00000593223,;SMAD4,stop_gained,p.Arg349Ter,ENST00000588745,;SMAD4,upstream_gene_variant,,ENST00000586253,;SMAD4,3_prime_UTR_variant,,ENST00000592186,;SMAD4,non_coding_transcript_exon_variant,,ENST00000590499,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;	T	ENSG00000141646	ENST00000342988	Transcript	stop_gained	1871	1333	445	R/*	Cga/Tga	rs377767360,CM000742,COSM1389083,COSM14096	.	.	1	SMAD4	HGNC	6770	protein_coding	YES	CCDS11950.1	ENSP00000341551	SMAD4_HUMAN	Q9BYG6_HUMAN,K7ENG8_HUMAN,K7ENG1_HUMAN,K7EL18_HUMAN,K7EL15_HUMAN,K7EIJ2_HUMAN	UPI0000053431	.	.	.	11/12	.	PROSITE_profiles:PS51076,hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF33,Pfam_domain:PF03166,Gene3D:2.60.200.10,SMART_domains:SM00524,Superfamily_domains:SSF49879	.	.	.	.	.	.	.	.	.	pathogenic	0,0,1,1	10764709	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R445*|c.1333C>T|21,CODON|p.0?|c.1_1659del1659|28,BUFFER|p.R441R|c.1323T>C|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATCGACAG	byCluster	5	ESCA
PTPRM	0	.	GRCh37	18	8376571	8376571	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3438G>A	p.%3D	p.R1146R	ENST00000580170	26/33	73	59	13	46	46	0	PTPRM,synonymous_variant,p.%3D,ENST00000332175,;PTPRM,synonymous_variant,p.%3D,ENST00000444013,;PTPRM,synonymous_variant,p.%3D,ENST00000583153,;PTPRM,synonymous_variant,p.%3D,ENST00000400053,;PTPRM,synonymous_variant,p.%3D,ENST00000400060,;PTPRM,synonymous_variant,p.%3D,ENST00000580170,;PTPRM,non_coding_transcript_exon_variant,,ENST00000577827,;	A	ENSG00000173482	ENST00000580170	Transcript	synonymous_variant	4475	3438	1146	R	cgG/cgA	.	.	.	1	PTPRM	HGNC	9675	protein_coding	YES	CCDS58613.1	ENSP00000463325	PTPRM_HUMAN	Q49AC9_HUMAN	UPI00015CFC03	.	.	.	26/33	.	Prints_domain:PR00700,Superfamily_domains:SSF52799,SMART_domains:SM00194,SMART_domains:SM00404,Gene3D:3.90.190.10,Pfam_domain:PF00102,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACGGAGGGT	.	5	ESCA
KRI1	0	.	GRCh37	19	10673510	10673510	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.296C>T	p.Ser99Leu	p.S99L	ENST00000312962	4/19	56	43	13	43	43	0	KRI1,missense_variant,p.Ser37Leu,ENST00000543682,;KRI1,missense_variant,p.Ser99Leu,ENST00000312962,;KRI1,missense_variant,p.Ser95Leu,ENST00000361821,;KRI1,missense_variant,p.Ser90Leu,ENST00000539027,;CDKN2D,downstream_gene_variant,,ENST00000335766,;CDKN2D,downstream_gene_variant,,ENST00000393599,;KRI1,intron_variant,,ENST00000537964,;KRI1,3_prime_UTR_variant,,ENST00000432197,;KRI1,3_prime_UTR_variant,,ENST00000546063,;KRI1,non_coding_transcript_exon_variant,,ENST00000536689,;KRI1,non_coding_transcript_exon_variant,,ENST00000478863,;KRI1,intron_variant,,ENST00000544397,;KRI1,upstream_gene_variant,,ENST00000543842,;KRI1,upstream_gene_variant,,ENST00000536714,;KRI1,upstream_gene_variant,,ENST00000537433,;KRI1,upstream_gene_variant,,ENST00000537363,;	A	ENSG00000129347	ENST00000312962	Transcript	missense_variant	316	296	99	S/L	tCg/tTg	.	.	.	-1	KRI1	HGNC	25769	protein_coding	YES	CCDS12242.1	ENSP00000320917	KRI1_HUMAN	.	UPI0000246DCC	.	tolerated(0.14)	benign(0.007)	4/19	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14490	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACGATGCT	.	5	ESCA
NOTCH3	0	.	GRCh37	19	15292532	15292532	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2647C>T	p.Arg883Ter	p.R883*	ENST00000263388	17/33	161	108	53	131	131	0	NOTCH3,stop_gained,p.Arg883Ter,ENST00000263388,;NOTCH3,stop_gained,p.Arg830Ter,ENST00000601011,;NOTCH3,upstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595045,;	A	ENSG00000074181	ENST00000263388	Transcript	stop_gained	2723	2647	883	R/*	Cga/Tga	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	.	.	17/33	.	Superfamily_domains:SSF57184,SMART_domains:SM00181,PIRSF_domain:PIRSF002279,SMART_domains:SM00179,Gene3D:2gy5A03,Pfam_domain:PF00008,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCGTGGGC	.	5	ESCA
ATP13A1	0	.	GRCh37	19	19760397	19760397	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2611G>T	p.Ala871Ser	p.A871S	ENST00000357324	19/26	41	29	12	29	29	0	ATP13A1,missense_variant,p.Ala753Ser,ENST00000291503,;ATP13A1,missense_variant,p.Ala871Ser,ENST00000357324,;ATP13A1,downstream_gene_variant,,ENST00000496082,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000469641,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000497556,;ATP13A1,non_coding_transcript_exon_variant,,ENST00000473243,;ATP13A1,downstream_gene_variant,,ENST00000497762,;ATP13A1,upstream_gene_variant,,ENST00000467160,;ATP13A1,downstream_gene_variant,,ENST00000491221,;ATP13A1,downstream_gene_variant,,ENST00000497156,;ATP13A1,downstream_gene_variant,,ENST00000471063,;	A	ENSG00000105726	ENST00000357324	Transcript	missense_variant	2638	2611	871	A/S	Gcc/Tcc	.	.	.	-1	ATP13A1	HGNC	24215	protein_coding	YES	CCDS32970.2	ENSP00000349877	AT131_HUMAN	Q8N3E5_HUMAN	UPI0000126647	.	deleterious(0)	probably_damaging(1)	19/26	.	Prints_domain:PR00119,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01494,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01657,Pfam_domain:PF12710,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF82	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCGCCCA	.	5	ESCA
ZNF493	0	.	GRCh37	19	21606488	21606488	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1027C>T	p.His343Tyr	p.H343Y	ENST00000392288	4/4	91	56	35	87	87	0	ZNF493,missense_variant,p.His215Tyr,ENST00000355504,;ZNF493,missense_variant,p.His343Tyr,ENST00000392288,;ZNF493,downstream_gene_variant,,ENST00000596302,;CTD-2561J22.3,intron_variant,,ENST00000600810,;ZNF493,downstream_gene_variant,,ENST00000598152,;	T	ENSG00000196268	ENST00000392288	Transcript	missense_variant	1136	1027	343	H/Y	Cac/Tac	.	.	.	1	ZNF493	HGNC	23708	protein_coding	YES	CCDS42536.1	ENSP00000376110	ZN493_HUMAN	.	UPI000022ABBF	.	deleterious(0)	unknown(0)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF247,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATTCACACT	.	5	ESCA
KMT2B	0	.	GRCh37	19	36212415	36212415	+	Silent	SNP	C	C	T	rs368953229	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2166C>T	p.%3D	p.H722H	ENST00000222270	3/37	113	101	12	121	121	0	KMT2B,missense_variant,p.Thr578Met,ENST00000341701,;KMT2B,synonymous_variant,p.%3D,ENST00000222270,;KMT2B,synonymous_variant,p.%3D,ENST00000420124,;ZBTB32,downstream_gene_variant,,ENST00000392197,;ZBTB32,downstream_gene_variant,,ENST00000262630,;KMT2B,non_coding_transcript_exon_variant,,ENST00000606995,;KMT2B,non_coding_transcript_exon_variant,,ENST00000607650,;ZBTB32,downstream_gene_variant,,ENST00000481182,;	T	ENSG00000272333	ENST00000222270	Transcript	synonymous_variant	2166	2166	722	H	caC/caT	rs368953229	.	.	1	KMT2B	Uniprot_gn	15840	protein_coding	YES	CCDS46055.1	ENSP00000222270	KMT2B_HUMAN	.	UPI00001376B5	.	.	.	3/37	.	hmmpanther:PTHR22884:SF280,hmmpanther:PTHR22884,PIRSF_domain:PIRSF010354	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCACGGGGC	.	4	ESCA
EEF2	0	.	GRCh37	19	3980008	3980008	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1403A>G	p.Asn468Ser	p.N468S	ENST00000309311	10/15	37	28	8	12	12	0	EEF2,missense_variant,p.Asn468Ser,ENST00000309311,;EEF2,upstream_gene_variant,,ENST00000600794,;SNORD37,downstream_gene_variant,,ENST00000384048,;EEF2,downstream_gene_variant,,ENST00000600720,;EEF2,downstream_gene_variant,,ENST00000598436,;EEF2,downstream_gene_variant,,ENST00000598182,;EEF2,upstream_gene_variant,,ENST00000596417,;EEF2,downstream_gene_variant,,ENST00000594885,;	C	ENSG00000167658	ENST00000309311	Transcript	missense_variant	1492	1403	468	N/S	aAc/aGc	.	.	.	-1	EEF2	HGNC	3214	protein_coding	YES	CCDS12117.1	ENSP00000307940	EF2_HUMAN	Q8TA90_HUMAN,B4DMC6_HUMAN	UPI00001649F3	.	deleterious(0.01)	probably_damaging(0.998)	10/15	.	hmmpanther:PTHR23115:SF103,hmmpanther:PTHR23115,Gene3D:2.40.30.10,Pfam_domain:PF03144,Superfamily_domains:SSF50447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATGTTCCCA	.	5	ESCA
KLK5	0	.	GRCh37	19	51451943	51451943	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.679G>A	p.Asp227Asn	p.D227N	ENST00000336334	5/6	28	18	10	21	21	0	KLK5,missense_variant,p.Asp227Asn,ENST00000391809,;KLK5,missense_variant,p.Asp227Asn,ENST00000336334,;KLK5,missense_variant,p.Asp227Asn,ENST00000593428,;KLK5,downstream_gene_variant,,ENST00000594846,;CTB-147C22.8,upstream_gene_variant,,ENST00000594939,;CTB-147C22.8,upstream_gene_variant,,ENST00000601506,;KLK5,non_coding_transcript_exon_variant,,ENST00000595585,;	T	ENSG00000167754	ENST00000336334	Transcript	missense_variant	1032	679	227	D/N	Gac/Aac	.	.	.	-1	KLK5	HGNC	6366	protein_coding	YES	CCDS12810.1	ENSP00000337733	KLK5_HUMAN	M0QXX2_HUMAN	UPI000013E718	.	tolerated(0.53)	benign(0.154)	5/6	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24275:SF51,hmmpanther:PTHR24275,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGTCATCTA	.	5	ESCA
PPP2R1A	0	.	GRCh37	19	52724234	52724234	+	Missense_Mutation	SNP	T	T	C	rs746735616	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1366T>C	p.Tyr456His	p.Y456H	ENST00000322088	12/15	36	21	14	33	33	0	PPP2R1A,missense_variant,p.Tyr277His,ENST00000462990,;PPP2R1A,missense_variant,p.Tyr401His,ENST00000444322,;PPP2R1A,missense_variant,p.Tyr456His,ENST00000322088,;PPP2R1A,downstream_gene_variant,,ENST00000454220,;PPP2R1A,upstream_gene_variant,,ENST00000391791,;CTD-2525I3.3,downstream_gene_variant,,ENST00000593857,;PPP2R1A,downstream_gene_variant,,ENST00000473820,;	C	ENSG00000105568	ENST00000322088	Transcript	missense_variant	1424	1366	456	Y/H	Tat/Cat	rs746735616	.	.	1	PPP2R1A	HGNC	9302	protein_coding	YES	CCDS12849.1	ENSP00000324804	2AAA_HUMAN	B4DDF7_HUMAN,B3KQV6_HUMAN,A8K7B7_HUMAN	UPI000006EB9C	.	tolerated(0.08)	possibly_damaging(0.787)	12/15	.	hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Pfam_domain:PF13646,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTATATGCC	byFrequency	5	ESCA
ZNF766	0	.	GRCh37	19	52794236	52794236	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1192C>A	p.Leu398Ile	p.L398I	ENST00000439461	4/4	79	57	22	60	60	0	ZNF766,missense_variant,p.Leu413Ile,ENST00000359102,;ZNF766,missense_variant,p.Leu413Ile,ENST00000593612,;ZNF766,missense_variant,p.Leu398Ile,ENST00000439461,;ZNF766,3_prime_UTR_variant,,ENST00000599581,;ZNF766,downstream_gene_variant,,ENST00000593703,;ZNF766,downstream_gene_variant,,ENST00000600821,;ZNF766,downstream_gene_variant,,ENST00000595149,;ZNF766,downstream_gene_variant,,ENST00000595000,;CTD-2525I3.5,intron_variant,,ENST00000594865,;	A	ENSG00000196214	ENST00000439461	Transcript	missense_variant	1235	1192	398	L/I	Ctt/Att	.	.	.	1	ZNF766	HGNC	28063	protein_coding	YES	CCDS46163.1	ENSP00000409652	ZN766_HUMAN	M0R1P9_HUMAN,M0R139_HUMAN,M0QXI4_HUMAN	UPI0000202AF7	.	deleterious(0.01)	probably_damaging(0.994)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF5,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATCTTGCA	.	5	ESCA
CNOT3	0	.	GRCh37	19	54646887	54646887	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.58G>A	p.Glu20Lys	p.E20K	ENST00000406403	2/17	17	14	3	15	15	0	CNOT3,missense_variant,p.Glu20Lys,ENST00000406403,;CNOT3,missense_variant,p.Glu20Lys,ENST00000221232,;CNOT3,5_prime_UTR_variant,,ENST00000358389,;CNOT3,upstream_gene_variant,,ENST00000440571,;CNOT3,non_coding_transcript_exon_variant,,ENST00000482247,;CNOT3,upstream_gene_variant,,ENST00000447684,;	A	ENSG00000088038	ENST00000406403	Transcript	missense_variant	1661	58	20	E/K	Gag/Aag	COSM96799	.	.	1	CNOT3	HGNC	7879	protein_coding	YES	CCDS12880.1	ENSP00000383954	CNOT3_HUMAN	.	UPI00000729AD	.	deleterious(0)	probably_damaging(0.994)	2/17	.	PIRSF_domain:PIRSF005290,Pfam_domain:PF04065,hmmpanther:PTHR23326,hmmpanther:PTHR23326:SF1	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.E20K|c.58G>A|7	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCCGAGGGC	.	5	ESCA
EPN1	0	.	GRCh37	19	56200328	56200328	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.904G>A	p.Ala302Thr	p.A302T	ENST00000411543	5/11	28	19	9	24	24	0	EPN1,missense_variant,p.Ala302Thr,ENST00000411543,;EPN1,missense_variant,p.Ala191Thr,ENST00000270460,;EPN1,missense_variant,p.Ala191Thr,ENST00000085079,;EPN1,upstream_gene_variant,,ENST00000589704,;AC010525.2,downstream_gene_variant,,ENST00000390145,;EPN1,non_coding_transcript_exon_variant,,ENST00000591743,;EPN1,upstream_gene_variant,,ENST00000586194,;	A	ENSG00000063245	ENST00000411543	Transcript	missense_variant	1451	904	302	A/T	Gcc/Acc	.	.	.	1	EPN1	HGNC	21604	protein_coding	YES	CCDS46198.1	ENSP00000406209	EPN1_HUMAN	.	UPI000059D7B7	.	deleterious(0)	unknown(0)	5/11	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50330,hmmpanther:PTHR12276:SF48,hmmpanther:PTHR12276,SMART_domains:SM00726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGGCCCTG	.	5	ESCA
AC003002.6	0	.	GRCh37	19	57924970	57924970	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.52-4310T>C	.	.	ENST00000596400	.	42	26	16	31	31	0	AC003002.6,missense_variant,p.Ile62Thr,ENST00000596617,;ZNF17,5_prime_UTR_variant,,ENST00000307658,;ZNF17,5_prime_UTR_variant,,ENST00000597350,;AC003002.6,intron_variant,,ENST00000596400,;AC004076.7,intron_variant,,ENST00000597410,;ZNF17,intron_variant,,ENST00000601808,;ZNF17,non_coding_transcript_exon_variant,,ENST00000595206,;ZNF17,intron_variant,,ENST00000599867,;AC003002.6,downstream_gene_variant,,ENST00000600421,;ZNF17,3_prime_UTR_variant,,ENST00000595162,;	C	ENSG00000269533	ENST00000596400	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	AC003002.6	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000472277	.	M0R233_HUMAN	UPI0002A476BC	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCATAGCAG	.	5	ESCA
PRTN3	0	.	GRCh37	19	846367	846367	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590G>A	p.Gly197Asp	p.G197D	ENST00000234347	4/5	42	22	20	48	48	0	PRTN3,missense_variant,p.Gly156Asp,ENST00000544537,;PRTN3,missense_variant,p.Gly197Asp,ENST00000234347,;ELANE,upstream_gene_variant,,ENST00000590230,;	A	ENSG00000196415	ENST00000234347	Transcript	missense_variant	636	590	197	G/D	gGc/gAc	.	.	.	1	PRTN3	HGNC	9495	protein_coding	YES	CCDS32860.1	ENSP00000234347	PRTN3_HUMAN	U3KPS2_HUMAN	UPI0000132263	.	tolerated(0.05)	probably_damaging(0.998)	4/5	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24257:SF15,hmmpanther:PTHR24257,PROSITE_patterns:PS00135,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCGGCATCT	.	5	ESCA
DPH5	0	.	GRCh37	1	101455897	101455897	+	3'UTR	DEL	A	A	-	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67delT	.	.	ENST00000370109	8/8	35	23	12	11	11	0	DPH5,3_prime_UTR_variant,,ENST00000427040,;AC093157.1,5_prime_UTR_variant,,ENST00000593496,;DPH5,3_prime_UTR_variant,,ENST00000342173,;DPH5,3_prime_UTR_variant,,ENST00000370109,;DPH5,downstream_gene_variant,,ENST00000488176,;DPH5,non_coding_transcript_exon_variant,,ENST00000488789,;DPH5,non_coding_transcript_exon_variant,,ENST00000498372,;DPH5,non_coding_transcript_exon_variant,,ENST00000481871,;DPH5,non_coding_transcript_exon_variant,,ENST00000370105,;DPH5,non_coding_transcript_exon_variant,,ENST00000477293,;DPH5,non_coding_transcript_exon_variant,,ENST00000492067,;DPH5,non_coding_transcript_exon_variant,,ENST00000466807,;DPH5,non_coding_transcript_exon_variant,,ENST00000464270,;DPH5,downstream_gene_variant,,ENST00000490732,;	-	ENSG00000117543	ENST00000370109	Transcript	3_prime_UTR_variant	1038	.	.	.	.	.	.	.	-1	DPH5	HGNC	24270	protein_coding	YES	CCDS41358.1	ENSP00000359127	DPH5_HUMAN	Q96DC6_HUMAN,B3KWP1_HUMAN	UPI000003B000	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GTGGGGATACAT	.	2	ESCA
OLFM3	0	.	GRCh37	1	102268974	102268974	+	3'UTR	SNP	T	T	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*820A>T	.	.	ENST00000370103	6/6	84	58	25	48	48	0	OLFM3,3_prime_UTR_variant,,ENST00000370103,;OLFM3,downstream_gene_variant,,ENST00000338858,;OLFM3,downstream_gene_variant,,ENST00000536598,;OLFM3,downstream_gene_variant,,ENST00000462354,;OLFM3,downstream_gene_variant,,ENST00000465523,;	A	ENSG00000118733	ENST00000370103	Transcript	3_prime_UTR_variant	2411	.	.	.	.	.	.	.	-1	OLFM3	HGNC	17990	protein_coding	YES	CCDS30781.1	ENSP00000359121	NOE3_HUMAN	.	UPI000002AF6A	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAGTTGTTG	.	5	ESCA
AADACL4	0	.	GRCh37	1	12711295	12711295	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.322T>A	p.Ser108Thr	p.S108T	ENST00000376221	2/4	106	72	33	59	59	0	AADACL4,missense_variant,p.Ser108Thr,ENST00000376221,;	A	ENSG00000204518	ENST00000376221	Transcript	missense_variant	322	322	108	S/T	Tcc/Acc	.	.	.	1	AADACL4	HGNC	32038	protein_coding	YES	CCDS30590.1	ENSP00000365395	ADCL4_HUMAN	.	UPI0000160609	.	deleterious(0.05)	possibly_damaging(0.881)	2/4	.	hmmpanther:PTHR23024,hmmpanther:PTHR23024:SF95,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF037251,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCATCCTCC	.	5	ESCA
PDE4DIP	0	.	GRCh37	1	144916732	144916732	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1623G>A	p.%3D	p.L541L	ENST00000369356	13/44	107	83	24	71	71	0	PDE4DIP,synonymous_variant,p.%3D,ENST00000479408,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369354,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369349,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369359,;PDE4DIP,synonymous_variant,p.%3D,ENST00000313431,;PDE4DIP,synonymous_variant,p.%3D,ENST00000530740,;PDE4DIP,synonymous_variant,p.%3D,ENST00000313382,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369356,;PDE4DIP,synonymous_variant,p.%3D,ENST00000529945,;PDE4DIP,synonymous_variant,p.%3D,ENST00000369351,;PDE4DIP,downstream_gene_variant,,ENST00000532801,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000467859,;PDE4DIP,upstream_gene_variant,,ENST00000533963,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000496263,;PDE4DIP,intron_variant,,ENST00000525886,;	T	ENSG00000178104	ENST00000369356	Transcript	synonymous_variant	1914	1623	541	L	ctG/ctA	.	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	MYOME_HUMAN	I1VE15_HUMAN	UPI0000458A81	.	.	.	13/44	.	hmmpanther:PTHR13895:SF2,hmmpanther:PTHR13895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCAGGAG	.	5	ESCA
SLC50A1	0	.	GRCh37	1	155110819	155110820	+	3'UTR	INS	-	-	CAG	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*64_*66dupAGC	.	.	ENST00000368404	6/6	58	32	26	49	49	0	SLC50A1,3_prime_UTR_variant,,ENST00000368401,;SLC50A1,3_prime_UTR_variant,,ENST00000484157,;SLC50A1,3_prime_UTR_variant,,ENST00000303343,;SLC50A1,3_prime_UTR_variant,,ENST00000368404,;EFNA1,downstream_gene_variant,,ENST00000368406,;EFNA1,downstream_gene_variant,,ENST00000368407,;DPM3,downstream_gene_variant,,ENST00000341298,;DPM3,downstream_gene_variant,,ENST00000368400,;DPM3,downstream_gene_variant,,ENST00000368399,;RNU7-150P,upstream_gene_variant,,ENST00000515971,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000488609,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000484027,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000479579,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000368405,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000490770,;SLC50A1,non_coding_transcript_exon_variant,,ENST00000490276,;SLC50A1,downstream_gene_variant,,ENST00000465546,;EFNA1,downstream_gene_variant,,ENST00000469878,;SLC50A1,downstream_gene_variant,,ENST00000475824,;EFNA1,downstream_gene_variant,,ENST00000474413,;EFNA1,downstream_gene_variant,,ENST00000497282,;SLC50A1,downstream_gene_variant,,ENST00000506037,;	CAG	ENSG00000169241	ENST00000368404	Transcript	3_prime_UTR_variant	790-791	.	.	.	.	.	.	.	1	SLC50A1	HGNC	30657	protein_coding	YES	CCDS1093.1	ENSP00000357389	SWET1_HUMAN	.	UPI00000361FB	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTGTTTCAGCT	.	3	ESCA
GON4L	0	.	GRCh37	1	155740961	155740961	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2543A>T	p.Asn848Ile	p.N848I	ENST00000437809	19/32	169	109	60	98	98	0	GON4L,missense_variant,p.Asn848Ile,ENST00000437809,;GON4L,missense_variant,p.Asn848Ile,ENST00000361040,;GON4L,missense_variant,p.Asn848Ile,ENST00000368331,;GON4L,missense_variant,p.Asn848Ile,ENST00000271883,;GON4L,non_coding_transcript_exon_variant,,ENST00000496021,;GON4L,non_coding_transcript_exon_variant,,ENST00000490801,;GON4L,non_coding_transcript_exon_variant,,ENST00000497369,;GON4L,non_coding_transcript_exon_variant,,ENST00000471341,;GON4L,downstream_gene_variant,,ENST00000482386,;	A	ENSG00000116580	ENST00000437809	Transcript	missense_variant	2666	2543	848	N/I	aAt/aTt	.	.	.	-1	GON4L	HGNC	25973	protein_coding	YES	CCDS44242.1	ENSP00000396117	GON4L_HUMAN	Q9NXJ9_HUMAN	UPI0000603C24	.	deleterious(0.02)	benign(0.147)	19/32	.	hmmpanther:PTHR16088,hmmpanther:PTHR16088:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGATTAGGA	.	5	ESCA
SMG5	0	.	GRCh37	1	156220038	156220038	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*340G>A	.	.	ENST00000361813	22/22	37	17	20	25	25	0	SMG5,3_prime_UTR_variant,,ENST00000361813,;SMG5,intron_variant,,ENST00000368267,;PAQR6,upstream_gene_variant,,ENST00000540423,;PAQR6,upstream_gene_variant,,ENST00000368270,;PAQR6,upstream_gene_variant,,ENST00000340183,;PAQR6,upstream_gene_variant,,ENST00000335852,;PAQR6,upstream_gene_variant,,ENST00000292291,;PAQR6,upstream_gene_variant,,ENST00000356983,;PAQR6,upstream_gene_variant,,ENST00000491107,;PAQR6,upstream_gene_variant,,ENST00000480773,;PAQR6,upstream_gene_variant,,ENST00000492619,;PAQR6,upstream_gene_variant,,ENST00000468632,;PAQR6,upstream_gene_variant,,ENST00000475507,;PAQR6,upstream_gene_variant,,ENST00000470198,;SMG5,non_coding_transcript_exon_variant,,ENST00000476954,;SMG5,downstream_gene_variant,,ENST00000468993,;SMG5,downstream_gene_variant,,ENST00000473643,;	T	ENSG00000198952	ENST00000361813	Transcript	3_prime_UTR_variant	3536	.	.	.	.	.	.	.	-1	SMG5	HGNC	24644	protein_coding	YES	CCDS1137.1	ENSP00000355261	SMG5_HUMAN	.	UPI0000050C24	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCTCAGAGA	.	5	ESCA
CROCC	0	.	GRCh37	1	17263342	17263342	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1167C>T	p.%3D	p.D389D	ENST00000375541	9/37	125	101	24	99	99	0	CROCC,synonymous_variant,p.%3D,ENST00000445545,;CROCC,synonymous_variant,p.%3D,ENST00000375541,;CROCC,non_coding_transcript_exon_variant,,ENST00000466256,;CROCC,non_coding_transcript_exon_variant,,ENST00000467715,;CROCC,non_coding_transcript_exon_variant,,ENST00000467938,;CROCC,intron_variant,,ENST00000492631,;CROCC,upstream_gene_variant,,ENST00000494191,;	T	ENSG00000058453	ENST00000375541	Transcript	synonymous_variant	1236	1167	389	D	gaC/gaT	.	.	.	1	CROCC	HGNC	21299	protein_coding	YES	CCDS30616.1	ENSP00000364691	CROCC_HUMAN	.	UPI00001AE5A0	.	.	.	9/37	.	hmmpanther:PTHR23159:SF11,hmmpanther:PTHR23159	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGACCTGGA	.	5	ESCA
IER5	0	.	GRCh37	1	181058181	181058181	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143T>A	p.Leu48Gln	p.L48Q	ENST00000367577	1/1	51	29	22	23	23	0	IER5,missense_variant,p.Leu48Gln,ENST00000367577,;RP11-309G3.3,upstream_gene_variant,,ENST00000606938,;	A	ENSG00000162783	ENST00000367577	Transcript	missense_variant	544	143	48	L/Q	cTg/cAg	.	.	.	1	IER5	HGNC	5393	protein_coding	YES	CCDS1343.1	ENSP00000356549	IER5_HUMAN	.	UPI000013E1C9	.	deleterious(0)	probably_damaging(0.998)	1/1	.	Pfam_domain:PF05760,hmmpanther:PTHR15895,hmmpanther:PTHR15895:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTACCTGAGCG	.	5	ESCA
FAM129A	0	.	GRCh37	1	184853931	184853931	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.437C>A	p.Ser146Tyr	p.S146Y	ENST00000367511	5/14	69	39	29	70	70	0	FAM129A,missense_variant,p.Ser146Tyr,ENST00000367511,;FAM129A,downstream_gene_variant,,ENST00000496299,;	T	ENSG00000135842	ENST00000367511	Transcript	missense_variant	631	437	146	S/Y	tCc/tAc	.	.	.	-1	FAM129A	HGNC	16784	protein_coding	YES	CCDS1364.1	ENSP00000356481	NIBAN_HUMAN	.	UPI00000375B3	.	tolerated(0.16)	possibly_damaging(0.583)	5/14	.	hmmpanther:PTHR14392:SF3,hmmpanther:PTHR14392	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTGGAGGCT	.	5	ESCA
UCHL5	0	.	GRCh37	1	192985454	192985454	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*27C>T	.	.	ENST00000367455	11/11	66	50	15	62	62	0	UCHL5,3_prime_UTR_variant,,ENST00000367451,;UCHL5,3_prime_UTR_variant,,ENST00000449480,;UCHL5,3_prime_UTR_variant,,ENST00000420791,;UCHL5,3_prime_UTR_variant,,ENST00000367455,;UCHL5,3_prime_UTR_variant,,ENST00000367450,;UCHL5,3_prime_UTR_variant,,ENST00000367454,;UCHL5,downstream_gene_variant,,ENST00000416915,;UCHL5,downstream_gene_variant,,ENST00000367449,;UCHL5,downstream_gene_variant,,ENST00000367452,;UCHL5,downstream_gene_variant,,ENST00000367448,;UCHL5,downstream_gene_variant,,ENST00000530098,;UCHL5,downstream_gene_variant,,ENST00000443327,;	A	ENSG00000116750	ENST00000367455	Transcript	3_prime_UTR_variant	1253	.	.	.	.	.	.	.	-1	UCHL5	HGNC	19678	protein_coding	YES	CCDS1378.1	ENSP00000356425	UCHL5_HUMAN	.	UPI000013CF2A	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCAGAAATG	.	5	ESCA
LGR6	0	.	GRCh37	1	202287572	202287572	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2141C>T	p.Ser714Phe	p.S714F	ENST00000367278	18/18	46	30	16	26	26	0	LGR6,missense_variant,p.Ser662Phe,ENST00000255432,;LGR6,missense_variant,p.Ser714Phe,ENST00000367278,;LGR6,missense_variant,p.Ser575Phe,ENST00000439764,;LGR6,3_prime_UTR_variant,,ENST00000487787,;	T	ENSG00000133067	ENST00000367278	Transcript	missense_variant	2230	2141	714	S/F	tCc/tTc	.	.	.	1	LGR6	HGNC	19719	protein_coding	YES	CCDS30971.1	ENSP00000356247	LGR6_HUMAN	.	UPI0000161221	.	deleterious(0)	probably_damaging(0.954)	18/18	.	Prints_domain:PR00373,Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCCCCAC	.	5	ESCA
LPGAT1	0	.	GRCh37	1	211919546	211919546	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3695G>A	.	.	ENST00000366997	8/8	131	88	43	95	95	0	LPGAT1,3_prime_UTR_variant,,ENST00000366997,;LPGAT1,downstream_gene_variant,,ENST00000366996,;	T	ENSG00000123684	ENST00000366997	Transcript	3_prime_UTR_variant	5035	.	.	.	.	.	.	.	-1	LPGAT1	HGNC	28985	protein_coding	YES	CCDS31018.1	ENSP00000355964	LGAT1_HUMAN	Q53YL2_HUMAN	UPI0000139467	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGAGCAAAGA	.	5	ESCA
OBSCN	0	.	GRCh37	1	228560180	228560180	+	Missense_Mutation	SNP	C	C	T	rs776508320	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.24572C>T	p.Ser8191Leu	p.S8191L	ENST00000570156	105/116	72	45	27	62	62	0	OBSCN,missense_variant,p.Ser4868Leu,ENST00000366707,;OBSCN,missense_variant,p.Ser1851Leu,ENST00000441106,;OBSCN,missense_variant,p.Ser7234Leu,ENST00000422127,;OBSCN,missense_variant,p.Ser8191Leu,ENST00000570156,;	T	ENSG00000154358	ENST00000570156	Transcript	missense_variant	24646	24572	8191	S/L	tCg/tTg	rs776508320	.	.	1	OBSCN	HGNC	15719	protein_coding	YES	CCDS59204.1	ENSP00000455507	.	H3BPX2_HUMAN	UPI00027FCDB5	.	.	benign(0.397)	105/116	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF17,Gene3D:1.10.510.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGTCGGAGG	byFrequency	5	ESCA
TRIM17	0	.	GRCh37	1	228602544	228602544	+	Missense_Mutation	SNP	T	T	A	rs769444776	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.230A>T	p.Asn77Ile	p.N77I	ENST00000366697	1/6	74	53	21	60	60	0	TRIM17,missense_variant,p.Asn77Ile,ENST00000366697,;TRIM17,missense_variant,p.Asn77Ile,ENST00000456946,;TRIM17,missense_variant,p.Asn77Ile,ENST00000366698,;TRIM17,missense_variant,p.Asn77Ile,ENST00000295033,;TRIM17,missense_variant,p.Asn50Ile,ENST00000479800,;TRIM17,missense_variant,p.Asn77Ile,ENST00000355586,;TRIM17,downstream_gene_variant,,ENST00000457345,;TRIM17,downstream_gene_variant,,ENST00000520264,;	A	ENSG00000162931	ENST00000366697	Transcript	missense_variant	1187	230	77	N/I	aAc/aTc	rs769444776	.	.	-1	TRIM17	HGNC	13430	protein_coding	YES	CCDS1571.1	ENSP00000355658	TRI17_HUMAN	J3KQG0_HUMAN,J3KNZ3_HUMAN,E5RJW6_HUMAN,E5RI62_HUMAN	UPI000000163B	.	deleterious(0.01)	benign(0.096)	1/6	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF313,Gene3D:3.30.40.10,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGGTTGGGC	byFrequency	5	ESCA
CNST	0	.	GRCh37	1	246784932	246784932	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.581A>G	p.His194Arg	p.H194R	ENST00000366513	3/11	36	13	22	43	43	0	CNST,missense_variant,p.His194Arg,ENST00000366513,;CNST,missense_variant,p.His194Arg,ENST00000366512,;CNST,intron_variant,,ENST00000366511,;CNST,non_coding_transcript_exon_variant,,ENST00000483271,;	G	ENSG00000162852	ENST00000366513	Transcript	missense_variant	850	581	194	H/R	cAt/cGt	.	.	.	1	CNST	HGNC	26486	protein_coding	YES	CCDS1628.1	ENSP00000355470	CNST_HUMAN	.	UPI000013E1DF	.	deleterious(0)	probably_damaging(0.999)	3/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTCATCAGG	.	5	ESCA
DNALI1	0	.	GRCh37	1	38023339	38023339	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283C>A	p.Leu95Ile	p.L95I	ENST00000296218	2/6	19	15	4	14	14	0	DNALI1,stop_gained,p.Tyr3Ter,ENST00000541606,;DNALI1,missense_variant,p.Leu95Ile,ENST00000296218,;SNIP1,upstream_gene_variant,,ENST00000296215,;DNALI1,non_coding_transcript_exon_variant,,ENST00000490312,;DNALI1,non_coding_transcript_exon_variant,,ENST00000466723,;DNALI1,upstream_gene_variant,,ENST00000467277,;SNIP1,upstream_gene_variant,,ENST00000493916,;SNIP1,upstream_gene_variant,,ENST00000468040,;DNALI1,upstream_gene_variant,,ENST00000497858,;RP3-423B22.5,downstream_gene_variant,,ENST00000423216,;RP3-423B22.5,downstream_gene_variant,,ENST00000368565,;	A	ENSG00000163879	ENST00000296218	Transcript	missense_variant	293	283	95	L/I	Cta/Ata	.	.	.	1	DNALI1	HGNC	14353	protein_coding	YES	CCDS420.1	ENSP00000296218	IDLC_HUMAN	.	UPI00001D6A0B	.	tolerated(0.11)	possibly_damaging(0.592)	2/6	.	hmmpanther:PTHR13183,Pfam_domain:PF10211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCATACTACCC	.	2	ESCA
SZT2	0	.	GRCh37	1	43891189	43891189	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2690A>T	p.Glu897Val	p.E897V	ENST00000562955	19/71	15	11	4	16	16	0	SZT2,missense_variant,p.Glu55Val,ENST00000372442,;SZT2,missense_variant,p.Glu897Val,ENST00000562955,;SZT2,non_coding_transcript_exon_variant,,ENST00000470139,;SZT2,upstream_gene_variant,,ENST00000478140,;	T	ENSG00000198198	ENST00000562955	Transcript	missense_variant	2690	2690	897	E/V	gAg/gTg	.	.	.	1	SZT2	HGNC	29040	protein_coding	YES	CCDS30694.2	ENSP00000457168	SZT2_HUMAN	.	UPI0001E24F46	.	deleterious(0)	probably_damaging(0.983)	19/71	.	hmmpanther:PTHR14918	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGGAGGGAG	.	5	ESCA
CST1	0	.	GRCh37	20	23728452	23728452	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1G>A	.	.	ENST00000304749	3/3	88	73	14	45	45	0	CST1,3_prime_UTR_variant,,ENST00000398402,;CST1,3_prime_UTR_variant,,ENST00000304749,;	T	ENSG00000170373	ENST00000304749	Transcript	3_prime_UTR_variant	498	.	.	.	.	.	.	.	-1	CST1	HGNC	2473	protein_coding	YES	CCDS13160.1	ENSP00000305731	CYTN_HUMAN	.	UPI000013E9BC	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATCCCTAGG	.	5	ESCA
PYGB	0	.	GRCh37	20	25277028	25277028	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2402A>G	p.Lys801Arg	p.K801R	ENST00000216962	20/20	87	67	19	62	62	0	PYGB,missense_variant,p.Lys801Arg,ENST00000216962,;PYGB,missense_variant,p.Lys220Arg,ENST00000428458,;ABHD12,intron_variant,,ENST00000376542,;ABHD12,downstream_gene_variant,,ENST00000339157,;PYGB,non_coding_transcript_exon_variant,,ENST00000471359,;ABHD12,intron_variant,,ENST00000465694,;	G	ENSG00000100994	ENST00000216962	Transcript	missense_variant	2512	2402	801	K/R	aAg/aGg	.	.	.	1	PYGB	HGNC	9723	protein_coding	YES	CCDS13171.1	ENSP00000216962	PYGB_HUMAN	Q8TDG6_HUMAN	UPI0000131A0A	.	tolerated(0.23)	benign(0.062)	20/20	.	hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF1,Gene3D:3.40.50.2000,TIGRFAM_domain:TIGR02093,Pfam_domain:PF00343,PIRSF_domain:PIRSF000460,Superfamily_domains:SSF53756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGAAGGTCA	.	5	ESCA
MYH7B	0	.	GRCh37	20	33568835	33568835	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.626-1G>C	.	p.X209_splice	ENST00000262873	.	65	53	12	46	46	0	MYH7B,splice_acceptor_variant,,ENST00000262873,;MYH7B,splice_acceptor_variant,,ENST00000481922,;MYH7B,splice_acceptor_variant,,ENST00000470929,;	C	ENSG00000078814	ENST00000262873	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	MYH7B	HGNC	15906	protein_coding	YES	CCDS42869.1	ENSP00000262873	MYH7B_HUMAN	.	UPI0000253BD4	.	.	.	.	6/42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCAGACCGA	.	5	ESCA
STK4	0	.	GRCh37	20	43704769	43704769	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*952G>A	.	.	ENST00000372806	11/11	16	7	9	9	9	0	STK4,3_prime_UTR_variant,,ENST00000499879,;STK4,3_prime_UTR_variant,,ENST00000372806,;STK4,downstream_gene_variant,,ENST00000372801,;	A	ENSG00000101109	ENST00000372806	Transcript	3_prime_UTR_variant	2511	.	.	.	.	.	.	.	1	STK4	HGNC	11408	protein_coding	YES	CCDS13341.1	ENSP00000361892	STK4_HUMAN	Q9BS84_HUMAN	UPI00001360FF	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	TAGAGGGGATT	.	2	ESCA
ZNFX1	0	.	GRCh37	20	47866096	47866096	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3465C>T	p.%3D	p.T1155T	ENST00000396105	14/14	53	36	16	32	32	0	ZNFX1,synonymous_variant,p.%3D,ENST00000371752,;ZNFX1,synonymous_variant,p.%3D,ENST00000396105,;ZNFX1,intron_variant,,ENST00000371754,;ZNFX1,upstream_gene_variant,,ENST00000469991,;	A	ENSG00000124201	ENST00000396105	Transcript	synonymous_variant	3712	3465	1155	T	acC/acT	.	.	.	-1	ZNFX1	HGNC	29271	protein_coding	YES	CCDS13417.1	ENSP00000379412	ZNFX1_HUMAN	Q5JXR5_HUMAN	UPI000012DD83	.	.	.	14/14	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF341,Pfam_domain:PF13087,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGGATGGTGAT	.	4	ESCA
SNAI1	0	.	GRCh37	20	48604672	48604672	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*79T>C	.	.	ENST00000244050	3/3	32	11	20	21	21	0	SNAI1,3_prime_UTR_variant,,ENST00000244050,;	C	ENSG00000124216	ENST00000244050	Transcript	3_prime_UTR_variant	935	.	.	.	.	.	.	.	1	SNAI1	HGNC	11128	protein_coding	YES	CCDS13423.1	ENSP00000244050	SNAI1_HUMAN	.	UPI0000135B17	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACATCCTTC	.	5	ESCA
AURKA	0	.	GRCh37	20	54959346	54959346	+	Silent	SNP	C	C	T	.	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.354G>A	p.%3D	p.Q118Q	ENST00000395909	6/11	98	79	19	63	63	0	AURKA,synonymous_variant,p.%3D,ENST00000395909,;AURKA,synonymous_variant,p.%3D,ENST00000395913,;AURKA,synonymous_variant,p.%3D,ENST00000420474,;AURKA,synonymous_variant,p.%3D,ENST00000422322,;AURKA,synonymous_variant,p.%3D,ENST00000347343,;AURKA,synonymous_variant,p.%3D,ENST00000371356,;AURKA,synonymous_variant,p.%3D,ENST00000395915,;AURKA,synonymous_variant,p.%3D,ENST00000441357,;AURKA,synonymous_variant,p.%3D,ENST00000395907,;AURKA,synonymous_variant,p.%3D,ENST00000395911,;AURKA,synonymous_variant,p.%3D,ENST00000395914,;AURKA,synonymous_variant,p.%3D,ENST00000312783,;AURKA,downstream_gene_variant,,ENST00000456249,;AURKA,downstream_gene_variant,,ENST00000451915,;	T	ENSG00000087586	ENST00000395909	Transcript	synonymous_variant	920	354	118	Q	caG/caA	COSM4099636	.	.	-1	AURKA	HGNC	11393	protein_coding	YES	CCDS13451.1	ENSP00000379245	AURKA_HUMAN	Q5QPD4_HUMAN,Q5QPD2_HUMAN,Q5QPD1_HUMAN,A3KFJ2_HUMAN,A3KFJ1_HUMAN	UPI000013C70F	.	.	.	6/11	.	hmmpanther:PTHR24350,hmmpanther:PTHR24350:SF5,Gene3D:3.30.200.20	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTCTGTTT	.	5	ESCA
RAB22A	0	.	GRCh37	20	56935539	56935539	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*780G>A	.	.	ENST00000244040	7/7	78	61	17	47	46	0	RAB22A,3_prime_UTR_variant,,ENST00000244040,;	A	ENSG00000124209	ENST00000244040	Transcript	3_prime_UTR_variant	1646	.	.	.	.	.	.	.	1	RAB22A	HGNC	9764	protein_coding	YES	CCDS33497.1	ENSP00000244040	RB22A_HUMAN	Q96IY7_HUMAN	UPI0000132F68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGAAGAG	.	5	ESCA
GNAS	0	.	GRCh37	20	57484444	57484444	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2554G>C	p.Glu852Gln	p.E852Q	ENST00000371100	8/13	107	79	27	79	79	0	GNAS,missense_variant,p.Glu209Gln,ENST00000371085,;GNAS,missense_variant,p.Glu195Gln,ENST00000306090,;GNAS,missense_variant,p.Glu150Gln,ENST00000604005,;GNAS,missense_variant,p.Glu210Gln,ENST00000354359,;GNAS,missense_variant,p.Glu195Gln,ENST00000371095,;GNAS,missense_variant,p.Glu838Gln,ENST00000371102,;GNAS,missense_variant,p.Glu194Gln,ENST00000265620,;GNAS,missense_variant,p.Glu852Gln,ENST00000371100,;GNAS,3_prime_UTR_variant,,ENST00000313949,;GNAS,3_prime_UTR_variant,,ENST00000371075,;GNAS,downstream_gene_variant,,ENST00000419558,;GNAS,downstream_gene_variant,,ENST00000349036,;GNAS,downstream_gene_variant,,ENST00000603546,;GNAS,downstream_gene_variant,,ENST00000450130,;GNAS,non_coding_transcript_exon_variant,,ENST00000477931,;GNAS,non_coding_transcript_exon_variant,,ENST00000481039,;GNAS,non_coding_transcript_exon_variant,,ENST00000482112,;GNAS,non_coding_transcript_exon_variant,,ENST00000467321,;GNAS,non_coding_transcript_exon_variant,,ENST00000480232,;GNAS,non_coding_transcript_exon_variant,,ENST00000472183,;GNAS,non_coding_transcript_exon_variant,,ENST00000464788,;GNAS,non_coding_transcript_exon_variant,,ENST00000488652,;GNAS,non_coding_transcript_exon_variant,,ENST00000493958,;GNAS,non_coding_transcript_exon_variant,,ENST00000488546,;GNAS,non_coding_transcript_exon_variant,,ENST00000470512,;GNAS,non_coding_transcript_exon_variant,,ENST00000492907,;GNAS,non_coding_transcript_exon_variant,,ENST00000468895,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,non_coding_transcript_exon_variant,,ENST00000480975,;GNAS,non_coding_transcript_exon_variant,,ENST00000476935,;GNAS,intron_variant,,ENST00000494081,;GNAS,downstream_gene_variant,,ENST00000485673,;GNAS,downstream_gene_variant,,ENST00000469431,;GNAS,downstream_gene_variant,,ENST00000490374,;GNAS,downstream_gene_variant,,ENST00000478585,;GNAS,downstream_gene_variant,,ENST00000467227,;GNAS,non_coding_transcript_exon_variant,,ENST00000479025,;GNAS,non_coding_transcript_exon_variant,,ENST00000487862,;GNAS,non_coding_transcript_exon_variant,,ENST00000476196,;GNAS,non_coding_transcript_exon_variant,,ENST00000487981,;GNAS,non_coding_transcript_exon_variant,,ENST00000496934,;GNAS,upstream_gene_variant,,ENST00000475610,;	C	ENSG00000087460	ENST00000371100	Transcript	missense_variant	3106	2554	852	E/Q	Gag/Cag	.	.	.	1	GNAS	HGNC	4392	protein_coding	YES	CCDS46622.1	ENSP00000360141	GNAS1_HUMAN	S4R3W4_HUMAN,S4R3V9_HUMAN,S4R3F1_HUMAN,S4R3E3_HUMAN,S4R379_HUMAN,B0AZR9_HUMAN	UPI0000E444AE	.	deleterious(0.01)	probably_damaging(0.999)	8/13	.	hmmpanther:PTHR10218:SF36,hmmpanther:PTHR10218,Pfam_domain:PF00503,Gene3D:3.40.50.300,SMART_domains:SM00275,Superfamily_domains:SSF52540,Prints_domain:PR00318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTGAGACC	.	5	ESCA
LAMA5	0	.	GRCh37	20	60912751	60912751	+	Missense_Mutation	SNP	C	C	T	rs757840397	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2059G>A	p.Ala687Thr	p.A687T	ENST00000252999	16/80	36	32	4	39	39	0	LAMA5,missense_variant,p.Ala687Thr,ENST00000252999,;LAMA5,downstream_gene_variant,,ENST00000370692,;LAMA5,upstream_gene_variant,,ENST00000474128,;	T	ENSG00000130702	ENST00000252999	Transcript	missense_variant	2126	2059	687	A/T	Gca/Aca	rs757840397	.	.	-1	LAMA5	HGNC	6485	protein_coding	YES	CCDS33502.1	ENSP00000252999	LAMA5_HUMAN	O75079_HUMAN	UPI0000161FDC	.	.	benign(0.094)	16/80	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF261,hmmpanther:PTHR10574,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCTGCGTGCA	byFrequency	2	ESCA
IFNGR2	0	.	GRCh37	21	34787211	34787211	+	Silent	SNP	G	G	T	rs546201964	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90G>T	p.%3D	p.L30L	ENST00000290219	2/7	26	13	13	39	39	0	IFNGR2,synonymous_variant,p.%3D,ENST00000381995,;IFNGR2,synonymous_variant,p.%3D,ENST00000290219,;IFNGR2,5_prime_UTR_variant,,ENST00000405436,;IFNGR2,3_prime_UTR_variant,,ENST00000439213,;IFNGR2,intron_variant,,ENST00000545369,;	T	ENSG00000159128	ENST00000290219	Transcript	synonymous_variant	738	90	30	L	ctG/ctT	rs546201964	.	.	1	IFNGR2	HGNC	5440	protein_coding	YES	CCDS33544.1	ENSP00000290219	INGR2_HUMAN	B5MCZ0_HUMAN,A8K881_HUMAN,A1Z2N6_HUMAN	UPI00001514B0	.	.	.	2/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF9,Pfam_domain:PF01108,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGCCCGC	byFrequency|by1000G	5	ESCA
NEFH	0	.	GRCh37	22	29879448	29879448	+	Missense_Mutation	SNP	G	G	A	rs756952361	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.968G>A	p.Arg323His	p.R323H	ENST00000310624	2/4	31	21	9	20	20	0	NEFH,missense_variant,p.Arg323His,ENST00000310624,;	A	ENSG00000100285	ENST00000310624	Transcript	missense_variant	1001	968	323	R/H	cGt/cAt	rs756952361,COSM1217023	.	.	1	NEFH	HGNC	7737	protein_coding	YES	CCDS13858.1	ENSP00000311997	NFH_HUMAN	.	UPI00001AEF71	.	deleterious(0.03)	unknown(0)	2/4	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23214:SF1,hmmpanther:PTHR23214,Pfam_domain:PF00038	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGCGTCAGC	.	5	ESCA
GRAMD4	0	.	GRCh37	22	47069673	47069688	+	Frame_Shift_Del	DEL	AGATCTTCAATCTGAC	AGATCTTCAATCTGAC	-	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	AGATCTTCAATCTGAC	AGATCTTCAATCTGAC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1349_1364delTCTTCAATCTGACAGA	p.Ile450LysfsTer59	p.I450Kfs*59	ENST00000406902	15/19	75	54	21	56	56	0	GRAMD4,frameshift_variant,p.Ile450LysfsTer59,ENST00000406902,;GRAMD4,frameshift_variant,p.Ile450LysfsTer59,ENST00000361034,;GRAMD4,downstream_gene_variant,,ENST00000456069,;GRAMD4,upstream_gene_variant,,ENST00000408031,;	-	ENSG00000075240	ENST00000406902	Transcript	frameshift_variant	1559-1574	1346-1361	449-454	EIFNLT/X	gAGATCTTCAATCTGACa/ga	.	.	.	1	GRAMD4	HGNC	29113	protein_coding	YES	CCDS33672.1	ENSP00000385689	GRAM4_HUMAN	.	UPI0000161A59	.	.	.	15/19	.	hmmpanther:PTHR16122,Pfam_domain:PF02893,SMART_domains:SM00568	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCACGAGATCTTCAATCTGACAGAAA	.	3	ESCA
EPB41L5	0	.	GRCh37	2	120799579	120799579	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181-3C>T	.	.	ENST00000263713	.	93	57	36	69	69	0	EPB41L5,splice_region_variant,,ENST00000331393,;EPB41L5,splice_region_variant,,ENST00000443902,;EPB41L5,splice_region_variant,,ENST00000263713,;EPB41L5,splice_region_variant,,ENST00000452780,;EPB41L5,splice_region_variant,,ENST00000443124,;EPB41L5,splice_region_variant,,ENST00000466241,;	T	ENSG00000115109	ENST00000263713	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	EPB41L5	HGNC	19819	protein_coding	YES	CCDS2130.1	ENSP00000263713	E41L5_HUMAN	Q53RT1_HUMAN,Q4ZG32_HUMAN	UPI00001B078A	.	.	.	.	2/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTCAGAAA	.	4	ESCA
SLC4A10	0	.	GRCh37	2	162757652	162757652	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1442+131A>G	.	.	ENST00000446997	.	22	15	7	14	14	0	SLC4A10,intron_variant,,ENST00000446997,;SLC4A10,intron_variant,,ENST00000421911,;SLC4A10,intron_variant,,ENST00000272716,;SLC4A10,intron_variant,,ENST00000535165,;SLC4A10,intron_variant,,ENST00000415876,;SLC4A10,intron_variant,,ENST00000375514,;SLC4A10,non_coding_transcript_exon_variant,,ENST00000493021,;SLC4A10,intron_variant,,ENST00000446228,;	G	ENSG00000144290	ENST00000446997	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	SLC4A10	HGNC	13811	protein_coding	YES	CCDS54411.1	ENSP00000393066	S4A10_HUMAN	.	UPI00001D4707	.	.	.	.	12/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCCAATTAG	.	5	ESCA
CCDC141	0	.	GRCh37	2	179736884	179736884	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2055G>A	p.%3D	p.A685A	ENST00000420890	13/24	52	29	23	42	42	0	CCDC141,synonymous_variant,p.%3D,ENST00000420890,;CCDC141,synonymous_variant,p.%3D,ENST00000443758,;CCDC141,synonymous_variant,p.%3D,ENST00000343876,;CCDC141,synonymous_variant,p.%3D,ENST00000446116,;CCDC141,synonymous_variant,p.%3D,ENST00000295723,;CCDC141,downstream_gene_variant,,ENST00000409284,;	T	ENSG00000163492	ENST00000420890	Transcript	synonymous_variant	2173	2055	685	A	gcG/gcA	.	.	.	-1	CCDC141	HGNC	26821	protein_coding	YES	.	ENSP00000395995	.	H7C0P1_HUMAN,E7ERF0_HUMAN	UPI0000EE2F1C	.	.	.	13/24	.	hmmpanther:PTHR19897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGCCGCCCA	.	5	ESCA
NT5C1B	0	.	GRCh37	2	18768420	18768420	+	Missense_Mutation	SNP	G	G	T	rs776002305	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.140C>A	p.Pro47Gln	p.P47Q	ENST00000359846	3/10	16	5	11	20	20	0	NT5C1B,missense_variant,p.Pro47Gln,ENST00000359846,;NT5C1B,missense_variant,p.Pro47Gln,ENST00000600945,;NT5C1B-RDH14,missense_variant,p.Pro47Gln,ENST00000532967,;NT5C1B,missense_variant,p.Pro47Gln,ENST00000416783,;NT5C1B,intron_variant,,ENST00000304081,;NT5C1B-RDH14,intron_variant,,ENST00000444297,;NT5C1B,upstream_gene_variant,,ENST00000418427,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,intron_variant,,ENST00000460052,;NT5C1B,intron_variant,,ENST00000406971,;NT5C1B,upstream_gene_variant,,ENST00000490687,;	T	ENSG00000185013	ENST00000359846	Transcript	missense_variant	218	140	47	P/Q	cCg/cAg	rs776002305	.	.	-1	NT5C1B	HGNC	17818	protein_coding	YES	CCDS33150.1	ENSP00000352904	5NT1B_HUMAN	B4DZ86_HUMAN	UPI000035B1B0	.	deleterious_low_confidence(0)	probably_damaging(0.91)	3/10	.	hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTCGGATTG	byFrequency	5	ESCA
CFLAR	0	.	GRCh37	2	202005016	202005016	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.524-64A>G	.	.	ENST00000309955	.	136	87	49	102	102	0	CFLAR,intron_variant,,ENST00000341222,;CFLAR,intron_variant,,ENST00000494258,;CFLAR,intron_variant,,ENST00000443227,;CFLAR,intron_variant,,ENST00000340870,;CFLAR,intron_variant,,ENST00000457277,;CFLAR,intron_variant,,ENST00000341582,;CFLAR,intron_variant,,ENST00000342795,;CFLAR,intron_variant,,ENST00000355558,;CFLAR,intron_variant,,ENST00000462763,;CFLAR,intron_variant,,ENST00000479953,;CFLAR,intron_variant,,ENST00000309955,;CFLAR,intron_variant,,ENST00000440180,;CFLAR,intron_variant,,ENST00000470178,;CFLAR,intron_variant,,ENST00000423241,;CFLAR,downstream_gene_variant,,ENST00000395148,;RNU7-45P,upstream_gene_variant,,ENST00000459460,;CFLAR-AS1,non_coding_transcript_exon_variant,,ENST00000415011,;CFLAR-AS1,non_coding_transcript_exon_variant,,ENST00000474886,;CFLAR-AS1,downstream_gene_variant,,ENST00000598453,;CFLAR-AS1,downstream_gene_variant,,ENST00000594911,;CFLAR,non_coding_transcript_exon_variant,,ENST00000474842,;CFLAR,intron_variant,,ENST00000439154,;CFLAR,intron_variant,,ENST00000461422,;CFLAR,downstream_gene_variant,,ENST00000461820,;CFLAR,downstream_gene_variant,,ENST00000460961,;IMPDH1P10,upstream_gene_variant,,ENST00000440965,;	G	ENSG00000003402	ENST00000309955	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CFLAR	HGNC	1876	protein_coding	YES	CCDS2337.1	ENSP00000312455	CFLAR_HUMAN	M0QYM0_HUMAN,C9JV51_HUMAN,C9JSU3_HUMAN,C9J4Q0_HUMAN,C9J408_HUMAN	UPI0000030475	.	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTATTGAA	.	5	ESCA
ATIC	0	.	GRCh37	2	216214455	216214455	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*77A>T	.	.	ENST00000236959	16/16	26	14	12	12	12	0	ATIC,3_prime_UTR_variant,,ENST00000540518,;ATIC,3_prime_UTR_variant,,ENST00000236959,;ATIC,3_prime_UTR_variant,,ENST00000435675,;ATIC,3_prime_UTR_variant,,ENST00000442048,;ATIC,downstream_gene_variant,,ENST00000426233,;ATIC,downstream_gene_variant,,ENST00000446622,;ATIC,3_prime_UTR_variant,,ENST00000443953,;ATIC,non_coding_transcript_exon_variant,,ENST00000479093,;ATIC,non_coding_transcript_exon_variant,,ENST00000478734,;ATIC,downstream_gene_variant,,ENST00000459796,;ATIC,downstream_gene_variant,,ENST00000467388,;	T	ENSG00000138363	ENST00000236959	Transcript	3_prime_UTR_variant	2182	.	.	.	.	.	.	.	1	ATIC	HGNC	794	protein_coding	YES	CCDS2398.1	ENSP00000236959	PUR9_HUMAN	F5GWY2_HUMAN,C9JLK0_HUMAN	UPI000000122D	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTTTAAAAAA	.	4	ESCA
ANTXR1	0	.	GRCh37	2	69399605	69399605	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089+2184G>T	.	.	ENST00000303714	.	47	29	18	57	57	0	ANTXR1,3_prime_UTR_variant,,ENST00000409349,;ANTXR1,intron_variant,,ENST00000303714,;	T	ENSG00000169604	ENST00000303714	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ANTXR1	HGNC	21014	protein_coding	YES	CCDS1892.1	ENSP00000301945	ANTR1_HUMAN	.	UPI0000049806	.	.	.	.	14/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATAGTCTCA	.	5	ESCA
TCF7L1	0	.	GRCh37	2	85361007	85361007	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.200C>A	p.Ser67Ter	p.S67*	ENST00000282111	1/12	49	35	14	45	45	0	TCF7L1,stop_gained,p.Ser67Ter,ENST00000282111,;TCF7L1,upstream_gene_variant,,ENST00000494519,;	A	ENSG00000152284	ENST00000282111	Transcript	stop_gained	475	200	67	S/*	tCg/tAg	.	.	.	1	TCF7L1	HGNC	11640	protein_coding	YES	CCDS1971.1	ENSP00000282111	TF7L1_HUMAN	Q53T87_HUMAN,C9JPE3_HUMAN	UPI0000136846	.	.	.	1/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10373,hmmpanther:PTHR10373:SF25,Pfam_domain:PF08347,Gene3D:4.10.900.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAGTCGTCCC	.	5	ESCA
DIRC2	0	.	GRCh37	3	122598588	122598588	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*363G>A	.	.	ENST00000261038	9/9	78	64	13	40	40	0	DIRC2,3_prime_UTR_variant,,ENST00000261038,;DIRC2,3_prime_UTR_variant,,ENST00000477647,;	A	ENSG00000138463	ENST00000261038	Transcript	3_prime_UTR_variant	2198	.	.	.	.	.	.	.	1	DIRC2	HGNC	16628	protein_coding	YES	CCDS3018.1	ENSP00000261038	DIRC2_HUMAN	.	UPI0000073CC7	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATATGAAGAT	.	5	ESCA
KALRN	0	.	GRCh37	3	124303670	124303670	+	Translation_Start_Site	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2T>C	p.Met1?	p.M1?	ENST00000454902	1/4	30	23	7	16	16	0	KALRN,start_lost,p.Met1?,ENST00000454902,;KALRN,start_lost,p.Met1?,ENST00000291478,;KALRN,start_lost,p.Met1?,ENST00000428018,;KALRN,intron_variant,,ENST00000393496,;KALRN,intron_variant,,ENST00000354186,;KALRN,intron_variant,,ENST00000360013,;KALRN,intron_variant,,ENST00000471431,;	C	ENSG00000160145	ENST00000454902	Transcript	start_lost	142	2	1	M/T	aTg/aCg	.	.	.	1	KALRN	HGNC	4814	protein_coding	.	.	ENSP00000400064	.	C9J1B4_HUMAN	UPI0000E5A8DD	.	deleterious_low_confidence(0)	benign(0.01)	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACATGAAGG	.	5	ESCA
NPHP3	0	.	GRCh37	3	132415603	132415604	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2142dupT	p.Val715CysfsTer19	p.V715Cfs*19	ENST00000337331	15/27	82	63	19	44	44	0	NPHP3,frameshift_variant,p.Val715CysfsTer19,ENST00000337331,;NPHP3,intron_variant,,ENST00000326682,;NPHP3,3_prime_UTR_variant,,ENST00000471702,;NPHP3,non_coding_transcript_exon_variant,,ENST00000490993,;NPHP3,intron_variant,,ENST00000465756,;NPHP3,upstream_gene_variant,,ENST00000474871,;NPHP3,downstream_gene_variant,,ENST00000469232,;NPHP3,upstream_gene_variant,,ENST00000515289,;	A	ENSG00000113971	ENST00000337331	Transcript	frameshift_variant	2229-2230	2142-2143	714-715	-/X	-/T	.	.	.	-1	NPHP3	HGNC	7907	protein_coding	YES	CCDS3078.1	ENSP00000338766	NPHP3_HUMAN	.	UPI00001B6B30	.	.	.	15/27	.	Superfamily_domains:SSF52540,hmmpanther:PTHR19959:SF133,hmmpanther:PTHR19959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTGACATAAA	.	3	ESCA
PFN2	0	.	GRCh37	3	149683756	149683756	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*520A>G	.	.	ENST00000239940	3/3	109	94	15	46	46	0	PFN2,3_prime_UTR_variant,,ENST00000494827,;PFN2,3_prime_UTR_variant,,ENST00000239940,;PFN2,3_prime_UTR_variant,,ENST00000452853,;PFN2,3_prime_UTR_variant,,ENST00000481767,;PFN2,intron_variant,,ENST00000423691,;PFN2,downstream_gene_variant,,ENST00000461868,;PFN2,downstream_gene_variant,,ENST00000475518,;RNF13,downstream_gene_variant,,ENST00000361785,;PFN2,downstream_gene_variant,,ENST00000497148,;RNF13,downstream_gene_variant,,ENST00000344229,;RNF13,downstream_gene_variant,,ENST00000482083,;PFN2,downstream_gene_variant,,ENST00000461930,;PFN2,downstream_gene_variant,,ENST00000498307,;RNF13,downstream_gene_variant,,ENST00000392894,;RNF13,downstream_gene_variant,,ENST00000491086,;PFN2,downstream_gene_variant,,ENST00000489155,;PFN2,downstream_gene_variant,,ENST00000490975,;RNF13,downstream_gene_variant,,ENST00000468289,;PFN2,downstream_gene_variant,,ENST00000481275,;ANKUB1,intron_variant,,ENST00000481585,;PFN2,3_prime_UTR_variant,,ENST00000460404,;PFN2,3_prime_UTR_variant,,ENST00000468323,;PFN2,downstream_gene_variant,,ENST00000497060,;PFN2,downstream_gene_variant,,ENST00000498169,;RNF13,downstream_gene_variant,,ENST00000493238,;	C	ENSG00000070087	ENST00000239940	Transcript	3_prime_UTR_variant	1196	.	.	.	.	.	.	.	-1	PFN2	HGNC	8882	protein_coding	YES	CCDS3148.1	ENSP00000239940	PROF2_HUMAN	C9J712_HUMAN	UPI000013CA98	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTATTGTGC	.	5	ESCA
SERP1	0	.	GRCh37	3	150261710	150261710	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*535T>G	.	.	ENST00000479209	4/4	67	51	16	31	31	0	SERP1,3_prime_UTR_variant,,ENST00000239944,;SERP1,3_prime_UTR_variant,,ENST00000479209,;EIF2A,upstream_gene_variant,,ENST00000460851,;SERP1,downstream_gene_variant,,ENST00000487153,;EIF2A,upstream_gene_variant,,ENST00000406576,;EIF2A,upstream_gene_variant,,ENST00000482093,;EIF2A,upstream_gene_variant,,ENST00000487799,;SERP1,downstream_gene_variant,,ENST00000491660,;EIF2A,upstream_gene_variant,,ENST00000273435,;SERP1,downstream_gene_variant,,ENST00000491195,;EIF2A,upstream_gene_variant,,ENST00000474505,;EIF2A,upstream_gene_variant,,ENST00000462221,;EIF2A,upstream_gene_variant,,ENST00000469331,;EIF2A,upstream_gene_variant,,ENST00000473499,;EIF2A,upstream_gene_variant,,ENST00000463863,;EIF2A,upstream_gene_variant,,ENST00000494558,;EIF2A,upstream_gene_variant,,ENST00000490505,;	C	ENSG00000120742	ENST00000479209	Transcript	3_prime_UTR_variant	2009	.	.	.	.	.	.	.	-1	SERP1	HGNC	10759	protein_coding	YES	CCDS3150.1	ENSP00000420076	SERP1_HUMAN	.	UPI0000022CDB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTAAAGGTT	.	5	ESCA
CCDC39	0	.	GRCh37	3	180397551	180397551	+	5'Flank	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000442201	.	172	75	97	86	86	0	CCDC39,missense_variant,p.Leu32Pro,ENST00000273654,;CCDC39,intron_variant,,ENST00000471307,;CCDC39,upstream_gene_variant,,ENST00000442201,;CCDC39-AS1,upstream_gene_variant,,ENST00000495357,;CCDC39,5_prime_UTR_variant,,ENST00000476379,;	G	ENSG00000145075	ENST00000442201	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	263	-1	CCDC39	HGNC	25244	protein_coding	YES	CCDS46964.1	ENSP00000405708	CCD39_HUMAN	.	UPI00015D7298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGCAGCTGG	.	5	ESCA
SETD2	0	.	GRCh37	3	47098822	47098822	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6452C>T	p.Pro2151Leu	p.P2151L	ENST00000409792	15/21	40	15	24	41	41	0	SETD2,missense_variant,p.Pro2151Leu,ENST00000409792,;SETD2,downstream_gene_variant,,ENST00000492397,;SETD2,3_prime_UTR_variant,,ENST00000445387,;SETD2,3_prime_UTR_variant,,ENST00000330022,;SETD2,3_prime_UTR_variant,,ENST00000431180,;	A	ENSG00000181555	ENST00000409792	Transcript	missense_variant	6495	6452	2151	P/L	cCc/cTc	.	.	.	-1	SETD2	HGNC	18420	protein_coding	YES	CCDS2749.2	ENSP00000386759	SETD2_HUMAN	C9JG86_HUMAN	UPI00017E10FB	.	deleterious(0)	possibly_damaging(0.804)	15/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAGGGCAGT	.	5	ESCA
FAM3D	0	.	GRCh37	3	58635041	58635041	+	Splice_Site	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.145+1G>A	.	p.X49_splice	ENST00000358781	.	33	18	15	41	41	0	FAM3D,splice_donor_variant,,ENST00000489857,;FAM3D,splice_donor_variant,,ENST00000498347,;FAM3D,splice_donor_variant,,ENST00000358781,;FAM3D,splice_donor_variant,,ENST00000483787,;FAM3D,splice_donor_variant,,ENST00000482623,;	T	ENSG00000198643	ENST00000358781	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	FAM3D	HGNC	18665	protein_coding	YES	CCDS2893.1	ENSP00000351632	FAM3D_HUMAN	C9IZW7_HUMAN	UPI00000015C6	.	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E47K|c.139G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCACGGATC	.	5	ESCA
LRIG1	0	.	GRCh37	3	66436586	66436586	+	Silent	SNP	G	G	A	rs770509956	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1608C>T	p.%3D	p.V536V	ENST00000273261	13/19	24	11	13	69	69	0	LRIG1,synonymous_variant,p.%3D,ENST00000383703,;LRIG1,synonymous_variant,p.%3D,ENST00000273261,;SLC25A26,intron_variant,,ENST00000536651,;LRIG1,non_coding_transcript_exon_variant,,ENST00000496559,;LRIG1,non_coding_transcript_exon_variant,,ENST00000495037,;SLC25A26,intron_variant,,ENST00000464350,;	A	ENSG00000144749	ENST00000273261	Transcript	synonymous_variant	2133	1608	536	V	gtC/gtT	rs770509956	.	.	-1	LRIG1	HGNC	17360	protein_coding	YES	CCDS33783.1	ENSP00000273261	LRIG1_HUMAN	.	UPI000004C5BE	.	.	.	13/19	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,SMART_domains:SM00408,Gene3D:2.60.40.10,Pfam_domain:PF07679,hmmpanther:PTHR24367:SF245,hmmpanther:PTHR24367,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAGGACTTC	.	5	ESCA
CPOX	0	.	GRCh37	3	98298944	98298944	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*583C>T	.	.	ENST00000264193	7/7	40	22	18	37	37	0	CPOX,3_prime_UTR_variant,,ENST00000264193,;CPOX,intron_variant,,ENST00000512905,;CPOX,downstream_gene_variant,,ENST00000510489,;	A	ENSG00000080819	ENST00000264193	Transcript	3_prime_UTR_variant	2167	.	.	.	.	.	.	.	-1	CPOX	HGNC	2321	protein_coding	YES	CCDS2932.1	ENSP00000264193	HEM6_HUMAN	.	UPI0000073C93	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	ATGCAGAGATT	.	2	ESCA
GAB1	0	.	GRCh37	4	144390657	144390657	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*315C>A	.	.	ENST00000262995	11/11	76	43	33	50	50	0	GAB1,3_prime_UTR_variant,,ENST00000505913,;GAB1,3_prime_UTR_variant,,ENST00000262995,;GAB1,downstream_gene_variant,,ENST00000512843,;GAB1,downstream_gene_variant,,ENST00000262994,;GAB1,downstream_gene_variant,,ENST00000508833,;GAB1,non_coding_transcript_exon_variant,,ENST00000511109,;	A	ENSG00000109458	ENST00000262995	Transcript	3_prime_UTR_variant	2917	.	.	.	.	.	.	.	1	GAB1	HGNC	4066	protein_coding	YES	CCDS3760.1	ENSP00000262995	GAB1_HUMAN	D6RF42_HUMAN	UPI0000232A33	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCCCAATG	.	5	ESCA
DCAF4L1	0	.	GRCh37	4	41987702	41987702	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2702A>C	.	.	ENST00000333141	1/1	49	33	16	34	34	0	DCAF4L1,3_prime_UTR_variant,,ENST00000333141,;SLC30A9,upstream_gene_variant,,ENST00000264451,;RP11-814H16.2,downstream_gene_variant,,ENST00000608029,;SLC30A9,upstream_gene_variant,,ENST00000510460,;SLC30A9,upstream_gene_variant,,ENST00000513699,;	C	ENSG00000182308	ENST00000333141	Transcript	3_prime_UTR_variant	3990	.	.	.	.	.	.	.	1	DCAF4L1	HGNC	27723	protein_coding	YES	CCDS33978.1	ENSP00000327796	DC4L1_HUMAN	.	UPI0000160C25	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGATATTAAC	.	5	ESCA
CYTL1	0	.	GRCh37	4	5016849	5016849	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*29G>A	.	.	ENST00000307746	4/4	61	42	18	37	37	0	CYTL1,3_prime_UTR_variant,,ENST00000307746,;CYTL1,3_prime_UTR_variant,,ENST00000506508,;CYTL1,downstream_gene_variant,,ENST00000509419,;	T	ENSG00000170891	ENST00000307746	Transcript	3_prime_UTR_variant	467	.	.	.	.	.	.	.	-1	CYTL1	HGNC	24435	protein_coding	YES	CCDS3379.1	ENSP00000303550	CYTL1_HUMAN	.	UPI00000015F6	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTCTTGGG	.	5	ESCA
FGF5	0	.	GRCh37	4	81188197	81188197	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.219C>T	p.%3D	p.G73G	ENST00000312465	1/3	75	53	21	76	76	0	FGF5,synonymous_variant,p.%3D,ENST00000456523,;FGF5,synonymous_variant,p.%3D,ENST00000312465,;FGF5,non_coding_transcript_exon_variant,,ENST00000380628,;FGF5,upstream_gene_variant,,ENST00000503413,;FGF5,synonymous_variant,p.%3D,ENST00000507780,;	T	ENSG00000138675	ENST00000312465	Transcript	synonymous_variant	445	219	73	G	ggC/ggT	.	.	.	1	FGF5	HGNC	3683	protein_coding	YES	CCDS34021.1	ENSP00000311697	FGF5_HUMAN	Q8NF90_HUMAN,Q8NBG6_HUMAN	UPI0000039721	.	.	.	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTGGCTTGGA	.	5	ESCA
SEC31A	0	.	GRCh37	4	83784392	83784392	+	Intron	SNP	G	G	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1509+79C>G	.	.	ENST00000395310	.	124	78	46	77	77	0	SEC31A,intron_variant,,ENST00000448323,;SEC31A,intron_variant,,ENST00000505984,;SEC31A,intron_variant,,ENST00000264405,;SEC31A,intron_variant,,ENST00000512664,;SEC31A,intron_variant,,ENST00000311785,;SEC31A,intron_variant,,ENST00000500777,;SEC31A,intron_variant,,ENST00000510167,;SEC31A,intron_variant,,ENST00000395310,;SEC31A,intron_variant,,ENST00000509142,;SEC31A,intron_variant,,ENST00000508502,;SEC31A,intron_variant,,ENST00000505472,;SEC31A,intron_variant,,ENST00000432794,;SEC31A,intron_variant,,ENST00000507828,;SEC31A,intron_variant,,ENST00000513858,;SEC31A,intron_variant,,ENST00000355196,;SEC31A,intron_variant,,ENST00000443462,;SEC31A,intron_variant,,ENST00000508479,;SEC31A,intron_variant,,ENST00000326950,;SEC31A,intron_variant,,ENST00000348405,;SEC31A,non_coding_transcript_exon_variant,,ENST00000436790,;SEC31A,upstream_gene_variant,,ENST00000512732,;	C	ENSG00000138674	ENST00000395310	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SEC31A	HGNC	17052	protein_coding	YES	CCDS3596.1	ENSP00000378721	SC31A_HUMAN	U3KQC9_HUMAN,D6REC0_HUMAN,D6REA9_HUMAN,D6RE64_HUMAN,D6RCQ9_HUMAN,D6RBT0_HUMAN	UPI000003E7E1	.	.	.	.	12/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTGAGATA	.	5	ESCA
HERC3	0	.	GRCh37	4	89571101	89571101	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337G>A	p.Asp113Asn	p.D113N	ENST00000402738	4/26	74	47	27	50	50	0	HERC3,missense_variant,p.Asp113Asn,ENST00000402738,;HERC3,missense_variant,p.Asp113Asn,ENST00000426683,;HERC3,missense_variant,p.Asp113Asn,ENST00000407637,;HERC3,missense_variant,p.Asp113Asn,ENST00000264345,;HERC3,missense_variant,p.Asp113Asn,ENST00000452979,;HERC3,missense_variant,p.Asp113Asn,ENST00000431413,;HERC3,downstream_gene_variant,,ENST00000422770,;HERC3,downstream_gene_variant,,ENST00000513325,;	A	ENSG00000138641	ENST00000402738	Transcript	missense_variant	576	337	113	D/N	Gat/Aat	.	.	.	1	HERC3	HGNC	4876	protein_coding	YES	CCDS34028.1	ENSP00000385684	HERC3_HUMAN	Q4W5H5_HUMAN,F5GWU0_HUMAN,D6RAT5_HUMAN,C9JKA7_HUMAN,C9JFL2_HUMAN,C9J8E7_HUMAN,C9J6Z1_HUMAN,B4DK41_HUMAN	UPI000012C614	.	tolerated(0.37)	possibly_damaging(0.761)	4/26	.	Prints_domain:PR00633,Superfamily_domains:SSF50985,Gene3D:2.130.10.30,Pfam_domain:PF00415,hmmpanther:PTHR11254:SF285,hmmpanther:PTHR11254,PROSITE_profiles:PS50012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGTGATGGT	.	5	ESCA
SPRY4	0	.	GRCh37	5	141693705	141693705	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*69A>G	.	.	ENST00000344120	3/3	24	16	8	17	17	0	SPRY4,3_prime_UTR_variant,,ENST00000344120,;SPRY4,3_prime_UTR_variant,,ENST00000434127,;SPRY4,downstream_gene_variant,,ENST00000511815,;SPRY4,downstream_gene_variant,,ENST00000503582,;	C	ENSG00000187678	ENST00000344120	Transcript	3_prime_UTR_variant	1225	.	.	.	.	.	.	.	-1	SPRY4	HGNC	15533	protein_coding	YES	CCDS4274.1	ENSP00000344967	SPY4_HUMAN	D6RB56_HUMAN	UPI0000167871	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGCTGCAGT	.	5	ESCA
C5orf46	0	.	GRCh37	5	147281335	147281335	+	Missense_Mutation	SNP	G	G	C	rs753733525,rs768741514	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72C>G	p.Asp24Glu	p.D24E	ENST00000318315	2/4	38	27	11	44	44	0	C5orf46,missense_variant,p.Asp24Glu,ENST00000515291,;C5orf46,missense_variant,p.Asp24Glu,ENST00000318315,;C5orf46,splice_region_variant,,ENST00000510432,;	C	ENSG00000178776	ENST00000318315	Transcript	missense_variant	73	72	24	D/E	gaC/gaG	rs753733525,rs768741514	.	.	-1	C5orf46	HGNC	33768	protein_coding	YES	CCDS34267.1	ENSP00000315370	CE046_HUMAN	.	UPI000020CF20	.	tolerated(0.25)	possibly_damaging(0.621)	2/4	.	Low_complexity_(Seg):seg,Pfam_domain:PF15144	.	.	.	.	.	.	.	-:0.0002	-:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTCGTCTGA	byFrequency	5	ESCA
RNF145	0	.	GRCh37	5	158635064	158635064	+	Intron	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51+1797C>T	.	.	ENST00000518802	.	14	11	3	9	9	0	RNF145,5_prime_UTR_variant,,ENST00000521606,;RNF145,5_prime_UTR_variant,,ENST00000519865,;RNF145,intron_variant,,ENST00000518802,;RNF145,intron_variant,,ENST00000424310,;RNF145,upstream_gene_variant,,ENST00000520638,;RNF145,upstream_gene_variant,,ENST00000274542,;CTB-11I22.1,upstream_gene_variant,,ENST00000521204,;RNF145,intron_variant,,ENST00000520548,;	A	ENSG00000145860	ENST00000518802	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RNF145	HGNC	20853	protein_coding	YES	CCDS56393.1	ENSP00000430955	RN145_HUMAN	Q8NDT8_HUMAN,Q8NC08_HUMAN,Q8N783_HUMAN,Q6MZY8_HUMAN,B7Z249_HUMAN,B3KWZ2_HUMAN	UPI0001E8F5CB	.	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTGCGACGCA	.	2	ESCA
MAT2B	0	.	GRCh37	5	162932668	162932668	+	5'UTR	SNP	A	A	T	rs761436765	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-25A>T	.	.	ENST00000321757	1/7	190	122	68	148	148	0	MAT2B,5_prime_UTR_variant,,ENST00000321757,;MAT2B,5_prime_UTR_variant,,ENST00000421814,;MAT2B,5_prime_UTR_variant,,ENST00000518095,;MAT2B,intron_variant,,ENST00000280969,;MAT2B,5_prime_UTR_variant,,ENST00000520449,;MAT2B,non_coding_transcript_exon_variant,,ENST00000523606,;MAT2B,intron_variant,,ENST00000519719,;	T	ENSG00000038274	ENST00000321757	Transcript	5_prime_UTR_variant	115	.	.	.	.	rs761436765	.	.	1	MAT2B	HGNC	6905	protein_coding	YES	CCDS4365.1	ENSP00000325425	MAT2B_HUMAN	.	UPI0000037B81	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTGAGGCTG	.	5	ESCA
GOLPH3	0	.	GRCh37	5	32125003	32125003	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1315A>G	.	.	ENST00000265070	4/4	236	173	63	158	158	0	GOLPH3,3_prime_UTR_variant,,ENST00000265070,;CTD-2152M20.2,upstream_gene_variant,,ENST00000503441,;GOLPH3,downstream_gene_variant,,ENST00000512668,;GOLPH3,downstream_gene_variant,,ENST00000503610,;	C	ENSG00000113384	ENST00000265070	Transcript	3_prime_UTR_variant	2528	.	.	.	.	.	.	.	-1	GOLPH3	HGNC	15452	protein_coding	YES	CCDS3896.1	ENSP00000265070	GOLP3_HUMAN	B3KQJ9_HUMAN,B3KS18_HUMAN,B3KQ71_HUMAN	UPI000006EEF4	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTATGGTAA	.	5	ESCA
RICTOR	0	.	GRCh37	5	38945607	38945607	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4619T>A	p.Ile1540Lys	p.I1540K	ENST00000357387	34/38	60	41	18	65	65	0	RICTOR,missense_variant,p.Ile1540Lys,ENST00000357387,;RICTOR,missense_variant,p.Ile1564Lys,ENST00000296782,;RICTOR,3_prime_UTR_variant,,ENST00000511516,;OSMR,3_prime_UTR_variant,,ENST00000509237,;RICTOR,upstream_gene_variant,,ENST00000505927,;OSMR,downstream_gene_variant,,ENST00000508882,;	T	ENSG00000164327	ENST00000357387	Transcript	missense_variant	4650	4619	1540	I/K	aTa/aAa	.	.	.	-1	RICTOR	HGNC	28611	protein_coding	YES	CCDS34148.1	ENSP00000349959	RICTR_HUMAN	.	UPI00003529F3	.	tolerated(0.35)	benign(0.014)	34/38	.	hmmpanther:PTHR13298:SF11,hmmpanther:PTHR13298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACATATTGCA	.	5	ESCA
LINC01020	0	.	GRCh37	5	5057902	5057902	+	RNA	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.585T>C	.	.	ENST00000508201	4/8	76	49	27	75	75	0	LINC01020,non_coding_transcript_exon_variant,,ENST00000507599,;LINC01020,non_coding_transcript_exon_variant,,ENST00000508201,;LINC01020,non_coding_transcript_exon_variant,,ENST00000514474,;LINC01020,non_coding_transcript_exon_variant,,ENST00000509382,;	C	ENSG00000215231	ENST00000508201	Transcript	non_coding_transcript_exon_variant	585	.	.	.	.	.	.	.	1	LINC01020	HGNC	27968	lincRNA	YES	.	.	.	.	.	.	.	.	4/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAAGTGAACT	.	5	ESCA
SGTB	0	.	GRCh37	5	65000152	65000152	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.328C>G	p.Gln110Glu	p.Q110E	ENST00000381007	5/11	149	100	49	88	88	0	SGTB,missense_variant,p.Gln110Glu,ENST00000381007,;SGTB,missense_variant,p.Gln110Glu,ENST00000506816,;	C	ENSG00000197860	ENST00000381007	Transcript	missense_variant	564	328	110	Q/E	Cag/Gag	.	.	.	-1	SGTB	HGNC	23567	protein_coding	YES	CCDS3988.1	ENSP00000370395	SGTB_HUMAN	O75589_HUMAN,D6RFW1_HUMAN	UPI000004D24F	.	tolerated(0.18)	benign(0.007)	5/11	.	PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR22904:SF290,hmmpanther:PTHR22904,Pfam_domain:PF13414,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTGTGTGT	.	5	ESCA
AIM1	0	.	GRCh37	6	106960342	106960342	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126C>T	p.%3D	p.D42D	ENST00000369066	1/20	67	63	4	51	51	0	AIM1,synonymous_variant,p.%3D,ENST00000369066,;	T	ENSG00000112297	ENST00000369066	Transcript	synonymous_variant	613	126	42	D	gaC/gaT	.	.	.	1	AIM1	HGNC	356	protein_coding	YES	CCDS34506.1	ENSP00000358062	AIM1_HUMAN	B3KPT0_HUMAN	UPI000013C91D	.	.	.	1/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACGACGAGGT	.	2	ESCA
NR2E1	0	.	GRCh37	6	108497939	108497939	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.492C>A	p.%3D	p.P164P	ENST00000368986	4/9	24	18	6	12	12	0	NR2E1,synonymous_variant,p.%3D,ENST00000368986,;NR2E1,synonymous_variant,p.%3D,ENST00000368983,;NR2E1,downstream_gene_variant,,ENST00000426403,;NR2E1,non_coding_transcript_exon_variant,,ENST00000484978,;	A	ENSG00000112333	ENST00000368986	Transcript	synonymous_variant	1200	492	164	P	ccC/ccA	.	.	.	1	NR2E1	HGNC	7973	protein_coding	YES	CCDS5063.1	ENSP00000357982	NR2E1_HUMAN	B6ZGT9_HUMAN,A6PVF6_HUMAN	UPI0000130478	.	.	.	4/9	.	hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF79,Gene3D:1.10.565.10,Superfamily_domains:SSF48508	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACGCCCAAGGT	.	4	ESCA
FOXO3	0	.	GRCh37	6	109005360	109005360	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4365C>T	.	.	ENST00000406360	3/3	71	59	12	51	50	1	FOXO3,3_prime_UTR_variant,,ENST00000406360,;FOXO3,3_prime_UTR_variant,,ENST00000343882,;FOXO3,downstream_gene_variant,,ENST00000540898,;	T	ENSG00000118689	ENST00000406360	Transcript	3_prime_UTR_variant	6730	.	.	.	.	.	.	.	1	FOXO3	HGNC	3821	protein_coding	YES	CCDS5068.1	ENSP00000385824	FOXO3_HUMAN	B4DVZ6_HUMAN	UPI000012ADEA	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GGTCACTTATT	.	2	ESCA
TUBE1	0	.	GRCh37	6	112392560	112392560	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*55C>T	.	.	ENST00000368662	12/12	63	42	20	62	62	0	TUBE1,3_prime_UTR_variant,,ENST00000368662,;WISP3,downstream_gene_variant,,ENST00000361714,;WISP3,downstream_gene_variant,,ENST00000409166,;WISP3,downstream_gene_variant,,ENST00000368663,;WISP3,downstream_gene_variant,,ENST00000230529,;WISP3,downstream_gene_variant,,ENST00000368666,;WISP3,downstream_gene_variant,,ENST00000604763,;TUBE1,non_coding_transcript_exon_variant,,ENST00000604814,;TUBE1,downstream_gene_variant,,ENST00000441191,;TUBE1,3_prime_UTR_variant,,ENST00000605457,;TUBE1,downstream_gene_variant,,ENST00000604689,;TUBE1,downstream_gene_variant,,ENST00000603651,;WISP3,downstream_gene_variant,,ENST00000454589,;WISP3,downstream_gene_variant,,ENST00000368664,;TUBE1,downstream_gene_variant,,ENST00000604743,;	A	ENSG00000074935	ENST00000368662	Transcript	3_prime_UTR_variant	1562	.	.	.	.	.	.	.	-1	TUBE1	HGNC	20775	protein_coding	YES	CCDS5100.1	ENSP00000357651	TBE_HUMAN	.	UPI0000136A4E	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACAGAAAGG	.	5	ESCA
ADTRP	0	.	GRCh37	6	11768590	11768590	+	Silent	SNP	G	G	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.234C>A	p.%3D	p.V78V	ENST00000229583	3/7	95	66	29	66	66	0	ADTRP,synonymous_variant,p.%3D,ENST00000414691,;ADTRP,synonymous_variant,p.%3D,ENST00000229583,;ADTRP,synonymous_variant,p.%3D,ENST00000379413,;ADTRP,synonymous_variant,p.%3D,ENST00000506810,;ADTRP,synonymous_variant,p.%3D,ENST00000379415,;ADTRP,upstream_gene_variant,,ENST00000512139,;ADTRP,stop_gained,p.Ser80Ter,ENST00000485323,;ADTRP,upstream_gene_variant,,ENST00000505099,;	T	ENSG00000111863	ENST00000229583	Transcript	synonymous_variant	278	234	78	V	gtC/gtA	.	.	.	-1	ADTRP	HGNC	21214	protein_coding	YES	CCDS47374.1	ENSP00000229583	ADTRP_HUMAN	.	UPI00017A7DC7	.	.	.	3/7	.	hmmpanther:PTHR10989,hmmpanther:PTHR10989:SF15,Pfam_domain:PF04750	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGTGACCCC	.	5	ESCA
HBS1L	0	.	GRCh37	6	135376037	135376037	+	5'Flank	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000367837	.	17	8	9	14	14	0	HBS1L,intron_variant,,ENST00000529882,;HBS1L,upstream_gene_variant,,ENST00000415177,;HBS1L,upstream_gene_variant,,ENST00000367824,;HBS1L,upstream_gene_variant,,ENST00000367837,;HBS1L,upstream_gene_variant,,ENST00000367820,;HBS1L,upstream_gene_variant,,ENST00000524715,;HBS1L,upstream_gene_variant,,ENST00000445176,;HBS1L,upstream_gene_variant,,ENST00000525067,;HBS1L,upstream_gene_variant,,ENST00000367822,;HBS1L,upstream_gene_variant,,ENST00000367826,;HBS1L,upstream_gene_variant,,ENST00000314674,;HBS1L,upstream_gene_variant,,ENST00000533274,;CTA-212D2.2,upstream_gene_variant,,ENST00000447508,;HBS1L,upstream_gene_variant,,ENST00000526100,;	A	ENSG00000112339	ENST00000367837	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1	-1	HBS1L	HGNC	4834	protein_coding	YES	CCDS5173.1	ENSP00000356811	HBS1L_HUMAN	E9PS53_HUMAN,E9PHZ9_HUMAN,D9YZV0_HUMAN,B7Z524_HUMAN,B7Z1K2_HUMAN	UPI00000372EA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCTGAGGGC	.	2	ESCA
AIG1	0	.	GRCh37	6	143457998	143457998	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168C>G	p.Ile56Met	p.I56M	ENST00000357847	2/6	53	27	25	40	40	0	AIG1,missense_variant,p.Ile56Met,ENST00000494282,;AIG1,missense_variant,p.Ile52Met,ENST00000367601,;AIG1,missense_variant,p.Ile56Met,ENST00000357847,;AIG1,missense_variant,p.Ile56Met,ENST00000275235,;AIG1,missense_variant,p.Ile56Met,ENST00000367598,;AIG1,5_prime_UTR_variant,,ENST00000458219,;AIG1,intron_variant,,ENST00000344492,;AIG1,intron_variant,,ENST00000447498,;	G	ENSG00000146416	ENST00000357847	Transcript	missense_variant	218	168	56	I/M	atC/atG	.	.	.	1	AIG1	HGNC	21607	protein_coding	YES	CCDS5198.1	ENSP00000350509	AIG1_HUMAN	Q5THU2_HUMAN,Q5T2H0_HUMAN	UPI000006F22E	.	deleterious(0)	possibly_damaging(0.768)	2/6	.	Transmembrane_helices:TMhelix,Pfam_domain:PF04750,hmmpanther:PTHR10989,hmmpanther:PTHR10989:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATCTGTGT	.	5	ESCA
TAGAP	0	.	GRCh37	6	159457656	159457656	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1399G>A	p.Ala467Thr	p.A467T	ENST00000367066	10/10	54	38	16	35	35	0	TAGAP,missense_variant,p.Ala289Thr,ENST00000326965,;TAGAP,missense_variant,p.Ala467Thr,ENST00000367066,;TAGAP,downstream_gene_variant,,ENST00000338313,;RP1-111C20.4,intron_variant,,ENST00000606470,;RP1-111C20.4,intron_variant,,ENST00000606466,;RP1-111C20.4,intron_variant,,ENST00000607796,;RP1-111C20.4,intron_variant,,ENST00000607391,;	T	ENSG00000164691	ENST00000367066	Transcript	missense_variant	1731	1399	467	A/T	Gcg/Acg	.	.	.	-1	TAGAP	HGNC	15669	protein_coding	YES	CCDS5261.1	ENSP00000356033	TAGAP_HUMAN	.	UPI0000071CD5	.	tolerated(0.37)	benign(0.007)	10/10	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23179,hmmpanther:PTHR23179:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACGCGTCCA	.	5	ESCA
QKI	0	.	GRCh37	6	163989702	163989702	+	Intron	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1009+1875A>G	.	.	ENST00000361752	.	75	47	28	59	59	0	QKI,3_prime_UTR_variant,,ENST00000453779,;QKI,3_prime_UTR_variant,,ENST00000275262,;QKI,3_prime_UTR_variant,,ENST00000392127,;QKI,intron_variant,,ENST00000544361,;QKI,intron_variant,,ENST00000361195,;QKI,intron_variant,,ENST00000537883,;QKI,intron_variant,,ENST00000361752,;QKI,downstream_gene_variant,,ENST00000424802,;QKI,intron_variant,,ENST00000361758,;QKI,intron_variant,,ENST00000545607,;QKI,intron_variant,,ENST00000541696,;QKI,downstream_gene_variant,,ENST00000540719,;	G	ENSG00000112531	ENST00000361752	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	QKI	HGNC	21100	protein_coding	YES	CCDS5285.1	ENSP00000355094	QKI_HUMAN	F5H8C8_HUMAN,F5H5U6_HUMAN,F5GYM3_HUMAN	UPI0000029EBD	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAGTATAAGC	.	5	ESCA
RNF39	0	.	GRCh37	6	30041253	30041253	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570T>C	p.%3D	p.D190D	ENST00000244360	2/4	94	68	26	80	80	0	RNF39,synonymous_variant,p.%3D,ENST00000376751,;RNF39,synonymous_variant,p.%3D,ENST00000244360,;PPP1R11,downstream_gene_variant,,ENST00000376769,;PPP1R11,downstream_gene_variant,,ENST00000376763,;PPP1R11,downstream_gene_variant,,ENST00000376772,;PPP1R11,downstream_gene_variant,,ENST00000376765,;PPP1R11,downstream_gene_variant,,ENST00000376773,;PPP1R11,downstream_gene_variant,,ENST00000376758,;	G	ENSG00000204618	ENST00000244360	Transcript	synonymous_variant	668	570	190	D	gaT/gaC	.	.	.	-1	RNF39	HGNC	18064	protein_coding	YES	CCDS4673.1	ENSP00000244360	RNF39_HUMAN	Q96QB5_HUMAN	UPI000000D735	.	.	.	2/4	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATATCCTA	.	5	ESCA
HSPA1B	0	.	GRCh37	6	31795547	31795547	+	5'UTR	SNP	C	C	T	rs572178551	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-181C>T	.	.	ENST00000375650	1/1	14	5	9	14	14	0	HSPA1B,5_prime_UTR_variant,,ENST00000375650,;HSPA1B,upstream_gene_variant,,ENST00000545241,;	T	ENSG00000204388	ENST00000375650	Transcript	5_prime_UTR_variant	36	.	.	.	.	rs572178551	.	.	1	HSPA1B	HGNC	5233	protein_coding	YES	CCDS34415.1	ENSP00000364801	HSP71_HUMAN	A8K5I0_HUMAN	UPI0000000C40	.	.	.	1/1	.	.	G:0.0002	G:0	G:0.0014	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGTCCGCTT	by1000G	5	ESCA
FUT9	0	.	GRCh37	6	96663051	96663051	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10940G>A	.	.	ENST00000302103	3/3	111	105	6	76	76	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	A	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	12346	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAGGCAAGA	.	2	ESCA
USP45	0	.	GRCh37	6	99881193	99881193	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2399A>G	.	.	ENST00000327681	18/18	139	96	43	133	133	0	USP45,3_prime_UTR_variant,,ENST00000392738,;USP45,3_prime_UTR_variant,,ENST00000500704,;USP45,3_prime_UTR_variant,,ENST00000327681,;USP45,3_prime_UTR_variant,,ENST00000539675,;USP45,downstream_gene_variant,,ENST00000369233,;RP11-98I9.4,downstream_gene_variant,,ENST00000418945,;USP45,3_prime_UTR_variant,,ENST00000496518,;	C	ENSG00000123552	ENST00000327681	Transcript	3_prime_UTR_variant	5377	.	.	.	.	.	.	.	-1	USP45	HGNC	20080	protein_coding	YES	CCDS34501.1	ENSP00000333376	UBP45_HUMAN	F5H1L5_HUMAN,D6RE98_HUMAN	UPI0000253B80	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTAATTCATT	.	5	ESCA
MTPN	0	.	GRCh37	7	135613632	135613632	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1042C>T	.	.	ENST00000393085	4/4	35	32	3	43	43	0	MTPN,3_prime_UTR_variant,,ENST00000393085,;AC015987.2,downstream_gene_variant,,ENST00000416501,;LUZP6,upstream_gene_variant,,ENST00000589735,;MTPN,downstream_gene_variant,,ENST00000435723,;AC015987.1,intron_variant,,ENST00000419211,;	A	ENSG00000105887	ENST00000393085	Transcript	3_prime_UTR_variant	1615	.	.	.	.	.	.	.	-1	MTPN	HGNC	15667	protein_coding	YES	CCDS5842.1	ENSP00000376800	MTPN_HUMAN	Q69YG1_HUMAN	UPI00000012BC	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGGGCTAAA	.	2	ESCA
OR2F2	0	.	GRCh37	7	143632543	143632543	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218A>T	p.Tyr73Phe	p.Y73F	ENST00000408955	1/1	36	14	21	50	50	0	OR2F2,missense_variant,p.Tyr73Phe,ENST00000408955,;	T	ENSG00000221910	ENST00000408955	Transcript	missense_variant	285	218	73	Y/F	tAt/tTt	.	.	.	1	OR2F2	HGNC	8247	protein_coding	YES	CCDS43666.1	ENSP00000386222	OR2F2_HUMAN	.	UPI0000041C25	.	tolerated(0.44)	probably_damaging(0.973)	1/1	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26453:SF63,hmmpanther:PTHR26453,PROSITE_profiles:PS50262,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D70N|c.208G>A|3,BUFFER|p.T75A|c.223A>G|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTATGCCA	.	5	ESCA
KMT2C	0	.	GRCh37	7	151878602	151878602	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6343G>T	p.Ala2115Ser	p.A2115S	ENST00000262189	36/59	34	18	15	41	41	0	KMT2C,missense_variant,p.Ala2115Ser,ENST00000355193,;KMT2C,missense_variant,p.Ala2115Ser,ENST00000262189,;KMT2C,intron_variant,,ENST00000558665,;KMT2C,upstream_gene_variant,,ENST00000360104,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;	A	ENSG00000055609	ENST00000262189	Transcript	missense_variant	6562	6343	2115	A/S	Gct/Tct	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	benign(0.05)	36/59	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAGCCCTTG	.	5	ESCA
CCDC126	0	.	GRCh37	7	23684068	23684068	+	3'UTR	SNP	G	G	A	rs184562874	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1334G>A	.	.	ENST00000307471	4/4	151	106	44	105	105	0	CCDC126,3_prime_UTR_variant,,ENST00000307471,;CCDC126,3_prime_UTR_variant,,ENST00000409765,;CCDC126,downstream_gene_variant,,ENST00000448353,;CCDC126,downstream_gene_variant,,ENST00000410069,;CCDC126,downstream_gene_variant,,ENST00000472407,;	A	ENSG00000169193	ENST00000307471	Transcript	3_prime_UTR_variant	2214	.	.	.	.	rs184562874	.	.	1	CCDC126	HGNC	22398	protein_coding	YES	CCDS5384.1	ENSP00000304355	CC126_HUMAN	C9J0J0_HUMAN	UPI0000048F13	.	.	.	4/4	.	.	A:0.0008	A:0.0015	A:0.0014	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTTCGTCATT	byFrequency|byCluster|by1000G	5	ESCA
GBAS	0	.	GRCh37	7	56067716	56067717	+	3'UTR	INS	-	-	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*952dupT	.	.	ENST00000322090	10/10	87	72	15	58	58	0	GBAS,3_prime_UTR_variant,,ENST00000322090,;GBAS,3_prime_UTR_variant,,ENST00000446778,;GBAS,non_coding_transcript_exon_variant,,ENST00000497279,;GBAS,downstream_gene_variant,,ENST00000415967,;	T	ENSG00000146729	ENST00000322090	Transcript	3_prime_UTR_variant	1841-1842	.	.	.	.	.	.	.	1	GBAS	HGNC	4179	protein_coding	YES	CCDS5521.1	ENSP00000313050	NIPS2_HUMAN	C9K068_HUMAN,C9J7B1_HUMAN	UPI00000015EB	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTACCATGTGA	.	3	ESCA
ASL	0	.	GRCh37	7	65546811	65546811	+	Missense_Mutation	SNP	C	C	T	rs564735357	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34C>T	p.Arg12Trp	p.R12W	ENST00000304874	3/17	58	33	25	32	32	0	ASL,missense_variant,p.Arg12Trp,ENST00000380839,;ASL,missense_variant,p.Arg12Trp,ENST00000395331,;ASL,missense_variant,p.Arg12Trp,ENST00000304874,;ASL,missense_variant,p.Arg12Trp,ENST00000395332,;ASL,intron_variant,,ENST00000362000,;ASL,non_coding_transcript_exon_variant,,ENST00000496336,;ASL,non_coding_transcript_exon_variant,,ENST00000487982,;	T	ENSG00000126522	ENST00000304874	Transcript	missense_variant	136	34	12	R/W	Cgg/Tgg	rs564735357	.	.	1	ASL	HGNC	746	protein_coding	YES	CCDS5531.1	ENSP00000307188	ARLY_HUMAN	.	UPI0000001634	.	deleterious(0)	probably_damaging(1)	3/17	.	HAMAP:MF_00006,hmmpanther:PTHR11444,hmmpanther:PTHR11444:SF3,Gene3D:1.10.275.10,Pfam_domain:PF00206,TIGRFAM_domain:TIGR00838,Superfamily_domains:SSF48557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGCCGGTTT	.	5	ESCA
RP1L1	0	.	GRCh37	8	10468842	10468842	+	Silent	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2766G>T	p.%3D	p.L922L	ENST00000382483	4/4	67	27	40	55	55	0	RP1L1,synonymous_variant,p.%3D,ENST00000382483,;	A	ENSG00000183638	ENST00000382483	Transcript	synonymous_variant	2990	2766	922	L	ctG/ctT	.	.	.	-1	RP1L1	HGNC	15946	protein_coding	YES	CCDS43708.1	ENSP00000371923	.	A6NKC6_HUMAN	UPI00001AF9CC	.	.	.	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23005:SF3,hmmpanther:PTHR23005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGGACAGCCC	.	5	ESCA
SNTG1	0	.	GRCh37	8	51617179	51617179	+	Missense_Mutation	SNP	G	G	A	rs150099561	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000522124	16/19	65	47	18	38	38	0	SNTG1,missense_variant,p.Arg353Gln,ENST00000517473,;SNTG1,missense_variant,p.Arg353Gln,ENST00000518864,;SNTG1,missense_variant,p.Arg353Gln,ENST00000276467,;SNTG1,missense_variant,p.Arg353Gln,ENST00000522124,;SNTG1,3_prime_UTR_variant,,ENST00000520825,;SNTG1,3_prime_UTR_variant,,ENST00000524004,;	A	ENSG00000147481	ENST00000522124	Transcript	missense_variant	1719	1058	353	R/Q	cGa/cAa	rs150099561	.	.	1	SNTG1	HGNC	13740	protein_coding	YES	CCDS6147.1	ENSP00000429842	SNTG1_HUMAN	E5RIN0_HUMAN	UPI000004A0DD	.	tolerated(0.89)	benign(0)	16/19	.	PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	A:0.0007	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGACCGACGGA	byFrequency|byCluster|by1000G	5	ESCA
NSMAF	0	.	GRCh37	8	59506838	59506838	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1997G>T	p.Gly666Val	p.G666V	ENST00000427130	23/31	118	96	22	69	69	0	NSMAF,missense_variant,p.Gly635Val,ENST00000038176,;NSMAF,missense_variant,p.Gly666Val,ENST00000427130,;NSMAF,non_coding_transcript_exon_variant,,ENST00000523177,;NSMAF,downstream_gene_variant,,ENST00000523982,;NSMAF,non_coding_transcript_exon_variant,,ENST00000519166,;NSMAF,non_coding_transcript_exon_variant,,ENST00000523106,;NSMAF,non_coding_transcript_exon_variant,,ENST00000519174,;NSMAF,non_coding_transcript_exon_variant,,ENST00000524148,;NSMAF,downstream_gene_variant,,ENST00000519227,;NSMAF,upstream_gene_variant,,ENST00000517612,;NSMAF,upstream_gene_variant,,ENST00000521712,;	A	ENSG00000035681	ENST00000427130	Transcript	missense_variant	2185	1997	666	G/V	gGa/gTa	.	.	.	-1	NSMAF	HGNC	8017	protein_coding	YES	CCDS47864.1	ENSP00000411012	FAN_HUMAN	.	UPI000192950C	.	tolerated(0.06)	probably_damaging(0.997)	23/31	.	PROSITE_profiles:PS50294,hmmpanther:PTHR13743,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGATTCCAGTA	.	4	ESCA
CDK5RAP2	0	.	GRCh37	9	123165255	123165255	+	Silent	SNP	C	C	G	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5136G>C	p.%3D	p.L1712L	ENST00000349780	34/38	70	43	27	34	34	0	CDK5RAP2,synonymous_variant,p.%3D,ENST00000416449,;CDK5RAP2,synonymous_variant,p.%3D,ENST00000349780,;CDK5RAP2,synonymous_variant,p.%3D,ENST00000360822,;CDK5RAP2,synonymous_variant,p.%3D,ENST00000425647,;CDK5RAP2,synonymous_variant,p.%3D,ENST00000360190,;CDK5RAP2,synonymous_variant,p.%3D,ENST00000359309,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000433194,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000480467,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000484546,;CDK5RAP2,downstream_gene_variant,,ENST00000483412,;CDK5RAP2,upstream_gene_variant,,ENST00000474262,;	G	ENSG00000136861	ENST00000349780	Transcript	synonymous_variant	5316	5136	1712	L	ctG/ctC	.	.	.	-1	CDK5RAP2	HGNC	18672	protein_coding	YES	CCDS6823.1	ENSP00000343818	CK5P2_HUMAN	F8WBJ0_HUMAN,C9K0C9_HUMAN	UPI0000367673	.	.	.	34/38	.	hmmpanther:PTHR13895,hmmpanther:PTHR13895:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGACCAGGCG	.	5	ESCA
TRAF1	0	.	GRCh37	9	123688278	123688278	+	Missense_Mutation	SNP	C	C	T	rs753124357	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76G>A	p.Val26Ile	p.V26I	ENST00000373887	2/8	85	55	30	42	42	0	TRAF1,missense_variant,p.Val26Ile,ENST00000540010,;TRAF1,missense_variant,p.Val26Ile,ENST00000373887,;	T	ENSG00000056558	ENST00000373887	Transcript	missense_variant	2522	76	26	V/I	Gtc/Atc	rs753124357	.	.	-1	TRAF1	HGNC	12031	protein_coding	YES	CCDS6825.1	ENSP00000362994	TRAF1_HUMAN	.	UPI0000001079	.	tolerated(1)	benign(0)	2/8	.	PIRSF_domain:PIRSF015614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGACGGTGG	byFrequency	5	ESCA
OLFM1	0	.	GRCh37	9	137968928	137968928	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96+1280G>T	.	.	ENST00000252854	.	71	10	60	63	63	0	OLFM1,missense_variant,p.Gly123Cys,ENST00000371799,;OLFM1,intron_variant,,ENST00000277415,;OLFM1,intron_variant,,ENST00000252854,;OLFM1,downstream_gene_variant,,ENST00000371801,;	T	ENSG00000130558	ENST00000252854	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	OLFM1	HGNC	17187	protein_coding	YES	CCDS6986.1	ENSP00000252854	NOE1_HUMAN	Q6IMJ8_HUMAN,Q96BL8_HUMAN,F5H810_HUMAN,F5GZQ2_HUMAN,B3KR22_HUMAN	UPI000013CD8C	.	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTCTTGGCCCC	.	4	ESCA
C9orf142	0	.	GRCh37	9	139888246	139888246	+	Missense_Mutation	SNP	G	G	A	rs370085766	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.604G>A	p.Asp202Asn	p.D202N	ENST00000371620	7/7	145	99	46	58	58	0	C9orf142,missense_variant,p.Asp202Asn,ENST00000371620,;CLIC3,downstream_gene_variant,,ENST00000494426,;C9orf142,non_coding_transcript_exon_variant,,ENST00000492564,;C9orf142,non_coding_transcript_exon_variant,,ENST00000463765,;C9orf142,non_coding_transcript_exon_variant,,ENST00000498095,;C9orf142,non_coding_transcript_exon_variant,,ENST00000483807,;C9orf142,non_coding_transcript_exon_variant,,ENST00000493968,;C9orf142,non_coding_transcript_exon_variant,,ENST00000467845,;C9orf142,downstream_gene_variant,,ENST00000481187,;CLIC3,downstream_gene_variant,,ENST00000480181,;CLIC3,downstream_gene_variant,,ENST00000473911,;C9orf142,downstream_gene_variant,,ENST00000468484,;C9orf142,downstream_gene_variant,,ENST00000488678,;	A	ENSG00000148362	ENST00000371620	Transcript	missense_variant	630	604	202	D/N	Gat/Aat	rs370085766,COSM1106997	.	.	1	C9orf142	HGNC	27849	protein_coding	YES	CCDS7020.1	ENSP00000360682	CI142_HUMAN	.	UPI00001BD908	.	deleterious(0)	probably_damaging(0.949)	7/7	.	Pfam_domain:PF15384	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTCGATGAG	byFrequency|byCluster	5	ESCA
SPATA31E1	0	.	GRCh37	9	90503589	90503589	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4187G>C	p.Arg1396Thr	p.R1396T	ENST00000325643	4/4	72	68	4	45	45	0	SPATA31E1,missense_variant,p.Arg1396Thr,ENST00000325643,;	C	ENSG00000177992	ENST00000325643	Transcript	missense_variant	4253	4187	1396	R/T	aGa/aCa	.	.	.	1	SPATA31E1	HGNC	26672	protein_coding	YES	CCDS6676.1	ENSP00000322640	S31E1_HUMAN	.	UPI000036764A	.	deleterious(0.02)	possibly_damaging(0.661)	4/4	.	hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCAGAGACA	.	2	ESCA
DCAF12L1	0	.	GRCh37	X	125685998	125685998	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7D-01A-11D-A403-09	TCGA-VR-AA7D-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>T	p.%3D	p.F198F	ENST00000371126	1/2	48	16	32	44	44	0	DCAF12L1,synonymous_variant,p.%3D,ENST00000371126,;	A	ENSG00000198889	ENST00000371126	Transcript	synonymous_variant	837	594	198	F	ttC/ttT	.	.	.	-1	DCAF12L1	HGNC	29395	protein_coding	YES	CCDS14610.1	ENSP00000360167	DC121_HUMAN	.	UPI0000160112	.	.	.	1/2	.	PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR19860:SF9,hmmpanther:PTHR19860,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGGCGAAGAT	.	5	ESCA
DHX32	0	.	GRCh37	10	127548228	127548228	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.793G>A	p.Glu265Lys	p.E265K	ENST00000284690	3/11	70	63	7	99	99	0	DHX32,missense_variant,p.Glu265Lys,ENST00000284688,;DHX32,missense_variant,p.Glu265Lys,ENST00000284690,;DHX32,upstream_gene_variant,,ENST00000368721,;	T	ENSG00000089876	ENST00000284690	Transcript	missense_variant	1284	793	265	E/K	Gaa/Aaa	.	.	.	-1	DHX32	HGNC	16717	protein_coding	YES	CCDS7652.1	ENSP00000284690	DHX32_HUMAN	.	UPI00000467F4	.	deleterious(0.01)	possibly_damaging(0.611)	3/11	.	hmmpanther:PTHR18934:SF88,hmmpanther:PTHR18934,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AATTTCAAAGA	.	3	ESCA
SYNPO2L	0	.	GRCh37	10	75405286	75405286	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1190T>G	.	.	ENST00000394810	4/4	12	8	4	21	21	0	SYNPO2L,3_prime_UTR_variant,,ENST00000372873,;SYNPO2L,3_prime_UTR_variant,,ENST00000394810,;MYOZ1,upstream_gene_variant,,ENST00000359322,;	C	ENSG00000166317	ENST00000394810	Transcript	3_prime_UTR_variant	4274	.	.	.	.	.	.	.	-1	SYNPO2L	HGNC	23532	protein_coding	YES	CCDS44438.1	ENSP00000378289	SYP2L_HUMAN	U3KQD0_HUMAN	UPI000042704D	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TTTTCATTTCC	.	3	ESCA
CCSER2	0	.	GRCh37	10	86273532	86273532	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*233C>G	.	.	ENST00000224756	11/11	45	32	13	50	50	0	CCSER2,missense_variant,p.Pro885Ala,ENST00000372088,;CCSER2,3_prime_UTR_variant,,ENST00000224756,;CCSER2,downstream_gene_variant,,ENST00000543283,;CCSER2,non_coding_transcript_exon_variant,,ENST00000480006,;CCSER2,non_coding_transcript_exon_variant,,ENST00000494144,;CCSER2,downstream_gene_variant,,ENST00000498300,;CCSER2,downstream_gene_variant,,ENST00000493409,;CCSER2,downstream_gene_variant,,ENST00000466105,;	G	ENSG00000107771	ENST00000224756	Transcript	3_prime_UTR_variant	2923	.	.	.	.	.	.	.	1	CCSER2	HGNC	29197	protein_coding	YES	CCDS31235.1	ENSP00000224756	CCSE2_HUMAN	B4DFY4_HUMAN	UPI00005E1AE0	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATACCCACT	.	5	ESCA
MARCH5	0	.	GRCh37	10	94113635	94113635	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2671C>G	.	.	ENST00000358935	6/6	113	84	28	127	127	0	MARCH5,3_prime_UTR_variant,,ENST00000358935,;MARCH5,downstream_gene_variant,,ENST00000462465,;MARCH5,downstream_gene_variant,,ENST00000467521,;MARCH5,downstream_gene_variant,,ENST00000492319,;	G	ENSG00000198060	ENST00000358935	Transcript	3_prime_UTR_variant	3840	.	.	.	.	.	.	.	1	MARCH5	HGNC	26025	protein_coding	YES	CCDS7420.1	ENSP00000351813	MARH5_HUMAN	B4DGV8_HUMAN	UPI000006D0BC	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTGCTGTAA	.	5	ESCA
SLIT1	0	.	GRCh37	10	98760861	98760861	+	3'UTR	SNP	G	G	T	rs201384867	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8C>A	.	.	ENST00000266058	37/37	25	21	4	49	49	0	SLIT1,3_prime_UTR_variant,,ENST00000266058,;ARHGAP19-SLIT1,3_prime_UTR_variant,,ENST00000453547,;SLIT1,downstream_gene_variant,,ENST00000371070,;SLIT1,upstream_gene_variant,,ENST00000494968,;	T	ENSG00000187122	ENST00000266058	Transcript	3_prime_UTR_variant	4859	.	.	.	.	rs201384867	.	.	-1	SLIT1	HGNC	11085	protein_coding	YES	CCDS7453.1	ENSP00000266058	SLIT1_HUMAN	.	UPI00001F9491	.	.	.	37/37	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCACGCCCAG	byCluster|by1000G	2	ESCA
DRD2	0	.	GRCh37	11	113295305	113295305	+	Silent	SNP	G	G	A	rs200831689	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.69C>T	p.%3D	p.N23N	ENST00000362072	2/8	37	32	5	88	88	0	DRD2,synonymous_variant,p.%3D,ENST00000542968,;DRD2,synonymous_variant,p.%3D,ENST00000543292,;DRD2,synonymous_variant,p.%3D,ENST00000544518,;DRD2,synonymous_variant,p.%3D,ENST00000362072,;DRD2,synonymous_variant,p.%3D,ENST00000355319,;DRD2,synonymous_variant,p.%3D,ENST00000346454,;DRD2,synonymous_variant,p.%3D,ENST00000538967,;DRD2,downstream_gene_variant,,ENST00000542616,;DRD2,upstream_gene_variant,,ENST00000535984,;DRD2,non_coding_transcript_exon_variant,,ENST00000540600,;	A	ENSG00000149295	ENST00000362072	Transcript	synonymous_variant	414	69	23	N	aaC/aaT	rs200831689	.	.	-1	DRD2	HGNC	3023	protein_coding	YES	CCDS8361.1	ENSP00000354859	DRD2_HUMAN	Q6LDH7_HUMAN	UPI0000001315	.	.	.	2/8	.	hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF68,Superfamily_domains:SSF81321	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCCGTTGAA	byCluster|by1000G	4	ESCA
OR51L1	0	.	GRCh37	11	5020730	5020730	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.518G>A	p.Gly173Asp	p.G173D	ENST00000321543	1/1	28	18	10	47	47	0	OR51L1,missense_variant,p.Gly173Asp,ENST00000321543,;	A	ENSG00000176798	ENST00000321543	Transcript	missense_variant	518	518	173	G/D	gGc/gAc	.	.	.	1	OR51L1	HGNC	14759	protein_coding	YES	CCDS31369.1	ENSP00000322156	O51L1_HUMAN	.	UPI0000041B76	.	tolerated(0.11)	benign(0.004)	1/1	.	Superfamily_domains:SSF81321,Pfam_domain:PF13853,Gene3D:1.20.1070.10,hmmpanther:PTHR26450:SF37,hmmpanther:PTHR26450,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGGCAATG	.	5	ESCA
OR5J2	0	.	GRCh37	11	55944718	55944718	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.625G>A	p.Ala209Thr	p.A209T	ENST00000312298	1/1	38	33	5	55	55	0	OR5J2,missense_variant,p.Ala209Thr,ENST00000312298,;	A	ENSG00000174957	ENST00000312298	Transcript	missense_variant	625	625	209	A/T	Gcc/Acc	COSM3449274	.	.	1	OR5J2	HGNC	19612	protein_coding	YES	CCDS31522.1	ENSP00000310788	OR5J2_HUMAN	.	UPI000004B232	.	tolerated(0.41)	benign(0.014)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF102,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATGGCCACC	.	4	ESCA
APLNR	0	.	GRCh37	11	57004575	57004575	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-97C>T	.	.	ENST00000606794	1/1	27	24	3	38	38	0	APLNR,5_prime_UTR_variant,,ENST00000606794,;APLNR,5_prime_UTR_variant,,ENST00000257254,;	A	ENSG00000134817	ENST00000606794	Transcript	5_prime_UTR_variant	101	.	.	.	.	.	.	.	-1	APLNR	HGNC	339	protein_coding	YES	CCDS7950.1	ENSP00000475344	APJ_HUMAN	.	UPI0000001622	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGAGCCTCA	.	2	ESCA
DLG2	0	.	GRCh37	11	83170085	83170085	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*776G>C	.	.	ENST00000376104	28/28	29	20	9	54	54	0	DLG2,3_prime_UTR_variant,,ENST00000426717,;DLG2,3_prime_UTR_variant,,ENST00000398309,;DLG2,3_prime_UTR_variant,,ENST00000376104,;DLG2,downstream_gene_variant,,ENST00000330014,;DLG2,downstream_gene_variant,,ENST00000532653,;DLG2,downstream_gene_variant,,ENST00000531015,;DLG2,downstream_gene_variant,,ENST00000418306,;DLG2,downstream_gene_variant,,ENST00000524982,;DLG2,downstream_gene_variant,,ENST00000280241,;DLG2,downstream_gene_variant,,ENST00000457267,;DLG2,downstream_gene_variant,,ENST00000537455,;DLG2,downstream_gene_variant,,ENST00000376106,;DLG2,downstream_gene_variant,,ENST00000543673,;DLG2,downstream_gene_variant,,ENST00000404783,;DLG2,downstream_gene_variant,,ENST00000529159,;AP003026.1,upstream_gene_variant,,ENST00000420284,;	G	ENSG00000150672	ENST00000376104	Transcript	3_prime_UTR_variant	4016	.	.	.	.	.	.	.	-1	DLG2	HGNC	2901	protein_coding	YES	CCDS44690.1	ENSP00000365272	DLG2_HUMAN	F8W750_HUMAN,E9PQT9_HUMAN	UPI0000E59399	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTTACAAAAT	.	5	ESCA
C11orf73	0	.	GRCh37	11	86056753	86056753	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*73A>G	.	.	ENST00000278483	5/5	43	22	21	61	61	0	C11orf73,3_prime_UTR_variant,,ENST00000278483,;C11orf73,downstream_gene_variant,,ENST00000533986,;C11orf73,non_coding_transcript_exon_variant,,ENST00000531485,;C11orf73,downstream_gene_variant,,ENST00000530208,;C11orf73,non_coding_transcript_exon_variant,,ENST00000529405,;C11orf73,downstream_gene_variant,,ENST00000528004,;	G	ENSG00000149196	ENST00000278483	Transcript	3_prime_UTR_variant	893	.	.	.	.	.	.	.	1	C11orf73	HGNC	26938	protein_coding	YES	CCDS8275.1	ENSP00000278483	HIKES_HUMAN	.	UPI000006CF46	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTATGAGG	.	5	ESCA
TAS2R50	0	.	GRCh37	12	11138694	11138694	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.766C>T	p.Arg256Trp	p.R256W	ENST00000506868	1/1	51	41	9	76	75	1	TAS2R50,missense_variant,p.Arg256Trp,ENST00000506868,;PRR4,intron_variant,,ENST00000539853,;PRR4,intron_variant,,ENST00000541977,;PRR4,intron_variant,,ENST00000535024,;TAS2R14,intron_variant,,ENST00000381852,;PRR4,intron_variant,,ENST00000536668,;PRR4,intron_variant,,ENST00000536086,;PRR4,intron_variant,,ENST00000534923,;	A	ENSG00000212126	ENST00000506868	Transcript	missense_variant	818	766	256	R/W	Cgg/Tgg	COSM180765	.	.	-1	TAS2R50	HGNC	18882	protein_coding	YES	CCDS8638.1	ENSP00000424040	T2R50_HUMAN	Q50KE4_HUMAN,Q50KE2_HUMAN	UPI000000D81E	.	deleterious(0)	benign(0.001)	1/1	.	Superfamily_domains:SSF81321,Pfam_domain:PF05296,Gene3D:1.20.1070.10,hmmpanther:PTHR11394:SF43,hmmpanther:PTHR11394	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTCCGCAGCC	.	5	ESCA
GALNT9	0	.	GRCh37	12	132811451	132811451	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301C>T	p.%3D	p.H101H	ENST00000411988	3/8	34	26	8	43	43	0	GALNT9,synonymous_variant,p.%3D,ENST00000411988,;GALNT9,synonymous_variant,p.%3D,ENST00000535228,;GALNT9,intron_variant,,ENST00000328957,;	A	ENSG00000182870	ENST00000411988	Transcript	synonymous_variant	301	303	101	H	caC/caT	.	.	.	-1	GALNT9	HGNC	4131	protein_coding	.	.	ENSP00000394446	.	F5H557_HUMAN,F5H317_HUMAN,B3KNR7_HUMAN	UPI000204AB92	.	.	.	3/8	.	hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCTCCGTGCGT	.	4	ESCA
ZNF268	0	.	GRCh37	12	133780251	133780251	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1979G>A	p.Gly660Glu	p.G660E	ENST00000536435	6/6	48	40	8	57	57	0	ZNF268,missense_variant,p.Gly660Glu,ENST00000536435,;ZNF268,missense_variant,p.Gly499Glu,ENST00000537565,;ZNF268,missense_variant,p.Gly660Glu,ENST00000228289,;ZNF268,3_prime_UTR_variant,,ENST00000542986,;ZNF268,3_prime_UTR_variant,,ENST00000541009,;ZNF268,3_prime_UTR_variant,,ENST00000536899,;ZNF268,downstream_gene_variant,,ENST00000416488,;CTD-2140B24.4,downstream_gene_variant,,ENST00000540096,;ZNF268,downstream_gene_variant,,ENST00000591951,;ZNF268,downstream_gene_variant,,ENST00000500625,;ZNF268,downstream_gene_variant,,ENST00000539248,;ZNF268,downstream_gene_variant,,ENST00000592241,;ZNF268,downstream_gene_variant,,ENST00000541211,;ZNF268,downstream_gene_variant,,ENST00000542711,;ZNF268,downstream_gene_variant,,ENST00000534953,;ZNF268,downstream_gene_variant,,ENST00000585488,;ZNF268,downstream_gene_variant,,ENST00000588312,;	A	ENSG00000090612	ENST00000536435	Transcript	missense_variant	2309	1979	660	G/E	gGa/gAa	.	.	.	1	ZNF268	HGNC	13061	protein_coding	YES	CCDS45012.1	ENSP00000444412	ZN268_HUMAN	Q9H337_HUMAN,K7EMS6_HUMAN,F5H467_HUMAN	UPI000013C33E	.	tolerated(0.11)	benign(0.2)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF255,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAGGAGTGC	.	5	ESCA
ATF7IP	0	.	GRCh37	12	14650645	14650645	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3451C>G	p.Leu1151Val	p.L1151V	ENST00000261168	15/15	25	19	6	25	24	0	ATF7IP,missense_variant,p.Leu1151Val,ENST00000261168,;ATF7IP,missense_variant,p.Leu1151Val,ENST00000540793,;ATF7IP,missense_variant,p.Leu1159Val,ENST00000544627,;ATF7IP,missense_variant,p.Leu1150Val,ENST00000536444,;	G	ENSG00000171681	ENST00000261168	Transcript	missense_variant	3604	3451	1151	L/V	Ctg/Gtg	COSM3954480	.	.	1	ATF7IP	HGNC	20092	protein_coding	YES	CCDS8663.1	ENSP00000261168	MCAF1_HUMAN	F8WE35_HUMAN,F5H8I0_HUMAN,F5H6X8_HUMAN,F5H502_HUMAN,F5H3C4_HUMAN,F5H2W9_HUMAN,F5H2H9_HUMAN,F5H221_HUMAN,F5H1K9_HUMAN,F5GZ98_HUMAN,F5GZ10_HUMAN,F5GYR7_HUMAN,A8MV73_HUMAN	UPI00001FB6B1	.	deleterious_low_confidence(0.03)	unknown(0)	15/15	.	hmmpanther:PTHR23210:SF20,hmmpanther:PTHR23210	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCGTCTGCCC	.	5	ESCA
PRICKLE1	0	.	GRCh37	12	42860064	42860064	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.707G>A	p.Arg236His	p.R236H	ENST00000455697	6/8	56	40	16	80	80	0	PRICKLE1,missense_variant,p.Arg236His,ENST00000345127,;PRICKLE1,missense_variant,p.Arg236His,ENST00000455697,;PRICKLE1,missense_variant,p.Arg236His,ENST00000445766,;PRICKLE1,missense_variant,p.Arg236His,ENST00000552240,;PRICKLE1,missense_variant,p.Arg236His,ENST00000548696,;PRICKLE1,downstream_gene_variant,,ENST00000547113,;PRICKLE1,downstream_gene_variant,,ENST00000551050,;PRICKLE1,downstream_gene_variant,,ENST00000552108,;RP11-328C8.4,downstream_gene_variant,,ENST00000547824,;	T	ENSG00000139174	ENST00000455697	Transcript	missense_variant	993	707	236	R/H	cGc/cAc	COSM1221975	.	.	-1	PRICKLE1	HGNC	17019	protein_coding	YES	CCDS8742.1	ENSP00000401060	PRIC1_HUMAN	Q687H4_HUMAN,Q687H3_HUMAN,F8W1Q8_HUMAN,F8W1J1_HUMAN,F8VUG8_HUMAN	UPI000013D6F5	.	tolerated(0.18)	benign(0.072)	6/8	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24211,hmmpanther:PTHR24211:SF14,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGCGGCCG	.	5	ESCA
VWF	0	.	GRCh37	12	6128145	6128145	+	Missense_Mutation	SNP	G	G	A	rs778742589	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4439C>T	p.Pro1480Leu	p.P1480L	ENST00000261405	28/52	59	37	22	98	98	0	VWF,missense_variant,p.Pro1480Leu,ENST00000261405,;VWF,intron_variant,,ENST00000538635,;VWF,downstream_gene_variant,,ENST00000539641,;	A	ENSG00000110799	ENST00000261405	Transcript	missense_variant	4694	4439	1480	P/L	cCg/cTg	rs778742589,COSM3812735	.	.	-1	VWF	HGNC	12726	protein_coding	YES	CCDS8539.1	ENSP00000261405	VWF_HUMAN	H2DLA2_HUMAN	UPI00001AE7EE	.	deleterious(0.04)	probably_damaging(0.913)	28/52	.	hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF259,PIRSF_domain:PIRSF002495,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGGGCCC	byFrequency	5	ESCA
CCT2	0	.	GRCh37	12	69986782	69986782	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.777C>T	p.%3D	p.D259D	ENST00000299300	9/16	95	64	30	115	115	0	CCT2,synonymous_variant,p.%3D,ENST00000543146,;CCT2,synonymous_variant,p.%3D,ENST00000544368,;CCT2,synonymous_variant,p.%3D,ENST00000299300,;CCT2,synonymous_variant,p.%3D,ENST00000550010,;CCT2,non_coding_transcript_exon_variant,,ENST00000548787,;CCT2,non_coding_transcript_exon_variant,,ENST00000553169,;CCT2,downstream_gene_variant,,ENST00000546850,;CCT2,downstream_gene_variant,,ENST00000546859,;CCT2,downstream_gene_variant,,ENST00000551620,;CCT2,downstream_gene_variant,,ENST00000550638,;	T	ENSG00000166226	ENST00000299300	Transcript	synonymous_variant	965	777	259	D	gaC/gaT	.	.	.	1	CCT2	HGNC	1615	protein_coding	YES	CCDS8991.1	ENSP00000299300	TCPB_HUMAN	Q9H369_HUMAN	UPI0000136AF3	.	.	.	9/16	.	hmmpanther:PTHR11353,TIGRFAM_domain:TIGR02341,Pfam_domain:PF00118,Gene3D:3.50.7.10,Superfamily_domains:SSF52029	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GTTGACTCTAC	.	3	ESCA
ZFC3H1	0	.	GRCh37	12	72024395	72024395	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3709A>G	p.Ile1237Val	p.I1237V	ENST00000378743	18/35	83	57	26	97	97	0	ZFC3H1,missense_variant,p.Ile1237Val,ENST00000378743,;ZFC3H1,missense_variant,p.Ile1237Val,ENST00000552994,;ZFC3H1,downstream_gene_variant,,ENST00000546606,;	C	ENSG00000133858	ENST00000378743	Transcript	missense_variant	4068	3709	1237	I/V	Att/Gtt	.	.	.	-1	ZFC3H1	HGNC	28328	protein_coding	YES	CCDS41813.1	ENSP00000368017	ZC3H1_HUMAN	.	UPI00003668E9	.	tolerated(0.26)	benign(0.004)	18/35	.	hmmpanther:PTHR21563	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAATTTCTT	.	5	ESCA
ACSS3	0	.	GRCh37	12	81627164	81627164	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1633G>A	p.Glu545Lys	p.E545K	ENST00000548058	13/16	96	81	15	139	139	0	ACSS3,missense_variant,p.Glu544Lys,ENST00000261206,;ACSS3,missense_variant,p.Glu545Lys,ENST00000548058,;ACSS3,missense_variant,p.Glu227Lys,ENST00000548324,;	A	ENSG00000111058	ENST00000548058	Transcript	missense_variant	2543	1633	545	E/K	Gaa/Aaa	COSM3465895	.	.	1	ACSS3	HGNC	24723	protein_coding	YES	CCDS9022.1	ENSP00000449535	ACSS3_HUMAN	F8VZB4_HUMAN	UPI000007060A	.	deleterious(0.04)	benign(0.094)	13/16	.	hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF0,Gene3D:2.30.38.10,Pfam_domain:PF00501,Superfamily_domains:SSF56801	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGATGAAGAA	.	4	ESCA
CCER1	0	.	GRCh37	12	91347661	91347661	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.859G>A	p.Glu287Lys	p.E287K	ENST00000358859	1/1	33	21	12	49	49	0	CCER1,missense_variant,p.Glu287Lys,ENST00000358859,;CCER1,intron_variant,,ENST00000548187,;CCER1,upstream_gene_variant,,ENST00000549707,;	T	ENSG00000197651	ENST00000358859	Transcript	missense_variant	1293	859	287	E/K	Gag/Aag	.	.	.	-1	CCER1	HGNC	28373	protein_coding	YES	CCDS9036.1	ENSP00000351727	CCER1_HUMAN	.	UPI000006EE70	.	tolerated(0.07)	possibly_damaging(0.486)	1/1	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCATCAT	.	5	ESCA
USPL1	0	.	GRCh37	13	31232748	31232748	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2534A>G	p.His845Arg	p.H845R	ENST00000255304	9/9	16	6	10	22	22	0	USPL1,missense_variant,p.His845Arg,ENST00000255304,;	G	ENSG00000132952	ENST00000255304	Transcript	missense_variant	2876	2534	845	H/R	cAt/cGt	.	.	.	1	USPL1	HGNC	20294	protein_coding	YES	CCDS9336.1	ENSP00000255304	USPL1_HUMAN	.	UPI000013CEA3	.	tolerated(0.5)	benign(0.008)	9/9	.	hmmpanther:PTHR15294,Pfam_domain:PF15509	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGCTCATGCTG	.	4	ESCA
TRPC4	0	.	GRCh37	13	38211399	38211399	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2590C>A	p.Gln864Lys	p.Q864K	ENST00000379681	11/11	46	27	19	83	83	0	TRPC4,missense_variant,p.Gln686Lys,ENST00000338947,;TRPC4,missense_variant,p.Gln864Lys,ENST00000379681,;TRPC4,missense_variant,p.Gln686Lys,ENST00000379679,;TRPC4,missense_variant,p.Gln859Lys,ENST00000379705,;TRPC4,intron_variant,,ENST00000379673,;TRPC4,intron_variant,,ENST00000447043,;TRPC4,intron_variant,,ENST00000355779,;TRPC4,intron_variant,,ENST00000358477,;TRPC4,intron_variant,,ENST00000426868,;TRPC4,3_prime_UTR_variant,,ENST00000488717,;	T	ENSG00000133107	ENST00000379681	Transcript	missense_variant	2825	2590	864	Q/K	Caa/Aaa	.	.	.	-1	TRPC4	HGNC	12336	protein_coding	YES	CCDS45037.1	ENSP00000369003	TRPC4_HUMAN	.	UPI000006E5BE	.	tolerated_low_confidence(0.89)	benign(0.023)	11/11	.	hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTGCTCAG	.	5	ESCA
PCDH9	0	.	GRCh37	13	67802560	67802560	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13G>A	p.Asp5Asn	p.D5N	ENST00000544246	2/5	54	38	16	128	128	0	PCDH9,missense_variant,p.Asp5Asn,ENST00000377861,;PCDH9,missense_variant,p.Asp5Asn,ENST00000328454,;PCDH9,missense_variant,p.Asp5Asn,ENST00000544246,;PCDH9,missense_variant,p.Asp5Asn,ENST00000377865,;PCDH9,missense_variant,p.Asp5Asn,ENST00000456367,;	T	ENSG00000184226	ENST00000544246	Transcript	missense_variant	705	13	5	D/N	Gat/Aat	.	.	.	-1	PCDH9	HGNC	8661	protein_coding	YES	CCDS9444.1	ENSP00000442186	PCDH9_HUMAN	.	UPI00001FCE90	.	tolerated(0.47)	benign(0.056)	2/5	.	Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24027:SF25,hmmpanther:PTHR24027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATCCCTCA	.	5	ESCA
MBNL2	0	.	GRCh37	13	98044732	98044732	+	3'UTR	DEL	A	A	-	rs142668758	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1148delA	.	.	ENST00000345429	9/9	58	48	10	64	64	0	MBNL2,3_prime_UTR_variant,,ENST00000343600,;MBNL2,3_prime_UTR_variant,,ENST00000376673,;MBNL2,3_prime_UTR_variant,,ENST00000345429,;MBNL2,3_prime_UTR_variant,,ENST00000397601,;MBNL2,downstream_gene_variant,,ENST00000449284,;MBNL2,downstream_gene_variant,,ENST00000445661,;MBNL2,downstream_gene_variant,,ENST00000469707,;	-	ENSG00000139793	ENST00000345429	Transcript	3_prime_UTR_variant	3027	.	.	.	.	rs142668758	.	.	1	MBNL2	HGNC	16746	protein_coding	YES	CCDS9484.1	ENSP00000267287	MBNL2_HUMAN	A0PJJ3_HUMAN	UPI000013F22B	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	6	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCATGGAAAAAA	.	3	ESCA
CLEC14A	0	.	GRCh37	14	38725073	38725073	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.155A>C	p.Glu52Ala	p.E52A	ENST00000342213	1/1	35	26	9	17	17	0	CLEC14A,missense_variant,p.Glu52Ala,ENST00000342213,;	G	ENSG00000176435	ENST00000342213	Transcript	missense_variant	502	155	52	E/A	gAg/gCg	.	.	.	-1	CLEC14A	HGNC	19832	protein_coding	YES	CCDS9667.1	ENSP00000353013	CLC14_HUMAN	.	UPI000000CBD4	.	tolerated(0.08)	possibly_damaging(0.557)	1/1	.	PROSITE_profiles:PS50041,hmmpanther:PTHR24838:SF258,hmmpanther:PTHR24838,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGCCTCCTCG	.	5	ESCA
LRFN5	0	.	GRCh37	14	42356936	42356936	+	Missense_Mutation	SNP	G	G	T	rs774865393	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1108G>T	p.Val370Leu	p.V370L	ENST00000298119	3/6	82	34	48	88	88	0	LRFN5,missense_variant,p.Val370Leu,ENST00000298119,;LRFN5,missense_variant,p.Val370Leu,ENST00000554120,;LRFN5,missense_variant,p.Val370Leu,ENST00000554171,;	T	ENSG00000165379	ENST00000298119	Transcript	missense_variant	2297	1108	370	V/L	Gtg/Ttg	rs774865393	.	.	1	LRFN5	HGNC	20360	protein_coding	YES	CCDS9678.1	ENSP00000298119	LRFN5_HUMAN	.	UPI000000DA1E	.	deleterious(0)	benign(0.395)	3/6	.	Superfamily_domains:SSF48726,SMART_domains:SM00409,Pfam_domain:PF07679,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATAGTGGAT	.	5	ESCA
STYX	0	.	GRCh37	14	53238879	53238879	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1055A>G	.	.	ENST00000354586	11/11	18	8	10	22	22	0	STYX,3_prime_UTR_variant,,ENST00000442123,;STYX,3_prime_UTR_variant,,ENST00000354586,;GNPNAT1,downstream_gene_variant,,ENST00000216410,;GNPNAT1,downstream_gene_variant,,ENST00000554230,;RP11-589M4.1,upstream_gene_variant,,ENST00000555689,;RP11-589M4.1,upstream_gene_variant,,ENST00000555969,;STYX,intron_variant,,ENST00000556861,;GNPNAT1,downstream_gene_variant,,ENST00000554421,;	G	ENSG00000198252	ENST00000354586	Transcript	3_prime_UTR_variant	2020	.	.	.	.	.	.	.	1	STYX	HGNC	11447	protein_coding	YES	CCDS9711.1	ENSP00000346599	STYX_HUMAN	.	UPI00000434EF	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATAAATTAGT	.	2	ESCA
SPTLC2	0	.	GRCh37	14	78018491	78018491	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1251G>A	p.%3D	p.E417E	ENST00000216484	9/12	40	34	6	67	67	0	SPTLC2,synonymous_variant,p.%3D,ENST00000554901,;SPTLC2,synonymous_variant,p.%3D,ENST00000216484,;RN7SL587P,upstream_gene_variant,,ENST00000459853,;SPTLC2,non_coding_transcript_exon_variant,,ENST00000556264,;SPTLC2,synonymous_variant,p.%3D,ENST00000556607,;SPTLC2,non_coding_transcript_exon_variant,,ENST00000554365,;	T	ENSG00000100596	ENST00000216484	Transcript	synonymous_variant	1445	1251	417	E	gaG/gaA	.	.	.	-1	SPTLC2	HGNC	11278	protein_coding	YES	CCDS9865.1	ENSP00000216484	SPTC2_HUMAN	.	UPI0000000C6B	.	.	.	9/12	.	Superfamily_domains:SSF53383,Pfam_domain:PF00155,Gene3D:3.90.1150.10,hmmpanther:PTHR13693:SF52,hmmpanther:PTHR13693	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATCTGCTCCAC	.	4	ESCA
LRRK1	0	.	GRCh37	15	101591974	101591974	+	Silent	SNP	G	G	T	rs199698040	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3498G>T	p.%3D	p.P1166P	ENST00000388948	24/34	42	27	15	95	95	0	LRRK1,synonymous_variant,p.%3D,ENST00000388948,;LRRK1,synonymous_variant,p.%3D,ENST00000284395,;RP11-505E24.2,intron_variant,,ENST00000559857,;RP11-505E24.3,upstream_gene_variant,,ENST00000558979,;LRRK1,3_prime_UTR_variant,,ENST00000531270,;LRRK1,3_prime_UTR_variant,,ENST00000525284,;LRRK1,upstream_gene_variant,,ENST00000526457,;	T	ENSG00000154237	ENST00000388948	Transcript	synonymous_variant	3857	3498	1166	P	ccG/ccT	rs199698040	.	.	1	LRRK1	HGNC	18608	protein_coding	YES	CCDS42086.1	ENSP00000373600	LRRK1_HUMAN	E9PMK9_HUMAN,E9PLF8_HUMAN,E9PK39_HUMAN,B3KSX5_HUMAN	UPI0000D4FE63	.	.	.	24/34	.	.	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCCGGTCTG	byCluster|by1000G	5	ESCA
SEMA6D	0	.	GRCh37	15	48065596	48065596	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1614A>G	.	.	ENST00000316364	19/19	26	18	8	29	28	0	SEMA6D,3_prime_UTR_variant,,ENST00000389432,;SEMA6D,3_prime_UTR_variant,,ENST00000537942,;SEMA6D,3_prime_UTR_variant,,ENST00000358066,;SEMA6D,3_prime_UTR_variant,,ENST00000354744,;SEMA6D,3_prime_UTR_variant,,ENST00000389428,;SEMA6D,3_prime_UTR_variant,,ENST00000355997,;SEMA6D,3_prime_UTR_variant,,ENST00000389433,;SEMA6D,3_prime_UTR_variant,,ENST00000558014,;SEMA6D,3_prime_UTR_variant,,ENST00000316364,;SEMA6D,downstream_gene_variant,,ENST00000560006,;SEMA6D,downstream_gene_variant,,ENST00000536845,;SEMA6D,downstream_gene_variant,,ENST00000558816,;	G	ENSG00000137872	ENST00000316364	Transcript	3_prime_UTR_variant	5275	.	.	.	.	.	.	.	1	SEMA6D	HGNC	16770	protein_coding	YES	CCDS32225.1	ENSP00000324857	SEM6D_HUMAN	Q9HAH9_HUMAN,H0YMV0_HUMAN,H0YMA6_HUMAN,H0YL82_HUMAN	UPI000006E201	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CAGAAACCACT	.	4	ESCA
FAM227B	0	.	GRCh37	15	49867238	49867238	+	Silent	SNP	G	G	A	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615C>T	p.%3D	p.S205S	ENST00000299338	8/16	94	82	11	136	136	0	FAM227B,synonymous_variant,p.%3D,ENST00000561064,;FAM227B,synonymous_variant,p.%3D,ENST00000299338,;FAM227B,downstream_gene_variant,,ENST00000559905,;FAM227B,downstream_gene_variant,,ENST00000558579,;FAM227B,downstream_gene_variant,,ENST00000558594,;FAM227B,downstream_gene_variant,,ENST00000560246,;FAM227B,non_coding_transcript_exon_variant,,ENST00000561319,;FAM227B,non_coding_transcript_exon_variant,,ENST00000558615,;FAM227B,downstream_gene_variant,,ENST00000561116,;	A	ENSG00000166262	ENST00000299338	Transcript	synonymous_variant	919	615	205	S	tcC/tcT	COSM270901	.	.	-1	FAM227B	HGNC	26543	protein_coding	YES	CCDS32237.1	ENSP00000299338	F227B_HUMAN	H0YLX5_HUMAN	UPI0000D6133A	.	.	.	8/16	.	Pfam_domain:PF14922	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAAAGGAGTC	.	4	ESCA
ZWILCH	0	.	GRCh37	15	66821208	66821208	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.988G>A	p.Ala330Thr	p.A330T	ENST00000307897	11/19	35	28	7	46	46	0	ZWILCH,missense_variant,p.Ala330Thr,ENST00000307897,;ZWILCH,missense_variant,p.Ala216Thr,ENST00000535141,;ZWILCH,missense_variant,p.Ala216Thr,ENST00000565627,;ZWILCH,missense_variant,p.Ala216Thr,ENST00000446801,;RPL4,upstream_gene_variant,,ENST00000568588,;ZWILCH,non_coding_transcript_exon_variant,,ENST00000562645,;ZWILCH,non_coding_transcript_exon_variant,,ENST00000561583,;	A	ENSG00000174442	ENST00000307897	Transcript	missense_variant	1368	988	330	A/T	Gct/Act	.	.	.	1	ZWILCH	HGNC	25468	protein_coding	YES	CCDS10219.1	ENSP00000311429	ZWILC_HUMAN	H3BSG1_HUMAN,H3BQ07_HUMAN,H3BPI7_HUMAN	UPI000013EC73	.	tolerated(0.08)	benign(0.053)	11/19	.	hmmpanther:PTHR15995,Pfam_domain:PF09817	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACACTGCTGCA	.	5	ESCA
GLCE	0	.	GRCh37	15	69561944	69561944	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*361A>G	.	.	ENST00000261858	5/5	58	52	6	60	60	0	GLCE,3_prime_UTR_variant,,ENST00000261858,;GLCE,3_prime_UTR_variant,,ENST00000559420,;GLCE,downstream_gene_variant,,ENST00000559500,;	G	ENSG00000138604	ENST00000261858	Transcript	3_prime_UTR_variant	2443	.	.	.	.	.	.	.	1	GLCE	HGNC	17855	protein_coding	YES	CCDS32277.1	ENSP00000261858	GLCE_HUMAN	H0YNP1_HUMAN	UPI00001D7785	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTAGTATGGAG	.	2	ESCA
PTPN9	0	.	GRCh37	15	75763081	75763081	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1299T>A	p.Asn433Lys	p.N433K	ENST00000306726	11/13	75	63	11	149	148	0	PTPN9,missense_variant,p.Asn433Lys,ENST00000306726,;PTPN9,intron_variant,,ENST00000563835,;PTPN9,non_coding_transcript_exon_variant,,ENST00000568108,;	T	ENSG00000169410	ENST00000306726	Transcript	missense_variant	1812	1299	433	N/K	aaT/aaA	.	.	.	-1	PTPN9	HGNC	9661	protein_coding	YES	CCDS10280.1	ENSP00000303554	PTN9_HUMAN	.	UPI0000000CAC	.	deleterious(0.02)	probably_damaging(0.913)	11/13	.	PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF194,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTAGATTGGT	.	4	ESCA
CLDN9	0	.	GRCh37	16	3063367	3063367	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4G>A	p.Ala2Thr	p.A2T	ENST00000445369	1/1	23	13	10	51	51	0	CLDN9,missense_variant,p.Ala2Thr,ENST00000445369,;CLDN6,downstream_gene_variant,,ENST00000572154,;CLDN6,downstream_gene_variant,,ENST00000396925,;CLDN6,downstream_gene_variant,,ENST00000328796,;	A	ENSG00000213937	ENST00000445369	Transcript	missense_variant	911	4	2	A/T	Gct/Act	.	.	.	1	CLDN9	HGNC	2051	protein_coding	YES	CCDS10487.1	ENSP00000398017	CLD9_HUMAN	.	UPI0000035DA5	.	deleterious(0.05)	probably_damaging(0.931)	1/1	.	hmmpanther:PTHR12002:SF42,hmmpanther:PTHR12002	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGGCTTCG	.	5	ESCA
ADCY7	0	.	GRCh37	16	50334726	50334726	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1177G>A	p.Asp393Asn	p.D393N	ENST00000394697	9/26	47	34	13	74	74	0	ADCY7,missense_variant,p.Asp393Asn,ENST00000537579,;ADCY7,missense_variant,p.Asp393Asn,ENST00000254235,;ADCY7,missense_variant,p.Asp393Asn,ENST00000538642,;ADCY7,missense_variant,p.Asp393Asn,ENST00000394697,;ADCY7,missense_variant,p.Asp393Asn,ENST00000566433,;ADCY7,upstream_gene_variant,,ENST00000568731,;ADCY7,downstream_gene_variant,,ENST00000563677,;ADCY7,downstream_gene_variant,,ENST00000564044,;ADCY7,missense_variant,p.Asp393Asn,ENST00000567277,;ADCY7,upstream_gene_variant,,ENST00000570187,;	A	ENSG00000121281	ENST00000394697	Transcript	missense_variant	1517	1177	393	D/N	Gac/Aac	.	.	.	1	ADCY7	HGNC	238	protein_coding	YES	CCDS10741.1	ENSP00000378187	ADCY7_HUMAN	I3L3Q5_HUMAN	UPI000004C5DB	.	deleterious(0)	probably_damaging(1)	9/26	.	Superfamily_domains:SSF55073,SMART_domains:SM00044,Pfam_domain:PF00211,Gene3D:3.30.70.1230,hmmpanther:PTHR11920:SF273,hmmpanther:PTHR11920,PROSITE_profiles:PS50125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTATGACGTG	.	5	ESCA
NLRC5	0	.	GRCh37	16	57074572	57074572	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2881C>A	p.Leu961Ile	p.L961I	ENST00000262510	17/49	33	28	5	43	43	0	NLRC5,missense_variant,p.Leu260Ile,ENST00000543030,;NLRC5,missense_variant,p.Leu961Ile,ENST00000308149,;NLRC5,missense_variant,p.Leu714Ile,ENST00000538805,;NLRC5,missense_variant,p.Leu468Ile,ENST00000538110,;NLRC5,missense_variant,p.Leu961Ile,ENST00000539144,;NLRC5,missense_variant,p.Leu961Ile,ENST00000436936,;NLRC5,missense_variant,p.Leu961Ile,ENST00000262510,;NLRC5,missense_variant,p.Leu689Ile,ENST00000545081,;NLRC5,missense_variant,p.Leu112Ile,ENST00000538453,;NLRC5,3_prime_UTR_variant,,ENST00000539881,;NLRC5,upstream_gene_variant,,ENST00000537056,;NLRC5,upstream_gene_variant,,ENST00000540182,;NLRC5,upstream_gene_variant,,ENST00000538778,;NLRC5,upstream_gene_variant,,ENST00000541020,;NLRC5,upstream_gene_variant,,ENST00000534931,;NLRC5,upstream_gene_variant,,ENST00000538930,;	A	ENSG00000140853	ENST00000262510	Transcript	missense_variant	3106	2881	961	L/I	Ctt/Att	.	.	.	1	NLRC5	HGNC	29933	protein_coding	YES	CCDS10773.1	ENSP00000262510	NLRC5_HUMAN	F5H274_HUMAN,F5GYP0_HUMAN	UPI00001AEE94	.	tolerated(0.16)	benign(0.339)	17/49	.	hmmpanther:PTHR24106:SF69,hmmpanther:PTHR24106	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATTTCTTGAC	.	4	ESCA
FLJ00418	0	.	GRCh37	16	70696512	70696512	+	5'UTR	SNP	C	C	A	rs137920455	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2180C>A	.	.	ENST00000597002	1/1	16	9	7	34	34	0	FLJ00418,5_prime_UTR_variant,,ENST00000597002,;MTSS1L,3_prime_UTR_variant,,ENST00000338779,;IL34,downstream_gene_variant,,ENST00000288098,;IL34,downstream_gene_variant,,ENST00000429149,;IL34,downstream_gene_variant,,ENST00000566361,;	A	ENSG00000268927	ENST00000597002	Transcript	5_prime_UTR_variant	943	.	.	.	.	rs137920455	.	.	1	FLJ00418	Uniprot_gn	.	protein_coding	YES	.	ENSP00000469464	.	Q86YU6_HUMAN	UPI000000D805	.	.	.	1/1	.	.	T:0.0094	T:0.0333	T:0.0043	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCACCGGGCT	byFrequency|byCluster|by1000G	2	ESCA
SLC38A8	0	.	GRCh37	16	84070482	84070482	+	Silent	SNP	G	G	A	rs149748570	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.213C>T	p.%3D	p.S71S	ENST00000299709	2/10	52	40	11	107	107	0	SLC38A8,synonymous_variant,p.%3D,ENST00000299709,;SLC38A8,synonymous_variant,p.%3D,ENST00000568178,;SLC38A8,5_prime_UTR_variant,,ENST00000569816,;RNA5SP432,downstream_gene_variant,,ENST00000362480,;	A	ENSG00000166558	ENST00000299709	Transcript	synonymous_variant	213	213	71	S	agC/agT	rs149748570	.	.	-1	SLC38A8	HGNC	32434	protein_coding	YES	CCDS32495.1	ENSP00000299709	S38A8_HUMAN	H3BUP5_HUMAN,H3BP02_HUMAN	UPI0000D61A1F	.	.	.	2/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22950:SF226,hmmpanther:PTHR22950,Pfam_domain:PF01490	A:0.0002	A:0	A:0	.	A:0	A:0	A:0.001	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCCGCTGAT	byCluster|by1000G	2	ESCA
VPS9D1	0	.	GRCh37	16	89777128	89777128	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1124A>G	p.Asp375Gly	p.D375G	ENST00000389386	10/15	75	54	21	119	118	1	VPS9D1,missense_variant,p.Asp375Gly,ENST00000389386,;VPS9D1,missense_variant,p.Asp305Gly,ENST00000561976,;VPS9D1,upstream_gene_variant,,ENST00000565023,;VPS9D1-AS1,upstream_gene_variant,,ENST00000562866,;VPS9D1,downstream_gene_variant,,ENST00000565452,;VPS9D1,downstream_gene_variant,,ENST00000567379,;VPS9D1,downstream_gene_variant,,ENST00000568691,;VPS9D1,downstream_gene_variant,,ENST00000563798,;	C	ENSG00000075399	ENST00000389386	Transcript	missense_variant	1249	1124	375	D/G	gAc/gGc	.	.	.	-1	VPS9D1	HGNC	13526	protein_coding	YES	CCDS42220.1	ENSP00000374037	VP9D1_HUMAN	H3BM58_HUMAN	UPI00001FF749	.	tolerated(0.23)	possibly_damaging(0.58)	10/15	.	hmmpanther:PTHR23101:SF25,hmmpanther:PTHR23101	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTGTCTGGC	.	5	ESCA
MYH8	0	.	GRCh37	17	10307898	10307898	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2437G>T	p.Ala813Ser	p.A813S	ENST00000403437	22/40	32	20	12	69	69	0	MYH8,missense_variant,p.Ala813Ser,ENST00000403437,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	A	ENSG00000133020	ENST00000403437	Transcript	missense_variant	2532	2437	813	A/S	Gca/Tca	.	.	.	-1	MYH8	HGNC	7578	protein_coding	YES	CCDS11153.1	ENSP00000384330	MYH8_HUMAN	.	UPI000012FB7D	.	tolerated(0.82)	benign(0.002)	22/40	.	PROSITE_profiles:PS50096,hmmpanther:PTHR13140:SF340,hmmpanther:PTHR13140,Gene3D:1wdcA00,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAGTGCTTCTC	.	4	ESCA
CDRT15	0	.	GRCh37	17	14140173	14140173	+	5'Flank	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000420162	.	31	12	19	68	68	0	CDRT15,5_prime_UTR_variant,,ENST00000431716,;CDRT15,upstream_gene_variant,,ENST00000420162,;	G	ENSG00000223510	ENST00000420162	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	7	-1	CDRT15	HGNC	14395	protein_coding	YES	CCDS32569.1	ENSP00000402355	CDRTF_HUMAN	.	UPI00000702CA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCACCAAG	.	5	ESCA
CDK5R1	0	.	GRCh37	17	30817544	30817544	+	3'UTR	SNP	C	C	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1982C>G	.	.	ENST00000313401	2/2	73	59	14	116	116	0	CDK5R1,3_prime_UTR_variant,,ENST00000313401,;MYO1D,downstream_gene_variant,,ENST00000394649,;MYO1D,downstream_gene_variant,,ENST00000318217,;CDK5R1,downstream_gene_variant,,ENST00000584792,;MYO1D,downstream_gene_variant,,ENST00000577576,;CDK5R1,downstream_gene_variant,,ENST00000584716,;MYO1D,downstream_gene_variant,,ENST00000577352,;	G	ENSG00000176749	ENST00000313401	Transcript	3_prime_UTR_variant	3595	.	.	.	.	.	.	.	1	CDK5R1	HGNC	1775	protein_coding	YES	CCDS11273.1	ENSP00000318486	CD5R1_HUMAN	.	UPI000012738E	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTCTAGTT	.	5	ESCA
DHRS11	0	.	GRCh37	17	34956684	34956684	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*52C>T	.	.	ENST00000251312	7/7	39	32	7	69	69	0	DHRS11,3_prime_UTR_variant,,ENST00000590554,;DHRS11,3_prime_UTR_variant,,ENST00000585376,;DHRS11,3_prime_UTR_variant,,ENST00000251312,;DHRS11,downstream_gene_variant,,ENST00000491046,;MRM1,upstream_gene_variant,,ENST00000585770,;MRM1,upstream_gene_variant,,ENST00000250156,;DHRS11,downstream_gene_variant,,ENST00000394445,;DHRS11,non_coding_transcript_exon_variant,,ENST00000593204,;DHRS11,non_coding_transcript_exon_variant,,ENST00000586848,;DHRS11,downstream_gene_variant,,ENST00000590527,;	T	ENSG00000108272	ENST00000251312	Transcript	3_prime_UTR_variant	1047	.	.	.	.	.	.	.	1	DHRS11	HGNC	28639	protein_coding	YES	CCDS11315.2	ENSP00000251312	DHR11_HUMAN	K7EK68_HUMAN	UPI0000038A01	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGCCTCTG	.	5	ESCA
C17orf78	0	.	GRCh37	17	35736300	35736300	+	Missense_Mutation	SNP	G	G	C	rs750590762	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.371G>C	p.Gly124Ala	p.G124A	ENST00000300618	3/7	39	28	10	38	38	0	C17orf78,missense_variant,p.Gly124Ala,ENST00000300618,;C17orf78,missense_variant,p.Gly124Ala,ENST00000586700,;ACACA,intron_variant,,ENST00000416895,;ACACA,intron_variant,,ENST00000353139,;ACACA,intron_variant,,ENST00000451642,;ACACA,intron_variant,,ENST00000413318,;ACACA,intron_variant,,ENST00000587545,;ACACA,intron_variant,,ENST00000456066,;	C	ENSG00000167230	ENST00000300618	Transcript	missense_variant	421	371	124	G/A	gGa/gCa	rs750590762	.	.	1	C17orf78	HGNC	26831	protein_coding	YES	CCDS45655.1	ENSP00000300618	CQ078_HUMAN	.	UPI0000140B91	.	deleterious(0.02)	possibly_damaging(0.807)	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGGATCTC	.	5	ESCA
KRT14	0	.	GRCh37	17	39740153	39740165	+	Frame_Shift_Del	DEL	GCCTCTCAGGGCA	GCCTCTCAGGGCA	-	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	GCCTCTCAGGGCA	GCCTCTCAGGGCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774_786delTGCCCTGAGAGGC	p.Ala259ArgfsTer18	p.A259Rfs*18	ENST00000167586	4/8	42	34	8	55	55	0	KRT14,frameshift_variant,p.Ala259ArgfsTer18,ENST00000167586,;KRT14,non_coding_transcript_exon_variant,,ENST00000476662,;KRT14,upstream_gene_variant,,ENST00000441550,;	-	ENSG00000186847	ENST00000167586	Transcript	frameshift_variant	861-873	774-786	258-262	NALRG/X	aaTGCCCTGAGAGGC/aa	.	.	.	-1	KRT14	HGNC	6416	protein_coding	YES	CCDS11400.1	ENSP00000167586	K1C14_HUMAN	K7ENV3_HUMAN	UPI00001AE5AA	.	.	.	4/8	.	Coiled-coils_(Ncoils):Coil,Superfamily_domains:SSF46579,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CACCTGGCCTCTCAGGGCATTCAT	.	2	ESCA
MLX	0	.	GRCh37	17	40720545	40720545	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.299G>T	p.Gly100Val	p.G100V	ENST00000246912	3/8	73	53	20	99	99	0	MLX,missense_variant,p.Gly46Val,ENST00000435881,;MLX,missense_variant,p.Gly100Val,ENST00000246912,;MLX,intron_variant,,ENST00000346833,;MLX,intron_variant,,ENST00000591024,;PSMC3IP,downstream_gene_variant,,ENST00000253789,;PSMC3IP,downstream_gene_variant,,ENST00000590760,;COASY,downstream_gene_variant,,ENST00000421097,;PSMC3IP,downstream_gene_variant,,ENST00000587209,;COASY,downstream_gene_variant,,ENST00000449624,;COASY,downstream_gene_variant,,ENST00000591779,;COASY,downstream_gene_variant,,ENST00000393818,;COASY,downstream_gene_variant,,ENST00000420359,;COASY,downstream_gene_variant,,ENST00000590958,;PSMC3IP,downstream_gene_variant,,ENST00000393795,;MLX,non_coding_transcript_exon_variant,,ENST00000586393,;MLX,non_coding_transcript_exon_variant,,ENST00000591195,;MLX,non_coding_transcript_exon_variant,,ENST00000588320,;MLX,non_coding_transcript_exon_variant,,ENST00000590084,;MLX,intron_variant,,ENST00000590050,;MLX,intron_variant,,ENST00000585403,;MLX,downstream_gene_variant,,ENST00000592717,;COASY,downstream_gene_variant,,ENST00000588353,;PSMC3IP,downstream_gene_variant,,ENST00000588544,;COASY,downstream_gene_variant,,ENST00000591583,;PSMC3IP,downstream_gene_variant,,ENST00000589505,;COASY,downstream_gene_variant,,ENST00000591753,;PSMC3IP,downstream_gene_variant,,ENST00000590931,;PSMC3IP,downstream_gene_variant,,ENST00000586337,;	T	ENSG00000108788	ENST00000246912	Transcript	missense_variant	352	299	100	G/V	gGt/gTt	.	.	.	1	MLX	HGNC	11645	protein_coding	YES	CCDS11430.1	ENSP00000246912	MLX_HUMAN	.	UPI000012F237	.	deleterious(0)	probably_damaging(0.999)	3/8	.	hmmpanther:PTHR15741,hmmpanther:PTHR15741:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCGGTTCCA	.	5	ESCA
TBX4	0	.	GRCh37	17	59560599	59560599	+	Missense_Mutation	SNP	C	C	T	rs370445781	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1360C>T	p.Arg454Trp	p.R454W	ENST00000240335	8/8	19	10	9	46	45	0	TBX4,missense_variant,p.Arg454Trp,ENST00000240335,;TBX4,missense_variant,p.Arg455Trp,ENST00000393853,;TBX4,downstream_gene_variant,,ENST00000589003,;TBX4,non_coding_transcript_exon_variant,,ENST00000589449,;TBX4,downstream_gene_variant,,ENST00000586874,;TBX4,downstream_gene_variant,,ENST00000593249,;TBX4,downstream_gene_variant,,ENST00000590174,;	T	ENSG00000121075	ENST00000240335	Transcript	missense_variant	1405	1360	454	R/W	Cgg/Tgg	rs370445781,COSM26950	.	.	1	TBX4	HGNC	11603	protein_coding	YES	CCDS11629.1	ENSP00000240335	TBX4_HUMAN	K7EPY2_HUMAN	UPI000013CAA9	.	deleterious(0)	probably_damaging(0.997)	8/8	.	hmmpanther:PTHR11267:SF29,hmmpanther:PTHR11267	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TGCCGCGGCTG	byFrequency|byCluster	4	ESCA
SMARCD2	0	.	GRCh37	17	61910294	61910294	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4C>T	.	.	ENST00000448276	13/13	49	35	14	64	64	0	SMARCD2,3_prime_UTR_variant,,ENST00000450364,;SMARCD2,3_prime_UTR_variant,,ENST00000323347,;SMARCD2,3_prime_UTR_variant,,ENST00000448276,;SMARCD2,3_prime_UTR_variant,,ENST00000225742,;PSMC5,downstream_gene_variant,,ENST00000581882,;PSMC5,downstream_gene_variant,,ENST00000579708,;PSMC5,downstream_gene_variant,,ENST00000580864,;PSMC5,downstream_gene_variant,,ENST00000375812,;PSMC5,downstream_gene_variant,,ENST00000581842,;PSMC5,downstream_gene_variant,,ENST00000585123,;PSMC5,downstream_gene_variant,,ENST00000584320,;PSMC5,downstream_gene_variant,,ENST00000310144,;PSMC5,downstream_gene_variant,,ENST00000582130,;FTSJ3,upstream_gene_variant,,ENST00000580295,;SMARCD2,downstream_gene_variant,,ENST00000584483,;PSMC5,downstream_gene_variant,,ENST00000583283,;PSMC5,downstream_gene_variant,,ENST00000584657,;PSMC5,downstream_gene_variant,,ENST00000580265,;PSMC5,downstream_gene_variant,,ENST00000578570,;PSMC5,downstream_gene_variant,,ENST00000584536,;SMARCD2,downstream_gene_variant,,ENST00000578234,;PSMC5,downstream_gene_variant,,ENST00000580063,;PSMC5,downstream_gene_variant,,ENST00000579031,;PSMC5,downstream_gene_variant,,ENST00000581764,;SMARCD2,downstream_gene_variant,,ENST00000580054,;SMARCD2,downstream_gene_variant,,ENST00000581832,;PSMC5,downstream_gene_variant,,ENST00000584880,;SMARCD2,downstream_gene_variant,,ENST00000584400,;SMARCD2,downstream_gene_variant,,ENST00000577686,;PSMC5,downstream_gene_variant,,ENST00000579147,;PSMC5,downstream_gene_variant,,ENST00000585242,;	A	ENSG00000108604	ENST00000448276	Transcript	3_prime_UTR_variant	1866	.	.	.	.	.	.	.	-1	SMARCD2	HGNC	11107	protein_coding	YES	CCDS45756.1	ENSP00000392617	SMRD2_HUMAN	J3KT18_HUMAN,J3KMX2_HUMAN	UPI0000D695F8	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGAGCAGTT	.	5	ESCA
SMARCD2	0	.	GRCh37	17	61910295	61910295	+	3'UTR	SNP	C	C	A	rs775428184	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3G>T	.	.	ENST00000448276	13/13	49	35	14	67	67	0	SMARCD2,3_prime_UTR_variant,,ENST00000450364,;SMARCD2,3_prime_UTR_variant,,ENST00000323347,;SMARCD2,3_prime_UTR_variant,,ENST00000448276,;SMARCD2,3_prime_UTR_variant,,ENST00000225742,;PSMC5,downstream_gene_variant,,ENST00000581882,;PSMC5,downstream_gene_variant,,ENST00000579708,;PSMC5,downstream_gene_variant,,ENST00000580864,;PSMC5,downstream_gene_variant,,ENST00000375812,;PSMC5,downstream_gene_variant,,ENST00000581842,;PSMC5,downstream_gene_variant,,ENST00000585123,;PSMC5,downstream_gene_variant,,ENST00000584320,;PSMC5,downstream_gene_variant,,ENST00000310144,;PSMC5,downstream_gene_variant,,ENST00000582130,;FTSJ3,upstream_gene_variant,,ENST00000580295,;SMARCD2,downstream_gene_variant,,ENST00000584483,;PSMC5,downstream_gene_variant,,ENST00000583283,;PSMC5,downstream_gene_variant,,ENST00000584657,;PSMC5,downstream_gene_variant,,ENST00000580265,;PSMC5,downstream_gene_variant,,ENST00000578570,;PSMC5,downstream_gene_variant,,ENST00000584536,;SMARCD2,downstream_gene_variant,,ENST00000578234,;PSMC5,downstream_gene_variant,,ENST00000580063,;PSMC5,downstream_gene_variant,,ENST00000579031,;PSMC5,downstream_gene_variant,,ENST00000581764,;SMARCD2,downstream_gene_variant,,ENST00000580054,;SMARCD2,downstream_gene_variant,,ENST00000581832,;PSMC5,downstream_gene_variant,,ENST00000584880,;SMARCD2,downstream_gene_variant,,ENST00000584400,;SMARCD2,downstream_gene_variant,,ENST00000577686,;PSMC5,downstream_gene_variant,,ENST00000579147,;PSMC5,downstream_gene_variant,,ENST00000585242,;	A	ENSG00000108604	ENST00000448276	Transcript	3_prime_UTR_variant	1865	.	.	.	.	rs775428184	.	.	-1	SMARCD2	HGNC	11107	protein_coding	YES	CCDS45756.1	ENSP00000392617	SMRD2_HUMAN	J3KT18_HUMAN,J3KMX2_HUMAN	UPI0000D695F8	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGAGCAGTTA	.	5	ESCA
TP53	0	.	GRCh37	17	7578478	7578478	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452C>A	p.Pro151His	p.P151H	ENST00000269305	5/11	16	11	4	50	50	0	TP53,missense_variant,p.Pro151His,ENST00000508793,;TP53,missense_variant,p.Pro151His,ENST00000413465,;TP53,missense_variant,p.Pro151His,ENST00000420246,;TP53,missense_variant,p.Pro151His,ENST00000269305,;TP53,missense_variant,p.Pro19His,ENST00000509690,;TP53,missense_variant,p.Pro151His,ENST00000359597,;TP53,missense_variant,p.Pro58His,ENST00000514944,;TP53,missense_variant,p.Pro151His,ENST00000445888,;TP53,missense_variant,p.Pro151His,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	642	452	151	P/H	cCc/cAc	TP53_g.12440C>A,TP53_g.12440C>T,TP53_g.12440C>G,COSM44003,COSM44288,COSM11476,COSM259150,COSM707868,COSM259149,COSM707869,COSM259151,COSM707871,COSM4139888,COSM3388218,COSM4139887,COSM2744918,COSM259152,COSM707870	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	possibly_damaging(0.773)	5/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.P58H|c.173C>A|6,SITE|p.P151H|c.452C>A|29,SITE|p.P151H|c.452C>A|6,SITE|p.P151H|c.452C>A|6,SITE|p.P19H|c.56C>A|6,CODON|p.0?|c.1_1182del1182|6,CODON|p.T150fs*16|c.448_460del13|4,CODON|p.P151P|c.453C>T|8,CODON|p.P151P|c.453C>G|4,CODON|p.P152fs*18|c.451delC|9,CODON|p.P151R|c.452C>G|8,CODON|p.P19R|c.56C>G|3,CODON|p.P151L|c.452C>T|7,BUFFER|p.P152fs*14|c.454_466del13|5,BUFFER|p.T62P|c.184A>C|3,BUFFER|p.T155P|c.463A>C|16,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T23P|c.67A>C|4,BUFFER|p.T155P|c.463A>C|3,BUFFER|p.T155A|c.463A>G|8,BUFFER|p.G154I|c.460_461GG>AT|3,BUFFER|p.G154G|c.462C>T|9,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G154V|c.461G>T|3,BUFFER|p.G61V|c.182G>T|3,BUFFER|p.G22V|c.65G>T|4,BUFFER|p.G154D|c.461G>A|6,BUFFER|p.G154V|c.461G>T|38,BUFFER|p.G154S|c.460G>A|9,BUFFER|p.P153P|c.459C>T|6,BUFFER|p.P153L|c.458C>T|6,BUFFER|p.P153T|c.457C>A|3,BUFFER|p.P153S|c.457C>T|8,BUFFER|p.P153fs*28|c.456_457insN|4,BUFFER|p.P153fs*28|c.455_456insN|3,BUFFER|p.P152fs*18|c.455delC|6,BUFFER|p.P152P|c.456G>A|4,BUFFER|p.P152Q|c.455C>A|5,BUFFER|p.P152L|c.455C>T|70,BUFFER|p.P20L|c.59C>T|10,BUFFER|p.P152L|c.455C>T|10,BUFFER|p.P152R|c.455C>G|6,BUFFER|p.P59L|c.176C>T|10,BUFFER|p.P152L|c.455C>T|10,BUFFER|p.P152L|c.455C>T|4,BUFFER|p.P152L|c.455C>T|3,BUFFER|p.P152fs*18|c.454delC|3,BUFFER|p.P152fs*29|c.453_454insN|5,BUFFER|p.P152T|c.454C>A|7,BUFFER|p.P152S|c.454C>T|24,BUFFER|p.P151T|c.451C>A|3,BUFFER|p.P19T|c.55C>A|3,BUFFER|p.P58S|c.172C>T|6,BUFFER|p.P151T|c.451C>A|16,BUFFER|p.P151A|c.451C>G|14,BUFFER|p.P151A|c.451C>G|3,BUFFER|p.P151S|c.451C>T|68,BUFFER|p.P151S|c.451C>T|6,BUFFER|p.P58T|c.172C>A|3,BUFFER|p.P151S|c.451C>T|3,BUFFER|p.P151A|c.451C>G|7,BUFFER|p.P151A|c.451C>G|7,BUFFER|p.P151S|c.451C>T|4,BUFFER|p.P151T|c.451C>A|3,BUFFER|p.P19A|c.55C>G|7,BUFFER|p.P58A|c.172C>G|7,BUFFER|p.P19S|c.55C>T|6,BUFFER|p.P151A|c.451C>G|3,BUFFER|p.P151fs*30|c.450_451insN|5,BUFFER|p.T150I|c.449C>T|4,BUFFER|p.S149S|c.447C>T|6,BUFFER|p.S149F|c.446C>T|5,BUFFER|p.S149fs*32|c.444_445insN|5,BUFFER|p.S149P|c.445T>C|4,BUFFER|p.D148N|c.442G>A|5,BUFFER|p.V147V|c.441T>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGGGGTGTG	.	5	ESCA
C1QTNF1	0	.	GRCh37	17	77021988	77021988	+	Intron	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-232+1412T>C	.	.	ENST00000339142	.	56	52	3	83	83	0	C1QTNF1,5_prime_UTR_variant,,ENST00000354124,;C1QTNF1,5_prime_UTR_variant,,ENST00000392445,;C1QTNF1,intron_variant,,ENST00000311661,;C1QTNF1-AS1,intron_variant,,ENST00000577521,;C1QTNF1,intron_variant,,ENST00000339142,;C1QTNF1,intron_variant,,ENST00000578229,;C1QTNF1,intron_variant,,ENST00000580454,;C1QTNF1,intron_variant,,ENST00000579760,;C1QTNF1-AS1,intron_variant,,ENST00000581579,;C1QTNF1,downstream_gene_variant,,ENST00000582295,;	C	ENSG00000173918	ENST00000339142	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	C1QTNF1	HGNC	14324	protein_coding	YES	CCDS11761.1	ENSP00000340864	C1QT1_HUMAN	.	UPI0000035539	.	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCATCATCA	.	2	ESCA
KDM6B	0	.	GRCh37	17	7749410	7749410	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.251G>C	p.Arg84Thr	p.R84T	ENST00000254846	6/22	35	24	11	46	46	0	KDM6B,missense_variant,p.Arg84Thr,ENST00000448097,;KDM6B,missense_variant,p.Arg84Thr,ENST00000570632,;KDM6B,missense_variant,p.Arg84Thr,ENST00000254846,;KDM6B,downstream_gene_variant,,ENST00000575521,;KDM6B,downstream_gene_variant,,ENST00000571047,;	C	ENSG00000132510	ENST00000254846	Transcript	missense_variant	640	251	84	R/T	aGa/aCa	.	.	.	1	KDM6B	HGNC	29012	protein_coding	YES	CCDS32552.1	ENSP00000254846	KDM6B_HUMAN	D3DTQ7_HUMAN	UPI00006C175B	.	.	unknown(0)	6/22	.	hmmpanther:PTHR14017,hmmpanther:PTHR14017:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGACCCC	.	5	ESCA
USP43	0	.	GRCh37	17	9615292	9615292	+	Silent	SNP	C	C	T	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2178C>T	p.%3D	p.T726T	ENST00000285199	14/15	38	28	10	43	43	0	USP43,synonymous_variant,p.%3D,ENST00000574408,;USP43,synonymous_variant,p.%3D,ENST00000570475,;USP43,synonymous_variant,p.%3D,ENST00000285199,;USP43,synonymous_variant,p.%3D,ENST00000573955,;USP43,non_coding_transcript_exon_variant,,ENST00000570827,;	T	ENSG00000154914	ENST00000285199	Transcript	synonymous_variant	2274	2178	726	T	acC/acT	COSM1270093	.	.	1	USP43	HGNC	20072	protein_coding	YES	CCDS45610.1	ENSP00000285199	UBP43_HUMAN	.	UPI0000047AFB	.	.	.	14/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24006:SF408,hmmpanther:PTHR24006	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTACCAGCTC	.	5	ESCA
RNF138	0	.	GRCh37	18	29709647	29709647	+	3'UTR	SNP	G	G	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*497G>T	.	.	ENST00000261593	8/8	289	205	84	288	288	0	RNF138,3_prime_UTR_variant,,ENST00000257190,;RNF138,3_prime_UTR_variant,,ENST00000261593,;GAREM,intron_variant,,ENST00000583696,;RNF138,downstream_gene_variant,,ENST00000580499,;RNF138,downstream_gene_variant,,ENST00000577999,;	T	ENSG00000134758	ENST00000261593	Transcript	3_prime_UTR_variant	1693	.	.	.	.	.	.	.	1	RNF138	HGNC	17765	protein_coding	YES	CCDS11903.1	ENSP00000261593	RN138_HUMAN	J3KSI2_HUMAN,J3KRU4_HUMAN	UPI00000702BA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTAGCTGAA	.	5	ESCA
RNF138	0	.	GRCh37	18	29709648	29709648	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*498C>T	.	.	ENST00000261593	8/8	287	203	83	283	283	0	RNF138,3_prime_UTR_variant,,ENST00000257190,;RNF138,3_prime_UTR_variant,,ENST00000261593,;GAREM,intron_variant,,ENST00000583696,;RNF138,downstream_gene_variant,,ENST00000580499,;RNF138,downstream_gene_variant,,ENST00000577999,;	T	ENSG00000134758	ENST00000261593	Transcript	3_prime_UTR_variant	1694	.	.	.	.	.	.	.	1	RNF138	HGNC	17765	protein_coding	YES	CCDS11903.1	ENSP00000261593	RN138_HUMAN	J3KSI2_HUMAN,J3KRU4_HUMAN	UPI00000702BA	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTAGCTGAAA	.	5	ESCA
MC4R	0	.	GRCh37	18	58038634	58038634	+	Missense_Mutation	SNP	T	T	A	rs778685158	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.949A>T	p.Ile317Phe	p.I317F	ENST00000299766	1/1	38	18	20	45	45	0	MC4R,missense_variant,p.Ile317Phe,ENST00000299766,;	A	ENSG00000166603	ENST00000299766	Transcript	missense_variant	1368	949	317	I/F	Atc/Ttc	CM052897,rs778685158	.	.	-1	MC4R	HGNC	6932	protein_coding	YES	CCDS11976.1	ENSP00000299766	MC4R_HUMAN	K4N7A9_HUMAN,A0N0W8_HUMAN	UPI000013E5E3	.	tolerated(0.36)	benign(0.08)	1/1	.	hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF6,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01062,Prints_domain:PR00535,Prints_domain:PR00534	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGATGATCT	byFrequency	5	ESCA
VAPA	0	.	GRCh37	18	9931846	9931846	+	Missense_Mutation	SNP	G	G	T	rs759982166	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.119G>T	p.Arg40Leu	p.R40L	ENST00000340541	2/7	74	43	31	96	96	0	VAPA,missense_variant,p.Arg40Leu,ENST00000340541,;VAPA,missense_variant,p.Arg40Leu,ENST00000400000,;VAPA,non_coding_transcript_exon_variant,,ENST00000584796,;VAPA,3_prime_UTR_variant,,ENST00000585042,;VAPA,non_coding_transcript_exon_variant,,ENST00000577901,;VAPA,non_coding_transcript_exon_variant,,ENST00000583879,;VAPA,upstream_gene_variant,,ENST00000583475,;	T	ENSG00000101558	ENST00000340541	Transcript	missense_variant	314	119	40	R/L	cGa/cTa	rs759982166	.	.	1	VAPA	HGNC	12648	protein_coding	YES	CCDS11847.2	ENSP00000345656	VAPA_HUMAN	.	UPI000059D45E	.	tolerated(0.2)	benign(0.06)	2/7	.	PROSITE_profiles:PS50202,hmmpanther:PTHR10809,hmmpanther:PTHR10809:SF40,Pfam_domain:PF00635,Gene3D:2.60.40.360,PIRSF_domain:PIRSF019693,Superfamily_domains:SSF49354	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGCGAAATC	byFrequency	5	ESCA
KXD1	0	.	GRCh37	19	18679911	18679911	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*470A>G	.	.	ENST00000602094	5/5	21	14	7	22	22	0	KXD1,3_prime_UTR_variant,,ENST00000595073,;KXD1,3_prime_UTR_variant,,ENST00000602094,;KXD1,3_prime_UTR_variant,,ENST00000539106,;KXD1,3_prime_UTR_variant,,ENST00000540691,;KXD1,3_prime_UTR_variant,,ENST00000601630,;KXD1,3_prime_UTR_variant,,ENST00000222307,;UBA52,upstream_gene_variant,,ENST00000599551,;UBA52,upstream_gene_variant,,ENST00000430157,;UBA52,upstream_gene_variant,,ENST00000594527,;UBA52,upstream_gene_variant,,ENST00000597451,;KXD1,downstream_gene_variant,,ENST00000596785,;UBA52,upstream_gene_variant,,ENST00000596273,;KXD1,downstream_gene_variant,,ENST00000600372,;KXD1,downstream_gene_variant,,ENST00000599000,;UBA52,upstream_gene_variant,,ENST00000595683,;UBA52,upstream_gene_variant,,ENST00000442744,;UBA52,upstream_gene_variant,,ENST00000598780,;KXD1,downstream_gene_variant,,ENST00000600099,;KXD1,downstream_gene_variant,,ENST00000599319,;UBA52,upstream_gene_variant,,ENST00000596272,;UBA52,upstream_gene_variant,,ENST00000599595,;UBA52,upstream_gene_variant,,ENST00000596304,;KXD1,downstream_gene_variant,,ENST00000598830,;UBA52,upstream_gene_variant,,ENST00000599256,;KXD1,downstream_gene_variant,,ENST00000595870,;KXD1,downstream_gene_variant,,ENST00000597438,;UBA52,upstream_gene_variant,,ENST00000595158,;AC005253.4,intron_variant,,ENST00000593791,;CRLF1,downstream_gene_variant,,ENST00000594325,;UBA52,upstream_gene_variant,,ENST00000598814,;KXD1,downstream_gene_variant,,ENST00000600654,;	G	ENSG00000105700	ENST00000602094	Transcript	3_prime_UTR_variant	2461	.	.	.	.	.	.	.	1	KXD1	HGNC	28420	protein_coding	YES	CCDS12381.1	ENSP00000472836	KXDL1_HUMAN	M0R228_HUMAN,M0QXP3_HUMAN,M0QXN9_HUMAN,M0QX74_HUMAN	UPI000013C7F8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAAGTATCAAA	.	4	ESCA
ZNF85	0	.	GRCh37	19	21106139	21106139	+	5'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-68T>C	.	.	ENST00000328178	1/4	77	65	12	123	123	0	ZNF85,5_prime_UTR_variant,,ENST00000596476,;ZNF85,5_prime_UTR_variant,,ENST00000328178,;ZNF85,5_prime_UTR_variant,,ENST00000595854,;ZNF85,5_prime_UTR_variant,,ENST00000300540,;ZNF85,5_prime_UTR_variant,,ENST00000597314,;ZNF85,5_prime_UTR_variant,,ENST00000599885,;ZNF85,5_prime_UTR_variant,,ENST00000601284,;ZNF85,5_prime_UTR_variant,,ENST00000601924,;ZNF85,upstream_gene_variant,,ENST00000345030,;	C	ENSG00000105750	ENST00000328178	Transcript	5_prime_UTR_variant	46	.	.	.	.	.	.	.	1	ZNF85	HGNC	13160	protein_coding	YES	CCDS32977.1	ENSP00000329793	ZNF85_HUMAN	M0R385_HUMAN,M0R120_HUMAN,M0QZN6_HUMAN	UPI0000203897	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTGTGGCCC	.	5	ESCA
DMRTC2	0	.	GRCh37	19	42355790	42355790	+	3'UTR	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*26C>T	.	.	ENST00000269945	9/9	32	28	3	43	43	0	DMRTC2,3_prime_UTR_variant,,ENST00000269945,;DMRTC2,3_prime_UTR_variant,,ENST00000596827,;DMRTC2,downstream_gene_variant,,ENST00000600017,;DMRTC2,downstream_gene_variant,,ENST00000596258,;DMRTC2,downstream_gene_variant,,ENST00000596660,;DMRTC2,downstream_gene_variant,,ENST00000602098,;DMRTC2,3_prime_UTR_variant,,ENST00000601660,;DMRTC2,downstream_gene_variant,,ENST00000599022,;	T	ENSG00000142025	ENST00000269945	Transcript	3_prime_UTR_variant	1181	.	.	.	.	.	.	.	1	DMRTC2	HGNC	13911	protein_coding	YES	CCDS33034.1	ENSP00000269945	DMRTD_HUMAN	M0R2D7_HUMAN,M0R1Z9_HUMAN,M0QZH7_HUMAN	UPI0000071B2A	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	TCTTGCTATGG	.	3	ESCA
TRPM4	0	.	GRCh37	19	49693513	49693513	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2068A>T	p.Ile690Phe	p.I690F	ENST00000252826	15/25	42	35	7	81	81	0	TRPM4,missense_variant,p.Ile336Phe,ENST00000355712,;TRPM4,missense_variant,p.Ile690Phe,ENST00000427978,;TRPM4,missense_variant,p.Ile690Phe,ENST00000252826,;TRPM4,3_prime_UTR_variant,,ENST00000595519,;TRPM4,3_prime_UTR_variant,,ENST00000598502,;TRPM4,3_prime_UTR_variant,,ENST00000598697,;TRPM4,non_coding_transcript_exon_variant,,ENST00000596338,;TRPM4,non_coding_transcript_exon_variant,,ENST00000595071,;TRPM4,intron_variant,,ENST00000595882,;	T	ENSG00000130529	ENST00000252826	Transcript	missense_variant	2194	2068	690	I/F	Atc/Ttc	.	.	.	1	TRPM4	HGNC	17993	protein_coding	YES	CCDS33073.1	ENSP00000252826	TRPM4_HUMAN	.	UPI0000070598	.	deleterious(0.02)	possibly_damaging(0.796)	15/25	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR13800:SF6,hmmpanther:PTHR13800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCATCTGG	.	5	ESCA
FLT3LG	0	.	GRCh37	19	49979702	49979702	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.221G>A	p.Trp74Ter	p.W74*	ENST00000594009	4/8	38	23	15	89	89	0	FLT3LG,stop_gained,p.Trp74Ter,ENST00000600429,;FLT3LG,stop_gained,p.Trp74Ter,ENST00000597551,;FLT3LG,stop_gained,p.Trp74Ter,ENST00000344019,;FLT3LG,stop_gained,p.Trp34Ter,ENST00000598555,;FLT3LG,stop_gained,p.Trp74Ter,ENST00000596435,;FLT3LG,stop_gained,p.Trp74Ter,ENST00000594009,;FLT3LG,5_prime_UTR_variant,,ENST00000595510,;FLT3LG,5_prime_UTR_variant,,ENST00000204637,;FLT3LG,upstream_gene_variant,,ENST00000597914,;CTD-3148I10.15,non_coding_transcript_exon_variant,,ENST00000595815,;FLT3LG,3_prime_UTR_variant,,ENST00000600084,;FLT3LG,3_prime_UTR_variant,,ENST00000601800,;FLT3LG,non_coding_transcript_exon_variant,,ENST00000593422,;FLT3LG,non_coding_transcript_exon_variant,,ENST00000598472,;CTD-3148I10.9,intron_variant,,ENST00000599536,;	A	ENSG00000090554	ENST00000594009	Transcript	stop_gained	300	221	74	W/*	tGg/tAg	.	.	.	1	FLT3LG	HGNC	3766	protein_coding	YES	CCDS12767.1	ENSP00000469613	FLT3L_HUMAN	Q05C96_HUMAN	UPI0000037544	.	.	.	4/8	.	hmmpanther:PTHR11032,hmmpanther:PTHR11032:SF1,Pfam_domain:PF02947,Gene3D:1.20.1250.10,Superfamily_domains:SSF47266	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTGGCGGC	.	5	ESCA
SHANK1	0	.	GRCh37	19	51189602	51189602	+	Silent	SNP	G	G	A	rs369883291	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2469C>T	p.%3D	p.D823D	ENST00000293441	20/23	31	21	10	60	60	0	SHANK1,synonymous_variant,p.%3D,ENST00000391814,;SHANK1,synonymous_variant,p.%3D,ENST00000391813,;SHANK1,synonymous_variant,p.%3D,ENST00000359082,;SHANK1,synonymous_variant,p.%3D,ENST00000293441,;	A	ENSG00000161681	ENST00000293441	Transcript	synonymous_variant	2488	2469	823	D	gaC/gaT	rs369883291	.	.	-1	SHANK1	HGNC	15474	protein_coding	YES	CCDS12799.1	ENSP00000293441	SHAN1_HUMAN	.	UPI000013E109	.	.	.	20/23	.	hmmpanther:PTHR24135:SF3,hmmpanther:PTHR24135	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCGTCCAG	byFrequency|byCluster	5	ESCA
ZNF160	0	.	GRCh37	19	53571447	53571448	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2339dupT	p.Met780IlefsTer13	p.M780Ifs*13	ENST00000429604	7/7	79	61	18	113	113	0	ZNF160,frameshift_variant,p.Met780IlefsTer13,ENST00000418871,;ZNF160,frameshift_variant,p.Met744IlefsTer13,ENST00000601421,;ZNF160,frameshift_variant,p.Met780IlefsTer13,ENST00000429604,;ZNF160,frameshift_variant,p.Met780IlefsTer13,ENST00000599056,;ZNF160,downstream_gene_variant,,ENST00000355147,;ZNF160,downstream_gene_variant,,ENST00000601982,;ZNF160,downstream_gene_variant,,ENST00000599247,;	A	ENSG00000170949	ENST00000429604	Transcript	frameshift_variant	2755-2756	2339-2340	780	M/IX	atg/atTg	.	.	.	-1	ZNF160	HGNC	12948	protein_coding	YES	CCDS12859.1	ENSP00000406201	ZN160_HUMAN	M0QZI7_HUMAN,M0QZ49_HUMAN,M0QXU9_HUMAN	UPI0000202B37	.	.	.	7/7	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF132,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTGCCATATG	.	2	ESCA
EPN1	0	.	GRCh37	19	56204348	56204348	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1467G>C	p.Glu489Asp	p.E489D	ENST00000411543	9/11	20	16	4	21	21	0	EPN1,missense_variant,p.Glu403Asp,ENST00000270460,;EPN1,missense_variant,p.Glu377Asp,ENST00000085079,;EPN1,missense_variant,p.Glu20Asp,ENST00000589704,;EPN1,missense_variant,p.Glu489Asp,ENST00000411543,;AC010525.7,upstream_gene_variant,,ENST00000589698,;AC010525.6,upstream_gene_variant,,ENST00000587937,;AC010525.4,downstream_gene_variant,,ENST00000585559,;EPN1,downstream_gene_variant,,ENST00000591743,;EPN1,non_coding_transcript_exon_variant,,ENST00000586194,;AC010525.1,upstream_gene_variant,,ENST00000366135,;	C	ENSG00000063245	ENST00000411543	Transcript	missense_variant	2014	1467	489	E/D	gaG/gaC	.	.	.	1	EPN1	HGNC	21604	protein_coding	YES	CCDS46198.1	ENSP00000406209	EPN1_HUMAN	.	UPI000059D7B7	.	tolerated(0.49)	possibly_damaging(0.487)	9/11	.	hmmpanther:PTHR12276:SF48,hmmpanther:PTHR12276	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACGAGTTCTC	.	4	ESCA
ZNF460	0	.	GRCh37	19	57802649	57802649	+	Missense_Mutation	SNP	A	A	T	rs768088713	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.740A>T	p.Asn247Ile	p.N247I	ENST00000360338	3/3	37	19	18	50	50	0	ZNF460,missense_variant,p.Asn206Ile,ENST00000537645,;ZNF460,missense_variant,p.Asn247Ile,ENST00000360338,;ZNF460,downstream_gene_variant,,ENST00000599602,;	T	ENSG00000197714	ENST00000360338	Transcript	missense_variant	1062	740	247	N/I	aAt/aTt	rs768088713	.	.	1	ZNF460	HGNC	21628	protein_coding	YES	CCDS12949.1	ENSP00000353491	ZN460_HUMAN	M0R0J6_HUMAN,B4DNX9_HUMAN	UPI0000202D11	.	deleterious(0)	benign(0.281)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF15,hmmpanther:PTHR24384,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACAATGGAG	byFrequency	5	ESCA
ZNF587	0	.	GRCh37	19	58371221	58371221	+	Missense_Mutation	SNP	A	A	G	rs762919845	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1441A>G	p.Ile481Val	p.I481V	ENST00000339656	3/3	81	47	34	101	101	0	ZNF587,missense_variant,p.Ile480Val,ENST00000423137,;ZNF587,missense_variant,p.Ile438Val,ENST00000419854,;ZNF587,missense_variant,p.Ile481Val,ENST00000339656,;ZNF814,intron_variant,,ENST00000597342,;ZNF814,intron_variant,,ENST00000595295,;ZNF814,intron_variant,,ENST00000596604,;ZNF814,intron_variant,,ENST00000597832,;CTD-2583A14.10,downstream_gene_variant,,ENST00000598031,;ZNF814,downstream_gene_variant,,ENST00000595048,;CTD-2583A14.10,downstream_gene_variant,,ENST00000597134,;ZNF814,downstream_gene_variant,,ENST00000600634,;ZNF587B,downstream_gene_variant,,ENST00000316462,;CTD-2583A14.10,downstream_gene_variant,,ENST00000593873,;CTD-2583A14.10,downstream_gene_variant,,ENST00000596498,;CTD-2583A14.10,downstream_gene_variant,,ENST00000603271,;ZNF814,upstream_gene_variant,,ENST00000597652,;ZNF587,upstream_gene_variant,,ENST00000596433,;ZNF814,non_coding_transcript_exon_variant,,ENST00000596184,;ZNF814,intron_variant,,ENST00000595894,;CTD-2583A14.10,downstream_gene_variant,,ENST00000604231,;ZNF814,downstream_gene_variant,,ENST00000597348,;	G	ENSG00000198466	ENST00000339656	Transcript	missense_variant	1623	1441	481	I/V	Ata/Gta	rs762919845	.	.	1	ZNF587	HGNC	30955	protein_coding	YES	CCDS12964.1	ENSP00000345479	ZN587_HUMAN	M0R2A6_HUMAN,M0R178_HUMAN,M0R0V5_HUMAN,M0R0M6_HUMAN,M0QXF5_HUMAN,E7EP41_HUMAN	UPI0000073916	.	tolerated(0.28)	benign(0.394)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF22,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGACTATACAT	byFrequency	5	ESCA
LRRC8E	0	.	GRCh37	19	7966108	7966108	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*310C>A	.	.	ENST00000306708	3/3	32	14	18	62	62	0	LRRC8E,3_prime_UTR_variant,,ENST00000306708,;AC010336.1,5_prime_UTR_variant,,ENST00000539278,;MAP2K7,upstream_gene_variant,,ENST00000545011,;MAP2K7,upstream_gene_variant,,ENST00000397979,;LRRC8E,downstream_gene_variant,,ENST00000599367,;LRRC8E,downstream_gene_variant,,ENST00000600345,;MAP2K7,upstream_gene_variant,,ENST00000397981,;MAP2K7,upstream_gene_variant,,ENST00000397983,;LRRC8E,downstream_gene_variant,,ENST00000598224,;LRRC8E,downstream_gene_variant,,ENST00000593511,;RN7SL115P,downstream_gene_variant,,ENST00000392196,;MAP2K7,upstream_gene_variant,,ENST00000468058,;MAP2K7,upstream_gene_variant,,ENST00000475022,;	A	ENSG00000171017	ENST00000306708	Transcript	3_prime_UTR_variant	2802	.	.	.	.	.	.	.	1	LRRC8E	HGNC	26272	protein_coding	YES	CCDS12189.1	ENSP00000306524	LRC8E_HUMAN	M0R3C1_HUMAN,M0R2K8_HUMAN,M0R2D8_HUMAN,M0QZ48_HUMAN	UPI0000201F4F	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCCTCTCC	.	5	ESCA
MUC16	0	.	GRCh37	19	9065422	9065423	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.22023dupT	p.Thr7342TyrfsTer32	p.T7342Yfs*32	ENST00000397910	3/84	95	65	30	74	74	0	MUC16,frameshift_variant,p.Thr7342TyrfsTer32,ENST00000397910,;	A	ENSG00000181143	ENST00000397910	Transcript	frameshift_variant	22227-22228	22023-22024	7341-7342	-/X	-/T	.	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	3/84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TAATGTAAAGG	.	3	ESCA
AMY1B	0	.	GRCh37	1	104234015	104234015	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1002G>A	p.%3D	p.R334R	ENST00000330330	8/11	139	124	15	191	190	1	AMY1B,synonymous_variant,p.%3D,ENST00000330330,;AMY1B,synonymous_variant,p.%3D,ENST00000370080,;AMY1B,downstream_gene_variant,,ENST00000425410,;AMY1B,downstream_gene_variant,,ENST00000446703,;AMY1B,downstream_gene_variant,,ENST00000464691,;	T	ENSG00000174876	ENST00000330330	Transcript	synonymous_variant	1297	1002	334	R	agG/agA	.	.	.	-1	AMY1B	HGNC	475	protein_coding	YES	CCDS30783.1	ENSP00000330484	AMY1_HUMAN	Q5T085_HUMAN,Q5T084_HUMAN	UPI0000125AA9	.	.	.	8/11	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF105,Gene3D:3.20.20.80,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TACAGCCTGAA	.	2	ESCA
PRKAB2	0	.	GRCh37	1	146633344	146633344	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.688C>T	p.Leu230Phe	p.L230F	ENST00000254101	7/8	120	70	50	100	100	0	PRKAB2,missense_variant,p.Leu230Phe,ENST00000254101,;PRKAB2,missense_variant,p.Leu148Phe,ENST00000425272,;PRKAB2,non_coding_transcript_exon_variant,,ENST00000496858,;PRKAB2,downstream_gene_variant,,ENST00000474939,;	A	ENSG00000131791	ENST00000254101	Transcript	missense_variant	827	688	230	L/F	Ctc/Ttc	.	.	.	-1	PRKAB2	HGNC	9379	protein_coding	YES	CCDS925.1	ENSP00000254101	AAKB2_HUMAN	.	UPI00001250AF	.	deleterious(0)	probably_damaging(0.999)	7/8	.	hmmpanther:PTHR10343:SF43,hmmpanther:PTHR10343,Pfam_domain:PF04739,SMART_domains:SM01010,Superfamily_domains:SSF160219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGAGTAAGG	.	5	ESCA
GON4L	0	.	GRCh37	1	155717813	155717813	+	3'Flank	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000437809	.	43	30	12	74	74	0	MSTO1,3_prime_UTR_variant,,ENST00000452804,;GON4L,downstream_gene_variant,,ENST00000437809,;MSTO1,downstream_gene_variant,,ENST00000538143,;GON4L,downstream_gene_variant,,ENST00000368331,;GON4L,downstream_gene_variant,,ENST00000271883,;GON4L,downstream_gene_variant,,ENST00000473267,;MSTO2P,non_coding_transcript_exon_variant,,ENST00000538914,;MSTO2P,non_coding_transcript_exon_variant,,ENST00000314835,;MSTO2P,downstream_gene_variant,,ENST00000545423,;	A	ENSG00000116580	ENST00000437809	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1695	-1	GON4L	HGNC	25973	protein_coding	YES	CCDS44242.1	ENSP00000396117	GON4L_HUMAN	Q9NXJ9_HUMAN	UPI0000603C24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGGTCTCGTG	.	5	ESCA
FCRL2	0	.	GRCh37	1	157740416	157740416	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.93A>G	p.%3D	p.G31G	ENST00000361516	3/12	32	23	9	57	57	0	FCRL2,synonymous_variant,p.%3D,ENST00000361516,;FCRL2,synonymous_variant,p.%3D,ENST00000392274,;FCRL2,synonymous_variant,p.%3D,ENST00000368181,;FCRL2,upstream_gene_variant,,ENST00000469986,;FCRL2,non_coding_transcript_exon_variant,,ENST00000462774,;FCRL2,upstream_gene_variant,,ENST00000368178,;	C	ENSG00000132704	ENST00000361516	Transcript	synonymous_variant	142	93	31	G	ggA/ggG	.	.	.	-1	FCRL2	HGNC	14875	protein_coding	YES	CCDS1168.1	ENSP00000355157	FCRL2_HUMAN	.	UPI000006E1F3	.	.	.	3/12	.	Superfamily_domains:SSF48726,SMART_domains:SM00408,SMART_domains:SM00409,Pfam_domain:PF13895,Gene3D:2.60.40.10,hmmpanther:PTHR11481:SF41,hmmpanther:PTHR11481	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.F29F|c.87C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCTCCTTC	.	5	ESCA
TADA1	0	.	GRCh37	1	166825867	166825867	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*937T>C	.	.	ENST00000367874	8/8	67	44	22	93	93	0	TADA1,3_prime_UTR_variant,,ENST00000367874,;POGK,downstream_gene_variant,,ENST00000367876,;POGK,downstream_gene_variant,,ENST00000537173,;POGK,downstream_gene_variant,,ENST00000367875,;TADA1,non_coding_transcript_exon_variant,,ENST00000467021,;	G	ENSG00000152382	ENST00000367874	Transcript	3_prime_UTR_variant	2039	.	.	.	.	.	.	.	-1	TADA1	HGNC	30631	protein_coding	YES	CCDS1255.1	ENSP00000356848	TADA1_HUMAN	.	UPI00000709B6	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTATACAT	.	5	ESCA
ASTN1	0	.	GRCh37	1	176926901	176926901	+	Silent	SNP	C	C	A	rs367953854	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1800G>T	p.%3D	p.P600P	ENST00000361833	11/23	40	28	12	65	64	1	ASTN1,synonymous_variant,p.%3D,ENST00000367654,;ASTN1,synonymous_variant,p.%3D,ENST00000424564,;ASTN1,synonymous_variant,p.%3D,ENST00000361833,;ASTN1,synonymous_variant,p.%3D,ENST00000367657,;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,;	A	ENSG00000152092	ENST00000361833	Transcript	synonymous_variant	1814	1800	600	P	ccG/ccT	rs367953854,COSM4025431,COSM4025432	.	.	-1	ASTN1	HGNC	773	protein_coding	YES	CCDS1319.1	ENSP00000354536	ASTN1_HUMAN	Q96BL7_HUMAN	UPI0000160388	.	.	.	11/23	.	hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF8	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCACCGGCCC	byFrequency|byCluster	5	ESCA
RP11-568K15.1	0	.	GRCh37	1	178000792	178000792	+	RNA	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.388C>T	.	.	ENST00000476232	6/10	89	64	24	106	106	0	RP11-568K15.1,non_coding_transcript_exon_variant,,ENST00000476232,;RP11-568K15.1,intron_variant,,ENST00000512906,;RP11-568K15.1,downstream_gene_variant,,ENST00000481349,;RP4-798P15.3,intron_variant,,ENST00000464428,;RP11-568K15.1,non_coding_transcript_exon_variant,,ENST00000462729,;	A	ENSG00000242193	ENST00000476232	Transcript	non_coding_transcript_exon_variant	388	.	.	.	.	.	.	.	-1	RP11-568K15.1	Clone_based_vega_gene	.	processed_transcript	YES	.	.	.	.	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAGGTCCT	.	5	ESCA
C1orf21	0	.	GRCh37	1	184594863	184594863	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6173A>G	.	.	ENST00000235307	6/6	11	6	5	12	12	0	C1orf21,3_prime_UTR_variant,,ENST00000235307,;	G	ENSG00000116667	ENST00000235307	Transcript	3_prime_UTR_variant	6974	.	.	.	.	.	.	.	1	C1orf21	HGNC	15494	protein_coding	YES	CCDS1362.1	ENSP00000235307	CA021_HUMAN	.	UPI0000071170	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAGAAAGTTTG	.	3	ESCA
KLHDC7A	0	.	GRCh37	1	18809788	18809788	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2313T>C	p.%3D	p.D771D	ENST00000400664	1/1	35	31	4	48	48	0	KLHDC7A,synonymous_variant,p.%3D,ENST00000400664,;	C	ENSG00000179023	ENST00000400664	Transcript	synonymous_variant	2365	2313	771	D	gaT/gaC	.	.	.	1	KLHDC7A	HGNC	26791	protein_coding	YES	CCDS185.2	ENSP00000383505	KLD7A_HUMAN	A4FU39_HUMAN	UPI0000E0501F	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24412:SF144,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCCGATTTGCC	.	3	ESCA
CDC42BPA	0	.	GRCh37	1	227178477	227178477	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3492T>C	.	.	ENST00000366769	36/36	58	42	15	87	87	0	CDC42BPA,3_prime_UTR_variant,,ENST00000366767,;CDC42BPA,3_prime_UTR_variant,,ENST00000366764,;CDC42BPA,3_prime_UTR_variant,,ENST00000366766,;CDC42BPA,3_prime_UTR_variant,,ENST00000366769,;CDC42BPA,3_prime_UTR_variant,,ENST00000448940,;CDC42BPA,3_prime_UTR_variant,,ENST00000334218,;ADCK3,downstream_gene_variant,,ENST00000433743,;CDC42BPA,downstream_gene_variant,,ENST00000442054,;ADCK3,downstream_gene_variant,,ENST00000458507,;ADCK3,downstream_gene_variant,,ENST00000366779,;CDC42BPA,downstream_gene_variant,,ENST00000366765,;ADCK3,downstream_gene_variant,,ENST00000366778,;ADCK3,downstream_gene_variant,,ENST00000366777,;CDC42BPA,downstream_gene_variant,,ENST00000535525,;RP5-1087E8.3,upstream_gene_variant,,ENST00000433837,;ADCK3,downstream_gene_variant,,ENST00000464693,;ADCK3,downstream_gene_variant,,ENST00000479852,;ADCK3,downstream_gene_variant,,ENST00000478406,;ADCK3,downstream_gene_variant,,ENST00000485462,;	G	ENSG00000143776	ENST00000366769	Transcript	3_prime_UTR_variant	9944	.	.	.	.	.	.	.	-1	CDC42BPA	HGNC	1737	protein_coding	YES	CCDS1558.1	ENSP00000355731	MRCKA_HUMAN	Q9NYF6_HUMAN	UPI000019097D	.	.	.	36/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTAACAAAA	.	5	ESCA
NUP133	0	.	GRCh37	1	229644018	229644018	+	5'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-22C>T	.	.	ENST00000261396	1/26	16	13	3	19	19	0	NUP133,5_prime_UTR_variant,,ENST00000537506,;NUP133,5_prime_UTR_variant,,ENST00000366678,;NUP133,5_prime_UTR_variant,,ENST00000261396,;RP4-613A2.1,upstream_gene_variant,,ENST00000417605,;	A	ENSG00000069248	ENST00000261396	Transcript	5_prime_UTR_variant	71	.	.	.	.	.	.	.	-1	NUP133	HGNC	18016	protein_coding	YES	CCDS1579.1	ENSP00000261396	NU133_HUMAN	.	UPI000013D17A	.	.	.	1/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACTAGGACAG	.	2	ESCA
RYR2	0	.	GRCh37	1	237947228	237947228	+	Silent	SNP	G	G	A	rs746200625	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12216G>A	p.%3D	p.T4072T	ENST00000366574	90/105	38	33	5	35	35	0	RYR2,synonymous_variant,p.%3D,ENST00000542537,;RYR2,synonymous_variant,p.%3D,ENST00000366574,;RYR2,synonymous_variant,p.%3D,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,;	A	ENSG00000198626	ENST00000366574	Transcript	synonymous_variant	12533	12216	4072	T	acG/acA	rs746200625	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	.	90/105	.	Superfamily_domains:SSF47473,Gene3D:1.10.238.10,hmmpanther:PTHR13715:SF75,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGACGGATGA	byFrequency	4	ESCA
KIAA1522	0	.	GRCh37	1	33240253	33240254	+	3'UTR	DEL	TA	TA	-	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1766_*1767delAT	.	.	ENST00000401073	7/7	79	54	25	99	99	0	KIAA1522,3_prime_UTR_variant,,ENST00000373481,;KIAA1522,3_prime_UTR_variant,,ENST00000373480,;KIAA1522,3_prime_UTR_variant,,ENST00000401073,;YARS,downstream_gene_variant,,ENST00000373477,;KIAA1522,downstream_gene_variant,,ENST00000294521,;YARS,downstream_gene_variant,,ENST00000469100,;YARS,downstream_gene_variant,,ENST00000490826,;YARS,downstream_gene_variant,,ENST00000487404,;YARS,downstream_gene_variant,,ENST00000478828,;	-	ENSG00000162522	ENST00000401073	Transcript	3_prime_UTR_variant	5120-5121	.	.	.	.	.	.	.	1	KIAA1522	HGNC	29301	protein_coding	YES	CCDS41298.1	ENSP00000383851	K1522_HUMAN	.	UPI000022ACD0	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAACTCTATCCTG	.	3	ESCA
GJB4	0	.	GRCh37	1	35228281	35228281	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*625G>A	.	.	ENST00000339480	2/2	29	21	8	45	45	0	GJB4,3_prime_UTR_variant,,ENST00000339480,;GJB5,downstream_gene_variant,,ENST00000338513,;RP1-34M23.5,intron_variant,,ENST00000542839,;SMIM12,intron_variant,,ENST00000426886,;	A	ENSG00000189433	ENST00000339480	Transcript	3_prime_UTR_variant	1796	.	.	.	.	.	.	.	1	GJB4	HGNC	4286	protein_coding	YES	CCDS383.1	ENSP00000345868	CXB4_HUMAN	.	UPI0000051E4B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGGATAGG	.	5	ESCA
ZMYND12	0	.	GRCh37	1	42921632	42921632	+	Missense_Mutation	SNP	G	G	A	rs746894765	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37C>T	p.Arg13Cys	p.R13C	ENST00000372565	1/8	29	20	9	62	61	1	ZMYND12,missense_variant,p.Arg13Cys,ENST00000372565,;ZMYND12,5_prime_UTR_variant,,ENST00000433602,;PPCS,upstream_gene_variant,,ENST00000455780,;PPCS,upstream_gene_variant,,ENST00000372561,;PPCS,upstream_gene_variant,,ENST00000372562,;PPCS,upstream_gene_variant,,ENST00000372560,;PPCS,upstream_gene_variant,,ENST00000372556,;ZMYND12,non_coding_transcript_exon_variant,,ENST00000461083,;PPCS,upstream_gene_variant,,ENST00000471420,;PPCS,upstream_gene_variant,,ENST00000482168,;PPCS,upstream_gene_variant,,ENST00000472013,;PPCS,upstream_gene_variant,,ENST00000469615,;	A	ENSG00000066185	ENST00000372565	Transcript	missense_variant	307	37	13	R/C	Cgc/Tgc	rs746894765	.	.	-1	ZMYND12	HGNC	21192	protein_coding	YES	CCDS467.1	ENSP00000361646	ZMY12_HUMAN	.	UPI000020587B	.	tolerated(0.09)	probably_damaging(0.951)	1/8	.	hmmpanther:PTHR12298,Superfamily_domains:SSF144232	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGCGCCCCT	byFrequency	5	ESCA
USP24	0	.	GRCh37	1	55595244	55595244	+	Silent	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3541C>T	p.%3D	p.L1181L	ENST00000294383	32/68	50	43	7	77	77	0	USP24,synonymous_variant,p.%3D,ENST00000407756,;USP24,synonymous_variant,p.%3D,ENST00000294383,;	A	ENSG00000162402	ENST00000294383	Transcript	synonymous_variant	3541	3541	1181	L	Cta/Tta	.	.	.	-1	USP24	HGNC	12623	protein_coding	YES	CCDS44154.2	ENSP00000294383	UBP24_HUMAN	.	UPI000059CFDE	.	.	.	32/68	.	hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTAGAACCT	.	4	ESCA
LRRC7	0	.	GRCh37	1	70385205	70385205	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534-11985C>T	.	.	ENST00000035383	.	70	58	12	82	82	0	LRRC7,intron_variant,,ENST00000415775,;LRRC7,intron_variant,,ENST00000035383,;LRRC7,intron_variant,,ENST00000310961,;PIN1P1,non_coding_transcript_exon_variant,,ENST00000412108,;PIN1P1,non_coding_transcript_exon_variant,,ENST00000439639,;	T	ENSG00000033122	ENST00000035383	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LRRC7	HGNC	18531	protein_coding	YES	CCDS645.1	ENSP00000035383	LRRC7_HUMAN	.	UPI000006F29B	.	.	.	.	5/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGTCCGCCGC	.	5	ESCA
SRSF11	0	.	GRCh37	1	70716908	70716908	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*420A>G	.	.	ENST00000370950	13/13	50	35	14	66	66	0	SRSF11,3_prime_UTR_variant,,ENST00000370951,;SRSF11,3_prime_UTR_variant,,ENST00000370949,;SRSF11,3_prime_UTR_variant,,ENST00000370950,;SRSF11,downstream_gene_variant,,ENST00000405432,;SRSF11,downstream_gene_variant,,ENST00000395136,;SRSF11,non_coding_transcript_exon_variant,,ENST00000461935,;SRSF11,non_coding_transcript_exon_variant,,ENST00000484162,;SRSF11,downstream_gene_variant,,ENST00000460795,;SRSF11,downstream_gene_variant,,ENST00000463859,;SRSF11,downstream_gene_variant,,ENST00000489188,;	G	ENSG00000116754	ENST00000370950	Transcript	3_prime_UTR_variant	1957	.	.	.	.	.	.	.	1	SRSF11	HGNC	10782	protein_coding	YES	CCDS647.1	ENSP00000359988	SRS11_HUMAN	Q6N079_HUMAN	UPI00001358C5	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAATATCCTA	.	5	ESCA
SLC45A1	0	.	GRCh37	1	8397968	8397968	+	Missense_Mutation	SNP	G	G	A	rs778651345	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1690G>A	p.Glu564Lys	p.E564K	ENST00000471889	7/9	36	33	3	91	91	0	SLC45A1,missense_variant,p.Glu564Lys,ENST00000289877,;SLC45A1,missense_variant,p.Glu598Lys,ENST00000377479,;SLC45A1,missense_variant,p.Glu564Lys,ENST00000471889,;SLC45A1,downstream_gene_variant,,ENST00000481265,;SLC45A1,non_coding_transcript_exon_variant,,ENST00000497660,;	A	ENSG00000162426	ENST00000471889	Transcript	missense_variant	2075	1690	564	E/K	Gag/Aag	rs778651345	.	.	1	SLC45A1	HGNC	17939	protein_coding	YES	CCDS30577.1	ENSP00000418096	S45A1_HUMAN	.	UPI000040EA42	.	tolerated(0.07)	benign(0.397)	7/9	.	hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF6,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATCAGAGGCG	byFrequency	2	ESCA
MCOLN3	0	.	GRCh37	1	85499887	85499887	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.444C>A	p.Asn148Lys	p.N148K	ENST00000370589	4/13	72	60	12	113	113	0	MCOLN3,missense_variant,p.Asn92Lys,ENST00000341115,;MCOLN3,missense_variant,p.Asn148Lys,ENST00000370589,;MCOLN3,missense_variant,p.Asn148Lys,ENST00000370587,;WDR63,intron_variant,,ENST00000370596,;MCOLN3,upstream_gene_variant,,ENST00000475312,;MCOLN3,3_prime_UTR_variant,,ENST00000490600,;	T	ENSG00000055732	ENST00000370589	Transcript	missense_variant	497	444	148	N/K	aaC/aaA	.	.	.	-1	MCOLN3	HGNC	13358	protein_coding	YES	CCDS701.1	ENSP00000359621	MCLN3_HUMAN	.	UPI0000073A4B	.	tolerated(0.73)	benign(0)	4/13	.	hmmpanther:PTHR12127,hmmpanther:PTHR12127:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTGTTCTC	.	5	ESCA
CLCA2	0	.	GRCh37	1	86900239	86900239	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783A>C	p.Glu261Asp	p.E261D	ENST00000370565	6/14	53	35	18	62	62	0	CLCA2,missense_variant,p.Glu261Asp,ENST00000370565,;	C	ENSG00000137975	ENST00000370565	Transcript	missense_variant	945	783	261	E/D	gaA/gaC	.	.	.	1	CLCA2	HGNC	2016	protein_coding	YES	CCDS708.1	ENSP00000359596	CLCA2_HUMAN	.	UPI0000035838	.	deleterious(0.05)	probably_damaging(0.999)	6/14	.	hmmpanther:PTHR10579:SF39,hmmpanther:PTHR10579,Pfam_domain:PF08434,TIGRFAM_domain:TIGR00868	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGAAGCACC	.	5	ESCA
FRG1B	0	.	GRCh37	20	29614264	29614264	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-123-1G>A	.	.	ENST00000278882	.	109	97	12	133	133	0	FRG1B,splice_acceptor_variant,,ENST00000278882,;FRG1B,5_prime_UTR_variant,,ENST00000439954,;FRG1B,5_prime_UTR_variant,,ENST00000358464,;FRG1B,non_coding_transcript_exon_variant,,ENST00000482423,;FRG1B,downstream_gene_variant,,ENST00000468180,;	A	ENSG00000149531	ENST00000278882	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	FRG1B	HGNC	15792	protein_coding	YES	.	ENSP00000278882	FRG1B_HUMAN	.	UPI000012AC05	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTAAGAAGAA	.	4	ESCA
DHX35	0	.	GRCh37	20	37650518	37650518	+	Silent	SNP	C	C	T	rs534416816	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1533C>T	p.%3D	p.I511I	ENST00000252011	16/22	47	40	7	83	83	0	DHX35,synonymous_variant,p.%3D,ENST00000252011,;DHX35,synonymous_variant,p.%3D,ENST00000373325,;DHX35,synonymous_variant,p.%3D,ENST00000373323,;DHX35,synonymous_variant,p.%3D,ENST00000449559,;DHX35,3_prime_UTR_variant,,ENST00000484417,;	T	ENSG00000101452	ENST00000252011	Transcript	synonymous_variant	1566	1533	511	I	atC/atT	rs534416816	.	.	1	DHX35	HGNC	15861	protein_coding	YES	CCDS13310.1	ENSP00000252011	DHX35_HUMAN	.	UPI0000129088	.	.	.	16/22	.	hmmpanther:PTHR18934,Pfam_domain:PF04408,SMART_domains:SM00847,Superfamily_domains:SSF52540	T:0.0004	T:0	T:0.0029	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCATCGCTGC	byFrequency|by1000G	4	ESCA
ATP9A	0	.	GRCh37	20	50221436	50221436	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2927G>T	p.Trp976Leu	p.W976L	ENST00000338821	27/28	36	28	8	58	58	0	ATP9A,missense_variant,p.Trp976Leu,ENST00000338821,;ATP9A,missense_variant,p.Trp855Leu,ENST00000402822,;ATP9A,missense_variant,p.Trp840Leu,ENST00000311637,;	A	ENSG00000054793	ENST00000338821	Transcript	missense_variant	3192	2927	976	W/L	tGg/tTg	.	.	.	-1	ATP9A	HGNC	13540	protein_coding	YES	CCDS33489.1	ENSP00000342481	ATP9A_HUMAN	Q2NLD0_HUMAN,B4DR18_HUMAN	UPI000004D334	.	deleterious(0)	possibly_damaging(0.885)	27/28	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24092:SF49,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCCAGGTC	.	5	ESCA
ZBTB46	0	.	GRCh37	20	62421604	62421604	+	Silent	SNP	C	C	T	rs374159825	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507G>A	p.%3D	p.P169P	ENST00000245663	2/5	17	13	4	39	39	0	ZBTB46,synonymous_variant,p.%3D,ENST00000302995,;ZBTB46,synonymous_variant,p.%3D,ENST00000395104,;ZBTB46,synonymous_variant,p.%3D,ENST00000245663,;ZBTB46,upstream_gene_variant,,ENST00000480766,;	T	ENSG00000130584	ENST00000245663	Transcript	synonymous_variant	658	507	169	P	ccG/ccA	rs374159825	.	.	-1	ZBTB46	HGNC	16094	protein_coding	YES	CCDS13538.1	ENSP00000245663	ZBT46_HUMAN	.	UPI0000206406	.	.	.	2/5	.	hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF118	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCACGGGGA	byCluster|by1000G	5	ESCA
COL6A1	0	.	GRCh37	21	47423346	47423346	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2506G>A	p.Gly836Ser	p.G836S	ENST00000361866	35/35	28	7	21	41	41	0	COL6A1,missense_variant,p.Gly836Ser,ENST00000361866,;COL6A1,non_coding_transcript_exon_variant,,ENST00000486023,;COL6A1,non_coding_transcript_exon_variant,,ENST00000498614,;COL6A1,downstream_gene_variant,,ENST00000463060,;COL6A1,downstream_gene_variant,,ENST00000466285,;	A	ENSG00000142156	ENST00000361866	Transcript	missense_variant	2620	2506	836	G/S	Ggc/Agc	.	.	.	1	COL6A1	HGNC	2211	protein_coding	YES	CCDS13727.1	ENSP00000355180	CO6A1_HUMAN	Q05BT9_HUMAN	UPI000019B179	.	tolerated(1)	benign(0.086)	35/35	.	Superfamily_domains:SSF53300,SMART_domains:SM00327,Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGACGGCTCC	.	5	ESCA
OR11H1	0	.	GRCh37	22	16449141	16449141	+	Missense_Mutation	SNP	T	T	A	rs775913492	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664A>T	p.Ile222Phe	p.I222F	ENST00000252835	1/1	82	69	13	112	112	0	OR11H1,missense_variant,p.Ile222Phe,ENST00000252835,;	A	ENSG00000130538	ENST00000252835	Transcript	missense_variant	665	664	222	I/F	Att/Ttt	rs775913492	.	.	-1	OR11H1	HGNC	15404	protein_coding	YES	CCDS33594.1	ENSP00000252835	O11H1_HUMAN	.	UPI000004B1CF	.	deleterious(0)	probably_damaging(0.925)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF201,hmmpanther:PTHR24242,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AAAAATAACTA	byFrequency	3	ESCA
DGCR8	0	.	GRCh37	22	20077713	20077713	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1238C>T	p.Ala413Val	p.A413V	ENST00000351989	5/14	39	31	8	39	39	0	DGCR8,missense_variant,p.Ala413Val,ENST00000351989,;DGCR8,missense_variant,p.Ala413Val,ENST00000383024,;DGCR8,missense_variant,p.Ala413Val,ENST00000407755,;DGCR8,downstream_gene_variant,,ENST00000457069,;MIR1306,downstream_gene_variant,,ENST00000408439,;MIR3618,downstream_gene_variant,,ENST00000580330,;DGCR8,non_coding_transcript_exon_variant,,ENST00000495826,;DGCR8,non_coding_transcript_exon_variant,,ENST00000498171,;DGCR8,upstream_gene_variant,,ENST00000491892,;	T	ENSG00000128191	ENST00000351989	Transcript	missense_variant	1667	1238	413	A/V	gCt/gTt	.	.	.	1	DGCR8	HGNC	2847	protein_coding	YES	CCDS13773.1	ENSP00000263209	DGCR8_HUMAN	C9JSD5_HUMAN	UPI0000129225	.	tolerated(0.38)	benign(0.013)	5/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13482,hmmpanther:PTHR13482:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGGCTGAGG	.	2	ESCA
ZNF70	0	.	GRCh37	22	24086011	24086011	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1317G>T	p.Lys439Asn	p.K439N	ENST00000341976	2/2	32	23	8	72	72	0	ZNF70,missense_variant,p.Lys439Asn,ENST00000341976,;LL22NC03-N27C7.1,upstream_gene_variant,,ENST00000602816,;	A	ENSG00000187792	ENST00000341976	Transcript	missense_variant	1778	1317	439	K/N	aaG/aaT	.	.	.	-1	ZNF70	HGNC	13140	protein_coding	YES	CCDS13812.1	ENSP00000339314	ZNF70_HUMAN	.	UPI0000001C98	.	deleterious(0)	possibly_damaging(0.522)	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF82,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCTTCTG	.	5	ESCA
TRABD	0	.	GRCh37	22	50637604	50637604	+	3'UTR	SNP	C	C	T	rs202137436	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*656C>T	.	.	ENST00000303434	10/10	89	64	25	103	103	0	TRABD,3_prime_UTR_variant,,ENST00000395827,;TRABD,3_prime_UTR_variant,,ENST00000303434,;TRABD,3_prime_UTR_variant,,ENST00000395829,;TRABD,3_prime_UTR_variant,,ENST00000380909,;SELO,upstream_gene_variant,,ENST00000380903,;RP3-402G11.26,non_coding_transcript_exon_variant,,ENST00000608025,;TRABD,non_coding_transcript_exon_variant,,ENST00000463233,;TRABD,downstream_gene_variant,,ENST00000472677,;	T	ENSG00000170638	ENST00000303434	Transcript	3_prime_UTR_variant	1906	.	.	.	.	rs202137436	.	.	1	TRABD	HGNC	28805	protein_coding	YES	CCDS14086.1	ENSP00000305664	TRABD_HUMAN	.	UPI0000049DAE	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATTCGTGTT	byCluster	5	ESCA
SBF1	0	.	GRCh37	22	50885850	50885850	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5484G>A	p.%3D	p.E1828E	ENST00000380817	40/41	33	25	8	53	53	0	SBF1,synonymous_variant,p.%3D,ENST00000418590,;SBF1,synonymous_variant,p.%3D,ENST00000390679,;SBF1,synonymous_variant,p.%3D,ENST00000348911,;SBF1,synonymous_variant,p.%3D,ENST00000380817,;PPP6R2,downstream_gene_variant,,ENST00000395741,;PPP6R2,downstream_gene_variant,,ENST00000359139,;PPP6R2,downstream_gene_variant,,ENST00000401672,;PPP6R2,downstream_gene_variant,,ENST00000427222,;PPP6R2,downstream_gene_variant,,ENST00000395744,;PPP6R2,downstream_gene_variant,,ENST00000216061,;SBF1,non_coding_transcript_exon_variant,,ENST00000473724,;SBF1,non_coding_transcript_exon_variant,,ENST00000470434,;PPP6R2,downstream_gene_variant,,ENST00000470046,;	T	ENSG00000100241	ENST00000380817	Transcript	synonymous_variant	5668	5484	1828	E	gaG/gaA	.	.	.	-1	SBF1	HGNC	10542	protein_coding	YES	CCDS14091.2	ENSP00000370196	MTMR5_HUMAN	Q86TK5_HUMAN	UPI00001D69ED	.	.	.	40/41	.	PROSITE_profiles:PS50003,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF43,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCACTCTGT	.	5	ESCA
TMEM182	0	.	GRCh37	2	103378750	103378750	+	Missense_Mutation	SNP	T	T	G	rs762064596	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.74T>G	p.Phe25Cys	p.F25C	ENST00000412401	1/5	62	33	29	82	82	0	TMEM182,missense_variant,p.Phe25Cys,ENST00000412401,;TMEM182,intron_variant,,ENST00000454536,;TMEM182,intron_variant,,ENST00000409528,;TMEM182,intron_variant,,ENST00000409173,;TMEM182,intron_variant,,ENST00000469971,;TMEM182,intron_variant,,ENST00000488134,;TMEM182,upstream_gene_variant,,ENST00000486293,;	G	ENSG00000170417	ENST00000412401	Transcript	missense_variant	279	74	25	F/C	tTt/tGt	rs762064596	.	.	1	TMEM182	HGNC	26391	protein_coding	YES	CCDS2064.1	ENSP00000394178	TM182_HUMAN	.	UPI0000366F4E	.	tolerated(0.07)	probably_damaging(0.963)	1/5	.	Pfam_domain:PF13903,hmmpanther:PTHR32012,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTTTGGAT	byFrequency	5	ESCA
GCC2	0	.	GRCh37	2	109086172	109086172	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387A>G	p.%3D	p.K129K	ENST00000309863	6/23	84	56	28	98	98	0	GCC2,synonymous_variant,p.%3D,ENST00000409821,;GCC2,synonymous_variant,p.%3D,ENST00000309863,;GCC2,synonymous_variant,p.%3D,ENST00000409896,;GCC2,upstream_gene_variant,,ENST00000492785,;GCC2,upstream_gene_variant,,ENST00000462897,;GCC2,non_coding_transcript_exon_variant,,ENST00000485546,;GCC2,downstream_gene_variant,,ENST00000478207,;GCC2,3_prime_UTR_variant,,ENST00000482325,;	G	ENSG00000135968	ENST00000309863	Transcript	synonymous_variant	1101	387	129	K	aaA/aaG	.	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	.	.	6/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAAGAAAT	.	5	ESCA
LINC00116	0	.	GRCh37	2	110970017	110970017	+	RNA	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1732G>A	.	.	ENST00000414416	8/9	37	25	12	74	74	0	LINC00116,non_coding_transcript_exon_variant,,ENST00000414416,;LINC00116,non_coding_transcript_exon_variant,,ENST00000426713,;	T	ENSG00000175701	ENST00000414416	Transcript	non_coding_transcript_exon_variant	1732	.	.	.	.	.	.	.	-1	LINC00116	HGNC	27339	lincRNA	YES	.	.	.	.	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAGTCGGTTC	.	5	ESCA
EN1	0	.	GRCh37	2	119600737	119600737	+	Missense_Mutation	SNP	T	T	G	rs769146878	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956A>C	p.Lys319Thr	p.K319T	ENST00000295206	2/2	34	21	13	57	57	0	EN1,missense_variant,p.Lys319Thr,ENST00000295206,;EN1,downstream_gene_variant,,ENST00000546667,;	G	ENSG00000163064	ENST00000295206	Transcript	missense_variant	1467	956	319	K/T	aAg/aCg	rs769146878	.	.	-1	EN1	HGNC	3342	protein_coding	YES	CCDS2123.1	ENSP00000295206	HME1_HUMAN	.	UPI000013E21D	.	deleterious(0)	possibly_damaging(0.753)	2/2	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24341,hmmpanther:PTHR24341:SF4,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00026	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCCTTGAGT	.	5	ESCA
ACVR2A	0	.	GRCh37	2	148686474	148686474	+	3'UTR	SNP	A	A	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1631A>T	.	.	ENST00000241416	11/11	80	62	17	102	102	0	ACVR2A,3_prime_UTR_variant,,ENST00000241416,;ACVR2A,downstream_gene_variant,,ENST00000404590,;ACVR2A,downstream_gene_variant,,ENST00000535787,;ORC4,downstream_gene_variant,,ENST00000392857,;ACVR2A,downstream_gene_variant,,ENST00000495775,;	T	ENSG00000121989	ENST00000241416	Transcript	3_prime_UTR_variant	3809	.	.	.	.	.	.	.	1	ACVR2A	HGNC	173	protein_coding	YES	CCDS33301.1	ENSP00000241416	AVR2A_HUMAN	B4DWQ2_HUMAN	UPI0000126673	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAATCCAT	.	5	ESCA
KCNJ3	0	.	GRCh37	2	155712210	155712210	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*385A>G	.	.	ENST00000295101	3/3	21	16	5	35	35	0	KCNJ3,3_prime_UTR_variant,,ENST00000295101,;KCNJ3,downstream_gene_variant,,ENST00000544049,;KCNJ3,downstream_gene_variant,,ENST00000493505,;	G	ENSG00000162989	ENST00000295101	Transcript	3_prime_UTR_variant	2368	.	.	.	.	.	.	.	1	KCNJ3	HGNC	6264	protein_coding	YES	CCDS2200.1	ENSP00000295101	IRK3_HUMAN	Q53R59_HUMAN	UPI000012D899	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGAATAGCT	.	2	ESCA
COBLL1	0	.	GRCh37	2	165548881	165548881	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3264G>C	p.Gln1088His	p.Q1088H	ENST00000342193	13/14	61	52	9	86	86	0	COBLL1,missense_variant,p.Gln1050His,ENST00000375458,;COBLL1,missense_variant,p.Gln1088His,ENST00000409184,;COBLL1,missense_variant,p.Gln1088His,ENST00000342193,;COBLL1,missense_variant,p.Gln1126His,ENST00000392717,;COBLL1,missense_variant,p.Gln1155His,ENST00000194871,;SNORA70F,upstream_gene_variant,,ENST00000384142,;COBLL1,downstream_gene_variant,,ENST00000493713,;COBLL1,upstream_gene_variant,,ENST00000495084,;COBLL1,non_coding_transcript_exon_variant,,ENST00000493868,;COBLL1,non_coding_transcript_exon_variant,,ENST00000489955,;AC019181.3,upstream_gene_variant,,ENST00000417151,;	G	ENSG00000082438	ENST00000342193	Transcript	missense_variant	3480	3264	1088	Q/H	caG/caC	.	.	.	-1	COBLL1	HGNC	23571	protein_coding	YES	CCDS2223.2	ENSP00000341360	COBL1_HUMAN	C9JWZ0_HUMAN,C9JAU3_HUMAN,B3KMG7_HUMAN	UPI000007132B	.	deleterious(0.03)	benign(0.194)	13/14	.	hmmpanther:PTHR21557:SF2,hmmpanther:PTHR21557	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAATTCTGTTC	.	4	ESCA
XIRP2	0	.	GRCh37	2	168107984	168107984	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10082A>C	p.Asn3361Thr	p.N3361T	ENST00000409195	9/11	35	30	5	39	39	0	XIRP2,missense_variant,p.Asn3139Thr,ENST00000409273,;XIRP2,missense_variant,p.Asn3361Thr,ENST00000409195,;XIRP2,missense_variant,p.Asn3361Thr,ENST00000295237,;XIRP2,intron_variant,,ENST00000409605,;XIRP2,intron_variant,,ENST00000420519,;XIRP2,intron_variant,,ENST00000409756,;XIRP2,intron_variant,,ENST00000409043,;XIRP2,intron_variant,,ENST00000409728,;	C	ENSG00000163092	ENST00000409195	Transcript	missense_variant	10171	10082	3361	N/T	aAc/aCc	.	.	.	1	XIRP2	HGNC	14303	protein_coding	YES	CCDS42769.1	ENSP00000386840	.	J3KNB1_HUMAN	UPI0000E9BBED	.	.	benign(0.135)	9/11	.	hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACAAACCATA	.	4	ESCA
OLA1	0	.	GRCh37	2	174939494	174939494	+	3'UTR	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*660A>G	.	.	ENST00000284719	11/11	21	13	8	23	23	0	OLA1,3_prime_UTR_variant,,ENST00000284719,;OLA1,downstream_gene_variant,,ENST00000428402,;OLA1,downstream_gene_variant,,ENST00000344357,;OLA1,downstream_gene_variant,,ENST00000409546,;OLA1,downstream_gene_variant,,ENST00000392560,;OLA1,downstream_gene_variant,,ENST00000497760,;	C	ENSG00000138430	ENST00000284719	Transcript	3_prime_UTR_variant	2098	.	.	.	.	.	.	.	-1	OLA1	HGNC	28833	protein_coding	YES	CCDS2255.1	ENSP00000284719	OLA1_HUMAN	Q53SW9_HUMAN,Q53SQ6_HUMAN,C9JTK6_HUMAN,C9JCJ9_HUMAN	UPI00001328C1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTATCATCT	.	5	ESCA
TTN	0	.	GRCh37	2	179456788	179456788	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59843T>C	p.Leu19948Pro	p.L19948P	ENST00000589042	302/363	68	54	13	60	60	0	TTN,missense_variant,p.Leu11008Pro,ENST00000359218,;TTN,missense_variant,p.Leu18307Pro,ENST00000591111,;TTN,missense_variant,p.Leu19948Pro,ENST00000589042,;TTN,missense_variant,p.Leu11075Pro,ENST00000342175,;TTN,missense_variant,p.Leu17380Pro,ENST00000342992,;TTN,missense_variant,p.Leu10883Pro,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000590743,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	60068	59843	19948	L/P	cTc/cCc	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	302/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAAGAGGTAC	.	5	ESCA
TTN	0	.	GRCh37	2	179482140	179482140	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.47672T>C	p.Ile15891Thr	p.I15891T	ENST00000589042	254/363	32	24	8	36	36	0	TTN,missense_variant,p.Ile6951Thr,ENST00000359218,;TTN,missense_variant,p.Ile14250Thr,ENST00000591111,;TTN,missense_variant,p.Ile15891Thr,ENST00000589042,;TTN,missense_variant,p.Ile13323Thr,ENST00000342992,;TTN,missense_variant,p.Ile7018Thr,ENST00000342175,;TTN,missense_variant,p.Ile6826Thr,ENST00000460472,;RP11-171I2.4,downstream_gene_variant,,ENST00000605334,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000589234,;TTN-AS1,upstream_gene_variant,,ENST00000604956,;	G	ENSG00000155657	ENST00000589042	Transcript	missense_variant	47897	47672	15891	I/T	aTa/aCa	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	254/363	.	PROSITE_profiles:PS50853,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTAATATTGGG	.	5	ESCA
SATB2	0	.	GRCh37	2	200135821	200135821	+	3'UTR	SNP	A	A	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1113T>G	.	.	ENST00000417098	11/11	32	28	4	30	30	0	SATB2,3_prime_UTR_variant,,ENST00000260926,;SATB2,3_prime_UTR_variant,,ENST00000443023,;SATB2,3_prime_UTR_variant,,ENST00000417098,;SATB2,downstream_gene_variant,,ENST00000428695,;SATB2,downstream_gene_variant,,ENST00000457245,;	C	ENSG00000119042	ENST00000417098	Transcript	3_prime_UTR_variant	4132	.	.	.	.	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAGTAAAAAAC	.	2	ESCA
CTLA4	0	.	GRCh37	2	204738398	204738398	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*863A>G	.	.	ENST00000302823	4/4	14	6	8	16	16	0	CTLA4,3_prime_UTR_variant,,ENST00000302823,;CTLA4,downstream_gene_variant,,ENST00000427473,;CTLA4,downstream_gene_variant,,ENST00000295854,;CTLA4,downstream_gene_variant,,ENST00000472206,;CTLA4,downstream_gene_variant,,ENST00000487393,;	G	ENSG00000163599	ENST00000302823	Transcript	3_prime_UTR_variant	1692	.	.	.	.	.	.	.	1	CTLA4	HGNC	2505	protein_coding	YES	CCDS2362.1	ENSP00000303939	CTLA4_HUMAN	Q9BZK2_HUMAN,Q8TDA6_HUMAN,Q0Q5F1_HUMAN,E9L3G3_HUMAN,E9L3G1_HUMAN,E9L3G0_HUMAN	UPI0000031FDF	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACAGCTGG	.	5	ESCA
MAP2	0	.	GRCh37	2	210594936	210594936	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5299C>T	p.His1767Tyr	p.H1767Y	ENST00000360351	15/15	34	25	8	38	38	0	MAP2,missense_variant,p.His1767Tyr,ENST00000360351,;MAP2,missense_variant,p.His1763Tyr,ENST00000447185,;MAP2,missense_variant,p.His499Tyr,ENST00000199940,;MAP2,missense_variant,p.His411Tyr,ENST00000392194,;MAP2,missense_variant,p.His411Tyr,ENST00000361559,;MAP2,downstream_gene_variant,,ENST00000475600,;	T	ENSG00000078018	ENST00000360351	Transcript	missense_variant	5805	5299	1767	H/Y	Cat/Tat	.	.	.	1	MAP2	HGNC	6839	protein_coding	YES	CCDS2384.1	ENSP00000353508	MTAP2_HUMAN	A8MZ31_HUMAN	UPI000013D119	.	deleterious(0)	probably_damaging(0.943)	15/15	.	hmmpanther:PTHR11501:SF15,hmmpanther:PTHR11501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGAGCATGCT	.	5	ESCA
SNED1	0	.	GRCh37	2	242003535	242003535	+	Nonsense_Mutation	SNP	C	C	A	rs778898633	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2592C>A	p.Cys864Ter	p.C864*	ENST00000310397	19/32	46	32	13	75	75	0	SNED1,stop_gained,p.Cys864Ter,ENST00000405547,;SNED1,stop_gained,p.Cys864Ter,ENST00000342631,;SNED1,stop_gained,p.Cys864Ter,ENST00000310397,;SNED1,stop_gained,p.Cys864Ter,ENST00000401884,;AC005237.4,upstream_gene_variant,,ENST00000458377,;SNED1,non_coding_transcript_exon_variant,,ENST00000466618,;	A	ENSG00000162804	ENST00000310397	Transcript	stop_gained	2592	2592	864	C/*	tgC/tgA	rs778898633	.	.	1	SNED1	HGNC	24696	protein_coding	YES	CCDS46562.1	ENSP00000308893	SNED1_HUMAN	.	UPI0000DD7AB0	.	.	.	19/32	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF28,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CACTGCGAGAC	.	3	ESCA
DTNB	0	.	GRCh37	2	25610220	25610220	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1763T>A	p.Leu588Gln	p.L588Q	ENST00000406818	18/21	30	26	4	93	93	0	DTNB,missense_variant,p.Leu524Gln,ENST00000496972,;DTNB,missense_variant,p.Leu551Gln,ENST00000407186,;DTNB,missense_variant,p.Leu588Gln,ENST00000406818,;DTNB,missense_variant,p.Leu588Gln,ENST00000407661,;DTNB,missense_variant,p.Leu377Gln,ENST00000545439,;DTNB,intron_variant,,ENST00000405222,;DTNB,intron_variant,,ENST00000404103,;DTNB,intron_variant,,ENST00000288642,;DTNB,intron_variant,,ENST00000407038,;DTNB,downstream_gene_variant,,ENST00000481841,;DTNB,upstream_gene_variant,,ENST00000497476,;DTNB,3_prime_UTR_variant,,ENST00000398951,;DTNB,3_prime_UTR_variant,,ENST00000356599,;DTNB,non_coding_transcript_exon_variant,,ENST00000498437,;DTNB,non_coding_transcript_exon_variant,,ENST00000479898,;DTNB,intron_variant,,ENST00000489949,;DTNB,downstream_gene_variant,,ENST00000482145,;	T	ENSG00000138101	ENST00000406818	Transcript	missense_variant	2013	1763	588	L/Q	cTg/cAg	.	.	.	-1	DTNB	HGNC	3058	protein_coding	YES	CCDS46237.1	ENSP00000384084	DTNB_HUMAN	Q53TC8_HUMAN,Q53T51_HUMAN,Q53SF9_HUMAN,Q53QV1_HUMAN,F8W9U0_HUMAN,E9PE76_HUMAN,E7ES64_HUMAN	UPI0000129949	.	deleterious(0)	probably_damaging(0.999)	18/21	.	hmmpanther:PTHR11915:SF227,hmmpanther:PTHR11915,PIRSF_domain:PIRSF038204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGCAGGTCA	.	4	ESCA
GALNT14	0	.	GRCh37	2	31147091	31147091	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000324589	14/16	73	64	9	105	105	0	GALNT14,missense_variant,p.Arg390Gln,ENST00000420311,;GALNT14,missense_variant,p.Arg430Gln,ENST00000324589,;GALNT14,missense_variant,p.Arg392Gln,ENST00000430167,;GALNT14,missense_variant,p.Arg392Gln,ENST00000356174,;GALNT14,missense_variant,p.Arg425Gln,ENST00000349752,;GALNT14,missense_variant,p.Arg405Gln,ENST00000406653,;GALNT14,non_coding_transcript_exon_variant,,ENST00000475320,;GALNT14,intron_variant,,ENST00000486564,;GALNT14,downstream_gene_variant,,ENST00000455477,;	T	ENSG00000158089	ENST00000324589	Transcript	missense_variant	1350	1289	430	R/Q	cGa/cAa	COSM1020081	.	.	-1	GALNT14	HGNC	22946	protein_coding	YES	CCDS58706.1	ENSP00000314500	GLT14_HUMAN	.	UPI0000073A6F	.	tolerated(0.31)	possibly_damaging(0.821)	14/16	.	PROSITE_profiles:PS50231,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF8,Gene3D:2.80.10.50,Pfam_domain:PF00652,SMART_domains:SM00458,Superfamily_domains:SSF50370	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TCTGTCGGATA	.	3	ESCA
MSH6	0	.	GRCh37	2	48023133	48023134	+	Frame_Shift_Ins	INS	-	-	AAGAG	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562_563insGAAGA	p.Ile188ArgfsTer25	p.I188Rfs*25	ENST00000234420	3/10	46	36	10	69	69	0	MSH6,frameshift_variant,p.Ile89ArgfsTer25,ENST00000411819,;MSH6,frameshift_variant,p.Ile188ArgfsTer25,ENST00000234420,;MSH6,frameshift_variant,p.Ile89ArgfsTer?,ENST00000420813,;MSH6,frameshift_variant,p.Ile89ArgfsTer25,ENST00000455383,;MSH6,5_prime_UTR_variant,,ENST00000538136,;FBXO11,intron_variant,,ENST00000405808,;MSH6,intron_variant,,ENST00000540021,;MSH6,downstream_gene_variant,,ENST00000606499,;MSH6,3_prime_UTR_variant,,ENST00000456246,;FBXO11,intron_variant,,ENST00000434234,;MSH6,intron_variant,,ENST00000445503,;RPL36AP15,downstream_gene_variant,,ENST00000444514,;	AAGAG	ENSG00000116062	ENST00000234420	Transcript	frameshift_variant	710-711	558-559	186-187	-/KX	-/AAGAG	.	.	.	1	MSH6	HGNC	7329	protein_coding	YES	CCDS1836.1	ENSP00000234420	MSH6_HUMAN	U3KQ72_HUMAN,F5H2F9_HUMAN,C9JH55_HUMAN,C9J8Y8_HUMAN,C9J7Y7_HUMAN	UPI00000405F8	.	.	.	3/10	.	Gene3D:2.30.30.160,PIRSF_domain:PIRSF037677,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAAGACAAGAT	.	3	ESCA
DYSF	0	.	GRCh37	2	71906280	71906280	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5978A>C	p.Glu1993Ala	p.E1993A	ENST00000410020	53/56	61	54	6	112	112	0	DYSF,missense_variant,p.Glu1992Ala,ENST00000409582,;DYSF,missense_variant,p.Glu1993Ala,ENST00000410020,;DYSF,missense_variant,p.Glu1962Ala,ENST00000409744,;DYSF,missense_variant,p.Glu1975Ala,ENST00000429174,;DYSF,missense_variant,p.Glu1971Ala,ENST00000409762,;DYSF,missense_variant,p.Glu1972Ala,ENST00000410041,;DYSF,missense_variant,p.Glu1986Ala,ENST00000409651,;DYSF,missense_variant,p.Glu1955Ala,ENST00000394120,;DYSF,missense_variant,p.Glu1976Ala,ENST00000409366,;DYSF,missense_variant,p.Glu1985Ala,ENST00000413539,;DYSF,missense_variant,p.Glu1954Ala,ENST00000258104,;DYSF,non_coding_transcript_exon_variant,,ENST00000479049,;	C	ENSG00000135636	ENST00000410020	Transcript	missense_variant	6119	5978	1993	E/A	gAa/gCa	.	.	.	1	DYSF	HGNC	3097	protein_coding	YES	CCDS46328.1	ENSP00000386881	DYSF_HUMAN	A0FK00_HUMAN	UPI000171F710	.	tolerated(0.64)	benign(0.012)	53/56	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF35,Gene3D:2.60.40.150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCAGAATGGT	.	4	ESCA
RGPD1	0	.	GRCh37	2	87201286	87201286	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1340A>C	p.Lys447Thr	p.K447T	ENST00000559485	10/23	86	77	9	128	128	0	RGPD1,missense_variant,p.Lys455Thr,ENST00000398193,;RGPD1,missense_variant,p.Lys447Thr,ENST00000559485,;RGPD1,missense_variant,p.Lys447Thr,ENST00000409776,;RGPD1,upstream_gene_variant,,ENST00000428128,;	C	ENSG00000187627	ENST00000559485	Transcript	missense_variant	1356	1340	447	K/T	aAa/aCa	.	.	.	1	RGPD1	HGNC	32414	protein_coding	YES	CCDS46358.2	ENSP00000453170	RGPD1_HUMAN	Q9NYL8_HUMAN,I1Z9D1_HUMAN	UPI00018815D1	.	tolerated(0.06)	benign(0.249)	10/23	.	hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	CCGAAAATGGC	.	2	ESCA
PARP9	0	.	GRCh37	3	122247052	122247065	+	3'UTR	DEL	ACTAAGATGCTAGT	ACTAAGATGCTAGT	-	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	ACTAAGATGCTAGT	ACTAAGATGCTAGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*146_*159delACTAGCATCTTAGT	.	.	ENST00000360356	11/11	28	17	11	29	29	0	PARP9,3_prime_UTR_variant,,ENST00000477522,;PARP9,3_prime_UTR_variant,,ENST00000471785,;PARP9,3_prime_UTR_variant,,ENST00000492382,;PARP9,3_prime_UTR_variant,,ENST00000360356,;PARP9,downstream_gene_variant,,ENST00000462315,;PARP9,non_coding_transcript_exon_variant,,ENST00000489652,;	-	ENSG00000138496	ENST00000360356	Transcript	3_prime_UTR_variant	2939-2952	.	.	.	.	.	.	.	-1	PARP9	HGNC	24118	protein_coding	YES	CCDS3014.1	ENSP00000353512	PARP9_HUMAN	Q658Y0_HUMAN	UPI000013D133	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|PINDEL	AAAGGCACTAAGATGCTAGTATGTG	.	2	ESCA
ZIC1	0	.	GRCh37	3	147132126	147132126	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*788G>A	.	.	ENST00000282928	3/3	76	64	12	114	114	0	ZIC1,3_prime_UTR_variant,,ENST00000282928,;ZIC1,downstream_gene_variant,,ENST00000488404,;ZIC1,intron_variant,,ENST00000472523,;	A	ENSG00000152977	ENST00000282928	Transcript	3_prime_UTR_variant	2861	.	.	.	.	.	.	.	1	ZIC1	HGNC	12872	protein_coding	YES	CCDS3136.1	ENSP00000282928	ZIC1_HUMAN	.	UPI000013DD09	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGTGATATT	.	5	ESCA
ARHGEF26	0	.	GRCh37	3	153973619	153973619	+	3'UTR	SNP	G	G	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*357G>C	.	.	ENST00000356448	15/15	11	2	9	8	8	0	ARHGEF26,3_prime_UTR_variant,,ENST00000465093,;ARHGEF26,3_prime_UTR_variant,,ENST00000356448,;ARHGEF26,intron_variant,,ENST00000465817,;ARHGEF26,non_coding_transcript_exon_variant,,ENST00000483068,;ARHGEF26,3_prime_UTR_variant,,ENST00000496710,;	C	ENSG00000114790	ENST00000356448	Transcript	3_prime_UTR_variant	3257	.	.	.	.	.	.	.	1	ARHGEF26	HGNC	24490	protein_coding	YES	CCDS46938.1	ENSP00000348828	ARHGQ_HUMAN	.	UPI00001410D0	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGTGACTGT	.	2	ESCA
SLITRK3	0	.	GRCh37	3	164906571	164906571	+	Missense_Mutation	SNP	C	C	T	rs756131997	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2048G>A	p.Arg683Gln	p.R683Q	ENST00000475390	2/2	45	24	21	36	36	0	SLITRK3,missense_variant,p.Arg683Gln,ENST00000475390,;SLITRK3,missense_variant,p.Arg683Gln,ENST00000241274,;SLITRK3,downstream_gene_variant,,ENST00000497724,;	T	ENSG00000121871	ENST00000475390	Transcript	missense_variant	2492	2048	683	R/Q	cGa/cAa	rs756131997,COSM1040814	.	.	-1	SLITRK3	HGNC	23501	protein_coding	YES	CCDS3197.1	ENSP00000420091	SLIK3_HUMAN	C9K0R4_HUMAN	UPI000004F259	.	tolerated(0.11)	benign(0.032)	2/2	.	hmmpanther:PTHR24373:SF14,hmmpanther:PTHR24373	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCTTTCGACGC	.	4	ESCA
ATP11B	0	.	GRCh37	3	182586882	182586883	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1707dupT	p.Leu570SerfsTer4	p.L570Sfs*4	ENST00000323116	16/30	180	159	21	122	122	0	ATP11B,frameshift_variant,p.Leu570SerfsTer4,ENST00000323116,;ATP11B,frameshift_variant,p.Leu371SerfsTer4,ENST00000498086,;ATP11B,non_coding_transcript_exon_variant,,ENST00000490303,;ATP11B,upstream_gene_variant,,ENST00000466758,;	T	ENSG00000058063	ENST00000323116	Transcript	frameshift_variant	1965-1966	1705-1706	569	I/IX	att/aTtt	.	.	.	1	ATP11B	HGNC	13553	protein_coding	YES	CCDS33896.1	ENSP00000321195	AT11B_HUMAN	B4E3T1_HUMAN	UPI000004124E	.	.	.	16/30	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF57,Gene3D:3.40.1110.10,Pfam_domain:PF00702,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF81660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TTCATATTCTG	.	3	ESCA
CMTM8	0	.	GRCh37	3	32409471	32409471	+	Silent	SNP	G	G	T	rs373166159	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.429G>T	p.%3D	p.A143A	ENST00000307526	3/4	13	6	7	35	35	0	CMTM8,synonymous_variant,p.%3D,ENST00000307526,;CMTM8,synonymous_variant,p.%3D,ENST00000458535,;	T	ENSG00000170293	ENST00000307526	Transcript	synonymous_variant	723	429	143	A	gcG/gcT	rs373166159	.	.	1	CMTM8	HGNC	19179	protein_coding	YES	CCDS2652.1	ENSP00000307741	CKLF8_HUMAN	.	UPI000019745A	.	.	.	3/4	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51225,hmmpanther:PTHR22776:SF10,hmmpanther:PTHR22776,Pfam_domain:PF01284,Prints_domain:PR01884	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	TGGGCGGCCTC	byCluster	4	ESCA
CLASP2	0	.	GRCh37	3	33686848	33686848	+	Intron	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.716-453G>A	.	.	ENST00000468888	.	47	28	18	56	56	0	CLASP2,5_prime_UTR_variant,,ENST00000487200,;CLASP2,5_prime_UTR_variant,,ENST00000313350,;CLASP2,5_prime_UTR_variant,,ENST00000485378,;CLASP2,intron_variant,,ENST00000307312,;CLASP2,intron_variant,,ENST00000359576,;CLASP2,intron_variant,,ENST00000461133,;CLASP2,intron_variant,,ENST00000496954,;CLASP2,intron_variant,,ENST00000468888,;CLASP2,intron_variant,,ENST00000399362,;CLASP2,intron_variant,,ENST00000480013,;CLASP2,upstream_gene_variant,,ENST00000333778,;CLASP2,upstream_gene_variant,,ENST00000539981,;CLASP2,non_coding_transcript_exon_variant,,ENST00000476433,;CLASP2,intron_variant,,ENST00000482896,;CLASP2,intron_variant,,ENST00000498331,;CLASP2,intron_variant,,ENST00000486796,;	T	ENSG00000163539	ENST00000468888	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CLASP2	HGNC	17078	protein_coding	YES	.	ENSP00000419974	.	Q6N029_HUMAN,Q07A20_HUMAN,E7EW49_HUMAN,B2RTR1_HUMAN	UPI0001B7944B	.	.	.	.	7/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTCCCAATA	.	5	ESCA
ARPP21	0	.	GRCh37	3	35763159	35763159	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.956T>G	p.Leu319Arg	p.L319R	ENST00000458225	13/20	19	10	9	41	41	0	ARPP21,missense_variant,p.Leu299Arg,ENST00000337271,;ARPP21,missense_variant,p.Leu319Arg,ENST00000417925,;ARPP21,missense_variant,p.Leu319Arg,ENST00000458225,;ARPP21,missense_variant,p.Leu126Arg,ENST00000425289,;ARPP21,missense_variant,p.Leu353Arg,ENST00000187397,;ARPP21,missense_variant,p.Leu299Arg,ENST00000444190,;ARPP21,intron_variant,,ENST00000476327,;ARPP21,missense_variant,p.Ser104Ala,ENST00000427590,;ARPP21,missense_variant,p.Leu11Arg,ENST00000457165,;ARPP21,non_coding_transcript_exon_variant,,ENST00000481854,;ARPP21,downstream_gene_variant,,ENST00000446068,;	G	ENSG00000172995	ENST00000458225	Transcript	missense_variant	1181	956	319	L/R	cTc/cGc	.	.	.	1	ARPP21	HGNC	16968	protein_coding	YES	CCDS58823.1	ENSP00000414351	ARP21_HUMAN	C9JTX6_HUMAN,C9JTF2_HUMAN,C9JQQ6_HUMAN,C9JI74_HUMAN,C9J5R1_HUMAN,C9J2U3_HUMAN	UPI0000209B3D	.	deleterious(0.01)	possibly_damaging(0.777)	13/20	.	hmmpanther:PTHR15672:SF14,hmmpanther:PTHR15672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACTCAAGT	.	5	ESCA
PARP3	0	.	GRCh37	3	51976714	51976714	+	Silent	SNP	G	G	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>C	p.%3D	p.L3L	ENST00000398755	1/11	21	13	7	52	52	0	PARP3,synonymous_variant,p.%3D,ENST00000398755,;PARP3,5_prime_UTR_variant,,ENST00000417220,;PARP3,5_prime_UTR_variant,,ENST00000431474,;PARP3,upstream_gene_variant,,ENST00000498510,;RRP9,upstream_gene_variant,,ENST00000232888,;PARP3,upstream_gene_variant,,ENST00000486510,;PARP3,synonymous_variant,p.%3D,ENST00000471971,;PARP3,upstream_gene_variant,,ENST00000475782,;PARP3,upstream_gene_variant,,ENST00000470601,;PARP3,upstream_gene_variant,,ENST00000470749,;	C	ENSG00000041880	ENST00000398755	Transcript	synonymous_variant	340	9	3	L	ctG/ctC	.	.	.	1	PARP3	HGNC	273	protein_coding	YES	CCDS46839.1	ENSP00000381740	PARP3_HUMAN	C9J9C7_HUMAN	UPI00015E16A5	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTGCTTTT	.	5	ESCA
FAM208A	0	.	GRCh37	3	56681036	56681036	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1729C>T	p.Pro577Ser	p.P577S	ENST00000493960	14/24	95	54	41	153	152	0	FAM208A,missense_variant,p.Pro577Ser,ENST00000355628,;FAM208A,missense_variant,p.Pro577Ser,ENST00000493960,;FAM208A,missense_variant,p.Pro181Ser,ENST00000431842,;	A	ENSG00000163946	ENST00000493960	Transcript	missense_variant	1740	1729	577	P/S	Cca/Tca	.	.	.	-1	FAM208A	HGNC	30314	protein_coding	YES	CCDS46853.1	ENSP00000417509	F208A_HUMAN	.	UPI0000422561	.	tolerated(0.32)	benign(0.007)	14/24	.	hmmpanther:PTHR16207:SF1,hmmpanther:PTHR16207	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATGGAAACA	.	5	ESCA
PRICKLE2	0	.	GRCh37	3	64085307	64085307	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1955G>A	p.Ser652Asn	p.S652N	ENST00000295902	8/8	20	17	3	26	26	0	PRICKLE2,missense_variant,p.Ser652Asn,ENST00000295902,;PRICKLE2,missense_variant,p.Ser708Asn,ENST00000564377,;RP11-129B22.1,non_coding_transcript_exon_variant,,ENST00000482609,;PRICKLE2-AS1,intron_variant,,ENST00000476308,;PRICKLE2-AS2,upstream_gene_variant,,ENST00000484703,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000460946,;	T	ENSG00000163637	ENST00000295902	Transcript	missense_variant	2541	1955	652	S/N	aGc/aAc	.	.	.	-1	PRICKLE2	HGNC	20340	protein_coding	YES	CCDS2902.1	ENSP00000295902	PRIC2_HUMAN	C9JY03_HUMAN	UPI0000160A8B	.	tolerated(1)	benign(0.001)	8/8	.	hmmpanther:PTHR24218:SF5,hmmpanther:PTHR24218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTGCTGCCC	.	2	ESCA
EMCN	0	.	GRCh37	4	101331439	101331439	+	Intron	SNP	G	G	A	rs572396865	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*39C>T	.	.	ENST00000296420	11/12	87	59	28	139	139	0	EMCN,splice_region_variant,,ENST00000511970,;EMCN,splice_region_variant,,ENST00000305864,;EMCN,splice_region_variant,,ENST00000296420,;EMCN,splice_region_variant,,ENST00000506300,;	A	ENSG00000164035	ENST00000296420	Transcript	splice_region_variant	1004	.	.	.	.	rs572396865	.	.	-1	EMCN	HGNC	16041	protein_coding	YES	CCDS3655.1	ENSP00000296420	MUCEN_HUMAN	Q53H40_HUMAN,Q4W5J1_HUMAN	UPI000003777D	.	.	.	11/12	.	.	A:0.0004	A:0.0008	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTACGTAATT	byFrequency|by1000G	5	ESCA
UBE2D3	0	.	GRCh37	4	103747741	103747741	+	Intron	SNP	G	G	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.31-16729C>A	.	.	ENST00000357194	.	19	15	3	43	43	0	UBE2D3,5_prime_UTR_variant,,ENST00000508238,;UBE2D3,5_prime_UTR_variant,,ENST00000453744,;UBE2D3,5_prime_UTR_variant,,ENST00000502690,;UBE2D3,5_prime_UTR_variant,,ENST00000321805,;UBE2D3,5_prime_UTR_variant,,ENST00000349311,;UBE2D3,5_prime_UTR_variant,,ENST00000343106,;UBE2D3,5_prime_UTR_variant,,ENST00000338145,;UBE2D3,5_prime_UTR_variant,,ENST00000394804,;UBE2D3,5_prime_UTR_variant,,ENST00000394801,;UBE2D3,5_prime_UTR_variant,,ENST00000394803,;UBE2D3,5_prime_UTR_variant,,ENST00000508249,;UBE2D3,intron_variant,,ENST00000357194,;UBE2D3,upstream_gene_variant,,ENST00000502404,;UBE2D3,upstream_gene_variant,,ENST00000505207,;UBE2D3,upstream_gene_variant,,ENST00000508476,;UBE2D3,upstream_gene_variant,,ENST00000350435,;UBE2D3,upstream_gene_variant,,ENST00000504211,;UBE2D3,upstream_gene_variant,,ENST00000507845,;RP11-10L12.4,upstream_gene_variant,,ENST00000501133,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000513098,;UBE2D3,5_prime_UTR_variant,,ENST00000505307,;UBE2D3,5_prime_UTR_variant,,ENST00000503418,;UBE2D3,5_prime_UTR_variant,,ENST00000508974,;UBE2D3,5_prime_UTR_variant,,ENST00000502563,;UBE2D3,5_prime_UTR_variant,,ENST00000514755,;UBE2D3,5_prime_UTR_variant,,ENST00000510129,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000503742,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000508818,;UBE2D3,non_coding_transcript_exon_variant,,ENST00000503282,;UBE2D3,upstream_gene_variant,,ENST00000508635,;	T	ENSG00000109332	ENST00000357194	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	UBE2D3	HGNC	12476	protein_coding	YES	CCDS3659.1	ENSP00000349722	UB2D3_HUMAN	D6RFM0_HUMAN,D6RAW0_HUMAN,D6RAH7_HUMAN	UPI00001B31EA	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ATCCCGGCGGC	.	2	ESCA
SEC24B	0	.	GRCh37	4	110384393	110384393	+	Missense_Mutation	SNP	A	A	T	rs558781877	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.470A>T	p.Asn157Ile	p.N157I	ENST00000265175	2/24	23	11	12	31	31	0	SEC24B,missense_variant,p.Asn157Ile,ENST00000265175,;SEC24B,missense_variant,p.Asn188Ile,ENST00000504968,;SEC24B,missense_variant,p.Asn157Ile,ENST00000399100,;	T	ENSG00000138802	ENST00000265175	Transcript	missense_variant	525	470	157	N/I	aAt/aTt	rs558781877	.	.	1	SEC24B	HGNC	10704	protein_coding	YES	CCDS47124.1	ENSP00000265175	SC24B_HUMAN	B4E2E1_HUMAN	UPI00004F6ED7	.	deleterious_low_confidence(0)	possibly_damaging(0.51)	2/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGAATCACT	.	5	ESCA
PITX2	0	.	GRCh37	4	111539588	111539588	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668C>G	p.Ser223Cys	p.S223C	ENST00000306732	3/3	50	23	27	104	104	0	PITX2,missense_variant,p.Ser216Cys,ENST00000394598,;PITX2,missense_variant,p.Ser216Cys,ENST00000354925,;PITX2,missense_variant,p.Ser170Cys,ENST00000355080,;PITX2,missense_variant,p.Ser216Cys,ENST00000511837,;PITX2,missense_variant,p.Ser223Cys,ENST00000306732,;PITX2,synonymous_variant,p.%3D,ENST00000394595,;PITX2,downstream_gene_variant,,ENST00000557119,;PITX2,downstream_gene_variant,,ENST00000511990,;RP11-380D23.2,upstream_gene_variant,,ENST00000513690,;RP11-380D23.2,upstream_gene_variant,,ENST00000503456,;PITX2,downstream_gene_variant,,ENST00000556049,;PITX2,non_coding_transcript_exon_variant,,ENST00000607868,;	C	ENSG00000164093	ENST00000306732	Transcript	missense_variant	1311	668	223	S/C	tCt/tGt	.	.	.	-1	PITX2	HGNC	9005	protein_coding	YES	CCDS3694.1	ENSP00000304169	PITX2_HUMAN	.	UPI000002B122	.	deleterious(0.02)	probably_damaging(0.997)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24329:SF287,hmmpanther:PTHR24329,PIRSF_domain:PIRSF000563	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATAGAGTTG	.	5	ESCA
FAM71B	0	.	GRCh37	5	156592876	156592876	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.304T>C	p.Trp102Arg	p.W102R	ENST00000302938	1/2	24	13	11	68	68	0	FAM71B,missense_variant,p.Trp102Arg,ENST00000302938,;ITK,intron_variant,,ENST00000521769,;	G	ENSG00000170613	ENST00000302938	Transcript	missense_variant	400	304	102	W/R	Tgg/Cgg	.	.	.	-1	FAM71B	HGNC	28397	protein_coding	YES	CCDS4335.1	ENSP00000305596	FA71B_HUMAN	.	UPI000006F9DC	.	tolerated(0.57)	benign(0)	1/2	.	hmmpanther:PTHR22574:SF2,hmmpanther:PTHR22574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCATCTGA	.	5	ESCA
FBXL7	0	.	GRCh37	5	15928102	15928102	+	Silent	SNP	G	G	A	rs561477427	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.231G>A	p.%3D	p.S77S	ENST00000504595	3/4	78	68	9	50	50	0	FBXL7,synonymous_variant,p.%3D,ENST00000329673,;FBXL7,synonymous_variant,p.%3D,ENST00000510662,;FBXL7,synonymous_variant,p.%3D,ENST00000504595,;	A	ENSG00000183580	ENST00000504595	Transcript	synonymous_variant	712	231	77	S	tcG/tcA	rs561477427	.	.	1	FBXL7	HGNC	13604	protein_coding	YES	CCDS54833.1	ENSP00000423630	FBXL7_HUMAN	J3KNM9_HUMAN,D6RDY7_HUMAN	UPI00000724E0	.	.	.	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23125:SF70,hmmpanther:PTHR23125	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTCGTCCTC	by1000G	4	ESCA
GABRA1	0	.	GRCh37	5	161317917	161317917	+	Silent	SNP	T	T	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.717T>G	p.%3D	p.V239V	ENST00000428797	9/11	47	27	20	79	79	0	GABRA1,synonymous_variant,p.%3D,ENST00000444819,;GABRA1,synonymous_variant,p.%3D,ENST00000420560,;GABRA1,synonymous_variant,p.%3D,ENST00000393943,;GABRA1,synonymous_variant,p.%3D,ENST00000023897,;GABRA1,synonymous_variant,p.%3D,ENST00000437025,;GABRA1,synonymous_variant,p.%3D,ENST00000428797,;GABRA1,non_coding_transcript_exon_variant,,ENST00000519542,;	G	ENSG00000022355	ENST00000428797	Transcript	synonymous_variant	1072	717	239	V	gtT/gtG	.	.	.	1	GABRA1	HGNC	4075	protein_coding	YES	CCDS4357.1	ENSP00000393097	GBRA1_HUMAN	E5RK60_HUMAN,E5RJS3_HUMAN	UPI000012AF95	.	.	.	9/11	.	hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGTTATGAC	.	5	ESCA
UGT3A2	0	.	GRCh37	5	36035772	36035772	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*28T>C	.	.	ENST00000282507	7/7	35	20	14	30	29	0	UGT3A2,3_prime_UTR_variant,,ENST00000513300,;UGT3A2,3_prime_UTR_variant,,ENST00000545528,;UGT3A2,3_prime_UTR_variant,,ENST00000282507,;UGT3A2,downstream_gene_variant,,ENST00000504954,;UGT3A2,3_prime_UTR_variant,,ENST00000504685,;	G	ENSG00000168671	ENST00000282507	Transcript	3_prime_UTR_variant	1702	.	.	.	.	.	.	.	-1	UGT3A2	HGNC	27266	protein_coding	YES	CCDS3914.1	ENSP00000282507	UD3A2_HUMAN	F5H377_HUMAN,D6RDU1_HUMAN	UPI000013DCE8	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAAACAGAC	.	5	ESCA
GPR98	0	.	GRCh37	5	90144561	90144561	+	Silent	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17127C>T	p.%3D	p.F5709F	ENST00000405460	79/90	65	57	8	100	100	0	GPR98,synonymous_variant,p.%3D,ENST00000405460,;GPR98,synonymous_variant,p.%3D,ENST00000425867,;GPR98,non_coding_transcript_exon_variant,,ENST00000505845,;	T	ENSG00000164199	ENST00000405460	Transcript	synonymous_variant	17223	17127	5709	F	ttC/ttT	.	.	.	1	GPR98	HGNC	17416	protein_coding	YES	CCDS47246.1	ENSP00000384582	GPR98_HUMAN	.	UPI00002127A7	.	.	.	79/90	.	hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GGATTCAGTCA	.	3	ESCA
C6orf58	0	.	GRCh37	6	127911258	127911258	+	Missense_Mutation	SNP	C	C	T	rs780579826	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.701C>T	p.Ala234Val	p.A234V	ENST00000329722	5/6	76	67	9	94	94	0	C6orf58,missense_variant,p.Ala234Val,ENST00000329722,;	T	ENSG00000184530	ENST00000329722	Transcript	missense_variant	713	701	234	A/V	gCg/gTg	rs780579826	.	.	1	C6orf58	HGNC	20960	protein_coding	YES	CCDS34533.1	ENSP00000328069	CF058_HUMAN	.	UPI00001D80C9	.	tolerated(0.08)	benign(0.046)	5/6	.	hmmpanther:PTHR18820,hmmpanther:PTHR18820:SF2,Pfam_domain:PF05612	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAGCGCATT	byFrequency	4	ESCA
BCLAF1	0	.	GRCh37	6	136599485	136599485	+	Silent	SNP	C	C	T	rs369195148	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.534G>A	p.%3D	p.P178P	ENST00000531224	4/13	82	75	7	93	93	0	BCLAF1,synonymous_variant,p.%3D,ENST00000392348,;BCLAF1,synonymous_variant,p.%3D,ENST00000529826,;BCLAF1,synonymous_variant,p.%3D,ENST00000353331,;BCLAF1,synonymous_variant,p.%3D,ENST00000531224,;BCLAF1,synonymous_variant,p.%3D,ENST00000530767,;BCLAF1,synonymous_variant,p.%3D,ENST00000527536,;BCLAF1,synonymous_variant,p.%3D,ENST00000527759,;BCLAF1,synonymous_variant,p.%3D,ENST00000534269,;BCLAF1,synonymous_variant,p.%3D,ENST00000527613,;BCLAF1,synonymous_variant,p.%3D,ENST00000530429,;BCLAF1,synonymous_variant,p.%3D,ENST00000532384,;BCLAF1,upstream_gene_variant,,ENST00000533621,;BCLAF1,upstream_gene_variant,,ENST00000476194,;BCLAF1,downstream_gene_variant,,ENST00000528229,;	T	ENSG00000029363	ENST00000531224	Transcript	synonymous_variant	787	534	178	P	ccG/ccA	rs369195148,COSM1238298,COSM594525	.	.	-1	BCLAF1	HGNC	16863	protein_coding	YES	CCDS5177.1	ENSP00000435210	BCLF1_HUMAN	B0AZU3_HUMAN	UPI000006FCE7	.	.	.	4/13	.	Pfam_domain:PF15440,hmmpanther:PTHR15268,hmmpanther:PTHR15268:SF4	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	TTCAACGGACT	byFrequency|byCluster	2	ESCA
ARID1B	0	.	GRCh37	6	157527315	157527315	+	Silent	SNP	C	C	T	rs766430210	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5040C>T	p.%3D	p.L1680L	ENST00000346085	20/20	36	29	7	59	59	0	ARID1B,synonymous_variant,p.%3D,ENST00000367148,;ARID1B,synonymous_variant,p.%3D,ENST00000350026,;ARID1B,synonymous_variant,p.%3D,ENST00000414678,;ARID1B,synonymous_variant,p.%3D,ENST00000275248,;ARID1B,synonymous_variant,p.%3D,ENST00000346085,;	T	ENSG00000049618	ENST00000346085	Transcript	synonymous_variant	5041	5040	1680	L	ctC/ctT	rs766430210,COSM3622293,COSM3622292	.	.	1	ARID1B	HGNC	18040	protein_coding	YES	CCDS55072.1	ENSP00000344546	ARI1B_HUMAN	.	UPI000058E4B2	.	.	.	20/20	.	hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCGAACT	byFrequency	5	ESCA
FNDC1	0	.	GRCh37	6	159653105	159653105	+	Silent	SNP	C	C	A	rs369480414	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1561C>A	p.%3D	p.R521R	ENST00000297267	11/23	29	24	5	55	55	0	FNDC1,synonymous_variant,p.%3D,ENST00000340366,;FNDC1,synonymous_variant,p.%3D,ENST00000297267,;FNDC1,synonymous_variant,p.%3D,ENST00000329629,;	A	ENSG00000164694	ENST00000297267	Transcript	synonymous_variant	1761	1561	521	R	Cga/Aga	rs369480414	.	.	1	FNDC1	HGNC	21184	protein_coding	YES	CCDS47512.1	ENSP00000297267	FNDC1_HUMAN	.	UPI0000579B80	.	.	.	11/23	.	hmmpanther:PTHR23197:SF8,hmmpanther:PTHR23197	.	.	.	.	.	.	.	T:0.0003	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCCCCGAAAA	byCluster	4	ESCA
SLC22A1	0	.	GRCh37	6	160577066	160577066	+	Missense_Mutation	SNP	G	G	A	rs760456949	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1558G>A	p.Ala520Thr	p.A520T	ENST00000366963	10/11	62	43	19	82	81	1	SLC22A1,missense_variant,p.Arg482His,ENST00000324965,;SLC22A1,missense_variant,p.Ala520Thr,ENST00000366963,;SLC22A1,intron_variant,,ENST00000457470,;SLC22A1,3_prime_UTR_variant,,ENST00000539263,;SLC22A1,non_coding_transcript_exon_variant,,ENST00000478607,;SLC22A1,intron_variant,,ENST00000460902,;	A	ENSG00000175003	ENST00000366963	Transcript	missense_variant	1705	1558	520	A/T	Gct/Act	rs760456949,COSM207420	.	.	1	SLC22A1	HGNC	10963	protein_coding	YES	CCDS5274.1	ENSP00000355930	S22A1_HUMAN	F5GY86_HUMAN	UPI0000070FB1	.	tolerated(0.54)	benign(0.021)	10/11	.	Superfamily_domains:SSF103473,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00898,Pfam_domain:PF00083,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF214	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGGTCGCTTTG	byFrequency	4	ESCA
LINC00242	0	.	GRCh37	6	170190213	170190213	+	RNA	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1091C>T	.	.	ENST00000437615	2/2	68	61	7	78	78	0	LINC00242,non_coding_transcript_exon_variant,,ENST00000437615,;LINC00574,upstream_gene_variant,,ENST00000420557,;	A	ENSG00000229214	ENST00000437615	Transcript	non_coding_transcript_exon_variant	1091	.	.	.	.	.	.	.	-1	LINC00242	HGNC	21249	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACCGGGTTGC	.	3	ESCA
PRR3	0	.	GRCh37	6	30530332	30530332	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*60C>A	.	.	ENST00000376560	4/4	34	23	11	39	39	0	PRR3,3_prime_UTR_variant,,ENST00000376557,;PRR3,3_prime_UTR_variant,,ENST00000376560,;PRR3,non_coding_transcript_exon_variant,,ENST00000498336,;PRR3,non_coding_transcript_exon_variant,,ENST00000481741,;PRR3,non_coding_transcript_exon_variant,,ENST00000470703,;PRR3,downstream_gene_variant,,ENST00000491173,;	A	ENSG00000204576	ENST00000376560	Transcript	3_prime_UTR_variant	1086	.	.	.	.	.	.	.	1	PRR3	HGNC	21149	protein_coding	YES	CCDS43440.1	ENSP00000365744	PRR3_HUMAN	Q96QB9_HUMAN,A6NDA2_HUMAN	UPI000000D739	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTTCTCTGT	.	5	ESCA
CCHCR1	0	.	GRCh37	6	31122453	31122453	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.621G>C	p.Gln207His	p.Q207H	ENST00000396268	4/18	22	14	7	29	29	0	CCHCR1,missense_variant,p.Gln118His,ENST00000507751,;CCHCR1,missense_variant,p.Gln118His,ENST00000502557,;CCHCR1,missense_variant,p.Gln118His,ENST00000448162,;CCHCR1,missense_variant,p.Gln82His,ENST00000508683,;CCHCR1,missense_variant,p.Gln207His,ENST00000396268,;CCHCR1,missense_variant,p.Gln92His,ENST00000513222,;CCHCR1,missense_variant,p.Gln82His,ENST00000448141,;CCHCR1,missense_variant,p.Gln216His,ENST00000426967,;CCHCR1,missense_variant,p.Gln118His,ENST00000503934,;CCHCR1,missense_variant,p.Gln118His,ENST00000455279,;CCHCR1,missense_variant,p.Gln171His,ENST00000451521,;CCHCR1,missense_variant,p.Gln118His,ENST00000396263,;CCHCR1,missense_variant,p.Gln82His,ENST00000503420,;CCHCR1,missense_variant,p.Gln118His,ENST00000376266,;CCHCR1,downstream_gene_variant,,ENST00000506831,;TCF19,upstream_gene_variant,,ENST00000376255,;CCHCR1,downstream_gene_variant,,ENST00000507892,;CCHCR1,downstream_gene_variant,,ENST00000507226,;CCHCR1,downstream_gene_variant,,ENST00000428174,;CCHCR1,downstream_gene_variant,,ENST00000507829,;TCF19,upstream_gene_variant,,ENST00000376257,;CCHCR1,intron_variant,,ENST00000480060,;CCHCR1,non_coding_transcript_exon_variant,,ENST00000509552,;CCHCR1,non_coding_transcript_exon_variant,,ENST00000464012,;CCHCR1,intron_variant,,ENST00000505392,;CCHCR1,intron_variant,,ENST00000507459,;CCHCR1,intron_variant,,ENST00000508852,;CCHCR1,intron_variant,,ENST00000512418,;CCHCR1,downstream_gene_variant,,ENST00000475684,;CCHCR1,downstream_gene_variant,,ENST00000488920,;	G	ENSG00000204536	ENST00000396268	Transcript	missense_variant	810	621	207	Q/H	caG/caC	.	.	.	-1	CCHCR1	HGNC	13930	protein_coding	YES	CCDS43445.1	ENSP00000379566	CCHCR_HUMAN	E9PGB6_HUMAN,E7EQE8_HUMAN,E7EQC5_HUMAN,D6RDI7_HUMAN,D6RD84_HUMAN,D6RBG1_HUMAN,D6RB88_HUMAN,B4DIA2_HUMAN,B0V092_HUMAN,A9XAL3_HUMAN,A9XAG5_HUMAN,A9XAF5_HUMAN,A9XAC7_HUMAN,A2ABH4_HUMAN,A2ABH3_HUMAN	UPI0000E5ACDF	.	deleterious(0)	probably_damaging(0.999)	4/18	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23161:SF4,hmmpanther:PTHR23161,Pfam_domain:PF07111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCTTCTGCTG	.	5	ESCA
VPS52	0	.	GRCh37	6	33218515	33218515	+	3'UTR	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*103G>T	.	.	ENST00000445902	20/20	35	21	14	52	51	1	VPS52,3_prime_UTR_variant,,ENST00000436044,;VPS52,3_prime_UTR_variant,,ENST00000482399,;VPS52,3_prime_UTR_variant,,ENST00000445902,;HCG25,intron_variant,,ENST00000422366,;HCG25,intron_variant,,ENST00000450514,;HCG25,intron_variant,,ENST00000442228,;HCG25,intron_variant,,ENST00000427196,;VPS52,non_coding_transcript_exon_variant,,ENST00000495981,;VPS52,non_coding_transcript_exon_variant,,ENST00000478934,;XXbac-BPG157A10.21,upstream_gene_variant,,ENST00000606432,;VPS52,downstream_gene_variant,,ENST00000493674,;VPS52,downstream_gene_variant,,ENST00000471309,;	A	ENSG00000223501	ENST00000445902	Transcript	3_prime_UTR_variant	2494	.	.	.	.	.	.	.	-1	VPS52	HGNC	10518	protein_coding	YES	CCDS4770.2	ENSP00000409952	VPS52_HUMAN	B4DS44_HUMAN,B4DNI9_HUMAN	UPI000006E468	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GGAAGCAAGGG	.	4	ESCA
DNAH8	0	.	GRCh37	6	38854597	38854597	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7639G>T	p.Glu2547Ter	p.E2547*	ENST00000359357	55/91	50	37	13	45	45	0	DNAH8,stop_gained,p.Glu2547Ter,ENST00000359357,;DNAH8,stop_gained,p.Glu2752Ter,ENST00000327475,;DNAH8,stop_gained,p.Glu2511Ter,ENST00000441566,;DNAH8,stop_gained,p.Glu2764Ter,ENST00000449981,;	T	ENSG00000124721	ENST00000359357	Transcript	stop_gained	7893	7639	2547	E/*	Gaa/Taa	COSM3626724,COSM3626725,COSM3626726	.	.	1	DNAH8	HGNC	2952	protein_coding	YES	.	ENSP00000352312	DYH8_HUMAN	.	UPI00003677EB	.	.	.	55/91	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Gene3D:3.40.50.300,Pfam_domain:PF12775,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF229	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATGGAAATG	.	5	ESCA
HSP90AB1	0	.	GRCh37	6	44221086	44221086	+	Missense_Mutation	SNP	G	G	A	rs199811663	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2036G>A	p.Arg679His	p.R679H	ENST00000371554	11/12	49	40	9	90	90	0	HSP90AB1,missense_variant,p.Arg679His,ENST00000371646,;HSP90AB1,missense_variant,p.Arg679His,ENST00000353801,;HSP90AB1,missense_variant,p.Arg679His,ENST00000371554,;SLC35B2,downstream_gene_variant,,ENST00000538577,;SLC35B2,downstream_gene_variant,,ENST00000537814,;SLC35B2,downstream_gene_variant,,ENST00000393810,;NFKBIE,downstream_gene_variant,,ENST00000275015,;SLC35B2,downstream_gene_variant,,ENST00000393812,;MIR4647,downstream_gene_variant,,ENST00000583964,;SLC35B2,downstream_gene_variant,,ENST00000495706,;	A	ENSG00000096384	ENST00000371554	Transcript	missense_variant	2250	2036	679	R/H	cGc/cAc	rs199811663	.	.	1	HSP90AB1	HGNC	5258	protein_coding	YES	CCDS4909.1	ENSP00000360609	HS90B_HUMAN	A8K3W9_HUMAN	UPI00001411EF	.	deleterious(0.01)	probably_damaging(0.991)	11/12	.	HAMAP:MF_00505,hmmpanther:PTHR11528,Pfam_domain:PF00183,PIRSF_domain:PIRSF002583,Superfamily_domains:0043579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACCGCATCT	byCluster	5	ESCA
GFRAL	0	.	GRCh37	6	55266676	55266676	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*25A>G	.	.	ENST00000340465	9/9	51	36	15	30	30	0	GFRAL,3_prime_UTR_variant,,ENST00000340465,;	G	ENSG00000187871	ENST00000340465	Transcript	3_prime_UTR_variant	1296	.	.	.	.	.	.	.	1	GFRAL	HGNC	32789	protein_coding	YES	CCDS4957.1	ENSP00000343636	GFRAL_HUMAN	.	UPI000023780D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATAACAATC	.	5	ESCA
UBE3D	0	.	GRCh37	6	83732251	83732251	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.767A>G	p.Gln256Arg	p.Q256R	ENST00000369747	7/10	66	46	20	60	60	0	UBE3D,missense_variant,p.Gln256Arg,ENST00000369747,;UBE3D,missense_variant,p.Gln256Arg,ENST00000509102,;UBE3D,3_prime_UTR_variant,,ENST00000430071,;UBE3D,3_prime_UTR_variant,,ENST00000237186,;UBE3D,3_prime_UTR_variant,,ENST00000369746,;	C	ENSG00000118420	ENST00000369747	Transcript	missense_variant	890	767	256	Q/R	cAg/cGg	COSM3875749	.	.	-1	UBE3D	HGNC	21381	protein_coding	YES	CCDS34491.1	ENSP00000358762	UBE3D_HUMAN	D6RHY9_HUMAN	UPI0000160DBE	.	tolerated(0.23)	benign(0.02)	7/10	.	hmmpanther:PTHR31531,hmmpanther:PTHR31531:SF2,Pfam_domain:PF09814	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACTGGGCG	.	5	ESCA
KLHL32	0	.	GRCh37	6	97578788	97578788	+	Silent	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1569T>C	p.%3D	p.T523T	ENST00000369261	9/11	82	65	17	91	91	0	KLHL32,synonymous_variant,p.%3D,ENST00000539200,;KLHL32,synonymous_variant,p.%3D,ENST00000544166,;KLHL32,synonymous_variant,p.%3D,ENST00000536676,;KLHL32,synonymous_variant,p.%3D,ENST00000369261,;KLHL32,3_prime_UTR_variant,,ENST00000369254,;	C	ENSG00000186231	ENST00000369261	Transcript	synonymous_variant	1932	1569	523	T	acT/acC	.	.	.	1	KLHL32	HGNC	21221	protein_coding	YES	CCDS5038.1	ENSP00000358265	KLH32_HUMAN	.	UPI000020DFAB	.	.	.	9/11	.	Superfamily_domains:0052715,SMART_domains:SM00612,PIRSF_domain:PIRSF037037,Pfam_domain:PF01344,Gene3D:1zgkA00,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF65	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACTGACCA	.	5	ESCA
PMPCB	0	.	GRCh37	7	102940749	102940749	+	Missense_Mutation	SNP	C	C	T	rs768813815	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.452C>T	p.Pro151Leu	p.P151L	ENST00000249269	4/13	46	41	5	58	58	0	PMPCB,missense_variant,p.Pro151Leu,ENST00000428154,;PMPCB,missense_variant,p.Pro151Leu,ENST00000249269,;PMPCB,missense_variant,p.Pro46Leu,ENST00000420236,;PMPCB,missense_variant,p.Pro151Leu,ENST00000456433,;PMPCB,3_prime_UTR_variant,,ENST00000444457,;PMPCB,3_prime_UTR_variant,,ENST00000453466,;PMPCB,3_prime_UTR_variant,,ENST00000443722,;PMPCB,non_coding_transcript_exon_variant,,ENST00000498530,;	T	ENSG00000105819	ENST00000249269	Transcript	missense_variant	490	452	151	P/L	cCa/cTa	rs768813815	.	.	1	PMPCB	HGNC	9119	protein_coding	YES	CCDS5730.1	ENSP00000249269	MPPB_HUMAN	.	UPI00000712F7	.	deleterious(0)	possibly_damaging(0.873)	4/13	.	hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF103,Gene3D:3.30.830.10,Pfam_domain:PF00675,Superfamily_domains:SSF63411	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGCCAAGAG	byFrequency	2	ESCA
PRKAR2B	0	.	GRCh37	7	106797765	106797765	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1121delT	p.Leu374Ter	p.L374*	ENST00000265717	10/11	72	58	14	69	69	0	PRKAR2B,frameshift_variant,p.Leu374Ter,ENST00000265717,;	-	ENSG00000005249	ENST00000265717	Transcript	frameshift_variant	1378	1119	373	C/X	tgT/tg	.	.	.	1	PRKAR2B	HGNC	9392	protein_coding	YES	CCDS5740.1	ENSP00000265717	KAP3_HUMAN	Q75MP1_HUMAN,O60380_HUMAN,A3R6R8_HUMAN	UPI000013D669	.	.	.	10/11	.	PROSITE_profiles:PS50042,hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF121,Pfam_domain:PF00027,Gene3D:2.60.120.10,SMART_domains:SM00100,PIRSF_domain:PIRSF000548,Superfamily_domains:SSF51206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAAATGTTTAGG	.	3	ESCA
AGBL3	0	.	GRCh37	7	134719125	134719125	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.783C>G	p.Asp261Glu	p.D261E	ENST00000436302	7/17	26	19	7	61	61	0	AGBL3,missense_variant,p.Asp235Glu,ENST00000458078,;AGBL3,missense_variant,p.Asp261Glu,ENST00000436302,;AGBL3,missense_variant,p.Asp261Glu,ENST00000435976,;AGBL3,missense_variant,p.Asp261Glu,ENST00000275763,;	G	ENSG00000146856	ENST00000436302	Transcript	missense_variant	1036	783	261	D/E	gaC/gaG	.	.	.	1	AGBL3	HGNC	27981	protein_coding	YES	CCDS47718.1	ENSP00000388275	CBPC3_HUMAN	.	UPI000192952B	.	tolerated(0.26)	benign(0.044)	7/17	.	hmmpanther:PTHR12756:SF6,hmmpanther:PTHR12756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGACCAAAT	.	5	ESCA
ITGB8	0	.	GRCh37	7	20452349	20452349	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2729G>A	.	.	ENST00000222573	14/14	134	87	46	151	150	1	ITGB8,3_prime_UTR_variant,,ENST00000222573,;ITGB8,downstream_gene_variant,,ENST00000537992,;	A	ENSG00000105855	ENST00000222573	Transcript	3_prime_UTR_variant	5723	.	.	.	.	.	.	.	1	ITGB8	HGNC	6163	protein_coding	YES	CCDS5370.1	ENSP00000222573	ITB8_HUMAN	B4DHD4_HUMAN	UPI000012DA14	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAGGGCTTGT	.	5	ESCA
FTSJ2	0	.	GRCh37	7	2274620	2274620	+	3'UTR	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*137C>T	.	.	ENST00000242257	3/3	12	9	3	23	23	0	FTSJ2,3_prime_UTR_variant,,ENST00000440306,;FTSJ2,3_prime_UTR_variant,,ENST00000242257,;MAD1L1,upstream_gene_variant,,ENST00000402746,;FTSJ2,downstream_gene_variant,,ENST00000407040,;MAD1L1,upstream_gene_variant,,ENST00000399654,;MAD1L1,upstream_gene_variant,,ENST00000455998,;MAD1L1,upstream_gene_variant,,ENST00000406869,;MAD1L1,upstream_gene_variant,,ENST00000265854,;MAD1L1,upstream_gene_variant,,ENST00000429779,;FTSJ2,non_coding_transcript_exon_variant,,ENST00000486040,;FTSJ2,non_coding_transcript_exon_variant,,ENST00000467199,;	A	ENSG00000122687	ENST00000242257	Transcript	3_prime_UTR_variant	907	.	.	.	.	.	.	.	-1	FTSJ2	HGNC	16352	protein_coding	YES	CCDS5328.1	ENSP00000242257	RRMJ2_HUMAN	Q68D18_HUMAN	UPI00000373C0	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAAAGAGAGA	.	2	ESCA
LFNG	0	.	GRCh37	7	2565180	2565180	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.714G>T	p.Glu238Asp	p.E238D	ENST00000222725	4/8	27	21	6	29	29	0	LFNG,missense_variant,p.Glu167Asp,ENST00000402506,;LFNG,missense_variant,p.Glu109Asp,ENST00000402045,;LFNG,missense_variant,p.Glu238Asp,ENST00000222725,;LFNG,missense_variant,p.Glu109Asp,ENST00000338732,;LFNG,missense_variant,p.Glu238Asp,ENST00000359574,;MIR4648,upstream_gene_variant,,ENST00000580107,;LFNG,non_coding_transcript_exon_variant,,ENST00000493850,;	T	ENSG00000106003	ENST00000222725	Transcript	missense_variant	734	714	238	E/D	gaG/gaT	.	.	.	1	LFNG	HGNC	6560	protein_coding	YES	CCDS34587.1	ENSP00000222725	LFNG_HUMAN	.	UPI000012E5D5	.	tolerated(0.1)	benign(0.147)	4/8	.	PIRSF_domain:PIRSF038073,Pfam_domain:PF02434,hmmpanther:PTHR10811,hmmpanther:PTHR10811:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGGAGCGGGT	.	5	ESCA
SEMA3C	0	.	GRCh37	7	80427447	80427447	+	Silent	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1092T>C	p.%3D	p.I364I	ENST00000265361	11/18	96	53	43	110	110	0	SEMA3C,synonymous_variant,p.%3D,ENST00000265361,;SEMA3C,synonymous_variant,p.%3D,ENST00000544525,;SEMA3C,synonymous_variant,p.%3D,ENST00000536800,;SEMA3C,synonymous_variant,p.%3D,ENST00000419255,;SEMA3C,non_coding_transcript_exon_variant,,ENST00000475955,;SEMA3C,3_prime_UTR_variant,,ENST00000458729,;	G	ENSG00000075223	ENST00000265361	Transcript	synonymous_variant	1654	1092	364	I	atT/atC	.	.	.	-1	SEMA3C	HGNC	10725	protein_coding	YES	CCDS5596.1	ENSP00000265361	SEM3C_HUMAN	Q75MX0_HUMAN,Q75L25_HUMAN	UPI000011C137	.	.	.	11/18	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF25,hmmpanther:PTHR11036,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGAAATCAG	.	5	ESCA
EMC2	0	.	GRCh37	8	109498839	109498839	+	3'UTR	SNP	C	C	G	rs368777392	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*12C>G	.	.	ENST00000220853	11/11	26	22	4	38	38	0	EMC2,3_prime_UTR_variant,,ENST00000220853,;EMC2,downstream_gene_variant,,ENST00000519642,;EMC2,non_coding_transcript_exon_variant,,ENST00000520294,;EMC2,non_coding_transcript_exon_variant,,ENST00000519450,;	G	ENSG00000104412	ENST00000220853	Transcript	3_prime_UTR_variant	941	.	.	.	.	rs368777392	.	.	1	EMC2	HGNC	28963	protein_coding	YES	CCDS6309.1	ENSP00000220853	EMC2_HUMAN	.	UPI000013927E	.	.	.	11/11	.	.	.	.	.	.	.	.	.	G:0.0002	G:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAACTCTTT	byCluster	2	ESCA
CSMD3	0	.	GRCh37	8	113314147	113314147	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8315G>A	p.Gly2772Glu	p.G2772E	ENST00000297405	53/71	68	56	11	75	75	0	CSMD3,missense_variant,p.Gly2702Glu,ENST00000352409,;CSMD3,missense_variant,p.Gly2603Glu,ENST00000455883,;CSMD3,missense_variant,p.Gly2772Glu,ENST00000297405,;CSMD3,missense_variant,p.Gly2042Glu,ENST00000339701,;CSMD3,missense_variant,p.Gly2732Glu,ENST00000343508,;	T	ENSG00000164796	ENST00000297405	Transcript	missense_variant	8560	8315	2772	G/E	gGa/gAa	COSM1700492,COSM1700493	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	deleterious(0.02)	probably_damaging(0.994)	53/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTTCCAATC	.	5	ESCA
KLHL38	0	.	GRCh37	8	124658211	124658211	+	Missense_Mutation	SNP	G	G	A	rs763669952	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1514C>T	p.Ala505Val	p.A505V	ENST00000325995	3/3	67	53	14	74	74	0	KLHL38,missense_variant,p.Ala505Val,ENST00000325995,;CTD-2552K11.2,intron_variant,,ENST00000524355,;	A	ENSG00000175946	ENST00000325995	Transcript	missense_variant	1538	1514	505	A/V	gCg/gTg	rs763669952,COSM216090	.	.	-1	KLHL38	HGNC	34435	protein_coding	YES	CCDS43766.1	ENSP00000321475	KLH38_HUMAN	.	UPI00001D82D1	.	deleterious(0.01)	possibly_damaging(0.557)	3/3	.	Superfamily_domains:0052715,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Pfam_domain:PF01344,Gene3D:1zgkA00,hmmpanther:PTHR24412:SF8,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCCGCACAT	byFrequency	5	ESCA
MAK16	0	.	GRCh37	8	33342693	33342693	+	5'UTR	SNP	G	G	C	rs371185171	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-32G>C	.	.	ENST00000360128	1/10	22	19	3	53	53	0	MAK16,5_prime_UTR_variant,,ENST00000360128,;TTI2,intron_variant,,ENST00000519356,;MAK16,upstream_gene_variant,,ENST00000519089,;MAK16,upstream_gene_variant,,ENST00000517567,;MAK16,upstream_gene_variant,,ENST00000518389,;MAK16,upstream_gene_variant,,ENST00000520763,;	C	ENSG00000198042	ENST00000360128	Transcript	5_prime_UTR_variant	426	.	.	.	.	rs371185171	.	.	1	MAK16	HGNC	13703	protein_coding	YES	CCDS6089.1	ENSP00000353246	MAK16_HUMAN	.	UPI000019080B	.	.	.	1/10	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATCCGACCGG	byCluster	2	ESCA
COL15A1	0	.	GRCh37	9	101818559	101818559	+	Silent	SNP	A	A	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3210A>C	p.%3D	p.T1070T	ENST00000375001	35/42	27	9	18	54	54	0	COL15A1,synonymous_variant,p.%3D,ENST00000375001,;	C	ENSG00000204291	ENST00000375001	Transcript	synonymous_variant	3633	3210	1070	T	acA/acC	.	.	.	1	COL15A1	HGNC	2192	protein_coding	YES	CCDS35081.1	ENSP00000364140	COFA1_HUMAN	.	UPI0000211506	.	.	.	35/42	.	hmmpanther:PTHR24023:SF398,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGACAGTCGT	.	5	ESCA
ALDOB	0	.	GRCh37	9	104183929	104183929	+	3'UTR	SNP	A	A	G	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*162T>C	.	.	ENST00000374855	9/9	22	16	6	27	27	0	ALDOB,3_prime_UTR_variant,,ENST00000374855,;ALDOB,downstream_gene_variant,,ENST00000468981,;	G	ENSG00000136872	ENST00000374855	Transcript	3_prime_UTR_variant	1382	.	.	.	.	.	.	.	-1	ALDOB	HGNC	417	protein_coding	YES	CCDS6756.1	ENSP00000363988	ALDOB_HUMAN	.	UPI000016A4A9	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	TTTCAATAACT	.	3	ESCA
SLC44A1	0	.	GRCh37	9	108147756	108147756	+	Silent	SNP	C	C	T	rs151307942	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1923C>T	p.%3D	p.V641V	ENST00000374720	15/16	57	24	33	52	51	1	SLC44A1,synonymous_variant,p.%3D,ENST00000374720,;SLC44A1,synonymous_variant,p.%3D,ENST00000374724,;SLC44A1,synonymous_variant,p.%3D,ENST00000343170,;SLC44A1,synonymous_variant,p.%3D,ENST00000374723,;SLC44A1,upstream_gene_variant,,ENST00000436716,;SLC44A1,synonymous_variant,p.%3D,ENST00000470972,;	T	ENSG00000070214	ENST00000374720	Transcript	synonymous_variant	2170	1923	641	V	gtC/gtT	rs151307942	.	.	1	SLC44A1	HGNC	18798	protein_coding	YES	CCDS6763.1	ENSP00000363852	CTL1_HUMAN	B3KMS7_HUMAN	UPI0000062328	.	.	.	15/16	.	hmmpanther:PTHR12385,hmmpanther:PTHR12385:SF35	.	.	.	.	.	.	.	T:0.0002	T:0.0005	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGTCGCTGA	byCluster	5	ESCA
PALM2	0	.	GRCh37	9	112706118	112706118	+	3'Flank	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000314527	.	49	26	23	65	65	0	PALM2,3_prime_UTR_variant,,ENST00000448454,;PALM2,3_prime_UTR_variant,,ENST00000374531,;PALM2-AKAP2,intron_variant,,ENST00000374530,;PALM2-AKAP2,intron_variant,,ENST00000413420,;PALM2-AKAP2,intron_variant,,ENST00000302798,;AKAP2,intron_variant,,ENST00000510514,;AKAP2,intron_variant,,ENST00000555236,;PALM2,downstream_gene_variant,,ENST00000497711,;PALM2,downstream_gene_variant,,ENST00000314527,;PALM2,downstream_gene_variant,,ENST00000483909,;	T	ENSG00000243444	ENST00000314527	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	367	1	PALM2	HGNC	15845	protein_coding	YES	CCDS48002.2	ENSP00000323805	PALM2_HUMAN	.	UPI0000071924	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTTGCCTCCT	.	5	ESCA
STOML2	0	.	GRCh37	9	35101143	35101143	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.713A>G	p.Asn238Ser	p.N238S	ENST00000356493	7/10	19	13	6	49	49	0	STOML2,missense_variant,p.Asn193Ser,ENST00000452248,;STOML2,missense_variant,p.Asn238Ser,ENST00000356493,;PIGO,upstream_gene_variant,,ENST00000341666,;FAM214B,downstream_gene_variant,,ENST00000605244,;FAM214B,downstream_gene_variant,,ENST00000322813,;PIGO,upstream_gene_variant,,ENST00000361778,;FAM214B,downstream_gene_variant,,ENST00000378554,;FAM214B,downstream_gene_variant,,ENST00000378566,;PIGO,upstream_gene_variant,,ENST00000298004,;PIGO,upstream_gene_variant,,ENST00000378617,;FAM214B,downstream_gene_variant,,ENST00000603301,;FAM214B,downstream_gene_variant,,ENST00000488109,;FAM214B,downstream_gene_variant,,ENST00000378557,;FAM214B,downstream_gene_variant,,ENST00000378561,;RP11-182N22.8,downstream_gene_variant,,ENST00000431804,;PIGO,upstream_gene_variant,,ENST00000472208,;PIGO,upstream_gene_variant,,ENST00000492770,;STOML2,downstream_gene_variant,,ENST00000487490,;STOML2,missense_variant,p.Asn49Ser,ENST00000488050,;PIGO,upstream_gene_variant,,ENST00000474436,;PIGO,upstream_gene_variant,,ENST00000465745,;	C	ENSG00000165283	ENST00000356493	Transcript	missense_variant	776	713	238	N/S	aAt/aGt	.	.	.	-1	STOML2	HGNC	14559	protein_coding	YES	CCDS6577.1	ENSP00000348886	STML2_HUMAN	.	UPI000006E47E	.	deleterious(0.02)	possibly_damaging(0.897)	7/10	.	hmmpanther:PTHR10264:SF27,hmmpanther:PTHR10264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGATTTATC	.	5	ESCA
CNTNAP3	0	.	GRCh37	9	39073896	39073899	+	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	TTCT	TTCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3855_3858delAGAA	p.Glu1286SerfsTer26	p.E1286Sfs*26	ENST00000297668	24/24	242	188	54	355	355	0	CNTNAP3,frameshift_variant,p.Glu1286SerfsTer26,ENST00000297668,;CNTNAP3,frameshift_variant,p.Glu1205SerfsTer26,ENST00000377656,;CNTNAP3,non_coding_transcript_exon_variant,,ENST00000493965,;CNTNAP3,downstream_gene_variant,,ENST00000477002,;	-	ENSG00000106714	ENST00000297668	Transcript	frameshift_variant	3929-3932	3855-3858	1285-1286	KE/X	aaAGAA/aa	.	.	.	-1	CNTNAP3	HGNC	13834	protein_coding	YES	CCDS6616.1	ENSP00000297668	CNTP3_HUMAN	.	UPI000013E43B	.	.	.	24/24	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GCACTCTTCTTTTTT	.	3	ESCA
BICD2	0	.	GRCh37	9	95481107	95481107	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1820C>T	p.Pro607Leu	p.P607L	ENST00000356884	5/7	17	7	9	36	36	0	BICD2,missense_variant,p.Pro607Leu,ENST00000375512,;BICD2,missense_variant,p.Pro607Leu,ENST00000356884,;	A	ENSG00000185963	ENST00000356884	Transcript	missense_variant	1888	1820	607	P/L	cCc/cTc	.	.	.	-1	BICD2	HGNC	17208	protein_coding	YES	CCDS35064.1	ENSP00000349351	BICD2_HUMAN	.	UPI00001BBAF1	.	tolerated(0.08)	possibly_damaging(0.454)	5/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31233,hmmpanther:PTHR31233:SF7,Pfam_domain:PF09730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGAGGGGCTG	.	5	ESCA
GRIA3	0	.	GRCh37	X	122318472	122318472	+	Nonsense_Mutation	SNP	G	G	T	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.85G>T	p.Gly29Ter	p.G29*	ENST00000264357	1/16	170	85	85	170	170	0	GRIA3,stop_gained,p.Gly29Ter,ENST00000542149,;GRIA3,stop_gained,p.Gly29Ter,ENST00000264357,;GRIA3,stop_gained,p.Gly29Ter,ENST00000371264,;GRIA3,stop_gained,p.Gly29Ter,ENST00000371256,;GRIA3,stop_gained,p.Gly29Ter,ENST00000371251,;GRIA3,stop_gained,p.Gly29Ter,ENST00000371266,;GRIA3,upstream_gene_variant,,ENST00000541091,;GRIA3,non_coding_transcript_exon_variant,,ENST00000479118,;	T	ENSG00000125675	ENST00000264357	Transcript	stop_gained	377	85	29	G/*	Gga/Tga	COSM3557372,COSM3557373,COSM3557371,COSM3557374	.	.	1	GRIA3	HGNC	4573	protein_coding	YES	CCDS14604.1	ENSP00000264357	GRIA3_HUMAN	Q9UHA9_HUMAN	UPI000013D503	.	.	.	1/16	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGGAGGATTC	.	5	ESCA
DCAF12L1	0	.	GRCh37	X	125685222	125685222	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1370A>G	p.Asn457Ser	p.N457S	ENST00000371126	1/2	60	27	32	63	63	0	DCAF12L1,missense_variant,p.Asn457Ser,ENST00000371126,;	C	ENSG00000198889	ENST00000371126	Transcript	missense_variant	1613	1370	457	N/S	aAc/aGc	COSM422242	.	.	-1	DCAF12L1	HGNC	29395	protein_coding	YES	CCDS14610.1	ENSP00000360167	DC121_HUMAN	.	UPI0000160112	.	deleterious(0.02)	benign(0.303)	1/2	.	hmmpanther:PTHR19860:SF9,hmmpanther:PTHR19860	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATAGTTCCCA	.	5	ESCA
ACTRT1	0	.	GRCh37	X	127186302	127186302	+	5'UTR	SNP	T	T	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-117A>T	.	.	ENST00000371124	1/1	62	23	38	59	58	1	ACTRT1,5_prime_UTR_variant,,ENST00000371124,;	A	ENSG00000123165	ENST00000371124	Transcript	5_prime_UTR_variant	81	.	.	.	.	.	.	.	-1	ACTRT1	HGNC	24027	protein_coding	YES	CCDS14611.1	ENSP00000360165	ACTT1_HUMAN	.	UPI0000072276	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGTTGTCAC	.	5	ESCA
MAGEC1	0	.	GRCh37	X	140994796	140994796	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1606C>T	p.Leu536Phe	p.L536F	ENST00000285879	4/4	71	33	38	83	83	0	MAGEC1,missense_variant,p.Leu536Phe,ENST00000285879,;MAGEC1,intron_variant,,ENST00000406005,;	T	ENSG00000155495	ENST00000285879	Transcript	missense_variant	1892	1606	536	L/F	Ctt/Ttt	.	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	tolerated_low_confidence(0.27)	possibly_damaging(0.587)	4/4	.	hmmpanther:PTHR11736:SF17,hmmpanther:PTHR11736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGTCTTCCT	.	5	ESCA
MAGEB4	0	.	GRCh37	X	30261127	30261127	+	Missense_Mutation	SNP	T	T	G	rs776963174	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.875T>G	p.Val292Gly	p.V292G	ENST00000378982	1/1	31	22	9	49	48	0	MAGEB4,missense_variant,p.Val292Gly,ENST00000378982,;MAGEB1,upstream_gene_variant,,ENST00000397548,;MAGEB1,upstream_gene_variant,,ENST00000397550,;MAGEB1,upstream_gene_variant,,ENST00000378981,;	G	ENSG00000120289	ENST00000378982	Transcript	missense_variant	1071	875	292	V/G	gTg/gGg	rs776963174	.	.	1	MAGEB4	HGNC	6811	protein_coding	YES	CCDS14221.1	ENSP00000368266	MAGB4_HUMAN	.	UPI000012F055	.	deleterious(0)	probably_damaging(0.944)	1/1	.	hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF75,PROSITE_profiles:PS50838	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGGTGAATG	.	5	ESCA
TMEM47	0	.	GRCh37	X	34646085	34646086	+	3'UTR	INS	-	-	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2344dupT	.	.	ENST00000275954	3/3	72	50	22	75	75	0	TMEM47,3_prime_UTR_variant,,ENST00000275954,;	A	ENSG00000147027	ENST00000275954	Transcript	3_prime_UTR_variant	3149-3150	.	.	.	.	.	.	.	-1	TMEM47	HGNC	18515	protein_coding	YES	CCDS14235.1	ENSP00000275954	TMM47_HUMAN	.	UPI0000073CBB	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAGGGAAAAA	.	3	ESCA
TAF1	0	.	GRCh37	X	70612774	70612774	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-VR-AA7I-01A-11D-A403-09	TCGA-VR-AA7I-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3041C>A	p.Ala1014Glu	p.A1014E	ENST00000276072	20/38	35	22	12	48	48	0	TAF1,missense_variant,p.Ala993Glu,ENST00000373790,;TAF1,missense_variant,p.Ala993Glu,ENST00000449580,;TAF1,missense_variant,p.Ala1014Glu,ENST00000276072,;TAF1,missense_variant,p.Ala1014Glu,ENST00000423759,;TAF1,upstream_gene_variant,,ENST00000483985,;TAF1,downstream_gene_variant,,ENST00000478305,;TAF1,downstream_gene_variant,,ENST00000474917,;TAF1,downstream_gene_variant,,ENST00000472567,;	A	ENSG00000147133	ENST00000276072	Transcript	missense_variant	3051	3041	1014	A/E	gCa/gAa	.	.	.	1	TAF1	HGNC	11535	protein_coding	YES	CCDS14412.1	ENSP00000276072	TAF1_HUMAN	.	UPI000013DA9F	.	deleterious(0)	probably_damaging(0.987)	20/38	.	hmmpanther:PTHR13900:SF0,hmmpanther:PTHR13900,Pfam_domain:PF12157,PIRSF_domain:PIRSF003047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATGCAGACC	.	5	ESCA
TMEM26	0	.	GRCh37	10	63188874	63188874	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.415G>A	p.Val139Ile	p.V139I	ENST00000399298	4/6	30	23	7	45	45	0	TMEM26,missense_variant,p.Val49Ile,ENST00000277749,;TMEM26,missense_variant,p.Val139Ile,ENST00000399298,;TMEM26,missense_variant,p.Val139Ile,ENST00000399293,;TMEM26,missense_variant,p.Val139Ile,ENST00000503886,;TMEM26,missense_variant,p.Val139Ile,ENST00000488505,;	T	ENSG00000196932	ENST00000399298	Transcript	missense_variant	784	415	139	V/I	Gta/Ata	.	.	.	-1	TMEM26	HGNC	28550	protein_coding	YES	CCDS41530.1	ENSP00000382237	TMM26_HUMAN	.	UPI00001C0B3F	.	tolerated(0.35)	benign(0.04)	4/6	.	Pfam_domain:PF09772,hmmpanther:PTHR22168:SF2,hmmpanther:PTHR22168	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATACTGTAG	.	5	ESCA
C11orf63	0	.	GRCh37	11	122774866	122774866	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578G>T	p.Ser193Ile	p.S193I	ENST00000227349	3/9	13	7	5	27	27	0	C11orf63,missense_variant,p.Ser193Ile,ENST00000531316,;C11orf63,missense_variant,p.Ser193Ile,ENST00000227349,;C11orf63,missense_variant,p.Ser193Ile,ENST00000307257,;	T	ENSG00000109944	ENST00000227349	Transcript	missense_variant	875	578	193	S/I	aGt/aTt	.	.	.	1	C11orf63	HGNC	26288	protein_coding	YES	CCDS8438.1	ENSP00000227349	CK063_HUMAN	.	UPI00001FA5AB	.	deleterious(0)	probably_damaging(0.989)	3/9	.	hmmpanther:PTHR14726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	TGGTAGTGAAT	.	4	ESCA
RAG1	0	.	GRCh37	11	36596040	36596040	+	Missense_Mutation	SNP	C	C	T	rs104894289	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1186C>T	p.Arg396Cys	p.R396C	ENST00000299440	2/2	38	29	8	43	43	0	RAG1,missense_variant,p.Arg396Cys,ENST00000299440,;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.Arg396Cys,ENST00000534663,;	T	ENSG00000166349	ENST00000299440	Transcript	missense_variant	1298	1186	396	R/C	Cgc/Tgc	CM981692,rs104894289,RAG1base_RAG1_DNA:g.7478C>T,RAG1base_HSRAG1:g.1298C>T	.	.	1	RAG1	HGNC	9831	protein_coding	YES	CCDS7902.1	ENSP00000299440	RAG1_HUMAN	.	UPI000013E5A0	.	deleterious_low_confidence(0)	probably_damaging(0.982)	2/2	.	hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0,PROSITE_profiles:PS51487	.	.	.	.	.	.	.	.	.	not_provided,pathogenic	.	10606976	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCCCGCCAA	byCluster	5	ESCA
UBQLNL	0	.	GRCh37	11	5537115	5537115	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.557C>A	p.Ser186Tyr	p.S186Y	ENST00000380184	1/1	12	8	3	9	9	0	UBQLNL,missense_variant,p.Ser186Tyr,ENST00000380184,;HBG2,intron_variant,,ENST00000380259,;AC087380.14,downstream_gene_variant,,ENST00000411807,;	T	ENSG00000175518	ENST00000380184	Transcript	missense_variant	821	557	186	S/Y	tCc/tAc	.	.	.	-1	UBQLNL	HGNC	28294	protein_coding	YES	CCDS31385.1	ENSP00000369531	UBQLN_HUMAN	.	UPI000066D8EC	.	deleterious(0.01)	probably_damaging(0.915)	1/1	.	hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGTTGGACAGA	.	3	ESCA
OR5T2	0	.	GRCh37	11	56000005	56000005	+	Silent	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657T>C	p.%3D	p.D219D	ENST00000313264	1/1	65	59	6	71	71	0	OR5T2,synonymous_variant,p.%3D,ENST00000313264,;	G	ENSG00000181718	ENST00000313264	Transcript	synonymous_variant	733	657	219	D	gaT/gaC	.	.	.	-1	OR5T2	HGNC	15296	protein_coding	YES	CCDS31523.1	ENSP00000323688	OR5T2_HUMAN	.	UPI0000061E97	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF79,hmmpanther:PTHR24247,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGATATCACA	.	3	ESCA
MS4A6E	0	.	GRCh37	11	60105265	60105265	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199G>A	p.Gly67Ser	p.G67S	ENST00000300182	2/4	95	67	27	92	92	0	MS4A6E,missense_variant,p.Gly67Ser,ENST00000300182,;MS4A6E,missense_variant,p.Gly42Ser,ENST00000532756,;MS4A6E,3_prime_UTR_variant,,ENST00000530509,;	A	ENSG00000166926	ENST00000300182	Transcript	missense_variant	264	199	67	G/S	Ggt/Agt	.	.	.	1	MS4A6E	HGNC	14285	protein_coding	YES	CCDS7984.1	ENSP00000300182	M4A6E_HUMAN	H0YD45_HUMAN	UPI0000073D4C	.	deleterious(0.01)	probably_damaging(0.983)	2/4	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR23320:SF53,hmmpanther:PTHR23320,Pfam_domain:PF04103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTGGGTTTC	.	5	ESCA
MS4A14	0	.	GRCh37	11	60183805	60183805	+	Missense_Mutation	SNP	T	T	C	rs780026614	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1463T>C	p.Met488Thr	p.M488T	ENST00000531783	6/6	42	30	11	56	56	0	MS4A14,missense_variant,p.Met438Thr,ENST00000395005,;MS4A14,missense_variant,p.Met488Thr,ENST00000531783,;MS4A14,missense_variant,p.Met343Thr,ENST00000531787,;MS4A14,missense_variant,p.Met455Thr,ENST00000300187,;MS4A14,downstream_gene_variant,,ENST00000395001,;MS4A14,3_prime_UTR_variant,,ENST00000527841,;MS4A14,3_prime_UTR_variant,,ENST00000525397,;MS4A14,3_prime_UTR_variant,,ENST00000530662,;	C	ENSG00000166928	ENST00000531783	Transcript	missense_variant	1554	1463	488	M/T	aTg/aCg	rs780026614	.	.	1	MS4A14	HGNC	30706	protein_coding	YES	CCDS58136.1	ENSP00000433761	.	E9PJE3_HUMAN	UPI0001F77AC2	.	deleterious(0.04)	benign(0.099)	6/6	.	hmmpanther:PTHR23320:SF10,hmmpanther:PTHR23320	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAATGTCAT	byFrequency	5	ESCA
PELI3	0	.	GRCh37	11	66241210	66241210	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.654G>A	p.%3D	p.E218E	ENST00000320740	7/8	111	91	19	127	127	0	PELI3,synonymous_variant,p.%3D,ENST00000349459,;PELI3,synonymous_variant,p.%3D,ENST00000320740,;PELI3,synonymous_variant,p.%3D,ENST00000526296,;PELI3,synonymous_variant,p.%3D,ENST00000528752,;PELI3,synonymous_variant,p.%3D,ENST00000524466,;PELI3,downstream_gene_variant,,ENST00000527230,;CTD-3074O7.5,non_coding_transcript_exon_variant,,ENST00000527092,;CTD-3074O7.5,downstream_gene_variant,,ENST00000533502,;CTD-3074O7.5,downstream_gene_variant,,ENST00000602951,;CTD-3074O7.5,downstream_gene_variant,,ENST00000525142,;CTD-3074O7.5,downstream_gene_variant,,ENST00000527274,;PELI3,intron_variant,,ENST00000531856,;PELI3,splice_region_variant,,ENST00000532970,;	A	ENSG00000174516	ENST00000320740	Transcript	synonymous_variant	814	654	218	E	gaG/gaA	.	.	.	1	PELI3	HGNC	30010	protein_coding	YES	CCDS31615.1	ENSP00000322532	PELI3_HUMAN	H0YEM6_HUMAN,E9PQX6_HUMAN,E9PI91_HUMAN	UPI00000707EF	.	.	.	7/8	.	hmmpanther:PTHR12098,hmmpanther:PTHR12098:SF6,Pfam_domain:PF04710,PIRSF_domain:PIRSF038886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGAGCGAGC	.	4	ESCA
ANKRD13D	0	.	GRCh37	11	67068775	67068775	+	Silent	SNP	C	C	T	.	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1254C>T	p.%3D	p.L418L	ENST00000511455	12/15	53	45	8	65	65	0	ANKRD13D,synonymous_variant,p.%3D,ENST00000515828,;ANKRD13D,synonymous_variant,p.%3D,ENST00000511455,;ANKRD13D,synonymous_variant,p.%3D,ENST00000447274,;ANKRD13D,synonymous_variant,p.%3D,ENST00000308440,;ANKRD13D,synonymous_variant,p.%3D,ENST00000514166,;SSH3,upstream_gene_variant,,ENST00000308127,;SSH3,upstream_gene_variant,,ENST00000308298,;SSH3,upstream_gene_variant,,ENST00000376757,;ANKRD13D,intron_variant,,ENST00000508422,;SSH3,upstream_gene_variant,,ENST00000534112,;ANKRD13D,upstream_gene_variant,,ENST00000504236,;SSH3,upstream_gene_variant,,ENST00000532181,;ANKRD13D,non_coding_transcript_exon_variant,,ENST00000512231,;ANKRD13D,non_coding_transcript_exon_variant,,ENST00000513750,;ANKRD13D,non_coding_transcript_exon_variant,,ENST00000507915,;ANKRD13D,intron_variant,,ENST00000508417,;ANKRD13D,downstream_gene_variant,,ENST00000506119,;ANKRD13D,downstream_gene_variant,,ENST00000504186,;SSH3,upstream_gene_variant,,ENST00000532881,;ANKRD13D,downstream_gene_variant,,ENST00000506531,;SSH3,upstream_gene_variant,,ENST00000532600,;	T	ENSG00000172932	ENST00000511455	Transcript	synonymous_variant	1424	1254	418	L	ctC/ctT	COSM348524	.	.	1	ANKRD13D	HGNC	27880	protein_coding	YES	CCDS31616.2	ENSP00000427130	AN13D_HUMAN	B3KND9_HUMAN	UPI00001981D2	.	.	.	12/15	.	Pfam_domain:PF11904,hmmpanther:PTHR12447,hmmpanther:PTHR12447:SF2	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGCTCAATGC	.	4	ESCA
KDM2B	0	.	GRCh37	12	121867624	121867624	+	3'UTR	SNP	C	C	A	rs547482960	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*467G>T	.	.	ENST00000377071	23/23	15	10	5	22	22	0	KDM2B,3_prime_UTR_variant,,ENST00000542973,;KDM2B,3_prime_UTR_variant,,ENST00000377071,;KDM2B,3_prime_UTR_variant,,ENST00000377069,;RNF34,intron_variant,,ENST00000392464,;KDM2B,downstream_gene_variant,,ENST00000536437,;KDM2B,non_coding_transcript_exon_variant,,ENST00000538503,;KDM2B,downstream_gene_variant,,ENST00000543025,;	A	ENSG00000089094	ENST00000377071	Transcript	3_prime_UTR_variant	4551	.	.	.	.	rs547482960	.	.	-1	KDM2B	HGNC	13610	protein_coding	YES	CCDS41850.1	ENSP00000366271	KDM2B_HUMAN	F5H7T7_HUMAN,F5H6N6_HUMAN,F5H4A7_HUMAN,F5GXC2_HUMAN	UPI000006F36E	.	.	.	23/23	.	.	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGTTCTGCAT	by1000G	5	ESCA
R3HDM2	0	.	GRCh37	12	57648738	57648738	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2749A>G	p.Thr917Ala	p.T917A	ENST00000347140	24/24	45	25	19	59	59	0	R3HDM2,missense_variant,p.Thr931Ala,ENST00000402412,;R3HDM2,missense_variant,p.Thr682Ala,ENST00000429355,;R3HDM2,missense_variant,p.Thr917Ala,ENST00000347140,;R3HDM2,missense_variant,p.Thr917Ala,ENST00000358907,;R3HDM2,missense_variant,p.Thr951Ala,ENST00000403821,;R3HDM2,missense_variant,p.Thr612Ala,ENST00000441731,;R3HDM2,intron_variant,,ENST00000413953,;STAC3,upstream_gene_variant,,ENST00000332782,;STAC3,upstream_gene_variant,,ENST00000546246,;STAC3,upstream_gene_variant,,ENST00000553489,;STAC3,upstream_gene_variant,,ENST00000554578,;R3HDM2,downstream_gene_variant,,ENST00000548161,;R3HDM2,downstream_gene_variant,,ENST00000546843,;R3HDM2,non_coding_transcript_exon_variant,,ENST00000393811,;RP11-123K3.4,intron_variant,,ENST00000548184,;STAC3,upstream_gene_variant,,ENST00000553294,;STAC3,upstream_gene_variant,,ENST00000557176,;	C	ENSG00000179912	ENST00000347140	Transcript	missense_variant	3140	2749	917	T/A	Act/Gct	.	.	.	-1	R3HDM2	HGNC	29167	protein_coding	YES	CCDS8937.2	ENSP00000317903	R3HD2_HUMAN	C9J7N6_HUMAN	UPI00005A60D3	.	tolerated(0.32)	benign(0.05)	24/24	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15672:SF13,hmmpanther:PTHR15672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGTCCCAC	.	5	ESCA
KRR1	0	.	GRCh37	12	75905384	75905384	+	5'UTR	SNP	G	G	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-7C>G	.	.	ENST00000229214	1/10	22	18	4	35	35	0	KRR1,5_prime_UTR_variant,,ENST00000229214,;KRR1,upstream_gene_variant,,ENST00000438169,;KRR1,non_coding_transcript_exon_variant,,ENST00000550898,;KRR1,non_coding_transcript_exon_variant,,ENST00000550023,;	C	ENSG00000111615	ENST00000229214	Transcript	5_prime_UTR_variant	18	.	.	.	.	.	.	.	-1	KRR1	HGNC	5176	protein_coding	YES	CCDS9012.1	ENSP00000229214	KRR1_HUMAN	.	UPI00001403EE	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCAAGCTGCT	.	4	ESCA
SNORD115-29	0	.	GRCh37	15	25468394	25468394	+	RNA	SNP	G	G	T	rs564840815	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2G>T	.	.	ENST00000362834	1/1	115	66	48	91	91	0	SNORD115-29,non_coding_transcript_exon_variant,,ENST00000362834,;SNORD115-27,downstream_gene_variant,,ENST00000364430,;SNORD115-31,upstream_gene_variant,,ENST00000365318,;SNORD115-28,downstream_gene_variant,,ENST00000363931,;SNORD115-30,upstream_gene_variant,,ENST00000364117,;SNHG14,downstream_gene_variant,,ENST00000365067,;SNHG14,intron_variant,,ENST00000453082,;SNHG14,downstream_gene_variant,,ENST00000424208,;	T	ENSG00000199704	ENST00000362834	Transcript	non_coding_transcript_exon_variant	2	.	.	.	.	rs564840815	.	.	1	SNORD115-29	HGNC	33048	snoRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	A:0.0168	A:0.0613	A:0.0043	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTGGGTCAA	byFrequency|by1000G	5	ESCA
SNORD115-40	0	.	GRCh37	15	25490534	25490534	+	3'Flank	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000606510	.	34	13	21	41	41	0	SNORD115-40,downstream_gene_variant,,ENST00000606510,;SNORD115-43,upstream_gene_variant,,ENST00000365503,;SNORD115-42,upstream_gene_variant,,ENST00000364273,;SNORD115-41,upstream_gene_variant,,ENST00000363608,;SNORD115-39,downstream_gene_variant,,ENST00000363694,;SNHG14,non_coding_transcript_exon_variant,,ENST00000453082,;	A	ENSG00000272460	ENST00000606510	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1692	1	SNORD115-40	HGNC	33059	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACCCTCCGT	.	5	ESCA
ALDH1A2	0	.	GRCh37	15	58306478	58306478	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.119T>A	p.Ile40Asn	p.I40N	ENST00000249750	2/13	25	20	5	47	47	0	ALDH1A2,missense_variant,p.Ile40Asn,ENST00000249750,;ALDH1A2,missense_variant,p.Ile11Asn,ENST00000558231,;ALDH1A2,missense_variant,p.Ile19Asn,ENST00000537372,;ALDH1A2,missense_variant,p.Ile40Asn,ENST00000347587,;ALDH1A2,splice_region_variant,,ENST00000561070,;ALDH1A2,splice_region_variant,,ENST00000557967,;ALDH1A2,splice_region_variant,,ENST00000558239,;ALDH1A2,upstream_gene_variant,,ENST00000559517,;ALDH1A2,splice_region_variant,,ENST00000560122,;ALDH1A2,splice_region_variant,,ENST00000558073,;ALDH1A2,splice_region_variant,,ENST00000558595,;ALDH1A2,splice_region_variant,,ENST00000559266,;ALDH1A2,splice_region_variant,,ENST00000559297,;ALDH1A2,splice_region_variant,,ENST00000430119,;	T	ENSG00000128918	ENST00000249750	Transcript	missense_variant	887	119	40	I/N	aTc/aAc	.	.	.	-1	ALDH1A2	HGNC	15472	protein_coding	YES	CCDS10163.1	ENSP00000249750	AL1A2_HUMAN	Q9UED3_HUMAN,H0YKL3_HUMAN	UPI00001678B4	.	deleterious(0.01)	probably_damaging(0.998)	2/13	.	hmmpanther:PTHR11699:SF102,hmmpanther:PTHR11699,Gene3D:3.40.605.10,Superfamily_domains:SSF53720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAAGATCTAA	.	2	ESCA
FURIN	0	.	GRCh37	15	91418967	91418967	+	5'UTR	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4C>A	.	.	ENST00000268171	2/16	60	46	13	57	57	0	FURIN,5_prime_UTR_variant,,ENST00000268171,;FURIN,5_prime_UTR_variant,,ENST00000560824,;FURIN,5_prime_UTR_variant,,ENST00000559353,;FURIN,upstream_gene_variant,,ENST00000558794,;FURIN,upstream_gene_variant,,ENST00000560018,;	A	ENSG00000140564	ENST00000268171	Transcript	5_prime_UTR_variant	276	.	.	.	.	.	.	.	1	FURIN	HGNC	8568	protein_coding	YES	CCDS10364.1	ENSP00000268171	FURIN_HUMAN	H0YNB5_HUMAN,H0YKB2_HUMAN	UPI0000000CC7	.	.	.	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCCCCCAT	.	5	ESCA
RPS2	0	.	GRCh37	16	2012996	2012997	+	Intron	DEL	AG	AG	-	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	AG	AG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376-87_376-86delCT	.	.	ENST00000343262	.	79	61	18	78	78	0	RPS2,intron_variant,,ENST00000533186,;RPS2,intron_variant,,ENST00000526522,;RPS2,intron_variant,,ENST00000530225,;RPS2,intron_variant,,ENST00000527302,;RPS2,intron_variant,,ENST00000343262,;RPS2,intron_variant,,ENST00000529806,;RPS2,intron_variant,,ENST00000526586,;RNF151,upstream_gene_variant,,ENST00000321392,;NDUFB10,downstream_gene_variant,,ENST00000543683,;NDUFB10,downstream_gene_variant,,ENST00000268668,;NDUFB10,downstream_gene_variant,,ENST00000569148,;RPS2,downstream_gene_variant,,ENST00000563194,;RNF151,upstream_gene_variant,,ENST00000569714,;RNF151,upstream_gene_variant,,ENST00000569210,;NDUFB10,downstream_gene_variant,,ENST00000570172,;SNORA64,non_coding_transcript_exon_variant,,ENST00000384674,;SNHG9,upstream_gene_variant,,ENST00000564014,;SNHG9,upstream_gene_variant,,ENST00000459373,;SNORA10,upstream_gene_variant,,ENST00000384084,;SNHG9,upstream_gene_variant,,ENST00000531523,;RPS2,non_coding_transcript_exon_variant,,ENST00000527826,;RPS2,non_coding_transcript_exon_variant,,ENST00000527109,;RPS2,non_coding_transcript_exon_variant,,ENST00000527871,;RPS2,non_coding_transcript_exon_variant,,ENST00000533872,;RPS2,intron_variant,,ENST00000526908,;RPS2,intron_variant,,ENST00000532746,;RPS2,intron_variant,,ENST00000531065,;RPS2,intron_variant,,ENST00000534461,;RPS2,intron_variant,,ENST00000533161,;NDUFB10,downstream_gene_variant,,ENST00000565031,;AC005363.9,downstream_gene_variant,,ENST00000530779,;	-	ENSG00000140988	ENST00000343262	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RPS2	HGNC	10404	protein_coding	YES	CCDS10452.1	ENSP00000341885	RS2_HUMAN	Q9BSW5_HUMAN,Q8NI62_HUMAN,O60249_HUMAN,H3BNG3_HUMAN,E9PMM9_HUMAN	UPI000000128D	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGGAAAGAGAGG	.	3	ESCA
TBL3	0	.	GRCh37	16	2025698	2025698	+	Missense_Mutation	SNP	G	G	A	rs749067239	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.974G>A	p.Arg325Gln	p.R325Q	ENST00000568546	10/22	22	18	4	25	25	0	TBL3,missense_variant,p.Arg325Gln,ENST00000568546,;TBL3,missense_variant,p.Arg233Gln,ENST00000332704,;NOXO1,downstream_gene_variant,,ENST00000354249,;NOXO1,downstream_gene_variant,,ENST00000567471,;NOXO1,downstream_gene_variant,,ENST00000566005,;NOXO1,downstream_gene_variant,,ENST00000397280,;NOXO1,downstream_gene_variant,,ENST00000356120,;TBL3,non_coding_transcript_exon_variant,,ENST00000569628,;TBL3,downstream_gene_variant,,ENST00000561907,;NOXO1,downstream_gene_variant,,ENST00000563181,;TBL3,upstream_gene_variant,,ENST00000569792,;TBL3,upstream_gene_variant,,ENST00000564171,;TBL3,upstream_gene_variant,,ENST00000567615,;NOXO1,downstream_gene_variant,,ENST00000569739,;	A	ENSG00000183751	ENST00000568546	Transcript	missense_variant	1102	974	325	R/Q	cGg/cAg	rs749067239	.	.	1	TBL3	HGNC	11587	protein_coding	YES	CCDS10453.1	ENSP00000454836	TBL3_HUMAN	A0JLS5_HUMAN	UPI000006F172	.	tolerated(1)	benign(0.001)	10/22	.	Superfamily_domains:0049172,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR19854:SF15,hmmpanther:PTHR19854,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGCGGCTGC	.	4	ESCA
ITGAD	0	.	GRCh37	16	31419760	31419760	+	Missense_Mutation	SNP	G	G	A	rs748457412	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1024G>A	p.Ala342Thr	p.A342T	ENST00000389202	10/30	35	32	3	32	32	0	ITGAD,missense_variant,p.Ala342Thr,ENST00000389202,;RP11-120K18.2,downstream_gene_variant,,ENST00000567545,;ITGAD,non_coding_transcript_exon_variant,,ENST00000444228,;	A	ENSG00000156886	ENST00000389202	Transcript	missense_variant	1073	1024	342	A/T	Gca/Aca	rs748457412	.	.	1	ITGAD	HGNC	6146	protein_coding	YES	CCDS32438.1	ENSP00000373854	ITAD_HUMAN	Q59H14_HUMAN	UPI000004B27A	.	tolerated(0.42)	benign(0)	10/30	.	Superfamily_domains:SSF69318,Gene3D:3nigC00,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19,PROSITE_profiles:PS51470	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CCAGGGCAAGC	.	3	ESCA
NLRC3	0	.	GRCh37	16	3613869	3613869	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1210C>T	p.Pro404Ser	p.P404S	ENST00000448023	3/19	29	20	9	21	21	0	NLRC3,missense_variant,p.Pro357Ser,ENST00000301749,;NLRC3,missense_variant,p.Pro339Ser,ENST00000324659,;NLRC3,missense_variant,p.Pro357Ser,ENST00000359128,;NLRC3,missense_variant,p.Pro404Ser,ENST00000448023,;NLRC3,non_coding_transcript_exon_variant,,ENST00000603128,;NLRC3,non_coding_transcript_exon_variant,,ENST00000419350,;NLRC3,downstream_gene_variant,,ENST00000603055,;NLRC3,missense_variant,p.Pro404Ser,ENST00000603507,;	A	ENSG00000167984	ENST00000448023	Transcript	missense_variant	1397	1210	404	P/S	Ccg/Tcg	.	.	.	-1	NLRC3	HGNC	29889	protein_coding	YES	.	ENSP00000414415	.	C9JLH9_HUMAN	UPI0000246E58	.	deleterious(0)	probably_damaging(0.998)	3/19	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCGGGGGCC	.	5	ESCA
FAM86A	0	.	GRCh37	16	5147684	5147684	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.57C>T	p.%3D	p.R19R	ENST00000427587	1/8	81	58	23	73	73	0	FAM86A,synonymous_variant,p.%3D,ENST00000587133,;FAM86A,synonymous_variant,p.%3D,ENST00000458008,;FAM86A,synonymous_variant,p.%3D,ENST00000427587,;RP11-10K17.6,upstream_gene_variant,,ENST00000589323,;FAM86A,synonymous_variant,p.%3D,ENST00000585436,;FAM86A,synonymous_variant,p.%3D,ENST00000587200,;FAM86A,synonymous_variant,p.%3D,ENST00000587161,;FAM86A,non_coding_transcript_exon_variant,,ENST00000585975,;FAM86A,non_coding_transcript_exon_variant,,ENST00000586444,;	A	ENSG00000118894	ENST00000427587	Transcript	synonymous_variant	126	57	19	R	cgC/cgT	.	.	.	-1	FAM86A	HGNC	32221	protein_coding	YES	CCDS10529.1	ENSP00000398502	FA86A_HUMAN	.	UPI000013D29B	.	.	.	1/8	.	Pfam_domain:PF14904,hmmpanther:PTHR23109,hmmpanther:PTHR23109:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGCGGCG	.	5	ESCA
RSPRY1	0	.	GRCh37	16	57220329	57220329	+	5'UTR	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-789C>T	.	.	ENST00000537866	1/15	181	167	13	123	123	0	RSPRY1,5_prime_UTR_variant,,ENST00000568505,;RSPRY1,5_prime_UTR_variant,,ENST00000564435,;RSPRY1,5_prime_UTR_variant,,ENST00000537866,;RSPRY1,5_prime_UTR_variant,,ENST00000562959,;RSPRY1,5_prime_UTR_variant,,ENST00000394420,;RSPRY1,intron_variant,,ENST00000562439,;FAM192A,upstream_gene_variant,,ENST00000565760,;FAM192A,upstream_gene_variant,,ENST00000566681,;FAM192A,upstream_gene_variant,,ENST00000566481,;FAM192A,upstream_gene_variant,,ENST00000309137,;FAM192A,upstream_gene_variant,,ENST00000564108,;FAM192A,upstream_gene_variant,,ENST00000568671,;FAM192A,upstream_gene_variant,,ENST00000570184,;FAM192A,upstream_gene_variant,,ENST00000562324,;FAM192A,upstream_gene_variant,,ENST00000565458,;FAM192A,upstream_gene_variant,,ENST00000562406,;FAM192A,upstream_gene_variant,,ENST00000566584,;FAM192A,upstream_gene_variant,,ENST00000566077,;FAM192A,upstream_gene_variant,,ENST00000567044,;FAM192A,upstream_gene_variant,,ENST00000567439,;FAM192A,upstream_gene_variant,,ENST00000565353,;FAM192A,upstream_gene_variant,,ENST00000562400,;RSPRY1,non_coding_transcript_exon_variant,,ENST00000566352,;	T	ENSG00000159579	ENST00000537866	Transcript	5_prime_UTR_variant	85	.	.	.	.	.	.	.	1	RSPRY1	HGNC	29420	protein_coding	YES	CCDS10775.1	ENSP00000443176	RSPRY_HUMAN	H3BSC7_HUMAN,H3BQQ7_HUMAN,H3BQG6_HUMAN	UPI000006E516	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCCGCCCCCT	.	2	ESCA
SLC9A5	0	.	GRCh37	16	67304865	67304865	+	Silent	SNP	C	C	T	rs745511053	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2443C>T	p.%3D	p.L815L	ENST00000299798	16/16	54	51	3	90	90	0	SLC9A5,synonymous_variant,p.%3D,ENST00000566626,;SLC9A5,synonymous_variant,p.%3D,ENST00000299798,;SLC9A5,3_prime_UTR_variant,,ENST00000564812,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000564704,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000563723,;	T	ENSG00000135740	ENST00000299798	Transcript	synonymous_variant	2508	2443	815	L	Ctg/Ttg	rs745511053	.	.	1	SLC9A5	HGNC	11078	protein_coding	YES	CCDS42178.1	ENSP00000299798	SL9A5_HUMAN	.	UPI000012FD2D	.	.	.	16/16	.	hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF56	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGCCTGCCT	.	2	ESCA
PCGF2	0	.	GRCh37	17	36891779	36891779	+	Silent	SNP	G	G	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.732C>G	p.%3D	p.P244P	ENST00000580830	12/12	25	20	5	20	20	0	PCGF2,missense_variant,p.Leu192Val,ENST00000578109,;PCGF2,missense_variant,p.Leu246Val,ENST00000579882,;PCGF2,missense_variant,p.Leu246Val,ENST00000585100,;PCGF2,synonymous_variant,p.%3D,ENST00000578487,;PCGF2,synonymous_variant,p.%3D,ENST00000581345,;PCGF2,synonymous_variant,p.%3D,ENST00000360797,;PCGF2,synonymous_variant,p.%3D,ENST00000580830,;CISD3,downstream_gene_variant,,ENST00000439660,;RNA5SP440,upstream_gene_variant,,ENST00000363245,;CISD3,downstream_gene_variant,,ENST00000578573,;CISD3,downstream_gene_variant,,ENST00000581668,;	C	ENSG00000056661	ENST00000580830	Transcript	synonymous_variant	1434	732	244	P	ccC/ccG	.	.	.	-1	PCGF2	HGNC	12929	protein_coding	YES	CCDS32638.1	ENSP00000461961	PCGF2_HUMAN	.	UPI0000001279	.	.	.	12/12	.	hmmpanther:PTHR10825:SF22,hmmpanther:PTHR10825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCGGAGGGGGT	.	2	ESCA
ZZEF1	0	.	GRCh37	17	3978660	3978660	+	Missense_Mutation	SNP	C	C	A	rs745636921	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3298G>T	p.Ala1100Ser	p.A1100S	ENST00000381638	22/55	64	49	14	92	92	0	ZZEF1,missense_variant,p.Ala1100Ser,ENST00000381638,;ZZEF1,downstream_gene_variant,,ENST00000574474,;ZZEF1,upstream_gene_variant,,ENST00000572426,;ZZEF1,upstream_gene_variant,,ENST00000572699,;ZZEF1,upstream_gene_variant,,ENST00000570365,;	A	ENSG00000074755	ENST00000381638	Transcript	missense_variant	3423	3298	1100	A/S	Gcc/Tcc	rs745636921	.	.	-1	ZZEF1	HGNC	29027	protein_coding	YES	CCDS11043.1	ENSP00000371051	ZZEF1_HUMAN	.	UPI00004569F7	.	deleterious(0.03)	benign(0.002)	22/55	.	Gene3D:2.60.120.290,hmmpanther:PTHR22772,hmmpanther:PTHR22772:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGGCAGATT	byFrequency	5	ESCA
PSME3	0	.	GRCh37	17	40993560	40993560	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.769C>T	p.Arg257Trp	p.R257W	ENST00000293362	11/11	65	52	13	57	57	0	PSME3,missense_variant,p.Arg244Trp,ENST00000590720,;PSME3,missense_variant,p.Arg255Trp,ENST00000441946,;PSME3,missense_variant,p.Arg257Trp,ENST00000293362,;PSME3,missense_variant,p.Arg183Trp,ENST00000545225,;PSME3,missense_variant,p.Arg188Trp,ENST00000592169,;PSME3,3_prime_UTR_variant,,ENST00000541124,;PSME3,downstream_gene_variant,,ENST00000589469,;PSME3,downstream_gene_variant,,ENST00000586114,;PSME3,downstream_gene_variant,,ENST00000591152,;PSME3,downstream_gene_variant,,ENST00000585805,;AOC2,upstream_gene_variant,,ENST00000253799,;AOC2,upstream_gene_variant,,ENST00000452774,;PSME3,3_prime_UTR_variant,,ENST00000543428,;PSME3,downstream_gene_variant,,ENST00000593111,;PSME3,downstream_gene_variant,,ENST00000586312,;PSME3,downstream_gene_variant,,ENST00000591722,;	T	ENSG00000131467	ENST00000293362	Transcript	missense_variant	930	769	257	R/W	Cgg/Tgg	.	.	.	1	PSME3	HGNC	9570	protein_coding	YES	CCDS11442.1	ENSP00000293362	PSME3_HUMAN	.	UPI000002B1BA	.	deleterious(0)	possibly_damaging(0.854)	11/11	.	hmmpanther:PTHR10660,hmmpanther:PTHR10660:SF4,Pfam_domain:PF02252,Gene3D:1.20.120.180,Superfamily_domains:SSF47216	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAAACGGCCC	.	5	ESCA
ITGA3	0	.	GRCh37	17	48157713	48157713	+	Nonsense_Mutation	SNP	C	C	T	rs776593477	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2794C>T	p.Arg932Ter	p.R932*	ENST00000007722	22/25	33	27	6	48	48	0	ITGA3,stop_gained,p.Arg932Ter,ENST00000320031,;ITGA3,stop_gained,p.Arg932Ter,ENST00000007722,;ITGA3,intron_variant,,ENST00000506827,;ITGA3,downstream_gene_variant,,ENST00000544892,;ITGA3,stop_gained,p.Arg12Ter,ENST00000504417,;ITGA3,non_coding_transcript_exon_variant,,ENST00000505306,;ITGA3,downstream_gene_variant,,ENST00000507771,;ITGA3,downstream_gene_variant,,ENST00000506401,;ITGA3,downstream_gene_variant,,ENST00000510809,;ITGA3,downstream_gene_variant,,ENST00000505612,;ITGA3,downstream_gene_variant,,ENST00000515147,;	T	ENSG00000005884	ENST00000007722	Transcript	stop_gained	2794	2794	932	R/*	Cga/Tga	rs776593477	.	.	1	ITGA3	HGNC	6139	protein_coding	YES	CCDS11557.1	ENSP00000007722	ITA3_HUMAN	Q86SW1_HUMAN	UPI0000140781	.	.	.	22/25	.	Superfamily_domains:SSF69179,Gene3D:1jv2A04,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGGCACGAGTG	.	3	ESCA
TANC2	0	.	GRCh37	17	61086934	61086934	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.14G>A	p.Ser5Asn	p.S5N	ENST00000424789	1/25	43	32	10	65	65	0	TANC2,missense_variant,p.Ser5Asn,ENST00000389520,;TANC2,missense_variant,p.Ser5Asn,ENST00000424789,;RP11-180P8.5,upstream_gene_variant,,ENST00000606304,;	A	ENSG00000170921	ENST00000424789	Transcript	missense_variant	18	14	5	S/N	aGt/aAt	.	.	.	1	TANC2	HGNC	30212	protein_coding	YES	CCDS45754.1	ENSP00000387593	TANC2_HUMAN	.	UPI00015D57DF	.	deleterious_low_confidence(0.01)	benign(0)	1/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATAGTCTCA	.	5	ESCA
KIAA0753	0	.	GRCh37	17	6510250	6510250	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1952G>A	p.Arg651Lys	p.R651K	ENST00000361413	12/19	47	36	11	38	38	0	KIAA0753,missense_variant,p.Arg352Lys,ENST00000542606,;KIAA0753,missense_variant,p.Arg107Lys,ENST00000589033,;KIAA0753,missense_variant,p.Arg651Lys,ENST00000361413,;KIAA0753,missense_variant,p.Arg352Lys,ENST00000572370,;KIAA0753,upstream_gene_variant,,ENST00000575027,;KIAA0753,3_prime_UTR_variant,,ENST00000570790,;KIAA0753,3_prime_UTR_variant,,ENST00000542826,;	T	ENSG00000198920	ENST00000361413	Transcript	missense_variant	2311	1952	651	R/K	aGa/aAa	.	.	.	-1	KIAA0753	HGNC	29110	protein_coding	YES	CCDS42247.1	ENSP00000355250	K0753_HUMAN	I3L1P2_HUMAN,I3L0P7_HUMAN,B7Z6L6_HUMAN	UPI000013D2BF	.	tolerated(0.17)	probably_damaging(0.971)	12/19	.	hmmpanther:PTHR15732:SF3,hmmpanther:PTHR15732	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTCTTCTA	.	5	ESCA
GPRC5C	0	.	GRCh37	17	72442995	72442995	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1289G>A	p.Gly430Glu	p.G430E	ENST00000392627	4/4	71	59	11	82	82	0	GPRC5C,missense_variant,p.Gly397Glu,ENST00000392629,;GPRC5C,missense_variant,p.Gly70Glu,ENST00000342648,;GPRC5C,missense_variant,p.Gly405Glu,ENST00000392628,;GPRC5C,missense_variant,p.Gly430Glu,ENST00000392627,;GPRC5C,3_prime_UTR_variant,,ENST00000481232,;GPRC5C,intron_variant,,ENST00000581590,;GPRC5C,non_coding_transcript_exon_variant,,ENST00000582873,;GPRC5C,non_coding_transcript_exon_variant,,ENST00000577663,;GPRC5C,non_coding_transcript_exon_variant,,ENST00000482723,;	A	ENSG00000170412	ENST00000392627	Transcript	missense_variant	2415	1289	430	G/E	gGa/gAa	.	.	.	1	GPRC5C	HGNC	13309	protein_coding	YES	CCDS11699.1	ENSP00000376403	GPC5C_HUMAN	J9JIE0_HUMAN,J3QQN3_HUMAN	UPI0000231CB2	.	tolerated(0.69)	possibly_damaging(0.614)	4/4	.	hmmpanther:PTHR14511,hmmpanther:PTHR14511:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGAAGGAGCTT	.	4	ESCA
ACOX1	0	.	GRCh37	17	73945584	73945584	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1576G>T	p.Ala526Ser	p.A526S	ENST00000293217	11/14	105	86	18	107	107	0	ACOX1,missense_variant,p.Ala488Ser,ENST00000537812,;ACOX1,missense_variant,p.Ala11Ser,ENST00000588968,;ACOX1,missense_variant,p.Ala526Ser,ENST00000301608,;ACOX1,missense_variant,p.Ala526Ser,ENST00000293217,;ACOX1,upstream_gene_variant,,ENST00000587927,;RP11-552F3.13,downstream_gene_variant,,ENST00000587348,;ACOX1,3_prime_UTR_variant,,ENST00000573078,;ACOX1,3_prime_UTR_variant,,ENST00000572047,;ACOX1,downstream_gene_variant,,ENST00000589744,;	A	ENSG00000161533	ENST00000293217	Transcript	missense_variant	1866	1576	526	A/S	Gca/Tca	.	.	.	-1	ACOX1	HGNC	119	protein_coding	YES	CCDS11734.1	ENSP00000293217	ACOX1_HUMAN	.	UPI000013E0F5	.	deleterious(0.04)	probably_damaging(0.923)	11/14	.	Gene3D:1.20.140.10,Pfam_domain:PF01756,PIRSF_domain:PIRSF000168,Superfamily_domains:SSF47203	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTGCTCGAA	.	5	ESCA
TP53	0	.	GRCh37	17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A	rs397516436	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	6/11	72	43	28	75	75	0	TP53,stop_gained,p.Arg213Ter,ENST00000413465,;TP53,stop_gained,p.Arg213Ter,ENST00000420246,;TP53,stop_gained,p.Arg213Ter,ENST00000269305,;TP53,stop_gained,p.Arg81Ter,ENST00000509690,;TP53,stop_gained,p.Arg213Ter,ENST00000359597,;TP53,stop_gained,p.Arg120Ter,ENST00000514944,;TP53,stop_gained,p.Arg213Ter,ENST00000445888,;TP53,stop_gained,p.Arg213Ter,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	A	ENSG00000141510	ENST00000269305	Transcript	stop_gained	827	637	213	R/*	Cga/Tga	CM951226,rs397516436,TP53_g.12706del,TP53_g.12706C>T,TP53_g.12706C>G,TP53_g.12706C>A,COSM10654,COSM43798,COSM43807,COSM44102,COSM99618,COSM99615,COSM99616,COSM707891,COSM3378350,COSM1638393,COSM99617	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	pathogenic	0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R213*|c.637C>T|45,SITE|p.R120*|c.358C>T|84,SITE|p.R213*|c.637C>T|84,SITE|p.R213*|c.637C>T|84,SITE|p.R81*|c.241C>T|87,SITE|p.R213*|c.637C>T|267,SITE|p.R213*|c.637C>T|33,CODON|p.0?|c.1_1182del1182|6,CODON|p.R213R|c.639A>G|6,CODON|p.R81Q|c.242G>A|9,CODON|p.R213L|c.638G>T|12,CODON|p.R213L|c.638G>T|4,CODON|p.R213L|c.638G>T|39,CODON|p.R213Q|c.638G>A|9,CODON|p.R213Q|c.638G>A|31,CODON|p.R120L|c.359G>T|12,CODON|p.R213P|c.638G>C|6,CODON|p.R120Q|c.359G>A|9,CODON|p.R81L|c.242G>T|12,CODON|p.R213L|c.638G>T|6,CODON|p.R213L|c.638G>T|12,CODON|p.R213Q|c.638G>A|4,CODON|p.R213Q|c.638G>A|9,CODON|p.R213Q|c.638G>A|3,CODON|p.R213fs*34|c.637delC|3,BUFFER|p.V218delV|c.646_648delGTG|8,BUFFER|p.V216G|c.647T>G|5,BUFFER|p.V216A|c.647T>C|3,BUFFER|p.V216E|c.647T>A|4,BUFFER|p.V216M|c.646G>A|20,BUFFER|p.V216M|c.646G>A|12,BUFFER|p.V123M|c.367G>A|20,BUFFER|p.V216L|c.646G>T|8,BUFFER|p.V216M|c.646G>A|20,BUFFER|p.V216M|c.646G>A|7,BUFFER|p.V216M|c.646G>A|70,BUFFER|p.V84M|c.250G>A|20,BUFFER|p.S215R|c.645T>G|3,BUFFER|p.S215R|c.645T>A|4,BUFFER|p.S122R|c.366T>A|4,BUFFER|p.S215R|c.645T>G|13,BUFFER|p.S215R|c.645T>A|4,BUFFER|p.S83R|c.249T>A|4,BUFFER|p.S122R|c.366T>G|3,BUFFER|p.S215R|c.645T>G|3,BUFFER|p.S83R|c.249T>G|3,BUFFER|p.S215R|c.645T>A|8,BUFFER|p.S215I|c.644G>T|4,BUFFER|p.S215I|c.644G>T|4,BUFFER|p.S215I|c.644G>T|19,BUFFER|p.S215T|c.644G>C|3,BUFFER|p.S83I|c.248G>T|4,BUFFER|p.S122I|c.365G>T|4,BUFFER|p.S215N|c.644G>A|8,BUFFER|p.S215C|c.643A>T|4,BUFFER|p.S215G|c.643A>G|3,BUFFER|p.S83G|c.247A>G|3,BUFFER|p.S215G|c.643A>G|10,BUFFER|p.S215G|c.643A>G|3,BUFFER|p.S122G|c.364A>G|3,BUFFER|p.H214Q|c.642T>G|3,BUFFER|p.H214R|c.641A>G|66,BUFFER|p.H214R|c.641A>G|16,BUFFER|p.H214R|c.641A>G|5,BUFFER|p.H82R|c.245A>G|18,BUFFER|p.H121R|c.362A>G|16,BUFFER|p.H214R|c.641A>G|16,BUFFER|p.H214R|c.641A>G|6,BUFFER|p.H214Y|c.640C>T|5,BUFFER|p.H214D|c.640C>G|4,BUFFER|p.F212fs*3|c.635_636delTT|5,BUFFER|p.F212fs*3|c.634_635delTT|6,BUFFER|p.R213fs*34|c.634delT|5,BUFFER|p.T211T|c.633T>C|9,BUFFER|p.T211I|c.632C>T|3,BUFFER|p.T211I|c.632C>T|11,BUFFER|p.T211N|c.632C>A|4,BUFFER|p.T118I|c.353C>T|3,BUFFER|p.T79I|c.236C>T|3,BUFFER|p.T211I|c.632C>T|3,BUFFER|p.T211fs*36|c.631delA|4,BUFFER|p.T211A|c.631A>G|3,BUFFER|p.N210fs*37|c.628delA|3,BUFFER|p.R209fs*6|c.626_627delGA|3,BUFFER|p.R116fs*6|c.347_348delGA|3,BUFFER|p.R209fs*6|c.626_627delGA|3,BUFFER|p.R209fs*6|c.626_627delGA|11,BUFFER|p.R77fs*6|c.230_231delGA|3,BUFFER|p.R209fs*6|c.625_626delAG|23,BUFFER|p.R209K|c.626G>A|6,BUFFER|p.R209T|c.626G>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTCGAAAAG	byCluster	5	ESCA
ELL	0	.	GRCh37	19	18554169	18554169	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1393C>T	.	.	ENST00000262809	12/12	101	96	5	115	115	0	ELL,3_prime_UTR_variant,,ENST00000262809,;ELL,downstream_gene_variant,,ENST00000596124,;CTD-3137H5.1,non_coding_transcript_exon_variant,,ENST00000594590,;ELL,3_prime_UTR_variant,,ENST00000594635,;ELL,downstream_gene_variant,,ENST00000608165,;ELL,downstream_gene_variant,,ENST00000610152,;AC010335.1,non_coding_transcript_exon_variant,,ENST00000541164,;	A	ENSG00000105656	ENST00000262809	Transcript	3_prime_UTR_variant	3331	.	.	.	.	.	.	.	-1	ELL	HGNC	23114	protein_coding	YES	CCDS12380.1	ENSP00000262809	ELL_HUMAN	Q75MS0_HUMAN	UPI0000062324	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGTCAGGAGGC	.	2	ESCA
MEGF8	0	.	GRCh37	19	42873013	42873013	+	Missense_Mutation	SNP	C	C	T	rs372350131	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6299C>T	p.Pro2100Leu	p.P2100L	ENST00000334370	36/41	74	69	5	73	73	0	MEGF8,missense_variant,p.Pro2100Leu,ENST00000334370,;MEGF8,missense_variant,p.Pro2167Leu,ENST00000251268,;MEGF8,intron_variant,,ENST00000598762,;MEGF8,upstream_gene_variant,,ENST00000378073,;MEGF8,upstream_gene_variant,,ENST00000593647,;MEGF8,upstream_gene_variant,,ENST00000599787,;	T	ENSG00000105429	ENST00000334370	Transcript	missense_variant	6934	6299	2100	P/L	cCg/cTg	rs372350131	.	.	1	MEGF8	HGNC	3233	protein_coding	YES	CCDS12604.2	ENSP00000334219	MEGF8_HUMAN	.	UPI00003CF1A7	.	tolerated(0.18)	benign(0.013)	36/41	.	hmmpanther:PTHR10574:SF241,hmmpanther:PTHR10574,SMART_domains:SM00423	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCGTCCGGGGG	byCluster|by1000G	2	ESCA
CCDC114	0	.	GRCh37	19	48800199	48800199	+	3'UTR	SNP	G	G	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*34C>G	.	.	ENST00000315396	14/14	41	31	9	43	43	0	CCDC114,3_prime_UTR_variant,,ENST00000315396,;CCDC114,non_coding_transcript_exon_variant,,ENST00000497273,;CCDC114,non_coding_transcript_exon_variant,,ENST00000474199,;	C	ENSG00000105479	ENST00000315396	Transcript	3_prime_UTR_variant	2730	.	.	.	.	.	.	.	-1	CCDC114	HGNC	26560	protein_coding	YES	CCDS12714.2	ENSP00000318429	CC114_HUMAN	.	UPI0000EE7B5F	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAGCCAGG	.	5	ESCA
ZNF836	0	.	GRCh37	19	52659498	52659498	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1438A>T	p.Ser480Cys	p.S480C	ENST00000322146	5/5	76	58	18	62	62	0	ZNF836,missense_variant,p.Ser480Cys,ENST00000597252,;ZNF836,missense_variant,p.Ser480Cys,ENST00000322146,;ZNF836,downstream_gene_variant,,ENST00000596428,;ZNF836,downstream_gene_variant,,ENST00000597065,;CTC-471J1.8,intron_variant,,ENST00000598982,;CTC-471J1.8,intron_variant,,ENST00000594362,;ZNF836,upstream_gene_variant,,ENST00000599618,;	A	ENSG00000196267	ENST00000322146	Transcript	missense_variant	1960	1438	480	S/C	Agt/Tgt	.	.	.	-1	ZNF836	HGNC	34333	protein_coding	YES	CCDS46162.1	ENSP00000325038	ZN836_HUMAN	M0QZ88_HUMAN,M0QYS4_HUMAN	UPI00001D818C	.	tolerated(0.11)	possibly_damaging(0.851)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF229,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACTGAAGA	.	5	ESCA
TMC4	0	.	GRCh37	19	54664700	54664700	+	Missense_Mutation	SNP	T	T	C	rs748646342	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1906A>G	p.Ile636Val	p.I636V	ENST00000376591	13/15	33	28	4	30	30	0	TMC4,missense_variant,p.Ile636Val,ENST00000376591,;TMC4,missense_variant,p.Ile630Val,ENST00000301187,;TMC4,missense_variant,p.Ile218Val,ENST00000416963,;LENG1,upstream_gene_variant,,ENST00000222224,;TMC4,downstream_gene_variant,,ENST00000476013,;TMC4,downstream_gene_variant,,ENST00000479750,;TMC4,missense_variant,p.Ile4Val,ENST00000449860,;TMC4,non_coding_transcript_exon_variant,,ENST00000465790,;TMC4,upstream_gene_variant,,ENST00000494594,;TMC4,downstream_gene_variant,,ENST00000497518,;TMC4,downstream_gene_variant,,ENST00000468343,;TMC4,downstream_gene_variant,,ENST00000495398,;	C	ENSG00000167608	ENST00000376591	Transcript	missense_variant	2038	1906	636	I/V	Att/Gtt	rs748646342	.	.	-1	TMC4	HGNC	22998	protein_coding	YES	CCDS46174.1	ENSP00000365776	TMC4_HUMAN	C9JFU4_HUMAN	UPI000040C55F	.	tolerated(0.56)	benign(0.406)	13/15	.	hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGAAATAGACT	.	4	ESCA
LILRB1	0	.	GRCh37	19	55146736	55146736	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1589A>T	p.Glu530Val	p.E530V	ENST00000324602	12/15	67	49	18	60	60	0	LILRB1,stop_gained,p.Lys504Ter,ENST00000448689,;LILRB1,missense_variant,p.Glu513Val,ENST00000396317,;LILRB1,missense_variant,p.Glu529Val,ENST00000396331,;LILRB1,missense_variant,p.Glu530Val,ENST00000396315,;LILRB1,missense_variant,p.Glu579Val,ENST00000427581,;LILRB1,missense_variant,p.Glu530Val,ENST00000396327,;LILRB1,missense_variant,p.Glu513Val,ENST00000418536,;LILRB1,missense_variant,p.Glu529Val,ENST00000434867,;LILRB1,missense_variant,p.Glu530Val,ENST00000324602,;LILRB1,missense_variant,p.Glu529Val,ENST00000396332,;LILRB1,missense_variant,p.Glu529Val,ENST00000396321,;AC009892.10,downstream_gene_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,downstream_gene_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,stop_gained,p.Lys504Ter,ENST00000421584,;LILRB1,non_coding_transcript_exon_variant,,ENST00000480375,;LILRB1,non_coding_transcript_exon_variant,,ENST00000487425,;	T	ENSG00000104972	ENST00000324602	Transcript	missense_variant	1814	1589	530	E/V	gAa/gTa	.	.	.	1	LILRB1	HGNC	6605	protein_coding	YES	CCDS42614.1	ENSP00000315997	LIRB1_HUMAN	.	UPI0000034BFC	.	deleterious(0)	benign(0.408)	12/15	.	hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF89	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGAAGAAA	.	5	ESCA
ZNF772	0	.	GRCh37	19	57986507	57986507	+	Silent	SNP	T	T	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207A>T	p.%3D	p.T69T	ENST00000343280	4/5	41	33	7	43	43	0	ZNF772,synonymous_variant,p.%3D,ENST00000343280,;ZNF772,intron_variant,,ENST00000600175,;ZNF772,intron_variant,,ENST00000425074,;ZNF772,intron_variant,,ENST00000601768,;AC004076.9,intron_variant,,ENST00000596831,;ZNF772,intron_variant,,ENST00000427512,;ZNF772,intron_variant,,ENST00000356584,;AC003005.2,upstream_gene_variant,,ENST00000595422,;AC003005.2,upstream_gene_variant,,ENST00000594562,;AC004076.9,intron_variant,,ENST00000415705,;ZNF772,downstream_gene_variant,,ENST00000450712,;	A	ENSG00000197128	ENST00000343280	Transcript	synonymous_variant	468	207	69	T	acA/acT	.	.	.	-1	ZNF772	HGNC	33106	protein_coding	YES	CCDS33133.1	ENSP00000341165	ZN772_HUMAN	.	UPI000022AA0A	.	.	.	4/5	.	Superfamily_domains:0044637,SMART_domains:SM00349,hmmpanther:PTHR24387:SF75,hmmpanther:PTHR24387,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGATGTATG	.	5	ESCA
ZNF135	0	.	GRCh37	19	58578877	58578877	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1097C>A	p.Thr366Asn	p.T366N	ENST00000401053	4/4	49	41	8	63	63	0	ZNF135,missense_variant,p.Thr366Asn,ENST00000401053,;ZNF135,missense_variant,p.Thr300Asn,ENST00000506786,;ZNF135,missense_variant,p.Thr342Asn,ENST00000313434,;ZNF135,missense_variant,p.Thr354Asn,ENST00000359978,;ZNF135,missense_variant,p.Thr354Asn,ENST00000511556,;ZNF135,missense_variant,p.Thr342Asn,ENST00000439855,;RN7SL526P,upstream_gene_variant,,ENST00000469492,;ZNF135,intron_variant,,ENST00000515535,;	A	ENSG00000176293	ENST00000401053	Transcript	missense_variant	1100	1097	366	T/N	aCc/aAc	.	.	.	1	ZNF135	HGNC	12919	protein_coding	YES	CCDS54329.1	ENSP00000441410	ZN135_HUMAN	.	UPI0001B3CB2A	.	deleterious(0.03)	possibly_damaging(0.535)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF245,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCACCCAGC	.	4	ESCA
CTSS	0	.	GRCh37	1	150727558	150727558	+	Silent	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318A>G	p.%3D	p.T106T	ENST00000368985	4/8	34	29	5	42	42	0	CTSS,synonymous_variant,p.%3D,ENST00000368985,;CTSS,intron_variant,,ENST00000448301,;CTSS,non_coding_transcript_exon_variant,,ENST00000480760,;CTSS,upstream_gene_variant,,ENST00000472977,;CTSS,upstream_gene_variant,,ENST00000483930,;	C	ENSG00000163131	ENST00000368985	Transcript	synonymous_variant	579	318	106	T	acA/acG	.	.	.	-1	CTSS	HGNC	2545	protein_coding	YES	CCDS968.1	ENSP00000357981	CATS_HUMAN	.	UPI000013DFE1	.	.	.	4/8	.	hmmpanther:PTHR12411:SF54,hmmpanther:PTHR12411,Gene3D:3.90.70.10,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTATATGTGAT	.	2	ESCA
IQGAP3	0	.	GRCh37	1	156496073	156496073	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*205A>G	.	.	ENST00000361170	38/38	24	20	3	32	32	0	IQGAP3,3_prime_UTR_variant,,ENST00000361170,;snoU13,upstream_gene_variant,,ENST00000458777,;IQGAP3,3_prime_UTR_variant,,ENST00000491900,;	C	ENSG00000183856	ENST00000361170	Transcript	3_prime_UTR_variant	5112	.	.	.	.	.	.	.	-1	IQGAP3	HGNC	20669	protein_coding	YES	CCDS1144.1	ENSP00000354451	IQGA3_HUMAN	F2Z2E2_HUMAN	UPI000046FFDD	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUSE|VARSCANS	GACTCTGGGCA	.	2	ESCA
PADI4	0	.	GRCh37	1	17657501	17657501	+	Missense_Mutation	SNP	G	G	A	rs767499070	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.130G>A	p.Ala44Thr	p.A44T	ENST00000375448	2/16	33	29	4	59	59	0	PADI4,missense_variant,p.Ala44Thr,ENST00000375448,;PADI4,missense_variant,p.Ala44Thr,ENST00000375453,;AC004824.2,intron_variant,,ENST00000602074,;	A	ENSG00000159339	ENST00000375448	Transcript	missense_variant	156	130	44	A/T	Gcc/Acc	rs767499070,COSM1336546	.	.	1	PADI4	HGNC	18368	protein_coding	YES	CCDS180.1	ENSP00000364597	PADI4_HUMAN	Q6EVJ1_HUMAN	UPI000013DFF1	.	tolerated(0.1)	benign(0.063)	2/16	.	hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF3,Pfam_domain:PF08526,PIRSF_domain:PIRSF001247,Superfamily_domains:SSF49503	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAACGCCTCC	byFrequency	3	ESCA
TAS1R2	0	.	GRCh37	1	19180792	19180792	+	Missense_Mutation	SNP	G	G	A	rs768209495	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1172C>T	p.Ala391Val	p.A391V	ENST00000375371	3/6	36	31	4	39	39	0	TAS1R2,missense_variant,p.Ala391Val,ENST00000375371,;RP13-279N23.2,3_prime_UTR_variant,,ENST00000494072,;	A	ENSG00000179002	ENST00000375371	Transcript	missense_variant	1194	1172	391	A/V	gCg/gTg	rs768209495	.	.	-1	TAS1R2	HGNC	14905	protein_coding	YES	CCDS187.1	ENSP00000364520	TS1R2_HUMAN	.	UPI0000456168	.	deleterious(0)	probably_damaging(0.97)	3/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF3,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AGACCGCAGAG	byFrequency	3	ESCA
NR5A2	0	.	GRCh37	1	200012970	200012970	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271G>A	p.Asp91Asn	p.D91N	ENST00000367362	3/8	62	55	7	55	55	0	NR5A2,missense_variant,p.Asp19Asn,ENST00000544748,;NR5A2,missense_variant,p.Asp45Asn,ENST00000236914,;NR5A2,missense_variant,p.Asp91Asn,ENST00000367362,;NR5A2,missense_variant,p.Asp12Asn,ENST00000367357,;NR5A2,downstream_gene_variant,,ENST00000447034,;NR5A2,3_prime_UTR_variant,,ENST00000474307,;	A	ENSG00000116833	ENST00000367362	Transcript	missense_variant	517	271	91	D/N	Gat/Aat	.	.	.	1	NR5A2	HGNC	7984	protein_coding	YES	CCDS1401.1	ENSP00000356331	NR5A2_HUMAN	Q8WY08_HUMAN,B4E2P3_HUMAN	UPI0000130482	.	deleterious(0)	probably_damaging(0.997)	3/8	.	PROSITE_profiles:PS51030,hmmpanther:PTHR24086:SF18,hmmpanther:PTHR24086,PROSITE_patterns:PS00031,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,PIRSF_domain:PIRSF002530,Superfamily_domains:SSF57716,Prints_domain:PR00047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGAGATAAA	.	4	ESCA
NFASC	0	.	GRCh37	1	204987304	204987304	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1637G>A	.	.	ENST00000339876	30/30	47	30	16	34	34	0	NFASC,3_prime_UTR_variant,,ENST00000404076,;NFASC,3_prime_UTR_variant,,ENST00000367170,;NFASC,3_prime_UTR_variant,,ENST00000447819,;NFASC,3_prime_UTR_variant,,ENST00000338515,;NFASC,3_prime_UTR_variant,,ENST00000360049,;NFASC,3_prime_UTR_variant,,ENST00000425360,;NFASC,3_prime_UTR_variant,,ENST00000401399,;NFASC,3_prime_UTR_variant,,ENST00000404907,;NFASC,3_prime_UTR_variant,,ENST00000367171,;NFASC,3_prime_UTR_variant,,ENST00000539706,;NFASC,3_prime_UTR_variant,,ENST00000367173,;NFASC,3_prime_UTR_variant,,ENST00000339876,;NFASC,3_prime_UTR_variant,,ENST00000430393,;NFASC,3_prime_UTR_variant,,ENST00000367169,;NFASC,3_prime_UTR_variant,,ENST00000367172,;NFASC,3_prime_UTR_variant,,ENST00000338586,;NFASC,downstream_gene_variant,,ENST00000413225,;NFASC,downstream_gene_variant,,ENST00000513543,;NFASC,non_coding_transcript_exon_variant,,ENST00000495396,;NFASC,non_coding_transcript_exon_variant,,ENST00000503221,;NFASC,downstream_gene_variant,,ENST00000504476,;	A	ENSG00000163531	ENST00000339876	Transcript	3_prime_UTR_variant	5688	.	.	.	.	.	.	.	1	NFASC	HGNC	29866	protein_coding	YES	CCDS53460.1	ENSP00000344786	NFASC_HUMAN	D6RHX4_HUMAN	UPI0000237208	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAGGAACCC	.	5	ESCA
TMEM206	0	.	GRCh37	1	212558750	212558750	+	Missense_Mutation	SNP	C	C	T	rs369443875	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.544G>A	p.Gly182Ser	p.G182S	ENST00000535273	5/9	81	66	14	65	65	0	TMEM206,missense_variant,p.Gly121Ser,ENST00000261455,;TMEM206,missense_variant,p.Gly182Ser,ENST00000535273,;TMEM206,non_coding_transcript_exon_variant,,ENST00000471937,;TMEM206,non_coding_transcript_exon_variant,,ENST00000467822,;	T	ENSG00000065600	ENST00000535273	Transcript	missense_variant	688	544	182	G/S	Ggt/Agt	rs369443875	.	.	-1	TMEM206	HGNC	25593	protein_coding	YES	CCDS55687.1	ENSP00000438863	TM206_HUMAN	B4DHQ5_HUMAN	UPI0001914DBE	.	deleterious_low_confidence(0.02)	probably_damaging(1)	5/9	.	hmmpanther:PTHR16087:SF0,hmmpanther:PTHR16087,Pfam_domain:PF15122	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGACCGGGGT	byFrequency|byCluster	5	ESCA
SKI	0	.	GRCh37	1	2160898	2160898	+	Silent	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693G>T	p.%3D	p.L231L	ENST00000378536	1/7	66	34	32	50	50	0	SKI,synonymous_variant,p.%3D,ENST00000378536,;SKI,upstream_gene_variant,,ENST00000508416,;	T	ENSG00000157933	ENST00000378536	Transcript	synonymous_variant	765	693	231	L	ctG/ctT	.	.	.	1	SKI	HGNC	10896	protein_coding	YES	CCDS39.1	ENSP00000367797	SKI_HUMAN	Q7Z462_HUMAN,Q7Z461_HUMAN,Q7Z459_HUMAN	UPI00001359DE	.	.	.	1/7	.	Superfamily_domains:SSF63763,SMART_domains:SM01046,Pfam_domain:PF08782,Gene3D:3.10.390.10,hmmpanther:PTHR10005:SF15,hmmpanther:PTHR10005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTGCTGGT	.	5	ESCA
HNRNPR	0	.	GRCh37	1	23645059	23645059	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.943G>A	p.Gly315Arg	p.G315R	ENST00000374616	8/11	46	39	7	63	63	0	HNRNPR,missense_variant,p.Gly315Arg,ENST00000374616,;HNRNPR,missense_variant,p.Gly214Arg,ENST00000478691,;HNRNPR,missense_variant,p.Gly312Arg,ENST00000302271,;HNRNPR,missense_variant,p.Gly274Arg,ENST00000427764,;HNRNPR,missense_variant,p.Gly173Arg,ENST00000606561,;HNRNPR,missense_variant,p.Gly312Arg,ENST00000374612,;HNRNPR,missense_variant,p.Gly152Arg,ENST00000426846,;HNRNPR,non_coding_transcript_exon_variant,,ENST00000476451,;HNRNPR,non_coding_transcript_exon_variant,,ENST00000463552,;HNRNPR,non_coding_transcript_exon_variant,,ENST00000470941,;	T	ENSG00000125944	ENST00000374616	Transcript	missense_variant	1052	943	315	G/R	Gga/Aga	.	.	.	-1	HNRNPR	HGNC	5047	protein_coding	YES	CCDS44085.1	ENSP00000363745	HNRPR_HUMAN	S4R3J4_HUMAN,Q7Z334_HUMAN	UPI000006F30B	.	deleterious(0.01)	probably_damaging(1)	8/11	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011:SF131,hmmpanther:PTHR24011,Gene3D:3.30.70.330,TIGRFAM_domain:TIGR01648,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTCCACTCA	.	4	ESCA
TINAGL1	0	.	GRCh37	1	32052456	32052456	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1283delG	p.Gly428AlafsTer55	p.G428Afs*55	ENST00000271064	12/12	78	68	10	55	55	0	TINAGL1,frameshift_variant,p.Gly428AlafsTer55,ENST00000271064,;TINAGL1,frameshift_variant,p.Gly397AlafsTer55,ENST00000457433,;TINAGL1,downstream_gene_variant,,ENST00000537531,;TINAGL1,non_coding_transcript_exon_variant,,ENST00000481165,;TINAGL1,non_coding_transcript_exon_variant,,ENST00000463112,;TINAGL1,downstream_gene_variant,,ENST00000461030,;TINAGL1,downstream_gene_variant,,ENST00000468635,;TINAGL1,downstream_gene_variant,,ENST00000480586,;TINAGL1,downstream_gene_variant,,ENST00000478398,;TINAGL1,downstream_gene_variant,,ENST00000498429,;	-	ENSG00000142910	ENST00000271064	Transcript	frameshift_variant	1356	1280	427	W/X	tGg/tg	.	.	.	1	TINAGL1	HGNC	19168	protein_coding	YES	CCDS343.1	ENSP00000271064	TINAL_HUMAN	B4DVG5_HUMAN	UPI000003B0A6	.	.	.	12/12	.	hmmpanther:PTHR12411:SF270,hmmpanther:PTHR12411,Pfam_domain:PF00112,Gene3D:3.90.70.10,SMART_domains:SM00645,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	3	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACTCCTGGGGCC	.	3	ESCA
SLC25A3P1	0	.	GRCh37	1	53904088	53904088	+	RNA	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1151G>A	.	.	ENST00000566100	1/1	34	29	4	32	32	0	SLC25A3P1,non_coding_transcript_exon_variant,,ENST00000566100,;SLC25A3P1,non_coding_transcript_exon_variant,,ENST00000569142,;SLC25A3P1,intron_variant,,ENST00000563752,;SLC25A3P1,downstream_gene_variant,,ENST00000562700,;SLC25A3P1,non_coding_transcript_exon_variant,,ENST00000443844,;	T	ENSG00000236253	ENST00000566100	Transcript	non_coding_transcript_exon_variant	1151	.	.	.	.	.	.	.	-1	SLC25A3P1	HGNC	26869	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGGGCGAGGC	.	4	ESCA
SLC25A3P1	0	.	GRCh37	1	53904463	53904463	+	RNA	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.776G>A	.	.	ENST00000566100	1/1	20	16	4	27	27	0	SLC25A3P1,non_coding_transcript_exon_variant,,ENST00000562700,;SLC25A3P1,non_coding_transcript_exon_variant,,ENST00000566100,;SLC25A3P1,non_coding_transcript_exon_variant,,ENST00000569142,;SLC25A3P1,intron_variant,,ENST00000563752,;SLC25A3P1,non_coding_transcript_exon_variant,,ENST00000443844,;	T	ENSG00000236253	ENST00000566100	Transcript	non_coding_transcript_exon_variant	776	.	.	.	.	.	.	.	-1	SLC25A3P1	HGNC	26869	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCCACGCCCT	.	4	ESCA
KCNAB2	0	.	GRCh37	1	6111666	6111666	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70C>A	p.His24Asn	p.H24N	ENST00000378083	2/16	14	10	4	10	10	0	KCNAB2,missense_variant,p.His24Asn,ENST00000378083,;KCNAB2,intron_variant,,ENST00000435937,;KCNAB2,intron_variant,,ENST00000389632,;KCNAB2,intron_variant,,ENST00000472700,;KCNAB2,intron_variant,,ENST00000602612,;KCNAB2,intron_variant,,ENST00000164247,;KCNAB2,intron_variant,,ENST00000428161,;KCNAB2,intron_variant,,ENST00000341524,;KCNAB2,intron_variant,,ENST00000378092,;KCNAB2,intron_variant,,ENST00000378111,;KCNAB2,intron_variant,,ENST00000445501,;KCNAB2,intron_variant,,ENST00000378097,;KCNAB2,intron_variant,,ENST00000378087,;KCNAB2,intron_variant,,ENST00000352527,;KCNAB2,intron_variant,,ENST00000458166,;KCNAB2,intron_variant,,ENST00000478098,;	A	ENSG00000069424	ENST00000378083	Transcript	missense_variant	359	70	24	H/N	Cac/Aac	.	.	.	1	KCNAB2	HGNC	6229	protein_coding	YES	CCDS55570.1	ENSP00000367323	KCAB2_HUMAN	.	UPI000035E741	.	tolerated_low_confidence(1)	benign(0)	2/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT	CCCTGCACCCC	.	3	ESCA
CACHD1	0	.	GRCh37	1	65143953	65143953	+	Silent	SNP	G	G	A	rs368444781	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3051G>A	p.%3D	p.V1017V	ENST00000290039	23/27	110	68	42	97	97	0	CACHD1,synonymous_variant,p.%3D,ENST00000290039,;CACHD1,synonymous_variant,p.%3D,ENST00000371073,;CACHD1,non_coding_transcript_exon_variant,,ENST00000495994,;CACHD1,non_coding_transcript_exon_variant,,ENST00000470527,;	A	ENSG00000158966	ENST00000290039	Transcript	synonymous_variant	3157	3051	1017	V	gtG/gtA	rs368444781	.	.	1	CACHD1	HGNC	29314	protein_coding	YES	CCDS628.2	ENSP00000290039	.	.	UPI0000458A70	.	.	.	23/27	.	hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF28	A:0.0006	A:0.0023	A:0	.	A:0	A:0	A:0	A:0.0009	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTGGGAGC	byFrequency|byCluster|by1000G	5	ESCA
MACROD2	0	.	GRCh37	20	15967423	15967423	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1037A>G	p.Gln346Arg	p.Q346R	ENST00000217246	14/17	31	24	7	43	43	0	MACROD2,missense_variant,p.Gln111Arg,ENST00000378058,;MACROD2,missense_variant,p.Gln346Arg,ENST00000217246,;MACROD2,missense_variant,p.Gln111Arg,ENST00000402914,;MACROD2,missense_variant,p.Gln346Arg,ENST00000310348,;MACROD2,5_prime_UTR_variant,,ENST00000407045,;MACROD2,non_coding_transcript_exon_variant,,ENST00000486914,;	G	ENSG00000172264	ENST00000217246	Transcript	missense_variant	1432	1037	346	Q/R	cAg/cGg	.	.	.	1	MACROD2	HGNC	16126	protein_coding	YES	CCDS13120.2	ENSP00000217246	MACD2_HUMAN	.	UPI00005B2E12	.	deleterious_low_confidence(0)	possibly_damaging(0.707)	14/17	.	hmmpanther:PTHR11106,hmmpanther:PTHR11106:SF54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGCAGAGCT	.	5	ESCA
INSM1	0	.	GRCh37	20	20351274	20351274	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*830T>C	.	.	ENST00000310227	1/1	71	59	11	99	99	0	INSM1,3_prime_UTR_variant,,ENST00000310227,;	C	ENSG00000173404	ENST00000310227	Transcript	3_prime_UTR_variant	2510	.	.	.	.	.	.	.	1	INSM1	HGNC	6090	protein_coding	YES	CCDS13143.1	ENSP00000312631	INSM1_HUMAN	.	UPI0000046C2F	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAGATTTTTT	.	5	ESCA
HM13	0	.	GRCh37	20	30126009	30126009	+	Silent	SNP	C	C	T	.	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310C>T	p.%3D	p.L104L	ENST00000398174	3/13	39	29	10	42	42	0	HM13,synonymous_variant,p.%3D,ENST00000376127,;HM13,synonymous_variant,p.%3D,ENST00000344042,;HM13,synonymous_variant,p.%3D,ENST00000335574,;HM13,synonymous_variant,p.%3D,ENST00000398174,;HM13,synonymous_variant,p.%3D,ENST00000340852,;HM13,non_coding_transcript_exon_variant,,ENST00000466766,;HM13,non_coding_transcript_exon_variant,,ENST00000496438,;HM13,non_coding_transcript_exon_variant,,ENST00000492709,;HM13,non_coding_transcript_exon_variant,,ENST00000469126,;HM13,intron_variant,,ENST00000460225,;HM13,non_coding_transcript_exon_variant,,ENST00000498035,;	T	ENSG00000101294	ENST00000398174	Transcript	synonymous_variant	434	310	104	L	Ctg/Ttg	COSM3545051,COSM3545050	.	.	1	HM13	HGNC	16435	protein_coding	YES	CCDS42861.1	ENSP00000381237	HM13_HUMAN	.	UPI000001358F	.	.	.	3/13	.	hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF23,Pfam_domain:PF04258,SMART_domains:SM00730	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTCCTGCTG	.	5	ESCA
BMP2	0	.	GRCh37	20	6750872	6750872	+	Silent	SNP	C	C	T	rs750303403	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99C>T	p.%3D	p.F33F	ENST00000378827	2/3	56	51	5	51	51	0	BMP2,synonymous_variant,p.%3D,ENST00000378827,;	T	ENSG00000125845	ENST00000378827	Transcript	synonymous_variant	1318	99	33	F	ttC/ttT	rs750303403	.	.	1	BMP2	HGNC	1069	protein_coding	YES	CCDS13099.1	ENSP00000368104	BMP2_HUMAN	U3N491_HUMAN,C8C069_HUMAN,C8C060_HUMAN	UPI0000126A21	.	.	.	2/3	.	hmmpanther:PTHR11848:SF143,hmmpanther:PTHR11848	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGTTCGCGGC	.	3	ESCA
MCM3AP	0	.	GRCh37	21	47704296	47704296	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.905G>T	p.Arg302Met	p.R302M	ENST00000397708	2/29	39	21	18	58	58	0	MCM3AP,missense_variant,p.Arg302Met,ENST00000291688,;MCM3AP,missense_variant,p.Arg302Met,ENST00000397708,;YBEY,upstream_gene_variant,,ENST00000339195,;YBEY,upstream_gene_variant,,ENST00000397701,;YBEY,upstream_gene_variant,,ENST00000397692,;MCM3AP,downstream_gene_variant,,ENST00000426537,;YBEY,upstream_gene_variant,,ENST00000397694,;YBEY,upstream_gene_variant,,ENST00000397691,;YBEY,upstream_gene_variant,,ENST00000329319,;MCM3AP,downstream_gene_variant,,ENST00000495475,;YBEY,upstream_gene_variant,,ENST00000492864,;YBEY,upstream_gene_variant,,ENST00000468924,;	A	ENSG00000160294	ENST00000397708	Transcript	missense_variant	1160	905	302	R/M	aGg/aTg	.	.	.	-1	MCM3AP	HGNC	6946	protein_coding	YES	CCDS13734.1	ENSP00000380820	GANP_HUMAN	N0GVG8_HUMAN,B3KWZ4_HUMAN	UPI000012ED4A	.	deleterious(0.01)	probably_damaging(0.997)	2/29	.	hmmpanther:PTHR12436:SF18,hmmpanther:PTHR12436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTCCTTGGG	.	5	ESCA
ZNF70	0	.	GRCh37	22	24086332	24086332	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.996C>T	p.%3D	p.G332G	ENST00000341976	2/2	41	32	9	52	52	0	ZNF70,synonymous_variant,p.%3D,ENST00000341976,;LL22NC03-N27C7.1,upstream_gene_variant,,ENST00000602816,;	A	ENSG00000187792	ENST00000341976	Transcript	synonymous_variant	1457	996	332	G	ggC/ggT	.	.	.	-1	ZNF70	HGNC	13140	protein_coding	YES	CCDS13812.1	ENSP00000339314	ZNF70_HUMAN	.	UPI0000001C98	.	.	.	2/2	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF82,Pfam_domain:PF13465,Gene3D:3.30.160.60,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCGCCAGT	.	5	ESCA
TNRC6B	0	.	GRCh37	22	40718961	40718961	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5218A>G	p.Ser1740Gly	p.S1740G	ENST00000454349	23/23	42	21	21	47	47	0	TNRC6B,missense_variant,p.Ser1740Gly,ENST00000454349,;TNRC6B,missense_variant,p.Ser936Gly,ENST00000402203,;TNRC6B,missense_variant,p.Ser936Gly,ENST00000301923,;TNRC6B,missense_variant,p.Ser1630Gly,ENST00000335727,;TNRC6B,downstream_gene_variant,,ENST00000446273,;	G	ENSG00000100354	ENST00000454349	Transcript	missense_variant	5429	5218	1740	S/G	Agt/Ggt	.	.	.	1	TNRC6B	HGNC	29190	protein_coding	YES	CCDS54533.1	ENSP00000401946	TNR6B_HUMAN	.	UPI00017A6F19	.	deleterious(0.01)	benign(0.39)	23/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCAAGTGCG	.	5	ESCA
CPT1B	0	.	GRCh37	22	51010669	51010669	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1421C>T	p.Ala474Val	p.A474V	ENST00000360719	12/19	32	25	6	37	37	0	CPT1B,missense_variant,p.Ala474Val,ENST00000312108,;CPT1B,missense_variant,p.Ala474Val,ENST00000360719,;CPT1B,missense_variant,p.Ala474Val,ENST00000395650,;CPT1B,missense_variant,p.Ala271Val,ENST00000434492,;CPT1B,missense_variant,p.Ala440Val,ENST00000457250,;CPT1B,missense_variant,p.Ala474Val,ENST00000405237,;CPT1B,missense_variant,p.Ala393Val,ENST00000440709,;CPT1B,downstream_gene_variant,,ENST00000417176,;CHKB-CPT1B,3_prime_UTR_variant,,ENST00000453634,;CHKB-CPT1B,non_coding_transcript_exon_variant,,ENST00000492556,;CPT1B,non_coding_transcript_exon_variant,,ENST00000497224,;CPT1B,non_coding_transcript_exon_variant,,ENST00000475238,;CPT1B,downstream_gene_variant,,ENST00000476790,;CPT1B,downstream_gene_variant,,ENST00000479886,;CPT1B,downstream_gene_variant,,ENST00000460853,;CPT1B,downstream_gene_variant,,ENST00000461117,;CPT1B,downstream_gene_variant,,ENST00000423069,;	A	ENSG00000205560	ENST00000360719	Transcript	missense_variant	1559	1421	474	A/V	gCg/gTg	.	.	.	-1	CPT1B	HGNC	2329	protein_coding	YES	CCDS14098.1	ENSP00000353945	CPT1B_HUMAN	C9J7C3_HUMAN	UPI0000128314	.	deleterious(0)	benign(0.228)	12/19	.	hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF58,PROSITE_patterns:PS00440,Pfam_domain:PF00755,Superfamily_domains:SSF52777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCACGCATGC	.	5	ESCA
IL18RAP	0	.	GRCh37	2	103067351	103067351	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1254C>A	p.Ser418Arg	p.S418R	ENST00000264260	11/12	69	64	5	62	62	0	IL18RAP,missense_variant,p.Ser276Arg,ENST00000409369,;IL18RAP,missense_variant,p.Ser418Arg,ENST00000264260,;	A	ENSG00000115607	ENST00000264260	Transcript	missense_variant	1843	1254	418	S/R	agC/agA	.	.	.	1	IL18RAP	HGNC	5989	protein_coding	YES	CCDS2061.1	ENSP00000264260	I18RA_HUMAN	Q3KPE8_HUMAN,C9JLE2_HUMAN	UPI0000071CAF	.	tolerated(0.09)	benign(0.029)	11/12	.	Superfamily_domains:SSF52200,SMART_domains:SM00255,Gene3D:3.40.50.10140,Pfam_domain:PF01582,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF4,PROSITE_profiles:PS50104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGAGCTCTTT	.	2	ESCA
PTPN4	0	.	GRCh37	2	120677751	120677751	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.935G>C	p.Arg312Thr	p.R312T	ENST00000263708	12/27	39	34	4	29	29	0	PTPN4,missense_variant,p.Arg312Thr,ENST00000263708,;snoU13,downstream_gene_variant,,ENST00000459555,;PTPN4,3_prime_UTR_variant,,ENST00000433888,;PTPN4,3_prime_UTR_variant,,ENST00000430976,;	C	ENSG00000088179	ENST00000263708	Transcript	missense_variant	1706	935	312	R/T	aGa/aCa	.	.	.	1	PTPN4	HGNC	9656	protein_coding	YES	CCDS2129.1	ENSP00000263708	PTN4_HUMAN	Q580X3_HUMAN,Q53QV5_HUMAN,Q53Q76_HUMAN,Q4ZG31_HUMAN,J3KQP5_HUMAN,F5H1A0_HUMAN	UPI0000000CA9	.	tolerated(0.1)	benign(0.342)	12/27	.	PROSITE_profiles:PS50057,hmmpanther:PTHR19134:SF187,hmmpanther:PTHR19134,Pfam_domain:PF09380,PIRSF_domain:PIRSF000927,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGACAGACCAC	.	3	ESCA
SAP130	0	.	GRCh37	2	128699581	128699581	+	Nonstop_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3251A>G	p.Ter1084TrpextTer31	p.*1084Wext*31	ENST00000357702	21/21	21	18	3	21	21	0	SAP130,stop_lost,p.Ter1049TrpextTer31,ENST00000259235,;SAP130,stop_lost,p.Ter1057TrpextTer31,ENST00000259234,;SAP130,stop_lost,p.Ter1084TrpextTer31,ENST00000357702,;	C	ENSG00000136715	ENST00000357702	Transcript	stop_lost	3383	3251	1084	*/W	tAg/tGg	.	.	.	-1	SAP130	HGNC	29813	protein_coding	YES	CCDS54397.1	ENSP00000350333	SP130_HUMAN	Q96DP1_HUMAN,C9J683_HUMAN	UPI00005989D6	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTCTAGACT	.	2	ESCA
FIGN	0	.	GRCh37	2	164468194	164468194	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148T>C	p.Tyr50His	p.Y50H	ENST00000333129	3/3	71	52	18	48	48	0	FIGN,missense_variant,p.Tyr50His,ENST00000333129,;FIGN,intron_variant,,ENST00000409634,;FIGN,non_coding_transcript_exon_variant,,ENST00000482917,;	G	ENSG00000182263	ENST00000333129	Transcript	missense_variant	463	148	50	Y/H	Tat/Cat	.	.	.	-1	FIGN	HGNC	13285	protein_coding	YES	CCDS2221.2	ENSP00000333836	FIGN_HUMAN	.	UPI000022BD13	.	tolerated(0.13)	probably_damaging(0.987)	3/3	.	hmmpanther:PTHR23074:SF14,hmmpanther:PTHR23074	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGATAGGTGC	.	5	ESCA
DNAH7	0	.	GRCh37	2	196746602	196746602	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5878G>C	p.Ala1960Pro	p.A1960P	ENST00000312428	36/65	70	53	16	86	86	0	DNAH7,missense_variant,p.Ala1960Pro,ENST00000312428,;	G	ENSG00000118997	ENST00000312428	Transcript	missense_variant	5979	5878	1960	A/P	Gca/Cca	.	.	.	-1	DNAH7	HGNC	18661	protein_coding	YES	CCDS42794.1	ENSP00000311273	DYH7_HUMAN	C9JUY3_HUMAN	UPI0000141B95	.	deleterious(0.02)	possibly_damaging(0.629)	36/65	.	hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Pfam_domain:PF12775,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R1957*|c.5869C>T|4	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAATGCAGAGT	.	5	ESCA
SATB2	0	.	GRCh37	2	200136363	200136363	+	3'UTR	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*571C>A	.	.	ENST00000417098	11/11	113	96	17	140	140	0	SATB2,3_prime_UTR_variant,,ENST00000260926,;SATB2,3_prime_UTR_variant,,ENST00000443023,;SATB2,3_prime_UTR_variant,,ENST00000417098,;SATB2,downstream_gene_variant,,ENST00000428695,;SATB2,downstream_gene_variant,,ENST00000457245,;	T	ENSG00000119042	ENST00000417098	Transcript	3_prime_UTR_variant	3590	.	.	.	.	.	.	.	-1	SATB2	HGNC	21637	protein_coding	YES	CCDS2327.1	ENSP00000401112	SATB2_HUMAN	Q59FT3_HUMAN	UPI00000336B1	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGCAGTTTAT	.	4	ESCA
CPS1	0	.	GRCh37	2	211421465	211421465	+	Missense_Mutation	SNP	G	G	A	rs750705469	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.26G>A	p.Arg9Lys	p.R9K	ENST00000430249	2/39	61	43	17	85	85	0	CPS1,missense_variant,p.Arg3Lys,ENST00000417946,;CPS1,missense_variant,p.Arg9Lys,ENST00000430249,;CPS1,missense_variant,p.Arg3Lys,ENST00000518043,;CPS1,missense_variant,p.Arg3Lys,ENST00000233072,;CPS1,missense_variant,p.Arg9Lys,ENST00000523702,;	A	ENSG00000021826	ENST00000430249	Transcript	missense_variant	81	26	9	R/K	aGg/aAg	rs750705469	.	.	1	CPS1	HGNC	2323	protein_coding	YES	CCDS46505.1	ENSP00000402608	CPSM_HUMAN	Q5R207_HUMAN,E7EWJ3_HUMAN,C9JTA4_HUMAN,B7ZAW0_HUMAN	UPI000166C19F	.	tolerated_low_confidence(0.44)	benign(0.006)	2/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACGAGGATTT	byFrequency	5	ESCA
MARCH4	0	.	GRCh37	2	217234789	217234789	+	Silent	SNP	G	G	A	.	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.195C>T	p.%3D	p.H65H	ENST00000273067	1/4	33	26	7	43	43	0	MARCH4,synonymous_variant,p.%3D,ENST00000273067,;	A	ENSG00000144583	ENST00000273067	Transcript	synonymous_variant	1962	195	65	H	caC/caT	COSM3380032	.	.	-1	MARCH4	HGNC	29269	protein_coding	YES	CCDS33376.1	ENSP00000273067	MARH4_HUMAN	.	UPI00001C1DB9	.	.	.	1/4	.	hmmpanther:PTHR23012:SF51,hmmpanther:PTHR23012	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCCGTGCAT	.	5	ESCA
MEIS1	0	.	GRCh37	2	66796256	66796256	+	3'UTR	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*16C>T	.	.	ENST00000272369	12/13	85	67	18	82	82	0	MEIS1,3_prime_UTR_variant,,ENST00000495021,;MEIS1,3_prime_UTR_variant,,ENST00000488550,;MEIS1,3_prime_UTR_variant,,ENST00000272369,;MEIS1,intron_variant,,ENST00000444274,;MEIS1,intron_variant,,ENST00000407092,;MEIS1,intron_variant,,ENST00000398506,;MEIS1,downstream_gene_variant,,ENST00000450027,;MEIS1,downstream_gene_variant,,ENST00000606455,;MEIS1,downstream_gene_variant,,ENST00000560281,;AC007392.3,upstream_gene_variant,,ENST00000433396,;MEIS1,non_coding_transcript_exon_variant,,ENST00000409517,;MEIS1,intron_variant,,ENST00000542964,;MEIS1,downstream_gene_variant,,ENST00000475239,;	T	ENSG00000143995	ENST00000272369	Transcript	3_prime_UTR_variant	1646	.	.	.	.	.	.	.	1	MEIS1	HGNC	7000	protein_coding	YES	CCDS46309.1	ENSP00000272369	MEIS1_HUMAN	Q8IZZ2_HUMAN,Q53RD5_HUMAN,Q53R57_HUMAN	UPI000000DA5A	.	.	.	12/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTAACCAATC	.	5	ESCA
FABP1	0	.	GRCh37	2	88427516	88427516	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21C>T	p.%3D	p.Y7Y	ENST00000295834	1/4	58	36	22	49	49	0	FABP1,synonymous_variant,p.%3D,ENST00000295834,;FABP1,synonymous_variant,p.%3D,ENST00000393750,;FABP1,non_coding_transcript_exon_variant,,ENST00000495375,;FABP1,non_coding_transcript_exon_variant,,ENST00000472846,;	A	ENSG00000163586	ENST00000295834	Transcript	synonymous_variant	120	21	7	Y	taC/taT	.	.	.	-1	FABP1	HGNC	3555	protein_coding	YES	CCDS2001.1	ENSP00000295834	FABPL_HUMAN	Q6FGL7_HUMAN	UPI00000527AB	.	.	.	1/4	.	Prints_domain:PR00178,Superfamily_domains:SSF50814,Pfam_domain:PF14651,Gene3D:2.40.128.20,PROSITE_patterns:PS00214,hmmpanther:PTHR11955:SF73,hmmpanther:PTHR11955	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTGGTACTT	.	5	ESCA
PLA1A	0	.	GRCh37	3	119325794	119325794	+	Missense_Mutation	SNP	G	G	A	rs141940849	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247G>A	p.Gly83Arg	p.G83R	ENST00000273371	2/11	24	10	14	40	40	0	PLA1A,missense_variant,p.Gly67Arg,ENST00000494440,;PLA1A,missense_variant,p.Gly83Arg,ENST00000273371,;PLA1A,missense_variant,p.Gly83Arg,ENST00000495992,;PLA1A,intron_variant,,ENST00000488919,;PLA1A,upstream_gene_variant,,ENST00000475963,;PLA1A,non_coding_transcript_exon_variant,,ENST00000472126,;	A	ENSG00000144837	ENST00000273371	Transcript	missense_variant	319	247	83	G/R	Gga/Aga	rs141940849	.	.	1	PLA1A	HGNC	17661	protein_coding	YES	CCDS2991.1	ENSP00000273371	PLA1A_HUMAN	.	UPI0000073F97	.	tolerated(0.16)	benign(0.114)	2/11	.	Prints_domain:PR00821,Superfamily_domains:SSF53474,PIRSF_domain:PIRSF000865,Gene3D:3.40.50.1820,Pfam_domain:PF00151,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF86	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTGGGAACC	byCluster	5	ESCA
GOLGB1	0	.	GRCh37	3	121437303	121437303	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817T>G	p.Leu273Val	p.L273V	ENST00000393667	8/22	57	30	27	66	66	0	GOLGB1,missense_variant,p.Leu273Val,ENST00000393667,;GOLGB1,missense_variant,p.Leu268Val,ENST00000340645,;GOLGB1,missense_variant,p.Leu232Val,ENST00000494517,;GOLGB1,missense_variant,p.Leu139Val,ENST00000489400,;GOLGB1,3_prime_UTR_variant,,ENST00000482512,;	C	ENSG00000173230	ENST00000393667	Transcript	missense_variant	928	817	273	L/V	Ttg/Gtg	.	.	.	-1	GOLGB1	HGNC	4429	protein_coding	YES	CCDS58847.1	ENSP00000377275	GOGB1_HUMAN	C9J8Q0_HUMAN	UPI0001AE7645	.	.	probably_damaging(0.999)	8/22	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18887,hmmpanther:PTHR18887:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACCAAGGATT	.	5	ESCA
TOPBP1	0	.	GRCh37	3	133320091	133320091	+	3'UTR	SNP	C	C	T	rs555920620	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3G>A	.	.	ENST00000260810	28/28	34	27	6	49	49	0	TOPBP1,3_prime_UTR_variant,,ENST00000260810,;TOPBP1,intron_variant,,ENST00000503464,;TOPBP1,intron_variant,,ENST00000503338,;	T	ENSG00000163781	ENST00000260810	Transcript	3_prime_UTR_variant	4704	.	.	.	.	rs555920620	.	.	-1	TOPBP1	HGNC	17008	protein_coding	YES	CCDS46919.1	ENSP00000260810	TOPB1_HUMAN	A0AV47_HUMAN	UPI000020A292	.	.	.	28/28	.	.	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	AGATGCGATTA	by1000G	4	ESCA
SLITRK3	0	.	GRCh37	3	164907746	164907746	+	Silent	SNP	A	A	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.873T>A	p.%3D	p.A291A	ENST00000475390	2/2	49	45	4	63	63	0	SLITRK3,synonymous_variant,p.%3D,ENST00000475390,;SLITRK3,synonymous_variant,p.%3D,ENST00000241274,;SLITRK3,downstream_gene_variant,,ENST00000497724,;	T	ENSG00000121871	ENST00000475390	Transcript	synonymous_variant	1317	873	291	A	gcT/gcA	.	.	.	-1	SLITRK3	HGNC	23501	protein_coding	YES	CCDS3197.1	ENSP00000420091	SLIK3_HUMAN	C9K0R4_HUMAN	UPI000004F259	.	.	.	2/2	.	hmmpanther:PTHR24373:SF14,hmmpanther:PTHR24373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AAACTAGCCTC	.	2	ESCA
KLHL6	0	.	GRCh37	3	183273443	183273443	+	5'UTR	SNP	G	G	A	rs755964120	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-2C>T	.	.	ENST00000341319	1/7	77	61	16	39	39	0	KLHL6,5_prime_UTR_variant,,ENST00000341319,;KLHL6-AS1,downstream_gene_variant,,ENST00000491676,;KLHL6,non_coding_transcript_exon_variant,,ENST00000489245,;KLHL6,upstream_gene_variant,,ENST00000468734,;	A	ENSG00000172578	ENST00000341319	Transcript	5_prime_UTR_variant	35	.	.	.	.	rs755964120	.	.	-1	KLHL6	HGNC	18653	protein_coding	YES	CCDS3245.2	ENSP00000341342	KLHL6_HUMAN	.	UPI0000169CB9	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATCGAGACT	byFrequency	5	ESCA
CMC1	0	.	GRCh37	3	28361202	28361202	+	3'UTR	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*82A>G	.	.	ENST00000466830	4/4	25	15	10	21	21	0	CMC1,3_prime_UTR_variant,,ENST00000423894,;CMC1,3_prime_UTR_variant,,ENST00000466830,;CMC1,3_prime_UTR_variant,,ENST00000418849,;AZI2,intron_variant,,ENST00000429369,;AZI2,downstream_gene_variant,,ENST00000479665,;CMC1,non_coding_transcript_exon_variant,,ENST00000495428,;CMC1,non_coding_transcript_exon_variant,,ENST00000469102,;CMC1,non_coding_transcript_exon_variant,,ENST00000467644,;CMC1,non_coding_transcript_exon_variant,,ENST00000482499,;AZI2,downstream_gene_variant,,ENST00000295748,;CMC1,downstream_gene_variant,,ENST00000468330,;CMC1,3_prime_UTR_variant,,ENST00000334841,;CMC1,non_coding_transcript_exon_variant,,ENST00000396610,;CMC1,non_coding_transcript_exon_variant,,ENST00000477739,;AZI2,downstream_gene_variant,,ENST00000476174,;AZI2,downstream_gene_variant,,ENST00000492044,;	G	ENSG00000187118	ENST00000466830	Transcript	3_prime_UTR_variant	602	.	.	.	.	.	.	.	1	CMC1	HGNC	28783	protein_coding	YES	CCDS33722.1	ENSP00000418348	COXM1_HUMAN	.	UPI0000161ABD	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATATATGTTT	.	5	ESCA
SCN11A	0	.	GRCh37	3	38924792	38924792	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3151C>A	p.Gln1051Lys	p.Q1051K	ENST00000302328	18/26	43	25	17	63	63	0	SCN11A,missense_variant,p.Gln1051Lys,ENST00000450244,;SCN11A,missense_variant,p.Gln1051Lys,ENST00000302328,;SCN11A,missense_variant,p.Gln1051Lys,ENST00000444237,;SCN11A,missense_variant,p.Gln1013Lys,ENST00000456224,;	T	ENSG00000168356	ENST00000302328	Transcript	missense_variant	3350	3151	1051	Q/K	Caa/Aaa	.	.	.	-1	SCN11A	HGNC	10583	protein_coding	YES	CCDS33737.1	ENSP00000307599	SCNBA_HUMAN	.	UPI000006CCD7	.	tolerated(0.56)	possibly_damaging(0.669)	18/26	.	hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF22,Gene3D:1.20.120.350,Pfam_domain:PF06512	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTTGGTAGC	.	5	ESCA
P4HTM	0	.	GRCh37	3	49041623	49041623	+	Missense_Mutation	SNP	C	C	T	rs199611252	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.817C>T	p.Arg273Trp	p.R273W	ENST00000343546	5/9	24	19	5	20	20	0	P4HTM,missense_variant,p.Arg273Trp,ENST00000383729,;P4HTM,missense_variant,p.Arg273Trp,ENST00000343546,;P4HTM,missense_variant,p.Arg65Trp,ENST00000472796,;P4HTM,missense_variant,p.Arg203Trp,ENST00000444213,;P4HTM,intron_variant,,ENST00000491739,;P4HTM,downstream_gene_variant,,ENST00000475629,;WDR6,upstream_gene_variant,,ENST00000491365,;WDR6,upstream_gene_variant,,ENST00000419837,;WDR6,upstream_gene_variant,,ENST00000395474,;WDR6,upstream_gene_variant,,ENST00000608424,;WDR6,upstream_gene_variant,,ENST00000448293,;WDR6,upstream_gene_variant,,ENST00000415265,;WDR6,upstream_gene_variant,,ENST00000429900,;WDR6,upstream_gene_variant,,ENST00000489427,;WDR6,upstream_gene_variant,,ENST00000438660,;P4HTM,non_coding_transcript_exon_variant,,ENST00000468374,;P4HTM,downstream_gene_variant,,ENST00000486817,;WDR6,upstream_gene_variant,,ENST00000489684,;WDR6,upstream_gene_variant,,ENST00000461687,;WDR6,upstream_gene_variant,,ENST00000472878,;P4HTM,non_coding_transcript_exon_variant,,ENST00000484115,;P4HTM,non_coding_transcript_exon_variant,,ENST00000472301,;WDR6,upstream_gene_variant,,ENST00000452875,;WDR6,upstream_gene_variant,,ENST00000471162,;WDR6,upstream_gene_variant,,ENST00000488572,;WDR6,upstream_gene_variant,,ENST00000462064,;WDR6,upstream_gene_variant,,ENST00000473238,;WDR6,upstream_gene_variant,,ENST00000420783,;P4HTM,downstream_gene_variant,,ENST00000485210,;	T	ENSG00000178467	ENST00000343546	Transcript	missense_variant	1185	817	273	R/W	Cgg/Tgg	rs199611252	.	.	1	P4HTM	HGNC	28858	protein_coding	YES	CCDS2781.2	ENSP00000341422	P4HTM_HUMAN	.	UPI0000209C68	.	deleterious(0)	probably_damaging(0.998)	5/9	.	hmmpanther:PTHR10869,Gene3D:1.10.238.10,SMART_domains:SM00702,Superfamily_domains:SSF47473	T:0.0004	T:0	T:0	.	T:0	T:0.002	T:0	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	TGGTGCGGAAC	byFrequency|byCluster|by1000G	3	ESCA
FHIT	0	.	GRCh37	3	59997128	59997128	+	Splice_Site	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250-2A>G	.	p.X84_splice	ENST00000468189	.	48	33	15	70	70	0	FHIT,splice_acceptor_variant,,ENST00000476844,;FHIT,splice_acceptor_variant,,ENST00000468189,;FHIT,splice_acceptor_variant,,ENST00000492590,;FHIT,splice_acceptor_variant,,ENST00000341848,;FHIT,downstream_gene_variant,,ENST00000488467,;FHIT,splice_acceptor_variant,,ENST00000466788,;	C	ENSG00000189283	ENST00000468189	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	FHIT	HGNC	3701	protein_coding	YES	CCDS2894.1	ENSP00000417480	FHIT_HUMAN	Q71VB2_HUMAN,Q45QG9_HUMAN,Q1WAB3_HUMAN,Q194U8_HUMAN,E9PBZ0_HUMAN,A2IAT6_HUMAN,A2IAS9_HUMAN	UPI000000160B	.	.	.	.	6/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCTAGAAG	.	5	ESCA
NPY2R	0	.	GRCh37	4	156138173	156138173	+	3'UTR	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1936A>G	.	.	ENST00000329476	2/2	37	33	4	69	69	0	NPY2R,3_prime_UTR_variant,,ENST00000506608,;NPY2R,3_prime_UTR_variant,,ENST00000329476,;	G	ENSG00000185149	ENST00000329476	Transcript	3_prime_UTR_variant	3571	.	.	.	.	.	.	.	1	NPY2R	HGNC	7957	protein_coding	YES	CCDS3791.1	ENSP00000332591	NPY2R_HUMAN	.	UPI000003B342	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CATTAATAAAA	.	3	ESCA
ARAP2	0	.	GRCh37	4	36230983	36230983	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.126T>A	p.Asn42Lys	p.N42K	ENST00000303965	2/33	29	24	5	51	51	0	ARAP2,missense_variant,p.Asn42Lys,ENST00000506189,;ARAP2,missense_variant,p.Asn42Lys,ENST00000303965,;ARAP2,non_coding_transcript_exon_variant,,ENST00000508066,;	T	ENSG00000047365	ENST00000303965	Transcript	missense_variant	616	126	42	N/K	aaT/aaA	.	.	.	-1	ARAP2	HGNC	16924	protein_coding	YES	CCDS3441.1	ENSP00000302895	ARAP2_HUMAN	D6RAD6_HUMAN	UPI000013E917	.	deleterious(0.01)	benign(0.222)	2/33	.	PROSITE_profiles:PS50105,Pfam_domain:PF00536,Gene3D:1.10.150.50,SMART_domains:SM00454,Superfamily_domains:SSF47769	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTCATTTAT	.	5	ESCA
ATP8A1	0	.	GRCh37	4	42487656	42487656	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2181T>A	p.Cys727Ter	p.C727*	ENST00000381668	25/37	59	51	8	45	44	1	ATP8A1,stop_gained,p.Cys727Ter,ENST00000381668,;ATP8A1,stop_gained,p.Cys712Ter,ENST00000264449,;ATP8A1,intron_variant,,ENST00000514372,;ATP8A1,upstream_gene_variant,,ENST00000506602,;	T	ENSG00000124406	ENST00000381668	Transcript	stop_gained	2413	2181	727	C/*	tgT/tgA	.	.	.	-1	ATP8A1	HGNC	13531	protein_coding	YES	CCDS3466.1	ENSP00000371084	AT8A1_HUMAN	H0YAJ4_HUMAN	UPI0000125063	.	.	.	25/37	.	hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF56,TIGRFAM_domain:TIGR01652,Pfam_domain:PF12710	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GTAGTACAGTG	.	2	ESCA
HSD17B13	0	.	GRCh37	4	88239522	88239522	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277G>C	p.Asp93His	p.D93H	ENST00000328546	2/7	43	38	5	42	42	0	HSD17B13,missense_variant,p.Asp93His,ENST00000328546,;HSD17B13,intron_variant,,ENST00000302219,;RP11-529H2.2,non_coding_transcript_exon_variant,,ENST00000508163,;	G	ENSG00000170509	ENST00000328546	Transcript	missense_variant	342	277	93	D/H	Gac/Cac	.	.	.	-1	HSD17B13	HGNC	18685	protein_coding	YES	CCDS3618.1	ENSP00000333300	DHB13_HUMAN	.	UPI00000350AE	.	deleterious(0)	probably_damaging(0.994)	2/7	.	Superfamily_domains:SSF51735,PIRSF_domain:PIRSF000126,Pfam_domain:PF00106,Gene3D:3.40.50.720,hmmpanther:PTHR24316,hmmpanther:PTHR24316:SF247	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGTCTACCA	.	2	ESCA
FBN2	0	.	GRCh37	5	127728955	127728955	+	Silent	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1338C>A	p.%3D	p.G446G	ENST00000508053	16/71	44	32	12	52	52	0	FBN2,synonymous_variant,p.%3D,ENST00000262464,;FBN2,synonymous_variant,p.%3D,ENST00000508053,;FBN2,synonymous_variant,p.%3D,ENST00000508989,;	T	ENSG00000138829	ENST00000508053	Transcript	synonymous_variant	2313	1338	446	G	ggC/ggA	.	.	.	-1	FBN2	HGNC	3604	protein_coding	YES	CCDS34222.1	ENSP00000424571	FBN2_HUMAN	.	UPI0000519468	.	.	.	16/71	.	Low_complexity_(Seg):seg,PIRSF_domain:PIRSF036312,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTGCCACT	.	5	ESCA
PCDHB7	0	.	GRCh37	5	140555366	140555366	+	3'UTR	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*568A>G	.	.	ENST00000231137	1/1	23	18	5	44	44	0	PCDHB7,3_prime_UTR_variant,,ENST00000231137,;PCDHB8,upstream_gene_variant,,ENST00000239444,;	G	ENSG00000113212	ENST00000231137	Transcript	3_prime_UTR_variant	3124	.	.	.	.	.	.	.	1	PCDHB7	HGNC	8692	protein_coding	YES	CCDS4249.1	ENSP00000231137	PCDB7_HUMAN	.	UPI00001273E3	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTCAGTGAC	.	5	ESCA
PCDHB13	0	.	GRCh37	5	140595492	140595492	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1797C>T	p.%3D	p.N599N	ENST00000341948	1/1	33	23	10	37	37	0	PCDHB13,synonymous_variant,p.%3D,ENST00000341948,;PCDHB12,downstream_gene_variant,,ENST00000541609,;PCDHB12,downstream_gene_variant,,ENST00000239450,;	T	ENSG00000187372	ENST00000341948	Transcript	synonymous_variant	1984	1797	599	N	aaC/aaT	.	.	.	1	PCDHB13	HGNC	8684	protein_coding	YES	CCDS4255.1	ENSP00000345491	PCDBD_HUMAN	.	UPI0000047816	.	.	.	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CAGAACGCCTG	.	3	ESCA
PCDHB14	0	.	GRCh37	5	140603871	140603871	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.794C>T	p.Ser265Leu	p.S265L	ENST00000239449	1/1	62	47	14	72	72	0	PCDHB14,missense_variant,p.Ser265Leu,ENST00000239449,;PCDHB14,missense_variant,p.Ser112Leu,ENST00000515856,;	T	ENSG00000120327	ENST00000239449	Transcript	missense_variant	794	794	265	S/L	tCa/tTa	.	.	.	1	PCDHB14	HGNC	8685	protein_coding	YES	CCDS4256.1	ENSP00000239449	PCDBE_HUMAN	B4DPE2_HUMAN	UPI00001273E7	.	tolerated_low_confidence(0.07)	possibly_damaging(0.858)	1/1	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCAGCTA	.	5	ESCA
GRIA1	0	.	GRCh37	5	153144164	153144188	+	Frame_Shift_Del	DEL	AAGCAGGATCTACTAAGGAGTTCTT	AAGCAGGATCTACTAAGGAGTTCTT	-	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	AAGCAGGATCTACTAAGGAGTTCTT	AAGCAGGATCTACTAAGGAGTTCTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2024_2048delAAGCAGGATCTACTAAGGAGTTCTT	p.Glu675AlafsTer16	p.E675Afs*16	ENST00000518783	12/16	59	54	5	77	77	0	GRIA1,frameshift_variant,p.Glu585AlafsTer16,ENST00000518142,;GRIA1,frameshift_variant,p.Glu675AlafsTer16,ENST00000518783,;GRIA1,frameshift_variant,p.Glu596AlafsTer16,ENST00000521843,;GRIA1,frameshift_variant,p.Glu665AlafsTer16,ENST00000285900,;GRIA1,frameshift_variant,p.Glu675AlafsTer16,ENST00000448073,;GRIA1,frameshift_variant,p.Glu665AlafsTer16,ENST00000340592,;	-	ENSG00000155511	ENST00000518783	Transcript	frameshift_variant	2051-2075	2024-2048	675-683	EAGSTKEFF/X	gAAGCAGGATCTACTAAGGAGTTCTTc/gc	.	.	.	1	GRIA1	HGNC	4571	protein_coding	YES	CCDS58987.1	ENSP00000428994	GRIA1_HUMAN	.	UPI0001E8F433	.	.	.	12/16	.	Superfamily_domains:SSF53850,SMART_domains:SM00079,Pfam_domain:PF00060,Gene3D:1.10.287.70,Pfam_domain:PF00497,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CGCTGGAAGCAGGATCTACTAAGGAGTTCTTCAGGG	.	2	ESCA
BASP1	0	.	GRCh37	5	17216508	17216508	+	5'Flank	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000322611	.	38	30	8	31	31	0	BASP1,intron_variant,,ENST00000606445,;BASP1,upstream_gene_variant,,ENST00000322611,;AC091878.1,non_coding_transcript_exon_variant,,ENST00000399760,;	A	ENSG00000176788	ENST00000322611	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1161	1	BASP1	HGNC	957	protein_coding	YES	CCDS3888.1	ENSP00000319281	BASP1_HUMAN	U3KQP0_HUMAN	UPI0000140E98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCACGTTACG	.	5	ESCA
FLT4	0	.	GRCh37	5	180048054	180048054	+	Intron	SNP	G	G	A	rs778740732	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2168-47C>T	.	.	ENST00000261937	.	28	22	6	45	45	0	FLT4,intron_variant,,ENST00000502649,;FLT4,intron_variant,,ENST00000261937,;FLT4,intron_variant,,ENST00000393347,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,non_coding_transcript_exon_variant,,ENST00000424276,;FLT4,intron_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,;	A	ENSG00000037280	ENST00000261937	Transcript	intron_variant	.	.	.	.	.	rs778740732	.	.	-1	FLT4	HGNC	3767	protein_coding	YES	CCDS4457.1	ENSP00000261937	VGFR3_HUMAN	D6RFF2_HUMAN	UPI00001488E7	.	.	.	.	14/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATCGTCGGC	.	5	ESCA
ADCY2	0	.	GRCh37	5	7817053	7817053	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2958C>T	p.%3D	p.A986A	ENST00000338316	23/25	137	128	9	95	95	0	ADCY2,synonymous_variant,p.%3D,ENST00000338316,;ADCY2,synonymous_variant,p.%3D,ENST00000537121,;ADCY2,downstream_gene_variant,,ENST00000382531,;ADCY2,3_prime_UTR_variant,,ENST00000493243,;ADCY2,non_coding_transcript_exon_variant,,ENST00000489501,;	T	ENSG00000078295	ENST00000338316	Transcript	synonymous_variant	3047	2958	986	A	gcC/gcT	.	.	.	1	ADCY2	HGNC	233	protein_coding	YES	CCDS3872.2	ENSP00000342952	ADCY2_HUMAN	Q7RTV6_HUMAN,Q71UM8_HUMAN,D6REB8_HUMAN	UPI000066D9F2	.	.	.	23/25	.	Superfamily_domains:SSF55073,SMART_domains:SM00044,Pfam_domain:PF00211,Gene3D:3.30.70.1230,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,PROSITE_profiles:PS50125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATGCCATCAA	.	2	ESCA
REV3L	0	.	GRCh37	6	111694997	111694997	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4561G>T	p.Gly1521Cys	p.G1521C	ENST00000358835	14/33	41	29	12	57	56	1	REV3L,missense_variant,p.Gly1443Cys,ENST00000435970,;REV3L,missense_variant,p.Gly1521Cys,ENST00000358835,;REV3L,missense_variant,p.Gly1521Cys,ENST00000368802,;REV3L,missense_variant,p.Gly1521Cys,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000434009,;REV3L,3_prime_UTR_variant,,ENST00000422377,;	A	ENSG00000009413	ENST00000358835	Transcript	missense_variant	5016	4561	1521	G/C	Ggt/Tgt	.	.	.	-1	REV3L	HGNC	9968	protein_coding	YES	CCDS5091.2	ENSP00000351697	DPOLZ_HUMAN	Q9UID5_HUMAN,C4TNX2_HUMAN,C4TNX1_HUMAN,C4TNX0_HUMAN,C4B7Q4_HUMAN	UPI0000140023	.	tolerated(0.06)	possibly_damaging(0.503)	14/33	.	hmmpanther:PTHR10322:SF16,hmmpanther:PTHR10322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTCACCAAATG	.	4	ESCA
NEDD9	0	.	GRCh37	6	11190694	11190694	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1408G>A	p.Val470Ile	p.V470I	ENST00000379446	5/7	43	28	14	65	65	0	NEDD9,missense_variant,p.Val470Ile,ENST00000504387,;NEDD9,missense_variant,p.Val470Ile,ENST00000379446,;RP3-510L9.1,intron_variant,,ENST00000500636,;NEDD9,3_prime_UTR_variant,,ENST00000448183,;NEDD9,downstream_gene_variant,,ENST00000505589,;	T	ENSG00000111859	ENST00000379446	Transcript	missense_variant	1575	1408	470	V/I	Gtt/Att	.	.	.	-1	NEDD9	HGNC	7733	protein_coding	YES	CCDS4520.1	ENSP00000368759	CASL_HUMAN	D6RGD7_HUMAN	UPI000000D981	.	tolerated(0.1)	benign(0.027)	5/7	.	Pfam_domain:PF08824,hmmpanther:PTHR10654:SF6,hmmpanther:PTHR10654	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAACAGCTC	.	5	ESCA
BCLAF1	0	.	GRCh37	6	136596728	136596728	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1794C>T	p.%3D	p.S598S	ENST00000531224	6/13	46	40	6	77	77	0	BCLAF1,synonymous_variant,p.%3D,ENST00000529826,;BCLAF1,synonymous_variant,p.%3D,ENST00000527536,;BCLAF1,synonymous_variant,p.%3D,ENST00000392348,;BCLAF1,synonymous_variant,p.%3D,ENST00000530767,;BCLAF1,synonymous_variant,p.%3D,ENST00000531224,;BCLAF1,synonymous_variant,p.%3D,ENST00000353331,;BCLAF1,synonymous_variant,p.%3D,ENST00000527759,;BCLAF1,synonymous_variant,p.%3D,ENST00000527613,;BCLAF1,synonymous_variant,p.%3D,ENST00000534269,;BCLAF1,synonymous_variant,p.%3D,ENST00000530429,;BCLAF1,synonymous_variant,p.%3D,ENST00000532384,;BCLAF1,3_prime_UTR_variant,,ENST00000533621,;BCLAF1,upstream_gene_variant,,ENST00000476194,;BCLAF1,upstream_gene_variant,,ENST00000532076,;BCLAF1,upstream_gene_variant,,ENST00000534792,;BCLAF1,downstream_gene_variant,,ENST00000528229,;	A	ENSG00000029363	ENST00000531224	Transcript	synonymous_variant	2047	1794	598	S	agC/agT	.	.	.	-1	BCLAF1	HGNC	16863	protein_coding	YES	CCDS5177.1	ENSP00000435210	BCLF1_HUMAN	B0AZU3_HUMAN	UPI000006FCE7	.	.	.	6/13	.	Pfam_domain:PF15440,hmmpanther:PTHR15268,hmmpanther:PTHR15268:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTTTGCTGGC	.	5	ESCA
AGPAT4	0	.	GRCh37	6	161653331	161653331	+	5'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-86C>T	.	.	ENST00000320285	2/9	18	9	8	11	11	0	AGPAT4,5_prime_UTR_variant,,ENST00000366911,;AGPAT4,5_prime_UTR_variant,,ENST00000457520,;AGPAT4,5_prime_UTR_variant,,ENST00000366905,;AGPAT4,5_prime_UTR_variant,,ENST00000320285,;AGPAT4,5_prime_UTR_variant,,ENST00000366908,;AGPAT4,intron_variant,,ENST00000366906,;AGPAT4,upstream_gene_variant,,ENST00000436279,;	A	ENSG00000026652	ENST00000320285	Transcript	5_prime_UTR_variant	128	.	.	.	.	.	.	.	-1	AGPAT4	HGNC	20885	protein_coding	YES	CCDS5280.1	ENSP00000314036	PLCD_HUMAN	Q6PJN9_HUMAN	UPI0000035BB6	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAGGCGTCT	.	5	ESCA
OR2J3	0	.	GRCh37	6	29080478	29080478	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811C>G	p.Gln271Glu	p.Q271E	ENST00000377169	1/1	24	18	5	32	32	0	OR2J3,missense_variant,p.Gln271Glu,ENST00000377169,;	G	ENSG00000204701	ENST00000377169	Transcript	missense_variant	811	811	271	Q/E	Caa/Gaa	.	.	.	1	OR2J3	HGNC	8261	protein_coding	YES	CCDS43433.1	ENSP00000366374	OR2J3_HUMAN	.	UPI000014073A	.	tolerated(0.12)	possibly_damaging(0.492)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF209,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATTCTCAAGAT	.	4	ESCA
TRIM15	0	.	GRCh37	6	30136085	30136085	+	Silent	SNP	C	C	A	.	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486C>A	p.%3D	p.I162I	ENST00000376694	3/7	39	33	5	33	33	0	TRIM15,synonymous_variant,p.%3D,ENST00000376694,;TRIM15,intron_variant,,ENST00000376688,;TRIM15,upstream_gene_variant,,ENST00000433744,;TRIM15,upstream_gene_variant,,ENST00000477944,;	A	ENSG00000204610	ENST00000376694	Transcript	synonymous_variant	955	486	162	I	atC/atA	COSM3430453	.	.	1	TRIM15	HGNC	16284	protein_coding	YES	CCDS4677.1	ENSP00000365884	TRI15_HUMAN	Q5SRL0_HUMAN	UPI0000137066	.	.	.	3/7	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF259	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGATCGAAAG	.	2	ESCA
OPN5	0	.	GRCh37	6	47779443	47779443	+	Silent	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032T>C	p.%3D	p.S344S	ENST00000371211	6/7	31	27	3	30	30	0	OPN5,synonymous_variant,p.%3D,ENST00000489301,;OPN5,synonymous_variant,p.%3D,ENST00000393699,;OPN5,synonymous_variant,p.%3D,ENST00000371211,;OPN5,non_coding_transcript_exon_variant,,ENST00000244799,;	C	ENSG00000124818	ENST00000371211	Transcript	synonymous_variant	1060	1032	344	S	tcT/tcC	.	.	.	1	OPN5	HGNC	19992	protein_coding	YES	CCDS4923.1	ENSP00000360255	OPN5_HUMAN	.	UPI0000223E5B	.	.	.	6/7	.	hmmpanther:PTHR24240:SF0,hmmpanther:PTHR24240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCTTCTGCTGT	.	3	ESCA
DST	0	.	GRCh37	6	56342211	56342211	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.13738A>G	p.Ile4580Val	p.I4580V	ENST00000244364	72/84	82	71	10	77	77	0	DST,missense_variant,p.Ile6668Val,ENST00000446842,;DST,missense_variant,p.Ile4797Val,ENST00000370788,;DST,missense_variant,p.Ile4580Val,ENST00000244364,;DST,missense_variant,p.Ile7172Val,ENST00000370754,;DST,missense_variant,p.Ile6883Val,ENST00000361203,;DST,missense_variant,p.Ile6994Val,ENST00000370769,;DST,missense_variant,p.Ile4906Val,ENST00000421834,;DST,3_prime_UTR_variant,,ENST00000312431,;DST,upstream_gene_variant,,ENST00000523943,;DST,non_coding_transcript_exon_variant,,ENST00000517840,;DST,upstream_gene_variant,,ENST00000492944,;	C	ENSG00000151914	ENST00000244364	Transcript	missense_variant	13946	13738	4580	I/V	Atc/Gtc	.	.	.	-1	DST	HGNC	1090	protein_coding	YES	CCDS47443.1	ENSP00000244364	DYST_HUMAN	Q86T18_HUMAN	UPI00001C1577	.	.	benign(0.015)	72/84	.	Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGATAGCCA	.	4	ESCA
COL9A1	0	.	GRCh37	6	70926288	70926288	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*312A>G	.	.	ENST00000357250	38/38	49	43	6	68	68	0	COL9A1,3_prime_UTR_variant,,ENST00000370499,;COL9A1,3_prime_UTR_variant,,ENST00000320755,;COL9A1,3_prime_UTR_variant,,ENST00000357250,;COL9A1,non_coding_transcript_exon_variant,,ENST00000486080,;COL9A1,downstream_gene_variant,,ENST00000489611,;	C	ENSG00000112280	ENST00000357250	Transcript	3_prime_UTR_variant	3237	.	.	.	.	.	.	.	-1	COL9A1	HGNC	2217	protein_coding	YES	CCDS4971.1	ENSP00000349790	CO9A1_HUMAN	.	UPI000020D14B	.	.	.	38/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATAGGTATAGC	.	4	ESCA
UFL1	0	.	GRCh37	6	96986512	96986512	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.984G>A	p.%3D	p.L328L	ENST00000369278	10/19	13	7	6	39	39	0	UFL1,synonymous_variant,p.%3D,ENST00000369278,;	A	ENSG00000014123	ENST00000369278	Transcript	synonymous_variant	1050	984	328	L	ctG/ctA	.	.	.	1	UFL1	HGNC	23039	protein_coding	YES	CCDS5034.1	ENSP00000358283	UFL1_HUMAN	B7ZAY8_HUMAN	UPI0000072D61	.	.	.	10/19	.	hmmpanther:PTHR31057,hmmpanther:PTHR31057:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	CCTCTGCTACC	.	4	ESCA
COG5	0	.	GRCh37	7	106888850	106888850	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1937A>G	p.Asp646Gly	p.D646G	ENST00000297135	17/22	98	85	12	88	88	0	COG5,missense_variant,p.Asp625Gly,ENST00000347053,;COG5,missense_variant,p.Asp646Gly,ENST00000393603,;COG5,missense_variant,p.Asp646Gly,ENST00000297135,;COG5,non_coding_transcript_exon_variant,,ENST00000468350,;COG5,non_coding_transcript_exon_variant,,ENST00000462342,;COG5,non_coding_transcript_exon_variant,,ENST00000464542,;	C	ENSG00000164597	ENST00000297135	Transcript	missense_variant	2462	1937	646	D/G	gAc/gGc	.	.	.	-1	COG5	HGNC	14857	protein_coding	YES	CCDS5742.1	ENSP00000297135	COG5_HUMAN	U3KQU7_HUMAN,B3KMW0_HUMAN	UPI0000246D05	.	deleterious(0)	possibly_damaging(0.868)	17/22	.	hmmpanther:PTHR13228:SF3,hmmpanther:PTHR13228	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAAAGTCTTCT	.	3	ESCA
WDR91	0	.	GRCh37	7	134882799	134882799	+	Silent	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.996C>A	p.%3D	p.R332R	ENST00000354475	7/15	38	29	9	47	47	0	WDR91,synonymous_variant,p.%3D,ENST00000354475,;WDR91,synonymous_variant,p.%3D,ENST00000344400,;WDR91,synonymous_variant,p.%3D,ENST00000423565,;AC009542.2,upstream_gene_variant,,ENST00000595902,;AC009542.2,upstream_gene_variant,,ENST00000412549,;WDR91,non_coding_transcript_exon_variant,,ENST00000485942,;WDR91,upstream_gene_variant,,ENST00000476775,;WDR91,non_coding_transcript_exon_variant,,ENST00000466182,;WDR91,upstream_gene_variant,,ENST00000462707,;WDR91,upstream_gene_variant,,ENST00000497853,;WDR91,upstream_gene_variant,,ENST00000474411,;WDR91,upstream_gene_variant,,ENST00000479698,;	T	ENSG00000105875	ENST00000354475	Transcript	synonymous_variant	1028	996	332	R	cgC/cgA	.	.	.	-1	WDR91	HGNC	24997	protein_coding	YES	CCDS34758.1	ENSP00000346466	WDR91_HUMAN	.	UPI000006F2DE	.	.	.	7/15	.	hmmpanther:PTHR13083	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGGCGCCG	.	5	ESCA
EPHA1	0	.	GRCh37	7	143088289	143088290	+	3'UTR	INS	-	-	AT	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*259_*260dupAT	.	.	ENST00000275815	18/18	44	33	11	43	43	0	EPHA1,3_prime_UTR_variant,,ENST00000275815,;ZYX,downstream_gene_variant,,ENST00000392910,;ZYX,downstream_gene_variant,,ENST00000322764,;ZYX,downstream_gene_variant,,ENST00000354434,;ZYX,downstream_gene_variant,,ENST00000449423,;ZYX,downstream_gene_variant,,ENST00000446634,;EPHA1,non_coding_transcript_exon_variant,,ENST00000458129,;EPHA1,downstream_gene_variant,,ENST00000488068,;ZYX,downstream_gene_variant,,ENST00000436448,;EPHA1,downstream_gene_variant,,ENST00000494989,;EPHA1,downstream_gene_variant,,ENST00000465208,;ZYX,downstream_gene_variant,,ENST00000497119,;	AT	ENSG00000146904	ENST00000275815	Transcript	3_prime_UTR_variant	3278-3279	.	.	.	.	.	.	.	-1	EPHA1	HGNC	3385	protein_coding	YES	CCDS5884.1	ENSP00000275815	EPHA1_HUMAN	.	UPI000013DA82	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ACAAAAATATA	.	2	ESCA
RARRES2	0	.	GRCh37	7	150035455	150035455	+	3'UTR	SNP	C	C	T	rs754733189	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*84G>A	.	.	ENST00000466675	5/5	134	108	26	98	98	0	RARRES2,missense_variant,p.Arg150His,ENST00000467793,;RARRES2,3_prime_UTR_variant,,ENST00000223271,;RARRES2,3_prime_UTR_variant,,ENST00000466675,;LRRC61,downstream_gene_variant,,ENST00000359623,;RARRES2,downstream_gene_variant,,ENST00000482669,;LRRC61,downstream_gene_variant,,ENST00000323078,;LRRC61,downstream_gene_variant,,ENST00000493307,;RP4-584D14.7,upstream_gene_variant,,ENST00000563946,;RARRES2,non_coding_transcript_exon_variant,,ENST00000478771,;	T	ENSG00000106538	ENST00000466675	Transcript	3_prime_UTR_variant	1610	.	.	.	.	rs754733189	.	.	-1	RARRES2	HGNC	9868	protein_coding	YES	CCDS5902.1	ENSP00000418009	RARR2_HUMAN	.	UPI0000136F55	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGAACGGGTT	byFrequency	5	ESCA
UBE3C	0	.	GRCh37	7	156979534	156979534	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1150G>A	p.Gly384Ser	p.G384S	ENST00000348165	10/23	65	50	14	75	75	0	UBE3C,missense_variant,p.Gly341Ser,ENST00000389103,;UBE3C,missense_variant,p.Gly384Ser,ENST00000348165,;	A	ENSG00000009335	ENST00000348165	Transcript	missense_variant	1510	1150	384	G/S	Ggc/Agc	.	.	.	1	UBE3C	HGNC	16803	protein_coding	YES	CCDS34789.1	ENSP00000309198	UBE3C_HUMAN	.	UPI000020E72A	.	tolerated(0.29)	benign(0.003)	10/23	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF85	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGGCAGA	.	5	ESCA
AEBP1	0	.	GRCh37	7	44152676	44152676	+	Silent	SNP	C	C	T	rs748511270	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2656C>T	p.%3D	p.L886L	ENST00000223357	19/21	39	35	4	36	36	0	AEBP1,synonymous_variant,p.%3D,ENST00000223357,;AEBP1,synonymous_variant,p.%3D,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000406581,;POLD2,downstream_gene_variant,,ENST00000223361,;POLD2,downstream_gene_variant,,ENST00000433715,;AEBP1,downstream_gene_variant,,ENST00000455443,;POLD2,downstream_gene_variant,,ENST00000436400,;POLD2,downstream_gene_variant,,ENST00000456038,;POLD2,downstream_gene_variant,,ENST00000452185,;POLD2,downstream_gene_variant,,ENST00000418438,;POLD2,downstream_gene_variant,,ENST00000436844,;MIR4649,downstream_gene_variant,,ENST00000582839,;AEBP1,downstream_gene_variant,,ENST00000454218,;AEBP1,3_prime_UTR_variant,,ENST00000413907,;POLD2,downstream_gene_variant,,ENST00000481104,;POLD2,downstream_gene_variant,,ENST00000463464,;AEBP1,downstream_gene_variant,,ENST00000434445,;POLD2,downstream_gene_variant,,ENST00000496539,;AEBP1,downstream_gene_variant,,ENST00000431035,;POLD2,downstream_gene_variant,,ENST00000467469,;POLD2,downstream_gene_variant,,ENST00000470867,;POLD2,downstream_gene_variant,,ENST00000461116,;POLD2,downstream_gene_variant,,ENST00000464871,;AEBP1,downstream_gene_variant,,ENST00000453052,;POLD2,downstream_gene_variant,,ENST00000489883,;	T	ENSG00000106624	ENST00000223357	Transcript	synonymous_variant	2961	2656	886	L	Ctg/Ttg	rs748511270	.	.	1	AEBP1	HGNC	303	protein_coding	YES	CCDS5476.1	ENSP00000223357	AEBP1_HUMAN	B4DJB3_HUMAN	UPI00000746E2	.	.	.	19/21	.	hmmpanther:PTHR11532:SF48,hmmpanther:PTHR11532,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	GTGAGCTGCCC	byFrequency	2	ESCA
ZNF479	0	.	GRCh37	7	57188226	57188226	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.896G>C	p.Cys299Ser	p.C299S	ENST00000331162	5/5	117	110	7	125	125	0	ZNF479,missense_variant,p.Cys299Ser,ENST00000331162,;	G	ENSG00000185177	ENST00000331162	Transcript	missense_variant	1167	896	299	C/S	tGt/tCt	.	.	.	-1	ZNF479	HGNC	23258	protein_coding	YES	CCDS43590.1	ENSP00000333776	ZN479_HUMAN	I0EZ75_HUMAN	UPI000006E615	.	deleterious(0.01)	probably_damaging(0.999)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF103,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCACATTTG	.	2	ESCA
SEMA3A	0	.	GRCh37	7	83643617	83643617	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.718G>C	p.Asp240His	p.D240H	ENST00000265362	7/17	54	37	17	51	51	0	SEMA3A,missense_variant,p.Asp240His,ENST00000265362,;SEMA3A,missense_variant,p.Asp240His,ENST00000436949,;	G	ENSG00000075213	ENST00000265362	Transcript	missense_variant	1033	718	240	D/H	Gat/Cat	.	.	.	-1	SEMA3A	HGNC	10723	protein_coding	YES	CCDS5599.1	ENSP00000265362	SEM3A_HUMAN	Q86UJ2_HUMAN,Q75MQ2_HUMAN,C9JD25_HUMAN,C9J9C4_HUMAN	UPI0000135A60	.	deleterious(0)	probably_damaging(0.996)	7/17	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF23,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCATCTTCAG	.	5	ESCA
DMTF1	0	.	GRCh37	7	86795900	86795901	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212dupT	p.Ser72IlefsTer11	p.S72Ifs*11	ENST00000394703	6/20	146	120	26	117	117	0	DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000394703,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000434534,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000446796,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000453049,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000394702,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000430405,;DMTF1,frameshift_variant,p.Ser72IlefsTer?,ENST00000432366,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000449088,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000425705,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000413276,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000331242,;DMTF1,5_prime_UTR_variant,,ENST00000414194,;DMTF1,5_prime_UTR_variant,,ENST00000432937,;DMTF1,5_prime_UTR_variant,,ENST00000420131,;DMTF1,intron_variant,,ENST00000411766,;DMTF1,downstream_gene_variant,,ENST00000448598,;DMTF1,downstream_gene_variant,,ENST00000582925,;DMTF1,downstream_gene_variant,,ENST00000428819,;DMTF1,downstream_gene_variant,,ENST00000423590,;DMTF1,downstream_gene_variant,,ENST00000579592,;DMTF1,downstream_gene_variant,,ENST00000414630,;DMTF1,downstream_gene_variant,,ENST00000583833,;DMTF1,downstream_gene_variant,,ENST00000580710,;DMTF1,downstream_gene_variant,,ENST00000584457,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000447863,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000412139,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000579677,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000584619,;DMTF1,frameshift_variant,p.Ser72IlefsTer11,ENST00000547146,;DMTF1,intron_variant,,ENST00000579850,;DMTF1,intron_variant,,ENST00000425406,;	T	ENSG00000135164	ENST00000394703	Transcript	frameshift_variant	774-775	211-212	71	I/IX	ata/aTta	.	.	.	1	DMTF1	HGNC	14603	protein_coding	YES	CCDS5601.1	ENSP00000378193	DMTF1_HUMAN	J3KRC1_HUMAN,D6W5P0_HUMAN,C9K0L9_HUMAN,C9K0K9_HUMAN,C9JZZ6_HUMAN,C9JVQ7_HUMAN,C9JLR5_HUMAN,C9JGT5_HUMAN,C9JFR2_HUMAN,C9JED5_HUMAN,C9J8Y5_HUMAN,C9J4F7_HUMAN,B3KVS2_HUMAN	UPI000006FB78	.	.	.	6/20	.	hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTTGCATATCA	.	3	ESCA
ZNF804B	0	.	GRCh37	7	88962978	88962978	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682C>A	p.His228Asn	p.H228N	ENST00000333190	4/4	27	18	8	33	33	0	ZNF804B,missense_variant,p.His228Asn,ENST00000333190,;	A	ENSG00000182348	ENST00000333190	Transcript	missense_variant	1291	682	228	H/N	Cac/Aac	.	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	tolerated(0.29)	possibly_damaging(0.876)	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTGCACCTA	.	5	ESCA
PRSS51	0	.	GRCh37	8	10355439	10355439	+	RNA	SNP	C	C	T	rs775783959	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.392G>A	.	.	ENST00000523024	3/5	49	36	12	67	67	0	PRSS51,non_coding_transcript_exon_variant,,ENST00000523024,;PRSS51,intron_variant,,ENST00000521149,;	T	ENSG00000253649	ENST00000523024	Transcript	non_coding_transcript_exon_variant	392	.	.	.	.	rs775783959	.	.	-1	PRSS51	HGNC	37321	antisense	YES	.	.	.	.	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTCGTTCC	.	5	ESCA
EXT1	0	.	GRCh37	8	118817064	118817064	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1952A>T	p.Asn651Ile	p.N651I	ENST00000378204	10/11	92	79	13	117	117	0	EXT1,missense_variant,p.Asn651Ile,ENST00000378204,;EXT1,3_prime_UTR_variant,,ENST00000437196,;	A	ENSG00000182197	ENST00000378204	Transcript	missense_variant	2759	1952	651	N/I	aAt/aTt	.	.	.	-1	EXT1	HGNC	3512	protein_coding	YES	CCDS6324.1	ENSP00000367446	EXT1_HUMAN	T2FFJ4_HUMAN,S5Y321_HUMAN,D7RTA7_HUMAN	UPI000012A3A1	.	deleterious(0.01)	probably_damaging(0.973)	10/11	.	Superfamily_domains:SSF53448,Pfam_domain:PF09258,Gene3D:3.90.550.10,hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACAATTGGCC	.	4	ESCA
TMEM65	0	.	GRCh37	8	125326108	125326108	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*93A>G	.	.	ENST00000297632	7/7	41	32	9	41	41	0	TMEM65,3_prime_UTR_variant,,ENST00000297632,;	C	ENSG00000164983	ENST00000297632	Transcript	3_prime_UTR_variant	1351	.	.	.	.	.	.	.	-1	TMEM65	HGNC	25203	protein_coding	YES	CCDS6348.1	ENSP00000297632	TMM65_HUMAN	.	UPI00003675D1	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTATACTGT	.	5	ESCA
ADCY8	0	.	GRCh37	8	132052132	132052132	+	Silent	SNP	G	G	T	.	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448C>A	p.%3D	p.R150R	ENST00000286355	1/18	76	48	27	106	106	0	ADCY8,synonymous_variant,p.%3D,ENST00000286355,;ADCY8,synonymous_variant,p.%3D,ENST00000377928,;	T	ENSG00000155897	ENST00000286355	Transcript	synonymous_variant	2541	448	150	R	Cga/Aga	COSM1454866	.	.	-1	ADCY8	HGNC	239	protein_coding	YES	CCDS6363.1	ENSP00000286355	ADCY8_HUMAN	E5RFR2_HUMAN	UPI000012887C	.	.	.	1/18	.	hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF229	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTCGGTAGC	.	5	ESCA
RNF122	0	.	GRCh37	8	33406939	33406939	+	Silent	SNP	G	G	A	rs777531296	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342C>T	p.%3D	p.A114A	ENST00000256257	5/6	39	32	7	40	40	0	RNF122,synonymous_variant,p.%3D,ENST00000256257,;	A	ENSG00000133874	ENST00000256257	Transcript	synonymous_variant	744	342	114	A	gcC/gcT	rs777531296	.	.	-1	RNF122	HGNC	21147	protein_coding	YES	CCDS6091.1	ENSP00000256257	RN122_HUMAN	.	UPI000013CEFB	.	.	.	5/6	.	Superfamily_domains:SSF57850,SMART_domains:SM00184,Gene3D:3.30.40.10,Pfam_domain:PF13639,hmmpanther:PTHR22766:SF137,hmmpanther:PTHR22766,PROSITE_profiles:PS50089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAAAGGCGTG	byFrequency	5	ESCA
KAT6A	0	.	GRCh37	8	41836217	41836217	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.986G>A	p.Arg329Gln	p.R329Q	ENST00000396930	7/18	60	39	21	90	90	0	KAT6A,missense_variant,p.Arg329Gln,ENST00000396930,;KAT6A,missense_variant,p.Arg329Gln,ENST00000406337,;KAT6A,missense_variant,p.Arg329Gln,ENST00000485568,;KAT6A,missense_variant,p.Arg329Gln,ENST00000265713,;KAT6A,upstream_gene_variant,,ENST00000463961,;KAT6A,upstream_gene_variant,,ENST00000470574,;	T	ENSG00000083168	ENST00000396930	Transcript	missense_variant	1530	986	329	R/Q	cGg/cAg	COSM3900252	.	.	-1	KAT6A	HGNC	13013	protein_coding	YES	CCDS6124.1	ENSP00000380136	KAT6A_HUMAN	A5PKX7_HUMAN	UPI000013D666	.	.	probably_damaging(0.998)	7/18	.	hmmpanther:PTHR10615:SF26,hmmpanther:PTHR10615	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGCCGTTTT	.	5	ESCA
DKK4	0	.	GRCh37	8	42232393	42232393	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301G>A	p.Glu101Lys	p.E101K	ENST00000220812	3/4	46	39	6	71	71	0	DKK4,missense_variant,p.Glu101Lys,ENST00000220812,;POLB,downstream_gene_variant,,ENST00000521492,;POLB,downstream_gene_variant,,ENST00000518579,;POLB,downstream_gene_variant,,ENST00000538005,;POLB,downstream_gene_variant,,ENST00000521290,;POLB,downstream_gene_variant,,ENST00000265421,;POLB,downstream_gene_variant,,ENST00000517393,;POLB,downstream_gene_variant,,ENST00000524208,;POLB,downstream_gene_variant,,ENST00000522610,;POLB,downstream_gene_variant,,ENST00000521418,;	T	ENSG00000104371	ENST00000220812	Transcript	missense_variant	488	301	101	E/K	Gaa/Aaa	.	.	.	-1	DKK4	HGNC	2894	protein_coding	YES	CCDS6130.1	ENSP00000220812	DKK4_HUMAN	.	UPI0000051057	.	tolerated(0.11)	benign(0.412)	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTCTAATA	.	5	ESCA
PCMTD1	0	.	GRCh37	8	52773576	52773576	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136T>C	p.Tyr46His	p.Y46H	ENST00000360540	3/7	33	25	7	38	38	0	PCMTD1,missense_variant,p.Tyr46His,ENST00000522514,;PCMTD1,missense_variant,p.Tyr46His,ENST00000521344,;PCMTD1,missense_variant,p.Tyr46His,ENST00000360540,;PCMTD1,intron_variant,,ENST00000544451,;PCMTD1,intron_variant,,ENST00000519559,;PCMTD1,non_coding_transcript_exon_variant,,ENST00000521046,;PCMTD1,upstream_gene_variant,,ENST00000519975,;	G	ENSG00000168300	ENST00000360540	Transcript	missense_variant	543	136	46	Y/H	Tac/Cac	.	.	.	-1	PCMTD1	HGNC	30483	protein_coding	YES	CCDS6148.1	ENSP00000353739	PCMD1_HUMAN	.	UPI0000047CC0	.	tolerated(0.49)	benign(0.009)	3/7	.	hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF4,Gene3D:3.40.50.150,Pfam_domain:PF01135	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTAGCCTT	.	5	ESCA
TMEM64	0	.	GRCh37	8	91637885	91637885	+	3'UTR	SNP	G	G	A	rs776823600	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*14C>T	.	.	ENST00000458549	3/3	45	41	4	55	55	0	TMEM64,3_prime_UTR_variant,,ENST00000418210,;TMEM64,3_prime_UTR_variant,,ENST00000422900,;TMEM64,3_prime_UTR_variant,,ENST00000458549,;TMEM64,downstream_gene_variant,,ENST00000519519,;	A	ENSG00000180694	ENST00000458549	Transcript	3_prime_UTR_variant	1335	.	.	.	.	rs776823600	.	.	-1	TMEM64	HGNC	25441	protein_coding	YES	CCDS34920.2	ENSP00000414786	TMM64_HUMAN	B3KW24_HUMAN	UPI0000DBEF28	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCACGTATCT	byFrequency	2	ESCA
KIAA0368	0	.	GRCh37	9	114124436	114124436	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5928G>T	p.Trp1976Cys	p.W1976C	ENST00000259335	51/51	17	11	6	40	40	0	KIAA0368,missense_variant,p.Trp1798Cys,ENST00000338205,;KIAA0368,missense_variant,p.Trp1976Cys,ENST00000259335,;KIAA0368,intron_variant,,ENST00000374383,;KIAA0368,intron_variant,,ENST00000374378,;KIAA0368,downstream_gene_variant,,ENST00000465499,;	A	ENSG00000136813	ENST00000259335	Transcript	missense_variant	5928	5928	1976	W/C	tgG/tgT	.	.	.	-1	KIAA0368	HGNC	29020	protein_coding	YES	CCDS48006.1	ENSP00000259335	.	J3KN16_HUMAN	UPI0000DD7F7A	.	tolerated(0.18)	probably_damaging(0.918)	51/51	.	hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF19,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATTCCCACTG	.	2	ESCA
CRAT	0	.	GRCh37	9	131857450	131857450	+	3'UTR	SNP	T	T	A	rs575299367	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*226A>T	.	.	ENST00000318080	14/14	35	20	14	40	40	0	CRAT,3_prime_UTR_variant,,ENST00000318080,;DOLPP1,downstream_gene_variant,,ENST00000406974,;DOLPP1,downstream_gene_variant,,ENST00000540102,;CRAT,downstream_gene_variant,,ENST00000455396,;DOLPP1,downstream_gene_variant,,ENST00000372546,;RP11-247A12.1,upstream_gene_variant,,ENST00000434250,;CRAT,downstream_gene_variant,,ENST00000467343,;DOLPP1,downstream_gene_variant,,ENST00000327812,;CRAT,downstream_gene_variant,,ENST00000458362,;	A	ENSG00000095321	ENST00000318080	Transcript	3_prime_UTR_variant	2402	.	.	.	.	rs575299367	.	.	-1	CRAT	HGNC	2342	protein_coding	YES	CCDS6919.1	ENSP00000315013	CACP_HUMAN	.	UPI000014021A	.	.	.	14/14	.	.	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCTGCACT	by1000G	5	ESCA
IFNA10	0	.	GRCh37	9	21206920	21206920	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.177C>A	p.Phe59Leu	p.F59L	ENST00000357374	1/1	144	109	34	176	175	1	IFNA10,missense_variant,p.Phe59Leu,ENST00000357374,;IFNA7,upstream_gene_variant,,ENST00000239347,;IFNWP18,downstream_gene_variant,,ENST00000437472,;	T	ENSG00000186803	ENST00000357374	Transcript	missense_variant	223	177	59	F/L	ttC/ttA	.	.	.	-1	IFNA10	HGNC	5418	protein_coding	YES	CCDS6499.1	ENSP00000369566	IFN10_HUMAN	Q9UMJ2_HUMAN	UPI0000047765	.	deleterious(0)	possibly_damaging(0.849)	1/1	.	Prints_domain:PR00266,Superfamily_domains:SSF47266,SMART_domains:SM00076,Gene3D:1.20.1250.10,Pfam_domain:PF00143,hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCGGAAATC	.	5	ESCA
FAM166B	0	.	GRCh37	9	35563176	35563176	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.273C>G	p.Ile91Met	p.I91M	ENST00000399742	2/6	39	33	6	38	38	0	FAM166B,missense_variant,p.Ile91Met,ENST00000399742,;RUSC2,downstream_gene_variant,,ENST00000361226,;RUSC2,downstream_gene_variant,,ENST00000455600,;FAM166B,non_coding_transcript_exon_variant,,ENST00000492890,;FAM166B,upstream_gene_variant,,ENST00000478246,;FAM166B,upstream_gene_variant,,ENST00000480287,;FAM166B,missense_variant,p.Ile91Met,ENST00000447837,;	C	ENSG00000215187	ENST00000399742	Transcript	missense_variant	344	273	91	I/M	atC/atG	.	.	.	-1	FAM166B	HGNC	34242	protein_coding	YES	CCDS56572.1	ENSP00000382646	F166B_HUMAN	.	UPI0000160C8C	.	deleterious(0)	possibly_damaging(0.863)	2/6	.	hmmpanther:PTHR22146,hmmpanther:PTHR22146:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGGGATCAT	.	4	ESCA
XPNPEP2	0	.	GRCh37	X	128881662	128881662	+	Silent	SNP	G	G	T	rs777481000	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570G>T	p.%3D	p.L190L	ENST00000371106	7/21	51	44	7	56	56	0	XPNPEP2,synonymous_variant,p.%3D,ENST00000371106,;XPNPEP2,downstream_gene_variant,,ENST00000371105,;	T	ENSG00000122121	ENST00000371106	Transcript	synonymous_variant	762	570	190	L	ctG/ctT	rs777481000	.	.	1	XPNPEP2	HGNC	12823	protein_coding	YES	CCDS14613.1	ENSP00000360147	XPP2_HUMAN	.	UPI000013901A	.	.	.	7/21	.	hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF84	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCTGGTATG	byFrequency	4	ESCA
TLR7	0	.	GRCh37	X	12905425	12905425	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1798A>T	p.Lys600Ter	p.K600*	ENST00000380659	3/3	52	31	21	62	62	0	TLR7,stop_gained,p.Lys600Ter,ENST00000380659,;	T	ENSG00000196664	ENST00000380659	Transcript	stop_gained	1937	1798	600	K/*	Aaa/Taa	.	.	.	1	TLR7	HGNC	15631	protein_coding	YES	CCDS14151.1	ENSP00000370034	TLR7_HUMAN	B2R9N9_HUMAN	UPI000004BAF6	.	.	.	3/3	.	Superfamily_domains:SSF52058,SMART_domains:SM00369,Gene3D:3.80.10.10,hmmpanther:PTHR24365:SF222,hmmpanther:PTHR24365	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAGAAACTG	.	5	ESCA
AIFM1	0	.	GRCh37	X	129299683	129299683	+	5'UTR	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-53G>T	.	.	ENST00000287295	1/16	36	28	7	20	19	1	AIFM1,5_prime_UTR_variant,,ENST00000319908,;AIFM1,5_prime_UTR_variant,,ENST00000287295,;AIFM1,upstream_gene_variant,,ENST00000535724,;AIFM1,upstream_gene_variant,,ENST00000346424,;AIFM1,5_prime_UTR_variant,,ENST00000529877,;AIFM1,upstream_gene_variant,,ENST00000416073,;AIFM1,upstream_gene_variant,,ENST00000527892,;	A	ENSG00000156709	ENST00000287295	Transcript	5_prime_UTR_variant	179	.	.	.	.	.	.	.	-1	AIFM1	HGNC	8768	protein_coding	YES	CCDS14618.1	ENSP00000287295	AIFM1_HUMAN	E9PMA0_HUMAN	UPI00001313DB	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	ACGACCGACGG	.	3	ESCA
SLITRK4	0	.	GRCh37	X	142717585	142717585	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1340G>T	p.Gly447Val	p.G447V	ENST00000381779	2/2	37	24	12	31	31	0	SLITRK4,missense_variant,p.Gly447Val,ENST00000381779,;SLITRK4,missense_variant,p.Gly447Val,ENST00000338017,;SLITRK4,missense_variant,p.Gly447Val,ENST00000356928,;	A	ENSG00000179542	ENST00000381779	Transcript	missense_variant	1566	1340	447	G/V	gGt/gTt	.	.	.	-1	SLITRK4	HGNC	23502	protein_coding	YES	CCDS14679.1	ENSP00000371198	SLIK4_HUMAN	.	UPI000004E650	.	deleterious(0)	probably_damaging(1)	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,SMART_domains:SM00365,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGACCTGAA	.	5	ESCA
MAGEA12	0	.	GRCh37	X	151896131	151896131	+	3'Flank	SNP	C	C	T	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000393900	.	141	132	9	95	95	0	MAGEA12,downstream_gene_variant,,ENST00000357916,;MAGEA12,downstream_gene_variant,,ENST00000393900,;MAGEA12,downstream_gene_variant,,ENST00000393869,;CSAG4,non_coding_transcript_exon_variant,,ENST00000361201,;CSAG4,downstream_gene_variant,,ENST00000535353,;CSAG4,downstream_gene_variant,,ENST00000583763,;	T	ENSG00000213401	ENST00000393900	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3171	-1	MAGEA12	HGNC	6799	protein_coding	YES	CCDS14710.1	ENSP00000377478	MAGAC_HUMAN	Q6FHH8_HUMAN	UPI0000000C51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTGGCTGCCC	.	2	ESCA
RENBP	0	.	GRCh37	X	153208330	153208330	+	Missense_Mutation	SNP	G	G	A	rs782506926	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.664C>T	p.Arg222Trp	p.R222W	ENST00000393700	6/11	75	54	20	34	34	0	RENBP,missense_variant,p.Arg222Trp,ENST00000412763,;RENBP,missense_variant,p.Arg222Trp,ENST00000393700,;RENBP,missense_variant,p.Arg208Trp,ENST00000369997,;HCFC1,downstream_gene_variant,,ENST00000444191,;HCFC1,downstream_gene_variant,,ENST00000369984,;HCFC1,downstream_gene_variant,,ENST00000310441,;HCFC1,downstream_gene_variant,,ENST00000354233,;RENBP,upstream_gene_variant,,ENST00000451114,;RENBP,non_coding_transcript_exon_variant,,ENST00000462086,;RENBP,missense_variant,p.Arg127Trp,ENST00000442361,;RENBP,3_prime_UTR_variant,,ENST00000423624,;RENBP,upstream_gene_variant,,ENST00000457282,;RENBP,downstream_gene_variant,,ENST00000475904,;RENBP,downstream_gene_variant,,ENST00000464227,;RENBP,downstream_gene_variant,,ENST00000471056,;	A	ENSG00000102032	ENST00000393700	Transcript	missense_variant	745	664	222	R/W	Cgg/Tgg	rs782506926	.	.	-1	RENBP	HGNC	9959	protein_coding	YES	CCDS14738.2	ENSP00000377303	RENBP_HUMAN	.	UPI0000E5B00C	.	deleterious(0)	possibly_damaging(0.818)	6/11	.	hmmpanther:PTHR15108,hmmpanther:PTHR15108:SF0,Gene3D:1.50.10.10,Pfam_domain:PF07221,Superfamily_domains:SSF48208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCCGGGCGC	byFrequency	5	ESCA
CDK16	0	.	GRCh37	X	47088143	47088143	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1689C>G	p.Phe563Leu	p.F563L	ENST00000276052	16/16	12	5	6	15	15	0	CDK16,missense_variant,p.Phe495Leu,ENST00000457458,;CDK16,missense_variant,p.Pro85Ala,ENST00000520141,;CDK16,missense_variant,p.Phe253Leu,ENST00000523344,;CDK16,missense_variant,p.Phe489Leu,ENST00000357227,;CDK16,missense_variant,p.Phe563Leu,ENST00000276052,;CDK16,missense_variant,p.Phe489Leu,ENST00000518022,;CDK16,intron_variant,,ENST00000517426,;CDK16,intron_variant,,ENST00000462827,;CDK16,downstream_gene_variant,,ENST00000520893,;CDK16,downstream_gene_variant,,ENST00000523034,;USP11,upstream_gene_variant,,ENST00000377107,;CDK16,downstream_gene_variant,,ENST00000519758,;USP11,upstream_gene_variant,,ENST00000377080,;USP11,upstream_gene_variant,,ENST00000218348,;CDK16,downstream_gene_variant,,ENST00000518391,;CDK16,non_coding_transcript_exon_variant,,ENST00000462483,;CDK16,non_coding_transcript_exon_variant,,ENST00000428400,;USP11,upstream_gene_variant,,ENST00000478596,;CDK16,downstream_gene_variant,,ENST00000522234,;CDK16,downstream_gene_variant,,ENST00000523699,;CDK16,downstream_gene_variant,,ENST00000520295,;USP11,upstream_gene_variant,,ENST00000469080,;CDK16,downstream_gene_variant,,ENST00000493213,;CDK16,downstream_gene_variant,,ENST00000523543,;	G	ENSG00000102225	ENST00000276052	Transcript	missense_variant	1767	1689	563	F/L	ttC/ttG	.	.	.	1	CDK16	HGNC	8749	protein_coding	YES	CCDS55408.1	ENSP00000276052	CDK16_HUMAN	Q96GA5_HUMAN,E5RJQ8_HUMAN,E5RJM2_HUMAN,E5RIY8_HUMAN,E5RIU4_HUMAN	UPI0001C00100	.	deleterious_low_confidence(0.05)	benign(0.009)	16/16	.	hmmpanther:PTHR24056:SF174,hmmpanther:PTHR24056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCTTTCCGCGT	.	3	ESCA
PQBP1	0	.	GRCh37	X	48759676	48759676	+	Missense_Mutation	SNP	A	A	C	rs782495605	.	TCGA-XP-A8T6-01A-11D-A36J-09	TCGA-XP-A8T6-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.459A>C	p.Arg153Ser	p.R153S	ENST00000218224	4/6	18	7	11	21	21	0	PQBP1,missense_variant,p.Arg153Ser,ENST00000218224,;PQBP1,missense_variant,p.Arg153Ser,ENST00000396763,;PQBP1,missense_variant,p.Arg153Ser,ENST00000376563,;PQBP1,missense_variant,p.Arg153Ser,ENST00000443648,;PQBP1,missense_variant,p.Arg153Ser,ENST00000447146,;PQBP1,intron_variant,,ENST00000456306,;PQBP1,intron_variant,,ENST00000247140,;PQBP1,intron_variant,,ENST00000376566,;TIMM17B,upstream_gene_variant,,ENST00000396779,;SLC35A2,downstream_gene_variant,,ENST00000413561,;SLC35A2,downstream_gene_variant,,ENST00000446885,;SLC35A2,downstream_gene_variant,,ENST00000452555,;SLC35A2,downstream_gene_variant,,ENST00000376529,;PQBP1,downstream_gene_variant,,ENST00000376548,;SLC35A2,downstream_gene_variant,,ENST00000247138,;TIMM17B,upstream_gene_variant,,ENST00000490755,;SLC35A2,downstream_gene_variant,,ENST00000376512,;TIMM17B,upstream_gene_variant,,ENST00000495490,;SLC35A2,downstream_gene_variant,,ENST00000376515,;SLC35A2,downstream_gene_variant,,ENST00000445167,;SLC35A2,downstream_gene_variant,,ENST00000376521,;TIMM17B,upstream_gene_variant,,ENST00000376582,;TIMM17B,upstream_gene_variant,,ENST00000465150,;PQBP1,non_coding_transcript_exon_variant,,ENST00000474671,;PQBP1,non_coding_transcript_exon_variant,,ENST00000463529,;PQBP1,non_coding_transcript_exon_variant,,ENST00000470059,;PQBP1,non_coding_transcript_exon_variant,,ENST00000473764,;PQBP1,non_coding_transcript_exon_variant,,ENST00000465859,;PQBP1,non_coding_transcript_exon_variant,,ENST00000477997,;PQBP1,intron_variant,,ENST00000470062,;PQBP1,intron_variant,,ENST00000472742,;PQBP1,downstream_gene_variant,,ENST00000486150,;TIMM17B,upstream_gene_variant,,ENST00000466995,;TIMM17B,upstream_gene_variant,,ENST00000464663,;	C	ENSG00000102103	ENST00000218224	Transcript	missense_variant	713	459	153	R/S	agA/agC	CD033719,rs782495605	.	.	1	PQBP1	HGNC	9330	protein_coding	YES	CCDS14309.1	ENSP00000218224	PQBP1_HUMAN	C9JQA1_HUMAN	UPI0000073DB7	.	tolerated(0.62)	benign(0.304)	4/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21737	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGAGAGCG	byFrequency	5	ESCA
CALHM2	0	.	GRCh37	10	105209038	105209038	+	Intron	SNP	G	G	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555+106C>A	.	.	ENST00000260743	.	36	22	14	30	30	0	CALHM2,3_prime_UTR_variant,,ENST00000393235,;CALHM2,intron_variant,,ENST00000369788,;CALHM2,intron_variant,,ENST00000260743,;CALHM1,downstream_gene_variant,,ENST00000329905,;PDCD11,downstream_gene_variant,,ENST00000369797,;RP11-225H22.7,upstream_gene_variant,,ENST00000608063,;RP11-225H22.4,upstream_gene_variant,,ENST00000411906,;CALHM2,downstream_gene_variant,,ENST00000474797,;CALHM2,downstream_gene_variant,,ENST00000480642,;CALHM2,downstream_gene_variant,,ENST00000463878,;CALHM2,downstream_gene_variant,,ENST00000461631,;CALHM2,downstream_gene_variant,,ENST00000494180,;PDCD11,downstream_gene_variant,,ENST00000478543,;	T	ENSG00000138172	ENST00000260743	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CALHM2	HGNC	23493	protein_coding	YES	CCDS7549.1	ENSP00000260743	CAHM2_HUMAN	.	UPI0000070F1F	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACAGACCTC	.	5	ESCA
ITPRIP	0	.	GRCh37	10	106072200	106072200	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1966C>T	.	.	ENST00000278071	3/3	49	35	13	24	24	0	ITPRIP,3_prime_UTR_variant,,ENST00000337478,;ITPRIP,3_prime_UTR_variant,,ENST00000358187,;ITPRIP,3_prime_UTR_variant,,ENST00000278071,;ITPRIP,downstream_gene_variant,,ENST00000458723,;RP11-127L20.5,intron_variant,,ENST00000472915,;	A	ENSG00000148841	ENST00000278071	Transcript	3_prime_UTR_variant	4063	.	.	.	.	.	.	.	-1	ITPRIP	HGNC	29370	protein_coding	YES	CCDS7557.1	ENSP00000278071	IPRI_HUMAN	.	UPI0000074521	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGGGCCATA	.	5	ESCA
CCDC147	0	.	GRCh37	10	106160486	106160486	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1864G>A	p.Asp622Asn	p.D622N	ENST00000369704	13/18	33	26	7	41	41	0	CCDC147,missense_variant,p.Asp622Asn,ENST00000369704,;snoU13,downstream_gene_variant,,ENST00000458914,;	A	ENSG00000120051	ENST00000369704	Transcript	missense_variant	1998	1864	622	D/N	Gat/Aat	.	.	.	1	CCDC147	HGNC	26676	protein_coding	YES	CCDS31282.1	ENSP00000358718	CC147_HUMAN	B4DK97_HUMAN	UPI0000160405	.	deleterious(0)	possibly_damaging(0.869)	13/18	.	hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAATGATGAG	.	5	ESCA
SORCS3	0	.	GRCh37	10	106849543	106849543	+	Missense_Mutation	SNP	G	G	A	rs530482370	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1039G>A	p.Gly347Arg	p.G347R	ENST00000369701	6/27	28	20	7	22	22	0	SORCS3,missense_variant,p.Gly347Arg,ENST00000369701,;	A	ENSG00000156395	ENST00000369701	Transcript	missense_variant	1266	1039	347	G/R	Gga/Aga	rs530482370	.	.	1	SORCS3	HGNC	16699	protein_coding	YES	CCDS7558.1	ENSP00000358715	SORC3_HUMAN	B7Z891_HUMAN	UPI0000135CE1	.	deleterious(0.02)	benign(0.394)	6/27	.	hmmpanther:PTHR12106:SF10,hmmpanther:PTHR12106,SMART_domains:SM00602	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCGGATTG	by1000G	5	ESCA
RASGEF1A	0	.	GRCh37	10	43701554	43701554	+	Missense_Mutation	SNP	G	G	A	rs760968520	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11C>T	p.Thr4Met	p.T4M	ENST00000395809	2/13	36	22	14	34	34	0	RASGEF1A,missense_variant,p.Thr12Met,ENST00000374459,;RASGEF1A,missense_variant,p.Thr4Met,ENST00000395810,;RASGEF1A,missense_variant,p.Thr4Met,ENST00000395809,;RASGEF1A,upstream_gene_variant,,ENST00000374455,;RASGEF1A,upstream_gene_variant,,ENST00000472864,;	A	ENSG00000198915	ENST00000395809	Transcript	missense_variant	2518	11	4	T/M	aCg/aTg	rs760968520	.	.	-1	RASGEF1A	HGNC	24246	protein_coding	YES	CCDS7202.2	ENSP00000379154	RGF1A_HUMAN	.	UPI00002289AF	.	deleterious(0)	possibly_damaging(0.708)	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGGACGTCTGG	.	4	ESCA
PARG	0	.	GRCh37	10	51027247	51027247	+	3'UTR	SNP	G	G	A	rs567335155	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*139C>T	.	.	ENST00000402038	14/14	26	16	9	28	28	0	PARG,3_prime_UTR_variant,,ENST00000402038,;RP11-507K13.6,downstream_gene_variant,,ENST00000444021,;	A	ENSG00000227345	ENST00000402038	Transcript	3_prime_UTR_variant	1615	.	.	.	.	rs567335155	.	.	-1	PARG	HGNC	8605	protein_coding	YES	.	ENSP00000384408	PARG_HUMAN	B4DX76_HUMAN,B4DHS4_HUMAN	UPI0000404B69	.	.	.	14/14	.	.	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGGAAGAG	by1000G	5	ESCA
ANK3	0	.	GRCh37	10	61830987	61830987	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9652C>A	p.Leu3218Ile	p.L3218I	ENST00000280772	37/44	82	53	29	79	78	1	ANK3,missense_variant,p.Leu3218Ile,ENST00000280772,;ANK3,intron_variant,,ENST00000373827,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000355288,;ANK3,intron_variant,,ENST00000511043,;ANK3,intron_variant,,ENST00000503366,;	T	ENSG00000151150	ENST00000280772	Transcript	missense_variant	9844	9652	3218	L/I	Ctt/Att	.	.	.	-1	ANK3	HGNC	494	protein_coding	YES	CCDS7258.1	ENSP00000280772	ANK3_HUMAN	D6RFK6_HUMAN,D6RBY7_HUMAN,B1AQT1_HUMAN	UPI0000141BA9	.	.	benign(0.01)	37/44	.	hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAAGGGAGG	.	5	ESCA
UNC5B	0	.	GRCh37	10	73039676	73039676	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.178G>A	p.Val60Met	p.V60M	ENST00000335350	2/17	56	34	22	31	31	0	UNC5B,missense_variant,p.Val60Met,ENST00000335350,;UNC5B,missense_variant,p.Val60Met,ENST00000373192,;	A	ENSG00000107731	ENST00000335350	Transcript	missense_variant	594	178	60	V/M	Gtg/Atg	.	.	.	1	UNC5B	HGNC	12568	protein_coding	YES	CCDS7309.1	ENSP00000334329	UNC5B_HUMAN	.	UPI000000D753	.	deleterious(0)	probably_damaging(0.999)	2/17	.	hmmpanther:PTHR12582:SF6,hmmpanther:PTHR12582,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTGTGAAG	.	5	ESCA
C10orf99	0	.	GRCh37	10	85936240	85936240	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75G>C	p.Lys25Asn	p.K25N	ENST00000372126	2/3	22	17	5	34	34	0	C10orf99,missense_variant,p.Lys25Asn,ENST00000372126,;C10orf99,upstream_gene_variant,,ENST00000472542,;	C	ENSG00000188373	ENST00000372126	Transcript	missense_variant	189	75	25	K/N	aaG/aaC	.	.	.	1	C10orf99	HGNC	31428	protein_coding	YES	CCDS7371.1	ENSP00000361199	CJ099_HUMAN	.	UPI0000046D02	.	deleterious(0.01)	benign(0.322)	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGAAGAGGCG	.	5	ESCA
GLUD1	0	.	GRCh37	10	88820542	88820542	+	Missense_Mutation	SNP	T	T	C	rs766896575	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1100A>G	p.Tyr367Cys	p.Y367C	ENST00000277865	8/13	78	50	27	76	76	0	GLUD1,missense_variant,p.Tyr367Cys,ENST00000277865,;GLUD1,missense_variant,p.Tyr200Cys,ENST00000537649,;GLUD1,missense_variant,p.Tyr234Cys,ENST00000544149,;GLUD1,non_coding_transcript_exon_variant,,ENST00000465164,;GLUD1,upstream_gene_variant,,ENST00000487058,;GLUD1,downstream_gene_variant,,ENST00000474574,;	C	ENSG00000148672	ENST00000277865	Transcript	missense_variant	1197	1100	367	Y/C	tAt/tGt	rs766896575	.	.	-1	GLUD1	HGNC	4335	protein_coding	YES	CCDS7382.1	ENSP00000277865	DHE3_HUMAN	Q9UQV0_HUMAN,E9KL48_HUMAN,B3KV55_HUMAN	UPI0000001C96	.	tolerated(0.05)	benign(0.112)	8/13	.	hmmpanther:PTHR11606:SF10,hmmpanther:PTHR11606,Gene3D:3.40.50.720,Pfam_domain:PF00208,SMART_domains:SM00839,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCATAGGGC	byFrequency	5	ESCA
PLCE1	0	.	GRCh37	10	95993928	95993928	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2073G>A	p.%3D	p.V691V	ENST00000371380	5/32	67	38	29	54	54	0	PLCE1,synonymous_variant,p.%3D,ENST00000371380,;PLCE1,synonymous_variant,p.%3D,ENST00000260766,;PLCE1,synonymous_variant,p.%3D,ENST00000371375,;PLCE1,synonymous_variant,p.%3D,ENST00000371385,;	A	ENSG00000138193	ENST00000371380	Transcript	synonymous_variant	2308	2073	691	V	gtG/gtA	.	.	.	1	PLCE1	HGNC	17175	protein_coding	YES	CCDS41552.1	ENSP00000360431	PLCE1_HUMAN	B7ZM61_HUMAN	UPI00001F93EE	.	.	.	5/32	.	Superfamily_domains:0041591,SMART_domains:SM00147,Gene3D:2ii0A02,Pfam_domain:PF00617,PROSITE_profiles:PS50009	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTGACACG	.	5	ESCA
YAP1	0	.	GRCh37	11	102100570	102100570	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1414C>G	p.Pro472Ala	p.P472A	ENST00000282441	9/9	38	13	24	58	58	0	YAP1,missense_variant,p.Pro418Ala,ENST00000526343,;YAP1,missense_variant,p.Pro226Ala,ENST00000529029,;YAP1,missense_variant,p.Pro460Ala,ENST00000537274,;YAP1,missense_variant,p.Pro456Ala,ENST00000531439,;YAP1,missense_variant,p.Pro472Ala,ENST00000282441,;YAP1,missense_variant,p.Pro294Ala,ENST00000524575,;YAP1,missense_variant,p.Pro422Ala,ENST00000345877,;RP11-864G5.3,downstream_gene_variant,,ENST00000526310,;YAP1,non_coding_transcript_exon_variant,,ENST00000528834,;	G	ENSG00000137693	ENST00000282441	Transcript	missense_variant	1802	1414	472	P/A	Cca/Gca	COSM1474942,COSM428285	.	.	1	YAP1	HGNC	16262	protein_coding	YES	CCDS44716.1	ENSP00000282441	YAP1_HUMAN	.	UPI00000746D8	.	deleterious(0.02)	possibly_damaging(0.456)	9/9	.	hmmpanther:PTHR17616,hmmpanther:PTHR17616:SF10	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGATGCCAAGT	.	5	ESCA
NPAT	0	.	GRCh37	11	108058908	108058908	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.557-2A>T	.	p.X186_splice	ENST00000278612	.	28	13	15	35	35	0	NPAT,splice_acceptor_variant,,ENST00000278612,;NPAT,splice_acceptor_variant,,ENST00000610253,;NPAT,downstream_gene_variant,,ENST00000531384,;	A	ENSG00000149308	ENST00000278612	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	NPAT	HGNC	7896	protein_coding	YES	CCDS41710.1	ENSP00000278612	NPAT_HUMAN	.	UPI00001FA306	.	.	.	.	6/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGCTGTATT	.	5	ESCA
MICAL2	0	.	GRCh37	11	12278428	12278428	+	Missense_Mutation	SNP	G	G	A	rs757654823	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3052G>A	p.Glu1018Lys	p.E1018K	ENST00000256194	24/28	40	35	5	28	28	0	MICAL2,missense_variant,p.Glu792Lys,ENST00000379612,;MICAL2,missense_variant,p.Glu1018Lys,ENST00000256194,;MICAL2,missense_variant,p.Glu828Lys,ENST00000527546,;MICAL2,missense_variant,p.Glu997Lys,ENST00000342902,;MICAL2,missense_variant,p.Glu828Lys,ENST00000537344,;RP11-265D17.2,downstream_gene_variant,,ENST00000527288,;MICAL2,non_coding_transcript_exon_variant,,ENST00000534563,;MICAL2,non_coding_transcript_exon_variant,,ENST00000526672,;MICAL2,non_coding_transcript_exon_variant,,ENST00000526604,;MICAL2,non_coding_transcript_exon_variant,,ENST00000525979,;MICAL2,non_coding_transcript_exon_variant,,ENST00000528931,;MICAL2,non_coding_transcript_exon_variant,,ENST00000525075,;MICAL2,non_coding_transcript_exon_variant,,ENST00000530691,;MICAL2,non_coding_transcript_exon_variant,,ENST00000525618,;MICAL2,non_coding_transcript_exon_variant,,ENST00000530021,;MICAL2,upstream_gene_variant,,ENST00000525444,;	A	ENSG00000133816	ENST00000256194	Transcript	missense_variant	3340	3052	1018	E/K	Gag/Aag	rs757654823	.	.	1	MICAL2	HGNC	24693	protein_coding	YES	CCDS7809.1	ENSP00000256194	MICA2_HUMAN	E9PRE0_HUMAN,E9PNC3_HUMAN,E9PL42_HUMAN,E9PKI3_HUMAN,E9PJB0_HUMAN	UPI000000DA92	.	deleterious(0)	probably_damaging(0.999)	24/28	.	Superfamily_domains:SSF57716,SMART_domains:SM00132,Gene3D:2.10.110.10,Pfam_domain:PF00412,PROSITE_patterns:PS00478,hmmpanther:PTHR11915:SF239,hmmpanther:PTHR11915,PROSITE_profiles:PS50023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCGCCGAGGGC	.	4	ESCA
OR5L2	0	.	GRCh37	11	55594834	55594834	+	Missense_Mutation	SNP	C	C	A	rs779534429	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.140C>A	p.Ala47Glu	p.A47E	ENST00000378397	1/1	84	61	23	56	56	0	OR5L2,missense_variant,p.Ala47Glu,ENST00000378397,;	A	ENSG00000205030	ENST00000378397	Transcript	missense_variant	140	140	47	A/E	gCa/gAa	rs779534429	.	.	1	OR5L2	HGNC	8351	protein_coding	YES	CCDS31511.1	ENSP00000367650	OR5L2_HUMAN	.	UPI0000041C49	.	deleterious(0.01)	possibly_damaging(0.649)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF154,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACTGCACTGA	.	5	ESCA
TAF6L	0	.	GRCh37	11	62549432	62549432	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598G>A	p.Val200Ile	p.V200I	ENST00000294168	7/11	65	49	15	44	44	0	TAF6L,missense_variant,p.Val200Ile,ENST00000294168,;TMEM223,intron_variant,,ENST00000528367,;TAF6L,downstream_gene_variant,,ENST00000529509,;RP11-727F15.12,downstream_gene_variant,,ENST00000601484,;TMEM223,intron_variant,,ENST00000527073,;TAF6L,non_coding_transcript_exon_variant,,ENST00000533823,;TAF6L,non_coding_transcript_exon_variant,,ENST00000524976,;TAF6L,downstream_gene_variant,,ENST00000531265,;TAF6L,downstream_gene_variant,,ENST00000525405,;TAF6L,downstream_gene_variant,,ENST00000532915,;	A	ENSG00000162227	ENST00000294168	Transcript	missense_variant	799	598	200	V/I	Gtc/Atc	.	.	.	1	TAF6L	HGNC	17305	protein_coding	YES	CCDS8035.1	ENSP00000294168	TAF6L_HUMAN	E9PP94_HUMAN,E9PLV8_HUMAN	UPI00000720C0	.	tolerated(0.5)	benign(0.012)	7/11	.	hmmpanther:PTHR10221:SF9,hmmpanther:PTHR10221	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTGGTCAGT	.	5	ESCA
SHANK2	0	.	GRCh37	11	70348384	70348384	+	Silent	SNP	C	C	T	rs367733874	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2208G>A	p.%3D	p.P736P	ENST00000338508	25/33	349	328	21	25	25	0	SHANK2,synonymous_variant,p.%3D,ENST00000409530,;SHANK2,synonymous_variant,p.%3D,ENST00000409161,;SHANK2,synonymous_variant,p.%3D,ENST00000412252,;SHANK2,synonymous_variant,p.%3D,ENST00000424924,;SHANK2,synonymous_variant,p.%3D,ENST00000423696,;SHANK2,synonymous_variant,p.%3D,ENST00000357171,;SHANK2,synonymous_variant,p.%3D,ENST00000294018,;SHANK2,synonymous_variant,p.%3D,ENST00000449116,;SHANK2,synonymous_variant,p.%3D,ENST00000338508,;SHANK2,synonymous_variant,p.%3D,ENST00000449833,;SHANK2,intron_variant,,ENST00000426687,;	T	ENSG00000162105	ENST00000338508	Transcript	synonymous_variant	2208	2208	736	P	ccG/ccA	rs367733874	.	.	-1	SHANK2	HGNC	14295	protein_coding	YES	.	ENSP00000345193	.	C9JFP8_HUMAN,A6NHU9_HUMAN	UPI00020653A9	.	.	.	25/33	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGGCGGGGG	.	2	ESCA
RNF121	0	.	GRCh37	11	71671862	71671862	+	Silent	SNP	C	C	T	rs763254619	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.168C>T	p.%3D	p.L56L	ENST00000361756	3/9	142	129	13	40	40	0	RNF121,synonymous_variant,p.%3D,ENST00000361756,;RNF121,synonymous_variant,p.%3D,ENST00000530137,;RNF121,synonymous_variant,p.%3D,ENST00000533380,;RNF121,synonymous_variant,p.%3D,ENST00000393713,;RNF121,5_prime_UTR_variant,,ENST00000545854,;RNF121,non_coding_transcript_exon_variant,,ENST00000490867,;RNF121,synonymous_variant,p.%3D,ENST00000525243,;RNF121,synonymous_variant,p.%3D,ENST00000530655,;RNF121,synonymous_variant,p.%3D,ENST00000393711,;RNF121,synonymous_variant,p.%3D,ENST00000530058,;RNF121,synonymous_variant,p.%3D,ENST00000526549,;RNF121,non_coding_transcript_exon_variant,,ENST00000528683,;RNF121,non_coding_transcript_exon_variant,,ENST00000526903,;	T	ENSG00000137522	ENST00000361756	Transcript	synonymous_variant	529	168	56	L	ctC/ctT	rs763254619	.	.	1	RNF121	HGNC	21070	protein_coding	YES	CCDS8203.1	ENSP00000354571	RN121_HUMAN	Q9NUW5_HUMAN,E9PLR7_HUMAN,B3KSW8_HUMAN,A0PJP0_HUMAN	UPI000006FB75	.	.	.	3/9	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR13407,hmmpanther:PTHR13407:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GTCCTCATCCT	.	3	ESCA
TBX5	0	.	GRCh37	12	114841727	114841727	+	5'UTR	SNP	G	G	A	rs769107196	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-24C>T	.	.	ENST00000310346	2/9	112	74	38	81	81	0	TBX5,5_prime_UTR_variant,,ENST00000310346,;TBX5,5_prime_UTR_variant,,ENST00000405440,;TBX5,intron_variant,,ENST00000349716,;TBX5,upstream_gene_variant,,ENST00000526441,;TBX5-AS1,upstream_gene_variant,,ENST00000531024,;TBX5-AS1,upstream_gene_variant,,ENST00000528549,;TBX5-AS1,upstream_gene_variant,,ENST00000532697,;TBX5-AS1,upstream_gene_variant,,ENST00000531202,;TBX5,non_coding_transcript_exon_variant,,ENST00000552726,;	A	ENSG00000089225	ENST00000310346	Transcript	5_prime_UTR_variant	644	.	.	.	.	rs769107196	.	.	-1	TBX5	HGNC	11604	protein_coding	YES	CCDS9173.1	ENSP00000309913	TBX5_HUMAN	.	UPI0000136AA2	.	.	.	2/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCCGCGCAA	byFrequency	5	ESCA
CIT	0	.	GRCh37	12	120127977	120127977	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6165C>T	p.%3D	p.T2055T	ENST00000392521	47/48	10	6	4	14	14	0	CIT,synonymous_variant,p.%3D,ENST00000392520,;CIT,synonymous_variant,p.%3D,ENST00000261833,;CIT,synonymous_variant,p.%3D,ENST00000392521,;CIT,non_coding_transcript_exon_variant,,ENST00000537607,;CIT,downstream_gene_variant,,ENST00000469414,;CIT,non_coding_transcript_exon_variant,,ENST00000545913,;CIT,downstream_gene_variant,,ENST00000544872,;	A	ENSG00000122966	ENST00000392521	Transcript	synonymous_variant	6221	6165	2055	T	acC/acT	.	.	.	-1	CIT	HGNC	1985	protein_coding	YES	CCDS55891.1	ENSP00000376306	CTRO_HUMAN	.	UPI0000683C41	.	.	.	47/48	.	PIRSF_domain:PIRSF038145,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGCGGGGTCCT	.	3	ESCA
SETD8	0	.	GRCh37	12	123893629	123893629	+	3'UTR	SNP	G	G	C	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1379G>C	.	.	ENST00000402868	8/8	83	58	25	90	90	0	SETD8,3_prime_UTR_variant,,ENST00000330479,;SETD8,3_prime_UTR_variant,,ENST00000402868,;SETD8,downstream_gene_variant,,ENST00000437502,;SETD8,downstream_gene_variant,,ENST00000485469,;SETD8,downstream_gene_variant,,ENST00000437519,;SETD8,downstream_gene_variant,,ENST00000461103,;	C	ENSG00000183955	ENST00000402868	Transcript	3_prime_UTR_variant	2864	.	.	.	.	.	.	.	1	SETD8	HGNC	29489	protein_coding	YES	CCDS9247.1	ENSP00000384629	SETD8_HUMAN	.	UPI000002B371	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACAGGTATG	.	5	ESCA
NOC4L	0	.	GRCh37	12	132635841	132635842	+	Frame_Shift_Ins	INS	-	-	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1003dupG	p.Asp335GlyfsTer18	p.D335Gfs*18	ENST00000330579	11/15	87	71	16	88	88	0	NOC4L,frameshift_variant,p.Asp335GlyfsTer18,ENST00000330579,;NOC4L,5_prime_UTR_variant,,ENST00000538784,;NOC4L,downstream_gene_variant,,ENST00000541954,;NOC4L,non_coding_transcript_exon_variant,,ENST00000535343,;	G	ENSG00000184967	ENST00000330579	Transcript	frameshift_variant	1042-1043	1001-1002	334	L/LX	ttg/ttGg	.	.	.	1	NOC4L	HGNC	28461	protein_coding	YES	CCDS9277.1	ENSP00000328854	NOC4L_HUMAN	F5H5K6_HUMAN	UPI00000723C4	.	.	.	11/15	.	Superfamily_domains:SSF48371,Pfam_domain:PF03914,hmmpanther:PTHR12455:SF0,hmmpanther:PTHR12455	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTCTTGGACC	.	3	ESCA
GOLGA3	0	.	GRCh37	12	133365650	133365650	+	Missense_Mutation	SNP	G	G	A	rs200604051	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2774C>T	p.Ala925Val	p.A925V	ENST00000204726	13/24	45	30	14	39	39	0	GOLGA3,missense_variant,p.Ala925Val,ENST00000204726,;GOLGA3,missense_variant,p.Ala925Val,ENST00000537452,;GOLGA3,missense_variant,p.Ala925Val,ENST00000450791,;GOLGA3,missense_variant,p.Ala925Val,ENST00000456883,;GOLGA3,missense_variant,p.Ala925Val,ENST00000545875,;	A	ENSG00000090615	ENST00000204726	Transcript	missense_variant	3333	2774	925	A/V	gCg/gTg	rs200604051	.	.	-1	GOLGA3	HGNC	4426	protein_coding	YES	CCDS9281.1	ENSP00000204726	GOGA3_HUMAN	.	UPI0000190979	.	tolerated(1)	benign(0.002)	13/24	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902:SF20,hmmpanther:PTHR18902	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGCGCCGAC	byCluster|by1000G	5	ESCA
TNFRSF19	0	.	GRCh37	13	24242195	24242195	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813G>A	p.%3D	p.V271V	ENST00000382258	8/9	17	14	3	27	27	0	TNFRSF19,synonymous_variant,p.%3D,ENST00000382258,;TNFRSF19,synonymous_variant,p.%3D,ENST00000382263,;TNFRSF19,synonymous_variant,p.%3D,ENST00000403372,;TNFRSF19,synonymous_variant,p.%3D,ENST00000248484,;	A	ENSG00000127863	ENST00000382258	Transcript	synonymous_variant	1017	813	271	V	gtG/gtA	.	.	.	1	TNFRSF19	HGNC	11915	protein_coding	YES	CCDS9302.1	ENSP00000371693	TNR19_HUMAN	.	UPI00001372A7	.	.	.	8/9	.	hmmpanther:PTHR12120,hmmpanther:PTHR12120:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGGGTGCATTC	.	3	ESCA
SLC7A1	0	.	GRCh37	13	30088299	30088299	+	3'UTR	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*318G>C	.	.	ENST00000380752	13/13	43	30	13	46	46	0	SLC7A1,3_prime_UTR_variant,,ENST00000380752,;SLC7A1,downstream_gene_variant,,ENST00000473577,;	G	ENSG00000139514	ENST00000380752	Transcript	3_prime_UTR_variant	2595	.	.	.	.	.	.	.	-1	SLC7A1	HGNC	11057	protein_coding	YES	CCDS9333.1	ENSP00000370128	CTR1_HUMAN	Q5JR49_HUMAN	UPI0000128653	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTTCTGCCT	.	5	ESCA
TNFSF11	0	.	GRCh37	13	43148538	43148538	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99G>A	p.%3D	p.P33P	ENST00000239849	1/5	26	17	9	11	11	0	TNFSF11,synonymous_variant,p.%3D,ENST00000239849,;TNFSF11,5_prime_UTR_variant,,ENST00000398795,;TNFSF11,intron_variant,,ENST00000358545,;TNFSF11,intron_variant,,ENST00000544862,;TNFSF11,intron_variant,,ENST00000405262,;	A	ENSG00000120659	ENST00000239849	Transcript	synonymous_variant	250	99	33	P	ccG/ccA	.	.	.	1	TNFSF11	HGNC	11926	protein_coding	YES	CCDS9384.1	ENSP00000239849	TNF11_HUMAN	Q5T9Y4_HUMAN,Q54A98_HUMAN	UPI000003BC8E	.	.	.	1/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF3,PIRSF_domain:PIRSF038013	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCCCCGCCGCC	.	4	ESCA
MYCBP2	0	.	GRCh37	13	77739514	77739514	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6239T>A	p.Leu2080His	p.L2080H	ENST00000544440	42/83	58	37	20	42	42	0	MYCBP2,missense_variant,p.Leu2080His,ENST00000357337,;MYCBP2,missense_variant,p.Leu2080His,ENST00000544440,;MYCBP2,missense_variant,p.Leu2118His,ENST00000407578,;MYCBP2,5_prime_UTR_variant,,ENST00000360084,;	T	ENSG00000005810	ENST00000544440	Transcript	missense_variant	6257	6239	2080	L/H	cTt/cAt	.	.	.	-1	MYCBP2	HGNC	23386	protein_coding	YES	.	ENSP00000444596	MYCB2_HUMAN	.	UPI0000212757	.	.	benign(0.418)	42/83	.	hmmpanther:PTHR12846:SF14,hmmpanther:PTHR12846	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAAGGGCC	.	5	ESCA
TGDS	0	.	GRCh37	13	95229646	95229647	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.862dupT	p.Trp288LeufsTer3	p.W288Lfs*3	ENST00000261296	10/12	122	90	32	79	79	0	TGDS,frameshift_variant,p.Trp288LeufsTer3,ENST00000261296,;TGDS,downstream_gene_variant,,ENST00000498294,;TGDS,downstream_gene_variant,,ENST00000470480,;	A	ENSG00000088451	ENST00000261296	Transcript	frameshift_variant	983-984	862-863	288	W/LX	tgg/tTgg	.	.	.	-1	TGDS	HGNC	20324	protein_coding	YES	CCDS9471.1	ENSP00000261296	TGDS_HUMAN	Q2TU31_HUMAN	UPI000006E8F4	.	.	.	10/12	.	Superfamily_domains:SSF51735,Gene3D:3.90.25.10,hmmpanther:PTHR10366:SF41,hmmpanther:PTHR10366	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAACCCAATTT	.	3	ESCA
IGHV3-38	0	.	GRCh37	14	106866572	106866572	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.182G>A	p.Gly61Glu	p.G61E	ENST00000390618	2/2	179	153	25	130	130	0	IGHV3-38,missense_variant,p.Gly61Glu,ENST00000390618,;	T	ENSG00000211958	ENST00000390618	Transcript	missense_variant	260	182	61	G/E	gGg/gAg	.	.	.	-1	IGHV3-38	HGNC	5601	IG_V_gene	YES	.	ENSP00000375027	.	.	UPI0000F30366	.	tolerated_low_confidence(0.08)	possibly_damaging(0.737)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF91,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCTTCCCTGGA	.	3	ESCA
METTL17	0	.	GRCh37	14	21462709	21462709	+	Silent	SNP	A	A	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.705A>T	p.%3D	p.S235S	ENST00000382985	8/13	52	19	33	33	33	0	METTL17,synonymous_variant,p.%3D,ENST00000556670,;METTL17,synonymous_variant,p.%3D,ENST00000382985,;METTL17,synonymous_variant,p.%3D,ENST00000555670,;METTL17,synonymous_variant,p.%3D,ENST00000339374,;METTL17,downstream_gene_variant,,ENST00000554751,;METTL17,upstream_gene_variant,,ENST00000556733,;METTL17,downstream_gene_variant,,ENST00000553564,;SLC39A2,upstream_gene_variant,,ENST00000298681,;SLC39A2,upstream_gene_variant,,ENST00000554422,;METTL17,downstream_gene_variant,,ENST00000554283,;RP11-84C10.4,downstream_gene_variant,,ENST00000557335,;METTL17,intron_variant,,ENST00000554354,;METTL17,downstream_gene_variant,,ENST00000555177,;METTL17,3_prime_UTR_variant,,ENST00000555533,;METTL17,3_prime_UTR_variant,,ENST00000557550,;METTL17,3_prime_UTR_variant,,ENST00000555640,;METTL17,non_coding_transcript_exon_variant,,ENST00000555902,;SLC39A2,upstream_gene_variant,,ENST00000554128,;METTL17,downstream_gene_variant,,ENST00000553441,;METTL17,upstream_gene_variant,,ENST00000554849,;METTL17,downstream_gene_variant,,ENST00000554985,;METTL17,downstream_gene_variant,,ENST00000555390,;METTL17,downstream_gene_variant,,ENST00000553536,;METTL17,upstream_gene_variant,,ENST00000553389,;METTL17,downstream_gene_variant,,ENST00000554588,;METTL17,downstream_gene_variant,,ENST00000557701,;METTL17,downstream_gene_variant,,ENST00000554949,;METTL17,downstream_gene_variant,,ENST00000556442,;METTL17,downstream_gene_variant,,ENST00000557279,;	T	ENSG00000165792	ENST00000382985	Transcript	synonymous_variant	728	705	235	S	tcA/tcT	.	.	.	1	METTL17	HGNC	19280	protein_coding	YES	CCDS41913.1	ENSP00000372445	MET17_HUMAN	G3V4P2_HUMAN,G3V3X6_HUMAN,G3V353_HUMAN	UPI00001410AF	.	.	.	8/13	.	hmmpanther:PTHR21320:SF2,hmmpanther:PTHR21320,Pfam_domain:PF09243,Gene3D:3.40.50.150,Superfamily_domains:SSF53335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTCAGAATC	.	5	ESCA
SUPT16H	0	.	GRCh37	14	21830353	21830353	+	Intron	SNP	C	C	T	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1793+3G>A	.	.	ENST00000216297	.	46	12	34	40	40	0	SUPT16H,splice_region_variant,,ENST00000216297,;SUPT16H,upstream_gene_variant,,ENST00000557394,;	T	ENSG00000092201	ENST00000216297	Transcript	splice_region_variant	.	.	.	.	.	COSM3955891	.	.	-1	SUPT16H	HGNC	11465	protein_coding	YES	CCDS9569.1	ENSP00000216297	SP16H_HUMAN	.	UPI0000035D5C	.	.	.	.	15/25	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGACTCACATT	.	4	ESCA
LRFN5	0	.	GRCh37	14	42357161	42357161	+	Missense_Mutation	SNP	C	C	T	rs548468008	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1333C>T	p.Arg445Cys	p.R445C	ENST00000298119	3/6	33	10	23	51	51	0	LRFN5,missense_variant,p.Arg445Cys,ENST00000298119,;LRFN5,missense_variant,p.Arg445Cys,ENST00000554120,;LRFN5,missense_variant,p.Arg445Cys,ENST00000554171,;	T	ENSG00000165379	ENST00000298119	Transcript	missense_variant	2522	1333	445	R/C	Cgt/Tgt	rs548468008,COSM71470	.	.	1	LRFN5	HGNC	20360	protein_coding	YES	CCDS9678.1	ENSP00000298119	LRFN5_HUMAN	.	UPI000000DA1E	.	deleterious(0.02)	possibly_damaging(0.593)	3/6	.	Superfamily_domains:SSF49265,Gene3D:2.60.40.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R445C|c.1333C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATACGTATG	byFrequency|byCluster	5	ESCA
FOS	0	.	GRCh37	14	75748401	75748401	+	3'UTR	SNP	G	G	C	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*274G>C	.	.	ENST00000303562	4/4	102	42	60	37	37	0	FOS,3_prime_UTR_variant,,ENST00000303562,;FOS,downstream_gene_variant,,ENST00000555347,;FOS,downstream_gene_variant,,ENST00000555686,;FOS,downstream_gene_variant,,ENST00000555242,;FOS,downstream_gene_variant,,ENST00000555672,;FOS,downstream_gene_variant,,ENST00000554212,;FOS,downstream_gene_variant,,ENST00000557139,;FOS,downstream_gene_variant,,ENST00000535987,;FOS,downstream_gene_variant,,ENST00000554617,;FOS,downstream_gene_variant,,ENST00000556324,;	C	ENSG00000170345	ENST00000303562	Transcript	3_prime_UTR_variant	1626	.	.	.	.	.	.	.	1	FOS	HGNC	3796	protein_coding	YES	CCDS9841.1	ENSP00000306245	FOS_HUMAN	Q76MZ0_HUMAN,Q76MY9_HUMAN,Q6FG41_HUMAN,G3V2V7_HUMAN,A8K4E2_HUMAN	UPI000000D8F5	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGTTGAGCCA	.	5	ESCA
GPATCH2L	0	.	GRCh37	14	76640108	76640108	+	Intron	SNP	G	G	C	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.984+140G>C	.	.	ENST00000261530	.	21	17	3	23	23	0	GPATCH2L,3_prime_UTR_variant,,ENST00000556663,;GPATCH2L,3_prime_UTR_variant,,ENST00000557263,;GPATCH2L,intron_variant,,ENST00000554799,;GPATCH2L,intron_variant,,ENST00000312858,;GPATCH2L,intron_variant,,ENST00000261530,;GPATCH2L,non_coding_transcript_exon_variant,,ENST00000554125,;GPATCH2L,intron_variant,,ENST00000554375,;	C	ENSG00000089916	ENST00000261530	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GPATCH2L	HGNC	20210	protein_coding	YES	CCDS9848.1	ENSP00000261530	GPT2L_HUMAN	G3V5D0_HUMAN	UPI000006FA38	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAAGAGTGA	.	5	ESCA
NOXRED1	0	.	GRCh37	14	77873059	77873059	+	Intron	SNP	G	G	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.682+8C>A	.	.	ENST00000380835	.	56	20	36	61	61	0	NOXRED1,synonymous_variant,p.%3D,ENST00000298358,;NOXRED1,splice_region_variant,,ENST00000380835,;NOXRED1,downstream_gene_variant,,ENST00000555603,;NOXRED1,non_coding_transcript_exon_variant,,ENST00000555901,;	T	ENSG00000165555	ENST00000380835	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	NOXRED1	HGNC	20487	protein_coding	YES	CCDS45142.1	ENSP00000370215	NXRD1_HUMAN	G3V2D4_HUMAN	UPI0000407F20	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGAGCCGTG	.	5	ESCA
SYNE3	0	.	GRCh37	14	95905383	95905383	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2363G>A	p.Arg788Lys	p.R788K	ENST00000334258	13/17	62	44	17	56	56	0	SYNE3,missense_variant,p.Arg545Lys,ENST00000554873,;SYNE3,missense_variant,p.Arg788Lys,ENST00000334258,;SYNE3,missense_variant,p.Arg788Lys,ENST00000557275,;SYNE3,downstream_gene_variant,,ENST00000553340,;SYNE3,non_coding_transcript_exon_variant,,ENST00000555759,;	T	ENSG00000176438	ENST00000334258	Transcript	missense_variant	2378	2363	788	R/K	aGg/aAg	.	.	.	-1	SYNE3	HGNC	19861	protein_coding	YES	CCDS9935.1	ENSP00000334308	SYNE3_HUMAN	.	UPI0000246F54	.	tolerated(0.3)	benign(0.009)	13/17	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGCCTGGGA	.	5	ESCA
PAPOLA	0	.	GRCh37	14	97033008	97033008	+	3'UTR	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1621C>T	.	.	ENST00000216277	22/22	21	15	6	16	16	0	PAPOLA,3_prime_UTR_variant,,ENST00000216277,;PAPOLA,downstream_gene_variant,,ENST00000392990,;PAPOLA,downstream_gene_variant,,ENST00000555626,;PAPOLA,downstream_gene_variant,,ENST00000556459,;PAPOLA,downstream_gene_variant,,ENST00000553689,;PAPOLA,downstream_gene_variant,,ENST00000555508,;PAPOLA,downstream_gene_variant,,ENST00000553940,;	T	ENSG00000090060	ENST00000216277	Transcript	3_prime_UTR_variant	4079	.	.	.	.	.	.	.	1	PAPOLA	HGNC	14981	protein_coding	YES	CCDS9946.1	ENSP00000216277	PAPOA_HUMAN	G3V2A0_HUMAN,B7ZA53_HUMAN,B4DZL2_HUMAN	UPI0000074269	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCCACATC	.	5	ESCA
DNM1P47	0	.	GRCh37	15	102303947	102303947	+	RNA	SNP	A	A	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.11993A>G	.	.	ENST00000561463	2/4	39	32	7	21	21	0	DNM1P47,non_coding_transcript_exon_variant,,ENST00000561463,;DNM1P47,non_coding_transcript_exon_variant,,ENST00000571780,;	G	ENSG00000259660	ENST00000561463	Transcript	non_coding_transcript_exon_variant	11993	.	.	.	.	.	.	.	1	DNM1P47	HGNC	35200	processed_transcript	YES	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	TGGGAACGAGA	.	2	ESCA
NPAP1	0	.	GRCh37	15	24922699	24922699	+	Missense_Mutation	SNP	C	C	T	rs759345390	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1685C>T	p.Ser562Phe	p.S562F	ENST00000329468	1/1	32	25	7	20	20	0	NPAP1,missense_variant,p.Ser562Phe,ENST00000329468,;	T	ENSG00000185823	ENST00000329468	Transcript	missense_variant	2159	1685	562	S/F	tCt/tTt	rs759345390,COSM3500114	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	tolerated(0.17)	probably_damaging(0.982)	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCATCTGCCC	byFrequency	5	ESCA
SNORD115-11	0	.	GRCh37	15	25436407	25436407	+	3'Flank	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000363616	.	32	25	7	16	16	0	SNORD115-11,downstream_gene_variant,,ENST00000363616,;SNORD115-10,downstream_gene_variant,,ENST00000365073,;SNHG14,upstream_gene_variant,,ENST00000363358,;SNORD115-14,upstream_gene_variant,,ENST00000363090,;SNORD115-12,upstream_gene_variant,,ENST00000362583,;SNHG14,non_coding_transcript_exon_variant,,ENST00000424208,;SNHG14,non_coding_transcript_exon_variant,,ENST00000414175,;SNHG14,upstream_gene_variant,,ENST00000456576,;	T	ENSG00000200486	ENST00000363616	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1765	1	SNORD115-11	HGNC	33030	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGACTTGCG	.	5	ESCA
SNORD115-33	0	.	GRCh37	15	25474026	25474026	+	5'Flank	SNP	T	T	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000363723	.	28	17	11	38	38	0	SNORD115-33,upstream_gene_variant,,ENST00000363723,;SNORD115-31,downstream_gene_variant,,ENST00000365318,;SNORD115-30,downstream_gene_variant,,ENST00000364117,;SNORD115-32,upstream_gene_variant,,ENST00000364079,;SNORD115-34,upstream_gene_variant,,ENST00000362441,;SNHG14,non_coding_transcript_exon_variant,,ENST00000453082,;	A	ENSG00000200593	ENST00000363723	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1959	1	SNORD115-33	HGNC	33052	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTTCCTGG	.	5	ESCA
RNU6-354P	0	.	GRCh37	15	44028270	44028270	+	5'Flank	SNP	C	C	G	rs191643915	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000383862	.	55	39	16	36	36	0	RNU6-354P,upstream_gene_variant,,ENST00000383862,;CATSPER2P1,non_coding_transcript_exon_variant,,ENST00000381680,;CATSPER2P1,downstream_gene_variant,,ENST00000416302,;CATSPER2P1,intron_variant,,ENST00000439564,;	G	ENSG00000206589	ENST00000383862	Transcript	upstream_gene_variant	.	.	.	.	.	rs191643915	.	1787	-1	RNU6-354P	HGNC	47317	snRNA	YES	.	.	.	.	.	.	.	.	.	.	.	T:0.0004	T:0.0008	T:0.0014	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCACCCGGCCA	byFrequency|by1000G	5	ESCA
ALDH1A2	0	.	GRCh37	15	58284926	58284926	+	Missense_Mutation	SNP	T	T	G	rs772058025	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775A>C	p.Ile259Leu	p.I259L	ENST00000249750	7/13	61	50	10	27	27	0	ALDH1A2,missense_variant,p.Ile163Leu,ENST00000559517,;ALDH1A2,missense_variant,p.Ile259Leu,ENST00000249750,;ALDH1A2,missense_variant,p.Ile230Leu,ENST00000558231,;ALDH1A2,missense_variant,p.Ile238Leu,ENST00000537372,;ALDH1A2,intron_variant,,ENST00000347587,;ALDH1A2,downstream_gene_variant,,ENST00000561070,;ALDH1A2,non_coding_transcript_exon_variant,,ENST00000560923,;ALDH1A2,downstream_gene_variant,,ENST00000559266,;ALDH1A2,3_prime_UTR_variant,,ENST00000430119,;	G	ENSG00000128918	ENST00000249750	Transcript	missense_variant	1543	775	259	I/L	Att/Ctt	rs772058025	.	.	-1	ALDH1A2	HGNC	15472	protein_coding	YES	CCDS10163.1	ENSP00000249750	AL1A2_HUMAN	Q9UED3_HUMAN,H0YKL3_HUMAN	UPI00001678B4	.	tolerated(0.12)	benign(0.037)	7/13	.	hmmpanther:PTHR11699:SF102,hmmpanther:PTHR11699,Pfam_domain:PF00171,Gene3D:3.40.605.10,Superfamily_domains:SSF53720	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCAATCTTGT	byFrequency	5	ESCA
ZNF609	0	.	GRCh37	15	64977379	64977379	+	3'UTR	SNP	A	A	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3494A>T	.	.	ENST00000326648	9/9	125	118	7	58	58	0	ZNF609,3_prime_UTR_variant,,ENST00000326648,;OAZ2,downstream_gene_variant,,ENST00000560258,;OAZ2,downstream_gene_variant,,ENST00000559753,;OAZ2,downstream_gene_variant,,ENST00000326005,;OAZ2,downstream_gene_variant,,ENST00000560837,;OAZ2,downstream_gene_variant,,ENST00000558194,;	T	ENSG00000180357	ENST00000326648	Transcript	3_prime_UTR_variant	7858	.	.	.	.	.	.	.	1	ZNF609	HGNC	29003	protein_coding	YES	CCDS32270.1	ENSP00000316527	ZN609_HUMAN	.	UPI00001D7783	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATATAAATATA	.	2	ESCA
ALPK3	0	.	GRCh37	15	85400143	85400143	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2780A>T	p.Glu927Val	p.E927V	ENST00000258888	6/14	44	28	15	37	37	0	ALPK3,missense_variant,p.Glu927Val,ENST00000258888,;SNORA25,upstream_gene_variant,,ENST00000364121,;	T	ENSG00000136383	ENST00000258888	Transcript	missense_variant	2947	2780	927	E/V	gAg/gTg	.	.	.	1	ALPK3	HGNC	17574	protein_coding	YES	CCDS10333.1	ENSP00000258888	ALPK3_HUMAN	.	UPI000013D013	.	deleterious_low_confidence(0)	possibly_damaging(0.46)	6/14	.	hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTGAGCAAG	.	5	ESCA
BLM	0	.	GRCh37	15	91341471	91341471	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3262G>T	p.Val1088Phe	p.V1088F	ENST00000355112	17/22	61	49	12	34	34	0	BLM,missense_variant,p.Val1088Phe,ENST00000560509,;BLM,missense_variant,p.Val1088Phe,ENST00000355112,;BLM,non_coding_transcript_exon_variant,,ENST00000560136,;BLM,3_prime_UTR_variant,,ENST00000559724,;BLM,non_coding_transcript_exon_variant,,ENST00000558825,;BLM,downstream_gene_variant,,ENST00000560559,;	T	ENSG00000197299	ENST00000355112	Transcript	missense_variant	3380	3262	1088	V/F	Gtt/Ttt	.	.	.	1	BLM	HGNC	1058	protein_coding	YES	CCDS10363.1	ENSP00000347232	BLM_HUMAN	.	UPI00001269FA	.	deleterious(0)	possibly_damaging(0.816)	17/22	.	hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF70,Gene3D:1.10.10.10,TIGRFAM_domain:TIGR00614,Pfam_domain:PF09382,SMART_domains:SM00956,Superfamily_domains:SSF52540,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTTGTTCAA	.	5	ESCA
DNAH3	0	.	GRCh37	16	20970694	20970694	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10633G>C	p.Gly3545Arg	p.G3545R	ENST00000261383	54/62	46	29	16	33	33	0	DNAH3,missense_variant,p.Gly3545Arg,ENST00000261383,;DNAH3,3_prime_UTR_variant,,ENST00000415178,;	G	ENSG00000158486	ENST00000261383	Transcript	missense_variant	10633	10633	3545	G/R	Gga/Cga	.	.	.	-1	DNAH3	HGNC	2949	protein_coding	YES	CCDS10594.1	ENSP00000261383	DYH3_HUMAN	.	UPI00001100F2	.	deleterious(0.02)	probably_damaging(0.934)	54/62	.	Pfam_domain:PF03028,hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTCCCATAC	.	5	ESCA
METTL9	0	.	GRCh37	16	21666980	21666980	+	3'UTR	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*227C>G	.	.	ENST00000358154	5/5	78	42	35	53	53	0	METTL9,3_prime_UTR_variant,,ENST00000396014,;METTL9,3_prime_UTR_variant,,ENST00000358154,;IGSF6,upstream_gene_variant,,ENST00000569602,;METTL9,downstream_gene_variant,,ENST00000568826,;METTL9,downstream_gene_variant,,ENST00000567404,;IGSF6,upstream_gene_variant,,ENST00000268389,;METTL9,non_coding_transcript_exon_variant,,ENST00000564733,;IGSF6,upstream_gene_variant,,ENST00000565499,;	G	ENSG00000197006	ENST00000358154	Transcript	3_prime_UTR_variant	1442	.	.	.	.	.	.	.	1	METTL9	HGNC	24586	protein_coding	YES	CCDS10598.2	ENSP00000350874	METL9_HUMAN	Q8TD49_HUMAN,H3BM54_HUMAN,B2R7Q6_HUMAN	UPI0000071713	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACTCAGAGC	.	5	ESCA
SCNN1B	0	.	GRCh37	16	23360218	23360218	+	Missense_Mutation	SNP	G	G	T	rs763646515	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298G>T	p.Ala100Ser	p.A100S	ENST00000343070	2/13	29	18	10	17	17	0	SCNN1B,missense_variant,p.Ala145Ser,ENST00000307331,;SCNN1B,missense_variant,p.Ala100Ser,ENST00000568923,;SCNN1B,missense_variant,p.Ala100Ser,ENST00000343070,;SCNN1B,missense_variant,p.Ala100Ser,ENST00000568085,;SCNN1B,non_coding_transcript_exon_variant,,ENST00000569789,;SCNN1B,missense_variant,p.Ala100Ser,ENST00000564275,;SCNN1B,non_coding_transcript_exon_variant,,ENST00000566870,;	T	ENSG00000168447	ENST00000343070	Transcript	missense_variant	474	298	100	A/S	Gct/Tct	rs763646515	.	.	1	SCNN1B	HGNC	10600	protein_coding	YES	CCDS10609.1	ENSP00000345751	SCNNB_HUMAN	B2R812_HUMAN	UPI0000135616	.	tolerated(0.14)	benign(0.052)	2/13	.	hmmpanther:PTHR11690:SF18,hmmpanther:PTHR11690,Gene3D:2qtsA02,TIGRFAM_domain:TIGR00859,Pfam_domain:PF00858,Prints_domain:PR01078	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAATGCTAGC	.	5	ESCA
FAM192A	0	.	GRCh37	16	57201049	57201049	+	Silent	SNP	C	C	T	rs771274396	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.438G>A	p.%3D	p.K146K	ENST00000309137	5/7	59	36	22	28	28	0	FAM192A,synonymous_variant,p.%3D,ENST00000565458,;FAM192A,synonymous_variant,p.%3D,ENST00000566077,;FAM192A,synonymous_variant,p.%3D,ENST00000389447,;FAM192A,synonymous_variant,p.%3D,ENST00000309137,;FAM192A,synonymous_variant,p.%3D,ENST00000569266,;FAM192A,synonymous_variant,p.%3D,ENST00000564108,;FAM192A,synonymous_variant,p.%3D,ENST00000567044,;FAM192A,synonymous_variant,p.%3D,ENST00000565956,;FAM192A,synonymous_variant,p.%3D,ENST00000567439,;FAM192A,synonymous_variant,p.%3D,ENST00000562324,;FAM192A,downstream_gene_variant,,ENST00000562406,;FAM192A,downstream_gene_variant,,ENST00000566584,;FAM192A,3_prime_UTR_variant,,ENST00000566403,;	T	ENSG00000172775	ENST00000309137	Transcript	synonymous_variant	697	438	146	K	aaG/aaA	rs771274396	.	.	-1	FAM192A	HGNC	29856	protein_coding	YES	CCDS42168.1	ENSP00000335808	F192A_HUMAN	H3BUL4_HUMAN,H3BU93_HUMAN,H3BTP8_HUMAN,H3BTI2_HUMAN,H3BSY6_HUMAN,H3BSF0_HUMAN,H3BQQ6_HUMAN,H3BPH9_HUMAN,H3BPF9_HUMAN,H3BP64_HUMAN,H3BN22_HUMAN,H3BMX9_HUMAN	UPI000003620C	.	.	.	5/7	.	hmmpanther:PTHR13495,hmmpanther:PTHR13495:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAACTTGTT	.	5	ESCA
FAM106A	0	.	GRCh37	17	18429102	18429102	+	3'UTR	SNP	T	T	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*506A>C	.	.	ENST00000392176	1/1	20	5	14	36	36	0	FAM106A,3_prime_UTR_variant,,ENST00000392176,;CTD-2303H24.2,intron_variant,,ENST00000581595,;CTD-2303H24.2,intron_variant,,ENST00000608313,;CTD-2303H24.2,intron_variant,,ENST00000608141,;CTD-2303H24.2,intron_variant,,ENST00000425211,;CTD-2303H24.2,intron_variant,,ENST00000609805,;USP32P2,intron_variant,,ENST00000608376,;CTD-2303H24.2,intron_variant,,ENST00000609272,;CTD-2303H24.2,intron_variant,,ENST00000609193,;CTD-2303H24.2,intron_variant,,ENST00000608216,;CTD-2303H24.2,intron_variant,,ENST00000609831,;CTD-2303H24.2,intron_variant,,ENST00000609832,;CTD-2303H24.2,intron_variant,,ENST00000610155,;USP32P2,upstream_gene_variant,,ENST00000412260,;USP32P2,upstream_gene_variant,,ENST00000610104,;USP32P2,upstream_gene_variant,,ENST00000578409,;USP32P2,upstream_gene_variant,,ENST00000577869,;CTD-2303H24.2,downstream_gene_variant,,ENST00000446853,;CTD-2303H24.2,upstream_gene_variant,,ENST00000608726,;CTD-2303H24.2,intron_variant,,ENST00000609578,;CTD-2303H24.2,intron_variant,,ENST00000608385,;CTD-2303H24.2,intron_variant,,ENST00000420856,;USP32P2,upstream_gene_variant,,ENST00000414432,;SRP68P2,upstream_gene_variant,,ENST00000456184,;	G	ENSG00000213077	ENST00000392176	Transcript	3_prime_UTR_variant	1059	.	.	.	.	.	.	.	-1	FAM106A	HGNC	25682	protein_coding	YES	.	ENSP00000437812	F106A_HUMAN	.	UPI000006FE37	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTTAGAAG	.	5	ESCA
ULK2	0	.	GRCh37	17	19679415	19679415	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*247C>T	.	.	ENST00000395544	27/27	36	21	14	15	15	0	ULK2,3_prime_UTR_variant,,ENST00000395544,;ULK2,intron_variant,,ENST00000361658,;ULK2,downstream_gene_variant,,ENST00000571454,;ULK2,upstream_gene_variant,,ENST00000570983,;	A	ENSG00000083290	ENST00000395544	Transcript	3_prime_UTR_variant	3858	.	.	.	.	.	.	.	-1	ULK2	HGNC	13480	protein_coding	YES	CCDS11213.1	ENSP00000378914	ULK2_HUMAN	.	UPI000013D19B	.	.	.	27/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGGGAGCCA	.	5	ESCA
ACACA	0	.	GRCh37	17	35598921	35598921	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2980G>C	p.Glu994Gln	p.E994Q	ENST00000353139	23/56	47	36	11	35	35	0	ACACA,missense_variant,p.Glu899Gln,ENST00000360679,;ACACA,missense_variant,p.Glu994Gln,ENST00000353139,;ACACA,missense_variant,p.Glu957Gln,ENST00000394406,;ACACA,missense_variant,p.Glu879Gln,ENST00000335166,;ACACA,non_coding_transcript_exon_variant,,ENST00000590888,;	G	ENSG00000132142	ENST00000353139	Transcript	missense_variant	3462	2980	994	E/Q	Gaa/Caa	COSM1283208,COSM1283207	.	.	-1	ACACA	HGNC	84	protein_coding	YES	CCDS42302.1	ENSP00000344789	ACACA_HUMAN	Q7Z5W8_HUMAN,K7EII5_HUMAN,K4DID9_HUMAN,B4DWK9_HUMAN,B4DK31_HUMAN,B4DIW1_HUMAN,B2ZZ90_HUMAN,A8MYL5_HUMAN	UPI00002263AC	.	deleterious(0.01)	benign(0.431)	23/56	.	hmmpanther:PTHR18866:SF89,hmmpanther:PTHR18866,Pfam_domain:PF08326	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CCGTTCAGATT	.	4	ESCA
MLLT6	0	.	GRCh37	17	36883042	36883042	+	3'UTR	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1191C>T	.	.	ENST00000325718	20/20	74	37	37	58	58	0	MLLT6,3_prime_UTR_variant,,ENST00000325718,;AC006449.1,downstream_gene_variant,,ENST00000595377,;CISD3,upstream_gene_variant,,ENST00000439660,;MLLT6,intron_variant,,ENST00000582830,;CISD3,upstream_gene_variant,,ENST00000578573,;MLLT6,non_coding_transcript_exon_variant,,ENST00000484263,;MLLT6,non_coding_transcript_exon_variant,,ENST00000494578,;CISD3,upstream_gene_variant,,ENST00000581668,;	T	ENSG00000108292	ENST00000325718	Transcript	3_prime_UTR_variant	4564	.	.	.	.	.	.	.	1	MLLT6	HGNC	7138	protein_coding	YES	CCDS11327.1	ENSP00000316426	AF17_HUMAN	.	UPI000013C86A	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCCCTCCCA	.	5	ESCA
PCGF2	0	.	GRCh37	17	36892358	36892358	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642delC	p.Tyr215ThrfsTer24	p.Y215Tfs*24	ENST00000580830	11/12	31	18	12	11	11	0	PCGF2,frameshift_variant,p.Leu162TyrfsTer131,ENST00000578109,;PCGF2,frameshift_variant,p.Leu216TyrfsTer131,ENST00000579882,;PCGF2,frameshift_variant,p.Leu216TyrfsTer131,ENST00000585100,;PCGF2,frameshift_variant,p.Tyr215ThrfsTer24,ENST00000581345,;PCGF2,frameshift_variant,p.Tyr215ThrfsTer24,ENST00000360797,;PCGF2,frameshift_variant,p.Tyr215ThrfsTer24,ENST00000580830,;CISD3,downstream_gene_variant,,ENST00000439660,;PCGF2,upstream_gene_variant,,ENST00000578487,;RNA5SP440,upstream_gene_variant,,ENST00000363245,;CISD3,downstream_gene_variant,,ENST00000578573,;CISD3,downstream_gene_variant,,ENST00000581668,;	-	ENSG00000056661	ENST00000580830	Transcript	frameshift_variant	1344	642	214	I/X	atC/at	.	.	.	-1	PCGF2	HGNC	12929	protein_coding	YES	CCDS32638.1	ENSP00000461961	PCGF2_HUMAN	.	UPI0000001279	.	.	.	11/12	.	hmmpanther:PTHR10825:SF22,hmmpanther:PTHR10825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GGGGTAGATGTA	.	2	ESCA
LRRC37A2	0	.	GRCh37	17	44626126	44626126	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3621G>A	p.%3D	p.G1207G	ENST00000576629	10/15	173	136	37	119	119	0	LRRC37A2,synonymous_variant,p.%3D,ENST00000576629,;LRRC37A2,synonymous_variant,p.%3D,ENST00000333412,;ARL17A,intron_variant,,ENST00000337845,;ARL17A,intron_variant,,ENST00000573185,;ARL17A,intron_variant,,ENST00000445552,;ARL17A,intron_variant,,ENST00000329240,;ARL17A,downstream_gene_variant,,ENST00000570550,;LRRC37A2,non_coding_transcript_exon_variant,,ENST00000572638,;	A	ENSG00000238083	ENST00000576629	Transcript	synonymous_variant	4116	3621	1207	G	ggG/ggA	.	.	.	1	LRRC37A2	HGNC	32404	protein_coding	YES	CCDS42353.1	ENSP00000459551	L37A2_HUMAN	.	UPI0000E59258	.	.	.	10/15	.	hmmpanther:PTHR23045	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGGGAGTCC	.	5	ESCA
C17orf47	0	.	GRCh37	17	56620587	56620587	+	Missense_Mutation	SNP	C	C	T	rs373119715	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.961G>A	p.Val321Met	p.V321M	ENST00000321691	1/2	29	17	12	29	29	0	C17orf47,missense_variant,p.Val321Met,ENST00000321691,;SEPT4,upstream_gene_variant,,ENST00000457347,;SEPT4,upstream_gene_variant,,ENST00000412945,;RP11-112H10.4,intron_variant,,ENST00000580589,;RP11-112H10.4,intron_variant,,ENST00000578022,;RP11-112H10.4,intron_variant,,ENST00000580769,;SEPT4,upstream_gene_variant,,ENST00000581921,;	T	ENSG00000181013	ENST00000321691	Transcript	missense_variant	1143	961	321	V/M	Gtg/Atg	rs373119715	.	.	-1	C17orf47	HGNC	26844	protein_coding	YES	CCDS32691.1	ENSP00000354874	CQ047_HUMAN	.	UPI0000140BFA	.	tolerated(0.46)	benign(0.011)	1/2	.	Pfam_domain:PF15548	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCACGTTGG	byFrequency|byCluster	5	ESCA
RPS6KB1	0	.	GRCh37	17	58024245	58024245	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*96G>A	.	.	ENST00000225577	15/15	57	38	19	57	57	0	RPS6KB1,3_prime_UTR_variant,,ENST00000225577,;RPS6KB1,3_prime_UTR_variant,,ENST00000443572,;RPS6KB1,3_prime_UTR_variant,,ENST00000393021,;RP11-178C3.1,intron_variant,,ENST00000591035,;RPS6KB1,intron_variant,,ENST00000406116,;RPS6KB1,upstream_gene_variant,,ENST00000587061,;RPS6KB1,3_prime_UTR_variant,,ENST00000472940,;RPS6KB1,non_coding_transcript_exon_variant,,ENST00000475155,;	A	ENSG00000108443	ENST00000225577	Transcript	3_prime_UTR_variant	1695	.	.	.	.	.	.	.	1	RPS6KB1	HGNC	10436	protein_coding	YES	CCDS11621.1	ENSP00000225577	KS6B1_HUMAN	K7EIM2_HUMAN,B4DLT4_HUMAN	UPI000013C873	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCAGAGAGT	.	5	ESCA
MAP3K3	0	.	GRCh37	17	61744308	61744308	+	Silent	SNP	C	C	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.483C>A	p.%3D	p.S161S	ENST00000361357	7/17	88	49	38	62	62	0	MAP3K3,synonymous_variant,p.%3D,ENST00000579585,;MAP3K3,synonymous_variant,p.%3D,ENST00000361357,;MAP3K3,synonymous_variant,p.%3D,ENST00000577395,;MAP3K3,synonymous_variant,p.%3D,ENST00000584573,;MAP3K3,synonymous_variant,p.%3D,ENST00000361733,;MAP3K3,3_prime_UTR_variant,,ENST00000577597,;MAP3K3,upstream_gene_variant,,ENST00000585302,;	A	ENSG00000198909	ENST00000361357	Transcript	synonymous_variant	801	483	161	S	tcC/tcA	.	.	.	1	MAP3K3	HGNC	6855	protein_coding	YES	CCDS32701.1	ENSP00000354927	M3K3_HUMAN	Q7Z4E6_HUMAN	UPI0000074003	.	.	.	7/17	.	hmmpanther:PTHR24360:SF38,hmmpanther:PTHR24360	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTCCTCTCC	.	5	ESCA
CD300A	0	.	GRCh37	17	72477866	72477866	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.668C>G	p.Ala223Gly	p.A223G	ENST00000360141	6/7	73	45	28	56	56	0	CD300A,missense_variant,p.Ala110Gly,ENST00000310828,;CD300A,missense_variant,p.Ala223Gly,ENST00000360141,;CD300A,missense_variant,p.Ala93Gly,ENST00000577511,;CD300A,missense_variant,p.Ala27Gly,ENST00000361933,;CD300A,intron_variant,,ENST00000392625,;CD300A,non_coding_transcript_exon_variant,,ENST00000582319,;	G	ENSG00000167851	ENST00000360141	Transcript	missense_variant	956	668	223	A/G	gCt/gGt	.	.	.	1	CD300A	HGNC	19319	protein_coding	YES	CCDS32720.1	ENSP00000353259	CLM8_HUMAN	J3QKQ4_HUMAN	UPI0000073EA9	.	tolerated(0.14)	benign(0.112)	6/7	.	hmmpanther:PTHR11860:SF40,hmmpanther:PTHR11860,Pfam_domain:PF15330	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAGGCTGCCA	.	5	ESCA
TP53	0	.	GRCh37	17	7577062	7577062	+	Frame_Shift_Del	DEL	T	T	-	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.876delA	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	8/11	86	50	36	30	30	0	TP53,frameshift_variant,p.Glu294SerfsTer57,ENST00000420246,;TP53,frameshift_variant,p.Glu294SerfsTer51,ENST00000269305,;TP53,frameshift_variant,p.Glu162SerfsTer?,ENST00000509690,;TP53,frameshift_variant,p.Glu294SerfsTer58,ENST00000359597,;TP53,frameshift_variant,p.Glu294SerfsTer51,ENST00000445888,;TP53,frameshift_variant,p.Glu294SerfsTer49,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	-	ENSG00000141510	ENST00000269305	Transcript	frameshift_variant	1066	876	292	K/X	aaA/aa	TP53_g.13856A>T,TP53_g.13856del,TP53_g.13856A>G,TP53_g.13856A>C,COSM46259,COSM44976,COSM45611	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	.	.	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Gene3D:2.60.40.720	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1	.	.	.	.	.	HIGH	.	deletion	.	.	0,0,0,0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.K291fs*48|c.871_889del19|8,CODON|p.E294fs*51|c.877delG|3,CODON|p.G293R|c.877G>A|4,CODON|p.G293fs*13|c.876_877insN|3,BUFFER|p.H296L|c.887A>T|4,BUFFER|p.H296Y|c.886C>T|4,BUFFER|p.P295P|c.885T>C|3,BUFFER|p.P295L|c.884C>T|4,BUFFER|p.E294E|c.882G>A|4,BUFFER|p.E294fs*51|c.880delG|9,BUFFER|p.E294*|c.880G>T|50,BUFFER|p.E294fs*12|c.879_880insN|3,BUFFER|p.E294K|c.880G>A|3,BUFFER|p.E294*|c.880G>T|5,BUFFER|p.E294*|c.880G>T|12,BUFFER|p.E294*|c.880G>T|5,BUFFER|p.G293G|c.879G>C|3,BUFFER|p.G293G|c.879G>A|4,BUFFER|p.K292T|c.875A>C|4,BUFFER|p.K292R|c.875A>G|5,BUFFER|p.K292*|c.874A>T|5,BUFFER|p.K292*|c.874A>T|3,BUFFER|p.K291N|c.873G>C|3,BUFFER|p.N288fs*13|c.859_872del14|17,BUFFER|p.K291R|c.872A>G|3,BUFFER|p.K291T|c.872A>C|3,BUFFER|p.K291*|c.871A>T|6,BUFFER|p.R290L|c.869G>T|4,BUFFER|p.R290H|c.869G>A|19,BUFFER|p.R290C|c.868C>T|6,BUFFER|p.L289L|c.867C>T|3,BUFFER|p.L289F|c.865C>T|3	INDELOCATOR*|VARSCANI*|PINDEL	CTCCCCTTTCTT	.	3	ESCA
LAMA1	0	.	GRCh37	18	7050775	7050775	+	Missense_Mutation	SNP	C	C	T	rs377017068	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.506G>A	p.Arg169Gln	p.R169Q	ENST00000389658	4/63	46	29	17	58	58	0	LAMA1,missense_variant,p.Arg169Gln,ENST00000389658,;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;	T	ENSG00000101680	ENST00000389658	Transcript	missense_variant	600	506	169	R/Q	cGa/cAa	rs377017068	.	.	-1	LAMA1	HGNC	6481	protein_coding	YES	CCDS32787.1	ENSP00000374309	LAMA1_HUMAN	Q7Z5W6_HUMAN,Q6P6D3_HUMAN	UPI00001C1FF9	.	tolerated(0.13)	benign(0.085)	4/63	.	PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF38,hmmpanther:PTHR10574,Pfam_domain:PF00055,SMART_domains:SM00136	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCGTCTT	byCluster	4	ESCA
AP1M1	0	.	GRCh37	19	16317176	16317176	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.224C>T	p.Ala75Val	p.A75V	ENST00000444449	3/13	31	19	11	25	25	0	AP1M1,missense_variant,p.Ala75Val,ENST00000291439,;AP1M1,missense_variant,p.Ala49Val,ENST00000591775,;AP1M1,missense_variant,p.Ala75Val,ENST00000444449,;AP1M1,missense_variant,p.Ala49Val,ENST00000590945,;AP1M1,missense_variant,p.Ala49Val,ENST00000589822,;AP1M1,missense_variant,p.Ala75Val,ENST00000429941,;AP1M1,missense_variant,p.Ala75Val,ENST00000590263,;AP1M1,intron_variant,,ENST00000590756,;AP1M1,intron_variant,,ENST00000541844,;AP1M1,non_coding_transcript_exon_variant,,ENST00000586957,;AP1M1,non_coding_transcript_exon_variant,,ENST00000589991,;AP1M1,non_coding_transcript_exon_variant,,ENST00000589782,;AP1M1,upstream_gene_variant,,ENST00000586461,;AP1M1,upstream_gene_variant,,ENST00000591966,;	T	ENSG00000072958	ENST00000444449	Transcript	missense_variant	317	224	75	A/V	gCg/gTg	COSM3692459	.	.	1	AP1M1	HGNC	13667	protein_coding	YES	CCDS46008.1	ENSP00000388996	AP1M1_HUMAN	Q59EK3_HUMAN,K7ER75_HUMAN,K7EQ90_HUMAN,K7EPJ8_HUMAN,K7ENA7_HUMAN	UPI000051DDEE	.	tolerated(0.17)	benign(0.072)	3/13	.	hmmpanther:PTHR11998,hmmpanther:PTHR11998:SF22,Pfam_domain:PF01217,Gene3D:3.30.450.60,PIRSF_domain:PIRSF005992,Superfamily_domains:SSF64356	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACGCGTGCG	.	5	ESCA
NPHS1	0	.	GRCh37	19	36333045	36333045	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2644C>T	p.%3D	p.L882L	ENST00000378910	19/29	43	31	12	46	46	0	NPHS1,synonymous_variant,p.%3D,ENST00000378910,;NPHS1,synonymous_variant,p.%3D,ENST00000353632,;NPHS1,downstream_gene_variant,,ENST00000585400,;	A	ENSG00000161270	ENST00000378910	Transcript	synonymous_variant	2644	2644	882	L	Ctg/Ttg	.	.	.	-1	NPHS1	HGNC	7908	protein_coding	YES	CCDS32996.1	ENSP00000368190	NPHN_HUMAN	.	UPI000004EF61	.	.	.	19/29	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11640:SF31,hmmpanther:PTHR11640,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.P881S|c.2641C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCAGAGGGA	.	5	ESCA
KPTN	0	.	GRCh37	19	47986768	47986768	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.300G>A	p.%3D	p.T100T	ENST00000338134	2/12	46	34	11	59	59	0	KPTN,synonymous_variant,p.%3D,ENST00000338134,;KPTN,5_prime_UTR_variant,,ENST00000536339,;KPTN,5_prime_UTR_variant,,ENST00000600271,;KPTN,intron_variant,,ENST00000595554,;NAPA,downstream_gene_variant,,ENST00000595227,;NAPA,downstream_gene_variant,,ENST00000263354,;NAPA-AS1,upstream_gene_variant,,ENST00000594367,;NAPA-AS1,upstream_gene_variant,,ENST00000593284,;KPTN,non_coding_transcript_exon_variant,,ENST00000595484,;KPTN,non_coding_transcript_exon_variant,,ENST00000602193,;KPTN,non_coding_transcript_exon_variant,,ENST00000598699,;KPTN,synonymous_variant,p.%3D,ENST00000594208,;KPTN,non_coding_transcript_exon_variant,,ENST00000594139,;NAPA,downstream_gene_variant,,ENST00000597778,;NAPA,downstream_gene_variant,,ENST00000594001,;NAPA,downstream_gene_variant,,ENST00000597271,;NAPA,downstream_gene_variant,,ENST00000594217,;	T	ENSG00000118162	ENST00000338134	Transcript	synonymous_variant	408	300	100	T	acG/acA	.	.	.	-1	KPTN	HGNC	6404	protein_coding	YES	CCDS42583.1	ENSP00000337850	KPTN_HUMAN	M0R238_HUMAN,M0QZ83_HUMAN,B4DQ76_HUMAN	UPI000007002E	.	.	.	2/12	.	hmmpanther:PTHR15435:SF2,hmmpanther:PTHR15435	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGAACGTGAT	.	5	ESCA
NAPA	0	.	GRCh37	19	47998746	47998746	+	Intron	SNP	A	A	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.342+61T>C	.	.	ENST00000263354	.	28	19	8	43	43	0	NAPA,intron_variant,,ENST00000595227,;NAPA,intron_variant,,ENST00000594155,;NAPA,intron_variant,,ENST00000598615,;NAPA,intron_variant,,ENST00000593761,;NAPA,intron_variant,,ENST00000597118,;NAPA,intron_variant,,ENST00000263354,;NAPA-AS1,non_coding_transcript_exon_variant,,ENST00000593284,;NAPA-AS1,intron_variant,,ENST00000594367,;NAPA,intron_variant,,ENST00000596892,;NAPA,intron_variant,,ENST00000595826,;NAPA,downstream_gene_variant,,ENST00000597160,;NAPA,downstream_gene_variant,,ENST00000593785,;NAPA,intron_variant,,ENST00000594288,;NAPA,intron_variant,,ENST00000597778,;NAPA,intron_variant,,ENST00000601927,;NAPA,intron_variant,,ENST00000597274,;NAPA,intron_variant,,ENST00000602174,;NAPA,intron_variant,,ENST00000594001,;NAPA,intron_variant,,ENST00000601208,;NAPA,intron_variant,,ENST00000602082,;NAPA,intron_variant,,ENST00000594740,;NAPA,upstream_gene_variant,,ENST00000593905,;NAPA,upstream_gene_variant,,ENST00000597271,;NAPA,upstream_gene_variant,,ENST00000594217,;	G	ENSG00000105402	ENST00000263354	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	NAPA	HGNC	7641	protein_coding	YES	CCDS12702.1	ENSP00000263354	SNAA_HUMAN	M0R213_HUMAN,M0R058_HUMAN,M0R027_HUMAN	UPI00000012C7	.	.	.	.	4/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGGACGCAA	.	5	ESCA
NUCB1	0	.	GRCh37	19	49425673	49425679	+	Frame_Shift_Del	DEL	CATCTGT	CATCTGT	-	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	CATCTGT	CATCTGT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1378_1384delCATCTGT	p.His460Asp	p.H460D	ENST00000405315	13/13	39	23	16	53	53	0	NUCB1,frameshift_variant,p.His460Asp,ENST00000263273,;NUCB1,frameshift_variant,p.His460Asp,ENST00000405315,;NUCB1,frameshift_variant,p.His460Asp,ENST00000407032,;NUCB1,downstream_gene_variant,,ENST00000452087,;NUCB1,downstream_gene_variant,,ENST00000424608,;CTD-2639E6.4,upstream_gene_variant,,ENST00000569130,;NUCB1-AS1,upstream_gene_variant,,ENST00000416432,;NUCB1,non_coding_transcript_exon_variant,,ENST00000485798,;NUCB1,non_coding_transcript_exon_variant,,ENST00000492367,;NUCB1,downstream_gene_variant,,ENST00000460125,;NUCB1,downstream_gene_variant,,ENST00000469291,;NUCB1,downstream_gene_variant,,ENST00000465524,;	-	ENSG00000104805	ENST00000405315	Transcript	frameshift_variant	1712-1718	1378-1384	460-462	HL*/X	CATCTGTga/ga	.	.	.	1	NUCB1	HGNC	8043	protein_coding	YES	CCDS12740.1	ENSP00000385923	NUCB1_HUMAN	Q96BA4_HUMAN,C9JBD3_HUMAN,C9J3C1_HUMAN,B4DZX0_HUMAN,B3KUR6_HUMAN	UPI0000161F57	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCCCAGCATCTGTGATCC	.	3	ESCA
PPP2R1A	0	.	GRCh37	19	52714685	52714685	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.443G>A	p.Cys148Tyr	p.C148Y	ENST00000322088	4/15	88	59	28	67	67	0	PPP2R1A,missense_variant,p.Cys188Tyr,ENST00000454220,;PPP2R1A,missense_variant,p.Cys93Tyr,ENST00000444322,;PPP2R1A,missense_variant,p.Cys148Tyr,ENST00000322088,;PPP2R1A,5_prime_UTR_variant,,ENST00000462990,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000473455,;PPP2R1A,downstream_gene_variant,,ENST00000495876,;PPP2R1A,3_prime_UTR_variant,,ENST00000490868,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000468280,;PPP2R1A,upstream_gene_variant,,ENST00000473820,;PPP2R1A,upstream_gene_variant,,ENST00000462047,;	A	ENSG00000105568	ENST00000322088	Transcript	missense_variant	501	443	148	C/Y	tGc/tAc	COSM333322	.	.	1	PPP2R1A	HGNC	9302	protein_coding	YES	CCDS12849.1	ENSP00000324804	2AAA_HUMAN	B4DDF7_HUMAN,B3KQV6_HUMAN,A8K7B7_HUMAN	UPI000006EB9C	.	deleterious(0)	probably_damaging(0.985)	4/15	.	hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTGCGGCC	.	5	ESCA
BIRC8	0	.	GRCh37	19	53793366	53793366	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.262G>A	p.Glu88Lys	p.E88K	ENST00000426466	1/1	61	47	14	51	51	0	BIRC8,missense_variant,p.Glu88Lys,ENST00000426466,;	T	ENSG00000163098	ENST00000426466	Transcript	missense_variant	1510	262	88	E/K	Gag/Aag	COSM440217	.	.	-1	BIRC8	HGNC	14878	protein_coding	YES	CCDS12863.1	ENSP00000412957	BIRC8_HUMAN	.	UPI000003966A	.	tolerated(0.1)	benign(0.004)	1/1	.	hmmpanther:PTHR10044:SF10,hmmpanther:PTHR10044	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTCAAGTG	.	5	ESCA
MBOAT7	0	.	GRCh37	19	54678123	54678125	+	In_Frame_Del	DEL	CTC	CTC	-	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	CTC	CTC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032_1034delGAG	p.Ser345del	p.S345del	ENST00000245615	8/8	75	53	22	47	47	0	MBOAT7,inframe_deletion,p.Gly117del,ENST00000449249,;MBOAT7,inframe_deletion,p.Ser272del,ENST00000431666,;MBOAT7,inframe_deletion,p.Ser272del,ENST00000338624,;MBOAT7,inframe_deletion,p.Ser345del,ENST00000245615,;TMC4,upstream_gene_variant,,ENST00000376591,;MBOAT7,downstream_gene_variant,,ENST00000391754,;TMC4,upstream_gene_variant,,ENST00000446291,;TMC4,upstream_gene_variant,,ENST00000301187,;TMC4,upstream_gene_variant,,ENST00000479750,;TMC4,upstream_gene_variant,,ENST00000476013,;MBOAT7,splice_region_variant,,ENST00000494142,;MBOAT7,splice_region_variant,,ENST00000437868,;	-	ENSG00000125505	ENST00000245615	Transcript	inframe_deletion	1513-1515	1032-1034	344-345	RS/R	cgGAGc/cgc	.	.	.	-1	MBOAT7	HGNC	15505	protein_coding	YES	CCDS12883.1	ENSP00000245615	MBOA7_HUMAN	C9J4E9_HUMAN,A9C4B8_HUMAN	UPI000013CBAC	.	.	.	8/8	.	hmmpanther:PTHR13906:SF8,hmmpanther:PTHR13906,Pfam_domain:PF03062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CAGGCGCTCCTGAG	.	3	ESCA
ZNF587B	0	.	GRCh37	19	58352646	58352646	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.604G>C	p.Glu202Gln	p.E202Q	ENST00000442832	3/4	86	65	21	48	48	0	ZNF587B,missense_variant,p.Glu152Gln,ENST00000594328,;ZNF587B,missense_variant,p.Glu202Gln,ENST00000594901,;ZNF587B,missense_variant,p.Glu202Gln,ENST00000442832,;CTD-2583A14.10,intron_variant,,ENST00000598031,;ZNF587B,intron_variant,,ENST00000316462,;CTD-2583A14.10,intron_variant,,ENST00000597134,;CTD-2583A14.10,intron_variant,,ENST00000593873,;CTD-2583A14.10,intron_variant,,ENST00000596498,;CTD-2583A14.10,intron_variant,,ENST00000603271,;CTD-2583A14.10,intron_variant,,ENST00000604231,;	C	ENSG00000269343	ENST00000442832	Transcript	missense_variant	838	604	202	E/Q	Gag/Cag	.	.	.	1	ZNF587B	HGNC	37142	protein_coding	YES	CCDS56109.1	ENSP00000392410	Z587B_HUMAN	.	UPI0001AE657B	.	tolerated(0.29)	possibly_damaging(0.552)	3/4	.	hmmpanther:PTHR24387:SF191,hmmpanther:PTHR24387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AAACTGAGTGT	.	4	ESCA
VANGL1	0	.	GRCh37	1	116238114	116238114	+	3'UTR	SNP	T	T	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4114T>A	.	.	ENST00000355485	8/8	38	32	6	22	22	0	VANGL1,3_prime_UTR_variant,,ENST00000355485,;VANGL1,3_prime_UTR_variant,,ENST00000369510,;VANGL1,downstream_gene_variant,,ENST00000369509,;CASQ2,downstream_gene_variant,,ENST00000261448,;VANGL1,downstream_gene_variant,,ENST00000310260,;	A	ENSG00000173218	ENST00000355485	Transcript	3_prime_UTR_variant	5960	.	.	.	.	.	.	.	1	VANGL1	HGNC	15512	protein_coding	YES	CCDS883.1	ENSP00000347672	VANG1_HUMAN	.	UPI0000070B72	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTATTCAGTG	.	4	ESCA
VANGL1	0	.	GRCh37	1	116238115	116238115	+	3'UTR	SNP	C	C	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4115C>A	.	.	ENST00000355485	8/8	39	33	6	22	22	0	VANGL1,3_prime_UTR_variant,,ENST00000355485,;VANGL1,3_prime_UTR_variant,,ENST00000369510,;VANGL1,downstream_gene_variant,,ENST00000369509,;CASQ2,downstream_gene_variant,,ENST00000261448,;VANGL1,downstream_gene_variant,,ENST00000310260,;	A	ENSG00000173218	ENST00000355485	Transcript	3_prime_UTR_variant	5961	.	.	.	.	.	.	.	1	VANGL1	HGNC	15512	protein_coding	YES	CCDS883.1	ENSP00000347672	VANG1_HUMAN	.	UPI0000070B72	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTATTCAGTGC	.	4	ESCA
UBE2J2	0	.	GRCh37	1	1190236	1190236	+	3'Flank	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000400930	.	33	24	9	56	56	0	UBE2J2,3_prime_UTR_variant,,ENST00000349431,;UBE2J2,3_prime_UTR_variant,,ENST00000347370,;UBE2J2,downstream_gene_variant,,ENST00000502382,;UBE2J2,downstream_gene_variant,,ENST00000339385,;UBE2J2,downstream_gene_variant,,ENST00000422076,;UBE2J2,downstream_gene_variant,,ENST00000509720,;UBE2J2,downstream_gene_variant,,ENST00000348298,;UBE2J2,downstream_gene_variant,,ENST00000400930,;UBE2J2,downstream_gene_variant,,ENST00000400929,;UBE2J2,downstream_gene_variant,,ENST00000360466,;UBE2J2,downstream_gene_variant,,ENST00000435198,;RP5-902P8.12,upstream_gene_variant,,ENST00000565563,;UBE2J2,downstream_gene_variant,,ENST00000491779,;UBE2J2,downstream_gene_variant,,ENST00000467339,;UBE2J2,3_prime_UTR_variant,,ENST00000450390,;UBE2J2,downstream_gene_variant,,ENST00000477894,;UBE2J2,downstream_gene_variant,,ENST00000473215,;UBE2J2,downstream_gene_variant,,ENST00000503294,;UBE2J2,downstream_gene_variant,,ENST00000464036,;UBE2J2,downstream_gene_variant,,ENST00000471154,;UBE2J2,downstream_gene_variant,,ENST00000466752,;	T	ENSG00000160087	ENST00000400930	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	322	-1	UBE2J2	HGNC	19268	protein_coding	YES	CCDS15.1	ENSP00000383719	UB2J2_HUMAN	D6REN4_HUMAN,D6RD90_HUMAN,D6R9H0_HUMAN,B1AMF1_HUMAN,A6NGS0_HUMAN	UPI00001D69F8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGCCCGCG	.	5	ESCA
HRNR	0	.	GRCh37	1	152191117	152191117	+	Silent	SNP	G	G	A	rs150171173	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2988C>T	p.%3D	p.H996H	ENST00000368801	3/3	101	60	41	87	87	0	HRNR,synonymous_variant,p.%3D,ENST00000368801,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	A	ENSG00000197915	ENST00000368801	Transcript	synonymous_variant	3064	2988	996	H	caC/caT	rs150171173	.	.	-1	HRNR	HGNC	20846	protein_coding	YES	CCDS30859.1	ENSP00000357791	HORN_HUMAN	Q5W8V9_HUMAN	UPI00001D7CAD	.	.	.	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF23,hmmpanther:PTHR22571	A:0.0006	A:0.0008	A:0	.	A:0.002	A:0	A:0	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCCGTGGCC	byFrequency|byCluster|by1000G	5	ESCA
HSPA6	0	.	GRCh37	1	161495361	161495361	+	Missense_Mutation	SNP	G	G	C	rs781731364	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.913G>C	p.Glu305Gln	p.E305Q	ENST00000309758	1/1	68	44	23	81	81	0	HSPA6,missense_variant,p.Glu305Gln,ENST00000309758,;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR2A,downstream_gene_variant,,ENST00000491841,;FCGR2A,downstream_gene_variant,,ENST00000467525,;	C	ENSG00000173110	ENST00000309758	Transcript	missense_variant	1326	913	305	E/Q	Gag/Cag	rs781731364,COSM2087228	.	.	1	HSPA6	HGNC	5239	protein_coding	YES	CCDS1231.1	ENSP00000310219	HSP76_HUMAN	.	UPI0000074238	.	deleterious_low_confidence(0)	probably_damaging(0.992)	1/1	.	Superfamily_domains:SSF53067,Gene3D:3.90.640.10,Pfam_domain:PF00012,hmmpanther:PTHR19375:SF168,hmmpanther:PTHR19375	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTTGAGGAA	.	5	ESCA
DNAH14	0	.	GRCh37	1	225490958	225490958	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6494C>T	p.Thr2165Met	p.T2165M	ENST00000445597	37/61	53	34	19	40	40	0	DNAH14,missense_variant,p.Thr2165Met,ENST00000445597,;DNAH14,missense_variant,p.Thr2818Met,ENST00000430092,;DNAH14,missense_variant,p.Thr2818Met,ENST00000439375,;DNAH14,missense_variant,p.Thr616Met,ENST00000327794,;	T	ENSG00000185842	ENST00000445597	Transcript	missense_variant	6494	6494	2165	T/M	aCg/aTg	.	.	.	1	DNAH14	HGNC	2945	protein_coding	.	.	ENSP00000409472	DYH14_HUMAN	C9JU64_HUMAN	UPI0001642868	.	deleterious(0)	probably_damaging(0.999)	37/61	.	Superfamily_domains:SSF52540,Pfam_domain:PF12780,Gene3D:3.40.50.300,hmmpanther:PTHR10676:SF132,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCACGATCG	.	5	ESCA
FMN2	0	.	GRCh37	1	240255968	240255968	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559C>T	p.His187Tyr	p.H187Y	ENST00000319653	1/18	67	47	20	86	86	0	FMN2,missense_variant,p.His187Tyr,ENST00000319653,;FMN2,intron_variant,,ENST00000447095,;	T	ENSG00000155816	ENST00000319653	Transcript	missense_variant	789	559	187	H/Y	Cat/Tat	COSM1502046	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	unknown(0)	1/18	.	hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTCCATTCG	.	5	ESCA
OR11L1	0	.	GRCh37	1	248004653	248004653	+	Silent	SNP	C	C	A	rs777477000	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.546G>T	p.%3D	p.P182P	ENST00000355784	1/1	30	22	7	49	49	0	OR11L1,synonymous_variant,p.%3D,ENST00000355784,;	A	ENSG00000197591	ENST00000355784	Transcript	synonymous_variant	602	546	182	P	ccG/ccT	rs777477000,COSM3386019	.	.	-1	OR11L1	HGNC	14998	protein_coding	YES	CCDS31098.1	ENSP00000348033	O11L1_HUMAN	.	UPI0000061EBC	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF12,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGGCGGGAG	.	5	ESCA
HCRTR1	0	.	GRCh37	1	32084943	32084943	+	Silent	SNP	C	C	T	rs201247112	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150C>T	p.%3D	p.I50I	ENST00000403528	3/9	36	24	12	39	39	0	HCRTR1,synonymous_variant,p.%3D,ENST00000373705,;HCRTR1,synonymous_variant,p.%3D,ENST00000373706,;HCRTR1,synonymous_variant,p.%3D,ENST00000403528,;HCRTR1,non_coding_transcript_exon_variant,,ENST00000468521,;HCRTR1,intron_variant,,ENST00000485464,;	T	ENSG00000121764	ENST00000403528	Transcript	synonymous_variant	535	150	50	I	atC/atT	rs201247112	.	.	1	HCRTR1	HGNC	4848	protein_coding	YES	CCDS344.1	ENSP00000384387	OX1R_HUMAN	.	UPI0000038135	.	.	.	3/9	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF30,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCGCAGC	byCluster	5	ESCA
NCDN	0	.	GRCh37	1	36028834	36028834	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1417G>A	p.Val473Ile	p.V473I	ENST00000373243	5/7	18	9	8	32	32	0	NCDN,missense_variant,p.Val67Ile,ENST00000423723,;NCDN,missense_variant,p.Val456Ile,ENST00000373253,;NCDN,missense_variant,p.Val473Ile,ENST00000373243,;NCDN,missense_variant,p.Val473Ile,ENST00000356090,;NCDN,downstream_gene_variant,,ENST00000437806,;NCDN,downstream_gene_variant,,ENST00000459931,;	A	ENSG00000020129	ENST00000373243	Transcript	missense_variant	1800	1417	473	V/I	Gtt/Att	COSM4007376,COSM4007375	.	.	1	NCDN	HGNC	17597	protein_coding	YES	CCDS392.1	ENSP00000362340	NCDN_HUMAN	C9J5H8_HUMAN,B4DJ92_HUMAN	UPI000007147C	.	deleterious(0)	benign(0.017)	5/7	.	hmmpanther:PTHR13109,Pfam_domain:PF05536	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGACCGTTGAA	.	5	ESCA
RLF	0	.	GRCh37	1	40705442	40705442	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5068C>T	p.Gln1690Ter	p.Q1690*	ENST00000372771	8/8	37	29	8	53	53	0	RLF,stop_gained,p.Gln1690Ter,ENST00000372771,;	T	ENSG00000117000	ENST00000372771	Transcript	stop_gained	5095	5068	1690	Q/*	Cag/Tag	.	.	.	1	RLF	HGNC	10025	protein_coding	YES	CCDS448.1	ENSP00000361857	RLF_HUMAN	.	UPI000013C9DA	.	.	.	8/8	.	hmmpanther:PTHR15507:SF18,hmmpanther:PTHR15507	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAGTTCAGCCT	.	3	ESCA
CYP4X1	0	.	GRCh37	1	47501605	47501605	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.620G>A	p.Ser207Asn	p.S207N	ENST00000371901	5/12	57	43	14	46	46	0	CYP4X1,missense_variant,p.Ser207Asn,ENST00000371901,;CYP4X1,missense_variant,p.Ser206Asn,ENST00000538609,;CYP4X1,upstream_gene_variant,,ENST00000466294,;	A	ENSG00000186377	ENST00000371901	Transcript	missense_variant	870	620	207	S/N	aGc/aAc	.	.	.	1	CYP4X1	HGNC	20244	protein_coding	YES	CCDS544.1	ENSP00000360968	CP4X1_HUMAN	.	UPI000003F043	.	tolerated(0.25)	probably_damaging(0.932)	5/12	.	hmmpanther:PTHR24290:SF6,hmmpanther:PTHR24290,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACAGGTCAG	.	5	ESCA
EPS15	0	.	GRCh37	1	51820874	51820874	+	3'UTR	SNP	A	A	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1498T>C	.	.	ENST00000371733	25/25	25	13	12	33	33	0	EPS15,3_prime_UTR_variant,,ENST00000371730,;EPS15,3_prime_UTR_variant,,ENST00000371733,;EPS15,downstream_gene_variant,,ENST00000396122,;	G	ENSG00000085832	ENST00000371733	Transcript	3_prime_UTR_variant	4286	.	.	.	.	.	.	.	-1	EPS15	HGNC	3419	protein_coding	YES	CCDS557.1	ENSP00000360798	EPS15_HUMAN	.	UPI0000161B29	.	.	.	25/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATGGAAAGAA	.	5	ESCA
C1orf173	0	.	GRCh37	1	75065555	75065555	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1550G>A	p.Gly517Glu	p.G517E	ENST00000326665	11/15	84	60	24	37	37	0	C1orf173,missense_variant,p.Gly320Glu,ENST00000420661,;C1orf173,missense_variant,p.Gly517Glu,ENST00000326665,;RP4-612J11.1,intron_variant,,ENST00000416017,;	T	ENSG00000178965	ENST00000326665	Transcript	missense_variant	1769	1550	517	G/E	gGa/gAa	.	.	.	-1	C1orf173	HGNC	25346	protein_coding	YES	CCDS30755.1	ENSP00000322609	CA173_HUMAN	.	UPI0000237200	.	deleterious(0.01)	possibly_damaging(0.861)	11/15	.	hmmpanther:PTHR23034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGTCCTTCT	.	5	ESCA
BPIFB2	0	.	GRCh37	20	31600673	31600673	+	Missense_Mutation	SNP	C	C	T	rs757877643	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.268C>T	p.Arg90Cys	p.R90C	ENST00000170150	4/16	66	35	31	64	64	0	BPIFB2,missense_variant,p.Arg90Cys,ENST00000170150,;	T	ENSG00000078898	ENST00000170150	Transcript	missense_variant	463	268	90	R/C	Cgc/Tgc	rs757877643	.	.	1	BPIFB2	HGNC	16177	protein_coding	YES	CCDS13210.1	ENSP00000170150	BPIB2_HUMAN	.	UPI00000377B0	.	deleterious(0.01)	probably_damaging(0.912)	4/16	.	Superfamily_domains:SSF55394,Pfam_domain:PF01273,hmmpanther:PTHR10504:SF68,hmmpanther:PTHR10504	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGTGCGCCTG	byFrequency	5	ESCA
SEZ6L	0	.	GRCh37	22	26706706	26706706	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1585C>A	p.Pro529Thr	p.P529T	ENST00000248933	7/17	31	26	5	29	29	0	SEZ6L,missense_variant,p.Pro529Thr,ENST00000529632,;SEZ6L,missense_variant,p.Pro529Thr,ENST00000248933,;SEZ6L,missense_variant,p.Pro529Thr,ENST00000360929,;SEZ6L,missense_variant,p.Pro529Thr,ENST00000343706,;SEZ6L,missense_variant,p.Pro302Thr,ENST00000402979,;SEZ6L,missense_variant,p.Pro302Thr,ENST00000403121,;SEZ6L,missense_variant,p.Pro529Thr,ENST00000404234,;	A	ENSG00000100095	ENST00000248933	Transcript	missense_variant	1680	1585	529	P/T	Cct/Act	.	.	.	1	SEZ6L	HGNC	10763	protein_coding	YES	CCDS13833.1	ENSP00000248933	SE6L1_HUMAN	.	UPI0000136779	.	deleterious(0)	probably_damaging(1)	7/17	.	Superfamily_domains:SSF49854,SMART_domains:SM00042,Pfam_domain:PF00431,Gene3D:2.60.120.290,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF81,PROSITE_profiles:PS01180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGTCCCTTTT	.	4	ESCA
UPK3A	0	.	GRCh37	22	45684984	45684984	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531G>C	p.Glu177Asp	p.E177D	ENST00000216211	4/6	22	13	9	28	28	0	UPK3A,missense_variant,p.Glu177Asp,ENST00000216211,;UPK3A,intron_variant,,ENST00000396082,;	C	ENSG00000100373	ENST00000216211	Transcript	missense_variant	563	531	177	E/D	gaG/gaC	.	.	.	1	UPK3A	HGNC	12580	protein_coding	YES	CCDS14064.1	ENSP00000216211	UPK3A_HUMAN	.	UPI0000161B8E	.	tolerated(0.18)	benign(0.023)	4/6	.	hmmpanther:PTHR15446,hmmpanther:PTHR15446:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAGAGGACCA	.	5	ESCA
ATXN10	0	.	GRCh37	22	46098707	46098707	+	Missense_Mutation	SNP	A	A	T	rs577007698	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.627A>T	p.Lys209Asn	p.K209N	ENST00000252934	5/12	70	50	19	75	75	0	ATXN10,missense_variant,p.Lys145Asn,ENST00000381061,;ATXN10,missense_variant,p.Lys209Asn,ENST00000252934,;ATXN10,non_coding_transcript_exon_variant,,ENST00000498009,;ATXN10,upstream_gene_variant,,ENST00000476998,;ATXN10,downstream_gene_variant,,ENST00000470722,;	T	ENSG00000130638	ENST00000252934	Transcript	missense_variant	892	627	209	K/N	aaA/aaT	rs577007698	.	.	1	ATXN10	HGNC	10549	protein_coding	YES	CCDS14070.1	ENSP00000252934	ATX10_HUMAN	Q9NTC6_HUMAN	UPI0000052A56	.	tolerated(0.07)	possibly_damaging(0.756)	5/12	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13255,hmmpanther:PTHR13255:SF0,Superfamily_domains:SSF48371	G:0.0002	G:0.0008	G:0	.	G:0	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAAACATCC	by1000G	5	ESCA
PPP6R2	0	.	GRCh37	22	50860746	50860746	+	Silent	SNP	C	C	T	rs547118539	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.912C>T	p.%3D	p.S304S	ENST00000395741	9/23	34	19	15	59	59	0	PPP6R2,synonymous_variant,p.%3D,ENST00000395741,;PPP6R2,synonymous_variant,p.%3D,ENST00000395744,;PPP6R2,synonymous_variant,p.%3D,ENST00000359139,;PPP6R2,synonymous_variant,p.%3D,ENST00000401672,;PPP6R2,synonymous_variant,p.%3D,ENST00000216061,;PPP6R2,upstream_gene_variant,,ENST00000427222,;	T	ENSG00000100239	ENST00000395741	Transcript	synonymous_variant	1287	912	304	S	agC/agT	rs547118539	.	.	1	PPP6R2	HGNC	19253	protein_coding	YES	CCDS56235.1	ENSP00000379090	PP6R2_HUMAN	.	UPI0000453B02	.	.	.	9/23	.	Superfamily_domains:SSF48371,Pfam_domain:PF04499,hmmpanther:PTHR12634:SF15,hmmpanther:PTHR12634	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCAGCGTACT	by1000G	5	ESCA
MYO3B	0	.	GRCh37	2	171243657	171243660	+	Frame_Shift_Del	DEL	CTCC	CTCC	-	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	CTCC	CTCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1418_1421delCCCT	p.Ser473TrpfsTer25	p.S473Wfs*25	ENST00000408978	14/35	42	29	13	30	30	0	MYO3B,frameshift_variant,p.Ser482TrpfsTer25,ENST00000484338,;MYO3B,frameshift_variant,p.Ser473TrpfsTer25,ENST00000408978,;MYO3B,frameshift_variant,p.Ser482TrpfsTer25,ENST00000334231,;MYO3B,frameshift_variant,p.Ser473TrpfsTer25,ENST00000409044,;MYO3B,downstream_gene_variant,,ENST00000442690,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,frameshift_variant,p.Ser473TrpfsTer25,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,;	-	ENSG00000071909	ENST00000408978	Transcript	frameshift_variant	1559-1562	1416-1419	472-473	NS/X	aaCTCC/aa	.	.	.	1	MYO3B	HGNC	15576	protein_coding	YES	CCDS42773.1	ENSP00000386213	MYO3B_HUMAN	.	UPI000020907B	.	.	.	14/35	.	Prints_domain:PR00193,Superfamily_domains:SSF52540,SMART_domains:SM00242,Pfam_domain:PF00063,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF311,PROSITE_profiles:PS51456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTCAACTCCCTGGT	.	3	ESCA
RAPGEF4	0	.	GRCh37	2	173883429	173883429	+	Missense_Mutation	SNP	G	G	A	rs776601135	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2054G>A	p.Arg685Gln	p.R685Q	ENST00000397081	22/31	26	16	9	27	27	0	RAPGEF4,missense_variant,p.Arg541Gln,ENST00000397087,;RAPGEF4,missense_variant,p.Arg685Gln,ENST00000409036,;RAPGEF4,missense_variant,p.Arg684Gln,ENST00000264111,;RAPGEF4,missense_variant,p.Arg465Gln,ENST00000535187,;RAPGEF4,missense_variant,p.Arg532Gln,ENST00000539331,;RAPGEF4,missense_variant,p.Arg514Gln,ENST00000538974,;RAPGEF4,missense_variant,p.Arg685Gln,ENST00000397081,;RAPGEF4,missense_variant,p.Arg532Gln,ENST00000540783,;	A	ENSG00000091428	ENST00000397081	Transcript	missense_variant	2197	2054	685	R/Q	cGg/cAg	rs776601135	.	.	1	RAPGEF4	HGNC	16626	protein_coding	YES	CCDS42775.1	ENSP00000380271	RPGF4_HUMAN	Q53TH3_HUMAN,Q53QY2_HUMAN,B7Z283_HUMAN,B7Z278_HUMAN	UPI000006D4C7	.	tolerated(0.27)	possibly_damaging(0.695)	22/31	.	hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF175,Pfam_domain:PF00788,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTCGGGTGC	.	5	ESCA
COL5A2	0	.	GRCh37	2	189901379	189901379	+	Missense_Mutation	SNP	G	G	A	rs745580343	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4076C>T	p.Pro1359Leu	p.P1359L	ENST00000374866	52/54	55	37	18	66	66	0	COL5A2,missense_variant,p.Pro1359Leu,ENST00000374866,;	A	ENSG00000204262	ENST00000374866	Transcript	missense_variant	4351	4076	1359	P/L	cCt/cTt	rs745580343	.	.	-1	COL5A2	HGNC	2210	protein_coding	YES	CCDS33350.1	ENSP00000364000	CO5A2_HUMAN	D3DPH5_HUMAN	UPI00006C511C	.	.	unknown(0)	52/54	.	SMART_domains:SM00038,Pfam_domain:PF01410,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF481,PROSITE_profiles:PS51461	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACAGGTTTA	byFrequency	5	ESCA
COL4A3	0	.	GRCh37	2	228169785	228169785	+	Missense_Mutation	SNP	C	C	T	rs373382431	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000396578	47/52	66	45	21	33	33	0	COL4A3,missense_variant,p.Ser1413Phe,ENST00000396578,;AC097662.2,intron_variant,,ENST00000433324,;AC097662.2,intron_variant,,ENST00000396588,;AC097662.2,intron_variant,,ENST00000439598,;COL4A3,downstream_gene_variant,,ENST00000468753,;COL4A3,upstream_gene_variant,,ENST00000469504,;COL4A3,downstream_gene_variant,,ENST00000471862,;	T	ENSG00000169031	ENST00000396578	Transcript	missense_variant	4400	4238	1413	S/F	tCt/tTt	rs373382431	.	.	1	COL4A3	HGNC	2204	protein_coding	YES	CCDS42829.1	ENSP00000379823	CO4A3_HUMAN	Q548X1_HUMAN,A9QVI3_HUMAN	UPI000013E9F3	.	.	unknown(0)	47/52	.	hmmpanther:PTHR24023:SF417,hmmpanther:PTHR24023,Pfam_domain:PF01391	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTCTAAAG	.	5	ESCA
MYT1L	0	.	GRCh37	2	2328522	2328522	+	Intron	SNP	A	A	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-521+6217T>C	.	.	ENST00000428368	.	37	25	12	31	31	0	MYT1L,intron_variant,,ENST00000399161,;MYT1L,intron_variant,,ENST00000428368,;MYT1L-AS1,non_coding_transcript_exon_variant,,ENST00000422175,;MYT1L-AS1,non_coding_transcript_exon_variant,,ENST00000448106,;MYT1L,intron_variant,,ENST00000460585,;MYT1L,intron_variant,,ENST00000476547,;MYT1L,upstream_gene_variant,,ENST00000479156,;	G	ENSG00000186487	ENST00000428368	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MYT1L	HGNC	7623	protein_coding	YES	CCDS46222.1	ENSP00000396103	MYT1L_HUMAN	.	UPI00004E55EA	.	.	.	.	1/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGGAAGCAT	.	5	ESCA
UGT1A7	0	.	GRCh37	2	234591302	234591302	+	Missense_Mutation	SNP	C	C	T	rs371311391	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.719C>T	p.Thr240Met	p.T240M	ENST00000373426	1/5	84	59	25	51	51	0	UGT1A7,missense_variant,p.Thr240Met,ENST00000373426,;UGT1A7,missense_variant,p.Thr97Met,ENST00000485022,;UGT1A10,intron_variant,,ENST00000373445,;UGT1A10,intron_variant,,ENST00000344644,;UGT1A8,intron_variant,,ENST00000373450,;UGT1A8,intron_variant,,ENST00000609637,;UGT1A9,intron_variant,,ENST00000354728,;	T	ENSG00000244122	ENST00000373426	Transcript	missense_variant	719	719	240	T/M	aCg/aTg	rs371311391,COSM3050261	.	.	1	UGT1A7	HGNC	12539	protein_coding	YES	CCDS2506.1	ENSP00000362525	UD17_HUMAN	Q5DSZ7_HUMAN	UPI000013EA12	.	deleterious(0)	probably_damaging(0.958)	1/5	.	Superfamily_domains:SSF53756,Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF138	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCACGGCAT	byCluster	5	ESCA
ANKMY1	0	.	GRCh37	2	241451391	241451391	+	Missense_Mutation	SNP	G	G	A	rs758507744	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1906C>T	p.Leu636Phe	p.L636F	ENST00000391987	11/18	56	42	13	31	31	0	ANKMY1,missense_variant,p.Leu636Phe,ENST00000272972,;ANKMY1,missense_variant,p.Leu636Phe,ENST00000391987,;ANKMY1,missense_variant,p.Leu406Phe,ENST00000373320,;ANKMY1,missense_variant,p.Leu574Phe,ENST00000403283,;ANKMY1,missense_variant,p.Leu495Phe,ENST00000373318,;ANKMY1,missense_variant,p.Leu725Phe,ENST00000401804,;ANKMY1,missense_variant,p.Leu397Phe,ENST00000406958,;ANKMY1,intron_variant,,ENST00000361678,;ANKMY1,intron_variant,,ENST00000391988,;ANKMY1,downstream_gene_variant,,ENST00000536462,;ANKMY1,upstream_gene_variant,,ENST00000489677,;	A	ENSG00000144504	ENST00000391987	Transcript	missense_variant	2273	1906	636	L/F	Ctc/Ttc	rs758507744	.	.	-1	ANKMY1	HGNC	20987	protein_coding	YES	CCDS2536.1	ENSP00000375847	ANKY1_HUMAN	C9JZ56_HUMAN	UPI000013D98C	.	tolerated(0.1)	probably_damaging(0.997)	11/18	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50297,hmmpanther:PTHR15897:SF1,hmmpanther:PTHR15897,Pfam_domain:PF12796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGAGCTTCA	.	5	ESCA
EPCAM	0	.	GRCh37	2	47604906	47604906	+	Intron	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555+690C>T	.	.	ENST00000263735	.	75	44	31	54	54	0	EPCAM,intron_variant,,ENST00000405271,;EPCAM,intron_variant,,ENST00000263735,;EPCAM,downstream_gene_variant,,ENST00000419334,;MIR559,non_coding_transcript_exon_variant,,ENST00000385188,;EPCAM,intron_variant,,ENST00000456133,;EPCAM,intron_variant,,ENST00000490733,;EPCAM,downstream_gene_variant,,ENST00000474691,;	T	ENSG00000119888	ENST00000263735	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	EPCAM	HGNC	11529	protein_coding	YES	CCDS1833.1	ENSP00000263735	EPCAM_HUMAN	.	UPI000013D450	.	.	.	.	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTCCCATC	.	5	ESCA
LHCGR	0	.	GRCh37	2	48921377	48921377	+	Silent	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933G>C	p.%3D	p.V311V	ENST00000294954	10/11	71	53	18	47	47	0	LHCGR,synonymous_variant,p.%3D,ENST00000403273,;LHCGR,synonymous_variant,p.%3D,ENST00000344775,;LHCGR,synonymous_variant,p.%3D,ENST00000401907,;LHCGR,synonymous_variant,p.%3D,ENST00000294954,;LHCGR,intron_variant,,ENST00000405626,;STON1-GTF2A1L,intron_variant,,ENST00000402114,;GTF2A1L,intron_variant,,ENST00000508440,;LHCGR,3_prime_UTR_variant,,ENST00000602369,;	G	ENSG00000138039	ENST00000294954	Transcript	synonymous_variant	955	933	311	V	gtG/gtC	.	.	.	-1	LHCGR	HGNC	6585	protein_coding	YES	CCDS1842.1	ENSP00000294954	LSHR_HUMAN	Q53S49_HUMAN,Q4ZFZ4_HUMAN	UPI000013E1E1	.	.	.	10/11	.	hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTATTCACTTT	.	4	ESCA
REG1P	0	.	GRCh37	2	79364421	79364421	+	RNA	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.214G>C	.	.	ENST00000444841	3/4	87	65	22	48	48	0	REG1P,non_coding_transcript_exon_variant,,ENST00000414597,;REG1P,non_coding_transcript_exon_variant,,ENST00000377435,;REG1P,non_coding_transcript_exon_variant,,ENST00000444841,;REG1P,non_coding_transcript_exon_variant,,ENST00000443710,;REG1P,non_coding_transcript_exon_variant,,ENST00000450249,;REG1P,downstream_gene_variant,,ENST00000434852,;REG1P,non_coding_transcript_exon_variant,,ENST00000447469,;	G	ENSG00000204787	ENST00000444841	Transcript	non_coding_transcript_exon_variant	214	.	.	.	.	.	.	.	-1	REG1P	HGNC	9953	processed_transcript	YES	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCTGGGC	.	5	ESCA
COL6A5	0	.	GRCh37	3	130107707	130107707	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2146C>T	p.Gln716Ter	p.Q716*	ENST00000265379	6/42	50	37	13	46	46	0	COL6A5,stop_gained,p.Gln716Ter,ENST00000432398,;COL6A5,stop_gained,p.Gln716Ter,ENST00000265379,;COL6A5,stop_gained,p.Gln716Ter,ENST00000312481,;	T	ENSG00000172752	ENST00000265379	Transcript	stop_gained	2640	2146	716	Q/*	Caa/Taa	.	.	.	1	COL6A5	HGNC	26674	protein_coding	YES	.	ENSP00000265379	.	E9PAL5_HUMAN	UPI0002064ECE	.	.	.	6/42	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF93,hmmpanther:PTHR22992,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGTCAATAC	.	5	ESCA
PIK3CA	0	.	GRCh37	3	178938934	178938934	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	14/21	134	99	35	82	82	0	PIK3CA,missense_variant,p.Glu726Lys,ENST00000263967,;PIK3CA,non_coding_transcript_exon_variant,,ENST00000462255,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	2333	2176	726	E/K	Gaa/Aaa	COSM87306,COSM446019	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	tolerated(0.36)	benign(0.4)	14/21	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Gene3D:3.30.1010.10,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.E726K|c.2176G>A|22,SITE|p.E726K|c.2176G>A|21,BUFFER|p.E726G|c.2177A>G|4,BUFFER|p.E726G|c.2177A>G|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGAAACA	.	5	ESCA
LAMP3	0	.	GRCh37	3	182871574	182871574	+	Nonsense_Mutation	SNP	G	G	A	rs773351046	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.655C>T	p.Gln219Ter	p.Q219*	ENST00000265598	2/6	65	47	18	30	30	0	LAMP3,stop_gained,p.Gln219Ter,ENST00000265598,;LAMP3,stop_gained,p.Gln195Ter,ENST00000466939,;LAMP3,downstream_gene_variant,,ENST00000470251,;LAMP3,downstream_gene_variant,,ENST00000476015,;LAMP3,downstream_gene_variant,,ENST00000486686,;	A	ENSG00000078081	ENST00000265598	Transcript	stop_gained	911	655	219	Q/*	Cag/Tag	rs773351046	.	.	-1	LAMP3	HGNC	14582	protein_coding	YES	CCDS3242.1	ENSP00000265598	LAMP3_HUMAN	E7ETP9_HUMAN,C9JYP5_HUMAN,C9JDI8_HUMAN	UPI000006DB7A	.	.	.	2/6	.	PROSITE_profiles:PS51407,hmmpanther:PTHR11506,hmmpanther:PTHR11506:SF30,Pfam_domain:PF01299	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTGAGGTG	byFrequency	5	ESCA
DGKG	0	.	GRCh37	3	185929635	185929635	+	Silent	SNP	C	C	T	rs547522584	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1866G>A	p.%3D	p.S622S	ENST00000265022	21/25	47	36	11	51	51	0	DGKG,synonymous_variant,p.%3D,ENST00000544847,;DGKG,synonymous_variant,p.%3D,ENST00000382164,;DGKG,synonymous_variant,p.%3D,ENST00000265022,;DGKG,synonymous_variant,p.%3D,ENST00000344484,;DGKG,non_coding_transcript_exon_variant,,ENST00000480809,;DGKG,non_coding_transcript_exon_variant,,ENST00000490452,;	T	ENSG00000058866	ENST00000265022	Transcript	synonymous_variant	2406	1866	622	S	tcG/tcA	rs547522584	.	.	-1	DGKG	HGNC	2853	protein_coding	YES	CCDS3274.1	ENSP00000265022	DGKG_HUMAN	.	UPI000013D5AB	.	.	.	21/25	.	hmmpanther:PTHR11255:SF36,hmmpanther:PTHR11255,Pfam_domain:PF00609,SMART_domains:SM00045,Superfamily_domains:SSF111331	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTCCGAGGT	byCluster|by1000G	5	ESCA
GLYCTK	0	.	GRCh37	3	52327044	52327044	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1474T>A	p.Phe492Ile	p.F492I	ENST00000436784	5/5	17	9	8	17	17	0	GLYCTK,missense_variant,p.Phe492Ile,ENST00000436784,;GLYCTK,3_prime_UTR_variant,,ENST00000354773,;GLYCTK,intron_variant,,ENST00000473032,;GLYCTK,intron_variant,,ENST00000471180,;GLYCTK,intron_variant,,ENST00000461183,;GLYCTK,intron_variant,,ENST00000305690,;GLYCTK,downstream_gene_variant,,ENST00000477382,;MIR135A1,downstream_gene_variant,,ENST00000385191,;GLYCTK-AS1,splice_region_variant,,ENST00000493616,;GLYCTK-AS1,downstream_gene_variant,,ENST00000472761,;GLYCTK,3_prime_UTR_variant,,ENST00000486393,;GLYCTK,non_coding_transcript_exon_variant,,ENST00000489173,;GLYCTK-AS1,non_coding_transcript_exon_variant,,ENST00000467187,;GLYCTK,downstream_gene_variant,,ENST00000473583,;	A	ENSG00000168237	ENST00000436784	Transcript	missense_variant	1534	1474	492	F/I	Ttc/Atc	.	.	.	1	GLYCTK	HGNC	24247	protein_coding	YES	CCDS2852.1	ENSP00000389175	GLCTK_HUMAN	.	UPI000004FD5A	.	deleterious(0.04)	probably_damaging(0.986)	5/5	.	Superfamily_domains:0051940,Pfam_domain:PF05161,Gene3D:1x3lA01,hmmpanther:PTHR12227,hmmpanther:PTHR12227:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACCTTCTTC	.	5	ESCA
CHMP2B	0	.	GRCh37	3	87304621	87304621	+	3'UTR	SNP	A	A	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1649A>T	.	.	ENST00000263780	6/6	48	23	25	52	52	0	CHMP2B,3_prime_UTR_variant,,ENST00000263780,;POU1F1,downstream_gene_variant,,ENST00000561167,;POU1F1,downstream_gene_variant,,ENST00000344265,;CHMP2B,downstream_gene_variant,,ENST00000471660,;POU1F1,downstream_gene_variant,,ENST00000350375,;CHMP2B,downstream_gene_variant,,ENST00000494980,;POU1F1,downstream_gene_variant,,ENST00000560656,;CHMP2B,downstream_gene_variant,,ENST00000472024,;CHMP2B,downstream_gene_variant,,ENST00000466696,;	T	ENSG00000083937	ENST00000263780	Transcript	3_prime_UTR_variant	2529	.	.	.	.	.	.	.	1	CHMP2B	HGNC	24537	protein_coding	YES	CCDS2918.1	ENSP00000263780	CHM2B_HUMAN	B2RE76_HUMAN	UPI00000701F8	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAATAAAGAT	.	5	ESCA
KIAA1109	0	.	GRCh37	4	123145797	123145797	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2758G>T	p.Ala920Ser	p.A920S	ENST00000264501	23/86	38	11	26	43	43	0	KIAA1109,missense_variant,p.Ala752Ser,ENST00000424425,;KIAA1109,missense_variant,p.Ala920Ser,ENST00000455637,;KIAA1109,missense_variant,p.Ala920Ser,ENST00000264501,;KIAA1109,missense_variant,p.Ala920Ser,ENST00000388738,;KIAA1109,missense_variant,p.Ala128Ser,ENST00000449251,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000495260,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000482114,;	T	ENSG00000138688	ENST00000264501	Transcript	missense_variant	3131	2758	920	A/S	Gct/Tct	.	.	.	1	KIAA1109	HGNC	26953	protein_coding	YES	CCDS43267.1	ENSP00000264501	K1109_HUMAN	B3KN93_HUMAN	UPI0000DD87B4	.	.	benign(0.278)	23/86	.	hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGGCTGGA	.	5	ESCA
FBXW7	0	.	GRCh37	4	153250883	153250883	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	8/12	37	7	30	43	43	0	FBXW7,stop_gained,p.Arg393Ter,ENST00000603548,;FBXW7,stop_gained,p.Arg313Ter,ENST00000263981,;FBXW7,stop_gained,p.Arg275Ter,ENST00000296555,;FBXW7,stop_gained,p.Arg217Ter,ENST00000393956,;FBXW7,stop_gained,p.Arg393Ter,ENST00000281708,;FBXW7,stop_gained,p.Arg393Ter,ENST00000603841,;FBXW7,non_coding_transcript_exon_variant,,ENST00000604069,;FBXW7,upstream_gene_variant,,ENST00000603821,;	A	ENSG00000109670	ENST00000281708	Transcript	stop_gained	2407	1177	393	R/*	Cga/Tga	COSM22973,COSM1052102,COSM1052104,COSM1052103	.	.	-1	FBXW7	HGNC	16712	protein_coding	YES	CCDS3777.1	ENSP00000281708	FBXW7_HUMAN	S4R3N3_HUMAN,H9CWI3_HUMAN,H9CWI2_HUMAN,G0Z2K0_HUMAN,A7BJS8_HUMAN	UPI000007007E	.	.	.	8/12	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Pfam_domain:PF00400,Gene3D:2.130.10.10,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF116,PROSITE_profiles:PS50294,PROSITE_profiles:PS50082	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R393*|c.1177C>T|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTCGGTTAC	.	5	ESCA
PCDHB2	0	.	GRCh37	5	140476081	140476081	+	Silent	SNP	C	C	T	rs200168689	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1707C>T	p.%3D	p.N569N	ENST00000194155	1/1	117	64	53	92	92	0	PCDHB2,synonymous_variant,p.%3D,ENST00000194155,;PCDHB3,upstream_gene_variant,,ENST00000231130,;AC005754.7,downstream_gene_variant,,ENST00000607216,;	T	ENSG00000112852	ENST00000194155	Transcript	synonymous_variant	1855	1707	569	N	aaC/aaT	rs200168689	.	.	1	PCDHB2	HGNC	8687	protein_coding	YES	CCDS4244.1	ENSP00000194155	PCDB2_HUMAN	.	UPI00001273DC	.	.	.	1/1	.	hmmpanther:PTHR24028:SF77,hmmpanther:PTHR24028,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CAGAACGGCTC	byCluster	4	ESCA
CDH10	0	.	GRCh37	5	24487941	24487941	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2198T>A	p.Leu733His	p.L733H	ENST00000264463	12/12	63	38	25	54	53	0	CDH10,missense_variant,p.Leu733His,ENST00000264463,;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,;	T	ENSG00000040731	ENST00000264463	Transcript	missense_variant	2706	2198	733	L/H	cTt/cAt	.	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	deleterious(0)	probably_damaging(0.996)	12/12	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Gene3D:4.10.900.10,Pfam_domain:PF01049	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Y730Y|c.2190C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCAAGTGAG	.	5	ESCA
CDH10	0	.	GRCh37	5	24511486	24511486	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.952G>C	p.Asp318His	p.D318H	ENST00000264463	6/12	55	16	38	47	47	0	CDH10,missense_variant,p.Asp318His,ENST00000264463,;CDH10,missense_variant,p.Asp318His,ENST00000510477,;	G	ENSG00000040731	ENST00000264463	Transcript	missense_variant	1460	952	318	D/H	Gac/Cac	.	.	.	-1	CDH10	HGNC	1749	protein_coding	YES	CCDS3892.1	ENSP00000264463	CAD10_HUMAN	.	UPI0000167B7B	.	deleterious(0.02)	possibly_damaging(0.746)	6/12	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF293,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGTCAAACA	.	5	ESCA
C5orf42	0	.	GRCh37	5	37183047	37183047	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5236C>T	p.%3D	p.L1746L	ENST00000425232	26/52	40	15	24	43	43	0	C5orf42,synonymous_variant,p.%3D,ENST00000274258,;C5orf42,synonymous_variant,p.%3D,ENST00000508244,;C5orf42,synonymous_variant,p.%3D,ENST00000425232,;C5orf42,synonymous_variant,p.%3D,ENST00000514429,;C5orf42,synonymous_variant,p.%3D,ENST00000509849,;	A	ENSG00000197603	ENST00000425232	Transcript	synonymous_variant	5467	5236	1746	L	Ctg/Ttg	.	.	.	-1	C5orf42	HGNC	25801	protein_coding	YES	CCDS34146.2	ENSP00000389014	CE042_HUMAN	.	UPI0001AAB3EA	.	.	.	26/52	.	hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCAGTCTTC	.	5	ESCA
GPBP1	0	.	GRCh37	5	56510008	56510008	+	Silent	SNP	A	A	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51A>G	p.%3D	p.P17P	ENST00000264779	1/11	53	12	40	46	46	0	GPBP1,synonymous_variant,p.%3D,ENST00000264779,;GPBP1,synonymous_variant,p.%3D,ENST00000506184,;GPBP1,synonymous_variant,p.%3D,ENST00000454432,;GPBP1,synonymous_variant,p.%3D,ENST00000424459,;GPBP1,synonymous_variant,p.%3D,ENST00000538707,;GPBP1,synonymous_variant,p.%3D,ENST00000511209,;GPBP1,intron_variant,,ENST00000514387,;	G	ENSG00000062194	ENST00000264779	Transcript	synonymous_variant	61	51	17	P	ccA/ccG	.	.	.	1	GPBP1	HGNC	29520	protein_coding	YES	CCDS47211.1	ENSP00000264779	GPBP1_HUMAN	.	UPI000006F55F	.	.	.	1/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR14339:SF11,hmmpanther:PTHR14339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCATCATC	.	5	ESCA
CMYA5	0	.	GRCh37	5	79029456	79029456	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4868A>G	p.Glu1623Gly	p.E1623G	ENST00000446378	2/13	24	14	9	33	33	0	CMYA5,missense_variant,p.Glu1623Gly,ENST00000446378,;CMYA5,upstream_gene_variant,,ENST00000506603,;	G	ENSG00000164309	ENST00000446378	Transcript	missense_variant	4899	4868	1623	E/G	gAg/gGg	.	.	.	1	CMYA5	HGNC	14305	protein_coding	YES	CCDS47238.1	ENSP00000394770	CMYA5_HUMAN	.	UPI00004F9478	.	.	benign(0.188)	2/13	.	hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTGAGAAGA	.	5	ESCA
HSPA1A	0	.	GRCh37	6	31785566	31785571	+	3'UTR	DEL	TTTTGG	TTTTGG	-	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	TTTTGG	TTTTGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*108_*113delTTTGGT	.	.	ENST00000375651	1/1	64	49	15	55	55	0	HSPA1A,3_prime_UTR_variant,,ENST00000375651,;HSPA1A,3_prime_UTR_variant,,ENST00000608703,;HSPA1L,upstream_gene_variant,,ENST00000417199,;HSPA1A,downstream_gene_variant,,ENST00000458062,;HSPA1L,upstream_gene_variant,,ENST00000375654,;	-	ENSG00000204389	ENST00000375651	Transcript	3_prime_UTR_variant	2276-2281	.	.	.	.	.	.	.	1	HSPA1A	HGNC	5232	protein_coding	YES	CCDS34414.1	ENSP00000364802	HSP71_HUMAN	A8K5I0_HUMAN	UPI0000000C40	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAATTTTTTGGTGAAG	.	3	ESCA
ICK	0	.	GRCh37	6	52876632	52876632	+	Missense_Mutation	SNP	C	C	T	rs55895113	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1427G>A	p.Arg476Gln	p.R476Q	ENST00000356971	12/15	26	17	8	29	29	0	ICK,missense_variant,p.Arg476Gln,ENST00000350082,;ICK,missense_variant,p.Arg476Gln,ENST00000356971,;	T	ENSG00000112144	ENST00000356971	Transcript	missense_variant	1917	1427	476	R/Q	cGa/cAa	rs55895113	.	.	-1	ICK	HGNC	21219	protein_coding	YES	CCDS4949.1	ENSP00000349458	ICK_HUMAN	.	UPI0000073DE8	.	tolerated(0.59)	benign(0.001)	12/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTCGCCGC	.	5	ESCA
KMT2C	0	.	GRCh37	7	151962148	151962148	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1159G>C	p.Glu387Gln	p.E387Q	ENST00000262189	8/59	208	190	18	131	130	0	KMT2C,missense_variant,p.Glu387Gln,ENST00000355193,;KMT2C,missense_variant,p.Glu387Gln,ENST00000262189,;KMT2C,missense_variant,p.Glu387Gln,ENST00000558084,;	G	ENSG00000055609	ENST00000262189	Transcript	missense_variant	1378	1159	387	E/Q	Gag/Cag	.	.	.	-1	KMT2C	HGNC	13726	protein_coding	YES	CCDS5931.1	ENSP00000262189	KMT2C_HUMAN	Q6N019_HUMAN,Q75MN6_HUMAN,H0YMU7_HUMAN	UPI0000141B9F	.	.	possibly_damaging(0.597)	8/59	.	PROSITE_profiles:PS50089,PROSITE_profiles:PS50016,Gene3D:3.30.40.10,SMART_domains:SM00184,SMART_domains:SM00249,Superfamily_domains:SSF57903,Superfamily_domains:SSF57903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCACTCAGGAC	.	3	ESCA
INTS1	0	.	GRCh37	7	1533526	1533526	+	Silent	SNP	G	G	C	rs778502259	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1932C>G	p.%3D	p.S644S	ENST00000404767	15/48	77	57	19	75	75	0	INTS1,synonymous_variant,p.%3D,ENST00000404767,;INTS1,synonymous_variant,p.%3D,ENST00000389470,;INTS1,downstream_gene_variant,,ENST00000496988,;INTS1,upstream_gene_variant,,ENST00000468115,;	C	ENSG00000164880	ENST00000404767	Transcript	synonymous_variant	2018	1932	644	S	tcC/tcG	rs778502259	.	.	-1	INTS1	HGNC	24555	protein_coding	YES	CCDS47526.1	ENSP00000385722	INT1_HUMAN	.	UPI0000D7211C	.	.	.	15/48	.	hmmpanther:PTHR21224:SF1,hmmpanther:PTHR21224	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCTCGGAGCA	byFrequency	3	ESCA
LFNG	0	.	GRCh37	7	2565060	2565060	+	Missense_Mutation	SNP	C	C	A	rs571692564	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>A	p.His198Gln	p.H198Q	ENST00000222725	4/8	69	44	24	83	83	0	LFNG,missense_variant,p.His127Gln,ENST00000402506,;LFNG,missense_variant,p.His69Gln,ENST00000402045,;LFNG,missense_variant,p.His198Gln,ENST00000222725,;LFNG,missense_variant,p.His69Gln,ENST00000338732,;LFNG,missense_variant,p.His198Gln,ENST00000359574,;MIR4648,upstream_gene_variant,,ENST00000580107,;LFNG,non_coding_transcript_exon_variant,,ENST00000493850,;	A	ENSG00000106003	ENST00000222725	Transcript	missense_variant	614	594	198	H/Q	caC/caA	rs571692564	.	.	1	LFNG	HGNC	6560	protein_coding	YES	CCDS34587.1	ENSP00000222725	LFNG_HUMAN	.	UPI000012E5D5	.	deleterious(0)	probably_damaging(0.993)	4/8	.	PIRSF_domain:PIRSF038073,Pfam_domain:PF02434,hmmpanther:PTHR10811,hmmpanther:PTHR10811:SF7	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCACGTGGA	by1000G	5	ESCA
GLI3	0	.	GRCh37	7	42003915	42003915	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*13A>G	.	.	ENST00000395925	15/15	41	27	13	51	51	0	GLI3,3_prime_UTR_variant,,ENST00000395925,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,;	C	ENSG00000106571	ENST00000395925	Transcript	3_prime_UTR_variant	4841	.	.	.	.	.	.	.	-1	GLI3	HGNC	4319	protein_coding	YES	CCDS5465.1	ENSP00000379258	GLI3_HUMAN	C9J9N4_HUMAN	UPI000020EE4C	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTTTTTTTC	.	5	ESCA
ZNF804B	0	.	GRCh37	7	88964137	88964137	+	Missense_Mutation	SNP	G	G	T	rs772613804	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1841G>T	p.Arg614Ile	p.R614I	ENST00000333190	4/4	39	18	20	62	62	0	ZNF804B,missense_variant,p.Arg614Ile,ENST00000333190,;	T	ENSG00000182348	ENST00000333190	Transcript	missense_variant	2450	1841	614	R/I	aGa/aTa	rs772613804	.	.	1	ZNF804B	HGNC	21958	protein_coding	YES	CCDS5613.1	ENSP00000329638	Z804B_HUMAN	.	UPI00001A92D2	.	deleterious(0.02)	benign(0.169)	4/4	.	hmmpanther:PTHR17614:SF12,hmmpanther:PTHR17614	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCAGAAAGG	byFrequency	5	ESCA
ARHGEF10	0	.	GRCh37	8	1893811	1893811	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3387C>T	p.%3D	p.N1129N	ENST00000349830	27/29	16	11	5	22	22	0	ARHGEF10,synonymous_variant,p.%3D,ENST00000522435,;ARHGEF10,synonymous_variant,p.%3D,ENST00000262112,;ARHGEF10,synonymous_variant,p.%3D,ENST00000398564,;ARHGEF10,synonymous_variant,p.%3D,ENST00000349830,;ARHGEF10,synonymous_variant,p.%3D,ENST00000520359,;ARHGEF10,synonymous_variant,p.%3D,ENST00000518288,;ARHGEF10,non_coding_transcript_exon_variant,,ENST00000523596,;ARHGEF10,non_coding_transcript_exon_variant,,ENST00000521927,;ARHGEF10,non_coding_transcript_exon_variant,,ENST00000523980,;	T	ENSG00000104728	ENST00000349830	Transcript	synonymous_variant	3572	3387	1129	N	aaC/aaT	.	.	.	1	ARHGEF10	HGNC	14103	protein_coding	YES	CCDS34794.1	ENSP00000340297	ARHGA_HUMAN	.	UPI00005054FE	.	.	.	27/29	.	hmmpanther:PTHR12877:SF14,hmmpanther:PTHR12877,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CACAACATGCT	.	2	ESCA
REXO1L1P	0	.	GRCh37	8	86573332	86573332	+	3'UTR	SNP	G	G	A	rs552670242	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*367C>T	.	.	ENST00000379010	1/1	184	170	13	142	142	0	REXO1L1P,3_prime_UTR_variant,,ENST00000379010,;REXO1L3P,upstream_gene_variant,,ENST00000608646,;	A	ENSG00000205176	ENST00000379010	Transcript	3_prime_UTR_variant	2395	.	.	.	.	rs552670242	.	.	-1	REXO1L1P	HGNC	24660	protein_coding	YES	.	ENSP00000368295	GOR_HUMAN	.	UPI000057A11F	.	.	.	1/1	.	.	T:0.0006	T:0	T:0	.	T:0	T:0.001	T:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGCTGGCCTTG	byFrequency|by1000G	3	ESCA
TMEM55A	0	.	GRCh37	8	92032388	92032388	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359A>T	p.Asn120Ile	p.N120I	ENST00000285419	3/7	62	41	20	56	56	0	TMEM55A,missense_variant,p.Asn120Ile,ENST00000285419,;TMEM55A,missense_variant,p.Asn126Ile,ENST00000520014,;GS1-251I9.3,downstream_gene_variant,,ENST00000517920,;TMEM55A,missense_variant,p.Asn120Ile,ENST00000518359,;TMEM55A,3_prime_UTR_variant,,ENST00000518869,;TMEM55A,intron_variant,,ENST00000520709,;	A	ENSG00000155099	ENST00000285419	Transcript	missense_variant	674	359	120	N/I	aAc/aTc	.	.	.	-1	TMEM55A	HGNC	25452	protein_coding	YES	CCDS6252.1	ENSP00000285419	TM55A_HUMAN	.	UPI0000071563	.	deleterious(0.03)	possibly_damaging(0.765)	3/7	.	hmmpanther:PTHR21014:SF5,hmmpanther:PTHR21014,Pfam_domain:PF09788	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCAGTTGGGT	.	5	ESCA
PDP1	0	.	GRCh37	8	94936733	94936733	+	3'UTR	DEL	A	A	-	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*832delA	.	.	ENST00000396200	3/3	40	20	20	19	19	0	PDP1,3_prime_UTR_variant,,ENST00000396200,;PDP1,3_prime_UTR_variant,,ENST00000297598,;PDP1,downstream_gene_variant,,ENST00000517764,;PDP1,downstream_gene_variant,,ENST00000521144,;PDP1,downstream_gene_variant,,ENST00000520614,;PDP1,downstream_gene_variant,,ENST00000520728,;PDP1,downstream_gene_variant,,ENST00000518827,;PDP1,downstream_gene_variant,,ENST00000518107,;PDP1,downstream_gene_variant,,ENST00000518573,;PDP1,downstream_gene_variant,,ENST00000523021,;	-	ENSG00000164951	ENST00000396200	Transcript	3_prime_UTR_variant	2797	.	.	.	.	.	.	.	1	PDP1	HGNC	9279	protein_coding	YES	CCDS55262.1	ENSP00000379503	PDP1_HUMAN	Q6P1N1_HUMAN,E5RIV4_HUMAN,E5RIE5_HUMAN,E5RI96_HUMAN,E5RHB9_HUMAN,E5RFL8_HUMAN,B4DYX8_HUMAN,B3KPZ7_HUMAN	UPI0000D4BFBD	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR|VARSCANI	ACTCTTATGTAA	.	2	ESCA
SEC16A	0	.	GRCh37	9	139341801	139341801	+	Missense_Mutation	SNP	C	C	G	rs752180026	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6575G>C	p.Arg2192Pro	p.R2192P	ENST00000313050	25/30	40	32	8	25	25	0	SEC16A,missense_variant,p.Arg2014Pro,ENST00000290037,;SEC16A,missense_variant,p.Arg2192Pro,ENST00000313050,;SEC16A,missense_variant,p.Arg198Pro,ENST00000313084,;SEC16A,missense_variant,p.Arg914Pro,ENST00000453963,;SEC16A,missense_variant,p.Arg586Pro,ENST00000277537,;SEC16A,missense_variant,p.Arg2014Pro,ENST00000431893,;SEC16A,missense_variant,p.Arg2014Pro,ENST00000371706,;SEC16A,3_prime_UTR_variant,,ENST00000398335,;SEC16A,upstream_gene_variant,,ENST00000467838,;	G	ENSG00000148396	ENST00000313050	Transcript	missense_variant	6649	6575	2192	R/P	cGc/cCc	rs752180026	.	.	-1	SEC16A	HGNC	29006	protein_coding	YES	CCDS55351.1	ENSP00000325827	.	J3KNL6_HUMAN,G1UI25_HUMAN,A0PJ75_HUMAN	UPI0000F0888B	.	deleterious(0)	probably_damaging(0.999)	25/30	.	hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGTAGCGAGCT	.	4	ESCA
CDKN2A	0	.	GRCh37	9	21968242	21968242	+	Splice_Site	SNP	C	C	T	.	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*151-1G>A	.	.	ENST00000498124	.	64	26	38	106	106	0	CDKN2A,splice_acceptor_variant,,ENST00000578845,;CDKN2A,splice_acceptor_variant,,ENST00000579755,;CDKN2A,splice_acceptor_variant,,ENST00000494262,;CDKN2A,splice_acceptor_variant,,ENST00000498628,;CDKN2A,splice_acceptor_variant,,ENST00000530628,;CDKN2A,splice_acceptor_variant,,ENST00000304494,;CDKN2A,splice_acceptor_variant,,ENST00000361570,;CDKN2A,splice_acceptor_variant,,ENST00000498124,;CDKN2A,splice_acceptor_variant,,ENST00000579122,;C9orf53,downstream_gene_variant,,ENST00000441769,;CDKN2A,downstream_gene_variant,,ENST00000446177,;CDKN2A,downstream_gene_variant,,ENST00000479692,;CDKN2A,downstream_gene_variant,,ENST00000497750,;CDKN2A,downstream_gene_variant,,ENST00000380150,;CDKN2A,downstream_gene_variant,,ENST00000577854,;CDKN2A,splice_acceptor_variant,,ENST00000380151,;RP11-145E5.5,intron_variant,,ENST00000404796,;	T	ENSG00000147889	ENST00000498124	Transcript	splice_acceptor_variant	.	.	.	.	.	COSM21562,COSM3952628,COSM99937	.	.	-1	CDKN2A	HGNC	1787	protein_coding	YES	CCDS56565.1	ENSP00000418915	CD2A1_HUMAN	Q9UPB7_HUMAN	UPI0001565711	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.0?|c.1_471del471|15	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGTCTGCAG	.	5	ESCA
TLE4	0	.	GRCh37	9	82341159	82341159	+	3'Flank	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000376552	.	35	7	27	20	20	0	TLE4,3_prime_UTR_variant,,ENST00000376544,;TLE4,3_prime_UTR_variant,,ENST00000376520,;TLE4,downstream_gene_variant,,ENST00000376534,;TLE4,downstream_gene_variant,,ENST00000376552,;TLE4,downstream_gene_variant,,ENST00000376537,;TLE4,downstream_gene_variant,,ENST00000265284,;TLE4,downstream_gene_variant,,ENST00000478290,;TLE4,downstream_gene_variant,,ENST00000462803,;TLE4,downstream_gene_variant,,ENST00000470872,;RP11-79D8.2,non_coding_transcript_exon_variant,,ENST00000440700,;	A	ENSG00000106829	ENST00000376552	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	745	1	TLE4	HGNC	11840	protein_coding	YES	CCDS43837.1	ENSP00000365735	TLE4_HUMAN	B3KQ29_HUMAN	UPI00001CE3BA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATGGACAC	.	5	ESCA
SPATA31E1	0	.	GRCh37	9	90502226	90502226	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2824A>G	p.Thr942Ala	p.T942A	ENST00000325643	4/4	22	13	8	33	33	0	SPATA31E1,missense_variant,p.Thr942Ala,ENST00000325643,;	G	ENSG00000177992	ENST00000325643	Transcript	missense_variant	2890	2824	942	T/A	Acc/Gcc	.	.	.	1	SPATA31E1	HGNC	26672	protein_coding	YES	CCDS6676.1	ENSP00000322640	S31E1_HUMAN	.	UPI000036764A	.	tolerated(0.54)	benign(0.113)	4/4	.	hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGATACCCAT	.	5	ESCA
MAGEA8	0	.	GRCh37	X	149013037	149013037	+	5'UTR	SNP	C	C	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-10C>A	.	.	ENST00000535454	4/4	116	93	22	93	93	0	MAGEA8,5_prime_UTR_variant,,ENST00000542674,;MAGEA8,5_prime_UTR_variant,,ENST00000535454,;MAGEA8,5_prime_UTR_variant,,ENST00000286482,;MAGEA8-AS1,upstream_gene_variant,,ENST00000427671,;MAGEA8,non_coding_transcript_exon_variant,,ENST00000493910,;MAGEA8,non_coding_transcript_exon_variant,,ENST00000345830,;	A	ENSG00000156009	ENST00000535454	Transcript	5_prime_UTR_variant	540	.	.	.	.	.	.	.	1	MAGEA8	HGNC	6806	protein_coding	YES	CCDS14692.1	ENSP00000438293	MAGA8_HUMAN	.	UPI0000071C79	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGACCTGAGT	.	5	ESCA
MAGEA6	0	.	GRCh37	X	151870172	151870172	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.862C>A	p.His288Asn	p.H288N	ENST00000329342	3/3	118	87	30	153	153	0	MAGEA6,missense_variant,p.His288Asn,ENST00000329342,;MAGEA6,downstream_gene_variant,,ENST00000412733,;MAGEA6,downstream_gene_variant,,ENST00000457643,;	A	ENSG00000197172	ENST00000329342	Transcript	missense_variant	1087	862	288	H/N	Cac/Aac	.	.	.	1	MAGEA6	HGNC	6804	protein_coding	YES	CCDS14708.1	ENSP00000329199	MAGA6_HUMAN	E7EUF2_HUMAN,E7ETG4_HUMAN,B9A060_HUMAN	UPI000000D9B0	.	deleterious(0.03)	benign(0.001)	3/3	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCTGCACCAT	.	5	ESCA
DCAF8L2	0	.	GRCh37	X	27766027	27766027	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1015G>A	p.Glu339Lys	p.E339K	ENST00000451261	5/5	45	33	12	46	46	0	DCAF8L2,missense_variant,p.Glu339Lys,ENST00000451261,;DCAF8L2,downstream_gene_variant,,ENST00000431122,;DCAF8L2,downstream_gene_variant,,ENST00000583068,;AC107613.1,non_coding_transcript_exon_variant,,ENST00000545306,;	A	ENSG00000189186	ENST00000451261	Transcript	missense_variant	1414	1015	339	E/K	Gaa/Aaa	.	.	.	1	DCAF8L2	HGNC	31811	protein_coding	YES	CCDS59162.1	ENSP00000462745	DC8L2_HUMAN	J3QRI4_HUMAN	UPI000183CBD9	.	deleterious(0.04)	probably_damaging(0.919)	5/5	.	PROSITE_profiles:PS50294,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF36,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CAGGTGAAGAT	.	3	ESCA
MAGIX	0	.	GRCh37	X	49023631	49023631	+	3'Flank	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000412696	.	68	45	22	80	80	0	MAGIX,3_prime_UTR_variant,,ENST00000376338,;MAGIX,downstream_gene_variant,,ENST00000425285,;MAGIX,downstream_gene_variant,,ENST00000415364,;MAGIX,downstream_gene_variant,,ENST00000425661,;PLP2,upstream_gene_variant,,ENST00000376327,;MAGIX,downstream_gene_variant,,ENST00000458388,;MAGIX,downstream_gene_variant,,ENST00000412696,;MAGIX,downstream_gene_variant,,ENST00000376339,;PLP2,upstream_gene_variant,,ENST00000376322,;MAGIX,downstream_gene_variant,,ENST00000454342,;MAGIX,downstream_gene_variant,,ENST00000498742,;	A	ENSG00000017621	ENST00000412696	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	660	1	MAGIX	HGNC	30006	protein_coding	YES	CCDS48106.1	ENSP00000387928	MAGIX_HUMAN	.	UPI00018132AC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGGGAGAGGCC	.	5	ESCA
TRO	0	.	GRCh37	X	54953052	54953052	+	Missense_Mutation	SNP	G	G	A	rs201094980	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1694G>A	p.Arg565His	p.R565H	ENST00000173898	9/13	87	45	42	76	76	0	TRO,missense_variant,p.Arg565His,ENST00000375022,;TRO,missense_variant,p.Arg168His,ENST00000399736,;TRO,missense_variant,p.Arg565His,ENST00000319167,;TRO,missense_variant,p.Arg168His,ENST00000375041,;TRO,missense_variant,p.Arg96His,ENST00000420798,;TRO,missense_variant,p.Arg565His,ENST00000173898,;TRO,downstream_gene_variant,,ENST00000431115,;TRO,downstream_gene_variant,,ENST00000411534,;TRO,downstream_gene_variant,,ENST00000449980,;TRO,downstream_gene_variant,,ENST00000430420,;TRO,downstream_gene_variant,,ENST00000440759,;TRO,downstream_gene_variant,,ENST00000440072,;TRO,downstream_gene_variant,,ENST00000427099,;TRO,downstream_gene_variant,,ENST00000453081,;TRO,downstream_gene_variant,,ENST00000442098,;TRO,downstream_gene_variant,,ENST00000416704,;TRO,downstream_gene_variant,,ENST00000452830,;SNORA11,upstream_gene_variant,,ENST00000408823,;TRO,downstream_gene_variant,,ENST00000484031,;TRO,downstream_gene_variant,,ENST00000492142,;TRO,downstream_gene_variant,,ENST00000474933,;TRO,upstream_gene_variant,,ENST00000475183,;TRO,missense_variant,p.Arg565His,ENST00000445561,;TRO,non_coding_transcript_exon_variant,,ENST00000492706,;TRO,upstream_gene_variant,,ENST00000469211,;	A	ENSG00000067445	ENST00000173898	Transcript	missense_variant	1806	1694	565	R/H	cGc/cAc	rs201094980,COSM4110343,COSM4110342	.	.	1	TRO	HGNC	12326	protein_coding	YES	CCDS43959.1	ENSP00000173898	TROP_HUMAN	F5GY27_HUMAN,E7ERU6_HUMAN,B1AKF6_HUMAN,B1AKF5_HUMAN,B1AKF4_HUMAN,B1AKF3_HUMAN,B1AKF2_HUMAN,B1AKE7_HUMAN,B1AKE6_HUMAN,B1AKE5_HUMAN	UPI000021208F	.	tolerated(0.67)	unknown(0)	9/13	.	PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF57,hmmpanther:PTHR11736,Pfam_domain:PF01454	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCGCCCTG	byFrequency|byCluster	5	ESCA
APEX2	0	.	GRCh37	X	55033867	55033867	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1556G>A	p.%3D	p.%3D	ENST00000374987	6/6	37	16	20	59	59	0	APEX2,stop_retained_variant,p.%3D,ENST00000374987,;ALAS2,downstream_gene_variant,,ENST00000396198,;ALAS2,downstream_gene_variant,,ENST00000335854,;ALAS2,downstream_gene_variant,,ENST00000330807,;APEX2,downstream_gene_variant,,ENST00000471758,;ALAS2,downstream_gene_variant,,ENST00000498636,;	A	ENSG00000169188	ENST00000374987	Transcript	stop_retained_variant	1622	1556	519	*	tGa/tAa	.	.	.	1	APEX2	HGNC	17889	protein_coding	YES	CCDS14365.1	ENSP00000364126	APEX2_HUMAN	E5KN95_HUMAN,B7ZA71_HUMAN	UPI0000071F5B	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTGAACCA	.	5	ESCA
ACRC	0	.	GRCh37	X	70823523	70823523	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396C>T	p.%3D	p.N132N	ENST00000373695	7/12	77	56	21	129	129	0	ACRC,synonymous_variant,p.%3D,ENST00000373695,;ACRC,synonymous_variant,p.%3D,ENST00000373696,;	T	ENSG00000147174	ENST00000373695	Transcript	synonymous_variant	933	396	132	N	aaC/aaT	.	.	.	1	ACRC	HGNC	15805	protein_coding	YES	CCDS35326.1	ENSP00000362799	ACRC_HUMAN	.	UPI0000072023	.	.	.	7/12	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23099,hmmpanther:PTHR23099:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACAACGGTAA	.	5	ESCA
XIST	0	.	GRCh37	X	73068515	73068515	+	RNA	SNP	G	G	A	novel	.	TCGA-XP-A8T7-01A-11D-A36J-09	TCGA-XP-A8T7-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.4074C>T	.	.	ENST00000429829	1/6	17	13	4	20	20	0	XIST,non_coding_transcript_exon_variant,,ENST00000429829,;	A	ENSG00000229807	ENST00000429829	Transcript	non_coding_transcript_exon_variant	4074	.	.	.	.	.	.	.	-1	XIST	HGNC	12810	lincRNA	YES	.	.	.	.	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACAGAAGGT	.	5	ESCA
FAM208B	0	.	GRCh37	10	5754877	5754877	+	5'UTR	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-196A>G	.	.	ENST00000328090	2/21	54	40	14	111	111	0	FAM208B,5_prime_UTR_variant,,ENST00000496681,;FAM208B,5_prime_UTR_variant,,ENST00000328090,;RP11-336A10.2,intron_variant,,ENST00000411512,;RP11-336A10.2,intron_variant,,ENST00000596567,;FAM208B,non_coding_transcript_exon_variant,,ENST00000473789,;FAM208B,non_coding_transcript_exon_variant,,ENST00000463468,;FAM208B,non_coding_transcript_exon_variant,,ENST00000480839,;FAM208B,downstream_gene_variant,,ENST00000532424,;FAM208B,downstream_gene_variant,,ENST00000482419,;FAM208B,downstream_gene_variant,,ENST00000477043,;FAM208B,non_coding_transcript_exon_variant,,ENST00000527124,;	G	ENSG00000108021	ENST00000328090	Transcript	5_prime_UTR_variant	430	.	.	.	.	.	.	.	1	FAM208B	HGNC	23484	protein_coding	YES	CCDS41485.1	ENSP00000328426	F208B_HUMAN	.	UPI00004589BB	.	.	.	2/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAAAGCAGG	.	5	ESCA
TAF3	0	.	GRCh37	10	8019276	8019276	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2305C>A	p.Gln769Lys	p.Q769K	ENST00000344293	4/7	59	40	18	80	80	0	TAF3,missense_variant,p.Gln769Lys,ENST00000344293,;	A	ENSG00000165632	ENST00000344293	Transcript	missense_variant	2511	2305	769	Q/K	Caa/Aaa	.	.	.	1	TAF3	HGNC	17303	protein_coding	YES	CCDS41487.1	ENSP00000340271	TAF3_HUMAN	.	UPI00004588FA	.	deleterious_low_confidence(0)	benign(0.042)	4/7	.	hmmpanther:PTHR12321:SF34,hmmpanther:PTHR12321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCCAAGAC	.	5	ESCA
RGR	0	.	GRCh37	10	86018276	86018276	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.769A>G	p.Ile257Val	p.I257V	ENST00000359452	7/7	48	40	8	77	77	0	RGR,missense_variant,p.Ile215Val,ENST00000358110,;RGR,missense_variant,p.Ile257Val,ENST00000359452,;RGR,non_coding_transcript_exon_variant,,ENST00000479725,;RGR,non_coding_transcript_exon_variant,,ENST00000478727,;RGR,non_coding_transcript_exon_variant,,ENST00000483660,;RGR,downstream_gene_variant,,ENST00000497161,;RGR,downstream_gene_variant,,ENST00000483744,;RGR,non_coding_transcript_exon_variant,,ENST00000483771,;	G	ENSG00000148604	ENST00000359452	Transcript	missense_variant	807	769	257	I/V	Att/Gtt	.	.	.	1	RGR	HGNC	9990	protein_coding	YES	CCDS7374.1	ENSP00000352427	RGR_HUMAN	.	UPI0000072293	.	tolerated(0.29)	benign(0.015)	7/7	.	Transmembrane_helices:TMhelix,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,PROSITE_patterns:PS00238,hmmpanther:PTHR24227,hmmpanther:PTHR24227:SF32,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCATTGCC	.	5	ESCA
ZNF518A	0	.	GRCh37	10	97921704	97921704	+	RNA	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.6480A>G	.	.	ENST00000534948	7/7	42	28	13	65	65	0	ZNF518A,non_coding_transcript_exon_variant,,ENST00000567632,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000534948,;ZNF518A,intron_variant,,ENST00000563195,;ZNF518A,intron_variant,,ENST00000442635,;ZNF518A,downstream_gene_variant,,ENST00000478086,;ZNF518A,downstream_gene_variant,,ENST00000316045,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000371192,;	G	ENSG00000177853	ENST00000534948	Transcript	non_coding_transcript_exon_variant	6480	.	.	.	.	.	.	.	1	ZNF518A	HGNC	29009	processed_transcript	YES	.	.	.	.	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAATGGAT	.	5	ESCA
EIF4G2	0	.	GRCh37	11	10828881	10828881	+	5'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-39A>G	.	.	ENST00000526148	2/22	39	27	12	67	67	0	EIF4G2,5_prime_UTR_variant,,ENST00000396525,;EIF4G2,5_prime_UTR_variant,,ENST00000532082,;EIF4G2,5_prime_UTR_variant,,ENST00000527526,;EIF4G2,5_prime_UTR_variant,,ENST00000531416,;EIF4G2,5_prime_UTR_variant,,ENST00000527419,;EIF4G2,5_prime_UTR_variant,,ENST00000339995,;EIF4G2,5_prime_UTR_variant,,ENST00000530702,;EIF4G2,5_prime_UTR_variant,,ENST00000525681,;EIF4G2,5_prime_UTR_variant,,ENST00000526148,;EIF4G2,5_prime_UTR_variant,,ENST00000524932,;EIF4G2,5_prime_UTR_variant,,ENST00000532570,;EIF4G2,intron_variant,,ENST00000530211,;RP11-685M7.3,upstream_gene_variant,,ENST00000499765,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000531507,;EIF4G2,intron_variant,,ENST00000525995,;EIF4G2,intron_variant,,ENST00000525972,;EIF4G2,upstream_gene_variant,,ENST00000532120,;ZBED5,downstream_gene_variant,,ENST00000525350,;EIF4G2,5_prime_UTR_variant,,ENST00000528562,;EIF4G2,5_prime_UTR_variant,,ENST00000531647,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000534246,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000533485,;EIF4G2,non_coding_transcript_exon_variant,,ENST00000532383,;EIF4G2,upstream_gene_variant,,ENST00000527015,;EIF4G2,upstream_gene_variant,,ENST00000532349,;EIF4G2,upstream_gene_variant,,ENST00000534605,;EIF4G2,upstream_gene_variant,,ENST00000532152,;	C	ENSG00000110321	ENST00000526148	Transcript	5_prime_UTR_variant	473	.	.	.	.	.	.	.	-1	EIF4G2	HGNC	3297	protein_coding	YES	CCDS31428.1	ENSP00000433664	.	Q59G42_HUMAN,Q2TU89_HUMAN,H0YEN8_HUMAN,H0YEC5_HUMAN,H0YDC0_HUMAN,H0YD99_HUMAN,H0YD77_HUMAN,H0YCF8_HUMAN,D3DQV9_HUMAN,B4DZF2_HUMAN	UPI000013C8BE	.	.	.	2/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATAATATTAA	.	5	ESCA
MUC5B	0	.	GRCh37	11	1269981	1269981	+	Silent	SNP	C	C	T	rs775871178	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11871C>T	p.%3D	p.T3957T	ENST00000529681	31/49	97	70	27	181	181	0	MUC5B,synonymous_variant,p.%3D,ENST00000529681,;MUC5B,synonymous_variant,p.%3D,ENST00000447027,;RP11-532E4.2,intron_variant,,ENST00000532061,;	T	ENSG00000117983	ENST00000529681	Transcript	synonymous_variant	11929	11871	3957	T	acC/acT	rs775871178	.	.	1	MUC5B	HGNC	7516	protein_coding	YES	CCDS44515.2	ENSP00000436812	MUC5B_HUMAN	Q93043_HUMAN	UPI0001DD21C7	.	.	.	31/49	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCACCGGCTC	.	5	ESCA
KBTBD4	0	.	GRCh37	11	47593922	47593922	+	3'UTR	SNP	A	A	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*560T>G	.	.	ENST00000430070	4/4	58	52	6	65	65	0	KBTBD4,3_prime_UTR_variant,,ENST00000533290,;KBTBD4,3_prime_UTR_variant,,ENST00000430070,;KBTBD4,3_prime_UTR_variant,,ENST00000526005,;KBTBD4,3_prime_UTR_variant,,ENST00000395288,;PTPMT1,downstream_gene_variant,,ENST00000426530,;KBTBD4,downstream_gene_variant,,ENST00000525720,;PTPMT1,downstream_gene_variant,,ENST00000534775,;PTPMT1,downstream_gene_variant,,ENST00000326674,;PTPMT1,downstream_gene_variant,,ENST00000326656,;RNU5E-10P,downstream_gene_variant,,ENST00000363506,;PTPMT1,non_coding_transcript_exon_variant,,ENST00000527079,;NDUFS3,intron_variant,,ENST00000533507,;KBTBD4,downstream_gene_variant,,ENST00000530668,;	C	ENSG00000123444	ENST00000430070	Transcript	3_prime_UTR_variant	2229	.	.	.	.	.	.	.	-1	KBTBD4	HGNC	23761	protein_coding	YES	CCDS44594.1	ENSP00000415106	KBTB4_HUMAN	E9PJY1_HUMAN,E9PJ66_HUMAN	UPI0000D4DDB6	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACCAAAGTTA	.	4	ESCA
OR4S2	0	.	GRCh37	11	55418475	55418475	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96C>G	p.Phe32Leu	p.F32L	ENST00000312422	1/1	100	76	23	113	113	0	OR4S2,missense_variant,p.Phe32Leu,ENST00000312422,;	G	ENSG00000174982	ENST00000312422	Transcript	missense_variant	96	96	32	F/L	ttC/ttG	.	.	.	1	OR4S2	HGNC	15183	protein_coding	YES	CCDS31505.1	ENSP00000310337	OR4S2_HUMAN	.	UPI00001D77D2	.	tolerated(0.52)	benign(0.059)	1/1	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF110,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTCTACAT	.	5	ESCA
DNHD1	0	.	GRCh37	11	6579838	6579838	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9126C>T	p.%3D	p.D3042D	ENST00000254579	26/43	37	33	4	76	76	0	DNHD1,synonymous_variant,p.%3D,ENST00000527990,;DNHD1,synonymous_variant,p.%3D,ENST00000254579,;DNHD1,synonymous_variant,p.%3D,ENST00000524401,;DNHD1,non_coding_transcript_exon_variant,,ENST00000531903,;DNHD1,non_coding_transcript_exon_variant,,ENST00000534210,;DNHD1,upstream_gene_variant,,ENST00000526027,;	T	ENSG00000179532	ENST00000254579	Transcript	synonymous_variant	9690	9126	3042	D	gaC/gaT	.	.	.	1	DNHD1	HGNC	26532	protein_coding	YES	CCDS44532.1	ENSP00000254579	DNHD1_HUMAN	.	UPI0001929529	.	.	.	26/43	.	hmmpanther:PTHR10676:SF244,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	ATTGACCGCTA	.	2	ESCA
MRPL11	0	.	GRCh37	11	66204663	66204663	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.385G>A	p.Ala129Thr	p.A129T	ENST00000310999	4/5	71	67	4	75	75	0	MRPL11,missense_variant,p.Ala129Thr,ENST00000329819,;MRPL11,missense_variant,p.Ala11Thr,ENST00000528272,;MRPL11,missense_variant,p.Ala103Thr,ENST00000430466,;MRPL11,missense_variant,p.Ala129Thr,ENST00000310999,;SNORA43,downstream_gene_variant,,ENST00000364863,;MRPL11,non_coding_transcript_exon_variant,,ENST00000524576,;MRPL11,3_prime_UTR_variant,,ENST00000534488,;	T	ENSG00000174547	ENST00000310999	Transcript	missense_variant	479	385	129	A/T	Gca/Aca	.	.	.	-1	MRPL11	HGNC	14042	protein_coding	YES	CCDS8139.1	ENSP00000308897	RM11_HUMAN	.	UPI0000049CE5	.	tolerated(0.6)	benign(0.177)	4/5	.	Superfamily_domains:SSF46906,SMART_domains:SM00649,Pfam_domain:PF00298,TIGRFAM_domain:TIGR01632,Gene3D:1vq8I00,hmmpanther:PTHR11661,HAMAP:MF_00736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATGCCTCAT	.	2	ESCA
PELI3	0	.	GRCh37	11	66239874	66239874	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.389A>C	p.Tyr130Ser	p.Y130S	ENST00000320740	5/8	64	45	18	52	52	0	PELI3,missense_variant,p.Tyr106Ser,ENST00000349459,;PELI3,missense_variant,p.Tyr130Ser,ENST00000320740,;PELI3,missense_variant,p.Tyr23Ser,ENST00000526296,;PELI3,missense_variant,p.Tyr130Ser,ENST00000524466,;PELI3,upstream_gene_variant,,ENST00000528752,;PELI3,downstream_gene_variant,,ENST00000527230,;CTD-3074O7.5,downstream_gene_variant,,ENST00000527092,;CTD-3074O7.5,downstream_gene_variant,,ENST00000533502,;CTD-3074O7.5,downstream_gene_variant,,ENST00000602951,;CTD-3074O7.5,downstream_gene_variant,,ENST00000527274,;PELI3,intron_variant,,ENST00000531856,;PELI3,3_prime_UTR_variant,,ENST00000532970,;	C	ENSG00000174516	ENST00000320740	Transcript	missense_variant	549	389	130	Y/S	tAt/tCt	.	.	.	1	PELI3	HGNC	30010	protein_coding	YES	CCDS31615.1	ENSP00000322532	PELI3_HUMAN	H0YEM6_HUMAN,E9PQX6_HUMAN,E9PI91_HUMAN	UPI00000707EF	.	deleterious(0)	probably_damaging(0.997)	5/8	.	hmmpanther:PTHR12098,hmmpanther:PTHR12098:SF6,Pfam_domain:PF04710,PIRSF_domain:PIRSF038886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGTATACAC	.	5	ESCA
CLEC7A	0	.	GRCh37	12	10271066	10271066	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.735T>G	p.Phe245Leu	p.F245L	ENST00000304084	6/6	48	38	9	80	80	0	CLEC7A,missense_variant,p.Phe199Leu,ENST00000353231,;CLEC7A,missense_variant,p.Phe245Leu,ENST00000304084,;CLEC7A,missense_variant,p.Phe166Leu,ENST00000396484,;CLEC7A,3_prime_UTR_variant,,ENST00000298523,;CLEC7A,3_prime_UTR_variant,,ENST00000533022,;CLEC7A,missense_variant,p.Phe245Leu,ENST00000529761,;CLEC7A,3_prime_UTR_variant,,ENST00000465100,;CLEC7A,3_prime_UTR_variant,,ENST00000349926,;CLEC7A,non_coding_transcript_exon_variant,,ENST00000534609,;CLEC7A,downstream_gene_variant,,ENST00000531192,;	C	ENSG00000172243	ENST00000304084	Transcript	missense_variant	890	735	245	F/L	ttT/ttG	.	.	.	-1	CLEC7A	HGNC	14558	protein_coding	YES	CCDS41753.1	ENSP00000302569	CLC7A_HUMAN	.	UPI0000073FA0	.	tolerated(1)	benign(0.001)	6/6	.	hmmpanther:PTHR22800:SF4,hmmpanther:PTHR22800,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGAAAACTT	.	5	ESCA
TRIAP1	0	.	GRCh37	12	120882537	120882537	+	3'UTR	SNP	A	A	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*138T>G	.	.	ENST00000546954	2/2	14	5	9	42	42	0	TRIAP1,3_prime_UTR_variant,,ENST00000546954,;AL021546.6,intron_variant,,ENST00000551806,;GATC,upstream_gene_variant,,ENST00000229384,;COX6A1,downstream_gene_variant,,ENST00000229379,;GATC,upstream_gene_variant,,ENST00000551765,;TRIAP1,non_coding_transcript_exon_variant,,ENST00000302432,;COX6A1,downstream_gene_variant,,ENST00000549525,;GATC,upstream_gene_variant,,ENST00000548171,;	C	ENSG00000170855	ENST00000546954	Transcript	3_prime_UTR_variant	409	.	.	.	.	.	.	.	-1	TRIAP1	HGNC	26937	protein_coding	YES	CCDS9198.1	ENSP00000449795	TRIA1_HUMAN	.	UPI0000124E0B	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGAAAACATC	.	5	ESCA
PGAM5	0	.	GRCh37	12	133291604	133291604	+	Missense_Mutation	SNP	C	C	T	rs376090046	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.352C>T	p.Arg118Cys	p.R118C	ENST00000498926	2/6	24	18	6	30	30	0	PGAM5,missense_variant,p.Arg118Cys,ENST00000498926,;PGAM5,missense_variant,p.Arg118Cys,ENST00000317555,;PXMP2,missense_variant,p.Pro157Leu,ENST00000545677,;PGAM5,5_prime_UTR_variant,,ENST00000454808,;PGAM5,5_prime_UTR_variant,,ENST00000543955,;RP13-672B3.2,downstream_gene_variant,,ENST00000537262,;PGAM5,upstream_gene_variant,,ENST00000541034,;	T	ENSG00000247077	ENST00000498926	Transcript	missense_variant	410	352	118	R/C	Cgc/Tgc	rs376090046	.	.	1	PGAM5	HGNC	28763	protein_coding	YES	CCDS53845.1	ENSP00000438465	PGAM5_HUMAN	F5GXG4_HUMAN	UPI0000406AB5	.	tolerated(0.06)	benign(0.013)	2/6	.	hmmpanther:PTHR20935,Gene3D:3.40.50.1240,Pfam_domain:PF00300,SMART_domains:SM00855,Superfamily_domains:SSF53254	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGGACCGCACT	byFrequency|byCluster	4	ESCA
AEBP2	0	.	GRCh37	12	19626251	19626251	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.949A>G	p.Arg317Gly	p.R317G	ENST00000398864	3/9	58	32	26	76	76	0	AEBP2,missense_variant,p.Arg317Gly,ENST00000266508,;AEBP2,missense_variant,p.Arg88Gly,ENST00000541908,;AEBP2,missense_variant,p.Arg101Gly,ENST00000360995,;AEBP2,missense_variant,p.Arg317Gly,ENST00000398864,;AEBP2,missense_variant,p.Arg88Gly,ENST00000538425,;	G	ENSG00000139154	ENST00000398864	Transcript	missense_variant	975	949	317	R/G	Agg/Ggg	.	.	.	1	AEBP2	HGNC	24051	protein_coding	YES	CCDS44841.1	ENSP00000381840	AEBP2_HUMAN	G5EA50_HUMAN,F5GZR7_HUMAN	UPI00002290BB	.	deleterious_low_confidence(0.02)	possibly_damaging(0.777)	3/9	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAAAGGCAT	.	5	ESCA
TM7SF3	0	.	GRCh37	12	27133537	27133537	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.998A>T	p.Tyr333Phe	p.Y333F	ENST00000343028	8/12	34	20	13	63	63	0	TM7SF3,missense_variant,p.Tyr124Phe,ENST00000543655,;TM7SF3,missense_variant,p.Tyr114Phe,ENST00000545303,;TM7SF3,missense_variant,p.Tyr124Phe,ENST00000535819,;TM7SF3,missense_variant,p.Tyr2Phe,ENST00000537406,;TM7SF3,missense_variant,p.Tyr47Phe,ENST00000545344,;TM7SF3,missense_variant,p.Tyr333Phe,ENST00000343028,;RP11-421F16.3,downstream_gene_variant,,ENST00000500632,;TM7SF3,intron_variant,,ENST00000542667,;TM7SF3,missense_variant,p.Tyr124Phe,ENST00000535260,;TM7SF3,3_prime_UTR_variant,,ENST00000543882,;TM7SF3,upstream_gene_variant,,ENST00000541081,;TM7SF3,upstream_gene_variant,,ENST00000544179,;	A	ENSG00000064115	ENST00000343028	Transcript	missense_variant	1224	998	333	Y/F	tAt/tTt	.	.	.	-1	TM7SF3	HGNC	23049	protein_coding	YES	CCDS8710.1	ENSP00000342322	TM7S3_HUMAN	F5H587_HUMAN,F5H3K5_HUMAN,F5GXE1_HUMAN,F5GWC3_HUMAN	UPI0000136849	.	tolerated(1)	benign(0.023)	8/12	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR15937,Pfam_domain:PF13886	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTATATAAAAG	.	5	ESCA
CACNA1C	0	.	GRCh37	12	2801925	2801925	+	3'Flank	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000347598	.	57	44	12	76	76	0	CACNA1C,3_prime_UTR_variant,,ENST00000399655,;CACNA1C,downstream_gene_variant,,ENST00000399644,;CACNA1C,downstream_gene_variant,,ENST00000399595,;CACNA1C,downstream_gene_variant,,ENST00000406454,;CACNA1C,downstream_gene_variant,,ENST00000399617,;CACNA1C,downstream_gene_variant,,ENST00000347598,;CACNA1C,downstream_gene_variant,,ENST00000402845,;CACNA1C,downstream_gene_variant,,ENST00000327702,;CACNA1C,downstream_gene_variant,,ENST00000399634,;CACNA1C,downstream_gene_variant,,ENST00000399641,;CACNA1C,downstream_gene_variant,,ENST00000399603,;CACNA1C,downstream_gene_variant,,ENST00000399629,;CACNA1C,downstream_gene_variant,,ENST00000399601,;CACNA1C,downstream_gene_variant,,ENST00000399597,;CACNA1C,downstream_gene_variant,,ENST00000399606,;CACNA1C,downstream_gene_variant,,ENST00000399637,;CACNA1C,downstream_gene_variant,,ENST00000335762,;CACNA1C,downstream_gene_variant,,ENST00000399591,;CACNA1C,downstream_gene_variant,,ENST00000399621,;CACNA1C,downstream_gene_variant,,ENST00000399638,;CACNA1C,downstream_gene_variant,,ENST00000344100,;CACNA1C,downstream_gene_variant,,ENST00000399649,;CACNA1C-AS1,upstream_gene_variant,,ENST00000544517,;CACNA1C-AS1,upstream_gene_variant,,ENST00000501371,;CACNA1C-AS1,upstream_gene_variant,,ENST00000541673,;	A	ENSG00000151067	ENST00000347598	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1466	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTTGAAGAA	.	5	ESCA
ATP8A2	0	.	GRCh37	13	25946268	25946268	+	5'UTR	SNP	C	C	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-83C>A	.	.	ENST00000381655	1/37	8	2	6	14	14	0	ATP8A2,5_prime_UTR_variant,,ENST00000381655,;	A	ENSG00000132932	ENST00000381655	Transcript	5_prime_UTR_variant	60	.	.	.	.	.	.	.	1	ATP8A2	HGNC	13533	protein_coding	YES	CCDS41873.1	ENSP00000371070	AT8A2_HUMAN	.	UPI0000229592	.	.	.	1/37	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGGTCCTCGG	.	2	ESCA
C14orf23	0	.	GRCh37	14	29261391	29261391	+	Missense_Mutation	SNP	G	G	A	rs747501043	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.428G>A	p.Ser143Asn	p.S143N	ENST00000399387	3/3	50	33	16	77	77	0	C14orf23,missense_variant,p.Ser143Asn,ENST00000399387,;C14orf23,intron_variant,,ENST00000548213,;C14orf23,intron_variant,,ENST00000550266,;	A	ENSG00000186960	ENST00000399387	Transcript	missense_variant	532	428	143	S/N	aGt/aAt	rs747501043	.	.	1	C14orf23	HGNC	19828	protein_coding	YES	.	ENSP00000382318	CN023_HUMAN	.	UPI0000160243	.	tolerated_low_confidence(0.64)	benign(0)	3/3	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTAAGTTTAT	.	5	ESCA
PCNX	0	.	GRCh37	14	71445317	71445317	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2263A>C	p.Asn755His	p.N755H	ENST00000304743	6/36	47	29	17	77	77	0	PCNX,missense_variant,p.Asn755His,ENST00000238570,;PCNX,missense_variant,p.Asn755His,ENST00000439984,;PCNX,missense_variant,p.Asn755His,ENST00000304743,;PCNX,downstream_gene_variant,,ENST00000553428,;PCNX,downstream_gene_variant,,ENST00000553272,;PCNX,non_coding_transcript_exon_variant,,ENST00000556846,;PCNX,non_coding_transcript_exon_variant,,ENST00000554879,;	C	ENSG00000100731	ENST00000304743	Transcript	missense_variant	2709	2263	755	N/H	Aac/Cac	.	.	.	1	PCNX	HGNC	19740	protein_coding	YES	CCDS9806.1	ENSP00000304192	PCX1_HUMAN	Q05BT4_HUMAN	UPI000013E9BB	.	deleterious(0)	benign(0.281)	6/36	.	hmmpanther:PTHR12372:SF2,hmmpanther:PTHR12372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCAAACCAG	.	5	ESCA
HERC2	0	.	GRCh37	15	28451412	28451412	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7186G>A	p.Ala2396Thr	p.A2396T	ENST00000261609	45/93	133	69	64	258	258	0	HERC2,missense_variant,p.Ala2396Thr,ENST00000261609,;HERC2,upstream_gene_variant,,ENST00000567869,;	T	ENSG00000128731	ENST00000261609	Transcript	missense_variant	7295	7186	2396	A/T	Gcc/Acc	.	.	.	-1	HERC2	HGNC	4868	protein_coding	YES	CCDS10021.1	ENSP00000261609	HERC2_HUMAN	.	UPI00004578F7	.	.	possibly_damaging(0.858)	45/93	.	hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGCCTTCA	.	4	ESCA
PPIP5K1	0	.	GRCh37	15	43827200	43827200	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3974G>T	p.Cys1325Phe	p.C1325F	ENST00000420765	31/31	34	24	9	71	71	0	PPIP5K1,missense_variant,p.Cys1325Phe,ENST00000396923,;PPIP5K1,missense_variant,p.Cys1300Phe,ENST00000360301,;PPIP5K1,missense_variant,p.Cys1321Phe,ENST00000381885,;PPIP5K1,missense_variant,p.Cys1301Phe,ENST00000381879,;PPIP5K1,missense_variant,p.Cys1325Phe,ENST00000420765,;PPIP5K1,missense_variant,p.Cys1298Phe,ENST00000348806,;PPIP5K1,missense_variant,p.Cys1298Phe,ENST00000360135,;PPIP5K1,missense_variant,p.Cys1300Phe,ENST00000334933,;MAP1A,downstream_gene_variant,,ENST00000300231,;MAP1A,downstream_gene_variant,,ENST00000382031,;MAP1A,downstream_gene_variant,,ENST00000399453,;	A	ENSG00000168781	ENST00000420765	Transcript	missense_variant	4157	3974	1325	C/F	tGc/tTc	.	.	.	-1	PPIP5K1	HGNC	29023	protein_coding	YES	CCDS45252.1	ENSP00000400887	VIP1_HUMAN	C9JZX6_HUMAN,C9J5E6_HUMAN,C9J490_HUMAN	UPI00001CE036	.	tolerated_low_confidence(0.42)	benign(0.002)	31/31	.	hmmpanther:PTHR12750,hmmpanther:PTHR12750:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGGCAAACT	.	5	ESCA
WDR72	0	.	GRCh37	15	53908157	53908157	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2246G>C	p.Ser749Thr	p.S749T	ENST00000396328	15/20	33	14	19	65	65	0	WDR72,missense_variant,p.Ser749Thr,ENST00000560036,;WDR72,missense_variant,p.Ser759Thr,ENST00000559418,;WDR72,missense_variant,p.Ser746Thr,ENST00000557913,;WDR72,missense_variant,p.Ser749Thr,ENST00000396328,;WDR72,missense_variant,p.Ser749Thr,ENST00000360509,;	G	ENSG00000166415	ENST00000396328	Transcript	missense_variant	2486	2246	749	S/T	aGc/aCc	.	.	.	-1	WDR72	HGNC	26790	protein_coding	YES	CCDS10151.1	ENSP00000379619	WDR72_HUMAN	H0YN02_HUMAN	UPI00001D777D	.	tolerated(0.68)	benign(0.004)	15/20	.	hmmpanther:PTHR12816:SF18,hmmpanther:PTHR12816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGGCTTTCA	.	5	ESCA
PML	0	.	GRCh37	15	74290730	74290730	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.515A>T	p.Gln172Leu	p.Q172L	ENST00000268058	2/9	9	3	6	14	14	0	PML,missense_variant,p.Gln172Leu,ENST00000563500,;PML,missense_variant,p.Gln172Leu,ENST00000395135,;PML,missense_variant,p.Gln172Leu,ENST00000569477,;PML,missense_variant,p.Gln172Leu,ENST00000565898,;PML,missense_variant,p.Gln172Leu,ENST00000435786,;PML,missense_variant,p.Gln172Leu,ENST00000436891,;PML,missense_variant,p.Gln172Leu,ENST00000359928,;PML,missense_variant,p.Gln172Leu,ENST00000564428,;PML,missense_variant,p.Gln172Leu,ENST00000567543,;PML,missense_variant,p.Gln172Leu,ENST00000354026,;PML,missense_variant,p.Gln172Leu,ENST00000569965,;PML,missense_variant,p.Gln172Leu,ENST00000268059,;PML,missense_variant,p.Gln172Leu,ENST00000268058,;PML,missense_variant,p.Gln172Leu,ENST00000395132,;STOML1,upstream_gene_variant,,ENST00000561656,;PML,non_coding_transcript_exon_variant,,ENST00000564725,;STOML1,upstream_gene_variant,,ENST00000563229,;	T	ENSG00000140464	ENST00000268058	Transcript	missense_variant	611	515	172	Q/L	cAg/cTg	.	.	.	1	PML	HGNC	9113	protein_coding	YES	CCDS10255.1	ENSP00000268058	PML_HUMAN	Q9UE85_HUMAN,Q05835_HUMAN	UPI000013D78F	.	deleterious(0)	benign(0.322)	2/9	.	hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF256	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	CAACCAGTCGG	.	3	ESCA
ALPK3	0	.	GRCh37	15	85411669	85411669	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5706G>C	p.Lys1902Asn	p.K1902N	ENST00000258888	14/14	46	26	19	110	110	0	ALPK3,missense_variant,p.Lys1902Asn,ENST00000258888,;ALPK3,downstream_gene_variant,,ENST00000558077,;	C	ENSG00000136383	ENST00000258888	Transcript	missense_variant	5873	5706	1902	K/N	aaG/aaC	COSM3887653,COSM3887654	.	.	1	ALPK3	HGNC	17574	protein_coding	YES	CCDS10333.1	ENSP00000258888	ALPK3_HUMAN	.	UPI000013D013	.	deleterious_low_confidence(0)	possibly_damaging(0.848)	14/14	.	hmmpanther:PTHR19897,hmmpanther:PTHR19897:SF21	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAAGGCCCA	.	5	ESCA
RGMA	0	.	GRCh37	15	93617030	93617030	+	5'UTR	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-45G>C	.	.	ENST00000557301	1/4	54	43	10	80	80	0	RGMA,5_prime_UTR_variant,,ENST00000556087,;RGMA,5_prime_UTR_variant,,ENST00000557301,;RGMA,intron_variant,,ENST00000555598,;RGMA,intron_variant,,ENST00000556950,;RGMA,intron_variant,,ENST00000329082,;RGMA,intron_variant,,ENST00000543599,;RGMA,upstream_gene_variant,,ENST00000557420,;RGMA,upstream_gene_variant,,ENST00000538818,;RGMA,upstream_gene_variant,,ENST00000556658,;RGMA,upstream_gene_variant,,ENST00000425933,;RGMA,upstream_gene_variant,,ENST00000542321,;RGMA,upstream_gene_variant,,ENST00000557608,;RGMA,upstream_gene_variant,,ENST00000554387,;	G	ENSG00000182175	ENST00000557301	Transcript	5_prime_UTR_variant	63	.	.	.	.	.	.	.	-1	RGMA	HGNC	30308	protein_coding	YES	CCDS53974.1	ENSP00000452126	.	G3V518_HUMAN,G3V4C2_HUMAN,F5H7G2_HUMAN,F5GZU6_HUMAN	UPI0002065681	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCGCTGC	.	5	ESCA
USP31	0	.	GRCh37	16	23093847	23093847	+	Missense_Mutation	SNP	T	T	C	rs771953230	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1862A>G	p.His621Arg	p.H621R	ENST00000219689	12/16	57	31	26	64	64	0	USP31,missense_variant,p.His621Arg,ENST00000219689,;USP31,non_coding_transcript_exon_variant,,ENST00000563525,;	C	ENSG00000103404	ENST00000219689	Transcript	missense_variant	1862	1862	621	H/R	cAc/cGc	rs771953230	.	.	-1	USP31	HGNC	20060	protein_coding	YES	CCDS10607.1	ENSP00000219689	UBP31_HUMAN	.	UPI0000366B06	.	deleterious(0.02)	probably_damaging(0.999)	12/16	.	Superfamily_domains:SSF54001,Pfam_domain:PF00443,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF400,PROSITE_profiles:PS50235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAGTGTGGG	.	5	ESCA
MT1M	0	.	GRCh37	16	56667702	56667702	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.134C>T	p.Ala45Val	p.A45V	ENST00000379818	3/3	92	53	39	95	95	0	MT1M,missense_variant,p.Ala45Val,ENST00000379818,;AC026461.1,upstream_gene_variant,,ENST00000600389,;MT1A,upstream_gene_variant,,ENST00000290705,;MT1M,downstream_gene_variant,,ENST00000570233,;MT1JP,upstream_gene_variant,,ENST00000564564,;MT1JP,upstream_gene_variant,,ENST00000563395,;MT1JP,upstream_gene_variant,,ENST00000444023,;	T	ENSG00000205364	ENST00000379818	Transcript	missense_variant	633	134	45	A/V	gCc/gTc	.	.	.	1	MT1M	HGNC	14296	protein_coding	YES	CCDS42166.1	ENSP00000369146	MT1M_HUMAN	.	UPI0000071D97	.	deleterious(0.05)	possibly_damaging(0.787)	3/3	.	Prints_domain:PR00860,Superfamily_domains:SSF57868,Gene3D:4mt2A00,Pfam_domain:PF00131,hmmpanther:PTHR23299,hmmpanther:PTHR23299:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGCCCACG	.	5	ESCA
SLC9A5	0	.	GRCh37	16	67298363	67298363	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1951A>T	p.Thr651Ser	p.T651S	ENST00000299798	13/16	86	77	9	102	102	0	SLC9A5,missense_variant,p.Thr104Ser,ENST00000566626,;SLC9A5,missense_variant,p.Thr651Ser,ENST00000299798,;SLC9A5,missense_variant,p.Thr137Ser,ENST00000567247,;SLC9A5,downstream_gene_variant,,ENST00000566345,;SLC9A5,3_prime_UTR_variant,,ENST00000564812,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000564704,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000563723,;SLC9A5,non_coding_transcript_exon_variant,,ENST00000566638,;CTC-277H1.7,downstream_gene_variant,,ENST00000573063,;	T	ENSG00000135740	ENST00000299798	Transcript	missense_variant	2016	1951	651	T/S	Acc/Tcc	.	.	.	1	SLC9A5	HGNC	11078	protein_coding	YES	CCDS42178.1	ENSP00000299798	SL9A5_HUMAN	.	UPI000012FD2D	.	tolerated(0.13)	benign(0.222)	13/16	.	hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF56	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AGTCCACCAAG	.	3	ESCA
HYDIN	0	.	GRCh37	16	70995941	70995941	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5889G>A	p.Trp1963Ter	p.W1963*	ENST00000393567	38/86	23	20	3	36	36	0	HYDIN,stop_gained,p.Trp1963Ter,ENST00000393567,;HYDIN,non_coding_transcript_exon_variant,,ENST00000543521,;HYDIN,non_coding_transcript_exon_variant,,ENST00000309900,;HYDIN,upstream_gene_variant,,ENST00000546297,;	T	ENSG00000157423	ENST00000393567	Transcript	stop_gained	6040	5889	1963	W/*	tgG/tgA	.	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	.	38/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	GCGTGCCATTC	.	2	ESCA
RP11-303E16.5	0	.	GRCh37	16	81087509	81087509	+	5'Flank	SNP	G	G	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000562450	.	10	7	3	19	19	0	C16orf46,3_prime_UTR_variant,,ENST00000378611,;RP11-303E16.5,upstream_gene_variant,,ENST00000562450,;RP11-303E16.8,non_coding_transcript_exon_variant,,ENST00000564536,;	T	ENSG00000261141	ENST00000562450	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	1397	1	RP11-303E16.5	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATAAGACCTT	.	2	ESCA
ANKRD11	0	.	GRCh37	16	89341252	89341252	+	Silent	SNP	G	G	A	rs781285799	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7683C>T	p.%3D	p.S2561S	ENST00000301030	11/13	37	28	8	88	88	0	ANKRD11,synonymous_variant,p.%3D,ENST00000378330,;ANKRD11,synonymous_variant,p.%3D,ENST00000301030,;ANKRD11,synonymous_variant,p.%3D,ENST00000562194,;AC137932.1,downstream_gene_variant,,ENST00000602042,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;	A	ENSG00000167522	ENST00000301030	Transcript	synonymous_variant	8144	7683	2561	S	tcC/tcT	rs781285799	.	.	-1	ANKRD11	HGNC	21316	protein_coding	YES	CCDS32513.1	ENSP00000301030	ANR11_HUMAN	.	UPI00004569E1	.	.	.	11/13	.	hmmpanther:PTHR24145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTCGGAGTC	byFrequency	5	ESCA
SYNRG	0	.	GRCh37	17	35913272	35913273	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2552dupT	p.Met851IlefsTer3	p.M851Ifs*3	ENST00000339208	14/22	52	42	10	56	56	0	SYNRG,frameshift_variant,p.Met773IlefsTer3,ENST00000394378,;SYNRG,frameshift_variant,p.Met773IlefsTer3,ENST00000502449,;SYNRG,frameshift_variant,p.Met690IlefsTer3,ENST00000591288,;SYNRG,frameshift_variant,p.Met851IlefsTer3,ENST00000339208,;SYNRG,frameshift_variant,p.Met773IlefsTer3,ENST00000345615,;SYNRG,frameshift_variant,p.Met772IlefsTer3,ENST00000585472,;SYNRG,frameshift_variant,p.Met851IlefsTer3,ENST00000346661,;SYNRG,downstream_gene_variant,,ENST00000588194,;SYNRG,downstream_gene_variant,,ENST00000587040,;SYNRG,non_coding_transcript_exon_variant,,ENST00000421408,;	A	ENSG00000006114	ENST00000339208	Transcript	frameshift_variant	2693-2694	2552-2553	851	M/IX	atg/atTg	.	.	.	-1	SYNRG	HGNC	557	protein_coding	YES	CCDS11321.1	ENSP00000343610	SYNRG_HUMAN	.	UPI000013C4EA	.	.	.	14/22	.	hmmpanther:PTHR15463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCAGACATGAC	.	3	ESCA
KRT10	0	.	GRCh37	17	38975181	38975181	+	Missense_Mutation	SNP	C	C	T	rs764225659	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1606G>A	p.Gly536Ser	p.G536S	ENST00000269576	7/8	21	15	6	14	14	0	KRT10,missense_variant,p.Gly536Ser,ENST00000269576,;TMEM99,upstream_gene_variant,,ENST00000436612,;TMEM99,upstream_gene_variant,,ENST00000301665,;TMEM99,upstream_gene_variant,,ENST00000496847,;	T	ENSG00000186395	ENST00000269576	Transcript	missense_variant	1616	1606	536	G/S	Ggc/Agc	rs764225659	.	.	-1	KRT10	HGNC	6413	protein_coding	YES	CCDS11377.1	ENSP00000269576	K1C10_HUMAN	.	UPI000013D842	.	tolerated_low_confidence(0.41)	unknown(0)	7/8	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GCCGCCGGAAC	.	2	ESCA
KRT10	0	.	GRCh37	17	38975189	38975191	+	In_Frame_Del	DEL	CCA	CCA	-	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	CCA	CCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1596_1598delTGG	p.Gly533del	p.G533del	ENST00000269576	7/8	24	16	8	12	12	0	KRT10,inframe_deletion,p.Gly533del,ENST00000269576,;TMEM99,upstream_gene_variant,,ENST00000436612,;TMEM99,upstream_gene_variant,,ENST00000301665,;TMEM99,upstream_gene_variant,,ENST00000496847,;	-	ENSG00000186395	ENST00000269576	Transcript	inframe_deletion	1606-1608	1596-1598	532-533	GG/G	ggTGGc/ggc	.	.	.	-1	KRT10	HGNC	6413	protein_coding	YES	CCDS11377.1	ENSP00000269576	K1C10_HUMAN	.	UPI000013D842	.	.	.	7/8	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	GAACTGCCACCACC	.	2	ESCA
CXCL16	0	.	GRCh37	17	4637861	4637861	+	Intron	DEL	A	A	-	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*23+17delT	.	.	ENST00000293778	.	82	53	29	98	98	0	CXCL16,3_prime_UTR_variant,,ENST00000574412,;CXCL16,intron_variant,,ENST00000293778,;CXCL16,downstream_gene_variant,,ENST00000573123,;MED11,downstream_gene_variant,,ENST00000575284,;MED11,downstream_gene_variant,,ENST00000573708,;MED11,downstream_gene_variant,,ENST00000293777,;RP11-314A20.5,upstream_gene_variant,,ENST00000570493,;CXCL16,intron_variant,,ENST00000576153,;CXCL16,downstream_gene_variant,,ENST00000575168,;	-	ENSG00000161921	ENST00000293778	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CXCL16	HGNC	16642	protein_coding	YES	CCDS11052.1	ENSP00000293778	CXL16_HUMAN	I3L333_HUMAN	UPI000013E11E	.	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGTAAGAATAAG	.	3	ESCA
AKAP1	0	.	GRCh37	17	55183839	55183839	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1014G>T	p.Leu338Phe	p.L338F	ENST00000337714	2/11	39	29	10	75	75	0	AKAP1,missense_variant,p.Leu338Phe,ENST00000314126,;AKAP1,missense_variant,p.Leu338Phe,ENST00000571629,;AKAP1,missense_variant,p.Leu338Phe,ENST00000337714,;AKAP1,missense_variant,p.Leu338Phe,ENST00000572557,;AKAP1,missense_variant,p.Leu338Phe,ENST00000539273,;AKAP1,intron_variant,,ENST00000576295,;AKAP1,downstream_gene_variant,,ENST00000575322,;AKAP1,downstream_gene_variant,,ENST00000574683,;AKAP1,downstream_gene_variant,,ENST00000575186,;AKAP1,downstream_gene_variant,,ENST00000576591,;AKAP1,downstream_gene_variant,,ENST00000573085,;AKAP1,downstream_gene_variant,,ENST00000572156,;AKAP1,downstream_gene_variant,,ENST00000572814,;AKAP1,downstream_gene_variant,,ENST00000570423,;AKAP1,missense_variant,p.Leu338Phe,ENST00000481416,;AKAP1,upstream_gene_variant,,ENST00000573326,;	T	ENSG00000121057	ENST00000337714	Transcript	missense_variant	1247	1014	338	L/F	ttG/ttT	.	.	.	1	AKAP1	HGNC	367	protein_coding	YES	CCDS11594.1	ENSP00000337736	AKAP1_HUMAN	I3L3L9_HUMAN,I3L3K1_HUMAN,I3L364_HUMAN,I3L2N7_HUMAN,I3L2A2_HUMAN,I3L0K6_HUMAN	UPI0000125778	.	deleterious(0.04)	benign(0.374)	2/11	.	hmmpanther:PTHR12727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GGCTTGGATAG	.	3	ESCA
AKAP1	0	.	GRCh37	17	55183841	55183841	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1016A>G	p.Asp339Gly	p.D339G	ENST00000337714	2/11	38	29	9	72	71	1	AKAP1,missense_variant,p.Asp339Gly,ENST00000314126,;AKAP1,missense_variant,p.Asp339Gly,ENST00000571629,;AKAP1,missense_variant,p.Asp339Gly,ENST00000337714,;AKAP1,missense_variant,p.Asp339Gly,ENST00000572557,;AKAP1,missense_variant,p.Asp339Gly,ENST00000539273,;AKAP1,intron_variant,,ENST00000576295,;AKAP1,downstream_gene_variant,,ENST00000575322,;AKAP1,downstream_gene_variant,,ENST00000574683,;AKAP1,downstream_gene_variant,,ENST00000575186,;AKAP1,downstream_gene_variant,,ENST00000576591,;AKAP1,downstream_gene_variant,,ENST00000573085,;AKAP1,downstream_gene_variant,,ENST00000572156,;AKAP1,downstream_gene_variant,,ENST00000572814,;AKAP1,downstream_gene_variant,,ENST00000570423,;AKAP1,missense_variant,p.Asp339Gly,ENST00000481416,;AKAP1,upstream_gene_variant,,ENST00000573326,;	G	ENSG00000121057	ENST00000337714	Transcript	missense_variant	1249	1016	339	D/G	gAt/gGt	.	.	.	1	AKAP1	HGNC	367	protein_coding	YES	CCDS11594.1	ENSP00000337736	AKAP1_HUMAN	I3L3L9_HUMAN,I3L3K1_HUMAN,I3L364_HUMAN,I3L2N7_HUMAN,I3L2A2_HUMAN,I3L0K6_HUMAN	UPI0000125778	.	deleterious(0.01)	benign(0.013)	2/11	.	hmmpanther:PTHR12727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTTGGATAGAA	.	3	ESCA
TP53	0	.	GRCh37	17	7579369	7579369	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	4/11	82	26	55	108	108	0	TP53,missense_variant,p.Ser106Arg,ENST00000508793,;TP53,missense_variant,p.Ser106Arg,ENST00000413465,;TP53,missense_variant,p.Ser106Arg,ENST00000604348,;TP53,missense_variant,p.Ser106Arg,ENST00000420246,;TP53,missense_variant,p.Ser106Arg,ENST00000269305,;TP53,missense_variant,p.Ser106Arg,ENST00000359597,;TP53,missense_variant,p.Ser106Arg,ENST00000445888,;TP53,missense_variant,p.Ser106Arg,ENST00000503591,;TP53,missense_variant,p.Ser106Arg,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	508	318	106	S/R	agC/agG	CM013441,TP53_g.11549C>G,COSM45944,COSM1735720,COSM1610878,COSM1610879,COSM3717683,COSM2745028	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.41)	benign(0.27)	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S106R|c.318C>G|3,SITE|p.S106R|c.318C>G|3,SITE|p.S106R|c.318C>G|6,CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,BUFFER|p.R110fs*13|c.329delG|3,BUFFER|p.R110fs*13|c.328delC|4,BUFFER|p.R110L|c.329G>T|27,BUFFER|p.R110P|c.329G>C|11,BUFFER|p.R110L|c.329G>T|5,BUFFER|p.R110L|c.329G>T|8,BUFFER|p.R110L|c.329G>T|8,BUFFER|p.R110C|c.328C>T|6,BUFFER|p.F109C|c.326T>G|3,BUFFER|p.F109C|c.326T>G|4,BUFFER|p.F109C|c.326T>G|3,BUFFER|p.G108delG|c.322_324delGGT|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.Y107*|c.321C>A|6,BUFFER|p.Y107Y|c.321C>T|3,BUFFER|p.Y107*|c.321C>G|3,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|8,BUFFER|p.G105D|c.314G>A|3,BUFFER|p.G105C|c.313G>T|7,BUFFER|p.G105R|c.313G>C|4,BUFFER|p.Q104*|c.310C>T|8,BUFFER|p.Q104*|c.310C>T|8,BUFFER|p.Q104*|c.310C>T|14,BUFFER|p.Y103*|c.309C>G|5,BUFFER|p.Y103*|c.309C>A|3,BUFFER|p.Y103fs*20|c.306delC|8,BUFFER|p.Y103fs*20|c.306delC|8,BUFFER|p.Y103fs*20|c.306delC|8,BUFFER|p.Y103fs*20|c.306delC|9	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGTAGCTGCC	.	5	ESCA
GAS7	0	.	GRCh37	17	9818705	9818705	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1840A>G	.	.	ENST00000432992	14/14	22	14	8	50	50	0	GAS7,3_prime_UTR_variant,,ENST00000432992,;GAS7,3_prime_UTR_variant,,ENST00000323816,;GAS7,3_prime_UTR_variant,,ENST00000437099,;GAS7,3_prime_UTR_variant,,ENST00000540214,;GAS7,3_prime_UTR_variant,,ENST00000585266,;GAS7,downstream_gene_variant,,ENST00000396115,;GAS7,downstream_gene_variant,,ENST00000583882,;GAS7,downstream_gene_variant,,ENST00000580865,;GAS7,downstream_gene_variant,,ENST00000579158,;GAS7,downstream_gene_variant,,ENST00000542249,;GAS7,downstream_gene_variant,,ENST00000581112,;GAS7,downstream_gene_variant,,ENST00000578456,;	C	ENSG00000007237	ENST00000432992	Transcript	3_prime_UTR_variant	3432	.	.	.	.	.	.	.	-1	GAS7	HGNC	4169	protein_coding	YES	CCDS11152.1	ENSP00000407552	GAS7_HUMAN	J3QS26_HUMAN,J3QLH8_HUMAN,J3KTK6_HUMAN,J3KTB1_HUMAN,J3KS47_HUMAN,B7Z1Q2_HUMAN	UPI00001B4B17	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTCTAAAAT	.	5	ESCA
WBP11P1	0	.	GRCh37	18	30091939	30091939	+	RNA	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.314G>A	.	.	ENST00000567636	1/1	38	26	12	103	103	0	WBP11P1,non_coding_transcript_exon_variant,,ENST00000567636,;WBP11P1,non_coding_transcript_exon_variant,,ENST00000562560,;	A	ENSG00000260389	ENST00000567636	Transcript	non_coding_transcript_exon_variant	314	.	.	.	.	.	.	.	1	WBP11P1	HGNC	26250	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCTGAAGTT	.	5	ESCA
CDH20	0	.	GRCh37	18	59195231	59195231	+	Missense_Mutation	SNP	C	C	A	rs748048718	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1049C>A	p.Thr350Asn	p.T350N	ENST00000262717	7/12	20	9	11	53	53	0	CDH20,missense_variant,p.Thr350Asn,ENST00000538374,;CDH20,missense_variant,p.Thr350Asn,ENST00000536675,;CDH20,missense_variant,p.Thr350Asn,ENST00000262717,;	A	ENSG00000101542	ENST00000262717	Transcript	missense_variant	1447	1049	350	T/N	aCc/aAc	rs748048718	.	.	1	CDH20	HGNC	1760	protein_coding	YES	CCDS11977.1	ENSP00000262717	CAD20_HUMAN	Q8N9J3_HUMAN,K7ESP2_HUMAN	UPI000013D30D	.	tolerated(0.14)	benign(0.011)	7/12	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Gene3D:2.60.40.60,Pfam_domain:PF00028,hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTACACCTTAA	.	5	ESCA
FBXO15	0	.	GRCh37	18	71814970	71814970	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.51G>C	p.Gln17His	p.Q17H	ENST00000419743	1/10	18	11	7	51	51	0	FBXO15,missense_variant,p.Gln17His,ENST00000582526,;FBXO15,missense_variant,p.Gln17His,ENST00000419743,;FBXO15,5_prime_UTR_variant,,ENST00000269500,;TIMM21,upstream_gene_variant,,ENST00000169551,;TIMM21,upstream_gene_variant,,ENST00000580087,;FBXO15,missense_variant,p.Gln17His,ENST00000583443,;FBXO15,missense_variant,p.Arg6Thr,ENST00000585174,;FBXO15,missense_variant,p.Gln17His,ENST00000580552,;TIMM21,upstream_gene_variant,,ENST00000577952,;TIMM21,upstream_gene_variant,,ENST00000581467,;FBXO15,upstream_gene_variant,,ENST00000581214,;	G	ENSG00000141665	ENST00000419743	Transcript	missense_variant	131	51	17	Q/H	caG/caC	.	.	.	-1	FBXO15	HGNC	13617	protein_coding	YES	CCDS45884.1	ENSP00000393154	FBX15_HUMAN	J3QRE7_HUMAN	UPI00003CF23D	.	tolerated(0.24)	benign(0.201)	1/10	.	hmmpanther:PTHR20995:SF16,hmmpanther:PTHR20995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	AGCGTCTGGAG	.	4	ESCA
RPSAP58	0	.	GRCh37	19	24010564	24010568	+	Frame_Shift_Del	DEL	CTGTA	CTGTA	-	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	CTGTA	CTGTA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.603_607delGTACT	p.Tyr202LeufsTer5	p.Y202Lfs*5	ENST00000496398	4/4	44	28	16	96	96	0	RPSAP58,frameshift_variant,p.Tyr202LeufsTer5,ENST00000354585,;RPSAP58,frameshift_variant,p.Tyr202LeufsTer5,ENST00000496398,;RPSAP58,downstream_gene_variant,,ENST00000486528,;RP11-255H23.4,intron_variant,,ENST00000599944,;RP11-255H23.2,intron_variant,,ENST00000475499,;RP11-255H23.2,intron_variant,,ENST00000471224,;RP11-255H23.2,intron_variant,,ENST00000472297,;	-	ENSG00000205246	ENST00000496398	Transcript	frameshift_variant	1024-1028	601-605	201-202	LY/X	CTGTAc/c	.	.	.	1	RPSAP58	HGNC	36809	protein_coding	YES	.	ENSP00000417240	.	C9JQR9_HUMAN,A6NE09_HUMAN	UPI00001972FD	.	.	.	4/4	.	HAMAP:MF_03016,HAMAP:MF_03015,hmmpanther:PTHR11489,TIGRFAM_domain:TIGR01012,Gene3D:3.40.50.10490	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	2	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCTGATCTGTACTTCT	.	3	ESCA
ARHGAP33	0	.	GRCh37	19	36283304	36283304	+	3'Flank	SNP	G	G	A	rs556740058	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000314737	.	22	15	7	47	47	0	ARHGAP33,downstream_gene_variant,,ENST00000007510,;ARHGAP33,downstream_gene_variant,,ENST00000378944,;ARHGAP33,downstream_gene_variant,,ENST00000587447,;ARHGAP33,downstream_gene_variant,,ENST00000314737,;ARHGAP33,downstream_gene_variant,,ENST00000588248,;AC002398.5,non_coding_transcript_exon_variant,,ENST00000564335,;AC002398.5,non_coding_transcript_exon_variant,,ENST00000433059,;AC002398.5,non_coding_transcript_exon_variant,,ENST00000567313,;	A	ENSG00000004777	ENST00000314737	Transcript	downstream_gene_variant	.	.	.	.	.	rs556740058	.	3580	1	ARHGAP33	HGNC	23085	protein_coding	YES	CCDS12477.1	ENSP00000320038	RHG33_HUMAN	.	UPI000013F8F9	.	.	.	.	.	.	A:0.0008	A:0.003	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CGAACGCTGAT	byFrequency|by1000G	4	ESCA
ZNF260	0	.	GRCh37	19	37005581	37005581	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.560C>A	p.Thr187Asn	p.T187N	ENST00000523638	3/3	59	50	9	100	100	0	ZNF260,missense_variant,p.Thr187Asn,ENST00000588993,;ZNF260,missense_variant,p.Thr187Asn,ENST00000592282,;ZNF260,missense_variant,p.Thr187Asn,ENST00000523638,;ZNF260,missense_variant,p.Thr187Asn,ENST00000593142,;	T	ENSG00000254004	ENST00000523638	Transcript	missense_variant	1682	560	187	T/N	aCt/aAt	.	.	.	-1	ZNF260	HGNC	13499	protein_coding	YES	CCDS33003.1	ENSP00000429803	ZN260_HUMAN	.	UPI00001984F1	.	deleterious(0.04)	benign(0.066)	3/3	.	Superfamily_domains:SSF57667,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24377:SF133,hmmpanther:PTHR24377,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCAGTATGG	.	5	ESCA
ZNF461	0	.	GRCh37	19	37130748	37130748	+	Frame_Shift_Del	DEL	T	T	-	rs765868153	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.499delA	p.Ile167LeufsTer98	p.I167Lfs*98	ENST00000588268	6/6	83	72	11	114	114	0	ZNF461,frameshift_variant,p.Ile79LeufsTer?,ENST00000591370,;ZNF461,frameshift_variant,p.Ile144LeufsTer98,ENST00000360357,;ZNF461,frameshift_variant,p.Ile167LeufsTer98,ENST00000588268,;ZNF461,non_coding_transcript_exon_variant,,ENST00000540605,;ZNF461,upstream_gene_variant,,ENST00000589442,;ZNF461,3_prime_UTR_variant,,ENST00000396893,;ZNF461,non_coding_transcript_exon_variant,,ENST00000590487,;ZNF461,downstream_gene_variant,,ENST00000590361,;ZNF461,downstream_gene_variant,,ENST00000588844,;	-	ENSG00000197808	ENST00000588268	Transcript	frameshift_variant	727	499	167	I/X	Att/tt	rs765868153	.	.	-1	ZNF461	HGNC	21629	protein_coding	YES	CCDS54257.1	ENSP00000467931	ZN461_HUMAN	K7EJM1_HUMAN,K7EIW1_HUMAN	UPI00002021CA	.	.	.	6/6	.	hmmpanther:PTHR24377:SF277,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GGTTAATCATAA	.	3	ESCA
PSG1	0	.	GRCh37	19	43373155	43373155	+	Silent	SNP	G	G	A	rs769102835	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.741C>T	p.%3D	p.N247N	ENST00000244296	4/5	134	104	30	225	225	0	PSG1,synonymous_variant,p.%3D,ENST00000244296,;PSG1,synonymous_variant,p.%3D,ENST00000595356,;PSG1,synonymous_variant,p.%3D,ENST00000312439,;PSG1,synonymous_variant,p.%3D,ENST00000436291,;PSG1,synonymous_variant,p.%3D,ENST00000595124,;PSG1,synonymous_variant,p.%3D,ENST00000403380,;PSG1,intron_variant,,ENST00000597058,;PSG1,downstream_gene_variant,,ENST00000595930,;PSG1,non_coding_transcript_exon_variant,,ENST00000602039,;	A	ENSG00000231924	ENST00000244296	Transcript	synonymous_variant	879	741	247	N	aaC/aaT	rs769102835,COSM3414071,COSM3414073,COSM3414072,COSM3414074,COSM3414075	.	.	-1	PSG1	HGNC	9514	protein_coding	YES	CCDS12612.1	ENSP00000244296	PSG1_HUMAN	Q9UMI0_HUMAN,M0QY44_HUMAN	UPI0000001071	.	.	.	4/5	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955,hmmpanther:PTHR19955:SF114,Gene3D:2.60.40.10,SMART_domains:SM00409	.	.	.	.	.	.	.	.	.	.	0,1,1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGTTGTTGAT	byFrequency|byCluster	3	ESCA
PSG7	0	.	GRCh37	19	43430802	43430802	+	Missense_Mutation	SNP	G	G	T	rs199532805	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.776C>A	p.Thr259Asn	p.T259N	ENST00000406070	4/6	107	66	41	237	237	0	PSG7,non_coding_transcript_exon_variant,,ENST00000599226,;PSG7,downstream_gene_variant,,ENST00000599620,;PSG7,missense_variant,p.Thr259Asn,ENST00000406070,;PSG7,missense_variant,p.Thr259Asn,ENST00000446844,;	T	ENSG00000221878	ENST00000406070	Transcript	missense_variant	873	776	259	T/N	aCc/aAc	rs199532805	.	.	-1	PSG7	HGNC	9524	polymorphic_pseudogene	YES	.	ENSP00000421986	.	.	.	.	tolerated(0.22)	benign(0.003)	4/6	.	.	.	.	.	.	.	.	.	A:0	A:0.0023	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	TGAAGGTTGAG	byFrequency|byCluster	2	ESCA
PSG7	0	.	GRCh37	19	43430805	43430805	+	Missense_Mutation	SNP	G	G	A	rs373637874	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.773C>T	p.Ser258Leu	p.S258L	ENST00000406070	4/6	104	63	41	239	239	0	PSG7,non_coding_transcript_exon_variant,,ENST00000599226,;PSG7,downstream_gene_variant,,ENST00000599620,;PSG7,missense_variant,p.Ser258Leu,ENST00000406070,;PSG7,missense_variant,p.Ser258Leu,ENST00000446844,;	A	ENSG00000221878	ENST00000406070	Transcript	missense_variant	870	773	258	S/L	tCa/tTa	rs373637874	.	.	-1	PSG7	HGNC	9524	polymorphic_pseudogene	YES	.	ENSP00000421986	.	.	.	.	tolerated(0.75)	benign(0.001)	4/6	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	AGGTTGAGACA	byCluster|by1000G	2	ESCA
ZNF347	0	.	GRCh37	19	53652593	53652593	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.43A>G	p.Ile15Val	p.I15V	ENST00000452676	3/5	107	33	74	185	185	0	ZNF347,missense_variant,p.Ile15Val,ENST00000601469,;ZNF347,missense_variant,p.Ile15Val,ENST00000452676,;ZNF347,missense_variant,p.Ile15Val,ENST00000334197,;ZNF347,missense_variant,p.Ile15Val,ENST00000599096,;ZNF347,5_prime_UTR_variant,,ENST00000595967,;ZNF347,intron_variant,,ENST00000601804,;ZNF347,intron_variant,,ENST00000597183,;ZNF347,non_coding_transcript_exon_variant,,ENST00000595710,;	C	ENSG00000197937	ENST00000452676	Transcript	missense_variant	470	43	15	I/V	Ata/Gta	.	.	.	-1	ZNF347	HGNC	16447	protein_coding	YES	CCDS54314.1	ENSP00000405218	ZN347_HUMAN	M0R1E9_HUMAN,M0QXR8_HUMAN	UPI000059D78C	.	tolerated(0.08)	probably_damaging(0.953)	3/5	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF95,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTATAGCCA	.	5	ESCA
CACNG8	0	.	GRCh37	19	54485599	54485599	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774G>A	p.%3D	p.S258S	ENST00000270458	4/4	11	7	4	20	20	0	CACNG8,synonymous_variant,p.%3D,ENST00000270458,;MIR935,non_coding_transcript_exon_variant,,ENST00000401179,;	A	ENSG00000142408	ENST00000270458	Transcript	synonymous_variant	877	774	258	S	tcG/tcA	.	.	.	1	CACNG8	HGNC	13628	protein_coding	YES	CCDS33104.1	ENSP00000270458	CCG8_HUMAN	.	UPI000013D88B	.	.	.	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12107,hmmpanther:PTHR12107:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTCGGCCAT	.	2	ESCA
ZNF71	0	.	GRCh37	19	57133981	57133981	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1326G>T	p.Gln442His	p.Q442H	ENST00000328070	3/3	58	39	19	107	107	0	ZNF71,missense_variant,p.Gln442His,ENST00000328070,;ZNF71,downstream_gene_variant,,ENST00000599599,;	T	ENSG00000197951	ENST00000328070	Transcript	missense_variant	1560	1326	442	Q/H	caG/caT	.	.	.	1	ZNF71	HGNC	13141	protein_coding	YES	CCDS12947.1	ENSP00000328245	ZNF71_HUMAN	M0R0C0_HUMAN	UPI00000437FA	.	deleterious(0.02)	probably_damaging(0.996)	3/3	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF115,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCAGTGCGG	.	5	ESCA
TRIP10	0	.	GRCh37	19	6750388	6750388	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1313C>T	p.Ala438Val	p.A438V	ENST00000313285	12/14	57	44	13	90	90	0	TRIP10,missense_variant,p.Ala438Val,ENST00000313285,;TRIP10,missense_variant,p.Ala438Val,ENST00000596758,;TRIP10,missense_variant,p.Ala330Val,ENST00000600428,;TRIP10,missense_variant,p.Ala494Val,ENST00000313244,;SH2D3A,downstream_gene_variant,,ENST00000245908,;SH2D3A,downstream_gene_variant,,ENST00000597687,;SH2D3A,downstream_gene_variant,,ENST00000437152,;CTD-3128G10.6,intron_variant,,ENST00000594056,;SH2D3A,downstream_gene_variant,,ENST00000597254,;SH2D3A,downstream_gene_variant,,ENST00000599563,;SH2D3A,downstream_gene_variant,,ENST00000597168,;TRIP10,3_prime_UTR_variant,,ENST00000600677,;TRIP10,non_coding_transcript_exon_variant,,ENST00000595305,;SH2D3A,downstream_gene_variant,,ENST00000595681,;TRIP10,downstream_gene_variant,,ENST00000598843,;	T	ENSG00000125733	ENST00000313285	Transcript	missense_variant	1395	1313	438	A/V	gCt/gTt	.	.	.	1	TRIP10	HGNC	12304	protein_coding	YES	CCDS12172.1	ENSP00000320493	CIP4_HUMAN	M0R0F9_HUMAN,M0R070_HUMAN	UPI00001279E3	.	tolerated(0.55)	benign(0.002)	12/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12602:SF7,hmmpanther:PTHR12602,Superfamily_domains:SSF50044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCGCTAGCG	.	5	ESCA
MUC16	0	.	GRCh37	19	9071105	9071105	+	Silent	SNP	C	C	T	rs760769858	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16341G>A	p.%3D	p.S5447S	ENST00000397910	3/84	42	36	6	48	48	0	MUC16,synonymous_variant,p.%3D,ENST00000397910,;	T	ENSG00000181143	ENST00000397910	Transcript	synonymous_variant	16545	16341	5447	S	tcG/tcA	rs760769858,COSM1494525,COSM1494526,COSM1494524	.	.	-1	MUC16	HGNC	15582	protein_coding	YES	CCDS54212.1	ENSP00000381008	.	F8WE81_HUMAN,B5ME49_HUMAN	UPI000065CA24	.	.	.	3/84	.	.	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S5447S|c.16341G>A|3,SITE|p.S5447S|c.16341G>A|3,CODON|p.S1080S|c.3240G>A|3	RADIA|MUTECT|MUSE|VARSCANS	GCTTTCGATGT	.	4	ESCA
PHTF1	0	.	GRCh37	1	114253027	114253027	+	Missense_Mutation	SNP	C	C	A	rs148397701	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118G>T	p.Arg373Leu	p.R373L	ENST00000369604	11/19	32	12	20	63	63	0	PHTF1,missense_variant,p.Arg129Leu,ENST00000412670,;PHTF1,missense_variant,p.Arg373Leu,ENST00000357783,;PHTF1,missense_variant,p.Arg320Leu,ENST00000369596,;PHTF1,missense_variant,p.Arg320Leu,ENST00000369600,;PHTF1,missense_variant,p.Arg373Leu,ENST00000369604,;PHTF1,missense_variant,p.Arg373Leu,ENST00000393357,;PHTF1,missense_variant,p.Arg328Leu,ENST00000369598,;PHTF1,3_prime_UTR_variant,,ENST00000447664,;PHTF1,non_coding_transcript_exon_variant,,ENST00000474926,;PHTF1,upstream_gene_variant,,ENST00000481652,;	A	ENSG00000116793	ENST00000369604	Transcript	missense_variant	1602	1118	373	R/L	cGc/cTc	rs148397701	.	.	-1	PHTF1	HGNC	8939	protein_coding	YES	CCDS861.1	ENSP00000358617	PHTF1_HUMAN	F6T5D1_HUMAN	UPI000013C9D0	.	tolerated(0.07)	probably_damaging(0.916)	11/19	.	hmmpanther:PTHR12680,hmmpanther:PTHR12680:SF8	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGGCGGGTG	byCluster	5	ESCA
HNRNPCL1	0	.	GRCh37	1	12908030	12908030	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113C>T	p.Ser38Phe	p.S38F	ENST00000317869	2/2	219	198	21	350	350	0	HNRNPCL1,missense_variant,p.Ser38Phe,ENST00000317869,;	A	ENSG00000179172	ENST00000317869	Transcript	missense_variant	339	113	38	S/F	tCc/tTc	.	.	.	-1	HNRNPCL1	HGNC	29295	protein_coding	YES	CCDS30591.1	ENSP00000365370	HNRCL_HUMAN	.	UPI0000134525	.	deleterious(0)	probably_damaging(0.958)	2/2	.	PROSITE_profiles:PS50102,hmmpanther:PTHR13968:SF17,hmmpanther:PTHR13968,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,PIRSF_domain:PIRSF037992,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A35A|c.105G>A|4	MUTECT|MUSE|VARSCANS	ACTTGGAAAAG	.	3	ESCA
FLG	0	.	GRCh37	1	152277313	152277313	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10049C>G	p.Ser3350Ter	p.S3350*	ENST00000368799	3/3	96	80	16	119	119	0	FLG,stop_gained,p.Ser3350Ter,ENST00000368799,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;	C	ENSG00000143631	ENST00000368799	Transcript	stop_gained	10085	10049	3350	S/*	tCa/tGa	.	.	.	-1	FLG	HGNC	3748	protein_coding	YES	CCDS30860.1	ENSP00000357789	FILA_HUMAN	Q4JFL9_HUMAN,I0B0K8_HUMAN,I0B0K6_HUMAN,I0B0K5_HUMAN,I0B0K3_HUMAN	UPI0000470CB3	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTCTGACTCT	.	5	ESCA
FAM189B	0	.	GRCh37	1	155221327	155221327	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.860A>T	p.Tyr287Phe	p.Y287F	ENST00000361361	7/12	67	54	13	69	69	0	FAM189B,missense_variant,p.Tyr191Phe,ENST00000350210,;FAM189B,missense_variant,p.Tyr287Phe,ENST00000361361,;FAM189B,missense_variant,p.Tyr269Phe,ENST00000368368,;FAM189B,missense_variant,p.Tyr191Phe,ENST00000491082,;SCAMP3,downstream_gene_variant,,ENST00000302631,;SCAMP3,downstream_gene_variant,,ENST00000355379,;FAM189B,non_coding_transcript_exon_variant,,ENST00000472550,;SCAMP3,downstream_gene_variant,,ENST00000472397,;SCAMP3,downstream_gene_variant,,ENST00000490999,;SCAMP3,downstream_gene_variant,,ENST00000478737,;FAM189B,non_coding_transcript_exon_variant,,ENST00000368366,;FAM189B,non_coding_transcript_exon_variant,,ENST00000497941,;FAM189B,intron_variant,,ENST00000487649,;FAM189B,downstream_gene_variant,,ENST00000481822,;	A	ENSG00000160767	ENST00000361361	Transcript	missense_variant	1370	860	287	Y/F	tAt/tTt	.	.	.	-1	FAM189B	HGNC	1233	protein_coding	YES	CCDS1103.1	ENSP00000354958	F189B_HUMAN	.	UPI00000710DE	.	deleterious(0)	probably_damaging(0.965)	7/12	.	hmmpanther:PTHR17615:SF7,hmmpanther:PTHR17615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCATAAGAA	.	5	ESCA
FAM189B	0	.	GRCh37	1	155221328	155221328	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.859T>A	p.Tyr287Asn	p.Y287N	ENST00000361361	7/12	68	55	13	70	70	0	FAM189B,missense_variant,p.Tyr191Asn,ENST00000350210,;FAM189B,missense_variant,p.Tyr287Asn,ENST00000361361,;FAM189B,missense_variant,p.Tyr269Asn,ENST00000368368,;FAM189B,missense_variant,p.Tyr191Asn,ENST00000491082,;SCAMP3,downstream_gene_variant,,ENST00000302631,;SCAMP3,downstream_gene_variant,,ENST00000355379,;FAM189B,non_coding_transcript_exon_variant,,ENST00000472550,;SCAMP3,downstream_gene_variant,,ENST00000472397,;SCAMP3,downstream_gene_variant,,ENST00000490999,;SCAMP3,downstream_gene_variant,,ENST00000478737,;FAM189B,non_coding_transcript_exon_variant,,ENST00000368366,;FAM189B,non_coding_transcript_exon_variant,,ENST00000497941,;FAM189B,intron_variant,,ENST00000487649,;FAM189B,downstream_gene_variant,,ENST00000481822,;	T	ENSG00000160767	ENST00000361361	Transcript	missense_variant	1369	859	287	Y/N	Tat/Aat	.	.	.	-1	FAM189B	HGNC	1233	protein_coding	YES	CCDS1103.1	ENSP00000354958	F189B_HUMAN	.	UPI00000710DE	.	deleterious(0)	probably_damaging(0.99)	7/12	.	hmmpanther:PTHR17615:SF7,hmmpanther:PTHR17615	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCATAAGAAG	.	5	ESCA
FDPS	0	.	GRCh37	1	155290347	155290347	+	Missense_Mutation	SNP	C	C	A	rs749598288	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1207C>A	p.Pro403Thr	p.P403T	ENST00000356657	11/11	38	31	7	51	51	0	FDPS,missense_variant,p.Pro403Thr,ENST00000356657,;FDPS,missense_variant,p.Pro337Thr,ENST00000447866,;FDPS,missense_variant,p.Pro403Thr,ENST00000368356,;RUSC1,upstream_gene_variant,,ENST00000368352,;RUSC1,upstream_gene_variant,,ENST00000368354,;RUSC1,upstream_gene_variant,,ENST00000292254,;RUSC1,upstream_gene_variant,,ENST00000368347,;RUSC1,upstream_gene_variant,,ENST00000368349,;RUSC1-AS1,non_coding_transcript_exon_variant,,ENST00000450199,;RUSC1-AS1,intron_variant,,ENST00000443642,;RUSC1-AS1,intron_variant,,ENST00000543656,;RUSC1-AS1,intron_variant,,ENST00000446880,;FDPS,non_coding_transcript_exon_variant,,ENST00000490140,;FDPS,non_coding_transcript_exon_variant,,ENST00000492244,;FDPS,non_coding_transcript_exon_variant,,ENST00000489324,;FDPS,downstream_gene_variant,,ENST00000470171,;RUSC1,upstream_gene_variant,,ENST00000497930,;RUSC1,upstream_gene_variant,,ENST00000471876,;RUSC1,upstream_gene_variant,,ENST00000479924,;RUSC1,upstream_gene_variant,,ENST00000467820,;RUSC1,upstream_gene_variant,,ENST00000489860,;FDPS,downstream_gene_variant,,ENST00000474345,;FDPS,downstream_gene_variant,,ENST00000461507,;FDPS,downstream_gene_variant,,ENST00000471117,;RUSC1,upstream_gene_variant,,ENST00000468764,;RUSC1,upstream_gene_variant,,ENST00000484664,;RUSC1,upstream_gene_variant,,ENST00000462780,;FDPS,downstream_gene_variant,,ENST00000467076,;RUSC1,upstream_gene_variant,,ENST00000490373,;FDPS,downstream_gene_variant,,ENST00000489003,;FDPS,downstream_gene_variant,,ENST00000495308,;RUSC1,upstream_gene_variant,,ENST00000473331,;FDPS,downstream_gene_variant,,ENST00000468479,;FDPS,downstream_gene_variant,,ENST00000465559,;RUSC1,upstream_gene_variant,,ENST00000492536,;FDPS,downstream_gene_variant,,ENST00000477057,;FDPS,downstream_gene_variant,,ENST00000491013,;FDPS,downstream_gene_variant,,ENST00000492887,;	A	ENSG00000160752	ENST00000356657	Transcript	missense_variant	1369	1207	403	P/T	Ccc/Acc	rs749598288	.	.	1	FDPS	HGNC	3631	protein_coding	YES	CCDS1110.1	ENSP00000349078	FPPS_HUMAN	.	UPI000006E4F7	.	deleterious(0.05)	benign(0.395)	11/11	.	hmmpanther:PTHR11525:SF0,hmmpanther:PTHR11525,Gene3D:1.10.600.10,Superfamily_domains:SSF48576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTGCCCCCA	byFrequency	2	ESCA
FMO2	0	.	GRCh37	1	171154891	171154891	+	Silent	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39T>C	p.%3D	p.S13S	ENST00000441535	2/10	75	64	11	146	146	0	FMO2,synonymous_variant,p.%3D,ENST00000209929,;FMO2,synonymous_variant,p.%3D,ENST00000441535,;FMO2,non_coding_transcript_exon_variant,,ENST00000483192,;FMO2,non_coding_transcript_exon_variant,,ENST00000462643,;FMO2,intron_variant,,ENST00000529935,;FMO2,intron_variant,,ENST00000489354,;FMO2,non_coding_transcript_exon_variant,,ENST00000493513,;	C	ENSG00000094963	ENST00000441535	Transcript	synonymous_variant	156	39	13	S	agT/agC	.	.	.	1	FMO2	HGNC	3770	protein_coding	YES	CCDS1293.1	ENSP00000405905	FMO2_HUMAN	B4E2Q9_HUMAN	UPI000013C672	.	.	.	2/10	.	hmmpanther:PTHR23023:SF84,hmmpanther:PTHR23023,Gene3D:3.50.50.60,Pfam_domain:PF00743,Superfamily_domains:SSF51905,Prints_domain:PR00370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCAGTGGCCT	.	4	ESCA
NPHS2	0	.	GRCh37	1	179533884	179533884	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319C>G	p.Leu107Val	p.L107V	ENST00000367615	2/8	74	67	7	98	98	0	NPHS2,missense_variant,p.Leu107Val,ENST00000367616,;NPHS2,missense_variant,p.Leu107Val,ENST00000367615,;	C	ENSG00000116218	ENST00000367615	Transcript	missense_variant	388	319	107	L/V	Ctc/Gtc	.	.	.	-1	NPHS2	HGNC	13394	protein_coding	YES	CCDS1331.1	ENSP00000356587	PODO_HUMAN	.	UPI000003F549	.	tolerated(0.76)	benign(0.009)	2/8	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10264,hmmpanther:PTHR10264:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.S109F|c.326C>T|4	MUTECT|MUSE	AATGAGGACAA	.	2	ESCA
CACNA1E	0	.	GRCh37	1	181724429	181724429	+	Silent	SNP	G	G	A	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3885G>A	p.%3D	p.V1295V	ENST00000367573	28/48	29	23	6	45	45	0	CACNA1E,synonymous_variant,p.%3D,ENST00000358338,;CACNA1E,synonymous_variant,p.%3D,ENST00000367567,;CACNA1E,synonymous_variant,p.%3D,ENST00000357570,;CACNA1E,synonymous_variant,p.%3D,ENST00000360108,;CACNA1E,synonymous_variant,p.%3D,ENST00000526775,;CACNA1E,synonymous_variant,p.%3D,ENST00000367573,;CACNA1E,synonymous_variant,p.%3D,ENST00000367570,;	A	ENSG00000198216	ENST00000367573	Transcript	synonymous_variant	3885	3885	1295	V	gtG/gtA	COSM4025796,COSM4025797,COSM4025795	.	.	1	CACNA1E	HGNC	1392	protein_coding	YES	CCDS55664.1	ENSP00000356545	CAC1E_HUMAN	Q9UN68_HUMAN,Q9NYZ6_HUMAN,Q9NY05_HUMAN,E9PIE8_HUMAN	UPI00004588C2	.	.	.	28/48	.	Superfamily_domains:SSF81324,Pfam_domain:PF00520,hmmpanther:PTHR10037:SF57,hmmpanther:PTHR10037,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTGTGTACAA	.	5	ESCA
LAMC2	0	.	GRCh37	1	183212909	183212909	+	3'UTR	DEL	T	T	-	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*374delT	.	.	ENST00000264144	23/23	58	48	10	55	55	0	LAMC2,3_prime_UTR_variant,,ENST00000264144,;NMNAT2,downstream_gene_variant,,ENST00000294868,;LAMC2,downstream_gene_variant,,ENST00000493293,;NMNAT2,downstream_gene_variant,,ENST00000287713,;LAMC2,intron_variant,,ENST00000476255,;LAMC2,downstream_gene_variant,,ENST00000461729,;	-	ENSG00000058085	ENST00000264144	Transcript	3_prime_UTR_variant	4021	.	.	.	.	.	.	.	1	LAMC2	HGNC	6493	protein_coding	YES	CCDS1352.1	ENSP00000264144	LAMC2_HUMAN	.	UPI000013D4CA	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAGTAATGTGAC	.	3	ESCA
BRINP3	0	.	GRCh37	1	190129936	190129936	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1046C>T	p.Ser349Phe	p.S349F	ENST00000367462	7/8	44	20	24	77	77	0	BRINP3,missense_variant,p.Ser247Phe,ENST00000534846,;BRINP3,missense_variant,p.Ser349Phe,ENST00000367462,;	A	ENSG00000162670	ENST00000367462	Transcript	missense_variant	1278	1046	349	S/F	tCt/tTt	.	.	.	-1	BRINP3	HGNC	22393	protein_coding	YES	CCDS1373.1	ENSP00000356432	BRNP3_HUMAN	.	UPI00001C1D9A	.	tolerated(0.52)	benign(0.165)	7/8	.	hmmpanther:PTHR15564:SF2,hmmpanther:PTHR15564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTAGAATCC	.	5	ESCA
PTPN14	0	.	GRCh37	1	214560236	214560236	+	Silent	SNP	G	G	A	rs138976528	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1017C>T	p.%3D	p.P339P	ENST00000366956	12/19	56	42	13	59	59	0	PTPN14,synonymous_variant,p.%3D,ENST00000366956,;PTPN14,3_prime_UTR_variant,,ENST00000543945,;	A	ENSG00000152104	ENST00000366956	Transcript	synonymous_variant	1212	1017	339	P	ccC/ccT	rs138976528	.	.	-1	PTPN14	HGNC	9647	protein_coding	YES	CCDS1514.1	ENSP00000355923	PTN14_HUMAN	.	UPI000013DCA6	.	.	.	12/19	.	Superfamily_domains:SSF50729,PIRSF_domain:PIRSF000934,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF77	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACGGGAGG	byCluster	5	ESCA
PLCH2	0	.	GRCh37	1	2429014	2429014	+	Silent	SNP	C	C	T	rs777973464	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2109C>T	p.%3D	p.C703C	ENST00000449969	16/22	53	25	27	75	75	0	PLCH2,synonymous_variant,p.%3D,ENST00000419816,;PLCH2,synonymous_variant,p.%3D,ENST00000449969,;PLCH2,synonymous_variant,p.%3D,ENST00000378486,;PLCH2,intron_variant,,ENST00000288766,;PLCH2,intron_variant,,ENST00000278878,;PLCH2,intron_variant,,ENST00000378488,;RP3-395M20.3,upstream_gene_variant,,ENST00000442305,;RP3-395M20.2,upstream_gene_variant,,ENST00000424657,;PLCH2,non_coding_transcript_exon_variant,,ENST00000343889,;PLCH2,upstream_gene_variant,,ENST00000462379,;PLCH2,upstream_gene_variant,,ENST00000473964,;	T	ENSG00000149527	ENST00000449969	Transcript	synonymous_variant	2270	2109	703	C	tgC/tgT	rs777973464	.	.	1	PLCH2	HGNC	29037	protein_coding	YES	.	ENSP00000397289	PLCH2_HUMAN	.	UPI00006C0134	.	.	.	16/22	.	Superfamily_domains:SSF51695,SMART_domains:SM00149,Gene3D:3.20.20.190,Pfam_domain:PF00387,hmmpanther:PTHR10336:SF21,hmmpanther:PTHR10336,PROSITE_profiles:PS50008	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTGCGGCTA	.	5	ESCA
MACF1	0	.	GRCh37	1	39853455	39853455	+	Missense_Mutation	SNP	C	C	T	rs766474090	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8755C>T	p.Arg2919Trp	p.R2919W	ENST00000545844	53/94	25	11	13	50	50	0	MACF1,missense_variant,p.Arg2032Trp,ENST00000372925,;MACF1,missense_variant,p.Arg2919Trp,ENST00000361689,;MACF1,missense_variant,p.Arg3421Trp,ENST00000289893,;MACF1,missense_variant,p.Arg4981Trp,ENST00000564288,;MACF1,missense_variant,p.Arg2898Trp,ENST00000539005,;MACF1,missense_variant,p.Arg4986Trp,ENST00000372915,;MACF1,missense_variant,p.Arg2919Trp,ENST00000317713,;MACF1,missense_variant,p.Arg5018Trp,ENST00000567887,;MACF1,missense_variant,p.Arg2919Trp,ENST00000545844,;	T	ENSG00000127603	ENST00000545844	Transcript	missense_variant	8863	8755	2919	R/W	Cgg/Tgg	rs766474090,COSM171995,COSM171996	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	probably_damaging(0.999)	53/94	.	Superfamily_domains:SSF46966,SMART_domains:SM00150,Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915:SF37,hmmpanther:PTHR11915	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATCCGGGAT	byFrequency	5	ESCA
ZFYVE9	0	.	GRCh37	1	52798549	52798549	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3548A>G	p.Tyr1183Cys	p.Y1183C	ENST00000287727	14/19	30	10	20	59	59	0	ZFYVE9,missense_variant,p.Tyr1183Cys,ENST00000371591,;ZFYVE9,missense_variant,p.Tyr1124Cys,ENST00000357206,;ZFYVE9,missense_variant,p.Tyr1183Cys,ENST00000287727,;ZFYVE9,non_coding_transcript_exon_variant,,ENST00000469134,;	G	ENSG00000157077	ENST00000287727	Transcript	missense_variant	3720	3548	1183	Y/C	tAt/tGt	.	.	.	1	ZFYVE9	HGNC	6775	protein_coding	YES	CCDS563.1	ENSP00000287727	ZFYV9_HUMAN	.	UPI0000001620	.	deleterious(0)	probably_damaging(1)	14/19	.	Pfam_domain:PF11979,PIRSF_domain:PIRSF037289	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTATCAGA	.	5	ESCA
GLIS1	0	.	GRCh37	1	54060185	54060185	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391G>C	p.Glu131Gln	p.E131Q	ENST00000312233	3/10	14	9	5	33	33	0	GLIS1,missense_variant,p.Glu131Gln,ENST00000312233,;	G	ENSG00000174332	ENST00000312233	Transcript	missense_variant	958	391	131	E/Q	Gag/Cag	.	.	.	-1	GLIS1	HGNC	29525	protein_coding	YES	CCDS582.1	ENSP00000309653	GLIS1_HUMAN	.	UPI000013F293	.	tolerated_low_confidence(0.12)	possibly_damaging(0.56)	3/10	.	hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF75	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCTCATGGC	.	2	ESCA
SNX5	0	.	GRCh37	20	17922937	17922937	+	3'UTR	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*64A>T	.	.	ENST00000377768	14/14	23	16	7	60	60	0	SNX5,3_prime_UTR_variant,,ENST00000377759,;SNX5,3_prime_UTR_variant,,ENST00000377768,;SNX5,non_coding_transcript_exon_variant,,ENST00000476648,;SNX5,non_coding_transcript_exon_variant,,ENST00000490175,;SNX5,non_coding_transcript_exon_variant,,ENST00000491090,;SNX5,non_coding_transcript_exon_variant,,ENST00000483485,;SNX5,non_coding_transcript_exon_variant,,ENST00000606570,;SNX5,non_coding_transcript_exon_variant,,ENST00000484809,;SNX5,downstream_gene_variant,,ENST00000463050,;	A	ENSG00000089006	ENST00000377768	Transcript	3_prime_UTR_variant	1592	.	.	.	.	.	.	.	-1	SNX5	HGNC	14969	protein_coding	YES	CCDS13130.1	ENSP00000366998	SNX5_HUMAN	.	UPI0000135B43	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGATTTAAG	.	5	ESCA
DHX35	0	.	GRCh37	20	37591011	37591012	+	Frame_Shift_Ins	INS	-	-	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2dupT	p.Met1?	p.M1?	ENST00000252011	1/22	205	139	66	140	140	0	DHX35,frameshift_variant,p.Met1?,ENST00000252011,;DHX35,frameshift_variant,p.Met1?,ENST00000373325,;DHX35,frameshift_variant,p.Met1?,ENST00000373323,;RP4-616B8.4,upstream_gene_variant,,ENST00000570096,;DHX35,frameshift_variant,p.Met1?,ENST00000484417,;	T	ENSG00000101452	ENST00000252011	Transcript	frameshift_variant	34-35	1-2	1	M/IX	atg/aTtg	.	.	.	1	DHX35	HGNC	15861	protein_coding	YES	CCDS13310.1	ENSP00000252011	DHX35_HUMAN	.	UPI0000129088	.	.	.	1/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCAACATGGCT	.	3	ESCA
STK4	0	.	GRCh37	20	43629138	43629138	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937G>T	p.Asp313Tyr	p.D313Y	ENST00000372806	8/11	100	51	48	107	107	0	STK4,missense_variant,p.Asp258Tyr,ENST00000499879,;STK4,missense_variant,p.Asp313Tyr,ENST00000372806,;STK4,missense_variant,p.Asp313Tyr,ENST00000372801,;STK4,missense_variant,p.Asp313Tyr,ENST00000396731,;Y_RNA,upstream_gene_variant,,ENST00000516212,;	T	ENSG00000101109	ENST00000372806	Transcript	missense_variant	1032	937	313	D/Y	Gac/Tac	.	.	.	1	STK4	HGNC	11408	protein_coding	YES	CCDS13341.1	ENSP00000361892	STK4_HUMAN	Q9BS84_HUMAN	UPI00001360FF	.	deleterious(0.03)	benign(0.008)	8/11	.	hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF275,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTGGACCAG	.	5	ESCA
SS18L1	0	.	GRCh37	20	60736518	60736518	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.258C>T	p.%3D	p.G86G	ENST00000331758	4/11	24	15	8	36	36	0	SS18L1,synonymous_variant,p.%3D,ENST00000421564,;SS18L1,synonymous_variant,p.%3D,ENST00000450482,;SS18L1,synonymous_variant,p.%3D,ENST00000370848,;SS18L1,synonymous_variant,p.%3D,ENST00000331758,;SS18L1,upstream_gene_variant,,ENST00000491916,;SS18L1,upstream_gene_variant,,ENST00000492466,;	T	ENSG00000184402	ENST00000331758	Transcript	synonymous_variant	284	258	86	G	ggC/ggT	.	.	.	1	SS18L1	HGNC	15592	protein_coding	YES	CCDS13491.1	ENSP00000333012	CREST_HUMAN	.	UPI000013543D	.	.	.	4/11	.	hmmpanther:PTHR23107,hmmpanther:PTHR23107:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGGCCCTGG	.	5	ESCA
TFIP11	0	.	GRCh37	22	26906094	26906094	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.145G>T	p.Ala49Ser	p.A49S	ENST00000407690	4/15	52	41	10	72	72	0	TFIP11,missense_variant,p.Ala49Ser,ENST00000407431,;TFIP11,missense_variant,p.Ala49Ser,ENST00000418876,;TFIP11,missense_variant,p.Ala49Ser,ENST00000407148,;TFIP11,missense_variant,p.Ala49Ser,ENST00000407690,;TFIP11,missense_variant,p.Ala49Ser,ENST00000405938,;TFIP11,missense_variant,p.Ala49Ser,ENST00000455080,;TFIP11,missense_variant,p.Ala49Ser,ENST00000420242,;TFIP11,downstream_gene_variant,,ENST00000440258,;TFIP11,upstream_gene_variant,,ENST00000450493,;CTA-445C9.14,upstream_gene_variant,,ENST00000565764,;CTA-445C9.14,upstream_gene_variant,,ENST00000566814,;TFIP11,upstream_gene_variant,,ENST00000496523,;TFIP11,non_coding_transcript_exon_variant,,ENST00000472918,;TFIP11,non_coding_transcript_exon_variant,,ENST00000479489,;TFIP11,upstream_gene_variant,,ENST00000493698,;TFIP11,downstream_gene_variant,,ENST00000464449,;	A	ENSG00000100109	ENST00000407690	Transcript	missense_variant	429	145	49	A/S	Gcc/Tcc	.	.	.	-1	TFIP11	HGNC	17165	protein_coding	YES	CCDS13838.1	ENSP00000384421	TFP11_HUMAN	F6XM96_HUMAN,F6UQ07_HUMAN,F6UKU9_HUMAN,F6SQZ1_HUMAN	UPI0000137191	.	tolerated(0.06)	probably_damaging(0.955)	4/15	.	hmmpanther:PTHR23329,hmmpanther:PTHR23329:SF1,Pfam_domain:PF12457,PIRSF_domain:PIRSF017706	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGGCTTCTT	.	5	ESCA
EWSR1	0	.	GRCh37	22	29664103	29664103	+	5'Flank	DEL	T	T	-	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000414183	.	36	24	12	37	37	0	EWSR1,5_prime_UTR_variant,,ENST00000397938,;EWSR1,5_prime_UTR_variant,,ENST00000444626,;RHBDD3,5_prime_UTR_variant,,ENST00000414672,;EWSR1,5_prime_UTR_variant,,ENST00000332050,;EWSR1,upstream_gene_variant,,ENST00000406548,;EWSR1,upstream_gene_variant,,ENST00000332035,;RHBDD3,upstream_gene_variant,,ENST00000406335,;EWSR1,upstream_gene_variant,,ENST00000415761,;EWSR1,upstream_gene_variant,,ENST00000447973,;RHBDD3,upstream_gene_variant,,ENST00000216085,;EWSR1,upstream_gene_variant,,ENST00000414183,;EWSR1,upstream_gene_variant,,ENST00000436425,;EWSR1,upstream_gene_variant,,ENST00000455726,;EWSR1,upstream_gene_variant,,ENST00000333395,;EWSR1,upstream_gene_variant,,ENST00000331029,;EWSR1,upstream_gene_variant,,ENST00000437155,;EWSR1,upstream_gene_variant,,ENST00000485037,;RHBDD3,upstream_gene_variant,,ENST00000496342,;EWSR1,upstream_gene_variant,,ENST00000493426,;RHBDD3,upstream_gene_variant,,ENST00000493894,;RHBDD3,upstream_gene_variant,,ENST00000413137,;EWSR1,upstream_gene_variant,,ENST00000483415,;RHBDD3,upstream_gene_variant,,ENST00000488106,;	-	ENSG00000182944	ENST00000414183	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	202	1	EWSR1	HGNC	3508	protein_coding	YES	CCDS13852.2	ENSP00000400142	EWS_HUMAN	.	UPI000006DE88	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ATGCTATTTTGG	.	3	ESCA
ATF4	0	.	GRCh37	22	39917510	39917510	+	Silent	SNP	C	C	T	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.60C>T	p.%3D	p.F20F	ENST00000337304	1/2	61	53	7	68	68	0	ATF4,synonymous_variant,p.%3D,ENST00000396680,;ATF4,synonymous_variant,p.%3D,ENST00000337304,;ATF4,synonymous_variant,p.%3D,ENST00000404241,;MIEF1,downstream_gene_variant,,ENST00000325301,;	T	ENSG00000128272	ENST00000337304	Transcript	synonymous_variant	942	60	20	F	ttC/ttT	COSM445015	.	.	1	ATF4	HGNC	786	protein_coding	YES	CCDS13996.1	ENSP00000336790	ATF4_HUMAN	Q96AQ3_HUMAN,B4DJD4_HUMAN	UPI000000DABF	.	.	.	1/2	.	hmmpanther:PTHR13044:SF2,hmmpanther:PTHR13044	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCTTCGACCA	.	4	ESCA
MOV10L1	0	.	GRCh37	22	50599160	50599160	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3368T>G	p.Leu1123Trp	p.L1123W	ENST00000262794	25/27	42	37	5	77	77	0	MOV10L1,missense_variant,p.Leu1103Trp,ENST00000540615,;MOV10L1,missense_variant,p.Leu1123Trp,ENST00000545383,;MOV10L1,missense_variant,p.Leu250Trp,ENST00000395852,;MOV10L1,missense_variant,p.Leu1123Trp,ENST00000262794,;MOV10L1,intron_variant,,ENST00000395858,;MOV10L1,downstream_gene_variant,,ENST00000395843,;MOV10L1,downstream_gene_variant,,ENST00000354853,;	G	ENSG00000073146	ENST00000262794	Transcript	missense_variant	3451	3368	1123	L/W	tTg/tGg	.	.	.	1	MOV10L1	HGNC	7201	protein_coding	YES	CCDS14084.1	ENSP00000262794	M10L1_HUMAN	.	UPI00000421FB	.	deleterious(0)	probably_damaging(1)	25/27	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF321,Pfam_domain:PF13087,Gene3D:3.40.50.300,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTTTTTGGGTT	.	3	ESCA
GRHL1	0	.	GRCh37	2	10098951	10098951	+	Frame_Shift_Del	DEL	G	G	-	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.244delG	p.Glu82ArgfsTer18	p.E82Rfs*18	ENST00000324907	3/16	128	79	49	84	84	0	GRHL1,frameshift_variant,p.Glu82ArgfsTer18,ENST00000405379,;GRHL1,frameshift_variant,p.Glu82ArgfsTer18,ENST00000324907,;GRHL1,5_prime_UTR_variant,,ENST00000324883,;GRHL1,frameshift_variant,p.Glu82ArgfsTer18,ENST00000472167,;GRHL1,frameshift_variant,p.Glu82ArgfsTer20,ENST00000439493,;GRHL1,frameshift_variant,p.Glu85ArgfsTer18,ENST00000464418,;GRHL1,non_coding_transcript_exon_variant,,ENST00000497403,;GRHL1,upstream_gene_variant,,ENST00000494520,;	-	ENSG00000134317	ENST00000324907	Transcript	frameshift_variant	380	244	82	E/X	Gag/ag	.	.	.	1	GRHL1	HGNC	17923	protein_coding	YES	CCDS33144.2	ENSP00000324693	GRHL1_HUMAN	F8WFB0_HUMAN,C9JYY8_HUMAN	UPI00001E0586	.	.	.	3/16	.	hmmpanther:PTHR11037,hmmpanther:PTHR11037:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AAGCCAGAGGTG	.	3	ESCA
IL1RL2	0	.	GRCh37	2	102808451	102808451	+	Silent	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.360T>C	p.%3D	p.T120T	ENST00000264257	4/12	62	53	8	71	71	0	IL1RL2,synonymous_variant,p.%3D,ENST00000264257,;IL1RL2,synonymous_variant,p.%3D,ENST00000539491,;IL1RL2,synonymous_variant,p.%3D,ENST00000421464,;IL1RL2,intron_variant,,ENST00000441515,;IL1RL2,intron_variant,,ENST00000481806,;	C	ENSG00000115598	ENST00000264257	Transcript	synonymous_variant	486	360	120	T	acT/acC	.	.	.	1	IL1RL2	HGNC	5999	protein_coding	YES	CCDS2056.1	ENSP00000264257	ILRL2_HUMAN	C9K0I8_HUMAN	UPI000013D4ED	.	.	.	4/12	.	hmmpanther:PTHR11890:SF9,hmmpanther:PTHR11890	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACACTTCCAT	.	4	ESCA
AMER3	0	.	GRCh37	2	131522133	131522133	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2488C>T	p.Pro830Ser	p.P830S	ENST00000423981	2/2	33	13	20	22	22	0	AMER3,missense_variant,p.Pro830Ser,ENST00000321420,;AMER3,missense_variant,p.Pro830Ser,ENST00000423981,;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,;	T	ENSG00000178171	ENST00000423981	Transcript	missense_variant	2598	2488	830	P/S	Cca/Tca	.	.	.	1	AMER3	HGNC	26771	protein_coding	YES	CCDS2164.1	ENSP00000392700	AMER3_HUMAN	C9JS07_HUMAN,C9J4B8_HUMAN	UPI0000D61239	.	tolerated(0.5)	benign(0.115)	2/2	.	hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCCCCAGAA	.	5	ESCA
RIF1	0	.	GRCh37	2	152325154	152325154	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6826-1G>C	.	p.X2276_splice	ENST00000243326	.	64	46	18	75	75	0	RIF1,splice_acceptor_variant,,ENST00000444746,;RIF1,splice_acceptor_variant,,ENST00000453091,;RIF1,splice_acceptor_variant,,ENST00000428287,;RIF1,splice_acceptor_variant,,ENST00000243326,;RIF1,splice_acceptor_variant,,ENST00000430328,;RIF1,splice_acceptor_variant,,ENST00000454583,;	C	ENSG00000080345	ENST00000243326	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	RIF1	HGNC	23207	protein_coding	YES	CCDS2194.1	ENSP00000243326	RIF1_HUMAN	C9J1D6_HUMAN,B4DRJ4_HUMAN	UPI000023729F	.	.	.	.	31/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTAAGATTTC	.	5	ESCA
PXDN	0	.	GRCh37	2	1635906	1635906	+	3'UTR	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2070G>A	.	.	ENST00000252804	23/23	27	10	17	32	32	0	PXDN,3_prime_UTR_variant,,ENST00000252804,;PXDN,downstream_gene_variant,,ENST00000453308,;PXDN,downstream_gene_variant,,ENST00000478155,;PXDN,downstream_gene_variant,,ENST00000493654,;	T	ENSG00000130508	ENST00000252804	Transcript	3_prime_UTR_variant	6561	.	.	.	.	.	.	.	-1	PXDN	HGNC	14966	protein_coding	YES	CCDS46221.1	ENSP00000252804	PXDN_HUMAN	.	UPI00001C1DC2	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCGCAGACA	.	5	ESCA
TTN	0	.	GRCh37	2	179456146	179456146	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.60306A>G	p.Ile20102Met	p.I20102M	ENST00000589042	304/363	43	38	5	45	45	0	TTN,missense_variant,p.Ile11162Met,ENST00000359218,;TTN,missense_variant,p.Ile18461Met,ENST00000591111,;TTN,missense_variant,p.Ile20102Met,ENST00000589042,;TTN,missense_variant,p.Ile11229Met,ENST00000342175,;TTN,missense_variant,p.Ile17534Met,ENST00000342992,;TTN,missense_variant,p.Ile11037Met,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,downstream_gene_variant,,ENST00000590743,;	C	ENSG00000155657	ENST00000589042	Transcript	missense_variant	60531	60306	20102	I/M	atA/atG	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	304/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTCTTATAAT	.	4	ESCA
SSFA2	0	.	GRCh37	2	182794901	182794901	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*627T>C	.	.	ENST00000431877	18/18	38	31	7	40	40	0	SSFA2,3_prime_UTR_variant,,ENST00000409001,;SSFA2,3_prime_UTR_variant,,ENST00000409136,;SSFA2,3_prime_UTR_variant,,ENST00000431877,;SSFA2,3_prime_UTR_variant,,ENST00000320370,;SSFA2,downstream_gene_variant,,ENST00000428267,;SSFA2,downstream_gene_variant,,ENST00000451836,;SSFA2,downstream_gene_variant,,ENST00000467172,;SSFA2,3_prime_UTR_variant,,ENST00000416081,;SSFA2,3_prime_UTR_variant,,ENST00000440623,;SSFA2,non_coding_transcript_exon_variant,,ENST00000491720,;SSFA2,downstream_gene_variant,,ENST00000454579,;	C	ENSG00000138434	ENST00000431877	Transcript	3_prime_UTR_variant	4586	.	.	.	.	.	.	.	1	SSFA2	HGNC	11319	protein_coding	YES	CCDS46467.1	ENSP00000388731	SSFA2_HUMAN	B3KXT1_HUMAN	UPI000019B17A	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTTTATCAT	.	5	ESCA
GLS	0	.	GRCh37	2	191827731	191827731	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*19T>C	.	.	ENST00000320717	18/18	89	82	7	89	89	0	GLS,synonymous_variant,p.%3D,ENST00000412247,;GLS,3_prime_UTR_variant,,ENST00000320717,;GLS,3_prime_UTR_variant,,ENST00000409428,;STAT1,downstream_gene_variant,,ENST00000415035,;	C	ENSG00000115419	ENST00000320717	Transcript	3_prime_UTR_variant	2287	.	.	.	.	.	.	.	1	GLS	HGNC	4331	protein_coding	YES	CCDS2308.1	ENSP00000317379	GLSK_HUMAN	Q53TX0_HUMAN,Q53S89_HUMAN,Q53RX0_HUMAN,C9JIJ6_HUMAN,B7Z509_HUMAN	UPI000012B7F6	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAAGATTTAAA	.	2	ESCA
STK11IP	0	.	GRCh37	2	220479262	220479262	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2896G>C	p.Val966Leu	p.V966L	ENST00000295641	23/25	34	31	3	62	62	0	STK11IP,missense_variant,p.Val955Leu,ENST00000456909,;STK11IP,missense_variant,p.Val55Leu,ENST00000447191,;STK11IP,missense_variant,p.Val966Leu,ENST00000295641,;STK11IP,downstream_gene_variant,,ENST00000483319,;STK11IP,missense_variant,p.Val148Leu,ENST00000413891,;STK11IP,non_coding_transcript_exon_variant,,ENST00000495941,;STK11IP,upstream_gene_variant,,ENST00000494777,;STK11IP,downstream_gene_variant,,ENST00000475396,;	C	ENSG00000144589	ENST00000295641	Transcript	missense_variant	2939	2896	966	V/L	Gtt/Ctt	.	.	.	1	STK11IP	HGNC	19184	protein_coding	YES	CCDS46521.1	ENSP00000295641	S11IP_HUMAN	C9JQV3_HUMAN	UPI0001AE7798	.	tolerated(0.33)	probably_damaging(0.98)	23/25	.	hmmpanther:PTHR15454:SF16,hmmpanther:PTHR15454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCTGGTTGAA	.	2	ESCA
IRS1	0	.	GRCh37	2	227600553	227600553	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*435C>T	.	.	ENST00000305123	2/2	37	19	18	61	61	0	IRS1,3_prime_UTR_variant,,ENST00000305123,;	A	ENSG00000169047	ENST00000305123	Transcript	3_prime_UTR_variant	5185	.	.	.	.	.	.	.	-1	IRS1	HGNC	6125	protein_coding	YES	CCDS2463.1	ENSP00000304895	IRS1_HUMAN	.	UPI000003BB52	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAACGTGAAC	.	5	ESCA
NLRC4	0	.	GRCh37	2	32460524	32460524	+	Missense_Mutation	SNP	C	C	G	rs144418059	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2728G>C	p.Val910Leu	p.V910L	ENST00000404025	9/10	30	23	6	48	48	0	NLRC4,missense_variant,p.Val910Leu,ENST00000402280,;NLRC4,missense_variant,p.Val910Leu,ENST00000360906,;NLRC4,missense_variant,p.Val245Leu,ENST00000342905,;NLRC4,missense_variant,p.Val910Leu,ENST00000404025,;	G	ENSG00000091106	ENST00000404025	Transcript	missense_variant	3217	2728	910	V/L	Gtc/Ctc	rs144418059	.	.	-1	NLRC4	HGNC	16412	protein_coding	YES	CCDS33174.1	ENSP00000385090	NLRC4_HUMAN	.	UPI0000126FAD	.	tolerated(0.6)	benign(0.001)	9/10	.	hmmpanther:PTHR10044:SF97,hmmpanther:PTHR10044,Gene3D:3.80.10.10,Superfamily_domains:SSF52047	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGACGAGTT	byCluster	5	ESCA
SMEK2	0	.	GRCh37	2	55826102	55826102	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.371A>G	p.Glu124Gly	p.E124G	ENST00000345102	4/17	23	19	3	30	30	0	SMEK2,missense_variant,p.Glu124Gly,ENST00000345102,;SMEK2,missense_variant,p.Glu124Gly,ENST00000272313,;SMEK2,missense_variant,p.Glu124Gly,ENST00000407823,;SMEK2,non_coding_transcript_exon_variant,,ENST00000470801,;	C	ENSG00000138041	ENST00000345102	Transcript	missense_variant	673	371	124	E/G	gAa/gGa	.	.	.	-1	SMEK2	HGNC	29267	protein_coding	YES	CCDS46289.1	ENSP00000339769	P4R3B_HUMAN	.	UPI00001C1DBA	.	deleterious(0.01)	benign(0.028)	4/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23318:SF2,hmmpanther:PTHR23318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GCATTTCTTCA	.	2	ESCA
VPS54	0	.	GRCh37	2	64141399	64141399	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2251A>T	p.Ile751Phe	p.I751F	ENST00000272322	17/23	46	16	30	85	85	0	VPS54,missense_variant,p.Ile598Phe,ENST00000354504,;VPS54,missense_variant,p.Ile751Phe,ENST00000272322,;VPS54,missense_variant,p.Ile739Phe,ENST00000409558,;VPS54,missense_variant,p.Ile46Phe,ENST00000416400,;	A	ENSG00000143952	ENST00000272322	Transcript	missense_variant	2406	2251	751	I/F	Att/Ttt	.	.	.	-1	VPS54	HGNC	18652	protein_coding	YES	CCDS33208.1	ENSP00000272322	VPS54_HUMAN	.	UPI0000053408	.	deleterious(0.01)	possibly_damaging(0.717)	17/23	.	hmmpanther:PTHR12965:SF0,hmmpanther:PTHR12965,Pfam_domain:PF07928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATAATTCTTA	.	5	ESCA
POLR1A	0	.	GRCh37	2	86327110	86327110	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263A>T	p.Tyr88Phe	p.Y88F	ENST00000263857	2/34	90	43	47	97	97	0	POLR1A,missense_variant,p.Tyr88Phe,ENST00000409681,;POLR1A,missense_variant,p.Tyr88Phe,ENST00000263857,;POLR1A,non_coding_transcript_exon_variant,,ENST00000486964,;POLR1A,intron_variant,,ENST00000409024,;POLR1A,intron_variant,,ENST00000424089,;	A	ENSG00000068654	ENST00000263857	Transcript	missense_variant	642	263	88	Y/F	tAt/tTt	.	.	.	-1	POLR1A	HGNC	17264	protein_coding	YES	CCDS42706.1	ENSP00000263857	RPA1_HUMAN	Q96AG9_HUMAN,Q53T12_HUMAN,B7Z8X7_HUMAN	UPI0000D7DB86	.	tolerated(0.11)	probably_damaging(0.988)	2/34	.	hmmpanther:PTHR19376,hmmpanther:PTHR19376:SF11,Pfam_domain:PF04997,Superfamily_domains:SSF64484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTATACACT	.	5	ESCA
RMND5A	0	.	GRCh37	2	87000518	87000518	+	Missense_Mutation	SNP	A	A	G	rs202224251	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1160A>G	p.Lys387Arg	p.K387R	ENST00000283632	9/9	61	29	31	96	96	0	RMND5A,missense_variant,p.Lys387Arg,ENST00000283632,;RMND5A,non_coding_transcript_exon_variant,,ENST00000472843,;RMND5A,non_coding_transcript_exon_variant,,ENST00000471113,;	G	ENSG00000153561	ENST00000283632	Transcript	missense_variant	1655	1160	387	K/R	aAa/aGa	rs202224251	.	.	1	RMND5A	HGNC	25850	protein_coding	YES	CCDS1991.1	ENSP00000283632	RMD5A_HUMAN	B4DZV7_HUMAN	UPI000000DC2B	.	tolerated(0.76)	benign(0.034)	9/9	.	hmmpanther:PTHR12170,hmmpanther:PTHR12170:SF5,Gene3D:3.30.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCAAACAGA	.	5	ESCA
ZBTB11	0	.	GRCh37	3	101389956	101389956	+	Intron	SNP	G	G	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.778+18C>G	.	.	ENST00000312938	.	38	30	8	36	36	0	ZBTB11,3_prime_UTR_variant,,ENST00000461821,;ZBTB11,intron_variant,,ENST00000312938,;	C	ENSG00000066422	ENST00000312938	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ZBTB11	HGNC	16740	protein_coding	YES	CCDS2943.1	ENSP00000326200	ZBT11_HUMAN	Q59H97_HUMAN,B3KN38_HUMAN	UPI000013D5E3	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAGAGTAATA	.	5	ESCA
STXBP5L	0	.	GRCh37	3	121100286	121100286	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2566G>C	p.Gly856Arg	p.G856R	ENST00000273666	23/28	123	108	15	113	113	0	STXBP5L,missense_variant,p.Gly799Arg,ENST00000471262,;STXBP5L,missense_variant,p.Gly832Arg,ENST00000472879,;STXBP5L,missense_variant,p.Gly856Arg,ENST00000273666,;STXBP5L,missense_variant,p.Gly832Arg,ENST00000471454,;STXBP5L,missense_variant,p.Gly856Arg,ENST00000492541,;STXBP5L,missense_variant,p.Gly830Arg,ENST00000497029,;	C	ENSG00000145087	ENST00000273666	Transcript	missense_variant	2837	2566	856	G/R	Gga/Cga	.	.	.	1	STXBP5L	HGNC	30757	protein_coding	YES	CCDS43137.1	ENSP00000273666	STB5L_HUMAN	C9JUZ7_HUMAN	UPI00001C1DEA	.	deleterious(0)	probably_damaging(0.999)	23/28	.	hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Pfam_domain:PF08596,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TCGTTGGAACC	.	3	ESCA
SERP1	0	.	GRCh37	3	150261660	150261660	+	3'UTR	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*585A>G	.	.	ENST00000479209	4/4	27	24	3	13	13	0	SERP1,3_prime_UTR_variant,,ENST00000239944,;SERP1,3_prime_UTR_variant,,ENST00000479209,;EIF2A,upstream_gene_variant,,ENST00000460851,;SERP1,downstream_gene_variant,,ENST00000487153,;EIF2A,upstream_gene_variant,,ENST00000406576,;EIF2A,upstream_gene_variant,,ENST00000482093,;EIF2A,upstream_gene_variant,,ENST00000487799,;SERP1,downstream_gene_variant,,ENST00000491660,;EIF2A,upstream_gene_variant,,ENST00000273435,;SERP1,downstream_gene_variant,,ENST00000491195,;EIF2A,upstream_gene_variant,,ENST00000474505,;EIF2A,upstream_gene_variant,,ENST00000462221,;EIF2A,upstream_gene_variant,,ENST00000469331,;EIF2A,upstream_gene_variant,,ENST00000473499,;EIF2A,upstream_gene_variant,,ENST00000463863,;EIF2A,upstream_gene_variant,,ENST00000494558,;EIF2A,upstream_gene_variant,,ENST00000490505,;	C	ENSG00000120742	ENST00000479209	Transcript	3_prime_UTR_variant	2059	.	.	.	.	.	.	.	-1	SERP1	HGNC	10759	protein_coding	YES	CCDS3150.1	ENSP00000420076	SERP1_HUMAN	.	UPI0000022CDB	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCATCTCCC	.	2	ESCA
MBNL1	0	.	GRCh37	3	152180663	152180663	+	3'UTR	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*508A>G	.	.	ENST00000282486	10/10	37	7	30	22	22	0	MBNL1,3_prime_UTR_variant,,ENST00000478535,;MBNL1,3_prime_UTR_variant,,ENST00000545754,;MBNL1,3_prime_UTR_variant,,ENST00000282486,;MBNL1,3_prime_UTR_variant,,ENST00000324196,;MBNL1,3_prime_UTR_variant,,ENST00000498502,;MBNL1,3_prime_UTR_variant,,ENST00000493459,;MBNL1,3_prime_UTR_variant,,ENST00000357472,;MBNL1,3_prime_UTR_variant,,ENST00000463374,;MBNL1,3_prime_UTR_variant,,ENST00000282488,;MBNL1,3_prime_UTR_variant,,ENST00000324210,;MBNL1,3_prime_UTR_variant,,ENST00000355460,;MBNL1,3_prime_UTR_variant,,ENST00000485910,;MBNL1,downstream_gene_variant,,ENST00000485509,;MBNL1,downstream_gene_variant,,ENST00000465907,;MBNL1,downstream_gene_variant,,ENST00000492948,;MBNL1,downstream_gene_variant,,ENST00000464596,;RP11-362A9.3,intron_variant,,ENST00000463255,;MBNL1,non_coding_transcript_exon_variant,,ENST00000497971,;	G	ENSG00000152601	ENST00000282486	Transcript	3_prime_UTR_variant	3517	.	.	.	.	.	.	.	1	MBNL1	HGNC	6923	protein_coding	YES	CCDS3165.1	ENSP00000282486	MBNL1_HUMAN	C9JCX1_HUMAN,C9J7P7_HUMAN	UPI000003B440	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTCATTTTT	.	5	ESCA
FYTTD1	0	.	GRCh37	3	197510287	197510287	+	3'UTR	SNP	A	A	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1507A>T	.	.	ENST00000241502	9/9	90	68	22	85	85	0	FYTTD1,3_prime_UTR_variant,,ENST00000241502,;FYTTD1,3_prime_UTR_variant,,ENST00000428395,;FYTTD1,downstream_gene_variant,,ENST00000424384,;FYTTD1,downstream_gene_variant,,ENST00000415708,;FYTTD1,downstream_gene_variant,,ENST00000492360,;	T	ENSG00000122068	ENST00000241502	Transcript	3_prime_UTR_variant	2686	.	.	.	.	.	.	.	1	FYTTD1	HGNC	25407	protein_coding	YES	CCDS3329.1	ENSP00000241502	UIF_HUMAN	H9KVC6_HUMAN,H9KVC1_HUMAN,F6VVD0_HUMAN	UPI0000073CEC	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTTGAGTTGC	.	5	ESCA
LRCH3	0	.	GRCh37	3	197607434	197607434	+	Nonsense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.392A>T	p.Arg132Ter	p.R132*	ENST00000428136	5/5	63	58	5	58	58	0	LRCH3,stop_gained,p.Arg132Ter,ENST00000428136,;LRCH3,stop_gained,p.Arg754Ter,ENST00000438796,;LRCH3,intron_variant,,ENST00000441090,;LRCH3,intron_variant,,ENST00000433298,;LRCH3,intron_variant,,ENST00000425562,;LRCH3,intron_variant,,ENST00000414675,;LRCH3,intron_variant,,ENST00000536618,;LRCH3,downstream_gene_variant,,ENST00000452660,;LRCH3,non_coding_transcript_exon_variant,,ENST00000473177,;LRCH3,non_coding_transcript_exon_variant,,ENST00000471667,;LRCH3,intron_variant,,ENST00000476664,;LRCH3,downstream_gene_variant,,ENST00000466054,;LRCH3,downstream_gene_variant,,ENST00000483442,;	T	ENSG00000186001	ENST00000428136	Transcript	stop_gained	392	394	132	R/*	Aga/Tga	.	.	.	1	LRCH3	HGNC	28637	protein_coding	.	.	ENSP00000394763	.	.	UPI000198CC08	.	.	.	5/5	.	PROSITE_profiles:PS50021,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TTAAAAGAACT	.	3	ESCA
OXSR1	0	.	GRCh37	3	38295029	38295029	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*647G>A	.	.	ENST00000311806	18/18	12	4	8	20	20	0	OXSR1,3_prime_UTR_variant,,ENST00000311806,;OXSR1,downstream_gene_variant,,ENST00000446845,;OXSR1,downstream_gene_variant,,ENST00000467900,;	A	ENSG00000172939	ENST00000311806	Transcript	3_prime_UTR_variant	2603	.	.	.	.	.	.	.	1	OXSR1	HGNC	8508	protein_coding	YES	CCDS2675.1	ENSP00000311713	OXSR1_HUMAN	.	UPI000006E0D0	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCTAGCCTTA	.	3	ESCA
CTBP1	0	.	GRCh37	4	1235290	1235290	+	Intron	SNP	G	G	A	rs749744584	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.41-3165C>T	.	.	ENST00000290921	.	38	26	12	84	83	1	CTBP1,5_prime_UTR_variant,,ENST00000513420,;CTBP1,5_prime_UTR_variant,,ENST00000382952,;CTBP1,5_prime_UTR_variant,,ENST00000510568,;CTBP1,5_prime_UTR_variant,,ENST00000515399,;CTBP1,5_prime_UTR_variant,,ENST00000514210,;CTBP1,intron_variant,,ENST00000290921,;CTBP1,intron_variant,,ENST00000506180,;CTBP1,intron_variant,,ENST00000514495,;CTBP1,upstream_gene_variant,,ENST00000515690,;	A	ENSG00000159692	ENST00000290921	Transcript	intron_variant	.	.	.	.	.	rs749744584	.	.	-1	CTBP1	HGNC	2494	protein_coding	YES	CCDS3348.1	ENSP00000290921	CTBP1_HUMAN	.	UPI0000128637	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGCGTCGGG	.	5	ESCA
TBC1D9	0	.	GRCh37	4	141590791	141590791	+	Silent	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1434A>G	p.%3D	p.K478K	ENST00000442267	8/21	53	33	20	59	59	0	TBC1D9,synonymous_variant,p.%3D,ENST00000442267,;TBC1D9,downstream_gene_variant,,ENST00000514787,;	C	ENSG00000109436	ENST00000442267	Transcript	synonymous_variant	1509	1434	478	K	aaA/aaG	.	.	.	-1	TBC1D9	HGNC	21710	protein_coding	YES	CCDS47136.1	ENSP00000411197	TBCD9_HUMAN	.	UPI00001C1E18	.	.	.	8/21	.	hmmpanther:PTHR22957:SF190,hmmpanther:PTHR22957	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.P477P|c.1431G>A|3,BUFFER|p.P477P|c.1431G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAATTTCGG	.	5	ESCA
ZNF732	0	.	GRCh37	4	265711	265711	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.935G>T	p.Gly312Val	p.G312V	ENST00000419098	4/4	36	22	14	51	51	0	ZNF732,missense_variant,p.Gly312Val,ENST00000419098,;RP11-478C6.5,upstream_gene_variant,,ENST00000507882,;RP11-478C6.6,upstream_gene_variant,,ENST00000511111,;	A	ENSG00000186777	ENST00000419098	Transcript	missense_variant	946	935	312	G/V	gGc/gTc	.	.	.	-1	ZNF732	HGNC	37138	protein_coding	YES	CCDS46990.1	ENSP00000415774	ZN732_HUMAN	.	UPI00017A8291	.	deleterious(0)	probably_damaging(0.999)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF81,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTTTGCCACAT	.	4	ESCA
WDR19	0	.	GRCh37	4	39276490	39276490	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3628G>A	p.Ala1210Thr	p.A1210T	ENST00000399820	33/37	38	25	13	71	71	0	WDR19,missense_variant,p.Ala1050Thr,ENST00000288634,;WDR19,missense_variant,p.Ala1210Thr,ENST00000399820,;WDR19,3_prime_UTR_variant,,ENST00000506869,;WDR19,non_coding_transcript_exon_variant,,ENST00000512534,;WDR19,non_coding_transcript_exon_variant,,ENST00000512095,;WDR19,upstream_gene_variant,,ENST00000512588,;WDR19,upstream_gene_variant,,ENST00000510315,;WDR19,upstream_gene_variant,,ENST00000503733,;	A	ENSG00000157796	ENST00000399820	Transcript	missense_variant	3782	3628	1210	A/T	Gct/Act	.	.	.	1	WDR19	HGNC	18340	protein_coding	YES	CCDS47042.1	ENSP00000382717	WDR19_HUMAN	D6RE75_HUMAN,B4DGR6_HUMAN	UPI000004CC24	.	deleterious(0)	probably_damaging(0.987)	33/37	.	hmmpanther:PTHR14920,hmmpanther:PTHR14920:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTGCTTTC	.	5	ESCA
COX18	0	.	GRCh37	4	73930518	73930518	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.697G>A	p.Val233Ile	p.V233I	ENST00000295890	4/6	40	20	20	75	75	0	COX18,missense_variant,p.Val234Ile,ENST00000507544,;COX18,missense_variant,p.Val233Ile,ENST00000295890,;COX18,downstream_gene_variant,,ENST00000421792,;COX18,3_prime_UTR_variant,,ENST00000449739,;COX18,3_prime_UTR_variant,,ENST00000510031,;	T	ENSG00000163626	ENST00000295890	Transcript	missense_variant	789	697	233	V/I	Gtc/Atc	.	.	.	-1	COX18	HGNC	26801	protein_coding	YES	CCDS3554.1	ENSP00000295890	COX18_HUMAN	.	UPI000006FD5F	.	tolerated(0.3)	benign(0.021)	4/6	.	Transmembrane_helices:TMhelix,Pfam_domain:PF02096,hmmpanther:PTHR12428:SF17,hmmpanther:PTHR12428	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGACGCCAA	.	5	ESCA
CNOT6L	0	.	GRCh37	4	78678024	78678024	+	Missense_Mutation	SNP	T	T	C	rs754850131	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.482A>G	p.Asn161Ser	p.N161S	ENST00000264903	5/12	66	31	35	74	74	0	CNOT6L,missense_variant,p.Asn161Ser,ENST00000504123,;CNOT6L,missense_variant,p.Asn161Ser,ENST00000264903,;CNOT6L,missense_variant,p.Asn161Ser,ENST00000515441,;CNOT6L,missense_variant,p.Asn190Ser,ENST00000515506,;CNOT6L,missense_variant,p.Asn168Ser,ENST00000512485,;CNOT6L,non_coding_transcript_exon_variant,,ENST00000506166,;CNOT6L,3_prime_UTR_variant,,ENST00000504804,;	C	ENSG00000138767	ENST00000264903	Transcript	missense_variant	564	482	161	N/S	aAt/aGt	rs754850131	.	.	-1	CNOT6L	HGNC	18042	protein_coding	YES	CCDS47082.1	ENSP00000264903	CNO6L_HUMAN	D6RGK9_HUMAN	UPI0000E445DF	.	tolerated(0.61)	benign(0.128)	5/12	.	hmmpanther:PTHR12121,hmmpanther:PTHR12121:SF35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGAGATTGTCA	byFrequency	5	ESCA
UNC5C	0	.	GRCh37	4	96127865	96127865	+	Missense_Mutation	SNP	C	C	T	rs777197285	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1816G>A	p.Val606Ile	p.V606I	ENST00000453304	11/16	27	18	9	77	77	0	UNC5C,missense_variant,p.Val625Ile,ENST00000513796,;UNC5C,missense_variant,p.Val606Ile,ENST00000453304,;	T	ENSG00000182168	ENST00000453304	Transcript	missense_variant	2165	1816	606	V/I	Gtc/Atc	rs777197285,COSM4126821	.	.	-1	UNC5C	HGNC	12569	protein_coding	YES	CCDS3643.1	ENSP00000406022	UNC5C_HUMAN	Q4W5H4_HUMAN	UPI000004E6A5	.	tolerated(1)	benign(0.002)	11/16	.	SMART_domains:SM00218,Pfam_domain:PF00791,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7,PROSITE_profiles:PS51145	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGACGACTG	byFrequency	5	ESCA
SLC2A9	0	.	GRCh37	4	9982321	9982321	+	Silent	SNP	G	G	T	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.576C>A	p.%3D	p.I192I	ENST00000264784	5/12	17	11	6	18	18	0	SLC2A9,synonymous_variant,p.%3D,ENST00000506583,;SLC2A9,synonymous_variant,p.%3D,ENST00000513129,;SLC2A9,synonymous_variant,p.%3D,ENST00000309065,;SLC2A9,synonymous_variant,p.%3D,ENST00000264784,;SLC2A9,non_coding_transcript_exon_variant,,ENST00000505104,;SLC2A9,downstream_gene_variant,,ENST00000506839,;	T	ENSG00000109667	ENST00000264784	Transcript	synonymous_variant	630	576	192	I	atC/atA	COSM180393,COSM180394	.	.	-1	SLC2A9	HGNC	13446	protein_coding	YES	CCDS3407.1	ENSP00000264784	GTR9_HUMAN	.	UPI000013D56E	.	.	.	5/12	.	PROSITE_profiles:PS50850,hmmpanther:PTHR24063:SF8,hmmpanther:PTHR24063,PROSITE_patterns:PS00217,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00879,Pfam_domain:PF00083,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTGAGATCTC	.	5	ESCA
DMXL1	0	.	GRCh37	5	118485616	118485616	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4094C>G	p.Ser1365Cys	p.S1365C	ENST00000311085	18/43	49	32	17	63	63	0	DMXL1,missense_variant,p.Ser1365Cys,ENST00000539542,;DMXL1,missense_variant,p.Ser1365Cys,ENST00000311085,;MIR5706,upstream_gene_variant,,ENST00000579841,;DMXL1,downstream_gene_variant,,ENST00000512281,;	G	ENSG00000172869	ENST00000311085	Transcript	missense_variant	4174	4094	1365	S/C	tCt/tGt	.	.	.	1	DMXL1	HGNC	2937	protein_coding	YES	CCDS4125.1	ENSP00000309690	DMXL1_HUMAN	F1T0K4_HUMAN,E7EMZ0_HUMAN	UPI000013F0EC	.	deleterious(0.03)	possibly_damaging(0.838)	18/43	.	hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12,Pfam_domain:PF12234	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGAATCTAATC	.	5	ESCA
PCDHA8	0	.	GRCh37	5	140221052	140221052	+	Missense_Mutation	SNP	C	C	T	rs562900530	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.146C>T	p.Ala49Val	p.A49V	ENST00000531613	1/4	82	77	5	136	136	0	PCDHA8,missense_variant,p.Ala49Val,ENST00000531613,;PCDHA8,missense_variant,p.Ala49Val,ENST00000378123,;PCDHA4,intron_variant,,ENST00000530339,;PCDHA1,intron_variant,,ENST00000504120,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA2,intron_variant,,ENST00000526136,;PCDHA1,intron_variant,,ENST00000394633,;PCDHA3,intron_variant,,ENST00000522353,;PCDHA7,intron_variant,,ENST00000525929,;PCDHA6,intron_variant,,ENST00000527624,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA6,intron_variant,,ENST00000529310,;PCDHA5,intron_variant,,ENST00000529859,;PCDHA7,downstream_gene_variant,,ENST00000378125,;	T	ENSG00000204962	ENST00000531613	Transcript	missense_variant	146	146	49	A/V	gCg/gTg	rs562900530	.	.	1	PCDHA8	HGNC	8674	protein_coding	YES	CCDS54919.1	ENSP00000434655	PCDA8_HUMAN	.	UPI00001273D0	.	deleterious_low_confidence(0.01)	possibly_damaging(0.897)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF83,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.I48I|c.144C>T|3,BUFFER|p.I48I|c.144C>T|3	MUTECT|MUSE	GATCGCGCAGG	by1000G	2	ESCA
PCDHB18	0	.	GRCh37	5	140615725	140615725	+	RNA	SNP	C	C	T	rs782636530	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1788C>T	.	.	ENST00000526308	1/1	144	111	33	214	214	0	PCDHB18,non_coding_transcript_exon_variant,,ENST00000526308,;PCDHB18,non_coding_transcript_exon_variant,,ENST00000524813,;PCDHB19P,upstream_gene_variant,,ENST00000570871,;	T	ENSG00000146001	ENST00000526308	Transcript	non_coding_transcript_exon_variant	1788	.	.	.	.	rs782636530	.	.	1	PCDHB18	HGNC	14548	processed_transcript	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCGCCGCAGA	byFrequency	5	ESCA
SLC25A2	0	.	GRCh37	5	140683267	140683267	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.166G>T	p.Ala56Ser	p.A56S	ENST00000239451	1/1	38	29	9	57	57	0	SLC25A2,missense_variant,p.Ala56Ser,ENST00000239451,;	A	ENSG00000120329	ENST00000239451	Transcript	missense_variant	346	166	56	A/S	Gcc/Tcc	COSM1062897	.	.	-1	SLC25A2	HGNC	22921	protein_coding	YES	CCDS4258.1	ENSP00000239451	ORNT2_HUMAN	.	UPI0000130E9F	.	tolerated(0.43)	benign(0.004)	1/1	.	PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF251,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGGCGTATG	.	5	ESCA
PCDHGB3	0	.	GRCh37	5	140752321	140752321	+	Missense_Mutation	SNP	G	G	T	rs201408759	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2360G>T	p.Trp787Leu	p.W787L	ENST00000576222	1/4	23	13	9	41	41	0	PCDHGB3,missense_variant,p.Trp787Leu,ENST00000576222,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGA6,upstream_gene_variant,,ENST00000517434,;	T	ENSG00000262209	ENST00000576222	Transcript	missense_variant	2491	2360	787	W/L	tGg/tTg	rs201408759	.	.	1	PCDHGB3	HGNC	8710	protein_coding	YES	CCDS58980.1	ENSP00000461862	PCDGF_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000006FA6F	.	tolerated(0.79)	benign(0.001)	1/4	.	hmmpanther:PTHR24028:SF106,hmmpanther:PTHR24028	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTTGGTTTG	byFrequency|byCluster	5	ESCA
PCDHGB7	0	.	GRCh37	5	140797618	140797618	+	Silent	SNP	C	C	T	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.192C>T	p.%3D	p.R64R	ENST00000398594	1/4	60	42	17	62	62	0	PCDHGB7,synonymous_variant,p.%3D,ENST00000398594,;PCDHGB6,intron_variant,,ENST00000520790,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGA10,intron_variant,,ENST00000398610,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGA11,upstream_gene_variant,,ENST00000398587,;PCDHGA11,upstream_gene_variant,,ENST00000518882,;	T	ENSG00000254122	ENST00000398594	Transcript	synonymous_variant	192	192	64	R	cgC/cgT	COSM448981	.	.	1	PCDHGB7	HGNC	8714	protein_coding	YES	CCDS47293.1	ENSP00000381594	PCDGJ_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000007141F	.	.	.	1/4	.	hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF113,Pfam_domain:PF08266,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCGCGAGCT	.	5	ESCA
CCDC69	0	.	GRCh37	5	150563967	150563967	+	Silent	SNP	C	C	T	rs369963539	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.651G>A	p.%3D	p.T217T	ENST00000355417	8/9	54	46	8	57	57	0	CCDC69,synonymous_variant,p.%3D,ENST00000355417,;CCDC69,non_coding_transcript_exon_variant,,ENST00000521308,;CCDC69,3_prime_UTR_variant,,ENST00000518189,;CCDC69,non_coding_transcript_exon_variant,,ENST00000519448,;CCDC69,downstream_gene_variant,,ENST00000522964,;	T	ENSG00000198624	ENST00000355417	Transcript	synonymous_variant	826	651	217	T	acG/acA	rs369963539	.	.	-1	CCDC69	HGNC	24487	protein_coding	YES	CCDS4312.1	ENSP00000347586	CCD69_HUMAN	.	UPI000020CFF2	.	.	.	8/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24200,hmmpanther:PTHR24200:SF6	.	.	.	.	.	.	.	T:0.0005	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGTCGTAAT	byFrequency|byCluster	4	ESCA
FAT2	0	.	GRCh37	5	150923012	150923012	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7676C>T	p.Ala2559Val	p.A2559V	ENST00000261800	9/23	38	31	7	62	62	0	FAT2,missense_variant,p.Ala2559Val,ENST00000261800,;	A	ENSG00000086570	ENST00000261800	Transcript	missense_variant	7689	7676	2559	A/V	gCt/gTt	.	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	probably_damaging(1)	9/23	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	CCCGAGCCATG	.	4	ESCA
FAT2	0	.	GRCh37	5	150923013	150923013	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7675G>T	p.Ala2559Ser	p.A2559S	ENST00000261800	9/23	38	31	7	62	61	0	FAT2,missense_variant,p.Ala2559Ser,ENST00000261800,;	A	ENSG00000086570	ENST00000261800	Transcript	missense_variant	7688	7675	2559	A/S	Gct/Tct	.	.	.	-1	FAT2	HGNC	3596	protein_coding	YES	CCDS4317.1	ENSP00000261800	FAT2_HUMAN	.	UPI0000055B22	.	.	probably_damaging(1)	9/23	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	CCGAGCCATGA	.	4	ESCA
LSM11	0	.	GRCh37	5	157178533	157178533	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.584A>G	p.Asn195Ser	p.N195S	ENST00000286307	2/4	61	49	12	72	72	0	LSM11,missense_variant,p.Asn195Ser,ENST00000286307,;CTC-370J7.1,upstream_gene_variant,,ENST00000518369,;	G	ENSG00000155858	ENST00000286307	Transcript	missense_variant	640	584	195	N/S	aAt/aGt	.	.	.	1	LSM11	HGNC	30860	protein_coding	YES	CCDS4342.1	ENSP00000286307	LSM11_HUMAN	.	UPI0000072830	.	deleterious(0)	probably_damaging(0.983)	2/4	.	hmmpanther:PTHR21415,hmmpanther:PTHR21415:SF1,Pfam_domain:PF01423,Gene3D:2.30.30.100,SMART_domains:SM00651,Superfamily_domains:SSF50182,Superfamily_domains:SSF50182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAATATGG	.	5	ESCA
FAM153B	0	.	GRCh37	5	175530248	175530248	+	Frame_Shift_Del	DEL	T	T	-	rs764878632	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453delT	p.Gln152ArgfsTer16	p.Q152Rfs*16	ENST00000515817	12/20	385	300	85	420	420	0	FAM153B,frameshift_variant,p.Gln229ArgfsTer16,ENST00000253490,;FAM153B,frameshift_variant,p.Gln152ArgfsTer16,ENST00000510151,;FAM153B,frameshift_variant,p.Gln152ArgfsTer16,ENST00000515817,;FAM153B,intron_variant,,ENST00000512862,;FAM153B,downstream_gene_variant,,ENST00000503724,;FAM153B,non_coding_transcript_exon_variant,,ENST00000393522,;FAM153B,frameshift_variant,p.Gln152ArgfsTer16,ENST00000508296,;	-	ENSG00000182230	ENST00000515817	Transcript	frameshift_variant	736	452	151	L/X	cTt/ct	rs764878632	.	.	1	FAM153B	HGNC	27323	protein_coding	YES	CCDS43401.2	ENSP00000427684	.	H0YL08_HUMAN,D6RF84_HUMAN,D6RA46_HUMAN	UPI00001D7EF3	.	.	.	12/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	ATGTACTTCAGG	.	2	ESCA
PRDM9	0	.	GRCh37	5	23522934	23522934	+	Silent	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.822C>T	p.%3D	p.G274G	ENST00000296682	8/11	103	87	15	73	73	0	PRDM9,synonymous_variant,p.%3D,ENST00000296682,;	T	ENSG00000164256	ENST00000296682	Transcript	synonymous_variant	1004	822	274	G	ggC/ggT	.	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	.	.	8/11	.	Superfamily_domains:SSF82199,Gene3D:2.170.270.10,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50280	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTGGCCCTTA	.	4	ESCA
PRDM9	0	.	GRCh37	5	23527045	23527045	+	Silent	SNP	C	C	A	rs545024531	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1848C>A	p.%3D	p.G616G	ENST00000296682	11/11	180	161	19	147	147	0	PRDM9,synonymous_variant,p.%3D,ENST00000296682,;	A	ENSG00000164256	ENST00000296682	Transcript	synonymous_variant	2030	1848	616	G	ggC/ggA	rs545024531	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	.	.	11/11	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50157	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R619W|c.1855C>T|3	RADIA|MUTECT|MUSE|VARSCANS	CGGGGCTTTAG	by1000G	4	ESCA
TARS	0	.	GRCh37	5	33441104	33441104	+	5'UTR	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-89C>G	.	.	ENST00000455217	1/20	33	22	11	42	42	0	TARS,5_prime_UTR_variant,,ENST00000265112,;TARS,5_prime_UTR_variant,,ENST00000541634,;TARS,5_prime_UTR_variant,,ENST00000455217,;TARS,5_prime_UTR_variant,,ENST00000414361,;TARS,intron_variant,,ENST00000514259,;TARS,intron_variant,,ENST00000502553,;TARS,upstream_gene_variant,,ENST00000506040,;CTD-2203K17.1,upstream_gene_variant,,ENST00000507251,;TARS,non_coding_transcript_exon_variant,,ENST00000502508,;TARS,5_prime_UTR_variant,,ENST00000509731,;TARS,5_prime_UTR_variant,,ENST00000507716,;TARS,5_prime_UTR_variant,,ENST00000513066,;TARS,5_prime_UTR_variant,,ENST00000505012,;TARS,5_prime_UTR_variant,,ENST00000508361,;	G	ENSG00000113407	ENST00000455217	Transcript	5_prime_UTR_variant	34	.	.	.	.	.	.	.	1	TARS	HGNC	11572	protein_coding	YES	CCDS58943.1	ENSP00000387710	SYTC_HUMAN	D6RBR8_HUMAN	UPI00017A6D60	.	.	.	1/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGTCCCGGGC	.	3	ESCA
KIF2A	0	.	GRCh37	5	61681734	61681734	+	3'Flank	DEL	T	T	-	rs200992864	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000407818	.	57	45	12	55	55	0	KIF2A,3_prime_UTR_variant,,ENST00000381103,;DIMT1,downstream_gene_variant,,ENST00000199320,;KIF2A,downstream_gene_variant,,ENST00000407818,;KIF2A,downstream_gene_variant,,ENST00000401507,;KIF2A,downstream_gene_variant,,ENST00000506857,;KIF2A,intron_variant,,ENST00000509663,;DIMT1,downstream_gene_variant,,ENST00000514605,;	-	ENSG00000068796	ENST00000407818	Transcript	downstream_gene_variant	.	.	.	.	.	rs200992864	.	279	1	KIF2A	HGNC	6318	protein_coding	YES	CCDS47216.1	ENSP00000385000	KIF2A_HUMAN	D6RD93_HUMAN	UPI0001533DB2	.	.	.	.	.	.	-:0.0080	-:0	-:0.0072	.	-:0	-:0.0149	-:0.0204	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAGCATTTCCT	byFrequency|byCluster|by1000G	3	ESCA
SEMA5A	0	.	GRCh37	5	9063121	9063121	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2396A>C	p.Asp799Ala	p.D799A	ENST00000382496	18/23	55	46	9	65	65	0	SEMA5A,missense_variant,p.Asp799Ala,ENST00000382496,;	G	ENSG00000112902	ENST00000382496	Transcript	missense_variant	3062	2396	799	D/A	gAc/gCc	.	.	.	-1	SEMA5A	HGNC	10736	protein_coding	YES	CCDS3875.1	ENSP00000371936	SEM5A_HUMAN	D6RAF4_HUMAN,B4DE33_HUMAN	UPI000004F25D	.	tolerated(0.09)	probably_damaging(1)	18/23	.	PROSITE_profiles:PS50092,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCAGTCACGG	.	5	ESCA
MCHR2	0	.	GRCh37	6	100391010	100391010	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.402C>T	p.%3D	p.A134A	ENST00000281806	4/6	40	30	10	53	53	0	MCHR2,synonymous_variant,p.%3D,ENST00000369212,;MCHR2,synonymous_variant,p.%3D,ENST00000281806,;	A	ENSG00000152034	ENST00000281806	Transcript	synonymous_variant	717	402	134	A	gcC/gcT	.	.	.	-1	MCHR2	HGNC	20867	protein_coding	YES	CCDS5044.1	ENSP00000281806	MCHR2_HUMAN	.	UPI000003730F	.	.	.	4/6	.	Prints_domain:PR00237,Superfamily_domains:SSF81321,Pfam_domain:PF00001,Gene3D:1.20.1070.10,PROSITE_patterns:PS00237,hmmpanther:PTHR24230:SF7,hmmpanther:PTHR24230,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGAGGGCAAA	.	5	ESCA
HDDC2	0	.	GRCh37	6	125614053	125614053	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.312A>T	p.Glu104Asp	p.E104D	ENST00000398153	4/6	41	17	23	69	69	0	HDDC2,missense_variant,p.Glu104Asp,ENST00000398153,;HDDC2,missense_variant,p.Glu70Asp,ENST00000368377,;HDDC2,intron_variant,,ENST00000608295,;HDDC2,downstream_gene_variant,,ENST00000608284,;HDDC2,missense_variant,p.Lys70Met,ENST00000609477,;HDDC2,missense_variant,p.Lys70Met,ENST00000318787,;HDDC2,splice_region_variant,,ENST00000608461,;HDDC2,non_coding_transcript_exon_variant,,ENST00000608532,;	A	ENSG00000111906	ENST00000398153	Transcript	missense_variant	355	312	104	E/D	gaA/gaT	.	.	.	-1	HDDC2	HGNC	21078	protein_coding	YES	CCDS43503.1	ENSP00000381220	HDDC2_HUMAN	H0UI53_HUMAN,H0UI52_HUMAN	UPI0000070B81	.	tolerated(0.15)	benign(0.012)	4/6	.	hmmpanther:PTHR11845,Gene3D:1.10.3210.10,Pfam_domain:PF13023,SMART_domains:SM00471,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGCTTCCTG	.	5	ESCA
SGK1	0	.	GRCh37	6	134491990	134491990	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1387A>G	p.Ile463Val	p.I463V	ENST00000367858	13/14	57	39	18	49	49	0	SGK1,missense_variant,p.Ile368Val,ENST00000237305,;SGK1,missense_variant,p.Ile463Val,ENST00000367858,;SGK1,missense_variant,p.Ile396Val,ENST00000528577,;SGK1,missense_variant,p.Ile382Val,ENST00000413996,;SGK1,missense_variant,p.Ile358Val,ENST00000367857,;SGK1,missense_variant,p.Ile324Val,ENST00000475719,;SGK1,downstream_gene_variant,,ENST00000461976,;SGK1,downstream_gene_variant,,ENST00000524387,;SGK1,downstream_gene_variant,,ENST00000489458,;SGK1,downstream_gene_variant,,ENST00000531575,;SGK1,non_coding_transcript_exon_variant,,ENST00000531782,;SGK1,non_coding_transcript_exon_variant,,ENST00000474427,;SGK1,non_coding_transcript_exon_variant,,ENST00000477460,;SGK1,non_coding_transcript_exon_variant,,ENST00000367855,;SGK1,downstream_gene_variant,,ENST00000534658,;SGK1,downstream_gene_variant,,ENST00000524764,;SGK1,downstream_gene_variant,,ENST00000530421,;SGK1,downstream_gene_variant,,ENST00000532021,;SGK1,downstream_gene_variant,,ENST00000473704,;SGK1,downstream_gene_variant,,ENST00000472859,;SGK1,downstream_gene_variant,,ENST00000532856,;SGK1,downstream_gene_variant,,ENST00000525877,;SGK1,downstream_gene_variant,,ENST00000475882,;SGK1,downstream_gene_variant,,ENST00000490149,;SGK1,downstream_gene_variant,,ENST00000525700,;	C	ENSG00000118515	ENST00000367858	Transcript	missense_variant	1985	1387	463	I/V	Att/Gtt	.	.	.	-1	SGK1	HGNC	10810	protein_coding	YES	CCDS47476.1	ENSP00000356832	SGK1_HUMAN	E9PP33_HUMAN,E9PJN2_HUMAN,B7Z1G1_HUMAN	UPI000013CA0E	.	tolerated(0.25)	benign(0.011)	13/14	.	PROSITE_profiles:PS51285,hmmpanther:PTHR24356:SF148,hmmpanther:PTHR24356,SMART_domains:SM00133,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.K367delK|c.1100_1102delAGA|3,CODON|p.K462delK|c.1385_1387delAGA|3,CODON|p.K395delK|c.1184_1186delAGA|3,CODON|p.K381delK|c.1142_1144delAGA|3,CODON|p.K357delK|c.1070_1072delAGA|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTAATCTTCT	.	5	ESCA
UTRN	0	.	GRCh37	6	144800995	144800995	+	Silent	SNP	G	G	T	rs112708396	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3384G>T	p.%3D	p.A1128A	ENST00000367545	25/74	58	39	19	82	82	0	UTRN,synonymous_variant,p.%3D,ENST00000367545,;	T	ENSG00000152818	ENST00000367545	Transcript	synonymous_variant	3384	3384	1128	A	gcG/gcT	rs112708396	.	.	1	UTRN	HGNC	12635	protein_coding	YES	CCDS34547.1	ENSP00000356515	UTRO_HUMAN	Q6LBS5_HUMAN,Q5SYY2_HUMAN,Q5JT45_HUMAN	UPI00003673F1	.	.	.	25/74	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF225,hmmpanther:PTHR11915,SMART_domains:SM00150,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGCGAACCT	byCluster	5	ESCA
AKAP12	0	.	GRCh37	6	151677302	151677302	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*453G>A	.	.	ENST00000402676	5/5	50	22	28	73	73	0	AKAP12,3_prime_UTR_variant,,ENST00000359755,;AKAP12,3_prime_UTR_variant,,ENST00000354675,;AKAP12,3_prime_UTR_variant,,ENST00000253332,;AKAP12,3_prime_UTR_variant,,ENST00000402676,;	A	ENSG00000131016	ENST00000402676	Transcript	3_prime_UTR_variant	6042	.	.	.	.	.	.	.	1	AKAP12	HGNC	370	protein_coding	YES	CCDS5229.1	ENSP00000384537	AKA12_HUMAN	.	UPI000013CDC7	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGATGGGGCA	.	5	ESCA
OR5V1	0	.	GRCh37	6	29323224	29323224	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.749T>A	p.Leu250His	p.L250H	ENST00000377154	4/4	21	18	3	39	39	0	OR5V1,missense_variant,p.Leu250His,ENST00000543825,;OR5V1,missense_variant,p.Leu250His,ENST00000377154,;	T	ENSG00000243729	ENST00000377154	Transcript	missense_variant	1049	749	250	L/H	cTc/cAc	.	.	.	-1	OR5V1	HGNC	13972	protein_coding	YES	CCDS4657.1	ENSP00000366359	OR5V1_HUMAN	.	UPI000004186B	.	deleterious(0)	probably_damaging(0.992)	4/4	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF0,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAAGAGAAAG	.	2	ESCA
TAPBP	0	.	GRCh37	6	33268057	33268057	+	3'Flank	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000426633	.	68	52	16	78	78	0	TAPBP,3_prime_UTR_variant,,ENST00000434618,;TAPBP,downstream_gene_variant,,ENST00000489157,;TAPBP,downstream_gene_variant,,ENST00000456592,;RGL2,upstream_gene_variant,,ENST00000425946,;RGL2,upstream_gene_variant,,ENST00000444031,;TAPBP,downstream_gene_variant,,ENST00000467025,;RGL2,upstream_gene_variant,,ENST00000497454,;TAPBP,downstream_gene_variant,,ENST00000426633,;TAPBP,downstream_gene_variant,,ENST00000475304,;PFDN6,downstream_gene_variant,,ENST00000463584,;RGL2,upstream_gene_variant,,ENST00000437840,;RGL2,upstream_gene_variant,,ENST00000491168,;RGL2,upstream_gene_variant,,ENST00000485077,;RGL2,upstream_gene_variant,,ENST00000478610,;RGL2,upstream_gene_variant,,ENST00000460988,;RGL2,upstream_gene_variant,,ENST00000494550,;TAPBP,downstream_gene_variant,,ENST00000437116,;TAPBP,downstream_gene_variant,,ENST00000480730,;RGL2,upstream_gene_variant,,ENST00000476616,;RGL2,upstream_gene_variant,,ENST00000483151,;	A	ENSG00000231925	ENST00000426633	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3293	-1	TAPBP	HGNC	11566	protein_coding	YES	CCDS34428.2	ENSP00000404833	.	.	UPI0000E5AD4C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTCTCCAAA	.	5	ESCA
MOCS1	0	.	GRCh37	6	39893509	39893509	+	Missense_Mutation	SNP	C	C	T	rs200517455	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.331G>A	p.Ala111Thr	p.A111T	ENST00000373186	2/10	26	20	5	31	31	0	MOCS1,missense_variant,p.Ala111Thr,ENST00000425303,;MOCS1,missense_variant,p.Ala111Thr,ENST00000373188,;MOCS1,missense_variant,p.Ala24Thr,ENST00000373195,;MOCS1,missense_variant,p.Ala82Thr,ENST00000373175,;MOCS1,missense_variant,p.Ala111Thr,ENST00000340692,;MOCS1,missense_variant,p.Ala111Thr,ENST00000308559,;MOCS1,missense_variant,p.Ala111Thr,ENST00000373186,;MOCS1,missense_variant,p.Ala82Thr,ENST00000432280,;MOCS1,missense_variant,p.Ala24Thr,ENST00000373181,;MOCS1,3_prime_UTR_variant,,ENST00000487924,;MOCS1,non_coding_transcript_exon_variant,,ENST00000473742,;	T	ENSG00000124615	ENST00000373186	Transcript	missense_variant	469	331	111	A/T	Gcc/Acc	rs200517455,COSM1079075,COSM1079076	.	.	-1	MOCS1	HGNC	7190	protein_coding	YES	CCDS4846.1	ENSP00000362282	MOCS1_HUMAN	Q9NP27_HUMAN	UPI000006FA21	.	deleterious(0.02)	possibly_damaging(0.863)	2/10	.	HAMAP:MF_01225_B,hmmpanther:PTHR22960:SF0,hmmpanther:PTHR22960,TIGRFAM_domain:TIGR02666,Pfam_domain:PF04055,Pfam_domain:PF13353,Gene3D:3.20.20.70,SMART_domains:SM00729,Superfamily_domains:SSF102114	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGGGCGAGGG	byCluster|by1000G	5	ESCA
COL12A1	0	.	GRCh37	6	75840585	75840585	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6050C>G	p.Pro2017Arg	p.P2017R	ENST00000322507	36/66	36	22	13	86	86	0	COL12A1,missense_variant,p.Pro2017Arg,ENST00000416123,;COL12A1,missense_variant,p.Pro2017Arg,ENST00000322507,;COL12A1,missense_variant,p.Pro2017Arg,ENST00000483888,;COL12A1,missense_variant,p.Pro853Arg,ENST00000345356,;COL12A1,downstream_gene_variant,,ENST00000419671,;	C	ENSG00000111799	ENST00000322507	Transcript	missense_variant	6360	6050	2017	P/R	cCt/cGt	.	.	.	-1	COL12A1	HGNC	2188	protein_coding	YES	CCDS43482.1	ENSP00000325146	COCA1_HUMAN	.	UPI000045890B	.	.	benign(0.235)	36/66	.	PROSITE_profiles:PS50853,hmmpanther:PTHR22992:SF23,hmmpanther:PTHR22992,Gene3D:2.60.40.10,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCAGGGCTG	.	5	ESCA
ADCK2	0	.	GRCh37	7	140380866	140380866	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000072869	4/8	59	28	31	72	72	0	ADCK2,stop_gained,p.Gln250Ter,ENST00000483369,;ADCK2,stop_gained,p.Gln52Ter,ENST00000473512,;ADCK2,stop_gained,p.Gln412Ter,ENST00000476491,;ADCK2,stop_gained,p.Gln412Ter,ENST00000072869,;ADCK2,non_coding_transcript_exon_variant,,ENST00000498423,;	T	ENSG00000133597	ENST00000072869	Transcript	stop_gained	1412	1234	412	Q/*	Cag/Tag	.	.	.	1	ADCK2	HGNC	19039	protein_coding	YES	CCDS5861.1	ENSP00000072869	ADCK2_HUMAN	A4D1T6_HUMAN	UPI000003C962	.	.	.	4/8	.	hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF6,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTACCAGCAG	.	5	ESCA
NOBOX	0	.	GRCh37	7	144098371	144098371	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.612delG	p.Lys205SerfsTer63	p.K205Sfs*63	ENST00000467773	4/10	58	47	11	51	51	0	NOBOX,frameshift_variant,p.Lys120SerfsTer63,ENST00000223140,;NOBOX,frameshift_variant,p.Lys205SerfsTer63,ENST00000483238,;NOBOX,frameshift_variant,p.Lys205SerfsTer63,ENST00000467773,;	-	ENSG00000106410	ENST00000467773	Transcript	frameshift_variant	612	612	204	G/X	ggG/gg	.	.	.	-1	NOBOX	HGNC	22448	protein_coding	YES	.	ENSP00000419457	NOBOX_HUMAN	.	UPI00019B220B	.	.	.	4/10	.	hmmpanther:PTHR24329:SF282,hmmpanther:PTHR24329	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CTGCTTCCCGGG	.	3	ESCA
WDR60	0	.	GRCh37	7	158664026	158664026	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.263G>A	p.Arg88Lys	p.R88K	ENST00000407559	3/25	47	28	18	106	106	0	WDR60,missense_variant,p.Arg88Lys,ENST00000407559,;WDR60,missense_variant,p.Arg98Lys,ENST00000397143,;	A	ENSG00000126870	ENST00000407559	Transcript	missense_variant	421	263	88	R/K	aGa/aAa	.	.	.	1	WDR60	HGNC	21862	protein_coding	YES	CCDS47757.1	ENSP00000384290	WDR60_HUMAN	H7C1E8_HUMAN,A4D230_HUMAN	UPI000020E761	.	tolerated(1)	benign(0.001)	3/25	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACAGACAGA	.	5	ESCA
CCDC129	0	.	GRCh37	7	31682502	31682502	+	Missense_Mutation	SNP	T	T	A	rs766622377	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1596T>A	p.Phe532Leu	p.F532L	ENST00000451887	11/15	36	30	5	25	25	0	CCDC129,missense_variant,p.Phe532Leu,ENST00000451887,;CCDC129,missense_variant,p.Phe414Leu,ENST00000409210,;CCDC129,missense_variant,p.Phe358Leu,ENST00000319386,;CCDC129,missense_variant,p.Phe506Leu,ENST00000407970,;	A	ENSG00000180347	ENST00000451887	Transcript	missense_variant	1608	1596	532	F/L	ttT/ttA	rs766622377	.	.	1	CCDC129	HGNC	27363	protein_coding	YES	CCDS59050.1	ENSP00000395835	CC129_HUMAN	E7ERG9_HUMAN,E7EQ43_HUMAN,B8ZZ49_HUMAN	UPI00020655D9	.	tolerated(0.72)	benign(0.002)	11/15	.	hmmpanther:PTHR17469,hmmpanther:PTHR17469:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGTTTCTGCT	.	4	ESCA
TRGC1	0	.	GRCh37	7	38305167	38305167	+	Silent	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113C>T	p.%3D	p.F38F	ENST00000443402	1/3	99	90	9	118	118	0	TRGC1,synonymous_variant,p.%3D,ENST00000443402,;TRGJ1,downstream_gene_variant,,ENST00000390337,;	A	ENSG00000211689	ENST00000443402	Transcript	synonymous_variant	113	114	38	F	ttC/ttT	.	.	.	-1	TRGC1	HGNC	12275	TR_C_gene	YES	.	ENSP00000404817	.	Q0VGM3_HUMAN	UPI0000F3036A	.	.	.	1/3	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19256,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAGGGAAAAA	.	3	ESCA
AEBP1	0	.	GRCh37	7	44152463	44152463	+	Missense_Mutation	SNP	G	G	C	rs748270931,rs775904599	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2524G>C	p.Gly842Arg	p.G842R	ENST00000223357	18/21	89	80	9	116	116	0	AEBP1,missense_variant,p.Gly842Arg,ENST00000223357,;AEBP1,missense_variant,p.Gly417Arg,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000406581,;POLD2,downstream_gene_variant,,ENST00000223361,;POLD2,downstream_gene_variant,,ENST00000433715,;AEBP1,downstream_gene_variant,,ENST00000455443,;POLD2,downstream_gene_variant,,ENST00000436400,;POLD2,downstream_gene_variant,,ENST00000456038,;POLD2,downstream_gene_variant,,ENST00000452185,;POLD2,downstream_gene_variant,,ENST00000418438,;POLD2,downstream_gene_variant,,ENST00000436844,;MIR4649,downstream_gene_variant,,ENST00000582839,;AEBP1,downstream_gene_variant,,ENST00000454218,;AEBP1,3_prime_UTR_variant,,ENST00000413907,;POLD2,downstream_gene_variant,,ENST00000481104,;POLD2,downstream_gene_variant,,ENST00000463464,;AEBP1,downstream_gene_variant,,ENST00000434445,;POLD2,downstream_gene_variant,,ENST00000496539,;AEBP1,downstream_gene_variant,,ENST00000431035,;POLD2,downstream_gene_variant,,ENST00000467469,;POLD2,downstream_gene_variant,,ENST00000470867,;POLD2,downstream_gene_variant,,ENST00000461116,;POLD2,downstream_gene_variant,,ENST00000464871,;AEBP1,downstream_gene_variant,,ENST00000453052,;POLD2,downstream_gene_variant,,ENST00000489883,;	C	ENSG00000106624	ENST00000223357	Transcript	missense_variant	2829	2524	842	G/R	Ggc/Cgc	rs748270931,rs775904599	.	.	1	AEBP1	HGNC	303	protein_coding	YES	CCDS5476.1	ENSP00000223357	AEBP1_HUMAN	B4DJB3_HUMAN	UPI00000746E2	.	deleterious(0.02)	probably_damaging(0.969)	18/21	.	hmmpanther:PTHR11532:SF48,hmmpanther:PTHR11532,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCGGCGGCATG	.	3	ESCA
SNORA22	0	.	GRCh37	7	64530054	64530054	+	3'Flank	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000384614	.	58	46	11	117	117	0	SNORA22,downstream_gene_variant,,ENST00000384614,;SNORA15,upstream_gene_variant,,ENST00000384334,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000426828,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000419314,;CCT6P3,non_coding_transcript_exon_variant,,ENST00000452026,;	C	ENSG00000207344	ENST00000384614	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	3544	1	SNORA22	RFAM	.	snoRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTGTGGTGG	.	5	ESCA
POR	0	.	GRCh37	7	75610443	75610443	+	Silent	SNP	C	C	T	rs782083065	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>T	p.%3D	p.L198L	ENST00000461988	6/16	42	31	11	80	80	0	POR,synonymous_variant,p.%3D,ENST00000394893,;POR,synonymous_variant,p.%3D,ENST00000461988,;POR,synonymous_variant,p.%3D,ENST00000419840,;POR,synonymous_variant,p.%3D,ENST00000447222,;POR,synonymous_variant,p.%3D,ENST00000450476,;POR,intron_variant,,ENST00000545601,;POR,downstream_gene_variant,,ENST00000439297,;POR,downstream_gene_variant,,ENST00000432753,;POR,downstream_gene_variant,,ENST00000414186,;POR,downstream_gene_variant,,ENST00000453773,;POR,downstream_gene_variant,,ENST00000426184,;POR,downstream_gene_variant,,ENST00000412521,;POR,downstream_gene_variant,,ENST00000439963,;POR,upstream_gene_variant,,ENST00000439269,;POR,downstream_gene_variant,,ENST00000475509,;POR,non_coding_transcript_exon_variant,,ENST00000460892,;POR,intron_variant,,ENST00000454934,;POR,intron_variant,,ENST00000412064,;POR,upstream_gene_variant,,ENST00000487247,;POR,upstream_gene_variant,,ENST00000495770,;POR,downstream_gene_variant,,ENST00000448410,;POR,downstream_gene_variant,,ENST00000471238,;POR,upstream_gene_variant,,ENST00000493973,;POR,upstream_gene_variant,,ENST00000496888,;	T	ENSG00000127948	ENST00000461988	Transcript	synonymous_variant	699	594	198	L	ctC/ctT	rs782083065	.	.	1	POR	HGNC	9208	protein_coding	YES	CCDS5579.1	ENSP00000419970	NCPR_HUMAN	Q59ED7_HUMAN,E7EMD0_HUMAN,C9JQ78_HUMAN	UPI000013D5F4	.	.	.	6/16	.	PROSITE_profiles:PS50902,hmmpanther:PTHR19384,Pfam_domain:PF00258,Gene3D:3.40.50.360,PIRSF_domain:PIRSF000208,Superfamily_domains:SSF52218,Prints_domain:PR00369	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCGGCGC	.	5	ESCA
DLC1	0	.	GRCh37	8	13356564	13356564	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1017G>T	p.Lys339Asn	p.K339N	ENST00000276297	2/18	27	19	8	62	62	0	DLC1,missense_variant,p.Lys339Asn,ENST00000511869,;DLC1,missense_variant,p.Lys63Asn,ENST00000517868,;DLC1,missense_variant,p.Lys339Asn,ENST00000276297,;DLC1,missense_variant,p.Lys339Asn,ENST00000316609,;DLC1,downstream_gene_variant,,ENST00000517333,;	A	ENSG00000164741	ENST00000276297	Transcript	missense_variant	1427	1017	339	K/N	aaG/aaT	.	.	.	-1	DLC1	HGNC	2897	protein_coding	YES	CCDS5989.1	ENSP00000276297	RHG07_HUMAN	.	UPI0000210275	.	deleterious_low_confidence(0.01)	possibly_damaging(0.511)	2/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCTTACG	.	5	ESCA
PHF20L1	0	.	GRCh37	8	133859093	133859093	+	3'UTR	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*925G>A	.	.	ENST00000395386	21/21	69	52	17	75	75	0	PHF20L1,3_prime_UTR_variant,,ENST00000395390,;PHF20L1,3_prime_UTR_variant,,ENST00000395386,;PHF20L1,downstream_gene_variant,,ENST00000220847,;AF230666.2,upstream_gene_variant,,ENST00000429151,;AF230666.2,upstream_gene_variant,,ENST00000608375,;PHF20L1,3_prime_UTR_variant,,ENST00000460236,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000477051,;	A	ENSG00000129292	ENST00000395386	Transcript	3_prime_UTR_variant	4278	.	.	.	.	.	.	.	1	PHF20L1	HGNC	24280	protein_coding	YES	CCDS6367.2	ENSP00000378784	P20L1_HUMAN	E5RK91_HUMAN,B3KWX5_HUMAN	UPI0000DBD7AF	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTGTAAAT	.	5	ESCA
PPP3CC	0	.	GRCh37	8	22368688	22368688	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.574C>G	p.Leu192Val	p.L192V	ENST00000397775	5/15	79	60	18	81	81	0	PPP3CC,missense_variant,p.Leu18Val,ENST00000523620,;PPP3CC,missense_variant,p.Leu192Val,ENST00000240139,;PPP3CC,missense_variant,p.Leu42Val,ENST00000522034,;PPP3CC,missense_variant,p.Leu69Val,ENST00000521651,;PPP3CC,missense_variant,p.Leu192Val,ENST00000518852,;PPP3CC,missense_variant,p.Leu192Val,ENST00000397775,;PPP3CC,missense_variant,p.Leu192Val,ENST00000289963,;	G	ENSG00000120910	ENST00000397775	Transcript	missense_variant	848	574	192	L/V	Ctc/Gtc	COSM1098104	.	.	1	PPP3CC	HGNC	9316	protein_coding	YES	CCDS59093.1	ENSP00000380878	PP2BC_HUMAN	E5RJH4_HUMAN	UPI00017A7ABA	.	deleterious(0)	possibly_damaging(0.88)	5/15	.	hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF186,Gene3D:3.60.21.10,Pfam_domain:PF00149,SMART_domains:SM00156,Superfamily_domains:SSF56300,Prints_domain:PR00114	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTTCTCTGT	.	5	ESCA
CNGB3	0	.	GRCh37	8	87751931	87751931	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163A>G	p.Thr55Ala	p.T55A	ENST00000320005	2/18	43	36	6	42	42	0	CNGB3,missense_variant,p.Thr55Ala,ENST00000320005,;RP11-386D6.1,intron_variant,,ENST00000519041,;CNGB3,non_coding_transcript_exon_variant,,ENST00000519777,;	C	ENSG00000170289	ENST00000320005	Transcript	missense_variant	211	163	55	T/A	Acc/Gcc	COSM751545,COSM85131	.	.	-1	CNGB3	HGNC	2153	protein_coding	YES	CCDS6244.1	ENSP00000316605	CNGB3_HUMAN	.	UPI000014076F	.	tolerated(0.37)	benign(0.003)	2/18	.	.	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGGTTTTGA	.	5	ESCA
C9orf131	0	.	GRCh37	9	35042298	35042298	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.47G>A	p.Gly16Glu	p.G16E	ENST00000312292	1/2	49	31	17	52	52	0	C9orf131,missense_variant,p.Gly16Glu,ENST00000312292,;C9orf131,missense_variant,p.Gly16Glu,ENST00000378745,;C9orf131,intron_variant,,ENST00000421362,;C9orf131,intron_variant,,ENST00000534880,;C9orf131,intron_variant,,ENST00000537671,;C9orf131,intron_variant,,ENST00000354479,;FLJ00273,downstream_gene_variant,,ENST00000595331,;C9orf131,upstream_gene_variant,,ENST00000416537,;	A	ENSG00000174038	ENST00000312292	Transcript	missense_variant	94	47	16	G/E	gGg/gAg	.	.	.	1	C9orf131	HGNC	31418	protein_coding	YES	CCDS6572.2	ENSP00000308279	CI131_HUMAN	.	UPI00001605AC	.	tolerated(0.28)	benign(0.136)	1/2	.	hmmpanther:PTHR21777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGGGGCTTC	.	5	ESCA
SPAG8	0	.	GRCh37	9	35811389	35811389	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.654A>T	p.Arg218Ser	p.R218S	ENST00000340291	2/8	41	31	9	103	103	0	SPAG8,missense_variant,p.Arg216Ser,ENST00000497810,;SPAG8,missense_variant,p.Arg218Ser,ENST00000340291,;SPAG8,missense_variant,p.Arg216Ser,ENST00000484764,;SPAG8,missense_variant,p.Arg218Ser,ENST00000396638,;HINT2,downstream_gene_variant,,ENST00000259667,;TMEM8B,upstream_gene_variant,,ENST00000377996,;NPR2,downstream_gene_variant,,ENST00000447210,;NPR2,downstream_gene_variant,,ENST00000421267,;NPR2,downstream_gene_variant,,ENST00000342694,;AL133410.1,downstream_gene_variant,,ENST00000582432,;SPAG8,non_coding_transcript_exon_variant,,ENST00000479751,;SPAG8,intron_variant,,ENST00000463889,;HINT2,downstream_gene_variant,,ENST00000474848,;HINT2,downstream_gene_variant,,ENST00000474908,;HINT2,downstream_gene_variant,,ENST00000472085,;HINT2,downstream_gene_variant,,ENST00000490578,;SPAG8,upstream_gene_variant,,ENST00000489063,;HINT2,downstream_gene_variant,,ENST00000471774,;HINT2,downstream_gene_variant,,ENST00000461169,;SPAG8,missense_variant,p.Arg218Ser,ENST00000475644,;SPAG8,intron_variant,,ENST00000471631,;SPAG8,intron_variant,,ENST00000495667,;SPAG8,intron_variant,,ENST00000472605,;SPAG8,upstream_gene_variant,,ENST00000460836,;NPR2,downstream_gene_variant,,ENST00000448821,;FAM221B,downstream_gene_variant,,ENST00000388950,;NPR2,downstream_gene_variant,,ENST00000464810,;NPR2,downstream_gene_variant,,ENST00000469249,;	A	ENSG00000137098	ENST00000340291	Transcript	missense_variant	779	654	218	R/S	agA/agT	.	.	.	-1	SPAG8	HGNC	14105	protein_coding	YES	CCDS6592.1	ENSP00000340982	SPAG8_HUMAN	F8WBP3_HUMAN	UPI000013E78B	.	deleterious_low_confidence(0)	possibly_damaging(0.813)	2/8	.	hmmpanther:PTHR15510	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTTCTGAA	.	5	ESCA
SPAG8	0	.	GRCh37	9	35811390	35811390	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.653G>C	p.Arg218Thr	p.R218T	ENST00000340291	2/8	41	31	9	103	103	0	SPAG8,missense_variant,p.Arg216Thr,ENST00000497810,;SPAG8,missense_variant,p.Arg218Thr,ENST00000340291,;SPAG8,missense_variant,p.Arg216Thr,ENST00000484764,;SPAG8,missense_variant,p.Arg218Thr,ENST00000396638,;HINT2,downstream_gene_variant,,ENST00000259667,;TMEM8B,upstream_gene_variant,,ENST00000377996,;NPR2,downstream_gene_variant,,ENST00000447210,;NPR2,downstream_gene_variant,,ENST00000421267,;NPR2,downstream_gene_variant,,ENST00000342694,;AL133410.1,downstream_gene_variant,,ENST00000582432,;SPAG8,non_coding_transcript_exon_variant,,ENST00000479751,;SPAG8,intron_variant,,ENST00000463889,;HINT2,downstream_gene_variant,,ENST00000474848,;HINT2,downstream_gene_variant,,ENST00000474908,;HINT2,downstream_gene_variant,,ENST00000472085,;HINT2,downstream_gene_variant,,ENST00000490578,;SPAG8,upstream_gene_variant,,ENST00000489063,;HINT2,downstream_gene_variant,,ENST00000471774,;HINT2,downstream_gene_variant,,ENST00000461169,;SPAG8,missense_variant,p.Arg218Thr,ENST00000475644,;SPAG8,intron_variant,,ENST00000471631,;SPAG8,intron_variant,,ENST00000495667,;SPAG8,intron_variant,,ENST00000472605,;SPAG8,upstream_gene_variant,,ENST00000460836,;NPR2,downstream_gene_variant,,ENST00000448821,;FAM221B,downstream_gene_variant,,ENST00000388950,;NPR2,downstream_gene_variant,,ENST00000464810,;NPR2,downstream_gene_variant,,ENST00000469249,;	G	ENSG00000137098	ENST00000340291	Transcript	missense_variant	778	653	218	R/T	aGa/aCa	.	.	.	-1	SPAG8	HGNC	14105	protein_coding	YES	CCDS6592.1	ENSP00000340982	SPAG8_HUMAN	F8WBP3_HUMAN	UPI000013E78B	.	deleterious_low_confidence(0.05)	benign(0.376)	2/8	.	hmmpanther:PTHR15510	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTTCTGAAC	.	5	ESCA
PRUNE2	0	.	GRCh37	9	79321817	79321817	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5373A>C	p.Glu1791Asp	p.E1791D	ENST00000376718	8/19	28	20	8	31	31	0	PRUNE2,missense_variant,p.Glu1113Asp,ENST00000426088,;PRUNE2,missense_variant,p.Glu1791Asp,ENST00000376718,;PRUNE2,missense_variant,p.Glu1432Asp,ENST00000428286,;PRUNE2,upstream_gene_variant,,ENST00000480674,;	G	ENSG00000106772	ENST00000376718	Transcript	missense_variant	5497	5373	1791	E/D	gaA/gaC	.	.	.	-1	PRUNE2	HGNC	25209	protein_coding	YES	CCDS47982.1	ENSP00000365908	PRUN2_HUMAN	.	UPI0001612CC0	.	tolerated(0.14)	benign(0.179)	8/19	.	hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTGTTTCTGG	.	5	ESCA
ZNF484	0	.	GRCh37	9	95610494	95610494	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.581A>G	p.Tyr194Cys	p.Y194C	ENST00000395506	4/4	31	5	26	30	30	0	ZNF484,missense_variant,p.Tyr194Cys,ENST00000395506,;ZNF484,missense_variant,p.Tyr156Cys,ENST00000395505,;ZNF484,missense_variant,p.Tyr156Cys,ENST00000332591,;ZNF484,missense_variant,p.Tyr192Cys,ENST00000375495,;ANKRD19P,intron_variant,,ENST00000473204,;	C	ENSG00000127081	ENST00000395506	Transcript	missense_variant	677	581	194	Y/C	tAt/tGt	.	.	.	-1	ZNF484	HGNC	23385	protein_coding	YES	CCDS59136.1	ENSP00000378882	ZN484_HUMAN	.	UPI00017A7C2E	.	tolerated(0.15)	benign(0.005)	4/4	.	hmmpanther:PTHR24377:SF144,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATTATATAAG	.	5	ESCA
PTCH1	0	.	GRCh37	9	98242359	98242361	+	Frame_Shift_Ins	INS	GCC	GCC	TCCA	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	GCC	GCC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.957_959delGGCinsTGGA	p.Met319IlefsTer118	p.M319Ifs*118	ENST00000331920	7/24	34	31	3	75	75	0	PTCH1,frameshift_variant,p.Met168IlefsTer?,ENST00000547672,;PTCH1,frameshift_variant,p.Met319IlefsTer118,ENST00000331920,;PTCH1,frameshift_variant,p.Met253IlefsTer118,ENST00000430669,;PTCH1,frameshift_variant,p.Met168IlefsTer118,ENST00000418258,;PTCH1,frameshift_variant,p.Met168IlefsTer?,ENST00000553011,;PTCH1,frameshift_variant,p.Met168IlefsTer118,ENST00000421141,;PTCH1,frameshift_variant,p.Met36IlefsTer118,ENST00000375271,;PTCH1,frameshift_variant,p.Met168IlefsTer?,ENST00000551845,;PTCH1,frameshift_variant,p.Met168IlefsTer?,ENST00000546820,;PTCH1,frameshift_variant,p.Met318IlefsTer118,ENST00000375274,;PTCH1,frameshift_variant,p.Met39IlefsTer?,ENST00000548420,;PTCH1,frameshift_variant,p.Met168IlefsTer118,ENST00000429896,;PTCH1,frameshift_variant,p.Met253IlefsTer118,ENST00000437951,;PTCH1,downstream_gene_variant,,ENST00000551630,;PTCH1,downstream_gene_variant,,ENST00000468211,;PTCH1,downstream_gene_variant,,ENST00000548379,;PTCH1,downstream_gene_variant,,ENST00000553256,;PTCH1,downstream_gene_variant,,ENST00000548945,;PTCH1,frameshift_variant,p.Met198IlefsTer118,ENST00000375290,;PTCH1,non_coding_transcript_exon_variant,,ENST00000488809,;PTCH1,downstream_gene_variant,,ENST00000550914,;PTCH1,downstream_gene_variant,,ENST00000550136,;PTCH1,downstream_gene_variant,,ENST00000551623,;	TCCA	ENSG00000185920	ENST00000331920	Transcript	frameshift_variant	1257-1259	957-959	319-320	MA/IGX	atGGCc/atTGGAc	.	.	.	-1	PTCH1	HGNC	9585	protein_coding	YES	CCDS6714.1	ENSP00000332353	PTC1_HUMAN	Q6TKQ0_HUMAN,F8VXL8_HUMAN,F8VQS6_HUMAN	UPI00001AFF9C	.	.	.	7/24	.	TIGRFAM_domain:TIGR00918,hmmpanther:PTHR10796:SF61,hmmpanther:PTHR10796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	ACAAGGGCCATATC	.	3	ESCA
SLC25A5	0	.	GRCh37	X	118604452	118604452	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715A>G	p.Met239Val	p.M239V	ENST00000317881	3/4	15	5	9	30	30	0	SLC25A5,missense_variant,p.Met239Val,ENST00000317881,;SLC25A5-AS1,upstream_gene_variant,,ENST00000609227,;SLC25A5-AS1,upstream_gene_variant,,ENST00000446986,;SLC25A5-AS1,upstream_gene_variant,,ENST00000445759,;SLC25A5,non_coding_transcript_exon_variant,,ENST00000463551,;SLC25A5,non_coding_transcript_exon_variant,,ENST00000460013,;SLC25A5,downstream_gene_variant,,ENST00000475354,;SLC25A5-AS1,upstream_gene_variant,,ENST00000395539,;	G	ENSG00000005022	ENST00000317881	Transcript	missense_variant	831	715	239	M/V	Atg/Gtg	.	.	.	1	SLC25A5	HGNC	10991	protein_coding	YES	CCDS14578.1	ENSP00000360671	ADT2_HUMAN	Q6NVC0_HUMAN	UPI000013C4ED	.	deleterious(0.04)	possibly_damaging(0.472)	3/4	.	PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF160,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588,Prints_domain:PR00926	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATGATGATG	.	5	ESCA
TLR8	0	.	GRCh37	X	12938288	12938288	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1129T>C	p.Tyr377His	p.Y377H	ENST00000218032	2/2	51	17	33	97	97	0	TLR8,missense_variant,p.Tyr395His,ENST00000311912,;TLR8,missense_variant,p.Tyr377His,ENST00000218032,;	C	ENSG00000101916	ENST00000218032	Transcript	missense_variant	1216	1129	377	Y/H	Tat/Cat	.	.	.	1	TLR8	HGNC	15632	protein_coding	YES	CCDS14152.1	ENSP00000218032	TLR8_HUMAN	Q8NC00_HUMAN,B4DLJ2_HUMAN	UPI000004BAFC	.	deleterious(0)	probably_damaging(0.993)	2/2	.	hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF227,Gene3D:3.80.10.10,SMART_domains:SM00369	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTTATGTG	.	5	ESCA
FAM127A	0	.	GRCh37	X	134167513	134167513	+	3'UTR	SNP	A	A	G	novel	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*758A>G	.	.	ENST00000257013	1/1	25	19	6	60	60	0	FAM127A,3_prime_UTR_variant,,ENST00000257013,;FAM127A,non_coding_transcript_exon_variant,,ENST00000464369,;FAM127A,downstream_gene_variant,,ENST00000495563,;	G	ENSG00000134590	ENST00000257013	Transcript	3_prime_UTR_variant	1181	.	.	.	.	.	.	.	1	FAM127A	HGNC	2569	protein_coding	YES	CCDS43997.1	ENSP00000257013	F127A_HUMAN	.	UPI00000373C5	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTAATACAC	.	5	ESCA
TMEM257	0	.	GRCh37	X	144909318	144909318	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-XP-A8T8-01A-11D-A36J-09	TCGA-XP-A8T8-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.123C>A	p.Phe41Leu	p.F41L	ENST00000408967	1/1	37	7	30	70	70	0	TMEM257,missense_variant,p.Phe41Leu,ENST00000408967,;SLITRK2,downstream_gene_variant,,ENST00000370490,;SLITRK2,downstream_gene_variant,,ENST00000434188,;SLITRK2,downstream_gene_variant,,ENST00000428560,;SLITRK2,downstream_gene_variant,,ENST00000413937,;SLITRK2,downstream_gene_variant,,ENST00000447897,;SLITRK2,downstream_gene_variant,,ENST00000335565,;	A	ENSG00000221870	ENST00000408967	Transcript	missense_variant	391	123	41	F/L	ttC/ttA	COSM1116442	.	.	1	TMEM257	HGNC	2562	protein_coding	YES	CCDS14681.1	ENSP00000386149	TM257_HUMAN	.	UPI0000128753	.	tolerated_low_confidence(0.23)	benign(0.294)	1/1	.	Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCTGTTT	.	5	ESCA
GTPBP4	0	.	GRCh37	10	1061784	1061784	+	Missense_Mutation	SNP	G	G	C	rs201965992	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1700G>C	p.Ser567Thr	p.S567T	ENST00000360803	16/17	136	117	18	150	150	0	GTPBP4,missense_variant,p.Ser520Thr,ENST00000545048,;GTPBP4,missense_variant,p.Ser567Thr,ENST00000360803,;GTPBP4,missense_variant,p.Ser451Thr,ENST00000538293,;IDI2,downstream_gene_variant,,ENST00000277517,;GTPBP4,non_coding_transcript_exon_variant,,ENST00000483839,;	C	ENSG00000107937	ENST00000360803	Transcript	missense_variant	1782	1700	567	S/T	aGt/aCt	rs201965992,COSM1253892	.	.	1	GTPBP4	HGNC	21535	protein_coding	YES	CCDS31132.1	ENSP00000354040	NOG1_HUMAN	Q5T3R7_HUMAN,D2CFK9_HUMAN,B7Z7A3_HUMAN,B4DY13_HUMAN	UPI000000D960	.	tolerated(0.14)	benign(0.359)	16/17	.	hmmpanther:PTHR11702:SF23,hmmpanther:PTHR11702,PIRSF_domain:PIRSF038919	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGGAGTGGGA	byCluster	4	ESCA
SEC23IP	0	.	GRCh37	10	121685688	121685688	+	Silent	SNP	C	C	T	rs758619932	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2262C>T	p.%3D	p.C754C	ENST00000369075	13/19	116	104	11	70	70	0	SEC23IP,synonymous_variant,p.%3D,ENST00000543134,;SEC23IP,synonymous_variant,p.%3D,ENST00000369075,;SEC23IP,upstream_gene_variant,,ENST00000475542,;	T	ENSG00000107651	ENST00000369075	Transcript	synonymous_variant	2334	2262	754	C	tgC/tgT	rs758619932	.	.	1	SEC23IP	HGNC	17018	protein_coding	YES	CCDS7618.1	ENSP00000358071	S23IP_HUMAN	.	UPI000006FCCE	.	.	.	13/19	.	hmmpanther:PTHR15457,hmmpanther:PTHR15457:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCTTGCGTGTC	byFrequency	3	ESCA
ATE1	0	.	GRCh37	10	123659471	123659471	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.814-987C>G	.	.	ENST00000369043	.	50	43	6	43	43	0	ATE1,missense_variant,p.Phe281Leu,ENST00000423243,;ATE1,missense_variant,p.Phe284Leu,ENST00000224652,;ATE1,missense_variant,p.Phe169Leu,ENST00000543447,;ATE1,5_prime_UTR_variant,,ENST00000535655,;ATE1,intron_variant,,ENST00000369043,;ATE1,intron_variant,,ENST00000540606,;ATE1,intron_variant,,ENST00000369040,;ATE1,downstream_gene_variant,,ENST00000455628,;ATE1,intron_variant,,ENST00000481784,;	C	ENSG00000107669	ENST00000369043	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ATE1	HGNC	782	protein_coding	YES	CCDS31299.1	ENSP00000358039	ATE1_HUMAN	B4E107_HUMAN	UPI000002A471	.	.	.	.	6/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTTGAACTG	.	4	ESCA
GPR158	0	.	GRCh37	10	25465155	25465155	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806A>T	p.Tyr269Phe	p.Y269F	ENST00000376351	1/11	60	55	5	72	72	0	GPR158,missense_variant,p.Tyr269Phe,ENST00000376351,;GPR158-AS1,non_coding_transcript_exon_variant,,ENST00000449643,;	T	ENSG00000151025	ENST00000376351	Transcript	missense_variant	1165	806	269	Y/F	tAt/tTt	.	.	.	1	GPR158	HGNC	23689	protein_coding	YES	CCDS31166.1	ENSP00000365529	GP158_HUMAN	.	UPI0000199875	.	tolerated(0.78)	benign(0.002)	1/11	.	hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTATCTGG	.	2	ESCA
MYO3A	0	.	GRCh37	10	26482174	26482174	+	Silent	SNP	A	A	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4479A>C	p.%3D	p.P1493P	ENST00000265944	32/35	120	112	8	130	130	0	MYO3A,synonymous_variant,p.%3D,ENST00000265944,;MYO3A,intron_variant,,ENST00000543632,;	C	ENSG00000095777	ENST00000265944	Transcript	synonymous_variant	4645	4479	1493	P	ccA/ccC	.	.	.	1	MYO3A	HGNC	7601	protein_coding	YES	CCDS7148.1	ENSP00000265944	MYO3A_HUMAN	.	UPI000014140A	.	.	.	32/35	.	hmmpanther:PTHR13140:SF348,hmmpanther:PTHR13140,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCCCCAAGACG	.	2	ESCA
AGAP7	0	.	GRCh37	10	51465318	51465318	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1138C>A	p.Leu380Ile	p.L380I	ENST00000374095	7/7	291	234	57	256	256	0	AGAP7,missense_variant,p.Leu380Ile,ENST00000374095,;	T	ENSG00000204169	ENST00000374095	Transcript	missense_variant	1264	1138	380	L/I	Cta/Ata	COSM685061	.	.	-1	AGAP7	HGNC	23465	protein_coding	YES	CCDS41524.1	ENSP00000363208	AGAP7_HUMAN	.	UPI000016167D	.	tolerated(0.06)	benign(0.334)	7/7	.	SMART_domains:SM00233,Gene3D:2.30.29.30,hmmpanther:PTHR23180,Pfam_domain:PF00169,hmmpanther:PTHR23180:SF213,PROSITE_profiles:PS50003,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTTAGGTGTT	.	4	ESCA
ARID5B	0	.	GRCh37	10	63856031	63856031	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3242C>G	.	.	ENST00000279873	10/10	109	89	20	77	77	0	ARID5B,3_prime_UTR_variant,,ENST00000279873,;ARID5B,downstream_gene_variant,,ENST00000309334,;	G	ENSG00000150347	ENST00000279873	Transcript	3_prime_UTR_variant	7219	.	.	.	.	.	.	.	1	ARID5B	HGNC	17362	protein_coding	YES	CCDS31208.1	ENSP00000279873	ARI5B_HUMAN	.	UPI00001606F0	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTGTCTGATG	.	5	ESCA
WAPAL	0	.	GRCh37	10	88196064	88196064	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1236A>G	.	.	ENST00000298767	19/19	96	78	18	92	92	0	WAPAL,3_prime_UTR_variant,,ENST00000298767,;WAPAL,downstream_gene_variant,,ENST00000372075,;WAPAL,downstream_gene_variant,,ENST00000263070,;WAPAL,non_coding_transcript_exon_variant,,ENST00000484070,;	C	ENSG00000062650	ENST00000298767	Transcript	3_prime_UTR_variant	5282	.	.	.	.	.	.	.	-1	WAPAL	HGNC	23293	protein_coding	YES	CCDS7375.1	ENSP00000298767	WAPL_HUMAN	B3Y1W2_HUMAN,B2RTX8_HUMAN	UPI00001AE41A	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGATGTAAC	.	5	ESCA
BMPR1A	0	.	GRCh37	10	88683192	88683192	+	Missense_Mutation	SNP	G	G	A	rs199907158	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1402G>A	p.Glu468Lys	p.E468K	ENST00000372037	12/13	138	125	13	108	108	0	BMPR1A,missense_variant,p.Glu468Lys,ENST00000372037,;	A	ENSG00000107779	ENST00000372037	Transcript	missense_variant	1939	1402	468	E/K	Gaa/Aaa	rs199907158	.	.	1	BMPR1A	HGNC	1076	protein_coding	YES	CCDS7378.1	ENSP00000361107	BMR1A_HUMAN	.	UPI000006EB08	.	deleterious(0)	probably_damaging(0.998)	12/13	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255:SF50,hmmpanther:PTHR23255,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATACGAAGAT	byCluster|by1000G	4	ESCA
IDE	0	.	GRCh37	10	94274755	94274755	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.706G>C	p.Asp236His	p.D236H	ENST00000265986	5/25	112	99	13	86	86	0	IDE,missense_variant,p.Asp222His,ENST00000436178,;IDE,missense_variant,p.Asp236His,ENST00000265986,;IDE,3_prime_UTR_variant,,ENST00000478361,;	G	ENSG00000119912	ENST00000265986	Transcript	missense_variant	763	706	236	D/H	Gat/Cat	COSM1474865	.	.	-1	IDE	HGNC	5381	protein_coding	YES	CCDS7421.1	ENSP00000265986	IDE_HUMAN	.	UPI000013D6B6	.	deleterious(0.01)	possibly_damaging(0.894)	5/25	.	Superfamily_domains:SSF63411,Gene3D:3.30.830.10,hmmpanther:PTHR11851:SF85,hmmpanther:PTHR11851	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACATCAATGC	.	4	ESCA
OR10G8	0	.	GRCh37	11	123900508	123900508	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.179T>C	p.Phe60Ser	p.F60S	ENST00000431524	1/1	149	143	6	172	172	0	OR10G8,missense_variant,p.Phe60Ser,ENST00000431524,;	C	ENSG00000234560	ENST00000431524	Transcript	missense_variant	212	179	60	F/S	tTc/tCc	.	.	.	1	OR10G8	HGNC	14845	protein_coding	YES	CCDS31704.1	ENSP00000389072	O10G8_HUMAN	.	UPI0000040A8F	.	deleterious(0)	probably_damaging(0.955)	1/1	.	Transmembrane_helices:TMhelix,Prints_domain:PR00237,Superfamily_domains:SSF81321,Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF146,PROSITE_profiles:PS50262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTACTTCCTCA	.	2	ESCA
NTM	0	.	GRCh37	11	132016295	132016295	+	Missense_Mutation	SNP	C	C	T	rs758413842	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287C>T	p.Thr96Met	p.T96M	ENST00000425719	2/8	72	53	19	62	62	0	NTM,missense_variant,p.Thr96Met,ENST00000374784,;NTM,missense_variant,p.Thr96Met,ENST00000374791,;NTM,missense_variant,p.Thr96Met,ENST00000539799,;NTM,missense_variant,p.Thr96Met,ENST00000425719,;NTM,missense_variant,p.Thr87Met,ENST00000550167,;NTM,missense_variant,p.Thr96Met,ENST00000374786,;NTM,missense_variant,p.Thr87Met,ENST00000427481,;NTM,non_coding_transcript_exon_variant,,ENST00000467255,;NTM,intron_variant,,ENST00000498764,;NTM,non_coding_transcript_exon_variant,,ENST00000479431,;	T	ENSG00000182667	ENST00000425719	Transcript	missense_variant	307	287	96	T/M	aCg/aTg	rs758413842	.	.	1	NTM	HGNC	17941	protein_coding	YES	CCDS44777.1	ENSP00000396722	NTRI_HUMAN	.	UPI00001A58B9	.	tolerated(0.1)	probably_damaging(0.947)	2/8	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19831:SF46,hmmpanther:PTHR19831,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAACGCAGT	byFrequency	5	ESCA
E2F8	0	.	GRCh37	11	19246919	19246919	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2270G>C	p.Gly757Ala	p.G757A	ENST00000527884	12/13	58	52	6	46	46	0	E2F8,missense_variant,p.Gly757Ala,ENST00000527884,;E2F8,missense_variant,p.Gly757Ala,ENST00000250024,;RP11-428C19.4,intron_variant,,ENST00000527978,;E2F8,downstream_gene_variant,,ENST00000529188,;	G	ENSG00000129173	ENST00000527884	Transcript	missense_variant	2503	2270	757	G/A	gGa/gCa	.	.	.	-1	E2F8	HGNC	24727	protein_coding	YES	CCDS7849.1	ENSP00000434199	E2F8_HUMAN	E9PMT9_HUMAN	UPI00001F9E94	.	tolerated(0.98)	benign(0.007)	12/13	.	hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGATTCCAGAC	.	4	ESCA
OR8I2	0	.	GRCh37	11	55861330	55861330	+	Missense_Mutation	SNP	C	C	G	rs756072924	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547C>G	p.Leu183Val	p.L183V	ENST00000302124	1/1	40	28	12	22	22	0	OR8I2,missense_variant,p.Leu183Val,ENST00000302124,;OR8I4P,downstream_gene_variant,,ENST00000526965,;	G	ENSG00000172154	ENST00000302124	Transcript	missense_variant	578	547	183	L/V	Ctt/Gtt	rs756072924,COSM136009	.	.	1	OR8I2	HGNC	15310	protein_coding	YES	CCDS31517.1	ENSP00000303864	OR8I2_HUMAN	H0YLY8_HUMAN	UPI0000041D16	.	tolerated(0.11)	benign(0.275)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCTTTTA	.	5	ESCA
DAGLA	0	.	GRCh37	11	61496471	61496471	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.840C>T	p.%3D	p.L280L	ENST00000257215	8/20	59	39	20	54	54	0	DAGLA,synonymous_variant,p.%3D,ENST00000257215,;DAGLA,3_prime_UTR_variant,,ENST00000540717,;	T	ENSG00000134780	ENST00000257215	Transcript	synonymous_variant	956	840	280	L	ctC/ctT	.	.	.	1	DAGLA	HGNC	1165	protein_coding	YES	CCDS31578.1	ENSP00000257215	DGLA_HUMAN	.	UPI00001678B3	.	.	.	8/20	.	hmmpanther:PTHR21493,hmmpanther:PTHR21493:SF87	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCTCAAGAA	.	5	ESCA
METTL12	0	.	GRCh37	11	62435298	62435298	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*775C>G	.	.	ENST00000532971	3/3	16	12	4	10	10	0	METTL12,3_prime_UTR_variant,,ENST00000532971,;C11orf48,intron_variant,,ENST00000528115,;C11orf48,intron_variant,,ENST00000528862,;C11orf48,intron_variant,,ENST00000354588,;C11orf48,intron_variant,,ENST00000532208,;C11orf48,intron_variant,,ENST00000415855,;C11orf48,intron_variant,,ENST00000431002,;C11orf48,upstream_gene_variant,,ENST00000525675,;C11orf48,upstream_gene_variant,,ENST00000524958,;RP11-831H9.11,upstream_gene_variant,,ENST00000528405,;C11orf83,upstream_gene_variant,,ENST00000531323,;C11orf83,upstream_gene_variant,,ENST00000377953,;C11orf48,downstream_gene_variant,,ENST00000377954,;C11orf48,downstream_gene_variant,,ENST00000526490,;SNORA57,downstream_gene_variant,,ENST00000383870,;METTL12,downstream_gene_variant,,ENST00000398922,;METTL12,downstream_gene_variant,,ENST00000594728,;METTL12,non_coding_transcript_exon_variant,,ENST00000529868,;C11orf48,intron_variant,,ENST00000524759,;C11orf48,intron_variant,,ENST00000527679,;C11orf48,upstream_gene_variant,,ENST00000532786,;	G	ENSG00000214756	ENST00000532971	Transcript	3_prime_UTR_variant	1755	.	.	.	.	.	.	.	1	METTL12	HGNC	33113	protein_coding	YES	CCDS41657.1	ENSP00000431287	MET12_HUMAN	.	UPI0000D4EAB2	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCTCATACC	.	2	ESCA
ESRRA	0	.	GRCh37	11	64081786	64081786	+	Missense_Mutation	SNP	C	C	T	rs45585533	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.518C>T	p.Pro173Leu	p.P173L	ENST00000405666	4/7	65	56	9	87	87	0	ESRRA,missense_variant,p.Pro11Leu,ENST00000545035,;ESRRA,missense_variant,p.Pro173Leu,ENST00000405666,;ESRRA,missense_variant,p.Pro173Leu,ENST00000000442,;ESRRA,missense_variant,p.Pro173Leu,ENST00000406310,;ESRRA,missense_variant,p.Pro30Leu,ENST00000539594,;TRMT112,downstream_gene_variant,,ENST00000544844,;PRDX5,upstream_gene_variant,,ENST00000265462,;TRMT112,downstream_gene_variant,,ENST00000535750,;TRMT112,downstream_gene_variant,,ENST00000308774,;PRDX5,upstream_gene_variant,,ENST00000352435,;PRDX5,upstream_gene_variant,,ENST00000347941,;TRMT112,downstream_gene_variant,,ENST00000539854,;TRMT112,downstream_gene_variant,,ENST00000535126,;ESRRA,non_coding_transcript_exon_variant,,ENST00000467987,;TRMT112,downstream_gene_variant,,ENST00000537918,;	T	ENSG00000173153	ENST00000405666	Transcript	missense_variant	752	518	173	P/L	cCg/cTg	rs45585533,COSM930072	.	.	1	ESRRA	HGNC	3471	protein_coding	YES	CCDS41667.1	ENSP00000384851	ERR1_HUMAN	Q96I02_HUMAN,Q96F89_HUMAN,Q569H8_HUMAN,F5H0E9_HUMAN,F5GWT5_HUMAN	UPI0000167B87	.	tolerated(0.44)	benign(0.001)	4/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24084,Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527,PIRSF_domain:PIRSF500939	.	.	.	.	.	.	.	T:0	T:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTCCCGGGCC	byFrequency|byCluster	4	ESCA
SSSCA1	0	.	GRCh37	11	65338969	65338969	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.364C>G	p.Pro122Ala	p.P122A	ENST00000309328	4/4	41	28	13	47	47	0	SSSCA1,missense_variant,p.Pro85Ala,ENST00000531405,;SSSCA1,missense_variant,p.Pro122Ala,ENST00000309328,;SSSCA1,missense_variant,p.Pro116Ala,ENST00000533115,;SSSCA1,3_prime_UTR_variant,,ENST00000526877,;SSSCA1,intron_variant,,ENST00000526433,;SSSCA1,intron_variant,,ENST00000527920,;EHBP1L1,upstream_gene_variant,,ENST00000309295,;FAM89B,upstream_gene_variant,,ENST00000316409,;FAM89B,upstream_gene_variant,,ENST00000530349,;FAM89B,upstream_gene_variant,,ENST00000449319,;EHBP1L1,upstream_gene_variant,,ENST00000533237,;SSSCA1-AS1,upstream_gene_variant,,ENST00000567594,;SSSCA1,non_coding_transcript_exon_variant,,ENST00000527413,;	G	ENSG00000173465	ENST00000309328	Transcript	missense_variant	426	364	122	P/A	Ccg/Gcg	.	.	.	1	SSSCA1	HGNC	11328	protein_coding	YES	CCDS8104.1	ENSP00000312318	SSA27_HUMAN	H0YEB6_HUMAN,G3V1B8_HUMAN	UPI0000125070	.	tolerated(0.09)	benign(0.015)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGTCCGGAG	.	5	ESCA
SSSCA1	0	.	GRCh37	11	65339076	65339076	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.471C>G	p.%3D	p.L157L	ENST00000309328	4/4	51	39	11	73	73	0	SSSCA1,synonymous_variant,p.%3D,ENST00000531405,;SSSCA1,synonymous_variant,p.%3D,ENST00000309328,;SSSCA1,synonymous_variant,p.%3D,ENST00000533115,;SSSCA1,3_prime_UTR_variant,,ENST00000526877,;SSSCA1,intron_variant,,ENST00000526433,;SSSCA1,intron_variant,,ENST00000527920,;EHBP1L1,upstream_gene_variant,,ENST00000309295,;FAM89B,upstream_gene_variant,,ENST00000316409,;FAM89B,upstream_gene_variant,,ENST00000530349,;FAM89B,upstream_gene_variant,,ENST00000449319,;EHBP1L1,upstream_gene_variant,,ENST00000533237,;SSSCA1-AS1,upstream_gene_variant,,ENST00000567594,;SSSCA1,non_coding_transcript_exon_variant,,ENST00000527413,;	G	ENSG00000173465	ENST00000309328	Transcript	synonymous_variant	533	471	157	L	ctC/ctG	.	.	.	1	SSSCA1	HGNC	11328	protein_coding	YES	CCDS8104.1	ENSP00000312318	SSA27_HUMAN	H0YEB6_HUMAN,G3V1B8_HUMAN	UPI0000125070	.	.	.	4/4	.	hmmpanther:PTHR16537	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCTTGCA	.	5	ESCA
TMEM134	0	.	GRCh37	11	67232074	67232074	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11G>C	.	.	ENST00000308022	7/7	181	149	31	213	213	0	TMEM134,3_prime_UTR_variant,,ENST00000393877,;TMEM134,3_prime_UTR_variant,,ENST00000308022,;TMEM134,downstream_gene_variant,,ENST00000544903,;TMEM134,downstream_gene_variant,,ENST00000452789,;CTC-1337H24.1,downstream_gene_variant,,ENST00000602912,;CTC-1337H24.2,upstream_gene_variant,,ENST00000602944,;TMEM134,non_coding_transcript_exon_variant,,ENST00000541059,;TMEM134,non_coding_transcript_exon_variant,,ENST00000535813,;TMEM134,3_prime_UTR_variant,,ENST00000545682,;TMEM134,3_prime_UTR_variant,,ENST00000536020,;TMEM134,non_coding_transcript_exon_variant,,ENST00000543661,;TMEM134,non_coding_transcript_exon_variant,,ENST00000535175,;TMEM134,downstream_gene_variant,,ENST00000501408,;TMEM134,downstream_gene_variant,,ENST00000535585,;TMEM134,downstream_gene_variant,,ENST00000537601,;TMEM134,downstream_gene_variant,,ENST00000538561,;TMEM134,downstream_gene_variant,,ENST00000536773,;TMEM134,downstream_gene_variant,,ENST00000540133,;TMEM134,downstream_gene_variant,,ENST00000541598,;	G	ENSG00000172663	ENST00000308022	Transcript	3_prime_UTR_variant	641	.	.	.	.	.	.	.	-1	TMEM134	HGNC	26142	protein_coding	YES	CCDS8167.1	ENSP00000312615	TM134_HUMAN	.	UPI0000071C39	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACGCTGCGC	.	5	ESCA
PPFIA1	0	.	GRCh37	11	70218320	70218320	+	Splice_Site	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2866-1G>C	.	p.X956_splice	ENST00000253925	.	91	79	12	64	64	0	PPFIA1,splice_acceptor_variant,,ENST00000253925,;PPFIA1,splice_acceptor_variant,,ENST00000389547,;AP000487.5,downstream_gene_variant,,ENST00000530690,;AP000487.5,downstream_gene_variant,,ENST00000500185,;PPFIA1,splice_acceptor_variant,,ENST00000530548,;PPFIA1,splice_acceptor_variant,,ENST00000525922,;PPFIA1,splice_acceptor_variant,,ENST00000532504,;PPFIA1,splice_region_variant,,ENST00000526262,;PPFIA1,non_coding_transcript_exon_variant,,ENST00000531657,;	C	ENSG00000131626	ENST00000253925	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	PPFIA1	HGNC	9245	protein_coding	YES	CCDS31627.1	ENSP00000253925	LIPA1_HUMAN	E9PPF6_HUMAN,E9PID5_HUMAN,B3KVS8_HUMAN	UPI0000072426	.	.	.	.	21/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCAGACACT	.	4	ESCA
OR10A6	0	.	GRCh37	11	7949268	7949268	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.942C>G	p.Ile314Met	p.I314M	ENST00000309838	1/1	57	44	13	57	57	0	OR10A6,missense_variant,p.Ile314Met,ENST00000309838,;	C	ENSG00000175393	ENST00000309838	Transcript	missense_variant	942	942	314	I/M	atC/atG	.	.	.	-1	OR10A6	HGNC	15132	protein_coding	YES	CCDS31420.1	ENSP00000312470	O10A6_HUMAN	.	UPI0000041DF4	.	tolerated(0.12)	benign(0.007)	1/1	.	hmmpanther:PTHR26453:SF30,hmmpanther:PTHR26453	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCAGATTGT	.	5	ESCA
DLG2	0	.	GRCh37	11	83170250	83170250	+	3'UTR	SNP	T	T	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*611A>T	.	.	ENST00000376104	28/28	128	123	5	110	110	0	DLG2,3_prime_UTR_variant,,ENST00000418306,;DLG2,3_prime_UTR_variant,,ENST00000426717,;DLG2,3_prime_UTR_variant,,ENST00000280241,;DLG2,3_prime_UTR_variant,,ENST00000398309,;DLG2,3_prime_UTR_variant,,ENST00000376104,;DLG2,3_prime_UTR_variant,,ENST00000543673,;DLG2,downstream_gene_variant,,ENST00000330014,;DLG2,downstream_gene_variant,,ENST00000532653,;DLG2,downstream_gene_variant,,ENST00000531015,;DLG2,downstream_gene_variant,,ENST00000524982,;DLG2,downstream_gene_variant,,ENST00000457267,;DLG2,downstream_gene_variant,,ENST00000537455,;DLG2,downstream_gene_variant,,ENST00000376106,;DLG2,downstream_gene_variant,,ENST00000404783,;DLG2,downstream_gene_variant,,ENST00000529159,;AP003026.1,upstream_gene_variant,,ENST00000420284,;	A	ENSG00000150672	ENST00000376104	Transcript	3_prime_UTR_variant	3851	.	.	.	.	.	.	.	-1	DLG2	HGNC	2901	protein_coding	YES	CCDS44690.1	ENSP00000365272	DLG2_HUMAN	F8W750_HUMAN,E9PQT9_HUMAN	UPI0000E59399	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCCTGTCAG	.	2	ESCA
SCUBE2	0	.	GRCh37	11	9068959	9068959	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1946C>G	p.Ser649Cys	p.S649C	ENST00000520467	16/22	64	52	12	66	66	0	SCUBE2,missense_variant,p.Ser649Cys,ENST00000457346,;SCUBE2,missense_variant,p.Ser494Cys,ENST00000450649,;SCUBE2,missense_variant,p.Ser620Cys,ENST00000309263,;SCUBE2,missense_variant,p.Ser649Cys,ENST00000520467,;RP11-467K18.2,intron_variant,,ENST00000531592,;SCUBE2,downstream_gene_variant,,ENST00000530265,;	C	ENSG00000175356	ENST00000520467	Transcript	missense_variant	2017	1946	649	S/C	tCt/tGt	.	.	.	-1	SCUBE2	HGNC	30425	protein_coding	YES	CCDS7797.2	ENSP00000429969	SCUB2_HUMAN	.	UPI0001E5E848	.	tolerated(0.13)	possibly_damaging(0.754)	16/22	.	hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTCAGATGTT	.	5	ESCA
TMEM41B	0	.	GRCh37	11	9336018	9336018	+	5'UTR	SNP	G	G	C	rs374661073	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-30C>G	.	.	ENST00000528080	1/7	60	36	23	64	64	0	TMEM41B,5_prime_UTR_variant,,ENST00000527813,;TMEM41B,5_prime_UTR_variant,,ENST00000528080,;TMEM41B,5_prime_UTR_variant,,ENST00000533723,;TMEM41B,5_prime_UTR_variant,,ENST00000524543,;TMEM41B,5_prime_UTR_variant,,ENST00000299596,;RP11-682B13.2,upstream_gene_variant,,ENST00000533804,;	C	ENSG00000166471	ENST00000528080	Transcript	5_prime_UTR_variant	310	.	.	.	.	rs374661073	.	.	-1	TMEM41B	HGNC	28948	protein_coding	YES	CCDS31424.1	ENSP00000433126	TM41B_HUMAN	.	UPI00001C1EF6	.	.	.	1/7	.	.	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCGGTGCCG	byCluster	5	ESCA
SESN3	0	.	GRCh37	11	94906420	94906420	+	Nonstop_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1478G>T	p.Ter493LeuextTer18	p.*493Lext*18	ENST00000536441	10/10	46	40	5	42	42	0	SESN3,stop_lost,p.Ter354LeuextTer18,ENST00000278499,;SESN3,stop_lost,p.Ter493LeuextTer18,ENST00000536441,;RP11-712B9.2,intron_variant,,ENST00000534864,;RP11-712B9.2,intron_variant,,ENST00000534891,;	A	ENSG00000149212	ENST00000536441	Transcript	stop_lost	1815	1478	493	*/L	tGa/tTa	.	.	.	-1	SESN3	HGNC	23060	protein_coding	YES	CCDS8303.1	ENSP00000441927	SESN3_HUMAN	.	UPI0000135891	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACTTCAGGTC	.	4	ESCA
SWAP70	0	.	GRCh37	11	9759811	9759811	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1132C>T	p.Gln378Ter	p.Q378*	ENST00000318950	8/12	26	19	7	35	35	0	SWAP70,stop_gained,p.Gln320Ter,ENST00000447399,;SWAP70,stop_gained,p.Gln378Ter,ENST00000318950,;SWAP70,downstream_gene_variant,,ENST00000534662,;SWAP70,3_prime_UTR_variant,,ENST00000534562,;SWAP70,non_coding_transcript_exon_variant,,ENST00000524817,;	T	ENSG00000133789	ENST00000318950	Transcript	stop_gained	1235	1132	378	Q/*	Cag/Tag	.	.	.	1	SWAP70	HGNC	17070	protein_coding	YES	CCDS31426.1	ENSP00000315630	SWP70_HUMAN	E9PJM7_HUMAN	UPI0000073652	.	.	.	8/12	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14383,hmmpanther:PTHR14383:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCAGACT	.	5	ESCA
UTP20	0	.	GRCh37	12	101706052	101706052	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2550C>G	p.Ile850Met	p.I850M	ENST00000261637	21/62	95	89	5	84	84	0	UTP20,missense_variant,p.Ile850Met,ENST00000261637,;	G	ENSG00000120800	ENST00000261637	Transcript	missense_variant	2724	2550	850	I/M	atC/atG	.	.	.	1	UTP20	HGNC	17897	protein_coding	YES	CCDS9081.1	ENSP00000261637	UTP20_HUMAN	.	UPI00001FB38B	.	deleterious(0.02)	possibly_damaging(0.495)	21/62	.	hmmpanther:PTHR17695:SF11,hmmpanther:PTHR17695,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTATCAAGTA	.	2	ESCA
YBX3	0	.	GRCh37	12	10851899	10851899	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*389T>C	.	.	ENST00000228251	10/10	97	74	23	95	95	0	YBX3,3_prime_UTR_variant,,ENST00000279550,;YBX3,3_prime_UTR_variant,,ENST00000228251,;YBX3,downstream_gene_variant,,ENST00000546164,;YBX3,downstream_gene_variant,,ENST00000544504,;YBX3,downstream_gene_variant,,ENST00000540975,;YBX3,downstream_gene_variant,,ENST00000366286,;YBX3,downstream_gene_variant,,ENST00000539204,;YBX3,non_coding_transcript_exon_variant,,ENST00000540447,;YBX3,downstream_gene_variant,,ENST00000541351,;YBX3,downstream_gene_variant,,ENST00000536823,;YBX3,downstream_gene_variant,,ENST00000366290,;YBX3,downstream_gene_variant,,ENST00000542641,;YBX3,downstream_gene_variant,,ENST00000542002,;	G	ENSG00000060138	ENST00000228251	Transcript	3_prime_UTR_variant	1709	.	.	.	.	.	.	.	-1	YBX3	HGNC	2428	protein_coding	YES	CCDS8630.1	ENSP00000228251	YBOX3_HUMAN	.	UPI000013DBD6	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATATATTTCA	.	5	ESCA
CIT	0	.	GRCh37	12	120128164	120128164	+	Missense_Mutation	SNP	C	C	T	rs371376893	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5978G>A	p.Arg1993Gln	p.R1993Q	ENST00000392521	47/48	51	43	8	55	55	0	CIT,missense_variant,p.Arg1564Gln,ENST00000392520,;CIT,missense_variant,p.Arg1951Gln,ENST00000261833,;CIT,missense_variant,p.Arg1993Gln,ENST00000392521,;CIT,non_coding_transcript_exon_variant,,ENST00000537607,;CIT,downstream_gene_variant,,ENST00000469414,;CIT,non_coding_transcript_exon_variant,,ENST00000545913,;CIT,downstream_gene_variant,,ENST00000544872,;	T	ENSG00000122966	ENST00000392521	Transcript	missense_variant	6034	5978	1993	R/Q	cGa/cAa	rs371376893	.	.	-1	CIT	HGNC	1985	protein_coding	YES	CCDS55891.1	ENSP00000376306	CTRO_HUMAN	.	UPI0000683C41	.	tolerated_low_confidence(0.07)	benign(0.004)	47/48	.	PIRSF_domain:PIRSF038145,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF26	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCTCGCGGG	byFrequency|byCluster	5	ESCA
SPPL3	0	.	GRCh37	12	121205249	121205249	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.921G>A	p.%3D	p.G307G	ENST00000353487	9/11	94	86	8	124	124	0	SPPL3,synonymous_variant,p.%3D,ENST00000353487,;SPPL3,downstream_gene_variant,,ENST00000543608,;SPPL3,downstream_gene_variant,,ENST00000536996,;SPPL3,downstream_gene_variant,,ENST00000543854,;SPPL3,non_coding_transcript_exon_variant,,ENST00000545209,;SPPL3,non_coding_transcript_exon_variant,,ENST00000392495,;	T	ENSG00000157837	ENST00000353487	Transcript	synonymous_variant	1425	921	307	G	ggG/ggA	.	.	.	-1	SPPL3	HGNC	30424	protein_coding	YES	CCDS9208.1	ENSP00000288680	SPPL3_HUMAN	F5H7J2_HUMAN,F5H6I1_HUMAN,F5H4Y6_HUMAN,F5H4L1_HUMAN,F5H2A2_HUMAN	UPI0000013590	.	.	.	9/11	.	hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF22,Pfam_domain:PF04258,SMART_domains:SM00730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGCGCCCGGA	.	3	ESCA
MLXIP	0	.	GRCh37	12	122618301	122618301	+	Frame_Shift_Del	DEL	C	C	-	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1500delC	p.Phe501LeufsTer8	p.F501Lfs*8	ENST00000319080	9/17	102	89	13	76	76	0	MLXIP,frameshift_variant,p.Phe108LeufsTer8,ENST00000538698,;MLXIP,frameshift_variant,p.Phe501LeufsTer8,ENST00000319080,;MLXIP,frameshift_variant,p.Phe91LeufsTer8,ENST00000377037,;MLXIP,upstream_gene_variant,,ENST00000366272,;MLXIP,downstream_gene_variant,,ENST00000535430,;MLXIP,upstream_gene_variant,,ENST00000542417,;MLXIP,upstream_gene_variant,,ENST00000535996,;MLXIP,non_coding_transcript_exon_variant,,ENST00000539861,;MLXIP,non_coding_transcript_exon_variant,,ENST00000541750,;MLXIP,non_coding_transcript_exon_variant,,ENST00000538061,;MLXIP,downstream_gene_variant,,ENST00000535876,;	-	ENSG00000175727	ENST00000319080	Transcript	frameshift_variant	1631	1499	500	T/X	aCc/ac	.	.	.	1	MLXIP	HGNC	17055	protein_coding	YES	.	ENSP00000312834	MLXIP_HUMAN	F5H321_HUMAN	UPI0000D6226F	.	.	.	9/17	.	hmmpanther:PTHR15741,hmmpanther:PTHR15741:SF23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CCACCACCTTTA	.	3	ESCA
ATP6V0A2	0	.	GRCh37	12	124232204	124232204	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1656G>C	p.Met552Ile	p.M552I	ENST00000330342	14/20	160	153	7	151	151	0	ATP6V0A2,missense_variant,p.Met552Ile,ENST00000330342,;ATP6V0A2,downstream_gene_variant,,ENST00000504192,;ATP6V0A2,upstream_gene_variant,,ENST00000534943,;ATP6V0A2,non_coding_transcript_exon_variant,,ENST00000536426,;ATP6V0A2,downstream_gene_variant,,ENST00000545059,;	C	ENSG00000185344	ENST00000330342	Transcript	missense_variant	1904	1656	552	M/I	atG/atC	.	.	.	1	ATP6V0A2	HGNC	18481	protein_coding	YES	CCDS9254.1	ENSP00000332247	VPP2_HUMAN	F5H847_HUMAN,F5H5F3_HUMAN,B4DQF7_HUMAN	UPI00001AFC09	.	deleterious(0)	possibly_damaging(0.718)	14/20	.	hmmpanther:PTHR11629,hmmpanther:PTHR11629:SF22,Pfam_domain:PF01496,PIRSF_domain:PIRSF001293	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAATGAAAAT	.	2	ESCA
PIWIL1	0	.	GRCh37	12	130847365	130847365	+	Silent	SNP	C	C	G	rs377358932	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2025C>G	p.%3D	p.L675L	ENST00000245255	17/21	70	66	4	77	77	0	PIWIL1,synonymous_variant,p.%3D,ENST00000245255,;PIWIL1,upstream_gene_variant,,ENST00000541480,;	G	ENSG00000125207	ENST00000245255	Transcript	synonymous_variant	2297	2025	675	L	ctC/ctG	rs377358932	.	.	1	PIWIL1	HGNC	9007	protein_coding	YES	CCDS9268.1	ENSP00000245255	PIWL1_HUMAN	F5H889_HUMAN,F5H3U6_HUMAN,F5H2F7_HUMAN,F5GZL9_HUMAN,F5GYG0_HUMAN,F5GWW4_HUMAN	UPI000007059F	.	.	.	17/21	.	Superfamily_domains:SSF53098,SMART_domains:SM00950,Pfam_domain:PF02171,Gene3D:3.30.420.10,hmmpanther:PTHR22892,hmmpanther:PTHR22892:SF31,PROSITE_profiles:PS50822	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCTCAAAGT	byFrequency|byCluster	2	ESCA
PXMP2	0	.	GRCh37	12	133277856	133277856	+	Silent	SNP	C	C	T	rs201001554	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.420C>T	p.%3D	p.F140F	ENST00000317479	4/5	136	110	26	157	157	0	PXMP2,missense_variant,p.Arg12Cys,ENST00000539093,;PXMP2,missense_variant,p.Arg12Cys,ENST00000545677,;RP13-672B3.2,missense_variant,p.Arg12Cys,ENST00000537262,;PXMP2,synonymous_variant,p.%3D,ENST00000317479,;PXMP2,synonymous_variant,p.%3D,ENST00000428960,;PXMP2,intron_variant,,ENST00000543589,;PXMP2,non_coding_transcript_exon_variant,,ENST00000454379,;	T	ENSG00000176894	ENST00000317479	Transcript	synonymous_variant	485	420	140	F	ttC/ttT	rs201001554	.	.	1	PXMP2	HGNC	9716	protein_coding	YES	CCDS9279.1	ENSP00000321271	PXMP2_HUMAN	.	UPI000016788C	.	.	.	4/5	.	hmmpanther:PTHR11266:SF7,hmmpanther:PTHR11266,Pfam_domain:PF04117	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTCGCCGC	byCluster|by1000G	5	ESCA
SOX5	0	.	GRCh37	12	23687057	23687057	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*96G>C	.	.	ENST00000451604	15/15	79	67	11	62	62	0	SOX5,3_prime_UTR_variant,,ENST00000309359,;SOX5,3_prime_UTR_variant,,ENST00000381381,;SOX5,3_prime_UTR_variant,,ENST00000546136,;SOX5,3_prime_UTR_variant,,ENST00000537393,;SOX5,3_prime_UTR_variant,,ENST00000541536,;SOX5,3_prime_UTR_variant,,ENST00000451604,;SOX5,3_prime_UTR_variant,,ENST00000396007,;SOX5,3_prime_UTR_variant,,ENST00000545921,;SOX5,downstream_gene_variant,,ENST00000367206,;	G	ENSG00000134532	ENST00000451604	Transcript	3_prime_UTR_variant	2490	.	.	.	.	.	.	.	-1	SOX5	HGNC	11201	protein_coding	YES	CCDS8699.1	ENSP00000398273	SOX5_HUMAN	T2CYZ2_HUMAN,F5GWL1_HUMAN	UPI000007405E	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGTCAGTGT	.	5	ESCA
CNTN1	0	.	GRCh37	12	41408098	41408098	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2182G>C	p.Ala728Pro	p.A728P	ENST00000551295	18/24	109	102	7	88	88	0	CNTN1,missense_variant,p.Ala728Pro,ENST00000551295,;CNTN1,missense_variant,p.Ala728Pro,ENST00000347616,;CNTN1,missense_variant,p.Ala717Pro,ENST00000348761,;CNTN1,splice_region_variant,,ENST00000550305,;	C	ENSG00000018236	ENST00000551295	Transcript	missense_variant	2299	2182	728	A/P	Gcg/Ccg	.	.	.	1	CNTN1	HGNC	2171	protein_coding	YES	CCDS8737.1	ENSP00000447006	CNTN1_HUMAN	F8VX96_HUMAN,F8VUI9_HUMAN,F8VUI8_HUMAN,F8VQW3_HUMAN	UPI0000127EBA	.	deleterious(0.01)	benign(0.275)	18/24	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF531,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATGGGCGGTA	.	2	ESCA
SCAF11	0	.	GRCh37	12	46349783	46349783	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.220-4273G>C	.	.	ENST00000369367	.	24	21	3	16	16	0	SCAF11,3_prime_UTR_variant,,ENST00000395454,;SCAF11,intron_variant,,ENST00000419565,;SCAF11,intron_variant,,ENST00000266589,;SCAF11,intron_variant,,ENST00000369367,;SCAF11,downstream_gene_variant,,ENST00000395453,;SCAF11,intron_variant,,ENST00000547018,;	G	ENSG00000139218	ENST00000369367	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SCAF11	HGNC	10784	protein_coding	YES	CCDS8748.2	ENSP00000358374	SCAFB_HUMAN	F8VXG7_HUMAN	UPI0000D481F2	.	.	.	.	3/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATAATCTTCCT	.	2	ESCA
SLC48A1	0	.	GRCh37	12	48174229	48174229	+	3'UTR	SNP	T	T	C	rs780184509	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*165T>C	.	.	ENST00000442218	3/3	99	77	22	97	97	0	SLC48A1,3_prime_UTR_variant,,ENST00000442218,;SLC48A1,intron_variant,,ENST00000442892,;HDAC7,downstream_gene_variant,,ENST00000552960,;HDAC7,downstream_gene_variant,,ENST00000380610,;HDAC7,downstream_gene_variant,,ENST00000354334,;SLC48A1,downstream_gene_variant,,ENST00000549243,;SLC48A1,downstream_gene_variant,,ENST00000548498,;HDAC7,downstream_gene_variant,,ENST00000080059,;HDAC7,downstream_gene_variant,,ENST00000548080,;HDAC7,downstream_gene_variant,,ENST00000427332,;SLC48A1,downstream_gene_variant,,ENST00000547002,;AC004466.1,upstream_gene_variant,,ENST00000599515,;HDAC7,downstream_gene_variant,,ENST00000549883,;SLC48A1,downstream_gene_variant,,ENST00000461620,;SLC48A1,downstream_gene_variant,,ENST00000476104,;SLC48A1,3_prime_UTR_variant,,ENST00000551301,;HDAC7,downstream_gene_variant,,ENST00000477203,;HDAC7,downstream_gene_variant,,ENST00000548938,;HDAC7,downstream_gene_variant,,ENST00000459625,;HDAC7,downstream_gene_variant,,ENST00000470668,;HDAC7,downstream_gene_variant,,ENST00000547259,;	C	ENSG00000211584	ENST00000442218	Transcript	3_prime_UTR_variant	703	.	.	.	.	rs780184509	.	.	1	SLC48A1	HGNC	26035	protein_coding	YES	CCDS8755.2	ENSP00000415998	HRG1_HUMAN	F8VQX9_HUMAN	UPI00001FC0AF	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCCTTTCGA	.	5	ESCA
ASIC1	0	.	GRCh37	12	50474327	50474327	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1252G>C	p.Glu418Gln	p.E418Q	ENST00000228468	9/12	95	90	5	68	68	0	ASIC1,missense_variant,p.Glu17Gln,ENST00000552633,;ASIC1,missense_variant,p.Glu418Gln,ENST00000228468,;ASIC1,missense_variant,p.Glu452Gln,ENST00000552438,;ASIC1,missense_variant,p.Glu286Gln,ENST00000453327,;ASIC1,missense_variant,p.Glu418Gln,ENST00000447966,;SMARCD1,upstream_gene_variant,,ENST00000550477,;SMARCD1,upstream_gene_variant,,ENST00000394963,;SMARCD1,upstream_gene_variant,,ENST00000551966,;SMARCD1,upstream_gene_variant,,ENST00000381513,;ASIC1,3_prime_UTR_variant,,ENST00000550558,;ASIC1,non_coding_transcript_exon_variant,,ENST00000551199,;SMARCD1,upstream_gene_variant,,ENST00000547637,;SMARCD1,upstream_gene_variant,,ENST00000547247,;ASIC1,downstream_gene_variant,,ENST00000549792,;ASIC1,downstream_gene_variant,,ENST00000548350,;	C	ENSG00000110881	ENST00000228468	Transcript	missense_variant	1637	1252	418	E/Q	Gag/Cag	.	.	.	1	ASIC1	HGNC	100	protein_coding	YES	CCDS8796.1	ENSP00000228468	ASIC1_HUMAN	.	UPI000013C8D6	.	deleterious(0)	probably_damaging(0.976)	9/12	.	hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF110,Gene3D:1.10.287.770,Pfam_domain:PF00858,Prints_domain:PR01078	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTATGAGACC	.	2	ESCA
KRT81	0	.	GRCh37	12	52681085	52681085	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1048G>T	p.Val350Leu	p.V350L	ENST00000327741	7/9	58	49	9	53	53	0	KRT81,missense_variant,p.Val350Leu,ENST00000327741,;KRT86,intron_variant,,ENST00000423955,;KRT86,intron_variant,,ENST00000544024,;KRT86,intron_variant,,ENST00000553310,;	A	ENSG00000205426	ENST00000327741	Transcript	missense_variant	1117	1048	350	V/L	Gtg/Ttg	COSM694235	.	.	-1	KRT81	HGNC	6458	protein_coding	YES	CCDS31805.1	ENSP00000369349	KRT81_HUMAN	Q8NFV1_HUMAN,Q8N120_HUMAN	UPI0000DBEEF8	.	deleterious(0.02)	benign(0.17)	7/9	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF143,hmmpanther:PTHR23239,Pfam_domain:PF00038,Gene3D:1.20.5.170,Superfamily_domains:SSF64593	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCACCGCGG	.	4	ESCA
KRT6A	0	.	GRCh37	12	52884424	52884424	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1006G>A	p.Glu336Lys	p.E336K	ENST00000330722	5/9	143	133	10	138	138	0	KRT6A,missense_variant,p.Glu336Lys,ENST00000330722,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549600,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549898,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549754,;KRT6A,upstream_gene_variant,,ENST00000548735,;	T	ENSG00000205420	ENST00000330722	Transcript	missense_variant	1075	1006	336	E/K	Gag/Aag	.	.	.	-1	KRT6A	HGNC	6443	protein_coding	YES	CCDS41786.1	ENSP00000369317	K2C6A_HUMAN	.	UPI000013CD4C	.	deleterious(0)	probably_damaging(0.983)	5/9	.	Pfam_domain:PF00038,hmmpanther:PTHR23239:SF141,hmmpanther:PTHR23239	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCTCAGCGA	.	2	ESCA
KRT5	0	.	GRCh37	12	52908628	52908628	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*98G>A	.	.	ENST00000252242	9/9	78	71	6	69	69	0	KRT5,3_prime_UTR_variant,,ENST00000252242,;KRT5,downstream_gene_variant,,ENST00000551275,;KRT5,downstream_gene_variant,,ENST00000548409,;KRT5,downstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000549420,;KRT5,downstream_gene_variant,,ENST00000547890,;KRT5,downstream_gene_variant,,ENST00000549511,;KRT5,downstream_gene_variant,,ENST00000551013,;KRT5,downstream_gene_variant,,ENST00000552952,;KRT5,downstream_gene_variant,,ENST00000552629,;	T	ENSG00000186081	ENST00000252242	Transcript	3_prime_UTR_variant	2262	.	.	.	.	.	.	.	-1	KRT5	HGNC	6442	protein_coding	YES	CCDS8830.1	ENSP00000252242	K2C5_HUMAN	Q9UEK9_HUMAN,F8VV57_HUMAN,B4DL32_HUMAN	UPI000013CD4B	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCTCCAGAAA	.	2	ESCA
KRT8	0	.	GRCh37	12	53294964	53294964	+	Silent	SNP	G	G	A	rs202170959	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.657C>T	p.%3D	p.N219N	ENST00000552150	4/9	79	65	14	63	63	0	KRT8,synonymous_variant,p.%3D,ENST00000546900,;KRT8,synonymous_variant,p.%3D,ENST00000546826,;KRT8,synonymous_variant,p.%3D,ENST00000548998,;KRT8,synonymous_variant,p.%3D,ENST00000546897,;KRT8,synonymous_variant,p.%3D,ENST00000552551,;KRT8,synonymous_variant,p.%3D,ENST00000293308,;KRT8,synonymous_variant,p.%3D,ENST00000552150,;KRT8,intron_variant,,ENST00000547176,;KRT8,downstream_gene_variant,,ENST00000546542,;KRT8,downstream_gene_variant,,ENST00000547413,;KRT8,non_coding_transcript_exon_variant,,ENST00000550170,;KRT8,non_coding_transcript_exon_variant,,ENST00000549176,;KRT8,non_coding_transcript_exon_variant,,ENST00000547031,;KRT8,non_coding_transcript_exon_variant,,ENST00000546583,;	A	ENSG00000170421	ENST00000552150	Transcript	synonymous_variant	677	657	219	N	aaC/aaT	rs202170959	.	.	-1	KRT8	HGNC	6446	protein_coding	YES	CCDS58234.1	ENSP00000449404	K2C8_HUMAN	Q969I0_HUMAN,Q7L4M3_HUMAN,F8VUG2_HUMAN,F8VRG4_HUMAN,F8VP67_HUMAN	UPI0001892789	.	.	.	4/9	.	Coiled-coils_(Ncoils):Coil,Prints_domain:PR01276,Superfamily_domains:SSF64593,Pfam_domain:PF00038,hmmpanther:PTHR23239:SF104,hmmpanther:PTHR23239	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	A:0.0002	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATTCGTTCTC	byCluster|by1000G	5	ESCA
TESPA1	0	.	GRCh37	12	55360994	55360994	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283G>A	p.Glu95Lys	p.E95K	ENST00000449076	5/11	35	31	4	53	53	0	TESPA1,missense_variant,p.Glu95Lys,ENST00000316577,;TESPA1,missense_variant,p.Glu95Lys,ENST00000449076,;TESPA1,5_prime_UTR_variant,,ENST00000526532,;TESPA1,5_prime_UTR_variant,,ENST00000532757,;TESPA1,5_prime_UTR_variant,,ENST00000533446,;TESPA1,5_prime_UTR_variant,,ENST00000531122,;TESPA1,5_prime_UTR_variant,,ENST00000532804,;TESPA1,5_prime_UTR_variant,,ENST00000524622,;TESPA1,upstream_gene_variant,,ENST00000528240,;TESPA1,downstream_gene_variant,,ENST00000524668,;TESPA1,non_coding_transcript_exon_variant,,ENST00000524959,;TESPA1,3_prime_UTR_variant,,ENST00000525978,;TESPA1,5_prime_UTR_variant,,ENST00000524923,;	T	ENSG00000135426	ENST00000449076	Transcript	missense_variant	416	283	95	E/K	Gaa/Aaa	.	.	.	-1	TESPA1	HGNC	29109	protein_coding	YES	CCDS44913.1	ENSP00000400892	TESP1_HUMAN	E9PN46_HUMAN,E9PM24_HUMAN,E9PIT9_HUMAN,E9PIN8_HUMAN,E9PHY9_HUMAN,B4DHC1_HUMAN	UPI00001FC438	.	deleterious(0)	possibly_damaging(0.779)	5/11	.	hmmpanther:PTHR17469:SF1,hmmpanther:PTHR17469	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTTCAAAGC	.	2	ESCA
MYO1A	0	.	GRCh37	12	57423252	57423252	+	Silent	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2844C>G	p.%3D	p.L948L	ENST00000442789	27/29	54	42	12	69	69	0	MYO1A,synonymous_variant,p.%3D,ENST00000300119,;MYO1A,synonymous_variant,p.%3D,ENST00000544473,;MYO1A,synonymous_variant,p.%3D,ENST00000442789,;TAC3,upstream_gene_variant,,ENST00000415231,;MYO1A,non_coding_transcript_exon_variant,,ENST00000477864,;MYO1A,3_prime_UTR_variant,,ENST00000554234,;MYO1A,downstream_gene_variant,,ENST00000487083,;	C	ENSG00000166866	ENST00000442789	Transcript	synonymous_variant	3132	2844	948	L	ctC/ctG	.	.	.	-1	MYO1A	HGNC	7595	protein_coding	YES	CCDS8929.1	ENSP00000393392	MYO1A_HUMAN	Q13871_HUMAN,G3V587_HUMAN,F5GWY8_HUMAN,C9JU63_HUMAN	UPI000012FAC2	.	.	.	27/29	.	hmmpanther:PTHR13140:SF291,hmmpanther:PTHR13140,Pfam_domain:PF06017	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTTGAGGCT	.	5	ESCA
NOP2	0	.	GRCh37	12	6669279	6669279	+	Missense_Mutation	SNP	G	G	A	rs765511648	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1873C>T	p.Pro625Ser	p.P625S	ENST00000382421	16/17	98	89	8	103	103	0	NOP2,missense_variant,p.Pro588Ser,ENST00000399466,;NOP2,missense_variant,p.Pro592Ser,ENST00000322166,;NOP2,missense_variant,p.Pro625Ser,ENST00000382421,;NOP2,missense_variant,p.Pro592Ser,ENST00000537442,;NOP2,missense_variant,p.Pro588Ser,ENST00000545200,;NOP2,missense_variant,p.Pro588Ser,ENST00000541778,;IFFO1,upstream_gene_variant,,ENST00000336604,;NOP2,downstream_gene_variant,,ENST00000536124,;NOP2,downstream_gene_variant,,ENST00000542944,;IFFO1,upstream_gene_variant,,ENST00000356896,;NOP2,downstream_gene_variant,,ENST00000542867,;IFFO1,upstream_gene_variant,,ENST00000396840,;NOP2,non_coding_transcript_exon_variant,,ENST00000542015,;NOP2,non_coding_transcript_exon_variant,,ENST00000544630,;NOP2,downstream_gene_variant,,ENST00000537708,;IFFO1,upstream_gene_variant,,ENST00000488007,;IFFO1,upstream_gene_variant,,ENST00000487279,;NOP2,downstream_gene_variant,,ENST00000538420,;NOP2,downstream_gene_variant,,ENST00000536506,;NOP2,downstream_gene_variant,,ENST00000400580,;NOP2,downstream_gene_variant,,ENST00000542919,;	A	ENSG00000111641	ENST00000382421	Transcript	missense_variant	1949	1873	625	P/S	Cct/Tct	rs765511648	.	.	-1	NOP2	HGNC	7867	protein_coding	YES	CCDS58204.1	ENSP00000371858	NOP2_HUMAN	.	UPI00005C3039	.	deleterious(0.03)	possibly_damaging(0.766)	16/17	.	hmmpanther:PTHR22807,hmmpanther:PTHR22807:SF30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTGAGGGATAG	.	3	ESCA
KERA	0	.	GRCh37	12	91449833	91449833	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.226C>G	p.Leu76Val	p.L76V	ENST00000266719	2/3	83	66	16	84	84	0	KERA,missense_variant,p.Leu76Val,ENST00000266719,;	C	ENSG00000139330	ENST00000266719	Transcript	missense_variant	474	226	76	L/V	Ctt/Gtt	.	.	.	-1	KERA	HGNC	6309	protein_coding	YES	CCDS9037.1	ENSP00000266719	KERA_HUMAN	.	UPI000000161F	.	tolerated(0.17)	probably_damaging(0.951)	2/3	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24371:SF60,hmmpanther:PTHR24371,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAAGATACC	.	5	ESCA
GAS6	0	.	GRCh37	13	114535349	114535349	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1066G>A	p.Glu356Lys	p.E356K	ENST00000327773	10/15	45	40	5	46	46	0	GAS6,missense_variant,p.Glu302Lys,ENST00000355761,;GAS6,missense_variant,p.Glu356Lys,ENST00000327773,;GAS6,missense_variant,p.Glu399Lys,ENST00000357389,;GAS6,missense_variant,p.Glu83Lys,ENST00000450766,;GAS6,missense_variant,p.Glu57Lys,ENST00000418959,;GAS6-AS1,intron_variant,,ENST00000458001,;GAS6,non_coding_transcript_exon_variant,,ENST00000610073,;GAS6,non_coding_transcript_exon_variant,,ENST00000480426,;	T	ENSG00000183087	ENST00000327773	Transcript	missense_variant	1213	1066	356	E/K	Gag/Aag	.	.	.	-1	GAS6	HGNC	4168	protein_coding	YES	CCDS45072.1	ENSP00000331831	GAS6_HUMAN	B4DZY7_HUMAN	UPI0000073CCA	.	deleterious(0)	probably_damaging(0.997)	10/15	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24035:SF21,hmmpanther:PTHR24035,Gene3D:2.60.120.200,Pfam_domain:PF00054,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCTCCAGCC	.	4	ESCA
WARS	0	.	GRCh37	14	100801253	100801253	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1375G>C	p.Glu459Gln	p.E459Q	ENST00000355338	11/11	50	38	11	57	57	0	WARS,missense_variant,p.Glu459Gln,ENST00000355338,;WARS,missense_variant,p.Glu459Gln,ENST00000392882,;WARS,missense_variant,p.Glu418Gln,ENST00000358655,;WARS,missense_variant,p.Glu418Gln,ENST00000344102,;WARS,missense_variant,p.Glu459Gln,ENST00000557135,;WARS,missense_variant,p.Glu418Gln,ENST00000556645,;SLC25A47,downstream_gene_variant,,ENST00000557052,;SLC25A47,downstream_gene_variant,,ENST00000361529,;RP11-638I2.8,intron_variant,,ENST00000557226,;RP11-638I2.9,upstream_gene_variant,,ENST00000556212,;WARS,downstream_gene_variant,,ENST00000557614,;WARS,downstream_gene_variant,,ENST00000554950,;	G	ENSG00000140105	ENST00000355338	Transcript	missense_variant	1994	1375	459	E/Q	Gag/Cag	.	.	.	-1	WARS	HGNC	12729	protein_coding	YES	CCDS9960.1	ENSP00000347495	SYWC_HUMAN	P78534_HUMAN,G3V5W1_HUMAN,G3V5U1_HUMAN,G3V5H5_HUMAN,G3V4S4_HUMAN,G3V4N8_HUMAN,G3V4C7_HUMAN,G3V456_HUMAN,G3V423_HUMAN,G3V3Y5_HUMAN,G3V3X0_HUMAN,G3V3S7_HUMAN,G3V3R3_HUMAN,G3V3P2_HUMAN,G3V3H8_HUMAN,G3V339_HUMAN,G3V313_HUMAN,G3V2F2_HUMAN,G3V2C0_HUMAN,G3V277_HUMAN,G3V227_HUMAN,B4DTK8_HUMAN	UPI0000000E0E	.	tolerated(0.57)	benign(0.003)	11/11	.	hmmpanther:PTHR10055:SF1,hmmpanther:PTHR10055,Gene3D:1.10.240.10,TIGRFAM_domain:TIGR00233,Superfamily_domains:SSF52374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAACTCTTTCA	.	5	ESCA
WDR20	0	.	GRCh37	14	102659849	102659849	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.250-1426G>C	.	.	ENST00000454394	.	56	53	3	52	52	0	WDR20,splice_region_variant,,ENST00000499851,;WDR20,intron_variant,,ENST00000322340,;WDR20,intron_variant,,ENST00000545563,;WDR20,intron_variant,,ENST00000558854,;WDR20,intron_variant,,ENST00000335263,;WDR20,intron_variant,,ENST00000299135,;WDR20,intron_variant,,ENST00000556511,;WDR20,intron_variant,,ENST00000342702,;WDR20,intron_variant,,ENST00000424963,;WDR20,intron_variant,,ENST00000558567,;WDR20,intron_variant,,ENST00000556807,;WDR20,intron_variant,,ENST00000454394,;WDR20,upstream_gene_variant,,ENST00000559478,;WDR20,intron_variant,,ENST00000559708,;WDR20,intron_variant,,ENST00000558448,;WDR20,intron_variant,,ENST00000555973,;WDR20,intron_variant,,ENST00000558135,;WDR20,intron_variant,,ENST00000557186,;WDR20,intron_variant,,ENST00000557485,;WDR20,splice_region_variant,,ENST00000555879,;WDR20,intron_variant,,ENST00000556094,;	C	ENSG00000140153	ENST00000454394	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	WDR20	HGNC	19667	protein_coding	YES	CCDS55943.1	ENSP00000406084	WDR20_HUMAN	H0YNU0_HUMAN,F5H8E6_HUMAN,B3KPG5_HUMAN	UPI0000E23AC1	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAACTGAGGTG	.	2	ESCA
MOK	0	.	GRCh37	14	102695441	102695441	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*185G>C	.	.	ENST00000361847	12/12	159	145	14	137	137	0	MOK,3_prime_UTR_variant,,ENST00000517966,;MOK,3_prime_UTR_variant,,ENST00000522874,;MOK,3_prime_UTR_variant,,ENST00000361847,;MOK,3_prime_UTR_variant,,ENST00000522867,;MOK,3_prime_UTR_variant,,ENST00000523231,;MOK,3_prime_UTR_variant,,ENST00000524370,;MOK,intron_variant,,ENST00000559838,;MOK,intron_variant,,ENST00000193029,;MOK,intron_variant,,ENST00000561150,;MOK,downstream_gene_variant,,ENST00000522534,;MOK,downstream_gene_variant,,ENST00000524214,;WDR20,downstream_gene_variant,,ENST00000559478,;MOK,downstream_gene_variant,,ENST00000521937,;MOK,downstream_gene_variant,,ENST00000522537,;MOK,downstream_gene_variant,,ENST00000519058,;MOK,non_coding_transcript_exon_variant,,ENST00000520266,;MOK,intron_variant,,ENST00000557823,;MOK,downstream_gene_variant,,ENST00000524120,;MOK,downstream_gene_variant,,ENST00000519477,;MOK,upstream_gene_variant,,ENST00000559512,;MOK,3_prime_UTR_variant,,ENST00000521766,;MOK,non_coding_transcript_exon_variant,,ENST00000523485,;MOK,non_coding_transcript_exon_variant,,ENST00000519569,;MOK,non_coding_transcript_exon_variant,,ENST00000521249,;MOK,non_coding_transcript_exon_variant,,ENST00000518686,;MOK,intron_variant,,ENST00000559138,;MOK,downstream_gene_variant,,ENST00000562292,;MOK,downstream_gene_variant,,ENST00000520046,;MOK,downstream_gene_variant,,ENST00000521388,;MOK,downstream_gene_variant,,ENST00000520252,;	G	ENSG00000080823	ENST00000361847	Transcript	3_prime_UTR_variant	1677	.	.	.	.	.	.	.	-1	MOK	HGNC	9833	protein_coding	YES	CCDS9971.1	ENSP00000355304	MOK_HUMAN	Q49A77_HUMAN	UPI0000035B77	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGAACATCCT	.	3	ESCA
AHNAK2	0	.	GRCh37	14	105404547	105404547	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17241G>C	p.Glu5747Asp	p.E5747D	ENST00000333244	7/7	97	87	10	79	79	0	AHNAK2,missense_variant,p.Glu5747Asp,ENST00000333244,;AHNAK2,missense_variant,p.Glu745Asp,ENST00000557457,;PLD4,downstream_gene_variant,,ENST00000553861,;PLD4,downstream_gene_variant,,ENST00000540372,;PLD4,downstream_gene_variant,,ENST00000392593,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;	G	ENSG00000185567	ENST00000333244	Transcript	missense_variant	17361	17241	5747	E/D	gaG/gaC	.	.	.	-1	AHNAK2	HGNC	20125	protein_coding	YES	CCDS45177.1	ENSP00000353114	AHNK2_HUMAN	.	UPI00015BB2CA	.	.	benign(0.083)	7/7	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCACCCTCTTC	.	3	ESCA
MYH6	0	.	GRCh37	14	23876283	23876283	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.150G>C	p.Lys50Asn	p.K50N	ENST00000405093	3/39	73	60	12	57	57	0	MYH6,missense_variant,p.Lys50Asn,ENST00000405093,;MYH6,missense_variant,p.Lys50Asn,ENST00000356287,;MYH6,non_coding_transcript_exon_variant,,ENST00000557461,;	G	ENSG00000197616	ENST00000405093	Transcript	missense_variant	221	150	50	K/N	aaG/aaC	.	.	.	-1	MYH6	HGNC	7576	protein_coding	YES	CCDS9600.1	ENSP00000386041	MYH6_HUMAN	Q9UQV1_HUMAN,A8CLL2_HUMAN	UPI0000160969	.	tolerated(0.17)	benign(0.143)	3/39	.	hmmpanther:PTHR13140:SF260,hmmpanther:PTHR13140,Pfam_domain:PF02736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAATCTTGGC	.	5	ESCA
COCH	0	.	GRCh37	14	31355479	31355479	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1438G>A	p.Asp480Asn	p.D480N	ENST00000396618	11/12	86	75	11	63	63	0	COCH,missense_variant,p.Asp331Asn,ENST00000382493,;COCH,missense_variant,p.Asp364Asn,ENST00000468826,;COCH,missense_variant,p.Asp480Asn,ENST00000216361,;COCH,missense_variant,p.Asp368Asn,ENST00000460581,;COCH,missense_variant,p.Asp480Asn,ENST00000475087,;COCH,missense_variant,p.Asp480Asn,ENST00000396618,;COCH,downstream_gene_variant,,ENST00000555881,;RP11-829H16.3,non_coding_transcript_exon_variant,,ENST00000556786,;RP11-829H16.3,non_coding_transcript_exon_variant,,ENST00000468444,;RP11-829H16.3,non_coding_transcript_exon_variant,,ENST00000555108,;RP11-829H16.3,upstream_gene_variant,,ENST00000555421,;COCH,downstream_gene_variant,,ENST00000557065,;COCH,downstream_gene_variant,,ENST00000553772,;	A	ENSG00000100473	ENST00000396618	Transcript	missense_variant	1494	1438	480	D/N	Gat/Aat	.	.	.	1	COCH	HGNC	2180	protein_coding	YES	CCDS9640.1	ENSP00000379862	COCH_HUMAN	G3V5G6_HUMAN,G3V4C4_HUMAN	UPI0000048EBB	.	deleterious(0)	probably_damaging(0.999)	11/12	.	PROSITE_profiles:PS50234,hmmpanther:PTHR22992:SF84,hmmpanther:PTHR22992,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTATGATGAT	.	4	ESCA
RALGAPA1	0	.	GRCh37	14	36277997	36277997	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45G>C	p.Gln15His	p.Q15H	ENST00000307138	1/40	69	54	15	83	83	0	RALGAPA1,missense_variant,p.Gln15His,ENST00000389698,;RALGAPA1,missense_variant,p.Gln15His,ENST00000553892,;RALGAPA1,missense_variant,p.Gln15His,ENST00000258840,;RALGAPA1,missense_variant,p.Gln15His,ENST00000382366,;RALGAPA1,missense_variant,p.Gln15His,ENST00000307138,;AL162311.1,downstream_gene_variant,,ENST00000582013,;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000556192,;	G	ENSG00000174373	ENST00000307138	Transcript	missense_variant	514	45	15	Q/H	caG/caC	COSM1748832,COSM3931930,COSM1748831	.	.	-1	RALGAPA1	HGNC	17770	protein_coding	YES	CCDS32064.1	ENSP00000302647	RGPA1_HUMAN	Q9H984_HUMAN	UPI00003B5C51	.	deleterious(0)	probably_damaging(0.997)	1/40	.	hmmpanther:PTHR10063:SF3,hmmpanther:PTHR10063	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCTTCTGGGT	.	5	ESCA
SSTR1	0	.	GRCh37	14	38680415	38680415	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*645C>T	.	.	ENST00000267377	3/3	162	138	23	153	153	0	SSTR1,3_prime_UTR_variant,,ENST00000267377,;	T	ENSG00000139874	ENST00000267377	Transcript	3_prime_UTR_variant	2438	.	.	.	.	.	.	.	1	SSTR1	HGNC	11330	protein_coding	YES	CCDS9666.1	ENSP00000267377	SSR1_HUMAN	.	UPI0000001C3C	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCTGTCCCCCT	.	4	ESCA
CLEC14A	0	.	GRCh37	14	38724231	38724231	+	Missense_Mutation	SNP	C	C	A	rs780657376	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.997G>T	p.Val333Phe	p.V333F	ENST00000342213	1/1	40	33	6	37	37	0	CLEC14A,missense_variant,p.Val333Phe,ENST00000342213,;	A	ENSG00000176435	ENST00000342213	Transcript	missense_variant	1344	997	333	V/F	Gtc/Ttc	rs780657376	.	.	-1	CLEC14A	HGNC	19832	protein_coding	YES	CCDS9667.1	ENSP00000353013	CLC14_HUMAN	.	UPI000000CBD4	.	tolerated(0.06)	possibly_damaging(0.748)	1/1	.	hmmpanther:PTHR24838:SF258,hmmpanther:PTHR24838	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGACAAGTG	.	5	ESCA
LRFN5	0	.	GRCh37	14	42356105	42356105	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277C>G	p.His93Asp	p.H93D	ENST00000298119	3/6	62	49	13	55	55	0	LRFN5,missense_variant,p.His93Asp,ENST00000298119,;LRFN5,missense_variant,p.His93Asp,ENST00000554120,;LRFN5,missense_variant,p.His93Asp,ENST00000554171,;	G	ENSG00000165379	ENST00000298119	Transcript	missense_variant	1466	277	93	H/D	Cat/Gat	.	.	.	1	LRFN5	HGNC	20360	protein_coding	YES	CCDS9678.1	ENSP00000298119	LRFN5_HUMAN	.	UPI000000DA1E	.	tolerated(0.16)	benign(0.281)	3/6	.	Superfamily_domains:SSF52058,SMART_domains:SM00369,Gene3D:3.80.10.10,Pfam_domain:PF13306,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCTCATGCT	.	5	ESCA
MDGA2	0	.	GRCh37	14	47504275	47504275	+	Silent	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1758C>A	p.%3D	p.T586T	ENST00000439988	8/17	85	72	13	62	62	0	MDGA2,synonymous_variant,p.%3D,ENST00000357362,;MDGA2,synonymous_variant,p.%3D,ENST00000439988,;MDGA2,synonymous_variant,p.%3D,ENST00000426342,;MDGA2,synonymous_variant,p.%3D,ENST00000399232,;MDGA2,downstream_gene_variant,,ENST00000554762,;MDGA2,3_prime_UTR_variant,,ENST00000557238,;	T	ENSG00000272781	ENST00000439988	Transcript	synonymous_variant	1758	1758	586	T	acC/acA	.	.	.	-1	MDGA2	Uniprot_gn	19835	protein_coding	YES	.	ENSP00000400011	MDGA2_HUMAN	F8WE89_HUMAN	UPI0001DD21C1	.	.	.	8/17	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCTGGTCTG	.	5	ESCA
NIN	0	.	GRCh37	14	51223236	51223236	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4512G>A	p.%3D	p.E1504E	ENST00000382041	18/30	66	57	8	29	29	0	NIN,synonymous_variant,p.%3D,ENST00000245441,;NIN,synonymous_variant,p.%3D,ENST00000324330,;NIN,synonymous_variant,p.%3D,ENST00000382041,;NIN,synonymous_variant,p.%3D,ENST00000389869,;NIN,synonymous_variant,p.%3D,ENST00000530853,;NIN,synonymous_variant,p.%3D,ENST00000453196,;NIN,synonymous_variant,p.%3D,ENST00000530997,;NIN,intron_variant,,ENST00000389868,;NIN,intron_variant,,ENST00000382043,;NIN,synonymous_variant,p.%3D,ENST00000476352,;	T	ENSG00000100503	ENST00000382041	Transcript	synonymous_variant	4703	4512	1504	E	gaG/gaA	.	.	.	-1	NIN	HGNC	14906	protein_coding	YES	CCDS32079.1	ENSP00000371472	NIN_HUMAN	H7C162_HUMAN,E9PJH9_HUMAN	UPI0000DBEF14	.	.	.	18/30	.	hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF11,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCATCTCACT	.	4	ESCA
DLGAP5	0	.	GRCh37	14	55644016	55644016	+	Missense_Mutation	SNP	C	C	G	rs760482885	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.813G>C	p.Leu271Phe	p.L271F	ENST00000247191	8/19	62	40	22	37	37	0	DLGAP5,missense_variant,p.Leu271Phe,ENST00000247191,;DLGAP5,missense_variant,p.Leu271Phe,ENST00000395425,;DLGAP5,downstream_gene_variant,,ENST00000557645,;	G	ENSG00000126787	ENST00000247191	Transcript	missense_variant	1030	813	271	L/F	ttG/ttC	rs760482885	.	.	-1	DLGAP5	HGNC	16864	protein_coding	YES	CCDS9723.1	ENSP00000247191	DLGP5_HUMAN	G3V543_HUMAN,G3V4E5_HUMAN	UPI000013CC13	.	deleterious(0)	possibly_damaging(0.555)	8/19	.	hmmpanther:PTHR12353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATTCAAAGT	.	5	ESCA
ACTR10	0	.	GRCh37	14	58690395	58690395	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.690A>C	p.Lys230Asn	p.K230N	ENST00000254286	9/13	110	98	11	85	85	0	ACTR10,missense_variant,p.Lys230Asn,ENST00000254286,;ACTR10,missense_variant,p.Lys14Asn,ENST00000554642,;C14orf37,intron_variant,,ENST00000554218,;ACTR10,missense_variant,p.Lys230Asn,ENST00000554402,;ACTR10,missense_variant,p.Lys19Asn,ENST00000553907,;ACTR10,3_prime_UTR_variant,,ENST00000555229,;ACTR10,3_prime_UTR_variant,,ENST00000556748,;ACTR10,3_prime_UTR_variant,,ENST00000545307,;ACTR10,non_coding_transcript_exon_variant,,ENST00000556449,;ACTR10,non_coding_transcript_exon_variant,,ENST00000555965,;ACTR10,non_coding_transcript_exon_variant,,ENST00000557711,;ACTR10,non_coding_transcript_exon_variant,,ENST00000554790,;ACTR10,non_coding_transcript_exon_variant,,ENST00000556694,;ACTR10,non_coding_transcript_exon_variant,,ENST00000557583,;ACTR10,intron_variant,,ENST00000555337,;	C	ENSG00000131966	ENST00000254286	Transcript	missense_variant	770	690	230	K/N	aaA/aaC	.	.	.	1	ACTR10	HGNC	17372	protein_coding	YES	CCDS32090.1	ENSP00000254286	ARP10_HUMAN	Q86SY7_HUMAN	UPI0000126067	.	tolerated(0.08)	possibly_damaging(0.511)	9/13	.	hmmpanther:PTHR11937:SF14,hmmpanther:PTHR11937,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAAAATTTAA	.	4	ESCA
RTN1	0	.	GRCh37	14	60069967	60069967	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2192C>T	p.Ser731Leu	p.S731L	ENST00000267484	7/9	107	96	11	62	62	0	RTN1,missense_variant,p.Ser148Leu,ENST00000395090,;RTN1,missense_variant,p.Ser163Leu,ENST00000342503,;RTN1,missense_variant,p.Ser731Leu,ENST00000267484,;RTN1,non_coding_transcript_exon_variant,,ENST00000557422,;RTN1,non_coding_transcript_exon_variant,,ENST00000474911,;RTN1,non_coding_transcript_exon_variant,,ENST00000481205,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,;RTN1,downstream_gene_variant,,ENST00000490111,;	A	ENSG00000139970	ENST00000267484	Transcript	missense_variant	2528	2192	731	S/L	tCa/tTa	.	.	.	-1	RTN1	HGNC	10467	protein_coding	YES	CCDS9740.1	ENSP00000267484	RTN1_HUMAN	Q2NKQ5_HUMAN,Q2L7A7_HUMAN	UPI00001352DA	.	tolerated(0.08)	probably_damaging(0.997)	7/9	.	PROSITE_profiles:PS50845,hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994,Pfam_domain:PF02453	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACATTGAAACC	.	3	ESCA
MNAT1	0	.	GRCh37	14	61278748	61278748	+	Missense_Mutation	SNP	G	G	A	rs373266719	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.464G>A	p.Arg155Gln	p.R155Q	ENST00000261245	5/8	98	92	6	65	65	0	MNAT1,missense_variant,p.Arg155Gln,ENST00000261245,;MNAT1,missense_variant,p.Arg50Gln,ENST00000554002,;MNAT1,missense_variant,p.Arg155Gln,ENST00000539616,;MNAT1,missense_variant,p.Arg15Gln,ENST00000557134,;MNAT1,non_coding_transcript_exon_variant,,ENST00000556525,;MNAT1,downstream_gene_variant,,ENST00000553354,;MNAT1,non_coding_transcript_exon_variant,,ENST00000554641,;MNAT1,downstream_gene_variant,,ENST00000556764,;	A	ENSG00000020426	ENST00000261245	Transcript	missense_variant	565	464	155	R/Q	cGa/cAa	rs373266719	.	.	1	MNAT1	HGNC	7181	protein_coding	YES	CCDS9750.1	ENSP00000261245	MAT1_HUMAN	H0YJ92_HUMAN	UPI000002FC14	.	tolerated(0.5)	benign(0.028)	5/8	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF003338,TIGRFAM_domain:TIGR00570,Pfam_domain:PF06391,hmmpanther:PTHR12683,PROSITE_profiles:PS50330	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAACGACAGG	byFrequency|byCluster	2	ESCA
SYT16	0	.	GRCh37	14	62567939	62567939	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*514C>G	.	.	ENST00000430451	6/6	19	13	6	23	23	0	SYT16,3_prime_UTR_variant,,ENST00000430451,;RP11-355I22.2,downstream_gene_variant,,ENST00000554252,;SYT16,3_prime_UTR_variant,,ENST00000555409,;	G	ENSG00000139973	ENST00000430451	Transcript	3_prime_UTR_variant	2649	.	.	.	.	.	.	.	1	SYT16	HGNC	23142	protein_coding	YES	CCDS45121.1	ENSP00000394700	SYT16_HUMAN	.	UPI0000EE1AC0	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATCAAAGA	.	5	ESCA
RAB15	0	.	GRCh37	14	65438753	65438753	+	Silent	SNP	G	G	A	rs774084170	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.42C>T	p.%3D	p.I14I	ENST00000267512	1/7	122	115	7	101	101	0	RAB15,synonymous_variant,p.%3D,ENST00000533601,;RAB15,synonymous_variant,p.%3D,ENST00000267512,;FNTB,intron_variant,,ENST00000447296,;CHURC1-FNTB,intron_variant,,ENST00000549987,;CHURC1-FNTB,intron_variant,,ENST00000553743,;RAB15,intron_variant,,ENST00000554593,;FNTB,intron_variant,,ENST00000542227,;RAB15,upstream_gene_variant,,ENST00000436278,;CHURC1-FNTB,intron_variant,,ENST00000551823,;CHURC1-FNTB,intron_variant,,ENST00000552941,;RAB15,upstream_gene_variant,,ENST00000585059,;	A	ENSG00000139998	ENST00000267512	Transcript	synonymous_variant	123	42	14	I	atC/atT	rs774084170	.	.	-1	RAB15	HGNC	20150	protein_coding	YES	CCDS9768.1	ENSP00000267512	RAB15_HUMAN	Q6MZX6_HUMAN,G5EMR7_HUMAN	UPI00001C1D4D	.	.	.	1/7	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF367,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00176,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCCGATCAG	byFrequency	2	ESCA
ZNF410	0	.	GRCh37	14	74371761	74371761	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.939G>A	p.%3D	p.L313L	ENST00000442160	8/14	116	106	10	77	77	0	ZNF410,synonymous_variant,p.%3D,ENST00000442160,;ZNF410,synonymous_variant,p.%3D,ENST00000540593,;ZNF410,synonymous_variant,p.%3D,ENST00000324593,;ZNF410,synonymous_variant,p.%3D,ENST00000334521,;ZNF410,synonymous_variant,p.%3D,ENST00000554316,;ZNF410,synonymous_variant,p.%3D,ENST00000555044,;RP5-1021I20.5,intron_variant,,ENST00000554009,;RP5-1021I20.6,upstream_gene_variant,,ENST00000602874,;Y_RNA,downstream_gene_variant,,ENST00000362602,;ZNF410,non_coding_transcript_exon_variant,,ENST00000412490,;ZNF410,non_coding_transcript_exon_variant,,ENST00000541357,;ZNF410,downstream_gene_variant,,ENST00000555602,;ZNF410,3_prime_UTR_variant,,ENST00000556396,;RP5-1021I20.4,3_prime_UTR_variant,,ENST00000556551,;ZNF410,3_prime_UTR_variant,,ENST00000398139,;ZNF410,non_coding_transcript_exon_variant,,ENST00000555620,;ZNF410,non_coding_transcript_exon_variant,,ENST00000557679,;ZNF410,downstream_gene_variant,,ENST00000554582,;	A	ENSG00000119725	ENST00000442160	Transcript	synonymous_variant	1133	939	313	L	ctG/ctA	.	.	.	1	ZNF410	HGNC	20144	protein_coding	YES	CCDS55929.1	ENSP00000407130	ZN410_HUMAN	G3V4E6_HUMAN	UPI00017A6BE1	.	.	.	8/14	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR11389:SF363,hmmpanther:PTHR11389,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AACCTGAAGAA	.	3	ESCA
PTPN21	0	.	GRCh37	14	88938602	88938602	+	Missense_Mutation	SNP	C	C	T	rs112928496	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2857G>A	p.Ala953Thr	p.A953T	ENST00000556564	15/19	116	96	19	67	66	0	PTPN21,missense_variant,p.Ala953Thr,ENST00000556564,;PTPN21,missense_variant,p.Ala953Thr,ENST00000328736,;SPATA7,downstream_gene_variant,,ENST00000556406,;PTPN21,upstream_gene_variant,,ENST00000553531,;PTPN21,3_prime_UTR_variant,,ENST00000536337,;PTPN21,non_coding_transcript_exon_variant,,ENST00000557249,;PTPN21,non_coding_transcript_exon_variant,,ENST00000554270,;	T	ENSG00000070778	ENST00000556564	Transcript	missense_variant	3142	2857	953	A/T	Gca/Aca	rs112928496,COSM958457	.	.	-1	PTPN21	HGNC	9651	protein_coding	YES	CCDS9884.1	ENSP00000452414	PTN21_HUMAN	Q8WX29_HUMAN,G3V3S6_HUMAN	UPI000013D15F	.	deleterious(0)	probably_damaging(1)	15/19	.	PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF78,hmmpanther:PTHR19134,Pfam_domain:PF00102,Gene3D:3.90.190.10,PIRSF_domain:PIRSF000934,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGATGCGTTGA	.	4	ESCA
UBE3A	0	.	GRCh37	15	25605546	25605546	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1746C>G	p.Ile582Met	p.I582M	ENST00000397954	5/11	71	62	9	54	54	0	UBE3A,missense_variant,p.Ile559Met,ENST00000566215,;UBE3A,missense_variant,p.Ile582Met,ENST00000397954,;UBE3A,missense_variant,p.Ile559Met,ENST00000438097,;UBE3A,missense_variant,p.Ile559Met,ENST00000428984,;UBE3A,missense_variant,p.Ile579Met,ENST00000232165,;UBE3A,upstream_gene_variant,,ENST00000604860,;SNHG14,intron_variant,,ENST00000554726,;	C	ENSG00000114062	ENST00000397954	Transcript	missense_variant	1746	1746	582	I/M	atC/atG	.	.	.	-1	UBE3A	HGNC	12496	protein_coding	YES	CCDS45192.1	ENSP00000381045	UBE3A_HUMAN	Q9UBN9_HUMAN,Q9H2G0_HUMAN,Q96GR7_HUMAN	UPI0000161F3B	.	deleterious(0)	possibly_damaging(0.82)	5/11	.	PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF301,Pfam_domain:PF00632,SMART_domains:SM00119,PIRSF_domain:PIRSF037201,Superfamily_domains:SSF56204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAAGATTTC	.	4	ESCA
RYR3	0	.	GRCh37	15	34064135	34064135	+	Nonsense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8831C>G	p.Ser2944Ter	p.S2944*	ENST00000389232	63/104	73	65	8	64	64	0	RYR3,stop_gained,p.Ser2944Ter,ENST00000389232,;RYR3,stop_gained,p.Ser2944Ter,ENST00000415757,;	G	ENSG00000198838	ENST00000389232	Transcript	stop_gained	8901	8831	2944	S/*	tCa/tGa	COSM1478053	.	.	1	RYR3	HGNC	10485	protein_coding	YES	CCDS45210.1	ENSP00000373884	RYR3_HUMAN	.	UPI0000E5B01A	.	.	.	63/104	.	hmmpanther:PTHR13715:SF16,hmmpanther:PTHR13715	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGTCAGGCT	.	4	ESCA
MGA	0	.	GRCh37	15	42057139	42057139	+	Silent	SNP	G	G	A	rs372185993	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7800G>A	p.%3D	p.P2600P	ENST00000219905	23/24	72	47	25	56	56	0	MGA,synonymous_variant,p.%3D,ENST00000219905,;MGA,synonymous_variant,p.%3D,ENST00000570161,;MGA,synonymous_variant,p.%3D,ENST00000545763,;MGA,synonymous_variant,p.%3D,ENST00000389936,;MGA,synonymous_variant,p.%3D,ENST00000566586,;MGA,downstream_gene_variant,,ENST00000564190,;MGA,downstream_gene_variant,,ENST00000568255,;	A	ENSG00000174197	ENST00000219905	Transcript	synonymous_variant	7981	7800	2600	P	ccG/ccA	rs372185993	.	.	1	MGA	HGNC	14010	protein_coding	YES	CCDS55959.1	ENSP00000219905	MGAP_HUMAN	H3BTF4_HUMAN,H3BP52_HUMAN	UPI0001B2337E	.	.	.	23/24	.	hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCCGCAAGG	byFrequency|byCluster	5	ESCA
PLA2G4F	0	.	GRCh37	15	42444892	42444892	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595G>T	p.Glu199Ter	p.E199*	ENST00000382396	7/20	67	60	7	64	64	0	PLA2G4F,stop_gained,p.Glu199Ter,ENST00000397272,;PLA2G4F,stop_gained,p.Glu199Ter,ENST00000382396,;PLA2G4F,stop_gained,p.Glu199Ter,ENST00000569985,;PLA2G4F,3_prime_UTR_variant,,ENST00000290497,;PLA2G4F,3_prime_UTR_variant,,ENST00000561627,;PLA2G4F,downstream_gene_variant,,ENST00000565553,;PLA2G4F,upstream_gene_variant,,ENST00000561893,;	A	ENSG00000168907	ENST00000382396	Transcript	stop_gained	682	595	199	E/*	Gag/Tag	.	.	.	-1	PLA2G4F	HGNC	27396	protein_coding	YES	CCDS32204.1	ENSP00000371833	PA24F_HUMAN	.	UPI0000160965	.	.	.	7/20	.	hmmpanther:PTHR10728,hmmpanther:PTHR10728:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTACTCTTCCC	.	4	ESCA
C15orf61	0	.	GRCh37	15	67813772	67813772	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186G>A	p.%3D	p.Q62Q	ENST00000342683	1/2	34	29	4	34	34	0	C15orf61,synonymous_variant,p.%3D,ENST00000342683,;C15orf61,upstream_gene_variant,,ENST00000557807,;IQCH-AS1,intron_variant,,ENST00000559298,;IQCH-AS1,intron_variant,,ENST00000561232,;IQCH-AS1,upstream_gene_variant,,ENST00000559702,;IQCH-AS1,upstream_gene_variant,,ENST00000559285,;C15orf61,upstream_gene_variant,,ENST00000560547,;C15orf61,upstream_gene_variant,,ENST00000560041,;	A	ENSG00000189227	ENST00000342683	Transcript	synonymous_variant	367	186	62	Q	caG/caA	.	.	.	1	C15orf61	HGNC	34453	protein_coding	YES	CCDS45289.1	ENSP00000342254	CO061_HUMAN	.	UPI0000039EE4	.	.	.	1/2	.	Pfam_domain:PF15031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCAGTTCGG	.	2	ESCA
NEO1	0	.	GRCh37	15	73418907	73418907	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.874G>A	p.Glu292Lys	p.E292K	ENST00000339362	5/30	98	86	12	66	66	0	NEO1,missense_variant,p.Glu292Lys,ENST00000261908,;NEO1,missense_variant,p.Glu292Lys,ENST00000558964,;NEO1,missense_variant,p.Glu292Lys,ENST00000339362,;NEO1,missense_variant,p.Glu292Lys,ENST00000560262,;NEO1,non_coding_transcript_exon_variant,,ENST00000558485,;	A	ENSG00000067141	ENST00000339362	Transcript	missense_variant	1321	874	292	E/K	Gaa/Aaa	.	.	.	1	NEO1	HGNC	7754	protein_coding	YES	CCDS10247.1	ENSP00000341198	NEO1_HUMAN	.	UPI000013D221	.	tolerated(0.25)	benign(0.021)	5/30	.	PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF55,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACACAGAAAGG	.	4	ESCA
CYP11A1	0	.	GRCh37	15	74654407	74654407	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.269+5251G>C	.	.	ENST00000268053	.	79	69	9	100	100	0	CYP11A1,intron_variant,,ENST00000569662,;CYP11A1,intron_variant,,ENST00000358632,;CYP11A1,intron_variant,,ENST00000419019,;CYP11A1,intron_variant,,ENST00000541301,;CYP11A1,intron_variant,,ENST00000416978,;CYP11A1,intron_variant,,ENST00000268053,;CYP11A1,intron_variant,,ENST00000450547,;CYP11A1,upstream_gene_variant,,ENST00000566674,;CTD-2311M21.3,upstream_gene_variant,,ENST00000568496,;CTD-2311M21.2,non_coding_transcript_exon_variant,,ENST00000562009,;CYP11A1,intron_variant,,ENST00000467407,;CTD-2311M21.2,downstream_gene_variant,,ENST00000564109,;CYP11A1,intron_variant,,ENST00000466978,;CYP11A1,intron_variant,,ENST00000435365,;CTD-2311M21.2,downstream_gene_variant,,ENST00000569235,;	G	ENSG00000140459	ENST00000268053	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CYP11A1	HGNC	2590	protein_coding	YES	CCDS32291.1	ENSP00000268053	CP11A_HUMAN	Q2HZF3_HUMAN,H3BSZ1_HUMAN,H3BS93_HUMAN,C9JPU9_HUMAN	UPI00000725F7	.	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTATCTTAAC	.	4	ESCA
KIF7	0	.	GRCh37	15	90176221	90176221	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2725G>C	p.Glu909Gln	p.E909Q	ENST00000394412	14/19	60	45	14	66	66	0	KIF7,missense_variant,p.Glu909Gln,ENST00000394412,;TICRR,downstream_gene_variant,,ENST00000560985,;TICRR,downstream_gene_variant,,ENST00000268138,;KIF7,upstream_gene_variant,,ENST00000558928,;TICRR,downstream_gene_variant,,ENST00000561095,;	G	ENSG00000166813	ENST00000394412	Transcript	missense_variant	2802	2725	909	E/Q	Gag/Cag	.	.	.	-1	KIF7	HGNC	30497	protein_coding	YES	CCDS32325.2	ENSP00000377934	KIF7_HUMAN	B7ZKY4_HUMAN	UPI00015F81C7	.	deleterious(0)	possibly_damaging(0.557)	14/19	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF342,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCAATCT	.	4	ESCA
SV2B	0	.	GRCh37	15	91827399	91827399	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1656G>A	p.%3D	p.G552G	ENST00000394232	11/13	54	48	6	82	81	1	SV2B,synonymous_variant,p.%3D,ENST00000330276,;SV2B,synonymous_variant,p.%3D,ENST00000394232,;SV2B,synonymous_variant,p.%3D,ENST00000545111,;SV2B,synonymous_variant,p.%3D,ENST00000557410,;	A	ENSG00000185518	ENST00000394232	Transcript	synonymous_variant	2126	1656	552	G	ggG/ggA	COSM198065	.	.	1	SV2B	HGNC	16874	protein_coding	YES	CCDS10370.1	ENSP00000377779	SV2B_HUMAN	.	UPI000006FCF1	.	.	.	11/13	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24065,hmmpanther:PTHR24065:SF1,Gene3D:1.20.1250.20,Pfam_domain:PF07690,TIGRFAM_domain:TIGR01299,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCCGGGAACAT	.	3	ESCA
GNPTG	0	.	GRCh37	16	1412296	1412296	+	Silent	SNP	C	C	T	rs756686252	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.501C>T	p.%3D	p.L167L	ENST00000204679	7/11	72	56	16	107	107	0	GNPTG,synonymous_variant,p.%3D,ENST00000204679,;UNKL,downstream_gene_variant,,ENST00000248104,;UNKL,downstream_gene_variant,,ENST00000403703,;UNKL,downstream_gene_variant,,ENST00000402641,;UNKL,downstream_gene_variant,,ENST00000397464,;GNPTG,downstream_gene_variant,,ENST00000529110,;UNKL,downstream_gene_variant,,ENST00000508903,;UNKL,downstream_gene_variant,,ENST00000391893,;UNKL,downstream_gene_variant,,ENST00000389221,;LA16c-316G12.2,upstream_gene_variant,,ENST00000569831,;UNKL,downstream_gene_variant,,ENST00000562537,;GNPTG,non_coding_transcript_exon_variant,,ENST00000527076,;GNPTG,non_coding_transcript_exon_variant,,ENST00000527168,;GNPTG,non_coding_transcript_exon_variant,,ENST00000529957,;UNKL,downstream_gene_variant,,ENST00000511095,;GNPTG,downstream_gene_variant,,ENST00000526820,;GNPTG,downstream_gene_variant,,ENST00000527876,;GNPTG,downstream_gene_variant,,ENST00000534197,;	T	ENSG00000090581	ENST00000204679	Transcript	synonymous_variant	544	501	167	L	ctC/ctT	rs756686252	.	.	1	GNPTG	HGNC	23026	protein_coding	YES	CCDS10436.1	ENSP00000204679	GNPTG_HUMAN	Q96RZ2_HUMAN	UPI0000073F3C	.	.	.	7/11	.	hmmpanther:PTHR12630,hmmpanther:PTHR12630:SF6,Pfam_domain:PF13015,Gene3D:2.70.130.10,Superfamily_domains:SSF50911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCTCGTCTG	.	5	ESCA
KIAA0430	0	.	GRCh37	16	15714339	15714339	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2689C>T	p.%3D	p.L897L	ENST00000396368	13/27	108	101	7	99	99	0	KIAA0430,synonymous_variant,p.%3D,ENST00000551742,;KIAA0430,synonymous_variant,p.%3D,ENST00000602337,;KIAA0430,synonymous_variant,p.%3D,ENST00000540441,;KIAA0430,synonymous_variant,p.%3D,ENST00000548025,;KIAA0430,synonymous_variant,p.%3D,ENST00000396368,;C16orf45,intron_variant,,ENST00000565857,;KIAA0430,intron_variant,,ENST00000344181,;KIAA0430,downstream_gene_variant,,ENST00000551678,;KIAA0430,synonymous_variant,p.%3D,ENST00000552553,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000546864,;KIAA0430,upstream_gene_variant,,ENST00000552535,;	A	ENSG00000166783	ENST00000396368	Transcript	synonymous_variant	2896	2689	897	L	Ctg/Ttg	.	.	.	-1	KIAA0430	HGNC	29562	protein_coding	YES	CCDS10562.2	ENSP00000379654	MARF1_HUMAN	F8VRS5_HUMAN	UPI00006881BC	.	.	.	13/27	.	hmmpanther:PTHR14379:SF3,hmmpanther:PTHR14379,PROSITE_profiles:PS51644	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAACAGAGGCA	.	2	ESCA
DNAH3	0	.	GRCh37	16	21042473	21042473	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5333A>G	p.Glu1778Gly	p.E1778G	ENST00000261383	37/62	81	71	10	61	61	0	DNAH3,missense_variant,p.Glu1778Gly,ENST00000261383,;DNAH3,missense_variant,p.Glu1778Gly,ENST00000415178,;DNAH3,non_coding_transcript_exon_variant,,ENST00000572931,;DNAH3,non_coding_transcript_exon_variant,,ENST00000572640,;	C	ENSG00000158486	ENST00000261383	Transcript	missense_variant	5333	5333	1778	E/G	gAg/gGg	.	.	.	-1	DNAH3	HGNC	2949	protein_coding	YES	CCDS10594.1	ENSP00000261383	DYH3_HUMAN	.	UPI00001100F2	.	tolerated(0.06)	benign(0.111)	37/62	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTGCTCCCGG	.	4	ESCA
HBA2	0	.	GRCh37	16	223305	223305	+	Missense_Mutation	SNP	C	C	T	rs281864876	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277C>T	p.Arg93Trp	p.R93W	ENST00000251595	2/3	95	85	10	124	124	0	HBA2,missense_variant,p.Arg61Trp,ENST00000397806,;HBA2,missense_variant,p.Arg93Trp,ENST00000251595,;HBA1,upstream_gene_variant,,ENST00000320868,;HBA1,upstream_gene_variant,,ENST00000397797,;HBA2,non_coding_transcript_exon_variant,,ENST00000482565,;HBA2,non_coding_transcript_exon_variant,,ENST00000484216,;HBA1,upstream_gene_variant,,ENST00000472694,;HBA1,upstream_gene_variant,,ENST00000487791,;Z84721.4,downstream_gene_variant,,ENST00000438841,;	T	ENSG00000188536	ENST00000251595	Transcript	missense_variant	343	277	93	R/W	Cgg/Tgg	rs281864876	.	.	1	HBA2	HGNC	4824	protein_coding	YES	CCDS10398.1	ENSP00000251595	HBA_HUMAN	D1MGQ2_HUMAN,Q7Z6G4_HUMAN,P78461_HUMAN,G3V1N2_HUMAN	UPI0000000239	.	deleterious(0)	benign(0.39)	2/3	.	Superfamily_domains:SSF46458,Gene3D:1.10.490.10,Pfam_domain:PF00042,hmmpanther:PTHR11442,hmmpanther:PTHR11442:SF41,PROSITE_profiles:PS01033	.	.	.	.	.	.	.	.	.	.	.	8148419	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCTTCGGGTG	.	4	ESCA
LUC7L	0	.	GRCh37	16	238990	238990	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*207G>C	.	.	ENST00000293872	10/10	32	27	5	42	42	0	LUC7L,3_prime_UTR_variant,,ENST00000397783,;LUC7L,3_prime_UTR_variant,,ENST00000293872,;LUC7L,3_prime_UTR_variant,,ENST00000337351,;LUC7L,3_prime_UTR_variant,,ENST00000429378,;LUC7L,downstream_gene_variant,,ENST00000397780,;LUC7L,downstream_gene_variant,,ENST00000430864,;LUC7L,downstream_gene_variant,,ENST00000442701,;LA16c-OS12.2,upstream_gene_variant,,ENST00000595428,;LUC7L,3_prime_UTR_variant,,ENST00000426094,;LUC7L,non_coding_transcript_exon_variant,,ENST00000468732,;LUC7L,non_coding_transcript_exon_variant,,ENST00000490762,;LUC7L,downstream_gene_variant,,ENST00000418978,;LUC7L,downstream_gene_variant,,ENST00000495349,;LUC7L,downstream_gene_variant,,ENST00000419516,;LUC7L,downstream_gene_variant,,ENST00000464711,;	G	ENSG00000007392	ENST00000293872	Transcript	3_prime_UTR_variant	1434	.	.	.	.	.	.	.	-1	LUC7L	HGNC	6723	protein_coding	YES	CCDS32348.1	ENSP00000293872	LUC7L_HUMAN	Q1W6G4_HUMAN,B8ZZ12_HUMAN,B8ZZ10_HUMAN,B8ZZ09_HUMAN,A8MYV2_HUMAN,D3DU41_HUMAN	UPI00000467F8	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCTCAGGAG	.	2	ESCA
ZKSCAN2	0	.	GRCh37	16	25251879	25251879	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2162G>C	p.Arg721Thr	p.R721T	ENST00000328086	7/7	49	45	3	55	55	0	ZKSCAN2,missense_variant,p.Arg721Thr,ENST00000328086,;CTD-2547G23.2,downstream_gene_variant,,ENST00000569456,;ZKSCAN2,3_prime_UTR_variant,,ENST00000569150,;	G	ENSG00000155592	ENST00000328086	Transcript	missense_variant	2966	2162	721	R/T	aGa/aCa	.	.	.	-1	ZKSCAN2	HGNC	25677	protein_coding	YES	CCDS32410.1	ENSP00000331626	ZKSC2_HUMAN	.	UPI0000229E7F	.	deleterious(0.02)	possibly_damaging(0.798)	7/7	.	hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGTCTAATT	.	2	ESCA
ZNF720	0	.	GRCh37	16	31765249	31765249	+	Intron	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361+28A>G	.	.	ENST00000316491	.	62	48	13	39	39	0	ZNF720,missense_variant,p.Tyr60Cys,ENST00000398696,;ZNF720,intron_variant,,ENST00000539915,;ZNF720,intron_variant,,ENST00000316491,;ZNF720,intron_variant,,ENST00000399681,;ZNF720,intron_variant,,ENST00000529515,;ZNF720,intron_variant,,ENST00000534369,;ZNF720,downstream_gene_variant,,ENST00000530881,;ZNF720,intron_variant,,ENST00000544044,;ZNF720,intron_variant,,ENST00000542684,;ZNF720,intron_variant,,ENST00000533488,;ZNF720,intron_variant,,ENST00000531864,;ZNF720,3_prime_UTR_variant,,ENST00000529943,;ZNF720,intron_variant,,ENST00000534277,;ZNF720,intron_variant,,ENST00000398707,;	G	ENSG00000197302	ENST00000316491	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZNF720	HGNC	26987	protein_coding	YES	CCDS45473.1	ENSP00000319222	ZN720_HUMAN	.	UPI000003603E	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	ATATTATGATG	.	4	ESCA
C16orf89	0	.	GRCh37	16	5106102	5106102	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.715G>A	p.Glu239Lys	p.E239K	ENST00000315997	5/8	51	35	16	78	78	0	C16orf89,missense_variant,p.Glu277Lys,ENST00000350219,;C16orf89,missense_variant,p.Glu239Lys,ENST00000315997,;C16orf89,missense_variant,p.Glu277Lys,ENST00000422873,;C16orf89,missense_variant,p.Glu239Lys,ENST00000474471,;C16orf89,missense_variant,p.Glu239Lys,ENST00000472572,;ALG1,intron_variant,,ENST00000588623,;C16orf89,non_coding_transcript_exon_variant,,ENST00000592343,;C16orf89,upstream_gene_variant,,ENST00000586629,;C16orf89,downstream_gene_variant,,ENST00000591875,;	T	ENSG00000153446	ENST00000315997	Transcript	missense_variant	917	715	239	E/K	Gag/Aag	.	.	.	-1	C16orf89	HGNC	28687	protein_coding	YES	CCDS42116.2	ENSP00000324672	CP089_HUMAN	.	UPI000166306A	.	tolerated(0.05)	benign(0.132)	5/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTCAGCTC	.	5	ESCA
SLC6A2	0	.	GRCh37	16	55705923	55705923	+	Silent	SNP	C	C	T	rs768139475	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.480C>T	p.%3D	p.L160L	ENST00000219833	3/14	77	61	15	60	59	1	SLC6A2,synonymous_variant,p.%3D,ENST00000568529,;SLC6A2,synonymous_variant,p.%3D,ENST00000561820,;SLC6A2,synonymous_variant,p.%3D,ENST00000566163,;SLC6A2,synonymous_variant,p.%3D,ENST00000379906,;SLC6A2,synonymous_variant,p.%3D,ENST00000219833,;SLC6A2,synonymous_variant,p.%3D,ENST00000568943,;SLC6A2,synonymous_variant,p.%3D,ENST00000568655,;SLC6A2,synonymous_variant,p.%3D,ENST00000414754,;SLC6A2,synonymous_variant,p.%3D,ENST00000567238,;	T	ENSG00000103546	ENST00000219833	Transcript	synonymous_variant	531	480	160	L	ctC/ctT	rs768139475	.	.	1	SLC6A2	HGNC	11048	protein_coding	YES	CCDS54011.1	ENSP00000219833	SC6A2_HUMAN	Q9Y6W9_HUMAN,H3BMY5_HUMAN	UPI00000734FD	.	.	.	3/14	.	Prints_domain:PR00176,Superfamily_domains:0053687,Pfam_domain:PF00209,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF37,PROSITE_profiles:PS50267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCACTCTACTA	byFrequency	5	ESCA
CNGB1	0	.	GRCh37	16	57917826	57917826	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*242C>T	.	.	ENST00000251102	33/33	14	11	3	11	11	0	CNGB1,3_prime_UTR_variant,,ENST00000564448,;CNGB1,3_prime_UTR_variant,,ENST00000251102,;CNGB1,downstream_gene_variant,,ENST00000565942,;	A	ENSG00000070729	ENST00000251102	Transcript	3_prime_UTR_variant	4059	.	.	.	.	.	.	.	-1	CNGB1	HGNC	2151	protein_coding	YES	CCDS42169.1	ENSP00000251102	CNGB1_HUMAN	H3BQC3_HUMAN	UPI000013CCDF	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGATAGTGAGA	.	2	ESCA
CAPN15	0	.	GRCh37	16	597619	597619	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.781G>A	p.Glu261Lys	p.E261K	ENST00000219611	4/14	25	18	7	39	39	0	CAPN15,missense_variant,p.Glu261Lys,ENST00000219611,;CAPN15,5_prime_UTR_variant,,ENST00000568988,;CAPN15,downstream_gene_variant,,ENST00000562370,;MIR3176,downstream_gene_variant,,ENST00000582210,;LA16c-366D1.3,intron_variant,,ENST00000565879,;CAPN15,upstream_gene_variant,,ENST00000565010,;	A	ENSG00000103326	ENST00000219611	Transcript	missense_variant	1144	781	261	E/K	Gag/Aag	.	.	.	1	CAPN15	HGNC	11182	protein_coding	YES	CCDS10410.1	ENSP00000219611	CAN15_HUMAN	H3BR03_HUMAN	UPI0000071B68	.	tolerated_low_confidence(0.19)	benign(0.141)	4/14	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10183:SF279,hmmpanther:PTHR10183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCTGAGGCT	.	5	ESCA
FAM65A	0	.	GRCh37	16	67577114	67577114	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2485C>T	p.Pro829Ser	p.P829S	ENST00000422602	13/22	198	162	36	188	188	0	FAM65A,missense_variant,p.Pro823Ser,ENST00000428437,;FAM65A,missense_variant,p.Pro829Ser,ENST00000422602,;FAM65A,missense_variant,p.Pro829Ser,ENST00000540839,;FAM65A,missense_variant,p.Pro809Ser,ENST00000042381,;FAM65A,missense_variant,p.Pro813Ser,ENST00000379312,;FAM65A,downstream_gene_variant,,ENST00000566559,;FAM65A,downstream_gene_variant,,ENST00000569253,;FAM65A,downstream_gene_variant,,ENST00000569179,;FAM65A,upstream_gene_variant,,ENST00000568959,;FAM65A,downstream_gene_variant,,ENST00000562755,;FAM65A,downstream_gene_variant,,ENST00000566920,;FAM65A,downstream_gene_variant,,ENST00000565176,;FAM65A,downstream_gene_variant,,ENST00000566907,;FAM65A,downstream_gene_variant,,ENST00000562116,;CTD-2012K14.4,upstream_gene_variant,,ENST00000564717,;CTD-2012K14.3,upstream_gene_variant,,ENST00000563083,;CTD-2012K14.2,upstream_gene_variant,,ENST00000567122,;FAM65A,downstream_gene_variant,,ENST00000566522,;FAM65A,non_coding_transcript_exon_variant,,ENST00000569733,;FAM65A,non_coding_transcript_exon_variant,,ENST00000564616,;FAM65A,upstream_gene_variant,,ENST00000565190,;FAM65A,downstream_gene_variant,,ENST00000561534,;FAM65A,upstream_gene_variant,,ENST00000565679,;FAM65A,downstream_gene_variant,,ENST00000569474,;FAM65A,downstream_gene_variant,,ENST00000566730,;FAM65A,downstream_gene_variant,,ENST00000566815,;	T	ENSG00000039523	ENST00000422602	Transcript	missense_variant	2581	2485	829	P/S	Cct/Tct	COSM3888768,COSM3888767	.	.	1	FAM65A	HGNC	25836	protein_coding	YES	CCDS54026.1	ENSP00000400099	FA65A_HUMAN	H3BQI5_HUMAN,H3BV02_HUMAN,H3BUP6_HUMAN,H3BSV5_HUMAN,H3BS40_HUMAN	UPI0001AE68C6	.	deleterious(0.05)	possibly_damaging(0.641)	13/22	.	hmmpanther:PTHR15829,hmmpanther:PTHR15829:SF1	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGTTTCCTGAG	.	4	ESCA
VAC14	0	.	GRCh37	16	70796488	70796488	+	Silent	SNP	G	G	A	rs760811310	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1326C>T	p.%3D	p.S442S	ENST00000261776	12/19	56	42	14	74	74	0	VAC14,synonymous_variant,p.%3D,ENST00000261776,;VAC14-AS1,intron_variant,,ENST00000562507,;VAC14-AS1,intron_variant,,ENST00000398177,;VAC14,missense_variant,p.Ala186Val,ENST00000568886,;VAC14,3_prime_UTR_variant,,ENST00000568548,;VAC14,non_coding_transcript_exon_variant,,ENST00000563662,;	A	ENSG00000103043	ENST00000261776	Transcript	synonymous_variant	1587	1326	442	S	agC/agT	rs760811310	.	.	-1	VAC14	HGNC	25507	protein_coding	YES	CCDS10896.1	ENSP00000261776	VAC14_HUMAN	Q9NTB8_HUMAN,B3KSM8_HUMAN	UPI00001A832B	.	.	.	12/19	.	hmmpanther:PTHR16023:SF0,hmmpanther:PTHR16023,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGAGGCTGTC	byFrequency	5	ESCA
WDR24	0	.	GRCh37	16	740071	740071	+	5'UTR	SNP	G	G	A	rs568055066	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-431C>T	.	.	ENST00000293883	1/9	52	45	6	69	69	0	WDR24,synonymous_variant,p.%3D,ENST00000248142,;WDR24,5_prime_UTR_variant,,ENST00000293883,;FBXL16,downstream_gene_variant,,ENST00000324361,;FBXL16,downstream_gene_variant,,ENST00000397621,;FBXL16,downstream_gene_variant,,ENST00000562563,;LA16c-313D11.12,intron_variant,,ENST00000566927,;FBXL16,downstream_gene_variant,,ENST00000562585,;LA16c-313D11.12,non_coding_transcript_exon_variant,,ENST00000575305,;WDR24,upstream_gene_variant,,ENST00000567014,;FBXL16,downstream_gene_variant,,ENST00000562648,;	A	ENSG00000127580	ENST00000293883	Transcript	5_prime_UTR_variant	330	.	.	.	.	rs568055066,COSM165562	.	.	-1	WDR24	HGNC	20852	protein_coding	YES	CCDS10420.1	ENSP00000293883	WDR24_HUMAN	.	UPI0000037D32	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODIFIER	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTGAGGGC	.	4	ESCA
PIEZO1	0	.	GRCh37	16	88804229	88804229	+	Intron	SNP	A	A	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1021-7T>A	.	.	ENST00000301015	.	55	47	8	56	56	0	PIEZO1,splice_region_variant,,ENST00000301015,;RP5-1142A6.2,splice_region_variant,,ENST00000440406,;RP5-1142A6.2,non_coding_transcript_exon_variant,,ENST00000567968,;RP5-1142A6.7,upstream_gene_variant,,ENST00000566114,;RP5-1142A6.8,upstream_gene_variant,,ENST00000567588,;RP5-1142A6.8,upstream_gene_variant,,ENST00000333666,;PIEZO1,upstream_gene_variant,,ENST00000490756,;	T	ENSG00000103335	ENST00000301015	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	-1	PIEZO1	HGNC	28993	protein_coding	YES	CCDS54058.1	ENSP00000301015	PIEZ1_HUMAN	.	UPI0001B300F3	.	.	.	.	8/50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGCAGAGACCA	.	4	ESCA
ANKRD11	0	.	GRCh37	16	89348761	89348761	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4189C>T	p.%3D	p.L1397L	ENST00000301030	9/13	23	19	4	23	23	0	ANKRD11,synonymous_variant,p.%3D,ENST00000378330,;ANKRD11,synonymous_variant,p.%3D,ENST00000301030,;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;ANKRD11,downstream_gene_variant,,ENST00000562275,;ANKRD11,downstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000378332,;	A	ENSG00000167522	ENST00000301030	Transcript	synonymous_variant	4650	4189	1397	L	Ctg/Ttg	.	.	.	-1	ANKRD11	HGNC	21316	protein_coding	YES	CCDS32513.1	ENSP00000301030	ANR11_HUMAN	.	UPI00004569E1	.	.	.	9/13	.	hmmpanther:PTHR24145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCAGGAAGT	.	4	ESCA
ANKRD11	0	.	GRCh37	16	89348762	89348762	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4188C>T	p.%3D	p.F1396F	ENST00000301030	9/13	23	19	4	24	24	0	ANKRD11,synonymous_variant,p.%3D,ENST00000378330,;ANKRD11,synonymous_variant,p.%3D,ENST00000301030,;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;ANKRD11,downstream_gene_variant,,ENST00000562275,;ANKRD11,downstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000378332,;	A	ENSG00000167522	ENST00000301030	Transcript	synonymous_variant	4649	4188	1396	F	ttC/ttT	.	.	.	-1	ANKRD11	HGNC	21316	protein_coding	YES	CCDS32513.1	ENSP00000301030	ANR11_HUMAN	.	UPI00004569E1	.	.	.	9/13	.	hmmpanther:PTHR24145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAGGAAGTC	.	4	ESCA
ANKRD11	0	.	GRCh37	16	89348979	89348979	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3971C>G	p.Ser1324Cys	p.S1324C	ENST00000301030	9/13	53	45	7	38	38	0	ANKRD11,missense_variant,p.Ser1324Cys,ENST00000378330,;ANKRD11,missense_variant,p.Ser1324Cys,ENST00000301030,;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;ANKRD11,downstream_gene_variant,,ENST00000562275,;ANKRD11,downstream_gene_variant,,ENST00000568100,;ANKRD11,downstream_gene_variant,,ENST00000378332,;	C	ENSG00000167522	ENST00000301030	Transcript	missense_variant	4432	3971	1324	S/C	tCt/tGt	.	.	.	-1	ANKRD11	HGNC	21316	protein_coding	YES	CCDS32513.1	ENSP00000301030	ANR11_HUMAN	.	UPI00004569E1	.	.	possibly_damaging(0.815)	9/13	.	hmmpanther:PTHR24145	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAAAGAGACC	.	5	ESCA
FANCA	0	.	GRCh37	16	89828391	89828391	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2818C>A	p.Gln940Lys	p.Q940K	ENST00000389301	29/43	84	64	19	97	97	0	FANCA,missense_variant,p.Gln940Lys,ENST00000568369,;FANCA,missense_variant,p.Gln940Lys,ENST00000389301,;FANCA,missense_variant,p.Gln66Lys,ENST00000561660,;FANCA,missense_variant,p.Gln53Lys,ENST00000567988,;FANCA,3_prime_UTR_variant,,ENST00000563318,;FANCA,3_prime_UTR_variant,,ENST00000563510,;FANCA,non_coding_transcript_exon_variant,,ENST00000305699,;	T	ENSG00000187741	ENST00000389301	Transcript	missense_variant	2849	2818	940	Q/K	Caa/Aaa	.	.	.	-1	FANCA	HGNC	3582	protein_coding	YES	CCDS32515.1	ENSP00000373952	FANCA_HUMAN	H3BT53_HUMAN	UPI0000520A1A	.	tolerated(0.26)	benign(0.042)	29/43	.	hmmpanther:PTHR12047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGTTGAATTT	.	5	ESCA
MYH8	0	.	GRCh37	17	10293733	10293733	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*38G>A	.	.	ENST00000403437	40/40	52	36	16	42	42	0	MYH8,3_prime_UTR_variant,,ENST00000403437,;CTC-297N7.11,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,;	T	ENSG00000133020	ENST00000403437	Transcript	3_prime_UTR_variant	5947	.	.	.	.	.	.	.	-1	MYH8	HGNC	7578	protein_coding	YES	CCDS11153.1	ENSP00000384330	MYH8_HUMAN	.	UPI000012FB7D	.	.	.	40/40	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGTGCCTTTC	.	5	ESCA
ZNF624	0	.	GRCh37	17	16527278	16527278	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.922G>A	p.Glu308Lys	p.E308K	ENST00000311331	6/6	63	53	9	64	64	0	ZNF624,missense_variant,p.Glu308Lys,ENST00000311331,;ZNF624,non_coding_transcript_exon_variant,,ENST00000579528,;	T	ENSG00000197566	ENST00000311331	Transcript	missense_variant	1014	922	308	E/K	Gaa/Aaa	.	.	.	-1	ZNF624	HGNC	29254	protein_coding	YES	CCDS11180.1	ENSP00000310472	ZN624_HUMAN	J3QKY7_HUMAN,C9J5H1_HUMAN	UPI0000456A22	.	deleterious(0.01)	probably_damaging(0.987)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF207,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACATTCATTAC	.	4	ESCA
TEFM	0	.	GRCh37	17	29231387	29231387	+	Silent	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.192C>G	p.%3D	p.L64L	ENST00000581216	2/4	61	56	5	54	54	0	TEFM,synonymous_variant,p.%3D,ENST00000580840,;TEFM,synonymous_variant,p.%3D,ENST00000581216,;ADAP2,upstream_gene_variant,,ENST00000583688,;TEFM,synonymous_variant,p.%3D,ENST00000306049,;TEFM,non_coding_transcript_exon_variant,,ENST00000541382,;	C	ENSG00000172171	ENST00000581216	Transcript	synonymous_variant	814	192	64	L	ctC/ctG	.	.	.	-1	TEFM	HGNC	26223	protein_coding	YES	CCDS42291.1	ENSP00000462963	TEFM_HUMAN	.	UPI00000708D5	.	.	.	2/4	.	hmmpanther:PTHR21053:SF1,hmmpanther:PTHR21053,Superfamily_domains:SSF47781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGAAGAGCTT	.	3	ESCA
KRT16	0	.	GRCh37	17	39768500	39768500	+	Silent	SNP	C	C	A	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.441G>T	p.%3D	p.V147V	ENST00000301653	1/8	154	138	16	209	209	0	KRT16,synonymous_variant,p.%3D,ENST00000301653,;KRT16,5_prime_UTR_variant,,ENST00000593067,;KRT16,downstream_gene_variant,,ENST00000590990,;KRT16,non_coding_transcript_exon_variant,,ENST00000588319,;	A	ENSG00000186832	ENST00000301653	Transcript	synonymous_variant	506	441	147	V	gtG/gtT	COSM3517501	.	.	-1	KRT16	HGNC	6423	protein_coding	YES	CCDS11401.1	ENSP00000301653	K1C16_HUMAN	K7ENW6_HUMAN,K7ENV3_HUMAN	UPI0000001C7B	.	.	.	1/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF105,Pfam_domain:PF00038,Superfamily_domains:SSF64593	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ATCTTCACTTC	.	3	ESCA
SPATA32	0	.	GRCh37	17	43344462	43344465	+	5'Flank	DEL	CTCA	CTCA	-	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	CTCA	CTCA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000331780	.	42	37	5	60	60	0	SPATA32,upstream_gene_variant,,ENST00000331780,;MAP3K14-AS1,intron_variant,,ENST00000590100,;MAP3K14-AS1,intron_variant,,ENST00000591263,;MAP3K14-AS1,intron_variant,,ENST00000585351,;MAP3K14-AS1,intron_variant,,ENST00000586450,;MAP3K14-AS1,intron_variant,,ENST00000588504,;MAP3K14-AS1,intron_variant,,ENST00000588160,;MAP3K14-AS1,intron_variant,,ENST00000585346,;MAP3K14-AS1,intron_variant,,ENST00000592422,;MAP3K14-AS1,intron_variant,,ENST00000588698,;MAP3K14-AS1,intron_variant,,ENST00000585780,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000587332,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000344686,;MAP3K14,downstream_gene_variant,,ENST00000376926,;MAP3K14,non_coding_transcript_exon_variant,,ENST00000592267,;MAP3K14,downstream_gene_variant,,ENST00000586644,;	-	ENSG00000184361	ENST00000331780	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4983	-1	SPATA32	HGNC	26349	protein_coding	YES	CCDS32669.1	ENSP00000331532	SPT32_HUMAN	K7EQM9_HUMAN,B7Z7K7_HUMAN	UPI000049DE53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CACCTTCTCACTGTC	.	2	ESCA
HOXB7	0	.	GRCh37	17	46687889	46687889	+	Missense_Mutation	SNP	C	C	T	rs749136655	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.392G>A	p.Arg131Gln	p.R131Q	ENST00000239165	1/2	95	88	7	119	119	0	HOXB7,missense_variant,p.Arg131Gln,ENST00000239165,;HOXB8,downstream_gene_variant,,ENST00000468443,;HOXB8,downstream_gene_variant,,ENST00000498634,;HOXB8,downstream_gene_variant,,ENST00000576562,;HOXB8,downstream_gene_variant,,ENST00000239144,;HOXB-AS3,downstream_gene_variant,,ENST00000491264,;HOXB-AS3,downstream_gene_variant,,ENST00000487849,;HOXB-AS3,downstream_gene_variant,,ENST00000467155,;HOXB-AS3,downstream_gene_variant,,ENST00000494420,;HOXB-AS3,downstream_gene_variant,,ENST00000466037,;HOXB7,intron_variant,,ENST00000567101,;HOXB7,upstream_gene_variant,,ENST00000467314,;	T	ENSG00000260027	ENST00000239165	Transcript	missense_variant	491	392	131	R/Q	cGa/cAa	rs749136655	.	.	-1	HOXB7	HGNC	5118	protein_coding	YES	CCDS11532.1	ENSP00000239165	HXB7_HUMAN	Q9HB12_HUMAN	UPI00001AE6AD	.	tolerated(0.07)	possibly_damaging(0.862)	1/2	.	hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF129,PROSITE_patterns:PS00032,Gene3D:1.10.10.60,Superfamily_domains:SSF46689,Prints_domain:PR00025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTTCGCATC	.	2	ESCA
TM4SF5	0	.	GRCh37	17	4686468	4686468	+	3'UTR	SNP	C	C	G	rs762780205	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*45C>G	.	.	ENST00000270560	5/5	84	62	22	57	57	0	TM4SF5,3_prime_UTR_variant,,ENST00000270560,;VMO1,downstream_gene_variant,,ENST00000441199,;VMO1,downstream_gene_variant,,ENST00000328739,;VMO1,downstream_gene_variant,,ENST00000416307,;VMO1,downstream_gene_variant,,ENST00000354194,;TM4SF5,non_coding_transcript_exon_variant,,ENST00000576530,;	G	ENSG00000142484	ENST00000270560	Transcript	3_prime_UTR_variant	670	.	.	.	.	rs762780205	.	.	1	TM4SF5	HGNC	11857	protein_coding	YES	CCDS11054.1	ENSP00000270560	T4S5_HUMAN	.	UPI0000152C4B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	ACGCTCACTCC	byFrequency	4	ESCA
IGF2BP1	0	.	GRCh37	17	47103868	47103868	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326A>G	p.Asn109Ser	p.N109S	ENST00000290341	4/15	119	88	30	79	79	0	IGF2BP1,missense_variant,p.Asn109Ser,ENST00000290341,;IGF2BP1,missense_variant,p.Asn109Ser,ENST00000431824,;IGF2BP1,non_coding_transcript_exon_variant,,ENST00000499130,;IGF2BP1,non_coding_transcript_exon_variant,,ENST00000515586,;IGF2BP1,non_coding_transcript_exon_variant,,ENST00000505562,;	G	ENSG00000159217	ENST00000290341	Transcript	missense_variant	660	326	109	N/S	aAc/aGc	.	.	.	1	IGF2BP1	HGNC	28866	protein_coding	YES	CCDS11543.1	ENSP00000290341	IF2B1_HUMAN	D3DTW3_HUMAN	UPI0000117170	.	tolerated(0.29)	benign(0.1)	4/15	.	PROSITE_profiles:PS50102,hmmpanther:PTHR10288:SF136,hmmpanther:PTHR10288,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGAACTGTG	.	5	ESCA
TBX4	0	.	GRCh37	17	59533820	59533820	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-32G>A	.	.	ENST00000240335	1/8	79	50	29	130	130	0	TBX4,5_prime_UTR_variant,,ENST00000240335,;TBX4,intron_variant,,ENST00000589003,;TBX4,intron_variant,,ENST00000393853,;RP11-15K2.2,downstream_gene_variant,,ENST00000592766,;	A	ENSG00000121075	ENST00000240335	Transcript	5_prime_UTR_variant	14	.	.	.	.	.	.	.	1	TBX4	HGNC	11603	protein_coding	YES	CCDS11629.1	ENSP00000240335	TBX4_HUMAN	K7EPY2_HUMAN	UPI000013CAA9	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGCGAGTGA	.	5	ESCA
KCNJ2	0	.	GRCh37	17	68175037	68175037	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2573G>A	.	.	ENST00000243457	2/2	77	70	7	64	64	0	KCNJ2,3_prime_UTR_variant,,ENST00000243457,;KCNJ2,downstream_gene_variant,,ENST00000535240,;	A	ENSG00000123700	ENST00000243457	Transcript	3_prime_UTR_variant	4240	.	.	.	.	.	.	.	1	KCNJ2	HGNC	6263	protein_coding	YES	CCDS11688.1	ENSP00000243457	IRK2_HUMAN	.	UPI000004F21A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCTGAGAGC	.	2	ESCA
ALOX12	0	.	GRCh37	17	6909289	6909289	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1361G>A	p.Gly454Glu	p.G454E	ENST00000251535	10/14	83	75	8	74	74	0	ALOX12,missense_variant,p.Gly454Glu,ENST00000251535,;AC027763.2,intron_variant,,ENST00000399541,;AC027763.2,intron_variant,,ENST00000575889,;AC027763.2,intron_variant,,ENST00000574377,;AC027763.2,intron_variant,,ENST00000399540,;AC027763.2,intron_variant,,ENST00000573939,;AC027763.2,intron_variant,,ENST00000575727,;RP11-589P10.7,intron_variant,,ENST00000572547,;AC027763.2,intron_variant,,ENST00000572385,;AC027763.2,intron_variant,,ENST00000571010,;AC027763.2,intron_variant,,ENST00000570562,;ALOX12,upstream_gene_variant,,ENST00000406228,;	A	ENSG00000108839	ENST00000251535	Transcript	missense_variant	1414	1361	454	G/E	gGa/gAa	.	.	.	1	ALOX12	HGNC	429	protein_coding	YES	CCDS11084.1	ENSP00000251535	LOX12_HUMAN	.	UPI000013CD03	.	tolerated(0.11)	benign(0.034)	10/14	.	Superfamily_domains:SSF48484,Pfam_domain:PF00305,Gene3D:1.20.245.10,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF4,PROSITE_profiles:PS51393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGGGACTCC	.	4	ESCA
UNC13D	0	.	GRCh37	17	73827202	73827202	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2602G>A	p.Ala868Thr	p.A868T	ENST00000207549	27/32	102	68	33	139	139	0	UNC13D,missense_variant,p.Ala868Thr,ENST00000207549,;UNC13D,missense_variant,p.Ala868Thr,ENST00000412096,;UNC13D,downstream_gene_variant,,ENST00000586147,;UNC13D,upstream_gene_variant,,ENST00000589670,;UNC13D,downstream_gene_variant,,ENST00000586930,;UNC13D,downstream_gene_variant,,ENST00000591616,;UNC13D,upstream_gene_variant,,ENST00000590856,;UNC13D,upstream_gene_variant,,ENST00000586519,;UNC13D,downstream_gene_variant,,ENST00000587105,;UNC13D,downstream_gene_variant,,ENST00000591563,;	T	ENSG00000092929	ENST00000207549	Transcript	missense_variant	2982	2602	868	A/T	Gcc/Acc	.	.	.	-1	UNC13D	HGNC	23147	protein_coding	YES	CCDS11730.1	ENSP00000207549	UN13D_HUMAN	K7EIH3_HUMAN	UPI000015FC91	.	tolerated(0.96)	benign(0.021)	27/32	.	Pfam_domain:PF10540,hmmpanther:PTHR15015:SF20,hmmpanther:PTHR15015,PROSITE_profiles:PS51259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.K867E|c.2599A>G|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGGCCTTGG	.	5	ESCA
FXR2	0	.	GRCh37	17	7494747	7494747	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*401C>T	.	.	ENST00000250113	17/17	109	103	6	103	103	0	FXR2,3_prime_UTR_variant,,ENST00000250113,;MPDU1,intron_variant,,ENST00000584378,;MPDU1,intron_variant,,ENST00000423172,;MPDU1,downstream_gene_variant,,ENST00000581380,;SOX15,upstream_gene_variant,,ENST00000538513,;MPDU1,downstream_gene_variant,,ENST00000585217,;SOX15,upstream_gene_variant,,ENST00000250055,;SOX15,upstream_gene_variant,,ENST00000570788,;MPDU1,downstream_gene_variant,,ENST00000396501,;MPDU1,downstream_gene_variant,,ENST00000250124,;MPDU1,downstream_gene_variant,,ENST00000579445,;FXR2,downstream_gene_variant,,ENST00000573057,;FXR2,downstream_gene_variant,,ENST00000574490,;FXR2,downstream_gene_variant,,ENST00000571079,;MPDU1,downstream_gene_variant,,ENST00000571822,;MPDU1,downstream_gene_variant,,ENST00000576066,;MPDU1,downstream_gene_variant,,ENST00000584479,;MPDU1,downstream_gene_variant,,ENST00000577088,;MPDU1,downstream_gene_variant,,ENST00000580834,;FXR2,downstream_gene_variant,,ENST00000573957,;MPDU1,downstream_gene_variant,,ENST00000576272,;MPDU1,downstream_gene_variant,,ENST00000572719,;MPDU1,downstream_gene_variant,,ENST00000585188,;MPDU1,downstream_gene_variant,,ENST00000580708,;MPDU1,downstream_gene_variant,,ENST00000581886,;MPDU1,downstream_gene_variant,,ENST00000571877,;MPDU1,downstream_gene_variant,,ENST00000359822,;MPDU1,downstream_gene_variant,,ENST00000574558,;MPDU1,downstream_gene_variant,,ENST00000572836,;MPDU1,downstream_gene_variant,,ENST00000578267,;MPDU1,downstream_gene_variant,,ENST00000572936,;MPDU1,downstream_gene_variant,,ENST00000571391,;MPDU1,downstream_gene_variant,,ENST00000570458,;	A	ENSG00000129245	ENST00000250113	Transcript	3_prime_UTR_variant	2758	.	.	.	.	.	.	.	-1	FXR2	HGNC	4024	protein_coding	YES	CCDS45604.1	ENSP00000250113	FXR2_HUMAN	.	UPI0000072727	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGATGAGGCC	.	2	ESCA
TP53	0	.	GRCh37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.818G>A	p.Arg273His	p.R273H	ENST00000269305	8/11	45	34	10	47	47	0	TP53,missense_variant,p.Arg273His,ENST00000420246,;TP53,missense_variant,p.Arg273His,ENST00000269305,;TP53,missense_variant,p.Arg141His,ENST00000509690,;TP53,missense_variant,p.Arg273His,ENST00000359597,;TP53,missense_variant,p.Arg273His,ENST00000445888,;TP53,missense_variant,p.Arg273His,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	T	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1008	818	273	R/H	cGt/cAt	CM920677,CM010472,rs28934576,CM004342,TP53_g.13798G>C,TP53_g.13798del,TP53_g.13798G>A,TP53_g.13798G>T,COSM10660,COSM43896,COSM44440,COSM10779,COSM318169,COSM99729,COSM165077,COSM3356963,COSM3675521,COSM1640828,COSM1645335,COSM1646808	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	tolerated(0.13)	possibly_damaging(0.631)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	T:0.0002	T:0,T:0	T:0,T:0	.	T:0,T:0	T:0.001,T:0.001	T:0,T:0	.	.	pathogenic	0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	25105660	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R273H|c.818G>A|116,SITE|p.R273H|c.818G>A|64,SITE|p.R273H|c.818G>A|588,SITE|p.R273H|c.818G>A|83,CODON|p.0?|c.1_1182del1182|6,CODON|p.R273L|c.818G>T|98,CODON|p.R273P|c.818G>C|4,CODON|p.R273L|c.818G>T|5,CODON|p.R273P|c.818G>C|29,CODON|p.R273L|c.818G>T|18,CODON|p.R273L|c.818G>T|12,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274A|c.821T>C|8,BUFFER|p.V274A|c.821T>C|22,BUFFER|p.V274G|c.821T>G|8,BUFFER|p.V274D|c.821T>A|3,BUFFER|p.V274D|c.821T>A|10,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274L|c.820G>C|11,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3,BUFFER|p.E271Q|c.811G>C|4,BUFFER|p.E271K|c.811G>A|35,BUFFER|p.E271*|c.811G>T|16,BUFFER|p.E271*|c.811G>T|3,BUFFER|p.E271K|c.811G>A|13,BUFFER|p.E271K|c.811G>A|4,BUFFER|p.E271K|c.811G>A|8,BUFFER|p.F270L|c.810T>G|4,BUFFER|p.F270L|c.810T>A|5,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270Y|c.809T>A|5,BUFFER|p.F270C|c.809T>G|16,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270S|c.809T>C|14,BUFFER|p.F270S|c.809T>C|6,BUFFER|p.F270L|c.808T>C|16,BUFFER|p.F270I|c.808T>A|3,BUFFER|p.F270V|c.808T>G|8,BUFFER|p.F270L|c.808T>C|3,BUFFER|p.F270I|c.808T>A|6,BUFFER|p.S269S|c.807C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACACGCACC	byCluster|by1000G	5	ESCA
LGALS3BP	0	.	GRCh37	17	76969204	76969204	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.477G>C	p.%3D	p.V159V	ENST00000262776	5/6	28	17	11	28	28	0	LGALS3BP,synonymous_variant,p.%3D,ENST00000589906,;LGALS3BP,synonymous_variant,p.%3D,ENST00000585407,;LGALS3BP,synonymous_variant,p.%3D,ENST00000589775,;LGALS3BP,synonymous_variant,p.%3D,ENST00000262776,;LGALS3BP,synonymous_variant,p.%3D,ENST00000589527,;LGALS3BP,intron_variant,,ENST00000591778,;LGALS3BP,downstream_gene_variant,,ENST00000591274,;LGALS3BP,stop_lost,p.Ter19SerextTer17,ENST00000586720,;LGALS3BP,3_prime_UTR_variant,,ENST00000587311,;LGALS3BP,3_prime_UTR_variant,,ENST00000588198,;LGALS3BP,3_prime_UTR_variant,,ENST00000587251,;LGALS3BP,3_prime_UTR_variant,,ENST00000587310,;LGALS3BP,non_coding_transcript_exon_variant,,ENST00000588508,;LGALS3BP,non_coding_transcript_exon_variant,,ENST00000592255,;LGALS3BP,non_coding_transcript_exon_variant,,ENST00000588587,;LGALS3BP,downstream_gene_variant,,ENST00000588205,;LGALS3BP,downstream_gene_variant,,ENST00000586300,;LGALS3BP,downstream_gene_variant,,ENST00000588899,;LGALS3BP,downstream_gene_variant,,ENST00000588990,;	G	ENSG00000108679	ENST00000262776	Transcript	synonymous_variant	786	477	159	V	gtG/gtC	.	.	.	-1	LGALS3BP	HGNC	6564	protein_coding	YES	CCDS11759.1	ENSP00000262776	LG3BP_HUMAN	K7ESM3_HUMAN,K7ES75_HUMAN,K7EP36_HUMAN,K7EKQ5_HUMAN,B4DVE1_HUMAN	UPI000006E64A	.	.	.	5/6	.	PROSITE_profiles:PS50097,hmmpanther:PTHR19331:SF249,hmmpanther:PTHR19331,Gene3D:3.30.710.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACATTCACGCT	.	5	ESCA
RP11-1055B8.7	0	.	GRCh37	17	79409094	79409094	+	Missense_Mutation	SNP	C	C	T	rs781998556	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.719C>T	p.Ala240Val	p.A240V	ENST00000307745	9/32	36	32	4	40	40	0	RP11-1055B8.7,missense_variant,p.Ala121Val,ENST00000571813,;RP11-1055B8.7,missense_variant,p.Ala240Val,ENST00000307745,;RP11-1055B8.7,upstream_gene_variant,,ENST00000570375,;	T	ENSG00000171282	ENST00000307745	Transcript	missense_variant	719	719	240	A/V	gCg/gTg	rs781998556	.	.	1	RP11-1055B8.7	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000303486	.	J3QLH5_HUMAN,F8WBW8_HUMAN	UPI0001AE66BF	.	.	benign(0.011)	9/32	.	hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAGCGGCAG	.	2	ESCA
ZNF750	0	.	GRCh37	17	80790253	80790253	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.78delA	p.Lys26AsnfsTer19	p.K26Nfs*19	ENST00000269394	2/3	68	51	17	61	61	0	ZNF750,frameshift_variant,p.Lys26AsnfsTer19,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	-	ENSG00000141579	ENST00000269394	Transcript	frameshift_variant	912	78	26	K/X	aaA/aa	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	.	.	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678,Pfam_domain:PF15269	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GAAACATTTATA	.	3	ESCA
CHMP1B	0	.	GRCh37	18	11852310	11852310	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*200A>G	.	.	ENST00000526991	1/1	83	70	13	59	59	0	CHMP1B,3_prime_UTR_variant,,ENST00000526991,;GNAL,intron_variant,,ENST00000535121,;GNAL,intron_variant,,ENST00000585642,;GNAL,intron_variant,,ENST00000334049,;GNAL,intron_variant,,ENST00000269162,;GNAL,intron_variant,,ENST00000423027,;GNAL,intron_variant,,ENST00000590228,;RP11-78A19.3,non_coding_transcript_exon_variant,,ENST00000586474,;RP11-78A19.4,downstream_gene_variant,,ENST00000609238,;CHMP1B,upstream_gene_variant,,ENST00000588284,;	G	ENSG00000255112	ENST00000526991	Transcript	3_prime_UTR_variant	916	.	.	.	.	.	.	.	1	CHMP1B	HGNC	24287	protein_coding	YES	CCDS54180.1	ENSP00000432279	CHM1B_HUMAN	B2RA72_HUMAN	UPI00000373BD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGTATAGCT	.	5	ESCA
IMPA2	0	.	GRCh37	18	12030535	12030535	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*78C>T	.	.	ENST00000269159	8/8	33	29	4	34	34	0	IMPA2,3_prime_UTR_variant,,ENST00000269159,;IMPA2,downstream_gene_variant,,ENST00000588927,;IMPA2,downstream_gene_variant,,ENST00000589238,;RP11-703I16.1,downstream_gene_variant,,ENST00000587619,;IMPA2,downstream_gene_variant,,ENST00000588752,;IMPA2,3_prime_UTR_variant,,ENST00000590107,;IMPA2,non_coding_transcript_exon_variant,,ENST00000589374,;IMPA2,downstream_gene_variant,,ENST00000588167,;IMPA2,downstream_gene_variant,,ENST00000586230,;IMPA2,downstream_gene_variant,,ENST00000590138,;	T	ENSG00000141401	ENST00000269159	Transcript	3_prime_UTR_variant	1187	.	.	.	.	.	.	.	1	IMPA2	HGNC	6051	protein_coding	YES	CCDS11855.1	ENSP00000269159	IMPA2_HUMAN	K7EII9_HUMAN	UPI000012FB90	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCACGCTCC	.	4	ESCA
TMEM241	0	.	GRCh37	18	20932234	20932234	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.691C>T	p.Leu231Phe	p.L231F	ENST00000383233	13/15	71	48	23	75	75	0	TMEM241,missense_variant,p.Leu192Phe,ENST00000578520,;TMEM241,missense_variant,p.Leu231Phe,ENST00000383233,;TMEM241,missense_variant,p.Leu110Phe,ENST00000450466,;TMEM241,3_prime_UTR_variant,,ENST00000542162,;TMEM241,3_prime_UTR_variant,,ENST00000473688,;TMEM241,3_prime_UTR_variant,,ENST00000581444,;TMEM241,3_prime_UTR_variant,,ENST00000477053,;TMEM241,3_prime_UTR_variant,,ENST00000460322,;TMEM241,non_coding_transcript_exon_variant,,ENST00000583048,;TMEM241,downstream_gene_variant,,ENST00000482411,;TMEM241,downstream_gene_variant,,ENST00000497608,;TMEM241,downstream_gene_variant,,ENST00000577531,;	A	ENSG00000134490	ENST00000383233	Transcript	missense_variant	744	691	231	L/F	Ctc/Ttc	.	.	.	-1	TMEM241	HGNC	31723	protein_coding	YES	CCDS11876.2	ENSP00000372720	TM241_HUMAN	.	UPI000022A6E0	.	deleterious(0.04)	possibly_damaging(0.659)	13/15	.	hmmpanther:PTHR11132:SF29,hmmpanther:PTHR11132,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATGAGAAAGA	.	5	ESCA
EPG5	0	.	GRCh37	18	43510751	43510751	+	Missense_Mutation	SNP	T	T	C	rs61736031	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2303A>G	p.Asn768Ser	p.N768S	ENST00000282041	12/44	88	71	16	131	131	0	EPG5,missense_variant,p.Asn768Ser,ENST00000282041,;EPG5,non_coding_transcript_exon_variant,,ENST00000587974,;	C	ENSG00000152223	ENST00000282041	Transcript	missense_variant	2338	2303	768	N/S	aAt/aGt	rs61736031	.	.	-1	EPG5	HGNC	29331	protein_coding	YES	CCDS11926.2	ENSP00000282041	EPG5_HUMAN	Q9BYJ3_HUMAN,Q9BTI0_HUMAN	UPI00004F6F8A	.	tolerated(0.09)	probably_damaging(0.953)	12/44	.	hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4	C:0.0004	C:0.0015	C:0	.	C:0	C:0	C:0	C:0.0019	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTATTCATA	byFrequency|byCluster|by1000G	5	ESCA
MAPK4	0	.	GRCh37	18	48256223	48256223	+	Silent	SNP	G	G	A	rs746873598	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1763G>A	p.%3D	p.%3D	ENST00000400384	6/6	23	17	6	27	27	0	MAPK4,stop_retained_variant,p.%3D,ENST00000540640,;MAPK4,stop_retained_variant,p.%3D,ENST00000400384,;MAPK4,3_prime_UTR_variant,,ENST00000592595,;	A	ENSG00000141639	ENST00000400384	Transcript	stop_retained_variant	2799	1763	588	*	tGa/tAa	rs746873598	.	.	1	MAPK4	HGNC	6878	protein_coding	YES	CCDS42437.1	ENSP00000383234	MK04_HUMAN	Q0VG04_HUMAN,B4E104_HUMAN,B4DEW2_HUMAN	UPI0000201D20	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTGAGGGC	byFrequency	5	ESCA
PIGN	0	.	GRCh37	18	59749943	59749943	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2539G>C	p.Glu847Gln	p.E847Q	ENST00000357637	28/31	37	31	6	58	58	0	PIGN,missense_variant,p.Glu847Gln,ENST00000400334,;PIGN,missense_variant,p.Glu847Gln,ENST00000357637,;PIGN,splice_region_variant,,ENST00000587942,;	G	ENSG00000197563	ENST00000357637	Transcript	missense_variant	2955	2539	847	E/Q	Gaa/Caa	.	.	.	-1	PIGN	HGNC	8967	protein_coding	YES	CCDS45879.1	ENSP00000350263	PIGN_HUMAN	K7ESH9_HUMAN,K7ERX5_HUMAN,K7EQG0_HUMAN,K7EPN0_HUMAN,K7ENC3_HUMAN,K7EMD7_HUMAN,K7EM45_HUMAN,K7ELE1_HUMAN,K7EL34_HUMAN,K7EK83_HUMAN	UPI0000070A47	.	tolerated(0.16)	benign(0.196)	28/31	.	hmmpanther:PTHR12250,Pfam_domain:PF04987	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTTCAAAAG	.	5	ESCA
DDX39A	0	.	GRCh37	19	14520777	14520777	+	Intron	DEL	G	G	-	rs766547609	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.733-92delC	.	.	ENST00000242776	.	50	45	5	46	46	0	DDX39A,frameshift_variant,p.Ser250CysfsTer?,ENST00000454233,;DDX39A,intron_variant,,ENST00000242776,;CD97,downstream_gene_variant,,ENST00000242786,;CD97,downstream_gene_variant,,ENST00000357355,;CD97,downstream_gene_variant,,ENST00000358600,;DDX39A,downstream_gene_variant,,ENST00000586993,;DDX39A,downstream_gene_variant,,ENST00000592632,;DDX39A,downstream_gene_variant,,ENST00000589675,;DDX39A,downstream_gene_variant,,ENST00000590315,;DDX39A,downstream_gene_variant,,ENST00000590696,;DDX39A,downstream_gene_variant,,ENST00000591275,;DDX39A,downstream_gene_variant,,ENST00000590239,;CTC-548K16.5,upstream_gene_variant,,ENST00000590626,;DDX39A,intron_variant,,ENST00000592927,;DDX39A,downstream_gene_variant,,ENST00000593008,;DDX39A,frameshift_variant,p.Ser250CysfsTer76,ENST00000588692,;DDX39A,non_coding_transcript_exon_variant,,ENST00000589318,;DDX39A,non_coding_transcript_exon_variant,,ENST00000588542,;DDX39A,non_coding_transcript_exon_variant,,ENST00000592391,;DDX39A,non_coding_transcript_exon_variant,,ENST00000587730,;DDX39A,intron_variant,,ENST00000324340,;DDX39A,downstream_gene_variant,,ENST00000590260,;CD97,downstream_gene_variant,,ENST00000591565,;DDX39A,downstream_gene_variant,,ENST00000586558,;DDX39A,downstream_gene_variant,,ENST00000590556,;DDX39A,downstream_gene_variant,,ENST00000593026,;	-	ENSG00000123136	ENST00000242776	Transcript	intron_variant	.	.	.	.	.	rs766547609	.	.	-1	DDX39A	HGNC	17821	protein_coding	YES	CCDS12308.1	ENSP00000242776	DX39A_HUMAN	K7ENP6_HUMAN,K7EN69_HUMAN,K7EL56_HUMAN,K7EIL8_HUMAN	UPI00000713A1	.	.	.	.	6/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	TTGTGCGACACT	.	2	ESCA
CLEC17A	0	.	GRCh37	19	14717876	14717876	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.966G>A	p.%3D	p.G322G	ENST00000417570	13/14	69	57	12	83	83	0	CLEC17A,synonymous_variant,p.%3D,ENST00000417570,;CLEC17A,intron_variant,,ENST00000397439,;CLEC17A,intron_variant,,ENST00000547437,;CLEC17A,3_prime_UTR_variant,,ENST00000339847,;CLEC17A,3_prime_UTR_variant,,ENST00000551730,;	A	ENSG00000187912	ENST00000417570	Transcript	synonymous_variant	1004	966	322	G	ggG/ggA	.	.	.	1	CLEC17A	HGNC	34520	protein_coding	YES	CCDS56087.1	ENSP00000393719	CL17A_HUMAN	.	UPI0001747A7C	.	.	.	13/14	.	PROSITE_profiles:PS50041,hmmpanther:PTHR22802:SF214,hmmpanther:PTHR22802,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAGGGGACTG	.	5	ESCA
NOTCH3	0	.	GRCh37	19	15288489	15288489	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4250G>C	p.Cys1417Ser	p.C1417S	ENST00000263388	24/33	20	17	3	28	28	0	NOTCH3,missense_variant,p.Cys1417Ser,ENST00000263388,;NOTCH3,downstream_gene_variant,,ENST00000601011,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,;	G	ENSG00000074181	ENST00000263388	Transcript	missense_variant	4326	4250	1417	C/S	tGc/tCc	.	.	.	-1	NOTCH3	HGNC	7883	protein_coding	YES	CCDS12326.1	ENSP00000263388	NOTC3_HUMAN	.	UPI000013D3FA	.	deleterious(0)	probably_damaging(0.999)	24/33	.	Prints_domain:PR01452,Superfamily_domains:0042228,SMART_domains:SM00004,PIRSF_domain:PIRSF002279,Pfam_domain:PF00066,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF47,PROSITE_profiles:PS50258	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GCGAGCAGTCG	.	2	ESCA
CYP4F8	0	.	GRCh37	19	15734900	15734900	+	RNA	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2820G>C	.	.	ENST00000589787	5/9	168	136	32	148	148	0	CYP4F8,non_coding_transcript_exon_variant,,ENST00000589019,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000441682,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000443973,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000325723,;CYP4F8,upstream_gene_variant,,ENST00000589778,;CYP4F8,upstream_gene_variant,,ENST00000589722,;CYP4F8,downstream_gene_variant,,ENST00000592615,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000585349,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000589927,;CYP4F8,non_coding_transcript_exon_variant,,ENST00000589787,;CYP4F8,upstream_gene_variant,,ENST00000590745,;CYP4F8,downstream_gene_variant,,ENST00000587680,;	C	ENSG00000186526	ENST00000589787	Transcript	non_coding_transcript_exon_variant	2820	.	.	.	.	.	.	.	1	CYP4F8	HGNC	2648	retained_intron	YES	.	.	.	.	.	.	.	.	5/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTGAATGG	.	5	ESCA
ZNF90	0	.	GRCh37	19	20229526	20229526	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1163A>T	p.Lys388Met	p.K388M	ENST00000418063	4/4	85	78	7	68	68	0	ZNF90,missense_variant,p.Lys388Met,ENST00000418063,;ZNF90,intron_variant,,ENST00000474284,;ZNF90,intron_variant,,ENST00000469078,;ZNF90,upstream_gene_variant,,ENST00000484032,;ZNF90,downstream_gene_variant,,ENST00000473524,;	T	ENSG00000213988	ENST00000418063	Transcript	missense_variant	1275	1163	388	K/M	aAg/aTg	.	.	.	1	ZNF90	HGNC	13165	protein_coding	YES	CCDS46028.1	ENSP00000410466	ZNF90_HUMAN	.	UPI00002376E6	.	deleterious(0.02)	probably_damaging(0.934)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF92,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACATAAGATAA	.	3	ESCA
ZNF676	0	.	GRCh37	19	22363402	22363402	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1117G>T	p.Ala373Ser	p.A373S	ENST00000397121	3/3	85	74	11	78	78	0	ZNF676,missense_variant,p.Ala373Ser,ENST00000397121,;	A	ENSG00000196109	ENST00000397121	Transcript	missense_variant	1435	1117	373	A/S	Gcc/Tcc	COSM993861	.	.	-1	ZNF676	HGNC	20429	protein_coding	YES	CCDS42539.1	ENSP00000380310	ZN676_HUMAN	.	UPI00002376EC	.	tolerated(0.06)	benign(0.094)	3/3	.	Superfamily_domains:SSF57667,Superfamily_domains:SSF57667,SMART_domains:SM00355,Pfam_domain:PF13465,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF112,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAAGGCTTTGC	.	4	ESCA
ZNF91	0	.	GRCh37	19	23544105	23544105	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1676C>G	p.Ser559Ter	p.S559*	ENST00000300619	4/4	105	91	13	69	68	0	ZNF91,stop_gained,p.Ser527Ter,ENST00000397082,;ZNF91,stop_gained,p.Ser559Ter,ENST00000300619,;ZNF91,intron_variant,,ENST00000599743,;ZNF91,downstream_gene_variant,,ENST00000595533,;ZNF91,intron_variant,,ENST00000596989,;ZNF91,upstream_gene_variant,,ENST00000593341,;ZNF91,upstream_gene_variant,,ENST00000599281,;ZNF91,upstream_gene_variant,,ENST00000596528,;	C	ENSG00000167232	ENST00000300619	Transcript	stop_gained	1882	1676	559	S/*	tCa/tGa	.	.	.	-1	ZNF91	HGNC	13166	protein_coding	YES	CCDS42541.1	ENSP00000300619	ZNF91_HUMAN	M0R186_HUMAN	UPI00002038F9	.	.	.	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF100,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTTGAGAAT	.	4	ESCA
ZNF91	0	.	GRCh37	19	23544477	23544477	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1304A>C	p.Lys435Thr	p.K435T	ENST00000300619	4/4	54	48	6	54	54	0	ZNF91,missense_variant,p.Lys403Thr,ENST00000397082,;ZNF91,missense_variant,p.Lys435Thr,ENST00000300619,;ZNF91,intron_variant,,ENST00000599743,;ZNF91,downstream_gene_variant,,ENST00000595533,;ZNF91,intron_variant,,ENST00000596989,;ZNF91,upstream_gene_variant,,ENST00000593341,;ZNF91,upstream_gene_variant,,ENST00000599281,;ZNF91,upstream_gene_variant,,ENST00000596528,;	G	ENSG00000167232	ENST00000300619	Transcript	missense_variant	1510	1304	435	K/T	aAg/aCg	.	.	.	-1	ZNF91	HGNC	13166	protein_coding	YES	CCDS42541.1	ENSP00000300619	ZNF91_HUMAN	M0R186_HUMAN	UPI00002038F9	.	tolerated(0.11)	possibly_damaging(0.734)	4/4	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF100,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CACACTTGTAA	.	3	ESCA
ZNF681	0	.	GRCh37	19	23938284	23938284	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73C>G	p.Gln25Glu	p.Q25E	ENST00000402377	2/4	134	112	22	124	124	0	ZNF681,missense_variant,p.Gln25Glu,ENST00000402377,;ZNF681,intron_variant,,ENST00000395385,;ZNF681,intron_variant,,ENST00000528059,;ZNF681,intron_variant,,ENST00000531570,;	C	ENSG00000196172	ENST00000402377	Transcript	missense_variant	215	73	25	Q/E	Cag/Gag	.	.	.	-1	ZNF681	HGNC	26457	protein_coding	YES	CCDS12414.2	ENSP00000384000	ZN681_HUMAN	E9PSC0_HUMAN,E9PJB6_HUMAN	UPI000022ABC8	.	deleterious(0)	possibly_damaging(0.523)	2/4	.	PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF279,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTGTATAG	.	5	ESCA
TMPRSS9	0	.	GRCh37	19	2425186	2425186	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2802C>T	p.%3D	p.I934I	ENST00000332578	15/17	21	17	4	37	37	0	TMPRSS9,synonymous_variant,p.%3D,ENST00000332578,;LMNB2,downstream_gene_variant,,ENST00000582871,;TIMM13,downstream_gene_variant,,ENST00000215570,;LMNB2,downstream_gene_variant,,ENST00000325327,;TIMM13,downstream_gene_variant,,ENST00000591871,;LMNB2,downstream_gene_variant,,ENST00000532465,;LMNB2,downstream_gene_variant,,ENST00000475819,;	T	ENSG00000178297	ENST00000332578	Transcript	synonymous_variant	2802	2802	934	I	atC/atT	.	.	.	1	TMPRSS9	HGNC	30079	protein_coding	YES	CCDS12088.1	ENSP00000330264	TMPS9_HUMAN	.	UPI00001B4EC6	.	.	.	15/17	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF108,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,PIRSF_domain:PIRSF037931,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCATCTGCCT	.	2	ESCA
GNA15	0	.	GRCh37	19	3162843	3162843	+	Silent	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.951G>T	p.%3D	p.T317T	ENST00000262958	7/7	68	59	9	71	71	0	GNA15,synonymous_variant,p.%3D,ENST00000262958,;	T	ENSG00000060558	ENST00000262958	Transcript	synonymous_variant	1209	951	317	T	acG/acT	.	.	.	1	GNA15	HGNC	4383	protein_coding	YES	CCDS12104.1	ENSP00000262958	GNA15_HUMAN	.	UPI000013D36D	.	.	.	7/7	.	hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF50,Pfam_domain:PF00503,Gene3D:3.40.50.300,SMART_domains:SM00275,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACACGAGGAT	.	4	ESCA
NFIC	0	.	GRCh37	19	3359661	3359661	+	5'UTR	SNP	C	C	G	rs551469624	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-20C>G	.	.	ENST00000395111	1/10	35	31	4	43	43	0	NFIC,5_prime_UTR_variant,,ENST00000395111,;NFIC,5_prime_UTR_variant,,ENST00000346156,;NFIC,5_prime_UTR_variant,,ENST00000589123,;NFIC,upstream_gene_variant,,ENST00000586919,;	G	ENSG00000141905	ENST00000395111	Transcript	5_prime_UTR_variant	17	.	.	.	.	rs551469624	.	.	1	NFIC	HGNC	7786	protein_coding	.	CCDS58640.1	ENSP00000378543	NFIC_HUMAN	.	UPI000002AF19	.	.	.	1/10	.	.	A:0.0004	A:0.0015	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCGCCTC	byFrequency|by1000G	4	ESCA
GAPDHS	0	.	GRCh37	19	36035690	36035690	+	Intron	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1057-121G>A	.	.	ENST00000222286	.	42	19	22	16	16	0	GAPDHS,intron_variant,,ENST00000222286,;GAPDHS,downstream_gene_variant,,ENST00000585510,;TMEM147,upstream_gene_variant,,ENST00000392205,;TMEM147,upstream_gene_variant,,ENST00000392204,;TMEM147,upstream_gene_variant,,ENST00000222284,;AD000090.2,non_coding_transcript_exon_variant,,ENST00000588286,;AD000090.2,non_coding_transcript_exon_variant,,ENST00000590717,;AD000090.2,intron_variant,,ENST00000444728,;AD000090.2,intron_variant,,ENST00000589137,;AD000090.2,upstream_gene_variant,,ENST00000590125,;TMEM147,upstream_gene_variant,,ENST00000596232,;TMEM147,upstream_gene_variant,,ENST00000593027,;TMEM147,upstream_gene_variant,,ENST00000599895,;TMEM147,upstream_gene_variant,,ENST00000477168,;GAPDHS,downstream_gene_variant,,ENST00000586334,;TMEM147,upstream_gene_variant,,ENST00000595467,;TMEM147,upstream_gene_variant,,ENST00000595180,;	A	ENSG00000105679	ENST00000222286	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GAPDHS	HGNC	24864	protein_coding	YES	CCDS12465.1	ENSP00000222286	G3PT_HUMAN	K7EP73_HUMAN	UPI000012AE83	.	.	.	.	9/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTAGGGCTA	.	5	ESCA
ZFP14	0	.	GRCh37	19	36853058	36853058	+	Missense_Mutation	SNP	T	T	C	rs751461218	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92A>G	p.Tyr31Cys	p.Y31C	ENST00000270001	3/5	258	242	16	85	85	0	ZFP14,missense_variant,p.Tyr31Cys,ENST00000270001,;ZFP14,missense_variant,p.Tyr31Cys,ENST00000589280,;	C	ENSG00000142065	ENST00000270001	Transcript	missense_variant	208	92	31	Y/C	tAt/tGt	rs751461218	.	.	-1	ZFP14	HGNC	29312	protein_coding	YES	CCDS33002.1	ENSP00000270001	ZFP14_HUMAN	.	UPI000013AD55	.	deleterious(0)	possibly_damaging(0.873)	3/5	.	Superfamily_domains:0044637,SMART_domains:SM00349,Pfam_domain:PF01352,hmmpanther:PTHR24377:SF253,hmmpanther:PTHR24377,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCTATATAAG	.	2	ESCA
ZNF790	0	.	GRCh37	19	37310963	37310963	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283G>C	p.Glu95Gln	p.E95Q	ENST00000356725	5/5	113	104	8	80	80	0	ZNF790,missense_variant,p.Glu95Gln,ENST00000586323,;ZNF790,missense_variant,p.Glu95Gln,ENST00000528994,;ZNF790,missense_variant,p.Glu95Gln,ENST00000525288,;ZNF790,missense_variant,p.Glu95Gln,ENST00000356725,;ZNF790,downstream_gene_variant,,ENST00000527645,;CTD-2162K18.5,intron_variant,,ENST00000588906,;CTD-2162K18.5,intron_variant,,ENST00000587278,;	G	ENSG00000197863	ENST00000356725	Transcript	missense_variant	404	283	95	E/Q	Gag/Cag	.	.	.	-1	ZNF790	HGNC	33114	protein_coding	YES	CCDS12496.1	ENSP00000349161	ZN790_HUMAN	K7EQ58_HUMAN,E9PRR6_HUMAN,E9PQ03_HUMAN,E9PL27_HUMAN	UPI0000160EF0	.	deleterious(0.01)	benign(0.075)	5/5	.	hmmpanther:PTHR24377:SF224,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTCTCAAAAA	.	2	ESCA
ZNF568	0	.	GRCh37	19	37488248	37488248	+	Missense_Mutation	SNP	G	G	T	rs148872903	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1463G>T	p.Arg488Leu	p.R488L	ENST00000455427	9/9	62	50	12	66	66	0	ZNF568,missense_variant,p.Arg488Leu,ENST00000455427,;ZNF568,missense_variant,p.Arg552Leu,ENST00000444991,;ZNF568,downstream_gene_variant,,ENST00000455817,;ZNF568,downstream_gene_variant,,ENST00000433993,;ZNF568,downstream_gene_variant,,ENST00000588596,;ZNF568,non_coding_transcript_exon_variant,,ENST00000591887,;	T	ENSG00000198453	ENST00000455427	Transcript	missense_variant	1792	1463	488	R/L	cGa/cTa	rs148872903,COSM4077504	.	.	1	ZNF568	HGNC	25392	protein_coding	.	CCDS56093.1	ENSP00000413396	ZN568_HUMAN	K7ELK8_HUMAN,K7EL97_HUMAN,C9K0F2_HUMAN,C9JXQ5_HUMAN	UPI0001AE649F	.	tolerated(0.27)	probably_damaging(0.999)	9/9	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF107,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACCCGACATC	by1000G	5	ESCA
CADM4	0	.	GRCh37	19	44130331	44130331	+	Silent	SNP	G	G	A	rs199788280	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609C>T	p.%3D	p.N203N	ENST00000222374	5/9	43	38	5	42	42	0	CADM4,synonymous_variant,p.%3D,ENST00000222374,;CADM4,upstream_gene_variant,,ENST00000593506,;	A	ENSG00000105767	ENST00000222374	Transcript	synonymous_variant	658	609	203	N	aaC/aaT	rs199788280	.	.	-1	CADM4	HGNC	30825	protein_coding	YES	CCDS12627.1	ENSP00000222374	CADM4_HUMAN	.	UPI000004EE93	.	.	.	5/9	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF50,Pfam_domain:PF08205,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTGGTTCTG	byCluster	4	ESCA
ZNF227	0	.	GRCh37	19	44732371	44732371	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61-228G>C	.	.	ENST00000313040	.	11	8	3	9	9	0	ZNF227,intron_variant,,ENST00000589005,;ZNF227,intron_variant,,ENST00000313040,;ZNF227,intron_variant,,ENST00000586048,;ZNF227,intron_variant,,ENST00000391961,;ZNF227,intron_variant,,ENST00000588394,;ZNF227,intron_variant,,ENST00000586228,;ZNF227,intron_variant,,ENST00000588219,;ZNF227,intron_variant,,ENST00000589707,;ZNF227,non_coding_transcript_exon_variant,,ENST00000589237,;ZNF227,intron_variant,,ENST00000591019,;ZNF235,downstream_gene_variant,,ENST00000592844,;	C	ENSG00000131115	ENST00000313040	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	ZNF227	HGNC	13020	protein_coding	YES	CCDS12636.1	ENSP00000321049	ZN227_HUMAN	Q86WM4_HUMAN,Q658S5_HUMAN,K7EIL7_HUMAN,B7Z5P9_HUMAN	UPI000000DC17	.	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTGAGACTCC	.	2	ESCA
FOSB	0	.	GRCh37	19	45976867	45976867	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*597C>T	.	.	ENST00000353609	4/4	145	108	36	152	152	0	FOSB,3_prime_UTR_variant,,ENST00000592811,;FOSB,3_prime_UTR_variant,,ENST00000586615,;FOSB,3_prime_UTR_variant,,ENST00000417353,;FOSB,3_prime_UTR_variant,,ENST00000585836,;FOSB,3_prime_UTR_variant,,ENST00000591858,;FOSB,3_prime_UTR_variant,,ENST00000443841,;FOSB,3_prime_UTR_variant,,ENST00000353609,;ERCC1,intron_variant,,ENST00000423698,;FOSB,downstream_gene_variant,,ENST00000589593,;FOSB,downstream_gene_variant,,ENST00000592436,;FOSB,downstream_gene_variant,,ENST00000590335,;FOSB,downstream_gene_variant,,ENST00000586113,;FOSB,downstream_gene_variant,,ENST00000587358,;	T	ENSG00000125740	ENST00000353609	Transcript	3_prime_UTR_variant	2206	.	.	.	.	.	.	.	1	FOSB	HGNC	3797	protein_coding	YES	CCDS12664.1	ENSP00000245919	FOSB_HUMAN	Q49AD7_HUMAN,K7ERZ8_HUMAN,K7EKC1_HUMAN,K7EKA0_HUMAN	UPI000004F5D2	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAATTCGATGC	.	5	ESCA
GYS1	0	.	GRCh37	19	49484891	49484891	+	Silent	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1065G>T	p.%3D	p.V355V	ENST00000323798	8/16	60	52	7	70	70	0	GYS1,stop_lost,p.Ter236LeuextTer41,ENST00000540532,;GYS1,synonymous_variant,p.%3D,ENST00000263276,;GYS1,synonymous_variant,p.%3D,ENST00000323798,;GYS1,synonymous_variant,p.%3D,ENST00000541188,;GYS1,splice_region_variant,,ENST00000544287,;GYS1,splice_region_variant,,ENST00000484289,;GYS1,upstream_gene_variant,,ENST00000496048,;GYS1,upstream_gene_variant,,ENST00000472004,;	A	ENSG00000104812	ENST00000323798	Transcript	synonymous_variant	1262	1065	355	V	gtG/gtT	.	.	.	-1	GYS1	HGNC	4706	protein_coding	YES	CCDS12747.1	ENSP00000317904	GYS1_HUMAN	F5H1N8_HUMAN	UPI0000000C44	.	.	.	8/16	.	hmmpanther:PTHR10176,hmmpanther:PTHR10176:SF2,Pfam_domain:PF05693,Superfamily_domains:SSF53756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGTTCACCTG	.	4	ESCA
ARHGEF18	0	.	GRCh37	19	7505303	7505303	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.477G>A	p.Met159Ile	p.M159I	ENST00000359920	1/20	44	39	5	44	44	0	ARHGEF18,start_lost,p.Met1?,ENST00000319670,;ARHGEF18,start_lost,p.Met1?,ENST00000599752,;ARHGEF18,missense_variant,p.Met159Ile,ENST00000359920,;CTD-2207O23.3,missense_variant,p.Met117Ile,ENST00000593531,;ARHGEF18,upstream_gene_variant,,ENST00000595600,;	A	ENSG00000104880	ENST00000359920	Transcript	missense_variant	730	477	159	M/I	atG/atA	.	.	.	1	ARHGEF18	HGNC	17090	protein_coding	YES	CCDS45946.1	ENSP00000352995	ARHGI_HUMAN	M0R125_HUMAN	UPI0000D6170D	.	deleterious(0.01)	probably_damaging(0.993)	1/20	.	hmmpanther:PTHR22825,hmmpanther:PTHR22825:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTATGACGGT	.	2	ESCA
FBXL12	0	.	GRCh37	19	9929551	9929551	+	5'UTR	SNP	G	G	C	rs191599755	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-62C>G	.	.	ENST00000247977	1/3	66	54	12	61	61	0	FBXL12,5_prime_UTR_variant,,ENST00000588922,;FBXL12,5_prime_UTR_variant,,ENST00000586469,;FBXL12,5_prime_UTR_variant,,ENST00000592067,;FBXL12,5_prime_UTR_variant,,ENST00000589626,;FBXL12,5_prime_UTR_variant,,ENST00000590277,;FBXL12,5_prime_UTR_variant,,ENST00000247977,;FBXL12,intron_variant,,ENST00000585379,;FBXL12,upstream_gene_variant,,ENST00000586073,;FBXL12,upstream_gene_variant,,ENST00000586651,;SNORA70,upstream_gene_variant,,ENST00000363367,;AC008752.1,upstream_gene_variant,,ENST00000401283,;FBXL12,upstream_gene_variant,,ENST00000590808,;FBXL12,upstream_gene_variant,,ENST00000592732,;FBXL12,upstream_gene_variant,,ENST00000589438,;RPL10P15,upstream_gene_variant,,ENST00000585756,;	C	ENSG00000127452	ENST00000247977	Transcript	5_prime_UTR_variant	181	.	.	.	.	rs191599755	.	.	-1	FBXL12	HGNC	13611	protein_coding	YES	CCDS12218.1	ENSP00000247977	FXL12_HUMAN	K7EPN7_HUMAN,K7ELM5_HUMAN	UPI000006EBD0	.	.	.	1/3	.	.	A:0.0002	A:0	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGCCGAGGCG	by1000G	5	ESCA
COL11A1	0	.	GRCh37	1	103491477	103491477	+	Intron	SNP	C	C	A	rs569376136	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.897+295G>T	.	.	ENST00000370096	.	54	50	4	60	60	0	COL11A1,missense_variant,p.Arg271Met,ENST00000427239,;COL11A1,missense_variant,p.Arg271Met,ENST00000358392,;COL11A1,intron_variant,,ENST00000512756,;COL11A1,intron_variant,,ENST00000353414,;COL11A1,intron_variant,,ENST00000370096,;COL11A1,downstream_gene_variant,,ENST00000447608,;	A	ENSG00000060718	ENST00000370096	Transcript	intron_variant	.	.	.	.	.	rs569376136	.	.	-1	COL11A1	HGNC	2186	protein_coding	YES	CCDS778.1	ENSP00000359114	COBA1_HUMAN	Q4FAC4_HUMAN,B4DQZ0_HUMAN	UPI00002053EF	.	.	.	.	6/66	.	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGTCCTCATC	byCluster|by1000G	2	ESCA
CASZ1	0	.	GRCh37	1	10708141	10708141	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3214C>T	p.Pro1072Ser	p.P1072S	ENST00000377022	16/21	90	73	17	91	91	0	CASZ1,missense_variant,p.Pro1072Ser,ENST00000344008,;CASZ1,missense_variant,p.Pro1072Ser,ENST00000377022,;CASZ1,upstream_gene_variant,,ENST00000447850,;RP4-734G22.3,non_coding_transcript_exon_variant,,ENST00000606802,;CASZ1,downstream_gene_variant,,ENST00000496432,;CASZ1,downstream_gene_variant,,ENST00000490176,;	A	ENSG00000130940	ENST00000377022	Transcript	missense_variant	3532	3214	1072	P/S	Ccg/Tcg	.	.	.	-1	CASZ1	HGNC	26002	protein_coding	YES	CCDS41246.1	ENSP00000366221	CASZ1_HUMAN	.	UPI0000EBB7D6	.	tolerated(0.15)	benign(0.027)	16/21	.	hmmpanther:PTHR12451	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCGGAAAGG	.	5	ESCA
CSF1	0	.	GRCh37	1	110453483	110453483	+	5'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-163G>C	.	.	ENST00000329608	1/9	183	162	20	219	218	0	CSF1,5_prime_UTR_variant,,ENST00000329608,;CSF1,5_prime_UTR_variant,,ENST00000357302,;CSF1,5_prime_UTR_variant,,ENST00000344188,;CSF1,intron_variant,,ENST00000527192,;CSF1,intron_variant,,ENST00000525659,;CSF1,upstream_gene_variant,,ENST00000488198,;CSF1,upstream_gene_variant,,ENST00000420111,;CSF1,upstream_gene_variant,,ENST00000369801,;CSF1,upstream_gene_variant,,ENST00000369802,;CSF1,upstream_gene_variant,,ENST00000526001,;	C	ENSG00000184371	ENST00000329608	Transcript	5_prime_UTR_variant	229	.	.	.	.	.	.	.	1	CSF1	HGNC	2432	protein_coding	YES	CCDS816.1	ENSP00000327513	CSF1_HUMAN	H7BY18_HUMAN,E9PKP4_HUMAN	UPI00001AFA6F	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCCGGGGAA	.	4	ESCA
IGSF3	0	.	GRCh37	1	117156526	117156526	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.693C>T	p.%3D	p.L231L	ENST00000369483	4/12	102	92	10	80	80	0	IGSF3,synonymous_variant,p.%3D,ENST00000318837,;IGSF3,synonymous_variant,p.%3D,ENST00000369486,;IGSF3,synonymous_variant,p.%3D,ENST00000369483,;IGSF3,downstream_gene_variant,,ENST00000481589,;	A	ENSG00000143061	ENST00000369483	Transcript	synonymous_variant	1398	693	231	L	ctC/ctT	.	.	.	-1	IGSF3	HGNC	5950	protein_coding	YES	CCDS30814.1	ENSP00000358495	IGSF3_HUMAN	.	UPI0000140437	.	.	.	4/12	.	PROSITE_profiles:PS50835,hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF21,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGGTGAGGCG	.	4	ESCA
IVL	0	.	GRCh37	1	152883367	152883367	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1094T>A	p.Leu365His	p.L365H	ENST00000368764	2/2	91	78	13	95	95	0	IVL,missense_variant,p.Leu365His,ENST00000368764,;IVL,missense_variant,p.Leu219His,ENST00000392667,;	A	ENSG00000163207	ENST00000368764	Transcript	missense_variant	1158	1094	365	L/H	cTc/cAc	.	.	.	1	IVL	HGNC	6187	protein_coding	YES	CCDS1030.1	ENSP00000357753	INVO_HUMAN	J3KPN6_HUMAN	UPI000013E24A	.	tolerated(0.14)	benign(0.444)	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGGCTCCCAG	.	4	ESCA
FCRL3	0	.	GRCh37	1	157650813	157650813	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1915A>C	p.Lys639Gln	p.K639Q	ENST00000368184	12/15	56	46	9	57	57	0	FCRL3,missense_variant,p.Lys639Gln,ENST00000368186,;FCRL3,missense_variant,p.Lys639Gln,ENST00000368184,;FCRL3,non_coding_transcript_exon_variant,,ENST00000494724,;FCRL3,non_coding_transcript_exon_variant,,ENST00000473231,;FCRL3,non_coding_transcript_exon_variant,,ENST00000468507,;FCRL3,non_coding_transcript_exon_variant,,ENST00000480682,;FCRL3,upstream_gene_variant,,ENST00000457799,;FCRL3,missense_variant,p.Lys639Gln,ENST00000485028,;FCRL3,missense_variant,p.Lys544Gln,ENST00000477837,;FCRL3,missense_variant,p.Lys645Gln,ENST00000492769,;	G	ENSG00000160856	ENST00000368184	Transcript	missense_variant	2207	1915	639	K/Q	Aaa/Caa	.	.	.	-1	FCRL3	HGNC	18506	protein_coding	YES	CCDS1167.1	ENSP00000357167	FCRL3_HUMAN	R4GNJ6_HUMAN	UPI000006D60E	.	tolerated(0.07)	benign(0.035)	12/15	.	hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTTTAGAGT	.	5	ESCA
KCNJ9	0	.	GRCh37	1	160054107	160054107	+	Missense_Mutation	SNP	C	C	G	rs764258969	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.287C>G	p.Ala96Gly	p.A96G	ENST00000368088	2/3	74	69	4	88	88	0	KCNJ9,missense_variant,p.Ala96Gly,ENST00000368088,;RP11-536C5.2,downstream_gene_variant,,ENST00000435580,;	G	ENSG00000162728	ENST00000368088	Transcript	missense_variant	529	287	96	A/G	gCg/gGg	rs764258969	.	.	1	KCNJ9	HGNC	6270	protein_coding	YES	CCDS1194.1	ENSP00000357067	IRK9_HUMAN	.	UPI000013E1B3	.	tolerated(0.46)	benign(0.015)	2/3	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11767:SF17,hmmpanther:PTHR11767,Gene3D:1.10.287.70,Pfam_domain:PF01007,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACCGCGTGGA	.	2	ESCA
VANGL2	0	.	GRCh37	1	160388955	160388955	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.356C>G	p.Ser119Cys	p.S119C	ENST00000368061	4/8	12	8	4	21	21	0	VANGL2,missense_variant,p.Ser119Cys,ENST00000368061,;VANGL2,upstream_gene_variant,,ENST00000483408,;	G	ENSG00000162738	ENST00000368061	Transcript	missense_variant	830	356	119	S/C	tCt/tGt	.	.	.	1	VANGL2	HGNC	15511	protein_coding	YES	CCDS30915.1	ENSP00000357040	VANG2_HUMAN	.	UPI00001C1D79	.	deleterious(0.02)	benign(0.007)	4/8	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR20886,hmmpanther:PTHR20886:SF10,Pfam_domain:PF06638,PIRSF_domain:PIRSF007991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTGTCTTTCC	.	2	ESCA
LHX4	0	.	GRCh37	1	180243439	180243439	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.898C>G	p.Gln300Glu	p.Q300E	ENST00000263726	6/6	82	62	19	78	78	0	LHX4,missense_variant,p.Gln300Glu,ENST00000263726,;RP5-1180C10.2,intron_variant,,ENST00000415414,;RP5-1180C10.2,intron_variant,,ENST00000440959,;ACBD6,downstream_gene_variant,,ENST00000496993,;LHX4,downstream_gene_variant,,ENST00000561113,;	G	ENSG00000121454	ENST00000263726	Transcript	missense_variant	1142	898	300	Q/E	Cag/Gag	COSM3789180	.	.	1	LHX4	HGNC	21734	protein_coding	YES	CCDS1338.1	ENSP00000263726	LHX4_HUMAN	Q96JP7_HUMAN,Q5RLJ3_HUMAN,Q5RLJ2_HUMAN,Q5RLJ1_HUMAN	UPI000007340D	.	tolerated(0.51)	benign(0.007)	6/6	.	hmmpanther:PTHR24208:SF15,hmmpanther:PTHR24208	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTATCAGGAC	.	5	ESCA
ZNF281	0	.	GRCh37	1	200378496	200378496	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.338C>G	p.Ser113Trp	p.S113W	ENST00000294740	2/2	77	58	18	92	92	0	ZNF281,missense_variant,p.Ser113Trp,ENST00000367353,;ZNF281,missense_variant,p.Ser77Trp,ENST00000367352,;ZNF281,missense_variant,p.Ser113Trp,ENST00000294740,;	C	ENSG00000162702	ENST00000294740	Transcript	missense_variant	463	338	113	S/W	tCg/tGg	.	.	.	-1	ZNF281	HGNC	13075	protein_coding	YES	CCDS1402.1	ENSP00000294740	ZN281_HUMAN	B3KMX4_HUMAN	UPI000013C345	.	deleterious(0.01)	benign(0.277)	2/2	.	hmmpanther:PTHR11389:SF327,hmmpanther:PTHR11389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGCGAGGGG	.	5	ESCA
PROX1	0	.	GRCh37	1	214169993	214169993	+	Missense_Mutation	SNP	G	G	A	rs765586199	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.115G>A	p.Ala39Thr	p.A39T	ENST00000366958	2/5	74	64	9	72	72	0	PROX1,missense_variant,p.Ala39Thr,ENST00000498508,;PROX1,missense_variant,p.Ala39Thr,ENST00000366958,;PROX1,missense_variant,p.Ala39Thr,ENST00000607425,;PROX1,missense_variant,p.Ala39Thr,ENST00000471129,;PROX1,missense_variant,p.Ala39Thr,ENST00000261454,;PROX1,missense_variant,p.Ala39Thr,ENST00000435016,;	A	ENSG00000117707	ENST00000366958	Transcript	missense_variant	723	115	39	A/T	Gca/Aca	rs765586199	.	.	1	PROX1	HGNC	9459	protein_coding	YES	CCDS31021.1	ENSP00000355925	PROX1_HUMAN	U3KPY6_HUMAN,C9JU29_HUMAN,B4DP41_HUMAN	UPI0000071D14	.	tolerated_low_confidence(0.12)	benign(0.272)	2/5	.	hmmpanther:PTHR12198:SF2,hmmpanther:PTHR12198	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAGAGCAACG	byFrequency	4	ESCA
URB2	0	.	GRCh37	1	229771164	229771164	+	Silent	SNP	G	G	T	rs749934225	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.804G>T	p.%3D	p.T268T	ENST00000258243	4/10	41	35	6	38	38	0	URB2,synonymous_variant,p.%3D,ENST00000258243,;	T	ENSG00000135763	ENST00000258243	Transcript	synonymous_variant	940	804	268	T	acG/acT	rs749934225	.	.	1	URB2	HGNC	28967	protein_coding	YES	CCDS31052.1	ENSP00000258243	URB2_HUMAN	Q5VYD0_HUMAN	UPI000013CFBD	.	.	.	4/10	.	hmmpanther:PTHR15682	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	AAGACGGGAGC	byFrequency	3	ESCA
ARID4B	0	.	GRCh37	1	235357397	235357397	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2056G>C	p.Asp686His	p.D686H	ENST00000264183	19/24	122	112	10	97	97	0	ARID4B,missense_variant,p.Asp86His,ENST00000444620,;ARID4B,missense_variant,p.Asp686His,ENST00000366603,;ARID4B,missense_variant,p.Asp600His,ENST00000349213,;ARID4B,missense_variant,p.Asp686His,ENST00000264183,;MIR4753,upstream_gene_variant,,ENST00000585119,;ARID4B,missense_variant,p.Asp686His,ENST00000421364,;ARID4B,non_coding_transcript_exon_variant,,ENST00000471257,;ARID4B,non_coding_transcript_exon_variant,,ENST00000491632,;ARID4B,upstream_gene_variant,,ENST00000474953,;	G	ENSG00000054267	ENST00000264183	Transcript	missense_variant	2554	2056	686	D/H	Gat/Cat	.	.	.	-1	ARID4B	HGNC	15550	protein_coding	YES	CCDS31061.1	ENSP00000264183	ARI4B_HUMAN	.	UPI00000437FE	.	deleterious_low_confidence(0)	possibly_damaging(0.681)	19/24	.	hmmpanther:PTHR13964:SF21,hmmpanther:PTHR13964	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGCATCAGTGA	.	3	ESCA
MTR	0	.	GRCh37	1	237052504	237052504	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2875C>G	p.Gln959Glu	p.Q959E	ENST00000366577	28/33	149	121	28	138	138	0	MTR,missense_variant,p.Gln513Glu,ENST00000366576,;MTR,missense_variant,p.Gln959Glu,ENST00000366577,;MTR,missense_variant,p.Gln908Glu,ENST00000535889,;	G	ENSG00000116984	ENST00000366577	Transcript	missense_variant	3269	2875	959	Q/E	Cag/Gag	.	.	.	1	MTR	HGNC	7468	protein_coding	YES	CCDS1614.1	ENSP00000355536	METH_HUMAN	.	UPI0000036BC4	.	tolerated(0.05)	benign(0)	28/33	.	Superfamily_domains:SSF56507,PIRSF_domain:PIRSF000381,TIGRFAM_domain:TIGR02082,hmmpanther:PTHR21091:SF97,hmmpanther:PTHR21091,PROSITE_profiles:PS50974	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGACCCAGGTC	.	4	ESCA
FMN2	0	.	GRCh37	1	240371346	240371346	+	Silent	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3234C>A	p.%3D	p.P1078P	ENST00000319653	5/18	57	46	11	92	92	0	FMN2,synonymous_variant,p.%3D,ENST00000319653,;FMN2,downstream_gene_variant,,ENST00000447095,;	A	ENSG00000155816	ENST00000319653	Transcript	synonymous_variant	3464	3234	1078	P	ccC/ccA	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	.	5/18	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,Pfam_domain:PF06346,Pfam_domain:PF06346,SMART_domains:SM00498	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGCCCCCACT	.	5	ESCA
OR1C1	0	.	GRCh37	1	247921358	247921358	+	Silent	SNP	C	C	G	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.351G>C	p.%3D	p.V117V	ENST00000408896	1/1	60	54	6	47	47	0	OR1C1,synonymous_variant,p.%3D,ENST00000408896,;	G	ENSG00000221888	ENST00000408896	Transcript	synonymous_variant	625	351	117	V	gtG/gtC	COSM1502396	.	.	-1	OR1C1	HGNC	8182	protein_coding	YES	CCDS41481.1	ENSP00000386138	OR1C1_HUMAN	.	UPI000004B1DC	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF108,hmmpanther:PTHR26451,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCATCACACA	.	3	ESCA
OR2M2	0	.	GRCh37	1	248344136	248344136	+	Silent	SNP	C	C	T	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.849C>T	p.%3D	p.P283P	ENST00000359682	1/1	124	114	10	102	102	0	OR2M2,synonymous_variant,p.%3D,ENST00000359682,;	T	ENSG00000198601	ENST00000359682	Transcript	synonymous_variant	849	849	283	P	ccC/ccT	COSM680459,COSM358381	.	.	1	OR2M2	HGNC	8268	protein_coding	YES	CCDS31106.1	ENSP00000352710	OR2M2_HUMAN	.	UPI00001612E4	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF204,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTCCCATGCT	.	2	ESCA
ZMYM6	0	.	GRCh37	1	35472675	35472675	+	Nonsense_Mutation	SNP	G	G	A	rs748753112	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1690C>T	p.Arg564Ter	p.R564*	ENST00000357182	12/16	91	75	16	77	77	0	ZMYM6,stop_gained,p.Arg564Ter,ENST00000357182,;ZMYM6,stop_gained,p.Arg564Ter,ENST00000373340,;ZMYM6,non_coding_transcript_exon_variant,,ENST00000466345,;ZMYM6,non_coding_transcript_exon_variant,,ENST00000493328,;ZMYM6,downstream_gene_variant,,ENST00000472971,;RP11-244H3.4,stop_gained,p.Arg564Ter,ENST00000487874,;	A	ENSG00000163867	ENST00000357182	Transcript	stop_gained	1918	1690	564	R/*	Cga/Tga	rs748753112	.	.	-1	ZMYM6	HGNC	13050	protein_coding	YES	CCDS387.2	ENSP00000349708	ZMYM6_HUMAN	Q7L9K1_HUMAN,A4Z946_HUMAN	UPI000040EBC6	.	.	.	12/16	.	hmmpanther:PTHR11697:SF92,hmmpanther:PTHR11697,SMART_domains:SM00746	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTCGTTTAC	byFrequency	5	ESCA
ZMYM1	0	.	GRCh37	1	35563128	35563128	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.380C>A	p.Ser127Ter	p.S127*	ENST00000373330	5/11	101	86	15	78	78	0	ZMYM1,stop_gained,p.Ser127Ter,ENST00000417119,;ZMYM1,stop_gained,p.Ser127Ter,ENST00000373330,;ZMYM1,stop_gained,p.Ser127Ter,ENST00000359858,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000373329,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000475654,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000488455,;ZMYM1,non_coding_transcript_exon_variant,,ENST00000466390,;ZMYM1,downstream_gene_variant,,ENST00000476269,;	A	ENSG00000197056	ENST00000373330	Transcript	stop_gained	554	380	127	S/*	tCa/tAa	.	.	.	1	ZMYM1	HGNC	26253	protein_coding	YES	CCDS41302.1	ENSP00000362427	ZMYM1_HUMAN	Q9H5R2_HUMAN,Q5SW02_HUMAN,Q5SVZ7_HUMAN	UPI0000203ED6	.	.	.	5/11	.	hmmpanther:PTHR11697:SF88,hmmpanther:PTHR11697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTTCACCAG	.	4	ESCA
AGO1	0	.	GRCh37	1	36383283	36383283	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2118G>A	p.%3D	p.Q706Q	ENST00000373204	16/19	71	53	18	78	77	1	AGO1,synonymous_variant,p.%3D,ENST00000373204,;AGO1,synonymous_variant,p.%3D,ENST00000373206,;	A	ENSG00000092847	ENST00000373204	Transcript	synonymous_variant	2331	2118	706	Q	caG/caA	.	.	.	1	AGO1	HGNC	3262	protein_coding	YES	CCDS398.1	ENSP00000362300	AGO1_HUMAN	Q5TA58_HUMAN	UPI000012D07D	.	.	.	16/19	.	PROSITE_profiles:PS50822,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF17,Pfam_domain:PF02171,Gene3D:3.30.420.10,SMART_domains:SM00950,Superfamily_domains:SSF53098	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGCAGAAACG	.	5	ESCA
C1orf122	0	.	GRCh37	1	38274899	38274899	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*154C>T	.	.	ENST00000373042	3/3	54	45	8	56	56	0	C1orf122,3_prime_UTR_variant,,ENST00000446260,;C1orf122,3_prime_UTR_variant,,ENST00000373042,;C1orf122,3_prime_UTR_variant,,ENST00000468084,;C1orf122,3_prime_UTR_variant,,ENST00000373043,;MTF1,downstream_gene_variant,,ENST00000373036,;YRDC,upstream_gene_variant,,ENST00000373044,;C1orf122,downstream_gene_variant,,ENST00000419397,;	T	ENSG00000197982	ENST00000373042	Transcript	3_prime_UTR_variant	746	.	.	.	.	.	.	.	1	C1orf122	HGNC	24789	protein_coding	YES	CCDS427.2	ENSP00000362133	CA122_HUMAN	.	UPI00001D7EAD	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGTTCACTCC	.	4	ESCA
GJA9	0	.	GRCh37	1	39341814	39341814	+	5'UTR	SNP	G	G	C	rs374468698	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-44C>G	.	.	ENST00000357771	2/2	114	99	14	85	85	0	GJA9,5_prime_UTR_variant,,ENST00000454994,;GJA9,5_prime_UTR_variant,,ENST00000357771,;GJA9,5_prime_UTR_variant,,ENST00000360786,;MYCBP,upstream_gene_variant,,ENST00000397572,;RP5-864K19.4,non_coding_transcript_exon_variant,,ENST00000443161,;RP5-864K19.4,non_coding_transcript_exon_variant,,ENST00000456813,;RP5-864K19.4,intron_variant,,ENST00000433671,;MYCBP,non_coding_transcript_exon_variant,,ENST00000489803,;MYCBP,non_coding_transcript_exon_variant,,ENST00000489575,;MYCBP,upstream_gene_variant,,ENST00000465771,;MYCBP,upstream_gene_variant,,ENST00000462027,;MYCBP,upstream_gene_variant,,ENST00000495043,;MYCBP,upstream_gene_variant,,ENST00000494695,;	C	ENSG00000131233	ENST00000357771	Transcript	5_prime_UTR_variant	238	.	.	.	.	rs374468698	.	.	-1	GJA9	HGNC	19155	protein_coding	YES	CCDS432.1	ENSP00000350415	CXA9_HUMAN	.	UPI000006E09A	.	.	.	2/2	.	.	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATAAGAGGCA	byCluster	4	ESCA
RLF	0	.	GRCh37	1	40702082	40702082	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1708C>T	p.Leu570Phe	p.L570F	ENST00000372771	8/8	65	60	5	57	57	0	RLF,missense_variant,p.Leu570Phe,ENST00000372771,;	T	ENSG00000117000	ENST00000372771	Transcript	missense_variant	1735	1708	570	L/F	Ctt/Ttt	.	.	.	1	RLF	HGNC	10025	protein_coding	YES	CCDS448.1	ENSP00000361857	RLF_HUMAN	.	UPI000013C9DA	.	deleterious(0.01)	probably_damaging(0.981)	8/8	.	SMART_domains:SM00355,hmmpanther:PTHR15507:SF18,hmmpanther:PTHR15507	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAATTCTTCAT	.	2	ESCA
TMEM59	0	.	GRCh37	1	54518838	54518838	+	Silent	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.24C>A	p.%3D	p.L8L	ENST00000234831	1/8	120	93	27	117	117	0	TMEM59,synonymous_variant,p.%3D,ENST00000371337,;TMEM59,synonymous_variant,p.%3D,ENST00000234831,;TMEM59,synonymous_variant,p.%3D,ENST00000452421,;TMEM59,intron_variant,,ENST00000440019,;TMEM59,intron_variant,,ENST00000420738,;TMEM59,intron_variant,,ENST00000371341,;TCEANC2,upstream_gene_variant,,ENST00000234827,;TCEANC2,upstream_gene_variant,,ENST00000371331,;MIR4781,upstream_gene_variant,,ENST00000585250,;TCEANC2,upstream_gene_variant,,ENST00000498272,;	T	ENSG00000116209	ENST00000234831	Transcript	synonymous_variant	274	24	8	L	ctC/ctA	.	.	.	-1	TMEM59	HGNC	1239	protein_coding	YES	CCDS586.1	ENSP00000234831	TMM59_HUMAN	Q5T6Z8_HUMAN	UPI0000001BF9	.	.	.	1/8	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCAGAGGCT	.	5	ESCA
PGM1	0	.	GRCh37	1	64089294	64089294	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.163G>C	p.Glu55Gln	p.E55Q	ENST00000371083	1/11	72	65	7	71	71	0	PGM1,missense_variant,p.Glu55Gln,ENST00000371083,;PGM1,intron_variant,,ENST00000371084,;PGM1,intron_variant,,ENST00000540265,;	C	ENSG00000079739	ENST00000371083	Transcript	missense_variant	531	163	55	E/Q	Gag/Cag	.	.	.	1	PGM1	HGNC	8905	protein_coding	YES	CCDS53323.1	ENSP00000360124	PGM1_HUMAN	.	UPI000016A812	.	tolerated(0.13)	benign(0.049)	1/11	.	hmmpanther:PTHR22573:SF37,hmmpanther:PTHR22573,Gene3D:3.40.120.10,Pfam_domain:PF02878,Superfamily_domains:SSF53738	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTGGAGAAT	.	2	ESCA
NEXN	0	.	GRCh37	1	78408248	78408248	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1762C>A	p.Leu588Ile	p.L588I	ENST00000334785	13/13	106	96	9	75	75	0	NEXN,missense_variant,p.Leu488Ile,ENST00000342754,;NEXN,missense_variant,p.Leu588Ile,ENST00000334785,;NEXN,missense_variant,p.Leu574Ile,ENST00000457030,;NEXN,missense_variant,p.Leu524Ile,ENST00000330010,;NEXN,non_coding_transcript_exon_variant,,ENST00000480732,;FUBP1,downstream_gene_variant,,ENST00000483894,;FUBP1,downstream_gene_variant,,ENST00000492724,;FUBP1,downstream_gene_variant,,ENST00000488814,;FUBP1,downstream_gene_variant,,ENST00000474632,;FUBP1,downstream_gene_variant,,ENST00000492405,;FUBP1,downstream_gene_variant,,ENST00000480673,;FUBP1,downstream_gene_variant,,ENST00000489495,;NEXN,non_coding_transcript_exon_variant,,ENST00000470735,;FUBP1,downstream_gene_variant,,ENST00000294623,;	A	ENSG00000162614	ENST00000334785	Transcript	missense_variant	1946	1762	588	L/I	Ctt/Att	.	.	.	1	NEXN	HGNC	29557	protein_coding	YES	CCDS41351.1	ENSP00000333938	NEXN_HUMAN	B4DDI0_HUMAN	UPI000022ABDC	.	deleterious(0.01)	probably_damaging(0.999)	13/13	.	PROSITE_profiles:PS50835,hmmpanther:PTHR22964,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGCCTCTTAAA	.	3	ESCA
SYDE2	0	.	GRCh37	1	85624705	85624705	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3313G>C	p.Glu1105Gln	p.E1105Q	ENST00000341460	7/7	93	74	19	61	61	0	SYDE2,missense_variant,p.Glu1105Gln,ENST00000341460,;	G	ENSG00000097096	ENST00000341460	Transcript	missense_variant	3363	3313	1105	E/Q	Gaa/Caa	.	.	.	-1	SYDE2	HGNC	25841	protein_coding	YES	CCDS44169.1	ENSP00000340594	SYDE2_HUMAN	.	UPI0001553B04	.	deleterious(0.02)	possibly_damaging(0.623)	7/7	.	hmmpanther:PTHR23178:SF24,hmmpanther:PTHR23178	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCTTTTG	.	5	ESCA
JAG1	0	.	GRCh37	20	10653641	10653641	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.95C>A	p.Ser32Ter	p.S32*	ENST00000254958	2/26	143	113	30	128	128	0	JAG1,stop_gained,p.Ser32Ter,ENST00000254958,;RP11-103J8.1,non_coding_transcript_exon_variant,,ENST00000605292,;	T	ENSG00000101384	ENST00000254958	Transcript	stop_gained	611	95	32	S/*	tCg/tAg	.	.	.	-1	JAG1	HGNC	6188	protein_coding	YES	CCDS13112.1	ENSP00000254958	JAG1_HUMAN	B7U6M8_HUMAN,B4DYR1_HUMAN	UPI00000498B5	.	.	.	2/26	.	hmmpanther:PTHR24044:SF212,hmmpanther:PTHR24044,Pfam_domain:PF07657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCCGAGGCC	.	5	ESCA
ABHD12	0	.	GRCh37	20	25295561	25295561	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.619G>A	p.Gly207Ser	p.G207S	ENST00000376542	6/13	70	59	10	68	68	0	ABHD12,missense_variant,p.Gly207Ser,ENST00000339157,;ABHD12,missense_variant,p.Gly50Ser,ENST00000471287,;ABHD12,missense_variant,p.Gly50Ser,ENST00000491682,;ABHD12,missense_variant,p.Gly162Ser,ENST00000450393,;ABHD12,missense_variant,p.Gly207Ser,ENST00000376542,;ABHD12,upstream_gene_variant,,ENST00000481556,;	T	ENSG00000100997	ENST00000376542	Transcript	missense_variant	899	619	207	G/S	Ggt/Agt	.	.	.	-1	ABHD12	HGNC	15868	protein_coding	YES	CCDS13172.1	ENSP00000365725	ABD12_HUMAN	I3L440_HUMAN,I3L294_HUMAN	UPI000006F03A	.	deleterious(0)	probably_damaging(1)	6/13	.	hmmpanther:PTHR12277:SF47,hmmpanther:PTHR12277,Gene3D:3.40.50.1820,Pfam_domain:PF12695,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCACCTCTGT	.	4	ESCA
ASXL1	0	.	GRCh37	20	31017787	31017787	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.649A>G	p.Ile217Val	p.I217V	ENST00000375687	8/13	49	41	7	41	41	0	ASXL1,missense_variant,p.Ile217Val,ENST00000375687,;ASXL1,missense_variant,p.Ile212Val,ENST00000306058,;ASXL1,upstream_gene_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000542461,;ASXL1,downstream_gene_variant,,ENST00000470145,;ASXL1,upstream_gene_variant,,ENST00000555564,;	G	ENSG00000171456	ENST00000375687	Transcript	missense_variant	1073	649	217	I/V	Att/Gtt	.	.	.	1	ASXL1	HGNC	18318	protein_coding	YES	CCDS13201.1	ENSP00000364839	ASXL1_HUMAN	.	UPI000036702C	.	tolerated(0.16)	benign(0.091)	8/13	.	hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTATTCGT	.	5	ESCA
MYH7B	0	.	GRCh37	20	33581979	33581979	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2601C>G	p.Ile867Met	p.I867M	ENST00000262873	25/43	49	46	3	43	43	0	MYH7B,missense_variant,p.Ile867Met,ENST00000262873,;MIR499A,downstream_gene_variant,,ENST00000384903,;	G	ENSG00000078814	ENST00000262873	Transcript	missense_variant	2693	2601	867	I/M	atC/atG	.	.	.	1	MYH7B	HGNC	15906	protein_coding	YES	CCDS42869.1	ENSP00000262873	MYH7B_HUMAN	.	UPI0000253BD4	.	.	possibly_damaging(0.61)	25/43	.	hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF310,Gene3D:1wdcA00,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	AACATCCGTGC	.	2	ESCA
MMP24	0	.	GRCh37	20	33851658	33851658	+	Silent	SNP	C	C	T	rs768177318	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.882C>T	p.%3D	p.S294S	ENST00000246186	5/9	67	61	6	56	56	0	MMP24,synonymous_variant,p.%3D,ENST00000246186,;EDEM2,intron_variant,,ENST00000540582,;MMP24-AS1,intron_variant,,ENST00000453892,;MMP24-AS1,intron_variant,,ENST00000456350,;MMP24-AS1,intron_variant,,ENST00000438751,;MMP24-AS1,intron_variant,,ENST00000566203,;MMP24-AS1,intron_variant,,ENST00000454184,;MMP24-AS1,intron_variant,,ENST00000433764,;RP4-614O4.11,downstream_gene_variant,,ENST00000444717,;	T	ENSG00000125966	ENST00000246186	Transcript	synonymous_variant	967	882	294	S	agC/agT	rs768177318	.	.	1	MMP24	HGNC	7172	protein_coding	YES	CCDS46593.1	ENSP00000246186	MMP24_HUMAN	Q86VV6_HUMAN	UPI000012F259	.	.	.	5/9	.	hmmpanther:PTHR10201:SF138,hmmpanther:PTHR10201,Pfam_domain:PF00413,Gene3D:3.40.390.10,SMART_domains:SM00235,PIRSF_domain:PIRSF001191,Superfamily_domains:SSF55486,Prints_domain:PR00138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCAGCGACCC	.	4	ESCA
ERGIC3	0	.	GRCh37	20	34130306	34130306	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.204G>A	p.%3D	p.L68L	ENST00000357394	3/14	47	34	12	43	43	0	ERGIC3,synonymous_variant,p.%3D,ENST00000413587,;ERGIC3,synonymous_variant,p.%3D,ENST00000357394,;ERGIC3,synonymous_variant,p.%3D,ENST00000447986,;ERGIC3,synonymous_variant,p.%3D,ENST00000348547,;ERGIC3,synonymous_variant,p.%3D,ENST00000416206,;ERGIC3,synonymous_variant,p.%3D,ENST00000411577,;ERGIC3,synonymous_variant,p.%3D,ENST00000279052,;ERGIC3,non_coding_transcript_exon_variant,,ENST00000486268,;ERGIC3,upstream_gene_variant,,ENST00000482338,;ERGIC3,upstream_gene_variant,,ENST00000489071,;ERGIC3,synonymous_variant,p.%3D,ENST00000438317,;ERGIC3,non_coding_transcript_exon_variant,,ENST00000496172,;ERGIC3,non_coding_transcript_exon_variant,,ENST00000461043,;ERGIC3,non_coding_transcript_exon_variant,,ENST00000492184,;ERGIC3,non_coding_transcript_exon_variant,,ENST00000476926,;RPL36P4,downstream_gene_variant,,ENST00000456725,;	A	ENSG00000125991	ENST00000357394	Transcript	synonymous_variant	264	204	68	L	ctG/ctA	.	.	.	1	ERGIC3	HGNC	15927	protein_coding	YES	CCDS13258.1	ENSP00000349970	ERGI3_HUMAN	.	UPI000013CBE0	.	.	.	3/14	.	hmmpanther:PTHR10984,hmmpanther:PTHR10984:SF25,Pfam_domain:PF13850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTGAAGAT	.	5	ESCA
C20orf27	0	.	GRCh37	20	3734504	3734504	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*201C>G	.	.	ENST00000217195	6/6	77	59	18	108	108	0	C20orf27,3_prime_UTR_variant,,ENST00000379772,;C20orf27,3_prime_UTR_variant,,ENST00000399672,;C20orf27,3_prime_UTR_variant,,ENST00000399683,;C20orf27,3_prime_UTR_variant,,ENST00000217195,;HSPA12B,downstream_gene_variant,,ENST00000542646,;HSPA12B,downstream_gene_variant,,ENST00000254963,;HSPA12B,downstream_gene_variant,,ENST00000399701,;	C	ENSG00000101220	ENST00000217195	Transcript	3_prime_UTR_variant	953	.	.	.	.	.	.	.	-1	C20orf27	HGNC	15873	protein_coding	YES	CCDS33436.1	ENSP00000217195	CT027_HUMAN	.	UPI0000470A46	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGAGAGGAG	.	5	ESCA
TTPAL	0	.	GRCh37	20	43115331	43115331	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.735G>C	p.Glu245Asp	p.E245D	ENST00000372904	5/6	69	60	9	61	61	0	TTPAL,missense_variant,p.Glu245Asp,ENST00000262605,;TTPAL,missense_variant,p.Glu245Asp,ENST00000372904,;TTPAL,missense_variant,p.Glu211Asp,ENST00000456317,;TTPAL,intron_variant,,ENST00000372906,;TTPAL,non_coding_transcript_exon_variant,,ENST00000461134,;	C	ENSG00000124120	ENST00000372904	Transcript	missense_variant	878	735	245	E/D	gaG/gaC	.	.	.	1	TTPAL	HGNC	16114	protein_coding	YES	CCDS13332.2	ENSP00000361995	TTPAL_HUMAN	B2RA57_HUMAN	UPI000020657C	.	tolerated(0.09)	possibly_damaging(0.676)	5/6	.	PROSITE_profiles:PS50191,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF110,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087,Prints_domain:PR00180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGGAGAAAAT	.	2	ESCA
ATP9A	0	.	GRCh37	20	50235275	50235275	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2276G>T	p.Arg759Leu	p.R759L	ENST00000338821	21/28	67	62	5	85	85	0	ATP9A,missense_variant,p.Arg759Leu,ENST00000338821,;ATP9A,missense_variant,p.Arg638Leu,ENST00000402822,;ATP9A,missense_variant,p.Arg623Leu,ENST00000311637,;	A	ENSG00000054793	ENST00000338821	Transcript	missense_variant	2541	2276	759	R/L	cGa/cTa	.	.	.	-1	ATP9A	HGNC	13540	protein_coding	YES	CCDS33489.1	ENSP00000342481	ATP9A_HUMAN	Q2NLD0_HUMAN,B4DR18_HUMAN	UPI000004D334	.	deleterious(0.02)	probably_damaging(0.961)	21/28	.	hmmpanther:PTHR24092:SF49,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,Gene3D:3.40.50.1000,Pfam_domain:PF00702,TIGRFAM_domain:TIGR01494,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACATCGGCAG	.	2	ESCA
HELZ2	0	.	GRCh37	20	62192573	62192573	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7008C>T	p.%3D	p.V2336V	ENST00000467148	14/19	57	50	7	63	63	0	HELZ2,synonymous_variant,p.%3D,ENST00000467148,;HELZ2,synonymous_variant,p.%3D,ENST00000427522,;C20orf195,downstream_gene_variant,,ENST00000370097,;C20orf195,downstream_gene_variant,,ENST00000370098,;HELZ2,non_coding_transcript_exon_variant,,ENST00000478861,;	A	ENSG00000130589	ENST00000467148	Transcript	synonymous_variant	7078	7008	2336	V	gtC/gtT	.	.	.	-1	HELZ2	HGNC	30021	protein_coding	YES	CCDS33508.1	ENSP00000417401	HELZ2_HUMAN	Q3C1U4_HUMAN	UPI0000246BF7	.	.	.	14/19	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF332,Pfam_domain:PF13086,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATGACCTC	.	4	ESCA
PDE9A	0	.	GRCh37	21	44153470	44153470	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.502T>C	p.Phe168Leu	p.F168L	ENST00000291539	7/20	117	94	23	119	119	0	PDE9A,missense_variant,p.Phe108Leu,ENST00000335512,;PDE9A,missense_variant,p.Phe41Leu,ENST00000398224,;PDE9A,missense_variant,p.Phe67Leu,ENST00000398234,;PDE9A,missense_variant,p.Phe40Leu,ENST00000539837,;PDE9A,missense_variant,p.Phe168Leu,ENST00000291539,;PDE9A,missense_variant,p.Phe40Leu,ENST00000349112,;PDE9A,missense_variant,p.Phe101Leu,ENST00000398232,;PDE9A,missense_variant,p.Phe127Leu,ENST00000398225,;PDE9A,missense_variant,p.Phe82Leu,ENST00000398236,;PDE9A,missense_variant,p.Phe34Leu,ENST00000398229,;PDE9A,missense_variant,p.Phe66Leu,ENST00000335440,;PDE9A,missense_variant,p.Phe8Leu,ENST00000398227,;PDE9A,missense_variant,p.Phe142Leu,ENST00000328862,;PDE9A,missense_variant,p.Phe115Leu,ENST00000380328,;AP001627.1,downstream_gene_variant,,ENST00000437426,;PDE9A,non_coding_transcript_exon_variant,,ENST00000460905,;PDE9A,non_coding_transcript_exon_variant,,ENST00000462571,;PDE9A,non_coding_transcript_exon_variant,,ENST00000495521,;PDE9A,non_coding_transcript_exon_variant,,ENST00000490803,;PDE9A,non_coding_transcript_exon_variant,,ENST00000470987,;PDE9A,non_coding_transcript_exon_variant,,ENST00000497805,;PDE9A,non_coding_transcript_exon_variant,,ENST00000468805,;PDE9A,non_coding_transcript_exon_variant,,ENST00000495343,;PDE9A,non_coding_transcript_exon_variant,,ENST00000460989,;PDE9A,non_coding_transcript_exon_variant,,ENST00000467403,;PDE9A,non_coding_transcript_exon_variant,,ENST00000467162,;	C	ENSG00000160191	ENST00000291539	Transcript	missense_variant	562	502	168	F/L	Ttc/Ctc	.	.	.	1	PDE9A	HGNC	8795	protein_coding	YES	CCDS13690.1	ENSP00000291539	PDE9A_HUMAN	.	UPI0000127C02	.	tolerated(0.36)	possibly_damaging(0.742)	7/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGCATTCAAA	.	5	ESCA
MCM3AP	0	.	GRCh37	21	47669700	47669700	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4290+1743C>G	.	.	ENST00000397708	.	47	43	4	50	50	0	MCM3AP,intron_variant,,ENST00000291688,;MCM3AP,intron_variant,,ENST00000397708,;MCM3AP-AS1,non_coding_transcript_exon_variant,,ENST00000414659,;MCM3AP-AS1,non_coding_transcript_exon_variant,,ENST00000455567,;MCM3AP-AS1,intron_variant,,ENST00000590829,;AP001469.9,downstream_gene_variant,,ENST00000447037,;AP001469.7,downstream_gene_variant,,ENST00000444966,;MCM3AP-AS1,downstream_gene_variant,,ENST00000588753,;AP001469.9,downstream_gene_variant,,ENST00000430259,;MCM3AP,intron_variant,,ENST00000467026,;MCM3AP,downstream_gene_variant,,ENST00000481113,;MCM3AP,intron_variant,,ENST00000496607,;MCM3AP,intron_variant,,ENST00000486937,;	C	ENSG00000160294	ENST00000397708	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MCM3AP	HGNC	6946	protein_coding	YES	CCDS13734.1	ENSP00000380820	GANP_HUMAN	N0GVG8_HUMAN,B3KWZ4_HUMAN	UPI000012ED4A	.	.	.	.	21/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCAAGAGCCA	.	2	ESCA
KLHL22	0	.	GRCh37	22	20825674	20825674	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.356A>T	p.Asn119Ile	p.N119I	ENST00000328879	3/7	90	46	43	56	56	0	KLHL22,missense_variant,p.Asn153Ile,ENST00000443285,;KLHL22,missense_variant,p.Asn119Ile,ENST00000431430,;KLHL22,missense_variant,p.Asn151Ile,ENST00000444967,;KLHL22,missense_variant,p.Asn119Ile,ENST00000328879,;KLHL22,missense_variant,p.Asn119Ile,ENST00000458248,;KLHL22,missense_variant,p.Asn42Ile,ENST00000451553,;KLHL22,intron_variant,,ENST00000440659,;KLHL22-IT1,downstream_gene_variant,,ENST00000532431,;KLHL22,intron_variant,,ENST00000494929,;KLHL22,non_coding_transcript_exon_variant,,ENST00000479601,;	A	ENSG00000099910	ENST00000328879	Transcript	missense_variant	513	356	119	N/I	aAt/aTt	.	.	.	-1	KLHL22	HGNC	25888	protein_coding	YES	CCDS13780.1	ENSP00000331682	KLH22_HUMAN	C9J2T1_HUMAN,C9J191_HUMAN,B7Z2G1_HUMAN	UPI0000072F37	.	deleterious(0.01)	benign(0.361)	3/7	.	hmmpanther:PTHR24412:SF180,hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,PIRSF_domain:PIRSF037037,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTACATTGCTC	.	5	ESCA
PI4KA	0	.	GRCh37	22	21174836	21174836	+	Missense_Mutation	SNP	G	G	C	rs371865226	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520C>G	p.Gln174Glu	p.Q174E	ENST00000255882	5/55	122	108	13	64	64	0	PI4KA,missense_variant,p.Gln116Glu,ENST00000572273,;PI4KA,missense_variant,p.Gln174Glu,ENST00000255882,;PI4KA,downstream_gene_variant,,ENST00000449120,;PI4KA,non_coding_transcript_exon_variant,,ENST00000485963,;	C	ENSG00000241973	ENST00000255882	Transcript	missense_variant	607	520	174	Q/E	Caa/Gaa	rs371865226	.	.	-1	PI4KA	HGNC	8983	protein_coding	YES	CCDS33603.2	ENSP00000255882	.	Q4LE69_HUMAN,J3KN10_HUMAN,C9JLI1_HUMAN	UPI0000E06BD6	.	tolerated(0.63)	benign(0.028)	5/55	.	.	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTTGAATCT	.	4	ESCA
IGLC7	0	.	GRCh37	22	23264889	23264889	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>A	p.Trp42Ter	p.W42*	ENST00000390331	1/1	246	184	61	172	172	0	IGLC7,stop_gained,p.Trp42Ter,ENST00000390331,;IGLJ7,downstream_gene_variant,,ENST00000390330,;IGLJ6,downstream_gene_variant,,ENST00000390328,;IGLC6,downstream_gene_variant,,ENST00000410078,;	A	ENSG00000211685	ENST00000390331	Transcript	stop_gained	124	125	42	W/*	tGg/tAg	.	.	.	1	IGLC7	HGNC	5861	IG_C_gene	YES	.	ENSP00000374859	.	.	UPI000059D86A	.	.	.	1/1	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266:SF75,hmmpanther:PTHR23266,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTGGAAGG	.	5	ESCA
SUSD2	0	.	GRCh37	22	24583631	24583631	+	Missense_Mutation	SNP	G	G	C	rs372525863	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1984G>C	p.Glu662Gln	p.E662Q	ENST00000358321	12/15	38	28	10	46	46	0	SUSD2,missense_variant,p.Glu662Gln,ENST00000358321,;SUSD2,non_coding_transcript_exon_variant,,ENST00000463101,;	C	ENSG00000099994	ENST00000358321	Transcript	missense_variant	2245	1984	662	E/Q	Gag/Cag	rs372525863	.	.	1	SUSD2	HGNC	30667	protein_coding	YES	CCDS13824.1	ENSP00000351075	SUSD2_HUMAN	.	UPI000006CC92	.	tolerated(0.61)	benign(0.004)	12/15	.	hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF43,PROSITE_profiles:PS51233	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTCGAGCCC	byFrequency|byCluster	5	ESCA
SFI1	0	.	GRCh37	22	32009828	32009828	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2983C>A	p.His995Asn	p.H995N	ENST00000400288	27/33	81	72	9	103	103	0	SFI1,missense_variant,p.His913Asn,ENST00000400289,;SFI1,missense_variant,p.His842Asn,ENST00000414585,;SFI1,missense_variant,p.His842Asn,ENST00000443011,;SFI1,missense_variant,p.His578Asn,ENST00000417682,;SFI1,missense_variant,p.His995Asn,ENST00000400288,;SFI1,missense_variant,p.His964Asn,ENST00000432498,;SFI1,missense_variant,p.His940Asn,ENST00000540643,;SFI1,missense_variant,p.His913Asn,ENST00000443326,;PISD,downstream_gene_variant,,ENST00000397500,;PISD,downstream_gene_variant,,ENST00000266095,;PISD,downstream_gene_variant,,ENST00000382151,;SFI1,non_coding_transcript_exon_variant,,ENST00000474741,;SFI1,downstream_gene_variant,,ENST00000463436,;SFI1,downstream_gene_variant,,ENST00000466991,;SFI1,3_prime_UTR_variant,,ENST00000452250,;SFI1,non_coding_transcript_exon_variant,,ENST00000382162,;SFI1,downstream_gene_variant,,ENST00000524296,;PISD,downstream_gene_variant,,ENST00000473770,;SFI1,downstream_gene_variant,,ENST00000495107,;SFI1,upstream_gene_variant,,ENST00000357852,;PISD,downstream_gene_variant,,ENST00000460723,;SFI1,downstream_gene_variant,,ENST00000491973,;SFI1,upstream_gene_variant,,ENST00000476577,;SFI1,upstream_gene_variant,,ENST00000464333,;PISD,downstream_gene_variant,,ENST00000437808,;	A	ENSG00000198089	ENST00000400288	Transcript	missense_variant	3088	2983	995	H/N	Cac/Aac	.	.	.	1	SFI1	HGNC	29064	protein_coding	YES	CCDS43004.1	ENSP00000383145	SFI1_HUMAN	.	UPI00004703B1	.	tolerated(0.31)	benign(0.164)	27/33	.	hmmpanther:PTHR22028:SF2,hmmpanther:PTHR22028	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGCCCCACGCC	.	4	ESCA
RPL3	0	.	GRCh37	22	39714546	39714546	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55C>G	p.Arg19Gly	p.R19G	ENST00000216146	2/10	144	136	8	121	121	0	RPL3,missense_variant,p.Arg46Gly,ENST00000453303,;RPL3,missense_variant,p.Arg19Gly,ENST00000216146,;RPL3,missense_variant,p.Arg51Gly,ENST00000427905,;RPL3,5_prime_UTR_variant,,ENST00000401609,;RPL3,5_prime_UTR_variant,,ENST00000402527,;SNORD83A,upstream_gene_variant,,ENST00000386747,;SNORD83B,upstream_gene_variant,,ENST00000386745,;SNORD43,downstream_gene_variant,,ENST00000583861,;RPL3,non_coding_transcript_exon_variant,,ENST00000465618,;RPL3,non_coding_transcript_exon_variant,,ENST00000459859,;RPL3,upstream_gene_variant,,ENST00000471290,;RPL3,missense_variant,p.Arg19Gly,ENST00000420536,;RPL3,non_coding_transcript_exon_variant,,ENST00000498462,;RPL3,non_coding_transcript_exon_variant,,ENST00000460589,;RPL3,non_coding_transcript_exon_variant,,ENST00000484615,;RPL3,non_coding_transcript_exon_variant,,ENST00000461967,;RPL3,upstream_gene_variant,,ENST00000464182,;RPL3,upstream_gene_variant,,ENST00000473638,;RPL3,upstream_gene_variant,,ENST00000484358,;RPL3,upstream_gene_variant,,ENST00000481985,;RPL3,upstream_gene_variant,,ENST00000467105,;	C	ENSG00000100316	ENST00000216146	Transcript	missense_variant	229	55	19	R/G	Cgg/Ggg	.	.	.	-1	RPL3	HGNC	10332	protein_coding	YES	CCDS13988.1	ENSP00000346001	RL3_HUMAN	Q9NY85_HUMAN,Q9BT63_HUMAN,Q8TBW1_HUMAN,Q49AJ9_HUMAN,G5E9G0_HUMAN,B5MCW2_HUMAN,B4DN06_HUMAN	UPI0000167B7E	.	deleterious(0)	possibly_damaging(0.798)	2/10	.	hmmpanther:PTHR11363,Superfamily_domains:SSF50447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTCCGAGGCA	.	2	ESCA
POLR3H	0	.	GRCh37	22	41940236	41940236	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-131C>T	.	.	ENST00000355209	1/6	32	26	6	52	52	0	POLR3H,5_prime_UTR_variant,,ENST00000355209,;POLR3H,5_prime_UTR_variant,,ENST00000337566,;POLR3H,intron_variant,,ENST00000396504,;POLR3H,intron_variant,,ENST00000407461,;POLR3H,non_coding_transcript_exon_variant,,ENST00000420561,;POLR3H,5_prime_UTR_variant,,ENST00000431534,;POLR3H,5_prime_UTR_variant,,ENST00000432789,;POLR3H,intron_variant,,ENST00000442616,;POLR3H,intron_variant,,ENST00000483837,;	A	ENSG00000100413	ENST00000355209	Transcript	5_prime_UTR_variant	214	.	.	.	.	.	.	.	-1	POLR3H	HGNC	30349	protein_coding	YES	CCDS14018.1	ENSP00000347345	RPC8_HUMAN	.	UPI0000073CE5	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGCACGGGGCG	.	2	ESCA
CERK	0	.	GRCh37	22	47108115	47108115	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.455G>C	p.Arg152Thr	p.R152T	ENST00000216264	4/13	261	251	9	222	222	0	CERK,missense_variant,p.Arg152Thr,ENST00000216264,;CERK,5_prime_UTR_variant,,ENST00000541677,;CERK,missense_variant,p.Arg152Thr,ENST00000443629,;	G	ENSG00000100422	ENST00000216264	Transcript	missense_variant	568	455	152	R/T	aGa/aCa	.	.	.	-1	CERK	HGNC	19256	protein_coding	YES	CCDS14077.1	ENSP00000216264	CERK1_HUMAN	Q6NX59_HUMAN	UPI000004BBBD	.	tolerated(0.3)	benign(0.016)	4/13	.	PROSITE_profiles:PS50146,hmmpanther:PTHR12358,hmmpanther:PTHR12358:SF25,Pfam_domain:PF00781,SMART_domains:SM00046,Superfamily_domains:SSF111331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTTCTTTCA	.	2	ESCA
SBF1	0	.	GRCh37	22	50885091	50885091	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*480C>T	.	.	ENST00000380817	41/41	33	28	5	32	32	0	SBF1,3_prime_UTR_variant,,ENST00000380817,;PPP6R2,downstream_gene_variant,,ENST00000395741,;SBF1,downstream_gene_variant,,ENST00000418590,;SBF1,downstream_gene_variant,,ENST00000390679,;SBF1,downstream_gene_variant,,ENST00000348911,;PPP6R2,downstream_gene_variant,,ENST00000359139,;PPP6R2,downstream_gene_variant,,ENST00000401672,;PPP6R2,downstream_gene_variant,,ENST00000427222,;PPP6R2,downstream_gene_variant,,ENST00000395744,;PPP6R2,downstream_gene_variant,,ENST00000216061,;PPP6R2,downstream_gene_variant,,ENST00000470046,;SBF1,downstream_gene_variant,,ENST00000473724,;SBF1,downstream_gene_variant,,ENST00000470434,;	A	ENSG00000100241	ENST00000380817	Transcript	3_prime_UTR_variant	6346	.	.	.	.	.	.	.	-1	SBF1	HGNC	10542	protein_coding	YES	CCDS14091.2	ENSP00000370196	MTMR5_HUMAN	Q86TK5_HUMAN	UPI00001D69ED	.	.	.	41/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCGAGCTG	.	4	ESCA
GCC2	0	.	GRCh37	2	109125700	109125700	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1614G>C	.	.	ENST00000309863	23/23	72	64	8	43	43	0	GCC2,3_prime_UTR_variant,,ENST00000309863,;AC012487.2,intron_variant,,ENST00000322353,;AC012487.2,downstream_gene_variant,,ENST00000440975,;GCC2,3_prime_UTR_variant,,ENST00000482325,;GCC2,non_coding_transcript_exon_variant,,ENST00000480863,;	C	ENSG00000135968	ENST00000309863	Transcript	3_prime_UTR_variant	7383	.	.	.	.	.	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTGAAATA	.	4	ESCA
CYTIP	0	.	GRCh37	2	158300421	158300421	+	Missense_Mutation	SNP	C	C	T	rs370374268	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.112G>A	p.Asp38Asn	p.D38N	ENST00000264192	1/8	102	91	11	71	71	0	CYTIP,missense_variant,p.Asp38Asn,ENST00000264192,;CYTIP,missense_variant,p.Asp3Asn,ENST00000435117,;CYTIP,missense_variant,p.Asp3Asn,ENST00000439355,;CYTIP,intron_variant,,ENST00000540637,;CYTIP,upstream_gene_variant,,ENST00000418920,;AC019201.1,downstream_gene_variant,,ENST00000401235,;CYTIP,intron_variant,,ENST00000497432,;CYTIP,missense_variant,p.Asp38Asn,ENST00000457793,;CYTIP,non_coding_transcript_exon_variant,,ENST00000483929,;CYTIP,non_coding_transcript_exon_variant,,ENST00000462109,;	T	ENSG00000115165	ENST00000264192	Transcript	missense_variant	234	112	38	D/N	Gat/Aat	rs370374268	.	.	-1	CYTIP	HGNC	9506	protein_coding	YES	CCDS2204.1	ENSP00000264192	CYTIP_HUMAN	C9JSM2_HUMAN,C9JRF8_HUMAN,C9JNN8_HUMAN,B4DWH9_HUMAN	UPI0000035D67	.	tolerated(0.07)	probably_damaging(0.998)	1/8	.	hmmpanther:PTHR15963,hmmpanther:PTHR15963:SF1	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTATCGTCCA	byCluster	4	ESCA
RBMS1	0	.	GRCh37	2	161143552	161143552	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.684G>C	p.Gln228His	p.Q228H	ENST00000348849	7/14	102	88	14	99	98	1	RBMS1,missense_variant,p.Gln228His,ENST00000392753,;RBMS1,missense_variant,p.Gln195His,ENST00000409972,;RBMS1,missense_variant,p.Gln228His,ENST00000348849,;RBMS1,missense_variant,p.Gln195His,ENST00000409289,;RBMS1,missense_variant,p.Gln195His,ENST00000409075,;RBMS1,non_coding_transcript_exon_variant,,ENST00000474820,;RBMS1,non_coding_transcript_exon_variant,,ENST00000491781,;RBMS1,upstream_gene_variant,,ENST00000490637,;RBMS1,upstream_gene_variant,,ENST00000477965,;	G	ENSG00000153250	ENST00000348849	Transcript	missense_variant	1115	684	228	Q/H	caG/caC	.	.	.	-1	RBMS1	HGNC	9907	protein_coding	YES	CCDS2213.1	ENSP00000294904	RBMS1_HUMAN	Q9UEK5_HUMAN,E7EPF2_HUMAN	UPI00000713D4	.	deleterious(0.03)	probably_damaging(0.956)	7/14	.	hmmpanther:PTHR24011:SF211,hmmpanther:PTHR24011,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	TTTTTCTGTCC	.	3	ESCA
GCG	0	.	GRCh37	2	163003871	163003871	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.246G>C	p.Lys82Asn	p.K82N	ENST00000418842	3/6	59	52	7	60	60	0	GCG,missense_variant,p.Lys82Asn,ENST00000418842,;GCG,missense_variant,p.Lys82Asn,ENST00000375497,;GCG,non_coding_transcript_exon_variant,,ENST00000497568,;GCG,non_coding_transcript_exon_variant,,ENST00000492913,;GCG,upstream_gene_variant,,ENST00000483769,;	G	ENSG00000115263	ENST00000418842	Transcript	missense_variant	501	246	82	K/N	aaG/aaC	.	.	.	-1	GCG	HGNC	4191	protein_coding	YES	CCDS46439.1	ENSP00000387662	GLUC_HUMAN	.	UPI000012B832	.	deleterious(0)	benign(0.099)	3/6	.	hmmpanther:PTHR11418:SF0,hmmpanther:PTHR11418	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTTGGT	.	4	ESCA
UBR3	0	.	GRCh37	2	170940487	170940487	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2134A>G	.	.	ENST00000418381	39/39	91	62	29	74	74	0	UBR3,3_prime_UTR_variant,,ENST00000392631,;UBR3,3_prime_UTR_variant,,ENST00000392632,;UBR3,3_prime_UTR_variant,,ENST00000418381,;UBR3,3_prime_UTR_variant,,ENST00000272793,;UBR3,downstream_gene_variant,,ENST00000439681,;UBR3,3_prime_UTR_variant,,ENST00000444475,;UBR3,3_prime_UTR_variant,,ENST00000430321,;UBR3,non_coding_transcript_exon_variant,,ENST00000474426,;UBR3,downstream_gene_variant,,ENST00000484596,;	G	ENSG00000144357	ENST00000418381	Transcript	3_prime_UTR_variant	7801	.	.	.	.	.	.	.	1	UBR3	HGNC	30467	protein_coding	YES	CCDS2238.2	ENSP00000396068	UBR3_HUMAN	Q68DC1_HUMAN	UPI00015FA088	.	.	.	39/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGATATCTTG	.	5	ESCA
MLTK	0	.	GRCh37	2	174131459	174131459	+	Missense_Mutation	SNP	G	G	A	rs761040219	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2384G>A	p.Arg795His	p.R795H	ENST00000375213	20/20	50	42	8	31	31	0	MLTK,missense_variant,p.Arg795His,ENST00000375213,;MLTK,missense_variant,p.Arg795His,ENST00000409176,;MLK7-AS1,intron_variant,,ENST00000422703,;MLK7-AS1,intron_variant,,ENST00000423106,;	A	ENSG00000091436	ENST00000375213	Transcript	missense_variant	2462	2384	795	R/H	cGt/cAt	rs761040219	.	.	1	MLTK	Uniprot_gn	.	protein_coding	YES	CCDS42777.1	ENSP00000364361	MLTK_HUMAN	C9J3F7_HUMAN	UPI0000073F69	.	deleterious_low_confidence(0.04)	possibly_damaging(0.863)	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACCGTGGAT	.	5	ESCA
AGPS	0	.	GRCh37	2	178305725	178305725	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.670C>G	p.Leu224Val	p.L224V	ENST00000264167	6/20	87	62	24	68	68	0	AGPS,missense_variant,p.Leu224Val,ENST00000264167,;AGPS,intron_variant,,ENST00000409888,;AGPS,non_coding_transcript_exon_variant,,ENST00000460342,;	G	ENSG00000018510	ENST00000264167	Transcript	missense_variant	816	670	224	L/V	Cta/Gta	.	.	.	1	AGPS	HGNC	327	protein_coding	YES	CCDS2275.1	ENSP00000264167	ADAS_HUMAN	Q53SN7_HUMAN,Q53SG6_HUMAN,Q53S12_HUMAN,B7Z3Q4_HUMAN	UPI00001254E8	.	tolerated(0.05)	possibly_damaging(0.457)	6/20	.	PROSITE_profiles:PS51387,hmmpanther:PTHR11748,hmmpanther:PTHR11748:SF3,Pfam_domain:PF01565,Gene3D:3.30.43.10,Superfamily_domains:SSF56176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAATCTAGCT	.	5	ESCA
FARSB	0	.	GRCh37	2	223520793	223520793	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-1C>T	.	.	ENST00000281828	1/17	42	28	13	45	45	0	FARSB,5_prime_UTR_variant,,ENST00000281828,;FARSB,upstream_gene_variant,,ENST00000536361,;	A	ENSG00000116120	ENST00000281828	Transcript	5_prime_UTR_variant	264	.	.	.	.	.	.	.	-1	FARSB	HGNC	17800	protein_coding	YES	CCDS2454.1	ENSP00000281828	SYFB_HUMAN	F5H6Y1_HUMAN	UPI00002096AC	.	.	.	1/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCATGGTGTG	.	5	ESCA
HDLBP	0	.	GRCh37	2	242179158	242179158	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2469G>A	p.%3D	p.L823L	ENST00000391975	19/28	56	38	18	65	65	0	HDLBP,synonymous_variant,p.%3D,ENST00000310931,;HDLBP,synonymous_variant,p.%3D,ENST00000427183,;HDLBP,synonymous_variant,p.%3D,ENST00000373292,;HDLBP,synonymous_variant,p.%3D,ENST00000391976,;HDLBP,synonymous_variant,p.%3D,ENST00000427487,;HDLBP,synonymous_variant,p.%3D,ENST00000391975,;HDLBP,downstream_gene_variant,,ENST00000452931,;HDLBP,upstream_gene_variant,,ENST00000470482,;HDLBP,upstream_gene_variant,,ENST00000483086,;HDLBP,downstream_gene_variant,,ENST00000471294,;HDLBP,non_coding_transcript_exon_variant,,ENST00000487169,;HDLBP,non_coding_transcript_exon_variant,,ENST00000479169,;HDLBP,upstream_gene_variant,,ENST00000479894,;HDLBP,downstream_gene_variant,,ENST00000459788,;	T	ENSG00000115677	ENST00000391975	Transcript	synonymous_variant	2697	2469	823	L	ttG/ttA	.	.	.	-1	HDLBP	HGNC	4857	protein_coding	YES	CCDS2547.1	ENSP00000375836	VIGLN_HUMAN	Q96CF6_HUMAN,C9JZI8_HUMAN,C9JT62_HUMAN,C9JQ82_HUMAN,C9JMQ6_HUMAN,C9JKQ5_HUMAN,C9JIZ1_HUMAN,C9JHZ8_HUMAN,C9JHS7_HUMAN,C9JHN6_HUMAN,C9JES8_HUMAN,C9JEJ8_HUMAN,C9JBS3_HUMAN,C9J5E5_HUMAN	UPI00001AEF85	.	.	.	19/28	.	PROSITE_profiles:PS50084,hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGCAAGAC	.	5	ESCA
EML4	0	.	GRCh37	2	42559543	42559543	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2196G>A	.	.	ENST00000318522	23/23	116	105	10	97	97	0	EML4,3_prime_UTR_variant,,ENST00000318522,;EML4,downstream_gene_variant,,ENST00000401738,;COX7A2L,downstream_gene_variant,,ENST00000468711,;EML4,downstream_gene_variant,,ENST00000453191,;EML4,downstream_gene_variant,,ENST00000402711,;EML4,non_coding_transcript_exon_variant,,ENST00000406175,;	A	ENSG00000143924	ENST00000318522	Transcript	3_prime_UTR_variant	5404	.	.	.	.	.	.	.	1	EML4	HGNC	1316	protein_coding	YES	CCDS1807.1	ENSP00000320663	EMAL4_HUMAN	F2Z2B5_HUMAN	UPI0000140350	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTAGATGTT	.	4	ESCA
THADA	0	.	GRCh37	2	43514140	43514140	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5071G>A	p.Glu1691Lys	p.E1691K	ENST00000405006	35/38	68	64	4	58	58	0	THADA,missense_variant,p.Glu1691Lys,ENST00000405006,;THADA,missense_variant,p.Glu1691Lys,ENST00000405975,;THADA,missense_variant,p.Glu931Lys,ENST00000407351,;THADA,missense_variant,p.Glu1372Lys,ENST00000415080,;THADA,intron_variant,,ENST00000330266,;THADA,3_prime_UTR_variant,,ENST00000398653,;THADA,non_coding_transcript_exon_variant,,ENST00000485018,;	T	ENSG00000115970	ENST00000405006	Transcript	missense_variant	5423	5071	1691	E/K	Gaa/Aaa	.	.	.	-1	THADA	HGNC	19217	protein_coding	YES	CCDS46268.1	ENSP00000385995	THADA_HUMAN	Q6YHU4_HUMAN	UPI00001C0473	.	deleterious(0.02)	benign(0.071)	35/38	.	hmmpanther:PTHR14387:SF0,hmmpanther:PTHR14387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCTTCACATG	.	2	ESCA
PPP1R21	0	.	GRCh37	2	48698298	48698298	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.970A>G	p.Ser324Gly	p.S324G	ENST00000294952	10/22	93	82	11	87	87	0	PPP1R21,missense_variant,p.Ser324Gly,ENST00000449090,;PPP1R21,missense_variant,p.Ser324Gly,ENST00000281394,;PPP1R21,missense_variant,p.Ser324Gly,ENST00000294952,;PPP1R21,3_prime_UTR_variant,,ENST00000416913,;PPP1R21,3_prime_UTR_variant,,ENST00000431614,;PPP1R21,non_coding_transcript_exon_variant,,ENST00000460299,;PPP1R21,upstream_gene_variant,,ENST00000455978,;	G	ENSG00000162869	ENST00000294952	Transcript	missense_variant	1127	970	324	S/G	Agt/Ggt	.	.	.	1	PPP1R21	HGNC	30595	protein_coding	YES	CCDS46278.1	ENSP00000294952	PPR21_HUMAN	F8W7E1_HUMAN	UPI000015C523	.	tolerated(0.14)	benign(0.003)	10/22	.	hmmpanther:PTHR21448,Pfam_domain:PF10212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGAAAGTATC	.	4	ESCA
MTIF2	0	.	GRCh37	2	55489519	55489519	+	Silent	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.264A>G	p.%3D	p.K88K	ENST00000394600	6/17	92	81	11	65	65	0	MTIF2,synonymous_variant,p.%3D,ENST00000394600,;MTIF2,synonymous_variant,p.%3D,ENST00000403721,;MTIF2,synonymous_variant,p.%3D,ENST00000263629,;MTIF2,downstream_gene_variant,,ENST00000417363,;MTIF2,downstream_gene_variant,,ENST00000420637,;MTIF2,downstream_gene_variant,,ENST00000412530,;MTIF2,downstream_gene_variant,,ENST00000366137,;MTIF2,downstream_gene_variant,,ENST00000441307,;MTIF2,downstream_gene_variant,,ENST00000404297,;MTIF2,non_coding_transcript_exon_variant,,ENST00000417741,;MTIF2,non_coding_transcript_exon_variant,,ENST00000446660,;	C	ENSG00000085760	ENST00000394600	Transcript	synonymous_variant	1001	264	88	K	aaA/aaG	.	.	.	-1	MTIF2	HGNC	7441	protein_coding	YES	CCDS1853.1	ENSP00000378099	IF2M_HUMAN	E7EW07_HUMAN,E7ESE3_HUMAN,C9JIY5_HUMAN,B5MCU1_HUMAN	UPI000013D42F	.	.	.	6/17	.	HAMAP:MF_00100_B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ACCTTTTTAGA	.	4	ESCA
FER1L5	0	.	GRCh37	2	97357862	97357862	+	RNA	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1695T>C	.	.	ENST00000457909	14/35	118	111	7	110	109	1	FER1L5,non_coding_transcript_exon_variant,,ENST00000457909,;FER1L5,non_coding_transcript_exon_variant,,ENST00000436930,;FER1L5,non_coding_transcript_exon_variant,,ENST00000414152,;FER1L5,non_coding_transcript_exon_variant,,ENST00000424961,;FER1L5,upstream_gene_variant,,ENST00000397978,;	C	ENSG00000249715	ENST00000457909	Transcript	non_coding_transcript_exon_variant	1695	.	.	.	.	.	.	.	1	FER1L5	HGNC	19044	retained_intron	.	.	.	.	.	.	.	.	.	14/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCTTCTGCT	.	2	ESCA
ANKRD36	0	.	GRCh37	2	97845601	97845601	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1666A>T	p.Thr556Ser	p.T556S	ENST00000420699	24/76	259	234	25	166	166	0	ANKRD36,missense_variant,p.Thr556Ser,ENST00000461153,;ANKRD36,missense_variant,p.Thr556Ser,ENST00000420699,;	T	ENSG00000135976	ENST00000420699	Transcript	missense_variant	1910	1666	556	T/S	Aca/Tca	.	.	.	1	ANKRD36	HGNC	24079	protein_coding	YES	CCDS54379.1	ENSP00000391950	AN36A_HUMAN	.	UPI0001B23BB4	.	deleterious_low_confidence(0.01)	probably_damaging(0.956)	24/76	.	hmmpanther:PTHR24176,hmmpanther:PTHR24176:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTACAAGT	.	4	ESCA
DZIP3	0	.	GRCh37	3	108409884	108409884	+	Intron	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*6+134G>A	.	.	ENST00000361582	.	42	35	7	32	32	0	DZIP3,3_prime_UTR_variant,,ENST00000463306,;DZIP3,intron_variant,,ENST00000361582,;DZIP3,intron_variant,,ENST00000495008,;	A	ENSG00000198919	ENST00000361582	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	DZIP3	HGNC	30938	protein_coding	YES	CCDS2952.1	ENSP00000355028	DZIP3_HUMAN	Q5MY58_HUMAN,D3DN61_HUMAN,C9JRX4_HUMAN,C9J9M8_HUMAN,C9J702_HUMAN	UPI000006E7D4	.	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGAAGTCAGG	.	2	ESCA
CHST13	0	.	GRCh37	3	126260800	126260800	+	Silent	SNP	G	G	A	rs779745607	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405G>A	p.%3D	p.P135P	ENST00000319340	3/3	20	16	3	34	34	0	CHST13,synonymous_variant,p.%3D,ENST00000319340,;C3orf22,intron_variant,,ENST00000505070,;	A	ENSG00000180767	ENST00000319340	Transcript	synonymous_variant	455	405	135	P	ccG/ccA	rs779745607	.	.	1	CHST13	HGNC	21755	protein_coding	YES	CCDS3039.1	ENSP00000317404	CHSTD_HUMAN	Q3ZCU8_HUMAN,Q3ZCR4_HUMAN	UPI00000492E5	.	.	.	3/3	.	hmmpanther:PTHR12137:SF31,hmmpanther:PTHR12137,Pfam_domain:PF03567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GACCCGCGCGC	byFrequency	2	ESCA
GATA2	0	.	GRCh37	3	128198513	128198513	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1349G>A	.	.	ENST00000341105	6/6	84	67	17	106	106	0	GATA2,3_prime_UTR_variant,,ENST00000341105,;GATA2,downstream_gene_variant,,ENST00000430265,;GATA2,downstream_gene_variant,,ENST00000487848,;GATA2,downstream_gene_variant,,ENST00000489987,;	T	ENSG00000179348	ENST00000341105	Transcript	3_prime_UTR_variant	3124	.	.	.	.	.	.	.	-1	GATA2	HGNC	4171	protein_coding	YES	CCDS3049.1	ENSP00000345681	GATA2_HUMAN	C9J965_HUMAN	UPI00000730CD	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCCCGCCCA	.	5	ESCA
HMCES	0	.	GRCh37	3	129009630	129009630	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.436C>G	p.Gln146Glu	p.Q146E	ENST00000383463	4/7	135	98	36	122	122	0	HMCES,missense_variant,p.Gln146Glu,ENST00000509551,;HMCES,missense_variant,p.Gln146Glu,ENST00000502878,;HMCES,missense_variant,p.Gln98Glu,ENST00000509042,;HMCES,missense_variant,p.Gln146Glu,ENST00000389735,;HMCES,missense_variant,p.Gln146Glu,ENST00000383463,;HMCES,intron_variant,,ENST00000417226,;HMCES,intron_variant,,ENST00000510314,;HMCES,intron_variant,,ENST00000511665,;	G	ENSG00000183624	ENST00000383463	Transcript	missense_variant	525	436	146	Q/E	Caa/Gaa	.	.	.	1	HMCES	HGNC	24446	protein_coding	YES	CCDS33852.1	ENSP00000372955	HMCES_HUMAN	D6RAZ3_HUMAN	UPI000006FF4D	.	deleterious(0.02)	possibly_damaging(0.612)	4/7	.	hmmpanther:PTHR13604,hmmpanther:PTHR13604:SF0,Pfam_domain:PF02586,Gene3D:2icuA00,Superfamily_domains:SSF143081	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCAAATC	.	5	ESCA
NEK11	0	.	GRCh37	3	130889714	130889714	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1382C>G	p.Ser461Cys	p.S461C	ENST00000383366	14/18	98	88	10	108	108	0	NEK11,missense_variant,p.Ser461Cys,ENST00000383366,;NEK11,missense_variant,p.Ser356Cys,ENST00000510769,;NEK11,missense_variant,p.Ser461Cys,ENST00000511262,;NEK11,missense_variant,p.Ser461Cys,ENST00000508196,;NEK11,missense_variant,p.Ser277Cys,ENST00000412440,;NEK11,missense_variant,p.Ser461Cys,ENST00000510688,;NEK11,missense_variant,p.Ser461Cys,ENST00000429253,;NEK11,missense_variant,p.Ser461Cys,ENST00000356918,;NEK11,missense_variant,p.Ser461Cys,ENST00000507910,;NEK11,3_prime_UTR_variant,,ENST00000514915,;NEK11,3_prime_UTR_variant,,ENST00000510474,;NEK11,non_coding_transcript_exon_variant,,ENST00000510823,;	G	ENSG00000114670	ENST00000383366	Transcript	missense_variant	1675	1382	461	S/C	tCt/tGt	.	.	.	1	NEK11	HGNC	18593	protein_coding	YES	CCDS3069.1	ENSP00000372857	NEK11_HUMAN	.	UPI000013F25D	.	tolerated(0.08)	benign(0.005)	14/18	.	hmmpanther:PTHR24362:SF242,hmmpanther:PTHR24362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACATCTGACC	.	4	ESCA
IL20RB	0	.	GRCh37	3	136699269	136699269	+	Intron	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.89-39G>A	.	.	ENST00000329582	.	103	77	26	68	68	0	IL20RB,5_prime_UTR_variant,,ENST00000309741,;IL20RB,intron_variant,,ENST00000329582,;IL20RB-AS1,intron_variant,,ENST00000462176,;IL20RB,intron_variant,,ENST00000484501,;IL20RB,3_prime_UTR_variant,,ENST00000469964,;IL20RB,3_prime_UTR_variant,,ENST00000491483,;IL20RB,upstream_gene_variant,,ENST00000475972,;	A	ENSG00000174564	ENST00000329582	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	IL20RB	HGNC	6004	protein_coding	YES	CCDS3093.1	ENSP00000328133	I20RB_HUMAN	.	UPI000003E7F6	.	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTATGAGCCC	.	5	ESCA
ARMC8	0	.	GRCh37	3	137928707	137928707	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.52G>C	p.Asp18His	p.D18H	ENST00000481646	3/23	81	73	7	61	61	0	ARMC8,missense_variant,p.Asp32His,ENST00000469044,;ARMC8,missense_variant,p.Asp32His,ENST00000471709,;ARMC8,missense_variant,p.Asp18His,ENST00000358441,;ARMC8,missense_variant,p.Asp32His,ENST00000538260,;ARMC8,missense_variant,p.Asp18His,ENST00000468560,;ARMC8,missense_variant,p.Asp32His,ENST00000461600,;ARMC8,missense_variant,p.Asp22His,ENST00000393058,;ARMC8,missense_variant,p.Asp18His,ENST00000481646,;ARMC8,missense_variant,p.Asp32His,ENST00000461822,;ARMC8,missense_variant,p.Asp32His,ENST00000470821,;ARMC8,missense_variant,p.Asp18His,ENST00000471453,;ARMC8,intron_variant,,ENST00000485396,;ARMC8,intron_variant,,ENST00000463485,;ARMC8,intron_variant,,ENST00000489213,;ARMC8,intron_variant,,ENST00000491704,;ARMC8,intron_variant,,ENST00000466749,;	C	ENSG00000114098	ENST00000481646	Transcript	missense_variant	458	52	18	D/H	Gat/Cat	.	.	.	1	ARMC8	HGNC	24999	protein_coding	YES	CCDS54646.1	ENSP00000420333	ARMC8_HUMAN	C9J8P8_HUMAN,C9J625_HUMAN,B7Z979_HUMAN	UPI000007471D	.	deleterious(0)	probably_damaging(0.979)	3/23	.	Superfamily_domains:SSF48371,Gene3D:1.25.10.10,hmmpanther:PTHR15651,hmmpanther:PTHR15651:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCCTGATCCC	.	3	ESCA
PLSCR1	0	.	GRCh37	3	146251305	146251305	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.46A>C	p.Asn16His	p.N16H	ENST00000342435	3/9	77	68	9	57	57	0	PLSCR1,missense_variant,p.Asn16His,ENST00000462666,;PLSCR1,missense_variant,p.Asn9His,ENST00000487389,;PLSCR1,missense_variant,p.Asn16His,ENST00000472349,;PLSCR1,missense_variant,p.Gln7His,ENST00000486631,;PLSCR1,missense_variant,p.Gln7His,ENST00000448787,;PLSCR1,missense_variant,p.Asn16His,ENST00000342435,;PLSCR1,5_prime_UTR_variant,,ENST00000448205,;PLSCR1,upstream_gene_variant,,ENST00000483300,;PLSCR1,missense_variant,p.Asn16His,ENST00000463777,;PLSCR1,missense_variant,p.Asn16His,ENST00000489775,;PLSCR1,missense_variant,p.Asn16His,ENST00000468985,;PLSCR1,missense_variant,p.Asn16His,ENST00000478267,;PLSCR1,missense_variant,p.Asn16His,ENST00000493432,;PLSCR1,missense_variant,p.Asn16His,ENST00000488253,;PLSCR1,non_coding_transcript_exon_variant,,ENST00000490745,;PLSCR1,non_coding_transcript_exon_variant,,ENST00000494568,;PLSCR1,non_coding_transcript_exon_variant,,ENST00000469266,;	G	ENSG00000188313	ENST00000342435	Transcript	missense_variant	457	46	16	N/H	Aac/Cac	.	.	.	-1	PLSCR1	HGNC	9092	protein_coding	YES	CCDS3135.1	ENSP00000345494	PLS1_HUMAN	C9JSI9_HUMAN,C9JE06_HUMAN,C9J7K9_HUMAN	UPI0000001627	.	tolerated(0.36)	benign(0.001)	3/9	.	hmmpanther:PTHR23248,hmmpanther:PTHR23248:SF26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAAGTTTGTTT	.	4	ESCA
SEC62	0	.	GRCh37	3	169711087	169711087	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*236G>A	.	.	ENST00000337002	8/8	68	62	5	61	61	0	SEC62,3_prime_UTR_variant,,ENST00000337002,;SEC62,intron_variant,,ENST00000480708,;SEC62,downstream_gene_variant,,ENST00000470355,;SEC62,downstream_gene_variant,,ENST00000469515,;	A	ENSG00000008952	ENST00000337002	Transcript	3_prime_UTR_variant	1494	.	.	.	.	.	.	.	1	SEC62	HGNC	11846	protein_coding	YES	CCDS3210.1	ENSP00000337688	SEC62_HUMAN	D3DNQ1_HUMAN	UPI000007186C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGTAGGTCTCA	.	2	ESCA
FNDC3B	0	.	GRCh37	3	172115069	172115069	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3419G>T	p.Gly1140Val	p.G1140V	ENST00000336824	26/26	47	39	7	40	40	0	FNDC3B,missense_variant,p.Gly1140Val,ENST00000416957,;FNDC3B,missense_variant,p.Gly1140Val,ENST00000415807,;FNDC3B,missense_variant,p.Gly1140Val,ENST00000336824,;	T	ENSG00000075420	ENST00000336824	Transcript	missense_variant	3518	3419	1140	G/V	gGa/gTa	.	.	.	1	FNDC3B	HGNC	24670	protein_coding	YES	CCDS3217.1	ENSP00000338523	FND3B_HUMAN	.	UPI00001AE8B2	.	deleterious(0)	probably_damaging(0.997)	26/26	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19900,hmmpanther:PTHR19900:SF54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	AAGCGGAGCCT	.	3	ESCA
ECE2	0	.	GRCh37	3	184005730	184005730	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1723G>C	p.Glu575Gln	p.E575Q	ENST00000402825	11/19	56	44	12	73	73	0	ECE2,missense_variant,p.Glu449Gln,ENST00000430587,;ECE2,missense_variant,p.Glu428Gln,ENST00000359140,;ECE2,missense_variant,p.Glu503Gln,ENST00000357474,;ECE2,missense_variant,p.Glu457Gln,ENST00000404464,;ECE2,missense_variant,p.Glu575Gln,ENST00000402825,;EIF2B5,intron_variant,,ENST00000444495,;ECE2,non_coding_transcript_exon_variant,,ENST00000488401,;ECE2,non_coding_transcript_exon_variant,,ENST00000490579,;	C	ENSG00000145194	ENST00000402825	Transcript	missense_variant	1723	1723	575	E/Q	Gaa/Caa	.	.	.	1	ECE2	HGNC	13275	protein_coding	YES	CCDS3256.2	ENSP00000384223	ECE2_HUMAN	.	UPI0001596888	.	tolerated(0.16)	benign(0.14)	11/19	.	hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF122,Gene3D:3.40.390.10,Pfam_domain:PF05649,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAAGAAATT	.	5	ESCA
SLC6A20	0	.	GRCh37	3	45837804	45837804	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108G>C	p.Gln36His	p.Q36H	ENST00000358525	1/11	50	42	7	51	51	0	SLC6A20,missense_variant,p.Gln36His,ENST00000353278,;SLC6A20,missense_variant,p.Gln36His,ENST00000456124,;SLC6A20,missense_variant,p.Gln36His,ENST00000358525,;SLC6A20,missense_variant,p.Gln36His,ENST00000413781,;SLC6A20,non_coding_transcript_exon_variant,,ENST00000470226,;	G	ENSG00000163817	ENST00000358525	Transcript	missense_variant	224	108	36	Q/H	caG/caC	.	.	.	-1	SLC6A20	HGNC	30927	protein_coding	YES	CCDS43077.1	ENSP00000346298	S6A20_HUMAN	.	UPI0000046064	.	deleterious(0.01)	probably_damaging(0.997)	1/11	.	PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF44,PROSITE_patterns:PS00610,Pfam_domain:PF00209,Superfamily_domains:0053687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACATCTGGCA	.	4	ESCA
FBXW12	0	.	GRCh37	3	48423318	48423318	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1114C>G	p.Leu372Val	p.L372V	ENST00000296438	9/11	76	66	10	84	84	0	FBXW12,missense_variant,p.Leu353Val,ENST00000445170,;FBXW12,missense_variant,p.Leu215Val,ENST00000436231,;FBXW12,missense_variant,p.Leu372Val,ENST00000296438,;FBXW12,missense_variant,p.Leu302Val,ENST00000415155,;RN7SL321P,downstream_gene_variant,,ENST00000581742,;FBXW12,non_coding_transcript_exon_variant,,ENST00000468158,;FBXW12,non_coding_transcript_exon_variant,,ENST00000477542,;	G	ENSG00000164049	ENST00000296438	Transcript	missense_variant	1300	1114	372	L/V	Ctg/Gtg	.	.	.	1	FBXW12	HGNC	20729	protein_coding	YES	CCDS2764.1	ENSP00000296438	FBW12_HUMAN	C9JK86_HUMAN	UPI00004123F1	.	tolerated(0.38)	possibly_damaging(0.803)	9/11	.	hmmpanther:PTHR22844:SF113,hmmpanther:PTHR22844,Gene3D:2.130.10.10,Superfamily_domains:SSF50969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTTCCTGCTG	.	4	ESCA
PLXNB1	0	.	GRCh37	3	48455320	48455320	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4370C>G	p.Ser1457Cys	p.S1457C	ENST00000358536	22/38	57	54	3	65	65	0	PLXNB1,missense_variant,p.Ser1457Cys,ENST00000358536,;PLXNB1,missense_variant,p.Ser1457Cys,ENST00000296440,;PLXNB1,missense_variant,p.Ser1274Cys,ENST00000358459,;PLXNB1,missense_variant,p.Ser68Cys,ENST00000448774,;PLXNB1,missense_variant,p.Ser1274Cys,ENST00000456774,;PLXNB1,non_coding_transcript_exon_variant,,ENST00000465117,;PLXNB1,downstream_gene_variant,,ENST00000484485,;PLXNB1,3_prime_UTR_variant,,ENST00000449094,;PLXNB1,non_coding_transcript_exon_variant,,ENST00000485535,;PLXNB1,non_coding_transcript_exon_variant,,ENST00000473996,;PLXNB1,downstream_gene_variant,,ENST00000464294,;PLXNB1,upstream_gene_variant,,ENST00000461261,;PLXNB1,upstream_gene_variant,,ENST00000478171,;PLXNB1,downstream_gene_variant,,ENST00000467913,;PLXNB1,upstream_gene_variant,,ENST00000483676,;PLXNB1,upstream_gene_variant,,ENST00000497627,;PLXNB1,upstream_gene_variant,,ENST00000470525,;PLXNB1,downstream_gene_variant,,ENST00000462738,;	C	ENSG00000164050	ENST00000358536	Transcript	missense_variant	4640	4370	1457	S/C	tCt/tGt	.	.	.	-1	PLXNB1	HGNC	9103	protein_coding	YES	CCDS2765.1	ENSP00000351338	PLXB1_HUMAN	G8JLJ7_HUMAN,B3KRL1_HUMAN	UPI0000038131	.	deleterious(0.01)	benign(0.155)	22/38	.	hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF36,Gene3D:2.60.40.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAAAGAGTCA	.	2	ESCA
WDR6	0	.	GRCh37	3	49044854	49044854	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.80C>G	p.Ser27Trp	p.S27W	ENST00000395474	1/6	44	38	6	60	60	0	WDR6,missense_variant,p.Ser27Trp,ENST00000395474,;WDR6,5_prime_UTR_variant,,ENST00000608424,;WDR6,5_prime_UTR_variant,,ENST00000415265,;WDR6,5_prime_UTR_variant,,ENST00000429900,;WDR6,5_prime_UTR_variant,,ENST00000438660,;P4HTM,downstream_gene_variant,,ENST00000383729,;P4HTM,downstream_gene_variant,,ENST00000491739,;WDR6,upstream_gene_variant,,ENST00000491365,;WDR6,upstream_gene_variant,,ENST00000419837,;P4HTM,downstream_gene_variant,,ENST00000343546,;P4HTM,downstream_gene_variant,,ENST00000472796,;WDR6,upstream_gene_variant,,ENST00000448293,;WDR6,upstream_gene_variant,,ENST00000489427,;P4HTM,downstream_gene_variant,,ENST00000444213,;WDR6,non_coding_transcript_exon_variant,,ENST00000489684,;P4HTM,downstream_gene_variant,,ENST00000486817,;P4HTM,downstream_gene_variant,,ENST00000468374,;WDR6,upstream_gene_variant,,ENST00000461687,;WDR6,upstream_gene_variant,,ENST00000472878,;WDR6,5_prime_UTR_variant,,ENST00000452875,;WDR6,5_prime_UTR_variant,,ENST00000488572,;WDR6,5_prime_UTR_variant,,ENST00000462064,;WDR6,5_prime_UTR_variant,,ENST00000473238,;WDR6,5_prime_UTR_variant,,ENST00000420783,;WDR6,non_coding_transcript_exon_variant,,ENST00000471162,;P4HTM,downstream_gene_variant,,ENST00000484115,;P4HTM,downstream_gene_variant,,ENST00000472301,;P4HTM,downstream_gene_variant,,ENST00000485210,;	G	ENSG00000178252	ENST00000395474	Transcript	missense_variant	360	80	27	S/W	tCg/tGg	.	.	.	1	WDR6	HGNC	12758	protein_coding	YES	CCDS2782.2	ENSP00000378857	WDR6_HUMAN	Q8NDH0_HUMAN,Q6PKC6_HUMAN,Q6AZD6_HUMAN,E9PDU5_HUMAN	UPI0000E5A634	.	deleterious_low_confidence(0.01)	benign(0.147)	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCTCGAGGA	.	4	ESCA
ACOX2	0	.	GRCh37	3	58520773	58520773	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61G>A	p.Asp21Asn	p.D21N	ENST00000302819	2/15	71	54	17	102	102	0	ACOX2,missense_variant,p.Asp21Asn,ENST00000459701,;ACOX2,missense_variant,p.Asp21Asn,ENST00000302819,;ACOX2,missense_variant,p.Asp21Asn,ENST00000474098,;ACOX2,non_coding_transcript_exon_variant,,ENST00000475143,;ACOX2,non_coding_transcript_exon_variant,,ENST00000480791,;ACOX2,non_coding_transcript_exon_variant,,ENST00000466689,;ACOX2,upstream_gene_variant,,ENST00000489472,;ACOX2,upstream_gene_variant,,ENST00000492530,;ACOX2,upstream_gene_variant,,ENST00000466810,;	T	ENSG00000168306	ENST00000302819	Transcript	missense_variant	353	61	21	D/N	Gac/Aac	.	.	.	-1	ACOX2	HGNC	120	protein_coding	YES	CCDS33775.1	ENSP00000307697	ACOX2_HUMAN	C9JY29_HUMAN,B4DPM1_HUMAN	UPI000000DC36	.	deleterious(0)	probably_damaging(0.973)	2/15	.	hmmpanther:PTHR10909:SF266,hmmpanther:PTHR10909,PIRSF_domain:PIRSF000168,Superfamily_domains:SSF56645	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGTCGGGGT	.	5	ESCA
MAGI1	0	.	GRCh37	3	65342522	65342522	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3920C>A	p.Ala1307Glu	p.A1307E	ENST00000402939	23/23	37	27	10	32	32	0	MAGI1,missense_variant,p.Ala1307Glu,ENST00000402939,;MAGI1,3_prime_UTR_variant,,ENST00000330909,;MAGI1,downstream_gene_variant,,ENST00000463103,;MAGI1,downstream_gene_variant,,ENST00000472257,;MAGI1,downstream_gene_variant,,ENST00000460329,;MAGI1,downstream_gene_variant,,ENST00000483466,;MAGI1,downstream_gene_variant,,ENST00000497477,;RP11-88H12.2,downstream_gene_variant,,ENST00000602316,;	T	ENSG00000151276	ENST00000402939	Transcript	missense_variant	3920	3920	1307	A/E	gCg/gAg	.	.	.	-1	MAGI1	HGNC	946	protein_coding	YES	CCDS33780.1	ENSP00000385450	MAGI1_HUMAN	.	UPI0000457132	.	tolerated(0.96)	benign(0.198)	23/23	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCGCGTCC	.	5	ESCA
TMF1	0	.	GRCh37	3	69088142	69088142	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1846G>T	p.Glu616Ter	p.E616*	ENST00000398559	7/17	37	26	10	38	38	0	TMF1,stop_gained,p.Glu616Ter,ENST00000398559,;TMF1,stop_gained,p.Glu619Ter,ENST00000543976,;CTD-2013N24.2,intron_variant,,ENST00000596523,;CTD-2013N24.2,intron_variant,,ENST00000597950,;CTD-2013N24.2,intron_variant,,ENST00000596732,;CTD-2013N24.2,intron_variant,,ENST00000598783,;CTD-2013N24.2,intron_variant,,ENST00000601735,;CTD-2013N24.2,intron_variant,,ENST00000595925,;CTD-2013N24.2,intron_variant,,ENST00000482368,;CTD-2013N24.2,intron_variant,,ENST00000596274,;CTD-2013N24.2,downstream_gene_variant,,ENST00000601511,;CTD-2013N24.2,downstream_gene_variant,,ENST00000599467,;TMF1,stop_gained,p.Glu616Ter,ENST00000488010,;TMF1,downstream_gene_variant,,ENST00000477872,;	A	ENSG00000144747	ENST00000398559	Transcript	stop_gained	2063	1846	616	E/*	Gag/Tag	.	.	.	-1	TMF1	HGNC	11870	protein_coding	YES	CCDS43105.1	ENSP00000381567	TMF1_HUMAN	.	UPI000013D9A7	.	.	.	7/17	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF285	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCTCTTCTT	.	5	ESCA
ARL13B	0	.	GRCh37	3	93772169	93772169	+	3'UTR	SNP	C	C	G	rs778211409	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62C>G	.	.	ENST00000394222	10/10	83	67	15	53	53	0	ARL13B,3_prime_UTR_variant,,ENST00000394222,;ARL13B,3_prime_UTR_variant,,ENST00000303097,;ARL13B,3_prime_UTR_variant,,ENST00000535334,;ARL13B,3_prime_UTR_variant,,ENST00000539730,;ARL13B,intron_variant,,ENST00000471138,;DHFRL1,downstream_gene_variant,,ENST00000314636,;DHFRL1,downstream_gene_variant,,ENST00000394221,;DHFRL1,intron_variant,,ENST00000481631,;ARL13B,3_prime_UTR_variant,,ENST00000335438,;ARL13B,3_prime_UTR_variant,,ENST00000460371,;	G	ENSG00000169379	ENST00000394222	Transcript	3_prime_UTR_variant	1624	.	.	.	.	rs778211409	.	.	1	ARL13B	HGNC	25419	protein_coding	YES	CCDS2925.1	ENSP00000377769	AR13B_HUMAN	B4DRI8_HUMAN	UPI00001B94DF	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTCTCAGAAG	.	5	ESCA
FAM193A	0	.	GRCh37	4	2696769	2696769	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2316G>A	p.%3D	p.E772E	ENST00000324666	15/20	49	45	4	50	50	0	FAM193A,synonymous_variant,p.%3D,ENST00000545951,;FAM193A,synonymous_variant,p.%3D,ENST00000513350,;FAM193A,synonymous_variant,p.%3D,ENST00000324666,;FAM193A,synonymous_variant,p.%3D,ENST00000382839,;FAM193A,synonymous_variant,p.%3D,ENST00000505311,;FAM193A,synonymous_variant,p.%3D,ENST00000502458,;FAM193A,synonymous_variant,p.%3D,ENST00000512465,;FAM193A,synonymous_variant,p.%3D,ENST00000513898,;FAM193A,upstream_gene_variant,,ENST00000506120,;	A	ENSG00000125386	ENST00000324666	Transcript	synonymous_variant	2667	2316	772	E	gaG/gaA	.	.	.	1	FAM193A	HGNC	16822	protein_coding	YES	CCDS58875.1	ENSP00000324587	F193A_HUMAN	E7EUR8_HUMAN,D6R990_HUMAN	UPI0000551BCA	.	.	.	15/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15109:SF2,hmmpanther:PTHR15109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTGAGCACAG	.	3	ESCA
LIMCH1	0	.	GRCh37	4	41633278	41633278	+	Intron	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.936-7671C>T	.	.	ENST00000313860	.	87	82	4	77	77	0	LIMCH1,missense_variant,p.Ser462Phe,ENST00000503057,;LIMCH1,intron_variant,,ENST00000512632,;LIMCH1,intron_variant,,ENST00000512820,;LIMCH1,intron_variant,,ENST00000508501,;LIMCH1,intron_variant,,ENST00000313860,;LIMCH1,intron_variant,,ENST00000513024,;LIMCH1,intron_variant,,ENST00000396595,;LIMCH1,intron_variant,,ENST00000514096,;LIMCH1,intron_variant,,ENST00000509277,;LIMCH1,intron_variant,,ENST00000508466,;LIMCH1,intron_variant,,ENST00000511496,;LIMCH1,intron_variant,,ENST00000381753,;LIMCH1,intron_variant,,ENST00000512946,;	T	ENSG00000064042	ENST00000313860	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LIMCH1	HGNC	29191	protein_coding	YES	CCDS33977.1	ENSP00000316891	LIMC1_HUMAN	D6RJ93_HUMAN,D6RGH8_HUMAN,D6R8Y0_HUMAN	UPI0000D61554	.	.	.	.	8/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCTTCCAGCC	.	2	ESCA
JAKMIP1	0	.	GRCh37	4	6082040	6082040	+	Splice_Site	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1102-1G>C	.	p.X368_splice	ENST00000409021	.	41	37	4	49	49	0	JAKMIP1,splice_acceptor_variant,,ENST00000409021,;JAKMIP1,splice_acceptor_variant,,ENST00000409831,;JAKMIP1,splice_acceptor_variant,,ENST00000282924,;JAKMIP1,splice_acceptor_variant,,ENST00000409371,;JAKMIP1,splice_acceptor_variant,,ENST00000410077,;JAKMIP1,splice_acceptor_variant,,ENST00000457227,;JAKMIP1,splice_acceptor_variant,,ENST00000473053,;	G	ENSG00000152969	ENST00000409021	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	-1	JAKMIP1	HGNC	26460	protein_coding	YES	CCDS47005.1	ENSP00000386711	JKIP1_HUMAN	F2Z2K5_HUMAN	UPI00015734C1	.	.	.	.	6/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTTTCTGCAG	.	3	ESCA
TADA2B	0	.	GRCh37	4	7056573	7056573	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1055C>G	p.Ser352Ter	p.S352*	ENST00000310074	2/2	63	59	4	71	71	0	TADA2B,stop_gained,p.Ser260Ter,ENST00000515646,;TADA2B,stop_gained,p.Ser352Ter,ENST00000310074,;TADA2B,stop_gained,p.Ser277Ter,ENST00000512388,;TADA2B,downstream_gene_variant,,ENST00000506692,;GRPEL1,downstream_gene_variant,,ENST00000264954,;TADA2B,downstream_gene_variant,,ENST00000510704,;	G	ENSG00000173011	ENST00000310074	Transcript	stop_gained	1244	1055	352	S/*	tCa/tGa	.	.	.	1	TADA2B	HGNC	30781	protein_coding	YES	CCDS47007.1	ENSP00000308022	TAD2B_HUMAN	D6RJ05_HUMAN,D6RC20_HUMAN	UPI00001996F4	.	.	.	2/2	.	hmmpanther:PTHR12374,PIRSF_domain:PIRSF025024,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGTCAGATC	.	2	ESCA
DCK	0	.	GRCh37	4	71889340	71889340	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.466C>G	p.Gln156Glu	p.Q156E	ENST00000286648	4/7	127	121	6	125	125	0	DCK,missense_variant,p.Gln156Glu,ENST00000286648,;DCK,missense_variant,p.Gln156Glu,ENST00000504952,;DCK,missense_variant,p.Gln156Glu,ENST00000504730,;MOB1B,downstream_gene_variant,,ENST00000511449,;DCK,3_prime_UTR_variant,,ENST00000503359,;DCK,upstream_gene_variant,,ENST00000509764,;	G	ENSG00000156136	ENST00000286648	Transcript	missense_variant	863	466	156	Q/E	Caa/Gaa	.	.	.	1	DCK	HGNC	2704	protein_coding	YES	CCDS3548.1	ENSP00000286648	DCK_HUMAN	F5CTF3_HUMAN,B4E0A5_HUMAN	UPI0000128FC6	.	deleterious(0)	benign(0.084)	4/7	.	hmmpanther:PTHR10513:SF19,hmmpanther:PTHR10513,Pfam_domain:PF01712,Gene3D:3.40.50.300,PIRSF_domain:PIRSF000705,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTATCAAGAC	.	2	ESCA
WDFY3	0	.	GRCh37	4	85696107	85696107	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4620G>C	p.Met1540Ile	p.M1540I	ENST00000295888	29/68	58	53	5	79	78	0	WDFY3,missense_variant,p.Met1540Ile,ENST00000295888,;WDFY3,missense_variant,p.Met1540Ile,ENST00000322366,;	G	ENSG00000163625	ENST00000295888	Transcript	missense_variant	5028	4620	1540	M/I	atG/atC	.	.	.	-1	WDFY3	HGNC	20751	protein_coding	YES	CCDS3609.1	ENSP00000295888	WDFY3_HUMAN	D6RJE4_HUMAN,A7E1Z6_HUMAN	UPI000013E2C7	.	deleterious(0.01)	benign(0.027)	29/68	.	hmmpanther:PTHR13743:SF55,hmmpanther:PTHR13743	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTCTCATTAA	.	3	ESCA
ARHGAP24	0	.	GRCh37	4	86916190	86916190	+	Silent	SNP	G	G	A	rs778915879	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1383G>A	p.%3D	p.R461R	ENST00000395184	9/10	53	41	11	59	59	0	ARHGAP24,synonymous_variant,p.%3D,ENST00000264343,;ARHGAP24,synonymous_variant,p.%3D,ENST00000514229,;ARHGAP24,synonymous_variant,p.%3D,ENST00000395184,;ARHGAP24,synonymous_variant,p.%3D,ENST00000395183,;	A	ENSG00000138639	ENST00000395184	Transcript	synonymous_variant	1849	1383	461	R	agG/agA	rs778915879	.	.	1	ARHGAP24	HGNC	25361	protein_coding	YES	CCDS34025.1	ENSP00000378611	RHG24_HUMAN	D6RHH1_HUMAN,B3KUX7_HUMAN	UPI00001AF1D9	.	.	.	9/10	.	hmmpanther:PTHR13521,hmmpanther:PTHR13521:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAAGGAGCTC	.	5	ESCA
PTPN13	0	.	GRCh37	4	87684273	87684273	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3947C>G	p.Ser1316Ter	p.S1316*	ENST00000436978	24/48	43	37	5	35	35	0	PTPN13,stop_gained,p.Ser1316Ter,ENST00000411767,;PTPN13,stop_gained,p.Ser1316Ter,ENST00000436978,;PTPN13,stop_gained,p.Ser1125Ter,ENST00000316707,;PTPN13,stop_gained,p.Ser1316Ter,ENST00000511467,;PTPN13,stop_gained,p.Ser1297Ter,ENST00000427191,;PTPN13,non_coding_transcript_exon_variant,,ENST00000511105,;PTPN13,downstream_gene_variant,,ENST00000508063,;	G	ENSG00000163629	ENST00000436978	Transcript	stop_gained	4427	3947	1316	S/*	tCa/tGa	.	.	.	1	PTPN13	HGNC	9646	protein_coding	YES	CCDS47093.1	ENSP00000394794	PTN13_HUMAN	Q4W5F5_HUMAN,D6R9X4_HUMAN	UPI000016075D	.	.	.	24/48	.	hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF197,PIRSF_domain:PIRSF000933	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTACTCAGACC	.	4	ESCA
FBN2	0	.	GRCh37	5	127594174	127594174	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*973G>T	.	.	ENST00000508053	71/71	39	33	6	44	44	0	FBN2,3_prime_UTR_variant,,ENST00000262464,;FBN2,3_prime_UTR_variant,,ENST00000508053,;	A	ENSG00000138829	ENST00000508053	Transcript	3_prime_UTR_variant	10687	.	.	.	.	.	.	.	-1	FBN2	HGNC	3604	protein_coding	YES	CCDS34222.1	ENSP00000424571	FBN2_HUMAN	.	UPI0000519468	.	.	.	71/71	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGCACCATTA	.	4	ESCA
CLPTM1L	0	.	GRCh37	5	1344846	1344846	+	Silent	SNP	G	G	A	rs760266337	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.111C>T	p.%3D	p.S37S	ENST00000320895	1/17	34	30	4	33	33	0	CLPTM1L,synonymous_variant,p.%3D,ENST00000320927,;CLPTM1L,synonymous_variant,p.%3D,ENST00000320895,;CLPTM1L,upstream_gene_variant,,ENST00000507807,;	A	ENSG00000049656	ENST00000320895	Transcript	synonymous_variant	369	111	37	S	tcC/tcT	rs760266337	.	.	-1	CLPTM1L	HGNC	24308	protein_coding	YES	CCDS3862.1	ENSP00000313854	CLP1L_HUMAN	B3KY18_HUMAN	UPI00000707DF	.	.	.	1/17	.	hmmpanther:PTHR21347:SF1,hmmpanther:PTHR21347,Pfam_domain:PF05602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGCCGGAGCA	.	4	ESCA
SPOCK1	0	.	GRCh37	5	136313840	136313840	+	3'UTR	SNP	G	G	A	rs575603062	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*503C>T	.	.	ENST00000394945	11/11	128	112	15	108	108	0	SPOCK1,3_prime_UTR_variant,,ENST00000394945,;SPOCK1,downstream_gene_variant,,ENST00000282223,;SPOCK1,downstream_gene_variant,,ENST00000509978,;SPOCK1,downstream_gene_variant,,ENST00000515091,;	A	ENSG00000152377	ENST00000394945	Transcript	3_prime_UTR_variant	1993	.	.	.	.	rs575603062	.	.	-1	SPOCK1	HGNC	11251	protein_coding	YES	CCDS4191.1	ENSP00000378401	TICN1_HUMAN	D6RB21_HUMAN,D6RAM7_HUMAN,D3DQB3_HUMAN	UPI0000136F50	.	.	.	11/11	.	.	A:0.0008	A:0	A:0	.	A:0	A:0	A:0.0041	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCACCGGCAGT	byFrequency|by1000G	4	ESCA
PFDN1	0	.	GRCh37	5	139682640	139682640	+	Missense_Mutation	SNP	G	G	C	rs371310256	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19C>G	p.Leu7Val	p.L7V	ENST00000261813	1/4	99	76	22	96	96	0	PFDN1,missense_variant,p.Leu7Val,ENST00000261813,;PFDN1,missense_variant,p.Leu7Val,ENST00000524074,;PFDN1,missense_variant,p.Leu7Val,ENST00000510217,;PFDN1,upstream_gene_variant,,ENST00000514611,;PFDN1,non_coding_transcript_exon_variant,,ENST00000507185,;	C	ENSG00000113068	ENST00000261813	Transcript	missense_variant	67	19	7	L/V	Cta/Gta	rs371310256	.	.	-1	PFDN1	HGNC	8866	protein_coding	YES	CCDS4222.1	ENSP00000261813	PFD1_HUMAN	.	UPI000013171E	.	deleterious(0.03)	benign(0.232)	1/4	.	hmmpanther:PTHR20903	.	.	.	.	.	.	.	C:0	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCTAGATCCA	.	5	ESCA
SLC4A9	0	.	GRCh37	5	139743751	139743751	+	Missense_Mutation	SNP	G	G	A	rs372321175	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439G>A	p.Arg480His	p.R480H	ENST00000230993	10/22	69	54	14	73	73	0	SLC4A9,missense_variant,p.Arg480His,ENST00000230993,;SLC4A9,missense_variant,p.Arg480His,ENST00000507527,;SLC4A9,missense_variant,p.Arg456His,ENST00000506757,;SLC4A9,missense_variant,p.Arg456His,ENST00000506545,;SLC4A9,missense_variant,p.Arg445His,ENST00000432095,;SLC4A9,upstream_gene_variant,,ENST00000514849,;	A	ENSG00000113073	ENST00000230993	Transcript	missense_variant	1474	1439	480	R/H	cGc/cAc	rs372321175,COSM3238473,COSM3238472,COSM3238474	.	.	1	SLC4A9	HGNC	11035	protein_coding	YES	CCDS58973.1	ENSP00000230993	B3A4_HUMAN	.	UPI000018336F	.	deleterious(0.03)	benign(0.262)	10/22	.	Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834,hmmpanther:PTHR11453:SF33,hmmpanther:PTHR11453	.	.	.	.	.	.	.	A:0.0003	A:0	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGCGCCTGC	byFrequency|byCluster	5	ESCA
ARL10	0	.	GRCh37	5	175795982	175795982	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558G>C	p.Lys186Asn	p.K186N	ENST00000310389	3/4	130	105	25	148	148	0	ARL10,missense_variant,p.Lys11Asn,ENST00000503175,;ARL10,missense_variant,p.Lys44Asn,ENST00000514533,;ARL10,missense_variant,p.Lys186Asn,ENST00000310389,;MIR1271,downstream_gene_variant,,ENST00000408537,;ARL10,non_coding_transcript_exon_variant,,ENST00000507151,;	C	ENSG00000175414	ENST00000310389	Transcript	missense_variant	654	558	186	K/N	aaG/aaC	.	.	.	1	ARL10	HGNC	22042	protein_coding	YES	CCDS4400.1	ENSP00000308496	ARL10_HUMAN	.	UPI000006FEF9	.	deleterious(0)	probably_damaging(0.936)	3/4	.	PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF126,Pfam_domain:PF00025,Gene3D:3.40.50.300,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAAGCAGGT	.	5	ESCA
FAF2	0	.	GRCh37	5	175936545	175936545	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2594G>C	.	.	ENST00000261942	11/11	31	22	8	24	24	0	FAF2,3_prime_UTR_variant,,ENST00000261942,;	C	ENSG00000113194	ENST00000261942	Transcript	3_prime_UTR_variant	3985	.	.	.	.	.	.	.	1	FAF2	HGNC	24666	protein_coding	YES	CCDS34296.1	ENSP00000261942	FAF2_HUMAN	.	UPI000007478A	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCAAAGACACT	.	5	ESCA
GRM6	0	.	GRCh37	5	178413676	178413676	+	Missense_Mutation	SNP	G	G	A	rs149199617	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1579C>T	p.Arg527Trp	p.R527W	ENST00000231188	8/10	61	48	13	70	70	0	GRM6,missense_variant,p.Arg527Trp,ENST00000231188,;GRM6,missense_variant,p.Arg527Trp,ENST00000517717,;RP11-281O15.4,intron_variant,,ENST00000519491,;GRM6,non_coding_transcript_exon_variant,,ENST00000518082,;GRM6,upstream_gene_variant,,ENST00000519003,;	A	ENSG00000113262	ENST00000231188	Transcript	missense_variant	1758	1579	527	R/W	Cgg/Tgg	rs149199617	.	.	-1	GRM6	HGNC	4598	protein_coding	YES	CCDS4442.1	ENSP00000231188	GRM6_HUMAN	.	UPI000013C947	.	deleterious(0.01)	probably_damaging(0.985)	8/10	.	Pfam_domain:PF07562,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF24	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	A:0	A:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCCGCTCCC	byCluster|by1000G	5	ESCA
NPR3	0	.	GRCh37	5	32789284	32789284	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2833C>G	.	.	ENST00000265074	8/8	22	17	5	15	15	0	NPR3,3_prime_UTR_variant,,ENST00000265074,;AC026703.1,5_prime_UTR_variant,,ENST00000326958,;NPR3,downstream_gene_variant,,ENST00000434067,;NPR3,downstream_gene_variant,,ENST00000415167,;NPR3,downstream_gene_variant,,ENST00000415685,;	G	ENSG00000113389	ENST00000265074	Transcript	3_prime_UTR_variant	4802	.	.	.	.	.	.	.	1	NPR3	HGNC	7945	protein_coding	YES	CCDS56357.1	ENSP00000265074	ANPRC_HUMAN	.	UPI0000125B46	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCATCCAGTC	.	5	ESCA
ELOVL7	0	.	GRCh37	5	60053363	60053363	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.609G>A	p.Trp203Ter	p.W203*	ENST00000508821	8/9	109	100	8	68	68	0	ELOVL7,stop_gained,p.Trp190Ter,ENST00000505959,;ELOVL7,stop_gained,p.Trp203Ter,ENST00000425382,;ELOVL7,stop_gained,p.Trp203Ter,ENST00000508821,;ELOVL7,stop_gained,p.Trp203Ter,ENST00000438340,;ELOVL7,3_prime_UTR_variant,,ENST00000504455,;	T	ENSG00000164181	ENST00000508821	Transcript	stop_gained	924	609	203	W/*	tgG/tgA	.	.	.	-1	ELOVL7	HGNC	26292	protein_coding	YES	CCDS34164.1	ENSP00000424123	ELOV7_HUMAN	D6RBM2_HUMAN	UPI000004CAF4	.	.	.	8/9	.	hmmpanther:PTHR11157:SF8,hmmpanther:PTHR11157,Pfam_domain:PF01151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTCCACCA	.	2	ESCA
NLN	0	.	GRCh37	5	65088483	65088483	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1527+1G>A	.	p.X509_splice	ENST00000380985	.	48	44	4	65	65	0	NLN,splice_donor_variant,,ENST00000509935,;NLN,splice_donor_variant,,ENST00000502464,;NLN,splice_donor_variant,,ENST00000380985,;NLN,intron_variant,,ENST00000511299,;NLN,splice_donor_variant,,ENST00000506799,;NLN,non_coding_transcript_exon_variant,,ENST00000506539,;	A	ENSG00000123213	ENST00000380985	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	NLN	HGNC	16058	protein_coding	YES	CCDS3989.1	ENSP00000370372	NEUL_HUMAN	Q8NDD9_HUMAN,E9PCB6_HUMAN	UPI000003989D	.	.	.	.	9/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CACAGGTGAGT	.	2	ESCA
BDP1	0	.	GRCh37	5	70809019	70809019	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4255C>G	p.Leu1419Val	p.L1419V	ENST00000358731	19/39	94	87	6	96	96	0	BDP1,missense_variant,p.Leu1419Val,ENST00000358731,;BDP1,5_prime_UTR_variant,,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;BDP1,downstream_gene_variant,,ENST00000508157,;	G	ENSG00000145734	ENST00000358731	Transcript	missense_variant	4518	4255	1419	L/V	Ctt/Gtt	.	.	.	1	BDP1	HGNC	13652	protein_coding	YES	CCDS43328.1	ENSP00000351575	BDP1_HUMAN	.	UPI000020CA90	.	deleterious(0.02)	probably_damaging(0.996)	19/39	.	hmmpanther:PTHR22929:SF0,hmmpanther:PTHR22929	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATCTCTTCCT	.	2	ESCA
ARHGEF28	0	.	GRCh37	5	73168821	73168821	+	Intron	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2567-3C>T	.	.	ENST00000545377	.	50	42	8	49	49	0	ARHGEF28,splice_region_variant,,ENST00000437974,;ARHGEF28,splice_region_variant,,ENST00000296799,;ARHGEF28,splice_region_variant,,ENST00000513042,;ARHGEF28,splice_region_variant,,ENST00000287898,;ARHGEF28,splice_region_variant,,ENST00000545377,;ARHGEF28,splice_region_variant,,ENST00000426542,;ARHGEF28,splice_region_variant,,ENST00000296794,;	T	ENSG00000214944	ENST00000545377	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	ARHGEF28	HGNC	30322	protein_coding	YES	CCDS47231.2	ENSP00000441913	ARG28_HUMAN	D6RAP0_HUMAN	UPI00004DF58E	.	.	.	.	21/36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATTTCAGAGC	.	4	ESCA
ANKRD31	0	.	GRCh37	5	74526426	74526426	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.139G>C	p.Glu47Gln	p.E47Q	ENST00000506364	2/26	67	55	11	46	45	1	ANKRD31,missense_variant,p.Glu47Gln,ENST00000506364,;ANKRD31,missense_variant,p.Glu47Gln,ENST00000274361,;SUMO2P5,downstream_gene_variant,,ENST00000506790,;	G	ENSG00000145700	ENST00000506364	Transcript	missense_variant	331	139	47	E/Q	Gag/Cag	.	.	.	-1	ANKRD31	HGNC	26853	protein_coding	YES	.	ENSP00000427262	.	H0YAM5_HUMAN,D6RJB7_HUMAN	UPI0003B9283E	.	deleterious(0.01)	benign(0.106)	2/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	GAACTCAGATT	.	3	ESCA
VCAN	0	.	GRCh37	5	82818043	82818043	+	Silent	SNP	G	G	A	rs768841073	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3918G>A	p.%3D	p.A1306A	ENST00000265077	7/15	47	35	11	52	52	0	VCAN,synonymous_variant,p.%3D,ENST00000342785,;VCAN,synonymous_variant,p.%3D,ENST00000265077,;VCAN,synonymous_variant,p.%3D,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000343200,;VCAN,intron_variant,,ENST00000515397,;	A	ENSG00000038427	ENST00000265077	Transcript	synonymous_variant	4483	3918	1306	A	gcG/gcA	rs768841073,COSM288257	.	.	1	VCAN	HGNC	2464	protein_coding	YES	CCDS4060.1	ENSP00000265077	CSPG2_HUMAN	.	UPI000013178B	.	.	.	7/15	.	hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGGCGCTTTC	byFrequency	5	ESCA
KIAA0825	0	.	GRCh37	5	93856381	93856381	+	Missense_Mutation	SNP	T	T	G	rs779873863	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.542A>C	p.Glu181Ala	p.E181A	ENST00000329378	5/5	50	42	8	48	48	0	KIAA0825,missense_variant,p.Glu181Ala,ENST00000427991,;KIAA0825,missense_variant,p.Glu181Ala,ENST00000312498,;KIAA0825,missense_variant,p.Glu181Ala,ENST00000329378,;KIAA0825,missense_variant,p.Glu181Ala,ENST00000513200,;	G	ENSG00000185261	ENST00000329378	Transcript	missense_variant	792	542	181	E/A	gAa/gCa	rs779873863	.	.	-1	KIAA0825	HGNC	28532	protein_coding	YES	CCDS4070.1	ENSP00000331385	K0825_HUMAN	.	UPI00000746AF	.	deleterious(0.02)	possibly_damaging(0.547)	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTATTTCATTA	.	5	ESCA
TBC1D7	0	.	GRCh37	6	13281263	13281263	+	Intron	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*40-13196G>A	.	.	ENST00000606214	.	58	48	9	52	52	0	PHACTR1,intron_variant,,ENST00000379329,;PHACTR1,intron_variant,,ENST00000415087,;PHACTR1,intron_variant,,ENST00000379335,;PHACTR1,intron_variant,,ENST00000332995,;TBC1D7,intron_variant,,ENST00000606214,;PHACTR1,intron_variant,,ENST00000457702,;PHACTR1,downstream_gene_variant,,ENST00000379350,;RP1-257A7.4,non_coding_transcript_exon_variant,,ENST00000606150,;RP1-257A7.4,intron_variant,,ENST00000399446,;PHACTR1,intron_variant,,ENST00000489548,;PHACTR1,intron_variant,,ENST00000481706,;TBC1D7,intron_variant,,ENST00000421203,;	T	ENSG00000145979	ENST00000606214	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TBC1D7	HGNC	21066	protein_coding	YES	CCDS4523.1	ENSP00000475727	TBCD7_HUMAN	U3KQ23_HUMAN,Q5SZM2_HUMAN,Q5SZM1_HUMAN,Q5SZL8_HUMAN,Q5SZL4_HUMAN	UPI0000073B32	.	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTCTGAGC	.	5	ESCA
NHSL1	0	.	GRCh37	6	138751558	138751558	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3936G>A	p.%3D	p.E1312E	ENST00000427025	5/7	63	52	10	75	75	0	NHSL1,synonymous_variant,p.%3D,ENST00000343505,;NHSL1,synonymous_variant,p.%3D,ENST00000427025,;NHSL1,downstream_gene_variant,,ENST00000342260,;MIR3145,downstream_gene_variant,,ENST00000580727,;	T	ENSG00000135540	ENST00000427025	Transcript	synonymous_variant	4565	3936	1312	E	gaG/gaA	.	.	.	-1	NHSL1	HGNC	21021	protein_coding	YES	CCDS55063.1	ENSP00000394546	NHSL1_HUMAN	B4DS58_HUMAN	UPI0001750345	.	.	.	5/7	.	hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGCTCTCCCC	.	5	ESCA
NHSL1	0	.	GRCh37	6	138751653	138751653	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3841G>A	p.Glu1281Lys	p.E1281K	ENST00000427025	5/7	43	29	13	41	41	0	NHSL1,missense_variant,p.Glu1277Lys,ENST00000343505,;NHSL1,missense_variant,p.Glu1281Lys,ENST00000427025,;NHSL1,downstream_gene_variant,,ENST00000342260,;MIR3145,downstream_gene_variant,,ENST00000580727,;	T	ENSG00000135540	ENST00000427025	Transcript	missense_variant	4470	3841	1281	E/K	Gaa/Aaa	.	.	.	-1	NHSL1	HGNC	21021	protein_coding	YES	CCDS55063.1	ENSP00000394546	NHSL1_HUMAN	B4DS58_HUMAN	UPI0001750345	.	tolerated(0.2)	benign(0.044)	5/7	.	hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCTTCCACTC	.	5	ESCA
NHSL1	0	.	GRCh37	6	138754450	138754450	+	Silent	SNP	G	G	A	rs774115580	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1044C>T	p.%3D	p.L348L	ENST00000427025	5/7	39	30	9	58	58	0	NHSL1,synonymous_variant,p.%3D,ENST00000343505,;NHSL1,synonymous_variant,p.%3D,ENST00000427025,;NHSL1,downstream_gene_variant,,ENST00000342260,;MIR3145,downstream_gene_variant,,ENST00000580727,;	A	ENSG00000135540	ENST00000427025	Transcript	synonymous_variant	1673	1044	348	L	ctC/ctT	rs774115580	.	.	-1	NHSL1	HGNC	21021	protein_coding	YES	CCDS55063.1	ENSP00000394546	NHSL1_HUMAN	B4DS58_HUMAN	UPI0001750345	.	.	.	5/7	.	Pfam_domain:PF15273,hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGCCGAGGGC	.	4	ESCA
EZR	0	.	GRCh37	6	159187344	159187344	+	3'UTR	SNP	A	A	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*602T>G	.	.	ENST00000367075	14/14	23	19	4	40	39	1	EZR,3_prime_UTR_variant,,ENST00000337147,;EZR,3_prime_UTR_variant,,ENST00000367075,;SYTL3,downstream_gene_variant,,ENST00000367081,;SYTL3,downstream_gene_variant,,ENST00000297239,;SYTL3,downstream_gene_variant,,ENST00000360448,;EZR,downstream_gene_variant,,ENST00000392177,;MIR3918,upstream_gene_variant,,ENST00000581555,;	C	ENSG00000092820	ENST00000367075	Transcript	3_prime_UTR_variant	2532	.	.	.	.	.	.	.	-1	EZR	HGNC	12691	protein_coding	YES	CCDS5258.1	ENSP00000356042	EZRI_HUMAN	B7Z9R6_HUMAN	UPI0000167BA1	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	AAAAAACAAAA	.	2	ESCA
LPA	0	.	GRCh37	6	161071369	161071369	+	Splice_Site	SNP	C	C	T	rs533200556	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.209+1G>A	.	p.X70_splice	ENST00000447678	.	270	258	11	228	228	0	LPA,splice_donor_variant,,ENST00000316300,;LPA,splice_donor_variant,,ENST00000447678,;	T	ENSG00000198670	ENST00000447678	Transcript	splice_donor_variant	.	.	.	.	.	rs533200556,COSM1213578	.	.	-1	LPA	HGNC	6667	protein_coding	YES	CCDS43523.1	ENSP00000395608	APOA_HUMAN	Q9UKJ7_HUMAN,Q9UIR8_HUMAN,Q9UIR6_HUMAN,Q9UIR5_HUMAN	UPI0000458AC9	.	.	.	.	3/39	.	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.?|c.209+1G>A|3	MUTECT|MUSE	ACATACGCATT	byFrequency|by1000G	2	ESCA
DEK	0	.	GRCh37	6	18255979	18255979	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.556C>G	p.Pro186Ala	p.P186A	ENST00000397239	6/11	54	50	4	49	49	0	DEK,missense_variant,p.Pro186Ala,ENST00000397239,;DEK,missense_variant,p.Pro119Ala,ENST00000503715,;DEK,missense_variant,p.Pro152Ala,ENST00000244776,;DEK,downstream_gene_variant,,ENST00000515742,;DEK,missense_variant,p.Pro62Ala,ENST00000515770,;DEK,missense_variant,p.Pro158Ala,ENST00000505224,;DEK,non_coding_transcript_exon_variant,,ENST00000512145,;	C	ENSG00000124795	ENST00000397239	Transcript	missense_variant	1004	556	186	P/A	Cca/Gca	.	.	.	-1	DEK	HGNC	2768	protein_coding	YES	CCDS34344.1	ENSP00000380414	DEK_HUMAN	D6RDA2_HUMAN	UPI0000001C2C	.	deleterious(0)	probably_damaging(0.993)	6/11	.	Low_complexity_(Seg):seg,hmmpanther:PTHR13468	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTGGATGCA	.	2	ESCA
HIST1H3E	0	.	GRCh37	6	26225833	26225833	+	3'UTR	SNP	C	C	T	rs750607982	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*40C>T	.	.	ENST00000360408	1/1	47	37	10	50	50	0	HIST1H3E,3_prime_UTR_variant,,ENST00000360408,;	T	ENSG00000196966	ENST00000360408	Transcript	3_prime_UTR_variant	451	.	.	.	.	rs750607982	.	.	1	HIST1H3E	HGNC	4769	protein_coding	YES	CCDS4596.1	ENSP00000353581	H31_HUMAN	.	UPI00000003C7	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCTCAGAGC	.	5	ESCA
HLA-V	0	.	GRCh37	6	29761162	29761162	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.670+679C>G	.	.	ENST00000476601	.	36	31	5	30	30	0	HLA-V,non_coding_transcript_exon_variant,,ENST00000457107,;HLA-V,intron_variant,,ENST00000476601,;HLA-V,downstream_gene_variant,,ENST00000446817,;HCG4,upstream_gene_variant,,ENST00000418983,;HCG4,upstream_gene_variant,,ENST00000320533,;HLA-V,downstream_gene_variant,,ENST00000429037,;	G	ENSG00000181126	ENST00000476601	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	HLA-V	HGNC	23482	processed_transcript	YES	.	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GGTCTCTACAG	.	3	ESCA
PPP1R18	0	.	GRCh37	6	30652519	30652519	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1277C>A	p.Pro426Gln	p.P426Q	ENST00000274853	1/3	16	12	4	16	16	0	PPP1R18,missense_variant,p.Pro426Gln,ENST00000399199,;PPP1R18,missense_variant,p.Pro426Gln,ENST00000274853,;NRM,downstream_gene_variant,,ENST00000376420,;NRM,downstream_gene_variant,,ENST00000376421,;NRM,downstream_gene_variant,,ENST00000444096,;NRM,downstream_gene_variant,,ENST00000259953,;PPP1R18,intron_variant,,ENST00000467662,;PPP1R18,intron_variant,,ENST00000488324,;NRM,downstream_gene_variant,,ENST00000462857,;NRM,downstream_gene_variant,,ENST00000482141,;NRM,downstream_gene_variant,,ENST00000474864,;NRM,downstream_gene_variant,,ENST00000470733,;NRM,downstream_gene_variant,,ENST00000495946,;	T	ENSG00000146112	ENST00000274853	Transcript	missense_variant	3154	1277	426	P/Q	cCa/cAa	.	.	.	-1	PPP1R18	HGNC	29413	protein_coding	YES	CCDS43444.1	ENSP00000274853	PPR18_HUMAN	.	UPI00001C1E5E	.	tolerated_low_confidence(0.07)	possibly_damaging(0.708)	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21685	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	GTGGTGGGGGC	.	2	ESCA
C6orf106	0	.	GRCh37	6	34574418	34574418	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.775C>G	p.Gln259Glu	p.Q259E	ENST00000374023	4/5	93	84	9	112	112	0	C6orf106,missense_variant,p.Gln185Glu,ENST00000374021,;C6orf106,missense_variant,p.Gln193Glu,ENST00000374026,;C6orf106,missense_variant,p.Gln259Glu,ENST00000374023,;	C	ENSG00000196821	ENST00000374023	Transcript	missense_variant	1019	775	259	Q/E	Caa/Gaa	.	.	.	-1	C6orf106	HGNC	21215	protein_coding	YES	CCDS4796.1	ENSP00000363135	CF106_HUMAN	Q5TH58_HUMAN	UPI000006F934	.	deleterious_low_confidence(0.04)	benign(0.009)	4/5	.	hmmpanther:PTHR20930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCTTGCTCAG	.	4	ESCA
CMTR1	0	.	GRCh37	6	37414120	37414120	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339G>A	p.%3D	p.R113R	ENST00000373451	4/24	79	69	10	69	69	0	CMTR1,synonymous_variant,p.%3D,ENST00000373451,;CMTR1,synonymous_variant,p.%3D,ENST00000455891,;CMTR1,downstream_gene_variant,,ENST00000471097,;	A	ENSG00000137200	ENST00000373451	Transcript	synonymous_variant	503	339	113	R	cgG/cgA	.	.	.	1	CMTR1	HGNC	21077	protein_coding	YES	CCDS4835.1	ENSP00000362550	CMTR1_HUMAN	.	UPI00000700C2	.	.	.	4/24	.	SMART_domains:SM00443,Pfam_domain:PF01585,hmmpanther:PTHR16121:SF0,hmmpanther:PTHR16121,PROSITE_profiles:PS50174	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGTCGGAAGGA	.	4	ESCA
CYP39A1	0	.	GRCh37	6	46554852	46554852	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1212C>G	p.Phe404Leu	p.F404L	ENST00000275016	10/12	110	82	27	75	75	0	CYP39A1,missense_variant,p.Phe404Leu,ENST00000275016,;CYP39A1,non_coding_transcript_exon_variant,,ENST00000489657,;CYP39A1,non_coding_transcript_exon_variant,,ENST00000476076,;CYP39A1,downstream_gene_variant,,ENST00000480804,;	C	ENSG00000146233	ENST00000275016	Transcript	missense_variant	1416	1212	404	F/L	ttC/ttG	.	.	.	-1	CYP39A1	HGNC	17449	protein_coding	YES	CCDS4916.1	ENSP00000275016	CP39A_HUMAN	.	UPI000013DA3D	.	deleterious(0)	possibly_damaging(0.856)	10/12	.	hmmpanther:PTHR24304,hmmpanther:PTHR24304:SF4,Pfam_domain:PF00067,Gene3D:1.10.630.10,PIRSF_domain:PIRSF000047,Superfamily_domains:SSF48264,Prints_domain:PR00465	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCATGAAGCA	.	5	ESCA
IL17F	0	.	GRCh37	6	52103596	52103596	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.186C>G	p.Ile62Met	p.I62M	ENST00000336123	2/3	138	111	26	136	136	0	IL17F,missense_variant,p.Ile62Met,ENST00000336123,;IL17F,non_coding_transcript_exon_variant,,ENST00000478427,;	C	ENSG00000112116	ENST00000336123	Transcript	missense_variant	294	186	62	I/M	atC/atG	.	.	.	-1	IL17F	HGNC	16404	protein_coding	YES	CCDS4938.1	ENSP00000337432	IL17F_HUMAN	.	UPI0000038A0C	.	deleterious(0.04)	benign(0.445)	2/3	.	Superfamily_domains:SSF57501,Gene3D:2.10.90.10,hmmpanther:PTHR21295,hmmpanther:PTHR21295:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATTGATGAT	.	5	ESCA
RELN	0	.	GRCh37	7	103155684	103155684	+	Silent	SNP	G	G	A	rs776667611	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8067C>T	p.%3D	p.A2689A	ENST00000428762	50/65	84	72	11	52	52	0	RELN,synonymous_variant,p.%3D,ENST00000424685,;RELN,synonymous_variant,p.%3D,ENST00000428762,;RELN,synonymous_variant,p.%3D,ENST00000343529,;CTB-107G13.1,downstream_gene_variant,,ENST00000422488,;	A	ENSG00000189056	ENST00000428762	Transcript	synonymous_variant	8227	8067	2689	A	gcC/gcT	rs776667611	.	.	-1	RELN	HGNC	9957	protein_coding	YES	CCDS47680.1	ENSP00000392423	RELN_HUMAN	Q75MM8_HUMAN	UPI00001678BC	.	.	.	50/65	.	hmmpanther:PTHR11841	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGGCCGGCATC	byFrequency	4	ESCA
NRCAM	0	.	GRCh37	7	107789577	107789577	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*778C>T	.	.	ENST00000379028	33/33	95	90	5	59	59	0	NRCAM,3_prime_UTR_variant,,ENST00000351718,;NRCAM,3_prime_UTR_variant,,ENST00000413765,;NRCAM,3_prime_UTR_variant,,ENST00000379024,;NRCAM,3_prime_UTR_variant,,ENST00000379028,;NRCAM,downstream_gene_variant,,ENST00000379022,;NRCAM,downstream_gene_variant,,ENST00000445634,;NRCAM,downstream_gene_variant,,ENST00000425651,;NRCAM,non_coding_transcript_exon_variant,,ENST00000522550,;NRCAM,downstream_gene_variant,,ENST00000415105,;	A	ENSG00000091129	ENST00000379028	Transcript	3_prime_UTR_variant	5164	.	.	.	.	.	.	.	-1	NRCAM	HGNC	7994	protein_coding	YES	CCDS47686.1	ENSP00000368314	NRCAM_HUMAN	C9JUR7_HUMAN,C9JF43_HUMAN,B3KRX0_HUMAN	UPI00005E2661	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGATGATTTG	.	2	ESCA
C7orf66	0	.	GRCh37	7	108524135	108524135	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.277G>A	p.Ala93Thr	p.A93T	ENST00000379007	2/2	81	63	17	55	55	0	C7orf66,missense_variant,p.Ala93Thr,ENST00000379007,;	T	ENSG00000205174	ENST00000379007	Transcript	missense_variant	332	277	93	A/T	Gca/Aca	.	.	.	-1	C7orf66	HGNC	33712	protein_coding	YES	CCDS34735.1	ENSP00000368292	CG066_HUMAN	.	UPI0000160BC7	.	deleterious_low_confidence(0.01)	benign(0.035)	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATATGCACCTT	.	5	ESCA
MGAM	0	.	GRCh37	7	141796214	141796214	+	Missense_Mutation	SNP	G	G	A	rs369519766	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5003G>A	p.Arg1668His	p.R1668H	ENST00000549489	42/48	94	88	5	87	87	0	MGAM,missense_variant,p.Arg2564His,ENST00000475668,;MGAM,missense_variant,p.Arg1668His,ENST00000549489,;MGAM,downstream_gene_variant,,ENST00000485078,;	A	ENSG00000257335	ENST00000549489	Transcript	missense_variant	5098	5003	1668	R/H	cGt/cAt	rs369519766	.	.	1	MGAM	HGNC	7043	protein_coding	YES	CCDS47727.1	ENSP00000447378	MGA_HUMAN	Q8TE25_HUMAN,E9PEQ5_HUMAN,E7EW87_HUMAN	UPI000183CB7B	.	deleterious(0.03)	benign(0)	42/48	.	Superfamily_domains:SSF51011,Pfam_domain:PF01055	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGAGCGTGTGA	byFrequency|byCluster	2	ESCA
SSPO	0	.	GRCh37	7	149477372	149477372	+	RNA	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1443C>T	.	.	ENST00000378016	12/109	46	38	8	49	49	0	SSPO,non_coding_transcript_exon_variant,,ENST00000378016,;SSPO,non_coding_transcript_exon_variant,,ENST00000262089,;SSPO,intron_variant,,ENST00000486824,;SSPO,downstream_gene_variant,,ENST00000465080,;SSPO,upstream_gene_variant,,ENST00000477518,;SSPO,upstream_gene_variant,,ENST00000493502,;	T	ENSG00000197558	ENST00000378016	Transcript	non_coding_transcript_exon_variant	1443	.	.	.	.	.	.	.	1	SSPO	HGNC	21998	processed_transcript	YES	.	.	.	.	.	.	.	.	12/109	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCTCTGCCC	.	5	ESCA
SNX13	0	.	GRCh37	7	17832356	17832356	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1313C>T	.	.	ENST00000428135	26/26	105	98	7	63	63	0	SNX13,3_prime_UTR_variant,,ENST00000428135,;SNX13,downstream_gene_variant,,ENST00000409389,;SNX13,downstream_gene_variant,,ENST00000496855,;SNX13,downstream_gene_variant,,ENST00000409076,;	A	ENSG00000071189	ENST00000428135	Transcript	3_prime_UTR_variant	4386	.	.	.	.	.	.	.	-1	SNX13	HGNC	21335	protein_coding	YES	CCDS47551.1	ENSP00000398789	SNX13_HUMAN	B3KN60_HUMAN	UPI000002B3E8	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAATGAAAGT	.	2	ESCA
DPY19L2P3	0	.	GRCh37	7	29727025	29727025	+	Intron	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.870+10T>C	.	.	ENST00000414296	.	199	173	26	196	196	0	DPY19L2P3,non_coding_transcript_exon_variant,,ENST00000602965,;DPY19L2P3,non_coding_transcript_exon_variant,,ENST00000602980,;ZNRF2P2,upstream_gene_variant,,ENST00000426767,;ZNRF2P2,upstream_gene_variant,,ENST00000442865,;DPY19L2P3,intron_variant,,ENST00000414296,;ZNRF2P2,upstream_gene_variant,,ENST00000454624,;	C	ENSG00000227855	ENST00000414296	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	DPY19L2P3	HGNC	22367	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	.	6/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTCTTCCAA	.	4	ESCA
FAM220A	0	.	GRCh37	7	6370417	6370417	+	Silent	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369A>G	p.%3D	p.E123E	ENST00000313324	2/2	104	92	11	96	96	0	FAM220A,synonymous_variant,p.%3D,ENST00000313324,;FAM220A,downstream_gene_variant,,ENST00000524898,;FAM220A,downstream_gene_variant,,ENST00000578372,;FAM220A,downstream_gene_variant,,ENST00000530143,;FAM220A,downstream_gene_variant,,ENST00000533877,;	C	ENSG00000178397	ENST00000313324	Transcript	synonymous_variant	837	369	123	E	gaA/gaG	.	.	.	-1	FAM220A	HGNC	22422	protein_coding	YES	CCDS34599.1	ENSP00000317289	F220A_HUMAN	E9PQY0_HUMAN,E9PQC6_HUMAN	UPI000013F4F0	.	.	.	2/2	.	hmmpanther:PTHR31980,Pfam_domain:PF15487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAGCTTCAAC	.	4	ESCA
GUSB	0	.	GRCh37	7	65444728	65444728	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567G>C	p.%3D	p.L189L	ENST00000304895	3/12	88	72	16	97	96	1	GUSB,synonymous_variant,p.%3D,ENST00000345660,;GUSB,synonymous_variant,p.%3D,ENST00000304895,;GUSB,intron_variant,,ENST00000421103,;GUSB,non_coding_transcript_exon_variant,,ENST00000478118,;GUSB,intron_variant,,ENST00000476486,;GUSB,intron_variant,,ENST00000475316,;GUSB,intron_variant,,ENST00000479038,;GUSB,upstream_gene_variant,,ENST00000465785,;GUSB,intron_variant,,ENST00000446111,;GUSB,intron_variant,,ENST00000430730,;GUSB,intron_variant,,ENST00000447929,;GUSB,upstream_gene_variant,,ENST00000462371,;GUSB,upstream_gene_variant,,ENST00000489482,;GUSB,upstream_gene_variant,,ENST00000466883,;	G	ENSG00000169919	ENST00000304895	Transcript	synonymous_variant	698	567	189	L	ctG/ctC	.	.	.	-1	GUSB	HGNC	4696	protein_coding	YES	CCDS5530.1	ENSP00000302728	BGLR_HUMAN	.	UPI000013E9E0	.	.	.	3/12	.	hmmpanther:PTHR10066:SF51,hmmpanther:PTHR10066,Pfam_domain:PF02837,Gene3D:2.60.120.260,Superfamily_domains:SSF49785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCAGTCAGGTA	.	5	ESCA
POM121	0	.	GRCh37	7	72413681	72413681	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2354C>T	p.Pro785Leu	p.P785L	ENST00000395270	14/16	159	150	9	176	176	0	POM121,missense_variant,p.Pro785Leu,ENST00000446813,;POM121,missense_variant,p.Pro785Leu,ENST00000257622,;POM121,missense_variant,p.Pro1050Leu,ENST00000434423,;POM121,missense_variant,p.Pro785Leu,ENST00000358357,;POM121,missense_variant,p.Pro785Leu,ENST00000395270,;NSUN5P2,downstream_gene_variant,,ENST00000602348,;	T	ENSG00000196313	ENST00000395270	Transcript	missense_variant	3395	2354	785	P/L	cCc/cTc	.	.	.	1	POM121	HGNC	19702	protein_coding	YES	CCDS59059.1	ENSP00000378687	P121A_HUMAN	A8MY32_HUMAN	UPI000013DA6B	.	deleterious(0.05)	benign(0.11)	14/16	.	hmmpanther:PTHR23193:SF5,hmmpanther:PTHR23193	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGCTCCCGCCA	.	2	ESCA
MLXIPL	0	.	GRCh37	7	73030405	73030405	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396C>T	p.%3D	p.I132I	ENST00000313375	2/17	63	51	11	78	78	0	MLXIPL,synonymous_variant,p.%3D,ENST00000313375,;MLXIPL,synonymous_variant,p.%3D,ENST00000456640,;MLXIPL,synonymous_variant,p.%3D,ENST00000434326,;MLXIPL,synonymous_variant,p.%3D,ENST00000395189,;MLXIPL,synonymous_variant,p.%3D,ENST00000429400,;MLXIPL,synonymous_variant,p.%3D,ENST00000354613,;MLXIPL,synonymous_variant,p.%3D,ENST00000453275,;MLXIPL,synonymous_variant,p.%3D,ENST00000414749,;MLXIPL,synonymous_variant,p.%3D,ENST00000345114,;	A	ENSG00000009950	ENST00000313375	Transcript	synonymous_variant	444	396	132	I	atC/atT	.	.	.	-1	MLXIPL	HGNC	12744	protein_coding	YES	CCDS5553.1	ENSP00000320886	MLXPL_HUMAN	S5LSP3_HUMAN	UPI0000138F98	.	.	.	2/17	.	hmmpanther:PTHR15741:SF14,hmmpanther:PTHR15741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGGATATA	.	5	ESCA
GRM3	0	.	GRCh37	7	86416063	86416063	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.955G>A	p.Gly319Ser	p.G319S	ENST00000361669	3/6	51	46	5	39	38	1	GRM3,missense_variant,p.Gly191Ser,ENST00000536043,;GRM3,missense_variant,p.Gly319Ser,ENST00000439827,;GRM3,missense_variant,p.Gly317Ser,ENST00000394720,;GRM3,missense_variant,p.Gly319Ser,ENST00000361669,;GRM3,intron_variant,,ENST00000546348,;GRM3,downstream_gene_variant,,ENST00000454217,;AC005009.2,upstream_gene_variant,,ENST00000418031,;AC005009.2,upstream_gene_variant,,ENST00000452471,;	A	ENSG00000198822	ENST00000361669	Transcript	missense_variant	2054	955	319	G/S	Ggc/Agc	.	.	.	1	GRM3	HGNC	4595	protein_coding	YES	CCDS5600.1	ENSP00000355316	GRM3_HUMAN	C9JUH9_HUMAN,C9JIT1_HUMAN,A4D1D0_HUMAN	UPI0000153EFC	.	deleterious(0.01)	possibly_damaging(0.835)	3/6	.	hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00593	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTACGGCGCC	.	2	ESCA
GNGT1	0	.	GRCh37	7	93538863	93538863	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97-1239C>G	.	.	ENST00000248572	.	108	94	14	111	111	0	GNGT1,3_prime_UTR_variant,,ENST00000455502,;GNGT1,3_prime_UTR_variant,,ENST00000430875,;GNGT1,3_prime_UTR_variant,,ENST00000428834,;GNGT1,intron_variant,,ENST00000429473,;GNGT1,intron_variant,,ENST00000248572,;	G	ENSG00000127928	ENST00000248572	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GNGT1	HGNC	4411	protein_coding	YES	CCDS5633.1	ENSP00000248572	GBG1_HUMAN	Q6LCP6_HUMAN	UPI0000001316	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCTCTGTTC	.	4	ESCA
ADAP1	0	.	GRCh37	7	938496	938496	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*62G>C	.	.	ENST00000265846	11/11	77	63	14	139	139	0	ADAP1,3_prime_UTR_variant,,ENST00000449296,;ADAP1,3_prime_UTR_variant,,ENST00000446141,;ADAP1,3_prime_UTR_variant,,ENST00000539900,;ADAP1,3_prime_UTR_variant,,ENST00000265846,;ADAP1,downstream_gene_variant,,ENST00000437486,;ADAP1,downstream_gene_variant,,ENST00000453175,;GET4,downstream_gene_variant,,ENST00000407192,;ADAP1,downstream_gene_variant,,ENST00000453823,;GET4,downstream_gene_variant,,ENST00000265857,;ADAP1,downstream_gene_variant,,ENST00000454383,;COX19,3_prime_UTR_variant,,ENST00000457254,;ADAP1,non_coding_transcript_exon_variant,,ENST00000478000,;ADAP1,non_coding_transcript_exon_variant,,ENST00000495809,;GET4,downstream_gene_variant,,ENST00000464468,;SUN1,downstream_gene_variant,,ENST00000457861,;	G	ENSG00000105963	ENST00000265846	Transcript	3_prime_UTR_variant	1407	.	.	.	.	.	.	.	-1	ADAP1	HGNC	16486	protein_coding	YES	CCDS5318.1	ENSP00000265846	ADAP1_HUMAN	H7C2Q4_HUMAN	UPI000013D694	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATCCACGG	.	5	ESCA
PABPC1	0	.	GRCh37	8	101721918	101721918	+	Silent	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1014A>G	p.%3D	p.V338V	ENST00000318607	8/15	133	107	25	92	91	1	PABPC1,synonymous_variant,p.%3D,ENST00000522387,;PABPC1,synonymous_variant,p.%3D,ENST00000519004,;PABPC1,synonymous_variant,p.%3D,ENST00000519100,;PABPC1,synonymous_variant,p.%3D,ENST00000318607,;PABPC1,intron_variant,,ENST00000517403,;PABPC1,upstream_gene_variant,,ENST00000518293,;PABPC1,downstream_gene_variant,,ENST00000523555,;PABPC1,upstream_gene_variant,,ENST00000520868,;PABPC1,upstream_gene_variant,,ENST00000522658,;PABPC1,upstream_gene_variant,,ENST00000517990,;AP001205.1,upstream_gene_variant,,ENST00000579868,;PABPC1,non_coding_transcript_exon_variant,,ENST00000519596,;PABPC1,synonymous_variant,p.%3D,ENST00000523636,;PABPC1,non_coding_transcript_exon_variant,,ENST00000518716,;PABPC1,intron_variant,,ENST00000519622,;PABPC1,downstream_gene_variant,,ENST00000517921,;PABPC1,upstream_gene_variant,,ENST00000519848,;	C	ENSG00000070756	ENST00000318607	Transcript	synonymous_variant	2143	1014	338	V	gtA/gtG	.	.	.	-1	PABPC1	HGNC	8554	protein_coding	YES	CCDS6289.1	ENSP00000313007	PABP1_HUMAN	H0YB75_HUMAN,E7EQV3_HUMAN,E5RJM8_HUMAN,E5RJB9_HUMAN,E5RHG7_HUMAN,E5RH24_HUMAN,E5RGH3_HUMAN,E5RGC4_HUMAN,E5RFD8_HUMAN	UPI0000000BC4	.	.	.	8/15	.	PROSITE_profiles:PS50102,hmmpanther:PTHR24011:SF239,hmmpanther:PTHR24011,Gene3D:3.30.70.330,TIGRFAM_domain:TIGR01628,Pfam_domain:PF00076,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACATACAAA	.	5	ESCA
RIMS2	0	.	GRCh37	8	105260958	105260958	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3506C>G	p.Ser1169Cys	p.S1169C	ENST00000406091	21/24	81	67	14	57	57	0	RIMS2,missense_variant,p.Ser1169Cys,ENST00000406091,;RIMS2,missense_variant,p.Ser1176Cys,ENST00000408894,;RIMS2,missense_variant,p.Ser105Cys,ENST00000339750,;RIMS2,missense_variant,p.Ser983Cys,ENST00000507740,;RIMS2,missense_variant,p.Ser1008Cys,ENST00000262231,;RIMS2,missense_variant,p.Ser105Cys,ENST00000523362,;RIMS2,missense_variant,p.Ser1187Cys,ENST00000436393,;	G	ENSG00000176406	ENST00000406091	Transcript	missense_variant	3506	3506	1169	S/C	tCt/tGt	.	.	.	1	RIMS2	HGNC	17283	protein_coding	YES	CCDS55269.1	ENSP00000384892	RIMS2_HUMAN	E9PFB6_HUMAN	UPI0001597063	.	deleterious_low_confidence(0)	possibly_damaging(0.754)	21/24	.	hmmpanther:PTHR12157:SF15,hmmpanther:PTHR12157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCCTCTGATA	.	4	ESCA
TRPS1	0	.	GRCh37	8	116680850	116680850	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-200C>T	.	.	ENST00000395715	1/7	174	135	39	129	129	0	TRPS1,5_prime_UTR_variant,,ENST00000395715,;TRPS1,5_prime_UTR_variant,,ENST00000519674,;TRPS1,5_prime_UTR_variant,,ENST00000220888,;TRPS1,intron_variant,,ENST00000422939,;TRPS1,intron_variant,,ENST00000519815,;TRPS1,upstream_gene_variant,,ENST00000520276,;TRPS1,upstream_gene_variant,,ENST00000451156,;TRPS1,upstream_gene_variant,,ENST00000517323,;	A	ENSG00000104447	ENST00000395715	Transcript	5_prime_UTR_variant	379	.	.	.	.	.	.	.	-1	TRPS1	HGNC	12340	protein_coding	YES	CCDS6318.2	ENSP00000379065	TRPS1_HUMAN	F8W8T0_HUMAN,E7EVN4_HUMAN,C9J6L7_HUMAN	UPI00002104B8	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTGTTGTT	.	5	ESCA
DLC1	0	.	GRCh37	8	12946153	12946153	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4135G>C	p.Glu1379Gln	p.E1379Q	ENST00000276297	16/18	100	87	13	89	89	0	DLC1,missense_variant,p.Glu942Gln,ENST00000358919,;DLC1,missense_variant,p.Glu868Gln,ENST00000520226,;DLC1,missense_variant,p.Glu976Gln,ENST00000512044,;DLC1,missense_variant,p.Glu1379Gln,ENST00000276297,;DLC1,non_coding_transcript_exon_variant,,ENST00000510318,;DLC1,non_coding_transcript_exon_variant,,ENST00000521730,;	G	ENSG00000164741	ENST00000276297	Transcript	missense_variant	4545	4135	1379	E/Q	Gag/Cag	.	.	.	-1	DLC1	HGNC	2897	protein_coding	YES	CCDS5989.1	ENSP00000276297	RHG07_HUMAN	.	UPI0000210275	.	tolerated(0.25)	probably_damaging(0.992)	16/18	.	PROSITE_profiles:PS50848,hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF2,Pfam_domain:PF01852,Gene3D:3.30.530.20,SMART_domains:SM00234,Superfamily_domains:SSF55961	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTGGCA	.	4	ESCA
EFR3A	0	.	GRCh37	8	132982840	132982840	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1109C>A	p.Ser370Tyr	p.S370Y	ENST00000254624	10/23	139	124	14	72	72	0	EFR3A,missense_variant,p.Ser370Tyr,ENST00000254624,;EFR3A,missense_variant,p.Ser334Tyr,ENST00000519656,;EFR3A,missense_variant,p.Ser370Tyr,ENST00000334503,;	A	ENSG00000132294	ENST00000254624	Transcript	missense_variant	1334	1109	370	S/Y	tCc/tAc	COSM1096151	.	.	1	EFR3A	HGNC	28970	protein_coding	YES	CCDS34942.2	ENSP00000254624	EFR3A_HUMAN	E5RJS1_HUMAN,B4DZ89_HUMAN	UPI00001C1E8F	.	tolerated(0.06)	benign(0.382)	10/23	.	hmmpanther:PTHR12444,hmmpanther:PTHR12444:SF1,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGTTCCAAAG	.	4	ESCA
ZFAT	0	.	GRCh37	8	135669872	135669872	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128A>T	p.Asp43Val	p.D43V	ENST00000377838	2/16	105	71	34	107	107	0	ZFAT,missense_variant,p.Asp31Val,ENST00000429442,;ZFAT,missense_variant,p.Asp31Val,ENST00000518191,;ZFAT,missense_variant,p.Asp31Val,ENST00000520214,;ZFAT,missense_variant,p.Asp43Val,ENST00000377838,;ZFAT,missense_variant,p.Asp43Val,ENST00000523399,;ZFAT,missense_variant,p.Asp31Val,ENST00000520727,;ZFAT,missense_variant,p.Asp31Val,ENST00000520356,;ZFAT,missense_variant,p.Asp43Val,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000522974,;	A	ENSG00000066827	ENST00000377838	Transcript	missense_variant	303	128	43	D/V	gAt/gTt	.	.	.	-1	ZFAT	HGNC	19899	protein_coding	YES	CCDS47924.1	ENSP00000367069	ZFAT_HUMAN	.	UPI0000210061	.	deleterious(0)	possibly_damaging(0.598)	2/16	.	hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCATCAACA	.	5	ESCA
TOP1MT	0	.	GRCh37	8	144403488	144403488	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1029C>T	p.%3D	p.L343L	ENST00000329245	8/14	87	63	23	69	69	0	TOP1MT,synonymous_variant,p.%3D,ENST00000523676,;TOP1MT,synonymous_variant,p.%3D,ENST00000519148,;TOP1MT,synonymous_variant,p.%3D,ENST00000521193,;TOP1MT,synonymous_variant,p.%3D,ENST00000329245,;TOP1MT,synonymous_variant,p.%3D,ENST00000519139,;TOP1MT,downstream_gene_variant,,ENST00000522041,;TOP1MT,downstream_gene_variant,,ENST00000520950,;TOP1MT,downstream_gene_variant,,ENST00000518760,;TOP1MT,downstream_gene_variant,,ENST00000519591,;TOP1MT,downstream_gene_variant,,ENST00000518007,;TOP1MT,3_prime_UTR_variant,,ENST00000518951,;TOP1MT,downstream_gene_variant,,ENST00000523417,;TOP1MT,downstream_gene_variant,,ENST00000522121,;	A	ENSG00000184428	ENST00000329245	Transcript	synonymous_variant	1064	1029	343	L	ctC/ctT	.	.	.	-1	TOP1MT	HGNC	29787	protein_coding	YES	CCDS6400.1	ENSP00000328835	TOP1M_HUMAN	E5KMK7_HUMAN,Q8TBP3_HUMAN,E5RJ95_HUMAN,E5RJ33_HUMAN,E5RFS0_HUMAN	UPI000013716D	.	.	.	8/14	.	hmmpanther:PTHR10290,Pfam_domain:PF01028,Gene3D:3.90.15.10,SMART_domains:SM00435,Superfamily_domains:SSF56349,Prints_domain:PR00416	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACGCGGAGGGA	.	5	ESCA
ZNF707	0	.	GRCh37	8	144773832	144773832	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.205G>A	p.Glu69Lys	p.E69K	ENST00000532205	7/8	127	121	6	102	102	0	ZNF707,missense_variant,p.Glu69Lys,ENST00000534303,;ZNF707,missense_variant,p.Glu69Lys,ENST00000358656,;ZNF707,missense_variant,p.Glu69Lys,ENST00000532205,;ZNF707,missense_variant,p.Glu33Lys,ENST00000526315,;ZNF707,missense_variant,p.Glu69Lys,ENST00000532158,;ZNF707,missense_variant,p.Glu69Lys,ENST00000529833,;ZNF707,missense_variant,p.Glu69Lys,ENST00000418203,;ZNF707,missense_variant,p.Glu69Lys,ENST00000454097,;ZNF707,synonymous_variant,p.%3D,ENST00000530574,;ZNF707,3_prime_UTR_variant,,ENST00000442058,;ZNF707,downstream_gene_variant,,ENST00000526970,;RP11-429J17.2,upstream_gene_variant,,ENST00000531565,;ZNF707,non_coding_transcript_exon_variant,,ENST00000530341,;ZNF707,non_coding_transcript_exon_variant,,ENST00000531811,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,downstream_gene_variant,,ENST00000532571,;ZNF707,missense_variant,p.Glu69Lys,ENST00000525862,;ZNF707,missense_variant,p.Glu69Lys,ENST00000528456,;ZNF707,3_prime_UTR_variant,,ENST00000527293,;ZNF707,3_prime_UTR_variant,,ENST00000533031,;ZNF707,3_prime_UTR_variant,,ENST00000531985,;ZNF707,3_prime_UTR_variant,,ENST00000525185,;ZNF707,non_coding_transcript_exon_variant,,ENST00000534589,;ZNF707,non_coding_transcript_exon_variant,,ENST00000525538,;ZNF707,non_coding_transcript_exon_variant,,ENST00000531254,;ZNF707,non_coding_transcript_exon_variant,,ENST00000532486,;ZNF707,downstream_gene_variant,,ENST00000532003,;ZNF707,downstream_gene_variant,,ENST00000533254,;ZNF707,downstream_gene_variant,,ENST00000528134,;ZNF707,downstream_gene_variant,,ENST00000525619,;	A	ENSG00000181135	ENST00000532205	Transcript	missense_variant	1104	205	69	E/K	Gaa/Aaa	.	.	.	1	ZNF707	HGNC	27815	protein_coding	YES	CCDS47932.1	ENSP00000436212	ZN707_HUMAN	E9PS67_HUMAN,E9PQ20_HUMAN,E9PNV7_HUMAN,E9PHZ0_HUMAN	UPI0000160D8F	.	tolerated(0.81)	benign(0.212)	7/8	.	hmmpanther:PTHR24402:SF169,hmmpanther:PTHR24402,PROSITE_profiles:PS50805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTTGAAGAC	.	2	ESCA
PCM1	0	.	GRCh37	8	17813047	17813047	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357G>C	p.Val453Leu	p.V453L	ENST00000325083	10/39	120	94	25	84	84	0	PCM1,missense_variant,p.Val453Leu,ENST00000524226,;PCM1,missense_variant,p.Val453Leu,ENST00000519253,;PCM1,missense_variant,p.Val492Leu,ENST00000517730,;PCM1,missense_variant,p.Val453Leu,ENST00000325083,;PCM1,missense_variant,p.Val492Leu,ENST00000518537,;PCM1,downstream_gene_variant,,ENST00000523055,;PCM1,downstream_gene_variant,,ENST00000518930,;PCM1,upstream_gene_variant,,ENST00000518762,;PCM1,upstream_gene_variant,,ENST00000517836,;	C	ENSG00000078674	ENST00000325083	Transcript	missense_variant	1796	1357	453	V/L	Gtt/Ctt	.	.	.	1	PCM1	HGNC	8727	protein_coding	YES	CCDS47812.1	ENSP00000327077	PCM1_HUMAN	E5RGQ4_HUMAN	UPI0000210A25	.	tolerated(0.4)	benign(0.016)	10/39	.	hmmpanther:PTHR14164,hmmpanther:PTHR14164:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCGGTTGTC	.	5	ESCA
BMP1	0	.	GRCh37	8	22049619	22049620	+	Frame_Shift_Del	DEL	TA	TA	-	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	TA	TA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1136_1137delAT	p.Tyr379CysfsTer24	p.Y379Cfs*24	ENST00000306385	9/20	41	36	5	61	61	0	BMP1,frameshift_variant,p.Tyr379CysfsTer24,ENST00000306385,;BMP1,frameshift_variant,p.Tyr379CysfsTer24,ENST00000306349,;BMP1,frameshift_variant,p.Tyr379CysfsTer24,ENST00000397816,;BMP1,frameshift_variant,p.Tyr379CysfsTer24,ENST00000397814,;BMP1,3_prime_UTR_variant,,ENST00000354870,;BMP1,non_coding_transcript_exon_variant,,ENST00000523749,;BMP1,frameshift_variant,p.Tyr379CysfsTer24,ENST00000471755,;BMP1,frameshift_variant,p.Tyr379CysfsTer24,ENST00000521385,;BMP1,frameshift_variant,p.Tyr379CysfsTer24,ENST00000520970,;BMP1,3_prime_UTR_variant,,ENST00000483364,;BMP1,3_prime_UTR_variant,,ENST00000518913,;BMP1,3_prime_UTR_variant,,ENST00000520626,;BMP1,3_prime_UTR_variant,,ENST00000520982,;BMP1,non_coding_transcript_exon_variant,,ENST00000523457,;BMP1,upstream_gene_variant,,ENST00000517324,;	-	ENSG00000168487	ENST00000306385	Transcript	frameshift_variant	1805-1806	1135-1136	379	Y/X	TAt/t	.	.	.	1	BMP1	HGNC	1067	protein_coding	YES	CCDS6026.1	ENSP00000305714	BMP1_HUMAN	.	UPI0000049818	.	.	.	9/20	.	PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF305,hmmpanther:PTHR10127,Pfam_domain:PF00431,Gene3D:2.60.120.290,PIRSF_domain:PIRSF001199,SMART_domains:SM00042,Superfamily_domains:SSF49854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	VARSCANI*|PINDEL	TACGACTATGTGG	.	2	ESCA
ZFHX4	0	.	GRCh37	8	77777019	77777019	+	3'UTR	SNP	T	T	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*218T>A	.	.	ENST00000521891	11/11	156	128	28	108	107	1	ZFHX4,3_prime_UTR_variant,,ENST00000455469,;ZFHX4,3_prime_UTR_variant,,ENST00000518282,;ZFHX4,3_prime_UTR_variant,,ENST00000521891,;ZFHX4,downstream_gene_variant,,ENST00000050961,;	A	ENSG00000091656	ENST00000521891	Transcript	3_prime_UTR_variant	11517	.	.	.	.	.	.	.	1	ZFHX4	HGNC	30939	protein_coding	YES	CCDS47878.2	ENSP00000430497	.	Q9H7F3_HUMAN,Q86WW5_HUMAN,Q6DK57_HUMAN,G3V138_HUMAN,E5RI93_HUMAN,E5RHS1_HUMAN,E5RGK3_HUMAN,E5RG79_HUMAN	UPI0000424CC7	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATGCTAAAAT	.	4	ESCA
LRRCC1	0	.	GRCh37	8	86057866	86057866	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*120G>A	.	.	ENST00000360375	19/19	112	100	11	97	97	0	LRRCC1,3_prime_UTR_variant,,ENST00000360375,;LRRCC1,3_prime_UTR_variant,,ENST00000414626,;	A	ENSG00000133739	ENST00000360375	Transcript	3_prime_UTR_variant	3368	.	.	.	.	.	.	.	1	LRRCC1	HGNC	29373	protein_coding	YES	CCDS43750.1	ENSP00000353538	LRCC1_HUMAN	.	UPI000021002F	.	.	.	19/19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTATGAATAT	.	4	ESCA
PSKH2	0	.	GRCh37	8	87076243	87076243	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.803C>G	p.Thr268Arg	p.T268R	ENST00000276616	2/3	89	82	7	77	77	0	PSKH2,missense_variant,p.Thr268Arg,ENST00000276616,;ATP6V0D2,intron_variant,,ENST00000521564,;PSKH2,downstream_gene_variant,,ENST00000523010,;PSKH2,downstream_gene_variant,,ENST00000517981,;	C	ENSG00000147613	ENST00000276616	Transcript	missense_variant	878	803	268	T/R	aCa/aGa	.	.	.	-1	PSKH2	HGNC	18997	protein_coding	YES	CCDS6240.1	ENSP00000276616	KPSH2_HUMAN	.	UPI000006F951	.	deleterious(0.01)	possibly_damaging(0.756)	2/3	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF135,hmmpanther:PTHR24347,Gene3D:1.10.510.10,Pfam_domain:PF00069,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCTTGTCTGG	.	3	ESCA
ESRP1	0	.	GRCh37	8	95653507	95653507	+	5'UTR	SNP	C	C	A	rs753428619	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-40C>A	.	.	ENST00000433389	1/16	108	101	6	80	80	0	ESRP1,5_prime_UTR_variant,,ENST00000433389,;ESRP1,5_prime_UTR_variant,,ENST00000454170,;ESRP1,5_prime_UTR_variant,,ENST00000423620,;ESRP1,5_prime_UTR_variant,,ENST00000358397,;ESRP1,upstream_gene_variant,,ENST00000522756,;ESRP1,upstream_gene_variant,,ENST00000519505,;ESRP1,upstream_gene_variant,,ENST00000517610,;ESRP1,upstream_gene_variant,,ENST00000520385,;RP11-22C11.2,upstream_gene_variant,,ENST00000562760,;ESRP1,upstream_gene_variant,,ENST00000522920,;	A	ENSG00000104413	ENST00000433389	Transcript	5_prime_UTR_variant	151	.	.	.	.	rs753428619	.	.	1	ESRP1	HGNC	25966	protein_coding	YES	CCDS47897.1	ENSP00000405738	ESRP1_HUMAN	E5RI26_HUMAN,E5RGE9_HUMAN	UPI0000210327	.	.	.	1/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTACCGCCTC	.	2	ESCA
IKBKAP	0	.	GRCh37	9	111641030	111641030	+	Silent	SNP	C	C	A	rs751070000	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3573G>T	p.%3D	p.A1191A	ENST00000374647	34/37	32	25	7	21	21	0	IKBKAP,synonymous_variant,p.%3D,ENST00000537196,;IKBKAP,synonymous_variant,p.%3D,ENST00000374647,;IKBKAP,downstream_gene_variant,,ENST00000467959,;IKBKAP,synonymous_variant,p.%3D,ENST00000495759,;	A	ENSG00000070061	ENST00000374647	Transcript	synonymous_variant	3881	3573	1191	A	gcG/gcT	rs751070000	.	.	-1	IKBKAP	HGNC	5959	protein_coding	YES	CCDS6773.1	ENSP00000363779	ELP1_HUMAN	Q4LE38_HUMAN,F5H2T0_HUMAN,B3KNB2_HUMAN,B3KMT0_HUMAN	UPI000013D2D0	.	.	.	34/37	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12747,PIRSF_domain:PIRSF017233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTCCTGTT	.	5	ESCA
ASTN2	0	.	GRCh37	9	119976864	119976864	+	Missense_Mutation	SNP	T	T	G	rs146556453	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.788A>C	p.Gln263Pro	p.Q263P	ENST00000361209	3/22	32	19	12	35	35	0	ASTN2,missense_variant,p.Gln263Pro,ENST00000373996,;ASTN2,missense_variant,p.Gln263Pro,ENST00000313400,;ASTN2,missense_variant,p.Gln263Pro,ENST00000361209,;ASTN2,5_prime_UTR_variant,,ENST00000361477,;ASTN2,upstream_gene_variant,,ENST00000373986,;	G	ENSG00000148219	ENST00000361209	Transcript	missense_variant	920	788	263	Q/P	cAg/cCg	rs146556453	.	.	-1	ASTN2	HGNC	17021	protein_coding	YES	CCDS6815.1	ENSP00000354504	ASTN2_HUMAN	B7ZKP3_HUMAN,B2RCB6_HUMAN	UPI00002116D7	.	tolerated_low_confidence(0.08)	unknown(0)	3/22	.	hmmpanther:PTHR16592	.	.	.	.	.	.	.	C:0.0002	C:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	GCGCCTGGGGA	byCluster	4	ESCA
CNTRL	0	.	GRCh37	9	123870109	123870109	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838G>C	p.Glu280Gln	p.E280Q	ENST00000373855	8/44	56	50	5	61	61	0	CNTRL,missense_variant,p.Glu280Gln,ENST00000373855,;CNTRL,missense_variant,p.Glu280Gln,ENST00000373865,;CNTRL,missense_variant,p.Glu280Gln,ENST00000238341,;CNTRL,upstream_gene_variant,,ENST00000468952,;CNTRL,upstream_gene_variant,,ENST00000373851,;	C	ENSG00000119397	ENST00000373855	Transcript	missense_variant	1098	838	280	E/Q	Gaa/Caa	.	.	.	1	CNTRL	HGNC	1858	protein_coding	YES	CCDS35118.1	ENSP00000362962	CNTRL_HUMAN	Q5JVD3_HUMAN,Q5JVD6_HUMAN,Q5JVD1_HUMAN	UPI0000211718	.	.	probably_damaging(0.999)	8/44	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18877,hmmpanther:PTHR18877:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACCTAGAAAAA	.	3	ESCA
ODF2	0	.	GRCh37	9	131235307	131235307	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.697G>A	p.Gly233Arg	p.G233R	ENST00000434106	7/21	59	52	6	61	61	0	ODF2,missense_variant,p.Gly277Arg,ENST00000372814,;ODF2,missense_variant,p.Gly228Arg,ENST00000351030,;ODF2,missense_variant,p.Gly209Arg,ENST00000393527,;ODF2,missense_variant,p.Gly209Arg,ENST00000444119,;ODF2,missense_variant,p.Gly233Arg,ENST00000434106,;ODF2,missense_variant,p.Gly214Arg,ENST00000546203,;ODF2,missense_variant,p.Gly228Arg,ENST00000372807,;ODF2,missense_variant,p.Gly157Arg,ENST00000432065,;ODF2,missense_variant,p.Gly176Arg,ENST00000421776,;ODF2,missense_variant,p.Gly152Arg,ENST00000448249,;ODF2,missense_variant,p.Gly233Arg,ENST00000604420,;ODF2,missense_variant,p.Gly214Arg,ENST00000372791,;ODF2,missense_variant,p.Arg117Gln,ENST00000535026,;ODF2,missense_variant,p.Gly233Arg,ENST00000393533,;ODF2,downstream_gene_variant,,ENST00000497812,;ODF2,downstream_gene_variant,,ENST00000470061,;ODF2,downstream_gene_variant,,ENST00000446274,;AL359091.1,upstream_gene_variant,,ENST00000580080,;ODF2-AS1,upstream_gene_variant,,ENST00000420801,;ODF2,downstream_gene_variant,,ENST00000469582,;	A	ENSG00000136811	ENST00000434106	Transcript	missense_variant	1060	697	233	G/R	Ggg/Agg	.	.	.	1	ODF2	HGNC	8114	protein_coding	YES	CCDS56588.1	ENSP00000403453	ODFP2_HUMAN	S4R462_HUMAN,Q9UNM2_HUMAN,Q6PJQ8_HUMAN,Q5T4C7_HUMAN	UPI0000211922	.	tolerated(0.32)	benign(0.021)	7/21	.	hmmpanther:PTHR23162:SF8,hmmpanther:PTHR23162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCATCGGGAAG	.	4	ESCA
AIF1L	0	.	GRCh37	9	133996359	133996359	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*650C>G	.	.	ENST00000372309	7/7	27	21	6	46	46	0	AIF1L,3_prime_UTR_variant,,ENST00000372309,;AIF1L,3_prime_UTR_variant,,ENST00000372302,;AIF1L,3_prime_UTR_variant,,ENST00000247291,;AIF1L,3_prime_UTR_variant,,ENST00000372312,;AIF1L,3_prime_UTR_variant,,ENST00000372300,;AIF1L,intron_variant,,ENST00000372298,;NUP214,upstream_gene_variant,,ENST00000451030,;NUP214,upstream_gene_variant,,ENST00000359428,;AIF1L,downstream_gene_variant,,ENST00000372301,;AIF1L,downstream_gene_variant,,ENST00000372297,;NUP214,upstream_gene_variant,,ENST00000411637,;AIF1L,3_prime_UTR_variant,,ENST00000372314,;	G	ENSG00000126878	ENST00000372309	Transcript	3_prime_UTR_variant	1335	.	.	.	.	.	.	.	1	AIF1L	HGNC	28904	protein_coding	YES	CCDS55348.1	ENSP00000361383	AIF1L_HUMAN	A6PVM9_HUMAN	UPI00001C1012	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTCTCTGGCC	.	2	ESCA
SEC16A	0	.	GRCh37	9	139342717	139342717	+	Intron	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6313-104C>T	.	.	ENST00000313050	.	77	61	15	86	86	0	SEC16A,synonymous_variant,p.%3D,ENST00000313084,;SEC16A,synonymous_variant,p.%3D,ENST00000398335,;SEC16A,intron_variant,,ENST00000290037,;SEC16A,intron_variant,,ENST00000313050,;SEC16A,intron_variant,,ENST00000453963,;SEC16A,intron_variant,,ENST00000277537,;SEC16A,intron_variant,,ENST00000431893,;SEC16A,intron_variant,,ENST00000371706,;SEC16A,upstream_gene_variant,,ENST00000467838,;	A	ENSG00000148396	ENST00000313050	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SEC16A	HGNC	29006	protein_coding	YES	CCDS55351.1	ENSP00000325827	.	J3KNL6_HUMAN,G1UI25_HUMAN,A0PJ75_HUMAN	UPI0000F0888B	.	.	.	.	21/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCCAGAGTCG	.	5	ESCA
UAP1L1	0	.	GRCh37	9	139973475	139973475	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.718G>T	p.Glu240Ter	p.E240*	ENST00000409858	4/9	59	44	15	86	86	0	UAP1L1,stop_gained,p.Glu240Ter,ENST00000409858,;UAP1L1,stop_gained,p.Glu117Ter,ENST00000360271,;UAP1L1,non_coding_transcript_exon_variant,,ENST00000476184,;UAP1L1,non_coding_transcript_exon_variant,,ENST00000474787,;	T	ENSG00000197355	ENST00000409858	Transcript	stop_gained	750	718	240	E/*	Gag/Tag	.	.	.	1	UAP1L1	HGNC	28082	protein_coding	YES	CCDS7028.2	ENSP00000386935	UAP1L_HUMAN	.	UPI000016047B	.	.	.	4/9	.	Superfamily_domains:SSF53448,Pfam_domain:PF01704,Gene3D:3.90.550.10,hmmpanther:PTHR11952,hmmpanther:PTHR11952:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCTGGAGGAC	.	5	ESCA
SMARCA2	0	.	GRCh37	9	2161902	2161902	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4198A>G	p.Arg1400Gly	p.R1400G	ENST00000382203	28/34	55	44	11	58	58	0	SMARCA2,missense_variant,p.Arg1400Gly,ENST00000382203,;SMARCA2,missense_variant,p.Arg64Gly,ENST00000382186,;SMARCA2,missense_variant,p.Ser1400Gly,ENST00000357248,;SMARCA2,missense_variant,p.Ser64Gly,ENST00000416751,;SMARCA2,missense_variant,p.Arg1400Gly,ENST00000349721,;SMARCA2,missense_variant,p.Ser64Gly,ENST00000382185,;SMARCA2,missense_variant,p.Ser106Gly,ENST00000302401,;SMARCA2,missense_variant,p.Ser104Gly,ENST00000423555,;SMARCA2,missense_variant,p.Ser1400Gly,ENST00000382194,;SMARCA2,missense_variant,p.Ser64Gly,ENST00000382183,;SMARCA2,missense_variant,p.Arg64Gly,ENST00000452193,;SMARCA2,missense_variant,p.Ser104Gly,ENST00000417599,;SMARCA2,missense_variant,p.Ser64Gly,ENST00000324954,;RNU2-25P,downstream_gene_variant,,ENST00000411041,;	G	ENSG00000080503	ENST00000382203	Transcript	missense_variant	4407	4198	1400	R/G	Agg/Ggg	.	.	.	1	SMARCA2	HGNC	11098	protein_coding	YES	CCDS34977.1	ENSP00000371638	SMCA2_HUMAN	Q6LC24_HUMAN,Q56A76_HUMAN,F6XDY1_HUMAN,F6VDE0_HUMAN,F6RS74_HUMAN,F6QYQ1_HUMAN,B1ALG5_HUMAN,B1ALG2_HUMAN	UPI00001AE8EB	.	.	benign(0.152)	28/34	.	hmmpanther:PTHR10799:SF541,hmmpanther:PTHR10799,Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGATAGGTGA	.	5	ESCA
GRIA3	0	.	GRCh37	X	122318457	122318457	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.70G>A	p.Gly24Ser	p.G24S	ENST00000264357	1/16	232	151	81	208	208	0	GRIA3,missense_variant,p.Gly24Ser,ENST00000542149,;GRIA3,missense_variant,p.Gly24Ser,ENST00000264357,;GRIA3,missense_variant,p.Gly24Ser,ENST00000371264,;GRIA3,missense_variant,p.Gly24Ser,ENST00000371256,;GRIA3,missense_variant,p.Gly24Ser,ENST00000371251,;GRIA3,missense_variant,p.Gly24Ser,ENST00000371266,;GRIA3,upstream_gene_variant,,ENST00000541091,;GRIA3,non_coding_transcript_exon_variant,,ENST00000479118,;	A	ENSG00000125675	ENST00000264357	Transcript	missense_variant	362	70	24	G/S	Ggt/Agt	.	.	.	1	GRIA3	HGNC	4573	protein_coding	YES	CCDS14604.1	ENSP00000264357	GRIA3_HUMAN	Q9UHA9_HUMAN	UPI000013D503	.	tolerated_low_confidence(0.12)	possibly_damaging(0.855)	1/16	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTGGGTCAT	.	5	ESCA
LINC00087	0	.	GRCh37	X	134232496	134232496	+	RNA	SNP	C	C	T	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.169G>A	.	.	ENST00000433425	1/2	132	125	7	137	137	0	LINC00087,non_coding_transcript_exon_variant,,ENST00000433425,;LINC00087,non_coding_transcript_exon_variant,,ENST00000535837,;RP11-85L21.4,intron_variant,,ENST00000608079,;	T	ENSG00000196972	ENST00000433425	Transcript	non_coding_transcript_exon_variant	169	.	.	.	.	.	.	.	-1	LINC00087	HGNC	34500	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGTTCATGCG	.	2	ESCA
DDX26B	0	.	GRCh37	X	134716221	134716221	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*660T>C	.	.	ENST00000370752	17/17	25	15	10	18	18	0	DDX26B,3_prime_UTR_variant,,ENST00000370752,;DDX26B,non_coding_transcript_exon_variant,,ENST00000481429,;DDX26B,non_coding_transcript_exon_variant,,ENST00000481908,;DDX26B,non_coding_transcript_exon_variant,,ENST00000494957,;DDX26B,non_coding_transcript_exon_variant,,ENST00000493637,;RP11-432N13.2,downstream_gene_variant,,ENST00000439300,;	C	ENSG00000165359	ENST00000370752	Transcript	3_prime_UTR_variant	3580	.	.	.	.	.	.	.	1	DDX26B	HGNC	27334	protein_coding	YES	CCDS35401.1	ENSP00000359788	DX26B_HUMAN	.	UPI00004A3AAF	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGCATGTGAT	.	5	ESCA
FANCB	0	.	GRCh37	X	14863402	14863402	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1503G>C	p.%3D	p.L501L	ENST00000398334	8/10	36	28	8	33	33	0	FANCB,synonymous_variant,p.%3D,ENST00000324138,;FANCB,synonymous_variant,p.%3D,ENST00000398334,;FANCB,synonymous_variant,p.%3D,ENST00000452869,;	G	ENSG00000181544	ENST00000398334	Transcript	synonymous_variant	1771	1503	501	L	ctG/ctC	.	.	.	-1	FANCB	HGNC	3583	protein_coding	YES	CCDS14161.1	ENSP00000381378	FANCB_HUMAN	C9J5X9_HUMAN	UPI000006E70A	.	.	.	8/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATTCAGGGA	.	5	ESCA
OPN1LW	0	.	GRCh37	X	153420169	153420169	+	Silent	SNP	T	T	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.699T>G	p.%3D	p.A233A	ENST00000369951	4/6	74	46	28	57	57	0	OPN1LW,synonymous_variant,p.%3D,ENST00000442922,;OPN1LW,synonymous_variant,p.%3D,ENST00000369951,;TEX28P2,downstream_gene_variant,,ENST00000369941,;OPN1LW,intron_variant,,ENST00000463296,;	G	ENSG00000102076	ENST00000369951	Transcript	synonymous_variant	759	699	233	A	gcT/gcG	.	.	.	1	OPN1LW	HGNC	9936	protein_coding	YES	CCDS14742.1	ENSP00000358967	OPSR_HUMAN	.	UPI0000113560	.	.	.	4/6	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24240:SF17,hmmpanther:PTHR24240,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCGCTATCAT	.	5	ESCA
KDM6A	0	.	GRCh37	X	44949070	44949070	+	Frame_Shift_Del	DEL	A	A	-	rs367565349	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3631delA	p.Ile1211PhefsTer10	p.I1211Ffs*10	ENST00000377967	25/29	62	51	11	78	78	0	KDM6A,frameshift_variant,p.Ile854PhefsTer10,ENST00000433797,;KDM6A,frameshift_variant,p.Ile809PhefsTer10,ENST00000414389,;KDM6A,frameshift_variant,p.Ile1132PhefsTer10,ENST00000543216,;KDM6A,frameshift_variant,p.Ile1211PhefsTer10,ENST00000377967,;KDM6A,frameshift_variant,p.Ile1218PhefsTer10,ENST00000382899,;KDM6A,frameshift_variant,p.Ile1166PhefsTer10,ENST00000536777,;KDM6A,upstream_gene_variant,,ENST00000431196,;KDM6A,downstream_gene_variant,,ENST00000484732,;	-	ENSG00000147050	ENST00000377967	Transcript	frameshift_variant	3672	3631	1211	I/X	Att/tt	rs367565349	.	.	1	KDM6A	HGNC	12637	protein_coding	YES	CCDS14265.1	ENSP00000367203	KDM6A_HUMAN	Q68D33_HUMAN,Q59HG3_HUMAN,Q590H7_HUMAN	UPI000013DA92	.	.	.	25/29	.	PROSITE_profiles:PS51184,hmmpanther:PTHR14017:SF9,hmmpanther:PTHR14017,Pfam_domain:PF02373,SMART_domains:SM00558,Superfamily_domains:SSF51197	.	.	.	.	.	.	.	G:0.0003	G:0	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_4206del4206|5	INDELOCATOR*|VARSCANI*|PINDEL	AGGTTTATTCAG	byCluster	3	ESCA
IL2RG	0	.	GRCh37	X	70327739	70327739	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.957G>C	p.Glu319Asp	p.E319D	ENST00000374202	8/8	142	111	30	142	142	0	IL2RG,missense_variant,p.Glu48Asp,ENST00000374188,;IL2RG,missense_variant,p.Glu129Asp,ENST00000456850,;IL2RG,missense_variant,p.Glu319Asp,ENST00000374202,;IL2RG,3_prime_UTR_variant,,ENST00000482750,;CXorf65,upstream_gene_variant,,ENST00000374251,;IL2RG,downstream_gene_variant,,ENST00000464642,;IL2RG,downstream_gene_variant,,ENST00000473378,;IL2RG,downstream_gene_variant,,ENST00000487883,;FOXO4,downstream_gene_variant,,ENST00000374259,;IL2RG,non_coding_transcript_exon_variant,,ENST00000512747,;IL2RG,non_coding_transcript_exon_variant,,ENST00000276110,;CXorf65,upstream_gene_variant,,ENST00000466160,;CXorf65,upstream_gene_variant,,ENST00000483257,;CXorf65,upstream_gene_variant,,ENST00000438526,;	G	ENSG00000147168	ENST00000374202	Transcript	missense_variant	1049	957	319	E/D	gaG/gaC	.	.	.	-1	IL2RG	HGNC	6010	protein_coding	YES	CCDS14406.1	ENSP00000363318	IL2RG_HUMAN	Q6LER1_HUMAN,D6RDW9_HUMAN	UPI0000000DEA	.	tolerated(0.1)	possibly_damaging(0.723)	8/8	.	hmmpanther:PTHR23036:SF92,hmmpanther:PTHR23036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACTCTCAGC	.	5	ESCA
MAGT1	0	.	GRCh37	X	77112967	77112974	+	In_Frame_Del	DEL	TGAAAGTT	TGAAAGTT	AGAAA	novel	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	TGAAAGTT	TGAAAGTT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.507_514delAACTTTCAinsTTTCT	p.Thr170_Ile172delinsPhePhe	p.T170_I172delinsFF	ENST00000358075	4/10	96	57	39	89	89	0	MAGT1,protein_altering_variant,p.Thr170_Ile172delinsPhePhe,ENST00000358075,;MAGT1,non_coding_transcript_exon_variant,,ENST00000476168,;	AGAAA	ENSG00000102158	ENST00000358075	Transcript	protein_altering_variant	594-601	507-514	169-172	PTFI/PFF	ccAACTTTCAtc/ccTTTCTtc	.	.	.	-1	MAGT1	HGNC	28880	protein_coding	YES	CCDS14436.2	ENSP00000354649	MAGT1_HUMAN	Q96SP2_HUMAN	UPI0001881372	.	.	.	4/10	.	hmmpanther:PTHR12692,hmmpanther:PTHR12692:SF2,Gene3D:3.40.30.10,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	substitution	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	PINDEL|SOMATICSNIPER*|VARSCANI*|INDELOCATOR*|RADIA*|VARSCANS*	AGTTGATGAAAGTTGGAGC	.	6	ESCA
P2RY10	0	.	GRCh37	X	78216383	78216383	+	Nonsense_Mutation	SNP	T	T	A	rs780586346	.	TCGA-Z6-A8JD-01A-11D-A36J-09	TCGA-Z6-A8JD-10A-01D-A36M-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.366T>A	p.Cys122Ter	p.C122*	ENST00000171757	4/4	22	18	3	19	19	0	P2RY10,stop_gained,p.Cys122Ter,ENST00000544091,;P2RY10,stop_gained,p.Cys122Ter,ENST00000171757,;P2RY10,non_coding_transcript_exon_variant,,ENST00000475374,;P2RY10,downstream_gene_variant,,ENST00000461541,;	A	ENSG00000078589	ENST00000171757	Transcript	stop_gained	646	366	122	C/*	tgT/tgA	rs780586346	.	.	1	P2RY10	HGNC	19906	protein_coding	YES	CCDS14442.1	ENSP00000171757	P2Y10_HUMAN	.	UPI0000050471	.	.	.	4/4	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24232:SF6,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01157,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTTGTTTCCT	byFrequency	4	ESCA
FAM178A	0	.	GRCh37	10	102723612	102723612	+	3'Flank	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000370269	.	51	48	3	53	53	0	FAM178A,3_prime_UTR_variant,,ENST00000238961,;FAM178A,downstream_gene_variant,,ENST00000370269,;RP11-108L7.14,upstream_gene_variant,,ENST00000609801,;	C	ENSG00000119906	ENST00000370269	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	4265	1	FAM178A	HGNC	17814	protein_coding	YES	CCDS44470.1	ENSP00000359292	F178A_HUMAN	.	UPI0000458847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACTTTGATACA	.	2	ESCA
WDR96	0	.	GRCh37	10	105900686	105900686	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4345C>G	p.Leu1449Val	p.L1449V	ENST00000357060	34/38	51	39	12	36	36	0	WDR96,missense_variant,p.Leu298Val,ENST00000457071,;WDR96,missense_variant,p.Leu1421Val,ENST00000428666,;WDR96,missense_variant,p.Leu1449Val,ENST00000357060,;WDR96,missense_variant,p.Leu781Val,ENST00000434629,;WDR96,non_coding_transcript_exon_variant,,ENST00000479392,;	C	ENSG00000197748	ENST00000357060	Transcript	missense_variant	4461	4345	1449	L/V	Ctg/Gtg	.	.	.	-1	WDR96	HGNC	26684	protein_coding	YES	CCDS31281.1	ENSP00000349568	WDR96_HUMAN	.	UPI0000D60FC7	.	tolerated(0.32)	benign(0.014)	34/38	.	hmmpanther:PTHR14885	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCAGTTCTA	.	5	ESCA
ANKRD26	0	.	GRCh37	10	27349452	27349452	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1480C>T	p.Leu494Phe	p.L494F	ENST00000376087	14/34	54	17	36	40	40	0	ANKRD26,missense_variant,p.Leu494Phe,ENST00000376087,;ANKRD26,missense_variant,p.Leu510Phe,ENST00000436985,;	A	ENSG00000107890	ENST00000376087	Transcript	missense_variant	1646	1480	494	L/F	Ctt/Ttt	.	.	.	-1	ANKRD26	HGNC	29186	protein_coding	YES	CCDS41499.1	ENSP00000365255	ANR26_HUMAN	.	UPI000006FC41	.	tolerated(0.29)	benign(0.002)	14/34	.	hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAGATATC	.	5	ESCA
ZEB1	0	.	GRCh37	10	31809541	31809541	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1281G>T	p.Arg427Ser	p.R427S	ENST00000361642	7/9	72	53	18	23	23	0	ZEB1,missense_variant,p.Arg406Ser,ENST00000560721,;ZEB1,missense_variant,p.Arg410Ser,ENST00000446923,;ZEB1,missense_variant,p.Arg427Ser,ENST00000361642,;ZEB1,missense_variant,p.Arg426Ser,ENST00000320985,;ZEB1,missense_variant,p.Arg434Ser,ENST00000561212,;ZEB1,missense_variant,p.Arg359Ser,ENST00000542815,;ZEB1,downstream_gene_variant,,ENST00000424869,;ZEB1,downstream_gene_variant,,ENST00000558440,;ZEB1,downstream_gene_variant,,ENST00000559476,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558863,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558655,;	T	ENSG00000148516	ENST00000361642	Transcript	missense_variant	1344	1281	427	R/S	agG/agT	.	.	.	1	ZEB1	HGNC	11642	protein_coding	YES	CCDS53505.1	ENSP00000354487	ZEB1_HUMAN	F6TDF5_HUMAN	UPI000068F51D	.	deleterious(0)	probably_damaging(0.997)	7/9	.	hmmpanther:PTHR13919,hmmpanther:PTHR13919:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAAGGCAAGT	.	5	ESCA
DNAJC12	0	.	GRCh37	10	69565494	69565494	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.349G>C	p.Asp117His	p.D117H	ENST00000225171	4/5	77	73	4	62	62	0	DNAJC12,missense_variant,p.Asp147His,ENST00000483798,;DNAJC12,missense_variant,p.Asp117His,ENST00000225171,;RNU6-1250P,upstream_gene_variant,,ENST00000391218,;DNAJC12,3_prime_UTR_variant,,ENST00000480963,;	G	ENSG00000108176	ENST00000225171	Transcript	missense_variant	502	349	117	D/H	Gac/Cac	COSM3439737	.	.	-1	DNAJC12	HGNC	28908	protein_coding	YES	CCDS7271.1	ENSP00000225171	DJC12_HUMAN	Q6IAH1_HUMAN	UPI000012DAAA	.	deleterious(0.01)	possibly_damaging(0.592)	4/5	.	hmmpanther:PTHR24078:SF137,hmmpanther:PTHR24078	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTGTCAGATT	.	2	ESCA
MYPN	0	.	GRCh37	10	69948764	69948764	+	Missense_Mutation	SNP	G	G	A	rs763893618	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2806G>A	p.Glu936Lys	p.E936K	ENST00000358913	13/20	41	37	4	36	36	0	MYPN,missense_variant,p.Glu936Lys,ENST00000358913,;MYPN,missense_variant,p.Glu936Lys,ENST00000540630,;MYPN,missense_variant,p.Glu661Lys,ENST00000354393,;	A	ENSG00000138347	ENST00000358913	Transcript	missense_variant	3294	2806	936	E/K	Gag/Aag	rs763893618	.	.	1	MYPN	HGNC	23246	protein_coding	YES	CCDS7275.1	ENSP00000351790	MYPN_HUMAN	A5PKT7_HUMAN	UPI00002288CF	.	deleterious(0.02)	probably_damaging(0.952)	13/20	.	hmmpanther:PTHR19897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGATGAGATC	.	3	ESCA
USP54	0	.	GRCh37	10	75286503	75286503	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2096C>G	p.Pro699Arg	p.P699R	ENST00000339859	15/23	44	33	11	38	38	0	USP54,missense_variant,p.Pro549Arg,ENST00000428547,;USP54,missense_variant,p.Pro699Arg,ENST00000339859,;USP54,missense_variant,p.Pro699Arg,ENST00000408019,;USP54,5_prime_UTR_variant,,ENST00000394811,;USP54,downstream_gene_variant,,ENST00000319786,;USP54,upstream_gene_variant,,ENST00000422491,;RNU6-883P,downstream_gene_variant,,ENST00000384597,;USP54,non_coding_transcript_exon_variant,,ENST00000497106,;USP54,downstream_gene_variant,,ENST00000480210,;USP54,missense_variant,p.Pro260Arg,ENST00000418501,;USP54,missense_variant,p.Pro274Arg,ENST00000466048,;USP54,missense_variant,p.Pro497Arg,ENST00000424265,;USP54,non_coding_transcript_exon_variant,,ENST00000498143,;	C	ENSG00000166348	ENST00000339859	Transcript	missense_variant	2197	2096	699	P/R	cCt/cGt	.	.	.	-1	USP54	HGNC	23513	protein_coding	YES	CCDS7329.2	ENSP00000345216	UBP54_HUMAN	.	UPI0000DFF136	.	deleterious(0)	possibly_damaging(0.776)	15/23	.	hmmpanther:PTHR22975,hmmpanther:PTHR22975:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGAAGGAACC	.	5	ESCA
LARP4B	0	.	GRCh37	10	909779	909779	+	Missense_Mutation	SNP	C	C	T	rs375571598	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.334G>A	p.Ala112Thr	p.A112T	ENST00000316157	4/17	58	32	26	28	28	0	LARP4B,missense_variant,p.Ala112Thr,ENST00000316157,;LARP4B,missense_variant,p.Ala112Thr,ENST00000406525,;LARP4B,downstream_gene_variant,,ENST00000412411,;LARP4B,downstream_gene_variant,,ENST00000481118,;LARP4B,3_prime_UTR_variant,,ENST00000476529,;	T	ENSG00000107929	ENST00000316157	Transcript	missense_variant	375	334	112	A/T	Gca/Aca	rs375571598	.	.	-1	LARP4B	HGNC	28987	protein_coding	YES	CCDS31131.1	ENSP00000326128	LAR4B_HUMAN	B5MCU2_HUMAN	UPI00001F8C87	.	tolerated(0.39)	benign(0.002)	4/17	.	hmmpanther:PTHR22792,hmmpanther:PTHR22792:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATGCGGCAT	byFrequency|byCluster	5	ESCA
PANK1	0	.	GRCh37	10	91353688	91353688	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1369G>A	p.Glu457Lys	p.E457K	ENST00000307534	4/7	57	38	18	56	56	0	PANK1,missense_variant,p.Glu259Lys,ENST00000371774,;PANK1,missense_variant,p.Glu232Lys,ENST00000342512,;PANK1,missense_variant,p.Glu457Lys,ENST00000307534,;PANK1,intron_variant,,ENST00000322191,;MIR107,upstream_gene_variant,,ENST00000362127,;	T	ENSG00000152782	ENST00000307534	Transcript	missense_variant	1525	1369	457	E/K	Gaa/Aaa	.	.	.	-1	PANK1	HGNC	8598	protein_coding	YES	CCDS31244.1	ENSP00000302108	PANK1_HUMAN	.	UPI0000131D49	.	deleterious(0.01)	probably_damaging(0.996)	4/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12280,hmmpanther:PTHR12280:SF23,TIGRFAM_domain:TIGR00555,Pfam_domain:PF03630,Superfamily_domains:SSF53067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCAAAGG	.	5	ESCA
EXOC6	0	.	GRCh37	10	94608265	94608265	+	5'Flank	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000260762	.	16	5	10	14	14	0	EXOC6,5_prime_UTR_variant,,ENST00000371543,;EXOC6,intron_variant,,ENST00000371547,;EXOC6,intron_variant,,ENST00000371552,;EXOC6,upstream_gene_variant,,ENST00000260762,;EXOC6,upstream_gene_variant,,ENST00000443748,;	G	ENSG00000138190	ENST00000260762	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	12	1	EXOC6	HGNC	23196	protein_coding	YES	CCDS7424.2	ENSP00000260762	EXOC6_HUMAN	Q9NTA6_HUMAN,H0Y5J8_HUMAN,B1AP46_HUMAN	UPI0000141914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTCGCTGG	.	5	ESCA
MMP13	0	.	GRCh37	11	102815028	102815028	+	Silent	SNP	G	G	A	rs374512736	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1383C>T	p.%3D	p.R461R	ENST00000260302	10/10	36	24	11	36	36	0	MMP13,synonymous_variant,p.%3D,ENST00000260302,;MMP13,downstream_gene_variant,,ENST00000340273,;	A	ENSG00000137745	ENST00000260302	Transcript	synonymous_variant	1412	1383	461	R	cgC/cgT	rs374512736	.	.	-1	MMP13	HGNC	7159	protein_coding	YES	CCDS8324.1	ENSP00000260302	MMP13_HUMAN	Q6LBE5_HUMAN	UPI00000422BC	.	.	.	10/10	.	PROSITE_profiles:PS51642,hmmpanther:PTHR10201:SF130,hmmpanther:PTHR10201,Gene3D:2.110.10.10,Pfam_domain:PF00045,PIRSF_domain:PIRSF001191,SMART_domains:SM00120,Superfamily_domains:SSF50923	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.V462A|c.1385T>C|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACGCGAAC	byFrequency|byCluster	5	ESCA
RAB39A	0	.	GRCh37	11	107799511	107799511	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.217G>A	p.Glu73Lys	p.E73K	ENST00000320578	1/2	97	35	62	122	122	0	RAB39A,missense_variant,p.Glu73Lys,ENST00000320578,;SLC35F2,upstream_gene_variant,,ENST00000429869,;SLC35F2,upstream_gene_variant,,ENST00000525071,;	A	ENSG00000179331	ENST00000320578	Transcript	missense_variant	283	217	73	E/K	Gag/Aag	.	.	.	1	RAB39A	HGNC	16521	protein_coding	YES	CCDS8338.1	ENSP00000322594	RB39A_HUMAN	.	UPI000006FF11	.	deleterious(0)	possibly_damaging(0.851)	1/2	.	PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF312,Gene3D:3.40.50.300,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00176,Superfamily_domains:SSF52540,Prints_domain:PR00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACAGGAGCGG	.	5	ESCA
LAYN	0	.	GRCh37	11	111430916	111430916	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.882C>G	p.%3D	p.V294V	ENST00000375615	8/8	25	22	3	39	39	0	LAYN,synonymous_variant,p.%3D,ENST00000436913,;LAYN,synonymous_variant,p.%3D,ENST00000375615,;LAYN,synonymous_variant,p.%3D,ENST00000375614,;LAYN,3_prime_UTR_variant,,ENST00000525126,;LAYN,3_prime_UTR_variant,,ENST00000533265,;LAYN,downstream_gene_variant,,ENST00000533999,;LAYN,downstream_gene_variant,,ENST00000530962,;LAYN,downstream_gene_variant,,ENST00000528924,;LAYN,3_prime_UTR_variant,,ENST00000525866,;	G	ENSG00000204381	ENST00000375615	Transcript	synonymous_variant	1067	882	294	V	gtC/gtG	.	.	.	1	LAYN	HGNC	29471	protein_coding	YES	CCDS58178.1	ENSP00000364765	LAYN_HUMAN	E9PQY8_HUMAN,E9PK64_HUMAN,B4DDS5_HUMAN	UPI0000048EB1	.	.	.	8/8	.	hmmpanther:PTHR14789,hmmpanther:PTHR14789:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AATGTCATAAG	.	2	ESCA
PIH1D2	0	.	GRCh37	11	111941292	111941292	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681G>C	p.Gln227His	p.Q227H	ENST00000280350	5/6	43	14	29	43	43	0	PIH1D2,missense_variant,p.Gln227His,ENST00000431456,;PIH1D2,missense_variant,p.Gln227His,ENST00000530641,;PIH1D2,missense_variant,p.Gln227His,ENST00000528775,;PIH1D2,missense_variant,p.Gln227His,ENST00000280350,;PIH1D2,missense_variant,p.Gln227His,ENST00000532211,;PIH1D2,missense_variant,p.Gln183His,ENST00000525072,;C11orf57,upstream_gene_variant,,ENST00000531378,;C11orf57,upstream_gene_variant,,ENST00000526879,;C11orf57,upstream_gene_variant,,ENST00000530104,;C11orf57,upstream_gene_variant,,ENST00000525785,;C11orf57,upstream_gene_variant,,ENST00000420986,;C11orf57,upstream_gene_variant,,ENST00000393047,;C11orf57,upstream_gene_variant,,ENST00000280352,;C11orf57,upstream_gene_variant,,ENST00000532163,;PIH1D2,downstream_gene_variant,,ENST00000521853,;PIH1D2,downstream_gene_variant,,ENST00000525744,;C11orf57,upstream_gene_variant,,ENST00000524989,;	G	ENSG00000150773	ENST00000280350	Transcript	missense_variant	904	681	227	Q/H	caG/caC	.	.	.	-1	PIH1D2	HGNC	25210	protein_coding	YES	CCDS8355.1	ENSP00000280350	PIHD2_HUMAN	.	UPI000007007A	.	tolerated(0.18)	benign(0.05)	5/6	.	hmmpanther:PTHR22997,hmmpanther:PTHR22997:SF2,Pfam_domain:PF08190	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCACCTGGAT	.	5	ESCA
PDE3B	0	.	GRCh37	11	14889244	14889244	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3079G>A	p.Asp1027Asn	p.D1027N	ENST00000282096	15/16	38	16	22	36	36	0	PDE3B,missense_variant,p.Asp976Asn,ENST00000455098,;PDE3B,missense_variant,p.Asp1027Asn,ENST00000282096,;	A	ENSG00000152270	ENST00000282096	Transcript	missense_variant	3432	3079	1027	D/N	Gat/Aat	.	.	.	1	PDE3B	HGNC	8779	protein_coding	YES	CCDS7817.1	ENSP00000282096	PDE3B_HUMAN	.	UPI000013DCB7	.	tolerated(0.13)	benign(0.052)	15/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11347:SF29,hmmpanther:PTHR11347,Superfamily_domains:SSF109604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATGATGAA	.	5	ESCA
CCDC73	0	.	GRCh37	11	32697502	32697502	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495G>C	p.Glu165Asp	p.E165D	ENST00000335185	8/18	41	14	27	50	50	0	CCDC73,missense_variant,p.Glu165Asp,ENST00000335185,;CCDC73,downstream_gene_variant,,ENST00000531481,;CCDC73,non_coding_transcript_exon_variant,,ENST00000534415,;	G	ENSG00000186714	ENST00000335185	Transcript	missense_variant	539	495	165	E/D	gaG/gaC	.	.	.	-1	CCDC73	HGNC	23261	protein_coding	YES	CCDS41630.1	ENSP00000335325	CCD73_HUMAN	.	UPI000066725E	.	deleterious(0)	probably_damaging(0.999)	8/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATTTCTCAAT	.	5	ESCA
NRXN2	0	.	GRCh37	11	64418762	64418762	+	Silent	SNP	G	G	A	rs184068000	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2883C>T	p.%3D	p.N961N	ENST00000265459	14/23	43	36	7	49	49	0	NRXN2,synonymous_variant,p.%3D,ENST00000377551,;NRXN2,synonymous_variant,p.%3D,ENST00000265459,;NRXN2,synonymous_variant,p.%3D,ENST00000409571,;NRXN2,synonymous_variant,p.%3D,ENST00000377559,;AP001092.4,intron_variant,,ENST00000433606,;NRXN2,non_coding_transcript_exon_variant,,ENST00000486057,;	A	ENSG00000110076	ENST00000265459	Transcript	synonymous_variant	3345	2883	961	N	aaC/aaT	rs184068000	.	.	-1	NRXN2	HGNC	8009	protein_coding	YES	CCDS8077.1	ENSP00000265459	NRX2A_HUMAN	.	UPI0000130AA2	.	.	.	14/23	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF593,hmmpanther:PTHR10127,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899	A:0.0006	A:0	A:0	.	A:0.003	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCCGTTGCC	byFrequency|byCluster|by1000G	5	ESCA
ATG2A	0	.	GRCh37	11	64665158	64665158	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5052C>T	p.%3D	p.V1684V	ENST00000377264	36/41	58	42	15	74	74	0	ATG2A,synonymous_variant,p.%3D,ENST00000418259,;ATG2A,synonymous_variant,p.%3D,ENST00000377264,;ATG2A,synonymous_variant,p.%3D,ENST00000421419,;MIR194-2,upstream_gene_variant,,ENST00000413053,;ATG2A,non_coding_transcript_exon_variant,,ENST00000472525,;	A	ENSG00000110046	ENST00000377264	Transcript	synonymous_variant	5165	5052	1684	V	gtC/gtT	.	.	.	-1	ATG2A	HGNC	29028	protein_coding	YES	CCDS31602.1	ENSP00000366475	ATG2A_HUMAN	B4DV45_HUMAN	UPI00001C1F21	.	.	.	36/41	.	hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCGTGACGTG	.	5	ESCA
CDC42EP2	0	.	GRCh37	11	65088922	65088922	+	Missense_Mutation	SNP	G	G	A	rs145388901	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553G>A	p.Val185Met	p.V185M	ENST00000544348	2/2	51	42	9	37	37	0	CDC42EP2,missense_variant,p.Val185Met,ENST00000533419,;CDC42EP2,missense_variant,p.Val185Met,ENST00000544348,;CDC42EP2,missense_variant,p.Val185Met,ENST00000279249,;	A	ENSG00000149798	ENST00000544348	Transcript	missense_variant	1159	553	185	V/M	Gtg/Atg	rs145388901,COSM1200377	.	.	1	CDC42EP2	HGNC	16263	protein_coding	YES	CCDS8099.1	ENSP00000442534	BORG1_HUMAN	.	UPI000000D7F5	.	deleterious(0.01)	possibly_damaging(0.868)	2/2	.	hmmpanther:PTHR15344:SF4,hmmpanther:PTHR15344,Pfam_domain:PF14957,PIRSF_domain:PIRSF038036	.	.	.	.	.	.	.	A:0.0014	A:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCACGTGGAC	byFrequency|byCluster	5	ESCA
IGHMBP2	0	.	GRCh37	11	68701368	68701368	+	Silent	SNP	G	G	A	rs747627986	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1524G>A	p.%3D	p.S508S	ENST00000255078	10/15	184	162	22	95	95	0	IGHMBP2,synonymous_variant,p.%3D,ENST00000255078,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000541229,;IGHMBP2,downstream_gene_variant,,ENST00000536803,;IGHMBP2,downstream_gene_variant,,ENST00000568742,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000539064,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000537458,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000543739,;IGHMBP2,upstream_gene_variant,,ENST00000544521,;IGHMBP2,upstream_gene_variant,,ENST00000545475,;	A	ENSG00000132740	ENST00000255078	Transcript	synonymous_variant	1635	1524	508	S	tcG/tcA	rs747627986	.	.	1	IGHMBP2	HGNC	5542	protein_coding	YES	CCDS8187.1	ENSP00000255078	SMBP2_HUMAN	F5H5K3_HUMAN	UPI000013CE82	.	.	.	10/15	.	hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF140,Gene3D:3.40.50.300,Pfam_domain:PF13087,TIGRFAM_domain:TIGR00376,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTCGAAAGG	byFrequency	4	ESCA
FCHSD2	0	.	GRCh37	11	72547797	72547798	+	3'Flank	INS	-	-	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000409418	.	127	96	31	90	90	0	FCHSD2,3_prime_UTR_variant,,ENST00000409314,;FCHSD2,3_prime_UTR_variant,,ENST00000311172,;ATG16L2,intron_variant,,ENST00000534905,;FCHSD2,downstream_gene_variant,,ENST00000458644,;FCHSD2,downstream_gene_variant,,ENST00000409263,;FCHSD2,downstream_gene_variant,,ENST00000409418,;	T	ENSG00000137478	ENST00000409418	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1491	-1	FCHSD2	HGNC	29114	protein_coding	YES	CCDS8218.2	ENSP00000386722	FCSD2_HUMAN	C9JM66_HUMAN	UPI0000251F08	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	ATTCCATTTTT	.	2	ESCA
LRRC32	0	.	GRCh37	11	76371217	76371217	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1420T>G	p.Ser474Ala	p.S474A	ENST00000407242	3/3	28	22	6	26	26	0	LRRC32,missense_variant,p.Ser474Ala,ENST00000260061,;LRRC32,missense_variant,p.Ser474Ala,ENST00000407242,;LRRC32,missense_variant,p.Ser474Ala,ENST00000404995,;LRRC32,downstream_gene_variant,,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,;	C	ENSG00000137507	ENST00000407242	Transcript	missense_variant	1663	1420	474	S/A	Tct/Gct	.	.	.	-1	LRRC32	HGNC	4161	protein_coding	YES	CCDS8245.1	ENSP00000384126	LRC32_HUMAN	C9JYU3_HUMAN	UPI000012B0DF	.	deleterious(0.01)	possibly_damaging(0.883)	3/3	.	Superfamily_domains:SSF52058,Gene3D:3.80.10.10,hmmpanther:PTHR24365:SF237,hmmpanther:PTHR24365	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GGAAGAAAGGT	.	4	ESCA
KCTD14	0	.	GRCh37	11	77727566	77727566	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*73C>G	.	.	ENST00000353172	2/2	34	20	14	32	32	0	KCTD14,3_prime_UTR_variant,,ENST00000353172,;KCTD14,downstream_gene_variant,,ENST00000533144,;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000528251,;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000530054,;RP11-7I15.3,downstream_gene_variant,,ENST00000533697,;	C	ENSG00000151364	ENST00000353172	Transcript	3_prime_UTR_variant	886	.	.	.	.	.	.	.	-1	KCTD14	HGNC	23295	protein_coding	YES	CCDS8255.2	ENSP00000316482	KCD14_HUMAN	B2R9R8_HUMAN	UPI000003E7AB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAAGAAAAT	.	5	ESCA
NDUFC2	0	.	GRCh37	11	77790692	77790692	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.99C>G	p.Ile33Met	p.I33M	ENST00000281031	1/3	34	25	8	23	23	0	NDUFC2,missense_variant,p.Ile33Met,ENST00000534029,;NDUFC2,missense_variant,p.Ile33Met,ENST00000281031,;NDUFC2,missense_variant,p.Ile33Met,ENST00000528164,;NDUFC2-KCTD14,missense_variant,p.Ile33Met,ENST00000528251,;NDUFC2,missense_variant,p.Ile33Met,ENST00000525085,;NDUFC2,missense_variant,p.Ile33Met,ENST00000527806,;NDUFC2-KCTD14,missense_variant,p.Ile33Met,ENST00000530054,;	C	ENSG00000151366	ENST00000281031	Transcript	missense_variant	574	99	33	I/M	atC/atG	.	.	.	-1	NDUFC2	HGNC	7706	protein_coding	YES	CCDS8257.1	ENSP00000281031	NDUC2_HUMAN	.	UPI000012FC27	.	tolerated(0.33)	benign(0.037)	1/3	.	hmmpanther:PTHR13099,Pfam_domain:PF06374,PIRSF_domain:PIRSF017834	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCCGATGTA	.	5	ESCA
KDM4D	0	.	GRCh37	11	94730891	94730891	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355G>A	p.Glu119Lys	p.E119K	ENST00000335080	3/3	48	42	6	34	34	0	KDM4D,missense_variant,p.Glu119Lys,ENST00000536741,;KDM4D,missense_variant,p.Glu119Lys,ENST00000335080,;	A	ENSG00000186280	ENST00000335080	Transcript	missense_variant	1187	355	119	E/K	Gaa/Aaa	COSM1176937	.	.	1	KDM4D	HGNC	25498	protein_coding	YES	CCDS8302.1	ENSP00000334181	KDM4D_HUMAN	.	UPI00001A82EC	.	tolerated(0.07)	benign(0.02)	3/3	.	Superfamily_domains:SSF51197,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF21	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	ATTTCGAAGAT	.	3	ESCA
TMEM132D	0	.	GRCh37	12	129569203	129569203	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1488G>C	p.Met496Ile	p.M496I	ENST00000422113	6/9	44	41	3	61	61	0	TMEM132D,missense_variant,p.Met496Ile,ENST00000422113,;TMEM132D,missense_variant,p.Met34Ile,ENST00000389441,;	G	ENSG00000151952	ENST00000422113	Transcript	missense_variant	1815	1488	496	M/I	atG/atC	.	.	.	-1	TMEM132D	HGNC	29411	protein_coding	YES	CCDS9266.1	ENSP00000408581	T132D_HUMAN	.	UPI000023759C	.	tolerated(0.16)	benign(0.034)	6/9	.	hmmpanther:PTHR13388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTTTCATTTC	.	2	ESCA
TUBA1A	0	.	GRCh37	12	49578864	49578864	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1285G>C	p.Glu429Gln	p.E429Q	ENST00000301071	4/4	171	146	24	138	138	0	TUBA1A,missense_variant,p.Glu394Gln,ENST00000550767,;TUBA1A,missense_variant,p.Glu429Gln,ENST00000295766,;TUBA1A,missense_variant,p.Glu429Gln,ENST00000301071,;TUBA1A,downstream_gene_variant,,ENST00000546918,;TUBA1A,downstream_gene_variant,,ENST00000552924,;TUBA1A,downstream_gene_variant,,ENST00000547939,;TUBA1A,downstream_gene_variant,,ENST00000550811,;TUBA1C,upstream_gene_variant,,ENST00000549554,;TUBA1A,downstream_gene_variant,,ENST00000550254,;TUBA1A,downstream_gene_variant,,ENST00000548363,;	G	ENSG00000167552	ENST00000301071	Transcript	missense_variant	1630	1285	429	E/Q	Gag/Cag	.	.	.	-1	TUBA1A	HGNC	20766	protein_coding	YES	CCDS8781.1	ENSP00000301071	TBA1A_HUMAN	F8VXZ7_HUMAN,F8VX09_HUMAN,F8VWV9_HUMAN,F8VRZ4_HUMAN,F8VRK0_HUMAN,F8VQQ4_HUMAN	UPI0000000DB2	.	deleterious_low_confidence(0.02)	benign(0.142)	4/4	.	hmmpanther:PTHR11588:SF65,hmmpanther:PTHR11588,Gene3D:1.10.287.600,Superfamily_domains:SSF55307,Prints_domain:PR01162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTCAAGGG	.	5	ESCA
TUBA1A	0	.	GRCh37	12	49578975	49578975	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1174G>C	p.Asp392His	p.D392H	ENST00000301071	4/4	126	101	25	116	116	0	TUBA1A,missense_variant,p.Asp357His,ENST00000550767,;TUBA1A,missense_variant,p.Asp392His,ENST00000295766,;TUBA1A,missense_variant,p.Asp392His,ENST00000301071,;TUBA1A,downstream_gene_variant,,ENST00000546918,;TUBA1A,downstream_gene_variant,,ENST00000552924,;TUBA1A,downstream_gene_variant,,ENST00000547939,;TUBA1A,downstream_gene_variant,,ENST00000550811,;TUBA1C,upstream_gene_variant,,ENST00000549554,;TUBA1A,downstream_gene_variant,,ENST00000550254,;TUBA1A,downstream_gene_variant,,ENST00000548363,;	G	ENSG00000167552	ENST00000301071	Transcript	missense_variant	1519	1174	392	D/H	Gac/Cac	.	.	.	-1	TUBA1A	HGNC	20766	protein_coding	YES	CCDS8781.1	ENSP00000301071	TBA1A_HUMAN	F8VXZ7_HUMAN,F8VX09_HUMAN,F8VWV9_HUMAN,F8VRZ4_HUMAN,F8VRK0_HUMAN,F8VQQ4_HUMAN	UPI0000000DB2	.	deleterious_low_confidence(0.01)	probably_damaging(0.979)	4/4	.	hmmpanther:PTHR11588:SF65,hmmpanther:PTHR11588,Gene3D:1.10.287.600,Pfam_domain:PF03953,SMART_domains:SM00865,Superfamily_domains:SSF55307,Prints_domain:PR01161,Prints_domain:PR01162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGTCCAGGC	.	5	ESCA
POU6F1	0	.	GRCh37	12	51584241	51584241	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.695C>G	p.Ser232Cys	p.S232C	ENST00000389243	11/11	52	46	6	48	48	0	POU6F1,missense_variant,p.Ser232Cys,ENST00000389243,;POU6F1,missense_variant,p.Ser232Cys,ENST00000550824,;POU6F1,missense_variant,p.Ser232Cys,ENST00000333640,;POU6F1,downstream_gene_variant,,ENST00000552305,;	C	ENSG00000184271	ENST00000389243	Transcript	missense_variant	1635	695	232	S/C	tCc/tGc	.	.	.	-1	POU6F1	HGNC	9224	protein_coding	YES	CCDS31803.1	ENSP00000373895	PO6F1_HUMAN	F8VSI9_HUMAN	UPI0000131D97	.	deleterious(0)	possibly_damaging(0.487)	11/11	.	Superfamily_domains:SSF46689,Gene3D:1.10.10.60,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF6,PROSITE_profiles:PS50071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCTTGGAGGGC	.	4	ESCA
TIMELESS	0	.	GRCh37	12	56814440	56814440	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3141C>T	p.%3D	p.L1047L	ENST00000553532	26/29	88	71	17	61	61	0	TIMELESS,synonymous_variant,p.%3D,ENST00000553532,;TIMELESS,synonymous_variant,p.%3D,ENST00000554616,;TIMELESS,synonymous_variant,p.%3D,ENST00000229201,;TIMELESS,non_coding_transcript_exon_variant,,ENST00000553314,;TIMELESS,non_coding_transcript_exon_variant,,ENST00000557589,;TIMELESS,downstream_gene_variant,,ENST00000555808,;	A	ENSG00000111602	ENST00000553532	Transcript	synonymous_variant	3292	3141	1047	L	ctC/ctT	.	.	.	-1	TIMELESS	HGNC	11813	protein_coding	YES	CCDS8918.1	ENSP00000450607	TIM_HUMAN	.	UPI000013C8EA	.	.	.	26/29	.	Pfam_domain:PF05029,hmmpanther:PTHR22940:SF4,hmmpanther:PTHR22940	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGTGAGTGG	.	5	ESCA
AGAP2-AS1	0	.	GRCh37	12	58121936	58121936	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*354G>A	.	.	ENST00000542466	2/2	40	29	11	29	29	0	AGAP2-AS1,3_prime_UTR_variant,,ENST00000542466,;AGAP2,intron_variant,,ENST00000257897,;AGAP2,intron_variant,,ENST00000328568,;AGAP2,intron_variant,,ENST00000547588,;AGAP2,downstream_gene_variant,,ENST00000549129,;RP11-571M6.8,upstream_gene_variant,,ENST00000548410,;RP11-571M6.8,upstream_gene_variant,,ENST00000602413,;	A	ENSG00000255737	ENST00000542466	Transcript	3_prime_UTR_variant	1297	.	.	.	.	.	.	.	1	AGAP2-AS1	HGNC	48633	protein_coding	YES	.	ENSP00000437523	.	B7Z718_HUMAN	UPI000021D228	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACCGTCCTC	.	5	ESCA
GRIP1	0	.	GRCh37	12	66838411	66838411	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1484C>T	p.Ser495Phe	p.S495F	ENST00000398016	12/24	95	90	5	73	73	0	GRIP1,missense_variant,p.Ser495Phe,ENST00000538211,;GRIP1,missense_variant,p.Ser362Phe,ENST00000538164,;GRIP1,missense_variant,p.Ser547Phe,ENST00000286445,;GRIP1,missense_variant,p.Ser387Phe,ENST00000536215,;GRIP1,missense_variant,p.Ser495Phe,ENST00000398016,;GRIP1,missense_variant,p.Ser547Phe,ENST00000359742,;GRIP1,missense_variant,p.Ser439Phe,ENST00000540433,;GRIP1,intron_variant,,ENST00000540854,;GRIP1,downstream_gene_variant,,ENST00000543172,;GRIP1,downstream_gene_variant,,ENST00000535002,;	A	ENSG00000155974	ENST00000398016	Transcript	missense_variant	1553	1484	495	S/F	tCt/tTt	.	.	.	-1	GRIP1	HGNC	18708	protein_coding	YES	CCDS41807.1	ENSP00000381098	GRIP1_HUMAN	F5H5I0_HUMAN,F5H4P8_HUMAN,F5H424_HUMAN	UPI0000DD8148	.	deleterious(0)	probably_damaging(0.997)	12/24	.	PROSITE_profiles:PS50106,hmmpanther:PTHR10316:SF39,hmmpanther:PTHR10316,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTGAAGAGTCT	.	2	ESCA
OSBPL8	0	.	GRCh37	12	76749571	76749571	+	3'UTR	SNP	G	G	A	rs187324650	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*98C>T	.	.	ENST00000261183	24/24	39	30	9	51	51	0	OSBPL8,3_prime_UTR_variant,,ENST00000261183,;OSBPL8,3_prime_UTR_variant,,ENST00000393249,;OSBPL8,downstream_gene_variant,,ENST00000393250,;	A	ENSG00000091039	ENST00000261183	Transcript	3_prime_UTR_variant	3248	.	.	.	.	rs187324650	.	.	-1	OSBPL8	HGNC	16396	protein_coding	YES	CCDS31862.1	ENSP00000261183	OSBL8_HUMAN	Q96E43_HUMAN,Q6ZME5_HUMAN,F8VZB8_HUMAN,F8VVE7_HUMAN,F8VVD3_HUMAN,F8VQX7_HUMAN	UPI000006ECD1	.	.	.	24/24	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTCGGAATA	by1000G	2	ESCA
DPPA3	0	.	GRCh37	12	7869817	7869817	+	3'UTR	SNP	A	A	T	rs200786984	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*144A>T	.	.	ENST00000345088	4/4	30	18	12	16	16	0	DPPA3,3_prime_UTR_variant,,ENST00000345088,;	T	ENSG00000187569	ENST00000345088	Transcript	3_prime_UTR_variant	741	.	.	.	.	rs200786984	.	.	1	DPPA3	HGNC	19199	protein_coding	YES	CCDS8582.1	ENSP00000339250	DPPA3_HUMAN	.	UPI00001981F7	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CTACTATGATA	.	3	ESCA
ATP2B1	0	.	GRCh37	12	90103606	90103606	+	5'Flank	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000428670	.	21	17	4	30	30	0	ATP2B1,upstream_gene_variant,,ENST00000551310,;ATP2B1,upstream_gene_variant,,ENST00000428670,;LINC00936,non_coding_transcript_exon_variant,,ENST00000605386,;	G	ENSG00000070961	ENST00000428670	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	998	-1	ATP2B1	HGNC	814	protein_coding	YES	CCDS9035.1	ENSP00000392043	AT2B1_HUMAN	Q3L582_HUMAN	UPI000002A436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTGCCGCGAC	.	4	ESCA
CCDC41	0	.	GRCh37	12	94702532	94702532	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*57G>A	.	.	ENST00000397809	17/17	39	19	19	36	36	0	CCDC41,3_prime_UTR_variant,,ENST00000397809,;CCDC41,3_prime_UTR_variant,,ENST00000339839,;CCDC41,intron_variant,,ENST00000552632,;PLXNC1,downstream_gene_variant,,ENST00000545312,;PLXNC1,downstream_gene_variant,,ENST00000547057,;PLXNC1,downstream_gene_variant,,ENST00000258526,;CCDC41,downstream_gene_variant,,ENST00000546783,;PLXNC1,downstream_gene_variant,,ENST00000549217,;CCDC41,downstream_gene_variant,,ENST00000547232,;	T	ENSG00000173588	ENST00000397809	Transcript	3_prime_UTR_variant	2713	.	.	.	.	.	.	.	-1	CCDC41	HGNC	17966	protein_coding	YES	CCDS41820.1	ENSP00000380911	.	J3KNW7_HUMAN,H0YHH5_HUMAN	UPI0000D4BD6F	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AATGTCAAGTT	.	4	ESCA
TMPO	0	.	GRCh37	12	98938017	98938017	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.673C>G	p.Gln225Glu	p.Q225E	ENST00000556029	5/9	22	15	7	40	40	0	TMPO,missense_variant,p.Gln225Glu,ENST00000556029,;TMPO,intron_variant,,ENST00000393053,;TMPO,intron_variant,,ENST00000343315,;TMPO,intron_variant,,ENST00000556678,;TMPO,non_coding_transcript_exon_variant,,ENST00000548223,;TMPO,upstream_gene_variant,,ENST00000551987,;	G	ENSG00000120802	ENST00000556029	Transcript	missense_variant	1029	673	225	Q/E	Caa/Gaa	.	.	.	1	TMPO	HGNC	11875	protein_coding	.	CCDS31879.1	ENSP00000450627	LAP2B_HUMAN	Q9P1N8_HUMAN	UPI0000143267	.	tolerated(0.53)	benign(0.004)	5/9	.	hmmpanther:PTHR12019,hmmpanther:PTHR12019:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTCTCAAGCT	.	2	ESCA
TNFSF13B	0	.	GRCh37	13	108922373	108922373	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.130G>C	p.Asp44His	p.D44H	ENST00000375887	1/6	23	17	6	16	16	0	TNFSF13B,missense_variant,p.Asp44His,ENST00000430559,;TNFSF13B,missense_variant,p.Asp44His,ENST00000375887,;TNFSF13B,missense_variant,p.Asp44His,ENST00000542136,;TNFSF13B,intron_variant,,ENST00000486502,;TNFSF13B,upstream_gene_variant,,ENST00000479435,;	C	ENSG00000102524	ENST00000375887	Transcript	missense_variant	308	130	44	D/H	Gac/Cac	.	.	.	1	TNFSF13B	HGNC	11929	protein_coding	YES	CCDS9509.1	ENSP00000365048	TN13B_HUMAN	.	UPI0000001C02	.	deleterious(0.05)	possibly_damaging(0.541)	1/6	.	hmmpanther:PTHR15151,hmmpanther:PTHR15151:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAAAGACGGA	.	5	ESCA
SOX1	0	.	GRCh37	13	112722275	112722275	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.303C>G	p.Ile101Met	p.I101M	ENST00000330949	1/1	47	11	35	88	88	0	SOX1,missense_variant,p.Ile101Met,ENST00000330949,;	G	ENSG00000182968	ENST00000330949	Transcript	missense_variant	363	303	101	I/M	atC/atG	.	.	.	1	SOX1	HGNC	11189	protein_coding	YES	CCDS9523.1	ENSP00000330218	SOX1_HUMAN	.	UPI0000190FB0	.	deleterious(0)	probably_damaging(0.996)	1/1	.	PROSITE_profiles:PS50118,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF40,Pfam_domain:PF00505,Gene3D:1.10.30.10,SMART_domains:SM00398,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATCGACGA	.	5	ESCA
PDS5B	0	.	GRCh37	13	33316842	33316842	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2589C>A	p.Asp863Glu	p.D863E	ENST00000315596	23/35	52	38	13	34	34	0	PDS5B,missense_variant,p.Asp863Glu,ENST00000315596,;PDS5B,missense_variant,p.Asp863Glu,ENST00000450460,;	A	ENSG00000083642	ENST00000315596	Transcript	missense_variant	2775	2589	863	D/E	gaC/gaA	.	.	.	1	PDS5B	HGNC	20418	protein_coding	YES	CCDS41878.1	ENSP00000313851	PDS5B_HUMAN	.	UPI000006D4A9	.	deleterious(0)	possibly_damaging(0.499)	23/35	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGACTTGAC	.	5	ESCA
LACC1	0	.	GRCh37	13	44456456	44456456	+	Missense_Mutation	SNP	C	C	T	rs750807129	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.698C>T	p.Ala233Val	p.A233V	ENST00000441843	3/7	41	26	15	35	35	0	LACC1,missense_variant,p.Ala233Val,ENST00000441843,;LACC1,missense_variant,p.Ala233Val,ENST00000325686,;CCDC122,upstream_gene_variant,,ENST00000444614,;LACC1,downstream_gene_variant,,ENST00000425906,;CCDC122,upstream_gene_variant,,ENST00000476570,;	T	ENSG00000179630	ENST00000441843	Transcript	missense_variant	1183	698	233	A/V	gCg/gTg	rs750807129	.	.	1	LACC1	HGNC	26789	protein_coding	YES	CCDS9391.1	ENSP00000391747	LACC1_HUMAN	A2A3Z5_HUMAN	UPI00000746BB	.	deleterious(0)	possibly_damaging(0.804)	3/7	.	hmmpanther:PTHR30616,Gene3D:3.60.140.10,Pfam_domain:PF02578,Superfamily_domains:SSF64438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTGGCGAATG	.	5	ESCA
DACH1	0	.	GRCh37	13	72012894	72012894	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1893C>A	.	.	ENST00000305425	11/11	77	56	21	54	54	0	DACH1,3_prime_UTR_variant,,ENST00000305425,;DACH1,3_prime_UTR_variant,,ENST00000313174,;DACH1,3_prime_UTR_variant,,ENST00000354591,;DACH1,downstream_gene_variant,,ENST00000359684,;	T	ENSG00000165659	ENST00000305425	Transcript	3_prime_UTR_variant	4443	.	.	.	.	.	.	.	-1	DACH1	HGNC	2663	protein_coding	YES	CCDS41899.1	ENSP00000304994	DACH1_HUMAN	.	UPI00001FCE9E	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATAGGGAAACA	.	5	ESCA
KCTD12	0	.	GRCh37	13	77454951	77454951	+	3'UTR	SNP	A	A	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4355T>A	.	.	ENST00000377474	1/1	72	49	23	53	53	0	KCTD12,3_prime_UTR_variant,,ENST00000377474,;KCTD12,downstream_gene_variant,,ENST00000317765,;	T	ENSG00000178695	ENST00000377474	Transcript	3_prime_UTR_variant	5575	.	.	.	.	.	.	.	-1	KCTD12	HGNC	14678	protein_coding	YES	CCDS9455.1	ENSP00000366694	KCD12_HUMAN	.	UPI0000073DDF	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTAAAAAA	.	5	ESCA
SLITRK6	0	.	GRCh37	13	86369470	86369470	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1174C>G	p.Leu392Val	p.L392V	ENST00000400286	2/2	77	56	20	62	62	0	SLITRK6,missense_variant,p.Leu392Val,ENST00000400286,;	C	ENSG00000184564	ENST00000400286	Transcript	missense_variant	1773	1174	392	L/V	Ctt/Gtt	.	.	.	-1	SLITRK6	HGNC	23503	protein_coding	YES	CCDS41903.1	ENSP00000383143	SLIK6_HUMAN	.	UPI000004C9D6	.	deleterious(0)	probably_damaging(0.999)	2/2	.	Superfamily_domains:SSF52058,SMART_domains:SM00365,SMART_domains:SM00369,Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24373:SF5,hmmpanther:PTHR24373,PROSITE_profiles:PS51450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAGCATTT	.	5	ESCA
SLITRK5	0	.	GRCh37	13	88331714	88331714	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1194C>G	.	.	ENST00000325089	2/2	59	40	19	38	38	0	SLITRK5,3_prime_UTR_variant,,ENST00000325089,;SLITRK5,downstream_gene_variant,,ENST00000400028,;	G	ENSG00000165300	ENST00000325089	Transcript	3_prime_UTR_variant	4290	.	.	.	.	.	.	.	1	SLITRK5	HGNC	20295	protein_coding	YES	CCDS9465.1	ENSP00000366283	SLIK5_HUMAN	.	UPI000015F6F7	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCTATAC	.	5	ESCA
IPO5	0	.	GRCh37	13	98660331	98660331	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1789G>A	p.Asp597Asn	p.D597N	ENST00000261574	18/29	36	9	27	27	27	0	IPO5,missense_variant,p.Asp597Asn,ENST00000261574,;IPO5,missense_variant,p.Asp581Asn,ENST00000469360,;IPO5,missense_variant,p.Asp579Asn,ENST00000490680,;IPO5,missense_variant,p.Asp579Asn,ENST00000357602,;IPO5,missense_variant,p.Asp454Asn,ENST00000539640,;IPO5,downstream_gene_variant,,ENST00000493492,;IPO5,non_coding_transcript_exon_variant,,ENST00000491555,;IPO5,downstream_gene_variant,,ENST00000479736,;	A	ENSG00000065150	ENST00000261574	Transcript	missense_variant	1969	1789	597	D/N	Gat/Aat	COSM432644	.	.	1	IPO5	HGNC	6402	protein_coding	YES	CCDS31999.1	ENSP00000261574	IPO5_HUMAN	Q9BVS9_HUMAN,E7EX05_HUMAN,E7EWK4_HUMAN,E7ETV3_HUMAN,E7ESZ1_HUMAN,E7ESA1_HUMAN,C9JZD8_HUMAN,C9JZ53_HUMAN,C9JXE0_HUMAN,C9JQT6_HUMAN,C9J875_HUMAN,B3KWG6_HUMAN	UPI0000163C1C	.	tolerated(0.11)	benign(0.012)	18/29	.	hmmpanther:PTHR10527:SF22,hmmpanther:PTHR10527,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCAGATGTG	.	5	ESCA
IGHV3-43	0	.	GRCh37	14	106926220	106926220	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.322G>T	p.Glu108Ter	p.E108*	ENST00000434710	2/2	119	93	25	118	118	0	IGHV3-43,stop_gained,p.Glu108Ter,ENST00000434710,;IGHVII-43-1,downstream_gene_variant,,ENST00000522649,;	A	ENSG00000232216	ENST00000434710	Transcript	stop_gained	402	322	108	E/*	Gag/Tag	.	.	.	-1	IGHV3-43	HGNC	5604	IG_V_gene	YES	.	ENSP00000399826	.	.	UPI000011AACC	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF91,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTCAGTTC	.	5	ESCA
TRAV19	0	.	GRCh37	14	22476309	22476309	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.239T>C	p.Ile80Thr	p.I80T	ENST00000390447	2/2	72	68	4	26	26	0	TRAV19,missense_variant,p.Ile80Thr,ENST00000390447,;TRAV18,downstream_gene_variant,,ENST00000390446,;AE000660.4,upstream_gene_variant,,ENST00000553572,;	C	ENSG00000211799	ENST00000390447	Transcript	missense_variant	356	239	80	I/T	aTa/aCa	.	.	.	1	TRAV19	HGNC	12115	TR_V_gene	YES	.	ENSP00000452148	.	.	UPI000011D122	.	tolerated(1)	benign(0)	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR23267,hmmpanther:PTHR23267:SF115,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGAAATAAGTG	.	2	ESCA
HOMEZ	0	.	GRCh37	14	23745409	23745409	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1028G>C	p.Arg343Thr	p.R343T	ENST00000357460	2/2	60	50	9	26	26	0	HOMEZ,missense_variant,p.Arg345Thr,ENST00000431326,;HOMEZ,missense_variant,p.Arg345Thr,ENST00000561013,;HOMEZ,missense_variant,p.Arg173Thr,ENST00000606731,;HOMEZ,missense_variant,p.Arg343Thr,ENST00000357460,;HOMEZ,downstream_gene_variant,,ENST00000606006,;C14orf164,downstream_gene_variant,,ENST00000399905,;C14orf164,downstream_gene_variant,,ENST00000492621,;C14orf164,downstream_gene_variant,,ENST00000399910,;C14orf164,downstream_gene_variant,,ENST00000430154,;C14orf164,downstream_gene_variant,,ENST00000492355,;C14orf164,downstream_gene_variant,,ENST00000470818,;	G	ENSG00000215271	ENST00000357460	Transcript	missense_variant	1193	1028	343	R/T	aGa/aCa	.	.	.	-1	HOMEZ	HGNC	20164	protein_coding	YES	CCDS45085.1	ENSP00000350049	HOMEZ_HUMAN	B4DLB7_HUMAN	UPI0000EE4A53	.	deleterious(0.01)	benign(0.437)	2/2	.	hmmpanther:PTHR15467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAACTCTACCT	.	5	ESCA
AKAP6	0	.	GRCh37	14	33291681	33291681	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4662G>C	p.Gln1554His	p.Q1554H	ENST00000280979	13/14	68	57	11	27	27	0	AKAP6,missense_variant,p.Gln1554His,ENST00000280979,;AKAP6,intron_variant,,ENST00000557272,;	C	ENSG00000151320	ENST00000280979	Transcript	missense_variant	4832	4662	1554	Q/H	caG/caC	.	.	.	1	AKAP6	HGNC	376	protein_coding	YES	CCDS9644.1	ENSP00000280979	AKAP6_HUMAN	G3V569_HUMAN,G3V3H6_HUMAN,G3V3H2_HUMAN,G3V3B5_HUMAN,D3DS91_HUMAN	UPI000013DC48	.	tolerated_low_confidence(0.06)	benign(0.006)	13/14	.	hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCAGAATGC	.	5	ESCA
PNN	0	.	GRCh37	14	39651504	39651504	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*437C>G	.	.	ENST00000216832	9/9	69	49	20	74	74	0	PNN,3_prime_UTR_variant,,ENST00000216832,;PNN,downstream_gene_variant,,ENST00000553331,;PNN,downstream_gene_variant,,ENST00000556530,;PNN,intron_variant,,ENST00000557680,;PNN,downstream_gene_variant,,ENST00000554902,;	G	ENSG00000100941	ENST00000216832	Transcript	3_prime_UTR_variant	2658	.	.	.	.	.	.	.	1	PNN	HGNC	9162	protein_coding	YES	CCDS9671.1	ENSP00000216832	PININ_HUMAN	.	UPI000013C70D	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATCATTTT	.	5	ESCA
LRFN5	0	.	GRCh37	14	42357021	42357021	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1193C>G	p.Ser398Ter	p.S398*	ENST00000298119	3/6	55	38	17	30	30	0	LRFN5,stop_gained,p.Ser398Ter,ENST00000298119,;LRFN5,stop_gained,p.Ser398Ter,ENST00000554120,;LRFN5,stop_gained,p.Ser398Ter,ENST00000554171,;	G	ENSG00000165379	ENST00000298119	Transcript	stop_gained	2382	1193	398	S/*	tCa/tGa	.	.	.	1	LRFN5	HGNC	20360	protein_coding	YES	CCDS9678.1	ENSP00000298119	LRFN5_HUMAN	.	UPI000000DA1E	.	.	.	3/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTCAACTT	.	5	ESCA
KIAA0586	0	.	GRCh37	14	58924677	58924677	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1722C>G	p.Ile574Met	p.I574M	ENST00000354386	13/34	38	30	8	47	47	0	KIAA0586,missense_variant,p.Ile521Met,ENST00000261244,;KIAA0586,missense_variant,p.Ile477Met,ENST00000423743,;KIAA0586,missense_variant,p.Ile574Met,ENST00000354386,;KIAA0586,missense_variant,p.Ile506Met,ENST00000556134,;KIAA0586,non_coding_transcript_exon_variant,,ENST00000538571,;	G	ENSG00000100578	ENST00000354386	Transcript	missense_variant	1966	1722	574	I/M	atC/atG	.	.	.	1	KIAA0586	HGNC	19960	protein_coding	YES	CCDS58320.1	ENSP00000346359	TALD3_HUMAN	.	UPI0001AE6998	.	deleterious(0.03)	probably_damaging(0.975)	13/34	.	hmmpanther:PTHR15721,hmmpanther:PTHR15721:SF2,Pfam_domain:PF15324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTATCAATGC	.	5	ESCA
AL133373.1	0	.	GRCh37	14	92041204	92041204	+	5'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-248C>G	.	.	ENST00000596306	1/1	68	43	25	46	46	0	AL133373.1,5_prime_UTR_variant,,ENST00000596306,;	C	ENSG00000268657	ENST00000596306	Transcript	5_prime_UTR_variant	180	.	.	.	.	.	.	.	-1	AL133373.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000472226	.	M0R207_HUMAN	UPI0000141AC8	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGAGGAATG	.	5	ESCA
LRRK1	0	.	GRCh37	15	101549252	101549252	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.973G>A	p.Glu325Lys	p.E325K	ENST00000388948	7/34	16	4	11	11	11	0	LRRK1,missense_variant,p.Glu325Lys,ENST00000388948,;LRRK1,missense_variant,p.Glu322Lys,ENST00000284395,;LRRK1,missense_variant,p.Glu325Lys,ENST00000531270,;LRRK1,missense_variant,p.Glu325Lys,ENST00000525284,;	A	ENSG00000154237	ENST00000388948	Transcript	missense_variant	1332	973	325	E/K	Gaa/Aaa	.	.	.	1	LRRK1	HGNC	18608	protein_coding	YES	CCDS42086.1	ENSP00000373600	LRRK1_HUMAN	E9PMK9_HUMAN,E9PLF8_HUMAN,E9PK39_HUMAN,B3KSX5_HUMAN	UPI0000D4FE63	.	deleterious(0.02)	possibly_damaging(0.891)	7/34	.	hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF239,Gene3D:3.80.10.10,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGACGAAATC	.	5	ESCA
PLA2G4B	0	.	GRCh37	15	42138148	42138148	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2196G>C	p.Trp732Cys	p.W732C	ENST00000542534	21/25	50	15	35	60	60	0	PLA2G4B,missense_variant,p.Trp501Cys,ENST00000458483,;JMJD7-PLA2G4B,missense_variant,p.Trp732Cys,ENST00000342159,;PLA2G4B,missense_variant,p.Trp732Cys,ENST00000542534,;JMJD7-PLA2G4B,missense_variant,p.Trp732Cys,ENST00000382448,;PLA2G4B,missense_variant,p.Trp501Cys,ENST00000452633,;PLA2G4B,upstream_gene_variant,,ENST00000569354,;SPTBN5,downstream_gene_variant,,ENST00000320955,;JMJD7-PLA2G4B,3_prime_UTR_variant,,ENST00000487292,;PLA2G4B,non_coding_transcript_exon_variant,,ENST00000566076,;JMJD7-PLA2G4B,non_coding_transcript_exon_variant,,ENST00000490848,;JMJD7-PLA2G4B,non_coding_transcript_exon_variant,,ENST00000491746,;PLA2G4B,non_coding_transcript_exon_variant,,ENST00000483748,;PLA2G4B,downstream_gene_variant,,ENST00000461382,;SPTBN5,downstream_gene_variant,,ENST00000563899,;	C	ENSG00000243708	ENST00000542534	Transcript	missense_variant	2236	2196	732	W/C	tgG/tgC	.	.	.	1	PLA2G4B	HGNC	9036	protein_coding	YES	CCDS32202.1	ENSP00000441905	.	C9K0I3_HUMAN	UPI0000070A0F	.	deleterious(0)	probably_damaging(0.999)	21/25	.	PROSITE_profiles:PS51210,hmmpanther:PTHR10728:SF31,hmmpanther:PTHR10728,Gene3D:3.40.1090.10,Pfam_domain:PF01735,SMART_domains:SM00022,Superfamily_domains:SSF52151	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTGGAGCAA	.	5	ESCA
FBN1	0	.	GRCh37	15	48714182	48714182	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7537C>A	p.Pro2513Thr	p.P2513T	ENST00000316623	61/66	47	35	12	34	34	0	FBN1,missense_variant,p.Pro2513Thr,ENST00000316623,;FBN1,3_prime_UTR_variant,,ENST00000559133,;	T	ENSG00000166147	ENST00000316623	Transcript	missense_variant	7993	7537	2513	P/T	Ccc/Acc	.	.	.	-1	FBN1	HGNC	3603	protein_coding	YES	CCDS32232.1	ENSP00000325527	FBN1_HUMAN	Q75N89_HUMAN,Q75N88_HUMAN,H0YN80_HUMAN	UPI0000163B0B	.	.	probably_damaging(0.942)	61/66	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,PIRSF_domain:PIRSF036312,SMART_domains:SM00181,Superfamily_domains:SSF57184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCGGGAGGAC	.	5	ESCA
CHRNB4	0	.	GRCh37	15	78921615	78921615	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1032C>A	p.Phe344Leu	p.F344L	ENST00000261751	5/6	48	23	25	68	68	0	CHRNB4,missense_variant,p.Phe344Leu,ENST00000261751,;CHRNB4,intron_variant,,ENST00000412074,;RP11-335K5.2,downstream_gene_variant,,ENST00000559120,;CHRNB4,downstream_gene_variant,,ENST00000560511,;CHRNB4,downstream_gene_variant,,ENST00000559849,;	T	ENSG00000117971	ENST00000261751	Transcript	missense_variant	1144	1032	344	F/L	ttC/ttA	.	.	.	-1	CHRNB4	HGNC	1964	protein_coding	YES	CCDS10306.1	ENSP00000261751	ACHB4_HUMAN	.	UPI0000125276	.	tolerated(1)	benign(0.034)	5/6	.	hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF385,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAGGAAGGT	.	5	ESCA
GPRC5B	0	.	GRCh37	16	19883970	19883970	+	Silent	SNP	G	G	A	rs775838103	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.198C>T	p.%3D	p.G66G	ENST00000300571	2/4	66	52	14	84	84	0	GPRC5B,synonymous_variant,p.%3D,ENST00000562469,;GPRC5B,synonymous_variant,p.%3D,ENST00000300571,;GPRC5B,synonymous_variant,p.%3D,ENST00000537135,;GPRC5B,synonymous_variant,p.%3D,ENST00000569847,;GPRC5B,synonymous_variant,p.%3D,ENST00000569479,;GPRC5B,synonymous_variant,p.%3D,ENST00000566822,;GPRC5B,synonymous_variant,p.%3D,ENST00000535671,;GPRC5B,synonymous_variant,p.%3D,ENST00000568214,;GPRC5B,synonymous_variant,p.%3D,ENST00000570142,;GPRC5B,downstream_gene_variant,,ENST00000564449,;	A	ENSG00000167191	ENST00000300571	Transcript	synonymous_variant	390	198	66	G	ggC/ggT	rs775838103	.	.	-1	GPRC5B	HGNC	13308	protein_coding	YES	CCDS10581.1	ENSP00000300571	GPC5B_HUMAN	H3BT93_HUMAN,H3BT47_HUMAN,H3BSJ1_HUMAN,H3BQV9_HUMAN,H3BN33_HUMAN	UPI0000032747	.	.	.	2/4	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR14511:SF9,hmmpanther:PTHR14511,Pfam_domain:PF00003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGCGCCCGC	byFrequency	5	ESCA
RABEP2	0	.	GRCh37	16	28920007	28920007	+	Missense_Mutation	SNP	C	C	T	rs757390295	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1168G>A	p.Glu390Lys	p.E390K	ENST00000358201	8/13	60	41	19	78	78	0	RABEP2,missense_variant,p.Glu319Lys,ENST00000544477,;RABEP2,missense_variant,p.Glu390Lys,ENST00000358201,;RABEP2,missense_variant,p.Glu358Lys,ENST00000357573,;ATP2A1,downstream_gene_variant,,ENST00000395503,;ATP2A1,downstream_gene_variant,,ENST00000536376,;ATP2A1,downstream_gene_variant,,ENST00000564112,;ATP2A1,downstream_gene_variant,,ENST00000357084,;RABEP2,downstream_gene_variant,,ENST00000562590,;	T	ENSG00000177548	ENST00000358201	Transcript	missense_variant	1757	1168	390	E/K	Gag/Aag	rs757390295	.	.	-1	RABEP2	HGNC	24817	protein_coding	YES	CCDS42140.1	ENSP00000350934	RABE2_HUMAN	H3BU67_HUMAN,H3BNR8_HUMAN,H3BNR2_HUMAN	UPI0000367822	.	tolerated(1)	possibly_damaging(0.474)	8/13	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31179:SF6,hmmpanther:PTHR31179,Pfam_domain:PF09311	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCGGCCC	byFrequency	5	ESCA
LINC00514	0	.	GRCh37	16	3041080	3041080	+	RNA	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.231C>T	.	.	ENST00000571152	3/4	28	11	17	44	44	0	LINC00514,non_coding_transcript_exon_variant,,ENST00000571152,;LINC00514,non_coding_transcript_exon_variant,,ENST00000573465,;LINC00514,non_coding_transcript_exon_variant,,ENST00000572266,;	T	ENSG00000262152	ENST00000571152	Transcript	non_coding_transcript_exon_variant	231	.	.	.	.	.	.	.	1	LINC00514	HGNC	27549	lincRNA	YES	.	.	.	.	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCCCAGT	.	5	ESCA
SEPHS2	0	.	GRCh37	16	30455361	30455361	+	3'Flank	SNP	A	A	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000500504	.	49	44	4	60	60	0	SEPHS2,3_prime_UTR_variant,,ENST00000478753,;SEPHS2,3_prime_UTR_variant,,ENST00000542752,;SEPHS2,downstream_gene_variant,,ENST00000500504,;	T	ENSG00000179918	ENST00000500504	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	341	-1	SEPHS2	HGNC	19686	protein_coding	YES	CCDS42150.1	ENSP00000426234	SPS2_HUMAN	B4E093_HUMAN	UPI00001678A0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTTAATAATC	.	2	ESCA
MMP25	0	.	GRCh37	16	3105828	3105828	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.662-1206C>G	.	.	ENST00000336577	.	38	10	27	30	30	0	MMP25,intron_variant,,ENST00000336577,;RP11-473M20.7,non_coding_transcript_exon_variant,,ENST00000576250,;RP11-473M20.7,non_coding_transcript_exon_variant,,ENST00000572574,;RP11-473M20.7,non_coding_transcript_exon_variant,,ENST00000573130,;RP11-473M20.7,non_coding_transcript_exon_variant,,ENST00000572930,;RP11-473M20.7,non_coding_transcript_exon_variant,,ENST00000573878,;RP11-473M20.7,non_coding_transcript_exon_variant,,ENST00000570949,;RP11-473M20.7,downstream_gene_variant,,ENST00000573953,;RP11-473M20.7,upstream_gene_variant,,ENST00000597579,;RP11-473M20.7,downstream_gene_variant,,ENST00000572222,;RP11-473M20.7,downstream_gene_variant,,ENST00000572427,;MMP25,splice_region_variant,,ENST00000570755,;MMP25,upstream_gene_variant,,ENST00000575441,;	G	ENSG00000008516	ENST00000336577	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MMP25	HGNC	14246	protein_coding	YES	CCDS10492.1	ENSP00000337816	MMP25_HUMAN	.	UPI000003DC71	.	.	.	.	4/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTTCAGGCC	.	5	ESCA
CORO7	0	.	GRCh37	16	4407996	4407996	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2566A>G	p.Ser856Gly	p.S856G	ENST00000251166	25/28	38	12	26	43	43	0	CORO7,missense_variant,p.Ser636Gly,ENST00000539968,;CORO7,missense_variant,p.Ser771Gly,ENST00000574025,;CORO7-PAM16,missense_variant,p.Ser856Gly,ENST00000572467,;CORO7,missense_variant,p.Ser65Gly,ENST00000570779,;CORO7,missense_variant,p.Ser838Gly,ENST00000537233,;CORO7,missense_variant,p.Ser856Gly,ENST00000251166,;PAM16,upstream_gene_variant,,ENST00000576217,;CORO7,downstream_gene_variant,,ENST00000423908,;CORO7-PAM16,non_coding_transcript_exon_variant,,ENST00000572274,;CORO7-PAM16,3_prime_UTR_variant,,ENST00000575334,;CORO7,3_prime_UTR_variant,,ENST00000571227,;CORO7,non_coding_transcript_exon_variant,,ENST00000575714,;CORO7,non_coding_transcript_exon_variant,,ENST00000574849,;CORO7,non_coding_transcript_exon_variant,,ENST00000575531,;CORO7,intron_variant,,ENST00000576637,;CORO7,downstream_gene_variant,,ENST00000571756,;CORO7,downstream_gene_variant,,ENST00000576437,;CORO7,downstream_gene_variant,,ENST00000572666,;CORO7,downstream_gene_variant,,ENST00000574311,;CORO7,downstream_gene_variant,,ENST00000573773,;CORO7,downstream_gene_variant,,ENST00000572125,;	C	ENSG00000262246	ENST00000251166	Transcript	missense_variant	2712	2566	856	S/G	Agc/Ggc	.	.	.	-1	CORO7	HGNC	26161	protein_coding	YES	CCDS10513.1	ENSP00000251166	CORO7_HUMAN	I3L258_HUMAN,B3KSY4_HUMAN	UPI00001FF898	.	deleterious(0.01)	possibly_damaging(0.764)	25/28	.	hmmpanther:PTHR10856:SF20,hmmpanther:PTHR10856,Pfam_domain:PF08954	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGCTGAGAA	.	5	ESCA
CBLN1	0	.	GRCh37	16	49313380	49313380	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.517C>T	p.Arg173Trp	p.R173W	ENST00000219197	3/3	79	61	17	99	99	0	CBLN1,missense_variant,p.Arg173Trp,ENST00000536749,;CBLN1,missense_variant,p.Arg173Trp,ENST00000219197,;CBLN1,3_prime_UTR_variant,,ENST00000564786,;	A	ENSG00000102924	ENST00000219197	Transcript	missense_variant	883	517	173	R/W	Cgg/Tgg	.	.	.	-1	CBLN1	HGNC	1543	protein_coding	YES	CCDS10736.1	ENSP00000219197	CBLN1_HUMAN	.	UPI0000127506	.	deleterious(0)	probably_damaging(0.988)	3/3	.	PROSITE_profiles:PS50871,hmmpanther:PTHR22923:SF5,hmmpanther:PTHR22923,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCCGCTCCA	.	5	ESCA
CYLD	0	.	GRCh37	16	50818332	50818332	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1919T>C	p.Leu640Pro	p.L640P	ENST00000427738	11/18	103	97	6	67	67	0	CYLD,missense_variant,p.Leu455Pro,ENST00000568704,;CYLD,missense_variant,p.Leu637Pro,ENST00000564326,;CYLD,missense_variant,p.Leu637Pro,ENST00000569418,;CYLD,missense_variant,p.Leu637Pro,ENST00000566206,;CYLD,missense_variant,p.Leu640Pro,ENST00000540145,;CYLD,missense_variant,p.Leu640Pro,ENST00000427738,;CYLD,missense_variant,p.Leu637Pro,ENST00000398568,;CYLD,missense_variant,p.Leu640Pro,ENST00000311559,;RP11-327F22.4,intron_variant,,ENST00000564510,;RP11-327F22.4,intron_variant,,ENST00000575917,;CYLD,non_coding_transcript_exon_variant,,ENST00000563629,;CYLD,non_coding_transcript_exon_variant,,ENST00000569891,;	C	ENSG00000083799	ENST00000427738	Transcript	missense_variant	2124	1919	640	L/P	cTg/cCg	.	.	.	1	CYLD	HGNC	2584	protein_coding	YES	CCDS45482.1	ENSP00000392025	CYLD_HUMAN	H3BTB8_HUMAN,H3BSW9_HUMAN,H3BPZ5_HUMAN	UPI0000073A15	.	deleterious(0)	probably_damaging(0.998)	11/18	.	PROSITE_profiles:PS50235,hmmpanther:PTHR11830:SF3,hmmpanther:PTHR11830,Pfam_domain:PF00443,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTACTGAGGA	.	2	ESCA
RAB11FIP3	0	.	GRCh37	16	570264	570264	+	Missense_Mutation	SNP	G	G	A	rs752293510	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2003G>A	p.Arg668His	p.R668H	ENST00000262305	12/14	18	12	6	11	11	0	RAB11FIP3,missense_variant,p.Arg589His,ENST00000434585,;RAB11FIP3,missense_variant,p.Arg372His,ENST00000450428,;RAB11FIP3,missense_variant,p.Arg713His,ENST00000457159,;RAB11FIP3,missense_variant,p.Arg668His,ENST00000262305,;RAB11FIP3,downstream_gene_variant,,ENST00000461009,;RAB11FIP3,downstream_gene_variant,,ENST00000487899,;RAB11FIP3,downstream_gene_variant,,ENST00000464263,;	A	ENSG00000090565	ENST00000262305	Transcript	missense_variant	2391	2003	668	R/H	cGc/cAc	rs752293510	.	.	1	RAB11FIP3	HGNC	17224	protein_coding	YES	CCDS32351.1	ENSP00000262305	RFIP3_HUMAN	F6X994_HUMAN	UPI0000129C9C	.	tolerated(0.08)	benign(0.126)	12/14	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15726,hmmpanther:PTHR15726:SF6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGTCCGCAGGC	.	2	ESCA
C16orf80	0	.	GRCh37	16	58163023	58163023	+	5'UTR	SNP	G	G	A	rs763694566	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4C>T	.	.	ENST00000262498	1/6	145	35	110	107	107	0	C16orf80,5_prime_UTR_variant,,ENST00000262498,;C16orf80,5_prime_UTR_variant,,ENST00000565880,;RP11-459F6.3,upstream_gene_variant,,ENST00000569580,;C16orf80,non_coding_transcript_exon_variant,,ENST00000567660,;C16orf80,non_coding_transcript_exon_variant,,ENST00000567092,;C16orf80,non_coding_transcript_exon_variant,,ENST00000562622,;	A	ENSG00000070761	ENST00000262498	Transcript	5_prime_UTR_variant	332	.	.	.	.	rs763694566	.	.	-1	C16orf80	HGNC	29523	protein_coding	YES	CCDS10793.1	ENSP00000262498	CP080_HUMAN	.	UPI000006E0AD	.	.	.	1/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCGCCGGC	.	5	ESCA
HYDIN	0	.	GRCh37	16	70884449	70884449	+	Missense_Mutation	SNP	C	C	T	rs750919238	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.12553G>A	p.Glu4185Lys	p.E4185K	ENST00000393567	74/86	46	15	31	44	44	0	HYDIN,missense_variant,p.Glu4185Lys,ENST00000393567,;RNU6ATAC25P,upstream_gene_variant,,ENST00000408798,;HYDIN,3_prime_UTR_variant,,ENST00000378856,;	T	ENSG00000157423	ENST00000393567	Transcript	missense_variant	12704	12553	4185	E/K	Gag/Aag	rs750919238,COSM212801,COSM161640	.	.	-1	HYDIN	HGNC	19368	protein_coding	YES	CCDS59269.1	ENSP00000377197	HYDIN_HUMAN	K0A1M3_HUMAN,I1Z9D0_HUMAN,F5H8I6_HUMAN,F5GXK3_HUMAN	UPI0001FEF4F9	.	.	possibly_damaging(0.81)	74/86	.	hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF5	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E4184K|c.12550G>A|3,BUFFER|p.E4136K|c.12406G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCGGCCT	.	5	ESCA
ZFHX3	0	.	GRCh37	16	72828297	72828297	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8284G>T	p.Gly2762Ter	p.G2762*	ENST00000268489	9/10	46	9	37	34	34	0	ZFHX3,stop_gained,p.Gly1848Ter,ENST00000397992,;ZFHX3,stop_gained,p.Gly2762Ter,ENST00000268489,;RP5-991G20.4,downstream_gene_variant,,ENST00000569195,;	A	ENSG00000140836	ENST00000268489	Transcript	stop_gained	8957	8284	2762	G/*	Gga/Tga	.	.	.	-1	ZFHX3	HGNC	777	protein_coding	YES	CCDS10908.1	ENSP00000268489	ZFHX3_HUMAN	Q6TCJ2_HUMAN	UPI00001AE937	.	.	.	9/10	.	hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTCCTTTCA	.	5	ESCA
CLEC18B	0	.	GRCh37	16	74455186	74455186	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-18G>C	.	.	ENST00000339953	1/13	129	73	55	82	82	0	CLEC18B,5_prime_UTR_variant,,ENST00000339953,;RP11-252A24.5,upstream_gene_variant,,ENST00000566506,;RP11-252A24.5,upstream_gene_variant,,ENST00000567148,;CLEC18B,non_coding_transcript_exon_variant,,ENST00000425714,;	G	ENSG00000140839	ENST00000339953	Transcript	5_prime_UTR_variant	105	.	.	.	.	.	.	.	-1	CLEC18B	HGNC	33849	protein_coding	YES	CCDS32484.1	ENSP00000341051	CL18B_HUMAN	.	UPI000025210E	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGTCAGGCG	.	5	ESCA
SLC38A8	0	.	GRCh37	16	84075670	84075670	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.93C>A	p.Phe31Leu	p.F31L	ENST00000299709	1/10	98	19	78	49	49	0	SLC38A8,missense_variant,p.Phe31Leu,ENST00000299709,;SLC38A8,missense_variant,p.Phe31Leu,ENST00000568178,;SLC38A8,upstream_gene_variant,,ENST00000569816,;RNA5SP432,upstream_gene_variant,,ENST00000362480,;	T	ENSG00000166558	ENST00000299709	Transcript	missense_variant	93	93	31	F/L	ttC/ttA	.	.	.	-1	SLC38A8	HGNC	32434	protein_coding	YES	CCDS32495.1	ENSP00000299709	S38A8_HUMAN	H3BUP5_HUMAN,H3BP02_HUMAN	UPI0000D61A1F	.	deleterious(0)	probably_damaging(0.955)	1/10	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22950:SF226,hmmpanther:PTHR22950,Pfam_domain:PF01490	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGAAGAC	.	5	ESCA
SNORD3B-1	0	.	GRCh37	17	18965435	18965435	+	RNA	SNP	G	G	A	rs770265522	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.211G>A	.	.	ENST00000577988	1/1	22	14	8	26	26	0	SNORD3B-1,non_coding_transcript_exon_variant,,ENST00000577988,;SNORD3B-1,non_coding_transcript_exon_variant,,ENST00000363359,;SNORD3B-2,downstream_gene_variant,,ENST00000364880,;SNORD3B-2,downstream_gene_variant,,ENST00000571722,;	A	ENSG00000265185	ENST00000577988	Transcript	non_coding_transcript_exon_variant	211	.	.	.	.	rs770265522	.	.	1	SNORD3B-1	HGNC	10168	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GGTCTGAGTGG	byFrequency	3	ESCA
SUPT6H	0	.	GRCh37	17	27002024	27002024	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.382G>A	p.Glu128Lys	p.E128K	ENST00000314616	5/37	62	50	12	46	46	0	SUPT6H,missense_variant,p.Glu128Lys,ENST00000314616,;SUPT6H,missense_variant,p.Glu128Lys,ENST00000347486,;SUPT6H,downstream_gene_variant,,ENST00000577713,;AC010761.13,upstream_gene_variant,,ENST00000578819,;SUPT6H,non_coding_transcript_exon_variant,,ENST00000584285,;SUPT6H,downstream_gene_variant,,ENST00000584312,;	A	ENSG00000109111	ENST00000314616	Transcript	missense_variant	665	382	128	E/K	Gag/Aag	.	.	.	1	SUPT6H	HGNC	11470	protein_coding	YES	CCDS32596.1	ENSP00000319104	SPT6H_HUMAN	J3QS64_HUMAN	UPI000015FFA7	.	deleterious(0.02)	unknown(0)	5/37	.	PIRSF_domain:PIRSF036947,Pfam_domain:PF14632,hmmpanther:PTHR10145:SF6,hmmpanther:PTHR10145,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACGAGGAC	.	5	ESCA
MLLT6	0	.	GRCh37	17	36876638	36876638	+	Silent	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2169G>C	p.%3D	p.L723L	ENST00000325718	15/20	31	14	17	32	32	0	MLLT6,synonymous_variant,p.%3D,ENST00000325718,;MLLT6,synonymous_variant,p.%3D,ENST00000471200,;MIR4726,downstream_gene_variant,,ENST00000577947,;CTB-58E17.9,upstream_gene_variant,,ENST00000579499,;MLLT6,non_coding_transcript_exon_variant,,ENST00000494578,;MLLT6,downstream_gene_variant,,ENST00000466997,;MLLT6,downstream_gene_variant,,ENST00000578946,;MLLT6,upstream_gene_variant,,ENST00000484263,;MLLT6,downstream_gene_variant,,ENST00000433891,;	C	ENSG00000108292	ENST00000325718	Transcript	synonymous_variant	2260	2169	723	L	ctG/ctC	.	.	.	1	MLLT6	HGNC	7138	protein_coding	YES	CCDS11327.1	ENSP00000316426	AF17_HUMAN	.	UPI000013C86A	.	.	.	15/20	.	hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF82,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGCTGAAGGC	.	5	ESCA
MBTD1	0	.	GRCh37	17	49296311	49296311	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.383A>G	p.Asn128Ser	p.N128S	ENST00000586178	5/17	85	16	68	51	51	0	MBTD1,missense_variant,p.Asn128Ser,ENST00000376381,;MBTD1,missense_variant,p.Asn128Ser,ENST00000415868,;MBTD1,missense_variant,p.Asn128Ser,ENST00000586178,;MBTD1,missense_variant,p.Asn128Ser,ENST00000405860,;MBTD1,non_coding_transcript_exon_variant,,ENST00000591270,;	C	ENSG00000011258	ENST00000586178	Transcript	missense_variant	727	383	128	N/S	aAt/aGt	.	.	.	-1	MBTD1	HGNC	19866	protein_coding	YES	CCDS11581.2	ENSP00000468304	MBTD1_HUMAN	.	UPI00015DE7E3	.	tolerated(0.49)	benign(0.001)	5/17	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12247	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTGATTTTGC	.	5	ESCA
NLRP1	0	.	GRCh37	17	5486100	5486100	+	Missense_Mutation	SNP	G	G	A	rs201858694	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.338C>T	p.Ser113Phe	p.S113F	ENST00000572272	2/17	52	31	21	69	69	0	NLRP1,missense_variant,p.Ser113Phe,ENST00000572272,;NLRP1,missense_variant,p.Ser113Phe,ENST00000345221,;NLRP1,missense_variant,p.Ser113Phe,ENST00000269280,;NLRP1,missense_variant,p.Ser113Phe,ENST00000354411,;NLRP1,missense_variant,p.Ser113Phe,ENST00000577119,;NLRP1,missense_variant,p.Ser113Phe,ENST00000262467,;NLRP1,downstream_gene_variant,,ENST00000576905,;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,downstream_gene_variant,,ENST00000572143,;NLRP1,missense_variant,p.Ser113Phe,ENST00000544378,;NLRP1,missense_variant,p.Ser113Phe,ENST00000571451,;	A	ENSG00000091592	ENST00000572272	Transcript	missense_variant	338	338	113	S/F	tCc/tTc	rs201858694,COSM3958573,COSM3958572,COSM3958571	.	.	-1	NLRP1	HGNC	14374	protein_coding	YES	CCDS42246.1	ENSP00000460475	NALP1_HUMAN	I3L2G5_HUMAN,I3L0S2_HUMAN	UPI0000038309	.	deleterious(0.03)	probably_damaging(0.921)	2/17	.	hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF13	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGTGGAGGTG	.	5	ESCA
XAF1	0	.	GRCh37	17	6676639	6676639	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*151C>A	.	.	ENST00000361842	7/7	94	67	26	36	36	0	XAF1,3_prime_UTR_variant,,ENST00000361842,;XAF1,3_prime_UTR_variant,,ENST00000346752,;XAF1,3_prime_UTR_variant,,ENST00000441631,;FBXO39,upstream_gene_variant,,ENST00000321535,;XAF1,3_prime_UTR_variant,,ENST00000571217,;XAF1,downstream_gene_variant,,ENST00000571673,;XAF1,downstream_gene_variant,,ENST00000576724,;XAF1,downstream_gene_variant,,ENST00000575369,;XAF1,downstream_gene_variant,,ENST00000574962,;XAF1,downstream_gene_variant,,ENST00000573518,;	A	ENSG00000132530	ENST00000361842	Transcript	3_prime_UTR_variant	1296	.	.	.	.	.	.	.	1	XAF1	HGNC	30932	protein_coding	YES	CCDS11080.1	ENSP00000354822	XAF1_HUMAN	I3L3D9_HUMAN	UPI000020078D	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAACTCACGTA	.	5	ESCA
ABCA9	0	.	GRCh37	17	67039531	67039531	+	Intron	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.800+99G>T	.	.	ENST00000340001	.	9	5	4	13	13	0	ABCA9,3_prime_UTR_variant,,ENST00000495634,;ABCA9,intron_variant,,ENST00000370732,;ABCA9,intron_variant,,ENST00000453985,;ABCA9,intron_variant,,ENST00000340001,;ABCA9,intron_variant,,ENST00000461623,;	A	ENSG00000154258	ENST00000340001	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ABCA9	HGNC	39	protein_coding	YES	CCDS11681.1	ENSP00000342216	ABCA9_HUMAN	K7EJJ0_HUMAN	UPI00000747B1	.	.	.	.	6/38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	GCAGTCTGTGG	.	2	ESCA
NXN	0	.	GRCh37	17	704261	704261	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1236G>C	p.Glu412Asp	p.E412D	ENST00000336868	8/8	79	47	32	94	94	0	NXN,missense_variant,p.Glu304Asp,ENST00000575801,;NXN,missense_variant,p.Glu207Asp,ENST00000571684,;NXN,missense_variant,p.Glu163Asp,ENST00000537628,;NXN,missense_variant,p.Glu103Asp,ENST00000538650,;NXN,missense_variant,p.Glu412Asp,ENST00000336868,;NXN,non_coding_transcript_exon_variant,,ENST00000574018,;NXN,non_coding_transcript_exon_variant,,ENST00000571281,;	G	ENSG00000167693	ENST00000336868	Transcript	missense_variant	1328	1236	412	E/D	gaG/gaC	.	.	.	-1	NXN	HGNC	18008	protein_coding	YES	CCDS10998.1	ENSP00000337443	NXN_HUMAN	.	UPI00001B31EB	.	tolerated(0.17)	probably_damaging(0.978)	8/8	.	hmmpanther:PTHR13871,Pfam_domain:PF13848,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATCTCCTC	.	5	ESCA
WBP2	0	.	GRCh37	17	73843668	73843669	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.554dupT	p.Met185IlefsTer74	p.M185Ifs*74	ENST00000591399	7/9	152	102	50	96	96	0	WBP2,frameshift_variant,p.Met140IlefsTer74,ENST00000433525,;WBP2,frameshift_variant,p.Met181IlefsTer74,ENST00000590221,;WBP2,frameshift_variant,p.Met185IlefsTer74,ENST00000591399,;WBP2,frameshift_variant,p.Met119IlefsTer?,ENST00000589642,;WBP2,frameshift_variant,p.Met84IlefsTer74,ENST00000586257,;WBP2,frameshift_variant,p.Met105IlefsTer?,ENST00000587374,;WBP2,frameshift_variant,p.Met185IlefsTer74,ENST00000254806,;WBP2,frameshift_variant,p.Met163IlefsTer74,ENST00000585462,;WBP2,frameshift_variant,p.Met163IlefsTer?,ENST00000593002,;WBP2,frameshift_variant,p.Met163IlefsTer74,ENST00000344296,;UNC13D,upstream_gene_variant,,ENST00000590762,;UNC13D,upstream_gene_variant,,ENST00000412096,;UNC13D,upstream_gene_variant,,ENST00000592386,;UNC13D,upstream_gene_variant,,ENST00000586147,;UNC13D,upstream_gene_variant,,ENST00000586108,;UNC13D,upstream_gene_variant,,ENST00000207549,;UNC13D,upstream_gene_variant,,ENST00000585574,;UNC13D,upstream_gene_variant,,ENST00000587504,;WBP2,downstream_gene_variant,,ENST00000590450,;WBP2,frameshift_variant,p.Met185IlefsTer90,ENST00000591831,;WBP2,3_prime_UTR_variant,,ENST00000588373,;WBP2,non_coding_transcript_exon_variant,,ENST00000589236,;WBP2,non_coding_transcript_exon_variant,,ENST00000587642,;WBP2,non_coding_transcript_exon_variant,,ENST00000416574,;WBP2,downstream_gene_variant,,ENST00000589241,;WBP2,downstream_gene_variant,,ENST00000592802,;UNC13D,upstream_gene_variant,,ENST00000588774,;WBP2,downstream_gene_variant,,ENST00000589834,;UNC13D,upstream_gene_variant,,ENST00000591563,;	A	ENSG00000132471	ENST00000591399	Transcript	frameshift_variant	979-980	554-555	185	M/IX	atg/atTg	.	.	.	-1	WBP2	HGNC	12738	protein_coding	YES	CCDS11731.1	ENSP00000467579	WBP2_HUMAN	K7ESN4_HUMAN,K7EIJ0_HUMAN,A6NG10_HUMAN	UPI0000138EBB	.	.	.	7/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR31606:SF4,hmmpanther:PTHR31606,Pfam_domain:PF10349	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCCATCATGGG	.	3	ESCA
QRICH2	0	.	GRCh37	17	74303665	74303665	+	5'UTR	SNP	C	C	T	rs146819251	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-84G>A	.	.	ENST00000262765	1/19	95	90	5	54	54	0	QRICH2,5_prime_UTR_variant,,ENST00000262765,;PRPSAP1,downstream_gene_variant,,ENST00000324684,;PRPSAP1,downstream_gene_variant,,ENST00000446526,;PRPSAP1,downstream_gene_variant,,ENST00000588364,;QRICH2,upstream_gene_variant,,ENST00000524722,;	T	ENSG00000129646	ENST00000262765	Transcript	5_prime_UTR_variant	97	.	.	.	.	rs146819251	.	.	-1	QRICH2	HGNC	25326	protein_coding	YES	CCDS32741.1	ENSP00000262765	QRIC2_HUMAN	.	UPI000006FECD	.	.	.	1/19	.	.	A:0.0054	A:0.0197	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAGCCCGCTGG	byFrequency|byCluster|by1000G	2	ESCA
TP53	0	.	GRCh37	17	7578271	7578271	+	Missense_Mutation	SNP	T	T	C	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578A>G	p.His193Arg	p.H193R	ENST00000269305	6/11	80	23	57	60	60	0	TP53,missense_variant,p.His193Arg,ENST00000413465,;TP53,missense_variant,p.His193Arg,ENST00000420246,;TP53,missense_variant,p.His193Arg,ENST00000269305,;TP53,missense_variant,p.His61Arg,ENST00000509690,;TP53,missense_variant,p.His193Arg,ENST00000359597,;TP53,missense_variant,p.His100Arg,ENST00000514944,;TP53,missense_variant,p.His193Arg,ENST00000445888,;TP53,missense_variant,p.His193Arg,ENST00000455263,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;	C	ENSG00000141510	ENST00000269305	Transcript	missense_variant	768	578	193	H/R	cAt/cGt	CM083194,CM951225,TP53_g.12647A>T,TP53_g.12647A>C,TP53_g.12647A>G,COSM10742,COSM11066,COSM43833,COSM308307,COSM99919,COSM131458,COSM131459,COSM99916,COSM308306,COSM99917,COSM308308,COSM131461,COSM3820719,COSM3970355,COSM3732881,COSM1740322,COSM2744772,COSM3970354,COSM308309,COSM131460,COSM99918	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	6/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.H193R|c.578A>G|8,SITE|p.H193R|c.578A>G|89,SITE|p.H61R|c.182A>G|23,SITE|p.H193R|c.578A>G|21,SITE|p.H193R|c.578A>G|22,SITE|p.H100R|c.299A>G|22,SITE|p.H193R|c.578A>G|5,CODON|p.0?|c.1_1182del1182|6,CODON|p.A189_V197delAPPQHLIRV|c.565_591del27|4,CODON|p.H193fs*16|c.577_578insN|3,CODON|p.H193L|c.578A>T|8,CODON|p.H61P|c.182A>C|4,CODON|p.H100L|c.299A>T|8,CODON|p.H193L|c.578A>T|8,CODON|p.H100P|c.299A>C|4,CODON|p.H193P|c.578A>C|4,CODON|p.H193L|c.578A>T|3,CODON|p.H193L|c.578A>T|3,CODON|p.H193P|c.578A>C|16,CODON|p.H193P|c.578A>C|3,CODON|p.H193L|c.578A>T|37,CODON|p.H61L|c.182A>T|10,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.V65L|c.193G>T|3,BUFFER|p.V197M|c.589G>A|12,BUFFER|p.V197L|c.589G>T|5,BUFFER|p.V104L|c.310G>T|3,BUFFER|p.V197L|c.589G>T|3,BUFFER|p.R196R|c.588A>G|4,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R196P|c.587G>C|18,BUFFER|p.R64P|c.191G>C|7,BUFFER|p.R196Q|c.587G>A|4,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196P|c.587G>C|6,BUFFER|p.R103P|c.308G>C|7,BUFFER|p.R196P|c.587G>C|3,BUFFER|p.R196*|c.585_586CC>TT|7,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R64fs*>27|c.190delC|3,BUFFER|p.R196fs*51|c.586delC|3,BUFFER|p.R103fs*51|c.307delC|3,BUFFER|p.R196fs*51|c.586delC|7,BUFFER|p.R64*|c.190C>T|65,BUFFER|p.R196*|c.586C>T|45,BUFFER|p.R196*|c.586C>T|33,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R196*|c.586C>T|64,BUFFER|p.R103*|c.307C>T|64,BUFFER|p.R196*|c.586C>T|180,BUFFER|p.I102N|c.305T>A|10,BUFFER|p.I102T|c.305T>C|21,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I63S|c.188T>G|3,BUFFER|p.I195T|c.584T>C|88,BUFFER|p.I195N|c.584T>A|4,BUFFER|p.I195T|c.584T>C|21,BUFFER|p.I63N|c.188T>A|10,BUFFER|p.I195T|c.584T>C|12,BUFFER|p.I63T|c.188T>C|21,BUFFER|p.I195T|c.584T>C|21,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I195N|c.584T>A|23,BUFFER|p.I195T|c.584T>C|10,BUFFER|p.I195N|c.584T>A|10,BUFFER|p.I195S|c.584T>G|7,BUFFER|p.I195F|c.583A>T|6,BUFFER|p.I195F|c.583A>T|28,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.I63F|c.187A>T|9,BUFFER|p.I102F|c.304A>T|9,BUFFER|p.I195F|c.583A>T|5,BUFFER|p.I195F|c.583A>T|9,BUFFER|p.L194L|c.582T>C|3,BUFFER|p.L62R|c.185T>G|17,BUFFER|p.L194R|c.581T>G|50,BUFFER|p.L194R|c.581T>G|11,BUFFER|p.L194H|c.581T>A|6,BUFFER|p.L194P|c.581T>C|9,BUFFER|p.L101R|c.302T>G|17,BUFFER|p.L194R|c.581T>G|9,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194R|c.581T>G|17,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|3,BUFFER|p.L194F|c.580C>T|19,BUFFER|p.L101F|c.301C>T|3,BUFFER|p.L62F|c.184C>T|3,BUFFER|p.H193N|c.577C>A|6,BUFFER|p.H193D|c.577C>G|8,BUFFER|p.H193Y|c.577C>T|5,BUFFER|p.H193Y|c.577C>T|40,BUFFER|p.H100Y|c.298C>T|15,BUFFER|p.H193Y|c.577C>T|15,BUFFER|p.H61Y|c.181C>T|15,BUFFER|p.H193Y|c.577C>T|15,BUFFER|p.H193Y|c.577C>T|3,BUFFER|p.Q192H|c.576G>T|3,BUFFER|p.Q192Q|c.576G>A|3,BUFFER|p.Q192R|c.575A>G|5,BUFFER|p.P191delP|c.572_574delCTC|3,BUFFER|p.P191delP|c.572_574delCTC|3,BUFFER|p.P191delP|c.572_574delCTC|5,BUFFER|p.P59delP|c.176_178delCTC|3,BUFFER|p.P98delP|c.293_295delCTC|3,BUFFER|p.Q192*|c.574C>T|6,BUFFER|p.Q99*|c.295C>T|17,BUFFER|p.Q192*|c.574C>T|10,BUFFER|p.Q192*|c.574C>T|17,BUFFER|p.Q192*|c.574C>T|86,BUFFER|p.Q192*|c.574C>T|17,BUFFER|p.Q60*|c.178C>T|17,BUFFER|p.P191fs*56|c.571delC|3,BUFFER|p.P191L|c.572C>T|3,BUFFER|p.P191delP|c.568_570delCCT|6,BUFFER|p.P190fs*57|c.569delC|4,BUFFER|p.P190L|c.569C>T|4,BUFFER|p.P97L|c.290C>T|6,BUFFER|p.P190L|c.569C>T|6,BUFFER|p.P190L|c.569C>T|30,BUFFER|p.P190R|c.569C>G|3,BUFFER|p.P190L|c.569C>T|6,BUFFER|p.P190L|c.569C>T|3,BUFFER|p.P58L|c.173C>T|6,BUFFER|p.P190T|c.568C>A|4,BUFFER|p.P190S|c.568C>T|8	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGATGCTGA	.	5	ESCA
CD7	0	.	GRCh37	17	80273253	80273253	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.667G>A	p.Glu223Lys	p.E223K	ENST00000312648	4/4	112	94	18	123	123	0	CD7,missense_variant,p.Glu123Lys,ENST00000583376,;CD7,missense_variant,p.Glu223Lys,ENST00000312648,;CD7,3_prime_UTR_variant,,ENST00000584284,;CD7,downstream_gene_variant,,ENST00000582480,;CD7,downstream_gene_variant,,ENST00000578509,;CD7,downstream_gene_variant,,ENST00000581434,;CD7,downstream_gene_variant,,ENST00000581744,;	T	ENSG00000173762	ENST00000312648	Transcript	missense_variant	774	667	223	E/K	Gag/Aag	.	.	.	-1	CD7	HGNC	1695	protein_coding	YES	CCDS11807.1	ENSP00000312027	CD7_HUMAN	Q29VG3_HUMAN,Q29VG2_HUMAN,J3QLC7_HUMAN	UPI00000359A4	.	deleterious(0)	probably_damaging(0.999)	4/4	.	hmmpanther:PTHR15343,hmmpanther:PTHR15343:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTCCTCGTACA	.	4	ESCA
ZNF750	0	.	GRCh37	17	80790258	80790258	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.73T>G	p.Tyr25Asp	p.Y25D	ENST00000269394	2/3	89	23	66	56	56	0	ZNF750,missense_variant,p.Tyr25Asp,ENST00000269394,;TBCD,intron_variant,,ENST00000539345,;TBCD,intron_variant,,ENST00000397466,;ZNF750,intron_variant,,ENST00000572562,;TBCD,intron_variant,,ENST00000355528,;	C	ENSG00000141579	ENST00000269394	Transcript	missense_variant	907	73	25	Y/D	Tat/Gat	.	.	.	-1	ZNF750	HGNC	25843	protein_coding	YES	CCDS11819.1	ENSP00000269394	ZN750_HUMAN	I3L0W7_HUMAN,B4DWV0_HUMAN	UPI000013D82D	.	deleterious(0)	probably_damaging(0.999)	2/3	.	hmmpanther:PTHR14678:SF1,hmmpanther:PTHR14678,Pfam_domain:PF15269	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATACTTGA	.	5	ESCA
PFAS	0	.	GRCh37	17	8158990	8158990	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555G>C	p.Glu185Asp	p.E185D	ENST00000314666	5/28	107	49	57	92	92	0	PFAS,missense_variant,p.Glu185Asp,ENST00000314666,;PFAS,intron_variant,,ENST00000545834,;PFAS,downstream_gene_variant,,ENST00000585183,;PFAS,downstream_gene_variant,,ENST00000581242,;PFAS,downstream_gene_variant,,ENST00000584044,;PFAS,intron_variant,,ENST00000580356,;	C	ENSG00000178921	ENST00000314666	Transcript	missense_variant	688	555	185	E/D	gaG/gaC	COSM40458	.	.	1	PFAS	HGNC	8863	protein_coding	YES	CCDS11136.1	ENSP00000313490	PUR4_HUMAN	Q9BR56_HUMAN,Q6P4B4_HUMAN,J3QSH6_HUMAN,J3QL39_HUMAN,J3KTL4_HUMAN,F5GWT9_HUMAN	UPI00001A95E5	.	deleterious(0.03)	possibly_damaging(0.71)	5/28	.	Superfamily_domains:0049526,TIGRFAM_domain:TIGR01735,hmmpanther:PTHR10099:SF1,hmmpanther:PTHR10099	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGGAGAAGGC	.	5	ESCA
USP43	0	.	GRCh37	17	9549132	9549132	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.183C>T	p.%3D	p.F61F	ENST00000285199	1/15	20	12	8	16	16	0	USP43,synonymous_variant,p.%3D,ENST00000570475,;USP43,synonymous_variant,p.%3D,ENST00000285199,;WDR16,downstream_gene_variant,,ENST00000574097,;WDR16,downstream_gene_variant,,ENST00000299764,;WDR16,downstream_gene_variant,,ENST00000352665,;WDR16,downstream_gene_variant,,ENST00000396219,;RP11-55L4.2,upstream_gene_variant,,ENST00000584676,;RP11-55L4.1,downstream_gene_variant,,ENST00000572923,;USP43,intron_variant,,ENST00000570827,;WDR16,downstream_gene_variant,,ENST00000576630,;	T	ENSG00000154914	ENST00000285199	Transcript	synonymous_variant	279	183	61	F	ttC/ttT	.	.	.	1	USP43	HGNC	20072	protein_coding	YES	CCDS45610.1	ENSP00000285199	UBP43_HUMAN	.	UPI0000047AFB	.	.	.	1/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24006:SF408,hmmpanther:PTHR24006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCGCCTG	.	5	ESCA
GAREM	0	.	GRCh37	18	29868054	29868054	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.506A>G	p.Lys169Arg	p.K169R	ENST00000269209	4/6	71	56	14	54	54	0	GAREM,missense_variant,p.Lys169Arg,ENST00000399218,;GAREM,missense_variant,p.Lys169Arg,ENST00000269209,;GAREM,upstream_gene_variant,,ENST00000583696,;RP11-344B2.2,non_coding_transcript_exon_variant,,ENST00000579580,;GAREM,non_coding_transcript_exon_variant,,ENST00000578619,;	C	ENSG00000141441	ENST00000269209	Transcript	missense_variant	510	506	169	K/R	aAg/aGg	.	.	.	-1	GAREM	HGNC	26136	protein_coding	YES	CCDS56057.1	ENSP00000269209	GAREM_HUMAN	.	UPI00005A72DA	.	tolerated(0.18)	possibly_damaging(0.596)	4/6	.	hmmpanther:PTHR14454:SF6,hmmpanther:PTHR14454,Pfam_domain:PF12736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCCTTGAAT	.	5	ESCA
COLEC12	0	.	GRCh37	18	333120	333120	+	Missense_Mutation	SNP	A	A	T	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1840T>A	p.Phe614Ile	p.F614I	ENST00000400256	7/10	55	42	12	40	40	0	COLEC12,missense_variant,p.Phe614Ile,ENST00000400256,;COLEC12,non_coding_transcript_exon_variant,,ENST00000582147,;	T	ENSG00000158270	ENST00000400256	Transcript	missense_variant	2048	1840	614	F/I	Ttc/Atc	COSM4072019	.	.	-1	COLEC12	HGNC	16016	protein_coding	YES	CCDS32782.1	ENSP00000383115	COL12_HUMAN	.	UPI00002018EC	.	deleterious(0)	unknown(0)	7/10	.	Superfamily_domains:SSF56436,SMART_domains:SM00034,Gene3D:3.10.100.10,hmmpanther:PTHR24021,hmmpanther:PTHR24021:SF19,PROSITE_profiles:PS50041	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGAAGTTCT	.	5	ESCA
KIAA1328	0	.	GRCh37	18	34740346	34740346	+	Splice_Site	SNP	T	T	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1414+2T>A	.	p.X472_splice	ENST00000280020	.	53	35	17	52	52	0	KIAA1328,splice_donor_variant,,ENST00000543923,;KIAA1328,splice_donor_variant,,ENST00000435985,;KIAA1328,splice_donor_variant,,ENST00000587139,;KIAA1328,splice_donor_variant,,ENST00000586135,;KIAA1328,splice_donor_variant,,ENST00000591619,;KIAA1328,splice_donor_variant,,ENST00000280020,;KIAA1328,splice_donor_variant,,ENST00000592611,;KIAA1328,splice_donor_variant,,ENST00000590617,;	A	ENSG00000150477	ENST00000280020	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	1	KIAA1328	HGNC	29248	protein_coding	YES	CCDS45855.1	ENSP00000280020	K1328_HUMAN	.	UPI00001C1FF0	.	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGGTAAGTT	.	5	ESCA
TMEM200C	0	.	GRCh37	18	5890406	5890406	+	Missense_Mutation	SNP	C	C	A	rs770578061	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1657G>T	p.Ala553Ser	p.A553S	ENST00000581347	3/3	51	43	7	38	38	0	TMEM200C,missense_variant,p.Ala553Ser,ENST00000383490,;TMEM200C,missense_variant,p.Ala553Ser,ENST00000581347,;RP11-945C19.4,intron_variant,,ENST00000577694,;RP11-945C19.4,downstream_gene_variant,,ENST00000580845,;RP11-945C19.4,downstream_gene_variant,,ENST00000582939,;	A	ENSG00000206432	ENST00000581347	Transcript	missense_variant	2303	1657	553	A/S	Gca/Tca	rs770578061	.	.	-1	TMEM200C	HGNC	37208	protein_coding	YES	CCDS45825.1	ENSP00000463375	T200C_HUMAN	.	UPI000020198E	.	tolerated(0.29)	benign(0.019)	3/3	.	hmmpanther:PTHR31815,hmmpanther:PTHR31815:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTGCGTCCA	byFrequency	5	ESCA
C19orf57	0	.	GRCh37	19	14001054	14001054	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615G>C	p.Gln205His	p.Q205H	ENST00000346736	6/8	93	75	17	62	62	0	C19orf57,missense_variant,p.Gln205His,ENST00000586783,;C19orf57,missense_variant,p.Gln205His,ENST00000454313,;C19orf57,missense_variant,p.Gln205His,ENST00000346736,;C19orf57,intron_variant,,ENST00000591586,;C19orf57,upstream_gene_variant,,ENST00000589393,;C19orf57,downstream_gene_variant,,ENST00000585755,;C19orf57,upstream_gene_variant,,ENST00000591439,;C19orf57,upstream_gene_variant,,ENST00000588115,;	G	ENSG00000132016	ENST00000346736	Transcript	missense_variant	743	615	205	Q/H	caG/caC	.	.	.	-1	C19orf57	HGNC	28153	protein_coding	YES	CCDS12299.1	ENSP00000254336	CS057_HUMAN	.	UPI0000070B0B	.	deleterious(0.01)	possibly_damaging(0.891)	6/8	.	hmmpanther:PTHR14583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCTGTGA	.	5	ESCA
AP1M1	0	.	GRCh37	19	16308764	16308764	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-74C>G	.	.	ENST00000444449	1/13	57	45	12	54	54	0	AP1M1,5_prime_UTR_variant,,ENST00000291439,;AP1M1,5_prime_UTR_variant,,ENST00000444449,;AP1M1,5_prime_UTR_variant,,ENST00000429941,;AP1M1,5_prime_UTR_variant,,ENST00000590263,;AP1M1,5_prime_UTR_variant,,ENST00000590756,;AP1M1,5_prime_UTR_variant,,ENST00000541844,;AP1M1,upstream_gene_variant,,ENST00000591775,;AP1M1,upstream_gene_variant,,ENST00000590945,;AP1M1,upstream_gene_variant,,ENST00000589822,;AP1M1,non_coding_transcript_exon_variant,,ENST00000589991,;	G	ENSG00000072958	ENST00000444449	Transcript	5_prime_UTR_variant	20	.	.	.	.	.	.	.	1	AP1M1	HGNC	13667	protein_coding	YES	CCDS46008.1	ENSP00000388996	AP1M1_HUMAN	Q59EK3_HUMAN,K7ER75_HUMAN,K7EQ90_HUMAN,K7EPJ8_HUMAN,K7ENA7_HUMAN	UPI000051DDEE	.	.	.	1/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCTCAACGC	.	5	ESCA
CHERP	0	.	GRCh37	19	16653226	16653226	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-37C>T	.	.	ENST00000546361	1/17	10	5	5	15	15	0	CHERP,5_prime_UTR_variant,,ENST00000546361,;CHERP,5_prime_UTR_variant,,ENST00000198939,;CTD-3222D19.7,downstream_gene_variant,,ENST00000596487,;CTD-3222D19.7,downstream_gene_variant,,ENST00000595909,;RN7SL146P,upstream_gene_variant,,ENST00000472338,;CTD-3222D19.2,intron_variant,,ENST00000409035,;CHERP,upstream_gene_variant,,ENST00000551747,;CHERP,upstream_gene_variant,,ENST00000546538,;	A	ENSG00000085872	ENST00000546361	Transcript	5_prime_UTR_variant	116	.	.	.	.	.	.	.	-1	CHERP	HGNC	16930	protein_coding	YES	CCDS42518.1	ENSP00000439856	CHERP_HUMAN	.	UPI00001AE5BE	.	.	.	1/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT	CACACGATCGA	.	2	ESCA
NDUFA13	0	.	GRCh37	19	19627082	19627082	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.35C>T	p.Pro12Leu	p.P12L	ENST00000507754	1/5	41	24	17	62	62	0	NDUFA13,missense_variant,p.Pro12Leu,ENST00000428459,;NDUFA13,missense_variant,p.Pro12Leu,ENST00000512771,;NDUFA13,missense_variant,p.Pro12Leu,ENST00000507754,;NDUFA13,missense_variant,p.Pro95Leu,ENST00000252576,;NDUFA13,missense_variant,p.Pro12Leu,ENST00000503283,;CTC-260F20.3,missense_variant,p.Pro12Leu,ENST00000555938,;YJEFN3,missense_variant,p.Pro12Leu,ENST00000608404,;TSSK6,upstream_gene_variant,,ENST00000585580,;TSSK6,upstream_gene_variant,,ENST00000360913,;CTC-260F20.3,non_coding_transcript_exon_variant,,ENST00000586674,;NDUFA13,missense_variant,p.Pro12Leu,ENST00000502506,;NDUFA13,missense_variant,p.Pro5Leu,ENST00000606722,;NDUFA13,non_coding_transcript_exon_variant,,ENST00000511584,;NDUFA13,non_coding_transcript_exon_variant,,ENST00000511180,;TSSK6,upstream_gene_variant,,ENST00000602623,;TSSK6,upstream_gene_variant,,ENST00000587522,;	T	ENSG00000186010	ENST00000507754	Transcript	missense_variant	519	35	12	P/L	cCg/cTg	.	.	.	1	NDUFA13	HGNC	17194	protein_coding	YES	CCDS12404.2	ENSP00000423673	NDUAD_HUMAN	.	UPI00001699BB	.	deleterious(0)	probably_damaging(0.999)	1/5	.	hmmpanther:PTHR12966,hmmpanther:PTHR12966:SF0,Pfam_domain:PF06212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCCGCCGG	.	5	ESCA
ZNF492	0	.	GRCh37	19	22817269	22817269	+	5'UTR	SNP	T	T	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-101T>G	.	.	ENST00000456783	1/4	73	65	8	113	113	0	ZNF492,5_prime_UTR_variant,,ENST00000456783,;	G	ENSG00000229676	ENST00000456783	Transcript	5_prime_UTR_variant	144	.	.	.	.	.	.	.	1	ZNF492	HGNC	23707	protein_coding	YES	CCDS46032.1	ENSP00000413660	ZN492_HUMAN	.	UPI00001C200B	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGCCTAGAAA	.	4	ESCA
LTBP4	0	.	GRCh37	19	41111456	41111456	+	Silent	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.789G>T	p.%3D	p.A263A	ENST00000308370	6/34	58	36	22	40	40	0	LTBP4,synonymous_variant,p.%3D,ENST00000396819,;LTBP4,synonymous_variant,p.%3D,ENST00000204005,;LTBP4,synonymous_variant,p.%3D,ENST00000308370,;LTBP4,5_prime_UTR_variant,,ENST00000545697,;RN7SL758P,downstream_gene_variant,,ENST00000580450,;LTBP4,non_coding_transcript_exon_variant,,ENST00000602240,;LTBP4,non_coding_transcript_exon_variant,,ENST00000600509,;LTBP4,non_coding_transcript_exon_variant,,ENST00000599016,;LTBP4,non_coding_transcript_exon_variant,,ENST00000601209,;LTBP4,upstream_gene_variant,,ENST00000598677,;LTBP4,downstream_gene_variant,,ENST00000600026,;LTBP4,downstream_gene_variant,,ENST00000594537,;LTBP4,intron_variant,,ENST00000598717,;LTBP4,downstream_gene_variant,,ENST00000593738,;LTBP4,upstream_gene_variant,,ENST00000598256,;LTBP4,upstream_gene_variant,,ENST00000595529,;LTBP4,upstream_gene_variant,,ENST00000546155,;	T	ENSG00000090006	ENST00000308370	Transcript	synonymous_variant	789	789	263	A	gcG/gcT	.	.	.	1	LTBP4	HGNC	6717	protein_coding	YES	.	ENSP00000311905	LTBP4_HUMAN	.	UPI000179A7A0	.	.	.	6/34	.	hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF41,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GAGGCGGCAGC	.	4	ESCA
RABAC1	0	.	GRCh37	19	42460877	42460877	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*121C>T	.	.	ENST00000222008	5/5	51	24	27	38	38	0	RABAC1,3_prime_UTR_variant,,ENST00000222008,;RABAC1,3_prime_UTR_variant,,ENST00000601028,;RABAC1,3_prime_UTR_variant,,ENST00000600292,;RABAC1,3_prime_UTR_variant,,ENST00000601891,;RABAC1,downstream_gene_variant,,ENST00000601078,;RABAC1,non_coding_transcript_exon_variant,,ENST00000595226,;RABAC1,non_coding_transcript_exon_variant,,ENST00000598057,;RABAC1,downstream_gene_variant,,ENST00000599219,;RABAC1,downstream_gene_variant,,ENST00000601476,;RABAC1,downstream_gene_variant,,ENST00000596171,;	A	ENSG00000105404	ENST00000222008	Transcript	3_prime_UTR_variant	777	.	.	.	.	.	.	.	-1	RABAC1	HGNC	9794	protein_coding	YES	CCDS12593.1	ENSP00000222008	PRAF1_HUMAN	M0QXU8_HUMAN	UPI000006F3F6	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGGGATCCC	.	5	ESCA
PRR19	0	.	GRCh37	19	42814490	42814490	+	Silent	SNP	A	A	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.669A>T	p.%3D	p.P223P	ENST00000499536	2/2	36	24	12	34	34	0	PRR19,synonymous_variant,p.%3D,ENST00000341747,;PRR19,synonymous_variant,p.%3D,ENST00000499536,;PRR19,3_prime_UTR_variant,,ENST00000598490,;TMEM145,upstream_gene_variant,,ENST00000598766,;PRR19,downstream_gene_variant,,ENST00000595750,;TMEM145,upstream_gene_variant,,ENST00000301204,;TMEM145,upstream_gene_variant,,ENST00000601020,;TMEM145,upstream_gene_variant,,ENST00000595775,;	T	ENSG00000188368	ENST00000499536	Transcript	synonymous_variant	1480	669	223	P	ccA/ccT	.	.	.	1	PRR19	HGNC	33728	protein_coding	YES	CCDS33036.1	ENSP00000445247	PRR19_HUMAN	M0QXP7_HUMAN	UPI000016101F	.	.	.	2/2	.	Pfam_domain:PF15455	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCCAGAGCA	.	5	ESCA
PSG4	0	.	GRCh37	19	43698596	43698596	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1139C>G	p.Ser380Cys	p.S380C	ENST00000405312	5/6	192	185	7	129	129	0	PSG4,missense_variant,p.Ser258Cys,ENST00000596907,;PSG4,missense_variant,p.Ser165Cys,ENST00000599391,;PSG4,missense_variant,p.Ser287Cys,ENST00000244295,;PSG4,missense_variant,p.Ser172Cys,ENST00000597374,;PSG4,missense_variant,p.Ser380Cys,ENST00000405312,;PSG4,missense_variant,p.Ser287Cys,ENST00000433626,;PSG4,downstream_gene_variant,,ENST00000451895,;PSG4,downstream_gene_variant,,ENST00000600572,;PSG4,downstream_gene_variant,,ENST00000599746,;PSG4,downstream_gene_variant,,ENST00000599371,;PSG4,3_prime_UTR_variant,,ENST00000601041,;PSG4,non_coding_transcript_exon_variant,,ENST00000597349,;PSG4,non_coding_transcript_exon_variant,,ENST00000490769,;PSG4,downstream_gene_variant,,ENST00000595949,;PSG4,downstream_gene_variant,,ENST00000495316,;PSG4,downstream_gene_variant,,ENST00000596199,;	C	ENSG00000243137	ENST00000405312	Transcript	missense_variant	1377	1139	380	S/C	tCt/tGt	.	.	.	-1	PSG4	HGNC	9521	protein_coding	YES	CCDS46093.1	ENSP00000384770	PSG4_HUMAN	M0QYU2_HUMAN	UPI000034ECBA	.	tolerated(0.14)	probably_damaging(0.976)	5/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF105,hmmpanther:PTHR19955,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGATAGAGAGC	.	2	ESCA
PSG4	0	.	GRCh37	19	43699413	43699413	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.722A>T	p.Lys241Met	p.K241M	ENST00000405312	4/6	199	156	43	120	120	0	PSG4,missense_variant,p.Lys119Met,ENST00000596907,;PSG4,missense_variant,p.Lys33Met,ENST00000597374,;PSG4,missense_variant,p.Lys127Met,ENST00000599746,;PSG4,missense_variant,p.Lys241Met,ENST00000405312,;PSG4,missense_variant,p.Lys148Met,ENST00000433626,;PSG4,intron_variant,,ENST00000599391,;PSG4,intron_variant,,ENST00000244295,;PSG4,downstream_gene_variant,,ENST00000451895,;PSG4,downstream_gene_variant,,ENST00000600572,;PSG4,downstream_gene_variant,,ENST00000599371,;PSG4,3_prime_UTR_variant,,ENST00000595949,;PSG4,3_prime_UTR_variant,,ENST00000601041,;PSG4,upstream_gene_variant,,ENST00000597349,;PSG4,downstream_gene_variant,,ENST00000495316,;PSG4,upstream_gene_variant,,ENST00000490769,;PSG4,downstream_gene_variant,,ENST00000596199,;	A	ENSG00000243137	ENST00000405312	Transcript	missense_variant	960	722	241	K/M	aAg/aTg	.	.	.	-1	PSG4	HGNC	9521	protein_coding	YES	CCDS46093.1	ENSP00000384770	PSG4_HUMAN	M0QYU2_HUMAN	UPI000034ECBA	.	tolerated(0.1)	benign(0)	4/6	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19955:SF105,hmmpanther:PTHR19955	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGGCTTGGAC	.	5	ESCA
ERCC1	0	.	GRCh37	19	45922395	45922395	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.486G>T	p.Lys162Asn	p.K162N	ENST00000013807	4/8	25	15	10	24	24	0	ERCC1,missense_variant,p.Lys90Asn,ENST00000589381,;ERCC1,missense_variant,p.Lys162Asn,ENST00000591636,;ERCC1,missense_variant,p.Lys17Asn,ENST00000590701,;ERCC1,missense_variant,p.Lys162Asn,ENST00000589165,;ERCC1,missense_variant,p.Lys162Asn,ENST00000300853,;ERCC1,missense_variant,p.Lys90Asn,ENST00000423698,;ERCC1,missense_variant,p.Lys162Asn,ENST00000013807,;ERCC1,missense_variant,p.Lys162Asn,ENST00000592083,;ERCC1,missense_variant,p.Lys162Asn,ENST00000592023,;ERCC1,missense_variant,p.Lys162Asn,ENST00000340192,;ERCC1,downstream_gene_variant,,ENST00000589214,;ERCC1,upstream_gene_variant,,ENST00000592444,;ERCC1,upstream_gene_variant,,ENST00000592410,;ERCC1,upstream_gene_variant,,ENST00000588738,;ERCC1,3_prime_UTR_variant,,ENST00000587888,;ERCC1,non_coding_transcript_exon_variant,,ENST00000588300,;ERCC1,non_coding_transcript_exon_variant,,ENST00000592905,;	A	ENSG00000012061	ENST00000013807	Transcript	missense_variant	678	486	162	K/N	aaG/aaT	.	.	.	-1	ERCC1	HGNC	3433	protein_coding	YES	CCDS12663.1	ENSP00000013807	ERCC1_HUMAN	Q8WWH8_HUMAN,K7ER89_HUMAN,K7EP14_HUMAN,K7EK97_HUMAN	UPI000019C835	.	tolerated(0.12)	benign(0.072)	4/8	.	hmmpanther:PTHR12749:SF0,hmmpanther:PTHR12749,TIGRFAM_domain:TIGR00597,Pfam_domain:PF03834,Superfamily_domains:SSF52980	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTCTTCCC	.	5	ESCA
PTPRH	0	.	GRCh37	19	55698885	55698885	+	Silent	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2562G>T	p.%3D	p.L854L	ENST00000376350	14/20	62	34	27	50	50	0	PTPRH,synonymous_variant,p.%3D,ENST00000263434,;PTPRH,synonymous_variant,p.%3D,ENST00000376350,;	A	ENSG00000080031	ENST00000376350	Transcript	synonymous_variant	2585	2562	854	L	ctG/ctT	.	.	.	-1	PTPRH	HGNC	9672	protein_coding	YES	CCDS33110.1	ENSP00000365528	PTPRH_HUMAN	.	UPI000006EDE6	.	.	.	14/20	.	PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF254,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGGCAGCAC	.	5	ESCA
LONP1	0	.	GRCh37	19	5713256	5713256	+	Missense_Mutation	SNP	G	G	A	rs139555567	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.527C>T	p.Ser176Leu	p.S176L	ENST00000360614	3/18	75	44	31	70	70	0	LONP1,missense_variant,p.Ser62Leu,ENST00000590729,;LONP1,missense_variant,p.Ser176Leu,ENST00000360614,;LONP1,missense_variant,p.Ser112Leu,ENST00000593119,;LONP1,missense_variant,p.Ser62Leu,ENST00000585374,;LONP1,5_prime_UTR_variant,,ENST00000540670,;LONP1,intron_variant,,ENST00000587365,;LONP1,downstream_gene_variant,,ENST00000590511,;LONP1,downstream_gene_variant,,ENST00000590728,;LONP1,missense_variant,p.Ser89Leu,ENST00000590558,;LONP1,non_coding_transcript_exon_variant,,ENST00000587552,;LONP1,intron_variant,,ENST00000586617,;LONP1,upstream_gene_variant,,ENST00000591321,;	A	ENSG00000196365	ENST00000360614	Transcript	missense_variant	685	527	176	S/L	tCg/tTg	rs139555567	.	.	-1	LONP1	HGNC	9479	protein_coding	YES	CCDS12148.1	ENSP00000353826	LONM_HUMAN	K7EKE6_HUMAN,F5GZ27_HUMAN	UPI000012E7EF	.	deleterious(0.05)	benign(0.013)	3/18	.	HAMAP:MF_03120,hmmpanther:PTHR10046:SF23,hmmpanther:PTHR10046,Pfam_domain:PF02190,TIGRFAM_domain:TIGR00763,SMART_domains:SM00464,PIRSF_domain:PIRSF001174,Superfamily_domains:SSF88697	A:0.0010	A:0.0038	A:0	.	A:0	A:0	A:0	A:0.0023	A:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCCGACTCA	byFrequency|byCluster|by1000G	5	ESCA
NDUFA11	0	.	GRCh37	19	5903711	5903711	+	Silent	SNP	C	C	T	rs576231769	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>A	p.%3D	p.P3P	ENST00000418389	1/4	50	26	23	82	82	0	NDUFA11,synonymous_variant,p.%3D,ENST00000308961,;AC024592.12,synonymous_variant,p.%3D,ENST00000585661,;AC024592.12,synonymous_variant,p.%3D,ENST00000586349,;NDUFA11,synonymous_variant,p.%3D,ENST00000418389,;NDUFA11,synonymous_variant,p.%3D,ENST00000592634,;FUT5,5_prime_UTR_variant,,ENST00000252675,;VMAC,upstream_gene_variant,,ENST00000339485,;AC104532.3,downstream_gene_variant,,ENST00000589277,;AC104532.3,downstream_gene_variant,,ENST00000590441,;NDUFA11,non_coding_transcript_exon_variant,,ENST00000591160,;NDUFA11,synonymous_variant,p.%3D,ENST00000593233,;AC024592.12,synonymous_variant,p.%3D,ENST00000592091,;AC104532.2,upstream_gene_variant,,ENST00000588891,;	T	ENSG00000174886	ENST00000418389	Transcript	synonymous_variant	87	9	3	P	ccG/ccA	rs576231769	.	.	-1	NDUFA11	HGNC	20371	protein_coding	YES	CCDS54203.1	ENSP00000389160	NDUAB_HUMAN	.	UPI0001AE63D7	.	.	.	1/4	.	hmmpanther:PTHR21382,hmmpanther:PTHR21382:SF1	T:0.0002	T:0	T:0	.	T:0	T:0	T:0.001	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ACCTTCGGCGC	by1000G	4	ESCA
CDC14A	0	.	GRCh37	1	100950051	100950051	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1137+44C>G	.	.	ENST00000361544	.	34	15	18	25	25	0	CDC14A,3_prime_UTR_variant,,ENST00000370124,;CDC14A,intron_variant,,ENST00000336454,;CDC14A,intron_variant,,ENST00000361544,;CDC14A,intron_variant,,ENST00000542213,;CDC14A,intron_variant,,ENST00000544534,;CDC14A,intron_variant,,ENST00000370125,;RP5-837M10.4,intron_variant,,ENST00000432210,;	G	ENSG00000079335	ENST00000361544	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	CDC14A	HGNC	1718	protein_coding	YES	CCDS770.1	ENSP00000354916	CC14A_HUMAN	F5H7B3_HUMAN	UPI000006EC22	.	.	.	.	11/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTTCTGCAT	.	5	ESCA
KCNA3	0	.	GRCh37	1	111215886	111215886	+	Nonsense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1546C>T	p.Arg516Ter	p.R516*	ENST00000369769	1/1	26	10	16	45	45	0	KCNA3,stop_gained,p.Arg516Ter,ENST00000369769,;	A	ENSG00000177272	ENST00000369769	Transcript	stop_gained	1770	1546	516	R/*	Cga/Tga	COSM1211400	.	.	-1	KCNA3	HGNC	6221	protein_coding	YES	CCDS828.2	ENSP00000358784	KCNA3_HUMAN	Q6P2D3_HUMAN,B2RA23_HUMAN	UPI000013FB79	.	.	.	1/1	.	hmmpanther:PTHR11537:SF28,hmmpanther:PTHR11537	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TTTTCGGAGCT	.	4	ESCA
TRIM33	0	.	GRCh37	1	114942183	114942183	+	Missense_Mutation	SNP	C	C	A	rs763612749	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3016G>T	p.Val1006Leu	p.V1006L	ENST00000358465	18/20	86	82	4	52	52	0	TRIM33,missense_variant,p.Val1006Leu,ENST00000369543,;TRIM33,missense_variant,p.Val767Leu,ENST00000448034,;TRIM33,missense_variant,p.Val1006Leu,ENST00000358465,;TRIM33,missense_variant,p.Val638Leu,ENST00000450349,;TRIM33,non_coding_transcript_exon_variant,,ENST00000478032,;TRIM33,upstream_gene_variant,,ENST00000492227,;TRIM33,downstream_gene_variant,,ENST00000476908,;	A	ENSG00000197323	ENST00000358465	Transcript	missense_variant	3100	3016	1006	V/L	Gtg/Ttg	rs763612749,COSM894172	.	.	-1	TRIM33	HGNC	16290	protein_coding	YES	CCDS872.1	ENSP00000351250	TRI33_HUMAN	.	UPI000013D8CD	.	deleterious(0)	probably_damaging(0.935)	18/20	.	PROSITE_profiles:PS50014,Pfam_domain:PF00439,Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370,Prints_domain:PR00503	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCACGGTGG	.	2	ESCA
AMPD1	0	.	GRCh37	1	115219977	115219977	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1482G>A	p.%3D	p.R494R	ENST00000520113	10/16	68	54	14	54	54	0	AMPD1,synonymous_variant,p.%3D,ENST00000353928,;AMPD1,synonymous_variant,p.%3D,ENST00000520113,;AMPD1,synonymous_variant,p.%3D,ENST00000369538,;AMPD1,downstream_gene_variant,,ENST00000485564,;	T	ENSG00000116748	ENST00000520113	Transcript	synonymous_variant	1498	1482	494	R	agG/agA	.	.	.	-1	AMPD1	HGNC	468	protein_coding	YES	CCDS876.2	ENSP00000430075	AMPD1_HUMAN	Q6F4B9_HUMAN,Q6F4B8_HUMAN,Q6F4B7_HUMAN,Q6F4B6_HUMAN,Q6F4B5_HUMAN	UPI0000470A27	.	.	.	10/16	.	hmmpanther:PTHR11359,hmmpanther:PTHR11359:SF1,Pfam_domain:PF00962,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR01429,PIRSF_domain:PIRSF001251,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAGATCCTGGG	.	5	ESCA
PDE4DIP	0	.	GRCh37	1	144994964	144994964	+	5'UTR	SNP	G	G	A	rs782026248	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-233C>T	.	.	ENST00000369356	1/44	144	127	16	116	116	0	PDE4DIP,missense_variant,p.Leu11Phe,ENST00000534536,;PDE4DIP,5_prime_UTR_variant,,ENST00000369356,;PDE4DIP,intron_variant,,ENST00000533259,;PDE4DIP,intron_variant,,ENST00000369348,;PDE4DIP,intron_variant,,ENST00000532801,;PDE4DIP,intron_variant,,ENST00000531369,;PDE4DIP,intron_variant,,ENST00000369359,;PDE4DIP,intron_variant,,ENST00000530740,;PDE4DIP,intron_variant,,ENST00000313382,;AL590452.1,downstream_gene_variant,,ENST00000596396,;PDE4DIP,upstream_gene_variant,,ENST00000369354,;PDE4DIP,upstream_gene_variant,,ENST00000369347,;PDE4DIP,upstream_gene_variant,,ENST00000369349,;PDE4DIP,upstream_gene_variant,,ENST00000369351,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000464103,;PDE4DIP,intron_variant,,ENST00000497529,;PDE4DIP,intron_variant,,ENST00000528552,;PDE4DIP,intron_variant,,ENST00000533163,;PDE4DIP,intron_variant,,ENST00000533396,;PDE4DIP,intron_variant,,ENST00000532803,;PDE4DIP,upstream_gene_variant,,ENST00000530472,;PDE4DIP,upstream_gene_variant,,ENST00000533845,;PDE4DIP,missense_variant,p.Leu11Phe,ENST00000528129,;PDE4DIP,intron_variant,,ENST00000527063,;PDE4DIP,intron_variant,,ENST00000530822,;PDE4DIP,intron_variant,,ENST00000496572,;PDE4DIP,intron_variant,,ENST00000530078,;PDE4DIP,upstream_gene_variant,,ENST00000526445,;	A	ENSG00000178104	ENST00000369356	Transcript	5_prime_UTR_variant	59	.	.	.	.	rs782026248	.	.	-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	MYOME_HUMAN	I1VE15_HUMAN	UPI0000458A81	.	.	.	1/44	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGGAGATATT	byFrequency	4	ESCA
CRNN	0	.	GRCh37	1	152384689	152384689	+	Missense_Mutation	SNP	G	G	C	rs370534840	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.21C>G	p.Asn7Lys	p.N7K	ENST00000271835	2/3	64	46	18	53	53	0	CRNN,missense_variant,p.Asn7Lys,ENST00000271835,;RP1-91G5.3,intron_variant,,ENST00000411804,;	C	ENSG00000143536	ENST00000271835	Transcript	missense_variant	84	21	7	N/K	aaC/aaG	rs370534840	.	.	-1	CRNN	HGNC	1230	protein_coding	YES	CCDS1010.1	ENSP00000271835	CRNN_HUMAN	.	UPI000006E106	.	deleterious(0)	possibly_damaging(0.694)	2/3	.	hmmpanther:PTHR11639:SF26,hmmpanther:PTHR11639,Gene3D:1.10.238.10,Pfam_domain:PF01023,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTAATGTTTTG	byCluster	5	ESCA
SPEN	0	.	GRCh37	1	16256243	16256243	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000375759	11/15	25	17	8	36	34	1	SPEN,stop_gained,p.Arg1170Ter,ENST00000375759,;	T	ENSG00000065526	ENST00000375759	Transcript	stop_gained	3712	3508	1170	R/*	Cga/Tga	.	.	.	1	SPEN	HGNC	17575	protein_coding	YES	CCDS164.1	ENSP00000364912	MINT_HUMAN	.	UPI000006FF0C	.	.	.	11/15	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23189:SF9,hmmpanther:PTHR23189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|VARSCANS	GTTACCGAAAA	.	2	ESCA
MROH9	0	.	GRCh37	1	170952649	170952649	+	Missense_Mutation	SNP	C	C	G	rs773855378	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703C>G	p.Gln235Glu	p.Q235E	ENST00000367759	9/22	74	58	16	50	50	0	MROH9,missense_variant,p.Gln235Glu,ENST00000367759,;MROH9,missense_variant,p.Gln235Glu,ENST00000367758,;	G	ENSG00000117501	ENST00000367759	Transcript	missense_variant	857	703	235	Q/E	Caa/Gaa	rs773855378	.	.	1	MROH9	HGNC	26287	protein_coding	YES	CCDS53429.1	ENSP00000356733	MROH9_HUMAN	.	UPI0001B09232	.	tolerated(0.17)	benign(0.089)	9/22	.	hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTCAACAA	.	5	ESCA
GLUL	0	.	GRCh37	1	182354682	182354682	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.613C>G	p.Gln205Glu	p.Q205E	ENST00000311223	7/8	26	22	4	29	29	0	GLUL,missense_variant,p.Gln205Glu,ENST00000311223,;GLUL,missense_variant,p.Gln205Glu,ENST00000417584,;GLUL,missense_variant,p.Gln205Glu,ENST00000331872,;GLUL,missense_variant,p.Gln205Glu,ENST00000339526,;GLUL,non_coding_transcript_exon_variant,,ENST00000463851,;GLUL,non_coding_transcript_exon_variant,,ENST00000484996,;GLUL,non_coding_transcript_exon_variant,,ENST00000461447,;GLUL,non_coding_transcript_exon_variant,,ENST00000491322,;GLUL,downstream_gene_variant,,ENST00000475808,;GLUL,downstream_gene_variant,,ENST00000462444,;GLUL,downstream_gene_variant,,ENST00000489818,;GLUL,downstream_gene_variant,,ENST00000480604,;	C	ENSG00000135821	ENST00000311223	Transcript	missense_variant	1510	613	205	Q/E	Cag/Gag	.	.	.	-1	GLUL	HGNC	4341	protein_coding	YES	CCDS1344.1	ENSP00000307900	GLNA_HUMAN	B4DWM6_HUMAN,A8YXX4_HUMAN	UPI000012B6E3	.	deleterious(0.03)	probably_damaging(0.914)	7/8	.	hmmpanther:PTHR20852,hmmpanther:PTHR20852:SF45,Pfam_domain:PF00120,Gene3D:3.30.590.10,Superfamily_domains:SSF55931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AATCTGAAATT	.	3	ESCA
CFHR2	0	.	GRCh37	1	196928158	196928158	+	Missense_Mutation	SNP	G	G	A	rs370528458	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.761G>A	p.Arg254Gln	p.R254Q	ENST00000367415	5/5	29	19	9	10	10	0	CFHR2,missense_variant,p.Arg254Gln,ENST00000367421,;CFHR2,missense_variant,p.Arg254Gln,ENST00000367415,;CFHR2,missense_variant,p.Arg238Gln,ENST00000476712,;CFHR2,non_coding_transcript_exon_variant,,ENST00000473386,;CFHR2,non_coding_transcript_exon_variant,,ENST00000496448,;	A	ENSG00000080910	ENST00000367415	Transcript	missense_variant	861	761	254	R/Q	cGa/cAa	rs370528458,COSM678388	.	.	1	CFHR2	HGNC	4890	protein_coding	YES	CCDS30959.1	ENSP00000356385	FHR2_HUMAN	.	UPI000012A73B	.	tolerated(0.38)	benign(0.049)	5/5	.	hmmpanther:PTHR19325:SF325,hmmpanther:PTHR19325,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTCGAGCAA	byFrequency|byCluster	5	ESCA
PKP1	0	.	GRCh37	1	201292166	201292166	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1592C>T	p.Pro531Leu	p.P531L	ENST00000263946	10/15	71	59	12	75	75	0	PKP1,missense_variant,p.Pro531Leu,ENST00000352845,;PKP1,missense_variant,p.Pro531Leu,ENST00000263946,;PKP1,missense_variant,p.Pro510Leu,ENST00000367324,;PKP1,downstream_gene_variant,,ENST00000475988,;	T	ENSG00000081277	ENST00000263946	Transcript	missense_variant	1843	1592	531	P/L	cCt/cTt	.	.	.	1	PKP1	HGNC	9023	protein_coding	YES	CCDS30966.1	ENSP00000263946	PKP1_HUMAN	B4DRX5_HUMAN	UPI0000131B86	.	deleterious(0.05)	probably_damaging(0.987)	10/15	.	hmmpanther:PTHR10372:SF3,hmmpanther:PTHR10372,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTGCCTGAGG	.	5	ESCA
PPP1R12B	0	.	GRCh37	1	202561464	202561464	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11776G>C	.	.	ENST00000608999	24/24	144	80	64	126	126	0	PPP1R12B,3_prime_UTR_variant,,ENST00000608999,;SYT2,3_prime_UTR_variant,,ENST00000367267,;SYT2,3_prime_UTR_variant,,ENST00000367268,;PPP1R12B,downstream_gene_variant,,ENST00000391959,;PPP1R12B,downstream_gene_variant,,ENST00000336894,;PPP1R12B,downstream_gene_variant,,ENST00000367270,;	C	ENSG00000077157	ENST00000608999	Transcript	3_prime_UTR_variant	14878	.	.	.	.	.	.	.	1	PPP1R12B	HGNC	7619	protein_coding	YES	CCDS1426.1	ENSP00000476755	.	.	UPI0000458A57	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTGGAGCAG	.	5	ESCA
MARK1	0	.	GRCh37	1	220837154	220837154	+	3'Flank	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000366917	.	60	57	3	43	43	0	MARK1,3_prime_UTR_variant,,ENST00000366918,;MARK1,3_prime_UTR_variant,,ENST00000402574,;MARK1,downstream_gene_variant,,ENST00000366917,;RP11-322F10.2,upstream_gene_variant,,ENST00000446040,;	C	ENSG00000116141	ENST00000366917	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1354	1	MARK1	HGNC	6896	protein_coding	YES	CCDS31029.2	ENSP00000355884	MARK1_HUMAN	B4DIB3_HUMAN	UPI0000048D8B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCCTTTTTA	.	2	ESCA
CDC42BPA	0	.	GRCh37	1	227333345	227333345	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.988G>C	p.Gly330Arg	p.G330R	ENST00000366769	8/36	53	39	13	44	44	0	CDC42BPA,missense_variant,p.Gly330Arg,ENST00000366769,;CDC42BPA,missense_variant,p.Gly330Arg,ENST00000366765,;CDC42BPA,missense_variant,p.Gly330Arg,ENST00000366764,;CDC42BPA,missense_variant,p.Gly330Arg,ENST00000334218,;CDC42BPA,missense_variant,p.Gly330Arg,ENST00000366767,;CDC42BPA,missense_variant,p.Gly330Arg,ENST00000535525,;CDC42BPA,missense_variant,p.Gly330Arg,ENST00000366766,;	G	ENSG00000143776	ENST00000366769	Transcript	missense_variant	2280	988	330	G/R	Ggt/Cgt	.	.	.	-1	CDC42BPA	HGNC	1737	protein_coding	YES	CCDS1558.1	ENSP00000355731	MRCKA_HUMAN	Q9NYF6_HUMAN	UPI000019097D	.	deleterious(0)	probably_damaging(1)	8/36	.	PROSITE_profiles:PS50011,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF31,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGACCAAGTC	.	5	ESCA
RBM34	0	.	GRCh37	1	235294938	235294938	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*90G>C	.	.	ENST00000408888	11/11	37	28	9	29	29	0	RBM34,3_prime_UTR_variant,,ENST00000366606,;RBM34,3_prime_UTR_variant,,ENST00000408888,;RBM34,downstream_gene_variant,,ENST00000447801,;TOMM20,upstream_gene_variant,,ENST00000366607,;SNORA14B,upstream_gene_variant,,ENST00000384452,;RBM34,downstream_gene_variant,,ENST00000495224,;ARID4B,downstream_gene_variant,,ENST00000474953,;RBM34,downstream_gene_variant,,ENST00000474086,;	G	ENSG00000188739	ENST00000408888	Transcript	3_prime_UTR_variant	1614	.	.	.	.	.	.	.	-1	RBM34	HGNC	28965	protein_coding	YES	CCDS41477.2	ENSP00000386226	RBM34_HUMAN	.	UPI00001D7E4C	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAACTCAACAC	.	2	ESCA
FMN2	0	.	GRCh37	1	240421329	240421329	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4150C>G	p.His1384Asp	p.H1384D	ENST00000319653	7/18	57	45	12	39	39	0	FMN2,missense_variant,p.His30Asp,ENST00000441342,;FMN2,missense_variant,p.His1384Asp,ENST00000319653,;FMN2,intron_variant,,ENST00000545751,;FMN2,non_coding_transcript_exon_variant,,ENST00000463398,;	G	ENSG00000155816	ENST00000319653	Transcript	missense_variant	4380	4150	1384	H/D	Cat/Gat	.	.	.	1	FMN2	HGNC	14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	FMN2_HUMAN	Q96L17_HUMAN,B4DN09_HUMAN	UPI00015FA087	.	.	possibly_damaging(0.687)	7/18	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213:SF185,hmmpanther:PTHR23213,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACAACATGGT	.	5	ESCA
CEP170	0	.	GRCh37	1	243303405	243303405	+	Missense_Mutation	SNP	A	A	C	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4064T>G	p.Val1355Gly	p.V1355G	ENST00000366542	16/20	125	90	35	84	84	0	CEP170,missense_variant,p.Val1329Gly,ENST00000336415,;CEP170,missense_variant,p.Val1257Gly,ENST00000366544,;CEP170,missense_variant,p.Val1231Gly,ENST00000366543,;CEP170,missense_variant,p.Val91Gly,ENST00000481987,;CEP170,missense_variant,p.Val1355Gly,ENST00000366542,;CEP170,missense_variant,p.Val64Gly,ENST00000490813,;CEP170,missense_variant,p.Val64Gly,ENST00000464936,;CEP170,missense_variant,p.Val147Gly,ENST00000413359,;CEP170,missense_variant,p.Val64Gly,ENST00000492145,;RP11-261C10.5,non_coding_transcript_exon_variant,,ENST00000439562,;CEP170,non_coding_transcript_exon_variant,,ENST00000468254,;CEP170,upstream_gene_variant,,ENST00000468697,;CEP170,upstream_gene_variant,,ENST00000439296,;	C	ENSG00000143702	ENST00000366542	Transcript	missense_variant	4116	4064	1355	V/G	gTt/gGt	COSM906559	.	.	-1	CEP170	HGNC	28920	protein_coding	YES	CCDS44339.1	ENSP00000355500	CE170_HUMAN	Q9NSN9_HUMAN,E5RJT5_HUMAN,E5RIH6_HUMAN,E5RFU8_HUMAN	UPI0000470238	.	deleterious(0.02)	probably_damaging(0.999)	16/20	.	hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF17,Pfam_domain:PF15308	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCAACCAAC	.	5	ESCA
KIF26B	0	.	GRCh37	1	245849901	245849901	+	Missense_Mutation	SNP	C	C	T	rs777110547	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3616C>T	p.Arg1206Cys	p.R1206C	ENST00000407071	12/15	44	31	13	59	59	0	KIF26B,missense_variant,p.Arg1206Cys,ENST00000407071,;KIF26B,missense_variant,p.Arg825Cys,ENST00000366518,;KIF26B,non_coding_transcript_exon_variant,,ENST00000483253,;	T	ENSG00000162849	ENST00000407071	Transcript	missense_variant	4056	3616	1206	R/C	Cgc/Tgc	rs777110547	.	.	1	KIF26B	HGNC	25484	protein_coding	YES	CCDS44342.1	ENSP00000385545	KI26B_HUMAN	B4DF75_HUMAN	UPI0000695D71	.	deleterious(0.01)	unknown(0)	12/15	.	hmmpanther:PTHR24115:SF363,hmmpanther:PTHR24115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGCCGCCCC	.	5	ESCA
HIVEP3	0	.	GRCh37	1	42047900	42047900	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2569G>C	p.Glu857Gln	p.E857Q	ENST00000372583	4/9	46	30	16	37	37	0	HIVEP3,missense_variant,p.Glu857Gln,ENST00000429157,;HIVEP3,missense_variant,p.Glu857Gln,ENST00000372584,;HIVEP3,missense_variant,p.Glu857Gln,ENST00000247584,;HIVEP3,missense_variant,p.Glu857Gln,ENST00000372583,;HIVEP3,upstream_gene_variant,,ENST00000460604,;	G	ENSG00000127124	ENST00000372583	Transcript	missense_variant	3455	2569	857	E/Q	Gag/Cag	.	.	.	-1	HIVEP3	HGNC	13561	protein_coding	YES	CCDS463.1	ENSP00000361664	ZEP3_HUMAN	.	UPI000013CC24	.	.	probably_damaging(0.997)	4/9	.	hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTCAGGAA	.	5	ESCA
INSL5	0	.	GRCh37	1	67266918	67266918	+	5'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-14C>G	.	.	ENST00000304526	1/2	38	35	3	25	25	0	INSL5,5_prime_UTR_variant,,ENST00000304526,;	C	ENSG00000172410	ENST00000304526	Transcript	5_prime_UTR_variant	22	.	.	.	.	.	.	.	-1	INSL5	HGNC	6088	protein_coding	YES	CCDS634.1	ENSP00000302724	INSL5_HUMAN	.	UPI000013E991	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGACTGAATGT	.	4	ESCA
LINC00115	0	.	GRCh37	1	762524	762524	+	RNA	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.379C>G	.	.	ENST00000473798	1/1	89	76	13	86	86	0	LINC00115,non_coding_transcript_exon_variant,,ENST00000536430,;LINC00115,non_coding_transcript_exon_variant,,ENST00000473798,;LINC01128,upstream_gene_variant,,ENST00000445118,;LINC01128,upstream_gene_variant,,ENST00000416570,;LINC01128,upstream_gene_variant,,ENST00000608189,;LINC01128,upstream_gene_variant,,ENST00000449005,;LINC01128,upstream_gene_variant,,ENST00000448975,;LINC01128,upstream_gene_variant,,ENST00000415295,;LINC01128,upstream_gene_variant,,ENST00000609009,;LINC01128,upstream_gene_variant,,ENST00000441765,;LINC01128,upstream_gene_variant,,ENST00000610067,;LINC01128,upstream_gene_variant,,ENST00000609139,;	C	ENSG00000225880	ENST00000473798	Transcript	non_coding_transcript_exon_variant	379	.	.	.	.	.	.	.	-1	LINC00115	HGNC	26211	lincRNA	YES	.	.	.	.	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCCTGAGGGG	.	4	ESCA
UOX	0	.	GRCh37	1	84833343	84833343	+	RNA	SNP	T	T	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.826A>T	.	.	ENST00000471089	7/8	60	43	17	30	30	0	SAMD13,intron_variant,,ENST00000454967,;UOX,downstream_gene_variant,,ENST00000483236,;UOX,non_coding_transcript_exon_variant,,ENST00000471089,;	A	ENSG00000240520	ENST00000471089	Transcript	non_coding_transcript_exon_variant	826	.	.	.	.	.	.	.	-1	UOX	HGNC	12575	unitary_pseudogene	YES	.	.	.	.	.	.	.	.	7/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCTCTTCCTT	.	3	ESCA
UOX	0	.	GRCh37	1	84833375	84833375	+	RNA	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.794G>A	.	.	ENST00000471089	7/8	52	34	17	33	33	0	SAMD13,intron_variant,,ENST00000454967,;UOX,non_coding_transcript_exon_variant,,ENST00000483236,;UOX,non_coding_transcript_exon_variant,,ENST00000471089,;	T	ENSG00000240520	ENST00000471089	Transcript	non_coding_transcript_exon_variant	794	.	.	.	.	.	.	.	-1	UOX	HGNC	12575	unitary_pseudogene	YES	.	.	.	.	.	.	.	.	7/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CATGTCTATGT	.	3	ESCA
SLC44A3	0	.	GRCh37	1	95293099	95293099	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.315C>G	p.%3D	p.V105V	ENST00000271227	4/15	37	30	7	35	35	0	SLC44A3,synonymous_variant,p.%3D,ENST00000446120,;SLC44A3,synonymous_variant,p.%3D,ENST00000422520,;SLC44A3,synonymous_variant,p.%3D,ENST00000271227,;SLC44A3,synonymous_variant,p.%3D,ENST00000529450,;SLC44A3,synonymous_variant,p.%3D,ENST00000467909,;SLC44A3,synonymous_variant,p.%3D,ENST00000532427,;SLC44A3,synonymous_variant,p.%3D,ENST00000527077,;SLC44A3,non_coding_transcript_exon_variant,,ENST00000530397,;SLC44A3,3_prime_UTR_variant,,ENST00000475883,;	G	ENSG00000143036	ENST00000271227	Transcript	synonymous_variant	417	315	105	V	gtC/gtG	.	.	.	1	SLC44A3	HGNC	28689	protein_coding	YES	CCDS44176.1	ENSP00000271227	CTL3_HUMAN	F8W7F3_HUMAN	UPI0000206066	.	.	.	4/15	.	hmmpanther:PTHR12385,hmmpanther:PTHR12385:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGTCAAAGG	.	5	ESCA
MKKS	0	.	GRCh37	20	10388273	10388273	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1263C>G	p.Ile421Met	p.I421M	ENST00000347364	5/6	77	52	24	42	42	0	MKKS,missense_variant,p.Ile421Met,ENST00000399054,;MKKS,missense_variant,p.Ile421Met,ENST00000347364,;	C	ENSG00000125863	ENST00000347364	Transcript	missense_variant	2026	1263	421	I/M	atC/atG	.	.	.	-1	MKKS	HGNC	7108	protein_coding	YES	CCDS13111.1	ENSP00000246062	MKKS_HUMAN	B7Z3W9_HUMAN	UPI000012F199	.	deleterious(0)	probably_damaging(0.948)	5/6	.	hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF12,Pfam_domain:PF00118,Gene3D:1.10.560.10,Superfamily_domains:SSF48592	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTGATATA	.	5	ESCA
BTBD3	0	.	GRCh37	20	11904297	11904297	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1552C>T	p.Leu518Phe	p.L518F	ENST00000405977	5/5	50	42	8	52	52	0	BTBD3,missense_variant,p.Leu457Phe,ENST00000254977,;BTBD3,missense_variant,p.Leu457Phe,ENST00000399006,;BTBD3,missense_variant,p.Leu518Phe,ENST00000405977,;BTBD3,missense_variant,p.Leu518Phe,ENST00000378226,;BTBD3,downstream_gene_variant,,ENST00000430557,;BTBD3,downstream_gene_variant,,ENST00000422390,;BTBD3,downstream_gene_variant,,ENST00000455911,;RP4-742J24.2,upstream_gene_variant,,ENST00000439529,;BTBD3,downstream_gene_variant,,ENST00000473180,;BTBD3,downstream_gene_variant,,ENST00000471120,;BTBD3,downstream_gene_variant,,ENST00000488503,;BTBD3,downstream_gene_variant,,ENST00000473416,;BTBD3,downstream_gene_variant,,ENST00000449299,;	T	ENSG00000132640	ENST00000405977	Transcript	missense_variant	2177	1552	518	L/F	Ctt/Ttt	.	.	.	1	BTBD3	HGNC	15854	protein_coding	YES	CCDS13113.1	ENSP00000384545	BTBD3_HUMAN	Q9NST6_HUMAN,Q52M42_HUMAN,B4DK27_HUMAN,B0QYR1_HUMAN,B0QYR0_HUMAN,B0QYQ9_HUMAN	UPI0000126B03	.	deleterious(0)	possibly_damaging(0.817)	5/5	.	Pfam_domain:PF08005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGAACTTATA	.	2	ESCA
GZF1	0	.	GRCh37	20	23345551	23345551	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.531C>G	p.%3D	p.L177L	ENST00000338121	2/6	49	32	17	33	33	0	GZF1,synonymous_variant,p.%3D,ENST00000377051,;GZF1,synonymous_variant,p.%3D,ENST00000338121,;GZF1,intron_variant,,ENST00000544236,;GZF1,intron_variant,,ENST00000542987,;GZF1,downstream_gene_variant,,ENST00000424216,;GZF1,upstream_gene_variant,,ENST00000477239,;GZF1,upstream_gene_variant,,ENST00000461789,;	G	ENSG00000125812	ENST00000338121	Transcript	synonymous_variant	608	531	177	L	ctC/ctG	.	.	.	1	GZF1	HGNC	15808	protein_coding	YES	CCDS13151.1	ENSP00000338290	GZF1_HUMAN	Q5JXG1_HUMAN,F5H2R0_HUMAN,B4DF58_HUMAN	UPI000013C35D	.	.	.	2/6	.	hmmpanther:PTHR24402:SF170,hmmpanther:PTHR24402	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCACGGA	.	5	ESCA
BPIFB4	0	.	GRCh37	20	31680384	31680384	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1264A>G	p.Met422Val	p.M422V	ENST00000375483	9/16	52	40	11	12	12	0	BPIFB4,missense_variant,p.Met422Val,ENST00000375483,;BPIFB4,downstream_gene_variant,,ENST00000445356,;	G	ENSG00000186191	ENST00000375483	Transcript	missense_variant	1264	1264	422	M/V	Atg/Gtg	.	.	.	1	BPIFB4	HGNC	16179	protein_coding	YES	CCDS13213.2	ENSP00000364632	BPIB4_HUMAN	.	UPI0000206190	.	tolerated(0.27)	benign(0.001)	9/16	.	hmmpanther:PTHR10504:SF78,hmmpanther:PTHR10504,Pfam_domain:PF02886,Gene3D:1ewfA02,SMART_domains:SM00329,Superfamily_domains:SSF55394	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCCATGTCT	.	5	ESCA
ATRN	0	.	GRCh37	20	3629141	3629141	+	3'UTR	SNP	G	G	A	rs148911326	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1647G>A	.	.	ENST00000262919	29/29	46	27	18	30	30	0	ATRN,3_prime_UTR_variant,,ENST00000262919,;	A	ENSG00000088812	ENST00000262919	Transcript	3_prime_UTR_variant	6005	.	.	.	.	rs148911326	.	.	1	ATRN	HGNC	885	protein_coding	YES	CCDS13053.1	ENSP00000262919	ATRN_HUMAN	.	UPI000012661C	.	.	.	29/29	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTCGAGTTT	by1000G	5	ESCA
SDC4	0	.	GRCh37	20	43977033	43977033	+	5'UTR	SNP	G	G	T	rs760647418	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-9C>A	.	.	ENST00000372733	1/5	34	23	11	18	18	0	SDC4,5_prime_UTR_variant,,ENST00000372733,;SDC4,5_prime_UTR_variant,,ENST00000537976,;	T	ENSG00000124145	ENST00000372733	Transcript	5_prime_UTR_variant	32	.	.	.	.	rs760647418	.	.	-1	SDC4	HGNC	10661	protein_coding	YES	CCDS13350.1	ENSP00000361818	SDC4_HUMAN	B4E1S6_HUMAN	UPI000003B45C	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCGCGGACTG	byFrequency	5	ESCA
ADNP	0	.	GRCh37	20	49509522	49509522	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1729G>A	p.Glu577Lys	p.E577K	ENST00000396029	5/5	104	74	30	64	64	0	ADNP,missense_variant,p.Glu577Lys,ENST00000396032,;ADNP,missense_variant,p.Glu577Lys,ENST00000396029,;ADNP,missense_variant,p.Glu577Lys,ENST00000349014,;ADNP,missense_variant,p.Glu577Lys,ENST00000371602,;ADNP,downstream_gene_variant,,ENST00000534467,;	T	ENSG00000101126	ENST00000396029	Transcript	missense_variant	2297	1729	577	E/K	Gaa/Aaa	.	.	.	-1	ADNP	HGNC	15766	protein_coding	YES	CCDS13433.1	ENSP00000379346	ADNP_HUMAN	E9PQK8_HUMAN	UPI00000375B9	.	deleterious(0.01)	possibly_damaging(0.76)	5/5	.	hmmpanther:PTHR15740:SF1,hmmpanther:PTHR15740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTCAGCTG	.	5	ESCA
TAF4	0	.	GRCh37	20	60639546	60639546	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1321C>G	p.Gln441Glu	p.Q441E	ENST00000252996	1/15	32	23	8	21	21	0	TAF4,missense_variant,p.Gln441Glu,ENST00000252996,;hsa-mir-3195,upstream_gene_variant,,ENST00000585001,;TAF4,upstream_gene_variant,,ENST00000608887,;	C	ENSG00000130699	ENST00000252996	Transcript	missense_variant	1321	1321	441	Q/E	Cag/Gag	.	.	.	-1	TAF4	HGNC	11537	protein_coding	YES	CCDS33500.1	ENSP00000252996	TAF4_HUMAN	.	UPI000020630A	.	.	possibly_damaging(0.68)	1/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15138,hmmpanther:PTHR15138:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCTGAGGCG	.	5	ESCA
LAMA5	0	.	GRCh37	20	60926806	60926806	+	Missense_Mutation	SNP	C	C	T	rs780029947	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.910G>A	p.Gly304Ser	p.G304S	ENST00000252999	6/80	178	146	31	115	115	0	LAMA5,missense_variant,p.Gly304Ser,ENST00000252999,;LAMA5,missense_variant,p.Gly304Ser,ENST00000370677,;LAMA5,missense_variant,p.Gly304Ser,ENST00000370692,;RP11-157P1.5,upstream_gene_variant,,ENST00000487421,;RP11-157P1.5,upstream_gene_variant,,ENST00000477848,;RP11-157P1.5,upstream_gene_variant,,ENST00000456721,;RP11-157P1.5,upstream_gene_variant,,ENST00000478167,;LAMA5,non_coding_transcript_exon_variant,,ENST00000497053,;	T	ENSG00000130702	ENST00000252999	Transcript	missense_variant	977	910	304	G/S	Ggc/Agc	rs780029947	.	.	-1	LAMA5	HGNC	6485	protein_coding	YES	CCDS33502.1	ENSP00000252999	LAMA5_HUMAN	O75079_HUMAN	UPI0000161FDC	.	.	probably_damaging(1)	6/80	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF261,hmmpanther:PTHR10574,Pfam_domain:PF00053,Gene3D:2.10.25.10,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTGGCCGTGGC	byFrequency	4	ESCA
GATA5	0	.	GRCh37	20	61039868	61039868	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*24G>T	.	.	ENST00000252997	7/7	76	36	40	70	70	0	GATA5,3_prime_UTR_variant,,ENST00000252997,;	A	ENSG00000130700	ENST00000252997	Transcript	3_prime_UTR_variant	1280	.	.	.	.	.	.	.	-1	GATA5	HGNC	15802	protein_coding	YES	CCDS13499.1	ENSP00000252997	GATA5_HUMAN	D9ZGF7_HUMAN	UPI000012B10C	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTCCCCTGAC	.	5	ESCA
TCEA2	0	.	GRCh37	20	62697888	62697888	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132C>G	p.%3D	p.L44L	ENST00000343484	2/10	41	19	22	34	34	0	TCEA2,synonymous_variant,p.%3D,ENST00000343484,;TCEA2,synonymous_variant,p.%3D,ENST00000361317,;TCEA2,synonymous_variant,p.%3D,ENST00000440819,;TCEA2,synonymous_variant,p.%3D,ENST00000395053,;TCEA2,synonymous_variant,p.%3D,ENST00000458442,;TCEA2,synonymous_variant,p.%3D,ENST00000339217,;TCEA2,synonymous_variant,p.%3D,ENST00000415602,;TCEA2,non_coding_transcript_exon_variant,,ENST00000470559,;TCEA2,non_coding_transcript_exon_variant,,ENST00000487164,;TCEA2,non_coding_transcript_exon_variant,,ENST00000465111,;TCEA2,upstream_gene_variant,,ENST00000475236,;TCEA2,upstream_gene_variant,,ENST00000465433,;TCEA2,upstream_gene_variant,,ENST00000477783,;TCEA2,downstream_gene_variant,,ENST00000475792,;TCEA2,upstream_gene_variant,,ENST00000461072,;TCEA2,upstream_gene_variant,,ENST00000495168,;TCEA2,downstream_gene_variant,,ENST00000476113,;	G	ENSG00000171703	ENST00000343484	Transcript	synonymous_variant	301	132	44	L	ctC/ctG	.	.	.	1	TCEA2	HGNC	11614	protein_coding	YES	CCDS13553.1	ENSP00000343515	TCEA2_HUMAN	Q6IB64_HUMAN,Q5JRI8_HUMAN,Q5JRI7_HUMAN	UPI0000136AC0	.	.	.	2/10	.	PROSITE_profiles:PS51319,hmmpanther:PTHR11477,hmmpanther:PTHR11477:SF3,TIGRFAM_domain:TIGR01385,Gene3D:1.20.930.10,Pfam_domain:PF08711,SMART_domains:SM00509,PIRSF_domain:PIRSF006704,Superfamily_domains:SSF47676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCCAGGT	.	5	ESCA
SCRT2	0	.	GRCh37	20	643334	643334	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*981C>A	.	.	ENST00000246104	2/2	87	69	17	55	55	0	SCRT2,3_prime_UTR_variant,,ENST00000246104,;RP5-850E9.3,intron_variant,,ENST00000488788,;	T	ENSG00000215397	ENST00000246104	Transcript	3_prime_UTR_variant	2483	.	.	.	.	.	.	.	-1	SCRT2	HGNC	15952	protein_coding	YES	CCDS13006.1	ENSP00000246104	SCRT2_HUMAN	.	UPI00002318AA	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAGGGCATTG	.	5	ESCA
NRIP1	0	.	GRCh37	21	16333779	16333779	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3258A>G	.	.	ENST00000400202	3/3	29	19	10	41	41	0	NRIP1,3_prime_UTR_variant,,ENST00000400202,;NRIP1,3_prime_UTR_variant,,ENST00000318948,;NRIP1,3_prime_UTR_variant,,ENST00000400199,;AF127577.10,non_coding_transcript_exon_variant,,ENST00000446301,;	C	ENSG00000180530	ENST00000400202	Transcript	3_prime_UTR_variant	7448	.	.	.	.	.	.	.	-1	NRIP1	HGNC	8001	protein_coding	YES	CCDS13568.1	ENSP00000383063	NRIP1_HUMAN	N0GWB6_HUMAN,N0GW17_HUMAN,C9J130_HUMAN	UPI000004A0A8	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTATATTCC	.	5	ESCA
OLIG1	0	.	GRCh37	21	34443982	34443982	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*614C>T	.	.	ENST00000382348	1/1	93	65	27	127	127	0	OLIG1,3_prime_UTR_variant,,ENST00000333063,;OLIG1,3_prime_UTR_variant,,ENST00000426947,;OLIG1,3_prime_UTR_variant,,ENST00000382348,;AP000282.2,upstream_gene_variant,,ENST00000454622,;AP000282.2,upstream_gene_variant,,ENST00000420356,;OLIG1,non_coding_transcript_exon_variant,,ENST00000498799,;	T	ENSG00000184221	ENST00000382348	Transcript	3_prime_UTR_variant	1533	.	.	.	.	.	.	.	1	OLIG1	HGNC	16983	protein_coding	YES	CCDS42920.2	ENSP00000371785	OLIG1_HUMAN	Q59EM0_HUMAN	UPI0000130C80	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTCGGCGG	.	5	ESCA
MORC3	0	.	GRCh37	21	37705976	37705976	+	Silent	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72T>C	p.%3D	p.T24T	ENST00000400485	2/17	63	21	41	81	81	0	MORC3,synonymous_variant,p.%3D,ENST00000400485,;MORC3,intron_variant,,ENST00000487909,;MORC3,non_coding_transcript_exon_variant,,ENST00000492336,;MORC3,non_coding_transcript_exon_variant,,ENST00000485933,;	C	ENSG00000159256	ENST00000400485	Transcript	synonymous_variant	148	72	24	T	acT/acC	.	.	.	1	MORC3	HGNC	23572	protein_coding	YES	CCDS42924.1	ENSP00000383333	MORC3_HUMAN	Q86YD6_HUMAN,H0YHQ4_HUMAN,B4DHJ4_HUMAN,A2RU29_HUMAN	UPI0000167F94	.	.	.	2/17	.	hmmpanther:PTHR23336:SF12,hmmpanther:PTHR23336,Superfamily_domains:SSF55874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTACTAGTCA	.	5	ESCA
GNAZ	0	.	GRCh37	22	23466279	23466279	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*661G>T	.	.	ENST00000248996	3/3	24	20	4	24	24	0	GNAZ,3_prime_UTR_variant,,ENST00000248996,;RTDR1,intron_variant,,ENST00000216036,;RTDR1,downstream_gene_variant,,ENST00000421213,;GNAZ,downstream_gene_variant,,ENST00000479571,;	T	ENSG00000128266	ENST00000248996	Transcript	3_prime_UTR_variant	2395	.	.	.	.	.	.	.	1	GNAZ	HGNC	4395	protein_coding	YES	CCDS13804.1	ENSP00000248996	GNAZ_HUMAN	.	UPI0000001249	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	AACGAGTGGCA	.	2	ESCA
CABIN1	0	.	GRCh37	22	24479322	24479322	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2890G>A	p.Glu964Lys	p.E964K	ENST00000398319	20/37	19	8	11	17	17	0	CABIN1,missense_variant,p.Glu964Lys,ENST00000398319,;CABIN1,missense_variant,p.Glu914Lys,ENST00000405822,;CABIN1,missense_variant,p.Glu964Lys,ENST00000263119,;CABIN1,upstream_gene_variant,,ENST00000496016,;	A	ENSG00000099991	ENST00000398319	Transcript	missense_variant	3275	2890	964	E/K	Gag/Aag	.	.	.	1	CABIN1	HGNC	24187	protein_coding	YES	CCDS13823.1	ENSP00000381364	CABIN_HUMAN	.	UPI0000126D6C	.	deleterious(0.01)	probably_damaging(0.991)	20/37	.	hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTGGAGGAA	.	5	ESCA
MICALL1	0	.	GRCh37	22	38313800	38313800	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.424C>T	p.Gln142Ter	p.Q142*	ENST00000215957	4/16	26	17	9	30	30	0	MICALL1,stop_gained,p.Gln142Ter,ENST00000215957,;MICALL1,stop_gained,p.Gln58Ter,ENST00000445494,;MICALL1,intron_variant,,ENST00000489812,;	T	ENSG00000100139	ENST00000215957	Transcript	stop_gained	550	424	142	Q/*	Cag/Tag	.	.	.	1	MICALL1	HGNC	29804	protein_coding	YES	CCDS13961.1	ENSP00000215957	MILK1_HUMAN	Q68D58_HUMAN,Q641Q8_HUMAN,B0QY86_HUMAN	UPI000000DCAE	.	.	.	4/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGGCTCAGGTA	.	2	ESCA
MEI1	0	.	GRCh37	22	42114165	42114165	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.620C>G	p.Ser207Cys	p.S207C	ENST00000401548	6/31	38	14	23	34	34	0	MEI1,missense_variant,p.Ser207Cys,ENST00000401548,;MEI1,5_prime_UTR_variant,,ENST00000300398,;MEI1,5_prime_UTR_variant,,ENST00000540833,;MEI1,5_prime_UTR_variant,,ENST00000400107,;RNU6ATAC22P,downstream_gene_variant,,ENST00000516794,;	G	ENSG00000167077	ENST00000401548	Transcript	missense_variant	660	620	207	S/C	tCc/tGc	.	.	.	1	MEI1	HGNC	28613	protein_coding	YES	CCDS46718.1	ENSP00000384115	MEI1_HUMAN	.	UPI00006E232C	.	deleterious(0)	possibly_damaging(0.76)	6/31	.	hmmpanther:PTHR12044,hmmpanther:PTHR12044:SF10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATACTCCTCAC	.	5	ESCA
RNF149	0	.	GRCh37	2	101892823	101892823	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*877G>A	.	.	ENST00000295317	7/7	38	21	17	23	23	0	RNF149,3_prime_UTR_variant,,ENST00000295317,;SNORD89,upstream_gene_variant,,ENST00000390981,;RNF149,upstream_gene_variant,,ENST00000485752,;RNF149,intron_variant,,ENST00000424632,;	T	ENSG00000163162	ENST00000295317	Transcript	3_prime_UTR_variant	2188	.	.	.	.	.	.	.	-1	RNF149	HGNC	23137	protein_coding	YES	CCDS2051.1	ENSP00000295317	RN149_HUMAN	Q53SV6_HUMAN	UPI0000366F4A	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAATCTGCTT	.	5	ESCA
GCC2	0	.	GRCh37	2	109067569	109067569	+	Splice_Site	SNP	G	G	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.148+1G>A	.	p.X50_splice	ENST00000309863	.	119	65	53	56	56	0	GCC2,splice_donor_variant,,ENST00000409821,;GCC2,splice_donor_variant,,ENST00000309863,;GCC2,splice_donor_variant,,ENST00000409896,;GCC2,intron_variant,,ENST00000478207,;GCC2,intron_variant,,ENST00000482325,;GCC2,downstream_gene_variant,,ENST00000467566,;	A	ENSG00000135968	ENST00000309863	Transcript	splice_donor_variant	.	.	.	.	.	COSM569074	.	.	1	GCC2	HGNC	23218	protein_coding	YES	CCDS33268.1	ENSP00000307939	GCC2_HUMAN	B8ZZW2_HUMAN,B3KR21_HUMAN	UPI000049DF0C	.	.	.	.	3/22	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAGGTATTG	.	5	ESCA
ROCK2	0	.	GRCh37	2	11332613	11332613	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3913A>G	p.Met1305Val	p.M1305V	ENST00000315872	31/33	69	55	13	50	50	0	ROCK2,missense_variant,p.Met1305Val,ENST00000315872,;ROCK2,missense_variant,p.Met1062Val,ENST00000401753,;ROCK2,downstream_gene_variant,,ENST00000493096,;ROCK2,downstream_gene_variant,,ENST00000460262,;	C	ENSG00000134318	ENST00000315872	Transcript	missense_variant	4362	3913	1305	M/V	Atg/Gtg	.	.	.	-1	ROCK2	HGNC	10252	protein_coding	YES	CCDS42654.1	ENSP00000317985	ROCK2_HUMAN	Q14DU5_HUMAN,E9PF63_HUMAN	UPI000034ECB0	.	tolerated(0.32)	benign(0.002)	31/33	.	PROSITE_profiles:PS50003,PROSITE_profiles:PS50081,hmmpanther:PTHR22988:SF24,hmmpanther:PTHR22988,Gene3D:3.30.60.20,Pfam_domain:PF00169,SMART_domains:SM00109,SMART_domains:SM00233,PIRSF_domain:PIRSF037568,Superfamily_domains:SSF57889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCATATGAT	.	5	ESCA
POTEE	0	.	GRCh37	2	131976247	131976247	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.272T>C	p.Met91Thr	p.M91T	ENST00000356920	1/15	78	51	26	85	85	0	POTEE,missense_variant,p.Met91Thr,ENST00000356920,;POTEE,missense_variant,p.Met91Thr,ENST00000358087,;PLEKHB2,intron_variant,,ENST00000404460,;PLEKHB2,intron_variant,,ENST00000303908,;AC131180.1,intron_variant,,ENST00000514256,;	C	ENSG00000188219	ENST00000356920	Transcript	missense_variant	366	272	91	M/T	aTg/aCg	.	.	.	1	POTEE	HGNC	33895	protein_coding	YES	CCDS46414.1	ENSP00000439189	POTEE_HUMAN	.	UPI0000F58EC8	.	deleterious_low_confidence(0)	benign(0.042)	1/15	.	hmmpanther:PTHR24118:SF46,hmmpanther:PTHR24118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTATGAAGA	.	5	ESCA
MZT2A	0	.	GRCh37	2	132250426	132250426	+	5'Flank	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000309451	.	88	58	30	136	136	0	MZT2A,upstream_gene_variant,,ENST00000309451,;MIR4784,upstream_gene_variant,,ENST00000579560,;AC093838.4,non_coding_transcript_exon_variant,,ENST00000438378,;MZT2A,upstream_gene_variant,,ENST00000488586,;MZT2A,upstream_gene_variant,,ENST00000410036,;MZT2A,upstream_gene_variant,,ENST00000445782,;MZT2A,upstream_gene_variant,,ENST00000491265,;MZT2A,upstream_gene_variant,,ENST00000427024,;AC093838.4,non_coding_transcript_exon_variant,,ENST00000415574,;AC093838.4,upstream_gene_variant,,ENST00000416745,;AC093838.4,upstream_gene_variant,,ENST00000426369,;AC093838.4,upstream_gene_variant,,ENST00000538598,;AC093838.4,upstream_gene_variant,,ENST00000543513,;	T	ENSG00000173272	ENST00000309451	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	431	-1	MZT2A	HGNC	33187	protein_coding	YES	CCDS42758.1	ENSP00000311500	MZT2A_HUMAN	.	UPI0000421BEF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AGTGCGTGAGC	.	4	ESCA
LRP1B	0	.	GRCh37	2	140990552	140990552	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*203G>T	.	.	ENST00000389484	91/91	37	10	26	32	32	0	LRP1B,3_prime_UTR_variant,,ENST00000389484,;LRP1B,3_prime_UTR_variant,,ENST00000437977,;	A	ENSG00000168702	ENST00000389484	Transcript	3_prime_UTR_variant	14975	.	.	.	.	.	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	.	91/91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTTCTTTTT	.	5	ESCA
LRP1B	0	.	GRCh37	2	141267497	141267497	+	Missense_Mutation	SNP	C	C	T	rs376234911	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8398G>A	p.Ala2800Thr	p.A2800T	ENST00000389484	52/91	15	3	12	18	18	0	LRP1B,missense_variant,p.Ala2800Thr,ENST00000389484,;	T	ENSG00000168702	ENST00000389484	Transcript	missense_variant	9370	8398	2800	A/T	Gct/Act	rs376234911	.	.	-1	LRP1B	HGNC	6693	protein_coding	YES	CCDS2182.1	ENSP00000374135	LRP1B_HUMAN	Q8WY27_HUMAN,Q8WY26_HUMAN,Q580W7_HUMAN,Q53TB8_HUMAN,Q53S76_HUMAN,Q53S73_HUMAN,Q53S26_HUMAN,Q53RL0_HUMAN,Q53RG4_HUMAN,Q53RA0_HUMAN,Q53QP5_HUMAN,Q53QM8_HUMAN,Q4ZG53_HUMAN,Q4ZFV5_HUMAN	UPI00001B045B	.	.	possibly_damaging(0.499)	52/91	.	PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,SMART_domains:SM00192	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATACCGCAGC	.	5	ESCA
MBD5	0	.	GRCh37	2	149243356	149243356	+	Missense_Mutation	SNP	C	C	G	rs750939401	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2891C>G	p.Thr964Ser	p.T964S	ENST00000407073	11/15	59	23	36	40	40	0	MBD5,missense_variant,p.Thr964Ser,ENST00000407073,;MBD5,missense_variant,p.Thr1197Ser,ENST00000404807,;MBD5,missense_variant,p.Thr937Ser,ENST00000416015,;MBD5,non_coding_transcript_exon_variant,,ENST00000496893,;	G	ENSG00000204406	ENST00000407073	Transcript	missense_variant	3888	2891	964	T/S	aCt/aGt	rs750939401	.	.	1	MBD5	HGNC	20444	protein_coding	YES	CCDS33302.1	ENSP00000386049	MBD5_HUMAN	.	UPI0000208C40	.	tolerated_low_confidence(0.9)	unknown(0)	11/15	.	hmmpanther:PTHR16112,hmmpanther:PTHR16112:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGACTCATC	.	5	ESCA
GALNT5	0	.	GRCh37	2	158156146	158156146	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2084G>A	p.Trp695Ter	p.W695*	ENST00000259056	6/10	131	126	5	121	121	0	GALNT5,stop_gained,p.Trp695Ter,ENST00000259056,;RN7SKP281,upstream_gene_variant,,ENST00000410472,;GALNT5,upstream_gene_variant,,ENST00000461704,;GALNT5,upstream_gene_variant,,ENST00000463418,;	A	ENSG00000136542	ENST00000259056	Transcript	stop_gained	2569	2084	695	W/*	tGg/tAg	.	.	.	1	GALNT5	HGNC	4127	protein_coding	YES	CCDS2203.1	ENSP00000259056	GALT5_HUMAN	Q68VJ5_HUMAN	UPI000019AD19	.	.	.	6/10	.	hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF16,Gene3D:3.90.550.10,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.L692P|c.2075T>C|4,BUFFER|p.L692L|c.2076T>C|4	MUTECT|MUSE	TGTTTGGGGTG	.	2	ESCA
SCN7A	0	.	GRCh37	2	167262557	167262557	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4582G>T	p.Asp1528Tyr	p.D1528Y	ENST00000409855	25/25	47	25	22	39	39	0	SCN7A,missense_variant,p.Asp1528Tyr,ENST00000409855,;SCN7A,3_prime_UTR_variant,,ENST00000424326,;	A	ENSG00000136546	ENST00000409855	Transcript	missense_variant	4709	4582	1528	D/Y	Gat/Tat	COSM1741598,COSM1741597	.	.	-1	SCN7A	HGNC	10594	protein_coding	YES	CCDS46442.1	ENSP00000386796	SCN7A_HUMAN	Q16278_HUMAN,C9JW43_HUMAN,C9JII9_HUMAN	UPI0000209019	.	deleterious(0)	probably_damaging(0.98)	25/25	.	hmmpanther:PTHR10037:SF14,hmmpanther:PTHR10037	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CCTATCAGGAT	.	4	ESCA
TTN	0	.	GRCh37	2	179592389	179592389	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.19916C>G	p.Ser6639Cys	p.S6639C	ENST00000589042	68/363	42	30	12	51	51	0	TTN,missense_variant,p.Ser5395Cys,ENST00000342992,;TTN,missense_variant,p.Ser6322Cys,ENST00000591111,;TTN,missense_variant,p.Ser6639Cys,ENST00000589042,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000585451,;RP11-171I2.1,downstream_gene_variant,,ENST00000590024,;	C	ENSG00000155657	ENST00000589042	Transcript	missense_variant	20141	19916	6639	S/C	tCt/tGt	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	68/363	.	PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF6,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTAGAAGCA	.	5	ESCA
PMS1	0	.	GRCh37	2	190660632	190660632	+	Silent	SNP	C	C	T	rs149723996	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.270C>T	p.%3D	p.Y90Y	ENST00000441310	3/13	66	53	13	45	45	0	PMS1,synonymous_variant,p.%3D,ENST00000424766,;PMS1,synonymous_variant,p.%3D,ENST00000447232,;PMS1,synonymous_variant,p.%3D,ENST00000409823,;PMS1,synonymous_variant,p.%3D,ENST00000374826,;PMS1,synonymous_variant,p.%3D,ENST00000441310,;PMS1,synonymous_variant,p.%3D,ENST00000409985,;PMS1,5_prime_UTR_variant,,ENST00000418224,;PMS1,intron_variant,,ENST00000424307,;PMS1,intron_variant,,ENST00000432292,;PMS1,downstream_gene_variant,,ENST00000420421,;PMS1,downstream_gene_variant,,ENST00000446877,;PMS1,non_coding_transcript_exon_variant,,ENST00000424059,;PMS1,non_coding_transcript_exon_variant,,ENST00000421722,;PMS1,synonymous_variant,p.%3D,ENST00000342075,;PMS1,synonymous_variant,p.%3D,ENST00000450931,;PMS1,intron_variant,,ENST00000447734,;	T	ENSG00000064933	ENST00000441310	Transcript	synonymous_variant	503	270	90	Y	taC/taT	rs149723996	.	.	1	PMS1	HGNC	9121	protein_coding	YES	CCDS2302.1	ENSP00000406490	PMS1_HUMAN	Q5FBZ2_HUMAN,C9JKP0_HUMAN,C9JF76_HUMAN,C9J4L1_HUMAN,B7ZAA0_HUMAN	UPI00000405F5	.	.	.	3/13	.	hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF38,Gene3D:3.30.565.10,TIGRFAM_domain:TIGR00585,Pfam_domain:PF13589,Superfamily_domains:SSF55874	.	.	.	.	.	.	.	T:0	T:0.0003	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTACGGTTT	byFrequency|byCluster	5	ESCA
ALS2CR11	0	.	GRCh37	2	202357836	202357836	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3228C>G	p.Phe1076Leu	p.F1076L	ENST00000439140	15/16	40	16	24	46	46	0	ALS2CR11,missense_variant,p.Phe1076Leu,ENST00000439140,;ALS2CR11,intron_variant,,ENST00000439802,;ALS2CR11,intron_variant,,ENST00000286195,;ALS2CR11,intron_variant,,ENST00000482942,;	C	ENSG00000155754	ENST00000439140	Transcript	missense_variant	3273	3228	1076	F/L	ttC/ttG	.	.	.	-1	ALS2CR11	HGNC	14438	protein_coding	YES	CCDS54430.1	ENSP00000409937	AL2SA_HUMAN	Q96Q36_HUMAN	UPI000198C657	.	tolerated(0.18)	benign(0.048)	15/16	.	hmmpanther:PTHR21665:SF2,hmmpanther:PTHR21665	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATTGAAGAT	.	5	ESCA
PAX3	0	.	GRCh37	2	223163464	223163464	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-130C>T	.	.	ENST00000392069	1/10	24	5	18	41	41	0	PAX3,5_prime_UTR_variant,,ENST00000392070,;PAX3,5_prime_UTR_variant,,ENST00000336840,;PAX3,5_prime_UTR_variant,,ENST00000258387,;PAX3,5_prime_UTR_variant,,ENST00000392069,;PAX3,5_prime_UTR_variant,,ENST00000344493,;PAX3,5_prime_UTR_variant,,ENST00000409551,;PAX3,5_prime_UTR_variant,,ENST00000409828,;PAX3,5_prime_UTR_variant,,ENST00000350526,;CCDC140,intron_variant,,ENST00000295226,;CCDC140,upstream_gene_variant,,ENST00000440903,;	A	ENSG00000135903	ENST00000392069	Transcript	5_prime_UTR_variant	237	.	.	.	.	.	.	.	-1	PAX3	HGNC	8617	protein_coding	YES	CCDS2448.1	ENSP00000375921	PAX3_HUMAN	.	UPI00001A8BF0	.	.	.	1/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAGGGAGGG	.	5	ESCA
INPP5D	0	.	GRCh37	2	234115509	234115509	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*155G>A	.	.	ENST00000359570	29/29	13	5	8	21	21	0	INPP5D,3_prime_UTR_variant,,ENST00000359570,;INPP5D,3_prime_UTR_variant,,ENST00000435188,;INPP5D,3_prime_UTR_variant,,ENST00000415617,;INPP5D,3_prime_UTR_variant,,ENST00000445964,;INPP5D,3_prime_UTR_variant,,ENST00000450745,;INPP5D,3_prime_UTR_variant,,ENST00000455936,;INPP5D,3_prime_UTR_variant,,ENST00000417661,;ATG16L1,upstream_gene_variant,,ENST00000431917,;RN7SL32P,downstream_gene_variant,,ENST00000580514,;INPP5D,downstream_gene_variant,,ENST00000491070,;	A	ENSG00000168918	ENST00000359570	Transcript	3_prime_UTR_variant	3689	.	.	.	.	.	.	.	1	INPP5D	HGNC	6079	protein_coding	YES	.	ENSP00000352575	SHIP1_HUMAN	H0Y5Q9_HUMAN,C9JF09_HUMAN	UPI0002065B89	.	.	.	29/29	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCACAGAGTTC	.	3	ESCA
PDCD1	0	.	GRCh37	2	242795101	242795101	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108C>T	p.%3D	p.T36T	ENST00000334409	2/5	55	18	37	77	77	0	PDCD1,synonymous_variant,p.%3D,ENST00000334409,;PDCD1,upstream_gene_variant,,ENST00000343705,;PDCD1,synonymous_variant,p.%3D,ENST00000418831,;	A	ENSG00000188389	ENST00000334409	Transcript	synonymous_variant	178	108	36	T	acC/acT	.	.	.	-1	PDCD1	HGNC	8760	protein_coding	YES	CCDS33428.1	ENSP00000335062	PDCD1_HUMAN	E7ER21_HUMAN	UPI0000061E11	.	.	.	2/5	.	PROSITE_profiles:PS50835,hmmpanther:PTHR15264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGGTGGG	.	5	ESCA
DYSF	0	.	GRCh37	2	71801357	71801357	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3258C>T	p.%3D	p.G1086G	ENST00000410020	30/56	80	23	56	71	71	0	DYSF,synonymous_variant,p.%3D,ENST00000409582,;DYSF,synonymous_variant,p.%3D,ENST00000410020,;DYSF,synonymous_variant,p.%3D,ENST00000409744,;DYSF,synonymous_variant,p.%3D,ENST00000429174,;DYSF,synonymous_variant,p.%3D,ENST00000409762,;DYSF,synonymous_variant,p.%3D,ENST00000410041,;DYSF,synonymous_variant,p.%3D,ENST00000409651,;DYSF,synonymous_variant,p.%3D,ENST00000394120,;DYSF,synonymous_variant,p.%3D,ENST00000409366,;DYSF,synonymous_variant,p.%3D,ENST00000413539,;DYSF,synonymous_variant,p.%3D,ENST00000258104,;DYSF,upstream_gene_variant,,ENST00000475076,;DYSF,upstream_gene_variant,,ENST00000479049,;DYSF,downstream_gene_variant,,ENST00000461565,;	T	ENSG00000135636	ENST00000410020	Transcript	synonymous_variant	3399	3258	1086	G	ggC/ggT	.	.	.	1	DYSF	HGNC	3097	protein_coding	YES	CCDS46328.1	ENSP00000386881	DYSF_HUMAN	A0FK00_HUMAN	UPI000171F710	.	.	.	30/56	.	hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF35,SMART_domains:SM00694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GAGGGCTGGGA	.	4	ESCA
LBX2	0	.	GRCh37	2	74725123	74725123	+	Silent	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.516C>G	p.%3D	p.L172L	ENST00000460508	2/2	126	42	84	107	107	0	LBX2,synonymous_variant,p.%3D,ENST00000377566,;LBX2,synonymous_variant,p.%3D,ENST00000460508,;LBX2,3_prime_UTR_variant,,ENST00000341396,;TTC31,downstream_gene_variant,,ENST00000414247,;TTC31,downstream_gene_variant,,ENST00000442235,;TTC31,downstream_gene_variant,,ENST00000410003,;TTC31,downstream_gene_variant,,ENST00000233623,;RP11-523H20.3,upstream_gene_variant,,ENST00000606287,;AC005041.17,downstream_gene_variant,,ENST00000479098,;LBX2-AS1,upstream_gene_variant,,ENST00000548978,;LBX2-AS1,upstream_gene_variant,,ENST00000603175,;LBX2,non_coding_transcript_exon_variant,,ENST00000550249,;TTC31,downstream_gene_variant,,ENST00000491252,;TTC31,downstream_gene_variant,,ENST00000489152,;TTC31,downstream_gene_variant,,ENST00000424122,;TTC31,downstream_gene_variant,,ENST00000464241,;TTC31,downstream_gene_variant,,ENST00000449459,;	C	ENSG00000179528	ENST00000460508	Transcript	synonymous_variant	973	516	172	L	ctC/ctG	.	.	.	-1	LBX2	HGNC	15525	protein_coding	YES	CCDS33228.1	ENSP00000417116	LBX2_HUMAN	.	UPI00001AADF5	.	.	.	2/2	.	hmmpanther:PTHR24336,hmmpanther:PTHR24336:SF4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGAGGCC	.	5	ESCA
DNAH6	0	.	GRCh37	2	84937415	84937415	+	Missense_Mutation	SNP	A	A	C	rs61752525	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9257A>C	p.Asn3086Thr	p.N3086T	ENST00000389394	56/77	52	34	17	33	33	0	DNAH6,missense_variant,p.Asn3086Thr,ENST00000237449,;DNAH6,missense_variant,p.Asn3086Thr,ENST00000389394,;	C	ENSG00000115423	ENST00000389394	Transcript	missense_variant	9394	9257	3086	N/T	aAc/aCc	rs61752525	.	.	1	DNAH6	HGNC	2951	protein_coding	YES	CCDS46348.1	ENSP00000374045	DYH6_HUMAN	B0I1R8_HUMAN	UPI000163AC9D	.	deleterious(0)	possibly_damaging(0.824)	56/77	.	hmmpanther:PTHR10676:SF136,hmmpanther:PTHR10676,Pfam_domain:PF12781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCAAACCGTT	byFrequency	5	ESCA
ANKRD36C	0	.	GRCh37	2	96587555	96587555	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2147C>G	p.Ser716Cys	p.S716C	ENST00000456556	33/67	110	94	16	57	57	0	ANKRD36C,missense_variant,p.Ser716Cys,ENST00000456556,;ANKRD36C,5_prime_UTR_variant,,ENST00000419039,;ANKRD36C,5_prime_UTR_variant,,ENST00000295246,;ANKRD36C,5_prime_UTR_variant,,ENST00000420871,;ANKRD36C,3_prime_UTR_variant,,ENST00000534304,;	C	ENSG00000174501	ENST00000456556	Transcript	missense_variant	2232	2147	716	S/C	tCt/tGt	.	.	.	-1	ANKRD36C	HGNC	32946	protein_coding	.	.	ENSP00000403302	AN36C_HUMAN	I1Z9D5_HUMAN,I1Z9D4_HUMAN,I1Z9D3_HUMAN,I1Z9D2_HUMAN	UPI00016620F5	.	deleterious_low_confidence(0)	probably_damaging(0.977)	33/67	.	hmmpanther:PTHR24176:SF1,hmmpanther:PTHR24176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGAAGACACT	.	5	ESCA
FER1L5	0	.	GRCh37	2	97356256	97356256	+	RNA	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1132G>A	.	.	ENST00000457909	10/35	55	44	11	48	48	0	FER1L5,non_coding_transcript_exon_variant,,ENST00000457909,;FER1L5,non_coding_transcript_exon_variant,,ENST00000436930,;FER1L5,non_coding_transcript_exon_variant,,ENST00000414152,;FER1L5,non_coding_transcript_exon_variant,,ENST00000424961,;FER1L5,upstream_gene_variant,,ENST00000397978,;	A	ENSG00000249715	ENST00000457909	Transcript	non_coding_transcript_exon_variant	1132	.	.	.	.	.	.	.	1	FER1L5	HGNC	19044	retained_intron	.	.	.	.	.	.	.	.	.	10/35	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACGTGAAGTG	.	5	ESCA
SEMA4C	0	.	GRCh37	2	97526115	97526115	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*248C>T	.	.	ENST00000305476	15/15	56	29	27	23	23	0	SEMA4C,3_prime_UTR_variant,,ENST00000305476,;ANKRD39,upstream_gene_variant,,ENST00000393537,;SEMA4C,downstream_gene_variant,,ENST00000442264,;ANKRD23,upstream_gene_variant,,ENST00000462692,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000467747,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000474420,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000482925,;ANKRD39,upstream_gene_variant,,ENST00000443120,;	A	ENSG00000168758	ENST00000305476	Transcript	3_prime_UTR_variant	2883	.	.	.	.	.	.	.	-1	SEMA4C	HGNC	10731	protein_coding	YES	CCDS2029.1	ENSP00000306844	SEM4C_HUMAN	Q8NBN9_HUMAN,Q6P5A5_HUMAN,Q53RE7_HUMAN,C9JV89_HUMAN,C9J4M7_HUMAN	UPI00001A7981	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCTGGGGTC	.	5	ESCA
TSGA10	0	.	GRCh37	2	99634675	99634675	+	Missense_Mutation	SNP	C	C	A	rs148460657	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2060G>T	p.Arg687Leu	p.R687L	ENST00000393483	20/21	83	49	33	37	37	0	TSGA10,missense_variant,p.Arg687Leu,ENST00000410001,;TSGA10,missense_variant,p.Arg687Leu,ENST00000393482,;TSGA10,missense_variant,p.Arg617Leu,ENST00000409564,;TSGA10,missense_variant,p.Arg687Leu,ENST00000539964,;TSGA10,missense_variant,p.Arg687Leu,ENST00000355053,;TSGA10,missense_variant,p.Arg687Leu,ENST00000393483,;TSGA10,non_coding_transcript_exon_variant,,ENST00000489546,;	A	ENSG00000135951	ENST00000393483	Transcript	missense_variant	2905	2060	687	R/L	cGa/cTa	rs148460657	.	.	-1	TSGA10	HGNC	14927	protein_coding	YES	CCDS2037.1	ENSP00000377123	TSG10_HUMAN	F8WA32_HUMAN	UPI0000072CE3	.	tolerated(0.24)	possibly_damaging(0.569)	20/21	.	hmmpanther:PTHR23159:SF9,hmmpanther:PTHR23159	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGATCGATCT	.	5	ESCA
SEC13	0	.	GRCh37	3	10342753	10342753	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*192G>C	.	.	ENST00000350697	9/9	26	10	16	29	29	0	SEC13,3_prime_UTR_variant,,ENST00000397117,;SEC13,3_prime_UTR_variant,,ENST00000337354,;SEC13,3_prime_UTR_variant,,ENST00000350697,;SEC13,3_prime_UTR_variant,,ENST00000397109,;SEC13,3_prime_UTR_variant,,ENST00000383801,;SEC13,intron_variant,,ENST00000492602,;SEC13,non_coding_transcript_exon_variant,,ENST00000479868,;SEC13,downstream_gene_variant,,ENST00000476597,;SEC13,downstream_gene_variant,,ENST00000490283,;SEC13,downstream_gene_variant,,ENST00000477547,;	G	ENSG00000157020	ENST00000350697	Transcript	3_prime_UTR_variant	1287	.	.	.	.	.	.	.	-1	SEC13	HGNC	10697	protein_coding	YES	CCDS2599.1	ENSP00000312122	SEC13_HUMAN	A4UCS7_HUMAN	UPI0000072378	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTTCAGCTG	.	5	ESCA
RP11-298O21.5	0	.	GRCh37	3	167630684	167630684	+	RNA	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.483G>A	.	.	ENST00000481578	4/7	76	60	16	58	58	0	RP11-298O21.5,non_coding_transcript_exon_variant,,ENST00000481578,;RP11-298O21.5,non_coding_transcript_exon_variant,,ENST00000490897,;RP11-298O21.5,non_coding_transcript_exon_variant,,ENST00000459923,;RP11-298O21.5,non_coding_transcript_exon_variant,,ENST00000494887,;RP11-298O21.5,intron_variant,,ENST00000469060,;RP11-298O21.5,upstream_gene_variant,,ENST00000493529,;RP11-298O21.5,upstream_gene_variant,,ENST00000496891,;	A	ENSG00000244227	ENST00000481578	Transcript	non_coding_transcript_exon_variant	483	.	.	.	.	.	.	.	1	RP11-298O21.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	4/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGAAGACTGC	.	5	ESCA
KLHL24	0	.	GRCh37	3	183400678	183400678	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3604A>G	.	.	ENST00000454652	9/9	66	26	40	59	59	0	KLHL24,3_prime_UTR_variant,,ENST00000454652,;KLHL24,downstream_gene_variant,,ENST00000242810,;	G	ENSG00000114796	ENST00000454652	Transcript	3_prime_UTR_variant	5793	.	.	.	.	.	.	.	1	KLHL24	HGNC	25947	protein_coding	YES	CCDS3246.1	ENSP00000395012	KLH24_HUMAN	C9JXR5_HUMAN,C9JQ67_HUMAN,C9JN72_HUMAN,C9JMQ9_HUMAN,C9JCK3_HUMAN,C9J3M5_HUMAN,C9J2N4_HUMAN,C9J0A6_HUMAN	UPI000020A86F	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAGATTTAT	.	5	ESCA
C3orf70	0	.	GRCh37	3	184870595	184870595	+	Missense_Mutation	SNP	G	G	A	rs757159118	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.17C>T	p.Ser6Leu	p.S6L	ENST00000335012	1/2	36	27	8	31	31	0	C3orf70,missense_variant,p.Ser6Leu,ENST00000335012,;	A	ENSG00000187068	ENST00000335012	Transcript	missense_variant	208	17	6	S/L	tCg/tTg	rs757159118,COSM420098,COSM3774780	.	.	-1	C3orf70	HGNC	33731	protein_coding	YES	CCDS33900.1	ENSP00000334974	CC070_HUMAN	.	UPI000016128B	.	deleterious_low_confidence(0.02)	benign(0.001)	1/2	.	hmmpanther:PTHR31785:SF2,hmmpanther:PTHR31785	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.S6L|c.17C>T|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGGCGAGGCC	.	5	ESCA
MB21D2	0	.	GRCh37	3	192516720	192516720	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.931C>G	p.Gln311Glu	p.Q311E	ENST00000392452	2/2	34	23	11	28	28	0	MB21D2,missense_variant,p.Gln311Glu,ENST00000392452,;	C	ENSG00000180611	ENST00000392452	Transcript	missense_variant	1252	931	311	Q/E	Cag/Gag	COSM348040,COSM350832	.	.	-1	MB21D2	HGNC	30438	protein_coding	YES	CCDS3302.2	ENSP00000376246	M21D2_HUMAN	A8K332_HUMAN	UPI000013FAFE	.	tolerated(0.19)	possibly_damaging(0.569)	2/2	.	Pfam_domain:PF03281,hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF43	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.Q311E|c.931C>G|8,BUFFER|p.Q311*|c.931C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGCCTGATAGG	.	5	ESCA
ACAP2	0	.	GRCh37	3	195006581	195006581	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2180G>A	p.Arg727His	p.R727H	ENST00000326793	22/23	38	19	19	38	38	0	ACAP2,missense_variant,p.Arg727His,ENST00000326793,;ACAP2-IT1,upstream_gene_variant,,ENST00000419899,;ACAP2,non_coding_transcript_exon_variant,,ENST00000466876,;	T	ENSG00000114331	ENST00000326793	Transcript	missense_variant	2411	2180	727	R/H	cGt/cAt	.	.	.	-1	ACAP2	HGNC	16469	protein_coding	YES	CCDS33924.1	ENSP00000324287	ACAP2_HUMAN	C9J8L1_HUMAN	UPI0000141A1A	.	deleterious(0)	probably_damaging(0.981)	22/23	.	PROSITE_profiles:PS50297,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF241,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTAAACGTAAC	.	5	ESCA
APOD	0	.	GRCh37	3	195306288	195306288	+	Silent	SNP	G	G	A	rs757303997	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.45C>T	p.%3D	p.F15F	ENST00000343267	2/5	45	30	15	57	57	0	APOD,synonymous_variant,p.%3D,ENST00000421243,;APOD,synonymous_variant,p.%3D,ENST00000453131,;APOD,synonymous_variant,p.%3D,ENST00000343267,;APOD,synonymous_variant,p.%3D,ENST00000458447,;APOD,non_coding_transcript_exon_variant,,ENST00000463719,;	A	ENSG00000189058	ENST00000343267	Transcript	synonymous_variant	407	45	15	F	ttC/ttT	rs757303997	.	.	-1	APOD	HGNC	612	protein_coding	YES	CCDS33925.1	ENSP00000345179	APOD_HUMAN	C9JX71_HUMAN	UPI00000369E0	.	.	.	2/5	.	Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,Prints_domain:PR02058,Superfamily_domains:SSF50814,PIRSF_domain:PIRSF036893,Gene3D:2.40.128.20,hmmpanther:PTHR10612:SF7,hmmpanther:PTHR10612	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACCGAAGAG	byFrequency	5	ESCA
TRANK1	0	.	GRCh37	3	36873775	36873775	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7167C>T	p.%3D	p.F2389F	ENST00000429976	21/23	58	44	14	72	72	0	TRANK1,synonymous_variant,p.%3D,ENST00000428977,;TRANK1,synonymous_variant,p.%3D,ENST00000301807,;TRANK1,synonymous_variant,p.%3D,ENST00000429976,;	A	ENSG00000168016	ENST00000429976	Transcript	synonymous_variant	7415	7167	2389	F	ttC/ttT	COSM3592760,COSM3592759,COSM3592758	.	.	-1	TRANK1	HGNC	29011	protein_coding	YES	CCDS46789.2	ENSP00000416168	TRNK1_HUMAN	B7WP88_HUMAN	UPI00017BE82B	.	.	.	21/23	.	hmmpanther:PTHR21529:SF5,hmmpanther:PTHR21529	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATGAAACG	.	5	ESCA
TRAIP	0	.	GRCh37	3	49866540	49866540	+	Missense_Mutation	SNP	G	G	A	rs748874948	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1406C>T	p.Ser469Leu	p.S469L	ENST00000331456	15/15	17	7	10	37	37	0	TRAIP,missense_variant,p.Ser469Leu,ENST00000331456,;TRAIP,downstream_gene_variant,,ENST00000469027,;TRAIP,3_prime_UTR_variant,,ENST00000473195,;TRAIP,non_coding_transcript_exon_variant,,ENST00000491060,;TRAIP,downstream_gene_variant,,ENST00000475495,;	A	ENSG00000183763	ENST00000331456	Transcript	missense_variant	1520	1406	469	S/L	tCg/tTg	rs748874948	.	.	-1	TRAIP	HGNC	30764	protein_coding	YES	CCDS2806.1	ENSP00000328203	TRAIP_HUMAN	A4UCT7_HUMAN	UPI000006FE67	.	deleterious_low_confidence(0)	benign(0.32)	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCACGACCAC	byFrequency	5	ESCA
FLNB	0	.	GRCh37	3	58089741	58089741	+	Missense_Mutation	SNP	C	C	G	rs764967982	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1539C>G	p.Phe513Leu	p.F513L	ENST00000490882	10/47	47	21	25	70	70	0	FLNB,missense_variant,p.Phe513Leu,ENST00000429972,;FLNB,missense_variant,p.Phe513Leu,ENST00000295956,;FLNB,missense_variant,p.Phe513Leu,ENST00000348383,;FLNB,missense_variant,p.Phe344Leu,ENST00000493452,;FLNB,missense_variant,p.Phe513Leu,ENST00000358537,;FLNB,missense_variant,p.Phe513Leu,ENST00000490882,;FLNB,missense_variant,p.Phe344Leu,ENST00000419752,;FLNB,missense_variant,p.Phe513Leu,ENST00000357272,;	G	ENSG00000136068	ENST00000490882	Transcript	missense_variant	1704	1539	513	F/L	ttC/ttG	rs764967982,COSM1177344,COSM1177343	.	.	1	FLNB	HGNC	3755	protein_coding	YES	CCDS54599.1	ENSP00000420213	FLNB_HUMAN	.	UPI0001765F91	.	tolerated(0.08)	benign(0.02)	10/47	.	PROSITE_profiles:PS50194,hmmpanther:PTHR11915:SF238,hmmpanther:PTHR11915,Gene3D:2.60.40.10,Pfam_domain:PF00630,SMART_domains:SM00557,Superfamily_domains:SSF81296	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATTCGAGTA	.	5	ESCA
OR5K1	0	.	GRCh37	3	98188847	98188847	+	Missense_Mutation	SNP	C	C	G	rs771972823	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.427C>G	p.Gln143Glu	p.Q143E	ENST00000332650	1/1	146	104	42	94	94	0	OR5K1,missense_variant,p.Gln143Glu,ENST00000332650,;	G	ENSG00000232382	ENST00000332650	Transcript	missense_variant	524	427	143	Q/E	Cag/Gag	rs771972823	.	.	1	OR5K1	HGNC	8349	protein_coding	YES	CCDS43115.1	ENSP00000373193	OR5K1_HUMAN	.	UPI000013F5A3	.	deleterious(0)	benign(0.282)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF38,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTCAGATG	.	5	ESCA
DCBLD2	0	.	GRCh37	3	98518298	98518298	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2246T>C	p.Val749Ala	p.V749A	ENST00000326840	16/16	75	57	18	45	45	0	DCBLD2,missense_variant,p.Val749Ala,ENST00000326840,;DCBLD2,missense_variant,p.Val763Ala,ENST00000326857,;ST3GAL6,downstream_gene_variant,,ENST00000265261,;ST3GAL6,intron_variant,,ENST00000491912,;ST3GAL6,upstream_gene_variant,,ENST00000495502,;DCBLD2,downstream_gene_variant,,ENST00000494614,;ST3GAL6,downstream_gene_variant,,ENST00000469105,;ST3GAL6,downstream_gene_variant,,ENST00000486249,;DCBLD2,downstream_gene_variant,,ENST00000496736,;	G	ENSG00000057019	ENST00000326840	Transcript	missense_variant	2609	2246	749	V/A	gTg/gCg	.	.	.	-1	DCBLD2	HGNC	24627	protein_coding	YES	CCDS46878.1	ENSP00000321573	DCBD2_HUMAN	B7Z7Y3_HUMAN	UPI0000072ABB	.	tolerated(0.12)	benign(0.164)	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTACACCAAT	.	5	ESCA
ANXA5	0	.	GRCh37	4	122593740	122593740	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.573A>T	p.Glu191Asp	p.E191D	ENST00000296511	9/13	105	92	13	65	65	0	ANXA5,missense_variant,p.Glu91Asp,ENST00000515017,;ANXA5,missense_variant,p.Glu191Asp,ENST00000296511,;ANXA5,missense_variant,p.Glu131Asp,ENST00000501272,;ANXA5,3_prime_UTR_variant,,ENST00000506395,;ANXA5,non_coding_transcript_exon_variant,,ENST00000511552,;ANXA5,non_coding_transcript_exon_variant,,ENST00000509648,;ANXA5,upstream_gene_variant,,ENST00000515717,;	A	ENSG00000164111	ENST00000296511	Transcript	missense_variant	859	573	191	E/D	gaA/gaT	.	.	.	-1	ANXA5	HGNC	543	protein_coding	YES	CCDS3720.1	ENSP00000296511	ANXA5_HUMAN	.	UPI000002BA00	.	deleterious(0)	probably_damaging(0.998)	9/13	.	hmmpanther:PTHR10502,hmmpanther:PTHR10502:SF26,PROSITE_patterns:PS00223,Gene3D:1.10.220.10,Pfam_domain:PF00191,SMART_domains:SM00335,Superfamily_domains:SSF47874,Prints_domain:PR00196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTTCTTCATC	.	4	ESCA
BBS12	0	.	GRCh37	4	123664621	123664621	+	Missense_Mutation	SNP	G	G	A	rs776730549	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1574G>A	p.Arg525His	p.R525H	ENST00000542236	3/3	39	28	11	43	43	0	BBS12,missense_variant,p.Arg525His,ENST00000542236,;BBS12,missense_variant,p.Arg525His,ENST00000314218,;BBS12,downstream_gene_variant,,ENST00000433287,;	A	ENSG00000181004	ENST00000542236	Transcript	missense_variant	1955	1574	525	R/H	cGt/cAt	CM104181,rs776730549,COSM586019	.	.	1	BBS12	HGNC	26648	protein_coding	YES	CCDS3728.1	ENSP00000438273	BBS12_HUMAN	C9J8H7_HUMAN	UPI0000231CAC	.	deleterious(0.01)	probably_damaging(1)	3/3	.	hmmpanther:PTHR11353:SF30,hmmpanther:PTHR11353,Pfam_domain:PF00118	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTATCGTTTGT	.	5	ESCA
UVSSA	0	.	GRCh37	4	1341932	1341932	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.53C>A	p.Pro18His	p.P18H	ENST00000389851	2/14	25	16	9	40	40	0	UVSSA,missense_variant,p.Pro18His,ENST00000507531,;UVSSA,missense_variant,p.Pro18His,ENST00000389851,;UVSSA,missense_variant,p.Pro18His,ENST00000511216,;	A	ENSG00000163945	ENST00000389851	Transcript	missense_variant	500	53	18	P/H	cCc/cAc	.	.	.	1	UVSSA	HGNC	29304	protein_coding	YES	CCDS33938.1	ENSP00000374501	UVSSA_HUMAN	.	UPI00001C1E0C	.	tolerated(0.06)	probably_damaging(0.95)	2/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAACCCCGAC	.	5	ESCA
CRIPAK	0	.	GRCh37	4	1389723	1389723	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*83G>T	.	.	ENST00000324803	1/1	66	38	27	62	62	0	CRIPAK,3_prime_UTR_variant,,ENST00000324803,;	T	ENSG00000179979	ENST00000324803	Transcript	3_prime_UTR_variant	4384	.	.	.	.	.	.	.	1	CRIPAK	HGNC	26619	protein_coding	YES	CCDS3349.1	ENSP00000323978	CRPAK_HUMAN	.	UPI0000070390	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTCGTATCA	.	5	ESCA
SLC7A11	0	.	GRCh37	4	139100537	139100537	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1278C>T	p.%3D	p.F426F	ENST00000280612	11/12	10	6	4	16	16	0	SLC7A11,synonymous_variant,p.%3D,ENST00000280612,;SLC7A11-AS1,downstream_gene_variant,,ENST00000512786,;SLC7A11-AS1,downstream_gene_variant,,ENST00000510767,;SLC7A11-AS1,downstream_gene_variant,,ENST00000512538,;SLC7A11,3_prime_UTR_variant,,ENST00000509248,;	A	ENSG00000151012	ENST00000280612	Transcript	synonymous_variant	1558	1278	426	F	ttC/ttT	.	.	.	-1	SLC7A11	HGNC	11059	protein_coding	YES	CCDS3742.1	ENSP00000280612	XCT_HUMAN	Q9P1X0_HUMAN,Q4W5A5_HUMAN	UPI0000138FD5	.	.	.	11/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF248,Pfam_domain:PF13520,TIGRFAM_domain:TIGR00911,PIRSF_domain:PIRSF006060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGATGAACAG	.	2	ESCA
OTUD4	0	.	GRCh37	4	146095823	146095823	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.38A>G	p.Lys13Arg	p.K13R	ENST00000454497	2/21	60	44	15	63	63	0	OTUD4,missense_variant,p.Lys13Arg,ENST00000514973,;OTUD4,missense_variant,p.Lys13Arg,ENST00000504501,;OTUD4,missense_variant,p.Lys13Arg,ENST00000296579,;OTUD4,missense_variant,p.Lys78Arg,ENST00000447906,;OTUD4,missense_variant,p.Lys13Arg,ENST00000454497,;OTUD4,missense_variant,p.Lys13Arg,ENST00000509620,;OTUD4,non_coding_transcript_exon_variant,,ENST00000505976,;OTUD4,non_coding_transcript_exon_variant,,ENST00000455611,;OTUD4,non_coding_transcript_exon_variant,,ENST00000509985,;OTUD4,upstream_gene_variant,,ENST00000504331,;	C	ENSG00000164164	ENST00000454497	Transcript	missense_variant	176	38	13	K/R	aAa/aGa	.	.	.	-1	OTUD4	HGNC	24949	protein_coding	YES	CCDS47139.1	ENSP00000409279	OTUD4_HUMAN	D6RA27_HUMAN	UPI0000DA6D4D	.	tolerated(0.1)	benign(0.085)	2/21	.	PROSITE_profiles:PS50802,hmmpanther:PTHR12419,hmmpanther:PTHR12419:SF9,Pfam_domain:PF02338,Superfamily_domains:SSF54001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAATTTCTCT	.	5	ESCA
ETFDH	0	.	GRCh37	4	159627784	159627784	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1472C>T	p.Ser491Phe	p.S491F	ENST00000511912	12/13	46	21	24	53	53	0	ETFDH,missense_variant,p.Ser444Phe,ENST00000307738,;ETFDH,missense_variant,p.Ser491Phe,ENST00000511912,;PPID,downstream_gene_variant,,ENST00000307720,;PPID,downstream_gene_variant,,ENST00000507213,;ETFDH,non_coding_transcript_exon_variant,,ENST00000506422,;PPID,downstream_gene_variant,,ENST00000512699,;	T	ENSG00000171503	ENST00000511912	Transcript	missense_variant	1804	1472	491	S/F	tCt/tTt	.	.	.	1	ETFDH	HGNC	3483	protein_coding	YES	CCDS3800.1	ENSP00000426638	ETFD_HUMAN	D6RAD5_HUMAN,B4DEQ0_HUMAN	UPI000013EC48	.	deleterious(0)	benign(0.004)	12/13	.	Superfamily_domains:SSF51905,Pfam_domain:PF05187,hmmpanther:PTHR10617,hmmpanther:PTHR10617:SF98	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGTTCTGACT	.	5	ESCA
KLHL2	0	.	GRCh37	4	166220690	166220690	+	Missense_Mutation	SNP	G	G	A	rs751575614	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.815G>A	p.Ser272Asn	p.S272N	ENST00000514860	8/15	50	20	29	55	55	0	KLHL2,missense_variant,p.Ser272Asn,ENST00000514860,;KLHL2,missense_variant,p.Ser102Asn,ENST00000506761,;KLHL2,missense_variant,p.Ser268Asn,ENST00000226725,;KLHL2,missense_variant,p.Ser180Asn,ENST00000538127,;KLHL2,missense_variant,p.Ser171Asn,ENST00000421009,;KLHL2,non_coding_transcript_exon_variant,,ENST00000509028,;KLHL2,non_coding_transcript_exon_variant,,ENST00000506541,;KLHL2,3_prime_UTR_variant,,ENST00000506824,;	A	ENSG00000109466	ENST00000514860	Transcript	missense_variant	1065	815	272	S/N	aGc/aAc	rs751575614	.	.	1	KLHL2	HGNC	6353	protein_coding	YES	CCDS54815.1	ENSP00000424198	KLHL2_HUMAN	D6RGC3_HUMAN,B4DFZ5_HUMAN	UPI0000E20649	.	tolerated(1)	benign(0.003)	8/15	.	PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412:SF155,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATAGCAGTG	byFrequency	5	ESCA
SLBP	0	.	GRCh37	4	1695032	1695032	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*292C>G	.	.	ENST00000489418	8/8	10	6	4	10	10	0	SLBP,3_prime_UTR_variant,,ENST00000489418,;SLBP,3_prime_UTR_variant,,ENST00000483348,;SLBP,3_prime_UTR_variant,,ENST00000429429,;SLBP,3_prime_UTR_variant,,ENST00000318386,;SLBP,downstream_gene_variant,,ENST00000480936,;SLBP,downstream_gene_variant,,ENST00000488267,;	C	ENSG00000163950	ENST00000489418	Transcript	3_prime_UTR_variant	1472	.	.	.	.	.	.	.	-1	SLBP	HGNC	10904	protein_coding	YES	CCDS3350.1	ENSP00000417686	SLBP_HUMAN	Q53XR2_HUMAN,B3KSC5_HUMAN	UPI0000135A0D	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAGACGTGTCA	.	3	ESCA
TMEM129	0	.	GRCh37	4	1718680	1718680	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*227C>A	.	.	ENST00000382936	4/4	16	11	5	19	19	0	TMEM129,3_prime_UTR_variant,,ENST00000382936,;TMEM129,3_prime_UTR_variant,,ENST00000303277,;TMEM129,3_prime_UTR_variant,,ENST00000536901,;TACC3,upstream_gene_variant,,ENST00000313288,;SLBP,upstream_gene_variant,,ENST00000480936,;SLBP,upstream_gene_variant,,ENST00000489418,;SLBP,upstream_gene_variant,,ENST00000429429,;SLBP,upstream_gene_variant,,ENST00000483348,;TACC3,upstream_gene_variant,,ENST00000493975,;SLBP,upstream_gene_variant,,ENST00000318386,;SLBP,upstream_gene_variant,,ENST00000488267,;TACC3,upstream_gene_variant,,ENST00000485989,;RP11-572O17.1,downstream_gene_variant,,ENST00000605571,;TMEM129,3_prime_UTR_variant,,ENST00000460722,;TMEM129,non_coding_transcript_exon_variant,,ENST00000476253,;TACC3,upstream_gene_variant,,ENST00000467746,;TACC3,upstream_gene_variant,,ENST00000484651,;TMEM129,downstream_gene_variant,,ENST00000480360,;	T	ENSG00000168936	ENST00000382936	Transcript	3_prime_UTR_variant	1810	.	.	.	.	.	.	.	-1	TMEM129	HGNC	25137	protein_coding	YES	CCDS46998.1	ENSP00000372394	TM129_HUMAN	.	UPI000011DC08	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGAGGAGGTG	.	5	ESCA
GPM6A	0	.	GRCh37	4	176733208	176733208	+	Intron	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.37+134C>T	.	.	ENST00000280187	.	33	24	8	18	18	0	GPM6A,intron_variant,,ENST00000512610,;GPM6A,intron_variant,,ENST00000503397,;GPM6A,intron_variant,,ENST00000507540,;GPM6A,intron_variant,,ENST00000513365,;GPM6A,intron_variant,,ENST00000280187,;GPM6A,intron_variant,,ENST00000505375,;GPM6A,intron_variant,,ENST00000506894,;GPM6A,intron_variant,,ENST00000393658,;GPM6A,intron_variant,,ENST00000502754,;GPM6A,intron_variant,,ENST00000512509,;GPM6A,intron_variant,,ENST00000509865,;GPM6A,intron_variant,,ENST00000513667,;GPM6A,upstream_gene_variant,,ENST00000505561,;GPM6A,downstream_gene_variant,,ENST00000503563,;RP11-806K15.1,non_coding_transcript_exon_variant,,ENST00000514864,;	A	ENSG00000150625	ENST00000280187	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	GPM6A	HGNC	4460	protein_coding	YES	CCDS3824.1	ENSP00000280187	GPM6A_HUMAN	Q49AH3_HUMAN,D6RIF4_HUMAN,D6RFZ3_HUMAN,D6RFY0_HUMAN,D6REJ8_HUMAN,D6RD95_HUMAN,D6RBM6_HUMAN,D6RBH3_HUMAN,D6RAE4_HUMAN,D6R9T7_HUMAN	UPI000012EAE1	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACAGACTAA	.	5	ESCA
ZFP42	0	.	GRCh37	4	188924576	188924576	+	Silent	SNP	G	G	A	rs753581463	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615G>A	p.%3D	p.L205L	ENST00000326866	4/4	17	14	3	17	17	0	ZFP42,synonymous_variant,p.%3D,ENST00000326866,;ZFP42,synonymous_variant,p.%3D,ENST00000509524,;	A	ENSG00000179059	ENST00000326866	Transcript	synonymous_variant	1023	615	205	L	ctG/ctA	rs753581463	.	.	1	ZFP42	HGNC	30949	protein_coding	YES	CCDS3849.1	ENSP00000317686	ZFP42_HUMAN	.	UPI0000049CA7	.	.	.	4/4	.	hmmpanther:PTHR14003:SF8,hmmpanther:PTHR14003,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCTGAGAAA	.	2	ESCA
GABRB1	0	.	GRCh37	4	47163327	47163327	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.302G>C	p.Gly101Ala	p.G101A	ENST00000295454	4/9	97	79	18	52	52	0	GABRB1,missense_variant,p.Gly31Ala,ENST00000538619,;GABRB1,missense_variant,p.Gly68Ala,ENST00000513567,;GABRB1,missense_variant,p.Gly101Ala,ENST00000295454,;GABRB1,missense_variant,p.Trp78Cys,ENST00000510909,;	C	ENSG00000163288	ENST00000295454	Transcript	missense_variant	594	302	101	G/A	gGa/gCa	.	.	.	1	GABRB1	HGNC	4081	protein_coding	YES	CCDS3474.1	ENSP00000295454	GBRB1_HUMAN	D6REM0_HUMAN	UPI000012AFAC	.	tolerated(0.33)	benign(0.026)	4/9	.	hmmpanther:PTHR18945:SF198,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932,Prints_domain:PR01160	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTGGAATCC	.	5	ESCA
GABRB1	0	.	GRCh37	4	47408746	47408746	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.883G>A	p.Glu295Lys	p.E295K	ENST00000295454	8/9	71	58	13	36	36	0	GABRB1,missense_variant,p.Glu225Lys,ENST00000538619,;GABRB1,missense_variant,p.Glu295Lys,ENST00000295454,;GABRB1,downstream_gene_variant,,ENST00000510909,;	A	ENSG00000163288	ENST00000295454	Transcript	missense_variant	1175	883	295	E/K	Gag/Aag	.	.	.	1	GABRB1	HGNC	4081	protein_coding	YES	CCDS3474.1	ENSP00000295454	GBRB1_HUMAN	D6REM0_HUMAN	UPI000012AFAC	.	tolerated(0.06)	possibly_damaging(0.535)	8/9	.	hmmpanther:PTHR18945:SF198,hmmpanther:PTHR18945,Pfam_domain:PF02932,Gene3D:1.20.58.390,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCAGGGAGACC	.	3	ESCA
USP46	0	.	GRCh37	4	53461245	53461245	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2561G>A	.	.	ENST00000441222	9/9	36	31	5	32	32	0	USP46,3_prime_UTR_variant,,ENST00000451218,;USP46,3_prime_UTR_variant,,ENST00000441222,;USP46,downstream_gene_variant,,ENST00000508499,;USP46,downstream_gene_variant,,ENST00000503060,;USP46,downstream_gene_variant,,ENST00000514536,;	T	ENSG00000109189	ENST00000441222	Transcript	3_prime_UTR_variant	3847	.	.	.	.	.	.	.	-1	USP46	HGNC	20075	protein_coding	YES	CCDS47053.1	ENSP00000407818	UBP46_HUMAN	.	UPI0000006C18	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ACACCCAGCAG	.	3	ESCA
NPFFR2	0	.	GRCh37	4	72897591	72897592	+	5'UTR	DEL	AA	AA	-	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	AA	AA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-28_-27delAA	.	.	ENST00000308744	1/4	45	31	14	34	34	0	NPFFR2,5_prime_UTR_variant,,ENST00000308744,;NPFFR2,upstream_gene_variant,,ENST00000344413,;	-	ENSG00000056291	ENST00000308744	Transcript	5_prime_UTR_variant	71-72	.	.	.	.	.	.	.	1	NPFFR2	HGNC	4525	protein_coding	YES	CCDS3551.1	ENSP00000307822	NPFF2_HUMAN	A0PJM9_HUMAN	UPI000012FFBD	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	CACAAGAATGTAC	.	3	ESCA
CCNI	0	.	GRCh37	4	77996721	77996721	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-140G>C	.	.	ENST00000237654	1/7	61	36	25	29	29	0	CCNI,5_prime_UTR_variant,,ENST00000507788,;CCNI,5_prime_UTR_variant,,ENST00000537948,;CCNI,5_prime_UTR_variant,,ENST00000237654,;CCNI,upstream_gene_variant,,ENST00000513774,;CCNI,upstream_gene_variant,,ENST00000505609,;CCNI,5_prime_UTR_variant,,ENST00000511943,;CCNI,non_coding_transcript_exon_variant,,ENST00000515790,;	G	ENSG00000118816	ENST00000237654	Transcript	5_prime_UTR_variant	438	.	.	.	.	.	.	.	-1	CCNI	HGNC	1595	protein_coding	YES	CCDS3580.1	ENSP00000237654	CCNI_HUMAN	D6RH01_HUMAN,D6RG12_HUMAN	UPI000000D8E4	.	.	.	1/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTCTCATA	.	5	ESCA
CPLX1	0	.	GRCh37	4	786256	786256	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.172G>A	p.Glu58Lys	p.E58K	ENST00000304062	3/4	27	20	7	27	27	0	CPLX1,missense_variant,p.Glu43Lys,ENST00000504062,;CPLX1,missense_variant,p.Glu58Lys,ENST00000304062,;CPLX1,intron_variant,,ENST00000505203,;CPLX1,non_coding_transcript_exon_variant,,ENST00000506404,;	T	ENSG00000168993	ENST00000304062	Transcript	missense_variant	404	172	58	E/K	Gag/Aag	.	.	.	-1	CPLX1	HGNC	2309	protein_coding	YES	CCDS46995.1	ENSP00000305613	CPLX1_HUMAN	F1T0G1_HUMAN,D6RAG3_HUMAN	UPI0000127BB3	.	deleterious(0)	probably_damaging(0.995)	3/4	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16705:SF3,hmmpanther:PTHR16705,Pfam_domain:PF05835,Gene3D:1kilE00,Superfamily_domains:SSF58038	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCTCCGCCT	.	2	ESCA
SH3TC1	0	.	GRCh37	4	8226903	8226903	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1245C>G	p.Asp415Glu	p.D415E	ENST00000245105	11/18	42	28	14	45	45	0	SH3TC1,missense_variant,p.Asp415Glu,ENST00000245105,;SH3TC1,missense_variant,p.Asp339Glu,ENST00000539824,;SH3TC1,downstream_gene_variant,,ENST00000508641,;SH3TC1,splice_region_variant,,ENST00000514274,;SH3TC1,upstream_gene_variant,,ENST00000507801,;SH3TC1,splice_region_variant,,ENST00000502669,;SH3TC1,splice_region_variant,,ENST00000506360,;SH3TC1,splice_region_variant,,ENST00000515682,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000508438,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000509553,;SH3TC1,upstream_gene_variant,,ENST00000508183,;SH3TC1,upstream_gene_variant,,ENST00000513495,;SH3TC1,upstream_gene_variant,,ENST00000511002,;SH3TC1,upstream_gene_variant,,ENST00000502350,;	G	ENSG00000125089	ENST00000245105	Transcript	missense_variant	1312	1245	415	D/E	gaC/gaG	.	.	.	1	SH3TC1	HGNC	26009	protein_coding	YES	CCDS3399.1	ENSP00000245105	S3TC1_HUMAN	F5GXD3_HUMAN,E7EQR1_HUMAN,D6RC98_HUMAN	UPI000013CB93	.	tolerated(0.13)	benign(0.222)	11/18	.	hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGACTCAGT	.	5	ESCA
LIN54	0	.	GRCh37	4	83849047	83849047	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*208A>G	.	.	ENST00000340417	13/13	76	63	12	27	27	0	LIN54,3_prime_UTR_variant,,ENST00000395283,;LIN54,3_prime_UTR_variant,,ENST00000446851,;LIN54,3_prime_UTR_variant,,ENST00000340417,;LIN54,3_prime_UTR_variant,,ENST00000505397,;LIN54,3_prime_UTR_variant,,ENST00000442461,;LIN54,3_prime_UTR_variant,,ENST00000395282,;LIN54,3_prime_UTR_variant,,ENST00000510557,;LIN54,3_prime_UTR_variant,,ENST00000506560,;LIN54,intron_variant,,ENST00000505905,;LIN54,3_prime_UTR_variant,,ENST00000508171,;LIN54,3_prime_UTR_variant,,ENST00000510877,;	C	ENSG00000189308	ENST00000340417	Transcript	3_prime_UTR_variant	2836	.	.	.	.	.	.	.	-1	LIN54	HGNC	25397	protein_coding	YES	CCDS3599.1	ENSP00000341947	LIN54_HUMAN	.	UPI00001D75DE	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE	TTCAATTTAGA	.	3	ESCA
MAPK10	0	.	GRCh37	4	86985430	86985430	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1099G>A	p.Glu367Lys	p.E367K	ENST00000359221	11/14	58	51	7	48	48	0	MAPK10,missense_variant,p.Glu222Lys,ENST00000449047,;MAPK10,missense_variant,p.Glu222Lys,ENST00000395160,;MAPK10,missense_variant,p.Glu367Lys,ENST00000361569,;MAPK10,missense_variant,p.Glu329Lys,ENST00000395169,;MAPK10,missense_variant,p.Glu222Lys,ENST00000395157,;MAPK10,missense_variant,p.Glu367Lys,ENST00000359221,;MAPK10,missense_variant,p.Glu280Lys,ENST00000515400,;MAPK10,missense_variant,p.Glu329Lys,ENST00000395166,;MAPK10,missense_variant,p.Glu367Lys,ENST00000395161,;MAPK10,downstream_gene_variant,,ENST00000489368,;MAPK10,3_prime_UTR_variant,,ENST00000310816,;MAPK10,non_coding_transcript_exon_variant,,ENST00000508262,;	T	ENSG00000109339	ENST00000359221	Transcript	missense_variant	1626	1099	367	E/K	Gaa/Aaa	COSM3606768,COSM1058454,COSM3606769,COSM1058455	.	.	-1	MAPK10	HGNC	6872	protein_coding	YES	CCDS34026.1	ENSP00000352157	MK10_HUMAN	D6RJF9_HUMAN,D6RFZ7_HUMAN,D6RFX8_HUMAN,D6RDG1_HUMAN,D6RCB1_HUMAN,D6RC26_HUMAN,D6RBH2_HUMAN,D6RAU3_HUMAN,D6RAJ0_HUMAN,D6R9C1_HUMAN,B3KR72_HUMAN,A8MWW6_HUMAN	UPI0000049042	.	deleterious(0.01)	benign(0.39)	11/14	.	hmmpanther:PTHR24055:SF162,hmmpanther:PTHR24055,Superfamily_domains:SSF56112,Prints_domain:PR01772	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACTTCGGCTG	.	4	ESCA
EIF4E	0	.	GRCh37	4	99801180	99801180	+	3'Flank	SNP	G	G	C	rs55937026	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000505992	.	37	17	20	15	15	0	EIF4E,3_prime_UTR_variant,,ENST00000450253,;EIF4E,downstream_gene_variant,,ENST00000504432,;EIF4E,downstream_gene_variant,,ENST00000505992,;EIF4E,downstream_gene_variant,,ENST00000511644,;EIF4E,downstream_gene_variant,,ENST00000280892,;EIF4E,downstream_gene_variant,,ENST00000505194,;EIF4E,downstream_gene_variant,,ENST00000515638,;	C	ENSG00000151247	ENST00000505992	Transcript	downstream_gene_variant	.	.	.	.	.	rs55937026	.	869	-1	EIF4E	HGNC	3287	protein_coding	YES	CCDS54779.1	ENSP00000425561	IF4E_HUMAN	D6RFJ3_HUMAN	UPI00017BAF0A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATAAAGATGGA	byCluster	4	ESCA
FNIP1	0	.	GRCh37	5	131042140	131042140	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.878A>T	p.Gln293Leu	p.Q293L	ENST00000510461	9/18	47	41	6	54	54	0	FNIP1,missense_variant,p.Gln265Leu,ENST00000307968,;FNIP1,missense_variant,p.Gln293Leu,ENST00000510461,;FNIP1,missense_variant,p.Gln248Leu,ENST00000307954,;FNIP1,missense_variant,p.Gln293Leu,ENST00000511848,;CTC-432M15.3,intron_variant,,ENST00000514667,;	A	ENSG00000217128	ENST00000510461	Transcript	missense_variant	974	878	293	Q/L	cAa/cTa	.	.	.	-1	FNIP1	HGNC	29418	protein_coding	YES	CCDS34227.1	ENSP00000421985	FNIP1_HUMAN	B3KX44_HUMAN	UPI00001AEE81	.	deleterious(0.02)	probably_damaging(0.992)	9/18	.	hmmpanther:PTHR21634,hmmpanther:PTHR21634:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.R291H|c.872G>A|4	RADIA|MUTECT|MUSE|VARSCANS	TTGTTTGGCTG	.	4	ESCA
DNAH5	0	.	GRCh37	5	13864573	13864573	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4529G>A	p.Gly1510Glu	p.G1510E	ENST00000265104	28/79	129	121	7	36	36	0	DNAH5,missense_variant,p.Gly1510Glu,ENST00000265104,;CTB-51A17.1,intron_variant,,ENST00000503244,;	T	ENSG00000039139	ENST00000265104	Transcript	missense_variant	4634	4529	1510	G/E	gGg/gAg	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0)	28/79	.	Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CATTCCCCACA	.	2	ESCA
TMCO6	0	.	GRCh37	5	140021959	140021959	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558G>T	p.Gln186His	p.Q186H	ENST00000394671	5/12	16	4	12	23	23	0	TMCO6,missense_variant,p.Gln186His,ENST00000394671,;TMCO6,missense_variant,p.Gln186His,ENST00000252100,;TMCO6,3_prime_UTR_variant,,ENST00000511410,;TMCO6,intron_variant,,ENST00000537378,;IK,upstream_gene_variant,,ENST00000513256,;NDUFA2,downstream_gene_variant,,ENST00000252102,;NDUFA2,downstream_gene_variant,,ENST00000512088,;NDUFA2,intron_variant,,ENST00000510680,;TMCO6,non_coding_transcript_exon_variant,,ENST00000514449,;TMCO6,non_coding_transcript_exon_variant,,ENST00000510336,;TMCO6,non_coding_transcript_exon_variant,,ENST00000509605,;TMCO6,intron_variant,,ENST00000515653,;TMCO6,intron_variant,,ENST00000504069,;TMCO6,downstream_gene_variant,,ENST00000505086,;TMCO6,downstream_gene_variant,,ENST00000509217,;TMCO6,upstream_gene_variant,,ENST00000509269,;TMCO6,downstream_gene_variant,,ENST00000513002,;NDUFA2,downstream_gene_variant,,ENST00000502960,;TMCO6,downstream_gene_variant,,ENST00000394669,;TMCO6,upstream_gene_variant,,ENST00000515265,;	T	ENSG00000113119	ENST00000394671	Transcript	missense_variant	659	558	186	Q/H	caG/caT	.	.	.	1	TMCO6	HGNC	28814	protein_coding	YES	CCDS4233.2	ENSP00000378166	TMCO6_HUMAN	.	UPI00003E5FF0	.	tolerated(0.13)	benign(0.014)	5/12	.	Superfamily_domains:SSF48371,SMART_domains:SM00185,Gene3D:1.25.10.10,hmmpanther:PTHR16356	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGCTCCT	.	5	ESCA
PCDH12	0	.	GRCh37	5	141334669	141334669	+	Silent	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2748C>G	p.%3D	p.L916L	ENST00000231484	1/4	87	25	62	79	79	0	PCDH12,synonymous_variant,p.%3D,ENST00000231484,;RNF14,upstream_gene_variant,,ENST00000506822,;RNF14,upstream_gene_variant,,ENST00000511961,;PCDH12,downstream_gene_variant,,ENST00000510041,;AC005740.6,downstream_gene_variant,,ENST00000607378,;PCDH12,downstream_gene_variant,,ENST00000512221,;	C	ENSG00000113555	ENST00000231484	Transcript	synonymous_variant	3959	2748	916	L	ctC/ctG	.	.	.	-1	PCDH12	HGNC	8657	protein_coding	YES	CCDS4269.1	ENSP00000231484	PCD12_HUMAN	E5RJD4_HUMAN	UPI00001313B4	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTGAGATG	.	5	ESCA
RANBP17	0	.	GRCh37	5	170319525	170319525	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.391G>A	p.Glu131Lys	p.E131K	ENST00000523189	4/28	60	43	17	38	38	0	RANBP17,missense_variant,p.Glu131Lys,ENST00000523189,;RANBP17,downstream_gene_variant,,ENST00000519944,;RANBP17,missense_variant,p.Glu131Lys,ENST00000519949,;RANBP17,missense_variant,p.Glu131Lys,ENST00000389118,;RANBP17,missense_variant,p.Glu131Lys,ENST00000519256,;RANBP17,missense_variant,p.Glu131Lys,ENST00000522533,;RANBP17,missense_variant,p.Glu131Lys,ENST00000522066,;RANBP17,missense_variant,p.Glu131Lys,ENST00000520864,;RANBP17,non_coding_transcript_exon_variant,,ENST00000523727,;RANBP17,non_coding_transcript_exon_variant,,ENST00000443155,;RANBP17,non_coding_transcript_exon_variant,,ENST00000519130,;CTC-455F18.3,upstream_gene_variant,,ENST00000522096,;	A	ENSG00000204764	ENST00000523189	Transcript	missense_variant	555	391	131	E/K	Gaa/Aaa	COSM3429277	.	.	1	RANBP17	HGNC	14428	protein_coding	YES	CCDS34287.1	ENSP00000427975	RBP17_HUMAN	Q546R4_HUMAN,E5RHX1_HUMAN	UPI000000107C	.	tolerated(0.09)	benign(0.014)	4/28	.	Superfamily_domains:SSF48371,hmmpanther:PTHR12596,hmmpanther:PTHR12596:SF8	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGAGAAATT	.	5	ESCA
SH3PXD2B	0	.	GRCh37	5	171760943	171760943	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4430C>G	.	.	ENST00000311601	13/13	42	27	14	52	52	0	SH3PXD2B,3_prime_UTR_variant,,ENST00000311601,;SH3PXD2B,intron_variant,,ENST00000519643,;SH3PXD2B,intron_variant,,ENST00000518522,;SH3PXD2B,intron_variant,,ENST00000523651,;	C	ENSG00000174705	ENST00000311601	Transcript	3_prime_UTR_variant	7337	.	.	.	.	.	.	.	-1	SH3PXD2B	HGNC	29242	protein_coding	YES	CCDS34291.1	ENSP00000309714	SPD2B_HUMAN	.	UPI000020C12E	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTGGACACC	.	5	ESCA
TBC1D9B	0	.	GRCh37	5	179290535	179290535	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3666C>T	p.%3D	p.D1222D	ENST00000356834	22/22	43	9	33	42	42	0	TBC1D9B,synonymous_variant,p.%3D,ENST00000355235,;TBC1D9B,synonymous_variant,p.%3D,ENST00000524222,;TBC1D9B,synonymous_variant,p.%3D,ENST00000519746,;TBC1D9B,synonymous_variant,p.%3D,ENST00000356834,;TBC1D9B,synonymous_variant,p.%3D,ENST00000444477,;TBC1D9B,intron_variant,,ENST00000522472,;C5orf45,upstream_gene_variant,,ENST00000520698,;C5orf45,upstream_gene_variant,,ENST00000376931,;C5orf45,upstream_gene_variant,,ENST00000523084,;CTC-241N9.1,downstream_gene_variant,,ENST00000499601,;C5orf45,upstream_gene_variant,,ENST00000292586,;C5orf45,upstream_gene_variant,,ENST00000518219,;C5orf45,upstream_gene_variant,,ENST00000521333,;C5orf45,upstream_gene_variant,,ENST00000403396,;C5orf45,upstream_gene_variant,,ENST00000518235,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000518085,;C5orf45,upstream_gene_variant,,ENST00000517338,;TBC1D9B,downstream_gene_variant,,ENST00000522180,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000520794,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000521469,;C5orf45,upstream_gene_variant,,ENST00000519398,;TBC1D9B,downstream_gene_variant,,ENST00000520912,;C5orf45,upstream_gene_variant,,ENST00000519318,;C5orf45,upstream_gene_variant,,ENST00000520995,;TBC1D9B,downstream_gene_variant,,ENST00000522921,;C5orf45,upstream_gene_variant,,ENST00000520150,;TBC1D9B,downstream_gene_variant,,ENST00000519757,;C5orf45,upstream_gene_variant,,ENST00000523835,;C5orf45,upstream_gene_variant,,ENST00000521299,;C5orf45,upstream_gene_variant,,ENST00000522663,;C5orf45,upstream_gene_variant,,ENST00000519213,;C5orf45,upstream_gene_variant,,ENST00000524068,;C5orf45,upstream_gene_variant,,ENST00000523737,;C5orf45,upstream_gene_variant,,ENST00000522157,;C5orf45,upstream_gene_variant,,ENST00000519208,;	A	ENSG00000197226	ENST00000356834	Transcript	synonymous_variant	3704	3666	1222	D	gaC/gaT	.	.	.	-1	TBC1D9B	HGNC	29097	protein_coding	YES	CCDS43408.1	ENSP00000349291	TBC9B_HUMAN	.	UPI000034ECFF	.	.	.	22/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAATGTCCAC	.	5	ESCA
TARS	0	.	GRCh37	5	33467748	33467748	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2206G>A	p.Glu736Lys	p.E736K	ENST00000455217	20/20	98	85	13	51	51	0	TARS,missense_variant,p.Glu703Lys,ENST00000502553,;TARS,missense_variant,p.Glu703Lys,ENST00000265112,;TARS,missense_variant,p.Glu599Lys,ENST00000541634,;TARS,missense_variant,p.Glu736Lys,ENST00000455217,;TARS,missense_variant,p.Glu582Lys,ENST00000414361,;TARS,downstream_gene_variant,,ENST00000509410,;TARS,3_prime_UTR_variant,,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,non_coding_transcript_exon_variant,,ENST00000503422,;TARS,downstream_gene_variant,,ENST00000509731,;	A	ENSG00000113407	ENST00000455217	Transcript	missense_variant	2328	2206	736	E/K	Gaa/Aaa	.	.	.	1	TARS	HGNC	11572	protein_coding	YES	CCDS58943.1	ENSP00000387710	SYTC_HUMAN	D6RBR8_HUMAN	UPI00017A6D60	.	tolerated(0.14)	benign(0.009)	20/20	.	Superfamily_domains:SSF52954,Gene3D:3.40.50.800,Pfam_domain:PF03129,TIGRFAM_domain:TIGR00418,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF23,HAMAP:MF_00184	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCTGAAACT	.	4	ESCA
SPEF2	0	.	GRCh37	5	35628627	35628627	+	Missense_Mutation	SNP	G	G	A	rs755241823	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.124G>A	p.Glu42Lys	p.E42K	ENST00000356031	2/37	112	43	69	64	64	0	SPEF2,missense_variant,p.Glu42Lys,ENST00000440995,;SPEF2,missense_variant,p.Glu42Lys,ENST00000510777,;SPEF2,missense_variant,p.Glu42Lys,ENST00000282469,;SPEF2,missense_variant,p.Glu42Lys,ENST00000509059,;SPEF2,missense_variant,p.Glu42Lys,ENST00000356031,;RNU7-130P,downstream_gene_variant,,ENST00000459491,;SPEF2,missense_variant,p.Glu42Lys,ENST00000505847,;SPEF2,non_coding_transcript_exon_variant,,ENST00000505088,;	A	ENSG00000152582	ENST00000356031	Transcript	missense_variant	278	124	42	E/K	Gaa/Aaa	rs755241823,COSM1543688,COSM1543687	.	.	1	SPEF2	HGNC	26293	protein_coding	YES	CCDS43309.1	ENSP00000348314	SPEF2_HUMAN	.	UPI0001505B9F	.	deleterious(0.03)	possibly_damaging(0.574)	2/37	.	PROSITE_profiles:PS50021,hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0,Pfam_domain:PF06294	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTGAACTT	.	5	ESCA
UGT3A1	0	.	GRCh37	5	35962969	35962969	+	Intron	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.843+2519G>A	.	.	ENST00000274278	.	65	45	20	28	28	0	UGT3A1,3_prime_UTR_variant,,ENST00000333811,;UGT3A1,intron_variant,,ENST00000274278,;UGT3A1,intron_variant,,ENST00000507113,;UGT3A1,intron_variant,,ENST00000503189,;UGT3A1,intron_variant,,ENST00000513233,;UGT3A1,3_prime_UTR_variant,,ENST00000515801,;	T	ENSG00000145626	ENST00000274278	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	UGT3A1	HGNC	26625	protein_coding	YES	CCDS3913.1	ENSP00000274278	UD3A1_HUMAN	A8K444_HUMAN	UPI000003C38B	.	.	.	.	4/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGATTCTGAGG	.	5	ESCA
NIPBL	0	.	GRCh37	5	36876898	36876898	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-462C>G	.	.	ENST00000282516	1/47	142	120	22	75	75	0	NIPBL,5_prime_UTR_variant,,ENST00000448238,;NIPBL,5_prime_UTR_variant,,ENST00000282516,;	G	ENSG00000164190	ENST00000282516	Transcript	5_prime_UTR_variant	38	.	.	.	.	.	.	.	1	NIPBL	HGNC	28862	protein_coding	YES	CCDS3920.1	ENSP00000282516	NIPBL_HUMAN	A2RRA7_HUMAN	UPI00003761B5	.	.	.	1/47	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGGAACGAGAG	.	4	ESCA
RICTOR	0	.	GRCh37	5	38950435	38950435	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3515C>T	p.Thr1172Ile	p.T1172I	ENST00000357387	31/38	100	93	7	35	35	0	RICTOR,missense_variant,p.Thr1172Ile,ENST00000357387,;RICTOR,missense_variant,p.Thr1172Ile,ENST00000296782,;RICTOR,downstream_gene_variant,,ENST00000503698,;RICTOR,3_prime_UTR_variant,,ENST00000511516,;OSMR,downstream_gene_variant,,ENST00000509237,;	A	ENSG00000164327	ENST00000357387	Transcript	missense_variant	3546	3515	1172	T/I	aCt/aTt	.	.	.	-1	RICTOR	HGNC	28611	protein_coding	YES	CCDS34148.1	ENSP00000349959	RICTR_HUMAN	.	UPI00003529F3	.	tolerated(0.19)	benign(0.073)	31/38	.	Pfam_domain:PF14665,hmmpanther:PTHR13298:SF11,hmmpanther:PTHR13298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TACCAGTGTCT	.	2	ESCA
EMB	0	.	GRCh37	5	49736952	49736952	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.34G>A	p.Ala12Thr	p.A12T	ENST00000303221	1/9	16	9	7	18	18	0	EMB,missense_variant,p.Ala12Thr,ENST00000303221,;EMB,missense_variant,p.Ala12Thr,ENST00000508934,;EMB,intron_variant,,ENST00000506190,;	T	ENSG00000170571	ENST00000303221	Transcript	missense_variant	250	34	12	A/T	Gcg/Acg	.	.	.	-1	EMB	HGNC	30465	protein_coding	YES	CCDS3953.1	ENSP00000302289	EMB_HUMAN	B7Z902_HUMAN	UPI0000160A6D	.	tolerated_low_confidence(0.07)	benign(0.039)	1/9	.	Cleavage_site_(Signalp):SignalP-noTM	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGCGCCCTGG	.	5	ESCA
ERBB2IP	0	.	GRCh37	5	65350089	65350089	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2943C>A	p.Tyr981Ter	p.Y981*	ENST00000506030	21/26	28	22	6	19	19	0	ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000380935,;ERBB2IP,stop_gained,p.Tyr977Ter,ENST00000511297,;ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000284037,;ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000508515,;ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000380943,;ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000380938,;ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000380936,;ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000506030,;ERBB2IP,stop_gained,p.Tyr981Ter,ENST00000380939,;ERBB2IP,intron_variant,,ENST00000416865,;ERBB2IP,upstream_gene_variant,,ENST00000511671,;ERBB2IP,upstream_gene_variant,,ENST00000503913,;	A	ENSG00000112851	ENST00000506030	Transcript	stop_gained	3034	2943	981	Y/*	taC/taA	.	.	.	1	ERBB2IP	HGNC	15842	protein_coding	YES	CCDS58952.1	ENSP00000426632	LAP2_HUMAN	.	UPI0001D3B314	.	.	.	21/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAATACAGTAG	.	5	ESCA
RASA1	0	.	GRCh37	5	86658398	86658398	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1363G>T	p.Asp455Tyr	p.D455Y	ENST00000274376	10/25	43	35	8	52	52	0	RASA1,missense_variant,p.Asp288Tyr,ENST00000512763,;RASA1,missense_variant,p.Asp278Tyr,ENST00000456692,;RASA1,missense_variant,p.Asp455Tyr,ENST00000274376,;RASA1,missense_variant,p.Asp289Tyr,ENST00000506290,;RASA1,missense_variant,p.Asp455Tyr,ENST00000515800,;RASA1,non_coding_transcript_exon_variant,,ENST00000509953,;	T	ENSG00000145715	ENST00000274376	Transcript	missense_variant	1927	1363	455	D/Y	Gat/Tat	.	.	.	1	RASA1	HGNC	9871	protein_coding	YES	CCDS34200.1	ENSP00000274376	RASA1_HUMAN	B4DTL8_HUMAN	UPI00001351F3	.	deleterious(0)	possibly_damaging(0.87)	10/25	.	hmmpanther:PTHR10194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTGGATGGC	.	5	ESCA
PDSS2	0	.	GRCh37	6	107585550	107585550	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630+9683C>G	.	.	ENST00000369037	.	21	11	9	22	22	0	PDSS2,3_prime_UTR_variant,,ENST00000369031,;PDSS2,intron_variant,,ENST00000453874,;PDSS2,intron_variant,,ENST00000369037,;AL590489.1,upstream_gene_variant,,ENST00000366111,;	C	ENSG00000164494	ENST00000369037	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PDSS2	HGNC	23041	protein_coding	YES	CCDS5059.1	ENSP00000358033	DLP1_HUMAN	B4DWD3_HUMAN	UPI000013E3B4	.	.	.	.	3/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTAAAGAGTAC	.	5	ESCA
RP11-544L8__B.4	0	.	GRCh37	6	114238199	114238199	+	RNA	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.700C>T	.	.	ENST00000314481	2/4	13	5	8	24	24	0	RP11-544L8__B.4,non_coding_transcript_exon_variant,,ENST00000314481,;	T	ENSG00000175967	ENST00000314481	Transcript	non_coding_transcript_exon_variant	700	.	.	.	.	.	.	.	1	RP11-544L8__B.4	Clone_based_vega_gene	.	antisense	YES	.	.	.	.	.	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE	ACCCTCACTAG	.	4	ESCA
TSPYL4	0	.	GRCh37	6	116579745	116579745	+	5'Flank	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000420283	.	14	4	10	28	28	0	DSE,missense_variant,p.Asp47His,ENST00000540275,;DSE,5_prime_UTR_variant,,ENST00000430252,;TSPYL4,upstream_gene_variant,,ENST00000420283,;RP3-486I3.7,downstream_gene_variant,,ENST00000448740,;RP3-486I3.4,non_coding_transcript_exon_variant,,ENST00000435100,;	C	ENSG00000187189	ENST00000420283	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	4484	-1	TSPYL4	HGNC	21559	protein_coding	YES	CCDS5106.1	ENSP00000410943	TSYL4_HUMAN	Q69YV8_HUMAN	UPI00001BBB76	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCATTGATGAG	.	5	ESCA
NOL7	0	.	GRCh37	6	13615843	13615843	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.253G>C	p.Glu85Gln	p.E85Q	ENST00000451315	1/8	60	47	12	37	37	0	NOL7,missense_variant,p.Glu85Gln,ENST00000451315,;NOL7,missense_variant,p.Glu23Gln,ENST00000420088,;AL441883.1,3_prime_UTR_variant,,ENST00000600057,;SIRT5,downstream_gene_variant,,ENST00000359782,;SIRT5,downstream_gene_variant,,ENST00000397350,;SIRT5,downstream_gene_variant,,ENST00000606117,;RP1-223E5.4,upstream_gene_variant,,ENST00000566170,;NOL7,non_coding_transcript_exon_variant,,ENST00000474485,;SIRT5,downstream_gene_variant,,ENST00000379250,;	C	ENSG00000225921	ENST00000451315	Transcript	missense_variant	285	253	85	E/Q	Gag/Cag	.	.	.	1	NOL7	HGNC	21040	protein_coding	YES	CCDS4528.1	ENSP00000405674	NOL7_HUMAN	.	UPI000007196C	.	tolerated(0.1)	possibly_damaging(0.702)	1/8	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32337	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGCGGGAGACC	.	4	ESCA
UTRN	0	.	GRCh37	6	144814581	144814581	+	Silent	SNP	C	C	T	rs778079117	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4582C>T	p.%3D	p.L1528L	ENST00000367545	32/74	25	20	5	18	18	0	UTRN,synonymous_variant,p.%3D,ENST00000367545,;	T	ENSG00000152818	ENST00000367545	Transcript	synonymous_variant	4582	4582	1528	L	Ctg/Ttg	rs778079117,COSM1074129	.	.	1	UTRN	HGNC	12635	protein_coding	YES	CCDS34547.1	ENSP00000356515	UTRO_HUMAN	Q6LBS5_HUMAN,Q5SYY2_HUMAN,Q5JT45_HUMAN	UPI00003673F1	.	.	.	32/74	.	hmmpanther:PTHR11915:SF225,hmmpanther:PTHR11915,Gene3D:1.20.58.60,SMART_domains:SM00150,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGACCTGGGC	.	5	ESCA
QKI	0	.	GRCh37	6	163987371	163987371	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.935-382G>C	.	.	ENST00000361752	.	45	29	15	36	36	0	QKI,3_prime_UTR_variant,,ENST00000453779,;QKI,3_prime_UTR_variant,,ENST00000275262,;QKI,3_prime_UTR_variant,,ENST00000392127,;QKI,intron_variant,,ENST00000544361,;QKI,intron_variant,,ENST00000361195,;QKI,intron_variant,,ENST00000537883,;QKI,intron_variant,,ENST00000361752,;QKI,downstream_gene_variant,,ENST00000544823,;QKI,downstream_gene_variant,,ENST00000537041,;QKI,downstream_gene_variant,,ENST00000424802,;QKI,3_prime_UTR_variant,,ENST00000361758,;QKI,intron_variant,,ENST00000545607,;QKI,downstream_gene_variant,,ENST00000540719,;QKI,upstream_gene_variant,,ENST00000541696,;	C	ENSG00000112531	ENST00000361752	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	QKI	HGNC	21100	protein_coding	YES	CCDS5285.1	ENSP00000355094	QKI_HUMAN	F5H8C8_HUMAN,F5H5U6_HUMAN,F5GYM3_HUMAN	UPI0000029EBD	.	.	.	.	6/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAAGGTTAG	.	5	ESCA
CAP2	0	.	GRCh37	6	17556938	17556938	+	3'UTR	SNP	G	G	C	rs75059190	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*265G>C	.	.	ENST00000229922	13/13	58	47	10	52	52	0	CAP2,3_prime_UTR_variant,,ENST00000378990,;CAP2,3_prime_UTR_variant,,ENST00000229922,;CAP2,downstream_gene_variant,,ENST00000465994,;CAP2,downstream_gene_variant,,ENST00000489374,;CAP2,downstream_gene_variant,,ENST00000493172,;	C	ENSG00000112186	ENST00000229922	Transcript	3_prime_UTR_variant	2231	.	.	.	.	rs75059190	.	.	1	CAP2	HGNC	20039	protein_coding	YES	CCDS4539.1	ENSP00000229922	CAP2_HUMAN	.	UPI0000126EC6	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAGAATTC	.	5	ESCA
KIAA0319	0	.	GRCh37	6	24572926	24572926	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1735G>A	p.Gly579Arg	p.G579R	ENST00000378214	11/21	35	21	13	35	35	0	KIAA0319,missense_variant,p.Gly579Arg,ENST00000543707,;KIAA0319,missense_variant,p.Gly534Arg,ENST00000430948,;KIAA0319,missense_variant,p.Gly579Arg,ENST00000378214,;KIAA0319,missense_variant,p.Gly570Arg,ENST00000535378,;KIAA0319,missense_variant,p.Gly579Arg,ENST00000537886,;	T	ENSG00000137261	ENST00000378214	Transcript	missense_variant	2260	1735	579	G/R	Gga/Aga	.	.	.	-1	KIAA0319	HGNC	21580	protein_coding	YES	CCDS34348.1	ENSP00000367459	K0319_HUMAN	.	UPI000020D61A	.	deleterious(0)	probably_damaging(0.983)	11/21	.	Superfamily_domains:SSF49299,SMART_domains:SM00089,Pfam_domain:PF02010,Gene3D:2.60.40.670,hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF194,PROSITE_profiles:PS50093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACTCCCTAAG	.	5	ESCA
HIST1H4C	0	.	GRCh37	6	26104467	26104467	+	Silent	SNP	C	C	T	rs781429243	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292C>T	p.%3D	p.L98L	ENST00000377803	1/1	36	32	4	32	32	0	HIST1H4C,synonymous_variant,p.%3D,ENST00000377803,;HIST1H1T,downstream_gene_variant,,ENST00000338379,;	T	ENSG00000197061	ENST00000377803	Transcript	synonymous_variant	364	292	98	L	Ctg/Ttg	rs781429243	.	.	1	HIST1H4C	HGNC	4787	protein_coding	YES	CCDS4583.1	ENSP00000367034	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	.	.	1/1	.	hmmpanther:PTHR10484,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCACTCTGTAT	.	3	ESCA
HIST1H4L	0	.	GRCh37	6	27841093	27841093	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196G>C	p.Val66Leu	p.V66L	ENST00000355981	1/1	82	65	17	81	81	0	HIST1H4L,missense_variant,p.Val66Leu,ENST00000355981,;HIST1H3I,upstream_gene_variant,,ENST00000328488,;	G	ENSG00000198558	ENST00000355981	Transcript	missense_variant	197	196	66	V/L	Gta/Cta	.	.	.	-1	HIST1H4L	HGNC	4791	protein_coding	YES	CCDS4637.1	ENSP00000348258	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	tolerated(0.05)	benign(0.046)	1/1	.	hmmpanther:PTHR10484,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00803,SMART_domains:SM00417,Superfamily_domains:SSF47113,Prints_domain:PR00623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTACATTCT	.	5	ESCA
PSMB8	0	.	GRCh37	6	32812357	32812357	+	5'Flank	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000374882	.	21	11	10	23	23	0	PSMB8,5_prime_UTR_variant,,ENST00000374881,;PSMB9,intron_variant,,ENST00000395330,;TAP1,downstream_gene_variant,,ENST00000425148,;TAP1,downstream_gene_variant,,ENST00000354258,;PSMB8,upstream_gene_variant,,ENST00000395339,;PSMB9,upstream_gene_variant,,ENST00000414474,;PSMB8,upstream_gene_variant,,ENST00000374882,;TAPSAR1,non_coding_transcript_exon_variant,,ENST00000412095,;TAPSAR1,non_coding_transcript_exon_variant,,ENST00000458296,;TAPSAR1,intron_variant,,ENST00000413039,;TAPSAR1,intron_variant,,ENST00000415067,;TAPSAR1,intron_variant,,ENST00000453426,;TAPSAR1,intron_variant,,ENST00000429600,;PSMB8,non_coding_transcript_exon_variant,,ENST00000484003,;PSMB8,upstream_gene_variant,,ENST00000490613,;TAP1,downstream_gene_variant,,ENST00000487296,;TAP1,downstream_gene_variant,,ENST00000486332,;	T	ENSG00000204264	ENST00000374882	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	533	-1	PSMB8	HGNC	9545	protein_coding	YES	CCDS4757.1	ENSP00000364016	PSB8_HUMAN	.	UPI0000140B8A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCAGGTTCA	.	5	ESCA
TULP1	0	.	GRCh37	6	35465741	35465741	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*363G>C	.	.	ENST00000229771	15/15	31	17	14	23	23	0	TULP1,3_prime_UTR_variant,,ENST00000229771,;TULP1,3_prime_UTR_variant,,ENST00000322263,;TEAD3,upstream_gene_variant,,ENST00000402886,;TEAD3,upstream_gene_variant,,ENST00000338863,;TULP1,downstream_gene_variant,,ENST00000495781,;	G	ENSG00000112041	ENST00000229771	Transcript	3_prime_UTR_variant	2072	.	.	.	.	.	.	.	-1	TULP1	HGNC	12423	protein_coding	YES	CCDS4807.1	ENSP00000229771	TULP1_HUMAN	Q0QD38_HUMAN	UPI000045742A	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCGGAGC	.	5	ESCA
C6orf141	0	.	GRCh37	6	49518881	49518881	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376G>T	p.Glu126Ter	p.E126*	ENST00000529246	1/1	54	39	15	33	33	0	C6orf141,stop_gained,p.Glu126Ter,ENST00000529246,;C6orf141,non_coding_transcript_exon_variant,,ENST00000424426,;C6orf141,stop_gained,p.Glu126Ter,ENST00000414696,;C6orf141,stop_gained,p.Glu126Ter,ENST00000371194,;C6orf141,upstream_gene_variant,,ENST00000415078,;C6orf141,upstream_gene_variant,,ENST00000530382,;C6orf141,upstream_gene_variant,,ENST00000526429,;	T	ENSG00000197261	ENST00000529246	Transcript	stop_gained	769	376	126	E/*	Gag/Tag	.	.	.	1	C6orf141	HGNC	21351	protein_coding	YES	CCDS55018.1	ENSP00000434602	CF141_HUMAN	.	UPI000013E9DC	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGGCGAGGAG	.	5	ESCA
PKHD1	0	.	GRCh37	6	51824753	51824753	+	Silent	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5823A>G	p.%3D	p.Q1941Q	ENST00000371117	36/67	61	45	15	40	40	0	PKHD1,synonymous_variant,p.%3D,ENST00000340994,;PKHD1,synonymous_variant,p.%3D,ENST00000371117,;	C	ENSG00000170927	ENST00000371117	Transcript	synonymous_variant	6099	5823	1941	Q	caA/caG	.	.	.	-1	PKHD1	HGNC	9016	protein_coding	YES	CCDS4935.1	ENSP00000360158	PKHD1_HUMAN	.	UPI000013C4C0	.	.	.	36/67	.	PROSITE_profiles:PS51484,hmmpanther:PTHR11915:SF230,hmmpanther:PTHR11915,Pfam_domain:PF10162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATCTTGTGG	.	5	ESCA
COL21A1	0	.	GRCh37	6	55925539	55925539	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2407G>T	p.Ala803Ser	p.A803S	ENST00000244728	27/30	61	49	12	35	35	0	COL21A1,missense_variant,p.Ala800Ser,ENST00000370819,;COL21A1,missense_variant,p.Ala803Ser,ENST00000535941,;COL21A1,missense_variant,p.Ala803Ser,ENST00000244728,;COL21A1,missense_variant,p.Gly203Cys,ENST00000370808,;COL21A1,splice_region_variant,,ENST00000467216,;COL21A1,splice_region_variant,,ENST00000467045,;COL21A1,splice_region_variant,,ENST00000488912,;COL21A1,non_coding_transcript_exon_variant,,ENST00000482933,;	A	ENSG00000124749	ENST00000244728	Transcript	missense_variant	2805	2407	803	A/S	Gcc/Tcc	.	.	.	-1	COL21A1	HGNC	17025	protein_coding	YES	CCDS55025.1	ENSP00000244728	COLA1_HUMAN	A6PVD9_HUMAN	UPI0000071DFE	.	tolerated(0.47)	benign(0.012)	27/30	.	hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTACCTCTTA	.	5	ESCA
LCA5	0	.	GRCh37	6	80228704	80228704	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-93G>A	.	.	ENST00000392959	3/9	23	10	13	14	14	0	LCA5,5_prime_UTR_variant,,ENST00000369846,;LCA5,5_prime_UTR_variant,,ENST00000467898,;LCA5,5_prime_UTR_variant,,ENST00000392959,;	T	ENSG00000135338	ENST00000392959	Transcript	5_prime_UTR_variant	520	.	.	.	.	.	.	.	-1	LCA5	HGNC	31923	protein_coding	YES	CCDS4990.1	ENSP00000376686	LCA5_HUMAN	A7X9N5_HUMAN	UPI000007144D	.	.	.	3/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCAGATC	.	5	ESCA
LYRM2	0	.	GRCh37	6	90347493	90347493	+	Missense_Mutation	SNP	C	C	G	rs769238833	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154G>C	p.Glu52Gln	p.E52Q	ENST00000523377	2/3	82	69	12	74	74	0	LYRM2,missense_variant,p.Glu52Gln,ENST00000520318,;LYRM2,missense_variant,p.Glu52Gln,ENST00000523377,;LYRM2,missense_variant,p.Glu52Gln,ENST00000520441,;MDN1,downstream_gene_variant,,ENST00000369393,;ANKRD6,downstream_gene_variant,,ENST00000369408,;LYRM2,non_coding_transcript_exon_variant,,ENST00000524153,;LYRM2,non_coding_transcript_exon_variant,,ENST00000520897,;LYRM2,non_coding_transcript_exon_variant,,ENST00000523793,;LYRM2,non_coding_transcript_exon_variant,,ENST00000521961,;LYRM2,non_coding_transcript_exon_variant,,ENST00000523075,;LYRM2,non_coding_transcript_exon_variant,,ENST00000517396,;LYRM2,missense_variant,p.Glu52Gln,ENST00000412237,;ANKRD6,downstream_gene_variant,,ENST00000415924,;	G	ENSG00000083099	ENST00000523377	Transcript	missense_variant	191	154	52	E/Q	Gaa/Caa	rs769238833	.	.	-1	LYRM2	HGNC	25229	protein_coding	YES	CCDS5023.1	ENSP00000430025	LYRM2_HUMAN	.	UPI00000703DA	.	deleterious(0.04)	possibly_damaging(0.772)	2/3	.	hmmpanther:PTHR13675,Pfam_domain:PF05347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTCTTCTC	.	5	ESCA
ZCWPW1	0	.	GRCh37	7	100004374	100004374	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1113G>T	p.Trp371Cys	p.W371C	ENST00000398027	12/18	24	7	17	37	37	0	ZCWPW1,missense_variant,p.Trp121Cys,ENST00000471336,;ZCWPW1,missense_variant,p.Trp372Cys,ENST00000360951,;ZCWPW1,missense_variant,p.Trp371Cys,ENST00000398027,;ZCWPW1,missense_variant,p.Trp251Cys,ENST00000324725,;ZCWPW1,missense_variant,p.Trp251Cys,ENST00000490721,;ZCWPW1,non_coding_transcript_exon_variant,,ENST00000490089,;ZCWPW1,upstream_gene_variant,,ENST00000479315,;	A	ENSG00000078487	ENST00000398027	Transcript	missense_variant	1361	1113	371	W/C	tgG/tgT	.	.	.	-1	ZCWPW1	HGNC	23486	protein_coding	YES	CCDS43623.1	ENSP00000381109	ZCPW1_HUMAN	.	UPI000014146E	.	deleterious(0)	probably_damaging(1)	12/18	.	PROSITE_profiles:PS50812,hmmpanther:PTHR15999:SF2,hmmpanther:PTHR15999,Gene3D:2.30.30.160,Pfam_domain:PF00855,SMART_domains:SM00293,Superfamily_domains:SSF63748	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGATCCATGC	.	5	ESCA
KMT2E	0	.	GRCh37	7	104730616	104730616	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1519C>A	p.Gln507Lys	p.Q507K	ENST00000311117	14/27	70	65	5	46	46	0	KMT2E,missense_variant,p.Gln507Lys,ENST00000257745,;KMT2E,missense_variant,p.Gln507Lys,ENST00000476671,;KMT2E,missense_variant,p.Gln507Lys,ENST00000311117,;KMT2E,missense_variant,p.Gln507Lys,ENST00000334877,;KMT2E,5_prime_UTR_variant,,ENST00000334914,;KMT2E,downstream_gene_variant,,ENST00000478990,;KMT2E,missense_variant,p.Gln507Lys,ENST00000334884,;KMT2E,downstream_gene_variant,,ENST00000482560,;	A	ENSG00000005483	ENST00000311117	Transcript	missense_variant	2064	1519	507	Q/K	Cag/Aag	.	.	.	1	KMT2E	HGNC	18541	protein_coding	YES	CCDS34723.1	ENSP00000312379	KMT2E_HUMAN	O95038_HUMAN,C9JQ68_HUMAN,C9JNE1_HUMAN	UPI0000074133	.	deleterious(0.02)	benign(0.042)	14/27	.	hmmpanther:PTHR16286,hmmpanther:PTHR16286:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAATCAGAAT	.	2	ESCA
TNPO3	0	.	GRCh37	7	128615974	128615974	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2077C>T	p.His693Tyr	p.H693Y	ENST00000265388	17/23	34	10	24	28	28	0	TNPO3,missense_variant,p.His727Tyr,ENST00000393245,;TNPO3,missense_variant,p.His727Tyr,ENST00000471166,;TNPO3,missense_variant,p.His629Tyr,ENST00000471234,;TNPO3,missense_variant,p.His627Tyr,ENST00000482320,;TNPO3,missense_variant,p.His693Tyr,ENST00000265388,;RN7SL306P,downstream_gene_variant,,ENST00000492941,;	A	ENSG00000064419	ENST00000265388	Transcript	missense_variant	2221	2077	693	H/Y	Cac/Tac	.	.	.	-1	TNPO3	HGNC	17103	protein_coding	YES	CCDS5809.1	ENSP00000265388	TNPO3_HUMAN	E9PFH4_HUMAN,B3KMX1_HUMAN	UPI0000072FAB	.	tolerated(0.06)	benign(0.007)	17/23	.	hmmpanther:PTHR12363,hmmpanther:PTHR12363:SF5,Gene3D:1.25.10.10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TACGTGGTACA	.	4	ESCA
OR2A5	0	.	GRCh37	7	143748358	143748358	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.864G>C	p.Leu288Phe	p.L288F	ENST00000408906	1/1	65	23	42	59	59	0	OR2A5,missense_variant,p.Leu288Phe,ENST00000408906,;	C	ENSG00000221836	ENST00000408906	Transcript	missense_variant	898	864	288	L/F	ttG/ttC	COSM3635413	.	.	1	OR2A5	HGNC	8232	protein_coding	YES	CCDS43668.1	ENSP00000386208	OR2A5_HUMAN	.	UPI0000061F52	.	deleterious(0.02)	benign(0.295)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF232,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCTTGATCTA	.	3	ESCA
KIAA0895	0	.	GRCh37	7	36373465	36373465	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1306G>T	p.Gly436Trp	p.G436W	ENST00000297063	5/7	47	11	35	56	56	0	KIAA0895,missense_variant,p.Gly333Trp,ENST00000436884,;KIAA0895,missense_variant,p.Gly385Trp,ENST00000317020,;KIAA0895,missense_variant,p.Gly436Trp,ENST00000297063,;KIAA0895,missense_variant,p.Gly433Trp,ENST00000440378,;KIAA0895,missense_variant,p.Gly423Trp,ENST00000338533,;KIAA0895,missense_variant,p.Gly191Trp,ENST00000453212,;KIAA0895,downstream_gene_variant,,ENST00000431396,;Y_RNA,downstream_gene_variant,,ENST00000364562,;KIAA0895,non_coding_transcript_exon_variant,,ENST00000480192,;KIAA0895,non_coding_transcript_exon_variant,,ENST00000483360,;KIAA0895,downstream_gene_variant,,ENST00000483526,;	A	ENSG00000164542	ENST00000297063	Transcript	missense_variant	1357	1306	436	G/W	Ggg/Tgg	.	.	.	-1	KIAA0895	HGNC	22206	protein_coding	YES	CCDS43570.1	ENSP00000297063	K0895_HUMAN	.	UPI000013E3C0	.	deleterious(0)	probably_damaging(1)	5/7	.	hmmpanther:PTHR31817:SF3,hmmpanther:PTHR31817,Pfam_domain:PF08014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCACCTGGTT	.	5	ESCA
IKZF1	0	.	GRCh37	7	50471458	50471458	+	3'Flank	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000439701	.	12	7	5	17	17	0	IKZF1,3_prime_UTR_variant,,ENST00000331340,;IKZF1,3_prime_UTR_variant,,ENST00000349824,;IKZF1,3_prime_UTR_variant,,ENST00000343574,;IKZF1,3_prime_UTR_variant,,ENST00000346667,;IKZF1,3_prime_UTR_variant,,ENST00000357364,;IKZF1,downstream_gene_variant,,ENST00000426121,;IKZF1,downstream_gene_variant,,ENST00000440768,;IKZF1,downstream_gene_variant,,ENST00000438033,;IKZF1,downstream_gene_variant,,ENST00000359197,;IKZF1,downstream_gene_variant,,ENST00000439701,;IKZF1,downstream_gene_variant,,ENST00000471793,;	C	ENSG00000185811	ENST00000439701	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1194	1	IKZF1	HGNC	13176	protein_coding	YES	CCDS59055.1	ENSP00000413025	IKZF1_HUMAN	.	UPI000002ABBE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGAAAGAGCTG	.	3	ESCA
KIAA1324L	0	.	GRCh37	7	86569422	86569422	+	Nonsense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.751A>T	p.Lys251Ter	p.K251*	ENST00000450689	6/22	74	27	47	41	41	0	KIAA1324L,stop_gained,p.Lys251Ter,ENST00000444627,;KIAA1324L,stop_gained,p.Lys212Ter,ENST00000423294,;KIAA1324L,stop_gained,p.Lys251Ter,ENST00000450689,;KIAA1324L,stop_gained,p.Lys11Ter,ENST00000297222,;KIAA1324L,stop_gained,p.Lys84Ter,ENST00000416314,;KIAA1324L,downstream_gene_variant,,ENST00000425689,;KIAA1324L,downstream_gene_variant,,ENST00000398276,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;	A	ENSG00000164659	ENST00000450689	Transcript	stop_gained	937	751	251	K/*	Aaa/Taa	.	.	.	-1	KIAA1324L	HGNC	21945	protein_coding	YES	CCDS47632.1	ENSP00000413445	K132L_HUMAN	F1LLU5_HUMAN,C9JFK7_HUMAN	UPI000173AA00	.	.	.	6/22	.	hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTTCAGCA	.	5	ESCA
PABPC1	0	.	GRCh37	8	101715436	101715436	+	3'UTR	SNP	A	A	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*153T>G	.	.	ENST00000318607	15/15	86	70	15	54	54	0	PABPC1,3_prime_UTR_variant,,ENST00000519004,;PABPC1,3_prime_UTR_variant,,ENST00000522387,;PABPC1,3_prime_UTR_variant,,ENST00000520868,;PABPC1,3_prime_UTR_variant,,ENST00000318607,;PABPC1,intron_variant,,ENST00000518293,;PABPC1,downstream_gene_variant,,ENST00000517403,;PABPC1,downstream_gene_variant,,ENST00000522658,;PABPC1,downstream_gene_variant,,ENST00000517990,;AP001205.1,downstream_gene_variant,,ENST00000579868,;PABPC1,downstream_gene_variant,,ENST00000519596,;PABPC1,downstream_gene_variant,,ENST00000519848,;PABPC1,downstream_gene_variant,,ENST00000523636,;PABPC1,downstream_gene_variant,,ENST00000518716,;	C	ENSG00000070756	ENST00000318607	Transcript	3_prime_UTR_variant	3193	.	.	.	.	.	.	.	-1	PABPC1	HGNC	8554	protein_coding	YES	CCDS6289.1	ENSP00000313007	PABP1_HUMAN	H0YB75_HUMAN,E7EQV3_HUMAN,E5RJM8_HUMAN,E5RJB9_HUMAN,E5RHG7_HUMAN,E5RH24_HUMAN,E5RGH3_HUMAN,E5RGC4_HUMAN,E5RFD8_HUMAN	UPI0000000BC4	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|VARSCANS	CTGGCATTTGC	.	3	ESCA
RP1L1	0	.	GRCh37	8	10464952	10464952	+	Missense_Mutation	SNP	T	T	C	rs544346924	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6656A>G	p.Glu2219Gly	p.E2219G	ENST00000382483	4/4	48	41	7	75	75	0	RP1L1,missense_variant,p.Glu2219Gly,ENST00000382483,;	C	ENSG00000183638	ENST00000382483	Transcript	missense_variant	6880	6656	2219	E/G	gAg/gGg	rs544346924	.	.	-1	RP1L1	HGNC	15946	protein_coding	YES	CCDS43708.1	ENSP00000371923	.	A6NKC6_HUMAN	UPI00001AF9CC	.	.	unknown(0)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23005:SF3,hmmpanther:PTHR23005	C:0.0004	C:0	C:0	.	C:0.001	C:0.001	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CCTCCTCTTCA	byFrequency|by1000G	2	ESCA
RP1L1	0	.	GRCh37	8	10464968	10464968	+	Missense_Mutation	SNP	C	C	T	rs532233178	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6640G>A	p.Ala2214Thr	p.A2214T	ENST00000382483	4/4	50	41	9	84	84	0	RP1L1,missense_variant,p.Ala2214Thr,ENST00000382483,;	T	ENSG00000183638	ENST00000382483	Transcript	missense_variant	6864	6640	2214	A/T	Gcc/Acc	rs532233178	.	.	-1	RP1L1	HGNC	15946	protein_coding	YES	CCDS43708.1	ENSP00000371923	.	A6NKC6_HUMAN	UPI00001AF9CC	.	.	unknown(0)	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23005:SF3,hmmpanther:PTHR23005	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	CGGGGCCTCTA	by1000G	3	ESCA
RP1L1	0	.	GRCh37	8	10464975	10464975	+	Silent	SNP	A	A	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6633T>C	p.%3D	p.G2211G	ENST00000382483	4/4	54	45	8	79	79	0	RP1L1,synonymous_variant,p.%3D,ENST00000382483,;	G	ENSG00000183638	ENST00000382483	Transcript	synonymous_variant	6857	6633	2211	G	ggT/ggC	.	.	.	-1	RP1L1	HGNC	15946	protein_coding	YES	CCDS43708.1	ENSP00000371923	.	A6NKC6_HUMAN	UPI00001AF9CC	.	.	.	4/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23005:SF3,hmmpanther:PTHR23005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TCTACACCTTC	.	3	ESCA
KIAA1456	0	.	GRCh37	8	12881831	12881831	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2278C>T	.	.	ENST00000524591	5/5	29	25	3	44	44	0	KIAA1456,3_prime_UTR_variant,,ENST00000524591,;KIAA1456,intron_variant,,ENST00000447063,;KIAA1456,non_coding_transcript_exon_variant,,ENST00000529978,;KIAA1456,downstream_gene_variant,,ENST00000529706,;	T	ENSG00000250305	ENST00000524591	Transcript	3_prime_UTR_variant	4132	.	.	.	.	.	.	.	1	KIAA1456	HGNC	26725	protein_coding	YES	CCDS47808.1	ENSP00000432695	K1456_HUMAN	E9PK20_HUMAN	UPI0001596892	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	ACAGGCGTGAG	.	3	ESCA
KCNQ3	0	.	GRCh37	8	133141661	133141661	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2467G>T	p.Gly823Trp	p.G823W	ENST00000388996	15/15	40	27	13	26	26	0	KCNQ3,missense_variant,p.Gly703Trp,ENST00000521134,;KCNQ3,missense_variant,p.Gly823Trp,ENST00000388996,;KCNQ3,missense_variant,p.Gly811Trp,ENST00000519445,;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,;	A	ENSG00000184156	ENST00000388996	Transcript	missense_variant	2888	2467	823	G/W	Ggg/Tgg	COSM3645164	.	.	-1	KCNQ3	HGNC	6297	protein_coding	YES	CCDS34943.1	ENSP00000373648	KCNQ3_HUMAN	.	UPI00001279F0	.	tolerated(0.05)	probably_damaging(0.999)	15/15	.	Pfam_domain:PF11956	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	BUFFER|p.S824S|c.2472G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGACCCCCCAT	.	5	ESCA
TG	0	.	GRCh37	8	133899614	133899614	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1997G>C	p.Arg666Thr	p.R666T	ENST00000220616	9/48	44	31	13	25	25	0	TG,missense_variant,p.Arg666Thr,ENST00000220616,;TG,missense_variant,p.Arg666Thr,ENST00000377869,;TG,downstream_gene_variant,,ENST00000520769,;	C	ENSG00000042832	ENST00000220616	Transcript	missense_variant	2037	1997	666	R/T	aGg/aCg	.	.	.	1	TG	HGNC	11764	protein_coding	YES	CCDS34944.1	ENSP00000220616	THYG_HUMAN	Q9NYM1_HUMAN,Q9NYD9_HUMAN,E5RG33_HUMAN	UPI000013C79F	.	deleterious(0)	probably_damaging(1)	9/48	.	Superfamily_domains:SSF57610,PIRSF_domain:PIRSF001831,Pfam_domain:PF00086,PROSITE_profiles:PS51162	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAAAGGGCTC	.	5	ESCA
TG	0	.	GRCh37	8	134030045	134030045	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6585G>C	p.Glu2195Asp	p.E2195D	ENST00000220616	38/48	49	30	18	34	34	0	TG,missense_variant,p.Glu2195Asp,ENST00000220616,;TG,missense_variant,p.Glu565Asp,ENST00000542445,;TG,missense_variant,p.Arg35Thr,ENST00000518108,;TG,missense_variant,p.Glu2138Asp,ENST00000377869,;TG,missense_variant,p.Glu328Asp,ENST00000519543,;TG,missense_variant,p.Glu651Asp,ENST00000519178,;TG,non_coding_transcript_exon_variant,,ENST00000522523,;TG,3_prime_UTR_variant,,ENST00000523756,;TG,downstream_gene_variant,,ENST00000522797,;	C	ENSG00000042832	ENST00000220616	Transcript	missense_variant	6625	6585	2195	E/D	gaG/gaC	.	.	.	1	TG	HGNC	11764	protein_coding	YES	CCDS34944.1	ENSP00000220616	THYG_HUMAN	Q9NYM1_HUMAN,Q9NYD9_HUMAN,E5RG33_HUMAN	UPI000013C79F	.	tolerated(0.54)	benign(0.008)	38/48	.	PIRSF_domain:PIRSF001831,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF142	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGAGGCATC	.	5	ESCA
KHDRBS3	0	.	GRCh37	8	136594204	136594204	+	Missense_Mutation	SNP	G	G	A	rs749251634	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.695G>A	p.Arg232Gln	p.R232Q	ENST00000355849	6/9	63	32	31	38	38	0	KHDRBS3,missense_variant,p.Arg147Gln,ENST00000524282,;KHDRBS3,missense_variant,p.Arg204Gln,ENST00000524199,;KHDRBS3,missense_variant,p.Arg232Gln,ENST00000355849,;KHDRBS3,intron_variant,,ENST00000520981,;KHDRBS3,non_coding_transcript_exon_variant,,ENST00000522079,;KHDRBS3,missense_variant,p.Arg157Gln,ENST00000517859,;	A	ENSG00000131773	ENST00000355849	Transcript	missense_variant	1105	695	232	R/Q	cGa/cAa	rs749251634	.	.	1	KHDRBS3	HGNC	18117	protein_coding	YES	CCDS6374.1	ENSP00000348108	KHDR3_HUMAN	.	UPI0000073E6F	.	tolerated(0.26)	probably_damaging(0.997)	6/9	.	hmmpanther:PTHR11208:SF29,hmmpanther:PTHR11208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G233G|c.699G>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACCCGAGGGC	.	5	ESCA
CHRAC1	0	.	GRCh37	8	141521552	141521552	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-47C>T	.	.	ENST00000220913	1/3	35	22	13	18	18	0	CHRAC1,5_prime_UTR_variant,,ENST00000220913,;CHRAC1,5_prime_UTR_variant,,ENST00000519533,;CHRAC1,upstream_gene_variant,,ENST00000519618,;CHRAC1,upstream_gene_variant,,ENST00000518971,;CTA-204B4.2,upstream_gene_variant,,ENST00000564464,;CHRAC1,upstream_gene_variant,,ENST00000523569,;	T	ENSG00000104472	ENST00000220913	Transcript	5_prime_UTR_variant	156	.	.	.	.	.	.	.	1	CHRAC1	HGNC	13544	protein_coding	YES	CCDS6379.1	ENSP00000220913	CHRC1_HUMAN	.	UPI00000437B9	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCGCGGT	.	5	ESCA
AGO2	0	.	GRCh37	8	141567319	141567319	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.895G>A	p.Glu299Lys	p.E299K	ENST00000220592	8/19	52	36	15	58	58	0	AGO2,missense_variant,p.Glu299Lys,ENST00000519980,;AGO2,missense_variant,p.Glu299Lys,ENST00000220592,;AGO2,3_prime_UTR_variant,,ENST00000523609,;AGO2,upstream_gene_variant,,ENST00000521325,;	T	ENSG00000123908	ENST00000220592	Transcript	missense_variant	1008	895	299	E/K	Gag/Aag	.	.	.	-1	AGO2	HGNC	3263	protein_coding	YES	CCDS6380.1	ENSP00000220592	AGO2_HUMAN	E5RJY2_HUMAN	UPI0000168652	.	tolerated(0.09)	possibly_damaging(0.561)	8/19	.	Superfamily_domains:SSF101690,SMART_domains:SM00949,Pfam_domain:PF02170,Gene3D:2.170.260.10,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF18,HAMAP:MF_03031,PROSITE_profiles:PS50821	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTCCTGCT	.	5	ESCA
RHPN1	0	.	GRCh37	8	144462882	144462882	+	Nonsense_Mutation	SNP	C	C	G	rs754081765	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1340C>G	p.Ser447Ter	p.S447*	ENST00000289013	11/15	39	30	8	58	58	0	RHPN1,stop_gained,p.Ser447Ter,ENST00000289013,;RHPN1,non_coding_transcript_exon_variant,,ENST00000522335,;RHPN1,non_coding_transcript_exon_variant,,ENST00000522899,;	G	ENSG00000158106	ENST00000289013	Transcript	stop_gained	1441	1340	447	S/*	tCa/tGa	rs754081765	.	.	1	RHPN1	HGNC	19973	protein_coding	YES	CCDS47927.1	ENSP00000289013	RHPN1_HUMAN	.	UPI0000071870	.	.	.	11/15	.	PROSITE_profiles:PS51180,hmmpanther:PTHR23031:SF6,hmmpanther:PTHR23031,Gene3D:2xs1A01,Pfam_domain:PF03097,SMART_domains:SM01041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCTCACTGG	.	5	ESCA
ARHGAP39	0	.	GRCh37	8	145831062	145831062	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-63G>A	.	.	ENST00000377307	1/11	56	37	19	65	65	0	ARHGAP39,5_prime_UTR_variant,,ENST00000540274,;ARHGAP39,5_prime_UTR_variant,,ENST00000276826,;ARHGAP39,5_prime_UTR_variant,,ENST00000377307,;	T	ENSG00000147799	ENST00000377307	Transcript	5_prime_UTR_variant	23	.	.	.	.	.	.	.	-1	ARHGAP39	HGNC	29351	protein_coding	YES	CCDS34971.1	ENSP00000366522	RHG39_HUMAN	B3KS00_HUMAN	UPI000021015B	.	.	.	1/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCATCAGACG	.	5	ESCA
HTRA4	0	.	GRCh37	8	38831859	38831859	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77T>C	p.Val26Ala	p.V26A	ENST00000302495	1/9	66	34	32	40	40	0	HTRA4,missense_variant,p.Val26Ala,ENST00000302495,;PLEKHA2,downstream_gene_variant,,ENST00000420274,;PLEKHA2,downstream_gene_variant,,ENST00000521746,;CTD-2544N14.3,upstream_gene_variant,,ENST00000520863,;PLEKHA2,downstream_gene_variant,,ENST00000521784,;PLEKHA2,downstream_gene_variant,,ENST00000388745,;PLEKHA2,downstream_gene_variant,,ENST00000518571,;PLEKHA2,downstream_gene_variant,,ENST00000521123,;PLEKHA2,downstream_gene_variant,,ENST00000518939,;	C	ENSG00000169495	ENST00000302495	Transcript	missense_variant	177	77	26	V/A	gTc/gCc	.	.	.	1	HTRA4	HGNC	26909	protein_coding	YES	CCDS6110.1	ENSP00000305919	HTRA4_HUMAN	B4DTF7_HUMAN	UPI0000001BEC	.	tolerated(0.55)	benign(0.011)	1/9	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22939,hmmpanther:PTHR22939:SF16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCGTCCTCT	.	5	ESCA
ANK1	0	.	GRCh37	8	41566347	41566347	+	Silent	SNP	C	C	T	rs375243297	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2046G>A	p.%3D	p.E682E	ENST00000265709	17/43	45	33	12	37	37	0	ANK1,synonymous_variant,p.%3D,ENST00000265709,;ANK1,synonymous_variant,p.%3D,ENST00000352337,;ANK1,synonymous_variant,p.%3D,ENST00000396942,;ANK1,synonymous_variant,p.%3D,ENST00000379758,;ANK1,synonymous_variant,p.%3D,ENST00000289734,;ANK1,synonymous_variant,p.%3D,ENST00000347528,;ANK1,synonymous_variant,p.%3D,ENST00000396945,;ANK1,upstream_gene_variant,,ENST00000520299,;	T	ENSG00000029534	ENST00000265709	Transcript	synonymous_variant	2328	2046	682	E	gaG/gaA	rs375243297	.	.	-1	ANK1	HGNC	492	protein_coding	YES	CCDS47849.1	ENSP00000265709	ANK1_HUMAN	Q9UMG4_HUMAN	UPI0000E4453A	.	.	.	17/43	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF11,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCATCTCTGC	.	5	ESCA
PI15	0	.	GRCh37	8	75761594	75761594	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*106C>G	.	.	ENST00000260113	6/6	17	13	4	9	9	0	PI15,3_prime_UTR_variant,,ENST00000523773,;PI15,3_prime_UTR_variant,,ENST00000260113,;RP11-758M4.4,intron_variant,,ENST00000522914,;RP11-758M4.4,intron_variant,,ENST00000518128,;RP11-758M4.4,intron_variant,,ENST00000523860,;	G	ENSG00000137558	ENST00000260113	Transcript	3_prime_UTR_variant	1062	.	.	.	.	.	.	.	1	PI15	HGNC	8946	protein_coding	YES	CCDS6218.1	ENSP00000260113	PI15_HUMAN	.	UPI00000422F7	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CTAATCTTGTT	.	3	ESCA
OR13C2	0	.	GRCh37	9	107367331	107367331	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.578C>G	p.Ser193Ter	p.S193*	ENST00000542196	1/1	45	32	13	32	32	0	OR13C2,stop_gained,p.Ser193Ter,ENST00000542196,;	C	ENSG00000257019	ENST00000542196	Transcript	stop_gained	621	578	193	S/*	tCa/tGa	.	.	.	-1	OR13C2	HGNC	14701	protein_coding	YES	CCDS35092.1	ENSP00000438815	O13C2_HUMAN	.	UPI0000041B29	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF23,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTGAGATG	.	5	ESCA
RGS3	0	.	GRCh37	9	116298982	116298982	+	Intron	SNP	A	A	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1915-94A>G	.	.	ENST00000374140	.	25	18	6	32	32	0	RGS3,5_prime_UTR_variant,,ENST00000462143,;RGS3,intron_variant,,ENST00000317613,;RGS3,intron_variant,,ENST00000343817,;RGS3,intron_variant,,ENST00000374140,;RGS3,intron_variant,,ENST00000496113,;RGS3,intron_variant,,ENST00000394646,;RGS3,intron_variant,,ENST00000374136,;RGS3,intron_variant,,ENST00000350696,;RGS3,non_coding_transcript_exon_variant,,ENST00000492676,;RGS3,intron_variant,,ENST00000470775,;RGS3,intron_variant,,ENST00000496264,;RGS3,intron_variant,,ENST00000460000,;RGS3,intron_variant,,ENST00000478599,;	G	ENSG00000138835	ENST00000374140	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	RGS3	HGNC	9999	protein_coding	YES	CCDS43869.1	ENSP00000363255	RGS3_HUMAN	H7BXY1_HUMAN,C9J6G2_HUMAN	UPI00001C0F58	.	.	.	.	19/25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTCACCCTC	.	5	ESCA
GPSM1	0	.	GRCh37	9	139244051	139244051	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1291G>A	p.Asp431Asn	p.D431N	ENST00000440944	11/14	48	27	20	64	64	0	GPSM1,missense_variant,p.Asp431Asn,ENST00000440944,;GPSM1,missense_variant,p.Asp408Asn,ENST00000354753,;GPSM1,upstream_gene_variant,,ENST00000429455,;	A	ENSG00000160360	ENST00000440944	Transcript	missense_variant	1511	1291	431	D/N	Gac/Aac	.	.	.	1	GPSM1	HGNC	17858	protein_coding	YES	CCDS48055.1	ENSP00000392828	GPSM1_HUMAN	.	UPI0000481581	.	tolerated(0.23)	benign(0.021)	11/14	.	hmmpanther:PTHR10098,hmmpanther:PTHR10098:SF36	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGGAGACAGC	.	5	ESCA
ABCA2	0	.	GRCh37	9	139904091	139904091	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6636G>T	p.Glu2212Asp	p.E2212D	ENST00000341511	44/49	51	23	27	120	120	0	ABCA2,missense_variant,p.Glu2211Asp,ENST00000371605,;ABCA2,missense_variant,p.Glu2212Asp,ENST00000341511,;ABCA2,missense_variant,p.Glu2212Asp,ENST00000265662,;ABCA2,upstream_gene_variant,,ENST00000490486,;ABCA2,upstream_gene_variant,,ENST00000448336,;ABCA2,non_coding_transcript_exon_variant,,ENST00000437791,;ABCA2,non_coding_transcript_exon_variant,,ENST00000463603,;ABCA2,upstream_gene_variant,,ENST00000464157,;ABCA2,3_prime_UTR_variant,,ENST00000479446,;ABCA2,3_prime_UTR_variant,,ENST00000459850,;ABCA2,3_prime_UTR_variant,,ENST00000487109,;ABCA2,upstream_gene_variant,,ENST00000464520,;ABCA2,downstream_gene_variant,,ENST00000431584,;ABCA2,downstream_gene_variant,,ENST00000488535,;	A	ENSG00000107331	ENST00000341511	Transcript	missense_variant	6686	6636	2212	E/D	gaG/gaT	.	.	.	-1	ABCA2	HGNC	32	protein_coding	YES	CCDS43909.1	ENSP00000344155	ABCA2_HUMAN	Q9UPU0_HUMAN,B4DI99_HUMAN	UPI00015E02DC	.	deleterious(0)	benign(0.358)	44/49	.	Superfamily_domains:SSF52540,SMART_domains:SM00382,Gene3D:3.40.50.300,Pfam_domain:PF00005,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF116,PROSITE_profiles:PS50893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGGGCTCGTC	.	5	ESCA
SMC5	0	.	GRCh37	9	72929739	72929739	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1660T>G	p.Leu554Val	p.L554V	ENST00000361138	12/25	84	58	26	85	85	0	SMC5,missense_variant,p.Leu554Val,ENST00000361138,;Y_RNA,upstream_gene_variant,,ENST00000459091,;	G	ENSG00000198887	ENST00000361138	Transcript	missense_variant	1718	1660	554	L/V	Ttg/Gtg	.	.	.	1	SMC5	HGNC	20465	protein_coding	YES	CCDS6632.1	ENSP00000354957	SMC5_HUMAN	.	UPI000036763A	.	deleterious(0.04)	benign(0.074)	12/25	.	hmmpanther:PTHR19306:SF1,hmmpanther:PTHR19306,Pfam_domain:PF02463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTTTGAAT	.	5	ESCA
SPATA31D5P	0	.	GRCh37	9	84531499	84531499	+	RNA	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1521G>C	.	.	ENST00000527857	4/4	74	64	10	93	93	0	SPATA31D5P,non_coding_transcript_exon_variant,,ENST00000527857,;SPATA31D5P,non_coding_transcript_exon_variant,,ENST00000376459,;	C	ENSG00000240632	ENST00000527857	Transcript	non_coding_transcript_exon_variant	1521	.	.	.	.	.	.	.	1	SPATA31D5P	HGNC	38602	processed_transcript	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GTTTTGAGGAC	.	4	ESCA
COL4A6	0	.	GRCh37	X	107408226	107408226	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3854C>G	p.Ser1285Cys	p.S1285C	ENST00000372216	39/45	31	9	22	21	21	0	COL4A6,missense_variant,p.Ser1285Cys,ENST00000394872,;COL4A6,missense_variant,p.Ser1285Cys,ENST00000372216,;COL4A6,missense_variant,p.Ser1284Cys,ENST00000334504,;COL4A6,missense_variant,p.Ser1260Cys,ENST00000545689,;COL4A6,missense_variant,p.Ser1260Cys,ENST00000538570,;COL4A6,upstream_gene_variant,,ENST00000487645,;	C	ENSG00000197565	ENST00000372216	Transcript	missense_variant	3955	3854	1285	S/C	tCc/tGc	.	.	.	-1	COL4A6	HGNC	2208	protein_coding	YES	CCDS14541.1	ENSP00000361290	CO4A6_HUMAN	B4DU54_HUMAN	UPI000049E122	.	.	probably_damaging(0.95)	39/45	.	hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF164,Pfam_domain:PF01391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGAGGATGGC	.	5	ESCA
COL4A5	0	.	GRCh37	X	107939618	107939618	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*10G>A	.	.	ENST00000328300	53/53	73	40	33	50	50	0	COL4A5,3_prime_UTR_variant,,ENST00000504541,;COL4A5,3_prime_UTR_variant,,ENST00000328300,;COL4A5,3_prime_UTR_variant,,ENST00000361603,;COL4A5,3_prime_UTR_variant,,ENST00000515658,;	A	ENSG00000188153	ENST00000328300	Transcript	3_prime_UTR_variant	5330	.	.	.	.	.	.	.	1	COL4A5	HGNC	2207	protein_coding	YES	CCDS35366.1	ENSP00000331902	CO4A5_HUMAN	H0Y9R8_HUMAN,B4DFF0_HUMAN	UPI000002A538	.	.	.	53/53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGAATTC	.	5	ESCA
HTR2C	0	.	GRCh37	X	114058075	114058075	+	Intron	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.350-24491G>T	.	.	ENST00000276198	.	20	16	4	11	11	0	HTR2C,intron_variant,,ENST00000371950,;HTR2C,intron_variant,,ENST00000276198,;HTR2C,intron_variant,,ENST00000371951,;MIR448,non_coding_transcript_exon_variant,,ENST00000362131,;	T	ENSG00000147246	ENST00000276198	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	HTR2C	HGNC	5295	protein_coding	YES	CCDS14564.1	ENSP00000276198	5HT2C_HUMAN	B3VRF0_HUMAN,B3VRE5_HUMAN,B3VRE0_HUMAN	UPI000000126F	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAGGGGGCT	.	4	ESCA
MAGEC1	0	.	GRCh37	X	140996200	140996200	+	Silent	SNP	C	C	T	.	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3010C>T	p.%3D	p.L1004L	ENST00000285879	4/4	40	8	32	29	29	0	MAGEC1,synonymous_variant,p.%3D,ENST00000406005,;MAGEC1,synonymous_variant,p.%3D,ENST00000285879,;	T	ENSG00000155495	ENST00000285879	Transcript	synonymous_variant	3296	3010	1004	L	Ctg/Ttg	COSM1177102	.	.	1	MAGEC1	HGNC	6812	protein_coding	YES	CCDS35417.1	ENSP00000285879	MAGC1_HUMAN	A0PK03_HUMAN	UPI000006F2FD	.	.	.	4/4	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF17,hmmpanther:PTHR11736,Pfam_domain:PF01454	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATTCTGAGT	.	5	ESCA
PASD1	0	.	GRCh37	X	150840072	150840072	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1258G>A	p.Val420Ile	p.V420I	ENST00000370357	13/16	36	27	8	28	28	0	PASD1,missense_variant,p.Val420Ile,ENST00000370357,;PASD1,non_coding_transcript_exon_variant,,ENST00000464219,;RP11-45D17.1,downstream_gene_variant,,ENST00000413236,;	A	ENSG00000166049	ENST00000370357	Transcript	missense_variant	1503	1258	420	V/I	Gtc/Atc	.	.	.	1	PASD1	HGNC	20686	protein_coding	YES	CCDS35431.1	ENSP00000359382	PASD1_HUMAN	.	UPI0000074686	.	tolerated(0.49)	benign(0.347)	13/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGTTGTCATT	.	5	ESCA
RBBP7	0	.	GRCh37	X	16887221	16887221	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271C>T	p.Gln91Ter	p.Q91*	ENST00000380084	2/12	34	8	26	30	30	0	RBBP7,stop_gained,p.Gln91Ter,ENST00000380084,;RBBP7,stop_gained,p.Gln47Ter,ENST00000404022,;RBBP7,stop_gained,p.Gln13Ter,ENST00000468092,;RBBP7,stop_gained,p.Gln47Ter,ENST00000380087,;RBBP7,downstream_gene_variant,,ENST00000493145,;	A	ENSG00000102054	ENST00000380084	Transcript	stop_gained	516	271	91	Q/*	Cag/Tag	.	.	.	-1	RBBP7	HGNC	9890	protein_coding	YES	CCDS56598.1	ENSP00000369424	RBBP7_HUMAN	Q5JNZ6_HUMAN,C9J7L0_HUMAN	UPI00001AE848	.	.	.	2/12	.	hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF82,Pfam_domain:PF12265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTGAACGG	.	5	ESCA
MAGEB2	0	.	GRCh37	X	30236789	30236789	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.92C>G	p.Thr31Ser	p.T31S	ENST00000378988	2/2	42	21	21	32	32	0	MAGEB2,missense_variant,p.Thr31Ser,ENST00000378988,;	G	ENSG00000099399	ENST00000378988	Transcript	missense_variant	193	92	31	T/S	aCt/aGt	.	.	.	1	MAGEB2	HGNC	6809	protein_coding	YES	CCDS14219.1	ENSP00000368273	MAGB2_HUMAN	.	UPI000013C683	.	tolerated(0.07)	possibly_damaging(0.82)	2/2	.	Pfam_domain:PF12440,hmmpanther:PTHR11736:SF22,hmmpanther:PTHR11736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCACTGAAG	.	5	ESCA
PPP2R3B	0	.	GRCh37	X	307471	307471	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757G>A	p.Glu253Lys	p.E253K	ENST00000390665	5/13	51	27	23	104	104	0	PPP2R3B,missense_variant,p.Glu253Lys,ENST00000390665,;PPP2R3B,downstream_gene_variant,,ENST00000381625,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000475859,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000496630,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000445792,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000477110,;PPP2R3B,upstream_gene_variant,,ENST00000477636,;PPP2R3B,upstream_gene_variant,,ENST00000484364,;PPP2R3B,upstream_gene_variant,,ENST00000468169,;	T	ENSG00000167393	ENST00000390665	Transcript	missense_variant	776	757	253	E/K	Gag/Aag	.	.	.	-1	PPP2R3B	HGNC	13417	protein_coding	YES	CCDS14104.1	ENSP00000375080	P2R3B_HUMAN	Q96FD8_HUMAN	UPI00001BB8B8	.	deleterious(0.01)	possibly_damaging(0.52)	5/13	.	hmmpanther:PTHR14095,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTCCTTCA	.	5	ESCA
EFHC2	0	.	GRCh37	X	44007976	44007976	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*65G>C	.	.	ENST00000420999	15/15	34	12	21	31	31	0	EFHC2,3_prime_UTR_variant,,ENST00000420999,;EFHC2,non_coding_transcript_exon_variant,,ENST00000343571,;	G	ENSG00000183690	ENST00000420999	Transcript	3_prime_UTR_variant	2399	.	.	.	.	.	.	.	-1	EFHC2	HGNC	26233	protein_coding	YES	CCDS55405.1	ENSP00000404232	EFHC2_HUMAN	.	UPI00000717F2	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATATCTACTA	.	5	ESCA
FAM46D	0	.	GRCh37	X	79699842	79699842	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-A8JE-01A-11D-A37C-09	TCGA-Z6-A8JE-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*634G>T	.	.	ENST00000538312	5/5	87	58	29	46	46	0	FAM46D,3_prime_UTR_variant,,ENST00000308293,;FAM46D,3_prime_UTR_variant,,ENST00000538312,;	T	ENSG00000174016	ENST00000538312	Transcript	3_prime_UTR_variant	2138	.	.	.	.	.	.	.	1	FAM46D	HGNC	28399	protein_coding	YES	CCDS14446.1	ENSP00000443410	FA46D_HUMAN	.	UPI0000073CF3	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAAGCCCTG	.	5	ESCA
PDZD8	0	.	GRCh37	10	119044395	119044395	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1849G>T	p.Glu617Ter	p.E617*	ENST00000334464	5/5	28	19	9	36	36	0	PDZD8,stop_gained,p.Glu617Ter,ENST00000334464,;PDZD8,non_coding_transcript_exon_variant,,ENST00000482496,;PDZD8,downstream_gene_variant,,ENST00000489302,;	A	ENSG00000165650	ENST00000334464	Transcript	stop_gained	2089	1849	617	E/*	Gaa/Taa	.	.	.	-1	PDZD8	HGNC	26974	protein_coding	YES	CCDS7600.1	ENSP00000334642	PDZD8_HUMAN	.	UPI00000723CC	.	.	.	5/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21519,hmmpanther:PTHR21519:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CTTTTCAACGA	.	4	ESCA
GPR158	0	.	GRCh37	10	25464572	25464572	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.223G>T	p.Ala75Ser	p.A75S	ENST00000376351	1/11	33	23	9	33	33	0	GPR158,missense_variant,p.Ala75Ser,ENST00000376351,;GPR158-AS1,intron_variant,,ENST00000449643,;	T	ENSG00000151025	ENST00000376351	Transcript	missense_variant	582	223	75	A/S	Gcc/Tcc	COSM4013434	.	.	1	GPR158	HGNC	23689	protein_coding	YES	CCDS31166.1	ENSP00000365529	GP158_HUMAN	.	UPI0000199875	.	tolerated(0.36)	benign(0.01)	1/11	.	hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACTCGCCGAG	.	5	ESCA
GPR158	0	.	GRCh37	10	25464990	25464990	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.641C>T	p.Ala214Val	p.A214V	ENST00000376351	1/11	92	87	5	67	67	0	GPR158,missense_variant,p.Ala214Val,ENST00000376351,;GPR158-AS1,non_coding_transcript_exon_variant,,ENST00000449643,;	T	ENSG00000151025	ENST00000376351	Transcript	missense_variant	1000	641	214	A/V	gCc/gTc	.	.	.	1	GPR158	HGNC	23689	protein_coding	YES	CCDS31166.1	ENSP00000365529	GP158_HUMAN	.	UPI0000199875	.	tolerated(0.28)	benign(0.209)	1/11	.	hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTGGCCAACG	.	2	ESCA
C10ORF68	0	.	GRCh37	10	33103339	33103339	+	Missense_Mutation	SNP	A	A	G	rs530294108	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.952A>G	p.Ile318Val	p.I318V	ENST00000302316	12/23	41	20	20	30	30	0	C10ORF68,missense_variant,p.Ile294Val,ENST00000375028,;C10ORF68,missense_variant,p.Ile354Val,ENST00000375025,;C10ORF68,intron_variant,,ENST00000375030,;C10ORF68,missense_variant,p.Ile318Val,ENST00000302316,;	G	ENSG00000150076	ENST00000302316	Transcript	missense_variant	1425	952	318	I/V	Ata/Gta	rs530294108	.	.	1	C10ORF68	Uniprot_gn	.	nonsense_mediated_decay	YES	CCDS31177.1	ENSP00000303710	CJ068_HUMAN	.	UPI000049DCE8	.	tolerated(0.44)	possibly_damaging(0.658)	12/23	.	.	C:0.0002	C:0.0008	C:0	.	C:0	C:0	C:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATATACTA	by1000G	5	ESCA
AKR1C2	0	.	GRCh37	10	5043707	5043707	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.251delA	p.Lys84SerfsTer20	p.K84Sfs*20	ENST00000380753	2/9	120	102	18	84	84	0	AKR1C2,frameshift_variant,p.Lys84SerfsTer20,ENST00000604507,;AKR1C2,frameshift_variant,p.Lys84SerfsTer20,ENST00000380753,;AKR1C2,frameshift_variant,p.Lys84SerfsTer20,ENST00000455190,;AKR1C2,frameshift_variant,p.Lys84SerfsTer20,ENST00000421196,;AKR1C2,frameshift_variant,p.Lys84SerfsTer20,ENST00000407674,;U8,upstream_gene_variant,,ENST00000459141,;RP11-499O7.7,downstream_gene_variant,,ENST00000451575,;RP11-499O7.7,downstream_gene_variant,,ENST00000440414,;AKR1C2,splice_region_variant,,ENST00000604184,;AKR1C2,downstream_gene_variant,,ENST00000604428,;AKR1C2,downstream_gene_variant,,ENST00000604711,;AKR1C2,splice_region_variant,,ENST00000460124,;	-	ENSG00000151632	ENST00000380753	Transcript	frameshift_variant	439	251	84	K/X	aAg/ag	.	.	.	-1	AKR1C2	HGNC	385	protein_coding	YES	CCDS7062.1	ENSP00000370129	AK1C2_HUMAN	S4R3P0_HUMAN	UPI0000111D9F	.	.	.	2/9	.	Superfamily_domains:SSF51430,PIRSF_domain:PIRSF000097,Pfam_domain:PF00248,Gene3D:3.20.20.100,hmmpanther:PTHR11732:SF153,hmmpanther:PTHR11732	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGTACCTTTGAA	.	3	ESCA
ANK3	0	.	GRCh37	10	61832417	61832417	+	Frame_Shift_Del	DEL	T	T	-	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8222delA	p.Asp2741ValfsTer31	p.D2741Vfs*31	ENST00000280772	37/44	34	25	9	47	47	0	ANK3,frameshift_variant,p.Asp2741ValfsTer31,ENST00000280772,;ANK3,intron_variant,,ENST00000373827,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000355288,;ANK3,intron_variant,,ENST00000511043,;ANK3,intron_variant,,ENST00000503366,;	-	ENSG00000151150	ENST00000280772	Transcript	frameshift_variant	8414	8222	2741	D/X	gAt/gt	.	.	.	-1	ANK3	HGNC	494	protein_coding	YES	CCDS7258.1	ENSP00000280772	ANK3_HUMAN	D6RFK6_HUMAN,D6RBY7_HUMAN,B1AQT1_HUMAN	UPI0000141BA9	.	.	.	37/44	.	hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGGCCATCTGAC	.	3	ESCA
P4HA1	0	.	GRCh37	10	74813333	74813333	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.479C>A	p.Ser160Tyr	p.S160Y	ENST00000412021	7/16	34	24	9	33	33	0	P4HA1,missense_variant,p.Ser160Tyr,ENST00000307116,;P4HA1,missense_variant,p.Ser160Tyr,ENST00000440381,;P4HA1,missense_variant,p.Ser160Tyr,ENST00000394890,;P4HA1,missense_variant,p.Ser160Tyr,ENST00000412021,;P4HA1,missense_variant,p.Ser160Tyr,ENST00000263556,;P4HA1,missense_variant,p.Ser160Tyr,ENST00000373008,;	T	ENSG00000122884	ENST00000412021	Transcript	missense_variant	813	479	160	S/Y	tCt/tAt	.	.	.	-1	P4HA1	HGNC	8546	protein_coding	YES	CCDS41537.1	ENSP00000411688	P4HA1_HUMAN	.	UPI0000001C27	.	tolerated(0.05)	possibly_damaging(0.555)	7/16	.	hmmpanther:PTHR10869:SF40,hmmpanther:PTHR10869	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAAGATTTG	.	5	ESCA
MUC2	0	.	GRCh37	11	1093688	1093688	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5507C>T	p.Pro1836Leu	p.P1836L	ENST00000441003	30/49	43	21	22	111	111	0	MUC2,missense_variant,p.Pro124Leu,ENST00000333592,;MUC2,missense_variant,p.Pro1836Leu,ENST00000441003,;MUC2,intron_variant,,ENST00000361558,;MUC2,downstream_gene_variant,,ENST00000359061,;	T	ENSG00000198788	ENST00000441003	Transcript	missense_variant	5534	5507	1836	P/L	cCc/cTc	.	.	.	1	MUC2	HGNC	7512	protein_coding	YES	.	ENSP00000415183	.	Q9UMI9_HUMAN,Q9HBC6_HUMAN,H0Y2U6_HUMAN,E7EUV1_HUMAN	UPI00006C10F2	.	.	unknown(0)	30/49	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCCCCACCC	.	5	ESCA
ZDHHC13	0	.	GRCh37	11	19173823	19173823	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.703A>C	p.Lys235Gln	p.K235Q	ENST00000446113	7/17	57	38	19	32	32	0	ZDHHC13,missense_variant,p.Lys105Gln,ENST00000399351,;ZDHHC13,missense_variant,p.Lys235Gln,ENST00000446113,;ZDHHC13,non_coding_transcript_exon_variant,,ENST00000530698,;ZDHHC13,non_coding_transcript_exon_variant,,ENST00000532812,;ZDHHC13,downstream_gene_variant,,ENST00000532026,;ZDHHC13,non_coding_transcript_exon_variant,,ENST00000525490,;	C	ENSG00000177054	ENST00000446113	Transcript	missense_variant	824	703	235	K/Q	Aag/Cag	.	.	.	1	ZDHHC13	HGNC	18413	protein_coding	YES	CCDS44550.1	ENSP00000400113	ZDH13_HUMAN	.	UPI000015F967	.	deleterious(0.01)	benign(0.215)	7/17	.	Superfamily_domains:SSF48403,SMART_domains:SM00248,Gene3D:1.25.40.20,Pfam_domain:PF12796,hmmpanther:PTHR24161,hmmpanther:PTHR24161:SF16,PROSITE_profiles:PS50297,PROSITE_profiles:PS50088	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATAAGCTT	.	5	ESCA
CREB3L1	0	.	GRCh37	11	46342074	46342074	+	Missense_Mutation	SNP	C	C	A	rs773657140	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1518C>A	p.His506Gln	p.H506Q	ENST00000529193	11/12	15	9	6	57	57	0	CREB3L1,missense_variant,p.His506Gln,ENST00000288400,;CREB3L1,missense_variant,p.His506Gln,ENST00000529193,;CREB3L1,downstream_gene_variant,,ENST00000534616,;CREB3L1,non_coding_transcript_exon_variant,,ENST00000530244,;	A	ENSG00000157613	ENST00000529193	Transcript	missense_variant	1969	1518	506	H/Q	caC/caA	rs773657140	.	.	1	CREB3L1	HGNC	18856	protein_coding	YES	CCDS53620.1	ENSP00000434939	CR3L1_HUMAN	E9PK33_HUMAN	UPI000004ABFF	.	tolerated_low_confidence(0.17)	benign(0.005)	11/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	TTCCACGACAG	byFrequency	3	ESCA
HBE1	0	.	GRCh37	11	5289646	5289646	+	3'UTR	SNP	G	G	T	rs760307633	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*53C>A	.	.	ENST00000380237	5/5	44	30	14	49	49	0	HBE1,3_prime_UTR_variant,,ENST00000380237,;HBE1,3_prime_UTR_variant,,ENST00000292896,;HBG2,intron_variant,,ENST00000380252,;HBG2,intron_variant,,ENST00000380259,;HBE1,downstream_gene_variant,,ENST00000396895,;	T	ENSG00000213931	ENST00000380237	Transcript	3_prime_UTR_variant	842	.	.	.	.	rs760307633	.	.	-1	HBE1	HGNC	4830	protein_coding	YES	CCDS7756.1	ENSP00000369586	HBE_HUMAN	D9YZU7_HUMAN,A8MUF7_HUMAN	UPI00000004B9	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCATGTGCAG	.	5	ESCA
OR5M9	0	.	GRCh37	11	56230099	56230099	+	Missense_Mutation	SNP	C	C	A	rs758257323	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.779G>T	p.Arg260Ile	p.R260I	ENST00000279791	1/1	33	24	8	46	46	0	OR5M9,missense_variant,p.Arg260Ile,ENST00000279791,;	A	ENSG00000150269	ENST00000279791	Transcript	missense_variant	779	779	260	R/I	aGa/aTa	rs758257323	.	.	-1	OR5M9	HGNC	15294	protein_coding	YES	CCDS31531.1	ENSP00000279791	OR5M9_HUMAN	.	UPI0000061E81	.	deleterious(0)	benign(0.392)	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF13,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGTCTCCTG	.	5	ESCA
RTN3	0	.	GRCh37	11	63448929	63448929	+	5'Flank	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000377819	.	22	15	7	19	19	0	RTN3,5_prime_UTR_variant,,ENST00000356000,;RTN3,5_prime_UTR_variant,,ENST00000341307,;RTN3,upstream_gene_variant,,ENST00000537981,;RTN3,upstream_gene_variant,,ENST00000545432,;RTN3,upstream_gene_variant,,ENST00000354497,;RTN3,upstream_gene_variant,,ENST00000339997,;RTN3,upstream_gene_variant,,ENST00000542238,;RTN3,upstream_gene_variant,,ENST00000377819,;RTN3,upstream_gene_variant,,ENST00000543552,;RTN3,upstream_gene_variant,,ENST00000540798,;RTN3,upstream_gene_variant,,ENST00000538995,;RTN3,upstream_gene_variant,,ENST00000338850,;RTN3,upstream_gene_variant,,ENST00000543123,;RTN3,upstream_gene_variant,,ENST00000536011,;	T	ENSG00000133318	ENST00000377819	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	26	1	RTN3	HGNC	10469	protein_coding	YES	CCDS58141.1	ENSP00000367050	RTN3_HUMAN	.	UPI00004546A2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCGCGCTCG	.	5	ESCA
PRB4	0	.	GRCh37	12	11461454	11461454	+	Missense_Mutation	SNP	G	G	T	rs774045189	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.463C>A	p.Pro155Thr	p.P155T	ENST00000279575	3/4	79	58	21	100	100	0	PRB4,missense_variant,p.Pro155Thr,ENST00000279575,;PRB4,missense_variant,p.Pro155Thr,ENST00000535904,;PRB4,intron_variant,,ENST00000445719,;	T	ENSG00000230657	ENST00000279575	Transcript	missense_variant	497	463	155	P/T	Ccc/Acc	rs774045189	.	.	-1	PRB4	HGNC	9340	protein_coding	YES	CCDS8641.1	ENSP00000279575	.	E9PAL0_HUMAN	UPI000013DBDC	.	tolerated_low_confidence(0.1)	unknown(0)	3/4	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23203:SF4,hmmpanther:PTHR23203,Pfam_domain:PF15240,Pfam_domain:PF15240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGGGGACCTT	.	5	ESCA
RIMBP2	0	.	GRCh37	12	130926544	130926544	+	Silent	SNP	G	G	A	rs769245689	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1302C>T	p.%3D	p.A434A	ENST00000261655	8/19	43	17	26	65	65	0	RIMBP2,synonymous_variant,p.%3D,ENST00000536002,;RIMBP2,synonymous_variant,p.%3D,ENST00000261655,;RIMBP2,synonymous_variant,p.%3D,ENST00000535703,;	A	ENSG00000060709	ENST00000261655	Transcript	synonymous_variant	1466	1302	434	A	gcC/gcT	rs769245689	.	.	-1	RIMBP2	HGNC	30339	protein_coding	YES	CCDS31925.1	ENSP00000261655	RIMB2_HUMAN	F5H3X3_HUMAN	UPI00001C1F42	.	.	.	8/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.I431I|c.1293C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGCGGCCTT	byFrequency	5	ESCA
HIST4H4	0	.	GRCh37	12	14923992	14923992	+	Silent	SNP	C	C	T	rs755941297	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.27G>A	p.%3D	p.K9K	ENST00000539745	1/1	37	34	3	41	41	0	HIST4H4,synonymous_variant,p.%3D,ENST00000539745,;H2AFJ,upstream_gene_variant,,ENST00000544848,;RP11-174G6.5,upstream_gene_variant,,ENST00000562691,;HIST4H4,upstream_gene_variant,,ENST00000537853,;HIST4H4,upstream_gene_variant,,ENST00000537096,;HIST4H4,upstream_gene_variant,,ENST00000541592,;HIST4H4,upstream_gene_variant,,ENST00000540565,;HIST4H4,synonymous_variant,p.%3D,ENST00000358064,;H2AFJ,upstream_gene_variant,,ENST00000389078,;H2AFJ,upstream_gene_variant,,ENST00000501744,;	T	ENSG00000197837	ENST00000539745	Transcript	synonymous_variant	74	27	9	K	aaG/aaA	rs755941297	.	.	-1	HIST4H4	HGNC	20510	protein_coding	YES	CCDS8665.1	ENSP00000443017	H4_HUMAN	Q6B823_HUMAN,B2R4R0_HUMAN	UPI000000003C	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10484,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCCCCTTGCC	.	2	ESCA
PCED1B	0	.	GRCh37	12	47630264	47630264	+	3'UTR	SNP	G	G	A	rs144729661	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*119G>A	.	.	ENST00000546455	4/4	37	25	11	77	77	0	PCED1B,3_prime_UTR_variant,,ENST00000432328,;PCED1B,3_prime_UTR_variant,,ENST00000546455,;PCED1B,downstream_gene_variant,,ENST00000551777,;PCED1B,downstream_gene_variant,,ENST00000549630,;PCED1B,downstream_gene_variant,,ENST00000549500,;PCED1B,downstream_gene_variant,,ENST00000548348,;RP11-493L12.3,downstream_gene_variant,,ENST00000547748,;	A	ENSG00000179715	ENST00000546455	Transcript	3_prime_UTR_variant	2149	.	.	.	.	rs144729661	.	.	1	PCED1B	HGNC	28255	protein_coding	YES	CCDS8752.1	ENSP00000446688	PED1B_HUMAN	F8VYL8_HUMAN,F8VUZ9_HUMAN,F8VUD2_HUMAN,F8VRF7_HUMAN	UPI000006E8D2	.	.	.	4/4	.	.	A:0.0028	A:0.0098	A:0.0014	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTCGTCTTC	byFrequency|byCluster|by1000G	5	ESCA
KRT82	0	.	GRCh37	12	52800029	52800029	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33G>A	p.%3D	p.R11R	ENST00000257974	1/9	23	12	11	44	44	0	KRT82,synonymous_variant,p.%3D,ENST00000257974,;RP11-1020M18.10,upstream_gene_variant,,ENST00000548135,;RP3-416H24.4,downstream_gene_variant,,ENST00000547174,;	T	ENSG00000161850	ENST00000257974	Transcript	synonymous_variant	111	33	11	R	agG/agA	.	.	.	-1	KRT82	HGNC	6459	protein_coding	YES	CCDS8826.1	ENSP00000257974	KRT82_HUMAN	.	UPI000013CFA4	.	.	.	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCACACCTGGA	.	2	ESCA
FAM90A1	0	.	GRCh37	12	8376138	8376138	+	Silent	SNP	C	C	T	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.339G>A	p.%3D	p.Q113Q	ENST00000538603	6/7	165	87	78	199	198	0	FAM90A1,synonymous_variant,p.%3D,ENST00000538603,;FAM90A1,synonymous_variant,p.%3D,ENST00000307435,;FAM90A1,downstream_gene_variant,,ENST00000442295,;RP11-266K4.1,upstream_gene_variant,,ENST00000542600,;ALG1L10P,upstream_gene_variant,,ENST00000437882,;	T	ENSG00000171847	ENST00000538603	Transcript	synonymous_variant	898	339	113	Q	caG/caA	COSM431921	.	.	-1	FAM90A1	HGNC	25526	protein_coding	YES	CCDS31738.1	ENSP00000445418	F90A1_HUMAN	.	UPI000013EC10	.	.	.	6/7	.	hmmpanther:PTHR16035:SF8,hmmpanther:PTHR16035	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCTGCGG	.	5	ESCA
FGD6	0	.	GRCh37	12	95478413	95478413	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4117G>A	p.Ala1373Thr	p.A1373T	ENST00000343958	20/21	58	42	16	58	58	0	FGD6,missense_variant,p.Ala1373Thr,ENST00000343958,;FGD6,intron_variant,,ENST00000548069,;FGD6,downstream_gene_variant,,ENST00000546711,;FGD6,3_prime_UTR_variant,,ENST00000451107,;	T	ENSG00000180263	ENST00000343958	Transcript	missense_variant	4341	4117	1373	A/T	Gct/Act	COSM944608	.	.	-1	FGD6	HGNC	21740	protein_coding	YES	CCDS31878.1	ENSP00000344446	FGD6_HUMAN	F8VY01_HUMAN	UPI00001FB2F4	.	deleterious(0)	probably_damaging(0.999)	20/21	.	PROSITE_profiles:PS50003,hmmpanther:PTHR12673:SF12,hmmpanther:PTHR12673,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAAAGCGGCCA	.	5	ESCA
ELK3	0	.	GRCh37	12	96641019	96641019	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.509C>T	p.Pro170Leu	p.P170L	ENST00000228741	3/5	26	9	17	32	32	0	ELK3,missense_variant,p.Pro170Leu,ENST00000228741,;ELK3,intron_variant,,ENST00000552142,;ELK3,downstream_gene_variant,,ENST00000547860,;ELK3,missense_variant,p.Pro38Leu,ENST00000549985,;	T	ENSG00000111145	ENST00000228741	Transcript	missense_variant	835	509	170	P/L	cCc/cTc	.	.	.	1	ELK3	HGNC	3325	protein_coding	YES	CCDS9060.1	ENSP00000228741	ELK3_HUMAN	F8VZQ0_HUMAN,F8VUJ0_HUMAN	UPI0000000E09	.	tolerated(0.61)	benign(0)	3/5	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF172	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCCCGAAG	.	5	ESCA
ARHGEF7	0	.	GRCh37	13	111935538	111935538	+	Missense_Mutation	SNP	C	C	T	rs750833153	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1841C>T	p.Ala614Val	p.A614V	ENST00000375741	17/20	38	24	13	74	74	0	ARHGEF7,missense_variant,p.Ala436Val,ENST00000466143,;ARHGEF7,missense_variant,p.Ala436Val,ENST00000375736,;ARHGEF7,missense_variant,p.Ala511Val,ENST00000375737,;ARHGEF7,missense_variant,p.Ala358Val,ENST00000478679,;ARHGEF7,missense_variant,p.Ala436Val,ENST00000218789,;ARHGEF7,missense_variant,p.Ala564Val,ENST00000375739,;ARHGEF7,missense_variant,p.Ala436Val,ENST00000375723,;ARHGEF7,missense_variant,p.Ala436Val,ENST00000426073,;ARHGEF7,missense_variant,p.Ala614Val,ENST00000375741,;ARHGEF7,missense_variant,p.Ala593Val,ENST00000317133,;ARHGEF7,missense_variant,p.Ala521Val,ENST00000370623,;ARHGEF7,3_prime_UTR_variant,,ENST00000544132,;ARHGEF7,non_coding_transcript_exon_variant,,ENST00000491688,;ARHGEF7,3_prime_UTR_variant,,ENST00000469877,;	T	ENSG00000102606	ENST00000375741	Transcript	missense_variant	2091	1841	614	A/V	gCg/gTg	rs750833153	.	.	1	ARHGEF7	HGNC	15607	protein_coding	YES	CCDS45068.1	ENSP00000364893	ARHG7_HUMAN	Q5ZEZ3_HUMAN,E7EUY6_HUMAN,C9JDI6_HUMAN,C9JAD7_HUMAN,B1ANY6_HUMAN	UPI00002132CC	.	tolerated(0.54)	benign(0)	17/20	.	hmmpanther:PTHR22826:SF94,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCGCGCCGC	.	5	ESCA
GPR12	0	.	GRCh37	13	27333515	27333515	+	Silent	SNP	C	C	T	rs772800273	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.450G>A	p.%3D	p.S150S	ENST00000405846	2/2	12	4	7	23	23	0	GPR12,synonymous_variant,p.%3D,ENST00000405846,;GPR12,synonymous_variant,p.%3D,ENST00000381436,;	T	ENSG00000132975	ENST00000405846	Transcript	synonymous_variant	672	450	150	S	tcG/tcA	rs772800273	.	.	-1	GPR12	HGNC	4466	protein_coding	YES	CCDS9319.1	ENSP00000384932	GPR12_HUMAN	B4DG25_HUMAN,A8K2F5_HUMAN	UPI000003EC24	.	.	.	2/2	.	PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF8,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00644	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	CTCTCCGAATG	byFrequency	4	ESCA
CDX2	0	.	GRCh37	13	28536299	28536299	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*953A>G	.	.	ENST00000381020	3/3	21	16	5	38	38	0	CDX2,3_prime_UTR_variant,,ENST00000381020,;CDX2,downstream_gene_variant,,ENST00000548877,;	C	ENSG00000165556	ENST00000381020	Transcript	3_prime_UTR_variant	4028	.	.	.	.	.	.	.	-1	CDX2	HGNC	1806	protein_coding	YES	CCDS9328.1	ENSP00000370408	CDX2_HUMAN	.	UPI000013E4C8	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATCTCTTTTTC	.	2	ESCA
BTBD6	0	.	GRCh37	14	105717165	105717165	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*156C>T	.	.	ENST00000392554	4/4	37	34	3	61	61	0	BTBD6,3_prime_UTR_variant,,ENST00000536364,;BTBD6,3_prime_UTR_variant,,ENST00000392554,;BTBD6,3_prime_UTR_variant,,ENST00000327471,;BTBD6,3_prime_UTR_variant,,ENST00000463376,;BRF1,intron_variant,,ENST00000379937,;BRF1,intron_variant,,ENST00000546417,;BRF1,intron_variant,,ENST00000546474,;BRF1,intron_variant,,ENST00000327359,;BRF1,intron_variant,,ENST00000440513,;BRF1,upstream_gene_variant,,ENST00000550208,;BRF1,upstream_gene_variant,,ENST00000550375,;BRF1,downstream_gene_variant,,ENST00000550692,;BRF1,upstream_gene_variant,,ENST00000552127,;BRF1,upstream_gene_variant,,ENST00000392557,;BRF1,upstream_gene_variant,,ENST00000446501,;BRF1,upstream_gene_variant,,ENST00000551787,;BRF1,upstream_gene_variant,,ENST00000379932,;BTBD6,downstream_gene_variant,,ENST00000537513,;BTBD6,downstream_gene_variant,,ENST00000392553,;	T	ENSG00000184887	ENST00000392554	Transcript	3_prime_UTR_variant	1911	.	.	.	.	.	.	.	1	BTBD6	HGNC	19897	protein_coding	YES	CCDS10002.2	ENSP00000376337	BTBD6_HUMAN	F8VPC8_HUMAN	UPI00001FDD27	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CACAGCCAGAA	.	3	ESCA
TGM1	0	.	GRCh37	14	24728952	24728952	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.942C>T	p.%3D	p.G314G	ENST00000206765	6/15	45	36	9	64	63	0	TGM1,synonymous_variant,p.%3D,ENST00000206765,;TGM1,synonymous_variant,p.%3D,ENST00000559136,;TGM1,intron_variant,,ENST00000544573,;TGM1,downstream_gene_variant,,ENST00000558074,;TGM1,downstream_gene_variant,,ENST00000560226,;TGM1,downstream_gene_variant,,ENST00000560443,;TGM1,upstream_gene_variant,,ENST00000559669,;TGM1,downstream_gene_variant,,ENST00000560478,;TGM1,downstream_gene_variant,,ENST00000561067,;	A	ENSG00000092295	ENST00000206765	Transcript	synonymous_variant	1066	942	314	G	ggC/ggT	.	.	.	-1	TGM1	HGNC	11777	protein_coding	YES	CCDS9622.1	ENSP00000206765	TGM1_HUMAN	H0YNM4_HUMAN,H0YN27_HUMAN,H0YMQ8_HUMAN,H0YLT9_HUMAN,H0YLJ6_HUMAN,H0YKI6_HUMAN,B4DWR7_HUMAN	UPI000000164D	.	.	.	6/15	.	Superfamily_domains:SSF54001,PIRSF_domain:PIRSF000459,Gene3D:1ex0A02,hmmpanther:PTHR11590:SF13,hmmpanther:PTHR11590	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCACGGCCTCC	.	5	ESCA
PELI2	0	.	GRCh37	14	56765514	56765514	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1630A>G	.	.	ENST00000267460	6/6	12	6	6	12	12	0	PELI2,3_prime_UTR_variant,,ENST00000267460,;RP11-930O11.2,downstream_gene_variant,,ENST00000560296,;	G	ENSG00000139946	ENST00000267460	Transcript	3_prime_UTR_variant	3179	.	.	.	.	.	.	.	1	PELI2	HGNC	8828	protein_coding	YES	CCDS9726.1	ENSP00000267460	PELI2_HUMAN	Q659D8_HUMAN,H0YNF4_HUMAN,H0YK56_HUMAN	UPI0000062262	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCTTTATTTTT	.	2	ESCA
NRXN3	0	.	GRCh37	14	79175585	79175585	+	Missense_Mutation	SNP	G	G	A	rs780387298	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.128G>A	p.Arg43His	p.R43H	ENST00000554719	4/17	24	21	3	39	39	0	NRXN3,missense_variant,p.Arg43His,ENST00000554719,;NRXN3,missense_variant,p.Arg43His,ENST00000335750,;NRXN3,5_prime_UTR_variant,,ENST00000557081,;NRXN3,5_prime_UTR_variant,,ENST00000553631,;RP11-232C2.2,intron_variant,,ENST00000555680,;NRXN3,missense_variant,p.Arg414His,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,;	A	ENSG00000021645	ENST00000554719	Transcript	missense_variant	619	128	43	R/H	cGt/cAt	rs780387298,COSM958243,COSM958242	.	.	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	deleterious(0.01)	probably_damaging(0.921)	4/17	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127:SF405,hmmpanther:PTHR10127,Gene3D:2.60.120.200	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R43H|c.128G>A|4	MUTECT|MUSE	CATCCGTCTGG	byFrequency	2	ESCA
TRIP11	0	.	GRCh37	14	92470599	92470599	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3721C>A	p.Gln1241Lys	p.Q1241K	ENST00000267622	11/21	38	29	9	37	37	0	TRIP11,missense_variant,p.Gln957Lys,ENST00000554357,;TRIP11,missense_variant,p.Gln1241Lys,ENST00000267622,;TRIP11,upstream_gene_variant,,ENST00000557017,;	T	ENSG00000100815	ENST00000267622	Transcript	missense_variant	4095	3721	1241	Q/K	Cag/Aag	.	.	.	-1	TRIP11	HGNC	12305	protein_coding	YES	CCDS9899.1	ENSP00000267622	TRIPB_HUMAN	G3V4R7_HUMAN	UPI000013D767	.	deleterious(0.04)	possibly_damaging(0.798)	11/21	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18921:SF2,hmmpanther:PTHR18921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGCTGGGCTG	.	5	ESCA
MKRN3	0	.	GRCh37	15	23813044	23813044	+	3'UTR	SNP	T	T	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*591T>G	.	.	ENST00000314520	1/1	28	19	9	47	47	0	MKRN3,3_prime_UTR_variant,,ENST00000314520,;MKRN3,intron_variant,,ENST00000564592,;MKRN3,intron_variant,,ENST00000568252,;RP11-73C9.1,intron_variant,,ENST00000563044,;MKRN3,intron_variant,,ENST00000568945,;MKRN3,intron_variant,,ENST00000570112,;	G	ENSG00000179455	ENST00000314520	Transcript	3_prime_UTR_variant	2591	.	.	.	.	.	.	.	1	MKRN3	HGNC	7114	protein_coding	YES	CCDS10013.1	ENSP00000313881	MKRN3_HUMAN	.	UPI000000DAA1	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TATATTTAAGA	.	3	ESCA
MKRN3	0	.	GRCh37	15	23813065	23813065	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*612A>G	.	.	ENST00000314520	1/1	35	24	11	53	53	0	MKRN3,3_prime_UTR_variant,,ENST00000314520,;MKRN3,intron_variant,,ENST00000564592,;MKRN3,intron_variant,,ENST00000568252,;RP11-73C9.1,intron_variant,,ENST00000563044,;MKRN3,intron_variant,,ENST00000568945,;MKRN3,intron_variant,,ENST00000570112,;	G	ENSG00000179455	ENST00000314520	Transcript	3_prime_UTR_variant	2612	.	.	.	.	.	.	.	1	MKRN3	HGNC	7114	protein_coding	YES	CCDS10013.1	ENSP00000313881	MKRN3_HUMAN	.	UPI000000DAA1	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE	TAAAAATATAT	.	3	ESCA
KIAA1024	0	.	GRCh37	15	79749998	79749998	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1509C>T	p.%3D	p.T503T	ENST00000305428	2/4	20	14	6	23	23	0	KIAA1024,synonymous_variant,p.%3D,ENST00000305428,;KIAA1024,synonymous_variant,p.%3D,ENST00000559272,;	T	ENSG00000169330	ENST00000305428	Transcript	synonymous_variant	1584	1509	503	T	acC/acT	.	.	.	1	KIAA1024	HGNC	29172	protein_coding	YES	CCDS32306.1	ENSP00000307461	K1024_HUMAN	.	UPI00001B2F56	.	.	.	2/4	.	hmmpanther:PTHR31530,hmmpanther:PTHR31530:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACACCATGAA	.	5	ESCA
IFT140	0	.	GRCh37	16	1576045	1576045	+	Missense_Mutation	SNP	G	G	T	rs767213195	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2611C>A	p.Arg871Ser	p.R871S	ENST00000426508	21/31	43	27	16	61	61	0	IFT140,missense_variant,p.Arg65Ser,ENST00000361339,;IFT140,missense_variant,p.Arg871Ser,ENST00000426508,;TMEM204,upstream_gene_variant,,ENST00000253934,;IFT140,3_prime_UTR_variant,,ENST00000397417,;IFT140,non_coding_transcript_exon_variant,,ENST00000565298,;IFT140,non_coding_transcript_exon_variant,,ENST00000566818,;	T	ENSG00000187535	ENST00000426508	Transcript	missense_variant	2975	2611	871	R/S	Cgc/Agc	rs767213195	.	.	-1	IFT140	HGNC	29077	protein_coding	YES	CCDS10439.1	ENSP00000406012	IF140_HUMAN	Q9UG52_HUMAN,H3BTA5_HUMAN,H3BNC5_HUMAN	UPI0000073C64	.	deleterious(0)	probably_damaging(0.997)	21/31	.	hmmpanther:PTHR15722	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGCGCTTGC	.	5	ESCA
DNAH3	0	.	GRCh37	16	21045322	21045322	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5171C>T	p.Ala1724Val	p.A1724V	ENST00000261383	36/62	15	12	3	25	25	0	DNAH3,missense_variant,p.Ala1724Val,ENST00000261383,;DNAH3,missense_variant,p.Ala1724Val,ENST00000415178,;DNAH3,non_coding_transcript_exon_variant,,ENST00000572931,;DNAH3,non_coding_transcript_exon_variant,,ENST00000572640,;	A	ENSG00000158486	ENST00000261383	Transcript	missense_variant	5171	5171	1724	A/V	gCt/gTt	.	.	.	-1	DNAH3	HGNC	2949	protein_coding	YES	CCDS10594.1	ENSP00000261383	DYH3_HUMAN	.	UPI00001100F2	.	deleterious(0)	possibly_damaging(0.468)	36/62	.	Superfamily_domains:SSF52540,Gene3D:3.40.50.300,hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTGCAGCCAAC	.	2	ESCA
ANKRD26P1	0	.	GRCh37	16	46534066	46534066	+	RNA	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.849T>C	.	.	ENST00000571006	3/10	50	38	11	41	41	0	ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000571006,;ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000566201,;ANKRD26P1,downstream_gene_variant,,ENST00000574898,;ANKRD26P1,non_coding_transcript_exon_variant,,ENST00000569528,;	G	ENSG00000261239	ENST00000571006	Transcript	non_coding_transcript_exon_variant	849	.	.	.	.	.	.	.	-1	ANKRD26P1	HGNC	32955	processed_transcript	YES	.	.	.	.	.	.	.	.	3/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGTAACAGAT	.	5	ESCA
SALL1	0	.	GRCh37	16	51174226	51174226	+	Missense_Mutation	SNP	G	G	A	rs757169483	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1907C>T	p.Thr636Met	p.T636M	ENST00000251020	2/3	26	21	5	19	19	0	SALL1,missense_variant,p.Thr636Met,ENST00000251020,;SALL1,missense_variant,p.Thr539Met,ENST00000570206,;SALL1,missense_variant,p.Thr539Met,ENST00000440970,;SALL1,intron_variant,,ENST00000541611,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,;	A	ENSG00000103449	ENST00000251020	Transcript	missense_variant	1941	1907	636	T/M	aCg/aTg	rs757169483	.	.	-1	SALL1	HGNC	10524	protein_coding	YES	CCDS10747.1	ENSP00000251020	SALL1_HUMAN	H3BSM9_HUMAN	UPI000013CCD8	.	tolerated(0.06)	benign(0.003)	2/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCGCCGTCGGG	byFrequency	4	ESCA
DPEP3	0	.	GRCh37	16	68010044	68010044	+	Missense_Mutation	SNP	T	T	A	rs753738476	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1257A>T	p.Gln419His	p.Q419H	ENST00000268793	9/10	39	33	5	41	41	0	DPEP3,missense_variant,p.Gln419His,ENST00000268793,;DPEP3,downstream_gene_variant,,ENST00000574342,;	A	ENSG00000141096	ENST00000268793	Transcript	missense_variant	1631	1257	419	Q/H	caA/caT	rs753738476	.	.	-1	DPEP3	HGNC	23029	protein_coding	YES	CCDS10856.1	ENSP00000268793	DPEP3_HUMAN	.	UPI000006F093	.	deleterious(0.02)	probably_damaging(0.929)	9/10	.	PROSITE_profiles:PS51365,hmmpanther:PTHR10443:SF14,hmmpanther:PTHR10443,Gene3D:3.20.20.140,Pfam_domain:PF01244,Superfamily_domains:SSF51556	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ACACCTTGAAG	byFrequency	2	ESCA
MAF	0	.	GRCh37	16	79630648	79630648	+	Intron	DEL	T	T	-	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118+2034delA	.	.	ENST00000326043	.	41	30	11	39	39	0	MAF,3_prime_UTR_variant,,ENST00000393350,;MAF,intron_variant,,ENST00000326043,;MAF,intron_variant,,ENST00000569649,;	-	ENSG00000178573	ENST00000326043	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MAF	HGNC	6776	protein_coding	YES	CCDS10928.1	ENSP00000327048	MAF_HUMAN	Q8IX32_HUMAN	UPI000012EB25	.	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TGTGGATTTTTT	.	2	ESCA
TMEM199	0	.	GRCh37	17	26685980	26685980	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.253A>G	p.Ile85Val	p.I85V	ENST00000292114	2/6	25	13	12	60	60	0	TMEM199,missense_variant,p.Ile85Val,ENST00000509083,;TMEM199,missense_variant,p.Ile85Val,ENST00000292114,;TMEM199,intron_variant,,ENST00000395404,;POLDIP2,upstream_gene_variant,,ENST00000540200,;MIR4723,upstream_gene_variant,,ENST00000585070,;CTB-96E2.7,downstream_gene_variant,,ENST00000577850,;CTB-96E2.3,non_coding_transcript_exon_variant,,ENST00000591482,;TMEM199,non_coding_transcript_exon_variant,,ENST00000581386,;TMEM199,downstream_gene_variant,,ENST00000579762,;POLDIP2,upstream_gene_variant,,ENST00000003607,;TMEM199,missense_variant,p.Ile85Val,ENST00000555264,;TMEM199,non_coding_transcript_exon_variant,,ENST00000483505,;TMEM199,intron_variant,,ENST00000580868,;TMEM199,upstream_gene_variant,,ENST00000585027,;TMEM199,upstream_gene_variant,,ENST00000577317,;	G	ENSG00000244045	ENST00000292114	Transcript	missense_variant	343	253	85	I/V	Atc/Gtc	.	.	.	1	TMEM199	HGNC	18085	protein_coding	YES	CCDS11228.1	ENSP00000292114	TM199_HUMAN	K7EJL8_HUMAN,J3KS81_HUMAN	UPI0000039EBA	.	tolerated(0.13)	possibly_damaging(0.454)	2/6	.	Pfam_domain:PF11712,hmmpanther:PTHR31394:SF1,hmmpanther:PTHR31394	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGAAATCTAT	.	5	ESCA
KRT24	0	.	GRCh37	17	38856630	38856630	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.861G>T	p.Met287Ile	p.M287I	ENST00000264651	4/8	21	15	6	15	15	0	KRT24,missense_variant,p.Met287Ile,ENST00000264651,;	A	ENSG00000167916	ENST00000264651	Transcript	missense_variant	918	861	287	M/I	atG/atT	.	.	.	-1	KRT24	HGNC	18527	protein_coding	YES	CCDS11372.1	ENSP00000264651	K1C24_HUMAN	.	UPI000013D54D	.	deleterious(0.01)	benign(0.114)	4/8	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF101,hmmpanther:PTHR23239,Pfam_domain:PF00038,Superfamily_domains:SSF46579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTCATTTC	.	5	ESCA
MAPT	0	.	GRCh37	17	44061259	44061259	+	Silent	SNP	G	G	A	rs781182606	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1089G>A	p.%3D	p.P363P	ENST00000344290	6/15	56	43	12	64	64	0	MAPT,synonymous_variant,p.%3D,ENST00000262410,;MAPT,synonymous_variant,p.%3D,ENST00000571987,;MAPT,synonymous_variant,p.%3D,ENST00000415613,;MAPT,synonymous_variant,p.%3D,ENST00000344290,;MAPT,intron_variant,,ENST00000334239,;MAPT,intron_variant,,ENST00000340799,;MAPT,intron_variant,,ENST00000446361,;MAPT,intron_variant,,ENST00000574436,;MAPT,intron_variant,,ENST00000535772,;MAPT,intron_variant,,ENST00000576518,;MAPT,intron_variant,,ENST00000420682,;MAPT,intron_variant,,ENST00000351559,;MAPT,intron_variant,,ENST00000347967,;MAPT,intron_variant,,ENST00000431008,;MAPT,intron_variant,,ENST00000570299,;MAPT,upstream_gene_variant,,ENST00000577017,;MAPT,non_coding_transcript_exon_variant,,ENST00000576238,;MAPT,downstream_gene_variant,,ENST00000572440,;	A	ENSG00000186868	ENST00000344290	Transcript	synonymous_variant	1411	1089	363	P	ccG/ccA	rs781182606	.	.	1	MAPT	HGNC	6893	protein_coding	YES	CCDS45715.1	ENSP00000340820	TAU_HUMAN	.	UPI0001AE66E9	.	.	.	6/15	.	hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.R364W|c.1090C>T|4,CODON|p.R364W|c.1090C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTCCGCGGGG	byFrequency	5	ESCA
ST6GALNAC1	0	.	GRCh37	17	74625793	74625793	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.132G>A	p.%3D	p.R44R	ENST00000156626	2/9	13	7	5	23	23	0	ST6GALNAC1,synonymous_variant,p.%3D,ENST00000156626,;ST6GALNAC1,upstream_gene_variant,,ENST00000590784,;ST6GALNAC1,splice_region_variant,,ENST00000590878,;ST6GALNAC1,upstream_gene_variant,,ENST00000589004,;ST6GALNAC1,downstream_gene_variant,,ENST00000590915,;ST6GALNAC1,synonymous_variant,p.%3D,ENST00000359088,;ST6GALNAC1,splice_region_variant,,ENST00000589813,;ST6GALNAC1,splice_region_variant,,ENST00000592042,;ST6GALNAC1,upstream_gene_variant,,ENST00000585633,;ST6GALNAC1,upstream_gene_variant,,ENST00000588375,;	T	ENSG00000070526	ENST00000156626	Transcript	synonymous_variant	332	132	44	R	agG/agA	.	.	.	-1	ST6GALNAC1	HGNC	23614	protein_coding	YES	CCDS11748.1	ENSP00000156626	SIA7A_HUMAN	.	UPI0000001C00	.	.	.	2/9	.	hmmpanther:PTHR13713:SF1,hmmpanther:PTHR13713	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TGATGCCTAGG	.	2	ESCA
TP53	0	.	GRCh37	17	7579361	7579361	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	4/11	63	22	41	85	85	0	TP53,missense_variant,p.Phe109Ser,ENST00000508793,;TP53,missense_variant,p.Phe109Ser,ENST00000413465,;TP53,missense_variant,p.Phe109Ser,ENST00000604348,;TP53,missense_variant,p.Phe109Ser,ENST00000420246,;TP53,missense_variant,p.Phe109Ser,ENST00000269305,;TP53,missense_variant,p.Phe109Ser,ENST00000359597,;TP53,missense_variant,p.Phe109Ser,ENST00000445888,;TP53,missense_variant,p.Phe109Ser,ENST00000503591,;TP53,missense_variant,p.Phe109Ser,ENST00000455263,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000504937,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000510385,;	G	ENSG00000141510	ENST00000269305	Transcript	missense_variant	516	326	109	F/S	tTc/tCc	TP53_g.11557T>C,TP53_g.11557T>G,COSM45169,COSM78686,COSM148181,COSM265872,COSM148180,COSM265871	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0)	probably_damaging(1)	4/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417	.	.	.	.	.	.	.	.	.	.	0,0,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1182del1182|6,CODON|p.G59fs*23|c.175_374del200|3,CODON|p.F109C|c.326T>G|3,CODON|p.F109C|c.326T>G|4,CODON|p.F109C|c.326T>G|3,BUFFER|p.F113V|c.337T>G|3,BUFFER|p.F113V|c.337T>G|3,BUFFER|p.F113V|c.337T>G|6,BUFFER|p.L111R|c.332T>G|5,BUFFER|p.L111Q|c.332T>A|7,BUFFER|p.L111P|c.332T>C|9,BUFFER|p.L111Q|c.332T>A|3,BUFFER|p.L111R|c.332T>G|10,BUFFER|p.L111Q|c.332T>A|3,BUFFER|p.L111P|c.332T>C|3,BUFFER|p.L111R|c.332T>G|5,BUFFER|p.L111P|c.332T>C|3,BUFFER|p.R110fs*13|c.329delG|3,BUFFER|p.R110fs*13|c.328delC|4,BUFFER|p.R110L|c.329G>T|27,BUFFER|p.R110P|c.329G>C|11,BUFFER|p.R110L|c.329G>T|5,BUFFER|p.R110L|c.329G>T|8,BUFFER|p.R110L|c.329G>T|8,BUFFER|p.R110C|c.328C>T|6,BUFFER|p.G108delG|c.322_324delGGT|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.G108fs*15|c.323delG|3,BUFFER|p.Y107*|c.321C>A|6,BUFFER|p.Y107Y|c.321C>T|3,BUFFER|p.Y107*|c.321C>G|3,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|7,BUFFER|p.Y107D|c.319T>G|8,BUFFER|p.S106R|c.318C>G|3,BUFFER|p.S106R|c.318C>G|3,BUFFER|p.S106R|c.318C>G|6	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACGGAAACCG	.	5	ESCA
ENTHD2	0	.	GRCh37	17	79205329	79205329	+	Intron	SNP	G	G	A	rs766162493	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.815+49C>T	.	.	ENST00000300714	.	62	47	15	79	79	0	ENTHD2,intron_variant,,ENST00000374769,;ENTHD2,intron_variant,,ENST00000300714,;ENTHD2,downstream_gene_variant,,ENST00000571094,;AC027601.1,non_coding_transcript_exon_variant,,ENST00000575922,;AC027601.1,intron_variant,,ENST00000569559,;ENTHD2,intron_variant,,ENST00000576090,;ENTHD2,intron_variant,,ENST00000573295,;ENTHD2,intron_variant,,ENST00000571115,;ENTHD2,downstream_gene_variant,,ENST00000570854,;ENTHD2,downstream_gene_variant,,ENST00000574944,;	A	ENSG00000167302	ENST00000300714	Transcript	intron_variant	.	.	.	.	.	rs766162493	.	.	-1	ENTHD2	HGNC	26458	protein_coding	YES	CCDS11779.1	ENSP00000300714	AP4AT_HUMAN	.	UPI0000071221	.	.	.	.	9/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTCGCCCAC	byFrequency|byCluster	5	ESCA
P4HB	0	.	GRCh37	17	79813462	79813462	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.353C>G	p.Ala118Gly	p.A118G	ENST00000331483	3/11	50	41	8	81	81	0	P4HB,missense_variant,p.Ser49Cys,ENST00000573778,;P4HB,missense_variant,p.Ala118Gly,ENST00000331483,;P4HB,missense_variant,p.Ala82Gly,ENST00000574914,;P4HB,intron_variant,,ENST00000576380,;P4HB,intron_variant,,ENST00000576390,;P4HB,intron_variant,,ENST00000576052,;P4HB,intron_variant,,ENST00000576541,;P4HB,intron_variant,,ENST00000571617,;P4HB,intron_variant,,ENST00000570907,;P4HB,intron_variant,,ENST00000439918,;P4HB,splice_region_variant,,ENST00000472244,;P4HB,splice_region_variant,,ENST00000467086,;P4HB,splice_region_variant,,ENST00000471535,;P4HB,splice_region_variant,,ENST00000575069,;P4HB,splice_region_variant,,ENST00000574007,;P4HB,non_coding_transcript_exon_variant,,ENST00000477607,;P4HB,upstream_gene_variant,,ENST00000478034,;P4HB,downstream_gene_variant,,ENST00000466567,;	C	ENSG00000185624	ENST00000331483	Transcript	missense_variant	576	353	118	A/G	gCt/gGt	.	.	.	-1	P4HB	HGNC	8548	protein_coding	YES	CCDS11787.1	ENSP00000327801	PDIA1_HUMAN	B3KTQ9_HUMAN	UPI0000000CAA	.	tolerated(1)	benign(0.001)	3/11	.	PROSITE_profiles:PS51352,hmmpanther:PTHR18929:SF48,hmmpanther:PTHR18929,Gene3D:3.40.30.10,Pfam_domain:PF00085,TIGRFAM_domain:TIGR01130,TIGRFAM_domain:TIGR01126,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAGCTAAC	.	5	ESCA
FASN	0	.	GRCh37	17	80038423	80038423	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6870C>T	p.%3D	p.I2290I	ENST00000306749	40/43	33	29	4	34	34	0	FASN,synonymous_variant,p.%3D,ENST00000306749,;FASN,intron_variant,,ENST00000579758,;FASN,non_coding_transcript_exon_variant,,ENST00000578424,;FASN,intron_variant,,ENST00000580382,;FASN,upstream_gene_variant,,ENST00000584610,;FASN,downstream_gene_variant,,ENST00000579410,;	A	ENSG00000169710	ENST00000306749	Transcript	synonymous_variant	7089	6870	2290	I	atC/atT	.	.	.	-1	FASN	HGNC	3594	protein_coding	YES	CCDS11801.1	ENSP00000304592	FAS_HUMAN	.	UPI000013EB82	.	.	.	40/43	.	hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF227,Gene3D:3.40.50.1820,Pfam_domain:PF00975,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGTCGATGTA	.	4	ESCA
PFAS	0	.	GRCh37	17	8158846	8158846	+	Silent	SNP	G	G	T	rs143291952	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.411G>T	p.%3D	p.V137V	ENST00000314666	5/28	52	34	18	56	56	0	PFAS,synonymous_variant,p.%3D,ENST00000314666,;PFAS,intron_variant,,ENST00000545834,;PFAS,downstream_gene_variant,,ENST00000585183,;PFAS,downstream_gene_variant,,ENST00000581242,;PFAS,downstream_gene_variant,,ENST00000584044,;PFAS,intron_variant,,ENST00000580356,;	T	ENSG00000178921	ENST00000314666	Transcript	synonymous_variant	544	411	137	V	gtG/gtT	rs143291952	.	.	1	PFAS	HGNC	8863	protein_coding	YES	CCDS11136.1	ENSP00000313490	PUR4_HUMAN	Q9BR56_HUMAN,Q6P4B4_HUMAN,J3QSH6_HUMAN,J3QL39_HUMAN,J3KTL4_HUMAN,F5GWT9_HUMAN	UPI00001A95E5	.	.	.	5/28	.	Superfamily_domains:SSF82697,TIGRFAM_domain:TIGR01735,hmmpanther:PTHR10099:SF1,hmmpanther:PTHR10099	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAGGTGGAAGC	.	5	ESCA
MIB1	0	.	GRCh37	18	19450104	19450104	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5477C>A	.	.	ENST00000261537	21/21	38	31	7	48	48	0	MIB1,3_prime_UTR_variant,,ENST00000261537,;RP11-268I9.3,downstream_gene_variant,,ENST00000583436,;	A	ENSG00000101752	ENST00000261537	Transcript	3_prime_UTR_variant	8762	.	.	.	.	.	.	.	1	MIB1	HGNC	21086	protein_coding	YES	CCDS11871.1	ENSP00000261537	MIB1_HUMAN	B3KRA8_HUMAN	UPI000000D833	.	.	.	21/21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTATCGTTAA	.	5	ESCA
NCAN	0	.	GRCh37	19	19338453	19338453	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2024C>T	p.Thr675Ile	p.T675I	ENST00000252575	8/15	48	31	17	77	77	0	NCAN,missense_variant,p.Thr126Ile,ENST00000538881,;NCAN,missense_variant,p.Thr675Ile,ENST00000252575,;NCAN,non_coding_transcript_exon_variant,,ENST00000590187,;	T	ENSG00000130287	ENST00000252575	Transcript	missense_variant	2123	2024	675	T/I	aCc/aTc	.	.	.	1	NCAN	HGNC	2465	protein_coding	YES	CCDS12397.1	ENSP00000252575	NCAN_HUMAN	Q4LE67_HUMAN,F5H7X3_HUMAN	UPI000013CD70	.	tolerated(0.25)	benign(0.003)	8/15	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGAGACCAAGG	.	5	ESCA
TSHZ3	0	.	GRCh37	19	31767227	31767227	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*226G>A	.	.	ENST00000240587	2/2	47	43	4	34	34	0	TSHZ3,3_prime_UTR_variant,,ENST00000240587,;TSHZ3,downstream_gene_variant,,ENST00000560707,;	T	ENSG00000121297	ENST00000240587	Transcript	3_prime_UTR_variant	3800	.	.	.	.	.	.	.	-1	TSHZ3	HGNC	30700	protein_coding	YES	CCDS12421.2	ENSP00000240587	TSH3_HUMAN	A1L0U7_HUMAN	UPI0000202000	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGTTCCAAACA	.	3	ESCA
MAP3K10	0	.	GRCh37	19	40704445	40704445	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.846A>T	p.Lys282Asn	p.K282N	ENST00000253055	2/10	15	10	5	21	21	0	MAP3K10,missense_variant,p.Lys282Asn,ENST00000253055,;MAP3K10,intron_variant,,ENST00000593906,;MAP3K10,missense_variant,p.Lys32Asn,ENST00000597986,;MAP3K10,missense_variant,p.Lys48Asn,ENST00000594951,;MAP3K10,intron_variant,,ENST00000593502,;	T	ENSG00000130758	ENST00000253055	Transcript	missense_variant	1134	846	282	K/N	aaA/aaT	.	.	.	1	MAP3K10	HGNC	6849	protein_coding	YES	CCDS12549.1	ENSP00000253055	M3K10_HUMAN	.	UPI000013CDAC	.	deleterious(0)	probably_damaging(0.999)	2/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF370,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00220,PIRSF_domain:PIRSF000556,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCAAAAGCAG	.	2	ESCA
NKPD1	0	.	GRCh37	19	45656300	45656300	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1395C>T	p.%3D	p.Y465Y	ENST00000317951	4/4	21	15	6	45	45	0	NKPD1,synonymous_variant,p.%3D,ENST00000589776,;NKPD1,synonymous_variant,p.%3D,ENST00000317951,;NKPD1,synonymous_variant,p.%3D,ENST00000438936,;NKPD1,synonymous_variant,p.%3D,ENST00000429338,;MARK4,intron_variant,,ENST00000587566,;AC005757.7,upstream_gene_variant,,ENST00000589594,;PPP1R37,downstream_gene_variant,,ENST00000422370,;	A	ENSG00000179846	ENST00000317951	Transcript	synonymous_variant	1395	1395	465	Y	taC/taT	.	.	.	-1	NKPD1	HGNC	24739	protein_coding	YES	.	ENSP00000321976	.	J3KNK3_HUMAN	UPI000059D74A	.	.	.	4/4	.	hmmpanther:PTHR22674,hmmpanther:PTHR22674:SF4,Pfam_domain:PF07693	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCGGGTAGCA	.	5	ESCA
PRKD2	0	.	GRCh37	19	47207558	47207558	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757C>T	p.%3D	p.L253L	ENST00000433867	6/19	34	24	10	50	50	0	PRKD2,synonymous_variant,p.%3D,ENST00000595515,;PRKD2,synonymous_variant,p.%3D,ENST00000600194,;PRKD2,synonymous_variant,p.%3D,ENST00000601806,;PRKD2,synonymous_variant,p.%3D,ENST00000433867,;PRKD2,synonymous_variant,p.%3D,ENST00000291281,;PRKD2,intron_variant,,ENST00000601605,;PRKD2,downstream_gene_variant,,ENST00000598633,;PRKD2,downstream_gene_variant,,ENST00000595132,;MIR320E,downstream_gene_variant,,ENST00000390179,;PRKD2,downstream_gene_variant,,ENST00000597641,;	A	ENSG00000105287	ENST00000433867	Transcript	synonymous_variant	1235	757	253	L	Ctg/Ttg	.	.	.	-1	PRKD2	HGNC	17293	protein_coding	YES	CCDS12689.1	ENSP00000393978	KPCD2_HUMAN	M0R346_HUMAN,M0R2R2_HUMAN,M0R012_HUMAN	UPI000013E03A	.	.	.	6/19	.	PIRSF_domain:PIRSF000552,hmmpanther:PTHR22968	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCCAGCTCAA	.	5	ESCA
MYH14	0	.	GRCh37	19	50783349	50783349	+	Missense_Mutation	SNP	G	G	A	rs727504915	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4088G>A	p.Arg1363His	p.R1363H	ENST00000601313	31/43	79	72	7	109	109	0	MYH14,missense_variant,p.Arg1363His,ENST00000440075,;MYH14,missense_variant,p.Arg1363His,ENST00000601313,;MYH14,missense_variant,p.Arg1355His,ENST00000376970,;MYH14,missense_variant,p.Arg1322His,ENST00000596571,;MYH14,missense_variant,p.Arg1330His,ENST00000425460,;MYH14,missense_variant,p.Arg1330His,ENST00000598205,;MYH14,missense_variant,p.Arg1363His,ENST00000262269,;MYH14,upstream_gene_variant,,ENST00000595016,;	A	ENSG00000105357	ENST00000601313	Transcript	missense_variant	4118	4088	1363	R/H	cGt/cAt	rs727504915	.	.	1	MYH14	HGNC	23212	protein_coding	YES	CCDS54295.1	ENSP00000470298	MYH14_HUMAN	A1L2Z2_HUMAN	UPI0001641C2F	.	deleterious(0.02)	probably_damaging(0.91)	31/43	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF318,Pfam_domain:PF01576,Superfamily_domains:SSF90257	.	.	.	.	.	.	.	.	.	uncertain_significance	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	CATCCGTCTTA	byFrequency|byCluster	3	ESCA
SIGLEC8	0	.	GRCh37	19	51961657	51961657	+	5'UTR	SNP	C	C	T	rs373554885	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-16G>A	.	.	ENST00000321424	1/7	14	10	4	21	21	0	SIGLEC8,5_prime_UTR_variant,,ENST00000340550,;SIGLEC8,5_prime_UTR_variant,,ENST00000321424,;SIGLEC8,5_prime_UTR_variant,,ENST00000430817,;SIGLEC8,upstream_gene_variant,,ENST00000597352,;	T	ENSG00000105366	ENST00000321424	Transcript	5_prime_UTR_variant	52	.	.	.	.	rs373554885	.	.	-1	SIGLEC8	HGNC	10877	protein_coding	YES	CCDS33086.1	ENSP00000321077	SIGL8_HUMAN	.	UPI000013598B	.	.	.	1/7	.	.	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE	GAAGGCGCCAG	byFrequency|byCluster	4	ESCA
ZNF175	0	.	GRCh37	19	52090212	52090212	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628G>C	p.Glu210Gln	p.E210Q	ENST00000262259	5/5	33	27	6	42	42	0	ZNF175,missense_variant,p.Glu210Gln,ENST00000262259,;ZNF175,intron_variant,,ENST00000436511,;AC018755.1,downstream_gene_variant,,ENST00000301439,;ZNF175,non_coding_transcript_exon_variant,,ENST00000600460,;	C	ENSG00000105497	ENST00000262259	Transcript	missense_variant	986	628	210	E/Q	Gaa/Caa	COSM1395695	.	.	1	ZNF175	HGNC	12964	protein_coding	YES	CCDS12837.1	ENSP00000262259	ZN175_HUMAN	.	UPI000013C30A	.	tolerated(0.37)	benign(0.231)	5/5	.	hmmpanther:PTHR24377:SF37,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTAGAAGTG	.	5	ESCA
FPR2	0	.	GRCh37	19	52272212	52272212	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301A>G	p.Ile101Val	p.I101V	ENST00000598776	2/2	63	45	17	70	70	0	FPR2,missense_variant,p.Ile101Val,ENST00000599326,;FPR2,missense_variant,p.Ile101Val,ENST00000340023,;FPR2,missense_variant,p.Ile101Val,ENST00000598953,;FPR2,missense_variant,p.Ile101Val,ENST00000600722,;FPR2,missense_variant,p.Ile101Val,ENST00000598776,;FPR1,intron_variant,,ENST00000594900,;FPR2,downstream_gene_variant,,ENST00000600258,;	G	ENSG00000171049	ENST00000598776	Transcript	missense_variant	1073	301	101	I/V	Att/Gtt	.	.	.	1	FPR2	HGNC	3827	protein_coding	YES	CCDS12840.1	ENSP00000468897	FPR2_HUMAN	M0R222_HUMAN,M0QZ89_HUMAN,M0QXD3_HUMAN	UPI00000012D0	.	tolerated(0.61)	benign(0.006)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF16,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00526	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTAATTCAC	.	5	ESCA
FPR2	0	.	GRCh37	19	52272818	52272818	+	Missense_Mutation	SNP	G	G	A	rs373596683	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.907G>A	p.Val303Ile	p.V303I	ENST00000598776	2/2	19	7	12	31	31	0	FPR2,missense_variant,p.Val303Ile,ENST00000340023,;FPR2,missense_variant,p.Val303Ile,ENST00000598953,;FPR2,missense_variant,p.Val303Ile,ENST00000598776,;FPR1,intron_variant,,ENST00000594900,;FPR2,downstream_gene_variant,,ENST00000599326,;FPR2,downstream_gene_variant,,ENST00000600258,;FPR2,downstream_gene_variant,,ENST00000600722,;	A	ENSG00000171049	ENST00000598776	Transcript	missense_variant	1679	907	303	V/I	Gtc/Atc	rs373596683,COSM1395727	.	.	1	FPR2	HGNC	3827	protein_coding	YES	CCDS12840.1	ENSP00000468897	FPR2_HUMAN	M0R222_HUMAN,M0QZ89_HUMAN,M0QXD3_HUMAN	UPI00000012D0	.	deleterious(0)	possibly_damaging(0.899)	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR24225:SF16,hmmpanther:PTHR24225,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTACGTCTTT	byFrequency|byCluster	5	ESCA
ZNF579	0	.	GRCh37	19	56090030	56090030	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.976C>T	p.%3D	p.L326L	ENST00000325421	2/2	13	10	3	19	19	0	ZNF579,synonymous_variant,p.%3D,ENST00000325421,;ZNF579,downstream_gene_variant,,ENST00000592239,;CTD-2537I9.5,upstream_gene_variant,,ENST00000589396,;	A	ENSG00000218891	ENST00000325421	Transcript	synonymous_variant	1005	976	326	L	Ctg/Ttg	.	.	.	-1	ZNF579	HGNC	26646	protein_coding	YES	CCDS12927.1	ENSP00000320188	ZN579_HUMAN	.	UPI0000141657	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24409:SF8,hmmpanther:PTHR24409	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGCCAGCAGGC	.	2	ESCA
WDR18	0	.	GRCh37	19	994323	994323	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1279A>G	p.Ile427Val	p.I427V	ENST00000251289	10/10	24	16	8	34	34	0	WDR18,missense_variant,p.Ile389Val,ENST00000607440,;WDR18,missense_variant,p.Ile427Val,ENST00000251289,;WDR18,missense_variant,p.Ile404Val,ENST00000587001,;WDR18,3_prime_UTR_variant,,ENST00000590354,;WDR18,downstream_gene_variant,,ENST00000591997,;WDR18,3_prime_UTR_variant,,ENST00000591985,;WDR18,non_coding_transcript_exon_variant,,ENST00000591155,;WDR18,downstream_gene_variant,,ENST00000591276,;WDR18,downstream_gene_variant,,ENST00000586317,;WDR18,downstream_gene_variant,,ENST00000585809,;WDR18,downstream_gene_variant,,ENST00000590397,;	G	ENSG00000065268	ENST00000251289	Transcript	missense_variant	1302	1279	427	I/V	Atc/Gtc	.	.	.	1	WDR18	HGNC	17956	protein_coding	YES	CCDS12051.1	ENSP00000251289	WDR18_HUMAN	.	UPI000013CCF7	.	tolerated(0.08)	possibly_damaging(0.454)	10/10	.	hmmpanther:PTHR18763,Pfam_domain:PF14077	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTCATCACG	.	5	ESCA
TNFRSF8	0	.	GRCh37	1	12164486	12164486	+	Nonsense_Mutation	SNP	G	G	T	rs748922700	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.319G>T	p.Glu107Ter	p.E107*	ENST00000263932	4/15	30	22	8	54	54	0	TNFRSF8,stop_gained,p.Glu107Ter,ENST00000263932,;TNFRSF8,5_prime_UTR_variant,,ENST00000417814,;TNFRSF8,3_prime_UTR_variant,,ENST00000514649,;	T	ENSG00000120949	ENST00000263932	Transcript	stop_gained	541	319	107	E/*	Gaa/Taa	rs748922700,COSM3472364	.	.	1	TNFRSF8	HGNC	11923	protein_coding	YES	CCDS144.1	ENSP00000263932	.	A5D8T4_HUMAN	UPI000013D48C	.	.	.	4/15	.	PROSITE_profiles:PS50050,hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF85,Gene3D:2.10.50.10,Superfamily_domains:SSF57586	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTGCGAATGT	.	5	ESCA
VPS13D	0	.	GRCh37	1	12336369	12336369	+	Silent	SNP	T	T	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2724T>A	p.%3D	p.T908T	ENST00000358136	19/70	17	13	4	27	27	0	VPS13D,synonymous_variant,p.%3D,ENST00000358136,;VPS13D,synonymous_variant,p.%3D,ENST00000356315,;VPS13D,upstream_gene_variant,,ENST00000011700,;	A	ENSG00000048707	ENST00000358136	Transcript	synonymous_variant	2854	2724	908	T	acT/acA	.	.	.	1	VPS13D	HGNC	23595	protein_coding	YES	CCDS30588.1	ENSP00000350854	.	M0QXS2_HUMAN,J3KP14_HUMAN	UPI0000451CA9	.	.	.	19/70	.	hmmpanther:PTHR16166:SF93,hmmpanther:PTHR16166	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	AAAACTTCTGA	.	4	ESCA
AQP10	0	.	GRCh37	1	154296217	154296217	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.642C>T	p.%3D	p.N214N	ENST00000324978	5/6	39	28	11	54	54	0	AQP10,synonymous_variant,p.%3D,ENST00000324978,;AQP10,synonymous_variant,p.%3D,ENST00000484864,;ATP8B2,upstream_gene_variant,,ENST00000368487,;ATP8B2,upstream_gene_variant,,ENST00000368489,;AQP10,non_coding_transcript_exon_variant,,ENST00000355197,;ATP8B2,upstream_gene_variant,,ENST00000368490,;	T	ENSG00000143595	ENST00000324978	Transcript	synonymous_variant	682	642	214	N	aaC/aaT	.	.	.	1	AQP10	HGNC	16029	protein_coding	YES	CCDS1065.1	ENSP00000318355	AQP10_HUMAN	.	UPI000007028A	.	.	.	5/6	.	hmmpanther:PTHR19139:SF18,hmmpanther:PTHR19139,Pfam_domain:PF00230,TIGRFAM_domain:TIGR00861,Gene3D:1.20.1080.10,Superfamily_domains:SSF81338,Prints_domain:PR00783	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCAACCCTGC	.	5	ESCA
OR6Y1	0	.	GRCh37	1	158517456	158517456	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.440G>T	p.Gly147Val	p.G147V	ENST00000302617	1/1	36	21	15	43	43	0	OR6Y1,missense_variant,p.Gly147Val,ENST00000302617,;	A	ENSG00000197532	ENST00000302617	Transcript	missense_variant	440	440	147	G/V	gGc/gTc	COSM676150	.	.	-1	OR6Y1	HGNC	14823	protein_coding	YES	CCDS30899.1	ENSP00000304807	OR6Y1_HUMAN	.	UPI000004B1E2	.	tolerated(0.86)	benign(0.098)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF109,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTGCCACAG	.	5	ESCA
SPTA1	0	.	GRCh37	1	158637726	158637727	+	Frame_Shift_Ins	INS	-	-	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	-	-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1959dupT	p.Ala654CysfsTer3	p.A654Cfs*3	ENST00000368147	15/52	64	50	14	49	49	0	SPTA1,frameshift_variant,p.Ala654CysfsTer3,ENST00000368147,;	A	ENSG00000163554	ENST00000368147	Transcript	frameshift_variant	2140-2141	1959-1960	653-654	-/X	-/T	.	.	.	-1	SPTA1	HGNC	11272	protein_coding	YES	CCDS41423.1	ENSP00000357129	SPTA1_HUMAN	O60686_HUMAN	UPI0000458906	.	.	.	15/52	.	hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF240,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	insertion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AGAGGCATAGT	.	3	ESCA
PBX1	0	.	GRCh37	1	164529123	164529123	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.64C>A	p.Leu22Met	p.L22M	ENST00000420696	1/9	57	50	7	120	120	0	PBX1,missense_variant,p.Leu22Met,ENST00000540236,;PBX1,missense_variant,p.Leu22Met,ENST00000485769,;PBX1,missense_variant,p.Leu22Met,ENST00000559240,;PBX1,missense_variant,p.Leu22Met,ENST00000367897,;PBX1,missense_variant,p.Leu22Met,ENST00000420696,;PBX1,missense_variant,p.Leu22Met,ENST00000340699,;PBX1,missense_variant,p.Leu22Met,ENST00000401534,;PBX1,upstream_gene_variant,,ENST00000559578,;PBX1,intron_variant,,ENST00000467023,;PBX1,non_coding_transcript_exon_variant,,ENST00000498497,;PBX1,upstream_gene_variant,,ENST00000605467,;	A	ENSG00000185630	ENST00000420696	Transcript	missense_variant	252	64	22	L/M	Ctg/Atg	.	.	.	1	PBX1	HGNC	8632	protein_coding	YES	CCDS1246.1	ENSP00000405890	PBX1_HUMAN	Q68DD6_HUMAN,H0YLT4_HUMAN,H0YLM3_HUMAN,H0YLD4_HUMAN,H0YLB0_HUMAN,H0YKH1_HUMAN,F8WA05_HUMAN	UPI00000213E1	.	tolerated_low_confidence(0.5)	benign(0.018)	1/9	.	hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF58	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCGGCCTGTCC	.	4	ESCA
TNN	0	.	GRCh37	1	175086207	175086207	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2252G>C	p.Arg751Thr	p.R751T	ENST00000239462	10/19	68	64	4	76	76	0	TNN,missense_variant,p.Arg751Thr,ENST00000239462,;	C	ENSG00000120332	ENST00000239462	Transcript	missense_variant	2365	2252	751	R/T	aGg/aCg	.	.	.	1	TNN	HGNC	22942	protein_coding	YES	CCDS30943.1	ENSP00000239462	TENN_HUMAN	.	UPI00001D7DA9	.	tolerated(0.06)	benign(0.013)	10/19	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF167,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACCAGGGAGG	.	2	ESCA
CRB1	0	.	GRCh37	1	197396689	197396689	+	Missense_Mutation	SNP	C	C	T	rs28939720	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2234C>T	p.Thr745Met	p.T745M	ENST00000367400	7/12	29	21	8	37	37	0	CRB1,missense_variant,p.Thr633Met,ENST00000367399,;CRB1,missense_variant,p.Thr676Met,ENST00000535699,;CRB1,missense_variant,p.Thr126Met,ENST00000367397,;CRB1,missense_variant,p.Thr226Met,ENST00000544212,;CRB1,missense_variant,p.Thr745Met,ENST00000367400,;CRB1,3_prime_UTR_variant,,ENST00000543483,;CRB1,intron_variant,,ENST00000538660,;CRB1,non_coding_transcript_exon_variant,,ENST00000480086,;CRB1,missense_variant,p.Thr745Met,ENST00000484075,;	T	ENSG00000134376	ENST00000367400	Transcript	missense_variant	2369	2234	745	T/M	aCg/aTg	rs28939720,CM992150,RISN_CRB1:c.2234C>T,COSM32648	.	.	1	CRB1	HGNC	2343	protein_coding	YES	CCDS1390.1	ENSP00000356370	CRUM1_HUMAN	B7Z824_HUMAN	UPI0000073345	.	deleterious(0.04)	probably_damaging(1)	7/12	.	PROSITE_profiles:PS50025,hmmpanther:PTHR24049,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	not_provided,pathogenic	0,0,0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,0,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.T745M|c.2234C>T|4	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCGAACGCTTC	byFrequency|byCluster	5	ESCA
NAV1	0	.	GRCh37	1	201792024	201792024	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2964T>C	.	.	ENST00000367296	30/30	44	41	3	36	36	0	NAV1,3_prime_UTR_variant,,ENST00000367297,;NAV1,3_prime_UTR_variant,,ENST00000367300,;NAV1,3_prime_UTR_variant,,ENST00000295624,;NAV1,3_prime_UTR_variant,,ENST00000367302,;NAV1,3_prime_UTR_variant,,ENST00000367296,;NAV1,3_prime_UTR_variant,,ENST00000367295,;IPO9-AS1,intron_variant,,ENST00000413035,;IPO9-AS1,intron_variant,,ENST00000421449,;IPO9-AS1,intron_variant,,ENST00000421159,;	C	ENSG00000134369	ENST00000367296	Transcript	3_prime_UTR_variant	9018	.	.	.	.	.	.	.	1	NAV1	HGNC	15989	protein_coding	YES	CCDS1414.2	ENSP00000356265	NAV1_HUMAN	.	UPI00004562D4	.	.	.	30/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GACACTCATCC	.	2	ESCA
KCNH1	0	.	GRCh37	1	210857068	210857068	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2525A>T	p.Asp842Val	p.D842V	ENST00000271751	11/11	25	13	11	34	34	0	KCNH1,missense_variant,p.Asp815Val,ENST00000367007,;KCNH1,missense_variant,p.Asp842Val,ENST00000271751,;	A	ENSG00000143473	ENST00000271751	Transcript	missense_variant	2553	2525	842	D/V	gAt/gTt	.	.	.	-1	KCNH1	HGNC	6250	protein_coding	YES	CCDS1496.1	ENSP00000271751	KCNH1_HUMAN	.	UPI000003230D	.	tolerated_low_confidence(0.09)	benign(0.006)	11/11	.	hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCATCTTTG	.	5	ESCA
NVL	0	.	GRCh37	1	224492794	224492794	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.690G>T	p.Arg230Ser	p.R230S	ENST00000281701	7/23	61	32	29	39	39	0	NVL,missense_variant,p.Arg124Ser,ENST00000361463,;NVL,missense_variant,p.Arg14Ser,ENST00000340871,;NVL,missense_variant,p.Arg124Ser,ENST00000391875,;NVL,missense_variant,p.Arg230Ser,ENST00000281701,;NVL,missense_variant,p.Arg126Ser,ENST00000436927,;NVL,missense_variant,p.Arg139Ser,ENST00000488718,;NVL,missense_variant,p.Arg135Ser,ENST00000492281,;NVL,missense_variant,p.Arg113Ser,ENST00000469968,;NVL,missense_variant,p.Arg139Ser,ENST00000469075,;NVL,5_prime_UTR_variant,,ENST00000482491,;NVL,downstream_gene_variant,,ENST00000461546,;RNU6-1008P,upstream_gene_variant,,ENST00000384160,;NVL,downstream_gene_variant,,ENST00000470903,;NVL,downstream_gene_variant,,ENST00000461466,;NVL,missense_variant,p.Arg230Ser,ENST00000467882,;NVL,3_prime_UTR_variant,,ENST00000470989,;NVL,downstream_gene_variant,,ENST00000498767,;	A	ENSG00000143748	ENST00000281701	Transcript	missense_variant	950	690	230	R/S	agG/agT	.	.	.	-1	NVL	HGNC	8070	protein_coding	YES	CCDS1541.1	ENSP00000281701	NVL_HUMAN	Q96PA2_HUMAN	UPI0000073F3E	.	tolerated(0.07)	benign(0.037)	7/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23077,hmmpanther:PTHR23077:SF55	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTTCCTTTT	.	5	ESCA
FH	0	.	GRCh37	1	241665791	241665791	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1188C>T	p.%3D	p.V396V	ENST00000366560	8/10	39	35	4	39	37	1	FH,synonymous_variant,p.%3D,ENST00000366560,;	A	ENSG00000091483	ENST00000366560	Transcript	synonymous_variant	1227	1188	396	V	gtC/gtT	COSM3789719	.	.	-1	FH	HGNC	3700	protein_coding	YES	CCDS1617.1	ENSP00000355518	FUMH_HUMAN	B1ANK7_HUMAN	UPI000012AD6A	.	.	.	8/10	.	Superfamily_domains:SSF48557,TIGRFAM_domain:TIGR00979,Gene3D:1.20.200.10,hmmpanther:PTHR11444:SF1,hmmpanther:PTHR11444,HAMAP:MF_00743	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCTCCGACAGT	.	2	ESCA
RLF	0	.	GRCh37	1	40702244	40702244	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1870T>A	p.Ser624Thr	p.S624T	ENST00000372771	8/8	31	15	16	36	36	0	RLF,missense_variant,p.Ser624Thr,ENST00000372771,;	A	ENSG00000117000	ENST00000372771	Transcript	missense_variant	1897	1870	624	S/T	Tct/Act	.	.	.	1	RLF	HGNC	10025	protein_coding	YES	CCDS448.1	ENSP00000361857	RLF_HUMAN	.	UPI000013C9DA	.	tolerated(0.57)	benign(0.004)	8/8	.	hmmpanther:PTHR15507:SF18,hmmpanther:PTHR15507	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAGGCTCTCAA	.	5	ESCA
ST6GALNAC3	0	.	GRCh37	1	77094625	77094625	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*134G>C	.	.	ENST00000328299	5/5	18	9	8	45	45	0	ST6GALNAC3,3_prime_UTR_variant,,ENST00000328299,;	C	ENSG00000184005	ENST00000328299	Transcript	3_prime_UTR_variant	1200	.	.	.	.	.	.	.	1	ST6GALNAC3	HGNC	19343	protein_coding	YES	CCDS672.1	ENSP00000329214	SIA7C_HUMAN	.	UPI000006F75A	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCTCAGATGTG	.	5	ESCA
CCDC18	0	.	GRCh37	1	93652031	93652031	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.594C>A	p.His199Asn	p.H199N	ENST00000370276	4/29	22	10	11	30	30	0	CCDC18,missense_variant,p.His263Asn,ENST00000557479,;CCDC18,missense_variant,p.His145Asn,ENST00000401026,;CCDC18,missense_variant,p.His145Asn,ENST00000343253,;CCDC18,missense_variant,p.His199Asn,ENST00000370276,;CCDC18,5_prime_UTR_variant,,ENST00000334652,;CCDC18,5_prime_UTR_variant,,ENST00000338949,;CCDC18,downstream_gene_variant,,ENST00000448243,;CCDC18,downstream_gene_variant,,ENST00000528942,;CCDC18,missense_variant,p.His184Asn,ENST00000481180,;CCDC18,3_prime_UTR_variant,,ENST00000479653,;RP4-612C19.1,downstream_gene_variant,,ENST00000413542,;	A	ENSG00000122483	ENST00000370276	Transcript	missense_variant	594	595	199	H/N	Cac/Aac	.	.	.	1	CCDC18	HGNC	30370	protein_coding	YES	.	ENSP00000359299	.	.	UPI0001F78148	.	tolerated(1)	benign(0.02)	4/29	.	hmmpanther:PTHR18875:SF4,hmmpanther:PTHR18875	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATTCACTTT	.	5	ESCA
CST1	0	.	GRCh37	20	23731294	23731294	+	Silent	SNP	T	T	C	rs3188307	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.210A>G	p.%3D	p.V70V	ENST00000304749	1/3	52	10	41	52	52	0	CST1,synonymous_variant,p.%3D,ENST00000398402,;CST1,synonymous_variant,p.%3D,ENST00000304749,;	C	ENSG00000170373	ENST00000304749	Transcript	synonymous_variant	281	210	70	V	gtA/gtG	rs3188307	.	.	-1	CST1	HGNC	2473	protein_coding	YES	CCDS13160.1	ENSP00000305731	CYTN_HUMAN	.	UPI000013E9BC	.	.	.	1/3	.	hmmpanther:PTHR11413:SF35,hmmpanther:PTHR11413,Pfam_domain:PF00031,Gene3D:3.10.450.10,SMART_domains:SM00043,Superfamily_domains:SSF54403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTAGTACCCG	suspect	5	ESCA
TUBB1	0	.	GRCh37	20	57599831	57599831	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1349G>A	p.Gly450Glu	p.G450E	ENST00000217133	4/4	19	15	4	33	33	0	TUBB1,missense_variant,p.Gly450Glu,ENST00000217133,;ATP5E,downstream_gene_variant,,ENST00000395663,;ATP5E,downstream_gene_variant,,ENST00000395659,;ATP5E,downstream_gene_variant,,ENST00000243997,;	A	ENSG00000101162	ENST00000217133	Transcript	missense_variant	1618	1349	450	G/E	gGa/gAa	.	.	.	1	TUBB1	HGNC	16257	protein_coding	YES	CCDS13475.1	ENSP00000217133	TBB1_HUMAN	.	UPI0000071B14	.	tolerated_low_confidence(0.32)	benign(0)	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGGGACATT	.	5	ESCA
BACE2	0	.	GRCh37	21	42629162	42629162	+	Silent	SNP	G	G	A	rs764727127	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1212G>A	p.%3D	p.A404A	ENST00000330333	8/9	27	14	13	33	33	0	BACE2,synonymous_variant,p.%3D,ENST00000330333,;BACE2,synonymous_variant,p.%3D,ENST00000347667,;BACE2,intron_variant,,ENST00000328735,;BACE2,non_coding_transcript_exon_variant,,ENST00000475618,;BACE2,non_coding_transcript_exon_variant,,ENST00000465326,;BACE2,non_coding_transcript_exon_variant,,ENST00000466122,;BACE2,non_coding_transcript_exon_variant,,ENST00000487994,;BACE2,non_coding_transcript_exon_variant,,ENST00000463674,;	A	ENSG00000182240	ENST00000330333	Transcript	synonymous_variant	1675	1212	404	A	gcG/gcA	rs764727127	.	.	1	BACE2	HGNC	934	protein_coding	YES	CCDS13668.1	ENSP00000332979	BACE2_HUMAN	.	UPI00000396BC	.	.	.	8/9	.	hmmpanther:PTHR13683:SF262,hmmpanther:PTHR13683,Pfam_domain:PF00026,Gene3D:2.40.70.10,Superfamily_domains:SSF50630	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGCGCTGGT	.	5	ESCA
DPP10	0	.	GRCh37	2	116601514	116601514	+	3'Flank	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000393147	.	55	51	4	43	43	0	DPP10,3_prime_UTR_variant,,ENST00000410059,;DPP10,downstream_gene_variant,,ENST00000393147,;DPP10,downstream_gene_variant,,ENST00000409163,;DPP10,downstream_gene_variant,,ENST00000310323,;	A	ENSG00000175497	ENST00000393147	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1593	1	DPP10	HGNC	20823	protein_coding	YES	CCDS54388.1	ENSP00000376855	DPP10_HUMAN	J3KQK8_HUMAN,C9J4M8_HUMAN	UPI00015E0A22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCACCCTCCT	.	2	ESCA
CNTNAP5	0	.	GRCh37	2	125204397	125204397	+	Missense_Mutation	SNP	G	G	T	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801G>T	p.Gln267His	p.Q267H	ENST00000431078	6/24	26	11	14	16	16	0	CNTNAP5,missense_variant,p.Gln267His,ENST00000431078,;	T	ENSG00000155052	ENST00000431078	Transcript	missense_variant	1165	801	267	Q/H	caG/caT	COSM715989	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	tolerated(0.12)	probably_damaging(0.998)	6/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACCAGCACTG	.	5	ESCA
CNTNAP5	0	.	GRCh37	2	125204398	125204398	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.802C>T	p.His268Tyr	p.H268Y	ENST00000431078	6/24	26	11	14	16	16	0	CNTNAP5,missense_variant,p.His268Tyr,ENST00000431078,;	T	ENSG00000155052	ENST00000431078	Transcript	missense_variant	1166	802	268	H/Y	Cac/Tac	.	.	.	1	CNTNAP5	HGNC	18748	protein_coding	YES	CCDS46401.1	ENSP00000399013	CNTP5_HUMAN	.	UPI0000071988	.	deleterious(0.01)	possibly_damaging(0.703)	6/24	.	PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCAGCACTGG	.	5	ESCA
NEB	0	.	GRCh37	2	152432749	152432749	+	Silent	SNP	C	C	T	rs531949723	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16824G>A	p.%3D	p.T5608T	ENST00000397345	106/182	36	14	21	43	43	0	NEB,synonymous_variant,p.%3D,ENST00000603639,;NEB,synonymous_variant,p.%3D,ENST00000172853,;NEB,synonymous_variant,p.%3D,ENST00000427231,;NEB,synonymous_variant,p.%3D,ENST00000397345,;NEB,synonymous_variant,p.%3D,ENST00000604864,;NEB,synonymous_variant,p.%3D,ENST00000413693,;NEB,synonymous_variant,p.%3D,ENST00000409198,;	T	ENSG00000183091	ENST00000397345	Transcript	synonymous_variant	17027	16824	5608	T	acG/acA	rs531949723	.	.	-1	NEB	HGNC	7720	protein_coding	YES	CCDS54407.1	ENSP00000380505	.	H7C2D0_HUMAN,F8WCL5_HUMAN	UPI0002065BA0	.	.	.	106/182	.	hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227	T:0.0004	T:0	T:0	.	T:0	T:0	T:0.002	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGGCGTCCG	byFrequency|by1000G	5	ESCA
FAP	0	.	GRCh37	2	163027347	163027347	+	3'UTR	DEL	T	T	-	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*142delA	.	.	ENST00000188790	26/26	47	15	32	41	41	0	FAP,3_prime_UTR_variant,,ENST00000188790,;FAP,3_prime_UTR_variant,,ENST00000443424,;AC007750.5,non_coding_transcript_exon_variant,,ENST00000418968,;AC007750.5,downstream_gene_variant,,ENST00000609668,;FAP,3_prime_UTR_variant,,ENST00000462608,;FAP,3_prime_UTR_variant,,ENST00000422436,;FAP,non_coding_transcript_exon_variant,,ENST00000480044,;FAP,downstream_gene_variant,,ENST00000461506,;	-	ENSG00000078098	ENST00000188790	Transcript	3_prime_UTR_variant	2633	.	.	.	.	.	.	.	-1	FAP	HGNC	3590	protein_coding	YES	CCDS33311.1	ENSP00000188790	SEPR_HUMAN	C9J131_HUMAN	UPI00000012A2	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	CTCATCTTTTTT	.	2	ESCA
TTN	0	.	GRCh37	2	179611959	179611959	+	Intron	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11312-5311G>T	.	.	ENST00000589042	.	64	18	46	52	52	0	TTN,synonymous_variant,p.%3D,ENST00000360870,;TTN,intron_variant,,ENST00000359218,;TTN,intron_variant,,ENST00000342175,;TTN,intron_variant,,ENST00000342992,;TTN,intron_variant,,ENST00000589042,;TTN,intron_variant,,ENST00000591111,;TTN,intron_variant,,ENST00000460472,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000578746,;TTN-AS1,downstream_gene_variant,,ENST00000582847,;	A	ENSG00000155657	ENST00000589042	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TTN	HGNC	12403	protein_coding	YES	CCDS59435.1	ENSP00000467141	TITIN_HUMAN	C9JQJ2_HUMAN,A2TKE6_HUMAN	UPI000264F4A1	.	.	.	.	47/362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCTCCCCTGG	.	5	ESCA
HECW2	0	.	GRCh37	2	197189751	197189751	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.694C>T	p.Arg232Trp	p.R232W	ENST00000260983	6/29	24	19	5	18	18	0	HECW2,missense_variant,p.Arg232Trp,ENST00000260983,;HECW2,5_prime_UTR_variant,,ENST00000409111,;	A	ENSG00000138411	ENST00000260983	Transcript	missense_variant	877	694	232	R/W	Cgg/Tgg	.	.	.	-1	HECW2	HGNC	29853	protein_coding	YES	CCDS33354.1	ENSP00000260983	HECW2_HUMAN	C9JPI9_HUMAN,C9JHL2_HUMAN	UPI00001A75E8	.	deleterious(0)	probably_damaging(1)	6/29	.	PROSITE_profiles:PS50004,hmmpanther:PTHR11254:SF127,hmmpanther:PTHR11254,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGACCGTCTCT	.	2	ESCA
CLK1	0	.	GRCh37	2	201718664	201718664	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1399G>T	p.Ala467Ser	p.A467S	ENST00000434813	12/13	42	30	11	40	40	0	CLK1,missense_variant,p.Ala425Ser,ENST00000321356,;CLK1,missense_variant,p.Ala467Ser,ENST00000434813,;CLK1,missense_variant,p.Ala248Ser,ENST00000409769,;RNA5SP115,upstream_gene_variant,,ENST00000411160,;CLK1,3_prime_UTR_variant,,ENST00000409403,;CLK1,3_prime_UTR_variant,,ENST00000432425,;CLK1,non_coding_transcript_exon_variant,,ENST00000496205,;CLK1,non_coding_transcript_exon_variant,,ENST00000464454,;CLK1,non_coding_transcript_exon_variant,,ENST00000473565,;CLK1,non_coding_transcript_exon_variant,,ENST00000461981,;CLK1,non_coding_transcript_exon_variant,,ENST00000461326,;CLK1,non_coding_transcript_exon_variant,,ENST00000472679,;	A	ENSG00000013441	ENST00000434813	Transcript	missense_variant	1734	1399	467	A/S	Gcc/Tcc	.	.	.	-1	CLK1	HGNC	2068	protein_coding	YES	CCDS54427.1	ENSP00000394734	CLK1_HUMAN	.	UPI00017A7024	.	tolerated(0.37)	benign(0.121)	12/13	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Pfam_domain:PF00069,Gene3D:1.10.510.10,hmmpanther:PTHR24058:SF2,hmmpanther:PTHR24058,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCGGCAGAAC	.	5	ESCA
NYAP2	0	.	GRCh37	2	226447741	226447741	+	Missense_Mutation	SNP	G	G	T	rs758201076	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1608G>T	p.Glu536Asp	p.E536D	ENST00000272907	4/6	24	16	7	51	51	0	NYAP2,missense_variant,p.Glu536Asp,ENST00000272907,;NYAP2,intron_variant,,ENST00000409269,;	T	ENSG00000144460	ENST00000272907	Transcript	missense_variant	2021	1608	536	E/D	gaG/gaT	rs758201076	.	.	1	NYAP2	HGNC	29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	NYAP2_HUMAN	.	UPI00001C1DB6	.	tolerated(0.09)	benign(0.017)	4/6	.	hmmpanther:PTHR22633	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAAGAGCCTGC	.	5	ESCA
VPS54	0	.	GRCh37	2	64120194	64120194	+	3'UTR	SNP	A	A	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*370T>G	.	.	ENST00000272322	23/23	49	29	20	35	35	0	VPS54,3_prime_UTR_variant,,ENST00000354504,;VPS54,3_prime_UTR_variant,,ENST00000272322,;VPS54,3_prime_UTR_variant,,ENST00000409558,;UGP2,downstream_gene_variant,,ENST00000394417,;UGP2,downstream_gene_variant,,ENST00000467648,;UGP2,downstream_gene_variant,,ENST00000445915,;UGP2,downstream_gene_variant,,ENST00000337130,;VPS54,downstream_gene_variant,,ENST00000416400,;UGP2,downstream_gene_variant,,ENST00000475550,;	C	ENSG00000143952	ENST00000272322	Transcript	3_prime_UTR_variant	3459	.	.	.	.	.	.	.	-1	VPS54	HGNC	18652	protein_coding	YES	CCDS33208.1	ENSP00000272322	VPS54_HUMAN	.	UPI0000053408	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATTTCATTGCA	.	5	ESCA
AFTPH	0	.	GRCh37	2	64819492	64819492	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*323A>G	.	.	ENST00000238855	10/10	66	40	26	66	66	0	AFTPH,3_prime_UTR_variant,,ENST00000422803,;AFTPH,3_prime_UTR_variant,,ENST00000238855,;AFTPH,3_prime_UTR_variant,,ENST00000238856,;AFTPH,downstream_gene_variant,,ENST00000409183,;AFTPH,downstream_gene_variant,,ENST00000409933,;AFTPH,downstream_gene_variant,,ENST00000498706,;	G	ENSG00000119844	ENST00000238855	Transcript	3_prime_UTR_variant	3448	.	.	.	.	.	.	.	1	AFTPH	HGNC	25951	protein_coding	YES	CCDS46303.1	ENSP00000238855	AFTIN_HUMAN	.	UPI00003E1F8E	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAAAAAAAAC	.	5	ESCA
ABI3BP	0	.	GRCh37	3	100534892	100534892	+	Intron	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1598-7813G>A	.	.	ENST00000284322	.	17	13	4	21	21	0	ABI3BP,3_prime_UTR_variant,,ENST00000495063,;ABI3BP,intron_variant,,ENST00000478235,;ABI3BP,intron_variant,,ENST00000471901,;ABI3BP,intron_variant,,ENST00000495591,;ABI3BP,intron_variant,,ENST00000466947,;ABI3BP,intron_variant,,ENST00000284322,;ABI3BP,intron_variant,,ENST00000383691,;ABI3BP,intron_variant,,ENST00000528305,;ABI3BP,intron_variant,,ENST00000533795,;ABI3BP,intron_variant,,ENST00000471714,;ABI3BP,upstream_gene_variant,,ENST00000527943,;ABI3BP,upstream_gene_variant,,ENST00000482765,;ABI3BP,intron_variant,,ENST00000487012,;ABI3BP,intron_variant,,ENST00000470336,;	T	ENSG00000154175	ENST00000284322	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	ABI3BP	HGNC	17265	protein_coding	YES	CCDS46880.1	ENSP00000284322	TARSH_HUMAN	.	UPI000011C136	.	.	.	.	18/34	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAAACATGAG	.	2	ESCA
KALRN	0	.	GRCh37	3	124114025	124114025	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2000A>G	p.Asp667Gly	p.D667G	ENST00000240874	12/34	21	12	9	22	22	0	KALRN,missense_variant,p.Asp667Gly,ENST00000240874,;KALRN,missense_variant,p.Asp667Gly,ENST00000460856,;KALRN,missense_variant,p.Asp645Gly,ENST00000354186,;KALRN,missense_variant,p.Asp143Gly,ENST00000439170,;KALRN,missense_variant,p.Asp667Gly,ENST00000360013,;KALRN,non_coding_transcript_exon_variant,,ENST00000522553,;KALRN,non_coding_transcript_exon_variant,,ENST00000484224,;KALRN,non_coding_transcript_exon_variant,,ENST00000393501,;	G	ENSG00000160145	ENST00000240874	Transcript	missense_variant	2157	2000	667	D/G	gAt/gGt	.	.	.	1	KALRN	HGNC	4814	protein_coding	YES	CCDS3027.1	ENSP00000240874	KALRN_HUMAN	.	UPI000012C095	.	tolerated(0.17)	unknown(0)	12/34	.	hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGAGGATGTCT	.	5	ESCA
HEG1	0	.	GRCh37	3	124692645	124692645	+	Missense_Mutation	SNP	C	C	T	rs375137864	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3926G>A	p.Arg1309Gln	p.R1309Q	ENST00000311127	16/17	41	37	4	63	63	0	HEG1,missense_variant,p.Arg193Gln,ENST00000487661,;HEG1,missense_variant,p.Arg1309Gln,ENST00000311127,;HEG1,upstream_gene_variant,,ENST00000480667,;HEG1,missense_variant,p.Arg36Gln,ENST00000482699,;	T	ENSG00000173706	ENST00000311127	Transcript	missense_variant	3994	3926	1309	R/Q	cGa/cAa	rs375137864	.	.	-1	HEG1	HGNC	29227	protein_coding	YES	CCDS46898.1	ENSP00000311502	HEG1_HUMAN	.	UPI00006C069B	.	deleterious(0)	probably_damaging(0.999)	16/17	.	hmmpanther:PTHR24037:SF2,hmmpanther:PTHR24037	.	.	.	.	.	.	.	T:0	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CTTCTCGGCCC	byCluster	2	ESCA
SLC9A9	0	.	GRCh37	3	143412093	143412093	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.590G>T	p.Gly197Val	p.G197V	ENST00000316549	5/16	115	93	22	40	40	0	SLC9A9,missense_variant,p.Gly197Val,ENST00000316549,;SLC9A9,non_coding_transcript_exon_variant,,ENST00000483124,;SLC9A9,3_prime_UTR_variant,,ENST00000474727,;	A	ENSG00000181804	ENST00000316549	Transcript	missense_variant	799	590	197	G/V	gGa/gTa	.	.	.	-1	SLC9A9	HGNC	20653	protein_coding	YES	CCDS33872.1	ENSP00000320246	SL9A9_HUMAN	.	UPI0000074664	.	tolerated(0.11)	benign(0.178)	5/16	.	hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF61,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTCTCCATTT	.	5	ESCA
WDR49	0	.	GRCh37	3	167371112	167371112	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-129C>T	.	.	ENST00000308378	1/15	87	79	8	48	48	0	WDR49,synonymous_variant,p.%3D,ENST00000466760,;WDR49,synonymous_variant,p.%3D,ENST00000488012,;WDR49,synonymous_variant,p.%3D,ENST00000479765,;WDR49,5_prime_UTR_variant,,ENST00000308378,;WDR49,synonymous_variant,p.%3D,ENST00000460448,;WDR49,synonymous_variant,p.%3D,ENST00000471198,;	A	ENSG00000174776	ENST00000308378	Transcript	5_prime_UTR_variant	178	.	.	.	.	.	.	.	-1	WDR49	HGNC	26587	protein_coding	YES	CCDS3201.1	ENSP00000311343	WDR49_HUMAN	.	UPI00000746AD	.	.	.	1/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCTGTGCCATA	.	3	ESCA
CCDC39	0	.	GRCh37	3	180397475	180397475	+	5'Flank	SNP	G	G	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000442201	.	166	146	20	63	63	0	CCDC39,missense_variant,p.Phe57Leu,ENST00000273654,;CCDC39,intron_variant,,ENST00000471307,;CCDC39,upstream_gene_variant,,ENST00000442201,;CCDC39-AS1,upstream_gene_variant,,ENST00000495357,;CCDC39,5_prime_UTR_variant,,ENST00000476379,;	C	ENSG00000145075	ENST00000442201	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	187	-1	CCDC39	HGNC	25244	protein_coding	YES	CCDS46964.1	ENSP00000405708	CCD39_HUMAN	.	UPI00015D7298	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCACGAAAAG	.	4	ESCA
MB21D2	0	.	GRCh37	3	192516915	192516915	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736G>T	p.Ala246Ser	p.A246S	ENST00000392452	2/2	64	53	11	43	43	0	MB21D2,missense_variant,p.Ala246Ser,ENST00000392452,;	A	ENSG00000180611	ENST00000392452	Transcript	missense_variant	1057	736	246	A/S	Gca/Tca	.	.	.	-1	MB21D2	HGNC	30438	protein_coding	YES	CCDS3302.2	ENSP00000376246	M21D2_HUMAN	A8K332_HUMAN	UPI000013FAFE	.	tolerated(0.11)	possibly_damaging(0.596)	2/2	.	Pfam_domain:PF03281,hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF43	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACTGCAGGCC	.	5	ESCA
MUC4	0	.	GRCh37	3	195474152	195474152	+	Silent	SNP	G	G	A	rs199920657	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.16134C>T	p.%3D	p.G5378G	ENST00000463781	25/25	53	43	9	41	41	0	MUC4,synonymous_variant,p.%3D,ENST00000463781,;MUC4,synonymous_variant,p.%3D,ENST00000346145,;MUC4,synonymous_variant,p.%3D,ENST00000349607,;MUC4,synonymous_variant,p.%3D,ENST00000475231,;MUC4,3_prime_UTR_variant,,ENST00000339251,;MUC4,3_prime_UTR_variant,,ENST00000448861,;MUC4,3_prime_UTR_variant,,ENST00000470451,;MUC4,3_prime_UTR_variant,,ENST00000308466,;MUC4,3_prime_UTR_variant,,ENST00000415455,;MUC4,3_prime_UTR_variant,,ENST00000477086,;MUC4,3_prime_UTR_variant,,ENST00000392407,;MUC4,3_prime_UTR_variant,,ENST00000466475,;MUC4,3_prime_UTR_variant,,ENST00000478156,;MUC4,3_prime_UTR_variant,,ENST00000479406,;MUC4,3_prime_UTR_variant,,ENST00000477756,;MUC4,3_prime_UTR_variant,,ENST00000462323,;MUC4,3_prime_UTR_variant,,ENST00000480843,;MUC4,non_coding_transcript_exon_variant,,ENST00000464234,;MUC4,downstream_gene_variant,,ENST00000469992,;MUC4,downstream_gene_variant,,ENST00000467235,;	A	ENSG00000145113	ENST00000463781	Transcript	synonymous_variant	16594	16134	5378	G	ggC/ggT	rs199920657	.	.	-1	MUC4	HGNC	7514	protein_coding	YES	CCDS54700.1	ENSP00000417498	.	O75456_HUMAN,E9PDY6_HUMAN	UPI0001B3CB30	.	.	.	25/25	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF41	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCCGCCCAG	byCluster|by1000G	4	ESCA
TGFBR2	0	.	GRCh37	3	30715615	30715615	+	Missense_Mutation	SNP	A	A	G	rs104893817	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1348A>G	p.Met450Val	p.M450V	ENST00000359013	6/8	33	19	13	47	47	0	TGFBR2,missense_variant,p.Met425Val,ENST00000295754,;TGFBR2,missense_variant,p.Met450Val,ENST00000359013,;	G	ENSG00000163513	ENST00000359013	Transcript	missense_variant	1631	1348	450	M/V	Atg/Gtg	CM060084,rs104893817	.	.	1	TGFBR2	HGNC	11773	protein_coding	YES	CCDS33727.1	ENSP00000351905	TGFR2_HUMAN	D2JYI1_HUMAN	UPI000053030E	.	deleterious(0)	probably_damaging(1)	6/8	.	PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037393,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	pathogenic	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATACATGGCT	byCluster	5	ESCA
STT3B	0	.	GRCh37	3	31666481	31666481	+	Silent	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1803A>G	p.%3D	p.V601V	ENST00000295770	12/16	22	11	11	23	23	0	STT3B,synonymous_variant,p.%3D,ENST00000295770,;STT3B,downstream_gene_variant,,ENST00000423527,;STT3B,upstream_gene_variant,,ENST00000463044,;STT3B,downstream_gene_variant,,ENST00000453168,;STT3B,upstream_gene_variant,,ENST00000488151,;STT3B,downstream_gene_variant,,ENST00000436236,;	G	ENSG00000163527	ENST00000295770	Transcript	synonymous_variant	2012	1803	601	V	gtA/gtG	.	.	.	1	STT3B	HGNC	30611	protein_coding	YES	CCDS2650.1	ENSP00000295770	STT3B_HUMAN	.	UPI000006D7FB	.	.	.	12/16	.	hmmpanther:PTHR13872,hmmpanther:PTHR13872:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGAGTAATGTC	.	5	ESCA
MTNR1A	0	.	GRCh37	4	187455431	187455431	+	Silent	SNP	C	C	T	rs767642752	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.465G>A	p.%3D	p.T155T	ENST00000307161	2/2	34	25	8	36	36	0	MTNR1A,synonymous_variant,p.%3D,ENST00000307161,;RP11-215A19.2,intron_variant,,ENST00000509111,;	T	ENSG00000168412	ENST00000307161	Transcript	synonymous_variant	667	465	155	T	acG/acA	rs767642752	.	.	-1	MTNR1A	HGNC	7463	protein_coding	YES	CCDS3848.1	ENSP00000302811	MTR1A_HUMAN	.	UPI0000050407	.	.	.	2/2	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF52,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCAGCGTCAG	byFrequency	5	ESCA
SLIT2	0	.	GRCh37	4	20568920	20568920	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2761C>T	p.Pro921Ser	p.P921S	ENST00000504154	27/37	24	12	12	35	35	0	SLIT2,missense_variant,p.Pro925Ser,ENST00000273739,;SLIT2,missense_variant,p.Pro921Ser,ENST00000504154,;SLIT2,missense_variant,p.Pro913Ser,ENST00000503823,;SLIT2,missense_variant,p.Pro917Ser,ENST00000503837,;SLIT2,missense_variant,p.Pro52Ser,ENST00000509941,;SLIT2,missense_variant,p.Pro133Ser,ENST00000511508,;	T	ENSG00000145147	ENST00000504154	Transcript	missense_variant	3013	2761	921	P/S	Ccc/Tcc	.	.	.	1	SLIT2	HGNC	11086	protein_coding	YES	CCDS3426.1	ENSP00000422591	SLIT2_HUMAN	Q4W5N0_HUMAN,Q4W5K2_HUMAN,B3KNE2_HUMAN	UPI00000747E4	.	deleterious(0)	probably_damaging(0.998)	27/37	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24373:SF107,hmmpanther:PTHR24373,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAACCCCTGC	.	5	ESCA
PDS5A	0	.	GRCh37	4	39918704	39918704	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.840A>C	p.Leu280Phe	p.L280F	ENST00000303538	8/33	35	23	12	45	45	0	PDS5A,missense_variant,p.Leu280Phe,ENST00000503396,;PDS5A,missense_variant,p.Leu280Phe,ENST00000303538,;PDS5A,intron_variant,,ENST00000513798,;PDS5A,upstream_gene_variant,,ENST00000508625,;PDS5A,upstream_gene_variant,,ENST00000512643,;	G	ENSG00000121892	ENST00000303538	Transcript	missense_variant	1380	840	280	L/F	ttA/ttC	.	.	.	-1	PDS5A	HGNC	29088	protein_coding	YES	CCDS47045.1	ENSP00000303427	PDS5A_HUMAN	Q96DB6_HUMAN,G1UI16_HUMAN,B3KMN2_HUMAN	UPI00006C6A7E	.	deleterious(0)	probably_damaging(1)	8/33	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF2,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATAATAATAA	.	5	ESCA
DCUN1D4	0	.	GRCh37	4	52781181	52781181	+	3'UTR	SNP	C	C	T	rs183173568	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1431C>T	.	.	ENST00000334635	11/11	27	21	6	33	33	0	DCUN1D4,3_prime_UTR_variant,,ENST00000381441,;DCUN1D4,3_prime_UTR_variant,,ENST00000334635,;DCUN1D4,downstream_gene_variant,,ENST00000510808,;DCUN1D4,downstream_gene_variant,,ENST00000381437,;DCUN1D4,downstream_gene_variant,,ENST00000451288,;RP11-365H22.2,upstream_gene_variant,,ENST00000610270,;DCUN1D4,downstream_gene_variant,,ENST00000507659,;DCUN1D4,downstream_gene_variant,,ENST00000510587,;DCUN1D4,downstream_gene_variant,,ENST00000508257,;DCUN1D4,3_prime_UTR_variant,,ENST00000477560,;DCUN1D4,downstream_gene_variant,,ENST00000509376,;DCUN1D4,downstream_gene_variant,,ENST00000505634,;DCUN1D4,downstream_gene_variant,,ENST00000507741,;DCUN1D4,downstream_gene_variant,,ENST00000512199,;DCUN1D4,downstream_gene_variant,,ENST00000510518,;	T	ENSG00000109184	ENST00000334635	Transcript	3_prime_UTR_variant	2490	.	.	.	.	rs183173568	.	.	1	DCUN1D4	HGNC	28998	protein_coding	YES	CCDS33982.1	ENSP00000334625	DCNL4_HUMAN	B4DH26_HUMAN	UPI00001C1E10	.	.	.	11/11	.	.	T:0.0006	T:0.0023	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATCCGTGAT	byFrequency|by1000G	5	ESCA
UGT2B17	0	.	GRCh37	4	69403558	69403558	+	Nonsense_Mutation	SNP	G	G	A	rs267600213	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1378C>T	p.Arg460Ter	p.R460*	ENST00000317746	6/6	37	11	26	67	67	0	UGT2B17,stop_gained,p.Arg460Ter,ENST00000317746,;	A	ENSG00000197888	ENST00000317746	Transcript	stop_gained	1421	1378	460	R/*	Cga/Tga	rs267600213,COSM1694449	.	.	-1	UGT2B17	HGNC	12547	protein_coding	YES	CCDS3523.1	ENSP00000320401	UDB17_HUMAN	.	UPI0000137A9C	.	.	.	6/6	.	Superfamily_domains:SSF53756,Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF178	.	.	.	.	.	.	.	.	.	not_provided	0,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCTCGATCCA	byCluster	5	ESCA
ADAMTS3	0	.	GRCh37	4	73188757	73188757	+	Missense_Mutation	SNP	G	G	A	rs750800733	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.919C>T	p.Arg307Cys	p.R307C	ENST00000286657	6/22	20	16	4	38	38	0	ADAMTS3,missense_variant,p.Arg307Cys,ENST00000286657,;RP11-373J21.1,non_coding_transcript_exon_variant,,ENST00000503918,;	A	ENSG00000156140	ENST00000286657	Transcript	missense_variant	956	919	307	R/C	Cgc/Tgc	rs750800733,COSM1430879	.	.	-1	ADAMTS3	HGNC	219	protein_coding	YES	CCDS3553.1	ENSP00000286657	ATS3_HUMAN	Q96AY5_HUMAN	UPI00001AEAEA	.	deleterious(0)	probably_damaging(0.997)	6/22	.	PROSITE_profiles:PS50215,hmmpanther:PTHR13723:SF158,hmmpanther:PTHR13723,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATGCGCACCA	byFrequency	4	ESCA
TRIO	0	.	GRCh37	5	14406743	14406743	+	Missense_Mutation	SNP	G	G	A	rs775980433	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4921G>A	p.Ala1641Thr	p.A1641T	ENST00000344204	33/57	24	14	10	36	36	0	TRIO,missense_variant,p.Ala1641Thr,ENST00000537187,;TRIO,missense_variant,p.Ala1641Thr,ENST00000344204,;TRIO,missense_variant,p.Ala1374Thr,ENST00000513206,;TRIO,missense_variant,p.Ala1582Thr,ENST00000512070,;TRIO,non_coding_transcript_exon_variant,,ENST00000509354,;TRIO,non_coding_transcript_exon_variant,,ENST00000515144,;TRIO,non_coding_transcript_exon_variant,,ENST00000512303,;	A	ENSG00000038382	ENST00000344204	Transcript	missense_variant	4945	4921	1641	A/T	Gcc/Acc	rs775980433	.	.	1	TRIO	HGNC	12303	protein_coding	YES	CCDS3883.1	ENSP00000339299	TRIO_HUMAN	.	UPI000034ECE6	.	.	possibly_damaging(0.692)	33/57	.	hmmpanther:PTHR22826:SF104,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCGCCTCA	byFrequency	5	ESCA
TMED9	0	.	GRCh37	5	177022337	177022337	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628C>A	p.Gln210Lys	p.Q210K	ENST00000332598	5/5	23	7	16	45	45	0	TMED9,missense_variant,p.Gln210Lys,ENST00000332598,;B4GALT7,upstream_gene_variant,,ENST00000505468,;B4GALT7,upstream_gene_variant,,ENST00000510761,;B4GALT7,upstream_gene_variant,,ENST00000029410,;TMED9,downstream_gene_variant,,ENST00000507578,;TMED9,non_coding_transcript_exon_variant,,ENST00000513799,;TMED9,non_coding_transcript_exon_variant,,ENST00000510499,;TMED9,non_coding_transcript_exon_variant,,ENST00000507723,;TMED9,downstream_gene_variant,,ENST00000505521,;B4GALT7,upstream_gene_variant,,ENST00000505433,;B4GALT7,upstream_gene_variant,,ENST00000502420,;	A	ENSG00000184840	ENST00000332598	Transcript	missense_variant	685	628	210	Q/K	Cag/Aag	.	.	.	1	TMED9	HGNC	24878	protein_coding	YES	CCDS4428.1	ENSP00000330945	TMED9_HUMAN	.	UPI00001D6EC0	.	deleterious(0)	probably_damaging(0.999)	5/5	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR22811:SF37,hmmpanther:PTHR22811,Pfam_domain:PF01105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCTGCAGACC	.	5	ESCA
OR2V2	0	.	GRCh37	5	180582374	180582374	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.432G>C	p.Gln144His	p.Q144H	ENST00000328275	1/1	40	34	6	80	80	0	OR2V2,missense_variant,p.Gln144His,ENST00000328275,;	C	ENSG00000182613	ENST00000328275	Transcript	missense_variant	432	432	144	Q/H	caG/caC	.	.	.	1	OR2V2	HGNC	15341	protein_coding	YES	CCDS4461.1	ENSP00000332185	OR2V2_HUMAN	.	UPI0000041C79	.	tolerated(0.13)	possibly_damaging(0.89)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF235,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCAGATTAC	.	4	ESCA
BDP1	0	.	GRCh37	5	70751670	70751670	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-35C>T	.	.	ENST00000358731	1/39	56	29	27	77	77	0	BDP1,5_prime_UTR_variant,,ENST00000358731,;BDP1,5_prime_UTR_variant,,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;	T	ENSG00000145734	ENST00000358731	Transcript	5_prime_UTR_variant	229	.	.	.	.	.	.	.	1	BDP1	HGNC	13652	protein_coding	YES	CCDS43328.1	ENSP00000351575	BDP1_HUMAN	.	UPI000020CA90	.	.	.	1/39	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCGGCCGTGAG	.	5	ESCA
ZDHHC11	0	.	GRCh37	5	795724	795724	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*979G>C	.	.	ENST00000283441	13/13	29	24	5	35	35	0	ZDHHC11,3_prime_UTR_variant,,ENST00000283441,;ZDHHC11,intron_variant,,ENST00000424784,;ZDHHC11,non_coding_transcript_exon_variant,,ENST00000503758,;ZDHHC11,downstream_gene_variant,,ENST00000507800,;	G	ENSG00000188818	ENST00000283441	Transcript	3_prime_UTR_variant	2602	.	.	.	.	.	.	.	-1	ZDHHC11	HGNC	19158	protein_coding	YES	CCDS3857.1	ENSP00000283441	ZDH11_HUMAN	.	UPI000013C384	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATGCACGTAGT	.	2	ESCA
MEF2C	0	.	GRCh37	5	88027605	88027605	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.805C>A	p.Arg269Ser	p.R269S	ENST00000340208	9/12	30	14	15	63	63	0	MEF2C,missense_variant,p.Arg251Ser,ENST00000504921,;MEF2C,missense_variant,p.Arg251Ser,ENST00000510942,;MEF2C,missense_variant,p.Arg251Ser,ENST00000514028,;MEF2C,missense_variant,p.Arg251Ser,ENST00000514015,;MEF2C,missense_variant,p.Arg251Ser,ENST00000506554,;MEF2C,missense_variant,p.Arg269Ser,ENST00000340208,;MEF2C,missense_variant,p.Arg249Ser,ENST00000424173,;MEF2C,missense_variant,p.Arg251Ser,ENST00000437473,;MEF2C,missense_variant,p.Arg251Ser,ENST00000508569,;MEF2C,missense_variant,p.Arg203Ser,ENST00000539796,;MEF2C,downstream_gene_variant,,ENST00000513252,;MEF2C,downstream_gene_variant,,ENST00000506716,;MEF2C,downstream_gene_variant,,ENST00000503554,;MEF2C,non_coding_transcript_exon_variant,,ENST00000515715,;MEF2C,upstream_gene_variant,,ENST00000510980,;	T	ENSG00000081189	ENST00000340208	Transcript	missense_variant	1211	805	269	R/S	Cgt/Agt	.	.	.	-1	MEF2C	HGNC	6996	protein_coding	YES	CCDS54878.1	ENSP00000340874	MEF2C_HUMAN	H0YNI2_HUMAN,D6RJA7_HUMAN,D6RJ95_HUMAN,D6RG14_HUMAN	UPI0000D9B539	.	deleterious(0)	possibly_damaging(0.864)	9/12	.	hmmpanther:PTHR11945:SF25,hmmpanther:PTHR11945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTACGGTTAT	.	5	ESCA
RFX6	0	.	GRCh37	6	117245835	117245835	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1559C>G	p.Ser520Cys	p.S520C	ENST00000332958	15/19	41	30	11	48	48	0	RFX6,missense_variant,p.Ser520Cys,ENST00000332958,;RFX6,downstream_gene_variant,,ENST00000487683,;	G	ENSG00000185002	ENST00000332958	Transcript	missense_variant	1575	1559	520	S/C	tCt/tGt	COSM3777044,COSM257882	.	.	1	RFX6	HGNC	21478	protein_coding	YES	CCDS5113.1	ENSP00000332208	RFX6_HUMAN	.	UPI00001609BE	.	deleterious(0)	probably_damaging(0.99)	15/19	.	hmmpanther:PTHR12619:SF16,hmmpanther:PTHR12619	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGGTTCTTTTC	.	3	ESCA
RGS17	0	.	GRCh37	6	153365166	153365166	+	5'UTR	SNP	A	A	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-13T>G	.	.	ENST00000367225	1/4	25	20	5	29	28	0	RGS17,5_prime_UTR_variant,,ENST00000367225,;RGS17,5_prime_UTR_variant,,ENST00000206262,;	C	ENSG00000091844	ENST00000367225	Transcript	5_prime_UTR_variant	13	.	.	.	.	.	.	.	-1	RGS17	HGNC	14088	protein_coding	YES	CCDS5244.1	ENSP00000356194	RGS17_HUMAN	.	UPI000000D76A	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACTTCAGGACC	.	4	ESCA
OR2W1	0	.	GRCh37	6	29012060	29012060	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.893A>T	p.Lys298Met	p.K298M	ENST00000377175	1/1	40	26	13	33	33	0	OR2W1,missense_variant,p.Lys298Met,ENST00000377175,;	A	ENSG00000204704	ENST00000377175	Transcript	missense_variant	958	893	298	K/M	aAg/aTg	.	.	.	-1	OR2W1	HGNC	8281	protein_coding	YES	CCDS4656.1	ENSP00000366380	OR2W1_HUMAN	.	UPI000003FF8A	.	deleterious(0.01)	probably_damaging(0.999)	1/1	.	hmmpanther:PTHR26453:SF169,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	CATCCTTCATG	.	4	ESCA
FUT9	0	.	GRCh37	6	96661003	96661003	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*8892G>A	.	.	ENST00000302103	3/3	24	19	5	28	28	0	FUT9,3_prime_UTR_variant,,ENST00000302103,;	A	ENSG00000172461	ENST00000302103	Transcript	3_prime_UTR_variant	10298	.	.	.	.	.	.	.	1	FUT9	HGNC	4020	protein_coding	YES	CCDS5033.1	ENSP00000302599	FUT9_HUMAN	.	UPI000013E792	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGTGGCCATG	.	4	ESCA
CYP2W1	0	.	GRCh37	7	1024091	1024091	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.218G>A	p.Arg73His	p.R73H	ENST00000308919	2/9	18	13	5	24	24	0	CYP2W1,missense_variant,p.Arg17His,ENST00000340150,;CYP2W1,missense_variant,p.Arg73His,ENST00000308919,;CYP2W1,upstream_gene_variant,,ENST00000415893,;CYP2W1,upstream_gene_variant,,ENST00000468456,;CYP2W1,upstream_gene_variant,,ENST00000462453,;	A	ENSG00000073067	ENST00000308919	Transcript	missense_variant	231	218	73	R/H	cGc/cAc	.	.	.	1	CYP2W1	HGNC	20243	protein_coding	YES	CCDS5319.2	ENSP00000310149	CP2W1_HUMAN	.	UPI000013C59A	.	tolerated(0.55)	benign(0.009)	2/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF50,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCGCCAGA	.	5	ESCA
GRM8	0	.	GRCh37	7	126173579	126173579	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1857C>T	p.%3D	p.R619R	ENST00000339582	9/11	13	9	4	24	24	0	GRM8,synonymous_variant,p.%3D,ENST00000358373,;GRM8,synonymous_variant,p.%3D,ENST00000444921,;GRM8,synonymous_variant,p.%3D,ENST00000339582,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,synonymous_variant,p.%3D,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,;	A	ENSG00000179603	ENST00000339582	Transcript	synonymous_variant	2666	1857	619	R	cgC/cgT	COSM296098,COSM3949876,COSM3411545,COSM3949877	.	.	-1	GRM8	HGNC	4600	protein_coding	YES	CCDS5794.1	ENSP00000344173	GRM8_HUMAN	E7ETK3_HUMAN,C9J7I1_HUMAN	UPI000012F085	.	.	.	9/11	.	PROSITE_profiles:PS50259,hmmpanther:PTHR24060:SF26,hmmpanther:PTHR24060,Pfam_domain:PF00003,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.R619R|c.1857C>T|3	MUTECT|MUSE	AGTTCGCGTCC	.	2	ESCA
MKLN1	0	.	GRCh37	7	131175337	131175337	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2850A>G	.	.	ENST00000352689	18/18	16	12	4	18	18	0	MKLN1,3_prime_UTR_variant,,ENST00000352689,;MKLN1,downstream_gene_variant,,ENST00000421797,;RP11-180C16.1,downstream_gene_variant,,ENST00000610193,;MKLN1,downstream_gene_variant,,ENST00000498778,;MKLN1,downstream_gene_variant,,ENST00000458153,;MKLN1,downstream_gene_variant,,ENST00000468830,;	G	ENSG00000128585	ENST00000352689	Transcript	3_prime_UTR_variant	5098	.	.	.	.	.	.	.	1	MKLN1	HGNC	7109	protein_coding	YES	CCDS34754.1	ENSP00000323527	MKLN1_HUMAN	F8WEY7_HUMAN,C9JXB0_HUMAN,C9JWX9_HUMAN,C9JVL5_HUMAN,C9J7E8_HUMAN	UPI0000034CB0	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	AGCTGACAGAC	.	4	ESCA
RP11-1220K2.2	0	.	GRCh37	7	141820169	141820169	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.174G>T	p.Gln58His	p.Q58H	ENST00000550469	3/13	25	21	4	27	27	0	RP11-1220K2.2,missense_variant,p.Gln58His,ENST00000477922,;RP11-1220K2.2,missense_variant,p.Gln58His,ENST00000550469,;	T	ENSG00000257743	ENST00000550469	Transcript	missense_variant	233	174	58	Q/H	caG/caT	.	.	.	1	RP11-1220K2.2	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000447431	MGAL2_HUMAN	.	UPI00001411D7	.	tolerated(0.09)	benign(0.001)	3/13	.	PROSITE_profiles:PS51448,hmmpanther:PTHR22762:SF55,hmmpanther:PTHR22762,Gene3D:4.10.110.10,Pfam_domain:PF00088,SMART_domains:SM00018,Superfamily_domains:SSF57492	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCAGGAGGT	.	4	ESCA
GSTK1	0	.	GRCh37	7	142962173	142962173	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.372C>T	p.%3D	p.R124R	ENST00000479303	4/7	42	31	11	43	43	0	GSTK1,synonymous_variant,p.%3D,ENST00000409500,;GSTK1,synonymous_variant,p.%3D,ENST00000443571,;GSTK1,synonymous_variant,p.%3D,ENST00000436038,;GSTK1,synonymous_variant,p.%3D,ENST00000479303,;GSTK1,synonymous_variant,p.%3D,ENST00000358406,;AC073342.12,intron_variant,,ENST00000427392,;GSTK1,downstream_gene_variant,,ENST00000494735,;GSTK1,synonymous_variant,p.%3D,ENST00000442394,;GSTK1,non_coding_transcript_exon_variant,,ENST00000473649,;GSTK1,downstream_gene_variant,,ENST00000489654,;	T	ENSG00000197448	ENST00000479303	Transcript	synonymous_variant	430	372	124	R	cgC/cgT	.	.	.	1	GSTK1	HGNC	16906	protein_coding	YES	CCDS47730.1	ENSP00000431049	GSTK1_HUMAN	.	UPI000022839D	.	.	.	4/7	.	Superfamily_domains:SSF52833,Gene3D:3.40.30.10,Pfam_domain:PF01323,hmmpanther:PTHR13887	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATGCGCGTCTG	.	5	ESCA
ZNF746	0	.	GRCh37	7	149170918	149170918	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*557C>T	.	.	ENST00000458143	7/7	43	26	17	59	59	0	ZNF746,3_prime_UTR_variant,,ENST00000340622,;ZNF746,3_prime_UTR_variant,,ENST00000458143,;ZNF746,downstream_gene_variant,,ENST00000471735,;	A	ENSG00000181220	ENST00000458143	Transcript	3_prime_UTR_variant	2766	.	.	.	.	.	.	.	-1	ZNF746	HGNC	21948	protein_coding	YES	CCDS55180.1	ENSP00000395007	ZN746_HUMAN	Q96N48_HUMAN	UPI00015DA840	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCGGAGGG	.	5	ESCA
CDCA7L	0	.	GRCh37	7	21945956	21945956	+	Frame_Shift_Del	DEL	G	G	-	rs776311696	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.872delC	p.Ala291ValfsTer43	p.A291Vfs*43	ENST00000406877	6/10	63	49	14	57	57	0	CDCA7L,frameshift_variant,p.Ala291ValfsTer43,ENST00000406877,;CDCA7L,frameshift_variant,p.Ala245ValfsTer43,ENST00000373934,;CDCA7L,frameshift_variant,p.Ala257ValfsTer43,ENST00000356195,;CDCA7L,downstream_gene_variant,,ENST00000435031,;CDCA7L,upstream_gene_variant,,ENST00000435717,;CDCA7L,downstream_gene_variant,,ENST00000457951,;DNAH11,downstream_gene_variant,,ENST00000328843,;CDCA7L,downstream_gene_variant,,ENST00000447180,;DNAH11,downstream_gene_variant,,ENST00000409508,;CDCA7L,non_coding_transcript_exon_variant,,ENST00000465490,;CDCA7L,upstream_gene_variant,,ENST00000488845,;CDCA7L,upstream_gene_variant,,ENST00000489669,;	-	ENSG00000164649	ENST00000406877	Transcript	frameshift_variant	1152	872	291	A/X	gCt/gt	rs776311696	.	.	-1	CDCA7L	HGNC	30777	protein_coding	YES	CCDS5374.1	ENSP00000383986	CDA7L_HUMAN	C9JFL7_HUMAN	UPI000000D840	.	.	.	6/10	.	hmmpanther:PTHR31169:SF4,hmmpanther:PTHR31169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	AATTTAGCGGCT	.	3	ESCA
TNS3	0	.	GRCh37	7	47314791	47314791	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2883C>A	.	.	ENST00000398879	31/31	18	15	3	25	25	0	TNS3,3_prime_UTR_variant,,ENST00000398879,;TNS3,3_prime_UTR_variant,,ENST00000311160,;TNS3,3_prime_UTR_variant,,ENST00000428457,;TNS3,3_prime_UTR_variant,,ENST00000355730,;	T	ENSG00000136205	ENST00000398879	Transcript	3_prime_UTR_variant	7588	.	.	.	.	.	.	.	-1	TNS3	HGNC	21616	protein_coding	YES	CCDS5506.2	ENSP00000381854	TENS3_HUMAN	C9JWN9_HUMAN,C9JTD0_HUMAN	UPI00001AE9DA	.	.	.	31/31	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAGATGATATT	.	2	ESCA
PMS2	0	.	GRCh37	7	6035230	6035230	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.838G>C	p.Val280Leu	p.V280L	ENST00000265849	8/15	28	14	14	44	44	0	PMS2,missense_variant,p.Val280Leu,ENST00000265849,;PMS2,missense_variant,p.Val174Leu,ENST00000441476,;PMS2,missense_variant,p.Val280Leu,ENST00000406569,;PMS2,intron_variant,,ENST00000382321,;PMS2,intron_variant,,ENST00000469652,;	G	ENSG00000122512	ENST00000265849	Transcript	missense_variant	944	838	280	V/L	Gtt/Ctt	.	.	.	-1	PMS2	HGNC	9122	protein_coding	YES	CCDS5343.1	ENSP00000265849	PMS2_HUMAN	.	UPI000013D696	.	tolerated(0.19)	benign(0.003)	8/15	.	Superfamily_domains:SSF54211,Gene3D:3.30.230.10,Pfam_domain:PF01119,TIGRFAM_domain:TIGR00585,hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCAACTCCAT	.	5	ESCA
SLC25A40	0	.	GRCh37	7	87476367	87476367	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528C>T	p.%3D	p.Y176Y	ENST00000341119	8/12	32	23	8	40	40	0	SLC25A40,synonymous_variant,p.%3D,ENST00000341119,;SLC25A40,3_prime_UTR_variant,,ENST00000429674,;SLC25A40,upstream_gene_variant,,ENST00000470328,;SLC25A40,upstream_gene_variant,,ENST00000446236,;	A	ENSG00000075303	ENST00000341119	Transcript	synonymous_variant	875	528	176	Y	taC/taT	.	.	.	-1	SLC25A40	HGNC	29680	protein_coding	YES	CCDS5610.1	ENSP00000344831	S2540_HUMAN	.	UPI0000071FF6	.	.	.	8/12	.	PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF225,hmmpanther:PTHR24089,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCACGTAAGA	.	5	ESCA
FBXO43	0	.	GRCh37	8	101152954	101152954	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1528C>T	p.Leu510Phe	p.L510F	ENST00000428847	2/5	54	51	3	44	44	0	FBXO43,missense_variant,p.Leu510Phe,ENST00000428847,;FBXO43,3_prime_UTR_variant,,ENST00000517806,;FBXO43,non_coding_transcript_exon_variant,,ENST00000520987,;	A	ENSG00000156509	ENST00000428847	Transcript	missense_variant	1845	1528	510	L/F	Ctt/Ttt	COSM1551109,COSM1551108,COSM1551107	.	.	-1	FBXO43	HGNC	28521	protein_coding	YES	CCDS47904.1	ENSP00000403293	FBX43_HUMAN	.	UPI000013DE8F	.	deleterious(0)	probably_damaging(0.989)	2/5	.	hmmpanther:PTHR15493:SF1,hmmpanther:PTHR15493,Gene3D:1.20.1280.50	.	.	.	.	.	.	.	.	.	.	1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGCAAGAATAT	.	2	ESCA
CSMD3	0	.	GRCh37	8	113267520	113267520	+	Silent	SNP	T	T	A	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9999A>T	p.%3D	p.A3333A	ENST00000297405	62/71	50	31	18	32	32	0	CSMD3,synonymous_variant,p.%3D,ENST00000352409,;CSMD3,synonymous_variant,p.%3D,ENST00000455883,;CSMD3,synonymous_variant,p.%3D,ENST00000297405,;CSMD3,synonymous_variant,p.%3D,ENST00000339701,;CSMD3,synonymous_variant,p.%3D,ENST00000343508,;CSMD3,non_coding_transcript_exon_variant,,ENST00000534172,;	A	ENSG00000164796	ENST00000297405	Transcript	synonymous_variant	10244	9999	3333	A	gcA/gcT	COSM3374738,COSM3374739	.	.	-1	CSMD3	HGNC	19291	protein_coding	YES	CCDS6315.1	ENSP00000297405	CSMD3_HUMAN	.	UPI00001E0584	.	.	.	62/71	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF44,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATCTGCTTG	.	5	ESCA
COL22A1	0	.	GRCh37	8	139825204	139825204	+	Missense_Mutation	SNP	C	C	A	rs761241970	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1304G>T	p.Cys435Phe	p.C435F	ENST00000303045	8/65	42	37	5	23	23	0	COL22A1,missense_variant,p.Cys435Phe,ENST00000303045,;COL22A1,missense_variant,p.Cys435Phe,ENST00000435777,;	A	ENSG00000169436	ENST00000303045	Transcript	missense_variant	1751	1304	435	C/F	tGt/tTt	rs761241970	.	.	-1	COL22A1	HGNC	22989	protein_coding	YES	CCDS6376.1	ENSP00000303153	COMA1_HUMAN	.	UPI00001C1EA1	.	.	unknown(0)	8/65	.	hmmpanther:PTHR24023:SF379,hmmpanther:PTHR24023,Superfamily_domains:SSF49899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACAACAAGTC	.	4	ESCA
LYNX1	0	.	GRCh37	8	143853579	143853579	+	Intron	SNP	A	A	C	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154+3432T>G	.	.	ENST00000335822	.	211	175	35	198	198	0	LYNX1,3_prime_UTR_variant,,ENST00000395192,;LYNX1,3_prime_UTR_variant,,ENST00000398906,;LYNX1,intron_variant,,ENST00000523332,;LYNX1,intron_variant,,ENST00000335822,;LYNX1,upstream_gene_variant,,ENST00000317543,;LYNX1,upstream_gene_variant,,ENST00000521396,;LYNX1,downstream_gene_variant,,ENST00000345173,;LYNX1,downstream_gene_variant,,ENST00000520131,;LYNX1,downstream_gene_variant,,ENST00000522929,;LYNX1,downstream_gene_variant,,ENST00000522906,;	C	ENSG00000180155	ENST00000335822	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	LYNX1	HGNC	29604	protein_coding	YES	CCDS34951.1	ENSP00000337950	LYNX1_HUMAN	.	UPI0000168665	.	.	.	.	3/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGCCACTCCT	.	4	ESCA
ADAM28	0	.	GRCh37	8	24212043	24212043	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*126C>A	.	.	ENST00000265769	23/23	46	22	24	66	66	0	ADAM28,3_prime_UTR_variant,,ENST00000521629,;ADAM28,3_prime_UTR_variant,,ENST00000265769,;ADAM28,downstream_gene_variant,,ENST00000397649,;ADAM28,downstream_gene_variant,,ENST00000518326,;RP11-624C23.1,intron_variant,,ENST00000518988,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,;RP11-624C23.1,intron_variant,,ENST00000523700,;ADAM28,downstream_gene_variant,,ENST00000518737,;ADAM28,downstream_gene_variant,,ENST00000523236,;ADAM28,downstream_gene_variant,,ENST00000520448,;ADAM28,downstream_gene_variant,,ENST00000520665,;	A	ENSG00000042980	ENST00000265769	Transcript	3_prime_UTR_variant	2564	.	.	.	.	.	.	.	1	ADAM28	HGNC	206	protein_coding	YES	CCDS34865.1	ENSP00000265769	ADA28_HUMAN	E5RGY1_HUMAN	UPI000049E0B9	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	ATTTTCTGATT	.	4	ESCA
ADAM32	0	.	GRCh37	8	39079206	39079206	+	Silent	SNP	C	C	T	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1311C>T	p.%3D	p.C437C	ENST00000379907	13/25	41	27	14	22	22	0	ADAM32,synonymous_variant,p.%3D,ENST00000379907,;ADAM32,synonymous_variant,p.%3D,ENST00000519315,;ADAM32,synonymous_variant,p.%3D,ENST00000437682,;ADAM32,non_coding_transcript_exon_variant,,ENST00000520691,;ADAM32,non_coding_transcript_exon_variant,,ENST00000518259,;	T	ENSG00000197140	ENST00000379907	Transcript	synonymous_variant	1438	1311	437	C	tgC/tgT	COSM3648989	.	.	1	ADAM32	HGNC	15479	protein_coding	YES	CCDS47846.1	ENSP00000369238	ADA32_HUMAN	E5RJY7_HUMAN	UPI000013F62F	.	.	.	13/25	.	PROSITE_profiles:PS50214,hmmpanther:PTHR11905:SF24,hmmpanther:PTHR11905,PROSITE_patterns:PS00427,Pfam_domain:PF00200,Gene3D:4.10.70.10,SMART_domains:SM00050,Superfamily_domains:SSF57552	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTGCTGCAA	.	5	ESCA
XKR4	0	.	GRCh37	8	56436772	56436772	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1939G>A	p.Glu647Lys	p.E647K	ENST00000327381	3/3	51	31	20	41	41	0	XKR4,missense_variant,p.Glu647Lys,ENST00000327381,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,;	A	ENSG00000206579	ENST00000327381	Transcript	missense_variant	2039	1939	647	E/K	Gaa/Aaa	COSM1700114	.	.	1	XKR4	HGNC	29394	protein_coding	YES	CCDS34893.1	ENSP00000328326	XKR4_HUMAN	.	UPI000016098C	.	deleterious(0)	probably_damaging(0.981)	3/3	.	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTACGAAACC	.	5	ESCA
RRS1	0	.	GRCh37	8	67341994	67341994	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.628A>G	p.Thr210Ala	p.T210A	ENST00000320270	1/1	21	8	13	21	21	0	RRS1,missense_variant,p.Thr210Ala,ENST00000320270,;ADHFE1,upstream_gene_variant,,ENST00000415254,;ADHFE1,upstream_gene_variant,,ENST00000396623,;ADHFE1,upstream_gene_variant,,ENST00000379385,;ADHFE1,upstream_gene_variant,,ENST00000523113,;RP11-346I3.4,upstream_gene_variant,,ENST00000499642,;ADHFE1,upstream_gene_variant,,ENST00000496501,;ADHFE1,upstream_gene_variant,,ENST00000422166,;ADHFE1,upstream_gene_variant,,ENST00000449512,;ADHFE1,upstream_gene_variant,,ENST00000424777,;ADHFE1,upstream_gene_variant,,ENST00000466920,;ADHFE1,upstream_gene_variant,,ENST00000443372,;ADHFE1,upstream_gene_variant,,ENST00000419955,;ADHFE1,upstream_gene_variant,,ENST00000426810,;ADHFE1,upstream_gene_variant,,ENST00000276576,;ADHFE1,upstream_gene_variant,,ENST00000431959,;ADHFE1,upstream_gene_variant,,ENST00000463261,;ADHFE1,upstream_gene_variant,,ENST00000396621,;	G	ENSG00000179041	ENST00000320270	Transcript	missense_variant	732	628	210	T/A	Acc/Gcc	.	.	.	1	RRS1	HGNC	17083	protein_coding	YES	CCDS6189.1	ENSP00000322396	RRS1_HUMAN	.	UPI0000134B8A	.	tolerated(0.13)	benign(0.353)	1/1	.	hmmpanther:PTHR17602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCCTACCGGA	.	5	ESCA
TMEM67	0	.	GRCh37	8	94821160	94821160	+	Silent	SNP	C	C	T	rs771098362	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2532C>T	p.%3D	p.D844D	ENST00000453321	24/28	44	25	19	33	33	0	TMEM67,synonymous_variant,p.%3D,ENST00000409623,;TMEM67,synonymous_variant,p.%3D,ENST00000453321,;TMEM67,upstream_gene_variant,,ENST00000518896,;TMEM67,synonymous_variant,p.%3D,ENST00000323130,;TMEM67,non_coding_transcript_exon_variant,,ENST00000474944,;TMEM67,non_coding_transcript_exon_variant,,ENST00000519845,;	T	ENSG00000164953	ENST00000453321	Transcript	synonymous_variant	2590	2532	844	D	gaC/gaT	rs771098362	.	.	1	TMEM67	HGNC	28396	protein_coding	YES	CCDS6258.2	ENSP00000389998	MKS3_HUMAN	E5RG10_HUMAN,C9JRQ8_HUMAN	UPI0000D624E9	.	.	.	24/28	.	hmmpanther:PTHR21274:SF0,hmmpanther:PTHR21274,Pfam_domain:PF09773	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGACAGAAT	.	5	ESCA
NANS	0	.	GRCh37	9	100845271	100845271	+	Silent	SNP	T	T	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1014T>A	p.%3D	p.T338T	ENST00000210444	6/6	39	29	10	41	41	0	NANS,synonymous_variant,p.%3D,ENST00000210444,;TRIM14,intron_variant,,ENST00000375098,;NANS,downstream_gene_variant,,ENST00000427646,;TRIM14,downstream_gene_variant,,ENST00000342043,;NANS,downstream_gene_variant,,ENST00000415280,;TRIM14,downstream_gene_variant,,ENST00000341469,;TRIM14,downstream_gene_variant,,ENST00000538344,;NANS,non_coding_transcript_exon_variant,,ENST00000461452,;TRIM14,intron_variant,,ENST00000478530,;NANS,downstream_gene_variant,,ENST00000495319,;TRIM14,downstream_gene_variant,,ENST00000475147,;	A	ENSG00000095380	ENST00000210444	Transcript	synonymous_variant	1084	1014	338	T	acT/acA	.	.	.	1	NANS	HGNC	19237	protein_coding	YES	CCDS6733.1	ENSP00000210444	SIAS_HUMAN	.	UPI000013597F	.	.	.	6/6	.	PROSITE_profiles:PS50844,hmmpanther:PTHR23416,hmmpanther:PTHR23416:SF1,Gene3D:3.90.1210.10,Pfam_domain:PF08666,SMART_domains:SM00858,Superfamily_domains:SSF51269,Prints_domain:PR00357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTCACTGTTGA	.	5	ESCA
COL15A1	0	.	GRCh37	9	101706528	101706528	+	Silent	SNP	G	G	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96G>T	p.%3D	p.A32A	ENST00000375001	2/42	39	26	13	41	41	0	COL15A1,synonymous_variant,p.%3D,ENST00000375001,;RP11-92C4.6,upstream_gene_variant,,ENST00000605631,;COL15A1,downstream_gene_variant,,ENST00000467052,;COL15A1,non_coding_transcript_exon_variant,,ENST00000471477,;	T	ENSG00000204291	ENST00000375001	Transcript	synonymous_variant	519	96	32	A	gcG/gcT	.	.	.	1	COL15A1	HGNC	2192	protein_coding	YES	CCDS35081.1	ENSP00000364140	COFA1_HUMAN	.	UPI0000211506	.	.	.	2/42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGCGACAGG	.	5	ESCA
ZNF189	0	.	GRCh37	9	104161215	104161215	+	5'Flank	SNP	A	A	T	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000339664	.	11	7	4	21	21	0	ZNF189,5_prime_UTR_variant,,ENST00000374861,;ZNF189,upstream_gene_variant,,ENST00000339664,;ZNF189,upstream_gene_variant,,ENST00000259395,;MRPL50,upstream_gene_variant,,ENST00000374865,;MRPL50,upstream_gene_variant,,ENST00000539624,;	T	ENSG00000136870	ENST00000339664	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	95	1	ZNF189	HGNC	12980	protein_coding	YES	CCDS6754.1	ENSP00000342019	ZN189_HUMAN	.	UPI000013FAD5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAACCAGGCAG	.	3	ESCA
BRINP1	0	.	GRCh37	9	121930252	121930252	+	Missense_Mutation	SNP	C	C	T	rs758271912	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1396G>A	p.Val466Met	p.V466M	ENST00000265922	8/8	22	19	3	26	26	0	BRINP1,missense_variant,p.Val466Met,ENST00000265922,;BRINP1,intron_variant,,ENST00000482797,;	T	ENSG00000078725	ENST00000265922	Transcript	missense_variant	1858	1396	466	V/M	Gtg/Atg	rs758271912	.	.	-1	BRINP1	HGNC	2687	protein_coding	YES	CCDS6822.1	ENSP00000265922	BRNP1_HUMAN	B4DE75_HUMAN	UPI000013D6A7	.	deleterious(0)	probably_damaging(0.971)	8/8	.	hmmpanther:PTHR15564:SF7,hmmpanther:PTHR15564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCACGTTCT	byFrequency	2	ESCA
NOL6	0	.	GRCh37	9	33462777	33462777	+	Missense_Mutation	SNP	C	C	T	rs138187500	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000297990	26/26	37	32	4	30	30	0	NOL6,missense_variant,p.Arg1109Gln,ENST00000297990,;NOL6,missense_variant,p.Arg662Gln,ENST00000353159,;NOL6,missense_variant,p.Arg1057Gln,ENST00000455041,;NOL6,missense_variant,p.Arg163Gln,ENST00000379470,;NOL6,intron_variant,,ENST00000379471,;NOL6,intron_variant,,ENST00000464829,;	T	ENSG00000165271	ENST00000297990	Transcript	missense_variant	3414	3326	1109	R/Q	cGa/cAa	rs138187500	.	.	-1	NOL6	HGNC	19910	protein_coding	YES	CCDS6543.1	ENSP00000297990	NOL6_HUMAN	.	UPI0000050326	.	tolerated(0.65)	benign(0.001)	26/26	.	Pfam_domain:PF03813,hmmpanther:PTHR17972	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CACCTCGAGAC	byCluster	4	ESCA
UBAP1	0	.	GRCh37	9	34241681	34241681	+	Missense_Mutation	SNP	C	C	T	rs137993779	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.850C>T	p.Arg284Trp	p.R284W	ENST00000545103	3/6	36	32	3	29	29	0	UBAP1,missense_variant,p.Arg256Trp,ENST00000543944,;UBAP1,missense_variant,p.Arg220Trp,ENST00000540348,;UBAP1,missense_variant,p.Arg220Trp,ENST00000359544,;UBAP1,missense_variant,p.Arg220Trp,ENST00000379186,;UBAP1,missense_variant,p.Arg284Trp,ENST00000545103,;UBAP1,missense_variant,p.Arg220Trp,ENST00000297661,;UBAP1,missense_variant,p.Arg220Trp,ENST00000536252,;	T	ENSG00000165006	ENST00000545103	Transcript	missense_variant	860	850	284	R/W	Cgg/Tgg	rs137993779	.	.	1	UBAP1	HGNC	12461	protein_coding	YES	CCDS55303.1	ENSP00000441024	UBAP1_HUMAN	.	UPI0001C2BF9D	.	deleterious(0)	possibly_damaging(0.857)	3/6	.	hmmpanther:PTHR15960:SF2,hmmpanther:PTHR15960	T:0.0006	T:0.0023	T:0	.	T:0	T:0	T:0	T:0.0011	T:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	TGGAACGGGCA	byFrequency|byCluster|by1000G	3	ESCA
FAM205B	0	.	GRCh37	9	34834839	34834839	+	RNA	SNP	G	G	A	novel	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1462C>T	.	.	ENST00000399773	4/4	43	37	6	39	39	0	FAM205B,non_coding_transcript_exon_variant,,ENST00000455647,;FAM205B,downstream_gene_variant,,ENST00000378786,;FAM205B,non_coding_transcript_exon_variant,,ENST00000399773,;	A	ENSG00000257198	ENST00000399773	Transcript	non_coding_transcript_exon_variant	1462	.	.	.	.	.	.	.	-1	FAM205B	HGNC	24504	transcribed_unprocessed_pseudogene	YES	.	.	.	.	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGCTGACTGG	.	2	ESCA
SERPINA7	0	.	GRCh37	X	105279119	105279119	+	Missense_Mutation	SNP	G	G	A	rs182605024	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.880C>T	p.Arg294Cys	p.R294C	ENST00000327674	2/4	16	5	11	12	12	0	SERPINA7,missense_variant,p.Arg294Cys,ENST00000327674,;SERPINA7,missense_variant,p.Arg294Cys,ENST00000372563,;SERPINA7,non_coding_transcript_exon_variant,,ENST00000487487,;	A	ENSG00000123561	ENST00000327674	Transcript	missense_variant	1216	880	294	R/C	Cgc/Tgc	rs182605024	.	.	-1	SERPINA7	HGNC	11583	protein_coding	YES	CCDS14518.1	ENSP00000329374	THBG_HUMAN	.	UPI0000001067	.	deleterious(0.01)	possibly_damaging(0.856)	2/4	.	hmmpanther:PTHR11461:SF39,hmmpanther:PTHR11461,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574	A:0.0003	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAAGCGGTTCC	byCluster|by1000G	5	ESCA
SAGE1	0	.	GRCh37	X	134993792	134993792	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-A9VB-01A-21D-A37C-09	TCGA-Z6-A9VB-10A-01D-A37F-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2201C>A	p.Pro734His	p.P734H	ENST00000535938	18/20	14	4	10	21	21	0	SAGE1,missense_variant,p.Pro734His,ENST00000370709,;SAGE1,missense_variant,p.Pro734His,ENST00000535938,;SAGE1,missense_variant,p.Pro358His,ENST00000537770,;SAGE1,missense_variant,p.Pro734His,ENST00000324447,;	A	ENSG00000181433	ENST00000535938	Transcript	missense_variant	2368	2201	734	P/H	cCt/cAt	COSM610818	.	.	1	SAGE1	HGNC	30369	protein_coding	YES	CCDS14652.1	ENSP00000445959	SAGE1_HUMAN	.	UPI00001413AB	.	deleterious(0)	probably_damaging(1)	18/20	.	hmmpanther:PTHR12957:SF7,hmmpanther:PTHR12957	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACCCCTCCTG	.	5	ESCA
NDUFB8	0	.	GRCh37	10	102283650	102283650	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.505G>C	p.Glu169Gln	p.E169Q	ENST00000299166	5/5	47	37	10	39	39	0	NDUFB8,missense_variant,p.Glu169Gln,ENST00000299166,;NDUFB8,missense_variant,p.Glu138Gln,ENST00000370322,;NDUFB8,intron_variant,,ENST00000531258,;SEC31B,intron_variant,,ENST00000535773,;SEC31B,upstream_gene_variant,,ENST00000370329,;SEC31B,upstream_gene_variant,,ENST00000451524,;NDUFB8,downstream_gene_variant,,ENST00000370320,;SEC31B,upstream_gene_variant,,ENST00000370345,;NDUFB8,non_coding_transcript_exon_variant,,ENST00000464651,;NDUFB8,intron_variant,,ENST00000527595,;NDUFB8,intron_variant,,ENST00000557395,;NDUFB8,intron_variant,,ENST00000529568,;NDUFB8,intron_variant,,ENST00000533549,;NDUFB8,intron_variant,,ENST00000528174,;NDUFB8,downstream_gene_variant,,ENST00000528425,;NDUFB8,downstream_gene_variant,,ENST00000466088,;SEC31B,upstream_gene_variant,,ENST00000480905,;NDUFB8,downstream_gene_variant,,ENST00000529437,;NDUFB8,downstream_gene_variant,,ENST00000531418,;SEC31B,upstream_gene_variant,,ENST00000462434,;SEC31B,upstream_gene_variant,,ENST00000479697,;SEC31B,upstream_gene_variant,,ENST00000482456,;	G	ENSG00000166136	ENST00000299166	Transcript	missense_variant	518	505	169	E/Q	Gaa/Caa	.	.	.	-1	NDUFB8	HGNC	7703	protein_coding	YES	CCDS7497.1	ENSP00000299166	NDUB8_HUMAN	Q5W145_HUMAN,E9PIZ8_HUMAN	UPI000013005D	.	deleterious(0)	probably_damaging(0.923)	5/5	.	hmmpanther:PTHR12840,hmmpanther:PTHR12840:SF1,Pfam_domain:PF05821,PIRSF_domain:PIRSF009288	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGTTCCAGGT	.	5	ESCA
FAM178A	0	.	GRCh37	10	102703859	102703859	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2731G>C	p.Glu911Gln	p.E911Q	ENST00000370269	12/19	88	76	11	76	76	0	FAM178A,missense_variant,p.Glu911Gln,ENST00000370269,;FAM178A,missense_variant,p.Glu911Gln,ENST00000238961,;FAM178A,non_coding_transcript_exon_variant,,ENST00000481654,;	C	ENSG00000119906	ENST00000370269	Transcript	missense_variant	2863	2731	911	E/Q	Gaa/Caa	.	.	.	1	FAM178A	HGNC	17814	protein_coding	YES	CCDS44470.1	ENSP00000359292	F178A_HUMAN	.	UPI0000458847	.	deleterious(0)	probably_damaging(0.936)	12/19	.	hmmpanther:PTHR16046,hmmpanther:PTHR16046:SF10,Pfam_domain:PF14816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTCCTGAAACC	.	4	ESCA
MRPL43	0	.	GRCh37	10	102738242	102738242	+	3'Flank	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000342071	.	21	17	4	24	24	0	MRPL43,3_prime_UTR_variant,,ENST00000318325,;SEMA4G,intron_variant,,ENST00000517724,;MRPL43,intron_variant,,ENST00000523148,;SEMA4G,intron_variant,,ENST00000210633,;SEMA4G,intron_variant,,ENST00000519649,;SEMA4G,intron_variant,,ENST00000370250,;MRPL43,downstream_gene_variant,,ENST00000370241,;MRPL43,downstream_gene_variant,,ENST00000299179,;MRPL43,downstream_gene_variant,,ENST00000448244,;MRPL43,downstream_gene_variant,,ENST00000342071,;MRPL43,downstream_gene_variant,,ENST00000370242,;SEMA4G,downstream_gene_variant,,ENST00000518124,;MIR608,downstream_gene_variant,,ENST00000384820,;RP11-108L7.4,downstream_gene_variant,,ENST00000447344,;SEMA4G,intron_variant,,ENST00000519756,;MRPL43,downstream_gene_variant,,ENST00000476012,;SEMA4G,intron_variant,,ENST00000521006,;SEMA4G,upstream_gene_variant,,ENST00000518948,;	C	ENSG00000055950	ENST00000342071	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2892	-1	MRPL43	HGNC	14517	protein_coding	YES	CCDS7504.1	ENSP00000339844	.	C9J5Q3_HUMAN	UPI0000167F88	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTGAATAT	.	5	ESCA
USP6NL	0	.	GRCh37	10	11503122	11503122	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1318C>A	.	.	ENST00000277575	14/14	21	16	4	39	39	0	USP6NL,3_prime_UTR_variant,,ENST00000609104,;USP6NL,3_prime_UTR_variant,,ENST00000379237,;USP6NL,3_prime_UTR_variant,,ENST00000277575,;	T	ENSG00000148429	ENST00000277575	Transcript	3_prime_UTR_variant	3899	.	.	.	.	.	.	.	-1	USP6NL	HGNC	16858	protein_coding	YES	CCDS44357.1	ENSP00000277575	US6NL_HUMAN	.	UPI0000251ED1	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTTGAAAAC	.	5	ESCA
GFRA1	0	.	GRCh37	10	117825136	117825136	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1199C>T	p.Ala400Val	p.A400V	ENST00000355422	10/11	25	21	4	22	22	0	GFRA1,missense_variant,p.Ala395Val,ENST00000439649,;GFRA1,missense_variant,p.Ala400Val,ENST00000369234,;GFRA1,missense_variant,p.Ala279Val,ENST00000544592,;GFRA1,missense_variant,p.Ala395Val,ENST00000369236,;GFRA1,missense_variant,p.Ala400Val,ENST00000355422,;	A	ENSG00000151892	ENST00000355422	Transcript	missense_variant	1750	1199	400	A/V	gCa/gTa	.	.	.	-1	GFRA1	HGNC	4243	protein_coding	YES	CCDS44481.1	ENSP00000347591	GFRA1_HUMAN	.	UPI000012B3A8	.	tolerated(0.36)	benign(0.016)	10/11	.	hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF3,PIRSF_domain:PIRSF038071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCTGTGCCTGG	.	3	ESCA
PNLIPRP2	0	.	GRCh37	10	118383542	118383542	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.136C>T	p.Pro46Ser	p.P46S	ENST00000537242	4/14	69	61	8	75	75	0	PNLIPRP2,missense_variant,p.Pro46Ser,ENST00000537242,;PNLIPRP2,non_coding_transcript_exon_variant,,ENST00000298771,;PNLIPRP2,non_coding_transcript_exon_variant,,ENST00000429325,;PNLIPRP2,non_coding_transcript_exon_variant,,ENST00000444825,;PNLIPRP2,synonymous_variant,p.%3D,ENST00000433618,;	T	ENSG00000165862	ENST00000537242	Transcript	missense_variant	162	136	46	P/S	Ccc/Tcc	.	.	.	1	PNLIPRP2	HGNC	9157	protein_coding	YES	.	ENSP00000446346	.	F5H1V6_HUMAN	UPI0000D60FDD	.	deleterious(0.01)	possibly_damaging(0.705)	4/14	.	hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF85,Pfam_domain:PF00151,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474,Prints_domain:PR00823	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACTTCCCTGG	.	4	ESCA
EMX2	0	.	GRCh37	10	119308905	119308905	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1162A>G	.	.	ENST00000553456	3/3	80	62	17	89	89	0	EMX2,3_prime_UTR_variant,,ENST00000553456,;EMX2,downstream_gene_variant,,ENST00000442245,;EMX2OS,upstream_gene_variant,,ENST00000551288,;EMX2,downstream_gene_variant,,ENST00000546446,;	G	ENSG00000170370	ENST00000553456	Transcript	3_prime_UTR_variant	2745	.	.	.	.	.	.	.	1	EMX2	HGNC	3341	protein_coding	YES	CCDS7601.1	ENSP00000450962	EMX2_HUMAN	.	UPI000004CC07	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAGAGAGTG	.	5	ESCA
C10orf88	0	.	GRCh37	10	124697221	124697221	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1103G>C	p.Gly368Ala	p.G368A	ENST00000481909	5/6	43	36	7	35	35	0	C10orf88,missense_variant,p.Gly368Ala,ENST00000481909,;C10orf88,splice_region_variant,,ENST00000368891,;C10orf88,splice_region_variant,,ENST00000470158,;C10orf88,upstream_gene_variant,,ENST00000462191,;	G	ENSG00000119965	ENST00000481909	Transcript	missense_variant	1328	1103	368	G/A	gGa/gCa	.	.	.	-1	C10orf88	HGNC	25822	protein_coding	YES	CCDS7632.1	ENSP00000419126	CJ088_HUMAN	.	UPI000006CF9E	.	tolerated(0.43)	benign(0.002)	5/6	.	hmmpanther:PTHR14787	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTACCCAACA	.	4	ESCA
RP11-108K14.8	0	.	GRCh37	10	135209721	135209721	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247C>G	p.His83Asp	p.H83D	ENST00000468317	4/12	69	56	12	57	57	0	RP11-108K14.8,missense_variant,p.His83Asp,ENST00000468317,;MTG1,missense_variant,p.His37Asp,ENST00000477902,;MTG1,missense_variant,p.His78Asp,ENST00000432508,;MTG1,missense_variant,p.His78Asp,ENST00000317502,;PAOX,downstream_gene_variant,,ENST00000357296,;PAOX,downstream_gene_variant,,ENST00000368539,;PAOX,downstream_gene_variant,,ENST00000480071,;PAOX,downstream_gene_variant,,ENST00000278060,;PAOX,downstream_gene_variant,,ENST00000368535,;PAOX,downstream_gene_variant,,ENST00000530555,;MTG1,non_coding_transcript_exon_variant,,ENST00000460848,;MTG1,non_coding_transcript_exon_variant,,ENST00000495014,;MTG1,non_coding_transcript_exon_variant,,ENST00000473735,;MTG1,non_coding_transcript_exon_variant,,ENST00000498790,;PAOX,downstream_gene_variant,,ENST00000476834,;PAOX,downstream_gene_variant,,ENST00000529585,;PAOX,downstream_gene_variant,,ENST00000356306,;PAOX,downstream_gene_variant,,ENST00000483211,;	G	ENSG00000254536	ENST00000468317	Transcript	missense_variant	502	247	83	H/D	Cac/Gac	.	.	.	1	RP11-108K14.8	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000436767	.	U3KQ69_HUMAN,E9PI62_HUMAN	UPI0000D4C5CD	.	deleterious(0)	probably_damaging(0.98)	4/12	.	PROSITE_profiles:PS51721,hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF4,Gene3D:3.40.50.300,PIRSF_domain:PIRSF006230,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCCTCACTTG	.	5	ESCA
ARID5B	0	.	GRCh37	10	63852198	63852198	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2976G>C	p.Met992Ile	p.M992I	ENST00000279873	10/10	29	24	5	29	29	0	ARID5B,missense_variant,p.Met992Ile,ENST00000279873,;ARID5B,missense_variant,p.Met749Ile,ENST00000309334,;	C	ENSG00000150347	ENST00000279873	Transcript	missense_variant	3386	2976	992	M/I	atG/atC	.	.	.	1	ARID5B	HGNC	17362	protein_coding	YES	CCDS31208.1	ENSP00000279873	ARI5B_HUMAN	.	UPI00001606F0	.	tolerated(0.1)	benign(0.296)	10/10	.	hmmpanther:PTHR13964,hmmpanther:PTHR13964:SF22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATGGTCCA	.	5	ESCA
MYPN	0	.	GRCh37	10	69866502	69866502	+	5'Flank	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000358913	.	61	41	19	51	51	0	MYPN,missense_variant,p.Lys7Asn,ENST00000354393,;MYPN,upstream_gene_variant,,ENST00000358913,;MYPN,upstream_gene_variant,,ENST00000540630,;MYPN,upstream_gene_variant,,ENST00000373675,;	C	ENSG00000138347	ENST00000358913	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	2492	1	MYPN	HGNC	23246	protein_coding	YES	CCDS7275.1	ENSP00000351790	MYPN_HUMAN	A5PKT7_HUMAN	UPI00002288CF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGAAGACTTC	.	5	ESCA
DDX21	0	.	GRCh37	10	70734442	70734442	+	Missense_Mutation	SNP	G	G	C	rs771246089	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1685G>C	p.Arg562Pro	p.R562P	ENST00000354185	11/15	65	59	6	62	62	0	DDX21,missense_variant,p.Arg562Pro,ENST00000354185,;	C	ENSG00000165732	ENST00000354185	Transcript	missense_variant	1783	1685	562	R/P	cGa/cCa	rs771246089	.	.	1	DDX21	HGNC	2744	protein_coding	YES	CCDS31211.1	ENSP00000346120	DDX21_HUMAN	Q8NI92_HUMAN	UPI00001A92E8	.	deleterious(0)	possibly_damaging(0.887)	11/15	.	PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF197,Gene3D:3.40.50.300	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAAACGAATAG	.	3	ESCA
COL13A1	0	.	GRCh37	10	71562471	71562471	+	Missense_Mutation	SNP	G	G	A	rs201112703	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292G>A	p.Glu98Lys	p.E98K	ENST00000398978	1/40	55	48	7	63	63	0	COL13A1,missense_variant,p.Glu98Lys,ENST00000517713,;COL13A1,missense_variant,p.Glu98Lys,ENST00000354547,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398978,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398964,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398971,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398966,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398969,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398973,;COL13A1,missense_variant,p.Glu98Lys,ENST00000520133,;COL13A1,missense_variant,p.Glu98Lys,ENST00000520267,;COL13A1,missense_variant,p.Glu98Lys,ENST00000522165,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398968,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398974,;COL13A1,missense_variant,p.Glu98Lys,ENST00000356340,;COL13A1,missense_variant,p.Glu98Lys,ENST00000398972,;COL13A1,missense_variant,p.Glu98Lys,ENST00000357811,;COL13A1,missense_variant,p.Glu98Lys,ENST00000479733,;	A	ENSG00000197467	ENST00000398978	Transcript	missense_variant	784	292	98	E/K	Gag/Aag	rs201112703	.	.	1	COL13A1	HGNC	2190	protein_coding	YES	CCDS44419.1	ENSP00000381949	CODA1_HUMAN	Q9UP45_HUMAN	UPI000046FD72	.	deleterious_low_confidence(0.01)	benign(0.122)	1/40	.	.	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGACGAGGTC	byCluster|by1000G	4	ESCA
DLG5	0	.	GRCh37	10	79569442	79569442	+	Missense_Mutation	SNP	A	A	T	rs781491443	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4510T>A	p.Phe1504Ile	p.F1504I	ENST00000372391	24/32	32	21	11	53	53	0	DLG5,missense_variant,p.Phe465Ile,ENST00000424842,;DLG5,missense_variant,p.Phe1164Ile,ENST00000372388,;DLG5,missense_variant,p.Phe1504Ile,ENST00000372391,;DLG5,non_coding_transcript_exon_variant,,ENST00000459739,;DLG5,non_coding_transcript_exon_variant,,ENST00000489547,;DLG5,upstream_gene_variant,,ENST00000484525,;DLG5,3_prime_UTR_variant,,ENST00000468332,;DLG5,non_coding_transcript_exon_variant,,ENST00000463362,;DLG5,non_coding_transcript_exon_variant,,ENST00000475613,;	T	ENSG00000151208	ENST00000372391	Transcript	missense_variant	4516	4510	1504	F/I	Ttc/Atc	rs781491443	.	.	-1	DLG5	HGNC	2904	protein_coding	YES	CCDS7353.2	ENSP00000361467	DLG5_HUMAN	.	UPI0000470041	.	tolerated(0.39)	benign(0.195)	24/32	.	PROSITE_profiles:PS50106,hmmpanther:PTHR13865,Gene3D:2.30.42.10,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATGAAGACAA	.	5	ESCA
ZCCHC24	0	.	GRCh37	10	81154181	81154181	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.463G>C	p.Glu155Gln	p.E155Q	ENST00000372336	3/4	43	35	7	24	24	0	ZCCHC24,missense_variant,p.Arg95Pro,ENST00000372333,;ZCCHC24,missense_variant,p.Glu155Gln,ENST00000372336,;RP11-342M3.5,intron_variant,,ENST00000438554,;	G	ENSG00000165424	ENST00000372336	Transcript	missense_variant	650	463	155	E/Q	Gag/Cag	.	.	.	-1	ZCCHC24	HGNC	26911	protein_coding	YES	CCDS7359.1	ENSP00000361411	ZCH24_HUMAN	.	UPI000006F100	.	deleterious(0.01)	probably_damaging(0.97)	3/4	.	hmmpanther:PTHR15439,hmmpanther:PTHR15439:SF2,Gene3D:4.10.60.10,Pfam_domain:PF13696,Superfamily_domains:SSF57756	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.G154G|c.462C>T|3	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCCTCGCCTT	.	5	ESCA
BTAF1	0	.	GRCh37	10	93768818	93768818	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3956C>G	p.Ser1319Ter	p.S1319*	ENST00000265990	28/38	109	97	12	83	83	0	BTAF1,stop_gained,p.Ser147Ter,ENST00000544642,;BTAF1,stop_gained,p.Ser1319Ter,ENST00000265990,;	G	ENSG00000095564	ENST00000265990	Transcript	stop_gained	4264	3956	1319	S/*	tCa/tGa	.	.	.	1	BTAF1	HGNC	17307	protein_coding	YES	CCDS7419.1	ENSP00000265990	BTAF1_HUMAN	Q8N6J1_HUMAN,Q2M1V9_HUMAN,B4E0W6_HUMAN	UPI0000136782	.	.	.	28/38	.	Superfamily_domains:SSF52540,Superfamily_domains:SSF48371,SMART_domains:SM00487,Pfam_domain:PF00176,Gene3D:1.25.10.10,hmmpanther:PTHR10799:SF225,hmmpanther:PTHR10799,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGATCAAAAT	.	4	ESCA
KIF11	0	.	GRCh37	10	94408026	94408026	+	Missense_Mutation	SNP	C	C	T	rs149407589	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2605C>T	p.Arg869Cys	p.R869C	ENST00000260731	19/22	124	114	10	87	87	0	KIF11,missense_variant,p.Arg869Cys,ENST00000260731,;	T	ENSG00000138160	ENST00000260731	Transcript	missense_variant	2695	2605	869	R/C	Cgt/Tgt	rs149407589	.	.	1	KIF11	HGNC	6388	protein_coding	YES	CCDS7422.1	ENSP00000260731	KIF11_HUMAN	.	UPI000013D0FC	.	tolerated(0.09)	benign(0.001)	19/22	.	hmmpanther:PTHR24115:SF105,hmmpanther:PTHR24115	.	.	.	.	.	.	.	T:0	T:0.0002	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGGACGTAAG	byCluster	3	ESCA
CYP2C9	0	.	GRCh37	10	96748714	96748714	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1402G>C	p.Asp468His	p.D468H	ENST00000260682	9/9	93	85	8	62	62	0	CYP2C9,missense_variant,p.Asp468His,ENST00000260682,;	C	ENSG00000138109	ENST00000260682	Transcript	missense_variant	1414	1402	468	D/H	Gac/Cac	.	.	.	1	CYP2C9	HGNC	2623	protein_coding	YES	CCDS7437.1	ENSP00000260682	CP2C9_HUMAN	S5RV20_HUMAN,Q9UEH3_HUMAN	UPI0000128258	.	deleterious(0)	probably_damaging(0.963)	9/9	.	hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF131,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	ACCTTGACACC	.	2	ESCA
HOGA1	0	.	GRCh37	10	99361729	99361729	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.816C>T	p.%3D	p.L272L	ENST00000370646	6/7	38	24	14	37	37	0	HOGA1,synonymous_variant,p.%3D,ENST00000370647,;PI4K2A,synonymous_variant,p.%3D,ENST00000370649,;HOGA1,synonymous_variant,p.%3D,ENST00000370646,;HOGA1,synonymous_variant,p.%3D,ENST00000370642,;PI4K2A,synonymous_variant,p.%3D,ENST00000555577,;HOGA1,downstream_gene_variant,,ENST00000465608,;	T	ENSG00000241935	ENST00000370646	Transcript	synonymous_variant	1177	816	272	L	ctC/ctT	.	.	.	1	HOGA1	HGNC	25155	protein_coding	YES	CCDS7467.1	ENSP00000359680	HOGA1_HUMAN	.	UPI000000DAE5	.	.	.	6/7	.	Superfamily_domains:SSF51569,PIRSF_domain:PIRSF001365,Pfam_domain:PF00701,Gene3D:3.20.20.70,hmmpanther:PTHR12128,hmmpanther:PTHR12128:SF15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCCTCATTGA	.	5	ESCA
TRPC6	0	.	GRCh37	11	101341989	101341989	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2334G>A	p.%3D	p.L778L	ENST00000344327	9/13	50	42	8	54	54	0	TRPC6,synonymous_variant,p.%3D,ENST00000532133,;TRPC6,synonymous_variant,p.%3D,ENST00000348423,;TRPC6,synonymous_variant,p.%3D,ENST00000344327,;TRPC6,synonymous_variant,p.%3D,ENST00000360497,;	T	ENSG00000137672	ENST00000344327	Transcript	synonymous_variant	2759	2334	778	L	ctG/ctA	.	.	.	-1	TRPC6	HGNC	12338	protein_coding	YES	CCDS8311.1	ENSP00000340913	TRPC6_HUMAN	B3KNL3_HUMAN	UPI00001374BA	.	.	.	9/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF7,TIGRFAM_domain:TIGR00870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTCAGTAA	.	5	ESCA
MMP3	0	.	GRCh37	11	102707181	102707181	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1334-224C>G	.	.	ENST00000299855	.	31	18	12	41	41	0	MMP3,intron_variant,,ENST00000299855,;MMP3,downstream_gene_variant,,ENST00000434103,;WTAPP1,non_coding_transcript_exon_variant,,ENST00000525739,;WTAPP1,downstream_gene_variant,,ENST00000371455,;WTAPP1,downstream_gene_variant,,ENST00000544704,;WTAPP1,downstream_gene_variant,,ENST00000537774,;	C	ENSG00000149968	ENST00000299855	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	MMP3	HGNC	7173	protein_coding	YES	CCDS8323.1	ENSP00000299855	MMP3_HUMAN	.	UPI00000422BF	.	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGTTGAGGTT	.	5	ESCA
DYNC2H1	0	.	GRCh37	11	103041718	103041718	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5255C>T	p.Ser1752Leu	p.S1752L	ENST00000398093	34/90	83	52	30	66	66	0	DYNC2H1,missense_variant,p.Ser1752Leu,ENST00000398093,;DYNC2H1,missense_variant,p.Ser1752Leu,ENST00000375735,;DYNC2H1,intron_variant,,ENST00000334267,;	T	ENSG00000187240	ENST00000398093	Transcript	missense_variant	5255	5255	1752	S/L	tCa/tTa	.	.	.	1	DYNC2H1	HGNC	2962	protein_coding	YES	CCDS44717.1	ENSP00000381167	DYHC2_HUMAN	.	UPI0000481AC7	.	.	probably_damaging(1)	34/90	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF34,Gene3D:3.40.50.300,Pfam_domain:PF12774,SMART_domains:SM00382,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTGTCAGCAG	.	5	ESCA
ADM	0	.	GRCh37	11	10328411	10328411	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*223C>T	.	.	ENST00000528655	3/3	14	11	3	13	13	0	ADM,3_prime_UTR_variant,,ENST00000534464,;ADM,3_prime_UTR_variant,,ENST00000530439,;ADM,3_prime_UTR_variant,,ENST00000278175,;ADM,3_prime_UTR_variant,,ENST00000525063,;ADM,3_prime_UTR_variant,,ENST00000528655,;ADM,downstream_gene_variant,,ENST00000524948,;ADM,downstream_gene_variant,,ENST00000528544,;ADM,downstream_gene_variant,,ENST00000526492,;RP11-351I24.1,upstream_gene_variant,,ENST00000526906,;AMPD3,upstream_gene_variant,,ENST00000527261,;	T	ENSG00000148926	ENST00000528655	Transcript	3_prime_UTR_variant	1398	.	.	.	.	.	.	.	1	ADM	HGNC	259	protein_coding	YES	CCDS7801.1	ENSP00000436607	ADML_HUMAN	E9PL83_HUMAN	UPI00001255F0	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGGGCGGGGT	.	5	ESCA
ATM	0	.	GRCh37	11	108186589	108186589	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6046G>C	p.Asp2016His	p.D2016H	ENST00000278616	41/63	71	48	22	49	49	0	ATM,missense_variant,p.Asp2016His,ENST00000278616,;ATM,missense_variant,p.Asp2016His,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,non_coding_transcript_exon_variant,,ENST00000532765,;ATM,3_prime_UTR_variant,,ENST00000529588,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;	C	ENSG00000149311	ENST00000278616	Transcript	missense_variant	6431	6046	2016	D/H	Gat/Cat	COSM93917	.	.	1	ATM	HGNC	795	protein_coding	YES	CCDS31669.1	ENSP00000278616	ATM_HUMAN	M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN	UPI0000DBEF44	.	deleterious(0)	probably_damaging(1)	41/63	.	hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66,PROSITE_profiles:PS51189	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCCAGATAGT	.	5	ESCA
CSNK2A3	0	.	GRCh37	11	11374595	11374595	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.72G>C	p.Trp24Cys	p.W24C	ENST00000528848	1/1	97	84	13	91	91	0	CSNK2A3,missense_variant,p.Trp24Cys,ENST00000528848,;GALNT18,intron_variant,,ENST00000227756,;RP11-567I13.1,intron_variant,,ENST00000526867,;	G	ENSG00000254598	ENST00000528848	Transcript	missense_variant	310	72	24	W/C	tgG/tgC	.	.	.	-1	CSNK2A3	HGNC	2458	protein_coding	YES	CCDS59224.1	ENSP00000473553	CSK23_HUMAN	.	UPI00001F9D63	.	deleterious(0)	probably_damaging(0.999)	1/1	.	hmmpanther:PTHR24054:SF28,hmmpanther:PTHR24054,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TAATCCCAGTA	.	4	ESCA
BSX	0	.	GRCh37	11	122852178	122852178	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.202C>G	p.His68Asp	p.H68D	ENST00000343035	1/3	24	20	4	15	15	0	BSX,missense_variant,p.His68Asp,ENST00000343035,;	C	ENSG00000188909	ENST00000343035	Transcript	missense_variant	251	202	68	H/D	Cac/Gac	.	.	.	-1	BSX	HGNC	20450	protein_coding	YES	CCDS41728.1	ENSP00000344285	BSH_HUMAN	.	UPI000036683F	.	deleterious(0.02)	benign(0.302)	1/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24327:SF27,hmmpanther:PTHR24327	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCGTGAGGAG	.	5	ESCA
VWA5A	0	.	GRCh37	11	124006970	124006970	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1494C>G	p.Ile498Met	p.I498M	ENST00000456829	13/19	41	36	5	22	22	0	VWA5A,missense_variant,p.Ile498Met,ENST00000456829,;VWA5A,missense_variant,p.Ile498Met,ENST00000392748,;VWA5A,intron_variant,,ENST00000360334,;	G	ENSG00000110002	ENST00000456829	Transcript	missense_variant	1745	1494	498	I/M	atC/atG	.	.	.	1	VWA5A	HGNC	6658	protein_coding	YES	CCDS8444.1	ENSP00000407726	VMA5A_HUMAN	.	UPI0000158B80	.	deleterious(0.04)	probably_damaging(0.942)	13/19	.	hmmpanther:PTHR10338:SF100,hmmpanther:PTHR10338	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAATCAGCTA	.	5	ESCA
FEZ1	0	.	GRCh37	11	125325912	125325912	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.758A>G	p.Gln253Arg	p.Q253R	ENST00000278919	6/10	21	16	5	11	11	0	FEZ1,missense_variant,p.Gln253Arg,ENST00000278919,;FEZ1,missense_variant,p.Gln186Arg,ENST00000577924,;FEZ1,non_coding_transcript_exon_variant,,ENST00000527350,;FEZ1,upstream_gene_variant,,ENST00000526507,;FEZ1,upstream_gene_variant,,ENST00000532778,;FEZ1,non_coding_transcript_exon_variant,,ENST00000524427,;FEZ1,non_coding_transcript_exon_variant,,ENST00000533294,;FEZ1,non_coding_transcript_exon_variant,,ENST00000392709,;FEZ1,upstream_gene_variant,,ENST00000530096,;FEZ1,downstream_gene_variant,,ENST00000534022,;FEZ1,upstream_gene_variant,,ENST00000528863,;	C	ENSG00000149557	ENST00000278919	Transcript	missense_variant	993	758	253	Q/R	cAg/cGg	.	.	.	-1	FEZ1	HGNC	3659	protein_coding	YES	CCDS31716.1	ENSP00000278919	FEZ1_HUMAN	E9PNH2_HUMAN	UPI000012A6FE	.	deleterious(0.01)	probably_damaging(0.977)	6/10	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12394:SF4,hmmpanther:PTHR12394,Pfam_domain:PF07763	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CCAGCTGCTGC	.	3	ESCA
AP000708.1	0	.	GRCh37	11	125365498	125365498	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.274G>C	p.Glu92Gln	p.E92Q	ENST00000527818	1/2	25	18	6	24	24	0	AP000708.1,missense_variant,p.Glu92Gln,ENST00000527818,;FEZ1,5_prime_UTR_variant,,ENST00000524435,;FEZ1,intron_variant,,ENST00000527534,;FEZ1,intron_variant,,ENST00000278919,;FEZ1,intron_variant,,ENST00000366139,;FEZ1,intron_variant,,ENST00000532981,;FEZ1,intron_variant,,ENST00000392709,;	C	ENSG00000255537	ENST00000527818	Transcript	missense_variant	389	274	92	E/Q	Gag/Cag	.	.	.	1	AP000708.1	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000434154	YK038_HUMAN	.	UPI00001AFDD3	.	tolerated_low_confidence(0.15)	possibly_damaging(0.742)	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|VARSCANS	GGCACGAGCGG	.	4	ESCA
PRDM10	0	.	GRCh37	11	129794884	129794884	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1783G>C	p.Glu595Gln	p.E595Q	ENST00000358825	13/22	35	27	8	36	36	0	PRDM10,missense_variant,p.Glu509Gln,ENST00000526082,;PRDM10,missense_variant,p.Glu591Gln,ENST00000360871,;PRDM10,missense_variant,p.Glu565Gln,ENST00000528746,;PRDM10,missense_variant,p.Glu595Gln,ENST00000358825,;PRDM10,missense_variant,p.Glu308Gln,ENST00000533431,;PRDM10,missense_variant,p.Glu509Gln,ENST00000423662,;PRDM10,missense_variant,p.Glu505Gln,ENST00000304538,;	G	ENSG00000170325	ENST00000358825	Transcript	missense_variant	2015	1783	595	E/Q	Gaa/Caa	.	.	.	-1	PRDM10	HGNC	13995	protein_coding	YES	CCDS44771.1	ENSP00000351686	PRD10_HUMAN	.	UPI00002371B3	.	tolerated(0.1)	benign(0.355)	13/22	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,PROSITE_patterns:PS00028,hmmpanther:PTHR11389:SF415,hmmpanther:PTHR11389,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	GGATTCTGGGC	.	4	ESCA
B3GAT1	0	.	GRCh37	11	134252719	134252719	+	Missense_Mutation	SNP	C	C	T	rs368413334	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.803G>A	p.Arg268Gln	p.R268Q	ENST00000524765	4/6	33	26	6	39	39	0	B3GAT1,missense_variant,p.Arg268Gln,ENST00000524765,;B3GAT1,missense_variant,p.Arg281Gln,ENST00000537389,;B3GAT1,missense_variant,p.Arg268Gln,ENST00000312527,;B3GAT1,missense_variant,p.Arg268Gln,ENST00000392580,;GLB1L2,downstream_gene_variant,,ENST00000389881,;GLB1L2,downstream_gene_variant,,ENST00000529077,;B3GAT1,downstream_gene_variant,,ENST00000531510,;B3GAT1,non_coding_transcript_exon_variant,,ENST00000531778,;	T	ENSG00000109956	ENST00000524765	Transcript	missense_variant	5348	803	268	R/Q	cGa/cAa	rs368413334,COSM1352787	.	.	-1	B3GAT1	HGNC	921	protein_coding	YES	CCDS8500.1	ENSP00000433847	B3GA1_HUMAN	Q8ND18_HUMAN	UPI0000073281	.	tolerated(0.26)	benign(0.215)	4/6	.	hmmpanther:PTHR10896,hmmpanther:PTHR10896:SF21,Gene3D:3.90.550.10,Pfam_domain:PF03360,Superfamily_domains:SSF53448	.	.	.	.	.	.	.	T:0	T:0.0002	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTCGCTGC	byFrequency|byCluster	5	ESCA
SPON1	0	.	GRCh37	11	14277295	14277295	+	RNA	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1730C>T	.	.	ENST00000310358	10/17	50	33	17	36	36	0	SPON1,non_coding_transcript_exon_variant,,ENST00000533633,;SPON1,non_coding_transcript_exon_variant,,ENST00000310358,;	T	ENSG00000152268	ENST00000310358	Transcript	non_coding_transcript_exon_variant	1730	.	.	.	.	.	.	.	1	SPON1	HGNC	11252	processed_transcript	YES	.	.	.	.	.	.	.	.	10/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTCAAGTA	.	5	ESCA
GAS2	0	.	GRCh37	11	22747876	22747876	+	Silent	SNP	A	A	C	rs202203862	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.306A>C	p.%3D	p.A102A	ENST00000454584	4/8	69	60	9	53	52	0	GAS2,synonymous_variant,p.%3D,ENST00000533363,;GAS2,synonymous_variant,p.%3D,ENST00000433790,;GAS2,synonymous_variant,p.%3D,ENST00000534801,;GAS2,synonymous_variant,p.%3D,ENST00000528582,;GAS2,synonymous_variant,p.%3D,ENST00000532398,;GAS2,synonymous_variant,p.%3D,ENST00000278187,;GAS2,synonymous_variant,p.%3D,ENST00000454584,;GAS2,synonymous_variant,p.%3D,ENST00000524701,;	C	ENSG00000148935	ENST00000454584	Transcript	synonymous_variant	611	306	102	A	gcA/gcC	rs202203862	.	.	1	GAS2	HGNC	4167	protein_coding	YES	CCDS7858.1	ENSP00000401145	GAS2_HUMAN	E9PRR5_HUMAN,E9PQ74_HUMAN,E9PQ37_HUMAN,E9PM28_HUMAN	UPI000000D98C	.	.	.	4/8	.	PROSITE_profiles:PS50021,hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF114,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AGTGCACCCTC	byCluster|by1000G	3	ESCA
GAS2	0	.	GRCh37	11	22747881	22747881	+	Missense_Mutation	SNP	C	C	G	rs769844769	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.311C>G	p.Ser104Trp	p.S104W	ENST00000454584	4/8	67	58	8	57	57	0	GAS2,missense_variant,p.Ser104Trp,ENST00000533363,;GAS2,missense_variant,p.Ser104Trp,ENST00000433790,;GAS2,missense_variant,p.Ser104Trp,ENST00000534801,;GAS2,missense_variant,p.Ser104Trp,ENST00000528582,;GAS2,missense_variant,p.Ser104Trp,ENST00000532398,;GAS2,missense_variant,p.Ser104Trp,ENST00000278187,;GAS2,missense_variant,p.Ser104Trp,ENST00000454584,;GAS2,missense_variant,p.Ser104Trp,ENST00000524701,;	G	ENSG00000148935	ENST00000454584	Transcript	missense_variant	616	311	104	S/W	tCg/tGg	rs769844769,COSM3935424	.	.	1	GAS2	HGNC	4167	protein_coding	YES	CCDS7858.1	ENSP00000401145	GAS2_HUMAN	E9PRR5_HUMAN,E9PQ74_HUMAN,E9PQ37_HUMAN,E9PM28_HUMAN	UPI000000D98C	.	deleterious(0)	probably_damaging(0.991)	4/8	.	PROSITE_profiles:PS50021,hmmpanther:PTHR25069,hmmpanther:PTHR25069:SF114,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	ACCCTCGGGCT	byFrequency	3	ESCA
KIAA1549L	0	.	GRCh37	11	33667496	33667496	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4783C>T	p.Pro1595Ser	p.P1595S	ENST00000321505	16/20	43	30	13	39	39	0	KIAA1549L,missense_variant,p.Pro1595Ser,ENST00000321505,;KIAA1549L,missense_variant,p.Pro1601Ser,ENST00000389726,;	T	ENSG00000110427	ENST00000321505	Transcript	missense_variant	4963	4783	1595	P/S	Ccg/Tcg	.	.	.	1	KIAA1549L	HGNC	24836	protein_coding	YES	CCDS44565.2	ENSP00000315295	K154L_HUMAN	.	UPI0000E59322	.	deleterious(0)	probably_damaging(0.999)	16/20	.	hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCTCCGGGG	.	5	ESCA
KIAA1549L	0	.	GRCh37	11	33667497	33667497	+	Missense_Mutation	SNP	C	C	T	rs762094891	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4784C>T	p.Pro1595Leu	p.P1595L	ENST00000321505	16/20	43	30	13	39	39	0	KIAA1549L,missense_variant,p.Pro1595Leu,ENST00000321505,;KIAA1549L,missense_variant,p.Pro1601Leu,ENST00000389726,;	T	ENSG00000110427	ENST00000321505	Transcript	missense_variant	4964	4784	1595	P/L	cCg/cTg	rs762094891	.	.	1	KIAA1549L	HGNC	24836	protein_coding	YES	CCDS44565.2	ENSP00000315295	K154L_HUMAN	.	UPI0000E59322	.	deleterious(0)	probably_damaging(0.999)	16/20	.	hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCTCCGGGGA	byFrequency	5	ESCA
SLC35C1	0	.	GRCh37	11	45833064	45833064	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*178G>C	.	.	ENST00000314134	2/2	94	78	15	107	107	0	SLC35C1,3_prime_UTR_variant,,ENST00000442528,;SLC35C1,3_prime_UTR_variant,,ENST00000456334,;SLC35C1,3_prime_UTR_variant,,ENST00000314134,;CTD-2210P24.6,upstream_gene_variant,,ENST00000534128,;	C	ENSG00000181830	ENST00000314134	Transcript	3_prime_UTR_variant	2669	.	.	.	.	.	.	.	1	SLC35C1	HGNC	20197	protein_coding	YES	CCDS7914.1	ENSP00000313318	FUCT1_HUMAN	Q96K20_HUMAN,E9PS26_HUMAN,E9PPI4_HUMAN,B3KQH0_HUMAN	UPI000012A5BB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATCAGAAAGT	.	5	ESCA
OR4C3	0	.	GRCh37	11	48346987	48346987	+	Silent	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495C>G	p.%3D	p.L165L	ENST00000319856	1/1	38	34	4	40	40	0	OR4C3,synonymous_variant,p.%3D,ENST00000319856,;	G	ENSG00000176547	ENST00000319856	Transcript	synonymous_variant	516	495	165	L	ctC/ctG	COSM1508100,COSM3448088	.	.	1	OR4C3	HGNC	14697	protein_coding	YES	CCDS31489.1	ENSP00000321419	OR4C3_HUMAN	.	UPI0000061EA2	.	.	.	1/1	.	PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	LOW	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CATCTCTGTGC	.	4	ESCA
OR51S1	0	.	GRCh37	11	4870196	4870196	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.243G>C	p.Leu81Phe	p.L81F	ENST00000322101	1/1	36	33	3	13	13	0	OR51S1,missense_variant,p.Leu81Phe,ENST00000322101,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	G	ENSG00000176922	ENST00000322101	Transcript	missense_variant	319	243	81	L/F	ttG/ttC	COSM97958	.	.	-1	OR51S1	HGNC	15204	protein_coding	YES	CCDS31362.1	ENSP00000322754	O51S1_HUMAN	.	UPI0000041C33	.	deleterious(0)	probably_damaging(1)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF73,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGACCAATCC	.	2	ESCA
OR5I1	0	.	GRCh37	11	55703532	55703532	+	Silent	SNP	G	G	A	rs768904558	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.345C>T	p.%3D	p.F115F	ENST00000301532	1/1	49	35	14	42	42	0	OR5I1,synonymous_variant,p.%3D,ENST00000301532,;	A	ENSG00000167825	ENST00000301532	Transcript	synonymous_variant	345	345	115	F	ttC/ttT	rs768904558,COSM1475529	.	.	-1	OR5I1	HGNC	8347	protein_coding	YES	CCDS7949.1	ENSP00000301532	OR5I1_HUMAN	.	UPI00000405D5	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF69,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGGATGAAGGA	.	5	ESCA
OR8K3	0	.	GRCh37	11	56085848	56085848	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66G>C	p.Glu22Asp	p.E22D	ENST00000312711	1/1	53	37	16	44	44	0	OR8K3,missense_variant,p.Glu22Asp,ENST00000312711,;	C	ENSG00000181689	ENST00000312711	Transcript	missense_variant	66	66	22	E/D	gaG/gaC	.	.	.	1	OR8K3	HGNC	15313	protein_coding	YES	CCDS31527.1	ENSP00000323555	OR8K3_HUMAN	.	UPI0000041BE7	.	tolerated_low_confidence(0.06)	benign(0.093)	1/1	.	hmmpanther:PTHR26452:SF161,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GCTGAGCTGCA	.	4	ESCA
LRRC55	0	.	GRCh37	11	56954739	56954739	+	Missense_Mutation	SNP	C	C	T	rs202161364	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.811C>T	p.Arg271Trp	p.R271W	ENST00000497933	2/2	38	31	6	27	27	0	LRRC55,missense_variant,p.Arg271Trp,ENST00000497933,;	T	ENSG00000183908	ENST00000497933	Transcript	missense_variant	958	811	271	R/W	Cgg/Tgg	rs202161364	.	.	1	LRRC55	HGNC	32324	protein_coding	YES	CCDS31539.1	ENSP00000419542	LRC55_HUMAN	.	UPI00001C0E6F	.	tolerated(0.21)	benign(0.019)	2/2	.	SMART_domains:SM00082,Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF99	T:0.0002	T:0	T:0	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTGCCGGGGC	byCluster|by1000G	5	ESCA
MED19	0	.	GRCh37	11	57472496	57472496	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.423C>G	p.Phe141Leu	p.F141L	ENST00000337672	2/4	54	41	13	48	48	0	MED19,missense_variant,p.Phe141Leu,ENST00000337672,;MED19,missense_variant,p.Phe141Leu,ENST00000431606,;ZDHHC5,downstream_gene_variant,,ENST00000287169,;ZDHHC5,downstream_gene_variant,,ENST00000527985,;MED19,non_coding_transcript_exon_variant,,ENST00000534677,;MED19,non_coding_transcript_exon_variant,,ENST00000528205,;ZDHHC5,downstream_gene_variant,,ENST00000529480,;	C	ENSG00000156603	ENST00000337672	Transcript	missense_variant	445	423	141	F/L	ttC/ttG	.	.	.	-1	MED19	HGNC	29600	protein_coding	YES	CCDS7966.1	ENSP00000337340	MED19_HUMAN	.	UPI00000746CC	.	tolerated(0.81)	benign(0.017)	2/4	.	hmmpanther:PTHR22536,Pfam_domain:PF10278	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATTGAAAGA	.	5	ESCA
C11orf31	0	.	GRCh37	11	57509011	57509011	+	5'Flank	SNP	G	G	C	rs572613984	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000388857	.	54	34	19	41	41	0	C11orf31,5_prime_UTR_variant,,ENST00000534355,;BTBD18,downstream_gene_variant,,ENST00000436147,;C11orf31,upstream_gene_variant,,ENST00000528798,;TMX2,downstream_gene_variant,,ENST00000378312,;BTBD18,downstream_gene_variant,,ENST00000527995,;BTBD18,downstream_gene_variant,,ENST00000422652,;TMX2,downstream_gene_variant,,ENST00000278422,;C11orf31,upstream_gene_variant,,ENST00000388857,;C11orf31,non_coding_transcript_exon_variant,,ENST00000533321,;TMX2-CTNND1,intron_variant,,ENST00000528395,;RP11-691N7.6,upstream_gene_variant,,ENST00000531074,;TMX2,downstream_gene_variant,,ENST00000525035,;C11orf31,upstream_gene_variant,,ENST00000534386,;TMX2,downstream_gene_variant,,ENST00000528110,;TMX2,downstream_gene_variant,,ENST00000530114,;TMX2,downstream_gene_variant,,ENST00000529403,;TMX2,downstream_gene_variant,,ENST00000528042,;TMX2,downstream_gene_variant,,ENST00000524972,;TMX2,downstream_gene_variant,,ENST00000533602,;	C	ENSG00000211450	ENST00000388857	Transcript	upstream_gene_variant	.	.	.	.	.	rs572613984	.	33	1	C11orf31	HGNC	18251	protein_coding	YES	CCDS44602.1	ENSP00000373509	SELH_HUMAN	.	UPI0000163E14	.	.	.	.	.	.	A:0.0004	A:0	A:0	.	A:0	A:0	A:0.002	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTCGCGTCT	byFrequency|by1000G	5	ESCA
OR52L1	0	.	GRCh37	11	6007166	6007166	+	3'UTR	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*5A>C	.	.	ENST00000332249	1/1	44	38	6	38	38	0	OR52L1,3_prime_UTR_variant,,ENST00000332249,;	G	ENSG00000183313	ENST00000332249	Transcript	3_prime_UTR_variant	1050	.	.	.	.	.	.	.	-1	OR52L1	HGNC	14785	protein_coding	YES	CCDS44529.1	ENSP00000330338	O52L1_HUMAN	.	UPI00001B006D	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATGTTCAGAT	.	5	ESCA
RAB3IL1	0	.	GRCh37	11	61674023	61674023	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572G>A	p.Arg191His	p.R191H	ENST00000394836	5/10	72	54	18	53	53	0	RAB3IL1,missense_variant,p.Arg238His,ENST00000531922,;RAB3IL1,missense_variant,p.Arg191His,ENST00000394836,;RAB3IL1,intron_variant,,ENST00000301773,;RAB3IL1,upstream_gene_variant,,ENST00000530888,;	T	ENSG00000167994	ENST00000394836	Transcript	missense_variant	730	572	191	R/H	cGc/cAc	.	.	.	-1	RAB3IL1	HGNC	9780	protein_coding	YES	CCDS8014.1	ENSP00000378313	R3GEF_HUMAN	.	UPI000007260E	.	tolerated(0.07)	probably_damaging(0.996)	5/10	.	hmmpanther:PTHR14430:SF1,hmmpanther:PTHR14430	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGGCGAGAG	.	5	ESCA
AHNAK	0	.	GRCh37	11	62297376	62297376	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4513G>C	p.Asp1505His	p.D1505H	ENST00000378024	5/5	96	85	11	67	67	0	AHNAK,missense_variant,p.Asp1505His,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000528508,;	G	ENSG00000124942	ENST00000378024	Transcript	missense_variant	4788	4513	1505	D/H	Gac/Cac	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	probably_damaging(1)	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCAGTCTGGGC	.	4	ESCA
AHNAK	0	.	GRCh37	11	62298039	62298039	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3850G>T	p.Asp1284Tyr	p.D1284Y	ENST00000378024	5/5	108	91	17	85	85	0	AHNAK,missense_variant,p.Asp1284Tyr,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000531324,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000528508,;	A	ENSG00000124942	ENST00000378024	Transcript	missense_variant	4125	3850	1284	D/Y	Gat/Tat	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	possibly_damaging(0.665)	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACATCAATGT	.	5	ESCA
AHNAK	0	.	GRCh37	11	62298750	62298750	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3139G>C	p.Glu1047Gln	p.E1047Q	ENST00000378024	5/5	69	60	8	61	61	0	AHNAK,missense_variant,p.Glu1047Gln,ENST00000378024,;AHNAK,intron_variant,,ENST00000257247,;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000531324,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000528508,;	G	ENSG00000124942	ENST00000378024	Transcript	missense_variant	3414	3139	1047	E/Q	Gaa/Caa	.	.	.	-1	AHNAK	HGNC	347	protein_coding	YES	CCDS31584.1	ENSP00000367263	AHNK_HUMAN	E9PQE3_HUMAN,E9PLK4_HUMAN,E9PKR9_HUMAN	UPI00004EC29C	.	.	probably_damaging(0.939)	5/5	.	hmmpanther:PTHR23348:SF40,hmmpanther:PTHR23348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTTCAGGTC	.	5	ESCA
TUT1	0	.	GRCh37	11	62343608	62343608	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1697C>G	p.Ser566Cys	p.S566C	ENST00000308436	9/9	59	54	5	33	33	0	TUT1,missense_variant,p.Ser528Cys,ENST00000476907,;TUT1,missense_variant,p.Ser566Cys,ENST00000308436,;TUT1,downstream_gene_variant,,ENST00000278279,;EEF1G,upstream_gene_variant,,ENST00000329251,;EEF1G,upstream_gene_variant,,ENST00000378019,;TUT1,downstream_gene_variant,,ENST00000494385,;EEF1G,upstream_gene_variant,,ENST00000524420,;EEF1G,upstream_gene_variant,,ENST00000532986,;TUT1,non_coding_transcript_exon_variant,,ENST00000469480,;MIR3654,intron_variant,,ENST00000534745,;MIR3654,intron_variant,,ENST00000496634,;MIR3654,intron_variant,,ENST00000526409,;TUT1,downstream_gene_variant,,ENST00000463241,;EEF1G,upstream_gene_variant,,ENST00000525340,;	C	ENSG00000149016	ENST00000308436	Transcript	missense_variant	1735	1697	566	S/C	tCt/tGt	.	.	.	-1	TUT1	HGNC	26184	protein_coding	YES	CCDS8021.2	ENSP00000308000	.	F5H0R1_HUMAN,C9JBX0_HUMAN	UPI000199421A	.	deleterious(0.01)	possibly_damaging(0.769)	9/9	.	Superfamily_domains:SSF81631,Pfam_domain:PF03828,hmmpanther:PTHR12271,hmmpanther:PTHR12271:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GATTAGAAGGC	.	3	ESCA
ATG2A	0	.	GRCh37	11	64662007	64662007	+	3'Flank	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000377264	.	23	20	3	17	17	0	ATG2A,3_prime_UTR_variant,,ENST00000421419,;ATG2A,downstream_gene_variant,,ENST00000418259,;ATG2A,downstream_gene_variant,,ENST00000377264,;MIR194-2,upstream_gene_variant,,ENST00000413053,;RP11-665N17.4,upstream_gene_variant,,ENST00000601517,;MIR192,upstream_gene_variant,,ENST00000384915,;MIR194-2,upstream_gene_variant,,ENST00000384864,;ATG2A,downstream_gene_variant,,ENST00000472525,;AP001187.1,upstream_gene_variant,,ENST00000366222,;	C	ENSG00000110046	ENST00000377264	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	11	-1	ATG2A	HGNC	29028	protein_coding	YES	CCDS31602.1	ENSP00000366475	ATG2A_HUMAN	B4DV45_HUMAN	UPI00001C1F21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GATCTGAGAGG	.	2	ESCA
C11orf85	0	.	GRCh37	11	64707168	64707168	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.618G>C	p.Arg206Ser	p.R206S	ENST00000301896	10/11	30	22	8	26	26	0	C11orf85,missense_variant,p.Arg206Ser,ENST00000432175,;C11orf85,missense_variant,p.Arg206Ser,ENST00000301896,;C11orf85,missense_variant,p.Glu122Gln,ENST00000536065,;C11orf85,missense_variant,p.Glu150Gln,ENST00000530444,;C11orf85,missense_variant,p.Arg49Ser,ENST00000532617,;GPHA2,upstream_gene_variant,,ENST00000532246,;GPHA2,upstream_gene_variant,,ENST00000533257,;GPHA2,upstream_gene_variant,,ENST00000279168,;C11orf85,3_prime_UTR_variant,,ENST00000530735,;C11orf85,non_coding_transcript_exon_variant,,ENST00000530287,;	G	ENSG00000168070	ENST00000301896	Transcript	missense_variant	692	618	206	R/S	agG/agC	COSM1604992	.	.	-1	C11orf85	HGNC	27441	protein_coding	YES	CCDS31603.1	ENSP00000301896	CK085_HUMAN	.	UPI00005C40BB	.	deleterious_low_confidence(0.01)	benign(0.402)	10/11	.	Pfam_domain:PF15077	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|SOMATICSNIPER|MUSE|VARSCANS	TCGCTCCTTAG	.	4	ESCA
SLC25A45	0	.	GRCh37	11	65144518	65144518	+	Silent	SNP	G	G	A	rs370182084	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.369C>T	p.%3D	p.I123I	ENST00000398802	6/7	100	73	26	97	97	0	SLC25A45,synonymous_variant,p.%3D,ENST00000377152,;SLC25A45,synonymous_variant,p.%3D,ENST00000526432,;SLC25A45,synonymous_variant,p.%3D,ENST00000398802,;SLC25A45,synonymous_variant,p.%3D,ENST00000360662,;SLC25A45,synonymous_variant,p.%3D,ENST00000417511,;SLC25A45,synonymous_variant,p.%3D,ENST00000527174,;SLC25A45,synonymous_variant,p.%3D,ENST00000294187,;SLC25A45,synonymous_variant,p.%3D,ENST00000534028,;SLC25A45,downstream_gene_variant,,ENST00000530936,;RP11-867O8.5,downstream_gene_variant,,ENST00000533886,;SLC25A45,3_prime_UTR_variant,,ENST00000533629,;SLC25A45,3_prime_UTR_variant,,ENST00000526259,;SLC25A45,3_prime_UTR_variant,,ENST00000526898,;SLC25A45,non_coding_transcript_exon_variant,,ENST00000534338,;SLC25A45,non_coding_transcript_exon_variant,,ENST00000531791,;SLC25A45,downstream_gene_variant,,ENST00000529431,;SLC25A45,downstream_gene_variant,,ENST00000524438,;SLC25A45,downstream_gene_variant,,ENST00000529962,;SLC25A45,downstream_gene_variant,,ENST00000525944,;	A	ENSG00000162241	ENST00000398802	Transcript	synonymous_variant	573	369	123	I	atC/atT	rs370182084	.	.	-1	SLC25A45	HGNC	27442	protein_coding	YES	CCDS41670.1	ENSP00000381782	S2545_HUMAN	E9PK53_HUMAN	UPI0000199B26	.	.	.	6/7	.	Prints_domain:PR00926,Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF249,PROSITE_profiles:PS50920	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTTTGATGAG	byFrequency|byCluster	5	ESCA
CNIH2	0	.	GRCh37	11	66045989	66045991	+	In_Frame_Del	DEL	TCT	TCT	-	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	TCT	TCT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66_68delCTT	p.Phe23del	p.F23del	ENST00000311445	1/6	40	34	6	34	34	0	CNIH2,inframe_deletion,p.Phe23del,ENST00000528852,;CNIH2,inframe_deletion,p.Phe23del,ENST00000311445,;RAB1B,downstream_gene_variant,,ENST00000311481,;RAB1B,downstream_gene_variant,,ENST00000527397,;RP11-867G23.3,non_coding_transcript_exon_variant,,ENST00000501708,;RP11-867G23.4,upstream_gene_variant,,ENST00000526951,;RP11-867G23.4,upstream_gene_variant,,ENST00000528650,;CNIH2,non_coding_transcript_exon_variant,,ENST00000530519,;CNIH2,inframe_deletion,p.Phe23del,ENST00000534826,;CNIH2,inframe_deletion,p.Phe23del,ENST00000528063,;CNIH2,upstream_gene_variant,,ENST00000531936,;	-	ENSG00000174871	ENST00000311445	Transcript	inframe_deletion	320-322	62-64	21-22	IF/I	aTCTtc/atc	.	.	.	1	CNIH2	HGNC	28744	protein_coding	YES	CCDS8131.1	ENSP00000310003	CNIH2_HUMAN	.	UPI000000DC89	.	.	.	1/6	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR12290,hmmpanther:PTHR12290:SF13,Pfam_domain:PF03311	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	deletion	.	4	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANI*|PINDEL	CCCTCATCTTCTTT	.	2	ESCA
C11orf80	0	.	GRCh37	11	66555679	66555679	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.572C>G	p.Ser191Ter	p.S191*	ENST00000360962	5/17	80	66	14	73	73	0	C11orf80,stop_gained,p.Ser191Ter,ENST00000360962,;C11orf80,stop_gained,p.Ser17Ter,ENST00000532089,;C11orf80,stop_gained,p.Ser36Ter,ENST00000525449,;C11orf80,stop_gained,p.Ser142Ter,ENST00000525908,;C11orf80,stop_gained,p.Ser25Ter,ENST00000540737,;C11orf80,stop_gained,p.Ser36Ter,ENST00000346672,;C11orf80,5_prime_UTR_variant,,ENST00000532565,;C11orf80,intron_variant,,ENST00000524551,;C11orf80,intron_variant,,ENST00000527634,;C11orf80,non_coding_transcript_exon_variant,,ENST00000527368,;C11orf80,stop_gained,p.Ser17Ter,ENST00000526260,;C11orf80,stop_gained,p.Ser25Ter,ENST00000531400,;C11orf80,stop_gained,p.Ser25Ter,ENST00000532727,;	G	ENSG00000173715	ENST00000360962	Transcript	stop_gained	579	572	191	S/*	tCa/tGa	.	.	.	1	C11orf80	HGNC	26197	protein_coding	YES	CCDS53664.1	ENSP00000354227	CK080_HUMAN	E9PIE7_HUMAN	UPI0001711D28	.	.	.	5/17	.	hmmpanther:PTHR14652	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTCAGAGG	.	5	ESCA
PPFIA1	0	.	GRCh37	11	70229214	70229214	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*118G>C	.	.	ENST00000253925	28/28	46	38	8	33	33	0	PPFIA1,missense_variant,p.Trp75Cys,ENST00000528853,;PPFIA1,3_prime_UTR_variant,,ENST00000253925,;PPFIA1,downstream_gene_variant,,ENST00000389547,;AP000487.5,intron_variant,,ENST00000530690,;AP000487.5,intron_variant,,ENST00000524619,;AP000487.5,intron_variant,,ENST00000500185,;PPFIA1,non_coding_transcript_exon_variant,,ENST00000530548,;PPFIA1,3_prime_UTR_variant,,ENST00000532504,;PPFIA1,3_prime_UTR_variant,,ENST00000526262,;PPFIA1,non_coding_transcript_exon_variant,,ENST00000531657,;	C	ENSG00000131626	ENST00000253925	Transcript	3_prime_UTR_variant	3942	.	.	.	.	.	.	.	1	PPFIA1	HGNC	9245	protein_coding	YES	CCDS31627.1	ENSP00000253925	LIPA1_HUMAN	E9PPF6_HUMAN,E9PID5_HUMAN,B3KVS8_HUMAN	UPI0000072426	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATGGACCCT	.	5	ESCA
KRTAP5-7	0	.	GRCh37	11	71238747	71238747	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.401C>G	p.Ser134Ter	p.S134*	ENST00000398536	1/1	102	83	18	88	88	0	KRTAP5-7,stop_gained,p.Ser134Ter,ENST00000398536,;NADSYN1,downstream_gene_variant,,ENST00000527963,;	G	ENSG00000244411	ENST00000398536	Transcript	stop_gained	435	401	134	S/*	tCa/tGa	.	.	.	1	KRTAP5-7	HGNC	23602	protein_coding	YES	CCDS41682.1	ENSP00000417330	KRA57_HUMAN	.	UPI0000376061	.	.	.	1/1	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23262:SF47,hmmpanther:PTHR23262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCCTCAGGCT	.	5	ESCA
DEFB108B	0	.	GRCh37	11	71548582	71548582	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.196G>C	p.Glu66Gln	p.E66Q	ENST00000328698	2/2	395	303	92	336	336	0	DEFB108B,missense_variant,p.Glu66Gln,ENST00000328698,;DEFB108B,non_coding_transcript_exon_variant,,ENST00000529157,;	C	ENSG00000184276	ENST00000328698	Transcript	missense_variant	196	196	66	E/Q	Gag/Cag	.	.	.	1	DEFB108B	HGNC	29966	protein_coding	YES	CCDS31631.1	ENSP00000333234	D108B_HUMAN	.	UPI00001AF853	.	tolerated(0.07)	benign(0.042)	2/2	.	hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAATTGAGAGC	.	5	ESCA
ARHGEF17	0	.	GRCh37	11	73076558	73076558	+	Missense_Mutation	SNP	G	G	C	rs372726461	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5674G>C	p.Glu1892Gln	p.E1892Q	ENST00000263674	19/21	19	9	10	19	19	0	ARHGEF17,missense_variant,p.Glu1892Gln,ENST00000263674,;ARHGEF17,non_coding_transcript_exon_variant,,ENST00000543530,;ARHGEF17,downstream_gene_variant,,ENST00000536481,;	C	ENSG00000110237	ENST00000263674	Transcript	missense_variant	6024	5674	1892	E/Q	Gag/Cag	rs372726461	.	.	1	ARHGEF17	HGNC	21726	protein_coding	YES	CCDS8221.1	ENSP00000263674	ARHGH_HUMAN	.	UPI000004980B	.	tolerated(0.09)	possibly_damaging(0.586)	19/21	.	hmmpanther:PTHR12877:SF15,hmmpanther:PTHR12877,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	C:0.0002	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTTTGAGCAG	byFrequency|byCluster	5	ESCA
C2CD3	0	.	GRCh37	11	73745207	73745207	+	3'Flank	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000313663	.	36	27	9	13	13	0	C2CD3,missense_variant,p.Arg2000Gly,ENST00000334126,;C2CD3,downstream_gene_variant,,ENST00000414160,;C2CD3,downstream_gene_variant,,ENST00000313663,;C2CD3,downstream_gene_variant,,ENST00000538361,;C2CD3,non_coding_transcript_exon_variant,,ENST00000538625,;C2CD3,downstream_gene_variant,,ENST00000540452,;C2CD3,upstream_gene_variant,,ENST00000542452,;C2CD3,3_prime_UTR_variant,,ENST00000442398,;	C	ENSG00000168014	ENST00000313663	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	272	-1	C2CD3	HGNC	24564	protein_coding	YES	CCDS31636.1	ENSP00000323339	C2CD3_HUMAN	.	UPI0000D62650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATCGTTCTT	.	5	ESCA
DGAT2	0	.	GRCh37	11	75511769	75511769	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*216C>G	.	.	ENST00000228027	8/8	55	49	6	38	38	0	DGAT2,3_prime_UTR_variant,,ENST00000228027,;DGAT2,3_prime_UTR_variant,,ENST00000376262,;DGAT2,downstream_gene_variant,,ENST00000603276,;DGAT2,downstream_gene_variant,,ENST00000604935,;DGAT2,downstream_gene_variant,,ENST00000605099,;DGAT2,downstream_gene_variant,,ENST00000604733,;RP11-535A19.2,downstream_gene_variant,,ENST00000533945,;RP11-535A19.1,downstream_gene_variant,,ENST00000534354,;RP11-535A19.2,downstream_gene_variant,,ENST00000533590,;RP11-535A19.2,downstream_gene_variant,,ENST00000525580,;DGAT2,non_coding_transcript_exon_variant,,ENST00000603363,;DGAT2,downstream_gene_variant,,ENST00000603865,;	G	ENSG00000062282	ENST00000228027	Transcript	3_prime_UTR_variant	1643	.	.	.	.	.	.	.	1	DGAT2	HGNC	16940	protein_coding	YES	CCDS31642.1	ENSP00000228027	DGAT2_HUMAN	S4R449_HUMAN,S4R3Z3_HUMAN,S4R383_HUMAN	UPI0000048F05	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TAAATCTGGGC	.	3	ESCA
DGAT2	0	.	GRCh37	11	75511780	75511780	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*227C>G	.	.	ENST00000228027	8/8	50	42	7	34	34	0	DGAT2,3_prime_UTR_variant,,ENST00000228027,;DGAT2,3_prime_UTR_variant,,ENST00000376262,;DGAT2,downstream_gene_variant,,ENST00000603276,;DGAT2,downstream_gene_variant,,ENST00000604935,;DGAT2,downstream_gene_variant,,ENST00000605099,;DGAT2,downstream_gene_variant,,ENST00000604733,;RP11-535A19.2,downstream_gene_variant,,ENST00000533945,;RP11-535A19.1,downstream_gene_variant,,ENST00000534354,;RP11-535A19.2,downstream_gene_variant,,ENST00000533590,;RP11-535A19.2,downstream_gene_variant,,ENST00000525580,;DGAT2,non_coding_transcript_exon_variant,,ENST00000603363,;DGAT2,downstream_gene_variant,,ENST00000603865,;	G	ENSG00000062282	ENST00000228027	Transcript	3_prime_UTR_variant	1654	.	.	.	.	.	.	.	1	DGAT2	HGNC	16940	protein_coding	YES	CCDS31642.1	ENSP00000228027	DGAT2_HUMAN	S4R449_HUMAN,S4R3Z3_HUMAN,S4R383_HUMAN	UPI0000048F05	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CTAATCTGGGT	.	3	ESCA
LRRC32	0	.	GRCh37	11	76370959	76370959	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1678G>A	p.Glu560Lys	p.E560K	ENST00000407242	3/3	39	32	7	37	37	0	LRRC32,missense_variant,p.Glu560Lys,ENST00000260061,;LRRC32,missense_variant,p.Glu560Lys,ENST00000407242,;LRRC32,missense_variant,p.Glu560Lys,ENST00000404995,;LRRC32,downstream_gene_variant,,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,;	T	ENSG00000137507	ENST00000407242	Transcript	missense_variant	1921	1678	560	E/K	Gag/Aag	.	.	.	-1	LRRC32	HGNC	4161	protein_coding	YES	CCDS8245.1	ENSP00000384126	LRC32_HUMAN	C9JYU3_HUMAN	UPI000012B0DF	.	deleterious(0)	possibly_damaging(0.733)	3/3	.	Superfamily_domains:SSF52058,SMART_domains:SM00368,Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24365:SF237,hmmpanther:PTHR24365	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCCAGGC	.	5	ESCA
TUB	0	.	GRCh37	11	8122402	8122402	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1410G>C	p.Gln470His	p.Q470H	ENST00000305253	12/13	34	29	5	39	39	0	TUB,missense_variant,p.Gln421His,ENST00000534099,;TUB,missense_variant,p.Gln415His,ENST00000299506,;TUB,missense_variant,p.Gln470His,ENST00000305253,;	C	ENSG00000166402	ENST00000305253	Transcript	missense_variant	1651	1410	470	Q/H	caG/caC	.	.	.	1	TUB	HGNC	12406	protein_coding	YES	CCDS7786.1	ENSP00000305426	TUB_HUMAN	Q9H4D2_HUMAN	UPI000013EA27	.	deleterious(0.03)	benign(0.006)	12/13	.	hmmpanther:PTHR16517:SF20,hmmpanther:PTHR16517,Pfam_domain:PF01167,Gene3D:3c5nA00,Superfamily_domains:SSF54518	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.T474M|c.1421C>T|3	RADIA|MUTECT|MUSE|VARSCANS	TGGCAGAATAA	.	4	ESCA
NOX4	0	.	GRCh37	11	89135696	89135696	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.644A>T	p.Tyr215Phe	p.Y215F	ENST00000263317	9/18	61	47	14	39	39	0	NOX4,missense_variant,p.Tyr49Phe,ENST00000527626,;NOX4,missense_variant,p.Tyr191Phe,ENST00000535633,;NOX4,missense_variant,p.Tyr215Phe,ENST00000534731,;NOX4,missense_variant,p.Tyr215Phe,ENST00000263317,;NOX4,missense_variant,p.Tyr191Phe,ENST00000527956,;NOX4,missense_variant,p.Tyr191Phe,ENST00000542487,;NOX4,missense_variant,p.Tyr190Phe,ENST00000528341,;NOX4,missense_variant,p.Tyr191Phe,ENST00000343727,;NOX4,missense_variant,p.Tyr236Phe,ENST00000413594,;NOX4,missense_variant,p.Tyr191Phe,ENST00000532825,;NOX4,missense_variant,p.Tyr191Phe,ENST00000424319,;NOX4,intron_variant,,ENST00000531342,;NOX4,intron_variant,,ENST00000375979,;NOX4,intron_variant,,ENST00000525196,;NOX4,intron_variant,,ENST00000529343,;	A	ENSG00000086991	ENST00000263317	Transcript	missense_variant	883	644	215	Y/F	tAt/tTt	.	.	.	-1	NOX4	HGNC	7891	protein_coding	YES	CCDS8285.1	ENSP00000263317	NOX4_HUMAN	E7EMD7_HUMAN	UPI000045655B	.	tolerated(0.27)	benign(0.049)	9/18	.	hmmpanther:PTHR11972	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTGATACTTC	.	5	ESCA
NOX4	0	.	GRCh37	11	89222104	89222104	+	Intron	SNP	G	G	A	rs750163966	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.153+1522C>T	.	.	ENST00000263317	.	154	122	31	137	137	0	NOX4,3_prime_UTR_variant,,ENST00000393282,;NOX4,intron_variant,,ENST00000375979,;NOX4,intron_variant,,ENST00000535633,;NOX4,intron_variant,,ENST00000527956,;NOX4,intron_variant,,ENST00000542487,;NOX4,intron_variant,,ENST00000343727,;NOX4,intron_variant,,ENST00000413594,;NOX4,intron_variant,,ENST00000532825,;NOX4,intron_variant,,ENST00000531342,;NOX4,intron_variant,,ENST00000527626,;NOX4,intron_variant,,ENST00000534731,;NOX4,intron_variant,,ENST00000263317,;NOX4,intron_variant,,ENST00000525196,;NOX4,intron_variant,,ENST00000528341,;NOX4,intron_variant,,ENST00000424319,;NOX4,intron_variant,,ENST00000525278,;NOX4,intron_variant,,ENST00000529343,;	A	ENSG00000086991	ENST00000263317	Transcript	intron_variant	.	.	.	.	.	rs750163966	.	.	-1	NOX4	HGNC	7891	protein_coding	YES	CCDS8285.1	ENSP00000263317	NOX4_HUMAN	E7EMD7_HUMAN	UPI000045655B	.	.	.	.	2/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGGGCGAGGTG	byFrequency	5	ESCA
MYBPC1	0	.	GRCh37	12	102061578	102061578	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2404A>G	p.Thr802Ala	p.T802A	ENST00000452455	22/30	52	41	10	47	47	0	MYBPC1,missense_variant,p.Thr765Ala,ENST00000536007,;MYBPC1,missense_variant,p.Thr758Ala,ENST00000547405,;MYBPC1,missense_variant,p.Thr802Ala,ENST00000550270,;MYBPC1,missense_variant,p.Thr809Ala,ENST00000361685,;MYBPC1,missense_variant,p.Thr685Ala,ENST00000551300,;MYBPC1,missense_variant,p.Thr809Ala,ENST00000361466,;MYBPC1,missense_variant,p.Thr802Ala,ENST00000452455,;MYBPC1,missense_variant,p.Thr815Ala,ENST00000549145,;MYBPC1,missense_variant,p.Thr771Ala,ENST00000392934,;MYBPC1,missense_variant,p.Thr784Ala,ENST00000553190,;MYBPC1,missense_variant,p.Thr784Ala,ENST00000545503,;MYBPC1,missense_variant,p.Thr802Ala,ENST00000441232,;MYBPC1,missense_variant,p.Thr802Ala,ENST00000360610,;MYBPC1,missense_variant,p.Thr770Ala,ENST00000547509,;MYBPC1,missense_variant,p.Thr772Ala,ENST00000541119,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000548532,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000548298,;MYBPC1,intron_variant,,ENST00000550501,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000549608,;	G	ENSG00000196091	ENST00000452455	Transcript	missense_variant	2506	2404	802	T/A	Aca/Gca	.	.	.	1	MYBPC1	HGNC	7549	protein_coding	YES	CCDS58268.1	ENSP00000400908	MYPC1_HUMAN	F8W1Z9_HUMAN	UPI0001AE6B26	.	deleterious(0.01)	benign(0.005)	22/30	.	PROSITE_profiles:PS50853,hmmpanther:PTHR19900:SF43,hmmpanther:PTHR19900,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCAACAGAT	.	5	ESCA
CRY1	0	.	GRCh37	12	107385586	107385586	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*194G>C	.	.	ENST00000008527	13/13	242	222	20	160	160	0	CRY1,3_prime_UTR_variant,,ENST00000008527,;MTERFD3,upstream_gene_variant,,ENST00000550496,;MTERFD3,upstream_gene_variant,,ENST00000240050,;MTERFD3,upstream_gene_variant,,ENST00000548101,;MTERFD3,upstream_gene_variant,,ENST00000392830,;CRY1,downstream_gene_variant,,ENST00000549356,;MTERFD3,upstream_gene_variant,,ENST00000552029,;MTERFD3,upstream_gene_variant,,ENST00000547115,;CRY1,non_coding_transcript_exon_variant,,ENST00000552790,;	G	ENSG00000008405	ENST00000008527	Transcript	3_prime_UTR_variant	2823	.	.	.	.	.	.	.	-1	CRY1	HGNC	2384	protein_coding	YES	CCDS9112.1	ENSP00000008527	CRY1_HUMAN	H0YHT0_HUMAN,A2I2P0_HUMAN	UPI0000073E80	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAGTTCTTTAT	.	3	ESCA
HVCN1	0	.	GRCh37	12	111087122	111087122	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*93G>C	.	.	ENST00000356742	7/7	46	25	21	32	32	0	HVCN1,3_prime_UTR_variant,,ENST00000439744,;HVCN1,3_prime_UTR_variant,,ENST00000356742,;HVCN1,3_prime_UTR_variant,,ENST00000242607,;TCTN1,3_prime_UTR_variant,,ENST00000551590,;HVCN1,intron_variant,,ENST00000548312,;TCTN1,downstream_gene_variant,,ENST00000377654,;TCTN1,downstream_gene_variant,,ENST00000397655,;HVCN1,downstream_gene_variant,,ENST00000549442,;TCTN1,downstream_gene_variant,,ENST00000397659,;TCTN1,downstream_gene_variant,,ENST00000549123,;TCTN1,downstream_gene_variant,,ENST00000463313,;TCTN1,downstream_gene_variant,,ENST00000397656,;TCTN1,downstream_gene_variant,,ENST00000495659,;TCTN1,downstream_gene_variant,,ENST00000490514,;TCTN1,downstream_gene_variant,,ENST00000547461,;TCTN1,downstream_gene_variant,,ENST00000460357,;TCTN1,downstream_gene_variant,,ENST00000480648,;TCTN1,downstream_gene_variant,,ENST00000464809,;HVCN1,downstream_gene_variant,,ENST00000547887,;TCTN1,downstream_gene_variant,,ENST00000481093,;TCTN1,downstream_gene_variant,,ENST00000485445,;TCTN1,downstream_gene_variant,,ENST00000491068,;TCTN1,downstream_gene_variant,,ENST00000552038,;	G	ENSG00000122986	ENST00000356742	Transcript	3_prime_UTR_variant	1669	.	.	.	.	.	.	.	-1	HVCN1	HGNC	28240	protein_coding	YES	CCDS31900.1	ENSP00000349181	HVCN1_HUMAN	F8W0B3_HUMAN,F8VPF7_HUMAN	UPI0000038CA3	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTCTCACC	.	5	ESCA
ACAD10	0	.	GRCh37	12	112143731	112143731	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.526G>C	p.Asp176His	p.D176H	ENST00000455480	4/22	62	30	31	49	49	0	ACAD10,missense_variant,p.Asp176His,ENST00000549590,;ACAD10,missense_variant,p.Asp176His,ENST00000313698,;ACAD10,missense_variant,p.Asp176His,ENST00000455480,;ACAD10,5_prime_UTR_variant,,ENST00000392636,;ACAD10,intron_variant,,ENST00000515283,;ACAD10,downstream_gene_variant,,ENST00000514615,;ACAD10,non_coding_transcript_exon_variant,,ENST00000413681,;ACAD10,non_coding_transcript_exon_variant,,ENST00000502746,;ACAD10,non_coding_transcript_exon_variant,,ENST00000509936,;ACAD10,non_coding_transcript_exon_variant,,ENST00000507135,;	C	ENSG00000111271	ENST00000455480	Transcript	missense_variant	703	526	176	D/H	Gat/Cat	COSM380864	.	.	1	ACAD10	HGNC	21597	protein_coding	YES	CCDS44973.1	ENSP00000389813	ACD10_HUMAN	F8VXK4_HUMAN,D6RFF6_HUMAN	UPI000013F5E7	.	deleterious(0)	probably_damaging(0.999)	4/22	.	Pfam_domain:PF13419,TIGRFAM_domain:TIGR01509,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR02247,Superfamily_domains:SSF56784,Prints_domain:PR00413	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTTGATGTG	.	5	ESCA
COX6A1	0	.	GRCh37	12	120875903	120875903	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-27C>T	.	.	ENST00000229379	1/3	69	36	33	67	67	0	COX6A1,5_prime_UTR_variant,,ENST00000229379,;AL021546.6,upstream_gene_variant,,ENST00000551806,;COX6A1,non_coding_transcript_exon_variant,,ENST00000550009,;COX6A1,upstream_gene_variant,,ENST00000549525,;	T	ENSG00000111775	ENST00000229379	Transcript	5_prime_UTR_variant	11	.	.	.	.	.	.	.	1	COX6A1	HGNC	2277	protein_coding	YES	CCDS9197.1	ENSP00000229379	CX6A1_HUMAN	Q9UEG9_HUMAN,H6SG15_HUMAN	UPI0000128144	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGCTTCCGGCG	.	5	ESCA
HCAR1	0	.	GRCh37	12	123214080	123214080	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.807G>A	p.Met269Ile	p.M269I	ENST00000432564	1/2	89	81	7	49	49	0	HCAR1,missense_variant,p.Met269Ile,ENST00000432564,;HCAR1,missense_variant,p.Met269Ile,ENST00000356987,;HCAR1,missense_variant,p.Met269Ile,ENST00000436083,;RP11-324E6.9,upstream_gene_variant,,ENST00000602891,;	T	ENSG00000196917	ENST00000432564	Transcript	missense_variant	1050	807	269	M/I	atG/atA	.	.	.	-1	HCAR1	HGNC	4532	protein_coding	YES	CCDS9236.1	ENSP00000389255	HCAR1_HUMAN	.	UPI000003BC7A	.	tolerated(0.08)	benign(0.003)	1/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24231:SF29,hmmpanther:PTHR24231,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CTGTTCATGTA	.	3	ESCA
EP400	0	.	GRCh37	12	132467003	132467003	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1909C>G	p.Gln637Glu	p.Q637E	ENST00000389561	5/53	23	14	9	26	26	0	EP400,missense_variant,p.Gln636Glu,ENST00000389562,;EP400,missense_variant,p.Gln600Glu,ENST00000332482,;EP400,missense_variant,p.Gln637Glu,ENST00000389561,;EP400,missense_variant,p.Gln673Glu,ENST00000333577,;EP400,missense_variant,p.Gln637Glu,ENST00000330386,;	G	ENSG00000183495	ENST00000389561	Transcript	missense_variant	2018	1909	637	Q/E	Cag/Gag	.	.	.	1	EP400	HGNC	11958	protein_coding	YES	CCDS31929.2	ENSP00000374212	EP400_HUMAN	.	UPI00004566BC	.	.	unknown(0)	5/53	.	hmmpanther:PTHR10799:SF599,hmmpanther:PTHR10799	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTCAGCTT	.	5	ESCA
PLEKHA5	0	.	GRCh37	12	19529232	19529232	+	3'UTR	SNP	G	G	C	rs541818547	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*779G>C	.	.	ENST00000429027	32/32	123	65	58	98	98	0	PLEKHA5,3_prime_UTR_variant,,ENST00000538972,;PLEKHA5,3_prime_UTR_variant,,ENST00000424268,;PLEKHA5,3_prime_UTR_variant,,ENST00000317589,;PLEKHA5,3_prime_UTR_variant,,ENST00000429027,;PLEKHA5,3_prime_UTR_variant,,ENST00000299275,;PLEKHA5,3_prime_UTR_variant,,ENST00000355397,;PLEKHA5,3_prime_UTR_variant,,ENST00000359180,;PLEKHA5,downstream_gene_variant,,ENST00000543806,;PLEKHA5,downstream_gene_variant,,ENST00000538714,;PLEKHA5,downstream_gene_variant,,ENST00000539256,;	C	ENSG00000052126	ENST00000429027	Transcript	3_prime_UTR_variant	4660	.	.	.	.	rs541818547	.	.	1	PLEKHA5	HGNC	30036	protein_coding	YES	CCDS58213.1	ENSP00000404296	PKHA5_HUMAN	F5H1X3_HUMAN,B4DHK5_HUMAN	UPI000204ABA8	.	.	.	32/32	.	.	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATGAGCAC	byCluster|by1000G	5	ESCA
CACNA1C	0	.	GRCh37	12	2783715	2783715	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4879G>C	p.Glu1627Gln	p.E1627Q	ENST00000347598	41/49	52	44	8	50	50	0	CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399644,;CACNA1C,missense_variant,p.Glu1587Gln,ENST00000399595,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000406454,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399617,;CACNA1C,missense_variant,p.Glu1627Gln,ENST00000347598,;CACNA1C,missense_variant,p.Glu1598Gln,ENST00000402845,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000327702,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399634,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399641,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399603,;CACNA1C,missense_variant,p.Glu1596Gln,ENST00000399629,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399601,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399597,;CACNA1C,missense_variant,p.Glu1579Gln,ENST00000399655,;CACNA1C,missense_variant,p.Glu1599Gln,ENST00000399606,;CACNA1C,missense_variant,p.Glu1598Gln,ENST00000399637,;CACNA1C,missense_variant,p.Glu1604Gln,ENST00000335762,;CACNA1C,missense_variant,p.Glu1587Gln,ENST00000399591,;CACNA1C,missense_variant,p.Glu1598Gln,ENST00000399621,;CACNA1C,missense_variant,p.Glu1607Gln,ENST00000399638,;CACNA1C,missense_variant,p.Glu1620Gln,ENST00000344100,;CACNA1C,missense_variant,p.Glu1585Gln,ENST00000399649,;CACNA1C-AS1,downstream_gene_variant,,ENST00000501371,;CACNA1C-AS2,upstream_gene_variant,,ENST00000545526,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000465934,;	C	ENSG00000151067	ENST00000347598	Transcript	missense_variant	4879	4879	1627	E/Q	Gaa/Caa	.	.	.	1	CACNA1C	HGNC	1390	protein_coding	YES	CCDS44788.1	ENSP00000266376	CAC1C_HUMAN	Q86XX0_HUMAN,O95234_HUMAN	UPI0000E593E5	.	deleterious(0.01)	possibly_damaging(0.877)	41/49	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTAGAACAA	.	5	ESCA
KDM5A	0	.	GRCh37	12	393434	393434	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1188G>C	.	.	ENST00000399788	28/28	125	75	50	95	95	0	KDM5A,3_prime_UTR_variant,,ENST00000399788,;KDM5A,downstream_gene_variant,,ENST00000382815,;KDM5A,downstream_gene_variant,,ENST00000540838,;	G	ENSG00000073614	ENST00000399788	Transcript	3_prime_UTR_variant	6624	.	.	.	.	.	.	.	-1	KDM5A	HGNC	9886	protein_coding	YES	CCDS41736.1	ENSP00000382688	KDM5A_HUMAN	.	UPI0000DB2E73	.	.	.	28/28	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ATAATCTATGT	.	4	ESCA
PLEKHA8P1	0	.	GRCh37	12	45567423	45567423	+	RNA	SNP	C	C	T	rs368700010	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.1263G>A	.	.	ENST00000256692	3/3	83	68	15	48	48	0	PLEKHA8P1,non_coding_transcript_exon_variant,,ENST00000256692,;PLEKHA8P1,downstream_gene_variant,,ENST00000545609,;PLEKHA8P1,downstream_gene_variant,,ENST00000550498,;PLEKHA8P1,non_coding_transcript_exon_variant,,ENST00000336399,;	T	ENSG00000134297	ENST00000256692	Transcript	non_coding_transcript_exon_variant	1263	.	.	.	.	rs368700010	.	.	-1	PLEKHA8P1	HGNC	30222	processed_transcript	YES	.	.	.	.	.	.	.	.	3/3	.	.	.	.	.	.	.	.	.	A:0.0002	A:0	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCATCTTAAC	byFrequency|byCluster	5	ESCA
PFKM	0	.	GRCh37	12	48531621	48531621	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1267G>A	p.Val423Ile	p.V423I	ENST00000340802	13/25	38	33	5	31	31	0	PFKM,missense_variant,p.Val423Ile,ENST00000340802,;PFKM,missense_variant,p.Val321Ile,ENST00000395233,;PFKM,missense_variant,p.Val352Ile,ENST00000547587,;PFKM,missense_variant,p.Val352Ile,ENST00000359794,;PFKM,missense_variant,p.Val352Ile,ENST00000312352,;PFKM,missense_variant,p.Val321Ile,ENST00000551804,;PFKM,intron_variant,,ENST00000546465,;PFKM,downstream_gene_variant,,ENST00000549003,;PFKM,downstream_gene_variant,,ENST00000549941,;PFKM,downstream_gene_variant,,ENST00000548345,;PFKM,downstream_gene_variant,,ENST00000550345,;PFKM,downstream_gene_variant,,ENST00000550924,;PFKM,downstream_gene_variant,,ENST00000551339,;PFKM,upstream_gene_variant,,ENST00000553055,;PFKM,downstream_gene_variant,,ENST00000549022,;PFKM,missense_variant,p.Val17Ile,ENST00000552752,;PFKM,3_prime_UTR_variant,,ENST00000547581,;PFKM,non_coding_transcript_exon_variant,,ENST00000546964,;PFKM,non_coding_transcript_exon_variant,,ENST00000547148,;PFKM,upstream_gene_variant,,ENST00000552818,;PFKM,upstream_gene_variant,,ENST00000550802,;PFKM,downstream_gene_variant,,ENST00000551485,;PFKM,downstream_gene_variant,,ENST00000552989,;PFKM,upstream_gene_variant,,ENST00000552214,;	A	ENSG00000152556	ENST00000340802	Transcript	missense_variant	1491	1267	423	V/I	Gtc/Atc	.	.	.	1	PFKM	HGNC	8877	protein_coding	YES	CCDS53786.1	ENSP00000345771	K6PF_HUMAN	Q7KYX9_HUMAN,P78457_HUMAN,F8W1J8_HUMAN,F8VZQ1_HUMAN,F8VYK8_HUMAN,F8VW30_HUMAN,F8VUB8_HUMAN,F8VSL1_HUMAN,F8VNX2_HUMAN	UPI0000D621DC	.	deleterious(0.02)	possibly_damaging(0.867)	13/25	.	Superfamily_domains:SSF53784,PIRSF_domain:PIRSF000533,TIGRFAM_domain:TIGR02478,Gene3D:3.40.50.450,hmmpanther:PTHR13697:SF13,hmmpanther:PTHR13697,HAMAP:MF_00339	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATGTGTCCAG	.	4	ESCA
KMT2D	0	.	GRCh37	12	49427918	49427918	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10672G>T	p.Glu3558Ter	p.E3558*	ENST00000301067	38/54	36	28	8	25	25	0	KMT2D,stop_gained,p.Glu3558Ter,ENST00000301067,;KMT2D,downstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,;	A	ENSG00000167548	ENST00000301067	Transcript	stop_gained	10672	10672	3558	E/*	Gaa/Taa	.	.	.	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	KMT2D_HUMAN	Q6PIA1_HUMAN,Q59FG6_HUMAN,F8VWW4_HUMAN	UPI0000EE84D6	.	.	.	38/54	.	hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF324	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTTCTGGGA	.	4	ESCA
NCKAP5L	0	.	GRCh37	12	50186476	50186476	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3634G>C	p.Glu1212Gln	p.E1212Q	ENST00000335999	11/13	22	16	6	22	22	0	NCKAP5L,missense_variant,p.Glu1212Gln,ENST00000335999,;NCKAP5L,missense_variant,p.Glu927Gln,ENST00000433948,;	G	ENSG00000167566	ENST00000335999	Transcript	missense_variant	3836	3634	1212	E/Q	Gag/Cag	.	.	.	-1	NCKAP5L	HGNC	29321	protein_coding	YES	CCDS41781.2	ENSP00000337998	NCK5L_HUMAN	.	UPI00006C1298	.	tolerated(1)	benign(0)	11/13	.	hmmpanther:PTHR21740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTCTCATGGC	.	5	ESCA
ATF1	0	.	GRCh37	12	51213786	51213786	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*224C>G	.	.	ENST00000262053	7/7	47	39	8	34	34	0	ATF1,3_prime_UTR_variant,,ENST00000262053,;ATF1,3_prime_UTR_variant,,ENST00000539132,;ATF1,3_prime_UTR_variant,,ENST00000551831,;	G	ENSG00000123268	ENST00000262053	Transcript	3_prime_UTR_variant	1062	.	.	.	.	.	.	.	1	ATF1	HGNC	783	protein_coding	YES	CCDS8803.1	ENSP00000262053	ATF1_HUMAN	F8VYN3_HUMAN,F8VS03_HUMAN,B4DRF9_HUMAN	UPI0000126227	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATATTCAAGGA	.	5	ESCA
SLC11A2	0	.	GRCh37	12	51393017	51393017	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.702G>A	p.%3D	p.R234R	ENST00000394904	8/16	87	80	7	58	58	0	SLC11A2,synonymous_variant,p.%3D,ENST00000541174,;SLC11A2,synonymous_variant,p.%3D,ENST00000262052,;SLC11A2,synonymous_variant,p.%3D,ENST00000394904,;SLC11A2,synonymous_variant,p.%3D,ENST00000547198,;SLC11A2,synonymous_variant,p.%3D,ENST00000545993,;SLC11A2,synonymous_variant,p.%3D,ENST00000546743,;SLC11A2,synonymous_variant,p.%3D,ENST00000547688,;SLC11A2,synonymous_variant,p.%3D,ENST00000547579,;SLC11A2,synonymous_variant,p.%3D,ENST00000262051,;SLC11A2,synonymous_variant,p.%3D,ENST00000546488,;SLC11A2,downstream_gene_variant,,ENST00000548193,;SLC11A2,downstream_gene_variant,,ENST00000547732,;SLC11A2,downstream_gene_variant,,ENST00000550714,;SLC11A2,downstream_gene_variant,,ENST00000549110,;SLC11A2,synonymous_variant,p.%3D,ENST00000546636,;SLC11A2,3_prime_UTR_variant,,ENST00000547510,;SLC11A2,non_coding_transcript_exon_variant,,ENST00000550061,;SLC11A2,upstream_gene_variant,,ENST00000550782,;	T	ENSG00000110911	ENST00000394904	Transcript	synonymous_variant	752	702	234	R	cgG/cgA	.	.	.	-1	SLC11A2	HGNC	10908	protein_coding	YES	CCDS53793.1	ENSP00000378364	NRAM2_HUMAN	F8W1P7_HUMAN,F8W1F2_HUMAN,F8W154_HUMAN,F8VZL6_HUMAN,F8VWB0_HUMAN,B3KY44_HUMAN	UPI00001FC234	.	.	.	8/16	.	HAMAP:MF_00221,hmmpanther:PTHR11706:SF27,hmmpanther:PTHR11706,TIGRFAM_domain:TIGR01197,Pfam_domain:PF01566,Prints_domain:PR00447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AGCTTCCGCAA	.	3	ESCA
CSRNP2	0	.	GRCh37	12	51457583	51457583	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1578G>C	p.Gln526His	p.Q526H	ENST00000228515	5/5	45	36	8	37	36	0	CSRNP2,missense_variant,p.Gln526His,ENST00000228515,;LETMD1,downstream_gene_variant,,ENST00000547008,;LETMD1,downstream_gene_variant,,ENST00000553043,;LETMD1,downstream_gene_variant,,ENST00000552739,;CSRNP2,downstream_gene_variant,,ENST00000548206,;LETMD1,downstream_gene_variant,,ENST00000418425,;LETMD1,downstream_gene_variant,,ENST00000551931,;LETMD1,downstream_gene_variant,,ENST00000550929,;LETMD1,downstream_gene_variant,,ENST00000262055,;LETMD1,downstream_gene_variant,,ENST00000547256,;LETMD1,downstream_gene_variant,,ENST00000380123,;LETMD1,downstream_gene_variant,,ENST00000547660,;LETMD1,downstream_gene_variant,,ENST00000548516,;LETMD1,downstream_gene_variant,,ENST00000549395,;LETMD1,downstream_gene_variant,,ENST00000546814,;LETMD1,downstream_gene_variant,,ENST00000552645,;LETMD1,downstream_gene_variant,,ENST00000550100,;LETMD1,downstream_gene_variant,,ENST00000550274,;LETMD1,downstream_gene_variant,,ENST00000547555,;LETMD1,downstream_gene_variant,,ENST00000380135,;LETMD1,downstream_gene_variant,,ENST00000547318,;LETMD1,downstream_gene_variant,,ENST00000547877,;LETMD1,downstream_gene_variant,,ENST00000549686,;	G	ENSG00000110925	ENST00000228515	Transcript	missense_variant	1876	1578	526	Q/H	caG/caC	.	.	.	-1	CSRNP2	HGNC	16006	protein_coding	YES	CCDS8807.1	ENSP00000228515	CSRN2_HUMAN	F8W1G8_HUMAN,F8VZY2_HUMAN,F8VVN1_HUMAN,F8VTU0_HUMAN	UPI0000073111	.	tolerated_low_confidence(0.12)	benign(0.14)	5/5	.	hmmpanther:PTHR13580:SF6,hmmpanther:PTHR13580	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCATTCTGCTG	.	4	ESCA
SCN8A	0	.	GRCh37	12	52056610	52056610	+	Silent	SNP	G	G	A	rs778177119	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>A	p.%3D	p.A3A	ENST00000354534	2/27	10	7	3	15	15	0	SCN8A,synonymous_variant,p.%3D,ENST00000550891,;SCN8A,synonymous_variant,p.%3D,ENST00000354534,;SCN8A,synonymous_variant,p.%3D,ENST00000355133,;SCN8A,synonymous_variant,p.%3D,ENST00000545061,;SCN8A,downstream_gene_variant,,ENST00000546961,;	A	ENSG00000196876	ENST00000354534	Transcript	synonymous_variant	187	9	3	A	gcG/gcA	rs778177119	.	.	1	SCN8A	HGNC	10596	protein_coding	YES	CCDS44891.1	ENSP00000346534	SCN8A_HUMAN	Q9P2Q6_HUMAN,Q8WWN3_HUMAN	UPI000006FD85	.	.	.	2/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCAGCGCGGCT	.	2	ESCA
RP11-923I11.6	0	.	GRCh37	12	52213863	52213863	+	RNA	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.2023G>C	.	.	ENST00000562343	2/2	28	21	7	19	19	0	RP11-923I11.6,non_coding_transcript_exon_variant,,ENST00000562343,;RP11-923I11.4,upstream_gene_variant,,ENST00000567167,;RP11-923I11.7,downstream_gene_variant,,ENST00000564840,;	C	ENSG00000261586	ENST00000562343	Transcript	non_coding_transcript_exon_variant	2023	.	.	.	.	.	.	.	1	RP11-923I11.6	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATGGAGAGA	.	5	ESCA
ACVR1B	0	.	GRCh37	12	52380666	52380666	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1324G>A	p.Ala442Thr	p.A442T	ENST00000541224	8/10	42	36	6	37	37	0	ACVR1B,missense_variant,p.Ala401Thr,ENST00000415850,;ACVR1B,missense_variant,p.Ala401Thr,ENST00000426655,;ACVR1B,missense_variant,p.Ala442Thr,ENST00000541224,;ACVR1B,missense_variant,p.Ala401Thr,ENST00000257963,;ACVR1B,missense_variant,p.Ala349Thr,ENST00000542485,;RNU6-574P,upstream_gene_variant,,ENST00000384265,;ACVR1B,intron_variant,,ENST00000563121,;	A	ENSG00000135503	ENST00000541224	Transcript	missense_variant	1367	1324	442	A/T	Gct/Act	.	.	.	1	ACVR1B	HGNC	172	protein_coding	YES	CCDS44894.2	ENSP00000442656	ACV1B_HUMAN	F5H5Q2_HUMAN	UPI0001915052	.	tolerated(0.17)	probably_damaging(0.999)	8/10	.	Superfamily_domains:SSF56112,SMART_domains:SM00220,Gene3D:1.10.510.10,Pfam_domain:PF00069,hmmpanther:PTHR23255:SF22,hmmpanther:PTHR23255,PROSITE_profiles:PS50011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.D443E|c.1329T>A|3,BUFFER|p.D402E|c.1206T>A|3	RADIA|MUTECT|MUSE|VARSCANS	AATGTGCTGAT	.	4	ESCA
KRT78	0	.	GRCh37	12	53242563	53242563	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.152C>G	p.Ser51Cys	p.S51C	ENST00000304620	1/9	38	28	9	35	35	0	KRT78,missense_variant,p.Ser51Cys,ENST00000304620,;KRT78,intron_variant,,ENST00000547110,;KRT78,upstream_gene_variant,,ENST00000359499,;KRT78,upstream_gene_variant,,ENST00000551581,;	C	ENSG00000170423	ENST00000304620	Transcript	missense_variant	216	152	51	S/C	tCt/tGt	.	.	.	-1	KRT78	HGNC	28926	protein_coding	YES	CCDS8840.1	ENSP00000306261	K2C78_HUMAN	F8VS93_HUMAN,B4DQ49_HUMAN	UPI00001AEDBE	.	deleterious(0.02)	possibly_damaging(0.7)	1/9	.	hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF127,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACGAGAGCCT	.	5	ESCA
NCKAP1L	0	.	GRCh37	12	54905766	54905766	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.818C>G	p.Ser273Cys	p.S273C	ENST00000293373	9/31	62	50	12	48	48	0	NCKAP1L,missense_variant,p.Ser273Cys,ENST00000293373,;NCKAP1L,missense_variant,p.Ser223Cys,ENST00000545638,;NCKAP1L,non_coding_transcript_exon_variant,,ENST00000552211,;NCKAP1L,missense_variant,p.Ser273Cys,ENST00000548221,;NCKAP1L,non_coding_transcript_exon_variant,,ENST00000548916,;	G	ENSG00000123338	ENST00000293373	Transcript	missense_variant	897	818	273	S/C	tCc/tGc	.	.	.	1	NCKAP1L	HGNC	4862	protein_coding	YES	CCDS31813.1	ENSP00000293373	NCKPL_HUMAN	Q9BV52_HUMAN,Q5XG97_HUMAN,B2RA26_HUMAN	UPI00001C0439	.	deleterious(0.01)	possibly_damaging(0.778)	9/31	.	hmmpanther:PTHR12093:SF9,hmmpanther:PTHR12093,Pfam_domain:PF09735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCCAATA	.	5	ESCA
ANO2	0	.	GRCh37	12	5672624	5672624	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2838G>C	p.%3D	p.L946L	ENST00000327087	26/26	28	13	15	14	14	0	ANO2,synonymous_variant,p.%3D,ENST00000327087,;ANO2,synonymous_variant,p.%3D,ENST00000546188,;ANO2,synonymous_variant,p.%3D,ENST00000356134,;ANO2,upstream_gene_variant,,ENST00000536751,;	G	ENSG00000047617	ENST00000327087	Transcript	synonymous_variant	2910	2838	946	L	ctG/ctC	.	.	.	-1	ANO2	HGNC	1183	protein_coding	YES	.	ENSP00000314048	ANO2_HUMAN	Q69YW4_HUMAN	UPI0001823FDD	.	.	.	26/26	.	hmmpanther:PTHR12308:SF20,hmmpanther:PTHR12308	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCAGGAA	.	5	ESCA
TIMELESS	0	.	GRCh37	12	56826260	56826260	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.580C>A	p.His194Asn	p.H194N	ENST00000553532	7/29	42	31	11	27	27	0	TIMELESS,missense_variant,p.His194Asn,ENST00000553532,;TIMELESS,missense_variant,p.His194Asn,ENST00000554616,;TIMELESS,missense_variant,p.His193Asn,ENST00000229201,;	T	ENSG00000111602	ENST00000553532	Transcript	missense_variant	731	580	194	H/N	Cac/Aac	.	.	.	-1	TIMELESS	HGNC	11813	protein_coding	YES	CCDS8918.1	ENSP00000450607	TIM_HUMAN	.	UPI000013C8EA	.	tolerated(0.05)	possibly_damaging(0.809)	7/29	.	Pfam_domain:PF04821,hmmpanther:PTHR22940:SF4,hmmpanther:PTHR22940	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGGTGAATCG	.	5	ESCA
HELB	0	.	GRCh37	12	66700240	66700240	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723G>C	p.Leu241Phe	p.L241F	ENST00000247815	3/13	97	87	9	89	89	0	HELB,missense_variant,p.Leu241Phe,ENST00000247815,;HELB,missense_variant,p.Leu241Phe,ENST00000440906,;HELB,missense_variant,p.Leu241Phe,ENST00000545134,;HELB,missense_variant,p.Leu241Phe,ENST00000542394,;	C	ENSG00000127311	ENST00000247815	Transcript	missense_variant	782	723	241	L/F	ttG/ttC	.	.	.	1	HELB	HGNC	17196	protein_coding	YES	CCDS8976.1	ENSP00000247815	HELB_HUMAN	.	UPI000013CC2D	.	deleterious(0.05)	possibly_damaging(0.473)	3/13	.	hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF97	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATGTTGAAAGA	.	4	ESCA
C1R	0	.	GRCh37	12	7188496	7188496	+	Silent	SNP	G	G	A	rs777050185	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1302C>T	p.%3D	p.R434R	ENST00000542285	11/11	28	18	10	19	19	0	C1R,synonymous_variant,p.%3D,ENST00000602480,;C1R,synonymous_variant,p.%3D,ENST00000542285,;C1R,synonymous_variant,p.%3D,ENST00000602286,;	A	ENSG00000159403	ENST00000542285	Transcript	synonymous_variant	1452	1302	434	R	cgC/cgT	rs777050185	.	.	-1	C1R	HGNC	1246	protein_coding	YES	.	ENSP00000438615	.	H0YFH3_HUMAN,F5H3A3_HUMAN,F5H1N6_HUMAN,F5GWL0_HUMAN	UPI00020653A8	.	.	.	11/11	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24265:SF78,hmmpanther:PTHR24265,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,PIRSF_domain:PIRSF001155,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCCCGCGCCC	byFrequency	5	ESCA
KRR1	0	.	GRCh37	12	75893570	75893570	+	3'UTR	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*19A>C	.	.	ENST00000229214	10/10	52	38	14	59	59	0	KRR1,3_prime_UTR_variant,,ENST00000229214,;GLIPR1,3_prime_UTR_variant,,ENST00000266659,;KRR1,downstream_gene_variant,,ENST00000438169,;GLIPR1,downstream_gene_variant,,ENST00000550491,;GLIPR1,downstream_gene_variant,,ENST00000456650,;GLIPR1,downstream_gene_variant,,ENST00000536703,;KRR1,downstream_gene_variant,,ENST00000551070,;	G	ENSG00000111615	ENST00000229214	Transcript	3_prime_UTR_variant	1189	.	.	.	.	.	.	.	-1	KRR1	HGNC	5176	protein_coding	YES	CCDS9012.1	ENSP00000229214	KRR1_HUMAN	.	UPI00001403EE	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTAGTCAAGG	.	5	ESCA
CCDC59	0	.	GRCh37	12	82752046	82752046	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.110G>T	p.Trp37Leu	p.W37L	ENST00000256151	1/4	70	55	15	36	36	0	CCDC59,missense_variant,p.Trp37Leu,ENST00000552377,;CCDC59,missense_variant,p.Trp37Leu,ENST00000256151,;METTL25,upstream_gene_variant,,ENST00000550058,;METTL25,upstream_gene_variant,,ENST00000248306,;METTL25,upstream_gene_variant,,ENST00000548200,;CCDC59,non_coding_transcript_exon_variant,,ENST00000552412,;CCDC59,intron_variant,,ENST00000548126,;METTL25,upstream_gene_variant,,ENST00000547985,;METTL25,upstream_gene_variant,,ENST00000547357,;METTL25,upstream_gene_variant,,ENST00000548569,;CCDC59,non_coding_transcript_exon_variant,,ENST00000552606,;CCDC59,intron_variant,,ENST00000547758,;CCDC59,upstream_gene_variant,,ENST00000550589,;	A	ENSG00000133773	ENST00000256151	Transcript	missense_variant	522	110	37	W/L	tGg/tTg	.	.	.	-1	CCDC59	HGNC	25005	protein_coding	YES	CCDS9023.1	ENSP00000256151	TAP26_HUMAN	.	UPI0000034DFE	.	deleterious(0)	probably_damaging(0.999)	1/4	.	Prints_domain:PR01854,hmmpanther:PTHR15657:SF1,hmmpanther:PTHR15657	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCGCCATGTC	.	5	ESCA
C12orf29	0	.	GRCh37	12	88442121	88442124	+	Frame_Shift_Del	DEL	TAAG	TAAG	-	rs754202444	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	TAAG	TAAG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.901_904delAAGT	p.Lys301ValfsTer7	p.K301Vfs*7	ENST00000356891	7/7	80	44	36	72	72	0	C12orf29,frameshift_variant,p.Lys301ValfsTer7,ENST00000356891,;CEP290,downstream_gene_variant,,ENST00000397838,;CEP290,downstream_gene_variant,,ENST00000309041,;CEP290,downstream_gene_variant,,ENST00000552810,;CEP290,downstream_gene_variant,,ENST00000547691,;RNA5SP364,upstream_gene_variant,,ENST00000516938,;C12orf29,downstream_gene_variant,,ENST00000549345,;C12orf29,downstream_gene_variant,,ENST00000548757,;C12orf29,3_prime_UTR_variant,,ENST00000552121,;C12orf29,3_prime_UTR_variant,,ENST00000550333,;C12orf29,non_coding_transcript_exon_variant,,ENST00000547468,;C12orf29,non_coding_transcript_exon_variant,,ENST00000548511,;C12orf29,downstream_gene_variant,,ENST00000453037,;C12orf29,downstream_gene_variant,,ENST00000552847,;C12orf29,downstream_gene_variant,,ENST00000552803,;	-	ENSG00000133641	ENST00000356891	Transcript	frameshift_variant	1103-1106	900-903	300-301	IK/X	atTAAG/at	rs754202444	.	.	1	C12orf29	HGNC	25322	protein_coding	YES	CCDS31866.1	ENSP00000349358	CL029_HUMAN	.	UPI000019908D	.	.	.	7/7	.	hmmpanther:PTHR31219,hmmpanther:PTHR31219:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TGATATTAAGTGTTT	byFrequency	3	ESCA
ATP2B1	0	.	GRCh37	12	90003718	90003718	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2438C>G	p.Ala813Gly	p.A813G	ENST00000428670	15/21	46	34	12	58	58	0	ATP2B1,missense_variant,p.Ala813Gly,ENST00000428670,;ATP2B1,missense_variant,p.Ala556Gly,ENST00000393164,;ATP2B1,missense_variant,p.Ala813Gly,ENST00000359142,;ATP2B1,missense_variant,p.Ala813Gly,ENST00000261173,;ATP2B1,missense_variant,p.Ala813Gly,ENST00000348959,;ATP2B1,non_coding_transcript_exon_variant,,ENST00000549727,;ATP2B1,non_coding_transcript_exon_variant,,ENST00000551009,;	C	ENSG00000070961	ENST00000428670	Transcript	missense_variant	2895	2438	813	A/G	gCa/gGa	.	.	.	-1	ATP2B1	HGNC	814	protein_coding	YES	CCDS9035.1	ENSP00000392043	AT2B1_HUMAN	Q3L582_HUMAN	UPI000002A436	.	deleterious(0)	possibly_damaging(0.663)	15/21	.	hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF245,TIGRFAM_domain:TIGR01494,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,Superfamily_domains:SSF56784,Prints_domain:PR00119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCATTGCAAAT	.	5	ESCA
ANKS1B	0	.	GRCh37	12	99447069	99447069	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2644G>A	p.Asp882Asn	p.D882N	ENST00000547776	17/26	63	52	10	57	57	0	ANKS1B,missense_variant,p.Asp108Asn,ENST00000546568,;ANKS1B,missense_variant,p.Asp108Asn,ENST00000549493,;ANKS1B,missense_variant,p.Asp108Asn,ENST00000550693,;ANKS1B,missense_variant,p.Asp108Asn,ENST00000546960,;ANKS1B,missense_variant,p.Asp108Asn,ENST00000332712,;ANKS1B,missense_variant,p.Asp882Asn,ENST00000329257,;ANKS1B,missense_variant,p.Asp51Asn,ENST00000549025,;ANKS1B,missense_variant,p.Asp154Asn,ENST00000550778,;ANKS1B,missense_variant,p.Asp108Asn,ENST00000549558,;ANKS1B,missense_variant,p.Asp77Asn,ENST00000547446,;ANKS1B,missense_variant,p.Asp458Asn,ENST00000547010,;ANKS1B,missense_variant,p.Asp882Asn,ENST00000547776,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000557083,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000552210,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000552245,;	T	ENSG00000185046	ENST00000547776	Transcript	missense_variant	2644	2644	882	D/N	Gat/Aat	.	.	.	-1	ANKS1B	HGNC	24600	protein_coding	YES	CCDS55872.1	ENSP00000449629	ANS1B_HUMAN	R4GN73_HUMAN,R4GN70_HUMAN,R4GN07_HUMAN	UPI00003FE521	.	deleterious(0.01)	probably_damaging(0.993)	17/26	.	hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3,Gene3D:1.10.150.50,SMART_domains:SM00454,Superfamily_domains:SSF47769	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCATCATGCC	.	5	ESCA
TMTC4	0	.	GRCh37	13	101266675	101266675	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1846C>G	p.Leu616Val	p.L616V	ENST00000342624	16/19	50	40	10	45	45	0	TMTC4,missense_variant,p.Leu597Val,ENST00000376234,;TMTC4,missense_variant,p.Leu486Val,ENST00000328767,;TMTC4,missense_variant,p.Leu616Val,ENST00000342624,;	C	ENSG00000125247	ENST00000342624	Transcript	missense_variant	2105	1846	616	L/V	Ctc/Gtc	.	.	.	-1	TMTC4	HGNC	25904	protein_coding	YES	CCDS9497.2	ENSP00000343871	TMTC4_HUMAN	C9K0R2_HUMAN	UPI000004B63E	.	tolerated(0.19)	benign(0.085)	16/19	.	PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF374,Gene3D:1.25.40.10,Pfam_domain:PF13414,SMART_domains:SM00028,Superfamily_domains:SSF48452	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGAGATCTG	.	5	ESCA
EFNB2	0	.	GRCh37	13	107187251	107187251	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.62G>C	p.Arg21Thr	p.R21T	ENST00000245323	1/5	137	101	35	90	90	0	EFNB2,missense_variant,p.Arg21Thr,ENST00000245323,;	G	ENSG00000125266	ENST00000245323	Transcript	missense_variant	212	62	21	R/T	aGa/aCa	.	.	.	-1	EFNB2	HGNC	3227	protein_coding	YES	CCDS9507.1	ENSP00000245323	EFNB2_HUMAN	Q2PDH7_HUMAN	UPI0000129C9B	.	tolerated(0.25)	benign(0.097)	1/5	.	hmmpanther:PTHR11304:SF18,hmmpanther:PTHR11304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCTGCAT	.	5	ESCA
COL4A2	0	.	GRCh37	13	111117830	111117830	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1855G>C	p.Gly619Arg	p.G619R	ENST00000360467	25/48	77	69	8	93	93	0	COL4A2,missense_variant,p.Gly619Arg,ENST00000360467,;COL4A2-AS2,upstream_gene_variant,,ENST00000458403,;COL4A2,downstream_gene_variant,,ENST00000478681,;COL4A2,upstream_gene_variant,,ENST00000494852,;	C	ENSG00000134871	ENST00000360467	Transcript	missense_variant	2161	1855	619	G/R	Ggc/Cgc	.	.	.	1	COL4A2	HGNC	2203	protein_coding	YES	CCDS41907.1	ENSP00000353654	CO4A2_HUMAN	A2A352_HUMAN	UPI000041C713	.	.	benign(0.013)	25/48	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF366,hmmpanther:PTHR24023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATGGGCCCC	.	4	ESCA
GAS6	0	.	GRCh37	13	114523706	114523706	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*131T>C	.	.	ENST00000327773	15/15	13	8	5	15	15	0	GAS6,3_prime_UTR_variant,,ENST00000355761,;GAS6,3_prime_UTR_variant,,ENST00000327773,;GAS6,3_prime_UTR_variant,,ENST00000357389,;GAS6,3_prime_UTR_variant,,ENST00000450766,;GAS6,3_prime_UTR_variant,,ENST00000418959,;GAS6-AS1,intron_variant,,ENST00000458001,;GAS6,non_coding_transcript_exon_variant,,ENST00000610073,;GAS6,non_coding_transcript_exon_variant,,ENST00000608763,;GAS6,non_coding_transcript_exon_variant,,ENST00000480426,;	G	ENSG00000183087	ENST00000327773	Transcript	3_prime_UTR_variant	2315	.	.	.	.	.	.	.	-1	GAS6	HGNC	4168	protein_coding	YES	CCDS45072.1	ENSP00000331831	GAS6_HUMAN	B4DZY7_HUMAN	UPI0000073CCA	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TACAGATATGT	.	3	ESCA
TPTE2	0	.	GRCh37	13	20039660	20039660	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.557G>T	p.Arg186Ile	p.R186I	ENST00000400230	8/20	171	152	19	120	120	0	TPTE2,missense_variant,p.Arg186Ile,ENST00000382977,;TPTE2,missense_variant,p.Arg109Ile,ENST00000255310,;TPTE2,missense_variant,p.Arg75Ile,ENST00000457266,;TPTE2,missense_variant,p.Arg146Ile,ENST00000382975,;TPTE2,missense_variant,p.Arg146Ile,ENST00000382978,;TPTE2,missense_variant,p.Arg109Ile,ENST00000390680,;TPTE2,missense_variant,p.Arg75Ile,ENST00000400103,;TPTE2,missense_variant,p.Arg186Ile,ENST00000400230,;TPTE2,missense_variant,p.Arg55Ile,ENST00000462409,;	A	ENSG00000132958	ENST00000400230	Transcript	missense_variant	602	557	186	R/I	aGa/aTa	COSM182365,COSM945747	.	.	-1	TPTE2	HGNC	17299	protein_coding	YES	CCDS45014.1	ENSP00000383089	TPTE2_HUMAN	.	UPI000040738D	.	deleterious(0)	probably_damaging(0.999)	8/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR12305,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAATTCTTATC	.	4	ESCA
DCLK1	0	.	GRCh37	13	36410271	36410271	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1128G>A	p.%3D	p.S376S	ENST00000255448	8/18	74	66	8	58	58	0	DCLK1,synonymous_variant,p.%3D,ENST00000360631,;DCLK1,synonymous_variant,p.%3D,ENST00000379893,;DCLK1,synonymous_variant,p.%3D,ENST00000255448,;	T	ENSG00000133083	ENST00000255448	Transcript	synonymous_variant	1340	1128	376	S	tcG/tcA	.	.	.	-1	DCLK1	HGNC	2700	protein_coding	YES	CCDS9354.1	ENSP00000255448	DCLK1_HUMAN	.	UPI000002A7C2	.	.	.	8/18	.	hmmpanther:PTHR24347:SF123,hmmpanther:PTHR24347	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTCCGACAC	.	4	ESCA
ELF1	0	.	GRCh37	13	41515340	41515340	+	Nonsense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.973C>T	p.Gln325Ter	p.Q325*	ENST00000239882	8/9	52	39	12	51	51	0	ELF1,stop_gained,p.Gln325Ter,ENST00000239882,;ELF1,stop_gained,p.Gln301Ter,ENST00000442101,;ELF1,non_coding_transcript_exon_variant,,ENST00000498824,;	A	ENSG00000120690	ENST00000239882	Transcript	stop_gained	1288	973	325	Q/*	Caa/Taa	.	.	.	-1	ELF1	HGNC	3316	protein_coding	YES	CCDS9374.1	ENSP00000239882	ELF1_HUMAN	Q6MZZ4_HUMAN,Q5T9E7_HUMAN,B3KTE9_HUMAN	UPI000007071F	.	.	.	8/9	.	hmmpanther:PTHR11849:SF156,hmmpanther:PTHR11849,Superfamily_domains:SSF46785	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTTTGATTCC	.	5	ESCA
FBXL3	0	.	GRCh37	13	77579580	77579580	+	3'UTR	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1700A>C	.	.	ENST00000355619	5/5	201	179	22	181	181	0	FBXL3,3_prime_UTR_variant,,ENST00000355619,;CLN5,downstream_gene_variant,,ENST00000377453,;FBXL3,downstream_gene_variant,,ENST00000417323,;FBXL3,intron_variant,,ENST00000477982,;FBXL3,intron_variant,,ENST00000485797,;	G	ENSG00000005812	ENST00000355619	Transcript	3_prime_UTR_variant	3312	.	.	.	.	.	.	.	-1	FBXL3	HGNC	13599	protein_coding	YES	CCDS9457.1	ENSP00000347834	FBXL3_HUMAN	.	UPI0000035C8B	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGTACTGTCAA	.	4	ESCA
MYCBP2	0	.	GRCh37	13	77671764	77671764	+	Missense_Mutation	SNP	G	G	C	rs776257927	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9411C>G	p.Ile3137Met	p.I3137M	ENST00000544440	56/83	64	49	15	44	44	0	MYCBP2,missense_variant,p.Ile3137Met,ENST00000544440,;MYCBP2,missense_variant,p.Ile3137Met,ENST00000357337,;MYCBP2,missense_variant,p.Ile3175Met,ENST00000407578,;MYCBP2,downstream_gene_variant,,ENST00000360084,;MYCBP2-AS1,intron_variant,,ENST00000593933,;MYCBP2,non_coding_transcript_exon_variant,,ENST00000485061,;MYCBP2,downstream_gene_variant,,ENST00000498073,;MYCBP2,downstream_gene_variant,,ENST00000462987,;MYCBP2,downstream_gene_variant,,ENST00000482517,;	C	ENSG00000005810	ENST00000544440	Transcript	missense_variant	9429	9411	3137	I/M	atC/atG	rs776257927	.	.	-1	MYCBP2	HGNC	23386	protein_coding	YES	.	ENSP00000444596	MYCB2_HUMAN	.	UPI0000212757	.	.	probably_damaging(0.983)	56/83	.	hmmpanther:PTHR12846:SF14,hmmpanther:PTHR12846	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTTTGATAGT	.	5	ESCA
SLITRK1	0	.	GRCh37	13	84453028	84453028	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*524C>T	.	.	ENST00000377084	1/1	27	21	6	21	21	0	SLITRK1,3_prime_UTR_variant,,ENST00000377084,;	A	ENSG00000178235	ENST00000377084	Transcript	3_prime_UTR_variant	3501	.	.	.	.	.	.	.	-1	SLITRK1	HGNC	20297	protein_coding	YES	CCDS9464.1	ENSP00000366288	SLIK1_HUMAN	.	UPI0000035971	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CATGCGAGCCA	.	2	ESCA
GPC6	0	.	GRCh37	13	93879852	93879852	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.143C>T	p.Pro48Leu	p.P48L	ENST00000377047	1/9	15	8	7	20	20	0	GPC6,missense_variant,p.Pro48Leu,ENST00000377047,;	T	ENSG00000183098	ENST00000377047	Transcript	missense_variant	758	143	48	P/L	cCc/cTc	.	.	.	1	GPC6	HGNC	4454	protein_coding	YES	CCDS9469.1	ENSP00000366246	GPC6_HUMAN	.	UPI0000032F5B	.	deleterious(0)	probably_damaging(0.982)	1/9	.	hmmpanther:PTHR10822:SF26,hmmpanther:PTHR10822,Pfam_domain:PF01153	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCCCCTACC	.	5	ESCA
GPR180	0	.	GRCh37	13	95271749	95271749	+	Silent	SNP	A	A	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.714A>C	p.%3D	p.P238P	ENST00000376958	5/9	69	57	12	51	51	0	GPR180,synonymous_variant,p.%3D,ENST00000376958,;	C	ENSG00000152749	ENST00000376958	Transcript	synonymous_variant	739	714	238	P	ccA/ccC	COSM1607267	.	.	1	GPR180	HGNC	28899	protein_coding	YES	CCDS9472.1	ENSP00000366157	GP180_HUMAN	.	UPI00001969C8	.	.	.	5/9	.	Pfam_domain:PF10192,hmmpanther:PTHR23252:SF26,hmmpanther:PTHR23252	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTACCATTTAT	.	5	ESCA
ABCC4	0	.	GRCh37	13	95858835	95858835	+	Nonsense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1112C>G	p.Ser371Ter	p.S371*	ENST00000376887	8/31	26	22	4	27	27	0	ABCC4,stop_gained,p.Ser371Ter,ENST00000431522,;ABCC4,stop_gained,p.Ser371Ter,ENST00000376887,;ABCC4,stop_gained,p.Ser371Ter,ENST00000412704,;ABCC4,stop_gained,p.Ser296Ter,ENST00000536256,;ABCC4,3_prime_UTR_variant,,ENST00000538287,;snoU13,upstream_gene_variant,,ENST00000459449,;	C	ENSG00000125257	ENST00000376887	Transcript	stop_gained	1227	1112	371	S/*	tCa/tGa	COSM1747538,COSM1747537	.	.	-1	ABCC4	HGNC	55	protein_coding	YES	CCDS9474.1	ENSP00000366084	MRP4_HUMAN	Q8IUA3_HUMAN	UPI00001A36E6	.	.	.	8/31	.	Superfamily_domains:SSF90123,Gene3D:2hydA01,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF205,PROSITE_profiles:PS50929,Transmembrane_helices:TMhelix	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCTGAGGGG	.	5	ESCA
PPP2R5C	0	.	GRCh37	14	102392292	102392292	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*683G>A	.	.	ENST00000422945	16/16	77	55	21	90	90	0	PPP2R5C,3_prime_UTR_variant,,ENST00000350249,;PPP2R5C,3_prime_UTR_variant,,ENST00000422945,;PPP2R5C,3_prime_UTR_variant,,ENST00000328724,;PPP2R5C,3_prime_UTR_variant,,ENST00000334743,;PPP2R5C,downstream_gene_variant,,ENST00000555237,;PPP2R5C,downstream_gene_variant,,ENST00000557268,;PPP2R5C,downstream_gene_variant,,ENST00000554147,;PPP2R5C,downstream_gene_variant,,ENST00000557071,;	A	ENSG00000078304	ENST00000422945	Transcript	3_prime_UTR_variant	2447	.	.	.	.	.	.	.	1	PPP2R5C	HGNC	9311	protein_coding	YES	CCDS53912.1	ENSP00000412324	2A5G_HUMAN	H0YJ75_HUMAN	UPI0001A7AE62	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGTAGAAGAG	.	5	ESCA
INF2	0	.	GRCh37	14	105172433	105172433	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763G>A	p.Asp255Asn	p.D255N	ENST00000392634	6/23	58	37	21	84	84	0	INF2,missense_variant,p.Asp255Asn,ENST00000330634,;INF2,missense_variant,p.Asp255Asn,ENST00000392634,;INF2,upstream_gene_variant,,ENST00000252527,;INF2,downstream_gene_variant,,ENST00000398337,;INF2,upstream_gene_variant,,ENST00000474229,;INF2,upstream_gene_variant,,ENST00000480763,;	A	ENSG00000203485	ENST00000392634	Transcript	missense_variant	875	763	255	D/N	Gac/Aac	.	.	.	1	INF2	HGNC	23791	protein_coding	YES	CCDS9989.2	ENSP00000376410	INF2_HUMAN	.	UPI000156D0FB	.	deleterious(0)	probably_damaging(0.999)	6/23	.	Low_complexity_(Seg):seg,PROSITE_profiles:PS51232,hmmpanther:PTHR23213:SF5,hmmpanther:PTHR23213,Pfam_domain:PF06367,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCGAGGACGAG	.	5	ESCA
JAG2	0	.	GRCh37	14	105617715	105617715	+	Missense_Mutation	SNP	G	G	C	rs372331234	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1172C>G	p.Ser391Trp	p.S391W	ENST00000331782	9/26	37	24	12	57	57	0	JAG2,missense_variant,p.Ser391Trp,ENST00000347004,;JAG2,missense_variant,p.Ser391Trp,ENST00000331782,;RP11-44N21.4,downstream_gene_variant,,ENST00000548203,;JAG2,upstream_gene_variant,,ENST00000546616,;JAG2,downstream_gene_variant,,ENST00000553051,;JAG2,upstream_gene_variant,,ENST00000553244,;	C	ENSG00000184916	ENST00000331782	Transcript	missense_variant	1576	1172	391	S/W	tCg/tGg	rs372331234,COSM1719192	.	.	-1	JAG2	HGNC	6189	protein_coding	YES	CCDS9998.1	ENSP00000328169	JAG2_HUMAN	.	UPI0000167BD5	.	deleterious(0)	probably_damaging(0.999)	9/26	.	PROSITE_profiles:PS50026,hmmpanther:PTHR24044:SF235,hmmpanther:PTHR24044,PROSITE_patterns:PS01187,Pfam_domain:PF00008,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196,Prints_domain:PR00010	.	.	.	.	.	.	.	A:0	A:0.0001	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTTCGAAGCA	byCluster	5	ESCA
SUPT16H	0	.	GRCh37	14	21852324	21852324	+	5'UTR	SNP	G	G	C	rs144114573	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-238C>G	.	.	ENST00000216297	1/26	16	10	5	19	19	0	SUPT16H,5_prime_UTR_variant,,ENST00000216297,;CHD8,downstream_gene_variant,,ENST00000557364,;SUPT16H,upstream_gene_variant,,ENST00000555943,;CHD8,downstream_gene_variant,,ENST00000553870,;CHD8,downstream_gene_variant,,ENST00000430710,;CHD8,downstream_gene_variant,,ENST00000399982,;RP11-524O1.4,upstream_gene_variant,,ENST00000565098,;SUPT16H,upstream_gene_variant,,ENST00000557652,;SUPT16H,upstream_gene_variant,,ENST00000555752,;SUPT16H,upstream_gene_variant,,ENST00000556217,;SUPT16H,upstream_gene_variant,,ENST00000556309,;CHD8,downstream_gene_variant,,ENST00000557727,;	C	ENSG00000092201	ENST00000216297	Transcript	5_prime_UTR_variant	102	.	.	.	.	rs144114573	.	.	-1	SUPT16H	HGNC	11465	protein_coding	YES	CCDS9569.1	ENSP00000216297	SP16H_HUMAN	.	UPI0000035D5C	.	.	.	1/26	.	.	A:0.0018	A:0.0068	A:0	.	A:0	A:0	A:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	ACGAGGGAAAA	byFrequency|by1000G	4	ESCA
TRAV8-4	0	.	GRCh37	14	22363081	22363081	+	Nonsense_Mutation	SNP	C	C	A	rs200696183	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.212C>A	p.Ser71Ter	p.S71*	ENST00000390438	2/2	61	43	18	58	58	0	TRAV8-4,stop_gained,p.Ser71Ter,ENST00000390438,;	A	ENSG00000211790	ENST00000390438	Transcript	stop_gained	340	212	71	S/*	tCa/tAa	rs200696183	.	.	1	TRAV8-4	HGNC	12149	TR_V_gene	YES	.	ENSP00000445942	TVA3_HUMAN	.	UPI000011C70D	.	.	.	2/2	.	PROSITE_profiles:PS50835,hmmpanther:PTHR19367,hmmpanther:PTHR19367:SF5,Gene3D:2.60.40.10,Pfam_domain:PF07686,Superfamily_domains:SSF48726	T:0.0006	T:0	T:0.0029	.	T:0	T:0.001	T:0	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACATCAGCGG	byFrequency|byCluster|by1000G	5	ESCA
RPL10L	0	.	GRCh37	14	47120658	47120658	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.282C>G	p.Phe94Leu	p.F94L	ENST00000298283	1/1	57	40	17	49	49	0	RPL10L,missense_variant,p.Phe94Leu,ENST00000298283,;	C	ENSG00000165496	ENST00000298283	Transcript	missense_variant	371	282	94	F/L	ttC/ttG	.	.	.	-1	RPL10L	HGNC	17976	protein_coding	YES	CCDS32071.1	ENSP00000298283	RL10L_HUMAN	.	UPI0000073CA8	.	deleterious(0.04)	benign(0.06)	1/1	.	hmmpanther:PTHR11726:SF9,hmmpanther:PTHR11726,TIGRFAM_domain:TIGR00279,Gene3D:3.90.1170.10,Pfam_domain:PF00252,PIRSF_domain:PIRSF005590,Superfamily_domains:SSF54686	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACATGGAAGGG	.	5	ESCA
TMX1	0	.	GRCh37	14	51721328	51721328	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*91G>C	.	.	ENST00000457354	8/8	73	51	22	71	71	0	TMX1,3_prime_UTR_variant,,ENST00000457354,;Y_RNA,upstream_gene_variant,,ENST00000364950,;TMX1,3_prime_UTR_variant,,ENST00000556683,;	C	ENSG00000139921	ENST00000457354	Transcript	3_prime_UTR_variant	1059	.	.	.	.	.	.	.	1	TMX1	HGNC	15487	protein_coding	YES	CCDS41953.1	ENSP00000393316	TMX1_HUMAN	.	UPI0000048EB4	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTGAATAT	.	5	ESCA
SIX4	0	.	GRCh37	14	61190785	61190785	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.8C>G	p.Ser3Cys	p.S3C	ENST00000216513	1/3	22	19	3	9	9	0	SIX4,missense_variant,p.Ser3Cys,ENST00000216513,;SIX4,intron_variant,,ENST00000556952,;SIX4,upstream_gene_variant,,ENST00000554079,;	C	ENSG00000100625	ENST00000216513	Transcript	missense_variant	68	8	3	S/C	tCt/tGt	.	.	.	-1	SIX4	HGNC	10890	protein_coding	YES	CCDS9749.2	ENSP00000216513	SIX4_HUMAN	.	UPI000066D924	.	deleterious_low_confidence(0)	probably_damaging(0.984)	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGAAGAGGAC	.	2	ESCA
KCNH5	0	.	GRCh37	14	63416702	63416702	+	Intron	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1369+149A>C	.	.	ENST00000322893	.	28	17	11	37	37	0	KCNH5,3_prime_UTR_variant,,ENST00000394964,;KCNH5,intron_variant,,ENST00000394968,;KCNH5,intron_variant,,ENST00000322893,;KCNH5,intron_variant,,ENST00000420622,;	G	ENSG00000140015	ENST00000322893	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	KCNH5	HGNC	6254	protein_coding	YES	CCDS9756.1	ENSP00000321427	KCNH5_HUMAN	.	UPI0000039E2D	.	.	.	.	7/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTATTTTCTAA	.	5	ESCA
ATP6V1D	0	.	GRCh37	14	67804908	67804908	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*430C>T	.	.	ENST00000216442	9/9	21	15	6	18	18	0	ATP6V1D,3_prime_UTR_variant,,ENST00000555474,;ATP6V1D,3_prime_UTR_variant,,ENST00000216442,;ATP6V1D,intron_variant,,ENST00000553408,;ATP6V1D,downstream_gene_variant,,ENST00000555723,;MPP5,downstream_gene_variant,,ENST00000555925,;MPP5,downstream_gene_variant,,ENST00000261681,;ATP6V1D,downstream_gene_variant,,ENST00000555431,;ATP6V1D,downstream_gene_variant,,ENST00000554236,;Y_RNA,upstream_gene_variant,,ENST00000362885,;ATP6V1D,upstream_gene_variant,,ENST00000553974,;ATP6V1D,intron_variant,,ENST00000555625,;ATP6V1D,intron_variant,,ENST00000554087,;	A	ENSG00000100554	ENST00000216442	Transcript	3_prime_UTR_variant	1725	.	.	.	.	.	.	.	-1	ATP6V1D	HGNC	13527	protein_coding	YES	CCDS9780.1	ENSP00000216442	VATD_HUMAN	H0YJH8_HUMAN,G3V5S7_HUMAN,G3V341_HUMAN,G3V2S6_HUMAN	UPI000013818E	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTTTGAGAAG	.	5	ESCA
NRXN3	0	.	GRCh37	14	80329346	80329346	+	3'Flank	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000554719	.	19	10	9	28	28	0	NRXN3,3_prime_UTR_variant,,ENST00000281127,;NRXN3,3_prime_UTR_variant,,ENST00000428277,;NRXN3,downstream_gene_variant,,ENST00000554719,;NRXN3,downstream_gene_variant,,ENST00000557594,;NRXN3,downstream_gene_variant,,ENST00000335750,;NRXN3,downstream_gene_variant,,ENST00000556003,;NRXN3,downstream_gene_variant,,ENST00000555387,;NRXN3,downstream_gene_variant,,ENST00000554738,;	A	ENSG00000021645	ENST00000554719	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	560	1	NRXN3	HGNC	8010	protein_coding	YES	CCDS9870.1	ENSP00000451648	NRX3A_HUMAN	G3V4R9_HUMAN,G3V247_HUMAN	UPI0000167BBA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTGAAATG	.	5	ESCA
KCNK13	0	.	GRCh37	14	90650758	90650758	+	Nonsense_Mutation	SNP	C	C	G	rs759324709	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.638C>G	p.Ser213Ter	p.S213*	ENST00000282146	2/2	18	12	6	27	27	0	KCNK13,stop_gained,p.Ser213Ter,ENST00000282146,;	G	ENSG00000152315	ENST00000282146	Transcript	stop_gained	1079	638	213	S/*	tCa/tGa	rs759324709	.	.	1	KCNK13	HGNC	6275	protein_coding	YES	CCDS9889.1	ENSP00000282146	KCNKD_HUMAN	B5TJL8_HUMAN	UPI0000127A55	.	.	.	2/2	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR11003:SF57,hmmpanther:PTHR11003,Gene3D:1.10.287.70,Pfam_domain:PF07885,Superfamily_domains:SSF81324,Prints_domain:PR01588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGCCTCAGCCA	.	5	ESCA
DDX24	0	.	GRCh37	14	94545833	94545833	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.256G>C	p.Glu86Gln	p.E86Q	ENST00000330836	2/9	20	16	4	21	21	0	DDX24,missense_variant,p.Glu43Gln,ENST00000555054,;DDX24,missense_variant,p.Glu86Gln,ENST00000330836,;DDX24,intron_variant,,ENST00000544005,;IFI27L1,upstream_gene_variant,,ENST00000555523,;IFI27L1,upstream_gene_variant,,ENST00000557066,;IFI27L1,upstream_gene_variant,,ENST00000554544,;IFI27L1,upstream_gene_variant,,ENST00000555341,;IFI27L1,upstream_gene_variant,,ENST00000554166,;IFI27L1,upstream_gene_variant,,ENST00000553664,;IFI27L1,upstream_gene_variant,,ENST00000556381,;IFI27L1,upstream_gene_variant,,ENST00000393115,;IFI27L1,upstream_gene_variant,,ENST00000557218,;IFI27L1,upstream_gene_variant,,ENST00000553350,;IFI27L1,upstream_gene_variant,,ENST00000555065,;DDX24,non_coding_transcript_exon_variant,,ENST00000555324,;DDX24,non_coding_transcript_exon_variant,,ENST00000555762,;IFI27L1,upstream_gene_variant,,ENST00000557600,;	G	ENSG00000089737	ENST00000330836	Transcript	missense_variant	388	256	86	E/Q	Gag/Cag	.	.	.	-1	DDX24	HGNC	13266	protein_coding	YES	CCDS9918.1	ENSP00000328690	DDX24_HUMAN	G3V529_HUMAN,F5GYL3_HUMAN	UPI0000129082	.	tolerated(0.16)	benign(0.011)	2/9	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCCTCTT	.	5	ESCA
BCL11B	0	.	GRCh37	14	99636165	99636165	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4323C>G	.	.	ENST00000357195	4/4	36	24	12	31	31	0	BCL11B,3_prime_UTR_variant,,ENST00000345514,;BCL11B,3_prime_UTR_variant,,ENST00000357195,;BCL11B,downstream_gene_variant,,ENST00000443726,;	C	ENSG00000127152	ENST00000357195	Transcript	3_prime_UTR_variant	7018	.	.	.	.	.	.	.	-1	BCL11B	HGNC	13222	protein_coding	YES	CCDS9950.1	ENSP00000349723	BC11B_HUMAN	L8B7P7_HUMAN	UPI000006E083	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTTAGAGTAA	.	5	ESCA
NPAP1	0	.	GRCh37	15	24921665	24921665	+	Silent	SNP	A	A	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.651A>T	p.%3D	p.S217S	ENST00000329468	1/1	50	40	10	23	23	0	NPAP1,synonymous_variant,p.%3D,ENST00000329468,;	T	ENSG00000185823	ENST00000329468	Transcript	synonymous_variant	1125	651	217	S	tcA/tcT	.	.	.	1	NPAP1	HGNC	1190	protein_coding	YES	CCDS10015.1	ENSP00000333735	NPAP1_HUMAN	.	UPI00001AFA1B	.	.	.	1/1	.	hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15,Pfam_domain:PF15229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCAGAAAA	.	5	ESCA
MEIS2	0	.	GRCh37	15	37183707	37183707	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*667G>C	.	.	ENST00000561208	12/12	63	45	18	62	62	0	MEIS2,3_prime_UTR_variant,,ENST00000219869,;MEIS2,3_prime_UTR_variant,,ENST00000397624,;MEIS2,3_prime_UTR_variant,,ENST00000338564,;MEIS2,3_prime_UTR_variant,,ENST00000340545,;MEIS2,3_prime_UTR_variant,,ENST00000444725,;MEIS2,3_prime_UTR_variant,,ENST00000382766,;MEIS2,3_prime_UTR_variant,,ENST00000559085,;MEIS2,3_prime_UTR_variant,,ENST00000557796,;MEIS2,3_prime_UTR_variant,,ENST00000561208,;MEIS2,downstream_gene_variant,,ENST00000424352,;MEIS2,downstream_gene_variant,,ENST00000559561,;MEIS2,downstream_gene_variant,,ENST00000397620,;MEIS2,downstream_gene_variant,,ENST00000607277,;RP11-122D10.1,upstream_gene_variant,,ENST00000558089,;MEIS2,downstream_gene_variant,,ENST00000559408,;MEIS2,3_prime_UTR_variant,,ENST00000314177,;MEIS2,3_prime_UTR_variant,,ENST00000560570,;MEIS2,non_coding_transcript_exon_variant,,ENST00000560702,;MEIS2,downstream_gene_variant,,ENST00000561264,;MEIS2,downstream_gene_variant,,ENST00000559371,;RP11-122D10.1,upstream_gene_variant,,ENST00000561259,;MEIS2,downstream_gene_variant,,ENST00000558643,;MEIS2,downstream_gene_variant,,ENST00000559972,;MEIS2,downstream_gene_variant,,ENST00000557992,;MEIS2,downstream_gene_variant,,ENST00000561284,;	G	ENSG00000134138	ENST00000561208	Transcript	3_prime_UTR_variant	2520	.	.	.	.	.	.	.	-1	MEIS2	HGNC	7001	protein_coding	YES	CCDS10044.1	ENSP00000453793	MEIS2_HUMAN	H0YKN2_HUMAN,H0YKE5_HUMAN	UPI000012EEBC	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAATCTTCAT	.	5	ESCA
C15orf54	0	.	GRCh37	15	39545303	39545303	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*415G>A	.	.	ENST00000318578	2/2	142	116	26	95	95	0	C15orf54,3_prime_UTR_variant,,ENST00000318578,;C15orf54,downstream_gene_variant,,ENST00000561223,;RP11-624L4.1,intron_variant,,ENST00000561058,;RP11-624L4.1,intron_variant,,ENST00000558209,;RP11-624L4.1,intron_variant,,ENST00000560484,;	A	ENSG00000175746	ENST00000318578	Transcript	3_prime_UTR_variant	1335	.	.	.	.	.	.	.	1	C15orf54	HGNC	33797	protein_coding	YES	CCDS10049.1	ENSP00000323686	CO054_HUMAN	.	UPI00000717BB	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAAACGAAGTT	.	5	ESCA
RPUSD2	0	.	GRCh37	15	40864051	40864051	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.855G>C	p.Lys285Asn	p.K285N	ENST00000315616	2/3	31	24	7	18	18	0	RPUSD2,missense_variant,p.Lys224Asn,ENST00000559271,;RPUSD2,missense_variant,p.Lys285Asn,ENST00000315616,;	C	ENSG00000166133	ENST00000315616	Transcript	missense_variant	893	855	285	K/N	aaG/aaC	.	.	.	1	RPUSD2	HGNC	24180	protein_coding	YES	CCDS10061.1	ENSP00000323288	RUSD2_HUMAN	B4DWW6_HUMAN	UPI0000163919	.	deleterious(0)	probably_damaging(0.992)	2/3	.	hmmpanther:PTHR10436,hmmpanther:PTHR10436:SF87,TIGRFAM_domain:TIGR00005,Pfam_domain:PF00849,Superfamily_domains:SSF55120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCAAGACAGC	.	5	ESCA
DLL4	0	.	GRCh37	15	41231089	41231089	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*857C>G	.	.	ENST00000249749	11/11	92	56	35	90	90	0	DLL4,3_prime_UTR_variant,,ENST00000249749,;DLL4,downstream_gene_variant,,ENST00000559440,;	G	ENSG00000128917	ENST00000249749	Transcript	3_prime_UTR_variant	3191	.	.	.	.	.	.	.	1	DLL4	HGNC	2910	protein_coding	YES	CCDS45232.1	ENSP00000249749	DLL4_HUMAN	.	UPI0000047825	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTCAAAGC	.	5	ESCA
MYO5C	0	.	GRCh37	15	52527916	52527916	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2913G>A	p.%3D	p.Q971Q	ENST00000261839	23/41	37	25	12	35	35	0	MYO5C,synonymous_variant,p.%3D,ENST00000261839,;MYO5C,3_prime_UTR_variant,,ENST00000443683,;MYO5C,3_prime_UTR_variant,,ENST00000558902,;MYO5C,3_prime_UTR_variant,,ENST00000560809,;MYO5C,downstream_gene_variant,,ENST00000559434,;	T	ENSG00000128833	ENST00000261839	Transcript	synonymous_variant	3075	2913	971	Q	caG/caA	.	.	.	-1	MYO5C	HGNC	7604	protein_coding	YES	CCDS42036.1	ENSP00000261839	MYO5C_HUMAN	Q14783_HUMAN,H0YM93_HUMAN	UPI000013D20E	.	.	.	23/41	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF313,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCTGTGT	.	5	ESCA
RFX7	0	.	GRCh37	15	56394372	56394372	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.598G>C	p.Asp200His	p.D200H	ENST00000423270	6/9	56	46	10	62	62	0	RFX7,missense_variant,p.Asp200His,ENST00000423270,;RFX7,missense_variant,p.Asp103His,ENST00000559447,;RFX7,missense_variant,p.Asp200His,ENST00000317318,;RFX7,missense_variant,p.Asp103His,ENST00000422057,;RFX7,downstream_gene_variant,,ENST00000560792,;RFX7,missense_variant,p.Asp103His,ENST00000559847,;	G	ENSG00000181827	ENST00000423270	Transcript	missense_variant	598	598	200	D/H	Gat/Cat	.	.	.	-1	RFX7	HGNC	25777	protein_coding	YES	.	ENSP00000397644	RFX7_HUMAN	H0YMH6_HUMAN,H0YLP2_HUMAN	UPI000057809D	.	deleterious(0)	probably_damaging(0.973)	6/9	.	hmmpanther:PTHR12619:SF2,hmmpanther:PTHR12619	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCATCTCCAG	.	5	ESCA
HCN4	0	.	GRCh37	15	73614969	73614969	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3465G>T	p.Lys1155Asn	p.K1155N	ENST00000261917	8/8	13	5	8	9	9	0	HCN4,missense_variant,p.Lys1155Asn,ENST00000261917,;	A	ENSG00000138622	ENST00000261917	Transcript	missense_variant	4459	3465	1155	K/N	aaG/aaT	.	.	.	-1	HCN4	HGNC	16882	protein_coding	YES	CCDS10248.1	ENSP00000261917	HCN4_HUMAN	.	UPI000003FFB5	.	deleterious_low_confidence(0.01)	probably_damaging(0.916)	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GATGTCTTCCG	.	2	ESCA
RPP25	0	.	GRCh37	15	75249552	75249552	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-628G>C	.	.	ENST00000322177	1/1	51	27	24	57	57	0	RPP25,5_prime_UTR_variant,,ENST00000322177,;RPP25,upstream_gene_variant,,ENST00000499788,;SCAMP5,upstream_gene_variant,,ENST00000568423,;	G	ENSG00000178718	ENST00000322177	Transcript	5_prime_UTR_variant	254	.	.	.	.	.	.	.	-1	RPP25	HGNC	30361	protein_coding	YES	CCDS10274.1	ENSP00000317691	RPP25_HUMAN	.	UPI0000072730	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCAAGGA	.	5	ESCA
HMG20A	0	.	GRCh37	15	77777784	77777784	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2479G>A	.	.	ENST00000381714	11/11	52	29	22	73	73	0	HMG20A,3_prime_UTR_variant,,ENST00000336216,;HMG20A,3_prime_UTR_variant,,ENST00000381714,;HMG20A,non_coding_transcript_exon_variant,,ENST00000558288,;HMG20A,downstream_gene_variant,,ENST00000559728,;	A	ENSG00000140382	ENST00000381714	Transcript	3_prime_UTR_variant	3951	.	.	.	.	.	.	.	1	HMG20A	HGNC	5001	protein_coding	YES	CCDS10295.1	ENSP00000371133	HM20A_HUMAN	H0YNS8_HUMAN,H0YMS9_HUMAN,H0YM80_HUMAN,H0YKM5_HUMAN,H0YK55_HUMAN,B4DMG1_HUMAN	UPI00000737EF	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTGACTGA	.	5	ESCA
CHRNA5	0	.	GRCh37	15	78873159	78873159	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113C>G	p.Ser38Cys	p.S38C	ENST00000299565	2/6	169	111	58	150	150	0	CHRNA5,missense_variant,p.Ser38Cys,ENST00000559554,;CHRNA5,missense_variant,p.Ser38Cys,ENST00000299565,;CHRNA5,upstream_gene_variant,,ENST00000394802,;	G	ENSG00000169684	ENST00000299565	Transcript	missense_variant	313	113	38	S/C	tCt/tGt	.	.	.	1	CHRNA5	HGNC	1959	protein_coding	YES	CCDS10304.1	ENSP00000299565	ACHA5_HUMAN	Q6EWN4_HUMAN	UPI0000001638	.	tolerated(0.08)	possibly_damaging(0.579)	2/6	.	hmmpanther:PTHR18945:SF76,hmmpanther:PTHR18945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTATCTGAAC	.	5	ESCA
AKAP13	0	.	GRCh37	15	86118491	86118491	+	Silent	SNP	A	A	G	rs139228217	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792A>G	p.%3D	p.E264E	ENST00000361243	6/37	54	34	19	33	33	0	AKAP13,synonymous_variant,p.%3D,ENST00000394518,;AKAP13,synonymous_variant,p.%3D,ENST00000559362,;AKAP13,synonymous_variant,p.%3D,ENST00000558166,;AKAP13,synonymous_variant,p.%3D,ENST00000361243,;AKAP13,synonymous_variant,p.%3D,ENST00000558811,;RP11-815J21.2,downstream_gene_variant,,ENST00000561409,;	G	ENSG00000170776	ENST00000361243	Transcript	synonymous_variant	873	792	264	E	gaA/gaG	rs139228217	.	.	1	AKAP13	HGNC	371	protein_coding	YES	CCDS32320.1	ENSP00000354718	AKP13_HUMAN	H0YMI5_HUMAN,A8MYJ1_HUMAN	UPI00001A8BEB	.	.	.	6/37	.	hmmpanther:PTHR13944:SF4,hmmpanther:PTHR13944	G:0.0002	G:0	G:0	.	G:0	G:0.001	G:0	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATGAACACCC	byCluster|by1000G	5	ESCA
ERCC4	0	.	GRCh37	16	14042187	14042187	+	Missense_Mutation	SNP	G	G	A	rs150077735	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2734G>A	p.Gly912Arg	p.G912R	ENST00000311895	11/11	66	60	5	41	41	0	ERCC4,missense_variant,p.Gly912Arg,ENST00000311895,;CTD-2135D7.3,upstream_gene_variant,,ENST00000576600,;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,;ERCC4,downstream_gene_variant,,ENST00000462862,;	A	ENSG00000175595	ENST00000311895	Transcript	missense_variant	2743	2734	912	G/R	Gga/Aga	rs150077735	.	.	1	ERCC4	HGNC	3436	protein_coding	YES	CCDS32390.1	ENSP00000310520	XPF_HUMAN	B4DXD8_HUMAN	UPI0000161BBF	.	deleterious(0.01)	possibly_damaging(0.448)	11/11	.	hmmpanther:PTHR10150	A:0.0002	A:0	A:0	.	A:0.001	A:0	A:0	.	.	not_provided	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAAAAGGAAAA	byCluster|by1000G	3	ESCA
IGFALS	0	.	GRCh37	16	1841183	1841183	+	Silent	SNP	G	G	C	rs774118306	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1350C>G	p.%3D	p.L450L	ENST00000415638	2/2	36	32	4	30	30	0	IGFALS,synonymous_variant,p.%3D,ENST00000415638,;IGFALS,synonymous_variant,p.%3D,ENST00000215539,;SPSB3,intron_variant,,ENST00000569769,;NUBP2,downstream_gene_variant,,ENST00000565134,;NUBP2,downstream_gene_variant,,ENST00000565987,;HAGH,downstream_gene_variant,,ENST00000564445,;NUBP2,downstream_gene_variant,,ENST00000262302,;NUBP2,downstream_gene_variant,,ENST00000562263,;NUBP2,downstream_gene_variant,,ENST00000543305,;IGFALS,downstream_gene_variant,,ENST00000568221,;NUBP2,downstream_gene_variant,,ENST00000563136,;NUBP2,downstream_gene_variant,,ENST00000568287,;NUBP2,downstream_gene_variant,,ENST00000568706,;NUBP2,downstream_gene_variant,,ENST00000569898,;NUBP2,downstream_gene_variant,,ENST00000565603,;NUBP2,downstream_gene_variant,,ENST00000563821,;NUBP2,downstream_gene_variant,,ENST00000566447,;NUBP2,downstream_gene_variant,,ENST00000567700,;NUBP2,downstream_gene_variant,,ENST00000568834,;NUBP2,downstream_gene_variant,,ENST00000564227,;NUBP2,downstream_gene_variant,,ENST00000566090,;	C	ENSG00000099769	ENST00000415638	Transcript	synonymous_variant	1430	1350	450	L	ctC/ctG	rs774118306	.	.	-1	IGFALS	HGNC	5468	protein_coding	YES	CCDS53982.1	ENSP00000416683	ALS_HUMAN	.	UPI00019863AB	.	.	.	2/2	.	PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF67,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	CGGCGGAGCCC	.	2	ESCA
SMG1	0	.	GRCh37	16	18937412	18937412	+	5'UTR	SNP	G	G	C	rs757287158	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-49C>G	.	.	ENST00000446231	1/63	25	18	7	25	25	0	SMG1,5_prime_UTR_variant,,ENST00000389467,;SMG1,5_prime_UTR_variant,,ENST00000532700,;SMG1,5_prime_UTR_variant,,ENST00000446231,;SMG1,upstream_gene_variant,,ENST00000569122,;AC092287.1,downstream_gene_variant,,ENST00000580939,;CTD-2288F12.1,upstream_gene_variant,,ENST00000565782,;SMG1,upstream_gene_variant,,ENST00000567737,;	C	ENSG00000157106	ENST00000446231	Transcript	5_prime_UTR_variant	365	.	.	.	.	rs757287158	.	.	-1	SMG1	HGNC	30045	protein_coding	YES	CCDS45430.1	ENSP00000402515	SMG1_HUMAN	H3BPS6_HUMAN	UPI00004F8E22	.	.	.	1/63	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGCGAGTCG	.	5	ESCA
C16orf62	0	.	GRCh37	16	19628044	19628044	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1405C>T	p.Gln469Ter	p.Q469*	ENST00000438132	14/31	76	55	21	72	72	0	C16orf62,stop_gained,p.Gln382Ter,ENST00000513947,;C16orf62,stop_gained,p.Gln129Ter,ENST00000543152,;C16orf62,stop_gained,p.Gln380Ter,ENST00000251143,;C16orf62,stop_gained,p.Gln469Ter,ENST00000438132,;C16orf62,stop_gained,p.Gln59Ter,ENST00000538552,;C16orf62,stop_gained,p.Gln230Ter,ENST00000448695,;C16orf62,intron_variant,,ENST00000417362,;C16orf62,intron_variant,,ENST00000542263,;C16orf62,downstream_gene_variant,,ENST00000540101,;C16orf62,non_coding_transcript_exon_variant,,ENST00000535164,;C16orf62,non_coding_transcript_exon_variant,,ENST00000541153,;C16orf62,non_coding_transcript_exon_variant,,ENST00000539705,;	T	ENSG00000103544	ENST00000438132	Transcript	stop_gained	1453	1405	469	Q/*	Caa/Taa	.	.	.	1	C16orf62	HGNC	24641	protein_coding	YES	CCDS32397.2	ENSP00000400815	.	I3L1U5_HUMAN,H3BV68_HUMAN,E7EWW0_HUMAN	UPI0001E1129C	.	.	.	14/31	.	hmmpanther:PTHR13673,hmmpanther:PTHR13673:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTCCAAGGA	.	5	ESCA
TBC1D24	0	.	GRCh37	16	2552628	2552628	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1669C>G	.	.	ENST00000293970	8/8	29	25	4	29	29	0	TBC1D24,3_prime_UTR_variant,,ENST00000293970,;TBC1D24,3_prime_UTR_variant,,ENST00000564879,;TBC1D24,3_prime_UTR_variant,,ENST00000567020,;RP11-20I23.1,intron_variant,,ENST00000564543,;TBC1D24,downstream_gene_variant,,ENST00000434757,;TBC1D24,downstream_gene_variant,,ENST00000569874,;	G	ENSG00000162065	ENST00000293970	Transcript	3_prime_UTR_variant	3482	.	.	.	.	.	.	.	1	TBC1D24	HGNC	29203	protein_coding	YES	CCDS55980.1	ENSP00000293970	TBC24_HUMAN	H3BV07_HUMAN,H3BNU1_HUMAN	UPI000041A97A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAACTCAGTTT	.	4	ESCA
SEZ6L2	0	.	GRCh37	16	29899913	29899913	+	Silent	SNP	G	G	A	rs776839200	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.987C>T	p.%3D	p.I329I	ENST00000308713	6/17	37	22	15	30	30	0	SEZ6L2,synonymous_variant,p.%3D,ENST00000308713,;SEZ6L2,synonymous_variant,p.%3D,ENST00000350527,;SEZ6L2,synonymous_variant,p.%3D,ENST00000346932,;SEZ6L2,synonymous_variant,p.%3D,ENST00000537485,;SEZ6L2,coding_sequence_variant,p.%3D,ENST00000563118,;SEZ6L2,non_coding_transcript_exon_variant,,ENST00000562159,;SEZ6L2,upstream_gene_variant,,ENST00000568407,;	A	ENSG00000174938	ENST00000308713	Transcript	synonymous_variant	1515	987	329	I	atC/atT	rs776839200	.	.	-1	SEZ6L2	HGNC	30844	protein_coding	YES	CCDS10659.1	ENSP00000312550	SE6L2_HUMAN	B3KNF3_HUMAN	UPI0000366B1B	.	.	.	6/17	.	PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF16,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCAGATGAG	.	5	ESCA
SEPT1	0	.	GRCh37	16	30392739	30392739	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.376G>C	p.Glu126Gln	p.E126Q	ENST00000605106	5/11	85	59	25	83	83	0	SEPT1,missense_variant,p.Glu121Gln,ENST00000571393,;SEPT1,missense_variant,p.Glu93Gln,ENST00000566517,;SEPT1,missense_variant,p.Glu126Gln,ENST00000605106,;SEPT1,missense_variant,p.Glu168Gln,ENST00000321367,;ZNF48,intron_variant,,ENST00000495929,;ZNF48,intron_variant,,ENST00000528032,;MYLPF,downstream_gene_variant,,ENST00000566955,;MYLPF,downstream_gene_variant,,ENST00000322861,;MYLPF,downstream_gene_variant,,ENST00000568749,;MYLPF,downstream_gene_variant,,ENST00000563718,;SEPT1,downstream_gene_variant,,ENST00000570039,;SEPT1,downstream_gene_variant,,ENST00000567783,;SEPT1,3_prime_UTR_variant,,ENST00000568577,;SEPT1,3_prime_UTR_variant,,ENST00000572252,;SEPT1,non_coding_transcript_exon_variant,,ENST00000573615,;SEPT1,non_coding_transcript_exon_variant,,ENST00000563957,;MYLPF,downstream_gene_variant,,ENST00000563728,;SEPT1,downstream_gene_variant,,ENST00000563743,;SEPT1,downstream_gene_variant,,ENST00000562152,;	G	ENSG00000270466	ENST00000605106	Transcript	missense_variant	376	376	126	E/Q	Gag/Cag	COSM164258	.	.	-1	SEPT1	Uniprot_gn	2879	protein_coding	YES	.	ENSP00000473960	.	S4R362_HUMAN,H3BS29_HUMAN	UPI000059D361	.	.	benign(0.406)	5/11	.	PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF6,Gene3D:3.40.50.300,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCTCATCCC	.	5	ESCA
STX1B	0	.	GRCh37	16	31004737	31004737	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606C>G	p.Ile202Met	p.I202M	ENST00000215095	8/10	29	19	10	24	24	0	STX1B,missense_variant,p.Ile118Met,ENST00000569638,;STX1B,missense_variant,p.Ile202Met,ENST00000565419,;STX1B,missense_variant,p.Ile202Met,ENST00000215095,;HSD3B7,downstream_gene_variant,,ENST00000297679,;HSD3B7,downstream_gene_variant,,ENST00000353250,;HSD3B7,downstream_gene_variant,,ENST00000262520,;STX1B,downstream_gene_variant,,ENST00000566211,;	C	ENSG00000099365	ENST00000215095	Transcript	missense_variant	838	606	202	I/M	atC/atG	.	.	.	-1	STX1B	HGNC	18539	protein_coding	YES	CCDS10699.1	ENSP00000215095	STX1B_HUMAN	H3BT82_HUMAN	UPI0000000C13	.	tolerated(0.81)	benign(0.159)	8/10	.	PROSITE_profiles:PS50192,hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF76,PROSITE_patterns:PS00914,Pfam_domain:PF05739,Gene3D:1.20.5.110,SMART_domains:SM00397,Superfamily_domains:SSF47661	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTTGATGAT	.	5	ESCA
ZNF267	0	.	GRCh37	16	31926132	31926132	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.562C>G	p.His188Asp	p.H188D	ENST00000300870	4/4	89	60	29	103	103	0	ZNF267,missense_variant,p.His188Asp,ENST00000300870,;ZNF267,downstream_gene_variant,,ENST00000394846,;ZNF267,downstream_gene_variant,,ENST00000562971,;ZNF267,non_coding_transcript_exon_variant,,ENST00000575471,;ZNF267,downstream_gene_variant,,ENST00000561814,;ZNF267,downstream_gene_variant,,ENST00000566541,;	G	ENSG00000185947	ENST00000300870	Transcript	missense_variant	771	562	188	H/D	Cac/Gac	.	.	.	1	ZNF267	HGNC	13060	protein_coding	YES	CCDS32440.1	ENSP00000300870	ZN267_HUMAN	H3BPW2_HUMAN	UPI000045696F	.	deleterious(0.01)	benign(0.101)	4/4	.	hmmpanther:PTHR24377:SF184,hmmpanther:PTHR24377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACATCACATA	.	5	ESCA
AC142381.1	0	.	GRCh37	16	32063551	32063551	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.241C>T	p.Gln81Ter	p.Q81*	ENST00000426099	1/1	33	25	8	29	29	0	AC142381.1,stop_gained,p.Gln81Ter,ENST00000426099,;RP11-1166P10.6,intron_variant,,ENST00000566806,;	T	ENSG00000223931	ENST00000426099	Transcript	stop_gained	241	241	81	Q/*	Caa/Taa	.	.	.	1	AC142381.1	Clone_based_ensembl_gene	.	protein_coding	YES	.	ENSP00000396505	.	.	UPI0000116410	.	.	.	1/1	.	Superfamily_domains:SSF48726,SMART_domains:SM00406,Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF91,PROSITE_profiles:PS50835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|VARSCANS	ATCTTCAAATG	.	2	ESCA
RP11-80F22.15	0	.	GRCh37	16	34739560	34739560	+	RNA	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.363C>T	.	.	ENST00000562591	2/2	52	41	11	39	39	0	RP11-80F22.15,non_coding_transcript_exon_variant,,ENST00000562591,;RP11-80F22.2,downstream_gene_variant,,ENST00000569755,;RP11-80F22.2,downstream_gene_variant,,ENST00000563487,;	A	ENSG00000260857	ENST00000562591	Transcript	non_coding_transcript_exon_variant	363	.	.	.	.	.	.	.	-1	RP11-80F22.15	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCACAGATGAG	.	5	ESCA
PHKB	0	.	GRCh37	16	47683022	47683022	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1704T>G	p.Ile568Met	p.I568M	ENST00000323584	18/31	91	80	10	72	72	0	PHKB,missense_variant,p.Ile568Met,ENST00000299167,;PHKB,missense_variant,p.Ile568Met,ENST00000323584,;PHKB,missense_variant,p.Ile561Met,ENST00000566044,;PHKB,missense_variant,p.Ile561Met,ENST00000455779,;PHKB,upstream_gene_variant,,ENST00000568171,;	G	ENSG00000102893	ENST00000323584	Transcript	missense_variant	1728	1704	568	I/M	atT/atG	.	.	.	1	PHKB	HGNC	8927	protein_coding	YES	CCDS10729.1	ENSP00000313504	KPBB_HUMAN	Q6LAJ4_HUMAN	UPI0000141140	.	deleterious(0.01)	probably_damaging(0.998)	18/31	.	hmmpanther:PTHR10749,hmmpanther:PTHR10749:SF3,Pfam_domain:PF00723	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCATTCTAGG	.	4	ESCA
GLYR1	0	.	GRCh37	16	4863802	4863802	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1055G>A	p.Arg352His	p.R352H	ENST00000321919	12/16	32	28	4	21	21	0	GLYR1,missense_variant,p.Arg352His,ENST00000321919,;GLYR1,missense_variant,p.Arg335His,ENST00000381983,;GLYR1,missense_variant,p.Arg323His,ENST00000589389,;GLYR1,missense_variant,p.Arg346His,ENST00000591451,;GLYR1,missense_variant,p.Arg271His,ENST00000436648,;GLYR1,downstream_gene_variant,,ENST00000588297,;GLYR1,3_prime_UTR_variant,,ENST00000588732,;GLYR1,3_prime_UTR_variant,,ENST00000587936,;GLYR1,downstream_gene_variant,,ENST00000591846,;GLYR1,downstream_gene_variant,,ENST00000586095,;	T	ENSG00000140632	ENST00000321919	Transcript	missense_variant	1132	1055	352	R/H	cGc/cAc	.	.	.	-1	GLYR1	HGNC	24434	protein_coding	YES	CCDS10524.1	ENSP00000322716	GLYR1_HUMAN	K7EPU6_HUMAN	UPI00001FF8EE	.	deleterious(0.05)	benign(0.151)	12/16	.	hmmpanther:PTHR22981,hmmpanther:PTHR22981:SF56,Gene3D:3.40.50.720,Pfam_domain:PF03446,Superfamily_domains:SSF51735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CAGGGCGGATC	.	4	ESCA
PPL	0	.	GRCh37	16	4949116	4949116	+	Missense_Mutation	SNP	G	G	C	rs761272518	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.774C>G	p.Phe258Leu	p.F258L	ENST00000345988	8/22	45	33	12	34	34	0	PPL,missense_variant,p.Phe256Leu,ENST00000590782,;PPL,missense_variant,p.Phe258Leu,ENST00000345988,;PPL,intron_variant,,ENST00000592772,;	C	ENSG00000118898	ENST00000345988	Transcript	missense_variant	864	774	258	F/L	ttC/ttG	rs761272518	.	.	-1	PPL	HGNC	9273	protein_coding	YES	CCDS10526.1	ENSP00000340510	PEPL_HUMAN	.	UPI00001AE832	.	deleterious(0)	possibly_damaging(0.895)	8/22	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23169,SMART_domains:SM00150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATGAAATT	byFrequency	5	ESCA
C16orf89	0	.	GRCh37	16	5094240	5094240	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*344G>C	.	.	ENST00000315997	8/8	27	20	7	19	19	0	C16orf89,3_prime_UTR_variant,,ENST00000350219,;C16orf89,3_prime_UTR_variant,,ENST00000315997,;C16orf89,3_prime_UTR_variant,,ENST00000422873,;C16orf89,3_prime_UTR_variant,,ENST00000474471,;C16orf89,3_prime_UTR_variant,,ENST00000472572,;ALG1,intron_variant,,ENST00000588623,;C16orf89,non_coding_transcript_exon_variant,,ENST00000586629,;ALG1,downstream_gene_variant,,ENST00000591961,;C16orf89,downstream_gene_variant,,ENST00000592343,;RP11-165E7.1,downstream_gene_variant,,ENST00000588778,;	G	ENSG00000153446	ENST00000315997	Transcript	3_prime_UTR_variant	1755	.	.	.	.	.	.	.	-1	C16orf89	HGNC	28687	protein_coding	YES	CCDS42116.2	ENSP00000324672	CP089_HUMAN	.	UPI000166306A	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTTATCCTCCA	.	2	ESCA
MMP2	0	.	GRCh37	16	55527132	55527132	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1399G>C	p.Glu467Gln	p.E467Q	ENST00000219070	9/13	34	20	14	33	33	0	MMP2,missense_variant,p.Glu391Gln,ENST00000543485,;MMP2,missense_variant,p.Glu391Gln,ENST00000570308,;MMP2,missense_variant,p.Glu467Gln,ENST00000219070,;MMP2,missense_variant,p.Glu92Gln,ENST00000570283,;MMP2,missense_variant,p.Glu417Gln,ENST00000437642,;	C	ENSG00000087245	ENST00000219070	Transcript	missense_variant	1908	1399	467	E/Q	Gag/Cag	.	.	.	1	MMP2	HGNC	7166	protein_coding	YES	CCDS10752.1	ENSP00000219070	MMP2_HUMAN	Q2EF79_HUMAN,H3BV48_HUMAN,H3BR66_HUMAN	UPI00000422C4	.	tolerated(0.07)	benign(0.062)	9/13	.	hmmpanther:PTHR10201:SF29,hmmpanther:PTHR10201,Gene3D:2.110.10.10,Superfamily_domains:SSF50923	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTGAGATC	.	5	ESCA
DPEP3	0	.	GRCh37	16	68009657	68009657	+	3'UTR	SNP	G	G	C	rs373064126	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*11C>G	.	.	ENST00000268793	10/10	27	21	6	30	30	0	DPEP3,3_prime_UTR_variant,,ENST00000268793,;DPEP3,downstream_gene_variant,,ENST00000574342,;	C	ENSG00000141096	ENST00000268793	Transcript	3_prime_UTR_variant	1927	.	.	.	.	rs373064126	.	.	-1	DPEP3	HGNC	23029	protein_coding	YES	CCDS10856.1	ENSP00000268793	DPEP3_HUMAN	.	UPI000006F093	.	.	.	10/10	.	.	.	.	.	.	.	.	.	A:0	A:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGGGGACCGA	byFrequency|byCluster	5	ESCA
WDR90	0	.	GRCh37	16	717619	717619	+	3'UTR	SNP	C	C	A	rs774918769	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*30C>A	.	.	ENST00000293879	41/41	47	35	12	26	26	0	WDR90,stop_gained,p.Ser62Ter,ENST00000546896,;WDR90,3_prime_UTR_variant,,ENST00000547944,;WDR90,3_prime_UTR_variant,,ENST00000551100,;WDR90,3_prime_UTR_variant,,ENST00000315764,;WDR90,3_prime_UTR_variant,,ENST00000549091,;WDR90,3_prime_UTR_variant,,ENST00000293879,;RHOT2,upstream_gene_variant,,ENST00000315082,;RHOT2,upstream_gene_variant,,ENST00000563134,;RHOT2,upstream_gene_variant,,ENST00000561929,;RHOT2,upstream_gene_variant,,ENST00000569943,;WDR90,downstream_gene_variant,,ENST00000548603,;WDR90,downstream_gene_variant,,ENST00000547543,;WDR90,3_prime_UTR_variant,,ENST00000552728,;WDR90,non_coding_transcript_exon_variant,,ENST00000553080,;WDR90,non_coding_transcript_exon_variant,,ENST00000549024,;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,;RHOT2,upstream_gene_variant,,ENST00000569358,;RHOT2,upstream_gene_variant,,ENST00000568950,;WDR90,downstream_gene_variant,,ENST00000548448,;RHOT2,upstream_gene_variant,,ENST00000566214,;RHOT2,upstream_gene_variant,,ENST00000570092,;WDR90,downstream_gene_variant,,ENST00000546923,;RHOT2,upstream_gene_variant,,ENST00000569706,;RHOT2,upstream_gene_variant,,ENST00000569675,;WDR90,downstream_gene_variant,,ENST00000552683,;RHOT2,upstream_gene_variant,,ENST00000602564,;RHOT2,upstream_gene_variant,,ENST00000570280,;RHOT2,upstream_gene_variant,,ENST00000562333,;RHOT2,upstream_gene_variant,,ENST00000562708,;RHOT2,upstream_gene_variant,,ENST00000567017,;RHOT2,upstream_gene_variant,,ENST00000567589,;RHOT2,upstream_gene_variant,,ENST00000566965,;RHOT2,upstream_gene_variant,,ENST00000563776,;RHOT2,upstream_gene_variant,,ENST00000561983,;RHOT2,upstream_gene_variant,,ENST00000568636,;RHOT2,upstream_gene_variant,,ENST00000563637,;WDR90,downstream_gene_variant,,ENST00000546516,;RHOT2,upstream_gene_variant,,ENST00000562598,;RHOT2,upstream_gene_variant,,ENST00000565004,;RHOT2,upstream_gene_variant,,ENST00000561711,;	A	ENSG00000161996	ENST00000293879	Transcript	3_prime_UTR_variant	5277	.	.	.	.	rs774918769	.	.	1	WDR90	HGNC	26960	protein_coding	YES	CCDS42092.1	ENSP00000293879	WDR90_HUMAN	.	UPI0000D67C48	.	.	.	41/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCATCACGCC	byFrequency	5	ESCA
FAM92B	0	.	GRCh37	16	85141485	85141485	+	Silent	SNP	C	C	G	rs764145326	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.393G>C	p.%3D	p.L131L	ENST00000539556	4/9	22	16	6	39	39	0	FAM92B,synonymous_variant,p.%3D,ENST00000539556,;	G	ENSG00000153789	ENST00000539556	Transcript	synonymous_variant	549	393	131	L	ctG/ctC	rs764145326	.	.	-1	FAM92B	HGNC	24781	protein_coding	YES	CCDS32500.1	ENSP00000443411	FA92B_HUMAN	.	UPI00001C0C61	.	.	.	4/9	.	Superfamily_domains:SSF103657,Pfam_domain:PF06730,Gene3D:1.20.1270.60,hmmpanther:PTHR21223:SF3,hmmpanther:PTHR21223,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TGCCTCAGTTT	.	3	ESCA
FAM92B	0	.	GRCh37	16	85141517	85141517	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.361G>C	p.Glu121Gln	p.E121Q	ENST00000539556	4/9	30	19	11	40	40	0	FAM92B,missense_variant,p.Glu121Gln,ENST00000539556,;	G	ENSG00000153789	ENST00000539556	Transcript	missense_variant	517	361	121	E/Q	Gag/Cag	.	.	.	-1	FAM92B	HGNC	24781	protein_coding	YES	CCDS32500.1	ENSP00000443411	FA92B_HUMAN	.	UPI00001C0C61	.	deleterious(0)	probably_damaging(0.998)	4/9	.	Superfamily_domains:SSF103657,Pfam_domain:PF06730,Gene3D:1.20.1270.60,hmmpanther:PTHR21223:SF3,hmmpanther:PTHR21223,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATCTCATGAT	.	5	ESCA
SREBF1	0	.	GRCh37	17	17721640	17721640	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1207C>G	p.Leu403Val	p.L403V	ENST00000355815	7/20	15	11	4	48	48	0	SREBF1,missense_variant,p.Leu373Val,ENST00000338854,;SREBF1,missense_variant,p.Leu119Val,ENST00000395757,;SREBF1,missense_variant,p.Leu403Val,ENST00000355815,;SREBF1,missense_variant,p.Leu373Val,ENST00000261646,;SREBF1,missense_variant,p.Leu373Val,ENST00000435530,;SREBF1,downstream_gene_variant,,ENST00000423161,;SREBF1,upstream_gene_variant,,ENST00000486311,;SREBF1,upstream_gene_variant,,ENST00000478616,;SREBF1,downstream_gene_variant,,ENST00000577897,;MIR33B,upstream_gene_variant,,ENST00000385104,;SREBF1,downstream_gene_variant,,ENST00000583732,;SREBF1,missense_variant,p.Leu2Val,ENST00000395756,;SREBF1,missense_variant,p.Leu119Val,ENST00000395751,;SREBF1,non_coding_transcript_exon_variant,,ENST00000487401,;SREBF1,non_coding_transcript_exon_variant,,ENST00000469356,;SREBF1,non_coding_transcript_exon_variant,,ENST00000470247,;SREBF1,upstream_gene_variant,,ENST00000490796,;SREBF1,upstream_gene_variant,,ENST00000581707,;SREBF1,upstream_gene_variant,,ENST00000447641,;SREBF1,upstream_gene_variant,,ENST00000583080,;SREBF1,downstream_gene_variant,,ENST00000476994,;SREBF1,upstream_gene_variant,,ENST00000584760,;SREBF1,upstream_gene_variant,,ENST00000578469,;SREBF1,upstream_gene_variant,,ENST00000471445,;SREBF1,upstream_gene_variant,,ENST00000485080,;SREBF1,upstream_gene_variant,,ENST00000580540,;	C	ENSG00000072310	ENST00000355815	Transcript	missense_variant	1377	1207	403	L/V	Ctg/Gtg	.	.	.	-1	SREBF1	HGNC	11289	protein_coding	YES	CCDS32583.1	ENSP00000348069	SRBP1_HUMAN	J3QLB6_HUMAN,B5MD58_HUMAN	UPI00004432F6	.	deleterious(0)	probably_damaging(0.96)	7/20	.	PROSITE_profiles:PS50888,hmmpanther:PTHR12565,hmmpanther:PTHR12565:SF5,Pfam_domain:PF00010,Gene3D:4.10.280.10,SMART_domains:SM00353,Superfamily_domains:SSF47459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGCAGAAAGC	.	5	ESCA
SGSM2	0	.	GRCh37	17	2278855	2278855	+	Missense_Mutation	SNP	G	G	C	rs758380631	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2170G>C	p.Glu724Gln	p.E724Q	ENST00000268989	18/24	37	24	13	48	48	0	SGSM2,missense_variant,p.Glu724Gln,ENST00000268989,;SGSM2,missense_variant,p.Glu679Gln,ENST00000426855,;SGSM2,missense_variant,p.Glu679Gln,ENST00000574563,;SGSM2,upstream_gene_variant,,ENST00000572925,;SGSM2,upstream_gene_variant,,ENST00000573851,;RP1-59D14.5,splice_region_variant,,ENST00000574290,;RP1-59D14.5,downstream_gene_variant,,ENST00000573007,;SGSM2,downstream_gene_variant,,ENST00000575367,;SGSM2,downstream_gene_variant,,ENST00000574857,;SGSM2,upstream_gene_variant,,ENST00000572841,;SGSM2,downstream_gene_variant,,ENST00000574250,;SGSM2,downstream_gene_variant,,ENST00000573717,;	C	ENSG00000141258	ENST00000268989	Transcript	missense_variant	2347	2170	724	E/Q	Gag/Cag	rs758380631	.	.	1	SGSM2	HGNC	29026	protein_coding	YES	CCDS32526.1	ENSP00000268989	SGSM2_HUMAN	I3L1Y7_HUMAN	UPI0000160300	.	tolerated(0.4)	benign(0.239)	18/24	.	PROSITE_profiles:PS50086,hmmpanther:PTHR22957:SF194,hmmpanther:PTHR22957,SMART_domains:SM00164	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTGAGCAG	.	5	ESCA
MNT	0	.	GRCh37	17	2290288	2290288	+	Silent	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1656G>T	p.%3D	p.V552V	ENST00000174618	6/6	48	31	16	50	50	0	MNT,synonymous_variant,p.%3D,ENST00000174618,;MNT,downstream_gene_variant,,ENST00000575394,;RP1-59D14.1,downstream_gene_variant,,ENST00000571775,;MNT,downstream_gene_variant,,ENST00000575374,;MNT,downstream_gene_variant,,ENST00000571232,;MNT,downstream_gene_variant,,ENST00000572892,;MNT,downstream_gene_variant,,ENST00000573384,;MNT,downstream_gene_variant,,ENST00000575402,;	A	ENSG00000070444	ENST00000174618	Transcript	synonymous_variant	2062	1656	552	V	gtG/gtT	.	.	.	-1	MNT	HGNC	7188	protein_coding	YES	CCDS11018.1	ENSP00000174618	MNT_HUMAN	K7ES66_HUMAN	UPI000012F2C6	.	.	.	6/6	.	hmmpanther:PTHR11969:SF15,hmmpanther:PTHR11969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGTGCACCAC	.	5	ESCA
MYO1D	0	.	GRCh37	17	30981621	30981621	+	Silent	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2364C>A	p.%3D	p.L788L	ENST00000318217	18/22	27	18	8	20	20	0	MYO1D,synonymous_variant,p.%3D,ENST00000318217,;MYO1D,synonymous_variant,p.%3D,ENST00000579584,;MYO1D,synonymous_variant,p.%3D,ENST00000394649,;RP11-220C2.1,intron_variant,,ENST00000582272,;MYO1D,non_coding_transcript_exon_variant,,ENST00000581059,;MYO1D,non_coding_transcript_exon_variant,,ENST00000582217,;MYO1D,non_coding_transcript_exon_variant,,ENST00000577352,;MYO1D,downstream_gene_variant,,ENST00000585094,;	T	ENSG00000176658	ENST00000318217	Transcript	synonymous_variant	2669	2364	788	L	ctC/ctA	.	.	.	-1	MYO1D	HGNC	7598	protein_coding	YES	CCDS32615.1	ENSP00000324527	MYO1D_HUMAN	Q8N618_HUMAN,K7EIG7_HUMAN	UPI0000186004	.	.	.	18/22	.	hmmpanther:PTHR13140:SF333,hmmpanther:PTHR13140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTGATGAGCTG	.	5	ESCA
OR3A3	0	.	GRCh37	17	3324821	3324821	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.960G>A	p.%3D	p.L320L	ENST00000291231	1/1	39	21	17	39	39	0	OR3A3,synonymous_variant,p.%3D,ENST00000291231,;	A	ENSG00000159961	ENST00000291231	Transcript	synonymous_variant	960	960	320	L	ctG/ctA	.	.	.	1	OR3A3	HGNC	8284	protein_coding	YES	CCDS11025.1	ENSP00000291231	OR3A3_HUMAN	.	UPI000013E033	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACTGACCTG	.	5	ESCA
ASPA	0	.	GRCh37	17	3385000	3385000	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340G>C	p.Asp114His	p.D114H	ENST00000263080	2/6	80	62	17	74	74	0	ASPA,missense_variant,p.Asp114His,ENST00000263080,;ASPA,missense_variant,p.Asp114His,ENST00000456349,;SPATA22,intron_variant,,ENST00000541913,;SPATA22,intron_variant,,ENST00000570318,;ASPA,3_prime_UTR_variant,,ENST00000571278,;	C	ENSG00000108381	ENST00000263080	Transcript	missense_variant	498	340	114	D/H	Gac/Cac	CM023014	.	.	1	ASPA	HGNC	756	protein_coding	YES	CCDS11028.1	ENSP00000263080	ACY2_HUMAN	Q6FH48_HUMAN,I3L0T3_HUMAN	UPI00000012D1	.	deleterious(0)	probably_damaging(0.988)	2/6	.	HAMAP:MF_00704,hmmpanther:PTHR15162:SF4,hmmpanther:PTHR15162,Pfam_domain:PF04952,Gene3D:3.40.630.10,PIRSF_domain:PIRSF018001,Superfamily_domains:SSF53187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTTTTGACCTT	.	5	ESCA
TAF15	0	.	GRCh37	17	34171853	34171853	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1550G>C	p.Gly517Ala	p.G517A	ENST00000588240	15/16	40	35	5	49	49	0	TAF15,missense_variant,p.Gly517Ala,ENST00000588240,;TAF15,missense_variant,p.Gly514Ala,ENST00000311979,;TAF15,intron_variant,,ENST00000585577,;TAF15,intron_variant,,ENST00000592237,;TAF15,upstream_gene_variant,,ENST00000586593,;TAF15,downstream_gene_variant,,ENST00000586970,;TAF15,downstream_gene_variant,,ENST00000591763,;TAF15,downstream_gene_variant,,ENST00000590051,;	C	ENSG00000172660	ENST00000588240	Transcript	missense_variant	1665	1550	517	G/A	gGa/gCa	.	.	.	1	TAF15	HGNC	11547	protein_coding	YES	CCDS32623.1	ENSP00000466950	RBP56_HUMAN	Q86X94_HUMAN,K7EJB3_HUMAN	UPI000013317D	.	deleterious_low_confidence(0)	unknown(0)	15/16	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23238,hmmpanther:PTHR23238:SF25	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGAGGAGATC	.	4	ESCA
SRCIN1	0	.	GRCh37	17	36719704	36719704	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.595G>A	p.Glu199Lys	p.E199K	ENST00000264659	5/19	47	29	17	49	49	0	SRCIN1,missense_variant,p.Glu199Lys,ENST00000264659,;SRCIN1,missense_variant,p.Glu259Lys,ENST00000584266,;SRCIN1,missense_variant,p.Glu233Lys,ENST00000578925,;SRCIN1,upstream_gene_variant,,ENST00000542707,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000398579,;SRCIN1,upstream_gene_variant,,ENST00000578160,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000577193,;	T	ENSG00000017373	ENST00000264659	Transcript	missense_variant	820	595	199	E/K	Gag/Aag	.	.	.	-1	SRCIN1	HGNC	29506	protein_coding	YES	CCDS45660.1	ENSP00000264659	SRCN1_HUMAN	.	UPI0000E27F82	.	deleterious(0.01)	probably_damaging(0.999)	5/19	.	hmmpanther:PTHR22741:SF5,hmmpanther:PTHR22741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTCGTGCG	.	5	ESCA
KRTAP9-9	0	.	GRCh37	17	39412234	39412234	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*87G>A	.	.	ENST00000394008	1/1	66	45	20	63	63	0	KRTAP9-9,3_prime_UTR_variant,,ENST00000394008,;	A	ENSG00000198083	ENST00000394008	Transcript	3_prime_UTR_variant	599	.	.	.	.	.	.	.	1	KRTAP9-9	HGNC	16773	protein_coding	YES	CCDS54127.1	ENSP00000377576	.	B5MDD6_HUMAN	UPI00002264BA	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCTGACAGC	.	5	ESCA
SLC25A39	0	.	GRCh37	17	42397473	42397473	+	Missense_Mutation	SNP	G	G	C	rs778758238	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.976C>G	p.Arg326Gly	p.R326G	ENST00000377095	12/12	55	35	20	78	78	0	SLC25A39,missense_variant,p.Arg318Gly,ENST00000590194,;SLC25A39,missense_variant,p.Arg318Gly,ENST00000225308,;SLC25A39,missense_variant,p.Arg326Gly,ENST00000377095,;SLC25A39,missense_variant,p.Arg233Gly,ENST00000588767,;SLC25A39,missense_variant,p.Arg194Gly,ENST00000586016,;SLC25A39,missense_variant,p.Arg303Gly,ENST00000537904,;SLC25A39,downstream_gene_variant,,ENST00000586633,;SLC25A39,downstream_gene_variant,,ENST00000585636,;RUNDC3A,downstream_gene_variant,,ENST00000426726,;RUNDC3A,downstream_gene_variant,,ENST00000225441,;RUNDC3A,downstream_gene_variant,,ENST00000590941,;SLC25A39,downstream_gene_variant,,ENST00000588049,;SLC25A39,downstream_gene_variant,,ENST00000585523,;SLC25A39,downstream_gene_variant,,ENST00000592857,;AC003102.3,upstream_gene_variant,,ENST00000588097,;SLC25A39,3_prime_UTR_variant,,ENST00000593166,;SLC25A39,non_coding_transcript_exon_variant,,ENST00000591006,;SLC25A39,non_coding_transcript_exon_variant,,ENST00000592372,;RUNDC3A,downstream_gene_variant,,ENST00000590834,;SLC25A39,downstream_gene_variant,,ENST00000585695,;RUNDC3A,downstream_gene_variant,,ENST00000588564,;SLC25A39,downstream_gene_variant,,ENST00000591151,;SLC25A39,downstream_gene_variant,,ENST00000588315,;RUNDC3A,downstream_gene_variant,,ENST00000587483,;RUNDC3A,downstream_gene_variant,,ENST00000593079,;	C	ENSG00000013306	ENST00000377095	Transcript	missense_variant	1096	976	326	R/G	Cgg/Ggg	rs778758238,COSM1383649	.	.	-1	SLC25A39	HGNC	24279	protein_coding	YES	CCDS45700.1	ENSP00000366299	S2539_HUMAN	K7EMW3_HUMAN,K7ELM7_HUMAN	UPI00001AE651	.	deleterious(0)	probably_damaging(1)	12/12	.	PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF193,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCCGAGGAA	byFrequency	5	ESCA
CRHR1	0	.	GRCh37	17	43907863	43907863	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.723C>A	p.Tyr241Ter	p.Y241*	ENST00000398285	8/14	30	19	11	25	25	0	CRHR1,stop_gained,p.Tyr241Ter,ENST00000398285,;CRHR1,stop_gained,p.Tyr37Ter,ENST00000293493,;CRHR1,stop_gained,p.Tyr111Ter,ENST00000339069,;CRHR1,stop_gained,p.Tyr172Ter,ENST00000352855,;CRHR1,stop_gained,p.Tyr212Ter,ENST00000577353,;CRHR1,stop_gained,p.Tyr212Ter,ENST00000314537,;CRHR1,upstream_gene_variant,,ENST00000580876,;CRHR1,3_prime_UTR_variant,,ENST00000347197,;CRHR1,non_coding_transcript_exon_variant,,ENST00000581479,;CRHR1,non_coding_transcript_exon_variant,,ENST00000582766,;CRHR1,intron_variant,,ENST00000583888,;CRHR1,downstream_gene_variant,,ENST00000580955,;CRHR1,upstream_gene_variant,,ENST00000535778,;	A	ENSG00000120088	ENST00000398285	Transcript	stop_gained	723	723	241	Y/*	taC/taA	.	.	.	1	CRHR1	HGNC	2357	protein_coding	YES	CCDS45712.1	ENSP00000381333	CRFR1_HUMAN	.	UPI0000128429	.	.	.	8/14	.	Transmembrane_helices:TMhelix,Prints_domain:PR00249,Superfamily_domains:SSF81321,Pfam_domain:PF00002,hmmpanther:PTHR12011:SF175,hmmpanther:PTHR12011,PROSITE_profiles:PS50261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTACCTGCA	.	5	ESCA
CRHR1	0	.	GRCh37	17	43912423	43912423	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*293C>G	.	.	ENST00000398285	14/14	59	41	17	71	71	0	CRHR1,3_prime_UTR_variant,,ENST00000398285,;CRHR1,3_prime_UTR_variant,,ENST00000314537,;CRHR1,downstream_gene_variant,,ENST00000580876,;CRHR1,downstream_gene_variant,,ENST00000293493,;CRHR1,downstream_gene_variant,,ENST00000339069,;CRHR1,downstream_gene_variant,,ENST00000352855,;CRHR1,downstream_gene_variant,,ENST00000577353,;CRHR1,3_prime_UTR_variant,,ENST00000535778,;CRHR1,3_prime_UTR_variant,,ENST00000347197,;CRHR1,downstream_gene_variant,,ENST00000580955,;CRHR1,downstream_gene_variant,,ENST00000581479,;CRHR1,downstream_gene_variant,,ENST00000582766,;CRHR1,downstream_gene_variant,,ENST00000583888,;	G	ENSG00000120088	ENST00000398285	Transcript	3_prime_UTR_variant	1628	.	.	.	.	.	.	.	1	CRHR1	HGNC	2357	protein_coding	YES	CCDS45712.1	ENSP00000381333	CRFR1_HUMAN	.	UPI0000128429	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACACCTACAG	.	5	ESCA
SP6	0	.	GRCh37	17	45922962	45922962	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1703C>G	.	.	ENST00000536300	2/2	30	26	4	36	36	0	SP6,3_prime_UTR_variant,,ENST00000536300,;SP6,3_prime_UTR_variant,,ENST00000342234,;SCRN2,upstream_gene_variant,,ENST00000290216,;SCRN2,upstream_gene_variant,,ENST00000407215,;SCRN2,upstream_gene_variant,,ENST00000578323,;SCRN2,upstream_gene_variant,,ENST00000584123,;SCRN2,upstream_gene_variant,,ENST00000582459,;SCRN2,upstream_gene_variant,,ENST00000578840,;SCRN2,upstream_gene_variant,,ENST00000583090,;SCRN2,upstream_gene_variant,,ENST00000581645,;SCRN2,upstream_gene_variant,,ENST00000579856,;SCRN2,upstream_gene_variant,,ENST00000580428,;SCRN2,upstream_gene_variant,,ENST00000581546,;	C	ENSG00000189120	ENST00000536300	Transcript	3_prime_UTR_variant	3166	.	.	.	.	.	.	.	-1	SP6	HGNC	14530	protein_coding	YES	CCDS11520.1	ENSP00000438209	SP6_HUMAN	.	UPI000022A416	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAAGAGATGCT	.	4	ESCA
SMG8	0	.	GRCh37	17	57288495	57288495	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1083G>A	p.%3D	p.V361V	ENST00000543872	2/5	64	40	23	64	64	0	SMG8,synonymous_variant,p.%3D,ENST00000543872,;SMG8,synonymous_variant,p.%3D,ENST00000578922,;SMG8,synonymous_variant,p.%3D,ENST00000300917,;CTD-2510F5.6,intron_variant,,ENST00000577660,;SMG8,upstream_gene_variant,,ENST00000582469,;SMG8,intron_variant,,ENST00000580498,;SMG8,upstream_gene_variant,,ENST00000580798,;	A	ENSG00000167447	ENST00000543872	Transcript	synonymous_variant	1347	1083	361	V	gtG/gtA	.	.	.	1	SMG8	HGNC	25551	protein_coding	YES	CCDS11615.1	ENSP00000438748	SMG8_HUMAN	.	UPI000006CCB5	.	.	.	2/5	.	hmmpanther:PTHR13091,hmmpanther:PTHR13091:SF0,Pfam_domain:PF10220	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTGAAGGA	.	5	ESCA
VMP1	0	.	GRCh37	17	57918648	57918648	+	3'Flank	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000262291	.	37	29	8	32	32	0	VMP1,downstream_gene_variant,,ENST00000536180,;VMP1,downstream_gene_variant,,ENST00000545362,;VMP1,downstream_gene_variant,,ENST00000262291,;VMP1,downstream_gene_variant,,ENST00000591877,;VMP1,downstream_gene_variant,,ENST00000537567,;VMP1,downstream_gene_variant,,ENST00000539763,;MIR21,non_coding_transcript_exon_variant,,ENST00000362134,;VMP1,downstream_gene_variant,,ENST00000591782,;VMP1,downstream_gene_variant,,ENST00000588617,;VMP1,non_coding_transcript_exon_variant,,ENST00000592790,;VMP1,downstream_gene_variant,,ENST00000592619,;VMP1,downstream_gene_variant,,ENST00000587470,;	T	ENSG00000062716	ENST00000262291	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	195	1	VMP1	HGNC	29559	protein_coding	YES	CCDS11619.1	ENSP00000262291	VMP1_HUMAN	K7ENU2_HUMAN,K7EMI0_HUMAN,K7EM96_HUMAN,K7EK01_HUMAN,D3DU01_HUMAN,B4DVV9_HUMAN	UPI0000037791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGACTGATGTT	.	5	ESCA
APPBP2	0	.	GRCh37	17	58571889	58571889	+	Missense_Mutation	SNP	G	G	C	rs747812788	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.317C>G	p.Ser106Cys	p.S106C	ENST00000083182	3/13	42	36	6	47	47	0	APPBP2,missense_variant,p.Ser106Cys,ENST00000585368,;APPBP2,missense_variant,p.Ser106Cys,ENST00000083182,;APPBP2,non_coding_transcript_exon_variant,,ENST00000590244,;APPBP2,3_prime_UTR_variant,,ENST00000588668,;APPBP2,3_prime_UTR_variant,,ENST00000589341,;	C	ENSG00000062725	ENST00000083182	Transcript	missense_variant	605	317	106	S/C	tCt/tGt	rs747812788	.	.	-1	APPBP2	HGNC	622	protein_coding	YES	CCDS32699.1	ENSP00000083182	APBP2_HUMAN	K7EIZ9_HUMAN	UPI000006D959	.	tolerated(0.11)	benign(0.003)	3/13	.	hmmpanther:PTHR19959,hmmpanther:PTHR19959:SF114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATAAGAGCAC	.	5	ESCA
DDX5	0	.	GRCh37	17	62496429	62496429	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1457G>C	p.Arg486Thr	p.R486T	ENST00000225792	13/13	29	17	12	26	26	0	DDX5,missense_variant,p.Arg486Thr,ENST00000578804,;DDX5,missense_variant,p.Arg407Thr,ENST00000450599,;DDX5,missense_variant,p.Arg486Thr,ENST00000225792,;DDX5,downstream_gene_variant,,ENST00000584279,;DDX5,downstream_gene_variant,,ENST00000583212,;DDX5,downstream_gene_variant,,ENST00000581806,;DDX5,downstream_gene_variant,,ENST00000583239,;DDX5,downstream_gene_variant,,ENST00000579091,;DDX5,downstream_gene_variant,,ENST00000578190,;POLG2,upstream_gene_variant,,ENST00000539111,;DDX5,downstream_gene_variant,,ENST00000581697,;DDX5,downstream_gene_variant,,ENST00000585060,;DDX5,downstream_gene_variant,,ENST00000579996,;DDX5,downstream_gene_variant,,ENST00000585111,;DDX5,downstream_gene_variant,,ENST00000577787,;DDX5,downstream_gene_variant,,ENST00000577922,;MIR3064,downstream_gene_variant,,ENST00000581130,;MIR5047,downstream_gene_variant,,ENST00000579212,;DDX5,non_coding_transcript_exon_variant,,ENST00000580026,;DDX5,non_coding_transcript_exon_variant,,ENST00000581237,;DDX5,downstream_gene_variant,,ENST00000578491,;DDX5,3_prime_UTR_variant,,ENST00000540698,;DDX5,3_prime_UTR_variant,,ENST00000581693,;DDX5,non_coding_transcript_exon_variant,,ENST00000578758,;DDX5,non_coding_transcript_exon_variant,,ENST00000581230,;DDX5,downstream_gene_variant,,ENST00000584549,;DDX5,downstream_gene_variant,,ENST00000585223,;DDX5,downstream_gene_variant,,ENST00000579461,;DDX5,downstream_gene_variant,,ENST00000578400,;DDX5,downstream_gene_variant,,ENST00000582326,;DDX5,downstream_gene_variant,,ENST00000583894,;DDX5,downstream_gene_variant,,ENST00000581551,;DDX5,downstream_gene_variant,,ENST00000583562,;POLG2,upstream_gene_variant,,ENST00000585141,;DDX5,downstream_gene_variant,,ENST00000583201,;POLG2,upstream_gene_variant,,ENST00000578997,;DDX5,downstream_gene_variant,,ENST00000585317,;	G	ENSG00000108654	ENST00000225792	Transcript	missense_variant	1859	1457	486	R/T	aGa/aCa	.	.	.	-1	DDX5	HGNC	2746	protein_coding	YES	CCDS11659.1	ENSP00000225792	DDX5_HUMAN	J3QS97_HUMAN,J3QRQ7_HUMAN,J3QRN5_HUMAN,J3QR62_HUMAN,J3QLG9_HUMAN,J3QKN9_HUMAN,J3KTQ4_HUMAN,J3KRZ1_HUMAN,J3KRX8_HUMAN	UPI000003B456	.	tolerated(0.09)	benign(0.002)	13/13	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24031:SF182,hmmpanther:PTHR24031	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTCCTCTACCC	.	5	ESCA
CDC42EP4	0	.	GRCh37	17	71282205	71282205	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.435G>A	p.%3D	p.K145K	ENST00000335793	2/2	40	18	22	19	19	0	CDC42EP4,synonymous_variant,p.%3D,ENST00000335793,;CDC42EP4,synonymous_variant,p.%3D,ENST00000439510,;CDC42EP4,intron_variant,,ENST00000581014,;CDC42EP4,downstream_gene_variant,,ENST00000580315,;CDC42EP4,downstream_gene_variant,,ENST00000579611,;CDC42EP4,downstream_gene_variant,,ENST00000581045,;	T	ENSG00000179604	ENST00000335793	Transcript	synonymous_variant	830	435	145	K	aaG/aaA	.	.	.	-1	CDC42EP4	HGNC	17147	protein_coding	YES	CCDS11695.1	ENSP00000338258	BORG4_HUMAN	J3QQS6_HUMAN,J3KRZ9_HUMAN,B2R6D8_HUMAN	UPI000003B4C8	.	.	.	2/2	.	hmmpanther:PTHR15344,hmmpanther:PTHR15344:SF14,Pfam_domain:PF14957	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCTTCAC	.	5	ESCA
KIAA0195	0	.	GRCh37	17	73494402	73494402	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3636C>G	p.%3D	p.P1212P	ENST00000314256	28/32	14	8	6	19	19	0	KIAA0195,synonymous_variant,p.%3D,ENST00000577245,;KIAA0195,synonymous_variant,p.%3D,ENST00000579208,;KIAA0195,synonymous_variant,p.%3D,ENST00000314256,;KIAA0195,synonymous_variant,p.%3D,ENST00000577247,;KIAA0195,synonymous_variant,p.%3D,ENST00000584694,;KIAA0195,synonymous_variant,p.%3D,ENST00000375248,;CASKIN2,downstream_gene_variant,,ENST00000321617,;KIAA0195,downstream_gene_variant,,ENST00000578853,;CASKIN2,downstream_gene_variant,,ENST00000433559,;AC100787.1,downstream_gene_variant,,ENST00000579379,;KIAA0195,splice_region_variant,,ENST00000579898,;KIAA0195,splice_region_variant,,ENST00000585105,;KIAA0195,splice_region_variant,,ENST00000581453,;KIAA0195,splice_region_variant,,ENST00000577194,;KIAA0195,splice_region_variant,,ENST00000581085,;CASKIN2,downstream_gene_variant,,ENST00000580021,;KIAA0195,downstream_gene_variant,,ENST00000581723,;KIAA0195,downstream_gene_variant,,ENST00000581867,;KIAA0195,downstream_gene_variant,,ENST00000578624,;	G	ENSG00000177728	ENST00000314256	Transcript	synonymous_variant	4030	3636	1212	P	ccC/ccG	.	.	.	1	KIAA0195	HGNC	28983	protein_coding	YES	CCDS32732.1	ENSP00000313885	K0195_HUMAN	J3QS17_HUMAN,J3QRT3_HUMAN,J3QLM7_HUMAN,J3KT63_HUMAN,J3KRU7_HUMAN	UPI0000139439	.	.	.	28/32	.	hmmpanther:PTHR13219:SF6,hmmpanther:PTHR13219,Pfam_domain:PF00689,Gene3D:1.20.1110.10,Superfamily_domains:0049473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCCCAGGTG	.	5	ESCA
TP53	0	.	GRCh37	17	7577118	7577118	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	8/11	29	21	8	33	33	0	TP53,missense_variant,p.Val274Leu,ENST00000420246,;TP53,missense_variant,p.Val274Leu,ENST00000269305,;TP53,missense_variant,p.Val142Leu,ENST00000509690,;TP53,missense_variant,p.Val274Leu,ENST00000359597,;TP53,missense_variant,p.Val274Leu,ENST00000445888,;TP53,missense_variant,p.Val274Leu,ENST00000455263,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,downstream_gene_variant,,ENST00000505014,;	G	ENSG00000141510	ENST00000269305	Transcript	missense_variant	1010	820	274	V/L	Gtt/Ctt	TP53_g.13800del,TP53_g.13800G>T,TP53_g.13800G>A,TP53_g.13800G>C,COSM44443,COSM43974,COSM10769,COSM43667,COSM165075,COSM172146,COSM3388171,COSM1679490	.	.	-1	TP53	HGNC	11998	protein_coding	YES	CCDS11118.1	ENSP00000269305	P53_HUMAN	S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN	UPI000002ED67	.	deleterious(0.04)	benign(0.126)	8/11	.	hmmpanther:PTHR11447:SF6,hmmpanther:PTHR11447,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386	.	.	.	.	.	.	.	.	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,0,0,0,1,1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.V274L|c.820G>C|11,CODON|p.0?|c.1_1182del1182|6,CODON|p.V274A|c.821T>C|8,CODON|p.V274A|c.821T>C|22,CODON|p.V274G|c.821T>G|8,CODON|p.V274D|c.821T>A|3,CODON|p.V274D|c.821T>A|10,BUFFER|p.C277*|c.831T>A|6,BUFFER|p.C277C|c.831T>C|4,BUFFER|p.C277Y|c.830G>A|15,BUFFER|p.C277F|c.830G>T|22,BUFFER|p.C277G|c.829T>G|5,BUFFER|p.A276D|c.827C>A|9,BUFFER|p.A276G|c.827C>G|4,BUFFER|p.A276D|c.827C>A|3,BUFFER|p.A276V|c.827C>T|7,BUFFER|p.A276P|c.826G>C|3,BUFFER|p.A276T|c.826G>A|7,BUFFER|p.A276S|c.826G>T|9,BUFFER|p.A276P|c.826G>C|16,BUFFER|p.C275C|c.825T>C|4,BUFFER|p.C275W|c.825T>G|8,BUFFER|p.C275*|c.825T>A|3,BUFFER|p.C275F|c.824G>T|10,BUFFER|p.C275S|c.824G>C|4,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275F|c.824G>T|43,BUFFER|p.C275F|c.824G>T|5,BUFFER|p.C275Y|c.824G>A|54,BUFFER|p.C275Y|c.824G>A|5,BUFFER|p.C275Y|c.824G>A|11,BUFFER|p.C275G|c.823T>G|7,BUFFER|p.C275R|c.823T>C|8,BUFFER|p.V274F|c.820G>T|8,BUFFER|p.V274I|c.820G>A|4,BUFFER|p.V274F|c.820G>T|3,BUFFER|p.V274F|c.820G>T|23,BUFFER|p.R273L|c.818G>T|98,BUFFER|p.R273P|c.818G>C|4,BUFFER|p.R273H|c.818G>A|116,BUFFER|p.R273H|c.818G>A|64,BUFFER|p.R273H|c.818G>A|588,BUFFER|p.R273L|c.818G>T|5,BUFFER|p.R273H|c.818G>A|83,BUFFER|p.R273P|c.818G>C|29,BUFFER|p.R273L|c.818G>T|18,BUFFER|p.R273L|c.818G>T|12,BUFFER|p.R273S|c.817C>A|4,BUFFER|p.R273C|c.817C>T|131,BUFFER|p.R273C|c.817C>T|571,BUFFER|p.R273C|c.817C>T|75,BUFFER|p.R273G|c.817C>G|10,BUFFER|p.R273S|c.817C>A|15,BUFFER|p.R273C|c.817C>T|59,BUFFER|p.V272E|c.815T>A|9,BUFFER|p.V272G|c.815T>G|7,BUFFER|p.V272A|c.815T>C|7,BUFFER|p.V272fs*73|c.814delG|3,BUFFER|p.V272L|c.814G>T|24,BUFFER|p.V272L|c.814G>T|4,BUFFER|p.V272M|c.814G>A|11,BUFFER|p.V272M|c.814G>A|84,BUFFER|p.V272M|c.814G>A|6,BUFFER|p.V272M|c.814G>A|22,BUFFER|p.V272L|c.814G>C|4,BUFFER|p.E271V|c.812A>T|8,BUFFER|p.E271G|c.812A>G|3,BUFFER|p.E271Q|c.811G>C|4,BUFFER|p.E271K|c.811G>A|35,BUFFER|p.E271*|c.811G>T|16,BUFFER|p.E271*|c.811G>T|3,BUFFER|p.E271K|c.811G>A|13,BUFFER|p.E271K|c.811G>A|4,BUFFER|p.E271K|c.811G>A|8,BUFFER|p.F270L|c.810T>G|4,BUFFER|p.F270L|c.810T>A|5,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270Y|c.809T>A|5,BUFFER|p.F270C|c.809T>G|16,BUFFER|p.F270S|c.809T>C|3,BUFFER|p.F270S|c.809T>C|14,BUFFER|p.F270S|c.809T>C|6	MUTECT|MUSE	ACAAACACGCA	.	2	ESCA
CHMP6	0	.	GRCh37	17	78969547	78969547	+	Missense_Mutation	SNP	A	A	G	rs749930438	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.337A>G	p.Lys113Glu	p.K113E	ENST00000325167	4/8	17	9	7	30	30	0	CHMP6,missense_variant,p.Lys92Glu,ENST00000572778,;CHMP6,missense_variant,p.Lys71Glu,ENST00000571457,;CHMP6,missense_variant,p.Lys113Glu,ENST00000325167,;CHMP6,missense_variant,p.Lys27Glu,ENST00000572525,;CTD-2561B21.7,downstream_gene_variant,,ENST00000577061,;CTD-2561B21.7,downstream_gene_variant,,ENST00000576215,;	G	ENSG00000176108	ENST00000325167	Transcript	missense_variant	415	337	113	K/E	Aag/Gag	rs749930438	.	.	1	CHMP6	HGNC	25675	protein_coding	YES	CCDS11774.1	ENSP00000317468	CHMP6_HUMAN	I3L3E4_HUMAN	UPI000003E7D8	.	tolerated(0.46)	benign(0.006)	4/8	.	hmmpanther:PTHR22761,Pfam_domain:PF03357	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAACAAGATG	.	5	ESCA
ACTG1	0	.	GRCh37	17	79477227	79477227	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*489G>A	.	.	ENST00000575842	5/5	69	35	34	86	86	0	ACTG1,3_prime_UTR_variant,,ENST00000575842,;ACTG1,3_prime_UTR_variant,,ENST00000573283,;ACTG1,3_prime_UTR_variant,,ENST00000331925,;ACTG1,3_prime_UTR_variant,,ENST00000575087,;ACTG1,downstream_gene_variant,,ENST00000575994,;ACTG1,downstream_gene_variant,,ENST00000571691,;ACTG1,downstream_gene_variant,,ENST00000571721,;ACTG1,downstream_gene_variant,,ENST00000575659,;ACTG1,downstream_gene_variant,,ENST00000570382,;AC139149.1,downstream_gene_variant,,ENST00000584254,;RP13-766D20.2,upstream_gene_variant,,ENST00000430912,;ACTG1,3_prime_UTR_variant,,ENST00000576544,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576209,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576917,;ACTG1,non_coding_transcript_exon_variant,,ENST00000574671,;ACTG1,downstream_gene_variant,,ENST00000576214,;ACTG1,downstream_gene_variant,,ENST00000572105,;RP13-766D20.1,upstream_gene_variant,,ENST00000448147,;	T	ENSG00000184009	ENST00000575842	Transcript	3_prime_UTR_variant	2044	.	.	.	.	.	.	.	-1	ACTG1	HGNC	144	protein_coding	YES	CCDS11782.1	ENSP00000458162	ACTG_HUMAN	Q9UE89_HUMAN,Q96FU6_HUMAN,Q96DE1_HUMAN,Q6PJ43_HUMAN,Q562Z7_HUMAN,I3L3R2_HUMAN,I3L3I0_HUMAN,I3L1U9_HUMAN,B4E3A4_HUMAN,B3KWQ3_HUMAN,A5GZ75_HUMAN,A4UCT3_HUMAN,A1E282_HUMAN	UPI0000000C38	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GACATCAGCTA	.	5	ESCA
ANKRD29	0	.	GRCh37	18	21218851	21218851	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.292C>G	p.Leu98Val	p.L98V	ENST00000592179	4/10	70	59	10	59	59	0	ANKRD29,missense_variant,p.Leu98Val,ENST00000284207,;ANKRD29,missense_variant,p.Leu98Val,ENST00000592179,;ANKRD29,missense_variant,p.Leu98Val,ENST00000322980,;ANKRD29,intron_variant,,ENST00000586087,;ANKRD29,intron_variant,,ENST00000591280,;	C	ENSG00000154065	ENST00000592179	Transcript	missense_variant	447	292	98	L/V	Ctc/Gtc	.	.	.	-1	ANKRD29	HGNC	27110	protein_coding	YES	CCDS11879.1	ENSP00000468354	ANR29_HUMAN	.	UPI00001618ED	.	deleterious(0)	probably_damaging(0.998)	4/10	.	PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24120:SF3,hmmpanther:PTHR24120,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGAGAAATC	.	5	ESCA
DSG4	0	.	GRCh37	18	28993211	28993211	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2833G>C	p.Asp945His	p.D945H	ENST00000359747	15/15	40	23	16	35	35	0	DSG4,missense_variant,p.Asp926His,ENST00000308128,;DSG4,missense_variant,p.Asp945His,ENST00000359747,;RP11-534N16.1,intron_variant,,ENST00000581856,;RP11-534N16.1,intron_variant,,ENST00000578477,;	C	ENSG00000175065	ENST00000359747	Transcript	missense_variant	2862	2833	945	D/H	Gat/Cat	COSM405035,COSM405034	.	.	1	DSG4	HGNC	21307	protein_coding	YES	CCDS45845.1	ENSP00000352785	DSG4_HUMAN	.	UPI000035DB4E	.	deleterious(0)	probably_damaging(0.991)	15/15	.	hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF10	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTTGATCCT	.	5	ESCA
COLEC12	0	.	GRCh37	18	346689	346689	+	Silent	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933G>T	p.%3D	p.L311L	ENST00000400256	5/10	70	56	14	52	52	0	COLEC12,synonymous_variant,p.%3D,ENST00000400256,;COLEC12,non_coding_transcript_exon_variant,,ENST00000582147,;	A	ENSG00000158270	ENST00000400256	Transcript	synonymous_variant	1141	933	311	L	ctG/ctT	.	.	.	-1	COLEC12	HGNC	16016	protein_coding	YES	CCDS32782.1	ENSP00000383115	COL12_HUMAN	.	UPI00002018EC	.	.	.	5/10	.	hmmpanther:PTHR24021,hmmpanther:PTHR24021:SF19,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTCAGGTT	.	5	ESCA
CELF4	0	.	GRCh37	18	35145938	35145938	+	5'UTR	SNP	T	T	C	rs567525723	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-334A>G	.	.	ENST00000420428	1/13	15	12	3	12	12	0	CELF4,5_prime_UTR_variant,,ENST00000420428,;CELF4,5_prime_UTR_variant,,ENST00000412753,;CELF4,upstream_gene_variant,,ENST00000361795,;CELF4,upstream_gene_variant,,ENST00000601392,;CELF4,upstream_gene_variant,,ENST00000588597,;CELF4,upstream_gene_variant,,ENST00000334919,;CELF4,upstream_gene_variant,,ENST00000603232,;CELF4,upstream_gene_variant,,ENST00000591282,;CELF4,upstream_gene_variant,,ENST00000591287,;CELF4,upstream_gene_variant,,ENST00000601019,;CELF4,upstream_gene_variant,,ENST00000587449,;	C	ENSG00000101489	ENST00000420428	Transcript	5_prime_UTR_variant	63	.	.	.	.	rs567525723	.	.	-1	CELF4	HGNC	14015	protein_coding	YES	CCDS32818.1	ENSP00000410584	CELF4_HUMAN	K7EJK3_HUMAN	UPI00000726FC	.	.	.	1/13	.	.	C:0.0160	C:0.0567	C:0.0014	.	C:0	C:0	C:0.0041	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTTTTTTT	byFrequency|by1000G	2	ESCA
SMAD4	0	.	GRCh37	18	48581229	48581229	+	Nonsense_Mutation	SNP	C	C	G	rs377767331	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	5/12	25	21	3	32	32	0	SMAD4,stop_gained,p.Ser178Ter,ENST00000342988,;SMAD4,stop_gained,p.Ser178Ter,ENST00000398417,;SMAD4,stop_gained,p.Ser178Ter,ENST00000588745,;SMAD4,3_prime_UTR_variant,,ENST00000452201,;SMAD4,non_coding_transcript_exon_variant,,ENST00000592911,;SMAD4,stop_gained,p.Ser178Ter,ENST00000592186,;RP11-729L2.2,3_prime_UTR_variant,,ENST00000590722,;SMAD4,non_coding_transcript_exon_variant,,ENST00000585448,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;	G	ENSG00000141646	ENST00000342988	Transcript	stop_gained	1071	533	178	S/*	tCa/tGa	rs377767331,CM994756,COSM1226725,COSM1582844	.	.	1	SMAD4	HGNC	6770	protein_coding	YES	CCDS11950.1	ENSP00000341551	SMAD4_HUMAN	Q9BYG6_HUMAN,K7ENG8_HUMAN,K7ENG1_HUMAN,K7EL18_HUMAN,K7EL15_HUMAN,K7EIJ2_HUMAN	UPI0000053431	.	.	.	5/12	.	hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF33	.	.	.	.	.	.	.	.	.	pathogenic	0,0,1,1	10441006	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	CODON|p.0?|c.1_1659del1659|28	RADIA|MUTECT|MUSE	ACATTCAATTC	.	3	ESCA
MC4R	0	.	GRCh37	18	58038944	58038944	+	Silent	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.639C>G	p.%3D	p.V213V	ENST00000299766	1/1	18	10	8	32	32	0	MC4R,synonymous_variant,p.%3D,ENST00000299766,;	C	ENSG00000166603	ENST00000299766	Transcript	synonymous_variant	1058	639	213	V	gtC/gtG	.	.	.	-1	MC4R	HGNC	6932	protein_coding	YES	CCDS11976.1	ENSP00000299766	MC4R_HUMAN	K4N7A9_HUMAN,A0N0W8_HUMAN	UPI000013E5E3	.	.	.	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF6,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATGTGGACATA	.	5	ESCA
CDH7	0	.	GRCh37	18	63430240	63430240	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.162C>G	p.Phe54Leu	p.F54L	ENST00000397968	2/12	60	39	21	72	72	0	CDH7,missense_variant,p.Phe54Leu,ENST00000397968,;CDH7,missense_variant,p.Phe54Leu,ENST00000536984,;CDH7,missense_variant,p.Phe54Leu,ENST00000323011,;CDH7,upstream_gene_variant,,ENST00000581601,;	G	ENSG00000081138	ENST00000397968	Transcript	missense_variant	588	162	54	F/L	ttC/ttG	.	.	.	1	CDH7	HGNC	1766	protein_coding	YES	CCDS11993.1	ENSP00000381058	CADH7_HUMAN	.	UPI000013D269	.	tolerated(0.08)	probably_damaging(0.999)	2/12	.	hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGTTCTTTGT	.	5	ESCA
CYB5A	0	.	GRCh37	18	71920714	71920714	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*105G>C	.	.	ENST00000340533	5/5	64	51	13	48	48	0	CYB5A,3_prime_UTR_variant,,ENST00000494131,;CYB5A,3_prime_UTR_variant,,ENST00000340533,;CYB5A,3_prime_UTR_variant,,ENST00000299438,;CYB5A,3_prime_UTR_variant,,ENST00000397914,;CYB5A,downstream_gene_variant,,ENST00000579064,;CYB5A,non_coding_transcript_exon_variant,,ENST00000583418,;CYB5A,non_coding_transcript_exon_variant,,ENST00000580678,;	G	ENSG00000166347	ENST00000340533	Transcript	3_prime_UTR_variant	651	.	.	.	.	.	.	.	-1	CYB5A	HGNC	2570	protein_coding	YES	CCDS12004.1	ENSP00000341625	CYB5_HUMAN	Q9UML1_HUMAN,J3KNC7_HUMAN	UPI0000000DF0	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCATTGT	.	5	ESCA
CYB5A	0	.	GRCh37	18	71920820	71920820	+	Nonstop_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.404G>T	p.Ter135LeuextTer73	p.*135Lext*73	ENST00000340533	5/5	31	24	7	28	28	0	CYB5A,stop_lost,p.Ter135LeuextTer73,ENST00000340533,;CYB5A,stop_lost,p.Ter61LeuextTer73,ENST00000299438,;CYB5A,stop_lost,p.Ter125LeuextTer?,ENST00000397914,;CYB5A,3_prime_UTR_variant,,ENST00000494131,;CYB5A,non_coding_transcript_exon_variant,,ENST00000579064,;CYB5A,non_coding_transcript_exon_variant,,ENST00000583418,;CYB5A,non_coding_transcript_exon_variant,,ENST00000580678,;	A	ENSG00000166347	ENST00000340533	Transcript	stop_lost	545	404	135	*/L	tGa/tTa	.	.	.	-1	CYB5A	HGNC	2570	protein_coding	YES	CCDS12004.1	ENSP00000341625	CYB5_HUMAN	Q9UML1_HUMAN,J3KNC7_HUMAN	UPI0000000DF0	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGTTCAGTCC	.	5	ESCA
RALBP1	0	.	GRCh37	18	9537334	9537334	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1399G>C	.	.	ENST00000019317	10/10	16	11	5	10	10	0	RALBP1,3_prime_UTR_variant,,ENST00000383432,;RALBP1,3_prime_UTR_variant,,ENST00000019317,;	C	ENSG00000017797	ENST00000019317	Transcript	3_prime_UTR_variant	3590	.	.	.	.	.	.	.	1	RALBP1	HGNC	9841	protein_coding	YES	CCDS11845.1	ENSP00000019317	RBP1_HUMAN	Q59E87_HUMAN,J3QLT3_HUMAN,E7ENF8_HUMAN	UPI00000703A3	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	GAGAAGATATT	.	3	ESCA
GRIN3B	0	.	GRCh37	19	1005401	1005401	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1901G>T	p.Ser634Ile	p.S634I	ENST00000234389	3/9	20	15	5	23	23	0	GRIN3B,missense_variant,p.Ser634Ile,ENST00000234389,;TMEM259,downstream_gene_variant,,ENST00000593068,;TMEM259,downstream_gene_variant,,ENST00000333175,;TMEM259,downstream_gene_variant,,ENST00000356663,;AC004528.4,upstream_gene_variant,,ENST00000588380,;GRIN3B,downstream_gene_variant,,ENST00000588335,;TMEM259,downstream_gene_variant,,ENST00000592052,;TMEM259,downstream_gene_variant,,ENST00000592618,;	T	ENSG00000116032	ENST00000234389	Transcript	missense_variant	1920	1901	634	S/I	aGc/aTc	.	.	.	1	GRIN3B	HGNC	16768	protein_coding	YES	CCDS32861.1	ENSP00000234389	NMD3B_HUMAN	.	UPI000004064B	.	tolerated(0.35)	benign(0.241)	3/9	.	hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Pfam_domain:PF00060,Gene3D:1.10.287.70,Pfam_domain:PF00497,SMART_domains:SM00079	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTCCAGCAAGA	.	2	ESCA
SBNO2	0	.	GRCh37	19	1107645	1107645	+	3'UTR	SNP	A	A	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*574T>A	.	.	ENST00000361757	32/32	37	25	11	50	50	0	SBNO2,3_prime_UTR_variant,,ENST00000438103,;SBNO2,3_prime_UTR_variant,,ENST00000587024,;SBNO2,3_prime_UTR_variant,,ENST00000361757,;GPX4,downstream_gene_variant,,ENST00000585362,;GPX4,downstream_gene_variant,,ENST00000587648,;GPX4,downstream_gene_variant,,ENST00000354171,;GPX4,downstream_gene_variant,,ENST00000589115,;GPX4,downstream_gene_variant,,ENST00000588919,;GPX4,downstream_gene_variant,,ENST00000593032,;SBNO2,downstream_gene_variant,,ENST00000587673,;GPX4,downstream_gene_variant,,ENST00000587932,;SBNO2,downstream_gene_variant,,ENST00000586109,;GPX4,downstream_gene_variant,,ENST00000585480,;GPX4,downstream_gene_variant,,ENST00000592940,;	T	ENSG00000064932	ENST00000361757	Transcript	3_prime_UTR_variant	4913	.	.	.	.	.	.	.	-1	SBNO2	HGNC	29158	protein_coding	YES	CCDS45894.1	ENSP00000354733	SBNO2_HUMAN	K7ERL2_HUMAN,K7ENA9_HUMAN	UPI0000140680	.	.	.	32/32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TAGGCAAAAGG	.	5	ESCA
EPOR	0	.	GRCh37	19	11488935	11488935	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1252G>A	p.Gly418Arg	p.G418R	ENST00000222139	8/8	23	15	8	23	23	0	EPOR,missense_variant,p.Gly418Arg,ENST00000222139,;EPOR,3_prime_UTR_variant,,ENST00000592375,;SWSAP1,downstream_gene_variant,,ENST00000312423,;CTD-2342J14.6,upstream_gene_variant,,ENST00000590399,;EPOR,3_prime_UTR_variant,,ENST00000586890,;EPOR,3_prime_UTR_variant,,ENST00000588859,;EPOR,3_prime_UTR_variant,,ENST00000591958,;EPOR,non_coding_transcript_exon_variant,,ENST00000588681,;EPOR,non_coding_transcript_exon_variant,,ENST00000590927,;EPOR,downstream_gene_variant,,ENST00000589402,;	T	ENSG00000187266	ENST00000222139	Transcript	missense_variant	1357	1252	418	G/R	Gga/Aga	.	.	.	-1	EPOR	HGNC	3416	protein_coding	YES	CCDS12260.1	ENSP00000222139	EPOR_HUMAN	I6R7G3_HUMAN	UPI000012A0AD	.	tolerated(0.36)	benign(0.035)	8/8	.	hmmpanther:PTHR23037:SF7,hmmpanther:PTHR23037,PIRSF_domain:PIRSF001959	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTCCCTCTG	.	5	ESCA
ECSIT	0	.	GRCh37	19	11616949	11616949	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*50G>C	.	.	ENST00000270517	8/8	22	16	6	27	27	0	ECSIT,3_prime_UTR_variant,,ENST00000252440,;ECSIT,3_prime_UTR_variant,,ENST00000270517,;ECSIT,3_prime_UTR_variant,,ENST00000417981,;ECSIT,3_prime_UTR_variant,,ENST00000588998,;ZNF653,upstream_gene_variant,,ENST00000293771,;ECSIT,downstream_gene_variant,,ENST00000591104,;ECSIT,downstream_gene_variant,,ENST00000592312,;ECSIT,downstream_gene_variant,,ENST00000585318,;ZNF653,upstream_gene_variant,,ENST00000593191,;ECSIT,downstream_gene_variant,,ENST00000591352,;ECSIT,3_prime_UTR_variant,,ENST00000592571,;ECSIT,non_coding_transcript_exon_variant,,ENST00000585898,;ZNF653,upstream_gene_variant,,ENST00000590548,;ECSIT,downstream_gene_variant,,ENST00000593231,;ZNF653,upstream_gene_variant,,ENST00000588541,;CTC-398G3.6,upstream_gene_variant,,ENST00000585656,;	G	ENSG00000130159	ENST00000270517	Transcript	3_prime_UTR_variant	1482	.	.	.	.	.	.	.	-1	ECSIT	HGNC	29548	protein_coding	YES	CCDS12262.1	ENSP00000270517	ECSIT_HUMAN	K7EPL5_HUMAN,K7EM98_HUMAN,K7EJI1_HUMAN,J3KTF5_HUMAN	UPI0000072F31	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCTTCAGTCC	.	2	ESCA
STK11	0	.	GRCh37	19	1220640	1220640	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	5/10	9	6	3	9	9	0	STK11,stop_gained,p.Gln220Ter,ENST00000326873,;STK11,upstream_gene_variant,,ENST00000586243,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,3_prime_UTR_variant,,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,upstream_gene_variant,,ENST00000585465,;	T	ENSG00000118046	ENST00000326873	Transcript	stop_gained	1831	658	220	Q/*	Cag/Tag	CM991157,KinMutBase_STK11_DNA:g.14728C>T,COSM13480	.	.	1	STK11	HGNC	11389	protein_coding	YES	CCDS45896.1	ENSP00000324856	STK11_HUMAN	Q9NS52_HUMAN	UPI0000136105	.	.	.	5/10	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF1,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,0,1	.	.	.	.	.	.	.	.	.	1	PASS	SITE|p.Q220*|c.658C>T|4,CODON|p.0?|c.1_1302del1302|16,BUFFER|p.S216F|c.647C>T|3	MUTECT|MUSE	CTTTCCAGCCG	.	2	ESCA
HOOK2	0	.	GRCh37	19	12882120	12882120	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.614C>G	p.Ser205Ter	p.S205*	ENST00000397668	9/23	57	39	17	75	75	0	HOOK2,stop_gained,p.Ser132Ter,ENST00000589400,;HOOK2,stop_gained,p.Ser132Ter,ENST00000592079,;HOOK2,stop_gained,p.Ser205Ter,ENST00000397668,;HOOK2,stop_gained,p.Ser205Ter,ENST00000264827,;HOOK2,stop_gained,p.Ser132Ter,ENST00000590839,;HOOK2,downstream_gene_variant,,ENST00000588052,;HOOK2,downstream_gene_variant,,ENST00000587178,;HOOK2,downstream_gene_variant,,ENST00000587964,;HOOK2,intron_variant,,ENST00000589965,;HOOK2,downstream_gene_variant,,ENST00000589765,;HOOK2,3_prime_UTR_variant,,ENST00000586719,;HOOK2,non_coding_transcript_exon_variant,,ENST00000586284,;HOOK2,intron_variant,,ENST00000586188,;HOOK2,upstream_gene_variant,,ENST00000589398,;HOOK2,downstream_gene_variant,,ENST00000592512,;HOOK2,upstream_gene_variant,,ENST00000591839,;HOOK2,upstream_gene_variant,,ENST00000592259,;HOOK2,downstream_gene_variant,,ENST00000589134,;HOOK2,downstream_gene_variant,,ENST00000591251,;HOOK2,downstream_gene_variant,,ENST00000592808,;HOOK2,downstream_gene_variant,,ENST00000591641,;HOOK2,downstream_gene_variant,,ENST00000593143,;	C	ENSG00000095066	ENST00000397668	Transcript	stop_gained	688	614	205	S/*	tCa/tGa	.	.	.	-1	HOOK2	HGNC	19885	protein_coding	YES	CCDS42508.1	ENSP00000380785	HOOK2_HUMAN	K7ENU5_HUMAN,K7EMR5_HUMAN,K7EJ48_HUMAN	UPI00003D0BC0	.	.	.	9/23	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947,Pfam_domain:PF05622	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTCTGACAGG	.	5	ESCA
hsa-mir-1199	0	.	GRCh37	19	14183884	14183884	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.189C>G	p.%3D	p.L63L	ENST00000269720	2/4	61	49	12	106	106	0	hsa-mir-1199,synonymous_variant,p.%3D,ENST00000269720,;hsa-mir-1199,5_prime_UTR_variant,,ENST00000587086,;hsa-mir-1199,upstream_gene_variant,,ENST00000590772,;hsa-mir-1199,non_coding_transcript_exon_variant,,ENST00000591982,;EEF1DP1,downstream_gene_variant,,ENST00000585891,;EEF1DP1,downstream_gene_variant,,ENST00000430596,;	G	ENSG00000141854	ENST00000269720	Transcript	synonymous_variant	189	189	63	L	ctC/ctG	.	.	.	1	hsa-mir-1199	miRBase	.	protein_coding	YES	.	ENSP00000269720	YS003_HUMAN	K7EJG0_HUMAN	UPI00001D826F	.	.	.	2/4	.	hmmpanther:PTHR18839,hmmpanther:PTHR18839:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTCCTCGAGCC	.	4	ESCA
OR7C2	0	.	GRCh37	19	15052578	15052578	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.278C>G	p.Thr93Ser	p.T93S	ENST00000248072	1/1	40	25	14	57	57	0	OR7C2,missense_variant,p.Thr93Ser,ENST00000248072,;	G	ENSG00000127529	ENST00000248072	Transcript	missense_variant	278	278	93	T/S	aCt/aGt	.	.	.	1	OR7C2	HGNC	8374	protein_coding	YES	CCDS12320.1	ENSP00000248072	OR7C2_HUMAN	.	UPI0000041E80	.	tolerated_low_confidence(0.5)	benign(0.05)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF307,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCACTTTTG	.	5	ESCA
BRD4	0	.	GRCh37	19	15366974	15366974	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1652A>G	p.His551Arg	p.H551R	ENST00000263377	9/20	37	28	9	51	51	0	BRD4,missense_variant,p.His551Arg,ENST00000594841,;BRD4,missense_variant,p.His551Arg,ENST00000371835,;BRD4,missense_variant,p.His551Arg,ENST00000263377,;BRD4,missense_variant,p.His551Arg,ENST00000360016,;BRD4,non_coding_transcript_exon_variant,,ENST00000602230,;BRD4,upstream_gene_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,;	C	ENSG00000141867	ENST00000263377	Transcript	missense_variant	1874	1652	551	H/R	cAc/cGc	.	.	.	-1	BRD4	HGNC	13575	protein_coding	YES	CCDS12328.1	ENSP00000263377	BRD4_HUMAN	Q96HN0_HUMAN,M0R0H4_HUMAN,M0QZD9_HUMAN	UPI0000126ACE	.	.	benign(0.227)	9/20	.	hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF143,Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGTGCTTT	.	5	ESCA
CTC-429P9.4	0	.	GRCh37	19	16770258	16770258	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.63G>C	p.%3D	p.L21L	ENST00000593459	3/5	19	14	5	23	23	0	CTC-429P9.4,synonymous_variant,p.%3D,ENST00000593459,;SMIM7,synonymous_variant,p.%3D,ENST00000487416,;SMIM7,synonymous_variant,p.%3D,ENST00000358726,;SMIM7,synonymous_variant,p.%3D,ENST00000597711,;TMEM38A,upstream_gene_variant,,ENST00000599479,;TMEM38A,upstream_gene_variant,,ENST00000187762,;SMIM7,splice_region_variant,,ENST00000461364,;SMIM7,splice_region_variant,,ENST00000397349,;CTC-429P9.4,splice_region_variant,,ENST00000593962,;SMIM7,intron_variant,,ENST00000594507,;CTC-429P9.4,synonymous_variant,p.%3D,ENST00000601636,;SMIM7,synonymous_variant,p.%3D,ENST00000481671,;CTC-429P9.4,synonymous_variant,p.%3D,ENST00000593991,;SMIM7,synonymous_variant,p.%3D,ENST00000600740,;SMIM7,synonymous_variant,p.%3D,ENST00000593404,;SMIM7,synonymous_variant,p.%3D,ENST00000599310,;SMIM7,synonymous_variant,p.%3D,ENST00000602194,;CTC-429P9.4,synonymous_variant,p.%3D,ENST00000600705,;SMIM7,synonymous_variant,p.%3D,ENST00000594662,;SMIM7,synonymous_variant,p.%3D,ENST00000597781,;SMIM7,synonymous_variant,p.%3D,ENST00000593409,;SMIM7,synonymous_variant,p.%3D,ENST00000598278,;CTC-429P9.4,synonymous_variant,p.%3D,ENST00000595505,;SMIM7,synonymous_variant,p.%3D,ENST00000487803,;SMIM7,synonymous_variant,p.%3D,ENST00000461488,;CTC-429P9.4,synonymous_variant,p.%3D,ENST00000594509,;SMIM7,synonymous_variant,p.%3D,ENST00000465250,;SMIM7,synonymous_variant,p.%3D,ENST00000463051,;TMEM38A,upstream_gene_variant,,ENST00000595452,;	G	ENSG00000268790	ENST00000593459	Transcript	synonymous_variant	63	63	21	L	ctG/ctC	.	.	.	-1	CTC-429P9.4	Clone_based_vega_gene	.	protein_coding	YES	.	ENSP00000470086	.	M0QYU9_HUMAN	UPI0002A47677	.	.	.	3/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTTTCCTACA	.	2	ESCA
CILP2	0	.	GRCh37	19	19653312	19653312	+	Missense_Mutation	SNP	G	G	A	rs774293541	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.721G>A	p.Asp241Asn	p.D241N	ENST00000291495	5/8	14	10	3	28	28	0	CILP2,missense_variant,p.Asp241Asn,ENST00000291495,;CILP2,missense_variant,p.Asp247Asn,ENST00000586018,;YJEFN3,downstream_gene_variant,,ENST00000436027,;YJEFN3,downstream_gene_variant,,ENST00000514277,;CILP2,non_coding_transcript_exon_variant,,ENST00000588333,;YJEFN3,downstream_gene_variant,,ENST00000458210,;	A	ENSG00000160161	ENST00000291495	Transcript	missense_variant	806	721	241	D/N	Gat/Aat	rs774293541	.	.	1	CILP2	HGNC	24213	protein_coding	YES	CCDS12405.1	ENSP00000291495	CILP2_HUMAN	.	UPI000013E04D	.	tolerated(0.16)	benign(0.038)	5/8	.	hmmpanther:PTHR15031:SF0,hmmpanther:PTHR15031,Gene3D:2.60.40.1120,Pfam_domain:PF13620,Superfamily_domains:SSF49464	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT	CCAGCGATGCT	byFrequency	2	ESCA
CTC-448F2.3	0	.	GRCh37	19	30414647	30414647	+	3'Flank	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000585753	.	27	23	4	60	60	0	URI1,synonymous_variant,p.%3D,ENST00000585655,;URI1,synonymous_variant,p.%3D,ENST00000360605,;URI1,5_prime_UTR_variant,,ENST00000574233,;URI1,5_prime_UTR_variant,,ENST00000570564,;URI1,non_coding_transcript_exon_variant,,ENST00000574766,;CTC-448F2.3,downstream_gene_variant,,ENST00000585753,;	T	ENSG00000267258	ENST00000585753	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	2087	1	CTC-448F2.3	Clone_based_vega_gene	.	processed_pseudogene	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GGGCTCTGGCA	.	4	ESCA
SLC7A9	0	.	GRCh37	19	33359402	33359402	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39G>C	p.Glu13Asp	p.E13D	ENST00000023064	2/13	38	33	5	23	23	0	SLC7A9,missense_variant,p.Glu13Asp,ENST00000023064,;SLC7A9,missense_variant,p.Glu13Asp,ENST00000590341,;SLC7A9,missense_variant,p.Glu13Asp,ENST00000587772,;SLC7A9,missense_variant,p.Glu13Asp,ENST00000592232,;SLC7A9,missense_variant,p.Glu13Asp,ENST00000590465,;SLC7A9,upstream_gene_variant,,ENST00000589659,;	G	ENSG00000021488	ENST00000023064	Transcript	missense_variant	231	39	13	E/D	gaG/gaC	.	.	.	-1	SLC7A9	HGNC	11067	protein_coding	YES	CCDS12425.1	ENSP00000023064	BAT1_HUMAN	K7EIF5_HUMAN	UPI0000037773	.	tolerated(0.52)	benign(0.001)	2/13	.	hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF305	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACTTCTCATC	.	4	ESCA
CEP89	0	.	GRCh37	19	33462550	33462550	+	Intron	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.39+192C>G	.	.	ENST00000305768	.	16	12	3	12	12	0	CEP89,intron_variant,,ENST00000590597,;CEP89,intron_variant,,ENST00000305768,;C19orf40,upstream_gene_variant,,ENST00000588258,;C19orf40,upstream_gene_variant,,ENST00000590179,;C19orf40,upstream_gene_variant,,ENST00000590281,;C19orf40,upstream_gene_variant,,ENST00000589646,;CEP89,non_coding_transcript_exon_variant,,ENST00000591863,;CEP89,non_coding_transcript_exon_variant,,ENST00000592401,;CEP89,intron_variant,,ENST00000591205,;CEP89,intron_variant,,ENST00000586984,;C19orf40,upstream_gene_variant,,ENST00000254262,;	C	ENSG00000121289	ENST00000305768	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	CEP89	HGNC	25907	protein_coding	YES	CCDS32987.1	ENSP00000306105	CEP89_HUMAN	.	UPI000020202C	.	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|SOMATICSNIPER|VARSCANS	AGAGCGAGACC	.	3	ESCA
ZNF567	0	.	GRCh37	19	37211573	37211573	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3G>C	.	.	ENST00000585696	3/3	62	55	7	69	69	0	ZNF567,3_prime_UTR_variant,,ENST00000360729,;ZNF567,3_prime_UTR_variant,,ENST00000536254,;ZNF567,3_prime_UTR_variant,,ENST00000585696,;ZNF567,intron_variant,,ENST00000392163,;ZNF567,intron_variant,,ENST00000589264,;ZNF567,intron_variant,,ENST00000588311,;ZNF850,intron_variant,,ENST00000589390,;ZNF567,intron_variant,,ENST00000591308,;	C	ENSG00000189042	ENST00000585696	Transcript	3_prime_UTR_variant	3084	.	.	.	.	.	.	.	1	ZNF567	HGNC	28696	protein_coding	YES	CCDS12495.1	ENSP00000467379	ZN567_HUMAN	.	UPI00001BBFD4	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TAAATGATGTG	.	2	ESCA
ZNF829	0	.	GRCh37	19	37382734	37382734	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1202G>T	p.Gly401Val	p.G401V	ENST00000520965	6/6	49	40	9	72	72	0	ZNF829,missense_variant,p.Gly401Val,ENST00000520965,;ZNF829,missense_variant,p.Gly320Val,ENST00000391711,;ZNF345,intron_variant,,ENST00000526123,;ZNF345,intron_variant,,ENST00000586933,;ZNF345,intron_variant,,ENST00000525851,;ZNF345,intron_variant,,ENST00000432005,;ZNF345,intron_variant,,ENST00000534729,;ZNF345,intron_variant,,ENST00000529989,;	A	ENSG00000185869	ENST00000520965	Transcript	missense_variant	1269	1202	401	G/V	gGt/gTt	.	.	.	-1	ZNF829	HGNC	34032	protein_coding	YES	CCDS59380.1	ENSP00000428679	.	.	UPI00002021CD	.	deleterious(0)	probably_damaging(0.999)	6/6	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Pfam_domain:PF13465,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCACCAGTA	.	5	ESCA
ZNF568	0	.	GRCh37	19	37464461	37464461	+	5'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-301C>T	.	.	ENST00000455817	1/4	98	81	17	78	78	0	ZNF568,5_prime_UTR_variant,,ENST00000455817,;ZNF568,5_prime_UTR_variant,,ENST00000586353,;ZNF568,5_prime_UTR_variant,,ENST00000433993,;ZNF568,intron_variant,,ENST00000427117,;ZNF568,intron_variant,,ENST00000455427,;ZNF568,intron_variant,,ENST00000444991,;ZNF568,intron_variant,,ENST00000592567,;ZNF568,upstream_gene_variant,,ENST00000588596,;	T	ENSG00000198453	ENST00000455817	Transcript	5_prime_UTR_variant	22	.	.	.	.	.	.	.	1	ZNF568	HGNC	25392	protein_coding	.	.	ENSP00000407153	.	K7ELK8_HUMAN,C9JXQ5_HUMAN	UPI000198C7C2	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGCGCTGGAG	.	5	ESCA
ZNF420	0	.	GRCh37	19	37619881	37619881	+	Missense_Mutation	SNP	G	G	A	rs140027212	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1988G>A	p.Arg663Lys	p.R663K	ENST00000337995	5/5	56	43	13	73	73	0	ZNF420,missense_variant,p.Arg663Lys,ENST00000337995,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF420,intron_variant,,ENST00000585862,;ZNF420,intron_variant,,ENST00000304239,;ZNF420,downstream_gene_variant,,ENST00000590332,;ZNF420,downstream_gene_variant,,ENST00000587029,;ZNF420,downstream_gene_variant,,ENST00000589245,;CTC-454I21.4,intron_variant,,ENST00000587645,;ZNF585A,intron_variant,,ENST00000588723,;ZNF420,intron_variant,,ENST00000586540,;ZNF585A,intron_variant,,ENST00000587817,;ZNF420,downstream_gene_variant,,ENST00000589461,;	A	ENSG00000197050	ENST00000337995	Transcript	missense_variant	2203	1988	663	R/K	aGa/aAa	rs140027212,COSM264994	.	.	1	ZNF420	HGNC	20649	protein_coding	YES	CCDS12498.1	ENSP00000338770	ZN420_HUMAN	K7ERS3_HUMAN,K7EQC9_HUMAN,K7ELF6_HUMAN	UPI000007049F	.	tolerated(0.18)	benign(0)	5/5	.	PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCAGAGAATTC	byCluster|by1000G	5	ESCA
HNRNPL	0	.	GRCh37	19	39327114	39327114	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*248G>A	.	.	ENST00000221419	13/13	31	27	3	50	50	0	HNRNPL,3_prime_UTR_variant,,ENST00000601449,;HNRNPL,3_prime_UTR_variant,,ENST00000221419,;AC104534.3,intron_variant,,ENST00000602021,;AC104534.3,intron_variant,,ENST00000594769,;ECH1,upstream_gene_variant,,ENST00000595470,;ECH1,upstream_gene_variant,,ENST00000602115,;ECH1,upstream_gene_variant,,ENST00000597205,;ECH1,upstream_gene_variant,,ENST00000221418,;ECH1,upstream_gene_variant,,ENST00000595567,;ECH1,upstream_gene_variant,,ENST00000601778,;HNRNPL,downstream_gene_variant,,ENST00000600873,;ECH1,upstream_gene_variant,,ENST00000601094,;ECH1,upstream_gene_variant,,ENST00000597805,;HNRNPL,3_prime_UTR_variant,,ENST00000388749,;HNRNPL,non_coding_transcript_exon_variant,,ENST00000595443,;HNRNPL,non_coding_transcript_exon_variant,,ENST00000595164,;HNRNPL,non_coding_transcript_exon_variant,,ENST00000595804,;HNRNPL,non_coding_transcript_exon_variant,,ENST00000597731,;HNRNPL,downstream_gene_variant,,ENST00000598985,;HNRNPL,downstream_gene_variant,,ENST00000601664,;ECH1,upstream_gene_variant,,ENST00000600178,;ECH1,upstream_gene_variant,,ENST00000594164,;ECH1,upstream_gene_variant,,ENST00000598707,;ECH1,upstream_gene_variant,,ENST00000601060,;ECH1,upstream_gene_variant,,ENST00000598316,;	T	ENSG00000104824	ENST00000221419	Transcript	3_prime_UTR_variant	2385	.	.	.	.	.	.	.	-1	HNRNPL	HGNC	5045	protein_coding	YES	CCDS33015.1	ENSP00000221419	HNRPL_HUMAN	Q6NTA2_HUMAN	UPI00004432FA	.	.	.	13/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAAATCACATG	.	2	ESCA
LYPD4	0	.	GRCh37	19	42343053	42343053	+	Missense_Mutation	SNP	C	C	T	rs368266342	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.113G>A	p.Arg38Lys	p.R38K	ENST00000330743	3/5	26	19	7	36	36	0	LYPD4,missense_variant,p.Arg38Lys,ENST00000330743,;LYPD4,intron_variant,,ENST00000343055,;LYPD4,intron_variant,,ENST00000601246,;AC020956.3,upstream_gene_variant,,ENST00000593354,;	T	ENSG00000183103	ENST00000330743	Transcript	missense_variant	1325	113	38	R/K	aGa/aAa	rs368266342,COSM1612305	.	.	-1	LYPD4	HGNC	28659	protein_coding	YES	CCDS12587.1	ENSP00000328737	LYPD4_HUMAN	A8K8E0_HUMAN	UPI0000366E14	.	tolerated(0.27)	probably_damaging(0.991)	3/5	.	hmmpanther:PTHR16529:SF6,hmmpanther:PTHR16529	.	.	.	.	.	.	.	T:0.0002	T:0	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCTGAAT	.	5	ESCA
ZNF233	0	.	GRCh37	19	44764147	44764147	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-56G>A	.	.	ENST00000391958	1/5	18	12	6	18	18	0	ZNF233,missense_variant,p.Gly85Glu,ENST00000334152,;ZNF233,5_prime_UTR_variant,,ENST00000588489,;ZNF233,5_prime_UTR_variant,,ENST00000391958,;ZNF233,intron_variant,,ENST00000592581,;ZNF235,intron_variant,,ENST00000589799,;ZNF233,intron_variant,,ENST00000590668,;ZNF233,upstream_gene_variant,,ENST00000589522,;ZNF235,intron_variant,,ENST00000592844,;	A	ENSG00000159915	ENST00000391958	Transcript	5_prime_UTR_variant	72	.	.	.	.	.	.	.	1	ZNF233	HGNC	30946	protein_coding	YES	CCDS33047.1	ENSP00000375820	ZN233_HUMAN	K7EN46_HUMAN	UPI000049DEBE	.	.	.	1/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CGTTGGACTCG	.	3	ESCA
GLTSCR1	0	.	GRCh37	19	48176990	48176990	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.55C>G	p.Leu19Val	p.L19V	ENST00000396720	4/15	43	40	3	41	41	0	GLTSCR1,missense_variant,p.Leu19Val,ENST00000594866,;GLTSCR1,missense_variant,p.Leu19Val,ENST00000396720,;CTD-2571L23.8,intron_variant,,ENST00000599924,;	G	ENSG00000063169	ENST00000396720	Transcript	missense_variant	249	55	19	L/V	Ctc/Gtc	.	.	.	1	GLTSCR1	HGNC	4332	protein_coding	YES	CCDS46134.1	ENSP00000379946	GSCR1_HUMAN	M0QYC3_HUMAN	UPI00016278EE	.	.	unknown(0)	4/15	.	hmmpanther:PTHR15572:SF1,hmmpanther:PTHR15572	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGCCCTCAAT	.	2	ESCA
RPL13A	0	.	GRCh37	19	49990672	49990672	+	5'Flank	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000391857	.	16	12	4	23	23	0	RPL13A,upstream_gene_variant,,ENST00000467825,;FLT3LG,downstream_gene_variant,,ENST00000598555,;FLT3LG,downstream_gene_variant,,ENST00000600429,;FLT3LG,downstream_gene_variant,,ENST00000597551,;FLT3LG,downstream_gene_variant,,ENST00000204637,;RPL13A,upstream_gene_variant,,ENST00000391857,;FLT3LG,downstream_gene_variant,,ENST00000596435,;FLT3LG,downstream_gene_variant,,ENST00000594009,;SNORD33,upstream_gene_variant,,ENST00000362761,;SNORD35A,upstream_gene_variant,,ENST00000363389,;SNORD34,upstream_gene_variant,,ENST00000365633,;SNORD32A,upstream_gene_variant,,ENST00000364805,;CTD-3148I10.15,non_coding_transcript_exon_variant,,ENST00000595815,;RPL13A,upstream_gene_variant,,ENST00000477613,;RPL13A,upstream_gene_variant,,ENST00000486930,;FLT3LG,downstream_gene_variant,,ENST00000600084,;FLT3LG,downstream_gene_variant,,ENST00000601800,;RPL13A,upstream_gene_variant,,ENST00000488946,;FLT3LG,downstream_gene_variant,,ENST00000598472,;RPL13A,upstream_gene_variant,,ENST00000474171,;RPL13A,upstream_gene_variant,,ENST00000476300,;RPL13A,upstream_gene_variant,,ENST00000484279,;RPL13A,upstream_gene_variant,,ENST00000476268,;RPL13A,upstream_gene_variant,,ENST00000472481,;RPL13A,upstream_gene_variant,,ENST00000468655,;CTD-3148I10.9,downstream_gene_variant,,ENST00000599536,;RPL13A,upstream_gene_variant,,ENST00000479992,;	A	ENSG00000142541	ENST00000391857	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	139	1	RPL13A	HGNC	10304	protein_coding	YES	CCDS12768.1	ENSP00000375730	RL13A_HUMAN	Q9BSQ6_HUMAN,Q8J015_HUMAN	UPI000013D896	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCTGACCGC	.	2	ESCA
LILRB4	0	.	GRCh37	19	55175698	55175698	+	Silent	SNP	C	C	T	rs541287083	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.417C>T	p.%3D	p.S139S	ENST00000391736	6/14	114	99	14	116	116	0	LILRB4,synonymous_variant,p.%3D,ENST00000434286,;LILRB4,synonymous_variant,p.%3D,ENST00000270452,;LILRB4,synonymous_variant,p.%3D,ENST00000391733,;LILRB4,synonymous_variant,p.%3D,ENST00000391736,;LILRB4,synonymous_variant,p.%3D,ENST00000391734,;LILRB4,synonymous_variant,p.%3D,ENST00000430952,;LILRB4,non_coding_transcript_exon_variant,,ENST00000494796,;LILRB4,upstream_gene_variant,,ENST00000461262,;LILRB4,upstream_gene_variant,,ENST00000470943,;	T	ENSG00000186818	ENST00000391736	Transcript	synonymous_variant	732	417	139	S	agC/agT	rs541287083,COSM1001195	.	.	1	LILRB4	HGNC	6608	protein_coding	YES	CCDS12902.1	ENSP00000375616	LIRB4_HUMAN	.	UPI000013D889	.	.	.	6/14	.	PROSITE_profiles:PS50835,hmmpanther:PTHR11738:SF30,hmmpanther:PTHR11738,Pfam_domain:PF13927,Gene3D:2.60.40.10,Superfamily_domains:SSF48726	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AAGAGCGTGAC	by1000G	4	ESCA
ZNF773	0	.	GRCh37	19	58018634	58018634	+	Missense_Mutation	SNP	G	G	A	rs761582727	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1171G>A	p.Glu391Lys	p.E391K	ENST00000282292	4/4	95	82	13	100	100	0	ZNF773,missense_variant,p.Glu391Lys,ENST00000282292,;ZNF773,missense_variant,p.Glu390Lys,ENST00000598770,;ZNF773,intron_variant,,ENST00000593916,;ZNF773,intron_variant,,ENST00000599847,;ZNF773,intron_variant,,ENST00000597061,;AC003005.4,downstream_gene_variant,,ENST00000599674,;AC003005.4,downstream_gene_variant,,ENST00000601674,;ZNF773,downstream_gene_variant,,ENST00000601958,;	A	ENSG00000152439	ENST00000282292	Transcript	missense_variant	1311	1171	391	E/K	Gaa/Aaa	rs761582727	.	.	1	ZNF773	HGNC	30487	protein_coding	YES	CCDS33134.1	ENSP00000282292	ZN773_HUMAN	.	UPI00001BD93D	.	tolerated(0.07)	benign(0.211)	4/4	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF40,hmmpanther:PTHR24387,PROSITE_patterns:PS00028,Pfam_domain:PF13465,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAATGAATGT	.	5	ESCA
MYO1F	0	.	GRCh37	19	8601234	8601234	+	Missense_Mutation	SNP	C	C	T	rs201646155	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1945G>A	p.Glu649Lys	p.E649K	ENST00000338257	19/28	23	16	7	36	36	0	MYO1F,missense_variant,p.Glu649Lys,ENST00000338257,;MYO1F,missense_variant,p.Arg143Gln,ENST00000598005,;MYO1F,non_coding_transcript_exon_variant,,ENST00000597222,;MYO1F,downstream_gene_variant,,ENST00000602136,;	T	ENSG00000142347	ENST00000338257	Transcript	missense_variant	2213	1945	649	E/K	Gaa/Aaa	rs201646155,COSM4083068	.	.	-1	MYO1F	HGNC	7600	protein_coding	YES	CCDS42494.1	ENSP00000344871	MYO1F_HUMAN	Q14779_HUMAN,M0QXU2_HUMAN	UPI00001678F0	.	tolerated(0.45)	benign(0.329)	19/28	.	Superfamily_domains:SSF52540,SMART_domains:SM00242,Pfam_domain:PF00063,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF288,PROSITE_profiles:PS51456	T:0.0002	T:0	T:0.0014	.	T:0	T:0	T:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGTTCGTCCC	byCluster|by1000G	5	ESCA
UBE4B	0	.	GRCh37	1	10218487	10218487	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3000T>A	p.Phe1000Leu	p.F1000L	ENST00000343090	22/28	76	71	5	76	76	0	UBE4B,missense_variant,p.Phe755Leu,ENST00000377157,;UBE4B,missense_variant,p.Phe871Leu,ENST00000253251,;UBE4B,missense_variant,p.Phe1000Leu,ENST00000343090,;RNU6-828P,upstream_gene_variant,,ENST00000364876,;UBE4B,missense_variant,p.Phe26Leu,ENST00000488228,;	A	ENSG00000130939	ENST00000343090	Transcript	missense_variant	3075	3000	1000	F/L	ttT/ttA	.	.	.	1	UBE4B	HGNC	12500	protein_coding	YES	CCDS41245.1	ENSP00000343001	UBE4B_HUMAN	.	UPI0000137944	.	tolerated(0.39)	benign(0.177)	22/28	.	hmmpanther:PTHR13931:SF13,hmmpanther:PTHR13931,Pfam_domain:PF10408	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTTTTAAAAG	.	2	ESCA
KIF1B	0	.	GRCh37	1	10434400	10434400	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4835C>G	p.Ser1612Cys	p.S1612C	ENST00000263934	44/47	63	43	20	66	66	0	KIF1B,missense_variant,p.Ser1658Cys,ENST00000377081,;KIF1B,missense_variant,p.Ser1658Cys,ENST00000377086,;KIF1B,missense_variant,p.Ser1612Cys,ENST00000263934,;	G	ENSG00000054523	ENST00000263934	Transcript	missense_variant	4988	4835	1612	S/C	tCt/tGt	.	.	.	1	KIF1B	HGNC	16636	protein_coding	YES	CCDS111.1	ENSP00000263934	KIF1B_HUMAN	B4DMF3_HUMAN	UPI000013EE7E	.	tolerated(0.05)	possibly_damaging(0.694)	44/47	.	hmmpanther:PTHR24115:SF328,hmmpanther:PTHR24115,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCTAGTC	.	5	ESCA
WDR47	0	.	GRCh37	1	109517260	109517260	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2539C>G	p.His847Asp	p.H847D	ENST00000400794	14/15	24	21	3	27	27	0	WDR47,missense_variant,p.His840Asp,ENST00000369965,;WDR47,missense_variant,p.His847Asp,ENST00000400794,;WDR47,missense_variant,p.His811Asp,ENST00000361054,;WDR47,missense_variant,p.His811Asp,ENST00000357672,;WDR47,missense_variant,p.His839Asp,ENST00000369962,;	C	ENSG00000085433	ENST00000400794	Transcript	missense_variant	2673	2539	847	H/D	Cat/Gat	.	.	.	-1	WDR47	HGNC	29141	protein_coding	YES	CCDS44186.1	ENSP00000383599	WDR47_HUMAN	E9PKZ6_HUMAN	UPI0001639B05	.	deleterious(0)	possibly_damaging(0.524)	14/15	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Pfam_domain:PF00400,Gene3D:2.130.10.10,hmmpanther:PTHR19863,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATGATAAC	.	4	ESCA
PSMA5	0	.	GRCh37	1	109955703	109955703	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.278G>C	p.Arg93Thr	p.R93T	ENST00000271308	4/9	57	43	13	49	49	0	PSMA5,missense_variant,p.Arg93Thr,ENST00000271308,;PSMA5,missense_variant,p.Arg35Thr,ENST00000538610,;PSMA5,non_coding_transcript_exon_variant,,ENST00000490870,;PSMA5,non_coding_transcript_exon_variant,,ENST00000484563,;PSMA5,downstream_gene_variant,,ENST00000491287,;PSMA5,upstream_gene_variant,,ENST00000477897,;	G	ENSG00000143106	ENST00000271308	Transcript	missense_variant	299	278	93	R/T	aGa/aCa	.	.	.	-1	PSMA5	HGNC	9534	protein_coding	YES	CCDS799.1	ENSP00000271308	PSA5_HUMAN	.	UPI0000026E6B	.	deleterious(0)	probably_damaging(0.988)	4/9	.	PROSITE_profiles:PS51475,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF14,Gene3D:3.60.20.10,Pfam_domain:PF00227,Superfamily_domains:SSF56235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACTCTGGCT	.	5	ESCA
TTLL10	0	.	GRCh37	1	1110887	1110887	+	Intron	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-28+1018C>T	.	.	ENST00000379290	.	15	11	4	28	28	0	TTLL10,intron_variant,,ENST00000379289,;TTLL10,intron_variant,,ENST00000379290,;TTLL10,upstream_gene_variant,,ENST00000379288,;TTLL10-AS1,non_coding_transcript_exon_variant,,ENST00000379317,;TTLL10,downstream_gene_variant,,ENST00000506177,;TTLL10,upstream_gene_variant,,ENST00000460998,;	T	ENSG00000162571	ENST00000379290	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	TTLL10	HGNC	26693	protein_coding	YES	CCDS44036.1	ENSP00000368592	TTL10_HUMAN	.	UPI0000205ADB	.	.	.	.	3/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCCCGGGTG	.	5	ESCA
PTCHD2	0	.	GRCh37	1	11561424	11561424	+	Silent	SNP	G	G	A	rs768397889	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375G>A	p.%3D	p.A125A	ENST00000294484	2/21	45	38	7	34	34	0	PTCHD2,synonymous_variant,p.%3D,ENST00000389575,;PTCHD2,synonymous_variant,p.%3D,ENST00000294484,;	A	ENSG00000204624	ENST00000294484	Transcript	synonymous_variant	513	375	125	A	gcG/gcA	rs768397889	.	.	1	PTCHD2	HGNC	29251	protein_coding	YES	CCDS41247.1	ENSP00000294484	PTHD2_HUMAN	.	UPI00001C1D7A	.	.	.	2/21	.	hmmpanther:PTHR10796:SF49,hmmpanther:PTHR10796	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGGCGCTTAA	byFrequency	4	ESCA
TBX15	0	.	GRCh37	1	119467289	119467289	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.355G>C	p.Glu119Gln	p.E119Q	ENST00000207157	4/8	93	77	16	95	95	0	TBX15,missense_variant,p.Glu225Gln,ENST00000369429,;TBX15,missense_variant,p.Glu119Gln,ENST00000207157,;	G	ENSG00000092607	ENST00000207157	Transcript	missense_variant	670	355	119	E/Q	Gag/Cag	.	.	.	-1	TBX15	HGNC	11594	protein_coding	YES	CCDS30816.1	ENSP00000207157	TBX15_HUMAN	Q8N8P2_HUMAN	UPI000046D38E	.	deleterious(0)	benign(0.345)	4/8	.	Superfamily_domains:SSF49417,SMART_domains:SM00425,Pfam_domain:PF00907,Gene3D:1h6fA00,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF98,PROSITE_profiles:PS50252	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCATTGT	.	5	ESCA
PLOD1	0	.	GRCh37	1	12012751	12012751	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538C>T	p.Gln180Ter	p.Q180*	ENST00000196061	5/19	51	32	19	44	44	0	PLOD1,stop_gained,p.Gln180Ter,ENST00000429000,;PLOD1,stop_gained,p.Gln227Ter,ENST00000376369,;PLOD1,stop_gained,p.Gln180Ter,ENST00000196061,;PLOD1,downstream_gene_variant,,ENST00000449038,;PLOD1,non_coding_transcript_exon_variant,,ENST00000485046,;PLOD1,non_coding_transcript_exon_variant,,ENST00000358133,;PLOD1,upstream_gene_variant,,ENST00000465920,;	T	ENSG00000083444	ENST00000196061	Transcript	stop_gained	565	538	180	Q/*	Cag/Tag	.	.	.	1	PLOD1	HGNC	9081	protein_coding	YES	CCDS142.1	ENSP00000196061	PLOD1_HUMAN	Q9UL44_HUMAN	UPI000013C611	.	.	.	5/19	.	hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCGATCAGCTG	.	3	ESCA
PLOD1	0	.	GRCh37	1	12012771	12012771	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.558C>G	p.Ile186Met	p.I186M	ENST00000196061	5/19	36	20	16	39	39	0	PLOD1,missense_variant,p.Ile186Met,ENST00000429000,;PLOD1,missense_variant,p.Ile233Met,ENST00000376369,;PLOD1,missense_variant,p.Ile186Met,ENST00000196061,;PLOD1,downstream_gene_variant,,ENST00000449038,;PLOD1,non_coding_transcript_exon_variant,,ENST00000485046,;PLOD1,non_coding_transcript_exon_variant,,ENST00000358133,;PLOD1,upstream_gene_variant,,ENST00000465920,;	G	ENSG00000083444	ENST00000196061	Transcript	missense_variant	585	558	186	I/M	atC/atG	.	.	.	1	PLOD1	HGNC	9081	protein_coding	YES	CCDS142.1	ENSP00000196061	PLOD1_HUMAN	Q9UL44_HUMAN	UPI000013C611	.	deleterious(0.01)	possibly_damaging(0.872)	5/19	.	hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAGATCTTCTT	.	3	ESCA
PDPN	0	.	GRCh37	1	13933769	13933769	+	Missense_Mutation	SNP	G	G	A	rs778306499	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.397G>A	p.Glu133Lys	p.E133K	ENST00000294489	2/6	43	36	6	50	50	0	PDPN,missense_variant,p.Glu52Lys,ENST00000509009,;PDPN,missense_variant,p.Glu15Lys,ENST00000513143,;PDPN,missense_variant,p.Glu15Lys,ENST00000487038,;PDPN,missense_variant,p.Glu133Lys,ENST00000376057,;PDPN,missense_variant,p.Glu133Lys,ENST00000294489,;PDPN,missense_variant,p.Glu124Lys,ENST00000510906,;PDPN,missense_variant,p.Glu15Lys,ENST00000475043,;PDPN,missense_variant,p.Glu15Lys,ENST00000376061,;PDPN,missense_variant,p.Glu15Lys,ENST00000488631,;PDPN,downstream_gene_variant,,ENST00000506205,;	A	ENSG00000162493	ENST00000294489	Transcript	missense_variant	738	397	133	E/K	Gaa/Aaa	rs778306499	.	.	1	PDPN	HGNC	29602	protein_coding	YES	CCDS30602.1	ENSP00000294489	PDPN_HUMAN	H0YA72_HUMAN	UPI000013E16D	.	tolerated(0.22)	benign(0.003)	2/6	.	Pfam_domain:PF05808,hmmpanther:PTHR16861	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAGCGAAGAC	byFrequency	5	ESCA
ANKRD34A	0	.	GRCh37	1	145475131	145475131	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*312C>G	.	.	ENST00000323397	4/4	44	28	15	36	36	0	ANKRD34A,3_prime_UTR_variant,,ENST00000323397,;POLR3GL,upstream_gene_variant,,ENST00000369313,;POLR3GL,upstream_gene_variant,,ENST00000369314,;LIX1L,upstream_gene_variant,,ENST00000369308,;RP11-315I20.1,downstream_gene_variant,,ENST00000600340,;POLR3GL,upstream_gene_variant,,ENST00000446572,;POLR3GL,upstream_gene_variant,,ENST00000471706,;	G	ENSG00000181039	ENST00000323397	Transcript	3_prime_UTR_variant	3096	.	.	.	.	.	.	.	1	ANKRD34A	HGNC	27639	protein_coding	YES	CCDS30829.1	ENSP00000314103	AN34A_HUMAN	.	UPI00001410C4	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCTCTTGCA	.	5	ESCA
CHD1L	0	.	GRCh37	1	146727518	146727518	+	Missense_Mutation	SNP	G	G	C	rs781957384	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.398G>C	p.Arg133Thr	p.R133T	ENST00000369258	4/23	48	36	12	47	47	0	CHD1L,missense_variant,p.Arg133Thr,ENST00000369258,;CHD1L,missense_variant,p.Arg133Thr,ENST00000431239,;CHD1L,intron_variant,,ENST00000369259,;CHD1L,intron_variant,,ENST00000361293,;CHD1L,non_coding_transcript_exon_variant,,ENST00000492728,;CHD1L,non_coding_transcript_exon_variant,,ENST00000467213,;CHD1L,intron_variant,,ENST00000488864,;RP11-337C18.10,downstream_gene_variant,,ENST00000606856,;	C	ENSG00000131778	ENST00000369258	Transcript	missense_variant	418	398	133	R/T	aGa/aCa	rs781957384	.	.	1	CHD1L	HGNC	1916	protein_coding	YES	CCDS927.1	ENSP00000358262	CHD1L_HUMAN	B5MDZ7_HUMAN	UPI000020566F	.	deleterious(0)	probably_damaging(1)	4/23	.	Superfamily_domains:SSF52540,SMART_domains:SM00487,Pfam_domain:PF00176,Gene3D:3.40.50.300,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF558,PROSITE_profiles:PS51192	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAAAGAGCCT	byFrequency	5	ESCA
RPRD2	0	.	GRCh37	1	150444823	150444823	+	Silent	SNP	A	A	G	rs764154888	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3399A>G	p.%3D	p.T1133T	ENST00000369068	11/11	64	44	20	38	38	0	RPRD2,synonymous_variant,p.%3D,ENST00000369068,;RPRD2,synonymous_variant,p.%3D,ENST00000401000,;RPRD2,downstream_gene_variant,,ENST00000539519,;RPRD2,non_coding_transcript_exon_variant,,ENST00000492220,;	G	ENSG00000163125	ENST00000369068	Transcript	synonymous_variant	3403	3399	1133	T	acA/acG	rs764154888	.	.	1	RPRD2	HGNC	29039	protein_coding	YES	CCDS44216.1	ENSP00000358064	RPRD2_HUMAN	.	UPI00001D7CA8	.	.	.	11/11	.	hmmpanther:PTHR12460,hmmpanther:PTHR12460:SF0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCACATCAGG	.	5	ESCA
POGZ	0	.	GRCh37	1	151377628	151377628	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3883G>C	p.Asp1295His	p.D1295H	ENST00000271715	19/19	35	21	13	22	22	0	POGZ,missense_variant,p.Asp1295His,ENST00000271715,;POGZ,missense_variant,p.Asp1242His,ENST00000392723,;POGZ,missense_variant,p.Asp1286His,ENST00000409503,;POGZ,missense_variant,p.Asp1242His,ENST00000361398,;POGZ,missense_variant,p.Asp1233His,ENST00000531094,;POGZ,missense_variant,p.Asp657His,ENST00000540984,;POGZ,missense_variant,p.Asp1200His,ENST00000368863,;POGZ,missense_variant,p.Asp1251His,ENST00000491586,;POGZ,downstream_gene_variant,,ENST00000529669,;PSMB4,downstream_gene_variant,,ENST00000290541,;POGZ,non_coding_transcript_exon_variant,,ENST00000358476,;PSMB4,downstream_gene_variant,,ENST00000495288,;POGZ,downstream_gene_variant,,ENST00000497787,;POGZ,downstream_gene_variant,,ENST00000492528,;PSMB4,downstream_gene_variant,,ENST00000476467,;PSMB4,downstream_gene_variant,,ENST00000495805,;PSMB4,downstream_gene_variant,,ENST00000466425,;PSMB4,downstream_gene_variant,,ENST00000493673,;PSMB4,downstream_gene_variant,,ENST00000474100,;	G	ENSG00000143442	ENST00000271715	Transcript	missense_variant	4198	3883	1295	D/H	Gat/Cat	.	.	.	-1	POGZ	HGNC	18801	protein_coding	YES	CCDS997.1	ENSP00000271715	POGZ_HUMAN	F5H8H4_HUMAN,E9PJY9_HUMAN,E9PIR8_HUMAN	UPI000035895F	.	deleterious(0.01)	benign(0.021)	19/19	.	hmmpanther:PTHR19303:SF65,hmmpanther:PTHR19303	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACATCAGAAT	.	5	ESCA
TCHHL1	0	.	GRCh37	1	152058803	152058803	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355G>A	p.Gly452Glu	p.G452E	ENST00000368806	3/3	71	48	23	45	45	0	TCHHL1,missense_variant,p.Gly452Glu,ENST00000368806,;	T	ENSG00000182898	ENST00000368806	Transcript	missense_variant	1420	1355	452	G/E	gGa/gAa	.	.	.	-1	TCHHL1	HGNC	31796	protein_coding	YES	CCDS30857.1	ENSP00000357796	TCHL1_HUMAN	.	UPI0000496834	.	tolerated(0.64)	possibly_damaging(0.575)	3/3	.	hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF53	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATCTCCTCCT	.	5	ESCA
RPTN	0	.	GRCh37	1	152127159	152127159	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*61G>A	.	.	ENST00000316073	3/3	34	25	9	29	29	0	RPTN,3_prime_UTR_variant,,ENST00000316073,;	T	ENSG00000215853	ENST00000316073	Transcript	3_prime_UTR_variant	2481	.	.	.	.	.	.	.	-1	RPTN	HGNC	26809	protein_coding	YES	CCDS41397.1	ENSP00000317895	RPTN_HUMAN	Q8N1M7_HUMAN,Q2M1U7_HUMAN	UPI00002371E2	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCCTCATAGT	.	2	ESCA
LCE3C	0	.	GRCh37	1	152573397	152573397	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.190C>G	p.Gln64Glu	p.Q64E	ENST00000333881	1/1	43	15	28	29	29	0	LCE3C,missense_variant,p.Gln64Glu,ENST00000333881,;	G	ENSG00000244057	ENST00000333881	Transcript	missense_variant	260	190	64	Q/E	Caa/Gaa	.	.	.	1	LCE3C	HGNC	16612	protein_coding	YES	CCDS1015.1	ENSP00000334644	LCE3C_HUMAN	.	UPI00001927D1	.	deleterious_low_confidence(0.03)	unknown(0)	1/1	.	hmmpanther:PTHR23263:SF27,hmmpanther:PTHR23263,Pfam_domain:PF14672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCATCAATGC	.	5	ESCA
SPRR2E	0	.	GRCh37	1	153066153	153066153	+	Silent	SNP	C	C	T	rs769693280	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.75G>A	p.%3D	p.E25E	ENST00000368751	2/2	100	82	18	62	62	0	SPRR2E,synonymous_variant,p.%3D,ENST00000368751,;SPRR2E,synonymous_variant,p.%3D,ENST00000368750,;SPRR2B,intron_variant,,ENST00000368752,;	T	ENSG00000203785	ENST00000368751	Transcript	synonymous_variant	150	75	25	E	gaG/gaA	rs769693280	.	.	-1	SPRR2E	HGNC	11265	protein_coding	YES	CCDS30866.1	ENSP00000357740	SPR2E_HUMAN	.	UPI000006E67B	.	.	.	2/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23263:SF16,hmmpanther:PTHR23263,Pfam_domain:PF14820,Prints_domain:PR00021	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|VARSCANS	CATGGCTCTGG	byFrequency	3	ESCA
SHC1	0	.	GRCh37	1	154935308	154935308	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*971C>G	.	.	ENST00000448116	12/12	72	54	18	55	55	0	SHC1,3_prime_UTR_variant,,ENST00000448116,;SHC1,3_prime_UTR_variant,,ENST00000368445,;SHC1,3_prime_UTR_variant,,ENST00000368449,;SHC1,3_prime_UTR_variant,,ENST00000606391,;SHC1,3_prime_UTR_variant,,ENST00000368453,;SHC1,3_prime_UTR_variant,,ENST00000368450,;SHC1,downstream_gene_variant,,ENST00000412170,;PYGO2,upstream_gene_variant,,ENST00000368456,;SHC1,downstream_gene_variant,,ENST00000414115,;SHC1,downstream_gene_variant,,ENST00000444664,;SHC1,downstream_gene_variant,,ENST00000444179,;PYGO2,upstream_gene_variant,,ENST00000368457,;RP11-307C12.12,downstream_gene_variant,,ENST00000605085,;PYGO2,intron_variant,,ENST00000483463,;SHC1,downstream_gene_variant,,ENST00000490667,;	C	ENSG00000160691	ENST00000448116	Transcript	3_prime_UTR_variant	2947	.	.	.	.	.	.	.	-1	SHC1	HGNC	10840	protein_coding	YES	CCDS44233.1	ENSP00000401303	SHC1_HUMAN	Q8NFT1_HUMAN,Q8NFT0_HUMAN,Q5T187_HUMAN,Q5T181_HUMAN,B4DL02_HUMAN	UPI00002048B4	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAAAGAATGC	.	5	ESCA
ZBTB7B	0	.	GRCh37	1	154987266	154987266	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.232G>C	p.Glu78Gln	p.E78Q	ENST00000417934	4/5	30	23	7	50	50	0	ZBTB7B,missense_variant,p.Glu44Gln,ENST00000535420,;ZBTB7B,missense_variant,p.Glu44Gln,ENST00000368426,;ZBTB7B,missense_variant,p.Glu44Gln,ENST00000292176,;ZBTB7B,missense_variant,p.Glu78Gln,ENST00000417934,;DCST2,downstream_gene_variant,,ENST00000368424,;ZBTB7B,non_coding_transcript_exon_variant,,ENST00000461530,;ZBTB7B,non_coding_transcript_exon_variant,,ENST00000487542,;ZBTB7B,downstream_gene_variant,,ENST00000483226,;DCST2,downstream_gene_variant,,ENST00000485982,;DCST2,downstream_gene_variant,,ENST00000368423,;DCST2,downstream_gene_variant,,ENST00000467991,;	C	ENSG00000160685	ENST00000417934	Transcript	missense_variant	501	232	78	E/Q	Gaa/Caa	.	.	.	1	ZBTB7B	HGNC	18668	protein_coding	YES	CCDS58030.1	ENSP00000406286	ZBT7B_HUMAN	.	UPI0001A5EB6F	.	deleterious(0)	possibly_damaging(0.61)	4/5	.	PROSITE_profiles:PS50097,hmmpanther:PTHR23228,hmmpanther:PTHR23228:SF129,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCCTTGAATAC	.	5	ESCA
SCAMP3	0	.	GRCh37	1	155228738	155228738	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.396G>T	p.Gln132His	p.Q132H	ENST00000302631	5/9	108	91	16	119	119	0	SCAMP3,missense_variant,p.Gln106His,ENST00000355379,;SCAMP3,missense_variant,p.Gln132His,ENST00000302631,;FAM189B,upstream_gene_variant,,ENST00000368368,;CLK2,downstream_gene_variant,,ENST00000536801,;CLK2,downstream_gene_variant,,ENST00000368361,;FAM189B,upstream_gene_variant,,ENST00000491082,;FAM189B,upstream_gene_variant,,ENST00000350210,;FAM189B,upstream_gene_variant,,ENST00000361361,;CLK2,downstream_gene_variant,,ENST00000361168,;CLK2,downstream_gene_variant,,ENST00000355560,;SCAMP3,non_coding_transcript_exon_variant,,ENST00000472397,;SCAMP3,non_coding_transcript_exon_variant,,ENST00000490999,;SCAMP3,non_coding_transcript_exon_variant,,ENST00000497470,;SCAMP3,intron_variant,,ENST00000465312,;SCAMP3,intron_variant,,ENST00000462151,;CLK2,downstream_gene_variant,,ENST00000497188,;FAM189B,upstream_gene_variant,,ENST00000472550,;CLK2,downstream_gene_variant,,ENST00000476983,;SCAMP3,downstream_gene_variant,,ENST00000480219,;SCAMP3,upstream_gene_variant,,ENST00000478737,;FAM189B,upstream_gene_variant,,ENST00000481822,;FAM189B,upstream_gene_variant,,ENST00000487649,;	A	ENSG00000116521	ENST00000302631	Transcript	missense_variant	504	396	132	Q/H	caG/caT	.	.	.	-1	SCAMP3	HGNC	10565	protein_coding	YES	CCDS1105.1	ENSP00000307275	SCAM3_HUMAN	.	UPI000013E800	.	deleterious(0.05)	possibly_damaging(0.841)	5/9	.	hmmpanther:PTHR10687:SF6,hmmpanther:PTHR10687,Pfam_domain:PF04144	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTTCTGTCG	.	4	ESCA
CADM3	0	.	GRCh37	1	159171026	159171026	+	3'UTR	SNP	T	T	A	rs371451747	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*314T>A	.	.	ENST00000368124	10/10	39	31	8	25	25	0	CADM3,3_prime_UTR_variant,,ENST00000368124,;CADM3,3_prime_UTR_variant,,ENST00000368125,;DARC,upstream_gene_variant,,ENST00000537147,;DARC,upstream_gene_variant,,ENST00000435307,;DARC,upstream_gene_variant,,ENST00000368121,;CADM3,downstream_gene_variant,,ENST00000416746,;DARC,upstream_gene_variant,,ENST00000368122,;CTA-134P22.2,non_coding_transcript_exon_variant,,ENST00000415675,;CTA-134P22.2,downstream_gene_variant,,ENST00000609696,;CADM3,non_coding_transcript_exon_variant,,ENST00000497636,;	A	ENSG00000162706	ENST00000368124	Transcript	3_prime_UTR_variant	1770	.	.	.	.	rs371451747	.	.	1	CADM3	HGNC	17601	protein_coding	YES	CCDS1182.1	ENSP00000357106	CADM3_HUMAN	.	UPI000006E8A2	.	.	.	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TGGGGTGAGAA	.	3	ESCA
ATP1A2	0	.	GRCh37	1	160113373	160113373	+	3'UTR	DEL	A	A	-	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000361216	23/23	103	77	26	65	65	0	ATP1A2,3_prime_UTR_variant,,ENST00000361216,;ATP1A2,3_prime_UTR_variant,,ENST00000447527,;ATP1A2,downstream_gene_variant,,ENST00000392233,;ATP1A2,downstream_gene_variant,,ENST00000459972,;ATP1A2,downstream_gene_variant,,ENST00000463989,;	-	ENSG00000018625	ENST00000361216	Transcript	3_prime_UTR_variant	5413	.	.	.	.	.	.	.	1	ATP1A2	HGNC	800	protein_coding	YES	CCDS1196.1	ENSP00000354490	AT1A2_HUMAN	Q58I22_HUMAN	UPI0000124FC1	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR|VARSCANI	TTTATGAAAAAA	.	2	ESCA
KLHDC9	0	.	GRCh37	1	161068192	161068192	+	5'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-134G>C	.	.	ENST00000368011	1/4	16	10	6	10	10	0	KLHDC9,5_prime_UTR_variant,,ENST00000392192,;KLHDC9,5_prime_UTR_variant,,ENST00000368011,;PFDN2,downstream_gene_variant,,ENST00000368010,;KLHDC9,splice_region_variant,,ENST00000469647,;KLHDC9,splice_region_variant,,ENST00000490724,;KLHDC9,upstream_gene_variant,,ENST00000494418,;PFDN2,downstream_gene_variant,,ENST00000468311,;KLHDC9,upstream_gene_variant,,ENST00000392191,;KLHDC9,splice_region_variant,,ENST00000471613,;KLHDC9,upstream_gene_variant,,ENST00000475934,;	C	ENSG00000162755	ENST00000368011	Transcript	5_prime_UTR_variant	9	.	.	.	.	.	.	.	1	KLHDC9	HGNC	28489	protein_coding	YES	CCDS30919.1	ENSP00000356990	KLDC9_HUMAN	D3DVF3_HUMAN	UPI0000420905	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTGAGGTG	.	5	ESCA
SPEN	0	.	GRCh37	1	16263970	16263970	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10339C>G	p.Leu3447Val	p.L3447V	ENST00000375759	12/15	49	41	8	44	44	0	SPEN,missense_variant,p.Leu3447Val,ENST00000375759,;ZBTB17,downstream_gene_variant,,ENST00000375733,;ZBTB17,downstream_gene_variant,,ENST00000375743,;ZBTB17,downstream_gene_variant,,ENST00000537142,;ZBTB17,downstream_gene_variant,,ENST00000440560,;ZBTB17,downstream_gene_variant,,ENST00000444358,;ZBTB17,downstream_gene_variant,,ENST00000462525,;SPEN,upstream_gene_variant,,ENST00000487496,;	G	ENSG00000065526	ENST00000375759	Transcript	missense_variant	10543	10339	3447	L/V	Ctt/Gtt	.	.	.	1	SPEN	HGNC	17575	protein_coding	YES	CCDS164.1	ENSP00000364912	MINT_HUMAN	.	UPI000006FF0C	.	.	benign(0.052)	12/15	.	hmmpanther:PTHR23189:SF9,hmmpanther:PTHR23189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTCTCTTCCC	.	5	ESCA
NADK	0	.	GRCh37	1	1684250	1684250	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*93C>T	.	.	ENST00000344463	14/14	68	58	9	60	60	0	NADK,3_prime_UTR_variant,,ENST00000378625,;NADK,3_prime_UTR_variant,,ENST00000344463,;NADK,3_prime_UTR_variant,,ENST00000341991,;NADK,3_prime_UTR_variant,,ENST00000342348,;NADK,3_prime_UTR_variant,,ENST00000341426,;NADK,downstream_gene_variant,,ENST00000469045,;NADK,downstream_gene_variant,,ENST00000400922,;NADK,downstream_gene_variant,,ENST00000492768,;NADK,downstream_gene_variant,,ENST00000460602,;NADK,downstream_gene_variant,,ENST00000477235,;NADK,downstream_gene_variant,,ENST00000480499,;NADK,downstream_gene_variant,,ENST00000497186,;NADK,downstream_gene_variant,,ENST00000498806,;NADK,downstream_gene_variant,,ENST00000492845,;NADK,downstream_gene_variant,,ENST00000497615,;NADK,downstream_gene_variant,,ENST00000489538,;NADK,downstream_gene_variant,,ENST00000497747,;	A	ENSG00000008130	ENST00000344463	Transcript	3_prime_UTR_variant	2091	.	.	.	.	.	.	.	-1	NADK	HGNC	29831	protein_coding	YES	CCDS55562.1	ENSP00000340925	NADK_HUMAN	.	UPI000013CBEB	.	.	.	14/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCACTGAGACA	.	4	ESCA
PRRX1	0	.	GRCh37	1	170688965	170688965	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.340G>C	p.Glu114Gln	p.E114Q	ENST00000239461	2/4	42	31	10	30	30	0	PRRX1,missense_variant,p.Glu114Gln,ENST00000497230,;PRRX1,missense_variant,p.Glu114Gln,ENST00000239461,;PRRX1,missense_variant,p.Glu114Gln,ENST00000367760,;PRRX1,non_coding_transcript_exon_variant,,ENST00000553786,;PRRX1,upstream_gene_variant,,ENST00000495280,;PRRX1,upstream_gene_variant,,ENST00000476867,;	C	ENSG00000116132	ENST00000239461	Transcript	missense_variant	653	340	114	E/Q	Gag/Cag	COSM1295466,COSM1295467	.	.	1	PRRX1	HGNC	9142	protein_coding	YES	CCDS1290.1	ENSP00000239461	PRRX1_HUMAN	.	UPI0000131D11	.	tolerated(0.11)	probably_damaging(0.992)	2/4	.	PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF300,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTGAGCGG	.	5	ESCA
ZBTB37	0	.	GRCh37	1	173854791	173854791	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1041G>C	p.Met347Ile	p.M347I	ENST00000367701	4/4	91	66	24	64	64	0	ZBTB37,missense_variant,p.Met347Ile,ENST00000427304,;ZBTB37,missense_variant,p.Met347Ile,ENST00000367701,;ZBTB37,3_prime_UTR_variant,,ENST00000367704,;	C	ENSG00000185278	ENST00000367701	Transcript	missense_variant	1232	1041	347	M/I	atG/atC	.	.	.	1	ZBTB37	HGNC	28365	protein_coding	YES	CCDS44278.1	ENSP00000356674	ZBT37_HUMAN	.	UPI0000203C09	.	tolerated(0.24)	benign(0)	4/4	.	hmmpanther:PTHR24375:SF2,hmmpanther:PTHR24375	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCAATGATGGG	.	5	ESCA
PADI2	0	.	GRCh37	1	17405696	17405696	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1310+63G>C	.	.	ENST00000375486	.	105	70	35	113	113	0	PADI2,3_prime_UTR_variant,,ENST00000375481,;PADI2,intron_variant,,ENST00000375486,;PADI2,intron_variant,,ENST00000444885,;PADI2,intron_variant,,ENST00000466151,;PADI2,upstream_gene_variant,,ENST00000479534,;	G	ENSG00000117115	ENST00000375486	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	PADI2	HGNC	18341	protein_coding	YES	CCDS177.1	ENSP00000364635	PADI2_HUMAN	Q96DA7_HUMAN	UPI00001314AF	.	.	.	.	11/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCACCCCAAAA	.	5	ESCA
ASTN1	0	.	GRCh37	1	177000021	177000021	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.933G>A	p.%3D	p.V311V	ENST00000361833	4/23	54	41	12	47	47	0	ASTN1,synonymous_variant,p.%3D,ENST00000367654,;ASTN1,synonymous_variant,p.%3D,ENST00000424564,;ASTN1,synonymous_variant,p.%3D,ENST00000361833,;ASTN1,synonymous_variant,p.%3D,ENST00000367657,;MIR488,upstream_gene_variant,,ENST00000365739,;ASTN1,non_coding_transcript_exon_variant,,ENST00000473640,;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,;	T	ENSG00000152092	ENST00000361833	Transcript	synonymous_variant	947	933	311	V	gtG/gtA	.	.	.	-1	ASTN1	HGNC	773	protein_coding	YES	CCDS1319.1	ENSP00000354536	ASTN1_HUMAN	Q96BL7_HUMAN	UPI0000160388	.	.	.	4/23	.	hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGTCCACAGG	.	5	ESCA
ABL2	0	.	GRCh37	1	179073137	179073137	+	3'UTR	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3716A>C	.	.	ENST00000502732	12/12	34	29	5	39	39	0	ABL2,3_prime_UTR_variant,,ENST00000408940,;ABL2,3_prime_UTR_variant,,ENST00000502732,;ABL2,downstream_gene_variant,,ENST00000507173,;ABL2,downstream_gene_variant,,ENST00000344730,;ABL2,downstream_gene_variant,,ENST00000512653,;ABL2,downstream_gene_variant,,ENST00000511413,;ABL2,downstream_gene_variant,,ENST00000504405,;ABL2,downstream_gene_variant,,ENST00000367623,;	G	ENSG00000143322	ENST00000502732	Transcript	3_prime_UTR_variant	7469	.	.	.	.	.	.	.	-1	ABL2	HGNC	77	protein_coding	YES	CCDS30947.1	ENSP00000427562	ABL2_HUMAN	.	UPI0000125140	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCACTGGGAA	.	4	ESCA
DHX9	0	.	GRCh37	1	182829167	182829167	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1180G>A	p.Glu394Lys	p.E394K	ENST00000367549	12/28	80	57	23	69	69	0	DHX9,missense_variant,p.Glu394Lys,ENST00000367549,;DHX9,non_coding_transcript_exon_variant,,ENST00000477802,;DHX9,downstream_gene_variant,,ENST00000479271,;	A	ENSG00000135829	ENST00000367549	Transcript	missense_variant	1290	1180	394	E/K	Gaa/Aaa	.	.	.	1	DHX9	HGNC	2750	protein_coding	YES	CCDS41444.1	ENSP00000356520	DHX9_HUMAN	.	UPI00001AEF15	.	tolerated(1)	benign(0.009)	12/28	.	hmmpanther:PTHR18934:SF84,hmmpanther:PTHR18934,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTGAAAGT	.	5	ESCA
LAMC1	0	.	GRCh37	1	183093999	183093999	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2635G>C	p.Asp879His	p.D879H	ENST00000258341	14/28	42	38	4	27	27	0	LAMC1,missense_variant,p.Asp879His,ENST00000258341,;LAMC1,upstream_gene_variant,,ENST00000478064,;LAMC1,upstream_gene_variant,,ENST00000466964,;	C	ENSG00000135862	ENST00000258341	Transcript	missense_variant	2892	2635	879	D/H	Gac/Cac	.	.	.	1	LAMC1	HGNC	6492	protein_coding	YES	CCDS1351.1	ENSP00000258341	LAMC1_HUMAN	R4GNC7_HUMAN	UPI000013CFC7	.	tolerated(0.06)	possibly_damaging(0.658)	14/28	.	PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF228,hmmpanther:PTHR10574,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CAGCAGACAAA	.	3	ESCA
PRG4	0	.	GRCh37	1	186275881	186275881	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1030C>G	p.Leu344Val	p.L344V	ENST00000445192	7/13	129	108	21	98	98	0	PRG4,missense_variant,p.Leu251Val,ENST00000367485,;PRG4,missense_variant,p.Leu210Val,ENST00000367482,;PRG4,missense_variant,p.Leu303Val,ENST00000367484,;PRG4,missense_variant,p.Leu301Val,ENST00000367486,;PRG4,missense_variant,p.Leu344Val,ENST00000445192,;PRG4,missense_variant,p.Leu303Val,ENST00000367483,;TPR,downstream_gene_variant,,ENST00000367478,;PRG4,downstream_gene_variant,,ENST00000533951,;	G	ENSG00000116690	ENST00000445192	Transcript	missense_variant	1075	1030	344	L/V	Ctc/Gtc	.	.	.	1	PRG4	HGNC	9364	protein_coding	YES	CCDS1369.1	ENSP00000399679	PRG4_HUMAN	B3KQ20_HUMAN	UPI0000070EF9	.	.	unknown(0)	7/13	.	hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTCTCACC	.	5	ESCA
TAS1R2	0	.	GRCh37	1	19166648	19166648	+	Silent	SNP	G	G	T	rs751000756	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1965C>A	p.%3D	p.I655I	ENST00000375371	6/6	34	21	13	23	23	0	TAS1R2,synonymous_variant,p.%3D,ENST00000375371,;	T	ENSG00000179002	ENST00000375371	Transcript	synonymous_variant	1987	1965	655	I	atC/atA	rs751000756,COSM3480500	.	.	-1	TAS1R2	HGNC	14905	protein_coding	YES	CCDS187.1	ENSP00000364520	TS1R2_HUMAN	.	UPI0000456168	.	.	.	6/6	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF3,Pfam_domain:PF00003,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A658T|c.1972G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGACGATCTG	byFrequency	5	ESCA
EMC1	0	.	GRCh37	1	19547522	19547522	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2588-180G>C	.	.	ENST00000477853	.	16	12	4	18	18	0	EMC1,intron_variant,,ENST00000375208,;EMC1,intron_variant,,ENST00000375199,;EMC1,intron_variant,,ENST00000486405,;EMC1,intron_variant,,ENST00000477853,;RP1-43E13.2,intron_variant,,ENST00000437898,;EMC1,non_coding_transcript_exon_variant,,ENST00000461353,;EMC1,non_coding_transcript_exon_variant,,ENST00000480380,;EMC1,intron_variant,,ENST00000496654,;EMC1,intron_variant,,ENST00000494770,;EMC1,intron_variant,,ENST00000462505,;EMC1,intron_variant,,ENST00000486238,;	G	ENSG00000127463	ENST00000477853	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	EMC1	HGNC	28957	protein_coding	YES	CCDS190.1	ENSP00000420608	EMC1_HUMAN	.	UPI0000070A23	.	.	.	.	20/22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	GTTCTCACTTT	.	4	ESCA
ZNF281	0	.	GRCh37	1	200376438	200376438	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2396C>G	p.Ser799Cys	p.S799C	ENST00000294740	2/2	47	36	10	31	31	0	ZNF281,missense_variant,p.Ser799Cys,ENST00000367353,;ZNF281,missense_variant,p.Ser763Cys,ENST00000367352,;ZNF281,missense_variant,p.Ser799Cys,ENST00000294740,;	C	ENSG00000162702	ENST00000294740	Transcript	missense_variant	2521	2396	799	S/C	tCt/tGt	.	.	.	-1	ZNF281	HGNC	13075	protein_coding	YES	CCDS1402.1	ENSP00000294740	ZN281_HUMAN	B3KMX4_HUMAN	UPI000013C345	.	deleterious(0)	possibly_damaging(0.87)	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGAAGACTCT	.	5	ESCA
NUAK2	0	.	GRCh37	1	205290713	205290713	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.44C>G	p.Ser15Trp	p.S15W	ENST00000367157	1/7	14	11	3	9	9	0	NUAK2,missense_variant,p.Ser15Trp,ENST00000367157,;	C	ENSG00000163545	ENST00000367157	Transcript	missense_variant	171	44	15	S/W	tCg/tGg	.	.	.	-1	NUAK2	HGNC	29558	protein_coding	YES	CCDS1453.1	ENSP00000356125	NUAK2_HUMAN	Q68E04_HUMAN,B4E0Y5_HUMAN	UPI0000037D77	.	deleterious_low_confidence(0.01)	possibly_damaging(0.563)	1/7	.	hmmpanther:PTHR24343:SF133,hmmpanther:PTHR24343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CGGCCGAGGGA	.	2	ESCA
CENPF	0	.	GRCh37	1	214814749	214814749	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3068T>G	p.Leu1023Arg	p.L1023R	ENST00000366955	12/20	60	51	9	45	45	0	CENPF,missense_variant,p.Leu1023Arg,ENST00000366955,;	G	ENSG00000117724	ENST00000366955	Transcript	missense_variant	3236	3068	1023	L/R	cTt/cGt	.	.	.	1	CENPF	HGNC	1857	protein_coding	YES	CCDS31023.1	ENSP00000355922	CENPF_HUMAN	.	UPI00001AE985	.	.	probably_damaging(0.948)	12/20	.	hmmpanther:PTHR18874	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	AAAACTTATTT	.	3	ESCA
USH2A	0	.	GRCh37	1	215931947	215931947	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.11379G>C	p.Trp3793Cys	p.W3793C	ENST00000307340	58/72	41	30	10	52	52	0	USH2A,missense_variant,p.Trp3793Cys,ENST00000366943,;USH2A,missense_variant,p.Trp3793Cys,ENST00000307340,;	G	ENSG00000042781	ENST00000307340	Transcript	missense_variant	11766	11379	3793	W/C	tgG/tgC	.	.	.	-1	USH2A	HGNC	12601	protein_coding	YES	CCDS31025.1	ENSP00000305941	USH2A_HUMAN	.	UPI000034E5B6	.	.	probably_damaging(1)	58/72	.	Superfamily_domains:SSF49265,SMART_domains:SM00060,Pfam_domain:PF00041,Gene3D:2.60.40.10,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF170,PROSITE_profiles:PS50853	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GGTATCCAAGC	.	5	ESCA
LDLRAD2	0	.	GRCh37	1	22148534	22148534	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.806-161C>G	.	.	ENST00000344642	.	12	8	4	29	29	0	LDLRAD2,intron_variant,,ENST00000344642,;LDLRAD2,intron_variant,,ENST00000543870,;HSPG2,downstream_gene_variant,,ENST00000374695,;LDLRAD2,non_coding_transcript_exon_variant,,ENST00000484271,;HSPG2,downstream_gene_variant,,ENST00000486901,;HSPG2,downstream_gene_variant,,ENST00000481644,;	G	ENSG00000187942	ENST00000344642	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	LDLRAD2	HGNC	32071	protein_coding	YES	CCDS30624.1	ENSP00000340988	LRAD2_HUMAN	.	UPI0000470177	.	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	TCTGTCTGATG	.	3	ESCA
HHIPL2	0	.	GRCh37	1	222713363	222713363	+	Missense_Mutation	SNP	T	T	C	rs140791930	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439A>G	p.Asn480Ser	p.N480S	ENST00000343410	4/9	40	30	10	25	25	0	HHIPL2,missense_variant,p.Asn480Ser,ENST00000343410,;HHIPL2,non_coding_transcript_exon_variant,,ENST00000494899,;HHIPL2,upstream_gene_variant,,ENST00000468172,;	C	ENSG00000143512	ENST00000343410	Transcript	missense_variant	1498	1439	480	N/S	aAt/aGt	rs140791930	.	.	-1	HHIPL2	HGNC	25842	protein_coding	YES	CCDS1530.2	ENSP00000342118	HIPL2_HUMAN	.	UPI000004C60D	.	tolerated(0.08)	benign(0.194)	4/9	.	Superfamily_domains:0046203,Pfam_domain:PF07995,Gene3D:2.120.10.30,hmmpanther:PTHR19328:SF31,hmmpanther:PTHR19328	.	.	.	.	.	.	.	C:0.0009	C:0	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCATTGTGA	byCluster	5	ESCA
ENAH	0	.	GRCh37	1	225684595	225684595	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*882G>C	.	.	ENST00000366844	15/15	98	72	26	127	127	0	ENAH,3_prime_UTR_variant,,ENST00000366844,;ENAH,downstream_gene_variant,,ENST00000366843,;ENAH,downstream_gene_variant,,ENST00000284563,;ENAH,intron_variant,,ENST00000488523,;ENAH,non_coding_transcript_exon_variant,,ENST00000358675,;ENAH,downstream_gene_variant,,ENST00000498108,;ENAH,downstream_gene_variant,,ENST00000483952,;	G	ENSG00000154380	ENST00000366844	Transcript	3_prime_UTR_variant	3110	.	.	.	.	.	.	.	-1	ENAH	HGNC	18271	protein_coding	YES	CCDS31041.1	ENSP00000355809	ENAH_HUMAN	.	UPI0000203FDB	.	.	.	15/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTGTCTGCAA	.	5	ESCA
CCSAP	0	.	GRCh37	1	229459933	229459933	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1049C>T	.	.	ENST00000284617	4/4	69	52	16	61	61	0	CCSAP,3_prime_UTR_variant,,ENST00000366687,;CCSAP,3_prime_UTR_variant,,ENST00000366686,;CCSAP,3_prime_UTR_variant,,ENST00000284617,;CCSAP,downstream_gene_variant,,ENST00000452552,;RP4-803J11.2,downstream_gene_variant,,ENST00000418348,;CCSAP,non_coding_transcript_exon_variant,,ENST00000483092,;	A	ENSG00000154429	ENST00000284617	Transcript	3_prime_UTR_variant	1987	.	.	.	.	.	.	.	-1	CCSAP	HGNC	29578	protein_coding	YES	CCDS1577.1	ENSP00000284617	CCSAP_HUMAN	.	UPI0000071365	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCAAGACTTT	.	5	ESCA
RYR2	0	.	GRCh37	1	237997115	237997115	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1168C>T	.	.	ENST00000366574	105/105	47	34	13	40	40	0	RYR2,3_prime_UTR_variant,,ENST00000542537,;RYR2,3_prime_UTR_variant,,ENST00000366574,;RYR2,downstream_gene_variant,,ENST00000360064,;RYR2,downstream_gene_variant,,ENST00000608590,;RYR2,downstream_gene_variant,,ENST00000462585,;	T	ENSG00000198626	ENST00000366574	Transcript	3_prime_UTR_variant	16389	.	.	.	.	.	.	.	1	RYR2	HGNC	10484	protein_coding	YES	CCDS55691.1	ENSP00000355533	RYR2_HUMAN	H0YGL9_HUMAN,D7UNU4_HUMAN,D7UNU3_HUMAN,D7UNU2_HUMAN	UPI0000DD0308	.	.	.	105/105	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TACATCACTCC	.	4	ESCA
CHML	0	.	GRCh37	1	241798135	241798135	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.934G>C	p.Asp312His	p.D312H	ENST00000366553	1/1	67	49	18	46	46	0	CHML,missense_variant,p.Asp312His,ENST00000366553,;OPN3,intron_variant,,ENST00000331838,;OPN3,intron_variant,,ENST00000366554,;OPN3,intron_variant,,ENST00000469376,;OPN3,intron_variant,,ENST00000490673,;OPN3,intron_variant,,ENST00000478849,;OPN3,intron_variant,,ENST00000463155,;	G	ENSG00000203668	ENST00000366553	Transcript	missense_variant	1098	934	312	D/H	Gat/Cat	.	.	.	-1	CHML	HGNC	1941	protein_coding	YES	CCDS31073.1	ENSP00000355511	RAE2_HUMAN	.	UPI0000073C74	.	deleterious(0)	possibly_damaging(0.746)	1/1	.	hmmpanther:PTHR11787,hmmpanther:PTHR11787:SF6,Gene3D:3.30.519.10,Pfam_domain:PF00996,PIRSF_domain:PIRSF016550,Superfamily_domains:SSF51905,Prints_domain:PR00893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATCAGGAT	.	5	ESCA
WDR64	0	.	GRCh37	1	241951283	241951283	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2808C>A	p.Ser936Arg	p.S936R	ENST00000366552	23/27	63	46	16	77	77	0	WDR64,missense_variant,p.Ser769Arg,ENST00000437684,;WDR64,missense_variant,p.Ser936Arg,ENST00000366552,;WDR64,missense_variant,p.Ser540Arg,ENST00000414635,;WDR64,missense_variant,p.Ser415Arg,ENST00000425826,;WDR64,missense_variant,p.Ser495Arg,ENST00000472717,;WDR64,3_prime_UTR_variant,,ENST00000468967,;WDR64,downstream_gene_variant,,ENST00000478331,;	A	ENSG00000162843	ENST00000366552	Transcript	missense_variant	3015	2808	936	S/R	agC/agA	.	.	.	1	WDR64	HGNC	26570	protein_coding	YES	.	ENSP00000355510	WDR64_HUMAN	D6RCR1_HUMAN	UPI0000519142	.	tolerated(0.06)	benign(0.319)	23/27	.	hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAAGCAAGTT	.	5	ESCA
AHCTF1	0	.	GRCh37	1	247076622	247076622	+	Silent	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.495A>G	p.%3D	p.A165A	ENST00000326225	4/36	82	55	27	59	59	0	AHCTF1,synonymous_variant,p.%3D,ENST00000391829,;AHCTF1,synonymous_variant,p.%3D,ENST00000366508,;AHCTF1,synonymous_variant,p.%3D,ENST00000326225,;AHCTF1,downstream_gene_variant,,ENST00000478568,;	C	ENSG00000153207	ENST00000326225	Transcript	synonymous_variant	592	495	165	A	gcA/gcG	.	.	.	-1	AHCTF1	HGNC	24618	protein_coding	YES	CCDS1629.2	ENSP00000355465	ELYS_HUMAN	C9J5C5_HUMAN	UPI0000204034	.	.	.	4/36	.	hmmpanther:PTHR21583	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCTGCCAC	.	5	ESCA
OR1C1	0	.	GRCh37	1	247920874	247920874	+	Missense_Mutation	SNP	A	A	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.835T>A	p.Ser279Thr	p.S279T	ENST00000408896	1/1	27	22	5	29	29	0	OR1C1,missense_variant,p.Ser279Thr,ENST00000408896,;	T	ENSG00000221888	ENST00000408896	Transcript	missense_variant	1109	835	279	S/T	Tca/Aca	.	.	.	-1	OR1C1	HGNC	8182	protein_coding	YES	CCDS41481.1	ENSP00000386138	OR1C1_HUMAN	.	UPI000004B1DC	.	tolerated(1)	benign(0.004)	1/1	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF108,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTGAATACA	.	5	ESCA
PGBD2	0	.	GRCh37	1	249211387	249211387	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.604G>A	p.Glu202Lys	p.E202K	ENST00000329291	3/3	55	42	13	37	37	0	PGBD2,missense_variant,p.Glu199Lys,ENST00000539153,;PGBD2,missense_variant,p.Glu202Lys,ENST00000329291,;PGBD2,intron_variant,,ENST00000355360,;RNU6-1205P,upstream_gene_variant,,ENST00000363625,;PGBD2,intron_variant,,ENST00000462488,;	A	ENSG00000185220	ENST00000329291	Transcript	missense_variant	751	604	202	E/K	Gaa/Aaa	.	.	.	1	PGBD2	HGNC	19399	protein_coding	YES	CCDS31128.1	ENSP00000331643	PGBD2_HUMAN	.	UPI000016196D	.	deleterious(0)	possibly_damaging(0.805)	3/3	.	Pfam_domain:PF13843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTGGGAAACC	.	5	ESCA
LAPTM5	0	.	GRCh37	1	31211805	31211805	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.492C>G	p.Phe164Leu	p.F164L	ENST00000294507	5/8	50	39	11	22	22	0	LAPTM5,missense_variant,p.Phe164Leu,ENST00000294507,;MIR4420,downstream_gene_variant,,ENST00000583944,;LAPTM5,non_coding_transcript_exon_variant,,ENST00000464569,;LAPTM5,downstream_gene_variant,,ENST00000476492,;	C	ENSG00000162511	ENST00000294507	Transcript	missense_variant	567	492	164	F/L	ttC/ttG	.	.	.	-1	LAPTM5	HGNC	29612	protein_coding	YES	CCDS337.1	ENSP00000294507	LAPM5_HUMAN	Q5TBB8_HUMAN	UPI000012E20A	.	tolerated(0.54)	benign(0.329)	5/8	.	Transmembrane_helices:TMhelix,TIGRFAM_domain:TIGR00799,Pfam_domain:PF03821,hmmpanther:PTHR12479:SF2,hmmpanther:PTHR12479	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACTTGAAGTT	.	5	ESCA
COL16A1	0	.	GRCh37	1	32126208	32126208	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3857G>C	p.Arg1286Thr	p.R1286T	ENST00000373672	62/71	51	39	11	27	27	0	COL16A1,missense_variant,p.Arg1286Thr,ENST00000271069,;COL16A1,missense_variant,p.Arg1286Thr,ENST00000373672,;COL16A1,missense_variant,p.Arg143Thr,ENST00000440437,;RP11-73M7.6,downstream_gene_variant,,ENST00000589462,;RP11-73M7.6,downstream_gene_variant,,ENST00000588288,;RP11-73M7.6,downstream_gene_variant,,ENST00000609338,;RP11-73M7.6,downstream_gene_variant,,ENST00000609373,;RP11-73M7.6,downstream_gene_variant,,ENST00000593188,;RP11-73M7.6,downstream_gene_variant,,ENST00000609625,;RP11-73M7.6,downstream_gene_variant,,ENST00000609033,;RP11-73M7.6,downstream_gene_variant,,ENST00000585413,;RP11-73M7.6,downstream_gene_variant,,ENST00000587445,;RP11-73M7.6,downstream_gene_variant,,ENST00000610216,;RP11-73M7.6,downstream_gene_variant,,ENST00000445166,;RP11-73M7.6,downstream_gene_variant,,ENST00000608332,;RP11-73M7.6,downstream_gene_variant,,ENST00000609549,;RP11-73M7.6,downstream_gene_variant,,ENST00000607926,;RP11-73M7.6,downstream_gene_variant,,ENST00000610043,;RP11-73M7.6,downstream_gene_variant,,ENST00000608246,;RP11-73M7.6,downstream_gene_variant,,ENST00000585660,;RP11-73M7.6,downstream_gene_variant,,ENST00000608888,;RP11-73M7.6,downstream_gene_variant,,ENST00000591592,;RP11-73M7.6,downstream_gene_variant,,ENST00000591929,;COL16A1,non_coding_transcript_exon_variant,,ENST00000466829,;COL16A1,upstream_gene_variant,,ENST00000461217,;COL16A1,non_coding_transcript_exon_variant,,ENST00000488128,;COL16A1,non_coding_transcript_exon_variant,,ENST00000482910,;COL16A1,non_coding_transcript_exon_variant,,ENST00000470799,;COL16A1,non_coding_transcript_exon_variant,,ENST00000488897,;	G	ENSG00000084636	ENST00000373672	Transcript	missense_variant	4374	3857	1286	R/T	aGa/aCa	.	.	.	-1	COL16A1	HGNC	2193	protein_coding	YES	CCDS41297.1	ENSP00000362776	COGA1_HUMAN	.	UPI0000203DD1	.	.	unknown(0)	62/71	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGGTCTTCCC	.	5	ESCA
BAI2	0	.	GRCh37	1	32222191	32222191	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.247T>G	p.Phe83Val	p.F83V	ENST00000373658	4/33	73	56	17	60	60	0	BAI2,missense_variant,p.Phe71Val,ENST00000398538,;BAI2,missense_variant,p.Phe83Val,ENST00000373658,;BAI2,missense_variant,p.Phe117Val,ENST00000533175,;BAI2,missense_variant,p.Phe71Val,ENST00000398547,;BAI2,missense_variant,p.Phe76Val,ENST00000420125,;BAI2,missense_variant,p.Phe83Val,ENST00000527361,;BAI2,missense_variant,p.Phe86Val,ENST00000398556,;BAI2,missense_variant,p.Phe83Val,ENST00000257070,;BAI2,missense_variant,p.Phe71Val,ENST00000398542,;BAI2,missense_variant,p.Phe83Val,ENST00000373655,;BAI2,downstream_gene_variant,,ENST00000436464,;MIR4254,downstream_gene_variant,,ENST00000581063,;BAI2,upstream_gene_variant,,ENST00000473952,;BAI2,upstream_gene_variant,,ENST00000530134,;	C	ENSG00000121753	ENST00000373658	Transcript	missense_variant	589	247	83	F/V	Ttc/Gtc	.	.	.	-1	BAI2	HGNC	944	protein_coding	YES	CCDS346.2	ENSP00000362762	BAI2_HUMAN	.	UPI0000E2A42F	.	tolerated(0.79)	probably_damaging(0.997)	4/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTTGAAGCGCA	.	5	ESCA
CLSPN	0	.	GRCh37	1	36211119	36211119	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2899G>A	p.Glu967Lys	p.E967K	ENST00000318121	16/25	50	42	8	52	52	0	CLSPN,missense_variant,p.Glu967Lys,ENST00000318121,;CLSPN,missense_variant,p.Glu914Lys,ENST00000520551,;CLSPN,missense_variant,p.Glu903Lys,ENST00000373220,;CLSPN,missense_variant,p.Glu967Lys,ENST00000251195,;RP11-435D7.3,downstream_gene_variant,,ENST00000373226,;CLSPN,downstream_gene_variant,,ENST00000517467,;	T	ENSG00000092853	ENST00000318121	Transcript	missense_variant	2957	2899	967	E/K	Gag/Aag	.	.	.	-1	CLSPN	HGNC	19715	protein_coding	YES	CCDS396.1	ENSP00000312995	CLSPN_HUMAN	.	UPI0000161087	.	tolerated(0.12)	benign(0.099)	16/25	.	hmmpanther:PTHR14396	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCTCCTTCT	.	5	ESCA
CEP104	0	.	GRCh37	1	3756340	3756340	+	Silent	SNP	C	C	T	rs778378591	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.567G>A	p.%3D	p.R189R	ENST00000378230	7/22	40	28	12	55	55	0	CEP104,synonymous_variant,p.%3D,ENST00000428079,;CEP104,synonymous_variant,p.%3D,ENST00000378230,;CEP104,upstream_gene_variant,,ENST00000443466,;CEP104,downstream_gene_variant,,ENST00000378223,;CEP104,upstream_gene_variant,,ENST00000460038,;CEP104,splice_region_variant,,ENST00000494951,;CEP104,splice_region_variant,,ENST00000494653,;	T	ENSG00000116198	ENST00000378230	Transcript	synonymous_variant	892	567	189	R	agG/agA	rs778378591	.	.	-1	CEP104	HGNC	24866	protein_coding	YES	CCDS30571.1	ENSP00000367476	CE104_HUMAN	.	UPI0000139AA8	.	.	.	7/22	.	hmmpanther:PTHR13371:SF0,hmmpanther:PTHR13371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATTTCCTAAA	.	5	ESCA
RSPO1	0	.	GRCh37	1	38078221	38078221	+	3'UTR	SNP	G	G	A	rs758416936	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*206C>T	.	.	ENST00000356545	8/9	28	25	3	25	25	0	RSPO1,3_prime_UTR_variant,,ENST00000401070,;RSPO1,3_prime_UTR_variant,,ENST00000401068,;RSPO1,3_prime_UTR_variant,,ENST00000401069,;RSPO1,3_prime_UTR_variant,,ENST00000401071,;RSPO1,3_prime_UTR_variant,,ENST00000356545,;RSPO1,3_prime_UTR_variant,,ENST00000373059,;	A	ENSG00000169218	ENST00000356545	Transcript	3_prime_UTR_variant	1786	.	.	.	.	rs758416936	.	.	-1	RSPO1	HGNC	21679	protein_coding	YES	CCDS41304.1	ENSP00000348944	RSPO1_HUMAN	.	UPI0000674A16	.	.	.	8/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCTGCGTGTGT	.	2	ESCA
MACF1	0	.	GRCh37	1	39800706	39800706	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4629+7681C>G	.	.	ENST00000545844	.	75	66	8	71	71	0	MACF1,missense_variant,p.Gln1256Glu,ENST00000289893,;MACF1,missense_variant,p.Gln2816Glu,ENST00000564288,;MACF1,missense_variant,p.Gln2821Glu,ENST00000372915,;MACF1,missense_variant,p.Gln2853Glu,ENST00000567887,;MACF1,intron_variant,,ENST00000372925,;MACF1,intron_variant,,ENST00000361689,;MACF1,intron_variant,,ENST00000530262,;MACF1,intron_variant,,ENST00000539005,;MACF1,intron_variant,,ENST00000317713,;MACF1,intron_variant,,ENST00000545844,;MACF1,intron_variant,,ENST00000476350,;MACF1,downstream_gene_variant,,ENST00000528611,;	G	ENSG00000127603	ENST00000545844	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	MACF1_HUMAN	Q8WXY4_HUMAN,Q8WXY3_HUMAN,Q8WXY0_HUMAN,Q8WXX9_HUMAN,B4DNC4_HUMAN	UPI00001B3DC6	.	.	.	.	36/93	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTTCAAGTT	.	4	ESCA
KIAA0754	0	.	GRCh37	1	39881069	39881069	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*848G>C	.	.	ENST00000530275	1/1	26	18	8	10	10	0	KIAA0754,3_prime_UTR_variant,,ENST00000530275,;MACF1,intron_variant,,ENST00000372925,;MACF1,intron_variant,,ENST00000361689,;MACF1,intron_variant,,ENST00000289893,;MACF1,intron_variant,,ENST00000564288,;MACF1,intron_variant,,ENST00000539005,;MACF1,intron_variant,,ENST00000372915,;MACF1,intron_variant,,ENST00000317713,;MACF1,intron_variant,,ENST00000482035,;MACF1,intron_variant,,ENST00000567887,;MACF1,intron_variant,,ENST00000545844,;	C	ENSG00000255103	ENST00000530275	Transcript	3_prime_UTR_variant	4919	.	.	.	.	.	.	.	1	KIAA0754	HGNC	29111	protein_coding	YES	.	ENSP00000431179	K0754_HUMAN	.	UPI0000DD78B2	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GTGGTGCGATC	.	2	ESCA
OXCT2	0	.	GRCh37	1	40236869	40236869	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.59C>G	p.Ser20Ter	p.S20*	ENST00000327582	1/1	10	7	3	17	17	0	OXCT2,stop_gained,p.Ser20Ter,ENST00000327582,;BMP8B,intron_variant,,ENST00000372827,;BMP8B,intron_variant,,ENST00000397360,;	C	ENSG00000198754	ENST00000327582	Transcript	stop_gained	152	59	20	S/*	tCa/tGa	.	.	.	-1	OXCT2	HGNC	18606	protein_coding	YES	CCDS445.1	ENSP00000361914	SCOT2_HUMAN	.	UPI000006DF0A	.	.	.	1/1	.	PROSITE_profiles:PS51257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCCTGAGCCG	.	2	ESCA
EXO5	0	.	GRCh37	1	40981820	40981820	+	3'Flank	SNP	G	G	C	rs541024680	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000372703	.	56	47	9	50	49	0	EXO5,3_prime_UTR_variant,,ENST00000296380,;EXO5,downstream_gene_variant,,ENST00000419161,;EXO5,downstream_gene_variant,,ENST00000415550,;EXO5,downstream_gene_variant,,ENST00000420209,;EXO5,downstream_gene_variant,,ENST00000358527,;EXO5,downstream_gene_variant,,ENST00000432259,;EXO5,downstream_gene_variant,,ENST00000372703,;EXO5,downstream_gene_variant,,ENST00000418186,;EXO5,downstream_gene_variant,,ENST00000443729,;RP11-656D10.6,intron_variant,,ENST00000437060,;RP11-656D10.5,upstream_gene_variant,,ENST00000453437,;EXO5,downstream_gene_variant,,ENST00000471429,;	C	ENSG00000164002	ENST00000372703	Transcript	downstream_gene_variant	.	.	.	.	.	rs541024680	.	111	1	EXO5	HGNC	26115	protein_coding	YES	CCDS453.1	ENSP00000361788	EXO5_HUMAN	.	UPI00000722CF	.	.	.	.	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTTGGAATCA	by1000G	5	ESCA
CDC20	0	.	GRCh37	1	43826244	43826244	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.828G>C	p.Trp276Cys	p.W276C	ENST00000372462	6/10	22	17	5	22	22	0	CDC20,missense_variant,p.Trp276Cys,ENST00000310955,;CDC20,missense_variant,p.Trp276Cys,ENST00000372462,;ELOVL1,downstream_gene_variant,,ENST00000413844,;ELOVL1,downstream_gene_variant,,ENST00000372458,;RP1-92O14.3,upstream_gene_variant,,ENST00000424948,;CDC20,non_coding_transcript_exon_variant,,ENST00000478882,;CDC20,upstream_gene_variant,,ENST00000482046,;ELOVL1,downstream_gene_variant,,ENST00000468865,;ELOVL1,downstream_gene_variant,,ENST00000482302,;ELOVL1,downstream_gene_variant,,ENST00000465321,;ELOVL1,downstream_gene_variant,,ENST00000478481,;ELOVL1,downstream_gene_variant,,ENST00000496932,;ELOVL1,downstream_gene_variant,,ENST00000497050,;ELOVL1,downstream_gene_variant,,ENST00000487209,;ELOVL1,downstream_gene_variant,,ENST00000470769,;ELOVL1,downstream_gene_variant,,ENST00000479439,;ELOVL1,downstream_gene_variant,,ENST00000470968,;ELOVL1,downstream_gene_variant,,ENST00000479686,;ELOVL1,downstream_gene_variant,,ENST00000464204,;ELOVL1,downstream_gene_variant,,ENST00000497569,;	C	ENSG00000117399	ENST00000372462	Transcript	missense_variant	1031	828	276	W/C	tgG/tgC	COSM909757	.	.	1	CDC20	HGNC	1723	protein_coding	YES	CCDS484.1	ENSP00000361540	CDC20_HUMAN	.	UPI0000072C04	.	deleterious(0)	probably_damaging(0.929)	6/10	.	Superfamily_domains:SSF50978,SMART_domains:SM00320,Gene3D:2.130.10.10,hmmpanther:PTHR19918,hmmpanther:PTHR19918:SF3,PROSITE_profiles:PS50294	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCTGGAACAG	.	5	ESCA
SLC6A9	0	.	GRCh37	1	44474228	44474228	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.606C>T	p.%3D	p.I202I	ENST00000360584	5/14	34	25	9	29	29	0	SLC6A9,synonymous_variant,p.%3D,ENST00000537678,;SLC6A9,synonymous_variant,p.%3D,ENST00000357730,;SLC6A9,synonymous_variant,p.%3D,ENST00000372306,;SLC6A9,synonymous_variant,p.%3D,ENST00000372310,;SLC6A9,synonymous_variant,p.%3D,ENST00000475075,;SLC6A9,synonymous_variant,p.%3D,ENST00000372307,;SLC6A9,synonymous_variant,p.%3D,ENST00000360584,;SLC6A9,downstream_gene_variant,,ENST00000528803,;SLC6A9,downstream_gene_variant,,ENST00000466926,;SLC6A9,non_coding_transcript_exon_variant,,ENST00000492434,;SLC6A9,downstream_gene_variant,,ENST00000489764,;	A	ENSG00000196517	ENST00000360584	Transcript	synonymous_variant	798	606	202	I	atC/atT	.	.	.	-1	SLC6A9	HGNC	11056	protein_coding	YES	CCDS41317.1	ENSP00000353791	SC6A9_HUMAN	B7Z589_HUMAN	UPI000053030B	.	.	.	5/14	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF110,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687,Prints_domain:PR00176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCGATGCA	.	5	ESCA
BEND5	0	.	GRCh37	1	49227056	49227056	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.313G>T	p.Glu105Ter	p.E105*	ENST00000371833	2/6	68	58	10	102	102	0	BEND5,stop_gained,p.Glu105Ter,ENST00000371833,;AGBL4,intron_variant,,ENST00000371839,;AGBL4,intron_variant,,ENST00000416121,;AGBL4,intron_variant,,ENST00000371838,;BEND5,intron_variant,,ENST00000480399,;BEND5,upstream_gene_variant,,ENST00000476079,;BEND5,upstream_gene_variant,,ENST00000476096,;BEND5,non_coding_transcript_exon_variant,,ENST00000463562,;BEND5,non_coding_transcript_exon_variant,,ENST00000489956,;	A	ENSG00000162373	ENST00000371833	Transcript	stop_gained	400	313	105	E/*	Gag/Tag	.	.	.	-1	BEND5	HGNC	25668	protein_coding	YES	CCDS552.2	ENSP00000360899	BEND5_HUMAN	.	UPI00002042F4	.	.	.	2/6	.	hmmpanther:PTHR14628	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACCTCTCCAT	.	5	ESCA
TTC39A	0	.	GRCh37	1	51767904	51767904	+	Intron	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903+125G>T	.	.	ENST00000413473	.	106	89	17	92	92	0	TTC39A,missense_variant,p.Arg371Ile,ENST00000262676,;TTC39A,intron_variant,,ENST00000447632,;TTC39A,intron_variant,,ENST00000413473,;TTC39A,intron_variant,,ENST00000262675,;TTC39A,intron_variant,,ENST00000451380,;TTC39A,intron_variant,,ENST00000411642,;TTC39A,intron_variant,,ENST00000371747,;TTC39A,intron_variant,,ENST00000371750,;TTC39A,downstream_gene_variant,,ENST00000422925,;TTC39A,downstream_gene_variant,,ENST00000439482,;TTC39A,upstream_gene_variant,,ENST00000530004,;TTC39A,downstream_gene_variant,,ENST00000380849,;TTC39A,intron_variant,,ENST00000524442,;TTC39A,intron_variant,,ENST00000431927,;TTC39A,upstream_gene_variant,,ENST00000534098,;	A	ENSG00000085831	ENST00000413473	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	TTC39A	HGNC	18657	protein_coding	YES	CCDS44143.1	ENSP00000406144	TT39A_HUMAN	E9PHX9_HUMAN,E9PAZ4_HUMAN,D3DQ30_HUMAN	UPI0000252149	.	.	.	.	11/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGGTTCTCTCT	.	4	ESCA
INADL	0	.	GRCh37	1	62237287	62237287	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.709C>G	p.Leu237Val	p.L237V	ENST00000371158	6/43	68	64	4	44	44	0	INADL,missense_variant,p.Leu237Val,ENST00000316485,;INADL,missense_variant,p.Leu237Val,ENST00000371158,;INADL,non_coding_transcript_exon_variant,,ENST00000459752,;INADL,non_coding_transcript_exon_variant,,ENST00000484562,;	G	ENSG00000132849	ENST00000371158	Transcript	missense_variant	823	709	237	L/V	Ctg/Gtg	.	.	.	1	INADL	HGNC	28881	protein_coding	YES	CCDS617.2	ENSP00000360200	INADL_HUMAN	.	UPI0000204487	.	tolerated(0.37)	benign(0.005)	6/43	.	hmmpanther:PTHR19964:SF11,hmmpanther:PTHR19964,Gene3D:2.30.42.10,Superfamily_domains:SSF50156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAACTCTGCCT	.	2	ESCA
RNF207	0	.	GRCh37	1	6266692	6266692	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.97G>C	p.Glu33Gln	p.E33Q	ENST00000377939	2/18	32	24	7	43	43	0	RNF207,missense_variant,p.Glu33Gln,ENST00000377939,;RNF207,5_prime_UTR_variant,,ENST00000377948,;RPL22,intron_variant,,ENST00000471204,;RPL22,intron_variant,,ENST00000465335,;RPL22,upstream_gene_variant,,ENST00000462296,;RP1-120G22.11,upstream_gene_variant,,ENST00000455744,;RNF207,upstream_gene_variant,,ENST00000463453,;RNF207,non_coding_transcript_exon_variant,,ENST00000484435,;RNF207,non_coding_transcript_exon_variant,,ENST00000466994,;RNF207,upstream_gene_variant,,ENST00000496329,;RNF207,upstream_gene_variant,,ENST00000485539,;RNF207,upstream_gene_variant,,ENST00000492476,;RNF207,upstream_gene_variant,,ENST00000496676,;	C	ENSG00000158286	ENST00000377939	Transcript	missense_variant	224	97	33	E/Q	Gag/Cag	COSM3491556	.	.	1	RNF207	HGNC	32947	protein_coding	YES	CCDS59.2	ENSP00000367173	RN207_HUMAN	.	UPI0000F0A526	.	tolerated(0.2)	possibly_damaging(0.531)	2/18	.	PROSITE_profiles:PS50089,hmmpanther:PTHR22635,Pfam_domain:PF00097,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTACGAGCGC	.	5	ESCA
ANGPTL3	0	.	GRCh37	1	63068045	63068045	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.925C>G	p.Leu309Val	p.L309V	ENST00000371129	5/7	71	58	13	60	60	0	ANGPTL3,missense_variant,p.Leu309Val,ENST00000371129,;DOCK7,intron_variant,,ENST00000404627,;DOCK7,intron_variant,,ENST00000251157,;DOCK7,intron_variant,,ENST00000340370,;ANGPTL3,non_coding_transcript_exon_variant,,ENST00000482591,;ANGPTL3,non_coding_transcript_exon_variant,,ENST00000493994,;	G	ENSG00000132855	ENST00000371129	Transcript	missense_variant	1005	925	309	L/V	Ctt/Gtt	COSM911405	.	.	1	ANGPTL3	HGNC	491	protein_coding	YES	CCDS622.1	ENSP00000360170	ANGL3_HUMAN	B1ALJ0_HUMAN	UPI000003722C	.	deleterious(0)	probably_damaging(0.96)	5/7	.	PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF18,Pfam_domain:PF00147,Gene3D:3.90.215.10,SMART_domains:SM00186,Superfamily_domains:SSF56496	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGAGGCTTGAT	.	5	ESCA
NEGR1	0	.	GRCh37	1	71871455	71871455	+	3'UTR	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1674A>C	.	.	ENST00000357731	7/7	80	62	18	70	70	0	NEGR1,3_prime_UTR_variant,,ENST00000306821,;NEGR1,3_prime_UTR_variant,,ENST00000357731,;NEGR1,downstream_gene_variant,,ENST00000434200,;ZRANB2-AS2,intron_variant,,ENST00000583678,;ZRANB2-AS2,intron_variant,,ENST00000594152,;ZRANB2-AS2,intron_variant,,ENST00000600103,;ZRANB2-AS2,intron_variant,,ENST00000599146,;ZRANB2-AS2,intron_variant,,ENST00000430605,;ZRANB2-AS2,intron_variant,,ENST00000608579,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585499,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587306,;ZRANB2-AS2,upstream_gene_variant,,ENST00000586006,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587066,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585415,;ZRANB2-AS2,upstream_gene_variant,,ENST00000590186,;NEGR1,downstream_gene_variant,,ENST00000474357,;	G	ENSG00000172260	ENST00000357731	Transcript	3_prime_UTR_variant	2979	.	.	.	.	.	.	.	-1	NEGR1	HGNC	17302	protein_coding	YES	CCDS661.1	ENSP00000350364	NEGR1_HUMAN	Q8N440_HUMAN,Q68DZ8_HUMAN	UPI00000477EE	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAATTTCTTGT	.	5	ESCA
FPGT-TNNI3K	0	.	GRCh37	1	74663999	74663999	+	Missense_Mutation	SNP	C	C	G	rs201738008	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.76C>G	p.Arg26Gly	p.R26G	ENST00000557284	1/27	38	34	4	48	48	0	FPGT-TNNI3K,missense_variant,p.Arg13Gly,ENST00000370895,;FPGT,missense_variant,p.Arg13Gly,ENST00000482102,;FPGT-TNNI3K,missense_variant,p.Arg13Gly,ENST00000370893,;FPGT-TNNI3K,missense_variant,p.Arg13Gly,ENST00000534632,;FPGT,missense_variant,p.Arg26Gly,ENST00000467578,;FPGT,missense_variant,p.Arg26Gly,ENST00000370898,;FPGT,missense_variant,p.Arg13Gly,ENST00000534056,;FPGT-TNNI3K,missense_variant,p.Arg13Gly,ENST00000370899,;TNNI3K,missense_variant,p.Arg13Gly,ENST00000370891,;FPGT,missense_variant,p.Arg13Gly,ENST00000609362,;FPGT,missense_variant,p.Arg13Gly,ENST00000370894,;FPGT-TNNI3K,missense_variant,p.Arg26Gly,ENST00000557284,;LRRIQ3,upstream_gene_variant,,ENST00000370911,;LRRIQ3,upstream_gene_variant,,ENST00000354431,;LRRIQ3,upstream_gene_variant,,ENST00000370909,;FPGT,upstream_gene_variant,,ENST00000472069,;FPGT,non_coding_transcript_exon_variant,,ENST00000524915,;FPGT-TNNI3K,non_coding_transcript_exon_variant,,ENST00000533006,;FPGT,missense_variant,p.Arg13Gly,ENST00000529485,;LRRIQ3,upstream_gene_variant,,ENST00000415760,;LRRIQ3,upstream_gene_variant,,ENST00000463724,;	G	ENSG00000259030	ENST00000557284	Transcript	missense_variant	81	76	26	R/G	Cga/Gga	rs201738008	.	.	1	FPGT-TNNI3K	HGNC	42952	protein_coding	YES	CCDS44161.2	ENSP00000450895	.	A6NHC7_HUMAN	UPI0001EECC26	.	deleterious_low_confidence(0)	benign(0.013)	1/27	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CGCTGCGAGAA	byCluster	4	ESCA
FPGT-TNNI3K	0	.	GRCh37	1	74715181	74715181	+	Missense_Mutation	SNP	G	G	A	rs567503494	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.530G>A	p.Arg177His	p.R177H	ENST00000557284	5/27	87	68	19	42	42	0	FPGT-TNNI3K,missense_variant,p.Arg164His,ENST00000370895,;TNNI3K,missense_variant,p.Arg164His,ENST00000370891,;FPGT-TNNI3K,missense_variant,p.Arg177His,ENST00000557284,;TNNI3K,missense_variant,p.Arg63His,ENST00000326637,;FPGT-TNNI3K,missense_variant,p.Arg164His,ENST00000370899,;FPGT-TNNI3K,intron_variant,,ENST00000534632,;FPGT-TNNI3K,non_coding_transcript_exon_variant,,ENST00000533006,;	A	ENSG00000259030	ENST00000557284	Transcript	missense_variant	535	530	177	R/H	cGc/cAc	rs567503494,COSM1229958	.	.	1	FPGT-TNNI3K	HGNC	42952	protein_coding	YES	CCDS44161.2	ENSP00000450895	.	A6NHC7_HUMAN	UPI0001EECC26	.	tolerated(0.07)	possibly_damaging(0.809)	5/27	.	Superfamily_domains:SSF48403,Gene3D:1.25.40.20,PROSITE_profiles:PS50297	A:0.0002	A:0.0008	A:0	.	A:0	A:0	A:0	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTACCGCACTG	by1000G	5	ESCA
SLC44A5	0	.	GRCh37	1	75805272	75805272	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.96C>T	p.%3D	p.A32A	ENST00000370855	4/24	93	80	13	96	96	0	SLC44A5,synonymous_variant,p.%3D,ENST00000370855,;SLC44A5,synonymous_variant,p.%3D,ENST00000370859,;SLC44A5,5_prime_UTR_variant,,ENST00000535611,;SLC44A5,non_coding_transcript_exon_variant,,ENST00000469525,;	A	ENSG00000137968	ENST00000370855	Transcript	synonymous_variant	210	96	32	A	gcC/gcT	.	.	.	-1	SLC44A5	HGNC	28524	protein_coding	YES	CCDS667.1	ENSP00000359892	CTL5_HUMAN	B7Z473_HUMAN	UPI000013E195	.	.	.	4/24	.	hmmpanther:PTHR12385:SF42,hmmpanther:PTHR12385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGTTGGCAAC	.	5	ESCA
PIGK	0	.	GRCh37	1	77676165	77676165	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103G>C	p.Glu35Gln	p.E35Q	ENST00000370812	2/11	170	138	31	135	135	0	PIGK,missense_variant,p.Glu35Gln,ENST00000370813,;PIGK,missense_variant,p.Glu35Gln,ENST00000370812,;PIGK,missense_variant,p.Glu35Gln,ENST00000359130,;PIGK,intron_variant,,ENST00000445065,;PIGK,non_coding_transcript_exon_variant,,ENST00000478391,;	G	ENSG00000142892	ENST00000370812	Transcript	missense_variant	127	103	35	E/Q	Gaa/Caa	.	.	.	-1	PIGK	HGNC	8965	protein_coding	YES	CCDS674.1	ENSP00000359848	GPI8_HUMAN	.	UPI000012B9D1	.	tolerated(0.22)	benign(0.01)	2/11	.	hmmpanther:PTHR12000:SF1,hmmpanther:PTHR12000,PIRSF_domain:PIRSF019663,PIRSF_domain:PIRSF500138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTCTGCTT	.	5	ESCA
USP33	0	.	GRCh37	1	78163138	78163138	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2693C>T	p.Ser898Phe	p.S898F	ENST00000370793	25/25	108	80	27	95	95	0	USP33,missense_variant,p.Ser898Phe,ENST00000370793,;USP33,missense_variant,p.Ser898Phe,ENST00000357428,;USP33,missense_variant,p.Ser867Phe,ENST00000370794,;USP33,3_prime_UTR_variant,,ENST00000481579,;USP33,downstream_gene_variant,,ENST00000533928,;	A	ENSG00000077254	ENST00000370793	Transcript	missense_variant	3040	2693	898	S/F	tCt/tTt	COSM3805907	.	.	-1	USP33	HGNC	20059	protein_coding	YES	CCDS678.1	ENSP00000359829	UBP33_HUMAN	Q9Y417_HUMAN,E9PQP0_HUMAN,E9PP47_HUMAN,E9PLK7_HUMAN	UPI000022ABDA	.	deleterious(0)	probably_damaging(0.999)	25/25	.	PROSITE_profiles:PS51283,hmmpanther:PTHR24006:SF369,hmmpanther:PTHR24006,Pfam_domain:PF06337,Gene3D:3jyuB01,SMART_domains:SM00695,Superfamily_domains:0050384	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTTCAGAAATC	.	5	ESCA
CCBL2	0	.	GRCh37	1	89426940	89426940	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.697G>C	p.Ala233Pro	p.A233P	ENST00000260508	8/14	51	44	7	41	41	0	CCBL2,missense_variant,p.Ala199Pro,ENST00000370491,;CCBL2,missense_variant,p.Ala233Pro,ENST00000370486,;CCBL2,missense_variant,p.Ala233Pro,ENST00000260508,;CCBL2,3_prime_UTR_variant,,ENST00000370485,;CCBL2,non_coding_transcript_exon_variant,,ENST00000446900,;	G	ENSG00000137944	ENST00000260508	Transcript	missense_variant	1035	697	233	A/P	Gct/Cct	.	.	.	-1	CCBL2	HGNC	33238	protein_coding	YES	CCDS30766.1	ENSP00000260508	KAT3_HUMAN	B4DW13_HUMAN	UPI0000155712	.	deleterious(0)	probably_damaging(0.999)	8/14	.	hmmpanther:PTHR11751:SF336,hmmpanther:PTHR11751,Gene3D:3.40.640.10,Pfam_domain:PF00155,Superfamily_domains:SSF53383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCAGCAATTA	.	5	ESCA
GCLM	0	.	GRCh37	1	94370138	94370138	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.133G>C	p.Asp45His	p.D45H	ENST00000370238	2/7	54	42	11	57	57	0	GCLM,missense_variant,p.Asp45His,ENST00000370238,;GCLM,non_coding_transcript_exon_variant,,ENST00000467772,;GCLM,non_coding_transcript_exon_variant,,ENST00000462183,;	G	ENSG00000023909	ENST00000370238	Transcript	missense_variant	380	133	45	D/H	Gat/Cat	.	.	.	-1	GCLM	HGNC	4312	protein_coding	YES	CCDS746.1	ENSP00000359258	GSH0_HUMAN	M5A959_HUMAN,D3DT44_HUMAN	UPI000000D9B9	.	deleterious(0)	possibly_damaging(0.838)	2/7	.	hmmpanther:PTHR13295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAATCATGAA	.	5	ESCA
ARHGAP29	0	.	GRCh37	1	94639155	94639155	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*270C>T	.	.	ENST00000260526	23/23	121	102	19	104	104	0	ARHGAP29,3_prime_UTR_variant,,ENST00000260526,;ARHGAP29,downstream_gene_variant,,ENST00000482481,;ARHGAP29,intron_variant,,ENST00000552844,;	A	ENSG00000137962	ENST00000260526	Transcript	3_prime_UTR_variant	4239	.	.	.	.	.	.	.	-1	ARHGAP29	HGNC	30207	protein_coding	YES	CCDS748.1	ENSP00000260526	RHG29_HUMAN	.	UPI000013D0E4	.	.	.	23/23	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTGAACTT	.	5	ESCA
CLSTN1	0	.	GRCh37	1	9796040	9796040	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1637C>T	p.Ser546Phe	p.S546F	ENST00000377298	12/19	27	23	4	47	47	0	CLSTN1,missense_variant,p.Ser347Phe,ENST00000435891,;CLSTN1,missense_variant,p.Ser546Phe,ENST00000377298,;CLSTN1,missense_variant,p.Ser527Phe,ENST00000377288,;CLSTN1,missense_variant,p.Ser536Phe,ENST00000361311,;CLSTN1,upstream_gene_variant,,ENST00000477264,;	A	ENSG00000171603	ENST00000377298	Transcript	missense_variant	2430	1637	546	S/F	tCc/tTc	COSM122206	.	.	-1	CLSTN1	HGNC	17447	protein_coding	YES	CCDS30580.1	ENSP00000366513	CSTN1_HUMAN	.	UPI0000127B95	.	deleterious(0)	possibly_damaging(0.892)	12/19	.	Superfamily_domains:SSF49899,Pfam_domain:PF13385,hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF4	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	TCCCGGAACGG	.	3	ESCA
LPPR4	0	.	GRCh37	1	99771566	99771566	+	Missense_Mutation	SNP	G	G	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1292G>A	p.Arg431Lys	p.R431K	ENST00000370185	7/7	45	27	18	28	28	0	LPPR4,missense_variant,p.Arg431Lys,ENST00000370185,;LPPR4,missense_variant,p.Arg373Lys,ENST00000457765,;LPPR4,missense_variant,p.Arg273Lys,ENST00000370184,;	A	ENSG00000117600	ENST00000370185	Transcript	missense_variant	1789	1292	431	R/K	aGa/aAa	COSM145888	.	.	1	LPPR4	Uniprot_gn	.	protein_coding	YES	CCDS757.1	ENSP00000359204	LPPR4_HUMAN	.	UPI0000161229	.	deleterious(0.01)	probably_damaging(0.91)	7/7	.	hmmpanther:PTHR10165:SF13,hmmpanther:PTHR10165	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGAAGAAATG	.	5	ESCA
JAG1	0	.	GRCh37	20	10619280	10619280	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*866C>G	.	.	ENST00000254958	26/26	88	70	18	72	72	0	JAG1,3_prime_UTR_variant,,ENST00000254958,;JAG1,intron_variant,,ENST00000423891,;SLX4IP,downstream_gene_variant,,ENST00000488816,;	C	ENSG00000101384	ENST00000254958	Transcript	3_prime_UTR_variant	5039	.	.	.	.	.	.	.	-1	JAG1	HGNC	6188	protein_coding	YES	CCDS13112.1	ENSP00000254958	JAG1_HUMAN	B7U6M8_HUMAN,B4DYR1_HUMAN	UPI00000498B5	.	.	.	26/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTGACGTC	.	5	ESCA
CRNKL1	0	.	GRCh37	20	20024186	20024186	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1405G>C	p.Glu469Gln	p.E469Q	ENST00000377340	8/15	61	34	26	41	41	0	CRNKL1,missense_variant,p.Glu469Gln,ENST00000377340,;CRNKL1,missense_variant,p.Glu457Gln,ENST00000377327,;CRNKL1,missense_variant,p.Glu308Gln,ENST00000536226,;CRNKL1,3_prime_UTR_variant,,ENST00000496549,;CRNKL1,3_prime_UTR_variant,,ENST00000490910,;CRNKL1,upstream_gene_variant,,ENST00000490258,;	G	ENSG00000101343	ENST00000377340	Transcript	missense_variant	1437	1405	469	E/Q	Gaa/Caa	.	.	.	-1	CRNKL1	HGNC	15762	protein_coding	YES	CCDS33446.1	ENSP00000366557	CRNL1_HUMAN	.	UPI00004A39A7	.	deleterious(0.01)	probably_damaging(0.979)	8/15	.	Superfamily_domains:SSF48452,hmmpanther:PTHR11246,hmmpanther:PTHR11246:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATCTTCAATAC	.	5	ESCA
VSX1	0	.	GRCh37	20	25059403	25059403	+	Intron	SNP	G	G	A	rs373947722	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.627+62C>T	.	.	ENST00000376709	.	118	108	9	96	96	0	VSX1,missense_variant,p.Ser230Leu,ENST00000376707,;VSX1,intron_variant,,ENST00000429762,;VSX1,intron_variant,,ENST00000444511,;VSX1,intron_variant,,ENST00000424574,;VSX1,intron_variant,,ENST00000451258,;VSX1,intron_variant,,ENST00000376709,;VSX1,downstream_gene_variant,,ENST00000398332,;VSX1,intron_variant,,ENST00000409958,;VSX1,intron_variant,,ENST00000409285,;VSX1,upstream_gene_variant,,ENST00000557285,;	A	ENSG00000100987	ENST00000376709	Transcript	intron_variant	.	.	.	.	.	rs373947722	.	.	-1	VSX1	HGNC	12723	protein_coding	YES	CCDS13168.1	ENSP00000365899	VSX1_HUMAN	.	UPI0000138E43	.	.	.	.	3/4	.	.	.	.	.	.	.	.	C:0	C:0.0002	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUSE|VARSCANS	TCACTGAATGT	byFrequency|byCluster	2	ESCA
TMC2	0	.	GRCh37	20	2597825	2597825	+	Missense_Mutation	SNP	A	A	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2048A>G	p.Glu683Gly	p.E683G	ENST00000358864	16/20	38	20	18	49	49	0	TMC2,missense_variant,p.Glu683Gly,ENST00000358864,;TMC2,non_coding_transcript_exon_variant,,ENST00000496948,;	G	ENSG00000149488	ENST00000358864	Transcript	missense_variant	2063	2048	683	E/G	gAa/gGa	COSM4134377	.	.	1	TMC2	HGNC	16527	protein_coding	YES	CCDS13029.2	ENSP00000351732	TMC2_HUMAN	.	UPI0000246C98	.	deleterious(0)	probably_damaging(0.938)	16/20	.	Pfam_domain:PF07810,hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCATGAACGCG	.	5	ESCA
TPX2	0	.	GRCh37	20	30358170	30358170	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381G>A	p.%3D	p.Q127Q	ENST00000300403	6/18	147	122	25	109	109	0	TPX2,synonymous_variant,p.%3D,ENST00000300403,;TPX2,synonymous_variant,p.%3D,ENST00000340513,;	A	ENSG00000088325	ENST00000300403	Transcript	synonymous_variant	909	381	127	Q	caG/caA	.	.	.	1	TPX2	HGNC	1249	protein_coding	YES	CCDS13190.1	ENSP00000300403	TPX2_HUMAN	Q96FC3_HUMAN,Q643R0_HUMAN,B3KM90_HUMAN	UPI00000015BB	.	.	.	6/18	.	hmmpanther:PTHR14326,hmmpanther:PTHR14326:SF9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTCAGAAGGA	.	5	ESCA
C20orf112	0	.	GRCh37	20	31115602	31115602	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154A>G	p.Lys52Glu	p.K52E	ENST00000201961	2/6	40	30	9	37	37	0	C20orf112,missense_variant,p.Lys52Glu,ENST00000201961,;C20orf112,missense_variant,p.Lys11Glu,ENST00000375678,;C20orf112,non_coding_transcript_exon_variant,,ENST00000470428,;	C	ENSG00000197183	ENST00000201961	Transcript	missense_variant	374	154	52	K/E	Aaa/Gaa	.	.	.	-1	C20orf112	HGNC	16106	protein_coding	.	.	ENSP00000201961	.	Q5W149_HUMAN	UPI000045880E	.	deleterious(0.01)	possibly_damaging(0.662)	2/6	.	hmmpanther:PTHR12449:SF16,hmmpanther:PTHR12449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCTTTGCCTG	.	5	ESCA
ITPA	0	.	GRCh37	20	3190102	3190102	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-96G>A	.	.	ENST00000380113	1/8	46	35	10	19	19	0	ITPA,5_prime_UTR_variant,,ENST00000380113,;ITPA,upstream_gene_variant,,ENST00000399838,;DDRGK1,upstream_gene_variant,,ENST00000354488,;ITPA,upstream_gene_variant,,ENST00000455664,;DDRGK1,upstream_gene_variant,,ENST00000380201,;ITPA,intron_variant,,ENST00000460676,;ITPA,intron_variant,,ENST00000483354,;ITPA,upstream_gene_variant,,ENST00000490838,;ITPA,upstream_gene_variant,,ENST00000460550,;ITPA,upstream_gene_variant,,ENST00000609835,;	A	ENSG00000125877	ENST00000380113	Transcript	5_prime_UTR_variant	97	.	.	.	.	.	.	.	1	ITPA	HGNC	6176	protein_coding	YES	CCDS13051.1	ENSP00000369456	ITPA_HUMAN	Q5NT82_HUMAN	UPI0000072BC2	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCGGAAACT	.	5	ESCA
RPN2	0	.	GRCh37	20	35869750	35869750	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*32G>A	.	.	ENST00000237530	17/17	38	27	10	35	35	0	RPN2,missense_variant,p.Glu125Lys,ENST00000456400,;RPN2,3_prime_UTR_variant,,ENST00000237530,;RPN2,3_prime_UTR_variant,,ENST00000437329,;RPN2,3_prime_UTR_variant,,ENST00000373622,;RPN2,non_coding_transcript_exon_variant,,ENST00000470352,;	A	ENSG00000118705	ENST00000237530	Transcript	3_prime_UTR_variant	2239	.	.	.	.	.	.	.	1	RPN2	HGNC	10382	protein_coding	YES	CCDS13291.1	ENSP00000237530	RPN2_HUMAN	.	UPI0000000C52	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AAACTGAATGT	.	5	ESCA
LPIN3	0	.	GRCh37	20	39987112	39987112	+	Missense_Mutation	SNP	G	G	C	rs146490125	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2341G>C	p.Glu781Gln	p.E781Q	ENST00000373257	19/20	15	11	4	11	11	0	LPIN3,missense_variant,p.Glu781Gln,ENST00000373257,;EMILIN3,downstream_gene_variant,,ENST00000332312,;LPIN3,downstream_gene_variant,,ENST00000445975,;LPIN3,non_coding_transcript_exon_variant,,ENST00000491528,;LPIN3,non_coding_transcript_exon_variant,,ENST00000496565,;	C	ENSG00000132793	ENST00000373257	Transcript	missense_variant	2432	2341	781	E/Q	Gag/Cag	rs146490125	.	.	1	LPIN3	HGNC	14451	protein_coding	YES	CCDS33469.1	ENSP00000362354	LPIN3_HUMAN	.	UPI0000470AE3	.	tolerated(0.29)	benign(0.035)	19/20	.	hmmpanther:PTHR12181:SF32,hmmpanther:PTHR12181,Gene3D:3.40.50.1000,Pfam_domain:PF08235,SMART_domains:SM00775,Superfamily_domains:SSF56784	.	.	.	.	.	.	.	C:0.0002	C:0.0006	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER	TGCCTGAGTCA	byFrequency|byCluster	2	ESCA
TBC1D20	0	.	GRCh37	20	418412	418412	+	3'UTR	SNP	T	T	C	rs553816000	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*818A>G	.	.	ENST00000354200	8/8	157	125	31	183	183	0	TBC1D20,3_prime_UTR_variant,,ENST00000354200,;TBC1D20,non_coding_transcript_exon_variant,,ENST00000494633,;TBC1D20,non_coding_transcript_exon_variant,,ENST00000461188,;TBC1D20,intron_variant,,ENST00000461304,;	C	ENSG00000125875	ENST00000354200	Transcript	3_prime_UTR_variant	2178	.	.	.	.	rs553816000	.	.	-1	TBC1D20	HGNC	16133	protein_coding	YES	CCDS13002.1	ENSP00000346139	TBC20_HUMAN	B9A6M1_HUMAN	UPI000006D549	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAACTATTTT	byCluster	5	ESCA
RBPJL	0	.	GRCh37	20	43942696	43942696	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.779G>C	p.Gly260Ala	p.G260A	ENST00000343694	8/12	62	56	6	56	56	0	RBPJL,missense_variant,p.Gly260Ala,ENST00000343694,;RBPJL,missense_variant,p.Gly260Ala,ENST00000372743,;RBPJL,missense_variant,p.Gly260Ala,ENST00000372741,;RBPJL,non_coding_transcript_exon_variant,,ENST00000464504,;	C	ENSG00000124232	ENST00000343694	Transcript	missense_variant	851	779	260	G/A	gGa/gCa	.	.	.	1	RBPJL	HGNC	13761	protein_coding	YES	CCDS13349.1	ENSP00000341243	RBPJL_HUMAN	.	UPI0000047297	.	tolerated(0.14)	benign(0.147)	8/12	.	hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2,Gene3D:2.80.10.50,Pfam_domain:PF09270,Superfamily_domains:0049692	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CCAAGGAGACT	.	3	ESCA
CSE1L	0	.	GRCh37	20	47704604	47704604	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1782C>T	p.%3D	p.L594L	ENST00000262982	17/25	71	61	10	56	56	0	CSE1L,synonymous_variant,p.%3D,ENST00000542325,;CSE1L,synonymous_variant,p.%3D,ENST00000396192,;CSE1L,synonymous_variant,p.%3D,ENST00000262982,;CSE1L,upstream_gene_variant,,ENST00000469700,;	T	ENSG00000124207	ENST00000262982	Transcript	synonymous_variant	1905	1782	594	L	ctC/ctT	.	.	.	1	CSE1L	HGNC	2431	protein_coding	YES	CCDS13412.1	ENSP00000262982	XPO2_HUMAN	.	UPI000013D377	.	.	.	17/25	.	hmmpanther:PTHR10997,hmmpanther:PTHR10997:SF8,Pfam_domain:PF03378,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACTCTCATCAC	.	5	ESCA
PCK1	0	.	GRCh37	20	56138676	56138676	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.854C>T	p.Pro285Leu	p.P285L	ENST00000319441	6/10	50	45	5	38	38	0	PCK1,missense_variant,p.Pro153Leu,ENST00000535860,;PCK1,missense_variant,p.Pro285Leu,ENST00000319441,;PCK1,intron_variant,,ENST00000543666,;PCK1,non_coding_transcript_exon_variant,,ENST00000467047,;PCK1,downstream_gene_variant,,ENST00000475833,;PCK1,downstream_gene_variant,,ENST00000498194,;PCK1,downstream_gene_variant,,ENST00000470051,;PCK1,upstream_gene_variant,,ENST00000485958,;	T	ENSG00000124253	ENST00000319441	Transcript	missense_variant	1018	854	285	P/L	cCc/cTc	.	.	.	1	PCK1	HGNC	8724	protein_coding	YES	CCDS13460.1	ENSP00000319814	PCKGC_HUMAN	.	UPI000013CB5A	.	deleterious(0)	probably_damaging(1)	6/10	.	HAMAP:MF_00452,hmmpanther:PTHR11561,hmmpanther:PTHR11561:SF1,PROSITE_patterns:PS00505,Gene3D:3.90.228.20,Pfam_domain:PF00821,PIRSF_domain:PIRSF001348,Superfamily_domains:SSF53795	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATTTCCCAGCG	.	4	ESCA
RAB22A	0	.	GRCh37	20	56941966	56941966	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*7207G>A	.	.	ENST00000244040	7/7	74	57	17	64	64	0	RAB22A,3_prime_UTR_variant,,ENST00000244040,;	A	ENSG00000124209	ENST00000244040	Transcript	3_prime_UTR_variant	8073	.	.	.	.	.	.	.	1	RAB22A	HGNC	9764	protein_coding	YES	CCDS33497.1	ENSP00000244040	RB22A_HUMAN	Q96IY7_HUMAN	UPI0000132F68	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTAGACATT	.	5	ESCA
SLCO4A1	0	.	GRCh37	20	61300307	61300307	+	Silent	SNP	C	C	T	rs201252224	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1902C>T	p.%3D	p.F634F	ENST00000217159	11/12	68	61	7	69	69	0	SLCO4A1,synonymous_variant,p.%3D,ENST00000370507,;SLCO4A1,synonymous_variant,p.%3D,ENST00000217159,;SLCO4A1,synonymous_variant,p.%3D,ENST00000451793,;RP11-93B14.5,upstream_gene_variant,,ENST00000433126,;RP11-93B14.5,upstream_gene_variant,,ENST00000411824,;RP11-93B14.5,upstream_gene_variant,,ENST00000451648,;SLCO4A1,non_coding_transcript_exon_variant,,ENST00000466961,;SLCO4A1,non_coding_transcript_exon_variant,,ENST00000497919,;SLCO4A1,non_coding_transcript_exon_variant,,ENST00000495889,;SLCO4A1,non_coding_transcript_exon_variant,,ENST00000466818,;SLCO4A1,non_coding_transcript_exon_variant,,ENST00000470412,;SLCO4A1,3_prime_UTR_variant,,ENST00000497209,;	T	ENSG00000101187	ENST00000217159	Transcript	synonymous_variant	2107	1902	634	F	ttC/ttT	rs201252224,COSM3799742	.	.	1	SLCO4A1	HGNC	10953	protein_coding	YES	CCDS13501.1	ENSP00000217159	SO4A1_HUMAN	.	UPI00000557C6	.	.	.	11/12	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF66,hmmpanther:PTHR11388,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCCTTCGGCTG	byCluster	4	ESCA
CXADR	0	.	GRCh37	21	18938077	18938077	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*67C>G	.	.	ENST00000284878	7/7	44	41	3	31	31	0	CXADR,3_prime_UTR_variant,,ENST00000400166,;CXADR,3_prime_UTR_variant,,ENST00000284878,;CXADR,intron_variant,,ENST00000400169,;CXADR,downstream_gene_variant,,ENST00000306618,;CXADR,downstream_gene_variant,,ENST00000356275,;CXADR,downstream_gene_variant,,ENST00000400165,;	G	ENSG00000154639	ENST00000284878	Transcript	3_prime_UTR_variant	1913	.	.	.	.	.	.	.	1	CXADR	HGNC	2559	protein_coding	YES	CCDS33519.1	ENSP00000284878	CXAR_HUMAN	.	UPI000004F892	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTATTCTGGTC	.	2	ESCA
DNAJC28	0	.	GRCh37	21	34860764	34860764	+	Missense_Mutation	SNP	C	C	G	rs762955572	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.937G>C	p.Asp313His	p.D313H	ENST00000314399	2/2	67	51	15	84	84	0	DNAJC28,missense_variant,p.Asp313His,ENST00000314399,;DNAJC28,missense_variant,p.Asp313His,ENST00000402202,;DNAJC28,missense_variant,p.Asp313His,ENST00000381947,;AP000302.58,upstream_gene_variant,,ENST00000450928,;	G	ENSG00000177692	ENST00000314399	Transcript	missense_variant	1376	937	313	D/H	Gat/Cat	rs762955572	.	.	-1	DNAJC28	HGNC	1297	protein_coding	YES	CCDS13626.1	ENSP00000320303	DJC28_HUMAN	.	UPI00001286AA	.	deleterious(0.02)	possibly_damaging(0.872)	2/2	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24016,hmmpanther:PTHR24016:SF10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATCATTAA	byFrequency	5	ESCA
SLC5A3	0	.	GRCh37	21	35468289	35468289	+	Missense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.792C>A	p.Phe264Leu	p.F264L	ENST00000608209	2/2	53	42	10	53	53	0	SLC5A3,missense_variant,p.Phe264Leu,ENST00000608209,;SLC5A3,missense_variant,p.Phe264Leu,ENST00000381151,;MRPS6,intron_variant,,ENST00000399312,;MRPS6,intron_variant,,ENST00000477091,;MRPS6,intron_variant,,ENST00000488492,;AP000320.7,intron_variant,,ENST00000362077,;	A	ENSG00000272962	ENST00000608209	Transcript	missense_variant	1304	792	264	F/L	ttC/ttA	.	.	.	1	SLC5A3	Uniprot_gn	11038	protein_coding	YES	CCDS33549.1	ENSP00000477068	.	.	UPI00001359F3	.	tolerated(1)	benign(0.326)	2/2	.	Transmembrane_helices:TMhelix,PROSITE_profiles:PS50283,hmmpanther:PTHR11819:SF123,hmmpanther:PTHR11819,TIGRFAM_domain:TIGR00813,Pfam_domain:PF00474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATTCATTCT	.	5	ESCA
COL18A1	0	.	GRCh37	21	46932395	46932395	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*83C>G	.	.	ENST00000355480	41/41	62	57	5	82	82	0	COL18A1,3_prime_UTR_variant,,ENST00000359759,;COL18A1,3_prime_UTR_variant,,ENST00000355480,;COL18A1,3_prime_UTR_variant,,ENST00000342220,;COL18A1,3_prime_UTR_variant,,ENST00000400337,;SLC19A1,intron_variant,,ENST00000567670,;SLC19A1,intron_variant,,ENST00000417954,;COL18A1,downstream_gene_variant,,ENST00000423214,;SLC19A1,downstream_gene_variant,,ENST00000311124,;SLC19A1,downstream_gene_variant,,ENST00000380010,;SLC19A1,downstream_gene_variant,,ENST00000485649,;SLC19A1,non_coding_transcript_exon_variant,,ENST00000468508,;SLC19A1,downstream_gene_variant,,ENST00000460174,;COL18A1,non_coding_transcript_exon_variant,,ENST00000473212,;	G	ENSG00000182871	ENST00000355480	Transcript	3_prime_UTR_variant	4685	.	.	.	.	.	.	.	1	COL18A1	HGNC	2195	protein_coding	YES	CCDS42972.1	ENSP00000347665	COIA1_HUMAN	D3DSM5_HUMAN	UPI000016A19D	.	.	.	41/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGCCCCTGGC	.	2	ESCA
TPTEP1	0	.	GRCh37	22	17119509	17119509	+	RNA	SNP	G	G	A	rs11089287	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.321G>A	.	.	ENST00000426585	4/5	151	112	38	164	164	0	TPTEP1,non_coding_transcript_exon_variant,,ENST00000383140,;TPTEP1,non_coding_transcript_exon_variant,,ENST00000588424,;TPTEP1,non_coding_transcript_exon_variant,,ENST00000426585,;TPTEP1,non_coding_transcript_exon_variant,,ENST00000585784,;TPTEP1,non_coding_transcript_exon_variant,,ENST00000400593,;TPTEP1,non_coding_transcript_exon_variant,,ENST00000558085,;	A	ENSG00000100181	ENST00000426585	Transcript	non_coding_transcript_exon_variant	321	.	.	.	.	rs11089287	.	.	1	TPTEP1	HGNC	43648	lincRNA	YES	.	.	.	.	.	.	.	.	4/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCTCGTCCTT	byCluster|by2Hit2Allele|byHapMap	5	ESCA
GAB4	0	.	GRCh37	22	17488987	17488987	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.18C>T	p.%3D	p.P6P	ENST00000400588	1/10	29	17	11	35	35	0	GAB4,synonymous_variant,p.%3D,ENST00000400588,;GAB4,upstream_gene_variant,,ENST00000523144,;GAB4,upstream_gene_variant,,ENST00000465611,;AC006548.26,upstream_gene_variant,,ENST00000605217,;	A	ENSG00000215568	ENST00000400588	Transcript	synonymous_variant	126	18	6	P	ccC/ccT	.	.	.	-1	GAB4	HGNC	18325	protein_coding	YES	CCDS42976.1	ENSP00000383431	GAB4_HUMAN	.	UPI00002326B5	.	.	.	1/10	.	hmmpanther:PTHR12156:SF20,hmmpanther:PTHR12156,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGAGGGGGA	.	5	ESCA
MN1	0	.	GRCh37	22	28193043	28193043	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3489G>C	p.Gln1163His	p.Q1163H	ENST00000302326	1/2	16	12	4	19	19	0	MN1,missense_variant,p.Gln1163His,ENST00000302326,;MN1,upstream_gene_variant,,ENST00000424656,;	G	ENSG00000169184	ENST00000302326	Transcript	missense_variant	4444	3489	1163	Q/H	caG/caC	.	.	.	-1	MN1	HGNC	7180	protein_coding	YES	CCDS42998.1	ENSP00000304956	MN1_HUMAN	A5HML1_HUMAN	UPI0000207445	.	.	probably_damaging(0.999)	1/2	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15821	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTCTGTAG	.	5	ESCA
SF3A1	0	.	GRCh37	22	30730595	30730595	+	Silent	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2370G>C	p.%3D	p.G790G	ENST00000215793	16/16	33	25	8	44	44	0	SF3A1,synonymous_variant,p.%3D,ENST00000215793,;SF3A1,synonymous_variant,p.%3D,ENST00000439242,;SF3A1,downstream_gene_variant,,ENST00000444440,;SF3A1,downstream_gene_variant,,ENST00000411423,;SF3A1,downstream_gene_variant,,ENST00000498259,;SF3A1,downstream_gene_variant,,ENST00000485618,;	G	ENSG00000099995	ENST00000215793	Transcript	synonymous_variant	2525	2370	790	G	ggG/ggC	COSM725960	.	.	-1	SF3A1	HGNC	10765	protein_coding	YES	CCDS13875.1	ENSP00000215793	SF3A1_HUMAN	.	UPI0000000C88	.	.	.	16/16	.	PROSITE_profiles:PS50053,hmmpanther:PTHR15316,Gene3D:3.10.20.90,Superfamily_domains:SSF54236	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCCCGCC	.	5	ESCA
RNF185	0	.	GRCh37	22	31602325	31602325	+	3'UTR	SNP	G	G	C	rs763456233	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1753G>C	.	.	ENST00000326132	7/7	69	39	30	86	86	0	RNF185,3_prime_UTR_variant,,ENST00000266252,;RNF185,3_prime_UTR_variant,,ENST00000326132,;RNF185,downstream_gene_variant,,ENST00000426256,;RNF185-AS1,upstream_gene_variant,,ENST00000526089,;RNF185,3_prime_UTR_variant,,ENST00000518626,;RNF185,non_coding_transcript_exon_variant,,ENST00000471384,;RNF185,downstream_gene_variant,,ENST00000494514,;	C	ENSG00000138942	ENST00000326132	Transcript	3_prime_UTR_variant	2491	.	.	.	.	rs763456233	.	.	1	RNF185	HGNC	26783	protein_coding	YES	CCDS13890.1	ENSP00000320508	RN185_HUMAN	.	UPI0000036022	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCCTGATAGA	.	5	ESCA
TOB2	0	.	GRCh37	22	41831698	41831698	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*617T>C	.	.	ENST00000327492	2/2	48	44	3	43	43	0	TOB2,3_prime_UTR_variant,,ENST00000327492,;TOB2,downstream_gene_variant,,ENST00000434408,;CTA-223H9.9,downstream_gene_variant,,ENST00000609612,;	G	ENSG00000183864	ENST00000327492	Transcript	3_prime_UTR_variant	2359	.	.	.	.	.	.	.	-1	TOB2	HGNC	11980	protein_coding	YES	CCDS14015.1	ENSP00000331305	TOB2_HUMAN	B0QXZ4_HUMAN	UPI00001370FC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGGGAGGGTG	.	2	ESCA
POLDIP3	0	.	GRCh37	22	42992255	42992255	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.750G>C	p.Leu250Phe	p.L250F	ENST00000252115	5/9	42	24	18	44	44	0	POLDIP3,missense_variant,p.Leu94Phe,ENST00000451060,;POLDIP3,missense_variant,p.Leu250Phe,ENST00000252115,;POLDIP3,missense_variant,p.Leu221Phe,ENST00000348657,;POLDIP3,intron_variant,,ENST00000339677,;POLDIP3,non_coding_transcript_exon_variant,,ENST00000491021,;POLDIP3,missense_variant,p.Leu250Phe,ENST00000445215,;POLDIP3,downstream_gene_variant,,ENST00000454057,;	G	ENSG00000100227	ENST00000252115	Transcript	missense_variant	855	750	250	L/F	ttG/ttC	.	.	.	-1	POLDIP3	HGNC	23782	protein_coding	YES	CCDS14038.1	ENSP00000252115	PDIP3_HUMAN	Q96DI9_HUMAN	UPI000006EEA7	.	deleterious(0.04)	possibly_damaging(0.842)	5/9	.	hmmpanther:PTHR19965,hmmpanther:PTHR19965:SF8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGTCAAGGC	.	5	ESCA
POLR1B	0	.	GRCh37	2	113331138	113331138	+	Splice_Site	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2272-1G>A	.	p.X758_splice	ENST00000263331	.	54	42	12	38	38	0	POLR1B,splice_acceptor_variant,,ENST00000541869,;POLR1B,splice_acceptor_variant,,ENST00000537335,;POLR1B,splice_acceptor_variant,,ENST00000263331,;POLR1B,splice_acceptor_variant,,ENST00000458012,;POLR1B,splice_acceptor_variant,,ENST00000417433,;POLR1B,splice_acceptor_variant,,ENST00000409894,;POLR1B,splice_acceptor_variant,,ENST00000448770,;POLR1B,splice_acceptor_variant,,ENST00000333990,;POLR1B,downstream_gene_variant,,ENST00000484574,;	A	ENSG00000125630	ENST00000263331	Transcript	splice_acceptor_variant	.	.	.	.	.	.	.	.	1	POLR1B	HGNC	20454	protein_coding	YES	CCDS2097.1	ENSP00000263331	RPA2_HUMAN	Q9BSR4_HUMAN,Q6DKI9_HUMAN,F5H643_HUMAN,C9JS83_HUMAN,C9JJG2_HUMAN,B7Z1W6_HUMAN	UPI00001B6B03	.	.	.	.	13/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCACAGATTGT	.	5	ESCA
DPP10	0	.	GRCh37	2	116601830	116601830	+	3'Flank	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000393147	.	126	100	25	95	95	0	DPP10,3_prime_UTR_variant,,ENST00000410059,;DPP10,downstream_gene_variant,,ENST00000393147,;DPP10,downstream_gene_variant,,ENST00000409163,;DPP10,downstream_gene_variant,,ENST00000310323,;	C	ENSG00000175497	ENST00000393147	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	1909	1	DPP10	HGNC	20823	protein_coding	YES	CCDS54388.1	ENSP00000376855	DPP10_HUMAN	J3KQK8_HUMAN,C9J4M8_HUMAN	UPI00015E0A22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATTTGAACCA	.	5	ESCA
LRP2	0	.	GRCh37	2	169984871	169984871	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*302G>C	.	.	ENST00000263816	79/79	33	22	11	34	34	0	LRP2,3_prime_UTR_variant,,ENST00000263816,;LRP2,downstream_gene_variant,,ENST00000491228,;	G	ENSG00000081479	ENST00000263816	Transcript	3_prime_UTR_variant	14556	.	.	.	.	.	.	.	-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	LRP2_HUMAN	Q9NP34_HUMAN,Q53TL0_HUMAN,Q4ZG84_HUMAN	UPI0000141BA5	.	.	.	79/79	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACATCTTTAT	.	5	ESCA
DCAF17	0	.	GRCh37	2	172336638	172336638	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1357G>C	p.Asp453His	p.D453H	ENST00000375255	13/14	55	44	11	69	69	0	DCAF17,missense_variant,p.Asp155His,ENST00000431110,;DCAF17,missense_variant,p.Asp453His,ENST00000375255,;DCAF17,missense_variant,p.Asp386His,ENST00000539783,;DCAF17,missense_variant,p.Asp204His,ENST00000339506,;DCAF17,non_coding_transcript_exon_variant,,ENST00000468592,;DCAF17,non_coding_transcript_exon_variant,,ENST00000498486,;	C	ENSG00000115827	ENST00000375255	Transcript	missense_variant	1684	1357	453	D/H	Gat/Cat	.	.	.	1	DCAF17	HGNC	25784	protein_coding	YES	CCDS2243.2	ENSP00000364404	DCA17_HUMAN	.	UPI00004C429A	.	deleterious(0.02)	probably_damaging(0.989)	13/14	.	hmmpanther:PTHR14815,hmmpanther:PTHR14815:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTGGATTTC	.	5	ESCA
HOXD12	0	.	GRCh37	2	176965274	176965274	+	Missense_Mutation	SNP	G	G	C	rs748039138	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.599G>C	p.Gly200Ala	p.G200A	ENST00000406506	2/2	82	58	24	61	61	0	HOXD12,missense_variant,p.Gly200Ala,ENST00000406506,;HOXD12,synonymous_variant,p.%3D,ENST00000404162,;HOXD13,downstream_gene_variant,,ENST00000392539,;HOXD11,upstream_gene_variant,,ENST00000498438,;	C	ENSG00000170178	ENST00000406506	Transcript	missense_variant	671	599	200	G/A	gGg/gCg	rs748039138	.	.	1	HOXD12	HGNC	5135	protein_coding	YES	CCDS46456.1	ENSP00000385586	HXD12_HUMAN	.	UPI0000EE2EA3	.	tolerated(1)	benign(0.162)	2/2	.	Superfamily_domains:SSF46689,Gene3D:1.10.10.60,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF40,PROSITE_profiles:PS50071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCGGGGAGGG	.	5	ESCA
TTC30A	0	.	GRCh37	2	178482187	178482187	+	Missense_Mutation	SNP	C	C	T	rs770640849	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1243G>A	p.Glu415Lys	p.E415K	ENST00000355689	1/1	60	54	6	45	45	0	TTC30A,missense_variant,p.Glu415Lys,ENST00000355689,;AC073834.3,non_coding_transcript_exon_variant,,ENST00000357045,;	T	ENSG00000197557	ENST00000355689	Transcript	missense_variant	1508	1243	415	E/K	Gaa/Aaa	rs770640849	.	.	-1	TTC30A	HGNC	25853	protein_coding	YES	CCDS2276.1	ENSP00000347915	TT30A_HUMAN	.	UPI0000209161	.	tolerated(0.15)	benign(0.279)	1/1	.	Superfamily_domains:SSF48452,hmmpanther:PTHR20931,hmmpanther:PTHR20931:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	ATATTCATTCA	.	4	ESCA
DFNB59	0	.	GRCh37	2	179319173	179319173	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.326C>G	p.Ser109Cys	p.S109C	ENST00000409117	3/7	48	35	13	56	56	0	DFNB59,missense_variant,p.Ser57Cys,ENST00000442710,;DFNB59,missense_variant,p.Ser109Cys,ENST00000375129,;DFNB59,missense_variant,p.Ser109Cys,ENST00000409117,;PRKRA,upstream_gene_variant,,ENST00000438687,;PRKRA,upstream_gene_variant,,ENST00000432031,;PRKRA,upstream_gene_variant,,ENST00000325748,;PRKRA,upstream_gene_variant,,ENST00000487082,;PRKRA,upstream_gene_variant,,ENST00000457633,;PRKRA,upstream_gene_variant,,ENST00000470200,;PRKRA,upstream_gene_variant,,ENST00000460433,;DFNB59,upstream_gene_variant,,ENST00000605419,;DFNB59,non_coding_transcript_exon_variant,,ENST00000437056,;PRKRA,upstream_gene_variant,,ENST00000424699,;PRKRA,upstream_gene_variant,,ENST00000466165,;PRKRA,upstream_gene_variant,,ENST00000463882,;DFNB59,upstream_gene_variant,,ENST00000444615,;PRKRA,upstream_gene_variant,,ENST00000448279,;AC009948.7,upstream_gene_variant,,ENST00000437039,;	G	ENSG00000204311	ENST00000409117	Transcript	missense_variant	682	326	109	S/C	tCc/tGc	.	.	.	1	DFNB59	HGNC	29502	protein_coding	YES	CCDS42787.1	ENSP00000386647	PJVK_HUMAN	A0PK15_HUMAN	UPI0000DAD718	.	tolerated(0.19)	benign(0.023)	3/7	.	hmmpanther:PTHR16399:SF10,hmmpanther:PTHR16399,Pfam_domain:PF04598	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGATTCCATTG	.	5	ESCA
CWC22	0	.	GRCh37	2	180846701	180846701	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.230G>C	p.Arg77Thr	p.R77T	ENST00000410053	5/20	24	20	4	20	20	0	CWC22,missense_variant,p.Arg77Thr,ENST00000404136,;CWC22,missense_variant,p.Arg77Thr,ENST00000410053,;CWC22,missense_variant,p.Arg77Thr,ENST00000295749,;	G	ENSG00000163510	ENST00000410053	Transcript	missense_variant	530	230	77	R/T	aGa/aCa	.	.	.	-1	CWC22	HGNC	29322	protein_coding	YES	CCDS46465.1	ENSP00000387006	CWC22_HUMAN	B7WP74_HUMAN	UPI00001C1DAE	.	deleterious(0.03)	benign(0.005)	5/20	.	Low_complexity_(Seg):seg,hmmpanther:PTHR18034:SF3,hmmpanther:PTHR18034	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTCTCTGCGT	.	2	ESCA
UBE2E3	0	.	GRCh37	2	181846835	181846835	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.66G>A	p.%3D	p.A22A	ENST00000410062	2/6	37	21	15	46	46	0	UBE2E3,synonymous_variant,p.%3D,ENST00000602710,;UBE2E3,synonymous_variant,p.%3D,ENST00000392415,;UBE2E3,synonymous_variant,p.%3D,ENST00000602303,;UBE2E3,synonymous_variant,p.%3D,ENST00000410062,;UBE2E3,synonymous_variant,p.%3D,ENST00000602959,;UBE2E3,synonymous_variant,p.%3D,ENST00000602632,;UBE2E3,synonymous_variant,p.%3D,ENST00000602475,;UBE2E3,synonymous_variant,p.%3D,ENST00000602499,;UBE2E3,synonymous_variant,p.%3D,ENST00000602479,;UBE2E3,synonymous_variant,p.%3D,ENST00000602291,;AC104076.3,upstream_gene_variant,,ENST00000428080,;UBE2E3,non_coding_transcript_exon_variant,,ENST00000602762,;UBE2E3,upstream_gene_variant,,ENST00000602888,;	A	ENSG00000170035	ENST00000410062	Transcript	synonymous_variant	459	66	22	A	gcG/gcA	COSM81875	.	.	1	UBE2E3	HGNC	12479	protein_coding	YES	CCDS2282.1	ENSP00000386788	UB2E3_HUMAN	R4GND1_HUMAN,R4GN77_HUMAN	UPI00000040F8	.	.	.	2/6	.	Low_complexity_(Seg):seg,hmmpanther:PTHR24068:SF25,hmmpanther:PTHR24068	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATGCGGACCA	.	5	ESCA
PGAP1	0	.	GRCh37	2	197777708	197777708	+	Silent	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.547T>C	p.%3D	p.L183L	ENST00000354764	4/27	53	35	17	43	43	0	PGAP1,synonymous_variant,p.%3D,ENST00000409475,;PGAP1,synonymous_variant,p.%3D,ENST00000409188,;PGAP1,synonymous_variant,p.%3D,ENST00000354764,;PGAP1,intron_variant,,ENST00000374738,;PGAP1,non_coding_transcript_exon_variant,,ENST00000485830,;PGAP1,3_prime_UTR_variant,,ENST00000423035,;PGAP1,intron_variant,,ENST00000470179,;	G	ENSG00000197121	ENST00000354764	Transcript	synonymous_variant	662	547	183	L	Ttg/Ctg	.	.	.	-1	PGAP1	HGNC	25712	protein_coding	YES	CCDS2318.1	ENSP00000346809	PGAP1_HUMAN	.	UPI000035154F	.	.	.	4/27	.	hmmpanther:PTHR15495,hmmpanther:PTHR15495:SF15,Pfam_domain:PF07819,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGCAATGCTC	.	5	ESCA
ADAM23	0	.	GRCh37	2	207346014	207346014	+	Missense_Mutation	SNP	T	T	C	rs111649087	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.491T>C	p.Leu164Pro	p.L164P	ENST00000264377	3/26	49	32	16	41	41	0	ADAM23,missense_variant,p.Leu164Pro,ENST00000374415,;ADAM23,missense_variant,p.Leu164Pro,ENST00000374416,;ADAM23,missense_variant,p.Leu164Pro,ENST00000264377,;	C	ENSG00000114948	ENST00000264377	Transcript	missense_variant	819	491	164	L/P	cTt/cCt	rs111649087	.	.	1	ADAM23	HGNC	202	protein_coding	YES	CCDS2369.1	ENSP00000264377	ADA23_HUMAN	Q53TK5_HUMAN,Q53TC0_HUMAN,Q53RX4_HUMAN	UPI0000044543	.	deleterious(0.02)	probably_damaging(0.974)	3/26	.	Pfam_domain:PF01562,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTCTTGACC	.	5	ESCA
UNC80	0	.	GRCh37	2	210737501	210737501	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3653G>C	p.Arg1218Thr	p.R1218T	ENST00000439458	23/64	33	23	9	29	29	0	UNC80,missense_variant,p.Arg1218Thr,ENST00000439458,;UNC80,missense_variant,p.Arg1213Thr,ENST00000272845,;UNC80,non_coding_transcript_exon_variant,,ENST00000477301,;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,;	C	ENSG00000144406	ENST00000439458	Transcript	missense_variant	3733	3653	1218	R/T	aGa/aCa	.	.	.	1	UNC80	HGNC	26582	protein_coding	YES	CCDS46504.1	ENSP00000391088	UNC80_HUMAN	.	UPI00017E10C9	.	.	probably_damaging(0.974)	23/64	.	hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCAGAGCAG	.	5	ESCA
STK36	0	.	GRCh37	2	219557016	219557016	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1915G>T	p.Gly639Ter	p.G639*	ENST00000295709	15/27	15	6	9	19	19	0	STK36,stop_gained,p.Gly639Ter,ENST00000392105,;STK36,stop_gained,p.Gly639Ter,ENST00000440309,;STK36,stop_gained,p.Gly639Ter,ENST00000295709,;STK36,stop_gained,p.Gly639Ter,ENST00000392106,;STK36,non_coding_transcript_exon_variant,,ENST00000480709,;STK36,downstream_gene_variant,,ENST00000470568,;STK36,upstream_gene_variant,,ENST00000419433,;STK36,upstream_gene_variant,,ENST00000486644,;STK36,downstream_gene_variant,,ENST00000414413,;STK36,upstream_gene_variant,,ENST00000473681,;STK36,upstream_gene_variant,,ENST00000492486,;STK36,downstream_gene_variant,,ENST00000422778,;STK36,upstream_gene_variant,,ENST00000462031,;	T	ENSG00000163482	ENST00000295709	Transcript	stop_gained	2194	1915	639	G/*	Gga/Tga	.	.	.	1	STK36	HGNC	17209	protein_coding	YES	CCDS2421.1	ENSP00000295709	STK36_HUMAN	C9JDA4_HUMAN,C9J1B8_HUMAN	UPI00000342FC	.	.	.	15/27	.	hmmpanther:PTHR22983:SF6,hmmpanther:PTHR22983,Gene3D:1.25.10.10,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	CCCAAGGTAAC	.	3	ESCA
CCDC108	0	.	GRCh37	2	219870902	219870902	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4763C>T	p.Ala1588Val	p.A1588V	ENST00000341552	31/35	31	19	12	42	42	0	CCDC108,missense_variant,p.Ala1588Val,ENST00000453220,;CCDC108,missense_variant,p.Ala1588Val,ENST00000341552,;CCDC108,missense_variant,p.Ala1588Val,ENST00000441968,;MIR375,upstream_gene_variant,,ENST00000362103,;AC097468.4,intron_variant,,ENST00000441450,;	A	ENSG00000181378	ENST00000341552	Transcript	missense_variant	4847	4763	1588	A/V	gCc/gTc	.	.	.	-1	CCDC108	HGNC	25325	protein_coding	YES	CCDS2430.2	ENSP00000340776	CC108_HUMAN	C9JLP9_HUMAN,C9JIV0_HUMAN	UPI0000609097	.	tolerated(0.13)	benign(0.06)	31/35	.	hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGCTGGCAGGC	.	5	ESCA
INHA	0	.	GRCh37	2	220437184	220437184	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.88C>G	p.Leu30Val	p.L30V	ENST00000243786	1/2	70	35	35	82	82	0	INHA,missense_variant,p.Leu30Val,ENST00000243786,;OBSL1,upstream_gene_variant,,ENST00000603926,;OBSL1,upstream_gene_variant,,ENST00000289656,;OBSL1,upstream_gene_variant,,ENST00000373876,;OBSL1,upstream_gene_variant,,ENST00000265318,;OBSL1,upstream_gene_variant,,ENST00000404537,;OBSL1,upstream_gene_variant,,ENST00000373873,;INHA,intron_variant,,ENST00000489456,;OBSL1,upstream_gene_variant,,ENST00000465589,;OBSL1,upstream_gene_variant,,ENST00000491370,;OBSL1,upstream_gene_variant,,ENST00000465149,;	G	ENSG00000123999	ENST00000243786	Transcript	missense_variant	268	88	30	L/V	Ctg/Gtg	COSM3909668	.	.	1	INHA	HGNC	6065	protein_coding	YES	CCDS2444.1	ENSP00000243786	INHA_HUMAN	.	UPI000002C8C6	.	deleterious(0)	possibly_damaging(0.893)	1/2	.	hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF117,PIRSF_domain:PIRSF037328	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGTTCTGGCC	.	5	ESCA
STK11IP	0	.	GRCh37	2	220476466	220476466	+	Missense_Mutation	SNP	C	C	G	rs776907199	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2278C>G	p.Pro760Ala	p.P760A	ENST00000295641	18/25	16	10	6	12	12	0	STK11IP,missense_variant,p.Pro749Ala,ENST00000456909,;STK11IP,missense_variant,p.Pro760Ala,ENST00000295641,;STK11IP,upstream_gene_variant,,ENST00000447191,;STK11IP,downstream_gene_variant,,ENST00000483319,;STK11IP,upstream_gene_variant,,ENST00000494777,;STK11IP,downstream_gene_variant,,ENST00000475396,;STK11IP,downstream_gene_variant,,ENST00000473899,;STK11IP,downstream_gene_variant,,ENST00000466648,;STK11IP,upstream_gene_variant,,ENST00000495941,;STK11IP,upstream_gene_variant,,ENST00000413891,;	G	ENSG00000144589	ENST00000295641	Transcript	missense_variant	2321	2278	760	P/A	Cct/Gct	rs776907199	.	.	1	STK11IP	HGNC	19184	protein_coding	YES	CCDS46521.1	ENSP00000295641	S11IP_HUMAN	C9JQV3_HUMAN	UPI0001AE7798	.	tolerated(0.32)	benign(0.117)	18/25	.	hmmpanther:PTHR15454:SF16,hmmpanther:PTHR15454	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACCCTCCTGGC	byFrequency	5	ESCA
TRIP12	0	.	GRCh37	2	230744786	230744786	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10C>T	p.Arg4Trp	p.R4W	ENST00000283943	2/41	37	19	17	27	27	0	TRIP12,missense_variant,p.Arg4Trp,ENST00000389045,;TRIP12,missense_variant,p.Arg4Trp,ENST00000543084,;TRIP12,missense_variant,p.Arg4Trp,ENST00000343290,;TRIP12,missense_variant,p.Arg4Trp,ENST00000409677,;TRIP12,missense_variant,p.Arg4Trp,ENST00000389044,;TRIP12,missense_variant,p.Arg4Trp,ENST00000283943,;TRIP12,missense_variant,p.Arg4Trp,ENST00000428959,;TRIP12,missense_variant,p.Arg4Trp,ENST00000430954,;TRIP12,missense_variant,p.Arg4Trp,ENST00000435716,;TRIP12,non_coding_transcript_exon_variant,,ENST00000479037,;	A	ENSG00000153827	ENST00000283943	Transcript	missense_variant	189	10	4	R/W	Cgg/Tgg	.	.	.	-1	TRIP12	HGNC	12306	protein_coding	YES	CCDS33391.1	ENSP00000283943	TRIPC_HUMAN	Q57Z94_HUMAN,F8W9P3_HUMAN,C9JSX9_HUMAN,C9JLJ5_HUMAN	UPI000013739D	.	deleterious_low_confidence(0)	probably_damaging(0.973)	2/41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCCGGTTGG	.	5	ESCA
COL6A3	0	.	GRCh37	2	238261195	238261195	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6723G>C	p.%3D	p.L2241L	ENST00000295550	26/44	26	18	8	32	32	0	COL6A3,synonymous_variant,p.%3D,ENST00000346358,;COL6A3,synonymous_variant,p.%3D,ENST00000347401,;COL6A3,synonymous_variant,p.%3D,ENST00000472056,;COL6A3,synonymous_variant,p.%3D,ENST00000353578,;COL6A3,synonymous_variant,p.%3D,ENST00000409809,;COL6A3,synonymous_variant,p.%3D,ENST00000295550,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;COL6A3,downstream_gene_variant,,ENST00000493475,;	G	ENSG00000163359	ENST00000295550	Transcript	synonymous_variant	7176	6723	2241	L	ctG/ctC	.	.	.	-1	COL6A3	HGNC	2213	protein_coding	YES	CCDS33412.1	ENSP00000295550	CO6A3_HUMAN	Q8N4Z1_HUMAN,D9ZGF2_HUMAN	UPI0000456F39	.	.	.	26/44	.	hmmpanther:PTHR22992,hmmpanther:PTHR22992:SF83	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCTATCAGCCC	.	5	ESCA
DNMT3A	0	.	GRCh37	2	25497920	25497920	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.529G>C	p.Glu177Gln	p.E177Q	ENST00000264709	6/23	78	69	9	76	76	0	DNMT3A,missense_variant,p.Glu177Gln,ENST00000321117,;DNMT3A,missense_variant,p.Glu177Gln,ENST00000264709,;DNMT3A,missense_variant,p.Glu177Gln,ENST00000380756,;	G	ENSG00000119772	ENST00000264709	Transcript	missense_variant	867	529	177	E/Q	Gag/Cag	.	.	.	-1	DNMT3A	HGNC	2978	protein_coding	YES	CCDS33157.1	ENSP00000264709	DNM3A_HUMAN	Q8WVA9_HUMAN,Q6PJ37_HUMAN	UPI000000DA70	.	deleterious(0)	probably_damaging(0.968)	6/23	.	Low_complexity_(Seg):seg,hmmpanther:PTHR23068:SF10,hmmpanther:PTHR23068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGACTCCCAGC	.	4	ESCA
IFT172	0	.	GRCh37	2	27679461	27679461	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3288G>C	p.Lys1096Asn	p.K1096N	ENST00000260570	30/48	35	30	5	29	29	0	IFT172,missense_variant,p.Lys1096Asn,ENST00000260570,;IFT172,upstream_gene_variant,,ENST00000443889,;IFT172,non_coding_transcript_exon_variant,,ENST00000507184,;IFT172,upstream_gene_variant,,ENST00000450564,;IFT172,upstream_gene_variant,,ENST00000509128,;IFT172,upstream_gene_variant,,ENST00000475909,;IFT172,downstream_gene_variant,,ENST00000476693,;AC074117.13,downstream_gene_variant,,ENST00000417130,;	G	ENSG00000138002	ENST00000260570	Transcript	missense_variant	3392	3288	1096	K/N	aaG/aaC	.	.	.	-1	IFT172	HGNC	30391	protein_coding	YES	CCDS1755.1	ENSP00000260570	IF172_HUMAN	H7C161_HUMAN	UPI0000353ABB	.	deleterious(0.02)	benign(0.16)	30/48	.	hmmpanther:PTHR15722,hmmpanther:PTHR15722:SF2,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTCTTTGC	.	4	ESCA
IFT172	0	.	GRCh37	2	27683889	27683889	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2514C>T	p.%3D	p.F838F	ENST00000260570	23/48	48	33	15	45	45	0	IFT172,synonymous_variant,p.%3D,ENST00000260570,;IFT172,non_coding_transcript_exon_variant,,ENST00000507184,;IFT172,downstream_gene_variant,,ENST00000489492,;IFT172,upstream_gene_variant,,ENST00000476693,;	A	ENSG00000138002	ENST00000260570	Transcript	synonymous_variant	2618	2514	838	F	ttC/ttT	COSM1019706	.	.	-1	IFT172	HGNC	30391	protein_coding	YES	CCDS1755.1	ENSP00000260570	IF172_HUMAN	H7C161_HUMAN	UPI0000353ABB	.	.	.	23/48	.	hmmpanther:PTHR15722,hmmpanther:PTHR15722:SF2	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A837T|c.2509G>A|5	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTCATGAATGC	.	5	ESCA
HEATR5B	0	.	GRCh37	2	37230747	37230747	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4988G>C	p.Gly1663Ala	p.G1663A	ENST00000233099	31/36	94	69	24	56	56	0	HEATR5B,missense_variant,p.Gly1663Ala,ENST00000233099,;HEATR5B,missense_variant,p.Gly1663Ala,ENST00000354531,;HEATR5B,downstream_gene_variant,,ENST00000471051,;	G	ENSG00000008869	ENST00000233099	Transcript	missense_variant	5084	4988	1663	G/A	gGa/gCa	.	.	.	-1	HEATR5B	HGNC	29273	protein_coding	YES	CCDS33181.1	ENSP00000233099	HTR5B_HUMAN	.	UPI0000160DCD	.	tolerated(0.13)	benign(0.001)	31/36	.	hmmpanther:PTHR21663:SF2,hmmpanther:PTHR21663,Superfamily_domains:SSF48371	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAACTCCAGTA	.	5	ESCA
PLEKHH2	0	.	GRCh37	2	43924327	43924327	+	Missense_Mutation	SNP	T	T	G	rs746212226	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.520T>G	p.Ser174Ala	p.S174A	ENST00000282406	7/30	101	89	12	65	65	0	PLEKHH2,missense_variant,p.Ser174Ala,ENST00000282406,;PLEKHH2,3_prime_UTR_variant,,ENST00000491692,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405000,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405223,;PLEKHH2,downstream_gene_variant,,ENST00000460356,;	G	ENSG00000152527	ENST00000282406	Transcript	missense_variant	630	520	174	S/A	Tca/Gca	rs746212226	.	.	1	PLEKHH2	HGNC	30506	protein_coding	YES	CCDS1812.1	ENSP00000282406	PKHH2_HUMAN	.	UPI000016021B	.	tolerated(0.78)	benign(0.003)	7/30	.	Low_complexity_(Seg):seg,hmmpanther:PTHR22903,hmmpanther:PTHR22903:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGAAGTCATCC	.	4	ESCA
LRPPRC	0	.	GRCh37	2	44190798	44190798	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1417G>C	p.Asp473His	p.D473H	ENST00000260665	12/38	46	41	5	49	49	0	LRPPRC,missense_variant,p.Asp473His,ENST00000260665,;LRPPRC,missense_variant,p.Asp473His,ENST00000409659,;LRPPRC,missense_variant,p.Asp473His,ENST00000409946,;LRPPRC,non_coding_transcript_exon_variant,,ENST00000467058,;	G	ENSG00000138095	ENST00000260665	Transcript	missense_variant	1475	1417	473	D/H	Gat/Cat	.	.	.	-1	LRPPRC	HGNC	15714	protein_coding	YES	CCDS33189.1	ENSP00000260665	LPPRC_HUMAN	E5KNY5_HUMAN	UPI000019B4D2	.	deleterious(0)	probably_damaging(0.933)	12/38	.	hmmpanther:PTHR24015:SF0,hmmpanther:PTHR24015	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGATCAGGAT	.	4	ESCA
SLC3A1	0	.	GRCh37	2	44547731	44547731	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2011C>T	p.Arg671Ter	p.R671*	ENST00000260649	10/10	28	19	8	20	20	0	SLC3A1,stop_gained,p.Arg671Ter,ENST00000260649,;SLC3A1,stop_gained,p.Arg393Ter,ENST00000409380,;SLC3A1,stop_gained,p.Arg302Ter,ENST00000409740,;PREPL,3_prime_UTR_variant,,ENST00000409957,;PREPL,3_prime_UTR_variant,,ENST00000541738,;PREPL,3_prime_UTR_variant,,ENST00000409936,;PREPL,3_prime_UTR_variant,,ENST00000409411,;PREPL,3_prime_UTR_variant,,ENST00000444696,;PREPL,downstream_gene_variant,,ENST00000260648,;PREPL,downstream_gene_variant,,ENST00000410081,;PREPL,downstream_gene_variant,,ENST00000378511,;PREPL,downstream_gene_variant,,ENST00000378520,;SLC3A1,downstream_gene_variant,,ENST00000409387,;PREPL,downstream_gene_variant,,ENST00000420756,;PREPL,downstream_gene_variant,,ENST00000409272,;PREPL,3_prime_UTR_variant,,ENST00000426481,;PREPL,3_prime_UTR_variant,,ENST00000425263,;	T	ENSG00000138079	ENST00000260649	Transcript	stop_gained	2087	2011	671	R/*	Cga/Tga	.	.	.	1	SLC3A1	HGNC	11025	protein_coding	YES	CCDS1819.1	ENSP00000260649	SLC31_HUMAN	E7ENC4_HUMAN	UPI000013D0F2	.	.	.	10/10	.	hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF73	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCAATCGAGCA	.	5	ESCA
PREPL	0	.	GRCh37	2	44586684	44586684	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.171G>A	p.%3D	p.K57K	ENST00000409936	2/15	76	63	12	89	89	0	PREPL,synonymous_variant,p.%3D,ENST00000260648,;PREPL,synonymous_variant,p.%3D,ENST00000410081,;PREPL,synonymous_variant,p.%3D,ENST00000378511,;PREPL,synonymous_variant,p.%3D,ENST00000378520,;PREPL,synonymous_variant,p.%3D,ENST00000409936,;PREPL,synonymous_variant,p.%3D,ENST00000409272,;PREPL,synonymous_variant,p.%3D,ENST00000438314,;PREPL,intron_variant,,ENST00000409957,;PREPL,intron_variant,,ENST00000541738,;PREPL,intron_variant,,ENST00000409411,;CAMKMT,upstream_gene_variant,,ENST00000407131,;CAMKMT,upstream_gene_variant,,ENST00000378494,;CAMKMT,upstream_gene_variant,,ENST00000403853,;CAMKMT,upstream_gene_variant,,ENST00000402247,;PREPL,intron_variant,,ENST00000477410,;PREPL,intron_variant,,ENST00000540817,;PREPL,synonymous_variant,p.%3D,ENST00000426481,;PREPL,synonymous_variant,p.%3D,ENST00000425263,;CAMKMT,upstream_gene_variant,,ENST00000454433,;	T	ENSG00000138078	ENST00000409936	Transcript	synonymous_variant	609	171	57	K	aaG/aaA	.	.	.	-1	PREPL	HGNC	30228	protein_coding	YES	CCDS33190.1	ENSP00000386543	PPCEL_HUMAN	C9JMT4_HUMAN	UPI0000208358	.	.	.	2/15	.	hmmpanther:PTHR11757,hmmpanther:PTHR11757:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GATATCTTGGG	.	5	ESCA
SOX11	0	.	GRCh37	2	5833136	5833136	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.283A>C	p.Lys95Gln	p.K95Q	ENST00000322002	1/1	31	24	6	47	47	0	SOX11,missense_variant,p.Lys95Gln,ENST00000322002,;AC010729.1,upstream_gene_variant,,ENST00000455579,;AC108025.2,upstream_gene_variant,,ENST00000453678,;AC107057.2,upstream_gene_variant,,ENST00000458264,;AC108025.2,upstream_gene_variant,,ENST00000420221,;	C	ENSG00000176887	ENST00000322002	Transcript	missense_variant	338	283	95	K/Q	Aag/Cag	.	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	deleterious(0)	probably_damaging(0.998)	1/1	.	PROSITE_profiles:PS50118,hmmpanther:PTHR10270:SF113,hmmpanther:PTHR10270,Pfam_domain:PF00505,Gene3D:1.10.30.10,SMART_domains:SM00398,PIRSF_domain:PIRSF038098,Superfamily_domains:SSF47095	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGAGAAGATC	.	5	ESCA
SOX11	0	.	GRCh37	2	5834742	5834742	+	3'UTR	SNP	G	G	C	rs770217948	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*563G>C	.	.	ENST00000322002	1/1	117	86	30	87	87	0	SOX11,3_prime_UTR_variant,,ENST00000322002,;AC010729.1,upstream_gene_variant,,ENST00000455579,;AC108025.2,upstream_gene_variant,,ENST00000453678,;AC107057.2,upstream_gene_variant,,ENST00000458264,;AC108025.2,upstream_gene_variant,,ENST00000420221,;	C	ENSG00000176887	ENST00000322002	Transcript	3_prime_UTR_variant	1944	.	.	.	.	rs770217948	.	.	1	SOX11	HGNC	11191	protein_coding	YES	CCDS1654.1	ENSP00000322568	SOX11_HUMAN	Q05CH0_HUMAN	UPI00001362AD	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TTAAAGAACTG	.	5	ESCA
BCL11A	0	.	GRCh37	2	60686532	60686532	+	3'UTR	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1007T>C	.	.	ENST00000335712	4/4	67	43	24	54	54	0	BCL11A,3_prime_UTR_variant,,ENST00000335712,;BCL11A,intron_variant,,ENST00000538214,;BCL11A,intron_variant,,ENST00000359629,;BCL11A,intron_variant,,ENST00000356842,;BCL11A,intron_variant,,ENST00000537768,;BCL11A,downstream_gene_variant,,ENST00000358510,;BCL11A,intron_variant,,ENST00000479026,;BCL11A,intron_variant,,ENST00000489516,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,downstream_gene_variant,,ENST00000477659,;	G	ENSG00000119866	ENST00000335712	Transcript	3_prime_UTR_variant	3743	.	.	.	.	.	.	.	-1	BCL11A	HGNC	13221	protein_coding	YES	CCDS1862.1	ENSP00000338774	BC11A_HUMAN	D6W5D9_HUMAN,Q53TS1_HUMAN,Q53TE8_HUMAN	UPI000013DC00	.	.	.	4/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATAAAACT	.	5	ESCA
WDPCP	0	.	GRCh37	2	63631310	63631310	+	Missense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1308C>A	p.Ser436Arg	p.S436R	ENST00000272321	10/18	54	31	23	51	51	0	WDPCP,missense_variant,p.Ser244Arg,ENST00000409199,;WDPCP,missense_variant,p.Ser244Arg,ENST00000409120,;WDPCP,missense_variant,p.Ser436Arg,ENST00000409562,;WDPCP,missense_variant,p.Ser277Arg,ENST00000398544,;WDPCP,missense_variant,p.Ser436Arg,ENST00000272321,;WDPCP,non_coding_transcript_exon_variant,,ENST00000409835,;WDPCP,missense_variant,p.Ser223Arg,ENST00000409354,;WDPCP,3_prime_UTR_variant,,ENST00000417238,;WDPCP,non_coding_transcript_exon_variant,,ENST00000493315,;	T	ENSG00000143951	ENST00000272321	Transcript	missense_variant	1836	1308	436	S/R	agC/agA	.	.	.	-1	WDPCP	HGNC	28027	protein_coding	YES	CCDS42688.1	ENSP00000272321	FRITZ_HUMAN	Q53TG5_HUMAN,Q53S85_HUMAN,Q53RX9_HUMAN,E9PFG9_HUMAN	UPI000013D946	.	tolerated(0.2)	possibly_damaging(0.878)	10/18	.	hmmpanther:PTHR13667,hmmpanther:PTHR13667:SF4,Pfam_domain:PF11768	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGACTGCTGGA	.	5	ESCA
PLEK	0	.	GRCh37	2	68620294	68620294	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.763G>A	p.Gly255Arg	p.G255R	ENST00000234313	7/9	71	42	28	75	75	0	PLEK,missense_variant,p.Gly255Arg,ENST00000234313,;PLEK,splice_region_variant,,ENST00000474788,;	A	ENSG00000115956	ENST00000234313	Transcript	missense_variant	942	763	255	G/R	Ggg/Agg	.	.	.	1	PLEK	HGNC	9070	protein_coding	YES	CCDS1887.1	ENSP00000234313	PLEK_HUMAN	.	UPI00002085C1	.	deleterious(0)	probably_damaging(1)	7/9	.	PROSITE_profiles:PS50003,hmmpanther:PTHR12092:SF1,hmmpanther:PTHR12092,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACAGGGGCAT	.	5	ESCA
HTRA2	0	.	GRCh37	2	74756658	74756658	+	5'UTR	SNP	G	G	A	rs760898459	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-476G>A	.	.	ENST00000258080	1/8	85	62	23	76	76	0	HTRA2,5_prime_UTR_variant,,ENST00000258080,;AUP1,intron_variant,,ENST00000377526,;HTRA2,upstream_gene_variant,,ENST00000352222,;DQX1,upstream_gene_variant,,ENST00000404568,;DQX1,upstream_gene_variant,,ENST00000393951,;HTRA2,upstream_gene_variant,,ENST00000437202,;LOXL3,downstream_gene_variant,,ENST00000409986,;LOXL3,downstream_gene_variant,,ENST00000264094,;LOXL3,downstream_gene_variant,,ENST00000409249,;LOXL3,downstream_gene_variant,,ENST00000409549,;DQX1,upstream_gene_variant,,ENST00000451518,;LOXL3,downstream_gene_variant,,ENST00000393937,;DQX1,upstream_gene_variant,,ENST00000498552,;HTRA2,upstream_gene_variant,,ENST00000462909,;HTRA2,upstream_gene_variant,,ENST00000484881,;HTRA2,upstream_gene_variant,,ENST00000467961,;AUP1,intron_variant,,ENST00000463900,;AUP1,intron_variant,,ENST00000466894,;AUP1,intron_variant,,ENST00000425118,;AUP1,intron_variant,,ENST00000472800,;HTRA2,upstream_gene_variant,,ENST00000484352,;AUP1,upstream_gene_variant,,ENST00000486234,;HTRA2,upstream_gene_variant,,ENST00000465521,;DQX1,upstream_gene_variant,,ENST00000473508,;LOXL3,downstream_gene_variant,,ENST00000470907,;AUP1,upstream_gene_variant,,ENST00000462297,;HTRA2,upstream_gene_variant,,ENST00000482205,;HTRA2,upstream_gene_variant,,ENST00000482331,;AUP1,upstream_gene_variant,,ENST00000464887,;	A	ENSG00000115317	ENST00000258080	Transcript	5_prime_UTR_variant	155	.	.	.	.	rs760898459	.	.	1	HTRA2	HGNC	14348	protein_coding	YES	CCDS1951.1	ENSP00000258080	HTRA2_HUMAN	.	UPI000012CB84	.	.	.	1/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGCCGAAGGC	.	5	ESCA
KCMF1	0	.	GRCh37	2	85276546	85276546	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.659C>T	p.Ser220Phe	p.S220F	ENST00000409785	6/7	36	17	19	26	26	0	KCMF1,missense_variant,p.Ser220Phe,ENST00000409785,;KCMF1,downstream_gene_variant,,ENST00000453448,;	T	ENSG00000176407	ENST00000409785	Transcript	missense_variant	1018	659	220	S/F	tCt/tTt	.	.	.	1	KCMF1	HGNC	20589	protein_coding	YES	CCDS46350.1	ENSP00000386738	KCMF1_HUMAN	C9JSW5_HUMAN,C9J3I2_HUMAN	UPI000003615C	.	deleterious(0)	possibly_damaging(0.889)	6/7	.	hmmpanther:PTHR12268:SF13,hmmpanther:PTHR12268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A224T|c.670G>A|5	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCCTCTGGCC	.	5	ESCA
TOMM70A	0	.	GRCh37	3	100086940	100086940	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1621G>C	p.Asp541His	p.D541H	ENST00000284320	11/12	44	28	15	36	36	0	TOMM70A,missense_variant,p.Asp541His,ENST00000284320,;TOMM70A,downstream_gene_variant,,ENST00000483945,;	G	ENSG00000154174	ENST00000284320	Transcript	missense_variant	2070	1621	541	D/H	Gac/Cac	.	.	.	-1	TOMM70A	HGNC	11985	protein_coding	YES	CCDS33807.1	ENSP00000284320	TOM70_HUMAN	B4DZ87_HUMAN,B3KQK5_HUMAN,B3KQK0_HUMAN	UPI0000000C55	.	deleterious(0)	probably_damaging(0.999)	11/12	.	Superfamily_domains:SSF48452,SMART_domains:SM00028,Gene3D:1.25.40.10,Pfam_domain:PF13414,hmmpanther:PTHR22904:SF178,hmmpanther:PTHR22904,PROSITE_profiles:PS50293	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTGTCAATTT	.	5	ESCA
FANCD2	0	.	GRCh37	3	10131997	10131997	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3705C>T	p.%3D	p.F1235F	ENST00000287647	37/43	54	45	9	58	58	0	FANCD2,synonymous_variant,p.%3D,ENST00000383807,;FANCD2,synonymous_variant,p.%3D,ENST00000287647,;FANCD2,synonymous_variant,p.%3D,ENST00000419585,;FANCD2OS,intron_variant,,ENST00000524279,;FANCD2,intron_variant,,ENST00000383806,;FANCD2OS,intron_variant,,ENST00000436517,;FANCD2OS,intron_variant,,ENST00000431315,;FANCD2OS,upstream_gene_variant,,ENST00000450616,;FANCD2,upstream_gene_variant,,ENST00000470028,;FANCD2,intron_variant,,ENST00000421731,;	T	ENSG00000144554	ENST00000287647	Transcript	synonymous_variant	3798	3705	1235	F	ttC/ttT	.	.	.	1	FANCD2	HGNC	3585	protein_coding	YES	CCDS2595.1	ENSP00000287647	FACD2_HUMAN	.	UPI000006F678	.	.	.	37/43	.	hmmpanther:PTHR32086,Pfam_domain:PF14631	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCCGTGT	.	5	ESCA
TMPRSS7	0	.	GRCh37	3	111799855	111799855	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2078C>G	p.Pro693Arg	p.P693R	ENST00000419127	16/16	69	63	6	63	63	0	TMPRSS7,missense_variant,p.Pro819Arg,ENST00000452346,;TMPRSS7,missense_variant,p.Pro693Arg,ENST00000419127,;TMPRSS7,3_prime_UTR_variant,,ENST00000435737,;	G	ENSG00000176040	ENST00000419127	Transcript	missense_variant	2160	2078	693	P/R	cCa/cGa	.	.	.	1	TMPRSS7	HGNC	30846	protein_coding	YES	CCDS43129.2	ENSP00000411645	TMPS7_HUMAN	.	UPI000192A2F1	.	tolerated(0.86)	possibly_damaging(0.779)	16/16	.	PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF17,hmmpanther:PTHR24256,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ACGACCAAACT	.	3	ESCA
C3orf30	0	.	GRCh37	3	118865898	118865898	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.862G>C	p.Glu288Gln	p.E288Q	ENST00000295622	1/3	48	24	24	39	39	0	C3orf30,missense_variant,p.Glu23Gln,ENST00000492792,;C3orf30,missense_variant,p.Glu288Gln,ENST00000295622,;C3orf30,missense_variant,p.Glu252Gln,ENST00000460150,;C3orf30,missense_variant,p.Glu81Gln,ENST00000473121,;IGSF11,upstream_gene_variant,,ENST00000425327,;RP11-484M3.5,upstream_gene_variant,,ENST00000490594,;IGSF11,upstream_gene_variant,,ENST00000354673,;IGSF11,upstream_gene_variant,,ENST00000441144,;IGSF11,upstream_gene_variant,,ENST00000494802,;C3orf30,missense_variant,p.Glu288Gln,ENST00000494105,;	C	ENSG00000163424	ENST00000295622	Transcript	missense_variant	902	862	288	E/Q	Gag/Cag	.	.	.	1	C3orf30	HGNC	26553	protein_coding	YES	CCDS2984.1	ENSP00000295622	CC030_HUMAN	.	UPI000013E280	.	deleterious(0.02)	probably_damaging(0.979)	1/3	.	hmmpanther:PTHR21847:SF1,hmmpanther:PTHR21847	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTTCTGAGCAG	.	5	ESCA
GPR156	0	.	GRCh37	3	119886160	119886160	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2164G>A	p.Glu722Lys	p.E722K	ENST00000464295	10/10	31	27	4	32	32	0	GPR156,missense_variant,p.Glu722Lys,ENST00000315843,;GPR156,missense_variant,p.Glu718Lys,ENST00000461057,;GPR156,missense_variant,p.Glu722Lys,ENST00000464295,;GPR156,3_prime_UTR_variant,,ENST00000495912,;	T	ENSG00000175697	ENST00000464295	Transcript	missense_variant	2610	2164	722	E/K	Gaa/Aaa	.	.	.	-1	GPR156	HGNC	20844	protein_coding	YES	CCDS2997.1	ENSP00000417261	GP156_HUMAN	.	UPI000004731C	.	tolerated(0.38)	benign(0.004)	10/10	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGTTCAGGCA	.	4	ESCA
STXBP5L	0	.	GRCh37	3	120957831	120957831	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1198G>A	p.Glu400Lys	p.E400K	ENST00000273666	13/28	79	60	19	59	59	0	STXBP5L,missense_variant,p.Glu400Lys,ENST00000471262,;STXBP5L,missense_variant,p.Glu400Lys,ENST00000472879,;STXBP5L,missense_variant,p.Glu400Lys,ENST00000273666,;STXBP5L,missense_variant,p.Glu400Lys,ENST00000471454,;STXBP5L,missense_variant,p.Glu400Lys,ENST00000492541,;STXBP5L,missense_variant,p.Glu400Lys,ENST00000497029,;	A	ENSG00000145087	ENST00000273666	Transcript	missense_variant	1469	1198	400	E/K	Gaa/Aaa	.	.	.	1	STXBP5L	HGNC	30757	protein_coding	YES	CCDS43137.1	ENSP00000273666	STB5L_HUMAN	C9JUZ7_HUMAN	UPI00001C1DEA	.	deleterious(0)	probably_damaging(0.995)	13/28	.	hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,SMART_domains:SM00320	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTGAAAAT	.	5	ESCA
POLQ	0	.	GRCh37	3	121207808	121207808	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3970C>G	p.Leu1324Val	p.L1324V	ENST00000264233	16/30	42	29	12	48	48	0	POLQ,missense_variant,p.Leu1324Val,ENST00000264233,;	C	ENSG00000051341	ENST00000264233	Transcript	missense_variant	4099	3970	1324	L/V	Ctg/Gtg	.	.	.	-1	POLQ	HGNC	9186	protein_coding	YES	CCDS33833.1	ENSP00000264233	DPOLQ_HUMAN	.	UPI0000D61B5F	.	deleterious(0)	probably_damaging(0.998)	16/30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATCCAGATAGA	.	5	ESCA
GOLGB1	0	.	GRCh37	3	121417367	121417367	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2003C>T	p.Ser668Leu	p.S668L	ENST00000393667	13/22	34	28	6	28	28	0	GOLGB1,missense_variant,p.Ser668Leu,ENST00000393667,;GOLGB1,missense_variant,p.Ser663Leu,ENST00000340645,;GOLGB1,missense_variant,p.Ser627Leu,ENST00000494517,;GOLGB1,missense_variant,p.Ser534Leu,ENST00000489400,;GOLGB1,3_prime_UTR_variant,,ENST00000482512,;	A	ENSG00000173230	ENST00000393667	Transcript	missense_variant	2114	2003	668	S/L	tCa/tTa	.	.	.	-1	GOLGB1	HGNC	4429	protein_coding	YES	CCDS58847.1	ENSP00000377275	GOGB1_HUMAN	C9J8Q0_HUMAN	UPI0001AE7645	.	.	benign(0.02)	13/22	.	hmmpanther:PTHR18887,hmmpanther:PTHR18887:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTGTTGATTTC	.	4	ESCA
CASR	0	.	GRCh37	3	122003196	122003196	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2425G>C	p.Glu809Gln	p.E809Q	ENST00000498619	7/7	37	25	12	17	17	0	CASR,missense_variant,p.Glu799Gln,ENST00000296154,;CASR,missense_variant,p.Glu809Gln,ENST00000498619,;CASR,missense_variant,p.Glu799Gln,ENST00000490131,;AC068754.1,downstream_gene_variant,,ENST00000408547,;	C	ENSG00000036828	ENST00000498619	Transcript	missense_variant	2863	2425	809	E/Q	Gag/Cag	CM013357,CASRdb_c.2395G>A,COSM3586279	.	.	1	CASR	HGNC	1514	protein_coding	YES	CCDS54632.1	ENSP00000420194	.	Q2F3K6_HUMAN,Q2F3K5_HUMAN,Q2F3K4_HUMAN,Q2F3K3_HUMAN,Q2F3K2_HUMAN,E7ENE0_HUMAN	UPI000020A065	.	deleterious(0)	probably_damaging(1)	7/7	.	PROSITE_profiles:PS50259,hmmpanther:PTHR24061:SF358,hmmpanther:PTHR24061,Pfam_domain:PF00003,Prints_domain:PR00248	.	.	.	.	.	.	.	.	.	.	0,0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGCCGGAGAAC	.	5	ESCA
PPARG	0	.	GRCh37	3	12447448	12447448	+	Silent	SNP	C	C	T	rs755427537	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.687C>T	p.%3D	p.I229I	ENST00000287820	5/7	41	29	12	27	27	0	PPARG,synonymous_variant,p.%3D,ENST00000287820,;PPARG,synonymous_variant,p.%3D,ENST00000397026,;PPARG,synonymous_variant,p.%3D,ENST00000397010,;PPARG,synonymous_variant,p.%3D,ENST00000397000,;PPARG,synonymous_variant,p.%3D,ENST00000397012,;PPARG,synonymous_variant,p.%3D,ENST00000539812,;PPARG,synonymous_variant,p.%3D,ENST00000309576,;PPARG,synonymous_variant,p.%3D,ENST00000397015,;PPARG,3_prime_UTR_variant,,ENST00000396999,;PPARG,3_prime_UTR_variant,,ENST00000397023,;PPARG,non_coding_transcript_exon_variant,,ENST00000497594,;PPARG,non_coding_transcript_exon_variant,,ENST00000477039,;	T	ENSG00000132170	ENST00000287820	Transcript	synonymous_variant	808	687	229	I	atC/atT	rs755427537	.	.	1	PPARG	HGNC	9236	protein_coding	YES	CCDS2609.1	ENSP00000287820	PPARG_HUMAN	Q9UEF6_HUMAN,Q6L9M1_HUMAN,E9PFJ1_HUMAN,E7EUD1_HUMAN,E7EU07_HUMAN,D2KUA6_HUMAN	UPI0000055911	.	.	.	5/7	.	hmmpanther:PTHR24082:SF14,hmmpanther:PTHR24082,Prints_domain:PR01288,Prints_domain:PR01291	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATATCGACCA	byFrequency	5	ESCA
SEC61A1	0	.	GRCh37	3	127774404	127774404	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.121A>C	p.Ile41Leu	p.I41L	ENST00000243253	3/12	111	94	17	68	68	0	SEC61A1,missense_variant,p.Ile41Leu,ENST00000243253,;SEC61A1,missense_variant,p.Ile47Leu,ENST00000464451,;SEC61A1,5_prime_UTR_variant,,ENST00000481210,;SEC61A1,intron_variant,,ENST00000424880,;SEC61A1,non_coding_transcript_exon_variant,,ENST00000491668,;	C	ENSG00000058262	ENST00000243253	Transcript	missense_variant	305	121	41	I/L	Atc/Ctc	.	.	.	1	SEC61A1	HGNC	18276	protein_coding	YES	CCDS3046.1	ENSP00000243253	S61A1_HUMAN	B3KNG2_HUMAN,C9JXC6_HUMAN,B3KNF6_HUMAN,B3KME8_HUMAN	UPI00000041A9	.	tolerated(0.09)	benign(0.033)	3/12	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR10906,Gene3D:1.10.3370.10,TIGRFAM_domain:TIGR00967,Pfam_domain:PF10559,PIRSF_domain:PIRSF004557,Superfamily_domains:0043235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTTTATCTTC	.	5	ESCA
TMCC1	0	.	GRCh37	3	129369054	129369054	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1270G>A	.	.	ENST00000393238	6/6	72	64	8	68	68	0	TMCC1,3_prime_UTR_variant,,ENST00000426664,;TMCC1,3_prime_UTR_variant,,ENST00000432054,;TMCC1,3_prime_UTR_variant,,ENST00000393238,;TMCC1,downstream_gene_variant,,ENST00000329333,;TMCC1,downstream_gene_variant,,ENST00000510323,;	T	ENSG00000172765	ENST00000393238	Transcript	3_prime_UTR_variant	3573	.	.	.	.	.	.	.	-1	TMCC1	HGNC	29116	protein_coding	YES	CCDS33855.1	ENSP00000376930	TMCC1_HUMAN	Q8N4H2_HUMAN,Q6N039_HUMAN,E9PC87_HUMAN,D6RBT7_HUMAN	UPI0000197B80	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACTCTTATA	.	4	ESCA
ANAPC13	0	.	GRCh37	3	134201686	134201686	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.61G>C	p.Glu21Gln	p.E21Q	ENST00000510994	2/3	43	35	8	52	52	0	ANAPC13,missense_variant,p.Glu21Gln,ENST00000354910,;ANAPC13,missense_variant,p.Glu21Gln,ENST00000514612,;ANAPC13,missense_variant,p.Glu21Gln,ENST00000511751,;ANAPC13,missense_variant,p.Glu21Gln,ENST00000510994,;CEP63,upstream_gene_variant,,ENST00000383229,;CEP63,upstream_gene_variant,,ENST00000511574,;CEP63,upstream_gene_variant,,ENST00000337090,;CEP63,upstream_gene_variant,,ENST00000354446,;CEP63,upstream_gene_variant,,ENST00000606977,;CEP63,upstream_gene_variant,,ENST00000512894,;CEP63,upstream_gene_variant,,ENST00000513612,;CEP63,upstream_gene_variant,,ENST00000332047,;CEP63,upstream_gene_variant,,ENST00000504013,;ANAPC13,non_coding_transcript_exon_variant,,ENST00000508755,;ANAPC13,non_coding_transcript_exon_variant,,ENST00000503439,;CEP63,upstream_gene_variant,,ENST00000514412,;	G	ENSG00000129055	ENST00000510994	Transcript	missense_variant	792	61	21	E/Q	Gaa/Caa	.	.	.	-1	ANAPC13	HGNC	24540	protein_coding	YES	CCDS3085.1	ENSP00000421842	APC13_HUMAN	A8K3Z6_HUMAN	UPI000007144A	.	tolerated(0.29)	possibly_damaging(0.448)	2/3	.	Pfam_domain:PF05839	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCTCGCC	.	5	ESCA
A4GNT	0	.	GRCh37	3	137850070	137850070	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.29C>G	p.Ser10Ter	p.S10*	ENST00000236709	2/3	39	34	5	31	31	0	A4GNT,stop_gained,p.Ser10Ter,ENST00000236709,;	C	ENSG00000118017	ENST00000236709	Transcript	stop_gained	231	29	10	S/*	tCa/tGa	.	.	.	-1	A4GNT	HGNC	17968	protein_coding	YES	CCDS3097.1	ENSP00000236709	A4GCT_HUMAN	.	UPI000003FF93	.	.	.	2/3	.	Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12042:SF16,hmmpanther:PTHR12042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TGACTGACAGG	.	4	ESCA
U2SURP	0	.	GRCh37	3	142772588	142772588	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2726C>G	p.Ser909Cys	p.S909C	ENST00000473835	26/28	120	101	18	84	84	0	U2SURP,missense_variant,p.Ser229Cys,ENST00000467348,;U2SURP,missense_variant,p.Ser909Cys,ENST00000473835,;U2SURP,missense_variant,p.Ser908Cys,ENST00000493598,;U2SURP,missense_variant,p.Ser476Cys,ENST00000480029,;U2SURP,missense_variant,p.Ser500Cys,ENST00000397933,;U2SURP,3_prime_UTR_variant,,ENST00000463563,;U2SURP,3_prime_UTR_variant,,ENST00000488497,;	G	ENSG00000163714	ENST00000473835	Transcript	missense_variant	2816	2726	909	S/C	tCc/tGc	.	.	.	1	U2SURP	HGNC	30855	protein_coding	YES	CCDS46928.1	ENSP00000418563	SR140_HUMAN	C9JDJ7_HUMAN,C9JB80_HUMAN,C9J5L1_HUMAN	UPI0000160746	.	tolerated(0.09)	benign(0.276)	26/28	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCGCTCCAAAG	.	5	ESCA
P2RY1	0	.	GRCh37	3	152555505	152555505	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*812G>A	.	.	ENST00000305097	1/1	91	62	29	70	70	0	P2RY1,3_prime_UTR_variant,,ENST00000305097,;RP11-38P22.2,upstream_gene_variant,,ENST00000460407,;	A	ENSG00000169860	ENST00000305097	Transcript	3_prime_UTR_variant	2770	.	.	.	.	.	.	.	1	P2RY1	HGNC	8539	protein_coding	YES	CCDS3169.1	ENSP00000304767	P2RY1_HUMAN	.	UPI0000001C06	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGCTGTGCAA	.	5	ESCA
GFM1	0	.	GRCh37	3	158363491	158363491	+	Nonsense_Mutation	SNP	C	C	G	rs746271799	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.155C>G	p.Ser52Ter	p.S52*	ENST00000486715	2/18	110	98	12	97	97	0	GFM1,stop_gained,p.Ser52Ter,ENST00000264263,;GFM1,stop_gained,p.Ser52Ter,ENST00000478576,;GFM1,stop_gained,p.Ser52Ter,ENST00000486715,;GFM1,5_prime_UTR_variant,,ENST00000464732,;LXN,downstream_gene_variant,,ENST00000482640,;GFM1,stop_gained,p.Ser52Ter,ENST00000478254,;GFM1,upstream_gene_variant,,ENST00000478251,;	G	ENSG00000168827	ENST00000486715	Transcript	stop_gained	512	155	52	S/*	tCa/tGa	rs746271799	.	.	1	GFM1	HGNC	13780	protein_coding	YES	CCDS33885.1	ENSP00000419038	EFGM_HUMAN	E5KND5_HUMAN,C9JA25_HUMAN	UPI000006232D	.	.	.	2/18	.	Prints_domain:PR00315,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00484,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00009,Gene3D:3.40.50.300,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF66,HAMAP:MF_00054_B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AATCTCAGCTC	.	4	ESCA
SI	0	.	GRCh37	3	164700087	164700087	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.5359C>T	p.%3D	p.L1787L	ENST00000264382	47/48	93	62	30	64	64	0	SI,synonymous_variant,p.%3D,ENST00000264382,;	A	ENSG00000090402	ENST00000264382	Transcript	synonymous_variant	5422	5359	1787	L	Cta/Tta	.	.	.	-1	SI	HGNC	10856	protein_coding	YES	CCDS3196.1	ENSP00000264382	SUIS_HUMAN	.	UPI000022C287	.	.	.	47/48	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CGTTAGAGTAA	.	5	ESCA
BCHE	0	.	GRCh37	3	165548470	165548470	+	Missense_Mutation	SNP	C	C	T	rs746209182	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.352G>A	p.Glu118Lys	p.E118K	ENST00000264381	2/4	66	43	23	54	54	0	BCHE,missense_variant,p.Glu118Lys,ENST00000264381,;BCHE,intron_variant,,ENST00000540653,;BCHE,intron_variant,,ENST00000479451,;BCHE,intron_variant,,ENST00000488954,;BCHE,missense_variant,p.Glu118Lys,ENST00000482958,;BCHE,missense_variant,p.Glu118Lys,ENST00000497011,;	T	ENSG00000114200	ENST00000264381	Transcript	missense_variant	519	352	118	E/K	Gaa/Aaa	rs746209182	.	.	-1	BCHE	HGNC	983	protein_coding	YES	CCDS3198.1	ENSP00000264381	CHLE_HUMAN	Q96HL2_HUMAN,F8WF14_HUMAN,D3DNN4_HUMAN	UPI0000127866	.	deleterious(0)	probably_damaging(1)	2/4	.	Superfamily_domains:SSF53474,Gene3D:3.40.50.1820,Pfam_domain:PF00135,PROSITE_patterns:PS00941,hmmpanther:PTHR11559:SF154,hmmpanther:PTHR11559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCTTCACTGA	.	5	ESCA
MECOM	0	.	GRCh37	3	169099121	169099121	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.301C>G	p.Pro101Ala	p.P101A	ENST00000486748	3/3	57	41	16	54	54	0	MECOM,missense_variant,p.Pro101Ala,ENST00000486748,;MECOM,missense_variant,p.Pro77Ala,ENST00000494292,;MECOM,non_coding_transcript_exon_variant,,ENST00000485957,;	C	ENSG00000085276	ENST00000486748	Transcript	missense_variant	319	301	101	P/A	Cct/Gct	COSM3589923	.	.	-1	MECOM	HGNC	3498	protein_coding	.	.	ENSP00000419537	.	C9JU02_HUMAN	UPI0001B797A5	.	deleterious(0)	probably_damaging(0.999)	3/3	.	Low_complexity_(Seg):seg,hmmpanther:PTHR21652,hmmpanther:PTHR21652:SF1,Gene3D:2.170.270.10	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCAGGAATGG	.	5	ESCA
PIK3CA	0	.	GRCh37	3	178952074	178952074	+	Missense_Mutation	SNP	G	G	A	rs121913283	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	21/21	29	18	11	42	42	0	PIK3CA,missense_variant,p.Met1043Ile,ENST00000263967,;RP11-245C23.3,downstream_gene_variant,,ENST00000609807,;	A	ENSG00000121879	ENST00000263967	Transcript	missense_variant	3286	3129	1043	M/I	atG/atA	rs121913283,COSM29313,COSM94984,COSM773,COSM419700,COSM446027,COSM94985	.	.	1	PIK3CA	HGNC	8975	protein_coding	YES	CCDS43171.1	ENSP00000263967	PK3CA_HUMAN	Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN	UPI000013D494	.	tolerated(0.11)	benign(0.054)	21/21	.	PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	likely_pathogenic	0,1,1,1,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1,1,1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	SITE|p.M1043I|c.3129G>A|8,SITE|p.M1043I|c.3129G>A|22,CODON|p.M1043I|c.3129G>T|4,CODON|p.M1043I|c.3129G>T|45,CODON|p.M1043I|c.3129G>C|4,CODON|p.M1043I|c.3129G>C|6,CODON|p.N1044D|c.3130A>G|4,CODON|p.N1044Y|c.3130A>T|3,BUFFER|p.M1040I|c.3120G>A|4,BUFFER|p.K1041K|c.3123A>G|3,BUFFER|p.K1041K|c.3123A>G|3,BUFFER|p.M1043V|c.3127A>G|26,BUFFER|p.M1043V|c.3127A>G|12,BUFFER|p.M1043T|c.3128T>C|8,BUFFER|p.M1043T|c.3128T>C|4,BUFFER|p.N1044S|c.3131A>G|5,BUFFER|p.N1044S|c.3131A>G|3,BUFFER|p.N1044K|c.3132T>G|5,BUFFER|p.N1044K|c.3132T>A|15,BUFFER|p.N1044K|c.3132T>A|7,BUFFER|p.D1045N|c.3133G>A|6,BUFFER|p.A1046T|c.3136G>A|6,BUFFER|p.A1046E|c.3137C>A|3,BUFFER|p.H1047Y|c.3139C>T|8,BUFFER|p.H1047Y|c.3139C>T|54,BUFFER|p.H1047R|c.3140A>G|1687,BUFFER|p.H1047R|c.3140A>G|242,BUFFER|p.H1047L|c.3140A>T|236,BUFFER|p.H1047L|c.3140A>T|45	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	CAAATGAATGA	byCluster	4	ESCA
RTP4	0	.	GRCh37	3	187089154	187089154	+	Missense_Mutation	SNP	C	C	T	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.734C>T	p.Ser245Leu	p.S245L	ENST00000259030	2/2	25	19	6	40	40	0	RTP4,missense_variant,p.Ser245Leu,ENST00000259030,;	T	ENSG00000136514	ENST00000259030	Transcript	missense_variant	844	734	245	S/L	tCa/tTa	COSM336723	.	.	1	RTP4	HGNC	23992	protein_coding	YES	CCDS33910.1	ENSP00000259030	RTP4_HUMAN	.	UPI000013D021	.	tolerated_low_confidence(1)	benign(0.184)	2/2	.	hmmpanther:PTHR14402:SF8,hmmpanther:PTHR14402	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACATCAGAAT	.	5	ESCA
OPA1	0	.	GRCh37	3	193409893	193409893	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2971G>C	p.Glu991Gln	p.E991Q	ENST00000361908	29/30	141	119	21	144	144	0	OPA1,missense_variant,p.Glu955Gln,ENST00000361150,;OPA1,missense_variant,p.Glu973Gln,ENST00000361715,;OPA1,missense_variant,p.Glu991Gln,ENST00000361908,;OPA1,missense_variant,p.Glu972Gln,ENST00000361828,;OPA1,missense_variant,p.Glu954Gln,ENST00000392438,;OPA1,missense_variant,p.Glu1009Gln,ENST00000361510,;OPA1,non_coding_transcript_exon_variant,,ENST00000495261,;	C	ENSG00000198836	ENST00000361908	Transcript	missense_variant	3205	2971	991	E/Q	Gaa/Caa	.	.	.	1	OPA1	HGNC	8140	protein_coding	YES	CCDS33917.1	ENSP00000354681	OPA1_HUMAN	Q6PEK6_HUMAN,E5KLJ7_HUMAN,C9JY58_HUMAN	UPI0000422960	.	tolerated(0.55)	benign(0.016)	29/30	.	hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCATTGAAGCT	.	5	ESCA
XXYLT1	0	.	GRCh37	3	194896403	194896403	+	Intron	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.653-19093C>A	.	.	ENST00000310380	.	26	18	8	40	40	0	XXYLT1,5_prime_UTR_variant,,ENST00000437101,;XXYLT1,intron_variant,,ENST00000310380,;XXYLT1,intron_variant,,ENST00000429994,;XXYLT1,upstream_gene_variant,,ENST00000355729,;XXYLT1,non_coding_transcript_exon_variant,,ENST00000476897,;XXYLT1,intron_variant,,ENST00000491138,;XXYLT1,downstream_gene_variant,,ENST00000494175,;XXYLT1,intron_variant,,ENST00000418940,;	T	ENSG00000173950	ENST00000310380	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	XXYLT1	HGNC	26639	protein_coding	YES	CCDS43188.1	ENSP00000309640	XXLT1_HUMAN	.	UPI000003B10F	.	.	.	.	2/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CACATGACTAG	.	5	ESCA
PCYT1A	0	.	GRCh37	3	195984695	195984695	+	Missense_Mutation	SNP	T	T	C	rs760187621	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.181A>G	p.Arg61Gly	p.R61G	ENST00000292823	4/10	82	61	21	83	83	0	PCYT1A,missense_variant,p.Arg61Gly,ENST00000419333,;PCYT1A,missense_variant,p.Arg61Gly,ENST00000441879,;PCYT1A,missense_variant,p.Arg61Gly,ENST00000431016,;PCYT1A,missense_variant,p.Arg61Gly,ENST00000412869,;PCYT1A,missense_variant,p.Arg61Gly,ENST00000443555,;PCYT1A,missense_variant,p.Arg61Gly,ENST00000411591,;PCYT1A,missense_variant,p.Arg61Gly,ENST00000292823,;PCYT1A,upstream_gene_variant,,ENST00000430755,;PCYT1A,non_coding_transcript_exon_variant,,ENST00000491544,;PCYT1A,missense_variant,p.Arg61Gly,ENST00000444822,;PCYT1A,synonymous_variant,p.%3D,ENST00000438634,;RP11-447L10.1,3_prime_UTR_variant,,ENST00000431391,;PCYT1A,non_coding_transcript_exon_variant,,ENST00000460677,;PCYT1A,non_coding_transcript_exon_variant,,ENST00000473978,;	C	ENSG00000161217	ENST00000292823	Transcript	missense_variant	354	181	61	R/G	Agg/Ggg	rs760187621	.	.	-1	PCYT1A	HGNC	8754	protein_coding	YES	CCDS3315.1	ENSP00000292823	PCY1A_HUMAN	C9JVS0_HUMAN,C9JPY0_HUMAN,C9J050_HUMAN	UPI000000DB72	.	deleterious(0)	possibly_damaging(0.591)	4/10	.	hmmpanther:PTHR10739,hmmpanther:PTHR10739:SF19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TACCCTGACAT	byFrequency	5	ESCA
CNTN4	0	.	GRCh37	3	3097920	3097920	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*16G>C	.	.	ENST00000397461	24/24	86	48	38	78	78	0	CNTN4,3_prime_UTR_variant,,ENST00000397459,;CNTN4,3_prime_UTR_variant,,ENST00000397461,;CNTN4,3_prime_UTR_variant,,ENST00000448906,;CNTN4,3_prime_UTR_variant,,ENST00000418658,;CNTN4,3_prime_UTR_variant,,ENST00000358480,;CNTN4,3_prime_UTR_variant,,ENST00000427331,;CNTN4-AS1,intron_variant,,ENST00000442749,;CNTN4,non_coding_transcript_exon_variant,,ENST00000484686,;	C	ENSG00000144619	ENST00000397461	Transcript	3_prime_UTR_variant	3481	.	.	.	.	.	.	.	1	CNTN4	HGNC	2174	protein_coding	YES	CCDS43041.1	ENSP00000380602	CNTN4_HUMAN	G3XAD4_HUMAN,C9JMQ2_HUMAN,C9JGK9_HUMAN	UPI000007446C	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAGGACTT	.	5	ESCA
OXSR1	0	.	GRCh37	3	38240282	38240282	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.362C>G	p.Ser121Cys	p.S121C	ENST00000311806	4/18	59	42	17	88	87	0	OXSR1,missense_variant,p.Ser121Cys,ENST00000311806,;OXSR1,missense_variant,p.Ser121Cys,ENST00000446845,;OXSR1,3_prime_UTR_variant,,ENST00000426620,;	G	ENSG00000172939	ENST00000311806	Transcript	missense_variant	734	362	121	S/C	tCt/tGt	.	.	.	1	OXSR1	HGNC	8508	protein_coding	YES	CCDS2675.1	ENSP00000311713	OXSR1_HUMAN	.	UPI000006E0D0	.	deleterious(0.04)	benign(0.351)	4/18	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF202,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TGAATCTACCA	.	4	ESCA
CCDC13	0	.	GRCh37	3	42799748	42799748	+	Missense_Mutation	SNP	C	C	T	rs757265443	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.90G>A	p.Met30Ile	p.M30I	ENST00000310232	2/16	52	34	17	52	52	0	CCDC13,missense_variant,p.Met30Ile,ENST00000310232,;CCDC13,non_coding_transcript_exon_variant,,ENST00000435327,;HIGD1A,3_prime_UTR_variant,,ENST00000431549,;CCDC13,non_coding_transcript_exon_variant,,ENST00000492806,;CCDC13,upstream_gene_variant,,ENST00000479576,;	T	ENSG00000244607	ENST00000310232	Transcript	missense_variant	174	90	30	M/I	atG/atA	rs757265443,COSM1044785	.	.	-1	CCDC13	HGNC	26358	protein_coding	YES	CCDS2705.1	ENSP00000309836	CCD13_HUMAN	.	UPI00001AEF4E	.	deleterious(0.01)	benign(0.269)	2/16	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31935,hmmpanther:PTHR31935:SF1	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTCCATCTG	byFrequency	5	ESCA
RBM6	0	.	GRCh37	3	50085751	50085751	+	Missense_Mutation	SNP	G	G	C	rs768599973	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1631G>C	p.Arg544Pro	p.R544P	ENST00000266022	7/21	41	23	17	53	53	0	RBM6,missense_variant,p.Arg22Pro,ENST00000442092,;RBM6,missense_variant,p.Arg544Pro,ENST00000266022,;RBM6,missense_variant,p.Arg22Pro,ENST00000422955,;RBM6,missense_variant,p.Arg412Pro,ENST00000443081,;RBM6,missense_variant,p.Arg22Pro,ENST00000446471,;RBM6,intron_variant,,ENST00000539992,;RBM6,splice_region_variant,,ENST00000464013,;RBM6,splice_region_variant,,ENST00000441115,;RBM6,missense_variant,p.Arg412Pro,ENST00000454079,;RBM6,missense_variant,p.Arg22Pro,ENST00000434592,;RBM6,synonymous_variant,p.%3D,ENST00000425608,;RBM6,splice_region_variant,,ENST00000483350,;RBM6,intron_variant,,ENST00000419610,;	C	ENSG00000004534	ENST00000266022	Transcript	missense_variant	1890	1631	544	R/P	cGa/cCa	rs768599973	.	.	1	RBM6	HGNC	9903	protein_coding	YES	CCDS2809.1	ENSP00000266022	RBM6_HUMAN	E9PGM9_HUMAN,C9JSL1_HUMAN,C9JMC8_HUMAN,C9JII0_HUMAN,B4DNY1_HUMAN	UPI000013D6C0	.	tolerated(0.08)	possibly_damaging(0.678)	7/21	.	hmmpanther:PTHR13948:SF22,hmmpanther:PTHR13948	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAACGAGTAA	.	5	ESCA
RBM6	0	.	GRCh37	3	50106179	50106179	+	Silent	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3000G>C	p.%3D	p.L1000L	ENST00000266022	18/21	116	91	25	132	132	0	RBM6,synonymous_variant,p.%3D,ENST00000539992,;RBM6,synonymous_variant,p.%3D,ENST00000442092,;RBM6,synonymous_variant,p.%3D,ENST00000266022,;RBM6,synonymous_variant,p.%3D,ENST00000422955,;RBM6,synonymous_variant,p.%3D,ENST00000443081,;RBM6,5_prime_UTR_variant,,ENST00000421682,;RBM6,downstream_gene_variant,,ENST00000438912,;RBM6,downstream_gene_variant,,ENST00000441115,;RBM6,3_prime_UTR_variant,,ENST00000454079,;RBM6,3_prime_UTR_variant,,ENST00000419610,;RBM6,3_prime_UTR_variant,,ENST00000434592,;	C	ENSG00000004534	ENST00000266022	Transcript	synonymous_variant	3259	3000	1000	L	ctG/ctC	.	.	.	1	RBM6	HGNC	9903	protein_coding	YES	CCDS2809.1	ENSP00000266022	RBM6_HUMAN	E9PGM9_HUMAN,C9JSL1_HUMAN,C9JMC8_HUMAN,C9JII0_HUMAN,B4DNY1_HUMAN	UPI000013D6C0	.	.	.	18/21	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13948:SF22,hmmpanther:PTHR13948	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TATCTGGAAAG	.	5	ESCA
FAM19A4	0	.	GRCh37	3	68781812	68781812	+	3'UTR	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*481G>T	.	.	ENST00000295569	6/6	16	8	8	14	14	0	FAM19A4,3_prime_UTR_variant,,ENST00000295569,;	A	ENSG00000163377	ENST00000295569	Transcript	3_prime_UTR_variant	1397	.	.	.	.	.	.	.	-1	FAM19A4	HGNC	21591	protein_coding	YES	CCDS2907.1	ENSP00000295569	F19A4_HUMAN	C9JUW7_HUMAN	UPI0000071129	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCTTCACCAG	.	5	ESCA
EIF4E3	0	.	GRCh37	3	71732114	71732114	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1719G>C	.	.	ENST00000425534	7/7	24	21	3	28	28	0	EIF4E3,3_prime_UTR_variant,,ENST00000295612,;EIF4E3,3_prime_UTR_variant,,ENST00000448225,;EIF4E3,3_prime_UTR_variant,,ENST00000425534,;EIF4E3,3_prime_UTR_variant,,ENST00000389826,;EIF4E3,downstream_gene_variant,,ENST00000421769,;EIF4E3,downstream_gene_variant,,ENST00000468147,;EIF4E3,downstream_gene_variant,,ENST00000481525,;	G	ENSG00000163412	ENST00000425534	Transcript	3_prime_UTR_variant	2402	.	.	.	.	.	.	.	-1	EIF4E3	HGNC	31837	protein_coding	YES	CCDS46867.1	ENSP00000393324	IF4E3_HUMAN	C9JUY2_HUMAN,C9J7Z6_HUMAN,C9J6E5_HUMAN	UPI00015887BF	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AAATTCTTGAG	.	2	ESCA
ENPEP	0	.	GRCh37	4	111397424	111397424	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-147G>A	.	.	ENST00000265162	1/20	15	11	4	12	12	0	ENPEP,5_prime_UTR_variant,,ENST00000265162,;ENPEP,intron_variant,,ENST00000510961,;	A	ENSG00000138792	ENST00000265162	Transcript	5_prime_UTR_variant	196	.	.	.	.	.	.	.	1	ENPEP	HGNC	3355	protein_coding	YES	CCDS3691.1	ENSP00000265162	AMPE_HUMAN	.	UPI000013D5C6	.	.	.	1/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGGCGCAAGA	.	5	ESCA
ANKRD50	0	.	GRCh37	4	125587651	125587651	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1022C>G	.	.	ENST00000504087	5/5	30	17	13	26	26	0	ANKRD50,3_prime_UTR_variant,,ENST00000504087,;ANKRD50,downstream_gene_variant,,ENST00000515641,;	C	ENSG00000151458	ENST00000504087	Transcript	3_prime_UTR_variant	6350	.	.	.	.	.	.	.	-1	ANKRD50	HGNC	29223	protein_coding	YES	CCDS34060.1	ENSP00000425658	ANR50_HUMAN	Q8TB46_HUMAN	UPI00002377E8	.	.	.	5/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTTTGAGTGG	.	5	ESCA
TMEM154	0	.	GRCh37	4	153564270	153564270	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.448G>C	p.Asp150His	p.D150H	ENST00000304385	5/7	74	53	20	74	74	0	TMEM154,missense_variant,p.Asp150His,ENST00000304385,;TMEM154,downstream_gene_variant,,ENST00000504064,;TMEM154,upstream_gene_variant,,ENST00000510252,;	G	ENSG00000170006	ENST00000304385	Transcript	missense_variant	680	448	150	D/H	Gat/Cat	COSM350975	.	.	-1	TMEM154	HGNC	26489	protein_coding	YES	CCDS3779.1	ENSP00000302144	TM154_HUMAN	.	UPI000006FAE5	.	deleterious(0)	probably_damaging(0.979)	5/7	.	Pfam_domain:PF15102	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTATCAAGCT	.	5	ESCA
BST1	0	.	GRCh37	4	15707200	15707200	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.251C>T	p.Ser84Phe	p.S84F	ENST00000265016	2/9	38	34	4	32	32	0	BST1,missense_variant,p.Ser99Phe,ENST00000382346,;BST1,missense_variant,p.Ser84Phe,ENST00000265016,;BST1,upstream_gene_variant,,ENST00000505785,;FAM200B,downstream_gene_variant,,ENST00000504598,;	T	ENSG00000109743	ENST00000265016	Transcript	missense_variant	446	251	84	S/F	tCc/tTc	.	.	.	1	BST1	HGNC	1118	protein_coding	YES	CCDS3416.1	ENSP00000265016	BST1_HUMAN	.	UPI0000072318	.	deleterious(0)	possibly_damaging(0.816)	2/9	.	hmmpanther:PTHR10912:SF4,hmmpanther:PTHR10912,Pfam_domain:PF02267,Gene3D:1.20.82.10,Superfamily_domains:SSF52309	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTGCTCCGTGC	.	4	ESCA
C4orf46	0	.	GRCh37	4	159589634	159589634	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1131C>G	.	.	ENST00000379205	2/2	84	59	25	47	47	0	C4orf46,3_prime_UTR_variant,,ENST00000508457,;C4orf46,3_prime_UTR_variant,,ENST00000379205,;ETFDH,upstream_gene_variant,,ENST00000507475,;ETFDH,upstream_gene_variant,,ENST00000307738,;ETFDH,upstream_gene_variant,,ENST00000512251,;ETFDH,upstream_gene_variant,,ENST00000511912,;ETFDH,upstream_gene_variant,,ENST00000436096,;C4orf46,downstream_gene_variant,,ENST00000508836,;ETFDH,upstream_gene_variant,,ENST00000510353,;ETFDH,upstream_gene_variant,,ENST00000506422,;	C	ENSG00000205208	ENST00000379205	Transcript	3_prime_UTR_variant	1718	.	.	.	.	.	.	.	-1	C4orf46	HGNC	27320	protein_coding	YES	CCDS34088.1	ENSP00000368503	CD046_HUMAN	.	UPI000015D968	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAAAGAATTA	.	5	ESCA
TRIM60	0	.	GRCh37	4	165961854	165961854	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.630G>A	p.Met210Ile	p.M210I	ENST00000512596	3/3	85	59	26	60	60	0	TRIM60,missense_variant,p.Met210Ile,ENST00000341062,;TRIM60,missense_variant,p.Met210Ile,ENST00000512596,;TRIM60,missense_variant,p.Met210Ile,ENST00000508504,;TRIM60,downstream_gene_variant,,ENST00000507119,;	A	ENSG00000176979	ENST00000512596	Transcript	missense_variant	846	630	210	M/I	atG/atA	.	.	.	1	TRIM60	HGNC	21162	protein_coding	YES	CCDS3808.1	ENSP00000421142	TRI60_HUMAN	D6RAS2_HUMAN	UPI000006DAAD	.	tolerated(0.21)	benign(0.048)	3/3	.	hmmpanther:PTHR24103:SF304,hmmpanther:PTHR24103	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAGATGAACAT	.	5	ESCA
SPOCK3	0	.	GRCh37	4	167713337	167713337	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.702G>A	p.%3D	p.L234L	ENST00000357154	8/12	65	49	16	51	51	0	SPOCK3,synonymous_variant,p.%3D,ENST00000512648,;SPOCK3,synonymous_variant,p.%3D,ENST00000357154,;SPOCK3,synonymous_variant,p.%3D,ENST00000511531,;SPOCK3,synonymous_variant,p.%3D,ENST00000357545,;SPOCK3,synonymous_variant,p.%3D,ENST00000506886,;SPOCK3,synonymous_variant,p.%3D,ENST00000510403,;SPOCK3,synonymous_variant,p.%3D,ENST00000511269,;SPOCK3,synonymous_variant,p.%3D,ENST00000421836,;SPOCK3,synonymous_variant,p.%3D,ENST00000541637,;SPOCK3,synonymous_variant,p.%3D,ENST00000541354,;SPOCK3,synonymous_variant,p.%3D,ENST00000512681,;SPOCK3,synonymous_variant,p.%3D,ENST00000534949,;SPOCK3,synonymous_variant,p.%3D,ENST00000502330,;SPOCK3,synonymous_variant,p.%3D,ENST00000504953,;SPOCK3,intron_variant,,ENST00000510741,;SPOCK3,intron_variant,,ENST00000535728,;SPOCK3,non_coding_transcript_exon_variant,,ENST00000507137,;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000515143,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,;SPOCK3,downstream_gene_variant,,ENST00000511226,;	T	ENSG00000196104	ENST00000357154	Transcript	synonymous_variant	840	702	234	L	ctG/ctA	.	.	.	-1	SPOCK3	HGNC	13565	protein_coding	YES	CCDS54817.1	ENSP00000349677	TICN3_HUMAN	Q4W5S3_HUMAN,Q4W5E2_HUMAN,E7EMP8_HUMAN	UPI000004BA60	.	.	.	8/12	.	hmmpanther:PTHR12036,hmmpanther:PTHR12036:SF4,Pfam_domain:PF10591,Gene3D:1.10.238.10,Superfamily_domains:SSF47473	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGCCTCAGCAA	.	5	ESCA
DDX60L	0	.	GRCh37	4	169377211	169377211	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.816G>C	p.Leu272Phe	p.L272F	ENST00000260184	7/38	38	27	11	25	25	0	DDX60L,missense_variant,p.Leu272Phe,ENST00000511577,;DDX60L,missense_variant,p.Leu272Phe,ENST00000505890,;DDX60L,missense_variant,p.Leu272Phe,ENST00000260184,;DDX60L,upstream_gene_variant,,ENST00000505863,;	G	ENSG00000181381	ENST00000260184	Transcript	missense_variant	1037	816	272	L/F	ttG/ttC	.	.	.	-1	DDX60L	HGNC	26429	protein_coding	YES	CCDS47161.1	ENSP00000260184	DDX6L_HUMAN	D6RIU1_HUMAN,D6RBA2_HUMAN,D6RB62_HUMAN	UPI0001553B03	.	deleterious(0)	probably_damaging(0.999)	7/38	.	hmmpanther:PTHR11752,hmmpanther:PTHR11752:SF56	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ATTCTCAAGGA	.	5	ESCA
FAM184B	0	.	GRCh37	4	17661649	17661649	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1756G>C	p.Glu586Gln	p.E586Q	ENST00000265018	9/18	50	37	13	74	74	0	FAM184B,missense_variant,p.Glu586Gln,ENST00000265018,;	G	ENSG00000047662	ENST00000265018	Transcript	missense_variant	1969	1756	586	E/Q	Gag/Cag	.	.	.	-1	FAM184B	HGNC	29235	protein_coding	YES	CCDS47033.1	ENSP00000265018	F184B_HUMAN	.	UPI000020BD7C	.	deleterious(0.04)	benign(0.442)	9/18	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18870:SF8,hmmpanther:PTHR18870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTCCTTCA	.	5	ESCA
LRP2BP	0	.	GRCh37	4	186291869	186291869	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.903C>G	p.Phe301Leu	p.F301L	ENST00000328559	7/8	66	49	16	38	38	0	LRP2BP,missense_variant,p.Phe275Leu,ENST00000510776,;LRP2BP,missense_variant,p.Phe301Leu,ENST00000505916,;LRP2BP,missense_variant,p.Phe301Leu,ENST00000328559,;LRP2BP,missense_variant,p.Phe303Leu,ENST00000362004,;LRP2BP,downstream_gene_variant,,ENST00000511404,;RP11-714G18.1,upstream_gene_variant,,ENST00000514884,;SNX25,downstream_gene_variant,,ENST00000504959,;	C	ENSG00000109771	ENST00000328559	Transcript	missense_variant	1715	903	301	F/L	ttC/ttG	.	.	.	-1	LRP2BP	HGNC	25434	protein_coding	YES	CCDS3840.1	ENSP00000332681	LR2BP_HUMAN	D6RGF6_HUMAN	UPI00001BB2BB	.	deleterious(0)	probably_damaging(1)	7/8	.	Superfamily_domains:SSF81901,SMART_domains:SM00671,Gene3D:1.25.40.10,Pfam_domain:PF08238,hmmpanther:PTHR11102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTAGAAGGA	.	5	ESCA
PGM2	0	.	GRCh37	4	37836311	37836311	+	Silent	SNP	C	C	T	rs758925694	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.321C>T	p.%3D	p.A107A	ENST00000381967	3/14	222	167	54	168	168	0	PGM2,synonymous_variant,p.%3D,ENST00000381967,;PGM2,5_prime_UTR_variant,,ENST00000544359,;PGM2,intron_variant,,ENST00000537241,;PGM2,synonymous_variant,p.%3D,ENST00000505986,;PGM2,synonymous_variant,p.%3D,ENST00000515668,;PGM2,intron_variant,,ENST00000512556,;	T	ENSG00000169299	ENST00000381967	Transcript	synonymous_variant	421	321	107	A	gcC/gcT	rs758925694	.	.	1	PGM2	HGNC	8906	protein_coding	YES	CCDS3443.1	ENSP00000371393	PGM2_HUMAN	Q4W5D6_HUMAN,F5H6V2_HUMAN	UPI000004A02B	.	.	.	3/14	.	hmmpanther:PTHR22573:SF43,hmmpanther:PTHR22573,Pfam_domain:PF02878,Gene3D:3.40.120.10,Superfamily_domains:SSF53738	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACGCCCGAGC	.	5	ESCA
KLB	0	.	GRCh37	4	39448748	39448748	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2402C>G	p.Ser801Trp	p.S801W	ENST00000257408	4/5	53	41	11	39	39	0	KLB,missense_variant,p.Ser801Trp,ENST00000257408,;	G	ENSG00000134962	ENST00000257408	Transcript	missense_variant	2499	2402	801	S/W	tCg/tGg	COSM3775831	.	.	1	KLB	HGNC	15527	protein_coding	YES	CCDS3451.1	ENSP00000257408	KLOTB_HUMAN	.	UPI000000D726	.	tolerated(0.18)	probably_damaging(0.998)	4/5	.	hmmpanther:PTHR10353:SF7,hmmpanther:PTHR10353,Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGCTCGGCCC	.	5	ESCA
PDS5A	0	.	GRCh37	4	39891930	39891930	+	Nonsense_Mutation	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1825G>T	p.Glu609Ter	p.E609*	ENST00000303538	17/33	117	88	28	64	64	0	PDS5A,stop_gained,p.Glu609Ter,ENST00000303538,;	A	ENSG00000121892	ENST00000303538	Transcript	stop_gained	2365	1825	609	E/*	Gag/Tag	.	.	.	-1	PDS5A	HGNC	29088	protein_coding	YES	CCDS47045.1	ENSP00000303427	PDS5A_HUMAN	Q96DB6_HUMAN,G1UI16_HUMAN,B3KMN2_HUMAN	UPI00006C6A7E	.	.	.	17/33	.	hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CATCTCTAGAA	.	5	ESCA
PHOX2B	0	.	GRCh37	4	41747647	41747647	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*177C>G	.	.	ENST00000226382	3/3	24	18	6	10	10	0	PHOX2B,3_prime_UTR_variant,,ENST00000226382,;PHOX2B,downstream_gene_variant,,ENST00000510424,;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,;	C	ENSG00000109132	ENST00000226382	Transcript	3_prime_UTR_variant	1482	.	.	.	.	.	.	.	-1	PHOX2B	HGNC	9143	protein_coding	YES	CCDS3463.1	ENSP00000226382	PHX2B_HUMAN	.	UPI000000D936	.	.	.	3/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGTTGAAATG	.	5	ESCA
GABRB1	0	.	GRCh37	4	47405694	47405694	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.801C>G	p.Ile267Met	p.I267M	ENST00000295454	7/9	35	22	13	32	32	0	GABRB1,missense_variant,p.Ile197Met,ENST00000538619,;GABRB1,missense_variant,p.Ile267Met,ENST00000295454,;GABRB1,downstream_gene_variant,,ENST00000510909,;	G	ENSG00000163288	ENST00000295454	Transcript	missense_variant	1093	801	267	I/M	atC/atG	.	.	.	1	GABRB1	HGNC	4081	protein_coding	YES	CCDS3474.1	ENSP00000295454	GBRB1_HUMAN	D6REM0_HUMAN	UPI000012AFAC	.	deleterious(0.04)	probably_damaging(0.985)	7/9	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF198,hmmpanther:PTHR18945,Pfam_domain:PF02932,Gene3D:1.20.58.390,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGGATCAACTA	.	5	ESCA
FRYL	0	.	GRCh37	4	48577189	48577189	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2791G>C	p.Glu931Gln	p.E931Q	ENST00000358350	25/64	159	126	33	112	112	0	FRYL,missense_variant,p.Glu931Gln,ENST00000358350,;FRYL,missense_variant,p.Glu931Gln,ENST00000503238,;FRYL,missense_variant,p.Glu931Gln,ENST00000507711,;FRYL,missense_variant,p.Glu931Gln,ENST00000537810,;FRYL,5_prime_UTR_variant,,ENST00000264319,;RNU5E-3P,upstream_gene_variant,,ENST00000515913,;FRYL,upstream_gene_variant,,ENST00000511343,;	G	ENSG00000075539	ENST00000358350	Transcript	missense_variant	3396	2791	931	E/Q	Gaa/Caa	.	.	.	-1	FRYL	HGNC	29127	protein_coding	YES	CCDS43227.1	ENSP00000351113	FRYL_HUMAN	.	UPI0000EBC149	.	deleterious(0.02)	benign(0.122)	25/64	.	Superfamily_domains:SSF48371,hmmpanther:PTHR12295:SF9,hmmpanther:PTHR12295	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GATTTCCATGC	.	5	ESCA
LNX1	0	.	GRCh37	4	54373487	54373487	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772G>A	p.Glu258Lys	p.E258K	ENST00000263925	4/11	52	39	13	38	38	0	LNX1,missense_variant,p.Glu162Lys,ENST00000306888,;LNX1,missense_variant,p.Glu258Lys,ENST00000263925,;FIP1L1,intron_variant,,ENST00000507166,;LNX1-AS1,intron_variant,,ENST00000514364,;LNX1-AS1,intron_variant,,ENST00000511989,;LNX1-AS1,intron_variant,,ENST00000510785,;LNX1,non_coding_transcript_exon_variant,,ENST00000511398,;	T	ENSG00000072201	ENST00000263925	Transcript	missense_variant	1087	772	258	E/K	Gaa/Aaa	.	.	.	-1	LNX1	HGNC	6657	protein_coding	YES	CCDS47057.1	ENSP00000263925	LNX1_HUMAN	D6RB76_HUMAN,D6RAH9_HUMAN	UPI000012E7A6	.	tolerated(0.08)	benign(0.297)	4/11	.	hmmpanther:PTHR19964:SF14,hmmpanther:PTHR19964	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTCAGGGG	.	5	ESCA
PRDM8	0	.	GRCh37	4	81123144	81123144	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.528C>T	p.%3D	p.F176F	ENST00000339711	10/10	24	20	4	31	31	0	PRDM8,synonymous_variant,p.%3D,ENST00000504452,;PRDM8,synonymous_variant,p.%3D,ENST00000515013,;PRDM8,synonymous_variant,p.%3D,ENST00000339711,;PRDM8,synonymous_variant,p.%3D,ENST00000415738,;PRDM8,downstream_gene_variant,,ENST00000509375,;PRDM8,downstream_gene_variant,,ENST00000511825,;	T	ENSG00000152784	ENST00000339711	Transcript	synonymous_variant	1759	528	176	F	ttC/ttT	.	.	.	1	PRDM8	HGNC	13993	protein_coding	YES	CCDS43243.1	ENSP00000339764	PRDM8_HUMAN	Q05CA1_HUMAN,E9PEH0_HUMAN	UPI0000422A1D	.	.	.	10/10	.	hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF0,SMART_domains:SM00355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|VARSCANS	CGTTTCCGCTG	.	3	ESCA
THAP9	0	.	GRCh37	4	83821902	83821902	+	5'Flank	SNP	C	C	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000302236	.	125	83	42	111	111	0	SEC31A,intron_variant,,ENST00000503210,;THAP9,upstream_gene_variant,,ENST00000302236,;SEC31A,upstream_gene_variant,,ENST00000355196,;SEC31A,upstream_gene_variant,,ENST00000507051,;SEC31A,upstream_gene_variant,,ENST00000506495,;SEC31A,upstream_gene_variant,,ENST00000507676,;THAP9-AS1,non_coding_transcript_exon_variant,,ENST00000504520,;THAP9-AS1,upstream_gene_variant,,ENST00000508772,;THAP9-AS1,upstream_gene_variant,,ENST00000511271,;THAP9-AS1,upstream_gene_variant,,ENST00000505028,;THAP9-AS1,upstream_gene_variant,,ENST00000504792,;THAP9-AS1,upstream_gene_variant,,ENST00000507660,;THAP9-AS1,upstream_gene_variant,,ENST00000503704,;THAP9-AS1,upstream_gene_variant,,ENST00000504869,;THAP9-AS1,upstream_gene_variant,,ENST00000513581,;THAP9-AS1,upstream_gene_variant,,ENST00000504718,;THAP9-AS1,upstream_gene_variant,,ENST00000509007,;THAP9-AS1,upstream_gene_variant,,ENST00000512932,;THAP9,5_prime_UTR_variant,,ENST00000514440,;THAP9,5_prime_UTR_variant,,ENST00000514244,;THAP9,upstream_gene_variant,,ENST00000505901,;THAP9,upstream_gene_variant,,ENST00000509353,;	A	ENSG00000168152	ENST00000302236	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	3	1	THAP9	HGNC	23192	protein_coding	YES	CCDS3598.1	ENSP00000305533	THAP9_HUMAN	.	UPI0000367262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTGGTCGTGAT	.	5	ESCA
SLCO6A1	0	.	GRCh37	5	101794130	101794130	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1087C>T	p.%3D	p.L363L	ENST00000506729	6/14	128	112	16	116	116	0	SLCO6A1,synonymous_variant,p.%3D,ENST00000379807,;SLCO6A1,synonymous_variant,p.%3D,ENST00000506729,;SLCO6A1,synonymous_variant,p.%3D,ENST00000389019,;SLCO6A1,intron_variant,,ENST00000513675,;SLCO6A1,intron_variant,,ENST00000379810,;SLCO6A1,non_coding_transcript_exon_variant,,ENST00000514551,;SLCO6A1,non_coding_transcript_exon_variant,,ENST00000505739,;	A	ENSG00000205359	ENST00000506729	Transcript	synonymous_variant	1259	1087	363	L	Ctg/Ttg	COSM1541380	.	.	-1	SLCO6A1	HGNC	23613	protein_coding	YES	CCDS34206.1	ENSP00000421339	SO6A1_HUMAN	H0Y8R6_HUMAN,D3DSZ4_HUMAN	UPI000020C392	.	.	.	6/14	.	hmmpanther:PTHR11388:SF3,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Superfamily_domains:SSF103473	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TTTCAGATCTT	.	4	ESCA
NKD2	0	.	GRCh37	5	1033539	1033539	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.255C>T	p.%3D	p.L85L	ENST00000296849	5/10	162	103	58	50	50	0	NKD2,synonymous_variant,p.%3D,ENST00000537972,;NKD2,synonymous_variant,p.%3D,ENST00000274150,;NKD2,synonymous_variant,p.%3D,ENST00000296849,;NKD2,upstream_gene_variant,,ENST00000382730,;NKD2,upstream_gene_variant,,ENST00000523688,;NKD2,upstream_gene_variant,,ENST00000513296,;NKD2,upstream_gene_variant,,ENST00000519933,;	T	ENSG00000145506	ENST00000296849	Transcript	synonymous_variant	484	255	85	L	ctC/ctT	.	.	.	1	NKD2	HGNC	17046	protein_coding	YES	CCDS3859.1	ENSP00000296849	NKD2_HUMAN	.	UPI0000073E19	.	.	.	5/10	.	hmmpanther:PTHR22611,hmmpanther:PTHR22611:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAGCGC	.	5	ESCA
SLC12A7	0	.	GRCh37	5	1085364	1085364	+	Silent	SNP	G	G	A	rs140320673	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.900C>T	p.%3D	p.F300F	ENST00000264930	7/24	117	110	7	42	42	0	SLC12A7,synonymous_variant,p.%3D,ENST00000264930,;SLC12A7,upstream_gene_variant,,ENST00000510943,;	A	ENSG00000113504	ENST00000264930	Transcript	synonymous_variant	944	900	300	F	ttC/ttT	rs140320673	.	.	-1	SLC12A7	HGNC	10915	protein_coding	YES	CCDS34129.1	ENSP00000264930	S12A7_HUMAN	.	UPI0000141815	.	.	.	7/24	.	hmmpanther:PTHR11827:SF47,hmmpanther:PTHR11827,TIGRFAM_domain:TIGR00930,Prints_domain:PR01081	.	.	.	.	.	.	.	A:0.0005	A:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GGGTCGAAGGC	byFrequency|byCluster	2	ESCA
SRFBP1	0	.	GRCh37	5	121356415	121356415	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.985G>C	p.Asp329His	p.D329H	ENST00000339397	6/8	54	43	10	46	46	0	SRFBP1,missense_variant,p.Asp329His,ENST00000339397,;SRFBP1,non_coding_transcript_exon_variant,,ENST00000504881,;	C	ENSG00000151304	ENST00000339397	Transcript	missense_variant	1057	985	329	D/H	Gac/Cac	.	.	.	1	SRFBP1	HGNC	26333	protein_coding	YES	CCDS43354.1	ENSP00000341324	SRFB1_HUMAN	.	UPI000006DEC3	.	deleterious(0)	possibly_damaging(0.717)	6/8	.	hmmpanther:PTHR23325	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GAAATGACAAA	.	3	ESCA
SRFBP1	0	.	GRCh37	5	121356424	121356424	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.994A>C	p.Lys332Gln	p.K332Q	ENST00000339397	6/8	53	43	10	41	41	0	SRFBP1,missense_variant,p.Lys332Gln,ENST00000339397,;SRFBP1,non_coding_transcript_exon_variant,,ENST00000504881,;	C	ENSG00000151304	ENST00000339397	Transcript	missense_variant	1066	994	332	K/Q	Aag/Cag	.	.	.	1	SRFBP1	HGNC	26333	protein_coding	YES	CCDS43354.1	ENSP00000341324	SRFB1_HUMAN	.	UPI000006DEC3	.	deleterious(0.01)	benign(0.398)	6/8	.	hmmpanther:PTHR23325	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	AAATCAAGCCA	.	3	ESCA
SLC6A19	0	.	GRCh37	5	1213667	1213667	+	Missense_Mutation	SNP	C	C	G	rs200597791	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.753C>G	p.Ile251Met	p.I251M	ENST00000304460	5/12	239	215	24	79	79	0	SLC6A19,missense_variant,p.Ile251Met,ENST00000304460,;SLC6A19,missense_variant,p.Arg221Gly,ENST00000515652,;	G	ENSG00000174358	ENST00000304460	Transcript	missense_variant	809	753	251	I/M	atC/atG	rs200597791	.	.	1	SLC6A19	HGNC	27960	protein_coding	YES	CCDS34130.1	ENSP00000305302	S6A19_HUMAN	B3KVZ8_HUMAN	UPI0000401AF8	.	deleterious(0)	probably_damaging(0.915)	5/12	.	PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF125,Pfam_domain:PF00209,Superfamily_domains:0053687	G:0.0002	G:0	G:0	.	G:0.001	G:0	G:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GGCATCGTCTT	byCluster|by1000G	4	ESCA
TERT	0	.	GRCh37	5	1264696	1264696	+	Missense_Mutation	SNP	C	C	T	rs532158398	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2666G>A	p.Arg889Gln	p.R889Q	ENST00000310581	11/16	139	131	8	55	55	0	TERT,missense_variant,p.Arg889Gln,ENST00000310581,;TERT,3_prime_UTR_variant,,ENST00000296820,;TERT,intron_variant,,ENST00000334602,;TERT,downstream_gene_variant,,ENST00000508104,;TERT,non_coding_transcript_exon_variant,,ENST00000503656,;TERT,intron_variant,,ENST00000484238,;TERT,intron_variant,,ENST00000460137,;	T	ENSG00000164362	ENST00000310581	Transcript	missense_variant	2724	2666	889	R/Q	cGa/cAa	rs532158398,COSM735863,COSM735864	.	.	-1	TERT	HGNC	11730	protein_coding	YES	CCDS3861.2	ENSP00000309572	TERT_HUMAN	Q9UNS6_HUMAN,Q9UNR4_HUMAN,Q9UBR6_HUMAN	UPI0000031309	.	tolerated(0.53)	benign(0.022)	11/16	.	PROSITE_profiles:PS50878,hmmpanther:PTHR12066:SF0,hmmpanther:PTHR12066,Pfam_domain:PF00078,Superfamily_domains:SSF56672	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CACCTCGGACC	.	2	ESCA
PRRC1	0	.	GRCh37	5	126887539	126887539	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269G>C	p.Gln423His	p.Q423H	ENST00000296666	9/9	24	20	4	33	33	0	PRRC1,missense_variant,p.Gln423His,ENST00000296666,;PRRC1,missense_variant,p.Gln423His,ENST00000512635,;PRRC1,3_prime_UTR_variant,,ENST00000442138,;PRRC1,non_coding_transcript_exon_variant,,ENST00000513427,;	C	ENSG00000164244	ENST00000296666	Transcript	missense_variant	1457	1269	423	Q/H	caG/caC	.	.	.	1	PRRC1	HGNC	28164	protein_coding	YES	CCDS4143.1	ENSP00000296666	PRRC1_HUMAN	.	UPI0000073C8E	.	tolerated(0.15)	probably_damaging(0.994)	9/9	.	Superfamily_domains:SSF52972,Gene3D:3.90.950.10,hmmpanther:PTHR23276,hmmpanther:PTHR23276:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCAGATGAT	.	5	ESCA
CLPTM1L	0	.	GRCh37	5	1318437	1318437	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*47G>C	.	.	ENST00000320895	17/17	70	60	10	24	24	0	CLPTM1L,3_prime_UTR_variant,,ENST00000320927,;CLPTM1L,3_prime_UTR_variant,,ENST00000320895,;CLPTM1L,3_prime_UTR_variant,,ENST00000507807,;CLPTM1L,downstream_gene_variant,,ENST00000507195,;CLPTM1L,downstream_gene_variant,,ENST00000506641,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000503534,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000503042,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000515719,;CLPTM1L,downstream_gene_variant,,ENST00000505605,;CLPTM1L,downstream_gene_variant,,ENST00000505914,;CLPTM1L,downstream_gene_variant,,ENST00000503151,;CLPTM1L,downstream_gene_variant,,ENST00000512451,;CLPTM1L,downstream_gene_variant,,ENST00000511268,;	G	ENSG00000049656	ENST00000320895	Transcript	3_prime_UTR_variant	1922	.	.	.	.	.	.	.	-1	CLPTM1L	HGNC	24308	protein_coding	YES	CCDS3862.1	ENSP00000313854	CLP1L_HUMAN	B3KY18_HUMAN	UPI00000707DF	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACTCATTGA	.	5	ESCA
CLPTM1L	0	.	GRCh37	5	1330463	1330463	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1012C>T	p.%3D	p.L338L	ENST00000320895	9/17	93	86	6	22	22	0	CLPTM1L,synonymous_variant,p.%3D,ENST00000320895,;CLPTM1L,intron_variant,,ENST00000320927,;CLPTM1L,intron_variant,,ENST00000507807,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000513250,;CLPTM1L,upstream_gene_variant,,ENST00000507195,;CLPTM1L,upstream_gene_variant,,ENST00000506641,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000508765,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000503042,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000503151,;CLPTM1L,upstream_gene_variant,,ENST00000503534,;CLPTM1L,downstream_gene_variant,,ENST00000511786,;	A	ENSG00000049656	ENST00000320895	Transcript	synonymous_variant	1270	1012	338	L	Ctg/Ttg	.	.	.	-1	CLPTM1L	HGNC	24308	protein_coding	YES	CCDS3862.1	ENSP00000313854	CLP1L_HUMAN	B3KY18_HUMAN	UPI00000707DF	.	.	.	9/17	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR21347:SF1,hmmpanther:PTHR21347,Pfam_domain:PF05602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAACAGAAAGA	.	2	ESCA
SEC24A	0	.	GRCh37	5	134007552	134007552	+	Missense_Mutation	SNP	G	G	A	rs769794390	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.793G>A	p.Glu265Lys	p.E265K	ENST00000398844	4/23	81	67	14	75	75	0	SEC24A,missense_variant,p.Glu265Lys,ENST00000322887,;SEC24A,missense_variant,p.Glu265Lys,ENST00000398844,;	A	ENSG00000113615	ENST00000398844	Transcript	missense_variant	1081	793	265	E/K	Gag/Aag	rs769794390	.	.	1	SEC24A	HGNC	10703	protein_coding	YES	CCDS43363.1	ENSP00000381823	SC24A_HUMAN	.	UPI0000185FF9	.	tolerated(0.45)	benign(0.047)	4/23	.	hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACGACGAGATT	.	5	ESCA
DNAH5	0	.	GRCh37	5	13868052	13868052	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3884A>C	p.Glu1295Ala	p.E1295A	ENST00000265104	25/79	188	180	7	32	32	0	DNAH5,missense_variant,p.Glu1295Ala,ENST00000265104,;CTB-51A17.1,intron_variant,,ENST00000503244,;	G	ENSG00000039139	ENST00000265104	Transcript	missense_variant	3989	3884	1295	E/A	gAg/gCg	.	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.292)	25/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CTATCTCTTCC	.	2	ESCA
DNAH5	0	.	GRCh37	5	13922323	13922323	+	Missense_Mutation	SNP	C	C	T	rs752339132	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.553G>A	p.Glu185Lys	p.E185K	ENST00000265104	5/79	146	139	7	37	37	0	DNAH5,missense_variant,p.Glu185Lys,ENST00000265104,;DNAH5,non_coding_transcript_exon_variant,,ENST00000508040,;	T	ENSG00000039139	ENST00000265104	Transcript	missense_variant	658	553	185	E/K	Gag/Aag	rs752339132,COSM3609258	.	.	-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	DYH5_HUMAN	O95496_HUMAN	UPI0000110101	.	.	benign(0.305)	5/79	.	hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF240	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	GAGCTCGCCCC	byFrequency	2	ESCA
CD14	0	.	GRCh37	5	140011383	140011383	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*58C>T	.	.	ENST00000302014	2/2	46	37	9	41	41	0	CD14,3_prime_UTR_variant,,ENST00000401743,;CD14,3_prime_UTR_variant,,ENST00000302014,;CD14,downstream_gene_variant,,ENST00000512545,;CD14,downstream_gene_variant,,ENST00000498971,;CD14,downstream_gene_variant,,ENST00000519715,;	A	ENSG00000170458	ENST00000302014	Transcript	3_prime_UTR_variant	1816	.	.	.	.	.	.	.	-1	CD14	HGNC	1628	protein_coding	YES	CCDS4232.1	ENSP00000304236	CD14_HUMAN	E7EVL5_HUMAN,D6RFL4_HUMAN,D6RD81_HUMAN	UPI000004A918	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTCCTGACGGG	.	5	ESCA
PCDHGA1	0	.	GRCh37	5	140710522	140710522	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.271G>C	p.Asp91His	p.D91H	ENST00000517417	1/4	31	26	4	27	27	0	PCDHGA1,missense_variant,p.Asp91His,ENST00000517417,;PCDHGA1,missense_variant,p.Asp91His,ENST00000378105,;AC005618.6,downstream_gene_variant,,ENST00000606901,;AC005618.6,downstream_gene_variant,,ENST00000606674,;	C	ENSG00000204956	ENST00000517417	Transcript	missense_variant	271	271	91	D/H	Gac/Cac	COSM735956,COSM735957	.	.	1	PCDHGA1	HGNC	8696	protein_coding	YES	CCDS54922.1	ENSP00000431083	PCDG1_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI0000070596	.	deleterious_low_confidence(0)	probably_damaging(0.995)	1/4	.	Prints_domain:PR00205,Superfamily_domains:SSF49313,SMART_domains:SM00112,Pfam_domain:PF08266,Gene3D:2.60.40.60,hmmpanther:PTHR24028:SF108,hmmpanther:PTHR24028,PROSITE_profiles:PS50268	.	.	.	.	.	.	.	.	.	.	1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.A87V|c.260C>T|3,BUFFER|p.A87V|c.260C>T|3	RADIA|MUTECT|MUSE|VARSCANS	GGATAGACCGG	.	4	ESCA
PCDHGA3	0	.	GRCh37	5	140723799	140723799	+	Missense_Mutation	SNP	G	G	A	rs762455729	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.199G>A	p.Val67Ile	p.V67I	ENST00000253812	1/4	38	32	6	49	49	0	PCDHGA3,missense_variant,p.Val67Ile,ENST00000253812,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA2,downstream_gene_variant,,ENST00000528330,;	A	ENSG00000254245	ENST00000253812	Transcript	missense_variant	199	199	67	V/I	Gtc/Atc	rs762455729,COSM1595036,COSM360106,COSM1063015	.	.	1	PCDHGA3	HGNC	8701	protein_coding	YES	CCDS47290.1	ENSP00000253812	PCDG3_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI0000161C1A	.	tolerated_low_confidence(0.12)	benign(0.147)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF75,Gene3D:2.60.40.60,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	0,1,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE	GCATCGTCTCC	.	3	ESCA
PCDHGA9	0	.	GRCh37	5	140783516	140783516	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.997G>C	p.Val333Leu	p.V333L	ENST00000573521	1/4	30	26	3	54	54	0	PCDHGA9,missense_variant,p.Val333Leu,ENST00000573521,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGB6,upstream_gene_variant,,ENST00000520790,;	C	ENSG00000261934	ENST00000573521	Transcript	missense_variant	997	997	333	V/L	Gtg/Ctg	.	.	.	1	PCDHGA9	HGNC	8707	protein_coding	YES	CCDS58981.1	ENSP00000460274	PCDG9_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI00000721C3	.	deleterious_low_confidence(0.05)	benign(0.396)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF86,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|VARSCANS	CAAAAGTGCTC	.	3	ESCA
PCDHGB7	0	.	GRCh37	5	140798107	140798107	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.681G>C	p.Gln227His	p.Q227H	ENST00000398594	1/4	59	53	6	76	76	0	PCDHGB7,missense_variant,p.Gln227His,ENST00000398594,;PCDHGB6,intron_variant,,ENST00000520790,;PCDHGA3,intron_variant,,ENST00000253812,;PCDHGA1,intron_variant,,ENST00000517417,;PCDHGA7,intron_variant,,ENST00000518325,;PCDHGA10,intron_variant,,ENST00000398610,;PCDHGB1,intron_variant,,ENST00000523390,;PCDHGA5,intron_variant,,ENST00000518069,;PCDHGA8,intron_variant,,ENST00000398604,;PCDHGB3,intron_variant,,ENST00000576222,;PCDHGA4,intron_variant,,ENST00000571252,;PCDHGA2,intron_variant,,ENST00000394576,;PCDHGA6,intron_variant,,ENST00000517434,;PCDHGB4,intron_variant,,ENST00000519479,;PCDHGA9,intron_variant,,ENST00000573521,;PCDHGB2,intron_variant,,ENST00000522605,;PCDHGA11,upstream_gene_variant,,ENST00000398587,;PCDHGA11,upstream_gene_variant,,ENST00000518882,;	C	ENSG00000254122	ENST00000398594	Transcript	missense_variant	681	681	227	Q/H	caG/caC	.	.	.	1	PCDHGB7	HGNC	8714	protein_coding	YES	CCDS47293.1	ENSP00000381594	PCDGJ_HUMAN	Q9UKW1_HUMAN,Q9BT64_HUMAN	UPI000007141F	.	tolerated(0.12)	benign(0.033)	1/4	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF113,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCTCAGATAAG	.	4	ESCA
SLC6A3	0	.	GRCh37	5	1422047	1422047	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.736C>G	p.Leu246Val	p.L246V	ENST00000270349	5/15	111	98	12	20	20	0	SLC6A3,missense_variant,p.Leu246Val,ENST00000270349,;SLC6A3,missense_variant,p.Leu172Val,ENST00000513308,;SLC6A3,missense_variant,p.Leu246Val,ENST00000453492,;	C	ENSG00000142319	ENST00000270349	Transcript	missense_variant	864	736	246	L/V	Ctg/Gtg	.	.	.	-1	SLC6A3	HGNC	11049	protein_coding	YES	CCDS3863.1	ENSP00000270349	SC6A3_HUMAN	Q6LC27_HUMAN,H0YBA7_HUMAN	UPI000013548F	.	tolerated(0.61)	benign(0.026)	5/15	.	Transmembrane_helices:TMhelix,Superfamily_domains:0053687,Pfam_domain:PF00209,hmmpanther:PTHR11616:SF38,hmmpanther:PTHR11616,PROSITE_profiles:PS50267	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCAGCACCA	.	4	ESCA
TRIO	0	.	GRCh37	5	14369614	14369614	+	Silent	SNP	G	G	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3198G>A	p.%3D	p.Q1066Q	ENST00000344204	18/57	133	120	12	35	35	0	TRIO,synonymous_variant,p.%3D,ENST00000537187,;TRIO,synonymous_variant,p.%3D,ENST00000509967,;TRIO,synonymous_variant,p.%3D,ENST00000344204,;TRIO,synonymous_variant,p.%3D,ENST00000513206,;TRIO,synonymous_variant,p.%3D,ENST00000512070,;TRIO,non_coding_transcript_exon_variant,,ENST00000515144,;	A	ENSG00000038382	ENST00000344204	Transcript	synonymous_variant	3222	3198	1066	Q	caG/caA	COSM1329008	.	.	1	TRIO	HGNC	12303	protein_coding	YES	CCDS3883.1	ENSP00000339299	TRIO_HUMAN	.	UPI000034ECE6	.	.	.	18/57	.	hmmpanther:PTHR22826:SF104,hmmpanther:PTHR22826	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	GAGCAGAAGGA	.	3	ESCA
PPP2R2B	0	.	GRCh37	5	145972589	145972589	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1006T>C	p.Tyr336His	p.Y336H	ENST00000336640	8/9	44	36	8	38	38	0	PPP2R2B,missense_variant,p.Tyr399His,ENST00000394414,;PPP2R2B,missense_variant,p.Tyr322His,ENST00000508545,;PPP2R2B,missense_variant,p.Tyr339His,ENST00000504198,;PPP2R2B,missense_variant,p.Tyr333His,ENST00000394411,;PPP2R2B,missense_variant,p.Tyr333His,ENST00000453001,;PPP2R2B,missense_variant,p.Tyr391His,ENST00000394409,;PPP2R2B,missense_variant,p.Tyr322His,ENST00000394410,;PPP2R2B,missense_variant,p.Tyr42His,ENST00000512984,;PPP2R2B,missense_variant,p.Tyr333His,ENST00000356826,;PPP2R2B,missense_variant,p.Tyr333His,ENST00000394413,;PPP2R2B,missense_variant,p.Tyr336His,ENST00000336640,;CTB-99A3.1,intron_variant,,ENST00000512730,;PPP2R2B,non_coding_transcript_exon_variant,,ENST00000530902,;PPP2R2B,3_prime_UTR_variant,,ENST00000512639,;	G	ENSG00000156475	ENST00000336640	Transcript	missense_variant	1237	1006	336	Y/H	Tat/Cat	.	.	.	-1	PPP2R2B	HGNC	9305	protein_coding	YES	CCDS4283.1	ENSP00000336591	2ABB_HUMAN	.	UPI0000026156	.	deleterious(0.04)	benign(0.351)	8/9	.	hmmpanther:PTHR11871:SF1,hmmpanther:PTHR11871,Gene3D:2.130.10.10,PIRSF_domain:PIRSF037309,Superfamily_domains:SSF50978,Prints_domain:PR00600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATAGAGGG	.	5	ESCA
CYFIP2	0	.	GRCh37	5	156752515	156752515	+	Silent	SNP	C	C	G	rs367974123	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1773C>G	p.%3D	p.L591L	ENST00000521420	16/30	72	58	14	46	46	0	CYFIP2,synonymous_variant,p.%3D,ENST00000521420,;CYFIP2,synonymous_variant,p.%3D,ENST00000377576,;CYFIP2,synonymous_variant,p.%3D,ENST00000541131,;CYFIP2,synonymous_variant,p.%3D,ENST00000318218,;CYFIP2,synonymous_variant,p.%3D,ENST00000435847,;CYFIP2,synonymous_variant,p.%3D,ENST00000347377,;CYFIP2,synonymous_variant,p.%3D,ENST00000522463,;CYFIP2,5_prime_UTR_variant,,ENST00000442283,;CYFIP2,non_coding_transcript_exon_variant,,ENST00000520960,;CYFIP2,3_prime_UTR_variant,,ENST00000523969,;CYFIP2,3_prime_UTR_variant,,ENST00000519153,;CYFIP2,3_prime_UTR_variant,,ENST00000523119,;CYFIP2,3_prime_UTR_variant,,ENST00000517753,;CYFIP2,3_prime_UTR_variant,,ENST00000520759,;CYFIP2,upstream_gene_variant,,ENST00000518555,;CYFIP2,upstream_gene_variant,,ENST00000520424,;	G	ENSG00000055163	ENST00000521420	Transcript	synonymous_variant	1864	1773	591	L	ctC/ctG	rs367974123,COSM3393375,COSM3393373,COSM3393374	.	.	1	CYFIP2	HGNC	13760	protein_coding	YES	.	ENSP00000430904	.	E7EVJ5_HUMAN	UPI0001D55E6B	.	.	.	16/30	.	hmmpanther:PTHR12195,hmmpanther:PTHR12195:SF1,Pfam_domain:PF05994,Prints_domain:PR01698	.	.	.	.	.	.	.	G:0	G:0.0001	.	0,1,1,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GACCTCTCCCA	byFrequency|byCluster	5	ESCA
ZNF622	0	.	GRCh37	5	16463720	16463720	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757G>A	p.Asp253Asn	p.D253N	ENST00000308683	2/6	107	94	13	33	33	0	ZNF622,missense_variant,p.Asp253Asn,ENST00000308683,;	T	ENSG00000173545	ENST00000308683	Transcript	missense_variant	884	757	253	D/N	Gac/Aac	.	.	.	-1	ZNF622	HGNC	30958	protein_coding	YES	CCDS3886.1	ENSP00000310042	ZN622_HUMAN	.	UPI0000072102	.	tolerated(0.07)	probably_damaging(0.923)	2/6	.	hmmpanther:PTHR13182,Pfam_domain:PF12756,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GCAGTCCGTGA	.	4	ESCA
MXD3	0	.	GRCh37	5	176734640	176734640	+	Silent	SNP	G	G	A	rs533160184	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.570C>T	p.%3D	p.F190F	ENST00000439742	6/6	59	47	12	66	66	0	MXD3,missense_variant,p.Ser216Leu,ENST00000423571,;MXD3,synonymous_variant,p.%3D,ENST00000513063,;MXD3,synonymous_variant,p.%3D,ENST00000439742,;MXD3,intron_variant,,ENST00000427908,;RAB24,upstream_gene_variant,,ENST00000303251,;PRELID1,downstream_gene_variant,,ENST00000303204,;MXD3,downstream_gene_variant,,ENST00000502529,;MXD3,downstream_gene_variant,,ENST00000513169,;PRELID1,downstream_gene_variant,,ENST00000503853,;RAB24,upstream_gene_variant,,ENST00000504395,;PRELID1,downstream_gene_variant,,ENST00000503216,;RAB24,upstream_gene_variant,,ENST00000303270,;RAB24,upstream_gene_variant,,ENST00000393611,;PRELID1,downstream_gene_variant,,ENST00000502670,;MXD3,non_coding_transcript_exon_variant,,ENST00000503782,;MXD3,intron_variant,,ENST00000509339,;MXD3,intron_variant,,ENST00000503473,;RAB24,upstream_gene_variant,,ENST00000393610,;RAB24,upstream_gene_variant,,ENST00000478234,;RAB24,upstream_gene_variant,,ENST00000471466,;PRELID1,downstream_gene_variant,,ENST00000510797,;PRELID1,downstream_gene_variant,,ENST00000504594,;PRELID1,downstream_gene_variant,,ENST00000511309,;RAB24,upstream_gene_variant,,ENST00000512758,;PRELID1,downstream_gene_variant,,ENST00000510701,;RAB24,upstream_gene_variant,,ENST00000495458,;	A	ENSG00000213347	ENST00000439742	Transcript	synonymous_variant	1049	570	190	F	ttC/ttT	rs533160184,COSM1319213	.	.	-1	MXD3	HGNC	14008	protein_coding	YES	CCDS4416.1	ENSP00000401867	MAD3_HUMAN	D6RD21_HUMAN	UPI00000437EB	.	.	.	6/6	.	hmmpanther:PTHR11969:SF6,hmmpanther:PTHR11969	A:0.0002	A:0	A:0	.	A:0	A:0.001	A:0	.	.	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCGACGAAGCC	by1000G	5	ESCA
RMND5B	0	.	GRCh37	5	177573128	177573128	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.708G>A	p.Met236Ile	p.M236I	ENST00000515098	9/12	41	33	7	57	57	0	RMND5B,missense_variant,p.Met236Ile,ENST00000515098,;RMND5B,missense_variant,p.Met236Ile,ENST00000313386,;RMND5B,missense_variant,p.Met223Ile,ENST00000542098,;NHP2,downstream_gene_variant,,ENST00000511078,;NHP2,downstream_gene_variant,,ENST00000314397,;RMND5B,downstream_gene_variant,,ENST00000502814,;RMND5B,downstream_gene_variant,,ENST00000508647,;NHP2,downstream_gene_variant,,ENST00000274606,;NHP2,downstream_gene_variant,,ENST00000502263,;NHP2,downstream_gene_variant,,ENST00000514354,;RMND5B,downstream_gene_variant,,ENST00000507457,;RMND5B,non_coding_transcript_exon_variant,,ENST00000513162,;RMND5B,non_coding_transcript_exon_variant,,ENST00000507575,;RMND5B,non_coding_transcript_exon_variant,,ENST00000515360,;RMND5B,non_coding_transcript_exon_variant,,ENST00000507937,;RMND5B,downstream_gene_variant,,ENST00000512811,;RMND5B,downstream_gene_variant,,ENST00000512663,;	A	ENSG00000145916	ENST00000515098	Transcript	missense_variant	1059	708	236	M/I	atG/atA	.	.	.	1	RMND5B	HGNC	26181	protein_coding	YES	CCDS4431.1	ENSP00000420875	RMD5B_HUMAN	Q659D3_HUMAN,D6RIF9_HUMAN,D6RFK1_HUMAN,D6RER3_HUMAN	UPI0000037C23	.	deleterious(0.03)	benign(0.021)	9/12	.	hmmpanther:PTHR12170,hmmpanther:PTHR12170:SF6,Pfam_domain:PF10607,SMART_domains:SM00757	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGATGATGGG	.	5	ESCA
HNRNPH1	0	.	GRCh37	5	179047895	179047895	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.395C>G	p.Ser132Ter	p.S132*	ENST00000356731	3/13	41	34	7	48	48	0	HNRNPH1,stop_gained,p.Ser132Ter,ENST00000504348,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000329433,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000510431,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000505811,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000442819,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000356731,;HNRNPH1,stop_gained,p.Ser80Ter,ENST00000519056,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000508103,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000506721,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000393432,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000513225,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000510411,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000503105,;HNRNPH1,stop_gained,p.Ser55Ter,ENST00000521790,;HNRNPH1,missense_variant,p.Gln23Glu,ENST00000521173,;HNRNPH1,intron_variant,,ENST00000523137,;HNRNPH1,downstream_gene_variant,,ENST00000503664,;HNRNPH1,upstream_gene_variant,,ENST00000523449,;HNRNPH1,upstream_gene_variant,,ENST00000523921,;HNRNPH1,downstream_gene_variant,,ENST00000515714,;HNRNPH1,downstream_gene_variant,,ENST00000521116,;HNRNPH1,upstream_gene_variant,,ENST00000511300,;HNRNPH1,downstream_gene_variant,,ENST00000522256,;HNRNPH1,upstream_gene_variant,,ENST00000523136,;HNRNPH1,downstream_gene_variant,,ENST00000515158,;HNRNPH1,upstream_gene_variant,,ENST00000519033,;HNRNPH1,splice_region_variant,,ENST00000518548,;HNRNPH1,splice_region_variant,,ENST00000524180,;HNRNPH1,non_coding_transcript_exon_variant,,ENST00000519455,;HNRNPH1,stop_gained,p.Ser79Ter,ENST00000519958,;HNRNPH1,stop_gained,p.Ser132Ter,ENST00000510678,;HNRNPH1,splice_region_variant,,ENST00000522958,;HNRNPH1,splice_region_variant,,ENST00000514332,;HNRNPH1,splice_region_variant,,ENST00000514731,;HNRNPH1,splice_region_variant,,ENST00000504779,;HNRNPH1,non_coding_transcript_exon_variant,,ENST00000519707,;HNRNPH1,non_coding_transcript_exon_variant,,ENST00000513972,;HNRNPH1,non_coding_transcript_exon_variant,,ENST00000519943,;HNRNPH1,downstream_gene_variant,,ENST00000513230,;HNRNPH1,upstream_gene_variant,,ENST00000502632,;HNRNPH1,downstream_gene_variant,,ENST00000515446,;HNRNPH1,downstream_gene_variant,,ENST00000512273,;HNRNPH1,upstream_gene_variant,,ENST00000524179,;HNRNPH1,downstream_gene_variant,,ENST00000505087,;HNRNPH1,upstream_gene_variant,,ENST00000515481,;HNRNPH1,upstream_gene_variant,,ENST00000504549,;HNRNPH1,upstream_gene_variant,,ENST00000520415,;HNRNPH1,upstream_gene_variant,,ENST00000502904,;HNRNPH1,upstream_gene_variant,,ENST00000521720,;	C	ENSG00000169045	ENST00000356731	Transcript	stop_gained	1931	395	132	S/*	tCa/tGa	.	.	.	-1	HNRNPH1	HGNC	5041	protein_coding	YES	CCDS4446.1	ENSP00000349168	HNRH1_HUMAN	Q68DG4_HUMAN,E7EQJ0_HUMAN,E5RJ94_HUMAN,E5RGH4_HUMAN,D6RIU0_HUMAN,D6RFM3_HUMAN,D6RF17_HUMAN,D6RDL0_HUMAN,D6RBM0_HUMAN,D6RAM1_HUMAN	UPI0000000C2B	.	.	.	3/13	.	PROSITE_profiles:PS50102,hmmpanther:PTHR13976:SF33,hmmpanther:PTHR13976,Pfam_domain:PF14259,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TACCTGAGAAG	.	4	ESCA
CANX	0	.	GRCh37	5	179150701	179150701	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1439G>A	p.Arg480His	p.R480H	ENST00000247461	12/15	65	59	6	48	48	0	CANX,missense_variant,p.Arg480His,ENST00000247461,;CANX,missense_variant,p.Arg515His,ENST00000415618,;CANX,missense_variant,p.Arg480His,ENST00000504734,;CANX,missense_variant,p.Arg372His,ENST00000512607,;CANX,missense_variant,p.Arg480His,ENST00000452673,;CANX,downstream_gene_variant,,ENST00000502673,;CANX,upstream_gene_variant,,ENST00000503303,;CANX,3_prime_UTR_variant,,ENST00000514032,;CANX,non_coding_transcript_exon_variant,,ENST00000505090,;	A	ENSG00000127022	ENST00000247461	Transcript	missense_variant	1639	1439	480	R/H	cGc/cAc	.	.	.	1	CANX	HGNC	1473	protein_coding	YES	CCDS4447.1	ENSP00000247461	CALX_HUMAN	D6RHJ3_HUMAN,D6RFW4_HUMAN,D6RFL1_HUMAN,D6RDP7_HUMAN,D6RB85_HUMAN,D6RAU8_HUMAN,D6RAQ8_HUMAN,B4E2T8_HUMAN	UPI000000D9F9	.	tolerated(0.42)	benign(0.015)	12/15	.	hmmpanther:PTHR11073,hmmpanther:PTHR11073:SF11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGAGCGCCCGT	.	2	ESCA
PRDM9	0	.	GRCh37	5	23527657	23527657	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2460C>T	p.%3D	p.L820L	ENST00000296682	11/11	101	88	13	61	61	0	PRDM9,synonymous_variant,p.%3D,ENST00000296682,;	T	ENSG00000164256	ENST00000296682	Transcript	synonymous_variant	2642	2460	820	L	ctC/ctT	.	.	.	1	PRDM9	HGNC	13994	protein_coding	YES	CCDS43307.1	ENSP00000296682	PRDM9_HUMAN	D6RD68_HUMAN,D2KI85_HUMAN,D2E453_HUMAN	UPI00006C9E90	.	.	.	11/11	.	Superfamily_domains:SSF57667,SMART_domains:SM00355,Gene3D:3.30.160.60,Pfam_domain:PF13465,PROSITE_patterns:PS00028,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF21,PROSITE_profiles:PS50157	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTCCTCAGACA	.	4	ESCA
RAI14	0	.	GRCh37	5	34821951	34821951	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1118T>C	p.Leu373Ser	p.L373S	ENST00000515799	16/20	44	36	8	37	37	0	RAI14,missense_variant,p.Leu362Ser,ENST00000506376,;RAI14,missense_variant,p.Leu370Ser,ENST00000265109,;RAI14,missense_variant,p.Leu363Ser,ENST00000397449,;RAI14,missense_variant,p.Leu373Ser,ENST00000515799,;RAI14,missense_variant,p.Leu370Ser,ENST00000428746,;RAI14,missense_variant,p.Leu341Ser,ENST00000512629,;RAI14,missense_variant,p.Leu370Ser,ENST00000503673,;RAI14,upstream_gene_variant,,ENST00000513772,;RAI14,downstream_gene_variant,,ENST00000508777,;RAI14,upstream_gene_variant,,ENST00000507883,;	C	ENSG00000039560	ENST00000515799	Transcript	missense_variant	1610	1118	373	L/S	tTa/tCa	.	.	.	1	RAI14	HGNC	14873	protein_coding	YES	CCDS54839.1	ENSP00000427123	RAI14_HUMAN	B3KMZ9_HUMAN	UPI00001B296B	.	deleterious(0.01)	possibly_damaging(0.868)	16/20	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24129	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAATTACAGG	.	5	ESCA
C5orf42	0	.	GRCh37	5	37201793	37201793	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3407C>G	p.Ser1136Cys	p.S1136C	ENST00000425232	19/52	61	48	13	45	45	0	C5orf42,missense_variant,p.Ser17Cys,ENST00000274258,;C5orf42,missense_variant,p.Ser1136Cys,ENST00000508244,;C5orf42,missense_variant,p.Ser1136Cys,ENST00000425232,;C5orf42,missense_variant,p.Ser184Cys,ENST00000514429,;C5orf42,missense_variant,p.Ser141Cys,ENST00000509849,;C5orf42,downstream_gene_variant,,ENST00000505431,;	C	ENSG00000197603	ENST00000425232	Transcript	missense_variant	3638	3407	1136	S/C	tCt/tGt	.	.	.	-1	C5orf42	HGNC	25801	protein_coding	YES	CCDS34146.2	ENSP00000389014	CE042_HUMAN	.	UPI0001AAB3EA	.	tolerated(0.06)	possibly_damaging(0.696)	19/52	.	hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGCAGAGTCT	.	5	ESCA
CENPH	0	.	GRCh37	5	68485511	68485511	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.50G>C	p.Gly17Ala	p.G17A	ENST00000283006	1/9	80	60	19	52	52	0	CENPH,missense_variant,p.Gly17Ala,ENST00000515001,;CENPH,missense_variant,p.Gly17Ala,ENST00000283006,;CENPH,upstream_gene_variant,,ENST00000502689,;CENPH,missense_variant,p.Gly17Ala,ENST00000513575,;CENPH,non_coding_transcript_exon_variant,,ENST00000514753,;	C	ENSG00000153044	ENST00000283006	Transcript	missense_variant	137	50	17	G/A	gGa/gCa	.	.	.	1	CENPH	HGNC	17268	protein_coding	YES	CCDS3998.1	ENSP00000283006	CENPH_HUMAN	.	UPI000006F610	.	tolerated(0.16)	benign(0.017)	1/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCGGAGGGG	.	5	ESCA
MRPS36	0	.	GRCh37	5	68524143	68524143	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.223G>A	p.Glu75Lys	p.E75K	ENST00000256441	3/4	79	56	22	71	71	0	MRPS36,missense_variant,p.Glu10Lys,ENST00000602380,;MRPS36,missense_variant,p.Glu10Lys,ENST00000512880,;MRPS36,missense_variant,p.Glu75Lys,ENST00000256441,;MRPS36,non_coding_transcript_exon_variant,,ENST00000507022,;MRPS36,downstream_gene_variant,,ENST00000503793,;	A	ENSG00000134056	ENST00000256441	Transcript	missense_variant	293	223	75	E/K	Gaa/Aaa	.	.	.	1	MRPS36	HGNC	16631	protein_coding	YES	CCDS34174.1	ENSP00000256441	RT36_HUMAN	D6R941_HUMAN	UPI0000052862	.	deleterious(0.01)	possibly_damaging(0.897)	3/4	.	hmmpanther:PTHR31601,hmmpanther:PTHR31601:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGCAGAAATA	.	5	ESCA
RP11-136K7.2	0	.	GRCh37	5	70741606	70741606	+	RNA	DEL	C	C	-	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.564delG	.	.	ENST00000502659	1/2	53	43	10	32	32	0	RP11-136K7.2,non_coding_transcript_exon_variant,,ENST00000517705,;RP11-136K7.2,non_coding_transcript_exon_variant,,ENST00000502659,;RP11-136K7.1,intron_variant,,ENST00000510180,;	-	ENSG00000250387	ENST00000502659	Transcript	non_coding_transcript_exon_variant	564	.	.	.	.	.	.	.	-1	RP11-136K7.2	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	1/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	GTTGAGCTCCTC	.	3	ESCA
BDP1	0	.	GRCh37	5	70840330	70840330	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.6559G>A	p.Glu2187Lys	p.E2187K	ENST00000358731	31/39	67	50	16	56	56	0	BDP1,missense_variant,p.Glu2187Lys,ENST00000358731,;BDP1,missense_variant,p.Glu323Lys,ENST00000380675,;BDP1,missense_variant,p.Glu209Lys,ENST00000525844,;BDP1,missense_variant,p.Glu443Lys,ENST00000514903,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;	A	ENSG00000145734	ENST00000358731	Transcript	missense_variant	6822	6559	2187	E/K	Gaa/Aaa	.	.	.	1	BDP1	HGNC	13652	protein_coding	YES	CCDS43328.1	ENSP00000351575	BDP1_HUMAN	.	UPI000020CA90	.	tolerated(0.25)	possibly_damaging(0.616)	31/39	.	hmmpanther:PTHR22929:SF0,hmmpanther:PTHR22929	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAACTGAAAGG	.	5	ESCA
JMY	0	.	GRCh37	5	78620720	78620720	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3295G>C	.	.	ENST00000396137	11/11	98	80	17	132	132	0	JMY,3_prime_UTR_variant,,ENST00000396137,;JMY,non_coding_transcript_exon_variant,,ENST00000412001,;	C	ENSG00000152409	ENST00000396137	Transcript	3_prime_UTR_variant	6724	.	.	.	.	.	.	.	1	JMY	HGNC	28916	protein_coding	YES	CCDS4047.3	ENSP00000379441	JMY_HUMAN	.	UPI0000E5AC67	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCTATGTAATA	.	5	ESCA
PAPD4	0	.	GRCh37	5	78940966	78940966	+	Missense_Mutation	SNP	C	C	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.772C>A	p.Gln258Lys	p.Q258K	ENST00000453514	8/15	55	47	8	72	72	0	PAPD4,missense_variant,p.Gln254Lys,ENST00000423041,;PAPD4,missense_variant,p.Gln258Lys,ENST00000504233,;PAPD4,missense_variant,p.Gln258Lys,ENST00000453514,;PAPD4,missense_variant,p.Gln258Lys,ENST00000296783,;PAPD4,missense_variant,p.Gln258Lys,ENST00000428308,;PAPD4,upstream_gene_variant,,ENST00000504982,;PAPD4,upstream_gene_variant,,ENST00000513735,;PAPD4,non_coding_transcript_exon_variant,,ENST00000509227,;	A	ENSG00000164329	ENST00000453514	Transcript	missense_variant	1465	772	258	Q/K	Cag/Aag	COSM1754343	.	.	1	PAPD4	HGNC	26776	protein_coding	YES	CCDS4048.1	ENSP00000397563	GLD2_HUMAN	.	UPI000013E386	.	deleterious(0.03)	probably_damaging(0.958)	8/15	.	hmmpanther:PTHR12271,Gene3D:3.30.460.10,Superfamily_domains:SSF81301	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GACCTCAGCTG	.	4	ESCA
GPR98	0	.	GRCh37	5	89949169	89949169	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3778G>C	p.Glu1260Gln	p.E1260Q	ENST00000405460	20/90	60	50	9	39	39	0	GPR98,missense_variant,p.Glu1260Gln,ENST00000405460,;GPR98,missense_variant,p.Glu849Gln,ENST00000504142,;	C	ENSG00000164199	ENST00000405460	Transcript	missense_variant	3874	3778	1260	E/Q	Gaa/Caa	.	.	.	1	GPR98	HGNC	17416	protein_coding	YES	CCDS47246.1	ENSP00000384582	GPR98_HUMAN	.	UPI00002127A7	.	.	possibly_damaging(0.727)	20/90	.	Superfamily_domains:SSF141072,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTGAAGAT	.	5	ESCA
SIM1	0	.	GRCh37	6	100838633	100838633	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1905G>C	p.Gln635His	p.Q635H	ENST00000369208	12/12	24	20	4	21	21	0	SIM1,missense_variant,p.Gln635His,ENST00000369208,;SIM1,missense_variant,p.Gln635His,ENST00000262901,;SIM1,downstream_gene_variant,,ENST00000505753,;	G	ENSG00000112246	ENST00000369208	Transcript	missense_variant	2688	1905	635	Q/H	caG/caC	.	.	.	-1	SIM1	HGNC	10882	protein_coding	YES	CCDS5045.1	ENSP00000358210	SIM1_HUMAN	.	UPI000013D355	.	tolerated_low_confidence(0.37)	benign(0.011)	12/12	.	PROSITE_profiles:PS51302,hmmpanther:PTHR23043:SF22,hmmpanther:PTHR23043,Pfam_domain:PF06621	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCTCTCTGCTG	.	4	ESCA
PRDM1	0	.	GRCh37	6	106553015	106553015	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.980C>G	p.Ser327Cys	p.S327C	ENST00000369096	5/7	19	14	5	19	19	0	PRDM1,missense_variant,p.Ser327Cys,ENST00000369096,;PRDM1,missense_variant,p.Ser291Cys,ENST00000369091,;PRDM1,missense_variant,p.Ser193Cys,ENST00000369089,;PRDM1,downstream_gene_variant,,ENST00000450060,;RP1-134E15.3,downstream_gene_variant,,ENST00000602426,;	G	ENSG00000057657	ENST00000369096	Transcript	missense_variant	1214	980	327	S/C	tCc/tGc	.	.	.	1	PRDM1	HGNC	9346	protein_coding	YES	CCDS5054.2	ENSP00000358092	PRDM1_HUMAN	Q5T4E8_HUMAN,B2REA5_HUMAN	UPI0000D49069	.	deleterious(0.02)	possibly_damaging(0.841)	5/7	.	Low_complexity_(Seg):seg,hmmpanther:PTHR11389,hmmpanther:PTHR11389:SF339,PIRSF_domain:PIRSF013212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCGCTCCCCCA	.	4	ESCA
TUBE1	0	.	GRCh37	6	112408695	112408695	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-58G>C	.	.	ENST00000368662	1/12	19	15	4	16	16	0	TUBE1,5_prime_UTR_variant,,ENST00000368662,;FAM229B,upstream_gene_variant,,ENST00000604268,;FAM229B,upstream_gene_variant,,ENST00000368656,;TUBE1,upstream_gene_variant,,ENST00000441191,;TUBE1,upstream_gene_variant,,ENST00000604814,;TUBE1,5_prime_UTR_variant,,ENST00000604743,;TUBE1,5_prime_UTR_variant,,ENST00000605457,;TUBE1,non_coding_transcript_exon_variant,,ENST00000603722,;TUBE1,non_coding_transcript_exon_variant,,ENST00000603621,;TUBE1,upstream_gene_variant,,ENST00000368657,;TUBE1,upstream_gene_variant,,ENST00000604967,;	G	ENSG00000074935	ENST00000368662	Transcript	5_prime_UTR_variant	22	.	.	.	.	.	.	.	-1	TUBE1	HGNC	20775	protein_coding	YES	CCDS5100.1	ENSP00000357651	TBE_HUMAN	.	UPI0000136A4E	.	.	.	1/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TCCCCCAGCAA	.	2	ESCA
PTPRK	0	.	GRCh37	6	128388853	128388853	+	Silent	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1968C>A	p.%3D	p.V656V	ENST00000368213	12/31	46	38	8	33	33	0	PTPRK,synonymous_variant,p.%3D,ENST00000532331,;PTPRK,synonymous_variant,p.%3D,ENST00000368226,;PTPRK,synonymous_variant,p.%3D,ENST00000368215,;PTPRK,synonymous_variant,p.%3D,ENST00000368207,;PTPRK,synonymous_variant,p.%3D,ENST00000368210,;PTPRK,synonymous_variant,p.%3D,ENST00000368227,;PTPRK,synonymous_variant,p.%3D,ENST00000368213,;PTPRK,upstream_gene_variant,,ENST00000415046,;RP11-103C16.2,intron_variant,,ENST00000417390,;PTPRK,non_coding_transcript_exon_variant,,ENST00000524534,;PTPRK,non_coding_transcript_exon_variant,,ENST00000524481,;PTPRK,upstream_gene_variant,,ENST00000434424,;PTPRK,3_prime_UTR_variant,,ENST00000531050,;	T	ENSG00000152894	ENST00000368213	Transcript	synonymous_variant	2193	1968	656	V	gtC/gtA	.	.	.	-1	PTPRK	HGNC	9674	protein_coding	YES	CCDS47473.1	ENSP00000357196	PTPRK_HUMAN	.	UPI0001747A04	.	.	.	12/31	.	hmmpanther:PTHR19134:SF209,hmmpanther:PTHR19134	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TATGTGACAGG	.	5	ESCA
CTAGE9	0	.	GRCh37	6	132030636	132030636	+	Missense_Mutation	SNP	C	C	G	rs774912126	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1522G>C	p.Asp508His	p.D508H	ENST00000314099	1/1	177	141	36	147	147	0	CTAGE9,missense_variant,p.Asp508His,ENST00000314099,;ENPP3,intron_variant,,ENST00000358229,;ENPP3,intron_variant,,ENST00000357639,;ENPP3,intron_variant,,ENST00000414305,;	G	ENSG00000236761	ENST00000314099	Transcript	missense_variant	1571	1522	508	D/H	Gat/Cat	rs774912126,COSM1595844,COSM1595843	.	.	-1	CTAGE9	HGNC	37275	protein_coding	YES	CCDS47475.1	ENSP00000395587	CTGE9_HUMAN	.	UPI0000073347	.	deleterious(0.03)	possibly_damaging(0.829)	1/1	.	hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF39	.	.	.	.	.	.	.	.	.	.	0,1,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACATCGAGTG	byFrequency	4	ESCA
HBS1L	0	.	GRCh37	6	135376021	135376021	+	5'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-192G>C	.	.	ENST00000367837	1/18	17	12	5	23	23	0	HBS1L,5_prime_UTR_variant,,ENST00000367837,;HBS1L,5_prime_UTR_variant,,ENST00000367822,;HBS1L,intron_variant,,ENST00000529882,;HBS1L,upstream_gene_variant,,ENST00000415177,;HBS1L,upstream_gene_variant,,ENST00000367824,;HBS1L,upstream_gene_variant,,ENST00000367820,;HBS1L,upstream_gene_variant,,ENST00000524715,;HBS1L,upstream_gene_variant,,ENST00000445176,;HBS1L,upstream_gene_variant,,ENST00000525067,;HBS1L,upstream_gene_variant,,ENST00000367826,;HBS1L,upstream_gene_variant,,ENST00000314674,;HBS1L,upstream_gene_variant,,ENST00000533274,;CTA-212D2.2,upstream_gene_variant,,ENST00000447508,;HBS1L,upstream_gene_variant,,ENST00000526100,;	G	ENSG00000112339	ENST00000367837	Transcript	5_prime_UTR_variant	16	.	.	.	.	.	.	.	-1	HBS1L	HGNC	4834	protein_coding	YES	CCDS5173.1	ENSP00000356811	HBS1L_HUMAN	E9PS53_HUMAN,E9PHZ9_HUMAN,D9YZV0_HUMAN,B7Z524_HUMAN,B7Z1K2_HUMAN	UPI00000372EA	.	.	.	1/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGGTCACTGT	.	2	ESCA
BCLAF1	0	.	GRCh37	6	136599709	136599709	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310A>T	p.Ser104Cys	p.S104C	ENST00000531224	4/13	121	114	7	70	70	0	BCLAF1,missense_variant,p.Ser102Cys,ENST00000392348,;BCLAF1,missense_variant,p.Ser104Cys,ENST00000529826,;BCLAF1,missense_variant,p.Ser102Cys,ENST00000353331,;BCLAF1,missense_variant,p.Ser104Cys,ENST00000531224,;BCLAF1,missense_variant,p.Ser104Cys,ENST00000530767,;BCLAF1,missense_variant,p.Ser104Cys,ENST00000527536,;BCLAF1,missense_variant,p.Ser102Cys,ENST00000527759,;BCLAF1,missense_variant,p.Ser102Cys,ENST00000534269,;BCLAF1,missense_variant,p.Ser104Cys,ENST00000527613,;BCLAF1,missense_variant,p.Ser102Cys,ENST00000530429,;BCLAF1,missense_variant,p.Ser104Cys,ENST00000532384,;BCLAF1,upstream_gene_variant,,ENST00000533621,;BCLAF1,downstream_gene_variant,,ENST00000528229,;	A	ENSG00000029363	ENST00000531224	Transcript	missense_variant	563	310	104	S/C	Agt/Tgt	.	.	.	-1	BCLAF1	HGNC	16863	protein_coding	YES	CCDS5177.1	ENSP00000435210	BCLF1_HUMAN	B0AZU3_HUMAN	UPI000006FCE7	.	deleterious_low_confidence(0)	benign(0.341)	4/13	.	hmmpanther:PTHR15268,hmmpanther:PTHR15268:SF4,Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AGGACTCCTAG	.	2	ESCA
KDM1B	0	.	GRCh37	6	18222817	18222817	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*594C>G	.	.	ENST00000297792	18/18	70	42	28	77	77	0	KDM1B,3_prime_UTR_variant,,ENST00000297792,;KDM1B,3_prime_UTR_variant,,ENST00000388870,;KDM1B,3_prime_UTR_variant,,ENST00000397244,;KDM1B,downstream_gene_variant,,ENST00000546309,;KDM1B,downstream_gene_variant,,ENST00000449850,;DEK,downstream_gene_variant,,ENST00000507591,;DEK,downstream_gene_variant,,ENST00000244776,;DEK,downstream_gene_variant,,ENST00000397239,;DEK,downstream_gene_variant,,ENST00000505224,;	G	ENSG00000165097	ENST00000297792	Transcript	3_prime_UTR_variant	2544	.	.	.	.	.	.	.	1	KDM1B	HGNC	21577	protein_coding	YES	CCDS34343.1	ENSP00000297792	KDM1B_HUMAN	Q08EI0_HUMAN	UPI000023739E	.	.	.	18/18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGTTCAAAAG	.	5	ESCA
BTN3A2	0	.	GRCh37	6	26376878	26376878	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*156G>C	.	.	ENST00000356386	11/11	65	56	8	76	76	0	BTN3A2,3_prime_UTR_variant,,ENST00000356386,;BTN3A2,downstream_gene_variant,,ENST00000396934,;BTN3A2,downstream_gene_variant,,ENST00000508906,;BTN3A2,downstream_gene_variant,,ENST00000527639,;BTN3A2,downstream_gene_variant,,ENST00000527417,;BTN3A2,downstream_gene_variant,,ENST00000377708,;BTN3A2,downstream_gene_variant,,ENST00000527422,;BTN3A2,downstream_gene_variant,,ENST00000396948,;BTN3A2,downstream_gene_variant,,ENST00000524682,;BTN3A2,downstream_gene_variant,,ENST00000532627,;BTN3A2,downstream_gene_variant,,ENST00000532994,;BTN3A2,downstream_gene_variant,,ENST00000604202,;BTN3A2,downstream_gene_variant,,ENST00000532294,;BTN3A2,downstream_gene_variant,,ENST00000531055,;	C	ENSG00000186470	ENST00000356386	Transcript	3_prime_UTR_variant	1349	.	.	.	.	.	.	.	1	BTN3A2	HGNC	1139	protein_coding	YES	CCDS4605.1	ENSP00000348751	BT3A2_HUMAN	E9PRX1_HUMAN,E9PRR1_HUMAN	UPI000006E484	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTGCTGAGGAG	.	5	ESCA
POM121L2	0	.	GRCh37	6	27278167	27278167	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1783C>G	p.Pro595Ala	p.P595A	ENST00000444565	1/1	23	20	3	14	14	0	POM121L2,missense_variant,p.Pro595Ala,ENST00000444565,;POM121L2,missense_variant,p.Pro531Ala,ENST00000377451,;POM121L2,intron_variant,,ENST00000429945,;	C	ENSG00000158553	ENST00000444565	Transcript	missense_variant	1783	1783	595	P/A	Cct/Gct	.	.	.	-1	POM121L2	HGNC	13973	protein_coding	YES	CCDS59497.1	ENSP00000392726	.	C9J1I7_HUMAN	UPI0000198C27	.	tolerated(0.08)	benign(0.344)	1/1	.	hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GAAAGGAGCTA	.	2	ESCA
ZSCAN12	0	.	GRCh37	6	28360708	28360708	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.518C>T	p.Ser173Phe	p.S173F	ENST00000361028	3/5	56	41	14	66	66	0	ZSCAN12,missense_variant,p.Ser173Phe,ENST00000396827,;ZSCAN12,missense_variant,p.Ser173Phe,ENST00000361028,;	A	ENSG00000158691	ENST00000361028	Transcript	missense_variant	664	518	173	S/F	tCt/tTt	.	.	.	-1	ZSCAN12	HGNC	13172	protein_coding	YES	.	ENSP00000354305	ZSC12_HUMAN	.	UPI000013C353	.	deleterious(0.02)	possibly_damaging(0.466)	3/5	.	hmmpanther:PTHR23226:SF19,hmmpanther:PTHR23226	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CTGGAGATTCA	.	5	ESCA
HLA-B	0	.	GRCh37	6	31324463	31324463	+	Splice_Site	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343+2T>C	.	p.X115_splice	ENST00000412585	.	53	43	10	44	44	0	HLA-B,splice_donor_variant,,ENST00000412585,;HLA-B,splice_donor_variant,,ENST00000434333,;HLA-B,splice_donor_variant,,ENST00000474381,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;HLA-B,upstream_gene_variant,,ENST00000497377,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,;	G	ENSG00000234745	ENST00000412585	Transcript	splice_donor_variant	.	.	.	.	.	.	.	.	-1	HLA-B	HGNC	4932	protein_coding	YES	CCDS34394.1	ENSP00000399168	1B73_HUMAN,1B07_HUMAN,1B42_HUMAN,1B67_HUMAN,1B81_HUMAN,1B48_HUMAN	T1R372_HUMAN,R4QQU0_HUMAN,N0A4A9_HUMAN,N0A0K3_HUMAN,M9XMA8_HUMAN,M9PAL2_HUMAN,M9P9U8_HUMAN,M9P9C4_HUMAN,M9P9A4_HUMAN,M9P990_HUMAN,M9P8G8_HUMAN,M1FXF1_HUMAN,M1FWX2_HUMAN,M1F4D0_HUMAN,E5FQ95_HUMAN,Q9UIP1_HUMAN,Q9TQC5_HUMAN,Q9TQC2_HUMAN,Q9TPU4_HUMAN,Q9GIM0_HUMAN,Q95IE1_HUMAN,Q95HL7_HUMAN,Q8SP64_HUMAN,Q8HWQ3_HUMAN,Q861E5_HUMAN,Q861D6_HUMAN,Q861D4_HUMAN,Q7YP17_HUMAN,Q7YNX2_HUMAN,Q7JGR7_HUMAN,Q710M8_HUMAN,Q710M7_HUMAN,Q70HJ6_HUMAN,Q709M5_HUMAN,Q6ZXT6_HUMAN,Q5QR88_HUMAN,Q5QR87_HUMAN,Q5QR86_HUMAN,Q5QR85_HUMAN,Q5QR84_HUMAN,Q5QR83_HUMAN,Q5QR76_HUMAN,Q5QR73_HUMAN,Q5QR69_HUMAN,Q5QR62_HUMAN,Q5QR60_HUMAN,Q5QR59_HUMAN,Q5QR58_HUMAN,Q5QR57_HUMAN,Q5QR48_HUMAN,Q5QR47_HUMAN,Q5QR46_HUMAN,Q5QR36_HUMAN,Q5QR34_HUMAN,Q5QR33_HUMAN,Q5QR31_HUMAN,Q5F311_HUMAN,Q53ZP0_HUMAN,Q29923_HUMAN,Q29843_HUMAN,Q256S0_HUMAN,O19782_HUMAN,O19746_HUMAN,O19644_HUMAN,O19638_HUMAN,O19563_HUMAN,L0RH50_HUMAN,L0BXM2_HUMAN,K9LCN4_HUMAN,K9L8E6_HUMAN,K7QT39_HUMAN,K7P5R9_HUMAN,K4JQY2_HUMAN,J9UP90_HUMAN,J9PWQ9_HUMAN,J9PW07_HUMAN,J7K017_HUMAN,J7F682_HUMAN,J7F577_HUMAN,I7A4E3_HUMAN,I6TRW4_HUMAN,I6RCX9_HUMAN,I6NXG0_HUMAN,I6NWI0_HUMAN,I6NVS4_HUMAN,I4EC43_HUMAN,I3VZ13_HUMAN,I3UI65_HUMAN,I3QHR8_HUMAN,I2B2Z4_HUMAN,I2B2W6_HUMAN,H9C5J4_HUMAN,H9BQ86_HUMAN,H9BQ83_HUMAN,H9BQ82_HUMAN,G9I2L1_HUMAN,G3D6I7_HUMAN,G1EPU3_HUMAN,G1EPN0_HUMAN,G1EPJ1_HUMAN,G1ENJ6_HUMAN,G1ENJ0_HUMAN,G1EMP0_HUMAN,G1EMK6_HUMAN,G0ZMJ0_HUMAN,G0ZMH5_HUMAN,G0Z8C9_HUMAN,G0WVB6_HUMAN,F8SKV9_HUMAN,F8RHF3_HUMAN,F6KRS1_HUMAN,F6KRR7_HUMAN,F6KRQ7_HUMAN,F4YU56_HUMAN,F4YTC4_HUMAN,F4NBP2_HUMAN,F4NBP0_HUMAN,F2X5W5_HUMAN,F2X5T3_HUMAN,F2VNN2_HUMAN,E9LY38_HUMAN,E7BYA5_HUMAN,E3SWI1_HUMAN,E3SWH9_HUMAN,E2GJN0_HUMAN,E2DH92_HUMAN,E2D5Q2_HUMAN,E2D5P9_HUMAN,E2D5N8_HUMAN,D9U3G7_HUMAN,D7NSR4_HUMAN,D5L9C9_HUMAN,D5FWA6_HUMAN,D5FI14_HUMAN,D5FHY1_HUMAN,D5FHV8_HUMAN,D5FHU6_HUMAN,D4HPL2_HUMAN,D4HPB9_HUMAN,D4HPB2_HUMAN,D4HP81_HUMAN,D3Y5Y4_HUMAN,D3U4B8_HUMAN,D2DL25_HUMAN,D2DKQ8_HUMAN,D2DKN8_HUMAN,D2DKN6_HUMAN,D2DKF7_HUMAN,D2DKF6_HUMAN,C9WEP9_HUMAN,C9WEN6_HUMAN,C9WD06_HUMAN,C9WCZ5_HUMAN,C9WCQ2_HUMAN,C9E1H2_HUMAN,C8CH80_HUMAN,C8CAX9_HUMAN,C7FDQ9_HUMAN,C6L830_HUMAN,C5JA70_HUMAN,C3VIU8_HUMAN,B9VWB1_HUMAN,B4DUK6_HUMAN,B2YG95_HUMAN,A7E1C3_HUMAN,A5PHP5_HUMAN,A2VC07_HUMAN	UPI0000000B17	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTCACCGGC	.	5	ESCA
HLA-B	0	.	GRCh37	6	31324464	31324464	+	Splice_Site	SNP	C	C	A	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.343+1G>T	.	p.X115_splice	ENST00000412585	.	54	44	10	44	44	0	HLA-B,splice_donor_variant,,ENST00000412585,;HLA-B,splice_donor_variant,,ENST00000434333,;HLA-B,splice_donor_variant,,ENST00000474381,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,upstream_gene_variant,,ENST00000481849,;HLA-B,upstream_gene_variant,,ENST00000463574,;HLA-B,upstream_gene_variant,,ENST00000497377,;XXbac-BPG248L24.12,non_coding_transcript_exon_variant,,ENST00000603274,;	A	ENSG00000234745	ENST00000412585	Transcript	splice_donor_variant	.	.	.	.	.	COSM127127	.	.	-1	HLA-B	HGNC	4932	protein_coding	YES	CCDS34394.1	ENSP00000399168	1B73_HUMAN,1B07_HUMAN,1B42_HUMAN,1B67_HUMAN,1B81_HUMAN,1B48_HUMAN	T1R372_HUMAN,R4QQU0_HUMAN,N0A4A9_HUMAN,N0A0K3_HUMAN,M9XMA8_HUMAN,M9PAL2_HUMAN,M9P9U8_HUMAN,M9P9C4_HUMAN,M9P9A4_HUMAN,M9P990_HUMAN,M9P8G8_HUMAN,M1FXF1_HUMAN,M1FWX2_HUMAN,M1F4D0_HUMAN,E5FQ95_HUMAN,Q9UIP1_HUMAN,Q9TQC5_HUMAN,Q9TQC2_HUMAN,Q9TPU4_HUMAN,Q9GIM0_HUMAN,Q95IE1_HUMAN,Q95HL7_HUMAN,Q8SP64_HUMAN,Q8HWQ3_HUMAN,Q861E5_HUMAN,Q861D6_HUMAN,Q861D4_HUMAN,Q7YP17_HUMAN,Q7YNX2_HUMAN,Q7JGR7_HUMAN,Q710M8_HUMAN,Q710M7_HUMAN,Q70HJ6_HUMAN,Q709M5_HUMAN,Q6ZXT6_HUMAN,Q5QR88_HUMAN,Q5QR87_HUMAN,Q5QR86_HUMAN,Q5QR85_HUMAN,Q5QR84_HUMAN,Q5QR83_HUMAN,Q5QR76_HUMAN,Q5QR73_HUMAN,Q5QR69_HUMAN,Q5QR62_HUMAN,Q5QR60_HUMAN,Q5QR59_HUMAN,Q5QR58_HUMAN,Q5QR57_HUMAN,Q5QR48_HUMAN,Q5QR47_HUMAN,Q5QR46_HUMAN,Q5QR36_HUMAN,Q5QR34_HUMAN,Q5QR33_HUMAN,Q5QR31_HUMAN,Q5F311_HUMAN,Q53ZP0_HUMAN,Q29923_HUMAN,Q29843_HUMAN,Q256S0_HUMAN,O19782_HUMAN,O19746_HUMAN,O19644_HUMAN,O19638_HUMAN,O19563_HUMAN,L0RH50_HUMAN,L0BXM2_HUMAN,K9LCN4_HUMAN,K9L8E6_HUMAN,K7QT39_HUMAN,K7P5R9_HUMAN,K4JQY2_HUMAN,J9UP90_HUMAN,J9PWQ9_HUMAN,J9PW07_HUMAN,J7K017_HUMAN,J7F682_HUMAN,J7F577_HUMAN,I7A4E3_HUMAN,I6TRW4_HUMAN,I6RCX9_HUMAN,I6NXG0_HUMAN,I6NWI0_HUMAN,I6NVS4_HUMAN,I4EC43_HUMAN,I3VZ13_HUMAN,I3UI65_HUMAN,I3QHR8_HUMAN,I2B2Z4_HUMAN,I2B2W6_HUMAN,H9C5J4_HUMAN,H9BQ86_HUMAN,H9BQ83_HUMAN,H9BQ82_HUMAN,G9I2L1_HUMAN,G3D6I7_HUMAN,G1EPU3_HUMAN,G1EPN0_HUMAN,G1EPJ1_HUMAN,G1ENJ6_HUMAN,G1ENJ0_HUMAN,G1EMP0_HUMAN,G1EMK6_HUMAN,G0ZMJ0_HUMAN,G0ZMH5_HUMAN,G0Z8C9_HUMAN,G0WVB6_HUMAN,F8SKV9_HUMAN,F8RHF3_HUMAN,F6KRS1_HUMAN,F6KRR7_HUMAN,F6KRQ7_HUMAN,F4YU56_HUMAN,F4YTC4_HUMAN,F4NBP2_HUMAN,F4NBP0_HUMAN,F2X5W5_HUMAN,F2X5T3_HUMAN,F2VNN2_HUMAN,E9LY38_HUMAN,E7BYA5_HUMAN,E3SWI1_HUMAN,E3SWH9_HUMAN,E2GJN0_HUMAN,E2DH92_HUMAN,E2D5Q2_HUMAN,E2D5P9_HUMAN,E2D5N8_HUMAN,D9U3G7_HUMAN,D7NSR4_HUMAN,D5L9C9_HUMAN,D5FWA6_HUMAN,D5FI14_HUMAN,D5FHY1_HUMAN,D5FHV8_HUMAN,D5FHU6_HUMAN,D4HPL2_HUMAN,D4HPB9_HUMAN,D4HPB2_HUMAN,D4HP81_HUMAN,D3Y5Y4_HUMAN,D3U4B8_HUMAN,D2DL25_HUMAN,D2DKQ8_HUMAN,D2DKN8_HUMAN,D2DKN6_HUMAN,D2DKF7_HUMAN,D2DKF6_HUMAN,C9WEP9_HUMAN,C9WEN6_HUMAN,C9WD06_HUMAN,C9WCZ5_HUMAN,C9WCQ2_HUMAN,C9E1H2_HUMAN,C8CH80_HUMAN,C8CAX9_HUMAN,C7FDQ9_HUMAN,C6L830_HUMAN,C5JA70_HUMAN,C3VIU8_HUMAN,B9VWB1_HUMAN,B4DUK6_HUMAN,B2YG95_HUMAN,A7E1C3_HUMAN,A5PHP5_HUMAN,A2VC07_HUMAN	UPI0000000B17	.	.	.	.	2/7	.	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	HIGH	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACTCACCGGCC	.	5	ESCA
BAG6	0	.	GRCh37	6	31615559	31615559	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.615G>A	p.%3D	p.Q205Q	ENST00000375964	7/25	91	59	31	121	121	0	BAG6,synonymous_variant,p.%3D,ENST00000375976,;BAG6,synonymous_variant,p.%3D,ENST00000424176,;BAG6,synonymous_variant,p.%3D,ENST00000362049,;BAG6,synonymous_variant,p.%3D,ENST00000435080,;BAG6,synonymous_variant,p.%3D,ENST00000437771,;BAG6,synonymous_variant,p.%3D,ENST00000375964,;BAG6,synonymous_variant,p.%3D,ENST00000441054,;BAG6,synonymous_variant,p.%3D,ENST00000452994,;BAG6,synonymous_variant,p.%3D,ENST00000211379,;BAG6,synonymous_variant,p.%3D,ENST00000451898,;BAG6,synonymous_variant,p.%3D,ENST00000428326,;BAG6,synonymous_variant,p.%3D,ENST00000404765,;BAG6,synonymous_variant,p.%3D,ENST00000456622,;BAG6,synonymous_variant,p.%3D,ENST00000434444,;BAG6,synonymous_variant,p.%3D,ENST00000439687,;BAG6,synonymous_variant,p.%3D,ENST00000424480,;BAG6,synonymous_variant,p.%3D,ENST00000433828,;APOM,upstream_gene_variant,,ENST00000375918,;BAG6,downstream_gene_variant,,ENST00000454165,;BAG6,upstream_gene_variant,,ENST00000453833,;APOM,upstream_gene_variant,,ENST00000375920,;BAG6,downstream_gene_variant,,ENST00000456286,;BAG6,upstream_gene_variant,,ENST00000438149,;BAG6,upstream_gene_variant,,ENST00000469182,;BAG6,upstream_gene_variant,,ENST00000470875,;BAG6,upstream_gene_variant,,ENST00000465348,;BAG6,upstream_gene_variant,,ENST00000462682,;	T	ENSG00000204463	ENST00000375964	Transcript	synonymous_variant	929	615	205	Q	caG/caA	.	.	.	-1	BAG6	HGNC	13919	protein_coding	YES	CCDS47403.1	ENSP00000365131	BAG6_HUMAN	F6TC96_HUMAN,F6RG75_HUMAN	UPI000047029D	.	.	.	7/25	.	Low_complexity_(Seg):seg,hmmpanther:PTHR15204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGTGGCTGCGG	.	5	ESCA
PPARD	0	.	GRCh37	6	35392450	35392450	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.972C>T	p.%3D	p.F324F	ENST00000311565	8/9	18	12	5	34	34	0	PPARD,synonymous_variant,p.%3D,ENST00000540939,;PPARD,synonymous_variant,p.%3D,ENST00000448077,;PPARD,synonymous_variant,p.%3D,ENST00000444397,;PPARD,synonymous_variant,p.%3D,ENST00000418635,;PPARD,synonymous_variant,p.%3D,ENST00000360694,;PPARD,synonymous_variant,p.%3D,ENST00000311565,;PPARD,synonymous_variant,p.%3D,ENST00000337400,;	T	ENSG00000112033	ENST00000311565	Transcript	synonymous_variant	1321	972	324	F	ttC/ttT	.	.	.	1	PPARD	HGNC	9235	protein_coding	YES	CCDS4803.1	ENSP00000310928	PPARD_HUMAN	F5H830_HUMAN	UPI000004EF98	.	.	.	8/9	.	hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF15,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCTTCAGTGA	.	5	ESCA
RUNX2	0	.	GRCh37	6	45517625	45517625	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2583G>C	.	.	ENST00000371438	8/8	164	118	46	135	135	0	RUNX2,3_prime_UTR_variant,,ENST00000359524,;RUNX2,3_prime_UTR_variant,,ENST00000371438,;RUNX2,3_prime_UTR_variant,,ENST00000371432,;RUNX2,intron_variant,,ENST00000576263,;RUNX2,downstream_gene_variant,,ENST00000352853,;RUNX2,downstream_gene_variant,,ENST00000541979,;RUNX2,downstream_gene_variant,,ENST00000371436,;RUNX2,downstream_gene_variant,,ENST00000465038,;RUNX2,intron_variant,,ENST00000478660,;RUNX2,downstream_gene_variant,,ENST00000483377,;	C	ENSG00000124813	ENST00000371438	Transcript	3_prime_UTR_variant	4507	.	.	.	.	.	.	.	1	RUNX2	HGNC	10472	protein_coding	YES	CCDS43467.2	ENSP00000360493	RUNX2_HUMAN	U3RG86_HUMAN	UPI000013532F	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCAAGCACTT	.	5	ESCA
BAI3	0	.	GRCh37	6	70082325	70082325	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4267G>C	p.Asp1423His	p.D1423H	ENST00000370598	30/32	59	38	21	48	48	0	BAI3,missense_variant,p.Asp387His,ENST00000546190,;BAI3,missense_variant,p.Asp629His,ENST00000238918,;BAI3,missense_variant,p.Asp1423His,ENST00000370598,;	C	ENSG00000135298	ENST00000370598	Transcript	missense_variant	5088	4267	1423	D/H	Gac/Cac	.	.	.	1	BAI3	HGNC	945	protein_coding	YES	CCDS4968.1	ENSP00000359630	BAI3_HUMAN	S4R3D0_HUMAN,B7Z1K0_HUMAN	UPI00001AE6A9	.	deleterious(0)	benign(0.026)	30/32	.	Prints_domain:PR01694	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACCTTGACTTT	.	5	ESCA
CD109	0	.	GRCh37	6	74537744	74537744	+	3'UTR	DEL	C	C	-	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*4388delC	.	.	ENST00000287097	33/33	87	67	20	60	60	0	CD109,3_prime_UTR_variant,,ENST00000287097,;CD109,3_prime_UTR_variant,,ENST00000437994,;CD109,3_prime_UTR_variant,,ENST00000422508,;	-	ENSG00000156535	ENST00000287097	Transcript	3_prime_UTR_variant	8837	.	.	.	.	.	.	.	1	CD109	HGNC	21685	protein_coding	YES	CCDS4982.1	ENSP00000287097	CD109_HUMAN	Q5XUN1_HUMAN,Q5XUM8_HUMAN,Q5XUM6_HUMAN,F1C639_HUMAN	UPI000013DE92	.	.	.	33/33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	1	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	INDELOCATOR*|VARSCANI*|PINDEL	TCTGGTCCTTCA	.	3	ESCA
COL12A1	0	.	GRCh37	6	75893760	75893760	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1098C>T	p.%3D	p.V366V	ENST00000322507	9/66	54	45	9	49	49	0	COL12A1,synonymous_variant,p.%3D,ENST00000416123,;COL12A1,synonymous_variant,p.%3D,ENST00000322507,;COL12A1,synonymous_variant,p.%3D,ENST00000483888,;COL12A1,intron_variant,,ENST00000345356,;COL12A1,non_coding_transcript_exon_variant,,ENST00000486533,;	A	ENSG00000111799	ENST00000322507	Transcript	synonymous_variant	1408	1098	366	V	gtC/gtT	.	.	.	-1	COL12A1	HGNC	2188	protein_coding	YES	CCDS43482.1	ENSP00000325146	COCA1_HUMAN	.	UPI000045890B	.	.	.	9/66	.	PROSITE_profiles:PS50853,hmmpanther:PTHR22992:SF23,hmmpanther:PTHR22992,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGATGACTTT	.	5	ESCA
CYB5R4	0	.	GRCh37	6	84669665	84669665	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*68G>C	.	.	ENST00000369681	16/16	29	25	4	19	19	0	CYB5R4,3_prime_UTR_variant,,ENST00000369681,;CYB5R4,downstream_gene_variant,,ENST00000479164,;	C	ENSG00000065615	ENST00000369681	Transcript	3_prime_UTR_variant	1774	.	.	.	.	.	.	.	1	CYB5R4	HGNC	20147	protein_coding	YES	CCDS5000.2	ENSP00000358695	NB5R4_HUMAN	B2R7W7_HUMAN	UPI000056D3CE	.	.	.	16/16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	TTTAAGAGAAC	.	2	ESCA
SYNCRIP	0	.	GRCh37	6	86324929	86324929	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1417G>C	p.Asp473His	p.D473H	ENST00000369622	11/11	82	60	22	74	74	0	SYNCRIP,missense_variant,p.Asp473His,ENST00000355238,;SYNCRIP,missense_variant,p.Asp473His,ENST00000369622,;RP11-321N4.5,missense_variant,p.Asp9His,ENST00000503906,;	G	ENSG00000135316	ENST00000369622	Transcript	missense_variant	1918	1417	473	D/H	Gat/Cat	.	.	.	-1	SYNCRIP	HGNC	16918	protein_coding	YES	CCDS5005.1	ENSP00000358635	HNRPQ_HUMAN	F6UXX1_HUMAN	UPI000013CF84	.	tolerated(0.14)	unknown(0)	11/11	.	Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR01648,hmmpanther:PTHR24011,hmmpanther:PTHR24011:SF131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GTAATCATAAC	.	5	ESCA
CNR1	0	.	GRCh37	6	88854985	88854985	+	Silent	SNP	C	C	T	rs371432780	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.9G>A	p.%3D	p.S3S	ENST00000537554	2/2	46	41	5	33	33	0	CNR1,synonymous_variant,p.%3D,ENST00000369499,;CNR1,synonymous_variant,p.%3D,ENST00000551417,;CNR1,synonymous_variant,p.%3D,ENST00000428600,;CNR1,synonymous_variant,p.%3D,ENST00000535130,;CNR1,synonymous_variant,p.%3D,ENST00000369501,;CNR1,synonymous_variant,p.%3D,ENST00000468898,;CNR1,synonymous_variant,p.%3D,ENST00000537554,;CNR1,synonymous_variant,p.%3D,ENST00000549890,;CNR1,synonymous_variant,p.%3D,ENST00000362094,;CNR1,upstream_gene_variant,,ENST00000549716,;	T	ENSG00000118432	ENST00000537554	Transcript	synonymous_variant	3572	9	3	S	tcG/tcA	rs371432780	.	.	-1	CNR1	HGNC	2159	protein_coding	YES	CCDS5015.1	ENSP00000441046	CNR1_HUMAN	S5TLS4_HUMAN,Q9BYY6_HUMAN,F8W187_HUMAN	UPI00000008AA	.	.	.	2/2	.	PIRSF_domain:PIRSF037995	.	.	.	.	.	.	.	T:0.0002	T:0	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGATCGACTT	byFrequency|byCluster	4	ESCA
SRSF12	0	.	GRCh37	6	89808431	89808431	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.652G>C	p.Asp218His	p.D218H	ENST00000452027	5/5	76	54	22	70	70	0	SRSF12,missense_variant,p.Asp218His,ENST00000452027,;SRSF12,downstream_gene_variant,,ENST00000488604,;SRSF12,downstream_gene_variant,,ENST00000524221,;	G	ENSG00000154548	ENST00000452027	Transcript	missense_variant	846	652	218	D/H	Gac/Cac	.	.	.	-1	SRSF12	HGNC	21220	protein_coding	YES	CCDS47459.1	ENSP00000414302	SRS12_HUMAN	B3KVR7_HUMAN	UPI00000721B8	.	deleterious_low_confidence(0.01)	probably_damaging(0.953)	5/5	.	hmmpanther:PTHR23147,hmmpanther:PTHR23147:SF3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGAGTCAGAAT	.	5	ESCA
MUC17	0	.	GRCh37	7	100685190	100685190	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10493C>G	p.Ser3498Cys	p.S3498C	ENST00000306151	3/13	44	30	14	58	58	0	MUC17,missense_variant,p.Ser3498Cys,ENST00000306151,;MUC17,missense_variant,p.Ser3498Cys,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,;	G	ENSG00000169876	ENST00000306151	Transcript	missense_variant	10557	10493	3498	S/C	tCt/tGt	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	benign(0.122)	3/13	.	Low_complexity_(Seg):seg	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTCATCTCCTA	.	5	ESCA
MUC17	0	.	GRCh37	7	100685292	100685292	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.10595C>G	p.Ser3532Cys	p.S3532C	ENST00000306151	3/13	55	43	11	59	59	0	MUC17,missense_variant,p.Ser3532Cys,ENST00000306151,;MUC17,missense_variant,p.Ser3532Cys,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,;	G	ENSG00000169876	ENST00000306151	Transcript	missense_variant	10659	10595	3532	S/C	tCt/tGt	.	.	.	1	MUC17	HGNC	16800	protein_coding	YES	CCDS34711.1	ENSP00000302716	MUC17_HUMAN	A1A4F7_HUMAN	UPI0000D5BB56	.	.	possibly_damaging(0.612)	3/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTCTGAGG	.	5	ESCA
COX19	0	.	GRCh37	7	1015230	1015230	+	5'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-85C>T	.	.	ENST00000344111	1/3	72	68	4	54	54	0	COX19,5_prime_UTR_variant,,ENST00000344111,;COX19,upstream_gene_variant,,ENST00000466146,;COX19,upstream_gene_variant,,ENST00000457254,;COX19,upstream_gene_variant,,ENST00000466853,;	A	ENSG00000240230	ENST00000344111	Transcript	5_prime_UTR_variant	6	.	.	.	.	.	.	.	-1	COX19	HGNC	28074	protein_coding	YES	CCDS34582.1	ENSP00000342015	COX19_HUMAN	.	UPI000015D70A	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCGCCGAGCAC	.	2	ESCA
ZNF862	0	.	GRCh37	7	149561375	149561375	+	3'UTR	SNP	G	G	T	rs377468102	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2G>T	.	.	ENST00000223210	8/8	24	20	4	39	39	0	ZNF862,3_prime_UTR_variant,,ENST00000223210,;RP4-751H13.7,upstream_gene_variant,,ENST00000608963,;ATP6V0E2-AS1,downstream_gene_variant,,ENST00000488315,;ATP6V0E2-AS1,downstream_gene_variant,,ENST00000461019,;ZNF862,downstream_gene_variant,,ENST00000478024,;	T	ENSG00000106479	ENST00000223210	Transcript	3_prime_UTR_variant	3757	.	.	.	.	rs377468102	.	.	1	ZNF862	HGNC	34519	protein_coding	YES	CCDS47741.1	ENSP00000223210	ZN862_HUMAN	C9JB70_HUMAN	UPI000016105C	.	.	.	8/8	.	.	.	.	.	.	.	.	.	A:0	A:0.0001	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE	CTGAGGGACAG	byFrequency|byCluster	2	ESCA
AGR3	0	.	GRCh37	7	16901016	16901016	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.359T>G	p.Met120Arg	p.M120R	ENST00000310398	6/8	69	53	15	65	65	0	AGR3,missense_variant,p.Met120Arg,ENST00000310398,;AGR3,missense_variant,p.Met120Arg,ENST00000402239,;AGR3,missense_variant,p.Met99Arg,ENST00000414935,;RAD17P1,downstream_gene_variant,,ENST00000418130,;	C	ENSG00000173467	ENST00000310398	Transcript	missense_variant	430	359	120	M/R	aTg/aGg	.	.	.	-1	AGR3	HGNC	24167	protein_coding	YES	CCDS5365.1	ENSP00000308606	AGR3_HUMAN	.	UPI0000040D21	.	deleterious(0)	probably_damaging(0.953)	6/8	.	hmmpanther:PTHR15337,hmmpanther:PTHR15337:SF5,Gene3D:3.40.30.10,Pfam_domain:PF13899,Superfamily_domains:SSF52833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAAACATGATT	.	5	ESCA
TWIST1	0	.	GRCh37	7	19155320	19155320	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*477C>G	.	.	ENST00000242261	2/2	78	58	19	42	42	0	TWIST1,3_prime_UTR_variant,,ENST00000242261,;AC003986.7,upstream_gene_variant,,ENST00000417460,;AC003986.6,downstream_gene_variant,,ENST00000419944,;TWIST1,intron_variant,,ENST00000443687,;TWIST1,intron_variant,,ENST00000354571,;	C	ENSG00000122691	ENST00000242261	Transcript	3_prime_UTR_variant	1437	.	.	.	.	.	.	.	-1	TWIST1	HGNC	12428	protein_coding	YES	CCDS5367.1	ENSP00000242261	TWST1_HUMAN	.	UPI00001377DC	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AGTTTGATCCC	.	5	ESCA
SNX8	0	.	GRCh37	7	2317768	2317768	+	Silent	SNP	G	G	A	rs759129958	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.267C>T	p.%3D	p.F89F	ENST00000222990	2/11	38	34	4	24	24	0	SNX8,synonymous_variant,p.%3D,ENST00000419693,;SNX8,synonymous_variant,p.%3D,ENST00000435336,;SNX8,synonymous_variant,p.%3D,ENST00000447136,;SNX8,synonymous_variant,p.%3D,ENST00000457286,;SNX8,synonymous_variant,p.%3D,ENST00000435060,;SNX8,synonymous_variant,p.%3D,ENST00000222990,;SNX8,non_coding_transcript_exon_variant,,ENST00000494722,;	A	ENSG00000106266	ENST00000222990	Transcript	synonymous_variant	310	267	89	F	ttC/ttT	rs759129958	.	.	-1	SNX8	HGNC	14972	protein_coding	YES	CCDS5331.1	ENSP00000222990	SNX8_HUMAN	C9JCB9_HUMAN,C9J8E6_HUMAN,C9J014_HUMAN,C9IYC5_HUMAN	UPI0000135B46	.	.	.	2/11	.	Superfamily_domains:SSF64268,SMART_domains:SM00312,Pfam_domain:PF00787,Gene3D:3.30.1520.10,hmmpanther:PTHR10555:SF15,hmmpanther:PTHR10555,PROSITE_profiles:PS50195	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|VARSCANS	TTCAGGAAGAG	.	2	ESCA
HNRNPA2B1	0	.	GRCh37	7	26231759	26231759	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*221G>A	.	.	ENST00000354667	12/12	68	61	6	43	43	0	HNRNPA2B1,3_prime_UTR_variant,,ENST00000354667,;HNRNPA2B1,3_prime_UTR_variant,,ENST00000356674,;HNRNPA2B1,upstream_gene_variant,,ENST00000476233,;HNRNPA2B1,non_coding_transcript_exon_variant,,ENST00000490912,;HNRNPA2B1,non_coding_transcript_exon_variant,,ENST00000463181,;HNRNPA2B1,intron_variant,,ENST00000360787,;HNRNPA2B1,downstream_gene_variant,,ENST00000495810,;	T	ENSG00000122566	ENST00000354667	Transcript	3_prime_UTR_variant	1452	.	.	.	.	.	.	.	-1	HNRNPA2B1	HGNC	5033	protein_coding	YES	CCDS43557.1	ENSP00000346694	ROA2_HUMAN	.	UPI000002F091	.	.	.	12/12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TCCTTCCTCCA	.	4	ESCA
AC005013.5	0	.	GRCh37	7	28997239	28997239	+	5'Flank	SNP	C	C	G	rs746364113	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000436594	.	76	66	10	47	47	0	AC005013.5,upstream_gene_variant,,ENST00000436594,;TRIL,non_coding_transcript_exon_variant,,ENST00000322982,;AC005013.1,non_coding_transcript_exon_variant,,ENST00000539664,;	G	ENSG00000228421	ENST00000436594	Transcript	upstream_gene_variant	.	.	.	.	.	rs746364113	.	44	1	AC005013.5	Clone_based_vega_gene	.	lincRNA	YES	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GATCTCGTTCC	byFrequency	4	ESCA
CAMK2B	0	.	GRCh37	7	44258960	44258964	+	3'UTR	DEL	TTTTG	TTTTG	-	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	TTTTG	TTTTG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*160_*164delCAAAA	.	.	ENST00000395749	24/24	32	28	4	24	24	0	CAMK2B,3_prime_UTR_variant,,ENST00000395749,;CAMK2B,3_prime_UTR_variant,,ENST00000353625,;CAMK2B,3_prime_UTR_variant,,ENST00000425809,;CAMK2B,3_prime_UTR_variant,,ENST00000457475,;CAMK2B,3_prime_UTR_variant,,ENST00000440254,;CAMK2B,3_prime_UTR_variant,,ENST00000358707,;CAMK2B,intron_variant,,ENST00000502837,;CAMK2B,intron_variant,,ENST00000350811,;CAMK2B,downstream_gene_variant,,ENST00000258682,;CAMK2B,downstream_gene_variant,,ENST00000395747,;CAMK2B,downstream_gene_variant,,ENST00000346990,;CAMK2B,downstream_gene_variant,,ENST00000347193,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000497584,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000489429,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000466584,;CAMK2B,intron_variant,,ENST00000523845,;CAMK2B,downstream_gene_variant,,ENST00000353185,;	-	ENSG00000058404	ENST00000395749	Transcript	3_prime_UTR_variant	2238-2242	.	.	.	.	.	.	.	-1	CAMK2B	HGNC	1461	protein_coding	YES	CCDS5483.1	ENSP00000379098	KCC2B_HUMAN	Q75LA8_HUMAN,Q75KE9_HUMAN,D3DVK8_HUMAN,A4D2J9_HUMAN	UPI0000164A3E	.	.	.	24/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	deletion	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	VARSCANS*|PINDEL	TTTTTTTTTTGTTTTT	.	2	ESCA
OGDH	0	.	GRCh37	7	44664045	44664045	+	Nonsense_Mutation	SNP	C	C	T	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.103C>T	p.Gln35Ter	p.Q35*	ENST00000222673	2/23	99	72	26	76	76	0	OGDH,stop_gained,p.Gln35Ter,ENST00000222673,;OGDH,stop_gained,p.Gln35Ter,ENST00000443864,;OGDH,stop_gained,p.Gln35Ter,ENST00000444676,;OGDH,stop_gained,p.Gln35Ter,ENST00000449767,;OGDH,stop_gained,p.Gln35Ter,ENST00000419661,;OGDH,stop_gained,p.Gln35Ter,ENST00000447398,;OGDH,stop_gained,p.Gln35Ter,ENST00000439616,;OGDH,upstream_gene_variant,,ENST00000543843,;	T	ENSG00000105953	ENST00000222673	Transcript	stop_gained	145	103	35	Q/*	Caa/Taa	COSM1313109,COSM254874,COSM1755293,COSM1313110	.	.	1	OGDH	HGNC	8124	protein_coding	YES	CCDS34627.1	ENSP00000222673	ODO1_HUMAN	C9J4G7_HUMAN	UPI000006D5FE	.	.	.	2/23	.	PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152:SF7,hmmpanther:PTHR23152	.	.	.	.	.	.	.	.	.	.	1,1,1,1	.	.	.	.	.	HIGH	.	SNV	.	.	1,1,1,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.Q35K|c.103C>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTCAACAG	.	5	ESCA
SEPT14	0	.	GRCh37	7	55886880	55886880	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.757G>A	p.Glu253Lys	p.E253K	ENST00000388975	7/10	69	41	28	51	51	0	SEPT14,missense_variant,p.Glu253Lys,ENST00000388975,;	T	ENSG00000154997	ENST00000388975	Transcript	missense_variant	874	757	253	E/K	Gaa/Aaa	.	.	.	-1	SEPT14	HGNC	33280	protein_coding	YES	CCDS5519.2	ENSP00000373627	SEP14_HUMAN	.	UPI0000E0AB69	.	tolerated(0.14)	benign(0.033)	7/10	.	PROSITE_profiles:PS51719,hmmpanther:PTHR18884:SF51,hmmpanther:PTHR18884,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,Superfamily_domains:SSF52540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CACTTCATCTG	.	5	ESCA
ZNF679	0	.	GRCh37	7	63726538	63726538	+	Missense_Mutation	SNP	C	C	A	rs375602152	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.527C>A	p.Thr176Lys	p.T176K	ENST00000421025	5/5	116	85	30	89	88	0	ZNF679,missense_variant,p.Thr176Lys,ENST00000255746,;ZNF679,missense_variant,p.Thr176Lys,ENST00000421025,;	A	ENSG00000197123	ENST00000421025	Transcript	missense_variant	796	527	176	T/K	aCa/aAa	rs375602152	.	.	1	ZNF679	HGNC	28650	protein_coding	YES	CCDS47592.1	ENSP00000416809	ZN679_HUMAN	.	UPI000045756A	.	tolerated(0.17)	possibly_damaging(0.526)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF91,Superfamily_domains:SSF57667	T:0.0002	T:0	T:0	.	T:0.001	T:0	T:0	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TAAGACAAGAC	byCluster|by1000G	5	ESCA
GRID2IP	0	.	GRCh37	7	6541650	6541650	+	Missense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3250G>A	p.Asp1084Asn	p.D1084N	ENST00000457091	19/22	52	35	16	21	21	0	GRID2IP,missense_variant,p.Asp1084Asn,ENST00000457091,;GRID2IP,missense_variant,p.Asp893Asn,ENST00000452113,;GRID2IP,missense_variant,p.Asp900Asn,ENST00000435185,;	T	ENSG00000215045	ENST00000457091	Transcript	missense_variant	3250	3250	1084	D/N	Gac/Aac	.	.	.	-1	GRID2IP	HGNC	18464	protein_coding	YES	CCDS47537.1	ENSP00000397351	GRD2I_HUMAN	.	UPI0001722D0B	.	deleterious(0)	probably_damaging(0.986)	19/22	.	PROSITE_profiles:PS51444,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF15,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CAGGTCCTGAG	.	5	ESCA
GTF2IRD1	0	.	GRCh37	7	73969808	73969808	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2103G>C	p.Lys701Asn	p.K701N	ENST00000455841	19/27	38	25	12	38	38	0	GTF2IRD1,missense_variant,p.Lys669Asn,ENST00000476977,;GTF2IRD1,missense_variant,p.Lys47Asn,ENST00000470715,;GTF2IRD1,missense_variant,p.Lys701Asn,ENST00000455841,;GTF2IRD1,missense_variant,p.Lys684Asn,ENST00000265755,;GTF2IRD1,missense_variant,p.Lys669Asn,ENST00000424337,;GTF2IRD1,intron_variant,,ENST00000489094,;	C	ENSG00000006704	ENST00000455841	Transcript	missense_variant	2316	2103	701	K/N	aaG/aaC	.	.	.	1	GTF2IRD1	HGNC	4661	protein_coding	YES	CCDS56492.1	ENSP00000397566	GT2D1_HUMAN	.	UPI00003BF92B	.	deleterious(0)	probably_damaging(0.958)	19/27	.	PIRSF_domain:PIRSF016441,hmmpanther:PTHR11697:SF84,hmmpanther:PTHR11697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTGAAGAGACA	.	5	ESCA
SEMA3A	0	.	GRCh37	7	83634746	83634746	+	Missense_Mutation	SNP	G	G	C	rs753997365	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1269C>G	p.Ile423Met	p.I423M	ENST00000265362	11/17	87	73	13	61	61	0	SEMA3A,missense_variant,p.Ile423Met,ENST00000265362,;SEMA3A,missense_variant,p.Ile423Met,ENST00000436949,;	C	ENSG00000075213	ENST00000265362	Transcript	missense_variant	1584	1269	423	I/M	atC/atG	rs753997365	.	.	-1	SEMA3A	HGNC	10723	protein_coding	YES	CCDS5599.1	ENSP00000265362	SEM3A_HUMAN	Q86UJ2_HUMAN,Q75MQ2_HUMAN,C9JD25_HUMAN,C9J9C4_HUMAN	UPI0000135A60	.	deleterious(0.03)	possibly_damaging(0.506)	11/17	.	PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF23,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GTTTTGATCAC	.	5	ESCA
AKAP9	0	.	GRCh37	7	91630582	91630582	+	Nonsense_Mutation	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1351G>T	p.Glu451Ter	p.E451*	ENST00000356239	8/50	44	32	12	62	62	0	AKAP9,stop_gained,p.Glu451Ter,ENST00000356239,;AKAP9,stop_gained,p.Glu463Ter,ENST00000359028,;AKAP9,stop_gained,p.Glu463Ter,ENST00000358100,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,;	T	ENSG00000127914	ENST00000356239	Transcript	stop_gained	1584	1351	451	E/*	Gaa/Taa	.	.	.	1	AKAP9	HGNC	379	protein_coding	YES	CCDS5622.1	ENSP00000348573	AKAP9_HUMAN	Q8IW64_HUMAN	UPI000002A38D	.	.	.	8/50	.	Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18932:SF10,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AACAAGAATTA	.	5	ESCA
AKAP9	0	.	GRCh37	7	91631495	91631495	+	Nonsense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2264T>G	p.Leu755Ter	p.L755*	ENST00000356239	8/50	225	213	11	178	178	0	AKAP9,stop_gained,p.Leu755Ter,ENST00000356239,;AKAP9,stop_gained,p.Leu767Ter,ENST00000359028,;AKAP9,stop_gained,p.Leu767Ter,ENST00000358100,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,;	G	ENSG00000127914	ENST00000356239	Transcript	stop_gained	2497	2264	755	L/*	tTa/tGa	.	.	.	1	AKAP9	HGNC	379	protein_coding	YES	CCDS5622.1	ENSP00000348573	AKAP9_HUMAN	Q8IW64_HUMAN	UPI000002A38D	.	.	.	8/50	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18932:SF10,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	ATTGTTAGAAA	.	2	ESCA
AKAP9	0	.	GRCh37	7	91631497	91631497	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2266G>C	p.Glu756Gln	p.E756Q	ENST00000356239	8/50	224	164	60	175	175	0	AKAP9,missense_variant,p.Glu756Gln,ENST00000356239,;AKAP9,missense_variant,p.Glu768Gln,ENST00000359028,;AKAP9,missense_variant,p.Glu768Gln,ENST00000358100,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,;	C	ENSG00000127914	ENST00000356239	Transcript	missense_variant	2499	2266	756	E/Q	Gaa/Caa	.	.	.	1	AKAP9	HGNC	379	protein_coding	YES	CCDS5622.1	ENSP00000348573	AKAP9_HUMAN	Q8IW64_HUMAN	UPI000002A38D	.	.	possibly_damaging(0.885)	8/50	.	Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18932:SF10,hmmpanther:PTHR18932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TGTTAGAAAAA	.	5	ESCA
GATAD1	0	.	GRCh37	7	92080020	92080020	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.381C>G	p.Ile127Met	p.I127M	ENST00000287957	3/5	31	27	4	23	23	0	GATAD1,missense_variant,p.Ile127Met,ENST00000287957,;GATAD1,non_coding_transcript_exon_variant,,ENST00000493878,;GATAD1,upstream_gene_variant,,ENST00000465247,;	G	ENSG00000157259	ENST00000287957	Transcript	missense_variant	658	381	127	I/M	atC/atG	COSM602798	.	.	1	GATAD1	HGNC	29941	protein_coding	YES	CCDS5625.1	ENSP00000287957	GATD1_HUMAN	.	UPI000006FF00	.	tolerated(0.09)	possibly_damaging(0.809)	3/5	.	hmmpanther:PTHR13340	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CCCATCAAAGC	.	4	ESCA
PEX1	0	.	GRCh37	7	92146692	92146692	+	Silent	SNP	C	C	T	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1137G>A	p.%3D	p.E379E	ENST00000248633	5/24	99	90	9	81	81	0	PEX1,synonymous_variant,p.%3D,ENST00000248633,;PEX1,synonymous_variant,p.%3D,ENST00000428214,;PEX1,5_prime_UTR_variant,,ENST00000541751,;PEX1,intron_variant,,ENST00000438045,;PEX1,synonymous_variant,p.%3D,ENST00000422866,;PEX1,non_coding_transcript_exon_variant,,ENST00000484913,;PEX1,upstream_gene_variant,,ENST00000476923,;	T	ENSG00000127980	ENST00000248633	Transcript	synonymous_variant	1233	1137	379	E	gaG/gaA	COSM1550896	.	.	-1	PEX1	HGNC	8850	protein_coding	YES	CCDS5627.1	ENSP00000248633	PEX1_HUMAN	Q96S70_HUMAN,Q96S69_HUMAN,B4DER6_HUMAN	UPI0000001C39	.	.	.	5/24	.	hmmpanther:PTHR23077:SF12,hmmpanther:PTHR23077	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	LOW	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GCCTTCTCATC	.	3	ESCA
BET1	0	.	GRCh37	7	93633539	93633539	+	5'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-11C>G	.	.	ENST00000222547	1/4	30	24	6	25	25	0	BET1,5_prime_UTR_variant,,ENST00000433727,;BET1,5_prime_UTR_variant,,ENST00000222547,;BET1,5_prime_UTR_variant,,ENST00000425626,;BET1,upstream_gene_variant,,ENST00000457139,;AC006378.2,intron_variant,,ENST00000426634,;AC006378.2,downstream_gene_variant,,ENST00000426193,;BET1,5_prime_UTR_variant,,ENST00000357520,;	C	ENSG00000105829	ENST00000222547	Transcript	5_prime_UTR_variant	149	.	.	.	.	.	.	.	-1	BET1	HGNC	14562	protein_coding	YES	CCDS5635.1	ENSP00000222547	BET1_HUMAN	Q53XK0_HUMAN	UPI000012689A	.	.	.	1/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CAGAGGAGAGA	.	2	ESCA
DYNC1I1	0	.	GRCh37	7	95705494	95705494	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1686C>T	p.%3D	p.L562L	ENST00000324972	15/17	32	27	4	32	32	0	DYNC1I1,synonymous_variant,p.%3D,ENST00000359388,;DYNC1I1,synonymous_variant,p.%3D,ENST00000457059,;DYNC1I1,synonymous_variant,p.%3D,ENST00000437599,;DYNC1I1,synonymous_variant,p.%3D,ENST00000447467,;DYNC1I1,synonymous_variant,p.%3D,ENST00000537881,;DYNC1I1,synonymous_variant,p.%3D,ENST00000324972,;	T	ENSG00000158560	ENST00000324972	Transcript	synonymous_variant	1879	1686	562	L	ctC/ctT	.	.	.	1	DYNC1I1	HGNC	2963	protein_coding	YES	CCDS5644.1	ENSP00000320130	DC1I1_HUMAN	Q75MI9_HUMAN,Q75LS9_HUMAN,A4D1I7_HUMAN	UPI0000129A01	.	.	.	15/17	.	PROSITE_profiles:PS50294,hmmpanther:PTHR12442:SF34,hmmpanther:PTHR12442,Gene3D:2.130.10.10,Superfamily_domains:SSF50978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AACCTCAACAA	.	4	ESCA
TECPR1	0	.	GRCh37	7	97862900	97862900	+	Missense_Mutation	SNP	G	G	C	rs749799075	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1505C>G	p.Ser502Trp	p.S502W	ENST00000447648	11/26	20	13	6	17	17	0	TECPR1,missense_variant,p.Ser502Trp,ENST00000447648,;TECPR1,missense_variant,p.Ser432Trp,ENST00000542604,;TECPR1,missense_variant,p.Ser502Trp,ENST00000379795,;TECPR1,non_coding_transcript_exon_variant,,ENST00000471397,;TECPR1,upstream_gene_variant,,ENST00000479975,;TECPR1,upstream_gene_variant,,ENST00000479911,;TECPR1,upstream_gene_variant,,ENST00000476659,;TECPR1,non_coding_transcript_exon_variant,,ENST00000490842,;TECPR1,downstream_gene_variant,,ENST00000463648,;TECPR1,upstream_gene_variant,,ENST00000483740,;	C	ENSG00000205356	ENST00000447648	Transcript	missense_variant	1805	1505	502	S/W	tCg/tGg	rs749799075,COSM3642695	.	.	-1	TECPR1	HGNC	22214	protein_coding	YES	CCDS47648.1	ENSP00000404923	TCPR1_HUMAN	C9JUV4_HUMAN	UPI0000161940	.	deleterious(0)	benign(0.049)	11/26	.	hmmpanther:PTHR23250,hmmpanther:PTHR23250:SF1	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CGGCCGAGTGG	byFrequency	5	ESCA
UBR5	0	.	GRCh37	8	103274200	103274200	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.7785C>G	p.Phe2595Leu	p.F2595L	ENST00000520539	55/59	68	56	12	86	86	0	UBR5,missense_variant,p.Phe2595Leu,ENST00000520539,;UBR5,missense_variant,p.Phe2588Leu,ENST00000521922,;UBR5,missense_variant,p.Phe323Leu,ENST00000518205,;UBR5,missense_variant,p.Phe2594Leu,ENST00000220959,;KB-431C1.5,downstream_gene_variant,,ENST00000606361,;UBR5,non_coding_transcript_exon_variant,,ENST00000517465,;UBR5,downstream_gene_variant,,ENST00000521767,;UBR5,downstream_gene_variant,,ENST00000521312,;	C	ENSG00000104517	ENST00000520539	Transcript	missense_variant	8392	7785	2595	F/L	ttC/ttG	.	.	.	-1	UBR5	HGNC	16806	protein_coding	YES	CCDS34933.1	ENSP00000429084	UBR5_HUMAN	Q49A65_HUMAN,E5RFK7_HUMAN,B3KML2_HUMAN	UPI0000129BCB	.	tolerated(0.26)	possibly_damaging(0.891)	55/59	.	PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF77,hmmpanther:PTHR11254,Gene3D:1c4zA02,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCTGAGAAAAC	.	5	ESCA
ZFPM2	0	.	GRCh37	8	106813358	106813358	+	Missense_Mutation	SNP	T	T	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1048T>A	p.Phe350Ile	p.F350I	ENST00000407775	8/8	59	54	5	48	48	0	ZFPM2,missense_variant,p.Phe218Ile,ENST00000517361,;ZFPM2,missense_variant,p.Phe81Ile,ENST00000378472,;ZFPM2,missense_variant,p.Phe218Ile,ENST00000520492,;ZFPM2,missense_variant,p.Phe350Ile,ENST00000407775,;RP11-152P17.2,intron_variant,,ENST00000524045,;RP11-152P17.2,intron_variant,,ENST00000509144,;RP11-152P17.2,intron_variant,,ENST00000521622,;RP11-152P17.2,intron_variant,,ENST00000520594,;RP11-152P17.2,intron_variant,,ENST00000520433,;RP11-152P17.2,intron_variant,,ENST00000518932,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;RP11-152P17.2,intron_variant,,ENST00000520078,;	A	ENSG00000169946	ENST00000407775	Transcript	missense_variant	1298	1048	350	F/I	Ttt/Att	.	.	.	1	ZFPM2	HGNC	16700	protein_coding	YES	CCDS47908.1	ENSP00000384179	FOG2_HUMAN	Q9NPQ0_HUMAN,F5H542_HUMAN,E7ET52_HUMAN,E5RJX0_HUMAN	UPI000057A0B4	.	tolerated(0.1)	possibly_damaging(0.718)	8/8	.	hmmpanther:PTHR12958:SF5,hmmpanther:PTHR12958,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE|VARSCANS	TCAACTTTCAC	.	3	ESCA
AARD	0	.	GRCh37	8	117950617	117950617	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.135C>G	p.Ile45Met	p.I45M	ENST00000378279	1/2	59	53	6	52	52	0	AARD,missense_variant,p.Ile45Met,ENST00000378279,;AARD,upstream_gene_variant,,ENST00000523536,;	G	ENSG00000205002	ENST00000378279	Transcript	missense_variant	180	135	45	I/M	atC/atG	.	.	.	1	AARD	HGNC	33842	protein_coding	YES	CCDS34935.1	ENSP00000367528	AARD_HUMAN	.	UPI0000419472	.	tolerated(0.08)	benign(0.033)	1/2	.	hmmpanther:PTHR32289:SF2,hmmpanther:PTHR32289	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	GACATCCAGGA	.	3	ESCA
SLC30A8	0	.	GRCh37	8	118186964	118186964	+	3'Flank	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000456015	.	57	49	7	65	65	0	SLC30A8,3_prime_UTR_variant,,ENST00000427715,;SLC30A8,downstream_gene_variant,,ENST00000456015,;SLC30A8,downstream_gene_variant,,ENST00000519688,;SLC30A8,downstream_gene_variant,,ENST00000521243,;	G	ENSG00000164756	ENST00000456015	Transcript	downstream_gene_variant	.	.	.	.	.	.	.	634	1	SLC30A8	HGNC	20303	protein_coding	YES	CCDS6322.1	ENSP00000415011	ZNT8_HUMAN	E5RG87_HUMAN	UPI00001B00D6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GAAATTCACTG	.	5	ESCA
COL14A1	0	.	GRCh37	8	121292979	121292979	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3676G>C	p.Asp1226His	p.D1226H	ENST00000297848	30/48	58	50	8	44	44	0	COL14A1,missense_variant,p.Asp1226His,ENST00000309791,;COL14A1,missense_variant,p.Asp1131His,ENST00000247781,;COL14A1,missense_variant,p.Asp1226His,ENST00000297848,;COL14A1,downstream_gene_variant,,ENST00000432943,;	C	ENSG00000187955	ENST00000297848	Transcript	missense_variant	3946	3676	1226	D/H	Gat/Cat	.	.	.	1	COL14A1	HGNC	2191	protein_coding	YES	CCDS34938.1	ENSP00000297848	COEA1_HUMAN	.	UPI000046D377	.	deleterious(0)	benign(0.221)	30/48	.	hmmpanther:PTHR22992:SF89,hmmpanther:PTHR22992	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCATTGATCTT	.	5	ESCA
MRPL13	0	.	GRCh37	8	121455468	121455468	+	Silent	SNP	A	A	G	rs148855915	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.108T>C	p.%3D	p.S36S	ENST00000306185	2/7	54	46	7	57	57	0	MRPL13,synonymous_variant,p.%3D,ENST00000306185,;MRPL13,synonymous_variant,p.%3D,ENST00000518918,;MTBP,upstream_gene_variant,,ENST00000305949,;MRPL13,synonymous_variant,p.%3D,ENST00000518696,;MRPL13,non_coding_transcript_exon_variant,,ENST00000520677,;MTBP,upstream_gene_variant,,ENST00000523373,;MTBP,upstream_gene_variant,,ENST00000522308,;MTBP,upstream_gene_variant,,ENST00000456899,;	G	ENSG00000172172	ENST00000306185	Transcript	synonymous_variant	400	108	36	S	tcT/tcC	rs148855915,COSM4138619	.	.	-1	MRPL13	HGNC	14278	protein_coding	YES	CCDS6332.1	ENSP00000306548	RM13_HUMAN	H0YAX3_HUMAN,E5RJI7_HUMAN	UPI00001342CD	.	.	.	2/7	.	hmmpanther:PTHR11545:SF6,hmmpanther:PTHR11545,Pfam_domain:PF00572,TIGRFAM_domain:TIGR01066,Gene3D:3.90.1180.10,PIRSF_domain:PIRSF002181,Superfamily_domains:SSF52161	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	T:0.002	T:0	.	0,1	.	.	.	.	.	LOW	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	CTTATAGATGC	byCluster|by1000G	4	ESCA
OPLAH	0	.	GRCh37	8	145113708	145113708	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.555C>T	p.%3D	p.R185R	ENST00000426825	5/28	49	42	7	60	60	0	OPLAH,synonymous_variant,p.%3D,ENST00000426825,;OPLAH,non_coding_transcript_exon_variant,,ENST00000534424,;OPLAH,downstream_gene_variant,,ENST00000567871,;OPLAH,upstream_gene_variant,,ENST00000527993,;OPLAH,upstream_gene_variant,,ENST00000531027,;	A	ENSG00000178814	ENST00000426825	Transcript	synonymous_variant	637	555	185	R	cgC/cgT	.	.	.	-1	OPLAH	HGNC	8149	protein_coding	YES	.	ENSP00000475943	OPLA_HUMAN	.	UPI000035154E	.	.	.	5/28	.	hmmpanther:PTHR11365:SF2,hmmpanther:PTHR11365,Pfam_domain:PF05378	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	AGGCTGCGGAT	.	4	ESCA
SCRT1	0	.	GRCh37	8	145556659	145556659	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*188G>A	.	.	ENST00000332135	2/2	26	21	5	31	31	0	SCRT1,3_prime_UTR_variant,,ENST00000332135,;	T	ENSG00000170616	ENST00000332135	Transcript	3_prime_UTR_variant	1347	.	.	.	.	.	.	.	-1	SCRT1	HGNC	15950	protein_coding	YES	CCDS6421.1	ENSP00000331692	SCRT1_HUMAN	.	UPI0000071337	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CCCCTCGGGAC	.	2	ESCA
ZNF251	0	.	GRCh37	8	145948071	145948071	+	Missense_Mutation	SNP	T	T	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.974A>C	p.Glu325Ala	p.E325A	ENST00000292562	5/5	43	39	4	46	46	0	ZNF251,missense_variant,p.Glu325Ala,ENST00000292562,;ZNF251,intron_variant,,ENST00000524394,;	G	ENSG00000198169	ENST00000292562	Transcript	missense_variant	1250	974	325	E/A	gAa/gCa	.	.	.	-1	ZNF251	HGNC	13045	protein_coding	YES	CCDS47944.1	ENSP00000292562	ZN251_HUMAN	.	UPI0000160D9A	.	deleterious(0.01)	possibly_damaging(0.484)	5/5	.	PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF202,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13465,SMART_domains:SM00355,Superfamily_domains:SSF57667	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CACATTCATTA	.	3	ESCA
PDLIM2	0	.	GRCh37	8	22451274	22451274	+	Missense_Mutation	SNP	C	C	T	rs147368012	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1660C>T	p.Arg554Trp	p.R554W	ENST00000308354	10/10	40	33	7	50	50	0	PDLIM2,missense_variant,p.Arg304Trp,ENST00000265810,;AC037459.4,missense_variant,p.Arg98Trp,ENST00000430850,;PDLIM2,missense_variant,p.Arg304Trp,ENST00000397760,;PDLIM2,missense_variant,p.Arg554Trp,ENST00000308354,;PDLIM2,missense_variant,p.Arg304Trp,ENST00000409417,;PDLIM2,missense_variant,p.Arg304Trp,ENST00000397761,;PDLIM2,synonymous_variant,p.%3D,ENST00000339162,;PDLIM2,synonymous_variant,p.%3D,ENST00000409141,;AC037459.4,intron_variant,,ENST00000450780,;AC037459.4,intron_variant,,ENST00000447849,;PDLIM2,downstream_gene_variant,,ENST00000456545,;PDLIM2,downstream_gene_variant,,ENST00000452226,;PDLIM2,non_coding_transcript_exon_variant,,ENST00000448520,;PDLIM2,non_coding_transcript_exon_variant,,ENST00000443561,;PDLIM2,non_coding_transcript_exon_variant,,ENST00000464275,;PDLIM2,downstream_gene_variant,,ENST00000416159,;	T	ENSG00000120913	ENST00000308354	Transcript	missense_variant	1699	1660	554	R/W	Cgg/Tgg	rs147368012	.	.	1	PDLIM2	HGNC	13992	protein_coding	YES	CCDS6032.2	ENSP00000312634	PDLI2_HUMAN	C9K0F0_HUMAN,C9JSR2_HUMAN,C9JS55_HUMAN,C9J760_HUMAN,C9J0X3_HUMAN,B3KPU0_HUMAN	UPI0000E5AE4E	.	deleterious(0)	probably_damaging(0.996)	10/10	.	PROSITE_profiles:PS50023,hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF1,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132	.	.	.	.	.	.	.	T:0.0002	T:0.0001	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGGCCGGTAC	byCluster	5	ESCA
PURG	0	.	GRCh37	8	30889113	30889113	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*142C>T	.	.	ENST00000475541	1/1	44	34	9	58	58	0	PURG,3_prime_UTR_variant,,ENST00000475541,;PURG,intron_variant,,ENST00000339382,;WRN,upstream_gene_variant,,ENST00000298139,;PURG,downstream_gene_variant,,ENST00000523392,;	A	ENSG00000172733	ENST00000475541	Transcript	3_prime_UTR_variant	2119	.	.	.	.	.	.	.	-1	PURG	HGNC	17930	protein_coding	YES	CCDS6081.1	ENSP00000418721	PURG_HUMAN	K7ENC1_HUMAN	UPI000006F2C7	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AATCAGACTTC	.	5	ESCA
LETM2	0	.	GRCh37	8	38251658	38251658	+	Missense_Mutation	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.403A>G	p.Met135Val	p.M135V	ENST00000523983	4/11	62	46	16	82	82	0	LETM2,missense_variant,p.Met182Val,ENST00000379957,;LETM2,missense_variant,p.Met135Val,ENST00000523983,;LETM2,3_prime_UTR_variant,,ENST00000519476,;LETM2,intron_variant,,ENST00000297720,;LETM2,intron_variant,,ENST00000524874,;LETM2,downstream_gene_variant,,ENST00000526356,;LETM2,upstream_gene_variant,,ENST00000527710,;LETM2,downstream_gene_variant,,ENST00000527334,;LETM2,intron_variant,,ENST00000523268,;LETM2,intron_variant,,ENST00000518121,;LETM2,intron_variant,,ENST00000518883,;	G	ENSG00000165046	ENST00000523983	Transcript	missense_variant	575	403	135	M/V	Atg/Gtg	.	.	.	1	LETM2	HGNC	14648	protein_coding	YES	CCDS56534.1	ENSP00000428765	LETM2_HUMAN	.	UPI000021093A	.	tolerated(0.22)	benign(0.008)	4/11	.	Transmembrane_helices:TMhelix,hmmpanther:PTHR14009:SF7,hmmpanther:PTHR14009,Pfam_domain:PF07766	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATTTATGGTG	.	5	ESCA
TGS1	0	.	GRCh37	8	56695312	56695312	+	Missense_Mutation	SNP	G	G	A	rs754206400	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.107G>A	p.Arg36Gln	p.R36Q	ENST00000260129	2/13	153	122	31	125	125	0	TGS1,missense_variant,p.Arg36Gln,ENST00000260129,;TGS1,intron_variant,,ENST00000523948,;	A	ENSG00000137574	ENST00000260129	Transcript	missense_variant	584	107	36	R/Q	cGa/cAa	rs754206400,COSM3779279	.	.	1	TGS1	HGNC	17843	protein_coding	YES	CCDS34894.1	ENSP00000260129	TGS1_HUMAN	.	UPI0000DBEF24	.	tolerated(0.06)	benign(0.241)	2/13	.	hmmpanther:PTHR14741,hmmpanther:PTHR14741:SF32	.	.	.	.	.	.	.	.	.	.	0,1	.	.	.	.	.	MODERATE	.	SNV	.	.	0,1	.	.	.	.	.	.	.	.	.	.	PASS	BUFFER|p.E34E|c.102G>A|3	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGATCGAAAAT	byFrequency	5	ESCA
LYN	0	.	GRCh37	8	56912040	56912040	+	Missense_Mutation	SNP	A	A	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1268A>C	p.Lys423Thr	p.K423T	ENST00000519728	12/13	107	94	12	91	91	0	LYN,missense_variant,p.Lys423Thr,ENST00000519728,;LYN,missense_variant,p.Lys402Thr,ENST00000520220,;LYN,downstream_gene_variant,,ENST00000420292,;	C	ENSG00000254087	ENST00000519728	Transcript	missense_variant	1564	1268	423	K/T	aAg/aCg	.	.	.	1	LYN	HGNC	6735	protein_coding	YES	CCDS6162.1	ENSP00000428924	LYN_HUMAN	E5RJ37_HUMAN,B4DQ79_HUMAN	UPI000013DACD	.	deleterious(0)	probably_damaging(0.988)	12/13	.	PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF42,hmmpanther:PTHR24418,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATTAAGTCTG	.	4	ESCA
CA8	0	.	GRCh37	8	61102468	61102468	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*112A>G	.	.	ENST00000317995	9/9	28	22	6	13	13	0	CA8,3_prime_UTR_variant,,ENST00000317995,;	C	ENSG00000178538	ENST00000317995	Transcript	3_prime_UTR_variant	1250	.	.	.	.	.	.	.	-1	CA8	HGNC	1382	protein_coding	YES	CCDS6174.1	ENSP00000314407	CAH8_HUMAN	B4DFA0_HUMAN	UPI000000D816	.	.	.	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	MUTECT|MUSE	CAGGCTTTGAG	.	2	ESCA
ASPH	0	.	GRCh37	8	62559369	62559369	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.559C>G	p.Leu187Val	p.L187V	ENST00000379454	6/25	68	55	13	57	57	0	ASPH,missense_variant,p.Leu202Val,ENST00000519234,;ASPH,missense_variant,p.Leu187Val,ENST00000356457,;ASPH,missense_variant,p.Leu173Val,ENST00000517847,;ASPH,missense_variant,p.Leu187Val,ENST00000379454,;ASPH,missense_variant,p.Leu173Val,ENST00000517903,;ASPH,missense_variant,p.Leu158Val,ENST00000541428,;ASPH,missense_variant,p.Leu173Val,ENST00000445642,;ASPH,intron_variant,,ENST00000522349,;ASPH,intron_variant,,ENST00000522835,;ASPH,intron_variant,,ENST00000518068,;ASPH,intron_variant,,ENST00000518306,;ASPH,upstream_gene_variant,,ENST00000522919,;ASPH,non_coding_transcript_exon_variant,,ENST00000519678,;ASPH,intron_variant,,ENST00000523927,;ASPH,intron_variant,,ENST00000524173,;ASPH,upstream_gene_variant,,ENST00000523897,;ASPH,non_coding_transcript_exon_variant,,ENST00000520198,;	C	ENSG00000198363	ENST00000379454	Transcript	missense_variant	747	559	187	L/V	Ctt/Gtt	.	.	.	-1	ASPH	HGNC	757	protein_coding	YES	CCDS34898.1	ENSP00000368767	ASPH_HUMAN	.	UPI0000161BFE	.	tolerated_low_confidence(0.62)	possibly_damaging(0.595)	6/25	.	Pfam_domain:PF05279,hmmpanther:PTHR12366,hmmpanther:PTHR12366:SF20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	1	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATAAGAAACT	.	5	ESCA
PREX2	0	.	GRCh37	8	69103972	69103972	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4362C>G	p.Asp1454Glu	p.D1454E	ENST00000288368	36/40	67	56	10	69	69	0	PREX2,missense_variant,p.Asp1454Glu,ENST00000288368,;PREX2,non_coding_transcript_exon_variant,,ENST00000522247,;PREX2,non_coding_transcript_exon_variant,,ENST00000520235,;	G	ENSG00000046889	ENST00000288368	Transcript	missense_variant	4639	4362	1454	D/E	gaC/gaG	.	.	.	1	PREX2	HGNC	22950	protein_coding	YES	CCDS6201.1	ENSP00000288368	PREX2_HUMAN	Q56UR8_HUMAN	UPI0000375435	.	tolerated(1)	benign(0.017)	36/40	.	hmmpanther:PTHR22829,hmmpanther:PTHR22829:SF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTGGACAAGTC	.	5	ESCA
MRPS28	0	.	GRCh37	8	80942328	80942328	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.156C>T	p.%3D	p.F52F	ENST00000276585	1/3	116	108	8	100	100	0	MRPS28,synonymous_variant,p.%3D,ENST00000521605,;MRPS28,synonymous_variant,p.%3D,ENST00000276585,;MRPS28,synonymous_variant,p.%3D,ENST00000518271,;TPD52,intron_variant,,ENST00000537855,;MRPS28,upstream_gene_variant,,ENST00000519120,;MRPS28,upstream_gene_variant,,ENST00000521434,;TPD52,downstream_gene_variant,,ENST00000379096,;MRPS28,upstream_gene_variant,,ENST00000519386,;MRPS28,upstream_gene_variant,,ENST00000520946,;RP11-92K15.3,downstream_gene_variant,,ENST00000607017,;MRPS28,non_coding_transcript_exon_variant,,ENST00000522987,;	A	ENSG00000147586	ENST00000276585	Transcript	synonymous_variant	179	156	52	F	ttC/ttT	.	.	.	-1	MRPS28	HGNC	14513	protein_coding	YES	CCDS6226.1	ENSP00000276585	RT28_HUMAN	E5RGC7_HUMAN	UPI00001352A5	.	.	.	1/3	.	hmmpanther:PTHR13447:SF1,hmmpanther:PTHR13447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	CTCGCGAAACC	.	2	ESCA
CDH17	0	.	GRCh37	8	95188895	95188895	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.298G>C	p.Asp100His	p.D100H	ENST00000027335	5/18	89	73	16	74	74	0	CDH17,missense_variant,p.Asp100His,ENST00000441892,;CDH17,missense_variant,p.Asp100His,ENST00000450165,;CDH17,missense_variant,p.Asp100His,ENST00000521491,;CDH17,missense_variant,p.Asp100His,ENST00000027335,;	G	ENSG00000079112	ENST00000027335	Transcript	missense_variant	423	298	100	D/H	Gac/Cac	.	.	.	-1	CDH17	HGNC	1756	protein_coding	YES	CCDS6260.1	ENSP00000027335	CAD17_HUMAN	E5RJT3_HUMAN	UPI000013C546	.	deleterious(0)	probably_damaging(0.937)	5/18	.	PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF292,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGCGTCCAGGG	.	5	ESCA
RAD54B	0	.	GRCh37	8	95444230	95444230	+	Intron	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.305-20687G>C	.	.	ENST00000336148	.	36	30	6	24	24	0	RAD54B,3_prime_UTR_variant,,ENST00000297592,;FSBP,3_prime_UTR_variant,,ENST00000481490,;RAD54B,intron_variant,,ENST00000336148,;RAD54B,intron_variant,,ENST00000523839,;RAD54B,intron_variant,,ENST00000463267,;RAD54B,intron_variant,,ENST00000518998,;FSBP,intron_variant,,ENST00000517506,;	G	ENSG00000197275	ENST00000336148	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	RAD54B	HGNC	17228	protein_coding	YES	CCDS6262.1	ENSP00000336606	RA54B_HUMAN	E5RHN9_HUMAN	UPI0000070088	.	.	.	.	3/14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	TATATCTAAAA	.	4	ESCA
OSR2	0	.	GRCh37	8	99961177	99961177	+	5'UTR	SNP	G	G	C	rs774614430	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-4G>C	.	.	ENST00000297565	2/4	30	25	5	34	34	0	OSR2,synonymous_variant,p.%3D,ENST00000520951,;OSR2,synonymous_variant,p.%3D,ENST00000457907,;OSR2,5_prime_UTR_variant,,ENST00000297565,;OSR2,5_prime_UTR_variant,,ENST00000522510,;OSR2,5_prime_UTR_variant,,ENST00000518199,;OSR2,5_prime_UTR_variant,,ENST00000523368,;OSR2,5_prime_UTR_variant,,ENST00000435298,;RP11-44N12.5,downstream_gene_variant,,ENST00000606778,;OSR2,intron_variant,,ENST00000520722,;OSR2,intron_variant,,ENST00000521044,;OSR2,downstream_gene_variant,,ENST00000520791,;	C	ENSG00000164920	ENST00000297565	Transcript	5_prime_UTR_variant	493	.	.	.	.	rs774614430	.	.	1	OSR2	HGNC	15830	protein_coding	YES	CCDS47901.1	ENSP00000297565	OSR2_HUMAN	E5RH47_HUMAN	UPI00001AEC4D	.	.	.	2/4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCCCGGAAAAT	.	4	ESCA
NANS	0	.	GRCh37	9	100839226	100839226	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.375G>A	p.%3D	p.L125L	ENST00000210444	3/6	109	77	32	81	81	0	NANS,synonymous_variant,p.%3D,ENST00000210444,;NANS,5_prime_UTR_variant,,ENST00000415280,;TRIM14,intron_variant,,ENST00000375098,;NANS,upstream_gene_variant,,ENST00000427646,;NANS,non_coding_transcript_exon_variant,,ENST00000461452,;NANS,non_coding_transcript_exon_variant,,ENST00000495319,;TRIM14,downstream_gene_variant,,ENST00000478530,;	A	ENSG00000095380	ENST00000210444	Transcript	synonymous_variant	445	375	125	L	ctG/ctA	.	.	.	1	NANS	HGNC	19237	protein_coding	YES	CCDS6733.1	ENSP00000210444	SIAS_HUMAN	.	UPI000013597F	.	.	.	3/6	.	hmmpanther:PTHR23416,hmmpanther:PTHR23416:SF1,Pfam_domain:PF03102,Gene3D:3.20.20.70,Superfamily_domains:SSF51569	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GAACTGAATGT	.	5	ESCA
ABCA1	0	.	GRCh37	9	107579672	107579672	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3476C>G	p.Ser1159Cys	p.S1159C	ENST00000374736	24/50	16	11	4	15	15	0	ABCA1,missense_variant,p.Ser1159Cys,ENST00000374736,;	C	ENSG00000165029	ENST00000374736	Transcript	missense_variant	3871	3476	1159	S/C	tCt/tGt	.	.	.	-1	ABCA1	HGNC	29	protein_coding	YES	CCDS6762.1	ENSP00000363868	ABCA1_HUMAN	Q9NS76_HUMAN,Q9NP93_HUMAN,Q9H002_HUMAN	UPI000013E441	.	tolerated(0.16)	benign(0.035)	24/50	.	hmmpanther:PTHR19229:SF34,hmmpanther:PTHR19229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|VARSCANS	TCTGAGAAACA	.	4	ESCA
SNX30	0	.	GRCh37	9	115580089	115580089	+	Silent	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.453C>G	p.%3D	p.L151L	ENST00000374232	3/9	44	37	7	44	44	0	SNX30,synonymous_variant,p.%3D,ENST00000374232,;	G	ENSG00000148158	ENST00000374232	Transcript	synonymous_variant	617	453	151	L	ctC/ctG	.	.	.	1	SNX30	HGNC	23685	protein_coding	YES	CCDS43865.1	ENSP00000363349	SNX30_HUMAN	.	UPI0000457796	.	.	.	3/9	.	PROSITE_profiles:PS50195,hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF123,Gene3D:3.30.1520.10,Pfam_domain:PF00787,SMART_domains:SM00312,Superfamily_domains:SSF64268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CATCTCATTCC	.	5	ESCA
TRIM32	0	.	GRCh37	9	119463515	119463515	+	3'UTR	SNP	T	T	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1532T>A	.	.	ENST00000450136	2/2	72	52	19	70	70	0	TRIM32,3_prime_UTR_variant,,ENST00000373983,;TRIM32,3_prime_UTR_variant,,ENST00000450136,;ASTN2,intron_variant,,ENST00000373996,;ASTN2,intron_variant,,ENST00000373986,;ASTN2,intron_variant,,ENST00000361209,;ASTN2,intron_variant,,ENST00000313400,;ASTN2,intron_variant,,ENST00000361477,;TRIM32,downstream_gene_variant,,ENST00000411410,;	A	ENSG00000119401	ENST00000450136	Transcript	3_prime_UTR_variant	3655	.	.	.	.	.	.	.	1	TRIM32	HGNC	16380	protein_coding	YES	CCDS6817.1	ENSP00000408292	TRI32_HUMAN	Q5JVY0_HUMAN	UPI000012CDB9	.	.	.	2/2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTTCTTTGGAT	.	5	ESCA
RBM18	0	.	GRCh37	9	125003773	125003773	+	3'UTR	SNP	C	C	T	rs192910977	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*390G>A	.	.	ENST00000417201	6/6	125	103	21	101	101	0	RBM18,3_prime_UTR_variant,,ENST00000417201,;RBM18,downstream_gene_variant,,ENST00000483428,;RBM18,downstream_gene_variant,,ENST00000491850,;	T	ENSG00000119446	ENST00000417201	Transcript	3_prime_UTR_variant	1104	.	.	.	.	rs192910977	.	.	-1	RBM18	HGNC	28413	protein_coding	YES	CCDS6839.1	ENSP00000409315	RBM18_HUMAN	.	UPI0000046802	.	.	.	6/6	.	.	T:0.0002	T:0.0008	T:0	.	T:0	T:0	T:0	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAGACACACG	by1000G	5	ESCA
LRSAM1	0	.	GRCh37	9	130265075	130265075	+	Missense_Mutation	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2069G>A	p.Cys690Tyr	p.C690Y	ENST00000323301	25/25	53	46	7	52	52	0	LRSAM1,missense_variant,p.Cys690Tyr,ENST00000300417,;LRSAM1,missense_variant,p.Cys690Tyr,ENST00000323301,;LRSAM1,missense_variant,p.Cys690Tyr,ENST00000373322,;LRSAM1,missense_variant,p.Cys663Tyr,ENST00000373324,;FAM129B,downstream_gene_variant,,ENST00000373312,;FAM129B,downstream_gene_variant,,ENST00000373314,;LRSAM1,non_coding_transcript_exon_variant,,ENST00000483302,;LRSAM1,intron_variant,,ENST00000476755,;FAM129B,downstream_gene_variant,,ENST00000468379,;LRSAM1,downstream_gene_variant,,ENST00000472068,;FAM129B,downstream_gene_variant,,ENST00000478917,;FAM129B,downstream_gene_variant,,ENST00000484348,;	A	ENSG00000148356	ENST00000323301	Transcript	missense_variant	2673	2069	690	C/Y	tGt/tAt	.	.	.	1	LRSAM1	HGNC	25135	protein_coding	YES	CCDS6873.1	ENSP00000322937	LRSM1_HUMAN	.	UPI000013DB12	.	deleterious(0)	probably_damaging(0.954)	25/25	.	PROSITE_profiles:PS50089,Pfam_domain:PF13920,Gene3D:3.30.40.10,Superfamily_domains:SSF57850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUSE|VARSCANS	CAACTGTGGCC	.	3	ESCA
STXBP1	0	.	GRCh37	9	130454790	130454790	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1753C>G	.	.	ENST00000373302	20/20	149	122	26	148	148	0	STXBP1,3_prime_UTR_variant,,ENST00000373302,;STXBP1,3_prime_UTR_variant,,ENST00000373299,;MIR3911,upstream_gene_variant,,ENST00000577791,;STXBP1,intron_variant,,ENST00000481942,;PTRH1,downstream_gene_variant,,ENST00000335223,;	G	ENSG00000136854	ENST00000373302	Transcript	3_prime_UTR_variant	3704	.	.	.	.	.	.	.	1	STXBP1	HGNC	11444	protein_coding	YES	CCDS6874.1	ENSP00000362399	STXB1_HUMAN	.	UPI0000006C0B	.	.	.	20/20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTTTCTCTGT	.	5	ESCA
URM1	0	.	GRCh37	9	131133692	131133692	+	Silent	SNP	C	C	T	rs752847603	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.33C>T	p.%3D	p.F11F	ENST00000452446	1/4	71	62	8	52	52	0	URM1,synonymous_variant,p.%3D,ENST00000372847,;URM1,synonymous_variant,p.%3D,ENST00000372850,;URM1,synonymous_variant,p.%3D,ENST00000452446,;URM1,synonymous_variant,p.%3D,ENST00000372853,;URM1,synonymous_variant,p.%3D,ENST00000470840,;	T	ENSG00000167118	ENST00000452446	Transcript	synonymous_variant	95	33	11	F	ttC/ttT	rs752847603	.	.	1	URM1	HGNC	28378	protein_coding	YES	CCDS48035.1	ENSP00000412922	URM1_HUMAN	.	UPI00017A7D83	.	.	.	1/4	.	HAMAP:MF_03048,hmmpanther:PTHR14986:SF4,hmmpanther:PTHR14986,Pfam_domain:PF09138,Gene3D:3.10.20.30,Superfamily_domains:SSF54285	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|MUTECT|MUSE|VARSCANS	GAGTTCGGGTG	.	4	ESCA
SPTAN1	0	.	GRCh37	9	131371527	131371527	+	Silent	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4722G>A	p.%3D	p.A1574A	ENST00000372739	36/57	113	88	25	105	105	0	SPTAN1,synonymous_variant,p.%3D,ENST00000372739,;SPTAN1,synonymous_variant,p.%3D,ENST00000358161,;SPTAN1,synonymous_variant,p.%3D,ENST00000372731,;SPTAN1,upstream_gene_variant,,ENST00000476825,;SPTAN1,downstream_gene_variant,,ENST00000461855,;	A	ENSG00000197694	ENST00000372739	Transcript	synonymous_variant	4832	4722	1574	A	gcG/gcA	.	.	.	1	SPTAN1	HGNC	11273	protein_coding	YES	CCDS48036.1	ENSP00000361824	SPTN1_HUMAN	.	UPI000045894C	.	.	.	36/57	.	hmmpanther:PTHR11915:SF250,hmmpanther:PTHR11915,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	ACAGCGAGTGA	.	5	ESCA
PMPCA	0	.	GRCh37	9	139310748	139310748	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.538G>C	p.Glu180Gln	p.E180Q	ENST00000371717	6/13	25	17	8	9	9	0	PMPCA,missense_variant,p.Glu49Gln,ENST00000399219,;PMPCA,missense_variant,p.Glu180Gln,ENST00000371717,;PMPCA,3_prime_UTR_variant,,ENST00000371720,;PMPCA,upstream_gene_variant,,ENST00000444897,;PMPCA,non_coding_transcript_exon_variant,,ENST00000462616,;	C	ENSG00000165688	ENST00000371717	Transcript	missense_variant	547	538	180	E/Q	Gaa/Caa	.	.	.	1	PMPCA	HGNC	18667	protein_coding	YES	CCDS35180.1	ENSP00000360782	MPPA_HUMAN	Q9BT52_HUMAN,Q5SXN0_HUMAN	UPI00000703D3	.	deleterious(0.04)	possibly_damaging(0.893)	6/13	.	hmmpanther:PTHR11851:SF49,hmmpanther:PTHR11851,Gene3D:3.30.830.10,Pfam_domain:PF00675,Superfamily_domains:SSF63411	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	ATGAAGAAGTC	.	3	ESCA
ANAPC2	0	.	GRCh37	9	140082363	140082363	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.310G>C	p.Glu104Gln	p.E104Q	ENST00000323927	2/13	20	15	5	17	17	0	ANAPC2,missense_variant,p.Glu104Gln,ENST00000323927,;TPRN,downstream_gene_variant,,ENST00000409012,;TPRN,downstream_gene_variant,,ENST00000321773,;TPRN,downstream_gene_variant,,ENST00000333046,;SSNA1,upstream_gene_variant,,ENST00000322310,;ANAPC2,upstream_gene_variant,,ENST00000495611,;ANAPC2,upstream_gene_variant,,ENST00000471131,;SSNA1,upstream_gene_variant,,ENST00000464553,;SSNA1,upstream_gene_variant,,ENST00000459860,;TPRN,downstream_gene_variant,,ENST00000541945,;SSNA1,upstream_gene_variant,,ENST00000463511,;TPRN,downstream_gene_variant,,ENST00000477345,;	G	ENSG00000176248	ENST00000323927	Transcript	missense_variant	315	310	104	E/Q	Gag/Cag	.	.	.	-1	ANAPC2	HGNC	19989	protein_coding	YES	CCDS7033.1	ENSP00000314004	ANC2_HUMAN	B4DJR9_HUMAN	UPI0000043E1B	.	tolerated(0.19)	benign(0.391)	2/13	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GGGCTCATCCG	.	5	ESCA
NSMF	0	.	GRCh37	9	140344061	140344061	+	Silent	SNP	G	G	C	rs780154049	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1485C>G	p.%3D	p.L495L	ENST00000371475	15/16	64	45	18	74	74	0	NSMF,synonymous_variant,p.%3D,ENST00000371474,;NSMF,synonymous_variant,p.%3D,ENST00000371475,;NSMF,synonymous_variant,p.%3D,ENST00000437259,;NSMF,synonymous_variant,p.%3D,ENST00000371473,;NSMF,synonymous_variant,p.%3D,ENST00000371482,;NSMF,synonymous_variant,p.%3D,ENST00000371472,;NSMF,synonymous_variant,p.%3D,ENST00000392812,;NSMF,synonymous_variant,p.%3D,ENST00000541195,;NSMF,synonymous_variant,p.%3D,ENST00000339554,;NSMF,synonymous_variant,p.%3D,ENST00000265663,;NSMF,downstream_gene_variant,,ENST00000371468,;NSMF,non_coding_transcript_exon_variant,,ENST00000484316,;NSMF,downstream_gene_variant,,ENST00000482448,;	C	ENSG00000165802	ENST00000371475	Transcript	synonymous_variant	1717	1485	495	L	ctC/ctG	rs780154049	.	.	-1	NSMF	HGNC	29843	protein_coding	YES	CCDS48069.1	ENSP00000360530	NSMF_HUMAN	Q9BT66_HUMAN,Q96AQ0_HUMAN,A8K7L5_HUMAN	UPI000035198D	.	.	.	15/16	.	hmmpanther:PTHR32061	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	GCTGAGAGCTC	.	5	ESCA
EHMT1	0	.	GRCh37	9	140672331	140672331	+	Intron	SNP	A	A	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2019-3A>C	.	.	ENST00000460843	.	62	53	8	55	55	0	EHMT1,splice_region_variant,,ENST00000334856,;EHMT1,splice_region_variant,,ENST00000462484,;EHMT1,splice_region_variant,,ENST00000460843,;EHMT1,splice_region_variant,,ENST00000371394,;EHMT1,downstream_gene_variant,,ENST00000465566,;EHMT1,splice_region_variant,,ENST00000462942,;	C	ENSG00000181090	ENST00000460843	Transcript	splice_region_variant	.	.	.	.	.	.	.	.	1	EHMT1	HGNC	24650	protein_coding	YES	CCDS7050.2	ENSP00000417980	EHMT1_HUMAN	Q71M33_HUMAN,A0PJE0_HUMAN	UPI000194EC2D	.	.	.	.	12/26	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCCTGAAGTGC	.	4	ESCA
SMARCA2	0	.	GRCh37	9	2058298	2058298	+	Missense_Mutation	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1355T>C	p.Leu452Pro	p.L452P	ENST00000382203	8/34	76	42	34	53	53	0	SMARCA2,missense_variant,p.Leu452Pro,ENST00000382194,;SMARCA2,missense_variant,p.Leu452Pro,ENST00000382203,;SMARCA2,missense_variant,p.Leu452Pro,ENST00000450198,;SMARCA2,missense_variant,p.Leu452Pro,ENST00000357248,;SMARCA2,missense_variant,p.Leu452Pro,ENST00000349721,;	C	ENSG00000080503	ENST00000382203	Transcript	missense_variant	1564	1355	452	L/P	cTg/cCg	.	.	.	1	SMARCA2	HGNC	11098	protein_coding	YES	CCDS34977.1	ENSP00000371638	SMCA2_HUMAN	Q6LC24_HUMAN,Q56A76_HUMAN,F6XDY1_HUMAN,F6VDE0_HUMAN,F6RS74_HUMAN,F6QYQ1_HUMAN,B1ALG5_HUMAN,B1ALG2_HUMAN	UPI00001AE8EB	.	.	benign(0.164)	8/34	.	PROSITE_profiles:PS51204,hmmpanther:PTHR10799:SF541,hmmpanther:PTHR10799,Pfam_domain:PF07529,SMART_domains:SM00573	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ATACCTGAACA	.	5	ESCA
UBAP2	0	.	GRCh37	9	33927920	33927920	+	Nonsense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2246C>G	p.Ser749Ter	p.S749*	ENST00000379238	20/29	25	18	7	32	32	0	UBAP2,stop_gained,p.Ser749Ter,ENST00000379238,;UBAP2,stop_gained,p.Ser482Ter,ENST00000379239,;UBAP2,stop_gained,p.Ser749Ter,ENST00000449054,;UBAP2,stop_gained,p.Ser504Ter,ENST00000539807,;UBAP2,stop_gained,p.Ser749Ter,ENST00000360802,;UBAP2,missense_variant,p.Gln674Glu,ENST00000418786,;UBAP2,5_prime_UTR_variant,,ENST00000379235,;UBAP2,non_coding_transcript_exon_variant,,ENST00000474372,;UBAP2,missense_variant,p.Gln105Glu,ENST00000488443,;	C	ENSG00000137073	ENST00000379238	Transcript	stop_gained	2364	2246	749	S/*	tCa/tGa	.	.	.	-1	UBAP2	HGNC	14185	protein_coding	YES	CCDS6547.1	ENSP00000368540	UBAP2_HUMAN	Q5JV03_HUMAN	UPI0000140784	.	.	.	20/29	.	Low_complexity_(Seg):seg,hmmpanther:PTHR16308,hmmpanther:PTHR16308:SF17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	AACTTGAGACG	.	2	ESCA
ZFAND5	0	.	GRCh37	9	74970020	74970020	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*849G>C	.	.	ENST00000237937	6/6	108	81	27	62	62	0	ZFAND5,3_prime_UTR_variant,,ENST00000237937,;ZFAND5,3_prime_UTR_variant,,ENST00000376960,;ZFAND5,3_prime_UTR_variant,,ENST00000376962,;ZFAND5,downstream_gene_variant,,ENST00000343431,;ZFAND5,downstream_gene_variant,,ENST00000376956,;ZFAND5,non_coding_transcript_exon_variant,,ENST00000488164,;ZFAND5,downstream_gene_variant,,ENST00000471197,;	G	ENSG00000107372	ENST00000237937	Transcript	3_prime_UTR_variant	2049	.	.	.	.	.	.	.	-1	ZFAND5	HGNC	13008	protein_coding	YES	CCDS6642.1	ENSP00000237937	ZFAN5_HUMAN	.	UPI000013C322	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TTATTCAGATA	.	5	ESCA
TMC1	0	.	GRCh37	9	75263520	75263520	+	5'UTR	SNP	C	C	G	rs768817345	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-45C>G	.	.	ENST00000297784	5/24	56	45	11	58	58	0	TMC1,5_prime_UTR_variant,,ENST00000297784,;TMC1,5_prime_UTR_variant,,ENST00000340019,;TMC1,upstream_gene_variant,,ENST00000396237,;TMC1,non_coding_transcript_exon_variant,,ENST00000492418,;	G	ENSG00000165091	ENST00000297784	Transcript	5_prime_UTR_variant	496	.	.	.	.	rs768817345	.	.	1	TMC1	HGNC	16513	protein_coding	YES	CCDS6643.1	ENSP00000297784	TMC1_HUMAN	.	UPI0000161FA9	.	.	.	5/24	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCTCTCCAAAC	byFrequency	5	ESCA
GADD45G	0	.	GRCh37	9	92220309	92220309	+	Intron	SNP	C	C	G	rs766068213	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.54-38C>G	.	.	ENST00000252506	.	24	17	7	19	19	0	GADD45G,5_prime_UTR_variant,,ENST00000375769,;GADD45G,intron_variant,,ENST00000252506,;GADD45G,non_coding_transcript_exon_variant,,ENST00000494726,;	G	ENSG00000130222	ENST00000252506	Transcript	intron_variant	.	.	.	.	.	rs766068213	.	.	1	GADD45G	HGNC	4097	protein_coding	YES	CCDS6686.1	ENSP00000252506	GA45G_HUMAN	Q5VZ88_HUMAN,Q5VZ87_HUMAN,Q5MAI3_HUMAN	UPI000012AEF1	.	.	.	.	1/3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCCTCCGGCC	.	5	ESCA
BICD2	0	.	GRCh37	9	95526873	95526873	+	Missense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.154G>C	p.Glu52Gln	p.E52Q	ENST00000356884	1/7	56	43	13	44	44	0	BICD2,missense_variant,p.Glu52Gln,ENST00000375512,;BICD2,missense_variant,p.Glu52Gln,ENST00000356884,;	G	ENSG00000185963	ENST00000356884	Transcript	missense_variant	222	154	52	E/Q	Gag/Cag	.	.	.	-1	BICD2	HGNC	17208	protein_coding	YES	CCDS35064.1	ENSP00000349351	BICD2_HUMAN	.	UPI00001BBAF1	.	deleterious(0)	probably_damaging(0.978)	1/7	.	hmmpanther:PTHR31233,hmmpanther:PTHR31233:SF7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CTCCTCGAGCA	.	5	ESCA
FGD3	0	.	GRCh37	9	95773521	95773521	+	Silent	SNP	C	C	T	rs140324424	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1002C>T	p.%3D	p.A334A	ENST00000375482	8/18	97	65	32	65	65	0	FGD3,synonymous_variant,p.%3D,ENST00000416701,;FGD3,synonymous_variant,p.%3D,ENST00000375482,;FGD3,synonymous_variant,p.%3D,ENST00000337352,;FGD3,upstream_gene_variant,,ENST00000538555,;FGD3,upstream_gene_variant,,ENST00000494553,;FGD3,synonymous_variant,p.%3D,ENST00000467786,;	T	ENSG00000127084	ENST00000375482	Transcript	synonymous_variant	1498	1002	334	A	gcC/gcT	rs140324424	.	.	1	FGD3	HGNC	16027	protein_coding	YES	CCDS43849.1	ENSP00000364631	FGD3_HUMAN	B4DXH4_HUMAN	UPI0000199249	.	.	.	8/18	.	PROSITE_profiles:PS50010,hmmpanther:PTHR12673:SF14,hmmpanther:PTHR12673,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065	T:0.0012	T:0.0045	T:0	.	T:0	T:0	T:0	T:0.0012	T:0.0001	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	ACAGCCGCCAA	byFrequency|byCluster|by1000G	5	ESCA
PTPDC1	0	.	GRCh37	9	96870182	96870182	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2377G>C	p.Glu793Gln	p.E793Q	ENST00000288976	9/9	95	76	18	91	91	0	PTPDC1,missense_variant,p.Glu793Gln,ENST00000288976,;PTPDC1,missense_variant,p.Glu741Gln,ENST00000375360,;PTPDC1,non_coding_transcript_exon_variant,,ENST00000467049,;	C	ENSG00000158079	ENST00000288976	Transcript	missense_variant	2444	2377	793	E/Q	Gaa/Caa	.	.	.	1	PTPDC1	HGNC	30184	protein_coding	YES	CCDS6708.1	ENSP00000288976	PTPC1_HUMAN	.	UPI000004DC48	.	deleterious(0.01)	possibly_damaging(0.786)	9/9	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGAAGAAAAA	.	5	ESCA
FBP2	0	.	GRCh37	9	97346898	97346898	+	Silent	SNP	G	G	A	rs758913276	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.387C>T	p.%3D	p.C129C	ENST00000375337	3/7	27	24	3	43	43	0	FBP2,synonymous_variant,p.%3D,ENST00000375337,;	A	ENSG00000130957	ENST00000375337	Transcript	synonymous_variant	454	387	129	C	tgC/tgT	rs758913276	.	.	-1	FBP2	HGNC	3607	protein_coding	YES	CCDS6711.1	ENSP00000364486	F16P2_HUMAN	.	UPI000013CDC2	.	.	.	3/7	.	Superfamily_domains:SSF56655,PIRSF_domain:PIRSF000904,PIRSF_domain:PIRSF500210,Pfam_domain:PF00316,Gene3D:3.30.540.10,hmmpanther:PTHR11556:SF13,hmmpanther:PTHR11556,HAMAP:MF_01855	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE	GCCAGGCAGTC	byFrequency	2	ESCA
ACSL4	0	.	GRCh37	X	108911423	108911423	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1345C>G	p.Gln449Glu	p.Q449E	ENST00000340800	12/17	42	22	19	26	26	0	ACSL4,missense_variant,p.Gln449Glu,ENST00000340800,;ACSL4,missense_variant,p.Gln408Glu,ENST00000348502,;ACSL4,missense_variant,p.Gln449Glu,ENST00000469796,;ACSL4,missense_variant,p.Gln53Glu,ENST00000514500,;	C	ENSG00000068366	ENST00000340800	Transcript	missense_variant	1850	1345	449	Q/E	Cag/Gag	.	.	.	-1	ACSL4	HGNC	3571	protein_coding	YES	CCDS14548.1	ENSP00000339787	ACSL4_HUMAN	Q5JWV8_HUMAN,D6RFW9_HUMAN,D6RF95_HUMAN,D6RDA8_HUMAN,D6RD96_HUMAN	UPI000012E293	.	tolerated(1)	benign(0.181)	12/17	.	Superfamily_domains:SSF56801,Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF126	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTCTGAGGAG	.	5	ESCA
ZCCHC16	0	.	GRCh37	X	111699597	111699597	+	3'UTR	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*708T>C	.	.	ENST00000340433	1/1	32	18	13	22	22	0	ZCCHC16,3_prime_UTR_variant,,ENST00000340433,;	C	ENSG00000187823	ENST00000340433	Transcript	3_prime_UTR_variant	1871	.	.	.	.	.	.	.	1	ZCCHC16	HGNC	25214	protein_coding	YES	CCDS35369.1	ENSP00000340590	ZCH16_HUMAN	.	UPI00001975B5	.	.	.	1/1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AACTGTTGGTC	.	5	ESCA
HTR2C	0	.	GRCh37	X	113886032	113886032	+	Intron	SNP	T	T	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.-80+37693T>C	.	.	ENST00000276198	.	48	18	29	26	26	0	HTR2C,intron_variant,,ENST00000371950,;HTR2C,intron_variant,,ENST00000276198,;HTR2C,intron_variant,,ENST00000371951,;MIR1912,non_coding_transcript_exon_variant,,ENST00000410389,;	C	ENSG00000147246	ENST00000276198	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	HTR2C	HGNC	5295	protein_coding	YES	CCDS14564.1	ENSP00000276198	5HT2C_HUMAN	B3VRF0_HUMAN,B3VRE5_HUMAN,B3VRE0_HUMAN	UPI000000126F	.	.	.	.	2/5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGTGCTCATTG	.	5	ESCA
GRIA3	0	.	GRCh37	X	122613989	122613989	+	Intron	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.2440-2661C>T	.	.	ENST00000264357	.	71	33	37	68	68	0	GRIA3,synonymous_variant,p.%3D,ENST00000371256,;GRIA3,3_prime_UTR_variant,,ENST00000542149,;GRIA3,intron_variant,,ENST00000264357,;GRIA3,intron_variant,,ENST00000371251,;GRIA3,upstream_gene_variant,,ENST00000460123,;	T	ENSG00000125675	ENST00000264357	Transcript	intron_variant	.	.	.	.	.	.	.	.	1	GRIA3	HGNC	4573	protein_coding	YES	CCDS14604.1	ENSP00000264357	GRIA3_HUMAN	Q9UHA9_HUMAN	UPI000013D503	.	.	.	.	14/15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGGTACGATAA	.	5	ESCA
FMR1	0	.	GRCh37	X	147031822	147031822	+	3'UTR	SNP	G	G	A	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*1458G>A	.	.	ENST00000370475	17/17	83	37	46	80	80	0	FMR1,3_prime_UTR_variant,,ENST00000218200,;FMR1,3_prime_UTR_variant,,ENST00000370475,;FMR1,3_prime_UTR_variant,,ENST00000370471,;FMR1,3_prime_UTR_variant,,ENST00000370477,;FMR1,3_prime_UTR_variant,,ENST00000439526,;FMR1,downstream_gene_variant,,ENST00000440235,;FMR1,downstream_gene_variant,,ENST00000370470,;FMR1-IT1,downstream_gene_variant,,ENST00000441414,;FMR1,downstream_gene_variant,,ENST00000478848,;FMR1,downstream_gene_variant,,ENST00000463120,;	A	ENSG00000102081	ENST00000370475	Transcript	3_prime_UTR_variant	3485	.	.	.	.	.	.	.	1	FMR1	HGNC	3775	protein_coding	YES	CCDS14682.1	ENSP00000359506	FMR1_HUMAN	.	UPI000012AACA	.	.	.	17/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAAATGGCAAC	.	5	ESCA
FATE1	0	.	GRCh37	X	150884668	150884668	+	Missense_Mutation	SNP	G	G	C	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.77G>C	p.Gly26Ala	p.G26A	ENST00000370350	1/5	25	13	12	30	30	0	FATE1,missense_variant,p.Gly18Ala,ENST00000417321,;FATE1,missense_variant,p.Gly26Ala,ENST00000370350,;	C	ENSG00000147378	ENST00000370350	Transcript	missense_variant	162	77	26	G/A	gGg/gCg	COSM3843891	.	.	1	FATE1	HGNC	24683	protein_coding	YES	CCDS14700.1	ENSP00000359375	FATE1_HUMAN	.	UPI0000073DB2	.	tolerated(0.63)	benign(0.355)	1/5	.	hmmpanther:PTHR21128	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CCAAGGGGAAA	.	5	ESCA
MECP2	0	.	GRCh37	X	153295862	153295862	+	Missense_Mutation	SNP	C	C	G	rs782115829	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1453G>C	p.Glu485Gln	p.E485Q	ENST00000453960	3/3	38	29	8	49	49	0	MECP2,missense_variant,p.Glu473Gln,ENST00000303391,;MECP2,missense_variant,p.Glu485Gln,ENST00000453960,;MECP2,downstream_gene_variant,,ENST00000407218,;MECP2,downstream_gene_variant,,ENST00000415944,;MECP2,downstream_gene_variant,,ENST00000488293,;MECP2,downstream_gene_variant,,ENST00000460227,;MECP2,downstream_gene_variant,,ENST00000486506,;MECP2,downstream_gene_variant,,ENST00000496908,;MECP2,downstream_gene_variant,,ENST00000481807,;MECP2,downstream_gene_variant,,ENST00000463644,;MECP2,downstream_gene_variant,,ENST00000369957,;	G	ENSG00000169057	ENST00000453960	Transcript	missense_variant	1508	1453	485	E/Q	Gag/Cag	rs782115829	.	.	-1	MECP2	HGNC	6990	protein_coding	YES	CCDS48193.1	ENSP00000395535	MECP2_HUMAN	.	UPI0000253F1B	.	deleterious(0)	unknown(0)	3/3	.	hmmpanther:PTHR15074:SF1,hmmpanther:PTHR15074,PIRSF_domain:PIRSF038006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGGCTCCTCTC	.	5	ESCA
RBBP7	0	.	GRCh37	X	16888524	16888524	+	5'Flank	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ENST00000380084	.	18	11	7	9	9	0	RBBP7,5_prime_UTR_variant,,ENST00000380087,;RBBP7,upstream_gene_variant,,ENST00000493145,;RBBP7,upstream_gene_variant,,ENST00000380084,;RBBP7,upstream_gene_variant,,ENST00000404022,;RBBP7,upstream_gene_variant,,ENST00000468092,;RNU4-6P,downstream_gene_variant,,ENST00000410804,;	T	ENSG00000102054	ENST00000380084	Transcript	upstream_gene_variant	.	.	.	.	.	.	.	515	-1	RBBP7	HGNC	9890	protein_coding	YES	CCDS56598.1	ENSP00000369424	RBBP7_HUMAN	Q5JNZ6_HUMAN,C9J7L0_HUMAN	UPI00001AE848	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|MUSE|VARSCANS	CGGCTCCGGCG	.	3	ESCA
NHS	0	.	GRCh37	X	17745851	17745851	+	Missense_Mutation	SNP	G	G	C	rs749817644	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.3562G>C	p.Glu1188Gln	p.E1188Q	ENST00000380060	6/8	21	9	12	13	13	0	NHS,missense_variant,p.Glu1188Gln,ENST00000380060,;NHS,missense_variant,p.Glu1032Gln,ENST00000398097,;NHS,downstream_gene_variant,,ENST00000485305,;	C	ENSG00000188158	ENST00000380060	Transcript	missense_variant	3900	3562	1188	E/Q	Gag/Cag	rs749817644	.	.	1	NHS	HGNC	7820	protein_coding	YES	CCDS14181.1	ENSP00000369400	NHS_HUMAN	.	UPI00001DFBF3	.	tolerated_low_confidence(0.13)	benign(0.026)	6/8	.	hmmpanther:PTHR23039:SF5,hmmpanther:PTHR23039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	CAGTTGAGATG	.	5	ESCA
ZFX	0	.	GRCh37	X	24231781	24231781	+	3'UTR	SNP	G	G	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*2288G>T	.	.	ENST00000379177	11/11	42	24	17	24	24	0	ZFX,3_prime_UTR_variant,,ENST00000379188,;ZFX,3_prime_UTR_variant,,ENST00000379177,;ZFX,3_prime_UTR_variant,,ENST00000539115,;ZFX,downstream_gene_variant,,ENST00000540034,;ZFX,downstream_gene_variant,,ENST00000304543,;ZFX,downstream_gene_variant,,ENST00000338565,;ZFX,downstream_gene_variant,,ENST00000459724,;	T	ENSG00000005889	ENST00000379177	Transcript	3_prime_UTR_variant	5133	.	.	.	.	.	.	.	1	ZFX	HGNC	12869	protein_coding	YES	CCDS14211.1	ENSP00000368475	ZFX_HUMAN	Q9BYX9_HUMAN,Q8WXB8_HUMAN,Q8NHZ5_HUMAN,C9JGU9_HUMAN,C9J682_HUMAN	UPI000013C504	.	.	.	11/11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|MUTECT|MUSE|VARSCANS	TCTTGGCCCCC	.	4	ESCA
MAOB	0	.	GRCh37	X	43661490	43661490	+	Nonsense_Mutation	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.405G>A	p.Trp135Ter	p.W135*	ENST00000378069	5/15	18	10	8	12	12	0	MAOB,stop_gained,p.Trp119Ter,ENST00000538942,;MAOB,stop_gained,p.Trp119Ter,ENST00000536181,;MAOB,stop_gained,p.Trp135Ter,ENST00000378069,;MAOB,non_coding_transcript_exon_variant,,ENST00000487544,;	T	ENSG00000069535	ENST00000378069	Transcript	stop_gained	553	405	135	W/*	tgG/tgA	.	.	.	-1	MAOB	HGNC	6834	protein_coding	YES	CCDS14261.1	ENSP00000367309	AOFB_HUMAN	H0YCD8_HUMAN,B7Z242_HUMAN	UPI0000049071	.	.	.	5/15	.	hmmpanther:PTHR10742,hmmpanther:PTHR10742:SF219,Pfam_domain:PF01593,Gene3D:1.10.405.10,Superfamily_domains:SSF51905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTTCCATGG	.	5	ESCA
PIM2	0	.	GRCh37	X	48770714	48770714	+	3'UTR	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*694G>C	.	.	ENST00000376509	6/6	24	15	8	20	20	0	PIM2,3_prime_UTR_variant,,ENST00000376509,;SLC35A2,upstream_gene_variant,,ENST00000376529,;SLC35A2,upstream_gene_variant,,ENST00000247138,;SLC35A2,upstream_gene_variant,,ENST00000376512,;SLC35A2,upstream_gene_variant,,ENST00000413561,;SLC35A2,upstream_gene_variant,,ENST00000445167,;SLC35A2,upstream_gene_variant,,ENST00000376515,;SLC35A2,upstream_gene_variant,,ENST00000446885,;SLC35A2,upstream_gene_variant,,ENST00000376521,;SLC35A2,upstream_gene_variant,,ENST00000452555,;PIM2,downstream_gene_variant,,ENST00000442430,;PIM2,downstream_gene_variant,,ENST00000485431,;	G	ENSG00000102096	ENST00000376509	Transcript	3_prime_UTR_variant	1820	.	.	.	.	.	.	.	-1	PIM2	HGNC	8987	protein_coding	YES	CCDS14312.1	ENSP00000365692	PIM2_HUMAN	C9J8V9_HUMAN	UPI0000049044	.	.	.	6/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	CCCATCCTAGT	.	5	ESCA
VSIG4	0	.	GRCh37	X	65241712	65241712	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*393C>G	.	.	ENST00000374737	8/8	43	30	12	27	27	0	VSIG4,3_prime_UTR_variant,,ENST00000455586,;VSIG4,3_prime_UTR_variant,,ENST00000412866,;VSIG4,3_prime_UTR_variant,,ENST00000374737,;VSIG4,3_prime_UTR_variant,,ENST00000427538,;MIR223,downstream_gene_variant,,ENST00000385204,;	C	ENSG00000155659	ENST00000374737	Transcript	3_prime_UTR_variant	1702	.	.	.	.	.	.	.	-1	VSIG4	HGNC	17032	protein_coding	YES	CCDS14383.1	ENSP00000363869	VSIG4_HUMAN	.	UPI000006F146	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAAAGAGAAA	.	5	ESCA
EDA	0	.	GRCh37	X	69259170	69259170	+	3'UTR	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*3711G>C	.	.	ENST00000374552	8/8	111	82	29	100	100	0	EDA,3_prime_UTR_variant,,ENST00000374553,;EDA,3_prime_UTR_variant,,ENST00000374552,;AWAT2,downstream_gene_variant,,ENST00000276101,;EDA,downstream_gene_variant,,ENST00000524573,;AWAT2,downstream_gene_variant,,ENST00000443056,;AWAT2,downstream_gene_variant,,ENST00000440401,;	C	ENSG00000158813	ENST00000374552	Transcript	3_prime_UTR_variant	5129	.	.	.	.	.	.	.	1	EDA	HGNC	3157	protein_coding	YES	CCDS14394.1	ENSP00000363680	EDA_HUMAN	D6RA95_HUMAN	UPI0000052244	.	.	.	8/8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	GCCTGGAGCAG	.	5	ESCA
NAP1L6	0	.	GRCh37	X	72347515	72347515	+	Silent	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.207G>A	p.%3D	p.L69L	ENST00000373518	1/1	34	24	9	21	21	0	NAP1L6,synonymous_variant,p.%3D,ENST00000373518,;	T	ENSG00000204118	ENST00000373518	Transcript	synonymous_variant	405	207	69	L	ctG/ctA	.	.	.	-1	NAP1L6	HGNC	31706	protein_coding	YES	.	ENSP00000362617	NP1L6_HUMAN	.	UPI0000161AD3	.	.	.	1/1	.	hmmpanther:PTHR11875:SF36,hmmpanther:PTHR11875,Pfam_domain:PF00956,Superfamily_domains:SSF143113	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	LOW	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TCCCTCAGGTA	.	5	ESCA
XIST	0	.	GRCh37	X	73048909	73048909	+	RNA	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	n.11940G>A	.	.	ENST00000429829	5/6	19	10	9	15	15	0	XIST,non_coding_transcript_exon_variant,,ENST00000429829,;TSIX,non_coding_transcript_exon_variant,,ENST00000604411,;XIST,non_coding_transcript_exon_variant,,ENST00000433732,;XIST,non_coding_transcript_exon_variant,,ENST00000445814,;XIST,non_coding_transcript_exon_variant,,ENST00000602587,;XIST,upstream_gene_variant,,ENST00000416330,;XIST,upstream_gene_variant,,ENST00000434839,;XIST,upstream_gene_variant,,ENST00000421322,;XIST,upstream_gene_variant,,ENST00000417942,;XIST,downstream_gene_variant,,ENST00000602863,;XIST,downstream_gene_variant,,ENST00000602495,;	T	ENSG00000229807	ENST00000429829	Transcript	non_coding_transcript_exon_variant	11940	.	.	.	.	.	.	.	-1	XIST	HGNC	12810	lincRNA	YES	.	.	.	.	.	.	.	.	5/6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	TCATTCAGCTA	.	5	ESCA
UPRT	0	.	GRCh37	X	74523419	74523419	+	3'UTR	SNP	C	C	T	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.*73C>T	.	.	ENST00000373383	7/7	43	25	18	35	35	0	UPRT,3_prime_UTR_variant,,ENST00000373379,;UPRT,3_prime_UTR_variant,,ENST00000530743,;UPRT,3_prime_UTR_variant,,ENST00000373383,;UPRT,non_coding_transcript_exon_variant,,ENST00000474175,;UPRT,downstream_gene_variant,,ENST00000526850,;UPRT,downstream_gene_variant,,ENST00000462237,;	T	ENSG00000094841	ENST00000373383	Transcript	3_prime_UTR_variant	1170	.	.	.	.	.	.	.	1	UPRT	HGNC	28334	protein_coding	YES	CCDS14429.1	ENSP00000362481	UPP_HUMAN	E9PSD7_HUMAN,A8KAF9_HUMAN	UPI000004B62E	.	.	.	7/7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGATTCACTTG	.	5	ESCA
CYLC1	0	.	GRCh37	X	83128291	83128291	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.575C>G	p.Ser192Ter	p.S192*	ENST00000329312	4/5	59	36	22	32	32	0	CYLC1,stop_gained,p.Ser192Ter,ENST00000329312,;	G	ENSG00000183035	ENST00000329312	Transcript	stop_gained	612	575	192	S/*	tCa/tGa	.	.	.	1	CYLC1	HGNC	2582	protein_coding	YES	CCDS35341.1	ENSP00000331556	CYLC1_HUMAN	.	UPI0000251E1D	.	.	.	4/5	.	hmmpanther:PTHR16742:SF1,hmmpanther:PTHR16742	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGTCTCAAAAA	.	5	ESCA
CYLC1	0	.	GRCh37	X	83129461	83129461	+	Nonsense_Mutation	SNP	C	C	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1745C>G	p.Ser582Ter	p.S582*	ENST00000329312	4/5	38	24	14	17	17	0	CYLC1,stop_gained,p.Ser582Ter,ENST00000329312,;	G	ENSG00000183035	ENST00000329312	Transcript	stop_gained	1782	1745	582	S/*	tCa/tGa	.	.	.	1	CYLC1	HGNC	2582	protein_coding	YES	CCDS35341.1	ENSP00000331556	CYLC1_HUMAN	.	UPI0000251E1D	.	.	.	4/5	.	hmmpanther:PTHR16742:SF1,hmmpanther:PTHR16742	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	HIGH	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS	AATGTCATCCA	.	5	ESCA
KLHL4	0	.	GRCh37	X	86880713	86880713	+	Missense_Mutation	SNP	C	C	G	.	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1241C>G	p.Ser414Cys	p.S414C	ENST00000373114	6/11	43	23	20	24	24	0	KLHL4,missense_variant,p.Ser414Cys,ENST00000373114,;KLHL4,missense_variant,p.Ser414Cys,ENST00000373119,;	G	ENSG00000102271	ENST00000373114	Transcript	missense_variant	1321	1241	414	S/C	tCc/tGc	COSM388791	.	.	1	KLHL4	HGNC	6355	protein_coding	YES	CCDS14456.1	ENSP00000362206	KLHL4_HUMAN	.	UPI000002ACC4	.	deleterious(0)	possibly_damaging(0.819)	6/11	.	Gene3D:1k3iA02,hmmpanther:PTHR24412:SF74,hmmpanther:PTHR24412	.	.	.	.	.	.	.	.	.	.	1	.	.	.	.	.	MODERATE	.	SNV	.	.	1	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AAGATCCATGA	.	5	ESCA
SHROOM2	0	.	GRCh37	X	9914723	9914723	+	Missense_Mutation	SNP	G	G	C	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.4597G>C	p.Glu1533Gln	p.E1533Q	ENST00000380913	10/10	18	3	15	10	10	0	SHROOM2,missense_variant,p.Glu1533Gln,ENST00000380913,;SHROOM2,missense_variant,p.Glu368Gln,ENST00000452575,;SHROOM2,missense_variant,p.Glu368Gln,ENST00000418909,;	C	ENSG00000146950	ENST00000380913	Transcript	missense_variant	4687	4597	1533	E/Q	Gag/Cag	.	.	.	1	SHROOM2	HGNC	630	protein_coding	YES	CCDS14135.1	ENSP00000370299	SHRM2_HUMAN	F5H3B6_HUMAN,C9IZC6_HUMAN	UPI0000125D05	.	tolerated(0.09)	probably_damaging(0.992)	10/10	.	PROSITE_profiles:PS51307,hmmpanther:PTHR15012,hmmpanther:PTHR15012:SF8,Pfam_domain:PF08687	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODERATE	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	TGCTTGAGAAG	.	5	ESCA
SYTL4	0	.	GRCh37	X	99940889	99940889	+	Intron	SNP	A	A	G	novel	.	TCGA-Z6-AAPN-01A-11D-A403-09	TCGA-Z6-AAPN-10A-01D-A403-09	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	c.1449+98T>C	.	.	ENST00000455616	.	22	12	10	17	17	0	SYTL4,3_prime_UTR_variant,,ENST00000372981,;SYTL4,intron_variant,,ENST00000372989,;SYTL4,intron_variant,,ENST00000454200,;SYTL4,intron_variant,,ENST00000263033,;SYTL4,intron_variant,,ENST00000455616,;SYTL4,intron_variant,,ENST00000276141,;	G	ENSG00000102362	ENST00000455616	Transcript	intron_variant	.	.	.	.	.	.	.	.	-1	SYTL4	HGNC	15588	protein_coding	YES	CCDS14472.1	ENSP00000390252	SYTL4_HUMAN	B3KUZ4_HUMAN	UPI00001AE9F2	.	.	.	.	14/17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MODIFIER	.	SNV	.	.	.	.	.	.	.	.	.	.	.	.	.	PASS	NONE	SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS	AGAGAAGACTA	.	5	ESCA